Modified sequence Experiment N duplicates Sequence Length Missed cleavages Proteins Leading proteins Gene names Protein names Phospho (STY) All Phospho (STY) Probabilities Max Score Min PEP Intensity Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Reporter intensity corrected 10 Phosphoproteome Fullproteome TMT Channel Normal 1 TMT Channel Normal 2 TMT Channel Normal 3 TMT Channel Normal 4 TMT Channel Normal 5 TMT Channel Normal 6 TMT Channel Normal 7 TMT Channel Normal 8 TMT Channel Normal 9 TMT Channel Normal 10 TMT Channel Ratio 1 TMT Channel Ratio 2 TMT Channel Ratio 3 TMT Channel Ratio 4 TMT Channel Ratio 5 TMT Channel Ratio 6 TMT Channel Ratio 7 TMT Channel Ratio 8 TMT Channel Ratio 9 TMT Channel Ratio 10 Curve signal Log EC50 Curve slope Curve top Curve bottom R2 Curve RMSE Log EC50 error Curve slope error Curve top error Curve bottom error EC50 pEC50 Curve effect size Regulation (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 AAAAAAAGDS(0.787)DS(0.213)WDADAFSVEDPVRK;AAAAAAAGDS(0.5)DS(0.5)WDADAFSVEDPVRK;AAAAAAAGDS(0.919)DS(0.081)WDADAFSVEDPVRK;AAAAAAAGDS(0.865)DS(0.135)WDADAFSVEDPVRK;AAAAAAAGDS(0.855)DS(0.145)WDADAFSVEDPVRK;AAAAAAAGDS(0.5)DS(0.5)WDADAFSVEDPVRK 125.97 7.14E-35 1526881000 862809 848541 1008146 803721 1195858 1303113 1068576 1013203 1068112 926892 TRUE FALSE 896873.3656 994271.316 1034419.113 962694.6149 992586.4843 1000484.755 984818.2209 999622.6711 1029670.858 1108498.741 0.809088303 0.89695304 0.933171211 0.868467035 0.895433118 0.902558314 0.888425205 0.90178061 0.928887711 1 20.0801757 -5 0.140949812 1.378754468 0.853641717 0.622614434 0.028356308 94.78389518 0.816632904 10.03274983 0.169654099 1.00E-05 5 -0.525112751 (ac)AAADGDDSLYPIAVLIDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAADGDDSLYPIAVLIDELR 20 0 P30153;C9J9C1;M0QXG4;M0R0K6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 67.115 3.88E-24 657650000 11242 11334 41842.4 23885.5 28544.6 41316.1 29897.8 38581 47074.8 32061.2 FALSE TRUE 11685.84284 13280.52633 42932.84732 28609.98061 23692.59909 31721.06193 27554.33231 38063.8848 45380.58714 38342.97829 0.304771391 0.346361366 1.119705595 0.746159581 0.617912331 0.827297809 0.718627857 0.992721132 1.183543615 1 15.22667478 4.256845113 24.38907271 0.87896723 0.32556551 0.641776077 0.171272153 117.3672519 156548.5358 0.043087947 0.117465237 18065.2973 -4.256845113 -0.553401721 (ac)AAAITDMADLEELSRLS(ph)PLPPGS(ph)PGSAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 2 AAAITDMADLEELSRLS(0.996)PLPPGS(0.868)PGS(0.136)AAR;AAAIT(0.001)DMADLEELS(0.025)RLS(0.974)PLPPGS(0.829)PGS(0.172)AAR;AAAITDMADLEELS(0.011)RLS(0.945)PLPPGS(0.826)PGS(0.217)AAR;AAAIT(0.005)DMADLEELS(0.081)RLS(0.916)PLPPGS(0.805)PGS(0.194)AAR 88.987 2.59E-12 104004400 10191.2 10351.5 9723 9515.4 14194 16282.9 11189.41 11893.7 14498.4 12487 TRUE FALSE 10593.55645 12129.2896 9976.389368 11397.51772 11781.30895 12501.44324 10312.35481 11734.28441 13976.60542 14933.58857 0.709377816 0.812215332 0.66805037 0.763213588 0.788913455 0.837135909 0.690547671 0.785764543 0.935917402 1 13.86627327 1.184313356 3.067084353 0.996018476 0.755250574 0.745783128 0.050236989 0.112221562 1.865201485 0.044929086 0.012350561 15.28668639 -1.184313356 -0.240767901 (ac)AAAITDMADLEELSRLS(ph)PLPPGSPGSAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAAITDMADLEELSRLSPLPPGSPGSAAR 29 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 AAAITDMADLEELS(0.007)RLS(0.952)PLPPGS(0.034)PGS(0.008)AAR 56.298 0.00023641 0 1035.5 1344.3 1704.9 1984.2 2834.9 1613.2 1538.2 617.29 1772.8 1460 TRUE FALSE 1076.38234 1575.173068 1749.331095 2376.668838 2353.024711 1238.558748 1417.631865 609.0162372 1708.997274 1746.059047 0.616463883 0.90213047 1.001873962 1.361161779 1.347620354 0.709345283 0.811903737 0.348794755 0.978774044 1 10.76988663 2.633407149 10.89865215 0.701249385 1.052848107 0.192411294 0.264661374 0.712878401 70.00695819 0.090417873 0.085223427 429.9393043 -2.633407149 0.351598723 (ac)AAAS(ph)PLRDCQAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAASPLRDCQAWK 13 1 A9UJP8;Q5R3I4;F8WBU8 A9UJP8 TTC38 Tetratricopeptide repeat protein 38 1 AAAS(1)PLRDCQAWK 60.563 0.0026323 0 58306 64967 57706 60039 82687 86372 64589 66293 66911 69922 TRUE FALSE 60607.9659 76124.57688 59209.86577 71914.535 68631.89328 66313.41198 59526.34541 65404.45077 64502.88618 83621.87716 0.724786 0.910342837 0.70806669 0.859996659 0.820740883 0.793015108 0.711851341 0.782145211 0.771363767 1 16.35159281 -1.351808936 6.004701111 1.000027194 0.787839659 0.519807165 0.061433325 2.08E-05 2.24E-06 0.055265704 0.013024584 0.044482692 1.351808936 -0.212187535 (ac)AAASVT(ph)PPGSLELLQPGFSK ddPTM_MDA-MB-175_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(0.071)VT(0.839)PPGS(0.09)LELLQPGFSK 67.358 1.50E-05 0 42221 53029 56734 55303 77879 65522 65975 69365 67512 40918 TRUE FALSE 43887.91768 62136.31824 58212.53465 66241.76834 64641.1554 50305.5085 60803.70711 68435.27563 65082.25631 48935.09868 0.896859695 1.269769959 1.189586539 1.353665776 1.320956883 1.02800464 1.242537744 1.398490603 1.329970881 1 15.57858199 4.740102867 24.14806443 1.25444695 0.8968595 0.385921386 0.127013092 82.78286062 1295985.221 0.030079743 0.190442945 54967.10534 -4.740102867 -0.35758745 (ac)AAAVAAAGAGEPQS(ph)PDELLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAAVAAAGAGEPQSPDELLPK 21 0 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 1 AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK;AAAVAAAGAGEPQS(1)PDELLPK 76.588 3.27E-22 134615000 117951 87194 96430 125904 122378 212913 122818 93161 123956 128708 TRUE FALSE 122607.7966 102168.8912 98943.04502 150807.4354 101576.2313 163467.1825 113191.2042 91912.32918 119494.8478 153925.8683 0.796537956 0.663753873 0.642796731 0.979740683 0.659903578 1.061986424 0.735361804 0.597120745 0.776314268 1 17.23187618 (ac)AADVSVTHRPPLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 AADVSVT(0.003)HRPPLS(0.997)PK;AADVSVT(0.001)HRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVTHRPPLS(0.999)PK;AADVSVTHRPPLS(1)PK;AADVSVT(0.005)HRPPLS(0.995)PK;AADVS(0.001)VT(0.008)HRPPLS(0.992)PK 121.44 9.12E-09 15630480000 3068730 3023590 3646270 2864930 4850880 6155820 4357430 3944950 3876410 2822450 TRUE FALSE 3189885.83 3542868.062 3741294.792 3431604.603 4026329.15 4726224.097 4015883.251 3892074.398 3736898.761 3375455.038 0.945023943 1.049597172 1.108382351 1.016634665 1.192825591 1.400173915 1.189730927 1.153051767 1.107079999 1 21.68665057 3.234397474 24.78357136 1.190726673 1.036920983 0.317345985 0.101385597 108.6884979 647033.2788 0.029489739 0.036471422 1715.526669 -3.234397474 -0.15380569 (ac)AAEVYFGDLELFEPFDHPEESIPKPVHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAEVYFGDLELFEPFDHPEESIPKPVHTR 29 1 Q6NZY4 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 0 ;; 82.342 3.78E-07 60680000 55530 58699 63203 51798 71793 76145 75499 62528 70718 59240 FALSE TRUE 57722.36728 68780.09664 64850.1221 62043.4898 59589.6515 58461.47774 69581.1911 61689.91444 68172.87299 70846.94378 0.814747457 0.970826587 0.915355252 0.87573982 0.841104052 0.825179953 0.982133983 0.870749127 0.962255665 1 16.112418 1.020944744 1.102063496 1.001380796 0.885443816 0.32838482 0.053936345 0.63620673 1.621605764 0.049887757 0.016058595 10.49408903 -1.020944744 -0.11593698 (ac)AAGGDHGS(ph)PDSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAGGDHGSPDSYR 13 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 1 AAGGDHGS(0.766)PDS(0.233)Y(0.001)R 43.177 5.59E-05 85867000 27144 17478 22242 23618 25348 36785 30431 20283 24351 17846 TRUE FALSE 28215.66608 20479.71054 22821.64479 28289.56991 21039.35601 28242.24123 28045.7387 20011.13956 23474.61227 21342.58202 1.322036202 0.959570427 1.069301023 1.325498943 0.985792441 1.323281373 1.314074308 0.93761568 1.09989561 1 14.3814471 1.707894588 11.88946267 1.015477981 1.175414681 0.244112704 0.138711192 0.177549171 52.4514725 0.064382015 0.035193508 51.03811057 -1.707894588 0.1599367 (ac)AALHTTPDS(ph)PAAQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 AALHTTPDS(1)PAAQLER;AALHTT(0.004)PDS(0.996)PAAQLER;AALHTTPDS(1)PAAQLER;AALHTTPDS(1)PAAQLER 133.16 1.62E-57 3683180000 439514 225950.4 199926 210401.6 340782.7 496832.9 261434.9 196933.2 205310.8 324176 TRUE FALSE 456866.3521 264755.6235 205136.2358 252018.4085 282856.5784 381450.9886 240942.9494 194293.6326 197921.7044 387692.0805 1.178425805 0.68290181 0.529121553 0.650047863 0.729590808 0.983901936 0.621480194 0.501154505 0.510512632 1 18.56455174 2.034944962 24.96437429 0.601675314 0.769125627 0.055042382 0.217143303 380.910004 272117.2062 0.080782389 0.059661479 108.3789557 -2.034944962 0.167450313 (ac)AAS(ph)DTERDGLAPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASDTERDGLAPEK 14 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AAS(0.994)DT(0.006)ERDGLAPEK 86.756 1.29E-05 191880000 329360 279940 352700 282220 417570 468820 410580 355900 387840 303250 TRUE FALSE 342363.3871 328017.5174 361891.6517 338042.2737 346591.6006 359943.66 378397.6667 351129.7426 373881.7142 362666.0314 0.944018346 0.904461651 0.997864758 0.93210349 0.955677043 0.992493448 1.043377747 0.968190324 1.03092565 1 18.4682821 2.724372048 3.409835016 1.006115265 0.94557926 0.531542426 0.028563252 0.200644176 4.952258841 0.009240013 0.009139816 530.1173861 -2.724372048 -0.060536005 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAAS(0.025)GS(0.973)PGPGEGS(0.002)AGGEKR;AASAAAASAAAASAASGS(1)PGPGEGSAGGEKR;AASAAAASAAAAS(0.004)AAS(0.067)GS(0.926)PGPGEGS(0.002)AGGEKR;AASAAAASAAAASAASGS(0.999)PGPGEGS(0.001)AGGEKR;AASAAAASAAAASAAS(0.003)GS(0.991)PGPGEGS(0.005)AGGEKR 231.28 4.99E-198 7661730000 4082618 3992198 4540610 3573219.1 5478859 5865665 4646866.6 4545274 4905854 4182062.4 TRUE FALSE 4243802.911 4677826.952 4658942.027 4279991.173 4547564.504 4503453.199 4282633.054 4484352.037 4729293.273 5001457.457 0.848513248 0.935292761 0.931516876 0.855748791 0.909247863 0.900428173 0.856277013 0.896609054 0.945583025 1 22.25391714 1.01768329 2.821314132 0.999356782 0.892377634 0.590416908 0.028840005 0.165120246 2.990756592 0.026906745 0.007164314 10.41557595 -1.01768329 -0.106979148 (ac)AASDTERDGLAPEKT(ph)SPDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASDTERDGLAPEKTSPDRDK 21 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AASDTERDGLAPEKT(0.5)S(0.5)PDRDK;AASDTERDGLAPEKT(0.581)S(0.419)PDRDK 110.68 1.40E-17 379720000 163807 120710 138262 87947 194403 233670 138556 126229 146259 146572 TRUE FALSE 170274.2268 141441.0035 141865.2213 105342.6541 161358.4475 179403.6838 127695.6187 124537.1067 140995.1672 175289.9771 0.971385984 0.806897267 0.809317359 0.600962222 0.920522954 1.023468009 0.728482146 0.710463363 0.804353845 1 17.41938398 -0.95954974 5.35085339 1.000000515 0.80993358 0.164989523 0.120055096 7.58E-07 1.47E-07 0.119554225 0.028179125 0.109761557 0.95954974 -0.190066935 (ac)AASDTERDGLAPEKTS(ph)PDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASDTERDGLAPEKTSPDRDK 21 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 AASDTERDGLAPEKT(0.185)S(0.815)PDRDK 123.65 4.65E-23 488720000 153880 73315 115180 42808 188820 172230 111290 89506 124300 63988 TRUE FALSE 159955.3012 85906.28094 118181.6854 51275.29463 156724.4438 132232.1927 102566.799 88306.31847 119826.4673 76525.22348 2.090229782 1.122587783 1.544349432 0.670044363 2.048010273 1.727955655 1.340300548 1.153950481 1.565842762 1 16.22364773 -3.503363375 0.18445683 1.17E-09 1.543933211 0.111588009 0.408595181 176.3224307 2.820182491 68.20940797 1.237989709 0.000313788 3.503363375 1.54393321 (ac)AATDLERFS(ph)NAEPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AATDLERFSNAEPEPR 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599 A0A087X142 8-Sep Septin-8 1 AAT(0.026)DLERFS(0.974)NAEPEPR;AAT(0.021)DLERFS(0.979)NAEPEPR;AAT(0.008)DLERFS(0.992)NAEPEPR 66.982 1.32E-19 1397800000 222179 51893.9 60537.1 35685.2 122289.1 135095.6 107544 68732.6 105734.5 45767.5 TRUE FALSE 230950.7985 60806.27365 62114.74656 42743.62605 101502.4425 103721.6943 99114.42027 67811.35192 101929.136 54734.76535 4.219453523 1.110925995 1.134831695 0.780922797 1.854441904 1.894987466 1.81081292 1.238908242 1.862237562 1 15.74016985 4.742521035 24.99606423 1.427731729 4.219454606 0.819987987 0.394852284 163.2358075 1030218.031 0.097725819 0.744476739 55274.01789 -4.742521035 2.791722877 (ac)ACRPRS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ACRPRSPPR 9 2 F8W8D3;Q14493;E7EUV9;Q14493-2 F8W8D3 SLBP Histone RNA hairpin-binding protein 1 ACRPRS(1)PPR;ACRPRS(1)PPR 71.085 0.0019172 303600000 51986 24720 29106 22961 43984 46162 41678 31465 24795.8 29421 TRUE FALSE 54038.44742 28965.46771 29864.52627 27502.61727 36507.61539 35441.57509 38411.16945 31043.26314 23903.404 35185.48165 1.535816618 0.823222146 0.848774121 0.781646747 1.037576116 1.007278384 1.09167667 0.882274782 0.679354179 1 15.10269264 4.743492717 24.9042633 0.910996665 1.53581689 0.706040328 0.121922111 281.460867 1421166.096 0.030160955 0.2495167 55397.8254 -4.743492717 0.624820224 (ac)ACS(ph)PDAVVSPSSAFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ACSPDAVVSPSSAFLR 16 0 Q93100-4;Q93100-2;I3L3F2;H3BV13;H3BQ89 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 ACS(1)PDAVVSPSSAFLR;ACS(1)PDAVVSPSSAFLR;ACS(0.997)PDAVVS(0.002)PS(0.001)SAFLR 83.314 3.02E-11 295510000 22849.9 24645.3 19445.5 25376.9 23670.4 32801.2 22370.6 23140.6 24382.5 27322 TRUE FALSE 23752.0317 28877.93856 19952.2657 30396.37508 19646.91386 25183.61841 20617.13392 22830.43811 23504.97859 32675.22279 0.726912617 0.883787044 0.610623708 0.930257623 0.60127865 0.770725224 0.630971487 0.698707955 0.719351747 1 14.99590945 -1.060917901 4.534783334 1.000014833 0.727992987 0.379014821 0.1035314 77429677094 16035034147 12645699.78 0.022206561 0.086912471 1.060917901 -0.272021846 (ac)ADANKAEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADANKAEVPGATGGDSPHLQPAEPPGEPR 29 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 ADANKAEVPGAT(0.015)GGDS(0.985)PHLQPAEPPGEPR;ADANKAEVPGAT(0.015)GGDS(0.985)PHLQPAEPPGEPR;ADANKAEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR;ADANKAEVPGAT(0.031)GGDS(0.969)PHLQPAEPPGEPR 79.534 1.76E-35 10694800000 3778560 3914300 4233130 2663760 5650500 5456780 3442900 4095750 4563400 4463500 TRUE FALSE 3927740.466 4586550.576 4343448.845 3190643.777 4690030.028 4189525.543 3173036.502 4040853.171 4399164.125 5338037.366 0.735802355 0.859220395 0.813678989 0.597718517 0.878605695 0.784843802 0.594420062 0.756992298 0.824116398 1 22.34787797 0.88642317 3.042080511 0.99968698 0.75136757 0.408039113 0.090201278 0.451134167 8.694960426 0.085949435 0.022507031 7.698802344 -0.88642317 -0.24831941 (ac)ADDKVAILT(ph)DDEEEQKRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADDKVAILTDDEEEQKRK 18 3 C9JAZ7;C9J134;C9JJH2;Q6ZSS7 C9JAZ7 MFSD6 Major facilitator superfamily domain-containing protein 6 1 ADDKVAILT(1)DDEEEQKRK 72.145 1.27E-05 83776000 113160 29908 55068 30900 103000 101360 76489 52086 66325 20611 TRUE FALSE 117627.6442 35044.46635 56503.11732 37011.92777 85492.09679 77820.67613 70493.59231 51387.87237 63937.97621 24649.33083 4.772042089 1.4217208 2.292277941 1.501538846 3.468333375 3.157111106 2.859858258 2.084757299 2.593903123 1 14.58926086 0.290630467 0.858653403 0.986342149 2.663728001 0.228538218 0.933380849 4.322087062 3.960245982 1.02218937 0.291386794 1.952677251 -0.290630467 1.677385851 (ac)ADEELEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADEELEALRR 10 1 O14737;O14737-2;Q3HM38;X6R2P6;K7ESJ4 O14737 PDCD5 Programmed cell death protein 5 0 ; 84.743 2.44E-05 1137920000 73091 81127 80516 78660 108915 127424 91698 96724 102738 72692 FALSE TRUE 75976.68912 95059.93117 82614.3131 94218.71322 90401.6672 97831.70713 84510.47115 95427.57299 99040.47945 86934.60563 0.873952192 1.0934648 0.950304111 1.083788355 1.03988126 1.125348259 0.972115426 1.097693747 1.139252646 1 16.40764296 5.341830946 1.98571091 1.057234363 3.21E-14 0.423301546 0.062163306 8.201410066 5.919112701 0.014907753 28.86385773 219700.4497 -5.341830946 -1.057234363 (ac)ADFDDRVSDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADFDDRVSDEEK 12 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 81.338 0.027813 237660000 260620 198100 247940 191650 336570 399180 290190 248330 274430 188930 FALSE TRUE 270909.4788 232122.134 254401.5201 229557.798 279359.9516 306476.4946 267444.1495 245001.5425 264553.3179 225947.2162 1.198994541 1.027329028 1.125933412 1.015979758 1.236394749 1.356407482 1.183657644 1.084330874 1.170863365 1 17.78562626 3.232066021 24.99390382 1.178985606 1.089855189 0.132216442 0.099215754 297.8750665 1146347.276 0.02933439 0.035842686 1706.341764 -3.232066021 -0.089130417 (ac)ADFDDRVSDEEKVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADFDDRVSDEEKVR 14 2 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 145.81 1.56E-05 381670000 152580 169670 197450 105140 270940 253940 124180 164750 199410 230660 FALSE TRUE 158603.9762 198809.5027 202595.7092 125936.3782 224885.7156 194966.2835 114446.4471 162541.7957 192233.2731 275853.4107 0.574957459 0.720707067 0.734432497 0.4565337 0.815236306 0.706774961 0.414881392 0.589232503 0.696867487 1 18.07354229 0.868499307 4.709715731 0.999976235 0.624946167 0.470299684 0.11847612 0.944937591 32.82591041 0.114478747 0.029008117 7.387530841 -0.868499307 -0.375030068 (ac)ADGDS(ph)GS(ph)ERGGGGGPCGFQPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 139.98 7.64E-12 2376740000 20358.5 29863.7 29577.9 34494.6 34709.9 44088.6 32495.6 31366.2 28636.5 17528.2 TRUE FALSE 21162.2693 34992.55817 30348.72437 41317.52892 28809.9236 33849.69082 29948.50996 30945.78739 27605.87796 20962.51519 1.00952911 1.669291965 1.447761592 1.971019629 1.374354334 1.614772393 1.428669684 1.476244006 1.316916301 1 14.35552421 0.825456557 1.104732563 0.999634277 1.528513155 0.305601217 0.230350282 0.819426458 1.912776956 0.204589424 0.06466598 6.690468914 -0.825456557 0.528878878 (ac)ADGDS(ph)GSERGGGGGPCGFQPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ADGDSGSERGGGGGPCGFQPASR 23 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 ADGDS(0.95)GS(0.05)ERGGGGGPCGFQPASR;ADGDS(0.624)GS(0.376)ERGGGGGPCGFQPASR;ADGDS(0.866)GS(0.134)ERGGGGGPCGFQPASR 156.39 1.41E-16 1557410000 16119.2 19709.8 18623.8 15364.2 17831.3 29085.9 16429.4 20975.8 15375.1 21614.4 TRUE FALSE 16755.59846 23094.80483 19109.15153 18403.1929 14800.342 22331.14053 15141.6207 20694.65371 14821.75315 25849.32785 0.648202482 0.893439279 0.739251389 0.711940868 0.572561967 0.863896371 0.585764581 0.800587692 0.573390273 1 14.65783915 -1.443745281 5.657993136 1.000201282 0.717453074 0.378142512 0.11122892 0.000257566 2.53E-05 0.098221044 0.023134601 0.035996039 1.443745281 -0.282748208 (ac)ADHS(ph)FSDGVPSDSVEAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADHSFSDGVPSDSVEAAK 18 0 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;E9PKT8;E9PS34;E9PNW0;E9PJJ2;E9PP22;E9PKI2;C9J1B1 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 ADHS(0.996)FS(0.004)DGVPSDSVEAAK;ADHS(0.998)FS(0.002)DGVPSDSVEAAK 98.942 5.37E-169 710930000 939060 797800 923550 745650 1180170 1267720 1043140 918030 985020 891340 TRUE FALSE 976134.8139 934815.944 947618.4717 893137.3445 979565.1249 973311.2425 961375.9611 905725.3094 949569.3226 1065981.007 0.915715015 0.876953658 0.888963748 0.837854838 0.918933 0.913066214 0.90186969 0.849663646 0.890793847 1 20.0237503 (ac)ADILSQSETLASQDLSGDFKKPALPVS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADILSQSETLASQDLSGDFKKPALPVSPAAR 31 2 A0A087X0M4;A0A087WWF4 A0A087X0M4 SLC4A1AP 1 ADILSQSETLASQDLSGDFKKPALPVS(1)PAAR 64.169 1.99E-08 159030000 89054 77253 90264 50734 124430 108790 77429 74143 96838 94693 TRUE FALSE 92569.92068 90520.60181 92616.35399 60769.03377 103279.433 83525.17123 71359.91266 73149.23436 93352.8193 113246.2803 0.817421291 0.799325166 0.817831312 0.536609534 0.911989628 0.73755333 0.6301303 0.64593057 0.82433453 1 16.78910414 0.966592892 8.301832538 0.999997033 0.731618002 0.37373308 0.103740735 0.522465279 128.1230988 0.100068763 0.025053822 9.259614198 -0.966592892 -0.268379031 (ac)ADLEEQLS(ph)DEEKVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADLEEQLSDEEKVR 14 1 P47755;F8W9N7;C9JUG7;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 1 ADLEEQLS(1)DEEKVR 69.345 0.00037847 124690000 101690 77602 93080 72324 132440 169070 102360 97906 105300 79093 TRUE FALSE 105704.7997 90929.53984 95505.74127 86629.47133 109927.8961 129806.0548 94336.75573 96593.73021 101510.2736 94589.75902 1.117507866 0.961304276 1.009683736 0.915844085 1.16215431 1.372305587 0.997325257 1.021185921 1.073163465 1 16.52939637 3.23004635 24.9990121 1.104530082 0.998857702 0.166674815 0.113079802 360.2391257 1057707.862 0.034859892 0.042299994 1698.424907 -3.23004635 -0.105672379 (ac)ADQLTEEQIAEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADQLTEEQIAEFK 13 0 P0DP25;P0DP24;P0DP23;M0QZ52;F8WBR5;G3V479 P0DP25 CALM3;CALM2;CALM1 0 ; 97.456 1.65E-07 50597000 118942 123299 133641 127599 140838 168717 152181 130785 133826 114124 FALSE TRUE 123637.922 144474.6441 137123.7942 152837.7014 116898.4071 129535.0337 140252.6556 129032.041 129009.6284 136484.4128 0.905875766 1.058543179 1.004684648 1.119817994 0.856496392 0.949082984 1.027609327 0.945397635 0.945233421 1 17.05837667 3.2400762 24.99999765 0.955702298 1.023570876 0.210173596 0.064753181 64.75984794 1068216.903 0.017813947 0.022896492 1738.105765 -3.2400762 0.067868578 (ac)ADSRDPASDQMQHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADSRDPASDQMQHWK 15 1 P04040 P04040 CAT Catalase 0 ; 57.679 0.00016469 681450000 321560 426680 358540 404400 462250 531400 363580 347970 364000 397060 FALSE TRUE 334255.4371 499958.9709 367883.8469 484389.113 383676.9101 407990.4034 335081.6496 343306.0313 350899.7111 474856.3048 0.703908601 1.05286371 0.774726677 1.020075143 0.807985292 0.859187083 0.705648522 0.722968249 0.738959781 1 18.85713148 2.572797478 2.280255183 0.763982973 0.887396886 0.051575742 0.126771547 0.533949073 5.508656772 0.043998312 0.039188653 373.9361718 -2.572797478 0.123413913 (ac)ADVLDLHEAGGEDFAMDEDGDES(ph)IHKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADVLDLHEAGGEDFAMDEDGDESIHKLK 28 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK;ADVLDLHEAGGEDFAMDEDGDES(1)IHKLK 223.4 4.76E-111 280713000 223631 132021 189659 122301 299908 265984 213500 185352 210501 132212 TRUE FALSE 232460.1246 154694.5798 194601.6693 146491.7728 248929.7453 204213.247 196765.3121 182867.6596 202925.1101 158116.41 1.47018342 0.978358791 1.230749353 0.926480513 1.574344783 1.291537336 1.244433213 1.156538145 1.283390573 1 17.27062758 -1.466027123 2.618540817 0.990901203 1.228542069 0.128063978 0.185532114 13799281.75 14134858.09 918677.7803 0.043534728 0.034195809 1.466027123 0.237640866 (ac)ADVLDLHEAGGEDFAMDEDGDESIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADVLDLHEAGGEDFAMDEDGDESIHK 26 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;;;; 156.28 1.54E-61 910683000 187762 243246 281404 225851 319018 350245 309977 275980 278906 241727 FALSE TRUE 195174.9887 285021.6083 288737.6194 270523.6537 264791.4343 268905.9068 285680.1928 272280.9395 268868.2275 289088.7775 0.675138587 0.985931072 0.998785293 0.935780545 0.915951967 0.930184524 0.988209211 0.941859251 0.930054186 1 18.14115308 4.742302314 24.99832883 0.955821544 0.67513848 0.886336541 0.030431156 115.3551182 770657.4539 0.00741436 0.055634667 55246.18759 -4.742302314 -0.280683064 (ac)AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLR 33 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 0 65.69 8.19E-08 52714000 1402.5 1898.4 1484.4 1385 2318 3020.7 2162.6 1929.9 2037.9 2261.7 FALSE TRUE 1457.871783 2224.435432 1523.084683 1658.948866 1923.987188 2319.188204 1993.089761 1904.032847 1964.556377 2704.836812 0.538986965 0.822391733 0.5630967 0.613326785 0.711313592 0.857422597 0.736861371 0.703936311 0.726312348 1 11.40132584 3.009454531 6.073539155 0.775528192 0.6443659 0.340290974 0.107951914 0.216683159 31.61436447 0.03073869 0.035635327 1022.008555 -3.009454531 -0.131162292 (ac)AEPPS(ph)PVHCVAAAAPTATVSEKEPFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEPPSPVHCVAAAAPTATVSEKEPFGK 27 1 Q6PCB5 Q6PCB5 RSBN1L Round spermatid basic protein 1-like protein 1 AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK;AEPPS(1)PVHCVAAAAPTATVSEKEPFGK 150.98 5.24E-25 977390000 1066980 722840 926950 697270 1265550 1247320 1108840 955610 1096220 719920 TRUE FALSE 1109105.194 846982.1471 951107.0785 835187.9249 1050432.263 957648.8333 1021926.223 942801.611 1056767.256 860974.5403 1.288197435 0.983748192 1.104686647 0.970049503 1.22005032 1.112284729 1.186941281 1.095040059 1.227408253 1 19.71561105 3.217563686 24.99985064 1.14343045 1.080605617 0.060476675 0.101969781 603.740692 718837.991 0.027287235 0.032644348 1650.302989 -3.217563686 -0.062824834 (ac)AESSESFTMASS(ph)PAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 AESSESFTMAS(0.011)S(0.988)PAQR;AESSESFTMAS(0.018)S(0.982)PAQR 116.58 8.71E-88 556650000 13273.4 18345.8 11930.9 17718.3 16395 23685 15529.1 23353.3 17063.2 19477.8 TRUE FALSE 13797.44408 21496.54844 12241.82906 21222.92686 13608.18376 18184.5177 14311.88856 23040.28721 16449.09877 23294.10198 0.592314917 0.922832245 0.525533419 0.911085856 0.584190099 0.780649012 0.61439967 0.989103904 0.706148654 1 14.50767709 1.022058025 0.624971535 0.99273602 0.71057023 0.224822467 0.151959416 1.130160964 1.055171045 0.140816587 0.060024496 10.52102434 -1.022058025 -0.28216579 (ac)AEYLASIFGTEKDKVNCSFYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 85.231 4.64E-05 165983000 115301 94470 138072 68152 191378 143707 110210 124833 143625 125581 FALSE TRUE 119853.1725 110694.4876 141670.2697 81632.26219 158847.6359 110333.2272 101571.4522 123159.8178 138455.9643 150186.1926 0.798030568 0.737048365 0.943297565 0.543540393 1.057671369 0.734642947 0.67630353 0.82004754 0.921895428 1 17.19639266 1.13849293 2.836985273 0.995189438 0.785430077 0.225611859 0.13231986 0.341928355 5.042601997 0.114919188 0.031255892 13.75602417 -1.13849293 -0.209759362 (ac)AGS(ph)PELVVLDPPWDKELAAGTESQALVSATPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSPELVVLDPPWDKELAAGTESQALVSATPR 32 1 Q5SY74;Q96IY1-2;Q96IY1 Q5SY74 NSL1 Kinetochore-associated protein NSL1 homolog 1 AGS(1)PELVVLDPPWDKELAAGTESQALVSATPR;AGS(1)PELVVLDPPWDKELAAGTESQALVSATPR;AGS(1)PELVVLDPPWDKELAAGTESQALVSATPR;AGS(0.999)PELVVLDPPWDKELAAGT(0.001)ESQALVSATPR 66.083 3.50E-19 137086000 92853 101652 111831 84168 131910 140447 99694 105712 125702 112663 TRUE FALSE 96518.90814 119109.9403 114745.4077 100816.1792 109487.9853 107830.3127 91879.72378 104295.1035 121178.0096 134737.1578 0.716349593 0.884017017 0.851624078 0.748243327 0.812604237 0.800301227 0.681918227 0.774063408 0.899365933 1 17.03978825 1.032338456 3.508179375 0.998539314 0.784330838 0.602955692 0.056783709 0.138485474 3.871983047 0.055911563 0.014509168 10.77304454 -1.032338456 -0.214208477 (ac)AHCVTLVQLSISCDHLIDKDIGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHCVTLVQLSISCDHLIDKDIGSK 24 1 Q99829;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57;Q5JX53 Q99829 CPNE1 Copine-1 0 70.917 2.06E-06 254170000 363390 269230 396860 261310 484930 447840 405790 372900 424980 272600 FALSE TRUE 377736.9178 315468.1582 407202.4976 312996.3381 402501.7718 343835.9471 373983.1195 367901.8854 409685.0528 326010.7508 1.158663992 0.967661825 1.249046225 0.960079805 1.234627296 1.054676713 1.147149653 1.128496176 1.256661174 1 18.31456001 3.213703255 24.99955939 1.139157872 1.08736145 0.056603733 0.105525183 709.1219599 713176.9615 0.02793183 0.033398718 1635.6985 -3.213703255 -0.051796422 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 AHSPVQSGLPGMQNLK 16 0 B4DR80;Q9Y6E0-2 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 1 AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(1)PVQSGLPGMQNLK;AHS(0.999)PVQS(0.001)GLPGMQNLK;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;AHS(1)PVQSGLPGMQNLK 124.42 1.00E-57 8652100000 3473425 3319440 3748810 3244632 4188580 4759280 4054709 3856060 3935810 3469008 TRUE FALSE 3610558.501 3889527.998 3846507.068 3886410.525 3476606.668 3654009.348 3736890.314 3804375.823 3794160.967 4148693.699 0.870288038 0.93753077 0.927161017 0.936779335 0.838000325 0.880761418 0.900739024 0.917005713 0.914543527 1 21.98422572 0.457617418 1.116295511 1.000047858 0.900868658 0.500681407 0.029635247 1.874376684 3.00106412 0.029728385 0.009118975 2.868252743 -0.457617418 -0.0991792 (ac)AKS(ph)PENSTLEEILGQYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKSPENSTLEEILGQYQR 18 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 AKS(1)PENSTLEEILGQYQR;AKS(0.995)PENS(0.003)T(0.002)LEEILGQYQR;AKS(0.999)PENS(0.001)T(0.001)LEEILGQYQR 120.03 1.20E-18 134439000 110125 94683 110502 90594 158428 167597 133543 130813 142886 114078 TRUE FALSE 114472.82 110944.0687 113381.7729 108513.2228 131498.4651 128675.1367 123075.5507 129059.6657 137743.5608 136429.3999 0.839062695 0.813197659 0.83106554 0.795380049 0.963857242 0.943162814 0.902118977 0.945981334 1.009632534 1 17.05779505 3.235057313 24.99999844 0.952525164 0.820027207 0.833675175 0.03074592 36.3261501 259228.2287 0.008893356 0.011038003 1718.13511 -3.235057313 -0.132497957 (ac)ALVTVSRS(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 ALVT(0.066)VS(0.243)RS(0.685)PPGS(0.685)GAS(0.245)T(0.075)PVGPWDQAVQR 47.38 0.0029052 143850000 6356.7 5295.4 3758.6 5164.8 6980.2 9572.9 4952.4 4423.6 5397.2 3909.7 TRUE FALSE 6607.667424 6204.843758 3856.552204 6186.382025 5793.708097 7349.739054 4564.217947 4364.308878 5202.955826 4675.730859 1.413183869 1.327031847 0.824802008 1.32308343 1.239102136 1.571890957 0.976150699 0.933396085 1.112757766 1 12.19097617 (ac)ALVTVSRS(ph)PPGSGAS(ph)TPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 ALVT(0.015)VS(0.108)RS(0.82)PPGS(0.458)GAS(0.526)T(0.072)PVGPWDQAVQR 65.071 0.00032454 108370000 6372.3 2899.5 2670.5 3237.3 5289.6 6637.7 5073.5 5054.8 5224.1 6056.7 TRUE FALSE 6623.883324 3397.46657 2740.095424 3877.628278 4390.475681 5096.19477 4675.825813 4987.048674 5036.085661 7243.394402 0.91447227 0.469043432 0.378288862 0.535333031 0.606135113 0.703564446 0.645529644 0.688496083 0.695265974 1 12.82245022 0.426497273 0.446901164 1.032135144 0.564514889 0.432455579 0.134481317 2.156101855 0.767517299 0.284510739 0.08288003 2.669914002 -0.426497273 -0.467620255 (ac)ALVTVSRS(ph)PPGSGAST(ph)PVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 ALVT(0.04)VS(0.135)RS(0.777)PPGS(0.049)GAS(0.052)T(0.947)PVGPWDQAVQR;ALVT(0.152)VS(0.123)RS(0.698)PPGS(0.032)GAS(0.16)T(0.835)PVGPWDQAVQR 76.691 2.61E-18 114511000 8308.9 2953.2 8664.2 10633 8121.9 11198.8 14652.2 7226.7 3748.1 4890.9 TRUE FALSE 8636.941788 3460.389127 8889.99617 12736.17566 6741.342339 8598.048419 13503.72228 7129.837907 3613.206613 5849.178213 1.476607734 0.591602615 1.519870971 2.177429923 1.152528115 1.469958361 2.308652906 1.218946944 0.617728932 1 12.51401823 4.186444481 24.99123662 1.490187625 1.034100812 0.077459671 0.521933798 189.3649765 90805.62889 0.128663254 0.277944961 15361.88398 -4.186444481 -0.456086813 (ac)ALVTVSRS(ph)PPGSGASTPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALVTVSRSPPGSGASTPVGPWDQAVQR 27 1 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 ALVT(0.012)VS(0.05)RS(0.437)PPGS(0.368)GAS(0.119)T(0.014)PVGPWDQAVQR;ALVT(0.001)VS(0.05)RS(0.881)PPGS(0.065)GAS(0.002)T(0.001)PVGPWDQAVQR;ALVT(0.013)VS(0.011)RS(0.664)PPGS(0.112)GAS(0.178)T(0.022)PVGPWDQAVQR;ALVT(0.002)VS(0.041)RS(0.802)PPGS(0.089)GAS(0.034)T(0.033)PVGPWDQAVQR;ALVT(0.005)VS(0.03)RS(0.814)PPGS(0.097)GAS(0.041)T(0.013)PVGPWDQAVQR;ALVT(0.002)VS(0.017)RS(0.561)PPGS(0.095)GAS(0.15)T(0.175)PVGPWDQAVQR 77.613 1.15E-81 7031200000 8693 5346.2 8672.4 18391.1 48678.3 17866.2 9125.2 6027.9 30939.6 13305.9 TRUE FALSE 9036.206352 6264.368262 8898.409868 22028.80469 40403.97995 13717.04581 8409.94298 5947.10586 29826.08984 15912.93635 0.567852856 0.393665137 0.559193456 1.384333112 2.539065014 0.86200595 0.528497242 0.373727748 1.874329739 1 13.95791245 3.818161159 6.457687331 1.145895263 0.486065963 0.222318974 0.602156297 0.456251768 30.53310486 0.1736552 0.316074666 6579.019285 -3.818161159 -0.6598293 (ac)AQES(ph)PKNSAAEIPVTSNGEVDDSREHSFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQESPKNSAAEIPVTSNGEVDDSREHSFNR 30 2 P53367;P53367-2;P53367-3 P53367 ARFIP1 Arfaptin-1 1 AQES(0.999)PKNS(0.001)AAEIPVTSNGEVDDSREHSFNR 84.035 4.42E-18 194330000 123630 111970 130260 70290 198140 219930 101110 134240 125600 162620 TRUE FALSE 128511.0079 131199.9765 133654.6826 84193.15221 164460.2336 168854.5906 93184.734 132440.7324 121079.6805 194482.2755 0.660785193 0.674611484 0.687233231 0.432909128 0.845630961 0.868226116 0.479142553 0.680991273 0.622574372 1 17.56927915 -1.78627551 2.692807784 1.090155605 0.66072544 0.38499302 0.128405957 21078126.51 16821755.48 12527594.19 0.030660241 0.016357785 1.78627551 -0.429430166 (ac)AQRHS(ph)DSSLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQRHSDSSLEEK 12 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 AQRHS(0.393)DS(0.393)S(0.213)LEEK 89.46 5.40E-05 249320000 335030 314400 375430 284820 486700 577580 400170 403730 430490 339550 TRUE FALSE 348257.2431 368395.7543 385214.0142 341156.5459 403970.9078 443445.7983 368803.6298 398318.6597 414996.749 406078.3214 0.857611019 0.907203697 0.948619992 0.84012499 0.994810327 1.092020369 0.908208122 0.980891219 1.021962334 1 18.63139849 3.217280233 24.54243499 0.995465395 0.894035927 0.538529716 0.050257495 162.9749026 187956.5657 0.014728527 0.017621307 1649.226227 -3.217280233 -0.101429468 (ac)AQS(ph)SPQLDIQVLHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSSPQLDIQVLHDLR 16 0 F6SS63;Q8N5C8-2;Q8N5C8;A0A0A0MQY2 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 AQS(0.5)S(0.5)PQLDIQVLHDLR;AQS(0.5)S(0.5)PQLDIQVLHDLR 62.924 0.0014651 31481000 8418.8 9337.6 10945.8 7318.3 9684.9 12381 9910.9 6539.9 10829.4 10501.1 TRUE FALSE 8751.180725 10941.26016 11231.05654 8765.837897 8038.664157 9505.700386 9134.057761 6452.243338 10439.65201 12558.58949 0.696828313 0.871217279 0.89429283 0.697995416 0.640092915 0.756908281 0.727315577 0.513771339 0.831275839 1 13.61638682 3.717548583 23.66856568 0.702864637 0.825823251 0.031139889 0.130922152 712.7364345 802846.8225 0.033753148 0.052367129 5218.534787 -3.717548583 0.122958614 (ac)AS(ph)GVAVSDGVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(0.998)GVAVS(0.002)DGVIK;AS(1)GVAVSDGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(0.997)GVAVS(0.003)DGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK 81.338 2.51E-21 57607349000 23829181 19132868 28063117 22980530 28304339 29979180 23732863 20792247 22660884 18879180 TRUE FALSE 24769975.47 22418789.25 28794464.88 27526010.24 23493177.57 23016969.78 21872619.18 20513560.94 21845323.21 22578193.86 1.097075152 0.992939886 1.275321891 1.219141372 1.040525106 1.019433615 0.968749729 0.90855633 0.967540776 1 24.42842675 2.780058485 2.000218677 0.953215964 1.14152436 0.529613521 0.07568309 0.264620152 2.09052854 0.029271814 0.029719681 602.6407367 -2.780058485 0.188308396 (ac)AS(ph)GVQVADEVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 76.943 6.71E-07 18064571000 261588.5 206728.29 252457.9 243265.2 275636.9 337641.7 211099.3 280455.74 271042.1 279799.1 TRUE FALSE 271916.216 242232.2657 259037.1603 291382.3305 228784.2382 259229.5322 194552.7853 276696.6895 261287.3478 334620.3766 0.812611051 0.723901719 0.774122493 0.870784778 0.683712811 0.774697389 0.581413443 0.826897311 0.780847091 1 18.35216577 0.61450692 1.586150139 0.999602491 0.751788041 0.476894701 0.0764534 1.34779642 4.499150837 0.070250734 0.02015421 4.11629906 -0.61450692 -0.24781445 (ac)AS(ph)PGKDNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPGKDNYR 9 1 O15131;Q5TD90 O15131 KPNA5 Importin subunit alpha-6 1 AS(1)PGKDNYR;AS(1)PGKDNYR 55.676 0.0037071 1369620000 1728330 1240160 1546750 1361540 2160600 2518700 2087300 1680190 1698560 1295600 TRUE FALSE 1796565.803 1453147.833 1587059.576 1630848.548 1793341.984 1933770.096 1923691.972 1657669.801 1637429.157 1549448.014 1.159487628 0.937848717 1.024274168 1.052535182 1.157407004 1.248038062 1.24153373 1.069845381 1.056782249 1 20.56332292 3.322653966 4.937567356 1.141065476 1.031920001 0.171461528 0.088983133 0.308206745 13.07808776 0.025564748 0.03466327 2102.102873 -3.322653966 -0.109145475 (ac)AS(ph)PPESDGFSDVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASPPESDGFSDVRK 14 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 AS(1)PPESDGFSDVRK;AS(1)PPESDGFSDVRK;AS(0.999)PPES(0.001)DGFSDVRK 148.56 2.22E-12 1419890000 1208210 1191290 1343730 1122370 1762170 1884240 1516210 1431890 1553280 1399920 TRUE FALSE 1255911.064 1395884.791 1378748.708 1344371.436 1462636.973 1446653.816 1397365.498 1412697.857 1497377.756 1674207.521 0.750152564 0.833758523 0.823523184 0.802989725 0.873629436 0.864082736 0.834642947 0.843800926 0.89438002 1 20.67504693 -4.999999999 0.117760384 1.545672917 0.750466786 0.818302565 0.026483354 65.92059509 0.506518162 8.547180164 0.274814278 1.00E-05 4.999999999 -0.795206131 (ac)AS(ph)PSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEER 37 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 AS(0.453)PS(0.453)KGNDLFS(0.094)PDEEGPAVVAGPGPGPGGAEGAAEER;AS(0.465)PS(0.465)KGNDLFS(0.069)PDEEGPAVVAGPGPGPGGAEGAAEER 85.239 1.73E-08 97896000 41790 47328 50159 40488 62649 68600 50917 49791 57897 49129 TRUE FALSE 43439.90147 55456.21584 51466.18475 48496.40556 51999.94536 52668.68964 46925.99249 49123.63309 55813.29828 58754.88692 0.739341079 0.943857077 0.875947303 0.825402075 0.885031835 0.896413769 0.798673863 0.8360774 0.949934571 1 15.84242123 1.090945844 4.100221314 0.998038045 0.852740238 0.474555155 0.053633688 0.165286491 4.834905167 0.048781995 0.012534082 12.32951075 -1.090945844 -0.145297807 (ac)AS(ph)PSLERPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPSLERPEK 10 1 Q13601-2;Q13601 Q13601-2 KRR1 KRR1 small subunit processome component homolog 1 AS(0.993)PS(0.007)LERPEK;AS(0.997)PS(0.003)LERPEK 85.67 6.18E-05 822120000 663440 587850 695670 514530 721980 837720 707420 642280 700820 582340 TRUE FALSE 689633.1235 688808.6647 713799.7317 616302.4983 599258.0975 643172.2258 651970.5719 633671.2872 675597.6251 696438.3734 0.990228497 0.989044675 1.024928779 0.884934722 0.860461055 0.923516352 0.936149696 0.90987417 0.970075244 1 19.40963617 3.743010634 24.99880987 0.919920042 1.000165055 0.43563798 0.038601276 324.3625388 1822162.942 0.009881481 0.017082807 5533.636588 -3.743010634 0.080245013 (ac)AS(ph)PSSFTYYCPPSSSPVWSEPLYSLRPEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPSSFTYYCPPSSSPVWSEPLYSLRPEHAR 31 1 P49356 P49356 FNTB Protein farnesyltransferase subunit beta 1 AS(0.997)PS(0.002)SFTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.997)PS(0.003)SFTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.941)PS(0.048)S(0.01)FTYYCPPSSSPVWSEPLYSLRPEHAR;AS(0.979)PS(0.019)S(0.002)FTYYCPPSSSPVWSEPLYSLRPEHAR 194.11 1.89E-105 3309110000 3152.6 5076.4 5544.5 5772.4 2514 16012.1 6969.9 6323.7 5440.3 11498.7 TRUE FALSE 3277.067082 5948.232211 5688.994225 6914.163491 2086.671178 12293.53244 6423.581026 6238.941145 5244.504666 13751.65011 0.238303553 0.432546797 0.413695388 0.502787915 0.151739694 0.893967803 0.467113472 0.453686728 0.381372753 1 13.74731712 -5 0.219219297 3.761140503 0.373551092 0.466433084 0.182448454 135.4357459 1.354830485 165.4873172 0.339678533 1.00E-05 5 -3.387589411 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 AS(0.443)PT(0.443)DGT(0.115)DLEASLLSFEK;AS(0.333)PT(0.333)DGT(0.333)DLEASLLSFEK;AS(0.467)PT(0.467)DGT(0.065)DLEAS(0.001)LLSFEK;AS(0.832)PT(0.158)DGT(0.009)DLEASLLSFEK 90.412 2.50E-40 200841000 204433 175547 204371 164424 237700 263496 232793 207304 216697 179034 TRUE FALSE 212504.1727 205695.8317 209697.0762 196946.5764 197295.8389 202303.0473 214546.0764 204525.429 208898.1173 214112.2845 0.9924894 0.960691406 0.979379005 0.919828477 0.921459688 0.944845588 1.002026002 0.955225103 0.97564751 1 17.70800805 2.266861153 24.99856448 0.977697996 0.951701779 0.251176351 0.024670711 359.5077557 317560.719 0.009062826 0.007581252 184.8677488 -2.266861153 -0.025996216 (ac)ASAVS(ph)PANLPAVLLQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.131)AVS(0.869)PANLPAVLLQPR;AS(0.209)AVS(0.791)PANLPAVLLQPR 72.652 9.09E-08 123430000 54524 43611 58899 40948 85307 77165 66121 59507 66202 50952 TRUE FALSE 56676.64962 51100.85 60433.95633 49047.39218 70806.54661 59244.5982 60938.26324 58709.406 63819.40295 60935.06887 0.93011546 0.838611508 0.991776287 0.804912394 1.161999944 0.972257836 1.000052423 0.963474844 1.04733455 1 15.89498514 3.256863833 24.99977027 1.01438107 0.894759663 0.457162674 0.070386565 235.0707349 321073.4979 0.018526964 0.025038665 1806.607601 -3.256863833 -0.119621407 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASEDNRVPSPPPTGDDGGGGGR 22 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 ASEDNRVPS(0.989)PPPT(0.011)GDDGGGGGR;ASEDNRVPS(0.996)PPPT(0.004)GDDGGGGGR;AS(0.006)EDNRVPS(0.947)PPPT(0.047)GDDGGGGGR;AS(0.014)EDNRVPS(0.846)PPPT(0.14)GDDGGGGGR;AS(0.001)EDNRVPS(0.997)PPPT(0.002)GDDGGGGGR;AS(0.002)EDNRVPS(0.981)PPPT(0.017)GDDGGGGGR;ASEDNRVPS(0.979)PPPT(0.021)GDDGGGGGR 131.11 3.88E-17 8325435000 9545.82 39704.8 33649.4 42868.1 40563.5 56030.8 53543.5 38318.2 34680.1 21522.1 TRUE FALSE 9922.696345 46523.79054 34526.33101 51347.28223 33668.53076 43018.49585 49346.62056 37804.6072 33431.96998 25738.94343 0.385512963 1.807525265 1.341404363 1.994925797 1.308077422 1.67133884 1.917196823 1.468770748 1.298886649 1 14.65166521 4.745839836 24.59935394 1.5672896 0.385512265 0.568040283 0.299270117 457.5859055 1546315.078 0.065196006 0.668419279 55698.03022 -4.745839836 -1.181777335 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREET(ph)PTEGGALSLKPGLPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 2 AS(0.012)EDNRVPS(0.973)PPPT(0.078)GDDGGGGGREET(0.752)PT(0.154)EGGALS(0.031)LKPGLPIR 45.282 0.0001279 47749000 16595 19867 19689 18860 21661 28832 19338 18077 18767 27046 TRUE FALSE 17250.18341 23279.00271 20202.11151 22590.45171 17979.07096 22136.20495 17822.23703 17834.70738 18091.57934 32345.14587 0.533315988 0.719706221 0.624579391 0.698418607 0.555850669 0.684374868 0.551001906 0.551387446 0.559329038 1 14.9812616 -1.206084693 3.585968809 1.00055391 0.608938712 0.758522559 0.066240785 64602093.15 111670072.3 410259.8214 0.015943324 0.062217894 1.206084693 -0.391615198 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGREETPTEGGALSLKPGLPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASEDNRVPSPPPTGDDGGGGGREETPTEGGALSLKPGLPIR 41 3 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 AS(0.001)EDNRVPS(0.986)PPPT(0.013)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.003)EDNRVPS(0.994)PPPT(0.002)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.983)PPPT(0.017)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.043)EDNRVPS(0.914)PPPT(0.04)GDDGGGGGREET(0.001)PT(0.001)EGGALSLKPGLPIR;ASEDNRVPS(0.991)PPPT(0.009)GDDGGGGGREETPTEGGALSLKPGLPIR;ASEDNRVPS(0.946)PPPT(0.054)GDDGGGGGREETPTEGGALSLKPGLPIR;AS(0.005)EDNRVPS(0.932)PPPT(0.062)GDDGGGGGREET(0.001)PTEGGALSLKPGLPIR 119.94 8.54E-55 29977910000 866135 960216 1035179 965355 1178835 1334514 1096583 1035442 1094966 1041930 TRUE FALSE 900330.6786 1125125.629 1062156.615 1156299.338 978457.0478 1024593.348 1010629.959 1021563.594 1055558.388 1246076.235 0.722532582 0.902934826 0.852400989 0.927952324 0.785230486 0.82225575 0.811049863 0.819824314 0.847105786 1 20.2489609 0.909733606 11.61179516 1 0.833426726 0.462843124 0.054366734 28.7942381 3705.045954 0.049957102 0.012492036 8.123320824 -0.909733606 -0.166573274 (ac)ASGEHS(ph)PGSGAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGEHSPGSGAAR 13 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 1 AS(0.016)GEHS(0.972)PGS(0.012)GAAR;AS(0.016)GEHS(0.972)PGS(0.012)GAAR 44.511 0.0037328 73447000 703.75 12145 4689.31 11561.1 4892.1 7131.4 2027.8 5998.3 1424.5 10838 TRUE FALSE 731.5345934 14230.80928 4811.517271 13847.85107 4060.542589 5475.240427 1868.855737 5917.9026 1373.232523 12961.49859 0.056439044 1.097929315 0.371216124 1.068383488 0.313277246 0.422423409 0.144185159 0.456575492 0.105947049 1 13.66194491 (ac)ASGRPEELWEAVVGAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGRPEELWEAVVGAAER 18 1 Q96B36;H9KV91;M0R2V8 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 68.034 1.84E-10 45746000 2621.1 2261.01 4003.5 3860.9 4706.5 5630.8 3910.8 4414.7 3315.8 2778.5 FALSE TRUE 2724.583052 2649.320879 4107.834499 4624.574496 3906.490811 4323.132036 3604.261277 4355.528167 3196.465006 3322.893877 0.819942843 0.797293256 1.236221995 1.391731023 1.175629122 1.301014175 1.084675409 1.310763548 0.961952179 1 11.6982245 4.240280772 24.99955072 1.205275309 0.808617895 0.559623709 0.131545048 26.68678979 387815.5974 0.030284402 0.074664697 17389.24684 -4.240280772 -0.396657414 (ac)ASHLRPPS(ph)PLLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ASHLRPPSPLLVR 13 1 Q8TDB6;Q8TDB6-2 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 ASHLRPPS(1)PLLVR;AS(0.003)HLRPPS(0.997)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;ASHLRPPS(1)PLLVR;AS(0.001)HLRPPS(0.999)PLLVR 111.7 9.07E-08 8116920000 35535 164466.5 98352.3 174206.7 112369.2 183584.4 106215.3 143857.1 91918 202207 TRUE FALSE 36937.94924 192712.342 100915.4417 208664.2653 93268.72352 140949.7053 97889.86724 141928.9309 88609.88914 241825.5902 0.152746238 0.796906324 0.417306711 0.862870903 0.385685913 0.582856865 0.40479532 0.58690617 0.366420647 1 17.88360739 -1.407754188 3.663025505 1.003233109 0.521932511 0.34990887 0.200872148 20990737.45 16146835.74 501738.8911 0.041667282 0.039106218 1.407754188 -0.481300598 (ac)ASLEVSRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASLEVSRSPR 10 1 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.024)RS(0.976)PR;ASLEVSRS(1)PR;ASLEVS(0.002)RS(0.998)PR;ASLEVSRS(1)PR 110.08 4.74E-07 4338350000 124807 109651 200863 144463 183147 241697 132283 153175 149875 201212 TRUE FALSE 129734.4767 128482.7063 206097.6548 173037.3502 152015.7384 185566.5347 121914.3128 151121.9397 144481.028 240635.639 0.53913243 0.533930497 0.856471866 0.719084467 0.631725787 0.771151503 0.506634484 0.628011463 0.600414089 1 17.8764908 -1.253632331 3.12604909 1.001644811 0.644500395 0.50766752 0.105474638 19533479.86 26513671.75 307278.3844 0.025438225 0.055765766 1.253632331 -0.357144417 (ac)ASLEVSRS(ph)PRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASLEVSRSPRR 11 2 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 ASLEVS(0.126)RS(0.874)PRR;ASLEVS(0.201)RS(0.799)PRR 92.457 7.21E-05 1075330000 27969.5 67428 57577 37321 65874 80295 53692 18671 62624 53614 TRUE FALSE 29073.75746 79008.23448 59077.50392 44702.98241 54676.76101 61647.70313 49483.48074 18420.74578 60370.17447 64118.6368 0.453436924 1.232219499 0.92137804 0.697191716 0.85274366 0.961463097 0.771748796 0.2872916 0.941538646 1 15.96845613 1.992932892 24.77244059 0.630195251 0.866335174 0 0.263913387 550.1359288 1928401.332 0.097797002 0.06940338 98.38590656 -1.992932892 0.236139923 (ac)AT(ph)PPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATPPKR 6 1 D6RCP9;D6RFG8;P27707;D6R9C6;D6RG38;Q9UBK9 D6RCP9 DCK;UXT Deoxycytidine kinase;Protein UXT 1 AT(1)PPKR 47.067 0.068895 2014100000 692080 440590 637860 539370 809960 862200 709520 620360 722940 519400 TRUE FALSE 719403.8528 516257.9052 654483.1556 646055.7761 672283.2885 661967.1168 653905.9684 612045.0889 696921.5306 621166.4855 1.158149819 0.831110366 1.053635653 1.040068631 1.082291631 1.06568389 1.052706454 0.985315697 1.121956105 1 19.24462047 (ac)ATSPQKS(ph)PSVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSPQKSPSVPK 12 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 AT(0.002)S(0.004)PQKS(0.985)PS(0.009)VPK;AT(0.006)S(0.018)PQKS(0.96)PS(0.016)VPK 69.602 0.00019446 833560000 1925900 1011060 1317260 977490 2001050 1831480 1741240 1337510 1526030 766380 TRUE FALSE 2001936.019 1184701.69 1351588.878 1170834.604 1660912.236 1406146.526 1604757.059 1319582.866 1471108.478 916537.4878 2.184238011 1.292583998 1.474668408 1.277454136 1.812159631 1.534194231 1.750890804 1.439747838 1.605071803 1 19.80583436 -0.725579042 0.744944727 0.934683699 1.58172447 0.326450772 0.256110635 29.66800712 9.960819721 5.23754014 0.08259001 0.188113931 0.725579042 0.647040771 (ac)AVPETRPNHTIYINNLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVPETRPNHTIYINNLNEK 19 1 P09012;M0R221;M0R2B8;M0R268;M0QXK2;M0R0G9 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 ; 93.812 1.75E-23 691540000 286440 221187 254154 232902 330800 359460 273850 278952 303720 260180 FALSE TRUE 297748.8724 259174.1467 260777.462 278969.3205 274570.7342 275980.8627 252384.9214 275213.1047 292789.1765 311157.2896 0.956907912 0.832936124 0.838088873 0.896554025 0.88241781 0.886949694 0.811116853 0.884482267 0.940968399 1 18.24728452 1.066272758 2.673599461 0.998495729 0.869581027 0.532175985 0.038324482 0.177184606 2.615761092 0.034841517 0.009405459 11.64857386 -1.066272758 -0.128914702 (ac)AYHSFLVEPISCHAWNK ddPTM_MDA-MB-175_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 ; 149.44 3.24E-72 1674610000 492710 1349100 1191850 1287490 1388530 1604400 1240690 1481370 1255600 1336430 FALSE TRUE 512162.5713 1580797.43 1222910.59 1542151.679 1152508.167 1231802.415 1143441.476 1461514.658 1210411.201 1598277.871 0.320446513 0.989062953 0.765142665 0.964883333 0.721093739 0.770706044 0.715420952 0.914430891 0.75732213 1 20.60808682 4.749375918 24.9029324 0.834565369 0.320446204 0.67862045 0.107951223 826.7008998 1903493.932 0.023880823 0.350991243 56153.382 -4.749375918 -0.514119165 (ac)AYHSGYGAHGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYHSGYGAHGSK 12 0 E9PIZ0;C9JST7;A6NGW1;O95070 E9PIZ0 YIF1A Protein YIF1A 0 ; 56.122 0.001468 242056000 60080 238642 226339 266860 250220 334050 207626 244880 192202 304430 FALSE TRUE 62452.00479 279626.9071 232237.5803 319644.1115 207687.6938 256471.9501 191351.7316 241597.7841 185284.6876 364077.2298 0.171535047 0.768042833 0.637879992 0.877956887 0.570449555 0.704443808 0.525580058 0.663589383 0.50891589 1 18.47388499 -2.440235745 2.200997692 4.545953975 0.619202694 0.301889509 0.179556058 5223833.264 302465.6588 93131706.9 0.041079141 0.00362881 2.440235745 -3.926751281 (ac)DDDIAALVVDNGSGMCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 DDDIAALVVDNGSGMCK 17 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7 C9JTX5;P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 ;;;;;;;; 176.42 9.89E-161 2434007000 2879380 2915747 3198360 2840560 3569920 4026550 3516200 3253010 3454930 3061730 FALSE TRUE 2993060.146 3416503.866 3281711.889 3402414.29 2963106.274 3091444.785 3240591.056 3209408.722 3330587.744 3661617.373 0.817414776 0.933058678 0.896246537 0.929210768 0.809234273 0.844283952 0.885016299 0.876500299 0.909594697 1 21.80404961 0.790168111 1.934134853 0.999967205 0.875264891 0.484521709 0.039326851 0.663489502 4.240490568 0.037372627 0.010403247 6.168337261 -0.790168111 -0.124702314 (ac)EEEIAALVIDNGSGMCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEEIAALVIDNGSGMCK 17 0 P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P63261 ACTG1 "Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;;; 160.67 4.43E-87 100941000 174450 179702 193373 171760 234015 245050 224047 196314 205636 184668 FALSE TRUE 181337.4207 210564.4206 198412.4592 205733.6153 194237.2139 188140.8513 206485.6107 193682.7319 198235.2005 220850.1589 0.821088025 0.95342662 0.898403063 0.931552942 0.879497732 0.851893665 0.934957945 0.876987062 0.897600443 1 17.75270834 -2.241885013 2.040174436 1.324914304 0.895719467 0.414368983 0.037774532 1758145.46 291746.3117 2631276.069 0.008837028 0.005729477 2.241885013 -0.429194837 (ac)GDKKS(ph)PTRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDKKSPTRPK 10 3 Q8IY57;Q8IY57-5;G3V1X5;A0A0B4J255;F8VRE5;G3V219;G3V212;Q8IY57-4 Q8IY57 YAF2 YY1-associated factor 2 1 GDKKS(0.975)PT(0.025)RPK;GDKKS(0.846)PT(0.154)RPK;GDKKS(0.967)PT(0.033)RPK 55.314 0.00068701 3482650000 5357200 1842730 3263100 1650110 4795400 4237500 4379900 3258420 3817130 1495730 TRUE FALSE 5568706.393 2159204.543 3348139.067 1976496.833 3980279.621 3253404.845 4036591.993 3214746.21 3679752.237 1788789.656 3.113114152 1.207075709 1.871734363 1.104935299 2.225124462 1.818774406 2.256605174 1.79716279 2.057118468 1 20.77055232 4.754037579 24.50780095 1.762175755 3.113115458 0.482544563 0.433960477 1914.338117 3031291.141 0.097476459 2.344304805 56759.37161 -4.754037579 1.350939703 (ac)GDPERPEAAGLDQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDPERPEAAGLDQDER 16 1 Q7LG56;Q7LG56-5 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 78.548 0.00010338 240330000 11711 23549 29205 23036 28720 24187 26097 31394 31348 30099 FALSE TRUE 12173.35932 27593.35756 29966.10629 27592.45204 23838.18466 18569.93581 24051.44895 30973.21478 30219.7916 35996.32277 0.338183414 0.766560455 0.832476875 0.766535299 0.662239441 0.515884245 0.668164054 0.860454969 0.839524409 1 15.13556191 1.673495779 3.367173039 0.901925578 0.660352187 0.40969945 0.138000638 0.22756432 6.025631494 0.084307995 0.037904722 47.15152881 -1.673495779 -0.241573391 (ac)GDREQLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDREQLLQR 9 1 Q04917;F8WEB6;A2IDB1 Q04917 YWHAH 14-3-3 protein eta 0 ;; 91.906 3.71E-05 2133150000 159547 143711 166221 150117 191608 200288 196528 179326 166064 184371 FALSE TRUE 165846.0388 168392.2463 170552.8558 179809.6945 159038.5406 153774.1474 181123.6218 176922.4283 160087.3891 220494.9675 0.752153397 0.763701087 0.773499993 0.815482079 0.721279685 0.697404341 0.821441069 0.802387602 0.726036476 1 17.7503862 -4.999999132 0.457117877 6.527775396 0.764700595 0.759558547 0.039716552 715.0575649 4.019215399 4008.356381 0.021482918 1.00E-05 4.999999132 -5.763074801 (ac)GDS(ph)DDEYDRR ddPTM_MDA-MB-175_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 71.491 1.07E-05 4846510000 23280 47127 45213 63539 40436 64719 19471 37616 39797 49175 TRUE FALSE 24199.11238 55220.69565 46391.28792 76106.82456 33562.70316 49688.99308 17944.81214 37111.81905 38364.71374 58809.89974 0.411480252 0.938969389 0.788834671 1.29411587 0.570698187 0.844908651 0.305132507 0.63104714 0.652351286 1 15.84377141 (ac)GDS(ph)DDEYDRRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDSDDEYDRRR 11 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A087X0F4 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 GDS(1)DDEYDRRR;GDS(1)DDEYDRRR 73.466 0.014218 179065000 129240 114682 142554 121406 164281 173121 139480 123573 147103 100720 TRUE FALSE 134342.495 134377.7414 146269.0743 145419.7444 136356.5743 132916.2714 128547.1931 121916.7061 141808.7918 120454.1556 1.115299795 1.115592407 1.214313227 1.207262163 1.132020507 1.10345941 1.067187699 1.012141968 1.177284346 1 16.87812464 2.611200243 2.106059785 1.060045726 1.162705062 0.399040232 0.054135345 0.318058745 2.797481172 0.020852629 0.018910144 408.5076961 -2.611200243 0.102659335 (ac)GS(ph)PEDDLIGIPFPDHSSELLSCLNEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSPEDDLIGIPFPDHSSELLSCLNEQR 27 0 O15156 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 GS(1)PEDDLIGIPFPDHSSELLSCLNEQR;GS(0.999)PEDDLIGIPFPDHSS(0.001)ELLSCLNEQR;GS(1)PEDDLIGIPFPDHSSELLSCLNEQR 58.08 0.0029084 49663100 975.61 3226 2162.22 2417.39 3101.5 3669.1 4300.4 2695.5 3310.82 3024.73 TRUE FALSE 1014.127836 3780.040405 2218.569229 2895.542527 2574.308138 2817.007131 3963.323411 2659.371231 3191.664235 3617.367932 0.280349651 1.044969845 0.61331036 0.80045563 0.71165228 0.778744984 1.095637349 0.73516747 0.882316727 1 11.82072463 4.752521801 24.87926094 0.834479465 0.280349251 0.569012829 0.148433231 1650.227298 2940701.776 0.033453974 0.696304605 56561.61496 -4.752521801 -0.554130213 (ac)GSELETAMETLINVFHAHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSELETAMETLINVFHAHSGK 21 0 P23297;Q5T7Y5;Q5T7Y4 P23297 S100A1 Protein S100-A1 0 ;;; 149.94 4.89E-55 1766740000 452506 444378 499634 421177 661700 646250 538681 477956 546826 562330 FALSE TRUE 470371.2863 520696.4647 512654.8725 504484.5535 549224.4704 496168.2315 496457.7756 471549.7816 527145.8391 672507.797 0.699428748 0.774260859 0.76230324 0.750154207 0.816681194 0.737788073 0.738218617 0.701181137 0.783850896 1 19.35919147 0.96541617 22.4927048 1.000000001 0.747804916 0.84551265 0.032196031 510.5836492 332075.2668 0.032063123 0.008015781 9.234559214 -0.96541617 -0.252195084 (ac)GTRDDEYDYLFK ddPTM_MDA-MB-175_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 1.33E-10 2653290000 2871820 2621390 2953290 2822360 3661710 3993450 3094820 2826230 2975590 2602550 FALSE TRUE 2985201.671 3071593.341 3030255.164 3380614.384 3039293.842 3066031.759 2852239.922 2788349.01 2868499.097 3112469.844 0.959110231 0.98686686 0.973585389 1.086151691 0.97648941 0.985079989 0.916391183 0.895863783 0.921615065 1 21.56962843 2.307714116 4.195228862 0.92115732 0.997935029 0.325617135 0.041702274 0.207408721 7.140289562 0.015152062 0.012212454 203.1019605 -2.307714116 0.076777709 (ac)MDDREDLVYQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MDDREDLVYQAK 12 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 98.033 6.26E-05 4568180000 4796230 4833010 5378290 4879310 6283170 6728540 5829190 5424520 5343320 4837450 FALSE TRUE 4985588.864 5663041.872 5518452.656 5844422.955 5215159.008 5165938.557 5372282.856 5351813.182 5151014.957 5785255.709 0.861775022 0.978874946 0.953882237 1.010227248 0.901456957 0.892949044 0.928616318 0.925078069 0.890369452 1 22.4639493 (ac)MDEET(ph)RHSLECIQANQIFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.5)RHS(0.5)LECIQANQIFPR 61.477 1.39E-16 58394000 5613.5 5800.6 4018 5056.5 5334.6 7592.7 4679 7261.2 5668.7 4879.1 TRUE FALSE 5835.125315 6796.807928 4122.712381 6056.660608 4427.826597 5829.410493 4312.247754 7163.875491 5464.684594 5835.066229 1.000010126 1.164821042 0.706540803 1.037976326 0.758830564 0.999030733 0.739022932 1.227728223 0.936524862 1 12.51053332 -1.431643619 6.111251537 1.000013482 0.959903091 0.005481533 0.166407284 2.92E-05 2.72E-06 0.153998018 0.036285482 0.037013178 1.431643619 -0.040110391 (ac)MDEETRHS(ph)LECIQANQIFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDEETRHSLECIQANQIFPR 20 1 Q13615-3;Q13615-2;Q13615;C9JLU3 Q13615-3 MTMR3 Myotubularin-related protein 3 1 MDEET(0.162)RHS(0.838)LECIQANQIFPR 74.579 1.09E-25 69208000 3489.4 3868.3 4348.5 6088.7 6776.5 5853.1 4682 4868.6 4467.6 4221.2 TRUE FALSE 3627.164206 4532.650434 4461.825482 7293.026687 5624.632951 4493.80623 4315.012606 4803.34438 4306.811949 5048.26332 0.718497427 0.897863314 0.883833746 1.444660515 1.114171863 0.890168746 0.854751888 0.951484516 0.853127437 1 12.30157145 -0.485225643 7.550028031 0.999988709 0.964367102 0.003223081 0.188293552 0 0 0.190158647 0.044820823 0.327170665 0.485225643 -0.035621607 (ac)MDEPS(ph)PLAQPLELNQHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MDEPSPLAQPLELNQHSR 18 0 Q13085;A0A0C4DGT1;A0A087X2F8;A0A087X126 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR 145.55 1.09E-18 1085589000 37079.7 17761.6 53887.3 26790.7 54016.8 64007 47319 45415 42135.1 30666.5 TRUE FALSE 38543.63519 20812.01663 55291.64731 32089.8205 44835.04363 49142.34429 43610.01313 44806.28621 40618.66598 36675.01353 1.05095081 0.567471274 1.507610822 0.874977741 1.222495626 1.339940727 1.189093307 1.221711511 1.10752968 1 15.16250988 4.245708782 24.99992338 1.18884704 0.809211137 0.367366939 0.196040397 151.9431256 531390.9733 0.043516487 0.113995372 17607.94941 -4.245708782 -0.379635903 (ac)MDFPT(ph)ISRSPSGPPAMDLEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDFPTISRSPSGPPAMDLEGPR 22 1 O96018 O96018 APBA3 Amyloid beta A4 precursor protein-binding family A member 3 1 MDFPT(0.345)IS(0.345)RS(0.263)PS(0.046)GPPAMDLEGPR 58.073 0.00074315 26842000 3552.4 3076.1 4430.6 2691.5 3109.5 4783.7 3514.3 2222.1 3966.4 3794.7 TRUE FALSE 3692.651495 3604.396246 4546.065076 3223.870667 2580.948301 3672.758173 3238.839983 2192.316384 3823.650039 4538.198811 0.813682178 0.794234981 1.001733345 0.710385508 0.568716446 0.80929865 0.713684023 0.483080728 0.842547935 1 12.1479041 3.573629302 9.807272605 0.692484991 0.861955492 0.116257132 0.147243303 0.65752485 62.96086606 0.03817083 0.059148712 3746.530754 -3.573629302 0.169470501 (ac)MDFPTISRS(ph)PSGPPAMDLEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDFPTISRSPSGPPAMDLEGPR 22 1 O96018 O96018 APBA3 Amyloid beta A4 precursor protein-binding family A member 3 1 MDFPTIS(0.031)RS(0.812)PS(0.156)GPPAMDLEGPR 90.22 3.40E-07 31338000 3856.9 3281.4 3224.4 4186.8 4184.9 3590.7 4778.2 3623.8 3901.1 3401.5 TRUE FALSE 4009.17339 3844.954924 3308.430513 5014.936544 3473.552193 2756.814343 4403.672198 3575.228888 3760.700173 4067.958799 0.985549163 0.9451804 0.813290074 1.232789414 0.853880869 0.677689839 1.082526254 0.878875393 0.924468599 1 11.99008935 (ac)MDLFGDLPEPERS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MDLFGDLPEPERSPR 15 1 Q9H0C8;E9PC05;F8SNU7;F8SNU6 Q9H0C8 ILKAP;ILKAP3;ILKAP2 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR 57.328 0.0033353 186053000 50086.8 44279.4 42185.6 41256 72606.1 91445.8 65737.6 45740.4 60844.6 60321.3 TRUE FALSE 52064.26554 51884.0425 43284.99139 49416.31366 60264.54106 70208.89882 60584.91514 45127.32475 58654.81473 72140.10381 0.721710433 0.719212196 0.600012879 0.685004748 0.835381956 0.9732298 0.839822955 0.625551148 0.813068067 1 16.13851388 3.244460265 22.06899113 0.820818375 0.678360243 0.373874731 0.101896275 45.18329427 169011.9941 0.031486058 0.041388689 1755.74025 -3.244460265 -0.142458132 (ac)MDLFGDLPEPERS(ph)PRPAAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 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;MDLFGDLPEPERS(1)PRPAAGK;MDLFGDLPEPERS(1)PRPAAGK 158.94 1.97E-29 3236112000 1870692 1753356 1882180 1588361 2328205 2455508 2040329 1951914 2106667 1961679 TRUE FALSE 1944548.365 2054481.254 1931231.157 1902534.065 1932457.546 1885253.481 1880402.682 1925751.786 2030848.466 2346032.441 0.828866784 0.87572585 0.823190303 0.810958123 0.823713053 0.803592247 0.801524586 0.820854713 0.865652337 1 21.16179153 0.825766409 2.736788464 0.999931313 0.823094789 0.880034281 0.019571545 0.245772879 3.153075834 0.020408492 0.005403035 6.695243996 -0.825766409 -0.176836523 (ac)MDPQRS(ph)PLLEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDPQRSPLLEVK 12 1 Q9BW19;A2AB20;A0A140T9E6 Q9BW19 KIFC1 Kinesin-like protein KIFC1 1 MDPQRS(1)PLLEVK;MDPQRS(1)PLLEVK 62.924 0.00022853 69489000 484910 438460 462180 368080 548900 685020 530010 425110 493230 428360 TRUE FALSE 504054.6212 513762.0943 474224.7905 440885.1254 455598.1741 525934.4866 488466.4313 419412.0958 475478.7486 512288.9406 0.983926416 1.00287563 0.925697888 0.860618082 0.889338297 1.026636425 0.953497904 0.818702226 0.928145644 1 18.96659822 4.190227231 5.839747593 0.914937119 0.99349294 0.160781688 0.058719855 0.273214165 21.02819116 0.015564311 0.035535235 15496.27203 -4.190227231 0.07855582 (ac)MDRNPS(ph)PPPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 82.278 2.25E-05 1792518000 78211.8 171398.2 145848.3 163070.1 123230.6 219891.9 123325 159090.5 117442.2 218733.1 TRUE FALSE 81299.66226 200834.5076 149649.2265 195324.8791 102283.9066 168825.3387 113658.4643 156958.1521 113215.4782 261589.663 0.310790806 0.767746344 0.572076223 0.746684241 0.391008977 0.645382301 0.43449142 0.600016645 0.432797982 1 17.99694601 -1.783846437 4.265764089 1.053255356 0.554935046 0.471145198 0.14438337 0.057853297 0.002931525 0.110599269 0.029660146 0.016449533 1.783846437 -0.49832031 (ac)MDSAGQDINLNS(ph)PNKGLLSDSMTDVPVDTGVAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 MDS(0.287)AGQDINLNS(0.712)PNKGLLSDSMTDVPVDTGVAAR;MDSAGQDINLNS(0.988)PNKGLLS(0.01)DS(0.002)MTDVPVDTGVAAR 101.21 2.54E-89 276890000 114191 108702 125589 97838 165231 190357 143229 119340 140943 124452 TRUE FALSE 118699.3489 127370.7229 128861.9525 117190.0644 137145.0936 146149.4716 132002.3367 117740.4425 135870.489 148835.9866 0.797517802 0.855779075 0.865798356 0.787377213 0.921451167 0.981949829 0.886897986 0.791075097 0.912887347 1 17.18336387 3.22709001 24.9994945 0.898762222 0.831499622 0.333164294 0.058726745 352.7420954 768778.8897 0.018608763 0.022421578 1686.902607 -3.22709001 -0.067262601 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-4;Q9NQC3-2 Q9NQC3-5;Q9NQC3-2 RTN4 Reticulon-4 1 MEDLDQSPLVSS(0.001)S(0.002)DS(0.997)PPRPQPAFK;MEDLDQSPLVSS(0.004)S(0.031)DS(0.965)PPRPQPAFK;MEDLDQSPLVSS(0.001)S(0.015)DS(0.983)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVS(0.002)S(0.002)S(0.007)DS(0.989)PPRPQPAFK;MEDLDQSPLVS(0.02)S(0.116)S(0.116)DS(0.748)PPRPQPAFK;MEDLDQSPLVSSS(0.004)DS(0.996)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.998)PPRPQPAFK;MEDLDQSPLVSSS(0.001)DS(0.999)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVSSSDS(1)PPRPQPAFK;MEDLDQSPLVS(0.004)S(0.018)S(0.103)DS(0.875)PPRPQPAFK 159.66 3.78E-33 2497602000 1921864 1979755 1925419 2270547 2342512 3097217 2134751 1957596 2121086 2226836 TRUE FALSE 1997740.675 2319762.521 1975597.001 2719654.42 1944332.647 2377935.291 1967423.638 1931357.628 2044748.529 2663141.879 0.75014429 0.871062312 0.741829422 1.021220252 0.730089772 0.892905973 0.738760354 0.7252177 0.767795567 1 21.34469786 2.226928911 24.99337519 0.776981816 0.835725361 0 0.109630304 661.6432278 1421681.053 0.03800399 0.02829843 168.6276978 -2.226928911 0.058743546 (ac)MEDMNEYSNIEEFAEGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEDMNEYSNIEEFAEGSK 18 0 O14979-2;O14979-3;A0A087WU03 O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 83.204 5.16E-12 15899000 20229 21759 21585 18743 27505 27205 22799 23904 22810 19289 FALSE TRUE 21027.65654 25495.93899 22147.52283 22450.30946 22829.70992 20887.05105 21011.95481 23583.60598 21989.07256 23068.31024 0.911538657 1.105236522 0.960084315 0.973209967 0.989656793 0.905443478 0.910857995 1.022337819 0.953215573 1 14.49362471 (ac)MEDS(ph)MDMDMSPLRPQNYLFGCELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.001)LFGCELK;MEDS(0.833)MDMDMS(0.165)PLRPQNY(0.003)LFGCELK;MEDS(0.5)MDMDMS(0.5)PLRPQNYLFGCELK;MEDS(0.499)MDMDMS(0.499)PLRPQNY(0.001)LFGCELK;MEDS(0.976)MDMDMS(0.024)PLRPQNYLFGCELK;MEDS(0.889)MDMDMS(0.111)PLRPQNYLFGCELK;MEDS(0.984)MDMDMS(0.015)PLRPQNYLFGCELK;MEDS(0.885)MDMDMS(0.114)PLRPQNYLFGCELK;MEDS(0.9)MDMDMS(0.1)PLRPQNYLFGCELK;MEDS(0.984)MDMDMS(0.016)PLRPQNYLFGCELK;MEDS(0.866)MDMDMS(0.134)PLRPQNY(0.001)LFGCELK 99.686 5.86E-26 1268350000 695477 653139 737669 626021 886140 961568 807569 746811 827077 701153 TRUE FALSE 722934.969 765310.5425 756893.2601 749846.0853 735514.2393 738258.4047 744269.6316 736801.2201 797310.6603 838530.506 0.862145102 0.912680621 0.902642486 0.894238289 0.877146668 0.880419257 0.88758802 0.878681473 0.95084276 1 19.67750374 1.044350019 3.428708366 0.999406957 0.887609223 0.879509341 0.013673977 0.063765453 1.627298578 0.013223187 0.003443275 11.07516026 -1.044350019 -0.111797734 (ac)MEDSMDMDMS(ph)PLRPQNYLFGCELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 33 MEDSMDMDMSPLRPQNYLFGCELK 24 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MEDS(0.107)MDMDMS(0.89)PLRPQNY(0.003)LFGCELK;MEDS(0.008)MDMDMS(0.991)PLRPQNY(0.001)LFGCELK;MEDS(0.002)MDMDMS(0.991)PLRPQNY(0.007)LFGCELK;MEDS(0.006)MDMDMS(0.994)PLRPQNYLFGCELK;MEDS(0.016)MDMDMS(0.979)PLRPQNY(0.004)LFGCELK;MEDS(0.437)MDMDMS(0.563)PLRPQNYLFGCELK;MEDS(0.013)MDMDMS(0.987)PLRPQNYLFGCELK;MEDS(0.194)MDMDMS(0.797)PLRPQNY(0.009)LFGCELK;MEDS(0.146)MDMDMS(0.842)PLRPQNY(0.012)LFGCELK;MEDS(0.199)MDMDMS(0.783)PLRPQNY(0.018)LFGCELK;MEDS(0.005)MDMDMS(0.994)PLRPQNY(0.001)LFGCELK;MEDS(0.043)MDMDMS(0.936)PLRPQNY(0.021)LFGCELK;MEDS(0.095)MDMDMS(0.902)PLRPQNY(0.002)LFGCELK;MEDS(0.416)MDMDMS(0.576)PLRPQNY(0.008)LFGCELK;MEDS(0.042)MDMDMS(0.937)PLRPQNY(0.021)LFGCELK;MEDS(0.016)MDMDMS(0.941)PLRPQNY(0.043)LFGCELK;MEDS(0.247)MDMDMS(0.745)PLRPQNY(0.007)LFGCELK;MEDS(0.098)MDMDMS(0.902)PLRPQNYLFGCELK;MEDS(0.072)MDMDMS(0.928)PLRPQNYLFGCELK;MEDS(0.466)MDMDMS(0.532)PLRPQNY(0.002)LFGCELK;MEDS(0.067)MDMDMS(0.933)PLRPQNYLFGCELK;MEDS(0.002)MDMDMS(0.991)PLRPQNY(0.007)LFGCELK;MEDS(0.208)MDMDMS(0.792)PLRPQNYLFGCELK;MEDS(0.02)MDMDMS(0.98)PLRPQNYLFGCELK;MEDS(0.164)MDMDMS(0.825)PLRPQNY(0.011)LFGCELK;MEDS(0.467)MDMDMS(0.531)PLRPQNY(0.002)LFGCELK;MEDS(0.132)MDMDMS(0.868)PLRPQNYLFGCELK;MEDS(0.466)MDMDMS(0.532)PLRPQNY(0.002)LFGCELK;MEDSMDMDMS(0.999)PLRPQNY(0.001)LFGCELK;MEDS(0.001)MDMDMS(0.998)PLRPQNY(0.001)LFGCELK;MEDS(0.008)MDMDMS(0.991)PLRPQNY(0.001)LFGCELK;MEDSMDMDMS(0.998)PLRPQNY(0.002)LFGCELK;MEDS(0.001)MDMDMS(0.983)PLRPQNY(0.015)LFGCELK 110.18 1.80E-45 3905082000 2136581 2275297 2651434 2143629 3141079 3277488 2886658 2633887 2727968 2348288 TRUE FALSE 2220934.868 2666061.56 2720532.548 2567632.418 2607159.514 2516341.083 2660394.203 2598584.053 2629788.965 2808390.073 0.790821364 0.949320248 0.968716054 0.914272003 0.928346649 0.896008395 0.947302239 0.925293134 0.936404451 1 21.4213119 7.999948212 0.013636764 1.707651072 1.23E-06 0.331877715 0.043036525 9115.928256 9.600024842 490.3212564 734.6730696 99988076.18 -7.999948212 -1.707649841 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHK 32 2 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPT(0.018)S(0.018)QKPGVGAGHGGDPKLS(0.963)PHK;MEFDLGAALEPTS(0.002)QKPGVGAGHGGDPKLS(0.998)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPTS(0.001)QKPGVGAGHGGDPKLS(0.999)PHK;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHK;MEFDLGAALEPT(0.002)S(0.007)QKPGVGAGHGGDPKLS(0.992)PHK 174.49 1.10E-73 8675200000 4400960 1765920 3064570 1900765 4316860 4231650 4631590 3164900 3706910 1478871 TRUE FALSE 4574713.299 2069203.023 3144435.212 2276730.644 3583081.679 3248913.419 4268553.873 3122479.692 3573499.033 1768627.458 2.586589549 1.16994849 1.777895734 1.287286723 2.025910919 1.836968777 2.413483888 1.765481859 2.020492794 1 20.75419876 (ac)MEFDLGAALEPTSQKPGVGAGHGGDPKLS(ph)PHKVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MEFDLGAALEPTSQKPGVGAGHGGDPKLSPHKVQGR 36 3 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 MEFDLGAALEPT(0.002)S(0.011)QKPGVGAGHGGDPKLS(0.987)PHKVQGR;MEFDLGAALEPT(0.001)S(0.001)QKPGVGAGHGGDPKLS(0.998)PHKVQGR;MEFDLGAALEPT(0.006)S(0.019)QKPGVGAGHGGDPKLS(0.975)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR;MEFDLGAALEPTSQKPGVGAGHGGDPKLS(1)PHKVQGR 115.82 1.96E-30 22050590000 9849340 4711990 7213050 4035600 11193880 9381840 8259940 6993370 8691170 4696500 TRUE FALSE 10238199.55 5521237.628 7401028.009 4833829.635 9291148.276 7203049.843 7612504.319 6899635.314 8378376.489 5616689.255 1.822817515 0.983005713 1.317685147 0.860619026 1.654203723 1.282436951 1.355336565 1.228416777 1.491693079 1 22.42128856 -1.422480563 3.07960945 0.994833471 1.310851135 0.115193035 0.270651881 37610205.7 48895797.7 1716160.877 0.060907948 0.037802406 1.422480563 0.316017663 (ac)MEGHDPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEGHDPKEPEQLR 13 1 P51991-2 P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 48.527 0.070994 137500000 76072 74884 101580 71844 98081 125880 97460 88883 81740 81914 FALSE TRUE 79075.3813 87744.74448 104227.2582 86054.52877 81409.22665 96646.27773 89820.83054 87691.66877 78798.19337 97963.47996 0.807192449 0.895688317 1.063939932 0.878434788 0.831016075 0.98655415 0.916880766 0.895146526 0.804362946 1 16.5799564 1.619274463 5.448603289 0.886100264 0.915031 0 0.082082253 0.751536143 47.82609219 0.044400161 0.021019941 41.61735386 -1.619274463 0.028930736 (ac)MELDLSPPHLSSS(ph)PEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 MELDLS(0.004)PPHLS(0.301)S(0.331)S(0.364)PEDLCPAPGT(0.956)PPGT(0.044)PRPPDTPLPEEVKR 93.227 1.25E-13 54790000 7850.3 26248 24225 23581 26593 43174 25081 30740 21846 29773 TRUE FALSE 8160.235906 30755.88982 24856.3234 28245.25142 22072.73136 33147.49281 23115.08568 30327.98058 21059.76673 35606.44931 0.229178592 0.863773008 0.698084866 0.793262231 0.619908241 0.930940699 0.649182553 0.851755263 0.591459332 1 15.11985096 4.744791052 24.78282457 0.768836962 0.22917832 0.614799549 0.130063258 375.4006008 1493186.057 0.027220254 0.254199109 55563.6864 -4.744791052 -0.539658641 (ac)MELDLSPPHLSSSPEDLCPAPGT(ph)PPGTPRPPDTPLPEEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MELDLSPPHLSSSPEDLCPAPGTPPGTPRPPDTPLPEEVKR 41 2 Q14451;Q14451-4;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 MELDLSPPHLS(0.015)S(0.015)S(0.015)PEDLCPAPGT(0.879)PPGT(0.074)PRPPDT(0.003)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.995)PPGT(0.005)PRPPDTPLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.941)PPGT(0.053)PRPPDT(0.007)PLPEEVKR;MELDLSPPHLSSSPEDLCPAPGT(0.991)PPGT(0.009)PRPPDTPLPEEVKR 164.39 3.28E-67 1087000000 53972 358968 273028 312642 304497 433807 255622 381290 311638 334950 TRUE FALSE 56102.85624 420617.9616 280143.334 374481.6545 252738.7087 333061.8987 235585.6797 376179.4312 300422.2093 400577.0395 0.140055097 1.050030132 0.699349454 0.934855515 0.630936583 0.83145529 0.588115784 0.939093842 0.749973612 1 18.6117202 4.751524282 24.85554177 0.81170399 0.140054633 0.653319842 0.149379414 1129.678086 2165916.973 0.032261971 0.597989055 56431.84921 -4.751524282 -0.671649357 (ac)MENGYTYEDYKNTAEWLLSHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MENGYTYEDYKNTAEWLLSHTK 22 1 P00491;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 137.12 1.92E-36 1073400000 591650 509090 668800 508340 860330 840940 797870 654820 776460 579220 FALSE TRUE 615008.7989 596522.2473 686229.4774 608888.1348 714091.4139 645644.4296 735330.8646 646043.209 748515.3563 692707.0692 0.887833871 0.86114647 0.990648873 0.878998009 1.030870689 0.932059825 1.061532208 0.932635507 1.080565494 1 19.40188587 4.282156104 0.44559333 1.013316222 0.807169061 0.408621396 0.057114688 3.355714796 0.701665724 0.039896107 0.352559549 19149.44116 -4.282156104 -0.206147161 (ac)MEQLS(ph)DEEIDHGAEEDS(ph)DKEDQDLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEQLSDEEIDHGAEEDSDKEDQDLDK 26 1 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6;C9J0R8;C9JLG4 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 2 MEQLS(1)DEEIDHGAEEDS(1)DKEDQDLDK 49.312 0.001514 354690000 419330 104770 154690 103580 243870 514200 310900 157710 181110 77145 TRUE FALSE 435885.4722 122763.4325 158721.3485 124067.8148 202417.0645 394784.8428 286530.8456 155596.1554 174591.8865 92260.08572 4.724529235 1.330623439 1.720368535 1.344761539 2.193983053 4.279042662 3.105685881 1.686494806 1.89238808 1 16.49341901 4.750169706 24.63492968 2.149204881 4.724531123 0.424620501 0.924927206 1569.398517 3330247.158 0.234822987 3.737284556 56256.111 -4.750169706 2.575326242 (ac)MESADFYEAEPRPPMS(ph)SHLQSPPHAPSSAAFGFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPR 35 1 P49715 P49715 CEBPA CCAAT/enhancer-binding protein alpha 1 MESADFY(0.005)EAEPRPPMS(0.317)S(0.317)HLQS(0.317)PPHAPS(0.022)S(0.022)AAFGFPR 43.728 0.00064488 58503000 3624.4 4519.1 5794.5 3948.9 5632.7 6286.5 6693.2 3949.4 3427.4 4873.5 TRUE FALSE 3767.494111 5295.220271 5945.50943 4729.980634 4675.255666 4826.555648 6168.569495 3896.464753 3304.048544 5828.369016 0.646406242 0.908525225 1.020098318 0.811544468 0.802155055 0.828114286 1.058369756 0.668534326 0.56689076 1 12.50887651 1.619468879 25 0.71328851 0.868691004 0.112785247 0.149960419 1.272196132 2734.45673 0.067189218 0.036863035 41.6359884 -1.619468879 0.155402494 (ac)MESYHKPDQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ;;;;;;;;; 99.283 3.51E-05 10363010000 4846080 6750620 8415240 6354120 12931630 10632930 9433310 8949810 9123950 7773950 FALSE TRUE 5037406.98 7909986.472 8634548.068 7610945.971 10733516.15 8163593.151 8693902.513 8829852.436 8795580.822 9297106.661 0.541825233 0.850800874 0.928734969 0.818635974 1.1545007 0.878078896 0.935119154 0.949741974 0.946055708 1 23.14835038 5.095169544 1.279478615 0.954810803 9.63E-16 0.697156341 0.081482319 1.635622912 1.268457147 0.021368156 2.545836364 124500.0552 -5.095169544 -0.954810803 (ac)METMAS(ph)PGKDNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 METMASPGKDNYR 13 1 O60684;S4R3E5 O60684 KPNA6 Importin subunit alpha-7 1 MET(0.069)MAS(0.931)PGKDNYR;MET(0.026)MAS(0.974)PGKDNYR;METMAS(1)PGKDNYR 92.781 2.19E-07 243740000 644760 462187 500380 360080 701790 859180 605740 509550 567870 407860 TRUE FALSE 670215.6227 541564.0219 513420.3139 431302.7493 582499.9865 659648.466 558260.516 502720.3157 547432.4696 487772.358 1.374033628 1.110280263 1.052581815 0.884229584 1.194204585 1.352369512 1.144510358 1.030645356 1.122311383 1 18.89584848 1.769065612 10.72310938 1.057374796 1.151193497 0.115619253 0.135245979 0.809708136 273.949152 0.067103987 0.037224495 58.75781148 -1.769065612 0.093818701 (ac)MEVAEPSS(ph)PTEEEEEEEEHSAEPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.102)S(0.765)PT(0.132)EEEEEEEEHSAEPRPR;MEVAEPS(0.005)S(0.581)PT(0.414)EEEEEEEEHSAEPRPR;MEVAEPS(0.031)S(0.83)PT(0.139)EEEEEEEEHSAEPRPR;MEVAEPS(0.414)S(0.477)PT(0.109)EEEEEEEEHSAEPRPR 115.54 1.29E-17 8772900000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)MEVKPPPGRPQPDS(ph)GR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 MEVKPPPGRPQPDS(1)GR 89.011 1.92E-06 247900000 122450 86046 106140 98929 132400 138920 124030 107860 103660 90689 TRUE FALSE 127284.4206 100823.7312 108906.0956 118496.8609 109894.6953 106657.9354 114308.2045 106414.3131 99929.29685 108457.7732 1.173585044 0.929612772 1.004133612 1.092562178 1.013248678 0.983405174 1.053942019 0.981158934 0.921365928 1 16.72677393 1.569250989 4.975866707 0.957882109 1.029585871 0.189910412 0.0644203 0.245884976 13.13144613 0.034950177 0.015746145 37.08950092 -1.569250989 0.071703763 (ac)MEVKPPPGRPQPDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;; 71.344 7.06E-06 5212810000 1665200 1609278 1703046 1561816 2039905 2209557 1901207 1777297 1857697 1524470 FALSE TRUE 1730943.382 1885658.978 1747428.778 1870738.543 1693162.677 1696420.873 1752185.427 1753475.241 1790838.848 1823160.709 0.949418981 1.034280176 0.958461187 1.026096347 0.92869634 0.930483454 0.9610702 0.96177766 0.982271524 1 20.79801031 5.078044115 20.59737425 0.97285824 3.29E-05 0.044921824 0.034127912 2136.718859 560494.0953 0.007877027 584.75488 119686.2102 -5.078044115 -0.972825376 (ac)MEVKPPPGRPQPDSGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MEVKPPPGRPQPDSGRR 17 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;; 51.888 0.0013434 2386320000 841730 887185 912984 812566 1119858 1130478 896985 919108 970134 952567 FALSE TRUE 874962.1504 1039552.122 936777.1131 973289.1295 929504.9372 867941.6171 826676.9719 906788.8606 935219.0668 1139204.266 0.768046765 0.91252478 0.822308291 0.854358747 0.815924734 0.7618841 0.72566176 0.795984432 0.820940629 1 20.11959502 5.05069348 14.75604109 0.820618704 0.473772668 0.039452984 0.074068334 2592096.318 21545023.04 0.017124489 25177480.6 112381.1521 -5.05069348 -0.346846035 (ac)MFCVT(ph)PPELETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MFCVTPPELETK 12 0 O60256;O60256-2;O60256-3;E7EPA1;C9K0K7;C9JJS3;C9JDU5;I3L1T1;I3L275;E7EW35;I3L164;I3L331;I3L2J4;I3L3B8;C9JDH0 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 MFCVT(1)PPELETK;MFCVT(1)PPELETK 81.865 0.00038238 22446000 61349 60832 64460 57576 85461 100162 70974 70463 70815 57710 TRUE FALSE 63771.10589 71279.42279 66139.88055 68964.36095 70934.36975 76900.89347 65410.87242 69518.55874 68266.38198 69017.16958 0.923989006 1.032778122 0.958310533 0.999234848 1.027778597 1.114228444 0.947747826 1.007264702 0.989121727 1 16.07466769 4.749802035 23.61185948 1.007903832 0.923988897 0.253799925 0.043459981 1119.651804 2351654.429 0.010346911 0.152298383 56208.50512 -4.749802035 -0.083914935 (ac)MFPFGPHS(ph)PGGDGSAGAGAEEPTPHEGQAAATGPPS(ph)PLHPGADATHPPPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MFPFGPHSPGGDGSAGAGAEEPTPHEGQAAATGPPSPLHPGADATHPPPPAR 52 0 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 2 MFPFGPHS(0.729)PGGDGS(0.262)AGAGAEEPT(0.012)PHEGQAAAT(0.114)GPPS(0.851)PLHPGADAT(0.033)HPPPPAR 46.542 1.61E-05 47645000 3202.7 11526 9138.7 11633 10101 14432 9130.7 10082 8963.7 12600 TRUE FALSE 3329.145069 13505.50084 9376.86203 13933.97268 8384.035628 11080.38672 8415.011875 9946.867281 8641.098188 15068.72876 0.220930718 0.896260133 0.622272932 0.924694638 0.556386392 0.735323258 0.558442056 0.660099962 0.573445732 1 13.87927009 -1.872278004 2.740457807 1.155437988 0.651844939 0.247905073 0.187554515 59510926.75 42157784.13 60309193.57 0.042979799 0.013419057 1.872278004 -0.503593049 (ac)MHGHGGYDS(ph)DFS(ph)DDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MHGHGGYDSDFSDDER 16 0 Q70Z53;Q70Z53-2;Q70Z53-4;Q70Z53-5;Q70Z53-3 Q70Z53 FRA10AC1 Protein FRA10AC1 2 MHGHGGY(0.031)DS(0.969)DFS(1)DDER;MHGHGGY(0.006)DS(0.994)DFS(1)DDER 118.32 3.19E-58 1059600000 26892 145397 108777 158263 151809 193200 132588 134153 137788 154617 TRUE FALSE 27953.71693 170367.8037 111611.818 189566.949 126004.5604 148332.228 122195.4061 132354.8985 132829.0368 184911.2408 0.151173703 0.921349091 0.603596717 1.02517807 0.681432669 0.802180697 0.660832763 0.715775298 0.718339438 1 17.4964734 4.747062492 24.8705546 0.772915582 0.151173367 0.653877677 0.139261198 588.5734651 1721714.207 0.030291184 0.351540072 55855.056 -4.747062492 -0.621742215 (ac)MLSLQYPDVYRDETAVQDYHGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MLSLQYPDVYRDETAVQDYHGHK 23 1 P48147 P48147 PREP Prolyl endopeptidase 0 ;;; 91.128 1.68E-06 630990000 413474 490758 535865 435642 639400 667410 493559 505923 559656 554180 FALSE TRUE 429798.2728 575041.8689 549830.0821 521810.6873 530715.0164 512414.1422 454872.5559 499141.9297 539514.0899 662760.9606 0.648496665 0.867645959 0.829605416 0.787328642 0.800763847 0.773150763 0.686329737 0.753125123 0.814040238 1 19.3381291 -2.019413507 3.739738582 1.267507546 0.773673922 0.547293045 0.061830178 0.04740664 0.000246094 0.02058004 0.013906955 0.009562831 2.019413507 -0.493833624 (ac)MMGHRPVLVLSQNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MMGHRPVLVLSQNTK 15 1 P49368;P49368-2;E9PRC8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 81.904 0.00030397 497340000 139660 239640 194780 191650 242750 280620 199150 201950 189940 278620 FALSE TRUE 145173.8846 280796.3059 199856.1268 229557.798 201487.4417 215450.2578 183540.1026 199243.1906 183104.0965 333210.2545 0.435682524 0.842700073 0.599789845 0.688927771 0.604685597 0.646589518 0.550823692 0.597950357 0.549515191 1 18.34607327 -2.006400878 2.892134883 1.398469703 0.618161054 0.574415744 0.099853106 15400923.81 8848811.29 40880774.6 0.023362982 0.009853695 2.006400878 -0.780308649 (ac)MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDK 32 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 48.204 0.0018605 26128000 7461.5 6057.9 9419.5 8705.7 10664 12315 10701 8632.7 9523.6 7387.4 FALSE TRUE 7756.085782 7098.297201 9664.979908 10427.66148 8851.337089 9455.027886 9862.227658 8516.992777 9180.847496 8834.81959 0.877899736 0.803445631 1.093964603 1.180291388 1.001869591 1.070200448 1.116290781 0.964025659 1.039166381 1 13.10898496 4.238389094 24.99997902 1.057809621 0.840672633 0.664294355 0.061861561 2.500287083 364682.449 0.015813196 0.037984884 17313.66835 -4.238389094 -0.217136988 (ac)MNLLPNIES(ph)PVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNLLPNIESPVTR 13 0 P17980;E9PM69 P17980 PSMC3 26S protease regulatory subunit 6A 1 MNLLPNIES(0.96)PVT(0.04)R 48.44 0.0011186 56478000 3431.4 5341.6 9012.8 7480.6 9909.2 11680 7610.1 6222.2 8833.3 3275.1 TRUE FALSE 3566.874322 6258.978248 9247.680972 8960.240353 8224.837723 8967.497012 7013.600477 6138.801586 8515.391258 3916.793139 0.91066191 1.597985399 2.361033795 2.287647071 2.09989076 2.289499775 1.790648683 1.567302987 2.174072246 1 11.93545722 2.003659011 24.82656919 1.652362968 1.961119235 0.083779074 0.483111104 276.6624715 1877153.609 0.187103326 0.137538757 100.8460777 -2.003659011 0.308756268 (ac)MNTAPSRPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.006)RPS(0.852)PT(0.142)R;MNTAPS(0.041)RPS(0.758)PT(0.201)R;MNTAPS(0.075)RPS(0.756)PT(0.168)R;MNTAPS(0.025)RPS(0.807)PT(0.168)R;MNT(0.001)APS(0.028)RPS(0.865)PT(0.106)R;MNTAPS(0.017)RPS(0.831)PT(0.152)R 76.24 6.42E-05 6693937000 250524.2 266494 332786 250158.2 329277 452581 344332 313495 342349 317149.1 TRUE FALSE 260415.0889 312262.2715 341458.6765 299638.7453 273306.6132 347475.9217 317342.3581 309293.1123 330027.9264 379288.394 0.686588604 0.823284541 0.900261337 0.79000241 0.720577317 0.916125901 0.836678272 0.815456305 0.870123979 1 18.5329357 -4.999999987 0.144095781 1.641044123 0.756570285 0.480304366 0.06324064 126.7208803 1.105415794 23.21560565 0.360050952 1.00E-05 4.999999987 -0.884473838 (ac)MNTAPSRPS(ph)PTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.06)RPS(0.47)PT(0.47)RR 53.168 0.001831 592450000 0 12181 8704.8 7090.1 4812.6 3980.6 0 5848.9 0 7744.4 TRUE FALSE 0 14272.99199 8931.654239 8492.500618 3994.555971 3056.165977 0 5770.505062 0 9261.766905 0 1.541065775 0.964357485 0.916941735 0.431295239 0.329976559 0 0.62304581 0 1 13.17707173 3.205228178 4.678542732 0.359642548 0.915560936 0.197358752 0.444080444 0.260100485 13.17200158 0.121012469 0.151373744 1604.087955 -3.205228178 0.555918388 (ac)MNTAPSRPSPT(ph)RR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MNTAPSRPSPTRR 13 2 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 MNTAPS(0.026)RPS(0.381)PT(0.592)RR;MNTAPS(0.028)RPS(0.385)PT(0.587)RR;MNT(0.001)APS(0.071)RPS(0.41)PT(0.519)RR 76.341 0.00054845 2838480000 31605 30864.6 26535.6 34030 65275 57952.4 38334 37706.4 38767 34128.8 TRUE FALSE 32852.7898 36165.35496 27227.13954 40761.03243 54179.57882 44493.83338 35329.28091 37201.00738 37371.78324 40815.68492 0.804906003 0.886065125 0.667075405 0.998660993 1.327420547 1.090116054 0.865580989 0.911439008 0.915623082 1 15.31683605 3.653256861 8.545180273 1.012889891 0.796373954 0.39156564 0.130945831 0.406850382 37.56167257 0.039111456 0.060680483 4500.459535 -3.653256861 -0.216515937 (ac)MNVDHEVNLLVEEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 MNVDHEVNLLVEEIHR 16 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 ;;;;;;;;;;;;;; 131.24 6.93E-20 4753528000 103753.65 115749.1 114043.1 144037 145459.4 158656.3 113683.9 133596.3 118171.9 151482.37 FALSE TRUE 107849.9242 135628.1075 117015.1569 172527.0887 120734.2631 121810.7788 104773.0589 131805.6601 113918.9164 181162.4401 0.595321658 0.748654674 0.645912899 0.952333655 0.666442023 0.672384291 0.578337644 0.727555116 0.628821937 1 17.46692435 -1.219436298 5.037121957 1.000035689 0.694983708 0.457779113 0.100905886 3.91E-05 6.06E-06 0.094478038 0.022266086 0.06033422 1.219436298 -0.30505198 (ac)MS(ph)PTPPLFSLPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;Q96FV9-2;J3KRD7;J3QQZ3;J3KT14 A0A087WWS1 THOC1 THO complex subunit 1 1 MS(0.498)PT(0.498)PPLFS(0.005)LPEAR 43.628 0.0078577 16786000 4233.2 3950.5 4431.3 3672.2 3601 5138.2 6179 4405.6 4298.8 4593.7 TRUE FALSE 4400.330005 4628.967644 4546.783318 4398.5502 2988.903306 3944.93092 5694.673834 4346.550138 4144.087028 5493.747563 0.80097055 0.842588341 0.82762873 0.80064658 0.544055451 0.718076481 1.036573626 0.791181263 0.754327894 1 12.42357491 (ac)MT(ph)TS(ph)QKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 32 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 MT(0.565)T(0.565)S(0.865)QKHRDFVAEPMGEKPVGS(0.004)LAGIGEVLGK 42.536 1.90E-05 170260000 136840 78622 149300 74587 195210 147130 138280 128840 167240 63142 TRUE FALSE 142242.5489 92124.71691 153190.8807 89340.08598 162028.2739 112961.2873 127441.2523 127113.1105 161221.0651 75513.46597 1.883671303 1.219977334 2.028656461 1.183101382 2.145687154 1.495909184 1.687662599 1.683317126 2.134997553 1 16.20444632 -0.729523361 6.555401808 0.999999998 1.700057181 0.301333837 0.326998631 1.25E-08 2.55E-09 0.280191983 0.066041883 0.18641319 0.729523361 0.700057183 (ac)MTTS(ph)QKHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTTSQKHR 8 1 O75531;E9PJJ8 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 MTT(0.022)S(0.978)QKHR 74.944 0.0053075 83856000 41074 58776 57662 38278 59524 74721 40088 54748 52801 93874 TRUE FALSE 42695.63324 68870.32079 59164.71909 45849.27415 49406.13174 57368.18016 36945.79781 54014.19261 50900.70232 112266.813 0.380305026 0.613452177 0.527000968 0.408395615 0.440077797 0.510998563 0.329089219 0.481123416 0.453390463 1 16.77657199 -1.262666879 3.757976317 1.000910928 0.461885201 0.819538148 0.075956435 45349865.99 74813870.99 473180.6511 0.017987211 0.054617664 1.262666879 -0.539025727 (ac)MVDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MVDYSVWDHIEVSDDEDETHPNIDTASLFR 30 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDY(0.001)S(0.004)VWDHIEVS(0.983)DDEDET(0.012)HPNIDTASLFR;MVDY(0.003)S(0.003)VWDHIEVS(0.988)DDEDET(0.005)HPNIDTASLFR;MVDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;MVDYSVWDHIEVS(0.998)DDEDET(0.002)HPNIDTASLFR;MVDY(0.017)S(0.019)VWDHIEVS(0.964)DDEDETHPNIDTASLFR;MVDY(0.02)S(0.021)VWDHIEVS(0.957)DDEDET(0.002)HPNIDTASLFR;MVDY(0.002)S(0.004)VWDHIEVS(0.991)DDEDET(0.003)HPNIDTASLFR 131.79 8.01E-35 455650300 26250.2 37439.1 38071.3 31641.8 41953.34 49062.3 37924.4 40071.9 35290.4 36471.04 TRUE FALSE 27286.57817 43868.97419 39063.46935 37900.4536 34822.12625 37668.32437 34951.78643 39534.80172 34020.3054 43616.84201 0.62559729 1.005780615 0.895605174 0.8689408 0.798364225 0.863618791 0.801336934 0.906411375 0.779980939 1 15.4125977 -2.314897195 2.360640383 1.840442019 0.848256996 0.2008553 0.09488468 3472780.574 1151879.811 15361709.4 0.021973005 0.00484287 2.314897195 -0.992185023 (ac)MVNPTVFFDIAVDGEPLGR ddPTM_MDA-MB-175_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 53.001 0.0081963 57690000 0 2638.9 0 2403.2 0 2073 0 2593.6 0 0 FALSE TRUE 0 3092.110547 0 2878.545787 0 1591.577167 0 2558.837034 0 0 0 (ac)MVSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVSVINTVDTSHEDMIHDAQMDYYGTR 27 0 P55735;P55735-4;P55735-3;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 ; 103.9 9.51E-12 83425000 1621.6 1084.6 4294.3 3133.3 4220.2 2781.83 1763.5 3479.4 1164.2 2224.5 FALSE TRUE 1685.62202 1270.871613 4406.212986 3753.057388 3502.851911 2135.792142 1625.272262 3432.764334 1122.300669 2660.348184 0.633609552 0.477708753 1.65625425 1.410739169 1.316689271 0.80282429 0.610924642 1.290344006 0.421862325 1 11.37739936 2.7148487 24.08622661 0.862228472 1.112761438 0.105590197 0.390065246 1397.195823 1419248.878 0.134517832 0.126901828 518.6193302 -2.7148487 0.250532966 (ac)S(ph)AADEVDGLGVARPHYGSVLDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 S(1)AADEVDGLGVARPHYGSVLDNER;S(1)AADEVDGLGVARPHYGSVLDNER;S(1)AADEVDGLGVARPHYGSVLDNER;S(1)AADEVDGLGVARPHYGSVLDNER 143.91 3.58E-52 1896510000 43764 11471.1 36276.5 29271.7 39114.7 50072.9 24703.2 25780 38610.5 14348 TRUE FALSE 45491.83651 13441.17219 37221.89539 35061.55489 32465.99727 38444.22784 22766.89863 25434.46127 37220.91565 17159.21589 2.651160566 0.783320886 2.169207243 2.043307521 1.892044338 2.240441992 1.326802972 1.482262443 2.169150146 1 14.06669601 -2.216839627 0.270022963 2.44E-16 1.902696516 0.197498844 0.510805103 61.23855089 2.253498744 38.25841488 0.635975638 0.006069604 2.216839627 1.902696516 (ac)S(ph)AIQNLHSFDPFADASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAIQNLHSFDPFADASK 17 0 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 1 S(1)AIQNLHSFDPFADASK 79.633 4.36E-05 17709000 22875 15787 17532 19037 24292 25484 22507 17529 18651 17346 TRUE FALSE 23778.12266 18498.29444 17988.89832 22802.46178 20162.85452 19565.72721 20742.84253 17294.05243 17979.75415 20744.61659 1.146231002 0.891715418 0.867159836 1.099198998 0.971955998 0.94317131 0.999914481 0.833664597 0.866719039 1 14.34044937 1.751130187 25 0.885157556 0.981970973 0.161361472 0.089531786 5.920340921 11793.85978 0.040206745 0.022296739 56.38066409 -1.751130187 0.096813416 (ac)S(ph)DAAVDTSSEITTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 S(0.992)DAAVDT(0.007)S(0.001)S(0.001)EITTK;S(0.857)DAAVDT(0.122)S(0.009)S(0.012)EITTK;S(0.997)DAAVDT(0.002)S(0.001)SEITTK;S(0.839)DAAVDT(0.064)S(0.064)S(0.027)EIT(0.003)T(0.003)K;S(0.951)DAAVDT(0.042)S(0.003)S(0.004)EITTK 75.695 1.23E-33 1379030000 1264525 1156612 1347320 1148370 1544480 1732060 1428790 1337017 1361170 1178140 TRUE FALSE 1314449.423 1355251.114 1382432.266 1375514.158 1281949.841 1329815.315 1316797.706 1319096.474 1312181.758 1408973.976 0.932912492 0.961870934 0.981162384 0.976252352 0.909846358 0.943818223 0.934579154 0.936210673 0.931303047 1 20.42621353 3.266465806 24.99999902 0.938794792 0.964259128 0.129314702 0.024713915 338.9411016 303651.8689 0.006440376 0.008718647 1846.995366 -3.266465806 0.025464336 (ac)S(ph)DKPDMAEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 S(1)DKPDMAEIEK;S(1)DKPDMAEIEK 62.303 0.0023327 193120000 672170 288592 435140 332610 622130 694920 693120 413060 511090 214919 TRUE FALSE 698707.7906 338155.4311 446480.1059 398399.2653 516380.5648 533535.3616 638791.4433 407523.6063 492695.9707 257028.2632 2.718408404 1.315635202 1.737085643 1.550021232 2.009041957 2.075784799 2.485296502 1.585520601 1.916894137 1 17.97156748 (ac)S(ph)DLEDDETPQLSAHALAALQEFYAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDLEDDETPQLSAHALAALQEFYAEQK 27 0 Q8WVE0 Q8WVE0 N6AMT2 Protein-lysine N-methyltransferase N6AMT2 1 S(0.494)DLEDDET(0.494)PQLS(0.012)AHALAALQEFYAEQK;S(0.479)DLEDDET(0.425)PQLS(0.096)AHALAALQEFY(0.001)AEQK;S(0.5)DLEDDET(0.5)PQLS(0.001)AHALAALQEFYAEQK;S(0.831)DLEDDET(0.089)PQLS(0.079)AHALAALQEFYAEQK 74.456 7.60E-18 127064000 53180.4 65382.4 74005 66002 90409 98274 74526 75470 88918 70272 TRUE FALSE 55280.00326 76611.3186 75933.6311 79056.9986 75041.31047 75451.35286 68684.45738 74458.44809 85717.85855 84040.45296 0.657778502 0.911600496 0.903536671 0.940701719 0.89291892 0.897798027 0.817278524 0.885983422 1.019959502 1 16.35879632 4.739006147 25 0.908387166 0.657778426 0.660156583 0.0557436 22.38664899 1255794.36 0.013048728 0.076999381 54828.47254 -4.739006147 -0.25060874 (ac)S(ph)DNDDIEVESDADKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDNDDIEVESDADKR 15 1 Q6V3B1;G3V563;G3V2R5;P61244-2;A0A494C130 Q6V3B1 MAX Protein max 1 S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR 88.441 7.76E-13 2478300000 1182850 957100 1147190 854830 1488560 1645480 1271830 1138110 1213610 804960 TRUE FALSE 1229549.831 1121474.48 1177086.714 1023912.823 1235535.103 1263342.207 1172140.641 1122855.497 1169932.413 962676.5001 1.277220158 1.164954665 1.222723016 1.063610489 1.283437482 1.312322683 1.217585182 1.166389225 1.215291339 1 19.87669155 -1.265812872 2.49649969 0.996916922 1.210000088 0.471234337 0.067815795 905823.441 972321.3475 21136.15412 0.01750723 0.054223448 1.265812872 0.213083166 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR 69.01 0.00026446 1929400000 874420 756410 857180 738160 1072400 1289270 946730 885350 879150 701700 TRUE FALSE 908942.7768 886317.5334 879518.815 884165.8448 890113.8311 989856.5816 872522.8288 873483.3314 847509.5632 839184.6801 1.083126037 1.056165055 1.048063479 1.053601032 1.060688847 1.179545582 1.039726832 1.040871398 1.009920204 1 19.67862882 1.612262325 2.184469574 1.00787074 1.076109136 0.367968359 0.037144155 0.326268706 3.387060154 0.028653728 0.010704456 40.95079385 -1.612262325 0.068238396 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SDQEAKPSTEDLGDKK 16 2 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.997)DQEAKPS(0.002)T(0.001)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.985)DQEAKPS(0.013)T(0.002)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK;S(0.987)DQEAKPS(0.01)T(0.003)EDLGDKK;S(1)DQEAKPSTEDLGDKK;S(1)DQEAKPSTEDLGDKK 108.34 1.25E-14 21502240000 13813810 3388275 6150070 3484020 9654110 10591690 10614180 6060410 7357670 2147707 TRUE FALSE 14359189.89 3970184.874 6310345.877 4173148.757 8013107.831 8131930.516 9782212.837 5979180.117 7092868.894 2568509.066 5.590476621 1.545715733 2.456812771 1.624735848 3.119750651 3.166011996 3.808517932 2.327879701 2.761473178 1 21.29249974 (ac)S(ph)DQEAKPSTEDLGDKKEGEYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDQEAKPSTEDLGDKKEGEYIK 22 3 B8ZZN6;P63165;B8ZZJ0;B9A032 B8ZZN6 SUMO1 Small ubiquitin-related modifier 1 1 S(0.972)DQEAKPS(0.012)T(0.016)EDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(1)DQEAKPSTEDLGDKKEGEYIK;S(0.793)DQEAKPS(0.103)T(0.103)EDLGDKKEGEYIK 130.09 5.63E-26 6789100000 13268560 3054611 6207509 1984328 12609430 9003358 5891395 5486635 7507618 2610746 TRUE FALSE 13792412.99 3579216.678 6369281.784 2376822.156 10466083.59 6912464.552 5429612.066 5413095.632 7237420.295 3122271.693 4.417428831 1.146350167 2.039951167 0.761247703 3.352073305 2.213921539 1.738994104 1.733704227 2.317998242 1 21.57416465 8 0.059783206 1.68E-15 6.268323325 0.157574877 0.970077411 777.9660095 3.473303022 73.95836325 425.093967 100000000 -8 6.268323325 (ac)S(ph)DSEKLNLDSIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSEKLNLDSIIGR 14 1 P62136;P62136-2;P62136-3;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 1 S(0.995)DS(0.005)EKLNLDSIIGR;S(0.5)DS(0.5)EKLNLDSIIGR 91.937 2.49E-05 72163000 175743 163105 187947 140489 230850 279500 209173 185123 203260 164332 TRUE FALSE 182681.4693 191117.015 192845.0532 168277.3049 191610.1995 214590.3609 192777.4737 182641.729 195944.7123 196529.7091 0.929536151 0.972458647 0.981251405 0.856243596 0.974968112 1.09189782 0.980907541 0.929333941 0.997023367 1 17.58438789 3.012654216 24.99507681 0.992952514 0.937711948 0.276629993 0.048842369 379.2465535 749096.5136 0.015241942 0.018207953 1029.566057 -3.012654216 -0.055240567 (ac)S(ph)DSGEQNYGERES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 S(0.829)DS(0.17)GEQNY(0.012)GERES(0.988)R 53.237 4.62E-06 0 0 0 24455 0 0 27915 0 0 20985 0 TRUE FALSE 0 0 25092.31739 0 0 21432.16431 0 0 20229.75395 0 0 (ac)S(ph)DVEENNFEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDVEENNFEGR 11 0 Q13595;F8WEH2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 S(1)DVEENNFEGR 61.78 0.00024794 68931000 30130 32914 49920 39240 42295 59475 43950 46317 42483 56520 TRUE FALSE 31319.55567 38566.72346 51220.95621 47001.55488 35105.71101 45662.8326 40505.08416 45696.19637 40954.04513 67594.01186 0.463348081 0.570564202 0.757773578 0.695350869 0.519361258 0.675545531 0.599240717 0.676039121 0.60588274 1 16.04460782 -5 0.314277526 4.425129916 0.607341582 0.660777543 0.082335333 189.4453686 1.700372207 430.388724 0.076050604 1.00E-05 5 -3.817788334 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_MDA-MB-175_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 103.88 1.71E-06 4343300000 19438.9 33280 30479 27856 35932 46569 19163 28939 17565 47007 TRUE FALSE 20206.36278 38995.58112 31273.30778 33365.83366 29824.29147 35754.05551 17660.95399 28551.12004 16932.83908 56217.12165 0.359434318 0.693660223 0.556295073 0.593517289 0.530519717 0.635999398 0.314156141 0.507872321 0.301204305 1 15.77872197 -0.995738428 4.896467505 1.000001749 0.506357863 0.579919378 0.12774259 0.075085644 80774408.02 1115.282928 0.028969751 0.100986093 0.995738428 -0.493643886 (ac)S(ph)EGESQTVLSSGSDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.723)EGES(0.265)QT(0.01)VLS(0.001)S(0.001)GSDPK 53.388 8.15E-27 135060000 288020 225180 291520 210890 352270 445740 317220 284180 297830 226920 TRUE FALSE 299391.252 263852.9133 299117.2507 252603.4126 292391.2712 342223.6403 292355.4675 280371.0319 287111.1565 271380.6294 1.103215262 0.97226141 1.102205605 0.930808559 1.077421303 1.261046675 1.077289371 1.033128387 1.057964812 1 18.04995822 3.023012814 24.92710115 1.091275569 1.025510579 0.106299585 0.080971516 481.6113452 521669.6623 0.023685423 0.028307899 1054.418007 -3.023012814 -0.065764991 (ac)S(ph)GDEMIFDPTMSK ddPTM_MDA-MB-175_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(0.999)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(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK 84.507 2.64E-41 11432241000 13683890 13934660 15314910 13234550 18012960 18988040 17111230 15244460 16283560 13930980 TRUE FALSE 14224140.54 16327829.46 15714029.14 15852304.49 14951123.49 14578355.48 15770007.08 15040132.95 15697517.86 16660488.81 0.853764899 0.980033038 0.943191362 0.95149096 0.89740005 0.875025676 0.946551285 0.902742598 0.942200318 1 23.98992739 0.938033077 7.035012576 0.999998877 0.921040016 0.314705019 0.036175011 0.9367662 105.2563239 0.033504833 0.008402204 8.670279088 -0.938033077 -0.078958861 (ac)S(ph)GDEMIFDPTMSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 SGDEMIFDPTMSKK 14 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 S(1)GDEMIFDPTMSKK;S(0.998)GDEMIFDPT(0.001)MS(0.001)KK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(0.999)GDEMIFDPT(0.001)MSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(0.993)GDEMIFDPT(0.006)MS(0.001)KK;S(0.999)GDEMIFDPT(0.001)MSKK 137.17 4.26E-17 7642358000 9443340 7897870 9754060 5909809 13739790 11168390 8385240 9019640 11026830 9087500 TRUE FALSE 9816170.355 9254267.736 10008258.82 7078751.581 11404305.4 8574700.681 7727982.978 8898746.479 10629976.54 10868021.63 0.903215938 0.851513555 0.920890586 0.651337642 1.049345114 0.788984506 0.711075414 0.818800954 0.978096741 1 23.37358601 1.220333836 8.538311088 0.990288047 0.832542627 0.251096695 0.10491181 0.274928266 100.1879969 0.088642411 0.02432385 16.60863097 -1.220333836 -0.15774542 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.962)GEDEQQEQT(0.038)IAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK 157.33 3.15E-191 3752041000 1617344 1674369 1815402 1535087 2037308 2304440 1860465 1825758 1891951 1717762 TRUE FALSE 1681197.99 1961928.851 1862712.867 1838722.627 1691007.114 1769268.734 1714636.892 1801286.7 1823860.053 2054324.575 0.818370189 0.955023794 0.906727637 0.895049716 0.823145054 0.861241089 0.83464751 0.87682673 0.887814942 1 20.97023271 0.682079585 2.623561717 0.999987237 0.872698915 0.487763128 0.039288185 2.080819951 16.07535906 0.03821946 0.010146229 4.809274708 -0.682079585 -0.127288322 (ac)S(ph)KGPAVGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKGPAVGIDLGTTYSCVGVFQHGK 24 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 S(1)KGPAVGIDLGTTYSCVGVFQHGK;S(1)KGPAVGIDLGTTYSCVGVFQHGK 126.02 1.86E-43 178350000 262466 144857 193336 144214 259571 286267 209243 192344 193810 126925 TRUE FALSE 272828.3603 169735.0629 198374.495 172739.0988 215449.2141 219785.8277 192841.9869 189765.9433 186834.816 151793.5236 1.797364959 1.118197001 1.306870611 1.137987278 1.419357091 1.447926252 1.270423021 1.250158365 1.230848402 1 17.21175071 -4.988006229 0.099162091 1.77E-13 1.538160641 0.305668708 0.174974877 257.5463051 1.746295017 53.61857942 2.922735171 1.03E-05 4.988006229 1.538160641 (ac)S(ph)KSESPKEPEQLR ddPTM_MDA-MB-175_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(0.333)KS(0.333)ES(0.333)PKEPEQLR 42.475 0.0001921 492170000 661640 244790 350510 133550 687760 668350 228370 296650 427470 324500 TRUE FALSE 687762.0581 286830.7783 359644.5785 159965.7914 570854.8009 513135.8414 210469.7627 292673.892 412085.4382 388079.5621 1.772219218 0.739103025 0.926728985 0.412198443 1.470973627 1.32224392 0.542336632 0.754159509 1.06185813 1 18.56599293 4.74503778 24.5809251 0.897642804 1.77221972 0.40859777 0.309015389 599.4439422 2274820.449 0.075392095 0.714397183 55595.26183 -4.74503778 0.874576916 (ac)S(ph)LPLNPKPFLNGLTGKPVMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPLNPKPFLNGLTGKPVMVK 21 2 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 1 S(1)LPLNPKPFLNGLTGKPVMVK;S(1)LPLNPKPFLNGLTGKPVMVK 99.86 1.17E-07 327960000 1019800 776330 1013670 754690 1408380 1176270 1174000 993700 1176790 937980 TRUE FALSE 1060062.491 909658.6385 1040087.073 903965.4295 1168984.071 903099.119 1081978.812 980381.0769 1134437.558 1121759.222 0.945000024 0.810921471 0.927192799 0.80584622 1.042098917 0.805073942 0.964537479 0.873967477 1.01130219 1 20.09733161 1.23331795 24.98271526 1.005651171 0.896025178 0.261123198 0.073211242 164.7609205 785087.2727 0.056236499 0.015692563 17.11267689 -1.23331795 -0.109625993 (ac)S(ph)SPPEGKLETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPEGKLETK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 1 S(0.5)S(0.5)PPEGKLETK 74.162 0.066051 1892600000 1138700 649900 937030 446820 1578500 1284700 835400 914440 1178300 850540 TRUE FALSE 1183656.755 761515.2695 961449.7716 535199.6624 1310187.134 986347.8948 769919.1651 902183.4275 1135893.213 1017187.028 1.16365695 0.748648231 0.945204515 0.526156594 1.288049392 0.969681944 0.756910129 0.886939572 1.116700451 1 19.95615354 3.23757935 24.9999822 0.971692695 0.8460609 0.118279349 0.199437627 71.23684576 1814945.747 0.05634572 0.071121539 1728.1417 -3.23757935 -0.125631795 (ac)S(ph)SSPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.333)S(0.333)S(0.333)PVKR;S(0.333)S(0.333)S(0.333)PVKR 42.124 0.085971 49202400000 19117700 18149600 20639200 17551300 26490200 27572300 25240900 22088600 21705600 18125400 TRUE FALSE 19872481.56 21266652.62 21177074.51 21022894.75 21987405.27 21169051.19 23262452.3 21792538.45 20924419.7 21676725.1 0.916765861 0.98108236 0.976949904 0.969837218 1.014332431 0.976579769 1.073153449 1.005342751 0.965294324 1 24.36964348 7.018590482 0.51339385 1.009502008 1.39E-13 0.424054876 0.029007214 36.85133877 1.056766949 0.014888798 36.15564899 10437355.64 -7.018590482 -1.009502008 (ac)S(ph)SSPVNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPVNVK 8 0 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.333)S(0.333)S(0.333)PVNVK 40.103 0.005959 185840000 354330 302970 359410 309750 405210 428760 415390 386300 366100 278590 TRUE FALSE 368319.222 355002.7407 368776.5199 371017.6255 336332.5489 329186.9879 382830.6464 381122.2804 352924.1325 333174.3766 1.105484839 1.065516335 1.106857387 1.113583912 1.009479037 0.988032127 1.149039882 1.143912339 1.059277536 1 18.34591793 0.986576139 24.11628394 0.999999994 1.087406018 0.211771273 0.049808756 756.8919688 1359778.15 0.052439995 0.013109999 9.695632355 -0.986576139 0.087406024 (ac)S(ph)SSPVNVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;S(0.333)S(0.333)S(0.333)PVNVKK 41.984 0.042703 24549100000 6837300 4533200 6152300 4180300 7549300 7075700 6641500 5775800 6320400 4110700 TRUE FALSE 7107241.884 5311741.837 6312633.992 5007150.863 6266072.683 5432475.908 6120921.876 5698384.848 6092930.039 4916112.961 1.445703534 1.080475953 1.284070167 1.018518269 1.274599004 1.105034801 1.245073481 1.159124067 1.239379584 1 22.22908664 -4.722320688 0.252034178 1.92E-28 1.214343753 0.221341796 0.115830426 238.6492314 2.692826086 123.2354618 0.147529982 1.90E-05 4.722320688 1.214343753 (ac)S(ph)TGGDFGNPLRK ddPTM_MDA-MB-175_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(0.768)T(0.232)GGDFGNPLRK 59.931 0.012918 110900000 334350 245930 296550 280570 367170 435410 336730 324140 340240 248640 TRUE FALSE 347550.3962 288166.5644 304278.3366 336065.9086 304758.5745 334292.6262 310336.2227 319795.4335 327994.8289 297356.2475 1.168801393 0.969095376 1.023278775 1.130179411 1.0248938 1.124215916 1.043651261 1.075462299 1.103036616 1 18.18183286 (ac)SAADEVDGLGVARPHYGSVLDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 190.88 4.21E-101 9619950000 48982.5 16329.8 20951.4 17256.6 30076.4 25357.7 29498.1 18811.9 22169.4 22821.4 FALSE TRUE 50916.36692 19134.31612 21497.4107 20669.90397 24964.02427 19468.75847 27185.96184 18559.75725 21371.52762 27292.81639 1.865559281 0.701075179 0.787658202 0.757338623 0.914673807 0.713329039 0.996084884 0.680023527 0.783045887 1 14.73623366 4.741973369 24.99581276 0.804908027 1.865559679 0.888601879 0.111561873 89.27771796 653862.6845 0.024263499 0.177076469 55204.35869 -4.741973369 1.060651652 (ac)SAEVPEAASAEEQKEMEDKVT(ph)SPEKAEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 SAEVPEAASAEEQKEMEDKVT(0.558)S(0.442)PEKAEEAK 94.48 6.12E-06 71702000 338720 32034 85090 26225 148080 277120 137330 72867 92174 20046 TRUE FALSE 352092.9271 37535.59031 87307.5153 31412.22673 122909.4145 212763.0798 126565.7158 71890.33705 88856.67575 23973.6299 14.68667568 1.565703253 3.641814597 1.310282459 5.126858762 8.874879637 5.279372223 2.998725573 3.70643395 1 14.54916075 4.746370126 24.95417626 3.937703476 14.686681 0.684074194 2.230973483 578.3643085 1848036.843 0.555140053 6.029449595 55766.08108 -4.746370126 10.74897753 (ac)SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAIQNLHSFDPFADASKGDDLLPAGTEDYIHIR 33 1 K7EM18;P41567 K7EM18 EIF1 Eukaryotic translation initiation factor 1 0 ; 89.793 5.25E-89 1164810000 394840 367120 446720 332310 553210 582230 469190 430670 455120 432640 FALSE TRUE 410428.5881 430170.0042 458361.8902 398039.9262 459175.5618 447015.9063 432413.6618 424897.5731 438740.3201 517407.5246 0.79324047 0.831394952 0.885881763 0.769296748 0.887454357 0.863953238 0.835731297 0.821204859 0.847958909 1 18.98094151 0.941011796 19.34193178 1 0.836971226 0.657919982 0.03527356 642.886025 210800.408 0.032220646 0.008055161 8.729950793 -0.941011796 -0.163028774 (ac)SCINLPTVLPGS(ph)PSKTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCINLPTVLPGSPSKTR 17 1 P04183;K7ERV3;K7ES52;K7ERJ1;K7ENW5 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 SCINLPT(0.001)VLPGS(0.51)PS(0.245)KT(0.245)R;SCINLPTVLPGS(0.737)PS(0.205)KT(0.058)R 92.633 8.44E-09 123802000 173246 166804 190410 91796 289790 255580 119433 179131 220629 282570 TRUE FALSE 180085.8859 195451.2894 195372.241 109952.9748 240531.5993 196225.4184 110071.5294 176730.0419 212688.6054 337934.1814 0.532902251 0.578370879 0.578136962 0.325368018 0.711770553 0.580661647 0.325718839 0.522971785 0.629378788 1 18.36638276 0.831575087 2.892663237 0.999741198 0.516889881 0.628046984 0.110983561 0.46249077 6.632158268 0.104948971 0.027603458 6.785394261 -0.831575087 -0.482851317 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK;SDEFSLADALPEHS(1)PAK 167.35 6.24E-88 4473190000 3573450 2687080 3209080 2445900 4284370 5242840 3971420 3459620 3839990 2848170 TRUE FALSE 3714532.565 3148565.087 3292711.261 2929691.72 3556114.318 4025269.866 3660129.723 3413249.453 3701789.51 3406214.38 1.090516377 0.92435905 0.966677635 0.860101976 1.044007781 1.181742961 1.074544733 1.002065364 1.086775258 1 21.69973781 3.02173231 24.88703139 1.068905816 0.957506923 0.344858148 0.071176622 249.2915854 285477.361 0.020757429 0.024808023 1051.313665 -3.02173231 -0.111398894 (ac)SDKPDLSEVEKFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKPDLSEVEKFDR 14 2 H3BU88;A0A087X1C1;P0CG35;P0CG34 H3BU88 TMSB15B;TMSB15A Thymosin beta-15B;Thymosin beta-15A 0 48.112 0.036895 208490000 171640 111800 140510 91438 198920 195190 165440 146630 151710 93792 FALSE TRUE 178416.4797 131000.7803 144171.806 109524.1635 165107.6495 149860.0806 152472.3805 144664.6647 146249.9867 112168.7466 1.590607768 1.167890203 1.285311732 0.976423173 1.471957692 1.336023492 1.35931251 1.289705636 1.303839002 1 16.77531123 -0.333915697 7.713117625 0.999999125 1.301223448 0.261508099 0.155288282 0 0 0.14167359 0.033392785 0.463536891 0.333915697 0.301224322 (ac)SDKPDMAEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKPDMAEIEK 11 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 90.15 0.00016005 226800000 337190 181020 271730 211340 370000 383790 447750 300870 334150 171380 FALSE TRUE 350502.5216 212108.7769 278811.507 253142.4212 307107.5322 294660.5889 412654.185 296837.3298 322124.0068 204958.6297 1.710113509 1.034885807 1.360330655 1.235090328 1.498387907 1.437658855 2.013353551 1.448279246 1.571653788 1 17.64497321 3.059946693 3.347544509 1.554174445 1.315907626 0.047712236 0.280758963 0.483998523 11.07432073 0.080842812 0.09662737 1148.012702 -3.059946693 -0.238266818 (ac)SDKPDMAEIEKFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;;;;;;;;;; 120.53 7.09E-08 38202865000 40469104 15335602 25710780 13925449 40487729 34647400 36324069 24644315 31841075 12597930 FALSE TRUE 42066855.47 17969372.35 26380824.05 16679861.25 33605639.29 26601066.44 33476893.56 24313998.27 30695120.93 15066253.18 2.792124556 1.192690189 1.750987703 1.10710082 2.230523998 1.765605962 2.221978693 1.613805236 2.0373427 1 23.84481734 (ac)SDQDHS(ph)MDEMTAVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDQDHSMDEMTAVVK 15 0 P08047;H3BUU5;P08047-3 P08047 SP1 Transcription factor Sp1 1 S(0.067)DQDHS(0.933)MDEMTAVVK;S(0.408)DQDHS(0.592)MDEMTAVVK;S(0.098)DQDHS(0.902)MDEMTAVVK 90.367 2.61E-07 271070000 172871 200936 227881 192516 261310 301556 225272 231344 235590 218989 TRUE FALSE 179696.0806 235445.1949 233819.7661 230595.0902 216892.6195 231524.1891 207614.592 228243.2121 227111.1619 261895.7018 0.686136043 0.899003662 0.892797264 0.88048444 0.828164105 0.884032031 0.792737684 0.871504231 0.867181708 1 17.99863286 -5 0.262637134 1.994378106 0.836607649 0.38725726 0.060199727 210.3777859 2.061293967 112.9944242 0.0746091 1.00E-05 5 -1.157770457 (ac)SDSGEQNYGERES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R 90.707 1.11E-11 2253480000 4074.7 19955.8 17532.6 22330.8 22511.3 26407.7 18759.7 27396.2 19430.7 27220.9 TRUE FALSE 4235.572302 23383.05342 17989.51396 26747.76559 18684.83727 20274.91189 17289.26569 27028.99875 18731.3929 32554.31418 0.130107865 0.718278176 0.552599998 0.821635051 0.573958867 0.622802612 0.531089846 0.830273942 0.575388958 1 14.99056113 -3.224907997 0.062540041 2.110012103 1.46E-16 0.402005222 0.171709872 270.5900484 1.744887851 56.24469798 14.46717923 0.000595788 3.224907997 -2.110012103 (ac)SEGES(ph)QTVLSSGSDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JHZ6;C9JDW7 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 S(0.405)EGES(0.591)QT(0.003)VLS(0.001)SGSDPK 70.195 1.22E-71 145570000 289520 246560 272730 229190 313300 423620 291200 273760 304220 206790 TRUE FALSE 300950.4732 288904.762 279837.5679 274523.0979 260045.3779 325240.675 268374.9831 270090.695 293271.1816 247306.5413 1.216912709 1.168205097 1.131541311 1.110051908 1.05151031 1.315131712 1.085191608 1.0921292 1.185860997 1 17.91594087 -5 0.210700751 0.306460191 1.165571459 0.27363867 0.072813328 201.4489891 2.009048238 59.10200071 0.151984593 1.00E-05 5 0.859111269 (ac)SEKS(ph)VEAAAELSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEKSVEAAAELSAK 14 1 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 1 S(0.02)EKS(0.98)VEAAAELSAK 73.156 8.73E-05 33741000 117850 82610 105260 65926 144780 136950 131720 100820 134870 65042 TRUE FALSE 122502.809 96797.62488 108003.1621 78965.96603 120170.3473 105145.438 121395.4422 99468.67281 130016.055 77785.7346 1.574875003 1.244413585 1.388470041 1.015172852 1.544889277 1.351731632 1.560638886 1.278752117 1.671463999 1 16.24721798 -0.964922044 5.518546592 0.999999247 1.388159394 0.296499764 0.185072013 1.59E-06 2.98E-07 0.165902164 0.039103439 0.10841215 0.964922044 0.388160147 (ac)SESSS(ph)KSSQPLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESSSKSSQPLASK 14 1 P17096;P17096-3;A0A669KAX1;A0A1W2PRV2;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 S(0.005)ES(0.005)S(0.141)S(0.82)KS(0.012)S(0.018)QPLASK;S(0.001)ES(0.002)S(0.133)S(0.835)KS(0.014)S(0.014)QPLASK 86.467 1.15E-05 237800000 920030 459300 644430 361150 958800 957850 663280 615340 755250 451850 TRUE FALSE 956353.4948 538181.2021 661224.3752 432584.3921 795823.5185 735403.8539 611290.3804 607092.3738 728068.7 540381.3563 1.769775148 0.995928516 1.223625441 0.80051687 1.472707208 1.360897902 1.131220338 1.123451738 1.34732387 1 19.04361838 7.968463672 0.020989494 7.63E-06 2.777020467 0.088718902 0.251463878 8922.56472 14.49591394 701.312923 1302.086087 92995872.19 -7.968463672 2.777012837 (ac)SETAPAAPAAPAPAEKT(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK;SETAPAAPAAPAPAEKT(1)PVK 128.38 2.05E-29 1127320000 1708360 762550 1320080 771959 1515940 1744660 1634950 1204790 1375430 657150 TRUE FALSE 1775807.372 893512.0307 1354482.369 924650.1861 1258261.06 1339489.156 1506798.347 1188641.761 1325928.543 785905.9606 2.259567252 1.136919779 1.723466212 1.176540493 1.601032596 1.704388594 1.917275631 1.512447825 1.687133842 1 19.58399717 -1.046836888 4.704815974 0.99997983 1.615436038 0.271959814 0.310347701 18928238.27 4211594.767 3949.774085 0.066650079 0.089776591 1.046836888 0.615456208 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 SETAPAAPAAPAPAEKT(1)PVKK;SETAPAAPAAPAPAEKT(1)PVKK 89.979 2.56E-11 609550000 2008540 719710 1318380 625040 1653270 1491530 1697490 1137940 1348940 596540 TRUE FALSE 2087838.71 843314.5939 1352738.066 748671.0464 1372247.756 1145144.762 1564436.298 1122687.776 1300391.913 713420.5916 2.926518711 1.182072124 1.896129831 1.049410481 1.923476519 1.605146775 2.192866756 1.573668869 1.822756349 1 19.44439333 -1.882962551 2.325331235 0.593345944 1.760995775 0.183330364 0.499431513 11241964.1 5846942.585 25117812.21 0.11431422 0.013092948 1.882962551 1.167649831 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 S(0.002)ET(0.002)APLAPTIPAPAEKT(0.996)PVK 45.916 0.001146 0 132910 69070 101710 55679 121720 133650 121720 89451 107360 56030 TRUE FALSE 138157.3894 80932.23521 104360.6462 66692.14001 101030.0779 102611.813 112179.2683 88252.05566 103496.1346 67008.00574 2.061804226 1.207799491 1.557435489 0.995286149 1.507731453 1.531336619 1.6741174 1.317037489 1.544533872 1 16.03204585 -1.76681284 2.368632374 0.869235328 1.466516833 0.22400162 0.270010241 10721017.79 6994292.955 8137558.324 0.064679751 0.017107524 1.76681284 0.597281505 (ac)SGDHLHNDS(ph)QIEADFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGDHLHNDSQIEADFR 16 0 P11387 P11387 TOP1 DNA topoisomerase 1 1 S(0.003)GDHLHNDS(0.997)QIEADFR 54.117 2.18E-07 152330000 8561.7 16776 13794 8907.3 19591 14868 12316 14724 12389 17904 TRUE FALSE 8899.722527 19657.1475 14153.48297 10669.13735 16260.92882 11415.13233 11350.63974 14526.64886 11943.12231 21411.94601 0.415642862 0.918045819 0.661008718 0.498279668 0.759432553 0.533119798 0.530107807 0.678436647 0.557778462 1 14.3861283 -1.446233767 3.429888569 1.004720911 0.625463802 0.408886814 0.137849027 389895205.2 448652773.7 17240694.5 0.031008055 0.035790374 1.446233767 -0.379257108 (ac)SGEDEQQEQT(ph)IAEDLVVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 S(0.434)GEDEQQEQT(0.565)IAEDLVVTK 42.789 0.0039539 0 16005 20334 24788 27035 28096 28960 23991 23724 24174 23196 TRUE FALSE 16636.88976 23826.20632 25433.99564 32382.44231 23320.25196 22234.47889 22110.52273 23406.01858 23303.98246 27740.81209 0.599726126 0.858886404 0.916843947 1.167321353 0.840647775 0.801507859 0.797039491 0.843739488 0.840061293 1 14.7597224 0.031717778 0.012881553 1.800853231 2.58E-06 0.079694361 0.133277427 8414.574158 33.88170674 2474.565123 2260.690863 1.075765909 -0.031717778 -1.800850656 (ac)SILKIHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SILKIHAR 8 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 57.177 0.0062412 378720000 514830 577990 609350 599630 690860 628020 563450 449290 523200 567200 FALSE TRUE 535155.8859 677255.2864 625230.1616 718235.0243 573427.864 482171.8727 519285.3167 443268.0024 504370.1342 678331.9803 0.78892917 0.998412733 0.921717064 1.058825244 0.845349889 0.710819903 0.765532706 0.653467646 0.743544678 1 19.37163199 2.99462792 5.99343616 0.747082571 0.946057073 0.335744848 0.107345856 0.140390615 20.3910944 0.030376813 0.034498358 987.7065192 -2.99462792 0.198974502 (ac)SKPHSEAGTAFIQTQQLHAAMADTFLEHMCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 157.42 1.43E-197 30438320000 2040383 2700990 3077210 2690064 3294270 4035650 2797030 2878570 3122660 3320310 FALSE TRUE 2120938.896 3164864.022 3157404.621 3222150.63 2734311.162 3098431.448 2577791.48 2839987.478 3010276.077 3970861.173 0.534125673 0.797022077 0.795143543 0.811448824 0.688593996 0.780292061 0.649176934 0.715206942 0.758091493 1 21.92102049 0.784714675 4.060045782 0.999994226 0.726337619 0.516837499 0.080214425 1.955713604 36.14257522 0.074093772 0.018913948 6.091365721 -0.784714675 -0.273656607 (ac)SKSES(ph)PKEPEQLRK ddPTM_MDA-MB-175_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(0.253)KS(0.253)ES(0.495)PKEPEQLRK 41.323 3.94E-05 906810000 2288600 730420 983030 256830 2456900 1889100 647640 947990 1265500 737470 TRUE FALSE 2378955.695 855863.9531 1008648.569 307630.2074 2039277.016 1450385.155 596876.2845 935283.7446 1219954.902 881963.1268 2.697341445 0.970407863 1.143640294 0.348801665 2.312202125 1.644496363 0.676758774 1.060456743 1.383226651 1 19.75035882 4.743159577 24.63479161 1.168687984 2.697342208 0.448833329 0.507382022 365.3391719 1956891.628 0.122162212 0.976865213 55355.34696 -4.743159577 1.528654223 (ac)SLHQFLLEPITCHAWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLHQFLLEPITCHAWNR 17 0 A0A1W2PNV4;E9PF58;F8WFD3;Q92747 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 ; 136.48 2.83E-28 1721090000 187438 90064 106965 78962 119936 140811 84785 82907 122127 149220 FALSE TRUE 194838.197 105531.7914 109752.5958 94580.44792 99549.32156 108109.7793 78139.33016 81795.76727 117731.6731 178456.802 1.091794736 0.591357629 0.615009316 0.529990714 0.557834279 0.605803635 0.437861316 0.458350516 0.65972085 1 17.44521537 0.968581235 21.71743912 1.000000009 0.589011488 0.304729581 0.172663979 794.7047584 549321.9561 0.164960526 0.041240131 9.302104944 -0.968581235 -0.410988521 (ac)SLICSISNEVPEHPCVSPVSNHVYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLICSISNEVPEHPCVSPVSNHVYER 26 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 102.67 1.38E-11 307840000 3826.1 4233.8 0 6968.5 5568.2 5836.2 7186.5 4133.8 5018.7 5480.2 FALSE TRUE 3977.157382 4960.922216 0 8346.848501 4621.719353 4480.830998 6623.203352 4078.393173 4838.077967 6553.940265 0.606834549 0.756937356 0 1.273561882 0.705181794 0.683685053 1.01056816 0.622281102 0.738193784 1 12.67814681 3.734453701 24.9997684 0.829262949 0.484825323 0.335087688 0.259062809 447.2835723 2722723.512 0.06600966 0.106484899 5425.674067 -3.734453701 -0.344437626 (ac)SQGDSNPAAIPHAAEDIQGDDRWMSQHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQGDSNPAAIPHAAEDIQGDDRWMSQHNR 29 1 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 94.08 8.38E-07 673480000 0 13530.6 6014.1 0 4504.9 0 0 0 0 13853.1 FALSE TRUE 0 15854.3753 6170.832387 0 3739.158707 0 0 0 0 16567.34971 0 0.956965089 0.372469495 0 0.225694439 0 0 0 0 1 14.01605521 -1.396753848 4.832330938 1.001005842 0.172792114 0.4239652 0.289264525 0.003297074 0.000411592 0.29459604 0.069361442 0.040109399 1.396753848 -0.828213728 (ac)SQPGQKPAAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQPGQKPAASPR 12 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 S(0.003)QPGQKPAAS(0.997)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR 89.26 0.00020868 2071480000 1453810 1247300 1341110 1403630 1528390 1700550 1568180 1412030 1347880 1123870 TRUE FALSE 1511207.541 1461514.072 1376060.428 1681263.825 1268594.814 1305623.035 1445261.954 1393104.047 1299370.062 1344070.809 1.124351137 1.087378777 1.023800546 1.250874443 0.943845224 0.971394532 1.075287064 1.036481143 0.966742268 1 20.35817771 3.207174319 24.99999316 1.007126323 1.112171341 0.467347926 0.063467761 200.7228515 159880.4026 0.018402852 0.02199767 1611.292254 -3.207174319 0.105045019 (ac)SQPGQKPAAS(ph)PRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR 100.58 4.09E-06 98119590000 11627870 11041810 11632770 10392920 13631680 14971770 12378790 11959950 11491960 11289850 TRUE FALSE 12086947.29 12938154.97 11935929.54 12448608.56 11314571.9 11494803.32 11408508.09 11799646.43 11078366.6 13501879.95 0.895204766 0.958248409 0.884019824 0.92199076 0.837999741 0.851348357 0.844957009 0.873926185 0.820505489 1 23.68665696 3.251784519 24.77270843 0.863173167 0.915761408 0.140941785 0.05003714 310.2918172 581274.8754 0.012630747 0.017002657 1785.601405 -3.251784519 0.052588242 (ac)SQPGQKPAASPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQPGQKPAASPRPR 14 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ; 80.746 0.0016843 115542000 70287 74872 84903 66440 89539 94851 81750 81616 86056 77633 FALSE TRUE 73061.98503 87730.68358 87115.64193 79581.6337 74319.19276 72823.29273 75342.22139 80522.07102 82958.86137 92843.69998 0.786935302 0.944928774 0.938304289 0.857157068 0.800476422 0.784364397 0.811495249 0.867286321 0.893532479 1 16.5025164 -1.986533673 7.817537996 1.114133408 0.854559181 0.381646291 0.055809764 0.040499683 6.98E-05 0.019713019 0.013519532 0.010314931 1.986533673 -0.259574227 (ac)SQQHTLPVTLSPALS(ph)QELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQQHTLPVTLSPALSQELLK 20 0 P07476 P07476 IVL Involucrin 1 SQQHTLPVTLS(0.001)PALS(0.999)QELLK;SQQHTLPVTLS(0.001)PALS(0.999)QELLK;SQQHTLPVTLSPALS(1)QELLK;SQQHTLPVTLSPALS(1)QELLK 161.51 2.46E-54 410029000 366588 550513 820538 603229 763865 870333 818522 682302 849571 573917 TRUE FALSE 381061.1773 645059.3254 841921.8944 722545.8957 634023.5001 668211.3508 754364.1068 673156.8577 818995.1057 686365.0478 0.555187329 0.939819601 1.226638648 1.05271371 0.923740948 0.973550959 1.099071273 0.980756319 1.193235448 1 19.38861656 4.694968139 3.577903015 1.048200969 0.519164201 0.724795029 0.092269715 0.12445068 2.820078126 0.022189137 0.163286077 49541.38445 -4.694968139 -0.529036768 (ac)SRLS(ph)WGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRLSWGYR 8 1 Q8N1Q1 Q8N1Q1 CA13 Carbonic anhydrase 13 1 S(0.001)RLS(0.999)WGYR;S(0.007)RLS(0.993)WGYR;S(0.087)RLS(0.913)WGYR 93.649 0.00071824 702312000 20465.9 39864 35661.3 41102 38831 51635 33354.5 36392 32851.3 48907 TRUE FALSE 21273.90954 46710.3319 36590.66277 49231.85292 32230.52049 39643.55379 30740.08713 35904.22477 31668.98813 58489.39027 0.363722539 0.798612051 0.625594875 0.841722793 0.551049008 0.677790512 0.525566893 0.613858763 0.541448423 1 15.83588733 -1.539122999 5.419247477 1.001198073 0.623218446 0.437567 0.130517104 0.001748741 0.000148721 0.116973576 0.027489725 0.028898613 1.539122999 -0.377979626 (ac)SS(ph)SPLSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPLSKK 8 1 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 S(0.021)S(0.595)S(0.379)PLS(0.005)KK;S(0.017)S(0.49)S(0.49)PLS(0.004)KK 58.676 0.012085 1912460000 7251400 4353100 5728400 3776800 8264500 7622400 6341300 5737700 6608700 4327100 TRUE FALSE 7537690.871 5100711.063 5877686.81 4523839.767 6859703.242 5852213.119 5844252.336 5660795.516 6370854.178 5174912.398 1.456583279 0.985661335 1.135804118 0.874186734 1.325568959 1.130881582 1.12934324 1.093892047 1.231103773 1 22.30310301 -1.1745508 4.040490037 0.999936199 1.138053414 0.073399119 0.154988155 8.16E-05 1.67E-05 0.137417086 0.032374568 0.066903556 1.1745508 0.138117215 (ac)SS(ph)SPVNVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 47.938 0.0479 5280800000 8011900 5285500 6780800 4702900 8902400 8099400 7256900 6456500 6931500 4847900 TRUE FALSE 8328215.999 6193243.51 6957513.218 5633119.583 7389173.228 6218437.098 6688085.216 6369961.178 6682036.669 5797753.186 1.436455767 1.068214412 1.200036117 0.971603896 1.274489098 1.072559817 1.153565011 1.098694783 1.152521754 1 22.46706249 4.743962617 24.62324904 1.116789058 1.436455936 0.563897914 0.085901234 317.1825984 1445717.444 0.018086134 0.156221539 55457.79738 -4.743962617 0.319666877 (ac)SSAPTT(ph)PPSVDKVDGFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSAPTTPPSVDKVDGFSR 18 1 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.037)S(0.028)APT(0.192)T(0.652)PPS(0.086)VDKVDGFS(0.004)R 55.864 0.062143 112410000 212220 175210 228360 181210 281230 295470 236820 217890 254250 208120 TRUE FALSE 220598.6095 205300.9546 234311.2492 217052.7971 233426.6251 226851.5704 218257.4296 214969.5409 245099.5922 248897.1293 0.886304354 0.824842597 0.941397958 0.872058259 0.937843782 0.911427026 0.876898139 0.86368831 0.984742543 1 17.92519007 -5 0.167504411 1.418205657 0.868859314 0.41546922 0.04041469 134.3630382 1.260491105 18.51669434 0.151614161 1.00E-05 5 -0.549346343 (ac)SSEPPPPPQPPTHQASVGLLDT(ph)PRSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSEPPPPPQPPTHQASVGLLDTPRSR 26 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 SSEPPPPPQPPT(0.022)HQAS(0.022)VGLLDT(0.567)PRS(0.389)R 57.078 0.048018 87368000 0 0 0 0 0 3279.5 0 3747.9 0 0 TRUE FALSE 0 0 0 0 0 2517.885826 0 3697.665531 0 0 0 (ac)SSILPFT(ph)PPVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSILPFTPPVVK 12 0 Q15796-2;Q15796;B7Z5N5;K7EJX0;K7ESI8;K7EL92;K7ERC7 Q15796-2 SMAD2 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 1 S(0.002)S(0.002)ILPFT(0.997)PPVVK;S(0.005)S(0.005)ILPFT(0.989)PPVVK 55.567 0.0098852 44491000 82642 80614 86492 80746 99101 106008 95353 85393 88725 72576 TRUE FALSE 85904.76997 94458.82741 88746.05257 96717.3178 82255.84742 81389.24857 87878.9827 84248.44651 85531.80458 86795.87765 0.989733295 1.088287024 1.02246852 1.114307735 0.94769302 0.937708688 1.012478761 0.970650321 0.985436255 1 16.4053389 3.222984873 24.99999203 0.974770622 1.053938961 0.506551227 0.037726505 181.6440118 291548.8123 0.010324698 0.01238205 1671.032411 -3.222984873 0.079168339 (ac)SSILPFT(ph)PPVVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.002)S(0.002)ILPFT(0.996)PPVVKR 62.891 0.0014716 35583000 86627 94150 92678 63157 129030 113340 66348 90367 96736 109930 TRUE FALSE 90047.10085 110319.5301 95093.26482 75649.2661 107097.5267 87018.50268 61147.47039 89155.77818 93254.49026 131468.6788 0.684931968 0.839131656 0.72331498 0.575416645 0.814623891 0.661895316 0.465110557 0.678152234 0.709328573 1 17.00435961 0.748193253 3.738646948 0.999989955 0.677384064 0.468862457 0.101422514 2.798179889 40.63921332 0.100894019 0.025891337 5.600067381 -0.748193253 -0.322605891 (ac)SSS(ph)PLSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPLSKK 8 1 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 S(0.087)S(0.128)S(0.768)PLS(0.017)KK 43.282 0.074224 669370000 3121600 1973800 2631800 1714500 3779700 3305900 2838100 2530200 3131700 2124600 TRUE FALSE 3244843.178 2312784.796 2700386.87 2053622.983 3137227.944 2538154.826 2615642.306 2496286.808 3018990.729 2540874.692 1.277057538 0.910231742 1.062778451 0.808234656 1.234703921 0.998929555 1.029425935 0.982451758 1.188169861 1 21.2768938 3.217047647 24.99851393 1.059101738 1.01056524 0.03567458 0.136423311 1074.453281 1248534.571 0.037610397 0.044989651 1648.343222 -3.217047647 -0.048536498 (ac)SSS(ph)PVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPVKR 7 1 P37837;F2Z393;E9PM01;E9PKI8 P37837 TALDO1 Transaldolase 1 S(0.037)S(0.044)S(0.918)PVKR 56.014 0.028524 43216000000 27967000 24316000 28103000 23265000 36085000 39555000 34243000 30209000 30151000 26087000 TRUE FALSE 29071158.76 28492083.85 28835387.27 27866747.56 29951284.59 30368950.71 31558944.18 29804097.77 29065871.4 31198248.18 0.931820229 0.913259093 0.924263026 0.893215138 0.960030974 0.97341846 1.011561418 0.955313183 0.931650753 1 24.89496169 3.09809846 5.632132892 0.97279037 0.916328526 0.603063296 0.022600488 0.148836501 7.102931554 0.00670755 0.00806398 1253.425311 -3.09809846 -0.056461844 (ac)SSS(ph)PVNVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPVNVKK 9 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.074)S(0.293)S(0.632)PVNVKK;S(0.01)S(0.145)S(0.845)PVNVKK;S(0.168)S(0.168)S(0.663)PVNVKK 52.79 0.019102 57904200000 18034200 12164000 16369500 11465800 20225500 18241500 17574400 15383000 16347500 10856700 TRUE FALSE 18746204.14 14253072.38 16796102.62 13733701.02 16787576.73 14005188.08 16196872.61 15176816.05 15759156.67 12983862.5 1.443807969 1.097752874 1.293613716 1.057751576 1.292957064 1.078661152 1.247461809 1.168898396 1.213749504 1 23.63021629 -5 0.119235624 0.393522838 1.297709836 0.279951349 0.108853097 209.1189445 1.62073293 31.26859684 0.964825829 1.00E-05 5 0.904186998 (ac)SVCTLSVPVSSLS(ph)PGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVCTLSVPVSSLSPGRR 17 1 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 SVCTLSVPVS(0.003)S(0.016)LS(0.98)PGRR;SVCTLS(0.001)VPVS(0.106)S(0.106)LS(0.786)PGRR 70.167 1.74E-05 117793000 36044 35842 41400 30714 44091 51472 40384 35173 34687 44871 TRUE FALSE 37467.04495 41997.58469 42478.91801 36789.13753 36596.42757 39518.40807 37218.59656 34701.56347 33438.62165 53662.61334 0.698196428 0.7826228 0.791592421 0.685563658 0.681972518 0.736423473 0.693566605 0.646661825 0.62312697 1 15.71162969 -1.006152739 4.802001387 1.000004993 0.704287762 0.753677959 0.050694791 2.98E-06 6.17E-07 0.05396956 0.012720533 0.098593268 1.006152739 -0.295717231 (ac)SYAEKPDEITKDEWMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYAEKPDEITKDEWMEK 17 2 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 51.888 0.0061556 0 79336 49035 68646 40099 84831 72884 80136 57377 71482 43836 FALSE TRUE 82468.24654 57456.37981 70434.97115 48030.46252 70411.45692 55957.79557 73854.73092 56607.95516 68909.37678 52424.82491 1.573076242 1.09597657 1.343542325 0.916177834 1.343093793 1.067391177 1.408774012 1.079792928 1.314441715 1 15.67796252 7.999998058 0.020982199 3.67E-06 2.777473309 0.14189874 0.184881838 6225.835767 10.06128989 486.3288428 905.4919576 99999552.93 -7.999998058 2.777469635 (ac)SYGRPPPDVEGMTSLKVDNLTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYGRPPPDVEGMTSLKVDNLTYR 23 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 79.635 9.27E-07 158910000 54017 66919 68760 48933 85459 83879 51307 58983 72253 90164 FALSE TRUE 56149.63287 78411.81769 70551.94209 58611.80135 70932.70971 64399.37345 47285.42327 58192.42936 69652.62864 107829.9095 0.520724103 0.727180594 0.654289171 0.54355792 0.657820358 0.597231081 0.438518622 0.539668721 0.64594906 1 16.71839788 0.868806567 5.770892036 0.99999648 0.584212862 0.719321297 0.077359001 1.125937245 49.25670858 0.078948889 0.01987038 7.392759316 -0.868806567 -0.415783618 (ac)SYGRPPPDVEGMTSLKVDNLTYRT(ph)SPDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLR 30 3 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 SYGRPPPDVEGMTSLKVDNLT(0.03)YRT(0.559)S(0.394)PDT(0.016)LR 76.658 2.82E-19 628730000 177610 256690 236450 160100 465340 314950 159860 227300 293770 475550 TRUE FALSE 184622.1799 300774.5107 242612.0812 191767.3021 386241.673 241807.6356 147329.7555 224253.4153 283197.2751 568724.9175 0.324624743 0.528857628 0.426589505 0.337188149 0.679136189 0.425175033 0.259052753 0.394309109 0.497951235 1 19.11737149 0.801761408 4.119934942 0.999983825 0.422681857 0.709577463 0.110284083 1.102759566 22.39560347 0.106532913 0.027172567 6.335215725 -0.801761408 -0.577301967 (ac)T(ph)T(ph)SQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 2 T(0.652)T(0.696)S(0.652)QKHRDFVAEPMGEKPVGSLAGIGEVLGK 59.275 0.0010485 2366500000 1052900 572770 1005000 436670 1218700 992750 946170 839880 1122200 435020 TRUE FALSE 1094469.305 671138.792 1031191.126 523042.0227 1011545.809 762198.8578 872006.723 828622.7824 1081812.241 520253.84 2.103721723 1.290021794 1.982092291 1.005359274 1.94433127 1.465051863 1.676117802 1.592727854 2.079393092 1 18.98885618 -2.001769411 3.053617743 0.336278904 1.655536214 0.261010041 0.341694306 88049661.14 61533324.26 410765810.5 0.072826802 0.009959341 2.001769411 1.31925731 (ac)T(ph)TSQKHRDFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGK 31 3 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 1 T(0.333)T(0.333)S(0.333)QKHRDFVAEPMGEKPVGSLAGIGEVLGK 61.499 6.67E-09 221940000 109460 69991 108780 38469 173420 131220 79560 90611 124440 101630 TRUE FALSE 113781.5653 82011.4098 111614.8962 46078.05338 143942.1303 100746.1437 73323.87931 89396.50775 119961.4287 121542.4527 0.936146695 0.674755264 0.918320255 0.379110775 1.184295093 0.828896747 0.60327793 0.735516733 0.986992002 1 16.89110078 1.230709336 23.12645894 0.993496577 0.774204016 0.145487617 0.203702403 136.2934863 401417.9297 0.171249117 0.046302704 17.0101967 -1.230709336 -0.219292562 (ac)TDRYTIHSQLEHLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDRYTIHSQLEHLQSK 16 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 57.788 1.04E-07 106710000 126570 142130 142210 134390 203510 195870 141420 138320 157970 152720 FALSE TRUE 131567.0813 166539.7219 145916.1094 160971.9409 168917.4429 150382.1609 130335.1309 136466.0466 152284.6906 182642.56 0.72035281 0.911834141 0.798916252 0.881349565 0.92485258 0.823368666 0.713607666 0.747175503 0.833785349 1 17.47866346 2.475005036 24.98487237 0.79033903 0.852611866 0 0.091391262 165.2145939 1950540.388 0.029944277 0.025206474 298.541724 -2.475005036 0.062272835 (ac)TECFLPPT(ph)SSPSEHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TECFLPPTSSPSEHRR 16 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.323)S(0.323)S(0.323)PS(0.031)EHRR 55.173 0.038579 536840000 18538 29837 33185 28764 22553 36854 32124 24638 23299 31873 TRUE FALSE 19269.89455 34961.27265 34049.82836 34453.43335 18719.44912 28295.21703 29606.03694 24307.76791 22460.47354 38117.9041 0.505533948 0.917187696 0.89327651 0.903864841 0.491093347 0.742307787 0.776696349 0.637699487 0.589236845 1 15.21818118 3.290749278 24.99995916 0.691483092 0.81928937 0.070912068 0.167088086 214.5438921 102771.3301 0.044136116 0.059760528 1953.211525 -3.290749278 0.127806278 (ac)TECFLPPTS(ph)SPSEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.042)S(0.415)S(0.307)PS(0.237)EHR;TECFLPPT(0.217)S(0.459)S(0.264)PS(0.059)EHR;TECFLPPT(0.169)S(0.375)S(0.375)PS(0.082)EHR;TECFLPPT(0.026)S(0.596)S(0.302)PS(0.076)EHR 56.514 0.0032369 681041000 146124 198604 184521 172425 216896 227358 187515 197056 203688 192186 TRUE FALSE 151893.0884 232712.6921 189329.7688 206530.1504 180028.0954 174557.5501 172817.0843 194414.7866 196357.3087 229841.1671 0.660861108 1.012493519 0.823741766 0.898577713 0.78327176 0.759470344 0.751897872 0.845865817 0.854317402 1 17.8102777 -1.699087155 7.795516825 1.000790403 0.82476551 0.263394117 0.089537237 0.001160793 4.48E-05 0.081817422 0.019201817 0.019994606 1.699087155 -0.176024893 (ac)TECFLPPTSS(ph)PSEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TECFLPPTSSPSEHR 15 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.006)S(0.159)S(0.677)PS(0.159)EHR 95.067 3.78E-06 631160000 48657 73302 59755 64337 67612 89418 47368 75316 59171 65001 TRUE FALSE 50578.01593 85891.04829 61312.26439 77062.66657 56119.33639 68652.02464 43655.17239 74306.51221 57041.44727 77736.70143 0.650632391 1.104897001 0.788717083 0.991329258 0.721915586 0.883135294 0.561577371 0.955874263 0.733777562 1 16.24630827 3.232031038 24.99950602 0.803819435 0.89288152 0.046575098 0.161978777 437.9772469 1676863.014 0.042765854 0.052261231 1706.204325 -3.232031038 0.089062086 (ac)TECFLPPTSS(ph)PSEHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TECFLPPTSSPSEHRR 16 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TECFLPPT(0.192)S(0.134)S(0.579)PS(0.095)EHRR 58.885 0.0017149 0 18725 20237 17147 17964 22730 24681 20622 20324 17717 19491 TRUE FALSE 19464.27746 23712.54733 17593.86491 21517.22558 18866.36272 18949.21179 19005.59375 20051.59002 17079.36863 23309.88827 0.83502234 1.017274174 0.754781177 0.923094325 0.809371649 0.812925895 0.815344695 0.860218195 0.732709159 1 14.50865447 3.225612901 24.98955572 0.830827145 0.883040821 0.052189309 0.088605937 601.9445681 1161772.848 0.023691484 0.028485268 1681.174916 -3.225612901 0.052213675 (ac)TEKAPEPHVEEDDDDELDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEKAPEPHVEEDDDDELDSK 20 1 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;; 115.76 1.34E-43 1014830000 1185980 528420 797760 500640 1215180 1131710 1007610 773180 961500 455730 FALSE TRUE 1232803.406 619172.0245 818550.281 599665.0977 1008624.138 868887.5037 928630.8953 762816.7868 926895.8028 545021.568 2.261935084 1.136050499 1.501867686 1.10025939 1.850613254 1.594225907 1.703842471 1.39960844 1.700658941 1 19.0559538 -1.019792319 4.467443287 0.999978182 1.555138515 0.223113418 0.322685724 19180787.32 4378437.47 4347.21156 0.06950226 0.095544937 1.019792319 0.555160333 (ac)TEKAPEPHVEEDDDDELDSKLNYKPPPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEKAPEPHVEEDDDDELDSKLNYKPPPQK 29 3 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 151.66 4.41E-81 3410210000 3636840 1314290 2172090 950930 3798580 2779660 2472120 2010670 2750540 1078780 FALSE TRUE 3780425.251 1540009.084 2228696.45 1139021.116 3152898.728 2134126.091 2278348.775 1983720.257 2651548.603 1290146.287 2.930229921 1.193670129 1.72747577 0.882861988 2.44383041 1.654173727 1.76596158 1.537593278 2.055230969 1 20.29910323 -1.734776685 2.473807844 0.834676646 1.749111698 0.151820083 0.555409096 24048690.02 17377554.73 24405304.72 0.128161071 0.018417188 1.734776685 0.914435052 (ac)VDYSVWDHIEVS(ph)DDEDETHPNIDTASLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 VDYSVWDHIEVSDDEDETHPNIDTASLFR 29 0 Q16543;K7EKQ2;K7EQA9;K7EJ06 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 1 VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.001)S(0.001)VWDHIEVS(0.993)DDEDET(0.005)HPNIDTASLFR;VDY(0.018)S(0.02)VWDHIEVS(0.961)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDY(0.001)S(0.005)VWDHIEVS(0.99)DDEDET(0.005)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR;VDYSVWDHIEVS(0.998)DDEDET(0.002)HPNIDTASLFR;VDYSVWDHIEVS(1)DDEDETHPNIDTASLFR 198.44 8.56E-121 2491383000 50780.2 54978.07 69128.1 68740.45 68982.4 95059.6 65188 71938 64027 63138.9 TRUE FALSE 52785.04151 64420.12585 70929.63508 82337.10584 57256.79629 72983.44854 60078.39422 70973.78878 61722.68078 75509.75859 0.699049269 0.85313643 0.939343952 1.090416754 0.758270154 0.966543264 0.795637482 0.939928694 0.817413298 1 16.20437548 4.678239886 3.012541415 0.908958003 0.678886013 0.31487603 0.095183846 0.372225054 5.264500311 0.022019901 0.189400279 47669.42204 -4.678239886 -0.23007199 (ac)VNPTVFFDIAVDGEPLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 42.789 0.01001 45021000 4932.3 9689.9 7945.9 8451.2 10113 10147 8996.7 9022.9 7602.4 12692 FALSE TRUE 5127.031013 11354.06495 8152.976682 10122.82214 8393.995872 7790.513029 8291.515145 8901.962784 7328.791109 15178.7544 0.337776795 0.748023497 0.537130812 0.666907302 0.553009532 0.513251142 0.546257942 0.586475184 0.482832182 1 13.88976578 -1.821334816 2.637712419 1.148093561 0.561635841 0.628739547 0.102963485 9280354.894 6132618.482 8719284.825 0.022723924 0.015089164 1.821334816 -0.58645772 (ac)VSVINTVDTSHEDMIHDAQMDYYGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 VSVINTVDTSHEDMIHDAQMDYYGTR 26 0 P55735 P55735 SEC13 Protein SEC13 homolog 0 ;;;;;;;;;;; 163.71 2.41E-70 3195296000 14257.3 23972.2 23993.9 21532.7 30801.5 47141.6 20721.2 20396.23 26563.4 30188.9 FALSE TRUE 14820.18921 28089.23887 24619.20075 25791.80379 25565.87203 36193.67784 19097.0182 20122.8519 25607.38842 36103.83695 0.410487928 0.778012567 0.681899843 0.71437847 0.708120637 1.002488403 0.528947054 0.55736048 0.709270554 1 15.13986455 4.745972509 24.24518831 0.715739505 0.410487704 0.289021376 0.151039435 821.1218016 2685885.93 0.03620551 0.371704245 55715.04801 -4.745972509 -0.305251801 (ac)VTAMALS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTAMALSK 8 0 Q5T1B0-3 Q5T1B0-3 1 VT(0.001)AMALS(0.999)K 40.103 0.033963 11770000 156610 245930 222000 243110 237260 278170 220030 245810 221610 276070 TRUE FALSE 162793.0837 288166.5644 227785.5024 291196.4324 196930.6299 213569.2332 202783.4737 242515.319 213634.2994 330160.6308 0.493072367 0.872807166 0.689923271 0.881984117 0.596469147 0.646864627 0.614196408 0.734537363 0.647061701 1 18.33280857 -1.647912155 3.603684046 1.016489452 0.693789857 0.404517894 0.113850354 0.014510215 0.00141768 0.106048664 0.024165189 0.022495096 1.647912155 -0.322699595 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 AAAAAATAPPS(1)PGPAQPGPR 170.06 2.83E-15 0 53052 50079 47107 45298 56512 63596 51475 53865 49315 52846 TRUE FALSE 55146.53393 58679.67869 48334.64712 54257.8092 46906.11043 48826.79281 47440.255 53143.02778 47540.16278 63200.1619 0.872569504 0.92847355 0.764786761 0.85850744 0.74218339 0.772573856 0.750635023 0.840868539 0.752215839 1 15.94764063 4.241664571 24.99991324 0.801556702 0.900521545 0.1805807 0.075150487 105.2682285 847812.3309 0.016629632 0.041742297 17444.74281 -4.241664571 0.098964843 AAAAPGAS(ph)PSPGGDAAWSEAGPGPRPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAAAPGASPSPGGDAAWSEAGPGPRPLAR 29 1 P52701;P52701-3;P52701-2;F8WAX8;F8W7G9 P52701 MSH6 DNA mismatch repair protein Msh6 1 AAAAPGAS(0.713)PS(0.287)PGGDAAWSEAGPGPRPLAR;AAAAPGAS(0.966)PS(0.034)PGGDAAWSEAGPGPRPLAR 185.38 4.50E-18 832870000 131107 156787 124641 147773 144712 188880 123847 141231 146969 151873 TRUE FALSE 136283.2056 183713.9476 127889.2469 177002.0583 120113.9059 145015.4825 114139.5485 139338.0295 141679.6144 181629.6066 0.750335852 1.011475778 0.704121147 0.97452206 0.661312372 0.798413239 0.628419291 0.767154827 0.780046916 1 17.47063986 5.077396832 15.43764005 0.798252343 5.99E-05 0.008082553 0.132284688 680810.9678 2411195.428 0.029884941 17834854.39 119507.9598 -5.077396832 -0.79819245 AAACPS(ph)SPHKIPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAACPSSPHKIPLTR 15 1 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 AAACPS(0.61)S(0.39)PHKIPLTR 78.012 0.014604 142130000 122890 126560 129250 110240 165010 164900 140020 131570 122130 110610 TRUE FALSE 127741.7921 148295.6955 132618.3612 132045.143 136961.6591 126604.4741 129044.8665 129806.5194 117734.5652 132281.9117 0.965678455 1.121058001 1.002543427 0.99821012 1.035377077 0.957080771 0.975529192 0.981286993 0.890027696 1 17.01325628 2.831697905 0.941064983 0.956238655 1.03651741 0.289316681 0.047271751 0.660313567 1.261848288 0.02490775 0.025626765 678.731343 -2.831697905 0.080278755 AAACPSS(ph)PHKIPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAACPSSPHKIPLTR 15 1 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 AAACPS(0.013)S(0.987)PHKIPLTR 119.8 0.00011105 78966000 194530 162540 220960 173900 259040 269330 225070 202050 221190 167670 TRUE FALSE 202210.1946 190454.9806 226718.3991 208296.901 215008.4733 206782.1892 207428.4253 199341.8502 213229.4151 200521.7263 1.008420376 0.949797232 1.130642566 1.038774725 1.072245274 1.031220871 1.034443644 0.994115969 1.063373127 1 17.61339903 -1.356602554 8.152101188 0.999999806 1.034131595 0.051066145 0.045855008 1.60E-07 1.26E-08 0.043770184 0.010316672 0.043994405 1.356602554 0.034131789 AAAGVGGS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAAGVGGSLR 10 0 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 1 AAAGVGGS(1)LR;AAAGVGGS(1)LR 73.841 0.045924 180265000 238260 290210 312600 320140 356670 389930 305400 317350 282920 322120 TRUE FALSE 247666.6888 340051.31 320746.6128 383462.7365 296043.3608 299374.6669 281461.95 313096.4423 272737.7645 385233.2466 0.642900609 0.882715376 0.832603664 0.995404057 0.768478223 0.777125727 0.73062736 0.812745123 0.707980858 1 18.55537269 AAAIGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 367.28 6.03E-113 2086661000 1608926 1580965 1744007 1503381 2046161 2119391 1876960 1804675 1870941 1727566 FALSE TRUE 1672447.641 1852483.441 1789457.255 1800745.275 1698355.284 1627194.56 1729838.971 1780486.283 1803606.199 2066049.481 0.809490603 0.896630723 0.866125072 0.871588648 0.822030304 0.78758741 0.837268897 0.861782982 0.87297338 1 20.97844338 0.615062328 1.432666464 0.999883322 0.844043327 0.706235987 0.030164324 0.842654275 2.410721437 0.030425278 0.008909194 4.12156666 -0.615062328 -0.155839996 AAAT(ph)PAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAATPAKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAAT(1)PAKK;AAAT(1)PAKK 105.98 0.0025107 778500000 2530800 1236090 1762160 968580 2154930 1747110 2002710 1558660 1796530 1021230 TRUE FALSE 2630717.938 1448378.842 1808083.337 1160162.233 1788635.768 1341370.18 1845732.357 1537768.712 1731873.236 1221320.466 2.153994805 1.185912201 1.480433177 0.9499245 1.464509781 1.098295016 1.511259664 1.259103368 1.418033419 1 20.22001037 4.742342192 24.73835194 1.279712455 2.153995195 0.654188159 0.193989785 178.848304 1169936.334 0.041110505 0.307874276 55251.26069 -4.742342192 0.87428274 AAAT(ph)PESQEPQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 AAAT(1)PESQEPQAK;AAAT(0.996)PES(0.004)QEPQAK;AAAT(1)PESQEPQAK 261.17 5.32E-23 1107230000 1625420 1291570 1604830 1202340 1813500 1970570 1752680 1589760 1724050 1274380 TRUE FALSE 1689592.837 1513387.1 1646653.188 1440159.263 1505241.918 1512934.982 1615300.362 1568451.868 1662001.777 1524070.362 1.108605534 0.99299031 1.080431212 0.944942766 0.987645948 0.992693658 1.059859441 1.029120379 1.090502 1 20.53949808 -0.737244055 7.677064467 0.999992131 1.02837966 0.031005086 0.050142909 0 0 0.046618186 0.010988012 0.183128503 0.737244055 0.028387528 AAATGNAS(ph)PGKLEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAATGNASPGKLEHSK 16 1 H0Y6H0;Q8NB78 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK;AAATGNAS(1)PGKLEHSK 192.19 3.47E-10 995190000 1877240 897510 1242600 793420 1741840 1589830 1564540 1243750 1446390 729240 TRUE FALSE 1951354.885 1051650.361 1274983.177 950356.1079 1445762.659 1220616.077 1441907.267 1227079.566 1394334.706 872120.6159 2.237482808 1.205854261 1.461934455 1.089707193 1.657755398 1.399595485 1.653334688 1.407006718 1.598786545 1 19.73416815 -2.045258634 2.551100172 0.349613493 1.498520508 0.215444462 0.296263915 18095164.47 8263264.389 68584982.19 0.068992638 0.009010344 2.045258634 1.148907015 AAAYDIS(ph)EDEED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAAYDISEDEED 12 0 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 AAAYDIS(1)EDEED;AAAYDIS(1)EDEED 332.56 3.43E-58 1445150000 863520 985350 979470 937680 1002490 1122710 957160 992930 898750 889570 TRUE FALSE 897612.4364 1154576.198 1004995.793 1123150.305 832087.1079 861977.6173 882135.2981 979621.3975 866404.1631 1063864.21 0.84372839 1.08526651 0.944665479 1.055727127 0.782136574 0.810232744 0.82918035 0.920814319 0.814393562 1 20.02088259 3.239854049 24.99998155 0.855741442 0.987006748 0.334876281 0.084645053 36.2933857 701482.9089 0.022534009 0.02890398 1737.216912 -3.239854049 0.131265306 AADAEAEVASLNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 214.23 1.11E-11 2093710000 1177340 1391810 1273240 1049990 1536330 1511620 1128630 1278230 1290570 1648660 FALSE TRUE 1223822.292 1630842.541 1306421.68 1257674.888 1275185.175 1160569.164 1040165.031 1261097.418 1244122.638 1971683.361 0.620699204 0.82713207 0.66259203 0.637868591 0.646749473 0.58861843 0.527551762 0.639604433 0.63099515 1 20.91099645 -1.689684063 6.525054525 1.003384554 0.641631465 0.691773915 0.071603166 0.003753918 0.000178527 0.073821596 0.017281755 0.020432238 1.689684063 -0.361753089 AADAVEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AADAVEDLR 9 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 114.89 0.0036389 243520000 1245540 991330 1027560 932200 1190660 1328170 1184490 1052860 1060520 1058040 FALSE TRUE 1294714.881 1161583.216 1054339.058 1116586.378 988272.0385 1019722.646 1091646.579 1038748.134 1022352.092 1265342.681 1.023212843 0.917998921 0.83324389 0.882437931 0.781031142 0.805886549 0.862728015 0.820922387 0.8079646 1 20.27109672 4.642626009 1.818446118 0.838766593 1.063507529 0.447806425 0.058697235 0.534857379 2.113545486 0.013927935 0.192621749 43916.32689 -4.642626009 0.224740936 AADEEAFEDNSEEYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AADEEAFEDNSEEYIR 16 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ; 350.8 4.84E-59 0 219969 183769 194978 226740 207690 253200 228540 206457 205274 166070 FALSE TRUE 228653.546 215329.8962 200059.2869 271588.4952 172386.928 194398.1373 210626.4376 203689.7816 197886.2288 198608.2369 1.15127927 1.084194188 1.007306092 1.367458367 0.867974716 0.978801989 1.060512096 1.02558577 0.996364662 1 17.59956593 3.206890974 24.99999925 0.99642064 1.137301723 0.401445358 0.097296911 224.0053525 176829.1147 0.027764296 0.033187477 1610.241345 -3.206890974 0.140881083 AADEEAFEDNSEEYIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AADEEAFEDNSEEYIRR 17 1 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;;; 292.44 8.07E-46 2925610000 569430 682460 734880 645040 832060 830810 542000 648020 669300 815300 FALSE TRUE 591911.5361 799667.1962 754031.5765 772626.9867 690626.7384 637866.9685 499516.6237 639334.3518 645212.0237 975042.4251 0.60706234 0.820135797 0.77333207 0.792403455 0.708304296 0.654194066 0.512302451 0.655699009 0.661727128 1 19.89510547 -1.244545962 4.58506044 1.000107778 0.68643202 0.535525602 0.087379316 0.00010556 1.74E-05 0.092771284 0.021858917 0.056944795 1.244545962 -0.313675758 AADESER ddPTM_MDA-MB-175_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 ; 140.98 0.0060195 1151340000 965570 1045530 1095180 1065200 1174710 1267990 1333380 1112410 1144030 1158230 FALSE TRUE 1003691.449 1225091.644 1123721.291 1275893.381 975033.2138 973518.5391 1228866.191 1097499.963 1102856.584 1385162.993 0.724601693 0.884438619 0.81125564 0.921114257 0.703912261 0.702818761 0.887163603 0.792325502 0.796192643 1 20.40162432 -1.456095546 2.946163273 1.004851854 0.805737989 0.393120041 0.073471764 13353029.96 15166840.38 531527.433 0.017126045 0.034986819 1.456095546 -0.199113865 AADIS(ph)LDNLVEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AADISLDNLVEGK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK 163.8 4.00E-05 46824000 123843 84476 97551 83942 120005 132387 116130 109165 112417 94432 TRUE FALSE 128732.4173 98984.09587 100093.2592 100545.4771 99606.59296 101642.1256 107027.4272 107701.8217 108371.1341 112934.1424 1.139889271 0.87647627 0.886297599 0.89030186 0.881988306 0.900012374 0.947697701 0.953669275 0.959595848 1 16.78512218 -0.730758847 7.81298863 1.000007284 0.931905046 0.055998334 0.074255872 0 0 0.068613953 0.016172464 0.185883633 0.730758847 -0.068102238 AADKLIQNLDANHDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;; 236.02 6.12E-20 8527780000 6356470 6946630 6783490 5702170 8257300 8644490 6176560 6530120 7067910 7946090 FALSE TRUE 6607428.344 8139659.665 6960273.322 6830042.207 6853727.095 6636938.206 5692425.088 6442594.423 6813537.3 9502974.198 0.695301093 0.856538121 0.732431045 0.718726797 0.721219163 0.698406422 0.599015105 0.677955584 0.716989982 1 23.17994768 0.921551565 20.39413114 1 0.709897159 0.673839084 0.059897975 4589.774199 1193200.407 0.062932444 0.015733111 8.347406532 -0.921551565 -0.290102841 AADPPAENSS(ph)APEAEQGGAE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AADPPAENSSAPEAEQGGAE 20 0 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 AADPPAENS(0.08)S(0.92)APEAEQGGAE;AADPPAENS(0.038)S(0.962)APEAEQGGAE 260.98 2.44E-36 396810000 226160 281800 250530 262670 259540 316980 254570 262080 249240 258470 TRUE FALSE 235088.9714 330196.9579 257059.0176 314625.342 215423.4835 243366.1989 234616.1382 258567.2463 240269.9011 309112.2478 0.760529462 1.06821053 0.831604116 1.01783525 0.696910216 0.787306878 0.758999813 0.836483343 0.777290136 1 18.23777129 3.240963167 24.99998092 0.799453919 0.923882323 0.192274536 0.109196016 87.27407578 908128.6634 0.027971334 0.036145807 1741.659157 -3.240963167 0.124428404 AADRLPNLS(ph)SPSAEGPPGPPSGPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.706)S(0.294)PS(0.001)AEGPPGPPSGPAPR 225.53 1.07E-34 2091300000 122390 119800 132450 128020 130070 157180 141550 135620 153440 136880 TRUE FALSE 127222.0517 140374.7181 135901.7558 153341.9739 107960.7479 120677.3271 130454.9411 133802.2357 147917.7244 163699.0153 0.777170538 0.857517181 0.830192873 0.936731193 0.659507619 0.737190306 0.796919523 0.817367383 0.903595688 1 17.32068612 1.032863417 2.149436624 0.999250601 0.800313056 0.464685651 0.068699349 0.276647448 2.693326784 0.067200443 0.018676214 10.78607454 -1.032863417 -0.198937544 AADRLPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784;O60784-4;O60784-2;O60784-3 O60784 TOM1 Target of Myb protein 1 1 AADRLPNLS(0.192)S(0.8)PS(0.008)AEGPPGPPSGPAPR;AADRLPNLS(0.18)S(0.814)PS(0.006)AEGPPGPPSGPAPR;AADRLPNLS(0.068)S(0.926)PS(0.006)AEGPPGPPSGPAPR;AADRLPNLS(0.251)S(0.747)PS(0.002)AEGPPGPPSGPAPR 238.18 3.26E-45 3823720000 314161 383576 336561 354772 401576 485395 383993 433214 420043 505759 TRUE FALSE 326564.3189 449452.1942 345332.0561 424944.8427 333316.255 372669.3675 353894.6253 427407.4749 404925.7345 604852.7927 0.539907103 0.743076993 0.570935706 0.702559115 0.551070044 0.616132342 0.585092157 0.706630572 0.669461627 1 19.20622454 0.291623752 0.845006696 1.0039108 0.621865692 0.751244496 0.064571365 1.235523045 1.106447544 0.068136884 0.019351345 1.957148377 -0.291623752 -0.382045108 AADTEEMDIEMDS(ph)GDEA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AADTEEMDIEMDSGDEA 17 0 Q9UBB5 Q9UBB5 MBD2 Methyl-CpG-binding domain protein 2 1 AADTEEMDIEMDS(1)GDEA 332.06 3.24E-72 220830000 197200 270030 251200 261870 276470 302000 258700 277270 243300 273330 TRUE FALSE 204985.6083 316405.552 257746.4784 313667.1044 229475.7282 231865.0769 238422.418 273553.6492 234543.6805 326883.7803 0.627090179 0.967945096 0.788495771 0.959567661 0.702010139 0.709319614 0.729379775 0.83685293 0.717513975 1 18.31841827 -1.553843701 3.114422373 1.008571995 0.789668491 0.273335097 0.105966345 301798005.5 282689952.1 21054945.58 0.024290993 0.02793549 1.553843701 -0.218903503 AAEAHVDAHYYEQNEQPTGTCAACITGDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAEAHVDAHYYEQNEQPTGTCAACITGDNR 30 0 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 145.67 2.24E-08 97294000 26349 26914 30278 26955 33443 36038 31911 28498 32151 29590 FALSE TRUE 27389.27887 31536.27014 31067.06955 32286.61855 27758.37081 27668.72066 29409.73244 28116.03092 30993.89179 35387.59397 0.773979686 0.891167401 0.8779085 0.912371115 0.784409667 0.781876289 0.831074655 0.794516602 0.875840607 1 15.11095605 0.935989622 7.091907156 0.999997851 0.832232071 0.546070514 0.046501225 0.676502091 74.3312684 0.046796652 0.011734234 8.629579263 -0.935989622 -0.16776578 AAEDDEDDDVDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;; 351.74 1.29E-75 19267800000 8592560.5 4017530 5297274 3881799 7129779 6855105 7039208 5377187 5859197 3434423 FALSE TRUE 8931801.423 4707509.525 5435325.312 4649607.256 5917861.712 5263110.754 6487456.483 5305114.604 5648325.645 4107332.431 2.174599104 1.146123331 1.323322474 1.132026037 1.440804174 1.281393908 1.579481718 1.29162046 1.37518103 1 21.96977029 7.999999968 0.032981313 1.60E-09 3.429022712 0.229049001 0.271472791 2083.475313 5.257383313 166.454309 441.1528059 99999992.54 -7.999999968 3.42902271 AAEDDEDDDVDTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;;;; 266.35 1.18E-24 51057868000 9454054 2629127 4618512 2801991 7017783 6829360 6712500 4298812 4914532 1855617 FALSE TRUE 9827307.352 3080659.11 4738874.217 3356216.457 5824902.752 5243344.64 6186356.71 4241193.457 4737658.953 2219189.623 4.428331518 1.388191022 2.135407523 1.512361279 2.624788207 2.362729433 2.787664761 1.911145137 2.134859907 1 21.08160152 0.5856054 1.039110041 1.001433413 2.358472911 0.217011308 0.799976104 2.148406491 3.558760337 0.717783759 0.226856964 3.851282713 -0.5856054 1.357039498 AAEEAEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAEEAEEAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 125.04 0.001193 443750000 672760 726270 727410 622660 804570 974210 730440 760990 659180 716010 FALSE TRUE 699321.0843 851001.2229 746366.9022 745820.2895 667809.4788 747964.4918 673186.2042 750790.1738 635456.2406 856298.4507 0.816679142 0.993813807 0.871620054 0.870981711 0.77987935 0.873485747 0.786158382 0.876785627 0.742096684 1 19.70775419 3.737235623 2.802216948 0.837427786 0.907653885 0.069084893 0.078301904 0.527255813 8.276998751 0.019504064 0.036381134 5460.540376 -3.737235623 0.0702261 AAEEAFVNDIDESSPGTEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAEEAFVNDIDESSPGTEWER 21 0 P09496-2;P09496-5 P09496-2 CLTA Clathrin light chain A 0 269.55 2.44E-37 175500000 88437 115750 107560 124190 118420 113850 115310 103960 101870 117470 FALSE TRUE 91928.56105 135629.1621 110363.102 148754.4113 98291.0107 87410.06291 106271.7009 102566.5862 98203.7186 140485.9974 0.654361024 0.965428332 0.785580798 1.058855787 0.699649876 0.622197689 0.756457603 0.730084052 0.699028518 1 17.10006681 5.03760408 14.81752974 0.797162822 0.139310393 0.095124987 0.139277401 2234160.387 26647834.21 0.033306401 38073651.23 109044.579 -5.03760408 -0.657852429 AAEEEDEADPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 ;;;;;; 195.25 7.86E-07 18146610000 5140790 2909573 3721630 2801673 4846720 4221970 4460650 3520240 3893820 2553985 FALSE TRUE 5343752.359 3409269.529 3818618.735 3355835.557 4022876.266 3241481.452 4111012.597 3473056.941 3753682.179 3054389.462 1.749532083 1.116186908 1.250206885 1.09869275 1.317080325 1.061253482 1.345935955 1.137070758 1.228946808 1 21.5424526 4.742750261 24.96668556 1.183968698 1.74953231 0.724622392 0.106457468 193.2640619 1151644.361 0.022149759 0.172572171 55303.1999 -4.742750261 0.565563612 AAEEPSKVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAEEPSKVEEK 11 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 ;; 94.767 0.0075316 592407000 492670 283766 363220 238030 515340 496210 501610 372410 436400 269935 FALSE TRUE 512120.992 332500.6031 372685.8116 285111.6236 427742.6909 380972.7476 462292.4975 367418.4531 420694.0492 322823.595 1.586380302 1.029976149 1.154456543 0.88318087 1.325004422 1.180126712 1.432028218 1.138140021 1.303170077 1 18.3003865 AAEEQGDDQDS(ph)EKSKPAGSDGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 AAEEQGDDQDS(0.971)EKS(0.013)KPAGS(0.016)DGER 49.888 0.071531 99099000 122330 34833 47217 39198 62199 82043 74331 43920 43244 22786 TRUE FALSE 127159.6829 40815.29679 48447.51381 46951.24741 51626.4362 62989.75662 68504.74199 43331.32424 41687.65689 27250.48044 4.66632811 1.497782649 1.77785907 1.722951179 1.894514716 2.311509948 2.513891164 1.590112304 1.5297953 1 14.73399404 4.742548007 24.99016765 1.822594135 4.66632922 0.820461314 0.406936822 160.2381159 1004221.124 0.096695193 0.741309985 55277.45089 -4.742548007 2.843735084 AAELWGEQAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAELWGEQAEAR 12 0 Q08379;Q08379-2 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 132.32 0.00050733 91106000 61798 76333 71020 67534 72497 89180 64646 72966 68705 78179 FALSE TRUE 64237.83276 89442.59896 72870.83954 80892.02363 60173.98584 68469.29654 59578.8776 71988.01012 66232.32047 93496.67822 0.687060054 0.956639323 0.779394957 0.86518607 0.643594906 0.732317959 0.637229886 0.769952596 0.708392231 1 16.51262749 5.040291385 15.99989179 0.77286244 0.30850672 0.050021985 0.116123536 6774206.871 74463863.93 0.026715368 91861216.28 109721.4112 -5.040291385 -0.46435572 AAEWQLDQPSWSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAEWQLDQPSWSGR 14 0 Q9NVZ3;Q9NVZ3-2;D6RAN6;F6SKB8;Q9NVZ3-3;H0Y970 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 0 134.49 4.07E-05 0 44868 54073 50772 47802 54610 64096 51000 46423 52003 52709 FALSE TRUE 46639.42329 63359.61712 52095.16003 57257.09293 45327.41171 49210.67538 47002.48674 45800.77562 50131.42219 63036.31938 0.739881766 1.005128754 0.826430866 0.908319101 0.719068184 0.780671776 0.745641357 0.726577568 0.795278384 1 15.94389568 3.246317152 24.9994392 0.773513159 0.876488656 0.10082886 0.098231359 265.23269 854844.1771 0.025066474 0.033324211 1763.263235 -3.246317152 0.102975498 AAFAHFPELYDFALSNVAEVDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAFAHFPELYDFALSNVAEVDTR 23 0 O60306;H0YH15 O60306 AQR Intron-binding protein aquarius 0 106.69 0.0014189 72228000 64825 41807 56503 47042 75856 75032 60795 38540 70028 45591 FALSE TRUE 67384.34106 48987.02704 57975.5146 56346.76719 62962.02422 57606.95512 56029.72904 38023.43434 67507.70596 54523.68356 1.235872866 0.8984541 1.063308838 1.033436546 1.154764684 1.056549216 1.027621859 0.697374643 1.238135459 1 15.73459541 1.982052965 24.57208802 0.924283312 1.065053943 0.039211036 0.148923267 1083.819781 1483904.643 0.057884725 0.038206882 95.95176427 -1.982052965 0.140770631 AAFDDAIAELDTLSEESYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AAFDDAIAELDTLSEESYK 19 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 153.95 4.06E-08 58172800 134771.6 102824.5 121695.8 116036.7 142997.7 156471.4 173161.6 123753.8 134843.9 94622.3 FALSE TRUE 140092.4868 120483.808 124867.2925 138988.4129 118691.002 120133.2887 159588.7413 122095.0827 129990.8944 113161.728 1.23798469 1.064704561 1.103441019 1.228228089 1.048861696 1.061607054 1.410271335 1.078943251 1.148717827 1 16.78802659 -2.451358075 1.026478439 0.558501522 1.151909994 0.156877286 0.106791298 13549.37541 1115.026693 13628.1281 0.031036271 0.003537056 2.451358075 0.593408472 AAFDDAIAELDTLSEESYKDSTLIMQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAFDDAIAELDTLSEESYKDSTLIMQLLR 29 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 180.42 1.01E-17 4806686000 1402755 1244412 1514697 1175406 1960511 1908682 1580728 1485085 1623567 1286784 FALSE TRUE 1458136.851 1458130.081 1554171.248 1407897.799 1627264.04 1465419.532 1456826.409 1465179.865 1565135.141 1538904.688 0.947516024 0.947511625 1.009920407 0.914870043 1.05741704 0.952248403 0.946664482 0.952092665 1.017044885 1 20.55347245 0.216544621 0.004141167 1.965898121 3.89E-07 0.071590828 0.04016289 57671.07132 83.9124307 20170.85352 19661.9079 1.646435117 -0.216544621 -1.965897732 AAFGISDSYVDGSSFDPQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAFGISDSYVDGSSFDPQRR 20 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 100.04 0.00091654 182010000 40146 51617 50908 36290 41428 56256 27094 42020 47710 49528 FALSE TRUE 41730.99508 60481.81823 52234.7043 43468.05369 34386.08336 43191.39657 24970.30148 41456.79063 45992.92642 59232.06333 0.704533875 1.021099297 0.881865351 0.733860197 0.580531581 0.729189465 0.421567308 0.69990455 0.776486988 1 15.85409072 3.633629024 3.755981432 0.66917725 0.884744667 0.166760008 0.15696845 0.30247268 7.708061055 0.040536272 0.065786939 4301.590097 -3.633629024 0.215567417 AAFNSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAFNSGK 7 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 124.83 0.0095567 9296000000 7002800 7201500 7606300 6877100 8922700 9183800 8438000 7732200 7504800 7524400 FALSE TRUE 7279275.951 8438301.605 7804526.427 8237369.854 7406022.641 7051001.632 7776607.511 7628562.506 7234703.714 8998662.117 0.808928689 0.937728464 0.86729853 0.915399395 0.823013749 0.783561105 0.864195967 0.847744077 0.803975482 1 23.10127909 5.061343391 14.41090668 0.863343089 0.392387914 0.07032547 0.062204494 1264265.547 7829934.556 0.014127745 17014043.93 115171.0671 -5.061343391 -0.470955174 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK 41 2 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 234.43 7.56E-55 1494750000 875310 740050 1386190 805920 1687520 1577450 1705200 1317700 1890400 861520 FALSE TRUE 909867.9147 867147.8307 1422315.25 965328.5706 1400675.953 1211111.144 1571541.968 1300038.387 1822364.873 1030318.349 0.883093964 0.841630969 1.380461924 0.936922623 1.359459389 1.175472751 1.525297467 1.261783203 1.768739608 1 19.97465874 4.351764837 0.554976685 1.387522754 0.62181015 0.340172932 0.233738208 2.823888455 0.894767838 0.123658256 1.324177798 22478.37112 -4.351764837 -0.765712603 AAFTTPDHAPLS(ph)PQSSVASSGSEQTEEQGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAFTTPDHAPLSPQSSVASSGSEQTEEQGSSR 32 0 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3 M0QZ22 SAMD4B Protein Smaug homolog 2 1 AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR;AAFTTPDHAPLS(1)PQSSVASSGSEQTEEQGSSR;AAFTTPDHAPLS(0.999)PQS(0.001)SVASSGSEQTEEQGSSR 270.73 1.62E-73 967170000 235476 313485 296883 325786 328669 358218 313912 353558 334643 381374 TRUE FALSE 244772.7743 367323.6102 304620.0149 390225.4984 272801.9608 275027.2983 289306.7572 348819.1333 322599.2638 456096.9335 0.536668318 0.805363034 0.667884374 0.855575799 0.598122769 0.603001858 0.634309806 0.764791665 0.707304172 1 18.79898094 0.329836081 1.017959589 1.000923699 0.683749736 0.505616276 0.09390706 2.386165929 2.909648132 0.092080526 0.027665224 2.137155297 -0.329836081 -0.317173963 AAGAGKVT(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGAGKVTK 9 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 1 AAGAGKVT(1)K;AAGAGKVT(1)K 84.507 0.02497 349040000 1310270 641550 935980 493870 1135680 1151620 973710 916600 1141560 638670 TRUE FALSE 1362000.471 751731.2219 960372.4077 591556.0119 942637.5193 884173.708 897388.0659 904314.4763 1100475.479 763805.1584 1.783177891 0.984192387 1.257352608 0.774485489 1.234133481 1.157590648 1.17489134 1.183959635 1.44078037 1 19.54284514 4.747340639 24.49842198 1.140234005 1.78317833 0.562952039 0.171482623 619.7813774 1729291.835 0.038999346 0.459398787 55890.84033 -4.747340639 0.642944325 AAGALGSASSGS(ph)MPNLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGALGSASSGSMPNLAAR 19 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 AAGALGSASS(0.009)GS(0.991)MPNLAAR;AAGALGSASS(0.01)GS(0.989)MPNLAAR 282.2 1.02E-39 679720000 338850 404910 389790 398270 443520 482350 367130 342430 361060 376980 TRUE FALSE 352228.0596 474450.1427 399948.2476 477046.6173 368130.6288 370331.5226 338353.3913 337840.286 348065.5211 450842.0133 0.781267161 1.052364529 0.887113969 1.058123696 0.816540203 0.821421943 0.750492149 0.749354044 0.772034351 1 18.78226244 3.09531316 8.464198138 0.795841532 0.948043297 0.259820227 0.100829746 0.275508597 21.82408796 0.027099338 0.032435324 1245.412326 -3.09531316 0.152201765 AAGARPLTS(ph)PESLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGARPLTSPESLSR 15 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 AAGARPLT(0.141)S(0.801)PES(0.04)LS(0.018)R;AAGARPLT(0.131)S(0.606)PES(0.198)LS(0.065)R 78.191 0.012589 156510000 274360 401710 376640 353060 389450 451770 327260 374590 330380 426120 TRUE FALSE 285191.9447 470700.5676 386455.5478 422894.2142 323251.4281 346853.2641 301608.5061 369569.2338 318489.6883 509610.0554 0.559627781 0.923648509 0.758335798 0.829838834 0.634311322 0.680624843 0.591841748 0.725200042 0.624967433 1 18.95903422 -1.13136129 3.792737944 1.000144888 0.708686416 0.411928363 0.106218406 17327944.57 38454751.78 33550.47401 0.025910626 0.073899025 1.13136129 -0.291458473 AAGGAPS(ph)PPPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAGGAPSPPPPVR 13 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR 162.72 4.19E-05 3960770000 940250 1024500 995660 971120 1139200 1254110 1114650 994310 995860 965230 TRUE FALSE 977371.796 1200449.905 1021607.718 1163204.637 945559.1909 962861.9587 1027280.82 980982.9008 960019.1931 1154348.338 0.846687056 1.03993731 0.885008176 1.00767212 0.819128126 0.834117334 0.889922727 0.849815319 0.831654676 1 20.13864721 3.231407153 24.99927911 0.862157014 0.947347107 0.203329431 0.070514327 211.2784395 738356.241 0.018445869 0.022481967 1703.755038 -3.231407153 0.085190093 AAGGAPS(ph)PPPPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAGGAPSPPPPVRR 14 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR;AAGGAPS(1)PPPPVRR 85.988 0.0046049 2146550000 2019210 1896440 1861710 1752450 2082910 2595810 1912140 1871620 1746990 1695840 TRUE FALSE 2098929.97 2222138.818 1910227.692 2099079.379 1728857.702 1992972.467 1762261.47 1846533.995 1684116.171 2028107.379 1.034920533 1.095671186 0.941876999 1.034994202 0.8524488 0.98267601 0.868919214 0.910471514 0.830388069 1 20.95170261 3.748062622 0.938635266 0.901440301 1.071312699 0.429146252 0.06365242 0.588013296 0.939825091 0.022180237 0.07449993 5598.383206 -3.748062622 0.169872398 AAGGGSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAGGGSYK 8 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 75.311 0.090077 911910000 1321700 1832800 1790500 1713000 1805900 2215800 1782500 1770900 1499600 2008200 FALSE TRUE 1373881.737 2147569.143 1837161.901 2051826.287 1498933.763 1701214.031 1642782.992 1747163.982 1445629.689 2401668.341 0.572053065 0.894198881 0.764952375 0.854333736 0.624121881 0.708346778 0.684017424 0.727479291 0.601927279 1 21.1956055 -1.093043104 4.558429677 1.00001922 0.721804726 0.428557426 0.098551865 1.95E-05 3.88E-06 0.090992566 0.021445581 0.080715492 1.093043104 -0.278214493 AAGIDEQENWHEGKENIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAGIDEQENWHEGKENIR 18 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ;; 205.31 5.87E-16 420810000 354132 307527 380490 251630 494500 418923 305575 334637 397691 381713 FALSE TRUE 368113.4048 360342.37 390405.882 301401.663 410445.0666 321634.4821 281623.233 330151.7384 383378.1786 456502.354 0.80637789 0.7893549 0.855211104 0.660241202 0.899108324 0.704562593 0.616915182 0.723220232 0.839816433 1 18.80026277 0.939114599 4.146332025 0.999798686 0.753311863 0.453778299 0.081485248 0.253623174 11.85817825 0.07966893 0.020331052 8.691897561 -0.939114599 -0.246486823 AAGISLIVPGKS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGISLIVPGKSPTR 15 1 J3KPC5;P47736-3;P47736;P47736-4;F2Z357 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 AAGISLIVPGKS(0.504)PT(0.496)R;AAGISLIVPGKS(0.997)PT(0.003)R 143.46 2.67E-06 2062390000 2215980 1615990 2109600 1724480 2592000 2528370 2321040 2156990 2275950 1906140 TRUE FALSE 2303468.602 1893523.712 2164577.909 2065576.997 2151412.766 1941194.385 2139110.82 2128079.077 2194039.004 2279611.638 1.010465363 0.830634342 0.949538015 0.906109165 0.943762845 0.851546094 0.938366336 0.933527028 0.962461749 1 21.12035663 1.13077123 1.362480051 0.998973798 0.914350434 0.227636306 0.04782355 0.529519054 1.964668179 0.04047738 0.012402538 13.51360531 -1.13077123 -0.084623364 AAGLATMISTMRPDIDNMDEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGLATMISTMRPDIDNMDEYVR 23 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 222.72 1.44E-32 602410000 232120 261240 289160 276350 273000 299520 289430 306270 281350 295360 FALSE TRUE 241284.2768 306105.9378 296695.7471 331011.2052 226595.5575 229961.0193 266743.7203 302164.9516 271224.2685 353230.137 0.683079532 0.866590661 0.839950265 0.937097859 0.64149554 0.651023215 0.755155612 0.855433668 0.767840113 1 18.43024891 -1.489874285 3.336062185 1.004304537 0.783346514 0.335343579 0.093642621 30996881.78 43374155.68 1234793.262 0.023494304 0.032368734 1.489874285 -0.220958022 AAGNESFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAGNESFR 8 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 107.01 0.0095055 126580000 35285 51087 44317 52012 53216 58827 51398 47597 46781 52518 FALSE TRUE 36678.07905 59860.79485 45471.93743 62299.81836 44170.36333 45165.32078 47369.29046 46959.04007 45097.36095 62807.89658 0.583972415 0.953077529 0.723984402 0.9919106 0.703261305 0.719102585 0.754193231 0.747661403 0.718020558 1 15.93865833 -1.020729646 4.660449595 1.000006235 0.771592551 0.27339206 0.114067717 6.81E-06 1.43E-06 0.101699479 0.023970143 0.095338948 1.020729646 -0.228413684 AAGQPYEQHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGQPYEQHAK 11 0 O14976-2;O14976;A0A087X1U9;H0Y8H5 O14976-2 GAK Cyclin-G-associated kinase 0 ; 163.12 0.0011423 71800000 141586 130049 149049 130825 177788 191735 162947 159022 152126 133628 FALSE TRUE 147175.9246 152383.9041 152933.3394 156701.7945 147567.6593 147207.452 150174.7884 156890.5702 146651.015 159809.8481 0.920944024 0.953532626 0.956970682 0.980551551 0.923395279 0.921141305 0.939709224 0.981732803 0.917659435 1 17.28599679 -1.474517054 2.878795785 1.001630534 0.946844391 0.342395861 0.022988387 13346792.92 16672863.98 177286.0205 0.005635837 0.033533814 1.474517054 -0.054786143 AAGS(ph)PSPLPAPDPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAGSPSPLPAPDPAPK 16 0 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3KRF7 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 AAGS(0.769)PS(0.231)PLPAPDPAPK;AAGS(0.74)PS(0.26)PLPAPDPAPK;AAGS(0.949)PS(0.051)PLPAPDPAPK 172.91 4.62E-09 774160000 1250900 857480 969960 841310 1283020 1440220 1249820 1021210 1089740 813130 TRUE FALSE 1300286.498 1004745.52 995237.9544 1007718.607 1064932.719 1105750.732 1151855.843 1007522.35 1050520.47 972447.2552 1.337128046 1.033213384 1.023436437 1.036270709 1.095105892 1.137080418 1.184491844 1.036068892 1.080285295 1 19.89126048 4.137921386 0.012559268 5.44E-06 2.236427054 0.163658762 0.088425276 7550.467238 18.05837393 1490.347749 1730.201442 13737.93274 -4.137921386 2.23642161 AAGSPS(ph)PLPAPDPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAGSPSPLPAPDPAPK 16 0 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3KRF7 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 AAGSPS(1)PLPAPDPAPK;AAGSPS(1)PLPAPDPAPK 188.92 1.16E-09 113870000 341190 192521 244860 176225 362630 364750 350010 278030 293020 186347 TRUE FALSE 354660.4447 225584.9841 251241.2528 211081.779 300990.2821 280042.3403 322575.3016 274303.4626 282474.2674 222858.1268 1.591418046 1.012235844 1.127359618 0.947157647 1.350591457 1.256594697 1.447446886 1.230843436 1.267507142 1 17.76576605 AAHACATVGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAHACATVGNR 11 0 G3V2H2;G3V3U8;Q9Y2U9-2;Q9Y2U9 G3V2H2 KLHDC2 Kelch domain-containing protein 2 0 74.533 0.040562 9691600 3431.2 6346.1 5373.3 5370.6 5616.1 6561.5 4783.8 5860.6 4740.7 6740.4 FALSE TRUE 3566.666425 7435.993309 5513.332612 6432.88865 4661.477328 5037.691065 4408.833256 5782.048243 4570.083133 8061.052327 0.442456677 0.922459377 0.683947007 0.798020952 0.578271563 0.624942112 0.546930237 0.717282063 0.566933813 1 12.97675247 -1.20581523 5.102544088 1.00002988 0.662915915 0.388438795 0.129957054 4.12E-05 6.42E-06 0.117451895 0.027681227 0.06225651 1.20581523 -0.337113965 AAHIFFTDTCPEPLFSELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAHIFFTDTCPEPLFSELGR 20 0 Q15833-2;Q15833;Q15833-3;M0R0M7;M0QZ54;M0R118;A0A087WUN8 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 ; 176.42 4.84E-13 310740000 186328 185131 205181 191870 230417 238302 212345 208366 194458 223252 FALSE TRUE 193684.3733 216925.8091 210528.1854 229821.3133 191250.8006 182959.972 195700.844 205573.1946 187459.4946 266993.955 0.725426062 0.812474609 0.788512929 0.860773471 0.716311351 0.685258855 0.732978558 0.769954491 0.702111381 1 18.02644755 -1.001243772 4.326475089 1.00001073 0.757474733 0.671585193 0.05139705 6772198.775 1567239.256 739.4639617 0.012514155 0.099714021 1.001243772 -0.242535996 AAHLCAEAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAHLCAEAALR 11 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 104.79 0.0021215 0 54911 116990 88960 94770 115600 128000 68177 99936 70039 158090 FALSE TRUE 57078.92868 137082.1224 91278.37068 113515.2231 95950.35329 98273.93986 62833.10859 98596.52138 67518.31007 189064.7087 0.30190155 0.725053996 0.482789048 0.600404084 0.507500072 0.519789973 0.332336527 0.52149617 0.357117468 1 17.52852057 -1.459411152 3.12680673 1.010338806 0.491193029 0.618819511 0.121545683 227221095 280313045.9 20602880.77 0.026957205 0.03472073 1.459411152 -0.519145777 AAHSEGNTTAGLDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AAHSEGNTTAGLDMR 15 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;;;; 200 5.82E-10 2758030000 1468320 1739818 1633358 1593129 1851688 2090022 1715617 1675458 1712365 1797104 FALSE TRUE 1526290.407 2038618.208 1675924.651 1908245.161 1536938.735 1604646.065 1581142.457 1653001.226 1650737.318 2149212.121 0.710162758 0.948542113 0.779785594 0.887881258 0.715117284 0.74662061 0.735684692 0.769119627 0.768066261 1 21.03537645 5.03497648 17.03733919 0.801858148 0.348595193 0.087479398 0.092645207 19469057.91 250526326.9 0.020962084 268866964 108386.8213 -5.03497648 -0.453262954 AAHSRNS(ph)MDRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAHSRNSMDRPK 12 2 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAHS(0.052)RNS(0.948)MDRPK;AAHS(0.116)RNS(0.884)MDRPK;AAHS(0.001)RNS(0.999)MDRPK;AAHS(0.026)RNS(0.974)MDRPK 98.943 0.002126 272752800 83261.8 71708 80430.3 47691.5 114443.2 87894.5 64086.7 74289.9 93230.8 92015.5 TRUE FALSE 86549.04016 84023.29119 82526.37969 57124.73636 94990.18574 67482.33443 59063.41699 73294.1654 89875.44172 110044.1755 0.786493604 0.763541467 0.749938644 0.519107314 0.863200486 0.613229497 0.536724608 0.666043115 0.816721479 1 16.74772326 0.97098873 3.428507591 0.999127451 0.682208431 0.466909266 0.10387671 0.199350999 6.155961676 0.099625989 0.025831662 9.353814008 -0.97098873 -0.31691902 AAHTEDINACTLT(ph)TSPRLPVF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAHTEDINACTLTTSPRLPVF 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 AAHTEDINACT(0.007)LT(0.517)T(0.092)S(0.384)PRLPVF 95.366 0.0023224 94234000 86749 110930 119220 104770 120820 121110 122320 107090 113780 164310 TRUE FALSE 90173.9175 129981.3646 122326.9711 125493.1933 100283.0596 92984.03794 112732.2388 105654.6337 109685.08 196503.3986 0.458892407 0.661471331 0.622518348 0.63863116 0.510337532 0.473193027 0.573691038 0.537673315 0.558184137 1 17.58419474 -1.440612329 4.180151999 1.002011992 0.561518004 0.808629709 0.064295233 0.001224897 0.000163916 0.063250732 0.014845902 0.03625665 1.440612329 -0.440493989 AAHTEDINACTLTT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAHTEDINACTLTTSPR 17 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 AAHTEDINACTLT(0.004)T(0.783)S(0.213)PR 145.55 1.73E-06 616240000 77800 75168 85349 76516 87302 110150 79955 69955 72911 88607 TRUE FALSE 80871.60407 88077.51927 87573.26505 91650.63642 72462.43722 84569.33184 73687.91818 69017.36765 70286.94735 105967.8452 0.763171167 0.831172127 0.826413568 0.864891008 0.683815332 0.798065977 0.695379981 0.651304814 0.663285615 1 16.69326703 3.238038041 24.99997169 0.724770596 0.822466381 0.086349802 0.099120817 23.22098072 1110913.648 0.026671176 0.033770929 1729.967884 -3.238038041 0.097695786 AAHTEDINACTLTTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAHTEDINACTLTTSPR 17 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 AAHTEDINACTLTT(0.002)S(0.998)PR;AAHTEDINACTLTT(0.017)S(0.983)PR 217.17 3.26E-15 595540000 179391 200663 199110 219321 221021 280530 241200 237030 222750 248210 TRUE FALSE 186473.4952 235125.3093 204298.9702 262702.0392 183451.9294 215381.159 222294.1137 233853.0006 214733.271 296841.9972 0.628191081 0.792089096 0.688241462 0.884989461 0.618012044 0.72557509 0.748863422 0.787802948 0.723392488 1 18.17933569 -4.99999999 0.291421897 3.067088214 0.723081542 0.537831029 0.074582332 184.6891241 1.735723684 232.1209062 0.073215435 1.00E-05 4.99999999 -2.344006672 AAHVLMPHESTVEHTHVDINEMES(ph)PLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAHVLMPHESTVEHTHVDINEMESPLATR 29 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHESTVEHTHVDINEMES(1)PLATR;AAHVLMPHES(0.002)T(0.002)VEHT(0.002)HVDINEMES(0.992)PLAT(0.002)R 198.95 1.72E-25 2355780000 351655 579899 546655 589937 568162 694959 556835 618086 518423 638004 TRUE FALSE 365538.6109 679492.1423 560901.2784 706624.7778 471586.0262 533565.3045 513188.8177 609801.5682 499765.0575 763008.6685 0.479075305 0.890543149 0.735117832 0.926103211 0.618061165 0.699291275 0.672585829 0.799206606 0.654992634 1 19.54133992 -2.009596995 2.855361009 1.286975548 0.730581747 0.310932778 0.12430565 10373185.83 11058153.58 19587719.13 0.027977397 0.009781445 2.009596995 -0.556393801 AAHVLMPHESTVEHTHVDINEMESPLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAHVLMPHESTVEHTHVDINEMESPLATR 29 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 104.3 0.00016633 435830000 50985 87733 86765 102750 94938 109720 90825 88139 88479 89710 FALSE TRUE 52997.92717 102800.4603 89026.16718 123073.6433 78800.47267 84239.19282 83705.89917 86957.64087 85294.65807 107286.9569 0.493982947 0.958182274 0.829794877 1.147144507 0.734483249 0.785176458 0.780205736 0.810514562 0.795014236 1 16.71111517 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAHVPENSDTEQDVLTVKPVR 21 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BS99 H3BSS6 ZNF106 Zinc finger protein 106 1 AAHVPENS(0.993)DT(0.007)EQDVLTVKPVR;AAHVPENS(1)DTEQDVLTVKPVR;AAHVPENS(0.952)DT(0.048)EQDVLTVKPVR 249.96 5.18E-31 800000000 534090 415974 489670 430360 573970 595280 526870 514790 550460 413935 TRUE FALSE 555176.2856 487414.2987 502431.2025 515483.9235 476406.7844 457035.2416 485572.5527 507890.0821 530649.0521 495037.638 1.12148298 0.984600485 1.014935358 1.041302487 0.962364774 0.923233319 0.980880069 1.025962559 1.071936781 1 18.91717869 4.743011734 24.52651486 0.999814997 1.121483044 0.455937552 0.03961364 343.2849037 1891477.381 0.010140228 0.080017779 55336.50596 -4.743011734 0.121668047 AAIDWFDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAIDWFDGK 9 0 Q92804-2;Q92804;A0A075B7D9;P35637-2;P35637;H3BPE7 Q92804-2;P35637-2 TAF15;FUS TATA-binding protein-associated factor 2N;RNA-binding protein FUS 0 ;;; 153.08 0.00018367 1471483000 3040310 2236950 2549100 2497070 3111830 3119530 3566700 2647010 2729380 1862607 FALSE TRUE 3160343.786 2621128.761 2615531.64 2990982.993 2582882.248 2395066.434 3287132.734 2611531.161 2631150.147 2227549.18 1.418753765 1.176687269 1.174174588 1.342723662 1.159517496 1.075202494 1.475672351 1.172378677 1.181186108 1 21.08702585 -4.142880631 0.275566246 9.12E-14 1.257415149 0.280546465 0.120149532 174.9914592 2.623193735 98.72470501 0.13771722 7.20E-05 4.142880631 1.257415149 AAIDWFDGKEFSGNPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAIDWFDGKEFSGNPIK 17 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;; 226.67 1.82E-15 1892340000 3499160 2376020 3342870 1972220 4593330 3849000 3219410 3123170 3531610 2577440 FALSE TRUE 3637309.539 2784082.952 3429987.938 2362319.23 3812557.407 2955128.082 2967064.232 3081309.015 3404508.046 3082440.02 1.180009835 0.903207503 1.11275091 0.766379626 1.236863453 0.958697676 0.962569981 0.999633081 1.104484767 1 21.55564139 AAIPPPVYEEQDRPRS(ph)PTGPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 AAIPPPVYEEQDRPRS(0.979)PT(0.021)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.72)PT(0.173)GPS(0.053)NS(0.053)FLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.722)PT(0.273)GPS(0.005)NSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.932)PT(0.068)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.983)PT(0.017)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.823)PT(0.177)GPSNSFLANMGGTVAHK;AAIPPPVYEEQDRPRS(0.97)PT(0.029)GPSNSFLANMGGTVAHK 262.6 2.04E-60 6559760000 1072111 1074509 1168240 852516 1441289 1412405 930888 1126035 1207044 1203348 TRUE FALSE 1114438.77 1259047.562 1198685.294 1021141.12 1196299.211 1084395.344 857922.5661 1110942.343 1163602.722 1439121.001 0.774388512 0.874872621 0.832928776 0.709558904 0.831270762 0.753512278 0.596143455 0.771958954 0.808550998 1 20.45675647 3.775544785 22.60365569 0.762380068 0.832144332 0.017493307 0.099548005 454.5017601 277774.4635 0.024427559 0.044034176 5964.098195 -3.775544785 0.069764264 AAKLS(ph)EGS(ph)QPAEEEEDQETPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;AAKLS(1)EGS(1)QPAEEEEDQETPSR 239.97 7.48E-31 1260130000 1903540 1156350 1581800 1161600 2400860 2474420 1978960 1874640 2040100 1350640 TRUE FALSE 1978693.229 1354944.117 1623023.007 1391361.013 1992762.675 1899773.455 1823843.944 1849513.517 1966677.2 1615272.048 1.224990695 0.838833383 1.004798547 0.861378747 1.233700959 1.176132192 1.129124933 1.145016729 1.217551682 1 20.62334574 3.231814705 24.99999897 1.156224588 0.973831142 0.339605421 0.114164861 156.2791723 579162.2053 0.030500559 0.037239339 1705.354633 -3.231814705 -0.182393446 AAKNS(ph)EEEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 243.04 1.53E-16 1761460000 3553570 755970 1299250 916230 1911540 2681160 2565180 1308400 1500360 535387 TRUE FALSE 3693867.688 885801.9669 1333109.522 1097457.559 1586617.114 2058501.223 2364114.489 1290863.038 1446362.337 640285.832 5.769091713 1.383447708 2.082053757 1.714011937 2.477982542 3.214972314 3.69227987 2.016073093 2.258932284 1 19.28835656 0.905645447 1.487509592 1.024008093 2.737040877 0.177948859 1.187860568 0.927158155 4.078345565 1.082933938 0.318607761 8.047212087 -0.905645447 1.713032784 AAKNS(ph)EEEEEEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 223.86 2.40E-12 3821060000 8958130 797225 1754513 650996 3492770 4834380 3415680 1839935 2091298 350957 TRUE FALSE 9311803.89 934142.1922 1800237.05 779761.0658 2899070.203 3711668.511 3147950.076 1815273.681 2016032.593 419720.3047 22.18573604 2.225630216 4.289135003 1.857811159 6.907147857 8.843195026 7.500113865 4.324960362 4.803276303 1 18.67906873 4.744116507 24.89306774 4.947460784 22.18574387 0.824225057 2.427171389 235.468842 1054980.617 0.597472388 5.251835371 55477.45204 -4.744116507 17.23828308 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 AAKPGPAEAPS(0.97)PT(0.03)AS(0.002)PSGDAS(0.997)PPAT(0.001)APYDPR;AAKPGPAEAPS(0.973)PT(0.025)AS(0.002)PS(0.017)GDAS(0.977)PPAT(0.006)APYDPR;AAKPGPAEAPS(0.978)PT(0.149)AS(0.274)PS(0.035)GDAS(0.558)PPAT(0.006)APYDPR 158.61 1.29E-12 1409770000 409482 355846 418056 316688 490057 506864 448684 423251 469223 380688 TRUE FALSE 425648.6655 416959.7824 428950.8828 379327.9412 406757.2862 389152.5176 413514.9757 417578.0126 452335.7559 455276.5249 0.934923376 0.915838528 0.942176588 0.833181419 0.893429079 0.85476078 0.908272123 0.917196451 0.993540697 1 18.79638355 1.295339608 2.540006129 1.003292355 0.896021943 0.606558417 0.03147556 0.188004222 2.006771253 0.028918369 0.008515449 19.73965725 -1.295339608 -0.107270412 AAKPGPAEAPSPTASPSGDAS(ph)PPATAPYDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 AAKPGPAEAPSPTASPSGDAS(0.999)PPATAPYDPR;AAKPGPAEAPSPTASPS(0.001)GDAS(0.996)PPAT(0.003)APYDPR;AAKPGPAEAPSPTASPS(0.001)GDAS(0.998)PPAT(0.001)APYDPR;AAKPGPAEAPSPTASPS(0.003)GDAS(0.995)PPAT(0.002)APYDPR 165.61 8.46E-13 1789650000 467630 427622 475046 401921 526334 572640 537290 489488 481010 435604 TRUE FALSE 486092.3935 501062.7521 487426.089 481419.7742 436867.9347 439653.0384 495175.8059 482927.214 463698.5441 520952.2637 0.933084329 0.961820856 0.93564444 0.924114948 0.838594945 0.843941123 0.950520499 0.927008572 0.890097954 1 18.99079165 -0.526443371 11.22461993 1 0.912830597 0.306697306 0.039815921 0 0 0.041697133 0.009828109 0.297547722 0.526443371 -0.087169403 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALAGGTTMIIDHVVPEPGTSLLAAFDQWR 30 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ; 214.78 1.90E-34 348630000 142716 189428 188425 190273 195580 215870 170123 192244 180156 198670 FALSE TRUE 148350.5379 221960.7855 193335.5103 227908.4315 162335.3815 165737.464 156788.3147 189667.2836 173672.2208 237595.5827 0.624382559 0.934195758 0.813716771 0.959228403 0.683242422 0.697561218 0.659895748 0.798277819 0.730957279 1 17.85814849 4.785379188 22.32279898 0.793250375 0.624379834 0.175490423 0.115553416 17768.2011 8470924.946 0.027311251 13.93572411 61006.9324 -4.785379188 -0.16887054 AALAPAKES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 137.81 4.28E-05 13899960000 11351130 8371340 9763600 7858460 12271010 12170880 11630660 10146000 10391820 8417990 TRUE FALSE 11799281.38 9809052.525 10018047.44 9412839.933 10185188.1 9344377.571 10719018.48 10010009.47 10017820.43 10067333.97 1.172036352 0.974344604 0.995104311 0.934988346 1.011706588 0.9281879 1.064732581 0.99430589 0.995081762 1 23.26317834 4.741505774 24.81303088 0.989653136 1.172036426 0.694329287 0.036485252 135.0064827 1137368.917 0.008354703 0.05877911 55144.95334 -4.741505774 0.18238329 AALAPAKES(ph)PRK ddPTM_MDA-MB-175_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 59.607 0.051047 50191000 78590 36258 57373 33726 74444 67618 68003 54140 70842 37846 TRUE FALSE 81692.79388 42485.02945 58868.18751 40396.90214 61790.03547 51914.74426 62672.74717 53414.34186 68292.41026 45261.19909 1.804918904 0.938663365 1.300632522 0.892528323 1.36518777 1.14700329 1.384690384 1.180135368 1.508851105 1 15.46598719 2.264751744 24.96140383 1.275979817 1.220173442 0 0.266979639 1636.340538 1559506.868 0.086068014 0.071988501 183.9720059 -2.264751744 -0.055806375 AALEAIDELDLFGAHGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AALEAIDELDLFGAHGGR 18 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 0 144.33 9.90E-08 11169000 10932 14655 15996 16212 14016 15473 12564 13511 14266 13457 FALSE TRUE 11363.6038 17171.88225 16412.8689 19418.68521 11633.56533 11879.63025 11579.20085 13329.90714 13752.56945 16093.6415 0.706092763 1.066997935 1.019835623 1.206606051 0.722867185 0.738156759 0.719489175 0.828271659 0.854534348 1 13.97420318 3.213980503 24.99999733 0.794455753 1.006102341 0.301854724 0.139649703 247.0484433 251267.9152 0.039427683 0.047144397 1636.743039 -3.213980503 0.211646588 AALEEVYPDLTPEETRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALEEVYPDLTPEETRR 17 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 211.57 3.77E-12 659530000 256430 302030 308470 324760 384580 357880 291200 291940 288720 418810 FALSE TRUE 266554.0544 353901.303 316508.9816 388996.5587 319209.229 274767.7937 268374.9831 288027.0218 278329.0236 500867.8009 0.532184449 0.706576271 0.6319212 0.776645171 0.637312337 0.548583465 0.535819996 0.575055975 0.555693584 1 18.93407034 -1.880406779 3.790463637 1.136525446 0.612271826 0.701835722 0.076043569 0.052063513 0.00164266 0.043692996 0.018407187 0.013170226 1.880406779 -0.52425362 AALGES(ph)GEQADGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AALGESGEQADGPK 14 0 E7EM83;Q92932-2;Q92932-4;Q92932;Q92932-3;A0A0A0MSD7 E7EM83 PTPRN2 Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase N2 1 AALGES(1)GEQADGPK 175.26 2.53E-06 411930000 476830 285350 340680 302120 472210 459900 442430 330560 346560 215640 TRUE FALSE 495655.6166 334356.6428 349558.4007 361878.4343 391943.9129 353095.1949 407751.1805 326129.3839 334087.3733 257890.5293 1.921961298 1.296506094 1.355452647 1.403224985 1.519807315 1.369166971 1.581101802 1.264603957 1.295461971 1 17.97639927 -3.419161449 0.107357058 3.51E-13 1.737337649 0.477573831 0.165218403 103.7937132 1.073948507 26.02545794 2.415708294 0.000380924 3.419161449 1.737337649 AALHS(ph)PVSEGAPVIPPSSGLPLPTPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALHSPVSEGAPVIPPSSGLPLPTPDAR 28 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 AALHS(0.958)PVS(0.042)EGAPVIPPSSGLPLPTPDAR;AALHS(0.858)PVS(0.142)EGAPVIPPSSGLPLPTPDAR 106.09 0.00058384 200702000 78584 98382 90668 107246 98469 127429 99581 113289 114135 125080 TRUE FALSE 81686.557 115278.3432 93030.88256 128458.9387 81731.27455 97835.54596 91775.58101 111770.5463 110027.3036 149587.0312 0.546080475 0.770643967 0.621918102 0.858757191 0.546379415 0.654037621 0.613526322 0.747194094 0.735540393 1 17.19062558 0.632263302 1.12296625 0.999465906 0.667541682 0.538064498 0.092637532 0.893473583 1.768357581 0.082221311 0.025539963 4.288084179 -0.632263302 -0.331924224 AALLELWELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALLELWELRR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 204.17 5.47E-08 1200030000 587590 814120 548060 637630 538790 745180 618070 625860 495560 758410 FALSE TRUE 610788.5069 953938.777 562342.8938 763751.3109 447206.6683 572123.2383 569624.0584 617471.3704 477724.8924 907005.9189 0.67341182 1.05174482 0.619999145 0.842057692 0.493058159 0.630782254 0.628026837 0.680779869 0.526705375 1 19.79075244 4.206061707 24.99729655 0.662470483 0.862578895 0.164106699 0.164075611 240.4068663 184914.5739 0.037075867 0.080102447 16071.69593 -4.206061707 0.200108412 AALLKAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AALLKASPK 9 1 P50914 P50914 RPL14 60S ribosomal protein L14 1 AALLKAS(1)PK 60.509 0.057688 2203800000 4412400 1431600 2319500 1235900 3624700 3854500 3032300 2430400 2826900 1512500 TRUE FALSE 4586604.959 1677466.164 2379948.075 1480357.331 3008574.789 2959350.791 2794620.403 2397824.463 2725160.421 1808845.416 2.535653361 0.927368446 1.315727731 0.818399028 1.663256993 1.636044055 1.544974699 1.325610492 1.506574523 1 20.78663769 -1.385822356 3.279560537 0.995765172 1.439253126 0.088104098 0.44523769 100773524.2 148542304 4125683.733 0.100369526 0.041131793 1.385822356 0.443487954 AALS(ph)SSELLELGDSLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.942)S(0.029)S(0.029)ELLELGDSLMR;AALS(0.985)S(0.014)S(0.001)ELLELGDSLMR;AALS(0.991)S(0.009)SELLELGDSLMR;AALS(0.997)S(0.003)SELLELGDSLMR;AALS(0.968)S(0.027)S(0.005)ELLELGDSLMR;AALS(0.984)S(0.016)SELLELGDSLMR;AALS(0.6)S(0.018)S(0.382)ELLELGDSLMR;AALS(0.944)S(0.046)S(0.009)ELLELGDSLMR 226.74 2.08E-15 421318000 290194.4 382179.1 379402.5 408883.9 469250.3 522371 442337.2 447641.2 437947.4 524480.5 TRUE FALSE 301651.499 447815.3875 389290.0408 489759.915 389487.3016 401058.2519 407665.6544 441641.3019 422185.7586 627242.4122 0.480916936 0.713943092 0.620637306 0.780814412 0.620951795 0.639399129 0.649933178 0.704099872 0.673082289 1 19.25866359 -5 0.259976528 3.205161228 0.631623994 0.684340413 0.071695104 106.9780095 1.051146583 125.917616 0.089064576 1.00E-05 5 -2.573537234 AALSEMVEYITHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALSEMVEYITHNR 14 0 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 ; 303.51 4.52E-44 269200000 359660 456780 434500 462710 491320 482240 454710 456430 428960 495800 FALSE TRUE 373859.6545 535228.4117 445823.4269 554232.6569 407805.6019 370247.0684 419068.642 450312.3024 413521.8134 592942.5173 0.630515849 0.902664923 0.751883048 0.934715661 0.687765829 0.624423207 0.706760992 0.759453555 0.697406243 1 19.17753272 -1.287469961 3.495633682 1.000809145 0.748527665 0.380069181 0.097945627 49937575.02 91248176.83 447834.3559 0.023402651 0.051585784 1.287469961 -0.25228148 AALSRDEILRYS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AALSRDEILRYSR 13 2 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 AALSRDEILRY(0.442)S(0.558)R 67.997 0.04066 2520500000 28480 1051900 657230 937850 421910 883740 379350 726810 435960 1165000 TRUE FALSE 29604.41239 1232555.642 674357.9537 1123353.931 350193.8889 678504.7782 349615.5558 717068.3008 420269.8848 1393259.445 0.021248313 0.884656226 0.484014629 0.806277636 0.251348656 0.486990977 0.250933562 0.514669614 0.3016451 1 20.4100325 -1.628188848 6.644355962 1.00182584 0.46060324 0.311123487 0.24688633 0.006153176 0.000344325 0.220276379 0.051784974 0.023540254 1.628188848 -0.5412226 AALSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALSSPR 7 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 AALS(0.146)S(0.854)PR;AALS(0.037)S(0.963)PR 82.529 0.038648 0 644000 723970 644140 644640 762330 837600 649320 712730 648120 821200 TRUE FALSE 669425.6173 848306.2158 660926.8176 772147.8679 632749.4189 643080.094 598424.6017 703177.0201 624794.2878 982098.4172 0.681627834 0.863769049 0.67297412 0.786222495 0.644283106 0.654802088 0.60933262 0.715994454 0.63618297 1 19.90550808 -1.038331472 4.3147148 1.000020751 0.697822281 0.610917724 0.072739159 0.420516798 41639845.29 1975.531639 0.016947707 0.091552146 1.038331472 -0.302198469 AALSS(ph)SELLELGDSLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.295)S(0.69)S(0.015)ELLELGDSLMR;AALS(0.031)S(0.965)S(0.004)ELLELGDSLMR 102.38 0.00099721 17445900 24235 25315 24751.4 26213 28201.5 34192 27665.8 25103.2 23696 26089.4 TRUE FALSE 25191.81651 29662.65433 25396.44182 31397.85316 23407.8191 26251.42618 25497.2823 24766.73266 22843.18559 31201.11842 0.807401074 0.950692021 0.813959342 1.006305375 0.750223719 0.841361705 0.817191293 0.79377708 0.73212714 1 14.92931012 3.212154538 24.99972289 0.811619759 0.892837663 0.133312564 0.087494545 364.9335838 345496.5912 0.023130024 0.027653111 1629.8759 -3.212154538 0.081217904 AALSSS(ph)ELLELGDSLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 AALS(0.124)S(0.268)S(0.608)ELLELGDSLMR 169.15 7.86E-09 60144000 90976 118840 146440 147730 170490 175260 163630 158990 142900 181800 TRUE FALSE 94567.80273 139249.8456 150256.3467 176950.5531 141510.1707 134558.5211 150804.253 156858.9991 137757.0569 217420.2292 0.43495402 0.640464073 0.691087243 0.813864256 0.650860185 0.618886851 0.693607276 0.721455403 0.633598159 1 17.73012665 -5 0.200933004 2.505406892 0.611296226 0.583229497 0.08892074 106.342987 1.053334634 64.45276752 0.214884013 1.00E-05 5 -1.894110665 AAMIWIVGEYAER ddPTM_MDA-MB-175_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 0 164.64 8.53E-05 149970000 131920 141850 164970 150860 164090 176260 172090 163710 155480 144830 FALSE TRUE 137128.3035 166211.6341 169269.2537 180699.6577 136198.0404 135326.2862 158601.1361 161515.7352 149884.3052 173206.6656 0.791703385 0.959614536 0.97726755 1.043260415 0.786332558 0.781299529 0.915675708 0.932503 0.865349522 1 17.40213493 -1.230178521 3.293295041 1.000282231 0.900321229 0.119592322 0.084451115 72608138.1 115722747.3 219600.1831 0.021082917 0.058860166 1.230178521 -0.099961001 AAMYDIIS(ph)SPSKDSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.529)S(0.406)PS(0.065)KDSTK 69.148 0.028476 275860000 231880 163640 183580 141810 227750 270680 210820 182320 197520 136480 TRUE FALSE 241034.8015 191743.8971 188364.2456 169859.5947 189037.1364 207818.6722 194295.3775 179876.2986 190411.2938 163220.6429 1.476742139 1.174752737 1.154046708 1.040674707 1.158169291 1.273237677 1.190384831 1.102043806 1.166588309 1 17.316464 4.746567646 3.561151768 1.142952758 1.518797976 0.66139948 0.072609035 0.181595701 4.062129536 0.017555135 0.184704652 55791.44967 -4.746567646 0.375845217 AAMYDIISS(ph)PSKDSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AAMYDIIS(0.019)S(0.964)PS(0.017)KDSTK 177.6 1.77E-09 428200000 695860 305190 467090 298820 677240 616990 632920 515370 525110 263190 TRUE FALSE 723333.0901 357604.0085 479262.7491 357925.7041 562122.9867 473703.4231 583310.0766 508462.3081 506211.3937 314757.0414 2.298068017 1.136127112 1.522643455 1.137149156 1.785894874 1.504981178 1.853207394 1.61541202 1.608260744 1 18.26387913 AANCNLHVPGPMAVNQFS(ph)PSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AANCNLHVPGPMAVNQFSPSLAR 23 0 Q99990;H0Y5G3 Q99990 VGLL1 Transcription cofactor vestigial-like protein 1 1 AANCNLHVPGPMAVNQFS(0.995)PS(0.005)LAR;AANCNLHVPGPMAVNQFS(0.82)PS(0.18)LAR;AANCNLHVPGPMAVNQFS(1)PSLAR;AANCNLHVPGPMAVNQFS(0.864)PS(0.136)LAR 210.79 3.86E-25 3004610000 1256550 1479620 1404120 1390590 1440860 1707230 1418490 1479660 1366480 1637690 TRUE FALSE 1306159.564 1733733.225 1440712.521 1665644.552 1195943.132 1310751.706 1307305.047 1459827.578 1317300.652 1958564 0.666896545 0.885206317 0.735596345 0.850441727 0.610622442 0.669241192 0.667481403 0.745356076 0.672584941 1 20.90136484 -1.08069679 3.927594549 1.000064658 0.725722258 0.505774639 0.082211441 12583598644 22856318075 10902829.47 0.019700759 0.083043034 1.08069679 -0.2743424 AAPAQVRPPS(ph)PGNIRPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAPAQVRPPSPGNIRPVK 18 2 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK;AAPAQVRPPS(1)PGNIRPVK 196.98 9.88E-16 10718900000 1591510 1193150 1335670 1325060 1438470 1695760 1845240 1380320 1462050 1116290 TRUE FALSE 1654344.044 1398064.231 1370478.657 1587152.913 1193959.383 1301945.439 1700605.267 1361819.068 1409431.106 1335005.653 1.239203774 1.04723469 1.026571427 1.188873552 0.894347811 0.9752359 1.273856229 1.02008487 1.055749167 1 20.34841442 4.740841796 23.95854447 1.058584883 1.239203891 0.229611489 0.10164346 179.8217032 1888384.174 0.023719154 0.158348554 55060.70863 -4.740841796 0.180619008 AAPAQVRPPS(ph)PGNIRPVKR ddPTM_MDA-MB-175_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 76.186 0.073689 11316000000 163680 123870 140340 125130 180210 174100 173570 142690 164350 155130 TRUE FALSE 170142.2128 145143.7089 143997.3757 149880.3405 149577.9686 133667.9135 159965.1299 140777.4739 158435.0756 185524.7534 0.917086317 0.782341474 0.776162604 0.807872469 0.806242649 0.720485601 0.862230656 0.758806959 0.853983486 1 17.50125216 0.928745107 6.135071821 0.999993297 0.800758863 0.567374673 0.05152349 0.4190879 35.18198969 0.045733579 0.011495144 8.486822265 -0.928745107 -0.199234433 AAPEAS(ph)SPPAS(ph)PLQHLLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.503)S(0.503)PPAS(0.995)PLQHLLPGK;AAPEAS(0.787)S(0.213)PPAS(1)PLQHLLPGK;AAPEAS(0.6)S(0.6)PPAS(0.799)PLQHLLPGK 145.13 7.84E-08 1477460000 686080 587732 710470 599546 879830 878260 809810 780640 838550 653250 TRUE FALSE 713166.9682 688670.3991 728985.4319 718134.4093 730276.8109 674297.4252 746334.9762 770176.7977 808370.7493 781241.8303 0.912863265 0.881507329 0.933111111 0.919221656 0.934764093 0.86310973 0.955318759 0.98583661 1.034725379 1 19.57540967 1.78626436 2.291051681 1.014015579 0.909431537 0.775569473 0.0238961 0.123841436 1.276247504 0.014507728 0.006548313 61.13140249 -1.78626436 -0.104584042 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.612)S(0.388)PPASPLQHLLPGK;AAPEAS(0.5)S(0.5)PPASPLQHLLPGK;AAPEAS(0.844)S(0.156)PPASPLQHLLPGK;AAPEAS(0.9)S(0.1)PPASPLQHLLPGK;AAPEAS(0.861)S(0.139)PPASPLQHLLPGK 234.51 1.04E-29 11015840000 983160 1181472 1339920 1209780 1595470 1693340 1533500 1414560 1434550 1235990 TRUE FALSE 1021975.916 1384380.625 1374839.416 1449070.873 1324272.579 1300087.448 1413300.263 1395600.137 1382920.826 1478158.576 0.691384492 0.936557584 0.93010279 0.980321663 0.895893445 0.879531783 0.956122223 0.944147779 0.935570005 1 20.49536962 4.738567379 10.65480122 0.936939735 0.690982097 0.830662225 0.03362678 0.025644523 133.8471598 0.007837244 0.045310227 54773.10725 -4.738567379 -0.245957639 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 AAPEAS(0.179)S(0.822)PPAS(0.999)PLQHLLPGK;AAPEAS(0.111)S(0.889)PPAS(1)PLQHLLPGK;AAPEAS(0.101)S(0.899)PPAS(1)PLQHLLPGK;AAPEAS(0.077)S(0.923)PPAS(1)PLQHLLPGK;AAPEAS(0.152)S(0.848)PPAS(1)PLQHLLPGK;AAPEAS(0.449)S(0.551)PPAS(1)PLQHLLPGK;AAPEAS(0.48)S(0.551)PPAS(0.969)PLQHLLPGK;AAPEAS(0.359)S(0.641)PPAS(1)PLQHLLPGK 236.64 7.48E-30 8259930000 3024789 2584695 3184760 2760166 3857186 4031693 3858443 3592205 3834450 3208983 TRUE FALSE 3144210.005 3028596.26 3267757.462 3306118.597 3201542.901 3095393.402 3556008.155 3544057.368 3696448.894 3837721.779 0.819290763 0.789165144 0.85148368 0.861479489 0.834230068 0.806570559 0.926593526 0.923479494 0.963188346 1 21.87181869 1.766814867 0.956674509 0.993649979 0.824529369 0.847580696 0.02645037 0.198141017 0.338389932 0.02361902 0.00989182 58.45408508 -1.766814867 -0.16912061 AAPEASS(ph)PPASPLQHLLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEAS(0.433)S(0.567)PPASPLQHLLPGK;AAPEAS(0.431)S(0.569)PPASPLQHLLPGK 226.16 2.97E-25 10722830000 517060 576430 731680 575810 861440 849010 756280 722310 772910 660160 TRUE FALSE 537473.9281 675427.3685 750748.1819 689703.4994 715012.7365 651840.2944 697000.7974 712628.6159 745093.1201 789505.7125 0.680772691 0.855506626 0.950909119 0.873588992 0.905646058 0.825630878 0.882831861 0.902626295 0.943746332 1 19.59059018 4.70544314 3.297779499 0.901529549 0.658370898 0.690327649 0.045859239 0.156180947 2.825061585 0.010610756 0.092017716 50750.82896 -4.70544314 -0.243158651 AAPEASSPPAS(ph)PLQHLLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AAPEASS(0.001)PPAS(0.999)PLQHLLPGK 162.72 1.33E-11 84688000 108140 100480 128680 143800 139860 171540 166140 124880 123130 122860 TRUE FALSE 112409.4507 117736.6584 132033.5065 172243.2108 116086.6472 131702.4347 153117.5127 123206.1879 118698.5754 146932.0647 0.765043702 0.801299965 0.898602404 1.172264278 0.79007021 0.896349173 1.042097332 0.838524852 0.807846644 1 17.16478974 4.233524264 4.222247429 0.929591248 0.777631951 0.228802726 0.10990606 0.29018277 11.91986849 0.027490829 0.072953554 17120.80827 -4.233524264 -0.151959298 AAPFSLEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAPFSLEYR 9 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 153.04 0.00018389 849180000 575640 842460 703860 666040 1264990 1091370 779250 717830 705150 1491730 FALSE TRUE 598366.7117 987145.9516 722203.1698 797780.7241 1049967.452 837915.8574 718170.3488 708208.663 679771.7892 1784005.933 0.335406234 0.553331092 0.404821058 0.447185017 0.588544821 0.469682215 0.402560516 0.39697663 0.381036731 1 20.76668898 -1.187326812 3.714964564 1.000518166 0.444402208 0.836446979 0.073994124 81443708.65 145765674 515455.9596 0.017808359 0.064964064 1.187326812 -0.556115958 AAPGAEFAPNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 140.39 9.56E-05 1409580000 1313520 1192110 1326200 1265280 1872370 1717920 1501060 1497550 1540130 1602090 FALSE TRUE 1365378.784 1396845.619 1360761.861 1515548.608 1554105.216 1318959.115 1383402.995 1477477.792 1484701.022 1915988.862 0.71262355 0.729046837 0.710213869 0.79100074 0.811124348 0.688396024 0.722030813 0.771130679 0.774900654 1 20.86965774 0.36255668 1.115313092 1.000511778 0.740504469 0.821036026 0.036033198 1.193976801 1.715051925 0.036736968 0.0110966 2.304393706 -0.36255668 -0.260007309 AT(ph)SMRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSMRK 6 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 AT(0.773)S(0.227)MRK;AT(0.843)S(0.157)MRK 58.194 0.08305 247215000 115085 165414 158847 136460 189516 179174 161073 169526 169119 263128 TRUE FALSE 119628.6447 193822.5678 162986.6833 163451.3807 157302.138 137563.5539 148447.6774 167253.7813 163032.4402 314682.8937 0.380156173 0.615929787 0.517939445 0.519416161 0.499875084 0.437149768 0.47173736 0.531499438 0.518084851 1 18.26353923 -0.005983436 1.21025069 1.001917493 0.499220653 0.869345568 0.058326915 3.856947674 4.252245332 0.079271705 0.016057537 0.986317104 0.005983436 -0.50269684 AAPLDSIHSLAAYYIDCIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 361.65 3.73E-91 23356930000 2477470 4482350 4140489 5118616 4664235 5575872 4487308 4268009 4193428 4723497 FALSE TRUE 2575282.429 5252158.745 4248393.545 6131062.967 3871410.001 4280960.231 4135581.074 4210803.32 4042507.345 5648975.8 0.45588484 0.929754159 0.752064391 1.085340632 0.685329542 0.757829451 0.732093962 0.745410048 0.715617749 1 22.42955789 -2.167691048 2.376550181 1.573764567 0.770832181 0.175270895 0.153750175 11960887.98 3243420.939 36859745.44 0.03726375 0.00679687 2.167691048 -0.802932386 AAPPPPPPPPPLES(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.599)S(0.401)PR 146.69 4.49E-07 192700000 33505 40740 49804 36077 50242 57315 55553 43022 39380 32002 TRUE FALSE 34827.80327 47736.77809 51101.93315 43212.92292 41701.88279 44004.45987 51198.6107 42445.36046 37962.72149 38272.17918 0.910003141 1.247297099 1.335224025 1.129094915 1.089613491 1.1497767 1.337750078 1.109039552 0.991914291 1 15.22400843 1.376767329 4.412130361 0.998819569 1.177936735 0.254645741 0.117700761 0.28500217 8.502112272 0.085531559 0.02964207 23.81043499 -1.376767329 0.179117166 AAPPPPPPPPPLESS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 AAPPPPPPPPPLES(0.219)S(0.781)PR 111.91 0.00051043 222930000 38563 39501 55494 51627 84764 60641 61930 67443 42353 45170 TRUE FALSE 40085.49702 46284.98947 56940.21923 61838.66651 70355.84556 46558.04677 57075.76478 66539.0369 40828.7238 54020.19667 0.742046484 0.856808978 1.054054275 1.144732347 1.302398916 0.861863704 1.056563439 1.2317437 0.755804797 1 15.72121127 4.349759184 2.871269121 1.074852683 0.756422964 0.304803562 0.153283045 0.288616246 4.543405683 0.038106553 0.141893336 22374.80113 -4.349759184 -0.31842972 AAPQS(ph)PSVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AAPQSPSVPK 10 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 1 AAPQS(0.999)PS(0.001)VPK;AAPQS(0.827)PS(0.173)VPK;AAPQS(1)PSVPK;AAPQS(0.996)PS(0.004)VPK;AAPQS(0.996)PS(0.004)VPK;AAPQS(0.98)PS(0.02)VPK;AAPQS(0.884)PS(0.116)VPK;AAPQS(0.882)PS(0.118)VPK 239.48 3.21E-12 5881703000 5562166 3873452 4791834 3932023 5519882 6029205 5829060 4772469 4851812 3277588 TRUE FALSE 5781764.609 4538687.25 4916713.131 4709765.413 4581614.429 4629013.512 5372163.046 4708501.859 4677196.234 3919768.615 1.475027017 1.157896727 1.254337593 1.201541692 1.168848184 1.180940501 1.370530654 1.201219337 1.193232737 1 21.90233706 -4.564805032 0.225630009 3.26E-16 1.270154664 0.402151824 0.093645778 132.6384293 1.589685027 60.47725269 0.164164482 2.72E-05 4.564805032 1.270154664 AAPTT(ph)PPPPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAPTTPPPPVK 11 0 Q9NZQ3-5;Q9NZQ3-4;Q9NZQ3-3;Q9NZQ3-2;Q9NZQ3;C9JC20;C9JMQ4;C9JSC3 Q9NZQ3-5 NCKIPSD NCK-interacting protein with SH3 domain 1 AAPT(0.015)T(0.985)PPPPVK 103.91 0.029857 131490000 449140 376940 390950 359790 495060 477200 454210 414560 396850 327980 TRUE FALSE 466872.394 441676.5128 401138.4782 430955.3881 410909.878 366377.532 418607.8333 409003.5013 382567.446 392241.4014 1.190268014 1.126032365 1.022682656 1.098699389 1.047594355 0.934061348 1.067219911 1.042734142 0.97533673 1 18.5813823 7.999999995 0.498093357 1.013264987 6.819310851 0.635105676 0.042902742 69.73971646 0.744274159 0.022794462 423.2384159 99999998.93 -7.999999995 5.806045864 AAQDRDQIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAQDRDQIYR 10 1 P62995;P62995-3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;;;; 218.11 6.33E-09 14110560000 4505940 5323090 4869690 4809880 5564710 5803030 4652750 4927510 4787360 5709720 FALSE TRUE 4683837.991 6237289.3 4996598.122 5761259.908 4618822.582 4455364.228 4288055.297 4861464.788 4615063.849 6828430.315 0.685931872 0.913429443 0.731734512 0.843716585 0.676410591 0.65247268 0.627970866 0.711944702 0.675860137 1 22.70312255 4.033696707 24.96432752 0.721117041 0.805406076 0.02074446 0.116734198 447.4499377 331489.2915 0.027305558 0.058986326 10806.78987 -4.033696707 0.084289035 AAQEEYVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 AAQEEYVKR 9 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;;;;;; 178.95 8.08E-05 60144367000 19012120 16584490 19096950 14428800 22659110 20637810 19737700 18175880 19107800 17738710 FALSE TRUE 19762733.18 19432747.15 19594632.21 17282773.57 18807522.58 15844991.4 18190607.5 17932262.06 18420114.01 21214270.6 0.931577312 0.916022404 0.923653355 0.814676776 0.886550518 0.746902484 0.857470325 0.845292417 0.868288821 1 24.33853174 3.757248033 23.55119248 0.849632061 0.92297819 0.17740807 0.060249364 532.683586 671320.8002 0.014280477 0.025672277 5718.051115 -3.757248033 0.073346128 AAQGQAGS(ph)PDKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAQGQAGSPDKSK 13 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 AAQGQAGS(0.998)PDKS(0.002)K;AAQGQAGS(1)PDKSK 145.04 2.52E-05 413480000 826300 280996 395000 254093 595580 607410 567360 426930 488030 248961 TRUE FALSE 858922.962 329254.8772 405294.0245 304351.837 494343.5243 466348.2329 522888.8407 421207.7017 470465.8956 297740.1413 2.884807397 1.105846446 1.36123407 1.022206262 1.6603187 1.566292777 1.756191954 1.414682279 1.580122497 1 18.18369421 4.746043788 24.9955952 1.417109714 2.884808094 0.755253532 0.255518758 443.8546601 1482546.129 0.060652862 0.635885317 55724.19304 -4.746043788 1.467698381 AAQLQHSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAQLQHSEK 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 121.73 0.0036779 0 22146 20718 19407 19139 33375 30204 27366 19996 23915 25544 FALSE TRUE 23020.34118 24276.15534 19912.76236 22924.63708 27701.92942 23189.57875 25220.98141 19727.98633 23054.30382 30548.85773 0.753558165 0.794666549 0.651833287 0.750425344 0.906807373 0.759098064 0.825594909 0.645784746 0.754669914 1 14.89883082 -2.309626766 2.235514186 2.197459159 0.756749994 0.497763043 0.072163243 4886636.305 610364.6335 29622041.8 0.017921633 0.004901999 2.309626766 -1.440709166 AAQMHSGYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAQMHSGYQR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;;;; 133.81 0.00018736 1408842000 449907 603279 564992 499568 741369 719132 607945 542889 523788 848398 FALSE TRUE 467669.6758 706887.4754 579716.1557 598381.0593 615351.3622 552124.4916 560292.6823 535612.4609 504936.9722 1014625.345 0.460928439 0.696698027 0.571359821 0.589755679 0.606481363 0.544165878 0.552216328 0.527891861 0.497658545 1 19.95251567 -1.516068563 3.016050734 1.015118545 0.563832853 0.824319574 0.060813277 20995049.95 23646234.45 2605853.298 0.014321418 0.030474139 1.516068563 -0.451285692 AAQQQQPSAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAQQQQPSASPR 12 0 Q86U86-8;Q86U86 Q86U86-8 PBRM1 Protein polybromo-1 1 AAQQQQPSAS(1)PR;AAQQQQPSAS(1)PR;AAQQQQPSAS(1)PR;AAQQQQPS(0.154)AS(0.846)PR 243.26 2.58E-16 1152820000 763479.1 830892 729994 744234.3 694434 871469 661627.2 714565.9 696771 850278 TRUE FALSE 793621.8444 973591.2376 749018.2433 891441.6232 576394.3567 669083.532 609767.1312 704988.3129 671694.3478 1016873.695 0.780452724 0.957435759 0.736589261 0.876649311 0.566829843 0.657980962 0.59964884 0.69328995 0.660548455 1 19.95570906 3.254153462 24.98833968 0.673889683 0.839100473 0.226485238 0.123891165 283.6951945 454633.4889 0.031387326 0.042350958 1795.367923 -3.254153462 0.16521079 AAREPNIDR ddPTM_MDA-MB-175_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 68.525 0.060638 0 49988 89300 81797 86701 93109 103950 70290 88107 82316 124870 FALSE TRUE 51961.56484 104636.5803 83928.69702 103850.199 77282.36544 79809.18788 64780.48613 86926.06978 79353.46324 149335.8857 0.34795096 0.70067941 0.562012919 0.695413554 0.517506995 0.534427392 0.433790484 0.582084268 0.531375716 1 17.18820136 -1.374426855 3.196255145 1.004477016 0.550879493 0.647888026 0.100539753 19389081.71 26349586.44 812048.68 0.022750146 0.042225339 1.374426855 -0.453597523 AAS(ph)ADYLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AASADYLRPR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 AAS(1)ADYLRPR;AAS(1)ADYLRPR;AAS(1)ADYLRPR;AAS(1)ADYLRPR 142.07 2.20E-05 1504670000 1393030 1719680 1697650 1624320 2029630 2173850 1794140 1733400 1757370 1996500 TRUE FALSE 1448027.9 2015021.663 1741892.154 1945605.648 1684634.218 1669006.283 1653510.619 1710166.608 1694122.597 2387675.95 0.606459139 0.843925937 0.729534573 0.814853309 0.705553958 0.699008709 0.692518857 0.716247365 0.709527856 1 21.18717562 -1.456964709 6.643062814 1.000067392 0.727087841 0.638128082 0.062276976 5.84E-05 4.77E-06 0.056624444 0.013343229 0.034916869 1.456964709 -0.27297955 AAS(ph)ALLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AASALLLR 8 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR;AAS(1)ALLLR 125.97 0.0012999 615905000 833539 876816 856082 862676 927127 1023442 963606 905918 890655 796009 TRUE FALSE 866447.7634 1027402.327 878392.2002 1033310.738 769534.2837 785763.1059 888076.0438 893775.651 858600.5005 951971.723 0.910161239 1.079236182 0.922708289 1.08544268 0.808358342 0.825405931 0.932880696 0.938867856 0.901918071 1 19.8605592 3.240492647 24.99993796 0.899735883 0.999613531 0.298946369 0.073610406 63.51659762 821875.6122 0.020196944 0.026013021 1739.773241 -3.240492647 0.099877648 AAS(ph)DDGSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASDDGSLK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5;A0A1B0GV45 Q92614;A0A1B0GV45 MYO18A Unconventional myosin-XVIIIa 1 AAS(0.999)DDGS(0.001)LK 157.97 0.0011909 0 818390 491990 560700 474480 814790 914670 824540 567080 710160 382270 TRUE FALSE 850700.6691 576485.4553 575312.3026 568330.7278 676292.2868 702251.7545 759910.4003 559479.2202 684601.4803 457168.4875 1.860803385 1.260991234 1.258425107 1.243153768 1.479306438 1.53608959 1.662210806 1.22379218 1.49748178 1 18.80236644 -0.595122952 0.83306563 0.970942079 1.431181786 0.308812116 0.198553696 32.30997503 13.94674202 3.120808043 0.063965542 0.254025344 0.595122952 0.460239707 AAS(ph)DPLLSSVS(ph)PAVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 2 AAS(1)DPLLS(0.008)S(0.004)VS(0.988)PAVSK 143.99 1.80E-05 0 127090 103450 117130 96157 137390 152170 155120 116150 130780 93431 TRUE FALSE 132107.6113 121216.7328 120182.504 115176.5676 114036.4969 116830.8237 142961.2891 114593.1992 126073.2533 111737.0156 1.182308393 1.084839541 1.075583623 1.030782565 1.020579405 1.045587472 1.279444312 1.02556166 1.128303389 1 16.76974767 AAS(ph)EDMTS(ph)DEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASEDMTSDEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 2 AAS(1)EDMT(0.159)S(0.841)DEER;AAS(1)EDMT(0.024)S(0.976)DEER 233.21 1.21E-15 335190000 683100 746820 726940 684470 898700 976400 813010 787340 785100 697700 TRUE FALSE 710069.3155 875080.5255 745884.6536 819856.1231 745939.295 749645.8975 749284.1518 776786.9951 756844.4044 834400.9567 0.850992931 1.048753023 0.893916345 0.982568532 0.893981831 0.898424063 0.897990523 0.930951707 0.907051218 1 19.67038129 3.224291264 24.99255555 0.916272148 0.947954429 0.030572235 0.056692718 646.0771285 1131591.849 0.014937036 0.017928064 1676.06657 -3.224291264 0.031682281 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;AAS(1)LNYLNQPSAAPLQVSR 400.22 5.56E-128 4238950000 1281890 1357590 1355180 1276230 1453490 1563280 1286720 1372170 1369910 1306150 TRUE FALSE 1332500.007 1590745.522 1390497.104 1528664.485 1206426.289 1200231.912 1185863.524 1353778.306 1320607.207 1562065.085 0.853037444 1.01836059 0.890165921 0.978617664 0.772327799 0.768362294 0.759163966 0.866659347 0.845423932 1 20.57502314 3.241601741 24.99884634 0.823162209 0.937790817 0.27353016 0.078071596 88.52970926 727731.1579 0.02080174 0.027002484 1744.221925 -3.241601741 0.114628608 AAS(ph)LRGGVGAPGSPSTPPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AASLRGGVGAPGSPSTPPTR 20 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 AAS(1)LRGGVGAPGSPSTPPTR;AAS(1)LRGGVGAPGSPSTPPTR;AAS(1)LRGGVGAPGSPSTPPTR 144.18 9.65E-08 1141503000 295726 213014 240861 172941 385975 369884 236843 227485 248903 339837 TRUE FALSE 307401.4908 249597.4975 247138.0355 207148.2136 320367.1074 283984.0466 218278.6268 224435.9357 239945.0297 406421.5536 0.756361192 0.6141345 0.608082995 0.509688061 0.788263084 0.698742584 0.537074436 0.552224491 0.590384608 1 18.63261739 -1.631034457 3.024348337 1.028991306 0.621387554 0.614846146 0.088095934 70017006.56 74835901.13 15979069.28 0.021899718 0.023386517 1.631034457 -0.407603751 AAS(ph)LTEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASLTEDR 8 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(0.865)LT(0.135)EDR;AAS(0.834)LT(0.166)EDR 115.82 0.0025063 131447000 359400 313300 292950 300720 263440 299030 306730 240470 256810 196702 TRUE FALSE 373589.3895 367106.8379 300584.5177 360201.5184 218660.5629 229584.8143 282687.7011 237246.893 247567.4583 235241.9908 1.588106733 1.560549784 1.277767275 1.531195673 0.929513316 0.975951672 1.201688951 1.008522722 1.052394844 1 17.84378608 3.242914741 24.99999967 1.036545731 1.479369745 0.82725234 0.103206343 45.38869969 260605.554 0.029498988 0.038598655 1749.503198 -3.242914741 0.442824014 AAS(ph)LTEDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AASLTEDRDR 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 AAS(1)LTEDRDR;AAS(1)LTEDRDR;AAS(1)LTEDRDR;AAS(1)LTEDRDR 211.26 3.76E-08 3592550000 3016510 2745170 2814920 2173040 2343140 2515870 2228070 2007400 2017540 1937140 TRUE FALSE 3135604.144 3216631.593 2888279.128 2602860.826 1944853.9 1931597.321 2053428.051 1980494.086 1944929.13 2316685.494 1.353487192 1.388462785 1.24672906 1.123527916 0.839498458 0.83377624 0.886364617 0.854882586 0.839530931 1 21.14363077 3.562009749 1.807693413 0.864003268 1.360848 0.928985042 0.056636321 0.075052199 0.484785478 0.016020883 0.029508704 3647.621349 -3.562009749 0.496844732 AAS(ph)PAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AASPAGPR 8 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 AAS(1)PAGPR;AAS(1)PAGPR;AAS(1)PAGPR 123.6 0.0014065 753837000 803690 891190 846980 840750 932850 982120 807170 887140 774870 846610 TRUE FALSE 835420.3018 1044244.95 869052.9946 1007047.841 774284.4902 754037.5142 743901.9063 875249.3394 746982.5801 1012487.02 0.825117049 1.031366259 0.858334949 0.994627902 0.764735226 0.744737956 0.734727351 0.864454874 0.737770031 1 19.94947198 3.230005305 24.98059918 0.797601921 0.929859981 0.278233218 0.093502691 204.7306086 597790.8164 0.02490685 0.030219657 1698.264397 -3.230005305 0.13225806 AAS(ph)PFR ddPTM_MDA-MB-175_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 106.38 0.033745 9245010000 2245130 2406600 2286050 2409860 2848750 2939070 2480740 2446550 2277820 2622680 TRUE FALSE 2333769.466 2819914.829 2345626.341 2886523.115 2364520.493 2256515.535 2286293.117 2413757.999 2195841.703 3136543.932 0.744057637 0.899051596 0.747837873 0.9202878 0.753861748 0.719427365 0.72892112 0.769559761 0.700083197 1 21.58074434 AAS(ph)PPASASDLIEQQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(0.994)PPAS(0.006)ASDLIEQQQK;AAS(1)PPASASDLIEQQQK;AAS(1)PPASASDLIEQQQK 390.45 6.96E-122 2976147000 1928601 1452510 1881460 1512040 2146571 2340910 2032200 1862660 2007016 1393410 TRUE FALSE 2004743.657 1701967.294 1930492.393 1811116.999 1781697.628 1797269.129 1872910.854 1837694.089 1934783.886 1666422.011 1.20302279 1.021330301 1.158465491 1.086829739 1.069175525 1.078519797 1.123911495 1.102778334 1.161040765 1 20.66832237 AAS(ph)PPASASDLIEQQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASPPASASDLIEQQQKR 18 1 Q5VSL9;Q5VSL9-2;Q5VSL9-3 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 AAS(1)PPASASDLIEQQQKR 135.98 4.44E-06 200900000 161790 172270 172970 101630 247100 199650 120280 131560 196120 222990 TRUE FALSE 168177.5941 201856.0324 177477.7403 121732.1107 205098.0303 153284.3132 110852.1393 129796.6534 189061.6795 266680.6211 0.630632978 0.756920513 0.665506701 0.456471528 0.769077368 0.574786097 0.415673771 0.486711981 0.7089442 1 18.02475347 -1.738313297 7.626944527 1.004078258 0.596034117 0.497718468 0.11790292 0.008644826 0.000296611 0.120702197 0.028310004 0.018267819 1.738313297 -0.408044141 AAS(ph)PPRPLLSNASATPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AASPPRPLLSNASATPVGR 19 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AAS(1)PPRPLLSNASATPVGR;AAS(0.999)PPRPLLS(0.001)NASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR;AAS(1)PPRPLLSNASATPVGR 185.71 3.70E-15 4451290000 796064 831487 814064 724587 936759 998352 890436 804968 832469 778882 TRUE FALSE 827493.2214 974288.4242 835279.1766 867908.1459 777529.0398 766499.8782 820641.2996 794178.7206 802508.6033 931489.0153 0.888355319 1.045947304 0.896713931 0.93174276 0.834716274 0.822875918 0.880999439 0.852590538 0.861533083 1 19.82917923 3.668671873 1.944374305 0.866739579 0.961505964 0.188008832 0.061598416 0.40620854 2.992329417 0.01654477 0.032662578 4663.069335 -3.668671873 0.094766385 AAS(ph)PQDLAGGYTSSLACHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASPQDLAGGYTSSLACHR 19 0 H0YJ92;P51948-2;P51948 H0YJ92 MNAT1 CDK-activating kinase assembly factor MAT1 1 AAS(1)PQDLAGGYTSSLACHR;AAS(1)PQDLAGGYTSSLACHR 184.59 1.58E-14 491000000 101761 166464 149218 138803 135076 182934 131784 156557 136892 168134 TRUE FALSE 105778.6029 195052.8971 153106.7437 166257.8191 112115.8298 140450.3509 121454.4257 154458.6095 131965.2837 201076.6382 0.526061127 0.970042561 0.76143477 0.826838068 0.557577602 0.698491641 0.604020571 0.768157907 0.656293465 1 17.61738595 -1.482118724 9.226794867 1.000004742 0.715210094 0.324456547 0.126126802 1.17E-05 6.57E-07 0.116123749 0.027370174 0.032951962 1.482118724 -0.284794648 AAS(ph)PS(ph)PQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 137.95 0.00011359 2027600000 2826270 2670990 2745920 2605500 3023260 3537970 3004000 2930110 2879410 2680260 TRUE FALSE 2937853.322 3129711.755 2817480.931 3120860.123 2509367.345 2716330.086 2768538.631 2890836.668 2775780.597 3205405.63 0.916530905 0.976385555 0.878977969 0.973624085 0.78285485 0.847421637 0.863709293 0.901862978 0.865968591 1 21.6120755 3.276830881 24.99996352 0.871958564 0.93513705 0.203122716 0.057111398 240.8652157 157343.079 0.014985204 0.02028968 1891.606862 -3.276830881 0.063178486 AAS(ph)PSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASPSPAR 8 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AAS(0.947)PS(0.053)PAR;AAS(0.996)PS(0.004)PAR 121.85 0.001485 1276750000 1094890 1310740 1244320 1146260 1277490 1359090 1161320 1237360 1100840 1209300 TRUE FALSE 1138117.103 1535849.399 1276748.001 1372986.807 1060342.706 1043461.945 1070292.704 1220775.213 1061220.983 1446239.182 0.786949432 1.061960856 0.882805568 0.949349751 0.733172438 0.721500259 0.740052349 0.844103264 0.733779721 1 20.46387474 3.245878795 24.99903122 0.784530045 0.927711684 0.264372825 0.10072841 190.7282558 651527.2231 0.026145122 0.03469945 1761.484374 -3.245878795 0.143181639 AAS(ph)PSPQS(ph)VRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASPSPQSVRR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 AAS(0.957)PS(0.395)PQS(0.649)VRR 72.374 0.031059 162520000 155140 207380 204400 179440 212070 253760 173880 227690 216230 250480 TRUE FALSE 161265.047 242995.9018 209726.8319 214932.6964 176022.4171 194828.0858 160250.8312 224638.188 208447.9245 299556.7603 0.538345544 0.811184837 0.700123849 0.717502407 0.587609564 0.650387878 0.534959822 0.749901914 0.695854516 1 18.19246987 0.484973397 1.273595629 0.999797733 0.661721745 0.593215831 0.084039013 1.500611313 3.00901962 0.078156829 0.023365361 3.054733985 -0.484973397 -0.338075988 AAS(ph)PSPQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 AAS(0.997)PS(0.003)PQSVR;AAS(0.996)PS(0.004)PQSVR;AAS(0.973)PS(0.027)PQSVR;AAS(0.981)PS(0.019)PQSVR;AAS(0.893)PS(0.107)PQSVR 175.74 2.84E-06 5869885000 2575699 2713150 2519050 2525140 2739140 3219240 2853550 2638760 2431610 2623140 TRUE FALSE 2677389.585 3179112.407 2584698.512 3024605.155 2273541.961 2471620.298 2629881.295 2603391.738 2344096.831 3137094.06 0.853461686 1.013394035 0.823914892 0.964142323 0.724728656 0.787869363 0.838317642 0.829873663 0.747219174 1 21.58099736 3.252932453 24.98895302 0.81382069 0.914431976 0.216891676 0.085289224 318.8934402 554470.9021 0.021814582 0.029402961 1790.32738 -3.252932453 0.100611286 AAS(ph)PVLLSSNSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASPVLLSSNSQK 13 0 G3V1Z7;P41970 G3V1Z7 ELK3 ETS domain-containing protein Elk-3 1 AAS(1)PVLLSSNSQK 151.54 1.36E-06 0 98789 80798 79824 70411 123240 103820 100900 87031 96717 78515 TRUE FALSE 102689.266 94674.42798 81904.27902 84338.08564 102291.7088 79709.37841 92991.19435 85864.4918 93236.17406 93898.51099 1.093619749 1.008263358 0.872263875 0.898183419 1.089385846 0.848888631 0.990337263 0.914439333 0.992946247 1 16.51881466 4.539860103 4.145791802 0.947066538 1.084649802 0.293852315 0.067903863 0.253991183 8.287996201 0.015435821 0.070227433 34662.51758 -4.539860103 0.137583264 AAS(ph)SDQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASSDQLR 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 AAS(0.698)S(0.302)DQLR 132.22 0.0010191 507000000 487430 500880 464530 510360 482380 548880 595470 479270 440990 356910 TRUE FALSE 506674.1128 586902.2437 476636.0334 611307.6847 400385.2199 421410.9384 548795.5054 472846.1696 425118.856 426839.681 1.187036106 1.37499457 1.116662894 1.432171637 0.938022489 0.987281542 1.285718104 1.107784001 0.995968451 1 18.70333478 3.732701294 0.270917165 1.004244224 1.406947602 0.251642826 0.142149862 7.622751064 0.726530331 0.201739738 0.996934 5403.825222 -3.732701294 0.402703377 AAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 AAS(0.917)S(0.093)DQLRDNS(0.989)PPPAFKPEPPK;AAS(0.804)S(0.196)DQLRDNS(1)PPPAFKPEPPK;AAS(0.882)S(0.119)DQLRDNS(0.998)PPPAFKPEPPK;AAS(0.95)S(0.05)DQLRDNS(1)PPPAFKPEPPK;AAS(0.948)S(0.052)DQLRDNS(1)PPPAFKPEPPK;AAS(0.78)S(0.22)DQLRDNS(1)PPPAFKPEPPK 139.19 1.70E-06 3022360000 2889250 1306160 2006980 1202070 2851090 2448230 2506120 1824710 2348790 1005586 TRUE FALSE 3003319.821 1530482.819 2059283.548 1439835.858 2366462.74 1879665.686 2309683.766 1800252.747 2264257.507 1202611.324 2.497332066 1.272632969 1.712343387 1.197257859 1.967770213 1.562986851 1.920557141 1.496953098 1.882784123 1 20.19773902 -1.837178977 2.680380889 0.747122567 1.690779525 0.26349371 0.35912243 34998856.62 23149716.28 56810019.24 0.078547929 0.014548594 1.837178977 0.943656958 AASAPAKES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 142.45 2.28E-05 10629480000 22937600 16813400 20505400 16192000 24519700 25148400 23421600 20308100 21343300 16643600 TRUE FALSE 23843194.16 19700970.66 21039787.57 19394729.27 20351850.15 19308065.23 21585753.79 20035903.14 20575158.8 19904594.76 1.19787388 0.989769995 1.057031697 0.974384533 1.022469957 0.970030561 1.084460852 1.006596888 1.033688907 1 24.24659816 4.743872144 24.94535866 1.017129423 1.197873959 0.720324741 0.034098051 273.8526217 1286095.233 0.00748654 0.064602748 55446.24555 -4.743872144 0.180744536 AASAPAKES(ph)PRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 128.64 0.00012961 380920000 752470 337840 495570 337780 678180 606240 683680 516680 606200 299420 TRUE FALSE 782178.0966 395861.392 508484.9613 404591.8758 562903.2058 465449.9477 630091.3751 509754.7497 584382.9804 358085.6163 2.184332632 1.105493698 1.420009456 1.129874693 1.571979382 1.299828663 1.75961096 1.423555503 1.631964407 1 18.44994504 4.752633976 24.54064042 1.401380819 2.184333322 0.518830456 0.233264761 1530.08329 2668047.137 0.052557995 1.088945929 56576.22623 -4.752633976 0.782952503 AASDIAMTELPPTHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AASDIAMTELPPTHPIR 17 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;; 157.8 1.21E-08 867780000 638870 721390 743920 798890 751940 848760 790030 792700 668090 654800 FALSE TRUE 664093.0809 845283.1209 763307.1663 956908.0576 624125.5074 651648.3531 728105.3842 782075.1531 644045.5714 783095.5231 0.848035854 1.079412531 0.974730596 1.221955725 0.796997926 0.832144143 0.929778504 0.998697004 0.822435517 1 19.57882877 3.210338741 24.99983043 0.90289613 1.030468049 0.268371102 0.108385993 300.8985657 266544.744 0.031070628 0.037143231 1623.075571 -3.210338741 0.127571919 AASDPLLS(ph)SVSPAVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.419)S(0.232)VS(0.35)PAVSK;AASDPLLS(0.383)S(0.235)VS(0.383)PAVSK 235.69 1.09E-19 592130000 954100 785310 884070 755600 1102560 1105140 1060630 915410 1025870 786930 TRUE FALSE 991768.6047 920180.8836 907109.5905 905055.4248 915147.245 848487.9836 977495.0492 903140.4263 988949.1391 941113.8668 1.053824239 0.977757226 0.963868053 0.961685357 0.972408629 0.901578452 1.038657578 0.959650536 1.050828358 1 19.84400976 AASDPLLSSVS(ph)PAVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 AASDPLLS(0.091)S(0.047)VS(0.861)PAVSK;AASDPLLS(0.068)S(0.009)VS(0.923)PAVSK 302.4 5.28E-46 1112840000 739480 592080 676560 575130 844050 853640 792040 696500 734990 590450 TRUE FALSE 768675.2414 693765.1343 694191.7094 688888.9974 700578.6825 655395.047 729957.8352 687164.5567 708537.8535 706137.3727 1.088563318 0.982478992 0.983083089 0.975573626 0.992128033 0.928141 1.033733468 0.973131551 1.003399453 1 19.42958935 4.73929296 24.52981718 0.984628306 1.08856336 0.595035081 0.025432644 29.88936826 1000902.031 0.005587951 0.033534734 54864.69388 -4.73929296 0.103935055 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK 266.41 2.82E-60 336601000 148526 111349 136026 116350 167530 162144 142431 140167 155011 126695 TRUE FALSE 154389.9212 130472.3246 139570.9493 139363.6827 139053.3104 124488.5133 131266.886 138288.2906 149432.1844 151518.4595 1.018951233 0.861098542 0.921148154 0.919780225 0.917731812 0.82160625 0.866342533 0.912682792 0.986230885 1 17.20913404 1.23698583 3.988859394 0.998424761 0.899998196 0.341135866 0.049108033 0.221339494 7.024108169 0.041758139 0.012062599 17.25781581 -1.23698583 -0.098426565 AASIFGGAKPVDTAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASIFGGAKPVDTAAR 16 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 139.08 2.83E-06 1515170000 1354700 1361230 1335900 1217360 1649620 1548190 1393920 1485800 1448840 1260050 FALSE TRUE 1408184.602 1595010.664 1370714.651 1458150.175 1369218.182 1188646.336 1284660.908 1465885.281 1396696.531 1506932.672 0.934470815 1.058448524 0.909605768 0.967627951 0.908612712 0.788785297 0.852500534 0.972760965 0.926847335 1 20.52318353 4.207523166 24.60644549 0.911863321 0.996459673 0.199625955 0.06417465 221.7670192 175816.6006 0.016516703 0.035686447 16125.87045 -4.207523166 0.084596352 AASLT(ph)EDRDR ddPTM_MDA-MB-175_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 1 AAS(0.02)LT(0.98)EDRDR 164.48 3.91E-05 220270000 711330 671470 647710 511330 558390 580280 490330 429220 480740 428900 TRUE FALSE 739413.8577 786789.7492 664589.8547 612469.5478 463475.0673 445518.7642 451896.6534 423467.008 463438.2613 512934.7432 1.441535921 1.533898336 1.295661609 1.194049645 0.90357511 0.868568117 0.881002231 0.825576769 0.903503355 1 18.96841577 3.574760666 1.413492012 0.87221281 1.487049682 0.936815502 0.062272483 0.083775359 0.331802298 0.018680936 0.038952797 3756.303424 -3.574760666 0.614836872 AASLTEDRDR ddPTM_MDA-MB-175_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 0 ;; 208.63 1.01E-07 3141400000 1450760 1806910 1745290 1727920 1984990 2185680 1807400 1741560 1603560 2006050 FALSE TRUE 1508037.125 2117232.737 1790773.691 2069697.419 1647582.109 1678088.944 1665731.265 1718217.237 1545848.189 2399097.089 0.628585284 0.882512319 0.746436524 0.862698483 0.68675091 0.699466875 0.694315904 0.71619329 0.644345823 1 21.19406011 -1.007657949 4.891710291 1.000002099 0.733159401 0.510670174 0.079480908 3.15E-06 6.38E-07 0.074883681 0.017650006 0.098252147 1.007657949 -0.266842699 AASPY(ph)SQRPAS(ph)PTAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 2 AAS(0.149)PY(0.778)S(0.255)QRPAS(0.815)PT(0.004)AIR 136.36 0.00035689 0 73275 90225 69782 72132 78312 98136 81604 79044 65979 81235 TRUE FALSE 76167.95358 105720.4419 71600.57625 86399.49431 65000.55421 75345.40127 75207.66525 77984.54447 63604.42868 97151.44291 0.784012582 1.088202488 0.736999617 0.889327958 0.669064218 0.77554588 0.774128134 0.802711129 0.654693608 1 16.5679478 4.208548899 24.99998349 0.780310632 0.936107967 0.202264474 0.117050412 232.9419489 194042.4566 0.026225968 0.056665867 16164.00211 -4.208548899 0.155797336 AASPYSQRPAS(ph)PTAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPYSQRPAS(0.893)PT(0.107)AIR;AASPYSQRPAS(0.972)PT(0.028)AIR 183.22 1.22E-09 1720840000 221850 264110 227760 264630 201508 273440 219467 217103 188690 186113 TRUE FALSE 230608.8093 309468.838 233695.6127 316973.0242 167255.7421 209937.704 202264.6031 214193.0894 181899.0838 222578.279 1.036079578 1.390382024 1.049947972 1.424096842 0.75144683 0.943208407 0.908734689 0.962327009 0.817236455 1 17.76395328 3.233297721 24.99999857 0.902772189 1.224417806 0.591415533 0.133496624 83.5548112 396905.0428 0.034814034 0.042792918 1711.187979 -3.233297721 0.321645617 AASPYSQRPASPT(ph)AIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AASPYSQRPAS(0.212)PT(0.788)AIR 218.05 2.21E-14 365540000 91056 107380 87243 99105 85771 120230 89057 87780 91962 93932 TRUE FALSE 94650.96119 125821.6797 89516.62425 118707.6732 71191.67606 92308.4046 82076.47963 86603.45268 88652.30558 112336.177 0.84256883 1.120045947 0.796863723 1.056718115 0.63373775 0.821715738 0.730632659 0.770931102 0.789169687 1 16.77746309 3.246650243 24.99998786 0.776525145 0.954678523 0.294305535 0.122434225 194.145628 599979.165 0.030836827 0.041037665 1764.616124 -3.246650243 0.178153379 AASS(ph)DQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 AAS(0.47)S(0.53)DQLRDNS(0.999)PPPAFKPEPPK 45.332 0.092183 1436000000 363100 171270 258570 157890 380640 303920 300540 204760 246010 126770 TRUE FALSE 377435.4684 200684.2902 265308.5466 189120.1707 315938.9488 233339.186 276982.8895 202015.5271 237156.1482 151608.1543 2.489545962 1.323703801 1.749962248 1.247427433 2.083917914 1.539093903 1.826965645 1.332484575 1.564270399 1 17.20998783 -1.778941045 0.110504433 3.12E-16 2.162856942 0.33009134 0.340844547 77.40024583 1.309401223 26.26779477 5.156979755 0.016636385 1.778941045 2.162856942 AASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 148.3 3.74E-08 4568230000 5758080 2894830 4045790 2577870 5831470 5470470 4897790 4345360 5154940 3068070 TRUE FALSE 5985413.445 3391994.534 4151226.611 3087764.992 4840238.812 4200036.248 4513888.422 4287117.557 4969414.716 3669199.575 1.631258623 0.924450814 1.131371169 0.841536397 1.319153868 1.144673699 1.230210658 1.168406752 1.354359341 1 21.80703395 2.263075362 21.98002893 1.199646563 1.145174731 0 0.217567749 376.4015439 337478.7359 0.072129764 0.060297595 183.2632406 -2.263075362 -0.054471832 AASSS(ph)SPGS(ph)PVASSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 2 AASS(0.003)S(0.996)S(0.004)PGS(0.997)PVASSPSR;AAS(0.021)S(0.175)S(0.803)S(0.007)PGS(0.994)PVASSPSR;AASS(0.008)S(0.941)S(0.056)PGS(0.995)PVASSPSR 202.79 1.50E-11 559725000 632509 682090 701420 745080 752460 890430 676920 703730 640970 734450 TRUE FALSE 657480.9437 799233.6516 719699.5814 892454.6002 624557.118 683641.1271 623861.2416 694297.6504 617901.6149 878351.4156 0.748539744 0.909924704 0.819375444 1.016056426 0.711056084 0.778323021 0.710263831 0.790455435 0.703478817 1 19.74443873 3.196904616 24.99990698 0.768208605 0.87221456 0.151273745 0.102634566 220.3792644 132260.2238 0.027228982 0.032545161 1573.637207 -3.196904616 0.104005955 AASSSSPGS(ph)PVASSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AASSSSPGSPVASSPSR 17 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 AASSSS(0.002)PGS(0.998)PVASSPSR;AASSSS(0.03)PGS(0.97)PVASSPSR;AASSSS(0.001)PGS(0.998)PVAS(0.001)SPSR;AASSSSPGS(1)PVASSPSR;AASSSSPGS(1)PVASSPSR 446.11 1.56E-182 1023344000 732151 820218 869244 973890 1005613 1148533 970244 999449 954408 1039802 TRUE FALSE 761056.8868 961084.0611 891897.2127 1166522.535 834679.2615 881803.6169 894193.74 986053.0209 920059.0425 1243531.294 0.612012654 0.772866808 0.717229407 0.938072521 0.671216933 0.709112526 0.719076186 0.792945884 0.739876067 1 20.24601138 -4.999999892 0.351317291 3.954929886 0.738629668 0.478586129 0.081156542 382.2283754 3.12022326 851.0443118 0.059557958 1.00E-05 4.999999892 -3.216300219 AASVAAATTS(ph)PTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 AASVAAATT(0.002)S(0.993)PT(0.004)PR;AASVAAATT(0.023)S(0.973)PT(0.004)PR;AASVAAAT(0.049)T(0.14)S(0.804)PT(0.007)PR;AASVAAAT(0.019)T(0.201)S(0.772)PT(0.008)PR 168.4 3.67E-06 954610000 1653450 1586060 1686030 1588950 1914810 1918160 1733280 1594800 1634470 1540720 TRUE FALSE 1718729.483 1858453.467 1729969.327 1903239.567 1589331.28 1472696.41 1597420.985 1573424.315 1575645.744 1842594.585 0.932776801 1.008606821 0.93887681 1.032912819 0.862550717 0.799251459 0.866941104 0.8539178 0.855123399 1 20.81330725 3.219870157 24.66597801 0.861264097 0.977643086 0.456279243 0.055450957 152.6849318 201499.2288 0.014746214 0.017655956 1659.090807 -3.219870157 0.11637899 AAT(ph)PLPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AATPLPSLR 9 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AAT(1)PLPSLR;AAT(1)PLPSLR;AAT(0.998)PLPS(0.002)LR;AAT(0.996)PLPS(0.004)LR;AAT(1)PLPSLR 134.57 0.0027422 1567070000 2416510 2273980 2346340 2203080 2952570 3178360 2578560 2397020 2374520 2444990 TRUE FALSE 2511915.681 2664518.376 2407487.548 2638842.648 2450693.206 2440234.059 2376445.729 2364891.868 2289061.489 2924038.978 0.859056839 0.911245847 0.823343179 0.902464936 0.838119199 0.834542247 0.812727104 0.808775767 0.782842331 1 21.47953111 3.087080887 8.326023454 0.831513323 0.872994264 0.016441412 0.060521307 0.604184981 51.1789192 0.016188055 0.019375442 1222.027242 -3.087080887 0.041480941 AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 AAT(0.001)AARPPAPPPAPQPPS(0.806)PT(0.195)PS(0.997)PPRPT(0.001)LAR;AAT(0.001)AARPPAPPPAPQPPS(0.939)PT(0.065)PS(0.985)PPRPT(0.011)LAR;AATAARPPAPPPAPQPPS(0.984)PT(0.017)PS(0.998)PPRPT(0.001)LAR;AAT(0.003)AARPPAPPPAPQPPS(0.85)PT(0.15)PS(0.995)PPRPT(0.002)LAR;AAT(0.001)AARPPAPPPAPQPPS(0.973)PT(0.027)PS(0.975)PPRPT(0.024)LAR 91.1 0.00054833 10535240000 521866 525157 568931 583386 644553 692933 562776 561084 563706 594235 TRUE FALSE 542469.6726 615348.6296 583757.8092 698778.0096 534992.1113 532009.8123 518664.1466 553563.5867 543418.3312 710663.9709 0.763327951 0.865878467 0.821425924 0.98327485 0.752806014 0.748609517 0.729830367 0.778938583 0.764662841 1 19.43880803 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36;Q96B36-3;H9KV91 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 AATAARPPAPPPAPQPPS(0.725)PT(0.203)PS(0.068)PPRPT(0.005)LAR;AATAARPPAPPPAPQPPS(0.996)PT(0.004)PSPPRPTLAR;AATAARPPAPPPAPQPPS(0.944)PT(0.056)PSPPRPTLAR 240.33 7.26E-46 1346610000 286494 306847 281213 275790 290666 314007 285546 260484 247730 263411 TRUE FALSE 297805.0043 359545.5853 288541.6418 330340.4388 241258.6971 241083.6331 263164.1584 256992.638 238814.2457 315021.3421 0.945348662 1.141337228 0.915943154 1.048628758 0.765848737 0.765293016 0.835385173 0.815794372 0.7580891 1 18.26509005 3.240844269 24.99998621 0.812685805 1.015075295 0.533107724 0.086480662 41.12630685 450219.8154 0.02245767 0.028997734 1741.182401 -3.240844269 0.20238949 AATEALGEKS(ph)PDSATVSGYDIMK ddPTM_MDA-MB-175_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(0.992)PDS(0.008)ATVSGYDIMK;AATEALGEKS(1)PDSATVSGYDIMK 255.84 8.89E-44 421470000 398520 189937 273940 164256 412500 382640 378780 289990 361670 183524 TRUE FALSE 414253.8773 222557.2022 281079.1014 196745.3465 342383.3973 293777.659 349090.2338 286103.1584 348653.5673 219482.014 1.887416056 1.014011117 1.280647541 0.896407605 1.55996107 1.33850448 1.590518637 1.303538058 1.588529105 1 17.74374319 AATFGLILDDVSLTHLTFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AATFGLILDDVSLTHLTFGK 20 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 ;;; 318.16 1.53E-66 390293000 575887 795969 641297 809483 774547 1074904 740035 644503 658396 735700 FALSE TRUE 598623.4634 932670.484 658009.7267 969596.3213 642889.7776 825273.8363 682029.123 635864.4915 634700.4566 879846.3292 0.680372746 1.060037933 0.747868923 1.10200644 0.730684162 0.937974972 0.775168459 0.722699488 0.72137649 1 19.74689204 2.217862297 23.91220519 0.775147497 0.882610575 0.037397893 0.148666771 317.3130049 366579.0767 0.05072576 0.037513439 165.1438089 -2.217862297 0.107463078 HLSNVSS(ph)TGSIDMVDSPQLATLADEVSASLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLSNVSSTGSIDMVDSPQLATLADEVSASLAK 32 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 HLS(0.057)NVS(0.159)S(0.207)T(0.207)GS(0.172)IDMVDS(0.159)PQLAT(0.04)LADEVSASLAK 45.748 0.063577 97533000 16192 15402 19866 15616 15273 28499 17445 20311 21318 32179 TRUE FALSE 16831.27266 18047.17369 20383.72428 18704.79819 12676.90092 21880.53916 16077.61532 20038.76427 20550.76934 38483.85895 0.437359275 0.468954366 0.529669447 0.486042687 0.329408257 0.568564062 0.417775549 0.520705688 0.534010099 1 15.23196585 0.142802471 0.883674375 1.006774811 0.46385739 0.868566024 0.061690823 1.309114811 1.091678177 0.079228163 0.018589318 1.389320585 -0.142802471 -0.54291742 AATQFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AATQFWR 7 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 121.52 0.027371 0 631570 763440 667780 699880 1002770 996220 765070 684760 677420 1079860 FALSE TRUE 656504.8713 894554.8813 685182.8954 838314.1751 832319.5136 764863.0029 705101.8143 675581.9122 653039.7865 1291437.892 0.508351873 0.692681303 0.530558147 0.649132398 0.644490547 0.5922569 0.545981978 0.523123811 0.505668752 1 20.30054683 -1.182104598 4.757371144 1.000054219 0.578128859 0.804246477 0.062616679 3.62E-05 6.23E-06 0.06098704 0.014372941 0.065749946 1.182104598 -0.42192536 AATSDLEHYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AATSDLEHYDK 11 0 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;; 145.23 3.63E-05 2071700000 4663650 4335440 4704350 5173600 8304500 7267800 6679500 4979800 5143860 5219900 FALSE TRUE 4847774.503 5080018.095 4826949.226 6196922.638 6892904.056 5579963.595 6155943.336 4913053.926 4958733.483 6242639.464 0.776558462 0.81376125 0.773222489 0.992676683 1.104165008 0.893846846 0.986112264 0.787015485 0.794332832 1 22.57372472 3.751308985 24.76970002 0.927660243 0.790438772 0.354621062 0.091522811 915.516339 1778815.556 0.026115774 0.046679554 5640.388068 -3.751308985 -0.137221471 AAVAGEDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 141.52 0.00024782 1386790000 1187990 1390940 1109670 1313860 1339700 1507790 1257080 1205470 987680 1448340 FALSE TRUE 1234892.763 1629823.125 1138588.912 1573737.587 1111978.273 1157628.623 1158546.785 1189312.646 952133.5897 1732114.493 0.712939455 0.940944223 0.657340445 0.908564412 0.64197735 0.668332624 0.668862705 0.68662473 0.549694373 1 20.72410286 4.21820015 24.98920956 0.709430673 0.826941984 0.078890674 0.136642551 438.3275798 537978.2047 0.03170185 0.068608928 16527.23302 -4.21820015 0.117511311 AAVEWFDGKDFQGSK ddPTM_MDA-MB-175_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 ; 226.67 7.61E-13 3594400000 4473700 2680300 3647500 2508700 4843100 4292600 4044900 3647900 4135800 2627000 FALSE TRUE 4650325.13 3140620.675 3742556.846 3004913.372 4019871.592 3295708.705 3727850.169 3599005.867 3986953.366 3141710.353 1.480189008 0.999653158 1.191248214 0.9564578 1.279516932 1.049017361 1.186567108 1.14555623 1.269039128 1 21.58311875 4.752028846 24.62739771 1.127974982 1.480189294 0.494156355 0.109135808 1464.432472 2677737.537 0.023552357 0.454004095 56497.44996 -4.752028846 0.352214312 AAVGQES(ph)PGGLEAGNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAVGQESPGGLEAGNAK 17 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK 301.38 2.19E-46 1771130000 2079440 1442600 1936250 1452830 2196330 2251700 2050410 1780370 1938510 1386940 TRUE FALSE 2161537.897 1690355.328 1986710.266 1740195.438 1822998.611 1728776.8 1889693.506 1756507.052 1868743.404 1658684.338 1.303164108 1.019094043 1.19776272 1.04914202 1.099063016 1.042257867 1.139272532 1.058976088 1.126641978 1 20.66160792 4.749881705 24.69050367 1.086506043 1.303164259 0.571128824 0.05750693 947.2281496 2065791.356 0.012178139 0.186316836 56218.81725 -4.749881705 0.216658216 AAVGRPLDKHEGALETLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AAVGRPLDKHEGALETLLR 19 2 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 185.96 1.30E-14 989030000 481560 404710 478030 385730 632700 575990 494980 439490 517330 464630 FALSE TRUE 500572.3606 474215.7943 490487.8545 462026.2427 525153.88 442225.0517 456182.1742 433599.3554 498711.3944 555665.3526 0.900852209 0.853419764 0.882703685 0.831482907 0.945090201 0.795847806 0.820965662 0.780324621 0.897503132 1 19.08385676 2.713179415 24.98771762 0.837010213 0.878236281 0 0.065721167 1942.286443 1912172.953 0.020027941 0.018890894 516.6297541 -2.713179415 0.041226068 AAVHLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAVHLEGK 8 0 P18206;P18206-2 P18206 VCL Vinculin 0 ; 75.38 0.03286 344330000 1100980 1220480 1196320 1283850 1297360 1624240 1570320 1300180 1140270 1214030 FALSE TRUE 1144447.541 1430087.946 1227497.082 1537791.698 1076835.211 1247034.876 1447234.215 1282753.214 1099231.905 1451895.934 0.788243505 0.984979648 0.845444259 1.059161102 0.741675202 0.858901004 0.996789219 0.883502173 0.757101029 1 20.46950662 1.4709925 24.99986054 0.859133245 0.900656161 0 0.106973476 5.014600345 20468.61196 0.054061344 0.025027188 29.57961384 -1.4709925 0.041522916 AAVLQELATHLHPAEPEEGDSNVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AAVLQELATHLHPAEPEEGDSNVAR 25 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ;; 163.31 1.05E-11 774563000 1094756 592795 700864 467239 1118883 1043972 818058 689959 856976 482184 FALSE TRUE 1137977.812 694602.9299 719129.0916 559657.4796 928695.6673 801525.3245 753936.4764 680711.2282 826133.6012 576658.7228 1.973399113 1.204530344 1.247061846 0.970517669 1.610477099 1.389947456 1.307422305 1.180440356 1.432621355 1 19.13735823 4.741787025 24.87249013 1.269390984 1.973399394 0.578064473 0.182613972 204.850122 1579117.755 0.042154644 0.303942465 55180.67702 -4.741787025 0.704008409 AAVLS(ph)DS(ph)EDEEKASAK ddPTM_MDA-MB-175_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 185.09 9.77E-10 597010000 2364200 663820 1059160 664010 1556620 1934270 1710440 1138340 1296370 516250 TRUE FALSE 2457540.442 777825.9212 1086762.58 795349.1961 1292026.288 1485065.107 1576371.243 1123082.414 1249713.897 617399.3033 3.980471679 1.259842564 1.760226443 1.288224965 2.092691523 2.405355981 2.553244286 1.819053582 2.024158256 1 19.23584433 0.42246377 1.399132604 1.000295006 2.092974012 0.175533028 0.734481118 5.81727645 12.24766688 0.670233714 0.196040049 2.645232013 -0.42246377 1.092679006 AAVPSGAS(ph)TGIYEALELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 AAVPSGAS(0.971)T(0.029)GIYEALELR;AAVPSGAS(0.595)T(0.405)GIYEALELR;AAVPS(0.001)GAS(0.997)T(0.003)GIYEALELR;AAVPSGAS(0.991)T(0.009)GIYEALELR;AAVPS(0.003)GAS(0.978)T(0.02)GIYEALELR 293.83 3.13E-49 313403000 41613.5 51283.3 51638.9 40866.3 60140.7 65838.4 47774.5 46616.9 46973.5 59981.4 TRUE FALSE 43256.43311 60090.80785 52984.65216 48949.53217 49918.0053 50548.42939 44029.80985 45992.07671 45282.93291 71733.60692 0.60301489 0.837693941 0.73863081 0.682379351 0.695880319 0.704668726 0.613796124 0.64115104 0.631265245 1 16.13036155 -1.088443174 5.161818739 1.000006226 0.684118508 0.676074588 0.06579011 4.87E-06 8.60E-07 0.065833387 0.015516772 0.081574952 1.088443174 -0.315887719 AAVPSGASTGIYEALELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798;P13929-3;P13929-2;P13929;E5RGZ4;P09104-2;F5H0C8;P09104;E5RI09;E5RG95;K7EPM1;K7EKN2;F5H1C3 P06733 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Beta-enolase;Gamma-enolase 0 ; 214.65 2.31E-18 400690000 17175.7 17310.1 23154 22700 29366 31600 23367 20698 19982.2 24118 FALSE TRUE 17853.8099 20282.97502 23757.41226 27189.99225 24374.37781 24261.3789 21535.43348 20420.57717 19263.04453 28843.46033 0.618989875 0.703208796 0.823667202 0.94267442 0.845057338 0.841139677 0.746631411 0.707979449 0.667847904 1 14.81595663 -2.29579196 2.39091202 2.169854796 0.770478652 0.364160772 0.0924756 3709162.296 914001.1866 23491926.62 0.025371248 0.00506067 2.29579196 -1.399376144 AAVPSGASTGIYEALELRDNDKTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAVPSGASTGIYEALELRDNDKTR 24 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ; 214.35 8.44E-33 271860000 123199 141645 194946 176848 62274 144654 82032 92738 206817 83894 FALSE TRUE 128062.9917 165971.4269 200026.4529 211828.0066 51688.68772 111060.3008 75602.11749 91494.9988 199373.6966 100331.4231 1.276399634 1.654231764 1.99365709 2.111282788 0.515179454 1.106934372 0.753523823 0.91192765 1.987151089 1 16.61441399 3.245927097 24.99898715 1.01550855 1.7681859 0.415906101 0.413010415 161.4910859 548034.8674 0.115683316 0.153562267 1761.680298 -3.245927097 0.75267735 AAVS(ph)PQKR ddPTM_MDA-MB-175_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 110.39 0.0021043 592434000 910480 664933 833556 661349 956190 1047230 978520 862257 845710 696632 TRUE FALSE 946426.4534 779130.0703 855279.1541 792161.8583 793657.1653 804026.7034 901821.0455 850699.8553 815273.0623 833123.7026 1.135997512 0.935191338 1.026593232 0.950833419 0.952628239 0.965074815 1.082457554 1.02109669 0.978573842 1 19.6681712 -0.299518931 8.115543102 1 1.004224695 0.000381046 0.060612357 0 0 0.055989267 0.013196797 0.501742707 0.299518931 0.004224695 AAVT(ph)PGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAVTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK;AAVT(1)PGKK 108.47 0.0022295 2327950000 12292100 4760250 6439000 3793300 8171800 8199200 7853600 6345100 6471600 3876500 TRUE FALSE 12777401.6 5577785.908 6606805.63 4543603.418 6782760.355 6295060.06 7238014.31 6260054.313 6238688.38 4636025.955 2.756110885 1.203139491 1.425101087 0.980064275 1.463054871 1.357856949 1.561254053 1.35030614 1.345697466 1 22.14445721 4.741490008 24.99773345 1.323621944 2.756111405 0.854028773 0.180515686 93.11682836 794565.0528 0.040896342 0.287667912 55142.95152 -4.741490008 1.432489461 AAVVESHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAVVESHK 8 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390;A0A2R8YF59;H0YC68 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ; 89.296 0.014006 514940000 209334 571320 404880 536140 1132980 863410 561990 535920 381150 943490 FALSE TRUE 217598.668 669439.7657 415431.5054 642186.8918 940396.4643 662896.1126 517939.7553 528736.869 367432.486 1128348.801 0.192846988 0.593291511 0.368176494 0.569138631 0.833427096 0.587492194 0.45902451 0.46859346 0.325637326 1 20.10578168 4.742493737 24.18980177 0.553899961 0.192846763 0.251052898 0.195685618 363.1063629 2233061.663 0.044865937 0.338048176 55270.54377 -4.742493737 -0.361053198 AAVVT(ph)SPPPTTAPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AAVVTSPPPTTAPHK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;P35611-5;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 P35611 ADD1 Alpha-adducin 1 AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK;AAVVT(0.5)S(0.5)PPPTTAPHK 107.82 0.0041468 841740000 1181140 952760 1145220 1049790 1399310 1455890 1423710 1297200 1334740 1189850 TRUE FALSE 1227772.319 1116389.119 1175065.374 1257435.329 1161455.786 1117781.612 1312115.89 1279813.156 1286702.968 1422978.326 0.862818707 0.784544007 0.825778828 0.883664428 0.816214671 0.785522584 0.922091268 0.899390477 0.904232302 1 20.44048226 1.282868075 0.626995209 0.99688529 0.824021054 0.661985159 0.037295274 0.416849889 0.395570968 0.03689243 0.017007766 19.18085997 -1.282868075 -0.172864236 AAYEAELGDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAYEAELGDAR 11 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 157.99 7.06E-05 2162942000 721330 905083 804578 859587 842963 1020411 863196 840597 814270 969315 FALSE TRUE 749808.6654 1060523.965 825545.9636 1029610.743 699676.4504 783436.0097 795536.442 829330.1722 784964.5818 1159233.716 0.646814059 0.914849137 0.712147993 0.888182192 0.603568065 0.675822312 0.686260614 0.715412398 0.677140917 1 20.14474003 -1.123150315 3.805632973 1.00012106 0.727030131 0.431198267 0.094896388 27680215.88 46679833.33 42199.09964 0.022164605 0.075309486 1.123150315 -0.273090929 AAYEAELGDARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AAYEAELGDARK 12 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 207.95 1.16E-07 5252770000 3800130 3205950 3257050 2434660 4484900 3787690 3479010 3490670 3628090 3175040 FALSE TRUE 3950162.067 3756546.974 3341931.399 2916228.481 3722558.3 2908056.4 3206316.105 3443883.278 3497515.75 3797128.298 1.040302501 0.989312628 0.880120748 0.768008941 0.980361475 0.765856767 0.844405523 0.906970481 0.921094963 1 21.85647732 4.325000469 3.563990024 0.874551491 1.029433211 0.340815876 0.073782651 0.223891338 5.399850414 0.017441007 0.05538622 21134.9132 -4.325000469 0.15488172 ACAELHQNVNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACAELHQNVNVK 12 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 84.821 0.012021 116450000 242860 154740 182050 132850 233660 240530 211210 205900 194340 140150 FALSE TRUE 252448.3003 181315.3913 186794.3726 159127.3335 193942.5567 184670.5528 194654.8083 203140.2473 187345.7414 167609.7092 1.506167522 1.081771409 1.114460335 0.949392098 1.157108127 1.101789113 1.161357592 1.21198377 1.117749934 1 17.3547462 4.741162879 24.93609604 1.111223014 1.506167667 0.730903121 0.073716305 127.4267716 1220991.539 0.018398397 0.125537947 55101.43121 -4.741162879 0.394944653 ACDHCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACDHCLR 7 0 C9IYN9;Q6GMV2 C9IYN9 SMYD5 SET and MYND domain-containing protein 5 0 72.138 0.052417 28063000 31202 39841 31105 32661 36087 45202 40013 27620 29699 51880 FALSE TRUE 32433.87905 46683.38183 31915.62185 39121.24832 29952.94463 34704.52054 36876.67651 27249.79908 28630.13879 62044.8927 0.522748572 0.752412967 0.514395633 0.630531324 0.482762454 0.559345323 0.594354747 0.439194878 0.461442313 1 15.92102484 -1.672546794 3.307173959 1.037174957 0.550014768 0.704523133 0.087270963 7202693.654 14940887.62 1620229.462 0.020686565 0.021254613 1.672546794 -0.487160189 ACELWEQILQDHPTDMLALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACELWEQILQDHPTDMLALK 20 0 A9UJP8;Q5R3I4;H7C2L7 A9UJP8 TTC38 Tetratricopeptide repeat protein 38 0 101.17 0.00041137 51594000 78136 83028 94252 79402 97450 97943 84796 91317 88341 75043 FALSE TRUE 81220.86961 97287.41313 96708.28455 95107.47861 80885.48381 75197.22259 78149.46795 90093.04498 85161.62467 89746.23906 0.90500583 1.084027745 1.077574788 1.059737763 0.901268785 0.837887174 0.870782651 1.003864295 0.948915805 1 16.45356386 3.239243931 24.99999004 0.924630812 1.03861722 0.363783122 0.067376544 19.61334811 717559.8298 0.019992244 0.025530053 1734.778102 -3.239243931 0.113986407 ACEVALEEIKAETEKQS(ph)PPHGEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ACEVALEEIKAETEKQSPPHGEAK 24 2 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 ACEVALEEIKAETEKQS(1)PPHGEAK;ACEVALEEIKAETEKQS(1)PPHGEAK;ACEVALEEIKAET(0.002)EKQS(0.998)PPHGEAK 256.12 3.51E-44 839857000 1614270 355157 738990 388369 1160630 1057920 1034470 662430 844600 305761 TRUE FALSE 1678002.626 416152.452 758248.6865 465187.229 963346.5272 812234.1129 953385.5383 653551.2094 814203.011 365669.0138 4.588856487 1.138057742 2.073592943 1.27215381 2.634476783 2.221227619 2.607236332 1.787275336 2.226611991 1 18.48017885 -1.665898588 0.225555162 1.21E-41 2.438200883 0.169515643 0.895546141 52.74764885 2.035171279 33.79116097 1.752558545 0.021582483 1.665898588 2.438200883 ACFHCETCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACFHCETCK 9 0 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 148.52 8.98E-05 233200000 227890 257070 164380 210790 657640 401650 249730 212640 206300 683710 FALSE TRUE 236887.2732 301219.7728 168663.8778 252483.6329 545854.5877 308372.8746 230155.5101 209789.9086 198875.3033 817669.8841 0.28971016 0.368387999 0.206273805 0.308784312 0.667573306 0.377136153 0.281477299 0.256570424 0.243221998 1 19.64115898 -1.050027027 4.254572934 1.000059108 0.333033443 0.727044789 0.122562462 7630812.87 3295744.69 4092.347048 0.030285554 0.089119548 1.050027027 -0.667025665 ACKVDS(ph)PTVTTTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACKVDSPTVTTTLK 14 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 Q07866-6 KLC1 Kinesin light chain 1 1 ACKVDS(0.859)PT(0.141)VTTTLK 123.19 6.32E-05 286820000 370500 205320 243420 173990 399690 358980 282770 261850 290660 209350 TRUE FALSE 385127.6261 240582.1128 249763.7252 208404.7027 331750.8366 275612.3354 260605.7485 258340.3291 280199.2034 250368.1243 1.538245443 0.960913509 0.997585958 0.832393114 1.325052211 1.100828375 1.040890286 1.031841932 1.11914887 1 17.93369137 4.744833566 24.76715986 1.047728312 1.538245693 0.603105346 0.119927694 430.4410675 1699435.611 0.028578244 0.265753676 55569.12598 -4.744833566 0.490517381 ACLISLGYDVENDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ACLISLGYDVENDR 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ; 172.13 6.76E-06 111488000 190125 220990 204059 261150 224891 293720 245730 201216 193511 263610 FALSE TRUE 197631.2818 258943.3134 209376.9452 312804.6905 186664.1081 225507.9814 226469.0405 198519.0286 186546.5769 315259.3324 0.626884795 0.821366053 0.664141942 0.992213896 0.59209701 0.715309455 0.718357927 0.62970072 0.591724202 1 18.26617955 -1.143130086 4.723164843 1.000026186 0.708119585 0.36515893 0.116354039 3.08E-05 5.58E-06 0.108073348 0.02547085 0.071923351 1.143130086 -0.291906601 ACLISLGYDVENDRQGEAEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ACLISLGYDVENDRQGEAEFNR 22 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 344.55 3.70E-82 3300930000 815960 1102180 852220 1039410 933040 1188620 954370 915900 836200 1323130 FALSE TRUE 848174.7309 1291470.841 874429.5533 1245002.196 774442.1941 912581.0187 879563.9856 903623.8586 806105.3253 1582371.991 0.536014752 0.816161338 0.55260682 0.78679489 0.489418543 0.576717121 0.555851589 0.57105653 0.509428459 1 20.59365736 -1.15653401 5.290429775 1.000013734 0.601812988 0.563724893 0.105721237 1.63E-05 2.60E-06 0.097462858 0.022971424 0.069737438 1.15653401 -0.398200746 ACNQLGQFLQHR ddPTM_MDA-MB-175_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 ; 151.07 6.87E-05 1660360000 1375870 1389370 1436290 1305700 1719040 1879600 1431820 1268170 1382110 1737570 FALSE TRUE 1430190.41 1627983.49 1473720.897 1563963.563 1426838.195 1443091.386 1319590.207 1251172.255 1332368.131 2078013.574 0.68824883 0.783432558 0.709196954 0.752624325 0.686635647 0.694457151 0.635024826 0.602100136 0.641173931 1 20.98677365 -1.068318502 5.168939281 1.000004813 0.685078258 0.769264591 0.051221575 3.32E-06 5.98E-07 0.057930387 0.013654115 0.085443986 1.068318502 -0.314926555 ACPGPPPPS(ph)PEPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ACPGPPPPSPEPLAR 15 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 ACPGPPPPS(1)PEPLAR;ACPGPPPPS(1)PEPLAR 147.35 3.91E-06 459710000 133381 155888 186959 167027 193019 201683 176802 171908 167606 174727 TRUE FALSE 138646.9849 182660.5514 191831.3051 200064.4421 160209.6993 154845.1798 162943.7973 169603.8544 161573.8928 208961.4103 0.663505212 0.87413533 0.918022638 0.957422913 0.766695148 0.74102285 0.779779372 0.811651559 0.773223595 1 17.67287701 4.746428587 24.24101389 0.836700639 0.663505082 0.291744983 0.084384244 893.3103402 2752164.924 0.020715816 0.221060987 55773.58837 -4.746428587 -0.173195557 ACPRPEGLNFQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACPRPEGLNFQDLK 14 1 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 111.64 0.00058337 793620000 213110 150590 179550 202070 242620 263200 213220 198490 195210 178270 FALSE TRUE 221523.7474 176452.6611 184229.2205 242038.8429 201379.5391 202075.7888 196507.2593 195829.5662 188184.4302 213198.5933 1.039048823 0.827644584 0.864120244 1.135274108 0.94456317 0.947828903 0.921709924 0.91853123 0.882672007 1 17.70183839 -0.103637716 7.794817318 1 0.940069526 0.040046601 0.083955488 10834572.77 1389970.855 0.079740642 0.019339946 0.78770261 0.103637716 -0.059930473 ACQSIYPLHDVFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ACQSIYPLHDVFVR 14 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;; 138.39 1.57E-05 11224895000 2823947 3738610 3873340 3655770 3516220 4113690 3541940 3631800 3436320 3898900 FALSE TRUE 2935438.608 4380687.185 3974282.422 4378870.395 2918534.18 3158347.841 3264313.488 3583121.661 3312647.514 4662814.806 0.629542182 0.93949414 0.852335464 0.939104506 0.625916812 0.677347905 0.700073587 0.768446059 0.710439435 1 22.1527697 5.020324147 10.489061 0.785426442 0.374878421 0.140806533 0.121734741 16537.63988 244294.4453 0.029277793 98806.82713 104791.0391 -5.020324147 -0.41054802 ACRPPGS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 132.79 0.00012979 10765560000 2384914 2609180 2373929 2668877 2490303 2958670 2793840 2476829 2152242 2280906 TRUE FALSE 2479072.246 3057286.368 2435795.54 3196772.905 2067002.186 2271563.732 2574851.52 2443631.159 2074783.231 2727805.86 0.9088155 1.120785908 0.892950476 1.171920976 0.757752674 0.832743915 0.943927703 0.895822974 0.760605167 1 21.37930954 3.22888178 24.99994871 0.866397753 1.021225369 0.352689987 0.105150696 216.7386675 559824.3384 0.028458074 0.034424003 1693.876644 -3.22888178 0.154827616 ACRPPGS(ph)PGRAPPPTPAPSGCDPR ddPTM_MDA-MB-175_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 110.47 0.0010236 13061550000 1684690 1861270 1761150 1508730 2077690 2143640 1439940 1778090 1695910 2168370 TRUE FALSE 1751202.862 2180928.644 1807047.016 1807152.291 1724524.996 1645812.097 1327073.74 1754257.612 1634874.53 2593220.586 0.675300386 0.841011619 0.696835057 0.696875654 0.665012844 0.634659507 0.511747341 0.676478361 0.630441752 1 21.3063135 -1.174985248 4.413679631 1.000071886 0.668841643 0.62586675 0.076582192 6.09E-05 1.14E-05 0.07919175 0.018661424 0.066836662 1.174985248 -0.331230242 ACRT(ph)PESFLGPSASSLVNLDSLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ACRTPESFLGPSASSLVNLDSLVK 24 1 Q9H201 Q9H201 EPN3 Epsin-3 1 ACRT(1)PESFLGPSASSLVNLDSLVK;ACRT(0.534)PES(0.465)FLGPSASSLVNLDSLVK;ACRT(0.832)PES(0.145)FLGPS(0.018)AS(0.002)S(0.002)LVNLDSLVK;ACRT(0.998)PES(0.002)FLGPSASSLVNLDSLVK;ACRT(0.709)PES(0.291)FLGPSASSLVNLDSLVK 277.28 7.16E-52 8963115000 3926921 3302698 3957655 3149330 4612213 4671381 3925794 3699010 3979905 3051918 TRUE FALSE 4081958.873 3869910.69 4060794.741 3772258.074 3828230.682 3586523.558 3618080.008 3649430.821 3836668.996 3649882.9 1.118380777 1.06028352 1.112582198 1.033528521 1.048863974 0.982640719 0.9912866 0.999876139 1.051175915 1 21.79941875 3.4020535 1.468999381 1.004722165 1.095296818 0.683790492 0.025732938 0.221252968 0.977921983 0.008209718 0.0140923 2523.791655 -3.4020535 0.090574653 ACS(ph)LAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ACSLAK 6 0 B7Z2E6;H0YB80;P63104-2;P31946-2;P31946;P63104;E7EX29;B0AZS6 B7Z2E6;P31946-2;P63104 YWHAZ;YWHAB "14-3-3 protein zeta/delta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 1 ACS(1)LAK;ACS(1)LAK 83.265 0.059984 188946000 683800 414880 565850 451910 741220 716350 715060 582690 632560 393660 TRUE FALSE 710796.952 486132.4127 580596.5159 541296.4492 615227.6892 549988.5689 659011.7287 574879.9936 609794.2892 470790.1399 1.509795749 1.032588348 1.233238478 1.149761652 1.306798161 1.168224485 1.399799343 1.221096078 1.295257138 1 18.84472458 -1.080946627 4.72322306 0.999990675 1.249798018 0.26932995 0.126631095 1.37E-05 2.67E-06 0.110657969 0.026081144 0.082995276 1.080946627 0.249807343 ACSMPQELPQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ACSMPQELPQSPR 13 0 Q8N5J2;Q8N5J2-3 Q8N5J2 FAM63A Protein FAM63A 1 ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR;ACSMPQELPQS(1)PR 176.56 1.72E-05 933270000 645159 757792 736310 748316 822838 963911 849718 876426 880542 1033310 TRUE FALSE 670630.3755 887936.8812 755498.8435 896330.6713 682972.2907 740057.2785 783114.8828 864678.943 848851.4654 1235767.311 0.542683376 0.718530806 0.611360114 0.725323177 0.552670624 0.598864586 0.633707395 0.69971016 0.686902347 1 20.23697569 0.30924718 0.81473009 1.004402021 0.629941233 0.779245649 0.058455496 1.113765024 0.959722793 0.064826662 0.018546368 2.038201796 -0.30924718 -0.374460788 ACSPSNIPAVIITDMGTQEDGALEETQGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ACSPSNIPAVIITDMGTQEDGALEETQGSPR 31 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 ACSPSNIPAVIITDMGTQEDGALEETQGS(1)PR;ACSPSNIPAVIITDMGTQEDGALEETQGS(1)PR 193.4 2.97E-19 45293000 66331 83923 75680 85024 87046 96832 72796 85132 81236 85545 TRUE FALSE 68949.7991 98336.12242 77652.28297 101841.4934 72249.95201 74344.2355 67090.0593 83990.94479 78312.33223 102305.9049 0.673957179 0.961196937 0.759020538 0.995460561 0.706214877 0.726685675 0.655778954 0.820978465 0.76547226 1 16.64252989 5.023730059 16.23688162 0.806419285 0.352471152 0.111094944 0.118487287 14885070.71 262772067.4 0.027177607 174319771.7 105616.0835 -5.023730059 -0.453948133 ACTGLSGPGSGSKS(ph)PPATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ACTGLSGPGSGSKSPPATR 19 1 I3L2J0;I3L2I4 I3L2J0 CIC 1 ACTGLSGPGS(0.002)GS(0.045)KS(0.953)PPATR;ACTGLSGPGS(0.062)GS(0.387)KS(0.55)PPATR;ACTGLSGPGSGS(0.005)KS(0.995)PPATR;ACTGLSGPGSGS(0.015)KS(0.984)PPAT(0.001)R;ACTGLSGPGSGS(0.04)KS(0.958)PPAT(0.002)R;ACTGLSGPGSGS(0.045)KS(0.955)PPATR 272.43 1.44E-39 2044850000 1606590 1246690 1521390 1030309 1904390 1753060 1400660 1484820 1583010 1352780 TRUE FALSE 1670019.414 1460799.31 1561038.673 1234101.045 1580682.468 1345938.383 1290872.609 1464918.417 1526037.779 1617831.34 1.032258043 0.902936711 0.964895805 0.762811929 0.977037858 0.831939862 0.79790308 0.905482778 0.943261353 1 20.62562978 5.399315956 1.173199632 0.884417045 1.46234821 0.211956059 0.075336059 8.67982306 3.31165031 0.020045879 8.953560725 250793.3152 -5.399315956 0.577931165 ACTLTVFPPEENPGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ACTLTVFPPEENPGSPSR 18 0 Q9P2J3 Q9P2J3 KLHL9 Kelch-like protein 9 1 ACTLTVFPPEENPGS(0.953)PS(0.047)R 75.911 0.016896 9202600 12593 17124 17572 16467 18419 21715 16717 16493 18179 18399 TRUE FALSE 13090.18136 20064.91379 18029.94076 19724.12345 15288.14496 16672.02034 15406.67786 16271.93831 17524.74134 22003.93178 0.594901925 0.911878568 0.819396321 0.896390865 0.694791509 0.757683695 0.700178405 0.739501398 0.796436815 1 14.42547371 0.94104958 14.55777013 1.000000002 0.768227814 0.379167705 0.089822818 59.15919206 14610.62932 0.084188048 0.021047925 8.73071035 -0.94104958 -0.231772188 ADAASSLT(ph)VDVTPPTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLT(0.839)VDVT(0.161)PPTAK 281.61 6.18E-35 280600000 341410 229570 265400 227370 337380 328950 334950 288930 284990 211650 TRUE FALSE 354889.1304 268996.8617 272316.542 272343.1074 280032.2681 252556.3478 308695.7438 285057.3659 274733.2656 253118.7652 1.402065667 1.062729827 1.075844937 1.075949889 1.106327569 0.997778049 1.21956878 1.126180296 1.085392722 1 17.94945494 4.741938675 24.93963156 1.092647661 1.402065787 0.712887465 0.060426189 173.621946 1281762.153 0.01430193 0.104684367 55199.94877 -4.741938675 0.309418126 ADAASSLTVDVT(ph)PPTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ADAASSLTVDVT(0.999)PPT(0.001)AK;ADAASSLTVDVT(0.999)PPT(0.001)AK;ADAASSLTVDVT(1)PPTAK;ADAASSLTVDVT(0.995)PPT(0.005)AK;ADAASSLTVDVT(1)PPTAK 334.96 4.23E-71 1242404000 1662117 1167125 1434268 1209601 1876049 1849978 1741841 1472436 1711336 1191648 TRUE FALSE 1727738.663 1367569.64 1471646.202 1448856.468 1557158.861 1420348.646 1605310.951 1452700.404 1649745.352 1425128.61 1.212338767 0.959611385 1.032640978 1.016649625 1.092644446 0.996645942 1.126432337 1.019346881 1.157611559 1 20.44266069 2.242766407 24.99957166 1.072982545 1.046960914 0.020315622 0.076775246 507.7132278 3017906.791 0.025360053 0.020488 174.8905754 -2.242766407 -0.02602163 ADADPSPTS(ph)PPTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADADPSPTSPPTAR 14 0 Q9NWZ5;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 ADADPS(0.001)PT(0.004)S(0.995)PPTAR 144.16 6.91E-06 0 194720 201620 206580 194880 226570 246920 190090 193430 203140 190580 TRUE FALSE 202407.696 236246.6666 211963.6445 233426.6823 188057.7123 189576.5721 175190.2491 190837.3872 195829.0311 227920.5021 0.888062698 1.036531003 0.929989371 1.024158337 0.82510222 0.831766209 0.768646293 0.837298029 0.85919884 1 17.79817118 3.228007748 24.99736879 0.838364321 0.971624615 0.394859986 0.068796848 169.3266177 401095.9904 0.018342205 0.022139886 1690.471092 -3.228007748 0.133260294 ADAEEEAATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADAEEEAATR 10 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 117.3 0.0058825 0 207188 179724 189121 192686 204828 222580 210159 191469 197134 180051 FALSE TRUE 215367.9422 210590.1989 194049.6486 230798.7157 170011.4097 170889.1682 193686.1884 188902.6712 190039.1858 215328.5462 1.000182958 0.977994802 0.901179393 1.07184449 0.789544223 0.793620592 0.89949146 0.87727649 0.882554539 1 17.71618007 3.234301633 24.99992814 0.866523231 0.980912792 0.402897391 0.067470019 106.0885286 622732.2001 0.018793441 0.023222652 1715.148124 -3.234301633 0.114389561 ADAETLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADAETLRK 8 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 149.65 0.00080453 4645150000 4295340 3690760 4086500 3217620 5087190 4715410 3476660 3978260 4093750 3580760 FALSE TRUE 4464923.34 4324619.32 4192997.547 3854055.632 4222471.261 3620327.49 3204150.305 3924937.932 3946416.737 4282341.364 1.042636016 1.009872626 0.97913669 0.899987952 0.986019306 0.84540843 0.748223935 0.916540182 0.92155585 1 22.02996837 3.880295332 0.972832433 0.881484325 1.048540303 0.361503008 0.067152764 0.747728784 1.207201806 0.024550796 0.098939838 7590.936031 -3.880295332 0.167055978 ADAHEEDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADAHEEDELR 10 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 0 ; 143.89 3.32E-05 222520000 283290 313320 298910 310860 367760 403370 325420 333920 302100 312440 FALSE TRUE 294474.5079 367130.2727 306699.8402 372347.1802 305248.2866 309693.4306 299912.7301 329444.3486 291227.48 373656.636 0.788088527 0.982533795 0.820806619 0.996495564 0.816921893 0.828818227 0.80264259 0.881676697 0.779398656 1 18.51135362 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADAPDAGAQSDSELPSYHQNDVSLDR 26 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 ADAPDAGAQS(0.993)DS(0.007)ELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(1)DSELPSYHQNDVSLDR;ADAPDAGAQS(0.998)DS(0.002)ELPSYHQNDVSLDR 345.7 5.57E-110 18941390000 1249269 2612370 2881490 3089340 2887650 3287460 2632870 2675460 2508120 2997690 TRUE FALSE 1298591.105 3061024.226 2956583.997 3700402.231 2396808.284 2523997.237 2426498.77 2639599.835 2417853.251 3585029.961 0.362226012 0.853835047 0.82470273 1.032181675 0.668560182 0.704037976 0.676841978 0.736283898 0.674430417 1 21.77355375 -2.269233438 2.25833902 2.065919596 0.737183056 0.202199908 0.161948079 9050365.247 1075037.447 49504158.37 0.038147738 0.005379805 2.269233438 -1.32873654 ADATNVNNWHWTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADATNVNNWHWTER 14 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;; 264 1.18E-24 3632000000 1441210 1756090 1701590 1667120 1860970 2181780 1506020 1743130 1582330 1866990 FALSE TRUE 1498110.084 2057684.797 1745934.833 1996871.36 1544642.984 1675094.66 1387974.217 1719766.194 1525382.252 2232790.945 0.670958509 0.921575216 0.781951771 0.894338704 0.691799198 0.750224585 0.621631963 0.770231623 0.683172894 1 21.09041675 5.032983489 15.83639107 0.775379664 0.323353588 0.079064224 0.112163853 8541222.271 116094184.6 0.025638421 105199870.4 107890.5703 -5.032983489 -0.452026076 ADDADEFGYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 300.71 1.87E-35 5916850000 1321870 1441480 1472270 1362120 1634980 1713970 1470150 1489890 1430930 1318760 FALSE TRUE 1374058.448 1689042.977 1510638.566 1631543.27 1357066.684 1315926.443 1354915.801 1469920.462 1379431.109 1577145.773 0.871231101 1.070949183 0.957830653 1.034491103 0.860457357 0.834372108 0.859093576 0.932013062 0.874637673 1 20.58888458 3.231889108 24.9998925 0.887943924 0.988020428 0.310818606 0.065361602 164.6124763 616846.005 0.017763145 0.021698294 1705.646816 -3.231889108 0.100076504 ADDGRPFPQVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ADDGRPFPQVIK 12 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;; 166.7 4.67E-05 44261020000 24170821 21765700 23080900 20278990 30944290 30530360 28206610 25693080 26445820 24629920 FALSE TRUE 25125103.68 25503789.66 23682407.22 24290113.7 25684390.64 23440146.58 25995702.2 25348706.29 25494040.1 29455681.26 0.852979887 0.865836014 0.804001341 0.824632555 0.871967293 0.79577676 0.882536105 0.860571041 0.865505024 1 24.81204258 -0.120055648 0.520452536 1.01683062 0.837545436 0.760910786 0.026249733 2.312621601 0.696882829 0.103634473 0.011979838 0.758480382 0.120055648 -0.179285184 ADDIQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADDIQKR 7 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 86.011 0.032694 128290000 268560 239230 270190 225020 291020 282070 324770 293190 275490 214260 FALSE TRUE 279162.9562 280315.8915 277231.3734 269528.2844 241552.5243 216563.5173 299313.6788 289260.2676 265575.1687 256240.1447 1.089458314 1.093957747 1.08192014 1.051858149 0.942680253 0.845158426 1.168098305 1.128863972 1.036430763 1 17.96713699 0.986630243 23.89044424 0.999999986 1.053891137 0.027334884 0.088465544 1887.285395 3372405.869 0.092740755 0.023185189 9.696840289 -0.986630243 0.053891151 ADDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADDLGK 6 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 99.919 0.088987 244860000 590200 357140 512130 385440 593630 594220 636230 532370 548830 350900 FALSE TRUE 613501.5517 418476.0168 525476.5285 461678.8816 492724.9846 456221.4105 586360.6301 525234.4509 529077.7155 419652.1366 1.461928817 0.997197394 1.252171698 1.100146625 1.174127192 1.087141875 1.397254009 1.251594845 1.26075306 1 18.6788344 2.269951742 24.99988166 1.254030443 1.170081136 0.010769903 0.147879858 538.3682168 428754.2381 0.047117342 0.039417501 186.1880236 -2.269951742 -0.083949307 ADDLGKGGNEESTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADDLGKGGNEESTK 14 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;; 208.39 7.40E-09 4033100000 3264019 1891399 2927980 1248765 4187500 3085150 2515635 2494743 3005432 1989410 FALSE TRUE 3392884.99 2216232.065 3004285.564 1495766.99 3475710.246 2368670.668 2318452.955 2461305.051 2897267.089 2379196.8 1.426063195 0.931504307 1.262731004 0.628685693 1.460875471 0.995575763 0.97446876 1.034510912 1.217750078 1 21.18204318 4.751496422 23.58568397 1.05629866 1.426063727 0.216752032 0.210906953 1386.543847 2527964.873 0.045752981 0.797497385 56428.22918 -4.751496422 0.369765067 ADDTDSQSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADDTDSQSWR 10 0 O75369-8 O75369-8 FLNB Filamin-B 0 ;;;; 236.03 9.14E-12 1306037000 1337460 1443080 1459510 1354190 1628380 1860310 1555060 1463670 1413050 1439950 FALSE TRUE 1390263.954 1690917.764 1497546.03 1622044.74 1351588.549 1428281.196 1433170.334 1444051.898 1362194.607 1722080.633 0.80731641 0.981903943 0.86961435 0.941909867 0.784857877 0.829392752 0.83223184 0.838550687 0.791016739 1 20.71572126 3.245638456 24.99997691 0.836466677 0.903839424 0.115044508 0.070410311 269.7697791 952859.8415 0.017818547 0.023630521 1760.509836 -3.245638456 0.067372747 ADDTDSQSWRS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADDTDSQSWRSPLK 14 1 O75369-8 O75369-8 FLNB Filamin-B 1 ADDTDSQSWRS(1)PLK;ADDTDSQS(0.001)WRS(0.999)PLK 185.55 7.06E-07 2316600000 2687900 1697600 2113470 1381190 2994700 2923000 2299160 2173270 2770100 2179200 TRUE FALSE 2794020.368 1989149.595 2168548.764 1654385.26 2485661.964 2244177.548 2118945.831 2144140.87 2670404.642 2606172.517 1.072078057 0.763245557 0.832081818 0.634794991 0.953759564 0.861100919 0.813048951 0.8227164 1.024646153 1 21.31350116 1.238339684 24.99968868 1.012323159 0.836159667 0.276744249 0.108170546 6.88293043 777985.9538 0.080477719 0.024935943 17.31169867 -1.238339684 -0.176163492 ADEAS(ph)ELACPTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 ADEAS(1)ELACPTPK 186.29 8.32E-06 147720000 330230 249390 280600 246120 374150 357660 315410 247350 292380 237630 TRUE FALSE 343267.7354 292220.7925 287912.6665 294801.8014 310552.1166 274598.8854 290687.34 244034.6778 281857.3009 284189.0488 1.207885163 1.028261975 1.013102608 1.037343989 1.092765953 0.966254282 1.022866086 0.858705425 0.991795082 1 18.11649144 2.488624599 1.603320895 0.942143677 1.06910096 0.366054516 0.067129554 0.381615321 1.987926981 0.030563712 0.023840522 308.0524013 -2.488624599 0.126957282 ADEASELACPT(ph)PK ddPTM_MDA-MB-175_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 314.55 1.18E-49 1.04674E+11 24192210 9983620 12638490 12321640 18973840 18887980 16351710 12792570 14091770 8131490 TRUE FALSE 25147337.13 11698229.07 12967859.43 14758823.62 15748673.45 14501532.9 15070020.24 12621106.52 13584609.95 9724699.779 2.585924265 1.202939869 1.333497149 1.517663676 1.619450864 1.49120623 1.549664317 1.297840222 1.396918184 1 23.21322228 4.744577548 24.89543926 1.404660479 2.585924815 0.808901956 0.175612373 259.1164827 1072079.262 0.040619559 0.371118266 55536.37751 -4.744577548 1.181264336 ADEASELACPT(ph)PKEDGLAQQQTQLNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 267.97 1.87E-53 3217439000 2064063 1493664 1765338 764220 3181410 2787450 735757 1511892 1965175 2536334 TRUE FALSE 2145553.801 1750189.173 1811344.159 915380.435 2640635.065 2140106.982 678086.4438 1491627.561 1894448.736 3033280.086 0.707337846 0.57699557 0.597156908 0.301779067 0.870554314 0.705542159 0.223548906 0.491753982 0.624554503 1 21.53244729 0.887090239 6.145262229 0.99999553 0.548779866 0.345005182 0.180676255 1.981060114 107.3048238 0.175917016 0.044213948 7.710636669 -0.887090239 -0.451215664 ADEASELACPTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADEASELACPTPK 13 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 134.98 1.24E-05 0 45609 40147 43073 44507 54445 58005 51005 46536 47576 44830 FALSE TRUE 47409.67854 47041.93495 44195.51776 53310.35176 45190.45835 44534.21782 47007.09482 45912.26104 45863.74905 53613.58018 0.884284884 0.877425734 0.824334387 0.994344186 0.84289201 0.830651818 0.876775896 0.856355067 0.855450222 1 15.71031086 -1.272404286 5.800598807 1.000007769 0.870923396 0.420440797 0.04529625 4.37E-06 5.48E-07 0.042085865 0.009919137 0.053406696 1.272404286 -0.129084373 ADEDPIMGFHQMFLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADEDPIMGFHQMFLLK 16 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 211.7 6.42E-12 2669100000 900980 834590 969800 843670 1233100 1205100 1163200 978190 989020 776660 FALSE TRUE 936551.3861 977924.3403 995073.7847 1010545.408 1023498.102 925233.7885 1072025.345 965078.963 953425.3634 928831.6569 1.008311225 1.052854231 1.07131769 1.08797477 1.101919917 0.996126458 1.154165382 1.039024624 1.02647811 1 19.82505762 -0.606392696 6.024300197 0.999996152 1.062597774 0.136142907 0.04468961 3.03E-10 5.02E-11 0.040619775 0.009574173 0.247518295 0.606392696 0.062601622 ADEESDSQMS(ph)PSHSSTDDHSNWFIIGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADEESDSQMSPSHSSTDDHSNWFIIGSK 28 0 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 ADEES(0.007)DS(0.157)QMS(0.692)PS(0.036)HS(0.036)S(0.036)T(0.036)DDHSNWFIIGSK 169.73 7.03E-12 75074000 13455 54563 49074 49056 46101 59686 46427 53808 44912 57846 TRUE FALSE 13986.21379 63933.77081 50352.90875 58759.13038 38264.76849 45824.83105 42787.93043 53086.79177 43295.62589 69179.81617 0.202171884 0.924167978 0.727855486 0.84936812 0.553120413 0.662401746 0.618503095 0.767373993 0.625841875 1 16.07806356 -5 0.3678268 5.203406911 0.667653107 0.228561222 0.186393394 782.5850822 6.081384741 2612.511773 0.121575428 1.00E-05 5 -4.535753804 ADEGISFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;;;;; 211.39 7.32E-05 19314800000 7745260 8376380 8203290 7620510 9262670 9763020 8807000 8240120 8012100 8097260 FALSE TRUE 8051048.845 9814958.106 8417074.476 9127824.133 7688204.662 7495706.565 8116684.327 8129674.67 7723746.086 9683763.066 0.83139672 1.01354794 0.869194591 0.94259061 0.793927382 0.774048943 0.83817461 0.839516066 0.79759759 1 23.20713635 3.243141461 24.99693993 0.829995216 0.918066587 0.184910645 0.073592066 152.8289575 833957.105 0.018976331 0.024857395 1750.416753 -3.243141461 0.08807137 ATLSSTSGLDLMSESGEGEIS(ph)PQREVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ATLSSTSGLDLMSESGEGEISPQREVSR 28 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ATLSSTSGLDLMSESGEGEIS(1)PQREVSR;ATLSSTSGLDLMSESGEGEIS(1)PQREVSR;ATLSSTSGLDLMSESGEGEIS(1)PQREVSR;ATLSSTSGLDLMSESGEGEIS(1)PQREVSR;ATLSSTSGLDLMSESGEGEIS(1)PQREVSR 364.02 1.50E-127 1818710000 246292 430544 375753 266994 458869 454004 262566 406784 396651 600546 TRUE FALSE 256015.7983 504486.5828 385545.4319 319804.6163 380870.6113 348568.4515 241985.3908 401331.7258 382375.608 718211.4906 0.356462966 0.702420651 0.536813233 0.44527917 0.530304258 0.485328425 0.336927763 0.55879324 0.532399736 1 19.45404921 0.429788453 1.679684078 0.999964216 0.496578556 0.702913016 0.098210545 2.360849922 6.358545704 0.090872119 0.025705449 2.690224061 -0.429788453 -0.503385661 ADEHVIDQGDDGDNFYVIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADEHVIDQGDDGDNFYVIER 20 0 P13861-2;P13861;H7C1L0 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 ;;; 289.76 1.97E-54 3067300000 1024900 1030720 1068050 1052870 1231980 1329320 1184050 1092320 1070480 1036950 FALSE TRUE 1065363.843 1207738.142 1095884.26 1261124.543 1022568.48 1020605.576 1091241.067 1077679.237 1031953.634 1240120.499 0.859080907 0.973887734 0.883691755 1.0169371 0.824571871 0.822989038 0.879947608 0.869011711 0.832139808 1 20.24204888 3.211459231 24.99999613 0.86370091 0.932740977 0.182425001 0.062982496 307.9282119 284051.1465 0.016802027 0.020086905 1627.268551 -3.211459231 0.069040067 ADELLCWEDSAGHWLYE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADELLCWEDSAGHWLYE 17 0 Q13232;H3BPR2 Q13232 NME3 Nucleoside diphosphate kinase 3;Nucleoside diphosphate kinase 0 ; 129.84 7.51E-05 11445000 45239 56338 61723 69906 69986 80056 60775 62993 56720 56331 FALSE TRUE 47025.07065 66013.61325 63331.55209 83733.19815 58089.80472 61464.20726 56011.29669 62148.68187 54678.65828 67367.98093 0.698032953 0.979895973 0.940083868 1.24292278 0.862276172 0.912365287 0.831423117 0.922525523 0.811641636 1 16.03977544 ADEVAPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 91.584 0.014128 0 388130 216500 305600 237150 476370 410040 386220 295440 344730 221720 FALSE TRUE 403453.6721 253682.1909 313564.1871 284057.5622 395396.7976 314814.4242 355947.0672 291480.11 332323.2346 265161.7889 1.521537752 0.956707193 1.182539114 1.071261298 1.491153002 1.187254112 1.342376926 1.099253822 1.253284781 1 18.01651337 -1.438068961 6.528627593 0.999952539 1.221297741 0.142077778 0.169918885 0.000108402 9.33E-06 0.151936801 0.035804187 0.036469603 1.438068961 0.221345202 ADEVVWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADEVVWVR 8 0 P14868;C9J7S3;H7C278;C9JLC1;C9JQM9 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 133.12 0.0037983 54143000 65934 87246 83014 81020 82034 96361 87351 88439 86605 81097 FALSE TRUE 68537.12523 102229.8218 85177.41304 97045.51418 68089.88998 73982.61812 80504.20037 87253.61986 83488.10297 96986.40445 0.706667348 1.054063427 0.878240755 1.000609464 0.702056029 0.76281432 0.830056551 0.899647949 0.860822746 1 16.5654949 0.338049719 1.253413915 1.000023838 0.858171657 0.137789086 0.108618401 8.030822514 13.15626975 0.103848164 0.030757905 2.177959094 -0.338049719 -0.141852181 ADEWLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADEWLMK 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;; 117.17 0.01231 529690000 728472 568109 717253 600713 955590 897400 850690 716892 812434 633798 FALSE TRUE 757232.6371 665677.3015 735945.2024 719532.2385 793159.1531 688992.4502 784010.6949 707283.2353 783194.659 757978.5833 0.999015874 0.878227058 0.970931394 0.949277795 1.046413673 0.908986699 1.034344126 0.933117704 1.033267531 1 19.53179756 3.662157832 2.597874757 0.984632289 0.940056972 0.116479474 0.050942147 0.571312056 7.525865498 0.013099559 0.023355305 4593.649259 -3.662157832 -0.044575317 ADFCIIHYAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADFCIIHYAGK 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;; 134.75 0.00013437 10898500000 16993510 14407420 16705880 14883200 21771200 20367830 19172980 17153000 18899070 15177090 FALSE TRUE 17664426.9 16881782.31 17141248.96 17827052.54 18070539.2 15637710.16 17670151.73 16923092.09 18218896.16 18150750.2 0.973206435 0.930087303 0.944382396 0.982166155 0.995580844 0.861546216 0.97352184 0.93236323 1.003754443 1 24.11352584 1.229031908 24.89458869 1.001877273 0.948473556 0.258503606 0.035736768 275.8153756 720564.9963 0.031377483 0.008254467 16.94462291 -1.229031908 -0.053403717 ADFDNTVAIHPTSSEELVTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ; 224.57 3.13E-25 558440000 198778 378590 360120 422930 1253080 736950 630150 459710 338390 1038820 FALSE TRUE 206625.9089 443609.8875 369505.023 506584.2917 1040081.909 565804.5311 580757.1964 453548.3394 326211.41 1242356.89 0.166317675 0.357071218 0.297422605 0.407760681 0.837184482 0.455428336 0.467464061 0.365070893 0.262574638 1 20.24464824 -2.413690508 2.321340645 6.370961753 0.41160068 0.528342485 0.169329725 11599124.77 1031119.353 328016625.1 0.042526624 0.003857532 2.413690508 -5.959361073 ADGATSDDLDLHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADGATSDDLDLHDDR 15 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 196.8 8.75E-09 154760000 170250 200600 193450 200270 213180 240320 215470 203370 190900 179760 FALSE TRUE 176971.6015 235051.4895 198491.4659 239882.8083 176943.7397 184509.3221 198580.8984 200644.1578 184029.5463 214980.5303 0.823198274 1.093361753 0.923299732 1.115835038 0.823068673 0.858260615 0.923715734 0.933313159 0.856028897 1 17.71384648 3.218337025 24.99937911 0.898194495 0.991696228 0.194556529 0.089488311 361.1232186 446401.2111 0.024158631 0.028907646 1653.244265 -3.218337025 0.093501733 ADGYEPPVQES(ph)V ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADGYEPPVQESV 12 0 P61247;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 1 ADGYEPPVQES(1)V 85.522 0.012196 52531000 56466 53087 56935 43963 60896 69957 56222 56332 50575 63075 TRUE FALSE 58695.32128 62204.27929 58418.77287 52658.75018 50544.91967 53710.54696 51815.17273 55576.96168 48754.81563 75433.33861 0.778108491 0.824625828 0.774442361 0.69808325 0.670060753 0.712026644 0.686900165 0.736769215 0.646329813 1 16.20291466 -1.081660407 4.414480438 1.000023084 0.725931991 0.716453279 0.051849839 0.411705835 32700667.69 1673.534468 0.013008612 0.082858982 1.081660407 -0.274091093 ADHDFVVQEDFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ADHDFVVQEDFMK 13 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 206.18 6.39E-08 1165210000 3905380 3179440 3986110 3039330 4951380 4766140 4433080 3925590 4122690 3053560 FALSE TRUE 4059567.418 3725484.087 4089991.301 3640500.403 4109746.196 3659276.217 4085603.606 3872973.887 3974315.192 3651846.618 1.111647844 1.020164447 1.119978939 0.99689302 1.125388502 1.002034477 1.118777439 1.060552179 1.08830288 1 21.80019474 ADHGEPIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 140.83 0.00010815 21627930000 4005190 4356210 4649140 4437030 5290270 5685190 4570760 4583700 4697050 4810720 FALSE TRUE 4163317.994 5104355.181 4770300.408 5314661.291 4391031.795 4364890.782 4212491.888 4522262.999 4528004.088 5753288.477 0.723641446 0.887206543 0.829143268 0.923760613 0.76322121 0.758677546 0.73218854 0.786030983 0.787028863 1 22.45595538 ADHGVPLPGS(ph)PPPTVALPLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADHGVPLPGSPPPTVALPLPSR 22 0 A0A1W2PRX0;V9GYJ6;V9GY36;Q9UK80-2;Q9UK80-3;Q9UK80 A0A1W2PRX0 USP21 Ubiquitin carboxyl-terminal hydrolase 21 1 ADHGVPLPGS(1)PPPTVALPLPSR;ADHGVPLPGS(0.999)PPPT(0.001)VALPLPSR 100.93 0.00050309 234500000 176246 225856 216650 222703 233896 270000 229109 248630 222280 281960 TRUE FALSE 183204.3282 264645.0111 222296.077 266752.9887 194138.4415 207296.5919 211150.8379 245297.5215 214280.1862 337204.6635 0.543303068 0.784820139 0.659231918 0.791071469 0.575728815 0.614750074 0.626180064 0.727444036 0.635460328 1 18.36326496 -1.473296771 2.811750419 1.010950506 0.668262563 0.622496792 0.078828661 10445867.45 11424802.16 893052.3279 0.018944405 0.03362817 1.473296771 -0.342687943 ADHPPAEVTSHAASGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADHPPAEVTSHAASGAK 17 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 198.87 7.98E-12 600890000 441340 435780 514190 453640 618820 621650 582280 537550 565980 419840 FALSE TRUE 458764.444 510621.8251 527590.2138 543368.638 513633.1974 477281.2087 536639.3721 530345.0215 545610.4904 502099.6097 0.913692094 1.016973157 1.050768022 1.082192911 1.022970716 0.950570762 1.068790658 1.056254598 1.086657866 1 18.93761408 4.723687104 2.966500417 1.041647099 0.894633758 0.483597645 0.038867356 0.319134942 4.182100581 0.009835006 0.109619213 52928.1975 -4.723687104 -0.147013341 ADHQPLTEASYVNLPTIALCNTDSPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADHQPLTEASYVNLPTIALCNTDSPLR 27 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 227.24 1.26E-34 1634350000 653187 743461 712361 679019 745905 838625 710695 721890 779109 773563 FALSE TRUE 678975.3271 871144.6434 730925.7129 813326.9315 619116.3345 643867.0532 654988.8688 712214.2453 751069.0193 925127.8591 0.733925933 0.941647833 0.79008075 0.879150837 0.669222452 0.695976288 0.707998211 0.769854932 0.811854288 1 19.81929324 5.050316808 15.10927196 0.791499907 0.402479711 0.023996418 0.102778045 4667469.315 38853881.52 0.024107273 52330306.61 112283.724 -5.050316808 -0.389020195 ADIDLTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADIDLTKR 8 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ; 76.478 0.05724 127770000 278560 219586 249720 212088 386410 331820 288600 277030 314480 278060 FALSE TRUE 289557.7639 257298.1874 256227.9083 254038.3734 320728.1662 254759.8338 265978.7779 273316.866 303161.9262 332540.5332 0.87074427 0.773734813 0.770516321 0.763932056 0.964478414 0.766101598 0.79983867 0.821905418 0.911654057 1 18.34317068 1.03593629 2.507668518 0.999200859 0.813394077 0.503430035 0.058703041 0.208754951 2.835309129 0.05454139 0.014804692 10.8626626 -1.03593629 -0.185806782 ADIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 666500000 996130 1153500 1063550 1151560 1297360 1330460 1220060 1137780 1078080 1106590 FALSE TRUE 1035457.982 1351604.652 1091266.987 1379335.131 1076835.211 1021480.828 1124428.509 1122529.92 1039280.111 1323405.124 0.782419505 1.021308311 0.824590269 1.042262197 0.813685236 0.771857997 0.849647995 0.84821337 0.785307608 1 20.33582334 ADIGTPSNFQHIGHVGWDPNTGFDLNNLDPELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADIGTPSNFQHIGHVGWDPNTGFDLNNLDPELK 33 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 195.55 4.52E-27 290780000 136880 120700 134970 111960 159900 163280 153010 148140 144320 98756 FALSE TRUE 142284.1281 141429.2861 138487.4291 134105.3538 132720.2551 125360.6945 141016.6764 146154.4256 139125.9514 118105.3474 1.20472215 1.197484188 1.172575435 1.135472329 1.123744674 1.061431148 1.193990615 1.237492026 1.177981814 1 16.84971476 4.079791809 2.930449201 1.148583448 1.202099341 0.127254253 0.06430068 0.670062619 11.51396007 0.017686035 0.045073869 12016.88235 -4.079791809 0.053515893 ADIKS(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ADIKS(0.494)PS(0.494)LDVT(0.012)VPEAELNLETPEISVGGK 116.73 9.16E-05 50037000 56944 47444 52113 34999 65075 67717 67623 43442 66808 39328 TRUE FALSE 59192.19309 55592.13794 53471.10759 41921.69774 54013.57474 51990.75301 62322.53256 42859.73105 64403.59313 47033.56862 1.258509503 1.181967254 1.136871157 0.891314416 1.148404774 1.105396731 1.325064935 0.911258327 1.369311218 1 15.52140318 4.413329897 2.644755035 1.102183658 1.250631984 0.091268249 0.146806249 0.671540937 8.710464372 0.035281769 0.159229774 25901.79711 -4.413329897 0.148448327 ADILEDKDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;; 134.13 0.00016308 7491530000 15271050 5523800 9164930 5462170 13863210 12097250 12886610 9072280 10687710 4381580 FALSE TRUE 15873962.85 6472469.681 9403775.605 6542570.923 11506746.52 9287847.023 11876523.84 8950680.926 10303061.4 5240066.711 3.029343656 1.235188412 1.794590818 1.248566342 2.195916035 1.772467325 2.266483328 1.708123469 1.966208061 1 22.32115375 -0.702748549 10.04432033 0.999999988 1.876872915 0.232153523 0.494209446 0 0 0.434764833 0.102475055 0.198267464 0.702748549 0.876872927 ADITGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADITGR 6 0 O95994;B5MC07;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;; 148.28 0.025091 6889700000 2255370 2808420 2644570 2478450 2827600 3034960 2549480 2323200 2227120 2576920 FALSE TRUE 2344413.749 3290744.289 2713489.667 2968680.013 2346965.562 2330136.535 2349645.096 2292061.304 2146966.386 3081818.136 0.760724237 1.067793148 0.880483386 0.963288514 0.761552259 0.756091512 0.762421724 0.743736717 0.69665577 1 21.5553503 3.231916755 24.99300948 0.76911088 0.926081747 0.262449883 0.105054059 162.0476162 609593.4142 0.027607639 0.033719154 1705.755402 -3.231916755 0.156970867 ADKDES(ph)T(ph)MINEIT(ph)LAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 55.656 0.053985 6151820000 4355220 2540868 3377830 2351162 4830750 4311570 3671520 3500320 4176150 2702910 TRUE FALSE 4527167.449 2977242.314 3465859.025 2816214.826 4009620.841 3310273.21 3383736.669 3453403.936 4025851.177 3232493.464 1.40051867 0.921035834 1.072193668 0.871220579 1.240411121 1.024061842 1.046788402 1.068340578 1.245432117 1 21.62421602 ADKDYHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ADKDYHFK 8 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 110.14 0.0027795 18889320000 47865540 29210360 42061590 31893650 51134580 47309420 52462630 41631180 44100020 23748960 FALSE TRUE 49755308.48 34227012.1 43157749.59 38202118.78 42442742.36 36322524.19 48350471.98 41073182.13 42512868.89 28402114.01 1.751817082 1.20508678 1.519525961 1.345044906 1.494351524 1.278866924 1.702354689 1.446131162 1.496820585 1 24.75949498 -1.09908975 5.374335374 0.99999331 1.464770413 0.433634866 0.161375283 1.16E-05 1.95E-06 0.14025451 0.033057829 0.079599484 1.09908975 0.464777103 ADKDYHFKVDNDENEHQLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADKDYHFKVDNDENEHQLSLR 21 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;; 205.02 2.99E-22 8182670000 8192850 6410190 8642320 3836368 13009030 9224450 5891500 7232440 8848900 7769490 FALSE TRUE 8516310.044 7511090.268 8867545.959 4595190.14 10797759.73 7082211.285 5429708.835 7135500.972 8530429.818 9291772.81 0.916543077 0.808359225 0.95434382 0.494543962 1.162077458 0.762202373 0.584356607 0.76793752 0.918062677 1 23.14752245 ADKVEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADKVEQR 7 1 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 90.657 0.015484 243570000 1321020 1115530 1346540 1069330 1502520 1508010 1523050 1376130 1438280 1040930 FALSE TRUE 1373174.89 1307113.6 1381631.939 1280840.282 1247122.187 1157797.532 1403669.361 1357685.228 1386516.584 1244880.304 1.103057768 1.04999139 1.109851232 1.028886294 1.001800883 0.930047273 1.127553675 1.090615077 1.113775019 1 20.2475756 -0.305347345 6.940761688 0.999999986 1.061255031 0.0914578 0.058352213 0 0 0.059104236 0.013931002 0.495054092 0.305347345 0.061255045 ADLAEEYSKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;;;; 146.36 3.27E-05 4891220000 4288370 3248870 3962610 3238550 4689880 4818640 4623730 3873260 4163980 2960740 FALSE TRUE 4457678.159 3806838.15 4065878.872 3879125.524 3892695.873 3699583.887 4261309.961 3821345.285 4014119.173 3540840.316 1.258932276 1.075122798 1.148280778 1.095538115 1.099370637 1.044832175 1.203474198 1.079219887 1.133662864 1 21.75566035 -2.729970927 0.014947525 6.62E-07 2.042085272 0.311197212 0.059633872 5155.259343 8.930030693 705.6151115 525.4579514 0.001862212 2.729970927 2.042084611 ADLNQGIGEPQS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 ADLNQGIGEPQS(1)PSR;ADLNQGIGEPQS(0.978)PS(0.022)R;ADLNQGIGEPQS(0.997)PS(0.003)R 270.94 2.31E-33 1058840000 921380 968000 890260 904060 945740 1153970 930560 902140 892450 916640 TRUE FALSE 957756.7939 1134246.47 913460.907 1082880.37 784983.4526 885977.9561 857620.2756 890048.2889 860330.8988 1096238.058 0.87367592 1.034671677 0.833268742 0.987814975 0.716070243 0.808198502 0.782330325 0.811911503 0.784802984 1 20.0641297 3.248154088 24.99999759 0.805518787 0.932588169 0.296206861 0.085816645 212.9583406 554952.9289 0.021674769 0.028974299 1770.737106 -3.248154088 0.127069382 ADLSIPDLHEIVTEELEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADLSIPDLHEIVTEELEER 19 0 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ;;;;; 292.55 1.39E-49 405701700 288379.2 363109.9 373658.9 397428.8 395267.4 456354.9 352232.6 366182.1 355384.9 374827.8 FALSE TRUE 299764.6335 425471.2007 383396.7579 476039.0304 328079.9885 350373.3906 324623.6884 361274.0279 342594.6669 448268.1309 0.668717254 0.949144433 0.855284441 1.061951537 0.731883366 0.781615659 0.724173025 0.805932885 0.764262822 1 18.77400241 ADPSLLGFSVNAS(ph)SER ddPTM_MDA-MB-175_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(0.864)S(0.135)ER;ADPSLLGFSVNAS(0.953)S(0.047)ER;ADPSLLGFS(0.001)VNAS(0.837)S(0.162)ER 146.81 1.14E-06 391459000 118824 159160 154586 144503 126442 176445 124542 143442 119901 189633 TRUE FALSE 123515.2633 186494.4919 158614.6382 173085.2621 104949.434 135468.3228 114780.0726 141519.3946 115585.7864 226787.9556 0.544628849 0.82232979 0.699396217 0.763203062 0.462764584 0.597334733 0.506111854 0.62401636 0.509664572 1 17.7909845 -1.138046022 4.650035966 1.000030225 0.61812742 0.519496092 0.111206344 4.39E-05 8.13E-06 0.109347153 0.025770846 0.072770269 1.138046022 -0.381902805 ADQEEQIHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADQEEQIHPR 10 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 185.18 1.48E-06 3283170000 1901320 2176320 2006490 2024540 2287630 2538120 2171380 2152730 2077190 2202510 FALSE TRUE 1976385.582 2550086.031 2058780.778 2424987.969 1898779.47 1948680.096 2001181.562 2123876.176 2002432.338 2634049.665 0.750322064 0.968123747 0.78160287 0.920631073 0.720859403 0.739803855 0.759735698 0.806315919 0.760210547 1 21.32885112 5.058271258 16.21262233 0.816905231 0.164193676 0.045367026 0.094952746 10045515.36 62088652.89 0.021532132 214925180.2 114359.2392 -5.058271258 -0.652711555 ADQELLMYSHDNIICGITSVAFSR ddPTM_MDA-MB-175_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 ;; 299.66 3.99E-62 639895000 448081 478459 436218 558166 427749 591545 521469 397645 434985 455411 FALSE TRUE 465771.5839 560630.6114 447586.1994 668569.5688 355040.3778 454167.6387 480594.8972 392315.2192 419329.9748 544640.0661 0.855191553 1.02935984 0.821801823 1.22754386 0.651880756 0.833885839 0.882408268 0.720320159 0.769921276 1 19.05494359 3.214386702 24.99972663 0.796979491 0.975204092 0.281089924 0.134938373 272.3982535 281703.0221 0.036395477 0.04352117 1638.274615 -3.214386702 0.1782246 ADRDESSPYAAMLAAQDVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;;;;;;;; 306.51 6.76E-56 12283063000 4035017 4708797 4996231 4718822 4944096 5594648 5222900 5029139 4921056 4880920 FALSE TRUE 4194322.587 5517496.255 5126436.884 5652190.907 4103700.328 4295375.79 4813515.45 4961731.618 4743948.156 5837242.823 0.718545161 0.945223014 0.878229164 0.968298061 0.703020322 0.735856965 0.824621417 0.850012886 0.812703583 1 22.47685565 -1.57377202 2.699921944 1.011964452 0.830614543 0.270181932 0.085387851 20673551.02 19699186.43 1769659.533 0.020567643 0.02668259 1.57377202 -0.181349909 ADRDQS(ph)PFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.999)PFS(0.001)K;ADRDQS(1)PFSK;ADRDQS(1)PFSK;ADRDQS(0.985)PFS(0.015)K 155.09 8.07E-06 4364930000 6060230 4595050 5586720 4452910 7009390 6746700 6861050 5737980 6047550 4222610 TRUE FALSE 6299492.56 5384214.093 5732314.513 5333682.307 5817936.391 5179881.172 6323262.973 5661071.764 5829899.857 5049949.583 1.247436723 1.066191653 1.135123117 1.056185259 1.152078114 1.025729284 1.252143783 1.121015501 1.154447141 1 22.26783755 ADRDQSPFS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADRDQSPFSK 10 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ADRDQS(0.163)PFS(0.837)K;ADRDQS(0.323)PFS(0.677)K 145.14 8.15E-05 1096050000 1817650 1360380 1623310 1328520 2024930 2121300 1992150 1709360 1853470 1251790 TRUE FALSE 1889412.226 1594014.683 1665614.792 1591297.291 1680733.122 1628660.224 1836000.077 1686448.825 1786763.977 1497054.284 1.26208665 1.064767457 1.112594787 1.062952298 1.122693506 1.087909932 1.226408486 1.126511472 1.193519832 1 20.5136951 ADRPS(ph)SLPLDFNDEFSDLDGVVQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADRPSSLPLDFNDEFSDLDGVVQQR 25 1 D6REP5;B7Z4W8;E9PD09;Q96HH9-5;Q96HH9-4;Q96HH9;Q96HH9-2;Q96HH9-3 D6REP5 GRAMD3 GRAM domain-containing protein 3 1 ADRPS(0.5)S(0.5)LPLDFNDEFSDLDGVVQQR 66.479 0.027256 28605000 6385.7 7007.2 5964.2 8695.8 4392.1 12424 7928.5 6764.4 4865.1 9473.1 TRUE FALSE 6637.812367 8210.632092 6119.631952 10415.80329 3645.532411 9538.714288 7307.043453 6673.734282 4690.006001 11329.17257 0.585904427 0.724733606 0.540165834 0.919378994 0.321782759 0.841960366 0.644975916 0.589075172 0.41397604 1 13.46775488 -1.867239024 2.526051818 1.172777687 0.625945352 0.308247272 0.170485708 32178232.72 18713338.92 33329796.24 0.03830795 0.013575661 1.867239024 -0.546832334 ADS(ph)LLAVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADSLLAVVK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 ADS(1)LLAVVK;ADS(1)LLAVVK 131.83 0.000338 77733000 342320 185673 258440 221810 361070 347680 362130 249760 278650 176978 TRUE FALSE 355835.0579 217560.8934 265175.1587 265683.356 299695.4504 266936.5891 333745.3043 246412.3757 268621.4409 211653.4507 1.681215481 1.027910921 1.252874252 1.255275334 1.415972428 1.26119649 1.576847924 1.164225648 1.269156917 1 17.69134448 0.787811235 1.347826393 1.003113582 1.325531744 0.236536813 0.179846026 1.084494194 3.531198807 0.159355151 0.047625254 6.134952927 -0.787811235 0.322418161 ADS(ph)PAGPESSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADSPAGPESSR 11 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ADS(0.999)PAGPESSR 75.89 0.038655 95959000 41538 28029 36916 31641 46357 70172 40994 38081 41170 30641 TRUE FALSE 43177.95231 32842.76271 37878.06129 37899.49536 38477.2537 53875.61647 37780.78316 37570.58648 39688.29974 36644.51729 1.178292293 0.896253113 1.033662444 1.034247363 1.050013932 1.470223118 1.0310078 1.025271698 1.083062424 1 15.16130974 2.979483376 24.96536042 1.122931132 1.027596339 0.08135954 0.139764771 1947.065507 2369261.681 0.04349833 0.046632956 953.8572308 -2.979483376 -0.095334792 ADS(ph)PAGPESSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADSPAGPESSRR 12 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ADS(1)PAGPESSRR 98.676 0.0025878 213920000 133390 159310 139250 157130 178770 205590 138370 142490 147230 165550 TRUE FALSE 138656.3402 186670.2532 142878.9694 188209.845 148382.7393 157844.8382 127524.1978 140580.1546 141931.2211 197986.3529 0.700332817 0.942844042 0.721660697 0.950620294 0.74945943 0.797251103 0.644106 0.710049721 0.716873759 1 17.59504146 3.049313071 24.99982639 0.7446412 0.831934991 0.033174349 0.116583626 233.5852245 118417.0515 0.031189177 0.037278188 1120.245146 -3.049313071 0.087293792 ADS(ph)PHVSGSEADVASLAPVDSSFSLLSVSHALYDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSR 36 0 A0A499FJD3;A0A3B3ISA1;Q96S15 A0A499FJD3 WDR24 WD repeat-containing protein 24 1 ADS(0.997)PHVS(0.002)GS(0.002)EADVASLAPVDSSFSLLSVSHALYDSR 112.32 2.32E-05 16809000 1968.3 2567.3 4979.8 5344 3767.8 5799.7 5420.6 5731.3 3363.5 4218 TRUE FALSE 2046.010004 3008.213804 5109.577679 6401.02725 3127.350702 4452.80757 4995.719208 5654.481298 3242.448292 5044.436342 0.405597348 0.596342901 1.012913502 1.268928145 0.619960386 0.882716575 0.990342403 1.120934216 0.642777126 1 12.30047736 4.374346619 3.898739346 0.955387832 0.442834712 0.479898953 0.18754077 0.171886755 4.735753881 0.046495001 0.148937853 23678.08736 -4.374346619 -0.51255312 ADSEQPSKRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ADSEQPSKRPR 11 2 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 0 ;; 114.83 0.00067735 183284000 195705 186815 197916 139678 264284 233878 156107 193710 197538 210656 FALSE TRUE 203431.5845 218899.023 203073.8535 167305.8915 219361.1001 179563.379 143870.9254 191113.6343 190428.646 251930.0099 0.807492464 0.86888824 0.806072502 0.664096713 0.870722389 0.712751049 0.57107498 0.758598129 0.755879167 1 17.94266346 2.7023534 24.79127904 0.730445424 0.799493065 0.003488803 0.113198902 1429.296617 978645.986 0.035292164 0.033274943 503.9104904 -2.7023534 0.06904764 ADSGPTQPPLSLS(ph)PAPETK ddPTM_MDA-MB-175_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 411.85 8.78E-148 11535200000 5382510 3536760 4574450 3592690 5448650 5647010 5470550 4726750 5056910 3418040 TRUE FALSE 5595015.651 4144171.018 4693663.925 4303313.359 4522490.419 4335577.509 5041753.996 4663395.648 4874912.797 4087739.496 1.368730971 1.013805068 1.148229707 1.052736693 1.106354851 1.060629601 1.233384368 1.140825058 1.192569341 1 21.96287183 2.261726264 24.98850143 1.154935196 1.116935808 0 0.106861858 1023.761744 1104317.018 0.034523318 0.028867635 182.6948326 -2.261726264 -0.037999388 ADSGPTQPPLSLS(ph)PAPETKRPGQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADSGPTQPPLSLSPAPETKRPGQAAK 26 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 ADSGPTQPPLSLS(1)PAPETKRPGQAAK;ADSGPTQPPLSLS(1)PAPETKRPGQAAK 228.76 5.18E-35 719970000 873650 765490 859150 351590 1528170 1052780 485550 764900 1027140 1249610 TRUE FALSE 908142.3766 896956.9528 881540.1548 421133.4526 1268412.209 808287.8 447491.3223 754647.7666 990173.432 1494447.154 0.607677812 0.600193155 0.589877101 0.281798825 0.848750125 0.540860744 0.29943603 0.50496785 0.662568381 1 20.51118045 0.892685525 3.561955825 0.999708709 0.52895734 0.460092197 0.152308586 0.408451113 10.90214577 0.1447283 0.037322312 7.810620284 -0.892685525 -0.470751369 ADSPSIDYAELLQHFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADSPSIDYAELLQHFEK 17 0 Q08AM6;Q08AM6-2 Q08AM6 VAC14 Protein VAC14 homolog 0 107.75 0.0015371 0 100770 83995 99719 85883 119650 153800 100830 101500 111210 87782 FALSE TRUE 104748.4774 98420.48786 102317.7591 102870.4011 99311.93574 118082.2809 92926.68113 100139.5585 107207.5738 104981.2022 0.997783176 0.937505818 0.974629333 0.979893532 0.945997318 1.124794519 0.88517448 0.953880851 1.021207336 1 16.6797715 4.007591756 24.23484829 0.981093671 0.96475028 0.010470114 0.059685966 872.8463067 2786266.907 0.014711211 0.031669295 10176.34346 -4.007591756 -0.016343391 ADTDHPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADTDHPSR 8 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ; 78.334 0.030893 96892000 42168 107722 86546 104670 93823 117812 88392 98154 91460 113294 FALSE TRUE 43832.8252 126222.4155 88801.45986 125373.4136 77874.99997 90451.94846 81463.60407 96838.40618 88168.37247 135491.7902 0.323509086 0.931587186 0.655401038 0.925321109 0.574758071 0.667582503 0.601243839 0.714717889 0.650728523 1 17.04784591 -1.465586305 2.887577461 1.009059465 0.68271828 0.261339972 0.164663064 44359070.57 49942974.06 3237200.212 0.035755411 0.034230536 1.465586305 -0.326341185 ADTLDPALLRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADTLDPALLRPGR 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 137.84 5.12E-05 2830330000 3532910 4047630 3877060 4004140 4047230 4685130 4369280 4072760 3848690 3579920 FALSE TRUE 3672392.015 4742778.966 3978099.369 4796146.941 3359283.29 3597079.561 4026804.417 4018171.314 3710176.399 4281336.782 0.857767609 1.107779931 0.929172259 1.120245191 0.784634207 0.840176736 0.94054839 0.938531939 0.86659298 1 22.0296299 3.237556075 24.99999399 0.895853737 1.00584621 0.256040058 0.090705689 36.15797911 899871.4696 0.024557207 0.030995396 1728.049086 -3.237556075 0.109992474 ADTLTLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ADTLTLEER 9 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40 Q9UHD8 9-Sep Septin-9 0 ;;; 173.48 0.00012889 271900000 582380 640820 626620 618630 700240 793470 652410 581190 606290 638090 FALSE TRUE 605372.8121 750875.8501 642950.232 740993.1676 581213.4549 609198.6177 601272.3994 573400.0987 584469.7413 763111.5185 0.793295341 0.983966081 0.842537711 0.971015572 0.761636328 0.79830877 0.78792206 0.751397515 0.765903445 1 19.54153438 3.225069402 24.95831787 0.793372265 0.89992486 0.18191825 0.085470849 280.8514361 519565.3015 0.022531161 0.027071313 1679.072318 -3.225069402 0.106552595 ADTQTYQPYNKDWIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADTQTYQPYNKDWIK 15 1 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 188.06 2.87E-07 5002000000 4004200 3072600 4052000 2752400 5102600 4640600 3588200 3926600 4413000 3142000 FALSE TRUE 4162288.908 3600295.148 4157598.449 3296816.505 4235261.875 3562890.979 3306947.508 3873970.35 4254176.992 3757614.743 1.107694427 0.958133123 1.106446172 0.877369483 1.12711445 0.948178891 0.880065609 1.030965284 1.13214826 1 21.84138573 4.756377745 23.20850757 1.004055427 1.107694662 0.102930793 0.089123286 3132.825403 4080620.611 0.020214838 0.568264635 57066.04117 -4.756377745 0.103639235 ADTSS(ph)AENILYTVGLWEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ADTSSAENILYTVGLWEAPR 20 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 ADT(0.002)S(0.007)S(0.992)AENILYTVGLWEAPR;ADTS(0.085)S(0.915)AENILYTVGLWEAPR;ADT(0.004)S(0.025)S(0.972)AENILYTVGLWEAPR;ADTS(0.002)S(0.998)AENILYTVGLWEAPR;ADTS(0.016)S(0.984)AENILYTVGLWEAPR;ADT(0.002)S(0.015)S(0.984)AENILYTVGLWEAPR 404.35 3.13E-151 1542410000 730991 822340 835910 785375 954530 1013380 808570 837010 858910 838700 TRUE FALSE 759851.0891 963570.4981 857694.5013 940719.8309 792279.3315 778037.8529 745192.1706 825791.25 827997.9969 1003027.207 0.757557805 0.960662374 0.855105919 0.937880672 0.789888176 0.77568968 0.742943128 0.823298954 0.82549904 1 19.93592931 3.219722128 24.99757546 0.810014024 0.882099203 0.065008815 0.082532185 432.1835261 573480.9433 0.022169292 0.026539334 1658.525405 -3.219722128 0.072085179 ADVFHAYLSLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADVFHAYLSLLK 12 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 191.29 5.55E-06 513610000 2250300 1947220 2351600 2044500 4107700 3146000 2868200 2180500 2438400 2815100 FALSE TRUE 2339143.582 2281639.888 2412884.628 2448895.998 3409474.621 2415389.178 2643382.989 2151273.964 2350642.46 3366664.947 0.694795478 0.677715164 0.71669877 0.727395222 1.012715751 0.717442697 0.785163665 0.638992593 0.698210988 1 21.68288872 3.465395121 24.9994227 0.782931548 0.699119717 0.147303773 0.115280154 541.6308902 1154720.763 0.032888424 0.044566169 2920.082493 -3.465395121 -0.083811831 ADVQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADVQKR 6 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 95.62 0.069169 165482000 415600 339120 411780 293840 552910 445930 407680 393820 473560 491150 FALSE TRUE 432008.2089 397361.222 422511.3251 351960.675 458926.5557 342369.5156 375724.9763 388541.4871 456516.6681 587381.4389 0.735481546 0.676496048 0.719313375 0.599202923 0.781309257 0.58287425 0.639660962 0.661480703 0.777206493 1 19.16393815 0.89613915 2.91230721 0.999715973 0.672021605 0.748827378 0.057310343 0.186981729 3.411100847 0.051719027 0.013616187 7.872980036 -0.89613915 -0.327694368 ADVVPQQADPEFPRAS(ph)PR ddPTM_MDA-MB-175_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 205.53 5.77E-16 5160830000 1604710 1672200 1628130 1538240 1752240 1977360 1514790 1657100 1566680 1770760 TRUE FALSE 1668065.19 1959387.342 1670560.405 1842499.281 1454394.871 1518148.107 1396056.802 1634889.285 1510295.493 2117706.519 0.787675334 0.925240266 0.788853597 0.870044675 0.686778294 0.716883144 0.659230535 0.772009375 0.713175069 1 21.01407124 3.248113059 24.98958967 0.739999163 0.844966834 0.142034059 0.096300962 289.0587743 756184.9472 0.024500444 0.0327576 1770.569828 -3.248113059 0.104967671 ADYDTLS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 ADYDTLS(1)LR;ADYDTLS(1)LR 104.82 0.0036312 99507000 158484 210455 268250 208359 374720 251140 162399 214505 193208 278070 TRUE FALSE 164741.0707 246599.0091 275240.8154 249571.7883 311025.2282 192816.5411 149669.742 211629.9113 186254.4818 332552.4925 0.495383659 0.741534088 0.827661261 0.750473366 0.935266568 0.579807836 0.45006351 0.63638047 0.560075435 1 18.34322256 ADYDTLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ADYDTLSLR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;; 210.37 1.60E-05 274486000 375484 434140 411110 368849 511040 554060 435840 413460 409760 514830 FALSE TRUE 390308.3983 508700.1679 421823.8643 441806.2313 424173.6033 425387.9619 401677.7219 407918.245 395012.8176 615701.0815 0.633925146 0.826212887 0.685111456 0.717566112 0.688927819 0.690900138 0.652390801 0.662526439 0.641565899 1 19.23187058 -1.938009354 4.966453217 1.152562958 0.6900278 0.763473934 0.051961341 0.032047894 0.000400018 0.01836912 0.011699487 0.011534284 1.938009354 -0.462535158 ADYNLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ADYNLTR 7 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 112.17 0.014922 139970000 85923 111850 102190 86981 159090 137290 98637 96687 94202 178090 FALSE TRUE 89315.30639 131059.3674 104853.1554 104185.5822 132047.9386 105406.4782 90905.5742 95391.06891 90811.68842 212983.3258 0.419353515 0.615350366 0.492306874 0.489172482 0.619991909 0.494904837 0.426820146 0.447880455 0.426379333 1 17.70038096 -1.604669889 6.195233012 1.001800389 0.493559377 0.830240407 0.068848537 0.001752243 0.000111814 0.068226747 0.01603484 0.024850213 1.604669889 -0.508241012 AEADKIYSFTDNAPS(ph)PSIGGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEADKIYSFTDNAPS(0.998)PS(0.001)IGGSSR 143.07 1.00E-07 267290000 253980 188930 220210 151620 263550 256110 204460 197880 208480 204820 TRUE FALSE 264007.3265 221377.2578 225948.8535 181609.9835 218751.8651 196632.3339 188433.8909 195227.7423 200976.8455 244950.5575 1.077798431 0.903763029 0.92242637 0.741414861 0.893044978 0.802742953 0.769273166 0.797008769 0.820479233 1 17.90213105 5.126093687 0.978868589 0.820333987 1.410841674 0.484182333 0.073033014 2.752411032 1.258100892 0.020542409 2.046689727 133688.388 -5.126093687 0.590507687 AEADKNDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEADKNDK 8 1 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 78.334 0.028174 184490000 174890 172430 160070 155740 217300 215830 217730 166880 185270 192370 FALSE TRUE 181794.7922 202043.5112 164241.5557 186544.9072 180363.4236 165706.7534 200663.7537 164643.2466 178602.1689 230061.2184 0.790201815 0.878216297 0.713903703 0.810848993 0.783980129 0.720272433 0.872218947 0.71564972 0.776324537 1 17.81165828 -0.582002108 8.522588538 0.999999983 0.783042333 0.572614226 0.055805917 0 0 0.050321682 0.011860934 0.26181703 0.582002108 -0.21695765 AEAEAEAGS(ph)PRPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEAEAEAGSPRPDPR 15 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAEAGS(1)PRPDPR 61.821 0.052179 283220000 507240 612350 596840 578500 623720 723950 591550 554140 554270 611480 TRUE FALSE 527266.2269 717516.3491 612394.1407 692925.5733 517700.2972 555823.5841 545182.7653 546712.6597 534321.931 731287.7985 0.721010562 0.981168222 0.837418786 0.947541549 0.707929625 0.76006134 0.745510545 0.7476026 0.73065889 1 19.48007977 3.234319217 24.99978717 0.764664668 0.877143169 0.145910386 0.101079055 149.9821936 884030.0367 0.026324944 0.03253439 1715.217572 -3.234319217 0.112478501 AEAEAGS(ph)PRPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR 65.172 0.035919 3668550000 3762190 4168060 4076640 4008360 4207060 4929210 4254490 3989440 4034440 4239320 TRUE FALSE 3910724.166 4883891.882 4182880.587 4801201.644 3491945.444 3784475.68 3921011.957 3935968.082 3889241.292 5069933.587 0.771356094 0.963304903 0.825036564 0.946994978 0.688755658 0.746454685 0.77338527 0.776335235 0.767118785 1 22.27353542 3.245784633 24.99993949 0.777432706 0.879172779 0.158057459 0.092041669 238.5949657 825693.6088 0.023427597 0.031075121 1761.102499 -3.245784633 0.101740073 AEAGVPAEFSIWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEAGVPAEFSIWTR 14 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 166.04 9.00E-06 74244000 90736 117010 119620 108530 131810 146440 129320 130020 118210 136860 FALSE TRUE 94318.32734 137105.5573 122737.3955 129996.9101 109404.9833 112431.5293 119183.5605 128277.2946 113955.6452 163675.0967 0.576253378 0.837669017 0.749884362 0.794237564 0.668427791 0.686918973 0.728171621 0.78373129 0.69623081 1 17.32047531 -4.790504373 0.546080237 9.999372692 0.730551206 0.576547967 0.070514553 2331.745333 11.39919087 25730.6055 0.028818937 1.62E-05 4.790504373 -9.268821486 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR;AEAPAGPALGLPS(1)PEAESGVDRGEPEPMEVEEGELEIVPVRR 287.24 6.53E-82 785280000 41071.2 53704.6 55227.5 55408.2 57897.8 62134.1 51951.5 48081.4 51114.1 61750 TRUE FALSE 42692.72269 62927.94729 56666.77402 66367.77658 48056.35264 47704.39693 47879.40568 47436.94748 49274.51353 73848.73022 0.57811045 0.852119557 0.767335794 0.898698954 0.650740405 0.645974505 0.648344332 0.64235292 0.667235758 1 16.17228549 -1.148125337 4.370109144 1.000055505 0.706833501 0.452977726 0.097029636 5.45E-05 1.06E-05 0.097578653 0.022995163 0.071100829 1.148125337 -0.293222004 AEAPLPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEAPLPSPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 AEAPLPS(1)PK;AEAPLPS(1)PK 124.42 0.00055603 91159000 691510 375810 415040 392050 585480 864010 681630 544530 533060 400250 TRUE FALSE 718811.3488 440352.4441 425856.2834 469596.3198 485960.3187 663356.7717 628202.0595 537231.466 513875.2747 478671.3243 1.501680406 0.919947408 0.889663244 0.981041262 1.015227556 1.385829353 1.312387076 1.122338939 1.073545142 1 18.86867586 AEAPPLEREDS(ph)GTFSLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEAPPLEREDSGTFSLGK 18 1 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 AEAPPLEREDS(0.852)GT(0.145)FS(0.003)LGK;AEAPPLEREDS(0.954)GT(0.046)FSLGK;AEAPPLEREDS(0.94)GT(0.06)FSLGK 198.84 1.02E-15 701300000 696100 571510 795090 518760 889180 791280 753370 724130 829370 567980 TRUE FALSE 723582.5655 669662.3968 815810.6986 621369.1797 738037.5012 607517.212 694318.8908 714424.2218 799521.1357 679264.8064 1.065243715 0.985863526 1.201020119 0.914767222 1.08652398 0.894374633 1.022162321 1.051760985 1.177038952 1 19.37361458 -1.022331553 3.996576435 0.999995044 1.040040605 0.017933209 0.093692585 3.86E-06 9.45E-07 0.084634628 0.019946104 0.094987935 1.022331553 0.040045561 AEASS(ph)PVPYLSPETNPASSTSAVNHNVNLTNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEASSPVPYLSPETNPASSTSAVNHNVNLTNVR 33 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 AEASS(1)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.021)S(0.979)PVPYLSPETNPASSTSAVNHNVNLTNVR;AEAS(0.005)S(0.995)PVPYLSPETNPASSTSAVNHNVNLTNVR 356.14 3.50E-132 5157600000 509800 987740 972010 920030 1016010 1372550 959470 1050900 1016370 1212500 TRUE FALSE 529927.2977 1157376.661 997341.3791 1102009.188 843308.9831 1053796.064 884264.2343 1036814.404 979791.0422 1450066.16 0.365450427 0.798154383 0.687790258 0.759971661 0.581565867 0.726722747 0.609809579 0.715011792 0.67568713 1 20.4676873 -5 0.272447099 3.326807092 0.642928491 0.456804421 0.113786974 187.9240316 1.819351939 246.2617829 0.126265628 1.00E-05 5 -2.683878601 AEASSGDHPTDTEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEASSGDHPTDTEMK 15 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 63.037 0.075896 0 52335 63522 75021 88738 78565 94645 107460 86307 96567 57392 FALSE TRUE 54401.22621 74431.40937 76976.10889 106290.1115 65210.54936 72665.13311 99037.00441 85150.19583 93091.57253 68636.86356 0.792594874 1.084423231 1.121498054 1.548586372 0.950080554 1.058689592 1.442912733 1.240589844 1.356291178 1 16.06669601 4.687684287 1.716477527 1.234647825 0.673366106 0.331812588 0.182448019 0.925260689 2.928126512 0.047015945 0.825347227 48717.42074 -4.687684287 -0.561281719 AEASSGDHPTDTEMKEEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 AEASSGDHPTDTEMKEEQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;;;;;; 333.69 1.39E-75 9576610000 7942150 5241983 7974550 4969017 11654170 9707440 10591400 8251950 9593700 4425811 FALSE TRUE 8255712.215 6142252.803 8182373.324 5951873.732 9673198.346 7453034.178 9761218.393 8141346.108 9248424.611 5292963.928 1.559752216 1.160456199 1.545896295 1.12448787 1.827557958 1.408102205 1.84418759 1.53814502 1.74730543 1 22.33564439 3.239604715 24.99996625 1.59616547 1.34843791 0.126618569 0.264798549 46.19563695 1106089.442 0.067279071 0.08615655 1736.219841 -3.239604715 -0.247727561 AEASWDSAVHGCPQLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEASWDSAVHGCPQLSR 17 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ; 176.21 1.13E-09 601180000 282820 407520 361990 358790 364890 429580 357000 376660 327710 398610 FALSE TRUE 293985.952 477508.3899 371423.7568 429757.5911 302866.1281 329816.5553 329017.4072 371611.4888 315915.7811 476709.9977 0.616697685 1.001674797 0.779139852 0.901507401 0.635325732 0.69185995 0.690183568 0.779533659 0.662700138 1 18.86275236 5.027852869 15.90268243 0.778780933 0.167270691 0.138310077 0.127726633 7338315.696 114982718.6 0.029376285 117451907.5 106623.4839 -5.027852869 -0.611510242 AECLEKFPVIQHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AECLEKFPVIQHFK 14 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;Q68CR8;B7ZBQ0 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 143.05 5.55E-06 805870000 1451830 1264770 1579780 1125630 2173300 1827840 1561660 1551380 1571130 1524630 FALSE TRUE 1509149.369 1481984.409 1620950.365 1348276.254 1803883.242 1403351.861 1439253.009 1530586.289 1514585.338 1823352.058 0.82767854 0.812780177 0.888994727 0.739449219 0.989322514 0.769654909 0.789344549 0.839435414 0.830659845 1 20.79816172 -1.115464295 4.165069945 1.000034784 0.831799072 0.373116718 0.065357529 22840952012 4850905121 7968588.032 0.013993455 0.076654156 1.115464295 -0.168235713 AEDEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEDEVQR 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ;; 149.48 0.0046838 1298880000 1189520 1320770 1189490 1299460 1404900 1675680 1321100 1250850 1239900 1216740 FALSE TRUE 1236483.168 1547601.973 1220489.087 1556489.309 1166095.6 1286528.715 1217548.73 1234084.402 1195276.241 1455136.907 0.849736655 1.063543895 0.838745193 1.069651455 0.801364871 0.884128984 0.83672452 0.848088173 0.821418408 1 20.47272347 3.213994388 24.99993212 0.856118694 0.954808742 0.200659095 0.086978301 303.2622291 308615.3815 0.022598913 0.02702228 1636.795371 -3.213994388 0.098690047 AEDFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDFRK 6 1 P32119;A6NIW5;P32119-2;Q86XL3;Q86XL3-2 P32119;Q86XL3 PRDX2;ANKLE2 Peroxiredoxin-2;Ankyrin repeat and LEM domain-containing protein 2 0 84.359 0.089697 1389900000 3478500 2836500 3309000 2677800 4251300 3759100 3577300 3363100 3495900 2954100 FALSE TRUE 3615833.866 3323646.81 3395235.258 3207460.848 3528665.545 2886105.995 3296901.878 3318023.145 3370083.242 3532899.335 1.02347492 0.940770312 0.961033683 0.907883453 0.99880161 0.816922794 0.933200062 0.939178513 0.953914313 1 21.75242121 AEDGATPS(ph)PSNETPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPS(0.998)PS(0.002)NETPK;AEDGATPS(0.997)PS(0.003)NETPK;AEDGATPS(1)PSNETPK;AEDGATPS(0.997)PS(0.003)NETPK 352.75 2.10E-82 2314110000 3040399 1719527 2466991 1883397 3157921 2903260 3087384 2452966 2648657 1626331 TRUE FALSE 3160436.3 2014842.386 2531282.812 2255927.305 2621138.716 2229021.864 2845386.775 2420088.003 2553332.352 1944979.421 1.624920174 1.035919642 1.301444521 1.159872069 1.347643418 1.146038791 1.46293927 1.244274349 1.312781166 1 20.89132346 -1.007110811 5.134532744 0.999997738 1.283430928 0.233278108 0.158456866 3.63E-06 7.03E-07 0.135917234 0.032035744 0.098376006 1.007110811 0.28343319 AEDGATPS(ph)PSNETPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGAT(0.115)PS(0.885)PSNETPKK 87.654 0.0039177 152230000 96577 58158 89698 55188 109970 105830 99974 86653 96587 53571 TRUE FALSE 100389.9345 68146.18409 92035.60357 66104.02168 91277.33868 81252.58637 92137.77665 85491.55827 93110.85274 64067.21177 1.566947144 1.06366708 1.436547666 1.031791768 1.424712207 1.268239777 1.438142446 1.334404228 1.453330809 1 15.96729858 AEDGATPSPS(ph)NETPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPS(0.28)PS(0.72)NETPK;AEDGATPS(0.02)PS(0.594)NET(0.385)PK 216.01 2.37E-12 226280000 393616 230925 323109 234936 420175 382975 414203 314491 338386 207403 TRUE FALSE 409156.2636 270584.5724 331529.486 281405.6396 348753.8036 294034.8603 381736.6865 310275.7625 326207.554 248039.6469 1.649559934 1.090892427 1.336598766 1.134518788 1.406040558 1.185434925 1.539014796 1.250911967 1.315142793 1 17.92021122 0.22437827 1.818496747 0.99998081 1.31536198 0.253918416 0.16568309 21.67983631 48.70997571 0.14320936 0.039824763 1.676402383 -0.22437827 0.315381169 AEDGATPSPSNET(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;AEDGATPSPS(0.008)NET(0.992)PK;AEDGATPSPSNET(1)PK;AEDGATPS(0.022)PS(0.149)NET(0.829)PK;AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK 423.92 3.74E-152 8850911000 8025286 3066822 3689594 2905690 5302818 6498084 5274967 4003269 3747596 2000765.4 TRUE FALSE 8342130.488 3593524.822 3785747.851 3480426.809 4401446.89 4989002.47 4861501.303 3949611.727 3612720.752 2392777.073 3.486380149 1.501821821 1.582156521 1.454555399 1.839472193 2.085026025 2.031740172 1.650639239 1.509844269 1 21.19025456 4.742011979 24.81949406 1.679446611 3.486380903 0.774643278 0.299507642 140.0365264 1006983.707 0.070914721 0.518271337 55209.26671 -4.742011979 1.806934292 AEDGATPSPSNET(ph)PKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK;AEDGATPSPSNET(1)PKK 247.89 1.42E-20 6073700000 4946180 1548950 2358040 1462620 3303620 3627270 3296510 2322080 2552120 1180640 TRUE FALSE 5141459.006 1814970.113 2419492.46 1751921.871 2742071.852 2784891.514 3038120.932 2290956.316 2460269.7 1411963.803 3.641353265 1.285422551 1.713565499 1.240769676 1.942027017 1.972353334 2.151698879 1.622531902 1.742445305 1 20.42927167 7.999999996 0.053056144 4.35E-08 5.311147829 0.236241242 0.606374274 800.5603597 3.194810027 71.86296498 340.9787985 99999999.12 -7.999999996 5.311147785 AEDGATPSPSNET(ph)PKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEDGATPSPSNETPKKK 17 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 AEDGATPSPSNET(1)PKKK;AEDGATPSPS(0.007)NET(0.993)PKKK 261.46 1.30E-25 1702130000 2886700 828370 1479400 504280 2862200 2095500 1335030 1286410 1685090 732750 TRUE FALSE 3000669.145 970636.1037 1517954.379 604025.0789 2375684.266 1608851.883 1230386.86 1269167.778 1624443.94 876318.3332 3.424177073 1.107629576 1.732195165 0.689275867 2.710983186 1.835921744 1.40404099 1.448295363 1.853714431 1 19.74109552 4.747207807 24.87399856 1.560039552 3.424178089 0.532006776 0.531980812 814.2458531 2342156.594 0.121537699 1.43985535 55873.74834 -4.747207807 1.864138537 AEDGENYDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AEDGENYDIKK 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;;;; 174.9 1.68E-05 4901870000 6954250 3245180 4836910 3247690 6524180 5669540 6537290 4800150 5785150 2505850 FALSE TRUE 7228809.16 3802514.421 4962963.848 3890073.389 5415202.214 4352875.258 6024880.128 4735811.841 5576943.582 2996823.33 2.412157262 1.268848378 1.656074884 1.298065638 1.806980798 1.452496453 2.010422192 1.580277287 1.860951737 1 21.51500261 4.75301756 24.51203038 1.587714606 2.412158015 0.434666419 0.292474107 1821.165912 3087752.995 0.063829298 1.378845099 56626.21842 -4.75301756 0.824443409 AEDGHAVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEDGHAVAK 9 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;; 104.2 0.0032987 528937000 1222780 1238620 1174130 1171510 1444850 1607360 1490350 1310640 1287710 1262240 FALSE TRUE 1271056.299 1451343.35 1204728.792 1403231.181 1199254.913 1234075 1373532.473 1293073.015 1241365.569 1509551.761 0.842009086 0.961439937 0.798070542 0.929568113 0.79444438 0.817510887 0.909894254 0.856594022 0.822340512 1 20.5256888 -1.48030929 5.67926072 1.000155221 0.861193764 0.377953324 0.054169257 9.88E-05 9.04E-06 0.048652783 0.011454809 0.033089539 1.48030929 -0.138961457 AEDKEWMPVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AEDKEWMPVTK 11 1 P15880;E9PQD7;E9PPT0;E9PMM9 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 155.08 2.89E-05 3745090000 7903100 4786940 7005930 4859250 8345500 7500710 8669780 6526240 7566800 4284870 FALSE TRUE 8215120.491 5609059.708 7188510.291 5820395.147 6926934.891 5758783.777 7990219.989 6438766.428 7294472.346 5124408.238 1.603135447 1.094577061 1.40279813 1.135818006 1.351753133 1.123794887 1.559247355 1.25648975 1.42347604 1 22.28895398 -2.172383943 2.542516565 0.128035365 1.317836279 0.252615273 0.168402595 8780338.125 2497697.351 45310553.63 0.036719814 0.00672382 2.172383943 1.189800914 AEDMYSAQSHQAAT(ph)PPKDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AEDMYSAQSHQAATPPKDGK 20 1 A8MXZ4;J9JIE0;A0A0C4DFY5;Q9NQ84;Q9NQ84-2 A8MXZ4 GPRC5C G-protein coupled receptor family C group 5 member C 1 AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK;AEDMYSAQSHQAAT(1)PPKDGK 198.68 2.25E-21 3201660000 3096630 2026311 2238710 2621050 3842990 4237230 4017180 2696700 2665200 1897286 TRUE FALSE 3218887.344 2374314.152 2297052.622 3139485.867 3189759.932 3253197.548 3702302.935 2660555.147 2569279.973 2269022.866 1.4186227 1.046403801 1.012353228 1.383629012 1.405785715 1.433743836 1.631672818 1.172555459 1.132328815 1 21.11363972 5.070064065 19.74216026 1.270412575 5.000489463 0.050227735 0.20171033 1112.250206 323089.2748 0.04889975 5597.83567 117507.0883 -5.070064065 3.730076888 AEDQTES(ph)SCESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.809)S(0.191)CESHR 188.96 3.65E-06 144330000 109350 154600 150220 162020 191560 193470 145960 140570 140670 190510 TRUE FALSE 113667.2224 181151.3474 154134.8566 194067.0724 158998.6996 148539.5246 134519.2738 138685.8891 135607.3142 227836.787 0.498897583 0.795092618 0.676514353 0.851781115 0.69786228 0.651955843 0.590419465 0.608707184 0.59519499 1 17.79764118 -1.118693473 4.419843927 1.000042498 0.666107768 0.519634447 0.097180255 29198624159 5822178651 13130518.27 0.023057373 0.076086311 1.118693473 -0.33393473 AEDQTES(ph)SCESHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDQTESSCESHRK 14 1 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.982)S(0.018)CESHRK 158.45 2.38E-06 551460000 287640 241630 306270 239520 445370 397010 287130 342090 347680 300920 TRUE FALSE 298996.2493 283128.0729 314251.6478 286896.3411 369666.1665 304810.4442 264624.0003 337504.8431 335167.0647 359879.5125 0.830823203 0.786730178 0.873213497 0.797201094 1.027194251 0.846979152 0.735312767 0.937827332 0.931331329 1 18.45715445 -4.999999997 0.09233475 1.472623473 0.747458937 0.285598859 0.076527742 278.5608215 1.779862575 25.44413802 1.674115382 1.00E-05 4.999999997 -0.725164536 AEDQTESS(ph)CESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 AEDQTES(0.38)S(0.62)CESHR 180.64 8.20E-06 191900000 127950 157400 156030 163060 203310 206840 156590 158850 167280 205090 TRUE FALSE 133001.5648 184432.2256 160096.27 195312.7813 168751.4388 158804.5447 144316.0666 156720.8756 161259.6255 245273.4588 0.542258284 0.751945304 0.652725618 0.796306222 0.688013451 0.647459148 0.588388435 0.638963858 0.657468714 1 17.9040316 -1.352527663 3.43969855 1.001987845 0.664084143 0.683513885 0.068866866 16803150.88 24599568.96 337074.7939 0.016296993 0.044409137 1.352527663 -0.337903702 AEDQTESSCESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEDQTESSCESHR 13 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 0 122.78 0.00023103 92644000 20248 42246 35474 42418 31945 53161 34067 35179 34624 44696 FALSE TRUE 21047.40667 49501.42187 36398.48158 50808.15379 26515.00031 40815.16341 31396.73952 34707.48305 33377.889 53453.32544 0.393752989 0.926068144 0.680939516 0.950514367 0.496040239 0.763566403 0.587367376 0.649304468 0.624430542 1 15.70599208 -0.875380061 4.07853354 1.000007965 0.681594252 0.260438093 0.164096704 341264466.8 736568554.8 42149.19407 0.03624817 0.133235495 0.875380061 -0.318413714 AEDS(ph)DS(ph)EPEPEDNVR ddPTM_MDA-MB-175_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 216.01 3.31E-12 430820000 287398 283090 295835 266613 293074 355470 272190 305920 309669 214817 TRUE FALSE 298744.695 331708.5054 303544.7031 319348.2556 243257.3862 272917.4797 250855.0366 301819.6428 298524.0732 256906.2782 1.162854785 1.291165431 1.181538673 1.243053528 0.946872096 1.062323123 0.976445723 1.174823927 1.161996021 1 17.97088262 3.263697943 24.99941603 1.065065166 1.222038742 0.530050219 0.07607216 196.6968377 195616.3933 0.021794419 0.029498105 1835.261454 -3.263697943 0.156973575 AEEAEAQKR ddPTM_MDA-MB-175_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 ;; 142.98 0.0001652 738237000 714222 602078 718225 573321 791143 833430 784526 690118 686285 558909 FALSE TRUE 742420.0361 705480.213 736942.5335 686722.1826 656664.7954 639878.5133 723032.8021 680868.097 661585.7369 668416.5176 1.110714676 1.055449999 1.102519932 1.027386614 0.982418564 0.957305058 1.081709956 1.018628474 0.989780652 1 19.35038786 3.61795283 4.620007872 1.009513849 1.085813551 0.559196853 0.033349356 0.187212236 6.235893661 0.009349528 0.014769205 4149.089758 -3.61795283 0.076299702 AEEAEELRLDLEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEEAEELRLDLEDVK 15 1 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 0 ; 197.88 7.48E-09 115152000 249050 145225 185218 145342 249130 260680 274020 208097 217265 116720 FALSE TRUE 258882.6863 170166.2641 190044.9332 174090.2138 206782.9716 200141.0206 252541.5964 205307.8001 209445.6751 139589.0493 1.854605986 1.219051673 1.361460188 1.247162401 1.481369582 1.433787405 1.809179142 1.470801622 1.500444886 1 17.09082624 3.029151496 24.66866434 1.497428577 1.397242769 0 0.247816381 724.0428122 612696.3747 0.068097626 0.081391226 1069.427864 -3.029151496 -0.100185808 AEEDEILNRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 207.39 4.79E-08 63720770000 19098260 23926160 21437360 29921670 26157210 35358840 24754000 22623940 22060450 29275750 TRUE FALSE 19852274.05 28035291.86 21996035.21 35840087.02 21711016.79 27147285.28 22813716.8 22320703.09 21266498.71 35011772.69 0.567017107 0.800739 0.62824683 1.023658166 0.620106185 0.775375915 0.651601306 0.637519936 0.607409939 1 25.06133677 2.239269335 24.99691069 0.686371006 0.741735442 0 0.158267724 87.58857528 3089434.751 0.05332695 0.042161187 173.4879579 -2.239269335 0.055364436 AEEELDAEVLEVFHPTHEWQALQPGQAVPAGSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEEELDAEVLEVFHPTHEWQALQPGQAVPAGSHVR 35 0 D6R940;D6RG16;D6RBP7;D6RAI3;D6RIU8;D6REA1;Q9H173 D6R940 SIL1 Nucleotide exchange factor SIL1 0 ; 91.407 0.00018882 84047000 18486.6 30103 27243 31247 32138 38541 27295 25286 22865.3 24589 FALSE TRUE 19216.46524 35272.95608 27952.97496 37427.56334 26675.19424 29590.43684 25155.54658 24947.08253 22042.38232 29406.74377 0.653471374 1.199485273 0.950563421 1.272754428 0.907111459 1.006246631 0.855434617 0.848345629 0.749568959 1 14.84385942 2.27707945 2.467384381 0.84594038 1.018545992 0.123005033 0.167776281 0.488175263 6.098576727 0.067454046 0.048780593 189.2689836 -2.27707945 0.172605612 AEEFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 97.071 0.066524 4137010000 4783770 2813340 3654940 2814050 5511420 4967510 5899230 4340950 4887950 2495530 FALSE TRUE 4972636.933 3296509.26 3750190.739 3370660.691 4574590.797 3813881.086 5436832.938 4282766.666 4712033.634 2984481.324 1.666164534 1.104550139 1.256563648 1.129395806 1.53279257 1.277904156 1.821701109 1.435012051 1.578845073 1 21.5090488 3.222113462 24.96399328 1.478943241 1.273652555 0.070247559 0.246142191 448.9326875 681402.1338 0.066761175 0.080011186 1667.682846 -3.222113462 -0.205290686 AEEGKS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEEGKSPFR 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 AEEGKS(1)PFR;AEEGKS(1)PFR 65.563 0.040095 565810000 573750 370630 400730 400370 546790 600460 576360 485730 495370 289030 TRUE FALSE 596402.093 434282.8194 411173.353 479561.991 453846.8311 461012.2651 531183.3972 479219.5838 477541.7305 345659.8947 1.725401478 1.25638764 1.189531558 1.38738106 1.312986661 1.333716385 1.536722673 1.38639047 1.381536411 1 18.3989937 0.773122194 10.7865653 1 1.382886851 0.40349385 0.142023341 1431.736318 68080.3408 0.132437827 0.033121061 5.930921748 -0.773122194 0.382886851 AEEKENDTVTIS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEEKENDTVTISPK 14 1 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 AEEKENDTVTIS(1)PK 168.09 2.15E-06 212310000 685810 180440 280050 143820 468580 473560 368560 281120 343260 132040 TRUE FALSE 712886.3084 211429.1664 287348.3331 172267.1667 388930.939 363582.8669 339671.3041 277352.0462 330906.1397 157910.7099 4.51448992 1.338915938 1.819688691 1.090915029 2.462980118 2.302458567 2.151033988 1.756385278 2.095526895 1 17.2687495 4.745075454 24.89515418 1.833743227 4.514491205 0.746000822 0.477786055 348.5448955 1331857.736 0.111302031 1.065474096 55600.08475 -4.745075454 2.680747978 AEEKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEEKLR 6 1 K7EM46 REV__Q08AD1-2 KIAA1328 0 74.743 0.072525 537470000 318500 238630 279310 235680 370100 363790 363250 310850 303030 230820 FALSE TRUE 331074.6259 279612.8462 286589.0481 282296.8006 307190.5342 279305.2858 334777.5158 306683.5642 292124.0095 276044.7597 1.199351244 1.012925754 1.038197749 1.022648649 1.112828711 1.011811585 1.212765336 1.110992161 1.058248705 1 18.07454269 AEEKS(ph)PISINVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AEEKSPISINVK 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 AEEKS(0.978)PIS(0.022)INVK;AEEKS(0.746)PIS(0.254)INVK;AEEKS(0.998)PIS(0.002)INVK;AEEKS(0.947)PIS(0.053)INVK;AEEKS(0.845)PIS(0.155)INVK;AEEKS(1)PISINVK;AEEKS(0.999)PIS(0.001)INVK;AEEKS(1)PISINVK 190.86 1.61E-05 9404920000 9745370 4181150 6376580 4226770 9091570 8353780 9024430 6563550 7317190 3317147 TRUE FALSE 10130124.73 4899229.988 6542758.913 5062812.49 7546188.179 6413741.198 8317071.596 6475576.348 7053845.761 3967078.444 2.553547875 1.234971795 1.649263811 1.276206801 1.902202915 1.616741713 2.0965231 1.632328788 1.778095861 1 21.91964549 -1.253029695 6.76149553 0.999993542 1.72568449 0.273774327 0.364148025 3.24E-05 3.58E-06 0.322607549 0.076038654 0.055843201 1.253029695 0.725690948 AEELHYPLGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEELHYPLGER 11 0 Q14257;Q14257-2;A8MXP8;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 94.191 0.0086877 141160000 66471 77040 70412 81635 82521 92152 74782 81255 67961 76987 FALSE TRUE 69095.32641 90271.02071 72246.99456 97782.15934 68494.1099 70751.09458 68920.39143 80165.90963 65515.09689 92071.12864 0.750455951 0.980448725 0.784686748 1.062028464 0.743926037 0.768439527 0.748555953 0.870695416 0.711570477 1 16.49046121 AEELS(ph)PAALS(ph)PSLEPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 2 AEELS(1)PAALS(0.953)PS(0.047)LEPIR;AEELS(1)PAALS(0.912)PS(0.088)LEPIR;AEELS(1)PAALS(1)PSLEPIR 229.4 1.64E-15 411148000 666690 719410 704870 680290 836780 859720 775420 752050 747030 794960 TRUE FALSE 693011.436 842963.0713 723239.4913 814849.3315 694544.4345 660063.0592 714640.5542 741969.9999 720144.5362 950717.1916 0.728935421 0.886660175 0.760730423 0.857089089 0.730547886 0.694279082 0.751685738 0.780431874 0.757475033 1 19.85865672 -1.963931619 8.03406703 1.116145848 0.773650531 0.60256202 0.05554034 0.030933034 0.000138872 0.014396856 0.012555781 0.010865967 1.963931619 -0.342495317 AEELS(ph)PAALSPLLEPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(1)PAALSPLLEPIR;AEELS(0.999)PAALS(0.001)PLLEPIR 183.7 7.10E-10 201793000 96551 111939 111865 112146 126163 135575 115181 121295 120196 134000 TRUE FALSE 100362.908 131163.6525 114780.2938 134328.1441 104717.8583 104089.7609 106152.8123 119669.2389 115870.1694 160254.7344 0.626271095 0.81846975 0.716236523 0.838216384 0.653446269 0.6495269 0.662400475 0.74674386 0.723037418 1 17.29000745 0.168301368 1.518235407 1.000133105 0.716205897 0.616195782 0.067529532 7.824659768 13.41132923 0.065322979 0.018357186 1.473334532 -0.168301368 -0.283927208 AEELSPAALS(ph)PLLEPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEELSPAALSPLLEPIR 17 0 A0A5F9ZH52;A5YM69 A0A5F9ZH52;A5YM69 ARHGEF35 Rho guanine nucleotide exchange factor 35 1 AEELS(0.001)PAALS(0.999)PLLEPIR 90.754 0.0039068 7827500 9050.8 10601 15039 13501 14028 15370 15269 13874 13487 14678 TRUE FALSE 9408.132573 12421.63929 15430.92869 16171.4575 11643.52557 11800.55043 14072.17588 13688.04172 13001.6055 17553.87307 0.535957651 0.707629549 0.879061198 0.921247262 0.663302368 0.672247679 0.801656468 0.779773311 0.740668766 1 14.09950176 -5 0.246428921 2.461231853 0.729067388 0.355554985 0.104432636 220.0127595 2.186686403 161.751653 0.162641431 1.00E-05 5 -1.732164465 AEELSPAALS(ph)PSLEPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AEELSPAALSPSLEPIR 17 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AEELSPAALS(0.989)PS(0.011)LEPIR;AEELSPAALS(0.921)PS(0.079)LEPIR;AEELSPAALS(0.983)PS(0.017)LEPIR;AEELSPAALS(0.995)PS(0.005)LEPIR;AEELSPAALS(0.982)PS(0.018)LEPIR;AEELSPAALS(0.985)PS(0.015)LEPIR 352.05 1.08E-87 1291486000 743868 829722 841763 840806 974563 1062906 913490 917324 903233 972926 TRUE FALSE 773236.483 972220.2992 863700.0353 1007114.917 808907.1294 816062.19 841888.2668 905028.7722 870725.8208 1163552.222 0.664548156 0.835562239 0.742295893 0.865551969 0.695204834 0.701354159 0.723550049 0.777815344 0.748334114 1 20.15010453 -1.588504154 2.652587737 1.019950243 0.753680075 0.615358965 0.059135753 14320115.03 13295897.26 1996326.026 0.014428223 0.025792643 1.588504154 -0.266270168 AEENLLMVLGTDMSDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEENLLMVLGTDMSDRR 17 1 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;Q9H9E3-3 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 ; 135.08 2.38E-05 85906000 40491 55412 63450 54294 67511 71168 55500 56156 54771 51760 FALSE TRUE 42089.61595 64928.57995 65103.55912 65033.19115 56035.50433 54640.31056 51149.76498 55403.32067 52799.80241 61901.38099 0.679946316 1.048903577 1.051730318 1.050593543 0.905238355 0.882699379 0.826310563 0.8950256 0.85296647 1 15.91768398 3.018688763 24.27858772 0.88179867 0.971874233 0.067120921 0.11035701 358.7529788 466051.6681 0.031331401 0.037441681 1043.97179 -3.018688763 0.090075564 AEEPGDRPAEEWLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEEPGDRPAEEWLGR 15 1 Q587I9 Q587I9 SFT2D3 Vesicle transport protein SFT2C 0 83.106 0.0081898 0 114900 86855 90911 82387 127990 149570 117860 94517 86667 94077 FALSE TRUE 119436.3407 101771.6706 93280.21534 98682.9027 106234.3055 114834.6343 108621.8252 93250.15421 83547.8716 112509.5869 1.061565898 0.904559988 0.829086817 0.877106613 0.944224474 1.020665326 0.965445063 0.82881963 0.742584467 1 16.77968841 1.708360077 7.353968481 0.840175001 0.937745675 0.161361036 0.08653577 0.199790234 25.04744182 0.04307829 0.022512745 51.09284387 -1.708360077 0.097570674 AEEPGGHAYETPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEEPGGHAYETPR 13 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 0 71.879 0.04107 170520000 86833 95588 92129 101790 98142 121150 107620 99883 92329 91341 FALSE TRUE 90261.23389 112004.4954 94529.95742 121923.7582 81459.8579 93014.74855 99184.46319 98544.23176 89006.09733 109237.5201 0.826284172 1.025329899 0.86536162 1.116134439 0.745713174 0.851490847 0.90797066 0.902109748 0.814794196 1 16.73710894 3.223370996 24.99990192 0.869770824 0.956430207 0.165194002 0.096796547 421.7247395 694095.8221 0.026248929 0.031485997 1672.518755 -3.223370996 0.086659383 AEEPPS(ph)PPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEEPPSPPVPK 11 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK;AEEPPS(1)PPVPK 225.1 6.00E-12 2622000000 2835660 2008180 2560390 2011440 3331350 3422670 3102300 2593660 2832180 1954880 TRUE FALSE 2947614.046 2353069.294 2627115.867 2409296.828 2765088.317 2627806.764 2859133.62 2558896.23 2730250.395 2337901.308 1.2607949 1.006487864 1.123706915 1.030538295 1.182722431 1.124002435 1.222948809 1.094527054 1.167821065 1 21.1567826 3.211662007 24.99983026 1.139582187 1.099626916 0.01685875 0.084479284 715.978578 665436.1312 0.022531779 0.026938173 1628.028512 -3.211662007 -0.039955271 AEEVEYYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEEVEYYYR 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 182.69 0.0001071 589720000 201174 228250 242470 209252 298470 288480 230140 225580 229810 285700 FALSE TRUE 209116.5049 267450.162 248788.9674 250641.421 247736.176 221484.892 212101.0254 222556.4691 221539.183 341677.4449 0.612029 0.782756269 0.728139861 0.733561506 0.725058618 0.648228015 0.620763906 0.651364239 0.648386911 1 18.38227549 -0.93392618 7.350502962 1.000000005 0.684115714 0.759080951 0.053512963 4.52E-09 5.60E-10 0.055202525 0.01301136 0.116432392 0.93392618 -0.315884291 AEEYEFLTPVEEAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEEYEFLTPVEEAPK 15 0 P52565;J3KTF8;J3QQX2;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 149.31 7.86E-06 64977000 216680 132965 170734 137008 221970 212440 229530 172273 195332 129906 FALSE TRUE 225234.6937 155800.7044 175183.4683 164107.7735 184239.6187 163104.0296 211538.8388 169963.9622 188302.0395 155358.5935 1.449772997 1.002845745 1.127607198 1.056316035 1.185899116 1.049855215 1.361616593 1.094010691 1.212047787 1 17.24524252 -2.248546878 2.321301305 0.389652437 1.161663585 0.12388368 0.134414748 5241255.333 952857.4657 16900886.73 0.029489447 0.00564226 2.248546878 0.772011148 AEFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEFAER 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;A0A494C034;A0A2R8Y6A3;A0A494C0I0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2 TPM3;TPM1;TPM4 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain 0 ;;;; 160.17 0.020687 18218020000 7843050 10479830 9489030 9336940 9869910 11194800 9750470 9266710 8863170 10653890 FALSE TRUE 8152699.67 12279659.28 9736321.917 11183758.86 8192226.224 8594977.359 8986202.683 9142504.91 8544186.243 12741315.76 0.639863247 0.963766969 0.764153569 0.877755412 0.642965481 0.674575336 0.705280589 0.717547942 0.670589004 1 23.60301093 5.040194469 15.95728998 0.762910732 0.101034943 0.093631726 0.120763288 6754549.889 74379872.93 0.027902128 130019357.1 109696.9289 -5.040194469 -0.661875789 AEFEDQDDEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEFEDQDDEAR 11 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 218.11 0.00077497 0 104970 103380 102520 99382 121700 121280 109800 108440 100120 104580 FALSE TRUE 109114.2967 121134.7108 105191.7554 119039.463 101013.4775 93114.55802 101193.5891 106986.5392 96516.70076 125070.4487 0.872422685 0.968531832 0.841060031 0.951779291 0.807652635 0.744496873 0.809092717 0.855410213 0.771698685 1 16.93238143 3.22580804 24.96994147 0.820987027 0.907926672 0.203720267 0.072909322 295.7283298 579044.2215 0.019642916 0.02362378 1681.930476 -3.22580804 0.086939645 AEFEVHEVYAVDVLVSSGEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEFEVHEVYAVDVLVSSGEGK 21 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;; 169.39 9.57E-12 107774000 141450 116964 137844 115600 159876 169932 167376 139148 156122 103402 FALSE TRUE 147034.5552 137051.6571 141436.3279 138465.335 132700.3346 130467.8683 154256.6318 137282.9487 150503.1997 123661.6421 1.189006976 1.108279453 1.143736452 1.119711275 1.073092127 1.055039106 1.24740889 1.110149811 1.217056454 1 16.91603854 AEFFQHLIEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEFFQHLIEDR 11 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 ;;; 184.1 5.06E-06 414865000 481171 518685 555891 560104 580502 656505 578014 522251 531257 485534 FALSE TRUE 500168.0026 607765.1139 570377.9761 670890.8995 481828.4774 504041.6632 532707.7523 515251.0796 512137.1643 580665.0912 0.861370884 1.046670659 0.98228391 1.155383559 0.82978723 0.868041959 0.91740964 0.887346402 0.881983732 1 19.14734678 3.20980319 24.99995476 0.891646795 1.011863209 0.332420065 0.078887527 220.651957 191820.7618 0.021729219 0.025975677 1621.075304 -3.20980319 0.120216414 AEFTS(ph)PPSLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEFTSPPSLFK 11 0 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 AEFT(0.007)S(0.85)PPS(0.144)LFK;AEFTS(0.988)PPS(0.011)LFK 162.22 0.0010743 50020000 730750 550190 660310 508830 821140 798540 756220 667770 708610 517960 TRUE FALSE 759600.5743 644680.8526 677518.2211 609475.0553 681562.9161 613091.187 696945.5004 658819.6354 683107.2645 619444.3451 1.226261213 1.040740557 1.093751564 0.983906077 1.100281117 0.989743779 1.125113993 1.063565501 1.102774236 1 19.24061514 4.74251128 24.43996376 1.059232285 1.226261303 0.526447862 0.048461082 212.6306902 1315323.258 0.010539393 0.079651367 55272.77644 -4.74251128 0.167029018 AEGDVAALNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEGDVAALNR 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 134.66 0.00038345 286660000 133670 122350 125040 159300 192040 240710 216680 178750 191630 129420 FALSE TRUE 138947.3948 143362.6607 128298.6451 190809.0645 159397.1094 184808.7505 199696.0554 176354.1486 184733.2737 154777.3711 0.89772422 0.92625078 0.82892379 1.232796908 1.029847634 1.194029522 1.290214803 1.139405246 1.193541875 1 17.23983504 3.73980895 24.99998692 1.163354635 0.888494706 0.676425238 0.085387235 60.08127407 1203219.451 0.021436561 0.036139994 5492.991791 -3.73980895 -0.27485993 AEGDVAALNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEGDVAALNRR 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;; 185.96 6.80E-06 3744830000 2916020 3630830 3415320 2855660 4218820 4063180 2812560 3319870 3372360 4514380 FALSE TRUE 3031146.721 4254396.809 3504326.045 3420501.025 3501706.483 3119568.023 2592104.198 3275372.573 3250989.422 5398886.328 0.561439256 0.788013777 0.649083132 0.633556778 0.648597928 0.577816948 0.480118313 0.606675595 0.602159265 1 22.36423041 -1.485498084 5.657224667 1.000471703 0.616008833 0.705707731 0.074317697 0.000463452 4.21E-05 0.075425386 0.017756797 0.032696549 1.485498084 -0.38446287 AEGEPQEES(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 150.34 7.14E-05 285300000 295750 155220 198370 154160 271100 304190 303890 222270 251960 118340 TRUE FALSE 307426.4384 181877.8276 203539.6852 184652.3879 225018.5188 233546.4825 280070.3077 219290.8342 242892.0088 141526.4572 2.172218851 1.285115385 1.438174099 1.304719919 1.5899396 1.650196628 1.978925447 1.549468831 1.716230403 1 17.11071225 3.007965696 24.80242718 1.638333047 1.513664629 0 0.327545873 742.8998768 2313111.346 0.090052554 0.107446146 1018.510935 -3.007965696 -0.124668418 AEGEPQEES(ph)PLKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(1)PLKSK;AEGEPQEES(1)PLKSK 217.35 3.51E-12 1050120000 1455970 574000 839860 491100 1280090 1183140 1104560 807800 990870 466080 TRUE FALSE 1513452.82 672580.0349 861747.4416 588238.1142 1062500.759 908373.6657 1017981.701 796972.7623 955208.7823 557399.4524 2.715203277 1.20663921 1.546014152 1.055325964 1.906174745 1.629663721 1.826305528 1.429805428 1.713688053 1 19.08835206 -2.556923004 0.338277939 2.86E-19 1.665460256 0.179200061 0.42932757 105.9495377 4.046930089 78.66100181 0.333107125 0.002773812 2.556923004 1.665460256 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 299.63 2.96E-55 3744764000 1715294 627954 991694 600844 1383348 1456717 1381231 969573 1131109 456890 TRUE FALSE 1783015.132 735800.2147 1017538.36 719689.1499 1148207.001 1118416.554 1272966.505 956577.4598 1090400.608 546408.8478 3.263152013 1.346611091 1.862228923 1.317125725 2.101369708 2.046849274 2.329695996 1.750662464 1.995576412 1 19.05962132 -0.676495723 6.357181733 0.999999996 1.960699992 0.247009316 0.520199066 2.77E-08 5.44E-09 0.464417403 0.109464231 0.210622264 0.676495723 0.960699995 AEGFVDALHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;;; 169.37 4.65E-06 3607460000 2251288 2390240 2345818 2215260 2830240 2866470 2496549 2377710 2443335 2623280 FALSE TRUE 2340170.589 2800745.127 2406951.944 2653431.816 2349156.816 2200775.784 2300862.966 2345840.687 2355399.851 3137261.49 0.745927809 0.892735634 0.767214321 0.845779615 0.748792163 0.701495808 0.73339853 0.747735149 0.750782126 1 21.58107435 AEGLEEADTGASGCHSHPEEQPT(ph)SISPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.467)S(0.467)IS(0.052)PS(0.014)R 170.01 5.27E-12 123150000 20126 30250 34953 36004 33849 41828 27495 32842 33547 32002 TRUE FALSE 20920.59002 35445.20219 35863.90389 43125.48374 28095.35907 32114.08091 25339.87006 32401.80671 32339.65002 38272.17918 0.54662657 0.926134935 0.937075041 1.126810249 0.734093529 0.839097266 0.662096348 0.84661515 0.84499108 1 15.22400843 AEGLEEADTGASGCHSHPEEQPTS(ph)ISPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.148)S(0.63)IS(0.21)PS(0.012)R 154.43 2.93E-08 227510000 53863 40513 40547 47477 55771 64291 53874 47071 47213 39193 TRUE FALSE 55989.55283 47470.7926 41603.68813 56867.8089 46291.06534 49360.38959 49651.21511 46440.09024 45513.81335 46872.11795 1.194517237 1.012772511 0.88759992 1.213254518 0.987603449 1.053086392 1.059291051 0.990782842 0.971021053 1 15.51644237 1.683774039 4.793414689 0.984196056 1.053059283 0.115637755 0.089134664 0.374072803 19.91495141 0.046676348 0.02260805 48.28075341 -1.683774039 0.068863227 AEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AEGLEEADTGASGCHSHPEEQPTSISPSR 29 0 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AEGLEEADTGASGCHSHPEEQPT(0.002)S(0.008)IS(0.876)PS(0.115)R;AEGLEEADTGASGCHSHPEEQPT(0.241)S(0.087)IS(0.584)PS(0.087)R;AEGLEEADTGASGCHSHPEEQPT(0.001)S(0.011)IS(0.986)PS(0.003)R;AEGLEEADTGASGCHSHPEEQPT(0.003)S(0.314)IS(0.64)PS(0.043)R;AEGLEEADTGASGCHSHPEEQPTSIS(0.962)PS(0.038)R;AEGLEEADTGASGCHSHPEEQPT(0.006)S(0.049)IS(0.852)PS(0.093)R;AEGLEEADTGASGCHSHPEEQPT(0.019)S(0.308)IS(0.66)PS(0.013)R 339.56 2.55E-105 7371170000 1133909 2011916 1867959 2037519 2029271 2445064 2101436 2222640 1949494 1920797 TRUE FALSE 1178676.603 2357446.922 1916639.546 2440534.177 1684336.24 1877234.941 1936719.955 2192849.146 1879332.092 2297140.396 0.513106036 1.026252869 0.834358905 1.062422733 0.733231736 0.817205141 0.843100386 0.954599532 0.818118081 1 21.1314076 4.751379344 24.78688582 0.893124589 0.513105764 0.561113566 0.102224179 1353.422631 2616988.306 0.02309686 0.422166103 56413.01922 -4.751379344 -0.380018825 AEGPLDS(ph)PSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_MDA-MB-175_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(0.669)PS(0.027)EGHS(0.302)YQNS(0.002)GLDHFQNSNIDQSFWETFGSAEPTK 140.03 4.63E-13 975210000 16813 21825 22987 22579 37657 32173 28872 29130 28246 21902 TRUE FALSE 17476.79022 25573.27398 23586.0601 27045.05881 31256.07659 24701.30834 26608.9372 28739.56 27229.43198 26193.27756 0.667224259 0.976329668 0.900462344 1.032519078 1.193286198 0.943039995 1.015868943 1.097211295 1.039558028 1 14.67690897 5.283348142 0.983276976 1.048155011 1.29E-14 0.687687296 0.073362029 2.794120213 1.021757487 0.022086219 4.000777844 192020.7413 -5.283348142 -1.048155011 AEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTK ddPTM_MDA-MB-175_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 75.298 0.00082101 77310000 20528 21039 28891 29006 33348 36047 32840 38714 29000 25915 FALSE TRUE 21338.46129 24652.28459 29643.92319 34743.30023 27679.51887 27675.63055 30265.91499 38195.10215 27956.29566 30992.54808 0.688502967 0.795426195 0.956485511 1.121021096 0.893102394 0.892976934 0.976554587 1.232396319 0.902032824 1 14.91963375 4.306357818 2.481755958 1.016426908 0.70014345 0.511726774 0.102013648 0.243645244 2.868285556 0.028690859 0.1104234 20246.86645 -4.306357818 -0.316283458 AEGS(ph)PNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEGSPNQGK 9 0 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGK;AEGS(1)PNQGK 110.93 0.0023149 108606000 283000 206341 236130 186228 320020 322380 306530 229565 270820 188051 TRUE FALSE 294173.0585 241778.4616 242283.7418 223063.3426 265623.1147 247512.1307 282503.3776 226488.0567 261073.2411 224895.993 1.308040462 1.075067894 1.077314622 0.99185112 1.181093141 1.100562653 1.256151227 1.007079111 1.160862128 1 17.77889843 -5 0.244191587 0.302786368 1.131260138 0.135273017 0.096151776 379.5432885 3.777504951 131.772442 0.140453455 1.00E-05 5 0.82847377 AEGS(ph)PNQGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEGSPNQGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(1)PNQGKK 111.83 0.001042 354590000 433180 198550 289920 179350 410010 400500 384940 283580 376580 202190 TRUE FALSE 450282.2809 232649.418 297475.5534 214824.8947 340316.6467 307489.9446 354767.3969 279779.0739 363026.9594 241805.2593 1.862169095 0.962135475 1.230227805 0.888421101 1.407399688 1.271642914 1.467161624 1.157042964 1.501319534 1 17.8834861 AEGS(ph)PSEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEGSPSEGKK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 AEGS(0.997)PS(0.003)EGKK 79.492 0.016442 82207000 113200 63192 77811 56918 95829 81740 89577 61519 83210 44610 TRUE FALSE 117669.2234 74044.73443 79838.81858 68176.21052 79540.02081 62757.12378 82555.72067 60694.43843 80215.28835 53350.47539 2.205589033 1.387892683 1.496496854 1.277893215 1.490896196 1.176317986 1.5474224 1.137655063 1.503553394 1 15.70321351 6.937218584 1.212503307 1.321068732 199.9796515 0.68893499 0.175301338 175.0994366 1.497925939 0.043492875 95424.39132 8654033.744 -6.937218584 198.6585828 AEGTNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEGTNFR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 106.43 0.017923 319860000 283640 309000 300230 305400 320130 397070 306720 310850 282130 305040 FALSE TRUE 294838.3262 362068.3463 308054.2404 365807.2085 265714.4169 304856.5102 282678.4849 306683.5642 271976.1964 364806.7477 0.808204147 0.992493556 0.844431312 1.002742441 0.728370346 0.835665766 0.774871865 0.840674045 0.745534994 1 18.47677289 3.236580164 24.99996156 0.812500451 0.912895651 0.196949956 0.089174328 72.155591 910850.2703 0.022886005 0.028690317 1724.170316 -3.236580164 0.1003952 AEGTTYRDELLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEGTTYRDELLTK 13 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ;; 90.689 0.0062707 690330000 377430 367234 379833 364811 453470 478570 493990 383787 384570 397961 FALSE TRUE 392331.2278 430303.5828 389731.76 436969.5269 376389.3314 367429.3703 455269.773 378642.963 370729.4008 475933.8385 0.824339847 0.904124792 0.818878021 0.918130823 0.790843813 0.772017748 0.956582063 0.795578991 0.778951549 1 18.86040151 -1.180676976 4.42548195 1.000037429 0.841837742 0.381876903 0.061048876 2.14E-05 3.97E-06 0.056208973 0.01324545 0.065966437 1.180676976 -0.158199687 AEGYEVAHGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEGYEVAHGGR 11 0 H0YDU8;P53041;A8MU39 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ;;; 114.86 0.0012005 1998530000 916280 1154300 1051480 1025190 1159530 1238770 1032600 1058780 960260 1204840 FALSE TRUE 952455.4419 1352542.046 1078882.433 1227969.522 962433.5048 951084.4412 951662.1138 1044588.786 925700.4302 1440905.33 0.661011811 0.938675163 0.748753169 0.85222082 0.667936668 0.660060326 0.660461235 0.7249531 0.642443616 1 20.45854412 5.038900625 16.91296848 0.750506886 0.253961167 0.051226596 0.119766532 1041562.713 11843159.27 0.027562139 16079536.03 109370.6076 -5.038900625 -0.496545719 AEHDQLLLNYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEHDQLLLNYAK 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 113.99 0.0011064 185140000 212420 411430 350540 377700 371360 468880 328420 394370 333100 599710 FALSE TRUE 220806.5056 482089.902 359675.3604 452407.9327 308236.3598 359989.7259 302677.5822 389084.1152 321111.7961 717211.6924 0.307867967 0.672172396 0.501491211 0.630787169 0.429770405 0.501929528 0.422019866 0.542495499 0.447722478 1 19.45203948 -1.392773666 2.983478731 1.007657678 0.502616354 0.696984083 0.099755549 18651663.13 22720888.79 1227057.464 0.021900358 0.040478679 1.392773666 -0.505041324 AEHDSILAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEHDSILAEK 10 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RBR8 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 69.01 0.05826 279040000 88695 524100 705960 555670 1080500 770040 1128600 830890 876650 393100 FALSE TRUE 92196.74709 614110.0981 724357.8976 665579.8675 896836.9959 591209.8801 1040137.383 819753.2786 845099.5377 470120.4186 0.196113046 1.306282547 1.54079225 1.415764645 1.907675056 1.25757116 2.212491399 1.743709156 1.797623554 1 18.84267082 4.682134367 2.154873427 1.667500802 1.57E-15 0.622200569 0.327461756 0.345870619 1.999784045 0.078465374 1.061088189 48098.81388 -4.682134367 -1.667500802 AEHIPAGK ddPTM_MDA-MB-175_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 ; 61.999 0.082414 248150000 630980 551230 615030 545250 786200 865520 778320 672480 691210 558650 FALSE TRUE 655891.5776 645899.4645 631058.1871 653098.8226 652562.0048 664516.0971 717313.2446 663466.5056 666333.4871 668106.7715 0.981716704 0.966760841 0.944546911 0.977536601 0.97673311 0.994625598 1.073650613 0.993054604 0.997345807 1 19.34971916 2.645411775 3.403095844 1.016614612 0.967942969 0.460723039 0.023435641 0.217418955 4.789975429 0.008027745 0.007578587 441.9893192 -2.645411775 -0.048671643 AEHLES(ph)PQLGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEHLESPQLGGK 12 0 Q9NYD6;D6RAG4 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 AEHLES(1)PQLGGK 139.6 3.80E-05 164970000 356430 280130 343870 267390 384480 440290 419110 336290 372160 301720 TRUE FALSE 370502.1316 328240.1484 352831.5347 320278.9439 319126.2269 338039.3202 386259.0631 331782.5826 358766.0343 360836.2572 1.026787426 0.909665096 0.977816191 0.88760189 0.884407319 0.936821933 1.070455242 0.919482386 0.994262708 1 18.46098478 2.433438043 24.99981566 0.987113269 0.932757035 0.222961389 0.052458522 220.8775465 126406.6276 0.017919483 0.014992523 271.2926598 -2.433438043 -0.054356234 AEHSVDIDVDIDWPIAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEHSVDIDVDIDWPIAEQR 19 0 Q8NFW8;Q8NFW8-2 Q8NFW8 CMAS N-acylneuraminate cytidylyltransferase 0 143.71 1.42E-07 27603000 19599 21933 23636 22362 24186 23701 24434 24995 21939 21620 FALSE TRUE 20372.78365 25699.82213 24251.97358 26785.13686 20074.87236 18196.80194 22518.79923 24659.98291 21149.41968 25856.02506 0.787931772 0.993958742 0.937962178 1.035934054 0.776409843 0.703774145 0.870930438 0.953742226 0.817968718 1 14.65821288 6.697931857 10.75024684 0.888807609 0.402367337 0 0.106809968 0 0 0.024054191 0 4988062.156 -6.697931857 -0.486440272 AEITFDDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;;; 205.09 1.55E-05 4817440000 5097140 3580260 4056170 3638410 5185090 4611790 5229710 4231730 4281950 3124877 FALSE TRUE 5298379.023 4195141.804 4161877.122 4358076.638 4303730.254 3540771.665 4819791.665 4175010.581 4127843.456 3737136.819 1.417764262 1.122555049 1.113653935 1.16615389 1.151611638 0.947455723 1.289701688 1.117168245 1.104547052 1 21.83350195 4.738552368 10.14943162 1.121869715 1.418421216 0.519994829 0.087564484 0.055748229 204.8068724 0.019574997 0.113382274 54771.21408 -4.738552368 0.2965515 AEKDEPGAWEETFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEKDEPGAWEETFK 14 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 206.95 9.23E-09 677220000 1102310 606216 809180 638396 1228340 1046100 1015100 730840 866580 436384 FALSE TRUE 1145830.05 710328.8823 830267.8955 764668.8234 1019547.206 803159.1288 935533.8095 721044.2852 835391.9551 521885.0897 2.195560043 1.361082921 1.590901737 1.465205346 1.953585618 1.538957799 1.792604978 1.381615033 1.600720104 1 18.99337266 -2.595476355 0.227140291 4.03E-16 1.738826862 0.422362087 0.240596726 43.34759832 1.148838888 21.78214587 0.433080778 0.002538187 2.595476355 1.738826862 AEKDNAEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AEKDNAEIR 9 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;; 106.37 0.0026882 3167260000 8287790 6004770 7691830 6550070 9691200 9085570 9693480 7694760 8340600 5168430 FALSE TRUE 8614998.349 7036042.537 7892285.409 7845654.296 8043893.286 6975584.061 8933679.708 7591624.328 8040423.435 6181084.903 1.393768001 1.138318377 1.276844685 1.269300522 1.301372399 1.128537169 1.445325513 1.228202564 1.300811033 1 22.55942865 -1.252949345 3.257613182 0.99901755 1.272230796 0.440150262 0.093245853 7963560.996 11689099.04 79987.99945 0.020953326 0.055853534 1.252949345 0.273213245 AEKEEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEKEEENR 8 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 93.111 0.010306 689570000 1733800 1280440 1596600 1224320 1999630 1969250 1947090 1588130 1879640 1242070 FALSE TRUE 1802251.763 1500345.61 1638208.708 1466486.842 1659733.607 1511921.532 1794471.998 1566843.715 1811992.124 1485429.836 1.213286363 1.010041386 1.102851625 0.987247466 1.117342312 1.017834364 1.20804898 1.054808297 1.219843631 1 20.50244903 2.267950629 24.99885286 1.120653655 1.071058824 0.06353902 0.085633798 549.494615 467393.0173 0.027150883 0.022712373 185.3320926 -2.267950629 -0.049594831 AEKEEENRR ddPTM_MDA-MB-175_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 ;; 88.496 0.0071683 568371000 892310 641270 876620 662270 1082730 1050150 1015630 857110 923620 677990 FALSE TRUE 927539.0878 751403.1341 899465.4374 793265.0293 898687.9413 806268.5777 936022.2667 845621.8424 890379.0966 810829.1596 1.143938987 0.92670956 1.109315602 0.978338063 1.108356712 0.99437541 1.154401338 1.042910004 1.098109369 1 19.62903845 AEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEKPPLSASSPQQRPPEPETGESAGTSR 28 2 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AEKPPLSAS(0.17)S(0.829)PQQRPPEPETGESAGTSR;AEKPPLS(0.001)AS(0.417)S(0.583)PQQRPPEPETGESAGTSR 136.12 4.63E-06 420920000 271290 252778 285340 235996 311030 361940 310500 318730 335580 278330 TRUE FALSE 282000.7387 296190.6552 292776.1948 282675.3044 258161.2317 277884.9203 286162.1987 314457.9457 323502.5414 332863.4346 0.847196506 0.88982635 0.879568509 0.84922306 0.775577023 0.83483162 0.85969851 0.944705585 0.971877676 1 18.34457087 1.631629353 2.237060505 0.985817979 0.845916626 0.798573124 0.029165201 0.13227157 1.453725969 0.023904335 0.009172543 42.81829333 -1.631629353 -0.139901354 AELAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AELAESR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;; 135.87 0.010169 2346224000 1118410 2027420 1849330 1880390 2104800 2556890 1868750 2068860 1727780 2047690 FALSE TRUE 1162565.69 2375613.614 1897525.059 2252325.53 1747026.848 1963091.048 1722272.492 2041130.316 1665597.535 2448895.65 0.474730596 0.970075476 0.774849291 0.919731116 0.713393749 0.801622988 0.703285373 0.833490114 0.680142306 1 21.22369987 -1.606381259 2.617593708 1.020880188 0.775896915 0.222158634 0.130928485 26070817.71 23588033.02 3730287.113 0.030928929 0.024752481 1.606381259 -0.244983273 AELDELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AELDELRR 8 1 O00291-3;O00291-4;O00291 O00291-3 HIP1 Huntingtin-interacting protein 1 0 103.8 0.0075398 34838000 56737 63139 68402 66874 79771 82330 77148 68160 71737 72645 FALSE TRUE 58977.02057 73982.6321 70184.61231 80101.4776 66211.55391 63210.10522 71100.93817 67246.42669 69155.19938 86878.39688 0.678845636 0.851565346 0.807848842 0.921995346 0.762117584 0.727569885 0.818396065 0.774029323 0.795999948 1 16.40670986 -2.072906168 2.208740949 1.295860266 0.795801892 0.492387184 0.062954798 4103182.76 1237973.784 6112726.564 0.015247994 0.008454615 2.072906168 -0.500058374 AELELELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AELELELGR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 157.91 0.00015683 219231000 356921 373313 379950 361219 443283 490129 430330 380848 381440 376222 FALSE TRUE 371012.5167 437426.6038 389851.8091 432667.0401 367933.914 376303.9677 396599.6101 375743.3555 367712.0489 449935.4977 0.824590455 0.972198473 0.866461551 0.961620148 0.817748135 0.836350921 0.881458814 0.835104937 0.817255031 1 18.77935867 3.227554761 24.99706031 0.855002506 0.908090858 0.080239843 0.064000987 399.2035795 906689.7344 0.016862711 0.02033573 1688.708778 -3.227554761 0.053088352 AELEQHLEQEQEFQVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AELEQHLEQEQEFQVNK 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 284.25 3.56E-36 802370000 528837 429194 493418 442891 615810 639430 596494 541679 600914 449183 FALSE TRUE 549715.8931 502904.7308 506276.8784 530493.5179 511134.8362 490932.0732 549739.2416 534418.679 579287.2225 537191.8087 1.02331399 0.936173491 0.942450853 0.987530914 0.951494099 0.913886 1.023357454 0.994837729 1.07836198 1 19.03507778 2.210399101 24.90344682 1.020603228 0.958281698 0.451061567 0.035033084 193.2420417 170884.2388 0.012759124 0.009425259 162.3301168 -2.210399101 -0.06232153 AELESDPPY(ph)MEMKGKLSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AELESDPPYMEMKGKLSAK 19 2 Q1MSJ5-1;Q1MSJ5;E5RI67;F2Z2M5 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 AELES(0.184)DPPY(0.764)MEMKGKLS(0.052)AK 41.348 0.068186 1790500000 1181200 781280 1315500 839370 1651700 1422400 1713100 869740 1487100 708380 TRUE FALSE 1227834.688 915458.7625 1349783.011 1005394.881 1370944.624 1092069.157 1578822.746 858082.5579 1433579.561 847173.4982 1.449330852 1.080603636 1.593278134 1.186763848 1.618257213 1.289073795 1.863635665 1.012877008 1.692191227 1 19.69229793 -1.410460243 3.155558428 0.994483194 1.401490466 0.182867352 0.263984462 156738076.1 200043466.2 7810054.027 0.057293587 0.038863307 1.410460243 0.407007272 AELGMGDSTSQS(ph)PPIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 AELGMGDSTSQSPPIKR 17 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 AELGMGDS(0.003)T(0.003)S(0.108)QS(0.887)PPIKR;AELGMGDS(0.004)T(0.019)S(0.08)QS(0.897)PPIKR;AELGMGDSTS(0.014)QS(0.986)PPIKR;AELGMGDSTS(0.029)QS(0.971)PPIKR;AELGMGDS(0.029)T(0.029)S(0.196)QS(0.746)PPIKR;AELGMGDSTS(0.004)QS(0.996)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTSQS(1)PPIKR;AELGMGDSTS(0.006)QS(0.994)PPIKR 314.9 1.86E-58 12989390000 4920960 3792980 4802100 3842240 5748440 5651150 5400770 4583510 5176320 3702720 TRUE FALSE 5115243.301 4444394.81 4927246.671 4602223.604 4771322.222 4338756.057 4977443.535 4522075.546 4990025.254 4428197.091 1.155152581 1.003657859 1.112698141 1.039299631 1.077486418 0.97980193 1.124033875 1.021200153 1.126875148 1 22.078288 4.76005757 23.71382014 1.055985202 1.155152787 0.257467678 0.051477627 3500.173606 3861001.691 0.010870369 0.472561923 57551.62221 -4.76005757 0.099167585 AELGSWSS(ph)QEHLEWEPACQTPQPSAR ddPTM_MDA-MB-175_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(0.002)WS(0.121)S(0.877)QEHLEWEPACQTPQPSAR;AELGS(0.028)WS(0.151)S(0.821)QEHLEWEPACQTPQPSAR 214.92 2.78E-34 428390000 121920 158279 152009 155294 136835 190998 160287 158914 153241 172458 TRUE FALSE 126733.4957 185462.187 155970.4794 186010.6897 113575.8356 146641.6091 147723.2861 156784.0178 147725.8863 206247.8432 0.61447186 0.899220007 0.756228414 0.901879442 0.550676477 0.710997055 0.716241604 0.760172884 0.716254212 1 17.65401951 -1.687013718 4.795781389 1.008174514 0.740895052 0.370913064 0.102890376 0.008748817 0.000570973 0.096919758 0.022326175 0.020558257 1.687013718 -0.267279461 AELKLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AELKLSR 7 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 AELKLS(1)R 62.463 0.051662 139170000 103380 63729 85508 68603 127150 121740 114600 99141 107610 83744 TRUE FALSE 107461.5222 74673.96001 87736.40873 82172.46864 105537.0884 93467.72999 105617.3525 97812.17706 103737.1371 100152.0334 1.072983928 0.74560603 0.876032225 0.820477287 1.053768803 0.933258435 1.054570226 0.976636956 1.035796614 1 16.61183219 3.238504362 24.9999987 1.00539997 0.869066899 0.361868149 0.084247446 1.48706817 660868.3724 0.022137018 0.028128432 1731.826426 -3.238504362 -0.136333071 AELMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AELMER 6 0 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 108.24 0.07115 202140000 190860 239550 254560 245420 263110 271650 233430 247150 225820 224130 FALSE TRUE 198395.3002 280690.8491 261194.0427 293963.3435 218386.6562 208563.4044 215133.1466 243837.3585 217692.7823 268043.9823 0.740159501 1.047182058 0.974444718 1.096698165 0.814741873 0.778093963 0.802603904 0.909691598 0.812153216 1 18.03211022 3.204536734 24.99969476 0.84582189 0.971220229 0.209449087 0.105507856 250.7224015 184222.3269 0.029469338 0.035224257 1601.536107 -3.204536734 0.12539834 AELNEFLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AELNEFLTR 9 0 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;H0YEU2;H0YF32;E9PQ96;E9PJH4;E9PK82;E9PQX2;H0YES8 P23396 RPS3 40S ribosomal protein S3 0 ;;;; 164.34 0.00014501 1665220000 1364360 1881040 1660250 1693230 1938650 2025440 1704860 1658630 1522600 1967630 FALSE TRUE 1418225.986 2204093.988 1703517.479 2028145.84 1609118.965 1555062.256 1571228.618 1636398.778 1467801.923 2353149.426 0.602692702 0.936657045 0.723930856 0.8618857 0.683815039 0.66084297 0.667713066 0.695407933 0.623760611 1 21.1661615 3.211551919 24.98926843 0.699797759 0.788291958 0.031315463 0.128351995 480.8019571 444851.2453 0.033757867 0.040358174 1627.615882 -3.211551919 0.088494199 AELNSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AELNSDKK 8 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 ; 107.79 0.0063107 821140000 1240480 547230 921070 571140 1084410 901150 986860 754010 863760 486910 FALSE TRUE 1289455.108 641212.4956 945073.8409 684109.7873 900082.3755 691871.5696 909507.3345 743903.7293 832673.4463 582310.692 2.214376493 1.10115185 1.622971815 1.17481921 1.545708138 1.18814849 1.561893585 1.277503126 1.429947033 1 19.15142958 4.748749122 24.74994562 1.346313989 2.214377046 0.634788989 0.202229147 719.9138326 1748776.597 0.041776596 0.576922514 56072.39702 -4.748749122 0.868063057 AELPGSS(ph)SPLLAQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 AELPGS(0.173)S(0.414)S(0.414)PLLAQPR 164.66 1.54E-06 118350000 179220 191060 176250 191240 188650 232980 192880 186050 150950 200720 TRUE FALSE 186295.744 223873.0688 180843.2198 229066.7012 156583.3404 178873.9258 177761.5616 183556.3041 145517.339 240047.241 0.776079505 0.932620878 0.753365125 0.954256755 0.652302187 0.745161349 0.74052741 0.764667418 0.606202922 1 17.87295883 3.234373003 24.99982754 0.740645687 0.852496623 0.162882 0.112331312 166.1461532 991883.5458 0.029256835 0.036167516 1715.430009 -3.234373003 0.111850937 AELRDDPIISTHLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AELRDDPIISTHLAK 15 1 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ;; 159.14 1.07E-06 1583990000 1767250 2664040 3065270 2652320 3591260 3835230 3175800 3327360 3186020 2975860 FALSE TRUE 1837022.395 3121568.147 3145153.454 3176940.98 2980818.908 2944555.956 2926872.498 3282762.182 3071355.763 3558922.791 0.516173714 0.877110387 0.883737479 0.892669262 0.837562117 0.827372812 0.822404045 0.922403315 0.863001516 1 21.7630092 4.738740634 24.49105704 0.875286443 0.516173585 0.82783163 0.049816352 4.032503014 548053.8815 0.011233801 0.06518102 54794.96245 -4.738740634 -0.359112859 AELSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AELSYR 6 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 158.53 0.021857 2738280000 1702090 2061690 1844700 1773190 2504790 2295180 1933120 1801260 1704790 2414610 FALSE TRUE 1769289.827 2415769.22 1892774.397 2123921.69 2079026.69 1762159.229 1781597.003 1777117.056 1643434.941 2887706.599 0.612697228 0.836570177 0.655459387 0.73550467 0.719957731 0.610227933 0.616959148 0.615407762 0.569114238 1 21.46149274 -1.135852348 5.053946157 1.000014381 0.664927024 0.64034347 0.075639737 1.26E-05 2.15E-06 0.075252644 0.017736457 0.07313877 1.135852348 -0.335087357 AEMDMVAWGVDLASVEQHINSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEMDMVAWGVDLASVEQHINSHR 23 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 47.808 0.088072 23293000 5106.5 9477.7 10694 9670.8 9063 10360 7460.5 8990.6 8936.4 7640.2 FALSE TRUE 5308.108563 11105.42125 10972.69443 11583.65538 7522.474497 7954.047007 6875.726516 8870.095713 8614.78071 9137.15091 0.580936948 1.215414012 1.20088795 1.267753536 0.823284476 0.870517198 0.752502239 0.970772596 0.942830079 1 13.15752867 3.215028863 24.9990908 0.886632787 1.086520065 0.161202233 0.190658633 368.8586328 391858.0932 0.054717442 0.065433949 1640.698809 -3.215028863 0.199887277 AEMDQILHGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEMDQILHGLDK 12 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ; 115.78 0.0009127 345630000 383080 296593 372860 314893 477230 454700 397770 361820 409360 282032 FALSE TRUE 398204.2942 347530.5406 382577.0379 377177.8955 396110.6151 349102.816 366591.748 356970.3947 394627.2136 337290.7706 1.180596473 1.03035888 1.134264769 1.118257386 1.174389131 1.035020364 1.086871566 1.058346169 1.169991141 1 18.36363332 2.72845139 24.98955558 1.073714474 1.122026721 0.204369744 0.055989963 1294.817224 3200726.586 0.017165317 0.01633803 535.1202548 -2.72845139 0.048312247 AEMELGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEMELGLR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 123.69 0.00311 55498000 58577 84465 72489 81832 75970 96810 74650 75684 66302 80653 FALSE TRUE 60889.66519 98971.2067 74378.12289 98018.12536 63056.64654 74327.34467 68798.73794 74669.57977 63915.80397 96455.41116 0.631272673 1.026082472 0.771114052 1.016201416 0.653738819 0.770587609 0.713269863 0.774135726 0.66264612 1 16.55757456 3.221338324 24.99994403 0.749953034 0.866514958 0.103356985 0.139308138 441.3901913 640722.2024 0.036473983 0.043693901 1664.708988 -3.221338324 0.116561924 AENGERS(ph)DLEEDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER 201.96 3.72E-09 942230000 448240 572300 589520 565490 563570 750970 704410 608560 590070 460670 TRUE FALSE 465936.8613 670588.0731 604883.3755 677342.2342 467774.5727 576568.5986 649196.5036 600403.2486 568833.496 550929.4664 0.8457287 1.217194058 1.097932516 1.229453633 0.849064356 1.046537958 1.178365913 1.089800574 1.032497862 1 19.0715081 4.760566615 24.03956103 1.086399389 0.845728272 0.304979201 0.106986576 4247.286193 4639650.209 0.025097647 1.183444423 57619.11915 -4.760566615 -0.240671117 AENGKLVINGNPITIFQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AENGKLVINGNPITIFQER 19 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 118.54 7.04E-05 1469880000 1083860 871310 1136830 792650 1372860 1268240 961890 1037730 1069760 890650 FALSE TRUE 1126651.63 1020950.715 1166456.724 949433.8042 1139501.748 973710.4804 886494.5484 1023820.927 1031259.547 1065155.815 1.057734102 0.958498935 1.09510431 0.89135673 1.069798176 0.914148397 0.832267482 0.961193576 0.968177174 1 20.02263306 2.714926459 24.69517826 0.926596939 1.009024268 0.243686911 0.068732246 910.1610071 951020.2753 0.021171778 0.019971253 518.7121961 -2.714926459 0.082427328 AENGKLVINGNPITIFQERDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AENGKLVINGNPITIFQERDPSK 23 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 229.2 3.22E-33 3458500000 2430300 1290140 2157730 1008930 2959000 2252900 2070590 1703240 2495700 1612160 FALSE TRUE 2526250.121 1511711.509 2213962.216 1208493.343 2456030.237 1729698.118 1908291.745 1680410.854 2405880.245 1928031.885 1.310274036 0.784069766 1.148301661 0.626801534 1.273853537 0.89713149 0.989761507 0.871567979 1.24784256 1 20.87869748 1.243194602 24.99936934 1.123921267 0.975857406 0.061339148 0.209039738 270.6132571 1459966.375 0.134765523 0.045544016 17.50630951 -1.243194602 -0.14806386 AENLQLLTENELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AENLQLLTENELHR 14 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ;; 187.37 9.56E-07 853639000 625219 705737 683930 683120 749604 840910 701704 735274 694642 735963 FALSE TRUE 649903.1289 826941.8399 701753.7777 818239.0971 622186.5798 645621.3966 646702.6069 725418.8547 669641.9701 880160.859 0.738391309 0.939534895 0.797301732 0.929647222 0.706900987 0.733526593 0.734755017 0.824188951 0.760817711 1 19.74740769 AENNS(ph)EVGASGYGVPGPTWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AENNSEVGASGYGVPGPTWDR 21 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 AENNS(1)EVGASGYGVPGPTWDR 181.82 4.27E-18 0 48221 57044 48467 37648 57684 62263 49481 46488 50079 48606 TRUE FALSE 50124.80231 66840.86326 49730.08984 45094.66203 47878.89428 47803.36185 45602.54993 45864.9044 48276.66657 58129.41508 0.862296692 1.149862994 0.855506455 0.775763217 0.823660348 0.822360965 0.784500409 0.789013692 0.830503223 1 15.82698077 4.056695982 10.641253 0.81799588 1.005774494 0.368611557 0.088559466 0.397606644 72.26587598 0.019641839 0.042488204 11394.51862 -4.056695982 0.187778614 AENSHNAGQVDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AENSHNAGQVDTR 13 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5;D6RHC4;Q8IWZ3-5;Q8IWZ3-3;Q8IWZ3-2 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 0 ; 181.26 1.22E-05 298040000 297450 342550 332910 325310 335440 403990 340540 362910 328040 340280 FALSE TRUE 309193.5557 401380.2978 341585.9081 389655.347 278422.0286 310169.445 313847.585 358045.7851 316233.9045 406951.3509 0.759780143 0.986310272 0.839377747 0.957498596 0.684165387 0.762178192 0.771216472 0.87982454 0.777080365 1 18.63449681 5.071877618 13.42163626 0.842185595 0.000155674 0.062954761 0.100521566 2307169.216 11272807.48 0.023367705 52746182.72 117998.8073 -5.071877618 -0.842029921 AENYDIPSADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 211.37 2.22E-08 1532940000 1637940 1873920 1694080 1802940 1865880 2090190 1826270 1872260 1717050 1743050 FALSE TRUE 1702607.136 2195751.183 1738229.117 2159556.151 1548718.384 1604775.05 1683122.185 1847165.417 1655253.706 2084567.275 0.81676766 1.053336685 0.83385609 1.035973354 0.742944784 0.769836056 0.80742042 0.886114562 0.794051469 1 20.9913165 3.23357243 24.99999718 0.827152509 0.936213865 0.207595338 0.096761663 175.0684738 877415.5341 0.025833834 0.031809139 1712.27072 -3.23357243 0.109061355 AEPAKIEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 145.91 2.70E-05 4794710000 5833970 5930300 6530900 4061520 9228300 7455000 4847060 5986930 6758820 7080420 FALSE TRUE 6064299.64 6948782.894 6701100.619 4864876.534 7659676.862 5723689.232 4467134.772 5906684.996 6515571.388 8467692.736 0.716169071 0.820622938 0.791372671 0.574522091 0.904576619 0.67594437 0.52755041 0.697555424 0.769462425 1 23.01353749 0.85032919 3.887637656 0.999947875 0.710983357 0.400796197 0.104738302 0.925876475 22.47979368 0.101623447 0.026021351 7.084826021 -0.85032919 -0.288964518 AEPDESNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEPDESNAR 9 0 P61088;F8VSD4;F8VV71;Q5JXB2;F8VZ29 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ; 197.5 6.49E-05 336430000 506800 571810 537030 544800 640350 687850 585300 544620 551050 572090 FALSE TRUE 526808.8553 670013.9194 551025.443 652559.8139 531503.5357 528107.262 539422.6566 537320.2597 531217.8181 684180.0822 0.769985665 0.979294687 0.805380714 0.953783705 0.776847426 0.77188342 0.788422041 0.78534917 0.77642982 1 19.38401658 3.21194639 24.99803143 0.80066749 0.879286474 0.088627058 0.086638135 368.0331407 345682.6802 0.022678129 0.027112783 1629.094922 -3.21194639 0.078618984 AEPEDHYFLLTEPPLNTPENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEPEDHYFLLTEPPLNTPENR 21 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 212.35 1.00E-22 750530000 277030 297420 327560 293480 343630 356230 379830 311240 340690 266980 FALSE TRUE 287967.3583 348499.5714 336096.4827 351529.468 285219.8953 273500.9812 350057.9321 307068.3369 328428.6335 319289.6194 0.901900159 1.091484189 1.052638302 1.100973683 0.893295234 0.856592149 1.096364902 0.961723521 1.02862296 1 18.28450612 3.249557527 24.99709843 0.973420201 1.041793656 0.130558237 0.080457499 440.7301688 1001818.154 0.022469977 0.030138618 1776.468566 -3.249557527 0.068373455 AEPHFLSILQHLLLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEPHFLSILQHLLLVR 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 199.68 2.17E-11 191071000 114482 152520 162413 171671 202304 217153 210797 177422 183362 153136 FALSE TRUE 119001.8378 178714.1236 166645.6162 205627.0114 167916.4383 166722.5067 194274.1803 175043.9483 176762.8374 183140.0672 0.649785924 0.975833013 0.909935323 1.122785497 0.916874395 0.910355168 1.060795615 0.955792749 0.965178402 1 17.48258793 4.739414684 6.734847133 0.979551984 0.643972851 0.70061027 0.064708563 0.06053532 18.4553221 0.014732076 0.091985673 54880.07343 -4.739414684 -0.335579133 AEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 40 2 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 AEPPKPEVVDSTESIPVS(0.999)DEDSDAMVDDPNDEDFVPFRPR 168.59 4.90E-19 78352000 34768 32254 45062 34221 41415 49840 38681 33544 34567 24220 TRUE FALSE 36140.66749 37793.3736 46236.35274 40989.81166 34375.29309 38265.41533 35649.08215 33094.39755 33322.94042 28965.44528 1.24771662 1.304774473 1.596259001 1.415127966 1.186769019 1.321071192 1.230745179 1.142547516 1.150437706 1 14.82204522 1.784651799 0.605107785 1.014730842 1.387312776 0.578568094 0.101120922 0.549866593 0.424498963 0.100856352 0.057702886 60.90483894 -1.784651799 0.372581934 AEPYCSVLPGFTFIQHLPLSER ddPTM_MDA-MB-175_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 ; 244.91 7.56E-31 1102990000 629680 996170 828520 814110 943890 1153020 809320 912490 863100 1172690 FALSE TRUE 654540.2526 1167254.448 850111.9118 975138.5281 783447.9149 885248.5792 745883.3836 900259.5641 832037.1996 1402456.153 0.466709958 0.832293007 0.606159351 0.695307676 0.558625604 0.631213017 0.531840787 0.641916371 0.593271453 1 20.41952424 -1.483590607 2.860652976 1.012582932 0.622171177 0.600633036 0.093503552 22134125.47 24744635.63 2205910.932 0.020416819 0.032840472 1.483590607 -0.390411756 AEQEEEFISNTLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEQEEEFISNTLFK 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 95.401 0.0088007 13530000 25535 45182 39406 41719 38272 46696 31638 36024 34267 57530 FALSE TRUE 26543.14152 52941.65703 40432.95273 49970.89368 31766.53911 35851.56168 29158.13089 35541.1572 33033.73736 68801.90202 0.38579081 0.769479556 0.58767202 0.72630105 0.461710188 0.521083875 0.423798326 0.516572306 0.480128258 1 16.07016083 -1.732597476 6.662404377 1.007528466 0.544749559 0.578878516 0.117315561 0.013041499 0.000523434 0.11292085 0.026532322 0.018509834 1.732597476 -0.462778907 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 271.05 1.49E-73 1568870000 879876 846416 1187680 654231 1664470 1360810 1172380 1204260 1330120 794204 TRUE FALSE 914614.1839 991781.3638 1218631.916 783635.9391 1381543.984 1044782.501 1080485.792 1188118.864 1282249.241 949813.0678 0.962941251 1.044185848 1.2830229 0.82504228 1.454543037 1.099987499 1.137577307 1.250897576 1.350001684 1 19.85728408 6.160131137 0.524109275 1.203877125 1.67E-15 0.132828513 0.170878445 30.45227807 1.993924888 0.081783977 31.11137219 1445876.292 -6.160131137 -1.203877125 AERPDVDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AERPDVDEK 9 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 123.29 0.00051248 1182390000 1462440 858320 1161350 945780 1602430 1513720 1491210 1172380 1238550 783970 FALSE TRUE 1520178.26 1005729.783 1191615.735 1132852.461 1330049.521 1162181.471 1374325.064 1156666.164 1193974.827 937573.9115 1.621395649 1.072693865 1.270956583 1.208280699 1.418607648 1.23956251 1.46583117 1.233679979 1.27347275 1 19.8385729 0.549315928 1.454518164 1.000273115 1.309370446 0.297159304 0.145381388 2.390363871 6.343906961 0.127107818 0.037033438 3.542549505 -0.549315928 0.309097331 AERPDVDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AERPDVDEKR 10 2 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 124.12 0.00024966 401580000 261150 320270 319790 335500 331970 382180 300540 277860 278860 388210 FALSE TRUE 271460.4037 375273.8811 328123.9901 401860.8986 275541.858 293424.487 276982.8895 274135.7412 268823.8831 464272.3168 0.584700819 0.80830553 0.706748988 0.865571528 0.593491897 0.63200944 0.596595747 0.59046325 0.579021995 1 18.82461173 -1.099104792 4.633812506 1.000022582 0.662441853 0.526049527 0.096281046 2.35E-05 4.58E-06 0.097728705 0.023033337 0.079596727 1.099104792 -0.337580729 AES(ph)GDSLGSEDRDLLYSIDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AES(0.995)GDS(0.004)LGS(0.001)EDRDLLYSIDAYR 192.3 6.78E-18 40301000 22161 25483 30551 27478 36691 33527 31339 30620 34196 27989 TRUE FALSE 23035.93339 29859.50702 31347.18416 32913.06639 30454.27693 25740.86236 28882.56729 30209.58898 32965.29264 33472.90867 0.688196345 0.892049965 0.93649418 0.983274764 0.90981866 0.769005843 0.862863983 0.902508631 0.984835019 1 15.0307063 7.999957828 0.024811712 1.546564618 6.30E-05 0.272583495 0.080246352 3429.791587 6.542467917 140.5357185 292.9548022 99990289.91 -7.999957828 -1.546501641 AES(ph)GPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AESGPDLR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR;AES(1)GPDLR 135.63 0.0008658 4786680000 8526810 8814400 8792800 8229900 9841000 11109100 8950400 8493800 7983900 7186400 TRUE FALSE 8863455.043 10328204.63 9021947.591 9857749.656 8168230.335 8529179.885 8248844.26 8379954.504 7696560.999 8594437.488 1.031301357 1.201731311 1.049742651 1.146991839 0.950408953 0.992406995 0.959788732 0.975043976 0.895528184 1 23.03497179 3.232785081 24.99999974 0.963146826 1.110055394 0.654498096 0.05168199 76.82083223 332526.7717 0.013594066 0.016666564 1709.16929 -3.232785081 0.146908568 AES(ph)KPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESKPR 6 1 E9PD25;O43897 E9PD25 TLL1 Metalloendopeptidase;Tolloid-like protein 1 1 AES(1)KPR 58.676 0.084193 56275000 122100 97539 94834 100330 120750 127080 120190 102960 111450 104230 TRUE FALSE 126920.6023 114290.5645 97305.45195 120174.9745 100224.9581 97567.59592 110769.1937 101579.9896 107438.9363 124651.8729 1.018200524 0.916878037 0.780617649 0.964084789 0.804038927 0.782720658 0.888628395 0.814909453 0.861911929 1 16.92754503 4.589010254 3.491655764 0.85337078 1.017671428 0.304614585 0.070549867 0.2646026 5.331825173 0.01578259 0.088031576 38815.95306 -4.589010254 0.164300648 AES(ph)PAEKVPEESVLPLVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AESPAEKVPEESVLPLVQK 19 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK;AES(1)PAEKVPEESVLPLVQK 255.83 3.68E-31 1409610000 2031810 816604 1271895 977914 1617480 1742440 2143820 1400103 1480769 560393 TRUE FALSE 2112027.428 956849.3847 1305041.629 1171342.47 1342541.327 1337784.717 1975781.787 1381336.909 1427476.413 670191.279 3.151380052 1.427725807 1.947267399 1.74777337 2.003221124 1.996123732 2.948086387 2.061108452 2.129953728 1 19.35421339 AES(ph)PDLR ddPTM_MDA-MB-175_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 112.41 0.0074808 8951110000 16427590 17634590 17651520 16731890 20715240 22996090 19366480 19153350 18346770 16977350 TRUE FALSE 17076163.94 20663193.65 18111533.11 20041407.9 17194070.9 17655596.61 17848484.69 18896630.67 17686473.33 20303736.68 0.84103553 1.017703981 0.892029551 0.987079778 0.846842686 0.869573758 0.879073885 0.93069719 0.871094499 1 24.27524193 AES(ph)PEEVACR ddPTM_MDA-MB-175_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 227.36 2.72E-09 3354609000 1260180 1327422 1270272 1300689 1517120 1666210 1397887 1293190 1265880 1213242 TRUE FALSE 1309932.879 1555396.403 1303376.332 1557961.402 1259240.484 1279257.979 1288316.964 1275856.903 1220321.226 1450953.541 0.902808286 1.071982223 0.898289501 1.073750026 0.867870989 0.881667085 0.887910555 0.879323057 0.84104776 1 20.46856989 3.20916669 24.99988578 0.885695371 0.986483054 0.3151138 0.067189012 208.8072794 177592.5305 0.017499533 0.020918909 1618.701206 -3.20916669 0.100787683 AES(ph)PESSAIESTQSTPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(1)PESSAIESTQSTPQK;AES(1)PESSAIESTQSTPQK 481.08 1.32E-239 2630800000 1650560 1242120 1777350 1369120 1897990 1872490 1862910 1577150 1805310 1170310 TRUE FALSE 1715725.383 1455444.448 1823669.201 1639927.85 1575370.338 1437632.575 1716890.246 1556010.884 1740337.246 1399609.838 1.225859763 1.039892982 1.302983983 1.171703575 1.125578211 1.027166669 1.22669204 1.111746175 1.243444565 1 20.41659328 3.303421266 5.625059059 1.129601501 1.184089854 0.095932928 0.093138386 0.579383002 34.73902817 0.024882218 0.033576798 2011.042579 -3.303421266 0.054488352 AES(ph)PGPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESPGPGSR 9 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 AES(1)PGPGSR 141.88 0.00011084 60675000 448490 422990 465040 432810 576700 629090 522780 484370 494500 447950 TRUE FALSE 466196.7315 495635.2421 477159.3244 518418.5262 478672.74 482993.3815 481803.1376 477877.8124 476703.0416 535717.226 0.870229123 0.925180707 0.890692517 0.967709271 0.893517544 0.901582697 0.899360921 0.892033687 0.889840794 1 19.03111216 -1.150239496 4.257904681 1.000023096 0.904118059 0.571191422 0.025114705 5.26E-06 1.05E-06 0.023244267 0.005477407 0.070755549 1.150239496 -0.095905037 AES(ph)PSPAPPPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 AES(0.931)PS(0.069)PAPPPGLR;AES(0.88)PS(0.12)PAPPPGLR;AES(0.887)PS(0.113)PAPPPGLR;AES(0.84)PS(0.16)PAPPPGLR 199.8 1.21E-07 1035720000 982100 986580 1037990 931920 1201150 1253940 1101410 1060750 1049120 1014050 TRUE FALSE 1020874.066 1156017.44 1065040.872 1116250.994 996978.952 962731.4386 1015078.606 1046532.381 1011362.376 1212733.682 0.841795756 0.953232731 0.878214968 0.920441982 0.822092242 0.793852313 0.837016916 0.862953175 0.833952574 1 20.20983134 5.074142083 14.98638593 0.870216914 0.47484956 0.016939096 0.060777827 4847527.673 19764891.44 0.014223185 60144562.68 118615.6745 -5.074142083 -0.395367354 AES(ph)PTPGMAQGMEPGAGQEGAMFVHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AESPTPGMAQGMEPGAGQEGAMFVHAR 27 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 AES(0.825)PT(0.175)PGMAQGMEPGAGQEGAMFVHAR;AES(0.82)PT(0.18)PGMAQGMEPGAGQEGAMFVHAR;AES(0.93)PT(0.07)PGMAQGMEPGAGQEGAMFVHAR;AES(0.993)PT(0.007)PGMAQGMEPGAGQEGAMFVHAR;AES(0.996)PT(0.004)PGMAQGMEPGAGQEGAMFVHAR 251.68 5.93E-53 1194017000 196236 244967 258307 228100 286298 315906 255473 264839 229053 232471 TRUE FALSE 203983.5488 287038.1767 265038.6926 273217.4992 237633.1682 242541.6191 235448.3587 261289.2664 220809.4273 278019.2415 0.73370299 1.032439967 0.95331061 0.982728741 0.854736409 0.872391485 0.846877926 0.939824398 0.794223544 1 18.08482521 3.224845919 24.98281119 0.882565033 0.935164118 0.043373201 0.089255926 622.6899924 1134294.837 0.024342163 0.029238343 1678.208509 -3.224845919 0.052599085 AESDLFLAEHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESDLFLAEHHK 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 71.558 0.025597 249600000 146680 103060 135730 108340 160500 172240 168800 122540 136160 88060 FALSE TRUE 152471.0397 120759.7533 139267.2353 129769.3286 133218.2673 132239.8703 155569.0149 120897.5517 131259.6282 105313.671 1.447780124 1.1466674 1.322404147 1.232217313 1.264966515 1.255676201 1.477196773 1.147975857 1.246368368 1 16.6843332 0.712885396 1.172310393 1.001942239 1.288941028 0.421333919 0.102053004 0.886391669 2.066276533 0.089946026 0.027744233 5.162801119 -0.712885396 0.286998789 AESGDS(ph)LGSEDRDLLYSIDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AESGDS(1)LGSEDRDLLYSIDAYR 221.26 5.75E-26 129630000 78451 83346 85178 80912 94325 122620 88922 86963 89253 105180 TRUE FALSE 81548.30606 97660.02716 87397.80865 96916.1521 78291.67019 94143.36332 81952.06129 85797.40323 86040.80196 125788.0072 0.648299531 0.776385836 0.694802395 0.770472116 0.622409655 0.748428768 0.651509338 0.682079358 0.68401435 1 16.94063485 -2.197493139 2.276579829 1.850261122 0.698060141 0.768835355 0.049744129 2744373.944 579758.2409 12011355.96 0.011083361 0.006346099 2.197493139 -1.152200981 AESGDSLGSEDRDLLYSIDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 159.67 1.77E-11 102140000 93852 107750 118320 98271 108820 129780 107370 115190 102650 122480 FALSE TRUE 97557.34943 126255.2243 121403.5164 117708.7105 90322.81527 99640.56183 98954.05884 113646.0665 98955.64655 146477.611 0.666022259 0.861942132 0.82881961 0.803595237 0.616632226 0.680244313 0.675557569 0.77585964 0.675568409 1 17.16032064 -1.550708905 9.273299569 1.000017995 0.736026199 0.5178961 0.077586344 3.00E-05 1.45E-06 0.078115345 0.018410711 0.028137862 1.550708905 -0.263991796 AESLQQEVEALKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AESLQQEVEALKER 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ; 140.49 9.06E-06 258420000 280612 227775 283888 171333 329766 335480 295945 271054 314208 239834 FALSE TRUE 291690.7784 266893.5844 291286.3545 205222.156 273712.4931 257569.8542 272748.0576 267420.9645 302899.7155 286824.8804 1.0169647 0.930510575 1.015554697 0.715496354 0.954284345 0.898003876 0.950921891 0.932349258 1.056044075 1 18.12981065 1.297139301 6.486526339 1.027573129 0.92387572 0.202083056 0.080316104 0.280140597 22.86702875 0.05468152 0.019344379 19.82162709 -1.297139301 -0.103697408 AESPES(ph)SAIESTQSTPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 AES(0.003)PES(0.716)S(0.282)AIESTQSTPQK;AESPES(0.88)S(0.12)AIESTQSTPQK 501.72 8.27E-267 2905600000 1133650 911610 1168250 874550 1278620 1192400 1118660 1029840 1082410 599280 TRUE FALSE 1178407.377 1068171.926 1198695.555 1047533.38 1061280.629 915483.171 1030976.506 1016036.679 1043454.276 716697.4421 1.644218757 1.490408453 1.672526626 1.461611718 1.480793103 1.277363525 1.438510096 1.417664721 1.455920189 1 19.45100468 -3.415732311 0.125670113 1.79E-15 1.720061215 0.763791584 0.087059982 44.67307242 0.533811437 12.80239001 0.813442168 0.000383944 3.415732311 1.720061215 AESSQTCHSEQGDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AESSQTCHSEQGDKK 15 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 ;;; 206.06 2.65E-09 404664000 312356 205378 293498 182418 391986 372933 352634 298669 339904 160698.2 FALSE TRUE 324688.0561 240650.0739 301146.799 218499.7359 325356.3597 286324.9626 324993.6256 294665.8306 327670.9214 192183.9355 1.689465122 1.25218621 1.566971756 1.136930282 1.692942539 1.489848576 1.691055107 1.533249019 1.70498601 1 17.55212822 AET(ph)PPLPIPPPPPDIQPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 121.27 0.00036418 206251000 162201.5 163361 158126 135494 196640 253600 195454 169023 165683 145896 TRUE FALSE 168605.3405 191416.981 162246.8935 162294.3088 163215.203 194705.2433 180133.8048 166757.5232 159720.1012 174481.5279 0.966322009 1.097061582 0.929880059 0.930151809 0.935429699 1.115907487 1.032394701 0.955731677 0.915398341 1 17.41271478 1.613473584 7.416422778 0.95053105 1.001051862 0.08482878 0.065332329 0.290163672 35.76237912 0.035575027 0.017440159 41.06516612 -1.613473584 0.050520812 AETEKQS(ph)PPHGEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AETEKQSPPHGEAK 14 1 Q9Y6D6;E5RJN9 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 AET(0.001)EKQS(0.999)PPHGEAK 163.56 2.57E-06 220820000 591190 228640 350280 301750 471390 541850 603480 401010 406280 159690 TRUE FALSE 614530.6377 267907.1414 359408.5846 361435.2494 391263.2962 416013.5493 556177.6607 395635.1169 391658.0622 190978.1981 3.217805194 1.402815317 1.881935154 1.892547176 2.048732788 2.178330058 2.912257349 2.071624515 2.050799862 1 17.54304842 2.763805805 6.411198705 2.17712519 2.027615022 0 0.616426637 1.255412997 197.5184674 0.182301857 0.189038612 580.5047869 -2.763805805 -0.149510168 AETEQGEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AETEQGEQQR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 144.65 7.40E-05 80064000 49572 84875 78951 88850 84372 101556 91437 81124 79555 82242 FALSE TRUE 51529.14084 99451.62101 81008.52792 106424.2648 70030.47758 77971.1581 84269.92901 80036.66547 76691.83109 98355.74528 0.523905753 1.01114196 0.823627818 1.082034044 0.712012068 0.79274635 0.856787052 0.813746724 0.77973921 1 16.58572171 -2.328192208 2.127139087 1.841834601 0.831342571 0.117228705 0.144603022 6319332.986 708809.3164 25626225.05 0.032847643 0.004696862 2.328192208 -1.01049203 AETLASSLQEDLAHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AETLASSLQEDLAHTR 16 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 200.94 3.42E-11 75515000 30063 37478 35831 37671 35003 47134 33311 36086 38693 42185 FALSE TRUE 31249.91045 43914.55496 36764.7853 45122.21136 29053.20256 36187.84282 30699.99678 35602.32619 37300.44649 50450.34307 0.619419186 0.870451067 0.728732117 0.894388593 0.575877205 0.717296268 0.608519088 0.705690468 0.739349709 1 15.62257646 0.777510418 4.728636372 0.999998763 0.716462167 0.428064423 0.098221189 4.403092241 92.99659781 0.091692207 0.023226615 5.991153096 -0.777510418 -0.283536596 AEVLGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEVLGHK 7 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJ51;K7ER34 Q9UHD8 9-Sep Septin-9 0 68.915 0.061157 160590000 269200 242190 282640 216020 319000 321630 326220 281890 308570 232550 FALSE TRUE 279828.2239 283784.2485 290005.8306 258748.1112 264776.4939 246936.3068 300650.024 278111.7256 297464.626 278113.7201 1.006164758 1.020389244 1.042759884 0.930368021 0.952043984 0.887896889 1.081032694 0.999992829 1.069579113 1 18.08531539 2.208162035 24.99976033 1.03516513 0.975655745 0.296110651 0.048483843 300.1162365 246813.5375 0.019062028 0.014079842 161.4960985 -2.208162035 -0.059509385 AEVLGHKT(ph)PEPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;AEVLGHKT(1)PEPAPR;AEVLGHKT(1)PEPAPR 209.25 1.01E-08 2973050000 2883470 1695790 2175670 1570610 2798970 3029370 2310760 2016320 2136790 1462210 TRUE FALSE 2997311.622 1987028.741 2232369.748 1881271.97 2323202.079 2325844.728 2129636.593 1989294.528 2059887.345 1748702.054 1.714020759 1.136287761 1.276586679 1.075810465 1.328529394 1.3300406 1.217838447 1.137583457 1.177952151 1 20.73785307 4.742742584 24.84540672 1.197752063 1.714020981 0.707523305 0.101482576 205.9268473 1223378.352 0.023297073 0.180299728 55302.22239 -4.742742584 0.516268917 AEVMLGHGLFSLLAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEVMLGHGLFSLLAER 16 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 226.39 6.00E-15 203327000 174306 207739 190893 213935 234830 260100 245550 212852 188849 205683 FALSE TRUE 181187.7355 243416.5573 195867.8284 256250.7045 194913.6805 199695.7169 226303.1494 209999.0671 182052.3614 245982.6458 0.736587473 0.98956801 0.796266858 1.041743021 0.792387934 0.811828478 0.919996403 0.85371497 0.74010246 1 17.90819701 AEVPGATGGDS(ph)PHLQPAEPPGEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 AEVPGATGGDSPHLQPAEPPGEPR 24 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 1 AEVPGAT(0.002)GGDS(0.998)PHLQPAEPPGEPR;AEVPGAT(0.008)GGDS(0.992)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGATGGDS(1)PHLQPAEPPGEPR;AEVPGAT(0.027)GGDS(0.973)PHLQPAEPPGEPR;AEVPGAT(0.018)GGDS(0.982)PHLQPAEPPGEPR;AEVPGAT(0.044)GGDS(0.956)PHLQPAEPPGEPR;AEVPGAT(0.001)GGDS(0.999)PHLQPAEPPGEPR 279.02 6.51E-53 22258300000 3491084 3781635 3655578 3959101 3542810 4400594 4252509 3929820 3560643 3261489 TRUE FALSE 3628914.692 4431101.394 3750845.366 4742199.361 2940604.422 3378622.735 3919186.233 3877147.191 3432496.154 3900515.325 0.930368013 1.136029736 0.961628158 1.215787907 0.753901517 0.866199067 1.00478678 0.994008962 0.880010939 1 21.89523331 3.242404658 24.99999938 0.925232893 1.059221339 0.314659155 0.103958584 130.8878379 851231.9562 0.028912086 0.037715883 1747.449596 -3.242404658 0.133988446 AEVSELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AEVSELK 7 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2;A0A494BX66;A0A590UJT6;Q2TAC2-2;Q2TAC2 P67936;P67936-2;A0A494BX66 TPM4;CCDC57 Tropomyosin alpha-4 chain;Coiled-coil domain-containing protein 57 0 91.906 0.037363 151010000 113140 143960 150840 150740 192770 206140 169900 156350 164790 164600 FALSE TRUE 117606.8546 168684.0101 154771.0143 180555.9221 160003.0243 158267.1091 156582.794 154254.384 158859.2401 196850.2185 0.597443353 0.856915534 0.786237452 0.9172249 0.812816086 0.80399763 0.795441302 0.783612968 0.807005658 1 17.58673879 -2.465577212 1.706358237 2.243968952 0.800318461 0.388946715 0.076644778 2182945.803 165042.5378 10449285.8 0.018188504 0.003423125 2.465577212 -1.44365049 AEVWDLDMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AEVWDLDMLR 10 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;; 155.84 2.79E-05 59030000 102949 132382 118411 129047 130035 158090 140946 119672 108965 144714 FALSE TRUE 107013.506 155117.5787 121496.8879 154572.1114 107931.6971 121375.9934 129898.2842 118067.9926 105043.3709 173067.9376 0.618332358 0.896281431 0.702018465 0.893129678 0.623637738 0.701319927 0.750562386 0.682206041 0.606948765 1 17.40097895 -1.02123882 4.518775694 1.000010418 0.724196008 0.422236536 0.098331823 12041684.53 2721408.343 1241.455671 0.021764452 0.095227236 1.02123882 -0.27581441 AEYLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AEYLCR 6 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 100.82 0.086601 386470000 465620 517950 504090 472080 581140 607770 468240 465840 435050 683580 FALSE TRUE 484003.0371 606903.8834 517226.9995 565456.015 482358.0304 466624.6283 431538.1253 459596.1768 419392.6355 817514.4131 0.592042207 0.742376983 0.632682423 0.69167712 0.590030002 0.570784589 0.527866076 0.562187246 0.51300947 1 19.64088464 -0.944347486 9.226146161 1 0.602577408 0.759997331 0.067010273 0 0 0.070510166 0.016619406 0.113671742 0.944347486 -0.397422592 AFAAVPTSHPPEDAPAQPPT(ph)PGPAASPEQLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.986)PGPAAS(0.014)PEQLSFR 268.75 1.07E-59 170200000 74957 101670 99023 111800 99224 138290 95810 102750 95792 113060 TRUE FALSE 77916.36024 119131.0316 101603.6207 133913.7063 82357.93992 106174.2433 88300.16185 101372.8043 92344.46463 135211.9423 0.576253539 0.881068858 0.751439695 0.990398511 0.609102558 0.785243089 0.653050021 0.749732624 0.682960862 1 17.04486305 -1.222497716 5.049482035 1.000029945 0.747469683 0.29878072 0.118257244 3.70E-05 5.70E-06 0.106411118 0.02507837 0.059910409 1.222497716 -0.252560263 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 AFAAVPTSHPPEDAPAQPPT(0.144)PGPAAS(0.856)PEQLSFR;AFAAVPTSHPPEDAPAQPPT(0.043)PGPAAS(0.957)PEQLSFR 216.86 3.98E-36 809230000 319540 411010 377980 397580 372900 489520 380540 377820 404030 441530 TRUE FALSE 332155.6859 481597.7703 387830.4693 476220.1373 309514.5912 375836.3987 350712.2804 372755.9409 389489.0392 528039.3499 0.629035859 0.912049018 0.734472666 0.901864866 0.586158193 0.711758317 0.664178305 0.705924551 0.737613663 1 19.01028592 0.912316908 18.85840086 1 0.731803571 0.396518194 0.099415733 4279.744238 920468.9742 0.092627623 0.023156906 8.171784546 -0.912316908 -0.26819643 AFAHITGGGLLENIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFAHITGGGLLENIPR 16 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 230.16 2.51E-15 1190160000 320870 511080 454160 473460 499820 553710 476030 507680 465040 528720 FALSE TRUE 333538.1954 598854.0143 465995.7827 567108.9749 414860.7749 425119.2441 438717.5247 500875.38 448303.3012 632312.561 0.527489435 0.947085431 0.736970624 0.896880767 0.656100796 0.672324528 0.693830159 0.792132579 0.708990029 1 19.27027835 -1.587261358 3.630212249 1.008089451 0.745162552 0.320792576 0.114292162 18819983.03 8273825.185 1209015.396 0.024824574 0.025866558 1.587261358 -0.262926899 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR 31 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ; 122.68 3.76E-05 595840000 138448 105576 144745 109930 174109 146368 147925 128903 147373 107743 FALSE TRUE 143914.0339 123707.8567 148517.1736 131673.8259 144514.0144 112376.2502 136330.252 127175.2661 142069.0745 128853.178 1.116883853 0.96006834 1.152607766 1.021890402 1.121540164 0.872126338 1.058027859 0.98697811 1.102565546 1 16.97536859 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFAMIIDKLEEDISSSMTNSTAASRPPVTLR 31 2 F8VZX2;F8W1G6;F8W0G4;F8VXH9;H3BND9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 124.08 3.45E-05 284930000 108290 72324 87684 85102 125510 92147 118370 105750 110230 76484 FALSE TRUE 112565.3728 84745.0844 89969.11707 101934.9216 104175.855 70747.25575 109091.8501 104332.5942 106262.8438 91469.57543 1.23063185 0.92648385 0.983596094 1.114413411 1.138912633 0.773451231 1.192657226 1.1406262 1.161728841 1 16.48100433 AFAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFASPR 6 0 M0R1U9;M0R364;Q8TBC5-2;Q8TBC5;Q8TBC5-3;M0R3C6 M0R1U9 ZSCAN18 Zinc finger and SCAN domain-containing protein 18 1 AFAS(1)PR 70.67 0.094676 349870000 499870 548840 477290 479060 486800 582140 487310 452450 455070 503760 TRUE FALSE 519605.2536 643099.0006 489728.5695 573816.6381 404053.9099 446946.8074 449113.3689 446385.6478 438692.1196 602462.1269 0.862469573 1.067451333 0.812878599 0.952452631 0.670671054 0.741867061 0.74546324 0.740935617 0.728165473 1 19.20051103 3.250599188 24.99991044 0.754259466 0.926149061 0.338182424 0.102960342 212.6789548 441657.3486 0.026213361 0.035225394 1780.73456 -3.250599188 0.171889595 AFCAENLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFCAENLEEK 10 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 157.66 0.0099654 0 70579 55577 59854 49256 82398 84299 71259 69456 59228 47461 FALSE TRUE 73365.51342 65121.91742 61413.84441 58998.68979 68392.01739 64721.83481 65673.53338 68525.05593 57096.39585 56760.07425 1.292554923 1.147319102 1.081990206 1.039439968 1.204931782 1.140270439 1.157037482 1.207275657 1.00592532 1 15.79258886 1.225367061 24.79115096 1.002962446 1.155402493 0.473632695 0.065655153 213.1571129 400516.3704 0.062693175 0.016066992 16.80223524 -1.225367061 0.152440047 AFDIIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFDIIER 7 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BV15;H3BRD9 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 140.98 0.0060195 107561000 199736 231554 230554 235316 256797 284602 239474 226694 209148 241646 FALSE TRUE 207621.7315 271321.5983 236562.4266 281860.8025 213146.7377 218507.4987 220703.4021 223655.5377 201620.8043 288991.9071 0.718434414 0.938855351 0.818578032 0.975324206 0.737552618 0.756102484 0.763700978 0.773916266 0.697669379 1 18.14066957 3.199327124 24.99902014 0.773784977 0.865072602 0.108067462 0.09997893 263.9163448 168162.9546 0.02644235 0.03160511 1582.439533 -3.199327124 0.091287625 AFDQDGDGHITVDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AFDQDGDGHITVDELR 16 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;; 219.68 1.22E-14 696830000 905490 1114480 1060560 1175950 1105780 1317930 1247600 1136770 1037370 986920 FALSE TRUE 941239.4444 1305883.271 1088199.065 1408549.4 917819.9106 1011860.731 1149809.852 1121533.458 1000035.256 1180288.078 0.797465857 1.106410625 0.921977511 1.193394584 0.777623639 0.857299798 0.974177299 0.950220101 0.847280655 1 20.1707076 3.214959857 24.99994649 0.905178275 1.00615268 0.161531082 0.115517277 425.3301934 450544.9629 0.031911338 0.038160627 1640.438138 -3.214959857 0.100974405 AFDQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFDQLR 6 0 Q9H0I9 Q9H0I9 TKTL2 Transketolase-like protein 2 0 108.98 0.069669 231050000 345490 387140 330970 354750 538090 424250 389320 334640 305970 506840 FALSE TRUE 359130.212 453628.2835 339595.3501 424918.4912 446625.654 325724.3671 358804.0811 330154.6982 294958.1995 606145.594 0.592481766 0.748381722 0.560253763 0.701017207 0.736829004 0.53736985 0.591943726 0.544678872 0.486612791 1 19.20930484 -1.356807029 5.042051948 1.000221725 0.612004734 0.655992778 0.084493214 0.000216026 2.76E-05 0.083920615 0.019769114 0.043973696 1.356807029 -0.388216991 AFDTAGNGYCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AFDTAGNGYCR 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;;; 254.83 4.43E-20 6900650000 1616460 1879770 1850210 2154120 2242750 2447170 1905310 1781520 1716520 2159500 FALSE TRUE 1680279.089 2202605.875 1898427.993 2580198.507 1861528.156 1878851.855 1755966.824 1757641.638 1654742.781 2582612.679 0.650612112 0.852859545 0.735080412 0.999065221 0.720792619 0.727500438 0.679918765 0.680567262 0.640724331 1 21.30039986 3.059297557 24.99981436 0.71778145 0.813790612 0.045960772 0.125368908 156.3724532 65925.04515 0.033930761 0.040555012 1146.298058 -3.059297557 0.096009162 AFEDDDITHVEGSVDPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 233.52 9.60E-24 282140000 397890 362840 406530 491130 468760 465540 535110 451840 431570 345410 FALSE TRUE 413599.0044 425154.9475 417124.5058 588274.0481 389080.3426 357425.3903 493166.68 445783.8239 416037.88 413086.4762 1.001240729 1.029215363 1.009775264 1.424094184 0.941885937 0.865255608 1.193858207 1.07915376 1.00714476 1 18.6560843 AFEDDDITHVEGSVDPIRDIEIIHEELQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AFEDDDITHVEGSVDPIRDIEIIHEELQLK 30 1 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;; 209.58 4.80E-26 255045000 268154.8 181255.4 240984.7 235036.9 296197 278178 361578 275759.7 283361.9 161792.1 FALSE TRUE 278741.7586 212384.605 247264.9593 281526.4973 245849.5397 213575.3753 333236.5716 272063.5923 273163.7606 193492.1643 1.44058422 1.097639306 1.277906835 1.454976217 1.270591709 1.103793407 1.722222565 1.406070335 1.41175619 1 17.56191562 2.276804988 24.99962069 1.428318869 1.274436057 0.053108965 0.197790059 332.6292911 217432.1344 0.065077996 0.054447237 189.1494089 -2.276804988 -0.153882812 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFEDDDITHVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDK 41 2 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 65.58 0.0011712 48114000 89014 40110 62790 47954 92487 87884 95274 67602 79670 28488 FALSE TRUE 92528.34145 46998.58049 64426.35898 57439.15807 76766.09278 67474.27289 87806.17493 66695.90576 76802.69226 34069.67816 2.715856047 1.379484134 1.89101754 1.685931924 2.253208627 1.980478729 2.577252844 1.957632398 2.254282881 1 15.0562007 3.235022547 24.99557824 2.082227496 1.877669343 0 0.498865496 349.8879704 2471874.108 0.131370151 0.163022731 1717.997576 -3.235022547 -0.204558153 AFEDEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFEDEKK 7 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 107.66 0.011908 584280000 1518300 548520 896650 554950 1187300 1147000 1201000 807360 940760 410880 FALSE TRUE 1578243.656 642724.0431 920017.4356 664717.4536 985483.1701 880626.633 1106862.482 796538.6598 906902.2314 491384.0692 3.211833177 1.30798714 1.872298052 1.352745226 2.005525274 1.79213509 2.252540428 1.621010345 1.845607719 1 18.90649156 -2.143075752 0.272656755 6.58E-25 1.975502877 0.241471723 0.504464661 53.15590125 2.043709007 34.42110066 0.605324011 0.007193235 2.143075752 1.975502877 AFEDWLNDDLGSYQGAQGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AFEDWLNDDLGSYQGAQGNR 20 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ;; 276.32 3.56E-44 86449000 59206 60052 63403 68324.2 64901.4 81058 67596.3 69088 63502 55510.5 FALSE TRUE 61543.4986 70365.46386 65055.33427 81838.52283 53869.48321 62233.50795 62297.92538 68161.98837 61216.57542 66386.71966 0.927045332 1.059932833 0.979945004 1.232754431 0.811449692 0.937439118 0.938409454 1.026741323 0.922120806 1 16.01860705 3.218262424 24.99992194 0.946381329 1.045636649 0.261350843 0.09048103 362.7372274 446758.0848 0.025767809 0.030831905 1652.960302 -3.218262424 0.09925532 AFELLHLHLDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFELLHLHLDLR 12 0 Q9H4A4;A6NKB8;A0A087WU27 Q9H4A4 RNPEP Aminopeptidase B 0 ; 231.67 1.67E-12 896240000 746740 705320 719590 662280 1302050 1047950 879530 776640 795810 1173930 FALSE TRUE 776221.8718 826453.2234 738343.1065 793277.0073 1080728.006 804579.4943 810590.1404 766230.4111 767168.9536 1403939.107 0.55288856 0.588667428 0.525908213 0.56503662 0.769782678 0.573087173 0.577368446 0.545771827 0.546440333 1 20.42104893 -1.2054054 5.123481112 1.000035404 0.58299495 0.78755913 0.065008651 10155258.09 2389236.035 4086.735453 0.015613821 0.062315287 1.2054054 -0.417040454 AFELMHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFELMHSGK 9 0 P11766 P11766 ADH5 Alcohol dehydrogenase class-3 0 ; 166.07 6.10E-05 1434470000 2650210 1579740 2096490 1578460 2725000 2771700 2468430 1956590 2344630 1825280 FALSE TRUE 2754842.337 1851048.056 2151126.252 1890674.677 2261805.473 2128014.681 2274948.007 1930365.111 2260247.224 2182908.669 1.262005313 0.847973203 0.985440336 0.866126331 1.036142971 0.974852824 1.042163623 0.884308693 1.03542913 1 21.05782034 4.752249977 24.85159692 0.960408559 1.262005531 0.626250705 0.069117605 1316.985288 2390803.604 0.015365588 0.30872087 56526.22419 -4.752249977 0.301596972 AFEVMDEFDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFEVMDEFDGR 11 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 ;;; 177.78 1.82E-05 451484000 374240 459870 444711 444157 523250 562700 462897 455788 472812 513160 FALSE TRUE 389015.2842 538849.0952 456300.534 532009.9289 434308.1519 432021.4528 426613.9236 449678.9074 455795.5885 613703.877 0.633881093 0.878027849 0.743519067 0.866883767 0.707683572 0.70395751 0.695146209 0.732729455 0.742696283 1 19.22718317 -1.698477322 8.431836649 1.000725959 0.746894143 0.535993547 0.071171646 0.000933874 3.34E-05 0.066257929 0.015575573 0.020022702 1.698477322 -0.253831817 AFFSEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFFSEVER 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 169.06 0.00070539 3173474000 1233015 1679436 1454858 1515023 1751859 1912197 1549592 1608528 1498060 1927305 FALSE TRUE 1281695.384 1967866.069 1492772.795 1814690.028 1454078.633 1468118.226 1428130.93 1586968.313 1444145.113 2304923.514 0.55606851 0.853766321 0.647645263 0.787310302 0.630857651 0.636948783 0.619600139 0.688512353 0.626547955 1 21.13628745 -1.929589502 3.477420376 1.18416814 0.67636059 0.585158834 0.082796079 0.05428389 0.001099135 0.036811504 0.017495904 0.011760086 1.929589502 -0.50780755 AFFSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFFSGR 6 0 P51659-3;P51659;P51659-2;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 102.81 0.08195 260840000 146670 139230 135230 157870 173240 218740 147120 150650 126620 181360 FALSE TRUE 152460.6449 163141.6694 138754.2049 189096.2148 143792.7267 167940.95 135588.35 148630.7832 122062.9709 216894.0197 0.702926918 0.752172281 0.639732737 0.871836923 0.662963077 0.774299588 0.625136415 0.685269162 0.562777024 1 17.72663075 2.258473629 24.97644052 0.688949159 0.733568148 0 0.123535469 1020.326777 1279769.579 0.039267167 0.032810342 181.3316566 -2.258473629 0.044618989 AFGFSHLEALLDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFGFSHLEALLDDSK 15 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 185.95 4.02E-07 928130000 2494300 1478370 2003110 1777340 2479900 2546900 2783000 2072400 2337120 1328790 FALSE TRUE 2592776.89 1732268.547 2055312.692 2128892.547 2058367.484 1955421.074 2564861.188 2044622.868 2253007.508 1589140.959 1.631558783 1.090066012 1.293348258 1.339649913 1.29527055 1.23048938 1.613992247 1.286621464 1.417751833 1 20.59981567 AFGFSHLEALLDDSKELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFGFSHLEALLDDSKELQR 19 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 208.2 1.69E-16 563120000 1089380 1022100 1141100 673730 1610630 1369750 951830 1122330 1236960 1203820 FALSE TRUE 1132389.564 1197637.724 1170838.003 806991.7831 1336855.688 1051646.321 877223.0775 1107287.002 1192442.051 1439685.48 0.786553437 0.831874559 0.813259576 0.56053339 0.928574821 0.730469492 0.609315777 0.769117295 0.828265665 1 20.45732224 0.890089248 2.653151713 0.999477986 0.75090008 0.358131375 0.100122992 0.466100212 6.89207803 0.093349784 0.024865449 7.764066527 -0.890089248 -0.248577906 AFGPGLQGGSAGS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 243.46 5.58E-20 1339360000 638040 696990 648060 673100 739360 816940 671640 677880 612320 729700 TRUE FALSE 663230.3119 816692.6107 664948.976 806237.171 613683.8513 627218.0658 618995.1018 668794.1274 590282.7228 872670.744 0.760000626 0.935854234 0.761970056 0.923873267 0.703224963 0.718733921 0.709311165 0.766376244 0.676409433 1 19.73507791 3.22588673 24.99944752 0.746400384 0.845922787 0.128274814 0.101099131 352.2363442 694790.8491 0.026433014 0.0317897 1682.235255 -3.22588673 0.099522403 AFGSGIDIKPGT(ph)PPIAGR ddPTM_MDA-MB-175_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 139.7 2.14E-07 6041490000 10401100 6699770 7784340 6154700 10100300 10233000 9428500 8058400 8619000 6415040 TRUE FALSE 10811743.46 7850403.381 7987206.295 7372081.29 8383454.614 7856540.833 8689469.533 7950390.329 8308803.874 7671944.265 1.4092573 1.023261263 1.041092847 0.960914344 1.092741856 1.02406125 1.132629387 1.036294068 1.083011501 1 22.87116081 4.740818588 24.99412756 1.046779675 1.409257426 0.847794621 0.046441542 71.34750412 789715.6451 0.0106413 0.071511548 55057.76625 -4.740818588 0.362477751 AFGSGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFGSGYR 7 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 148.28 0.0048727 138790000 111230 155910 127860 117740 173080 169000 143360 158630 133410 170430 FALSE TRUE 115621.4463 182686.3297 131192.1366 141028.6206 143659.9234 129752.3112 132123.0686 156503.8243 128608.6002 203822.4954 0.567265385 0.896301114 0.64365877 0.69191882 0.704828597 0.636594655 0.648226136 0.767843726 0.630983346 1 17.63695376 -1.694019553 2.844180792 1.041060496 0.695225336 0.539309751 0.086379645 19092380.87 18612036.92 5673915.818 0.018886138 0.020229281 1.694019553 -0.34583516 AFHAALRNS(ph)PVNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFHAALRNSPVNTK 14 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 1 AFHAALRNS(1)PVNTK 115.26 0.00026025 306670000 211170 199160 205460 207750 284110 276060 239610 211620 243720 238550 TRUE FALSE 219507.1547 233364.1808 210814.4564 248842.3299 235817.0837 211949.2487 220828.7421 208783.58 234948.5648 285289.3052 0.7694195 0.817991339 0.738949735 0.872245561 0.826589288 0.742927424 0.774051947 0.731831079 0.823544944 1 18.12206614 -2.497034068 1.216789366 1.862994341 0.78560398 0.679196989 0.043539782 21837.17648 1674.617738 51148.75138 0.01284149 0.003183948 2.497034068 -1.077390361 AFHNEAQVNPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 212.68 1.74E-08 5397160000 2613750 3111990 2659870 3162080 2926870 3446340 3022330 2951050 2666600 3022300 FALSE TRUE 2716942.868 3646450.075 2729188.397 3787529.986 2429361.683 2645979.765 2785431.877 2911496.002 2570629.587 3614461.82 0.751686697 1.008850074 0.755074623 1.04788214 0.672122657 0.732053594 0.770635302 0.805513005 0.711206734 1 21.78534942 3.219564081 24.99971702 0.771653802 0.889600482 0.161299917 0.120336611 379.3468646 499224.9211 0.031755891 0.038012484 1657.921947 -3.219564081 0.11794668 AFHNEAQVNPERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AFHNEAQVNPERK 13 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;;;; 174.39 1.30E-05 2399610000 2376670 2005280 2184990 1666980 2965200 2696000 2128110 2144680 2470670 2275940 FALSE TRUE 2470502.767 2349671.241 2241932.634 1996703.669 2461176.363 2069894.858 1961303.177 2115934.073 2381751.069 2721866.867 0.907650112 0.863257226 0.823674611 0.733578741 0.904223639 0.76046881 0.720572781 0.777383383 0.875043191 1 21.37616507 4.394800435 2.460060673 0.806362708 0.904571502 0.062155529 0.08220454 0.611190187 6.782765299 0.019924153 0.092196652 24819.92328 -4.394800435 0.098208794 AFHPFIAGPYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFHPFIAGPYNR 12 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 87.485 0.010522 1099570000 1303590 1474010 1322460 1173330 2320140 1916940 1633240 1490810 1404160 2444800 FALSE TRUE 1355056.74 1727159.751 1356924.394 1405411.172 1925763.432 1471759.737 1505222.381 1470828.13 1353624.556 2923811.751 0.463455535 0.59072194 0.464094309 0.480677722 0.658648229 0.50337021 0.51481508 0.503051583 0.462965701 1 21.479419 -1.431788384 3.156146637 1.007750978 0.518132358 0.854848174 0.059854982 18642630.47 23400187.19 1287857.525 0.01364807 0.037000843 1.431788384 -0.48961862 AFHPTYEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFHPTYEEK 9 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;; 148.52 8.98E-05 1906400000 2052490 2071230 2442580 1940670 3324450 3208400 2720980 2441320 2656490 2408220 FALSE TRUE 2133523.89 2426947.641 2506235.641 2324528.734 2759361.176 2463297.724 2507702.478 2408598.099 2560883.444 2880064.601 0.74079029 0.842671251 0.870201189 0.807109928 0.958090029 0.855292525 0.870710496 0.836300025 0.889175695 1 21.45766974 -5 0.091872104 1.428701078 0.744852168 0.51872772 0.047907769 186.873439 1.189162724 16.01706771 1.067808577 1.00E-05 5 -0.68384891 AFHRLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFHRLSR 7 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AFHRLS(1)R;AFHRLS(1)R 68.016 0.038513 179743000 82103 258851 255551 260844 263495 297378 218926 225885 258092 263977 TRUE FALSE 85344.48984 303306.6457 262210.869 312438.1647 218706.214 228316.4663 201766.0081 222857.381 248803.3193 315698.239 0.270335654 0.960748614 0.83057438 0.989673448 0.692769826 0.723211086 0.639110337 0.705918987 0.788104869 1 18.26818669 0.885320622 5.549786555 0.999994139 0.739389414 0.157328104 0.188039505 2.42261377 115.7321269 0.172096863 0.043359352 7.679282108 -0.885320622 -0.260604725 AFKPEETSSNSDPPS(ph)PPVLNNSHPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFKPEETSSNSDPPSPPVLNNSHPVPR 27 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 AFKPEETSSNSDPPS(1)PPVLNNSHPVPR 114.08 0.00056841 223100000 530460 369380 475600 347280 576370 591620 563090 482410 508880 342940 TRUE FALSE 551402.9704 432818.1416 487994.5267 415970.9475 478398.8333 454225.2211 518953.5344 475944.083 490565.5082 410132.527 1.344450718 1.055312888 1.189845951 1.014235448 1.166449383 1.107508406 1.265331326 1.160464122 1.196114611 1 18.64573064 AFLQAILEHEEENEEEDEVPDDETLNQMIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFLQAILEHEEENEEEDEVPDDETLNQMIAR 31 0 F6VDE0;P51531-2;P51531;A0A0U1RQZ9 F6VDE0 SMARCA2 Probable global transcription activator SNF2L2 0 92.822 0.00046946 16423000 5572.3 9267.6 10418 7772.8 7434.9 10458 7499.8 9507.9 9000.5 10760 FALSE TRUE 5792.298707 10859.23821 10689.50164 9310.236641 6171.118354 8029.287993 6911.946079 9380.462152 8676.573763 12868.21599 0.450124455 0.84388063 0.830690256 0.723506401 0.479562852 0.623962793 0.537133204 0.728963686 0.674263921 1 13.65152444 0.348375461 1.387383661 1.000055414 0.656880214 0.396723653 0.128100064 4.645612878 8.799016135 0.125392247 0.036590359 2.230362531 -0.348375461 -0.3431752 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFLQAILEHEEQDEEEDEVPDDETVNQMIAR 31 0 A0A2R8Y4P4;A0A2R8Y7S2;P51532-4;P51532-2;A0A0A0MT49;P51532-3;P51532-5;A0A2R8YF58;A0A2R8YF80;A0A2R8Y440;A0A2R8Y4C5 A0A2R8Y4P4 SMARCA4 Transcription activator BRG1 0 107.2 0.00013396 25758000 13923 19660 18132 15270 15998 18776 14754 17555 14194 18240 FALSE TRUE 14472.69079 23036.45207 18604.53482 18290.36042 13278.66567 14415.55855 13597.54293 17319.70394 13683.16071 21813.77877 0.663465553 1.056050504 0.852879962 0.838477396 0.608728355 0.660846463 0.623346513 0.793979994 0.627271453 1 14.41295209 3.390719439 6.860073736 0.705910429 0.872215577 0.174043357 0.140190478 0.298287818 19.69967992 0.036293513 0.049283739 2458.778683 -3.390719439 0.166305148 AFLS(ph)PPTLLEGPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.929)PPT(0.071)LLEGPLR;AFLS(0.968)PPT(0.032)LLEGPLR;AFLS(0.974)PPT(0.026)LLEGPLR;AFLS(0.943)PPT(0.057)LLEGPLR 112.02 0.00064792 397870100 157154.2 205660 176887 227004 209898 260836 187919 173296 168277 243345 TRUE FALSE 163358.7692 240980.5052 181496.8205 271904.7137 174219.6129 200260.792 173189.4177 170973.2506 162220.7436 291023.7936 0.561324444 0.828043997 0.623649421 0.934304066 0.59864388 0.688125151 0.59510398 0.587488907 0.557414023 1 18.15077758 -1.635510935 6.675426689 1.001234049 0.665456621 0.422567134 0.117891654 0.002128156 0.000116201 0.112195715 0.026357092 0.023146699 1.635510935 -0.335777428 AFMGT(ph)PVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFMGTPVQK 9 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AFMGT(1)PVQK;AFMGT(1)PVQK 113.63 0.018449 183313000 1320250 998110 1026570 830880 1114130 1127280 1002310 984790 1011970 1104020 TRUE FALSE 1372374.489 1169527.628 1053323.258 995225.5841 924750.5806 865486.3041 923746.3232 971590.5008 975549.3974 1320331.581 1.039416544 0.885783272 0.797771766 0.75376943 0.700392684 0.655506781 0.699632074 0.735868561 0.738866972 1 20.33246886 4.60825518 1.280563411 0.733958743 1.129159148 0.486834943 0.089340773 0.792204543 1.349208969 0.023305177 0.386773458 40574.68719 -4.60825518 0.395200405 AFQLEEGEET(ph)EPDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFQLEEGEETEPDCK 15 0 P38432 P38432 COIL Coilin 1 AFQLEEGEET(1)EPDCK 190.11 2.57E-06 48113000 79832 40568 61183 46150 87701 72390 55660 53904 65504 54866 TRUE FALSE 82983.829 47535.23842 62777.47924 55278.33226 72793.61535 55578.51958 51297.22376 53181.50505 63146.52384 65615.94223 1.264690046 0.724446481 0.95674126 0.84245277 1.109389165 0.847027684 0.781779885 0.810496706 0.962365573 1 16.00175876 AFREEAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFREEAIK 8 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 147.51 0.00048898 913600000 487710 460660 459230 317840 926070 727450 485070 436520 490050 736550 FALSE TRUE 506965.1674 539774.7716 471197.9111 380707.8033 768656.9522 558510.7621 447048.9459 430669.1634 472413.1962 880862.8704 0.575532452 0.612779571 0.534927657 0.432198718 0.872618177 0.634049613 0.507512532 0.488917376 0.53630731 1 19.74855792 -1.496261957 3.083319817 1.011890358 0.573740727 0.554793659 0.113584843 29969555.02 36810584.41 3045620.775 0.029201534 0.031896134 1.496261957 -0.438149631 AFS(ph)DPFVEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 1 AFS(1)DPFVEAEK;AFS(1)DPFVEAEK;AFS(1)DPFVEAEK;AFS(1)DPFVEAEK 198.74 5.52E-08 217697000 978700 626340 771710 578260 1081440 1054230 1013880 771230 861300 501755 TRUE FALSE 1017339.832 733909.0228 791821.3966 692638.1021 897617.2151 809401.0595 934409.4363 760892.9233 830301.9812 600064.2856 1.695384738 1.223050664 1.319560946 1.154273165 1.495868421 1.348857246 1.55718222 1.268019013 1.383688383 1 19.19475754 -0.008014491 1.14899844 0.998133329 1.375022564 0.355628838 0.154179786 11.83973239 12.22324834 0.219077272 0.042539798 0.981715185 0.008014491 0.376889235 AFS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFSFSK 6 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C103 Q9H8V3-2 ECT2 Protein ECT2 1 AFS(0.999)FS(0.001)K;AFS(0.762)FS(0.238)K 118.74 0.022663 339600000 745570 572350 868170 534300 1155870 919560 928820 829180 960640 617320 TRUE FALSE 775005.6793 670646.6602 890795.2234 639982.9453 959395.6303 706006.1261 856016.6614 818066.1984 926066.7541 738272.0347 1.049756246 0.908400466 1.206594834 0.866866027 1.299515064 0.956295367 1.159486776 1.108082333 1.254370626 1 19.49379299 3.626075781 0.763981428 1.126466623 0.993258008 0.077068476 0.135592666 2.067485518 2.250898454 0.059428475 0.184253845 4227.423729 -3.626075781 -0.133208615 AFS(ph)TEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFSTEK 6 0 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 AFS(0.838)T(0.162)EK 78.516 0.072985 1155500000 1383300 822490 1299200 752080 2162000 1565300 1471300 1273700 1729400 829400 TRUE FALSE 1437913.752 963746.2594 1333058.219 900839.1793 1794504.012 1201782.797 1355975.661 1256628.135 1667159.232 991905.0502 1.449648585 0.971611405 1.343937325 0.908190939 1.809148982 1.211590562 1.367041796 1.266883493 1.68076494 1 19.9198425 AFS(ph)WLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 87.323 0.055145 306670600 227042 242077 300477 210394 358451 336963 306013 282896 310300 226181 TRUE FALSE 236005.7935 283651.8417 308307.6775 252009.3052 297521.6271 258708.45 282026.9014 279104.2418 299132.3636 270496.8365 0.872490032 1.048632751 1.139782932 0.931653429 1.099907973 0.956419503 1.042625508 1.031820725 1.105862706 1 18.0452522 4.74054714 24.06526618 1.039452077 0.872489933 0.395962344 0.061931886 100.6138671 1218704.342 0.013623337 0.088675708 55023.36418 -4.74054714 -0.166962143 AFSDPFVEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFSDPFVEAEK 11 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 180.67 0.0018222 0 369830 289680 301500 254700 406610 419450 341980 317780 342070 262270 FALSE TRUE 384431.174 339430.2866 309357.3377 305078.8998 337494.5774 322039.0943 315174.714 313520.6789 329758.9675 313656.785 1.22564278 1.082171032 0.98629251 0.972652002 1.075999607 1.026724463 1.004839458 0.999566067 1.051336949 1 18.25882725 4.653201699 2.725370726 1.014740122 1.246540867 0.824738063 0.029504726 0.139562717 1.552330259 0.007422716 0.065932203 44998.87944 -4.653201699 0.231800746 AFSMDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFSMDDR 7 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 ; 110.9 0.015585 270880000 416830 544600 521460 504500 585160 665300 532560 483350 510150 671430 FALSE TRUE 433286.7703 638130.8136 535049.676 604288.5942 485694.7122 510794.1577 490816.5556 476871.4839 491789.8012 802983.8532 0.539595869 0.794699434 0.666326818 0.752553855 0.604862365 0.636120086 0.611240878 0.593874313 0.612452914 1 19.61501145 -1.892748321 4.497146188 1.116271296 0.646980257 0.684494034 0.072148443 0.045286581 0.001080032 0.037613547 0.01631429 0.012801229 1.892748321 -0.469291039 AFSNLSALRKHEIIHT(ph)GQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFSNLSALRKHEIIHTGQK 19 2 A0A0A0MS76;A8MXY4 A0A0A0MS76 ZNF99 Zinc finger protein 99 1 AFS(0.006)NLS(0.037)ALRKHEIIHT(0.957)GQK 71.601 0.019944 1230700000 9436.9 1939500 2026600 1665900 1900700 2344100 1561500 1912300 2221000 2210400 TRUE FALSE 9809.476099 2272594.038 2079414.861 1995410.048 1577619.693 1799718.3 1439105.55 1886668.746 2141066.644 2643485.559 0.003710811 0.859696029 0.786618581 0.754840533 0.596795276 0.680812609 0.544396978 0.713704957 0.809940738 1 21.33401002 -5 0.051637946 2.328911176 4.06E-16 0.290381827 0.215116697 798.8652978 3.045839519 145.524697 31.054129 1.00E-05 5 -2.328911176 AFTHTAQYDEAISDYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ;;; 287.57 1.08E-36 2476680000 567400 723290 701140 714480 804190 854050 722900 717750 648050 800470 FALSE TRUE 589801.3901 847509.4311 719412.2844 855802.0115 667494.071 655709.8308 666237.2091 708129.7353 624726.8071 957306.7706 0.616104898 0.885306003 0.751496079 0.89396841 0.697262457 0.684952672 0.695949543 0.739710359 0.652587892 1 19.86862179 -1.040516277 4.388050519 1.000014871 0.740505577 0.456564737 0.086478789 11015140.23 2611964.748 1687.375575 0.01963599 0.091092731 1.040516277 -0.259509293 AFVAIGDYNGHVGLGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AFVAIGDYNGHVGLGVK 17 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ;; 149.3 3.30E-07 1089789000 1143833 867449 1042889 816494 1198740 1369003 1310307 1054522 1206531 968698 FALSE TRUE 1188992.41 1016426.618 1070067.544 977994.0762 994978.603 1051072.801 1207601.713 1040387.857 1163108.185 1158495.826 1.026324293 0.877367527 0.923669745 0.844193008 0.858853852 0.907273705 1.042387626 0.898050588 1.003981334 1 20.14382142 2.438838142 24.96925717 0.971827597 0.900129127 0.295600726 0.058377462 219.4068297 143101.8336 0.019889111 0.016640458 274.6870224 -2.438838142 -0.07169847 AFVDFLSDEIKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFVDFLSDEIKEER 14 1 Q07021 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 160.48 4.33E-06 56568000 75215 52931 63102 60030 55454 91531 73949 51375 62848 50554 FALSE TRUE 78184.54628 62021.4875 64746.48996 71903.75483 46027.94889 70274.31242 68152.68415 50686.40216 60586.11276 60459.08839 1.293181031 1.025842254 1.070914096 1.189296047 0.761307359 1.16234489 1.127252924 0.83835869 1.002100997 1 15.88367161 8 0.643203492 0.992167516 23.88938788 0.279118943 0.129042357 283.0637265 1.864440409 0.050901729 9214.978098 100000000 -8 22.89722037 AFVDRT(ph)PPPAAVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AFVDRTPPPAAVAQR 15 1 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 AFVDRT(1)PPPAAVAQR;AFVDRT(1)PPPAAVAQR;AFVDRT(1)PPPAAVAQR;AFVDRT(1)PPPAAVAQR 132.14 7.97E-05 1757210000 967820 976200 1027430 991890 1121670 1242970 1115310 1099190 983660 1102760 TRUE FALSE 1006030.281 1143854.756 1054205.67 1188082.882 931008.9341 954309.0549 1027889.088 1084457.156 948258.2687 1318824.708 0.762823349 0.867328879 0.79935238 0.900864894 0.705938347 0.723605684 0.779397809 0.822290596 0.71901767 1 20.33082139 -1.25470379 3.579313441 1.000433912 0.790660339 0.525690091 0.060669343 20668612.98 28918386.33 98447.11078 0.014599566 0.055628354 1.25470379 -0.209773573 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFVEDSEDEDGAGEGGSSLLQK 22 0 A0A494C108;Q8N9T8;H0YFD2;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK 321.54 6.96E-68 332080000 358270 317450 359120 284770 413090 404180 388560 354710 402860 298310 TRUE FALSE 372414.7762 371969.5681 368478.9622 341096.656 342873.1094 310315.3204 358103.6519 349955.6926 388361.1473 356758.133 1.043885876 1.042637949 1.032853713 0.956100575 0.961080008 0.869819891 1.003771516 0.980932627 1.088583865 1 18.44458679 3.825069184 5.61282796 0.975842825 1.041506089 0.221733516 0.050981098 0.334922128 16.92491564 0.01357333 0.024879363 6684.503953 -3.825069184 0.065663264 AFVHWYVGEGMEEGEFSEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 20 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 ;;;;;;;;;;;;;;;;;;; 298.33 1.03E-54 5850135300 3593592.4 4145913.4 4188577 4620524.9 4435336.2 4995760.8 4648987.1 4336304.9 4059835 3924545.7 FALSE TRUE 3735470.203 4857941.776 4297734.758 5534450.934 3681419.337 3835571.066 4284587.343 4278183.826 3913722.331 4693485.29 0.795884076 1.03503931 0.915680884 1.17917722 0.784367929 0.817211694 0.912879679 0.911515337 0.833862703 1 22.16222821 AFWMAIGGDRDEIEGLS(ph)S(ph)DEEH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 2 AFWMAIGGDRDEIEGLS(1)S(1)DEEH 70.091 0.01172 13617000 22821 26282 27546 25033 29725 27810 29054 29696 26063 27836 TRUE FALSE 23721.9907 30795.72905 28263.87139 29984.45268 24672.35512 21351.54896 26776.67156 29297.97369 25124.99772 33289.93125 0.712587555 0.925076379 0.849021621 0.900706357 0.741135659 0.641381588 0.804347458 0.880085137 0.754732641 1 15.02279827 -1.354052232 2.982974007 1.002263382 0.808091077 0.324104266 0.085661397 16947552.76 21140583.55 335727.863 0.023220911 0.044253515 1.354052232 -0.194172305 AFWMAIGGDRDEIEGLSS(ph)DEEH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AFWMAIGGDRDEIEGLSSDEEH 22 1 Q6PD74;Q6PD74-2 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 1 AFWMAIGGDRDEIEGLS(0.033)S(0.967)DEEH;AFWMAIGGDRDEIEGLS(0.047)S(0.953)DEEH;AFWMAIGGDRDEIEGLS(0.012)S(0.988)DEEH 197.33 1.22E-22 77597000 67430 83302 78985 82257 85756 94920 73604 82022 75210 89614 TRUE FALSE 70092.18847 97608.4705 81043.41399 98527.18909 71179.22575 72876.26853 67834.72615 80922.62925 72503.20679 107172.1475 0.654014966 0.91076341 0.75619847 0.919335773 0.664157875 0.679992612 0.632951076 0.755071454 0.676511654 1 16.70957049 3.216731478 24.99807795 0.715597819 0.813421488 0.073044514 0.120038753 447.5284973 512495.1253 0.031822637 0.038065546 1647.143655 -3.216731478 0.097823669 AFYAELYHIISSNLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AFYAELYHIISSNLEK 16 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 359.86 1.00E-87 2338800000 2384450 2257570 2723970 2198610 3972200 3599520 3238230 2826830 2758520 2798300 FALSE TRUE 2478589.927 2645290.086 2794958.896 2633488.496 3297006.863 2763586.031 2984409.071 2788940.968 2659241.404 3346573.308 0.740635181 0.790447375 0.835170378 0.786920905 0.985188896 0.825795755 0.891780576 0.833372142 0.794616212 1 21.67425319 -5 0.020936358 2.065574241 1.53E-09 0.402872525 0.062840263 3253.073245 5.154373502 347.3763243 184.8099695 1.00E-05 5 -2.065574239 AFYGS(ph)EEDEAKGAGSEETAAAAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AFYGSEEDEAKGAGSEETAAAAAPSR 26 1 A0A590UJW5;A0A590UKD3;A0A590UJU7;A0A590UJU0;A0A590UJ60;A0A590UK04;A0A5F9UJV3;A0A2R8Y2A8;A0A590UKC4;Q13367-3;Q13367;Q13367-4 A0A590UJW5 AP3B2 AP-3 complex subunit beta-2 1 AFYGS(1)EEDEAKGAGSEETAAAAAPSR 272.55 9.49E-61 199020000 116580 74326 109300 57813 127110 122130 88210 84453 97368 76995 TRUE FALSE 121182.6684 87090.91232 112148.4478 69248.23885 105503.8876 93767.1584 81295.86971 83321.04567 93863.7447 92080.69609 1.31604857 0.945810751 1.217936577 0.752038612 1.14577639 1.018315047 0.882876359 0.90486985 1.019363978 1 16.49061112 7.951944098 0.943769576 0.967059085 199.9985021 0.36057678 0.127042263 1126.923355 2.187187184 0.036420162 483822.4194 89524952.2 -7.951944098 199.031443 AGAAAGDS(ph)DEESRADDK ddPTM_MDA-MB-175_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 250.86 1.01E-21 398210000 587780 368880 429430 397440 489720 546320 624990 411900 452930 222870 TRUE FALSE 610986.0083 432232.2705 440621.2986 476052.4458 406477.5693 419445.4596 576001.6507 406379.1542 436629.1378 266537.1094 2.292311227 1.621658881 1.653133027 1.786064413 1.525031806 1.573685032 2.161056117 1.52466257 1.638155148 1 18.02397688 -2.36411536 0.267046124 5.94E-12 1.822831206 0.480450602 0.243929627 35.9755494 1.224438551 21.77043088 0.315208205 0.00432399 2.36411536 1.822831206 AGAAAGDS(ph)DEESRADDKGVMDYYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(0.996)DEES(0.004)RADDKGVMDYYLK;AGAAAGDS(0.789)DEES(0.211)RADDKGVMDYYLK;AGAAAGDS(0.999)DEES(0.001)RADDKGVMDYYLK 149.07 1.57E-07 1933920000 470770 366000 409010 320693 508850 483020 502620 384370 410800 315546 TRUE FALSE 489356.3631 428857.6529 419669.1366 384125.1182 422355.8588 370845.9252 463223.331 379218.1489 396015.3882 377371.1972 1.296750697 1.136434514 1.112085765 1.017897288 1.119205339 0.982708612 1.227500494 1.004894257 1.049405443 1 18.52562479 5.0102822 1.221944006 1.063788394 1.536486377 0.51899926 0.068877672 2.000714935 1.654354051 0.018022677 1.396026087 102395.8133 -5.0102822 0.472697984 AGAAAGDSDEES(ph)RADDKGVMDYYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 AGAAAGDS(0.281)DEES(0.719)RADDKGVMDYYLK;AGAAAGDS(0.023)DEES(0.977)RADDKGVMDYYLK 193.34 2.85E-18 439420000 426520 295129 384620 266769 496210 447130 437780 345770 423160 258797 TRUE FALSE 443359.3389 345815.11 394643.5132 319535.112 411864.4014 343290.8338 403465.6597 341135.5187 407930.5543 309503.3172 1.43248655 1.11732279 1.275086538 1.03241256 1.330726938 1.109166897 1.303590745 1.10220311 1.318016744 1 18.23959535 -2.345182115 1.950508048 3.54E-05 1.212184693 0.226682676 0.122524604 1478763.775 168247.7563 6511534.549 0.027542647 0.004516665 2.345182115 1.212149283 AGAAS(ph)MIHYMVLISAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGAASMIHYMVLISAR 16 0 C9IYN1;Q9NV64 C9IYN1 TMEM39A Transmembrane protein 39A 1 AGAAS(0.995)MIHY(0.005)MVLISAR 49.482 0.066853 631540000 1168800 517910 880920 553950 1052600 1094300 958490 526390 881130 437940 TRUE FALSE 1214945.127 606857.0137 903877.4989 663519.6566 873679.428 840165.4093 883361.0493 519334.6031 849418.3034 523745.9581 2.319722201 1.158685818 1.725793746 1.266873083 1.668135886 1.604146812 1.686621225 0.9915773 1.621813572 1 18.99850768 7.999999728 0.053777674 0.174546459 4.018662565 0.289511369 0.325459386 551.8284164 2.230495807 35.43876621 171.6624245 99999937.48 -7.999999728 3.844116106 AGAEDDEEKGEGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGAEDDEEKGEGTPR 15 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AGAEDDEEKGEGT(1)PR 99.569 0.0038673 0 117200 50985 54647 60885 72741 109190 139380 63523 83842 29190 TRUE FALSE 121827.1465 59741.27714 56071.14571 72927.87128 60376.5108 83832.27729 128455.0314 62671.57809 80824.5428 34909.22162 3.489827067 1.71133226 1.606198681 2.089071824 1.72952899 2.401436451 3.679687642 1.795272858 2.315277713 1 15.09132057 2.626490415 18.27409929 2.365753595 2.07052402 0 0.799792095 14.59054188 2339.909865 0.252039793 0.237623817 423.1461709 -2.626490415 -0.295229575 AGAES(ph)PTMSVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGAESPTMSVDGR 13 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 AGAES(0.991)PT(0.009)MSVDGR;AGAES(0.993)PT(0.007)MSVDGR;AGAES(0.984)PT(0.016)MSVDGR;AGAES(0.997)PT(0.003)MSVDGR;AGAES(0.5)PT(0.5)MSVDGR;AGAES(0.994)PT(0.006)MSVDGR 356.46 3.55E-76 4014830000 2227950 2318690 2393030 2390680 2571390 2849910 2698360 2539470 2322400 2289650 TRUE FALSE 2315911.186 2716906.971 2455394.328 2863549.369 2134306.046 2188061.593 2486855.492 2505432.558 2238817.278 2738263.08 0.845759198 0.992200856 0.896697745 1.045753927 0.779437908 0.799069165 0.908187205 0.914971457 0.817604888 1 21.38482963 5.103537937 11.3745346 0.901957847 3.57E-05 0.041861302 0.084487783 839079.7928 2218942.216 0.019868821 18138882.08 126922.3009 -5.103537937 -0.901922186 AGAGMITQHSSNAS(ph)PINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AGAGMITQHSSNASPINR 18 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHSS(0.005)NAS(0.994)PINR;AGAGMITQHSSNAS(1)PINR;AGAGMITQHS(0.003)S(0.221)NAS(0.777)PINR;AGAGMITQHSS(0.015)NAS(0.984)PINR 262.8 4.75E-31 3066010000 299713 2261684 1663818 2105594 1609943 2593289 1361410 2249616 1569916 2623002 TRUE FALSE 311545.9007 2650110.634 1707178.464 2522074.209 1336285.464 1991036.931 1254699.127 2219463.577 1513415.03 3136929.021 0.099315572 0.844810519 0.544219666 0.803994668 0.425985241 0.634708952 0.399976894 0.707527509 0.482451155 1 21.58092146 -1.619068921 2.579034917 1.044948706 0.568096486 0.293638106 0.207898395 18080938.91 15801157.63 5451768.325 0.046594118 0.024039813 1.619068921 -0.47685222 AGAHLQGGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 AGAHLQGGAK 10 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;; 183.26 3.93E-06 1.58777E+11 109943040 97123620 108299540 89838510 137416220 137050130 129091480 109564450 109068560 105116660 FALSE TRUE 114283676.1 113803846.2 111121915 107608299.1 114058260 105222314.3 118972952.5 108095917.8 105143203.8 125712256.9 0.909089367 0.905272477 0.883938589 0.855988921 0.907296256 0.83700919 0.946391031 0.859867768 0.836379892 1 26.90555008 -1.732641882 7.582980438 1.001099981 0.882846163 0.523437438 0.033672031 0.000593054 2.09E-05 0.030878325 0.007213037 0.018507941 1.732641882 -0.118253818 AGAHLQGGAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGAHLQGGAKR 11 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;; 117.7 0.0013144 2024870000 3264578 3200568 3731527 2258380 4600363 3771443 2704458 3220592 3869917 4255205 FALSE TRUE 3393466.06 3750240.657 3828773.659 2705080.823 3818394.94 2895582.52 2492475.515 3177425.232 3730639.443 5088930.949 0.666832797 0.736940763 0.752372885 0.531561707 0.750333416 0.568996229 0.489783717 0.62437971 0.733089028 1 22.27893119 0.874385097 3.382654485 0.999807705 0.637529229 0.611208631 0.086434036 0.376674814 8.387304107 0.086346147 0.022361759 7.488332111 -0.874385097 -0.362278476 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 AGAPGALS(0.959)PS(0.041)YDGGLHGLQSK;AGAPGALS(0.981)PS(0.019)YDGGLHGLQSK;AGAPGALS(0.959)PS(0.041)YDGGLHGLQSK 401.9 1.22E-151 1165300000 1216700 1281420 1496270 1275050 1800150 1937200 1722880 1603240 1714280 1427160 TRUE FALSE 1264736.255 1501493.917 1535264.025 1527251.084 1494161.146 1487314.659 1587836.164 1581751.19 1652583.398 1706784.677 0.741005161 0.879720762 0.899506567 0.894811809 0.875424514 0.871413177 0.930308424 0.926743257 0.968243634 1 20.70284963 8 0.145129453 1.014530229 0.259164438 0.732929973 0.034050609 40.20680958 0.385350899 0.132989476 6.354871841 100000000 -8 -0.755365792 AGAPGESLECPAELRPQVPQPPS(ph)PAAVPRPPSNPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGAPGESLECPAELRPQVPQPPSPAAVPRPPSNPPAR 37 2 O43734-5;O43734-2;O43734 O43734-5 TRAF3IP2 Adapter protein CIKS 1 AGAPGESLECPAELRPQVPQPPS(0.999)PAAVPRPPS(0.001)NPPAR 86.8 0.00040981 114670000 16910 15258 15895 17387 15134 18001 12459 17057 15742 19164 TRUE FALSE 17577.61986 17878.44281 16309.23676 20826.0967 12561.52809 13820.54056 11482.43102 16828.37881 15175.4485 22918.81888 0.766951384 0.780076971 0.711608955 0.908689789 0.548087934 0.603021501 0.501004484 0.734260299 0.662139204 1 14.48424508 -1.43745877 2.777043756 1.008522149 0.688504557 0.401130185 0.113368401 13264623.42 14778567.51 887327.2163 0.031019792 0.03652088 1.43745877 -0.320017592 AGAPHALAPHPDRFS(ph)HDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGAPHALAPHPDRFSHDR 18 1 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 AGAPHALAPHPDRFS(1)HDR 125.09 1.53E-05 150810000 15176 29705 22475 27054 22864 33904 21579 23981 20378 28058 TRUE FALSE 15775.1602 34806.60268 23060.71696 32405.20045 18977.58545 26030.30982 19887.58159 23659.57392 19644.59976 33555.4279 0.470122457 1.037286807 0.687242524 0.965721568 0.565559334 0.775740661 0.592678527 0.705089322 0.585437319 1 15.03425853 3.224249546 24.99875344 0.686409004 0.800403586 0.042804904 0.185900127 586.2200867 1024014.385 0.048623097 0.058367895 1675.905577 -3.224249546 0.113994582 AGAPVGGS(ph)PGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGAPVGGSPGLAK 13 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK;AGAPVGGS(1)PGLAK 154.1 4.83E-05 275188000 493550 379050 453230 387580 557910 602010 557940 474400 462650 368265 TRUE FALSE 513035.7351 444148.8889 465041.5461 464242.1672 463076.6575 462202.301 514207.2049 468041.444 445999.3169 440419.4759 1.164879764 1.008467866 1.055905952 1.054090912 1.05144455 1.049459269 1.167539659 1.062717408 1.012669378 1 18.74851874 AGDEKPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGDEKPEK 8 1 Q8WW12;Q8WW12-2;G5E9V9;A0A0B4J1Z9 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 65.347 0.058831 332340000 537260 238000 383860 226670 561810 443370 476220 378530 449610 212040 FALSE TRUE 558471.4397 278874.6486 393863.7069 271504.6495 466313.7369 340404.0368 438892.632 373456.4245 433428.6239 253585.1782 2.202303161 1.099727715 1.553181103 1.070664505 1.838884039 1.342365667 1.730750334 1.472706043 1.709203302 1 17.9521109 -0.839523294 7.047992288 0.999999996 1.534501979 0.207162567 0.324484006 1.25E-08 3.55E-09 0.280062321 0.066011321 0.144702724 0.839523294 0.534501983 AGDKDDITEPAVCALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGDKDDITEPAVCALR 16 1 P14923 P14923 JUP Junction plakoglobin 0 ;;; 171.26 4.54E-09 1197620000 912070 727820 740940 698480 921040 1028300 951640 778320 861120 639210 FALSE TRUE 948079.2279 852817.4233 760249.5051 836637.2592 764481.9498 789492.909 877047.9702 767887.8935 830128.4594 764450.9611 1.240209348 1.115594677 0.994503956 1.094428946 1.000040537 1.032758083 1.147291343 1.004495949 1.0859146 1 19.54406443 4.62272933 3.050053708 1.047946853 1.249347369 0.601294748 0.048510432 0.187186445 2.7815855 0.011113898 0.077249526 41949.7455 -4.62272933 0.201400516 AGDLLEDS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 190.78 9.06E-07 86949280000 75139422 17812211 24014721 22694396 38224151 54284542 45062527 29682139 28349745 12018257 TRUE FALSE 78105984.4 20871319.68 24640564.36 27183279.79 31726823.47 41677779.81 41530408.38 29284298.48 27329443.22 14373004.36 5.434214202 1.452119485 1.714364217 1.891273329 2.207389818 2.899726374 2.889473026 2.037451444 1.901442631 1 23.77685832 4.74534593 24.80359601 2.091773894 5.434215918 0.771323845 0.559054789 346.3774899 1266140.415 0.137012683 1.347221063 55634.72305 -4.74534593 3.342442024 AGDLLEDS(ph)PKRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 216.01 1.47E-11 70739210000 31060090 10834587 17569210 9396797 27949360 24086060 21743090 16629270 21307510 9313195 TRUE FALSE 32286366.34 12695343.04 18027078.05 11255455.4 23198537.77 18492437.59 20038809.79 16406381.84 20540656.88 11137937.25 2.898774308 1.139828925 1.618529324 1.010551159 2.08283969 1.660310808 1.799149101 1.473017981 1.844206555 1 23.40897873 -2.090777473 1.846297832 9.20E-05 1.679860022 0.155196181 0.497586217 2220424.107 541822.3446 9326089.192 0.122060447 0.008113767 2.090777473 1.679767979 AGDNSQSVYIPMS(ph)PGAHHFDSLGYPSTTLPVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGDNSQSVYIPMSPGAHHFDSLGYPSTTLPVHR 33 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 AGDNSQSVYIPMS(0.583)PGAHHFDS(0.081)LGY(0.074)PS(0.097)T(0.097)T(0.068)LPVHR 73.492 0.0013694 120870000 5621.9 8634.2 7515.4 6614.6 10929 15236 9195.2 11864 10963 10782 TRUE FALSE 5843.856953 10117.05669 7711.257498 7922.948137 9071.292484 11697.6699 8474.456197 11704.98249 10568.44377 12894.52647 0.453204464 0.78460087 0.598025644 0.614442737 0.703499466 0.907181038 0.657213448 0.907748145 0.81960697 1 13.65447117 5.021716387 0.124266181 1.132823799 7.98E-08 0.613265765 0.099921005 26.29117011 0.490760221 0.811564751 5.099934946 105127.5121 -5.021716387 -1.132823719 AGDSAVLVLPPS(ph)PGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 280.69 1.87E-35 3237548000 1331749 1477740 1447483 1452580 1595070 1745600 1491480 1499770 1488580 1607880 TRUE FALSE 1384327.479 1731530.35 1485205.596 1739895.988 1323940.571 1340210.855 1374573.9 1479668.036 1435006.297 1922913.301 0.719911541 0.900472397 0.772372626 0.904822899 0.688507678 0.696968945 0.714839249 0.76949285 0.746266769 1 20.87486229 5.050846632 14.86259369 0.78500801 0.349030478 0.037718671 0.098892513 3361119.097 27765482.87 0.022571841 41455614.53 112420.7897 -5.050846632 -0.435977532 AGDTETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGDTETLK 8 0 C9JNG9;P12111 C9JNG9 COL6A3 Collagen alpha-3(VI) chain 0 ; 79.454 0.065131 3357040000 2022050 1282680 1519760 1116990 2258080 1847360 1683430 1587130 1852400 1400280 FALSE TRUE 2101882.095 1502970.312 1559366.194 1337927.288 1874252.368 1418338.637 1551478.358 1565857.118 1785732.486 1674638.056 1.255126197 0.897489644 0.931166104 0.798935199 1.119198481 0.84695235 0.92645593 0.93504212 1.066339368 1 20.67541789 4.743410797 24.85453254 0.94083173 1.255126337 0.508905284 0.09067958 355.4449173 1821396.347 0.020152303 0.165585475 55387.37685 -4.743410797 0.314294607 AGDVFHVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGDVFHVAR 9 0 Q13882;Q13882-2 Q13882 PTK6 Protein-tyrosine kinase 6 0 64.04 0.089858 0 49849 87028 70698 81158 65156 88490 69193 66174 55714 88387 FALSE TRUE 51817.07701 101974.382 72540.44796 97210.81017 54080.80639 67939.53858 63769.47186 65287.04577 53708.86402 105704.7404 0.490205802 0.96470964 0.686255391 0.919644756 0.511621392 0.642729345 0.603279206 0.617635931 0.5081027 1 16.68968055 3.230789994 24.99998828 0.624629277 0.773815134 0.087350486 0.177170198 320.8188991 1032151.714 0.046326124 0.056342654 1701.335618 -3.230789994 0.149185858 AGDWQCPNPGCGNQNFAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGDWQCPNPGCGNQNFAWR 19 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 245.55 3.19E-24 628310000 333450 358760 325900 353480 326760 416860 349560 338970 327830 350780 FALSE TRUE 346614.8635 420374.2392 334393.2217 423397.289 271217.4519 320050.5826 322160.5738 334426.6616 316031.4623 419508.6249 0.826240136 1.002063401 0.797106905 1.009269569 0.646512219 0.762917765 0.767947438 0.797186617 0.753337223 1 18.67834095 3.246266841 24.99989399 0.776886781 0.907372141 0.243806176 0.1030093 218.0809059 707475.549 0.026225066 0.034856017 1763.058979 -3.246266841 0.13048536 AGEAGKLEEVMQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 AGEAGKLEEVMQELR 15 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;;;;;;;; 184.41 4.24E-07 3009392000 2724315 2098301 2766416 1873512 3501364 3324517 3002880 2573034 2897533 1984897 FALSE TRUE 2831873.06 2458667.874 2838511.074 2244087.082 2906203.398 2552448.31 2767506.419 2538546.688 2793251.353 2373799.564 1.192970587 1.035752096 1.195766954 0.945356599 1.224283399 1.075258564 1.165855138 1.069402289 1.176700592 1 21.17876669 -1.426492525 3.008934956 0.997847436 1.115076242 0.154843647 0.083456225 16824386.64 20164024.18 309645.7492 0.017596889 0.037454799 1.426492525 0.117228806 AGELTEDEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;; 286.53 1.60E-27 3074210000 1832420 1941920 2046290 1929510 2430990 2486580 2236820 2083100 2071520 1820900 FALSE TRUE 1904765.357 2275429.654 2099617.998 2311161.319 2017771.188 1909109.479 2061492.204 2055179.452 1996966.4 2177670.492 0.874680244 1.044891623 0.964157804 1.061299828 0.926573233 0.876675092 0.946650199 0.943751343 0.917019543 1 21.05435424 AGEPDGES(ph)LDEQPSSSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGEPDGESLDEQPSSSSSK 19 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGEPDGES(1)LDEQPSSSSSK;AGEPDGES(1)LDEQPSSSSSK 293.35 1.38E-49 457760000 556445 373690 496046 394571 604765 672321 668689 516905 580004 356278 TRUE FALSE 578413.8783 437868.3506 508973.3663 472615.9661 501967.2613 516184.6369 616275.4089 509976.734 559129.7693 426083.8527 1.357511848 1.027657696 1.19453803 1.109208817 1.178095011 1.211462564 1.446371189 1.19689289 1.312252895 1 18.70077785 2.474245452 24.98291087 1.264987638 1.1660998 0.037409938 0.130377655 189.6315893 1647348.617 0.041596654 0.034981992 298.0200284 -2.474245452 -0.098887838 AGEPDGES(ph)LDEQPSSSSSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGEPDGESLDEQPSSSSSKR 20 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGEPDGES(1)LDEQPSSSSSKR 133.58 6.43E-06 214220000 141460 101210 142740 88076 194620 168780 132020 128670 160320 131780 TRUE FALSE 147044.95 118592.0302 146459.9217 105497.1699 161538.5619 129583.4029 121671.9274 126945.3891 154550.1145 157599.7679 0.933027707 0.752488609 0.929315592 0.669399272 1.024992385 0.822230925 0.772031133 0.805492234 0.980649379 1 17.26590588 1.228481576 21.56610901 0.990325817 0.834113923 0.28040512 0.096993503 49.5067495 105907.402 0.080596526 0.021393886 16.9231645 -1.228481576 -0.156211894 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_MDA-MB-175_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(0.998)PDVT(0.002)AGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR;AGEPNS(1)PDAEEANS(1)PDVTAGCDPAGVHPPR 228.42 2.48E-35 5219160000 792421 589020 611241 534405 718453 967080 647719 576195 572536 506220 TRUE FALSE 823706.393 690179.6031 627170.4426 640108.714 596330.6157 742490.3262 596949.0923 568472.0485 551930.5412 605404.1168 1.360589349 1.140031235 1.035953382 1.05732468 0.985012489 1.226437524 0.986034082 0.938996007 0.911672924 1 19.20753896 8 0.665406899 1.000080776 36.28461092 0.63829501 0.079833932 158.9011452 0.961150777 0.032593152 8287.478717 99999999.99 -8 35.28453015 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_MDA-MB-175_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 280.37 1.00E-71 4696940000 397173 440599 441890 412028 482954 579525 423573 398889 411584 412671 TRUE FALSE 412853.6967 516268.4509 453406.0164 493525.9086 400861.6516 444939.1015 390372.2415 393542.5454 396771.1722 493525.9814 0.836538931 1.046081605 0.918707492 0.999999853 0.81224022 0.901551526 0.790986202 0.797409985 0.803951944 1 18.91276651 3.232350943 24.99958193 0.836362509 0.954912342 0.264798065 0.078678628 156.6245549 630556.014 0.021125974 0.025848701 1707.46159 -3.232350943 0.118549833 AGERPELCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGERPELCR 9 1 P19174-2;P19174 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 107.79 0.0024777 185210000 44533 82583 89154 98776 73099 99024 70209 80139 67474 103220 FALSE TRUE 46291.19723 96765.98784 91477.42648 118313.598 60673.65809 76027.17672 64705.83512 79064.86779 65045.62392 123443.9827 0.3749976 0.783885822 0.74104403 0.958439572 0.491507619 0.615884023 0.524171642 0.640491874 0.526924217 1 16.91349699 -1.045708777 4.578924509 1.000015468 0.637507984 0.32972229 0.15840501 0.528946117 95320984.57 3241.598252 0.03655771 0.090010096 1.045708777 -0.362507485 AGEVFIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGEVFIHK 8 0 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 111.04 0.0033105 5389800000 7016000 5794100 7178300 5757000 8596300 8139900 8319300 7223000 7463700 5567070 FALSE TRUE 7292997.098 6789191.603 7365372.395 6895717.417 7135103.997 6249531.586 7667211.528 7126187.499 7195082.895 6657830.779 1.095401391 1.019730274 1.106272094 1.035730352 1.071685994 0.938673841 1.151608051 1.070346745 1.080694769 1 22.66662077 AGFAGDDAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 AGFAGDDAPR 10 0 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38;P0CG39 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI;POTEJ "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I;POTE ankyrin domain family member J" 0 ;;;;;;;;; 245.03 3.86E-12 78234500000 82036120 98935520 89078760 89398300 102088310 110345440 95994320 92292700 91970770 99393800 FALSE TRUE 85274969.36 115926925.9 91400225.66 107081016.9 84735375.53 84719383.86 88470034.36 91055667.32 88660759.95 118868112.1 0.717391467 0.975256727 0.76892132 0.900838879 0.712852034 0.712717501 0.744270543 0.766022659 0.745875058 1 26.8247865 AGFDSDYDQALADIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGFDSDYDQALADIR 15 0 P52701;P52701-3;P52701-2;A0A087WWJ1;A0A494C0M1;P52701-4 P52701 MSH6 DNA mismatch repair protein Msh6 0 88.187 0.016011 15328000 23656 29063 28142 32972 27948 32508 34463 27961 21357 25234 FALSE TRUE 24589.95715 34054.34417 28875.40364 39493.76319 23197.40894 24958.50966 31761.70001 27586.22853 20588.36574 30178.11917 0.814827359 1.128444884 0.956832448 1.308688688 0.768683059 0.827039933 1.052474471 0.914113579 0.68222826 1 14.88121527 3.19428229 24.99997488 0.882938883 1.050835539 0.242033987 0.153925229 198.7008307 112187.7753 0.04336117 0.051826742 1564.164013 -3.19428229 0.167896655 AGFNYES(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.576)PS(0.424)K;AGFNYES(0.774)PS(0.226)K 138.2 7.43E-05 542750000 1041360 536400 673950 562830 787270 938340 1031120 741600 728260 427590 TRUE FALSE 1082473.697 628522.5274 691513.6907 674156.0941 653450.1266 720424.7557 950298.1201 731660.065 702050.0649 511368.0738 2.116819083 1.229100055 1.352281705 1.318338255 1.277846937 1.408818408 1.858344642 1.430789489 1.372885991 1 18.96400257 4.746869002 24.66996041 1.396088012 2.116819516 0.543657783 0.205499755 715.7618854 2125242.818 0.049485525 0.561097008 55830.1766 -4.746869002 0.720731504 AGFNYES(ph)PSKGGNFPSFPHDEVTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGFNYESPSKGGNFPSFPHDEVTDR 25 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 AGFNYES(0.983)PS(0.017)KGGNFPSFPHDEVTDR;AGFNYES(0.967)PS(0.033)KGGNFPSFPHDEVTDR;AGFNYES(0.961)PS(0.039)KGGNFPSFPHDEVTDR 178.59 1.74E-17 1519770000 858000 621440 730640 583730 961910 935570 781830 794360 787920 657580 TRUE FALSE 891874.5025 728167.4859 749681.0786 699190.0517 798404.8818 718298.0462 720548.1217 783712.9035 759562.9131 786420.2109 1.134094076 0.925926719 0.953283077 0.889079454 1.015239526 0.91337689 0.916238051 0.996557429 0.965848668 1 19.58494087 4.743609691 24.65269221 0.951864088 1.134094169 0.650328245 0.039866938 262.6693511 1282461.68 0.009128878 0.076469602 55412.74844 -4.743609691 0.182230081 AGGAS(ph)PAASSTAQPPTQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGGASPAASSTAQPPTQHR 19 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR;AGGAS(1)PAASSTAQPPTQHR 183.63 1.72E-14 7572140000 809279 845113 837432 847664 904013 1007730 846740 879376 849925 938519 TRUE FALSE 841229.9598 990254.5837 859256.1659 1015329.409 750349.1932 773699.9798 780370.3063 867589.4031 819336.3653 1122403.829 0.749489567 0.8822623 0.765549924 0.904602589 0.668519809 0.689324074 0.695266967 0.772974379 0.72998358 1 20.09816041 5.070691693 14.39499227 0.776681395 0.466465621 0 0.102790678 2213955.293 10441398.91 0.023504719 20289034.56 117677.0285 -5.070691693 -0.310215774 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 366.06 5.73E-112 4489570000 2301520 2470090 2203650 2780720 2346960 2892880 2155520 2178190 1845880 2005972 TRUE FALSE 2392385.787 2894308.743 2261078.929 3330738.116 1948024.578 2221052.462 1986564.71 2148994.926 1779447.139 2399003.807 0.997241347 1.206462755 0.942507437 1.38838384 0.812013958 0.925822817 0.828079015 0.895786376 0.741744192 1 21.19400402 3.199583247 24.99997264 0.864442876 1.12519756 0.503153443 0.129565255 120.3970368 77221.97357 0.034164643 0.04083519 1583.373045 -3.199583247 0.260754684 AGGIETIANEFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGGIETIANEFSDR 14 0 Q92598-2;Q92598;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 312.48 2.12E-55 678366000 447727 578330 556384 530030 595671 666228 531260 556817 545881 614998 FALSE TRUE 465403.6077 677653.6787 570883.8241 634868.352 494419.0562 511506.6438 489618.453 549353.7789 526234.8494 735495.0833 0.63277596 0.921357184 0.776189858 0.863185039 0.672226188 0.695458957 0.665699152 0.746916997 0.715483844 1 19.48835617 -1.279318281 3.043918044 1.001621473 0.746170498 0.445992295 0.08579018 27092347.68 35455542.39 404153.9913 0.020294527 0.052563191 1.279318281 -0.255450975 AGGIETIANEYSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGGIETIANEYSDR 14 0 P34932;A0A087WYC1;A0A087WTS8;P34932-2 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 244.71 3.06E-17 1146480000 479550 464510 476720 449770 513300 569650 499410 553040 471630 473980 FALSE TRUE 498483.0043 544285.9791 489143.7148 538733.1636 426049.4493 437357.4206 460264.9392 545627.4034 454656.1284 566847.3061 0.87939556 0.960198581 0.862919713 0.950402618 0.751612374 0.771561258 0.811973408 0.962565046 0.802078661 1 19.11260064 -1.056744516 5.46659289 1.000000934 0.866088581 0.238623754 0.073841935 8.69E-07 1.50E-07 0.073923568 0.017423831 0.087751689 1.056744516 -0.133912353 AGGLDWPEATEVS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AGGLDWPEATEVSPSR 16 0 Q9Y446;Q9Y446-2;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 1 AGGLDWPEATEVS(0.929)PS(0.071)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.998)PS(0.002)R;AGGLDWPEATEVS(0.991)PS(0.009)R;AGGLDWPEATEVS(1)PSR;AGGLDWPEATEVS(0.995)PS(0.005)R;AGGLDWPEATEVS(0.985)PS(0.015)R 274.6 3.23E-35 6816573000 4475680 4882680 4568040 4309302 4988260 5777030 4527130 4743300 4684710 4824330 TRUE FALSE 4652383.302 5721242.308 4687086.875 5161669.074 4140357.347 4435402.334 4172281.721 4679723.822 4516108.202 5769565.096 0.806366377 0.991624535 0.812381314 0.894637462 0.717620354 0.768758522 0.723153592 0.811105126 0.782746728 1 22.46003114 3.261151321 24.95058392 0.785972928 0.8799311 0.137287464 0.088335022 345.117998 381167.311 0.022501969 0.030445815 1824.531311 -3.261151321 0.093958172 AGGPAT(ph)PLSPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPAT(0.992)PLS(0.008)PTR;AGGPAT(0.959)PLS(0.041)PTR 151.66 0.000773 756680000 259120 355210 315960 343060 356870 466820 341650 325540 325270 378420 TRUE FALSE 269350.2577 416214.5543 324194.1772 410916.2441 296209.3649 358408.1297 314870.5803 321176.6688 313563.5962 452564.1537 0.595164808 0.919680781 0.716349659 0.907973468 0.654513537 0.791949886 0.695747946 0.709682077 0.692859993 1 18.78776279 -1.150654778 5.159037798 1.00001054 0.746112803 0.379718097 0.098583468 1.09E-05 1.80E-06 0.087218851 0.020556827 0.070687923 1.150654778 -0.253897737 AGGPATPLS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 AGGPATPLS(0.993)PT(0.007)R;AGGPATPLS(0.978)PT(0.022)R;AGGPAT(0.029)PLS(0.922)PT(0.049)R 225.44 1.85E-11 906380000 728490 964390 815230 884250 945720 1041530 957810 901990 821950 984390 TRUE FALSE 757251.3477 1130016.481 836475.5635 1059152.011 784966.8522 799650.442 882734.3494 889900.2994 792368.1801 1177262.373 0.64323074 0.959868001 0.710526033 0.899673713 0.666773075 0.679245732 0.749819556 0.755906516 0.673059972 1 20.16700445 -1.1811013 3.78747781 1.000190877 0.754024783 0.36716879 0.0987592 22685200.22 46775506.46 55052.76962 0.022316913 0.065902016 1.1811013 -0.246166094 AGGPTTPLS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 AGGPTT(0.001)PLS(0.5)PT(0.5)R;AGGPTT(0.034)PLS(0.958)PT(0.008)R;AGGPTT(0.001)PLS(0.999)PTR;AGGPTTPLS(0.897)PT(0.103)R;AGGPTTPLS(0.997)PT(0.003)R 214.46 4.59E-11 2360670000 2105320 2540650 2406730 2252060 2863920 2986900 2745590 2600060 2341350 2700900 TRUE FALSE 2188439.659 2976986.874 2469451.361 2697510.746 2377111.901 2293237.742 2530383.482 2565210.449 2257085.271 3230089.643 0.677516695 0.921642184 0.764514807 0.835119469 0.735927533 0.709961021 0.783378717 0.794160761 0.698768616 1 21.62314277 -1.960724775 7.744007801 1.111824853 0.774739011 0.505399875 0.068343927 0.037235517 0.000188847 0.018674008 0.014591742 0.010946499 1.960724775 -0.337085842 AGGS(ph)PAS(ph)YHGSTSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGGSPASYHGSTSPR 15 0 I3L2B2;O95208-3;O95208-2;F6PQP6 I3L2B2 EPN2 Epsin-2 2 AGGS(1)PAS(1)YHGSTSPR 128.06 0.00010866 104910000 103690 230210 233740 224010 228920 318800 204770 252840 194380 238010 TRUE FALSE 107783.7613 269746.7767 239831.4564 268318.5094 190008.2602 244763.5315 188719.5923 249451.0934 187384.3018 284643.5025 0.378662293 0.947665323 0.842567824 0.942647582 0.667530643 0.859895024 0.663003338 0.876363209 0.65831224 1 18.11879664 -2.584200679 2.20710081 5.351515466 0.776546164 0.15224849 0.165893939 7548929 390292.528 166383357.9 0.036665049 0.00260495 2.584200679 -4.574969302 AGGSAALS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 AGGSAALS(0.988)PS(0.012)K;AGGSAALS(0.988)PS(0.012)K;AGGSAALS(0.988)PS(0.012)K;AGGSAALS(0.86)PS(0.14)K;AGGSAALS(0.914)PS(0.086)K;AGGSAALS(0.998)PS(0.002)K 253.72 2.14E-20 6052920000 9182910 5081970 6622310 4200190 9648270 8432140 7869160 6329720 6609000 5459940 TRUE FALSE 9545458.378 5954758.815 6794892.839 5030975.046 8008260.512 6473903.275 7252354.677 6244880.457 6371143.381 6529710.706 1.46185012 0.911948336 1.04061162 0.770474416 1.226434198 0.991453307 1.110670136 0.956379346 0.975716026 1 22.63858765 4.745445257 24.719321 1.001087918 1.461850369 0.601348649 0.113232681 450.8500211 1618729.463 0.025365288 0.25002421 55647.44864 -4.745445257 0.460762452 AGGSAALS(ph)PSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGGSAALSPSKK 12 1 Q92522 Q92522 H1FX Histone H1x 1 AGGS(0.005)AALS(0.951)PS(0.044)KK;AGGSAALS(0.986)PS(0.014)KK;AGGSAALS(0.99)PS(0.01)KK 91.969 0.0048995 1400620000 4764350 1798780 2987000 1800840 3887430 3643790 3792280 2911330 3052050 1517670 TRUE FALSE 4952450.217 2107706.472 3064843.674 2157040.777 3226646.037 2797574.995 3495031.184 2872308.383 2942207.317 1815028.379 2.728580046 1.161252627 1.688592702 1.188433637 1.777738615 1.541339533 1.925606908 1.58251431 1.621025517 1 20.79156068 -2.373159093 0.46199347 2.33E-16 1.674528313 0.200875767 0.413594779 153.2879924 8.502532067 156.2334179 0.195869506 0.004234878 2.373159093 1.674528313 AGHCAVAINTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGHCAVAINTR 11 0 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 ; 120.06 0.00050243 238260000 142076 146370 123748 142019 135972 167933 133215 143902 141363 131189 FALSE TRUE 147685.2702 171507.9089 126972.9745 170109.9343 112859.528 128933.1058 122773.2602 141973.2291 136275.3732 156892.9728 0.941312205 1.093152267 0.80929676 1.084241896 0.719340873 0.821790189 0.782528739 0.904904959 0.868588126 1 17.25942121 3.243022115 24.99999969 0.843150201 0.977604152 0.288883682 0.101434751 138.9788118 778761.4753 0.02686769 0.035179462 1749.935794 -3.243022115 0.13445395 AGHFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGHFDK 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 74.417 0.080382 147610000 445260 337170 419680 403280 483820 505710 539350 447400 442340 308470 FALSE TRUE 462839.2086 395076.3247 430617.2056 483047.5803 401580.4492 388266.5166 497074.3377 441403.3348 426420.2698 368908.7905 1.254616915 1.07093226 1.167272824 1.30939569 1.088562972 1.052472933 1.347417981 1.196510753 1.155896202 1 18.49290464 -2.563474595 1.303785773 0.000226944 1.184177495 0.254424056 0.093722021 129714.3655 8386.550629 378459.1189 0.026535409 0.002732281 2.563474595 1.183950551 AGHFDKEIVPVLVSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGHFDKEIVPVLVSTR 16 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 149.09 5.22E-07 823880000 2164300 2137400 2370700 1712300 3062700 2884100 2095100 2343300 2558500 2660300 FALSE TRUE 2249748.235 2504481.823 2432482.39 2050987.829 2542103.348 2214311.484 1930880.587 2311891.896 2466420.085 3181534.85 0.707126699 0.787192956 0.764562547 0.644653579 0.799017917 0.695988442 0.606902227 0.726659303 0.77522963 1 21.60129149 0.796244292 2.639786283 0.99985597 0.715595731 0.693383995 0.056470684 0.511506721 5.613185602 0.054788378 0.014561117 6.255244539 -0.796244292 -0.284260239 AGHYAASIIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGHYAASIIIR 11 0 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 84.658 0.013245 0 58347 79673 68812 59455 93542 85603 62358 69042 69472 76187 FALSE TRUE 60650.58461 93356.21798 70605.29725 71215.02154 77641.76425 65723.00058 57470.21702 68116.60492 66971.71629 91114.38396 0.665653237 1.024604611 0.774908353 0.781600209 0.852135095 0.721324095 0.630748017 0.747594419 0.735029019 1 16.47539121 2.735697723 24.41810766 0.739955261 0.826545427 0.020261129 0.122651647 420.1341116 3583377.985 0.036453204 0.035768126 544.123801 -2.735697723 0.086590166 AGIIQDTWHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGIIQDTWHK 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 149.23 2.37E-05 685940000 773380 727100 757000 710660 922860 922120 807470 706360 691820 783990 FALSE TRUE 803913.6396 851973.7689 776728.0419 851226.4269 765992.5868 707971.6049 744178.3915 696892.3996 666921.5333 937597.8301 0.857418409 0.908677198 0.828423464 0.907880116 0.816973506 0.755090917 0.793707459 0.743274331 0.711308742 1 19.83860971 3.040432776 5.318043994 0.781323818 0.874121494 0.153310471 0.077295987 0.256362571 17.6478426 0.021021374 0.024930382 1097.571384 -3.040432776 0.092797676 AGIPVYAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGIPVYAWK 9 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 154.11 0.00023706 175720000 662180 572680 627540 524720 901370 812390 700600 629030 637380 695130 FALSE TRUE 688323.3777 671033.3352 643894.2079 628508.0499 748155.4494 623724.7344 645685.1413 620598.8817 614440.8183 831327.4144 0.827981089 0.807182975 0.774537441 0.7560295 0.899952818 0.750275672 0.776691746 0.746515598 0.739108091 1 19.66505726 AGKEPAKPS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.7)PS(0.3)R;AGKEPAKPS(0.995)PS(0.005)R;AGKEPAKPS(0.5)PS(0.5)R;AGKEPAKPS(0.624)PS(0.376)R 98.943 0.002126 1764182000 1520130 833862 1223850 837816 1523590 1408640 1415520 1128870 1250010 673906 TRUE FALSE 1580145.906 977071.312 1255744.536 1003533.504 1264610.716 1081504.708 1304567.844 1113739.344 1205022.384 805944.978 1.960612634 1.212330046 1.558102067 1.245163791 1.569103041 1.341908862 1.618681026 1.381904937 1.495167061 1 19.62032182 -2.844743694 0.374583556 1.30E-14 1.487525354 0.338821812 0.204576799 99.07199088 3.438356244 79.2940663 0.1264478 0.001429737 2.844743694 1.487525354 AGKEPAKPS(ph)PSRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGKEPAKPSPSRDR 14 3 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.797)PS(0.203)RDR 84.375 0.045082 127400000 181320 102580 156510 100330 218230 176280 166590 145270 173900 101620 TRUE FALSE 188478.6536 120197.317 160588.7792 120174.9745 181135.3425 135341.6415 153532.2405 143322.8933 167641.373 121530.4934 1.550875409 0.989030108 1.321386713 0.988846266 1.4904518 1.11364348 1.263322778 1.179316312 1.379418188 1 16.89095882 -1.045134764 4.210746836 0.999977922 1.238208513 0.143450821 0.182245143 3.40E-05 7.70E-06 0.154265363 0.036357231 0.090129142 1.045134764 0.238230591 AGKEPAKPSPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGKEPAKPSPSR 12 2 Q15311 Q15311 RALBP1 RalA-binding protein 1 1 AGKEPAKPS(0.201)PS(0.799)R 66.577 0.045427 576120000 696280 426550 598890 438510 827030 677380 717040 627510 640270 378080 TRUE FALSE 723769.672 499806.6444 614497.5654 525245.9692 686451.736 520068.7608 660836.5312 619099.2548 617226.8078 452157.5372 1.600702438 1.10538165 1.359034219 1.161643732 1.518169398 1.150193722 1.461518335 1.369211401 1.365070262 1 18.78646599 -0.963877887 4.622756473 0.999994508 1.338402894 0.306807012 0.154701589 0.032655085 42640805.37 558.6055588 0.032397258 0.108673114 0.963877887 0.338408386 AGKES(ph)DEKEQEQDKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGKESDEKEQEQDKDR 16 3 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 AGKES(1)DEKEQEQDKDR 132.14 0.00022504 157060000 456300 50403 89568 53960 192730 309790 248500 110320 137440 24785 TRUE FALSE 474315.0763 59059.32317 91902.21566 64633.12695 159969.8234 237845.9674 229021.9207 108841.3408 132493.5612 29641.14621 16.00191413 1.992477711 3.100494664 2.1805205 5.396883855 8.024182523 7.726486656 3.671968016 4.469920303 1 14.85531362 4.746050959 24.99970054 4.445898034 16.0019196 0.715077191 2.233961531 529.4865759 1767167.572 0.562225621 5.957885569 55725.11318 -4.746050959 11.55602156 AGKPVICATQMLESMIK ddPTM_MDA-MB-175_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 ; 237.52 2.93E-20 1222570000 1864470 1440280 1791480 1422410 2247840 1996230 1962770 1730100 1969520 1298410 FALSE TRUE 1938080.715 1687636.886 1838167.441 1703758.453 1865752.96 1532635.836 1808922.959 1706910.839 1898637.36 1552808.58 1.24811309 1.086828672 1.183769503 1.09721087 1.201534422 0.987008866 1.164936221 1.099240989 1.222711791 1 20.56644856 4.748400098 23.79308098 1.120433955 1.248113229 0.212945239 0.075798581 1019.988977 2466357.681 0.016250445 0.206314909 56027.3521 -4.748400098 0.127679274 AGKPYQLQIYPNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGKPYQLQIYPNER 14 1 Q86TI2;Q86TI2-2 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 105.03 0.0023408 0 168700 155440 161280 165830 218760 216340 153640 157900 175250 181210 FALSE TRUE 175360.4063 182135.6108 165483.0893 198630.679 181575.2533 166098.3137 141597.2953 155783.6088 168942.7867 216714.63 0.809176594 0.840439849 0.763599067 0.916554083 0.837854156 0.766437936 0.65338134 0.718842142 0.779563367 1 17.72543702 2.690151726 5.270446039 0.750937758 0.834706772 0.011401202 0.092715555 0.38127677 25.07835635 0.028765935 0.027438362 489.9499592 -2.690151726 0.083769014 AGLESGAEPGDGDS(ph)DTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK;AGLESGAEPGDGDS(1)DTTK 468.24 1.84E-214 4352240000 6771690 3014610 4160100 3170660 5250190 6028870 5591760 4117550 4215530 2314340 TRUE FALSE 7039041.55 3532345.817 4268515.624 3797807.085 4357764.579 4628756.311 5153463.24 4062360.977 4063813.899 2767790.612 2.543198723 1.276233036 1.542210456 1.372143929 1.574456015 1.672365059 1.861941152 1.467726987 1.468251927 1 21.40030337 -2.796079811 0.182879025 1.80E-22 1.778188197 0.295166291 0.326684797 74.11350635 1.495814804 31.00494271 1.040054018 0.001599264 2.796079811 1.778188197 AGLESGAEPGDGDS(ph)DTTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.965)DT(0.018)T(0.018)KK;AGLESGAEPGDGDS(1)DTTKK;AGLESGAEPGDGDS(1)DTTKK;AGLESGAEPGDGDS(1)DTTKK 334.15 1.36E-75 2308090000 6520500 1818960 2945630 1724860 4571300 4715470 4242290 2944480 3345330 1448890 TRUE FALSE 6777934.375 2131352.23 3022395.538 2066032.16 3794272.059 3620373.556 3909768.225 2905014.062 3224932.227 1732772.255 3.911612941 1.230024445 1.744254347 1.192327586 2.189711919 2.089353374 2.256365898 1.676512337 1.861140273 1 20.72465062 8 0.052073102 5.55E-13 5.506436968 0.205169246 0.697818098 933.1205891 3.658446329 88.22713826 406.9886249 100000000 -8 5.506436968 AGLESGAEPGDGDS(ph)DTTKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGLESGAEPGDGDSDTTKKK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AGLESGAEPGDGDS(0.999)DT(0.001)TKKK 205.13 4.67E-22 394880000 1152100 254300 455650 173080 946210 758200 477780 436630 534600 219990 TRUE FALSE 1197585.798 297974.0468 467524.6133 207314.7074 785373.5622 582119.5406 440330.3552 430777.689 515359.8504 263092.8285 4.551951508 1.13258141 1.777032905 0.78799072 2.985157621 2.212601324 1.673669167 1.637360058 1.958851761 1 18.0052124 4.746111397 24.79150517 1.731247679 4.551953028 0.668852656 0.604390638 485.649369 1594491.298 0.140976796 1.485014801 55732.86864 -4.746111397 2.820705349 AGLGS(ph)PERPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;AGLGS(1)PERPPK 145.6 2.19E-05 4075650000 8077140 6468780 7465290 5984440 9436210 9170230 8603060 7670440 7512030 5711430 TRUE FALSE 8396031.724 7579742.645 7659841.59 7168144.37 7832246.395 7040583.059 7928729.677 7567630.298 7241673.508 6830475.357 1.229201671 1.10969475 1.121421452 1.049435654 1.14666198 1.030760334 1.160787392 1.10792147 1.060200517 1 22.70355455 7.999999981 0.013624675 2.13E-07 2.413183273 0.418853354 0.049457605 7417.408899 7.804265005 563.8894696 844.6084255 99999995.52 -7.999999981 2.41318306 AGLIPS(ph)K ddPTM_MDA-MB-175_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 88.948 0.019126 707340000 2167100 1011200 1265400 1085700 1913000 2274500 1842300 1513100 1569600 1027500 TRUE FALSE 2252658.781 1184865.734 1298377.364 1300448.22 1587828.943 1746281.845 1697895.712 1492819.369 1513110.403 1228818.952 1.833190135 0.964231331 1.056605907 1.058291148 1.292158573 1.421105886 1.381729757 1.214840776 1.231353406 1 20.22884094 0.609704428 1.882664195 1.000157585 1.261111863 0.109832226 0.232680626 5.082740513 21.51538639 0.216485389 0.060234904 4.071031177 -0.609704428 0.260954278 AGLLVLAVLSDGAGDHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGLLVLAVLSDGAGDHIR 18 0 Q8TEX9;Q8TEX9-2;H0YN14 Q8TEX9 IPO4 Importin-4 0 ; 147.12 7.89E-08 189994000 194385 207595 232080 249430 255540 296390 270860 231280 245350 197088 FALSE TRUE 202059.4699 243247.8264 238128.1955 298766.5095 212103.4021 227557.9143 249629.2854 228180.0699 236519.9014 235703.6201 0.857260783 1.032007172 1.010286543 1.267551637 0.899873332 0.965440897 1.059081253 0.968080464 1.003463168 1 17.84661439 1.689745247 16.83642727 0.989401212 1.017291432 0.008667515 0.103678567 1.099675935 344.6022405 0.048323479 0.026717494 48.94916042 -1.689745247 0.02789022 AGLNEMVEYITHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGLNEMVEYITHSR 14 0 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3 E9PFR3 PPP2R5D Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform 0 200.63 1.90E-08 255620000 186550 225780 205290 212330 276850 307810 236330 227510 238270 261300 FALSE TRUE 193915.138 264555.9587 210640.026 254328.2403 229791.1359 236325.7924 217805.8371 224460.6006 229694.7092 312496.7321 0.620534931 0.846587921 0.674055132 0.81385888 0.735339324 0.756250444 0.696985967 0.718281433 0.735030756 1 18.25348158 0.797708827 17.03502112 1 0.734940896 0.630014428 0.061368785 142804.885 12025728.08 0.052564934 0.013141233 6.276374174 -0.797708827 -0.265059104 AGLQFPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 191.44 8.35E-05 10825770000 4597280 6026080 5144280 4927680 6893550 6546190 5660180 5188760 4767680 7365130 FALSE TRUE 4778784.164 7061012.364 5278344.163 5902360.396 5721786.833 5025936.581 5216520.301 5119213.159 4596092.128 8808186.21 0.542538958 0.80164204 0.59925438 0.670099412 0.649598759 0.570598357 0.59223547 0.581188117 0.521797793 1 23.07041354 -1.870497307 4.581645036 1.097640726 0.617204897 0.701407164 0.075469756 0.044889113 0.001268815 0.043578559 0.01685533 0.013474191 1.870497307 -0.480435829 AGLQMKS(ph)PEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGLQMKSPEKK 11 2 Q9BRQ0 Q9BRQ0 PYGO2 Pygopus homolog 2 1 AGLQMKS(1)PEKK;AGLQMKS(1)PEKK 114.64 0.00064189 759710000 3177900 672290 1192880 594110 2243400 2107900 1705070 1295330 1556050 564520 TRUE FALSE 3303365.946 787750.5778 1223967.433 711623.1848 1862067.669 1618372.171 1571422.158 1277968.22 1500048.064 675126.8856 4.892955704 1.166818556 1.812944291 1.054058429 2.758100305 2.39713779 2.327595288 1.892930421 2.221875764 1 19.36479915 8 0.056793324 1.60E-10 6.386210568 0.168161854 0.984899223 899.1245331 3.82594909 91.38004602 482.445305 99999999.99 -8 6.386210568 AGLS(ph)PAEPLLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGLSPAEPLLSR 12 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 AGLS(0.994)PAEPLLS(0.006)R;AGLS(1)PAEPLLSR 128.21 0.0002685 80674000 109697 124463 122818 102508 127434 139477 126440 133737 124726 125118 TRUE FALSE 114027.9223 145838.5521 126018.738 122783.7764 105772.8142 107085.5805 116529.3024 131944.4743 120237.1356 149632.4766 0.762053298 0.974645046 0.842188413 0.820569032 0.706884071 0.715657343 0.778770125 0.881790353 0.803549726 1 17.19106381 -0.807609907 7.399016542 0.999999951 0.813636039 0.365476211 0.07510404 0 7.76E-11 0.077026886 0.018155411 0.155736386 0.807609907 -0.186363912 AGLS(ph)PANCQSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGLSPANCQSDR 12 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 1 AGLS(1)PANCQSDR 113.43 0.00020039 0 80322 134460 164480 140360 183220 196810 168670 171940 171650 150350 TRUE FALSE 83493.17458 157552.459 168766.4839 168122.7891 152076.3298 151103.8602 155449.2047 169635.4255 165472.35 179808.2039 0.464345746 0.876225087 0.938591679 0.935011782 0.845769696 0.840361323 0.864527876 0.943424281 0.920271414 1 17.45609932 4.737531002 4.645762033 0.904913693 0.437816406 0.889073968 0.047022038 0.056157077 3.2867032 0.01149667 0.085423431 54642.55554 -4.737531002 -0.467097287 AGLVGPEFHEK ddPTM_MDA-MB-175_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 ;;; 196.48 6.03E-08 2200310000 2766030 2159170 2571490 2225570 3247220 3132720 2912900 2605650 2868980 2236010 FALSE TRUE 2875235 2529990.651 2638505.142 2665781.103 2695258.704 2405193.257 2684579.287 2570725.524 2765725.97 2674113.349 1.075210593 0.946104492 0.986684107 0.996884109 1.007907427 0.899435792 1.003913797 0.961337531 1.034259065 1 21.35062919 1.23528121 24.98961595 1.01712953 0.981791452 0.077646879 0.043830955 204.5906325 1558883.041 0.034115338 0.009850252 17.19021108 -1.23528121 -0.035338077 AGLYGLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 2005590000 1771400 2033490 1957140 1890620 3162810 2580490 1886130 1880170 1887090 3030110 FALSE TRUE 1841336.24 2382726.089 2008144.676 2264578.993 2625196.686 1981210.305 1738290.202 1854969.396 1819174 3623802.04 0.508122745 0.657521041 0.554154077 0.624917964 0.724431593 0.54672145 0.479686855 0.511884859 0.502007003 1 21.78907272 -1.023628805 5.490065581 1.000001886 0.567648092 0.752698449 0.074334919 1.84E-06 3.27E-07 0.07719217 0.01819429 0.094704626 1.023628805 -0.432353794 AGMSSNQS(ph)IS(ph)SPVLDAVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.001)S(0.006)NQS(0.992)IS(0.797)S(0.204)PVLDAVPR 130.01 4.11E-05 88399000 58223 63931 63657 73129 69344 82338 75937 74821 65523 64691 TRUE FALSE 60521.689 74910.65194 65315.95371 87593.69793 57556.93165 63216.24734 69984.85952 73818.14688 63164.84003 77365.96287 0.782277978 0.96826368 0.844246634 1.132199415 0.743956768 0.817106709 0.904594953 0.954142418 0.81644224 1 16.23941137 -1.158143041 4.228356545 1.000029571 0.89271428 0.089915331 0.107323541 2.82E-05 5.62E-06 0.098093233 0.023114428 0.069479544 1.158143041 -0.107315292 AGMSSNQS(ph)ISS(ph)PVLDAVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMSS(0.001)NQS(0.925)IS(0.146)S(0.929)PVLDAVPR 148.83 2.04E-07 107810000 78147 79814 87218 98534 81187 103770 96882 90090 96419 83773 TRUE FALSE 81232.3039 93521.43363 89490.97273 118023.7311 67386.86274 79670.99015 89288.13569 88882.49091 92948.89902 100186.7154 0.810809133 0.933471401 0.893241907 1.178037733 0.672612756 0.795225094 0.891217317 0.887168429 0.927756725 1 16.6123317 0.913343882 2.239630601 0.999829263 0.884655114 0.081859988 0.121244965 1.127998604 12.06521061 0.11456061 0.031321396 8.1911312 -0.913343882 -0.115174149 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSIS(0.754)S(0.246)PVLDAVPR 258.67 1.91E-30 393780000 226900 290770 270230 285770 275800 346260 317540 307380 294760 284050 TRUE FALSE 235858.1872 340707.4856 277272.4158 342294.4531 228919.6145 265846.3626 292650.3851 303260.0739 284151.6452 339704.159 0.694304679 1.00295353 0.816217313 1.007625147 0.67387934 0.782582007 0.861486023 0.892718166 0.836467961 1 18.37391936 0.01969919 0.784926308 1.003771646 0.843249124 0.169334595 0.105251201 9.244935427 5.848393772 0.20482984 0.033884186 1.046403516 -0.01969919 -0.160522522 AGMSSNQSISS(ph)PVLDAVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQS(0.001)IS(0.213)S(0.786)PVLDAVPR;AGMSSNQS(0.001)IS(0.008)S(0.991)PVLDAVPR;AGMSSNQS(0.063)IS(0.24)S(0.696)PVLDAVPR;AGMSSNQSIS(0.023)S(0.977)PVLDAVPR;AGMSSNQS(0.009)IS(0.051)S(0.941)PVLDAVPR;AGMSSNQS(0.455)IS(0.057)S(0.488)PVLDAVPR;AGMSSNQS(0.01)IS(0.045)S(0.946)PVLDAVPR;AGMSSNQS(0.001)IS(0.016)S(0.984)PVLDAVPR;AGMSSNQSIS(0.092)S(0.908)PVLDAVPR;AGMSSNQSIS(0.029)S(0.971)PVLDAVPR;AGMSSNQSIS(0.013)S(0.987)PVLDAVPR;AGMSSNQSIS(0.033)S(0.967)PVLDAVPR;AGMSSNQSIS(0.183)S(0.817)PVLDAVPR;AGMSSNQSIS(0.209)S(0.791)PVLDAVPR;AGMSSNQSIS(0.492)S(0.508)PVLDAVPR;AGMSSNQSIS(0.023)S(0.977)PVLDAVPR 484.93 4.06E-240 11961048000 3347338 3842677 3736232 4006695 3718231 4489720 4060984 3900128 3695795 3624411 TRUE FALSE 3479493.489 4502626.883 3833601.275 4799207.312 3086207.423 3447050.572 3742673.463 3847853.163 3562784.06 4334544.942 0.802735589 1.038777298 0.884429929 1.107199804 0.712002636 0.795250855 0.863452453 0.887717907 0.821951118 1 22.04744911 3.233343036 24.99999976 0.843220443 0.958759643 0.220623122 0.102589745 184.6138409 884575.1302 0.027876917 0.0342704 1711.366536 -3.233343036 0.115539199 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AGMS(0.007)S(0.007)NQS(0.008)IS(0.251)S(0.728)PVLDAVPRT(0.806)PS(0.194)R;AGMS(0.006)S(0.006)NQS(0.005)IS(0.102)S(0.881)PVLDAVPRT(0.817)PS(0.183)R;AGMSSNQS(0.001)IS(0.048)S(0.951)PVLDAVPRT(0.883)PS(0.117)R;AGMSSNQSIS(0.158)S(0.842)PVLDAVPRT(0.904)PS(0.096)R;AGMSSNQSIS(0.008)S(0.992)PVLDAVPRT(0.975)PS(0.025)R;AGMSSNQSIS(0.008)S(0.992)PVLDAVPRT(0.749)PS(0.251)R;AGMSSNQS(0.001)IS(0.026)S(0.974)PVLDAVPRT(0.869)PS(0.131)R;AGMSSNQSIS(0.002)S(0.998)PVLDAVPRT(0.907)PS(0.093)R 187.89 5.25E-17 3442650000 1034784 1342692 1183239 1087304 1302813 1522413 1059627 1209576 1192540 1438890 TRUE FALSE 1075638.071 1573288.906 1214075.18 1302369.486 1081361.312 1168855.653 976570.6669 1193363.612 1149620.718 1720812.946 0.625075534 0.914270729 0.705524202 0.756833849 0.628401427 0.679246199 0.567505416 0.693488281 0.668068381 1 20.71465885 -1.178685087 4.407611234 1.000073395 0.694013814 0.518941456 0.0886258 13064251.28 3493650.171 9246.371524 0.020856352 0.066269686 1.178685087 -0.306059581 AGMSSNQSISSPVLDAVPRT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AGMSSNQSISSPVLDAVPRT(0.998)PS(0.002)R;AGMSSNQSISSPVLDAVPRT(0.998)PS(0.002)R 197.1 4.89E-24 1142000000 176146 218160 196905 198335 231600 262860 181506 212490 193136 250610 TRUE FALSE 183100.3801 255627.283 202036.5061 237565.071 192232.7147 201814.7487 167279.0854 209641.9191 186185.0731 299712.2313 0.610920613 0.852909078 0.674101638 0.792643897 0.641390957 0.673361737 0.558132328 0.699477356 0.621212796 1 18.19321844 -1.032291725 4.608629399 1.000010018 0.683131955 0.57571242 0.082266026 87456716863 18360479332 10651781.7 0.018706675 0.092834259 1.032291725 -0.316878062 AGMTHIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 AGMTHIVR 8 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;;;;; 163.77 0.00033395 3966850000 2790613.2 3207845 2907891 2858217 4050046 3929309 3162787 2993346 3010444 4283887 FALSE TRUE 2900788.764 3758767.425 2983673.028 3423563.792 3361620.628 3016786.534 2914879.491 2953225.093 2902098.708 5123232.638 0.566202819 0.733671042 0.582380938 0.668242892 0.656152251 0.588844339 0.568953178 0.576437828 0.566458507 1 22.28862297 -2.026608325 2.457913579 1.450595964 0.612384642 0.825651693 0.053498547 3680023.687 1474230.293 9344732.18 0.013016506 0.009405712 2.026608325 -0.838211322 AGNNMLLVGVHGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGNNMLLVGVHGPR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 126.95 8.24E-05 660560000 531300 649650 607090 610240 719870 773060 533880 604900 587760 822930 FALSE TRUE 552276.1343 761222.3339 622911.2641 730943.6506 597506.7545 593528.5308 492033.0906 596792.3049 566606.6324 984167.3776 0.561160781 0.773468367 0.632932241 0.74270258 0.607119041 0.603076818 0.499948588 0.606393098 0.575721819 1 19.90854417 -1.852031575 7.493557187 1.029334499 0.62313263 0.684200002 0.076938498 0.033205861 0.000655686 0.065604294 0.018020638 0.014059453 1.852031575 -0.40620187 AGNS(ph)DS(ph)EEDDANGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGNSDSEEDDANGR 14 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 2 AGNS(1)DS(1)EEDDANGR;AGNS(1)DS(1)EEDDANGR 185.96 1.63E-06 125188000 319490 299020 330950 329550 347560 451740 413360 335530 323160 244381 TRUE FALSE 332103.7119 350374.3589 339574.8289 394734.0064 288481.8753 346830.2312 380959.7631 331032.7692 311529.5347 292262.778 1.136318878 1.198833329 1.16188189 1.350613339 0.987063345 1.186706818 1.303483686 1.132654563 1.065922718 1 18.15690658 1.203789775 2.608486174 1.007936873 1.188111148 0.315664011 0.092202303 0.305271616 3.582197193 0.082264243 0.023138862 15.98783933 -1.203789775 0.180174275 AGNS(ph)DS(ph)EEDDANGRVELILEPK ddPTM_MDA-MB-175_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 142.28 6.60E-08 109960000 302870 195692 268844 176739 361470 349450 308650 251610 280980 192329 TRUE FALSE 314827.5415 229300.5787 275850.2955 211697.4467 300027.4585 268295.5335 284457.2065 248237.5795 270867.5847 230012.1852 1.368742883 0.996906223 1.199285574 0.920374921 1.304398105 1.166440522 1.236704944 1.079236647 1.177622761 1 17.81135077 -0.512710272 0.886972863 0.992659249 1.153612705 0.121869079 0.127831534 52.34721806 26.12632298 1.448819597 0.037321346 0.307107009 0.512710272 0.160953456 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGS(ph)AR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGS(1)AR 195.96 2.40E-25 550210000 256545 321190 322412 289368 324212 361760 281807 302274 312438 331869 TRUE FALSE 266673.5947 376351.884 330814.3216 346604.1267 269102.56 277746.7225 259718.231 298222.5115 301193.4174 396892.3765 0.671904049 0.948246694 0.833511403 0.873294997 0.678024008 0.699803622 0.65437949 0.751393902 0.758879321 1 18.59838833 6.852269094 12.04793986 0.77634861 0.686881284 0 0.115963352 0 0 0.025161406 0 7116543.265 -6.852269094 -0.089467326 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 AGPDLPSLPSHALEDEGWAAAAPS(0.96)PGS(0.04)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.815)PGS(0.185)AR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(1)PGSAR;AGPDLPSLPSHALEDEGWAAAAPS(0.999)PGS(0.001)AR 385.19 7.95E-155 9576498000 1747207 2360269 2157771 2124051 2343984 2773352 2158504 2336601 2195108 2503238 TRUE FALSE 1816188.081 2765626.84 2214004.285 2544181.948 1945554.437 2129283.029 1989314.816 2305282.686 2116106.492 2993699.559 0.606670124 0.923815762 0.739554602 0.84984545 0.649882996 0.711254749 0.664500488 0.770044769 0.706853327 1 21.51349801 -1.935165171 6.274731072 1.101639208 0.740652306 0.437967065 0.089628732 0.052769399 0.00054525 0.03593437 0.019166569 0.01161007 1.935165171 -0.360986902 AGPGSS(ph)PLFSLLPGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 AGPGS(0.015)S(0.985)PLFSLLPGYR 200.19 3.80E-11 412940000 302570 400980 347410 376830 429460 553680 461670 446310 431440 441950 TRUE FALSE 314515.6972 469845.1958 356463.79 451365.8493 356460.5426 425096.2111 425483.099 440327.9445 415912.5587 528541.6409 0.595063232 0.888946413 0.674428962 0.853983517 0.674422818 0.8042814 0.805013392 0.833099817 0.786905944 1 19.01165761 -4.999999983 0.134065195 1.780209635 0.683685953 0.460196471 0.082133525 119.9794751 1.003583524 24.95462987 0.510192701 1.00E-05 4.999999983 -1.096523682 AGPIWDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGPIWDLR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5;O43390;O43390-3;B4DT28;O43390-2;O43390-4 O60506-2;O43390;O43390-2 SYNCRIP;HNRNPR Heterogeneous nuclear ribonucleoprotein Q;Heterogeneous nuclear ribonucleoprotein R 0 ;;;;; 108.92 0.0086475 3743020000 5529330 6547900 5821300 5598640 7322700 7841390 6146880 5927550 5871910 7701590 FALSE TRUE 5747632.218 7672450.889 5973007.86 6706034.282 6077990.07 6020346.01 5665071.484 5848100.888 5660581.106 9210569.105 0.624025742 0.833005084 0.648494984 0.72808034 0.659892999 0.65363453 0.615062047 0.634933718 0.614574522 1 23.13485887 -1.028605638 8.983251824 1.000000001 0.668559644 0.711782045 0.06338441 8.90E-10 5.10E-11 0.061445534 0.014482851 0.093625546 1.028605638 -0.331440356 AGPPPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGPPPEKR 8 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 103.56 0.0076141 229520000 99536 245410 194502 212070 257130 306610 219745 249010 237920 284260 FALSE TRUE 103465.7581 287557.2585 199570.8819 254016.813 213423.1344 235404.4742 202520.8127 245672.4282 229357.3057 339955.3045 0.304351063 0.845867838 0.587050354 0.747206499 0.62779763 0.692457129 0.595727762 0.722660965 0.674669001 1 18.37498556 -5 0.200208269 2.568534286 0.59817329 0.419620816 0.131071881 132.4681957 1.311246399 83.10804661 0.282484484 1.00E-05 5 -1.970360996 AGPSAQEPGSQT(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGPSAQEPGSQTPLK 15 0 O60271;A0A087X2D8;O60271-4;O60271-2;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 AGPSAQEPGS(0.005)QT(0.995)PLK 104.41 0.0073615 0 86832 58125 63076 55824 82796 82075 76814 66888 68632 44669 TRUE FALSE 90260.19441 68107.5166 64719.81238 66865.82058 68722.36549 63014.32511 70793.11796 65991.47577 66161.94773 53421.03531 1.689600246 1.274919443 1.21150427 1.251675865 1.286428934 1.179578882 1.3251918 1.235308814 1.238499916 1 15.70512032 4.738775075 3.946699046 1.232882433 1.732125196 0.739751713 0.083269183 0.109103547 3.497095159 0.017868741 0.156805747 54799.30814 -4.738775075 0.499242763 AGQATEGHCPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGQATEGHCPR 11 0 C9J8T0;P57772-2;P57772 C9J8T0 EEFSEC Selenocysteine-specific elongation factor 0 ;; 109.72 0.0018907 249141000 66979 86947 82902 84673 81693 106004 81486 80100 80544 90393 FALSE TRUE 69623.38264 101879.4709 85062.49422 101421.0667 67806.85304 81386.17751 75098.9144 79026.39052 77645.23717 108103.7777 0.644042088 0.942422856 0.78685959 0.938182447 0.627238516 0.752852299 0.694692785 0.731023395 0.718247214 1 16.72205741 5.021293698 17.16613289 0.781549007 0.325020978 0.121126047 0.117005408 115832060.6 2235538365 0.026904426 1425683563 105025.2438 -5.021293698 -0.456528029 AGQDMGLEHGFEKPLDSAMS(ph)AEEDTDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGQDMGLEHGFEKPLDSAMSAEEDTDVR 28 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 AGQDMGLEHGFEKPLDS(0.002)AMS(0.998)AEEDTDVR;AGQDMGLEHGFEKPLDS(0.047)AMS(0.93)AEEDT(0.023)DVR 219.81 1.64E-34 98954000 81806 94447 113403 96951 140135 134995 145643 124704 124402 85691 TRUE FALSE 85035.76405 110667.5376 116358.3753 116127.6184 116314.9028 103644.4571 134227.1211 123032.5469 119924.7963 102480.5108 0.829774982 1.079888622 1.135419549 1.133167834 1.134995345 1.011357733 1.309781929 1.2005458 1.170220517 1 16.64499005 5.328503398 1.221865582 1.155348026 3.26E-13 0.53216059 0.084855577 3.989354406 1.839077182 0.023760328 8.286093833 213060.724 -5.328503398 -1.155348026 AGQEHLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 110.76 0.0033646 610490000 1147020 1600010 1374310 1588610 1359280 1722460 1346100 1463220 1293260 1732290 FALSE TRUE 1192305.235 1874799.271 1410125.648 1902832.316 1128230.071 1322444.769 1240589.165 1443607.929 1246715.825 2071699.059 0.575520479 0.904957341 0.680661432 0.918488768 0.54459168 0.638338258 0.598826919 0.696823181 0.601784231 1 20.98238302 -1.137372465 3.810313303 1.000157321 0.689092019 0.371206232 0.123075902 7734745406 15535941968 15854451.04 0.028645551 0.072883217 1.137372465 -0.311065302 AGQTQPNPGILPIQPALT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGQTQPNPGILPIQPALTPR 20 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 AGQTQPNPGILPIQPALT(1)PR 101.49 0.0040832 46025000 45299 37816 37308 34650 37151 45591 40150 35494 41080 39098 TRUE FALSE 47087.4395 44310.60383 38280.27713 41503.66658 30836.08629 35003.18119 37002.93809 35018.26099 39601.53882 46758.50452 1.007034763 0.947648011 0.818680527 0.887617493 0.65947546 0.748594968 0.791362736 0.748917472 0.846937669 1 15.51294117 4.338133737 1.385353597 0.787201287 1.033452 0.349851349 0.088013497 0.600321903 1.707711677 0.023585671 0.169942064 21783.8048 -4.338133737 0.246250713 AGRPQYDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGRPQYDTK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 163.16 5.77E-05 540810000 399420 373800 404410 373660 459340 501170 445550 393230 430500 455840 FALSE TRUE 415189.41 437997.2422 414949.2568 447568.8327 381261.5509 384780.8628 410626.6268 387959.395 415006.3891 545153.1204 0.761601456 0.803438935 0.761160931 0.820996553 0.699365988 0.705821628 0.753231728 0.711652159 0.761265732 1 19.05630198 0.939711435 22.24192802 1 0.750377527 0.795133453 0.037603223 3445.522373 1271139.654 0.038280533 0.009570133 8.703850742 -0.939711435 -0.249622473 AGRVTWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGRVTWLR 8 1 Q5THK1-4;H3BLU3 Q5THK1-4 PRR14L Protein PRR14L 0 ;;; 75.213 0.035543 1286840000 251499 415350 381108 254855 547845 407440 299172 380205 356046 439593 FALSE TRUE 261428.3747 486683.1315 391039.9876 305264.5583 454722.5026 312818.2348 275722.1169 375108.9739 343231.974 525722.8318 0.497274151 0.925740908 0.743813972 0.58065684 0.864947221 0.595025013 0.524462892 0.713510906 0.652876294 1 19.00394287 -1.556168543 8.423175862 1.000057951 0.682655004 0.347315974 0.132428823 0.000137084 7.22E-06 0.121963855 0.028741944 0.027786347 1.556168543 -0.317402947 AGS(ph)EECVFYTDETASPLAPDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGSEECVFYTDETASPLAPDLAK 23 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 AGS(0.979)EECVFY(0.021)TDETASPLAPDLAK 148.91 6.50E-08 69986000 115980 58467 67033 53737 122150 123900 112520 86710 96408 53508 TRUE FALSE 120558.98 68508.25244 68779.93505 64366.01821 101386.9866 95126.10272 103700.3884 85547.79428 92938.29491 63991.86813 1.88397344 1.070577472 1.074823053 1.005846838 1.584372977 1.486534235 1.620524473 1.336854147 1.452345394 1 15.96560096 3.22394552 24.99703285 1.440970424 1.232218711 0.059733833 0.280576985 520.5174331 890268.6499 0.078872475 0.094655515 1674.732775 -3.22394552 -0.208751713 AGS(ph)FTGTSDPEAAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSFTGTSDPEAAPAR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 AGS(0.862)FT(0.08)GT(0.033)S(0.025)DPEAAPAR;AGS(0.98)FT(0.016)GT(0.002)S(0.001)DPEAAPAR;AGS(1)FTGTSDPEAAPAR;AGS(0.983)FT(0.017)GTSDPEAAPAR 219.01 1.34E-14 2625500000 1633470 1488390 1631380 1488990 2071800 2359410 1943760 1657600 1600660 1240730 TRUE FALSE 1697960.657 1744009.404 1673895.103 1783507.778 1719636.176 1811472.785 1791403.012 1635382.583 1543052.559 1483827.288 1.144311518 1.175345283 1.12809295 1.201964536 1.158919363 1.220811073 1.207285394 1.102138097 1.039913858 1 20.50089175 1.376750184 2.285480009 1.009252992 1.176363848 0.831128965 0.028372874 0.113154224 1.023594243 0.025295662 0.007762085 23.80949499 -1.376750184 0.167110856 AGS(ph)ISTLDSLDFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 AGS(1)ISTLDSLDFAR;AGS(0.499)IS(0.499)T(0.001)LDSLDFAR;AGS(0.997)IS(0.002)TLDSLDFAR;AGS(0.877)IS(0.123)TLDSLDFAR 323.24 2.20E-56 207427000 251966 208342 246802 230818 287351 330644 312610 249098 254553 177334 TRUE FALSE 261913.8122 244123.1178 253233.8629 276473.1115 238507.1797 253856.942 288106.8113 245759.2488 245391.6873 212079.202 1.234981128 1.151094098 1.194053261 1.303631421 1.124613717 1.196991216 1.35848687 1.158808815 1.157075682 1 17.69424362 0.855947673 1.817802553 1.001179579 1.217541756 0.492818651 0.066538401 0.454933895 2.888582816 0.061905579 0.017469215 7.177078115 -0.855947673 0.216362177 AGS(ph)LQLSSMSAGNSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGSLQLSSMSAGNSSLR 17 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 AGS(1)LQLSSMSAGNSSLR;AGS(1)LQLSSMSAGNSSLR 161.86 3.06E-09 272930000 97150 97824 108310 107562 136665 168671 150316 114783 108032 90746 TRUE FALSE 100985.557 114624.511 111132.6476 128837.4426 113434.7321 129499.7165 138533.8391 113244.5216 104143.9494 108525.9413 0.930519983 1.056194581 1.0240192 1.187158029 1.045231498 1.193260477 1.276504378 1.043478825 0.959622632 1 16.72768041 4.85476771 1.164153351 1.108516002 0.819502462 0.205029192 0.094231617 3.006172359 2.87789561 0.027676961 1.124232851 71576.0471 -4.85476771 -0.289013541 AGS(ph)PDVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGSPDVLR 8 0 Q8NDX6 Q8NDX6 ZNF740 Zinc finger protein 740 1 AGS(1)PDVLR;AGS(1)PDVLR 141.48 0.00066382 1116120000 1269940 1382480 1443510 1278580 1808870 1822940 1594680 1464470 1447670 1079600 TRUE FALSE 1320078.212 1619910.186 1481129.056 1531479.308 1501398.924 1399589.812 1469684.815 1444841.175 1395568.639 1291126.95 1.02242325 1.254648264 1.147159895 1.18615703 1.162859255 1.08400635 1.138296133 1.119054308 1.080891883 1 20.30019943 0.792255359 0.53005748 0.995126793 1.158418686 0.374404954 0.057124299 1.185066968 0.743008074 0.065028576 0.026904917 6.198054047 -0.792255359 0.163291892 AGS(ph)PFSPPPSSSSLTGEAAISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.995)PFS(0.005)PPPSSSSLTGEAAISR;AGS(0.996)PFS(0.004)PPPSSSSLTGEAAISR;AGS(0.995)PFS(0.005)PPPSSSSLTGEAAISR;AGS(0.995)PFS(0.005)PPPSSSSLTGEAAISR;AGS(0.999)PFS(0.001)PPPSSSSLTGEAAISR;AGS(1)PFSPPPSSSSLTGEAAISR 263.09 2.25E-37 1402340000 716435 682414 752247 611377 901795 1041970 784031 742774 752117 571480 TRUE FALSE 744720.407 799613.2961 771851.1748 732305.5458 748508.208 799988.2587 722576.6015 732818.3295 725048.4561 683450.5644 1.089647805 1.169965083 1.129344557 1.071482831 1.095189977 1.170513714 1.057247794 1.072233118 1.060864522 1 19.38247746 1.225670864 0.565625412 0.998943909 1.124342653 0.538351554 0.034043535 0.602078276 0.486431986 0.035099759 0.017211634 16.81399305 -1.225670864 0.125398744 AGS(ph)PLCNSNLQDS(ph)EEDIEPSYSLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 AGS(1)PLCNSNLQDS(1)EEDIEPSYSLFR;AGS(1)PLCNSNLQDS(1)EEDIEPSYSLFR 135.75 1.95E-05 53627000 36000 33440 38874 32156 46726 56290 39017 37602 35333 32439 TRUE FALSE 37421.3078 39183.05987 39887.08838 38516.36082 38783.53121 43217.50058 35958.74559 37098.00669 34061.37223 38794.80097 0.964595948 1.010008014 1.02815551 0.992822746 0.999709503 1.114002379 0.926895994 0.956262328 0.877988065 1 15.2435757 AGS(ph)PLCNSNLQDSEEDIEPSYSLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSPLCNSNLQDSEEDIEPSYSLFR 25 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR;AGS(1)PLCNSNLQDSEEDIEPSYSLFR 217.74 9.66E-34 581390000 328154 308673 350647 316798 440609 489410 393469 347333 369252 305369 TRUE FALSE 341109.7733 361685.1866 359785.1489 379459.6989 365714.4396 375751.9446 362627.8716 342677.5693 355962.6926 365200.2089 0.93403499 0.990375081 0.985172352 1.039045678 1.001408079 1.028893017 0.992956364 0.938327966 0.974705611 1 18.47832807 4.741928108 4.87513914 0.992611611 0.930782651 0.320405011 0.026320353 0.262568109 18.4795029 0.007320422 0.055126271 55198.60569 -4.741928108 -0.06182896 AGS(ph)PRGS(ph)PLAEGPQAFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSPRGSPLAEGPQAFFPER 20 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 AGS(1)PRGS(1)PLAEGPQAFFPER;AGS(1)PRGS(1)PLAEGPQAFFPER;AGS(1)PRGS(1)PLAEGPQAFFPER;AGS(1)PRGS(1)PLAEGPQAFFPER 213.37 4.59E-23 353107000 195027 189428 217627 163478 277029 306217 205973 219158 233651 228787 TRUE FALSE 202726.8166 221960.7855 223298.5384 195813.4605 229939.7095 235102.7425 189828.298 216220.5455 225241.9462 273613.4323 0.740924212 0.811220354 0.816109562 0.715657338 0.840381657 0.859251465 0.693782818 0.790240975 0.823212312 1 18.06177953 0.776919524 2.771640929 0.999933749 0.783825389 0.623444512 0.050312023 0.731859232 8.099976839 0.0471268 0.012444529 5.983007175 -0.776919524 -0.21610836 AGS(ph)STPGDAPPAVAEVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.989)S(0.01)T(0.001)PGDAPPAVAEVQGR;AGS(0.882)S(0.059)T(0.059)PGDAPPAVAEVQGR;AGS(0.988)S(0.012)TPGDAPPAVAEVQGR 299.91 6.76E-48 197020000 330400 389540 429390 369710 431914 558110 391533 396710 386785 375730 TRUE FALSE 343444.4471 456440.4648 440580.2561 442837.5345 358497.4126 428497.4107 360843.6204 391392.7513 372864.6834 449347.0997 0.764318825 1.015785937 0.980489818 0.985513281 0.797818463 0.953600037 0.803039834 0.871025431 0.829792122 1 18.77747076 3.252968576 24.99982135 0.868252308 0.945328519 0.097140524 0.087133271 436.0765729 756649.3868 0.022718033 0.030619669 1790.476298 -3.252968576 0.077076211 AGSALPGFANS(ph)PAGSTSVVLVPPAHGTLVPDGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGSALPGFANSPAGSTSVVLVPPAHGTLVPDGNK 34 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AGSALPGFANS(0.894)PAGS(0.035)T(0.035)S(0.035)VVLVPPAHGTLVPDGNK 100.73 4.07E-05 295180000 77099 96354 118580 97136 135480 148010 131000 129220 126630 97908 TRUE FALSE 80142.92805 112902.05 121670.2922 116349.2109 112451.158 113636.9206 120731.8777 127488.0173 122072.611 117091.198 0.684448783 0.964223203 1.039107074 0.993663169 0.960372427 0.970499256 1.031092684 1.088792492 1.042543018 1 16.8372731 4.737042202 3.030523025 1.018849834 0.631189952 0.883622899 0.035852164 0.133483249 1.828225311 0.010526098 0.124572755 54581.08973 -4.737042202 -0.387659882 AGSATVLSGS(ph)IAGLEGGSQLALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSATVLSGSIAGLEGGSQLALR 23 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 AGSATVLSGS(1)IAGLEGGSQLALR;AGSATVLSGS(1)IAGLEGGSQLALR;AGSATVLS(0.001)GS(0.999)IAGLEGGSQLALR;AGSATVLS(0.002)GS(0.998)IAGLEGGSQLALR 303.34 4.44E-62 236194000 176425 192196 200466 221835 234540 237089 192886 197106 176393 200054 TRUE FALSE 183390.3952 225204.1679 205690.3086 265713.3009 194672.9746 182028.6729 177767.0913 194464.1165 170044.6504 239250.751 0.766519622 0.941289283 0.859726909 1.110605922 0.81367759 0.76082801 0.743015813 0.812804623 0.710738209 1 17.86816393 3.026611562 24.99754434 0.790159947 0.922482834 0.19913531 0.108601649 290.6745971 273042.8694 0.029562072 0.035332676 1063.191662 -3.026611562 0.132322886 AGSGKNDHAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGSGKNDHAEK 11 1 P43487;F6WQW2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 93.345 0.0055992 234850000 651821 456485 627746 322170 952440 705724 596151 618557 769605 634959 FALSE TRUE 677555.3964 534882.7478 644105.5765 385894.2644 790544.589 541830.2964 549423.1269 610266.2552 741907.0664 759367.059 0.892263351 0.704379709 0.848213744 0.508178831 1.041057259 0.713528839 0.723527733 0.803651209 0.977007177 1 19.53443789 1.248874563 3.852495563 0.999631072 0.772854663 0.290920098 0.131382278 0.248280855 7.072173454 0.104533458 0.030663769 17.73677115 -1.248874563 -0.226776409 AGSMKDPLLDDHGDFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 182.7 4.40E-10 1415120000 1752190 1574510 1814460 1538640 2269000 2202140 2094020 1930120 1990700 1577580 FALSE TRUE 1821367.814 1844919.845 1861746.318 1842978.4 1883316.19 1690726.359 1929885.241 1904249.898 1919055.096 1886676.596 0.96538422 0.977867562 0.986786141 0.976838533 0.998218875 0.896139997 1.022901988 1.009314422 1.017161659 1 20.84741571 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 AGSNEDPILAPS(0.212)GT(0.782)PPPT(0.005)IPPDETFGGR;AGSNEDPILAPS(0.046)GT(0.944)PPPT(0.01)IPPDETFGGR;AGSNEDPILAPS(0.148)GT(0.85)PPPT(0.002)IPPDETFGGR 93.667 0.0091417 260699000 251629 277976 278887 273402 319092 331047 278023 275825 278399 268902 TRUE FALSE 261563.5072 325716.2156 286155.0243 327480.0996 264852.8558 254166.3513 256230.8308 272128.017 268379.4744 321588.1985 0.81334921 1.012836345 0.889818176 1.01832126 0.82357766 0.790347259 0.796766896 0.84620026 0.834543916 1 18.29485494 3.208464971 24.99048042 0.83524115 0.936116438 0.211034805 0.077946616 242.3379068 201229.1732 0.02075091 0.024804968 1616.08787 -3.208464971 0.100875288 AGSPRGS(ph)PLAEGPQAFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGSPRGSPLAEGPQAFFPER 20 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AGS(0.028)PRGS(0.972)PLAEGPQAFFPER 45.099 0.091144 4023700000 75262 55124 78140 44726 113300 113370 92274 61642 85154 46495 TRUE FALSE 78233.40187 64591.11819 80176.39259 53572.66931 94041.30647 87041.53564 85041.32277 60815.78982 82089.32417 55604.80505 1.406953982 1.16161037 1.441896838 0.963453954 1.691244244 1.565359964 1.529388021 1.093714649 1.476299109 1 15.76292194 -0.518636354 0.787153403 0.975605465 1.360806469 0.201737158 0.217542368 31.07233946 13.07706158 2.489718136 0.072968851 0.3029449 0.518636354 0.385201004 AGSSPCLGSSSAASS(ph)PPPPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGSSPCLGSSSAASSPPPPASR 22 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 AGSSPCLGSSSAAS(0.025)S(0.975)PPPPASR;AGSSPCLGSSSAAS(0.066)S(0.934)PPPPASR 280.64 3.86E-44 96609000 252386 258323 253723 248980 294509 343487 262744 268146 269141 269885 TRUE FALSE 262350.3942 302687.9658 260335.2298 298227.5009 244448.4654 263717.3498 242149.4387 264551.9415 259454.668 322763.7985 0.81282472 0.937800234 0.806581256 0.923980639 0.757360232 0.817059878 0.750237294 0.819645644 0.803853063 1 18.30011925 5.103378688 15.02891104 0.835545191 5.63E-05 0 0.078198743 370591.3405 602457.1021 0.017588782 10307113.06 126875.7692 -5.103378688 -0.835488935 AGSST(ph)PGDAPPAVAEVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 AGS(0.009)S(0.043)T(0.948)PGDAPPAVAEVQGR 140.68 9.52E-07 0 177580 151830 163030 139900 194370 215000 183060 149550 163670 143630 TRUE FALSE 184590.9955 177905.6214 167278.6957 167571.8024 161331.0568 165069.5084 168711.2789 147545.5269 157779.5487 171771.5485 1.074630794 1.035710646 0.973844022 0.975550397 0.939218737 0.960982827 0.982184071 0.858963712 0.918542972 1 17.39013157 5.088789015 0.54149804 0.926978459 1.244255471 0.566701873 0.037426046 3.899841491 0.662757108 0.020326826 0.84625393 122684.3071 -5.088789015 0.317277012 AGT(ph)PVSELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGTPVSELTK 10 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 AGT(1)PVSELTK;AGT(1)PVSELTK;AGT(1)PVSELTK;AGT(0.999)PVS(0.001)ELTK 149.49 0.00025989 851281000 3489490 1064350 1491000 1119350 2276150 2903150 2414870 1627710 1698830 751800 TRUE FALSE 3627257.76 1247143.833 1529856.685 1340754.089 1889250.836 2228937.41 2225586.179 1605893.21 1637689.44 899100.8159 4.034317059 1.387101214 1.701540759 1.49121663 2.101266958 2.479073949 2.475346635 1.78611028 1.821474757 1 19.77812337 4.74651627 24.9694562 1.872964334 4.03431813 0.692732391 0.443373165 577.8554575 1813603.89 0.107507633 1.183835102 55784.85002 -4.74651627 2.161353796 AGTEDEEEEEEGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGTEDEEEEEEGRR 14 1 O95456;O95456-2;F8WBH7 O95456 PSMG1 Proteasome assembly chaperone 1 0 ; 302.63 8.76E-44 719270000 555450 493020 532620 501870 689230 895580 677980 588850 571010 445370 FALSE TRUE 577379.5949 577692.3498 546500.5148 601138.3881 572074.9308 687595.1176 624838.156 580957.4289 550459.4616 532631.7244 1.084012777 1.084599965 1.026038236 1.128619195 1.074053431 1.290939098 1.173114795 1.090730053 1.033471039 1 19.02277883 AGTEKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGTEKLR 7 1 A0A0G2JR78;Q9NY99-2;Q9NY99 A0A0G2JR78 SNTG2 Gamma-2-syntrophin 0 ; 119.56 0.0043366 896780000 734830 617720 737230 610450 820770 960220 787190 696080 732370 581550 FALSE TRUE 763841.6558 723808.6048 756442.8194 731195.188 681255.8086 737223.4573 725487.9909 686750.1862 706012.1468 695493.5881 1.09827275 1.040712118 1.087634498 1.051332752 0.979528525 1.060000365 1.043126786 0.987428494 1.015123876 1 19.40767769 6.90650851 0.226430261 0.993825115 1.338334002 0.490805603 0.027365674 26.28768228 0.524221205 0.042051886 3.019142802 8063220.003 -6.90650851 0.344508887 AGTFIAPPVYSNITPYQS(ph)HLRSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.014)PY(0.354)QS(0.429)HLRS(0.203)PVR 126.45 7.95E-05 1064400000 748410 1060400 912120 943440 1141900 1252400 915190 991960 1012900 1174800 TRUE FALSE 777957.8047 1242515.451 935890.5965 1130049.616 947800.2459 961549.0803 843455.0164 978664.3987 976445.9269 1404979.567 0.553714675 0.884365496 0.666123991 0.804317474 0.674600733 0.684386523 0.600332586 0.696568421 0.694989415 1 20.42211772 -0.322676942 8.292898951 1 0.698164217 0.516185494 0.088408367 0 0 0.079252388 0.018679967 0.475688945 0.322676942 -0.301835783 AGTFIAPPVYSNITPYQSHLRS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 AGTFIAPPVYSNIT(0.01)PY(0.06)QS(0.099)HLRS(0.831)PVR;AGTFIAPPVYSNIT(0.001)PYQS(0.067)HLRS(0.933)PVR 160.53 1.33E-11 2050640000 511210 804320 680660 715450 782700 871300 683490 825120 796040 997390 TRUE FALSE 531392.9655 942455.7033 698398.5588 856963.8746 649656.9336 668953.7797 629916.2678 814060.616 767390.6759 1192809.474 0.445496936 0.7901142 0.58550722 0.718441539 0.544644344 0.560821987 0.528094621 0.682473298 0.643347234 1 20.18593219 0.360682769 1.19299347 1.00035504 0.608913943 0.606721379 0.094653302 2.053842954 3.231389522 0.085968056 0.025730728 2.294472035 -0.360682769 -0.391441097 AGTFQAFEQFGQQLLAHGHYASPEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 221.29 1.61E-34 263450000 414080 172450 225620 171610 288180 365510 314620 247140 245710 189850 FALSE TRUE 430428.1981 202066.946 231499.8425 205553.9458 239195.2665 280625.8419 289959.2623 243827.4925 236866.9451 227047.4726 1.895763001 0.889976637 1.019609864 0.905334657 1.053503322 1.235978708 1.277086501 1.073905337 1.043248543 1 17.79263445 4.746153868 24.9850704 1.067963243 1.895763401 0.821386012 0.117431403 407.0512845 1339342.179 0.030686653 0.327442919 55738.3192 -4.746153868 0.827800157 AGTGYAS(ph)PDRTHVLAAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGTGYASPDRTHVLAAGK 18 1 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 AGT(0.156)GY(0.009)AS(0.68)PDRT(0.156)HVLAAGK;AGT(0.249)GYAS(0.75)PDRTHVLAAGK;AGT(0.003)GY(0.013)AS(0.984)PDRTHVLAAGK 119.41 4.50E-05 1035820000 799490 686300 792810 614170 961050 1030470 896930 734640 856340 696800 TRUE FALSE 831054.4825 804166.6863 813471.2799 735650.9929 797691.0643 791158.9594 826626.2829 724793.3524 825520.4907 833324.619 0.997275808 0.965010115 0.976175744 0.882790423 0.957239287 0.949400679 0.991961913 0.869761118 0.990634948 1 19.66851908 3.952932592 24.9931675 0.941189886 0.978505656 0.080754457 0.042253115 749.5444111 398014.4098 0.010481586 0.018896668 8972.895124 -3.952932592 0.037315771 AGTLSITEFADMLSGNAGGFRS(ph)R ddPTM_MDA-MB-175_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(0.034)GNAGGFRS(0.966)R 282.58 2.86E-52 2544119000 573116 936211 865497 399517 1166596 998341 350291 753544 799987 1690767 TRUE FALSE 595743.0622 1096997.957 888052.5628 478540.2702 968298.4286 766491.4328 322834.2761 743443.9752 771195.6241 2022040.422 0.294624705 0.54252029 0.439186355 0.236662069 0.478871944 0.379068304 0.159657677 0.367670185 0.381394761 1 20.94738041 0.596042355 3.660858374 0.999999209 0.361838142 0.761907854 0.106638976 7.53646307 67.71950904 0.102994046 0.026461591 3.944957741 -0.596042355 -0.638161067 AGTPIRDS(ph)HSPDLQLPTPEVIPSSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGTPIRDSHSPDLQLPTPEVIPSSGSK 27 1 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 AGT(0.024)PIRDS(0.489)HS(0.487)PDLQLPTPEVIPSSGSK 110.91 0.00081527 101530000 51936 45791 55681 36502 72542 63729 41663 49729 56370 56279 TRUE FALSE 53986.47338 53655.24805 57132.0926 43721.98665 60211.33675 48928.90557 38397.34519 49062.4641 54341.25471 67305.79252 0.802107387 0.797186186 0.84884362 0.649602137 0.894593682 0.726964259 0.570490945 0.728948613 0.807378573 1 16.03844305 0.879780643 4.168323807 0.999943219 0.748200191 0.410497524 0.088895875 0.678704178 21.68186743 0.087561007 0.022326229 7.581945234 -0.879780643 -0.251743028 AGTQIENIDEDFRDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AGTQIENIDEDFRDGLK 17 1 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ;; 272.76 1.11E-35 1919380000 649414 438818 574343 577326 969720 833130 980350 613595 690948 673225 FALSE TRUE 675053.3662 514181.578 589310.8504 691519.3597 804887.3408 639648.1837 903507.6053 605370.7627 666080.9164 805130.5491 0.838439638 0.638631311 0.731944467 0.858890972 0.999697927 0.794465176 1.122187708 0.751891433 0.827295545 1 19.6188632 3.668879538 3.967912335 0.903449739 0.725481485 0.329578693 0.113054036 0.257146542 7.916458768 0.029619767 0.048556527 4665.299594 -3.668879538 -0.177968254 AGTQIENIEEDFRDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGTQIENIEEDFRDGLK 17 1 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ;;;;; 277.44 7.87E-36 946449000 837713 639330 758899 588176 1020185 1008880 981398 804213 869013 590471 FALSE TRUE 870786.5561 749129.9542 778676.5314 704515.4573 846774.3181 774582.9097 904473.4604 793433.8402 837737.3919 706162.4872 1.233124914 1.060846431 1.102687477 0.997667633 1.199121071 1.09689048 1.280829096 1.123585371 1.186323838 1 19.42964066 3.181519316 24.99999927 1.158515725 1.096175053 0.061893792 0.087907524 181.7911632 79674.0928 0.023826377 0.028477984 1518.865494 -3.181519316 -0.062340671 AGVDYAPNLPPFPS(ph)PADVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVDYAPNLPPFPSPADVK 19 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 AGVDYAPNLPPFPS(1)PADVK 153.06 4.34E-10 0 68372 45148 61482 52613 66909 69859 80178 62379 62036 43983 TRUE FALSE 71071.37935 52901.8178 63084.27143 63019.69437 55535.83208 53635.30597 73893.43885 61542.91154 59803.33648 52600.62674 1.351150809 1.005725997 1.199306459 1.198078773 1.055801718 1.019670473 1.404801491 1.170003389 1.136932014 1 15.68279237 AGVHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVHIK 6 0 P12532;P12532-2;P12277;H0YJG0;H0YJK0 P12532;P12277 CKMT1A;CKB "Creatine kinase U-type, mitochondrial;Creatine kinase B-type" 0 78.002 0.070933 133770000 553270 543830 590860 536390 588480 694570 601010 516250 522980 468050 FALSE TRUE 575113.5268 637228.5721 606258.297 642486.341 488450.3798 533266.6438 553901.2658 509330.5132 504158.052 559755.4361 1.027437144 1.13840533 1.083077104 1.147798305 0.87261391 0.952677919 0.989541557 0.909916153 0.90067558 1 19.09443711 3.241991044 24.9999997 0.935820723 1.100831162 0.735680646 0.047444768 42.2462571 307876.2571 0.012775381 0.016626825 1745.786151 -3.241991044 0.165010439 AGVLAGHDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 168.83 4.82E-06 3371040000 2875210 3707440 2651920 3418740 3697500 4508060 3218400 2681480 2569800 5198040 FALSE TRUE 2988725.511 4344163.98 2721031.214 4094956.568 3069000.271 3461131.385 2966133.398 2645539.147 2477313.4 6216496.416 0.480773302 0.698812271 0.437711378 0.65872419 0.493686486 0.556765605 0.477139083 0.42556755 0.398506367 1 22.56767028 -1.786678874 3.025033329 1.10995655 0.514121837 0.709943838 0.093157768 48890516.27 56416830.82 40474967.56 0.02315887 0.016342599 1.786678874 -0.595834714 AGVLAHLEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 227.94 3.63E-12 20942430000 6033610 6667560 6843100 6732890 7283230 7828300 7031410 6687150 6634600 6205580 FALSE TRUE 6271821.582 7812661.564 7021436.808 8064635.546 6045229.166 6010295.964 6480269.711 6597519.692 6395822.042 7421444.588 0.845094443 1.052714397 0.946101089 1.086666545 0.814562326 0.809855264 0.873181715 0.888980523 0.861802843 1 22.8232686 3.223269771 24.99999415 0.867601235 0.985038949 0.314486285 0.077593681 250.0795426 408870.482 0.021107892 0.025317289 1672.128969 -3.223269771 0.117437713 AGVLT(ph)PPDLGPHPPPPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVLTPPDLGPHPPPPAPR 19 0 I3L2J0 I3L2J0 CIC 1 AGVLT(1)PPDLGPHPPPPAPR 70.072 0.081013 181330000 179790 213920 195860 169770 239650 271690 238230 211340 210710 198810 TRUE FALSE 186888.248 250659.0959 200964.2725 203349.9993 198914.3786 208594.115 219556.9101 208507.333 203126.5883 237763.0131 0.786027421 1.054239231 0.845229331 0.855263385 0.836607747 0.877319446 0.923427523 0.876954453 0.854323747 1 17.85916478 -1.772659885 2.528493038 1.031218215 0.882621205 0.223084183 0.067507829 16216283.74 11365610.43 3134839.352 0.01521991 0.016878744 1.772659885 -0.14859701 AGVMSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVMSDR 7 0 A0A087WXN0;Q9H0B3-3;Q9H0B3-5;Q9H0B3;Q9H0B3-4 A0A087WXN0 KIAA1683 Uncharacterized protein KIAA1683 0 82.263 0.088715 531950000 474920 503230 500310 439750 419510 587690 477630 508940 472620 276940 FALSE TRUE 493670.2083 589655.8379 513348.4896 526731.2375 348201.84 451207.904 440192.1125 502118.4918 455610.4985 331201.0907 1.490545237 1.780355967 1.549960142 1.590366857 1.051330596 1.362338219 1.329078089 1.516053256 1.375631033 1 18.3373479 7.99999943 0.038650696 5.05E-11 3.719534736 0.453499471 0.167514516 822.7857575 2.423140835 65.16301593 203.8320141 99999868.69 -7.99999943 3.719534736 AGVSVWVQAVEMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVSVWVQAVEMDR 14 0 Q9Y365;F5H0V7;F5H8G1;F5H1Z6;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 144.47 1.49E-05 0 75893 75527 88316 72960 101000 118400 85680 83984 70449 69953 FALSE TRUE 78889.31424 88498.17473 90617.58751 87391.27024 83832.05608 90903.39437 78964.17772 82858.33185 67913.55425 83658.95102 0.942987131 1.057844662 1.083178625 1.044613507 1.002069176 1.086594958 0.943881997 0.990429964 0.81179065 1 16.35223229 1.837547445 1.783547779 0.917749313 1.036746951 0.349171363 0.063285637 0.351084088 2.125524916 0.040766782 0.017850127 68.79350626 -1.837547445 0.118997638 AGVVGPELHEQLLSAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 204.13 9.06E-12 244080000 485500 388530 445460 373330 625200 547860 506710 480380 514820 382550 FALSE TRUE 504667.9149 455257.0052 457069.0535 447173.5597 518928.7273 420627.8179 466992.7462 473941.2918 496291.7288 457503.3481 1.103091195 0.995089997 0.999050729 0.977421393 1.134262141 0.919398338 1.020741702 1.035929669 1.084782725 1 18.80342278 1.605445663 4.453674879 1.047295036 1.018309376 0.017168444 0.060561263 0.616381081 27.35595975 0.033269518 0.015045794 40.31305052 -1.605445663 -0.02898566 AGVVNGTGAPGQS(ph)PGAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVVNGTGAPGQSPGAGR 18 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;Q13330-2 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 AGVVNGTGAPGQS(1)PGAGR 265.42 5.04E-31 82444000 55358 56642 54065 56853 61122 66289 59243 54967 54681 58303 TRUE FALSE 57543.57659 66369.82289 55473.97831 68098.35371 50732.50427 50894.38437 54599.37886 54230.25727 52713.04149 69726.35657 0.825277261 0.951861336 0.79559554 0.976651543 0.727594367 0.729916016 0.783052228 0.777758368 0.755998794 1 16.08941648 3.225252104 24.99547857 0.780538622 0.885401012 0.192673672 0.08863907 299.3095165 562149.1861 0.023358919 0.028072838 1679.77883 -3.225252104 0.104862391 AGVYPEKDQAENEDGAQENTFSMDPQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AGVYPEKDQAENEDGAQENTFSMDPQLER 29 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 206.4 1.77E-25 148840000 76073 63556 78429 68468 95299 92269 89630 83176 91585 62699 FALSE TRUE 79076.42078 74471.2486 80472.92417 82010.76604 79100.11002 70840.9231 82604.5664 82061.16177 88288.87374 74983.66861 1.054581914 0.993166245 1.073206015 1.093715039 1.05489784 0.944751363 1.101634102 1.094387128 1.177441373 1 16.19428879 2.096832843 21.5177447 1.100582157 1.037677721 0.196469839 0.05627277 7.819084369 1724.701742 0.020611015 0.015222232 124.9777907 -2.096832843 -0.062904436 AGYLRS(ph)PSWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AGYLRSPSWTR 11 1 D3DX86;H3BLZ2;Q9H9R9;Q9H9R9-2;Q9H9R9-3 D3DX86 MGC3101;DBNDD1 Dysbindin domain-containing protein 1 1 AGYLRS(0.709)PS(0.291)WTR;AGYLRS(0.936)PS(0.061)WT(0.003)R;AGYLRS(0.845)PS(0.155)WTR;AGYLRS(0.961)PS(0.038)WTR 146.96 2.15E-05 1826050000 731200 954330 920940 642660 1140910 1167330 686510 950070 962860 1613350 TRUE FALSE 760068.3406 1118228.754 944940.453 769776.2299 946978.5257 896235.2986 632699.5523 937335.8657 928206.8567 1929455.043 0.393929023 0.579556781 0.489744737 0.398960438 0.490801032 0.464501778 0.327916193 0.485803424 0.481072031 1 20.879762 0.418760542 2.067798185 0.999993004 0.45464158 0.863838368 0.064775269 2.711665506 9.208013646 0.061297186 0.016768468 2.622772021 -0.418760542 -0.545351425 AGYTDKVVIGMDVAASEFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 AGYTDKVVIGMDVAASEFFR 20 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;;;;;;;; 175.77 1.32E-12 4610282300 6077410 6396523 7361049 6018601 9504629 8525094 6315247 6409939 7963737 8101650 FALSE TRUE 6317350.84 7495076.067 7552883.984 7209062.314 7889035.558 6545270.118 5820241.438 6324024.252 7677123.661 9689013.202 0.65201179 0.77356444 0.779530776 0.74404505 0.814224874 0.675535267 0.600705285 0.652700551 0.792353514 1 23.20791831 0.929990604 5.793103661 0.999979414 0.711139913 0.651585239 0.063781791 0.357425631 28.32873437 0.068753359 0.017303725 8.511196244 -0.929990604 -0.288839502 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 AHAS(0.999)PFS(0.001)GALTPSAPPGPEMNR;AHAS(0.998)PFS(0.002)GALTPSAPPGPEMNR;AHAS(0.982)PFS(0.018)GALTPSAPPGPEMNR;AHAS(0.802)PFS(0.198)GALTPSAPPGPEMNR 222.18 5.63E-26 2251510000 614208 844430 719976 777607 807852 951400 746629 742710 696005 859163 TRUE FALSE 638457.4061 989454.2837 738739.166 931415.3437 670533.6056 730451.7686 688106.268 732755.1873 670955.916 1027499.54 0.621370016 0.96297297 0.71896788 0.906487358 0.652587743 0.710902283 0.669690098 0.713144054 0.652998751 1 19.97070632 AHATGAGPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHATGAGPAGR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 129.89 0.0002356 106362000 34265.1 78319 59263.1 63987 60479 79425 54867 61533 54068 84429 FALSE TRUE 35617.91261 91769.67901 60807.54507 76643.43762 50198.80118 60979.74745 50566.38117 60708.25078 52122.10324 100971.2461 0.352753026 0.908869432 0.602226351 0.759062016 0.497159371 0.603931811 0.500799813 0.601242959 0.516207388 1 16.62358498 -1.637157272 5.167826466 1.005313383 0.601453128 0.414173426 0.144733889 0.008255954 0.000579666 0.130578728 0.030494642 0.02305912 1.637157272 -0.403860256 AHCAICTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHCAICTDR 9 0 P41743 P41743 PRKCI Protein kinase C iota type 0 104.17 0.0033041 64304000 24158 21789 24705 23945 26542 30796 18487 19837 23842 23707 FALSE TRUE 25111.77649 25531.09126 25348.8326 28681.24953 22030.40032 23644.09572 17037.94063 19571.11746 22983.93108 28351.93275 0.885716565 0.900506201 0.894077762 1.01161532 0.777033457 0.833950049 0.600944591 0.69029218 0.810665406 1 14.79115947 3.111371183 6.747238047 0.752176873 0.918834992 0.264359387 0.10439481 0.234143544 13.05564924 0.029988561 0.035981327 1292.323325 -3.111371183 0.166658119 AHDGGIYAISWSPDSTHLLSASGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHDGGIYAISWSPDSTHLLSASGDK 25 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 193.4 2.03E-18 953141000 270028 404658 455878 389680 511481 617813 522299 540876 508615 419720 FALSE TRUE 280688.9139 474154.8637 467758.5552 466757.5409 424539.6423 474335.2938 481359.8396 533626.4419 490310.0455 501956.098 0.559190166 0.944614212 0.931871447 0.92987722 0.845770465 0.944973665 0.958968008 1.063093852 0.976798663 1 18.93720166 4.739805315 5.357431492 0.957922844 0.543049311 0.83744969 0.052347797 0.065985999 6.903635849 0.014577787 0.100711783 54929.4582 -4.739805315 -0.414873533 AHDPLADVSNDLGHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHDPLADVSNDLGHSGR 17 0 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 0 88.133 0.0025279 26952000 16907 20729 23025 18895 20961 22081 20488 18474 24851 21875 FALSE TRUE 17574.50142 24289.0445 23625.05042 22632.3746 17398.05671 16953.02239 18882.09702 18226.38625 23956.61736 26160.98743 0.671782801 0.92844525 0.903064171 0.86511928 0.665038227 0.648026854 0.721765456 0.696701006 0.91573827 1 14.67512937 5.017586135 15.86247447 0.792711026 0.441915204 0.08688941 0.12059603 2212582.171 45231451.26 0.029938571 18155603.57 104132.4617 -5.017586135 -0.350795822 AHEAQDAGYR ddPTM_MDA-MB-175_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 ; 141.1 3.81E-05 400360000 382670 394990 396570 382840 516910 433680 446760 371590 438510 384520 FALSE TRUE 397778.1071 462826.4599 406904.94 458564.6093 429045.8228 332964.3925 411741.7838 366609.4438 422728.1108 459859.3319 0.864999532 1.006452251 0.884846543 0.997184525 0.93299362 0.724057053 0.895364637 0.797220842 0.919255262 1 18.81083309 2.962569803 24.98823524 0.850042144 0.9426204 0.143292316 0.08025512 754.9696515 504014.3769 0.022431794 0.023798399 917.4233788 -2.962569803 0.092578256 AHEEQLK ddPTM_MDA-MB-175_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 ; 152.47 0.0018115 720720000 1444360 1349080 1481660 1214340 1742470 1915530 1644430 1377410 1468630 1189460 FALSE TRUE 1501384.448 1580773.996 1520273.277 1454532.828 1446285.572 1470677.188 1515535.28 1358948.072 1415774.293 1422511.913 1.055445957 1.111255365 1.06872446 1.02251012 1.016712449 1.033859312 1.065393734 0.955315776 0.995263576 1 20.4400093 3.331891189 0.465954464 0.986464283 1.101225333 0.509421855 0.029611981 1.21969481 0.478722037 0.026479828 0.067472012 2147.292411 -3.331891189 0.11476105 AHFGLPSVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHFGLPSVEK 10 0 Q9Y6Q5;K7ERH5;K7EL08;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 107.21 0.0036989 0 193860 212710 216640 223720 267320 305500 261290 212890 222550 216440 FALSE TRUE 201513.7425 249241.2878 222285.8164 267971.1483 221881.0419 234552.2549 240809.407 210036.5578 214540.469 258847.274 0.778504403 0.962889367 0.858752781 1.035248099 0.857189023 0.906141491 0.930314634 0.811430441 0.82883032 1 17.9817416 -0.12840444 8.03981226 1 0.887560291 0.182925366 0.072491234 0 0 0.067480104 0.015905213 0.744038759 0.12840444 -0.112439709 AHFLDADPGFVHSDGTISHHDMYDYLHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHFLDADPGFVHSDGTISHHDMYDYLHLSR 30 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;; 285.61 1.89E-72 2640620000 115332.1 1598502 1183368 1427404 927366 1685378 774181 1370753 887860 2081578 FALSE TRUE 119885.5004 1873032.284 1214207.542 1709740.251 769732.6586 1293974.502 713498.6703 1352380.298 855906.092 2489423.355 0.04815794 0.752396044 0.487746506 0.686801724 0.309201188 0.51978885 0.286612026 0.543250426 0.343817009 1 21.24738017 -1.425118126 3.42141944 1.005816776 0.457702599 0.420326305 0.195813129 765385310.2 1172323242 44366534.85 0.042760285 0.037573519 1.425118126 -0.548114177 AHFNAMFQPS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.576)S(0.408)PT(0.016)R 77.468 0.0066467 0 85549 112420 107410 117370 107770 129340 109080 114930 100290 109250 TRUE FALSE 88926.54058 131727.2605 110209.1928 140585.4357 89451.29389 99302.74517 100530.0246 113389.5513 96680.58249 130655.4458 0.680618707 1.008203368 0.843510136 1.076001347 0.684635021 0.760035256 0.769428507 0.867851705 0.739965961 1 16.99540773 4.802558992 21.69966344 0.851083724 0.680610704 0.15677526 0.123611825 39700.16609 13457983.4 0.028753727 71.74851003 63468.61077 -4.802558992 -0.17047302 AHFNAMFQPSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 AHFNAMFQPS(0.043)S(0.914)PT(0.043)R;AHFNAMFQPS(0.149)S(0.823)PT(0.027)R;AHFNAMFQPS(0.008)S(0.976)PT(0.016)R 153.75 4.06E-06 886176000 441860 483090 485190 497160 519810 634740 565580 513040 512250 532930 TRUE FALSE 459304.974 566056.9496 497834.45 595496.7641 431452.8819 487331.2546 521248.3617 506163.538 493814.2226 637347.4299 0.720650861 0.888145026 0.781103722 0.934336182 0.676950846 0.764624178 0.817840219 0.794172086 0.774795974 1 19.2817205 -1.137463176 4.894426204 1.000012148 0.79764466 0.432404736 0.070481109 8.73E-06 1.54E-06 0.063752933 0.015025808 0.072867996 1.137463176 -0.202367487 AHFNLDESGVLSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHFNLDESGVLSLDR 15 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 242.19 6.48E-18 361380000 152980 180367 173825 202151 192680 225160 189509 179429 159910 152259 FALSE TRUE 159019.7685 211343.6292 178355.0223 242135.8644 159928.3224 172870.0023 174654.7894 177024.0477 154154.8703 182091.2359 0.873297211 1.160646904 0.97948164 1.329750239 0.878286765 0.949359268 0.959160876 0.972172257 0.846580395 1 17.47430196 AHFPLDVQWNDLDYMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AHFPLDVQWNDLDYMDSR 18 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 ;;;; 232.18 3.85E-20 474283000 370497 481785 405264 434007 442547 528341 431563 390280 378863 470748 FALSE TRUE 385124.5076 564527.826 415825.5128 519852.2892 367323.019 405641.8098 397735.9644 385048.935 365227.7946 562982.0576 0.684079541 1.00274568 0.738612372 0.92339051 0.652459548 0.720523513 0.706480711 0.683945305 0.648737894 1 19.10272942 3.233324528 24.99999992 0.714843127 0.841988741 0.123087349 0.125985712 197.8129011 944469.1841 0.03271578 0.040226441 1711.293607 -3.233324528 0.127145614 AHGCFPEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHGCFPEGR 9 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;; 85.862 0.014528 483794000 196620 617150 461990 531751 327819 579110 349109 487890 317085 673620 FALSE TRUE 204382.7094 723140.7117 474029.8389 636929.7607 272096.4435 444620.479 321744.9244 481350.6326 305673.1728 805602.9418 0.253701543 0.897639115 0.588416221 0.790624919 0.337755027 0.551910198 0.399383999 0.597503569 0.379434033 1 19.61970943 -1.075630435 4.694033843 1.000020808 0.54578573 0.347437737 0.191304191 3.88E-05 7.65E-06 0.172714023 0.040707223 0.084017463 1.075630435 -0.454235079 AHGCFQDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHGCFQDGR 9 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 ;; 146.23 9.53E-05 143449000 106299 137475 121666 110039 145746 149105 119783 123699 116977 140035 FALSE TRUE 110495.7666 161085.2618 124836.7159 131804.3858 120972.147 114477.6235 110394.0955 122041.0172 112767.0206 167472.1771 0.659785813 0.961862828 0.745417645 0.787022585 0.722341759 0.683562043 0.659178721 0.728724134 0.673347792 1 17.35356191 5.028647679 17.07641971 0.757081843 0.359679115 0.068137019 0.112245085 17838369.98 277415677.2 0.025640679 205006072.2 106818.7961 -5.028647679 -0.397402728 AHGCFQDGRS(ph)PGPPPPVGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHGCFQDGRSPGPPPPVGVK 20 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 AHGCFQDGRS(1)PGPPPPVGVK 97.509 0.00056263 99283000 189210 127570 141390 82374 178820 203660 109390 124250 153410 150180 TRUE FALSE 196680.1569 149479.1551 145074.7396 98667.33134 148424.2403 156363.0515 100815.726 122584.632 147888.8041 179604.8956 1.095071246 0.832266596 0.807743793 0.549357694 0.826393065 0.870594596 0.561319476 0.68252389 0.823411876 1 17.45446715 4.786446442 1.770268198 0.737685925 1.242384283 0.346481069 0.132279901 1.019489526 2.915323734 0.03330732 0.896839397 61157.03779 -4.786446442 0.504698357 AHGGYSVFAGVGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHGGYSVFAGVGER 14 0 P06576;H0YH81;F8W079;F8W0P7;H0YI37 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ; 124.3 0.00052997 0 144958 230900 183167 238560 180214 290600 182618 178109 183912 244500 FALSE TRUE 150681.0538 270555.2788 187940.4825 285746.456 149581.2887 223112.5541 168303.924 175721.7402 177293.043 292405.0938 0.515316104 0.925275533 0.642740111 0.977228038 0.511555003 0.763025538 0.575584788 0.600953075 0.606326794 1 18.15760892 -0.961592633 4.877580076 1.000001426 0.681655529 0.282002035 0.153261411 18484764.41 3789740.294 544.2328282 0.033825894 0.109246458 0.961592633 -0.318345897 AHGLLAEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AHGLLAEENR 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;; 127.76 0.00034743 1403260000 541375 712920 608108 561118 785535 840430 584705 589460 523441 857300 FALSE TRUE 562748.903 835358.4643 623955.794 672105.4656 652010.0413 645252.8693 538874.2943 581559.2529 504602.4607 1025271.521 0.548877923 0.814768037 0.608576149 0.655538998 0.635938898 0.629348281 0.52559179 0.567224624 0.49216471 1 19.9675746 -1.058073909 4.758582455 1.000011925 0.610686329 0.657897735 0.084645834 1.17E-05 2.31E-06 0.083178005 0.019604598 0.087483488 1.058073909 -0.389325596 AHGNSGMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHGNSGMVR 9 0 C9K025;P18077 C9K025 RPL35A 60S ribosomal protein L35a 0 ;; 141.02 0.00010771 110928000 45828 51837 41153 37606 132252 81459 48614 49890 42276 160371 FALSE TRUE 47637.32483 60739.60151 42225.48099 45044.35456 109771.8523 62541.38177 44803.50765 49221.30615 40754.49502 191792.627 0.248379333 0.316694142 0.22016217 0.234859678 0.57234657 0.326088561 0.23360391 0.256638156 0.212492501 1 17.54918773 -1.131131146 4.831246427 1.000037345 0.292387429 0.816378095 0.100838018 5.01E-05 9.01E-06 0.100334271 0.023647521 0.073938197 1.131131146 -0.707649916 AHGPEVQAHNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHGPEVQAHNKR 12 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 0 97.214 0.002053 25875000 17139 21174 21408 18825 21287 25632 19078 21492 24091 28960 FALSE TRUE 17815.66095 24810.46979 21965.91007 22548.52881 17668.64334 19679.35646 17582.61651 21203.93489 23223.96962 34634.15753 0.514395678 0.716358403 0.634226776 0.651048861 0.510150805 0.568206587 0.507666932 0.612226091 0.670551019 1 15.07990796 0.733099111 2.134389712 0.999821215 0.590286645 0.785381039 0.064287995 0.516214742 3.42176169 0.062707197 0.017148637 5.408777439 -0.733099111 -0.40953457 AHGPGLEGGLVGKPAEFTIDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHGPGLEGGLVGKPAEFTIDTK 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 0 242.34 6.28E-31 975240000 1419500 855440 1100700 864760 1473100 1344000 1339800 1118100 1259100 891830 FALSE TRUE 1475542.956 1002355.166 1129385.146 1035806.947 1222702.988 1031876.369 1234782.975 1103113.698 1213785.237 1066567.013 1.38345077 0.939795768 1.058897502 0.971159743 1.146391153 0.967474482 1.157717199 1.034265718 1.13802998 1 20.02454318 4.750677811 24.68426882 1.050216401 1.383451013 0.643660945 0.07527125 926.3036467 1886957.172 0.016376296 0.273150166 56321.9667 -4.750677811 0.333234612 AHGS(ph)FSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHGSFSHVR 9 0 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 AHGS(0.98)FS(0.02)HVR;AHGS(0.989)FS(0.011)HVR 149.33 5.66E-05 209972000 38224 51935 43455 50593 70937 72813 54803 43384 47321 65339 TRUE FALSE 39733.11304 60854.43225 44587.473 60600.14439 58879.15408 55903.28424 50507.39766 42802.50844 45617.92645 78140.92606 0.508480191 0.778777976 0.570603335 0.775523755 0.753499569 0.715416198 0.646362927 0.547760445 0.583790451 1 16.25379073 4.760961273 23.23989571 0.684388004 0.508479695 0.156756493 0.128742031 4417.912698 4583236.991 0.029519773 1.356682137 57671.50339 -4.760961273 -0.17590831 AHGVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AHGVDK 6 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;; 121.68 0.019546 4608204000 12814100 10537640 13264100 9851940 16176500 15053720 16183070 13680040 14782950 12117190 FALSE TRUE 13320010.56 12347397.7 13609773.34 11800624.33 13426824.31 11557721.67 14914598.69 13496681.44 14250914.52 14491321.38 0.919171566 0.852054645 0.939167173 0.814323554 0.926542442 0.797561614 1.029209021 0.931363061 0.983410287 1 23.78868582 2.229246613 24.99888498 0.9767828 0.876297759 0.54642674 0.049333172 153.4488455 411855.0966 0.016816385 0.01258925 169.5300198 -2.229246613 -0.10048504 AHIAQLCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHIAQLCEK 9 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 150.27 8.56E-05 2231370000 3289960 2761050 2851410 2154650 6419300 4642110 3601390 2664370 3017330 5199040 FALSE TRUE 3419850.161 3235238.86 2925720.087 2580833.339 5328149.679 3564050.304 3319103.641 2628658.478 2908736.883 6217692.346 0.550019199 0.520327909 0.47054758 0.415078971 0.856933631 0.573211106 0.533815997 0.422770753 0.467816148 1 22.5679478 -1.562117847 5.968655165 1.00114121 0.531258721 0.579779109 0.118861391 0.001870277 0.00013721 0.119247137 0.028045486 0.027408303 1.562117847 -0.469882489 AHIISDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHIISDQK 8 0 A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 A0A669KAX4 CUL4B Cullin-4B 0 79.713 0.02771 0 172720 244710 252520 271360 325840 375330 337970 290890 266080 327880 FALSE TRUE 179539.119 286737.0389 259100.8786 325034.1981 270453.8332 288165.2957 311479.0283 286991.0954 256503.8328 392121.8084 0.457865681 0.731244814 0.660766306 0.8289113 0.689718928 0.734887195 0.794342527 0.731892716 0.654143247 1 18.58094236 -5 0.103663645 1.830026278 0.536358223 0.517057691 0.091419231 152.7450018 1.069197618 28.021255 1.337883951 1.00E-05 5 -1.293668054 AHIVFDFHQAADGIQEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHIVFDFHQAADGIQEQQR 19 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;; 310.3 9.63E-62 958100000 292854 360740 334393 339464 345430 391990 365790 363960 339280 408000 FALSE TRUE 304416.1021 422694.2888 343107.5563 406608.966 286713.932 300956.2632 337118.424 359081.7115 327069.3791 487939.7884 0.623880465 0.866283707 0.703176016 0.833317913 0.58760105 0.616789756 0.690901689 0.73591398 0.670306843 1 18.89634361 -1.111599238 4.563620991 1.000024703 0.70743945 0.519808526 0.085509591 2.20E-05 4.28E-06 0.081048654 0.019101667 0.077339394 1.111599238 -0.292585254 AHLLDNTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHLLDNTER 9 0 Q96AJ9-1;Q96AJ9 Q96AJ9-1 VTI1A Vesicle transport through interaction with t-SNAREs homolog 1A 0 80.239 0.022544 0 33773 39295 38344 45430 44533 53699 37488 39003 37919 46589 FALSE TRUE 35106.38412 46043.61058 39343.27614 54415.9184 36963.29657 41228.22107 34549.5926 38480.22858 36554.3026 55717.22255 0.630081374 0.826380219 0.706124145 0.97664449 0.663408815 0.739954707 0.620088207 0.690634364 0.656068284 1 15.76583572 -1.091049573 4.72236205 1.000013018 0.724927345 0.39867164 0.101942484 1.48E-05 2.85E-06 0.09695873 0.022852227 0.081086849 1.091049573 -0.275085674 AHLMEIQVNGGTVAEKLDWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHLMEIQVNGGTVAEKLDWAR 21 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 218.07 3.35E-25 721330000 717930 752180 803120 547230 1102300 985990 627360 742690 861510 996210 FALSE TRUE 746274.4308 881361.0639 824049.967 655470.4607 914931.4397 757008.7653 578185.8839 732735.4553 830504.4234 1191398.276 0.626385354 0.739770303 0.691666241 0.550169053 0.767947594 0.635395216 0.485300252 0.615021417 0.697083788 1 20.18422435 0.833623625 4.181282368 0.99997779 0.637182575 0.652326044 0.078662768 0.850829886 20.67019559 0.078179488 0.019925916 6.817476115 -0.833623625 -0.362795215 AHLTVGQAAAGGS(ph)GNLLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHLTVGQAAAGGSGNLLTER 20 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(0.986)GNLLT(0.014)ER;AHLTVGQAAAGGS(1)GNLLTER;AHLTVGQAAAGGS(1)GNLLTER 264.07 1.00E-36 721597000 275921 419721 332084 393310 386746 484428 347428 366284 348929 414347 TRUE FALSE 286814.5741 491804.8168 340738.3819 471105.5441 321007.0531 371926.9386 320195.6855 361374.5621 336371.1134 495530.3615 0.578803231 0.992481702 0.687623622 0.950709746 0.647805015 0.750563371 0.646167643 0.729268255 0.6788103 1 18.91861393 AHMGMFTELAILYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHMGMFTELAILYSK 15 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;A0A087WV74;A0A087WXH4;P53675;P53675-2 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 95.264 0.0041522 409270000 465350 419140 546130 485260 608290 692200 599430 521210 557460 447350 FALSE TRUE 483722.3773 491124.0345 560362.5965 581242.9796 504893.0831 531447.0404 552445.1103 514224.0325 537397.1235 534999.6675 0.904154538 0.91798942 1.047407373 1.086436151 0.943725976 0.993359571 1.032608325 0.961167013 1.004481229 1 19.02917847 4.311632883 7.578322012 1.006012962 0.909188174 0.502447172 0.038796914 0.198775661 17.47985858 0.009840127 0.027146071 20494.29025 -4.311632883 -0.096824787 AHPPELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHPPELK 7 0 P62308;A8MWD9;C9JVQ0 P62308 SNRPG;SNRPGP15 Small nuclear ribonucleoprotein G;Putative small nuclear ribonucleoprotein G-like protein 15 0 ; 88.029 0.018908 540530000 743270 720500 677790 627360 897750 886610 806700 720430 721520 851800 FALSE TRUE 772614.8735 844240.2703 695453.7642 751449.9355 745150.7757 680708.2642 743468.7461 710773.8142 695552.6361 1018693.901 0.758436732 0.828747742 0.682691595 0.737660189 0.731476624 0.668216687 0.729825461 0.697730509 0.682788652 1 19.95828918 -1.563986705 8.548121459 1.000051861 0.723349441 0.777024358 0.044324819 4.46E-05 2.27E-06 0.043649537 0.010286377 0.027290613 1.563986705 -0.27670242 AHPWTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHPWTK 6 0 A0A3B3ITW1;P49841;P49841-2;P49840;A8MT37 A0A3B3ITW1;P49840 GSK3B;GSK3A Glycogen synthase kinase-3 beta;Glycogen synthase kinase-3 alpha 0 ; 91.093 0.048284 893220000 1323890 1521740 1561420 1497430 1864280 1935950 1696490 1604680 1637610 1680340 FALSE TRUE 1376158.199 1783087.008 1602111.888 1793617.185 1547390.352 1486354.952 1563514.681 1583171.889 1578672.736 2009570.451 0.684802167 0.887297585 0.797240966 0.892537599 0.770010502 0.739638141 0.778034271 0.787816067 0.785577204 1 20.93845573 -0.753905568 6.325161143 1.000000003 0.794227219 0.532886757 0.058527346 2.41E-09 3.81E-10 0.053936087 0.012712857 0.176235921 0.753905568 -0.205772784 AHQGTGAGIS(ph)PVILNSGEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHQGTGAGISPVILNSGEGK 20 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 AHQGT(0.002)GAGIS(0.998)PVILNSGEGK 157.62 5.02E-11 0 351050 303440 363250 307570 390130 470760 353250 330740 377360 320520 TRUE FALSE 364909.7251 355553.4596 372716.5934 368406.428 323815.842 361433.1244 325561.342 326306.9713 363778.8873 383319.7573 0.951972128 0.927563614 0.972338593 0.961094285 0.844766897 0.942902414 0.849320537 0.851265726 0.949022012 1 18.54818883 3.267477266 24.99539904 0.893494541 0.952772039 0.152692956 0.049056162 289.0382302 249841.2839 0.013069235 0.017692703 1851.30198 -3.267477266 0.059277498 AHQLVHEGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHQLVHEGYK 10 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 196.76 1.89E-07 139604000 252510 168355 225188 198524 305190 281790 273810 231168 263410 201121 FALSE TRUE 262479.2898 197268.6616 231056.5843 237791.4547 253313.9128 216348.5431 252348.0567 228069.5711 253929.9256 240526.8093 1.091268331 0.82015249 0.960627154 0.988627652 1.053162904 0.899477874 1.049147318 0.948208525 1.055724002 1 17.87583818 3.800091941 4.575637965 0.995467669 0.942011724 0.049675549 0.076575717 0.534570797 22.89171746 0.01843322 0.033898591 6310.909338 -3.800091941 -0.053455944 AHQLVMEGYNWCHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 274.48 1.02E-33 3752780000 1042535 1130950 1031443 1051790 1110550 1340430 1126110 1107740 1128350 1138040 FALSE TRUE 1083695.087 1325181.865 1058323.252 1259830.923 921779.1077 1029135.447 1037842.556 1092892.557 1087740.904 1361017.149 0.796239113 0.973670219 0.777597294 0.925653967 0.677272221 0.756151712 0.762549213 0.802996904 0.799211755 1 20.37625381 4.20230814 24.99999838 0.800489752 0.884955168 0.073531062 0.095042751 304.6997653 210123.2772 0.02204208 0.047618618 15933.3883 -4.20230814 0.084465416 AHS(ph)IQIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 AHS(1)IQIMK 73.781 0.027489 148780000 400020 215910 303560 224060 431810 359170 352610 321610 357220 219300 TRUE FALSE 415813.0985 252990.863 311471.023 268378.3992 358411.0904 275758.2108 324971.5068 317299.344 344363.722 262267.6362 1.585453335 0.964628601 1.187607543 1.023299722 1.366585277 1.051438198 1.239083524 1.209830342 1.313024081 1 18.00068026 4.756752218 24.55853484 1.164077173 1.585453791 0.496864159 0.13064249 2553.984246 3447789.985 0.028947708 0.93581941 57115.26789 -4.756752218 0.421376618 AHS(ph)LLFENSDSFSEDSSTLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHSLLFENSDSFSEDSSTLGR 21 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 AHS(1)LLFENSDSFSEDSSTLGR;AHS(1)LLFENSDSFSEDSSTLGR;AHS(1)LLFENSDSFSEDSSTLGR 197.73 5.76E-22 337066000 209908 202124 225351 176635 268594 281816 210889 231418 210310 212416 TRUE FALSE 218195.3299 236837.2247 231223.8322 211572.8758 222938.4878 216368.505 194358.9691 228316.2202 202740.9842 254034.8483 0.85891889 0.932302109 0.91020517 0.832849813 0.877590178 0.851727653 0.765087823 0.898759449 0.798083356 1 17.95466689 3.749157128 24.13012146 0.853697808 0.903658067 0.072249595 0.061849726 916.4209372 2086842.494 0.014638673 0.026014754 5612.510003 -3.749157128 0.049960259 AHS(ph)NPMADHTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHSNPMADHTLR 12 0 Q9UBP6;F8VSD9;H0YHX0;Q9UBP6-2 Q9UBP6 METTL1 tRNA (guanine-N(7)-)-methyltransferase 1 AHS(1)NPMADHTLR;AHS(1)NPMADHTLR 115.8 0.00058643 328360000 123322 125317 143180 139097 178490 188273 162371 153598 162521 148098 TRUE FALSE 128190.8478 146839.2199 146911.3884 166609.9714 148150.3336 144549.4491 149643.9367 151539.27 156671.901 177114.9676 0.723771963 0.829061608 0.829469075 0.940688264 0.836464222 0.816133447 0.84489718 0.855598327 0.884577419 1 17.43432661 -5 0.128988604 1.519793243 0.77516618 0.568900626 0.046303188 117.6159272 0.960400034 15.86574596 0.373294351 1.00E-05 5 -0.744627063 AHS(ph)SLGPGRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSSLGPGRPR 11 1 Q9NRR6-2;Q9NRR6 Q9NRR6-2 INPP5E 72 kDa inositol polyphosphate 5-phosphatase 1 AHS(0.958)S(0.042)LGPGRPR 72.705 0.033896 0 3586.7 10383 14014 12856 10766 13543 10345 14775 10884 11291 TRUE FALSE 3728.305686 12166.19948 14379.21635 15398.87843 8935.999166 10397.8435 9534.131868 14576.96529 10492.28697 13503.25527 0.276104214 0.900982707 1.064870364 1.14038268 0.661766292 0.770024952 0.706061737 1.079514902 0.777019078 1 13.72101962 4.738481611 10.17344818 0.902928086 0.274735474 0.580037083 0.159263263 0.052116516 196.4396505 0.039269582 0.227041742 54762.29125 -4.738481611 -0.628192613 AHS(ph)SPASLQLGAVSPGTLTPTGVVSGPAATPTAQHLR ddPTM_MDA-MB-175_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(0.455)S(0.455)PAS(0.09)LQLGAVSPGTLTPTGVVSGPAATPTAQHLR 85.658 0.0014087 249630000 14626 28247 28619 32799 36024 43103 20989 31939 23377 31782 TRUE FALSE 15203.44577 33098.20252 29364.83465 39286.5443 29900.65335 33092.98148 19343.82734 31510.90995 22535.66634 38009.0744 0.399995159 0.870797383 0.772574316 1.033609603 0.786671442 0.87066002 0.508926556 0.829036498 0.592902266 1 15.21405627 -2.515330785 2.116580335 4.024260572 0.754605939 0.15362042 0.179988414 11725017.82 828629.9989 169929224.8 0.042090064 0.003052595 2.515330785 -3.269654633 AHSAPSSGTSSRPGS(ph)IR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSAPSSGTSSRPGSIR 17 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 AHS(0.001)APS(0.017)S(0.017)GT(0.013)S(0.013)S(0.013)RPGS(0.926)IR 67.251 0.02386 130160000 25730 51346 39034 40850 48503 61118 51868 46288 48836 50509 TRUE FALSE 26745.84027 60164.27608 40051.25811 48930.00807 40258.47738 46924.27075 47802.45063 45667.58507 47078.4019 60405.2715 0.442773281 0.996010358 0.663042432 0.810028775 0.666472915 0.776824101 0.791362235 0.756019863 0.779375719 1 15.88238684 -5 0.204259238 2.164325455 0.711417264 0.281796406 0.130072437 182.683347 1.814459251 86.8587853 0.265041246 1.00E-05 5 -1.45290819 AHSEVFTKPSGQQTLS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSEVFTKPSGQQTLSPDR 19 1 F5H212;P15822;A0A0D9SFF3;P15822-2;P15822-3 F5H212 HIVEP1 Zinc finger protein 40 1 AHSEVFTKPSGQQT(0.005)LS(0.995)PDR 77.576 0.0052903 0 23832 19112 26045 23240 29727 28813 30218 28629 26033 25180 TRUE FALSE 24772.90576 22394.33733 26723.7541 27836.80264 24674.01516 22121.61742 27849.4342 28245.27508 25096.07742 30113.5389 0.822650099 0.74366342 0.887433197 0.924394928 0.819366174 0.734607031 0.924814393 0.93795934 0.833381872 1 14.87812464 -4.999999961 0.081097885 1.515855122 0.700094877 0.358395838 0.065911402 277.348253 1.59035333 25.18940487 2.284370637 1.00E-05 4.999999961 -0.815760244 AHSIQIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AHSIQIMK 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;; 119.29 0.0017225 2949500000 3364230 2967470 3304390 2871300 4478880 4348430 3718070 3468210 3566800 3588440 FALSE TRUE 3497052.398 3477109.889 3390505.118 3439234.57 3717561.577 3338573.034 3426637.958 3421724.318 3438431.565 4291526.113 0.814873848 0.810226898 0.790046484 0.801401292 0.866256311 0.777945408 0.798466063 0.797321099 0.801214177 1 22.03305935 -1.243739112 6.297181418 1.000003356 0.805837027 0.872083436 0.022240969 1.03E-06 1.23E-07 0.021070632 0.00496631 0.057050688 1.243739112 -0.194166329 AHSLGGLDPAFT(ph)STEDLNCKENLEQDLGDDNSNDLLLSCPHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSLGGLDPAFTSTEDLNCKENLEQDLGDDNSNDLLLSCPHFR 43 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHS(0.005)LGGLDPAFT(0.433)S(0.433)T(0.129)EDLNCKENLEQDLGDDNSNDLLLSCPHFR 59.53 0.0060228 106920000 16863 16067 15544 9664.7 19015 17109 17175 15537 12971 19030 TRUE FALSE 17528.76426 18826.38227 15949.08941 11576.34881 15782.83709 13135.69404 15828.77862 15328.75193 12504.17624 22758.56415 0.770205192 0.827221882 0.700795064 0.508659015 0.693490019 0.577175869 0.695508667 0.673537743 0.549427291 1 14.47412192 -1.944231313 8.353256581 1.113818567 0.667291984 0.538296537 0.092730849 0.04665153 0.000311459 0.02130989 0.021640463 0.011370215 1.944231313 -0.446526583 AHSLGGLDPAFTS(ph)TEDLNCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHSLGGLDPAFTSTEDLNCK 20 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AHSLGGLDPAFT(0.014)S(0.947)T(0.039)EDLNCK 125.78 1.58E-05 155530000 133200 76157 110950 106660 143440 145330 141930 138020 118130 70837 TRUE FALSE 138458.8389 89236.37233 113841.4481 127757.0297 119058.12 111579.31 130805.1557 136170.0677 113878.5244 84716.15389 1.634385327 1.05335722 1.34379859 1.508059842 1.405376833 1.31709603 1.544040301 1.607368387 1.344236242 1 16.37034947 3.983906414 23.89528544 1.431690932 1.307548033 0 0.207022354 1108.171534 1645395.074 0.05006633 0.093770369 9636.2135 -3.983906414 -0.124142899 AHT(ph)PLNTPDPSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 AHT(1)PLNTPDPSTK;AHT(1)PLNTPDPSTK 159.81 0.00016531 705020000 1679440 935680 1267850 973650 1723850 1874990 1793760 1316320 1434660 815440 TRUE FALSE 1745745.588 1096375.761 1300891.213 1166235.064 1430830.593 1439551.988 1653160.404 1298676.883 1383026.867 975209.8555 1.790122996 1.124245982 1.333960281 1.19588113 1.467202761 1.476145857 1.695184267 1.331689663 1.418183849 1 19.89535318 AHT(ph)PTPGIYMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AHTPTPGIYMGR 12 0 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.994)PT(0.006)PGIYMGR;AHT(0.999)PT(0.001)PGIYMGR;AHT(1)PTPGIYMGR;AHT(0.997)PT(0.003)PGIYMGR;AHT(1)PTPGIYMGR;AHT(1)PTPGIYMGR 140.82 0.00022076 10394280000 2467320 2058970 2609530 2464390 2841330 3641590 3521610 2606910 2616810 1630130 TRUE FALSE 2564731.699 2412582.081 2677536.496 2951838.987 2358361.741 2795885.911 3245577.006 2571968.635 2522631.519 1949522.763 1.315568993 1.237524448 1.373431768 1.514134148 1.209712339 1.434138634 1.664805904 1.319281152 1.293973873 1 20.89468957 0.823909458 2.20924256 1.000935243 1.389182981 0.456951165 0.125899219 0.599887736 5.259240082 0.122682779 0.033469179 6.66667767 -0.823909458 0.388247738 AHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.946)PT(0.054)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.837)PT(0.163)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.833)PT(0.167)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.901)PT(0.094)PGIYMGRPT(0.003)HS(0.003)GGGGGGGGGGGGGGGGR;AHT(0.994)PT(0.006)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.626)PT(0.374)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.978)PT(0.022)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.984)PT(0.016)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.913)PT(0.087)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.744)PT(0.239)PGIY(0.013)MGRPT(0.004)HSGGGGGGGGGGGGGGGGR;AHT(0.984)PT(0.016)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.789)PT(0.211)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.925)PT(0.075)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.799)PT(0.201)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;AHT(0.953)PT(0.047)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 316.63 3.49E-104 23557091000 2124427.6 2148539.7 2255940 1981883 2880647 3453883 2525933 2282497 2369801 1907527.9 TRUE FALSE 2208301.642 2517534.68 2314731.65 2373893.542 2390995.652 2651771.017 2327943.771 2251903.861 2284512.325 2281271.47 0.968013527 1.10356646 1.014667338 1.040601074 1.048097819 1.162409232 1.020458898 0.987126649 1.001420635 1 21.12140671 2.00837437 24.97481651 0.997012216 1.058411128 0.239638657 0.04846597 253.0226878 754583.0763 0.017810787 0.013133599 101.946981 -2.00837437 0.061398912 AHTDFFEAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHTDFFEAFK 10 0 P61201;P61201-2;B4DIH5;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 129.85 0.00029216 304330000 349170 280550 329400 276970 411880 414710 389750 337960 356050 288680 FALSE TRUE 362955.5012 328732.2801 337984.4346 331753.8393 341868.7847 318399.8875 359200.3766 333430.199 343235.8301 345241.3189 1.051309566 0.952181162 0.978980256 0.960933183 0.990231372 0.922253132 1.040432755 0.9657888 0.994191052 1 18.39724561 2.224709992 24.99931216 0.99542327 0.974999622 0.094415275 0.035352969 668.0729893 1205814.304 0.012479679 0.009261948 167.7683339 -2.224709992 -0.020423648 AHTMTDDVTFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AHTMTDDVTFWK 12 0 A0A087WVQ6;Q00610-2;Q00610;J3KSQ2 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 160.15 4.98E-05 5613750000 6788680 5385720 7064150 6393960 7964200 8379400 8112080 7052320 7633400 5213530 FALSE TRUE 7056702.328 6310675.515 7248247.552 7658666.204 6610448.129 6433411.341 7476233.973 6957795.186 7358675.425 6235021.384 1.131784784 1.01213374 1.162505644 1.228330383 1.060212583 1.031818649 1.199071104 1.115921623 1.18021655 1 22.57196308 2.225902347 24.98840095 1.133926202 1.106524517 0.007655817 0.077389324 1103.042596 2177477.19 0.028777891 0.021415945 168.2295748 -2.225902347 -0.027401686 AHTPT(ph)PGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.116)PT(0.884)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 94.006 0.00040936 80279000 12833 10633 12746 10190 13066 17206 10711 10180 12065 9441.7 TRUE FALSE 13339.65675 12459.13504 13078.17123 12205.55159 10845.04599 13210.16726 9871.443832 10043.55375 11630.78301 11291.62034 1.181376662 1.103396559 1.158219178 1.080938892 0.960450817 1.169908911 0.874227395 0.889469664 1.030036669 1 13.46296491 3.091787119 0.780029847 0.942701332 1.158687424 0.444454129 0.079745854 0.575325562 0.779049648 0.046689543 0.068337887 1235.341749 -3.091787119 0.215986091 AHTPTPGIY(ph)MGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 AHT(0.244)PT(0.352)PGIY(0.398)MGRPT(0.006)HS(0.001)GGGGGGGGGGGGGGGGR;AHT(0.251)PT(0.343)PGIY(0.401)MGRPT(0.005)HSGGGGGGGGGGGGGGGGR 108.39 1.86E-05 307750000 67940 66012 93254 56325 90368 101338 83459 80569 85169 58977 TRUE FALSE 70622.32366 77349.0475 95684.27585 67465.91689 75007.27964 77803.78529 76917.2655 79489.10434 82103.78433 70532.41397 1.001274729 1.096645402 1.356600043 0.956523577 1.063444102 1.10309262 1.09052365 1.126986868 1.164057484 1 16.1059988 -2.54627272 1.765498309 9.75E-05 1.108527909 0.090725562 0.101044605 1460921.888 96903.7227 5819685.838 0.025042491 0.002842675 2.54627272 1.108430406 AHVDEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AHVDEFK 7 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;;; 134.66 0.0031526 1599710000 2780300 2146710 2650760 2080600 3339780 3445410 3196020 2626020 2738560 1815890 FALSE TRUE 2890068.391 2515390.743 2719840.983 2492136.47 2772085.389 2645265.743 2945507.601 2590822.497 2639999.761 2171678.878 1.330799143 1.158270115 1.252413978 1.147562144 1.276471129 1.218074076 1.356327416 1.193004418 1.215649232 1 21.05037936 0.537933908 1.62914896 1.000123126 1.240294144 0.560223178 0.063968332 1.697616105 5.193531877 0.056959125 0.016230957 3.450912185 -0.537933908 0.240171017 AHVIVMAATNRPNSIDPALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHVIVMAATNRPNSIDPALR 20 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 158.15 1.65E-11 669240000 118760 125510 118940 135480 148750 192740 144630 108810 126920 131800 FALSE TRUE 123448.7365 147065.3662 122039.6741 162277.5396 123465.5281 147979.056 133293.5227 107351.5799 122352.174 157623.6865 0.783186456 0.933015649 0.774247049 1.029525087 0.783292986 0.938812302 0.845643987 0.681062487 0.776229618 1 17.26612482 1.986048285 24.3809189 0.7785832 0.876282323 0.009162968 0.108110266 855.3255213 1494698.524 0.03976231 0.026827262 96.83855146 -1.986048285 0.097699122 AHVIVMAATNRPNSIDPALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHVIVMAATNRPNSIDPALRR 21 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 145.91 6.83E-08 1600210000 1239040 740230 856180 737050 1116260 1054640 1056250 779440 900100 770630 FALSE TRUE 1287958.256 867358.7443 878492.7542 882836.2901 926518.5239 809715.8432 973458.365 768992.8817 867705.5768 921620.1939 1.397493528 0.941123849 0.953204758 0.957917693 1.005314912 0.878578669 1.056246783 0.834392396 0.941500178 1 19.8138128 4.738950088 24.99997786 0.94618249 1.397493663 0.832742086 0.059840589 11.26864637 723083.0811 0.013568803 0.079632399 54821.39566 -4.738950088 0.451311173 AHYGGDIFITSVDAATTFEELCEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AHYGGDIFITSVDAATTFEELCEEVR 26 0 Q05513;F2Z3C5 Q05513 PRKCZ Protein kinase C zeta type 0 ; 157.88 2.85E-09 30404000 15034.6 20129.7 15417.5 23058 19286.7 24134 18301.2 17627.1 18822.7 21478.6 FALSE TRUE 15628.17762 23586.81939 15819.29272 27618.80358 16008.35362 18529.24425 16866.70412 17390.83756 18145.2747 25686.92044 0.608409936 0.918242397 0.615850108 1.075208826 0.623210309 0.721349385 0.656626168 0.677030849 0.706401328 1 14.64874632 -1.083518766 4.935102249 1.000007967 0.734399036 0.23974891 0.142314308 1.16E-05 2.15E-06 0.128112826 0.030195577 0.082505183 1.083518766 -0.265608931 AHYTHSDYQYSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AHYTHSDYQYSQR 13 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 0 122.46 0.00013577 95146000 21164 129760 99172 128180 87241 141310 77175 95407 78520 133840 FALSE TRUE 21999.57106 152045.2706 101756.5038 153533.6214 72411.80598 108492.8941 71125.82184 94128.22522 75694.08054 160063.3855 0.13744287 0.949906627 0.6357263 0.959205136 0.452394567 0.677812066 0.444360349 0.588068439 0.472900659 1 17.2882838 -1.232352227 4.967094575 1.000060823 0.604589093 0.217465825 0.231517744 0.000143948 2.22E-05 0.20692843 0.048766022 0.058566298 1.232352227 -0.39547173 AIAGDEHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AIAGDEHKR 9 1 H0YDU8;P53041;A8MU39;M0R196;A0A087WY80;E7EU14 H0YDU8 PPP5C;PPP5D1 Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5;Protein PPP5D1 0 ;;;;; 171.56 3.69E-05 884609000 2510290 2002650 2388810 1922563 2908700 2852680 2660410 2430390 2453860 2046240 FALSE TRUE 2609398.188 2346589.559 2451064.351 2302840.223 2414280.213 2190188.303 2451880.113 2397814.597 2365546.058 2447161.55 1.066295843 0.958902594 1.001594828 0.94102501 0.986563479 0.894991302 1.001928178 0.979835024 0.966648915 1 21.22267791 4.742510295 24.78429746 0.969738894 1.066295885 0.456742998 0.031448922 302.1365838 1895833.09 0.007080911 0.053294366 55272.65099 -4.742510295 0.096556991 AIAHYEQSADYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIAHYEQSADYYK 13 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R027;A0A087WZQ7;Q9H115-3;Q9H115-2;Q9H115 P54920 NAPA;NAPB Alpha-soluble NSF attachment protein;Beta-soluble NSF attachment protein 0 127.02 9.12E-05 0 125990 93799 98936 102670 117630 132740 142260 97585 105130 103730 FALSE TRUE 130964.1825 109908.2486 101514.3534 122977.8196 97635.29462 101913.1467 131109.2895 96277.03269 101346.3918 124053.9075 1.055703808 0.885971678 0.818308391 0.991325643 0.787039253 0.821523068 1.056873517 0.776090287 0.816954451 1 16.92060765 4.735206583 5.48978736 0.876212823 1.061960277 0.227108939 0.094368872 0.197092406 23.06127521 0.021417124 0.13773372 54350.88039 -4.735206583 0.185747454 AIAHYEQSADYYKGEESNSSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIAHYEQSADYYKGEESNSSANK 23 1 P54920;M0R0Y2;M0R2M1;M0R058;M0R027;A0A087WZQ7;Q9H115-3;Q9H115-2;Q9H115 P54920 NAPA;NAPB Alpha-soluble NSF attachment protein;Beta-soluble NSF attachment protein 0 295.4 7.14E-62 166970000 104810 49840 92321 59184 125380 98296 107080 93029 108300 39240 FALSE TRUE 108947.9797 58399.6323 94726.9611 70890.41855 104067.9524 75468.24369 98686.7898 91782.09842 104402.3042 46928.3267 2.321582451 1.244443099 2.018545466 1.510610404 2.217593503 1.608159698 2.102925817 1.955793118 2.224718235 1 15.5181714 3.25455448 24.99657825 1.908163848 1.753466796 0 0.431511868 1053.588987 1646629.24 0.108451627 0.146381506 1797.026494 -3.25455448 -0.154697051 AIAQGIQELSAELPPEESESSRVDFGS(ph)SER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AIAQGIQELSAELPPEESESSRVDFGSSER 30 1 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 AIAQGIQELSAELPPEESESSRVDFGS(0.5)S(0.5)ER;AIAQGIQELSAELPPEES(0.043)ES(0.043)S(0.043)RVDFGS(0.699)S(0.172)ER;AIAQGIQELSAELPPEES(0.001)ES(0.001)S(0.001)RVDFGS(0.96)S(0.038)ER;AIAQGIQELSAELPPEESESSRVDFGS(0.802)S(0.198)ER 164.83 1.95E-12 447772000 71778.7 99993 96167 77355 97860 116631 72548 99079 91657 115821 TRUE FALSE 74612.5785 117166.0199 98673.19102 92655.58812 81225.79215 89545.21781 66861.49819 97751.00807 88358.28247 138513.9074 0.538664889 0.845879104 0.71237028 0.668926246 0.586408929 0.646470954 0.482706029 0.705712588 0.637901884 1 17.07967131 -1.353323452 4.956904678 1.000217638 0.650653298 0.553292208 0.095048748 0.000225009 2.94E-05 0.090579931 0.021336736 0.044327838 1.353323452 -0.34956434 AICDHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AICDHVR 7 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;; 189.88 0.00054855 2175500000 1421430 1847750 1201920 1209390 3316950 2218610 1623530 1309190 1310310 3935850 FALSE TRUE 1477549.154 2165086.689 1233243.023 1448603.732 2753136.024 1703371.451 1496273.476 1291642.449 1263152.199 4707004.451 0.313904346 0.459971243 0.262001669 0.30775491 0.584901938 0.361880144 0.317882316 0.274408589 0.268355854 1 22.16637779 -1.569228785 4.348910186 1.00870295 0.349792719 0.805715686 0.095737758 0.008322577 0.000824374 0.095498196 0.022382083 0.026963186 1.569228785 -0.658910231 AIDDNMSLDEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIDDNMSLDEIEK 13 0 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 66.989 0.05437 57757000 4981.6 137840 122880 103520 119630 156970 74294 120740 115910 174910 FALSE TRUE 5178.277415 161512.9478 126082.3537 123995.947 99295.33533 120516.0964 68470.64215 119121.6778 111738.4217 209180.2656 0.024755095 0.772123256 0.602744974 0.592770769 0.474687873 0.576135115 0.327328402 0.569469005 0.534172865 1 17.67438723 0.382533433 1.663002916 0.999998173 0.505621925 0.387392344 0.189927223 5.50706627 13.69084833 0.167912986 0.047543106 2.412867276 -0.382533433 -0.494376248 AIDGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIDGLDR 7 0 A0A0A0MSS8;P42330;S4R3Z2;P42330-2 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 79.469 0.097493 0 74418 89974 84061 84326 96861 104980 101580 90916 91017 86288 FALSE TRUE 77356.0801 105426.3346 86251.69872 101005.4311 80396.60182 80599.98599 93617.89417 89697.41973 87741.31595 103194.4815 0.749614504 1.02162764 0.835816969 0.978787137 0.7790785 0.781049382 0.907198649 0.869207524 0.850252016 1 16.6550063 -1.39793495 2.964655592 1.002165196 0.868002037 0.195322283 0.082611562 13178965.52 15396012.44 240952.8494 0.01860197 0.040000466 1.39793495 -0.134163159 AIDVKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIDVKSPR 8 1 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;Q659C4-5 A0A3B3ISF0 LARP1B La-related protein 1B 1 AIDVKS(1)PR 60.434 0.05591 132160000 206610 156670 170440 127160 219690 205110 171180 171420 175810 149960 TRUE FALSE 214767.1223 183576.8538 174881.8064 152311.8685 182347.1723 157476.311 157762.4643 169122.3953 169482.6324 179341.7908 1.197529708 1.023614479 0.975131371 0.849282634 1.016757842 0.878079282 0.879674858 0.94301721 0.945025873 1 17.45235218 4.750911294 1.516381843 0.926955163 1.308171355 0.714234709 0.050793405 0.560347565 1.167877098 0.012859463 0.323074413 56352.25427 -4.750911294 0.381216192 AIEALKEFNEDGALAVLQQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIEALKEFNEDGALAVLQQFK 21 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 284.95 2.46E-45 1209740000 1765100 1157500 1586150 1014770 2199690 1907760 1731230 1570290 1813260 1259580 FALSE TRUE 1834787.511 1356291.621 1627486.372 1215488.477 1825787.48 1464711.652 1595531.669 1549242.831 1748001.127 1506370.585 1.21801868 0.90037049 1.080402385 0.806898707 1.212044033 0.972344831 1.059189342 1.028460624 1.160405776 1 20.5226453 3.208138379 24.99995554 1.06498232 0.999845254 0.073949117 0.120879031 584.7035373 480488.0252 0.032473948 0.038818258 1614.87302 -3.208138379 -0.065137066 AIEDEGGNPDEIEITSEGNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIEDEGGNPDEIEITSEGNKK 21 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7ES42 Q15424 SAFB Scaffold attachment factor B1 0 94.281 0.0018673 0 21274 13762 18777 11937 23131 22221 18118 17827 20090 13168 FALSE TRUE 22113.91395 16125.51645 19266.34405 14298.10297 19199.20088 17060.50951 16697.86382 17588.05822 19366.96482 15748.01748 1.404234785 1.023971205 1.223413935 0.907930347 1.219150341 1.083343318 1.060315296 1.116842691 1.229803361 1 13.9428826 4.747630076 24.58358891 1.100315561 1.404234986 0.457598787 0.100551968 805.1708641 2182429.356 0.021706862 0.264098048 55928.10132 -4.747630076 0.303919424 AIEKVDDLLESYMGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIEKVDDLLESYMGIR 16 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 213.99 4.43E-13 865570000 769740 737320 829950 501950 1128070 928490 768840 724620 901150 756810 FALSE TRUE 800129.9296 863948.9744 851579.1788 601234.2118 936321.0643 712862.2689 708576.3118 714907.6541 868717.7875 905092.4295 0.884031181 0.954542261 0.940875375 0.664279351 1.034503255 0.787612674 0.782877294 0.789872538 0.95981113 1 19.7877056 AIELDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIELDKK 7 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 ; 93.374 0.024023 792810000 1096230 588960 799920 578820 1165330 1050190 1136650 842040 935470 585390 FALSE TRUE 1139510.007 690109.2985 820766.5723 693308.8684 967247.6228 806299.2883 1047556.403 830753.8311 901802.6174 700085.9625 1.627671554 0.985749373 1.172379702 0.990319626 1.381612651 1.151714691 1.496325393 1.186645463 1.288131266 1 19.41717255 AIEMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AIEMER 6 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 120.9 0.046264 1494930000 2155470 1894230 1787200 1699280 2102540 2023760 1802860 1846800 1699480 1882420 FALSE TRUE 2240569.62 2219549.267 1833775.9 2035392.512 1745151.002 1553772.41 1661547.122 1822046.667 1638316.047 2251244.158 0.995258383 0.985921167 0.814561092 0.904118954 0.775194017 0.690183872 0.738057272 0.809350981 0.727738056 1 21.1022911 4.184560248 1.053965818 0.779591243 1.036912225 0.398908073 0.087086915 0.734887183 1.183137089 0.026586167 0.174032854 15295.37917 -4.184560248 0.257320982 AIEPPPLDAVIEAEHTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AIEPPPLDAVIEAEHTLR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 383.69 2.01E-126 1990876000 1028344 1315759 1271833 1294840 1324400 1506070 1242289 1303051 1185880 1372833 FALSE TRUE 1068943.815 1541730.373 1304978.013 1550955.487 1099278.961 1156308.067 1144915.142 1285585.733 1143200.41 1641813.342 0.651075118 0.939041201 0.794839449 0.944660058 0.669551729 0.704287167 0.697347934 0.783027948 0.696303521 1 20.64685869 5.016894883 14.73094878 0.788730009 0.406924296 0.127324054 0.113947303 1271822.196 25246136.46 0.026503136 10292793.86 103966.8494 -5.016894883 -0.381805713 AIEQADLLQEEDES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIEQADLLQEEDESPR 16 0 A0A2R8YGH5;H7C1E4;P61966 A0A2R8YGH5 AP1S1 AP-1 complex subunit sigma-1A 1 AIEQADLLQEEDES(1)PR;AIEQADLLQEEDES(1)PR 390.18 2.04E-121 304040000 215124 215370 208429 243590 206800 241500 251930 226710 200024 171990 TRUE FALSE 223617.2616 252358.1222 213860.831 291771.375 171648.2099 185415.285 232183.0683 223671.3233 192825.1753 205688.1476 1.087166491 1.226896762 1.039733371 1.41851331 0.834507053 0.901438839 1.12881112 1.087429324 0.937463717 1 17.65009914 3.224911073 24.999454 0.999189997 1.184540062 0.408873744 0.123313712 264.8054899 484996.4663 0.036145226 0.043417349 1678.4603 -3.224911073 0.185350065 AIEVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIEVGR 6 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 102.98 0.081604 346960000 233440 283410 239660 257590 273750 306380 257720 250090 231910 299860 FALSE TRUE 242656.3915 332083.4629 245905.7365 308540.5332 227218.0728 235227.8882 237519.233 246737.9526 223563.6044 358611.8258 0.676654739 0.926024852 0.685715637 0.860374675 0.633604517 0.655940132 0.662329616 0.688036297 0.623413921 1 18.45206354 AIEVLSDEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIEVLSDEHAR 11 0 Q9HCS7 Q9HCS7 XAB2 Pre-mRNA-splicing factor SYF1 0 ; 132.76 0.001007 0 92915 110497 101609 114315 120190 136407 105579 114338 101735 116612 FALSE TRUE 96583.35595 129474.0002 104257.014 136926.1658 99760.14673 104728.5415 97303.4421 112805.4861 98073.57722 139459.8887 0.69255294 0.928395981 0.747577063 0.981831888 0.715332184 0.750958161 0.697716333 0.808874058 0.703238602 1 17.08949071 AIFQEVHVQSLPQVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIFQEVHVQSLPQVDR 16 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;Q5T454;Q96T76-7;B0QZ77;F8WCH8 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 108.56 0.0010408 87678000 71904 81213 71854 92974 82499 97040 92924 77620 71573 77994 FALSE TRUE 74742.82544 95160.701 73726.57427 111363.9797 68475.84945 74503.93066 85640.37407 76579.63086 68997.10171 93275.43101 0.801313107 1.02021186 0.790417943 1.193926187 0.734125254 0.798751931 0.918145037 0.821005382 0.739713566 1 16.5092095 AIGDHFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AIGDHFYK 8 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;; 100.19 0.0062812 1166490000 1921620 1719760 1993910 1647580 2446300 2493000 2292630 2008860 2164860 1810540 FALSE TRUE 1997487.041 2015115.402 2045872.933 1973466.406 2030478.8 1914038.532 2112927.67 1981934.518 2086947.111 2165280.648 0.922507225 0.930648599 0.944853469 0.911413681 0.937743937 0.883967874 0.97582162 0.915324542 0.963822918 1 21.0461226 1.000551391 3.78593946 0.999908303 0.928571308 0.50938061 0.022609379 0.141912899 5.377746257 0.019710736 0.00507007 10.01270432 -1.000551391 -0.071336995 AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILT(0.008)AS(0.992)HNPGGPNGDFGIK;AIGGIILTAS(1)HNPGGPNGDFGIK 291.53 1.00E-61 14338230000 11200990 7960943 10162669 8537809 13157370 11973710 12374340 10702070 10906970 7221015 TRUE FALSE 11643213.73 9328173.033 10427516.5 10226562.14 10920884.95 9192997.316 11404406.9 10558626.26 10514430.28 8635834.635 1.348244174 1.080170409 1.207470609 1.184200783 1.264600981 1.064517526 1.320591162 1.222652668 1.217534926 1 23.04190419 -1.27660347 4.411458948 0.999864647 1.210234123 0.35611533 0.085571021 0.000103981 1.71E-05 0.075628426 0.017814356 0.052892797 1.27660347 0.210369477 AIGNNSATS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIGNNSATSPR 11 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 AIGNNSAT(0.002)S(0.998)PR;AIGNNS(0.001)AT(0.009)S(0.99)PR 101.56 0.0033524 385700000 391180 441790 423690 480580 532940 668740 462600 490030 481530 645410 TRUE FALSE 406624.0885 517663.9959 434731.7095 575637.2896 442351.0492 513435.2699 426340.2032 483461.9494 464199.8294 771865.7324 0.526806764 0.670665861 0.563221933 0.745773864 0.57309326 0.665187284 0.552350215 0.626354985 0.601399712 1 19.55799038 -2.077096809 2.346121048 1.581971241 0.616303235 0.773776745 0.062621943 7073283.4 2158754.346 22014343.33 0.014138006 0.008373426 2.077096809 -0.965668006 AIGPHDVLATLLNNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIGPHDVLATLLNNLK 16 0 O75533;H7C341 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 169.17 5.72E-09 274990000 382640 307930 354870 308830 465580 420200 423010 354070 382720 303200 FALSE TRUE 397746.9227 360814.5821 364118.2037 369915.6522 386440.8779 322614.9182 389853.3709 349324.2708 368945.982 362606.2349 1.096911427 0.995058958 1.004169727 1.020158002 1.065731476 0.889711448 1.075142492 0.963370834 1.017483834 1 18.46804421 4.741506046 24.12127609 1.002746816 1.096911483 0.245779667 0.049116867 225.9513142 1850242.841 0.010691363 0.074716161 55144.98797 -4.741506046 0.094164668 AIGSASEGAQSSLQEVYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AIGSASEGAQSSLQEVYHK 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 332.96 2.47E-75 924090000 859770 826880 911080 801120 1059990 1084460 981890 973260 986930 917420 FALSE TRUE 893714.3835 968890.2078 934823.4933 959579.1449 879813.2784 832610.6002 904926.8961 960215.0416 951410.5821 1097170.884 0.814562614 0.883080495 0.852030898 0.874594066 0.80189266 0.758870484 0.824782091 0.875173645 0.867148952 1 20.06535681 0.680359323 1.171946376 0.99937823 0.833262534 0.662056221 0.035537224 0.692524662 1.555370906 0.03679147 0.011329299 4.790262611 -0.680359323 -0.166115696 AIGSTSKPQES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AIGSTSKPQESPK 13 1 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGSTSKPQES(1)PK;AIGSTSKPQES(1)PK;AIGSTSKPQES(1)PK;AIGSTSKPQES(0.999)PK 147.12 2.58E-05 1831300000 4502280 1062130 1488700 1040520 2321970 2896730 2358500 1652300 1821490 736780 TRUE FALSE 4680033.491 1244542.565 1527496.745 1246331.75 1927282.369 2224008.358 2173634.607 1630153.621 1755934.931 881137.9345 5.311351728 1.412426496 1.733550089 1.414457035 2.187265232 2.524018398 2.466849425 1.850054977 1.992803694 1 19.74900835 4.74367818 24.98942277 1.909675813 5.311353148 0.835366696 0.461130094 211.0425854 1030503.093 0.111378776 0.941858098 55421.48777 -4.74367818 3.401677335 AIGSTSKPQES(ph)PKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIGSTSKPQESPKGK 15 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 AIGS(0.001)T(0.004)S(0.013)KPQES(0.982)PKGK;AIGSTS(0.002)KPQES(0.997)PKGK 133.09 2.27E-05 1012950000 4895600 1063840 1853020 1037840 2941600 2956800 2697600 1954390 2318700 776640 TRUE FALSE 5088882.068 1246546.244 1901311.223 1243121.654 2441587.883 2270128.011 2486155.063 1928194.599 2235250.44 928807.7383 5.478940214 1.342092871 2.047044986 1.33840579 2.628733356 2.444131242 2.67671657 2.075988947 2.406580337 1 19.82502047 4.746167816 24.96561638 2.074777783 5.478941873 0.775189972 0.561311117 414.5331508 1360399.056 0.12974514 1.382398432 55740.10926 -4.746167816 3.404164091 AIGTEPDSDVLSEIMHSFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIGTEPDSDVLSEIMHSFAK 20 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 317 1.74E-66 1053520000 718600 641300 833140 833360 916960 982830 1012350 781220 881890 593830 FALSE TRUE 746970.8829 751438.2864 854852.3128 998196.1207 761095.4667 754582.6274 932999.3617 770749.0237 850150.9512 710179.6189 1.051805576 1.058096102 1.203712821 1.405554446 1.071694324 1.062523631 1.313751249 1.085287444 1.19709286 1 19.43782443 -0.635013834 8.237466757 1.000001528 1.16205506 0.150045355 0.114975628 0 0 0.110377319 0.026016184 0.231732083 0.635013834 0.162053533 AIGVKPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIGVKPPR 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 111.01 0.0030244 2391800000 2215200 2139490 2274600 1925080 2506200 2558900 2438000 2353300 2252000 2104100 FALSE TRUE 2302657.807 2506930.765 2333877.945 2305855.078 2080197.019 1964634.256 2246903.189 2321757.863 2170950.96 2516358.11 0.91507556 0.996253576 0.927482434 0.916346155 0.826669706 0.780745097 0.892918691 0.922665917 0.862735297 1 21.26290582 3.647607813 2.798608146 0.876760487 0.953534067 0.195371074 0.058062952 0.397226446 6.037238525 0.016421105 0.028412956 4442.299274 -3.647607813 0.07677358 AIHDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIHDLGK 7 0 Q9BUP3-3;Q9BUP3;E9PI87 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 86.866 0.019762 131290000 308180 298410 334160 296790 431380 428180 348530 316660 341440 308050 FALSE TRUE 320347.1844 349659.5962 342868.4841 355494.1762 358054.1817 328741.6841 321211.3079 312415.6907 329151.6411 368406.4995 0.869548134 0.949113538 0.930679791 0.964950881 0.971899742 0.892334105 0.871893705 0.848018944 0.89344689 1 18.49093899 2.601385808 6.935797359 0.885071421 0.938945523 0.084755553 0.046456431 0.364198868 19.07956234 0.014589442 0.013721975 399.3795356 -2.601385808 0.053874102 AIHSWLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIHSWLTR 8 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 194.2 0.00016665 3722400000 1439720 1710020 1409360 1403180 1878070 1849110 1547370 1538840 1489450 2056020 FALSE TRUE 1496561.257 2003702.633 1446089.079 1680724.816 1558836.332 1419682.226 1426083.096 1518214.367 1435844.985 2458857.754 0.608640843 0.814891642 0.588114167 0.683538856 0.633967674 0.577374687 0.579977875 0.617447009 0.583947967 1 21.22955685 -1.692878705 5.876127023 1.005759751 0.632643709 0.722577163 0.068407577 0.005175196 0.000270486 0.066407352 0.015504486 0.020282491 1.692878705 -0.373116042 AIIEEYLHLNDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIIEEYLHLNDMK 13 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 155.42 1.35E-06 0 329730 255560 329660 264100 381320 364940 327630 312410 353880 254500 FALSE TRUE 342747.995 299450.442 338251.2104 316338.1917 316503.3626 280188.2157 301949.5045 308222.6549 341143.9279 304364.4023 1.12611065 0.98385501 1.111336306 1.039340308 1.039882983 0.920568285 0.992065768 1.012676425 1.120840431 1 18.21544011 4.753480303 23.55063687 1.023312182 1.126110816 0.227316289 0.056158341 1847.050367 2915446.787 0.013543118 0.286904216 56686.58618 -4.753480303 0.102798634 AIIESDQEQGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AIIESDQEQGRK 12 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;; 134.13 0.00024199 298020000 422929 363509 425670 323789 568950 553380 494120 455960 495590 459370 FALSE TRUE 439626.5635 425938.843 436763.3099 387833.4978 472240.0822 424865.8816 455389.5833 449848.602 477753.8127 549374.7563 0.800230732 0.775315644 0.795018892 0.705954348 0.859595525 0.773362585 0.828923386 0.818837409 0.869631899 1 19.06743109 0.513607657 0.519842272 1.011089974 0.777815212 0.76242315 0.036027103 0.809380583 0.399455447 0.051545602 0.016733044 3.262929249 -0.513607657 -0.233274762 AIIVEFAQQGLNAALFYENKDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIIVEFAQQGLNAALFYENKDPR 23 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 190.91 1.26E-17 500390000 661840 521920 622810 517030 734810 737480 708750 663440 685860 541900 FALSE TRUE 687969.9543 611555.7 639040.9402 619296.9908 609907.2587 566211.4466 653196.323 654547.672 661176.0326 648074.9297 1.061559278 0.94364968 0.98606027 0.955594735 0.941106083 0.873682071 1.007902471 1.009987645 1.020215414 1 19.3058011 2.050494696 24.99997808 1.01062038 0.958039624 0.230689156 0.043957619 148.4785638 73511.18143 0.016498928 0.012185263 112.329725 -2.050494696 -0.052580756 AIIYQYMEEIYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIIYQYMEEIYHR 13 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 232.25 1.06E-12 660530000 693490 912610 747720 943290 838670 979790 757390 744370 684490 773610 FALSE TRUE 720869.5207 1069343.668 767206.1975 1129869.947 696113.173 752248.6214 698023.7927 734392.9377 659855.3386 925184.0678 0.779163353 1.15581721 0.829247092 1.221238006 0.752405059 0.813079956 0.754470183 0.793780355 0.713215199 1 19.8193809 3.185130795 24.99948956 0.791367387 0.995821474 0.29965232 0.142860579 99.76840982 46680.57432 0.037210111 0.044474628 1531.548643 -3.185130795 0.204454087 AIKVEQATKPS(ph)FESGR ddPTM_MDA-MB-175_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" 1 AIKVEQAT(0.004)KPS(0.995)FES(0.001)GR;AIKVEQAT(0.001)KPS(0.792)FES(0.207)GR 119.38 0.00010382 964750000 1475090 905800 1191600 690390 1696110 1413670 1204310 1174610 1329290 905080 TRUE FALSE 1533327.692 1061364.104 1222654.075 826947.0814 1407805.828 1085366.567 1109913.035 1158866.274 1281449.113 1082413.097 1.416582723 0.980553641 1.129563268 0.763984733 1.30061788 1.002728598 1.025406139 1.070632162 1.183881751 1 20.04581977 4.745582577 24.75120783 1.052461429 1.416582917 0.401462254 0.133968237 691.0283479 2435685.803 0.029441765 0.292963918 55665.04655 -4.745582577 0.364121488 AIKVEQATKPSFESGR ddPTM_MDA-MB-175_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 ; 127.61 3.67E-05 2714100000 3675700 2863400 3833000 2731300 5070000 4305900 3876300 3911200 4232800 3311800 FALSE TRUE 3820819.474 3355166.676 3932891.129 3271542.988 4208203.211 3305919.982 3572465.477 3858776.761 4080462.355 3960683.802 0.964686823 0.847118034 0.99298286 0.826004587 1.06249411 0.834684147 0.901981995 0.974270342 1.030241887 1 21.9173181 1.543742397 3.751141599 1.012928256 0.91771273 0.235984648 0.070675987 0.254564266 7.977566817 0.041595058 0.016959308 34.97376577 -1.543742397 -0.095215527 AILDAEPGPRPALQPS(ph)PSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AILDAEPGPRPALQPSPSIR 20 1 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(1)PSIR;AILDAEPGPRPALQPS(0.981)PS(0.019)IR;AILDAEPGPRPALQPS(0.979)PS(0.021)IR;AILDAEPGPRPALQPS(0.5)PS(0.5)IR;AILDAEPGPRPALQPS(0.972)PS(0.028)IR 171.29 4.87E-12 2595830000 1757430 2033650 1789070 2375740 1865410 2425030 2106670 1974590 1576320 1800000 TRUE FALSE 1826814.693 2382913.568 1835694.634 2845654.281 1548328.275 1861853.534 1941543.701 1948123.851 1519588.551 2152675.537 0.848625193 1.106954358 0.852750265 1.321915092 0.719257616 0.864902073 0.901921199 0.90497793 0.705906917 1 21.03769945 AILDAEPGPRPALQPS(ph)PSIRLPLDAPLPGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AILDAEPGPRPALQPSPSIRLPLDAPLPGSK 31 2 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 AILDAEPGPRPALQPS(0.963)PS(0.037)IRLPLDAPLPGSK;AILDAEPGPRPALQPS(0.975)PS(0.025)IRLPLDAPLPGSK 202.68 4.62E-26 1222940000 1301630 1298760 1391840 1119300 1787780 1817840 1256020 1562520 1394190 1527550 TRUE FALSE 1353019.357 1521811.927 1428112.494 1340694.199 1483893.794 1395674.21 1157569.87 1541576.975 1344013.374 1826844.176 0.740632056 0.833027768 0.781737442 0.733885362 0.812271684 0.763980983 0.633644558 0.843846999 0.735702252 1 20.80092215 -1.157367489 4.313377978 1.000048345 0.767254858 0.601232261 0.057540408 2.85E-05 5.56E-06 0.053080388 0.01250827 0.06960373 1.157367489 -0.232793487 IKLYSESLAR ddPTM_MDA-MB-175_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 ; 167.11 4.87E-06 1868140000 1981790 2512300 2164400 1770710 4310500 3317500 2329370 2589400 2720800 4245200 FALSE TRUE 2060032.599 2943767.982 2220806.042 2120951.153 3577802.75 2547060.902 2146787.893 2554693.328 2622878.939 5076965.661 0.405760593 0.579828224 0.437427824 0.417759602 0.704712812 0.501689606 0.422848614 0.50319295 0.516623337 1 22.27553507 0.5288657 2.984452468 0.999998907 0.498760474 0.754240362 0.085877362 6.150893293 38.29081293 0.080284781 0.020990093 3.379603103 -0.5288657 -0.501238433 AILILDNDGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AILILDNDGDR 11 0 F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4;F8VXB1;F8VUC5;F8W156;F8W651;F8VXR1 F8VYZ4 COPZ1 Coatomer subunit zeta-1 0 ;;;;;;; 245.38 1.43E-15 1158669000 1311666 1409831 1440683 1599332 1384466 1641856 1655450 1434610 1324798 1208029 FALSE TRUE 1363451.587 1651958.507 1478228.383 1915675.096 1149134.964 1260559.827 1525691.503 1415381.399 1277118.779 1444719.153 0.943748536 1.143446118 1.023194286 1.325984425 0.795403703 0.872529324 1.056047121 0.979693109 0.883991034 1 20.46235764 3.221240191 24.99989876 0.939492119 1.105411579 0.366841009 0.114097348 277.8874062 401095.3032 0.032709933 0.039183101 1664.332872 -3.221240191 0.16591946 AILILDNDGDRLFAK ddPTM_MDA-MB-175_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 ; 236.4 9.54E-18 2816100000 1263980 1280290 1402970 1037410 1771340 1620000 1190900 1365010 1479430 1406620 FALSE TRUE 1313882.906 1500169.848 1439532.551 1242606.602 1470248.26 1243779.551 1097554.146 1346714.274 1426185.603 1682220.258 0.781040949 0.891779683 0.855733691 0.738670573 0.873992721 0.739367836 0.652443781 0.800557637 0.847799565 1 20.68193518 3.774703237 24.20084687 0.790458317 0.847744292 0.005858278 0.092232442 1129.069753 756012.3935 0.022790522 0.041084069 5952.552541 -3.774703237 0.057285975 AILTGHDYEVTCAAVCAELGLVLSGSQEGPCLIHSMNGDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AILTGHDYEVTCAAVCAELGLVLSGSQEGPCLIHSMNGDLLR 42 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6;A0A3B3IS13;H0YA17 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;;; 362.68 2.70E-155 406794000 76219 103323.1 88571.9 111330.6 102294.9 118199.6 103206.2 92850.7 99457.6 101848 FALSE TRUE 79228.18497 121068.0387 90880.15648 133351.4604 84906.84944 90749.53423 95116.62836 91606.18824 95878.1404 121803.1656 0.650460804 0.993964632 0.746123108 1.094811122 0.697082453 0.745050704 0.780904403 0.752083805 0.787156392 1 16.8941921 AILVDLEPGTMDS(ph)VR ddPTM_MDA-MB-175_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(0.001)MDS(0.999)VR;AILVDLEPGT(0.001)MDS(0.999)VR 144.68 4.40E-06 26389000 42278 62394 66271 50413 62303 68630 50306 61004 58579 68636 TRUE FALSE 43947.16809 73109.68414 67998.0767 60384.54093 51712.75831 52691.7226 46362.88427 60186.34116 56470.75323 82083.91008 0.53539321 0.890670097 0.828397144 0.735644061 0.62999872 0.641925105 0.564823048 0.733229461 0.687963733 1 16.32481184 -1.350756506 8.029189068 1.000001846 0.69864103 0.43542877 0.104344126 3.50E-06 2.83E-07 0.102580148 0.024178225 0.044590618 1.350756506 -0.301360816 AILVDLEPGTMDSVR ddPTM_MDA-MB-175_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 0 ; 140.14 1.16E-05 176433000 214863 254632 262982 262791 272430 301240 258388 267280 243373 277895 FALSE TRUE 223345.9572 298363.0652 269835.527 314770.2754 226122.4459 231281.5753 238134.8734 263697.5488 234614.0533 332343.2046 0.672034072 0.897755877 0.811918292 0.947124151 0.680388354 0.695911853 0.716533 0.793449498 0.705939071 1 18.34231433 4.795412889 20.72748053 0.792377211 0.672027235 0.11305528 0.106589154 15314.47012 5581850.894 0.024782387 23.24032206 62432.81095 -4.795412889 -0.120349977 AIMEMPSFYSHGLPR ddPTM_MDA-MB-175_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 ; 212.95 6.17E-10 1177090000 1058880 1305790 1194000 1138780 1384670 1692260 1209070 1208810 1152150 1477180 FALSE TRUE 1100685.4 1530049.275 1225116.621 1364027.285 1149304.288 1299258.261 1114299.934 1192607.879 1110684.347 1766605.139 0.623051171 0.866095791 0.69348639 0.772117807 0.650572255 0.735454818 0.630757779 0.675084575 0.628711149 1 20.75254818 -1.183101232 5.164110569 1.000018175 0.699376955 0.609049577 0.072747924 1.46E-05 2.31E-06 0.067660668 0.015946809 0.065599234 1.183101232 -0.300641219 AIPELDAYEAEGLALDDEDVEELTAS(ph)QR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AIPELDAYEAEGLALDDEDVEELTASQR 28 0 P49736;F8WDM3;C9J013;C9JZ21;H7C4N9 P49736 MCM2 DNA replication licensing factor MCM2 1 AIPELDAYEAEGLALDDEDVEELT(0.008)AS(0.992)QR;AIPELDAYEAEGLALDDEDVEELT(0.071)AS(0.929)QR;AIPELDAYEAEGLALDDEDVEELT(0.06)AS(0.94)QR;AIPELDAYEAEGLALDDEDVEELT(0.026)AS(0.974)QR;AIPELDAYEAEGLALDDEDVEELTAS(1)QR 170.6 3.86E-13 137780000 73133.6 87062.9 75524.1 87500.9 84683.3 101946.1 90281.4 83029.3 80789.8 90217.3 TRUE FALSE 76020.971 102015.2758 77492.32009 104808.3169 70288.86291 78270.66328 83204.90796 81916.42804 77882.19088 107893.6526 0.70459169 0.945516936 0.718228721 0.971403918 0.6514643 0.725442706 0.771175189 0.75923306 0.721842194 1 16.71925047 5.05037201 15.77797119 0.793456224 0.150725891 0.054600954 0.11605651 8154692.874 66401411.86 0.025638926 159827685.1 112297.9969 -5.05037201 -0.642730333 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AIPGDQHPES(1)PVHTEPMGIQGR;AIPGDQHPES(0.999)PVHT(0.001)EPMGIQGR 200 1.09E-22 325020000 136333 171967 150643 169276 165094 183349 152138 149817 151064 192125 TRUE FALSE 141715.5321 201500.9945 154568.8803 202758.2876 137031.3809 140768.9734 140213.026 147808.9482 145627.2361 229768.2153 0.616776049 0.876975061 0.672716547 0.882447066 0.59638963 0.612656425 0.610236824 0.643295888 0.633800615 1 17.80981971 -1.150102564 3.815591704 1.000176815 0.683351722 0.466283501 0.101803822 39701616.91 81154679.19 91725.30713 0.02474856 0.070777861 1.150102564 -0.316825093 AIPPERHS(ph)PHHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIPPERHSPHHLK 13 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 AIPPERHS(1)PHHLK;AIPPERHS(1)PHHLK 115.8 0.00031867 315540000 309210 261890 311530 270730 396780 403880 309700 296540 332340 299820 TRUE FALSE 321417.8496 306867.5703 319648.7277 324279.586 329335.4773 310084.9909 285424.9047 292565.3663 320379.1483 358563.9886 0.89640304 0.85582373 0.891469132 0.904384144 0.918484532 0.864796803 0.796022227 0.815936278 0.893506204 1 18.45187108 2.488805211 24.71064599 0.850941564 0.891732607 0 0.055189425 1108.669129 2344753.502 0.017731287 0.015860919 308.1805391 -2.488805211 0.040791044 AIPVS(ph)PSAVEEDEDEDGHTVVATAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 AIPVS(0.858)PS(0.142)AVEEDEDEDGHTVVATAR;AIPVS(0.83)PS(0.17)AVEEDEDEDGHTVVATAR 327.07 6.09E-88 2422600000 517680 549400 581840 512510 497890 695060 554910 540450 541740 631390 TRUE FALSE 538118.4061 643755.1763 597003.2284 613882.9483 413258.8356 533642.8487 511414.7042 533206.1517 522242.8832 755098.7818 0.71264637 0.852544318 0.790629309 0.81298363 0.54729109 0.706719255 0.677281856 0.706140924 0.691621938 1 19.52630586 -1.045632611 4.113748257 1.000031508 0.721806077 0.520637521 0.080030213 7368406.288 5621100.462 1894.771082 0.019570538 0.090025883 1.045632611 -0.278225431 AIQNEISSLKDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIQNEISSLKDER 13 1 Q15149-8 Q15149-8 PLEC Plectin 0 121.18 0.00022766 219890000 261280 195990 240960 194540 303000 291900 264480 223600 251500 195070 FALSE TRUE 271595.5362 229649.7579 247239.6156 233019.4314 251496.1682 224110.6488 243749.3665 220603.0077 242448.5641 233290.2317 1.164195921 0.984395087 1.059794119 0.998839213 1.078039858 0.960651662 1.044833145 0.945616137 1.039257248 1 17.83176637 4.744678788 24.54211362 1.010673361 1.164196009 0.554950044 0.040760463 378.4444449 1518017.578 0.0091726 0.084785028 55549.32524 -4.744678788 0.153522648 AIS(ph)ETEENSDELSGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AISETEENSDELSGER 16 0 Q00987-8;A7UKX8;F5GWH7;J3KN53;E7EPE2;Q00987-9;Q00987;Q00987-11 Q00987-8 MDM2;mdm2 E3 ubiquitin-protein ligase Mdm2 1 AIS(1)ETEENSDELSGER 194.94 1.39E-10 253420000 26252 38421 33816 38895 48235 59143 42897 45637 44100 51242 TRUE FALSE 27288.44923 45019.50788 34697.27274 46588.31491 40036.03193 45407.93457 39534.62105 45025.31066 42512.84961 61281.88881 0.445293867 0.7346299 0.566191307 0.760229748 0.653309366 0.740968261 0.645127326 0.73472459 0.693726163 1 15.90317314 -5 0.138163115 2.118058772 0.548352044 0.635149429 0.082302053 84.5580188 0.720156347 26.11018121 0.476741048 1.00E-05 5 -1.569706728 AIS(ph)SANLLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AISSANLLVR 10 0 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 AIS(0.94)S(0.06)ANLLVR;AIS(0.958)S(0.042)ANLLVR 71.888 0.052065 53057000 85295 157205 141327 153376 166356 166305 120127 142039 143881 223490 TRUE FALSE 88662.51246 184203.7359 145010.0977 183713.315 138078.8665 127683.1841 110711.1318 140135.1995 138702.7509 267278.5865 0.331723217 0.689182543 0.542542894 0.687347675 0.516610284 0.477715726 0.414216243 0.524303878 0.518944494 1 18.02798473 -1.199123275 3.482262324 1.000766821 0.526479001 0.659906436 0.102800152 68143233.47 110404947.5 577447.5508 0.024063516 0.063223237 1.199123275 -0.47428782 AIS(ph)SDMFFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.983)S(0.017)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.5)S(0.5)DMFFGR;AIS(0.947)S(0.053)DMFFGR;AIS(0.822)S(0.178)DMFFGR 231.07 8.98E-10 927855000 345856 350262 545926 360516 854409 487600 474446 482211 619177 549141 TRUE FALSE 359510.6619 410416.7738 560153.28 431824.9888 709176.8634 374362.2896 437257.6828 475747.7503 596892.9407 656734.665 0.547421479 0.624935451 0.852936977 0.657533418 1.079852947 0.57003583 0.665805699 0.724413946 0.908879906 1 19.32495108 -5 0.118582757 1.855701862 0.601898569 0.272762261 0.150332727 231.9625185 1.790975429 47.79625168 1.501907771 1.00E-05 5 -1.253803294 AIS(ph)SLDLLGDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AISSLDLLGDFK 12 0 Q9ULL8-2;Q9ULL8 Q9ULL8-2 SHROOM4 Protein Shroom4 1 AIS(0.874)S(0.126)LDLLGDFK 108.59 0.0017716 9619900 22052 24010 25655 18933 45870 32888 19390 21858 25967 28204 TRUE FALSE 22922.62999 28133.53073 26323.59038 22677.89089 38073.03378 25250.26042 17870.16113 21565.02926 25032.45274 33730.0338 0.679591077 0.83407953 0.780419923 0.672335255 1.128757653 0.748598729 0.529799681 0.639342059 0.742141348 1 15.04174614 2.478341127 24.98837297 0.67971891 0.822487067 0.035738835 0.164089346 89.7851582 1839268.041 0.054675228 0.046312195 300.8438422 -2.478341127 0.142768156 AIS(ph)TGSLASSTLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AISTGSLASSTLNK 14 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 AIS(0.966)T(0.031)GS(0.003)LASSTLNK;AIS(0.969)T(0.031)GSLASSTLNK;AIS(0.896)T(0.098)GS(0.005)LASSTLNK;AIS(0.951)T(0.048)GS(0.001)LASSTLNK;AIS(0.333)T(0.333)GS(0.333)LASSTLNK;AIS(0.998)T(0.001)GSLASSTLNK 266.2 8.05E-25 1507920000 2220601 2477880 2661770 2467730 3044670 3311120 2680610 2607650 2698500 2677050 TRUE FALSE 2308272.042 2903436.615 2731137.913 2955839.629 2527138.081 2542162.561 2470496.784 2572698.717 2601381.512 3201566.692 0.720982027 0.906879942 0.853062946 0.92324787 0.789344194 0.794037046 0.771652451 0.803574926 0.812533913 1 21.61034663 AISGVHTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AISGVHTVR 9 0 P41091;Q2VIR3;Q2VIR3-2;H7BZU1 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 120.12 0.0007167 220810000 110400 162640 147480 140720 154260 177060 138410 149660 150030 171480 FALSE TRUE 114758.6772 190572.1548 151323.45 168553.996 128038.9403 135940.4984 127561.0625 147654.0525 144630.4496 205078.2228 0.559584902 0.929265683 0.737881614 0.821900998 0.624341963 0.662871447 0.622011742 0.719988941 0.705245285 1 17.64581478 -1.275172783 9.242245901 1.000000057 0.712736928 0.428035934 0.100761752 1.16E-07 8.97E-09 0.094344139 0.022237122 0.053067328 1.275172783 -0.28726313 AISS(ph)DMFFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AISSDMFFGR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;Q8N6H7-3;H0YDN9;E9PMU9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 AIS(0.271)S(0.729)DMFFGR;AIS(0.306)S(0.694)DMFFGR;AIS(0.356)S(0.644)DMFFGR 252.51 4.87E-17 1177040000 216639 211032 344088 238302 564030 289173 294504 283937 411174 330177 TRUE FALSE 225192.075 247275.1044 353055.216 285437.4243 468156.3821 222016.9532 271420.0069 280131.2889 396375.9281 394868.8615 0.570295855 0.626220825 0.894107514 0.72286638 1.185599645 0.562254902 0.687367461 0.709428664 1.003816625 1 18.59101408 -4.999999994 0.032459442 2.162476599 1.21E-13 0.184547473 0.181789447 2608.262742 6.363766406 342.4544996 129.0165214 1.00E-05 4.999999994 -2.162476599 AISS(ph)PTVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AISSPTVSR 9 0 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 AIS(0.039)S(0.961)PTVSR 176.6 5.56E-05 163070000 138190 179400 150690 158530 183110 209940 144520 165460 144810 168530 TRUE FALSE 143645.8479 210210.5545 154617.1052 189886.7608 151985.0276 161184.6167 133192.1448 163242.2793 139598.3164 201550.2268 0.712704968 1.042968583 0.767139326 0.942131219 0.754080162 0.799724313 0.660838476 0.809933494 0.692622969 1 17.62077988 3.218065531 24.95140142 0.771246071 0.871781459 0.088188425 0.119921486 426.5043801 519239.3845 0.031467727 0.03765181 1652.211085 -3.218065531 0.100535388 AIT(ph)PPQQPYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 163.45 7.22E-05 763420000 1615380 1401650 1548820 1310780 1920780 1891690 1707680 1528050 1643220 1489110 TRUE FALSE 1679156.45 1642372.484 1589183.522 1570048.372 1594286.502 1452373.666 1573827.579 1507568.989 1584080.833 1780872.594 0.942884098 0.922229075 0.892362276 0.881617459 0.895227714 0.815540467 0.88373957 0.846533881 0.889497002 1 20.76415288 4.343382865 1.336930507 0.875687865 0.951075451 0.107440857 0.04533511 1.066919572 2.756223825 0.012023286 0.090807688 22048.69371 -4.343382865 0.075387586 AITGILRPPLEQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AITGILRPPLEQGR 14 1 O60437;K7EKI8 O60437 PPL Periplakin 0 87.519 0.0063024 188390000 122960 131480 122360 119140 155580 167750 140560 135340 135150 153900 FALSE TRUE 127814.5557 154060.6672 125548.8021 142705.5364 129134.5672 128792.6048 129542.5399 133525.9887 130285.9779 184053.7584 0.694441433 0.83704168 0.682131151 0.775347038 0.701613313 0.699755364 0.703829908 0.725472763 0.707869152 1 17.48976768 -1.19262057 5.58973585 1.000008398 0.726328354 0.774312724 0.04449163 4.34E-06 6.26E-07 0.040114845 0.00945487 0.064177003 1.19262057 -0.273680045 AITHLNNNFMFGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AITHLNNNFMFGQK 14 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 217.2 5.85E-12 1746110000 3028700 2820000 3136900 2838600 3979300 4103900 3575900 3408400 3329900 3102600 FALSE TRUE 3148275.415 3304313.063 3218650.191 3400066.608 3302900.007 3150831.42 3295611.614 3362715.973 3210057.549 3710495.067 0.848478534 0.890531588 0.867444945 0.916337725 0.890150761 0.849167392 0.888186497 0.906271512 0.865129179 1 21.82318026 -5 0.367573755 2.523146401 0.879446972 0.73046283 0.021739249 266.4622287 2.072279956 322.0615195 0.01508115 1.00E-05 5 -1.643699429 AITSLLGGGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AITSLLGGGSPK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 AITSLLGGGS(1)PK;AITSLLGGGS(1)PK 205.27 1.09E-07 2120100000 2727500 1182060 1551980 1127430 2098700 2348000 2015020 1635700 1608330 1025320 TRUE FALSE 2835183.806 1385069.61 1592425.874 1350432.289 1741963.724 1802712.584 1857077.467 1613776.117 1550446.517 1226211.823 2.312148483 1.129551668 1.298654803 1.101304247 1.420605878 1.470147776 1.514483413 1.316066349 1.264419808 1 20.22577679 4.744717852 24.96904545 1.305832511 2.312148934 0.790950141 0.158751138 304.0913992 1233128.355 0.037842996 0.349524406 55554.32199 -4.744717852 1.006316423 AITVFSPDGHLFQVEYAQEAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AITVFSPDGHLFQVEYAQEAVK 22 0 O14818;O14818-4;Q8TAA3-2;Q8TAA3-5;Q8TAA3;F5GY34 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 ; 240.94 1.20E-30 675620000 285940 346930 408270 326910 457080 461420 436950 425340 434410 314040 FALSE TRUE 297229.132 406512.5288 418909.8516 391571.8223 379385.7049 354262.1979 402700.7172 419639.013 418775.669 375570.1253 0.791407814 1.082387819 1.115397161 1.042606416 1.010159433 0.943265116 1.072238419 1.11733864 1.115039884 1 18.51872278 2.022515425 22.77534214 1.091569999 1.009238494 0.145130762 0.088959186 154.8815605 156667.6807 0.033245466 0.024550338 105.3211094 -2.022515425 -0.082331505 AIVDALPPPCESACTVPTDVDKWFHHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AIVDALPPPCESACTVPTDVDKWFHHQK 28 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 158.2 6.68E-12 1819750000 2401410 1652130 2297050 1705240 2803700 2546500 2639300 2300200 2628100 1664020 FALSE TRUE 2496219.521 1935870.476 2356913.01 2042531.382 2327128.075 1955113.968 2432424.769 2269369.581 2533515.194 1990052.859 1.25434835 0.972773395 1.184346938 1.026370417 1.169380032 0.982443234 1.222291538 1.140356434 1.273089397 1 20.92437532 2.196472791 24.99999815 1.169232002 1.096447431 0.068377635 0.10689071 327.7736733 194694.3643 0.036054465 0.026628232 157.2073296 -2.196472791 -0.072784571 AIVICPTDEDLKDR ddPTM_MDA-MB-175_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 ; 125.73 0.00039743 254600000 279683 216172 212653 173339 301473 274515 244971 214775 227610 203128 FALSE TRUE 290725.1008 253297.8594 218194.9119 207624.9368 250228.7271 210763.0516 225769.5329 211896.2924 219418.3606 242927.0425 1.196758903 1.042691076 0.898191118 0.854680215 1.030057109 0.867598146 0.92937176 0.872263089 0.903227398 1 17.89016357 4.543869761 2.484095704 0.913047073 1.208745706 0.716014991 0.054530167 0.173365037 1.739124782 0.013086788 0.089749527 34984.02392 -4.543869761 0.295698633 AIVQQWLEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIVQQWLEYR 10 0 O43324;H0YAL7;D6RBD7;C9J1V9;O43324-2;D6RCQ0 O43324 EEF1E1;EEF1E1-BLOC1S5 Eukaryotic translation elongation factor 1 epsilon-1 0 174.41 7.25E-06 147450000 71107 74234 61154 75835 104690 113810 75335 63609 79263 102750 FALSE TRUE 73914.35927 86983.11204 62747.72348 90834.93666 86894.83119 87379.35231 69430.04585 62756.4254 76410.34011 122881.8952 0.601507318 0.70785946 0.510634405 0.739205206 0.70714104 0.711084022 0.565014445 0.51070522 0.621819349 1 16.90691285 -1.185664407 5.545492426 1.000011411 0.625697785 0.656008136 0.080189681 1.21E-05 1.78E-06 0.083093008 0.019584613 0.065213212 1.185664407 -0.374313626 AIWHAFTALDQDHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AIWHAFTALDQDHSGK 16 0 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 153.23 2.72E-07 552850000 290100 222930 289650 217460 343780 346820 323190 276920 302870 253930 FALSE TRUE 301553.372 261216.4933 297198.517 260472.9389 285344.3984 266276.3111 297857.5233 273208.3403 291969.7679 303682.7217 0.992988242 0.860162514 0.978648095 0.857714056 0.939613544 0.876824041 0.980818143 0.899650592 0.961430292 1 18.2122053 1.004545341 4.843096569 0.999905331 0.921812455 0.209756124 0.047473336 0.203773032 15.26170774 0.039750825 0.010068507 10.10520994 -1.004545341 -0.078092876 AIYHDLEQSIR ddPTM_MDA-MB-175_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 ;;;; 264.17 7.54E-21 2818910000 1188858 1567371 1443730 1453175 1609868 1727970 1385997 1502943 1332212 1724594 FALSE TRUE 1235795.032 1836554.777 1481354.79 1740608.678 1336223.212 1326675.155 1277358.934 1482798.507 1284265.95 2062495.175 0.59917475 0.890452884 0.718234306 0.843933454 0.647867316 0.643237944 0.619326992 0.718934292 0.622675857 1 20.97595931 -1.180609759 4.539276395 1.000048903 0.705043486 0.48238471 0.092985479 5.19E-05 9.38E-06 0.088304111 0.020809516 0.065976647 1.180609759 -0.295005416 AKADS(ph)PVNGLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 AKADS(1)PVNGLPK 103.39 0.0013633 232020000 1129700 428090 660630 410620 1009800 902260 846720 697830 848590 412710 TRUE FALSE 1174301.428 501611.1274 677846.5605 491839.4104 838154.5567 692723.7889 780351.8739 688476.7303 818049.4117 493572.6227 2.379186718 1.016286367 1.373347162 0.996488435 1.698138264 1.403489086 1.581027468 1.394884357 1.65740435 1 18.91290285 -1.100144706 4.976236375 0.999991578 1.467979389 0.135498202 0.371041916 5.85E-05 1.06E-05 0.327704857 0.077238207 0.079406361 1.100144706 0.467987812 AKAEASSGDHPTDTEMKEEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKAEASSGDHPTDTEMKEEQK 21 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 111.66 0.00014607 204723000 178284 87936 165286 81610 251415 210682 217558 165172 178472 86107 FALSE TRUE 185322.79 103038.324 169593.4889 97752.21442 208679.5681 161754.2984 200505.2355 162958.1395 172048.8276 102978.018 1.799634461 1.000585619 1.646890202 0.949253212 2.026447703 1.57076531 1.947068309 1.582455582 1.67073353 1 16.65197688 3.233853962 24.99999002 1.674541667 1.345469046 0.128038615 0.352906789 195.224258 1036958.669 0.091503988 0.112786314 1713.381059 -3.233853962 -0.329072622 AKAEKPPLSAS(ph)SPQQRPPEPETGESAGTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.018)AS(0.491)S(0.491)PQQRPPEPETGESAGTSR 93.737 0.0048043 92501000 19282 16665 20928 11341 20153 23527 22578 16072 20943 16603 TRUE FALSE 20043.26825 19527.08411 21473.40087 13584.21595 16727.40026 18063.21081 20808.27736 15856.58113 20189.26552 19856.03997 1.009429286 0.983432958 1.081454354 0.684135204 0.842433853 0.909708624 1.047957065 0.798577217 1.016782075 1 14.2772903 AKAEKPPLSASS(ph)PQQRPPEPETGESAGTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKAEKPPLSASSPQQRPPEPETGESAGTSR 30 3 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 AKAEKPPLS(0.047)AS(0.242)S(0.711)PQQRPPEPETGESAGTSR;AKAEKPPLS(0.01)AS(0.159)S(0.831)PQQRPPEPETGESAGTSR 97.077 0.00048215 379750000 187791 129380 170192 116657 188741 203968 202007 155642 190570 140555 TRUE FALSE 195205.1337 151600.0086 174627.3433 139731.4064 156658.8722 156599.5232 186173.1635 153555.8736 183711.4229 168094.0612 1.16128513 0.901876054 1.038866823 0.831269144 0.931971488 0.931618417 1.107553486 0.913511593 1.092908468 1 17.35890923 AKDDATLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKDDATLSGK 10 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 76.522 0.032598 115370000 210480 160960 180800 185290 294810 267110 307600 233720 284120 191330 FALSE TRUE 218789.9129 188603.6279 185511.7965 221939.809 244698.3015 205077.7506 283489.5082 230587.3657 273894.5767 228817.4503 0.956176693 0.824253691 0.810741472 0.969942671 1.069404021 0.896250484 1.238933079 1.007735054 1.197000388 1 17.80383755 3.226308771 1.157512502 1.088108644 0.857669592 0.449186257 0.099843279 0.403756879 1.150713368 0.037249072 0.057624495 1683.870821 -3.226308771 -0.230439052 AKDDDDDDDDDAEM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKDDDDDDDDDAEM 14 1 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 0 154.28 1.34E-05 109610000 391420 209860 288690 176790 401270 400690 369940 300630 322020 183100 FALSE TRUE 406873.5638 245901.8225 296213.4986 211758.5343 333062.2687 307635.82 340943.1361 296600.5466 310430.5631 218974.9393 1.858082779 1.122967876 1.352727848 0.967044608 1.521006329 1.404890537 1.556996144 1.354495393 1.417653381 1 17.74040624 -1.4985461 6.516273002 0.999793633 1.382165683 0.211147185 0.227872011 0.000641204 4.93E-05 0.207080937 0.048783572 0.031728818 1.4985461 0.38237205 AKDPFAHLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKDPFAHLPK 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 91.937 0.0058935 5806000000 11912300 9060600 10728000 8365300 14935200 13492600 12251100 11270300 12172000 9449700 FALSE TRUE 12382606.8 10616687.57 11007580.49 10019931.37 12396520.04 10359148.13 11290826.77 11119240.06 11733932.1 11301187.79 1.095690739 0.939431126 0.974019784 0.886626393 1.09692187 0.916642421 0.999083192 0.983900124 1.038291931 1 23.42997108 1.262979435 22.04269724 1.019145861 0.983283191 0.0367827 0.065057442 172.922995 156099.2185 0.040227016 0.014661881 18.32227658 -1.262979435 -0.03586267 AKDYENAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKDYENAIK 9 1 H0YDU8;P53041 H0YDU8 PPP5C Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 5 0 91.936 0.0094993 83500000 88386 48039 85962 53947 102480 128820 100390 66078 76236 53532 FALSE TRUE 91875.54753 56289.32456 88202.24034 64617.55558 85060.4862 98903.50729 92521.16948 65192.33249 73492.28125 64020.57047 1.435094171 0.879238097 1.377717188 1.009324895 1.328643053 1.544870759 1.445178773 1.018302899 1.147947929 1 15.96624791 1.662995301 9.259038071 1.063394391 1.276467867 0.227799141 0.19530142 0.194762904 26.74320456 0.096200387 0.051183037 46.02515935 -1.662995301 0.213073477 AKEAAEQDVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKEAAEQDVEK 11 1 P26373;P26373-2;J3KS98 P26373 RPL13 60S ribosomal protein L13 0 ;; 168.31 1.66E-05 1948520000 2494350 1504340 1968720 1274000 3190100 2499420 2398050 2009540 2348360 1512450 FALSE TRUE 2592828.864 1762698.693 2020026.461 1525993.397 2647847.941 1918967.584 2210084.575 1982605.403 2263842.982 1808785.62 1.433463886 0.974520514 1.116786002 0.843656308 1.463881575 1.060914883 1.221860983 1.096097504 1.251581701 1 20.78659 4.757372502 23.74345183 1.121946253 1.433464438 0.257920157 0.161919187 2839.629338 3583927.186 0.03613043 1.174701279 57196.90142 -4.757372502 0.311518185 AKEALELTDTGLLSGSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKEALELTDTGLLSGSEER 19 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 74.047 0.014932 308230000 316130 162405 210650 156460 313990 298500 270750 224410 236640 158755 FALSE TRUE 328611.0565 190296.7954 216139.7121 187407.321 260618.092 229177.8988 249527.9075 221402.151 228123.3726 189860.0027 1.730807183 1.002300604 1.138416249 0.98708163 1.372685601 1.207088884 1.31427317 1.166133719 1.201534654 1 17.53457648 -4.999999999 0.028632368 5.93E-09 1.940460979 0.136109233 0.197736121 4279.545359 9.234282786 478.3120115 202.0337926 1.00E-05 4.999999999 1.940460973 AKEAQDDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AKEAQDDLVK 10 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 138.94 4.70E-05 3126910000 4577310 2960710 3780620 2610800 5630920 4900910 4903670 4009020 4658700 3215900 FALSE TRUE 4758025.733 3469188.911 3879146.063 3127208.448 4673778.23 3762747.927 4519307.532 3955285.644 4491034.297 3845994.033 1.237138096 0.902026597 1.008619886 0.813107982 1.215232834 0.978355113 1.175068784 1.028417 1.167717438 1 21.87492509 3.221551533 24.99993031 1.091198784 0.985237344 0.143454337 0.124024014 443.9764399 652554.6106 0.033482682 0.040113133 1665.526447 -3.221551533 -0.10596144 AKEEDREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 99.815 0.0036816 919850000 2305270 982440 1469740 797710 2397200 1805840 2049380 1542910 1871630 994490 FALSE TRUE 2396283.84 1151166.428 1508042.632 955494.6571 1989724.8 1386461.028 1888744.241 1522229.815 1804270.402 1189341.275 2.014799192 0.967902529 1.267964598 0.803381399 1.672963717 1.165738596 1.588059105 1.279893204 1.51703337 1 20.18173132 -1.145951691 5.394775236 0.999991581 1.341471657 0.092612273 0.335269528 3.11E-05 4.92E-06 0.296659494 0.069921588 0.071457581 1.145951691 0.341480076 AKEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AKEEELR 7 1 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9;E5RG12;Q9H6N6;Q5STV6;A0A0A0MRT5;Q9UBC1-2;Q9UBC1-3;Q9UBC1;Q07666-2;Q07666;Q5VWX1 O75525-2;Q07666-2 KHDRBS3;MYH16;NFKBIL1;KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 3;Putative uncharacterized protein MYH16;NF-kappa-B inhibitor-like protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 ;;;; 112.84 0.0057124 2444890000 5669550 4588560 5389840 4339130 6308690 6604930 6484040 5381050 5685420 4151260 FALSE TRUE 5893388.212 5376609.486 5530303.658 5197396.963 5236341.127 5071035.106 5975804.002 5308925.826 5480802.845 4964619.916 1.187077422 1.082985118 1.113943011 1.046887184 1.054731523 1.02143471 1.203678046 1.069351917 1.103972295 1 22.24325184 0.028246025 0.009238946 4.27E-07 2.122388329 0.196360006 0.056319608 7757.539765 22.34023152 2648.993869 2482.262116 1.067200512 -0.028246025 2.122387902 AKEEQQDDTVYMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKEEQQDDTVYMGK 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 81.632 0.011823 137860000 165830 62549 104390 51204 130620 139900 112310 93610 112600 63060 FALSE TRUE 172377.0964 73291.30419 107110.4892 61331.99837 108417.2591 107410.3452 103506.8487 92355.31107 108547.548 75415.39964 2.285701558 0.971834725 1.420273441 0.81325563 1.437601068 1.4242495 1.372489561 1.224621384 1.439328685 1 16.20257153 4.748177862 24.96014019 1.250783218 2.285702121 0.675633016 0.218380319 731.2012588 1897685.243 0.049023536 0.642319736 55998.68935 -4.748177862 1.034918903 AKEFTNVYIK ddPTM_MDA-MB-175_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 ; 167.18 4.85E-06 1307010000 2582800 2239300 2464600 1967780 4905800 3680600 3286300 2805100 3101200 3550900 FALSE TRUE 2684770.938 2623882.356 2528829.501 2357001.011 4071913.868 2825836.43 3028711.219 2767502.223 2989588.418 4246630.869 0.632211987 0.617873895 0.595490773 0.555028465 0.958857502 0.6654302 0.713203316 0.651693615 0.703990648 1 22.01788728 -5 0.201892055 2.464404183 0.625243413 0.485354106 0.102243656 126.6980076 1.256001518 75.04838352 0.24389747 1.00E-05 5 -1.83916077 AKEILQEEEDLAEIVQLVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKEILQEEEDLAEIVQLVGK 20 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 69.125 0.014825 0 226100 144840 211260 158940 244280 274840 214320 207870 264730 193820 FALSE TRUE 235026.6026 169715.1433 216765.6092 190377.8576 202757.3729 211012.5752 197521.0384 205083.8427 255202.419 231795.3181 1.013940249 0.732176753 0.935159566 0.821318822 0.87472592 0.910340109 0.852135582 0.884762662 1.100981768 1 17.8224919 1.253044776 21.83318113 1.050490624 0.873523189 0.470899786 0.072979075 33.13361495 49947.8657 0.043800061 0.01576139 17.90790476 -1.253044776 -0.176967435 AKELATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKELATK 7 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 65.305 0.064702 368680000 230100 162300 195500 136880 296260 229130 245630 193240 230000 175630 FALSE TRUE 239184.5257 190173.7625 200594.8906 163954.4555 245901.831 175918.03 226376.8788 190649.9339 221722.3449 210041.3359 1.138749783 0.905411126 0.95502578 0.780581854 1.170730656 0.837540046 1.077772991 0.907678163 1.055612906 1 17.68031375 1.218465622 24.99192581 1.027806446 0.967123029 0.032778266 0.119908043 1006.244619 1251422.638 0.102990011 0.025875192 16.53733872 -1.218465622 -0.060683417 AKEVELVS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKEVELVSE 9 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 AKEVELVS(1)E;AKEVELVS(1)E;AKEVELVS(1)E;AKEVELVS(1)E 126.66 0.0012293 5174600000 8301400 6772900 8124700 6128400 9764200 9434700 8150200 7745000 8029200 6957400 TRUE FALSE 8629145.682 7936092.889 8336436.357 7340579.229 8104484.772 7243633.909 7511366.027 7641190.943 7740230.66 8320569.323 1.037085967 0.953792052 1.001906965 0.882220789 0.974030076 0.870569504 0.902746643 0.918349532 0.93025253 1 22.98825082 4.771439129 0.842180074 0.920181434 1.095165442 0.357207789 0.042282798 2.398830109 1.266963737 0.013413742 0.39670696 59079.81525 -4.771439129 0.174984008 AKFAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKFAGR 6 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 80.555 0.058555 422870000 461330 628320 610840 502490 722890 637330 474590 514330 613190 912360 FALSE TRUE 479543.6646 736229.0723 626758.9922 601881.0222 600013.416 489319.7663 437390.3957 507436.2476 591121.4117 1091119.474 0.439496935 0.674746524 0.574418299 0.55161789 0.549906248 0.448456634 0.400863889 0.465060206 0.541756816 1 20.05737765 0.942475019 20.71555206 1.000000001 0.512310242 0.786892358 0.075652776 1150.510213 414316.2102 0.079218436 0.019804609 8.759413316 -0.942475019 -0.487689759 AKFDLSEGPSKPTTLAVQFLSEGSTLSGVDFELVGTGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKFDLSEGPSKPTTLAVQFLSEGSTLSGVDFELVGTGYR 39 2 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 0 129.84 5.65E-09 32548000 16670 11804 19089 16103 23064 19318 20602 16955 20192 11997 FALSE TRUE 17328.14447 13831.24518 19586.47502 19288.12534 19143.58952 14831.68727 18987.16141 16727.74596 19465.29386 14347.58245 1.207739668 0.964012245 1.365141137 1.344346715 1.334272835 1.033741211 1.323370085 1.165893001 1.356695034 1 13.80852004 -2.300095666 2.13585959 0.000207877 1.228526048 0.211763656 0.134516488 2816231.283 382711.1983 13608684.68 0.033537021 0.005010768 2.300095666 1.228318171 AKFEELNMDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKFEELNMDLFR 12 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 189.3 7.39E-06 5132858000 3484076 3678512 3464058 3392425 5947268 5131082 4247196 3507350 3579288 4327584 FALSE TRUE 3621630.011 4310267.821 3554334.197 4063436.54 4936353.51 3939465.968 3914289.68 3460339.71 3450470.124 5175491.228 0.699765462 0.83282294 0.686762674 0.785130601 0.953794199 0.761177209 0.756312687 0.668601212 0.666694227 1 22.30326437 -2.256056115 2.476359401 2.045637214 0.757190092 0.433868437 0.083346232 7943791.699 2012693.463 46317315.47 0.02102425 0.005545541 2.256056115 -1.288447122 AKFENLCK ddPTM_MDA-MB-175_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 ; 131.11 0.00092961 6651800000 7133500 5075300 6001100 4871700 13094400 9201200 8634600 6595100 7589300 8748700 FALSE TRUE 7415136.088 5946943.295 6157493.596 5835307.719 10868618.57 7064360.746 7957797.49 6506703.472 7316162.575 10462840.26 0.708711583 0.568387087 0.588510714 0.557717367 1.038782806 0.675185759 0.760577175 0.621886917 0.699252057 1 23.31877121 AKFFPEDVSEELIQEITQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKFFPEDVSEELIQEITQR 19 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-3;A0A2R8Y5P0;E9PNV3;E9PQ82 A0A2R8Y5S7 RDX Radixin 0 149.34 7.89E-08 66532000 82802 83430 88909 79053 96845 116600 90873 91316 101570 83335 FALSE TRUE 86071.0869 97758.4535 91226.04158 94689.44745 80383.32149 89521.41709 83750.13681 90092.05838 97914.51554 99662.89771 0.863622159 0.980891142 0.915346068 0.950097274 0.806552121 0.898242166 0.840334154 0.90396788 0.982457041 1 16.6047689 1.220971498 4.437451727 0.996697375 0.894613062 0.399036925 0.047611249 0.200137621 8.635599856 0.042369698 0.011939411 16.63303486 -1.220971498 -0.102084313 AKFFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKFFSR 6 1 P46776;E9PJD9;E9PLX7 P46776 RPL27A 60S ribosomal protein L27a 0 76.847 0.067469 255760000 222210 257500 210420 171760 412330 294900 230000 232080 232740 505850 FALSE TRUE 230983.0224 301723.6219 215903.7181 205733.6153 342242.2939 226413.9443 211971.999 228969.3472 224363.7329 604961.6224 0.38181434 0.498748368 0.356888289 0.340077135 0.565725628 0.374261665 0.350389167 0.37848574 0.370872671 1 19.2064841 -1.419767564 3.511470431 1.005484306 0.401646894 0.871662648 0.068846803 140558781.3 205089301.6 7741460.637 0.016364367 0.038039293 1.419767564 -0.603837412 AKGPS(ph)ESSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGPSESSK 9 1 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.998)ES(0.002)SK 71.241 0.030364 113790000 228300 79421 140010 111660 229380 218000 284660 171540 205610 98118 TRUE FALSE 237313.4603 93060.93894 143658.7756 133746.0147 190390.0695 167372.8038 262347.6054 169240.7869 198210.1363 117342.3435 2.022402597 0.793072101 1.224270552 1.139793281 1.622518043 1.426363228 2.235745405 1.442282315 1.689161221 1 16.84036418 3.227431725 24.55096563 1.619722714 1.253997033 0.087633116 0.406702328 307.3411684 678010.8318 0.110644012 0.133457098 1688.230435 -3.227431725 -0.365725681 AKGPS(ph)ESSKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.926)ES(0.037)S(0.037)KER;AKGPS(0.998)ES(0.001)S(0.001)KER 91.812 0.005459 137411000 163510 93216 134210 91868 297745 218547 196719 184354 237010 163108 TRUE FALSE 169965.5011 109225.1229 137707.6229 110039.2162 247134.4113 167792.7714 181299.6508 181883.0362 228480.0564 195065.8897 0.871323537 0.559939634 0.705954399 0.564113061 1.266927865 0.860185098 0.929427749 0.932418458 1.17129682 1 17.573602 3.256537335 24.99999769 1.003006451 0.669277524 0.601525517 0.139270253 168.9272255 234923.5722 0.037092907 0.050123814 1805.249921 -3.256537335 -0.333728928 AKGPSES(ph)SKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPSES(0.5)S(0.5)KER 60.401 0.048987 152190000 176420 84579 110040 69947 139080 150050 125640 93530 124910 71803 TRUE FALSE 183385.1978 99104.78532 112907.7328 83782.30783 115439.2313 115203.1615 115792.0085 92276.38333 120414.5135 85871.4231 2.135578883 1.154106707 1.314846415 0.975671589 1.344326519 1.341577412 1.348434722 1.074587797 1.402265261 1 16.38989048 4.741155021 24.98454964 1.222146836 2.13557921 0.773091807 0.149224144 103.2784413 994532.2571 0.033474328 0.229925513 55100.43413 -4.741155021 0.913432374 AKGPSESS(ph)KER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGPSESSKER 11 2 Q8TEA8;A0A087WZV9 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1;D-tyrosyl-tRNA(Tyr) deacylase 1 AKGPS(0.001)ES(0.033)S(0.967)KER 96.435 0.0055244 84305000 266500 106570 148060 82382 223730 213510 183860 149470 169840 83047 TRUE FALSE 277021.6258 124872.5685 151918.5652 98676.91371 185700.4545 163925.5383 169448.5728 147466.5991 163727.4916 99318.46962 2.789225678 1.257294529 1.529610412 0.993540417 1.869747442 1.650504069 1.706113409 1.484785254 1.648510012 1 16.59977441 8 0.041057924 4.76E-12 4.213519068 0.208091916 0.43287152 1460.787237 4.561272064 126.1172918 423.1489558 100000000 -8 4.213519068 AKGS(ph)ETPGATPGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.605)ET(0.395)PGATPGSK 77.527 0.064246 55688000 86650 55044 71305 44906 99128 82456 80600 72861 80347 51688 TRUE FALSE 90071.00891 64497.37882 73163.26688 53788.27277 82278.25797 63306.84363 74282.36139 71884.41747 77455.32716 61815.27397 1.457099566 1.043389031 1.183579109 0.870145343 1.33103443 1.024129468 1.20168296 1.162890866 1.253012762 1 15.91567574 4.747810944 24.42748575 1.127300937 1.457099807 0.379495696 0.12934352 915.6704171 2417954.371 0.028328739 0.350628354 55951.39821 -4.747810944 0.32979887 AKGSET(ph)PGAT(ph)PGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 AKGS(0.022)ET(0.978)PGAT(0.692)PGS(0.308)K 80.719 0.0082175 0 61290 27960 40730 33327 69395 59599 47357 40640 45331 27861 TRUE FALSE 63709.77653 32761.9125 41791.45726 39918.98113 57599.26269 45758.03548 43645.0346 40095.28727 43699.54616 33319.82952 1.912067902 0.983255706 1.254251833 1.198054783 1.728678193 1.373297407 1.30988169 1.203346111 1.3115177 1 15.0240934 0.820701735 0.701350573 1.003412686 1.380834985 0.178491082 0.25128279 1.726804493 1.796976338 0.244640276 0.092339463 6.617618627 -0.820701735 0.377422299 AKGSET(ph)PGATPGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.038)ET(0.962)PGATPGSK;AKGS(0.013)ET(0.987)PGATPGSK;AKGS(0.129)ET(0.871)PGATPGSK 156.83 8.83E-06 1450840000 3472860 2008650 2853350 1697580 3862280 3447290 3096670 2878340 3323430 1753850 TRUE FALSE 3609971.194 2353620.012 2927710.645 2033356.257 3205771.025 2646709.142 2853944.914 2839760.56 3203820.403 2097483.328 1.72109649 1.122116196 1.395820699 0.96942666 1.528389276 1.261849907 1.360652014 1.353889455 1.527459294 1 21.00022791 -2.200007112 2.309744671 6.60E-05 1.345150109 0.219044354 0.202208874 4706425.736 1789629.445 24233613.47 0.045329905 0.00630947 2.200007112 1.345084084 AKGSETPGAT(ph)PGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKGSETPGATPGSK 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 AKGS(0.053)ET(0.201)PGAT(0.744)PGS(0.002)K 66.777 0.087995 34488000 86968 52867 70582 48612 92941 93573 75538 63507 71947 42662 TRUE FALSE 90401.56379 61946.496 72421.4249 58227.30851 77142.92202 71842.08886 69617.13418 62655.79254 69357.64152 51020.80209 1.77185697 1.214141947 1.419448969 1.141246435 1.511989598 1.40809407 1.364485295 1.228044052 1.359399278 1 15.63879796 -4.389484467 0.121638267 2.02E-13 1.54598931 0.379404892 0.159794443 140.1035697 1.273242404 35.81613359 1.447666119 4.08E-05 4.389484467 1.54598931 AKHDELTYF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AKHDELTYF 9 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ;;;;; 116.98 0.0011182 2292290000 4874220 5237780 5003370 4860640 5845100 6310140 5439200 4889620 5608620 5180890 FALSE TRUE 5066657.969 6137327.971 5133761.933 5822060.084 4851551.99 4844705.616 5012861.291 4824082.642 5406766.862 6195986.201 0.817732287 0.990532866 0.828562519 0.939650266 0.783015299 0.78191033 0.809049783 0.778581889 0.872624097 1 22.5629025 3.235241642 24.99661044 0.818976542 0.896323514 0.083386041 0.078463808 137.2068766 1033363.861 0.020617887 0.025621711 1718.864501 -3.235241642 0.077346972 AKIDDPTDSKPEDWDKPEHIPDPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKIDDPTDSKPEDWDKPEHIPDPDAK 26 3 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ; 175.9 4.15E-13 601430000 3279330 563766 1042490 537807 2123890 1870710 1760290 934140 1304930 303132 FALSE TRUE 3408800.481 660588.425 1069658.146 644183.6194 1762871.936 1436265.953 1622313.87 921619.3812 1257965.824 362524.9116 9.402941347 1.822187673 2.950578323 1.776936147 4.86276082 3.961840711 4.475041075 2.542223587 3.470012085 1 18.46772061 7.999999973 0.08353035 3.44E-06 13.38437834 0.233263554 1.976687057 330.5793366 2.001486793 45.93935643 509.0024473 99999993.85 -7.999999973 13.38437491 AKLAEQAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 133.89 0.00024095 1802840000 1663390 1676597 1806782 1154007 3368540 2352620 1461690 1695202 2023790 2790470 FALSE TRUE 1729061.922 1964539.493 1853868.223 1382266.14 2795956.774 1806259.659 1347118.918 1672480.59 1950954.193 3337209.17 0.518116136 0.588677363 0.555514542 0.414198233 0.837812865 0.541248561 0.403666312 0.501161451 0.584606506 1 21.67021068 0.925440242 13.39654799 1.000000002 0.542987943 0.59069955 0.112931204 38.95803214 7000.688239 0.10887206 0.027220263 8.422484912 -0.925440242 -0.457012059 AKLDNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKLDNNK 7 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 60.682 0.087587 469510000 536590 383600 491520 397470 589730 638430 559190 480740 544310 435280 FALSE TRUE 557774.9875 449480.316 504329.415 476088.3797 489487.9052 490164.308 515359.2266 474296.4666 524720.3894 520564.7821 1.071480451 0.863447416 0.968812014 0.914561254 0.940301615 0.941600978 0.990000177 0.911119006 1.007982882 1 18.98971819 1.217417996 24.99118025 1.003991532 0.946386587 0.142171091 0.052231097 453.8121861 536405.0592 0.044332222 0.011127151 16.49749464 -1.217417996 -0.057604945 AKLNWLSVDFNNWKDWEDDS(ph)DEDMSNFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AKLNWLSVDFNNWKDWEDDSDEDMSNFDR 29 2 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(0.992)DEDMS(0.008)NFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(0.998)DEDMS(0.002)NFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR;AKLNWLSVDFNNWKDWEDDS(1)DEDMSNFDR 334.58 1.50E-105 19464098000 4000199 2350656 3374956 1590587.3 5166077 4037140 2994870 3087073 3843212 2892707 TRUE FALSE 4158129.945 2754362.882 3462910.126 1905200.721 4287949.077 3099575.418 2760124.264 3045695.836 3704895.551 3459477.552 1.201953151 0.796178857 1.000992223 0.550719203 1.239478798 0.895966333 0.797844247 0.880391848 1.070940769 1 21.72212275 -0.20463109 8.123062827 1.00000641 0.921791047 0.003749651 0.194718035 0 0 0.17285068 0.040741296 0.62426489 0.20463109 -0.078215363 AKLTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 360.73 5.49E-121 1957267200 917683.9 850866.9 1133898.6 933949.6 1418436.8 1332688.9 867854.5 977110.7 1224529.2 1173530.9 FALSE TRUE 953914.769 996996.6712 1163448.929 1118682.043 1177331.419 1023192.1 799829.7966 964014.1293 1180458.633 1403461.811 0.679687015 0.710383897 0.828985099 0.797087626 0.838876705 0.729048765 0.569897799 0.68688305 0.841104919 1 20.42055838 0.968567275 4.321890513 0.999639331 0.72932113 0.554124414 0.075314692 0.163921614 9.562698415 0.081436783 0.020738156 9.30180595 -0.968567275 -0.270318201 AKNECYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKNECYR 7 1 Q66K14-2;Q66K14;H0YB58 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 ; 84.743 0.037015 106840000 96392 216090 208916 201018 221720 268410 177069 197861 190284 255340 FALSE TRUE 100197.6306 253201.7766 214360.5226 240778.7604 184032.1136 206075.8453 163189.8691 195208.9969 183435.716 305368.9842 0.328119867 0.829166646 0.701972151 0.788484662 0.602654897 0.674842096 0.53440224 0.639256136 0.600701857 1 18.22019401 -0.859567623 5.416084651 1.000000239 0.641546272 0.408368801 0.132081111 3.55E-07 7.48E-08 0.119192929 0.028094024 0.138175924 0.859567623 -0.358453966 AKNEQEHHAGGDS(ph)QKDIMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKNEQEHHAGGDSQKDIMQR 20 2 Q86SF2;E9PBY3 Q86SF2 GALNT7 N-acetylgalactosaminyltransferase 7 1 AKNEQEHHAGGDS(1)QKDIMQR 161 1.10E-11 164650000 97461 50973 58055 56682 139270 126980 108390 76225 71897 72681 TRUE FALSE 101308.8355 59727.21624 59567.96099 67893.53042 115596.9351 97490.8194 99894.10858 75203.32855 69309.44101 86921.45039 1.165521687 0.687140124 0.68530795 0.78109063 1.329901131 1.121596786 1.149245763 0.865187226 0.797380171 1 16.40742463 AKNS(ph)PPQAPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AKNSPPQAPSTR 12 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR;AKNS(1)PPQAPSTR 106.6 0.0011535 2000750000 1224350 886803 1029470 859152 1293960 1278920 1144390 1038200 1089490 799071 TRUE FALSE 1272688.283 1039104.517 1056298.834 1029089.701 1074013.141 981910.2122 1054689.721 1024284.627 1050279.468 955633.6633 1.331774227 1.087346079 1.105338661 1.076866315 1.123875375 1.027496466 1.103654844 1.07183816 1.099039839 1 19.86609815 4.73984195 5.606031005 1.080511853 1.340544767 0.820307612 0.035719346 0.051748868 6.598444709 0.00763681 0.05151401 54934.09193 -4.73984195 0.260032914 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR;AKNWEDEDFYDS(1)DDDTFLDR 250.22 7.89E-31 849350000 1143080 941980 1166130 817200 1436970 1420140 1151190 1161440 1255010 932870 TRUE FALSE 1188209.681 1103757.737 1196520.306 978839.7209 1192714.353 1090334.007 1060956.72 1145872.797 1209842.435 1115648.016 1.065039927 0.989342267 1.072489073 0.877373246 1.069077645 0.977310041 0.950978001 1.027091682 1.084430231 1 20.0894505 1.501966405 8.29606721 1.046643645 0.99903393 0.076261446 0.059950673 0.241964166 38.86392109 0.030693204 0.014152316 31.76628331 -1.501966405 -0.047609715 AKPAMPQDSVPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.007)VPS(0.993)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDS(0.001)VPS(0.999)PR;AKPAMPQDSVPS(1)PR;AKPAMPQDSVPS(1)PR 201.57 1.45E-08 54565080000 23284400 20782630 23715330 20350110 27096030 26848100 24248300 23525620 23874620 21458510 TRUE FALSE 24203686.09 24351885.04 24333370.98 24375301.02 22490256.5 20613035.66 22347654.88 23210297.54 23015377.09 25662894.19 0.943139379 0.948914213 0.94819278 0.949826658 0.876372569 0.803223343 0.870815845 0.90443024 0.89683482 1 24.61318055 3.240975985 24.75636685 0.882979685 0.947666161 0.248766211 0.045744429 67.6248781 693114.221 0.012644059 0.016339725 1741.710561 -3.240975985 0.064686476 AKPAMPQDSVPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 0 119.31 0.00017763 66264000 137330 120050 123530 101370 158250 155480 161660 129550 143600 109130 FALSE TRUE 142751.8944 140667.6536 126749.2933 121420.6834 131350.7215 119372.1263 148988.6668 127813.5942 138431.8641 130511.9341 1.093784223 1.07781449 0.97117014 0.930341614 1.006426902 0.914645294 1.141571212 0.979324956 1.060683569 1 16.99382221 4.316619488 6.540944827 1.000916366 1.088478668 0.238684962 0.061029897 0.291151856 19.34184264 0.014605616 0.040622231 20730.96356 -4.316619488 0.087562302 AKPDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKPDFK 6 1 P13489;E9PMJ3;E9PLZ3;E9PIM9 P13489 RNH1 Ribonuclease inhibitor 0 ; 66.682 0.091899 2300600000 3217800 2406500 3202800 2351000 4171100 4036400 3749100 3160000 3808500 2363500 FALSE TRUE 3344841.229 2819797.655 3286267.599 2816020.783 3462097.912 3099007.272 3455235.746 3117645.369 3671432.829 2826582.573 1.183351677 0.997599604 1.162629258 0.996263406 1.224835229 1.09637953 1.222407503 1.102973392 1.298894596 1 21.43062741 3.227517493 24.9999667 1.160177032 1.084268607 0.121150698 0.095660463 413.4203925 935919.8555 0.024955729 0.030091724 1688.56387 -3.227517493 -0.075908425 AKPPADPAAAAS(ph)PCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKPPADPAAAASPCR 15 1 Q9GZT9-2;Q9GZT9 Q9GZT9-2 EGLN1 Egl nine homolog 1 1 AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR;AKPPADPAAAAS(1)PCR 157.28 1.20E-06 5515700000 5732030 4833110 5364790 4917470 6774970 6922030 5527720 5446240 5735940 5194520 TRUE FALSE 5958334.97 5663159.046 5504600.835 5890130.889 5623363.019 5314493.437 5094442.862 5373242.061 5529504.64 6212286.739 0.959121048 0.91160619 0.886082865 0.948142147 0.905200171 0.855481027 0.820059195 0.86493787 0.890091664 1 22.56669299 2.932744441 5.236888044 0.871697358 0.92288259 0.096510019 0.048189222 0.341382591 18.07427657 0.014104372 0.015218165 856.5336737 -2.932744441 0.051185232 AKPS(ph)PAPPSTTTAPDASGPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKPSPAPPSTTTAPDASGPQKR 22 2 Q5QNY5;P40855;E9PS71;B7Z8B3 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 1 AKPS(0.999)PAPPS(0.001)TTTAPDASGPQKR 98 0.00064001 87627000 89537 49409 66834 43769 85680 79662 72877 69862 81339 59192 TRUE FALSE 93071.9899 57894.6114 68575.74894 52426.37756 71116.1442 61161.70779 67164.71031 68925.61416 78411.62528 70789.5391 1.31477039 0.817841338 0.968727157 0.740594984 1.004613748 0.863993587 0.948794287 0.973669486 1.107672493 1 16.11124856 1.441962788 4.189254771 1.053441418 0.938699618 0.065561141 0.14571764 0.49758663 16.13406794 0.095440898 0.035078762 27.66704574 -1.441962788 -0.1147418 AKPS(ph)PHPIKDK ddPTM_MDA-MB-175_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 71.279 0.02581 1278660000 1195630 649030 825280 527370 1258820 1071610 1085000 805810 975280 664480 TRUE FALSE 1242834.396 760495.8537 846787.4748 631682.212 1044846.226 822744.8179 999954.8649 795009.435 940179.8633 794672.1338 1.563958698 0.956993232 1.065580934 0.794896644 1.314814225 1.035326121 1.258323807 1.000424453 1.183104105 1 19.60000023 4.74682208 24.87369496 1.071398686 1.563958961 0.516105737 0.14411191 763.7563293 2299469.84 0.03238767 0.366510768 55824.14495 -4.74682208 0.492560276 AKPVGS(ph)PLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKPVGSPLFK 10 1 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 AKPVGS(1)PLFK 62.68 0.050576 784720000 1663300 986750 1328700 951590 1969900 1821500 1656900 1490900 1569100 1040100 TRUE FALSE 1728968.368 1156216.637 1363327.014 1139811.662 1635057.102 1398484.23 1527027.848 1470916.924 1512628.398 1243887.681 1.389971454 0.92951852 1.096020995 0.916330051 1.314473265 1.124284975 1.227625188 1.182515871 1.216049022 1 20.24642479 3.229456086 24.99985062 1.18712985 1.072933027 0.091335079 0.142765399 380.5159878 1044845.493 0.038208978 0.046291167 1696.11809 -3.229456086 -0.114196823 AKQEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKQEAER 7 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2;A0A087WW69;F8W8L6 E9PMS6;Q8WWI1-3;A0A087WTA5 LMO7;EIF2B4 LIM domain only protein 7;Translation initiation factor eIF-2B subunit delta 0 69.954 0.053207 73789000 127150 119150 123710 112440 169350 140250 152780 133280 156560 146630 FALSE TRUE 132169.9802 139613.0856 126933.9842 134680.2964 140563.9475 107679.063 140804.7044 131493.5996 150925.4362 175359.3411 0.75370938 0.796154255 0.723850714 0.768024649 0.801576618 0.614048059 0.802949552 0.749852268 0.860663796 1 17.41995476 0.951743567 2.048133763 1.000056891 0.749797603 0.689634663 0.052289063 0.193658419 1.741918158 0.047090693 0.013095444 8.948362453 -0.951743567 -0.250259287 AKQGYVIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKQGYVIYR 9 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 100.02 0.0045099 241370000 176060 205910 192500 142040 304150 277340 164450 203960 232060 324430 FALSE TRUE 183010.9847 241273.4407 197516.7081 170135.0881 252450.6916 212931.9881 151559.9793 201226.2498 223708.2059 387995.8469 0.471682845 0.621845421 0.50906913 0.438497189 0.650653077 0.548799658 0.390622684 0.518629907 0.576573713 1 18.56568168 0.725066049 3.072221341 0.99997225 0.518831372 0.791834677 0.073568736 0.986275329 10.50896804 0.070362679 0.018359366 5.309651895 -0.725066049 -0.481140877 AKQTLENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKQTLENER 9 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 161.67 5.87E-05 1436800000 1675230 1705850 1603410 1375670 2958100 2359130 1701520 1528150 1714910 2461140 FALSE TRUE 1741369.374 1998816.468 1645196.182 1647773.42 2455283.219 1811257.81 1568150.416 1507667.649 1653190.724 2943353.262 0.591627718 0.679094995 0.558953016 0.559828629 0.834178911 0.615372213 0.532776829 0.512227896 0.56166915 1 21.48902927 -0.881108679 8.654186664 0.99999095 0.601787532 0.64188064 0.088463664 0 0 0.090942309 0.021435308 0.131489575 0.881108679 -0.398203418 AKQTLENERGELANEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKQTLENERGELANEVK 17 2 P35579 P35579 MYH9 Myosin-9 0 ;;; 272.4 6.97E-36 1161370000 825390 580180 760030 371870 1119720 869650 565610 645130 857390 674600 FALSE TRUE 857977.0345 679821.4018 779837.0062 445424.7761 929390.3944 667686.9672 521276.0103 636483.0876 826532.7014 806774.954 1.063465134 0.842640687 0.966610332 0.55210536 1.15198221 0.827600019 0.646123194 0.788922716 1.024489788 1 19.62180677 2.521610812 24.985775 0.821730618 0.903567447 0.004184728 0.179804009 1612.034112 905332.1935 0.056761824 0.053512986 332.3615781 -2.521610812 0.081836829 AKREELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKREELER 8 2 Q9NWB6 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 134.25 0.00049764 106130000 98297 114090 115360 73866 149390 122460 83759 94957 105440 148520 FALSE TRUE 102177.8415 133684.07 118366.3764 88476.47433 123996.7412 94020.5209 77193.75072 93684.25673 101645.235 177619.6504 0.575262034 0.752642344 0.666403611 0.498123232 0.698102608 0.529336257 0.434601411 0.527443087 0.572263456 1 17.43843167 -1.829817453 7.069177699 1.026318799 0.579934778 0.648364084 0.091912777 0.036602634 0.000881167 0.085440072 0.02242895 0.014797302 1.829817453 -0.446384021 AKS(ph)LDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 79.986 0.024524 1576880000 2870120 2150310 2579540 1911810 3480960 3395560 3059380 2620500 3107950 2358080 TRUE FALSE 2983434.554 2519609.015 2646764.932 2289960.312 2889267.663 2606992.65 2819577.801 2585376.484 2996095.487 2820100.628 1.057917765 0.893446493 0.938535634 0.812013688 1.024526442 0.924432492 0.999814607 0.916767458 1.062407297 1 21.42731521 1.240588387 24.99970175 1.031203661 0.942818484 0.20182865 0.067603603 73.52689976 906588.0456 0.047641749 0.015412567 17.40156817 -1.240588387 -0.088385177 AKS(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 36 AKSPQPPVEEEDEHFDDTVVCLDTYNCDLHFK 32 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(1)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK;AKS(0.991)PQPPVEEEDEHFDDT(0.009)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 326.37 1.62E-106 2.63947E+11 6640824.5 3690048.4 5333537.5 3951082.3 7046795 6305159.8 6581966.5 5294796.8 5961917.8 3194211.2 TRUE FALSE 6903009.379 4323785.508 5472533.869 4732594.586 5848983.303 4840881.992 6066054.767 5223828.709 5747349.543 3820055.728 1.807044156 1.131864511 1.43257959 1.238881033 1.531125125 1.267228108 1.587949286 1.367474477 1.504519817 1 21.86516225 -1.503775759 4.96663392 0.998569583 1.416896856 0.326302148 0.184451093 0.002588615 0.000258633 0.158243239 0.037180786 0.03134904 1.503775759 0.418327273 AKS(ph)PT(ph)PDGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.974)PT(0.988)PDGS(0.038)ER;AKS(0.999)PT(0.649)PDGS(0.352)ER 117.75 0.019466 1577840000 2855620 1389690 1570310 1208260 2271900 3153690 2183670 1749640 1860200 1146520 TRUE FALSE 2968362.083 1628358.447 1611233.569 1447250.222 1885723.25 2421293.292 2012508.239 1726188.938 1793251.765 1371158.643 2.164856779 1.187578444 1.175089095 1.055494366 1.375277222 1.765873924 1.46774281 1.25892722 1.307836825 1 20.38696407 -3.985763047 0.164105516 3.32E-29 1.50520415 0.167691062 0.305458087 196.9468694 2.484552817 67.26031305 1.286000718 0.000103333 3.985763047 1.50520415 AKS(ph)PTPDGS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.797)PT(0.204)PDGS(0.999)ER;AKS(0.895)PT(0.116)PDGS(0.99)ER 112.96 0.0174 395590000 1909020 874600 1082100 851580 1562180 1978610 1396830 1244760 1197580 851640 TRUE FALSE 1984389.584 1024805.747 1110300.415 1020019.982 1296641.202 1519107.814 1287342.815 1228076.028 1154479.33 1018502.552 1.948340315 1.006188688 1.090130223 1.001489864 1.273085864 1.491511052 1.263956395 1.205766275 1.133506565 1 19.95801817 AKS(ph)PTPDGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 AKS(0.84)PT(0.159)PDGS(0.001)ER;AKS(0.811)PT(0.189)PDGSER;AKS(0.919)PT(0.08)PDGS(0.001)ER 101.3 0.0025415 382000000 442170 361407 392720 341528 500740 521090 488940 405320 435930 355713 TRUE FALSE 459627.213 423475.8409 402954.6058 409081.219 415624.3937 400074.7447 450615.6052 399887.3484 420240.9645 425408.1518 1.080438189 0.995457748 0.947218816 0.961620546 0.977001479 0.940449173 1.059254749 0.940008664 0.987853577 1 18.69848815 4.707830166 3.519556222 0.975092027 1.08976709 0.457924265 0.033624699 0.213413952 4.679856356 0.007675244 0.061811737 51030.54025 -4.707830166 0.114675062 AKS(ph)PTPESSTIASYVTLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKSPTPESSTIASYVTLRK 19 2 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 AKS(0.788)PT(0.212)PESSTIASYVTLRK 76.161 0.006977 806950000 205540 168770 234930 110100 283030 221020 148570 176700 225620 192020 TRUE FALSE 213654.8779 197754.9347 241052.4688 131877.4514 234920.6617 169691.4546 136924.6952 174331.6255 217499.9803 229642.6426 0.930379809 0.861142044 1.049685137 0.574272487 1.02298362 0.73893704 0.596251174 0.759143091 0.947123661 1 17.80903104 3.766965561 24.99770343 0.787318721 0.938476272 0.146786846 0.151575938 1265.716789 1113887.096 0.037637101 0.067835688 5847.437135 -3.766965561 0.15115755 AKS(ph)VEDDAEGHLIYHVGDWLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKSVEDDAEGHLIYHVGDWLQER 23 1 B1AVT0;P49760-3;P49760 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 AKS(1)VEDDAEGHLIYHVGDWLQER 206.58 8.12E-25 93781000 101070 64274 81794 64361 105310 116110 104090 84738 93365 57686 TRUE FALSE 105060.3216 75312.55952 83925.61883 77091.4137 87409.44382 89145.21216 95931.15381 83602.22571 90004.81189 68988.46723 1.522867892 1.091668833 1.216516647 1.117453638 1.267015304 1.292175573 1.390538994 1.211829007 1.304635622 1 16.07406759 -1.280390769 5.403725072 0.999966453 1.25956432 0.310787192 0.119226537 4.54E-05 6.05E-06 0.108791634 0.025639125 0.052433546 1.280390769 0.259597868 AKSEDS(ph)DVELS(ph)D ddPTM_MDA-MB-175_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(0.011)EDS(0.989)DVELS(1)D;AKS(0.016)EDS(0.984)DVELS(1)D 122.63 0.0042458 317350000 1309540 715000 985310 737380 1426860 1385030 1147070 960700 1084130 690300 TRUE FALSE 1361241.65 837795.6881 1010987.988 883231.5631 1184322.847 1063377.773 1057159.656 947823.3879 1045112.373 825551.0684 1.648888485 1.014832056 1.224621985 1.069869081 1.434584597 1.288082365 1.280550285 1.14810994 1.265957265 1 19.65499794 -4.457062751 0.226877181 2.85E-10 1.280437418 0.185292232 0.170196354 214.5655694 2.691052226 98.22228458 0.289182897 3.49E-05 4.457062751 1.280437418 AKSEENTKEEKPDSK ddPTM_MDA-MB-175_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 ; 87.932 0.003058 575940000 1099170 331397 544550 286278 969940 770810 757670 511940 715030 259177 FALSE TRUE 1142566.08 388311.8568 558741.4204 342902.9339 805069.9453 591801.0592 698281.8456 505078.2817 689296.21 309957.7709 3.686199178 1.252789552 1.802637239 1.106289199 2.597353642 1.909295765 2.252828969 1.629506756 2.223839099 1 18.24171215 -2.001920738 2.9902084 0.000645041 1.986210943 0.164163208 0.697856006 17953598.25 102946999.7 123950546.4 0.154662263 0.009955871 2.001920738 1.985565901 AKSEGTYLNSVIESHTEFIFTTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKSEGTYLNSVIESHTEFIFTTIK 24 1 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 110.44 0.0011822 20253000 103750 107130 141450 110200 158200 152380 128510 119610 136920 104900 FALSE TRUE 107846.1301 125528.7441 145136.3032 131997.2311 131309.2205 116992.0543 118437.0504 118006.8236 131992.2759 125453.1466 0.859652652 1.000602596 1.156896476 1.052163574 1.046679371 0.932555759 0.944073972 0.94064459 1.052124076 1 16.93678913 2.748085226 24.27186798 0.965328757 1.030980372 0.085765814 0.075958355 933.7975753 2379624.747 0.024297927 0.02546045 559.8674589 -2.748085226 0.065651615 AKSELTLTPDPAPPMAHS(ph)PLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKSELTLTPDPAPPMAHSPLHR 22 1 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 AKSELTLTPDPAPPMAHS(1)PLHR;AKSELTLTPDPAPPMAHS(1)PLHR;AKSELTLTPDPAPPMAHS(1)PLHR;AKSELTLTPDPAPPMAHS(1)PLHR 156.41 7.23E-09 995870000 948210 879540 1014220 938560 1308780 1372240 1111540 1136910 1158720 1148690 TRUE FALSE 985646.063 1030594.153 1040651.406 1124204.367 1086314.043 1053558.056 1024414.59 1121671.581 1117017.894 1373753.813 0.717483769 0.750202943 0.757523944 0.818344857 0.79076326 0.766919114 0.745704639 0.81650116 0.813113589 1 20.38969205 -5 0.2042944 2.055750618 0.741137582 0.879594775 0.025954259 47.84752515 0.475246961 20.58905376 0.062766791 1.00E-05 5 -1.314613036 AKSPT(ph)PDGS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKSPTPDGSER 11 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 2 AKS(0.412)PT(0.795)PDGS(0.793)ER 153.39 0.00081495 1022800000 2170700 1046300 1192200 955590 1699400 2419200 1644200 1382300 1358000 829580 TRUE FALSE 2256400.912 1225993.886 1223269.711 1144602.85 1410536.595 1857377.463 1515323.308 1363772.529 1309125.845 992120.3177 2.274321846 1.235731054 1.232985243 1.153693589 1.42173945 1.872129247 1.527358407 1.374603972 1.319523269 1 19.92015557 0.928566737 1.480190052 1.004685282 1.496664619 0.200678675 0.318577508 0.84671467 3.732655125 0.300493951 0.088632897 8.483337332 -0.928566737 0.491979338 AKSPT(ph)PESSTIASYVTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKSPTPESSTIASYVTLR 18 1 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 AKS(0.385)PT(0.614)PESSTIASYVTLR;AKS(0.382)PT(0.617)PES(0.001)STIASYVTLR;AKS(0.335)PT(0.622)PES(0.042)STIASYVTLR 199.36 2.64E-15 3965420000 543390 464290 520320 486360 664380 634680 634580 518270 574210 417351 TRUE FALSE 564843.4568 544028.1958 533879.9666 582560.5564 551448.9249 487285.1887 584839.9614 511323.4384 553544.2943 499122.9378 1.131672007 1.089968332 1.069636208 1.167168471 1.104835869 0.976282899 1.171735292 1.024443879 1.109033972 1 18.92903568 2.971073143 24.93222612 1.062215976 1.112934016 0.193853582 0.05706406 1216.166531 1048221.785 0.016351295 0.017371972 935.5632273 -2.971073143 0.05071804 AKT(ph)GGAYGEDLGADYNLSQVCDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(1)GGAYGEDLGADYNLSQVCDGK 213.41 1.38E-25 231376000 138673 88512 111055 67646 155084 150572 117951 109248 118914 74498 TRUE FALSE 144147.9171 103713.2475 113949.1845 81026.1769 128722.8771 115603.9349 108705.6924 107783.7093 114634.3084 89094.45675 1.617922398 1.164081933 1.27897053 0.909441281 1.444791088 1.297543519 1.220117349 1.209768971 1.286660389 1 16.44304805 -5 0.17168273 0.030875609 1.315299838 0.1922953 0.171848588 239.816091 2.271721659 79.80704805 0.583541869 1.00E-05 5 1.284424229 AKT(ph)PVTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.979)PVT(0.021)LK;AKT(0.977)PVT(0.023)LK 94.767 0.01637 2306100000 4973800 2944700 3410500 3509800 5619400 6018200 5569300 3804400 4379500 3505300 TRUE FALSE 5170169.465 3450429.318 3499380.432 4204027.964 4664216.395 4620564.257 5132763.713 3753408.241 4221882.65 4192096.422 1.233313584 0.823079665 0.834756666 1.002846199 1.112621449 1.102208487 1.224390662 0.895353509 1.00710533 1 21.99924047 4.779034209 22.91496031 1.003955556 1.233315568 0.253981258 0.119674189 13220.16787 7484399.74 0.030733772 8.932087819 60122.10933 -4.779034209 0.229360013 AKT(ph)QTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.5)QT(0.5)PPVS(0.999)PAPQPT(0.212)EERLPS(0.421)S(0.366)PVYEDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPT(0.001)EERLPS(0.533)S(0.466)PVYEDAASFK;AKT(0.558)QT(0.47)PPVS(0.972)PAPQPT(0.01)EERLPS(0.56)S(0.427)PVY(0.003)EDAASFK;AKT(0.5)QT(0.5)PPVS(1)PAPQPT(0.015)EERLPS(0.528)S(0.457)PVYEDAASFK 173.96 8.47E-14 12501220000 1321800 830160 1184950 696990 1699540 1462490 1302620 1235400 1496220 1043360 TRUE FALSE 1373985.685 972733.5223 1215830.77 834852.5417 1410652.798 1122848.862 1200517.241 1218841.484 1442371.334 1247786.416 1.101138518 0.779567328 0.974390132 0.669066862 1.130524247 0.899872645 0.962117575 0.976802976 1.155944091 1 20.25093958 1.49891497 3.126984879 1.077411205 0.923523357 0.152993772 0.133386072 0.377380027 7.577724255 0.090159073 0.032767712 31.54386968 -1.49891497 -0.153887848 AKT(ph)QTPPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.499)QT(0.501)PPVS(0.995)PAPQPT(0.005)EERLPSSPVYEDAASFK 120.47 4.34E-07 13589000000 122420 99897 114650 105080 241880 154720 191580 112440 119840 115390 TRUE FALSE 127253.2361 117053.5327 117637.8732 125864.5104 200765.324 118788.6248 176563.459 110932.9257 115526.9818 137998.4612 0.922135182 0.848223463 0.852457862 0.912071839 1.454837411 0.860796735 1.279459622 0.803870744 0.837161377 1 17.07429265 3.456871383 24.99993788 1.036039529 0.873433278 0.139901025 0.19067148 476.3660399 588106.784 0.052875547 0.071601791 2863.329868 -3.456871383 -0.16260625 AKT(ph)QTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.499)QT(0.501)PPVS(0.155)PAPQPT(0.021)EERLPS(0.438)S(0.386)PVYEDAASFK;AKT(0.492)QT(0.492)PPVS(0.017)PAPQPTEERLPS(0.525)S(0.473)PVY(0.001)EDAASFK 167.07 8.48E-14 481450000 311250 200636 264390 169757 397410 330250 310397 269237 306060 212226 TRUE FALSE 323538.3903 235093.6723 271280.2206 203334.4279 329858.3902 253554.4425 286067.2721 265628.3184 295044.9604 253807.6214 1.274738672 0.92626719 1.068841901 0.801136021 1.299639421 0.999002477 1.127102766 1.046573452 1.162474786 1 17.95337587 3.232593688 24.9999058 1.100475809 1.01486147 0.087683024 0.138381481 369.9689676 1550073.441 0.037147243 0.045494945 1708.416229 -3.232593688 -0.085614339 AKTGGAYGEDLGADYNLSQVCDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 160.92 1.82E-11 271340000 91416 70482 82598 49211 145840 96597 67208 77947 101510 101790 FALSE TRUE 95025.17427 82586.73523 84750.57174 58944.78892 121050.1689 74163.81069 61940.06134 76902.24796 97856.67493 121733.8016 0.7805981 0.678420736 0.696195885 0.484210533 0.9943842 0.609229398 0.508815633 0.631724689 0.803857874 1 16.89337029 0.965376813 3.861824206 0.999406183 0.667317697 0.357534899 0.135772512 0.230711027 9.771839162 0.127574663 0.032730621 9.233722377 -0.965376813 -0.332088486 AKTHYDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTHYDAK 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 74.684 0.024238 77006000 322670 248990 290790 176080 451640 388360 305760 278920 324580 305950 FALSE TRUE 335409.2608 291752.0956 298368.2263 210908.0985 374870.3941 298169.2757 281793.7322 275181.5336 312898.4292 365895.0447 0.916681616 0.797365528 0.815447573 0.57641693 1.024529847 0.814903836 0.77014908 0.752077782 0.855158969 1 18.48107035 0.965976286 13.1762684 1.000000006 0.803584054 0.219618006 0.108301132 9.615731325 3725.146072 0.099791266 0.024950079 9.246476842 -0.965976286 -0.196415952 AKTQT(ph)PPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.001)QT(0.999)PPVS(0.999)PAPQPT(0.001)EER;AKT(0.052)QT(0.948)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(1)PAPQPTEER;AKT(0.001)QT(0.999)PPVS(1)PAPQPTEER;AKTQT(1)PPVS(1)PAPQPTEER;AKT(0.152)QT(0.848)PPVS(0.999)PAPQPT(0.001)EER 264.69 1.38E-29 15875970000 5009560 3466060 4519070 3847560 5129520 5944080 5817520 5267720 5323920 3439610 TRUE FALSE 5207341.297 4061328.843 4636840.677 4608595.884 4257606.023 4563657.503 5361527.581 5197114.83 5132313.159 4113535.724 1.265903993 0.987308514 1.127215366 1.120349061 1.035023471 1.109424546 1.303386658 1.26341794 1.247664662 1 21.97194754 2.316897287 8.449188931 1.232199748 1.099703655 0.149133124 0.10289626 0.332542171 32.00952218 0.03322692 0.027734917 207.4422848 -2.316897287 -0.132496093 AKTQT(ph)PPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 AKT(0.459)QT(0.552)PPVS(0.99)PAPQPT(0.104)EERLPS(0.465)S(0.423)PVY(0.008)EDAASFK;AKT(0.467)QT(0.54)PPVS(0.992)PAPQPT(0.159)EERLPS(0.434)S(0.403)PVY(0.004)EDAASFK 81.517 0.0041721 1736940000 141487 96637 116446 81752 195100 170450 146577 133649 158965 114815 TRUE FALSE 147073.016 113233.653 119480.6784 97922.30159 161936.9717 130865.5707 135087.9117 131857.6538 153243.8807 137310.801 1.071095755 0.824652192 0.870147706 0.713143474 1.179346202 0.95306101 0.983811257 0.960286101 1.116036609 1 17.06708559 3.240258371 24.99999992 1.018505291 0.86656555 0.357202296 0.105707762 52.99083763 780297.5957 0.029130588 0.037471712 1738.834993 -3.240258371 -0.151939742 AKTQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.451)QT(0.548)PPVS(0.538)PAPQPT(0.243)EERLPS(0.115)S(0.105)PVYEDAASFK;AKT(0.12)QT(0.88)PPVS(0.742)PAPQPT(0.04)EERLPS(0.115)S(0.103)PVYEDAASFK;AKT(0.452)QT(0.548)PPVS(1)PAPQPTEERLPSSPVYEDAASFK 138.78 1.13E-08 13138540000 677790 461151 586442 354524 1140540 672813 791900 596341 698053 480166 TRUE FALSE 704549.6726 540350.097 601725.1603 424647.7891 946671.4182 516562.3773 729828.8088 588348.0243 672930.2089 574245.3344 1.226914056 0.940974292 1.047853808 0.739488444 1.648548733 0.899549977 1.270935548 1.02455865 1.171851417 1 19.1313077 5.062891975 17.01004805 1.088955601 2.847095596 0.032512214 0.233833823 36248180.23 182173663.8 0.051750338 2257475751 115582.4711 -5.062891975 1.758139996 AKTQT(ph)PPVSPAPQPT(ph)EER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKTQT(1)PPVS(0.112)PAPQPT(0.888)EER 144.82 3.08E-07 576030000 510010 335470 443860 371930 509000 604910 604430 536000 544920 345230 TRUE FALSE 530145.5886 393084.3629 455427.3562 445496.6439 422480.3618 464428.82 557053.1972 528815.7967 525308.4356 412871.2087 1.284045914 0.952075017 1.103073662 1.079020853 1.023273972 1.124875773 1.349217832 1.280825075 1.272330026 1 18.65533229 2.405559754 6.787416902 1.255226181 1.080331555 0.219892865 0.116922427 0.233891186 17.94393886 0.037790162 0.031557016 254.4249827 -2.405559754 -0.174894626 AKTQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.221)QT(0.772)PPVS(0.075)PAPQPT(0.853)EERLPS(0.039)S(0.036)PVY(0.003)EDAAS(0.001)FK 68.831 0.0044412 920640000 137870 71368 112090 66500 150130 135640 111970 106530 126760 97192 TRUE FALSE 143313.2141 83624.89883 115011.1575 79653.50152 124610.9562 104139.6656 103193.4988 105102.1396 122197.9324 116234.9115 1.232961871 0.719447348 0.989471717 0.685280356 1.07206135 0.895941368 0.887801242 0.904221788 1.051301461 1 16.82668393 1.243955405 24.45844606 1.02565075 0.912868669 0.065726849 0.150061271 220.5495593 999958.1443 0.096404041 0.03288611 17.53700417 -1.243955405 -0.112782081 AKTQT(ph)PPVSPAPQPTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.084)QT(0.916)PPVSPAPQPTEER;AKT(0.015)QT(0.984)PPVSPAPQPTEER;AKT(0.052)QT(0.948)PPVSPAPQPTEER;AKT(0.073)QT(0.926)PPVS(0.001)PAPQPTEER;AKT(0.041)QT(0.959)PPVSPAPQPTEER;AKT(0.227)QT(0.772)PPVS(0.002)PAPQPTEER;AKT(0.015)QT(0.985)PPVSPAPQPTEER;AKTQT(1)PPVSPAPQPTEER 159.98 6.74E-11 32952030000 22343340 15677980 19267280 16227920 21669030 23478500 22943550 19595910 20526050 12823990 TRUE FALSE 23225472.32 18370551.11 19769401.15 19437754.14 17985736.02 18025974.2 21145174.6 19333258.88 19787321.47 15336605.31 1.514381563 1.197823817 1.289033704 1.267409166 1.172732535 1.175356204 1.378738917 1.260595711 1.290202171 1 23.87047585 -1.63891517 2.516028922 0.965846851 1.276688184 0.430369668 0.09741003 6632685.551 5505194.043 1468766.638 0.023883852 0.022965972 1.63891517 0.310841333 AKTQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 AKT(0.056)QT(0.943)PPVS(0.126)PAPQPT(0.063)EERLPS(0.435)S(0.377)PVYEDAASFK 163.31 1.18E-13 14809000000 199280 165360 178740 161290 325820 227330 248630 172800 207860 161520 TRUE FALSE 207147.7283 193759.2937 183398.1112 193192.6806 270437.2328 174536.0527 229141.7309 170483.8986 200379.1592 193166.7515 1.07237776 1.003067516 0.949428977 1.000134232 1.400019572 0.903551213 1.186237948 0.882573721 1.037337728 1 17.55948727 1.727303497 24.9999946 0.967655285 1.069257297 0.100326292 0.13682654 1.991044074 4401.385739 0.061991193 0.034377188 53.37077346 -1.727303497 0.101602012 AKTQT(ph)PPVSPAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKT(0.211)QT(0.789)PPVSPAPQPTEERLPSSPVYEDAASFK 180.69 8.15E-18 5849100000 415170 255810 335120 150010 446330 387200 280770 352180 329780 232790 TRUE FALSE 431561.2322 299743.3776 343853.5025 179681.5303 370462.986 297278.6681 258762.5137 347459.6032 317911.2822 278400.7435 1.550143964 1.076661556 1.235102673 0.645406072 1.330682459 1.067808456 0.92946057 1.248055586 1.14191966 1 18.08680354 4.739055568 23.39352517 1.082900592 1.550144242 0.375200209 0.183685943 17.25327668 814851.5467 0.041464003 0.244710654 54834.71221 -4.739055568 0.467243651 AKTQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 AKTQTPPVSPAPQPT(0.006)EERLPS(0.497)S(0.497)PVYEDAASFK;AKTQTPPVSPAPQPTEERLPS(0.59)S(0.409)PVYEDAASFK;AKTQTPPVS(0.001)PAPQPT(0.026)EERLPS(0.486)S(0.486)PVY(0.001)EDAASFK;AKTQTPPVSPAPQPT(0.001)EERLPS(0.579)S(0.42)PVYEDAASFK 183.82 7.04E-20 4818770000 494189 413953 554270 321632 749680 635450 462332 550265 674190 560220 TRUE FALSE 513699.9633 485046.2076 568714.7315 385249.8496 622249.6614 487876.3678 426093.2098 542889.5977 649926.0336 669984.3829 0.766734235 0.723966439 0.848847743 0.575013179 0.928752486 0.728190657 0.635974839 0.810301869 0.970061467 1 19.35376794 1.289228012 3.423353944 0.996203875 0.745987885 0.509417536 0.093327149 0.177217819 3.538025191 0.074289163 0.022481323 19.46381697 -1.289228012 -0.25021599 AKVDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AKVDEFPLCGHMVSDEYEQLSSEALEAAR 29 1 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;; 315.3 2.07E-92 885420000 354767 340425 404191 316275 482780 494570 417385 385985 451810 395214 FALSE TRUE 368773.4751 398890.3456 414724.5495 378833.251 400717.228 379713.6128 384669.2731 380811.5024 435549.4464 472648.6165 0.780227556 0.843946923 0.877447929 0.801511393 0.847812125 0.803374007 0.813858879 0.805696852 0.921507926 1 18.85040851 1.039585806 3.580819822 0.9990608 0.82281597 0.822940123 0.026965821 0.075941714 2.152411405 0.025711573 0.006661481 10.95432965 -1.039585806 -0.17624483 AKVEEAR ddPTM_MDA-MB-175_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 ; 105.57 0.0072026 347790000 1304590 1075720 1221750 992090 1532390 1516930 1449740 1278710 1252650 1161010 FALSE TRUE 1356096.221 1260466.542 1253589.809 1188322.441 1271914.895 1164645.997 1336105.591 1261570.984 1207567.371 1388487.681 0.97667141 0.907798146 0.902845467 0.855839384 0.916043342 0.838787418 0.962273997 0.908593574 0.869699737 1 20.40508295 AKWDAWNELK ddPTM_MDA-MB-175_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 ; 162.68 6.10E-06 2085200000 5890600 3508100 4149300 3711400 5491500 5266500 5913900 4383000 4541000 3099000 FALSE TRUE 6123165.437 4110588.886 4257434.167 4445503.843 4558056.792 4043435.19 5450353.065 4324253.054 4377570.297 3706189.716 1.652145709 1.109114536 1.148736166 1.199480918 1.22984983 1.0909952 1.470608221 1.166765165 1.181151164 1 21.8215053 -5 0.035030915 2.46E-08 1.891272314 0.220549665 0.161974635 2059.455133 5.412424473 244.9156534 85.45868867 1.00E-05 5 1.89127229 AKWDAWNELKGTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKWDAWNELKGTSK 14 2 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 104.41 0.00059569 778870000 930280 560800 693570 447160 927800 819280 751220 683750 766610 544380 FALSE TRUE 967008.1727 657113.0376 711645.004 535606.9134 770092.8874 629014.6363 692337.4135 674585.4496 739019.8558 651040.8382 1.485326443 1.00932691 1.093088117 0.822693266 1.18286418 0.966167711 1.06343162 1.036164569 1.135135943 1 19.31238852 4.740525739 24.82824798 1.03461732 1.485326613 0.675935002 0.093684439 85.30026506 1077635.315 0.020395369 0.133418611 55020.65285 -4.740525739 0.450709293 AKYAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AKYAYR 6 1 J3KS46 J3KS46 HEXDC 0 ; 65.619 0.094454 159227000 345240 358390 310310 270270 640210 495860 407210 324570 352850 583310 FALSE TRUE 358870.3418 419940.6946 318396.9335 323728.5993 531387.3329 380704.0298 375291.8162 320219.67 340150.9974 697598.4264 0.514436857 0.601980565 0.456418652 0.464061539 0.761738147 0.545735219 0.537976867 0.459031526 0.487602874 1 19.41203726 -1.414902512 5.604330529 1.000244386 0.53531736 0.718682883 0.086983076 0.000270621 2.83E-05 0.085811604 0.02021556 0.038467812 1.414902512 -0.464927026 AKYHGNVMLLR ddPTM_MDA-MB-175_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 ; 143.89 2.22E-05 2521400000 831180 820520 881490 734530 1583860 1254960 846380 810220 934870 1749200 FALSE TRUE 863995.6282 961437.9272 904462.3536 879817.8416 1314636.043 963514.5591 780038.524 799360.3262 901224.2113 2091922.25 0.413015172 0.45959544 0.43235945 0.420578653 0.628434467 0.460588131 0.372881222 0.382117608 0.430811523 1 20.9963978 -1.149449057 4.25066088 1.000134568 0.442147694 0.859781073 0.067295569 34416261.69 81952642.6 66478.57345 0.017419765 0.070884445 1.149449057 -0.557986874 AKYPDYEVTWANDGY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AKYPDYEVTWANDGY 15 1 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;; 175.48 6.96E-06 462540000 657670 636580 707820 591520 748720 839050 669760 668050 778930 681230 FALSE TRUE 683635.3194 745907.6631 726266.3707 708520.8905 621452.8418 644193.3534 617262.4611 659095.8825 750896.4615 814703.9756 0.839121129 0.915556675 0.891448173 0.869666666 0.762795887 0.790708494 0.757652448 0.80900045 0.921680124 1 19.63591642 5.123305318 18.12718239 0.843994501 0.001911384 0 0.075177773 7565.078935 1371707.613 0.017612079 61697.98715 132832.7971 -5.123305318 -0.842083117 AKYPS(ph)LGQKPGGSDFLMK ddPTM_MDA-MB-175_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 124.81 1.62E-05 256990000 321280 134440 308810 157140 367940 328200 296010 272780 311550 183940 TRUE FALSE 333964.3825 157529.0242 316857.8423 188221.823 305397.6902 251980.5239 272807.9627 269123.8303 300337.3764 219979.5213 1.518161239 0.716107678 1.440396999 0.855633388 1.388300549 1.145472644 1.240151634 1.223404018 1.365296981 1 17.7470097 ALAAFLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALAAFLKK 8 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 89.55 0.0246 0 221080 205230 224540 137670 448070 295750 210490 178780 244400 342850 FALSE TRUE 229808.4091 240476.656 230391.6969 164900.7151 371907.2214 227066.5446 193991.2438 176383.7465 235604.0917 410024.8932 0.560474286 0.58649282 0.561896852 0.402172448 0.907035713 0.553787217 0.473120649 0.430178141 0.574609239 1 18.64535198 0.94109854 21.91639172 1.000000001 0.552841043 0.503507463 0.130701962 4759.077745 1770788.104 0.127926125 0.031981531 8.731694657 -0.94109854 -0.447158958 ALAAGADS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALAAGADSPK 10 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(1)PK;ALAAGADS(1)PK 153.74 1.65E-05 488550000 1964420 941290 977240 1007750 1267480 1954200 1463430 1165310 1108660 820820 TRUE FALSE 2041976.818 1102949.235 1002707.677 1207079.942 1052034.202 1500366.666 1348722.533 1149690.926 1068759.543 981643.9635 2.080160317 1.123573593 1.02145759 1.229651469 1.071706486 1.528422444 1.373942675 1.171189319 1.088744578 1 19.90484034 4.741420423 24.95931623 1.196064395 2.080160644 0.748343962 0.156529736 135.9818191 1186735.703 0.038411172 0.270036314 55134.11693 -4.741420423 0.884096249 ALAAGADS(ph)PKTEEARPSPAPGPGTPTGTPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALAAGADSPKTEEARPSPAPGPGTPTGTPTR 31 2 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 ALAAGADS(0.996)PKT(0.004)EEARPSPAPGPGTPTGTPTR;ALAAGADS(0.999)PKT(0.001)EEARPSPAPGPGTPTGTPTR;ALAAGADS(0.999)PKT(0.001)EEARPSPAPGPGTPTGTPTR 231.9 2.60E-36 1014750000 718320 330400 388342 277401 611560 617000 463660 425165 447945 335995 TRUE FALSE 746679.8283 387143.6298 398462.5115 332270.0898 507607.2496 473711.1007 427317.1177 419466.3586 431823.547 401826.7872 1.85821317 0.963458988 0.991627547 0.826898804 1.263248907 1.178893782 1.063436115 1.043898446 1.074650971 1 18.61621422 4.742275358 24.98001009 1.049526758 1.858213483 0.825149078 0.112269976 147.1584797 989534.9488 0.027808354 0.208237458 55242.75864 -4.742275358 0.808686725 ALAEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALAEEAKR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 136.27 0.0012799 1096340000 1049269 862369 910250 759254 1259620 1109292 978497 822173 942914 865326 FALSE TRUE 1090694.95 1010474.167 933971.8628 909432.1751 1045510.242 851675.7445 901799.8483 811153.1157 908978.7093 1034870.062 1.053943862 0.976426128 0.902501577 0.878788757 1.010281658 0.822978435 0.871413602 0.783821221 0.87835057 1 19.9810182 2.730316291 24.9507573 0.852020273 0.956863468 0.280016471 0.070833332 688.1419585 2082598.531 0.022500892 0.021530956 537.4230519 -2.730316291 0.104843195 ALAEEAS(ph)EEELPSDVDLNDPYFAEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 ALAEEAS(1)EEELPSDVDLNDPYFAEEVK 153.48 3.71E-08 27147000 55025 34182 53063 44993 60771 62261 66223 48729 54739 43898 TRUE FALSE 57197.42949 40052.4926 54445.86537 53892.48111 50441.16713 47801.82632 61032.26822 48075.86746 52768.95408 52498.97262 1.089496168 0.762919551 1.037084397 1.026543538 0.960802938 0.910528796 1.162542145 0.915748729 1.005142605 1 15.68000157 ALALDLGS(ph)PAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALALDLGSPAALR 13 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 ALALDLGS(1)PAALR 113.59 0.00084987 16222000 81184 73370 78273 75710 96189 95268 80741 80622 80543 84897 TRUE FALSE 84389.20701 85970.72676 80312.85868 90685.21203 79838.82814 73143.4508 74412.30944 79541.39396 77644.27316 101530.9417 0.831167382 0.846744109 0.791018554 0.893178085 0.786349726 0.72040552 0.73290278 0.783420233 0.764735083 1 16.63155993 3.033337639 24.39322373 0.778452529 0.837725995 0.03363439 0.077537877 298.0156774 218056.3071 0.020704744 0.024746724 1079.785869 -3.033337639 0.059273467 ALAMPGRPES(ph)PPVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALAMPGRPESPPVFR 15 1 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ERU2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR;ALAMPGRPES(1)PPVFR 123 6.38E-05 3278270000 1276555 1487893 1424925 1388825 1623714 1776740 1506606 1478288 1453359 1502605 TRUE FALSE 1326954.377 1743427.049 1462059.716 1663530.44 1347715.674 1364119.062 1388514.285 1458473.967 1401052.893 1797011.681 0.738422789 0.970181256 0.813606128 0.925720438 0.749976023 0.759104171 0.77267961 0.811610733 0.779657088 1 20.77716836 5.035646067 16.61064594 0.830351961 0.37904829 0.100349121 0.08688619 25336867.24 318735014.3 0.019878097 338858710.3 108554.0591 -5.035646067 -0.45130367 ALAPTWEQLALGLEHSETVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALAPTWEQLALGLEHSETVK 20 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ; 298.81 9.79E-55 874090000 638910 675010 723940 682450 877930 875950 750050 637210 754190 551080 FALSE TRUE 664134.6601 790937.7167 742806.4711 817436.5731 728699.7722 672523.8877 691259.1211 628669.2422 727046.8492 659053.5749 1.007709669 1.200111412 1.127080558 1.240318851 1.105676078 1.020438874 1.048866355 0.953897022 1.103168053 1 19.33003622 2.843476532 3.760049563 1.01839423 1.148970478 0.412766058 0.066621065 0.210171508 5.39183901 0.020239346 0.021528639 697.391311 -2.843476532 0.130576248 ALASEKS(ph)PTADAKPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALASEKSPTADAKPAPK 17 2 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 ALASEKS(0.914)PT(0.085)ADAKPAPK;ALASEKS(0.904)PT(0.096)ADAKPAPK;ALASEKS(0.967)PT(0.032)ADAKPAPK 180.13 4.57E-10 2342890000 4529500 1458140 2423390 1468950 4019270 3362980 3898750 2646020 3122270 1261890 TRUE FALSE 4708328.158 1708564.202 2486545.534 1759503.926 3336075.921 2581978.861 3593155.788 2610554.43 3009900.113 1509133.185 3.119889089 1.132149382 1.647664738 1.165903674 2.210590791 1.710901918 2.380940147 1.729837006 1.99445625 1 20.5252887 ALASNTSFFSGCS(ph)PIEEEAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALASNTSFFSGCSPIEEEAH 20 0 O95239;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 ALASNTSFFS(0.007)GCS(0.993)PIEEEAH;ALASNTSFFSGCS(1)PIEEEAH 198.96 1.58E-21 122407000 88689 103673 88738 90601 93422 114335 90000 94211 98921 112995 TRUE FALSE 92190.5102 121478.0313 91050.58518 108521.6074 77542.16181 87782.42901 82945.56483 92948.25564 95360.85253 135134.2068 0.682214462 0.898943607 0.673778959 0.803065411 0.573815939 0.649594437 0.613801396 0.687821817 0.705675156 1 17.04403339 -1.378131489 9.357462461 1.000000459 0.69737746 0.513779906 0.087909867 8.48E-07 5.63E-08 0.085736298 0.020208209 0.041866679 1.378131489 -0.302622999 ALASVPS(ph)PALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALASVPSPALPR 12 0 O60336-4;O60336-3;O60336-6;O60336;O60336-2 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 ALAS(0.005)VPS(0.995)PALPR 91.961 0.0083951 101580000 51387 73274 71251 67181 68194 71628 54487 70002 65923 78294 TRUE FALSE 53415.79844 85858.23951 73107.85959 80469.20128 56602.40824 54993.48253 50216.16656 69063.73769 63550.44411 93634.21027 0.570473103 0.916953742 0.780781505 0.859399583 0.60450564 0.587322543 0.536301491 0.73759086 0.678709672 1 16.51474811 -1.320932903 2.750295749 1.004048905 0.700375182 0.36082242 0.120946769 6434648.259 7463559.899 213005.1764 0.031768523 0.047760306 1.320932903 -0.303673724 ALDDKNCWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALDDKNCWEK 10 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 128.85 0.00029072 1277970000 1661540 987400 1292800 919230 2061300 1763810 1688450 1367400 1546340 913740 FALSE TRUE 1727138.882 1156978.269 1326491.43 1101050.95 1710920.962 1354191.858 1556104.877 1349072.24 1490687.525 1092769.858 1.580514752 1.058757487 1.213879958 1.007578075 1.56567364 1.23922878 1.424000548 1.234543787 1.364136752 1 20.05955817 -1.151545364 4.703543566 0.999985271 1.288122765 0.194275159 0.181343745 5.21E-05 9.40E-06 0.163557541 0.038546948 0.070543115 1.151545364 0.288137494 ALDEEVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALDEEVHK 8 0 Q06210-2;Q06210;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 130.27 0.001055 401430000 534610 468663 468500 510870 542770 641710 612030 531400 526570 412420 FALSE TRUE 555716.8156 549152.2246 480709.4949 611918.5612 450510.1493 492682.5777 564057.4894 524277.4522 507618.8486 493225.8027 1.126698588 1.113389084 0.974623574 1.240645882 0.913395339 0.998898628 1.143609045 1.062956255 1.029181453 1 18.91188875 6.187682612 0.68651171 1.049879471 1.672027669 0.083440165 0.08774208 53.74078424 3.992638387 0.032268146 40.5434227 1540574.168 -6.187682612 0.622148198 ALDEYYDKHFTEFVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALDEYYDKHFTEFVPLR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 261.17 1.69E-27 827190000 697830 899370 935630 736240 984110 1098300 898760 853100 958320 873010 FALSE TRUE 725380.8672 1053829.801 960013.2864 881866.0745 816831.3337 843236.4699 828312.8427 841665.5899 923830.2504 1044059.595 0.6947696 1.009357901 0.919500468 0.84465109 0.782360833 0.807651665 0.793357819 0.806147076 0.884844366 1 19.99377263 4.809818163 22.48125752 0.855975924 0.694762539 0.290416717 0.079639394 81823.62348 25809593.61 0.019423824 132.814765 64538.39535 -4.809818163 -0.161213385 ALDIAENEMPGLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALDIAENEMPGLMR 14 0 P23526 P23526 AHCY Adenosylhomocysteinase 0 ;; 231.92 5.06E-09 65241000 89840 114202 102336 101212 104113 121296 93897 101353 101880 100990 FALSE TRUE 93386.95257 133815.3051 105002.9602 121231.4315 86415.90945 93126.84226 86537.10779 99994.52882 98213.3587 120777.0569 0.773217654 1.107953021 0.869394924 1.003762094 0.715499381 0.771064014 0.716502869 0.827926523 0.813178936 1 16.8819869 3.24304087 24.99888432 0.793097716 0.945737935 0.246336867 0.110485609 130.0377527 725578.2016 0.028470645 0.037279541 1750.011367 -3.24304087 0.152640219 ALDIDLDKPLADSEKLPIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALDIDLDKPLADSEKLPIQK 20 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 74.953 0.0073548 217650000 383130 221720 302370 197800 420320 372230 390360 276180 350480 166120 FALSE TRUE 398256.2682 259798.6853 310250.0106 236924.2496 348874.1565 285785.2237 359762.5632 272478.2588 337866.2933 198668.0334 2.004631854 1.307702506 1.561650383 1.192563522 1.756065888 1.43850633 1.810872927 1.371525424 1.700657561 1 17.60000023 -1.309626631 4.770340981 0.999719592 1.550948355 0.337192586 0.238837625 0.000639204 9.25E-05 0.207529995 0.048890878 0.049020007 1.309626631 0.551228763 ALDKLDGTEINGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALDKLDGTEINGR 13 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 188.13 5.81E-06 3645900000 4460600 3585170 4370100 3561390 5573200 5067500 4945400 4460800 4693200 3392740 FALSE TRUE 4636707.932 4200895.059 4483988.396 4265822.312 4625869.455 3890649.924 4557766.626 4401010.272 4524292.649 4057482.445 1.142754897 1.035345221 1.105115908 1.051347078 1.140083665 0.95888275 1.123299161 1.084665265 1.115049223 1 21.95215342 -2.289462993 2.283409454 0.6236961 1.082139335 0.180753706 0.05354748 2796090.833 627348.663 5425873.084 0.011675466 0.005134959 2.289462993 0.458443234 ALDLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALDLLDR 7 0 P27361;E9PBK7;E9PQW4;P27361-3;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;;; 162.31 0.0029707 378571000 587400 722498 653398 667821 767360 803572 656139 704019 653373 762253 FALSE TRUE 610591.0056 846581.4112 670426.0887 799914.0006 636924.4213 616954.5813 604709.1107 694582.7768 629858.2334 911601.8811 0.669800072 0.928674489 0.735437369 0.877481735 0.698687041 0.676780724 0.663347809 0.761936533 0.690935645 1 19.79804438 ALDSNSLENDDLSAPGREPGHFNPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALDSNSLENDDLSAPGREPGHFNPESR 27 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 136.53 9.07E-06 281090000 91759 87166 98974 85995 109210 113020 122080 89243 96627 79061 FALSE TRUE 95381.71617 102136.0824 101553.3437 103004.5543 90646.52321 86772.81783 112511.0506 88046.84356 93149.41315 94551.48924 1.008780686 1.080216539 1.07405335 1.089401713 0.958700111 0.917730842 1.189944775 0.931205254 0.985171296 1 16.52881256 3.247181673 24.9822462 0.999041724 1.065116199 0.162791136 0.073177423 353.3766769 1024014.909 0.020213862 0.026944194 1766.77674 -3.247181673 0.066074475 ALDVMVSTFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALDVMVSTFHK 11 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 212.89 4.38E-09 12296200000 4421100 6954400 7246400 6797000 9635800 9664300 7909000 7869100 7843200 8463500 FALSE TRUE 4595648.442 8148764.102 7435247.137 8141426.313 7997910.158 7419912.789 7289071.914 7763627.586 7560924.764 10121760.78 0.454036461 0.805073769 0.734580405 0.804348817 0.790169846 0.733065417 0.720138726 0.767023421 0.746996983 1 23.27095695 -5 0.156983817 1.933331957 0.663336314 0.469224275 0.091895515 123.9421796 1.12989096 36.3138376 0.39580566 1.00E-05 5 -1.269995642 ALDYYGLYDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALDYYGLYDDR 11 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 0 ; 94.692 0.019343 117852000 97251 126346 109486 105180 142738 141464 103182 113386 109270 143293 FALSE TRUE 101090.5446 148044.9427 112339.2951 125984.2901 118475.4457 108611.1299 95094.32522 111866.2461 105337.394 171368.5198 0.589901486 0.863898123 0.655542192 0.735165888 0.691348947 0.633786941 0.554911283 0.652781773 0.614683456 1 17.38674259 -0.986917359 4.560910677 1.000007162 0.667225659 0.601126332 0.081667235 0.07751221 49786793.55 925.8870151 0.019169751 0.103058221 0.986917359 -0.332781503 ALEAASLSQHPPSLCIS(ph)DS(ph)EEEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEAASLSQHPPSLCISDSEEEEEER 26 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 2 ALEAASLS(0.001)QHPPS(0.007)LCIS(0.995)DS(0.997)EEEEEER;ALEAAS(0.001)LS(0.002)QHPPS(0.006)LCIS(0.993)DS(0.997)EEEEEER 65.035 0.019779 98812000 74906 94230 74995 106270 97185 112498 98730 93817 85957 89795 TRUE FALSE 77863.34672 110413.2695 76949.43131 127289.8888 80665.52841 86372.04442 90991.28462 92559.53657 82863.42436 107388.611 0.725061494 1.028165542 0.716551137 1.18532019 0.751155338 0.804294269 0.847308516 0.861912038 0.771622089 1 16.71248147 ALEAELDAQHLS(ph)ETFDNIDNLSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLS(0.367)ET(0.367)FDNIDNLS(0.267)PK 95.652 0.011482 21926000 4397.5 30234 32891 25257 31716 24168 35417 19838 31196 25600 TRUE FALSE 4571.116696 35426.45431 33748.16648 30252.75922 26324.92565 18555.34827 32640.92299 19572.10406 30073.26205 30615.82986 0.14930566 1.157128664 1.102311015 0.988141081 0.859846876 0.606070401 1.066145296 0.639280534 0.982278194 1 14.90199017 4.750300848 24.86517165 0.91051161 0.149305168 0.639104237 0.176020311 1153.231721 2442433.796 0.043475416 0.713453844 56273.10092 -4.750300848 -0.761206442 ALEAELDAQHLSETFDNIDNLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALEAELDAQHLSETFDNIDNLSPK 24 0 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLS(0.296)ET(0.296)FDNIDNLS(0.409)PK;ALEAELDAQHLSETFDNIDNLS(1)PK;ALEAELDAQHLS(0.083)ET(0.367)FDNIDNLS(0.551)PK;ALEAELDAQHLSETFDNIDNLS(1)PK 261.26 3.04E-44 366904000 168522.9 342975 381989 308451 430551 374835 401243 335748 390354 315855 TRUE FALSE 175176.3142 401878.2883 391943.9471 369461.6872 357366.0948 287785.2519 369792.5252 331247.8472 376305.2358 377740.7398 0.463747475 1.063899775 1.037600412 0.978082712 0.946061828 0.761859184 0.978958545 0.876918511 0.996199764 1 18.52703686 4.746854683 24.9692261 0.950090602 0.463747229 0.765418755 0.08224712 516.3305317 1554374.066 0.020391238 0.232259899 55828.33589 -4.746854683 -0.486343372 ALEATTEHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;; 198.72 2.92E-07 654750000 350354 460241 396540 427678 469367 521071 435385 427926 412258 504675 FALSE TRUE 364186.2465 539283.8116 406874.1582 512271.4319 389584.165 400060.1572 401258.386 422190.3519 397420.9151 603556.4037 0.603400518 0.893510214 0.674127813 0.848754862 0.645480957 0.662838062 0.664823343 0.699504387 0.658465245 1 19.20312907 -1.025363141 4.611095698 1.000008505 0.708984003 0.503790647 0.087580191 7.88E-06 1.67E-06 0.079610074 0.018763673 0.094327182 1.025363141 -0.291024503 ALEEALEAKEEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEEALEAKEEFER 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 102.28 0.001079 83204000 80054 49642 75876 45508 87309 88132 56444 57426 75012 60261 FALSE TRUE 83214.59374 58167.62734 77853.39089 54509.34657 72468.24737 67664.67865 52019.77179 56656.2984 72312.33277 72067.98918 1.1546679 0.807121553 1.080276996 0.756360032 1.005553897 0.938900605 0.721815224 0.786150676 1.003390459 1 16.13707097 2.440049271 24.99701032 0.845066742 0.950007827 0.053564259 0.136963454 355.3613382 239612.3555 0.044876263 0.037546248 275.4541188 -2.440049271 0.104941085 ALEEGLTPQEICDKYHIIHADIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEEGLTPQEICDKYHIIHADIYR 24 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 93.583 0.0051505 245480000 221855 198768 262270 216830 281260 287710 244180 233750 247760 207600 FALSE TRUE 230614.0067 232904.8578 269104.9717 259718.3268 233451.5257 220893.7128 225040.5336 230616.9636 238843.166 248275.2453 0.928864279 0.938091341 1.083897718 1.046090304 0.940293203 0.889712998 0.906415512 0.928876189 0.962009586 1 17.9215809 3.098121321 7.702938887 0.928696206 1.000674267 0.247513896 0.051264911 0.306723701 21.20080226 0.015659668 0.018756094 1253.491292 -3.098121321 0.071978061 ALEELQEALAEKEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALEELQEALAEKEELR 16 1 Q9UJC3;Q9UJC3-2 Q9UJC3 HOOK1 Protein Hook homolog 1 0 ;;; 211.29 6.81E-12 274498000 245169 193083 241230 195769 285586 283268 284391 238383 253086 210694 FALSE TRUE 254848.4614 226243.5033 247516.652 234491.5239 237042.1937 217483.3 262099.6903 235187.8658 243977.4843 251975.4553 1.011401928 0.897879133 0.982304612 0.930612561 0.940735253 0.863113035 1.040179449 0.933376092 0.968258928 1 17.94292368 0.91710411 0.73945006 0.998782457 0.944493704 0.088181935 0.048991607 1.875046223 2.259154385 0.044797857 0.016886878 8.262359934 -0.91710411 -0.054288753 ALEHAFQLEHIMDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEHAFQLEHIMDLTR 16 0 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 212.9 1.91E-12 1330740000 403820 433910 560390 557360 567530 642540 455720 467390 514100 590530 FALSE TRUE 419763.1254 508430.6671 574994.2238 667604.1444 471061.4533 493319.8228 419999.4756 461125.4015 495597.6414 706233.0471 0.594369135 0.719919111 0.814170657 0.945302896 0.667005679 0.698522711 0.594703798 0.652936596 0.701748019 1 19.42978481 -0.96874323 4.922174894 1.000001683 0.70931539 0.43529525 0.099140332 2.86E-06 6.00E-07 0.103526742 0.024401282 0.107462458 0.96874323 -0.290686293 ALEHFTDLYDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEHFTDLYDIK 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 229.29 8.53E-12 223790000 445870 386420 507880 484930 590820 640050 681460 552610 535460 335220 FALSE TRUE 463473.2919 452784.6291 521115.77 580847.7066 490392.6274 491408.0876 628045.3845 545203.1668 516188.8992 400899.9408 1.156082216 1.129420544 1.299864921 1.448859547 1.223229483 1.225762435 1.566588868 1.359948235 1.287575394 1 18.61288268 4.18697791 5.129562668 1.330921506 1.141873683 0.142212641 0.143191329 0.262946457 14.65050418 0.03448957 0.080681387 15380.76406 -4.18697791 -0.189047823 ALEHFTDLYDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALEHFTDLYDIKR 13 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 196.5 9.18E-08 7668700000 5859200 6721800 7984200 6323400 9850100 9621600 7686200 7693500 8225000 7544000 FALSE TRUE 6090525.74 7876216.862 8192274.811 7574149.647 8175783.52 7387129.217 7083735.56 7590381.217 7928983.857 9022102.361 0.67506724 0.872991299 0.908022818 0.839510498 0.906194941 0.818781357 0.785153535 0.841309588 0.878839935 1 23.10503222 -4.999999672 0.339731736 2.743226361 0.833121369 0.377506442 0.064235309 428.8841357 3.615368701 542.0679167 0.050598847 1.00E-05 4.999999672 -1.910104992 ALEHSALAINHK ddPTM_MDA-MB-175_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 0 205.56 5.80E-08 156700000 673760 531910 677330 552560 701400 712830 765910 669420 662970 511560 FALSE TRUE 700360.5651 623261.4048 694981.7762 661854.7188 582176.2785 547286.0355 705875.9729 660447.5199 639109.8392 611790.3876 1.144772097 1.018749914 1.135980215 1.081832491 0.951594354 0.89456462 1.153787289 1.079532358 1.044654921 1 19.22267791 8 0.777115559 1.040261659 20.66958939 0.141161713 0.07550339 1100.495175 4.188270998 0.027558842 37942.56472 100000000 -8 19.62932774 ALEIIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALEIIPR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 121.29 0.010358 154777000 210040 265324 250766 262787 284281 286199 246961 271544 236640 288486 FALSE TRUE 218332.5414 310891.3331 257301.168 314765.4843 235959.0172 219733.6196 227603.5515 267904.3968 228123.3726 345009.3083 0.632830872 0.901109986 0.745780365 0.912339107 0.683920728 0.636891859 0.65970264 0.776513533 0.661209327 1 18.39627576 -1.316803387 3.490078354 1.001071265 0.740049308 0.399526935 0.097440136 28602257.28 44892854.19 321173.3403 0.023243829 0.048216603 1.316803387 -0.261021957 ALELDSNLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALELDSNLYR 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 255.84 8.78E-17 1657540000 1882660 1982650 1935120 1883820 2378270 2271740 2080020 1854530 1875040 2209290 FALSE TRUE 1956988.871 2323154.715 1985550.817 2256433.973 1974012.515 1744162.814 1916982.597 1829673.059 1807557.677 2642158.076 0.740678193 0.879264089 0.751488276 0.854011724 0.747121277 0.660128109 0.72553668 0.692491897 0.684121701 1 21.33328535 3.060693114 7.805758421 0.725720277 0.807202624 0.036135667 0.098633284 0.46932413 52.3935963 0.026061626 0.031171847 1149.987484 -3.060693114 0.081482347 ALELDSNNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALELDSNNEK 10 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 182.16 4.21E-06 334180000 398540 490370 506810 460590 708420 738650 607620 588930 589020 459820 FALSE TRUE 414274.6669 574587.233 520017.8849 551693.3273 588003.0214 567109.7318 559993.1567 581036.3566 567821.2853 549912.9252 0.753345935 1.044869481 0.945636775 1.003237607 1.069265686 1.031271872 1.018330596 1.056597017 1.03256581 1 19.06884367 4.74122616 24.88013598 1.024227207 0.753345832 0.857085294 0.032954942 82.49777791 769987.5724 0.008193339 0.056204548 55109.46059 -4.74122616 -0.270881375 ALELPLAASSIPRPRT(ph)PS(ph)PESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALELPLAASSIPRPRTPSPESHR 23 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 ALELPLAAS(0.01)S(0.311)IPRPRT(0.679)PS(0.996)PES(0.003)HR;ALELPLAASSIPRPRT(1)PS(1)PESHR 191.51 2.26E-17 590390000 116869 151038 162158 96980 194353 182884 73587 133656 125083 242279 TRUE FALSE 121483.0784 176977.6016 166383.9707 116162.3545 161316.9465 140411.9626 67819.05866 131864.5599 120581.2873 289748.9313 0.419270152 0.610796391 0.574234976 0.40090693 0.556747339 0.484598725 0.234061463 0.455099383 0.416157833 1 18.14444381 -1.001933153 5.022062821 1.000003527 0.460326239 0.715395821 0.101927829 6.21E-06 1.23E-06 0.102292052 0.024110234 0.099555864 1.001933153 -0.539677288 ALENDFFNS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALENDFFNSPPR 12 0 F5H148;H3BMT1;Q9NYV6-3;Q9NYV6;Q9NYV6-2;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR 186.42 1.24E-05 119069000 151919 184006 185275 188621 224776 265066 225344 219288 219986 256955 TRUE FALSE 157916.8794 215607.5991 190103.4187 225929.6708 186568.6558 203508.4386 207680.9485 216348.803 212068.7468 307300.4125 0.513884372 0.70161832 0.618624027 0.735207834 0.607121397 0.662245901 0.675823852 0.704030305 0.690102382 1 18.22929018 -5 0.214597734 2.685821002 0.613985328 0.794537488 0.054094232 59.67239398 0.596137317 43.29959638 0.100425807 1.00E-05 5 -2.071835674 ALEQQVEEMKTQLEELEDELQATEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALEQQVEEMKTQLEELEDELQATEDAK 27 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 66.282 0.026016 10530000 10213 8137.8 9875 10621 10313 11222 8905.7 9065.9 11487 10108 FALSE TRUE 10616.21713 9535.403847 10132.35061 12721.8021 8559.999944 8615.860571 8207.647963 8944.386439 11073.58511 12088.46907 0.878210224 0.788801608 0.838183111 1.0523915 0.708112822 0.712733806 0.678965046 0.739910603 0.916045287 1 13.56134393 4.749936506 21.9924167 0.80838461 0.878210448 0 0.12237635 1505.825408 2910813.385 0.02980041 0.405555334 56225.9117 -4.749936506 0.069825838 ALEQSQSLPLPAPTSTS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ALEQSQSLPLPAPTS(0.003)T(0.165)S(0.829)PS(0.003)R;ALEQSQSLPLPAPT(0.001)S(0.018)T(0.008)S(0.972)PS(0.001)R;ALEQSQSLPLPAPTST(0.015)S(0.803)PS(0.182)R;ALEQSQSLPLPAPTSTS(0.929)PS(0.071)R;ALEQSQSLPLPAPTS(0.004)T(0.018)S(0.974)PS(0.004)R;ALEQSQSLPLPAPTST(0.026)S(0.967)PS(0.007)R 421.75 1.73E-173 1908820000 1708917 1955883 1801241 1962701 1889870 2205470 1852689 1910829 1810552 1779303 TRUE FALSE 1776386.363 2291790.691 1848182.82 2350917.4 1568630.572 1693283.017 1707470.395 1885217.463 1745390.587 2127923.356 0.834798094 1.0770081 0.868538246 1.104794208 0.737164977 0.795744364 0.802411605 0.885942371 0.820231886 1 21.02101476 3.229037549 24.99951286 0.833577438 0.971497319 0.289452976 0.100250975 226.4974261 594589.602 0.026736 0.032348098 1694.484299 -3.229037549 0.137919881 ALERPYTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALERPYTSK 9 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;; 106.29 0.0026992 1453090000 1363220 1424160 1313390 1353800 2241850 2258990 1972670 1953520 1978870 1848590 FALSE TRUE 1417040.978 1668748.402 1347618.022 1621577.599 1860781.138 1734373.808 1818046.971 1927336.26 1907650.855 2210785.817 0.640967102 0.75482138 0.609565165 0.733484712 0.841683135 0.784505579 0.822353281 0.871787871 0.862883614 1 21.07612783 2.841150872 0.196411484 1.050456767 0.507927284 0.817692476 0.046577411 2.45258912 0.218466449 0.154537627 0.390795355 693.6667412 -2.841150872 -0.542529483 ALES(ph)PERPFLAILGGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 234.73 2.33E-20 3306986000 2578557 2045961 2520705 2098794 3117146 3086112 2838137 2628582 2725905 2173880 TRUE FALSE 2680360.421 2397338.886 2586396.643 2513929.189 2587294.636 2369409.258 2615676.406 2593350.158 2627800.212 2599810.165 1.03098313 0.922120745 0.994840577 0.966966444 0.995185984 0.911377796 1.006102846 0.997515201 1.010766189 1 21.30997485 ALESPERPFLAILGGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 200.94 1.09E-11 4186000000 544960 480010 570710 504300 728790 710260 616090 575610 616580 527760 FALSE TRUE 566475.4416 562447.9835 585583.1714 604049.0348 604910.5361 545312.8791 567799.2559 567894.8895 594389.4062 631164.4674 0.897508448 0.891127452 0.927782221 0.957039038 0.958403978 0.863979053 0.899605864 0.899757383 0.941734583 1 19.26765646 0.932258395 4.187061464 0.999953732 0.912166155 0.484943608 0.027746066 0.283039124 12.99268357 0.028601468 0.007293988 8.55575608 -0.932258395 -0.087787578 ALETNTHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALETNTHVK 9 0 Q9NYL9;H0YKU1;H0YNJ8;G5EA42;Q9NZR1 Q9NYL9 TMOD3;TMOD2 Tropomodulin-3;Tropomodulin-2 0 ; 117.67 0.0020101 269700000 257380 261410 273660 244270 345500 380190 323550 331170 299590 306280 FALSE TRUE 267541.5611 306305.134 280791.8044 292585.8769 286772.0334 291896.6343 298189.3056 326731.2078 288807.8144 366289.7019 0.730409727 0.836237362 0.766583944 0.7987827 0.782910445 0.796901013 0.814080505 0.892002167 0.788468289 1 18.48262562 -5 0.152081104 1.723196343 0.745002289 0.747483712 0.036275601 63.00681916 0.565530599 13.65700005 0.170178023 1.00E-05 5 -0.978194055 ALFDFNGNDEEDLPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALFDFNGNDEEDLPFK 16 0 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 158.2 2.23E-08 18534000 16011 14873 21441 16265 22047 23052 22281 16566 19404 14233 FALSE TRUE 16643.12664 17427.32205 21999.77007 19482.16845 18299.45881 17698.52236 20534.557 16343.95987 18705.65383 17021.68384 0.977760297 1.023830675 1.292455569 1.144550012 1.075067484 1.039763311 1.20637636 0.960184669 1.09893087 1 14.05508614 1.72403686 24.9999969 1.022059632 1.109810799 0.162844876 0.092227346 1.733628674 2971.859758 0.043614225 0.024186312 52.97084005 -1.72403686 0.087751168 ALFEEVPELLTEAEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 184.99 2.78E-09 50832000 105804 49912 66473 49566 115766 90431 100733 74109 88861 46956 FALSE TRUE 109981.2236 58483.99774 68205.34099 59370.00686 96088.13667 69429.77075 92837.28424 73115.69007 85662.90997 56156.12917 1.95849011 1.041453508 1.214566281 1.057231111 1.711089031 1.236370308 1.653199492 1.302007299 1.525441857 1 15.77715587 -1.579321924 6.297486455 0.999121887 1.391529854 0.155441409 0.284197009 0.003247688 0.000216948 0.255059056 0.059993227 0.026343779 1.579321924 0.392407966 ALFPGDSEIDQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALFPGDSEIDQLFR 14 0 G3V5T9;P24941;P24941-2;E7ESI2;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 0 ; 125.74 0.00020814 34899000 37559 45256 39489 39752 43367 50236 37820 39891 38000 42490 FALSE TRUE 39041.85832 53028.36596 40518.11578 47614.82695 35995.49283 38569.45033 34855.56958 39356.32639 36632.38742 50815.10198 0.768312112 1.04355524 0.797363662 0.937021183 0.708362109 0.759015506 0.685929344 0.774500589 0.720895679 1 15.6329697 3.239538655 24.99986447 0.757739573 0.891405399 0.193736241 0.108236406 33.16602511 847745.7647 0.027751302 0.035519218 1735.955768 -3.239538655 0.133665826 ALGALVDSCAPGLCPDWDSWDASKPVTNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALGALVDSCAPGLCPDWDSWDASKPVTNAR 30 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 138.92 1.57E-17 0 82782 66464 69353 74498 93779 101700 82051 76741 83693 82249 FALSE TRUE 86050.29728 77878.67498 71160.39615 89233.48205 77838.47908 78081.71628 75619.62822 75712.41242 80680.90528 98364.1168 0.874813907 0.79173867 0.723438572 0.907175146 0.791330026 0.79380285 0.768772502 0.769715775 0.820227009 1 16.5858445 0.954672345 20.48794097 1.000000001 0.799044775 0.579561831 0.050066367 634.2045071 286659.5462 0.046817472 0.011704368 9.008912007 -0.954672345 -0.200955226 ALGALVDSCAPGLCPDWESWDPQKPVDNAR ddPTM_MDA-MB-175_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 0 166.35 2.56E-12 143380000 31446 29229 24111 34779 51446 43153 42951 28829 32224 48351 FALSE TRUE 32687.51236 34248.85338 24739.35247 41658.1824 42701.2273 33131.36974 39584.38839 28442.59441 31064.26453 57824.45271 0.565288746 0.592290143 0.42783548 0.720425018 0.738463147 0.572964692 0.684561401 0.491878316 0.53721675 1 15.81939209 -1.549204602 3.055347721 1.017089808 0.591702429 0.630743731 0.093576736 49052561.42 57882303.71 6937453.529 0.023316928 0.028235494 1.549204602 -0.425387379 ALGDEDDLAKREDEFVDLGDV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALGDEDDLAKREDEFVDLGDV 21 2 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 0 98.816 0.0036884 42270000 71586 42416 60511 32968 79131 80164 60642 48616 61325 41853 FALSE TRUE 74412.27056 49700.61805 62087.96637 39488.972 65680.34088 61547.1259 55888.72158 47964.38204 59117.92523 50053.29403 1.486660808 0.992953991 1.24043717 0.788938526 1.312208161 1.229631877 1.116584286 0.958266243 1.181099594 1 15.6111774 4.747708519 24.10493548 1.091238744 1.486661155 0.383857466 0.150336028 752.5890271 1983018.403 0.034474732 0.41484838 55938.20412 -4.747708519 0.39542241 ALGDFDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALGDFDYK 8 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 91.318 0.028493 0 165080 135910 146080 123980 208510 199840 185380 142340 149620 143510 FALSE TRUE 171597.4859 159251.4853 149886.9648 148502.874 173067.5447 153430.1886 170849.4312 140432.1651 144235.2054 171628.0368 0.999821993 0.927887356 0.873324473 0.865259993 1.00838737 0.893969257 0.995463412 0.818235573 0.840394193 1 17.38892572 1.732753453 24.99999988 0.870091053 0.933122537 0.0951389 0.066474619 1.083828067 4630.326265 0.029576993 0.016401905 54.04474265 -1.732753453 0.063031484 ALGEYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALGEYLER 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 102.46 0.011539 66805000 93604 111800 112710 113610 118820 142920 108650 99460 102780 117050 FALSE TRUE 97299.5582 131000.7803 115647.3152 136081.7189 98623.01884 109728.996 100133.7291 98126.90138 99080.96788 139983.7064 0.695077739 0.935828774 0.826148401 0.972125416 0.70453213 0.783869771 0.715324173 0.700988021 0.707803575 1 17.09489939 3.214220593 24.99952786 0.747585407 0.860679958 0.119612295 0.108794288 342.9337974 352224.8297 0.029159747 0.034868384 1637.648127 -3.214220593 0.113094552 ALGHQLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALGHQLGR 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 155.51 0.00040783 396023000 363952 390963 404229 425437 497210 538420 421070 406123 406887 481050 FALSE TRUE 378321.106 458107.854 414763.5398 509587.1688 412694.4218 413380.1148 388065.4331 400679.5855 392243.2164 575302.5372 0.65760375 0.796290342 0.720948567 0.885772504 0.717351993 0.718543876 0.674541494 0.696467614 0.681803383 1 19.13396131 -0.87098438 8.71927907 1 0.728884976 0.620751068 0.063845049 0 0 0.062472524 0.014724915 0.134590876 0.87098438 -0.271115024 ALGNICYDSHEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALGNICYDSHEGR 13 0 P52306-4;P52306;P52306-5;D6RHH8 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 156.08 5.47E-06 275190000 275460 449460 347130 416420 375770 447500 355560 350370 334680 433500 FALSE TRUE 286335.3735 526651.2587 356176.493 498786.6331 311896.7496 343574.9069 327690.2781 345673.8632 322634.9322 518436.0251 0.552306089 1.015846186 0.687021109 0.962098714 0.601610873 0.662714183 0.632074667 0.666762814 0.62232352 1 18.98380645 3.215905357 24.9999639 0.674281436 0.811048951 0.083278761 0.162213984 422.9765592 466751.378 0.042411423 0.050725162 1644.013415 -3.215905357 0.136767514 ALGNNFYEYYVDDPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALGNNFYEYYVDDPPR 16 0 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 ; 136.24 4.30E-05 136037000 162613 166094 127109 223367 148379 179353 208945 165096 142613 114566 FALSE TRUE 169033.0868 194619.3525 130421.565 267548.3259 123157.5906 137700.9839 192567.3449 162883.1582 137480.386 137013.0142 1.233700957 1.420444281 0.951891802 1.952721991 0.898875127 1.005021199 1.405467547 1.188815231 1.003411149 1 17.06395341 ALGS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ALGSPTK 7 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 1 ALGS(0.999)PT(0.001)K;ALGS(0.999)PT(0.001)K;ALGS(1)PTK;ALGS(0.999)PT(0.001)K;ALGS(0.988)PT(0.012)K;ALGS(0.999)PT(0.001)K;ALGS(0.999)PT(0.001)K;ALGS(0.994)PT(0.006)K 130.66 0.0037155 12320760000 34589300 21073460 26022200 19968200 33600700 32982100 32761900 27523700 29537200 18930380 TRUE FALSE 35954912.27 24692662.83 26700359.91 23917850.36 27889265.02 25322507.12 30193936.67 27154789.82 28474161.94 22639425.52 1.588154799 1.090692995 1.179374445 1.056468961 1.231889254 1.118513679 1.333688289 1.199446947 1.25772458 1 24.43233401 -5 0.022227704 3.74E-06 2.022325469 0.174129514 0.144317113 6246.891406 10.5018916 665.1760787 340.4207319 1.00E-05 5 2.022321725 ALGSNDPMQSILNSLEQQHEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALGSNDPMQSILNSLEQQHEEEKR 24 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 149.32 9.50E-08 218320000 59795 57866 66847 57678 86641 85374 71371 65585 77193 64409 FALSE TRUE 62155.75277 67804.03537 68589.08774 69086.53625 71913.79377 65547.18236 65776.75453 64705.94035 74414.83901 77028.71037 0.8069167 0.880243679 0.890435364 0.896893326 0.933597271 0.850944824 0.853925169 0.840023675 0.966066271 1 16.23310865 1.111342671 4.956040226 0.997891219 0.870622952 0.659293858 0.033081234 0.122640147 4.417784392 0.033236419 0.00844014 12.92238487 -1.111342671 -0.127268267 ALHSLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALHSLLLR 8 0 M0R1K3;Q15102 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ; 194.44 0.00016534 1894380000 814700 995250 781050 790180 1731450 1206830 996000 823900 801880 1945250 FALSE TRUE 846864.9851 1166176.446 801404.8046 946475.2455 1437138.747 926562.0222 917930.9174 812856.9681 773020.4954 2326384.493 0.364026234 0.501282763 0.344485104 0.406843859 0.61775633 0.398284129 0.394574035 0.349407835 0.332284065 1 21.14965813 -1.228343966 4.015664408 1.000461604 0.41280183 0.820688656 0.082438995 10009770.45 6123872.247 38207.55163 0.019666753 0.05910933 1.228343966 -0.587659774 ALHSVLQAVPLNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALHSVLQAVPLNELR 15 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 153.24 2.69E-06 918950000 722990 948540 779340 824190 960140 1056270 808150 814370 755050 983160 FALSE TRUE 751534.2035 1111444.366 799650.2406 987212.322 796935.7458 810967.3004 744805.0913 803454.7022 727875.898 1175791.378 0.639173086 0.945273445 0.680095343 0.839615207 0.677786689 0.689720401 0.633450036 0.683331003 0.61905191 1 20.16520067 3.220096059 24.92757787 0.693556488 0.781274298 0.028591599 0.128128309 522.4438441 705309.7119 0.033683999 0.040329378 1659.954023 -3.220096059 0.08771781 ALHVNNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALHVNNDR 8 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 135.79 0.00081866 297771000 201808 195230 193459 219007 218678 246269 223154 208804 185379 204451 FALSE TRUE 209775.5357 228759.2338 198500.7005 262325.9309 181507.1917 189076.757 205662.6064 206005.3239 178707.246 244509.259 0.857945161 0.935585158 0.811833062 1.072867064 0.742332591 0.773290786 0.841124002 0.842525656 0.730881304 1 17.89952957 ALIEHEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALIEHEMK 8 0 O95372;Q5QPQ1;Q5QPQ3;Q5QPQ2;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 100.15 0.0063088 626090000 382610 325680 365210 314780 499400 492780 426510 388480 416870 312480 FALSE TRUE 397715.7382 381613.0066 374727.6726 377042.5445 414512.1664 378339.3132 393079.0317 383273.061 401866.9301 373704.4732 1.064252014 1.021162533 1.002737991 1.008932382 1.109197765 1.01240242 1.051844599 1.025604692 1.075360235 1 18.51153831 ALIEVLQPLIAEHQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALIEVLQPLIAEHQAR 16 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 199.33 3.84E-11 2966800000 906490 996600 1050640 1064780 1128220 1280860 1028350 1006710 1087520 1200320 FALSE TRUE 942278.9252 1167758.298 1078020.542 1275390.306 936445.5674 983399.6766 947745.2399 993216.6991 1048380.368 1435499.722 0.656411778 0.813485561 0.750972309 0.888464335 0.652348135 0.685057378 0.66021973 0.691896128 0.730324326 1 20.45312162 0.91687426 20.13665865 1 0.724626131 0.565705972 0.072177217 6066.785188 1469642.706 0.071499427 0.017874857 8.257988239 -0.91687426 -0.275373869 ALIQTCLNSPDS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALIQTCLNSPDSPPR 15 0 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR;ALIQTCLNSPDS(1)PPR 238.45 9.50E-18 297033000 171083 170201 161638 204292 159970 198989 187733 160141 161568 125340 TRUE FALSE 177837.4889 199431.6978 165850.4191 244700.3478 132778.3565 152776.8205 173017.9969 157994.5718 155753.1992 149897.9732 1.186390217 1.330449595 1.106422025 1.632446007 0.88579154 1.019205378 1.154238401 1.054014063 1.039061409 1 17.19362135 3.209384104 24.99999769 1.038296878 1.300285986 0.496858202 0.141624564 180.4571338 154624.8551 0.039119919 0.046764147 1619.511752 -3.209384104 0.261989108 ALIQTCLNSPDS(ph)PPRSDPTTDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALIQTCLNSPDSPPRSDPTTDQR 23 1 P11831 P11831 SRF Serum response factor 1 ALIQTCLNSPDS(1)PPRSDPTTDQR;ALIQTCLNSPDS(0.999)PPRSDPTTDQR;ALIQTCLNS(0.001)PDS(0.999)PPRSDPTTDQR;ALIQTCLNSPDS(1)PPRSDPTTDQR 243.75 1.26E-37 3232720000 723970 859470 757990 752970 882000 868170 679900 786570 762750 942910 TRUE FALSE 752552.8946 1007077.287 777743.8421 901905.2186 732077.955 666550.6747 626607.6614 776027.3157 735298.7765 1127655.161 0.667360839 0.893072032 0.689700069 0.799805871 0.649203746 0.591094421 0.55567312 0.68817786 0.652059957 1 20.10489453 -1.392844332 3.024193246 1.004551936 0.687090949 0.509544646 0.09202104 18666843.55 23360714.77 742044.2168 0.025853334 0.040472093 1.392844332 -0.317460987 ALIQYFSPYVSADMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALIQYFSPYVSADMHR 16 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ; 106.19 0.0012247 750090000 233000 388640 379720 399900 354880 485780 342250 360360 336140 418040 FALSE TRUE 242199.0199 455385.8968 389615.8151 478999.0264 294557.6244 372964.9571 315423.5507 355529.9636 324042.3871 499946.9341 0.484449455 0.910868466 0.77931434 0.958099738 0.589177779 0.746009089 0.630914061 0.711135401 0.648153564 1 18.93141545 -1.005208997 4.486439997 1.000009485 0.724501241 0.280022487 0.135451665 16456733.49 3687212.451 1532.353329 0.030193496 0.098807748 1.005208997 -0.275508244 ALIRS(ph)PSLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALIRSPSLAK 10 1 Q5SW96 Q5SW96 LDLRAP1 Low density lipoprotein receptor adapter protein 1 1 ALIRS(0.838)PS(0.162)LAK 83.204 0.0095461 251390000 1017900 691230 781530 576010 1038700 1043600 800470 648120 835570 755370 TRUE FALSE 1058087.478 809943.3755 801897.3138 689943.0588 862142.145 801239.7159 737727.0698 639433.0115 805497.9989 903370.2891 1.171266634 0.896579603 0.887672888 0.763743359 0.954361855 0.88694495 0.816638624 0.707830465 0.891658724 1 19.78495794 4.920740407 1.795593804 0.842964421 1.410627966 0.541669021 0.082731209 1.128219557 2.486569029 0.021931459 1.26019143 83318.30135 -4.920740407 0.567663545 ALIVLAHSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALIVLAHSER 10 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 202.36 2.25E-07 19198500000 4760130 5555360 4406320 4108977 10162900 7582380 5965510 4446030 4637815 11458060 FALSE TRUE 4948063.608 6509449.865 4521152.319 4921720.387 8435413.888 5821487.157 5497917.738 4386438.24 4470900.944 13703047.48 0.361092203 0.475036657 0.329937726 0.359169768 0.615586708 0.424831569 0.401218616 0.320106768 0.326270558 1 23.70799344 -1.328991035 5.263631866 1.000175903 0.401289139 0.816175646 0.085214799 0.000182012 2.32E-05 0.085374136 0.020117059 0.046882306 1.328991035 -0.598886764 ALKDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 86.011 0.018596 6589960000 9403110 4497190 6556190 4521640 9574620 9074610 10126350 6877860 8324020 4058120 FALSE TRUE 9774352.044 5269547.399 6727049.697 5416006.896 7947129.512 6967169.355 9332620.227 6785673.537 8024440.146 4853230.917 2.013988663 1.085781305 1.386097182 1.115959036 1.637492559 1.43557343 1.922970571 1.398176525 1.653422284 1 22.21051407 ALKDEEKMELQEIQLK ddPTM_MDA-MB-175_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 0 119.46 0.00010844 389230000 515930 228090 311710 162610 597220 495710 313980 295430 512870 292380 FALSE TRUE 536299.3148 267262.6832 319833.4187 194773.7727 495704.7577 380588.8651 289369.4272 291470.2441 494411.9089 349666.263 1.533746236 0.764336487 0.914681948 0.557027638 1.417651087 1.088434617 0.827558898 0.83356696 1.413953707 1 18.41561908 4.751609002 24.24722512 0.963373094 1.533746799 0.290545215 0.258606169 1773.629899 3295766.054 0.060587218 1.101396368 56442.85877 -4.751609002 0.570373705 ALKEDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALKEDDPK 8 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 84.213 0.016062 161150000 904160 372240 535490 329540 777730 793710 728380 504480 636570 332230 FALSE TRUE 939856.935 436169.3244 549445.3093 394722.0284 645531.7324 609382.8813 671287.6723 497718.2708 613659.97 397324.1076 2.365466673 1.097767077 1.382864263 0.993450991 1.624698125 1.53371736 1.689521626 1.252675741 1.544482095 1 18.59995681 -2.932656184 0.342542423 2.73E-20 1.487004552 0.144221669 0.360702882 168.632983 5.255711815 122.9467683 0.273841359 0.001167734 2.932656184 1.487004552 ALKEPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALKEPPR 7 1 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;; 89.55 0.016225 1025720000 2232530 1945810 2239830 2068920 2649970 2648140 2757140 2330600 2249450 1941730 FALSE TRUE 2320672.008 2279987.731 2298201.81 2478146.201 2199529.046 2033149.618 2541028.162 2299362.119 2168492.734 2322174.817 0.999352844 0.981832942 0.989676485 1.067166082 0.947184954 0.875536847 1.094244991 0.99017615 0.933819762 1 21.14704515 -1.696853317 2.787516775 1.001527009 0.98931051 0.002686122 0.059184976 19107425.22 21226467.65 203298.7371 0.014031878 0.020097715 1.696853317 -0.012216499 ALKEPPRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALKEPPRDR 9 2 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;; 103.7 0.0019009 7332860000 14745200 15216400 16231600 13026300 19997200 18743500 15165700 16290400 16380200 18088800 FALSE TRUE 15327351.88 17829698.33 16654608.83 15602863.26 16598083.09 14390606.19 13976972.81 16072053.83 15790679.8 21632954.03 0.708518673 0.824191569 0.76987215 0.721254399 0.767259204 0.66521688 0.646096358 0.742943096 0.729936364 1 24.36672735 0.017091885 2.752961467 1.000000754 0.730521775 0.733042817 0.048774562 270.4185138 751.3740374 0.049947936 0.013123087 1.040140208 -0.017091885 -0.269478979 ALLDFERHDDDELGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALLDFERHDDDELGFR 16 1 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ;;; 282.55 8.32E-36 246067000 220005 295539 290049 246092 340878 336249 223498 265672 284984 374531 FALSE TRUE 228690.9673 346295.5243 297607.9152 294768.2631 282935.6793 258160.2657 205979.6428 262111.1014 274727.4815 447913.1786 0.510569856 0.773130912 0.664432148 0.65809241 0.631675273 0.576362291 0.459865109 0.58518283 0.613349851 1 18.77285959 0.904184015 18.82928086 1 0.607286187 0.675328712 0.081534105 3981.196567 782369.0071 0.08266294 0.020665735 8.020178141 -0.904184015 -0.392713813 ALLDSLQLGPDSLTVHLIHEVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALLDSLQLGPDSLTVHLIHEVTK 23 0 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 243.37 1.26E-37 843750000 1133350 1138640 1282810 1288290 1688560 1644650 1359180 1257240 1339880 976480 FALSE TRUE 1178095.533 1334192.563 1316241.082 1543109.917 1401539.174 1262704.962 1252643.92 1240388.754 1291657.981 1167802.56 1.008813967 1.142481279 1.127109263 1.321379118 1.200150798 1.081265794 1.072650431 1.062156221 1.106058528 1 20.15536495 2.635629016 5.57807464 1.066931265 1.165881783 0.281063361 0.076297546 0.324834885 14.54563781 0.026189238 0.024633609 432.1445255 -2.635629016 0.098950519 ALLDSQFSYQHAIEESVVLIYDPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ALLDSQFSYQHAIEESVVLIYDPIK 25 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;;; 232.06 8.22E-35 1928560000 936395 965282.5 1184147 956845 1261094 1315784 1240606 1238479 1270818 854099 FALSE TRUE 973364.5977 1131062.261 1215006.844 1146106.085 1046733.692 1010213.107 1143364.06 1221879.215 1225081.508 1021443.346 0.952930577 1.107317664 1.189499983 1.122045671 1.024759421 0.989005519 1.11936121 1.196228082 1.199363149 1 19.96217776 2.005432219 24.75838698 1.15469882 1.071194412 0.1074918 0.08272594 226.1910167 1030902.972 0.031700079 0.02333725 101.25867 -2.005432219 -0.083504408 ALLELQLEPEELYQTFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 226.19 8.49E-19 419102000 338872 345814 386292 434149 397690 438959 472502 401177 376332 329687 FALSE TRUE 352250.9282 405204.8644 396359.0869 520022.3764 330090.7959 337017.4247 435466.0586 395799.8785 362787.8848 394282.8554 0.893396513 1.027700948 1.005265843 1.318906895 0.837192871 0.854760536 1.10445091 1.00384755 0.920120872 1 18.58887145 ALLENMEGLFLAVDEIVDGGVILESDPQQVVHR ddPTM_MDA-MB-175_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 0 227.48 2.09E-36 317480000 137070 184070 167640 179180 166860 208110 177340 159050 204280 182230 FALSE TRUE 142481.6294 215682.5906 172008.8361 214621.2692 138497.1968 159779.6064 163439.6274 156918.1949 196928.0027 217934.4795 0.653781952 0.989667129 0.789268575 0.984797218 0.635499243 0.733154326 0.749948461 0.720024639 0.903611045 1 17.73353494 5.019195163 16.04631743 0.811919229 0.332386598 0.137838571 0.124655063 7566449.042 149558406 0.02896981 87726845.72 104518.98 -5.019195163 -0.479532632 ALLEPELRPEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALLEPELRPEDR 12 1 P0DPD7;P0DPD8 P0DPD7 0 ;; 118.76 0.00053906 332060000 424989 634250 565060 607590 564320 678220 588350 583250 552080 618210 FALSE TRUE 441767.8939 743177.5037 579785.9278 727769.4885 468397.088 520713.6835 542233.5896 575432.4878 532210.7486 739336.4132 0.597519459 1.005195322 0.784197718 0.984354991 0.633537155 0.704298712 0.733405768 0.77830941 0.719849231 1 19.49587144 5.003806332 17.26285252 0.799568146 0.362519791 0.197484364 0.12832184 67444507.1 2044157451 0.029586071 625856508.4 100880.2923 -5.003806332 -0.437048355 ALLETAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALLETASPR 9 0 H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2;Q96BT3 H3BMP6 CENPT Centromere protein T 1 ALLETAS(1)PR 132.25 0.001188 0 95803 124160 114160 128890 114240 141610 110030 115640 104100 136400 TRUE FALSE 99585.37642 145483.5142 117135.1034 154384.0573 94821.52561 108723.2236 101405.5611 114090.0349 100353.4613 163124.9685 0.610485184 0.891853133 0.718069738 0.94641586 0.581281495 0.666502649 0.621643407 0.699402648 0.615193752 1 17.3156181 3.220001691 24.9999848 0.677252131 0.793599708 0.089285902 0.138985114 443.5760235 597522.0393 0.036605008 0.043824051 1659.593368 -3.220001691 0.116347577 ALLFIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALLFIPR 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 166.66 0.0025941 716510000 606220 653040 644000 691060 829730 779580 783060 668060 645970 750510 FALSE TRUE 630154.0337 765194.5401 660783.1691 827749.6054 688692.791 598534.3596 721681.7111 659105.7484 622721.6659 897558.0651 0.702076064 0.85252929 0.736201027 0.922224018 0.767296087 0.666847509 0.804050166 0.734332155 0.69379541 1 19.77564575 -0.996445912 7.078831757 1.000000018 0.767362743 0.478269531 0.073770736 2.06E-08 2.91E-09 0.069137587 0.016295884 0.100821717 0.996445912 -0.232637275 ALLFVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALLFVPR 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 181.07 0.0015755 2848600000 715210 901150 805940 854900 943050 953720 962850 818500 831440 873040 FALSE TRUE 743447.0431 1055915.503 826943.4585 1023996.668 782750.6978 732232.9838 887379.3011 807529.3463 801516.6368 1044095.473 0.71204891 1.011320832 0.792019006 0.980750032 0.749692646 0.701308456 0.849902451 0.773424814 0.76766604 1 19.99382221 5.044547126 15.65272185 0.834272942 0.103316056 0.114715519 0.107363394 4114325.36 40054302.95 0.024649524 87766791.62 110801.8792 -5.044547126 -0.730956887 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALLGPAPEDEDERPEAEDGPGAGDHALGLPAEVVEPEGPVAQR 43 1 A0A1B0GUA3;Q96EK5;A0A1B0GUH6;A0A1B0GTE6;A0A0D9SFK7;A0A1B0GU96;A0A1B0GVY9 A0A1B0GUA3 KIAA1279;KIF1BP KIF1-binding protein 0 82.311 0.00019943 32811000 6477 9455.3 8608.3 8794.7 11260 9910.1 8562.3 8056.9 11635 8456.6 FALSE TRUE 6732.716961 11079.17422 8832.63937 10534.26541 9346.029222 7608.629464 7891.164553 7948.910434 11216.25862 10113.50886 0.665715238 1.095482723 0.873350634 1.04160342 0.924113416 0.752323409 0.780259815 0.785969592 1.109037306 1 13.303996 ALLLLCGEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALLLLCGEDD 10 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 198.73 6.78E-07 277141000 335499 448726 377272 404719 423488 484947 276776 394568 370610 469166 FALSE TRUE 348744.7596 525791.1999 387104.0183 484771.2102 351503.661 372325.4087 255081.5739 389279.4613 357271.8185 561090.095 0.621548594 0.937088722 0.68991419 0.863981051 0.626465632 0.663575087 0.454617852 0.693791362 0.636745902 1 19.09787292 3.222589668 24.93389715 0.650253061 0.783185765 0.074392597 0.151148136 411.2599234 642059.0448 0.040292546 0.048303473 1669.512473 -3.222589668 0.132932704 ALLLVGDVAQAADVAIEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALLLVGDVAQAADVAIEHR 19 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 ; 120.9 3.41E-05 7556400 16177.4 20390 19994.4 20477.2 21862.6 25717.5 21760.1 19061.8 20377.4 20188.4 FALSE TRUE 16816.09624 23891.82389 20515.47049 24527.52904 18146.40306 19745.00038 20054.4865 18806.30775 19644.02135 24143.93045 0.696493733 0.989558181 0.84971544 1.015887993 0.751592749 0.817803896 0.830622278 0.778924864 0.813621518 1 14.55937293 3.203364509 24.99998967 0.817670294 0.892446258 0.055716046 0.102072387 375.9860742 267063.9001 0.027253849 0.032575828 1597.219152 -3.203364509 0.074775963 ALLQSGAPAVPQLLHMPDFEGLYPVHLAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALLQSGAPAVPQLLHMPDFEGLYPVHLAVR 30 0 Q00653;Q00653-4 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 141.38 3.01E-08 98428000 58487 69555 57955 56210 70873 71604 54578 67841 56194 62503 FALSE TRUE 60796.11192 81500.53019 59465.35491 67328.17023 58826.03278 54975.05617 50300.03375 66931.70236 54171.58892 74749.26616 0.813333897 1.0903188 0.795530953 0.90072015 0.786978064 0.735459477 0.672916757 0.89541618 0.724710645 1 16.1897718 3.752625715 1.599207007 0.795719412 0.939330537 0.134314255 0.114947945 0.627075444 3.089366761 0.032358411 0.076750665 5657.515006 -3.752625715 0.143611125 ALLT(ph)PVAIAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALLTPVAIAAGR 12 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 1 ALLT(1)PVAIAAGR;ALLT(1)PVAIAAGR;ALLT(1)PVAIAAGR 135.02 0.0015109 152528000 179468 215039 205893 271290 371930 355230 300439 226255 204941 353410 TRUE FALSE 186553.5352 251970.2755 211258.7407 324950.3523 308709.4715 272733.2161 276889.8061 223222.4218 197565.2134 422653.9231 0.441386025 0.596162159 0.499838589 0.768833162 0.730407207 0.645287317 0.655121817 0.528144682 0.467439677 1 18.68911732 3.767702187 24.457308 0.656324652 0.520832214 0.219670494 0.141745225 1012.497413 849742.7347 0.035808969 0.064541039 5857.363645 -3.767702187 -0.135492437 ALMDSLGPEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALMDSLGPEWR 11 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 98.249 0.013172 40381000 48524 62569 55833 63159 62643 77915 55419 53123 50225 94658 FALSE TRUE 50439.76499 73314.73903 57288.05385 75651.66169 51994.96524 59820.42206 51075.11397 52410.97308 48417.41206 113204.4228 0.445563554 0.647631402 0.506058442 0.668274789 0.459301536 0.528428312 0.451175959 0.462976373 0.427698944 1 16.7885708 -1.410261417 3.376913758 1.004973881 0.512089647 0.772232111 0.079702811 21019226.73 32988877.71 1034837.654 0.019739969 0.038881104 1.410261417 -0.492884234 ALMGS(ph)PQLVAAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ALMGSPQLVAAVVR 14 0 P14923;C9JTX4;C9J826;C9JK18;C9JKY1 P14923 JUP Junction plakoglobin 1 ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR;ALMGS(1)PQLVAAVVR 224.67 3.21E-12 1488082600 1101088 1405507 999656 1218936 1221413 1485688 1201340 1059689 941908 1431015 TRUE FALSE 1144559.804 1646891.894 1025707.857 1460037.903 1013797.655 1140659.478 1107175.832 1045485.602 908008.9151 1711394.991 0.668787633 0.962309638 0.599340224 0.853127367 0.592380871 0.666508599 0.64694348 0.610896729 0.530566538 1 20.70674134 3.23195358 24.99017017 0.650275197 0.77231032 0.076831883 0.150027136 296.911873 1123025.396 0.039467946 0.048211363 1705.900044 -3.23195358 0.122035123 ALNHSVEDIEPDLLT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALNHSVEDIEPDLLTPR 17 0 Q8IWR0;I3L2K5 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR 273.33 4.30E-35 621810000 467120 545190 500470 515840 573230 625670 547350 584480 576920 629630 TRUE FALSE 485562.2583 638822.1415 513512.6593 617871.6124 475792.5694 480367.6246 504447.2768 576646.0016 556156.7619 752993.9435 0.644842183 0.848376201 0.681961208 0.82055323 0.631867724 0.637943544 0.66992209 0.765804302 0.738593938 1 19.52227874 0.386584245 1.211835109 1.000151808 0.712581121 0.587483117 0.072033823 2.070429601 3.430014025 0.068111637 0.020408769 2.435478193 -0.386584245 -0.287570687 ALPAAHIPAPPHEGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 ALPAAHIPAPPHEGS(1)PR 91.889 0.0057568 63156000 30344 82230 79490 94525 65581 100150 60059 82167 68105 133930 TRUE FALSE 31542.00455 96352.36284 81561.5747 113221.7629 54433.56504 76891.68029 55351.41865 81065.68576 65653.91435 160171.0193 0.196927039 0.601559279 0.509215556 0.706880454 0.33984653 0.48005988 0.34557699 0.50611956 0.409898836 1 17.28925361 -1.258024762 3.419317711 1.001552999 0.464152179 0.589304257 0.136274511 61956811.23 94147680.1 1009191.652 0.030439215 0.055204596 1.258024762 -0.53740082 ALPDSQQVPSS(ph)PASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALPDSQQVPSSPASK 15 0 O14924-5;O14924-4;O14924;O14924-7;O14924-6;O14924-2;O14924-3 O14924-5 RGS12 Regulator of G-protein signaling 12 1 ALPDSQQVPS(0.013)S(0.986)PASK 180.7 1.72E-11 0 103220 99094 109740 80857 130400 136840 125600 103750 115180 90477 TRUE FALSE 107295.2053 116112.6237 112599.9146 96850.27327 108234.6546 105060.9838 115755.1438 102359.401 111034.6943 108204.2359 0.991598937 1.073087599 1.040623906 0.895069149 1.000281123 0.970950749 1.069783848 0.945983308 1.026158481 1 16.72339745 ALPESLGQHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALPESLGQHALR 12 0 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ;;; 223.08 2.33E-11 1457650000 571917 853140 755185 804270 824820 940830 742140 737160 736268 944420 FALSE TRUE 594496.7248 999660.1585 774865.7415 963352.2055 684617.391 722336.4909 683969.1276 727279.576 709769.8585 1129461.017 0.526354355 0.885077168 0.686049124 0.852930903 0.606145215 0.639540878 0.605571257 0.643917377 0.628414658 1 20.10720305 -1.085107225 4.619810286 1.000015001 0.678052679 0.45891426 0.105855755 2.02E-05 4.00E-06 0.099345555 0.023414584 0.082203967 1.085107225 -0.321962322 ALPFWNEEIVPQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALPFWNEEIVPQIK 14 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ; 184.88 2.89E-06 166282000 221180 193272 244500 172523 299070 280240 252080 212470 261450 199617 FALSE TRUE 229912.3572 226464.9626 250871.8709 206647.5345 248234.1882 215158.5071 232321.3109 209622.1872 252040.4656 238728.1293 0.963071917 0.948631245 1.050868499 0.865618707 1.039819601 0.901270025 0.9731627 0.878079126 1.055763585 1 17.86500904 3.76141647 24.99350143 0.951429702 0.983634596 0.028032728 0.065542367 2751.958116 3009331.794 0.015681367 0.0282413 5773.198226 -3.76141647 0.032204895 ALPLALVLHELGAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALPLALVLHELGAGR 15 0 C9JGI3;P19971;A0A494C0L6;P19971-2 C9JGI3 TYMP Thymidine phosphorylase 0 ; 186.49 1.14E-11 0 175674 201016 188789 197300 203289 227650 189055 190148 172642 220060 FALSE TRUE 182609.7452 235538.9343 193708.9964 236325.3511 168734.0084 174781.7376 174236.3751 187599.3771 166428.6481 263176.5437 0.69386786 0.894984526 0.736042026 0.897972698 0.641143797 0.664123539 0.662051308 0.712827118 0.632384048 1 18.00567139 4.033277082 24.95936891 0.72664045 0.799698035 0.0131749 0.121993689 549.0533568 411808.9257 0.028767244 0.062143878 10796.35314 -4.033277082 0.073057585 ALPPLPRPPT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALPPLPRPPTPK 12 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ALPPLPRPPT(1)PK;ALPPLPRPPT(1)PK 86.772 0.037113 70934000 201686 81742 104871 71299 154093 159234 121369 111965 116115 75083 TRUE FALSE 209648.719 95780.55264 107604.0244 85401.72939 127900.3269 122254.3167 111855.7806 110464.2923 111936.0438 89794.0763 2.334772266 1.066668945 1.198342127 0.951084224 1.424373769 1.361496457 1.245692202 1.230195764 1.246586061 1 16.45433265 4.742921673 24.9992491 1.207430666 2.334772713 0.852595682 0.142461726 158.4997122 908548.5874 0.033716211 0.267749082 55325.03196 -4.742921673 1.127342047 ALPQT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALPQTPR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ALPQT(1)PR 110.76 0.075253 1094600000 959000 992340 931870 1168300 921480 1100600 1218100 1084100 914180 855340 TRUE FALSE 996862.0605 1162766.676 956155.2977 1399386.253 764847.1587 845002.3298 1122622.139 1069569.413 881278.8404 1022927.497 0.974518784 1.136704879 0.934724407 1.368020957 0.747704174 0.826062778 1.097460126 1.045596503 0.861526201 1 19.96427246 3.218907651 24.99997594 0.946422528 1.093809974 0.248227515 0.146038244 407.9266236 518910.607 0.042828125 0.051254703 1655.417915 -3.218907651 0.147387446 ALPQT(ph)PRPR ddPTM_MDA-MB-175_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 122.69 0.00093559 36987396000 3567132 4226910 3819196 3648851 4118803 4750836 3515271 3856844 3610663 4453457 TRUE FALSE 3707965.126 4952848.912 3918727.385 4370582.837 3418690.337 3647526.339 3239734.874 3805149.315 3480715.944 5326026.633 0.696197256 0.929933185 0.735769394 0.820608521 0.641883823 0.684849437 0.608283641 0.71444429 0.653529579 1 22.34462821 4.022039499 24.95200054 0.712587311 0.818011807 0.051810521 0.119070865 455.65186 515858.3968 0.027387547 0.059156925 10520.57554 -4.022039499 0.105424495 ALPSLNTGSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 ALPSLNTGS(0.017)S(0.213)S(0.77)PR;ALPSLNTGS(0.001)S(0.112)S(0.887)PR;ALPSLNTGSS(0.166)S(0.833)PR;ALPSLNTGSS(0.035)S(0.964)PR;ALPSLNTGSS(0.001)S(0.999)PR;ALPSLNTGSS(0.009)S(0.991)PR;ALPSLNTGSS(0.247)S(0.753)PR;ALPSLNTGSS(0.066)S(0.934)PR 241.39 7.26E-17 26109320000 14518970 17661460 16208700 16712100 17383910 18772450 16000440 16839530 15465300 17944660 TRUE FALSE 15092190.15 20694678.37 16631112.04 20017703.5 14428999.19 14412832.99 14746283.7 16613823.64 14908706.87 21460572.56 0.70325198 0.964311568 0.774961246 0.932766516 0.672349219 0.671595921 0.68713375 0.774155657 0.694702196 1 24.35518523 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.635)S(0.365)PVGPSSSK 108.44 0.00025472 273340000 274190 232890 355840 260140 468230 413720 432440 381670 421140 287370 TRUE FALSE 285015.2329 272887.0459 365113.4827 311594.9156 388640.4318 317639.8 398544.2228 376554.3379 405983.2537 343674.6495 0.829317011 0.794027276 1.062381189 0.906656677 1.130838229 0.924245651 1.159655574 1.095670974 1.181301136 1 18.39068391 4.491228599 0.541458119 1.105325292 0.638085312 0.519342578 0.09140583 2.302596352 0.623567715 0.048751958 0.658382166 30990.50111 -4.491228599 -0.46723998 ALPTSKPEGSLHSS(ph)PVGPSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALPTSKPEGSLHSSPVGPSSSK 22 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 ALPTSKPEGSLHS(0.214)S(0.786)PVGPSSSK;ALPTSKPEGSLHS(0.188)S(0.812)PVGPSSSK 120.57 1.79E-05 746940000 588540 561260 746820 585830 985040 854230 865350 796960 840740 576660 TRUE FALSE 611776.0137 657652.039 766282.7427 701705.4255 817603.2526 655848.0285 797521.6058 786278.0548 810481.9316 689645.4862 0.887087679 0.95360885 1.111125583 1.017487158 1.185541367 0.950992998 1.15642257 1.140119192 1.175215307 1 19.39549541 4.362610222 3.00418583 1.099180106 0.893516592 0.45721185 0.075788784 0.208200731 3.579099589 0.018357523 0.067611552 23046.77819 -4.362610222 -0.205663514 ALQAPHS(ph)PSKTDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALQAPHSPSKTDGK 14 1 F2Z2Z8;Q5T173;Q96AQ6-3;Q96AQ6-2;Q96AQ6 F2Z2Z8 PBXIP1 Pre-B-cell leukemia transcription factor-interacting protein 1 1 ALQAPHS(0.73)PS(0.135)KT(0.135)DGK;ALQAPHS(0.968)PS(0.016)KT(0.016)DGK;ALQAPHS(0.977)PS(0.012)KT(0.012)DGK;ALQAPHS(0.49)PS(0.49)KT(0.019)DGK 131.48 3.38E-05 1132300000 1705089 817578 1156607 1004456 1698056 1751970 1541299 1160499 1315260 702883 TRUE FALSE 1772407.23 957990.6616 1186749.129 1203134.399 1409421.048 1345101.519 1420487.957 1144944.409 1267924.05 840599.4663 2.108503873 1.13965176 1.411789058 1.431281421 1.676685632 1.60016937 1.689851129 1.362057026 1.508356953 1 19.68105902 0.351840788 0.947979284 0.997906095 1.544675625 0.320040361 0.241609784 3.061633409 3.444496644 0.234995038 0.07125198 2.248230256 -0.351840788 0.54676953 ALQDEWDAVMLHSFTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALQDEWDAVMLHSFTLR 17 0 Q9UMS4;F5GY56 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ;;;; 241.32 2.34E-20 1049380000 664610 889784 941668 876036 1015371 1084147 1031001 934245 1025465 900641 FALSE TRUE 690849.316 1042597.48 966208.6417 1049313.306 842778.6001 832370.2897 950188.4476 921722.9739 988558.715 1077104.36 0.641394967 0.96796329 0.897042736 0.974198365 0.782448416 0.772785183 0.882169345 0.855741568 0.917792882 1 20.03872661 0.95037919 1.902276153 0.999979227 0.852183798 0.211149895 0.09319043 0.630887932 4.804195426 0.085431203 0.024053473 8.920294437 -0.95037919 -0.147795429 ALQEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALQEENR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 108 0.017104 418480000 422970 1325100 712870 1293620 635030 1227140 559740 852570 595610 1542380 FALSE TRUE 439669.1822 1552675.617 731447.9778 1549494.175 527087.8274 942155.3325 515866.1162 841142.6937 574174.1124 1844579.83 0.238357362 0.841750295 0.396539074 0.840025544 0.285749534 0.510769616 0.279665921 0.456007748 0.311276369 1 20.8148608 -1.383017181 5.603145508 1.000185076 0.469854908 0.375832025 0.207696498 0.000445238 4.90E-05 0.186463672 0.043934824 0.04139833 1.383017181 -0.530330168 ALQHTES(ph)PSETNKPHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALQHTESPSETNKPHSK 17 1 Q14669-3;Q14669;Q14669-2;G5E9G6;C9JLD7;C9JLJ5;C9JSX9 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 ALQHTES(0.984)PS(0.016)ETNKPHSK 220.36 2.44E-15 123730000 158670 118510 152940 101010 176730 175110 171420 151750 170090 100900 TRUE FALSE 164934.4141 138863.1706 156925.742 120989.4765 146689.4977 134443.3563 157983.6525 149716.0395 163968.4941 120669.4232 1.366828562 1.150773468 1.300459867 1.002652315 1.215631051 1.11414601 1.309226881 1.240712316 1.358823883 1 16.88070063 2.231269972 24.99938373 1.248763086 1.18731775 0.006261658 0.128193206 566.4105606 1942185.406 0.044451895 0.033503761 170.3216955 -2.231269972 -0.061445336 ALQKYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALQKYEK 7 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 92.439 0.01429 253640000 243760 248920 293390 196080 397390 351460 247530 267250 313830 293120 FALSE TRUE 253383.833 291670.0737 301035.9844 234864.0388 329841.7897 269838.7414 228127.9518 263667.9509 302535.3196 350551.2519 0.722815371 0.832032612 0.858750276 0.669984881 0.940923155 0.769755464 0.650769183 0.752152359 0.863027355 1 18.41926586 0.956678926 3.864270587 0.999645665 0.774641292 0.418264406 0.082246916 0.225650483 9.453811204 0.078470999 0.020127903 9.050632404 -0.956678926 -0.225004374 ALQLEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALQLEEER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 193.16 0.00040043 1402090000 1013420 1292690 1072940 1212880 1330300 1448490 1183930 1192570 1140320 1425910 FALSE TRUE 1053430.604 1514699.452 1100901.698 1452784.044 1104176.081 1112100.15 1091130.473 1176585.55 1099280.106 1705289.764 0.617742877 0.88823582 0.645580429 0.851927968 0.647500562 0.65214732 0.639850479 0.689962243 0.644629511 1 20.70158547 -1.05827223 4.658148176 1.000011134 0.700077918 0.506820152 0.089485634 1.08E-05 2.18E-06 0.08183663 0.019288287 0.087443548 1.05827223 -0.299933216 ALQLLHCFPLDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALQLLHCFPLDIR 13 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 106.13 0.0013983 376950000 422160 523460 420430 468910 595160 610820 482210 500350 438000 614820 FALSE TRUE 438827.2028 613360.183 431386.7512 561658.9984 493994.9158 468966.3121 444413.1202 493643.6267 422236.4656 735282.2076 0.596814663 0.834183361 0.586695485 0.763868611 0.671843968 0.637804515 0.604411634 0.671366207 0.574250895 1 19.48793855 -1.964278949 3.564406379 1.250637218 0.663976303 0.626742621 0.078633325 0.048477533 0.000485822 0.023566334 0.016561945 0.01085728 1.964278949 -0.586660915 ALQLSNS(ph)PGASSAFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALQLSNSPGASSAFLK 16 0 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ALQLSNS(0.998)PGAS(0.001)SAFLK;ALQLSNS(1)PGASSAFLK 202.81 3.09E-11 371660000 1384050 1082990 1282820 1179580 1613890 1573110 1381230 1339800 1338490 1138360 TRUE FALSE 1438693.363 1268985.108 1316251.343 1412897.403 1339561.554 1207779.043 1272965.583 1321842.172 1290318.006 1361399.847 1.056775029 0.932117857 0.966836706 1.037826915 0.983958943 0.887159673 0.935041668 0.970943383 0.947787683 1 20.37665942 2.976466006 24.74669998 0.946191837 0.993838126 0.243849197 0.041897688 1003.304463 1055005.447 0.01264713 0.013493521 947.2530368 -2.976466006 0.047646289 ALQQYTLEPSEKPFDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALQQYTLEPSEKPFDLK 17 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 93.152 0.0028568 484540000 437440 212940 325840 265700 427820 427210 410060 338170 390530 215120 FALSE TRUE 454710.469 249510.7886 334331.6581 318254.667 355099.3092 327996.9519 377918.4257 333637.3843 376474.9016 257268.6453 1.767453894 0.969845308 1.299542965 1.237051902 1.380266565 1.274920042 1.468964184 1.296844331 1.463353224 1 17.97291611 -0.939416007 4.1509599 0.999987242 1.335608642 0.225891298 0.19302067 5139953.07 1857384.847 592.3953682 0.040820218 0.114969857 0.939416007 0.3356214 ALQS(ph)PALGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALQSPALGLR 10 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR;ALQS(1)PALGLR 162.31 7.14E-06 3144470000 2933880 3088990 3031120 3278590 3076430 3448960 3386360 3061550 2775270 2875400 TRUE FALSE 3049711.848 3619500.003 3110113.477 3927085.316 2553499.527 2647991.309 3120928.255 3020514.93 2675388.575 3438779.577 0.886858776 1.052553652 0.904423621 1.141999721 0.742559815 0.770038105 0.907568567 0.878368288 0.778005253 1 21.71346521 3.227283681 24.99999727 0.843496914 0.993891779 0.364425138 0.097224451 226.2324017 501536.864 0.026788714 0.032290675 1687.65504 -3.227283681 0.150394864 ALQS(ph)PK ddPTM_MDA-MB-175_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 96.311 0.044426 366990000 2982600 1500280 1935810 1381280 2480800 3135300 2493800 2073980 2094650 1448800 TRUE FALSE 3100355.351 1757941.419 1986258.799 1654493.061 2059114.502 2407174.091 2298329.44 2046181.69 2019263.956 1732664.621 1.789356875 1.014588396 1.146360799 0.954883618 1.188409157 1.389290265 1.326471039 1.18094504 1.165409584 1 20.724561 7.99993986 0.020000014 1.09E-05 2.764539928 0.127428959 0.216217514 9210.268699 14.19354271 727.1043907 1315.080553 99986153.21 -7.99993986 2.764529016 ALQTS(ph)PQPPEGPGLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.005)S(0.995)PQPPEGPGLPR;ALQTS(1)PQPPEGPGLPR;ALQT(0.028)S(0.972)PQPPEGPGLPR;ALQT(0.003)S(0.997)PQPPEGPGLPR 262.36 7.35E-27 995693000 806190 941820 906290 928450 949400 1142280 889240 964560 917830 998470 TRUE FALSE 838019.0037 1103570.259 929908.6619 1112094.639 788021.3271 877002.7814 819539.0452 951631.6509 884797.4776 1194101.08 0.70179905 0.92418496 0.778752049 0.931323703 0.659928494 0.734446017 0.686323008 0.796943967 0.740973685 1 20.18749353 5.03774632 16.65482732 0.791969818 0.318342808 0.065167181 0.107183072 47467626.63 560395802.2 0.024330434 679347197.7 109080.2992 -5.03774632 -0.47362701 ALRPGDLPPS(ph)PDDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALRPGDLPPSPDDVK 15 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVK;ALRPGDLPPS(1)PDDVK;ALRPGDLPPS(1)PDDVK 141.31 2.90E-06 857120000 1351070 800830 952810 820594 1284310 1366780 1230790 1023530 960220 768349 TRUE FALSE 1404411.287 938366.3229 977641.0113 982905.044 1066003.445 1049366.059 1134317.464 1009811.255 925661.8698 918892.2756 1.528374244 1.02119296 1.063934301 1.069662974 1.160096208 1.141990293 1.23444009 1.098944111 1.007367125 1 19.80953621 4.74516352 24.78518978 1.100811421 1.528374463 0.773284159 0.071157948 327.0771109 1227706.489 0.017461928 0.167475177 55611.36052 -4.74516352 0.427563042 ALRPGDLPPS(ph)PDDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALRPGDLPPSPDDVKR 16 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR;ALRPGDLPPS(1)PDDVKR 139.98 9.10E-07 1637680000 1306380 869634 1061095 869751 1399060 1324540 1300197 1074435 1167913 845280 TRUE FALSE 1357956.891 1018986.875 1088748.007 1041785.152 1161248.281 1016935.659 1198284.162 1060033.956 1125880.039 1010896.432 1.343319501 1.008003236 1.077012415 1.030555771 1.148731209 1.00597413 1.185367881 1.048607872 1.113744201 1 19.94720377 4.74726672 24.95362272 1.073995152 1.343319642 0.649076884 0.060470678 635.3431831 1820993.357 0.013017677 0.154188965 55881.32825 -4.74726672 0.26932449 ALRPPT(ph)SPGVFGALQNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALRPPTSPGVFGALQNFK 18 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ALRPPT(0.5)S(0.5)PGVFGALQNFK;ALRPPT(0.5)S(0.5)PGVFGALQNFK 108.07 0.00064966 779350000 584520 520440 633910 587620 633540 670800 707050 534280 561280 490920 TRUE FALSE 607597.3009 609821.5215 650430.2154 703849.4821 525851.0971 515016.8661 651629.5735 527118.8505 541079.6424 587106.3748 1.034901556 1.038690002 1.107857525 1.198844898 0.895665794 0.877212185 1.109900354 0.897825119 0.921604101 1 19.1632624 3.225002883 24.99907657 0.949693095 1.091959266 0.465661311 0.075907445 213.1467305 393020.0963 0.022355629 0.026857807 1678.815164 -3.225002883 0.142266172 ALS(ph)GRASPVPAPSSGLHAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSGRASPVPAPSSGLHAAVR 21 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 ALS(0.636)GRAS(0.364)PVPAPSSGLHAAVR 217.7 3.45E-25 308490000 52524 165890 127640 112990 148620 162880 93286 135300 111390 178120 TRUE FALSE 54597.68808 194380.3171 130966.4033 135339.0848 123357.6255 125053.5885 85973.99956 133486.5248 107381.0957 213019.2037 0.256304066 0.912501379 0.614810313 0.635337483 0.579091572 0.587053122 0.403597413 0.626640803 0.504091151 1 17.70062397 -1.372768325 2.990465989 1.005594993 0.579418717 0.391399119 0.160811164 34122450.53 42930077.22 1662724.103 0.036022795 0.042386902 1.372768325 -0.426176275 ALS(ph)HDSIFIPESGQDATRPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(1)HDSIFIPESGQDATRPVR;ALS(0.999)HDS(0.001)IFIPESGQDATRPVR 134.47 4.95E-06 222765000 44799 182221 160397 179700 171893 207789 132592 192621 155528 183521 TRUE FALSE 46567.69911 213516.0393 164577.0776 215244.1236 142674.6893 159533.1538 122199.0926 190039.2306 149930.5777 219478.4262 0.21217438 0.972833836 0.749855375 0.980707431 0.650062476 0.726873965 0.556770406 0.865867474 0.683122165 1 17.74371961 -5 0.308400837 3.366736984 0.716499439 0.14244927 0.211039744 592.9398217 5.390618938 911.1555196 0.186758761 1.00E-05 5 -2.650237544 ALS(ph)IESLSPTDSSNGVNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALSIESLSPTDSSNGVNWR 19 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5;Q9Y3M8-3 STARD13 StAR-related lipid transfer protein 13 1 ALS(0.994)IES(0.006)LSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(0.974)IES(0.026)LSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR;ALS(1)IESLSPTDSSNGVNWR 388.66 6.47E-127 1200780000 653392 727707 676589 672477 780381 868164 698397 731772 698616 793741 TRUE FALSE 679188.4207 852685.0165 694221.4652 805490.9435 647732.1164 666546.0682 643654.8182 721963.7933 673472.9466 949259.3519 0.715492999 0.898263488 0.731329603 0.848546756 0.682355265 0.702174876 0.678060023 0.760554839 0.709472017 1 19.85644278 -1.159431405 3.699081617 1.000192225 0.74888602 0.549994188 0.068544461 18446949.74 33547468.19 43258.49525 0.016388213 0.069273734 1.159431405 -0.251306206 ALS(ph)LDDKGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSLDDKGWR 10 1 Q9NRR6-2;Q9NRR6 Q9NRR6-2 INPP5E 72 kDa inositol polyphosphate 5-phosphatase 1 ALS(1)LDDKGWR;ALS(1)LDDKGWR 130.2 0.00017136 273780000 318984 275006 319586 274172 378191 400674 327918 315386 345802 306714 TRUE FALSE 331577.7346 322236.1413 327914.6737 328402.4033 313906.2289 307623.5358 302214.9303 311158.7665 333356.6536 366808.7359 0.903952666 0.87848546 0.893966369 0.895296025 0.855776317 0.838648335 0.823903306 0.84828614 0.908802384 1 18.48466847 0.925391397 4.179530917 0.999932339 0.865491099 0.723446973 0.024923742 0.195670354 8.563296282 0.027353712 0.006976051 8.421537693 -0.925391397 -0.13444124 ALS(ph)LEENGVGSNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALSLEENGVGSNFK 14 0 Q8NF50-3;Q8NF50;Q8NF50-4;Q8NF50-2;E9PDJ4 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK;ALS(1)LEENGVGSNFK 295.22 1.41E-43 519390000 620170 487203 723640 485313 1184770 781690 762590 679440 820140 558790 TRUE FALSE 644654.7905 570876.3253 742498.6529 581306.4629 983383.2186 600154.3441 702816.2031 670333.2181 790623.3216 668274.2018 0.964656108 0.854254622 1.111068856 0.869862193 1.471526532 0.898066007 1.051688366 1.003081095 1.183082213 1 19.35008066 4.235562004 24.99897751 1.069660533 0.90945535 0.141270552 0.161598934 133.8951922 1116305.387 0.037783621 0.087608829 17201.32907 -4.235562004 -0.160205182 ALS(ph)PEGALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSPEGALR 9 0 I3L100;I3L2W2;Q96JN8-2;Q96JN8;K7EPS7;I3L2Z9 I3L100 NEURL4 Neuralized-like protein 4 1 ALS(1)PEGALR 110.38 0.0024919 0 54459 65270 53108 72557 64720 74222 61114 54856 52557 73884 TRUE FALSE 56609.08337 76479.61477 54492.03811 86908.55804 53718.91752 56985.06535 56323.72499 54120.74505 50665.48384 88360.15521 0.640663014 0.865544143 0.616703739 0.983571813 0.607954087 0.644918122 0.637433523 0.612501697 0.573397407 1 16.43110833 ALS(ph)PGLEESGLGLLAR ddPTM_MDA-MB-175_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 352.72 2.92E-87 2346934000 519541 611346 593747 587806 652174 679168 593086 586085 510209 597105 TRUE FALSE 540052.8799 716339.9199 609220.5346 704072.2724 541317.6964 521441.5249 546598.3696 578229.4892 491846.6778 714096.2925 0.756274589 1.003141912 0.853134992 0.985962649 0.758045802 0.73021178 0.765440705 0.809736019 0.688768004 1 19.4457591 3.220043346 24.99986883 0.779969061 0.903701394 0.208781028 0.100862177 303.5805965 409858.4293 0.026670504 0.031931117 1659.752555 -3.220043346 0.123732333 ALS(ph)PVIPLIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 178.71 7.79E-06 4296563000 1903085 2158873 2005069 1965827 2261737 2477931 2066543 1989876 2065042 1982418 TRUE FALSE 1978220.265 2529642.644 2057322.745 2354661.713 1877287.753 1902469.079 1904561.96 1963204.967 1990721.542 2370834.851 0.834398172 1.066983912 0.867762992 0.993178294 0.79182561 0.802446901 0.803329662 0.828064834 0.839671114 1 21.17696374 3.235506636 24.99998578 0.830618989 0.944408361 0.239078794 0.081976667 89.12175603 729554.5961 0.021312765 0.026525737 1719.91362 -3.235506636 0.113789372 ALS(ph)SAGPIPIRPPIVPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSSAGPIPIRPPIVPVK 18 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 ALS(0.872)S(0.128)AGPIPIRPPIVPVK 195.39 1.45E-15 405230000 391580 291090 419470 304030 570920 514350 471010 426800 518340 358290 TRUE FALSE 407039.8808 341082.4431 430401.7328 364166.2266 473875.2223 394900.0075 434091.0054 421079.4441 499685.0447 428490.0656 0.949940065 0.796010154 1.004461404 0.849882543 1.105918807 0.921608315 1.013071341 0.982705266 1.166153161 1 18.70890223 3.314180563 0.564425339 1.043898382 0.866537499 0.291690582 0.087338581 1.384896473 0.878855701 0.059451319 0.133150964 2061.486821 -3.314180563 -0.177360882 ALS(ph)SDSILS(ph)PAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 ALS(0.999)S(0.001)DSILS(1)PAPDAR;ALS(0.999)S(0.001)DSILS(1)PAPDAR;ALS(0.989)S(0.011)DSILS(1)PAPDAR;ALS(0.978)S(0.022)DS(0.018)ILS(0.982)PAPDAR;ALS(0.996)S(0.004)DS(0.098)ILS(0.902)PAPDAR;ALS(0.988)S(0.012)DSILS(1)PAPDAR 300.54 4.11E-44 1672130000 1892619 1991018 1961120 2097331 2125989 2739620 2364080 2168667 2092212 2139573 TRUE FALSE 1967341.06 2332959.854 2012228.398 2512176.812 1764614.149 2103384.774 2178777.232 2139599.566 2016913.699 2558781.365 0.768858601 0.911746461 0.786401068 0.981786426 0.689630686 0.822025986 0.851490191 0.836179126 0.788232135 1 21.28702545 -0.962670876 4.84010768 1.000001624 0.829675716 0.320586115 0.075730811 1.21E-06 2.59E-07 0.066811063 0.015747368 0.108975564 0.962670876 -0.170325908 ALS(ph)SDSILSPAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.988)S(0.011)DSILSPAPDAR;ALS(0.494)S(0.494)DS(0.011)ILSPAPDAR;ALS(0.498)S(0.498)DS(0.003)ILSPAPDAR;ALS(0.694)S(0.306)DSILSPAPDAR;ALS(0.498)S(0.498)DS(0.004)ILSPAPDAR;ALS(0.999)S(0.001)DSILSPAPDAR;ALS(0.98)S(0.02)DSILSPAPDAR;ALS(0.97)S(0.03)DSILSPAPDAR;ALS(0.989)S(0.009)DS(0.003)ILSPAPDAR 396.88 7.26E-115 26212211000 4172869 4719175 4310333 4450421 4783836 5173679 4628899 4753104 4215321 4407259 TRUE FALSE 4337617.09 5529656.596 4422663.819 5330700.991 3970681.265 3972170.46 4266073.801 4689396.415 4063612.421 5270777.019 0.822955909 1.049116018 0.839091429 1.011369096 0.753338882 0.75362142 0.809382333 0.889697363 0.770970277 1 22.32958423 3.235879262 24.99998499 0.82377133 0.932557482 0.2150442 0.094247083 98.04643485 914151.9405 0.025236263 0.03148951 1721.389944 -3.235879262 0.108786152 ALS(ph)TDCTPSGDLSPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSTDCTPSGDLSPLSR 17 0 J3KNM6;F8VVT9;Q99490-2;Q99490 J3KNM6 AGAP2 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2" 1 ALS(0.974)T(0.026)DCTPSGDLSPLSR;ALS(0.82)T(0.18)DCTPSGDLSPLSR 152.94 2.03E-07 341410000 84366 96694 124035 95089 114627 135164 107956 104074 113240 116417 TRUE FALSE 87696.83482 113300.4423 127267.454 113897.3204 95142.74348 103774.2094 99494.12663 102679.0583 109164.5145 139226.6822 0.629885259 0.813783971 0.914102469 0.818071066 0.683365731 0.745361505 0.714619677 0.737495548 0.78407754 1 17.0870762 -1.981006964 6.016268809 1.183353793 0.761462262 0.479599027 0.074961352 0.045531466 0.00014374 0.017925811 0.017708587 0.010447035 1.981006964 -0.421891531 ALS(ph)VGNIDDALQCYSEAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSVGNIDDALQCYSEAIK 19 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 ALS(1)VGNIDDALQCYSEAIK;ALS(1)VGNIDDALQCYSEAIK 98.035 0.00065754 20810900 24297 18027.5 20601 22779 31982 28092 24752 26774 25991 22007 TRUE FALSE 25256.26432 21123.58289 21137.87898 27284.61821 26545.71106 21568.05874 22811.87356 26415.13832 25055.58899 26318.8503 0.959626429 0.802602798 0.803145986 1.036694913 1.008619706 0.819490916 0.866750382 1.003658519 0.952001653 1 14.68380885 2.519754937 0.171703785 1.032475751 0.8183258 0.127565316 0.082260554 13.56026502 1.257802572 0.46971415 0.908180516 330.9443237 -2.519754937 -0.214149951 ALS(ph)YAS(ph)LDKEDLLSPINQNTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 2 ALS(0.966)Y(0.224)AS(0.811)LDKEDLLSPINQNTLQR 62.284 0.026431 135030000 155070 82606 125970 80923 159510 163760 156080 131190 141840 92632 TRUE FALSE 161192.2833 96792.93791 129252.8817 96929.32787 132396.5472 125729.2218 143846.0418 129431.6126 136735.2061 110781.4669 1.455047382 0.873728618 1.16673741 0.87495978 1.195114589 1.134930105 1.298466665 1.168350775 1.234278711 1 16.75735702 ALSAAVADSLTNS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSAAVADSLTNSPR 15 0 Q14687;Q14687-2;Q14687-3;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 1 ALSAAVADSLTNS(1)PR;ALSAAVADSLTNS(1)PR 242.1 6.86E-18 449780000 642620 591040 602320 585620 693250 790060 724970 631230 598270 580750 TRUE FALSE 667991.1338 692546.5223 618016.954 701453.8881 575411.6126 606580.5385 668144.957 622769.3943 576738.3796 694536.8434 0.961779264 0.997134319 0.889826018 1.009959219 0.828482489 0.873359771 0.96200074 0.896668622 0.830392779 1 19.4056917 3.249679918 24.99999604 0.896852068 0.9616469 0.239185886 0.057687707 321.8528444 723631.0518 0.015439839 0.020710925 1776.969272 -3.249679918 0.064794833 ALSAIADLLTNEHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALSAIADLLTNEHER 15 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ;;;; 272.97 1.95E-33 982395000 1069901 1455412 1206819 1212806 1277347 1518479 1267139 1305731 1183728 1445471 FALSE TRUE 1112141.518 1705367.689 1238269.695 1452695.407 1060224.013 1165835.265 1167817.334 1288229.812 1141125.861 1728683.367 0.643345993 0.986512465 0.716307982 0.840347882 0.613313018 0.67440648 0.675553057 0.745208658 0.660112709 1 20.72124221 5.049660931 15.5230428 0.752385524 7.65E-06 0.066677596 0.128474986 4212754.099 35247806.6 0.029062752 94279915.85 112114.2796 -5.049660931 -0.752377869 ALSAS(ph)HTDLAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALSASHTDLAH 11 0 Q07866-6;Q07866-4;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ALSAS(0.984)HT(0.016)DLAH;ALSAS(0.985)HT(0.015)DLAH;ALSAS(0.998)HT(0.002)DLAH;ALSAS(1)HTDLAH;ALSAS(0.997)HT(0.002)DLAH;ALS(0.014)AS(0.976)HT(0.01)DLAH 205.07 2.00E-08 14320550000 5401590 10309320 9983620 9525540 9973690 11573830 8623940 9485230 8442760 11338370 TRUE FALSE 5614848.944 12079865.51 10243801.34 11409663.38 8278365.736 8885983.386 7947973.048 9358096.007 8138906.717 13559906.52 0.414077261 0.890851681 0.755447785 0.841426404 0.610503157 0.655313027 0.586137747 0.690129832 0.600218498 1 23.6928439 -1.15506043 5.074941176 1.000016472 0.680288595 0.365024913 0.129493561 2.30E-05 3.83E-06 0.119443293 0.028151605 0.069974462 1.15506043 -0.319727877 ALSCHPDKNPDNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSCHPDKNPDNPR 14 1 H0YLQ7;Q9NVM6;S4R343;H0YK99 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 0 73.887 0.020779 86145000 18946 27805 24073 20238 26548 37851 22306 25700 27404 32899 FALSE TRUE 19694.00271 32580.29246 24700.36216 24241.016 22035.38044 29060.67889 20557.59743 25355.53354 26417.73539 39344.92916 0.500547418 0.828068398 0.627790231 0.61611538 0.560056427 0.738613069 0.522496745 0.644442221 0.671439394 1 15.26389009 0.657177159 2.604930079 0.999974341 0.632776753 0.589839678 0.092027937 1.865529893 13.37985058 0.081741528 0.021713367 4.541268279 -0.657177159 -0.367197587 ELPSFLGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPSFLGKR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 116.52 0.0020858 2285650000 1864880 2805500 2664400 2188620 3410800 3523400 1808530 2632100 2773600 4401100 FALSE TRUE 1938506.902 3287322.801 2733836.453 2621522.504 2831033.434 2705143.748 1666772.693 2596821.005 2673778.678 5263411.281 0.36829858 0.624561264 0.51940392 0.498065297 0.537870458 0.513952569 0.316671566 0.493372238 0.507993492 1 22.3275667 0.6046365 3.332982525 0.99999784 0.485717878 0.781343257 0.081547929 4.369526289 36.30130739 0.077544706 0.02007043 4.023801055 -0.6046365 -0.514279962 ALSFLVNDCSLIHNNVCMAAVFVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALSFLVNDCSLIHNNVCMAAVFVDR 25 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 ;; 303.8 1.82E-63 141499000 61267.4 67832.7 64480 76121.7 81416 82045 74682.7 72053 72831.1 79027 FALSE TRUE 63686.28426 79482.43856 66160.40177 91178.34506 67576.9374 62991.29215 68828.87483 71087.24739 70209.92294 94510.82759 0.673851726 0.840987648 0.700029864 0.964739675 0.715017942 0.666498154 0.728264439 0.752159823 0.74287703 1 16.528192 -2.003939545 5.109143119 1.255651651 0.755926344 0.433169253 0.084450958 0.048490197 3.74E-05 0.016122842 0.018510794 0.009909699 2.003939545 -0.499725307 ALSGRAS(ph)PVPAPSSGLHAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALSGRASPVPAPSSGLHAAVR 21 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 ALS(0.396)GRAS(0.604)PVPAPSSGLHAAVR;ALS(0.243)GRAS(0.757)PVPAPSSGLHAAVR;ALS(0.016)GRAS(0.984)PVPAPSSGLHAAVR 207.6 2.16E-22 618580000 109487 341747 246725 215238 300169 296883 171324 265422 235218 392753 TRUE FALSE 113809.6313 400439.3888 253154.8562 257811.434 249146.3806 227936.4226 157895.1772 261864.4522 226752.5501 469705.4306 0.242300012 0.852533019 0.538965146 0.548878972 0.530431126 0.485275255 0.33615787 0.557507823 0.482754798 1 18.84139675 -0.978529588 4.947515972 1.000004276 0.516069499 0.489768943 0.150368828 6.62E-06 1.37E-06 0.135863244 0.032022991 0.105067987 0.978529588 -0.483934778 ALSHDS(ph)IFIPESGQDATRPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSHDSIFIPESGQDATRPVR 21 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 ALS(0.325)HDS(0.675)IFIPESGQDATRPVR;ALS(0.087)HDS(0.913)IFIPESGQDATRPVR 285.4 1.45E-45 1219390000 80180 251024 230725 192416 232040 293810 206183 258780 207189 234758 TRUE FALSE 83345.56831 294135.4193 236737.883 230475.3105 192597.9237 225577.0802 190021.8377 255311.4774 199732.3084 280754.3354 0.296862979 1.047661184 0.843220756 0.82091452 0.686001601 0.803467843 0.676826014 0.909376794 0.711413087 1 18.09894878 -5 0.174954679 1.879420046 0.724139057 0.141561952 0.185444357 282.2704239 2.692601882 86.61964916 0.579746047 1.00E-05 5 -1.155280989 ALSQTVPSSGTNGVSLPADCTGAVPAAS(ph)PDTAAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ALSQTVPSSGTNGVSLPADCTGAVPAASPDTAAWR 35 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EN31 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.846)PDT(0.154)AAWR;ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.956)PDT(0.043)AAWR;ALSQTVPSSGTNGVSLPADCTGAVPAAS(0.944)PDT(0.056)AAWR 187.62 1.28E-20 886760000 312810 343503 310035 351738 341259 378734 318625 336111 324079 354505 TRUE FALSE 325159.9803 402496.9682 318114.7668 421310.7266 283251.9171 290778.7683 293650.3399 331605.9818 312415.4601 423963.4673 0.766952828 0.949367102 0.750335327 0.993742997 0.668104539 0.685858077 0.692631235 0.782156972 0.736892407 1 18.69358043 3.221283484 24.99997882 0.744414881 0.862921286 0.162978575 0.111897867 354.1592471 512466.594 0.029819806 0.03572069 1664.49879 -3.221283484 0.118506405 ALSS(ph)AGPIPIRPPIVPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSSAGPIPIRPPIVPVK 18 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 ALS(0.318)S(0.682)AGPIPIRPPIVPVK 213.93 1.72E-17 231080000 295770 254580 302470 227210 432840 354010 345450 345250 408420 284010 TRUE FALSE 307447.228 298302.1346 310352.6167 272151.4598 359266.0114 271796.5426 318372.7263 340622.4885 393721.044 339656.3218 0.905171517 0.878246968 0.913725424 0.801255394 1.057733916 0.800210463 0.93733785 1.002844542 1.159174786 1 18.37371618 1.624903306 2.813962438 1.079540218 0.896005833 0.474696495 0.077267317 0.175379319 3.232606857 0.047329531 0.019246754 42.16026247 -1.624903306 -0.183534385 ALSS(ph)DSILSPAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALS(0.248)S(0.748)DS(0.004)ILSPAPDAR;ALS(0.292)S(0.703)DS(0.005)ILSPAPDAR 434.95 8.93E-154 14553400000 582380 666950 662830 654790 752150 830330 721210 721280 681330 677060 TRUE FALSE 605372.8121 781493.4743 680103.8943 784305.5076 624299.8117 637498.4413 664679.6757 711612.4214 656809.0664 809716.9439 0.747635105 0.96514403 0.839927952 0.96861689 0.771009939 0.78731024 0.82087905 0.878840966 0.811158852 1 19.62705814 -1.338136288 3.1779907 1.001170154 0.848111086 0.299851416 0.071465693 20104772.62 25161056.15 221841.7676 0.0164383 0.045905393 1.338136288 -0.153059068 ALSSDSILS(ph)PAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 ALSSDS(0.001)ILS(0.999)PAPDAR;ALSSDS(0.001)ILS(0.999)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR;ALSSDSILS(1)PAPDAR 363.83 7.72E-85 2459600000 1434350 1583070 1485270 1863460 1862060 2244430 1858690 1743750 1659910 2193210 TRUE FALSE 1490979.246 1854949.958 1523977.356 2232046.826 1545547.706 1723195.147 1713001.021 1720377.883 1600170.163 2622927.508 0.568440889 0.707205957 0.581021531 0.850975416 0.5892453 0.656973989 0.653087444 0.655899897 0.610070297 1 21.3227465 -1.089131721 4.379686815 1.000033647 0.656210146 0.642021722 0.077791041 25506181093 5304863670 9454955.762 0.016603922 0.081445722 1.089131721 -0.343823501 ALSSEGKPYVTKEELYQNLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSSEGKPYVTKEELYQNLTR 21 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 164.58 8.89E-12 802260000 554120 485260 602920 323000 825160 749450 464550 568990 716160 640330 FALSE TRUE 575997.0855 568599.6302 618632.5905 386888.4359 684899.5979 575401.5955 428137.3571 561363.6197 690385.5415 765790.4036 0.752160229 0.742500334 0.807835391 0.505214526 0.894369523 0.751382614 0.559079031 0.733051259 0.901533289 1 19.54659006 1.124068459 3.335251601 0.994170949 0.713965834 0.446874211 0.106278704 0.194586588 3.919702178 0.097122994 0.025730174 13.30664158 -1.124068459 -0.280205116 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_MDA-MB-175_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(0.168)S(0.832)PPLS(1)PALPK;ALSSGGSIT(0.021)S(0.979)PPLS(1)PALPK;ALSSGGSIT(0.06)S(0.94)PPLS(1)PALPK;ALSSGGSIT(0.011)S(0.989)PPLS(1)PALPK 232.54 1.17E-20 658710000 907000 581256 751517 611355 999640 998250 944760 870190 894360 696956 TRUE FALSE 942809.0604 681082.1965 771102.1504 732279.1943 829721.5499 766421.5661 870707.2425 858526.5264 862172.1583 833511.1842 1.131129466 0.817124244 0.925125139 0.878547533 0.995453409 0.919509637 1.044625746 1.030012005 1.03438583 1 19.66884203 2.237325056 24.99999978 1.03031527 0.937132659 0.210095073 0.077759586 44.74440301 905316.3819 0.026586675 0.020732605 172.7130113 -2.237325056 -0.093182611 ALSSGGSITS(ph)PPLSPALPK ddPTM_MDA-MB-175_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(0.002)S(0.998)PPLSPALPK;ALSSGGSITS(1)PPLSPALPK;ALSSGGSIT(0.025)S(0.975)PPLSPALPK;ALSSGGSITS(1)PPLSPALPK;ALSSGGSITS(1)PPLSPALPK 314.41 1.30E-61 3387421000 3444427 2769450 3169710 2720994 3817038 3628135 3428329 3244444 3310333 2900205 TRUE FALSE 3580415.638 3245081.494 3252315.247 3259198.492 3168219.244 2785555.631 3159607.615 3200957.535 3191194.762 3468444.642 1.032282769 0.935601351 0.937686941 0.939671475 0.913440914 0.803113764 0.910958064 0.922879811 0.92006507 1 21.72585743 7.999999255 0.851080266 0.908623605 44.76483926 0.350347348 0.045884174 704.8704197 1.925499454 0.014658151 59862.39635 99999828.44 -7.999999255 43.85621565 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 ALS(0.001)S(0.004)LHGDDQDS(0.995)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALS(0.004)S(0.004)LHGDDQDS(0.991)EDEVLTIPEVK;ALS(0.067)S(0.067)LHGDDQDS(0.865)EDEVLT(0.001)IPEVK;ALSSLHGDDQDS(0.999)EDEVLTIPEVK;ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(0.999)EDEVLTIPEVK;ALS(0.006)S(0.006)LHGDDQDS(0.988)EDEVLTIPEVK 179.81 3.05E-17 4556414000 2227863 2508150 3033010 2576559 3583430 3686360 3248990 2989500 3146760 2419416 TRUE FALSE 2315820.752 2938905.252 3112052.732 3086194.68 2974319.849 2830258.757 2994325.674 2949430.642 3033508.722 2893454.243 0.800365431 1.015708218 1.075549316 1.066612575 1.027947774 0.978159155 1.034861941 1.019345873 1.048403903 1 21.4643614 4.735099206 4.843756999 1.031681546 0.788405955 0.863902372 0.027356422 0.058660516 4.051027952 0.006853386 0.047977399 54337.44411 -4.735099206 -0.24327559 ALSSQHQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ALSSQHQAR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;;;; 166.19 6.09E-05 858487000 196494 844736 472254 594216 1173418 1074120 546312 549866 436394 1737357 FALSE TRUE 204251.7348 989812.8369 484561.3272 711750.1512 973960.8275 824671.9084 503490.6379 542495.9457 420688.2652 2077758.84 0.09830387 0.476384852 0.23321346 0.342556671 0.468755473 0.396904536 0.242323906 0.261096685 0.202472133 1 20.98659678 -1.063925684 4.330976211 1.000056857 0.308335481 0.770232743 0.114255594 12618429.12 6202454.363 6867.5619 0.025851911 0.086312623 1.063925684 -0.691721376 ALSTGEK ddPTM_MDA-MB-175_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 ;; 117.93 0.01191 1592716000 2292160 1942280 2265420 1703150 2768730 2676520 2261420 2195640 2315820 1894640 FALSE TRUE 2382656.247 2275851.481 2324458.706 2040027.987 2298102.264 2054938.793 2084163.991 2166211.037 2232474.091 2265858.433 1.051546828 1.00441027 1.025862284 0.900333382 1.014230294 0.906914026 0.919812095 0.956022232 0.98526636 1 21.1116263 3.769103922 23.79344628 0.951486663 1.024986887 0.436455249 0.037667224 334.7026246 260733.865 0.009181162 0.016548144 5876.299492 -3.769103922 0.073500224 ALSTGLDYS(ph)PPSAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALSTGLDYSPPSAPR 15 0 P54253 P54253 ATXN1 Ataxin-1 1 ALSTGLDYS(1)PPSAPR;ALSTGLDYS(1)PPSAPR 276.34 1.62E-33 579110000 413460 462710 396430 426700 463440 514290 413180 442870 399180 486720 TRUE FALSE 429783.7201 542176.8431 406761.2915 511099.9864 384664.6343 394853.9416 380793.872 436934.052 384813.5898 582083.4652 0.738354112 0.931441753 0.698802347 0.878052748 0.660841026 0.678345916 0.654191185 0.750638144 0.661096926 1 19.15086651 4.214030435 24.98110537 0.734034217 0.834898109 0.074758675 0.114800154 402.5209751 409920.7812 0.026419145 0.057111318 16369.31233 -4.214030435 0.100863892 ALSVGNIDDALQCYSEAIKLDPHNHVLYSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSVGNIDDALQCYSEAIKLDPHNHVLYSNR 31 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 136.49 8.75E-07 149730000 79507 92883 100460 53275 146770 124900 50909 78448 113660 160340 FALSE TRUE 82645.99775 108834.9327 103078.0701 63812.63599 121822.0878 95893.86788 46918.61955 77396.53288 109569.3988 191755.5531 0.430996633 0.567571217 0.537549335 0.332781163 0.635298878 0.500083916 0.244679326 0.403620816 0.571401438 1 17.54890883 0.871672691 4.330833199 0.999936668 0.454250443 0.694475305 0.107970955 0.473537087 15.11629137 0.107906275 0.027453687 7.44170913 -0.871672691 -0.545686225 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 ALSYAS(1)LDKEDLLSPINQNTLQR 308.86 2.46E-73 802720000 369790 236130 319640 191140 358350 405940 335270 282050 328700 213970 TRUE FALSE 384389.5947 276683.4907 327970.081 228946.9215 297437.795 311666.5871 308990.6613 278269.5811 316870.1512 255893.3248 1.502147799 1.08124544 1.2816672 0.894696732 1.162350738 1.217955128 1.207497935 1.087443689 1.238290024 1 17.96518299 4.743840769 24.41314275 1.135293131 1.502148017 0.496218248 0.112344993 332.2196821 1535972.341 0.025182371 0.214563448 55442.2401 -4.743840769 0.366854885 ALTAHLYSLLQTQHALGDAFADLSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALTAHLYSLLQTQHALGDAFADLSQK 26 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 154.14 4.04E-08 601360000 694570 653750 845860 716700 995080 963230 967240 855300 905800 610010 FALSE TRUE 721992.1599 766026.477 867903.8065 858461.1209 825936.657 739534.4304 891425.2014 843836.1025 873200.4349 729529.7802 0.989667838 1.0500277 1.189675638 1.176732115 1.132149337 1.013713834 1.221917495 1.15668493 1.19693597 1 19.47660735 4.419153859 4.730190991 1.143397525 1.001877556 0.31078705 0.070895729 0.192207007 8.628481923 0.016776836 0.051707631 26251.48402 -4.419153859 -0.141519969 ALTHIDHSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALTHIDHSLSR 11 0 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;;;; 268.58 1.23E-21 855817000 313435 397652 405569 439046 488196 522980 380879 391135 382804 525639 FALSE TRUE 325809.6558 465945.6377 416138.4613 525887.9884 405212.6183 401525.8208 351024.7087 385892.4751 369026.9588 628627.8981 0.518286982 0.741210562 0.66197899 0.836564826 0.644598529 0.638733696 0.558398235 0.613864698 0.587035606 1 19.26184677 -1.195224719 4.192864231 1.000148598 0.647148947 0.604955115 0.086154956 19.44875385 48946735.79 13517.2521 0.020500611 0.063793331 1.195224719 -0.352999652 ALTHNGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALTHNGTPR 9 0 Q9HB90 Q9HB90 RRAGC Ras-related GTP-binding protein C 1 ALTHNGT(1)PR;ALTHNGT(1)PR;ALTHNGT(1)PR;ALTHNGT(1)PR 154.15 0.00028105 1881670000 1379710 1794840 1619200 1887290 1954120 2459540 1925720 1956720 1855140 2203580 TRUE FALSE 1434182.016 2103089.808 1661397.682 2260590.329 1621959.38 1888349.11 1774777.034 1930493.369 1788373.874 2635329.311 0.544213587 0.798036814 0.630432666 0.857801839 0.615467438 0.716551477 0.673455506 0.732543505 0.678614952 1 21.32955182 -1.617964847 2.527646626 1.032440777 0.700032928 0.533800612 0.085595484 5694150.45 4880814.318 1215174.14 0.01877219 0.024101005 1.617964847 -0.33240785 ALTNLPHTDFTLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALTNLPHTDFTLCK 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 179.39 1.87E-06 368540000 410720 347110 439580 341640 547790 487710 506720 420460 444900 379510 FALSE TRUE 426935.5427 406723.4424 451035.8159 409215.3723 454676.8515 374446.7438 467001.9623 414824.4214 428888.1359 453867.7183 0.940660738 0.896127717 0.993760511 0.901618149 1.001782751 0.825012947 1.028938485 0.913976484 0.944962857 1 18.79191235 -4.999998784 0.303432668 1.524803816 0.935295251 0.097259155 0.056466798 635.8264197 5.84046454 212.5227028 0.04939879 1.00E-05 4.999998784 -0.589508565 ALTQPS(ph)PVSTPSSVQFFLQEDDSADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALTQPSPVSTPSSVQFFLQEDDSADR 26 0 P04920-2;P04920-3;P04920;C9J9M9 P04920-2 SLC4A2 Anion exchange protein 2 1 ALT(0.015)QPS(0.721)PVS(0.2)T(0.057)PS(0.003)S(0.003)VQFFLQEDDSADR;ALT(0.025)QPS(0.811)PVS(0.137)T(0.026)PS(0.001)S(0.001)VQFFLQEDDSADR 91.722 0.0063026 107098000 41387 49545 40197 49164 43147 60530 50637 44874 39569 58322 TRUE FALSE 43020.99072 58053.96834 41244.56684 58888.49246 35812.88835 46472.82484 46667.93962 44272.53743 38144.91942 69749.07926 0.616796539 0.832325946 0.591327761 0.844290607 0.513453206 0.666285854 0.669083236 0.634740098 0.546887784 1 16.08988655 -1.560486117 8.390054636 1.000069677 0.66065921 0.500758829 0.102620032 0.000123358 6.46E-06 0.091642511 0.021595952 0.027511476 1.560486117 -0.339410467 ALTVPELTQQMFDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 179.67 1.54E-06 270410000 247880 214960 227120 173530 308770 294340 271970 252400 251280 220290 FALSE TRUE 257666.4938 251877.7078 233038.9338 207853.7161 256285.3857 225983.9958 250652.2807 249016.9908 242236.4819 263451.6078 0.978041075 0.956068213 0.884560682 0.788963551 0.972798716 0.857781805 0.951416781 0.945209608 0.919472399 1 18.00717846 2.130118597 21.5133664 0.949082305 0.905243414 0.142596423 0.056690299 8.125909306 1577.097435 0.021565642 0.015927279 134.9331308 -2.130118597 -0.043838891 ALVADSHPESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALVADSHPESER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 158.04 6.71E-05 2581500000 1576960 2070330 1813640 1811720 2038300 2149750 1812540 1870150 1844730 2188800 FALSE TRUE 1639219.598 2425893.073 1860904.948 2170072.809 1691830.494 1650503.142 1670468.379 1845083.698 1778338.528 2617653.453 0.626217193 0.926743404 0.710905772 0.829014554 0.646315689 0.63052775 0.6381549 0.704861714 0.679363621 1 21.31984268 -1.134523119 3.626978925 1.000205286 0.712200211 0.471409824 0.092029936 25735832.03 44336950.68 63329.2601 0.022203775 0.073362966 1.134523119 -0.288005075 ALVAT(ph)PGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALVATPGKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK;ALVAT(1)PGKK 122.7 0.00033898 9358870000 36439100 16137900 21948800 13324400 27064400 27007700 25926300 20256300 20659400 11295610 TRUE FALSE 37877743.81 18909458.79 22520803.76 15959926.55 22464002.96 20735570.98 23894128.86 19984797.43 19915872.23 13508768.51 2.803937589 1.399791459 1.667124856 1.181449407 1.66292012 1.534971227 1.76878661 1.47939447 1.474292213 1 23.68739283 4.741158974 24.96103194 1.49718595 2.803938063 0.766838102 0.221077257 102.3843394 983494.464 0.048079214 0.329896294 55100.93573 -4.741158974 1.306752113 ALVEFESNPEET(ph)REPGSPPSVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEET(0.752)REPGS(0.247)PPS(0.001)VQR 115.45 0.00092364 718030000 796250 1038500 830620 886360 910960 955290 819360 804300 755510 961720 TRUE FALSE 827686.5648 1216854.297 852266.6396 1061679.362 756115.3446 733438.3751 755136.4222 793519.6741 728319.3427 1150150.621 0.719633194 1.0579956 0.741004373 0.923078546 0.657405501 0.637688979 0.656554375 0.689926745 0.633238229 1 20.13339137 3.233633124 24.99888771 0.689626299 0.866009658 0.213545783 0.134725217 145.3184281 737251.0421 0.035121059 0.043237371 1712.510033 -3.233633124 0.176383359 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 ALVEFESNPEETREPGS(0.999)PPS(0.001)VQR;ALVEFESNPEETREPGS(1)PPSVQR;ALVEFESNPEETREPGS(0.999)PPS(0.001)VQR;ALVEFESNPEETREPGS(1)PPSVQR 297.62 5.90E-62 8079200000 2800850 3321910 3037900 3047490 3185650 3487300 2866750 3111590 2894170 3157740 TRUE FALSE 2911429.721 3892422.202 3117070.17 3650274.426 2644154.351 2677427.426 2642046.644 3069884.226 2790009.387 3776438.694 0.770945845 1.030712403 0.825399383 0.966591734 0.700171396 0.708982097 0.699613275 0.812904557 0.738793772 1 21.84859494 3.23812726 25 0.762366303 0.902647137 0.230790606 0.106788428 14.06434668 811388.3167 0.027933564 0.035392765 1730.323314 -3.23812726 0.140280834 ALVHERDEAAYGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALVHERDEAAYGELR 15 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 210.9 9.90E-10 2178270000 1247110 1670380 1560950 1291560 1864490 1793130 1173130 1492000 1520970 2212650 FALSE TRUE 1296346.866 1957254.771 1601629.639 1547026.713 1547564.656 1376702.733 1081177.005 1472002.18 1466230.587 2646176.404 0.489894349 0.739653928 0.605261855 0.584627204 0.584830495 0.520261133 0.40858085 0.556275152 0.554094045 1 21.33547781 -0.683145357 6.513739571 1.000000001 0.560239744 0.727907642 0.08063285 2.43E-09 1.86E-10 0.081396196 0.019185267 0.207421917 0.683145357 -0.439760257 ALVHQLS(ph)NESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALVHQLSNESR 11 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 ALVHQLS(1)NESR;ALVHQLS(1)NESR 159.52 1.84E-05 199962000 72350 86762 109562 89324 98977 92279 97849 97133 107352 94274 TRUE FALSE 75206.43387 101662.6986 112417.2757 106992.0206 82152.92489 70848.60075 90179.3397 95831.09101 103488.4225 112745.1853 0.667047854 0.901703237 0.997091587 0.94897197 0.728660161 0.628395798 0.799850916 0.849979454 0.917896602 1 16.7827063 1.091807195 2.104210716 0.997572001 0.817147689 0.231177087 0.111141879 0.498977638 4.349355858 0.114250837 0.032095681 12.35398855 -1.091807195 -0.180424312 ALVLDCHYPEDEVGQEDEAESDIFSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALVLDCHYPEDEVGQEDEAESDIFSIR 27 0 Q07021;I3L3Q7;I3L3B0 Q07021 C1QBP "Complement component 1 Q subcomponent-binding protein, mitochondrial" 0 ;;; 200.91 4.72E-25 249182000 80515 155381 105705 149122 97724 173906 105885 109877 103175 176010 FALSE TRUE 83693.79437 182066.4781 108459.7591 178617.8865 81112.90939 133518.9671 97585.45702 108404.2785 99461.7519 210495.7896 0.397603176 0.864941187 0.515258568 0.848558001 0.385342194 0.634307068 0.463598142 0.514994997 0.472511836 1 17.68343185 -1.681733205 8.425106569 1.000895288 0.570073256 0.394675458 0.161056441 0.002514504 9.50E-05 0.144776595 0.03406354 0.020809747 1.681733205 -0.430822032 ALVTGYFMQVAHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALVTGYFMQVAHLER 15 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 141.55 1.61E-05 0 168070 161310 194260 191310 228630 215620 207670 179610 150860 180460 FALSE TRUE 174705.5334 189013.7377 199322.5752 229150.547 189767.5543 165545.5228 191392.2828 177202.6217 145430.5781 215817.6819 0.809505189 0.875802835 0.923569253 1.061778372 0.879295675 0.767061908 0.88682392 0.821075549 0.673858494 1 17.71945354 2.995422177 24.82073294 0.82378709 0.922025809 0.151808996 0.097498169 310.4501877 1683262.79 0.028142816 0.03282496 989.514534 -2.995422177 0.098238719 ALVVPEPEPDSDS(ph)NQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALVVPEPEPDSDSNQER 17 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.004)DS(0.996)NQER;ALVVPEPEPDS(0.002)DS(0.998)NQER;ALVVPEPEPDS(0.038)DS(0.962)NQER;ALVVPEPEPDS(0.011)DS(0.989)NQER;ALVVPEPEPDSDS(1)NQER 334.04 4.33E-72 3321760000 1487340 1694000 1614470 1705460 1764890 1988800 1624200 1716190 1640350 1741750 TRUE FALSE 1546061.332 1984931.323 1656544.415 2042794.898 1464894.628 1526931.341 1496890.96 1693187.28 1581314.124 2083012.565 0.742223719 0.952913754 0.795263765 0.980692547 0.703257701 0.733039909 0.718618306 0.812855049 0.759147665 1 20.99024011 ALVVPEPEPDSDS(ph)NQERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALVVPEPEPDSDSNQERK 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 ALVVPEPEPDS(0.024)DS(0.976)NQERK 205.68 5.73E-16 56519000 128300 79934 103540 94993 125430 127840 143560 106570 128770 63128 TRUE FALSE 133365.3831 93662.0427 106238.3375 113782.3319 104109.4534 98151.09743 132307.3921 105141.6035 124135.5929 75496.72294 1.76650559 1.240610705 1.407191376 1.507116169 1.378993012 1.300070965 1.752491856 1.392664468 1.644251406 1 16.2041264 4.761759559 23.50583897 1.428645313 1.766506449 0.221531138 0.199340336 4303.949141 4360727.04 0.043709638 2.233617185 57777.60818 -4.761759559 0.337861136 ALWEDEGVR ddPTM_MDA-MB-175_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 ; 90.709 0.026165 214853000 298160 576570 413180 544690 404170 558290 379980 452500 359420 599800 FALSE TRUE 309931.587 675591.4124 423947.8102 652428.0563 335469.3278 428635.6085 350196.1747 446434.9776 346484.5444 717319.3261 0.4320692 0.941827981 0.591016852 0.909536426 0.467670834 0.597552015 0.488201226 0.622365746 0.48302692 1 19.45225598 -1.11867579 4.331979423 1.000057477 0.622100609 0.319310228 0.168417598 22257196.24 5747626.622 12090.13448 0.037269774 0.076089409 1.11867579 -0.377956869 ALWFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALWFER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;; 126.68 0.040453 1084085000 705064 927670 836493 782477 1170460 1088520 827684 800687 775632 1311350 FALSE TRUE 732900.4711 1086990.106 858292.6948 937248.6151 971505.6273 835727.7267 762807.9653 789955.1004 747717.1558 1568283.925 0.467326394 0.693107982 0.547281446 0.597626871 0.6194705 0.532893128 0.486396598 0.503706687 0.476774099 1 20.58075534 -1.946199156 8.961295942 1.148711854 0.54869424 0.799730195 0.067977048 0.026312209 0.00015797 0.008574823 0.015807719 0.011318812 1.946199156 -0.600017613 ALWFQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALWFQGR 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 177.42 0.0016994 1130140000 583260 737850 644340 574640 1085670 863120 733430 630310 616820 1188540 FALSE TRUE 606287.5552 864569.9978 661132.0297 688302.0769 901128.2012 662673.4607 675941.8401 621861.7254 594620.7687 1421411.657 0.426539034 0.608247437 0.465123546 0.484238379 0.633967082 0.466207982 0.475542632 0.437495867 0.418331147 1 20.43889301 -1.241523382 3.508225668 1.001104302 0.491997704 0.829275371 0.069332288 48267484.67 76064261.33 579722.9821 0.01713837 0.057342499 1.241523382 -0.509106597 ALYDYAGQEADELS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR 263.2 6.57E-27 318075000 249113 336276 293211 313995 323808 373633 301870 286480 313037 360940 TRUE FALSE 258948.1736 394028.7871 300852.3195 376102.2738 268767.2318 286862.3982 278208.6406 282640.2042 301770.8595 431659.2824 0.599890201 0.912823616 0.696967103 0.871294304 0.622637443 0.664557464 0.644509807 0.654776153 0.699095031 1 18.71953349 -1.128404631 4.410646679 1.000041856 0.707545511 0.443877922 0.098255384 3.96E-05 7.82E-06 0.09313379 0.021948708 0.074403843 1.128404631 -0.292496345 ALYDYAGQEADELSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ; 166.38 1.56E-08 159506000 126603 118260 122592 102581 153208 160323 118450 111030 122075 130453 FALSE TRUE 131601.3842 138570.2351 125786.8482 122871.2156 127165.7589 123090.413 109165.5795 109541.8245 117681.5446 156012.7677 0.843529579 0.888198044 0.806259963 0.78757154 0.81509841 0.788976536 0.699722088 0.702133717 0.75430714 1 17.25130457 3.773570056 0.986865142 0.762208777 0.870953679 0.035620514 0.082864825 1.182829546 2.084033894 0.029129214 0.098457234 5937.041111 -3.773570056 0.108744903 ALYDYEGQEHDELSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ALYDYEGQEHDELSFK 16 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;H0Y923 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;;;; 246.03 3.64E-20 2699584000 3326770 2823787 3307110 2749970 4179460 3889060 3758160 3411180 3707040 2923250 FALSE TRUE 3458113.448 3308750.451 3393296.003 3293905.858 3469036.882 2985884.754 3463585.599 3365458.712 3573624.355 3496004.868 0.989161508 0.946437598 0.970621075 0.942191439 0.992286056 0.854084839 0.990726767 0.962658474 1.022202339 1 21.73727576 1.438854328 2.227536469 1.010255488 0.952300453 0.234688977 0.038779161 0.407937089 3.743311366 0.031184426 0.009948652 27.46972601 -1.438854328 -0.057955035 ALYESELADARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALYESELADARR 12 1 Q03252 Q03252 LMNB2 Lamin-B2 0 146.17 0.00052189 0 83139 108310 85539 84113 124310 134650 87196 104090 95971 117580 FALSE TRUE 86421.39192 126911.4 87768.21661 100750.3003 103179.8306 103379.5781 80361.34968 102694.8438 92517.02246 140617.5498 0.614584681 0.902528882 0.624162608 0.716484539 0.733762114 0.735182616 0.571488764 0.730313136 0.657933683 1 17.10141714 -0.757541234 6.06316935 1.000000009 0.701512773 0.518241476 0.08716633 9.85E-09 2.01E-09 0.077773052 0.018331284 0.174766732 0.757541234 -0.298487235 ALYETELADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ALYETELADAR 11 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ; 110.14 0.0042691 251680000 246380 315000 264770 301150 313100 349830 314680 278000 256810 306580 FALSE TRUE 256107.2726 369098.7996 271670.1237 360716.5712 259879.3738 268587.2842 290014.5593 274273.8647 247567.4583 366648.4812 0.698509024 1.006683018 0.740955268 0.983821261 0.708797083 0.732547107 0.790988029 0.748056732 0.675217466 1 18.48403804 3.206688557 24.99999313 0.761635929 0.85982487 0.091525324 0.120857315 364.8940396 286216.7272 0.031681723 0.037869791 1609.491018 -3.206688557 0.098188941 ALYETELADARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ALYETELADARR 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 171.26 6.24E-05 330970000 109650 152810 123970 114050 167480 176040 101430 117200 112430 193270 FALSE TRUE 113979.0667 179053.9288 127200.76 136608.7496 139011.8094 135157.3779 93479.65156 115629.1257 108383.6663 231137.5561 0.493122228 0.774663935 0.550324933 0.591027922 0.601424588 0.584748667 0.404432984 0.50026109 0.468914131 1 17.81839217 -1.765591049 6.613471439 1.012623385 0.55184038 0.66871971 0.094574729 0.018138569 0.000642906 0.094358702 0.022431131 0.01715572 1.765591049 -0.460783005 AMASVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AMASVAR 7 0 H7C2G2;Q93070 H7C2G2 ART4 NAD(P)(+)--arginine ADP-ribosyltransferase;Ecto-ADP-ribosyltransferase 4 0 77.748 0.086555 39026000 68057 56689 62226 53614 81167 70163 58938 47407 54829 79503 FALSE TRUE 70743.94291 66424.89477 63847.66068 64218.68918 67370.26233 53868.70658 54318.28555 46771.58671 52855.715 95080.09067 0.744045808 0.69862044 0.671514512 0.675416785 0.708563295 0.566561372 0.571289795 0.491917776 0.555907284 1 16.53685566 -1.024807386 4.80310998 1.000005873 0.623858798 0.668932271 0.077595555 7.54E-06 1.53E-06 0.087497643 0.020622965 0.094447967 1.024807386 -0.376147074 AMAVLTDHPYASLTLPDDAAADCLFLRPGLPGVPPFLLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AMAVLTDHPYASLTLPDDAAADCLFLRPGLPGVPPFLLHR 40 1 O95865 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 231.53 3.16E-41 564010000 98734 131400 130840 203900 169260 196810 156720 154000 184450 186920 FALSE TRUE 102632.0946 153966.9278 134249.7979 244230.8114 140489.2457 151103.8602 144435.8769 151935.8819 177811.6805 223543.3952 0.45911486 0.688756327 0.600553632 1.092543178 0.628465205 0.675948668 0.646120082 0.679670637 0.795423548 1 17.7701954 -5 0.235111534 2.671648977 0.665671374 0.281863648 0.152335191 231.8404384 2.317008973 184.8667262 0.24982766 1.00E-05 5 -2.005977603 AMDQLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AMDQLAK 7 0 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ;; 141.78 0.0058941 604204000 1021660 945400 1053140 899810 1311940 1277910 1180250 1100550 1104780 1009200 FALSE TRUE 1061995.926 1107765.096 1080585.694 1077789.732 1088936.907 981134.7694 1087738.921 1085798.927 1065019.184 1206933.418 0.879912603 0.917834472 0.895315083 0.892998501 0.902234449 0.812915406 0.901241862 0.899634488 0.882417512 1 20.20291466 -1.168636257 3.921332617 1.000061299 0.888215557 0.613252174 0.026869751 30378.77279 13976471.67 1660.179731 0.006262104 0.06782093 1.168636257 -0.111845741 AMEGIFIKPSVEPSAGHDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AMEGIFIKPSVEPSAGHDEL 20 1 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 121.44 2.94E-05 46380000 39942 54808 56400 58972 70070 79001 52591 59849 59822 61422 FALSE TRUE 41518.941 64220.84765 57869.83033 70636.48559 58159.52643 60654.21502 48468.78 59046.82205 57669.01791 73456.4649 0.565218338 0.874270872 0.787811262 0.961610196 0.791755042 0.825716499 0.65983001 0.803834246 0.785077501 1 16.16460185 -1.949890559 2.189781135 1.163806062 0.789051835 0.283867076 0.102677089 11737394.47 4873624.314 9787911.648 0.024204575 0.011223012 1.949890559 -0.374754226 AMEVDERPTEQYSDIGGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AMEVDERPTEQYSDIGGLDK 20 1 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 200.74 1.21E-21 3489090000 3584020 2776260 3311800 2704900 4081270 3939850 3941080 3389940 3555640 2646580 FALSE TRUE 3725519.877 3253061.059 3398108.229 3239921.147 3387537.183 3024879.547 3632167.852 3344503.399 3427673.211 3165126.679 1.177052376 1.027782262 1.073608918 1.023630797 1.070269069 0.955689883 1.147558445 1.056672841 1.082949771 1 21.59383181 4.745962163 24.14621705 1.052961894 1.177052472 0.375907891 0.049344224 568.2751837 1853821.441 0.011069422 0.111572827 55713.72074 -4.745962163 0.124090579 AMGIMNSFVNDIFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 AMGIMNSFVNDIFER 15 0 Q16778;P33778;P23527;P06899;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;P57053;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;H2BFS;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type F-S;Histone H2B type 1-L 0 ;;;;;;;; 304.89 2.59E-44 25854036400 3585791.7 3727284.4 3290518.5 3446799.8 4127380.8 4461324 3408829.8 3512508 3087019.9 4125623.6 FALSE TRUE 3727361.525 4367416.501 3376272.115 4128566.513 3425810.086 3425249.113 3141636.813 3465428.576 2975918.657 4933960.555 0.755450208 0.885174588 0.684292482 0.836765205 0.694332686 0.69421899 0.636737318 0.70236244 0.603150071 1 22.23431475 3.221116341 24.99361669 0.699892505 0.789608179 0.062123551 0.112736985 467.9109859 670406.9176 0.029806348 0.035700421 1663.858313 -3.221116341 0.089715673 AMKDEEK ddPTM_MDA-MB-175_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 ;;; 114.89 0.0052918 3525990000 7615150 3061140 4904530 2986040 6672670 6137790 7650900 5136430 5759450 2730360 FALSE TRUE 7915802.002 3586866.983 5032346.081 3576669.8 5538451.937 4712381.292 7051202.466 5067584.557 5552168.52 3265321.766 2.424202749 1.098472751 1.541148604 1.095349878 1.69614278 1.443159857 2.15942041 1.551940336 1.700343463 1 21.63879373 AMKEYEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AMKEYEEEER 10 1 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 158.41 7.29E-06 2080960000 3653240 3161050 3738960 2606020 5043700 4593200 3477290 3536280 4203730 3712660 FALSE TRUE 3797472.736 3703935.748 3836400.369 3121482.978 4186373.676 3526498.911 3204730.924 3488881.951 4052438.578 4440084.644 0.855270347 0.83420386 0.864037665 0.703023304 0.942858979 0.79424137 0.721772484 0.785769243 0.912693992 1 22.08215575 1.028134491 3.977972289 0.998995876 0.809978864 0.457331484 0.065915637 0.157242244 5.891863137 0.062336785 0.015987076 10.66926472 -1.028134491 -0.189017012 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 AMKPPGGESS(0.001)NLFGS(0.995)PEEAT(0.001)PS(0.001)S(0.001)RPNR;AMKPPGGESS(0.002)NLFGS(0.993)PEEAT(0.002)PS(0.002)S(0.002)RPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR;AMKPPGGESSNLFGS(1)PEEATPSSRPNR 125.68 3.80E-05 528500000 273034 247055 269176 240957 313858 341694 322319 285466 332056 287122 TRUE FALSE 283813.5931 289484.7744 276190.9477 288617.5754 260508.5293 262340.7469 297054.7946 281639.7952 320105.3694 343378.0586 0.826533863 0.843049715 0.804334875 0.840524222 0.758663877 0.763999738 0.865095445 0.820203237 0.932224297 1 18.38943833 1.095398734 1.880792044 1.001531068 0.811857799 0.790023095 0.031972372 0.139345021 0.966169394 0.030591188 0.008751597 12.45657748 -1.095398734 -0.189673269 AMLDSGIYPPGS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK;AMLDSGIYPPGS(1)PGK 262.23 5.73E-25 2351730000 4895410 2876050 3508750 2863620 4972140 5059130 4547430 3972600 4188620 2954280 TRUE FALSE 5088684.567 3369989.215 3600190.907 3430035.489 4126977.419 3884223.729 4190990.554 3919353.795 4037872.384 3533114.603 1.440282906 0.953829579 1.018985035 0.97082486 1.168084787 1.099376659 1.186202834 1.109319746 1.14286482 1 21.75250912 AMLPGS(ph)PLFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 AMLPGSPLFTR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AMLPGS(0.999)PLFT(0.001)R;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR;AMLPGS(1)PLFTR 180.24 7.08E-06 3018059000 2405328 3293146 2678636 2713760 2979892 3468809 2449138 2849727 2367382 3191025 TRUE FALSE 2500292.207 3858718.208 2748443.455 3250533.628 2473371.022 2663230.68 2257168.164 2811531.071 2282180.384 3816245.253 0.655170735 1.011129514 0.720195709 0.851762246 0.64811637 0.697866752 0.591463078 0.73672704 0.598017222 1 21.86372246 3.241517455 24.99375602 0.692884104 0.817578569 0.095911546 0.138581219 134.463816 1136593.481 0.035406931 0.045930581 1743.883447 -3.241517455 0.124694464 AMREENGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AMREENGLK 9 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;; 151.22 7.60E-05 535410000 547790 558020 611500 501540 854620 845910 619790 632300 652660 767340 FALSE TRUE 569417.1722 653855.5942 627436.1924 600743.1151 709351.9977 649460.2224 571209.2403 623825.0527 629170.8941 917685.5814 0.620492665 0.712505032 0.683715866 0.654628478 0.772979343 0.707715404 0.622445478 0.679780815 0.685606167 1 19.80764041 -1.24720046 2.226594148 1.006675343 0.682896188 0.834900991 0.042394471 73311.28046 70220.91807 3325.270549 0.010934525 0.056597799 1.24720046 -0.323779155 AMS(ph)LNTLNVDAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(0.994)LNT(0.006)LNVDAPR;AMS(0.998)LNT(0.002)LNVDAPR;AMS(0.99)LNT(0.01)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.998)LNT(0.002)LNVDAPR;AMS(0.994)LNT(0.006)LNVDAPR;AMS(1)LNTLNVDAPR;AMS(1)LNTLNVDAPR 265.09 2.85E-24 4225791000 3046730 3430410 3721350 3400430 4107930 4239450 3574420 3681270 3639000 3870630 TRUE FALSE 3167017.253 4019556.233 3818331.438 4073024.905 3409665.526 3254901.987 3294247.62 3631928.597 3508033.101 4629005.841 0.68416791 0.868341145 0.824870732 0.879891935 0.736587 0.703153571 0.711653373 0.784602293 0.75783726 1 22.14227095 -1.267348553 3.64719872 1.000477594 0.774865162 0.528975523 0.064407447 17584988.46 32474332.84 95955.85499 0.016089647 0.05403205 1.267348553 -0.225612432 AMS(ph)TTSISSPQPGK ddPTM_MDA-MB-175_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(0.333)T(0.333)T(0.333)SISSPQPGK;AMS(0.989)T(0.01)TSISSPQPGK;AMS(0.631)T(0.365)T(0.004)SISSPQPGK;AMS(0.965)T(0.034)T(0.001)SISSPQPGK;AMS(0.969)T(0.031)TSISSPQPGK;AMS(0.84)T(0.149)T(0.01)SISSPQPGK;AMS(0.998)T(0.002)TSISSPQPGK;AMS(0.979)T(0.021)TSISSPQPGK;AMS(0.942)T(0.058)T(0.001)SISSPQPGK 321.34 3.50E-56 4166164000 3595558 2782452 4708046 2981208 6611309 4264162 4153555 3637043 4823712 3209394 TRUE FALSE 3737513.406 3260316.487 4830741.546 3570882.044 5487521.058 3273875 3827988.506 3588294.388 4650107.547 3838213.307 0.97376386 0.849435981 1.258591214 0.930350077 1.429707163 0.852968488 0.997336052 0.934886652 1.211529213 1 21.87200346 4.286368871 24.99962621 1.063079533 0.911599794 0.127443206 0.16997217 252.7902283 132183.4722 0.039491023 0.108150054 19336.09944 -4.286368871 -0.151479739 AMSLNT(ph)LNVDAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 AMS(0.245)LNT(0.755)LNVDAPR 254.61 9.15E-23 1242300000 344440 379960 411590 385310 451320 443410 369660 403490 391890 426800 TRUE FALSE 358038.7572 445215.1743 422316.3735 461523.168 374604.7876 340434.7474 340685.0833 398081.8765 377785.9555 510423.2884 0.701454587 0.872246985 0.82738461 0.904196925 0.733910063 0.666965546 0.667455994 0.779905395 0.740142474 1 18.96133463 5.034772771 14.73060323 0.784271097 0.432092522 0.060525629 0.101207058 2588280.768 33232317.6 0.024206739 22930749.1 108335.9936 -5.034772771 -0.352178575 AMSRPILYSNWLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AMSRPILYSNWLSK 14 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 64.665 0.055015 239520000 1070100 179780 344390 169060 399450 701720 482380 193210 348610 161760 FALSE TRUE 1112348.374 210655.8165 353365.0863 202499.5634 331551.6317 538756.1647 444569.7951 190620.336 336063.5942 193453.7749 5.74994401 1.088920682 1.826612515 1.046759431 1.713854546 2.784934876 2.298067305 0.985353406 1.737177754 1 17.56162936 4.74324122 24.98364507 1.6390496 5.749945688 0.824331882 0.573316296 195.7827795 1044993.53 0.141388216 1.144592602 55365.75419 -4.74324122 4.110896088 AMST(ph)TSISSPQPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.318)T(0.644)T(0.038)SISSPQPGK;AMS(0.237)T(0.58)T(0.183)SISSPQPGK;AMS(0.008)T(0.78)T(0.212)SISSPQPGK;AMS(0.058)T(0.769)T(0.172)SISSPQPGK 345.44 1.03E-80 5012020000 2868780 2289550 3730500 2350540 5256020 3205620 3187860 2851430 3798950 2474380 TRUE FALSE 2982041.65 2682762.402 3827719.895 2815469.796 4362603.598 2461163.337 2937987.203 2813211.245 3662226.532 2959187.386 1.007723155 0.906587536 1.293503721 0.951433427 1.474257297 0.831702429 0.992835809 0.950670193 1.237578448 1 21.49676963 AMSTTSISS(ph)PQPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;AMSTTS(0.002)IS(0.167)S(0.831)PQPGK;AMSTTSIS(0.074)S(0.926)PQPGK;AMSTTSIS(0.007)S(0.993)PQPGK;AMSTTSIS(0.062)S(0.938)PQPGK;AMSTT(0.001)S(0.025)IS(0.225)S(0.75)PQPGK;AMSTTSIS(0.104)S(0.896)PQPGK 320.4 4.14E-56 5560880000 9801970 7323920 7752610 6686910 8541260 9763810 8389900 7625490 7416780 6345340 TRUE FALSE 10188959.34 8581746.288 7954649.385 8009560.84 7089419.676 7496313.099 7732277.715 7523282.779 7149851.537 7588587.884 1.342668689 1.130875259 1.048238422 1.055474479 0.9342212 0.987840322 1.018934989 0.991394301 0.942184718 1 22.85540002 5.834696563 0.769204454 0.983213514 2.928201041 0.929082761 0.030103913 2.804163075 0.352179959 0.010470142 6.921320267 683433.9725 -5.834696563 1.944987527 AMT(ph)PEQEETASLLSSVTQGMESAYVSPSGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AMTPEQEETASLLSSVTQGMESAYVSPSGYR 31 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AMT(1)PEQEETASLLSSVTQGMESAYVSPSGYR;AMT(0.802)PEQEET(0.161)AS(0.037)LLSSVTQGMESAYVSPSGYR 193.23 1.83E-18 35474000 15681.5 18434.3 18167.7 18563.5 18379.2 25137 20334.8 18322.6 19354 17552.3 TRUE FALSE 16300.61773 21600.24763 18641.16519 22235.30489 15255.11015 19299.3127 18740.90524 18077.01552 18657.45332 20991.33713 0.776540229 1.029007704 0.888040865 1.059261007 0.726733607 0.919394157 0.892792352 0.861165509 0.888816811 1 14.35750645 4.799553668 22.29134932 0.908269629 0.776536323 0.173060341 0.090617649 44743.84729 16350183.83 0.020416174 44.11616934 63030.92314 -4.799553668 -0.131733306 AMTGVEQWPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AMTGVEQWPYR 11 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 125.75 0.0011438 393660000 73169 74256 66254 59546 103162 89398 75292 71605 74064 101081 FALSE TRUE 76057.76862 87008.89037 67980.63367 71324.02107 85626.56009 68636.66934 69390.4163 70645.2521 71398.45111 120885.8866 0.629169961 0.719760534 0.562353767 0.590011151 0.708325533 0.567780667 0.574015861 0.584396194 0.590626856 1 16.88328629 -1.953769235 2.678750776 1.291365199 0.612487986 0.823468083 0.05360511 11264198.9 6047007.776 20428938.54 0.012969564 0.011123226 1.953769235 -0.678877214 AMTVEKAS(ph)PVGDGNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AMTVEKASPVGDGNFR 16 1 Q86YS7;H0YFC4 Q86YS7 C2CD5 C2 domain-containing protein 5 1 AMTVEKAS(1)PVGDGNFR;AMTVEKAS(1)PVGDGNFR;AMTVEKAS(1)PVGDGNFR 190.79 4.84E-10 1000270000 1624130 1233290 1547320 1163560 1834190 1923320 1576570 1470570 1545440 1360920 TRUE FALSE 1688251.907 1445097.964 1587644.43 1393708.695 1522415.039 1476658.078 1452994.324 1450859.415 1489819.916 1627566.218 1.037286157 0.887888891 0.975471482 0.856314588 0.935393609 0.907279877 0.892740528 0.891428809 0.915366699 1 20.63428481 4.745571817 24.85979811 0.91258223 1.037286219 0.427957662 0.040951339 649.6609527 2303458.184 0.008803065 0.088226971 55663.66749 -4.745571817 0.12470399 ANAS(ph)PQKPLDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANASPQKPLDLK 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK;ANAS(1)PQKPLDLK 99.451 0.0022946 1653750000 3617760 1588870 2389930 1494820 3196960 3218960 3136390 2345130 2790150 1381350 TRUE FALSE 3760591.958 1861746.063 2452213.539 1790490.934 2653541.881 2471405.324 2890551.556 2313697.368 2689733.047 1651999.085 2.276388645 1.126965553 1.484391584 1.083832885 1.606261108 1.496008894 1.749729514 1.400543977 1.628168606 1 20.65578146 -1.179449582 4.061894282 0.999762867 1.513341293 0.202359089 0.317421718 21111304.99 6130124.49 44322.19214 0.068167133 0.066153133 1.179449582 0.513578425 ANCDASLIVTEELHLITFETEVYHQGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 255.96 8.87E-54 79841000 39545 33599 41848 35356 39698 45806 47027 39229 42843 26479 FALSE TRUE 41106.26714 39369.36689 42938.59326 42349.31127 32950.14814 35168.2507 43340.90086 38703.19942 41301.0888 31667.05308 1.298076807 1.243227994 1.355939031 1.337330353 1.040518297 1.110562786 1.368643326 1.222191384 1.304228995 1 14.950695 -1.39930965 3.221859103 0.997090089 1.251060523 0.360884429 0.101127413 13143153.9 19962717.48 363460.3757 0.024961119 0.03987405 1.39930965 0.253970434 ANEEYGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANEEYGLR 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 88.948 0.034261 0 71149 90376 102430 99839 114990 120250 103550 126730 104910 118160 FALSE TRUE 73958.01746 105897.375 105099.4099 119586.8562 95444.04087 92323.75991 95433.48042 125031.3916 101134.3096 141311.1897 0.523369859 0.749391292 0.743744428 0.846266007 0.675417432 0.653336513 0.6753427 0.8847947 0.715685076 1 17.10851618 -4.99999999 0.143348518 1.967703969 0.633426864 0.490023927 0.091142321 122.5401714 1.065867819 33.64955504 0.532694972 1.00E-05 4.99999999 -1.334277106 ANEFHDVNCEVVAVSVDSHFSHLAWINTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANEFHDVNCEVVAVSVDSHFSHLAWINTPR 30 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 126.05 4.72E-06 20280000 18422 28119 22073 26063 24964 33050 22516 21559 19747 27383 FALSE TRUE 19149.31478 32948.21951 22648.24051 31218.18361 20720.6282 25374.63838 20751.13709 21270.03687 19036.30933 32748.17457 0.584744494 1.006108583 0.691587877 0.953280115 0.632726204 0.774841307 0.633657825 0.649502977 0.581293754 1 14.99912687 3.211336965 24.99988776 0.689325076 0.814633009 0.072511526 0.157246814 418.441436 384260.0305 0.041546474 0.049669261 1626.810495 -3.211336965 0.125307933 ANEHQGIGFLNDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANEHQGIGFLNDPR 14 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ;;; 136.34 2.76E-05 1247020000 1595040 1519160 1660080 1762900 1929280 2076600 1957430 1797130 1721420 1536780 FALSE TRUE 1658013.411 1780063.913 1703343.049 2111596.358 1601341.675 1594341.121 1804001.522 1773042.412 1659466.43 1837882.618 0.902132375 0.968540589 0.92679643 1.148928848 0.871297035 0.867488003 0.981565147 0.964720159 0.902922969 1 20.8096132 ANEKEPCCWWLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANEKEPCCWWLAK 13 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7 Q06787 FMR1 Fragile X mental retardation protein 1 0 116.84 0.00050503 204700000 157790 97172 118840 106270 149910 146110 150970 125550 120230 107660 FALSE TRUE 164019.671 113860.5351 121937.068 127289.8888 124428.3517 112178.1668 139136.5769 123867.2076 115902.9458 128753.9157 1.273900449 0.884326775 0.94705522 0.988629263 0.966404408 0.871260235 1.080639576 0.96204614 0.900189677 1 16.97425678 4.746956319 24.94670793 0.958855227 1.273900611 0.726510497 0.058554465 533.527322 1585268.83 0.013574634 0.156462149 55841.40273 -4.746956319 0.315045384 ANESS(ph)PKPVGPPPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANESSPKPVGPPPER 15 1 Q9BQI0-3;Q9BQI0;Q9BQI0-2;A6PVM9 Q9BQI0-3 AIF1L Allograft inflammatory factor 1-like 1 ANES(0.432)S(0.568)PKPVGPPPER 75.55 0.019075 243020000 102850 63074 72378 51391 98145 91864 81898 68219 82227 54911 TRUE FALSE 106910.5974 73906.46885 74264.23014 61555.98641 81462.34796 70529.97821 75478.62076 67304.63589 79267.66633 65669.75912 1.628003496 1.125426221 1.130874106 0.937356665 1.240484952 1.074010003 1.149366493 1.024895428 1.207064978 1 16.00294154 4.742308151 4.421790134 1.095865322 1.66681489 0.766014714 0.08787396 0.08809946 4.24336 0.019398551 0.158192067 55246.9302 -4.742308151 0.570949568 ANFDKESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANFDKESER 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 181.53 4.32E-05 2395640000 4761450 3791370 4763750 3443410 6344550 5449680 4516020 4111110 4712550 4557650 FALSE TRUE 4949435.723 4442508.305 4887897.238 4124506.22 5266105.657 4184074.411 4162042.552 4056007.295 4542946.246 5450634.256 0.908047668 0.815044286 0.896757516 0.756702069 0.966145481 0.767630741 0.763588668 0.744134922 0.833471121 1 22.37799269 ANFWYQPSFHGVDLSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANFWYQPSFHGVDLSALR 18 0 K7EQA8;Q86X55-2;Q86X55-1;Q86X55 K7EQA8 CARM1 Histone-arginine methyltransferase CARM1 0 66.325 0.031996 201450000 47518 115720 82794 96285 141040 136920 86123 100150 99374 218810 FALSE TRUE 49394.04733 135594.0098 84951.67966 115329.8856 117066.0712 105122.405 79372.45422 98807.65306 95797.54915 261681.6301 0.188756266 0.518164037 0.324637536 0.440725952 0.447360677 0.401718703 0.303316875 0.377587273 0.366084349 1 17.99745313 -1.463035187 3.000321414 1.015207053 0.378794593 0.827553706 0.085670068 13456830.78 15852483.9 1712146.098 0.019428315 0.034432203 1.463035187 -0.63641246 ANGLPAGPEPAS(ph)EPGSPYPEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANGLPAGPEPASEPGSPYPEGPR 23 0 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 ANGLPAGPEPAS(0.808)EPGS(0.163)PY(0.029)PEGPR 56.428 0.09364 96136000 17814 31769 25128 35534 27082 36520 17867 25517 15179 40123 TRUE FALSE 18517.31048 37225.07862 25782.85632 42562.51914 22478.61131 28038.78347 16466.53785 25174.98635 14632.71076 47984.33365 0.385903254 0.775775671 0.537318211 0.887008653 0.468457299 0.584332038 0.343164875 0.524650119 0.30494767 1 15.55027584 -1.059810751 4.597627869 1.000020916 0.542053829 0.392197025 0.173582283 22737817.06 5241351.877 4996.906662 0.039678823 0.08713432 1.059810751 -0.457967086 ANGMELDGRR ddPTM_MDA-MB-175_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 ;;; 149.33 3.77E-05 3144210000 1686060 2012080 1885240 1649850 2340850 2353770 1757770 1989500 1931850 2187620 FALSE TRUE 1752626.951 2357639.088 1934370.903 1976185.406 1942953.153 1807142.589 1619991.394 1962834.007 1862323.096 2616242.254 0.669902394 0.901154732 0.739369949 0.755352606 0.742650322 0.690739776 0.619205424 0.750249333 0.711831289 1 21.3190647 -1.053965972 4.328453102 1.000020821 0.732640732 0.573492085 0.069541876 37335.13466 40281257.72 1893.609028 0.016346118 0.088314909 1.053965972 -0.26738009 ANGQENGHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ANGQENGHVK 10 0 P49006;P29966 P49006;P29966 MARCKSL1;MARCKS MARCKS-related protein;Myristoylated alanine-rich C-kinase substrate 0 ;;;; 179.57 2.09E-06 691749000 704727 550078 640998 518665 770010 705319 715212 662603 711404 571917 FALSE TRUE 732550.1661 644549.6175 657702.9345 621255.3889 639123.9752 541519.3515 659151.8146 653721.8906 685800.709 683973.1861 1.071021761 0.942360944 0.961591694 0.908303719 0.934428408 0.791725995 0.963710022 0.955771226 1.002671922 1 19.38358024 -0.858502334 5.857914153 1.000000012 0.943560026 0.047901756 0.067083822 1.01E-08 1.97E-09 0.064380793 0.015174695 0.138515274 0.858502334 -0.056439986 ANGQENGHVKS(ph)NGDLSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANGQENGHVKSNGDLSPK 18 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 ANGQENGHVKS(1)NGDLSPK;ANGQENGHVKS(1)NGDLSPK 143.29 6.44E-08 375220000 282640 216816 269014 155903 370520 358180 262079 261198 301030 212087 TRUE FALSE 293798.8454 254052.4614 276024.7258 186740.1481 307539.1427 274998.1233 241536.5632 257697.068 290195.9891 253641.387 1.158323761 1.001620691 1.088247975 0.736236898 1.212495904 1.084200518 0.952275833 1.015989824 1.144119233 1 17.95243065 4.744607195 23.3639206 1.023386183 1.158323911 0.096370993 0.121173902 638.6624902 2467601.513 0.027612612 0.242505051 55540.16875 -4.744607195 0.134937729 ANHGPGMAMNWPQFEEWSADLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANHGPGMAMNWPQFEEWSADLNR 23 0 Q9UNF0-2;Q9UNF0 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 203.4 1.91E-24 346220000 89364 102280 85853 95104 98339 115040 89386 89675 101480 118350 FALSE TRUE 92892.15972 119845.7944 88090.39971 113915.2873 81623.37191 88323.70345 82379.69175 88473.0533 97827.75462 141538.4166 0.656303511 0.84673686 0.622378022 0.804836525 0.57668705 0.624026364 0.582030616 0.625081554 0.691174573 1 17.11083416 -1.493294362 9.04856634 1.000008669 0.666616107 0.573016371 0.085437575 1.50E-05 8.38E-07 0.082798694 0.019515333 0.032114831 1.493294362 -0.333392562 ANIVAYHDSIMNPDYNVEFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANIVAYHDSIMNPDYNVEFFR 21 0 Q9UBT2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 202.47 6.37E-22 231720000 34101 162550 120430 192050 129920 234490 114030 146950 124280 187260 FALSE TRUE 35447.33381 190466.698 123568.5047 230036.9168 107836.2448 180033.2512 105092.0306 144980.3756 119807.1871 223950.0117 0.158282349 0.850487556 0.551768244 1.027179749 0.481519264 0.803899271 0.469265573 0.64737829 0.534972899 1 17.77281722 -2.334567241 2.078299611 2.844180377 0.62809604 0.20230381 0.228459854 6193704.976 686977.9809 53696671.85 0.050670581 0.00462842 2.334567241 -2.216084336 ANKLDHVVTIIK ddPTM_MDA-MB-175_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 ; 123.95 0.0001993 953390000 2197690 1481680 2091790 1565140 2553570 2255940 2279700 2088080 2287780 1599750 FALSE TRUE 2284456.498 1736147.014 2146303.766 1874720.021 2119515.084 1732032.124 2101011.157 2060092.703 2205443.245 1913190.383 1.194056022 0.907461709 1.121845366 0.979892036 1.107843266 0.905310908 1.098171502 1.076783953 1.152756811 1 20.86754901 ANKPGDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANKPGDVVR 9 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 83.862 0.014485 278820000 568790 564300 543380 449520 799850 696030 609770 522720 558030 580330 FALSE TRUE 591246.2684 661214.1354 557540.9292 538433.7143 663891.7827 534387.5809 561974.6341 515713.7934 537946.6093 694034.5524 0.851897454 0.952710687 0.803333101 0.775802462 0.956568777 0.769972589 0.809721407 0.743066453 0.775100616 1 19.40464796 2.662773587 24.99999998 0.798101723 0.864049113 0.045488865 0.085609303 265.3870068 87542.34368 0.026462931 0.024949493 460.0166882 -2.662773587 0.06594739 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANLEAFTVDKDITLTNDKPATAIGVIGNFTDAER 34 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 289.34 6.82E-90 976870000 1140420 742330 955770 749460 1258270 1207910 1222990 1033220 1149890 700150 FALSE TRUE 1185444.662 869819.403 980678.1514 897700.9511 1044389.715 927391.2086 1127128.848 1019371.376 1108505.684 837330.9873 1.415742019 1.038799968 1.171195341 1.072098089 1.247284205 1.107556298 1.346097141 1.217405532 1.323856038 1 19.67543849 2.262997305 24.99858436 1.241331459 1.167609359 0.01850331 0.131852535 633.6400255 648207.8461 0.042118635 0.035223568 183.230305 -2.262997305 -0.0737221 ANLQIDQINTDLNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANLQIDQINTDLNLER 16 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 251.63 3.83E-26 414975000 385986 436416 397466 445398 476915 491477 427006 431047 446855 478596 FALSE TRUE 401225.0253 511367.0532 407824.2905 533496.395 395849.1586 377338.9152 393536.1539 425269.52 430772.7758 572367.7229 0.700991704 0.893423987 0.712521469 0.932086793 0.691599374 0.659259598 0.687558257 0.743000527 0.752615423 1 19.12658279 -1.119836427 2.964706902 1.000605287 0.752691696 0.429901182 0.085482649 3922108.574 5448899.281 22986.36749 0.021230398 0.075886334 1.119836427 -0.247913591 ANNIDYTVHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANNIDYTVHSVR 12 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 178.15 2.24E-05 990300000 539740 632330 612050 604590 659370 760910 624420 621190 586180 681270 FALSE TRUE 561049.352 740927.7587 628000.5258 724176.0975 547290.5229 584200.1842 575476.3288 612863.9641 565083.4963 814751.8128 0.688613812 0.909390746 0.770787516 0.888830299 0.671726671 0.717028394 0.706321017 0.75220939 0.693565191 1 19.63600113 5.03897204 16.42385658 0.77544354 0.309535842 0.063994691 0.103651833 14501117.73 165053737.7 0.023442087 202270021.2 109388.5939 -5.03897204 -0.465907698 ANPFGGASHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 ;;; 176.32 8.79E-06 3071759000 3805270 3373990 3922380 3362870 5120670 4838800 4428850 3780950 4097020 4099980 FALSE TRUE 3955504.998 3953446.537 4024600.445 4028035.649 4250260.342 3715062.033 4081705.164 3730272.55 3949569.051 4903292.582 0.806703849 0.806284037 0.820795492 0.821496083 0.866817607 0.757666807 0.83244169 0.760768909 0.805493244 1 22.22531942 -1.178263633 3.555424074 1.00022982 0.807195777 0.781627765 0.030321798 43328402.57 72308129.91 113507.3732 0.007208922 0.066334028 1.178263633 -0.193034042 ANS(ph)DIISLNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANSDIISLNFR 11 0 Q8TC76 Q8TC76 FAM110B Protein FAM110B 1 ANS(1)DIISLNFR;ANS(1)DIISLNFR;ANS(1)DIISLNFR 154.72 3.34E-05 81903000 120072 111269 137765 107380 160783 166735 127796 124733 128459 112881 TRUE FALSE 124812.5353 130378.5852 141355.2691 128619.4435 133453.1631 128013.3231 117779.0156 123061.1582 123835.7857 134997.8707 0.924551881 0.965782531 1.047092582 0.952751646 0.988557541 0.948261795 0.872450913 0.911578512 0.917316585 1 17.04257713 2.474504291 24.6684267 0.914995147 0.976932736 0.229644382 0.041908526 79.88221483 752978.7288 0.014035326 0.011808847 298.1977009 -2.474504291 0.061937589 ANS(ph)FQSPTPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANSFQSPTPSK 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 ANS(0.983)FQS(0.017)PTPSK 174.95 1.09E-05 273690000 278090 202990 266120 170020 363290 315480 307730 278430 308640 162170 TRUE FALSE 289069.2079 237851.9535 273055.3058 203649.4485 301538.0956 242214.5511 283609.3185 274698.1013 297532.1067 193944.1066 1.490476886 1.226394334 1.407907209 1.050041954 1.554768025 1.248888432 1.462325015 1.416377667 1.534112647 1 17.56528141 3.189737496 24.99994583 1.392396673 1.29704754 0.029882834 0.184984236 336.8098255 172462.7257 0.049177695 0.058778704 1547.880739 -3.189737496 -0.095349133 ANS(ph)FVGTAQYVSPELLTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ANSFVGTAQYVSPELLTEK 19 0 E9PER6;O15530-5;O15530-2;O15530;O15530-4;Q6A1A2 E9PER6;Q6A1A2 PDPK1;PDPK2P 3-phosphoinositide-dependent protein kinase 1;Putative 3-phosphoinositide-dependent protein kinase 2 1 ANS(1)FVGTAQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(0.739)FVGT(0.261)AQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK;ANS(1)FVGTAQYVSPELLTEK 431.23 2.26E-169 2699384000 1519340 884153 1214351 891905 1731370 1568600 1514600 1210713 1346250 736738 TRUE FALSE 1579324.716 1035999.4 1245997.985 1068321.147 1437072.346 1204316.422 1395881.694 1194485.373 1297798.725 881087.7054 1.792471631 1.1758187 1.41415886 1.212502615 1.631020768 1.366851921 1.584270993 1.355694065 1.472950669 1 19.74892611 -1.172205168 4.075324796 0.999822308 1.432867088 0.35721041 0.17843996 11626367.97 3344163.715 18814.63743 0.037717781 0.067265881 1.172205168 0.43304478 ANS(ph)LDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANSLDNER 8 0 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 ANS(1)LDNER;ANS(1)LDNER 116.74 0.0023223 1032730000 1364220 1252260 1447460 1358980 1754730 1939180 1675050 1518020 1513210 1122020 TRUE FALSE 1418080.459 1467325.914 1485181.997 1627782.188 1456461.621 1488834.834 1543755.204 1497673.425 1458749.868 1341858.337 1.056803405 1.093502849 1.106809829 1.213080504 1.085406396 1.109532052 1.150460642 1.116118881 1.087111678 1 20.35580094 0.843728813 2.59118155 1.000094818 1.118818124 0.437827497 0.039662192 0.562192123 6.95621351 0.037866717 0.010101601 6.977965417 -0.843728813 0.118723307 ANS(ph)LGDLYAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ANSLGDLYAQK 11 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 ANS(1)LGDLYAQK;ANS(1)LGDLYAQK;ANS(1)LGDLYAQK;ANS(1)LGDLYAQK;ANS(1)LGDLYAQK;ANS(1)LGDLYAQK 184.51 5.11E-06 1322462000 2460830 1633970 2083340 1634560 2767220 2630370 2433620 2072000 2191120 1492910 TRUE FALSE 2557985.469 1914591.637 2137633.552 1957871.089 2296848.933 2019506.431 2242866.505 2044228.229 2112262.019 1785417.131 1.432710275 1.072349763 1.197274023 1.09659029 1.286449476 1.131111826 1.256214285 1.144958337 1.1830636 1 20.76782974 -5 0.214890554 0.048686753 1.219370391 0.286728819 0.098445436 192.0138635 1.918455123 78.87591438 0.181526327 1.00E-05 5 1.170683638 ANS(ph)LVTLGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANSLVTLGSHR 11 0 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ANS(1)LVTLGSHR;ANS(0.999)LVTLGSHR;ANS(1)LVTLGSHR 136.81 5.89E-05 500744000 394422 483400 466568 429352 671162 693070 507721 466885 508689 551810 TRUE FALSE 409994.0851 566420.1897 478727.1454 514276.5441 557078.123 532114.9961 467924.5013 460627.1702 490381.3823 659926.6045 0.621272248 0.858307857 0.725424831 0.779293547 0.844151636 0.80632451 0.709055368 0.697997576 0.743084729 1 19.33194605 -2.172312888 2.336891438 1.619482737 0.754911561 0.541770454 0.067899306 5932767.249 1109050.04 19512142.46 0.0163317 0.00672492 2.172312888 -0.864571175 ANS(ph)PEKPPEAGAAHKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANSPEKPPEAGAAHKPR 17 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR;ANS(1)PEKPPEAGAAHKPR 169.84 1.00E-09 4738900000 5273100 1754790 2861000 1677560 4217800 4377600 4300980 2961950 3458510 1284240 TRUE FALSE 5481286.06 2056161.532 2935560.01 2009376.361 3500859.863 3360968.743 3963857.949 2922249.905 3334038.901 1535862.24 3.568865695 1.338766902 1.911343306 1.308305074 2.279410075 2.188326958 2.580868158 1.902677095 2.170792936 1 20.55061739 4.751543912 24.7815569 1.922260357 3.568866887 0.535283169 0.475641976 1516.281255 2894108.083 0.110176463 2.047533372 56434.39996 -4.751543912 1.64660653 ANS(ph)RDGEAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 122.46 0.00029552 273580000 64829 72719 87207 54423 108641 96835 84320 80777 104683 86361 TRUE FALSE 67388.49898 85207.92257 89479.68606 65187.70696 90174.24163 74346.5388 77710.77807 79694.31644 100915.4793 103281.7845 0.652472257 0.825004361 0.86636464 0.631163639 0.873089501 0.719841734 0.752415138 0.771620251 0.977088843 1 16.65622631 1.22645926 5.008632597 0.996980361 0.764000258 0.586473035 0.076364718 0.116035052 7.522417848 0.061213731 0.017536495 16.84454403 -1.22645926 -0.232980103 ANSALT(ph)PPKPESGLTLQESNTPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANSALTPPKPESGLTLQESNTPGLR 25 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 ANS(0.001)ALT(0.998)PPKPESGLTLQESNTPGLR 130.45 0.00014679 348050000 445020 277930 330720 272780 514260 479520 424640 356780 449120 277460 TRUE FALSE 462589.7332 325662.3155 339338.8349 326735.0698 426846.2689 368158.7472 391355.6072 351997.9477 432956.2589 331822.9747 1.394085909 0.981433898 1.02265021 0.98466681 1.286367435 1.109503486 1.179410822 1.06080041 1.304780838 1 18.34005425 4.75532156 24.07036514 1.106269031 1.39408629 0.372763843 0.113104417 2165.29292 3109487.694 0.026325838 0.701222186 56927.4277 -4.75532156 0.287817259 ANSFTVSSVAAPSWLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANSFTVSSVAAPSWLHR 17 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 111.34 0.00051411 1041540000 294464 552290 470515 496654 566210 621990 449590 491980 491730 588250 FALSE TRUE 306089.6661 647141.5113 482777.0074 594890.6788 469965.8264 477542.2488 414349.961 485385.8128 474032.7334 703506.3248 0.435091563 0.919880161 0.686244019 0.845608146 0.668033548 0.678803064 0.588978303 0.689952308 0.673814459 1 19.42420387 -1.963941363 2.633587368 1.246288334 0.693503718 0.363538462 0.123855673 28284273.87 12323610.84 42492791.65 0.028673195 0.010865723 1.963941363 -0.552784616 ANSFVGT(ph)AQYVSPELLTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.372)FVGT(0.628)AQYVSPELLTEK 367.48 7.75E-107 1290100000 788340 447720 655950 481290 894660 788350 793660 616730 679960 372200 TRUE FALSE 819464.2719 524612.4272 673044.5959 576487.7255 742586.0128 605267.6601 731450.8554 608463.7431 655488.3724 445125.4638 1.8409737 1.178572043 1.512033462 1.295112889 1.668262261 1.35976867 1.643246489 1.366948855 1.472592394 1 18.76385251 -0.111277625 0.955741002 0.992632923 1.475577114 0.376724963 0.185949013 9.611190698 7.178319042 0.42192714 0.051293731 0.773966878 0.111277625 0.482944191 ANSWQLVET(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANSWQLVETPEK 12 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEK;ANSWQLVET(1)PEK;ANSWQLVET(1)PEK 150.05 0.00073012 264049000 865090 475450 576970 502890 844290 860780 719760 649190 726750 448920 TRUE FALSE 899244.4212 557104.839 592006.3122 602360.141 700777.8874 660876.8902 663343.3305 640488.6699 700594.4095 536877.2789 1.674953395 1.03767632 1.102684609 1.121969889 1.305285053 1.230964535 1.235558584 1.192988966 1.304943303 1 19.03423282 -2.321555092 1.988549218 0.00027041 1.229318482 0.158268651 0.166050779 3542781.275 387057.518 15935399.17 0.037921524 0.004769193 2.321555092 1.229048072 ANSWQLVET(ph)PEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANSWQLVETPEKR 13 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR 139.08 2.44E-05 1453230000 768130 427518 506120 435147 641060 620340 678270 564140 586290 421170 TRUE FALSE 798456.3655 500940.8909 519309.903 521217.7778 532092.8502 476275.4363 625105.4251 556578.626 565189.5374 503690.1977 1.585213231 0.994541671 1.03101054 1.034798335 1.056389131 0.945572176 1.2410514 1.105001901 1.122097551 1 18.94217713 4.74346613 24.98229609 1.067154119 1.585213445 0.80113368 0.078565303 226.8312745 1155144.796 0.019355071 0.160365171 55394.4341 -4.74346613 0.518059326 ANT(ph)PELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANTPELKK 8 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 1 ANT(1)PELKK;ANT(1)PELKK 98.105 0.0045466 866000000 1912800 565030 869920 505380 1565170 1963750 1323350 883310 1057920 389490 TRUE FALSE 1988318.821 662069.5072 892590.8298 605342.6556 1299122.962 1507698.823 1219622.369 871470.6743 1019845.666 465803.1083 4.268582123 1.421350557 1.916240605 1.29956766 2.788995907 3.236772784 2.618321663 1.870899225 2.189435081 1 18.82936074 0.685337673 1.12141472 1.00927035 2.399742751 0.209611509 0.837991753 1.745420936 3.657551714 0.789684197 0.24619371 4.845489678 -0.685337673 1.3904724 ANTIPIIGS(ph)PSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANTIPIIGSPSSK 13 0 E9PGM7;O94988-6;O94988-5;O94988-1;O94988 E9PGM7 FAM13A Protein FAM13A 1 ANTIPIIGS(0.812)PS(0.176)S(0.012)K;ANTIPIIGS(0.959)PS(0.024)S(0.018)K 126.42 0.00019797 626970000 1722990 1234200 1494870 1251150 1968850 1891150 1513460 1499920 1534870 1141360 TRUE FALSE 1791014.976 1446164.249 1533827.54 1498623.736 1634185.58 1451959.073 1394831.051 1479816.026 1479630.329 1364987.639 1.312110765 1.059470582 1.123693355 1.097902789 1.197216395 1.063715913 1.021863503 1.084124122 1.083988079 1 20.38045646 4.742666966 24.85641866 1.085928181 1.312110861 0.641829186 0.05161687 244.8000801 1481754.158 0.012302836 0.09496454 55292.59415 -4.742666966 0.22618268 ANTLS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANTLSPVR 8 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 ANT(0.071)LS(0.929)PVR 71.221 0.051717 235990000 247420 300560 260020 255010 259730 324730 237970 281120 271250 298500 TRUE FALSE 257188.3326 352178.842 266796.3348 305450.2169 215581.1874 249316.3788 219317.2896 277352.0462 261487.7655 356985.3599 0.720445042 0.986535812 0.747359317 0.855637937 0.603893637 0.698393847 0.614359339 0.776928349 0.732488765 1 18.44550538 3.279576815 24.99985385 0.72002001 0.833130783 0.103133262 0.122879853 259.2802377 158032.6242 0.031566305 0.042740536 1903.604902 -3.279576815 0.113110773 ANVNEILDFFHGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ANVNEILDFFHGYR 14 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 189.69 6.90E-07 220080000 94138 105960 103950 106750 112680 130360 109050 105040 100230 119580 FALSE TRUE 97854.64093 124157.8057 106659.0224 127864.8314 93526.69385 100085.8656 100502.3761 103632.1106 96622.74188 143009.4115 0.684253154 0.868179265 0.745818204 0.894100815 0.653989782 0.699855097 0.702767566 0.724652381 0.675639043 1 17.12575057 -1.149534268 3.879508657 1.000121895 0.740985872 0.513538995 0.076237778 18011063.63 39102636.9 30508.94836 0.018213568 0.070870538 1.149534268 -0.259136023 ANVS(ph)SPHREFPPATAR ddPTM_MDA-MB-175_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 75.349 0.018013 529000000 64949 78049 67812 65132 75305 93897 76947 66172 61791 84125 TRUE FALSE 67513.23667 91453.30861 69579.23643 78014.9152 62504.683 72090.84477 70915.69308 65285.07258 59567.15398 100607.6831 0.671054482 0.909009191 0.691589691 0.775436953 0.621271468 0.71655407 0.704873534 0.648907425 0.592073609 1 16.61838096 -1.124017612 4.293248076 1.000050411 0.705159764 0.527236475 0.084238205 11812303.27 3092586.839 5652.885173 0.019720053 0.075159241 1.124017612 -0.294890647 ANVSS(ph)PHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 ANVS(0.129)S(0.871)PHR;ANVS(0.133)S(0.867)PHR;ANVS(0.055)S(0.945)PHR;ANVS(0.058)S(0.942)PHR 84.896 0.011032 1103705000 1527970 1748400 1675090 1926710 1766660 2168030 2208580 1845410 1603820 1694040 TRUE FALSE 1588295.435 2048674.099 1718744.222 2307807.487 1466363.764 1664537.889 2035465.729 1820675.297 1546098.831 2025954.704 0.783973814 1.011214168 0.848362611 1.13912097 0.723789017 0.821606666 1.004694589 0.898675224 0.763145804 1 20.95017049 4.783088274 22.10995679 0.909365762 0.78397183 0.090683448 0.121580855 17687.18367 8781556.207 0.027593179 10.60778655 60685.9666 -4.783088274 -0.125393932 ANVSSPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ANVSSPHR 8 0 Q5QPM7;Q5QPM9;H0Y555;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ;; 89.355 0.013965 135410000 77379 137752 104516 113734 205631 166861 116822 108539 104017 241084 FALSE TRUE 80433.98267 161409.8344 107239.7728 136230.2457 170677.9161 128110.0616 107665.1864 107084.2122 100273.4485 288319.794 0.27897489 0.559829182 0.371947314 0.472497028 0.591974327 0.444333217 0.373422806 0.371407772 0.347785517 1 18.13731036 -1.36949931 3.819965568 1.002235934 0.426826413 0.779835916 0.09186854 70425344.11 121209901.5 1760446.154 0.022010455 0.04270716 1.36949931 -0.575409521 ANWEAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ANWEAQQR 8 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;; 135 0.0019835 825346000 643911 868937 710524 721730 965042 1009090 778248 762954 726922 1010890 FALSE TRUE 669333.1035 1018170.17 729040.8391 864486.0399 801004.5055 774744.1404 717246.8882 752727.8496 700760.2192 1208954.541 0.553646213 0.842190617 0.603034121 0.715069104 0.662559657 0.640838108 0.593278625 0.622627092 0.579641496 1 20.20532857 -1.96117921 3.701809873 1.252418351 0.648578677 0.646293738 0.07856993 0.047397377 0.000497055 0.022029446 0.016930048 0.01093505 1.96117921 -0.603839674 ANYWWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ANYWWLR 7 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 110.34 0.015881 680730000 901840 933090 831690 821570 2098400 1253840 922300 870650 822800 2084290 FALSE TRUE 937445.3396 1093340.949 853364.5246 984074.0939 1741714.718 962654.6621 850007.716 858980.3608 793187.5887 2492666.719 0.3760813 0.438622998 0.342350029 0.394787673 0.698735496 0.386194694 0.341003356 0.344602972 0.31820844 1 21.24925857 -1.167665113 4.646055155 1.000068708 0.404318451 0.74732687 0.103877139 9.03E-05 1.62E-05 0.104318255 0.024584729 0.067972757 1.167665113 -0.595750257 APAAHPEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APAAHPEGQLK 11 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 ; 82.171 0.015765 84509000 123381 102911 109048 132649 177939 181259 163739 127535 136124 156567 FALSE TRUE 128252.1772 120585.1637 111889.8805 158886.5763 147692.9923 139164.3443 150904.7093 125825.6019 131224.9238 187243.306 0.684949331 0.644002535 0.597564115 0.848556777 0.788775821 0.74322734 0.80592846 0.671989854 0.700825715 1 17.51455462 APAASEGNHTDGAEEAAGSCAQAPSHS(ph)PPNKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APAASEGNHTDGAEEAAGSCAQAPSHSPPNKPK 33 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 APAASEGNHTDGAEEAAGSCAQAPS(0.002)HS(0.998)PPNKPK;APAASEGNHTDGAEEAAGSCAQAPS(0.025)HS(0.975)PPNKPK 212.72 3.05E-28 372670000 209660 129219 189188 141177 228160 214664 237130 186487 218000 101182 TRUE FALSE 217937.5387 151411.3581 194118.3947 169101.3892 189377.4447 164811.5393 218543.131 183987.4468 210154.2226 121006.6757 1.801037319 1.251264505 1.604195749 1.397455044 1.565016506 1.362003694 1.806041938 1.520473526 1.736715941 1 16.88472711 APADPAPAPADPAS(ph)PQHQLAGPAPLLSTPAPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APADPAPAPADPASPQHQLAGPAPLLSTPAPEAR 34 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 APADPAPAPADPAS(1)PQHQLAGPAPLLSTPAPEAR 117.39 2.27E-06 150870000 31891 30573 27993 32817 29528 37084 36140 34143 29659 25020 TRUE FALSE 33150.08131 35823.67493 28722.52058 39308.10465 24508.84111 28471.80301 33307.25237 33685.36893 28591.57838 29922.18996 1.107876173 1.197227709 0.959907033 1.313677398 0.819085807 0.951528048 1.113128832 1.125765493 0.955530943 1 14.86892815 3.243655016 24.99999793 1.015034208 1.135228488 0.275345444 0.116298421 216.6575842 1063207.33 0.03334562 0.043802067 1752.487853 -3.243655016 0.12019428 APAGPSLEETSVSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APAGPSLEETSVSSPK 16 0 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 APAGPSLEETSVS(0.013)S(0.987)PK 139 2.37E-05 0 171930 60722 89272 66066 128340 155060 113230 79065 103770 51565 TRUE FALSE 178717.9292 71150.53115 91598.50166 79133.65761 106524.8126 119049.665 104354.7367 78005.263 100035.338 61668.17448 2.898057721 1.153764186 1.48534479 1.283217126 1.727387158 1.930487905 1.692197598 1.264919282 1.622155006 1 15.91223852 8 0.048398198 3.03E-08 4.463124016 0.237931711 0.445466085 900.1222592 3.291746767 73.18097123 303.7126625 99999999.89 -8 4.463123986 APAPLGTVADSLRAS(ph)DGQLQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 APAPLGTVADSLRAS(1)DGQLQAK;APAPLGTVADS(0.265)LRAS(0.735)DGQLQAK;APAPLGTVADS(0.001)LRAS(0.999)DGQLQAK;APAPLGTVADSLRAS(1)DGQLQAK 228.35 2.24E-26 2776180000 876201 701695 820322 654731 995500 1001120 802250 803501 883937 730927 TRUE FALSE 910794.0921 822205.6578 841700.2652 784234.8376 826285.2656 768625.0521 739367.5487 792731.3834 852124.28 874138.1512 1.041933807 0.940590062 0.96289158 0.897152054 0.945257068 0.87929471 0.845824596 0.906871966 0.974816485 1 19.73750178 APDMS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APDMSPQR 8 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 APDMS(1)PQR;APDMS(1)PQR 93.258 0.01043 0 1094310 1311960 1128910 1120740 1552220 1475320 1166420 1158980 1075360 1702690 TRUE FALSE 1137514.204 1537278.924 1158330.322 1342419.027 1288374.199 1132699.289 1074992.953 1143445.769 1036658.004 2036299.506 0.558618318 0.754937533 0.56884084 0.659244391 0.632703684 0.556253776 0.52791495 0.561531231 0.509089159 1 20.95751834 -1.20215379 6.038899803 1.000006184 0.593196733 0.758855947 0.068974877 5.85E-06 7.73E-07 0.068058258 0.016041241 0.062783599 1.20215379 -0.406809451 APDWVDAEECHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APDWVDAEECHR 12 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ;;; 182.08 1.73E-05 1558190000 2160180 2488690 2255700 2565290 2527280 2797620 2355080 2358140 2351910 2722710 FALSE TRUE 2245465.574 2916103.148 2314485.395 3072696.705 2097693.848 2147915.153 2170482.676 2326532.99 2267265.219 3256172.895 0.689602686 0.89556152 0.710799294 0.943652811 0.644220659 0.659644074 0.666574763 0.714499219 0.696297553 1 21.63474587 3.208373467 24.99990238 0.708611981 0.808943855 0.080083571 0.11955266 371.1343222 307359.0231 0.031539297 0.037700867 1615.747405 -3.208373467 0.100331874 APELPNTSSS(ph)PSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 APELPNTSS(0.005)S(0.995)PSLK;APELPNTSS(0.032)S(0.968)PSLK 299.31 9.46E-44 1365140000 2787900 2057090 2406100 1861800 2981800 2977900 2700700 2381100 2571800 2012830 TRUE FALSE 2897968.445 2410379.206 2468804.943 2230058.483 2474954.701 2286327.856 2489012.077 2349185.249 2479241.42 2407205.501 1.203872475 1.001318419 1.025589607 0.926409682 1.028144336 0.949785074 1.033984044 0.975897259 1.029925123 1 21.19892788 4.741675931 5.073327525 0.994522404 1.214174969 0.763878779 0.034538565 0.070804934 5.861590759 0.007462153 0.054559724 55166.56347 -4.741675931 0.219652565 APEPHVEEDDDDELDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APEPHVEEDDDDELDSK 17 0 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;; 304.71 9.97E-47 4974010000 4942520 2532560 3384120 3217400 3964850 4783270 5945480 3502140 3628710 1605470 FALSE TRUE 5137654.506 2967507.479 3472312.947 3853792.117 3290906.213 3672428.034 5479457.742 3455199.542 3498113.436 1920031.108 2.675818368 1.545551771 1.808467026 2.007150874 1.713985883 1.912691945 2.853838003 1.799553938 1.821904563 1 20.87269825 4.756543678 23.86713721 1.900334412 2.675819595 0.238269107 0.437798788 3126.757374 4149709.694 0.100525561 3.025842565 57087.84872 -4.756543678 0.775485183 APEPHVEEDDDDELDSKLNYKPPPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APEPHVEEDDDDELDSKLNYKPPPQK 26 2 P52566;F5H3P3;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;; 268.22 1.13E-53 4154600000 5113300 1880530 3176790 1989760 4608000 3846470 4605600 3131570 3979680 1438400 FALSE TRUE 5315177.032 2203496.399 3259579.757 2383328.589 3824733.806 2953185.636 4244601.038 3089596.426 3836452.094 1720226.94 3.089811529 1.280933549 1.894854499 1.385473354 2.223389087 1.716741883 2.467465739 1.796040019 2.230201146 1 20.71416747 APEPQLS(ph)PGSDASEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APEPQLSPGSDASEVR 16 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 APEPQLS(0.999)PGS(0.001)DASEVR;APEPQLS(0.998)PGS(0.002)DASEVR 269 1.21E-27 341480000 116252 168163 124237 139802 135257 165988 140407 138893 127069 153343 TRUE FALSE 120841.7187 197043.6871 127474.7183 167454.4183 112266.0635 127439.8026 129401.5325 137031.3665 122495.8115 183387.6249 0.658941511 1.07446556 0.695110798 0.91311733 0.612179058 0.694920405 0.705617582 0.747222538 0.667961165 1 17.48453676 3.25069831 24.99708659 0.722959322 0.842462982 0.092627605 0.144199273 425.6862508 876678.1387 0.036421272 0.048952959 1781.141037 -3.25069831 0.11950366 APESDTGDEDQDQERDTVFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APESDTGDEDQDQERDTVFLK 21 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 57.496 0.072994 33262000 30901 94457 69976 97182 60143 90022 57815 76337 70717 115320 FALSE TRUE 32120.99534 110679.255 71799.63205 116404.3095 49919.91434 69115.7548 53283.30923 75313.82738 68171.90898 137914.7461 0.23290472 0.802519369 0.520608812 0.844030917 0.361962123 0.501148403 0.386349616 0.546089737 0.494304713 1 17.07341719 -0.813074771 7.294160889 1.000000001 0.52902149 0.397252773 0.17672734 2.37E-09 3.25E-10 0.159229301 0.037530706 0.153788984 0.813074771 -0.470978511 APEYLHR ddPTM_MDA-MB-175_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 0 117.16 0.0052935 574890000 554010 717500 666660 624050 726350 828220 605680 624250 659450 817210 FALSE TRUE 575882.7426 840725.0436 684033.7073 747485.2274 602885.2864 635878.4568 558205.2189 615882.9498 635716.5233 977326.6531 0.58924285 0.860229321 0.699902847 0.764826402 0.616871836 0.650630426 0.571155219 0.630171036 0.650464736 1 19.89848131 -0.992666421 4.441725422 1.000009956 0.670141813 0.591490809 0.082176867 0.145849458 50197636.43 1288.500062 0.019846574 0.101702957 0.992666421 -0.329868143 APFDLFENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APFDLFENR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 128.38 0.00097451 409670000 144564 171992 138709 158254 195726 209053 139469 163599 152369 205086 FALSE TRUE 150271.4983 201530.2881 142323.8705 189556.1689 162456.5644 160503.609 128537.0553 161406.223 146885.2695 245268.6751 0.612681168 0.821671532 0.580277406 0.772851114 0.66236165 0.654399136 0.524066334 0.658079239 0.598874966 1 17.90400346 -1.754677223 7.902139235 1.003974581 0.654962391 0.608321752 0.08330642 0.005631107 0.000174818 0.07786488 0.018238842 0.017592306 1.754677223 -0.34901219 APGLITPGS(ph)PPPAQQNQYVHISSSPQNTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APGLITPGSPPPAQQNQYVHISSSPQNTGR 30 0 P54253 P54253 ATXN1 Ataxin-1 1 APGLITPGS(1)PPPAQQNQYVHISSSPQNTGR;APGLITPGS(1)PPPAQQNQYVHISSSPQNTGR;APGLIT(0.006)PGS(0.994)PPPAQQNQYVHISSSPQNTGR 235.97 1.24E-45 802860000 31566.3 440474 361536 445952 297576 501265 250925 435971 297820 505053 TRUE FALSE 32812.5619 516121.9831 370957.9252 534159.9746 246994.1378 384853.8005 231256.8428 430127.5218 287101.5164 604008.4655 0.054324672 0.854494618 0.614160142 0.884358424 0.40892496 0.637166236 0.382870201 0.712121678 0.475326974 1 19.20420924 -1.964710824 2.45659295 1.345234327 0.578471042 0.23995623 0.233390471 14165344.08 6660900.216 27848846.24 0.051870973 0.010846489 1.964710824 -0.766763285 APGLLTPRPPGS(ph)PRPPPPVTPAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APGLLTPRPPGSPRPPPPVTPAALR 25 2 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 APGLLT(0.102)PRPPGS(0.894)PRPPPPVT(0.004)PAALR 51.566 0.067828 242780000 110290 87549 118230 90899 96949 129640 99519 110230 97190 100610 TRUE FALSE 114644.3344 102584.8597 121311.1709 108878.5509 80469.64361 99533.07471 91718.44074 108752.5471 93692.15089 120322.6032 0.952807962 0.852581784 1.008215977 0.904888591 0.668782435 0.827218428 0.76227108 0.903841375 0.778674566 1 16.87654816 3.457984093 24.97469216 0.817760954 0.933875346 0.256631146 0.08944576 295.4369518 385554.802 0.023510813 0.031837867 2870.675436 -3.457984093 0.116114392 APGPRDT(ph)DDDEEEPDPYGFIVQTAEIAEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APGPRDTDDDEEEPDPYGFIVQTAEIAEIAR 31 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 APGPRDT(1)DDDEEEPDPYGFIVQTAEIAEIAR;APGPRDT(1)DDDEEEPDPYGFIVQTAEIAEIAR 120.31 1.87E-05 25790400 7228.7 6513 6882 6149.7 9378.4 8633.6 5152.3 7064.3 9622.3 7022.5 TRUE FALSE 7514.094658 7631.557086 7061.350574 7366.092305 7784.262918 6628.577243 4748.449263 6969.614613 9275.995303 8398.424421 0.894702897 0.908689143 0.84079468 0.877080264 0.926871819 0.78926438 0.56539763 0.829871684 1.104492323 1 13.03590298 4.236145327 24.1163811 0.843910344 0.901696025 0 0.134577083 177.3059266 1770522.115 0.034545101 0.080785453 17224.44855 -4.236145327 0.057785681 APGS(ph)PAAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 APGSPAAPR 9 0 Q5SPY9;Q9NQX5 Q5SPY9 NPDC1 Neural proliferation differentiation and control protein 1 1 APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR;APGS(1)PAAPR 112.83 0.0019913 3276160000 908822 1041668 874785 1113179 1109674 1301642 994113 906681 823000 1061529 TRUE FALSE 944702.9943 1220566.376 897582.6157 1333362.484 921052.0098 999355.3721 916191.8254 894528.4242 793380.3908 1269515.283 0.744144641 0.961442837 0.707027814 1.050292581 0.725514708 0.78719444 0.72168633 0.704622021 0.624947491 1 20.27584633 APGT(ph)PHSHTKPYVR ddPTM_MDA-MB-175_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 138.91 1.86E-05 130765000 88896 92205 101747 81998 119292 122101 90357 91687 94301 100073 TRUE FALSE 92405.68272 108040.4915 104398.6104 98216.95966 99014.78845 93744.89321 83274.58224 90458.08573 90907.12543 119680.3883 0.772103801 0.902741819 0.872311762 0.820660436 0.827326764 0.783293692 0.695808088 0.755830483 0.759582474 1 16.86882724 2.919039183 2.269235521 0.773125591 0.84880197 0.011599055 0.08249878 0.57965735 5.909226509 0.026083475 0.029000548 829.9256425 -2.919039183 0.075676379 APGTPHSHTKPYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APGTPHSHTKPYVR 14 1 J3QQ67;Q07020;F8VYV2;H0YHA7;Q07020-2;F8VUA6 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 194.3 1.03E-07 5909700000 1391170 2051420 1998840 1937760 2017530 2283440 1969030 2161040 1982660 2250090 FALSE TRUE 1446094.466 2403735.427 2050931.412 2321043.144 1674590.971 1753145.666 1814692.283 2132074.794 1911304.454 2690952.055 0.53739139 0.893265795 0.762158288 0.862536046 0.622304276 0.651496433 0.674368122 0.792312442 0.71027072 1 21.35968526 -1.279247069 3.594710877 1.000690461 0.730622352 0.38930072 0.10371352 5644722.871 4036604.815 27654.83845 0.023337325 0.05257181 1.279247069 -0.27006811 APIRPDIVNFVHTNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APIRPDIVNFVHTNLR 16 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 248.06 1.39E-20 9458500000 7502800 9157100 8192500 9276600 9188800 10640800 9503400 8701200 8423800 8849100 FALSE TRUE 7799016.337 10729760.69 8406003.28 11111483.79 7626891.058 8169635.463 8758498.675 8584574.646 8120629.083 10582911.72 0.736944288 1.013876046 0.794299669 1.049945808 0.720679834 0.771964813 0.827607648 0.811173227 0.767334104 1 23.33523328 3.208756979 24.99999361 0.806254061 0.899527035 0.114204137 0.110108438 371.1281821 311310.0857 0.029042142 0.034716479 1617.174852 -3.208756979 0.093272974 APIRPDIVNFVHTNLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APIRPDIVNFVHTNLRK 17 2 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 153.86 9.58E-08 1694270000 1724450 1636040 1782530 1230290 2380500 2051420 1557390 1740680 1882710 1955790 FALSE TRUE 1792532.618 1917017.143 1828984.196 1473637.69 1975863.46 1575008.795 1435317.702 1717349.032 1814951.635 2338989.605 0.766370493 0.819591989 0.78195482 0.63003174 0.844750852 0.673371438 0.613648603 0.734226877 0.775955409 1 21.15745402 -1.797314675 8.586689147 1.004835262 0.734040211 0.535077407 0.073257443 0.006873422 0.000162244 0.071897103 0.016795771 0.015947232 1.797314675 -0.270795051 APKPDGPGGGPGGSHMGGNYGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 APKPDGPGGGPGGSHMGGNYGDDR 24 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ;;;;;; 236.94 1.20E-37 6860010000 3163891 3250689 3299956 3260519 2981398 3896367 3268267 3185933 3882629 2701432 FALSE TRUE 3288803.86 3808969.549 3385955.564 3905439.927 2474621.033 2991494.814 3012091.693 3143230.779 3742893.941 3230725.878 1.017976759 1.178982585 1.048047928 1.208842865 0.765964407 0.925951296 0.932326606 0.97291782 1.158530337 1 21.62342691 3.262499055 24.99994296 0.955627473 1.113470032 0.346139809 0.103740141 260.0528171 271582.5052 0.02839513 0.038427109 1830.202122 -3.262499055 0.157842559 APKPEDIDEEDDDVPDLVENFDEASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APKPEDIDEEDDDVPDLVENFDEASK 26 1 Q96K17;Q96K17-2 Q96K17 BTF3L4 Transcription factor BTF3 homolog 4 0 ; 179.38 2.10E-17 105322000 366980 127216 206276 159616 282040 285570 351200 216052 246632 87453 FALSE TRUE 381468.6538 149064.3584 211651.722 191187.5684 234098.9415 219250.6954 323672.0263 213156.1763 237755.7625 104587.741 3.647355324 1.425256507 2.023676198 1.828011262 2.238301921 2.096332642 3.094741538 2.038060813 2.273266066 1 16.67435423 APKS(ph)PDALESAQSEEEVDELSLIDHNEIMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APKSPDALESAQSEEEVDELSLIDHNEIMSR 31 1 Q13905-2;Q13905;Q13905-4;Q13905-3;H0Y6R4 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 APKS(1)PDALESAQSEEEVDELSLIDHNEIMSR 120.31 7.00E-06 29754000 4362.6 5594.3 5809.5 3656.5 7792.2 7595 4600 7531.3 6651.7 5866.2 TRUE FALSE 4534.838817 6555.077507 5960.900343 4379.744786 6467.684627 5831.176353 4239.43998 7430.355242 6412.306616 7015.569575 0.646396386 0.934361414 0.84966734 0.624289267 0.921904424 0.83117647 0.604290206 1.059123591 0.914010837 1 12.77634452 1.679947884 10.15566071 0.988161339 0.784792123 0.41988702 0.116616582 0.11551636 17.51996224 0.053623426 0.028929482 47.85726595 -1.679947884 -0.203369215 APLATGEDDDDEVPDLVENFDEASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APLATGEDDDDEVPDLVENFDEASK 25 0 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ; 106.69 0.0038185 56535000 47978 36748 50706 42383 54295 50373 60230 49139 49781 25725 FALSE TRUE 49872.20849 43059.18314 52027.44002 50766.2309 45065.95529 38674.63416 55509.01522 48480.37208 47989.39153 30765.32122 1.621052748 1.399601286 1.691106673 1.650112168 1.464829669 1.257085336 1.804272246 1.575812316 1.559853421 1 14.90901744 -0.869556428 5.355305936 0.99999951 1.560551441 0.565389078 0.146805552 8.52E-07 1.81E-07 0.139805626 0.032952473 0.135034136 0.869556428 0.560551932 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 ;;; 223.64 1.36E-34 722590000 742720 535978 667573 526669 867610 835340 762810 690285 767170 565777 FALSE TRUE 772043.1591 628028.0522 684970.5008 630842.5562 720133.9621 641344.9447 703018.959 681032.8587 739559.7016 676630.1707 1.141012022 0.928170335 1.012326276 0.932329925 1.064294785 0.947851533 1.039000313 1.006506786 1.093004323 1 19.36800798 1.415406901 23.96930687 1.047587357 1.005155735 0.048554968 0.064801705 124.8980268 48510.20813 0.038589282 0.014295556 26.02596856 -1.415406901 -0.042431623 APLDIPIPDPPPKDDEMETDKQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLDIPIPDPPPKDDEMETDKQEK 24 2 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 56.766 0.051748 65736000 604100 130240 248130 132000 397490 430730 413110 248340 301210 79913 FALSE TRUE 627950.3345 152607.7069 254596.4716 158109.206 329924.7918 330699.4853 380729.3587 245011.4085 290369.5109 95570.42232 6.570551005 1.596808962 2.663967213 1.654373834 3.452164213 3.46027021 3.983757207 2.563674017 3.038277993 1 16.54427657 4.749225745 24.79792773 2.731043456 6.570553438 0.631359372 0.904997333 905.3333851 2104981.844 0.211661352 3.062555382 56133.96833 -4.749225745 3.839509982 APLDLDKYVEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 213.18 7.26E-09 3737420000 3803503 3235323 3746674 2833513 4802900 4772100 4360078 3953373 4028234 3283452 FALSE TRUE 3953668.235 3790964.558 3844315.402 3393973.414 3986504.774 3663852.097 4018323.693 3900384.501 3883258.645 3926781.554 1.006847002 0.965412643 0.978999048 0.864314291 1.015209203 0.933041995 1.023312257 0.993277688 0.988916392 1 21.90491591 2.234948838 24.99999014 1.000812095 0.959791261 0.196912582 0.040277166 152.9337235 1058560.694 0.014302899 0.010979506 171.770602 -2.234948838 -0.041020834 APLEHELAGEPQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APLEHELAGEPQLR 14 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;;; 145.43 8.58E-06 1055317000 879882 1108050 1003606 1088012 1112810 1266890 1136637 1069799 1061089 1308500 FALSE TRUE 914620.4208 1298348.968 1029760.797 1303217.526 923654.9537 972673.9974 1047544.422 1055460.094 1022900.614 1564875.522 0.584468482 0.829681946 0.658046459 0.832793093 0.590241806 0.62156637 0.669410702 0.674469042 0.653662607 1 20.57761647 -1.577409057 4.420577723 1.004303415 0.682378885 0.577089711 0.082306687 0.003329652 0.000318302 0.076013498 0.017711189 0.026460067 1.577409057 -0.32192453 APLKPYPVS(ph)PSDKVLIQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPYPVS(0.708)PS(0.292)DKVLIQEK 212.82 3.34E-17 2528100000 4850000 2157500 3829900 2379000 4719000 4274500 4343200 3643800 4346800 1871800 TRUE FALSE 5041481.745 2528033.842 3929710.34 2849559.099 3916866.066 3281812.156 4002768.635 3594960.821 4190359.517 2238543.372 2.252126006 1.129320912 1.755476525 1.272952374 1.749738743 1.466048054 1.788113058 1.605937533 1.871913481 1 21.09412884 4.764153261 24.05596217 1.55469799 2.252127499 0.368854703 0.28494941 5116.847984 4809481.219 0.061227853 4.287234409 58096.94033 -4.764153261 0.69742951 APLKPYPVSPS(ph)DKVLIQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLKPYPVSPSDKVLIQEK 19 2 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 APLKPYPVS(0.36)PS(0.64)DKVLIQEK 221.43 1.39E-19 2543900000 4065500 1935300 2942400 2014000 4436700 2976300 3604800 2966900 3578000 1449900 TRUE FALSE 4226009.079 2267672.72 3019081.361 2412363.189 3682551.319 2285099.431 3322246.357 2927133.558 3449228.479 1733980.145 2.437172704 1.30778471 1.741127988 1.391228842 2.123756336 1.317834831 1.915965628 1.688100966 1.989197217 1 20.72565595 -1.952085229 2.588917922 0.442397712 1.742012257 0.301675398 0.348535945 7766143.36 4735846.162 26092573.29 0.074781388 0.011166441 1.952085229 1.299614545 APLQGDHNHLFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLQGDHNHLFIR 13 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 0 61.11 0.050144 55998000 18163 25100 25408 28126 30371 36251 28434 28935 25234 26586 FALSE TRUE 18880.08926 29410.72975 26070.15335 33689.23885 25208.54827 27832.25464 26205.26878 28547.17365 24325.83327 31795.01768 0.593806535 0.925010643 0.819944609 1.059576038 0.792845864 0.875365283 0.824194188 0.897850536 0.765083181 1 14.95651309 -4.99999998 0.017106851 2.018238424 6.23E-27 0.145752932 0.114090451 10406.42618 13.49461238 1027.8956 613.5995111 1.00E-05 4.99999998 -2.018238424 APLS(ph)PSLNSRPSPISATPPALVPETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLSPSLNSRPSPISATPPALVPETR 26 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 APLS(0.871)PS(0.079)LNS(0.033)RPS(0.014)PIS(0.002)AT(0.001)PPALVPETR 55.765 0.05522 324370000 23037 53260 54983 53689 63291 55375 48977 59077 54133 49329 TRUE FALSE 23946.51855 62406.99069 56415.90215 64308.52395 52532.81843 42514.99547 45138.05476 58285.16945 52184.7639 58994.07309 0.405913972 1.057851873 0.956297797 1.090084488 0.890476207 0.720665539 0.765128637 0.987983477 0.884576385 1 15.8482824 4.748131385 24.56140868 0.921599085 0.405913618 0.66058528 0.112208012 670.5350041 1720744.402 0.0285778 0.366147851 55992.69676 -4.748131385 -0.515685467 APLSRPTPLEDLEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APLSRPTPLEDLEGR 15 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 98.507 0.0026461 219380000 134780 136260 125120 129750 156910 156830 143960 128370 135530 134980 FALSE TRUE 140101.2185 159661.595 128380.73 155414.1627 130238.4942 120408.6093 132676.039 126649.4101 130652.3018 161426.7467 0.867893465 0.989065309 0.795287848 0.962753484 0.806796252 0.745902471 0.821896258 0.784562737 0.809359691 1 17.30052011 3.213354452 24.92721564 0.811168416 0.902096678 0.156822453 0.08036363 297.715402 294419.8612 0.021355951 0.025534642 1634.385317 -3.213354452 0.090928263 APPARPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APPARPVK 8 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 77.058 0.031188 261720000 427100 266760 427870 291250 364060 424250 343130 279680 284000 331140 FALSE TRUE 443962.2378 312573.9549 439020.6437 348858.3807 302177.2112 325724.3671 316234.574 275931.3471 273778.8955 396020.5429 1.121058606 0.789287224 1.10858048 0.880909809 0.763034183 0.822493613 0.798530732 0.696760186 0.691324984 1 18.59521574 3.455567815 4.501270938 0.777719214 0.987117596 0.382916326 0.117609051 0.187892257 9.308222304 0.030860548 0.04417649 2854.748246 -3.455567815 0.209398382 APPGLTPAPAS(ph)PPVLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 APPGLTPAPASPPVLPR 17 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 APPGLTPAPAS(1)PPVLPR;APPGLT(0.002)PAPAS(0.998)PPVLPR;APPGLT(0.007)PAPAS(0.993)PPVLPR;APPGLT(0.023)PAPAS(0.977)PPVLPR;APPGLT(0.023)PAPAS(0.977)PPVLPR 174.62 1.40E-09 1287437000 309292 382768 389590 357570 419454 458581 348425 357521 361260 421091 TRUE FALSE 321503.087 448505.4265 399743.0355 428296.2788 348155.3589 352082.5126 321114.5381 352729.0158 348258.3232 503595.7192 0.638415051 0.890606114 0.793777668 0.850476409 0.691338996 0.699137223 0.637643502 0.700420997 0.691543454 1 18.94190649 3.226515609 24.98547977 0.71213215 0.800300683 0.029819356 0.112472628 440.575341 913903.0394 0.029933407 0.036032817 1684.672974 -3.226515609 0.088168533 APPHELTEEEKQQILHSEEFLSFFDHSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APPHELTEEEKQQILHSEEFLSFFDHSTR 29 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5;E7EV09 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 318.13 8.66E-93 361120000 66876 62347 75251 73025 107006 87265 96598 79502 81958 68597 FALSE TRUE 69516.31612 73054.61226 77212.10288 87469.12704 88817.15834 66999.02626 89026.39635 78436.40573 79008.34759 82037.26878 0.847374823 0.890505173 0.941183245 1.066212081 1.082644019 0.816690112 1.085194542 0.956106985 0.963078717 1 16.32399184 4.176700527 2.829293321 0.993648739 0.860931055 0.31193951 0.075016095 0.306450223 4.877968228 0.018841885 0.054528123 15021.05813 -4.176700527 -0.132717684 APPQTHLPSGASS(ph)GTGSASATHGGGSPPGTR ddPTM_MDA-MB-175_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(0.12)S(0.476)GT(0.12)GS(0.031)AS(0.12)AT(0.021)HGGGS(0.083)PPGT(0.029)R;APPQTHLPSGAS(0.104)S(0.43)GT(0.104)GS(0.104)AS(0.003)AT(0.001)HGGGS(0.251)PPGT(0.001)R 152 1.46E-08 1071148000 27386.3 103685 85507 109560 91401 127040 80750 100302 79437 106087 TRUE FALSE 28467.53227 121492.0922 87735.38266 131230.641 75864.69067 97536.88531 74420.604 98957.61575 76578.07789 126872.7165 0.224378677 0.957590375 0.691522851 1.034348792 0.597959063 0.768777465 0.586576894 0.779975542 0.603581921 1 16.95302233 -2.337299084 2.053199362 2.421341486 0.711503814 0.15324598 0.212271664 8433874.373 909619.2421 55675462.39 0.046660187 0.004599397 2.337299084 -1.709837671 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.003)S(0.003)GT(0.001)GS(0.001)AS(0.002)AT(0.005)HGGGS(0.762)PPGT(0.222)R;APPQTHLPSGAS(0.043)S(0.171)GT(0.137)GS(0.059)AS(0.002)AT(0.07)HGGGS(0.359)PPGT(0.159)R;APPQTHLPSGASSGTGSASATHGGGS(0.653)PPGT(0.346)R;APPQTHLPSGASSGTGS(0.001)ASAT(0.003)HGGGS(0.991)PPGT(0.005)R;APPQTHLPSGASSGTGSASAT(0.009)HGGGS(0.937)PPGT(0.054)R;APPQTHLPSGASSGTGSASAT(0.001)HGGGS(0.999)PPGTR 211.71 3.17E-26 20012510000 209677 862136 723380 823301 676826 1002266 652041 755564 633791 813981 TRUE FALSE 217955.2099 1010201.152 742231.8771 986147.4805 561779.3583 769504.911 600932.3226 745436.9004 610980.9857 973464.9923 0.2238963 1.037737525 0.762463861 1.013028191 0.577092513 0.790480312 0.61731272 0.765756248 0.627635293 1 19.89276957 -2.231550095 2.186508277 1.867483477 0.729649193 0.12913015 0.219861068 9124139.15 1510346.31 39162063.39 0.049386442 0.005867457 2.231550095 -1.137834285 APPQTHLPSGASSGTGSASATHGGGS(ph)PPGTRGPGASVHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 APPQTHLPS(0.003)GAS(0.011)S(0.055)GT(0.055)GS(0.055)AS(0.055)AT(0.284)HGGGS(0.44)PPGT(0.01)RGPGAS(0.031)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.999)PPGTRGPGAS(0.001)VHDR;APPQTHLPSGASSGTGSASATHGGGS(0.999)PPGTRGPGASVHDR;APPQTHLPSGASSGTGSASATHGGGS(0.998)PPGTRGPGASVHDR 217.34 2.81E-40 1348440000 9627.3 194167 138408 102561 135659 211627 57798.3 145785 107742 324897 TRUE FALSE 10007.39324 227513.6718 142015.0262 122847.2597 112599.7316 162479.8365 53267.91822 143830.9905 103864.3865 388554.3466 0.025755453 0.585538867 0.365495914 0.316164935 0.289791461 0.418165021 0.137092581 0.370169557 0.267309805 1 18.56775688 -1.327085279 3.493972573 1.003026642 0.317574159 0.67382667 0.144228466 356528385.2 539169095.5 11260022.3 0.031682258 0.047088485 1.327085279 -0.685452483 APPQTHLPSGASSGTGSASATHGGGSPPGTR ddPTM_MDA-MB-175_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 0 145.86 1.02E-08 50143000 2532 20330 14898 18269 14890 17992 13701 14253 13586 21768 FALSE TRUE 2631.965315 23821.51935 15286.25412 21882.55367 12359.00312 13813.63067 12627.07982 14061.96185 13097.04251 26033.02283 0.101101026 0.91505007 0.587187059 0.840569066 0.474743298 0.530619543 0.485040861 0.540158626 0.503093421 1 14.66805522 -1.498988485 3.030377594 1.013162434 0.565522661 0.291074525 0.208435583 49077097.41 58331814.97 5396883.251 0.045740617 0.031696515 1.498988485 -0.447639774 APQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APQSPR 6 0 P12270 P12270 TPR Nucleoprotein TPR 1 APQS(1)PR;APQS(1)PR 73.157 0.087801 321080000 366700 392550 381420 338940 404760 410650 387840 396120 387410 432690 TRUE FALSE 381177.5992 459967.4089 391360.1185 405981.3204 335959.0398 315282.761 357440.0874 390810.6593 373467.1898 517467.3211 0.736621587 0.888882042 0.756299195 0.78455451 0.64923721 0.609280525 0.690749102 0.755237371 0.721721304 1 18.98110823 -1.889696589 5.620822858 1.064034652 0.733061642 0.552085947 0.072279449 0.04619443 0.000906522 0.055738969 0.017858062 0.012891499 1.889696589 -0.33097301 APQTS(ph)SS(ph)PPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 APQT(0.02)S(0.86)S(0.124)S(0.996)PPPVR;APQT(0.169)S(0.632)S(0.346)S(0.854)PPPVR 154.13 0.00010414 842390000 848930 898720 798990 891280 873360 1099680 879100 910430 798170 897240 TRUE FALSE 882446.4119 1053068.169 819812.3358 1067572.524 724906.5792 844295.9858 810193.8449 898227.175 769444.0176 1073036.999 0.822382092 0.981390362 0.764011247 0.994907468 0.675565316 0.7868284 0.755047445 0.837088726 0.717071283 1 20.03326839 3.240366492 24.99999924 0.787587504 0.888105343 0.168429725 0.102945668 77.22193122 1069024.249 0.026460492 0.034064842 1739.26794 -3.240366492 0.100517839 APQTS(ph)SSPPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.153)S(0.309)S(0.309)S(0.229)PPPVR 102.9 0.0024166 160640000 109760 130630 105240 101270 124210 145890 114030 110320 106960 109550 TRUE FALSE 114093.4096 153064.6863 107982.6409 121300.9037 103096.8286 112009.2585 105092.0306 108841.3408 103110.5305 131014.225 0.870847494 1.168305856 0.824205469 0.92586056 0.786913242 0.854939671 0.802142138 0.83075972 0.787017825 1 16.99936394 4.205815767 24.98933859 0.842777996 1.01957691 0.345811238 0.091859071 149.1363884 113813.9173 0.020527979 0.044350409 16062.59712 -4.205815767 0.176798913 APQTSS(ph)SPPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.168)S(0.234)S(0.47)S(0.127)PPPVR 99.161 0.0041456 153450000 149780 167480 182820 173710 176000 217000 161750 163260 156210 152910 TRUE FALSE 155693.4301 196243.3872 187584.4394 208069.3195 146083.5829 166605.0387 149071.6123 161071.7667 150588.0326 182869.7869 0.851389575 1.07313182 1.025781473 1.137800416 0.798839357 0.911058308 0.815179013 0.88080032 0.823471363 1 17.48045721 3.228370956 24.99999681 0.864721485 1.025944521 0.420506245 0.086261401 175.9880222 431780.1387 0.023389264 0.028251002 1691.885452 -3.228370956 0.161223036 APQTSSS(ph)PPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQT(0.004)S(0.037)S(0.078)S(0.881)PPPVR;APQTS(0.032)S(0.032)S(0.936)PPPVR;APQT(0.003)S(0.031)S(0.066)S(0.899)PPPVR;APQT(0.109)S(0.188)S(0.188)S(0.514)PPPVR;APQT(0.007)S(0.254)S(0.254)S(0.485)PPPVR 153 7.37E-05 13139500000 1401320 1643480 1451340 1471290 1502370 1824710 1471660 1548950 1426610 1639900 TRUE FALSE 1456645.196 1925734.906 1489163.113 1762306.771 1246997.684 1400948.756 1356307.444 1528188.859 1375266.585 1961207.007 0.742728937 0.981913127 0.7593095 0.898582742 0.63583175 0.714329875 0.691567713 0.779208341 0.70123479 1 20.90331039 3.257339183 24.98601057 0.739373594 0.849201823 0.132831273 0.111386227 387.1402874 515110.2771 0.028186536 0.038100574 1808.586075 -3.257339183 0.10982823 APQTSSS(ph)PPPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 APQTS(0.002)S(0.022)S(0.977)PPPVRR;APQT(0.003)S(0.036)S(0.22)S(0.741)PPPVRR;APQT(0.003)S(0.019)S(0.419)S(0.56)PPPVRR;APQTS(0.001)S(0.03)S(0.969)PPPVRR 120.37 0.00016864 7143420000 905850 889040 919750 740160 992940 1076760 847970 832400 831840 982990 TRUE FALSE 941613.6575 1041725.704 943719.4406 886561.4388 824160.4135 826698.8085 781503.8956 821243.0395 801902.2409 1175588.07 0.800972451 0.886131572 0.80276371 0.754142936 0.701062247 0.703221502 0.664776987 0.698580617 0.682128597 1 20.16495119 3.746031171 2.359500483 0.71859265 0.843412112 0.128959744 0.094153107 0.408206748 4.447638692 0.024066635 0.047534855 5572.257424 -3.746031171 0.124819462 APRPFGSVSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APRPFGSVSSPK 12 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 APRPFGSVS(0.213)S(0.787)PK 54.501 0.081169 322170000 535370 281020 419500 308760 495160 653200 540110 442380 448240 359110 TRUE FALSE 556506.821 329282.999 430432.5146 369831.8064 410992.8801 501504.1993 497774.7669 436450.6197 432107.93 429470.7289 1.295796858 0.766718141 1.002239467 0.861133906 0.956975301 1.167726147 1.159042359 1.016252308 1.006140584 1 18.71220028 2.779403959 23.38649922 1.073704374 0.959926726 0.095945342 0.138245439 470.0150653 269124.4238 0.040176004 0.042612414 601.7331793 -2.779403959 -0.113777648 APRPSAPS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APRPSAPSPPPR 12 1 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 APRPS(0.012)APS(0.988)PPPR;APRPS(0.002)APS(0.998)PPPR;APRPS(0.027)APS(0.973)PPPR;APRPS(0.011)APS(0.989)PPPR 96.247 0.0033863 1695400000 185411 190313 180371 185085 219541 232131 188443 193495 171658 224751 TRUE FALSE 192731.1694 222997.7773 185071.6164 221694.2606 182223.4992 178222.0932 173672.3453 190901.516 165480.0621 268786.6553 0.717041436 0.829646014 0.688544661 0.824796381 0.677948461 0.663061539 0.646134552 0.710234352 0.615655796 1 18.03610199 -1.175274365 4.471011818 1.000056361 0.709665954 0.634252641 0.066485472 3.97E-05 7.32E-06 0.064629575 0.015230214 0.066792183 1.175274365 -0.290390407 APRPTRPDK ddPTM_MDA-MB-175_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 ;;;;; 112.75 0.0010755 8761350000 2546330 2105920 2336730 2141840 3216440 3213080 3125850 2844620 2951000 2447450 FALSE TRUE 2646861.075 2467595.378 2397627.103 2565489.559 2669710.678 2466890.865 2880837.709 2806492.522 2844794.086 2926980.968 0.90429733 0.843051392 0.819146803 0.876496837 0.912103873 0.842810695 0.984235204 0.958835248 0.971920937 1 21.48098193 2.234534192 24.99898698 0.97387001 0.865659982 0.79112101 0.028256141 47.88655529 297310.845 0.010656456 0.008161452 171.606681 -2.234534192 -0.108210028 APRS(ph)PPVGSGPASGVEPTSFPVESEAVMEDVLRPLEQALEDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APRSPPVGSGPASGVEPTSFPVESEAVMEDVLRPLEQALEDCR 43 2 Q9HD15 Q9HD15 SRA1 Steroid receptor RNA activator 1 1 APRS(0.998)PPVGS(0.001)GPASGVEPTSFPVESEAVMEDVLRPLEQALEDCR;APRS(0.998)PPVGS(0.002)GPAS(0.001)GVEPTSFPVESEAVMEDVLRPLEQALEDCR;APRS(0.999)PPVGS(0.001)GPASGVEPTSFPVESEAVMEDVLRPLEQALEDCR 240.98 4.15E-55 469733000 12047 23992.4 18805.8 13419.5 23356.3 28668.6 10266.2 21970.6 19864.4 32543.6 TRUE FALSE 12522.62486 28112.90807 19295.8946 16073.83705 19386.20447 22010.75213 9461.508418 21676.12004 19149.48412 38919.89534 0.321753817 0.722327432 0.495784853 0.412997952 0.498105257 0.565539859 0.243102103 0.556941889 0.492023012 1 15.24822021 0.272979819 1.728315193 1.000037352 0.480074693 0.607739332 0.125709692 6.868046931 15.45961563 0.113927883 0.031974792 1.874907381 -0.272979819 -0.51996266 APS(ph)APPGTGALPPAAPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSAPPGTGALPPAAPSGR 19 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 APS(1)APPGTGALPPAAPSGR;APS(1)APPGTGALPPAAPSGR 170.89 1.19E-11 208390000 80549 76384 65197 69501 91196 89704 80887 75327 79652 74724 TRUE FALSE 83729.13672 89502.35781 66896.08738 83248.09036 75694.53649 68871.60548 74546.86558 74317.36478 76785.34008 89364.73712 0.93693709 1.001539989 0.748573649 0.931554135 0.847029141 0.770679887 0.834186593 0.831618457 0.859235338 1 16.44741804 4.258367424 24.99947267 0.844940679 0.969238598 0.301962424 0.06995369 249.873906 315376.8856 0.015548736 0.04245828 18128.7318 -4.258367424 0.12429792 APS(ph)ASPLALHASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 APS(0.5)AS(0.5)PLALHASR 93.181 0.003692 353250000 68615 130540 139000 159970 182360 171830 124870 143570 128340 169530 TRUE FALSE 71323.97318 152959.2295 142622.4542 191611.5885 151362.5123 131925.0866 115082.3631 141645.679 123721.0685 202746.1577 0.351789519 0.754437131 0.703453303 0.945081232 0.746561681 0.650690934 0.567617973 0.698635578 0.610226452 1 17.62931505 4.741381626 23.70432677 0.725703417 0.35178923 0.442150876 0.13030982 123.0961861 1034228.508 0.030653024 0.211655723 55129.19184 -4.741381626 -0.373914187 APS(ph)DS(ph)SLGTPSDGRPELR ddPTM_MDA-MB-175_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(0.999)DS(0.549)S(0.449)LGT(0.003)PS(0.001)DGRPELR 83.436 0.0022787 253960000 111070 148520 182920 150580 203800 196630 209480 164100 187190 151560 TRUE FALSE 115455.1294 174027.1547 187687.0455 180364.2746 169158.1488 150965.6625 193060.4102 161900.5079 180453.0685 181255.2802 0.636975261 0.960121848 1.035484568 0.99508425 0.93325915 0.832889736 1.065129854 0.89321816 0.995574133 1 17.4676635 4.738255348 7.976633193 0.963683223 0.634309931 0.702000963 0.064627785 0.049403947 38.59979487 0.014978159 0.088331746 54733.76815 -4.738255348 -0.329373292 APS(ph)DSS(ph)LGTPSDGRPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.24)S(0.76)LGTPSDGRPELR;APS(1)DS(0.287)S(0.712)LGT(0.001)PSDGRPELR 147.08 4.51E-08 734800000 356490 398420 389740 381510 492960 526020 423020 405640 393220 451660 TRUE FALSE 370564.5005 466845.5357 399896.9446 456971.5393 409166.8353 403859.8269 389862.587 400203.0593 379068.089 540154.1294 0.686034745 0.864282082 0.740338586 0.846002121 0.757500152 0.747675163 0.721761745 0.740905304 0.701777638 1 19.0430116 -1.545587652 6.020443978 1.000443584 0.758598239 0.644815084 0.054246158 0.000309702 2.34E-05 0.05036435 0.011849667 0.028471631 1.545587652 -0.241845346 APS(ph)DSSLGTPSDGRPELR ddPTM_MDA-MB-175_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 1 APS(0.968)DS(0.026)S(0.005)LGTPSDGRPELR;APS(0.828)DS(0.138)S(0.034)LGTPSDGRPELR;APS(0.376)DS(0.312)S(0.312)LGTPSDGRPELR 212.26 1.28E-16 4376300000 1415270 1742850 1700870 1571300 1750090 1947040 1765820 1741420 1761830 1700890 TRUE FALSE 1471145.952 2042170.93 1745196.069 1882098.45 1452610.327 1494869.468 1627410.414 1718079.113 1698422.082 2034146.83 0.723225055 1.0039447 0.8579499 0.925252013 0.714112819 0.734887691 0.800045695 0.844619026 0.834955499 1 20.95599239 7.103179822 18.94745692 0.838545803 0.270303952 0 0.101182122 0 0 0.021607555 0 12681768.52 -7.103179822 -0.568241851 APS(ph)LTDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSLTDLVK 9 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 APS(0.992)LT(0.008)DLVK;APS(1)LTDLVK;APS(1)LTDLVK;APS(1)LTDLVK 175.33 5.66E-05 513788000 1591327 1277550 1520054 1189721 1790250 1730124 1505324 1343416 1304807 895725 TRUE FALSE 1654153.819 1496959.275 1559667.856 1425044.263 1485943.944 1328328.921 1387332.771 1325409.706 1257847.251 1071225.164 1.544170053 1.397427287 1.45596641 1.330293864 1.38714436 1.240009072 1.295089789 1.237283953 1.174213688 1 20.03083033 8 0.057911355 0.467473381 3.034411113 0.923958199 0.040428949 80.67846454 0.349638333 3.236982811 17.64240408 99999999.96 -8 2.566937731 APS(ph)PAPSSVPLGSEKPSNVSQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 APS(0.995)PAPS(0.004)S(0.001)VPLGSEKPSNVSQDR;APS(0.988)PAPS(0.009)S(0.003)VPLGSEKPSNVSQDR 192.35 5.72E-18 1267190000 517770 458263 510880 427459 646540 666050 550100 530030 567400 466853 TRUE FALSE 538211.9594 536966.1055 524193.9525 512009.1144 536641.3617 511369.9816 506981.7246 522925.8148 546979.3848 558323.9069 0.963977993 0.961746575 0.938870691 0.917046732 0.961164935 0.915901997 0.9080423 0.936599362 0.97968111 1 19.09074281 1.123350535 3.681767888 0.998751795 0.936530085 0.552039318 0.019075219 0.162778641 3.863575571 0.019074969 0.004988846 13.28466279 -1.123350535 -0.06222171 APS(ph)PARPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 83.869 0.010813 1791610000 3300280 2576170 2928400 2436490 3473590 3826250 3395880 2975260 2652100 2503260 TRUE FALSE 3430577.603 3018607.158 3004716.51 2918420.45 2883150.413 2937661.425 3129702.052 2935381.506 2556651.439 2993725.869 1.145922423 1.008311145 1.003671225 0.974845586 0.963064268 0.981272686 1.045420385 0.98051112 0.854003189 1 21.51351069 APS(ph)PEPAAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 APS(1)PEPAAPR;APS(1)PEPAAPR;APS(1)PEPAAPR;APS(1)PEPAAPR 120.06 0.0006395 2624990000 1726670 1894460 1799810 1852290 1952890 2263690 1981810 1851150 1873330 1819680 TRUE FALSE 1794840.265 2219818.768 1846714.527 2218667.433 1620938.455 1737982.304 1826470.554 1826338.362 1805909.219 2176211.456 0.824754534 1.020038178 0.848591492 1.019509123 0.744844188 0.798627495 0.8392891 0.839228356 0.829840875 1 21.05338732 3.237506194 24.99999999 0.83232374 0.929093535 0.196260581 0.084153991 38.51913614 913283.3128 0.021907646 0.027626011 1727.850624 -3.237506194 0.096769796 APS(ph)PGAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSPGAYK 8 0 P54259 P54259 ATN1 Atrophin-1 1 APS(1)PGAYK;APS(1)PGAYK 106.88 0.0043116 273220000 1061930 799490 1062690 840010 1123840 1192680 1207660 1008920 1119960 730760 TRUE FALSE 1103855.816 936796.1883 1090384.574 1006161.471 932810.0782 915698.1452 1113000.454 995397.0777 1079652.858 873938.4308 1.263081903 1.071924698 1.247667497 1.151295601 1.06736361 1.04778336 1.273545612 1.138978494 1.235387781 1 19.73717212 4.766940989 23.03170249 1.146285731 1.263082406 0.148824356 0.087949707 6673.953774 5415894.989 0.019975972 1.63337 58471.06302 -4.766940989 0.116796675 APS(ph)PGDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPGDYK 8 0 P55198 P55198 MLLT6 Protein AF-17 1 APS(1)PGDYK 63.283 0.089058 0 257690 192130 222990 198680 289390 334760 304720 224600 243990 158850 TRUE FALSE 267863.8002 225126.8329 228801.3026 237978.311 240199.5912 257017.0633 280835.2502 221589.6044 235208.8476 189973.6161 1.410005271 1.185042626 1.204384626 1.252691378 1.26438395 1.352909254 1.478285542 1.166423048 1.23811323 1 17.53543954 0.774478344 1.426112241 1.002251888 1.290658094 0.467762287 0.0934771 0.713832718 2.540287394 0.09026833 0.026616272 5.94947089 -0.774478344 0.288406206 APS(ph)PHVVQENLHSEVVEVCTSSTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSPHVVQENLHSEVVEVCTSSTLK 25 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 APS(0.924)PHVVQENLHS(0.076)EVVEVCTSSTLK;APS(0.815)PHVVQENLHS(0.185)EVVEVCTSSTLK 108.64 0.0055335 241090000 82252 61624 74838 69772 75791 83200 88447 81949 70350 55226 TRUE FALSE 85499.37247 72207.44263 76788.33976 83572.69335 62908.07289 63878.06091 81514.29303 80850.6077 67818.11724 66046.47733 1.294533424 1.093282269 1.162640959 1.265361859 0.95248188 0.967168326 1.234195923 1.224147161 1.026824139 1 16.011194 6.74600156 1.637162189 1.116991755 129.0702942 0.196590437 0.110677996 2067.884939 9.649710708 0.030536386 991263.5659 5571877.509 -6.74600156 127.9533024 APS(ph)PLGPTRDPVATFLETCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPLGPTRDPVATFLETCR 20 1 I3L2L9;E7EVV8;Q0VG06-3;Q0VG06 I3L2L9 C17orf70;FAAP100 Fanconi anemia-associated protein of 100 kDa 1 APS(0.999)PLGPT(0.001)RDPVATFLETCR 212.94 7.48E-23 101860000 22750 25038 22727 31496 26820 26687 26595 28318 24599 22981 TRUE FALSE 23648.18757 29338.08173 23319.28429 37725.81479 22261.14598 20489.3487 24510.41441 27938.44353 23713.6868 27483.68695 0.860444511 1.067472562 0.848477292 1.372662076 0.809976697 0.745509463 0.891816824 1.016546418 0.862827714 1 14.74628794 APS(ph)PLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPLPK 7 0 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 APS(1)PLPK 66.621 0.070675 205490000 564950 418970 519200 405540 627020 664350 607660 513260 553150 402960 TRUE FALSE 587254.6622 490924.8384 532730.7785 485754.6016 520439.3644 510064.7808 560030.0214 506380.5892 533242.2396 481912.2969 1.2185924 1.018701622 1.105451722 1.007973037 1.079946222 1.058418273 1.162099463 1.050773331 1.106513038 1 18.87841109 4.751482941 24.43333848 1.070338292 1.21859253 0.474894295 0.048043848 1329.138415 2513052.126 0.0106198 0.194927275 56426.47764 -4.751482941 0.148254238 APS(ph)PPLSQVFQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 APSPPLSQVFQTR 13 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 APS(0.999)PPLS(0.001)QVFQTR;APS(0.992)PPLS(0.008)QVFQTR;APS(1)PPLSQVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(1)PPLSQVFQTR;APS(0.999)PPLS(0.001)QVFQTR;APS(0.995)PPLS(0.005)QVFQTR 194 1.46E-06 6804309000 548455 551949 569897 472125 599098 687698 549617 575913 484461.3 539673 TRUE FALSE 570108.4269 646741.9472 584748.984 565509.9158 497263.536 527990.5617 506536.5834 568193.8282 467025.6324 645411.5917 0.883325361 1.002061251 0.906009423 0.876200433 0.770459568 0.818067987 0.784827217 0.880358883 0.723608994 1 19.29985996 3.664389886 2.616580632 0.824339798 0.941814507 0.258543833 0.075533195 0.320386399 4.283737475 0.019429555 0.034637098 4617.31906 -3.664389886 0.117474708 APS(ph)PPVEHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APSPPVEHPR 10 0 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 APS(1)PPVEHPR;APS(1)PPVEHPR;APS(1)PPVEHPR 102.97 0.0018528 1484050000 402077 346470 340536 329112 478840 463346 396076 361838 372051 370522 TRUE FALSE 417951.3104 405973.5273 349410.6479 394209.3713 397446.9478 355740.9136 365030.5282 356988.1535 358660.9572 443118.6918 0.943203973 0.91617333 0.788526086 0.889624786 0.896931127 0.802811798 0.823775965 0.805626483 0.809401553 1 18.75733366 2.749547762 24.45951318 0.831920975 0.883205674 0.049534064 0.0665156 1169.314678 2603118.159 0.019547289 0.020555556 561.7560553 -2.749547762 0.051284699 APS(ph)PRPGPGPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 APSPRPGPGPLR 12 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR;APS(1)PRPGPGPLR 100.18 0.002045 11289590000 1792180 2179050 1925340 2172700 1950810 2352230 1802500 1911000 1800250 2323780 TRUE FALSE 1862936.65 2553284.887 1975515.942 2602453.575 1619212.013 1805960.231 1661215.34 1885386.171 1735459.354 2779080.2 0.670342889 0.918751782 0.71085244 0.936444215 0.58264314 0.649840991 0.597757251 0.678420929 0.62447257 1 21.40617604 3.227721693 24.99911066 0.665542456 0.809912745 0.146887232 0.135121062 304.6073706 702551.3857 0.035305689 0.042589984 1689.357999 -3.227721693 0.144370289 APS(ph)PSGLMS(ph)PSRLPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSPSGLMSPSRLPGSR 17 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 APS(0.998)PS(0.004)GLMS(0.973)PS(0.026)RLPGSR;APS(0.998)PS(0.016)GLMS(0.882)PS(0.104)RLPGSR;APS(0.993)PS(0.007)GLMS(0.978)PS(0.022)RLPGSR;APS(0.89)PS(0.11)GLMS(0.998)PS(0.002)RLPGSR 140.51 3.75E-07 724660000 713420 703350 705230 701840 847070 1022390 732700 805390 798810 837360 TRUE FALSE 741586.3725 824144.8912 723608.8732 840661.8572 703085.344 784955.417 675269.0594 794595.0644 770060.9841 1001424.66 0.740531367 0.822972435 0.722579443 0.839465904 0.702085112 0.783838713 0.674308399 0.793464647 0.76896547 1 19.93362246 0.291168226 1.576005552 1.000038219 0.759640876 0.679075664 0.049374956 3.947195063 8.155256423 0.04319238 0.012304217 1.955096627 -0.291168226 -0.240397343 APS(ph)PSGLMSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 APSPSGLMSPSR 12 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 APS(0.787)PS(0.213)GLMSPSR;APS(0.974)PS(0.026)GLMSPSR;APS(0.974)PS(0.026)GLMSPSR;APS(0.859)PS(0.141)GLMSPSR;APS(0.875)PS(0.125)GLMSPSR;APS(0.922)PS(0.078)GLMSPSR;APS(0.928)PS(0.072)GLMSPSR;APS(0.985)PS(0.015)GLMSPSR;APS(0.99)PS(0.01)GLMSPSR;APS(0.99)PS(0.01)GLMSPSR;APS(0.989)PS(0.011)GLMSPSR 210.93 3.97E-08 5022940000 1376008 2150565 1818664 2132402 1921418 2420687 1779241 1893266 1618861 2386384 TRUE FALSE 1430333.858 2519907.81 1866059.878 2554184.751 1594816.055 1858519.13 1639779.441 1867889.866 1560598.509 2853950.255 0.501176871 0.882954356 0.653851578 0.894964706 0.55881004 0.651209364 0.574564829 0.65449279 0.546820501 1 21.44452876 -1.028818998 4.620601245 1.000010352 0.66378901 0.395176358 0.126856198 0.211133458 74091322.12 1813.25563 0.028159362 0.093579561 1.028818998 -0.336221341 APS(ph)PSINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.933)PS(0.067)INR;APS(0.912)PS(0.088)INR;APS(0.983)PS(0.017)INR;APS(0.991)PS(0.009)INR 157.99 0.00038601 1861700000 1323500 1383590 1363960 1308870 1403270 1523180 1182010 1251170 1115430 1159780 TRUE FALSE 1375752.802 1621210.82 1399505.918 1567760.579 1164742.667 1169444.529 1089360.968 1234400.113 1075285.892 1387016.686 0.991879057 1.16884738 1.009004385 1.130311261 0.839746687 0.843136597 0.785398603 0.889967745 0.77525087 1 20.40355371 3.231579701 24.99860877 0.847575211 1.076998437 0.667526188 0.075733203 82.40673315 295097.6051 0.019736987 0.024078897 1704.432085 -3.231579701 0.229423225 APS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 APSPSSR 7 0 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 APS(0.675)PS(0.299)S(0.025)R;APS(0.993)PS(0.006)S(0.001)R;APS(0.98)PS(0.02)SR;APS(0.991)PS(0.009)SR;APS(0.999)PS(0.001)SR;APS(0.824)PS(0.176)SR;APS(0.998)PS(0.002)SR;APS(0.983)PS(0.017)SR;APS(0.951)PS(0.049)SR;APS(0.84)PS(0.158)S(0.002)R 121.35 0.0046647 17202740000 1306190 1388941 1340229 1270606 1362426 1641798 1366065 1333424 1319176 1469076 TRUE FALSE 1357759.39 1627480.812 1375156.469 1521928.074 1130841.315 1260515.296 1258989.256 1315551.632 1271699.113 1756913.315 0.772809551 0.926329602 0.782711621 0.86625109 0.643652311 0.717460153 0.716591561 0.748785737 0.723825759 1 20.74461158 3.270629854 24.99983867 0.74160256 0.839524812 0.122687758 0.096885281 303.7912697 236820.9979 0.024478201 0.033141005 1864.789666 -3.270629854 0.097922253 APS(ph)PTAEQPPGGGDSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 APS(0.998)PT(0.002)AEQPPGGGDSAR 266.24 1.31E-27 232200000 44998 52522 48507 44821 55736 60830 52559 55245 47502 51481 TRUE FALSE 46774.55579 61542.24494 49771.13227 53686.46002 46262.01463 46703.15439 48439.28824 54504.53114 45792.4123 61567.71629 0.759725366 0.999586287 0.808396596 0.87199044 0.75140053 0.758565645 0.786764414 0.885277779 0.743773118 1 15.90988644 6.917000426 9.446959815 0.833676871 0.287402435 0 0.093873518 0 0 0.019350976 0 8260387.604 -6.917000426 -0.546274436 APS(ph)PTGPALIS(ph)GASPVHCAADGTVELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPTGPALISGASPVHCAADGTVELK 27 0 E7EWD6;Q76L83 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 2 APS(0.998)PT(0.044)GPALIS(0.639)GAS(0.319)PVHCAADGTVELK 88.683 0.0038754 169990000 50140 50395 46526 36359 53328 69577 47884 55122 57391 46726 TRUE FALSE 52119.56592 59049.94923 47738.50578 43550.70168 44263.32561 53418.7962 44130.72696 54383.17975 55325.50912 55881.06508 0.932687411 1.056707655 0.854287686 0.779346307 0.792098818 0.955937331 0.789725946 0.973195119 0.990058243 1 15.7700719 1.585007996 8.051236804 0.989831032 0.881257875 0.269519681 0.081591422 0.170028505 23.64771695 0.046713757 0.022169756 38.45988634 -1.585007996 -0.108573157 APS(ph)PTGPALISGAS(ph)PVHCAADGTVELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPTGPALISGASPVHCAADGTVELK 27 0 E7EWD6;Q76L83 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 2 APS(1)PT(0.001)GPALIS(0.167)GAS(0.833)PVHCAADGTVELK 153.55 3.00E-08 202520000 122220 107630 127780 121580 148050 180350 146540 129800 130700 119600 TRUE FALSE 127045.34 126114.6153 131110.0518 145628.1611 122884.5139 138466.4457 135053.8119 128060.2433 125996.1325 143033.3301 0.888221926 0.881714878 0.916639861 1.018141443 0.85913202 0.968071187 0.944212176 0.895317498 0.880886521 1 17.12599184 4.121795969 5.085854177 0.932319437 0.885556233 0.154645805 0.047762475 0.390511716 15.58296186 0.011608828 0.026311544 13237.19507 -4.121795969 -0.046763204 APS(ph)PTK ddPTM_MDA-MB-175_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(0.966)PT(0.034)K;APS(0.97)PT(0.03)K;APS(0.995)PT(0.005)K;APS(0.992)PT(0.008)K;APS(0.974)PT(0.026)K;APS(0.974)PT(0.026)K 109.36 0.031078 21786200000 34579200 20878800 28237000 19896600 34663000 34727900 36357000 27958800 30760900 19922600 TRUE FALSE 35944413.52 24464571.49 28972879.42 23832088.09 28770995.64 26662871.53 33507243.34 27584058.02 29653821.22 23826052.03 1.508618107 1.026799214 1.216016795 1.000253339 1.207543558 1.119063767 1.406327968 1.15772676 1.244596511 1 24.50603658 APS(ph)PTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.611)PT(0.389)KR;APS(0.995)PT(0.005)KR;APS(0.989)PT(0.011)KR;APS(0.713)PT(0.287)KR;APS(0.944)PT(0.056)KR;APS(0.993)PT(0.007)KR;APS(0.937)PT(0.063)KR;APS(0.997)PT(0.003)KR 105.1 0.0049015 8530440000 5137790 3313050 4149170 3232320 5042210 4586380 4919980 4186390 4268680 3081460 TRUE FALSE 5340633.916 3882040.566 4257300.779 3871663.248 4185136.945 3521262.752 4534339.112 4130278.29 4115051.041 3685213.089 1.44920627 1.053410067 1.1552387 1.050594133 1.135656703 0.955511301 1.230414362 1.120770547 1.116638561 1 21.81331661 4.743227402 24.96684963 1.099977994 1.449206415 0.666180137 0.07584447 271.7498603 1453784.569 0.016955585 0.137191167 55363.99265 -4.743227402 0.349228421 APS(ph)RQDVYGPQPQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 APSRQDVYGPQPQVR 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR;APS(1)RQDVYGPQPQVR 258.17 4.96E-25 16100820000 1233320 1570550 1170460 1287320 1310770 1483680 989160 1200850 1003230 1458260 TRUE FALSE 1282012.426 1840279.745 1200963.149 1541948.054 1087965.784 1139117.805 911627.0545 1184754.57 967123.9483 1743978.127 0.735108088 1.05521951 0.688634296 0.884155615 0.623841416 0.653172071 0.522728491 0.679340269 0.554550503 1 20.73395052 3.23580566 24.96321573 0.647114242 0.845229038 0.216606625 0.152461437 85.58655879 775518.6954 0.0398593 0.049707193 1721.09824 -3.23580566 0.198114796 APS(ph)SDEECFFDLLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSSDEECFFDLLTK 15 0 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 1 APS(0.5)S(0.5)DEECFFDLLTK 86.641 0.0078445 17519000 18541 14556 17756 16126 22678 22980 22956 20280 22952 15990 TRUE FALSE 19273.013 17055.87977 18218.73595 19315.67467 18823.20166 17643.24327 21156.64874 20008.17977 22125.962 19122.93435 1.007848097 0.89190704 0.952716545 1.010079014 0.984326009 0.922622174 1.106349494 1.046292342 1.157038015 1 14.2230163 2.235377832 24.99999999 1.078424665 0.961251144 0.557043326 0.050600705 59.44603454 466927.4871 0.017765828 0.013674691 171.9403602 -2.235377832 -0.117173521 APS(ph)VATVGSICDLNLK ddPTM_MDA-MB-175_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 317.67 6.96E-58 280970000 190449 175299 184955 189247 247800 242760 233938 211287 232957 173683 TRUE FALSE 197968.0736 205405.2396 189775.0792 226679.4918 205679.0445 186382.6691 215601.3283 208455.0434 224572.9231 207712.8585 0.953085307 0.988890342 0.91364146 1.091311792 0.990208531 0.897309249 1.037977763 1.003573129 1.081170057 1 17.664231 APSAS(ph)PLALHASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSASPLALHASR 13 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 APS(0.032)AS(0.968)PLALHASR;APS(0.038)AS(0.962)PLALHASR 160.93 2.77E-05 907160000 352750 657780 588110 567220 658750 759480 527250 645370 548400 694220 TRUE FALSE 366676.8424 770748.5982 603436.6297 679414.423 546775.9103 583102.28 485922.7673 636719.8708 528663.1911 830239.1174 0.441652091 0.928345319 0.726822691 0.818335837 0.658576426 0.702330531 0.585280502 0.766911432 0.636760157 1 19.66316738 -1.987837413 2.378790299 1.274797008 0.706240417 0.342537784 0.125599965 8850573.585 3750609.825 13351052.26 0.031377245 0.010284012 1.987837413 -0.568556591 APSDSSLGTPS(ph)DGRPELR ddPTM_MDA-MB-175_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 1 APSDS(0.028)S(0.006)LGT(0.154)PS(0.812)DGRPELR 211.17 8.74E-16 262140000 214680 252910 230740 226820 249070 284090 264810 251140 267940 264840 TRUE FALSE 223155.7322 296345.3251 236753.274 271684.319 206733.1704 218114.4029 244053.5002 247773.8791 258296.8917 316730.3273 0.704560672 0.935639248 0.747491647 0.857778039 0.652710374 0.688643884 0.770540359 0.782286563 0.81551045 1 18.27289549 0.668089466 1.645646323 0.999888012 0.768416795 0.446444474 0.077647912 1.204962373 4.66173282 0.073434358 0.020951505 4.656820152 -0.668089466 -0.231471216 APSEEELHGDQTDFGQGS(ph)QSPQKQEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.5)QS(0.5)PQKQEEQR 297.85 1.31E-71 2213500000 899950 518760 708230 563290 765990 843830 871950 677980 763150 405790 TRUE FALSE 935480.7209 607852.9946 726687.0556 674707.0807 635787.2934 647863.2709 803604.2806 668892.7871 735684.3806 485296.7812 1.927646663 1.25253869 1.497407532 1.390297869 1.31009996 1.334983655 1.655902762 1.378316966 1.515947373 1 18.88850777 -2.194436479 1.742015447 4.51E-05 1.45845586 0.360400613 0.188327555 952459.4775 168640.1737 3744899.992 0.045600428 0.006390922 2.194436479 1.458410775 APSEEELHGDQTDFGQGSQS(ph)PQKQEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 APSEEELHGDQTDFGQGS(0.005)QS(0.995)PQKQEEQR;APSEEELHGDQTDFGQGS(0.395)QS(0.605)PQKQEEQR;APSEEELHGDQTDFGQGS(0.133)QS(0.867)PQKQEEQR;APSEEELHGDQTDFGQGS(0.008)QS(0.992)PQKQEEQR;APSEEELHGDQTDFGQGSQS(1)PQKQEEQR;APSEEELHGDQTDFGQGS(0.025)QS(0.975)PQKQEEQR;APSEEELHGDQTDFGQGS(0.169)QS(0.831)PQKQEEQR 339.2 1.74E-96 10677700000 3330955 2008148 2391309 1981584 2897701 3233639 3201557 2508723 2645459 1501060 TRUE FALSE 3462463.675 2353031.798 2453628.477 2373535.401 2405150.819 2482675.349 2950610.597 2475097.672 2550249.447 1795163.967 1.928772936 1.310761491 1.36679909 1.322183067 1.339794505 1.382979713 1.643644063 1.378758552 1.420622012 1 20.77568419 -2.762324918 0.456794757 3.87E-12 1.449508576 0.361123864 0.181914485 157.3466734 6.480320579 154.4532565 0.091301889 0.001728523 2.762324918 1.449508576 APSEEELHGDQTDFGQGSQSPQKQEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSEEELHGDQTDFGQGSQSPQKQEEQR 28 1 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 177.6 1.06E-17 247080000 54077 49955 71668 48479 77089 71067 56470 64756 67246 63670 FALSE TRUE 56212.00172 58534.38265 73535.72696 58068.0015 63985.43932 54562.76628 52043.73384 63888.05174 64825.8296 76144.91746 0.73822395 0.768723437 0.965733885 0.762598522 0.840311362 0.716564783 0.683482701 0.839032385 0.851348084 1 16.21646012 0.872393025 1.846654157 0.998813434 0.788502454 0.426470035 0.074674641 0.507442805 3.40135177 0.072372876 0.020383672 7.454062415 -0.872393025 -0.21031098 APSGHLAPS(ph)PPAFDGELDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APSGHLAPSPPAFDGELDLQR 21 0 Q9P2Y4;G3V2Q8;G3V452;G3V2W3;G3V2E3;G3V4M7;G3V3F2 Q9P2Y4 ZNF219 Zinc finger protein 219 1 APSGHLAPS(1)PPAFDGELDLQR;APSGHLAPS(1)PPAFDGELDLQR;APSGHLAPS(1)PPAFDGELDLQR 145.63 7.50E-08 815030000 330932 552227 536216 474169 514371 532468 445270 482128 469081 573848 TRUE FALSE 343997.4509 647067.6915 550190.2295 567958.2129 426938.4011 408810.3766 410368.5739 475665.8628 452198.8664 686282.5286 0.501247572 0.942859048 0.801696395 0.827586583 0.622102973 0.59568816 0.597958649 0.693105016 0.658910649 1 19.3884431 -1.342418047 3.016624573 1.003105709 0.69841941 0.353830536 0.124111734 18071143.39 23110739.5 502519.059 0.03022724 0.04545503 1.342418047 -0.304686299 APSGSSLPSS(ph)PGSNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSGSSLPSSPGSNSR 16 0 Q96Q07-3;Q96Q07-2;Q96Q07 Q96Q07-3 BTBD9 BTB/POZ domain-containing protein 9 1 APS(0.002)GS(0.002)S(0.001)LPS(0.435)S(0.558)PGS(0.001)NS(0.001)R 65.472 0.04795 0 120590 111170 114200 105960 125930 141100 123750 129320 111460 111660 TRUE FALSE 125350.9863 130262.5827 117176.1458 126918.5717 104524.4636 108331.6634 114050.1516 127586.6769 107448.5764 133537.6391 0.938694043 0.975474657 0.877476542 0.950432946 0.782734098 0.811244411 0.854067455 0.955436068 0.804631391 1 17.02688691 3.987187844 1.655818919 0.872528692 0.95673056 0.151490032 0.068872731 0.727296519 3.774101172 0.019638283 0.061400112 9709.298286 -3.987187844 0.084201867 APSLPAPPYAGAPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSLPAPPYAGAPGSPR 17 0 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR;APSLPAPPYAGAPGS(1)PR 182.23 7.97E-10 1403460000 280763 315310 321578 316973 353566 354228 294526 320455 282941 340149 TRUE FALSE 291847.74 369462.0397 329958.5869 379669.3133 293466.9776 271963.9154 271440.2825 316159.8249 272758.0087 406794.684 0.717432532 0.908227305 0.811118237 0.93331926 0.72141301 0.668553268 0.667266051 0.777197533 0.670505342 1 18.6339413 5.097492075 10.68276347 0.782690468 0.000187061 0.030225824 0.113666552 273084.5965 900450.7056 0.026983548 4673391.29 125167.6433 -5.097492075 -0.782503408 APSPS(ph)INR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 APS(0.38)PS(0.62)INR 86.18 0.01701 168600000 76869 114730 105950 109040 96215 134180 85254 104810 87527 113910 TRUE FALSE 79903.84748 134433.985 108711.144 130607.7865 79860.40867 103018.7285 78571.56871 103405.1934 84376.92037 136228.4836 0.586542883 0.986827288 0.798005976 0.958740662 0.586224016 0.756220181 0.576763146 0.759057069 0.619377961 1 17.05566886 3.237735386 24.99999967 0.700542496 0.841084537 0.116323935 0.152613132 37.46830922 1135106.632 0.039462058 0.049859477 1728.762708 -3.237735386 0.140542041 APSPT(ph)KR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSPTKR 7 1 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BTY0;H3BUG0;H3BNU7;H3BNI3;H3BTR6;H3BP82;H3BTV0 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 1 APS(0.4)PT(0.6)KR 76.679 0.023502 3544500000 1002100 632160 788910 620520 916540 873410 987330 792070 831430 541310 TRUE FALSE 1041663.682 740728.5625 809469.6427 743257.0039 760746.8582 670573.7642 909940.4947 781453.5972 801506.9967 647369.3305 1.60907172 1.144213245 1.250398504 1.148118962 1.175135772 1.035844197 1.405597164 1.207121747 1.2380985 1 19.30422949 4.742637403 24.88092347 1.192625932 1.609071894 0.584760147 0.108299647 267.8729393 1634780.356 0.024549439 0.189534234 55288.83044 -4.742637403 0.416445962 APSPT(ph)SSAGEEGTKKPEPLSPASYHQPEGVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSPTSSAGEEGTKKPEPLSPASYHQPEGVAR 32 2 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 APS(0.219)PT(0.665)S(0.065)S(0.051)AGEEGTKKPEPLSPASYHQPEGVAR;APS(0.329)PT(0.4)S(0.134)S(0.134)AGEEGT(0.004)KKPEPLSPASYHQPEGVAR 166.46 2.27E-12 1320900000 320830 349720 462710 325215 576780 553280 533110 487890 483890 310804 TRUE FALSE 333496.6161 409781.6896 474768.6027 389541.5563 478739.1416 424789.105 491323.4452 481350.6326 466474.8934 371700.0931 0.89721962 1.10245248 1.277289437 1.04799962 1.287971541 1.142827545 1.321827609 1.294997342 1.254976531 1 18.50377952 5.420920756 1.017899441 1.226777856 2.12E-11 0.416652117 0.106461942 5.490907977 1.695016857 0.030151392 10.24968704 263585.039 -5.420920756 -1.226777856 APSQVSISAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APSQVSISASPR 12 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;Q8IVL1-6;Q8IVL1-7 Q8IVL1-9 NAV2 Neuron navigator 2 1 APSQVSISAS(1)PR;APSQVSISAS(1)PR;APSQVSISAS(1)PR;APSQVSISAS(1)PR 225.29 1.89E-11 3201490000 1553750 1436900 1647090 1345810 1769030 1859550 1439450 1385500 1735110 1473850 TRUE FALSE 1615093.25 1683676.397 1690014.518 1612007.201 1468330.912 1427697.694 1326622.148 1366929.639 1672663.73 1762622.689 0.91630118 0.955210896 0.958806742 0.914550352 0.833037565 0.809984861 0.752641025 0.775508932 0.948963009 1 20.74929225 3.31605778 3.416924159 0.828316866 0.943778675 0.197595941 0.073517736 0.270726011 6.287131244 0.020928407 0.028615378 2070.416785 -3.31605778 0.115461809 APSRPYQDT(ph)RGSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APSRPYQDTRGSYGSDAEEEEYRQQLSEHSK 31 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 APS(0.069)RPY(0.016)QDT(0.679)RGS(0.275)Y(0.334)GS(0.601)DAEEEEY(0.01)RQQLS(0.015)EHS(0.002)K 44.869 0.070166 460200000 27617 31386 40179 29789 48633 53100 34661 35158 38978 35316 TRUE FALSE 28707.34048 36776.30135 41226.09775 35681.17529 40366.38003 40768.32974 31944.18025 34686.76452 37575.18939 42235.49403 0.679697045 0.870743961 0.976100758 0.844814915 0.955745421 0.965262291 0.75633495 0.821270481 0.889659048 1 15.36616831 4.731059077 4.99724016 0.888064431 0.670445879 0.436187776 0.073860936 0.162123951 12.63993555 0.018457531 0.12092936 53834.30082 -4.731059077 -0.217618552 APSRPYQDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 69.721 0.051192 153790000 181200 223300 183980 235820 253130 259760 215850 199810 184910 249520 FALSE TRUE 188353.9159 261650.038 188774.6699 282464.4921 210103.053 199434.6767 198931.113 197131.8738 178255.1252 298408.6667 0.631194523 0.876817825 0.632604515 0.946569332 0.704078254 0.668327361 0.666639864 0.660610417 0.597352373 1 18.18692991 3.028611691 24.97245318 0.690133929 0.776351766 0.018195548 0.136867045 517.7269182 451871.5607 0.036205474 0.043273188 1068.099449 -3.028611691 0.086217837 APSRPYQDTRGS(ph)YGS(ph)DAEEEEYRQQLSEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APSRPYQDTRGSYGSDAEEEEYRQQLSEHSK 31 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 APS(0.004)RPYQDT(0.416)RGS(0.579)Y(0.026)GS(0.975)DAEEEEYRQQLSEHSK;APS(0.012)RPY(0.001)QDT(0.124)RGS(0.816)Y(0.05)GS(0.993)DAEEEEYRQQLS(0.002)EHSK 93.563 0.0002139 687300000 88569 95945 126645 103645 147470 133601 100520 114560 139016 111797 TRUE FALSE 92065.77251 112422.8074 129945.4727 124145.6717 122403.1021 102574.1925 92640.97974 113024.5106 134012.8413 133701.4817 0.688592014 0.840849376 0.9719075 0.928528765 0.91549548 0.767188151 0.692894189 0.845349724 1.002328767 1 17.02865593 1.24751385 7.353773614 1.00231288 0.833611393 0.365236479 0.089564583 0.144750585 45.72542476 0.074040681 0.023885754 17.68128605 -1.24751385 -0.168701488 APTVPPPLPPT(ph)PPQPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APTVPPPLPPTPPQPAR 17 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 APTVPPPLPPT(1)PPQPAR 82.349 0.082327 165710000 82635 94031 72867 77814 78383 90698 75916 77406 73838 79499 TRUE FALSE 85897.49361 110180.0928 74765.97388 93205.37695 65059.48566 69634.76404 69965.50555 76368.49918 71180.5848 95075.30695 0.90346796 1.158871807 0.786386879 0.980332117 0.684294248 0.732416926 0.735895658 0.803242205 0.748675835 1 16.53678307 3.798153947 1.460355172 0.777512812 1.015307221 0.288451512 0.121784064 0.442486431 1.795916109 0.034088268 0.090393849 6282.810293 -3.798153947 0.23779441 APTVPPPLPPT(ph)PPQPARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APTVPPPLPPTPPQPARR 18 1 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 APTVPPPLPPT(1)PPQPARR 83.395 0.0023512 205720000 35068 41751 45952 38252 51406 47721 31861 47457 34071 46242 TRUE FALSE 36452.51172 48921.40947 47149.54687 45818.13143 42668.02648 36638.52097 29363.65157 46820.91654 32844.79137 55302.23454 0.659150792 0.884619037 0.852579417 0.828504161 0.77154254 0.662514296 0.530966819 0.846636975 0.593914362 1 15.75505015 5.023356228 13.93183152 0.763495785 0.438431316 0.056212477 0.135192129 1963652.899 32648658.07 0.031529662 13516371.34 105525.2108 -5.023356228 -0.325064469 APVDEDRLS(ph)PLVAADSLLEHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 APVDEDRLSPLVAADSLLEHVR 22 1 Q01094 Q01094 E2F1 Transcription factor E2F1 1 APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR;APVDEDRLS(1)PLVAADSLLEHVR 305.75 1.57E-56 853259000 200278 263566 232084 238069 260077 279318 246755 248328 242621 269855 TRUE FALSE 208185.1301 308831.4102 238132.2997 285158.3376 215869.2044 214450.6276 227413.6983 244999.5693 233889.1176 322727.9206 0.64507939 0.956940477 0.73787325 0.883587442 0.66888915 0.664493569 0.704660749 0.759152071 0.724725388 1 18.29995887 -1.301758855 3.371276263 1.001090155 0.752857212 0.388890099 0.094124196 159638806.5 224008748.7 1749511.264 0.022027135 0.049916157 1.301758855 -0.248232943 APVDFGYVGIDSILEQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVDFGYVGIDSILEQMR 18 0 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 0 210.91 8.39E-16 71064000 99016 83931 91651 100410 131490 125830 129630 104590 118130 104970 FALSE TRUE 102925.2281 98345.49636 94039.50035 120270.7983 109139.3768 96607.88947 119469.2619 103188.1421 113878.5244 125536.8617 0.819880525 0.783399354 0.749098703 0.958051656 0.869381115 0.769557946 0.951666787 0.821974842 0.907132159 1 16.93775152 -5 0.079753652 1.51539625 0.689174389 0.407352597 0.064057346 256.6217791 1.450579986 23.25049885 2.191472853 1.00E-05 5 -0.826221861 APVHFVEPLS(ph)PTGVAGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APVHFVEPLSPTGVAGHR 18 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 APVHFVEPLS(0.992)PT(0.008)GVAGHR;APVHFVEPLS(0.999)PT(0.001)GVAGHR;APVHFVEPLS(0.99)PT(0.01)GVAGHR;APVHFVEPLS(0.997)PT(0.003)GVAGHR 176.67 1.83E-13 2737130000 637320 719031 749120 667460 792040 874550 840020 775310 732770 785880 TRUE FALSE 662481.8857 842518.981 768642.6826 799481.5958 657409.3237 671449.0164 774177.0374 764918.2376 706397.7508 939858.1394 0.70487434 0.896432074 0.817828404 0.850640711 0.699477183 0.714415281 0.823716905 0.813865631 0.751600397 1 19.84208349 -1.649957947 3.292814126 1.01472304 0.790766274 0.505377451 0.0633849 11078843.58 5630695.087 1169938.761 0.014794626 0.022389379 1.649957947 -0.223956766 APVILGSPDDVLEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APVILGSPDDVLEFLK 16 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 227.31 1.20E-14 187360000 172365 144425 176619 137007 214551 213294 179280 164526 177346 138273 FALSE TRUE 179170.1033 169228.8703 181221.8362 164106.5757 178081.6977 163759.701 165227.5651 162320.7981 170963.3521 165364.947 1.083482967 1.023366036 1.095890269 0.992390338 1.076901126 0.990292707 0.99916922 0.981591329 1.033854848 1 17.33529393 2.726693811 24.87109269 0.998192023 1.051541048 0.425223249 0.030881961 642.8432623 1347303.732 0.009220937 0.008744026 532.9590129 -2.726693811 0.053349024 APVPEPGLDLSLS(ph)PRPDS(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 2 APVPEPGLDLS(0.128)LS(0.872)PRPDS(1)PQPR 90.974 0.0013066 33310000 40268 34919 41035 38710 38391 45875 40660 35876 31394 38130 TRUE FALSE 41857.81173 40916.06662 42104.40581 46366.72246 31865.31153 35221.22649 37472.96295 35395.1409 30264.13607 45600.84346 0.917917489 0.897265566 0.923325154 1.016795282 0.698787766 0.772381031 0.821760303 0.776194873 0.663674919 1 15.47677289 3.238211011 24.99999949 0.779268426 0.934750084 0.403433935 0.08886748 8.676075232 620435.7183 0.023671854 0.030008801 1730.65703 -3.238211011 0.155481659 APVPEPGLDLSLS(ph)PRPDSPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLS(0.267)LS(0.733)PRPDSPQPR 68.657 0.011774 108570000 24612 28406 27715 35869 32274 37707 27497 28906 32290 43184 TRUE FALSE 25583.70076 33284.50953 28437.27567 42963.78114 26788.07701 28950.12071 25341.71329 28518.56235 31127.88921 51645.07799 0.495375392 0.644485609 0.550628962 0.831904662 0.518695644 0.560559144 0.490689806 0.55220291 0.602727122 1 15.65634324 0.930259433 18.13776944 1.000000001 0.581151995 0.639319443 0.094087006 602.895475 156799.575 0.089539089 0.022384772 8.516466308 -0.930259433 -0.418848006 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLS(0.048)LS(0.048)PRPDS(0.904)PQPR;APVPEPGLDLS(0.069)LS(0.043)PRPDS(0.888)PQPR 161 1.08E-11 2026070000 456289 583118 492132 524273 548286 612131 467892 501425 431738 578877 TRUE FALSE 474303.6421 683263.9805 504957.3642 627972.6346 455088.5416 469972.8522 431217.4024 494704.218 416199.8337 692296.8649 0.685115976 0.986952296 0.729394267 0.90708577 0.657360396 0.678860292 0.622879323 0.714583935 0.60118694 1 19.40103129 3.228079186 24.99588338 0.692011433 0.831570826 0.144464199 0.130959334 300.3448155 716254.6636 0.034168976 0.041251143 1690.749181 -3.228079186 0.139559393 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 APVPSTCSSTFPEELSPPSHQAK 23 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(0.949)PPS(0.051)HQAK;APVPSTCSSTFPEELS(1)PPSHQAK;APVPSTCSSTFPEELS(1)PPSHQAK 279.57 4.47E-52 15352770000 1374950 1157830 1341730 1156890 1489620 1603900 1471630 1315109 1414250 1169140 TRUE FALSE 1429234.088 1356678.296 1376696.586 1385719.389 1236414.924 1231418.532 1356279.795 1297482.115 1363351.419 1398210.598 1.022187995 0.970296104 0.984613182 0.991066289 0.884283759 0.880710341 0.970011096 0.927959004 0.97506872 1 20.41515025 3.290117095 24.99993 0.934987385 0.989957301 0.313584135 0.037524978 119.6366053 58011.30548 0.010331086 0.013988357 1950.370389 -3.290117095 0.054969917 APVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 APVQPQQSPAAAPGGTDEKPSGK 23 1 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 APVQPQQS(1)PAAAPGGTDEKPSGK;APVQPQQS(1)PAAAPGGTDEKPSGK;APVQPQQS(1)PAAAPGGTDEKPSGK 204.88 9.97E-25 1380760000 1207732 671815 900934 655086 1171849 1155070 1179529 934611 1084391 542385 TRUE FALSE 1255414.192 787194.0003 924413.0802 784660.0556 972658.5256 886822.4978 1087074.435 922084.0683 1045363.98 648654.9562 1.935411392 1.213578949 1.425122974 1.209672489 1.499500646 1.36717139 1.675890124 1.421532449 1.611587131 1 19.30709173 -2.121174222 2.493249484 0.060913523 1.468364317 0.327525815 0.207080244 8797926.323 3290106.665 46624696.07 0.046489217 0.007565293 2.121174222 1.407450794 APVS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APVSPLK 7 0 Q9UBS0 Q9UBS0 RPS6KB2 Ribosomal protein S6 kinase beta-2 1 APVS(1)PLK;APVS(1)PLK 90.919 0.017607 922210000 1103500 662110 890710 774900 1120080 1288550 1211160 996580 973830 608150 TRUE FALSE 1147067.032 775822.242 913922.6343 928172.9072 929689.2017 989303.7907 1116226.114 983222.4752 938782.0485 727305.3488 1.577146427 1.066707736 1.256587259 1.276180505 1.278265316 1.3602317 1.534742067 1.351870266 1.29076742 1 19.47220166 2.746197634 20.19747762 1.34970128 1.275785337 0 0.171763412 160.8294581 425336.9 0.050166473 0.052004655 557.4393642 -2.746197634 -0.073915944 APVSGSRS(ph)PDREASGSGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APVSGSRSPDREASGSGGR 19 2 Q8N5F7 Q8N5F7 NKAP NF-kappa-B-activating protein 1 APVS(0.031)GS(0.031)RS(0.9)PDREAS(0.031)GS(0.006)GGR;APVS(0.136)GS(0.136)RS(0.591)PDREAS(0.023)GS(0.113)GGR 67.877 0.019795 347776000 81862 117660 106933 84251 116931 124107 77456 101478 102466 162170 TRUE FALSE 85093.97497 137867.1897 109719.7618 100915.5963 97055.11039 95285.03011 71384.79633 100117.8534 98778.26868 193944.1066 0.438755147 0.710860424 0.565728775 0.5203334 0.500428253 0.491301498 0.368068912 0.516220138 0.509313072 1 17.56528141 -0.536211189 7.650503185 1 0.513731526 0.754965348 0.083157654 0 0 0.082853361 0.019528725 0.290930204 0.536211189 -0.486268475 APVSGSRSPDREAS(ph)GSGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVSGSRSPDREASGSGGR 19 2 Q8N5F7 Q8N5F7 NKAP NF-kappa-B-activating protein 1 APVS(0.001)GS(0.001)RS(0.117)PDREAS(0.721)GS(0.16)GGR 118.51 6.13E-05 232060000 55825 95428 81591 67203 82995 102140 62993 74954 84632 114010 TRUE FALSE 58029.01411 111817.0167 83717.32849 80495.55282 68887.53955 78419.53295 58055.44406 73949.36423 81586.11085 136348.0766 0.425594666 0.820085031 0.613997135 0.590368084 0.505232939 0.575142201 0.425788508 0.542357223 0.598366423 1 17.05693482 0.802620102 5.424857801 0.999999242 0.564388686 0.605314622 0.10540163 3.714501845 101.8515516 0.101086911 0.025483514 6.347754212 -0.802620102 -0.435610556 APVSSTESVIQSNT(ph)PT(ph)PPPSQPLNETAEEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 APVSSTESVIQSNT(1)PT(0.997)PPPS(0.003)QPLNETAEEESR 187.7 1.53E-19 101430000 29196 43917 39862 32138 39426 49482 35886 35941 40178 45627 TRUE FALSE 30348.68062 51459.40312 40900.83647 38494.80048 32724.3826 37990.55541 33073.16155 35459.26968 38732.00163 54566.73707 0.55617547 0.94305443 0.749556207 0.705462752 0.599713019 0.696221864 0.606104805 0.649833059 0.709809743 1 15.73573416 0.942045511 20.06991484 1.000000001 0.68988007 0.457542284 0.10127715 1526.45002 528619.2891 0.097708102 0.024427026 8.750754719 -0.942045511 -0.31011993 APVSSTESVIQSNTPT(ph)PPPSQPLNETAEEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 APVSSTESVIQS(0.001)NT(0.014)PT(0.985)PPPS(0.001)QPLNETAEEESR 105.96 3.64E-11 0 27464 27840 28017 28939 34844 34188 26788 36051 28523 32055 TRUE FALSE 28548.29993 32621.30343 28747.14604 34663.04783 28921.22933 26248.35512 24688.28656 35567.79531 27496.4628 38335.56352 0.744694934 0.850941018 0.749881922 0.904200816 0.754422961 0.684699864 0.644004791 0.927801552 0.7172573 1 15.22639577 -1.318176013 0.758713436 1.066397925 0.781439111 0.367339174 0.087804332 109.7649789 24.55483634 15.28920607 0.03011216 0.048064451 1.318176013 -0.284958814 APWNHGEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APWNHGEER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 125.48 0.0015992 0 26278 28757 35873 34676 32129 35181 31849 29443 25633 36853 FALSE TRUE 27315.47573 33695.79105 36807.87985 41534.8093 26667.72406 27010.74592 29352.59216 29048.36474 24710.47334 44073.63976 0.619769002 0.764533886 0.835144999 0.942395716 0.605071971 0.612854896 0.665989746 0.659087039 0.560663323 1 15.42762842 3.206941441 24.98640218 0.66229809 0.791801008 0.116563704 0.136019 327.3298293 258664.7441 0.037462444 0.044779966 1610.428474 -3.206941441 0.129502918 APYFSGSSTFS(ph)PTILSSDKETIEIIDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 APYFSGSSTFSPTILSSDKETIEIIDLAK 29 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 APYFSGSSTFS(0.781)PT(0.218)ILSSDKETIEIIDLAK;APYFS(0.007)GS(0.006)S(0.047)T(0.394)FS(0.466)PT(0.079)ILSSDKETIEIIDLAK 239.56 1.37E-45 259868000 402150 218335 299610 208377 422800 380070 402280 303630 372040 201056 TRUE FALSE 418027.1925 255832.3378 307418.0827 249593.3487 350932.607 291804.5025 370748.2424 299560.3365 358650.3531 240449.0738 1.73852694 1.063977223 1.278516394 1.038029986 1.459488288 1.213581313 1.541899233 1.245836933 1.491585505 1 17.87537184 APYS(ph)PTTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 APYS(0.903)PT(0.067)T(0.026)S(0.004)K;APYS(0.988)PT(0.011)TSK;APYS(0.625)PT(0.37)T(0.005)S(0.001)K;APYS(0.639)PT(0.24)T(0.095)S(0.026)K 110.39 0.0024076 2598260000 5263170 3921550 4466950 4044170 5531580 5603600 5608220 4564560 4556490 3137020 TRUE FALSE 5470964.016 4595045.707 4583362.387 4844094.755 4591324.007 4302248.823 5168633.062 4503379.539 4392502.815 3751659.007 1.458278592 1.224803666 1.221689492 1.291187378 1.223811652 1.146759025 1.377692656 1.200370164 1.170816113 1 21.83909727 -5 0.135737777 0.125161949 1.353972989 0.529182756 0.081762229 116.1655365 0.979000243 27.48367095 0.536535697 1.00E-05 5 1.228811039 APYTCGGDSDQYVLMS(ph)SPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 APYTCGGDSDQYVLMSSPVGR 21 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 APYTCGGDSDQYVLMS(0.5)S(0.5)PVGR 96.379 0.0013504 37763000 23197 23299 26138 26355 29137 40460 25229 29224 30498 31271 TRUE FALSE 24112.83547 27300.42201 26819.17775 31567.94034 24184.30315 31063.77818 23251.48506 28832.30008 29400.38294 37397.95373 0.644763498 0.729997748 0.717129551 0.84410876 0.646674503 0.83062775 0.621731478 0.770959296 0.786149508 1 15.19067171 0.721738175 1.631124272 0.999634502 0.725717994 0.576584021 0.070815816 0.655106425 2.739695764 0.061529524 0.017614112 5.269121035 -0.721738175 -0.273916508 AQAEAQQPTFDALRDELR ddPTM_MDA-MB-175_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 ;;;;; 237.31 6.92E-24 7842020000 2579230 3068990 2850790 2767090 2996380 3316820 2768430 2936270 2836700 3295370 FALSE TRUE 2681059.992 3596065.159 2925083.929 3314412.143 2487056.398 2546538.822 2551433.223 2896914.103 2734607.721 3941034.658 0.680293432 0.912467276 0.742212181 0.841000506 0.631066868 0.646159966 0.647401874 0.735064356 0.693880658 1 21.91014301 -1.42984631 3.007313195 1.005265009 0.726953106 0.481367684 0.08546459 12253043.55 14529248.37 547159.2277 0.021765821 0.037166673 1.42984631 -0.278311903 AQAGEGVRPSPMQLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AQAGEGVRPSPMQLELR 17 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;;; 263.07 2.03E-27 4942620000 1908010 2285840 1976670 1891240 2242680 2477800 2013530 2054390 2010250 2443850 FALSE TRUE 1983339.708 2678415.239 2028183.644 2265321.627 1861470.055 1902368.501 1855704.257 2026854.262 1937901.495 2922675.617 0.678604118 0.916425765 0.693947571 0.775084862 0.636906143 0.650899638 0.634933363 0.69349272 0.663057331 1 21.47885829 -1.157026086 3.697523312 1.000220573 0.70526251 0.547551756 0.080497011 29701609.87 54946526.85 80861.12727 0.01988637 0.069658467 1.157026086 -0.294958063 AQAGSNQSRGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQAGSNQSRGK 11 1 Q96PY0 Q96PY0 PSMG3-AS1 Putative uncharacterized protein PSMG3-AS1 0 64.439 0.062286 1320800000 19765 1757700 1709100 1682600 1413100 2013400 1313900 1754000 1536500 1868700 FALSE TRUE 20545.33746 2059571.302 1753640.55 2015413.258 1172901.767 1545818.363 1210913.085 1730490.499 1481201.665 2234835.987 0.009193219 0.921576042 0.784684228 0.901817077 0.524826776 0.691692085 0.541835326 0.774325503 0.662778689 1 21.09173753 -4.999999997 0.043206209 2.143782997 4.10E-12 0.187631733 0.242415953 1531.759135 4.930013628 230.3024176 63.03237784 1.00E-05 4.999999997 -2.143782997 AQAHAENNEFITWNDIQACVDHVNLVVQEEHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQAHAENNEFITWNDIQACVDHVNLVVQEEHER 33 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 205.42 1.28E-27 78491000 35979 40862 33919 43185 31620 41708 41401 36093 33917 33388 FALSE TRUE 37399.4787 47879.73064 34802.957 51726.86411 26245.24369 32021.94909 38155.88144 35609.23237 32696.3338 39929.73935 0.936632177 1.199099504 0.871604913 1.295447077 0.657285625 0.801957378 0.95557552 0.891797266 0.818846662 1 15.28517603 3.234245762 24.99998833 0.856418265 1.069932518 0.369715853 0.141553847 116.9689858 677711.2724 0.038312659 0.047333349 1714.927492 -3.234245762 0.213514252 AQALDRDGNLVEDFVFDAGVGDIGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQALDRDGNLVEDFVFDAGVGDIGNR 26 1 Q9H9P8 Q9H9P8 L2HGDH "L-2-hydroxyglutarate dehydrogenase, mitochondrial" 0 55.985 0.081934 19582000 13018 16344 14901 14500 14050 17307 9543.1 9907.5 11224 16731 FALSE TRUE 13531.96069 19150.95486 15289.3323 17368.05672 11661.78602 13287.71154 8795.086886 9774.706168 10820.05043 20009.11912 0.676289676 0.957111343 0.764118211 0.868007063 0.582823559 0.664082785 0.439553927 0.488512568 0.540755961 1 14.28837003 3.23109221 24.59865467 0.576903653 0.822700609 0.240682745 0.161126455 146.7325361 483291.8271 0.043724491 0.053258165 1702.519951 -3.23109221 0.245796957 AQAVS(ph)EEEEEEEGK ddPTM_MDA-MB-175_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 244.32 1.46E-17 750740000 523270 298610 402960 327360 447060 522550 549980 399370 457610 223140 TRUE FALSE 543929.1037 349893.9446 413461.4686 392110.8309 371068.9009 401195.6818 506871.1305 394017.0984 441140.7055 266860.0107 2.038256321 1.311151655 1.549357161 1.469350278 1.39050021 1.503393786 1.899389605 1.476493602 1.653079097 1 18.02572361 -2.069557256 2.303124684 0.170859657 1.573249636 0.403661369 0.213698728 3245389.718 1174879.514 14116137.22 0.049329431 0.008520062 2.069557256 1.402389978 AQAVS(ph)EEEEEEEGKSSSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQAVSEEEEEEEGKSSSPK 19 1 G3V529;Q9GZR7;Q9GZR7-2 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 AQAVS(1)EEEEEEEGKSSSPK;AQAVS(1)EEEEEEEGKSSSPK;AQAVS(1)EEEEEEEGKSSSPK 220.49 1.75E-19 770450000 498560 238752 358824 201327 502570 457140 399498 302072 419640 186628 TRUE FALSE 518243.5338 279755.7988 368175.2482 241148.8797 417143.3309 350976.163 368184.3029 298023.2189 404537.2384 223194.1834 2.321940142 1.253418859 1.64957367 1.080444284 1.868970439 1.572514829 1.649614238 1.335264273 1.812490058 1 17.7679399 -2.588420193 0.39549692 7.69E-18 1.597306007 0.225733538 0.334340869 121.7860008 5.160823502 105.0402642 0.196605207 0.002579763 2.588420193 1.597306007 AQCLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQCLSR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ; 106.42 0.074774 198028000 195013 211811 192414 168290 235410 234990 163604 184842 176273 247430 FALSE TRUE 202712.2638 248187.8916 197428.4669 201577.2597 195395.0923 180417.1338 150780.291 182364.4953 169928.9692 295909.1712 0.685048939 0.838729975 0.667192795 0.681213289 0.660321177 0.609704434 0.509549232 0.616285378 0.57426057 1 18.17479489 -1.14097654 3.836597543 1.000174511 0.646919898 0.624865006 0.081538392 18799949.19 32487687.57 40932.03867 0.021490632 0.072280885 1.14097654 -0.353254613 AQCPIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQCPIVER 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 98.933 0.016683 191916000 115095 190887 176535 178438 163414 218950 145781 156140 142777 212480 FALSE TRUE 119639.0395 223670.3574 181135.6471 213732.5038 135636.9467 168102.1807 134354.3043 154047.1987 137638.4837 254111.3878 0.470813372 0.880205957 0.712819873 0.8410977 0.53376965 0.661529505 0.528722091 0.606219186 0.541646263 1 17.9551015 -1.128704824 4.652347298 1.000031261 0.646347905 0.408096102 0.129290715 4.14E-05 7.76E-06 0.123652734 0.029142656 0.074352432 1.128704824 -0.353683356 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSR 33 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 375.4 1.88E-148 1065420000 256659 312156 297267 270333 346221 389884 291112 306390 279893 369830 FALSE TRUE 266792.0955 365766.3648 305014.0222 323804.0605 287370.4781 299339.3497 268293.8808 302283.3432 269819.7056 442291.1077 0.603204747 0.82698105 0.689622778 0.732106196 0.64973153 0.676792602 0.606600214 0.683448837 0.610050035 1 18.75463671 -1.944702102 6.363257991 1.14294853 0.678593626 0.695755877 0.0643651 0.03386961 0.000294333 0.016170939 0.014174979 0.011357896 1.944702102 -0.464354904 AQDGSHPLSLQDLIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQDGSHPLSLQDLIEK 16 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 222.3 9.78E-15 256950000 580190 445670 538780 449460 629170 659960 624300 555320 606450 381380 FALSE TRUE 603096.3492 522210.3557 552821.0494 538361.8465 522223.9081 506694.2918 575365.7347 547876.8437 584623.983 456104.109 1.322277825 1.144936749 1.21205014 1.1803486 1.144966462 1.11091806 1.261478955 1.201210059 1.281777496 1 18.79900364 -2.146943314 2.539215331 0.523207891 1.201898795 0.490263538 0.063049908 17644371.5 15942407.61 46621256.04 0.014611089 0.007129461 2.146943314 0.678690903 AQEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQEEAER 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 133.68 0.0075565 343680000 329660 406160 351020 396410 396350 403090 439900 382310 367610 379380 FALSE TRUE 342675.2314 475914.8205 360167.8696 474818.7148 328978.5686 309478.4564 405419.4885 377185.7598 354379.7879 453712.2473 0.755269961 1.048935362 0.793824438 1.046519501 0.725081967 0.682102937 0.893560822 0.831332551 0.781067273 1 18.79141808 3.220711567 24.99967022 0.810918762 0.912600616 0.122795862 0.119679965 451.4566149 632316.085 0.032586534 0.039023976 1662.308277 -3.220711567 0.101681854 AQEEAERLEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AQEEAERLEADR 12 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 200.16 1.49E-07 10585900000 7769320 9953430 8900010 7475570 10610750 11159700 7672850 8950880 9098810 11835310 FALSE TRUE 8076058.753 11662854.18 9131951.572 8954215.434 8807138.505 8568028.802 7071431.968 8830908.094 8771345.605 14154212.39 0.570576344 0.82398468 0.645175536 0.632618417 0.622227381 0.605334198 0.499599114 0.62390671 0.6196986 1 23.75472814 -1.344545805 5.397712058 1.000108116 0.626885239 0.679211337 0.076899094 0.000102349 1.24E-05 0.076166801 0.017947519 0.045232875 1.344545805 -0.373222877 AQELDALDNSHPIEVSVGHPSEVDEIFDAISYSK ddPTM_MDA-MB-175_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 ;; 260.79 6.58E-60 838110000 145383 325312 362188 373516 407156 466783 378037 380463 367254 327748 FALSE TRUE 151122.8331 381181.8054 371626.9168 447396.35 337947.7686 358379.7224 348405.4721 375363.5158 354036.6003 391963.9455 0.385552893 0.972492011 0.948115053 1.141422203 0.862190955 0.914318081 0.888871224 0.95764807 0.903237669 1 18.58036143 4.739837394 24.97432006 0.951716452 0.385552708 0.842237066 0.073832598 39.37307188 770069.8197 0.017521749 0.108982843 54933.51564 -4.739837394 -0.566163744 AQELGHSQSALASAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQELGHSQSALASAQR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 232.78 9.80E-17 505750000 278350 176123 182569 177267 223031 268580 207853 183974 180821 198387 FALSE TRUE 289339.4729 206370.7552 187326.8981 212329.8835 185120.2703 206206.3654 191560.9387 181508.1295 174313.2875 237257.1343 1.219518535 0.869818966 0.789552224 0.894935717 0.780251649 0.86912609 0.807398013 0.765027066 0.734701985 1 17.85609194 4.736527401 3.518589368 0.819819502 1.266673026 0.714505221 0.073137902 0.137011249 2.991526583 0.016555376 0.162294428 54516.42908 -4.736527401 0.446853525 AQEPPAGGGGSIHDLPLFT(ph)ETSPTSAPWDPLPGPPPVLPHSPHSHL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGS(0.002)IHDLPLFT(0.2)ET(0.2)S(0.2)PT(0.2)S(0.2)APWDPLPGPPPVLPHSPHSHL 54.349 0.026965 133340000 4638.6 13064 12353 14082 13680 17519 9922.8 13544 13123 15780 TRUE FALSE 4821.73551 15307.64038 12674.92933 16867.37757 11354.67849 13450.47775 9145.025008 13362.46483 12650.70579 18871.78887 0.255499653 0.81113881 0.671633697 0.893787954 0.601674731 0.712729347 0.484587077 0.708065617 0.670350112 1 14.20394356 0.403681227 1.761973117 0.999977539 0.653288838 0.288421259 0.166979971 7.226414754 19.86278082 0.149204016 0.04184882 2.533268526 -0.403681227 -0.346688701 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(ph)PHSHL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHSPHSHL 46 0 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 AQEPPAGGGGSIHDLPLFTETSPTSAPWDPLPGPPPVLPHS(0.952)PHS(0.048)HL;AQEPPAGGGGSIHDLPLFTETSPT(0.001)S(0.001)APWDPLPGPPPVLPHS(0.845)PHS(0.152)HL 235.54 2.67E-60 279840000 14879.3 63789 57906 66030 52859 73408 48252 60537 51881 73068 TRUE FALSE 15466.74625 74744.26454 59415.07793 79090.53692 43874.04606 56360.10451 44469.88216 59725.60053 50013.81294 87384.27563 0.176996904 0.855351423 0.679928711 0.905088889 0.502081705 0.644968492 0.508900278 0.683482241 0.572343395 1 16.41508608 -1.71431303 2.578739302 1.067992889 0.62908059 0.262098907 0.192703753 17035742.14 13452961.36 7480393.873 0.045403814 0.019305763 1.71431303 -0.438912299 AQEQS(ph)PR ddPTM_MDA-MB-175_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 116.12 0.0057988 70173000 111798 146068 129441 120442 129562 152187 136888 125162 120299 151692 TRUE FALSE 116211.8714 171154.0427 132814.3388 144265.0681 107539.0975 116843.8757 126158.3609 123484.4081 115969.4625 181413.1431 0.640592348 0.943448969 0.732109794 0.795229418 0.592785593 0.644076133 0.695420181 0.680680606 0.639256123 1 17.46891945 -1.120777387 3.809013115 1.000126842 0.709535533 0.458326708 0.095502997 21320466.17 35973638.11 33612.89751 0.024135289 0.075722094 1.120777387 -0.290591309 AQFSVAGVHTVPGS(ph)PQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQFSVAGVHTVPGSPQAR 18 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 AQFSVAGVHT(0.003)VPGS(0.997)PQAR;AQFSVAGVHT(0.001)VPGS(0.999)PQAR 119.34 4.93E-05 1090640000 659670 885260 776040 818830 915480 978430 745700 790250 771740 893790 TRUE FALSE 685714.281 1037296.519 796264.2399 980792.13 759867.0366 751204.4608 687250.0855 779657.9913 743965.2282 1068911.038 0.641507344 0.97042362 0.744930319 0.917561982 0.710879587 0.702775473 0.642944138 0.729394649 0.696002943 1 20.02771036 5.03344241 16.60849225 0.772798051 0.169822907 0.105288285 0.120743628 19937566.13 268430732.6 0.028055792 349893025.7 108004.639 -5.03344241 -0.602975144 AQGAGVTLPPT(ph)PSGSR ddPTM_MDA-MB-175_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(0.976)PS(0.024)GSR;AQGAGVTLPPT(0.997)PS(0.003)GS(0.001)R 215.51 1.79E-13 250700000 206905 225645 243412 265694 277147 311600 208890 212058 205366 282730 TRUE FALSE 215073.7692 264397.7735 249755.5167 318247.4802 230037.6519 239235.6223 192516.656 209215.7094 197974.9178 338125.5303 0.636076693 0.781951523 0.73864732 0.941211035 0.6803321 0.707534927 0.569364448 0.61875159 0.585507156 1 18.36719943 3.02860204 24.96402566 0.661613246 0.777237633 0.051796243 0.134565455 391.6579105 341838.5664 0.036860856 0.044056583 1068.075713 -3.02860204 0.115624387 AQGEPVAGHES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQGEPVAGHESPK 13 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 AQGEPVAGHES(1)PK;AQGEPVAGHES(1)PK 128.82 0.00016873 373450000 845970 340470 403640 388140 543880 716070 696740 464380 474030 213924 TRUE FALSE 879369.5488 398943.074 414159.19 464912.9335 451431.4719 549773.5946 642127.6982 458155.7457 456969.7529 255838.312 3.43720822 1.559356263 1.61883178 1.817213888 1.764518646 2.148910343 2.509896556 1.790801941 1.786166229 1 17.9648728 4.744810557 24.73262098 1.8405415 3.437209046 0.63749715 0.372775059 394.3040244 1560312.806 0.087521392 0.811369034 55566.18202 -4.744810557 1.596667547 AQGEPVAGHES(ph)PKIPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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(0.999)PKIPY(0.001)EK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(1)PKIPYEK 246.17 1.74E-24 53425743000 20242585 8273369 11822471 7626962 17680085 15304405 15146617 11839535 13246253 6443965 TRUE FALSE 21041777.89 9694255.768 12130574.31 9135552.319 14674830.47 11750188.88 13959385.58 11680845.4 12769522.94 7706536.565 2.730380594 1.257926396 1.574063031 1.18542905 1.90420565 1.524704227 1.811369539 1.515706219 1.656972991 1 22.87765121 -2.821448303 0.192424395 5.60E-40 1.794439042 0.224684404 0.401383035 87.63050389 1.83551492 39.04596251 1.092412786 0.001508522 2.821448303 1.794439042 AQGGQTQS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQGGQTQSPTK 11 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 AQGGQT(0.022)QS(0.978)PTK;AQGGQT(0.03)QS(0.969)PT(0.001)K;AQGGQT(0.038)QS(0.961)PT(0.001)K;AQGGQT(0.034)QS(0.802)PT(0.164)K 154.1 3.37E-05 285741000 744290 439419 571609 449497 693280 710900 730460 600685 639970 461412 TRUE FALSE 773675.1439 514885.795 586505.6001 538406.165 575436.5132 545804.2488 673204.6365 592633.8001 616937.6047 551816.8471 1.402050604 0.933073714 1.062862802 0.975697222 1.042803452 0.989103996 1.219978404 1.073968298 1.118011543 1 19.07382998 2.278727407 24.99995992 1.109342803 1.055964294 0.011709395 0.13097114 596.7613339 371424.1766 0.042992722 0.035969889 189.9885409 -2.278727407 -0.053378509 AQGGSSDSSLALHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQGGSSDSSLALHER 15 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ; 158.17 9.90E-09 0 95699 155833 128346 124770 144117 163378 124235 145200 127474 145090 FALSE TRUE 99477.27042 182596.1055 131690.8022 149449.1336 119620.0438 125435.9355 114497.1361 143253.8315 122886.2356 173517.6076 0.573297845 1.052320327 0.758947775 0.861290884 0.68938274 0.722900328 0.659858891 0.825586714 0.708206143 1 17.40472254 -1.546230158 3.076327365 1.009265037 0.769277003 0.247090348 0.124298531 407099620.6 428238661.5 30883271.12 0.02796429 0.028429541 1.546230158 -0.239988033 AQGPRPHQENNHQESYPLS(ph)VSPMENNHCPASSESHPKPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.931)VS(0.069)PMENNHCPAS(0.156)S(0.101)ES(0.28)HPKPS(0.375)S(0.089)PR;AQGPRPHQENNHQES(0.005)Y(0.001)PLS(0.248)VS(0.24)PMENNHCPAS(0.236)S(0.235)ES(0.093)HPKPS(0.471)S(0.471)PR 176.2 2.24E-21 593810000 77482 143926 148917 148586 178164 196142 170865 172290 170359 122854 TRUE FALSE 80541.04919 168644.1709 152797.8994 177975.8673 147879.7469 150590.9931 157472.1548 169980.7344 164227.8129 146924.8891 0.54817839 1.147825749 1.039972875 1.21133913 1.006498952 1.024952232 1.071786787 1.156922666 1.117767138 1 17.16471928 4.742169625 24.99767746 1.09158667 0.548178184 0.85103508 0.06751438 120.4824951 834482.8963 0.015708782 0.116501272 55229.31095 -4.742169625 -0.543408486 AQGPRPHQENNHQESYPLSVS(ph)PMENNHCPASSESHPKPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQGPRPHQENNHQESYPLSVSPMENNHCPASSESHPKPSSPR 42 2 P41212 P41212 ETV6 Transcription factor ETV6 2 AQGPRPHQENNHQESYPLS(0.442)VS(0.539)PMENNHCPAS(0.014)S(0.005)ES(0.017)HPKPS(0.515)S(0.467)PR;AQGPRPHQENNHQESYPLS(0.37)VS(0.443)PMENNHCPAS(0.09)S(0.096)ES(0.076)HPKPS(0.483)S(0.442)PR 107.88 3.11E-06 584640000 44780 83331 87812 72811 88422 94340 82265 84776 85188 68740 TRUE FALSE 46547.94898 97642.45102 90100.45286 87212.79848 73392.06002 72430.96474 75816.85434 83639.71639 82122.10052 82208.28689 0.566219669 1.187744627 1.096002073 1.060875999 0.892757443 0.881066465 0.922253184 1.017412229 0.99895161 1 16.32699621 1.670556639 9.377802331 1.005818738 0.959286897 0.024718218 0.157434842 0.7002513 95.48023205 0.074842151 0.039971816 46.83350262 -1.670556639 -0.046531841 AQGTHVLVHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQGTHVLVHCK 11 0 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 114.76 0.00070185 539510000 478850 353760 402880 382070 710580 606020 515310 429930 457430 539570 FALSE TRUE 497755.3678 414515.5281 413379.3838 457642.3056 589795.8654 465281.0393 474918.6557 424167.4916 440967.1837 645288.4108 0.771368832 0.642372498 0.640611821 0.709205834 0.914003499 0.721043539 0.735978901 0.657330094 0.683364487 1 19.29958459 -2.23023125 2.321999586 1.970370671 0.716676924 0.548186706 0.076364422 5495045.168 681021.7044 28190386.96 0.019320282 0.005885302 2.23023125 -1.253693748 AQGVRS(ph)PLLR ddPTM_MDA-MB-175_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 122.46 0.00029552 2390850000 1529850 1878620 1697700 1595650 2342460 2308030 1623610 1779270 1687250 2439970 TRUE FALSE 1590249.659 2201258.371 1741943.457 1911264.807 1944289.486 1772025.011 1496347.206 1755421.796 1626526.202 2918035.405 0.544972709 0.754363147 0.596957615 0.654983419 0.666300855 0.607266453 0.512792683 0.601576592 0.557404547 1 21.47656596 -1.972787902 2.888202714 1.323512776 0.612301557 0.761335627 0.065378778 43220210.2 38986493.22 93771775.56 0.015706693 0.010646628 1.972787902 -0.711211219 AQHEDQVEQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQHEDQVEQYK 11 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 160.52 2.74E-05 526900000 945520 733930 901760 800340 1064610 1177060 1167120 960810 1022710 681980 FALSE TRUE 982849.8597 859976.7683 925260.6064 958644.8632 883647.9725 903705.6535 1075638.085 947931.9135 985902.8669 815600.9237 1.20506222 1.054408772 1.134452622 1.17538472 1.083431795 1.108024313 1.318828919 1.162249681 1.208805481 1 19.63750388 AQHEDQVEQYKK ddPTM_MDA-MB-175_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 ;;;;; 222.79 1.56E-11 12487867000 13323551 7911380 11321500 7713080 14780121 13433905 12950716 11219273 13316116 7396920 FALSE TRUE 13849575.08 9270097.973 11616547.59 9238704.203 12267801.31 10314084.16 11935605.04 11068897 12836871.59 8846204.851 1.565595113 1.047918077 1.313167374 1.044369236 1.386786935 1.165933226 1.349234529 1.251259402 1.451116247 1 23.07662722 AQHTLPQDPAIVQSSLGSASAS(ph)PFQPHVPYSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQHTLPQDPAIVQSSLGSASASPFQPHVPYSPFR 34 0 Q9BX40;Q9BX40-2;Q5TBQ1;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 1 AQHTLPQDPAIVQSSLGSASAS(0.866)PFQPHVPYS(0.133)PFR 256.08 2.84E-59 742750000 184860 261860 242700 289960 245910 316560 248320 274930 211340 252810 TRUE FALSE 192158.4155 306832.418 249024.9614 347313.2226 204110.306 243043.7375 228856.0295 271245.013 203733.9147 302343.2792 0.635563708 1.014847821 0.823649734 1.148738029 0.67509457 0.803866844 0.756941018 0.897142526 0.673849656 1 18.20582798 AQIEDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQIEDTLRR 9 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ; 105.4 0.006008 376570000 292267 337250 294230 321923 393310 391350 326310 312480 332700 353940 FALSE TRUE 303805.9268 395170.0641 301897.8755 385598.4086 326455.3067 300464.8935 300732.9695 308291.7167 320726.192 423287.7664 0.717729051 0.933573081 0.713221358 0.910960437 0.771237283 0.709835996 0.710469315 0.728326546 0.757702484 1 18.69127927 3.0192659 24.87715204 0.754329811 0.822215255 0.001047436 0.103931775 549.4985052 709536.4904 0.027437452 0.032789955 1045.360054 -3.0192659 0.067885444 AQIHDLVLVGGS(ph)TR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQIHDLVLVGGSTR 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 1 AQIHDLVLVGGS(0.913)T(0.087)R;AQIHDLVLVGGS(0.977)T(0.023)R 87.772 0.0043865 107002000 72152 97035 87803 91555 80026 120153 86487 82651 79715 126085 TRUE FALSE 75000.61667 113700.0064 90091.21831 109664.3057 66423.2091 92249.28669 79707.92295 81543.19853 76846.07272 150788.9417 0.497388043 0.754034116 0.597465685 0.727270213 0.440504511 0.611777533 0.528605891 0.540777046 0.509626713 1 17.20217111 -1.480467395 4.621375621 1.001666362 0.580507021 0.642977072 0.094192469 0.001569067 0.000176394 0.088488129 0.020780935 0.033077494 1.480467395 -0.421159341 AQIHDLVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 167.69 3.61E-06 14639120000 5892200 7309590 6589620 6822410 7624020 7694290 6535840 6791960 6322300 7475860 FALSE TRUE 6124828.606 8564955.222 6761350.911 8171862.335 6328091.804 5907407.756 6023543.783 6700924.886 6094761.658 8940611.633 0.685057002 0.957983142 0.756251495 0.914016028 0.707791823 0.660738661 0.673728379 0.749492894 0.681694039 1 23.0919421 4.054514471 24.99998376 0.753052762 0.830419526 0.017876214 0.120938991 253.8950866 116430.9587 0.028690645 0.061978867 11337.42615 -4.054514471 0.077366764 AQIS(ph)SPNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQISSPNLR 9 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 AQIS(0.864)S(0.136)PNLR 141.08 0.00011282 933270000 750670 951310 820870 872670 927400 1026500 801200 853420 832450 963350 TRUE FALSE 780307.0312 1114690.092 842262.5466 1045281.521 769760.8793 788110.9318 738399.8505 841981.3008 802490.2871 1152099.988 0.677291068 0.967528951 0.73106723 0.907283684 0.668137217 0.684064699 0.640916464 0.730823114 0.696545695 1 20.1358345 5.037527089 16.81790561 0.763969678 0.306658719 0.043790773 0.124548631 20077101.63 237730033.8 0.02880775 280556725.8 109025.2494 -5.037527089 -0.45731096 AQISS(ph)PNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQISSPNLR 9 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 AQIS(0.203)S(0.797)PNLR;AQIS(0.247)S(0.753)PNLR 144.7 0.001503 1009600000 673710 807640 694870 731730 753510 905730 717140 778920 698190 879510 TRUE FALSE 700308.591 946345.8874 712978.883 876464.01 625428.6393 695387.934 660928.6929 768479.8515 673062.2783 1051833.145 0.665798177 0.899711035 0.677844092 0.833272857 0.594608225 0.661120005 0.628358876 0.730610035 0.639894532 1 20.00447443 -1.123009387 4.118242767 1.000068229 0.706368698 0.492177053 0.090319091 10134461.01 5527163.899 6098.855512 0.020561712 0.075333928 1.123009387 -0.293699531 AQIWDTAGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQIWDTAGLER 11 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 ;; 199.03 1.20E-07 245494000 257333 321945 334554 354244 349726 397985 290324 311641 314660 333298 FALSE TRUE 267492.7055 377236.5494 343272.7521 424312.4059 290279.6994 305559.0153 267567.6463 307463.9621 303335.4481 398601.3617 0.671078253 0.946400554 0.861193124 1.064503152 0.728245629 0.766577951 0.671266262 0.771357029 0.760999528 1 18.60458711 AQIWDTAGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQIWDTAGQER 11 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;; 207.67 5.16E-08 768660000 754170 955590 841560 1068550 948720 1085530 864990 801160 820870 948190 FALSE TRUE 783945.2139 1119705.149 863491.7449 1279906.001 787456.9133 833432.1089 797189.8236 790421.7606 791327.049 1133969.676 0.691328199 0.987420715 0.761476927 1.128695085 0.694425018 0.734968603 0.703008061 0.697039592 0.697837928 1 20.11295063 AQKLPDLS(ph)PVENK ddPTM_MDA-MB-175_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 132.51 7.15E-05 199040000 754030 342100 506160 349180 658560 660050 588790 452450 610840 289340 TRUE FALSE 783799.6866 400853.0138 519350.9454 418246.7618 546618.2064 506763.3907 542639.1013 446385.6478 588855.9877 346030.6333 2.26511647 1.15843216 1.500881412 1.208698657 1.579681548 1.464504417 1.568182262 1.290017718 1.701745254 1 18.40054024 -3.166635803 0.256175505 2.29E-50 1.542293275 0.211809639 0.298052271 106.7967436 2.453677955 58.69693352 0.389949082 0.00068134 3.166635803 1.542293275 AQLADSFHLQQFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQLADSFHLQQFFR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 181.26 1.66E-06 833290000 361278 621570 500057 589840 583050 706510 538970 608590 478659 643320 FALSE TRUE 375541.5344 728319.8124 513088.8962 706508.5915 483943.3693 542433.7598 496724.1231 600432.8465 461432.1561 769366.2369 0.488118033 0.946649044 0.666898119 0.918299449 0.629015605 0.705039725 0.64562766 0.780425261 0.599756181 1 19.55331099 -2.00773316 3.686559783 1.298851808 0.720135939 0.295135519 0.133959666 0.082386504 0.000172819 0.032476052 0.027323102 0.009823513 2.00773316 -0.578715869 AQLEPVAS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AQLEPVASPAK 11 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK 151.99 3.48E-05 1145164000 5123160 2318520 3049580 2728780 3867760 4440940 4945790 3259630 3491090 1957400 TRUE FALSE 5325426.313 2716707.774 3129054.56 3268524.539 3210319.537 3409598.988 4558126.056 3215939.992 3365446.353 2340915.053 2.274933601 1.160532404 1.336680097 1.396259354 1.371395144 1.456524013 1.947155686 1.373796109 1.437662741 1 21.15864115 4.749709549 24.70745086 1.42223821 2.274934186 0.56559675 0.231657862 1077.682483 2388227.415 0.054607241 0.83252812 56196.53642 -4.749709549 0.852695976 AQLEPVAS(ph)PAKKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQLEPVASPAKKPK 14 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 1 AQLEPVAS(1)PAKKPK 94.057 0.0022521 265090000 1014500 348280 558200 280370 875350 727230 702300 531360 724370 372120 TRUE FALSE 1054553.243 408094.3808 572747.1506 335826.3492 726558.3197 558341.8538 647251.8909 524237.9883 698300.0652 445029.7893 2.369623941 0.917004638 1.286986095 0.754615438 1.632606035 1.254616808 1.45440127 1.177984038 1.56910859 1 18.76354238 4.748887024 24.85508667 1.241098681 2.369624619 0.622000477 0.266921328 854.527547 2056756.34 0.059850391 0.836099229 56090.20452 -4.748887024 1.128525938 AQLGEDIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQLGEDIRR 9 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ;;; 121.61 0.00097667 642860000 392734 724750 552742 641326 655190 756890 501275 620656 538003 859130 FALSE TRUE 408239.4416 849220.1747 567146.9106 768178.3686 543821.0378 581113.7683 461983.7557 612337.1215 518640.3771 1027460.074 0.397328764 0.82652377 0.551989245 0.747647902 0.529286783 0.565582822 0.449636698 0.595971694 0.504779105 1 19.9706509 -1.079514929 4.919042189 1.000012445 0.580323754 0.52249205 0.1219651 1.55E-05 2.90E-06 0.109803936 0.025880269 0.08326933 1.079514929 -0.419688691 AQLGGPEAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQLGGPEAAK 10 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 150.08 5.17E-05 92336000 181210 119080 161520 124380 210430 193040 175960 161290 170710 139820 FALSE TRUE 188364.3107 139531.0637 165729.3439 148981.9928 174661.1838 148209.3855 162167.7954 159128.1714 164566.1804 167215.052 1.126479396 0.834440812 0.991114986 0.890960419 1.044530272 0.886339978 0.969815776 0.951637843 0.984158893 1 17.35134519 1.077231778 3.661383046 0.999732967 0.956718566 0.021233126 0.078839151 0.79930169 20.48647023 0.06622726 0.017179396 11.94625492 -1.077231778 -0.043014401 AQLGGPEAAKS(ph)DETAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(0.995)DET(0.005)AAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK;AQLGGPEAAKS(1)DETAAK 204.65 5.21E-12 13740600000 7761130 2425776 3874470 2371204 5591000 6214300 5530870 3479860 4747670 1780050 TRUE FALSE 8067545.405 2842384.158 3975441.871 2840221.074 4640643.817 4771123.004 5097345.957 3433218.169 4576802.284 2128816.716 3.789685295 1.3351944 1.867442059 1.334178303 2.179917032 2.241208915 2.394450362 1.612735442 2.149927821 1 21.02162031 -1.917215088 0.306385462 1.16E-14 2.126950461 0.201056473 0.66430255 54.05221107 2.623056562 40.4891327 0.642185089 0.012099987 1.917215088 2.126950461 AQLGINEDHS(ph)EGDEKSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQLGINEDHSEGDEKSEK 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1;C9JLY8 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 AQLGINEDHS(1)EGDEKSEK;AQLGINEDHS(1)EGDEKSEK;AQLGINEDHS(1)EGDEKSEK;AQLGINEDHS(1)EGDEKSEK 278.95 2.04E-39 663600000 1162450 443507 623660 425779 955730 1114150 1064210 743020 832650 377423 TRUE FALSE 1208344.424 519675.8772 639913.0919 509996.8154 793275.356 855405.5476 980794.4394 733061.0322 802683.0891 451371.8107 2.677048932 1.151325504 1.417707258 1.129881848 1.757476513 1.895123992 2.172919124 1.62407358 1.778319049 1 18.7839568 3.050982368 24.99998871 1.769177091 1.536517502 0 0.491964989 360.4983869 176773.3218 0.13659895 0.163266952 1124.559317 -3.050982368 -0.232659589 AQLLHALS(ph)LDEGGPEPEPSLSDSSSGGSFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQLLHALSLDEGGPEPEPSLSDSSSGGSFGR 31 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR;AQLLHALS(1)LDEGGPEPEPSLSDSSSGGSFGR 218.16 4.82E-35 574349000 132845.2 164788 143628 127782.9 206519 168389 154640 191921 167448 164498 TRUE FALSE 138090.0311 193089.0571 147371.0637 153057.9762 171414.9741 129283.2067 142518.9127 189348.6129 161421.5792 196728.2336 0.701932959 0.981501504 0.749109881 0.778017336 0.871328792 0.65716651 0.724445648 0.962488248 0.820530822 1 17.5858445 1.726900938 10.61197287 0.917075357 0.785710181 0.326446152 0.096263034 0.123293083 50.6045354 0.04459469 0.024230103 53.3213256 -1.726900938 -0.131365176 AQLNIGNVLPVGTMPEGTIVCCLEEKPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQLNIGNVLPVGTMPEGTIVCCLEEKPGDR 30 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ; 179.81 6.80E-18 492470000 246800 171486 227091 175333 258270 229200 229710 223920 245920 182294 FALSE TRUE 256543.8546 200937.3865 233009.178 210013.3441 214369.3577 175971.7736 211704.73 220918.7187 237069.3872 218011.0191 1.176747192 0.921684543 1.068795417 0.963315272 0.983295975 0.807169171 0.97107353 1.013337397 1.087419288 1 17.73404153 4.748963407 24.47637715 0.978258865 1.176747342 0.390518757 0.073884166 1179.325052 2774720.317 0.017931074 0.248100126 56100.07047 -4.748963407 0.198488476 AQLS(ph)PGIYDDTSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQLSPGIYDDTSAR 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR;AQLS(1)PGIYDDTSAR 222.09 4.22E-12 2269980000 1492290 1576320 1504350 1612790 1634580 1809560 1621330 1556780 1491870 1577900 TRUE FALSE 1551206.761 1847040.698 1543554.597 1931795.048 1356734.675 1389317.114 1494245.918 1535913.91 1438177.89 1887059.294 0.822023328 0.978793143 0.817968254 1.023706597 0.718967697 0.736233948 0.79183835 0.813919263 0.762126497 1 20.84770832 3.225600539 24.99997052 0.792183961 0.908873979 0.233838332 0.093239843 284.7599928 549300.702 0.024797001 0.02981321 1681.12706 -3.225600539 0.116690018 AQLSTILEEEKAQQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQLSTILEEEKAQQEER 17 1 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2 E7ESA6 PTK2 Focal adhesion kinase 1 0 180.08 8.03E-10 302650000 78555 68516 81275 63464 108280 110020 73666 72557 78975 75450 FALSE TRUE 81656.41206 80283.09002 83393.09327 76016.98978 89874.60428 84469.52237 67891.86643 71584.49209 76132.70518 90232.98292 0.904950822 0.889731087 0.924197456 0.842452364 0.996028297 0.936126898 0.752406318 0.793329554 0.843734771 1 16.46136726 2.259819442 24.99989999 0.823424188 0.915130469 0.149095536 0.071161197 299.506298 352211.7485 0.023688812 0.019801449 181.8944474 -2.259819442 0.091706281 AQLSVQTS(ph)PVPTPDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AQLSVQT(0.257)S(0.742)PVPTPDPK 174.52 4.03E-09 60795000 136410 67501 95184 75603 135280 121860 117410 92039 101230 63997 TRUE FALSE 141795.5721 79093.77167 97664.57323 90557.04775 112285.1539 93559.86181 108207.0974 90805.36775 97586.75207 76535.98685 1.852665366 1.033419375 1.276060808 1.183195664 1.467089647 1.222429679 1.413806784 1.18644015 1.275044016 1 16.22385064 -5 0.095435602 0.068722095 1.526512552 0.228876119 0.204120964 325.7949211 2.137783199 61.83142297 3.725366857 1.00E-05 5 1.457790457 AQLYLPSTS(ph)PPHEGLDGFAQELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2;I3L465 I3L1Z8 CNTROB Centrobin 1 AQLYLPS(0.02)T(0.11)S(0.87)PPHEGLDGFAQELSR;AQLYLPS(0.014)T(0.172)S(0.814)PPHEGLDGFAQELSR;AQLYLPS(0.246)T(0.154)S(0.6)PPHEGLDGFAQELSR 225.56 3.82E-33 485160000 152386 215276 198455 190862 207127 242646 198542 210914 187865 241937 TRUE FALSE 158402.3169 252247.9784 203626.9003 228613.9339 171919.6265 186295.1438 182979.7592 208087.0428 181103.7753 289339.923 0.547460977 0.871804954 0.703763581 0.790122329 0.594178725 0.643862561 0.63240412 0.719178469 0.625920452 1 18.14240587 -1.597769666 5.039605236 1.002939637 0.687121473 0.524383081 0.090981356 0.002870674 0.000229119 0.084154604 0.019673767 0.025248195 1.597769666 -0.315818164 AQNDLIWNIKDELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQNDLIWNIKDELKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 227.4 4.14E-13 2083200000 1818490 766400 1168700 687780 1809480 1406730 1599580 1132540 1394020 613130 FALSE TRUE 1890285.389 898023.2382 1199157.282 823820.8312 1501905.236 1080038.277 1474200.74 1117360.154 1343849.493 733261.0844 2.577915874 1.224697802 1.635375595 1.123502731 2.048254391 1.472924583 2.01047181 1.523823066 1.832702595 1 19.48396745 -0.455356346 12.21664271 1.000000023 1.685528494 0.214848724 0.407096543 0 0 0.354949779 0.083662465 0.350464194 0.455356346 0.685528471 AQNTWGCGNSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQNTWGCGNSLR 12 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 205.12 2.45E-07 1019540000 174406 218420 174832 182242 210759 219820 178583 205205 182234 234990 FALSE TRUE 181291.6836 255931.9359 179388.2655 218288.9237 174934.2605 168770.1364 164585.1978 202454.5626 175675.4339 281031.7913 0.64509315 0.910686776 0.638320187 0.776741032 0.622471428 0.600537525 0.58564619 0.720397367 0.625108758 1 18.10037382 -1.297215369 9.328622568 1.000000088 0.683422969 0.50828783 0.094219729 1.70E-07 1.28E-08 0.089895217 0.0211885 0.05044111 1.297215369 -0.316577119 AQPDVHFFQGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQPDVHFFQGLR 12 0 Q8TE68;B4DKV7;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 91.914 0.0080297 60962000 141220 167430 170100 159340 182300 213290 165930 167160 165860 217240 FALSE TRUE 146795.4746 196184.8001 174532.9457 190856.9764 151312.7111 163756.6299 152923.973 164919.4936 159890.731 259804.0187 0.56502388 0.755126118 0.671786936 0.734619031 0.582410972 0.630308302 0.588612808 0.634784229 0.615428244 1 17.98706422 -1.723643642 3.581768223 1.03645772 0.643845353 0.764530999 0.059594069 0.017326608 0.001336859 0.057624423 0.013438304 0.018895412 1.723643642 -0.392612367 AQPFGFIDS(ph)DTDAEEERIPATPVVIPMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQPFGFIDSDTDAEEERIPATPVVIPMK 28 1 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 AQPFGFIDS(0.992)DT(0.008)DAEEERIPATPVVIPMK 103.5 0.00064117 47688000 15902 45733 30245 41425 25482 42057 25116 33839 22578 47050 TRUE FALSE 16529.82324 53587.287 31033.20955 49618.74136 21150.57874 32289.89913 23147.34229 33385.44355 21765.42219 56268.54667 0.293766664 0.952348873 0.551519657 0.881820205 0.375886352 0.573853441 0.41137267 0.593323367 0.386813299 1 15.78004108 -1.085245166 4.820779163 1.000016759 0.569386376 0.29535666 0.204180574 3.41E-05 6.47E-06 0.183384267 0.043222405 0.082177861 1.085245166 -0.430630383 AQPGS(ph)PESSGQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQPGSPESSGQPK 13 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 AQPGS(0.973)PES(0.02)S(0.007)GQPK;AQPGS(0.884)PES(0.097)S(0.019)GQPK 81.128 0.010743 175030000 344140 324550 369590 330480 459870 483550 408640 377220 406130 336780 TRUE FALSE 357726.9129 380288.9379 379221.819 395847.9576 381701.4617 371252.8408 376609.729 372163.9829 391513.4606 402765.593 0.888176446 0.944194203 0.941544724 0.982824662 0.947701264 0.921759076 0.935059339 0.92402129 0.972062826 1 18.61958092 1.028761701 4.357944019 0.999764173 0.937113111 0.46407776 0.022576376 0.155349676 7.150477549 0.021992711 0.005604301 10.68468445 -1.028761701 -0.062651062 AQPPKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQPPKPER 8 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 63.565 0.090962 0 34789 33561 37191 33910 47206 44766 40108 37908 40049 35876 FALSE TRUE 36162.49658 39324.84068 38160.22801 40617.29679 39181.94098 34369.77494 36964.23016 37399.90526 38607.64431 42905.21531 0.842846174 0.916551529 0.88940768 0.946675049 0.913220938 0.80106287 0.861532331 0.871686693 0.899835697 1 15.3888654 0.838971987 4.515307015 0.999996429 0.881259028 0.459312359 0.038734464 1.469824939 40.29073097 0.038857703 0.009864335 6.901952839 -0.838971987 -0.118737401 AQPQDSATFAHT(ph)PPPAQATPAPGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQPQDSATFAHTPPPAQATPAPGFK 25 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 AQPQDSATFAHT(0.999)PPPAQATPAPGFK;AQPQDSATFAHT(1)PPPAQATPAPGFK 154.42 2.96E-07 488300000 282210 205646 283000 242658 297350 346150 289380 271661 293050 258736 TRUE FALSE 293351.8687 240964.1008 290375.2125 290655.0281 246806.5532 265761.9085 266697.6394 268019.8286 282503.1877 309430.3654 0.948038401 0.7787345 0.938418607 0.9393229 0.797615815 0.858874688 0.861898732 0.86617171 0.912978231 1 18.23925525 0.899213232 2.929173439 0.999891705 0.871080865 0.333592514 0.054158493 0.440700831 8.213340913 0.049157645 0.012934222 7.928905316 -0.899213232 -0.12881084 AQPSMS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQPSMSPK 8 0 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 1 AQPS(0.017)MS(0.983)PK 103.31 0.0050318 182340000 427100 211390 244300 213330 436870 424080 339760 262080 284660 242450 TRUE FALSE 443962.2378 247694.5881 250666.6587 255526.0373 362610.9934 325593.847 313128.7234 258567.2463 274415.1422 289953.4355 1.531150121 0.854256435 0.8645066 0.881265769 1.250583539 1.122917707 1.07992762 0.891754381 0.946411074 1 18.14546171 4.747500187 24.7866952 0.989512364 1.531150436 0.637033982 0.123000959 735.492582 2039246.844 0.03205721 0.387442649 55911.37677 -4.747500187 0.541638072 AQPYDPNFYDETYDYGGFTMMFDDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 AQPYDPNFYDETYDYGGFTMMFDDRR 26 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;; 198.6 9.71E-25 3927821000 910240 1192285 1172043 1122954 1156597 1360256 1085649 1164054 1064977 1305103 FALSE TRUE 946176.9781 1397050.674 1202587.403 1345070.95 959999.0551 1044357.159 1000552.995 1148451.76 1026648.686 1560812.945 0.606207798 0.895078862 0.770487846 0.86177588 0.615063489 0.669111031 0.641046064 0.735803585 0.657765358 1 20.57386622 -1.166286175 3.807463894 1.000182177 0.721378192 0.443408623 0.095027375 29938880.58 52417588.07 67367.18787 0.022848921 0.068188922 1.166286175 -0.278803986 AQQELVPPQQQAS(ph)PPQLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;AQQELVPPQQQAS(1)PPQLPK 129.27 1.28E-05 2864368000 2166500 1734499 1934780 1672918 2152250 2311150 1976123 2004877 2006610 1755880 TRUE FALSE 2252035.093 2032385.711 1985201.956 2003816.187 1786411.314 1774420.438 1821229.316 1978004.903 1934392.498 2099911.068 1.07244308 0.967843706 0.9453743 0.954238595 0.850708081 0.844997898 0.867288784 0.941946987 0.921178296 1 21.0018968 5.005252457 0.961401321 0.903443837 1.236602118 0.527367081 0.045951445 2.408538308 1.257571289 0.014652653 0.937915228 101216.766 -5.005252457 0.333158281 AQQEQAAHQASLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQQEQAAHQASLR 13 0 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 64.374 0.078398 0 103390 66949 87673 60893 144760 128950 91894 84394 109080 74023 FALSE TRUE 107471.917 78446.96996 89957.8304 72937.45365 120153.7469 99003.31676 84691.10816 83262.83647 105154.2321 88526.38959 1.214009941 0.886142204 1.016169651 0.82390634 1.357264737 1.118348068 0.956676405 0.940542553 1.187829218 1 16.43381996 4.777238342 22.6516978 1.028314645 1.214011427 0.120274007 0.147492387 13961.1735 8175826.973 0.035220627 8.225763891 59874.0095 -4.777238342 0.185696782 AQQEQAAHQASLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQQEQAAHQASLRK 14 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 0 100.11 0.0012422 37473000 75438 53234 72786 50483 88260 78598 70479 62965 88339 71265 FALSE TRUE 78416.35049 62376.5254 74682.86295 60468.38672 73257.59673 60344.80566 64954.67182 62121.05716 85159.69665 85228.0123 0.920077195 0.731878214 0.876271321 0.709489581 0.859548343 0.708039576 0.762128203 0.728880746 0.999198437 1 16.37904007 1.22992396 24.99932613 0.999599425 0.781583749 0.588133786 0.07103384 127.2382556 368284.9176 0.059185989 0.01571965 16.97946334 -1.22992396 -0.218015676 AQQNNVEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQQNNVEHK 9 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;; 159.4 6.61E-05 1406010000 1445990 1102280 1339950 1108660 1545100 1590680 1652910 1399230 1393100 947700 FALSE TRUE 1503078.802 1291588.015 1374870.198 1327949.639 1282464.454 1221268.677 1523350.595 1380475.611 1342962.603 1133383.67 1.326187099 1.13958587 1.213066885 1.17166823 1.131536026 1.07754215 1.344073181 1.218012617 1.184914375 1 20.11220489 4.748662344 23.83927797 1.179298606 1.326187257 0.220431278 0.08731565 1207.054996 2848441.14 0.020365829 0.269988584 56061.19411 -4.748662344 0.14688865 AQQNNVEHKVETFSGVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQQNNVEHKVETFSGVYK 18 1 P62081;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 264.88 3.20E-31 802460000 710660 521550 650920 442680 904360 829780 743720 678400 774150 518140 FALSE TRUE 738717.4055 611122.1554 667883.5099 530240.7827 750637.2102 637076.1704 685425.283 669307.1576 746288.4927 619659.6126 1.192134182 0.986222344 1.077823205 0.855696857 1.211370234 1.028106653 1.10613193 1.080120673 1.204352321 1 19.24111642 3.192771106 24.99999977 1.103538508 1.028545008 0.125006383 0.099806869 264.0373149 144157.141 0.02715396 0.032455289 1558.730761 -3.192771106 -0.0749935 AQRLS(ph)QETEALGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQRLSQETEALGR 13 1 Q02818 Q02818 NUCB1 Nucleobindin-1 1 AQRLS(0.823)QET(0.177)EALGR 81.526 0.012847 0 111160 114970 107810 116320 154490 176880 135880 120950 108580 144400 TRUE FALSE 115548.6826 134715.2032 110619.6172 139327.7488 128229.845 135802.3006 125229.3705 119328.8631 104672.227 172692.4153 0.669101086 0.78008755 0.640558631 0.806797152 0.742533161 0.786382543 0.725158487 0.690990759 0.606119422 1 17.3978452 -2.038414455 2.899433226 1.362061339 0.719854445 0.650748102 0.062280016 21607121.32 21029887.14 51596601.17 0.014707781 0.009153465 2.038414455 -0.642206893 AQS(ph)LLSTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSLLSTDR 9 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 1 AQS(0.743)LLS(0.256)T(0.001)DR;AQS(0.585)LLS(0.386)T(0.028)DR 195.29 3.30E-05 738740000 356200 412430 488340 365080 447590 485880 473870 448580 475760 343920 TRUE FALSE 370263.051 483261.6442 501066.5416 437291.7343 371508.8117 373041.7336 436726.8312 442567.5188 458637.4905 411304.5393 0.900216301 1.174948482 1.218237325 1.063182369 0.903245105 0.90697208 1.061808926 1.076009323 1.115080061 1 18.64984747 3.476910539 24.99999854 1.014395113 1.111381215 0.13075669 0.10016623 14.07152081 1669266.234 0.029111868 0.039802567 2998.544778 -3.476910539 0.096986102 AQS(ph)PGAVEEILDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;AQS(1)PGAVEEILDR 261.59 4.77E-24 2111242000 718622 783420 743506 933621 788770 1034218 836241 768728 782973 809516 TRUE FALSE 746993.7515 917966.2908 762882.3772 1118288.447 654695.1571 794036.5432 770694.2453 758424.4585 754793.9547 968125.1611 0.771587994 0.948189684 0.787999742 1.155107307 0.676250534 0.820179637 0.79606881 0.78339505 0.779645014 1 19.88483405 AQS(ph)PGS(ph)PLHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 2 AQS(1)PGS(1)PLHAR;AQS(1)PGS(1)PLHAR;AQS(1)PGS(1)PLHAR 105.58 0.0035765 988670000 1183350 1227250 1279840 1200020 1418210 1555890 1326300 1274990 1270510 1319500 TRUE FALSE 1230069.572 1438020.641 1313193.682 1437380.374 1177143.171 1194558.127 1222341.14 1257900.845 1224784.593 1578030.762 0.779496574 0.911275417 0.832172423 0.91086968 0.745957049 0.756992928 0.774599057 0.797133285 0.776147476 1 20.5896939 5.057384359 15.81645077 0.822415019 0.432570721 0.023055925 0.07908484 12994215.19 84265847.67 0.018230055 160314711.6 114125.9378 -5.057384359 -0.389844298 AQS(ph)PGSPLHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQS(0.947)PGS(0.053)PLHAR 94.287 0.0090381 116030000 55330 115730 102420 87785 109920 120770 87749 97600 90454 102080 TRUE FALSE 57514.47112 135605.7272 105089.1493 105148.611 91235.83766 92722.99779 80871.00409 96291.83164 87198.57821 122080.6216 0.471118761 1.110788309 0.860817614 0.861304682 0.747340868 0.759522655 0.662439321 0.788756073 0.714270431 1 16.89747469 4.78702056 23.1890109 0.815007478 0.471114802 0.407266728 0.129507534 19624.18311 9389910.323 0.030897094 22.38087165 61237.93822 -4.78702056 -0.343892677 AQS(ph)PTPSLPASWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQSPTPSLPASWK 13 0 H0Y9Y3;Q9UMS6-5;Q9UMS6;Q9UMS6-3;Q9UMS6-4;Q9UMS6-2 H0Y9Y3 SYNPO2 Synaptopodin-2 1 AQS(0.866)PT(0.133)PSLPASWK;AQS(0.959)PT(0.04)PS(0.001)LPASWK;AQS(0.976)PT(0.024)PSLPASWK;AQS(0.985)PT(0.015)PSLPASWK 246.18 3.85E-17 833960000 1387170 1134420 1325940 1094400 1530270 1692540 1507050 1414290 1513480 1194740 TRUE FALSE 1441936.543 1329247.81 1360495.086 1310869.054 1270155.252 1299473.236 1388923.483 1395333.756 1459010.15 1428826.428 1.009175442 0.930307408 0.952176597 0.917444574 0.888949999 0.909468925 0.972072923 0.976559313 1.021124835 1 20.44639924 1.746559533 1.928236865 1.006842653 0.933292309 0.458257087 0.031639208 0.286886178 2.144330915 0.022980336 0.00950464 55.79040739 -1.746559533 -0.073550344 AQS(ph)PVSGPNVAHLTDGATLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSPVSGPNVAHLTDGATLNDR 22 0 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 AQS(0.982)PVS(0.018)GPNVAHLTDGATLNDR 78.913 0.0008589 0 31984 46149 34345 45574 45490 54815 43819 54198 36235 50696 TRUE FALSE 33246.75302 54074.73176 35240.05891 54588.40118 37757.62605 42085.04698 40384.35228 53471.56446 34930.90943 60628.91057 0.548364678 0.891896807 0.58124183 0.900369158 0.622766032 0.694141567 0.66609068 0.881948298 0.576142786 1 15.88771828 -1.683972038 2.743803056 1.037735714 0.721758546 0.305508993 0.130837685 41373386.56 35964818.61 10862825.29 0.028185208 0.020702746 1.683972038 -0.315977168 AQS(ph)SPAAPASLSAPEPASQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI15;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 AQS(0.5)S(0.5)PAAPASLSAPEPASQAR;AQS(0.791)S(0.209)PAAPASLSAPEPASQAR;AQS(0.5)S(0.5)PAAPASLSAPEPASQAR 335.36 3.13E-80 468790000 154360 186808 178825 141222 224411 234020 181241 190512 199012 198593 TRUE FALSE 160454.252 218890.8208 183485.3264 169155.2901 186265.6984 179672.4016 167034.8568 187958.4983 191849.597 237503.4961 0.675586906 0.921631995 0.772558423 0.712222316 0.78426508 0.756504239 0.703294308 0.791392554 0.807775886 1 17.85758922 0.676289132 1.824357557 0.999854331 0.766335342 0.552728627 0.063375099 0.999460164 4.605372135 0.058106179 0.016277879 4.745578174 -0.676289132 -0.233518989 AQS(ph)SPASATFPVSVQEPPTKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSSPASATFPVSVQEPPTKPR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 AQS(0.8)S(0.113)PAS(0.058)AT(0.029)FPVSVQEPPTKPR;AQS(0.908)S(0.085)PAS(0.002)AT(0.005)FPVSVQEPPTKPR 172 6.14E-18 0 106044 86346 110634 84526 150422 137638 118142 109582 123621 89032 TRUE FALSE 110230.699 101175.2538 113517.2129 101244.9905 124853.3222 105673.6604 108881.7213 108113.2325 119171.9044 106476.1158 1.035262211 0.950215483 1.066128419 0.950870435 1.172594635 0.992463518 1.022592912 1.015375436 1.119236023 1 16.70017032 AQS(ph)TDS(ph)LGTSGSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 AQS(0.967)T(0.033)DS(0.952)LGT(0.048)SGSLQSK;AQS(0.959)T(0.041)DS(1)LGTSGSLQSK 192.72 7.16E-10 395390000 1166090 822850 1038850 895850 1266350 1265680 1093110 1028900 1050180 675900 TRUE FALSE 1212128.134 964168.0866 1065923.284 1073046.456 1051096.279 971745.0016 1007429.182 1015109.278 1012384.227 808329.6641 1.499546766 1.192790676 1.318673967 1.327486178 1.300331197 1.202164222 1.2463098 1.255810993 1.25243978 1 19.62458427 -5 0.128567609 0.060188801 1.404595476 0.632835195 0.072391215 92.55939392 0.7542229 22.45593551 0.53455262 1.00E-05 5 1.344406675 AQS(ph)TDSLGTSGSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQS(0.973)T(0.026)DS(0.001)LGTSGSLQSK;AQS(0.916)T(0.084)DSLGTSGSLQSK;AQS(0.985)T(0.007)DS(0.007)LGTSGSLQSK 347.14 4.38E-87 1185790000 1755930 1250210 1580080 1182520 1741530 1784190 1843360 1585820 1634110 992070 TRUE FALSE 1825255.472 1464923.842 1621258.183 1416418.927 1445505.353 1369838.912 1698872.626 1564564.677 1575298.7 1186447.122 1.538421256 1.234714818 1.366481618 1.193832325 1.218347894 1.154572241 1.431899151 1.318697351 1.32774455 1 20.17821637 -2.071439442 2.431103833 0.545585884 1.304629852 0.41226888 0.110697691 2983307.801 1180005.358 7511772.705 0.02691425 0.008483217 2.071439442 0.759043967 AQS(ph)YPDNHQEFSDYDNPIFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSYPDNHQEFSDYDNPIFEK 21 0 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 AQS(1)YPDNHQEFSDYDNPIFEK;AQS(1)YPDNHQEFSDYDNPIFEK 306.6 4.42E-56 369340000 241760 222932 259300 194563 318560 309940 256250 243380 285320 206134 TRUE FALSE 251304.8715 261218.8368 266057.571 233046.9807 264411.285 237961.1322 236164.4554 240117.8892 275051.3889 246522.0106 1.019401354 1.05961669 1.07924469 0.945339445 1.072566641 0.965273371 0.957985272 0.974022111 1.115727509 1 17.91135694 3.75973472 24.94916872 1.000100619 1.053440487 0.149572698 0.052104793 1375.920433 1621223.514 0.01312798 0.023639243 5750.885487 -3.75973472 0.053339868 AQSDGIWGEHEIDYILLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQSDGIWGEHEIDYILLVR 19 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ;;; 231.39 3.49E-20 722490000 540902 692840 682830 693780 732190 867930 775670 698480 678180 735340 FALSE TRUE 562257.2286 811829.8805 700625.1108 831007.6133 607732.6053 666366.4111 714870.9586 689118.0181 653772.4343 879415.7941 0.639353116 0.923146805 0.7966938 0.94495416 0.69106401 0.757737598 0.812893018 0.783608872 0.743416753 1 19.74618592 -1.839107963 8.588837284 1.008565996 0.793626735 0.338935201 0.08847877 0.013663214 0.000255949 0.080653795 0.018775839 0.014484117 1.839107963 -0.214939261 AQSDIEHLFQHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSDIEHLFQHNR 13 0 A0A087X211;Q8TCG1-2;Q8TCG1 A0A087X211 KIAA1524 Protein CIP2A 0 226.59 6.08E-12 48670000 21514 25521 23824 23708 26493 32787 23308 20353 22438 28113 FALSE TRUE 22363.38933 29904.03322 24444.87301 28397.37164 21989.72932 25172.71614 21481.05806 20080.20133 21630.46076 33621.20409 0.6651573 0.889439686 0.727067149 0.844626848 0.65404348 0.748715485 0.638914002 0.597248132 0.643357707 1 15.03708377 3.22821877 24.9993339 0.683956504 0.785384275 0.036879474 0.121803153 395.1546355 955205.4652 0.032900856 0.039730688 1691.292685 -3.22821877 0.101427771 AQSEGRPCEYNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSEGRPCEYNSR 13 1 O00622 O00622 CYR61 Protein CYR61 0 107.69 0.0011632 68757000 46141 39084 39882 37844 52169 116310 45513 51752 42617 47794 FALSE TRUE 47962.68231 45796.37297 40921.35768 45329.43025 43301.33201 89298.7652 41945.57213 51058.34909 41083.22249 57158.31923 0.839119886 0.801219728 0.715930038 0.793050441 0.757568322 1.562305652 0.733848943 0.8932794 0.718761906 1 15.80267587 AQSELAAHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AQSELAAHQK 10 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;;;; 122.42 0.00048899 1141910000 1817060 1474070 1756050 1523550 2196010 2237280 2179700 1850920 1901410 1587840 FALSE TRUE 1888798.932 1727230.056 1801814.106 1824903.643 1822733.005 1717705.626 2008849.418 1826111.445 1832978.626 1898946.847 0.99465603 0.909572618 0.948849152 0.96100828 0.959865205 0.904556981 1.057875539 0.961644318 0.965260628 1 20.85676809 2.259125005 24.99997201 0.991956484 0.9461282 0.33089208 0.034465177 292.0634332 355058.2933 0.011491011 0.009603559 181.6038308 -2.259125005 -0.045828284 AQSGSDS(ph)SPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSGSDSSPEPK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQS(0.006)GS(0.013)DS(0.491)S(0.491)PEPK;AQS(0.008)GS(0.008)DS(0.492)S(0.492)PEPK 77.593 0.029375 176713000 381140 223479 267990 204664 342610 396810 322410 279450 302530 198921 TRUE FALSE 396187.7015 261859.7798 274974.0396 245145.9283 284373.2746 304656.8912 297138.6617 275704.4298 291642.0044 237895.7614 1.665383608 1.100733272 1.155859348 1.030476234 1.195369236 1.280631859 1.249028818 1.158929559 1.2259235 1 17.85997004 4.743115542 24.80854983 1.165413504 1.665383833 0.757443398 0.086436197 204.6038838 1114338.196 0.020584327 0.164460125 55349.73447 -4.743115542 0.499970329 AQSLVISPPAPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSLVISPPAPSPR 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 AQSLVISPPAPS(1)PR 104.26 0.0011206 147550000 140640 160450 172770 155820 186390 159680 167520 157340 148910 171900 TRUE FALSE 146192.5758 188006.0394 177272.5281 186640.7309 154707.4944 122596.74 154389.3447 155231.1147 143550.7582 205580.5138 0.711120782 0.914512937 0.862302194 0.907871702 0.752539682 0.596344166 0.750992114 0.755086714 0.698270257 1 17.649344 3.148002307 7.314519952 0.738678507 0.85426884 0.126385206 0.108505507 0.346594224 23.95116248 0.029579803 0.035492358 1406.054993 -3.148002307 0.115590333 AQSNGSGNGS(ph)DSEMDTSSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 AQSNGS(0.001)GNGS(0.952)DS(0.047)EMDTSSLER;AQSNGS(0.137)GNGS(0.847)DS(0.016)EMDTSSLER;AQSNGSGNGS(0.997)DS(0.003)EMDTSSLER 176.61 6.91E-13 395874000 335282 409489 407135 403391 463773 486030 390698 394802 397580 439353 TRUE FALSE 348519.1923 479815.5504 417745.2726 483180.5358 384941.0311 373156.8984 360074.0699 389510.325 383271.1735 525435.8084 0.663295471 0.913176344 0.795045305 0.919580524 0.732612861 0.710185511 0.685286507 0.741309059 0.729434818 1 19.003155 3.165689978 24.99999999 0.744902995 0.827259402 0.039867341 0.106800803 84.3697301 28942.93268 0.028447354 0.034001102 1464.50203 -3.165689978 0.082356407 AQSPGS(ph)PLHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSPGSPLHAR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 AQSPGS(1)PLHAR;AQSPGS(1)PLHAR 130.72 0.00014064 828830000 219707 279100 249510 268580 273820 312850 245040 258850 260060 293610 TRUE FALSE 228381.202 327033.2539 256012.4356 321704.3224 227276.1742 240195.3288 225833.1245 255380.5391 250700.4914 351137.258 0.650404356 0.931354467 0.729095047 0.916178261 0.647257359 0.684049679 0.643147713 0.727295476 0.713967218 1 18.42167556 AQSPSYVISTGVS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSPSYVISTGVSPSR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 AQSPSYVISTGVS(0.997)PS(0.003)R;AQSPSYVISTGVS(0.999)PS(0.001)R 235.72 1.09E-19 540780000 209520 192818 180457 198172 213380 239640 192801 193075 204660 185833 TRUE FALSE 217792.0114 225932.9916 185159.8577 237369.8301 177109.7438 183987.2418 177688.7538 190487.1454 197294.3266 222243.4184 0.979970579 1.016601496 0.833139892 1.068062361 0.796917835 0.827863624 0.799523132 0.857110401 0.887739795 1 17.76178117 4.245233737 24.99210141 0.874865853 0.998286084 0.22551472 0.083569164 204.4297453 765608.0026 0.020135244 0.052555526 17588.69983 -4.245233737 0.123420231 AQSS(ph)PAAPASLSAPEPASQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI15;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 AQS(0.088)S(0.912)PAAPASLSAPEPASQAR 298.1 6.09E-55 222910000 86847 99066 93983 94412 115830 126050 89114 97984 110850 108640 TRUE FALSE 90275.78662 116079.8149 96432.27419 113086.4118 96141.25797 96776.79781 82129.01182 96670.68475 106860.5302 129925.928 0.694825029 0.893430716 0.742209624 0.870391411 0.739969762 0.744861317 0.632121803 0.744044597 0.822472711 1 16.98732984 0.885801702 3.708992723 0.999889896 0.758134395 0.507598219 0.071976357 0.435694641 12.03367804 0.069870381 0.017957707 7.687793373 -0.885801702 -0.241755501 AQSTDS(ph)LGTSGSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQSTDSLGTSGSLQSK 16 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 AQSTDS(0.995)LGT(0.004)S(0.002)GSLQSK;AQS(0.035)T(0.035)DS(0.926)LGT(0.003)SGSLQSK 317.31 7.24E-58 562980000 769350 556080 633320 507330 763760 789670 790120 586020 675930 405420 TRUE FALSE 799724.5321 651582.4143 649824.8395 607678.3598 633936.348 606281.1101 728188.3298 578165.3604 651603.4113 484854.2868 1.64941211 1.343872648 1.340247693 1.253321619 1.307478072 1.250439826 1.501870458 1.192451786 1.343915954 1 18.88719171 -4.787511549 0.078122664 2.64E-17 1.678533493 0.502073455 0.116210459 222.0238617 1.283255784 40.21044805 4.283516427 1.63E-05 4.787511549 1.678533493 AQT(ph)PPGPSLSGSK ddPTM_MDA-MB-175_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(0.994)PPGPS(0.006)LSGSK;AQT(0.986)PPGPS(0.014)LSGSK;AQT(0.988)PPGPS(0.011)LSGSK 156.25 0.00045647 2442280000 2305580 1590490 2019110 1672640 2383060 2570910 2662070 1995080 2204690 1269370 TRUE FALSE 2396606.079 1863644.285 2071729.665 2003483.2 1977988.312 1973855.115 2453409.997 1968339.216 2125343.638 1518078.748 1.578709986 1.227633473 1.364705005 1.319749191 1.302955011 1.300232361 1.616128281 1.296598888 1.400021995 1 20.5338152 -1.229494807 4.139774023 0.999759496 1.372254646 0.474692942 0.11929448 0.000246865 4.59E-05 0.107682154 0.025364678 0.058952903 1.229494807 0.37249515 AQT(ph)PPGPSLSGSKS(ph)PCPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 AQT(1)PPGPS(0.026)LS(0.046)GS(0.034)KS(0.894)PCPQEK;AQT(1)PPGPS(0.006)LS(0.017)GS(0.252)KS(0.726)PCPQEK 97.057 0.0022819 1728150000 2623300 1157830 1673610 1090540 2488000 2341400 2363900 1790220 1961210 922680 TRUE FALSE 2726869.91 1356678.296 1717225.651 1306245.557 2065090.649 1797645.334 2178611.341 1766225.029 1890626.435 1103461.48 2.471196284 1.229474993 1.556217124 1.183770871 1.871466006 1.62909659 1.974342902 1.600622279 1.713359704 1 20.07360484 AQTAPNKDVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQTAPNKDVQR 11 1 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 68.536 0.051957 71904000 73316 115760 88787 80302 116390 126020 79827 94519 92516 150150 FALSE TRUE 76210.57229 135640.8795 91100.86216 96185.49592 96606.06937 96753.76485 73569.95115 93252.12741 89186.36723 179569.0177 0.424408249 0.755369057 0.507330626 0.535646389 0.537988516 0.538811016 0.409702921 0.519310784 0.496669015 1 17.45417893 -1.247934859 3.66698486 1.000822816 0.526769074 0.722100059 0.088390813 24900500.83 41735593.56 233059.4843 0.02056663 0.056502172 1.247934859 -0.474053742 AQTAPTKTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AQTAPTKTSPR 11 1 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 AQTAPT(0.003)KT(0.027)S(0.969)PR;AQTAPT(0.001)KT(0.003)S(0.995)PR;AQT(0.002)APT(0.044)KT(0.17)S(0.784)PR;AQT(0.008)APT(0.016)KT(0.049)S(0.928)PR 119.88 0.0013857 1124810000 1988560 1561490 1787340 1392270 2064290 2071440 1901950 1661080 1815850 1359070 TRUE FALSE 2067069.884 1829663.761 1833919.549 1667656.85 1713402.723 1590379.453 1752870.189 1638815.94 1750497.913 1625353.746 1.271766156 1.125701876 1.128320253 1.026027014 1.054172194 0.978482043 1.078454579 1.008282624 1.076995034 1 20.63232231 5.458838628 0.722304044 1.028592198 1.77825945 0.817630603 0.03479068 2.620267614 0.488904521 0.011818755 2.030872522 287632.945 -5.458838628 0.749667252 AQTLPTSVVTITSESS(ph)PGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AQTLPTSVVTITSESSPGKR 20 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 AQTLPTSVVTITSES(0.064)S(0.936)PGKR;AQTLPTSVVTITSES(0.351)S(0.649)PGKR;AQTLPTSVVTIT(0.003)S(0.02)ES(0.242)S(0.734)PGKR;AQTLPTSVVTITSES(0.305)S(0.695)PGKR;AQTLPTSVVTITSES(0.024)S(0.976)PGKR;AQTLPTSVVTITSES(0.029)S(0.971)PGKR;AQTLPTSVVTITSES(0.056)S(0.944)PGKR 326.48 6.35E-80 7934710000 3815712 2356191 2765760 2202588 3555973 3622074 3465180 2830417 2980595 2058302 TRUE FALSE 3966359.256 2760848.476 2837837.978 2638253.332 2951529.98 2780902.207 3193570.137 2792479.89 2873323.968 2461586.868 1.611301761 1.121572637 1.152849007 1.07176934 1.199035475 1.129719305 1.297362355 1.134422646 1.167264908 1 21.23115722 4.740840843 24.99711729 1.151690003 1.611301921 0.782973365 0.07402098 87.60534722 960317.8788 0.016517255 0.110327072 55060.58773 -4.740840843 0.459611917 AQTPPGPSLSGS(ph)KSPCPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQT(0.001)PPGPS(0.099)LS(0.082)GS(0.422)KS(0.397)PCPQEK 61.37 0.030875 936270000 74371 44260 61633 51457 83569 85970 68242 65068 77157 50970 TRUE FALSE 77307.22451 51861.3107 63239.20661 61635.04102 69363.97123 66004.77039 62893.01372 64195.86989 74380.13464 60956.59562 1.268233958 0.850790799 1.037446497 1.011129975 1.137923969 1.082815891 1.031767163 1.053140669 1.22021471 1 15.89549471 3.26689031 24.94991189 1.083677565 1.027931486 0.032949602 0.110323104 674.5945069 594109.8429 0.028812352 0.03900402 1848.801608 -3.26689031 -0.055746078 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AQTPPGPSLSGS(0.028)KS(0.972)PCPQEK;AQTPPGPS(0.005)LS(0.065)GS(0.047)KS(0.883)PCPQEK 124.86 1.58E-05 3012540000 1651570 819680 1147280 817430 1600710 1513250 1426790 1174360 1383520 713390 TRUE FALSE 1716775.259 960453.6638 1177179.059 979115.2142 1328621.886 1161820.621 1314954.472 1158619.625 1333727.385 853165.1118 2.012242689 1.125753562 1.379778712 1.147626879 1.557285767 1.361776994 1.541266108 1.358025087 1.563269954 1 19.70246545 -1.315034896 5.203513175 0.999883167 1.428340585 0.237657211 0.23887632 0.000293199 3.86E-05 0.209453017 0.049355186 0.048413347 1.315034896 0.428457417 AQTSYGFAMLAES(ph)PHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQTSYGFAMLAESPHTR 17 0 Q8TF44 Q8TF44 C2CD4C C2 calcium-dependent domain-containing protein 4C 1 AQTSYGFAMLAES(0.991)PHT(0.009)R;AQTSYGFAMLAES(0.999)PHT(0.001)R 126.86 2.72E-05 376680000 425220 492260 575170 513430 667010 692730 591570 573640 629390 574680 TRUE FALSE 442008.0139 576801.8257 590159.4027 614984.9216 553631.8784 531853.9559 545201.1976 565951.2941 606738.3768 687277.5431 0.643128847 0.839256035 0.858691527 0.89481306 0.805543385 0.773856154 0.793276607 0.823468335 0.882814204 1 19.39053329 -5 0.20199101 1.860413675 0.78524366 0.473542998 0.063602332 134.8955156 1.337378895 46.74307888 0.151509078 1.00E-05 5 -1.075170015 AQVADVVVSR ddPTM_MDA-MB-175_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 ;; 167.09 1.24E-05 744490000 985590 929040 966950 1051140 1107690 1229970 1051380 1003940 950230 935000 FALSE TRUE 1024501.854 1088595.393 992149.5114 1259052.355 919405.2495 944328.1079 968970.0883 990483.8264 916031.4079 1118195.348 0.916210084 0.973528816 0.887277445 1.125968156 0.822222388 0.844510853 0.86654813 0.885787826 0.819205168 1 20.09274082 AQVARPGGDTIFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQVARPGGDTIFGK 14 1 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 156.17 5.15E-06 4838000000 4443100 4178300 4506200 3694900 5357200 5226300 4297500 4370800 4810300 4801700 FALSE TRUE 4618517.019 4895890.522 4623635.274 4425740.192 4446585.058 4012571.03 3960650.721 4312216.575 4637178.243 5742501.181 0.804269233 0.852571095 0.805160526 0.770699048 0.774328976 0.698749709 0.689708299 0.750930028 0.807518901 1 22.45324782 0.838090476 4.065293993 0.999981847 0.766071663 0.693148869 0.046011902 0.748846447 18.01031747 0.050761036 0.012959418 6.887957766 -0.838090476 -0.233910184 AQVLATIHGHAGAFPAAGDAGEGAPGGGSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQVLATIHGHAGAFPAAGDAGEGAPGGGSSPER 33 0 Q86WR7;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.195)S(0.805)PER;AQVLATIHGHAGAFPAAGDAGEGAPGGGS(0.063)S(0.937)PER 116.13 5.57E-06 472630000 77618 112046 102612 108943 114587 135899 97034 96215 108200 107748 TRUE FALSE 80682.41857 131289.0289 105286.153 130491.6002 95109.54267 104338.5168 89428.22153 94925.3953 104305.9031 128859.1576 0.626128713 1.018856799 0.8170638 1.012668425 0.738089123 0.809709754 0.693999737 0.736660064 0.809456658 1 16.97543554 AQVLVEDISDILEEHAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQVLVEDISDILEEHAEK 18 0 Q5VV41;Q5VV41-2;B0QZD3;B0QZD4 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;; 223.36 5.19E-19 106218000 231623 160169 202354 183904 250130 267786 267581 222045 224318 150533 FALSE TRUE 240767.6549 187676.7798 207627.5115 220279.6623 207612.9919 205596.7598 246607.302 219068.85 216244.839 180027.0592 1.337397033 1.04249206 1.153312798 1.22359196 1.153232147 1.142032541 1.369834641 1.216866236 1.201179645 1 17.45785424 AQYDELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;; 257.22 1.04E-12 45731920000 17279160 20730800 18528680 17884750 20933790 23221770 19795440 19612610 18964860 21522950 FALSE TRUE 17961354.58 24291153.64 19011552.62 21422300.17 17375471.85 17828865.85 18243821.69 19349735.04 18282318.39 25739959.97 0.697800408 0.94371373 0.738600707 0.832258488 0.675038806 0.692653208 0.708774284 0.751739127 0.710269884 1 24.61750647 -1.448389265 3.384612933 1.003366321 0.752147781 0.486137764 0.077053866 43781211.7 70483314.02 1447169.268 0.018424849 0.035613178 1.448389265 -0.251218541 AQYDELARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AQYDELARK 9 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 97.456 0.010709 350530000 509890 823050 686760 282360 1418220 918200 360130 629690 872450 1778130 FALSE TRUE 530020.8509 964402.4351 704657.5298 338209.9652 1177151.471 704961.9655 331902.0696 621250.0355 841050.6949 2126520.529 0.249243233 0.453511933 0.331366436 0.159043828 0.553557539 0.331509598 0.156077529 0.292143916 0.395505561 1 21.02006335 0.771880489 3.817653404 0.999982886 0.315856025 0.760350787 0.114512002 1.132555537 18.48355636 0.109005978 0.027934781 5.91398868 -0.771880489 -0.68412686 AQYEQTLAELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AQYEQTLAELHR 12 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ;; 174.39 3.05E-05 1261060000 450910 1066190 583230 744200 624130 863590 550740 641740 568680 1394550 FALSE TRUE 468712.275 1249299.839 598429.4529 891400.5388 518040.6055 663034.3103 507571.5597 633138.525 548213.3179 1667785.372 0.281038725 0.749077105 0.358816826 0.534481567 0.310615871 0.397553739 0.304338657 0.3796283 0.328707355 1 20.66950221 -1.355896848 5.499259795 1.000169904 0.408024952 0.641190647 0.133529571 0.000265565 3.11E-05 0.123434664 0.029085618 0.044065952 1.355896848 -0.592144952 AQYSLPGILHFLQHEWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AQYSLPGILHFLQHEWAR 18 0 O43815-2;O43815 O43815-2 STRN Striatin 0 80.142 0.005259 50010000 30284 39613 39715 47086 41474 55658 42957 42729 42386 55449 FALSE TRUE 31479.6357 46416.2246 40750.00553 56399.47026 34424.26429 42732.27301 39589.91809 42156.28765 40860.53614 66313.16991 0.474711671 0.699954846 0.614508484 0.850501798 0.519116555 0.644401 0.597014411 0.635715163 0.616175282 1 16.0170078 -1.255069278 4.964168268 1.000073673 0.632488607 0.575234716 0.095827122 7.22E-05 1.08E-05 0.085759776 0.020209736 0.055581559 1.255069278 -0.367585066 ARAPS(ph)PGDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARAPSPGDYK 10 1 P55198 P55198 MLLT6 Protein AF-17 1 ARAPS(0.998)PGDY(0.002)K;ARAPS(0.994)PGDY(0.006)K 92.457 0.0057256 400070000 579850 343530 456210 348820 693080 655230 733600 530800 501410 362980 TRUE FALSE 602742.9257 402528.6052 468099.2074 417815.5549 575270.5092 503062.7626 676098.5151 523685.4942 483364.352 434098.9813 1.388491915 0.927273784 1.078323672 0.962489139 1.325205849 1.15886649 1.55747547 1.20637347 1.113488796 1 18.72766451 3.229879288 24.99211348 1.254329256 1.076809492 0.110487943 0.180397281 309.9011632 892153.3875 0.049962744 0.060599147 1697.771692 -3.229879288 -0.177519764 ARDDLITDLLNEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ARDDLITDLLNEAK 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 ;;;;; 263.75 1.12E-24 1480741000 2665920 1833740 2228890 1744770 3024640 2768110 2735360 2252210 2449150 1721050 FALSE TRUE 2771172.58 2148670.58 2286976.704 2089880.298 2510512.773 2125258.404 2520955.336 2222022.809 2361005.57 2058256.796 1.346368726 1.043927359 1.111123116 1.015364216 1.219727673 1.032552599 1.224801172 1.079565394 1.147089894 1 20.97299156 ARDYDAMGSQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARDYDAMGSQTK 12 1 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ; 131.32 0.00022478 72510000 120528 80343 121963 78754 182330 134482 118463 123757 137706 130282 FALSE TRUE 125286.5385 94141.28527 125141.456 94331.30614 151337.6117 103250.5936 109177.5605 122098.2398 132749.988 155808.2635 0.804107149 0.604212403 0.803175988 0.605431984 0.971306709 0.662677263 0.700717395 0.783644186 0.852008648 1 17.24941223 0.982472562 1.664994804 0.998612695 0.735161473 0.384376567 0.103118019 0.382984079 2.188045872 0.090125481 0.0260562 9.60445138 -0.982472562 -0.263451221 AREEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AREEAER 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 63.419 0.072548 63352000 6363.8 10485 9302.1 9474.3 8603.3 11131 9983.3 7930.5 8302.3 11269 FALSE TRUE 6615.047738 12285.71719 9544.520368 11348.28826 7140.914139 8545.993942 9200.78286 7824.204619 8003.501845 13476.94479 0.490841792 0.911609966 0.708210987 0.842051996 0.529861497 0.634119533 0.682705391 0.580562193 0.593866189 1 13.71820586 -1.083335442 4.63838807 1.00001863 0.667300172 0.394226565 0.124972166 2.35E-05 4.64E-06 0.117885921 0.027784423 0.082540018 1.083335442 -0.332718458 AREEEEQKEGGDGAAGDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AREEEEQKEGGDGAAGDPK 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 149.94 4.53E-08 747560000 1382700 512140 803100 504830 1147100 1160300 1123500 791140 955250 401770 FALSE TRUE 1437290.064 600096.0611 824029.4458 604683.8672 952116.3517 890837.9095 1035437.134 780536.0623 920870.7391 480489.1391 2.991306039 1.24892742 1.714980379 1.25847562 1.981556448 1.854022988 2.154964701 1.624461406 1.916527688 1 18.8741443 -1.23248694 4.108043234 0.999422137 1.821867541 0.228088076 0.470117014 32642481.69 9793780.375 168424.5397 0.101395143 0.058548134 1.23248694 0.822445405 AREEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AREEEER 7 1 Q9NWB6 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 71.379 0.049681 101081000 44336 53606 51044 49747 58026 61053 52132 53194 49572 62260 FALSE TRUE 46086.41951 62812.4135 52374.24857 59586.80812 48162.76125 46874.36602 48045.75762 52481.02144 47787.9134 74458.65496 0.618953156 0.843587808 0.703400412 0.80026705 0.646838991 0.629535492 0.6452676 0.704834401 0.641804682 1 16.18415193 -1.893272554 7.301109207 1.050536103 0.696030165 0.62434725 0.071463166 0.039319123 0.000574766 0.046280438 0.016096929 0.012785786 1.893272554 -0.354505938 AREES(ph)WGPPR ddPTM_MDA-MB-175_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 113.69 0.00088066 966430000 1642443 2128926 1835667 1981400 2034790 2287090 1770190 1813110 1728000 2197430 TRUE FALSE 1707287.918 2494552.48 1883505.99 2373315.006 1688917.123 1755948.009 1631437.882 1788808.226 1665809.618 2627974.336 0.649659281 0.949230152 0.716713997 0.903096721 0.642668804 0.668175478 0.620796733 0.680679488 0.633875908 1 21.32551976 3.222652854 24.9158054 0.683620834 0.808717494 0.100199471 0.130712251 367.8320341 576121.9282 0.034212367 0.041017617 1669.75539 -3.222652854 0.125096659 AREESWGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AREESWGPPR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 166.29 5.10E-06 1160920000 551796 508424 497540 492370 602240 666420 545540 544510 501800 575700 FALSE TRUE 573581.3322 595741.867 510506.3011 589759.3164 499871.4599 511654.0547 502779.1493 537211.7341 483740.316 688497.3926 0.83309151 0.86527832 0.741478917 0.856589034 0.726032466 0.743145958 0.730255706 0.780266912 0.702602975 1 19.39309167 4.246141101 24.98829645 0.773764472 0.849184937 0.073807148 0.08355709 335.3416383 1105392.769 0.018397866 0.048352934 17625.486 -4.246141101 0.075420465 AREETDKEEPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AREETDKEEPASK 13 2 P05455 P05455 SSB Lupus La protein 0 ;;; 226.19 6.30E-12 3019060000 3447030 1535800 2288470 1430660 3344330 2905970 3027240 2253390 2594260 1255858 FALSE TRUE 3583121.406 1799561.703 2348109.408 1713640.278 2775861.981 2231102.508 2789957.019 2223186.993 2500893.089 1501919.33 2.38569498 1.198174673 1.563405811 1.140966924 1.848209771 1.485500894 1.857594454 1.480230628 1.665131435 1 20.5183759 -1.098392449 4.512167383 0.999948725 1.599943195 0.23115492 0.339192588 0.000158268 3.16E-05 0.297081538 0.070016828 0.079727391 1.098392449 0.59999447 ARENIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 122.18 0.0039821 2732520000 2450810 1713250 2237850 1684690 2827490 2755880 2677600 2366810 2435450 2277860 FALSE TRUE 2547569.871 2007487.36 2296170.209 2017916.654 2346874.26 2115868.636 2467722.715 2335086.783 2347798.63 2724163.055 0.935175252 0.736918944 0.842890151 0.740747383 0.861502859 0.776704108 0.905864541 0.85717585 0.861842182 1 21.37738163 0.537356897 0.489600724 1.008715797 0.811173363 0.421248308 0.060531901 1.609310682 0.730104597 0.090275787 0.030042317 3.446330291 -0.537356897 -0.197542434 AREQAEAEVASLNR ddPTM_MDA-MB-175_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 ;;; 289.18 1.81E-43 1513020000 722210 771920 802450 733420 912230 984200 756300 790590 829060 972500 FALSE TRUE 750723.4085 904491.2553 823362.5062 878488.287 757169.4704 755634.4657 697019.2298 779993.4342 799222.2925 1163042.755 0.64548221 0.777693899 0.707938296 0.755336193 0.651024622 0.649704804 0.599306626 0.670648977 0.687182211 1 20.1494727 -1.767842355 5.555048596 1.016324772 0.681950937 0.780110442 0.050535981 0.010917301 0.000456258 0.052283488 0.012232853 0.017067018 1.767842355 -0.334373835 AREQAEAEVASLNRR ddPTM_MDA-MB-175_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 0 175.27 4.87E-07 350550000 206130 216750 239070 141620 328460 285760 173420 228460 253420 362020 FALSE TRUE 214268.1716 253975.1264 245300.3606 169632.0133 272628.4865 219396.5707 159826.8873 225397.8674 244299.4637 432950.8877 0.494901795 0.586614172 0.566577798 0.391804286 0.629698412 0.506747017 0.369157084 0.520608396 0.564265996 1 18.72384385 0.679071766 2.647602864 0.999958341 0.507263182 0.788919717 0.075837572 1.060337451 8.218222724 0.072028089 0.019099459 4.776081907 -0.679071766 -0.492695159 ARES(ph)YVETELIFALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARESYVETELIFALAK 16 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 ARES(0.999)YVET(0.001)ELIFALAK 136.35 4.72E-05 7034200 14621 15477 16187 16037 17551 20660 14517 17683 16837 14485 TRUE FALSE 15198.24837 18135.05436 16608.84652 19209.07073 14567.68729 15862.02811 13379.11961 17445.98831 16231.03966 17323.05842 0.877342095 1.046873705 0.958771027 1.108872941 0.840941994 0.915659794 0.77233011 1.007096316 0.93696155 1 14.08040604 3.220986492 24.99998988 0.909584793 0.998658916 0.194919489 0.085323582 380.0729323 540669.8285 0.02399217 0.028736821 1663.360912 -3.220986492 0.089074123 ARFEELCSDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 211.77 2.55E-08 34035966000 9892430 9155050 9125646 8370503 16363457 12509642 11782942 10346170 10456842 17124204 FALSE TRUE 10282990.78 10727358.62 9363467.832 10026163.51 13582002.42 9604467.231 10859364.22 10207496.51 10080502.3 20479363.91 0.502114754 0.523813077 0.457214778 0.489573971 0.663204311 0.468982693 0.530258863 0.498428396 0.492227314 1 24.28766757 -1.339629831 4.75445107 1.000351965 0.514491738 0.878760754 0.054157606 0.000195967 2.72E-05 0.050859219 0.01197913 0.045747795 1.339629831 -0.485860226 ARFEELNADLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ARFEELNADLFR 12 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;; 231.74 2.47E-12 36070045000 10380574 9407958 10011366 8739166 16941410 13726344 13278555 11409677 10644610 18588260 FALSE TRUE 10790407.08 11023701.6 10272270.42 10467746.95 14061715.18 10538608.63 12237747.16 11256748.94 10261512.57 22230273.65 0.485392454 0.495886905 0.462084749 0.470878007 0.632548002 0.474065628 0.550499169 0.506370237 0.461600821 1 24.40602237 -1.789042548 2.699796493 1.132878152 0.506808764 0.899467218 0.049703596 7986207.205 5650823.554 6961055.133 0.011629553 0.016253895 1.789042548 -0.626069388 ARFEEVLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARFEEVLSK 9 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 96.113 0.00692 847920000 1023750 381500 641750 436240 918140 803380 851070 578350 639830 548670 FALSE TRUE 1064168.441 447019.6573 658474.5322 522526.97 762074.8908 616807.1703 784360.9095 570598.1642 616802.6433 656171.3816 1.621784294 0.681254425 1.003509983 0.796326973 1.161396111 0.940009253 1.195359828 0.869587093 0.940002354 1 19.32371315 4.754193981 24.91491282 0.959723176 1.621784806 0.653147572 0.145904553 1701.125569 2711038.603 0.032845053 0.822784076 56779.81608 -4.754193981 0.662061629 ARGDS(ph)EALDEES ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 222.55 6.46E-11 7451440000 2842709 3151350 3228940 3012335 3811900 4095620 3515300 3373130 3562630 3488770 TRUE FALSE 2954941.346 3692569.848 3313088.829 3608165.872 3163954.6 3144474.325 3239761.6 3327918.71 3434411.642 4172327.685 0.708223699 0.885014344 0.79406247 0.864784874 0.758318818 0.753649896 0.776487813 0.797616813 0.823140439 1 21.99242104 0.667157765 2.303276848 0.999979693 0.794707124 0.616163215 0.04888547 1.300690447 8.18085146 0.044649793 0.012057165 4.646840489 -0.667157765 -0.205272569 ARGQDTPKPAGQHGS(ph)LSPAAAHTAS(ph)PEPPTQSGPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARGQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 37 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 ARGQDT(0.013)PKPAGQHGS(0.637)LS(0.35)PAAAHT(0.312)AS(0.688)PEPPTQSGPLTR 130.25 2.15E-08 131330000 20585 26851 46593 28013 103240 70842 64619 72935 57926 64689 TRUE FALSE 21397.7117 31462.45038 47807.25186 33553.88779 85691.30168 54390.01912 59553.99393 71957.42562 55841.25458 77363.571 0.276586401 0.406683016 0.617955599 0.433716895 1.107644083 0.703044319 0.769793756 0.930120271 0.72180296 1 16.23936677 3.928287341 0.884246243 0.860587874 0.244831912 0.626668795 0.156653072 0.556490264 0.700050803 0.056805204 0.264067025 8477.881482 -3.928287341 -0.615755963 ARGQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARGQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 37 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 ARGQDT(0.035)PKPAGQHGS(0.25)LS(0.713)PAAAHT(0.303)AS(0.692)PEPPT(0.005)QS(0.002)GPLTR 56.089 0.06573 110750000 25915 27704 40522 24205 88869 62527 63895 65237 48438 61954 TRUE FALSE 26938.14421 32461.94649 41578.03661 28992.67676 73763.07912 48006.05186 58886.74294 64362.60472 46694.72584 74092.70012 0.363573526 0.43812611 0.561162389 0.391302742 0.995551235 0.64791878 0.794771183 0.868676734 0.630220329 1 16.17704379 3.251523863 24.99950102 0.81014465 0.44727012 0.693684492 0.124886224 129.2185564 249195.3181 0.032693497 0.043996227 1784.53004 -3.251523863 -0.36287453 ARGQGSS(ph)PVAMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARGQGSSPVAMQK 13 1 P18206;P18206-2 P18206 VCL Vinculin 1 ARGQGS(0.202)S(0.798)PVAMQK;ARGQGS(0.099)S(0.901)PVAMQK 103.79 0.0009585 162267000 251550 135699 177955 150905 300780 278670 347280 244500 215570 223140 TRUE FALSE 261481.3882 159004.2477 182592.6535 180753.5586 249653.523 213953.1158 320059.2862 241222.8774 207811.6778 266860.0107 0.979844779 0.595833925 0.684226359 0.67733475 0.93552242 0.801742888 1.199352744 0.903930404 0.778729182 1 18.02572361 3.230422041 24.44397293 0.941746914 0.720841406 0.323575379 0.142598053 148.0791041 444750.7401 0.040436522 0.049150773 1699.894784 -3.230422041 -0.220905507 ARHDS(ph)PDLAPNVTYSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 ARHDS(1)PDLAPNVTYSLPR;ARHDS(1)PDLAPNVTYSLPR 180.21 4.83E-14 693700000 120560 154529 143586 154434 167378 186803 151551 161974 143836 211429 TRUE FALSE 125319.8019 181068.1537 147327.9691 184980.5843 138927.1473 143420.8343 139672.0366 159803.0035 138659.3705 252854.4645 0.495620286 0.716096329 0.582659157 0.731569382 0.549435216 0.567207048 0.552381137 0.631995974 0.5483762 1 17.94794773 -1.724509598 2.812951911 1.066749502 0.602265304 0.7380507 0.071924326 15523305.15 13633405.07 7290065.205 0.016016924 0.018857773 1.724509598 -0.464484198 ARIPS(ph)GK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARIPSGK 7 1 Q9NTM9;A0A0B4J226 Q9NTM9 CUTC Copper homeostasis protein cutC homolog 1 ARIPS(1)GK;ARIPS(1)GK 63.32 0.048534 379770000 572670 332800 487500 338750 840850 683660 720000 600910 610640 490210 TRUE FALSE 595279.4538 389955.8112 500204.6505 405753.7389 697922.6173 524890.326 663564.5186 592855.7843 588663.1857 586257.2639 1.015389472 0.665161586 0.853216977 0.692108676 1.19047159 0.895324217 1.131865752 1.011255333 1.004103867 1 19.16117437 3.245309846 24.99939272 1.037287433 0.799714908 0.489770982 0.116101246 122.3537879 453200.0248 0.029549009 0.039125248 1759.178245 -3.245309846 -0.237572525 ARLEIEPEWAYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;; 148.52 3.95E-05 2383440000 2974090 2224720 2881260 2242420 3939540 3510290 3640340 3183090 3147010 2743660 FALSE TRUE 3091509.37 2606798.354 2956348.003 2685963.983 3269898.398 2695078.346 3355000.639 3140425.885 3033749.725 3281227.646 0.942180703 0.794458244 0.900988386 0.818585076 0.996547253 0.821362806 1.022483351 0.957088695 0.924577643 1 21.64580426 2.599862938 0.938288988 0.972682666 0.865589488 0.264359492 0.066845239 0.693620915 1.264263516 0.038913427 0.031202347 397.981549 -2.599862938 -0.107093178 ARLS(ph)PDGVAPTCPLCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARLSPDGVAPTCPLCGK 17 1 B2RXF5 B2RXF5 ZBTB42 Zinc finger and BTB domain-containing protein 42 1 ARLS(1)PDGVAPTCPLCGK;ARLS(1)PDGVAPTCPLCGK 195.15 2.06E-11 537910000 530460 558070 559890 465910 598410 626180 549760 538970 550220 514360 TRUE FALSE 551402.9704 653914.1813 574481.1934 558065.6074 496692.4819 480759.1848 506668.3747 531745.9887 530417.6897 615138.994 0.896387606 1.063034839 0.933904693 0.907218715 0.807447564 0.781545617 0.823664862 0.864432257 0.862272909 1 19.23055291 3.651742418 2.460452862 0.846177683 0.979230258 0.324928936 0.068024967 0.273393588 3.22619719 0.018182055 0.032630114 4484.793155 -3.651742418 0.133052575 ARLS(ph)SAYLLGVPGSEQPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARLSSAYLLGVPGSEQPDR 19 1 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 ARLS(0.776)S(0.222)AY(0.002)LLGVPGSEQPDR 94.606 0.00095051 112410000 152680 164380 133090 193220 196490 234990 166770 161540 163030 212180 TRUE FALSE 158707.9243 192610.9863 136558.4347 231438.3393 163090.7 180417.1338 153698.1316 159374.8205 157162.5821 253752.6086 0.625443518 0.759050271 0.538155787 0.912062897 0.642715363 0.710996174 0.605700696 0.628071654 0.619353563 1 17.95306313 -1.400283381 3.241239791 1.00373974 0.67128779 0.501259857 0.098366833 80454825.37 112947439.6 2829611.446 0.022330105 0.039784749 1.400283381 -0.332451951 ARLS(ph)YSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ARLSYSDK 8 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(1)YSDK;ARLS(1)YSDK;ARLS(1)YSDK;ARLS(0.995)YS(0.005)DK;ARLS(0.997)YS(0.003)DK;ARLS(0.97)YS(0.03)DK;ARLS(0.997)YS(0.003)DK 162.21 0.00020777 17611840000 9239250 5684370 7494190 7051340 8777500 8854870 10359290 7296480 7650220 4582330 TRUE FALSE 9604022.724 6660616.329 7689494.748 8446074.006 7285503.685 6798460.639 9547301.781 7198682.62 7374890.077 5480149.829 1.752510976 1.215407705 1.403154108 1.541212242 1.329435127 1.240561089 1.742160721 1.3135923 1.345746066 1 22.38578391 0.756931416 1.648927316 1.001374514 1.437902612 0.360761163 0.177850968 0.90044175 4.069412845 0.158091777 0.045221281 5.713883956 -0.756931416 0.436528098 ARLS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ARLSYSDKNLIDSMDQSAFAGFSFVNPK 28 2 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 ARLS(0.34)Y(0.29)S(0.34)DKNLIDS(0.014)MDQS(0.016)AFAGFSFVNPK;ARLS(0.398)Y(0.252)S(0.293)DKNLIDS(0.057)MDQS(0.001)AFAGFSFVNPK;ARLS(0.5)YS(0.5)DKNLIDSMDQSAFAGFSFVNPK 291.58 1.85E-71 18783680000 4694310 3247100 4701180 3272900 6265550 5132050 5000500 4546490 5164090 3762990 TRUE FALSE 4879644.984 3804764.166 4823696.613 3920269.851 5200534.049 3940209.164 4608547.744 4485551.738 4978235.41 4500275.844 1.084299086 0.845451323 1.071866877 0.87111768 1.155603396 0.875548367 1.024058947 0.996728177 1.106206727 1 22.101582 1.395499867 7.004418627 1.05399727 0.987289602 0.059680394 0.099005358 0.584584708 39.49616515 0.0594248 0.021881065 24.85992806 -1.395499867 -0.066707668 ARLSYS(ph)DK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.404)YS(0.596)DK 100.58 0.015784 2121300000 1190100 725100 976490 908350 1089300 1109500 1321600 883860 970470 607630 TRUE FALSE 1237086.067 849630.2845 1001938.132 1088018.919 904141.1751 851835.4396 1218009.539 872013.3024 935542.9743 726683.4647 1.702372666 1.16918896 1.37878207 1.49723913 1.244202213 1.172223507 1.676121169 1.199990566 1.287414699 1 19.47096755 -4.003448157 0.178829867 1.43E-10 1.447510114 0.304259634 0.181687749 114.7398148 1.523489589 41.80593161 0.566617127 9.92E-05 4.003448157 1.447510114 ARNS(ph)GTQS(ph)DGEEKQPGLVMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 2 ARNS(1)GT(0.017)QS(0.984)DGEEKQPGLVMER 146.25 5.44E-07 279410000 1014800 629390 753110 598550 1016000 1137500 936440 791330 919070 659280 TRUE FALSE 1054865.088 737482.8365 772736.6653 716941.4035 843300.6829 873332.864 863039.3859 780723.5157 885992.8502 788453.2933 1.337891663 0.935353867 0.980066507 0.909301045 1.06956327 1.107653264 1.094597985 0.990196277 1.12371 1 19.58866577 ARNS(ph)GTQSDGEEKQPGLVMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ARNSGTQSDGEEKQPGLVMER 21 2 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 ARNS(0.722)GT(0.065)QS(0.213)DGEEKQPGLVMER;ARNS(0.925)GT(0.058)QS(0.017)DGEEKQPGLVMER;ARNS(0.989)GT(0.011)QSDGEEKQPGLVMER;ARNS(0.937)GT(0.063)QSDGEEKQPGLVMER;ARNS(0.944)GT(0.056)QSDGEEKQPGLVMER 193.6 3.48E-18 2581630000 706305 617258 731570 589043 851530 1001390 810420 727740 799280 639953 TRUE FALSE 734190.4668 723267.2599 750635.3152 705553.9473 706787.2348 768832.3487 746897.1628 717985.8356 770514.0689 765339.5377 0.959300324 0.945027957 0.980787321 0.921883573 0.923494998 1.00456374 0.975903016 0.938127197 1.006761092 1 19.54574041 2.743729122 24.99991865 0.976957647 0.946621188 0.35982071 0.024834658 644.5790144 3117819.091 0.008068234 0.008304122 554.2798903 -2.743729122 -0.030336459 ARPAPSRDPS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARPAPSRDPSPPR 13 2 Q5C9Z4 Q5C9Z4 NOM1 Nucleolar MIF4G domain-containing protein 1 1 ARPAPS(0.093)RDPS(0.907)PPR;ARPAPS(0.138)RDPS(0.862)PPR 77.324 0.02068 439020000 160167 191221 194038 243240 195269 252360 232094 205453 201492 203459 TRUE FALSE 166490.5168 224061.7193 199094.7897 291352.146 162077.2451 193753.2146 213901.8658 202699.2386 194240.3423 243322.8956 0.684236954 0.920841085 0.818232864 1.197388948 0.666099443 0.796280244 0.879086472 0.833046303 0.798282224 1 17.89251255 -1.414629962 5.85060129 1.000056609 0.849460324 0.10023996 0.139513124 9.74E-05 9.74E-06 0.127700008 0.030087884 0.038491961 1.414629962 -0.150596285 ARPATDS(ph)FDDYPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 ARPAT(0.039)DS(0.961)FDDYPPR;ARPAT(0.022)DS(0.978)FDDYPPR 123.41 6.24E-05 298900000 333990 339990 549070 392140 576480 481890 511410 463340 631390 476410 TRUE FALSE 347176.1831 398380.6377 563379.2153 469704.1216 478490.1355 369978.3506 471324.3479 457129.6852 608666.3972 569753.4181 0.609344625 0.69921588 0.988812348 0.824398953 0.839819684 0.649365741 0.827242686 0.802328991 1.06829793 1 19.11997815 1.26368746 7.797227621 1.034454794 0.786062883 0.489945309 0.10354951 0.141405619 35.01769934 0.07516602 0.02602518 18.35217153 -1.26368746 -0.248391911 ARPATDSFDDYPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 97.45 0.0027085 663550000 325401 372030 347260 361350 343656 428520 332840 343490 338390 405650 FALSE TRUE 338248.0827 435923.2585 356309.8809 432823.9515 285241.4759 329002.7243 306751.1311 338886.0784 326211.41 485129.3509 0.697232773 0.898571191 0.734463665 0.892182571 0.587969941 0.678175261 0.632307921 0.698547878 0.672421509 1 18.88800994 5.055434206 16.23337056 0.73798177 0.373739452 0.002503107 0.127017042 27306578 184603759.2 0.029281677 322573084 113614.6162 -5.055434206 -0.364242317 ARPDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ARPDAEK 7 1 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;; 93.429 0.013627 1127967000 1066927 817522 946333 838029 1180310 1207880 1387940 1025436 977564 717644 FALSE TRUE 1109050.102 957925.0441 970995.2154 1003788.635 979681.3278 927368.1756 1279149.636 1011691.708 942381.6626 858252.6017 1.292218747 1.116134157 1.131362973 1.169572493 1.141483668 1.080530573 1.490411603 1.178780822 1.09802366 1 19.7110428 ARPDAEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ARPDAEKK 8 2 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;; 93.649 0.0061413 1113030000 1685470 900440 1323530 830600 2006750 1673060 1660860 1263880 1533110 985570 FALSE TRUE 1752013.657 1055083.566 1358022.279 994890.2009 1665643.352 1284517.17 1530677.453 1246939.756 1477933.671 1178673.572 1.486428218 0.89514484 1.152161474 0.844076108 1.413150674 1.089798907 1.298644078 1.057917803 1.253895655 1 20.1687328 4.76497058 23.68764394 1.120774022 1.486429218 0.307658684 0.168165222 5182.207836 4647874.2 0.037325113 2.775058233 58206.37866 -4.76497058 0.365655197 ARPEDVISEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ARPEDVISEGR 11 1 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 ;;;; 187.78 3.14E-06 2471870000 1354990 1615740 1519900 1542010 1672050 1852970 1463820 1590810 1490790 1823690 FALSE TRUE 1408486.051 1893230.776 1559509.843 1847014.976 1387835.538 1422645.8 1349081.963 1569487.794 1437136.759 2181007.139 0.645796167 0.868053452 0.715041145 0.846863333 0.636327829 0.652288465 0.618559169 0.719616074 0.658932625 1 21.05656306 -1.116054633 4.347353366 1.000041766 0.709163554 0.533343314 0.082242675 1.696263321 47725733.86 4057.202918 0.019278871 0.07655003 1.116054633 -0.290878212 ARPEYMLPVHFYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARPEYMLPVHFYGR 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 133.66 2.60E-05 4579100000 2108380 2673200 2385700 2774000 3004600 3115300 2624700 2671600 2388800 3266400 FALSE TRUE 2191620.47 3132301.305 2447873.302 3322688.92 2493879.165 2391818.788 2418969.156 2635791.572 2302827.555 3906388.541 0.561034942 0.801840696 0.626633341 0.850578197 0.638410424 0.612283894 0.619234142 0.674738712 0.589502946 1 21.89740402 -1.926549778 3.108892779 1.195908009 0.668561567 0.568640138 0.087756035 9996860.602 18296481.68 13413470.81 0.019447619 0.011842686 1.926549778 -0.527346441 ARPFPDGLAEDIDKGEVSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;; 240.44 5.94E-30 10459185000 2032837 1524460 1847398 1511034 2409815 2354780 2294186 1940565 2057152 1547289 FALSE TRUE 2113094.974 1786274.146 1895542.71 1809912.015 2000195.507 1807918.032 2114361.707 1914554.9 1983115.501 1850450.655 1.141935327 0.965318444 1.024368148 0.978092558 1.080923451 0.977014992 1.142619881 1.034642505 1.071693264 1 20.81944523 2.27289382 24.99999149 1.064627742 1.025075561 0.070856471 0.060060313 431.26271 314025.7095 0.01930297 0.016149367 187.4536148 -2.27289382 -0.03955218 ARPPS(ph)GSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARPPSGSSK 9 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 ARPPS(0.997)GS(0.002)S(0.001)K 57.003 0.071603 259510000 116680 118460 136620 113790 163530 180860 160340 146970 153100 135330 TRUE FALSE 121286.6165 138804.5835 140180.4294 136297.3224 135733.229 138858.006 147772.1318 145000.1075 147589.9609 161845.3225 0.749398343 0.857637289 0.866138281 0.842145576 0.838660191 0.857967372 0.913045429 0.895917814 0.911919842 1 17.30425614 5.173727954 0.030361492 1.600476562 8.61E-09 0.810537704 0.026722154 314.065723 1.308545209 26.61134474 44.0536732 149185.9603 -5.173727954 -1.600476553 ARPPSEGEFIDCFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARPPSEGEFIDCFQK 15 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 110.56 0.00083153 235380000 431620 353970 489600 360540 553580 537040 554350 452310 474100 374150 FALSE TRUE 448660.6909 414761.594 502359.3782 431853.7359 459482.6693 412320.5989 510898.5985 446247.5243 457037.2336 447457.529 1.002688885 0.926929523 1.122697342 0.965127879 1.026874373 0.921474268 1.141781209 0.997295822 1.021409193 1 18.77139123 ARPS(ph)AHSPGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARPSAHSPGKK 11 2 H9KVB4;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 ARPS(0.71)AHS(0.29)PGKK 74.769 0.020829 29325000 33559 29381 36221 24605 50232 46738 47115 38455 42322 23237 TRUE FALSE 34883.93523 34426.9582 37164.94902 29471.79556 41693.58258 35883.80782 43422.00319 37939.57362 40798.83949 27789.84525 1.25527634 1.23883231 1.337357178 1.060523918 1.500317192 1.291256122 1.562513314 1.365231554 1.468120427 1 14.76227018 3.22404839 24.99997172 1.391382743 1.232297001 0.147030386 0.158759327 363.0773111 625466.0901 0.041907145 0.050295315 1675.129514 -3.22404839 -0.159085742 ARPS(ph)ETGSDDDWEYLLNSDYHQNVESHLLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARPSETGSDDDWEYLLNSDYHQNVESHLLNR 31 1 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 ARPS(0.332)ET(0.332)GS(0.332)DDDWEY(0.004)LLNSDYHQNVESHLLNR 43.088 0.066929 53882000 10060 18586 15059 17290 14923 18094 14869 14757 12470 17956 TRUE FALSE 10457.17657 21778.00092 15451.44991 20709.91039 12386.39379 13891.94272 13703.52893 14559.20655 12021.20714 21474.13441 0.48696615 1.01415035 0.719537729 0.964411883 0.576805265 0.646915142 0.638141155 0.677988052 0.55979938 1 14.39031236 4.025171724 24.99795312 0.705429673 0.779629551 0 0.184648989 1001.627235 994698.294 0.043433099 0.09382047 10596.72647 -4.025171724 0.074199878 ARPTILSSGLPEEPDQNLSS(ph)PEEVFHSGHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARPTILSSGLPEEPDQNLSSPEEVFHSGHSR 31 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 ARPTILSSGLPEEPDQNLS(0.239)S(0.685)PEEVFHS(0.067)GHS(0.01)R;ARPTILSSGLPEEPDQNLS(0.176)S(0.799)PEEVFHS(0.024)GHS(0.001)R 206.5 3.57E-26 418690000 103900 160781 145619 151346 150233 197103 167006 158228 166746 181255 TRUE FALSE 108002.0522 188393.886 149413.9508 181281.7871 124696.4483 151328.8154 153915.6333 156107.2125 160744.844 216768.4469 0.498236961 0.869101978 0.689279057 0.836292319 0.575251842 0.698112744 0.710046298 0.72015653 0.741550933 1 17.72579525 0.328607959 1.178258998 1.000492661 0.704169795 0.43574797 0.101994929 3.139528713 4.683479113 0.090987691 0.027109925 2.131120268 -0.328607959 -0.296322866 ARQEELYSELQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 278.93 2.27E-32 2764980000 713292 927305 839108 819428 972318 1038540 821729 932858 844755 1155414 FALSE TRUE 741453.3189 1086562.42 860975.8438 981508.4127 807043.7337 797354.8242 757319.7338 920354.5644 814352.4326 1381795.252 0.536586964 0.786341116 0.623084963 0.710313928 0.584054499 0.577042672 0.548069428 0.666057119 0.589343777 1 20.39811243 -1.267969593 3.648766442 1.000790937 0.628632431 0.700690126 0.073573322 20211859.13 34483718.34 179875.0761 0.017077873 0.05395484 1.267969593 -0.372158506 ARQEFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARQEFEER 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 124.74 0.0011781 482490000 424620 424860 424650 433740 536300 565530 521180 494760 482260 547120 FALSE TRUE 441384.3255 497826.4 435716.7279 519532.4774 445139.9176 434194.2282 480328.5497 488128.5515 464903.5568 654317.6888 0.674571898 0.760832862 0.665910055 0.794006469 0.680311606 0.663583204 0.73409073 0.746011547 0.710516565 1 19.31963175 -2.603941148 0.451158723 1.539330252 0.711978577 0.807319942 0.041867595 45.27993203 2.084343971 23.84699347 0.021083886 0.002489195 2.603941148 -0.827351675 ARQELQEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARQELQEAK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 99.864 0.0046042 182326000 345920 222939 270430 208249 456690 398940 327650 277700 296170 319720 FALSE TRUE 359577.1887 261227.039 277477.628 249440.0306 379061.9969 306292.231 301967.9368 273977.8857 285510.8996 382363.0126 0.940407876 0.683191183 0.725691604 0.652364435 0.991366802 0.801050889 0.789741494 0.716538673 0.746701146 1 18.54458345 ARQPQS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARQPQSPPR 9 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 ARQPQS(1)PPR 83.182 0.0098994 64263000 23793 21379 25621 23674 28768 21689 22966 24832 22264 35237 TRUE FALSE 24732.36601 25050.67694 26288.70431 28356.64654 23878.02564 16652.05845 21165.86491 24499.16766 21462.72299 42141.0155 0.586895349 0.59444882 0.623827025 0.672898985 0.56662198 0.395150858 0.502262811 0.581361587 0.509307209 1 15.36293746 -1.155835381 5.152718534 1.000019668 0.559946381 0.769749698 0.072324374 1.77E-05 2.90E-06 0.075826433 0.017871664 0.069849712 1.155835381 -0.440073287 ARS(ph)DPTHQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSDPTHQHR 10 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 1 ARS(0.999)DPT(0.001)HQHR;ARS(0.989)DPT(0.011)HQHR 100.55 0.0023769 322870000 13471 12660 12502.8 11795.5 10814.6 14009.3 10378 8987.8 10085.8 14760 TRUE FALSE 14002.84548 14834.25652 12828.63324 14128.61469 8976.338155 10755.85239 9564.545242 8867.333242 9722.814028 17651.9394 0.793275184 0.84037545 0.726754888 0.800400136 0.508518523 0.609329782 0.541841042 0.502343286 0.550807127 1 14.10753908 3.24948037 24.9994669 0.582566766 0.789253435 0.241929844 0.140076033 231.7681914 530602.4311 0.035817528 0.048032017 1776.152987 -3.24948037 0.206686669 ARS(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELKK 24 2 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.984)MDS(0.012)S(0.004)DLSDGAVTLQEYLELKK 156.4 1.43E-08 215030000 127200 77970 99497 67040 159940 119390 93148 103190 127200 80726 TRUE FALSE 132221.9542 91360.74098 102089.9736 80300.31191 132753.4559 91663.48187 85846.81636 101806.9068 122622.0968 96542.71411 1.369569474 0.946324555 1.057459121 0.83175942 1.375074827 0.949460378 0.88921072 1.054527084 1.270133101 1 16.55887977 ARS(ph)NENLDKIDMSLDDIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARSNENLDKIDMSLDDIIK 19 2 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 ARS(1)NENLDKIDMSLDDIIK 98.703 0.00047689 46473000 106640 45988 78809 47413 114580 93316 91719 71223 86769 48731 TRUE FALSE 110850.2295 53886.08126 80862.82728 56791.14989 95103.73253 71644.77322 84529.82512 70268.37218 83646.20064 58278.90644 1.902064337 0.924624097 1.387514492 0.974471783 1.63187229 1.229343129 1.45043602 1.205725647 1.435274025 1 15.83068619 -1.516154962 2.880628198 0.986813702 1.326715873 0.12087786 0.27655164 31302486.4 33521464.66 3231368.96 0.062851519 0.030468077 1.516154962 0.339902172 ARS(ph)PDLGPQEQMNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSPDLGPQEQMNPK 15 1 H3BUW4;H3BMU4;A0A0C4DGM2;C9K0J8;Q8IWY8-4;Q8IWY8-3;Q8IWY8-2;Q8IWY8 H3BUW4 ZSCAN29 Zinc finger and SCAN domain-containing protein 29 1 ARS(1)PDLGPQEQMNPK;ARS(1)PDLGPQEQMNPK 185.61 2.52E-07 701230000 441470 380930 398650 360170 501840 514670 470400 397160 407040 336750 TRUE FALSE 458899.5765 446351.7643 409039.1465 431410.551 416537.4161 395145.6924 433528.8188 391836.7198 392390.7099 402729.715 1.139472851 1.108315944 1.015666665 1.071216091 1.03428528 0.981168455 1.076475866 0.972952095 0.974327682 1 18.6194524 7.999999999 0.329764297 0.990798842 2.58391066 0.65076328 0.033058438 34.32027725 0.490187129 0.028819581 33.30597192 99999999.68 -7.999999999 1.593111818 ARS(ph)PGREEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSPGREEVAR 11 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 ARS(1)PGREEVAR;ARS(1)PGREEVAR 85.163 0.012145 1817040000 834890 1006710 997750 1159500 1079900 1280490 1268510 1025820 1201320 1157110 TRUE FALSE 867852.1019 1179604.611 1023752.185 1388845.639 896338.9837 983115.6035 1169080.872 1012070.561 1158084.728 1383823.55 0.627140723 0.852424148 0.739799655 1.00362914 0.647726355 0.710434219 0.844819321 0.731358099 0.836873117 1 20.40022857 0.923047066 5.43917718 0.999984147 0.774972099 0.308738224 0.104178005 0.630725689 42.29936156 0.093729337 0.023629876 8.376200529 -0.923047066 -0.225012048 ARS(ph)PINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSPINR 7 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ARS(1)PINR;ARS(1)PINR 80.688 0.017704 254650000 43551 56948 54372 70955 50153 60055 58681 60357 53262 69461 TRUE FALSE 45270.42711 66728.37601 55788.97899 84989.68722 41628.01097 46108.13639 54081.42989 59548.01314 51345.11102 83070.55304 0.544963594 0.803273526 0.671585501 1.023102461 0.501116334 0.555047905 0.651030093 0.716836604 0.618090396 1 16.34204954 -1.589348855 4.801385182 1.003386484 0.68271949 0.314297511 0.143219883 0.005091989 0.000435506 0.136005396 0.031762923 0.025742525 1.589348855 -0.320666994 ARS(ph)PSPCPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARSPSPCPFR 10 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 ARS(0.996)PS(0.004)PCPFR 56.122 0.076401 178270000 54793 65561 59868 63719 76962 84039 73367 50873 64025 79053 TRUE FALSE 56956.26995 76820.59176 61428.20926 76322.42802 63880.02673 64522.21587 67616.30283 50191.13065 61720.75276 94541.92179 0.602444597 0.812555851 0.649745722 0.807286615 0.675679376 0.682472015 0.715199158 0.530887565 0.652840048 1 16.52866657 -0.953242724 5.31332893 1.000000883 0.678196946 0.584677438 0.080623292 8.66E-07 1.71E-07 0.080154637 0.018892577 0.111367194 0.953242724 -0.321803936 ARS(ph)PSVAAMASPQLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 ARSPSVAAMASPQLCR 16 1 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 ARS(1)PSVAAMASPQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(1)PSVAAMASPQLCR;ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.995)PS(0.005)VAAMASPQLCR;ARS(0.999)PS(0.001)VAAMASPQLCR;ARS(0.991)PS(0.009)VAAMASPQLCR;ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.998)PS(0.002)VAAMASPQLCR;ARS(0.619)PS(0.299)VAAMAS(0.082)PQLCR;ARS(0.989)PS(0.011)VAAMASPQLCR;ARS(0.997)PS(0.003)VAAMASPQLCR 221.05 6.62E-15 24724150000 4019144 4629070 4400614 4093873 5363160 5473580 4194920 4468295 4350689 5530800 TRUE FALSE 4177822.909 5424076.763 4515297.616 4903628.86 4451531.979 4202423.998 3866111.209 4408404.814 4194108.553 6614454.366 0.631620188 0.820033893 0.682640981 0.741350471 0.673000634 0.63533948 0.584494351 0.666480494 0.634082317 1 22.65719072 -0.973437801 12.75615984 1 0.675067685 0.710482996 0.06236451 0 0 0.062333117 0.014692057 0.106307082 0.973437801 -0.324932315 ARS(ph)PTDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ARSPTDDK 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.999)PT(0.001)DDK;ARS(0.991)PT(0.009)DDK;ARS(0.997)PT(0.003)DDK 75.378 0.023343 522200000 1011980 564227 771060 588180 950390 1140760 1194790 794070 829360 520468 TRUE FALSE 1051933.752 661128.5982 791154.457 704520.2485 788843.0473 875835.7784 1101139.238 783426.7905 799511.4956 622443.7396 1.690006156 1.062149968 1.271045729 1.131861731 1.267332286 1.407092276 1.769058258 1.258630685 1.284471904 1 19.24758392 2.747100102 20.79753114 1.386551294 1.262902421 0 0.237258519 204.8930282 499002.8955 0.070780254 0.073658184 558.5989337 -2.747100102 -0.123648873 ARS(ph)PTDDKVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ARSPTDDKVK 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.997)PT(0.003)DDKVK;ARS(0.997)PT(0.003)DDKVK;ARS(0.954)PT(0.046)DDKVK;ARS(0.966)PT(0.034)DDKVK;ARS(0.5)PT(0.5)DDKVK;ARS(0.991)PT(0.009)DDKVK;ARS(0.98)PT(0.02)DDKVK 156.08 9.11E-06 9938070000 7810640 3162152 4815220 3097110 7125230 6662960 6747670 4630910 5294800 2509304 TRUE FALSE 8119010.098 3705227.008 4940708.589 3709709.114 5914085.95 5115588.518 6218769.994 4568840.226 5104241.182 3000954.075 2.70547629 1.234683009 1.646379273 1.23617657 1.97073524 1.70465405 2.072264299 1.522462561 1.700872807 1 21.51698981 0.339167993 1.184177325 0.999349479 1.738522603 0.236721731 0.407416447 4.967778291 7.550294772 0.369104246 0.110159135 2.183574396 -0.339167993 0.739173124 ARS(ph)PTDDKVKIEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ARSPTDDKVKIEDK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 ARS(0.975)PT(0.025)DDKVKIEDK;ARS(0.882)PT(0.118)DDKVKIEDK;ARS(0.99)PT(0.01)DDKVKIEDK;ARS(0.996)PT(0.004)DDKVKIEDK 134.29 0.00021893 1681520000 3372320 955110 1598720 474828 3415610 2386140 1415730 1373970 1973510 992670 TRUE FALSE 3505461.798 1119142.713 1640383.957 568747.5612 2835025.832 1831995.147 1304761.383 1355554.18 1902483.761 1187164.681 2.952801624 0.942702163 1.381766138 0.479080595 2.388064502 1.543168507 1.099056773 1.141841736 1.602544105 1 20.17908865 4.746088837 24.89811333 1.294998313 2.952802462 0.520971348 0.479291537 692.2495272 2289421.835 0.111441925 1.176826947 55729.97361 -4.746088837 1.657804149 ARS(ph)PVRLPHEGSPSPGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSPVRLPHEGSPSPGEK 18 2 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 ARS(0.99)PVRLPHEGS(0.01)PSPGEK;ARS(1)PVRLPHEGSPSPGEK 188.23 2.03E-14 330190000 171992 203187 226300 191889 278190 273660 233580 216914 249480 207640 TRUE FALSE 178782.377 238082.7867 232197.5639 229844.0715 230903.3632 210106.6124 215271.3893 214006.6226 240501.2635 248323.0825 0.719958754 0.958762207 0.935062345 0.925584803 0.929850584 0.846101821 0.866900439 0.861807209 0.968501442 1 17.92185885 1.110399868 4.7486105 0.998132907 0.885217697 0.296444355 0.064307245 0.249173259 8.51754842 0.059337528 0.01510726 12.89436227 -1.110399868 -0.11291521 ARS(ph)PYSPAEEDALFMDLPTGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ARSPYSPAEEDALFMDLPTGPR 22 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 ARS(0.969)PY(0.001)S(0.03)PAEEDALFMDLPTGPR;ARS(1)PYSPAEEDALFMDLPTGPR;ARS(0.994)PYS(0.006)PAEEDALFMDLPTGPR;ARS(0.979)PYS(0.021)PAEEDALFMDLPTGPR;ARS(0.997)PYS(0.003)PAEEDALFMDLPTGPR;ARS(0.988)PY(0.005)S(0.007)PAEEDALFMDLPTGPR 333.23 4.78E-81 983611000 279390 326597 292726 288358 318492 358591 306842 304292 297884 340324 TRUE FALSE 290420.5329 382687.4942 300354.68 345394.3517 264354.8436 275313.6747 282790.9223 300213.4635 287163.213 407003.9719 0.713556999 0.940254938 0.737964985 0.848626489 0.649514162 0.676439774 0.69481121 0.737618019 0.705553834 1 18.63468335 5.081337043 14.38515079 0.761804439 6.61E-05 0.012524178 0.111723558 2383410.936 8190694.107 0.025550127 55233626.25 120597.1496 -5.081337043 -0.761738387 ARS(ph)VDALDDLTPPSTAESGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARSVDALDDLTPPSTAESGSR 21 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 ARS(1)VDALDDLTPPSTAESGSR 114.31 0.0001092 205350000 93697 135830 111790 160610 153440 186340 145610 134040 112480 153900 TRUE FALSE 97396.22991 159157.7459 114703.3392 192378.1786 127358.3236 143065.359 134196.7077 132243.413 108431.8668 184053.7584 0.529172731 0.864735104 0.623205634 1.0452282 0.691962635 0.777302024 0.729116911 0.718504279 0.5891315 1 17.48976768 -1.972097359 2.662718887 1.220076024 0.738817964 0.25121786 0.1391578 43544842.24 22568901.15 59077555.31 0.031927401 0.01066357 1.972097359 -0.48125806 ARS(ph)VS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSVSPPPK 9 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 ARS(1)VS(1)PPPK;ARS(1)VS(1)PPPK 62.042 0.048489 1435400000 777850 542480 695980 541920 859770 874290 781630 697650 722470 562460 TRUE FALSE 808560.1186 635646.7201 714117.8106 649110.1585 713626.6025 671249.3975 720363.7982 688299.1429 696468.4458 672663.2681 1.202028053 0.944970166 1.061627481 0.96498529 1.060897237 0.997898101 1.07091294 1.023244728 1.035389442 1 19.35952495 4.754353596 24.86412291 1.021460751 1.202028198 0.657298462 0.039833862 1649.967415 2597626.152 0.008532434 0.222988612 56800.68802 -4.754353596 0.180567447 ARS(ph)VS(ph)PPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ARSVSPPPKR 10 2 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 ARS(1)VS(1)PPPKR;ARS(1)VS(1)PPPKR 126.1 0.00021002 7051100000 185900 154226 183095 167179 239580 223830 199034 179387 180755 155869 TRUE FALSE 193239.4755 180713.1158 187866.6061 200246.5072 198856.2772 171848.8747 183433.195 176982.6107 174249.6629 186408.5463 1.036644936 0.969446516 1.007821851 1.074234584 1.066776611 0.921893755 0.984038547 0.949433995 0.934772929 1 17.50810848 2.736958497 24.99972777 0.956670027 1.028682025 0.52720631 0.034498393 126.224705 1969616.278 0.011425626 0.011291503 545.7057093 -2.736958497 0.072011998 ARSDEGQLS(ph)PATR ddPTM_MDA-MB-175_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(0.997)PAT(0.003)R;ARSDEGQLS(1)PATR;ARSDEGQLS(1)PATR;ARSDEGQLS(0.993)PAT(0.007)R;ARSDEGQLS(1)PATR 199.19 7.26E-08 3447140000 1056950 974795 1106580 892902 1595930 1361030 1220010 1148520 1214920 1428490 TRUE FALSE 1098679.202 1142208.458 1135418.384 1069515.351 1324654.389 1044951.409 1124382.428 1133125.968 1171195.267 1708375.265 0.643113503 0.668593418 0.664618838 0.6260424 0.775388415 0.61166386 0.658158925 0.663276969 0.685560889 1 20.70419348 0.53702159 2.499795148 0.999998239 0.664456624 0.854846333 0.041340027 2.133048502 11.10145445 0.03706927 0.009888181 3.4436705 -0.53702159 -0.335541614 ARSMDSSDLS(ph)DGAVTLQEYLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARSMDSSDLSDGAVTLQEYLELK 23 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 ARS(0.195)MDS(0.246)S(0.246)DLS(0.313)DGAVTLQEYLELK 57.293 0.017106 0 13747 8237.5 12901 8601.1 17843 19595 14356 12371 14473 7771.7 TRUE FALSE 14289.74217 9652.226546 13237.21066 10302.37191 14810.05323 15044.35822 13230.73921 12205.18698 13952.11956 9294.415817 1.537454581 1.038497388 1.424211152 1.108447493 1.59343562 1.618644841 1.423514879 1.313174192 1.501129262 1 13.18214847 5.062728028 21.45184812 1.355612856 5.567690967 0.068999699 0.211222965 1973.007157 714682.5531 0.047166453 23255.75529 115538.8466 -5.062728028 4.212078111 ART(ph)PLTAAQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ARTPLTAAQQK 11 1 I3L2J0 I3L2J0 CIC 1 ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK;ART(1)PLTAAQQK 158.31 4.85E-05 2168880000 1312910 1114740 1306610 974830 1805230 1650490 1433810 1294270 1435190 1161130 TRUE FALSE 1364744.701 1306187.924 1340661.33 1167648.464 1498377.649 1267188.711 1321424.226 1276922.428 1383537.792 1388631.192 0.982798534 0.940629831 0.96545529 0.840862909 1.079032113 0.912545187 0.951602004 0.919554764 0.996332071 1 20.40523205 1.204985628 17.55753145 0.998173008 0.947584715 0.106238359 0.056843659 19.3471456 10106.06639 0.050082104 0.012549679 16.03192335 -1.204985628 -0.050588293 ARTEKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARTEKEEK 8 2 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 72.643 0.02566 58675000 133300 55442 86071 43046 139780 113570 126310 95597 120410 67138 FALSE TRUE 138562.7869 64963.73222 88314.08097 51560.37032 116020.2455 87195.08867 116409.4922 94315.67858 116076.4676 80292.40567 1.725727182 0.809089374 1.099905779 0.642157498 1.444971596 1.085969314 1.449819459 1.174652544 1.445671812 1 16.29297592 ARVSS(ph)GYVPPPVATPFSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ARVSSGYVPPPVATPFSSK 19 1 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 ARVS(0.267)S(0.404)GY(0.328)VPPPVATPFSSK 98.175 0.00060464 236360000 197200 195900 196710 176650 263710 275300 247790 232610 222550 236410 TRUE FALSE 204985.6083 229544.3011 201836.4242 211590.8428 218884.6684 211365.7472 228367.5723 229492.2434 214540.469 282730.0132 0.725022455 0.811885157 0.71388397 0.748384794 0.774182641 0.747588644 0.807723134 0.811701032 0.758817455 1 18.10906551 -4.99999997 0.230974942 2.258002045 0.743583287 0.834857001 0.031512702 58.75751854 0.587833139 34.50836345 0.05197763 1.00E-05 4.99999997 -1.514418758 AS(ph)DGQLQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASDGQLQAK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 AS(1)DGQLQAK 142.1 0.00011029 487510000 868470 626800 788860 724530 885300 942110 1038800 803240 779480 474330 TRUE FALSE 902757.8662 734448.0242 809418.3397 867839.8715 734817.0222 723319.2303 957376.1416 792473.8816 751426.6671 567265.8819 1.591419289 1.294715666 1.426876471 1.529864388 1.295366151 1.275097363 1.687702667 1.397006072 1.324646327 1 19.11366557 0.836428388 2.509703362 1.000570577 1.435298736 0.515827165 0.127770347 0.500503573 5.720519127 0.118512208 0.031746039 6.861647255 -0.836428388 0.434728159 AS(ph)DKDITVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASDKDITVSK 10 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 AS(0.998)DKDIT(0.002)VSK;AS(1)DKDITVSK 147.56 1.62E-05 665360000 1807910 602510 940350 662240 1236210 1440030 1806620 1049880 1316220 410560 TRUE FALSE 1879287.683 705986.4056 964856.2935 793229.0954 1026079.466 1105604.856 1665012.404 1035808.076 1268849.499 491001.3714 3.827459132 1.437850171 1.965078612 1.61553336 2.089769043 2.251734763 3.391054487 2.109582857 2.584207649 1 18.90536753 2.473418992 24.99630049 2.4291754 2.108351766 0 0.822348656 467.1045955 3153664.589 0.269070804 0.22610562 297.4534373 -2.473418992 -0.320823635 AS(ph)DLEDEESAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASDLEDEESAAR 12 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 AS(1)DLEDEESAAR;AS(1)DLEDEESAAR 147.73 0.00024699 812990000 127130 106452 133482 135862 145980 187510 176438 144478 138567 103970 TRUE FALSE 132149.1906 124734.3029 136960.6506 162735.0981 121166.3717 143963.6442 162608.3285 142541.5087 133580.0007 124340.9309 1.062797179 1.003163657 1.101492884 1.308781404 0.974468913 1.157813789 1.307761872 1.1463764 1.074304332 1 16.92394176 4.005213516 18.00082521 1.152809146 1.037814687 0.125485098 0.1056162 7.68629057 26505.97582 0.025628072 0.054589066 10120.76909 -4.005213516 -0.114994459 AS(ph)DPGLPAEEPK ddPTM_MDA-MB-175_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 190.1 7.42E-06 1115440000 3579630 1190393 1736688 1879763 2256590 3435540 3143430 1826348 1992554 889551 TRUE FALSE 3720956.556 1394833.738 1781947.516 2251574.511 1873015.638 2637687.901 2897039.743 1801868.792 1920842.371 1063841.487 3.497660697 1.311129294 1.675012244 2.116456764 1.760615337 2.479399359 2.723187409 1.693738038 1.805571971 1 20.02085177 0.91599229 1.514537731 1.015312964 2.138962742 0.26841269 0.591232244 0.67520906 3.100983845 0.53818046 0.157835648 8.241234847 -0.91599229 1.123649778 AS(ph)DPGLPAEEPKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASDPGLPAEEPKEK 14 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 AS(1)DPGLPAEEPKEK;AS(1)DPGLPAEEPKEK 177.67 2.09E-06 144750000 798580 284530 475740 327380 745980 739200 655230 467030 585360 260060 TRUE FALSE 830108.555 333395.8142 488138.1752 392134.7869 619178.5861 567532.0027 603871.3605 460770.2268 564293.0079 311013.7779 2.669041098 1.071964774 1.569506594 1.260827702 1.990839732 1.824780904 1.941622537 1.481510658 1.814366591 1 18.24661897 -1.258182849 4.014245812 0.999263178 1.700208665 0.212644969 0.419832288 29689009.01 9306056.193 190498.9045 0.09101961 0.055184505 1.258182849 0.700945486 AS(ph)ETPPPVAQPKPEAPHPGLETTLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 AS(0.527)ET(0.473)PPPVAQPKPEAPHPGLETTLQER 56.476 0.044312 923070000 55885 50899 64748 56392 73740 89376 63848 74878 56882 47072 TRUE FALSE 58091.38295 59640.50731 66435.38607 67546.16929 61205.70114 68619.77851 58843.42692 73874.38289 54834.82793 56294.85715 1.031912787 1.059430831 1.180132421 1.199863943 1.087234327 1.218935121 1.045271805 1.312275874 0.974064607 1 15.78071551 4.347180884 5.502651836 1.146744257 1.039250298 0.071273137 0.100940634 0.357343374 15.58172363 0.02279684 0.064948958 22242.36092 -4.347180884 -0.107493959 AS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASGDYDNDCTNPITPLCTQPDQVIK 25 0 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 AS(0.468)GDY(0.468)DNDCT(0.064)NPITPLCTQPDQVIK 143.29 2.12E-07 114900000 53807 32285 41581 45362 68094 69551 72773 50288 60653 38499 TRUE FALSE 55931.34191 37829.69761 42664.63502 54334.46821 56519.4062 53398.83431 67068.8621 49613.97161 58470.11038 46042.14194 1.214785836 0.82163201 0.926643141 1.180102965 1.227558142 1.159781714 1.45668423 1.0775774 1.26992594 1 15.49066733 3.680347448 5.754302365 1.208360015 0.971325844 0.296010673 0.145900943 0.220035999 15.65424449 0.036797192 0.058125176 4790.131628 -3.680347448 -0.237034171 AS(ph)GEGHHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASGEGHHLK 9 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 AS(1)GEGHHLK 77.64 0.012409 0 76840 68102 79829 74604 90520 99324 83536 71516 92218 58494 TRUE FALSE 79873.70253 79797.98874 81909.40932 89360.44853 75133.44273 76257.50627 76988.23004 70557.445 88899.09219 69954.77936 1.1417905 1.140708176 1.170890825 1.27740305 1.074028728 1.090097159 1.100542818 1.008615074 1.270807985 1 16.09413501 3.180417155 24.99984618 1.086123644 1.178856979 0.249701445 0.077786417 107.0632305 46033.20463 0.021824354 0.026085106 1515.015776 -3.180417155 0.092733335 AS(ph)GEMASAQYITAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR;AS(1)GEMASAQYITAALR 353.33 2.76E-87 1694975000 1049404.3 772677.1 937141.2 1127751.8 972059.8 1241043.3 1613174 1082662.9 1040910.5 553336.6 TRUE FALSE 1090835.592 905378.3813 961563.8695 1350817.74 806829.4224 952829.8018 1486729.207 1068151.575 1003448.334 661752.3125 1.648404655 1.368152954 1.45305706 2.041273925 1.219231738 1.439858666 2.246655098 1.614125942 1.516350325 1 19.33593181 AS(ph)GQAFELILS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR 96.379 0.006234 49962000 130521 115462 126333 133293 166460 186472 167284 168647 175274 184175 TRUE FALSE 135674.0699 135291.7003 129625.3418 159657.9576 138165.1887 143166.704 154171.843 166386.5628 168965.923 220260.565 0.61597077 0.614234783 0.588509077 0.724859475 0.627280642 0.649987909 0.699952091 0.755407863 0.767118358 1 17.7488517 0.380481912 0.337588751 1.062827223 0.601524379 0.919323806 0.032712382 0.812618785 0.174707324 0.113366962 0.033370636 2.401496245 -0.380481912 -0.461302844 AS(ph)GQAFELILSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 226.74 1.08E-11 903631000 271044 299125 314673 331967 393814 456288 392892 361698 373830 397556 TRUE FALSE 281745.0264 350497.3919 322873.6369 397629.0818 326873.6369 350322.0271 362096.0984 356850.0299 360375.9313 475449.4865 0.592586667 0.737191651 0.679091357 0.836322455 0.687504448 0.736822811 0.761586895 0.750552982 0.757968915 1 18.85893255 -5 0.177390283 2.090719996 0.671318522 0.713451365 0.054601622 69.71295821 0.668228607 26.76913024 0.167767052 1.00E-05 5 -1.419401474 AS(ph)GVAVSDGVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASGVAVSDGVIK 12 0 P23528;E9PP50;E9PS23 P23528 CFL1 Cofilin-1 1 AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK 182.33 1.79E-05 556156000 922109 679210 943112 668733 1892450 1120003 1520170 848323 954984 720156 TRUE FALSE 958514.5753 795859.034 967690.2735 801006.3914 1570772.025 859899.2771 1401015.103 836952.6178 920614.3124 861256.78 1.112925434 0.924067076 1.123579281 0.930043641 1.823813828 0.998423812 1.626710101 0.971780585 1.068919669 1 19.71608391 AS(ph)HSS(ph)ERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 AS(1)HS(0.21)S(0.79)ERPPPR;AS(1)HS(0.264)S(0.736)ERPPPR 69.258 0.031293 404170000 454310 476160 441910 598320 502300 582320 465870 445690 347680 383430 TRUE FALSE 472246.5096 557936.776 453426.5376 716665.9102 416919.2254 447085.0051 429353.8921 439716.2546 335167.0647 458555.7673 1.029856221 1.216726112 0.988814382 1.562876233 0.909200702 0.974985023 0.936317723 0.958915547 0.730918873 1 18.80673767 AS(ph)HSSERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.718)HS(0.255)S(0.027)ERPPPR;AS(0.991)HS(0.009)SERPPPR;AS(0.99)HS(0.009)S(0.001)ERPPPR 174.72 6.47E-06 1902053000 108614.4 345214 247185.5 329138.8 295460.9 401229.8 275623 296196.3 229748.6 273067.3 TRUE FALSE 112902.5804 404501.8191 253627.3572 394241.4723 245238.5618 308050.2596 254018.9491 292226.2731 221479.9928 326569.6092 0.345722863 1.238638892 0.776641028 1.207220333 0.75095341 0.943291264 0.777840135 0.894836093 0.678201481 1 18.31703101 2.244776952 24.86439417 0.834188818 0.898220765 0.001603558 0.247749571 843.4001071 3373479.165 0.080391762 0.065680561 175.7020999 -2.244776952 0.064031947 AS(ph)LADALPLHIAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASLADALPLHIAPR 14 0 H3BRB6;Q8ND25;Q8ND25-2 H3BRB6 ZNRF1 E3 ubiquitin-protein ligase ZNRF1 1 AS(1)LADALPLHIAPR;AS(1)LADALPLHIAPR 154.46 3.94E-06 135452000 115170 110596 116564 112581 176337 146252 124532 118626 117938 125306 TRUE FALSE 119717.0005 129590.0027 119601.7536 134849.1858 146363.2997 112287.1895 114770.8564 117036.0125 113693.4344 149857.3116 0.79887327 0.864755956 0.798104226 0.89985056 0.976684409 0.749294034 0.765867579 0.780982998 0.758677927 1 17.19322995 2.680148937 24.99986732 0.792540374 0.865418721 0.083337383 0.083322898 490.1060809 209761.8542 0.025762329 0.024286455 478.7942621 -2.680148937 0.072878347 AS(ph)LEDAPVDDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 217.2 2.75E-11 958390000 1881180 1762930 2090490 2221420 2364850 2771590 3096760 2245550 2385520 1757640 TRUE FALSE 1955450.439 2065699.514 2144969.887 2660810.246 1962873.642 2127930.226 2854027.859 2215452.075 2299665.601 2102015.906 0.930273854 0.982723065 1.02043466 1.265837351 0.933805323 1.012328318 1.357757499 1.053965419 1.094028639 1 21.00334216 3.98905472 20.69559492 1.109182968 0.967767944 0.195525034 0.119706745 82.10393129 155256.9212 0.030008986 0.058704216 9751.124921 -3.98905472 -0.141415024 AS(ph)LSDLTDLEDIEGLTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASLSDLTDLEDIEGLTVR 18 0 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 AS(0.974)LS(0.026)DLTDLEDIEGLTVR;AS(0.998)LS(0.002)DLTDLEDIEGLTVR;AS(0.966)LS(0.034)DLTDLEDIEGLTVR;AS(0.994)LS(0.006)DLTDLEDIEGLTVR 122.1 3.86E-05 85483000 88602 83790 93322 102780 108556 124049 100124 85571 88530 80523 TRUE FALSE 92100.07538 98180.2807 95754.04798 123109.5772 90103.6899 95240.49973 92276.01925 84424.06071 85343.82259 96299.94014 0.95638767 1.019525875 0.994331334 1.278397235 0.935656759 0.988998535 0.95821471 0.876678226 0.886229238 1 16.55524728 2.57646441 1.718591612 0.915796851 1.050015773 0.236295168 0.092841502 0.480361168 2.852050479 0.039408758 0.033761015 377.10684 -2.57646441 0.134218922 AS(ph)LSEIGFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASLSEIGFGK 10 0 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 AS(0.971)LS(0.029)EIGFGK 132.03 0.0037152 0 87816 64933 91536 69853 107470 103760 116070 83292 101410 59733 TRUE FALSE 91283.04349 76084.73764 93921.50336 83669.71491 89202.28779 79663.3125 106972.1301 82175.60698 97760.27391 71436.53769 1.277820097 1.065067542 1.314754415 1.171245382 1.248692765 1.115162004 1.497442815 1.150330204 1.36849121 1 16.12437454 AS(ph)LSSAPVVLVGDHA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASLSSAPVVLVGDHA 15 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 AS(1)LSSAPVVLVGDHA 205.96 4.34E-09 22693000 32700 36528 33115 37367 40873 47914 34558 35924 31076 50394 TRUE FALSE 33991.02125 42801.39985 33978.0041 44758.08107 33925.42206 36786.69964 31849.25366 35442.49754 29957.58083 60267.73945 0.564000269 0.710187577 0.56378428 0.742654055 0.562911806 0.610387912 0.528462722 0.588084071 0.497074904 1 15.87909833 -1.945851781 2.863637557 1.280761195 0.59876313 0.736741366 0.072366512 26432600.09 8099148.049 49187096.57 0.016801119 0.011327869 1.945851781 -0.681998066 AS(ph)PALVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPALVAK 8 0 Q92783;Q92783-2;A6NMU3 Q92783 STAM Signal transducing adapter molecule 1 1 AS(1)PALVAK 65.933 0.066075 92861000 133810 126900 132770 131760 154150 158670 151910 129690 137420 133190 TRUE FALSE 139092.9221 148694.0879 136230.0953 157821.7347 127947.6381 121821.2972 140002.8973 127951.7177 132474.281 159286.0304 0.873227374 0.933503632 0.855254506 0.990807131 0.80325712 0.764795863 0.878940211 0.803282732 0.83167545 1 17.28126022 3.211629692 24.99940458 0.833512138 0.910509809 0.164472424 0.069105667 304.9100732 283040.7647 0.01848278 0.022096791 1627.907381 -3.211629692 0.076997671 AS(ph)PAPAPS(ph)RSPSAQCPFPGGTVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPAPAPSRSPSAQCPFPGGTVLSR 25 1 P78411-3;P78411-2;P78411;H0YML8 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 2 AS(1)PAPAPS(0.493)RS(0.254)PS(0.254)AQCPFPGGTVLSR 99.372 2.93E-06 0 46484 46841 37708 38185 48465 53311 46902 41943 46528 35951 TRUE FALSE 48319.22421 54885.57738 38690.70146 45737.87903 40226.93661 40930.32819 43225.69868 41380.82269 44853.46637 42994.91013 1.123835916 1.276559882 0.899890274 1.063797526 0.935620902 0.951980783 1.005367811 0.962458639 1.043227355 1 15.39187826 4.239435906 25 0.981754243 1.200197923 0.695204055 0.057577518 10.35954914 295843.7962 0.012788051 0.031174037 17355.45109 -4.239435906 0.21844368 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 AS(0.888)PAPGS(0.112)GHPEGPGAHLDMNSLDR;AS(0.991)PAPGS(0.009)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR;AS(0.998)PAPGS(0.002)GHPEGPGAHLDMNSLDR;AS(1)PAPGSGHPEGPGAHLDMNSLDR;AS(0.992)PAPGS(0.008)GHPEGPGAHLDMNSLDR 242.48 1.60E-37 4330610000 344885 413456 400054 561051 444662 818400 478512 391497 453986 613531 TRUE FALSE 358501.3261 484463.8518 410479.7359 672025.2132 369078.5121 628339.003 441004.9791 386249.6231 437647.1325 733740.6527 0.488594062 0.66026579 0.559434365 0.915889301 0.503009491 0.856350266 0.601036589 0.526411644 0.596460249 1 19.48491069 -2.140500001 2.356174371 1.783820138 0.634302455 0.391112842 0.136939245 7698506.352 1769438.967 32299121.93 0.03203226 0.007236024 2.140500001 -1.149517683 AS(ph)PATHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPATHR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 AS(0.996)PAT(0.004)HR 80.455 0.041442 0 14799 16158 14373 17722 18417 21601 23224 19068 17567 15203 TRUE FALSE 15383.27595 18933.01081 14747.57219 21227.35871 15286.48492 16584.49512 21403.6422 18812.42465 16934.7671 18181.73677 0.846083966 1.041320257 0.811120102 1.167509956 0.840760435 0.912151316 1.177205592 1.034687989 0.931416361 1 14.1502024 AS(ph)PDS(ph)SSCGERSPPPPPPPPSDEALLHCVLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPDSSSCGERSPPPPPPPPSDEALLHCVLEGK 33 1 Q9BRK4 Q9BRK4 LZTS2 Leucine zipper putative tumor suppressor 2 2 AS(0.998)PDS(0.311)S(0.281)S(0.254)CGERS(0.156)PPPPPPPPSDEALLHCVLEGK;AS(0.723)PDS(0.326)S(0.326)S(0.326)CGERS(0.301)PPPPPPPPSDEALLHCVLEGK 101.16 4.18E-05 103231000 58444 43754 53282 49355 69962 77884 80099 63436 63499 41850 TRUE FALSE 60751.41425 51268.40914 54670.57269 59117.27169 58069.88423 59796.62134 73820.63108 62585.74418 61213.68339 50049.70623 1.213821595 1.024349851 1.092325546 1.181171202 1.160244257 1.194744702 1.474946341 1.250471759 1.223057796 1 15.61107398 2.625658151 3.501055346 1.270445665 1.127581858 0.107568912 0.119441091 0.357863142 8.105751168 0.03920037 0.036706348 422.3360471 -2.625658151 -0.142863807 AS(ph)PEPELQLRPYQMEVAQPALEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPEPELQLRPYQMEVAQPALEGK 24 1 A0A3B3IRK8;Q9BYX4 A0A3B3IRK8 IFIH1 Interferon-induced helicase C domain-containing protein 1 1 AS(1)PEPELQLRPYQMEVAQPALEGK 154.02 4.08E-08 94268000 45959 35260 38824 36277 50334 60375 52739 39875 45483 30891 TRUE FALSE 47773.49681 41315.63072 39835.78533 43452.48232 41778.24466 46353.82124 48605.17937 39340.54085 43846.07571 36943.50001 1.293150265 1.118346413 1.078289424 1.176187484 1.130868614 1.254721974 1.315662549 1.064883967 1.186841412 1 15.17303293 0.448271788 1.086002341 1.000400661 1.17883506 0.301067279 0.081821734 2.815333003 4.283002691 0.079987819 0.024637517 2.807189872 -0.448271788 0.178434399 AS(ph)PEPPGPESSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ASPEPPGPESSSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(1)PEPPGPESSSR 270.16 8.29E-26 16654385000 5774710 5573720 5911688 5418238 6350185 7153016 6790283 5877413 5844491 4556519 TRUE FALSE 6002700.01 6530963.052 6065751.446 6489949.305 5270782.822 5491836.439 6258042.875 5798635.892 5634148.911 5449281.658 1.101558038 1.198499814 1.113128634 1.190973363 0.967243602 1.007809246 1.148416116 1.064110144 1.033925068 1 22.37763463 3.253266182 24.99999585 1.047964594 1.151722005 0.515290062 0.053583543 218.1568608 370872.4154 0.015217455 0.020518887 1791.703665 -3.253266182 0.10375741 AS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASPEPQRENASPAPGTTAEEAMSR 24 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 AS(1)PEPQRENAS(0.998)PAPGT(0.001)T(0.001)AEEAMSR;AS(1)PEPQRENAS(1)PAPGTTAEEAMSR;AS(1)PEPQRENAS(0.992)PAPGT(0.003)T(0.003)AEEAMS(0.003)R 109.56 0.0012101 1491020000 281614 323727 322794 322355 348569 398370 339632 315754 306945 253546 TRUE FALSE 292732.3382 379324.594 331206.2768 386115.8569 289319.3659 305854.6049 313010.7564 311521.8341 295898.1094 303223.4843 0.965401275 1.250973667 1.092284384 1.273370556 0.954145641 1.008677166 1.032277421 1.027367108 0.975841664 1 18.21002197 3.219178395 24.99996454 1.005474449 1.149239171 0.429026365 0.082188474 215.0012421 277316.5681 0.02202114 0.026356697 1656.450245 -3.219178395 0.143764722 AS(ph)PGLLPVANGNSLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPGLLPVANGNSLNK 16 0 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK 331.85 1.49E-71 3205710000 2847960 2122270 2513350 1968390 2736510 3020290 2740320 2491780 2532310 1906150 TRUE FALSE 2960399.66 2486753.364 2578849.966 2357731.667 2271359.008 2318873.42 2525526.558 2458381.765 2441172.658 2279623.597 1.298635294 1.090861389 1.131261305 1.034263582 0.996374582 1.017217677 1.107869984 1.078415651 1.07086655 1 21.1203642 6.896426965 1.005765923 1.052641345 21.16730325 0.768316117 0.040492309 69.76442265 1.124403399 0.012718982 3117.92371 7878199.34 -6.896426965 20.1146619 AS(ph)PHDVLETIFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPHDVLETIFVR 13 0 H0YEM7;O75143-4;O75143-3;O75143-2;O75143;O75143-5;H0YCL5 H0YEM7 ATG13 Autophagy-related protein 13 1 AS(1)PHDVLETIFVR 75.463 0.020175 11332000 17291 17212 19151 17855 24381 23641 24291 19374 20822 17850 TRUE FALSE 17973.66203 20168.02711 19650.09079 21386.66571 20236.72633 18150.73603 22387.00795 19114.32322 20072.62029 21347.36574 0.841961591 0.94475484 0.920492534 1.001840975 0.947972999 0.850256479 1.048701194 0.895394938 0.940285585 1 14.38177043 AS(ph)PIKMDLAPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPIKMDLAPSK 12 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK;AS(1)PIKMDLAPSK 151.48 4.18E-05 1859140000 4846710 2105693 3099610 2301590 4308060 4432220 5404590 3348010 3739850 1617798 TRUE FALSE 5038061.853 2467329.393 3180388.383 2756837.632 3575777.5 3402904.076 4980964.114 3303135.402 3605253.529 1934774.543 2.603952936 1.275254216 1.643803095 1.424888312 1.848162367 1.758811686 2.574441622 1.707245639 1.863397232 1 20.88373403 3.032907879 24.75912362 1.872422281 1.689737678 0 0.487243798 741.021303 557522.1908 0.133917865 0.16006142 1078.717883 -3.032907879 -0.182684603 AS(ph)PIPGTPDRLPCQQLLQQAQAAIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPIPGTPDRLPCQQLLQQAQAAIPR 26 1 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 AS(1)PIPGTPDRLPCQQLLQQAQAAIPR;AS(1)PIPGTPDRLPCQQLLQQAQAAIPR 128.43 1.67E-10 257310000 70710 72088.8 94687 60601 140237 123341 94942 83318 96381 101983 TRUE FALSE 73501.6854 84469.49063 97154.62101 72587.69692 116399.5648 94696.922 87500.19796 82201.25849 92912.26664 121964.6163 0.602647617 0.692573742 0.796580385 0.595153735 0.954371591 0.776429467 0.717422812 0.673976281 0.7617969 1 16.89610314 -2.52782623 1.361097871 2.410707043 0.730248152 0.403193199 0.098509427 135338.5252 9448.94515 582170.3881 0.02725654 0.002966018 2.52782623 -1.680458891 AS(ph)PNLIGATGANSLGK ddPTM_MDA-MB-175_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 98.196 0.0029539 100930000 101850 74983 90353 81325 116320 117180 107810 87266 75259 73902 TRUE FALSE 105871.1166 87860.74696 92707.67341 97410.84227 96547.96795 89966.72088 99359.57049 86096.34201 72550.44329 88381.68196 1.197885289 0.994105849 1.048946697 1.102160992 1.092397947 1.017934021 1.124209998 0.97414238 0.820876472 1 16.43145977 1.54449034 4.683924316 0.906077622 1.07589194 0.523028079 0.06737798 0.113129119 5.436281314 0.036859503 0.016072425 35.03404953 -1.54449034 0.169814317 AS(ph)PNPVAMETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPNPVAMETR 11 0 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 AS(1)PNPVAMETR;AS(1)PNPVAMETR 79.394 0.028599 1063500000 130589 666040 517670 611180 367390 729120 310399 567160 497400 1540369 TRUE FALSE 135744.7546 780427.1889 531160.9055 732069.5798 304941.179 559792.9299 286069.1153 559558.1479 479498.6712 1842174.813 0.073687227 0.423644479 0.288333605 0.397394197 0.165533247 0.303876117 0.1552888 0.303748669 0.260289451 1 20.81297854 -1.211298777 3.01430605 1.003062544 0.269068709 0.822807934 0.10250022 3858800.291 5222743.442 111169.5512 0.023549647 0.06147538 1.211298777 -0.733993836 AS(ph)PPALLPGPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASPPALLPGPAPR 13 0 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR;AS(1)PPALLPGPAPR 138.89 4.59E-05 743110000 345763 391872 373051 360568 450081 478651 383175 373274 371752 362635 TRUE FALSE 359413.9902 459172.9677 382773.0155 431887.2742 373576.3924 367491.5593 353140.7423 368270.8726 358372.7181 433686.3852 0.828741696 1.058767311 0.882603256 0.995851585 0.861397556 0.847367065 0.814276755 0.849164016 0.826340716 1 18.72629263 3.148191297 7.879898461 0.853403437 0.94547102 0.180155288 0.075358403 0.309894405 23.56980433 0.01984749 0.023788627 1406.666993 -3.148191297 0.092067583 AS(ph)PPPQGPLPGPPGALHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR 138.46 1.28E-06 2607550000 497374 529960 515092 445308 581554 656719 524358 564937 552599 554182 TRUE FALSE 517010.7096 620976.5075 528515.7207 533388.5933 482701.6588 504205.9649 483257.4498 557364.9436 532711.0699 662763.3524 0.78008343 0.93695058 0.797442584 0.804794941 0.728316762 0.760763194 0.729155358 0.840971278 0.803772671 1 19.33813431 0.285570032 1.343438769 1.000105493 0.796831181 0.53184239 0.056938481 4.327047329 7.29676926 0.057505978 0.016745367 1.930056543 -0.285570032 -0.203274312 AS(ph)PPRS(ph)PAEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPPRSPAEPK 11 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 2 AS(1)PPRS(1)PAEPK 79.771 0.0058214 0 251720 154740 172290 186900 239050 310810 320470 219580 208540 131460 TRUE FALSE 261658.1 181315.3913 176780.0189 223868.2622 198416.3664 238629.0879 295350.724 216636.8893 201034.6861 157217.07 1.664311006 1.153280564 1.124432728 1.423943736 1.262053582 1.517831924 1.878617404 1.377947631 1.278707751 1 17.26239834 2.738929365 24.99040048 1.467894962 1.310317882 0.000787708 0.251745918 89.71665708 6080241.002 0.077981554 0.078189741 548.187799 -2.738929365 -0.15757708 AS(ph)PRPWT(ph)PEDPWSLYGPSPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 AS(1)PRPWT(1)PEDPWSLYGPSPGGR;AS(1)PRPWT(0.978)PEDPWS(0.022)LYGPSPGGR;AS(1)PRPWT(0.996)PEDPWS(0.004)LYGPSPGGR 112.17 0.0006904 414146000 161700 168924 161045 153332 165089 192226 157323 161025 151128 170950 TRUE FALSE 168084.0409 197935.383 165241.965 183660.6119 137027.2307 147584.4247 144991.6122 158866.7233 145688.9328 204444.3795 0.822150461 0.968162507 0.808248999 0.898340235 0.670242103 0.721880568 0.709198328 0.777065741 0.712609137 1 17.64134888 3.255725136 24.99599078 0.75006045 0.876222754 0.231976046 0.094827645 288.6925479 420408.625 0.024048487 0.032482935 1801.876975 -3.255725136 0.126162304 AS(ph)PS(ph)PQPSSQPLQIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 AS(1)PS(1)PQPSSQPLQIHR;AS(1)PS(1)PQPSSQPLQIHR;AS(0.997)PS(0.454)PQPS(0.313)S(0.237)QPLQIHR 168.99 3.05E-09 1036740000 564950 567990 607240 550480 703530 786490 671260 619280 695590 549210 TRUE FALSE 587254.6622 665537.8642 623065.1733 659363.301 583944.2219 603839.6169 618644.8872 610979.5645 670555.8518 656817.1842 0.894091501 1.01327718 0.948612777 1.003876447 0.889051377 0.919341989 0.94188292 0.930212515 1.020917034 1 19.32513235 1.23689872 24.99983089 1.010458545 0.943854468 0.330317785 0.038644715 51.16686742 769582.9729 0.030503911 0.009153853 17.25435462 -1.23689872 -0.066604077 AS(ph)PSPQPSSQPLQIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.83)PS(0.17)PQPSSQPLQIHR 65.022 0.037691 21792000 8760.1 11966 13143 13457 13905 15939 11804 14230 11854 12647 TRUE FALSE 9105.955512 14021.06742 13485.51738 16118.75443 11541.43307 12237.40881 10878.77164 14039.27013 11427.37686 15124.93751 0.602049133 0.927016552 0.891608139 1.065707176 0.763073108 0.809088223 0.719260601 0.928220042 0.75553217 1 13.88464156 -2.215217295 2.170092537 1.469007651 0.840016656 0.14057562 0.124165935 7801472.631 1386561.105 17965494.1 0.029254962 0.00609232 2.215217295 -0.628990996 AS(ph)PSSPGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.393)PS(0.264)S(0.343)PGRQDS(1)DEDDGPQR 146.2 6.70E-08 203470000 170500 166480 152910 177760 154020 208360 198490 168420 179430 137740 TRUE FALSE 177231.4717 195071.645 156894.9602 212920.3974 127839.7354 159971.5477 182931.8351 166162.6054 172972.3493 164727.5158 1.075906905 1.184208018 0.952451444 1.292561212 0.776067889 0.971128272 1.110511709 1.0087119 1.050051344 1 17.32972203 3.252051335 24.99997021 0.995822178 1.118002917 0.263935801 0.113671911 365.7824511 677835.9263 0.030764844 0.041430549 1786.698758 -3.252051335 0.122180739 AS(ph)PSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.601)PS(0.2)S(0.2)PGRQDS(1)DEDDGPQRVEEVDQGR 111.56 0.00067888 292180000 78393 80469 82479 59792 83262 93663 85165 74092 78308 80380 TRUE FALSE 81488.01617 94288.92479 84628.4705 71618.67914 69109.15498 71911.18773 78489.54476 73098.91793 75489.71038 96128.92203 0.8476951 0.980859067 0.880364293 0.745027382 0.718921564 0.74807026 0.816502912 0.760425857 0.785296545 1 16.55268294 3.888787571 4.874841331 0.781819818 0.917854911 0.26183165 0.08049263 0.225439684 8.147086099 0.019164816 0.035946977 7740.830734 -3.888787571 0.136035093 AS(ph)PSVTCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPSVTCK 8 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 AS(0.996)PS(0.004)VTCK;AS(0.98)PS(0.015)VT(0.005)CK 125.57 0.0013179 477170000 761850 657440 709480 577470 796670 861700 729440 732460 774520 577700 TRUE FALSE 791928.4263 770350.2058 727969.6316 691691.8424 661252.318 661583.2342 672264.5868 722642.5718 746645.1765 690889.2543 1.146245106 1.115012574 1.053670508 1.001161674 0.957103203 0.957582174 0.97304247 1.045960069 1.080701678 1 19.39809495 4.146185464 2.059992305 1.001470693 1.142487292 0.668100719 0.036238428 0.220894934 1.813941891 0.011045451 0.037366863 14001.85141 -4.146185464 0.141016599 AS(ph)PTLDFTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPTLDFTER 10 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 AS(0.975)PT(0.025)LDFTER;AS(0.739)PT(0.261)LDFTER 131.17 0.00026975 710600000 303820 287500 297200 336000 359700 405890 369940 324790 317000 270970 TRUE FALSE 315815.0482 336875.8886 304945.2762 402459.7971 298558.3225 311628.1988 340943.1361 320436.7213 305591.2319 324061.3835 0.974553169 1.03954345 0.941010845 1.241924579 0.921301759 0.961633242 1.052094305 0.98881489 0.943004158 1 18.30590759 AS(ph)PTPLASPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPTPLASPGK 11 0 A0A1B0GTL5 A0A1B0GTL5 1 AS(0.98)PT(0.02)PLASPGK 106.67 0.001625 0 284290 218830 217310 216180 292940 324910 324260 232540 261150 146120 TRUE FALSE 295513.9887 256412.3502 222973.2771 258939.7588 243146.1634 249454.5766 298843.6539 229423.1817 251751.2625 174749.4164 1.691072822 1.467314487 1.275960068 1.481777531 1.391399001 1.427498768 1.710126764 1.312869516 1.440641507 1 17.41492811 0.360231098 1.109638465 0.999396908 1.468753007 0.53106003 0.132367589 2.280735451 3.244448892 0.126624742 0.038248876 2.292087002 -0.360231098 0.469356099 AS(ph)PTSDIESVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPTSDIESVER 12 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 AS(0.977)PT(0.023)SDIESVER;AS(0.996)PT(0.004)SDIESVER 273.02 9.81E-28 462730000 208394 161139 195179 197719 216050 247530 252450 213910 203784 134337 TRUE FALSE 216621.556 188813.3698 200265.5251 236827.2281 179325.8982 190044.9089 232662.3093 211042.8863 196449.8536 160657.7631 1.348341666 1.175252077 1.246535002 1.47411008 1.116198151 1.182917683 1.448185913 1.313617732 1.222784694 1 17.29363117 0.877744615 4.258536237 1.000049024 1.288534457 0.38458392 0.109374739 0.760109152 24.69381093 0.104492353 0.026610382 7.546483296 -0.877744615 0.288485433 AS(ph)PVAALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPVAALK 8 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 AS(1)PVAALK;AS(1)PVAALK 119.68 0.0017282 415450000 645470 493270 519430 531870 672030 663950 785100 584940 608270 415750 TRUE FALSE 670953.654 577985.2854 532966.7725 637072.2985 557798.5806 509757.6748 723561.8105 577099.8361 586378.4815 497208.2525 1.34944191 1.162461167 1.071918597 1.281298722 1.121861067 1.025239771 1.455248997 1.160680325 1.179341812 1 18.92349072 4.741241047 23.8473999 1.175265992 1.349442024 0.160776389 0.125214036 252.2943984 2244368.835 0.02861709 0.196812067 55111.34969 -4.741241047 0.174176031 AS(ph)PVPAPSSGLHAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPVPAPSSGLHAAVR 16 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 AS(0.997)PVPAPS(0.001)S(0.001)GLHAAVR 140.49 2.05E-05 0 35544 62777 66811 74651 74419 100360 66928 70826 76433 72322 TRUE FALSE 36947.30457 73558.46141 68552.14955 89416.74499 61769.28496 77052.91097 61682.00848 69876.69332 73682.19126 86492.11121 0.427175427 0.850464399 0.792582683 1.033813879 0.714160911 0.890866345 0.713151843 0.807896724 0.851894933 1 16.40028093 4.739667697 24.1939616 0.837805555 0.427175217 0.611245941 0.100829907 38.49394846 841065.5377 0.02239413 0.137686752 54912.05496 -4.739667697 -0.410630338 AS(ph)SDIVSLAGPSAGPGSSEGGCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 AS(0.5)S(0.5)DIVSLAGPSAGPGSSEGGCSR 301.38 3.30E-62 126180000 25374 21090 23170 20579 26837 30017 23579 19002 22522 19756 TRUE FALSE 26375.78511 24712.04344 23773.82923 24649.46478 22275.25633 23046.00666 21730.81637 18747.30927 21711.43762 23626.80995 1.116349823 1.04593229 1.006222562 1.043283661 0.942795764 0.975417617 0.919752451 0.793476111 0.91893225 1 14.52813723 3.112862137 0.825741264 0.882727408 1.0759187 0.544529868 0.057043965 0.431580194 0.652958634 0.031631696 0.046726373 1296.767557 -3.112862137 0.193191292 AS(ph)SGGGGGGLMEEMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSGGGGGGLMEEMNK 16 0 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3;G3V314;H0YJL6 H0YJN0 EVL Ena/VASP-like protein 1 AS(0.976)S(0.024)GGGGGGLMEEMNK;AS(0.998)S(0.002)GGGGGGLMEEMNK 206.59 2.06E-11 168092000 172192 128548 148023 141010 182226 214577 216069 167583 168367 111229 TRUE FALSE 178990.2731 150625.119 151880.601 168901.3571 151251.2896 164744.7437 199132.9472 165336.824 162307.5046 133022.1929 1.345567 1.132330747 1.141768885 1.269723145 1.13703801 1.238475626 1.49699041 1.242926615 1.220153577 1 17.02130743 2.476051998 24.99958141 1.279468073 1.199930977 0 0.129715381 99.71112183 2331156.888 0.042691711 0.03599309 299.2622924 -2.476051998 -0.079537096 AS(ph)SHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.461)S(0.461)HS(0.654)S(0.413)QT(0.011)QGGGSVTK 99.569 0.0012411 221650000 288230 289720 371650 281870 450120 447940 368720 381600 395190 321630 TRUE FALSE 299609.543 339477.1563 381335.5043 337623.0447 373608.7632 343912.7236 339818.7629 376485.2762 380967.1891 384647.2405 0.778920297 0.882567507 0.991390199 0.877747216 0.971302336 0.894099027 0.883455611 0.97878065 0.990432659 1 18.55317643 4.611527176 3.080457617 0.942587736 0.772787171 0.566602753 0.045326147 0.210405609 3.219870842 0.010867976 0.072348854 40881.53328 -4.611527176 -0.169800565 AS(ph)SHSS(ph)QTQGGGSVTKK ddPTM_MDA-MB-175_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(0.477)S(0.477)HS(0.049)S(0.987)QT(0.009)QGGGSVTKK 93.583 0.0030856 1178800000 310070 258270 356060 212260 481580 407260 365440 365360 403240 267660 TRUE FALSE 322311.803 302625.8634 365339.2161 254244.3945 399721.2036 312680.0371 336795.8579 360462.9468 388727.4712 320102.8523 1.006900753 0.945401958 1.141318215 0.794258447 1.248727403 0.976811156 1.052148881 1.12608477 1.214383028 1 18.28817601 2.806554218 0.86637092 1.111143709 0.992462025 0.102508432 0.122316614 1.259839851 2.050015861 0.069440299 0.070286555 640.5517448 -2.806554218 -0.118681684 AS(ph)SHSSQTQGGGSVTK ddPTM_MDA-MB-175_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 1 AS(0.465)S(0.465)HS(0.061)S(0.01)QTQGGGSVTK 192.46 3.42E-10 374960000 299940 344020 419050 329280 554130 483780 507880 468240 470400 349840 TRUE FALSE 311781.8628 403102.7589 429970.7873 394410.6012 459939.1805 371429.4268 468071.0385 461964.0087 453470.3959 418384.4499 0.745204232 0.963474524 1.02769304 0.942698997 1.099321881 0.88777063 1.118758211 1.104161516 1.08386054 1 18.67446971 5.461626969 0.905420737 1.049093772 1.08E-12 0.596657447 0.070914018 4.73616154 1.184702735 0.022536081 6.699769228 289485.6024 -5.461626969 -1.049093772 AS(ph)SHSSQTQGGGSVTKK ddPTM_MDA-MB-175_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(0.291)S(0.256)HS(0.225)S(0.175)QT(0.052)QGGGS(0.001)VTKK 60.032 0.049893 414940000 16548 39211 48684 39298 63214 72380 43748 65395 42777 44575 TRUE FALSE 17201.32782 45945.18423 49952.74503 47071.02711 52468.90686 55570.84193 40318.91745 64518.48699 41237.46413 53308.61781 0.322674429 0.861871609 0.937048213 0.88299095 0.98424812 1.042436368 0.756330198 1.210282495 0.773560933 1 15.70208116 4.816526702 2.24494109 0.962244971 0.071045609 0.690645859 0.124553862 0.430793316 2.103841735 0.029586198 0.818727638 65543.05823 -4.816526702 -0.891199362 AS(ph)SPAQCVTPVQTVV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPAQCVTPVQTVV 15 0 Q13614;Q13614-2 Q13614 MTMR2 Myotubularin-related protein 2 1 AS(0.5)S(0.5)PAQCVTPVQTVV 78.763 0.0094838 0 63781 64952 65215 61864 63050 84140 56702 74552 68838 66626 TRUE FALSE 66299.12313 76107.00074 66914.55647 74100.51455 52332.78352 64599.76015 52257.54908 73552.75238 66360.53383 79680.08907 0.832066378 0.955157074 0.839790182 0.929975298 0.656786208 0.810739056 0.655842001 0.92310078 0.832837094 1 16.28193164 0.652433671 1.376744719 0.998936712 0.822186133 0.22462836 0.097332925 1.899298444 5.384621506 0.092966858 0.027492383 4.491937151 -0.652433671 -0.176750579 AS(ph)SPCPEFEQFQIVPAVETPYLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPCPEFEQFQIVPAVETPYLAR 24 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 AS(0.5)S(0.5)PCPEFEQFQIVPAVETPYLAR 133.44 2.71E-05 116530000 117040 125620 123650 121460 124840 149620 130010 128120 119990 128480 TRUE FALSE 121660.8296 147194.2578 126872.4206 145484.4255 103619.7414 114873.0225 119819.4765 126402.761 115671.5833 153653.1961 0.791788473 0.957964179 0.825706356 0.946836312 0.674374136 0.747612321 0.779804648 0.822649734 0.752809484 1 17.22931825 3.257555187 24.99948821 0.78662244 0.882182583 0.165297125 0.091336127 372.125284 489765.3333 0.023459675 0.031712534 1809.48583 -3.257555187 0.095560142 AS(ph)SPFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.5)S(0.5)PFRR;AS(0.681)S(0.319)PFRR 110.22 0.0041975 847150000 696750 850700 856074 902780 918340 1058250 796261 901110 781430 1058530 TRUE FALSE 724258.228 996801.1075 878383.9917 1081347.189 762240.8948 812487.4754 733847.9822 889032.0944 753306.4869 1265928.687 0.572116135 0.787406998 0.693865303 0.854192816 0.602119932 0.64181141 0.579691407 0.7022766 0.59506234 1 20.27176471 -1.869135769 5.845597778 1.055881148 0.674729275 0.555618784 0.088483134 0.046909778 0.00105016 0.062366789 0.019633797 0.013516499 1.869135769 -0.381151873 AS(ph)SPPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.5)S(0.5)PPDR 80.676 0.0307 111050000 236830 226550 249550 260970 247290 311710 308770 272710 243490 205500 TRUE FALSE 246180.2313 265458.2002 256053.478 312589.0871 205255.7341 239320.0765 284567.8006 269054.7685 234726.8425 245763.7905 1.001694476 1.080135522 1.0418682 1.271908634 0.835174839 0.973780865 1.157891486 1.094769771 0.955091236 1 17.90691285 1.233834814 24.95163612 0.977545596 1.061047855 0.077725527 0.109030134 323.8606476 1709837.638 0.092784144 0.026140038 17.13305518 -1.233834814 0.083502259 AS(ph)SPPDRIDIFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR;AS(0.5)S(0.5)PPDRIDIFGR 230.38 2.54E-12 15986375000 1982737 2278972 2328293 1902405 2571964 2657919 1960091 2318845 2266327 2588659 TRUE FALSE 2061016.988 2670367.713 2388970.228 2278695.031 2134782.478 2040657.593 1806453.946 2287764.676 2184762.334 3095857.168 0.665733875 0.862561665 0.771666811 0.736046564 0.689561037 0.659157539 0.583506876 0.738976171 0.705705146 1 21.56190748 -1.067645119 4.488998717 1.000017808 0.713345595 0.600239865 0.070373614 1.39E-05 2.89E-06 0.07187125 0.016939111 0.085576571 1.067645119 -0.286672213 AS(ph)SPSEHGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPSEHGPR 10 0 C9J052;Q9NSU2-2;Q9NSU2;Q9NSU2-1 C9J052 TREX1 Three-prime repair exonuclease 1 1 AS(0.5)S(0.5)PSEHGPR 121.68 0.00032762 113390000 48556 129770 81995 145790 85485 160170 85911 88618 68262 141700 TRUE FALSE 50473.02837 152056.988 84131.85706 174626.8269 70954.29023 122972.9449 79177.07133 87430.22066 65805.26395 169463.402 0.297840288 0.897285114 0.496460333 1.030469262 0.418699787 0.725660783 0.467222246 0.515923908 0.38831549 1 17.37061421 AS(ph)SREDGRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSREDGRPR 10 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 AS(0.5)S(0.5)REDGRPR;AS(0.5)S(0.5)REDGRPR 79.875 0.020236 1823280000 710910 896970 920170 688970 848250 1001270 780930 805690 693730 929850 TRUE FALSE 738977.2757 1051017.62 944150.3861 825246.2096 704064.768 768740.2169 719718.666 794891.0434 668762.7928 1112036.304 0.664526214 0.945128874 0.849028384 0.742103658 0.633131099 0.691290576 0.647207886 0.714806738 0.601385755 1 20.08477246 3.577040954 4.280990682 0.695410535 0.830840448 0.113973808 0.122271009 0.34621282 10.85114996 0.030416609 0.047811944 3776.077978 -3.577040954 0.135429913 AS(ph)SSAESEDLAVHLYPGAVTIQGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSSAESEDLAVHLYPGAVTIQGVLR 26 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 AS(0.333)S(0.333)S(0.333)AES(0.002)EDLAVHLYPGAVTIQGVLR 121.96 2.81E-10 0 18431 25053 24339 24856 29149 27873 25134 25037 26494 22715 TRUE FALSE 19158.67011 29355.65786 24973.29433 29772.44261 24194.26339 21399.91817 23163.9314 24701.41997 25540.48612 27165.56935 0.705255608 1.080620012 0.919299501 1.095962401 0.890622357 0.787758868 0.852694494 0.909291451 0.940178569 1 14.72949166 3.044156263 24.99993317 0.885020535 0.961869822 0.041796933 0.11273956 318.1454313 180122.2359 0.031024794 0.037081745 1107.022029 -3.044156263 0.076849286 AS(ph)SWPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSWPHR 7 0 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AS(0.577)S(0.423)WPHR 60.59 0.062217 116490000 43830 58474 55748 61581 51678 66619 58610 54395 55103 52226 TRUE FALSE 45560.44224 68516.45464 57200.83868 73761.538 42893.79202 51147.74687 54015.99505 53665.924 53119.85379 62458.68477 0.729449274 1.096988431 0.915818815 1.180965278 0.686754647 0.818905282 0.86482761 0.859222768 0.850479865 1 15.93061457 3.228038385 24.99998931 0.841126136 0.98446236 0.200123426 0.130981378 304.2864659 722959.5573 0.035465319 0.042813263 1690.590349 -3.228038385 0.143336224 AS(ph)SWPHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASSWPHRR 8 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 AS(0.5)S(0.5)WPHRR;AS(0.5)S(0.5)WPHRR;AS(0.603)S(0.397)WPHRR;AS(0.5)S(0.5)WPHRR 95.358 0.0059455 970800000 543148 711990 702740 675500 830760 855740 734340 744220 666810 763330 TRUE FALSE 564591.9024 834268.744 721053.9817 809111.8838 689547.7119 657007.3539 676780.512 734244.9482 642811.6384 912889.8987 0.61846659 0.91387663 0.789858649 0.886319243 0.755345976 0.719700541 0.7413605 0.804308328 0.704150237 1 19.80008135 -1.089570552 4.568599829 1.000013256 0.777446464 0.411890882 0.081923288 1.21E-05 2.40E-06 0.07431028 0.017513888 0.081363467 1.089570552 -0.222566793 AS(ph)TDNEELLQFPLELCSDSLPSHPFPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASTDNEELLQFPLELCSDSLPSHPFPPAK 29 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(0.791)T(0.209)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.873)T(0.127)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.794)T(0.206)DNEELLQFPLELCSDSLPSHPFPPAK;AS(0.962)T(0.038)DNEELLQFPLELCSDSLPSHPFPPAK 297.73 4.46E-81 798469000 508700 499503 588081 490537 764102 757646 660390 608195 671665 488178 TRUE FALSE 528783.8688 585288.7547 603406.874 587563.7545 634220.215 581694.1987 608626.9062 600043.1408 647491.9079 583827.1324 0.905719929 1.002503519 1.033536882 1.00640022 1.086315075 0.996346635 1.04247794 1.027775359 1.109047305 1 19.15518173 5.452096186 1.097629748 1.039867589 0.479400107 0.577703189 0.034125347 4.608015319 1.474142443 0.00917248 4.373644855 283201.9151 -5.452096186 -0.560467481 AS(ph)TFCGTPDYIAPEILQGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.461)T(0.461)FCGT(0.078)PDYIAPEILQGLK 208.43 3.66E-22 129500000 105550 71864 121340 105800 195630 121740 149270 115160 148880 73357 TRUE FALSE 109717.1955 84206.08298 124502.2201 126726.9242 162376.8825 93467.72999 137569.8274 113616.4686 143521.8379 87729.89965 1.250624883 0.959833344 1.419153796 1.444512358 1.850872771 1.065403362 1.568106517 1.295071225 1.635951237 1 16.420781 4.220149732 24.37045477 1.426261437 1.105229215 0.191935686 0.248229 218.2576651 288908.4806 0.057040692 0.123613742 16601.59182 -4.220149732 -0.321032222 AS(ph)TPQPAPAGVPALASQHPPEEEVHYHLPVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASTPQPAPAGVPALASQHPPEEEVHYHLPVAR 32 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 AS(0.804)T(0.196)PQPAPAGVPALASQHPPEEEVHYHLPVAR 48.909 0.037539 202730000 21499 42474 43615 41039 44860 51748 40087 42316 33593 35847 TRUE FALSE 22347.79712 49768.5791 44751.64273 49156.39171 37234.71322 39730.31125 36944.87619 41748.82324 32383.99449 42870.53332 0.521285727 1.160904128 1.043878843 1.146624217 0.868538605 0.926751038 0.861777854 0.97383494 0.755390521 1 15.38769874 AS(ph)WESLDEEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(1)WESLDEEWR;AS(0.985)WES(0.015)LDEEWR;AS(0.938)WES(0.062)LDEEWR;AS(1)WESLDEEWR 216.84 1.24E-11 196350000 366456 371938 363516 368490 412924 443103 487275 397164 396258 333897 TRUE FALSE 380923.9658 435815.4582 372989.5256 441376.2222 342735.326 340199.0435 449081.1122 391840.6662 381996.752 399317.7243 0.953937035 1.091400235 0.934067042 1.105325898 0.858302312 0.851950772 1.124621035 0.981275416 0.956623583 1 18.60717758 3.257054158 24.99854823 0.968654046 1.019975498 0.096936536 0.086912035 720.418505 973816.2609 0.024428901 0.033018602 1807.399501 -3.257054158 0.051321453 AS(ph)WESLDEEWRAPQAGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASWESLDEEWRAPQAGSR 18 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 AS(0.603)WES(0.397)LDEEWRAPQAGSR 176.61 2.63E-13 74174000 22900 33243 29814 31269 31168 35671 32871 31687 39246 39167 TRUE FALSE 23804.10968 38952.22666 30590.97733 37453.91487 25870.07449 27386.95085 30294.48513 31262.28759 37833.54413 46841.02375 0.508189356 0.831583589 0.653080887 0.799596419 0.552295241 0.584678742 0.646751132 0.66741256 0.807701051 1 15.51548499 0.967358718 2.382292463 0.99926614 0.658540036 0.566489335 0.094632381 0.220457935 2.81531797 0.086351242 0.023469018 9.275956814 -0.967358718 -0.340726104 ASAGHAVS(ph)IAQDDAGADDWETDPDFVNDVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 1 AS(0.014)AGHAVS(0.986)IAQDDAGADDWETDPDFVNDVSEK;AS(0.009)AGHAVS(0.991)IAQDDAGADDWETDPDFVNDVSEK 105.67 3.50E-06 116386000 94212 115279 187171 125565 258870 162483 148017 144462 151892 120110 TRUE FALSE 97931.56251 135077.2715 192048.83 150401.3822 214867.3699 124748.7857 136415.0408 142525.7232 146425.4366 143643.2549 0.681769308 0.940366268 1.336984672 1.047047997 1.495840303 0.868462538 0.949679405 0.992220089 1.01936869 1 17.13213072 -0.762051994 7.260599682 0.999994779 1.044138581 0.001568098 0.217939352 0 0 0.209730164 0.049433874 0.172960928 0.762051994 0.044143802 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEK 32 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;; 404.84 5.20E-186 3243430000 844082 1173521 1459469 1328588 1715409 1871348 1766683 1699746 1604021 1178852 FALSE TRUE 877407.0091 1375064.103 1497503.961 1591378.741 1423824.391 1436755.788 1628205.77 1676963.685 1546292.598 1409825.479 0.622351505 0.97534349 1.062191018 1.128777118 1.009929535 1.019101874 1.154898812 1.189483174 1.096797171 1 20.42708515 4.898408091 1.588031118 1.098055482 0.290485146 0.837971298 0.060607752 0.627975529 1.107048581 0.01769974 0.881454513 79142.19489 -4.898408091 -0.807570336 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASAGHAVSIAQDDAGADDWETDPDFVNDVSEKEQR 35 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 322.66 1.65E-105 1717460000 164298 345291 401686 203983 496180 458960 234626 376845 374910 491080 FALSE TRUE 170784.6119 404592.0433 412154.2671 244330.2286 411839.5008 352373.4956 216235.401 371794.0092 361417.0623 587297.7237 0.290797333 0.688904498 0.701780801 0.416024477 0.701244844 0.59999125 0.368187024 0.633058829 0.615389857 1 19.16373252 0.589396678 1.620328921 0.999712823 0.555242422 0.485277375 0.138562958 1.550738701 5.123004077 0.125183233 0.035747266 3.885050587 -0.589396678 -0.444470401 ASAGRLT(ph)PESQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASAGRLTPESQSK 13 1 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2;H7BZ56;H7BZC2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 ASAGRLT(0.999)PES(0.001)QSK;ASAGRLT(0.999)PES(0.001)QSK 117.2 0.00084961 1050800000 1447020 1223630 1466490 1190540 2012030 2007910 1639270 1440560 1672420 1345510 TRUE FALSE 1504149.467 1433778.934 1504707.934 1426025.259 1670025.859 1541603.333 1510779.734 1421251.649 1612229.931 1609136.923 0.934755424 0.891023575 0.935102484 0.886205045 1.0378395 0.958031172 0.938875811 0.88323848 1.001922153 1 20.61785566 ASAGTPSLSAGVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASAGTPSLSAGVSPK 15 0 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 ASAGTPSLSAGVS(1)PK 175.48 8.96E-07 127600000 275350 129190 160180 122000 221000 255830 214470 162260 183900 96000 TRUE FALSE 286221.0306 151377.3775 164354.4224 146131.2359 183434.4989 196417.3596 197659.281 160085.1701 177281.4749 114809.362 2.493011247 1.318510746 1.431541989 1.272816375 1.597731194 1.710813093 1.721630341 1.394356413 1.544137794 1 16.80888076 -3.094908009 0.133849798 7.94E-37 1.835771775 0.280430127 0.319435054 117.7846314 1.627298819 38.00965377 2.477591936 0.000803696 3.094908009 1.835771775 ASALLFS(ph)SDEEDQWNIPASQTHLASDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.561)S(0.439)DEEDQWNIPASQTHLASDSR 237.79 2.27E-45 858490000 101120 191600 173990 201120 166490 226330 158160 203990 161560 193700 TRUE FALSE 105112.2957 224505.8096 178524.3223 240900.9357 138190.0893 173768.2876 145763.0059 201255.8477 155745.4872 231651.8064 0.453751246 0.969151992 0.77065802 1.03992686 0.596542248 0.750127056 0.629233194 0.868786006 0.672325805 1 17.82159841 -1.951853571 3.631649983 1.157974057 0.763714674 0.162931547 0.167401202 0.120196513 0.0015935 0.09098848 0.035129935 0.011172399 1.951853571 -0.394259384 ASALLFSS(ph)DEEDQWNIPASQTHLASDSR ddPTM_MDA-MB-175_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 AS(0.001)ALLFS(0.457)S(0.542)DEEDQWNIPASQTHLASDSR;ASALLFS(0.028)S(0.972)DEEDQWNIPASQTHLASDSR;ASALLFS(0.04)S(0.96)DEEDQWNIPASQTHLASDSR;ASALLFS(0.146)S(0.854)DEEDQWNIPASQTHLASDSR;ASALLFS(0.152)S(0.848)DEEDQWNIPASQTHLASDSR 297.54 1.44E-71 2023679000 229458 421410 405326 380222 457557 520985 387802 455501 370331 440936 TRUE FALSE 238517.179 493783.8894 415889.1285 455428.7768 379781.6246 399994.1294 357405.0659 449395.7541 357002.8597 527328.967 0.452311923 0.93638681 0.788671123 0.863652113 0.720198677 0.75852865 0.677764903 0.852211394 0.677002179 1 19.00834372 -2.067133081 2.408046208 1.346892581 0.76096657 0.256888942 0.127010999 12244663.41 3566106.708 23362243.78 0.027917145 0.008567753 2.067133081 -0.585926011 ASAPS(ph)PNAQVACDHCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASAPSPNAQVACDHCLK 17 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 AS(0.001)APS(0.999)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK;ASAPS(1)PNAQVACDHCLK 346.07 9.99E-88 6033500000 4699840 3670730 4151870 3409290 4772320 5309700 4564200 4436550 4761630 3894350 TRUE FALSE 4885393.312 4301149.323 4260071.143 4083637.386 3961122.751 4076602.644 4206446.078 4377085.304 4590259.866 4657373.321 1.048958925 0.92351397 0.914693938 0.876811264 0.850505742 0.875300811 0.903179923 0.939818435 0.985589849 1 22.1510851 -0.352446784 6.811986383 1 0.919451674 0.140180503 0.055123629 0 0 0.054547843 0.01285705 0.444174085 0.352446784 -0.080548326 ASAS(ph)PSTSSTSSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 AS(0.003)AS(0.711)PS(0.192)T(0.043)S(0.012)S(0.012)T(0.017)S(0.004)S(0.006)RPK 75.018 0.087017 17495000 19392 16314 17860 13420 19785 21321 17535 16421 15146 12945 TRUE FALSE 20157.61113 19115.80259 18325.44627 16074.43595 16421.95277 16369.52087 16160.56088 16200.90335 14600.89842 15481.3249 1.302059821 1.234765287 1.183713047 1.038311388 1.060758874 1.05737209 1.043874538 1.046480418 0.943129772 1 13.91824132 4.128853858 0.964227708 1.022775236 1.34016776 0.89963356 0.033674213 0.267535256 0.360327387 0.011596839 0.072816311 13454.07542 -4.128853858 0.317392524 ASASRPQPAPADGADPPPAEEPEARPDGEGS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASASRPQPAPADGADPPPAEEPEARPDGEGSPGK 34 2 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 ASASRPQPAPADGADPPPAEEPEARPDGEGS(1)PGK;ASASRPQPAPADGADPPPAEEPEARPDGEGS(1)PGK 96.316 0.00011807 711660000 564070 311532 376364 297235 484236 517680 433207 363089 382087 256461 TRUE FALSE 586339.9192 365035.1976 386172.355 356027.1958 401925.7377 397456.6655 399251.1034 358222.3858 368335.7635 306709.6227 1.911710216 1.190165455 1.259081315 1.16079565 1.310443846 1.295872826 1.301723434 1.167952876 1.200926662 1 18.2265139 4.7401835 24.99788917 1.222339613 1.911710445 0.8492308 0.088597639 47.88478096 737523.2822 0.019710363 0.12593893 54977.31175 -4.7401835 0.689370831 ASAVSELS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ASAVSELSPR 10 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVS(0.01)ELS(0.99)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR 176.61 2.56E-06 50314680000 4158547 4819975 4533845 4555503 4754886 5177536 4549705 4710464 4303326 4610287 TRUE FALSE 4322729.647 5647768.212 4652000.725 5456567.897 3946652.176 3975131.73 4193087.234 4647327.935 4148450.138 5513584.468 0.784014405 1.024336934 0.843734371 0.989658892 0.715805153 0.720970496 0.760501133 0.842886866 0.752405293 1 22.39455911 3.2376809 24.9999526 0.78848392 0.913807505 0.227458777 0.099674682 30.00660455 852746.7189 0.026353369 0.033281327 1728.545835 -3.2376809 0.125323585 ASCGPPS(ph)LPDPTFLPDAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASCGPPSLPDPTFLPDAER 19 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 ASCGPPS(1)LPDPTFLPDAER 156.22 1.90E-08 35050000 44259 43993 47742 43026 45962 54026 43657 43323 40471 44658 TRUE FALSE 46006.3795 51548.45553 48986.19574 51536.41438 38149.39566 41479.28027 40235.05026 42742.32605 39014.45662 53407.88007 0.861415571 0.965184453 0.91720914 0.964958997 0.714302751 0.77665094 0.753354191 0.800299993 0.730500004 1 15.704765 3.246617852 24.9999803 0.783307081 0.929192737 0.390773322 0.079402932 154.1185641 478196.0175 0.020102528 0.026751172 1764.484516 -3.246617852 0.145885655 ASDADRPCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASDADRPCR 9 1 Q86U44;H0YFV6;Q86U44-2 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 ; 99.305 0.0049496 224730000 371020 564850 511220 583050 525450 621080 464740 552330 474170 639830 FALSE TRUE 385668.1561 661858.5936 524542.8132 698375.5498 436134.1967 476843.5826 428312.4644 544926.9198 457104.7143 765192.4382 0.504014594 0.864957049 0.685504439 0.912679628 0.569966684 0.623168185 0.559744769 0.712143629 0.597372231 1 19.54546309 -0.937476288 4.25252268 1.000009162 0.67680294 0.384107424 0.125109072 4622635.257 1811722.777 399.9928483 0.028094527 0.115484504 0.937476288 -0.323206222 ASDDWWEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASDDWWEGR 9 0 B7ZM87;O75044;A0A075B7B5;Q5VZB4;A0A075B7E6;A0A075B7E9 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 0 125.04 0.001193 86846000 85155 97866 93245 87554 100660 120680 94843 89482 94297 106070 FALSE TRUE 88516.98515 114673.7242 95675.0413 104871.9199 83549.84915 92653.89892 87408.95783 88282.64015 90903.26939 126852.3857 0.697795195 0.903993438 0.754223429 0.826724065 0.658638375 0.730407224 0.689060418 0.695947811 0.716606699 1 16.95279113 4.022079941 24.969189 0.739128798 0.807947862 0 0.104172231 613.7108896 694007.3692 0.02388412 0.05158952 10521.55528 -4.022079941 0.068819065 ASDGSRS(ph)PTPSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASDGSRSPTPSQK 13 1 E7ENB6;B7ZAG0;Q9UPQ7 E7ENB6 PDZRN3 E3 ubiquitin-protein ligase PDZRN3 1 ASDGS(0.01)RS(0.982)PT(0.008)PSQK;ASDGS(0.212)RS(0.765)PT(0.023)PSQK 111.22 0.00060362 136728000 231789 169654 233886 181552 272774 278286 229103 222020 238847 172456 TRUE FALSE 240940.2087 198790.7548 239981.2613 217462.4437 226407.9729 213658.294 211145.3082 219044.1851 230250.9431 206245.4513 1.168220715 0.96385522 1.163571171 1.054386617 1.097759836 1.035941848 1.023757406 1.062055835 1.11639283 1 17.65400278 2.739915856 24.57675093 1.05028997 1.084732982 0.103298782 0.060691554 270.8920327 4912582.438 0.017719877 0.01789056 549.4344117 -2.739915856 0.034443012 ASDPQS(ph)PPQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASDPQSPPQVSR 12 0 Q7L7X3-3;Q7L7X3;Q7L7X3-2 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 ASDPQS(1)PPQVSR 128.95 0.00025477 314710000 227450 290220 245610 282340 249920 328400 266500 256290 224540 254050 TRUE FALSE 236429.9016 340063.0274 252010.7984 338186.0093 207438.6877 252134.077 245611.0336 252854.8518 216458.8493 303826.2334 0.778174745 1.119268154 0.829457007 1.113090221 0.682754367 0.829862761 0.80839311 0.832235087 0.712442921 1 18.21288692 3.232203806 24.99999993 0.80545933 0.962049682 0.24716497 0.127199649 188.879055 742821.023 0.033049256 0.04042226 1706.883207 -3.232203806 0.156590352 ASDSQEDQEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASDSQEDQEKR 11 1 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 0 71.241 0.079482 221170000 135260 136580 152820 125380 153980 210430 149280 153210 157220 132550 FALSE TRUE 140600.1692 160036.5526 156802.6147 150179.7898 127806.5346 161560.8216 137579.0435 151156.4706 151561.6829 158520.6347 0.886951844 1.009562906 0.989162168 0.947383223 0.806245413 1.019178493 0.867893595 0.953544445 0.956100657 1 17.27431112 0.914388354 2.162554705 0.999533138 0.935564401 0.091905961 0.062775737 1.031141449 10.21604486 0.057447685 0.015795009 8.21085446 -0.914388354 -0.063968737 ASDSSS(ph)PSCSSGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASDSSSPSCSSGPR 14 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 ASDSS(0.001)S(0.996)PS(0.001)CS(0.002)SGPR 201.72 1.07E-07 0 242970 272660 254520 243790 301280 315940 258290 251100 257030 260080 TRUE FALSE 252562.6432 319487.234 261153.0003 292010.9344 250068.5332 242567.7231 238044.5549 247734.4152 247779.5405 311037.6965 0.812000108 1.027165638 0.839618488 0.938828115 0.803981434 0.779865997 0.76532381 0.796477141 0.796622221 1 18.24672991 3.228856988 24.89372517 0.806629817 0.908544369 0.166569759 0.083117054 241.217791 618820.3145 0.021915125 0.026509115 1693.779953 -3.228856988 0.101914552 ASDVHEVR ddPTM_MDA-MB-175_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 ;;;;; 143.28 0.0006039 14724040000 16052160 24788400 22360280 25381060 24770740 28424230 24150450 24442990 22305110 25010910 FALSE TRUE 16685911.67 29045614.87 22943007.27 30401357.91 20560218.46 21823133.36 22257474.62 24115371.7 21502353.45 29911318.95 0.557846068 0.971057643 0.767034289 1.016383061 0.687372513 0.729594485 0.744115452 0.806228964 0.71887012 1 24.83418819 -1.021243908 4.491219844 1.000008596 0.786074871 0.215884903 0.126224747 1.67436E+11 36485891226 15597021.09 0.027392399 0.095226121 1.021243908 -0.213933725 ASDVHEVRK ddPTM_MDA-MB-175_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 ;;; 106.2 0.0019309 1081670000 2109830 2504800 2636120 1905160 3859790 3035030 2499950 2616100 2788240 3347850 FALSE TRUE 2193127.718 2934979.915 2704819.453 2281994.962 3203704.274 2330190.279 2303997.387 2581035.459 2687891.787 4003797.109 0.547761951 0.733049112 0.675563566 0.569957693 0.800166489 0.581995095 0.575453082 0.644646916 0.671335663 1 21.93293744 0.650863312 3.004460382 0.999993837 0.643362643 0.669376963 0.075219363 2.4941417 20.81070726 0.068503192 0.017905732 4.475724148 -0.650863312 -0.356631194 ASEAGEVPFNHEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASEAGEVPFNHEILR 15 0 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 ; 160.48 1.71E-06 938670000 510760 545800 567530 582730 569350 684830 614900 600090 586700 458170 FALSE TRUE 530925.1992 639536.9043 582320.298 697992.2547 472572.0904 525788.6112 566702.5313 592046.7751 565584.7816 547939.6393 0.968948331 1.167166707 1.06274534 1.273848805 0.862452826 0.959573963 1.034242626 1.080496341 1.032202712 1 19.06365745 3.234467045 24.99995785 1.005412943 1.117717101 0.304854421 0.090405174 144.530924 882669.4285 0.026138766 0.032341053 1715.801509 -3.234467045 0.112304158 ASEDTTS(ph)GSPPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDT(0.149)T(0.094)S(0.482)GS(0.275)PPKK 191.06 4.12E-06 250580000 524160 172740 265940 175710 398920 401430 376540 272470 309410 137120 TRUE FALSE 544854.2415 202406.7513 272870.6149 210464.9136 331111.7209 308203.9662 347025.8109 268817.9853 298274.3945 163986.0387 3.322564811 1.234292583 1.663986868 1.283431902 2.019145798 1.879452475 2.116191193 1.639273608 1.818901151 1 17.32321347 -2.188998893 0.322250289 1.31E-19 1.900022573 0.195702155 0.548754048 70.64377162 3.145364865 52.42523359 0.472042967 0.006471443 2.188998893 1.900022573 ASEDTTSGS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASEDTTSGSPPK 12 0 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTSGS(1)PPK;ASEDTTSGS(1)PPK;ASEDT(0.001)T(0.002)S(0.004)GS(0.994)PPK 203.74 1.27E-07 793830000 2017520 853980 1101020 886310 1488760 1637220 1494770 1145230 1276200 760670 TRUE FALSE 2097173.247 1000644.422 1129713.486 1061619.473 1235701.107 1257000.467 1377606.022 1129880.065 1230269.811 909708.7226 2.305323886 1.099961336 1.241840886 1.166988341 1.358348091 1.381761476 1.514337488 1.242023998 1.352377723 1 19.79504516 4.744830319 24.96001624 1.282306555 2.305324349 0.827172827 0.142803085 269.8984892 1074450.397 0.033425787 0.31379957 55568.71056 -4.744830319 1.023017794 ASEDTTSGS(ph)PPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ASEDTTSGSPPKK 13 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 ASEDTTS(0.004)GS(0.996)PPKK;ASEDTTS(0.007)GS(0.993)PPKK;ASEDT(0.003)T(0.012)S(0.06)GS(0.926)PPKK;ASEDTTS(0.002)GS(0.998)PPKK;ASEDT(0.001)T(0.029)S(0.125)GS(0.846)PPKK;ASEDT(0.001)T(0.002)S(0.161)GS(0.836)PPKK;ASEDTT(0.002)S(0.007)GS(0.991)PPKK;ASEDTT(0.002)S(0.011)GS(0.987)PPKK;ASEDT(0.072)T(0.061)S(0.402)GS(0.465)PPKK 225.21 1.36E-11 3530780000 6453930 2234449 3350768 2154440 4978170 4802410 4873330 3348206 3928691 1751709 TRUE FALSE 6708736.14 2618198.234 3438091.767 2580581.802 4131982.442 3687123.059 4491345.661 3303328.775 3787298.178 2094922.84 3.202378633 1.249782657 1.641154367 1.231826658 1.972379298 1.760028097 2.143919372 1.576825987 1.807846144 1 20.99846568 -2.251012671 0.341336251 3.67E-21 1.844887028 0.189595017 0.527979526 80.48896153 3.668036137 62.42325611 0.406732113 0.005610316 2.251012671 1.844887028 ASEEHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ASEEHLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;;;;;;; 116.54 0.0054322 24613770000 11477310 10463870 13372310 11019690 15285060 15309770 15693270 13443560 13894060 9247790 FALSE TRUE 11930443.06 12260958.27 13720803.38 13199351.79 12686910.96 11754307.94 14463190.49 13263371.07 13394015.49 11059717.39 1.078729468 1.108614067 1.240610668 1.193461942 1.147127952 1.062803644 1.307735992 1.199250451 1.211063088 1 23.39881119 2.255639994 24.99998438 1.20043883 1.144720847 0.026298362 0.087033362 621.5199207 909748.5719 0.02935598 0.024505319 180.1523758 -2.255639994 -0.055717984 ASEENLLSSSSVPSADRDS(ph)SPTTNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.663)S(0.332)PT(0.004)T(0.001)NSK 152.49 6.03E-08 1085800000 235530 160890 184210 167270 262370 225330 207600 193470 204710 172710 TRUE FALSE 244828.9063 188521.6059 189010.6639 200355.5067 217772.4411 173000.5224 191327.7695 190876.8511 197342.5271 206549.2178 1.185329622 0.912720019 0.915087774 0.970013389 1.054336799 0.837575297 0.926305951 0.924122847 0.955426165 1 17.65612607 2.752561343 24.78672462 0.92389204 0.995015771 0.177595413 0.08232122 1369.107966 2423851.947 0.024757867 0.026132598 565.66765 -2.752561343 0.071123732 ASEENLLSSSSVPSADRDSS(ph)PTTNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 ASEENLLSSSSVPSADRDS(0.226)S(0.766)PT(0.007)T(0.001)NSK;ASEENLLSSSSVPSADRDS(0.43)S(0.499)PT(0.06)T(0.01)NSK;ASEENLLSSSSVPSADRDS(0.202)S(0.769)PT(0.024)T(0.004)NSK 256.68 7.40E-53 2032560000 715450 596050 676200 530220 833220 840410 741950 696330 762030 575870 TRUE FALSE 743696.5184 698416.9509 693822.3275 635095.9335 691589.562 645237.514 683794.0203 686996.8353 734604.6892 688700.7008 1.079854453 1.014108088 1.007436651 0.922165365 1.004194654 0.936891037 0.992875453 0.997525971 1.06665303 1 19.39351762 -0.566073603 6.331233251 1.000006873 0.998139944 0 0.04615304 0 0 0.044129915 0.010401521 0.271597893 0.566073603 -0.001866928 ASEKPVS(ph)PK ddPTM_MDA-MB-175_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;AS(0.001)EKPVS(0.999)PK 92.906 0.011808 996230000 2276610 664641 876687 637170 1602120 1870830 1440300 1093255 1157305 511856 TRUE FALSE 2366492.321 778787.9216 899534.1834 763200.3242 1329792.215 1436358.085 1327405.522 1078601.705 1115653.819 612144.3831 3.865905473 1.272229139 1.469480417 1.246765216 2.172350595 2.346436764 2.168451691 1.762005394 1.822533784 1 19.22351245 0.615014452 1.261034368 1.001855406 1.991716981 0.159209629 0.713213375 2.640948038 6.177842684 0.657023753 0.197988306 4.121112326 -0.615014452 0.989861574 ASEPLLS(ph)PPPFGESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;ASEPLLS(1)PPPFGESR;ASEPLLS(1)PPPFGESR 290.37 7.12E-44 1012206000 205167 235940 215423 210851 255098 275280 222912 244622 221338 244354 TRUE FALSE 213267.1516 276460.8596 221037.1004 252556.6985 211736.5331 211350.3919 205439.575 241343.2422 213372.0886 292230.4879 0.729790903 0.946037019 0.756379329 0.864238021 0.724553193 0.723231835 0.703005277 0.825866062 0.730149993 1 18.15674717 -1.56480718 2.973034983 1.011086491 0.781760204 0.447068978 0.073921547 52418518.52 58570900.21 4631592.823 0.017057132 0.027239104 1.56480718 -0.229326287 ASES(ph)PARGPSGSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASESPARGPSGSPR 14 1 O43237;O43237-2;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 AS(0.013)ES(0.987)PARGPSGSPR;AS(0.205)ES(0.795)PARGPSGSPR 105.77 0.00059364 643850000 346980 424850 378770 346090 487700 510280 336520 423780 410440 527260 TRUE FALSE 360679.0383 497814.6826 388641.0574 414545.569 404800.9282 391775.2034 310142.6831 418099.9223 395668.3446 630566.502 0.571992069 0.789472135 0.616336352 0.657417683 0.641963896 0.621306717 0.491847699 0.663054445 0.627480755 1 19.26628901 -1.00026044 4.311280508 1.000015462 0.632347771 0.709404921 0.070807468 20164981.77 39817405.26 5126.29183 0.016689076 0.09994005 1.00026044 -0.36766769 ASET(ph)PPPVAQPKPEAPHPGLETTLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.012)ET(0.988)PPPVAQPKPEAPHPGLETTLQER 210.21 2.07E-25 4353280000 745780 656970 727200 615870 913070 908820 863540 859990 822290 655050 TRUE FALSE 775223.9703 769799.487 746151.4294 737687.2478 757866.6875 697760.3283 795853.4784 848463.2407 792695.9435 783394.5058 0.989570344 0.982646012 0.95245936 0.941654865 0.967413841 0.89068831 1.015903829 1.083059984 1.011873249 1 19.57937948 2.014261119 24.55057487 1.043025454 0.955169329 0.541060048 0.032955312 120.2645475 207034.889 0.012171848 0.008985151 103.3382539 -2.014261119 -0.087856125 ASETPPPVAQPKPEAPHPGLETTLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASETPPPVAQPKPEAPHPGLETTLQER 27 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 245.2 1.26E-45 144660000 64717 57203 66181 64760 79548 113220 80552 72370 76339 64700 FALSE TRUE 67272.07713 67027.17027 67905.73123 77569.33471 66026.45937 86926.37087 74238.12376 71399.99852 73591.5743 77376.72624 0.86940971 0.866244587 0.877598918 1.00248923 0.853311617 1.123417532 0.959437383 0.922758069 0.951081519 1 16.23961207 3.797515776 7.417692093 0.967652517 0.869915299 0.340472043 0.064821756 0.339193446 37.67600891 0.016449516 0.029748685 6273.584854 -3.797515776 -0.097737218 ASEYS(ph)PASLDAFGAFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASEYSPASLDAFGAFLK 17 0 P17029;E9PC66;B3KRF7 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 AS(0.003)EYS(0.997)PASLDAFGAFLK;ASEYS(1)PASLDAFGAFLK 229.54 9.55E-19 0 38462 38904 39487 31403 40443 47198 38353 37129 46488 36779 TRUE FALSE 39980.50946 45585.45937 40516.06366 37614.41967 33568.51331 36236.97979 35346.79164 36631.34649 44814.90596 43985.14087 0.908954903 1.036383162 0.921130701 0.855161969 0.763178488 0.823845941 0.803607558 0.832811849 1.018864668 1 15.42472861 3.916609371 3.744314702 0.85296706 0.974256104 0.169395867 0.083260766 0.297349913 7.792915529 0.021192829 0.042357912 8252.952977 -3.916609371 0.121289044 ASFDHS(ph)PDSLPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASFDHSPDSLPLR 13 0 H0Y6H0;Q8NB78;Q8NB78-2 H0Y6H0 KDM1B Lysine-specific histone demethylase 1B 1 AS(0.05)FDHS(0.95)PDSLPLR 106.3 0.00089201 71684000 36621 114370 105260 106760 97209 132750 84751 103370 103000 157180 TRUE FALSE 38066.82536 134012.1578 108003.1621 127876.8094 80685.4489 101920.8243 78107.99516 101984.4942 99293.05012 187976.4116 0.202508522 0.712920077 0.574556994 0.680281149 0.429231775 0.542200074 0.415520195 0.542538786 0.528220798 1 17.52019211 0.267032208 2.302096493 1.000002088 0.521530506 0.531241434 0.136759296 24.13648907 74.13036003 0.122084271 0.032879052 1.849405768 -0.267032208 -0.478471582 ASFNNPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASFNNPDR 8 0 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;;;; 165.26 0.00075678 1931350000 1309681 1684465 1554362 1589820 1657670 1810910 1545568 1559210 1474544 1676410 FALSE TRUE 1361388.217 1973758.76 1594869.951 1904281.651 1375899.846 1390353.597 1424422.342 1538311.34 1421475.449 2004870.443 0.679040495 0.984481949 0.795497762 0.949827785 0.686278682 0.693488002 0.710480992 0.767287156 0.709011126 1 20.93507758 3.227763068 24.99703758 0.744412061 0.857608846 0.118795575 0.116004895 336.7372922 779567.734 0.030605211 0.036922125 1689.518951 -3.227763068 0.113196784 ASFPGPSELHSEDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASFPGPSELHSEDSR 15 0 Q99988;A0A0A0MTT8 Q99988 GDF15 Growth/differentiation factor 15 0 ;;; 196.95 8.67E-09 1227620000 430746 758970 673670 644810 788480 924410 673820 801900 772290 917100 FALSE TRUE 447752.1847 889317.1935 691226.3936 772351.4934 654454.4512 709729.7871 621004.2277 791151.8421 744495.4338 1096788.186 0.408239431 0.810837685 0.630227789 0.704193848 0.596700858 0.647098315 0.566202513 0.721335124 0.678796 1 20.06485351 0.29967444 0.903827028 1.002689049 0.636485728 0.547416123 0.099553278 2.019786382 2.013174077 0.098732397 0.028743448 1.993767167 -0.29967444 -0.366203321 ASFTNSELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASFTNSELHR 10 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 106.16 0.0024538 139920000 62577 91664 92050 93335 96166 133390 95137 99180 95368 108840 FALSE TRUE 65047.58828 107406.579 94448.89862 111796.3844 79819.73767 102412.194 87679.91335 97850.65433 91935.72431 130165.1141 0.499731351 0.825156415 0.725608388 0.858881315 0.613219127 0.786786803 0.67360532 0.751742546 0.706300801 1 16.98998331 -1.468228226 2.559887684 1.012029817 0.722847563 0.423532498 0.099197222 4702527.051 4612522.375 402422.9677 0.022872648 0.034022935 1.468228226 -0.289182254 ASGDGES(ph)LDEDSEFTLASDFEIGHFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 AS(0.024)GDGES(0.974)LDEDS(0.002)EFT(0.001)LASDFEIGHFFR;AS(0.034)GDGES(0.949)LDEDS(0.013)EFT(0.004)LASDFEIGHFFR 62.945 0.022803 38324000 7879.8 12192.2 9832 11658.4 12044.1 14726.4 11661.2 10612.3 9738.3 11895.2 TRUE FALSE 8190.900589 14286.11551 10088.23 13964.39672 9996.848184 11306.41678 10747.16467 10470.05948 9387.820485 14225.83669 0.575776368 1.004237277 0.709148447 0.981622173 0.702724796 0.794780442 0.75546802 0.735989011 0.659913416 1 13.79622589 ASGDGESLDEDSEFTLASDFEIGHFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASGDGESLDEDSEFTLASDFEIGHFFR 27 0 Q99733;Q99733-2;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ;;;;; 330.78 3.20E-95 471097200 259744.4 336138.3 336296.4 329215.2 363872.4 373177 350068.9 330379.4 334480 341678.7 FALSE TRUE 269999.3095 393867.4382 345060.5605 394332.984 302021.4994 286512.2973 322629.5849 325951.2045 322442.1301 408624.0994 0.66075229 0.963886953 0.844444958 0.965026254 0.739118177 0.701163484 0.789551045 0.797679836 0.789092299 1 18.64041477 4.779679521 23.08297574 0.829357875 0.66075091 0.229849563 0.097281419 16056.94478 9013377.283 0.023195103 7.512606129 60211.51029 -4.779679521 -0.168606965 ASGDPGASGMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.006)GMS(0.994)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR 244.71 8.24E-12 3154620000 3986500 4577960 4569000 4422550 4698770 5423980 4672600 4457560 4310650 4477940 TRUE FALSE 4143890.098 5364189.018 4688071.893 5297317.19 3900074.754 4164342.846 4306349.402 4397813.699 4155510.549 5355306.608 0.773791381 1.001658619 0.875406814 0.989171597 0.728263578 0.777610537 0.804127516 0.821206706 0.775961276 1 22.35253775 3.239810562 24.99994736 0.807196705 0.914082182 0.19712856 0.089412317 44.15881271 883199.0864 0.023193093 0.029736461 1737.042972 -3.239810562 0.106885477 ASGEGHHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGEGHHLK 9 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ; 87.476 0.013435 98171000 90002 125989 143445 134096 181000 171020 135705 140235 143089 160183 FALSE TRUE 93555.34846 147626.6307 147183.2945 160619.7886 150233.6847 131303.1968 125068.0875 138355.3792 137939.2548 191567.792 0.488366794 0.770623439 0.768309187 0.838448817 0.78423248 0.68541374 0.652865945 0.722226726 0.720054522 1 17.5474955 -2.04241912 2.192529153 1.346747766 0.720097721 0.469938867 0.090787824 5478746.586 1794373.236 9530114.987 0.023168988 0.009069449 2.04241912 -0.626650045 ASGGAQS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;ASGGAQS(1)PLR 148.13 2.69E-05 4645194000 3546895 3457164 3323134 3361322 4366393 4363031 3493422 3519659 3184885 4224373 TRUE FALSE 3686929.153 4050905.024 3409737.602 4026181.459 3624195.077 3349783.173 3219598.455 3472483.728 3070261.611 5052058.009 0.729787573 0.801832643 0.674920517 0.796938882 0.717370044 0.663053189 0.637284538 0.687340431 0.607724932 1 22.26843977 -1.031873421 4.604657173 1.000009471 0.702143095 0.692532287 0.059607008 6.55E-06 1.38E-06 0.059568703 0.014039989 0.092923718 1.031873421 -0.297866377 ASGQAFELILS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 189.07 5.84E-06 8000338000 3741618 3930544 4194535 4052823 4360306 4970981 4828849 4707209 4628993 5511239 TRUE FALSE 3889339.968 4605584.357 4303848.028 4854459.293 3619142.744 3816545.999 4450351.198 4644116.563 4462396.446 6591060.763 0.590093174 0.698762236 0.652982605 0.736521702 0.549098677 0.579048826 0.675210161 0.704608367 0.677037674 1 22.65207924 0.064611575 0.73660271 1.010398725 0.642702936 0.783482165 0.055511485 1.955408353 1.168947394 0.111580362 0.019962056 1.160410299 -0.064611575 -0.36769579 ASGS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGSENEGDYNPGR 14 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 AS(0.001)GS(0.999)ENEGDYNPGR;AS(0.001)GS(0.999)ENEGDYNPGR 195.6 9.08E-08 0 236680 284980 277350 274410 302750 316290 311070 283770 262120 191846 TRUE FALSE 246024.3092 333923.0982 284577.9688 328687.479 251288.6631 242836.4409 286687.5206 279966.5273 252686.3524 229434.5506 1.07230715 1.455417666 1.240344874 1.432598003 1.095252056 1.058412695 1.249539443 1.220245715 1.101343942 1 17.80772314 3.220699094 24.99984163 1.143532608 1.306983293 0.335527546 0.120998226 291.3669949 407810.2488 0.03374757 0.040415376 1662.260534 -3.220699094 0.163450686 ASGYFTRPWQWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGYFTRPWQWEK 13 1 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ; 143.21 3.71E-05 715170000 455330 415300 421560 345910 892200 637420 458990 446260 478580 729110 FALSE TRUE 473306.78 486624.5444 432546.1999 414329.9656 740544.1627 489388.8652 423013.1645 440278.6146 461355.9993 871965.1448 0.542804701 0.558077977 0.496059048 0.475168036 0.84928184 0.561248197 0.485126231 0.504926851 0.52909913 1 19.73391094 -1.727182288 2.66808573 1.083448624 0.553756043 0.62901135 0.102341373 11505608.68 9516550.97 6399691.406 0.027585963 0.018742077 1.727182288 -0.529692581 ASGYQS(ph)SQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 ASGYQS(0.94)S(0.06)QKK 66.215 0.040817 102550000 100250 47771 75094 44441 90516 83765 89461 71424 81758 49961 TRUE FALSE 104207.9474 55975.29764 77051.01133 53231.29716 75130.12265 64311.84822 82448.81306 70466.67811 78815.54555 59749.90139 1.744068944 0.936826611 1.289558803 0.890901841 1.257409986 1.076350701 1.37989873 1.179360576 1.319090805 1 15.86664871 7.209095773 0.014945837 9.88E-07 2.608595809 0.071618475 0.23081439 20266.6606 26.65548841 1911.861037 2820.242489 16184369.04 -7.209095773 2.608594821 ASGYQSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASGYQSSQK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 82.261 0.044095 32832000 10153 6839.6 9297.5 9537.9 15174 13602 10525 9315.1 8203.7 11025 FALSE TRUE 10553.84828 8014.248095 9539.800488 11424.46815 12594.7289 10443.14164 9700.022998 9190.246321 7908.45044 13185.13766 0.800435198 0.607824378 0.723526802 0.866465595 0.955221646 0.792038878 0.735678553 0.697015576 0.599800369 1 13.68662501 3.985072886 24.15388853 0.790070419 0.694516242 0.108585392 0.119891672 1009.178489 1632987.53 0.031708778 0.059858742 9662.130211 -3.985072886 -0.095554178 ASGYQSSQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASGYQSSQKK 10 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 94.767 0.012634 686360000 524350 399700 484270 287620 718280 577450 496740 472720 532220 557900 FALSE TRUE 545051.7429 468345.3658 496890.474 344510.3775 596187.0222 443345.9888 457804.2208 466383.9616 513065.5062 667209.8234 0.816912047 0.701946149 0.744728954 0.516344882 0.893552525 0.66447761 0.686147303 0.699006437 0.768971751 1 19.347781 0.817647591 3.254547237 0.999957419 0.711866201 0.454965597 0.093051045 0.82213454 13.32621056 0.082567306 0.021442829 6.571243967 -0.817647591 -0.288091217 ASHDPLVPNS(ph)SPLPTNGISGSPESFASSLDGSGHAGPEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASHDPLVPNSSPLPTNGISGSPESFASSLDGSGHAGPEGSR 41 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 ASHDPLVPNS(0.5)S(0.5)PLPTNGISGSPESFASSLDGSGHAGPEGSR 94.079 0.00027431 74501000 18126 47540 37967 45407 44260 49601 40175 44824 37973 48287 TRUE FALSE 18841.62848 55704.62519 38956.45121 54388.36907 36736.70101 38081.91946 37025.97852 44223.2076 36606.35915 57747.91314 0.326273755 0.964617112 0.674594961 0.941823975 0.636156339 0.659451007 0.641165654 0.765797501 0.633899256 1 15.81748119 -1.511720478 3.247485253 1.007582848 0.70789512 0.222811194 0.169748884 74293487.71 95278781.42 5018668.32 0.037018703 0.030780773 1.511720478 -0.299687728 ASHEEVEGLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASHEEVEGLVEK 12 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ;; 157.03 7.37E-05 1074150000 1755700 1561880 1625830 1785830 3465110 2691200 2353050 1696670 1772800 2176770 FALSE TRUE 1825016.392 1830120.74 1668200.465 2139061.844 2876111.84 2066209.586 2168611.792 1673928.914 1708997.274 2603266.405 0.701048647 0.703009395 0.640810507 0.821683805 1.10480888 0.793698863 0.833034909 0.643010992 0.6564819 1 21.31189153 3.726767429 22.93093693 0.819759467 0.683761508 0.216046625 0.132292336 445.0437809 865354.6212 0.038283124 0.05995716 5330.493636 -3.726767429 -0.135997959 ASHGYGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASHGYGGK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 133.6 0.00091248 4866830000 6566060 6191200 7019880 5793200 8022160 7997370 7865310 7286590 7197200 6579830 FALSE TRUE 6825293.119 7254490.439 7202823.84 6939077.669 6658556.109 6140102.019 7248806.45 7188925.18 6938174.178 7869021.71 0.867362344 0.921904997 0.915339175 0.881822153 0.846173305 0.780287848 0.921182673 0.913572925 0.881707337 1 22.90775286 0.328687807 0.797945636 1.001053716 0.878068552 0.429275525 0.041245469 2.567587721 2.182118321 0.051762334 0.015014142 2.131512121 -0.328687807 -0.122985164 ASHPEDPASVVEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASHPEDPASVVEAR 14 0 Q9UHL4;R4GMR2 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ; 97.203 0.0030677 164267000 82830 125463 100858 112065 108037 143794 95830 102591 91283 119737 FALSE TRUE 86100.19236 147010.2943 103486.4423 134231.1225 89672.90933 110400.0227 88318.59419 101215.9355 87997.74266 143197.1726 0.601270198 1.02662847 0.722684955 0.937386682 0.626219832 0.770965101 0.616762137 0.706829147 0.614521509 1 17.12764348 3.229875151 24.99971716 0.703139752 0.829516032 0.085253199 0.150986535 344.6326194 991967.9619 0.039309686 0.047678385 1697.755518 -3.229875151 0.12637628 ASHS(ph)SERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 AS(0.032)HS(0.966)S(0.002)ERPPPR;AS(0.012)HS(0.987)S(0.001)ERPPPR 155.14 1.92E-05 499710000 159443 299420 290120 277170 358050 395920 274850 338570 310930 450810 TRUE FALSE 165737.9328 350843.0558 297680.7655 331993.3987 297188.7889 303973.5802 253306.5388 334032.0229 299739.69 539137.5882 0.307413054 0.650748647 0.552142481 0.615786037 0.551229956 0.563814482 0.46983654 0.619567306 0.555961403 1 19.04029397 -5 0.329073155 5.5234046 0.533125084 0.698485608 0.09062476 183.9593781 1.594184797 581.7308232 0.07087239 1.00E-05 5 -4.990279515 ASHSS(ph)ERPPPR ddPTM_MDA-MB-175_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(0.015)HS(0.026)S(0.959)ERPPPR 99.941 0.0026644 1712100000 161340 106160 96761 90335 108570 187480 119160 106910 106940 90410 TRUE FALSE 167709.8278 124392.1542 99282.67115 108202.9934 90115.31018 143940.6113 109819.9278 105477.0463 103091.2503 108124.1085 1.551086341 1.150457154 0.918228807 1.000729577 0.833443267 1.331253624 1.015684008 0.975518298 0.953452951 1 16.72232871 4.686267046 2.903529026 1.007465025 1.613241024 0.645748352 0.122011709 0.209691781 2.678056054 0.02972778 0.27890298 48558.69943 -4.686267046 0.605775998 ASHSSERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASHSSERPPPR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;; 90.653 0.0068055 334855000 3336.07 6146 6648.7 6966.5 8851.4 7858.6 6681 7581.7 6158.8 9632.1 FALSE TRUE 3467.78062 7201.527691 6821.970584 8344.452907 7346.84219 6033.559248 6157.325762 7480.079713 5937.145991 11519.32558 0.301040247 0.625169212 0.592219617 0.724387279 0.637784056 0.523777126 0.534521376 0.64935049 0.51540743 1 13.49176863 -1.81568478 2.453428474 1.148657964 0.578874053 0.58626955 0.108699235 9206924.573 5820414.299 8099231.411 0.026063897 0.015286752 1.81568478 -0.569783911 ASHTAPQVLFSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASHTAPQVLFSHR 13 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 186.13 4.67E-06 1954766000 764740 1028422 881785 1040719 1037941 1132485 1145038 1025833 895537 1086522 FALSE TRUE 794932.5257 1205045.478 904765.0415 1246570.112 861512.1596 869482.5217 1055286.93 1012083.387 863306.7983 1299405.183 0.611766473 0.927382385 0.696291698 0.959339033 0.66300502 0.669138874 0.812130768 0.778882061 0.664386143 1 20.30941993 -1.202120958 5.011477266 1.000023892 0.761875713 0.303628335 0.111316129 2.72E-05 4.33E-06 0.098757846 0.023275114 0.062788346 1.202120958 -0.238148178 ASIANSDGPTAGS(ph)QTPPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASIANSDGPTAGSQTPPFK 19 0 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPT(0.175)AGS(0.44)QT(0.385)PPFK 84.375 0.0033637 64949000 169640 111310 127030 114620 182420 174610 166420 153020 161860 105100 TRUE FALSE 176337.5182 130426.6266 130340.5062 137291.4939 151412.3136 134059.4737 153375.5655 150969.0172 156034.6902 125692.3327 1.402929792 1.037665733 1.036980564 1.092282169 1.20462649 1.066568428 1.220245994 1.201099653 1.241401817 1 16.93953712 2.216385144 24.99319219 1.185793881 1.131577895 0 0.1189703 861.9538274 971472.0438 0.042843169 0.031667631 164.5830641 -2.216385144 -0.054215985 ASIANSDGPTAGSQT(ph)PPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASIANSDGPTAGSQTPPFK 19 0 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPTAGS(0.002)QT(0.998)PPFK;ASIANSDGPT(0.001)AGS(0.085)QT(0.914)PPFK 181.61 3.47E-13 254000000 468900 357620 411750 346870 467590 463610 443480 418130 430510 300518 TRUE FALSE 487412.5341 419038.4531 422480.5433 415479.8507 388109.2188 355943.6036 408718.8788 412525.6513 415016.0292 359398.7483 1.356188736 1.165942995 1.175520352 1.156041452 1.079884726 0.990386319 1.137229555 1.147821614 1.154750903 1 18.45522586 7.999993118 0.735634615 1.100069571 41.61885475 0.6433892 0.058107607 235.977787 1.073438353 0.021437713 15815.40127 99998415.29 -7.999993118 40.51878517 ASIANSDGPTAGSQT(ph)PPFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASIANSDGPTAGSQTPPFKR 20 1 J3KP75;O75167-5;O75167-2;O75167;O75167-4;F6TH74;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 ASIANSDGPTAGS(0.126)QT(0.874)PPFKR;ASIANSDGPTAGS(0.061)QT(0.939)PPFKR 92.147 0.00099259 593750000 253740 237514 270062 221432 276302 286270 259724 235105 258250 229580 TRUE FALSE 263757.8511 278305.1819 277100.0376 265230.5887 229336.2847 219788.131 239366.1542 231953.802 248955.6329 274561.8054 0.960650192 1.013634003 1.009244666 0.966014149 0.835281092 0.80050512 0.871811554 0.844814528 0.906738039 1 18.06677142 3.348837899 4.883311639 0.863798763 0.994904409 0.512613328 0.052476643 0.142557769 5.513031868 0.01398744 0.019064823 2232.738695 -3.348837899 0.131105646 ASIGQS(ph)PGLPSTTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASIGQSPGLPSTTFK 15 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK;ASIGQS(1)PGLPSTTFK 235.4 1.17E-17 818791000 1753850 1415720 1763670 1362740 1988760 1942130 1878020 1707710 1869610 1433980 TRUE FALSE 1823093.352 1658858.897 1809632.689 1632285.905 1650711.286 1491099.741 1730815.885 1684820.941 1802323.101 1714940.926 1.063064812 0.967297982 1.055215758 0.951802992 0.962547025 0.869475863 1.009256855 0.982436721 1.050953461 1 20.70972745 7.999999696 0.927441208 0.977156172 49.50490224 0.170144326 0.050781262 1928.035344 3.677885404 0.015791045 198312.1946 99999929.98 -7.999999696 48.52774607 ASIHEAWTDGK ddPTM_MDA-MB-175_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 ;;; 178.53 7.50E-06 2593480000 2403010 5134480 4005770 4949440 5273360 6319900 6163300 4890870 4078160 6612600 FALSE TRUE 2497882.69 6016286.999 4110163.657 5928424.459 4376996.151 4852199.004 5680204.441 4825315.887 3931387.818 7908212.364 0.315859334 0.760764471 0.519733597 0.749654181 0.553474787 0.613564581 0.718266554 0.610165188 0.497127244 1 22.91492018 -1.909636554 2.4720722 1.235558208 0.605995393 0.474231422 0.127867719 13039672.23 6682528.038 17811430.57 0.027602963 0.012312988 1.909636554 -0.629562815 ASKSS(ph)PAGNSPAPL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASKSSPAGNSPAPL 14 1 B4DSP0;A0A087WZG9;Q86TG7-2 B4DSP0 PEG10 Retrotransposon-derived protein PEG10 1 AS(0.034)KS(0.203)S(0.763)PAGNSPAPL 104.26 0.0028102 233240000 323380 279850 318080 217860 428990 404330 286040 313910 359790 314940 TRUE FALSE 336147.2921 327912.0606 326369.4261 260952.0578 356070.433 310430.4852 263619.4374 309702.5499 346841.2282 376646.4631 0.89247431 0.87060969 0.866513981 0.692830236 0.945370441 0.824195939 0.699912154 0.822263263 0.920866813 1 18.52285146 1.049163791 3.443347234 0.998213928 0.822875838 0.359182436 0.07494948 0.218503745 5.527810531 0.071331742 0.018573753 11.1986015 -1.049163791 -0.175338091 ASLENSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ASLENSLR 8 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 303.14 7.15E-27 17497930000 4567660 5411050 4774080 4717290 6429490 6269780 5260170 4945510 4859790 6764190 FALSE TRUE 4747994.744 6340355.745 4898496.447 5650355.882 5336607.586 4813718.614 4847864.131 4879223.528 4684887.107 8089503.522 0.586932774 0.783775633 0.60553734 0.698479934 0.659695316 0.595057361 0.599278326 0.60315488 0.579131599 1 22.94761973 -1.105013896 6.360012446 1.00000074 0.635624438 0.764760977 0.060800945 6.32E-07 8.88E-08 0.058258414 0.013731612 0.078521051 1.105013896 -0.364376302 ASLGS(ph)LEGEAEAEASSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.071)LGS(0.929)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK 407.45 3.16E-147 1225007000 1287590 877036 1056435 857026 1364121 1495490 1433188 1133538 1247969 922994 TRUE FALSE 1338425.047 1027660.111 1083966.564 1026543.185 1132248.2 1148185.112 1320850.98 1118344.777 1203054.839 1103837.003 1.212520548 0.930989003 0.981998757 0.929977146 1.02573858 1.040176321 1.196599658 1.013143041 1.0898845 1 20.07409572 2.645267535 3.693860783 1.077248204 1.004464894 0.074568129 0.089526591 0.513400812 13.05639839 0.029207292 0.027562543 441.8425484 -2.645267535 -0.07278331 ASLGSLEGEAEAEASS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEASS(1)PK;ASLGSLEGEAEAEAS(0.022)S(0.978)PK;ASLGSLEGEAEAEAS(0.006)S(0.994)PK;ASLGSLEGEAEAEAS(0.016)S(0.984)PK;ASLGSLEGEAEAEAS(0.001)S(0.999)PK 424.46 1.01E-168 1100175000 2549539 1170520 1325872 1284452 1880105 2404386 2074773 1515080 1562728 1069936 TRUE FALSE 2650196.768 1371547.705 1360425.314 1538512.772 1560525.424 1846003.79 1912146.871 1494772.831 1506485.725 1279569.474 2.071162858 1.07188217 1.063189878 1.202367517 1.219570688 1.442675703 1.494367371 1.168184191 1.177337968 1 20.28722705 4.744886449 24.88231707 1.223780637 2.071163261 0.74871536 0.150265341 357.6795955 1406872.812 0.03790925 0.356733695 55575.89286 -4.744886449 0.847382624 ASLGSLEGEAEAEASS(ph)PKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ASLGSLEGEAEAEAS(0.491)S(0.509)PKGK;ASLGSLEGEAEAEAS(0.16)S(0.84)PKGK;ASLGSLEGEAEAEAS(0.136)S(0.864)PKGK 208.17 3.60E-22 613770000 938465 448752 569690 309749 1130071 992290 591819 605328 735006 507954 TRUE FALSE 975516.3229 525821.6652 584536.5894 371016.4277 937981.9351 761845.6858 545430.6803 597214.5683 708553.2776 607477.8609 1.605846707 0.86558161 0.962235214 0.610748887 1.544059455 1.254112676 0.897861001 0.983105075 1.16638535 1 19.21247231 1.590169926 0.015110608 5.43E-05 2.103730543 0.019009895 0.290091531 2806.250618 43.24765078 3001.428008 3008.502503 38.91973957 -1.590169926 2.103676282 ASLLHSMPTHS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASLLHSMPTHSSPR 14 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ASLLHSMPT(0.08)HS(0.46)S(0.46)PR;ASLLHSMPT(0.001)HS(0.577)S(0.422)PR 167.71 6.03E-06 161653000 37291 73347 72699 72778 85096 96442 66786 79258 68325 89101 TRUE FALSE 38763.27747 85943.77669 74593.59566 87173.27118 70631.41232 74044.80709 61551.13881 78195.67615 65865.9966 106558.635 0.363774156 0.806539767 0.700023941 0.818077964 0.662840814 0.694873832 0.577626945 0.733827682 0.618119748 1 16.70128798 -2.159091133 2.229472203 1.734864266 0.675291119 0.397889229 0.123304789 12043311.84 2732520.623 44697943.24 0.027455111 0.006932803 2.159091133 -1.059573147 ASLLHSMPTHSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASLLHSMPTHSSPR 14 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ASLLHSMPTHS(0.02)S(0.98)PR 130.01 0.00021634 105640000 23829 43863 38434 42264 43099 55445 40261 46527 38711 53305 TRUE FALSE 24769.78732 51396.12904 39435.62161 50623.69305 35773.04737 42568.73903 37105.23762 45903.38167 37317.79867 63749.09416 0.388551204 0.806225245 0.618606776 0.79410843 0.561153815 0.667754414 0.582051213 0.720063277 0.585385552 1 15.96011722 -2.279054892 2.235524337 2.484686339 0.647021759 0.46535219 0.116513129 5152888.005 658806.5304 38772009.18 0.025672374 0.005259508 2.279054892 -1.837664579 ASLPQAATFGELSGPLKPGS(ph)PYRPPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 ASLPQAATFGELSGPLKPGS(1)PYRPPVPR 228.34 4.91E-35 867410000 514490 376900 464000 344740 514040 582380 494020 446620 486790 374980 TRUE FALSE 534802.4625 441629.6431 476092.2212 412928.5431 426663.6644 447131.0711 455297.4215 440633.7894 469270.523 448450.1516 1.192557212 0.984790933 1.061639113 0.920790285 0.951418263 0.997058579 1.015268743 0.982570276 1.046427393 1 18.7745881 4.740145925 24.92935191 0.993827227 1.19255728 0.6964214 0.039006156 72.68870825 1142941.772 0.009223129 0.059004594 54972.55534 -4.740145925 0.198730053 ASLQVLGTVGEPINPEAWLWYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASLQVLGTVGEPINPEAWLWYHR 23 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ; 274.97 1.03E-51 868240000 448600 565200 556430 549750 571840 680310 588760 567130 540900 597860 FALSE TRUE 466311.0744 662268.7034 570931.0229 658488.9092 474638.8411 522318.3127 542611.4528 559528.55 521433.1147 714999.2203 0.652184032 0.926250945 0.798505798 0.920964514 0.663831271 0.730515919 0.758897964 0.782558266 0.729277879 1 19.44758214 -1.219784731 3.534140844 1.000368496 0.778438078 0.374227908 0.087608217 36450797.8 66377588.38 160983.0072 0.020313151 0.060285833 1.219784731 -0.221930417 ASMSEFLES(ph)EDGEVEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR 136.01 7.53E-06 123540000 102198 120013 130559 124359 146271 163181 122285 134153 124584 133942 TRUE FALSE 106232.856 140624.2992 133961.4748 148956.839 121407.9077 125284.6858 112699.9822 132354.8985 120100.2462 160185.3704 0.663187004 0.877884783 0.836290321 0.929902891 0.757921322 0.782123146 0.703559769 0.826260838 0.749757895 1 17.28938287 -0.983944718 4.471332626 1.00000543 0.79682717 0.403909011 0.075635347 9357444.735 2092764.525 531.9981941 0.017254718 0.103766049 0.983944718 -0.203178261 ASNDMYHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASNDMYHSR 9 0 P01034 P01034 CST3 Cystatin-C 0 ;;; 105.46 0.0023471 344960000 195131 255048 239692 239555 302686 309194 204153 224004 204197 333449 FALSE TRUE 202834.9226 298850.51 245938.5704 286938.264 251235.5418 237388.3794 188150.9544 221001.5928 196847.9899 398781.9473 0.508636171 0.749408322 0.616724433 0.719536744 0.63000731 0.595283666 0.471814122 0.554191568 0.493623122 1 18.60524058 -1.084855744 5.361243968 1.000005024 0.595051027 0.663133731 0.086963543 5.45E-06 9.31E-07 0.087896998 0.020717264 0.082251581 1.084855744 -0.404953998 ASNEDGDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASNEDGDIKR 10 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;; 136.81 0.00017303 909150000 1610980 1129370 1448760 1109150 1798620 1695100 1658640 1373080 1541690 1023910 FALSE TRUE 1674582.734 1323330.512 1486515.876 1328536.56 1492891.215 1301438.714 1528631.463 1354676.109 1486204.878 1224525.561 1.367535957 1.080688354 1.213952508 1.084939835 1.219158883 1.062810574 1.2483459 1.10628651 1.213698534 1 20.22379146 -5 0.196120708 0.272730416 1.197664715 0.262439766 0.090083319 187.1090048 1.844535901 53.57880807 0.203102839 1.00E-05 5 0.924934299 ASNGDAWVEAHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 161.82 4.15E-05 941790000 1344470 1372800 1331610 1451890 1359140 2064670 1379620 1261500 1358840 1369120 FALSE TRUE 1397550.714 1608567.721 1366312.851 1739069.509 1128113.868 1585181.683 1271481.779 1244591.656 1309935.614 1637372.851 0.85353236 0.982407715 0.834454321 1.062109652 0.688977998 0.968125056 0.77653772 0.760114995 0.800022801 1 20.64295145 3.23773042 24.99999833 0.818843418 0.929598135 0.171045219 0.106182542 34.12742552 1027702.197 0.028134657 0.035554251 1728.742943 -3.23773042 0.110754717 ASNTST(ph)PTKGNTETSASASQTNHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASNTSTPTKGNTETSASASQTNHVK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 AS(0.001)NT(0.006)S(0.383)T(0.607)PT(0.003)KGNTETSASASQTNHVK;ASNT(0.005)S(0.032)T(0.96)PT(0.003)KGNTETSASASQTNHVK;ASNT(0.008)S(0.036)T(0.946)PT(0.01)KGNTETSASASQTNHVK 221.3 1.68E-33 875940000 181918 172207 218834 145806 283370 263736 243552 231044 231854 167011 TRUE FALSE 189100.2631 201782.2127 224536.9938 174645.9916 235202.8686 202487.311 224461.7578 227947.2331 223509.6198 199733.6078 0.946762366 1.010256686 1.124182336 0.874394617 1.177582837 1.013786879 1.123805654 1.141256274 1.119038615 1 17.60771758 3.21949889 24.99998964 1.103593018 1.00008757 0.305692743 0.077770215 292.8411352 384068.512 0.021495433 0.02572964 1657.673099 -3.21949889 -0.103505449 ASPDQNASTHT(ph)PQSSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 ASPDQNASTHT(0.937)PQS(0.053)S(0.01)VK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK;ASPDQNASTHT(1)PQSSVK 263.75 7.42E-27 6466720000 1261000 2123310 2621760 2338500 2887760 3007260 2713060 2689190 2459700 1861360 TRUE FALSE 1310785.254 2487971.975 2690085.219 2801048.32 2396899.587 2308869.44 2500403.268 2653145.807 2371175.877 2226057.854 0.588837011 1.117658272 1.208452518 1.258299875 1.076746313 1.037201004 1.123242715 1.191858424 1.065190589 1 21.08605966 4.737881154 6.261035563 1.132573467 0.576439829 0.809310489 0.077137787 0.049119782 10.54049568 0.018641089 0.11647813 54686.62902 -4.737881154 -0.556133638 ASPDS(ph)RHSPATISSSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 AS(0.001)PDS(0.588)RHS(0.329)PAT(0.012)IS(0.02)S(0.02)S(0.027)T(0.001)R;AS(0.1)PDS(0.449)RHS(0.449)PAT(0.002)ISSSTR 74.047 0.010829 91763000 97168 255198 208460 207402 229989 291360 179080 227358 194794 254940 TRUE FALSE 101004.2677 299026.2713 213892.6389 248425.4966 190895.5519 223696.0556 165043.2417 224310.6379 187783.402 304890.6119 0.331280347 0.980765756 0.701538947 0.814802053 0.62611161 0.733692829 0.541319527 0.735708576 0.615904179 1 18.2179322 -2.259371122 2.25925814 2.204572397 0.687542592 0.261306497 0.162490095 7400537.19 1176325.936 45557164.51 0.035839302 0.005503372 2.259371122 -1.517029805 ASPDSRHS(ph)PATISSSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPDSRHSPATISSSTR 17 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 ASPDS(0.004)RHS(0.996)PATISSSTR;ASPDS(0.012)RHS(0.975)PAT(0.009)IS(0.002)S(0.001)S(0.001)T(0.001)R 140.48 3.99E-07 620040000 193211 648540 570360 556040 595640 682670 432850 600250 492150 690510 TRUE FALSE 200839.1195 759921.7001 585224.0502 666023.0524 494393.3256 524130.2385 398922.086 592204.6306 474437.6176 825802.2139 0.243204869 0.920222406 0.708673385 0.806516429 0.59868249 0.634692218 0.483072192 0.717126475 0.574517251 1 19.65543676 -1.791366019 6.021929034 1.0196315 0.645731515 0.282003086 0.174971044 0.041728981 0.00144573 0.153296731 0.03677228 0.016167169 1.791366019 -0.373899985 ASPEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPEPQRENASPAPGTTAEEAMSR 24 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 ASPEPQRENAS(1)PAPGTTAEEAMSR 185.38 1.44E-17 500120000 249300 339180 314780 237410 324040 362320 236560 272040 302330 410890 TRUE FALSE 259142.5565 397431.5265 322983.4254 284368.9894 268959.7965 278176.671 218017.8091 268393.7488 291449.2024 491396.0285 0.527359892 0.808780502 0.65727724 0.578696149 0.547338157 0.566094667 0.443670271 0.546186239 0.593104513 1 18.90652667 0.913165861 18.28837452 1 0.582602117 0.653799873 0.090523043 1786.402427 376241.9714 0.093782524 0.023445631 8.187774279 -0.913165861 -0.417397884 ASPITNDGEDEFVPS(ph)DGLDKDEYTFSPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 ASPITNDGEDEFVPS(0.999)DGLDKDEY(0.001)TFSPGK 127.14 1.65E-11 0 214530 117220 151900 104650 216400 194850 214030 142070 158670 72630 TRUE FALSE 222999.8101 137351.6232 155858.6388 125349.4577 179616.4053 149599.0405 197253.7693 140165.784 152959.4977 86860.45791 2.567334037 1.581290572 1.794356633 1.443113019 2.067873111 1.72229164 2.270927118 1.613689214 1.760979638 1 16.40641194 0.538827234 1.211964095 1.000861245 1.872977842 0.40467299 0.321540432 1.675677648 3.343507237 0.286935442 0.086976198 3.458017872 -0.538827234 0.872116597 ASPNVEAPQPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASPNVEAPQPHR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 120.87 0.00038631 761610000 201560 243449 238183 243436 244893 281730 244491 229959 235332 257867 FALSE TRUE 209517.7444 285259.472 244390.2446 291586.9142 203266.1753 216302.4772 225327.1566 226876.7757 226862.4473 308391.1015 0.679389721 0.924992552 0.792468536 0.945510142 0.65911816 0.701390138 0.730653886 0.735678736 0.735632274 1 18.23440161 5.034008136 15.19914574 0.786511236 0.327216546 0.084992851 0.110380216 1807178.309 23773274.23 0.025719379 21618240.33 108145.4211 -5.034008136 -0.45929469 ASPRPWT(ph)PEDPWSLYGPSPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 AS(0.001)PRPWT(0.999)PEDPWSLYGPSPGGR;AS(0.014)PRPWT(0.986)PEDPWSLYGPSPGGR;AS(0.002)PRPWT(0.998)PEDPWSLYGPSPGGR;AS(0.032)PRPWT(0.968)PEDPWSLYGPSPGGR 200.47 2.66E-22 2143200000 793850 976150 973090 908810 961300 1020280 868680 887350 949420 898440 TRUE FALSE 825191.811 1143796.169 998449.5248 1088569.905 797898.5694 783335.4325 800590.5917 875456.5247 915250.5597 1074472.116 0.767997418 1.064519173 0.929246566 1.013120665 0.742595882 0.729042123 0.74510132 0.814778263 0.851814157 1 20.03519661 3.236889477 24.99999924 0.796983404 0.95131552 0.26735222 0.10272883 47.94616198 717271.8325 0.027562502 0.034628042 1725.39874 -3.236889477 0.154332116 ASPS(ph)PQPSS(ph)QPLQIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 AS(0.231)PS(0.769)PQPS(0.231)S(0.769)QPLQIHR 204.13 3.80E-11 197360000 157830 165410 157210 155780 187800 208950 192390 181980 194690 173040 TRUE FALSE 164061.2503 193817.8808 161307.0217 186592.819 155877.8231 160424.5292 177309.9691 179540.8558 187683.1449 206943.8749 0.792781378 0.936572203 0.779472317 0.901659057 0.753237191 0.775207912 0.856802208 0.867582362 0.90692776 1 17.65888002 1.019119685 1.232009289 0.998315933 0.828176183 0.491387912 0.054766293 0.396176352 1.241236 0.049826163 0.01549099 10.45008167 -1.019119685 -0.17013975 ASPS(ph)PQPSSQPLQIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 AS(0.236)PS(0.761)PQPS(0.003)SQPLQIHR;AS(0.005)PS(0.995)PQPSSQPLQIHR;AS(0.017)PS(0.982)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.001)PS(0.999)PQPSSQPLQIHR;AS(0.001)PS(0.999)PQPSSQPLQIHR;ASPS(1)PQPSSQPLQIHR;AS(0.026)PS(0.974)PQPSSQPLQIHR;AS(0.141)PS(0.859)PQPSSQPLQIHR 276.14 2.89E-35 18003360000 3443694 4177732 3894426 3774516 4255138 4663205 3619937 4010459 3791386 4020893 TRUE FALSE 3579653.698 4895224.973 3995917.941 4521103.999 3531851.163 3580246.31 3336196.879 3956705.357 3654934.758 4808709.999 0.744410393 1.017991306 0.830975031 0.940190612 0.73446957 0.74453363 0.693782091 0.82282054 0.760065539 1 22.19721849 3.236157702 24.99975299 0.77769419 0.889262028 0.148070154 0.102625826 91.92230532 956356.3462 0.026917216 0.033638106 1722.493939 -3.236157702 0.111567838 ASPS(ph)SPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.279)PS(0.361)S(0.361)PGRQDS(0.999)DEDDGPQRVEEVDQGR 55.871 0.041258 344970000 43912 60593 59735 63544 68490 67771 65736 66730 64834 61810 TRUE FALSE 45645.67967 70999.3764 61291.74317 76112.81354 56848.09426 52032.21233 60583.44055 65835.5935 62500.637 73920.48608 0.617497017 0.960483084 0.82915774 1.029657915 0.769043837 0.703894348 0.819575787 0.890627172 0.845511716 1 16.17368662 0.527443428 1.053074917 0.999595681 0.831181637 0.176046543 0.111857053 3.017616948 4.788291457 0.105101737 0.032909998 3.368553331 -0.527443428 -0.168414044 ASPSS(ph)PGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 AS(0.008)PS(0.45)S(0.542)PGRQDS(1)DEDDGPQR 134.76 5.18E-06 140170000 175100 177200 174910 211170 184020 218180 228780 193770 183490 153880 TRUE FALSE 182013.0832 207632.7216 179468.2983 252938.7957 152740.3461 167511.0015 210847.6258 191172.8301 176886.2307 184029.8398 0.989041144 1.128255732 0.975213033 1.374444471 0.829975977 0.910238262 1.145725204 1.038814305 0.961182333 1 17.48958019 ASPSSPGRQDS(ph)DEDDGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASPSSPGRQDSDEDDGPQR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;AS(0.057)PS(0.052)S(0.052)PGRQDS(0.84)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR;ASPSSPGRQDS(1)DEDDGPQR 223.97 1.26E-19 2444083000 1215635 1286674 1170813 1287521 1213727 1800050 1406309 1285118 1228764 1102573 TRUE FALSE 1263629.208 1507650.251 1201325.349 1542188.811 1007418.118 1382015.668 1296078.826 1267893.095 1184541.024 1318601.069 0.958310468 1.143371021 0.911060499 1.169564356 0.764005234 1.04809233 0.982919593 0.961544113 0.898331612 1 20.33057673 3.264412347 24.99999573 0.949591172 1.042953483 0.199159249 0.100618678 385.4305691 372729.241 0.025705454 0.0347936 1838.282897 -3.264412347 0.093362311 ASPSSPGRQDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASPSSPGRQDSDEDDGPQRVEEVDQGR 27 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 AS(0.001)PS(0.003)S(0.019)PGRQDS(0.978)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPS(0.003)S(0.066)PGRQDS(0.932)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR;ASPSS(0.001)PGRQDS(0.999)DEDDGPQRVEEVDQGR;AS(0.009)PS(0.009)S(0.009)PGRQDS(0.973)DEDDGPQRVEEVDQGR;ASPSSPGRQDS(1)DEDDGPQRVEEVDQGR 179.54 1.51E-17 5293890000 813303 985083 958201 859078 1040551 1165637 780061 928127 981160 1109693 TRUE FALSE 845412.8304 1154263.342 983172.5052 1029001.064 863678.5127 894935.4721 718917.7805 915686.9757 945848.2433 1327116.097 0.637030048 0.869753102 0.740833833 0.775366275 0.650793487 0.674346031 0.54171431 0.68998257 0.712709495 1 20.33986315 0.750885071 5.051488669 0.999999663 0.697008068 0.54446841 0.082652745 7.493863538 151.5991339 0.083608959 0.021125125 5.63488518 -0.750885071 -0.302991595 ASPVPSDPEKPGT(ph)PGEGMLSSDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASPVPSDPEKPGTPGEGMLSSDLDR 25 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 ASPVPSDPEKPGT(1)PGEGMLSSDLDR 161.11 3.43E-11 81765000 233860 159030 189380 148080 252080 218790 226390 199560 223550 151170 TRUE FALSE 243092.9734 186342.1654 194315.3984 177369.782 209231.5316 167979.3383 208644.9602 196885.2246 215504.4792 180788.8672 1.344623578 1.030717037 1.074819492 0.981087966 1.157325309 0.929146473 1.154080799 1.089034008 1.192022952 1 17.46394631 4.743777549 24.833137 1.071199633 1.344623704 0.517777877 0.080139758 392.5796534 1868656.465 0.01786523 0.150746466 55434.16995 -4.743777549 0.273424071 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 ASQEPS(1)PKPGTEVIPAAPR;ASQEPS(1)PKPGTEVIPAAPR 203.79 2.96E-16 1011260000 756280 380500 464840 375170 641500 715500 588150 526700 590360 353850 TRUE FALSE 786138.5184 445847.9151 476954.1123 449377.5062 532458.0591 549335.9685 542049.2662 519640.448 569113.0589 423180.1326 1.857692405 1.053565328 1.127071135 1.061905963 1.258230286 1.298113796 1.280894882 1.227941503 1.344848246 1 18.69091237 4.746223144 24.98292242 1.196889136 1.857692725 0.763294289 0.112394116 453.5781711 1478812.28 0.027232825 0.290185813 55747.21095 -4.746223144 0.660803589 ASQSRPNS(ph)SALETLGGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 AS(0.003)QS(0.019)RPNS(0.938)S(0.039)ALETLGGEK 166.91 1.48E-11 118410000 66915 64561 67309 56062 103490 101360 95635 81829 94262 75952 TRUE FALSE 69556.85587 75648.84954 69063.12783 67150.89627 85898.80677 77820.67613 88138.8788 80732.2161 90869.52903 90833.34021 0.765763493 0.832831308 0.760327955 0.739275866 0.945674865 0.856741324 0.970336207 0.888794972 1.000398409 1 16.47093431 3.232798985 24.99996794 0.932730491 0.777696788 0.744042558 0.048322502 71.20010349 308940.2272 0.013298695 0.016306471 1709.224009 -3.232798985 -0.155033703 ASREEILAQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASREEILAQAK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 153.74 2.95E-05 993810000 1002050 871410 1072720 608640 1662480 1365330 792270 987750 1204100 1334080 FALSE TRUE 1041611.708 1021067.889 1100675.964 729027.1754 1379892.243 1048252.799 730169.8072 974510.8269 1160764.676 1595467.433 0.652856765 0.639980402 0.689876798 0.456936419 0.864882739 0.657019239 0.457652592 0.610799573 0.727538934 1 20.60554773 0.88177078 3.445369621 0.999785817 0.62592631 0.510106523 0.109691663 0.408596007 9.732372004 0.103650114 0.02680173 7.616768915 -0.88177078 -0.373859507 ASRVPS(ph)S(ph)DEEVVEEPQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASRVPSSDEEVVEEPQSR 18 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 AS(0.022)RVPS(0.99)S(0.988)DEEVVEEPQSR;AS(0.032)RVPS(0.973)S(0.995)DEEVVEEPQSR 99.838 0.00054736 425640000 210734 307600 302120 178151 334820 311220 162021 270710 263540 426060 TRUE FALSE 219053.941 360427.9072 309993.4954 213388.7361 277907.416 238943.8716 149321.3707 267081.5752 254055.2469 509538.2996 0.429906724 0.707361758 0.608381147 0.418788413 0.545410259 0.468941926 0.2930523 0.524163886 0.498598922 1 18.95883107 0.100045436 2.974068557 1.000000278 0.499445638 0.666819196 0.106156402 280.0614688 919.4504467 0.105420477 0.027558051 1.259057128 -0.100045436 -0.50055464 ASRYS(ph)IPDLAVDVEQVIGLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASRYSIPDLAVDVEQVIGLEK 21 1 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8;H0Y8N8 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 AS(0.293)RY(0.046)S(0.66)IPDLAVDVEQVIGLEK 60.379 0.034688 18740000 19932 15370 22306 17541 24558 26906 23645 22694 23844 17079 TRUE FALSE 20718.93075 18009.67794 22887.31268 21010.55745 20383.63993 20657.48926 21791.64312 22389.82405 22985.8591 20425.30305 1.014375684 0.881733695 1.120537239 1.028653401 0.99796022 1.011367577 1.066894482 1.096180751 1.125361961 1 14.31806986 2.177311376 3.704403202 1.083872943 1.00832856 0.195233006 0.061729225 0.335328664 9.301507336 0.024413758 0.01767369 150.4220061 -2.177311376 -0.075544384 ASS(ph)ESQIFELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSESQIFELNK 12 0 Q9BV36;Q9BV36-4 Q9BV36 MLPH Melanophilin 1 AS(0.039)S(0.961)ESQIFELNK;AS(0.025)S(0.975)ESQIFELNK 188.92 9.01E-06 126421000 374590 272400 329300 267700 499450 517160 436870 415410 456910 332730 TRUE FALSE 389379.1024 319182.581 337881.8285 320650.261 414553.6674 397057.4276 402626.9879 409842.1084 440465.8984 397922.073 0.978531046 0.802123337 0.849115572 0.805811697 1.041796109 0.997827099 1.011823709 1.029955703 1.106914967 1 18.6021264 3.231270255 24.99968726 1.029791146 0.8541417 0.711837899 0.053725191 84.3301263 289179.7896 0.014955528 0.018221392 1703.218068 -3.231270255 -0.175649446 ASS(ph)FADMMGILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 AS(0.001)S(0.999)FADMMGILK;AS(0.195)S(0.805)FADMMGILK 218.06 3.69E-11 410910000 1004440 957750 1144930 916910 1853880 1531560 1174730 1107240 1109280 1163280 TRUE FALSE 1044096.067 1122236.112 1174767.816 1098272.061 1538758.14 1175878.401 1082651.593 1092399.259 1069357.229 1391202.444 0.750499017 0.806666289 0.844426217 0.789440866 1.106063425 0.845224508 0.778212832 0.78521948 0.768656808 1 20.40790094 4.563889737 1.607776506 0.855727936 0.732747168 0.108804892 0.10318446 1.959087208 6.322579593 0.028767927 0.339722347 36634.4552 -4.563889737 -0.122980768 ASS(ph)FSGISILTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSFSGISILTR 12 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 AS(0.006)S(0.993)FS(0.001)GISILTR;AS(0.004)S(0.996)FSGISILTR 140.45 6.26E-05 76361000 141162 147228 184965 141752 256220 197433 187705 175232 196573 174131 TRUE FALSE 146735.1848 172513.2637 189785.3399 169790.1225 212667.8159 151582.1779 172992.1916 172883.3017 189498.3761 208248.6355 0.704615348 0.828400452 0.911340136 0.815324058 1.021220693 0.727890377 0.830700241 0.830177356 0.90996215 1 17.66794752 -4.999999999 0.215734145 1.779729813 0.821807323 0.262434623 0.084593327 217.4473372 2.173200274 73.48615069 0.165389725 1.00E-05 4.999999999 -0.95792249 ASS(ph)FSGISVLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSFSGISVLTR 12 0 Q15032-2;Q15032-4;Q15032;Q15032-3;H7C1X4;H7BZ47;H7C207 Q15032-2 R3HDM1 R3H domain-containing protein 1 1 AS(0.041)S(0.959)FSGISVLTR;AS(0.021)S(0.979)FS(0.001)GISVLTR 119.39 0.0005488 142291000 200571 254230 286700 235790 397700 312600 309540 277150 317100 340920 TRUE FALSE 208489.698 297892.0249 294171.6375 282428.5582 330099.0961 240003.3875 285277.446 273435.2576 305687.6329 407716.7467 0.511359172 0.730634754 0.721509822 0.69270777 0.809628495 0.588652268 0.699695189 0.670650053 0.749754911 1 18.63720769 -5 0.320640413 3.974690896 0.674921254 0.60354184 0.077563288 215.3194195 1.904573604 434.5690034 0.065421319 1.00E-05 5 -3.299769642 ASS(ph)HS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.198)S(0.578)HS(0.578)S(0.579)QT(0.067)QGGGSVTK 78.249 0.011442 76524000 24449 59780 61774 60421 36507 65990 40344 45096 58640 85419 TRUE FALSE 25414.2654 70046.74998 63383.88119 72372.09346 30301.55318 50664.82259 37181.73186 44491.56188 56529.55785 102155.2176 0.248780885 0.685689401 0.620466411 0.708452247 0.296622668 0.495959225 0.36397291 0.435529021 0.553369267 1 16.64040337 0.864823827 6.115810593 0.999998145 0.486941821 0.523413312 0.147374954 2.241027994 101.1545889 0.141617774 0.035596532 7.325273209 -0.864823827 -0.513056324 ASS(ph)HS(ph)SQTQGGGSVTKK ddPTM_MDA-MB-175_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(0.004)S(0.996)HS(0.659)S(0.337)QT(0.004)QGGGSVTKK 192.11 7.18E-10 548140000 491310 415810 566750 364330 804470 678310 582800 591980 652940 429820 TRUE FALSE 510707.2982 487222.1329 581519.9706 436393.3866 667726.4767 520782.7824 537118.6131 584045.4764 629440.8169 514034.9996 0.993526314 0.947838442 1.131284778 0.848956563 1.298990297 1.013127088 1.044906696 1.136197879 1.224509649 1 18.97150707 3.250408763 24.99987207 1.117008054 0.988853027 0.284293113 0.107835563 308.5998602 651149.1363 0.028502357 0.038289843 1779.953936 -3.250408763 -0.128155028 ASS(ph)HSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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 2 AS(0.006)S(0.994)HS(0.002)S(0.998)QT(0.001)QGGGSVTK;ASS(1)HSS(0.655)QT(0.345)QGGGSVTK;AS(0.037)S(0.959)HS(0.046)S(0.958)QTQGGGSVTK;AS(0.155)S(0.845)HS(0.004)S(0.996)QTQGGGSVTK;AS(0.002)S(0.998)HSS(0.967)QT(0.033)QGGGSVTK;AS(0.162)S(0.803)HS(0.228)S(0.798)QT(0.008)QGGGSVTK;AS(0.015)S(0.985)HS(0.246)S(0.752)QT(0.002)QGGGSVTK;AS(0.465)S(0.533)HS(0.19)S(0.727)QT(0.084)QGGGSVTK;AS(0.005)S(0.995)HS(0.045)S(0.955)QTQGGGSVTK 363.37 1.86E-88 22038364000 4526592 4383209 5484749 4404581 6634167 6641466 5961394 5805528 5884598 4352862 TRUE FALSE 4705305.347 5135991.049 5627686.065 5275793.975 5506493.663 5099086.174 5494124.361 5727714.393 5672812.467 5205721.968 0.903871812 0.986604947 1.081057747 1.013460574 1.057777134 0.979515657 1.055401036 1.100272821 1.089726363 1 22.31166683 4.559210701 2.891210178 1.050469437 0.901118391 0.578304759 0.037830784 0.216405542 3.056559325 0.009861926 0.060658158 36241.87855 -4.559210701 -0.149351046 ASS(ph)HSS(ph)QTQGGGSVTKK ddPTM_MDA-MB-175_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 2 AS(0.122)S(0.878)HS(0.002)S(0.998)QTQGGGSVTKK;AS(0.433)S(0.566)HS(0.004)S(0.995)QT(0.001)QGGGSVTKK 162.39 2.90E-09 889960000 623560 525740 710530 485130 1003920 843250 750030 774310 851550 559270 TRUE FALSE 648178.6303 616031.7553 729046.9955 581087.266 833274.037 647417.9671 691240.6888 763931.641 820902.8818 668848.2486 0.9690967 0.921033667 1.090003595 0.868787901 1.245834221 0.967959426 1.033479104 1.142159888 1.227338015 1 19.3513194 3.486545302 0.637182173 1.112526561 0.936255631 0.190069652 0.108479846 1.617746643 1.267095845 0.063603704 0.171295021 3065.810459 -3.486545302 -0.17627093 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_MDA-MB-175_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(0.001)S(0.999)HS(0.015)S(0.489)QT(0.496)QGGGSVTK 321.67 1.91E-57 9529700000 806050 835160 1018200 885080 1346400 1302400 1115400 1141600 1139200 867350 TRUE FALSE 837873.4764 978592.2334 1044735.128 1060146.182 1117539.409 999937.3381 1027972.033 1126298.719 1098200.415 1037290.626 0.807751902 0.943411816 1.007176872 1.022033898 1.077363837 0.963989564 0.991016411 1.08580825 1.05872008 1 19.98438873 4.807525354 1.330212519 1.032691129 0.683091954 0.776043755 0.036254556 0.720913377 1.002012633 0.010618806 0.355567727 64198.56989 -4.807525354 -0.349599175 AAPHKAEGLEEADTGASGCHSHPEEQPTSIS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AAPHKAEGLEEADTGASGCHSHPEEQPTSISPSR 34 1 Q9BV36-2;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 AAPHKAEGLEEADTGASGCHSHPEEQPT(0.002)S(0.041)IS(0.953)PS(0.003)R;AAPHKAEGLEEADTGASGCHSHPEEQPT(0.023)S(0.391)IS(0.58)PS(0.006)R 298.43 3.07E-90 1097470000 211282 331515 384934 212111 491567 503145 279215 438345 441513 568878 TRUE FALSE 219623.5765 388450.1224 394965.6963 254065.9227 408010.6169 386297.199 257329.3987 432469.7023 425623.0334 680338.7523 0.322815033 0.570965745 0.5805427 0.373440322 0.599716855 0.567801257 0.378237162 0.635668189 0.625604571 1 19.37589374 0.639443842 0.918372022 1.001154412 0.493852629 0.70310452 0.098923908 0.621845461 0.88916045 0.09075158 0.029889687 4.359571872 -0.639443842 -0.507301783 ASS(ph)KGGGGYTCQSGSGWDEFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSKGGGGYTCQSGSGWDEFTK 22 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 AS(0.16)S(0.826)KGGGGY(0.001)T(0.014)CQSGSGWDEFTK 89.723 0.00089408 0 91747 51048 67781 43430 92952 82879 82388 67907 82338 44016 TRUE FALSE 95369.2424 59815.0969 69547.42854 52020.32437 77152.05224 63631.60829 75930.21328 66996.81774 79374.67146 52640.09246 1.811722547 1.136303036 1.321187431 0.988226311 1.465651913 1.208805025 1.442440728 1.272733664 1.507874849 1 15.6838744 4.747996203 24.40155996 1.27526573 1.811722948 0.473249406 0.173869818 758.5665123 1961686.059 0.038150944 0.473910829 55975.27071 -4.747996203 0.536457219 ASS(ph)LEDLVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 AS(0.058)S(0.942)LEDLVLK;AS(0.002)S(0.998)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK;ASS(1)LEDLVLK 302.09 1.45E-32 6173393000 6735050 4719750 6068780 5055570 7849360 7504730 7031910 5767630 6171810 4151310 TRUE FALSE 7000954.975 5530330.348 6226937.392 6055546.657 6515128.591 5761870.193 6480730.52 5690324.354 5949687.764 4964679.713 1.410152392 1.11393497 1.254247555 1.219725543 1.312295851 1.160572389 1.305367293 1.146161421 1.198403141 1 22.24326922 -0.03429616 0.410368698 0.959933241 1.256200145 0.463049288 0.080807763 3.930525176 0.85944551 0.324629451 0.049223818 0.924067805 0.03429616 0.296266904 ASS(ph)LGEIDESSELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ASS(1)LGEIDESSELR;ASS(1)LGEIDESSELR;AS(0.001)S(0.999)LGEIDESSELR;AS(0.001)S(0.999)LGEIDESSELR;ASS(1)LGEIDESSELR 350.18 7.21E-82 2138500000 1473150 1583550 1587960 1582060 1824210 1944310 1710440 1578530 1611660 1598420 TRUE FALSE 1531311.1 1855512.394 1629343.542 1894986.746 1514131.436 1492773.469 1576371.243 1557372.387 1553656.671 1911599.795 0.801062599 0.970659444 0.852345531 0.991309348 0.792075538 0.780902714 0.824634553 0.814695833 0.81275206 1 20.86634909 3.210244613 24.99975281 0.824080732 0.904938381 0.137573748 0.077063872 309.9220267 273624.4779 0.020349334 0.024326595 1622.723826 -3.210244613 0.080857649 ASS(ph)LNENVDHSALLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASSLNENVDHSALLK 15 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 AS(0.026)S(0.974)LNENVDHSALLK;AS(0.123)S(0.877)LNENVDHSALLK;AS(0.088)S(0.912)LNENVDHSALLK 299.43 2.09E-44 1528490000 1163270 945300 1399170 901170 1504520 1475760 1414690 1292410 1500770 1022880 TRUE FALSE 1209196.798 1107647.922 1435633.52 1079418.736 1248782.228 1133037.105 1303802.901 1275087.358 1446757.581 1223293.752 0.988476232 0.905463565 1.173580358 0.88238719 1.020835941 0.926218338 1.065813423 1.042339468 1.182673891 1 20.22233945 2.128764216 8.387596273 1.073222784 0.985243887 0.204410128 0.086881541 0.407929335 28.81054466 0.0309091 0.022813988 134.5129866 -2.128764216 -0.087978897 ASS(ph)LNFLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 AS(0.001)S(0.999)LNFLNK;ASS(1)LNFLNK;AS(0.003)S(0.997)LNFLNK;AS(0.001)S(0.999)LNFLNK;AS(0.001)S(0.999)LNFLNK;AS(0.001)S(0.999)LNFLNK;ASS(1)LNFLNK;AS(0.003)S(0.997)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK;ASS(1)LNFLNK 236.23 3.35E-10 26361136000 24709585 20836504 24825960 19293112 31142280 29113000 27462802 24656622 27013008 20280852 TRUE FALSE 25685138.5 24415011.48 25472944.91 23109231.97 25848726.37 22351946.96 25310195.82 24326140.31 26040815.12 24254496.65 1.058984603 1.006617941 1.050235974 0.952781346 1.065729244 0.921558888 1.043525915 1.00295383 1.073648961 1 24.5317489 -1.460202816 2.914110922 0.999557732 1.016602971 0.011560777 0.04765757 5639520.597 8144439.887 20084.62195 0.010330145 0.034657496 1.460202816 0.017045239 ASS(ph)LNVLNVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ASSLNVLNVGGK 12 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;AS(0.021)S(0.979)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK;ASS(1)LNVLNVGGK 294.31 3.40E-36 26517618000 19380670 15077270 18650840 14700280 22383880 21602400 20873260 18455360 19546240 13964630 TRUE FALSE 20145833.82 17666673.84 19136896.21 17607951.51 18579076.07 16585569.99 19237159.34 18207996.09 18842774.64 16700731.88 1.206284489 1.057838301 1.145871711 1.054322148 1.112470771 0.993104381 1.151875228 1.090251386 1.128260413 1 23.99340799 -0.194999942 0.010555769 4.43E-07 2.118183095 0.223487207 0.057159188 5643.259935 16.38749854 1714.162116 1574.305584 0.638263571 0.194999942 2.118182652 ASS(ph)LSESSPPK ddPTM_MDA-MB-175_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(0.994)LS(0.006)ESSPPK;AS(0.012)S(0.964)LS(0.016)ES(0.007)S(0.001)PPK 142.97 3.92E-05 646810000 1004510 815720 1167110 812520 1343000 1198730 1261130 1001440 1336300 811890 TRUE FALSE 1044168.83 955813.5646 1197525.845 973234.0309 1114717.34 920343.1244 1162279.335 988017.3348 1288206.824 970964.3009 1.075393636 0.984396196 1.233336637 1.002337604 1.148051827 0.947865049 1.197036116 1.017562988 1.326729338 1 19.88905873 ASS(ph)PCPEFEQFQIVPAVETPYLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPCPEFEQFQIVPAVETPYLAR 24 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 AS(0.199)S(0.801)PCPEFEQFQIVPAVETPYLAR 101.41 0.002428 122330000 105380 120760 109400 121920 118270 142570 114700 118110 127050 115150 TRUE FALSE 109540.4838 141499.5906 112251.0539 146035.4121 98166.50764 109460.2782 105709.5143 116526.9286 122477.4953 137711.4378 0.7954349 1.027507902 0.81511787 1.060445047 0.712842079 0.794852482 0.767616082 0.846167395 0.889377798 1 17.07128886 ASS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSPFR 6 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.031)S(0.969)PFR;AS(0.017)S(0.983)PFR 116.9 0.024312 3585900000 3157600 3520000 3540800 3506000 3738700 4173800 4185800 3432100 3203300 3200900 TRUE FALSE 3282264.486 4124532.618 3633076.157 4199476.336 3103197.109 3204498.205 3857706.058 3386098.313 3088013.859 3828055.07 0.857423529 1.077448611 0.949065802 1.097026103 0.81064589 0.8371087 1.007745706 0.884547963 0.806679581 1 21.86818015 3.232340157 24.99838127 0.89092186 0.997814753 0.244543627 0.089606902 203.987032 819769.4886 0.024728889 0.030256418 1707.419185 -3.232340157 0.106892893 ASS(ph)PFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPFRR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 AS(0.276)S(0.724)PFRR 72.638 0.028347 0 366260 652090 624140 650730 557250 702390 544920 649160 590830 721540 TRUE FALSE 380720.2276 764081.3849 640405.6011 779442.4518 462528.844 539270.5673 502207.7465 640459.072 569566.1437 862911.9483 0.441204028 0.885468542 0.742144784 0.903269972 0.536009317 0.624942752 0.581991879 0.742206749 0.660051289 1 19.71885383 -1.361282943 3.994905216 1.000875198 0.688116889 0.324101709 0.138284884 0.001035592 0.000165573 0.12855513 0.030217895 0.043522823 1.361282943 -0.312758309 ASS(ph)PGYIDSPTYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPGYIDSPTYSR 14 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 AS(0.002)S(0.998)PGYIDSPTYSR 195.87 2.69E-08 132740000 162890 188670 195480 217180 202650 237710 219720 208290 190150 188790 TRUE FALSE 169321.023 221072.6049 200574.3694 260137.5558 168203.6254 182505.455 202497.7723 205498.2132 183306.5386 225779.7859 0.749938806 0.97915145 0.888362829 1.152173808 0.744989746 0.808333901 0.896881762 0.910170999 0.811881976 1 17.7845568 4.75785815 23.10242726 0.905601462 0.749938401 0.160921333 0.10934036 2873.398842 3439787.677 0.025557796 0.826830754 57260.8974 -4.75785815 -0.15566306 ASS(ph)PNSTVSNTSTEGFGGIMSFASSLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSPNSTVSNTSTEGFGGIMSFASSLYR 28 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 AS(0.076)S(0.561)PNS(0.117)T(0.117)VS(0.117)NT(0.013)STEGFGGIMSFASSLYR 197.1 3.56E-25 24427000 23671 13865 18375 15019 25073 20108 23460 17037 22759 13971 TRUE FALSE 24605.54936 16246.2059 18853.8676 17989.71337 20811.10042 15438.22174 21621.1439 16808.64688 21939.90804 16708.34996 1.472649868 0.972340532 1.128409905 1.076690003 1.245550905 0.923982427 1.294032262 1.006002802 1.313110396 1 14.02828165 4.752756388 24.21833428 1.109148425 1.472650256 0.412829221 0.130907591 1449.058491 2472063.248 0.027639212 0.56735775 56592.17536 -4.752756388 0.363501831 ASS(ph)PPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASSPPDR 7 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.183)S(0.817)PPDR;AS(0.043)S(0.957)PPDR;AS(0.004)S(0.996)PPDR 124.95 0.0042969 1439340000 834590 895250 901920 941540 918850 1058960 1137070 1005950 920740 824740 TRUE FALSE 867540.2576 1049002.223 925424.7761 1127773.802 762664.2052 813032.5887 1047943.482 992466.8857 887602.7473 986332.0124 0.879562102 1.063538657 0.938248748 1.143401803 0.773232741 0.824299099 1.062465244 1.006219887 0.899902605 1 19.91171383 -0.399833778 11.47340334 1 0.961793925 0.011323809 0.110022236 0 0 0.104756352 0.024691309 0.398259571 0.399833778 -0.038206075 ASS(ph)PPDRIDIFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASSPPDRIDIFGR 13 1 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 AS(0.169)S(0.831)PPDRIDIFGR;AS(0.098)S(0.902)PPDRIDIFGR;AS(0.145)S(0.855)PPDRIDIFGR;AS(0.496)S(0.504)PPDRIDIFGR 180.74 7.66E-06 19658920000 1979730 2237090 2256220 1949520 2716270 2749120 2152270 2308740 2315690 2666310 TRUE FALSE 2057891.269 2621292.805 2315018.947 2335129.237 2254559.396 2110678.543 1983569.453 2277795.117 2232348.769 3188722.395 0.645365452 0.822051117 0.726002035 0.732308727 0.707041604 0.661919817 0.622057742 0.714328447 0.700076235 1 21.60454707 -1.763321645 5.193729411 1.01743119 0.704491238 0.74361677 0.052233213 0.010872705 0.000495469 0.052157351 0.012113305 0.017245602 1.763321645 -0.312939952 ASS(ph)RPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.092)S(0.562)RPGS(0.336)PT(0.009)ADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 260.92 5.97E-68 281720000 111410 85632 108410 89162 123710 128880 132050 104830 113330 69464 TRUE FALSE 115808.5528 100338.6299 111235.2537 106797.9775 102681.8184 98949.5732 121699.576 103424.9253 109251.2754 83074.14083 1.394038526 1.207820254 1.338987711 1.285574264 1.236026245 1.191099567 1.464951364 1.244971351 1.315105692 1 16.34211185 -1.154416409 4.692964165 0.999968311 1.294585789 0.54863521 0.080942912 2.49E-05 4.48E-06 0.072593264 0.017108558 0.070078305 1.154416409 0.294617478 ASS(ph)RS(ph)PVFTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 2 AS(0.451)S(0.568)RS(0.981)PVFTPR;AS(0.434)S(0.566)RS(1)PVFTPR 95.067 0.0045718 904940000 517520 503710 545430 532810 682820 697320 568330 558280 537600 493870 TRUE FALSE 537952.0892 590218.2742 559644.3539 638198.2277 566754.5003 535377.998 523782.8095 550797.1698 518251.881 590634.3708 0.910803901 0.999295509 0.947530963 1.08053012 0.959569115 0.906445721 0.886813967 0.932551841 0.877449581 1 19.17190579 2.919020564 5.307782486 0.915891064 0.987047472 0.255098877 0.051103688 0.268021112 12.93855943 0.015023744 0.016133081 829.8900618 -2.919020564 0.071156408 ASS(ph)SAESEDLAVHLYPGAVTIQGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSSAESEDLAVHLYPGAVTIQGVLR 26 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 AS(0.112)S(0.443)S(0.443)AES(0.001)EDLAVHLYPGAVTIQGVLR 119.01 0.00030504 37259000 15331 18860 21302 21031 21239 28025 20143 20104 20942 24237 TRUE FALSE 15936.27972 22099.05829 21857.14762 25190.86903 17628.80237 21516.61847 18564.13903 19834.53876 20188.30151 28985.7761 0.549796551 0.762410439 0.754064598 0.86907692 0.60818804 0.742316452 0.640456856 0.68428524 0.696489942 1 14.82305749 -1.695375855 2.630677634 1.04682814 0.703575274 0.527694572 0.084885384 12067997.71 10062763.13 3753662.536 0.020725033 0.020166203 1.695375855 -0.343252866 ASS(ph)VTTFTGEPNTCPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASSVTTFTGEPNTCPR 16 0 P52943;H0YFA4;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 1 ASS(0.988)VT(0.011)TFTGEPNTCPR;AS(0.002)S(0.998)VTTFTGEPNTCPR;AS(0.001)S(0.885)VT(0.113)T(0.001)FTGEPNTCPR;AS(0.002)S(0.923)VT(0.075)TFTGEPNTCPR;ASS(0.986)VT(0.013)TFTGEPNTCPR;ASS(0.984)VT(0.016)TFTGEPNTCPR;AS(0.134)S(0.866)VTTFTGEPNTCPR 391.87 1.73E-121 4905865000 2553683 2686464 3784645 3258585 4096792 3290232 3130732 2937537 3578901 2956087 TRUE FALSE 2654504.377 3147843.294 3883275.958 3903123.387 3400420.759 2526125.482 2885337.045 2898164.121 3450097.052 3535275.65 0.750862066 0.890409576 1.098436541 1.104050652 0.961854491 0.714548378 0.816156173 0.819784483 0.975906094 1 21.75339128 2.96066552 24.74173849 0.846464151 0.974126759 0.121266742 0.121880865 793.0619568 498842.9985 0.038774958 0.041134017 913.409491 -2.96066552 0.127662608 ASSDIVSLAGPSAGPGS(ph)SEGGCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSDIVSLAGPSAGPGSSEGGCSR 24 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 ASSDIVSLAGPS(0.05)AGPGS(0.916)S(0.032)EGGCS(0.001)R 132.83 1.18E-09 0 29747 36541 36139 38952 34125 38674 38989 33823 35581 32758 TRUE FALSE 30921.43453 42816.6325 37080.81203 46656.58934 28324.44469 29692.54961 35932.9403 33369.65801 34300.44676 39176.30291 0.789289245 1.092921724 0.946511265 1.190939059 0.72299943 0.757921177 0.917211111 0.851781703 0.875540677 1 15.25769364 3.224929996 24.99993761 0.8472525 1.007029825 0.272351599 0.120307629 282.3941676 517938.4595 0.033271881 0.039967474 1678.533434 -3.224929996 0.159777325 ASSEGGTAAGAGLDSLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSEGGTAAGAGLDSLHK 18 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 165.16 2.89E-11 221390000 151820 150900 184040 139190 200540 194760 191370 192280 179130 124370 FALSE TRUE 157813.9708 176815.9012 188836.2336 166721.3666 166452.2824 149529.9416 176369.9193 189702.8011 172683.1463 148737.9203 1.061020421 1.188774865 1.269590386 1.120906936 1.119097821 1.005324946 1.185776425 1.275416523 1.160989383 1 17.18241298 0.895714426 20.90645747 1 1.162047458 0.245321606 0.080000666 64018.07278 12833964.91 0.08297527 0.020743818 7.865284316 -0.895714426 0.162047457 ASSGDIGS(ph)LDYQEFVVDIESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSGDIGSLDYQEFVVDIESR 21 0 J3KN59 J3KN59 BNIP2 1 ASSGDIGS(1)LDYQEFVVDIESR;ASSGDIGS(1)LDYQEFVVDIESR 167.61 1.25E-11 51547000 31492 31077 36513 31272 41041 42141 36313 39423 39072 40018 TRUE FALSE 32735.32848 36414.233 37464.55878 37457.50826 34064.86548 32354.3914 33466.69217 38894.59917 37665.80635 47858.76091 0.683998663 0.760868696 0.78281506 0.78266774 0.711779094 0.676039053 0.699280373 0.81269549 0.787020091 1 15.54649542 0.655860895 1.049484334 0.999233576 0.734172385 0.785754663 0.041409267 0.534749589 0.970887547 0.042465672 0.01346531 4.527525399 -0.655860895 -0.265061192 ASSHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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 1 ASS(0.045)HS(0.475)S(0.475)QT(0.005)QGGGSVTK 240.66 7.51E-20 882590000 45370 149670 158330 152300 184500 234040 155690 197770 173150 164670 TRUE FALSE 47161.24263 175374.6582 162456.2099 182424.4854 153138.7559 179687.7569 143486.611 195119.2166 166918.3653 196933.9337 0.239477482 0.89052534 0.824927461 0.92632327 0.777614873 0.912426587 0.728602777 0.990785148 0.847585595 1 17.5873522 4.739480137 24.98723973 0.873750962 0.239477282 0.844324268 0.082192069 25.53008366 693656.1155 0.017895833 0.108761308 54888.34509 -4.739480137 -0.634273679 RPS(ph)QGPPARS(ph)PSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RPS(0.497)QGPPARS(0.497)PS(0.497)QDFS(0.497)FIEDT(0.011)EILDSAMYR 69.766 0.0034918 18031000 5877.2 9391.1 10892 8767.2 14275 12657 9065.1 10110 11194 16656 TRUE FALSE 6109.236394 11003.94837 11175.85447 10501.32599 11848.5406 9717.603569 8354.553775 9974.491987 10791.13013 19919.4243 0.306697438 0.552423012 0.561053086 0.527190236 0.594823446 0.487845603 0.419417431 0.500741981 0.541739056 1 14.28188833 0.645929558 2.848803506 0.999989127 0.498986438 0.791026609 0.077545784 1.697384798 13.15198413 0.07307365 0.019207516 4.425165913 -0.645929558 -0.50100269 ASSHSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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 1 AS(0.003)S(0.021)HS(0.081)S(0.884)QT(0.011)QGGGSVTK 256.89 1.24E-26 8983100000 53087 264180 295080 273640 292630 392870 269370 353790 282880 290560 TRUE FALSE 55182.91575 309550.86 302770.0272 327765.1753 242888.8571 301631.8965 248256.0755 349048.0237 272699.2041 347489.6689 0.158804479 0.890820326 0.871306558 0.94323718 0.698981521 0.868031264 0.714427213 1.004484608 0.784769242 1 18.40661056 4.740009671 24.98430628 0.861546556 0.158804247 0.815520937 0.100615368 47.30979169 815626.7086 0.022586351 0.142488993 54955.3111 -4.740009671 -0.702742309 ASSHSSQT(ph)QGGGSVTK ddPTM_MDA-MB-175_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(0.06)S(0.06)HS(0.242)S(0.242)QT(0.397)QGGGSVTK;ASSHSSQT(0.522)QGGGS(0.478)VTK 137.52 0.00012964 186867000 48764 500563 334610 427508 178970 383142 186839 293974 273225 794787 TRUE FALSE 50689.24037 586530.8014 343330.2115 512067.8064 148548.7433 294163.0771 172194.071 290033.7594 263391.6856 950510.2955 0.05332845 0.617069383 0.3612062 0.538729363 0.15628315 0.309479107 0.181159606 0.30513479 0.277105558 1 19.85834273 -1.243050782 4.126871327 1.000475118 0.317106401 0.624401421 0.160238991 37179162.59 22576210.71 161194.3142 0.035727857 0.057141182 1.243050782 -0.683368718 ASSHSSQTQGGGS(ph)VTK ddPTM_MDA-MB-175_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 ASSHSSQTQGGGS(0.999)VT(0.001)K;ASSHSSQTQGGGS(1)VTK;ASSHSSQT(0.001)QGGGS(0.998)VT(0.001)K;ASSHSSQTQGGGS(0.999)VT(0.001)K;ASSHSSQTQGGGS(0.998)VT(0.001)K 191.4 4.52E-10 781896000 151394.2 1254310 1069790 1081172 1083349 1512789 887069 1371603 1041207 1391509 TRUE FALSE 157371.3599 1469727.985 1097669.606 1295024.595 899201.7239 1161466.681 817538.2139 1353218.905 1003734.163 1664148.547 0.094565693 0.88317115 0.659598332 0.778190503 0.540337415 0.697934499 0.491265167 0.813159924 0.603151783 1 20.66635279 -5 0.142238143 2.220176441 0.513824418 0.261072324 0.205203739 197.5326353 1.710692855 68.70641978 1.121376549 1.00E-05 5 -1.706352023 ASSHSSQTQGGGSVTK ddPTM_MDA-MB-175_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 0 82.663 0.0093654 59571000 4659.9 19376 16041 16486 17584 22908 15500 20311 17920 19702 FALSE TRUE 4843.87645 22703.67728 16459.04164 19746.88159 14595.07796 17587.96417 14285.0695 20038.76427 17275.0627 23562.22968 0.205578017 0.963562345 0.69853498 0.838073555 0.619426861 0.746447361 0.606269852 0.850461291 0.733167571 1 14.52418845 -5 0.040841497 2.219437845 2.43E-13 0.252340842 0.184910389 1262.383819 3.849105945 190.4556734 55.91146267 1.00E-05 5 -2.219437845 ASSIIDELFQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASSIIDELFQDR 12 0 E7ERK6;H0YC35;H0YLK8;P10909-4;P10909-6;P10909;P10909-5;P10909-2;P10909-3 E7ERK6 CLU Clusterin;Clusterin;Clusterin beta chain;Clusterin alpha chain 0 ; 234.9 3.48E-06 17891000 50061 64762 58469 61328 63812 72761 53087 64722 58999 69886 FALSE TRUE 52037.44694 75884.36972 59992.75017 73458.49535 52965.25903 55863.36045 48925.90222 63854.50745 56875.63751 83578.82365 0.622615211 0.907937758 0.717798451 0.878912769 0.633716254 0.668391322 0.585386347 0.764003424 0.680502967 1 16.35084983 -1.127633532 3.751264355 1.000146184 0.721462171 0.412750802 0.100929622 25956507.75 38199146.59 44613.46869 0.023749004 0.074536066 1.127633532 -0.278684014 ASSNKDFT(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSNKDFTPNR 11 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 AS(0.009)S(0.007)NKDFT(0.984)PNR 74.853 0.064161 473880000 2224200 1411700 1803900 1282100 2451300 2366300 2051100 1957000 2197000 1448400 TRUE FALSE 2312013.133 1654148.493 1850911.116 1535695.553 2034628.902 1816762.687 1890329.422 1930769.616 2117930.399 1732186.249 1.334737033 0.954948404 1.068540474 0.886564914 1.174601694 1.048826411 1.091296865 1.114643196 1.222692075 1 20.72416263 1.844130626 2.935471079 1.12605693 1.06786436 0.007364345 0.124099475 0.996895852 15.34543512 0.064698938 0.032895256 69.84424481 -1.844130626 -0.05819257 ASSPHGLGSPLVAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASSPHGLGSPLVASPR 16 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 ASSPHGLGSPLVAS(1)PR;ASSPHGLGSPLVAS(1)PR;ASSPHGLGSPLVAS(1)PR 133.45 2.17E-05 489110000 239128 465473 383349 414677 378232 509887 374259 437097 357728 513094 TRUE FALSE 248568.9581 545414.3669 393339.3899 496698.8729 313940.2597 391473.4717 344923.6016 431238.4297 344853.4392 613624.9455 0.405082877 0.888839952 0.641009452 0.809450262 0.511615869 0.63796864 0.56210818 0.702771999 0.56199384 1 19.22699761 -1.52771145 3.284058751 1.00995229 0.64587499 0.3981612 0.133854987 43151416.19 56113220.68 3847610.29 0.03039342 0.029668019 1.52771145 -0.3640773 ASSPS(ph)PLTIGTPESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR;ASSPS(1)PLTIGTPESQR 381.02 3.55E-105 1541030000 847660 937690 899810 996990 903780 1086270 975790 905450 848400 823940 TRUE FALSE 881126.2713 1098730.963 923259.7878 1194191.646 750155.7984 834000.2551 899305.03 893313.9238 817866.2497 985375.2677 0.894203762 1.115038097 0.936962615 1.211915587 0.761289453 0.846378311 0.912652326 0.906572301 0.830004848 1 19.91031374 3.224972657 24.99999924 0.875112716 1.037597251 0.388305613 0.100441519 226.4729649 416678.6526 0.027139857 0.032605522 1678.698324 -3.224972657 0.162484535 ASSRPGS(ph)PTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 45 1 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.005)S(0.005)RPGS(0.987)PT(0.004)ADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHK 339.99 1.31E-134 152230000 36986 23005 30615 31582 37113 41110 39417 36970 34528 25131 TRUE FALSE 38446.23584 26955.9298 31412.85205 37828.82534 30804.54552 31562.82553 36327.39254 36474.47762 33285.34402 30054.93829 1.279198629 0.896888542 1.045181053 1.258655898 1.024941233 1.050171031 1.208699622 1.213593496 1.107483359 1 14.87531444 2.245201157 24.97934 1.159118785 1.085944361 0.005035043 0.119579313 418.0161966 1572429.789 0.040986073 0.033558579 175.8738039 -2.245201157 -0.073174425 ASSRPGS(ph)PTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFK 48 2 H0Y9C1;H0Y9Z5;Q96LI5-2;Q96LI5 H0Y9C1 CNOT6L CCR4-NOT transcription complex subunit 6-like 1 AS(0.137)S(0.137)RPGS(0.553)PT(0.171)ADPNS(0.002)IPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFK 144.18 2.05E-15 127690000 166690 104600 151980 82524 218940 179180 134060 140480 176160 118550 TRUE FALSE 173271.0499 122564.2363 155940.7237 98847.00089 181724.657 137568.1605 123552.0269 138597.0954 169820.036 141777.6027 1.222132739 0.864482358 1.099896744 0.697197576 1.281758568 0.97030954 0.871449542 0.977566927 1.197791702 1 17.11327012 1.276428163 24.96043597 1.098896278 0.988798431 0.051457181 0.169380776 390.9324439 257683.4097 0.104418322 0.03812779 18.89853603 -1.276428163 -0.110097847 ASSRS(ph)PVFTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASSRSPVFTPR 11 1 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 AS(0.003)S(0.002)RS(0.994)PVFTPR;ASSRS(0.999)PVFTPR;AS(0.001)S(0.002)RS(0.997)PVFTPR;AS(0.008)S(0.016)RS(0.976)PVFTPR;ASSRS(1)PVFTPR;AS(0.084)S(0.066)RS(0.849)PVFTPR;AS(0.16)S(0.127)RS(0.713)PVFTPR 133.48 9.74E-05 5846930000 867502 991506 1006035 952631 1103065 1196457 911560 1009024 882116 1123405 TRUE FALSE 901751.6488 1161789.443 1032253.099 1141058.568 915566.4053 918597.9942 840109.5453 995499.6837 850368.8175 1343514.701 0.671188524 0.864738913 0.768322891 0.849308584 0.681471073 0.683727535 0.625307296 0.740966722 0.632943441 1 20.35758068 3.225350048 24.98793781 0.707606972 0.792409903 0.049905062 0.111333515 463.5434594 876795.9149 0.029369277 0.035296913 1680.157703 -3.225350048 0.084802932 ASSS(ph)AESEDLAVHLYPGAVTIQGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSSAESEDLAVHLYPGAVTIQGVLR 26 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 AS(0.044)S(0.183)S(0.773)AESEDLAVHLYPGAVTIQGVLR 165.77 7.92E-12 34065000 34119 42401 41058 43740 42753 48431 42232 44089 47015 46680 TRUE FALSE 35466.04447 49683.04192 42128.00521 52391.64145 35485.86033 37183.63423 38921.74549 43498.05907 45322.93933 55826.05226 0.635295584 0.889961584 0.754629846 0.938480142 0.635650541 0.666062398 0.697196809 0.779171324 0.81186001 1 15.76865092 0.776869538 1.902501645 0.999653569 0.751810182 0.383199301 0.095825757 0.864250938 5.22195874 0.090490627 0.025247304 5.982318595 -0.776869538 -0.247843388 ASSSGPRS(ph)PLDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASSSGPRSPLDQR 13 1 O14646;O14646-2 O14646 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 AS(0.01)S(0.01)S(0.008)GPRS(0.973)PLDQR;AS(0.068)S(0.068)S(0.014)GPRS(0.849)PLDQR;AS(0.089)S(0.089)S(0.089)GPRS(0.734)PLDQR;AS(0.059)S(0.059)S(0.059)GPRS(0.824)PLDQR 112.34 0.00055028 2177970000 2807530 2928870 2770480 2707960 3206920 4376170 2872760 2945340 2768340 3052030 TRUE FALSE 2918373.452 3431880.639 2842680.985 3243586.406 2661808.884 3359870.839 2647585.565 2905862.535 2668707.984 3650016.844 0.799550681 0.940236932 0.778813114 0.888649709 0.729259343 0.920508311 0.725362561 0.796123048 0.731149498 1 21.79947169 3.633984812 1.431860145 0.806321021 0.859004959 0 0.094148701 1.475309212 5.922623855 0.027459557 0.060700574 4305.115547 -3.633984812 0.052683938 ASSTST(ph)PEPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 ASST(0.001)S(0.116)T(0.883)PEPTR;ASST(0.001)S(0.104)T(0.895)PEPTR;ASSTS(0.265)T(0.734)PEPTR;ASST(0.001)S(0.125)T(0.874)PEPTR;ASST(0.001)S(0.045)T(0.954)PEPTR;ASSTS(0.001)T(0.998)PEPTR 272.65 5.06E-26 8013440000 4842010 5478430 5002410 4996500 5179440 6254210 4783430 4858620 4502600 4847810 TRUE FALSE 5033176.294 6419307.736 5132776.914 5984792.787 4299040.639 4801764.511 4408492.257 4793498.146 4340552.306 5797645.553 0.868141429 1.107226663 0.885320923 1.032279868 0.741514913 0.828226643 0.760393546 0.826800828 0.748675004 1 22.4670357 3.240545125 24.9998495 0.806938716 0.976532455 0.394229633 0.093924799 45.40491603 571982.2226 0.023852635 0.030744787 1739.983481 -3.240545125 0.169593739 ASSVGVLS(ph)PQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASSVGVLSPQKK 12 1 Q9UGU5 Q9UGU5 HMGXB4 HMG domain-containing protein 4 1 ASSVGVLS(1)PQKK 114.63 0.00063532 467200000 608150 278250 456100 264390 603430 477060 554120 406660 455010 220770 TRUE FALSE 632160.2316 326037.273 467986.3407 316685.5529 500859.1841 366270.0449 510686.6265 401209.3879 438634.279 264025.6546 2.394313661 1.23486967 1.772503287 1.19944993 1.897009535 1.387251725 1.934231078 1.519584862 1.661332039 1 18.01031859 -2.356346592 0.524814131 6.42E-10 1.651045967 0.253462216 0.342339768 184.691316 11.51662942 214.061555 0.136693062 0.004402034 2.356346592 1.651045966 ASSVSTKES(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASSVSTKESPAR 12 1 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASSVST(0.001)KES(0.999)PAR;ASSVSTKES(0.999)PAR;ASSVS(0.001)T(0.031)KES(0.969)PAR;ASSVSTKES(1)PAR;ASSVS(0.001)T(0.001)KES(0.999)PAR 256.4 9.52E-21 2296120000 3294240 2208750 2707010 2088662 3393350 3439200 3460830 2810430 3049270 2205350 TRUE FALSE 3424299.139 2588085.631 2777556.904 2501793.11 2816549.579 2640497.922 3189561.101 2772760.783 2939527.368 2637446.109 1.298338998 0.981284745 1.053123662 0.948566532 1.067907917 1.001157109 1.209336976 1.05130519 1.114535519 1 21.33071018 ASSVSTKES(ph)PARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASSVSTKESPARK 13 2 Q13428-4;Q13428;Q13428-3;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 ASS(0.001)VS(0.221)T(0.221)KES(0.557)PARK;ASSVS(0.155)T(0.155)KES(0.689)PARK;ASSVST(0.004)KES(0.996)PARK;ASSVSTKES(1)PARK 143.88 2.14E-05 2762660000 3198740 1653880 2145670 1664900 3284040 2822750 2628840 2288770 2656840 1628376 TRUE FALSE 3325028.725 1937921.025 2201587.923 1994212.251 2725820.054 2167209.092 2422784.652 2258092.782 2561220.847 1947425.1 1.707397489 0.995119671 1.130512246 1.024025135 1.399704694 1.112858765 1.244096449 1.15952741 1.315183237 1 20.89313641 7.999380008 0.017852064 5.02E-06 2.699955885 0.112478956 0.197336045 11453.77775 15.77023564 913.0529711 1549.737132 99857343.48 -7.999380008 2.699950867 AST(ph)DNEELLQFPLELCSDSLPSHPFPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASTDNEELLQFPLELCSDSLPSHPFPPAK 29 0 Q86YS7;Q86YS7-5;H0YFC4;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AS(0.45)T(0.55)DNEELLQFPLELCSDSLPSHPFPPAK 221.65 6.66E-34 67927000 48617 47329 51662 42370 66394 70819 64711 52228 61040 44157 TRUE FALSE 50536.4367 55457.38758 53008.35416 50750.65954 55108.3716 54372.36052 59638.78273 51527.96909 58843.18232 52808.71871 0.956971461 1.050155901 1.00378035 0.961028042 1.043546841 1.029609539 1.129335916 0.975747383 1.114270214 1 15.68848852 3.118550754 8.994127145 1.047658839 0.997908146 0.230070837 0.049678063 0.437905936 32.5462518 0.013697162 0.016391152 1313.86503 -3.118550754 -0.049750693 AST(ph)PDWVSEGPQPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.002)T(0.998)PDWVSEGPQPGLR;AS(0.016)T(0.984)PDWVSEGPQPGLR;AS(0.001)T(0.999)PDWVSEGPQPGLR;AST(1)PDWVSEGPQPGLR;AS(0.004)T(0.996)PDWVSEGPQPGLR;AS(0.017)T(0.983)PDWVSEGPQPGLR;AS(0.006)T(0.994)PDWVSEGPQPGLR 401.25 1.10E-122 14113550000 2951920 3190399 3196969 3010946 3704093 4175310 3742833 3213670 3202202 2828431 TRUE FALSE 3068464.081 3738325.21 3280284.638 3606502.132 3074472.595 3205657.53 3449459.969 3170596.01 3086955.376 3382607.901 0.907129697 1.105160669 0.969750185 1.066189827 0.908905994 0.947688181 1.01976347 0.937322948 0.912596277 1 21.68970452 3.235777882 24.99999689 0.95452143 1.015685853 0.184933182 0.059124211 113.4870279 1019563.175 0.015788193 0.019668725 1720.988157 -3.235777882 0.061164423 AST(ph)PDWVSEGPQPGLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ASTPDWVSEGPQPGLRR 17 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AS(0.03)T(0.97)PDWVSEGPQPGLRR;AS(0.005)T(0.995)PDWVSEGPQPGLRR;AS(0.019)T(0.981)PDWVSEGPQPGLRR;AS(0.004)T(0.996)PDWVSEGPQPGLRR;AS(0.001)T(0.999)PDWVSEGPQPGLRR 264.88 9.77E-28 8411910000 2737640 3744090 3389774 2515363 4321050 4488630 2308923 3113825 3301497 4615210 TRUE FALSE 2845724.141 4387108.333 3478114.295 3012894.294 3586559.464 3446213.708 2127943.582 3072089.269 3182676.768 5519472.036 0.515579049 0.794842025 0.630153441 0.545866393 0.649801184 0.624373796 0.3855339 0.556591147 0.57662703 1 22.39609884 -1.625916353 6.145578436 1.0020859 0.584803318 0.608739269 0.099419616 0.002941136 0.000179028 0.099642148 0.023388898 0.023663754 1.625916353 -0.417282582 AST(ph)PVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASTPVLK 7 0 Q04724;A0A669KBK8;A0A669KAE5;F6T2C8 Q04724 TLE1 Transducin-like enhancer protein 1 1 AS(0.071)T(0.929)PVLK;AS(0.076)T(0.924)PVLK 114.64 0.065504 782380000 3486900 2486600 2934800 2270300 3773100 3806200 3556400 3143300 3271300 2178900 TRUE FALSE 3624565.504 2913654.207 3011283.299 2719358.564 3131749.81 2922267.734 3277640.075 3101169.205 3153566.552 2605813.737 1.39095341 1.118136022 1.155601897 1.043573654 1.201831798 1.121441526 1.25781825 1.190096268 1.210204132 1 21.31330253 4.744145444 24.7409427 1.155309633 1.390953527 0.4892074 0.074853772 452.8813683 2006207.967 0.017218548 0.14900622 55481.14862 -4.744145444 0.235643895 ASTAS(ph)PCNNNINAATAVALQEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASTASPCNNNINAATAVALQEPR 23 0 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 AS(0.12)T(0.12)AS(0.76)PCNNNINAATAVALQEPR;AS(0.002)T(0.016)AS(0.982)PCNNNINAATAVALQEPR 284.86 1.86E-50 193470000 154966 167824 182239 181118 198690 217550 170380 185813 177033 204055 TRUE FALSE 161084.1773 196646.4665 186988.2981 216942.5998 164916.7448 167027.3095 157025.1704 183322.4807 170661.6169 244035.6704 0.660084557 0.80581034 0.766233468 0.888979056 0.675789505 0.684438096 0.643451714 0.751211822 0.699330621 1 17.89673251 -1.136009274 4.811135887 1.000018605 0.73306792 0.560534298 0.071533499 0.35682857 46777755.57 1731.305387 0.017074409 0.073112347 1.136009274 -0.266950685 ASTFCGT(ph)PDYIAPEILQGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.273)T(0.273)FCGT(0.455)PDYIAPEILQGLK 172.2 2.46E-11 143220000 124720 89262 159130 100390 241960 155240 174330 141980 180010 88014 TRUE FALSE 129644.0419 104592.0541 163277.0585 120246.8424 200831.7256 119187.8627 160665.5591 140076.9903 173531.4753 105258.6582 1.231671049 0.993666991 1.551198366 1.142393837 1.907982955 1.1323331 1.52638806 1.330788296 1.648619489 1 16.68357938 4.240263449 24.99956042 1.417279171 1.112668998 0.16396154 0.262836369 65.97163938 968461.1879 0.05803948 0.143068983 17388.55322 -4.240263449 -0.304610173 ASTRS(ph)PTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASTRSPTQR 9 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 AS(0.1)T(0.1)RS(0.747)PT(0.052)QR 87.363 0.0081828 86009000 12914 15395 14077 11934 14653 22851 11092 18766 15556 20909 TRUE FALSE 13423.85469 18038.97149 14443.85818 14294.50958 12162.28829 17544.20156 10222.58006 18514.47246 14996.1426 25005.71822 0.536831399 0.721393856 0.577622208 0.57164963 0.486380283 0.701607584 0.408809696 0.740409546 0.599708533 1 14.60997042 0.162614256 0.826687259 1.006192233 0.586072399 0.605178923 0.098886755 2.3753043 1.831572626 0.128892755 0.030204127 1.454166903 -0.162614256 -0.420119834 ASTS(ph)KSESSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.005)T(0.022)S(0.904)KS(0.067)ES(0.001)S(0.001)QK 115.12 0.0030672 44177000 106070 60215 93250 60584 180110 132270 158930 117190 154460 72189 TRUE FALSE 110257.7255 70556.45784 95680.17161 72567.33437 149494.9665 101552.2971 146472.6513 115619.2597 148901.0148 86333.05241 1.277120667 0.817258928 1.108268142 0.84055101 1.731607564 1.176285261 1.696599937 1.339223583 1.724727791 1 16.39762538 3.247172791 24.99962166 1.457935307 1.003937358 0.408272107 0.255581279 164.9633094 478856.4662 0.06403597 0.085368351 1766.740608 -3.247172791 -0.45399795 ASTSKS(ph)ESSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AS(0.001)T(0.004)S(0.038)KS(0.958)ESSQK;ASTS(0.005)KS(0.963)ES(0.031)S(0.001)QK 166.86 5.24E-05 252163000 348291 186952 290598 178333 520610 415040 458090 365540 457700 246141 TRUE FALSE 362041.7976 219059.5517 298171.2226 213606.7351 432116.8982 318653.25 422183.7088 360640.5342 441227.4664 294367.6163 1.229896828 0.744170009 1.01292128 0.725646176 1.46794985 1.082501037 1.434205685 1.225136578 1.498899478 1 18.16725944 3.236739956 24.99999409 1.291942223 0.921071012 0.431848705 0.200225557 40.71550127 559079.0499 0.051847366 0.065044666 1724.804816 -3.236739956 -0.370871211 ASTSKSES(ph)SQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASTSKSESSQK 11 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 AST(0.001)S(0.011)KS(0.294)ES(0.683)S(0.011)QK;ASTS(0.01)KS(0.285)ES(0.689)S(0.016)QK 182.33 1.54E-05 203988000 299090 174506 275770 168773 495690 397130 450790 342220 438310 219128 TRUE FALSE 310898.3041 204476.048 282956.7927 202155.7957 411432.7909 304902.5761 415455.9019 337633.1007 422535.3087 262061.9361 1.186354297 0.78025848 1.079732513 0.771404648 1.569983024 1.163475248 1.58533478 1.288371389 1.612349031 1 17.9995483 3.239177928 24.99999902 1.382770292 0.950945761 0.470182549 0.215794961 12.84395675 520139.9614 0.054982899 0.070196968 1734.514475 -3.239177928 -0.431824531 ASTVS(ph)PGGYMVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 AST(0.001)VS(0.999)PGGYMVPK;ASTVS(1)PGGYMVPK 194.86 3.97E-07 137710000 331526 295282 318556 283740 361987 436360 365952 321036 353609 275620 TRUE FALSE 344614.9025 345994.3865 326857.8311 339862.9251 300456.579 335022.0031 337267.726 316733.0375 340882.6812 329622.4619 1.045483674 1.049668716 0.991612735 1.031067249 0.911517308 1.016380987 1.023194002 0.960896402 1.034160958 1 18.33045503 4.23837525 24.99708658 0.993416212 1.047576212 0.253512011 0.035088684 5.691374858 768000.0943 0.008334026 0.02002432 17313.11646 -4.23837525 0.05416 ASVALT(ph)PTAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 ASVALT(0.986)PT(0.014)APSR;ASVALT(0.997)PT(0.003)APSR 139.19 0.00068253 418340000 356680 446620 373710 417150 402450 470200 359920 398280 380470 419930 TRUE FALSE 370762.0018 523323.5108 383449.1896 499661.0249 334041.6928 361003.1759 331708.5299 392941.7081 366776.959 502207.2435 0.738264943 1.042046919 0.763527796 0.994929945 0.665147102 0.718833073 0.660501286 0.782429392 0.730329886 1 18.93792331 3.2312019 24.99999787 0.742608218 0.887277399 0.188456922 0.12423987 223.7671618 760210.4922 0.032517836 0.039604389 1702.950011 -3.2312019 0.14466918 ASVAVSSFEHAGPSLPGLS(ph)PGACSLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASVAVSSFEHAGPSLPGLSPGACSLPAR 28 0 Q8TER5;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 ASVAVSSFEHAGPS(0.035)LPGLS(0.964)PGACS(0.001)LPAR 102.55 0.00071783 207680000 21929 39639 41010 41332 33994 59208 32935 45257 31654 34957 TRUE FALSE 22794.77385 46446.6899 42078.75429 49507.34624 28215.71202 45457.83931 30353.46864 44650.40394 30514.77872 41806.15486 0.545249233 1.11100124 1.006520557 1.184211904 0.674917656 1.08734801 0.726052629 1.068034219 0.729911154 1 15.35142774 3.24389445 24.99493938 0.895695625 0.975604952 0.030579387 0.207443412 555.8847351 2604917.725 0.054636408 0.071883063 1753.454294 -3.24389445 0.079909328 ASVITQVFHVPLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ASVITQVFHVPLEER 15 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62 Q00341 HDLBP Vigilin 0 ;;; 193.69 8.26E-08 1474031000 778810 963656 912240 978466 979827 1077338 954542 979563 927072 1084818 FALSE TRUE 809558.0202 1129156.422 936013.7238 1172003.654 813276.3565 827142.5767 879722.5038 966433.5602 893706.8598 1297367.317 0.624000628 0.870344433 0.721471638 0.903370725 0.626866691 0.637554658 0.678082831 0.744918997 0.688861857 1 20.30715557 -1.925087748 8.048515146 1.068435671 0.725706868 0.451835427 0.091859387 0.052662611 0.000490162 0.041522963 0.020410532 0.011882621 1.925087748 -0.342728803 ASVLDTSMSAGSGS(ph)PSK ddPTM_MDA-MB-175_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 ASVLDTSMSAGSGS(1)PSK;ASVLDTSMSAGSGS(1)PSK 348.63 1.39E-87 384430000 805490 476620 587850 482480 715750 782510 810330 630830 693220 404150 TRUE FALSE 837291.3672 558475.7774 603169.8539 577913.1039 594087.0707 600783.9116 746814.2172 622374.7557 668271.1476 483335.4546 1.732319364 1.155462055 1.247932152 1.195677036 1.229140269 1.242995741 1.545126082 1.287666257 1.382623893 1 18.8826653 -1.984447284 2.515285497 0.703916161 1.324024739 0.258852091 0.169290124 11740830.89 5879127.086 20195462.24 0.040030193 0.010364604 1.984447284 0.620108577 ASVSGPNS(ph)PSESRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ASVSGPNSPSESRR 14 1 A6PVI4;Q9UJV3-2;Q9UJV3 A6PVI4 MID2 Probable E3 ubiquitin-protein ligase MID2 1 ASVSGPNS(0.984)PS(0.015)ES(0.001)RR;ASVSGPNS(0.995)PS(0.005)ESRR;ASVSGPNS(0.995)PS(0.004)ESRR 175.39 6.03E-08 93742000 217196 282858 259183 253673 275564 314383 215365 227938 248232 284684 TRUE FALSE 225771.0658 331436.6612 265937.5219 303848.7623 228723.7297 241372.3128 198484.1285 224882.8639 239298.1788 340462.3792 0.663130729 0.973489823 0.781106924 0.89245914 0.671803241 0.708954432 0.582984026 0.660521919 0.702862323 1 18.37713586 3.229097393 24.96458755 0.691641487 0.834654045 0.117162804 0.127899731 272.660786 719295.6082 0.034034453 0.041187762 1694.717807 -3.229097393 0.143012558 ASVSQTS(ph)PQSASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.111)S(0.851)PQS(0.008)AS(0.015)S(0.015)PR 197.75 8.67E-09 121010000 267340 230350 248210 227740 311050 534750 290880 268900 262510 237210 TRUE FALSE 277894.7896 269910.8206 254678.5565 272786.2923 258177.8321 410562.4167 268080.0655 265295.8353 253062.3164 283686.7578 0.979583227 0.951439618 0.897745663 0.961575698 0.910080661 1.447238566 0.94498618 0.935171727 0.892048393 1 18.11393928 ASVSQTSPQS(ph)ASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 ASVSQT(0.114)S(0.261)PQS(0.599)AS(0.021)S(0.005)PR 241.11 7.58E-18 201750000 176020 208790 206270 179030 234220 339890 212760 206400 231310 218060 TRUE FALSE 182969.4055 244648.0583 211645.5657 214441.5996 194407.3681 260955.6986 196083.3153 203633.5456 222985.1983 260784.682 0.701611015 0.938122809 0.811572076 0.822293695 0.74547081 1.000655777 0.751897365 0.780849335 0.855054816 1 17.99249961 0.968485319 19.91179368 1.000000004 0.820898728 0.288040068 0.085104104 302.4536156 191099.935 0.076476667 0.019119167 9.300050751 -0.968485319 -0.179101276 ASYDDPYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 98.048 0.010066 189760000 1411500 705630 1040100 686300 1414700 1255200 1277600 1019900 1137800 569760 FALSE TRUE 1467227.11 826816.4635 1067205.86 822048.0916 1174229.799 963698.8227 1177458.374 1006229.909 1096850.8 681393.5633 2.153274097 1.213419833 1.566210657 1.206421862 1.723276917 1.414305733 1.728015111 1.476723531 1.609716997 1 19.37812879 -0.99943262 4.083996216 0.999956663 1.546710019 0.29346085 0.261844405 39401241.9 63823511.26 23101.72334 0.05647952 0.100130729 0.99943262 0.546753356 ASYDTLCVLDGDKDSVNCAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ASYDTLCVLDGDKDSVNCAR 20 1 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 156.13 2.00E-08 121640000 131220 76259 92500 87628 120360 127050 106820 81003 101530 68969 FALSE TRUE 136400.6669 89355.89004 94910.62599 104960.5569 99901.25019 97544.56296 98447.16928 79917.28728 97875.95513 82482.15506 1.653699116 1.083336026 1.150680725 1.272524424 1.211186227 1.182614141 1.193557191 0.968903967 1.186631885 1 16.33179441 4.742490644 24.73362762 1.140526612 1.653699348 0.744890441 0.090388853 176.5523002 1111080.604 0.022711894 0.172631502 55270.15009 -4.742490644 0.513172736 ASYHFSPEELDENTS(ph)PLLGDAR ddPTM_MDA-MB-175_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(0.298)S(0.702)PLLGDAR;ASYHFSPEELDENT(0.024)S(0.976)PLLGDAR;ASYHFSPEELDENT(0.013)S(0.987)PLLGDAR;ASYHFSPEELDENT(0.343)S(0.657)PLLGDAR 305.69 1.73E-56 888900000 56750 448308 419040 507000 398880 582040 408830 519470 427038 633240 TRUE FALSE 58990.53382 525301.4116 429960.5266 607283.0868 331078.5201 446870.0309 376784.8363 512507.3543 411668.9858 757311.2539 0.077894701 0.693640044 0.567746121 0.801893652 0.437176284 0.590074462 0.497529694 0.67674599 0.543592854 1 19.53052684 -5 0.17286584 2.70800648 0.459505041 0.38869063 0.179667367 141.4922058 1.343791987 83.17741055 0.589033227 1.00E-05 5 -2.248501439 ASYNNPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ASYNNPHR 8 0 P54725-2;P54725;A0A494C0B4;K7ELU6;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;;;;;;; 136.27 0.00079823 870742000 814358 1094357 954364 914151 1199398 1196407 941579 936957 926295 1232835 FALSE TRUE 846509.4827 1282304.302 979235.5099 1094967.339 995524.7564 918559.606 867775.5776 924398.624 892957.8239 1474385.414 0.574143962 0.869721234 0.664165218 0.742660182 0.675213378 0.623011865 0.588567663 0.626972171 0.605647489 1 20.49168227 -1.009533169 4.57314355 1.000008583 0.664871202 0.596896594 0.082989018 0.119916746 50943450.53 1150.375688 0.019562631 0.097828824 1.009533169 -0.335137381 AT(ph)PAQTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATPAQTPR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3ITP6;E5RFR3;E5RG53 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 AT(1)PAQTPR 88.056 0.04476 0 349270 243220 207870 202900 263410 347720 252970 204830 218320 211330 TRUE FALSE 363059.4493 284991.143 213287.263 243033.0144 218635.6623 266967.2997 233141.5504 202084.5889 210462.7058 252736.0673 1.436516177 1.127623556 0.84391304 0.961607961 0.865075035 1.056308672 0.922470437 0.799587455 0.832737124 1 17.94727204 4.586021627 2.46672773 0.903499555 1.475525442 0.814163563 0.077813741 0.155268343 1.454542696 0.020365182 0.161071795 38549.75542 -4.586021627 0.572025887 AT(ph)PARAS(ph)S(ph)FLIENLLAAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATPARASSFLIENLLAAEAK 20 1 F1T0J4;Q9NP08 F1T0J4 HMX1 Homeobox protein HMX1 3 AT(1)PARAS(1)S(1)FLIENLLAAEAK;AT(1)PARAS(1)S(1)FLIENLLAAEAK 69.605 0.016443 474560000 22715 605110 254520 594790 88440 354280 124050 194623 176681 1328390 TRUE FALSE 23611.80574 709032.9354 261153.0003 712437.6867 73407.00039 272003.8392 114326.6369 192014.397 170322.2853 1588662.587 0.014862694 0.446308071 0.164385441 0.448451227 0.046206791 0.171215613 0.071964077 0.120865437 0.107211114 1 20.59938132 -1.149733342 4.088852591 1.00025753 0.179474674 0.744818882 0.144539742 183502361.6 348805621.8 659835.3539 0.033705139 0.07083806 1.149733342 -0.820782856 AT(ph)SFSSAGEVPKPRPPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSFSSAGEVPKPRPPSTR 19 2 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H7BZT5 O15231-3 ZNF185 Zinc finger protein 185 1 AT(0.864)S(0.11)FS(0.026)SAGEVPKPRPPSTR;AT(0.498)S(0.498)FS(0.003)SAGEVPKPRPPSTR 195.09 8.07E-14 1576870000 352320 410110 418060 396940 613360 557740 497470 478790 485340 423270 TRUE FALSE 366229.8657 480543.2023 428954.987 475453.5473 509101.2863 428213.3376 458477.0015 472372.6032 467872.7082 506201.6525 0.723486112 0.949311801 0.847399421 0.939257201 1.005728219 0.845934294 0.905720081 0.933170804 0.924281274 1 18.94935269 4.743177447 24.94921255 0.923006929 0.72348603 0.591774376 0.050781113 319.4863469 1726433.886 0.011549668 0.093100899 55357.62467 -4.743177447 -0.1995209 AT(ph)SGSSLPVGINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSGSSLPVGINR 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 AT(0.77)S(0.228)GS(0.002)SLPVGINR 189.61 5.72E-05 279440000 97496 118530 108780 121040 126180 147850 114100 115230 126240 133470 TRUE FALSE 101345.2174 138886.6055 111614.8962 144981.3507 104731.9687 113514.0782 105156.5439 113685.5303 121696.6471 159620.8911 0.634911989 0.870102933 0.699249925 0.908285562 0.656129458 0.711148005 0.658789355 0.712222126 0.762410523 1 17.28428996 -1.973668657 6.871449123 1.174828214 0.734816801 0.462891178 0.085699322 0.041746413 0.000159972 0.015091889 0.018466913 0.010625059 1.973668657 -0.440011412 SLGSVQAPSYGARPVSSAASVYAGAGGS(ph)GSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVSSAASVYAGAGGS(0.812)GS(0.188)R 198.1 7.49E-26 588570000 69854 76581 74817 66846 94275 100410 44510 94715 92468 126990 TRUE FALSE 72611.88986 89733.19103 76766.79248 80067.93928 78250.16917 77091.29923 41021.18989 93445.50035 89140.09474 151871.2591 0.478114755 0.590850379 0.505472812 0.527209294 0.515240142 0.507609535 0.270105023 0.61529417 0.586945122 1 17.21248935 0.679663806 1.537785579 0.999024055 0.496781166 0.753811746 0.085634905 0.548634323 1.940936782 0.080459153 0.023266965 4.782597207 -0.679663806 -0.502242889 AT(ph)SNVFAMFDQSQIQEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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(0.585)S(0.415)NVFAMFDQSQIQEFK;AT(0.599)S(0.401)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(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.608)S(0.392)NVFAMFDQSQIQEFK;AT(0.564)S(0.436)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK;AT(0.571)S(0.429)NVFAMFDQSQIQEFK;AT(0.566)S(0.434)NVFAMFDQSQIQEFK;AT(0.584)S(0.416)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK 299.85 6.23E-49 6077482200 7052620 6446327 8625415 5943150 11487578 9266077 8060541 7898636 8762627 6966310 TRUE FALSE 7331062.883 7553433.517 8850200.401 7118687.331 9534923.595 7114171.046 7428734.734 7792767.704 8447261.766 8331225.066 0.879950166 0.906641395 1.0622928 0.854458651 1.144480376 0.85391656 0.891673754 0.935368765 1.013927928 1 22.99009722 4.45949704 24.81383653 0.961439967 0.886622861 0.106133554 0.087472732 423.0037332 595564.0742 0.020183972 0.055300443 28806.93414 -4.45949704 -0.074817106 AT(ph)SPSSSVSGDFDDGHHSVSTPGPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSPSSSVSGDFDDGHHSVSTPGPSR 26 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053;C9J409 Q86U86-8 PBRM1 Protein polybromo-1 1 AT(0.548)S(0.438)PS(0.014)SSVSGDFDDGHHSVSTPGPSR;AT(0.436)S(0.436)PS(0.127)S(0.001)SVSGDFDDGHHSVSTPGPSR 161.04 3.28E-11 596740000 33324.6 105888 104882 104000 82129 133914 101667 113182 107078 118244 TRUE FALSE 34640.28094 124073.4403 107615.3111 124570.8896 68168.74192 102814.503 93698.07488 111664.9804 103224.2837 141411.6479 0.244960592 0.877391942 0.761007404 0.880909681 0.482058889 0.727058234 0.662590927 0.789644857 0.72995602 1 17.10954143 -5 0.136033189 2.021215519 0.581937721 0.260675311 0.17644996 209.3026394 1.766226274 58.15305209 1.126044311 1.00E-05 5 -1.439277798 AT(ph)TPPNQGRPDS(ph)PVYANLQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 AT(0.5)T(0.5)PPNQGRPDS(0.998)PVY(0.002)ANLQELK 71.608 0.037122 686160000 92989 61848 79613 74523 114030 111640 105050 85227 92843 61899 TRUE FALSE 96660.27752 72469.91289 81687.78018 89263.42697 94647.22133 85713.30192 96815.9065 84084.67147 89501.59857 74026.92392 1.305744889 0.978966963 1.103487432 1.205823804 1.27855132 1.157866589 1.307847218 1.135866074 1.209041168 1 16.17576246 5.063534489 21.22128425 1.165673002 4.429912117 0.158787459 0.101769855 1119.239196 390330.3265 0.023113324 7537.199659 115753.5952 -5.063534489 3.264239116 ATAAVIFLHGLGDTGHGWAEAFAGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATAAVIFLHGLGDTGHGWAEAFAGIR 26 0 B4DP64;E5RGR0;O75608-2;O75608 B4DP64 LYPLA1 Acyl-protein thioesterase 1 0 206.48 1.73E-25 71519000 36022 63944 41117 41003 44275 54024 47759 53908 45123 83928 FALSE TRUE 37444.17638 74925.88458 42188.5428 49113.27102 36749.15131 41477.74474 44015.52479 53185.45144 43499.03204 100372.0847 0.373053688 0.746481303 0.420321476 0.489312055 0.366129202 0.413239845 0.438523569 0.529882901 0.433377788 1 16.61499856 -1.153939941 4.492636308 1.000082903 0.473581721 0.700477622 0.10433916 16.82191488 120493934 19537.35645 0.023549828 0.070155231 1.153939941 -0.526501181 ATAGDTHLGGEDFDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 212.7 3.82E-12 1.50426E+11 39526660 46558330 43102820 43374010 48299080 51275800 43148320 45069580 42372430 47610530 FALSE TRUE 41087203.06 54554361 44226114.9 51953259.72 40089219.63 39367772.54 39766241.93 44465496 40847454.52 56938901.79 0.721601607 0.958121061 0.776729327 0.912438738 0.704074339 0.691403791 0.698401983 0.780933502 0.717390979 1 25.76291133 ATANNDHTVVSLACAGGHLAVVELLLAHGADPTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATANNDHTVVSLACAGGHLAVVELLLAHGADPTHR 35 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;E9PDP5;H7C2F5;H3BLS9 Q8IWZ3-6 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 0 105.64 6.48E-06 37925000 90827 48191 57896 47699 73076 100620 68385 54540 54893 51460 FALSE TRUE 94412.92009 56467.42938 59404.81732 57133.71983 60654.56762 77252.52991 63024.80501 53808.98051 52917.41165 61542.60174 1.534106739 0.917533997 0.96526334 0.928360489 0.985570416 1.255269159 1.024084183 0.874337109 0.85985009 1 15.90929782 4.742437508 24.92585088 0.979036431 1.534106963 0.715096685 0.10513022 215.1597869 1383277.991 0.0271727 0.207083034 55263.38823 -4.742437508 0.555070532 ATAPAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATAPASPR 8 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 ATAPAS(1)PR;ATAPAS(1)PR;ATAPAS(1)PR;ATAPAS(1)PR 123.29 0.0014203 6653320000 5471370 6513640 5234270 5437780 5912570 7129410 5987350 5943010 5394660 6604330 TRUE FALSE 5687383.912 7632307.001 5370679.376 6513356.654 4907553.463 5473712.575 5518045.862 5863353.672 5200507.24 7898322.016 0.72007496 0.96632006 0.679977262 0.824650684 0.621341274 0.693022209 0.69863521 0.742354346 0.658431909 1 22.91311476 5.084349522 16.08240992 0.751761516 9.54E-05 0.001620357 0.12255798 25727255.45 64669221.4 0.027431204 676893469.1 121436.5784 -5.084349522 -0.751666111 ATAPQTQHVS(ph)PMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 25 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;ATAPQT(0.002)QHVS(0.998)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(0.002)QHVS(0.998)PMR 261.08 5.05E-24 1.09342E+11 18647691.6 22648644.8 19421603.5 20264965.8 20837925.1 24066811.3 19294996.7 20125301.4 19002609.4 21408443.8 TRUE FALSE 19383916.86 26538373.36 19927746.44 24273315.55 17295902.03 18477659.11 17782604.44 19855554.65 18318709.2 25603018.47 0.757094984 1.036532993 0.778335823 0.948064603 0.675541521 0.721698464 0.694551092 0.775516163 0.715490215 1 24.60981057 3.240624342 24.99999109 0.747759449 0.883925288 0.193006175 0.113490454 71.35649817 864404.4238 0.029076481 0.037495242 1740.300887 -3.240624342 0.136165839 ATAPQTQHVSPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 200.19 1.12E-07 1031456000 105432.9 852198 604673 765838 558878 1031781 495362 847465 556710 971472 FALSE TRUE 109595.4723 998556.3773 620431.2751 917318.4706 463880.1172 792165.4995 456534.2321 836106.1178 536674.1158 1161813.338 0.094331394 0.859480903 0.534019756 0.789557531 0.399272501 0.681835432 0.392949725 0.719656153 0.461928003 1 20.14794687 -1.850654106 2.435834344 1.186814806 0.568106254 0.27887503 0.215852853 15717159.89 9187146.269 17063010.85 0.047134856 0.014104117 1.850654106 -0.618708552 ATCIEMVTSLAYTHHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATCIEMVTSLAYTHHGR 17 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 79.97 0.0071781 261480000 164500 120600 136810 132060 168510 225850 168540 116610 148850 126900 FALSE TRUE 170994.587 141312.1119 140375.381 158181.0738 139866.7304 173399.7603 155329.3944 115047.0337 143492.9176 151763.6254 1.126716541 0.931132948 0.924960646 1.042285814 0.921609049 1.142564695 1.023495545 0.758067247 0.9455027 1 17.21146652 1.775053188 25 0.875960942 1.011571163 0.226516261 0.093642346 50.59933502 34678.98372 0.041897584 0.023254007 59.57350992 -1.775053188 0.135610221 ATCIS(ph)PGVVETQFAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATCISPGVVETQFAFK 16 0 A0A087WZN3;Q6UWP2-2;Q6UWP2 A0A087WZN3 DHRS11 Dehydrogenase/reductase SDR family member 11 1 ATCIS(1)PGVVETQFAFK;ATCIS(1)PGVVETQFAFK 216.71 1.57E-14 69718000 184856 163670 145394 142154 197505 204512 184254 170180 184610 167024 TRUE FALSE 192154.2576 191779.0493 149183.0871 170271.6369 163933.1706 157017.1874 169811.69 167899.0155 177965.9222 199749.1549 0.961977825 0.960099428 0.746852156 0.852427321 0.82069519 0.786071848 0.850124698 0.840549316 0.890947059 1 17.60782987 -0.998152072 5.558216341 1.0000004 0.851998356 0.304457544 0.064664533 3.25E-07 5.86E-08 0.063516445 0.014970929 0.100426408 0.998152072 -0.148002044 ATDAEADVASLNRR ddPTM_MDA-MB-175_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 ; 167.03 5.95E-06 257180000 227865 313620 258520 251972 310790 331380 252370 275880 273680 361610 FALSE TRUE 236861.2862 367481.7954 265257.2436 301811.3095 257962.0268 254422.0171 232588.58 272182.2798 263830.3103 432460.5561 0.547706104 0.849746388 0.613367485 0.697893265 0.596498393 0.588312653 0.537826113 0.62938059 0.610067916 1 18.72220903 -1.332099397 5.19469837 1.000124954 0.631622376 0.631915357 0.084688773 0.000119825 1.54E-05 0.080171477 0.018890233 0.046547955 1.332099397 -0.368502578 ATDCVGHDVVTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ATDCVGHDVVTLLR 14 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;; 199.41 2.07E-08 3755680000 3536770 4074070 3775610 4011410 3783460 4353740 3703300 3627880 2952460 3499650 FALSE TRUE 3676404.411 4773759.831 3874005.498 4804854.925 3140348.821 3342649.867 3413025.669 3579254.203 2846201.541 4185339.413 0.878400542 1.140590848 0.925613222 1.148020376 0.750321183 0.79865682 0.815471658 0.855188516 0.680040795 1 21.99691319 3.228135921 24.99728825 0.811766919 1.024577084 0.463180288 0.108852666 164.8172877 395213.368 0.02864621 0.034586278 1690.970073 -3.228135921 0.212810165 ATDDYHYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDDYHYEK 9 0 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 0 78.655 0.029157 144150000 343710 300160 385040 336160 420000 451400 375220 368950 411870 319850 FALSE TRUE 357279.9362 351710.1451 395074.4587 402651.4447 348608.55 346569.191 345809.2759 364004.8287 397046.8792 382518.4836 0.934020058 0.919459216 1.032824493 1.052632649 0.911350863 0.906019463 0.904032853 0.951600627 1.037980898 1 18.54516994 1.249074239 24.21448956 1.018990441 0.95129866 0.226951809 0.049828501 202.1732686 465647.3538 0.03739906 0.013314078 17.74492791 -1.249074239 -0.067691781 ATDFVADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDFVADR 8 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 89.542 0.032179 217570000 270930 340280 279620 286830 289210 420930 318030 278660 292220 332920 FALSE TRUE 281626.5256 398720.443 286907.1269 343564.1179 240050.1875 323175.3868 293101.9776 274925.0185 281703.0593 398149.2999 0.707338995 1.001434495 0.720601862 0.86290273 0.602915006 0.811693972 0.736160977 0.690507351 0.707531219 1 18.60295 ATDGAPADAPVGVLGRPFPTPS(ph)PASLDVYVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATDGAPADAPVGVLGRPFPTPSPASLDVYVAR 32 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 ATDGAPADAPVGVLGRPFPT(0.054)PS(0.941)PAS(0.005)LDVYVAR;ATDGAPADAPVGVLGRPFPT(0.013)PS(0.983)PAS(0.004)LDVYVAR;ATDGAPADAPVGVLGRPFPT(0.01)PS(0.979)PAS(0.01)LDVYVAR;ATDGAPADAPVGVLGRPFPT(0.01)PS(0.99)PASLDVYVAR 187.94 5.27E-20 681203000 202858 287777 251335 227020 296591 302468 216115 243724 239059 313141 TRUE FALSE 210866.9905 337200.4612 257884.9966 271923.8784 246176.5678 232224.3909 199175.3416 240457.2784 230455.3133 374494.9835 0.563070267 0.900413827 0.688620697 0.7261082 0.657356116 0.620100138 0.531850493 0.642084111 0.615376236 1 18.51458687 -1.091302547 4.34924187 1.000035771 0.661959035 0.527878715 0.096297556 1.701049538 56991293.46 4500.482206 0.02301171 0.081039631 1.091302547 -0.338076737 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ATDIPASASPPPVAGVPFFK 20 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPASAS(1)PPPVAGVPFFK;ATDIPAS(0.001)AS(0.999)PPPVAGVPFFK;ATDIPAS(0.003)AS(0.997)PPPVAGVPFFK 255.19 3.95E-36 2271735000 1961054 1636445 1884898 1694899 2053084 2211759 2205812 1927639 1991861 1535414 TRUE FALSE 2038477.926 1917491.699 1934019.99 2030144.963 1704101.515 1698111.492 2032914.692 1901802.152 1920174.312 1836248.976 1.110131552 1.044243849 1.053244966 1.105593517 0.928034018 0.92477192 1.107101879 1.035699503 1.045704769 1 20.80833026 4.827739751 0.862503166 1.021370825 1.157527103 0.177819364 0.05818371 5.415281032 2.825263676 0.020847051 0.72561477 67257.34983 -4.827739751 0.136156277 ATDKSFVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 94.297 0.0080418 88755000 128210 96095 120320 67836 191790 151740 88792 113770 138740 141670 FALSE TRUE 133271.8298 112598.5687 123455.638 81253.75833 159189.6043 116500.6846 81832.25103 112245.0992 133746.7745 169427.5241 0.786600823 0.664582507 0.728663414 0.479578267 0.939573456 0.687613688 0.482992663 0.662496249 0.789404055 1 17.37030874 0.933017312 3.392174562 0.999455786 0.67318545 0.373743637 0.126938187 0.307919244 8.783228055 0.118906044 0.030824971 8.570720088 -0.933017312 -0.326270336 ATDLRPIYISVQPPSLHVLEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDLRPIYISVQPPSLHVLEQR 22 1 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH5;B1ANH3 B1ANH0 GUK1 Guanylate kinase 0 60.635 0.032252 369100000 81436 203810 146840 173860 148930 196040 132240 186580 121870 325250 FALSE TRUE 84651.15616 238812.7821 150666.771 208248.9891 123614.9318 150512.681 121874.6833 184079.2003 117483.9225 388976.5102 0.217625368 0.61395168 0.387341567 0.535376774 0.317795364 0.386945425 0.313321448 0.473239888 0.302033463 1 18.56932351 -1.388065421 3.154371241 1.006991988 0.403816267 0.721062624 0.112896608 26668744.75 34452998.05 1695628.033 0.025203857 0.040919901 1.388065421 -0.603175722 ATDPPESTRQDAPPWGSGVELTHLGS(ph)PSAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATDPPESTRQDAPPWGSGVELTHLGSPSAQR 31 1 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 ATDPPESTRQDAPPWGSGVELTHLGS(0.951)PS(0.049)AQR;ATDPPESTRQDAPPWGSGVELTHLGS(0.97)PS(0.029)AQR 122.43 4.80E-06 175279000 46250 71395 54094 45503 60847 70845 44107 59546 47444 74462 TRUE FALSE 48075.98571 83656.53587 55503.73408 54503.35759 50504.24867 54392.32242 40649.77809 58747.88327 45736.49971 89051.40324 0.539867806 0.939418502 0.623277479 0.612043782 0.567135911 0.610796915 0.456475436 0.659707552 0.51359662 1 16.44235072 -1.120960804 9.421948036 1.000000002 0.618155962 0.470766556 0.122824765 5.45E-09 4.63E-10 0.117117552 0.027604872 0.07569012 1.120960804 -0.38184404 ATDSDLS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLS(0.869)S(0.131)PR 62.466 0.089061 364370000 333670 405590 394150 362930 419960 445140 376960 394030 380070 403840 TRUE FALSE 346843.5492 475246.9274 404421.8728 434716.4708 348575.3492 341762.9812 347412.8902 388748.6724 366391.3549 482964.716 0.718155049 0.984019974 0.837373538 0.900099855 0.721740818 0.707635506 0.719333895 0.804921477 0.758629653 1 18.88155827 ATDSDLSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 ATDSDLS(0.089)S(0.911)PR 96.113 0.0073024 99642000 502440 550740 533440 524620 614040 651520 558940 568730 557190 599120 TRUE FALSE 522276.7192 645325.3108 547341.8846 628388.2702 509665.7001 500214.3539 515128.8223 561107.1046 537136.8407 716506.0932 0.728921532 0.900655719 0.76390402 0.877017343 0.711320818 0.698129937 0.718945487 0.783115608 0.749661232 1 19.45061945 -1.284273952 3.23223989 1.001106433 0.771729171 0.530371849 0.064861514 62441690.54 84994853.04 670883.487 0.015867594 0.051966809 1.284273952 -0.229377262 ATDSSDPLKPYQDFIIDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATDSSDPLKPYQDFIIDSR 19 1 Q96Q11-2;Q96Q11 Q96Q11-2 TRNT1 "CCA tRNA nucleotidyltransferase 1, mitochondrial" 0 71.558 0.018156 51321000 147630 101800 155150 148260 169740 176010 153200 153950 155120 120250 FALSE TRUE 153458.5464 119283.3581 159193.3365 177585.3855 140887.6554 135134.345 141191.7837 151886.5521 149537.2615 143810.6852 1.067087235 0.829447116 1.106964592 1.234855291 0.979674461 0.93966832 0.981789243 1.056156237 1.039820242 1 17.13381135 -1.474076571 2.584814955 0.998899883 1.02527979 0.005869079 0.101566714 11027851.18 9934672.783 85660.63224 0.025069676 0.033567843 1.474076571 0.026379907 ATEDGEEDEEMIESIENLEDLKGHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 232.06 1.11E-35 59312000 48878 43695 56673 47635 68827 69173 61836 63402 59395 46360 FALSE TRUE 50807.74118 51199.27635 58149.94494 57057.06082 57127.81112 53108.61908 56989.13274 62552.19989 57257.38555 55443.35438 0.916390102 0.923451997 1.048817222 1.029105498 1.030381581 0.957889718 1.027880318 1.128218171 1.03271864 1 15.75872692 4.242877449 24.26187797 1.038159211 0.919920957 0.545796297 0.040529224 56.48587387 317449.6822 0.011311138 0.028768619 17493.5298 -4.242877449 -0.118238254 ATEEPEDVRSEAALDQEQITAAYSVEHNQLEAHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATEEPEDVRSEAALDQEQITAAYSVEHNQLEAHPK 35 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 118.93 1.56E-06 77910000 59420 55729 61909 46069 60902 69834 50029 56734 70500 57002 FALSE TRUE 61765.94748 65300.02224 63522.3994 55181.3107 50549.89979 53616.11184 46107.59625 55973.57353 67962.71877 68170.45053 0.906051625 0.957893365 0.931817216 0.809460848 0.741522161 0.78650077 0.676357511 0.821082641 0.996952759 1 16.0568589 3.742094374 9.224978836 0.811156726 0.934627117 0.152151196 0.097609382 0.171705496 238.0010582 0.025243932 0.042635696 5521.974208 -3.742094374 0.123470392 ATEETGQAQSGQANCQGLS(ph)PVSVASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATEETGQAQSGQANCQGLSPVSVASK 26 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 ATEETGQAQSGQANCQGLS(1)PVSVASK;ATEETGQAQSGQANCQGLS(0.992)PVS(0.008)VASK 235.69 4.11E-45 443034000 521630 340970 415810 351640 492430 542010 487990 447980 463170 319070 TRUE FALSE 542224.3552 399528.9451 426646.3502 421193.3425 408726.9245 416136.3917 449740.0687 441975.5608 446500.6022 381585.6575 1.42097677 1.047022961 1.118088014 1.103797625 1.071127587 1.090545159 1.178608419 1.158260412 1.170118932 1 18.54164742 4.746199203 24.99025956 1.113524393 1.420976917 0.754140436 0.054029058 470.5347525 1539356.553 0.012976336 0.139546265 55744.1378 -4.746199203 0.307452525 ATENDIYNFFS(ph)PLNPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 1 ATENDIYNFFS(1)PLNPMR 181.14 5.39E-14 0 54278 59949 58450 67549 63961 65932 55905 61483 57832 63838 TRUE FALSE 56420.93735 70244.77441 59973.25502 80909.99059 53088.93207 50620.29221 51523.02002 60658.92095 55750.63762 76345.83385 0.739017894 0.920086544 0.785547187 1.059782656 0.695374317 0.663039352 0.674863544 0.794528239 0.730238113 1 16.22026181 5.056144703 14.0906691 0.800884953 0.356665826 0.02014694 0.131211956 6347317.65 46239405.55 0.031344107 76458101.7 113800.6396 -5.056144703 -0.444219127 ATENDIYNFFS(ph)PLNPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ATENDIYNFFSPLNPVR 17 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P52597;P31943 HNRNPF;HNRNPH1 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 1 ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR 294.04 4.73E-46 562546000 561946 566900 542394 561794 591487 616626 563766 559711 546078 587091 TRUE FALSE 584132.062 664260.6651 556529.2332 672915.1764 490946.251 473423.9566 519576.5478 552208.9895 526424.7595 702120.2409 0.831954454 0.946078216 0.792640919 0.958404469 0.699233867 0.674277608 0.740010781 0.78648778 0.749764398 1 19.42135859 3.233330508 24.99995401 0.75908348 0.880425237 0.223973651 0.095112042 160.8121969 768683.4544 0.025425955 0.031260297 1711.317169 -3.233330508 0.121341757 ATENDIYNFFSPLNPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 127.71 9.16E-05 68360000 18333 20638 21612 18778 20281 27015 21130 22336 14289 18170 FALSE TRUE 19056.801 24182.41596 22175.22647 22492.23235 16833.64286 20741.17567 19473.77539 22036.62245 13774.74168 21730.06361 0.876978611 1.112855277 1.020486036 1.035074391 0.774670667 0.954492174 0.896167436 1.014107591 0.633902501 1 14.40740478 3.278459713 24.99516802 0.893365011 1.019251875 0.224367591 0.118473 239.5356232 150057.756 0.031341574 0.042436151 1898.7147 -3.278459713 0.125886864 ATENDIYNFFSPLNPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATENDIYNFFSPLNPVR 17 0 P52597;P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;H0YBG7 P52597;P31943 HNRNPF;HNRNPH1 "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ; 214.65 1.36E-14 147934000 160231 169497 170856 161460 184469 187563 185542 177656 160811 160664 FALSE TRUE 166557.0436 198606.7912 175308.6477 193396.3061 153113.0253 144004.3358 170998.7332 175274.8119 155023.4435 192143.0347 0.866838831 1.033640338 0.912386171 1.006522596 0.796870027 0.749464252 0.88995541 0.912210074 0.806812715 1 17.55182115 3.241994157 24.99999215 0.855948181 0.957442164 0.26451892 0.077955275 115.9596249 844308.4575 0.021497153 0.02797447 1745.798663 -3.241994157 0.101493983 ATEVS(ph)KTPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ATEVS(0.533)KT(0.467)PEAR 97.797 0.0036328 376560000 629270 389870 459250 373980 665600 711250 579310 540630 548740 370240 TRUE FALSE 654114.0655 456827.1397 471218.4323 447952.1278 552461.5497 546072.9666 533902.1685 533383.7391 528990.9546 442781.4393 1.477284293 1.03172152 1.064223543 1.011677744 1.247707109 1.23327881 1.205791664 1.204620817 1.19469993 1 18.75623522 ATEVSKT(ph)PEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 ATEVS(0.058)KT(0.942)PEAR;ATEVS(0.033)KT(0.967)PEAR 128.71 0.00042067 520500000 744560 466820 589720 489680 762180 809970 745050 635400 628140 472030 TRUE FALSE 773955.8037 546992.7036 605088.5877 586537.2425 632624.9158 621866.7427 686651.0342 626883.5023 605533.3641 564515.2409 1.371009581 0.968960028 1.071872899 1.039010464 1.120651614 1.101594249 1.216355174 1.110481094 1.07266079 1 19.10665301 1.731897205 0.009288237 6.49E-05 2.195172982 0.104114023 0.103437127 4254.188298 38.04086506 4475.250071 4508.90419 53.93829388 -1.731897205 2.195108097 ATFMVGS(ph)YGPRPEEYEFLTPVEEAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ATFMVGSYGPRPEEYEFLTPVEEAPK 26 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 1 ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;AT(0.165)FMVGS(0.835)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK;ATFMVGS(1)YGPRPEEYEFLTPVEEAPK 233.27 1.11E-44 880969000 1020481 677270 874744 687509 1201104 1095746 1063486 868584 1017497 702869 TRUE FALSE 1060770.378 793585.8541 897540.5473 823496.2282 996940.7711 841275.5977 980127.1884 856942.0522 980877.4817 840582.7233 1.261946443 0.944090132 1.067759927 0.979673036 1.186011494 1.000824279 1.1660092 1.01946189 1.166901787 1 19.68103028 3.271073408 24.99998287 1.08709661 1.055161465 0.01313444 0.101458137 967.2523022 743739.4881 0.025788378 0.034914685 1866.695189 -3.271073408 -0.031935145 ATFMVGSYGPRPEEYEFLTPVEEAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATFMVGSYGPRPEEYEFLTPVEEAPK 26 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 184.29 1.46E-17 1180150000 609624 395562 495391 412885 652390 633219 613670 477767 552073 424847 FALSE TRUE 633692.4263 463496.6965 508301.2964 494552.4207 541496.9808 486163.4838 565568.9419 471363.3148 532204.0006 508087.6355 1.247210879 0.912237701 1.00042052 0.973360472 1.065755084 0.956849665 1.113132661 0.927720499 1.047464971 1 18.95471783 4.751502826 24.61671323 0.999300316 1.247211076 0.612622335 0.05905432 1065.405328 2026408.125 0.012897462 0.236689746 56429.06136 -4.751502826 0.24791076 ATFYGEQVDYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATFYGEQVDYYK 12 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 213.16 2.76E-08 316280000 537950 436880 549990 443830 672580 618810 631390 562800 611690 389830 FALSE TRUE 559188.6814 511910.7415 564323.1912 531618.2493 558255.0918 475100.7557 581900.002 555256.5866 589675.3964 466209.7248 1.199435901 1.098026734 1.210449206 1.140298499 1.197433391 1.019070883 1.248150716 1.191001725 1.264828606 1 18.83061957 ATGDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATGDWK 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;; 114.02 0.059648 1330990000 2221120 1733200 2083710 1641320 2405830 2234800 2367450 1994680 2104100 1634780 FALSE TRUE 2308811.533 2030863.618 2138013.194 1965968.197 1996887.876 1715801.569 2181883.083 1967944.577 2028373.852 1955083.841 1.180927121 1.038760372 1.093565989 1.005567207 1.021382221 0.877610224 1.116004867 1.006578099 1.037486889 1 20.89879905 7.999999239 0.802098708 1.012962786 42.65653286 0.412622078 0.058911213 504.4765753 1.716913284 0.019043 38184.90394 99999824.76 -7.999999239 41.64357007 ATGEADVEFVTHEDAVAAMSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATGEADVEFVTHEDAVAAMSK 21 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 144.01 1.32E-07 67702000 71276 50670 61563 58330 78524 75556 69668 70240 64732 47125 FALSE TRUE 74090.03152 59372.17834 63167.38235 69867.4999 65176.51853 58009.26406 64207.24012 69298.54769 62402.30796 56358.24149 1.314626389 1.053478192 1.120818902 1.239703335 1.156468279 1.02929514 1.139269758 1.229608055 1.107243702 1 15.78233898 4.75583331 24.12213466 1.134025488 1.314626628 0.36156992 0.07559487 2640.214924 3687087.046 0.018120607 0.522051663 56994.54752 -4.75583331 0.18060114 ATGEPGTFVCTSHLPAAASAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAASAS(1)PK;ATGEPGTFVCTSHLPAAASAS(1)PK 295.95 7.31E-62 4039510000 8029900 3511100 4381870 3334440 6000840 7753200 5548280 4655300 4800330 2885420 TRUE FALSE 8346926.652 4114104.112 4496065.132 3993982.28 4980819.36 5952636.801 5113391.316 4592903.318 4627567.061 3450762.804 2.418864212 1.19223034 1.302919206 1.157420114 1.443396618 1.725020565 1.481814777 1.33098204 1.341027281 1 21.71848388 4.74396515 24.95912493 1.355981364 2.418864672 0.748465789 0.188757348 292.4907307 1350733.77 0.045797432 0.397186525 55458.1209 -4.74396515 1.062883308 ATGGGYESDDAYHNAELFFLDIHNIHVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATGGGYESDDAYHNAELFFLDIHNIHVMR 29 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 0 ;;; 155.45 1.27E-08 89468100 38466.2 47048.2 51684.4 45285.9 52867.4 59650.1 47630.1 53493.8 50742.6 50894.7 FALSE TRUE 39984.87528 55128.36237 53031.33792 54243.31586 43881.01823 45797.26828 43896.7283 52776.80311 48916.38374 60866.54203 0.656927007 0.905725223 0.871272396 0.891184451 0.720938249 0.752421063 0.721196356 0.867090545 0.80366622 1 15.89336178 0.28766031 1.168508532 1.000239935 0.801117295 0.361649804 0.080158111 4.605667318 6.494844626 0.079601582 0.023465822 1.939368378 -0.28766031 -0.19912264 ATGHSGGGCISQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATGHSGGGCISQGR 14 0 Q9HA64;I3L3W5;I3L139;I3L407 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;;; 210.38 5.32E-09 458400000 184371 253975 243606 256420 266459 294867 227802 258836 233604 275923 FALSE TRUE 191650.1094 297593.2306 249954.5725 307139.1107 221166.3944 226388.608 209946.284 255366.7268 225196.6377 329984.829 0.580784608 0.901839129 0.757472922 0.930767368 0.670232007 0.686057625 0.63623011 0.773874143 0.682445427 1 18.33204017 -1.055417438 4.508983232 1.000010767 0.741514155 0.359908492 0.105540101 1.45E-05 3.05E-06 0.098375642 0.023186085 0.088020243 1.055417438 -0.258496611 ATGPEAAGGGGAGGGGGGYRPIIQS(ph)PGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATGPEAAGGGGAGGGGGGYRPIIQSPGYK 29 1 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 ATGPEAAGGGGAGGGGGGYRPIIQS(1)PGYK 170.19 1.66E-12 203440000 103510 71788 72691 65389 98413 113150 89908 97433 87560 73362 TRUE FALSE 107596.6547 84117.03057 74585.38718 78322.74903 81684.79341 86872.6273 82860.77603 96127.07 84408.7327 87735.8793 1.22637005 0.958752921 0.850112722 0.892710595 0.931030658 0.990160787 0.944434326 1.095641495 0.962077697 1 16.42087933 1.771389455 25 1.028880764 0.961672424 0.040304946 0.099536959 83.03700694 63265.7174 0.046722158 0.02592015 59.07305826 -1.771389455 -0.06720834 ATGSAGLLGDPECEGS(ph)PPEHS(ph)PEQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATGSAGLLGDPECEGSPPEHSPEQGR 26 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 2 ATGSAGLLGDPECEGS(1)PPEHS(1)PEQGR 104.84 0.0017585 286510000 107990 109670 117390 120210 128550 161680 119580 121550 126850 133380 TRUE FALSE 112253.5286 128504.9694 120449.2798 143987.1792 106699.1169 124132.2703 110207.0071 119920.8211 122284.6933 159513.2573 0.703725386 0.805606829 0.755105136 0.902665908 0.668904383 0.778194066 0.690895597 0.75179219 0.766611474 1 17.28331681 0.753122937 5.743701626 0.999999965 0.757726336 0.57454874 0.062476417 11.72428865 272.7157436 0.057086815 0.014369079 5.66399599 -0.753122937 -0.242273629 ATGSAGLLGDPECEGS(ph)PPEHSPEQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATGSAGLLGDPECEGSPPEHSPEQGR 26 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 ATGSAGLLGDPECEGS(1)PPEHSPEQGR 163.19 9.78E-12 221640000 65454 79146 80309 88049 83434 100940 73304 80550 83564 96001 TRUE FALSE 68038.17446 92738.70983 82401.91851 105464.8294 69251.91848 77498.21476 67558.24094 79470.359 80556.54796 114810.5579 0.592612524 0.807754195 0.717720739 0.918598701 0.603184235 0.675009478 0.588432302 0.692186855 0.701647561 1 16.80889579 -1.211598027 9.006622157 1.000000024 0.700745075 0.46398536 0.096830073 4.61E-08 3.98E-09 0.092531 0.021809764 0.061433035 1.211598027 -0.299254948 ATGSAGLLGDPECEGSPPEHS(ph)PEQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATGSAGLLGDPECEGSPPEHSPEQGR 26 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 ATGSAGLLGDPECEGS(0.176)PPEHS(0.824)PEQGR 120.18 0.00015314 250260000 122240 142380 147400 167520 170500 206780 153090 145270 163020 195340 TRUE FALSE 127066.1296 166832.6574 151241.3651 200654.956 141518.4709 158758.4788 141090.4058 143322.8933 157152.942 233613.133 0.543916894 0.714140748 0.647400954 0.858919845 0.605781315 0.67957857 0.603948947 0.613505292 0.672705939 1 17.83376185 0.930281365 19.95175084 1.000000001 0.659405644 0.616803344 0.0804664 2059.922015 589501.1345 0.075716763 0.018929191 8.516896412 -0.930281365 -0.340594356 ATIAGGGVIPHIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATIAGGGVIPHIHK 14 0 Q71UI9;P0C0S5;Q71UI9-4;Q71UI9-3 Q71UI9 H2AFV;H2AFZ Histone H2A.V;Histone H2A.Z 0 ; 162.32 2.58E-06 5892400000 5720400 5454500 6618900 5073100 7366400 7056400 6555200 6272700 6516900 6144500 FALSE TRUE 5946245.809 6391267.945 6791393.971 6076544.038 6114261.959 5417658.041 6041386.295 6188624.717 6282358.042 7348397.131 0.809189501 0.869749937 0.924200727 0.826921018 0.832053828 0.737257111 0.822136608 0.842173416 0.854929031 1 22.80899817 0.590401301 1.885370794 0.999969077 0.833428485 0.558675732 0.044293046 1.870157652 7.64463372 0.045320719 0.012602579 3.894048005 -0.590401301 -0.166540592 ATIS(ph)DEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ATISDEEIER 10 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 ATIS(1)DEEIER;AT(0.001)IS(0.999)DEEIER;ATIS(1)DEEIER;ATIS(1)DEEIER;AT(0.004)IS(0.996)DEEIER 298.61 2.35E-32 7451290000 2096510 2228820 2156300 2067180 2452210 2525480 2233060 2329130 2117460 2262770 TRUE FALSE 2179281.834 2611602.497 2212494.949 2476062.034 2035384.22 1938975.544 2058026.922 2297911.822 2041253.028 2706116.458 0.805317091 0.965073949 0.817590441 0.914987242 0.752142139 0.716515928 0.76050937 0.849154816 0.754310858 1 21.3677925 3.240767505 24.99999985 0.794457561 0.877969327 0.131010016 0.085878244 97.59106207 1105516.702 0.022732338 0.029351404 1740.874666 -3.240767505 0.083511766 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATISPLHLAAYHGHHQALEVLVQSLLDLDVR 31 0 O15084-2;O15084;O15084-4;O15084-1;B4DIW9 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 0 74.474 0.0010607 81512000 8777.4 24848 25711 23781 28801 33035 25241 28326 23918 26168 FALSE TRUE 9123.93853 29115.45071 26381.04978 28484.81082 23905.41631 25363.1219 23262.54446 27946.3363 23057.19585 31295.11858 0.291545102 0.930351187 0.842976508 0.910199805 0.76387045 0.810449778 0.74332821 0.892993462 0.736766528 1 14.93365002 4.744319996 24.99789393 0.840228835 0.291544865 0.803142931 0.082551833 253.9598169 1102250.183 0.018237989 0.164829899 55503.45223 -4.744319996 -0.54868397 ATLAENPNLFDDHEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATLAENPNLFDDHEEGR 17 0 Q9BU68 Q9BU68 PRR15L Proline-rich protein 15-like protein 0 ;; 249.16 5.55E-21 798620000 276754 379660 335784 338452 341713 422362 351795 371602 350449 439421 FALSE TRUE 287680.4616 444863.6517 344534.8069 405396.7954 283628.7463 324274.8265 324220.3887 366621.283 337836.4089 525517.1317 0.547423565 0.846525498 0.65561099 0.771424509 0.539713606 0.617058526 0.616954937 0.69763907 0.642864692 1 19.00337827 -1.15453574 3.995063173 1.000133098 0.664041927 0.565754031 0.089421248 9805428.331 5667364.799 11146.46009 0.019897081 0.070059053 1.15453574 -0.33609117 ATLENITNLRPVGEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATLENITNLRPVGEDFR 17 1 Q9NWV4 Q9NWV4 C1orf123 UPF0587 protein C1orf123 0 ; 129.62 3.01E-05 761780000 486670 499560 516380 504780 551320 616250 528130 539970 483770 574720 FALSE TRUE 505884.1074 585355.544 529837.287 604623.9774 457606.8233 473135.2769 486733.7906 532732.5854 466359.2122 687325.3803 0.736018372 0.851642556 0.770868212 0.879676489 0.665779028 0.688371607 0.708156289 0.775080625 0.678513009 1 19.39063371 -1.265611424 3.565959513 1.000571461 0.753294235 0.547660421 0.067992896 1404054079 2367440991 9216486.214 0.016645284 0.054248605 1.265611424 -0.247277226 ATLLPEAGRS(ph)PEEAGFPGDPHEDKQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATLLPEAGRSPEEAGFPGDPHEDKQ 25 2 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 ATLLPEAGRS(1)PEEAGFPGDPHEDKQ;AT(0.1)LLPEAGRS(0.9)PEEAGFPGDPHEDKQ;AT(0.004)LLPEAGRS(0.996)PEEAGFPGDPHEDKQ;AT(0.013)LLPEAGRS(0.987)PEEAGFPGDPHEDKQ 131.9 3.97E-05 1259330000 947976 569820 713193 643213 997378 829244 862051 780951 901664 631485 TRUE FALSE 985402.8245 667682.1524 731779.3955 770438.6116 827844.0438 636664.6483 794481.1901 770483.6292 869213.2888 755212.3952 1.304802239 0.884098509 0.968971643 1.020161502 1.096173804 0.843027276 1.051997021 1.020221111 1.150952095 1 19.52652292 -0.937568043 3.948841451 0.999998391 1.026727684 0.001151917 0.124791265 1855.615298 30321083.26 126.4689861 0.026969075 0.115460107 0.937568043 0.026729294 ATLPDADKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATLPDADKER 10 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8 P12814-3 ACTN1 Alpha-actinin-1 0 ;; 93.959 0.0076883 819140000 1297770 1134810 1101170 1164900 1534300 1642460 1696160 1247800 1183230 1445520 FALSE TRUE 1349006.962 1329704.79 1129867.395 1395313.743 1273500.234 1261023.557 1563210.547 1231075.282 1140645.783 1728741.968 0.780340263 0.769174819 0.653577813 0.807126667 0.736662994 0.729445794 0.904247468 0.712122055 0.659812629 1 20.72129112 -1.194413504 4.31696149 1.000080782 0.752505443 0.539573148 0.069176548 5.31E-05 9.91E-06 0.064834879 0.015276652 0.063912602 1.194413504 -0.247575339 ATLPS(ph)PDKLPGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 ATLPS(1)PDKLPGFK;AT(0.001)LPS(0.999)PDKLPGFK 95.347 0.0028692 1097910000 1277490 418780 606540 433010 1019070 1088800 954620 620970 788450 375430 TRUE FALSE 1327926.292 490702.2073 622346.9307 518658.0856 845848.8454 835942.7009 879794.39 612646.9129 760073.8385 448988.3205 2.957596514 1.092906396 1.386109398 1.155170551 1.88389944 1.861836183 1.959503956 1.364505233 1.69285882 1 18.77631839 0.243265369 0.903557141 0.995072931 1.680521271 0.145810254 0.509058307 6.779160646 6.400647724 0.561986276 0.154789424 1.750916231 -0.243265369 0.685448341 ATLPSPDKLPGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 113.76 0.00072662 715640000 681280 401980 637260 414420 821380 664570 739250 586440 719030 441190 FALSE TRUE 708177.4605 471016.938 653867.5191 496391.0391 681762.121 510233.6892 681305.6533 578579.731 693152.2508 527632.7334 1.342178784 0.892698478 1.239247449 0.940788938 1.292114908 0.967024327 1.291249785 1.096557689 1.31370214 1 19.00917454 2.223599511 24.99932236 1.177967638 1.108500343 0.033753634 0.164220754 878.1935485 1467410.5 0.055097721 0.040852449 167.3399022 -2.223599511 -0.069467295 ATLSSTSGLDLMSESGEGEIS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATLSSTSGLDLMSESGEGEISPQR 24 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ATLSSTSGLDLMSESGEGEIS(1)PQR;ATLSSTSGLDLMSESGEGEIS(1)PQR 259.71 3.56E-44 222170000 231533 284058 288355 262652 260611 330084 319850 293528 296344 273914 TRUE FALSE 240674.1016 332842.7518 295869.7682 314603.7817 216312.4353 253426.9935 294779.3212 289593.7373 285678.6373 327582.2039 0.734698341 1.016058711 0.903192434 0.960381174 0.66033024 0.773628697 0.899863661 0.88403379 0.872082286 1 18.32149746 -0.574144885 6.395467907 0.99994973 0.860729978 0.153606147 0.100843685 7.26E-10 0 0.09747941 0.022976117 0.266596912 0.574144885 -0.139219752 GQLTKS(ph)PLAQMEEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQLTKSPLAQMEEERR 16 2 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 1 GQLT(0.131)KS(0.869)PLAQMEEERR;GQLT(0.089)KS(0.911)PLAQMEEERR 88.071 0.0032636 206507000 192568 284770 271220 161306 377560 362380 165666 271240 304690 453010 TRUE FALSE 200170.7333 333677.0323 278288.216 193211.8453 313382.4861 278222.7369 152680.666 267604.4715 293724.2664 541768.6361 0.369476415 0.615903192 0.513666162 0.356631655 0.578443389 0.5135453 0.281818946 0.493946038 0.542158122 1 19.04731735 0.698460212 2.444833514 0.999891806 0.466541392 0.727089591 0.097721242 0.905310261 6.671824045 0.091607657 0.024547239 4.994134238 -0.698460212 -0.533350414 ATLVDHGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATLVDHGIR 9 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 111.65 0.0020901 480390000 327453 445081 389893 470799 507492 512508 412100 399572 382270 522696 FALSE TRUE 340381.0973 521520.1995 400053.9319 563921.637 421228.6911 393485.7841 379798.5252 394216.3909 368512.1774 625108.2736 0.544515425 0.834287789 0.639975423 0.902118338 0.67384917 0.629468207 0.607572386 0.630636975 0.589517357 1 19.25374657 -1.021153888 4.64176244 1.000009278 0.675652032 0.464683695 0.105422243 13485239.85 2966654.31 1275.041454 0.024313475 0.095245861 1.021153888 -0.324357246 ATLYVTAIEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATLYVTAIEDR 11 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4;E9PNR9 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 132.25 0.00043372 156348000 109151 170961 160183 162664 161074 196120 138084 150601 142595 188110 FALSE TRUE 113460.3658 200322.2219 164357.5006 194838.4537 133694.699 150574.1022 127260.6153 148582.4399 137463.0338 224966.5529 0.504343265 0.890453355 0.730586385 0.866077429 0.594287005 0.669317729 0.565686826 0.66046458 0.61103765 1 17.779351 -1.051580038 4.416209763 1.000018919 0.681310452 0.404437651 0.117508995 15319358.55 3647818.865 3052.375877 0.027033603 0.088801431 1.051580038 -0.318708467 ATMAQNENVVVQPVVAENIPVIPLSDS(ph)PPPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ATMAQNENVVVQPVVAENIPVIPLS(0.222)DS(0.605)PPPS(0.174)R 78.642 0.00087697 20628000 34250 47340 46564 43376 46158 55980 41193 43997 41189 47179 TRUE FALSE 35602.21645 55470.27675 47777.49609 51955.64334 38312.07965 42979.49339 37964.18502 43407.29218 39706.61594 56422.82175 0.630989648 0.983117735 0.846776085 0.920826746 0.679017434 0.761739524 0.672851585 0.769321541 0.703733254 1 15.7839912 5.026953458 14.33053383 0.799091108 0.221900023 0.174918706 0.115348256 1169483.39 18124708.81 0.027348394 15326600.08 106402.8985 -5.026953458 -0.577191085 ATMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATMSPR 6 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AT(0.023)MS(0.977)PR;AT(0.001)MS(0.999)PR;AT(0.006)MS(0.994)PR 89.752 0.052248 1381100000 2155410 2389860 2089900 2197830 2903990 2934230 2438710 2339570 2091820 3318380 TRUE FALSE 2240507.251 2800299.864 2144364.511 2632554.214 2410370.817 2252799.551 2247557.538 2308211.891 2016535.807 3968553.027 0.56456528 0.705622388 0.540339135 0.66335367 0.607367673 0.567662706 0.566341818 0.581625564 0.508128729 1 21.92018165 -2.031085742 2.772218373 1.497869374 0.591748419 0.834661853 0.054809428 23096378.11 6671206.199 73175079.04 0.012622112 0.009309241 2.031085742 -0.906120955 ATNES(ph)EDEIPQLVPIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ATNESEDEIPQLVPIGK 17 0 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 ATNES(1)EDEIPQLVPIGK;AT(0.123)NES(0.877)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;ATNES(1)EDEIPQLVPIGK;AT(0.001)NES(0.999)EDEIPQLVPIGK;AT(0.01)NES(0.99)EDEIPQLVPIGK 316.02 2.88E-58 4320430000 3907490 2976940 3928630 2916700 4176140 4019790 3914810 3428530 3574920 2888165 TRUE FALSE 4061760.722 3488206.288 4031013.325 3493614.555 3466281.214 3086254.693 3607956.963 3382576.163 3446259.328 3454045.634 1.175942982 1.009890041 1.167041131 1.011455819 1.003542391 0.893518795 1.044559726 0.979308475 0.997745743 1 21.71985571 3.577302582 5.45313965 0.98637952 1.106357125 0.528604678 0.055289329 0.176724522 7.762592677 0.01389214 0.021644782 3778.353451 -3.577302582 0.119977605 ATPATAPGTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATPATAPGTSPR 12 0 Q96P47;Q96P47-2;Q96P47-4;H0Y873;Q96P47-5 Q96P47 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 ATPATAPGT(0.022)S(0.978)PR 101.38 0.0028358 174680000 198000 194990 194030 179950 240810 250930 231060 217250 188030 235400 TRUE FALSE 205817.1929 228478.0157 199086.5812 215543.5729 199877.2022 192655.3104 212948.9134 214338.1191 181262.837 281522.123 0.731087101 0.811581034 0.70717917 0.765636358 0.709987549 0.684334532 0.756419819 0.761354443 0.643867115 1 18.10288877 -1.054611311 4.976484813 1.000005246 0.734196551 0.764160678 0.04492166 2.51E-06 4.76E-07 0.041676458 0.009823041 0.088183775 1.054611311 -0.265808695 ATQPETTEEVTDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATQPETTEEVTDLKR 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 124.43 0.00015493 140110000 56779 47252 57801 51407 69648 79820 66166 61470 57535 51962 FALSE TRUE 59020.67876 55367.16343 59307.34154 61575.15117 57809.25784 61283.01468 60979.73603 60646.09519 55464.32659 62142.95903 0.949756492 0.890964388 0.954369449 0.990862877 0.930262394 0.986161838 0.9812815 0.975912576 0.89252793 1 15.92330332 4.052925258 8.958987349 0.965868621 0.920684381 0.223260444 0.03303862 0.412942716 64.55846201 0.00777431 0.016842992 11296.01493 -4.052925258 -0.04518424 ATQQQHDFTLTQTADGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ATQQQHDFTLTQTADGR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 264.88 1.67E-27 1773250000 946580 948490 1205670 1097180 1293840 1400500 1102110 1071310 1220140 1028720 FALSE TRUE 983951.7093 1111385.779 1237090.751 1314198.929 1073913.539 1075255.1 1015723.738 1056950.842 1176227.4 1230277.988 0.799779984 0.903361509 1.00553758 1.068212991 0.872903156 0.87399361 0.825605065 0.859115462 0.956066362 1 20.23055291 ATRPAS(ph)TSQPDPSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATRPASTSQPDPSPDR 16 1 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 AT(0.003)RPAS(0.3)T(0.3)S(0.3)QPDPS(0.098)PDR 118.21 0.00076363 579270000 382330 421070 390370 437470 402610 497340 468940 425720 401050 342490 TRUE FALSE 397424.6836 493385.497 400543.3629 524000.2603 334174.496 381840.3223 432183.2575 420013.9197 386616.2888 409594.3581 0.970288471 1.204571028 0.977902539 1.279315132 0.815866941 0.93224019 1.05514944 1.025438733 0.943900425 1 18.64383632 3.23409778 24.99999991 0.972561318 1.105621779 0.310521197 0.105810117 147.6755793 827251.6685 0.029271887 0.036132109 1714.343242 -3.23409778 0.133060461 ATRPASTS(ph)QPDPSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATRPASTSQPDPSPDR 16 1 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 AT(0.001)RPAS(0.284)T(0.055)S(0.494)QPDPS(0.167)PDR 123.02 0.00023715 487140000 376080 455480 408750 485660 373520 552630 451460 466890 434120 413320 TRUE FALSE 390927.9288 533705.1469 419402.3608 581722.0984 310029.2038 424290.0577 416073.3855 460632.1032 418496.106 494302.1405 0.790868371 1.079714416 0.848473689 1.176855309 0.627205869 0.858361765 0.841738992 0.931883691 0.846640287 1 18.91503363 3.244912835 24.99999336 0.853098698 0.972565882 0.167242163 0.13440277 277.2258855 1091051.259 0.035286706 0.046648818 1757.570825 -3.244912835 0.119467183 ATRPASTSQPDPS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATRPASTSQPDPSPDR 16 1 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 AT(0.015)RPAS(0.058)T(0.058)S(0.058)QPDPS(0.81)PDR 79.022 0.051326 73862000 51675 56820 55605 56137 46111 63954 56256 53766 53032 40056 TRUE FALSE 53715.1689 66578.393 57054.11198 67240.73105 38273.06869 49101.65273 51846.50772 53045.35471 51123.38868 47904.20628 1.121303808 1.389823528 1.191004223 1.403649831 0.798950064 1.024996687 1.082295517 1.107321441 1.067200412 1 15.54786472 3.254358765 24.99994676 1.029956134 1.278440837 0.568335014 0.111722213 184.8177619 292465.0267 0.030479671 0.041132971 1796.216846 -3.254358765 0.248484703 ATS(ph)FSSAGEVPKPRPPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSFSSAGEVPKPRPPSTR 19 2 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H7BZT5 O15231-3 ZNF185 Zinc finger protein 185 1 AT(0.001)S(0.941)FS(0.032)S(0.026)AGEVPKPRPPSTR;AT(0.122)S(0.878)FS(0.001)SAGEVPKPRPPSTR 180.41 1.76E-14 1310810000 402370 399720 507480 450040 664090 650100 552230 490830 513030 490270 TRUE FALSE 418255.8783 468368.8006 520705.3457 539056.5688 551208.219 499124.1274 508944.7696 484251.2267 494566.1505 586329.0197 0.713346712 0.798815656 0.888077049 0.919375556 0.940100525 0.851269698 0.868019069 0.825903563 0.843495945 1 19.16135094 4.500543814 2.566182748 0.882983078 0.711341797 0.567757478 0.049602426 0.254968858 2.904144372 0.012821732 0.074736976 31662.39875 -4.500543814 -0.17164128 ATS(ph)GSSLPVGINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSGSSLPVGINR 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 AT(0.116)S(0.883)GS(0.001)SLPVGINR 111.38 0.00042967 0 140640 175300 172330 190390 192290 238820 197450 176440 177730 202970 TRUE FALSE 146192.5758 205406.4114 176821.0614 228048.5737 159604.6145 183357.6744 181973.3531 174075.1104 171333.532 242738.0854 0.602264682 0.846205947 0.728443833 0.939484108 0.657517811 0.7553725 0.749669557 0.71713143 0.705837041 1 17.88904096 -1.120020341 4.279034885 1.000043139 0.74861494 0.425779445 0.08885209 1.745170468 46971925.58 4105.823216 0.019277303 0.075854205 1.120020341 -0.251428199 ATS(ph)LPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSLPSIPNPFPELCSPPSQSPILGGPSSAR 31 0 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 AT(0.467)S(0.526)LPS(0.007)IPNPFPELCS(0.367)PPS(0.117)QS(0.511)PILGGPS(0.003)S(0.002)AR;AT(0.467)S(0.526)LPS(0.008)IPNPFPELCS(0.024)PPS(0.227)QS(0.747)PILGGPS(0.001)S(0.001)AR 119.05 1.24E-05 151606000 62055 82625 77961 93163 95442 116651 85635 93451 92740 95597 TRUE FALSE 64504.97932 96815.20102 79992.72771 111590.3633 79218.80293 89560.57311 78922.70493 92198.4422 89402.30552 114327.4018 0.564212763 0.846824116 0.699681147 0.976059646 0.692911775 0.783369268 0.690321862 0.806442207 0.781984932 1 16.8028117 -4.99999994 0.30556972 3.023193788 0.753967093 0.33078615 0.10363381 323.612504 2.959597863 420.4198511 0.092572809 1.00E-05 4.99999994 -2.269226695 ATS(ph)NVFAMFDQSQIQEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.164)S(0.836)NVFAMFDQSQIQEFK 280.91 9.10E-39 441040000 769980 648140 828090 620040 1267800 994260 820370 836260 896640 693680 TRUE FALSE 800379.405 759453.0032 849670.7057 742682.0614 1052299.809 763358.1832 756067.2558 825051.3025 864370.1015 829593.3147 0.964785264 0.915452174 1.024201486 0.895236314 1.268452614 0.920159516 0.91137096 0.994525014 1.041920283 1 19.66204474 4.236387199 24.9969294 1.003493868 0.940118714 0.065560764 0.100284099 162.546433 1869581.841 0.024458788 0.057289382 17234.04408 -4.236387199 -0.063375153 ATS(ph)PGPTDLETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSPGPTDLETR 12 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 AT(0.042)S(0.956)PGPT(0.002)DLETR 116.81 0.00020339 0 138420 118560 133220 146160 162950 178950 159730 147500 144660 130690 TRUE FALSE 143884.9285 138921.7577 136691.8226 175070.0118 135251.8172 137391.5745 147209.9452 145523.0038 139453.7149 156296.2033 0.920591322 0.88883642 0.874569054 1.120116856 0.865355744 0.879046142 0.941865139 0.931071905 0.892239939 1 17.25392321 -2.328236218 2.183607005 1.389439288 0.925263314 0.096133274 0.070008147 9520917.764 1249782.836 18290487.68 0.016908121 0.004696386 2.328236218 -0.464175974 ATS(ph)PLVSLYPALECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 AT(0.018)S(0.982)PLVSLYPALECR;AT(0.022)S(0.978)PLVSLYPALECR;ATS(1)PLVSLYPALECR;AT(0.021)S(0.979)PLVSLYPALECR 261.39 6.32E-25 1067175000 1210600 1394650 1189330 1298360 1444720 1634340 1354740 1414210 1367220 1556220 TRUE FALSE 1258395.423 1634170.289 1220324.917 1555171.733 1199147.01 1254789.304 1248551.939 1395254.828 1318014.019 1861131.513 0.676145352 0.878052022 0.655689782 0.835605502 0.644310733 0.674207757 0.670856374 0.749680943 0.708178874 1 20.82774857 -1.27822282 4.538686918 1.000146471 0.723514854 0.55626415 0.074624 0.00010325 1.64E-05 0.067451264 0.015890036 0.052695943 1.27822282 -0.276631617 ATS(ph)PRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSPRPR 7 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 AT(0.154)S(0.846)PRPR 67.993 0.038552 226220000 363940 433450 390900 382000 413170 478760 436330 440620 405970 493200 TRUE FALSE 378308.6322 507891.6657 401087.1751 457558.4598 342939.511 367575.2457 402129.3145 434714.2096 391359.219 589833.0971 0.64138251 0.861076919 0.680001134 0.77574226 0.581417884 0.623185181 0.681767972 0.737012236 0.663508408 1 19.16994725 -1.29544009 4.900997098 1.000106465 0.697830262 0.590766472 0.076366826 8.76E-05 1.26E-05 0.072916341 0.017180518 0.050647721 1.29544009 -0.302276202 ATS(ph)PVKSTTSITDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATSPVKSTTSITDAK 15 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 AT(0.16)S(0.838)PVKS(0.002)TTSITDAK;AT(0.04)S(0.96)PVKSTTSITDAK;AT(0.018)S(0.982)PVKSTTSITDAK;AT(0.017)S(0.907)PVKS(0.056)T(0.014)T(0.006)SITDAK 171.04 6.70E-07 2230930000 2672720 1535350 2021110 1021940 3389890 2779940 1920130 1953930 2464820 1639830 TRUE FALSE 2778241.049 1799034.419 2073781.787 1224076.682 2813677.709 2134341.065 1769625.193 1927740.764 2376111.61 1961123.292 1.416658025 0.917348963 1.057445901 0.624171202 1.434727597 1.088325795 0.902352851 0.982977854 1.21160746 1 20.90324881 4.748056927 24.15236179 1.01977992 1.416658369 0.258116942 0.199406564 1096.039541 2787508.365 0.045873042 0.577777692 55983.0979 -4.748056927 0.396878449 ATS(ph)SPMLYEVVYEAGALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSSPMLYEVVYEAGALER 19 0 Q5T4L2;Q5T4K9;Q5T4L1;Q8TEY5-2;Q8TEY5 Q5T4L2 CREB3L4 Cyclic AMP-responsive element-binding protein 3-like protein 4;Processed cyclic AMP-responsive element-binding protein 3-like protein 4 1 AT(0.082)S(0.459)S(0.459)PMLYEVVYEAGALER;AT(0.06)S(0.47)S(0.47)PMLYEVVYEAGALER 85.563 0.0031642 127385000 46355 55673 54326 57567 62595 67244 51914 56713 52227 58445 TRUE FALSE 48185.13119 65234.40467 55741.78019 68953.58078 51955.12426 51627.60009 47844.84503 55952.855 50347.36047 69896.17875 0.689381481 0.933304307 0.797493957 0.986514313 0.743318522 0.738632655 0.684513029 0.800513791 0.720316352 1 16.09292596 ATS(ph)SSSGSLSATGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATS(0.981)S(0.017)S(0.001)SGSLSATGR 258.79 2.25E-24 203220000 252230 293680 233020 266780 266070 312540 273070 252300 246070 329320 TRUE FALSE 262188.2352 344117.2555 239092.6926 319548.2877 220843.5164 239957.3216 251666.0599 248918.3312 237213.9888 393843.9488 0.665716043 0.873740111 0.607074689 0.811357617 0.56073863 0.609270048 0.638999433 0.632022739 0.602304516 1 18.58726458 -1.08509247 4.335241683 1.000028702 0.666789128 0.531739687 0.093803044 1.45513444 53377475.97 4048.700351 0.021622131 0.08220676 1.08509247 -0.333239574 ATS(ph)VDYSSFADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSVDYSSFADR 12 0 Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 AT(0.007)S(0.993)VDYSSFADR;AT(0.001)S(0.999)VDYSSFADR 261.38 2.44E-21 544940000 626040 754590 686950 688910 879180 901560 728520 703310 770000 836860 TRUE FALSE 650756.5426 884184.9626 704852.4813 825174.3418 729737.2976 692186.3533 671416.6988 693883.2798 742287.8504 1000826.694 0.65021901 0.883454616 0.704270265 0.824492738 0.729134526 0.691614599 0.670862101 0.693310124 0.741674712 1 19.93276074 0.934030729 21.00631746 1 0.731067177 0.585397906 0.067686967 3506.417192 1116536.31 0.064091571 0.016022893 8.590743033 -0.934030729 -0.268932823 ATSACAPISS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSACAPISSPK 12 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 ATSACAPIS(0.016)S(0.984)PK;ATSACAPIS(0.037)S(0.963)PK 120.53 0.00020669 99426000 617690 292530 361720 301000 508110 592270 477040 417020 462480 293810 TRUE FALSE 642076.8782 342769.7519 371146.7204 360536.9016 421741.6437 454724.2684 439648.3583 411430.529 445835.4351 351376.4442 1.827319073 0.975505779 1.056265229 1.026070209 1.200255881 1.294122802 1.251217506 1.170910958 1.268825621 1 18.42265795 4.747813348 24.79853042 1.15030411 1.827319469 0.772839736 0.111918587 550.1107516 1474334.201 0.028222522 0.353709257 55951.70789 -4.747813348 0.67701536 ATSAGSS(ph)PSCSLAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSAGSSPSCSLAGR 15 0 Q9BXB5;Q9BXB5-2 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 ATSAGS(0.016)S(0.982)PS(0.002)CSLAGR;ATSAGS(0.128)S(0.835)PS(0.023)CS(0.014)LAGR 156.17 2.28E-06 262140000 518020 621020 572500 579900 646520 712680 533110 583100 523440 531530 TRUE FALSE 538471.8296 727675.3541 587419.8203 694602.4892 536624.7613 547170.8708 491323.4452 575284.4983 504601.4966 635673.1267 0.847089183 1.144731975 0.924091008 1.092703876 0.844183494 0.860773954 0.772918383 0.905000501 0.793806558 1 19.27792557 3.219716183 24.98884295 0.855122755 1.006762222 0.332059727 0.09638345 233.2714071 309331.1613 0.025262042 0.030241796 1658.5027 -3.219716183 0.151639467 ATSCFPRPMT(ph)PR ddPTM_MDA-MB-175_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 102.52 0.0037915 1576260000 1134320 1284620 1188920 1248530 1311290 1473920 1056970 1160710 1087970 1288570 TRUE FALSE 1179103.829 1505243.492 1219904.232 1495485.508 1088397.394 1131624.417 974121.9295 1145152.581 1048814.172 1541040.62 0.765134815 0.976770808 0.791610692 0.970438733 0.706274306 0.734324847 0.632119567 0.743103437 0.680588272 1 20.55547346 3.220498741 24.99729778 0.728613339 0.877160486 0.223618903 0.11158019 277.6086245 384204.3666 0.029291945 0.035075678 1661.493861 -3.220498741 0.148547147 ATSFS(ph)SAGEVPKPRPPSTR ddPTM_MDA-MB-175_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(0.002)S(0.326)FS(0.672)SAGEVPKPRPPSTR 185.92 1.13E-14 1429300000 302250 290790 314600 322390 481230 431290 408380 367020 377020 314700 TRUE FALSE 314183.0634 340730.9205 322798.7344 386157.7798 399430.6965 331129.4338 376370.1085 362100.6972 363451.1238 376359.4397 0.834795226 0.905333797 0.857687361 1.026034527 1.061301124 0.879822316 1.000028347 0.96211403 0.96570216 1 18.52175163 3.748734391 24.95428577 0.981979175 0.869878285 0.567365613 0.04755575 522.5213287 1281639.701 0.012221988 0.021725259 5607.049514 -3.748734391 -0.11210089 ATSFSSAGEVPKPRPPST(ph)R ddPTM_MDA-MB-175_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 ATS(0.053)FS(0.012)S(0.065)AGEVPKPRPPS(0.159)T(0.711)R 108.96 0.00042561 588380000 94900 88688 116590 103070 155640 140340 118760 121280 123880 115230 TRUE FALSE 98646.72528 103919.4741 119628.4312 123456.9384 129184.3684 107748.1619 109451.2809 119654.44 119421.583 137807.1123 0.715831887 0.754093692 0.868086046 0.895867683 0.937428891 0.78187664 0.794235356 0.868274779 0.866585048 1 17.07229082 -4.999998351 0.022305542 2.091979657 1.50E-06 0.467468882 0.060221611 2820.179086 4.757560991 310.9830695 158.7826365 1.00E-05 4.999998351 -2.091978154 ATSILS(ph)YLSDSDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSILSYLSDSDLR 14 0 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILS(0.669)YLS(0.315)DS(0.015)DLR 71.548 0.043123 18777000 26380 25761 28332 25879 31458 39973 32138 27493 26074 24235 TRUE FALSE 27421.50277 30185.25136 29070.35519 30997.78896 26110.7804 30689.87655 29618.93958 27124.5013 25135.60183 28983.38424 0.946111142 1.041467453 1.003000718 1.069502053 0.900887908 1.058878297 1.021928265 0.935863841 0.867241783 1 14.82293844 1.656119652 5.188800773 0.923984535 1.007517484 0.246959436 0.056616068 0.176616745 10.47276091 0.028614182 0.013783497 45.30223744 -1.656119652 0.083532949 ATSILSYLS(ph)DSDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ATSILSYLSDSDLR 14 0 A0A499FJE4;Q96MK2;Q96MK2-2 A0A499FJE4 FAM65C Protein FAM65C 1 ATSILS(0.021)YLS(0.975)DS(0.004)DLR;ATSILSYLS(1)DSDLR;ATSILS(0.028)YLS(0.971)DS(0.001)DLR;ATSILS(0.204)Y(0.004)LS(0.789)DS(0.002)DLR 178.14 2.12E-06 81147000 94583 159173 126019 160952 121613 170183 131211 144551 112285 158604 TRUE FALSE 98317.20987 186509.7246 129303.1587 192787.8252 100941.2657 130660.5774 120926.339 142613.5303 108243.8848 189679.4171 0.518333572 0.983289212 0.681693146 1.016387693 0.532167734 0.68884953 0.637530106 0.751866135 0.570667532 1 17.53320361 ATSLGRPEEEEDELAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSLGRPEEEEDELAHR 17 1 P36551;D6RER6;P36551-2 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 ; 141 3.85E-07 791290000 370470 589680 537280 605080 562650 707390 502300 520230 481990 539620 FALSE TRUE 385096.4417 690952.9529 551281.9582 724763.018 467010.954 543109.3931 462928.4135 513257.1678 464643.2741 645348.2074 0.5967266 1.070666882 0.854239544 1.123057304 0.72365732 0.841575737 0.717331215 0.795318189 0.719988479 1 19.29971827 ATSS(ph)PMLYEVVYEAGALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATSSPMLYEVVYEAGALER 19 0 Q5T4L2;Q5T4K9;Q5T4L1;Q8TEY5-2;Q8TEY5 Q5T4L2 CREB3L4 Cyclic AMP-responsive element-binding protein 3-like protein 4;Processed cyclic AMP-responsive element-binding protein 3-like protein 4 1 AT(0.024)S(0.141)S(0.835)PMLYEVVYEAGALER;AT(0.014)S(0.148)S(0.838)PMLYEVVYEAGALER;AT(0.002)S(0.014)S(0.984)PMLYEVVYEAGALER 199.08 7.46E-16 188721000 106578 125754 119402 132966 140662 164533 121780 132658 108095 135153 TRUE FALSE 110785.7817 147351.2713 122513.7142 159266.2779 116752.3235 126322.7043 112234.5654 130879.9365 104204.6821 161633.6427 0.685412887 0.911637385 0.757971621 0.985353515 0.722326872 0.781537198 0.694376267 0.809732023 0.644696737 1 17.30236799 ATSS(ph)SSGSLSATGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSS(0.93)S(0.07)SGSLSATGR;ATS(0.003)S(0.695)S(0.302)S(0.001)GSLSATGR 268.21 4.11E-25 660740000 557630 633970 506370 580350 571670 733910 568160 573300 479720 649200 TRUE FALSE 579645.663 742849.4159 519566.4182 695141.4978 474497.7376 563470.525 523626.1346 565615.8512 462454.9709 776398.3103 0.74658285 0.956789068 0.669200862 0.895341333 0.61115246 0.725749293 0.674429771 0.728512471 0.595641393 1 19.56643745 3.244166699 24.99998485 0.707505968 0.816409433 0.110175155 0.12716187 251.4726286 1121419.312 0.032251643 0.042488738 1754.553838 -3.244166699 0.108903464 ATSSHFS(ph)ASEESMDFLDK ddPTM_MDA-MB-175_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 AT(0.002)S(0.001)S(0.001)HFS(0.992)AS(0.004)EESMDFLDK 187.86 2.63E-14 108960000 90138 124060 139800 122030 170680 180740 162690 155510 152260 115890 TRUE FALSE 93696.71784 145366.3399 143443.3028 146167.1698 141667.8746 138765.8741 149937.9327 153425.6428 146780.1923 138596.4267 0.676039925 1.048846233 1.034971148 1.054624375 1.02216109 1.001222596 1.081831158 1.10699566 1.059047451 1 17.08053054 4.738614229 8.366890122 1.051094928 0.673600928 0.922212364 0.03215652 0.023768987 24.44200514 0.008580496 0.050600047 54779.01624 -4.738614229 -0.377494 ATSSSNPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 AT(0.005)S(0.005)S(0.005)S(0.005)NPS(0.49)S(0.49)PAPDWYKDFVTDADAEVLEHSGK 140.61 3.96E-10 65537000 61354 28506 50603 45888 78607 62513 80389 49519 70700 29288 TRUE FALSE 63776.3033 33401.68375 51921.75575 54964.50944 65245.41022 47995.30314 74087.90012 48855.2788 68155.52081 35026.42285 1.820805498 0.953613902 1.482359645 1.569229883 1.862748317 1.370259914 2.1152003 1.394812111 1.945831611 1 15.09615604 3.804339501 3.576532867 1.642810881 1.358272382 0.048814066 0.360562427 0.522124962 13.23057892 0.086732506 0.163885241 6372.935175 -3.804339501 -0.284538499 ATSSSNPSS(ph)PAPDWYKDFVTDADAEVLEHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100;P46100-4;P46100-2;P46100-5;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 ATSSS(0.002)NPS(0.154)S(0.844)PAPDWYKDFVTDADAEVLEHSGK 170.8 1.67E-14 61397000 74427 54143 76508 65365 107090 96372 104330 83811 100790 54529 TRUE FALSE 77365.43543 63441.63908 78501.86133 78294.0019 88886.88005 73991.06353 96152.34198 82687.65063 97162.58759 65212.91353 1.186351464 0.972838594 1.203777858 1.200590461 1.363025745 1.134607542 1.474437144 1.267964367 1.48992864 1 15.99287006 3.733369653 1.714016322 1.304842048 1.083396042 0.202080434 0.148946097 0.478155043 2.71783893 0.040517521 0.090531425 5412.147864 -3.733369653 -0.221446006 ATSSSS(ph)GSLSATGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSSS(0.026)S(0.86)GS(0.114)LSATGR;ATSSS(0.006)S(0.55)GS(0.444)LSATGR 248.76 5.69E-18 321440000 289270 313840 250763 298440 301400 377230 287050 276480 280880 353070 TRUE FALSE 300690.603 367739.5787 257298.0898 357470.5412 250168.1357 289624.0495 264550.2709 272774.2378 270771.1837 422247.3066 0.712119647 0.870910419 0.609354011 0.846590459 0.59246828 0.685910946 0.626529209 0.646005868 0.641262074 1 18.68772869 -1.09749141 4.348883355 1.000030018 0.690374872 0.509125312 0.090606942 12113070.7 3056875.389 4230.70778 0.020616769 0.079892974 1.09749141 -0.309655147 ATSSSSGS(ph)LSATGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 ATSSS(0.001)S(0.01)GS(0.987)LS(0.001)ATGR 178.03 2.13E-06 114020000 95769 114310 94287 113970 113350 129150 107650 102930 94963 114200 TRUE FALSE 99550.03407 133941.8533 96744.19668 136512.9258 94082.80749 99156.86979 99212.11171 101550.3917 91545.30018 136575.3035 0.728902162 0.980717962 0.708357911 0.999543273 0.688871304 0.726023426 0.726427906 0.743548717 0.670291757 1 17.0593371 3.196041187 24.99990715 0.742728476 0.852975368 0.118925468 0.122061703 235.9608537 138735.8097 0.03182626 0.038039914 1570.51174 -3.196041187 0.110246892 ATSTS(ph)PNSQSSK ddPTM_MDA-MB-175_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 ATSTS(0.992)PNS(0.008)QSSK;ATST(0.002)S(0.996)PNS(0.002)QSSK;ATST(0.003)S(0.995)PNS(0.003)QSSK;ATST(0.002)S(0.996)PNS(0.002)QSSK;ATST(0.028)S(0.971)PNS(0.001)QSSK;ATST(0.003)S(0.997)PNSQSSK;ATST(0.041)S(0.958)PNS(0.001)QSSK;ATSTS(1)PNSQSSK;ATST(0.013)S(0.984)PNS(0.003)QS(0.001)SK 279.68 5.73E-28 4608457000 13896957 10280380 12663833 9490252 14611473 14861473 14943128 13034737 13721906 10829999 TRUE FALSE 14445619.59 12045955.29 12993862.89 11367395.52 12127820.04 11410121.12 13771846.58 12860027.67 13228057.28 12951929.95 1.115325642 0.930050992 1.003237582 0.877660361 0.936371652 0.880959144 1.063304591 0.992904356 1.021319397 1 23.62666375 2.223009102 24.99485775 1.017606999 0.953551652 0.173885797 0.06598364 420.3517897 675597.6332 0.024242778 0.017967215 167.1125636 -2.223009102 -0.064055348 ATSVALPGWS(ph)PSETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWS(0.984)PS(0.016)ETR 161.24 1.74E-06 47347000 106620 124830 101390 113540 112250 130280 96527 99704 88918 104050 TRUE FALSE 110829.4399 146268.5815 104032.3067 135997.8731 93169.78509 100024.4444 88960.96151 98367.63096 85717.85855 124436.6053 0.890649818 1.175446574 0.836026557 1.092908897 0.748732938 0.803818492 0.714909903 0.790503973 0.688847613 1 16.92505142 3.228132044 24.99970292 0.776949154 0.999754908 0.419785649 0.118878278 170.8656644 409603.897 0.031088804 0.037536854 1690.954975 -3.228132044 0.222805755 ATSVALPGWSPS(ph)ETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-4;Q16513-5;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 ATSVALPGWS(0.352)PS(0.644)ET(0.004)R 112.96 0.0015724 0 85593 124320 106310 117980 97672 126680 85968 93191 86966 134500 TRUE FALSE 88972.27773 145670.9929 109080.5259 141316.0919 81069.74833 97260.48985 79229.60352 91941.92707 83836.11065 160852.6998 0.553128905 0.905617332 0.67813923 0.878543487 0.503999923 0.604655626 0.492559986 0.571590823 0.521198032 1 17.29538063 3.230693817 24.99988143 0.584294811 0.759288822 0.125672416 0.166418587 258.5701402 821708.2646 0.043449987 0.052827767 1700.958887 -3.230693817 0.174994011 ATT(ph)PPNQGRPDS(ph)PVYANLQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 AT(0.476)T(0.524)PPNQGRPDS(0.992)PVY(0.007)ANLQELK;AT(0.464)T(0.536)PPNQGRPDS(0.994)PVY(0.006)ANLQELK;AT(0.476)T(0.524)PPNQGRPDS(0.95)PVY(0.05)ANLQELK 89.659 0.0057208 4123590000 537960 379670 493930 378962 606180 622240 597470 496580 570490 369140 TRUE FALSE 559199.0762 444875.3691 506802.2216 453919.5525 503141.7401 477734.1901 550638.7402 489924.1573 549958.1763 441465.9154 1.266686865 1.007723028 1.147998529 1.028209736 1.139706878 1.08215419 1.247296158 1.109766667 1.245754558 1 18.75194253 ATTPPNQGRPDS(ph)PVYANLQELK ddPTM_MDA-MB-175_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 222.63 5.07E-26 328830000 282810 216320 238110 162680 295600 289240 221220 219860 248280 192760 TRUE FALSE 293975.5572 253471.2773 244315.3422 194857.6184 245354.0176 222068.3935 203880.1983 216913.1363 239344.4513 230527.6314 1.275229158 1.099526663 1.059809363 0.84526795 1.064315007 0.963304885 0.884406772 0.940942025 1.038246261 1 17.81458016 4.603250235 1.364223707 0.958424278 1.355628721 0.67971235 0.065523353 0.542247892 1.089437769 0.017806646 0.277709659 40109.77581 -4.603250235 0.397204442 ATTVPDFQETRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ATTVPDFQETRPR 13 1 B7ZC38;Q9NR46 B7ZC38 SH3GLB2 Endophilin-B2 0 ;;;; 220.4 1.90E-11 2740420000 1634627 1885034 1722100 1756351 1971353 2160950 1674273 1814727 1683111 2113952 FALSE TRUE 1699163.336 2208773.926 1766979.341 2103751.986 1636263.121 1659102.112 1543039.107 1790403.553 1622536.164 2528140.42 0.672100063 0.873675334 0.698924524 0.832134152 0.647220031 0.65625394 0.610345491 0.708189916 0.641790365 1 21.26964517 -1.125858204 3.817327134 1.000132583 0.706002846 0.549404899 0.080269172 17912423.29 32064143.54 29902.48668 0.020210293 0.074841382 1.125858204 -0.294129737 ATVMAATAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ATVMAATAAER 11 0 K7EL91;K7EMJ5;K7EPN1;K7ERP1;K7EPS3;Q9GZN7 K7EL91 ROGDI Protein rogdi homolog 0 ; 70.977 0.038148 504940000 72059 979850 558030 917340 424290 1020510 377860 659890 403210 1163860 FALSE TRUE 74903.94496 1148131.615 572572.7202 1098787.114 352169.3374 783512.0185 348242.3458 651045.2539 388698.5509 1391896.084 0.053814323 0.824868774 0.411361686 0.789417491 0.253014102 0.562909852 0.250192777 0.467739842 0.279258312 1 20.40862008 -1.251530677 4.115925922 1.000459476 0.446220615 0.350454296 0.231099092 63816497.28 19405255.76 262787.4212 0.048912675 0.056036283 1.251530677 -0.55423886 ATVMLYDDGNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ATVMLYDDGNKR 12 1 P50552;K7ENR7;K7ENL7;K7EIG8 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;; 131.69 0.00031141 886490000 642812 474114 573123 494084 751048 715917 688774 634129 701032 563873 FALSE TRUE 668190.7141 555539.3914 588059.0562 591812.3405 623385.1292 549656.1266 634786.0941 625629.538 675801.9953 674353.1183 0.990861755 0.823810814 0.87203431 0.877600065 0.924419436 0.815086505 0.941325956 0.927747675 1.002148543 1 19.36314472 1.511582991 1.54899069 1.003940026 0.883704966 0.435046581 0.049287619 0.314573306 1.454718598 0.039963531 0.013353147 32.47752985 -1.511582991 -0.120235059 ATVT(ph)PS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 ATVT(1)PS(1)PVK 169.52 0.00030985 463530000 957010 470280 586900 560610 688780 885010 956860 633360 631180 358250 TRUE FALSE 994793.4938 551046.9317 602195.0961 671496.9847 571701.4216 679479.84 881858.8129 624870.8452 608463.9551 428442.2284 2.321884791 1.28616391 1.405545617 1.567298787 1.334372253 1.585931066 2.05829107 1.458471653 1.420177365 1 18.70874116 4.747850121 24.78845656 1.49927996 2.321885279 0.497581781 0.257532641 969.655544 2587403.621 0.060472935 0.758863608 55956.44575 -4.747850121 0.822605319 ATVT(ph)PS(ph)PVKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 AT(0.065)VT(0.935)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;ATVT(1)PS(1)PVKGK;AT(0.001)VT(0.999)PS(1)PVKGK;AT(0.005)VT(0.995)PS(1)PVKGK;AT(0.007)VT(0.993)PS(1)PVKGK 134.61 0.00031434 8005840000 17472400 6899990 9389870 6311420 12570600 12905800 13047300 9685180 10516940 5562280 TRUE FALSE 18162223.84 8085009.608 9634577.726 7559800.038 10433853.9 9908623.539 12024618.53 9555366.004 10138437.38 6652102.27 2.730298349 1.215406691 1.448350812 1.136452768 1.568504734 1.489547685 1.807641862 1.43644304 1.524095237 1 22.66537892 4.744552431 24.95326695 1.436022196 2.730298928 0.760983624 0.222475915 307.6518157 1281197.509 0.051336137 0.470036609 55533.16562 -4.744552431 1.294276733 ATVT(ph)PSPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.619)PS(0.381)PVK 164.31 0.00069709 3877600000 1755100 1052300 1173400 1085000 1755500 1724700 1989400 1312800 1253500 926950 TRUE FALSE 1824392.703 1233024.339 1203979.768 1299609.762 1457100.737 1324164.563 1833465.63 1295204.063 1208386.78 1108568.105 1.645720001 1.112267558 1.08606748 1.172331908 1.314398935 1.194481924 1.653904367 1.168357684 1.090042889 1 20.08026597 1.359707238 4.037940368 1.044515537 1.292933913 0.233790122 0.190413045 0.347239247 8.85587568 0.143894702 0.048300202 22.89323878 -1.359707238 0.248418376 ATVTPS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.035)PS(0.965)PVK;ATVT(0.041)PS(0.959)PVK;ATVT(0.415)PS(0.585)PVK;ATVT(0.034)PS(0.966)PVK;ATVT(0.047)PS(0.953)PVK;ATVT(0.085)PS(0.915)PVK 199.03 2.67E-05 16056580000 9978100 6034790 6932620 6517170 10010600 10382900 11507300 7689900 7538400 5805700 TRUE FALSE 10372043.09 7071218.238 7113289.772 7806246.774 8309001.788 7971628.829 10605327.76 7586829.469 7267094.457 6943215.758 1.493838511 1.018435619 1.024494992 1.124298459 1.196707992 1.148117689 1.527437448 1.092696775 1.046646786 1 22.72717257 1.495880982 16.92200129 1.038772655 1.204639111 0.193405178 0.163167466 0.302452232 255.7234556 0.088478069 0.0409886 31.3242717 -1.495880982 0.165866457 ATVTPS(ph)PVKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 ATVT(0.001)PS(0.999)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.002)PS(0.998)PVKGK;ATVT(0.008)PS(0.992)PVKGK;ATVT(0.001)PS(0.999)PVKGK;ATVT(0.003)PS(0.997)PVKGK;ATVTPS(1)PVKGK 164.93 1.34E-05 98868100000 61202200 32046240 44001800 28299260 55195600 54830900 59025600 45124200 47591400 26571860 TRUE FALSE 63618510.11 37549932.43 45148523.06 33896769.16 45813471.63 42097254.45 54399019.24 44519383.91 45878594.81 31778107.22 2.001960333 1.181628981 1.42074299 1.066670489 1.441667728 1.324725043 1.711839502 1.40094511 1.443717038 1 24.92152986 -2.152421105 2.16419377 0.080499933 1.430201373 0.222778428 0.247498704 3996861.594 779754.6591 18067430.83 0.058167009 0.007040101 2.152421105 1.34970144 AVAAPRPDR ddPTM_MDA-MB-175_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 ;;; 76.827 0.03131 682340000 1412240 1573470 1600660 1450650 1738970 1883170 1616050 1584110 1597490 1661410 FALSE TRUE 1467996.326 1843701.233 1642374.515 1737584.24 1443380.501 1445832.307 1489379.778 1562877.597 1539996.647 1986931.48 0.738825843 0.927913847 0.826588401 0.874506372 0.726436978 0.727670945 0.749587891 0.786578507 0.775062785 1 20.92211069 AVAFNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVAFNKR 7 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 89.903 0.028111 901340000 855040 640510 786240 523780 1252050 970390 818110 756600 759240 856200 FALSE TRUE 888797.6394 750512.61 806730.0603 627382.1207 1039226.988 745031.6289 753984.4005 746459.0145 731915.1007 1023955.997 0.868003744 0.732953967 0.78785618 0.612704181 1.014913718 0.727601216 0.736344533 0.728995207 0.714791556 1 19.96572229 4.755117791 22.38539599 0.77172241 0.868004066 0.032909845 0.121065178 2341.020219 3164843.178 0.026672269 0.614358169 56900.72388 -4.755117791 0.096281656 AVAGVMITAS(ph)HNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AVAGVMITASHNR 13 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 1 AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMITAS(1)HNR;AVAGVMIT(0.001)AS(0.999)HNR;AVAGVMIT(0.003)AS(0.997)HNR;AVAGVMIT(0.02)AS(0.98)HNR;AVAGVMIT(0.015)AS(0.985)HNR 179.79 8.66E-06 2538077000 2042874 2058620 2450350 2490180 2853470 2637140 2148880 2043080 2228200 2416270 TRUE FALSE 2123528.243 2412171.971 2514208.134 2982730.172 2368438.189 2024704.201 1980445.171 2015695.854 2148007.517 2889691.844 0.734863216 0.83475059 0.870060986 1.032196626 0.819616179 0.7006644 0.685348223 0.697546992 0.743334457 1 21.46248422 2.992729067 24.58699849 0.738642616 0.873264903 0.141227162 0.10963992 381.3193304 1289456.857 0.031579573 0.036314214 983.3974257 -2.992729067 0.134622287 AVAHHTDCTFIR ddPTM_MDA-MB-175_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 ; 124.1 0.00019022 547060000 140853 240140 186437 202973 230120 253820 217380 192302 206551 294850 FALSE TRUE 146413.9852 281382.177 191295.7014 243120.4536 191004.2846 194874.1517 200341.1876 189724.5062 199117.2699 352620.2123 0.415217223 0.797975179 0.542497834 0.689468287 0.541671402 0.552646005 0.56815004 0.538042062 0.564679116 1 18.42775565 -1.689264054 2.699898338 1.06052454 0.582017509 0.632954235 0.096169011 17933122.25 15675592.03 7430156.064 0.022270115 0.020452008 1.689264054 -0.478507032 AVCMLSNTTAIAEAWAR ddPTM_MDA-MB-175_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 ; 214.18 2.80E-17 62722000 81282 103533 92678 90557 102045 111262 86479 81874 93298 82468 FALSE TRUE 84491.07612 121313.9874 95093.26482 108468.9043 84699.42735 85423.08669 79700.55001 80776.61295 89940.2232 98626.02565 0.856681343 1.230040312 0.964180237 1.099800013 0.858793881 0.866131289 0.808108706 0.819019244 0.911931943 1 16.58968078 3.228437124 24.86959237 0.859899856 1.04616616 0.359788299 0.102976446 166.7370425 409609.1742 0.027395786 0.033101406 1692.143243 -3.228437124 0.186266304 AVCS(ph)TYLQSR ddPTM_MDA-MB-175_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(0.398)T(0.398)Y(0.203)LQSR;AVCS(0.385)T(0.385)Y(0.229)LQSR 96.624 0.0069376 974890000 153115 510510 361450 463320 360150 603930 274870 479550 339680 615550 TRUE FALSE 159160.0984 598186.1213 370869.6839 554963.3131 298931.8316 463676.4101 253324.9712 473122.4166 327454.9832 736155.2371 0.216204532 0.812581493 0.503792767 0.753867235 0.406071731 0.629862272 0.344118955 0.642693813 0.444817841 1 19.4896505 -1.614537515 2.766863516 1.039293746 0.541420009 0.390277577 0.17621026 19991109.34 19148353.44 5678594.129 0.038485379 0.024291956 1.614537515 -0.497873737 AVDDLNLHSYSNLPIWVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVDDLNLHSYSNLPIWVNK 19 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 242.26 2.12E-24 559750000 1193800 1115420 1343100 1438760 1455100 1655310 1583110 1308720 1459280 1147980 FALSE TRUE 1240932.146 1306984.708 1378102.289 1723342.434 1207762.622 1270889.339 1459021.702 1291178.749 1406760.798 1372904.702 0.903873477 0.951985019 1.003785833 1.255252773 0.87971337 0.925693777 1.062726131 0.940472232 1.024660194 1 20.38880006 4.418616943 3.385795925 1.009129312 0.911348495 0.116822394 0.096078815 0.532986703 11.91002274 0.02417234 0.090096512 26219.04946 -4.418616943 -0.097780818 AVDFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AVDFAER 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ;;;;; 167.24 0.0025446 3678380000 3713650 4173730 4302860 4102250 4732910 5127740 4440290 4443050 4255630 4445980 FALSE TRUE 3860267.77 4890535.66 4414996.066 4913662.806 3928411.649 3936900.097 4092248.467 4383498.182 4102470.708 5317084.658 0.726012095 0.919777655 0.830341503 0.924127247 0.738828118 0.740424565 0.769641398 0.824417602 0.771563925 1 22.34220401 4.855303156 17.7299983 0.823723177 0.725752767 0.119627396 0.083795288 45311.5848 6839579.349 0.019268912 1097.09875 71664.34832 -4.855303156 -0.09797041 AVDIPHMDIEALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AVDIPHMDIEALK 13 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 210.41 3.02E-08 2311963000 5552609 4060470 5212072 4132292 6779350 6079528 6424341 5646052 5927916 4363286 FALSE TRUE 5771830.291 4757824.136 5347902.878 4949647.024 5626998.509 4667649.758 5920784.366 5570375.908 5714571.461 5218188.352 1.106098497 0.911777003 1.024858153 0.948537441 1.078343312 0.89449622 1.134643667 1.067492304 1.095125564 1 22.31511759 2.218771729 24.99950244 1.080559783 0.993447588 0.237547474 0.07011449 305.0355122 385351.8261 0.023777389 0.017583857 165.4899898 -2.218771729 -0.087112195 AVDIPHMDIEALKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVDIPHMDIEALKK 14 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 194.85 6.25E-08 2807700000 11020000 6170200 9466700 6355900 12975900 10633500 11721200 9581700 10937200 5910400 FALSE TRUE 11455078.11 7229883.853 9713409.979 7613078.05 10770261.15 8164030.777 10802461.72 9453272.984 10543572.31 7068429.719 1.620597299 1.022841584 1.374196302 1.077053653 1.52371341 1.154999215 1.528268957 1.337393645 1.491642802 1 22.75295832 2.24991011 24.99697484 1.369966805 1.287182288 0.000863967 0.219997164 889.3791513 1958833.76 0.069780724 0.05790536 177.7911382 -2.24991011 -0.082784517 AVDLGPPKPSDQETGEQVSS(ph)PSSHPALHTTTEDSAGVQTEF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVDLGPPKPSDQETGEQVSSPSSHPALHTTTEDSAGVQTEF 41 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 AVDLGPPKPS(0.004)DQET(0.014)GEQVS(0.144)S(0.526)PS(0.144)S(0.144)HPALHT(0.008)T(0.008)T(0.008)EDSAGVQTEF 94.07 9.92E-05 273480000 23353 22612 31864 25212 30038 38567 39384 29965 33291 27461 TRUE FALSE 24274.99447 26495.4351 32694.40202 30198.85835 24932.15149 29610.39874 36296.97917 29563.36819 32092.86341 32841.45718 0.739157046 0.806767951 0.995522271 0.919534666 0.759167029 0.901616471 1.105218291 0.900184423 0.97720583 1 15.00323052 2.468064707 24.95983964 0.984858182 0.852152757 0.416720952 0.083972216 224.7010955 619271.0692 0.030032883 0.025159698 293.8087378 -2.468064707 -0.132705425 AVDPDGDGHVSWDEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVDPDGDGHVSWDEYK 16 0 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;G3V1E2;Q9BRK5-4;Q9BRK5-3;H0Y3T6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 203.04 2.88E-11 376440000 269920 468520 507140 487620 709330 720710 560790 510580 521730 523860 FALSE TRUE 280576.65 548984.6654 520356.485 584069.7806 588758.34 553336.025 516833.8144 503736.5102 502953.0392 626500.3371 0.447847564 0.876271939 0.830576544 0.932273689 0.939757419 0.883217442 0.824953769 0.804048267 0.802797715 1 19.25695576 4.739237614 24.98275886 0.868090206 0.447847434 0.810569581 0.062116169 23.95090608 883664.2817 0.015300234 0.091709033 54857.70236 -4.739237614 -0.420242772 AVDTWSWGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVDTWSWGER 10 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 235.65 9.37E-12 1011600000 294830 401160 304320 383060 569920 497910 352590 326730 288140 565660 FALSE TRUE 306470.1161 470056.1094 312250.8292 458828.1247 473045.202 382277.9484 324953.0745 322350.7188 277769.8977 676490.2468 0.453029615 0.694845361 0.461574769 0.678247952 0.699263891 0.565090111 0.480351455 0.476504606 0.410604438 1 19.36770961 -1.708135692 2.696672058 1.073601013 0.549148537 0.633938034 0.103341977 12786785.77 11058199.84 6390977.678 0.026205526 0.019582327 1.708135692 -0.524452476 AVDVFFPPEAQNDFPVAMQISEKHDVVFLITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVDVFFPPEAQNDFPVAMQISEKHDVVFLITK 32 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 310.45 3.18E-104 159320000 170080 149630 237090 168700 275130 256490 212000 212890 254540 161080 FALSE TRUE 176794.8897 175327.7885 243268.7602 202068.3565 228363.5009 196924.0846 195382.886 210036.5578 245379.1551 192640.5419 0.917744977 0.910129232 1.262811855 1.04893993 1.185438426 1.022235936 1.01423555 1.090302984 1.273766948 1 17.55555183 4.275925365 24.99181382 1.106564007 0.913936528 0.412578169 0.094444173 157.7252498 105493.8307 0.022054603 0.060395884 18876.6692 -4.275925365 -0.192627479 AVDWIFSHIDDLDAEAAMDISEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVDWIFSHIDDLDAEAAMDISEGR 24 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 281.15 2.25E-52 148517000 83186 97987 99332 109820 112898 109477 95587 100195 94219 109327 FALSE TRUE 86470.24751 114815.505 101920.6735 131542.0682 93707.63829 84052.62589 88094.64117 98852.04991 90828.07659 130747.5325 0.661352806 0.87814663 0.779522731 1.00607687 0.716706744 0.642862043 0.673776702 0.756052891 0.694682912 1 16.99642419 AVEDIHGLFSLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEDIHGLFSLSK 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 136.99 6.59E-05 390100000 1279150 1148120 1309890 1226560 1802100 1732220 1627530 1372250 1406480 1231640 FALSE TRUE 1329651.83 1345300.679 1344026.809 1469169.907 1495779.686 1329938.157 1499959.946 1353857.233 1355861.06 1472956.277 0.90270964 0.913333749 0.912468911 0.997429408 1.015494967 0.902904029 1.018332974 0.919142852 0.920503263 1 20.49028318 3.825811969 8.425538624 0.964011807 0.909505746 0.30863606 0.039648421 0.4468197 39.58268196 0.0101267 0.01832136 6695.946413 -3.825811969 -0.054506061 AVEDINEHITDAQLEAMTELHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEDINEHITDAQLEAMTELHDR 23 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 152.5 3.54E-08 26307000 14962 23986 17004 24952 17382 24944 25554 23223 17470 19733 FALSE TRUE 15552.71131 28105.40891 17447.13821 29887.43113 14427.41385 19151.13403 23551.01071 22911.73367 16841.25811 23599.30354 0.65903264 1.190942303 0.739307335 1.266453948 0.611349137 0.811512679 0.997953633 0.970864824 0.713633692 1 14.52645666 3.220107567 24.99983669 0.865979554 0.964104425 0.064665802 0.205879934 810.7362624 1098367.823 0.05649594 0.067640341 1659.998007 -3.220107567 0.098124871 AVEDKNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEDKNR 7 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79;Q9NX05;F8W881 Q9NZB2;Q9NX05 FAM120A;FAM120C Constitutive coactivator of PPAR-gamma-like protein 1;Constitutive coactivator of PPAR-gamma-like protein 2 0 64.836 0.065862 73283000 61795 57058 65247 53748 83542 81347 69214 71086 64071 71592 FALSE TRUE 64234.71432 66857.26765 66947.39042 64379.19398 69341.56068 62455.39208 63788.82582 70133.20844 61765.09723 85619.08169 0.7502383 0.780868778 0.781921379 0.751925771 0.809884424 0.729456458 0.745030483 0.819130585 0.721394063 1 16.38564474 -1.868301849 2.850525823 1.097258725 0.769138325 0.83789306 0.030901969 14115675.45 10675605.49 9321538.532 0.00708057 0.013542478 1.868301849 -0.328120399 AVEEEDKMTPEQLAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEEEDKMTPEQLAIK 16 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 148.03 8.86E-07 55429000 119600 58228 84647 57285 113700 99726 103810 77661 85563 47282 FALSE TRUE 124321.9004 68228.20605 86852.97036 68615.80202 94373.31461 76566.14786 95673.10094 76620.08132 82483.60434 56546.00263 2.198597506 1.20659645 1.535970118 1.213450975 1.668965271 1.354050584 1.691951623 1.355004382 1.458699121 1 15.78713742 -3.409536825 0.16146857 1.56E-16 1.651770676 0.283349534 0.268628331 101.4984935 1.5071323 35.99412822 1.112049771 0.00038946 3.409536825 1.651770676 AVEEKIEWLESHQDADIEDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEEKIEWLESHQDADIEDFK 21 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 160.07 1.30E-11 276386000 326070 231110 268964 171189 402690 388660 249034 248488 291862 252084 FALSE TRUE 338943.4954 270801.3447 275973.4228 205049.6733 334240.8976 298399.6052 229514.0644 245157.4248 281357.9436 301475.0334 1.124283798 0.898254631 0.915410539 0.680154741 1.108685167 0.98979873 0.76130372 0.813193126 0.933271125 1 18.201679 2.257397313 24.98903069 0.852638426 0.9432849 0.059431731 0.13131589 592.2754379 785719.4613 0.045885612 0.038329702 180.8828169 -2.257397313 0.090646474 AVEEKIEWLESHQDADIEDFKAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEEKIEWLESHQDADIEDFKAK 23 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 201.87 1.31E-24 216450000 358490 188290 274570 108260 423200 360260 236250 247400 309840 161660 FALSE TRUE 372643.462 220627.3428 281725.5198 129673.5049 351264.6152 276595.0748 217732.1077 244084.0077 298688.9189 193334.1818 1.927457724 1.141170903 1.457194569 0.670722082 1.816877967 1.430657901 1.126195614 1.262497947 1.544935904 1 17.56073721 7.999959061 0.027409158 3.34E-07 3.18917929 0.097825154 0.341305434 4795.16952 10.09042618 389.0244872 875.4006482 99990573.91 -7.999959061 3.189178956 AVEELHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEELHK 7 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 116.54 0.0054322 216000000 492970 427460 480630 392798 611200 577920 552400 515210 535560 430350 FALSE TRUE 512432.8363 500872.9298 493155.6126 470492.272 507308.4423 443706.8385 509101.4446 508304.4527 516285.3002 514668.843 0.995655446 0.973194583 0.958199859 0.914165057 0.985698764 0.862121041 0.989182562 0.987634009 1.003140772 1 18.97328492 2.038173198 24.99999843 0.993765594 0.947902756 0.286828308 0.036215546 211.8007808 138709.5211 0.013351156 0.009860469 109.1875693 -2.038173198 -0.045862839 AVEES(ph)S(ph)DEERQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEESSDEERQR 12 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 AVEES(1)S(1)DEERQR 122.63 0.00372 0 291140 316810 298370 281420 333050 379950 287130 310610 287950 359910 TRUE FALSE 302634.432 371219.6531 306145.7673 337084.036 276438.28 291712.3707 264624.0003 306446.781 277586.7357 430427.4736 0.703102034 0.862444142 0.71125982 0.783137826 0.642241253 0.677727117 0.614793471 0.711959156 0.644909428 1 18.71541064 -1.167744039 4.221977554 1.000088711 0.706489472 0.621717124 0.068859526 10247440.18 2834312.093 8469.446953 0.016589596 0.067960405 1.167744039 -0.293599239 AVEHINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AVEHINK 7 0 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;;;; 138.37 0.0027925 21942600000 41672200 37214000 42343100 37695200 57804500 53761100 48777400 42297900 45452000 40602700 FALSE TRUE 43317450.63 43605215.02 43446595.97 45151198.05 47978911.74 41275899.28 44954099.93 41730965.84 43816191.4 48558021.68 0.892076101 0.898002297 0.894735709 0.929840148 0.988073856 0.850032556 0.925781125 0.85940416 0.902347128 1 25.53320631 3.794101476 23.39161118 0.913143298 0.895244411 0.045679662 0.045389972 674.3619508 284009.7949 0.011595266 0.020903655 6224.457073 -3.794101476 -0.017898886 AVEQHNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AVEQHNGK 8 0 Q9BRA2;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;;; 108.74 0.003752 810832000 1380980 1175390 1359220 1064870 1651350 1489770 1545550 1387580 1440780 1240150 FALSE TRUE 1435502.157 1377254.089 1394642.39 1275498.108 1370654.117 1143793.495 1424405.752 1368981.76 1388926.609 1483133.648 0.967884559 0.928610912 0.94033494 0.860002137 0.924160893 0.771200557 0.96040283 0.923033309 0.936481086 1 20.50021718 0.922741194 1.14852729 0.998353893 0.904680925 0.210097872 0.053942556 0.904258821 2.415693779 0.050509378 0.015894704 8.370303272 -0.922741194 -0.093672967 AVEQLAEGLLSHYLPDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEQLAEGLLSHYLPDLQR 19 0 H3BST1;Q9UL45;H3BPR6;H3BN13;Q9UL45-2 H3BST1 BLOC1S6 Biogenesis of lysosome-related organelles complex 1 subunit 6 0 ; 161.08 3.02E-11 135868000 173967 213574 228011 242363 245774 308870 279573 275710 241171 194355 FALSE TRUE 180835.3515 250253.6731 233953.154 290301.678 203997.4233 237139.6235 257659.3377 272014.5584 232491.3028 232435.1411 0.778003492 1.076660233 1.00653091 1.248957781 0.877653105 1.020239979 1.108521442 1.170281555 1.000241623 1 17.82646868 4.739793558 24.20205565 1.066739056 0.778003353 0.417378214 0.09807426 63.29130389 1242145.566 0.023077481 0.142922393 54927.97112 -4.739793558 -0.288735703 AVEVAWETLQEEFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEVAWETLQEEFSR 15 0 O60313-10;O60313-9;O60313-2;E5KLJ9;O60313-13;O60313;O60313-11;A0A2R8YDM2;A0A2R8Y3X5;C9JMB8;A0A2R8YE78;A0A2R8YFD1 O60313-10 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 84.718 0.019124 5769000 2452.9 4093.5 3740.9 2684.3 3979.9 3887 3182.5 3623.4 2699.6 2774.8 FALSE TRUE 2549.742386 4796.526782 3838.390927 3215.246528 3303.39802 2984.303158 2933.047334 3574.83425 2602.441923 3318.468933 0.76834903 1.445403552 1.156675263 0.968894569 0.995458474 0.899301219 0.883855595 1.077254096 0.784229708 1 11.69630205 3.720122131 5.644915772 0.950772379 1.156454437 0.181415565 0.1701554 0.240046396 27.3637514 0.04242841 0.069661785 5249.55066 -3.720122131 0.205682058 AVEVHVLLLDDLLLLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEVHVLLLDDLLLLLQR 18 0 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4;M0R2C7 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 0 57.973 0.05565 0 21249 26986 34586 27333 37952 54803 37121 35728 40898 37631 FALSE TRUE 22087.92693 31620.63558 35487.33957 32739.38582 31500.9326 42075.8338 34211.35902 35249.1246 39426.08897 45004.07396 0.490798387 0.702617181 0.788536158 0.727476047 0.699957355 0.934933887 0.760183601 0.783242971 0.876055999 1 15.45776799 6.337677048 0.148090905 1.006528112 5.23E-27 0.665855139 0.07771908 29.45438621 0.451120785 0.326236267 5.890067174 2176090.976 -6.337677048 -1.006528112 AVEYDTLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEYDTLFR 9 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 118.32 0.0040452 0 224610 210060 226850 191050 236510 278820 221040 183050 205880 218140 FALSE TRUE 233477.7762 246136.171 232761.8974 228839.1198 196308.1147 214068.2806 203714.3072 180596.5142 198470.419 260880.3565 0.894961121 0.94348296 0.892217032 0.87718034 0.752483312 0.820561132 0.780872542 0.692258001 0.760771802 1 17.99302879 3.373167591 3.919200072 0.779308716 0.910232966 0.26600601 0.078077837 0.232623806 6.688524928 0.021356068 0.029619054 2361.389299 -3.373167591 0.13092425 AVEYLLMGIPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEYLLMGIPGDR 13 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ; 161.62 9.73E-05 232690000 239670 254150 272360 281960 269020 316420 287070 262730 276930 270520 FALSE TRUE 249132.3567 297798.2855 279457.9253 337730.8464 223292.0765 242936.2504 264568.7033 259208.5341 266963.3434 323523.2146 0.770060217 0.92048506 0.863795588 1.04391534 0.69018873 0.750908248 0.817773475 0.801205361 0.825175231 1 18.30350971 5.038350171 11.50342702 0.844710161 0.563924484 0.049001031 0.102751778 151207.4943 1700826.021 0.024410203 794656.5101 109232.0717 -5.038350171 -0.280785676 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAAGENPLEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.992)PEPEHGS(0.008)VQESQVSEQPATEAAGENPLEFLR;AVEYLLTGIPGS(0.991)PEPEHGS(0.009)VQESQVSEQPATEAAGENPLEFLR 251.21 4.86E-56 497200000 26653.3 81510 69361 86311 67945 99547 55346 91633 65004 91467 TRUE FALSE 27705.59286 95508.70844 71168.60464 103383.0582 56395.73317 76428.7179 51007.8359 90404.80952 62664.51874 109388.2074 0.253277693 0.873117045 0.650605822 0.945102408 0.515555877 0.69869248 0.466301049 0.826458461 0.572863567 1 16.73909769 -2.008859026 2.794053228 1.357158451 0.662627627 0.221947517 0.197023531 13882405.69 10789664.2 31859390.57 0.043599947 0.00979808 2.008859026 -0.694530825 AVEYLLTGIPGS(ph)PEPEHGSVQESQVSEQPATEAGENPLEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAGENPLEFLR 42 0 P54725-3 P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLTGIPGS(0.833)PEPEHGS(0.131)VQES(0.036)QVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.999)PEPEHGS(0.001)VQESQVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.998)PEPEHGS(0.002)VQESQVSEQPATEAGENPLEFLR;AVEYLLTGIPGS(0.993)PEPEHGS(0.007)VQESQVSEQPATEAGENPLEFLR 240.56 1.95E-54 606260000 56654.9 228753 185979 217902 178049 257635 180767 230750 179981 249621 TRUE FALSE 58891.6792 268039.5483 190825.7655 261002.3652 147784.2946 197803.1757 166598.0102 227657.1737 173503.519 298529.4557 0.197272591 0.897866335 0.639219219 0.874293509 0.495040914 0.662591821 0.558062218 0.762595346 0.581193968 1 18.18751376 -4.999999994 0.383830533 6.096785901 0.639388684 0.248792229 0.191177057 861.9242659 6.362720293 3661.959726 0.115053251 1.00E-05 4.999999994 -5.457397217 AVEYLLTGIPGSPEPEHGS(ph)VQESQVSEQPATEAAGENPLEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVEYLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLR 43 0 P54725-2;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 AVEYLLT(0.002)GIPGS(0.408)PEPEHGS(0.57)VQES(0.019)QVS(0.001)EQPATEAAGENPLEFLR 121.92 1.24E-08 333160000 3117.6 10207 9445.2 12065 12716 10765 10597 11695 9989.1 14476 TRUE FALSE 3240.685255 11959.97285 9691.349671 14451.42099 10554.53886 8264.991895 9766.37945 11538.24765 9629.594242 17312.29504 0.187189812 0.690836935 0.559795778 0.834749001 0.609655672 0.477405906 0.564129679 0.666477069 0.556228635 1 14.07950937 -5 0.257432513 3.611446002 0.551752714 0.403985393 0.15745914 197.9467055 1.949916261 273.2277766 0.206420287 1.00E-05 5 -3.059693288 AVFHEEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVFHEEEQR 9 0 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 152.34 8.07E-05 970230000 1036440 1121760 1119050 1080560 1295500 1368690 1103750 1069560 1037490 1215280 FALSE TRUE 1077359.452 1314413.554 1148213.362 1294291.543 1075291.373 1050832.49 1017235.191 1055224.298 1000150.938 1453390.848 0.741273039 0.904377206 0.790023801 0.890532333 0.739850106 0.723021265 0.699904773 0.726043032 0.688150018 1 20.4709913 3.213712063 24.00062647 0.741767831 0.833787143 0.087196224 0.095179142 229.1858244 221364.1161 0.025093319 0.030007344 1635.731673 -3.213712063 0.092019312 AVFPS(ph)IVGRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 102.45 0.001736 719330000 764310 955570 906880 817540 997070 1045900 779220 882510 855630 1223760 TRUE FALSE 794485.549 1119681.714 930514.0378 979246.9719 827588.3975 803005.5758 718142.7003 870681.3969 824836.0434 1463532.342 0.542854795 0.765054302 0.63580012 0.66909828 0.565473255 0.548676345 0.490691377 0.59491777 0.563592631 1 20.4810232 -1.477024916 6.384318847 1.00018414 0.598219734 0.731211896 0.073235421 0.000201019 1.65E-05 0.074260404 0.017495456 0.033340728 1.477024916 -0.401964407 AVFPSIVGR ddPTM_MDA-MB-175_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 ; 192.58 8.04E-05 2254200000 559570 601160 542720 670790 647510 766250 751290 720300 568510 622580 FALSE TRUE 581662.2557 704404.5536 556863.729 803470.2599 537446.4815 588300.0501 692401.9267 710645.5567 548049.4362 744562.631 0.781213334 0.946064877 0.747907168 1.07911709 0.721828439 0.790128359 0.929944504 0.954446983 0.736068953 1 19.50603368 -1.828333547 2.49023634 1.050575335 0.864617757 0.124253919 0.113146095 19920653.47 13034075.49 6038239.695 0.026226138 0.014847949 1.828333547 -0.185957578 AVFPSIVGRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AVFPSIVGRPR 11 1 C9JTX5;F8WCH0;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63267-2;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6;Q6S8J3;A5A3E0;P0CG38 C9JTX5;P60709;P63261;P68133;Q6S8J3 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2;POTEE;POTEF;POTEI "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;POTE ankyrin domain family member I" 0 ;;;; 228.98 2.62E-12 1.43817E+11 15591281 18659630 16307470 15296250 22238700 21074610 16333696 17191480 15741539 25935210 FALSE TRUE 16206836.81 21864276.3 16732456.06 18321802.6 18458573.72 16180351.22 15053418.23 16961056.33 15175004.09 31016717.84 0.522519401 0.704919083 0.539465721 0.59070733 0.595116924 0.521665487 0.485332404 0.546835949 0.489252414 1 24.88654269 -1.438642835 3.070135963 1.008375454 0.556511309 0.827902091 0.060851189 18954515.73 23724127.79 1380348.03 0.015053587 0.036421444 1.438642835 -0.451864144 AVFVDLEPTVIDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 329.73 1.82E-68 2803323000 1254757 1462999 1348669 1452608 1426765 1633012 1429358 1363881 1309054 1549186 FALSE TRUE 1304295.775 1714257.698 1383816.422 1739929.527 1184243.995 1253769.712 1317321.185 1345600.406 1261941.402 1852719.336 0.703989941 0.925265724 0.746910984 0.939122021 0.639192333 0.676718641 0.711020369 0.726283998 0.681129288 1 20.82121292 5.062692426 15.21271585 0.768065927 0.128122293 0.024304681 0.120716007 4826148.535 27380618.59 0.027754439 95078058.24 115529.3755 -5.062692426 -0.639943635 AVFVDLEPTVIDEVRT(ph)GTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVFVDLEPTVIDEVRTGTYR 20 1 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 1 AVFVDLEPT(0.006)VIDEVRT(0.985)GT(0.008)YR 88.222 0.0036404 15011000 15338 20448 17166 16180 21342 23795 13118 19539 18560 28202 TRUE FALSE 15943.55608 23959.78494 17613.36006 19380.35571 17714.29446 18268.97187 12089.77688 19277.11166 17892.02923 33727.64194 0.472714817 0.710390159 0.522223288 0.574613421 0.525215919 0.5416617 0.358453073 0.57155231 0.530485625 1 15.04164384 -0.95925345 3.986204967 1.000029063 0.535072109 0.738831239 0.083090403 10224100.91 21574139.48 4797.913962 0.019568676 0.109836466 0.95925345 -0.464956954 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVGEPMRPLAEECCQLGLGLCDQVDDPDLRR 31 2 Q8TEX9;Q8TEX9-2;H0YN14;H0YMR4 Q8TEX9 IPO4 Importin-4 0 163.73 9.18E-13 164450000 45679 53114 58809 61621 61997 71574 44522 57849 62195 60029 FALSE TRUE 47482.44219 62235.91633 60341.61085 73809.44988 51458.77208 54952.02321 41032.2493 57073.62878 59956.6141 71790.53323 0.661402556 0.866909793 0.84052323 1.028122324 0.716790498 0.765449437 0.571555154 0.795002157 0.835160451 1 16.13150599 4.754847488 23.02645148 0.807478312 0.661402219 0.119668236 0.125277633 2517.921716 3559669.19 0.030500388 0.719172816 56865.3201 -4.754847488 -0.146076093 AVGHPFVIQLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVGHPFVIQLGR 12 0 O14980 O14980 XPO1 Exportin-1 0 ; 131.82 0.00019196 1399100000 1757110 1776110 1903530 1856730 2220500 2174000 1887050 1931840 1835960 2185040 FALSE TRUE 1826482.06 2081143.076 1953137.556 2223985.652 1843060.203 1669121.447 1739138.09 1905946.845 1769884.158 2613156.753 0.698956179 0.796409582 0.747424567 0.851072424 0.705300285 0.63873759 0.665531483 0.729365677 0.677297356 1 21.31736224 -0.989687115 4.335485564 1.00001052 0.72474837 0.657785697 0.059856648 8039533.68 1854782.93 870.9587127 0.014868139 0.102403048 0.989687115 -0.275262151 AVGIWHCGSCMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVGIWHCGSCMK 12 0 Q6P4E4;E9PEL3;P61513;M0R0A1;C9J4Z3;M0R2L6 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 ; 209.85 5.04E-08 1610330000 1342510 1785480 1816170 1503500 3070100 2577600 2132980 1881500 1975530 3149000 FALSE TRUE 1395513.331 2092122.301 1863500.882 1800887.813 2548245.499 1978991.464 1965791.454 1856281.57 1904431.061 3765986.259 0.370557202 0.55553105 0.494824132 0.47819819 0.676647583 0.525490888 0.521985828 0.492907154 0.505692515 1 21.84459631 -2.068181838 2.439802009 1.708526964 0.5169845 0.806056875 0.071567556 4245969.369 1548590.548 16729942.99 0.016797876 0.008547088 2.068181838 -1.191542463 AVGMPS(ph)PVSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPS(0.995)PVS(0.005)PK;AVGMPS(0.998)PVS(0.002)PK 117.98 0.00079699 56914000 286610 216230 251960 213540 325570 308890 290750 247610 269090 204600 TRUE FALSE 297925.5841 253365.8205 258526.2846 255777.5746 270229.7277 237154.9788 267960.2553 244291.193 259405.5035 244687.4527 1.217576058 1.035467155 1.056557178 1.045323623 1.104387351 0.969215937 1.095112366 0.998380547 1.060150411 1 17.9005806 4.739762522 24.37955756 1.041408459 1.217576139 0.634363087 0.04032325 42.0883818 853576.608 0.00869103 0.05366488 54924.04604 -4.739762522 0.17616768 AVGMPSPVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVGMPSPVSPK 11 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 AVGMPS(0.001)PVS(0.999)PK;AVGMPSPVS(1)PK;AVGMPS(0.007)PVS(0.993)PK 124.21 0.00040944 330187000 1127870 581100 672040 578700 1002550 1150170 943650 766670 809020 545840 TRUE FALSE 1172399.179 680899.4047 689553.9145 693165.1328 832136.9091 883060.4485 869684.2472 756394.0427 779903.5282 652786.8973 1.795990672 1.043065367 1.056323154 1.061855156 1.274745116 1.352754555 1.332263639 1.158715112 1.19472914 1 19.31625257 0.778580779 1.327424156 1.001810547 1.246883399 0.122740589 0.209517216 1.797320778 5.630680305 0.194193555 0.058221365 6.005937095 -0.778580779 0.245072853 AVHADFFNDFEDLFDDDDIQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVHADFFNDFEDLFDDDDIQ 20 0 Q8WXC6 Q8WXC6 MYEOV2 Myeloma-overexpressed gene 2 protein 0 149.36 9.99E-08 7440900 11885 15001 14563 12835 14240 17032 13797 14429 16126 14275 FALSE TRUE 12354.22898 17577.30506 14942.52374 15373.72469 11819.48989 13076.57612 12715.55509 14235.60286 15545.62841 17071.91294 0.723658153 1.029603719 0.875269444 0.90052736 0.692335412 0.765970174 0.744823098 0.833861027 0.910596748 1 14.0593371 5.041869438 16.34147103 0.845783988 0.133518565 0.123203541 0.102903432 10266977.32 107250030.9 0.024937712 221887132.9 110120.8202 -5.041869438 -0.712265423 AVHS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVHSPIR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 AVHS(1)PIR;AVHS(1)PIR 123.35 0.0061216 297380000 324200 1394420 909020 1338020 739350 1238100 659170 738460 822370 2749830 TRUE FALSE 336999.6663 1633900.788 932709.808 1602676.362 613675.5511 950570.0386 607502.533 728562.1516 792773.0643 3288606.54 0.102474912 0.496836812 0.283618547 0.487342083 0.186606559 0.289049489 0.184729467 0.221541295 0.24106656 1 21.64904498 -1.403315151 3.007057243 1.011569675 0.279283278 0.76521893 0.120132191 19460319.15 23863774.77 1938990.95 0.029260629 0.039507982 1.403315151 -0.732286397 AVIFCLSADKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVIFCLSADKK 11 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 158.56 4.76E-05 3041000000 1929500 1458900 1463300 1459300 4116800 3130500 3688000 2818300 3116600 2348500 FALSE TRUE 2005678.15 1709454.726 1501434.8 1747945.184 3417027.806 2403488.818 3398924.923 2780525.298 3004434.175 2808643.61 0.714109167 0.608640669 0.534576475 0.622344956 1.21661139 0.855747169 1.210165972 0.989988651 1.069710007 1 21.42144214 3.252982903 24.95072932 1.053301679 0.613016322 0.800941695 0.106724827 89.62610805 155053.2951 0.02731597 0.036819958 1790.535363 -3.252982903 -0.440285358 AVIFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVIFDR 6 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 106.76 0.074087 298240000 389440 1336540 660180 1257210 559890 1144440 522050 731480 435910 1412860 FALSE TRUE 404815.3919 1566080.348 677384.8331 1505882.386 464720.0978 878661.1542 481130.3569 721675.7071 420221.6843 1689682.866 0.239580693 0.926848688 0.400894657 0.891221907 0.275033917 0.520015425 0.284745952 0.427107194 0.248698553 1 20.68832106 -1.134293726 4.93849777 1.000027777 0.47642618 0.308074286 0.23879471 6.87E-05 1.20E-05 0.217505681 0.051263866 0.073401726 1.134293726 -0.523601598 AVIPGDEDASFPPLKSEDSGIGLSASS(ph)PELSEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVIPGDEDASFPPLKSEDSGIGLSASSPELSEHLR 35 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 AVIPGDEDASFPPLKSEDSGIGLSAS(0.069)S(0.927)PELS(0.004)EHLR;AVIPGDEDASFPPLKSEDSGIGLS(0.001)AS(0.411)S(0.582)PELS(0.006)EHLR 194.73 1.13E-21 485210000 126626 161928 205200 150162 231490 239890 185244 176718 219100 228060 TRUE FALSE 131625.2923 189737.8744 210547.6806 179863.5954 192141.4125 184179.1831 170724.0912 174349.3843 211214.6338 272743.9905 0.482596489 0.695662896 0.771960842 0.659459426 0.704475329 0.675282277 0.625949965 0.639241891 0.774406187 1 18.05718788 0.914155607 3.298048223 0.999719278 0.662026755 0.689596199 0.070332679 0.199312105 5.016439284 0.066399031 0.017252106 8.206455278 -0.914155607 -0.337692523 AVIVPGNGGGDVTTHGWYGWVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVIVPGNGGGDVTTHGWYGWVK 22 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 201.67 1.50E-22 301840000 381370 379850 358050 300170 500750 427530 337910 334440 393340 346770 FALSE TRUE 396426.7821 445086.2827 367381.0771 359542.7301 415632.6939 328242.6368 311423.7312 329957.3788 379183.7702 414712.9422 0.955906464 1.073239432 0.885868368 0.866967711 1.002217803 0.791493593 0.750938058 0.795628362 0.914328278 1 18.66175355 2.735000166 24.99923282 0.826257935 0.954370826 0.253607978 0.086322557 360.0028867 2527702.686 0.027447119 0.026847382 543.2505395 -2.735000166 0.128112891 AVIVSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVIVSSPK 8 0 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 AVIVS(0.034)S(0.966)PK;AVIVS(0.038)S(0.962)PK;AVIVS(0.003)S(0.997)PK 163.38 0.00035269 1517170000 6885700 3288730 4062280 3175370 6067930 7098700 5479890 4616180 4626240 3255890 TRUE FALSE 7157552.753 3853543.795 4168146.354 3803448.708 5036505.426 5450134.507 5050361.903 4554307.658 4459742.526 3893819.308 1.838183076 0.989656553 1.07045192 0.97679127 1.293461516 1.399688603 1.297020099 1.169624807 1.14533885 1 21.89275451 0.999075568 1.651094263 1.003670134 1.240505166 0.103779109 0.235117145 1.001378315 5.612623493 0.217279741 0.063002319 9.978736813 -0.999075568 0.236835032 AVLFCLS(ph)EDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 AVLFCLS(1)EDKK;AVLFCLS(1)EDKK 151.74 2.04E-05 878640000 1197770 434150 610670 372700 923300 1099640 774900 633190 783600 451300 TRUE FALSE 1245058.884 508711.8853 626584.5619 446418.9476 766357.7958 844265.2752 714161.3132 624703.1237 755398.3891 539723.5943 2.306845388 0.942541498 1.160936021 0.827125129 1.419907901 1.564254897 1.323198246 1.157450092 1.399602309 1 19.04186123 4.747354621 24.91613038 1.212814552 2.306845973 0.693831183 0.220527277 645.857709 1829872.962 0.05418671 0.648783802 55892.63972 -4.747354621 1.094031421 AVLFCLSEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVLFCLSEDKK 11 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;; 181.4 1.00E-05 19817885000 14548399 7733257 8838725 7668236 18880139 15008415 18196605 13090244 16319036 9207082 FALSE TRUE 15122781.03 9061383.733 9069069.435 9184990.193 15670899.72 11522938.07 16770307.55 12914790.69 15731717.08 11011033.44 1.37342068 0.822936719 0.823634719 0.83416241 1.423199721 1.046490153 1.523045738 1.17289542 1.428723032 1 23.39244654 3.242671895 24.99985988 1.274834528 0.943502482 0.315436696 0.217038922 112.190331 682202.0285 0.057520252 0.075164626 1748.525197 -3.242671895 -0.331332046 AVLGDDEITREPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVLGDDEITREPR 13 1 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 0 ; 122.45 0.00021425 184986000 320720 449550 357000 374410 392070 455080 342880 373580 346560 435190 FALSE TRUE 333382.2732 526756.7155 366303.7133 448467.1805 325426.0814 349394.5668 316004.1696 368572.7712 334087.3733 520457.1483 0.640556623 1.012103911 0.703811475 0.861679356 0.625269693 0.671322448 0.607166547 0.708171215 0.641911393 1 18.98941986 3.241964798 24.99196764 0.687001099 0.812169251 0.088090206 0.139462239 153.6041532 1127682.871 0.035595861 0.046310627 1745.680651 -3.241964798 0.125168152 AVLHTDS(ph)SLPFSFPDELPNSCLLAALSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVLHTDSSLPFSFPDELPNSCLLAALSDR 29 0 Q8NCE2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVLHT(0.021)DS(0.49)S(0.49)LPFSFPDELPNSCLLAALSDR 235.67 1.93E-45 104180000 18983 23572 26372 32058 32678 46379 33717 31541 30171 39907 TRUE FALSE 19732.4635 27620.30764 27059.27598 38398.97672 27123.40523 35608.18013 31074.17344 31118.24449 29085.1516 47726.01258 0.413453009 0.578726488 0.566971228 0.804571231 0.568314924 0.746095854 0.65109511 0.652018528 0.609419267 1 15.54248819 -5 0.147663124 2.254592375 0.511790535 0.605584379 0.09546341 95.99993966 0.848604293 35.72519257 0.502399656 1.00E-05 5 -1.74280184 AVLHTDSS(ph)LPFSFPDELPNSCLLAALSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVLHTDSSLPFSFPDELPNSCLLAALSDR 29 0 Q8NCE2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 AVLHT(0.028)DS(0.151)S(0.819)LPFS(0.001)FPDELPNSCLLAALSDR 167.61 2.46E-12 139550000 18402 29390 32621 38596 32372 44216 35806 37996 30435 40766 TRUE FALSE 19128.52517 34437.50388 33471.13006 46230.1736 26869.419 33947.5041 32999.43216 37486.72577 29339.6503 48753.31719 0.392353306 0.706362272 0.686540568 0.94824673 0.551130068 0.696311678 0.676865372 0.768906157 0.601798031 1 15.57321276 -5 0.231060113 2.682336137 0.648113171 0.343765719 0.13640122 190.5626442 1.906432261 150.4090419 0.226044843 1.00E-05 5 -2.034222966 AVLLDEDDDLWVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVLLDEDDDLWVELR 15 0 Q15833-2;Q15833;Q15833-3;M0R0M7 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 ; 195.25 4.24E-08 37180000 24839 32061 29215 30484 28684 34351 29224 26861 29750 31451 FALSE TRUE 25819.6629 37567.22735 29976.3669 36513.64421 23808.30393 26373.50084 26933.34652 26500.97223 28679.30331 37613.22128 0.686451785 0.998777187 0.796963564 0.970766208 0.632976999 0.70117634 0.716060619 0.704565345 0.762479318 1 15.19895225 3.237478391 24.99990037 0.731293484 0.868186919 0.14905214 0.12262633 40.74581583 941257.6909 0.031805479 0.04011032 1727.740012 -3.237478391 0.136893435 AVLPVTCHRDS(ph)FSR ddPTM_MDA-MB-175_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(0.937)FS(0.063)R 107.65 0.00052756 351130000 64440 84056 68101 86633 94629 112310 89936 73037 64712 114990 TRUE FALSE 66984.14096 98491.96414 69875.76801 103768.7488 78543.99638 86227.70457 82886.58132 72058.05848 62383.02776 137520.0889 0.487086225 0.716200556 0.508113168 0.754571566 0.57114562 0.627018971 0.602723442 0.523982053 0.453628472 1 17.06928286 -1.488740595 3.206943936 1.009438941 0.586791677 0.64859966 0.092099175 253936200 291904888.8 21021297.18 0.0210562 0.03245334 1.488740595 -0.422647263 AVLS(ph)PGSVFS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 2 AVLS(0.935)PGS(0.065)VFS(1)PGR;AVLS(0.993)PGS(0.03)VFS(0.976)PGR;AVLS(0.999)PGS(0.008)VFS(0.993)PGR 155.38 6.82E-05 168200000 268649 303543 309995 344549 365194 440877 371957 385490 374295 462911 TRUE FALSE 279255.47 355674.149 318073.7244 412699.7638 303118.4543 338489.9983 342802.0384 380323.1371 360824.1961 553609.5475 0.504426759 0.6424639 0.574545229 0.745470821 0.547531118 0.611423701 0.619212656 0.686988038 0.65176657 1 19.0785093 -4.999999996 0.234755814 3.100145179 0.583599439 0.787968116 0.060418197 69.1618556 0.691278666 69.03976438 0.094173376 1.00E-05 4.999999996 -2.51654574 AVLS(ph)PGSVFSPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 AVLS(0.556)PGS(0.444)VFSPGR;AVLS(1)PGSVFSPGR 185.95 8.63E-06 721300000 601180 813840 704640 759110 813320 963930 727360 746260 722100 992330 TRUE FALSE 624915.0506 953610.6892 723003.4973 909259.6923 675072.1569 740071.866 670347.6226 736257.6053 696111.7621 1186758.064 0.52657325 0.803542624 0.609225687 0.766171067 0.568837219 0.623608036 0.564856177 0.620394019 0.586565858 1 20.17859442 -1.848373268 3.359422243 1.113653911 0.632749327 0.638057867 0.083583371 693386.4077 35238621.61 788688.9479 0.018420788 0.014178384 1.848373268 -0.480904584 AVLSAEQLRDEEVHAGLGELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AVLSAEQLRDEEVHAGLGELLR 22 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;;;;; 314.74 1.55E-67 4686514000 1799387 2658497 2187216 2399358 2673108 2836462 1853191 2104786 2071500 2771566 FALSE TRUE 1870428.188 3115073.18 2244216.646 2873943.851 2218734.057 2177736.687 1707933.047 2076574.786 1996947.12 3314601.293 0.564299601 0.939803284 0.677069864 0.867055672 0.669381884 0.657013165 0.515275563 0.626493084 0.602469782 1 21.66040391 3.051489952 11.30604653 0.643456059 0.768742715 0.040573591 0.153242837 1.22358446 264.2077566 0.040716619 0.048669485 1125.87442 -3.051489952 0.125286656 AVLSPGS(ph)VFS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVLSPGSVFSPGR 13 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 2 AVLS(0.359)PGS(0.642)VFS(1)PGR 107.46 0.0018902 77814000 169930 194530 194620 221500 232340 296410 249120 259830 239140 322850 TRUE FALSE 176638.9676 227939.0143 199691.9571 265312.0389 192846.9298 227573.2696 229593.3234 256347.4038 230533.3981 386106.2762 0.457487947 0.590353041 0.517194279 0.687147698 0.499465929 0.589405777 0.594637636 0.663929648 0.597072393 1 18.55863848 -5 0.207370727 2.994883837 0.51980825 0.826076355 0.059759164 52.36798511 0.521264392 43.30446536 0.121649678 1.00E-05 5 -2.475075588 AVLVDLEPGTMDS(ph)VR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 1 AVLVDLEPGTMDS(1)VR 154.47 2.59E-06 17843000 31274 51184 41101 40852 44281 51511 37870 45646 43685 60911 TRUE FALSE 32508.72167 59974.45384 42172.12582 48932.40367 36754.13144 39548.35091 34901.65045 45034.19003 42112.78538 72845.34424 0.44627041 0.823312107 0.578926852 0.671730008 0.504550178 0.542908422 0.479119851 0.618216449 0.578112243 1 16.15254915 -1.155379586 4.251745917 1.000105784 0.586530223 0.600374762 0.102122841 13964984.31 3794884.844 13710.50242 0.022793491 0.069923058 1.155379586 -0.413575561 AVLVDLEPGTMDSVR ddPTM_MDA-MB-175_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 ;;; 210.79 3.97E-09 284598000 371357 432223 412975 433126 489603 549278 388027 400456 394312 468985 FALSE TRUE 386018.4611 506453.938 423737.4678 518797.03 406380.4569 421716.5089 357612.4298 395088.5423 380120.7881 560873.6315 0.68824498 0.902973343 0.755495434 0.924980247 0.72454905 0.7518922 0.637598934 0.704416325 0.677729825 1 19.09731623 3.105729208 22.75217843 0.725325711 0.820202645 0.058249443 0.11224117 9.907960543 2099.069724 0.029858582 0.035687865 1275.643169 -3.105729208 0.094876934 AVNENHKDYMFLECILFITEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVNENHKDYMFLECILFITEMK 22 1 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 ;; 144.88 5.83E-08 1853290000 2312690 1434510 2337780 1652540 3264740 2682650 2956150 2275840 2982800 1527890 FALSE TRUE 2403996.787 1680875.934 2398704.467 1979407.48 2709800.661 2059645.193 2724439.239 2245336.087 2875449.611 1827250.792 1.315635925 0.919893394 1.312739596 1.083270829 1.482993288 1.127182542 1.491004546 1.228805644 1.573648031 1 20.80124323 3.258464467 24.99987666 1.324845757 1.151946578 0.137453701 0.19482169 426.4715582 535658.6223 0.048814587 0.066008079 1813.27831 -3.258464467 -0.172899179 AVPAPSPGPTHNS(ph)PELGRPPAAGVLAPDMSDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVPAPSPGPTHNSPELGRPPAAGVLAPDMSDKDK 34 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 AVPAPSPGPT(0.001)HNS(0.999)PELGRPPAAGVLAPDMSDKDK 190.89 1.19E-20 406240000 215490 94076 140380 96896 212030 210780 186690 149620 159640 69853 TRUE FALSE 223997.7116 110232.8212 144038.4181 116061.7396 175989.2163 161829.5394 172056.75 147614.5886 153894.5876 83539.35793 2.681343467 1.319531583 1.72419829 1.3893061 2.106662305 1.937165229 2.059589087 1.767006502 1.842180637 1 16.35016843 0.090027266 1.699613271 0.999769293 1.848512649 0.338025216 0.364056559 28.4883278 51.08562826 0.338489936 0.092277465 1.230346013 -0.090027266 0.848743356 AVPEHAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVPEHAAR 8 0 X6RA56;X6RLR1;O75935-2;O75935 X6RA56 DCTN3 Dynactin subunit 3 0 ;; 167.24 0.00031378 175329000 326830 378995 345229 370445 436936 473945 394188 373376 359036 471841 FALSE TRUE 339733.5008 444084.4431 354225.9513 443717.9153 362665.7748 363878.4565 363290.5145 368371.5054 346114.3645 564289.21 0.602055639 0.786980214 0.627738303 0.786330675 0.64269486 0.644843903 0.643801987 0.652806219 0.613363428 1 19.10607524 -2.162626997 2.541660716 1.857107538 0.669115337 0.718499988 0.062564207 6163087.654 2318839.671 30210519.28 0.01453698 0.006876588 2.162626997 -1.187992201 AVPIGT(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVPIGTPPK 9 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 AVPIGT(1)PPK;AVPIGT(1)PPK;AVPIGT(1)PPK 101.38 0.044956 1554730000 2760170 1854150 2505010 2556410 3355230 3737980 3853400 3006700 3165270 1864220 TRUE FALSE 2869143.643 2172585.839 2570292.618 3062060.268 2784909.203 2869890.795 3551360.439 2966400.104 3051352.551 2229478.216 1.286912616 0.974481752 1.152867339 1.37344256 1.249130484 1.28724774 1.592911029 1.330535586 1.368639769 1 21.08827467 3.804031717 5.223189183 1.340667125 1.117046544 0.198235816 0.155769322 0.265305656 14.36072164 0.038364409 0.070176211 6368.420288 -3.804031717 -0.223620581 AVPKEDIYSGGGGGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVPKEDIYSGGGGGGSR 17 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 175.16 1.15E-09 250360000 200450 182130 207280 165710 248870 259900 176220 186510 206220 213820 FALSE TRUE 208363.9208 213409.4107 212681.8871 198486.9434 206567.1663 199542.1638 162407.4159 184010.1385 198798.1825 255713.9352 0.814832092 0.834563085 0.831718017 0.776206988 0.807805668 0.780333554 0.63511367 0.719593707 0.777424126 1 17.96417126 2.475089171 24.99820485 0.745523935 0.811300252 0 0.089918163 148.6477473 1828579.642 0.02926501 0.024639861 298.5995653 -2.475089171 0.065776317 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.999)PGS(0.001)SNDSSAR;AVPMAPAPAS(0.996)PGS(0.004)S(0.001)NDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR;AVPMAPAPAS(1)PGSSNDSSAR 280.43 1.09E-44 4889080000 4483108 4918594 4947106 4865920 5746354 6203248 5420901 4879065 4447061 4365769 TRUE FALSE 4660104.566 5763324.258 5076031.646 5828384.453 4769590.8 4762637.663 4995996.615 4813669.114 4287012.143 5221157.848 0.892542363 1.103840264 0.972204211 1.116301139 0.913512087 0.912180363 0.95687523 0.921954336 0.821084569 1 22.31593834 3.196975746 24.98985784 0.919508937 1.023622126 0.314614661 0.072462493 157.1512546 94437.3749 0.019473332 0.023275279 1573.894965 -3.196975746 0.104113189 AVPMIEGYMFEEHEMIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVPMIEGYMFEEHEMIR 17 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 219.29 4.38E-15 65961000 39633 54102 53473 61167 56634 63423 60472 57331 51704 52870 FALSE TRUE 41197.74144 63393.59764 54866.55031 73265.65003 47007.37291 48693.96943 55732.04663 56562.57172 49843.18314 63228.86424 0.651565419 1.002605351 0.867745309 1.158737404 0.743448004 0.770122475 0.881433619 0.89456884 0.788297935 1 15.94829568 AVPPGNDPVS(ph)PAMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVPPGNDPVSPAMVR 15 0 O94966-3;O94966;O94966-7;O94966-6;O94966-5;A0A0A0MR08;E7ESU0;O94966-2;O94966-4;H0YB23 O94966-3 USP19 Ubiquitin carboxyl-terminal hydrolase 19;Ubiquitin carboxyl-terminal hydrolase 1 AVPPGNDPVS(1)PAMVR 95.9 0.0040983 91669000 16285 78816 62264 77863 57508 72764 54445 65873 53165 82132 TRUE FALSE 16927.94437 92352.0349 63886.65099 93264.069 47732.8107 55865.66375 50177.45863 64990.08018 51251.60204 98224.19289 0.172339867 0.940216786 0.650416655 0.949502014 0.48595778 0.568756659 0.51084623 0.661650437 0.52178186 1 16.58379079 -1.527629835 2.765004192 1.018652474 0.622212503 0.23067463 0.213750557 29684267.42 30850419.86 4154515.952 0.048633407 0.029673595 1.527629835 -0.396439971 AVPPVS(ph)PELR ddPTM_MDA-MB-175_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 129.88 0.00030574 1744790000 909160 1016600 919240 916130 985630 1117080 961460 951600 873020 979170 TRUE FALSE 945054.3388 1191193.142 943196.1496 1097337.78 818092.9647 857655.0995 886098.2529 938845.3585 841600.1807 1171019.614 0.807035448 1.017227318 0.805448635 0.937078907 0.698615937 0.732400285 0.756689506 0.801733248 0.71869008 1 20.15933381 3.24770087 24.99864345 0.772552489 0.894503355 0.218053947 0.097606737 247.1972451 676081.9317 0.024877495 0.033218215 1768.890175 -3.24770087 0.121950866 AVPS(ph)PTTGEEGSVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVPSPTTGEEGSVHSR 16 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 AVPS(0.997)PT(0.003)TGEEGSVHSR;AVPS(0.982)PT(0.018)TGEEGSVHSR 150.23 4.89E-07 822810000 314751 391510 404080 385890 428560 561160 346530 438660 393560 444980 TRUE FALSE 327177.6125 458748.797 414610.6568 462217.8902 355713.5243 430839.0945 319368.0731 432780.4802 379395.8525 532165.3113 0.614804471 0.862041902 0.779101245 0.868560728 0.66842674 0.809596352 0.600129445 0.813244439 0.712928566 1 19.02151495 -1.444479633 5.627842734 1.000184645 0.752987053 0.404544478 0.091642105 0.000194362 1.92E-05 0.081229782 0.019131852 0.035935225 1.444479633 -0.247197593 AVPSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVPSQK 6 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 98.133 0.093712 114450000 475890 386940 475460 365370 565150 517950 500590 491490 514870 460430 FALSE TRUE 494678.5047 453393.935 487850.8782 437639.0955 469086.0049 397663.9621 461352.4478 484902.3805 496339.9293 550642.443 0.898366101 0.823390824 0.885966718 0.794779082 0.851888573 0.722181821 0.837843965 0.880612068 0.901383349 1 19.07075629 1.036802991 1.347795522 0.996934298 0.829339536 0.547816556 0.047084137 0.321692621 1.194901097 0.044013396 0.013382797 10.88436235 -1.036802991 -0.167594762 AVPTWASVQVVDDPGSLASVESPGT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVPTWASVQVVDDPGSLASVESPGTPK 27 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 AVPTWASVQVVDDPGSLAS(0.002)VES(0.032)PGT(0.966)PK 140.59 8.13E-07 118030000 285530 203660 207670 212090 289170 384360 266500 242830 256680 202040 TRUE FALSE 296802.9449 238637.0207 213082.0508 254040.769 240016.9867 295098.215 245611.0336 239575.261 247442.1369 241625.8697 1.228357482 0.987630261 0.881867703 1.051380671 0.993341429 1.221302236 1.016493118 0.99151329 1.024071376 1 17.8824154 1.737643196 0.006066171 1.79E-07 2.056677152 0.03074495 0.09999399 16500.35301 95.75161564 16185.96582 16268.27643 54.6566735 -1.737643196 2.056676973 AVPVES(ph)PVQKV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AVPVESPVQKV 11 1 Q8TB61-5;Q8TB61-4;Q8TB61-3;Q8TB61-2;Q8TB61 Q8TB61-5 SLC35B2 Adenosine 3-phospho 5-phosphosulfate transporter 1 1 AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV 149.41 3.64E-05 1344260000 1843410 1285020 1534860 1398060 1920900 2193110 1789430 1561760 1533030 1502010 TRUE FALSE 1916189.25 1505712.189 1574859.713 1674592.095 1594386.104 1683793.439 1649169.801 1540827.162 1477856.55 1796300.102 1.066742271 0.838229752 0.876724168 0.932245171 0.887594507 0.937367558 0.918092583 0.857778252 0.822722522 1 20.77659697 1.758557188 25 0.87872133 0.917044227 0.017650894 0.070740667 27.91581676 34932.40976 0.030749248 0.017052777 57.35313841 -1.758557188 0.038322897 AVQALCAVYEHWVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVQALCAVYEHWVPR 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 154.69 2.43E-06 4234800000 1197420 1356690 1420450 1508640 1030320 1409430 1300280 1514090 1362520 990310 FALSE TRUE 1244695.066 1589690.954 1457468.094 1807044.489 855186.5744 1082111.243 1198360.656 1493796.1 1313483.171 1184342.284 1.050958902 1.342256352 1.230613914 1.525778919 0.722077212 0.913681169 1.011836419 1.261287485 1.109040173 1 20.17565466 3.247991298 24.99996403 1.029019158 1.287263816 0.397608894 0.169696403 242.3387556 642416.4113 0.05062065 0.06763662 1770.07349 -3.247991298 0.258244658 AVQGMLDFDYVCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVQGMLDFDYVCSR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 191.26 1.19E-06 41908000 34747 45991 46350 37711 46890 51589 40806 39110 40944 40248 FALSE TRUE 36118.83839 53889.59649 47557.91908 45170.12324 38919.65455 39608.23659 37607.51909 38585.79442 39470.43344 48133.82501 0.750383714 1.119578519 0.988035318 0.938427878 0.808571821 0.822877396 0.781311668 0.80163574 0.820014479 1 15.55476345 3.3207739 4.437048971 0.822730525 0.968193473 0.202960878 0.10235067 0.251822627 9.124122376 0.027179964 0.036886872 2093.022516 -3.3207739 0.145462949 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;AVQQHQHGYDS(1)DEEVDSELGTWEHQLR 436.52 9.82E-188 6195610000 984201 1223928 1129574 1092375 1074774 1354309 1012284 1071796 1070611 1245171 TRUE FALSE 1023058.015 1434128.113 1159011.626 1308443.515 892084.2994 1039791.26 932938.535 1057430.328 1032079.919 1489138.417 0.687013379 0.963058972 0.778310205 0.878658088 0.599060698 0.698250242 0.626495512 0.710095392 0.693071851 1 20.50604643 3.253819816 24.99981706 0.699734217 0.83303509 0.137885619 0.122113641 345.0894215 565371.7108 0.030768312 0.041505967 1793.989168 -3.253819816 0.133300873 AVQTLAGSQPTSDKPS(ph)QRPSESTNCSPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.198)QRPS(0.198)ES(0.198)T(0.198)NCS(0.198)PT(0.008)R 45.408 0.060947 83076000 16319 14200 17260 17294 19053 17255 12104 14869 15065 15943 TRUE FALSE 16963.28672 16638.73954 17709.80978 20714.70158 15814.37787 13247.78775 11155.25685 14669.70538 14522.81359 19066.7256 0.88968012 0.872658467 0.928833306 1.086432039 0.829422849 0.694811895 0.58506411 0.769387764 0.761683673 1 14.21876949 3.003450376 24.5345141 0.737907119 0.940634935 0.363773978 0.11139142 77.15134165 548586.6446 0.031571421 0.037553662 1007.976427 -3.003450376 0.202727815 AVQTLAGSQPTSDKPSQRPS(ph)ESTNCSPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVQTLAGSQPTSDKPSQRPSESTNCSPTR 29 2 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 AVQTLAGSQPTSDKPS(0.018)QRPS(0.327)ES(0.236)T(0.236)NCS(0.163)PT(0.021)R;AVQTLAGSQPTSDKPS(0.11)QRPS(0.311)ES(0.217)T(0.217)NCS(0.122)PT(0.022)R 150.79 1.84E-08 501190000 111169 118159 115233 95155 132083 147545 115536 121073 122169 108939 TRUE FALSE 115558.038 138451.8891 118236.0666 113976.375 109631.5788 113279.9098 106479.9864 119450.2145 117772.1616 130283.5113 0.886973623 1.062696942 0.907529015 0.87483346 0.84148468 0.869487694 0.817294417 0.916848289 0.90396828 1 16.99129498 4.017391619 24.69806861 0.881540981 0.977404772 0.228576606 0.060956605 234.3200722 332755.5916 0.013999093 0.030231498 10408.58323 -4.017391619 0.095863791 AVQVHQDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVQVHQDTLR 10 0 Q9UKV8-2;Q9UKV8;Q5TA58;A0A6I8PTZ8;Q9UL18 Q9UKV8-2 AGO2;AGO1 Protein argonaute-2;Protein argonaute;Protein argonaute-1 0 ; 91.855 0.009865 279370000 97458 131477 93813 86057 162435 142055 110465 103602 103819 175465 FALSE TRUE 101305.7171 154057.152 96257.84385 103078.8177 134824.3567 109064.8791 101806.4647 102213.3846 100082.5745 209844.0073 0.482766787 0.734150829 0.458711426 0.4912164 0.642498008 0.519742644 0.485153071 0.487092226 0.476937968 1 17.67895774 -1.768277869 3.727655477 1.0641387 0.531294099 0.739065207 0.083616598 0.038069274 0.002366499 0.069151715 0.018691743 0.017049912 1.768277869 -0.532844601 AVS(ph)LDSPVSVGSSPPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 AVS(0.988)LDS(0.012)PVSVGSSPPVK 222.42 3.53E-15 62637000 98421 76631 97727 73276 205160 104580 111630 130270 141970 106980 TRUE FALSE 102306.7371 89791.77814 100273.8459 87769.77409 170286.9765 80292.87993 102880.1489 128523.9437 136860.5274 127940.6827 0.79964195 0.701823503 0.783752625 0.686019272 1.330983803 0.627578955 0.804123807 1.004558839 1.069718595 1 16.96511556 3.601099875 0.297626883 1.031227958 0.621350205 0.178067566 0.186650035 7.09403276 0.865844252 0.235522265 1.014546847 3991.166768 -3.601099875 -0.409877754 AVS(ph)MDNSNKYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVSMDNSNKYTK 12 1 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 AVS(1)MDNSNKYTK;AVS(1)MDNSNKYTK;AVS(1)MDNSNKYTK 101.39 0.0016352 493160000 1125380 801490 1055350 721343 1665540 1431800 1115190 1094600 1394700 976120 TRUE FALSE 1169810.871 939139.6728 1082853.288 864022.4924 1382432.106 1099286.149 1027778.494 1079928.677 1344505.019 1167372.025 1.002089177 0.804490473 0.927599141 0.740143222 1.18422583 0.94167594 0.880420699 0.925093847 1.151736542 1 20.15483297 3.258487015 24.99992553 0.992022834 0.868218343 0.278367787 0.111308361 373.3105514 468357.4069 0.030578354 0.041349993 1813.372458 -3.258487015 -0.123804491 AVS(ph)PAPQSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVSPAPQSSSR 11 0 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 AVS(1)PAPQSSSR;AVS(1)PAPQSSSR 154.1 7.81E-05 361500000 745330 840040 788780 826490 947470 993560 817840 814930 820400 966110 TRUE FALSE 774756.2039 984310.3354 809336.2548 989967.2552 786419.3878 762820.7475 753735.5638 804007.1963 790873.9643 1155400.757 0.670551927 0.851921144 0.70048098 0.856817212 0.680646419 0.660221783 0.652358551 0.695868677 0.684501857 1 20.13996191 -1.033162662 4.437707713 1.000013383 0.717455631 0.588376775 0.071000655 9363223.803 2179894.451 1314.448859 0.016777786 0.092648275 1.033162662 -0.282557752 AVS(ph)PAVPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR;AVS(1)PAVPFSR 161.19 7.50E-06 5144660000 3950340 4699840 4382290 4240840 5232420 5267710 4571070 4792800 4526610 5055260 TRUE FALSE 4106302.474 5507000.96 4496496.077 5079665.494 4343015.117 4044364.185 4212777.589 4728560.355 4363698.19 6045741.408 0.679205774 0.910889267 0.743746015 0.840205552 0.718359391 0.668960829 0.696817364 0.782130765 0.721780489 1 22.52748784 -1.026748381 9.413678398 0.999874946 0.754695949 0.519460959 0.071682502 4.94E-10 0 0.068038399 0.016036804 0.094026792 1.026748381 -0.245178997 AVS(ph)PLDPSKEVSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSPLDPSKEVSGK 14 1 Q14865;Q14865-2 Q14865 ARID5B AT-rich interactive domain-containing protein 5B 1 AVS(0.988)PLDPS(0.012)KEVSGK 82.877 0.0057456 353870000 416200 240160 312440 199760 466150 411880 386330 304160 371580 197940 TRUE FALSE 432631.8974 281405.6118 320582.4431 239271.9318 386913.9895 316227.1121 356048.4451 300083.2327 358206.9084 236722.5532 1.827590534 1.188757083 1.354253909 1.010769479 1.634461881 1.335855447 1.504074877 1.267657976 1.513192991 1 17.85283764 -1.196610376 5.332910128 0.999980001 1.384977711 0.228731195 0.220097015 4.80E-05 7.23E-06 0.195294805 0.046029039 0.063590117 1.196610376 0.38499771 AVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSPLLLTTTNSSEGLSMGNYIGLINR 27 0 P19525-2;P19525;C9JZT2 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 AVS(0.96)PLLLT(0.03)T(0.004)T(0.004)NS(0.001)SEGLSMGNYIGLINR 141.53 1.35E-07 17622000 17192 10472 10356 9074.8 12146 17777 15037 13029 11128 11842 TRUE FALSE 17870.75344 12270.48454 10625.88587 10869.76835 10081.42726 13648.56116 13858.36065 12854.36757 10727.50545 14162.21317 1.261861633 0.866424223 0.750298399 0.767519047 0.711853941 0.963730809 0.978544842 0.907652456 0.757473802 1 13.78975912 4.737245249 6.259460141 0.853551928 1.271075654 0.598565808 0.099760507 0.087519884 18.80223112 0.025204524 0.156067515 54606.61407 -4.737245249 0.417523726 AVS(ph)PPHLDGPPS(ph)PR ddPTM_MDA-MB-175_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 2 AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR;AVS(1)PPHLDGPPS(1)PR 161.08 2.46E-06 2233690000 1335640 1380370 1324260 1524940 1380460 1535200 1480440 1320160 1250650 1159290 TRUE FALSE 1388372.099 1617437.81 1358771.303 1826568.581 1145809.902 1178673.066 1364399.244 1302465.415 1205639.351 1386430.68 1.0014003 1.166620036 0.980049939 1.317461167 0.826445865 0.850149296 0.984109241 0.93943782 0.869599446 1 20.40294405 3.213820562 24.9999999 0.912915121 1.110233356 0.497272316 0.100778924 185.1442672 187089.1196 0.027631769 0.033040009 1636.140377 -3.213820562 0.197318235 AVS(ph)PQCPEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSPQCPEEPR 11 0 A0A2R8YFA9;E9PRG5;A0A2R8Y7K9 A0A2R8YFA9 MICALCL 1 AVS(1)PQCPEEPR 100.69 0.0040278 317980000 52360 127000 94456 116870 106990 156560 91564 107380 80677 139680 TRUE FALSE 54427.21323 148811.2621 96917.60096 139986.5372 88803.87802 120201.3127 84386.97442 105940.7467 77773.45053 167047.6217 0.325818546 0.890831372 0.580179472 0.838003773 0.531608155 0.719563149 0.505167171 0.634194882 0.465576521 1 17.34989992 -1.360765673 3.55127204 1.002025564 0.621562584 0.339172506 0.162562171 53141618.98 73590673.96 1098271.967 0.03520174 0.043574692 1.360765673 -0.38046298 AVS(ph)PSNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AVSPSNPK 8 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 AVS(0.981)PS(0.019)NPK;AVS(0.998)PS(0.002)NPK;AVS(0.993)PS(0.007)NPK;AVS(0.993)PS(0.007)NPK;AVS(0.986)PS(0.014)NPK 141.91 0.00065658 9001790000 6894200 5499940 6202800 4927310 7322900 7957300 7563200 6430600 6804400 5119140 TRUE FALSE 7166388.339 6444511.911 6364450.064 5901917.211 6078156.074 6109337.669 6970376.621 6344408.325 6559510.973 6122137.471 1.170569654 1.052657171 1.039579737 0.964028861 0.992816006 0.997909259 1.138552777 1.036306087 1.071441307 1 22.54560401 4.755188875 2.854034239 1.032774771 1.198290512 0.450806754 0.04621213 0.446504247 4.938039549 0.01206981 0.174686891 56910.03797 -4.755188875 0.165515741 AVSDWIDEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSDWIDEQEK 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7ERM6;K7ENK6;K7EQ75;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 177.57 1.84E-05 46790000 104270 62618 80921 70305 93402 103760 114440 74431 83070 52013 FALSE TRUE 108386.6601 73372.1544 83029.86774 84211.11916 77525.5614 79663.3125 105469.8938 73433.37419 80080.32693 62203.9515 1.74244011 1.179541695 1.334800535 1.353790509 1.246312485 1.280679291 1.69554974 1.180525874 1.287383277 1 15.92471861 0.887433915 1.427178648 1.005471985 1.374824467 0.286288992 0.183045116 0.698903026 2.792472758 0.163297263 0.048427639 7.716740844 -0.887433915 0.369352483 AVSEDVSNGSSGSPS(ph)PGDTLPWNLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 AVSEDVSNGSS(0.008)GS(0.026)PS(0.962)PGDT(0.003)LPWNLGK 120.63 9.67E-05 99888000 70441 67807 81954 61807 87715 91205 102030 76277 84186 87636 TRUE FALSE 73222.06507 79452.32478 84089.78857 74032.24012 72805.23563 70024.02098 94032.62199 75254.63158 81156.1623 104806.5963 0.698639853 0.758085155 0.802332978 0.706370045 0.694662723 0.668126086 0.897201372 0.718033351 0.774342123 1 16.67736999 -2.300066389 0.325001572 1.33658432 0.730795703 0.609191966 0.061933788 30.19844167 1.27893262 7.37990748 0.05463287 0.005011106 2.300066389 -0.605788617 AVSETPAVPPVS(ph)EDEDDDDDDATPPPVIAPRPEHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSETPAVPPVSEDEDDDDDDATPPPVIAPRPEHTK 36 1 E9PM17;B3KNX7;Q13153;Q13153-2;H0YCM0 E9PM17 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 AVSETPAVPPVS(0.999)EDEDDDDDDAT(0.001)PPPVIAPRPEHTK 84.073 0.00065414 321120000 78563 69654 68348 66821 82113 82756 71806 69319 70673 75224 TRUE FALSE 81664.7279 81616.53267 70129.20503 80037.99436 68155.46159 63537.17318 66177.65809 68389.89219 68129.49254 89962.70255 0.907762057 0.907226332 0.779536442 0.889679746 0.757596867 0.706261277 0.735612162 0.760202731 0.757308202 1 16.45703938 4.115180429 0.990757113 0.771519857 0.931156551 0.165612197 0.084542573 1.161957575 1.68950055 0.026828831 0.160836202 13037.08295 -4.115180429 0.159636694 AVSGGS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVSGGSPERR 10 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 AVS(0.161)GGS(0.839)PERR;AVS(0.034)GGS(0.966)PERR 73.951 0.046026 274730000 462980 609580 526510 546780 575520 621660 499180 536940 485800 647550 TRUE FALSE 481258.8079 714270.6231 540231.2831 654931.452 477693.316 477288.8863 460052.9672 529743.1976 468316.1529 774425.0244 0.621440156 0.922323789 0.697590168 0.84570027 0.616836105 0.616313873 0.594057466 0.684047107 0.604727557 1 19.56276605 3.231440633 24.9737749 0.662066551 0.777219796 0.071501234 0.13530972 294.4748093 1032887.642 0.035372944 0.043125269 1703.886388 -3.231440633 0.115153245 AVSGYQS(ph)HDDSSDNSECSFPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSGYQSHDDSSDNSECSFPFK 22 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 AVS(0.067)GYQS(0.868)HDDS(0.04)S(0.025)DNSECSFPFK 74.287 0.0085388 59575000 41137 33683 40463 32144 38347 54779 35294 35789 33044 37402 TRUE FALSE 42761.12052 39467.79323 41517.49902 38501.98726 31828.79064 42057.40743 32527.56406 35309.30699 31854.75289 44730.2058 0.955978623 0.88235215 0.9281759 0.860760342 0.71157264 0.940246232 0.727194599 0.78938396 0.712153059 1 15.44896178 3.475111344 24.84119374 0.800770097 0.914234047 0.213187277 0.09135193 77.42813857 956950.4845 0.023424959 0.031936046 2986.148107 -3.475111344 0.11346395 AVSLFSLNDPALSPDIPPAHS(ph)PVHSHLSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.946)PVHS(0.027)HLS(0.027)LER 229.5 2.88E-35 103930000 25807 76606 52631 69702 61103 81449 60300 71770 56010 79382 TRUE FALSE 26825.88029 89762.48459 54002.6071 83488.84756 50716.73389 62533.70412 55573.52844 70808.04054 53994.21104 94935.38304 0.282569885 0.945511375 0.568835405 0.879428142 0.534223724 0.658697549 0.585382675 0.74585511 0.568746966 1 16.53465827 -1.068988848 3.898984691 1.000074527 0.656587791 0.264486189 0.177892323 39205916.48 81542900.46 42311.77655 0.037792036 0.085312202 1.068988848 -0.343486735 AVSLFSLNDPALSPDIPPAHSPVHS(ph)HLSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.264)PVHS(0.368)HLS(0.368)LER 160.63 3.38E-12 206400000 20474 72553 72774 67531 76975 65440 48313 76231 63205 65371 TRUE FALSE 21282.32933 85013.41337 74670.55022 80888.43024 63890.81699 50242.55175 44526.10082 75209.24813 60930.2644 78179.19585 0.272224971 1.087417342 0.955120469 1.03465416 0.817235536 0.642658846 0.569538997 0.962011022 0.779366732 1 16.25449712 0.321862501 1.245752115 0.999853384 0.806888226 0.062219735 0.233956734 13.22978771 21.09983277 0.221887315 0.065602753 2.098275456 -0.321862501 -0.192965158 AVSLFSLNDPALSPDIPPAHSPVHSHLS(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSLFSLNDPALSPDIPPAHSPVHSHLSLER 31 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 AVSLFSLNDPALSPDIPPAHS(0.283)PVHS(0.186)HLS(0.531)LER 237.01 1.49E-45 134650000 6783.4 19729 18637 24852 19196 20851 18928 23418 20500 23628 TRUE FALSE 7051.21387 23117.30228 19122.69553 29767.65142 15933.07078 16008.67125 17444.3739 23104.12001 19762.209 28257.45421 0.249534647 0.818095717 0.67673101 1.053444206 0.563853724 0.566529141 0.617337067 0.817629212 0.699362683 1 14.78634388 -5 0.161512164 2.154002767 0.606080844 0.221568587 0.19509522 222.6879834 2.056840061 82.48088434 0.794699912 1.00E-05 5 -1.547921924 AVSPPHLDGPPS(ph)PR ddPTM_MDA-MB-175_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 1 AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR 193.64 1.51E-07 485370000 187509 245490 214520 239520 217330 250370 223550 238380 199258 231700 TRUE FALSE 194912.0001 287650.9979 220110.5674 286896.3411 180388.3242 192225.3619 206027.5669 235184.906 192086.7435 277097.1788 0.703406657 1.038087068 0.79434431 1.035363631 0.650993002 0.693711003 0.743520983 0.84874522 0.693210751 1 18.0800325 3.231710245 24.99732295 0.764609038 0.896145457 0.167673294 0.131531849 253.3766169 924581.8552 0.035270437 0.04304589 1704.944495 -3.231710245 0.131536419 AVSTVVVTTAPS(ph)PK ddPTM_MDA-MB-175_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;AVSTVVVTT(0.006)APS(0.994)PK 215.48 2.24E-08 90892000 558000 272300 308630 235637 451590 516190 368770 362720 345390 228671 TRUE FALSE 580030.2709 319065.4068 316673.1513 282245.2953 374828.8931 396312.6954 339864.8438 357858.3317 332959.4814 273474.7043 2.120964981 1.166709029 1.1579614 1.032070941 1.370616321 1.449174967 1.242765194 1.308560997 1.217514732 1 18.06104787 4.741241917 24.92061967 1.234749832 2.120965312 0.805680733 0.13302612 103.2890292 959937.0953 0.032381538 0.223469645 55111.46002 -4.741241917 0.886215479 AVSVEAAERDWEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVSVEAAERDWEEKR 15 2 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 0 98.507 0.0016318 46957000 55840 44627 50035 35490 68867 59236 45703 53209 57527 45453 FALSE TRUE 58044.60632 52291.3401 51338.9532 42509.81607 57161.01194 45479.33673 42120.67944 52495.82039 55456.61451 54358.6451 1.067808188 0.961969159 0.944448728 0.782024938 1.051553287 0.836653243 0.774866249 0.965730847 1.020198616 1 15.73022188 4.684235729 1.936380739 0.912340273 1.103084856 0.184114559 0.091617162 1.089733563 4.738543787 0.023264901 0.35759489 48332.10707 -4.684235729 0.190744583 AVT(ph)FSPDLGPVPHEGLGEYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 AVT(0.534)FS(0.466)PDLGPVPHEGLGEYNR 81.888 0.017428 199380000 15676 76148 61483 78285 41515 74013 35914 63712 39891 103090 TRUE FALSE 16294.90058 89225.82665 63085.29749 93769.53934 34458.29513 56824.60243 33098.96684 62858.04485 38455.3307 123288.5117 0.132168848 0.72371566 0.511688369 0.760569967 0.279493155 0.460907522 0.268467567 0.50984511 0.311913334 1 16.91167885 -1.278361608 3.492626386 1.001640313 0.452499928 0.437299806 0.190132427 115047059.6 177134012.7 2014288.209 0.042489244 0.052679106 1.278361608 -0.549140386 AVT(ph)PSSEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.858)PS(0.071)S(0.071)EAK;AVT(0.667)PS(0.128)S(0.205)EAK;AVT(0.978)PS(0.016)S(0.005)EAK;AVT(0.913)PS(0.086)S(0.002)EAK;AVT(0.503)PS(0.248)S(0.248)EAK;AVT(0.461)PS(0.211)S(0.328)EAK 150.04 0.00096341 3067130000 5779840 4148050 4752570 3985810 5966380 6663580 6268850 5015890 5279890 3813890 TRUE FALSE 6008032.546 4860445.32 4876425.878 4774191.322 4952216.859 5116064.533 5777481.156 4948660.199 5089867.79 4561148.724 1.317219172 1.065618688 1.069122314 1.046708101 1.085738957 1.121661415 1.26667239 1.084959184 1.115917962 1 22.12096578 0.624912434 1.904248264 1.000140168 1.127539236 0.175345408 0.085225183 3.597606305 15.9370118 0.080322249 0.02231347 4.216114857 -0.624912434 0.127399069 AVT(ph)PVPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AVTPVPTK 8 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.998)PVPT(0.002)K;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK;AVT(1)PVPTK 146.11 0.0062446 12617080000 22605800 17913600 20813600 20040300 23761700 25589900 28431400 22234200 22025800 15125300 TRUE FALSE 23498294.44 20990121.45 21356019.51 24004211.53 19722694.72 19647033.54 26202872.58 21936186.92 21233095.76 18088812.94 1.299051215 1.160392421 1.180620286 1.327019722 1.090325539 1.086142778 1.448567834 1.212693557 1.173824718 1 24.1085944 0.845126358 3.110216518 1.000180787 1.225823506 0.295233221 0.104675076 0.882295284 15.00428299 0.099339127 0.025926599 7.00045644 -0.845126358 0.225642718 AVT(ph)PVPTKTEEVSNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 AVT(0.997)PVPT(0.003)KTEEVSNLK;AVT(0.991)PVPT(0.007)KT(0.002)EEVSNLK;AVT(0.993)PVPT(0.004)KT(0.002)EEVSNLK;AVT(0.702)PVPT(0.294)KT(0.002)EEVS(0.001)NLK;AVT(1)PVPTKTEEVSNLK;AVT(0.938)PVPT(0.041)KT(0.021)EEVSNLK 222.77 5.95E-14 8563560000 10519780 6266969 9137590 5351576 12526790 10787220 9894440 8746940 10243340 6072000 TRUE FALSE 10935109.04 7343272.175 9375723.102 6410101.76 10397490.71 8282051.637 9118887.938 8629701.576 9874684.194 7261692.145 1.505862383 1.0112343 1.291120983 0.882728382 1.431827528 1.140512634 1.255752483 1.188387142 1.359832391 1 22.79187434 -1.071547232 4.331435709 0.999980075 1.217049864 0.126577138 0.178248082 0.417278595 45874448.69 2025.640826 0.037198283 0.084811114 1.071547232 0.217069789 AVT(ph)PVSQGSNSSSADPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVTPVSQGSNSSSADPK 17 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 AVT(0.916)PVS(0.084)QGSNSSSADPK;AVT(0.999)PVS(0.001)QGSNSSSADPK;AVT(1)PVSQGSNSSSADPK 232.78 3.82E-16 526440000 327042 200875 226761 200785 307832 290189 275347 243760 260414 187357 TRUE FALSE 339953.8707 235373.7187 232670.5779 240499.6737 255506.8266 222797.0026 253764.5827 240492.7959 251041.751 224066.017 1.51720406 1.050465938 1.038401901 1.073342923 1.140319402 0.994336426 1.132543819 1.073312228 1.120391902 1 17.77356433 4.740366575 24.95172833 1.073465893 1.517204213 0.884432247 0.048558088 44.60815966 616271.8084 0.010726209 0.069345871 55000.49205 -4.740366575 0.44373832 AVT(ph)TPGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.878)T(0.122)PGKK;AVT(0.563)T(0.437)PGKK 78.655 0.017617 1822130000 10655200 4866900 6235300 4205460 7829800 7504900 7299400 6224000 6344900 3811880 TRUE FALSE 11075875.52 5702752.216 6397797.04 5037287.436 6498893.393 5762000.713 6727253.955 6140577.46 6116548.288 4558744.903 2.429588792 1.250947868 1.403411943 1.104972431 1.425588299 1.263944536 1.475681157 1.34698861 1.341717604 1 22.12020525 4.740475606 24.93771792 1.312313745 2.429589185 0.855524316 0.140186139 53.05489867 690847.9964 0.030413297 0.198113522 55014.30183 -4.740475606 1.11727544 AVTDKFLSAIVSSVDKIPYGMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVTDKFLSAIVSSVDKIPYGMR 22 2 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 204.82 6.31E-23 841020000 580990 573760 673510 433450 902850 799410 568470 644530 782490 736850 FALSE TRUE 603927.9338 672298.8168 691062.2239 519185.1163 749383.8795 613759.1427 523911.836 635891.1296 754328.3378 881221.6497 0.685330341 0.762916818 0.784209312 0.589165185 0.850392044 0.696486682 0.594529011 0.721601801 0.856002957 1 19.74914541 1.02540514 2.890605122 0.99798328 0.70928727 0.601481261 0.075458455 0.154506922 2.90963968 0.070277207 0.018663568 10.60242332 -1.02540514 -0.288696011 AVTELNEPLSNEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AVTELNEPLSNEDR 14 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ;;; 313.52 8.29E-33 203094000 324041 363225 352427 364382 369108 427639 355544 343620 347876 375737 FALSE TRUE 336834.3889 425606.0683 361611.5371 436455.672 306367.154 328326.3232 327675.5322 339014.3359 335356.0107 449355.4712 0.749594498 0.94714785 0.804733803 0.971292662 0.68179242 0.730660567 0.72921229 0.754445773 0.746304501 1 18.77749764 3.229928393 24.99999155 0.756265468 0.869299156 0.161815765 0.100699456 258.3589411 748238.5175 0.026411521 0.032037518 1697.963667 -3.229928393 0.113033688 AVTEQGAELSNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVTEQGAELSNEER 14 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;; 284.76 3.32E-33 1345740000 211075 231509 246139 253667 261085 315995 276187 224153 205368 274395 FALSE TRUE 219408.404 271268.8699 252553.5845 303841.5755 216705.865 242609.9502 254538.7413 221148.5957 197976.8458 328157.4466 0.668607116 0.826642432 0.769611012 0.925901815 0.660371621 0.739309599 0.775660415 0.673910033 0.603298349 1 18.32402865 AVTEQGHELSNEER ddPTM_MDA-MB-175_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 ;;;;;;;;;; 314.55 7.76E-56 67219410000 15840149 20586495 19336564 20841285 20844000 22357609 19520689 19455003 19045497 20351119 FALSE TRUE 16465530.31 24122065.38 19840490.74 24963628.97 17300944.33 17165393.14 17990606.39 19194240.51 18360053.28 24338531.12 0.676521119 0.991106047 0.815188503 1.025683466 0.71084587 0.705276463 0.739182094 0.788635946 0.7543616 1 24.53673877 3.202384639 24.99934629 0.767297523 0.880842823 0.121964231 0.119076338 280.6434253 193937.3347 0.031803079 0.038013027 1593.619515 -3.202384639 0.1135453 AVTFSPDLGPVPHEGLGEYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTFSPDLGPVPHEGLGEYNR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 0 180.8 5.62E-18 0 63726 78731 73518 69623 73021 74543 68905 64677 66454 77702 FALSE TRUE 66241.95169 92252.43681 75433.93948 83394.2216 60608.9165 57231.51796 63504.04605 63810.11061 64062.33352 92926.21921 0.71284458 0.992749276 0.811761633 0.897424024 0.652226218 0.615881271 0.68338136 0.68667499 0.689389217 1 16.50379809 3.240320782 24.99997159 0.697286355 0.860632119 0.211106827 0.119874587 54.35013017 771935.8008 0.030991812 0.039880838 1739.084891 -3.240320782 0.163345764 AVTGQTTQVS(ph)PPVIAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTGQTTQVSPPVIAGR 17 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 AVTGQTTQVS(1)PPVIAGR 148.15 3.91E-07 80611000 83866 79770 93134 78057 77948 93889 75593 87820 65564 85056 TRUE FALSE 87177.09444 93469.87698 95561.14855 93496.44162 64698.4268 72084.70265 69667.82313 86642.91654 63204.36445 101721.0947 0.857020805 0.918883907 0.939442785 0.919145059 0.636037461 0.708650481 0.684890615 0.851769407 0.621349629 1 16.63425937 3.262747861 24.97245866 0.744250123 0.911557551 0.347121231 0.106036269 234.9052732 242529.5513 0.027640876 0.037407565 1831.250942 -3.262747861 0.167307428 AVTGYKDPYSGK ddPTM_MDA-MB-175_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 ; 139.46 5.37E-05 903590000 2982400 2145600 2644500 1927830 3557900 3235800 3127200 2670900 2927500 2110080 FALSE TRUE 3100147.455 2514090.11 2713417.842 2309149.02 2953129.429 2484334.489 2882081.893 2635100.954 2822139.847 2523509.776 1.22850622 0.996267236 1.07525553 0.915054517 1.170246875 0.984475873 1.14209262 1.044220624 1.118339177 1 21.26700024 AVTGYRDPYTEQTISLFQAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTGYRDPYTEQTISLFQAMK 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 172.3 5.27E-12 519490000 244290 245210 299440 242060 364670 309610 277590 295230 308500 279950 FALSE TRUE 253934.7578 287322.91 307243.6524 289938.7455 302683.5237 237707.7697 255831.7705 291272.9247 297397.1453 334800.8425 0.75846511 0.858190523 0.917690798 0.866003632 0.904070376 0.709997525 0.764131203 0.869988625 0.888280755 1 18.35294363 0.915581378 1.883516387 0.998770858 0.831393394 0.403049721 0.063435821 0.468198393 3.42285991 0.063593187 0.017893821 8.233441008 -0.915581378 -0.167377464 AVTIANS(ph)PSKPSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVTIANS(0.978)PS(0.022)KPSEK;AVTIANS(0.9)PS(0.1)KPSEK 180.62 1.05E-06 558910000 1360620 528320 806380 596460 967790 1080570 1331640 854950 877090 409230 TRUE FALSE 1414338.328 619054.8502 827394.9252 714438.0077 803285.4015 829623.9937 1227262.577 843490.7937 845523.7022 489410.7833 2.889879783 1.264898264 1.690593982 1.459792126 1.641331636 1.695148579 2.50763289 1.723482241 1.727636029 1 18.90068636 0.697771135 2.502786816 1.000288009 1.832607929 0.235243189 0.460583767 2.793550874 21.19674559 0.4200842 0.112215169 4.986216537 -0.697771135 0.832319919 AVTIANS(ph)PSKPSEKDSVVSLESQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTIANSPSKPSEKDSVVSLESQK 24 2 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 AVT(0.013)IANS(0.729)PS(0.253)KPS(0.005)EKDSVVSLESQK 112.6 0.00082293 732950000 666090 202790 351540 168850 568330 478520 448640 374230 427670 184620 TRUE FALSE 692387.7475 237617.605 360701.4212 202248.026 471725.4696 367390.982 413474.4245 369214.059 412278.2402 220792.7542 3.135916982 1.076202006 1.633665119 0.916008438 2.136507927 1.663963038 1.87268113 1.672219998 1.867263451 1 17.7523333 -1.262684036 6.110494227 0.999977148 1.731644513 0.13741628 0.57330258 0.000162964 1.97E-05 0.506815171 0.119453763 0.054615506 1.262684036 0.731667365 AVTIHDTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVTIHDTEK 9 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 159.37 9.78E-05 544000000 519340 529560 687170 554830 834630 919680 776230 694240 729970 576740 FALSE TRUE 539843.9442 620507.8106 705078.2147 664573.718 692759.8907 706098.2579 715387.0643 684934.8483 703698.5223 689741.1606 0.782676133 0.899624158 1.022235956 0.963511758 1.004376613 1.023714834 1.037181924 0.993031716 1.020235651 1 19.39569554 4.56031304 2.089155987 1.008414276 0.758951022 0.920510775 0.020934022 0.11529772 0.734589651 0.005369233 0.047104867 36333.98562 -4.56031304 -0.249463254 AVTKDEDEWKELEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AVTKDEDEWKELEQK 15 2 Q9UKY7;Q9UKY7-2 Q9UKY7 CDV3 Protein CDV3 homolog 0 129.62 3.64E-05 183090000 371320 107620 167760 81774 273640 254290 226910 163450 218140 68934 FALSE TRUE 385980.0003 126102.8978 172131.9634 97948.65313 227126.7705 195235.0013 209124.2013 161259.2201 210289.184 82440.29748 4.681933619 1.529626914 2.087959028 1.188116202 2.755045499 2.368198651 2.536674511 1.956072758 2.55080574 1 16.33106209 -1.683692514 0.33960914 2.75E-37 2.413117758 0.182969439 0.889101994 50.67528312 3.123476982 44.87261441 0.70911398 0.020716076 1.683692514 2.413117758 AVTLHDQGTAQWADLSSQFYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVTLHDQGTAQWADLSSQFYLR 22 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 311.18 3.36E-67 4231926000 1319585 1352550 1537007 1389559 1427007 1656746 1484957 1354286 1431028 1403109 FALSE TRUE 1371683.235 1584839.941 1577062.665 1664409.623 1184444.86 1271991.85 1368562.19 1336134.011 1379525.582 1678021.344 0.817440874 0.944469477 0.939834687 0.991888231 0.705858042 0.758030793 0.815580919 0.796255671 0.822114442 1 20.67832964 3.247598169 24.99999737 0.802980038 0.926085991 0.281419567 0.082158887 212.3593257 587432.4227 0.021691028 0.028955081 1768.471923 -3.247598169 0.123105952 AVTT(ph)PGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVTTPGKK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 AVT(0.032)T(0.968)PGKK;AVT(0.353)T(0.647)PGKK 70.363 0.030194 1849000000 13071200 5644940 7257100 4650690 9015600 9186600 9623100 7162300 7474500 4308350 TRUE FALSE 13587261.07 6614414.533 7446225.988 5570582.601 7483131.532 7053151.374 8868816.277 7066301.084 7205494.205 5152488.694 2.637028798 1.283731984 1.445170757 1.081144071 1.452333421 1.368882455 1.721268459 1.371434564 1.3984493 1 22.296838 4.741057633 24.98411041 1.374272481 2.637029247 0.802776038 0.19140264 93.16228076 932088.4584 0.043671874 0.297029554 55088.07962 -4.741057633 1.262756766 AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_MDA-MB-175_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 103.82 0.00035784 377400000 214886 270748 256268 238243 266508 304392 242943 254288 266224 284264 TRUE FALSE 223369.8652 317246.8629 262946.5546 285366.7543 221207.0654 233701.5711 223900.4928 250879.6853 256642.6502 339960.0882 0.657047321 0.933188553 0.773463014 0.83941252 0.650685398 0.687438259 0.658608174 0.737968056 0.754919942 1 18.37500586 0.736730704 5.065121266 0.999999856 0.743636051 0.449652809 0.085176854 11.14082634 213.9308485 0.083442124 0.021080865 5.45419554 -0.736730704 -0.256363805 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AVVHTHLLNPEWLVNYFGSLSVEDSLECLR 30 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 287.57 1.51E-72 2891650000 470140 497478 597567 660025 558219 676322 650152 566010 557675 542755 FALSE TRUE 488701.4902 582915.9767 613140.0869 790575.975 463333.1338 519256.4653 599191.3874 558423.5618 537604.3857 649097.4506 0.752893868 0.898040774 0.94460406 1.217961917 0.71381136 0.799966884 0.923114683 0.860307742 0.828233704 1 19.30807556 AVVIVDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 152.47 0.0010622 2886293000 3163440 3708850 3530070 3665880 3845040 4166770 3661410 3691420 3404060 3909380 FALSE TRUE 3288335.054 4345816.137 3622066.524 4390980.122 3191461.474 3199100.816 3374419.117 3641942.553 3281548.546 4675348.161 0.703334798 0.929517115 0.774715893 0.939177142 0.68261472 0.684248682 0.72174713 0.778967133 0.701883246 1 22.15664237 5.052268218 15.53047515 0.788396412 0.152034009 0.05537039 0.110301949 5915423.161 45588543.37 0.025359002 113598896.4 112789.3822 -5.052268218 -0.636362403 AVVMPLQLIQEQAAS(ph)PNAEIHILK ddPTM_MDA-MB-175_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 149.57 9.15E-08 103660000 86896 70043 70147 50042 71183 68088 50291 59704 75145 55787 TRUE FALSE 90326.72118 82072.34039 71975.08845 59940.15824 59083.33909 52275.59388 46349.06001 58903.76554 72440.54613 66717.39454 1.353870633 1.230149063 1.078805444 0.89841875 0.885576235 0.7835377 0.694707285 0.88288468 1.085782001 1 16.02577533 4.121621852 1.438968518 0.863489438 1.361242851 0.714561106 0.10246465 0.2595602 0.940800395 0.030805845 0.134976754 13231.8891 -4.121621852 0.497753413 AVVPGPAEHPLQYNYTFWYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVVPGPAEHPLQYNYTFWYSR 21 0 B9A044;B8ZZ50;O60573-2;O60573;C9JEL3 B9A044 EIF4E2 Eukaryotic translation initiation factor 4E type 2 0 ; 243.23 4.35E-30 513540000 233720 264750 263800 257590 293360 342700 262190 288600 254470 309620 FALSE TRUE 242947.4461 310218.753 270674.8447 308540.5332 243494.772 263113.1187 241638.8627 284731.7891 245311.6744 370284.111 0.656110913 0.837785754 0.730992329 0.833253505 0.657589037 0.710570913 0.652576915 0.76895492 0.662495816 1 18.49827312 -1.095431362 5.270740626 1.000004646 0.727845403 0.603058097 0.067241178 3.47E-06 5.95E-07 0.061466623 0.014487575 0.080272842 1.095431362 -0.272159242 AVVPSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AVVPSKR 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;G3V555;G3V575;P07910-2;G3V4C1;B2R5W2;G3V2D6 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 105.95 0.012527 3538600000 3242300 2655700 2499500 2585000 3755300 3770000 2827800 2631000 2197400 3272400 FALSE TRUE 3370308.508 3111795.817 2564639.023 3096305.285 3116975.447 2894474.635 2606149.647 2595735.748 2118316.003 3913564.126 0.861186478 0.795130913 0.655320557 0.791172748 0.79645442 0.739600666 0.665927416 0.663266441 0.541275404 1 21.90005165 2.429365568 4.499897292 0.68641434 0.774107305 0.031325336 0.119723696 0.469839305 20.6952862 0.039971283 0.033635494 268.7605793 -2.429365568 0.087692965 AVVS(ph)PPKFVFGSESVK ddPTM_MDA-MB-175_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 167.16 3.89E-09 1004540000 2254200 930070 1404110 857760 2049300 1905760 1810150 1449830 1595410 849490 TRUE FALSE 2343197.557 1089802.288 1440702.26 1027422.368 1700960.718 1463176.122 1668265.713 1430397.4 1537991.506 1015931.301 2.306452763 1.072712581 1.418109924 1.01131087 1.674287145 1.440231363 1.642104846 1.40796666 1.513873531 1 19.95437142 -1.501643485 6.25857979 0.999639675 1.47391319 0.159887264 0.338632157 0.001555533 0.000123864 0.299566309 0.070556726 0.031503334 1.501643485 0.474273516 AVVVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AVVVSPK 7 0 O75909;G3V5E1;O75909-1 O75909 CCNK Cyclin-K 1 AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK;AVVVS(1)PK 128.6 0.0039249 2624980000 7353200 3502150 4120530 4038480 5555490 7416300 6908270 4874110 4877400 2567490 TRUE FALSE 7643510.014 4103617.02 4227914.397 4837279.29 4611169.794 5693976.72 6366781.746 4808780.528 4701863.327 3070540.508 2.489304406 1.336447772 1.37692839 1.575383643 1.501745306 1.854389058 2.073505212 1.566102292 1.531281973 1 21.55006121 0.806535277 1.940631758 1.001920401 1.703099754 0.303540263 0.330232598 0.889726913 5.910286377 0.307997653 0.085742645 6.40523808 -0.806535277 0.701179353 AVVVS(ph)PKEENK ddPTM_MDA-MB-175_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 140.82 2.33E-05 3813790000 14377900 3833010 5971690 3339070 9807100 11632710 8429880 6223620 7137350 2883180 TRUE FALSE 14945550.59 4491299.651 6127317.147 3999528.08 8140092.645 8931189.398 7769123.978 6140202.554 6880478.168 3448083.919 4.334450943 1.302549403 1.777020888 1.159927709 2.360758275 2.590189104 2.253171373 1.780757864 1.995449742 1 21.71736346 7.99999988 0.054774943 1.87E-08 6.029306141 0.197496146 0.813746714 880.3149047 3.620494988 87.25908368 434.9049998 99999972.31 -7.99999988 6.029306122 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ;;;; 428.29 2.53E-187 940408000 217272.9 237260 240680 231394 244613 286000.7 250246 241443 234548 291490 FALSE TRUE 225851.0019 278007.5594 246952.3185 277163.0426 203033.7696 219581.3718 230631.0646 238206.8515 226106.6633 348601.8846 0.647876595 0.79749299 0.70840787 0.795070408 0.582423041 0.629891522 0.661588691 0.683320607 0.648609985 1 18.41122084 -1.65640567 5.857246429 1.003055648 0.685500431 0.68090997 0.064917597 0.00264818 0.000155346 0.064259135 0.015025807 0.022059432 1.65640567 -0.317555217 AWALLQLDGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AWALLQLDGTPR 12 0 A0A499FJE4;Q96MK2 A0A499FJE4 FAM65C Protein FAM65C 1 AWALLQLDGT(1)PR;AWALLQLDGT(1)PR;AWALLQLDGT(1)PR;AWALLQLDGT(1)PR 173.44 0.00036955 521298000 479055 620532 484550 613294 539496 685810 501094 542155 453243 587016 TRUE FALSE 497968.4613 727103.5439 497177.7711 734601.7227 447792.6626 526541.0211 461816.9429 534888.299 436930.873 702030.5461 0.709325918 1.035714967 0.708199627 1.046395669 0.637853531 0.750025799 0.657830269 0.761915991 0.622381569 1 19.42117428 AWDDFFPGSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 AWDDFFPGSDR 11 0 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ;;;;;; 154.85 7.40E-05 907264000 681158 974192 766790 1153894 930912 1308309 900388 840504 823630 1142188 FALSE TRUE 708050.6438 1141501.898 786773.1773 1382130.789 772675.9108 1004474.062 829813.2358 829238.4187 793987.7172 1365977.87 0.518347083 0.835666465 0.575977982 1.011825169 0.565657708 0.735351637 0.607486588 0.607065778 0.581259576 1 20.38150268 -1.020435124 4.824431735 1.000006126 0.674146868 0.319741358 0.143914334 8.81E-06 1.79E-06 0.129493564 0.030521352 0.095403625 1.020435124 -0.325859258 AWEDYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AWEDYYK 7 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 107.43 0.0174 182190000 224720 176670 208280 189170 282940 287520 240300 207630 222590 202050 FALSE TRUE 233592.1191 207011.6982 213707.9479 226587.2614 234845.9599 220747.8374 221464.6581 204847.0595 214579.0294 241637.829 0.966703434 0.856702359 0.884414286 0.937714357 0.97189236 0.913548339 0.916514848 0.847744164 0.888019191 1 17.8824868 4.789099275 21.8800257 0.907392705 0.966704862 0.100411654 0.045615376 19480.96875 8432868.972 0.011130643 7.315472618 61531.75117 -4.789099275 0.059312157 AWEEYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AWEEYYK 7 0 A0A087WTP3;Q92945;M0R3J3;M0R251;M0QYG1;M0R263;M0R0C6;Q96AE4;E9PEB5;Q96AE4-2 A0A087WTP3;Q96AE4 KHSRP;FUBP1 Far upstream element-binding protein 2;Far upstream element-binding protein 1 0 ;;;;; 172.26 0.0021099 3936620000 3368090 2743380 3205530 2666100 3914980 3824150 3868230 3165490 3283390 2488470 FALSE TRUE 3501064.794 3214534.174 3289068.745 3193446.622 3249513.098 2936049.118 3565028.025 3123061.784 3165221.435 2976038.052 1.176418021 1.080138801 1.1051837 1.073053021 1.091892322 0.98656303 1.197910767 1.049402504 1.063568872 1 21.50496154 -4.999881581 0.013422889 6.54E-06 1.941528087 0.264975532 0.054426796 10591.4578 10.7896985 954.1119606 636.3585077 1.00E-05 4.999881581 1.941521544 AWEVDTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AWEVDTCR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;; 161.9 0.00080229 1386870000 1475960 1612220 1566680 1520200 1939600 2002390 1677110 1676390 1523660 1867690 FALSE TRUE 1534232.04 1889106.244 1607508.968 1820891.023 1609907.485 1537365.269 1545653.736 1653920.734 1468823.774 2233628.096 0.686878914 0.845756841 0.719685148 0.815216743 0.720758969 0.688281667 0.691992431 0.740463794 0.657595495 1 21.09095756 -1.213930864 5.125638876 1.000024993 0.732742709 0.677084871 0.05597843 1.55E-05 2.38E-06 0.052571206 0.012389994 0.061103929 1.213930864 -0.267282284 AWGPGLHGGIVGR ddPTM_MDA-MB-175_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 ; 126.03 0.00019334 2892100000 788660 1099880 863450 817130 1186550 1270150 833110 891230 978930 1519800 FALSE TRUE 819796.9058 1288775.834 885952.2163 978755.8751 984860.6548 975176.9118 767808.6613 879284.5196 943698.5005 1817575.712 0.451038656 0.709063081 0.48743621 0.538495243 0.541853992 0.536526157 0.422435586 0.483767754 0.519207257 1 20.79358403 -1.246300999 3.454066993 1.001191875 0.520164423 0.794211858 0.073132026 21500025.98 32743631.44 272427.1849 0.018028154 0.056715139 1.246300999 -0.481027452 AWKPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AWKPSSK 7 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 80.067 0.028198 865450000 732640 620000 738220 624070 1006300 955360 939660 801080 846350 651550 FALSE TRUE 761565.1929 726480.1771 757458.6197 747509.1833 835249.4854 733492.1186 866006.9939 790342.8329 815890.0288 779208.7478 0.977357088 0.932330623 0.972086905 0.959318264 1.071920057 0.94132942 1.111392802 1.014288963 1.047075037 1 19.57165035 3.260700519 24.38674626 1.031916351 0.959121099 0.388255137 0.043474583 172.0542762 189513.3996 0.011200138 0.015151051 1822.638414 -3.260700519 -0.072795252 AWLDEDSNLS(ph)PSPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.003)NLS(0.984)PS(0.013)PLR 119.31 0.00023332 50330000 47141 46949 46162 56334 43378 52830 46117 46991 43307 49793 TRUE FALSE 49002.16308 55012.12554 47365.01964 67476.69706 36004.62305 40561.03315 42502.22904 46361.16251 41748.38953 59548.98501 0.822888301 0.923812984 0.795395919 1.133129256 0.604621944 0.681137271 0.713735575 0.778538249 0.701076425 1 15.8617893 3.218001862 24.9999994 0.733427975 0.910349329 0.298244481 0.128269785 274.3920313 333667.29 0.034811675 0.041652143 1651.968879 -3.218001862 0.176921354 AWLDEDSNLSPS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AWLDEDSNLSPSPLR 15 0 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDSNLSPS(1)PLR;AWLDEDSNLS(0.003)PS(0.997)PLR;AWLDEDSNLSPS(1)PLR;AWLDEDSNLS(0.002)PS(0.998)PLR 228.9 5.61E-13 310580000 204969 248734 232774 253035 251082 265789 260386 247505 214070 195961 TRUE FALSE 213061.3344 291452.1296 238840.2817 303084.5678 208403.1713 204063.5328 239976.2649 244187.6003 206365.6625 234355.8061 0.909136146 1.243630933 1.01913533 1.293266733 0.88925969 0.870742382 1.023982589 1.041952425 0.880565607 1 17.83834101 3.211276539 24.99965268 0.96050479 1.118448344 0.33037408 0.114740315 254.6690155 233345.6092 0.031918387 0.038158621 1626.584161 -3.211276539 0.157943554 AWLDEDSNLSPS(ph)PLRDLSGGLGGQEEEEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 Q9C086;B8ZZ93;B8ZZH7;F8WCL7;J3KQ70 Q9C086 INO80B;INO80B-WBP1 INO80 complex subunit B 1 AWLDEDS(0.069)NLS(0.063)PS(0.866)PLRDLS(0.002)GGLGGQEEEEEQR 42.782 0.082943 37230000 20029 22834 24016 19098 24001 24552 19325 22757 22046 21229 TRUE FALSE 20819.76039 26755.56188 24641.87669 22875.5274 19921.31859 18850.17009 17810.256 22451.97964 21252.56877 25388.4161 0.820049597 1.053849195 0.970595274 0.901022234 0.784661734 0.742471292 0.701511112 0.884339517 0.837097072 1 14.63188277 3.427209264 3.945674776 0.81203846 0.956662733 0.255394328 0.093536052 0.250287507 8.1667005 0.025819148 0.036703147 2674.294704 -3.427209264 0.144624273 AWMAFMSEAER ddPTM_MDA-MB-175_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 ; 149.72 7.96E-05 228100000 187942 261420 198831 196209 351380 345210 219990 220610 230190 358460 FALSE TRUE 195362.0953 306316.8514 204012.6992 235018.5546 291652.5531 265040.2092 202746.609 217653.0838 221905.5069 428693.3739 0.45571522 0.714536007 0.475894221 0.548220637 0.680329044 0.618251238 0.472940851 0.507712731 0.517632229 1 18.70958659 -1.447435618 3.343007584 1.006321741 0.555267244 0.713519973 0.084669814 41898619.98 59921053.43 2519866.862 0.020171694 0.035691466 1.447435618 -0.451054498 AWNAYPYCR ddPTM_MDA-MB-175_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 0 136.11 0.0029308 0 112990 108040 101950 93258 190690 150880 119050 108660 107670 201650 FALSE TRUE 117450.9324 126595.0296 104606.9008 111704.1541 158276.5819 115840.4066 109718.5499 107203.5904 103794.9777 241159.4567 0.487026029 0.524943253 0.43376653 0.463196242 0.656315054 0.480347767 0.454962668 0.444534052 0.430399783 1 17.87962786 -1.751751378 2.60495329 1.116051055 0.485522834 0.857206204 0.062914819 11872709.12 8891625.009 8854793.728 0.017001233 0.017711226 1.751751378 -0.630528221 AWNPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AWNPFR 6 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 120.06 0.047651 1989520000 1271580 1730680 1272070 1358300 2078100 1798670 1485480 1350610 1256890 2175500 FALSE TRUE 1321782.96 2027910.827 1305221.189 1626967.686 1724865.304 1380956.152 1369044.196 1332507.282 1211654.774 2601747.573 0.508036588 0.779441806 0.501670955 0.625336487 0.662964126 0.530780221 0.526201777 0.512158557 0.465708045 1 21.31104956 -1.860166079 2.606130398 1.185951942 0.569633008 0.672569636 0.09041338 17113383.96 10201787.26 19706435.06 0.022847523 0.013798565 1.860166079 -0.616318934 AWRDPDEPVLLEEPVVLALAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AWRDPDEPVLLEEPVVLALAEK 22 1 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 184.45 3.56E-17 592875000 462177 384060 449798 358874 561121 517754 464081 469562 492230 393457 FALSE TRUE 480424.1048 450019.3174 461520.1054 429858.2061 465741.8528 397513.4801 427705.1186 463268.2894 474514.7385 470547.366 1.020989893 0.956374108 0.980815405 0.913528025 0.989787398 0.844789513 0.908952317 0.984530619 1.008431399 1 18.84398043 1.553990902 5.634399922 1.001832694 0.943485028 0.218192639 0.04647983 0.218659218 14.47378082 0.026929062 0.012257668 35.80889353 -1.553990902 -0.058347666 AWSS(ph)QDEVSTNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AWSSQDEVSTNVR 13 0 A1L390-3;A1L390;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 AWS(0.027)S(0.973)QDEVSTNVR 172.82 6.20E-07 0 112970 113670 138560 122100 139240 147080 131330 110300 130860 147640 TRUE FALSE 117430.1428 133191.9383 142170.9874 146251.0156 115572.0345 112922.899 121036.0114 108821.6089 126150.3742 176567.2313 0.665073253 0.754341207 0.805194636 0.82830214 0.654549736 0.639546184 0.685495324 0.616318261 0.71446085 1 17.4298581 0.937680658 22.58716506 1 0.703291055 0.635013567 0.066632507 7856.927243 2847686.396 0.072331119 0.01808278 8.663246233 -0.937680658 -0.296708945 AWTVEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AWTVEQLR 8 0 Q00688;G3V5F2 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;; 166.68 0.00073762 1574080000 873120 1040250 955370 941450 1378830 1292370 999550 987550 985130 1640250 FALSE TRUE 907591.4518 1218904.845 980267.727 1127666 1144456.969 992236.6536 921202.6592 974313.5076 949675.3637 1961625.583 0.462673132 0.621374872 0.499722136 0.574863017 0.583422738 0.505823671 0.46961187 0.496686787 0.484126722 1 20.90361827 -1.680074037 2.73470671 1.063621019 0.522951555 0.889474787 0.050544536 17955838.97 15944202.51 7941435.65 0.013163455 0.0208894 1.680074037 -0.540669464 AWVESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 AWVESR 6 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;; 129.96 0.037149 4505060000 3718070 4825600 4420410 4525760 4788830 5384860 4354600 4646260 4284360 5439760 FALSE TRUE 3864862.275 5654359.262 4535609.516 5420941.82 3974826.387 4134307.873 4013275.073 4583984.484 4130166.721 6505576.822 0.594084488 0.869155713 0.697187911 0.833276121 0.610987541 0.635502122 0.616897653 0.704623834 0.634865567 1 22.63324555 -0.995264304 4.386995922 1.000011447 0.692298843 0.522152669 0.089328679 11064674.6 2522152.417 1274.659194 0.020440502 0.101096401 0.995264304 -0.307712605 AWVWNTHADFADECPKPELLAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AWVWNTHADFADECPKPELLAIR 23 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 204.82 9.96E-25 5567600000 1507350 1286530 1402890 1232400 1838670 1976540 1729820 1418440 1605560 1261160 FALSE TRUE 1566861.342 1507481.52 1439450.466 1476165.042 1526133.53 1517518.54 1594232.188 1399428.132 1547776.209 1508260.156 1.0388535 0.999483752 0.954378103 0.978720439 1.011850326 1.006138453 1.057000798 0.927842671 1.02619976 1 20.52445387 4.713248941 4.608407912 0.992123084 1.040887416 0.119315884 0.034307068 0.338810784 17.92105837 0.008200538 0.049891061 51671.2468 -4.713248941 0.048764331 AYAGDKAEEIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYAGDKAEEIGR 12 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 106.58 0.00079707 0 405300 286690 316190 289870 404470 399150 360220 331820 359540 285630 FALSE TRUE 421301.557 335926.7774 324430.1712 347205.4208 335718.3339 306453.4617 331985.0151 327372.4956 346600.2256 341593.7298 1.233341014 0.983410256 0.949754468 1.016427969 0.982800048 0.897128474 0.971870928 0.958367988 1.014656287 1 18.38192197 4.73782582 5.128790551 0.970505935 1.245206985 0.844709194 0.033235132 0.056092273 4.894193777 0.007881319 0.054581084 54679.66185 -4.73782582 0.27470105 AYAQQLTEWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYAQQLTEWAR 11 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 157.24 7.14E-05 806560000 379090 322740 367280 321680 426730 398300 382770 276880 314810 348690 FALSE TRUE 394056.7659 378168.0844 376851.6185 385307.3439 354194.587 305800.8613 352767.4872 273168.8765 303480.0496 417009.1294 0.944959566 0.906858046 0.903701123 0.923978198 0.849368904 0.733319344 0.845946677 0.655066897 0.72775397 1 18.66971944 2.989161338 3.198859702 0.766412057 0.917503513 0.295339021 0.087910249 0.250576291 5.296512085 0.026300125 0.030141624 975.3519077 -2.989161338 0.151091456 AYDATHLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYDATHLVK 9 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ;; 120.12 0.0007167 1099160000 2553690 2264110 2377690 1998960 3134650 2783460 2648800 2503640 2558750 2225670 FALSE TRUE 2654511.653 2652953.28 2439654.555 2394348.322 2601823.313 2137043.599 2441180.135 2470082.801 2466661.087 2661747.423 0.997281571 0.996696102 0.916561253 0.899540017 0.977486928 0.802872421 0.917134403 0.927992934 0.92670742 1 21.34394225 4.238413299 9.307232702 0.915982956 0.997150561 0.271929363 0.049159507 0.106540112 130.5335837 0.011558045 0.027963968 17314.63332 -4.238413299 0.081167605 AYDPDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 84.916 0.039812 1278670000 1071310 1367670 1201780 1247390 1493690 1542330 1256100 1333330 1314360 1402670 FALSE TRUE 1113606.146 1602556.684 1233099.374 1494120.019 1239793.107 1184147.232 1157643.6 1315458.892 1267056.44 1677496.331 0.663850123 0.955326491 0.735083202 0.890684523 0.739073514 0.705901533 0.690102016 0.784179892 0.755325909 1 20.67787818 -1.235639074 3.003857123 1.00115258 0.771673709 0.395740054 0.085628884 10653796.31 14240241.94 114035.0925 0.021071471 0.058124727 1.235639074 -0.22947887 AYEFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 AYEFAER 7 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;;;; 173.59 0.0019951 7941007000 4558060 5315160 5330190 5249290 5802220 6232000 5225310 5047360 5012680 5471610 FALSE TRUE 4738015.728 6227997.384 5469099.13 6287583.894 4815960.717 4784712.447 4815736.548 4979708.395 4832274.626 6543667.219 0.724061229 0.951759491 0.835785034 0.960865472 0.735972744 0.731197398 0.735938486 0.760996583 0.738465827 1 22.64166795 3.216597585 24.9999272 0.765695881 0.87178277 0.135564429 0.098015619 336.4652719 382988.4381 0.025959649 0.031051935 1646.635921 -3.216597585 0.106086888 AYEKPPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYEKPPEKK 9 2 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 72.006 0.026982 1120640000 770990 362620 507200 343800 677820 554180 618750 465070 556870 282560 FALSE TRUE 801429.2805 424897.1642 520418.0487 411802.6139 562604.3985 425480.0937 570250.7582 458836.4974 536828.3575 337922.2221 2.371638289 1.257381541 1.540052754 1.218631351 1.664893167 1.259106581 1.68752074 1.35781688 1.588615138 1 18.3663317 8 0.039847528 3.33E-14 3.922264761 0.278470035 0.30597689 1162.099433 3.525093181 95.21734374 308.4144729 100000000 -8 3.922264761 AYFETEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYFETEKK 8 1 P15170-2;P15170-3;P15170;H3BR35;H3BSV8 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 81.594 0.036006 78531000 115420 88761 102560 82814 146820 129360 124610 103620 109670 70940 FALSE TRUE 119976.8707 104005.0113 105232.7979 99194.36202 121863.5888 99318.10047 114842.7426 102231.1434 105722.9981 84839.33477 1.414165623 1.225905549 1.240377452 1.169202497 1.436404342 1.170661 1.35364973 1.204996994 1.246155435 1 16.37244569 0.067069143 0.679319485 0.989106552 1.28031006 0.46446953 0.089724768 3.420467093 1.811935976 0.176754526 0.03070183 1.166995398 -0.067069143 0.291203507 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHK 39 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 309.09 1.83E-110 5038500000 2979800 2864900 3310700 3147400 3894600 4185100 3998100 3566800 3616300 2800500 FALSE TRUE 3097444.805 3356924.289 3396979.562 3769946.326 3232597.283 3213173.951 3684718.475 3518992.88 3486150.069 3349204.356 0.924830042 1.002305005 1.014264643 1.125624454 0.965183649 0.959384262 1.100177261 1.050695182 1.040889029 1 21.67538698 4.701131664 1.930222843 1.03659373 0.896906251 0.295130612 0.04996518 0.898101428 3.761555517 0.013124152 0.218142196 50249.49069 -4.701131664 -0.139687479 AYGDRIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYGDRIER 8 1 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 0 ; 141.48 0.00057715 659880000 484920 867110 654550 467430 893990 872170 371820 560750 569080 1076090 FALSE TRUE 504065.016 1016029.397 671608.1107 559886.2589 742029.8991 669621.7354 342675.7768 553234.0635 548598.922 1286929.233 0.391680446 0.789499043 0.52186872 0.43505598 0.576589513 0.520325219 0.266273986 0.429886935 0.426285229 1 20.29550129 -1.650334972 6.4551894 1.00285952 0.483051722 0.585901614 0.130095799 0.005546716 0.000300455 0.130502267 0.030645865 0.022369951 1.650334972 -0.519807797 AYGELPEHAK ddPTM_MDA-MB-175_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 ;;; 132.78 0.0002146 3569110000 7064990 5582240 6652190 5490020 8051400 7774800 7678800 6913290 6910900 5621510 FALSE TRUE 7343921.261 6540946.296 6825551.536 6575929.57 6682825.904 5969220.528 7076915.591 6820628.655 6662178.059 6722937.254 1.092367961 0.972929844 1.015263311 0.978133414 0.994033657 0.887888776 1.052652334 1.014531059 0.990962403 1 22.68066025 4.745134937 24.54358378 0.991464991 1.09236802 0.369422125 0.040213564 664.3506255 2480102.172 0.009617449 0.091858883 55607.70055 -4.745134937 0.100903029 AYGSELYGPGRPLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYGSELYGPGRPLSPR 16 1 A7MCY6 A7MCY6 TBKBP1 TANK-binding kinase 1-binding protein 1 1 AYGSELYGPGRPLS(1)PR;AYGSELYGPGRPLS(1)PR 76.015 0.016889 489910000 367960 399670 419500 423790 464110 483850 435540 433690 391400 470180 TRUE FALSE 382487.3449 468310.2135 430432.5146 507614.3971 385220.748 371483.1703 401401.2367 427877.0949 377313.5905 562302.7689 0.680216008 0.832843513 0.765481763 0.902742126 0.685077096 0.660646169 0.713852499 0.760937201 0.671014996 1 19.10098763 -1.178588529 4.423412721 1.000055988 0.745509626 0.523414758 0.07392898 2.962796495 43904012.15 4914.807817 0.017430126 0.066284422 1.178588529 -0.254546362 AYGVPVKPMT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYGVPVKPMTPK 12 1 H3BT74;F8W872;Q15131-4;Q15131-3;Q15131-2;Q15131 H3BT74 CDK10 Cyclin-dependent kinase 10 1 AYGVPVKPMT(1)PK 82.908 0.012642 0 710420 273990 412900 262870 582800 575690 543830 455210 447430 243680 TRUE FALSE 738467.9302 321045.6512 423660.5132 314864.9014 483735.8642 441994.7222 501203.1836 449108.6545 431327.0817 291424.4305 2.53399459 1.101642888 1.453757712 1.080434131 1.659901551 1.516670107 1.719839283 1.541081006 1.480064938 1 18.1527623 0.720430609 2.973482219 1.000040823 1.54688832 0.166897053 0.379805378 4.03533426 40.71220675 0.338016965 0.088490815 5.253280721 -0.720430609 0.546847497 AYHEQLSVAEITNACFEPANQMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYHEQLSVAEITNACFEPANQMVK 24 0 P68363;P68363-2;C9JDS9;P68366-2;P68366 P68363;P68366-2 TUBA1B;TUBA4A Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 ; 228.29 2.82E-33 213926000 129368 106111 101131 106561 141905 141793 126348 109881 128781 110214 FALSE TRUE 134475.5485 124334.7388 103766.5569 127638.4477 117784.0388 108863.7246 116444.5136 108408.2249 124146.197 131808.3231 1.020235637 0.943299603 0.787253449 0.968364097 0.89360092 0.82592451 0.883438245 0.822468736 0.941869178 1 17.00808195 4.475586043 24.99693989 0.880266532 1.001001663 0.267810745 0.06433899 45.00977691 732885.2534 0.014622227 0.040720363 29894.13857 -4.475586043 0.120735131 AYHLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYHLQK 6 0 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ;; 142.27 0.011547 3468790000 5148110 5041280 5348150 4447050 8066560 6661440 5930580 5440370 5402360 6898730 FALSE TRUE 5351361.358 5907080.624 5487527.183 5326663.217 6695409.013 5114421.515 5465725.643 5367450.739 5207930.119 8250404.059 0.648618094 0.715974706 0.665122234 0.645624527 0.811524983 0.61989952 0.662479753 0.650568227 0.631233341 1 22.97603335 -1.051703908 4.127458452 1.000038827 0.673095064 0.777682605 0.052555816 4486933.695 3429902.361 1400.669772 0.011870195 0.088776106 1.051703908 -0.326943763 AYINKVEELK ddPTM_MDA-MB-175_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 ; 169.58 4.19E-06 2576100000 5054900 2755900 3352300 2718600 4448200 4244600 4411400 3597600 3850400 2307300 FALSE TRUE 5254471.355 3229204.387 3439663.692 3256330.966 3692096.553 3258855.978 4065622.941 3549380.056 3711824.856 2759371.259 1.904227761 1.170268182 1.246538928 1.180098892 1.33802095 1.18101396 1.473387435 1.286300292 1.345170514 1 21.39590815 7.999995152 0.026864217 1.22E-07 3.140434641 0.246241584 0.200904958 3088.684642 6.372165827 248.8673489 551.1066009 99998883.66 -7.999995152 3.140434519 AYINKVEELKK ddPTM_MDA-MB-175_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 ; 134.08 8.35E-05 1966570000 4612250 1934630 2922180 1875700 3987200 3493110 3845100 2801010 3312180 1562960 FALSE TRUE 4794345.191 2266887.653 2998334.411 2246707.862 3309457.168 2681888.141 3543711.015 2763467.042 3192975.289 1869192.087 2.564929107 1.212763348 1.604080411 1.201967351 1.770528129 1.434784664 1.89585171 1.478428601 1.70821143 1 20.8339834 -2.114269569 1.806960107 5.48E-05 1.621628296 0.211814443 0.373322076 1521156.71 344713.7713 6238252.786 0.091206469 0.007686532 2.114269569 1.621573481 AYLPVNESFGFTADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 234.04 2.67E-19 789686000 318766 311887 323731 338135 334242 381307 336706 339696 324051 302091 FALSE TRUE 331351.1278 365451.1661 332167.6958 405017.0938 277427.6642 292754.228 310314.1039 335142.9308 312388.4678 361279.9476 0.917158924 1.011545669 0.919419132 1.121061649 0.767902194 0.810325151 0.858929775 0.927654394 0.864671482 1 18.46275766 3.229057017 24.99999478 0.868468419 0.988465793 0.358510711 0.078974466 217.0320621 570919.7525 0.022274179 0.026954212 1694.560259 -3.229057017 0.119997374 AYLQAR ddPTM_MDA-MB-175_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 ; 117.54 0.052659 2038720000 809990 815490 769150 788170 1362550 1211260 868070 753150 799000 1516730 FALSE TRUE 841969.0306 955544.0639 789194.6809 944067.6735 1130944.238 929963.2218 800028.4051 743055.2562 770244.1461 1813904.204 0.464175026 0.526788604 0.435080684 0.520461704 0.623486199 0.512685962 0.441053284 0.409644156 0.42463331 1 20.79066684 -1.718537782 2.798690972 1.084324417 0.482728339 0.865689571 0.06094507 21062223.26 18267554.63 12443930.73 0.016937399 0.01911887 1.718537782 -0.601596077 AYMCPFMQFIEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYMCPFMQFIEGGR 14 0 O94855;O94855-2;P53992;G5EA31 O94855;P53992 SEC24D;SEC24C Protein transport protein Sec24D;Protein transport protein Sec24C 0 76.143 0.065804 41768000 29038 31710 30904 35820 44249 39401 30966 39762 39240 33655 FALSE TRUE 30184.44266 37155.94583 31709.38363 42905.08909 36727.57079 30250.71488 28538.80401 39229.05543 37827.76007 40249.05289 0.749941688 0.923150811 0.787829312 1.06599003 0.912507703 0.751588241 0.709055293 0.974657852 0.939842241 1 15.29666721 1.607148351 24.99999996 0.967952276 0.85088814 0.252733831 0.100645117 0.12859729 3957.976131 0.052372351 0.026470339 40.4714115 -1.607148351 -0.117064136 AYMCPFMQFIEGGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYMCPFMQFIEGGRR 15 1 O94855;O94855-2;P53992;G5EA31 O94855;P53992 SEC24D;SEC24C Protein transport protein Sec24D;Protein transport protein Sec24C 0 119.39 0.00034717 194200000 59737 94047 84352 56487 93708 100150 72137 70544 69973 118060 FALSE TRUE 62095.46289 110198.8407 86550.28242 67659.96 77779.54763 76891.68029 66482.71345 69598.47307 67454.6854 141191.5966 0.439795741 0.780491497 0.612998822 0.479206707 0.55087944 0.544591053 0.47086877 0.49293637 0.477752834 1 17.1072947 -1.487377636 6.138232761 1.000327913 0.540427092 0.685214444 0.093765964 0.000428904 3.58E-05 0.092542586 0.021797416 0.03255535 1.487377636 -0.459900822 AYPLADAHLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYPLADAHLTK 11 0 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 ;; 152.7 3.28E-05 785650000 1000310 955460 1032540 884370 1313880 1371350 1235030 1061320 1077940 1063070 FALSE TRUE 1039803.011 1119552.823 1059448.841 1059295.746 1090547.147 1052874.746 1138225.121 1047094.741 1039145.15 1271358.213 0.817867852 0.880595894 0.833320484 0.833200066 0.857781179 0.828149561 0.895282785 0.823603239 0.817350405 1 20.27793914 -1.468039997 3.183970757 1.003149406 0.844345385 0.774383075 0.025411288 7512959.187 9437533.275 209289.1241 0.005727764 0.034037684 1.468039997 -0.158804021 AYPVSGCFDYLSEDLPDTIHIGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYPVSGCFDYLSEDLPDTIHIGGR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 ; 216.49 1.33E-32 145993000 57936 71126 61749 71217 76937 81942 63473 66577 74622 70583 FALSE TRUE 60223.35802 83341.33722 63358.22967 85303.51004 63859.27622 62912.21234 58497.8204 65684.64421 71936.3688 84412.38746 0.713442183 0.987311694 0.750579762 1.010556775 0.756515461 0.745295972 0.693000425 0.77813987 0.852201566 1 16.36516711 5.033244369 16.41767187 0.824149089 0.324610225 0.085662922 0.113402705 42684451.18 576373056 0.026366914 610329696.8 107955.3994 -5.033244369 -0.499538864 AYQDQIS(ph)PVPGAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYQDQISPVPGAPK 14 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 1 AYQDQIS(1)PVPGAPK;AYQDQIS(1)PVPGAPK 154.51 6.40E-06 203263000 664490 431450 581070 476450 662720 743590 696090 565170 618980 459680 TRUE FALSE 690724.5783 505548.1813 596213.1616 570690.3879 550071.0911 570902.4917 641528.6469 557594.8206 596703.0307 549745.4949 1.256444272 0.919604046 1.08452578 1.038099254 1.000592267 1.038485075 1.166955715 1.014278108 1.085416863 1 19.06840435 AYRPPS(ph)GEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYRPPSGEK 9 1 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 AYRPPS(1)GEK 93.623 0.0056163 213870000 440010 251250 312310 285290 377280 433090 420070 298370 337090 222460 TRUE FALSE 457381.9346 294400.233 320449.0552 341719.5105 313150.0804 332511.411 387143.8158 294370.8382 324958.1967 266046.7777 1.719178629 1.106573196 1.20448388 1.284433938 1.17704895 1.24982311 1.455171978 1.106462708 1.22143256 1 18.0213204 8 0.02758465 1.25E-14 3.006584211 0.28499359 0.163796862 2403.955764 5.090481647 183.355759 414.7326545 100000000 -8 3.006584211 AYS(ph)FCGTVEYMAPEVVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 283.05 2.10E-39 2328566000 1487340 1550599 1800844 1750051 2048313 2124110 1738556 1784195 1722397 1546902 TRUE FALSE 1546061.332 1816902.316 1847775.474 2096205.864 1700141.488 1630817.644 1602283.438 1760280.784 1660408.268 1849987.83 0.835714326 0.982115821 0.998804124 1.133091705 0.919001445 0.88152885 0.866104853 0.951509386 0.897523887 1 20.81908435 3.044796886 24.99999364 0.913422468 0.992636957 0.160197503 0.075469321 213.942794 119394.5863 0.022004132 0.026299958 1108.65619 -3.044796886 0.079214489 AYS(ph)GSDLPSSSSGGANGTAGGGGGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 AYS(0.984)GS(0.016)DLPSSSSGGANGTAGGGGGAR;AYS(0.915)GS(0.073)DLPS(0.004)S(0.004)S(0.002)S(0.002)GGANGTAGGGGGAR;AYS(0.991)GS(0.009)DLPSSSSGGANGTAGGGGGAR;AYS(1)GSDLPSSSSGGANGTAGGGGGAR 351.35 6.25E-110 871020000 469504 541118 596556 537826 684529 771183 654525 668628 680528 623576 TRUE FALSE 488040.3805 634050.8072 612102.7394 644206.3775 568173.0051 592087.4356 603221.6202 659666.1353 656035.9302 745753.7781 0.654425622 0.850214676 0.82078396 0.863832536 0.761877475 0.793944936 0.808875044 0.884562914 0.879695081 1 19.50833986 -5 0.094441209 1.628550207 0.670176793 0.609306331 0.053465047 140.3014381 0.912931021 17.32165775 1.073499292 1.00E-05 5 -0.958373414 AYS(ph)PEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;AYS(1)PEYR 129.42 0.0038414 25201826000 12619250 14173370 13459380 13843650 15439420 16438140 14638590 14016090 13814940 12869670 TRUE FALSE 13117467.73 16607536.04 13810142.5 16581882.65 12815032.9 12620631.11 13491179.06 13828227.24 13317743.01 15391235.43 0.852268669 1.079025535 0.897273163 1.077358782 0.83261886 0.819988179 0.876549457 0.898448166 0.865280962 1 23.8756057 3.217104641 24.97702051 0.875435891 0.978148427 0.249303184 0.07966388 282.5938122 328968.2781 0.021198878 0.025359481 1648.559557 -3.217104641 0.102712536 AYS(ph)PEYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;AYS(1)PEYRR;AYS(1)PEYRR;AYS(1)PEYRR 130.53 0.00063929 4718000000 1637890 2048920 1840190 1256020 2470920 2258380 1210840 1737750 1779250 2858170 TRUE FALSE 1702555.162 2400806.072 1888146.863 1504457.007 2050913.901 1733905.471 1115931.197 1714458.304 1715215.14 3418173.689 0.498089131 0.702365149 0.552384705 0.440134746 0.600002834 0.507260786 0.32647001 0.501571441 0.501792857 1 21.70479428 -0.855217902 5.984098373 1.000000069 0.512111023 0.712434159 0.092533469 8.89E-08 1.67E-08 0.093261482 0.021981939 0.139566792 0.855217902 -0.487889046 AYSEAHEISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AYSEAHEISK 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 168.83 0.0029357 4893900000 7855895 10791180 10252440 9660550 13147550 14376160 11426490 11466690 10593650 11053600 FALSE TRUE 8166051.801 12644481.22 10519627.01 11571377.96 10912734.15 11037514.71 10530851.86 11312997.78 10212386.61 13219341.29 0.617735152 0.956513713 0.795775431 0.875336956 0.825512702 0.834951945 0.796624554 0.855791339 0.772533698 1 23.65614695 -1.752360875 2.790345456 1.036124888 0.822634233 0.309182446 0.082372504 30158987.62 23533092.37 7482914.675 0.01749313 0.017686387 1.752360875 -0.213490655 AYSPELIVHPVLDSPNAVHEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYSPELIVHPVLDSPNAVHEVEK 23 0 Q8IW45-2;Q8IW45 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 ; 233.66 2.75E-37 308290000 177505 139754 164483 133302 200850 208040 186356 172175 192786 146521 FALSE TRUE 184513.0345 163755.6624 168769.5621 159668.7377 166709.5887 159725.8629 171748.9298 169867.2757 185847.6695 175228.9846 1.052982387 0.934523833 0.963137248 0.911200496 0.951381354 0.911526499 0.980139959 0.969401701 1.060598907 1 17.41888191 1.404230743 3.906133037 1.029620895 0.954498811 0.321759416 0.040767576 0.237096769 6.027845434 0.028954637 0.010023086 25.36475915 -1.404230743 -0.075122084 AYSPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYSPKR 6 1 A6NM62 A6NM62 LRRC53 Leucine-rich repeat-containing protein 53 0 103.41 0.055655 273900000 375320 371390 378580 374860 761380 712040 633900 554700 604830 666400 FALSE TRUE 390137.9234 435173.3435 388446.1058 449006.1892 631960.8996 546679.5011 584213.2616 547265.1538 583062.2864 796968.321 0.489527517 0.546035936 0.487404701 0.563392769 0.79295611 0.685948847 0.733044522 0.686683698 0.73160033 1 19.60416285 1.797420381 0.085917232 1.438433775 8.82E-15 0.824535285 0.062823846 6.094158509 0.486141058 3.667682366 4.032834755 62.72206968 -1.797420381 -1.438433775 AYSSFGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYSSFGGGR 9 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;; 166.68 0.00014089 860880000 328811 447530 395650 390910 443240 483280 395750 383380 375960 514160 FALSE TRUE 341792.7122 524389.7962 405960.964 468230.8313 367898.2231 371045.5442 364730.0809 378241.4182 362429.273 614899.8078 0.555851064 0.852805269 0.660206685 0.761475 0.598305965 0.603424394 0.593153675 0.615126909 0.589411915 1 19.22999183 -1.054503384 4.638876933 1.000012428 0.649806882 0.596615977 0.086877778 11612200.53 2639670.117 1702.984151 0.020337683 0.088205693 1.054503384 -0.350205546 AYSSFGGGRGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 107.74 0.0010791 811460000 734950 541860 676360 468000 748530 731480 641690 532280 579910 728340 TRUE FALSE 763966.3935 634920.2399 693986.4972 560569.0032 621295.138 561604.8557 591392.6611 525145.6572 559039.1524 871044.2781 0.877069528 0.728918444 0.796729299 0.64355971 0.713276183 0.644748918 0.678946726 0.602892035 0.641803369 1 19.73238653 5.313796177 0.796250815 0.680211785 1.198363415 0.129605228 0.110571718 8.366241389 2.129533912 0.034812798 4.74581681 205966.3044 -5.313796177 0.51815163 AYT(ph)PPPPLGPHPNLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 AY(0.001)T(0.999)PPPPLGPHPNLGK;AY(0.002)T(0.998)PPPPLGPHPNLGK 109.72 0.0034977 468900000 766170 470740 676400 487110 856230 885560 779970 693340 708680 407610 TRUE FALSE 796418.9832 551585.9332 694027.5397 583458.9041 710688.3304 679902.1108 718833.9133 684046.9114 683174.7452 487473.3753 1.633769193 1.131520122 1.423723991 1.196904146 1.457901839 1.39474717 1.47461164 1.40324979 1.401460633 1 18.8949639 -0.726473241 6.620707221 0.999999999 1.385514022 0.436735656 0.133044993 1.75E-09 5.28E-10 0.11723933 0.027633575 0.187727008 0.726473241 0.385514023 AYT(ph)PVVVTLWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYTPVVVTLWYR 12 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 1 AYT(1)PVVVTLWYR;AYT(1)PVVVTLWYR 115.14 0.01098 1837030000 606480 469540 568540 543120 758670 890210 808830 592340 561760 427920 TRUE FALSE 630424.2987 550179.8425 583356.6195 650547.5149 629711.5444 683472.2188 745431.7911 584400.6512 541542.3673 511762.731 1.231868326 1.075068209 1.139896644 1.271189705 1.230475582 1.335525581 1.456596477 1.141936714 1.058190319 1 18.96511556 1.373090512 3.738282078 1.028308217 1.24438164 0.439655377 0.098620518 0.238411025 5.352337185 0.083625322 0.02787042 23.60970236 -1.373090512 0.216073422 AYT(ph)PVVVTQWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;AYT(1)PVVVTQWYR 127.3 0.0030429 932680000 525893 495459 560690 519497 746050 813760 708610 583180 566510 430192 TRUE FALSE 546655.6617 580550.2291 575302.042 622251.9561 619236.6875 624776.5727 653067.2966 575363.426 546121.4158 514479.8859 1.062540396 1.128421626 1.118220669 1.209477714 1.203616904 1.214384838 1.269373817 1.118339981 1.061501977 1 18.97275515 1.216035937 2.515770598 1.008017325 1.173268649 0.503130268 0.056375545 0.231011526 2.498915508 0.055648961 0.015773907 16.44507796 -1.216035937 0.165251324 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR 35 1 Q9Y4P8-2;Q9Y4P8-6;Q9Y4P8-3;Q9Y4P8-5 Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 101.14 3.83E-05 25654000 4701.4 7056.2 6808.1 7504.8 8962.6 9671.9 5163.8 5451.4 6019 8352 FALSE TRUE 4887.014902 8268.04746 6985.524679 8989.22704 7439.140453 7425.747804 4759.047863 5378.3329 5802.377366 9988.414491 0.489268332 0.827763752 0.699362715 0.89996536 0.744776907 0.743436089 0.476456786 0.53845712 0.580910751 1 13.28603997 2.30937844 14.91086789 0.597999131 0.744842025 0.022178372 0.16689572 2.85136274 597.3048196 0.054398442 0.045509949 203.881791 -2.30937844 0.146842894 AYTGFSSNSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYTGFSSNSER 11 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 98.943 0.006342 0 68322 33994 39241 36706 53235 56498 52888 48551 45571 35960 FALSE TRUE 71019.40532 39832.20506 40263.6527 43966.33724 44186.13372 43377.19574 48742.50036 47900.25326 43930.90861 43005.6735 1.651396189 0.926208145 0.936240487 1.02233807 1.027448941 1.008638912 1.133396977 1.11381242 1.021514257 1 15.39223938 4.744474316 24.99993113 1.030826101 1.651396458 0.901648606 0.062379146 214.7278262 907727.9013 0.017198629 0.155040708 55523.17797 -4.744474316 0.620570357 AYTNFDAERDALNIETAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 AYTNFDAERDALNIETAIK 19 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YNB8;H0YKN4;H0YMD9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 157.88 1.44E-09 79986000 106660 114540 135760 101300 136510 167570 99068 107620 124480 134620 FALSE TRUE 110871.0192 134211.354 139298.0171 121336.8376 113306.079 128654.407 91302.79129 106177.5299 119999.9891 160996.2115 0.688656075 0.83363051 0.865225435 0.753662689 0.703781026 0.7991145 0.567111427 0.659503282 0.745359086 1 17.29666721 3.487143572 7.363977767 0.7156939 0.801365776 0 0.114835301 0.332638124 111.4918002 0.030163056 0.043865055 3070.036737 -3.487143572 0.085671875 AYVFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYVFER 6 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PSE4;A0A1W2PS70;A0A1W2PNX7 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 111.69 0.064292 269760000 299860 364440 298710 340380 338630 388680 263810 272380 238820 364300 FALSE TRUE 311698.7043 427029.7351 306494.628 407706.1481 281069.7936 298414.9605 243131.8829 268729.1916 230224.9149 435677.6101 0.715434296 0.980150747 0.703489509 0.935797798 0.645132518 0.684944449 0.558054573 0.616807441 0.52842953 1 18.73290145 3.217478306 24.60438308 0.643824941 0.834875494 0.213456305 0.145867919 233.9547568 273039.1086 0.038643484 0.046235177 1649.978578 -3.217478306 0.191050553 AYVHEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AYVHEFK 7 0 Q9H4A4;A6NKB8;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 121.29 0.0044522 1988580000 3886900 2811720 3579520 3433590 4466940 4326860 4375010 3550370 3824790 2781140 FALSE TRUE 4040357.813 3294611.038 3672805.232 4112743.854 3707651.134 3322012.339 4032085.284 3502783.097 3687136.555 3326051.135 1.214761184 0.99054732 1.104253989 1.236524541 1.114730647 0.998785708 1.212273991 1.053135672 1.108562799 1 21.66537892 -0.08564439 0.492898109 0.986552286 1.119488285 0.159642499 0.081494807 9.223351025 2.612830511 0.315731066 0.039911574 0.821023542 0.08564439 0.132935998 AYVWDNNKDLAEWLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 AYVWDNNKDLAEWLEK 16 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 217.37 1.31E-14 399230000 428780 232797 367650 268875 495770 433820 385580 370230 425630 263565 FALSE TRUE 445708.5655 272778.0738 377231.261 322057.6725 411499.1925 333071.8796 355357.2321 365267.6724 410311.6594 315205.5155 1.414025274 0.865397528 1.196778744 1.021738696 1.305494899 1.056681635 1.127382659 1.158823861 1.30172741 1 18.26593325 AYWQVHLDQVEVASGLTLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 284.36 5.62E-45 6891098000 4296172 4123457 4255214 4109672 4941287 5899345 5363093 4709388 4595785 4536992 FALSE TRUE 4465788.188 4831628.664 4366108.373 4922552.855 4101368.801 4529311.529 4942719.757 4646266.357 4430383.596 5425928.716 0.823045864 0.890470354 0.804674849 0.907227705 0.755883281 0.834753231 0.91094447 0.856308035 0.816520789 1 22.37143866 -1.75179008 2.632717742 1.033923698 0.847213387 0.503056255 0.046313414 14962334.05 11353554.98 3297493.982 0.010754534 0.017709648 1.75179008 -0.186710311 AYYEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 AYYEFR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 103.28 0.080999 1384360000 1397920 1815170 1522360 1625130 1985890 1924170 1600220 1644530 1519150 2117260 FALSE TRUE 1453110.961 2126911.327 1562033.952 1946575.863 1648329.127 1477310.679 1474790.575 1622487.765 1464476.088 2532096.56 0.573876599 0.839980339 0.616893517 0.768760518 0.65097404 0.583433785 0.582438521 0.64076852 0.578365024 1 21.27190099 -1.104048372 9.03082722 1.000000003 0.651169274 0.609154696 0.084467147 4.84E-09 4.60E-10 0.079723261 0.018790953 0.078695813 1.104048372 -0.348830729 CAAPRPPSS(ph)SPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.011)S(0.495)S(0.495)PEQR;CAAPRPPS(0.088)S(0.456)S(0.456)PEQR;CAAPRPPS(0.057)S(0.585)S(0.358)PEQR;CAAPRPPS(0.067)S(0.467)S(0.467)PEQR;CAAPRPPS(0.058)S(0.581)S(0.361)PEQR 153.08 3.81E-07 1717070000 568655 761661 779911 776803 794247 1157495 775101 854323 716536 732194 TRUE FALSE 591105.9385 892470.3518 800236.1214 930452.3149 659241.1786 888684.3283 714346.5583 842872.1976 690748.0093 875653.3956 0.675045562 1.019205037 0.913873144 1.062580605 0.752856304 1.014881382 0.815786888 0.962563729 0.788837242 1 19.7400004 -1.796640193 0.007794437 1.886348443 7.07E-06 0.036665762 0.124013986 62142.63398 71.44015692 9176.622877 8135.638036 0.015972019 1.796640193 -1.886341375 CAAPRPPSSS(ph)PEQR ddPTM_MDA-MB-175_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(0.031)S(0.11)S(0.859)PEQR 144.46 5.36E-06 828780000 152770 161580 171180 160800 202740 248240 190570 173200 162310 128560 TRUE FALSE 158801.4776 189330.1081 175641.0914 192605.7601 168278.3272 190590.0221 175632.6254 170878.5373 156468.4948 153748.8706 1.032862726 1.231424383 1.142389474 1.252729593 1.094501225 1.239619006 1.142334411 1.111413285 1.017688743 1 17.23021629 1.37437209 1.912333104 0.997816442 1.168630132 0.471849249 0.064226598 0.252657871 1.641188754 0.052350338 0.016050485 23.67947613 -1.37437209 0.17081369 CAAPRPPSSSPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CAAPRPPSSSPEQR 14 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 162.94 3.97E-06 382768000 354852 370695 386538 381492 462350 593460 403167 437513 380315 300852 FALSE TRUE 368861.831 434358.9826 396611.4978 456949.979 383759.9121 455637.909 371565.7171 431648.8539 366627.5374 359798.1892 1.025190904 1.207229485 1.102316548 1.27001745 1.066597675 1.266370767 1.032705912 1.199697127 1.018981052 1 18.4568284 1.177333043 7.536662014 1.005955648 1.149028319 0.292307402 0.08506841 0.284079742 29.05020961 0.071077186 0.017953169 15.04295106 -1.177333043 0.143072671 CAHIEAK ddPTM_MDA-MB-175_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 ; 96.964 0.012345 1073930000 1322870 909970 1107070 969380 1600070 1737600 1387520 1308520 1352660 793440 FALSE TRUE 1375097.929 1066250.269 1135921.154 1161120.471 1328090.673 1334068.734 1278762.557 1290981.43 1303978.031 948899.3767 1.449150419 1.123670534 1.197093371 1.223649735 1.399611703 1.405911698 1.347627144 1.360504034 1.374200535 1 19.85589558 5.073242996 18.24698039 1.292183033 4.855675137 0.128193736 0.129015523 43662048.44 118475992.9 0.030552378 6181071891 118370.3674 -5.073242996 3.563492104 CAIKVEQSAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 123.2 0.00034184 838630000 813740 634300 827940 565310 1128110 1060440 757330 812610 814000 636540 FALSE TRUE 845867.0835 743236.0908 849516.7966 677126.6307 936354.2652 814168.8811 697968.4957 801718.2921 784704.299 761257.8257 1.111144024 0.976326372 1.115938343 0.889483967 1.230009379 1.069504777 0.916862162 1.053149492 1.030799648 1 19.53802563 CALGWDHQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CALGWDHQEK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 205.18 1.73E-07 6312420000 7928170 5586430 7177300 5654350 9360530 9958360 8670030 7697320 7940180 4671250 FALSE TRUE 8241180.273 6545855.896 7364346.334 6772763.553 7769430.454 7645681.81 7990450.394 7594150.016 7654414.473 5586492.001 1.475197722 1.171729217 1.318241632 1.212346416 1.39075299 1.368601586 1.430316269 1.359377229 1.37016476 1 22.41351121 -0.990729572 5.454731956 0.999998933 1.341549244 0.583209487 0.087239028 1.11E-06 2.05E-07 0.082714558 0.019495947 0.10215754 0.990729572 0.341550311 CALSS(ph)PSLAFTPPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 CALS(0.129)S(0.819)PS(0.052)LAFTPPIK;CALS(0.037)S(0.926)PS(0.037)LAFTPPIK 273.07 2.03E-33 1084450000 1817460 1462390 1816210 1383990 2347600 2519900 2005570 1960470 1983240 1397150 TRUE FALSE 1889214.724 1713544.107 1863541.925 1657739.091 1948555.791 1934691.414 1848368.183 1934193.106 1911863.58 1670894.792 1.13066049 1.025524835 1.115295788 0.992126553 1.166175033 1.157877458 1.106214581 1.157579229 1.144215416 1 20.67218947 3.213606377 24.99387329 1.132151475 1.066545893 0.167582974 0.058699655 310.9460358 311438.7923 0.015526834 0.018565035 1635.333665 -3.213606377 -0.065605582 CAPSAGS(ph)PAAAVGR ddPTM_MDA-MB-175_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(0.015)AGS(0.985)PAAAVGR;CAPS(0.022)AGS(0.978)PAAAVGR 301.95 6.49E-44 666610000 450300 445633 450704 482575 615038 760338 554939 545870 529408 391631 TRUE FALSE 468078.1917 522167.0012 462449.7165 578026.8947 510494.0604 583761.0225 511441.4311 538553.5055 510354.7095 468363.5962 0.999390635 1.114875292 0.987373315 1.234141379 1.089952474 1.246384278 1.091975199 1.149862009 1.089654947 1 18.83726942 3.755485111 24.99357867 1.136725599 1.041979306 0.243473465 0.07542992 1080.124708 1595089.636 0.017620449 0.031666528 5694.886994 -3.755485111 -0.094746293 CAPSAGSPAAAVGRES(ph)PGAAATSSSGPQAQQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CAPSAGSPAAAVGRESPGAAATSSSGPQAQQHR 33 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR;CAPSAGSPAAAVGRES(1)PGAAATSSSGPQAQQHR 307.82 2.73E-104 1263430000 114459 141582 144485 147966 189756 227083 134886 172087 141584 124178 TRUE FALSE 118977.9297 165897.6071 148250.3978 177233.2332 157501.3429 174346.4147 124313.2829 169780.4552 136488.4195 148508.3016 0.801153393 1.117093155 0.998263371 1.19342307 1.060555816 1.173984302 0.837079689 1.143238819 0.919062558 1 17.18018405 2.274526747 24.99999694 0.998197532 1.063761447 0.080909645 0.12582941 537.2586562 373445.3712 0.041754051 0.034932868 188.1597585 -2.274526747 0.065563915 CAS(ph)CLKEFRSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CASCLKEFRSK 11 2 J3QQI2;J3KTI4;H7BYU6;Q96K83 J3QQI2 ZNF521 Zinc finger protein 521 1 CAS(1)CLKEFRSK;CAS(1)CLKEFRSK 59.871 0.076582 6183370000 112830 12887670 13027340 11769980 11837100 16312700 9856470 12463650 12770500 14809160 TRUE FALSE 117284.6155 15101027.07 13366843.18 14098046.91 9825033.97 12524322.65 9083894.126 12296595.16 12310892.2 17710731.36 0.006622234 0.852648418 0.754731293 0.796017207 0.554750324 0.707160105 0.512903388 0.694301941 0.695109194 1 24.07812045 -5 0.147256321 2.232113307 0.520005789 0.243757418 0.220749169 218.1798304 1.925798052 79.48861794 1.130375956 1.00E-05 5 -1.712107518 CATITPDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CATITPDEKR 10 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;; 152.04 3.00E-05 1753840000 980300 725610 805800 727310 1313500 1277110 1103830 1062400 1024450 659550 FALSE TRUE 1019003.001 850227.873 826799.81 871169.7472 1090231.739 980520.5573 1017308.92 1048160.266 987580.2446 788776.1947 1.291878492 1.077907623 1.048205835 1.104457453 1.382181342 1.24309096 1.289730759 1.328843686 1.252041138 1 19.58925649 3.263671284 24.99576334 1.272157289 1.120961472 0.191987434 0.112950709 275.6424602 274379.2898 0.029402489 0.039794908 1835.148798 -3.263671284 -0.151195817 CAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 CAVSDVEMQEHYDEFFEEVFTEMEEK 26 0 P0DN76;Q01081 P0DN76 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ;;;;;; 227.51 1.29E-34 364700000 268869 216033 306362 227520 380583 400211 351480 316180 340273 197703 FALSE TRUE 279484.1557 253134.9872 314346.0454 272522.7769 315891.6376 307268.0605 323930.0792 311942.1243 328026.6412 236439.1176 1.182055485 1.070613822 1.329501009 1.1526129 1.336037965 1.299565248 1.3700359 1.31933382 1.387361975 1 17.85110922 4.234946161 24.99982988 1.290831706 1.126334637 0.201813897 0.113980761 106.4321156 736172.3896 0.026133105 0.060185112 17176.95434 -4.234946161 -0.16449707 CCLTYCFNKPEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CCLTYCFNKPEDK 13 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ; 213.67 3.71E-09 3134600000 3286000 1459560 2115000 1535150 3166100 3137000 2848200 2323800 2661600 986810 FALSE TRUE 3415733.817 1710228.076 2170118.637 1838798.088 2627927.453 2408479.292 2624950.642 2292653.262 2565809.536 1180156.526 2.894305749 1.449153598 1.838839671 1.558096784 2.226761786 2.040813434 2.224239399 1.9426688 2.174126465 1 20.17054679 4.755250176 24.40535843 1.888871851 2.894306846 0.409129775 0.378067767 2422.84108 3542871.107 0.084827226 2.303617062 56918.07137 -4.755250176 1.005434996 CCSFDGDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CCSFDGDADR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 146.79 0.012411 0 274580 287460 315220 305900 350710 458420 305640 355680 286460 233810 FALSE TRUE 285420.6304 336829.0189 323434.8922 366406.107 291096.4395 351958.9024 281683.1382 350912.6914 276150.3606 279620.5929 1.020742526 1.204593036 1.156691962 1.310368822 1.041040777 1.258701653 1.007376228 1.254960115 0.987589496 1 18.09311109 1.217978428 24.99937639 0.993794474 1.160260189 0.297242001 0.100149145 306.3403099 372074.8388 0.085818538 0.021551824 16.51879747 -1.217978428 0.166465715 CDDS(ph)PRTPSNTPSAEADWSPGLELHPDYK ddPTM_MDA-MB-175_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(0.514)PRT(0.466)PS(0.016)NT(0.003)PSAEADWSPGLELHPDYK 86.081 0.0011877 34409000 40641 36270 49599 38817 57878 57787 44750 47532 40183 46829 TRUE FALSE 42245.53806 42499.09036 50891.59069 46494.88674 48039.91823 44366.84502 41242.37807 46894.91129 38736.82168 56004.24595 0.754327415 0.758854791 0.908709506 0.830202888 0.857790645 0.792205024 0.736415201 0.837345642 0.691676515 1 15.77324859 -1.719410376 2.732671276 1.033965267 0.801342573 0.4993639 0.060979114 12919800.35 10291881.07 2987709.496 0.014452544 0.019080494 1.719410376 -0.232622694 CDDSPRT(ph)PSNTPSAEADWS(ph)PGLELHPDYK ddPTM_MDA-MB-175_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 2 CDDS(0.413)PRT(0.583)PS(0.003)NT(0.002)PS(0.002)AEADWS(0.998)PGLELHPDYK 90.336 0.024457 43915000 45133 31938 38223 27611 48495 54698 37729 41226 42516 31706 TRUE FALSE 46914.88569 37423.10306 39219.12278 33072.37339 40251.83722 41995.21846 34771.70239 40673.4329 40985.85747 37918.18365 1.237266166 0.986943452 1.03430911 0.872203524 1.061544445 1.107521891 0.917019199 1.072663007 1.080902446 1 15.21060224 4.743183224 24.47637043 1.015649601 1.237266287 0.472233806 0.070552948 311.2222801 1647821.579 0.016498575 0.131176192 55358.36106 -4.743183224 0.221616686 CDDSPRT(ph)PSNTPSAEADWSPGLELHPDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CDDSPRTPSNTPSAEADWSPGLELHPDYK 29 1 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8Y586;A0A2R8Y7R5;A0A2R8Y755 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 CDDS(0.173)PRT(0.821)PS(0.006)NTPSAEADWSPGLELHPDYK;CDDS(0.139)PRT(0.859)PS(0.001)NTPSAEADWSPGLELHPDYK 194.26 1.30E-18 575080000 446360 375056 394510 340299 597800 586360 414510 438380 454110 360036 TRUE FALSE 463982.6375 439468.9505 404791.2547 407609.1265 496186.1695 450186.7764 382019.6231 432504.2331 437766.6698 430578.1609 1.077580518 1.020648492 0.940110975 0.946655366 1.152371891 1.0455402 0.887224801 1.004473223 1.016695015 1 18.71591562 -1.00128727 4.306521036 0.999999815 1.006145795 0 0.070995234 2.14E-07 4.94E-08 0.07002429 0.016504058 0.099704034 1.00128727 0.00614598 CDENILWLDYK ddPTM_MDA-MB-175_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 ;;;; 186.72 9.08E-06 2219970000 2836440 2031376 2671430 2096872 3612918 3708850 3152831 2767282 3013584 1859320 FALSE TRUE 2948424.841 2380249.026 2741049.66 2511627.023 2998795.489 2847525.796 2905703.868 2730191.111 2905125.701 2223618.155 1.325958252 1.070439644 1.232698003 1.129522628 1.348610813 1.280582185 1.306745882 1.227814724 1.30648587 1 21.08447764 5.075735472 20.17642971 1.225726823 4.707309927 0.079384452 0.107503771 1105.788519 300486.7535 0.023466993 3477.593557 119051.6645 -5.075735472 3.481583104 CDILVQEELLAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CDILVQEELLASPK 14 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK;CDILVQEELLAS(1)PK 227.4 2.14E-12 597341000 1359540 439699 595184 545317 852255 1207183 1120943 762790 733750 291542 TRUE FALSE 1413215.689 515213.8829 610694.984 653179.075 707388.9995 926833.0433 1033080.559 752566.0477 707342.4808 348664.073 4.053230024 1.477679872 1.75152828 1.873376484 2.028855435 2.65824074 2.962968194 2.158427283 2.028722015 1 18.41147819 4.749836894 24.70498869 2.08740931 4.053231382 0.570314125 0.530775257 1120.361341 2454524.203 0.129448692 1.987168217 56213.01689 -4.749836894 1.965822072 CDLEDER ddPTM_MDA-MB-175_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 ; 116.3 0.012765 417910000 946230 1112010 998410 1353270 1662250 1803710 1372540 1120220 1013440 1140740 FALSE TRUE 983587.891 1302989.067 1024429.385 1620942.767 1379701.339 1384825.688 1264956.728 1105205.283 976966.4924 1364246.162 0.720975377 0.95509821 0.750912418 1.188160034 1.01132873 1.015084906 0.927220295 0.8101216 0.716121855 1 20.37967255 -0.885085297 4.760551513 1.000000462 0.906160807 0.039933588 0.144575491 7.16E-07 1.68E-07 0.141418306 0.033332451 0.130291086 0.885085297 -0.093839656 CDLVNYSYGEATHWPNSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CDLVNYSYGEATHWPNSGR 19 0 A0A494C0U1;Q5VZU9;P29144;A0A494C0X4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 201.52 9.80E-22 0 54704 60302 70195 57880 78304 97312 75634 61884 64256 60892 FALSE TRUE 56863.75616 70658.39942 72024.33937 69328.49125 64993.91405 74712.76278 69705.60945 61054.5462 61943.43911 72822.62155 0.780852913 0.970280909 0.989037992 0.952018614 0.892496214 1.025955413 0.9571972 0.838400828 0.850607102 1 16.15209906 -1.032281431 4.817207106 1.000001736 0.920336905 0.103418808 0.0724835 1.37E-06 2.76E-07 0.071256799 0.016795023 0.092836459 1.032281431 -0.079664831 CDNFTSSWR ddPTM_MDA-MB-175_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 ;;; 166.07 0.00014196 948400000 372844 403387 347843 348410 479930 608608 379393 399074 373135 382070 FALSE TRUE 387564.169 472665.5793 356908.0743 417324.4581 398351.67 467268.0155 349655.1853 393725.0658 359705.9442 456929.3013 0.848192856 1.034439197 0.781101307 0.913323914 0.871801543 1.022626507 0.765228197 0.861676116 0.787224508 1 18.80161144 2.217739016 24.99910626 0.84137083 0.909778337 0.082235538 0.091861571 517.8971556 621800.5923 0.031965612 0.023633176 165.096937 -2.217739016 0.068407508 CDPAPFYLFDEIDQALDAQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CDPAPFYLFDEIDQALDAQHR 21 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;;;;; 257.93 1.69E-36 192637500 117196 120811.7 135950 137560 153303 208426 162599 153606 143872 106600.8 FALSE TRUE 121822.9886 141560.1697 139492.9687 164768.9574 127244.6108 160022.2202 149854.0655 151547.1628 138694.0748 127487.1858 0.955570459 1.110387439 1.094172468 1.292435443 0.99809726 1.25520239 1.175444141 1.18872467 1.087906004 1 16.95999272 4.907426649 1.566383713 1.152752392 0.815340135 0.242567142 0.092809387 2.014744353 3.382308193 0.022532081 1.175620677 80802.84437 -4.907426649 -0.337412257 CDPDAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CDPDAAR 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 94.407 0.033089 1119930000 618160 698840 709660 780790 828030 1025860 711250 738640 713780 684940 FALSE TRUE 642565.4341 818860.3338 728154.3226 935227.9316 687281.7564 787619.5621 655500.3665 728739.739 688091.1972 819140.879 0.784438246 0.999657513 0.88892441 1.141718055 0.83902754 0.961519053 0.800229098 0.889639081 0.840015698 1 19.64375207 CDVDIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CDVDIRK 7 1 P60709;A0A2R8Y793;Q562R1;P63261 P60709;P63261 ACTB;ACTBL2;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 ;;; 91.041 0.02677 65507050000 51608500 40757550 46337000 33454520 67010700 66608300 50593100 48060600 50022900 33078610 FALSE TRUE 53646043.43 47757342.16 47544580.29 40071724.2 55620245.15 51139531.78 46627480.62 47416426.27 48222585.6 39559730.3 1.356077077 1.207221126 1.201842882 1.0129423 1.405981404 1.292716897 1.178660225 1.198603375 1.218981657 1 25.23752925 -0.291735033 0.619861199 0.979846735 1.232849935 0.321411155 0.101130466 9.527581019 3.324595909 0.553936557 0.039794989 0.510816559 0.291735033 0.2530032 CEAFGWHAIIVDGHSVEELCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CEAFGWHAIIVDGHSVEELCK 21 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 242.98 2.59E-30 704700000 482050 357940 470540 358540 971680 729410 660550 486950 505970 426680 FALSE TRUE 501081.7062 419413.4106 482802.659 429458.1419 806514.1807 560015.5818 608774.365 480423.2317 487760.2385 510279.7767 0.981974456 0.821928342 0.946152838 0.841613094 1.580533302 1.097467717 1.193020756 0.941489853 0.955868253 1 18.96092894 CEDCGKPLSIEADDNGCFPLDGHVLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CEDCGKPLSIEADDNGCFPLDGHVLCR 27 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 ; 207.46 1.43E-25 409790000 191130 195834 168751 180355 263150 312460 227485 248100 235273 174413 FALSE TRUE 198675.96 229466.9661 173148.7897 216028.6807 218419.857 239895.9004 209654.1313 244774.6253 226805.5707 208585.888 0.95248994 1.100107818 0.830107882 1.035682149 1.047145898 1.150106091 1.005121359 1.173495617 1.087348587 1 17.67028203 3.289917807 2.834708623 1.092570813 0.971292973 0.274149175 0.080988304 0.306382475 5.017085411 0.022850286 0.031247108 1949.475613 -3.289917807 -0.12127784 CEGINISGNFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CEGINISGNFYR 12 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 230.95 1.07E-11 294760000 155394 123785 105145 103112 164609 202853 168453 121699 142473 117915 FALSE TRUE 161529.0751 145044.1108 107885.1651 123507.2458 136628.821 155743.465 155249.2137 120067.824 137345.4246 141018.1866 1.145448534 1.028548972 0.765044337 0.875824947 0.968873762 1.10442113 1.100916253 0.85143503 0.973955401 1 17.10552171 -1.979319809 4.640563578 1.0230259 0.971280006 0 0.115830528 0.049318669 0.000219784 0.200451036 0.027658608 0.010487698 1.979319809 -0.051745895 CETS(ph)PPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.439)S(0.561)PPS(0.004)S(0.996)PR;CET(0.052)S(0.948)PPS(0.004)S(0.996)PR;CET(0.197)S(0.803)PPS(0.219)S(0.782)PR 139.48 5.99E-05 727910000 599890 727600 712520 707780 845890 1057690 706560 740340 724930 712300 TRUE FALSE 623574.1204 852559.6401 731088.8565 847776.7715 702105.9199 812057.5269 651177.9809 730416.9533 698839.9109 851861.5472 0.732013462 1.000819491 0.858224977 0.995204883 0.824201917 0.953274073 0.764417625 0.85743623 0.82036795 1 19.70025944 2.259030555 24.99980498 0.846604557 0.898621235 0.019530334 0.094222408 669.2933093 817401.7244 0.029824764 0.024925866 181.5643401 -2.259030555 0.052016678 CFLAQPVTLLDIYTHWQQTSELGR ddPTM_MDA-MB-175_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 ; 201.15 1.45E-24 164257000 68070 78369 96216 84678 120189 118153 101008 100160 101282 81022 FALSE TRUE 70757.45616 91828.26612 98723.468 101427.0557 99759.31671 90713.75638 93090.72902 98817.51903 97636.8806 96896.70964 0.730235902 0.947692305 1.018852636 1.046754385 1.029542872 0.936190266 0.960721261 1.019823267 1.007638763 1 16.56416006 4.726054993 2.851160627 1.00177298 0.68586172 0.874087251 0.03090084 0.137645354 1.601675087 0.008344786 0.099417365 53217.56423 -4.726054993 -0.31591126 CFSEENHEPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CFSEENHEPLR 11 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 149.49 3.43E-05 306500000 330150 304240 332920 305490 348270 424210 364600 343740 337940 249030 FALSE TRUE 343184.5769 356490.8533 341596.1687 365915.0102 289071.1898 325693.6565 336021.6993 339132.7275 325777.6054 297822.6605 1.152311837 1.196990359 1.146978434 1.228633877 0.970615162 1.093582523 1.128261022 1.13870693 1.093864398 1 18.184094 -4.999999994 0.020578889 3.29E-07 1.902631895 0.340818117 0.061707162 3734.59824 5.817254221 365.4726939 196.5372033 1.00E-05 4.999999994 1.902631565 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CFSIDNPGYEPEVVAVHPGGDTVAIGGVDGNVR 33 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 121.2 1.36E-07 159485000 143247 142102 156754 163669 183654 234735 179503 176882 168606 133341 FALSE TRUE 148902.5022 166506.9131 160839.138 196042.2397 152436.5587 180221.3537 165433.0858 174511.1861 162537.903 159466.616 0.933753446 1.044149034 1.008606955 1.229362262 0.955915178 1.130150989 1.037415166 1.09434307 1.019259749 1 17.2828949 4.875541397 1.67541665 1.067838871 0.852450438 0.202146682 0.073687747 2.006987595 4.188821862 0.0175686 0.772432923 75082.96198 -4.875541397 -0.215388433 CGAQDKEHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CGAQDKEHPR 10 1 Q96GX9 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 0 ; 152.7 1.06E-05 74920000 82373 67231 76492 66712 97500 110768 79241 75196 76028 55932 FALSE TRUE 85625.14965 78777.40127 78485.44436 79907.43448 80926.98483 85043.81071 73029.88336 74188.12062 73291.76713 66890.80452 1.280073551 1.177701507 1.173336827 1.194595207 1.209837218 1.271382686 1.09177762 1.109092964 1.095692714 1 16.02952028 1.546969363 0.866605327 1.014241431 1.213110231 0.705773704 0.044721586 0.303666013 0.456085956 0.041094857 0.016473821 35.23460139 -1.546969363 0.1988688 CGDLEEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CGDLEEELK 9 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 137.13 0.00040317 36424000 145420 114430 124730 125750 174170 188900 189550 142130 158940 81149 FALSE TRUE 151161.2939 134082.4624 127980.5663 150622.9747 144564.6456 145030.8378 174692.5757 140224.9798 153219.7804 97048.59286 1.557583572 1.381601303 1.318726655 1.552036668 1.48961094 1.494414638 1.800052639 1.444894518 1.578794457 1 16.56641967 -0.83400488 5.550148892 0.999999834 1.511162545 0.611014109 0.12280524 2.66E-07 5.57E-08 0.120021109 0.028289237 0.146553137 0.83400488 0.511162711 CGDLEEELKNVTNNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CGDLEEELKNVTNNLK 16 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ; 227.67 4.39E-15 359546000 722838 341829 454727 265014 788443 756150 620947 492660 577904 279717 FALSE TRUE 751376.2024 400535.4717 466577.5592 317432.9782 654423.7405 580545.6221 572275.5516 486056.6985 557105.3479 334522.1906 2.246117667 1.19733603 1.394758172 0.948914563 1.956293958 1.735447269 1.71072523 1.45298791 1.665376359 1 18.35174239 -1.698043208 2.549939163 0.90400599 1.565421646 0.199658947 0.351208829 25690439.46 20248121.46 15835503.91 0.08134795 0.020042726 1.698043208 0.661415657 CGEDDETIPSEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 261.41 1.08E-23 771370000 1085020 1028677 1071892 992159 1417680 1655380 1275330 1153590 1072870 851516 FALSE TRUE 1127857.427 1205344.273 1099826.386 1188405.089 1176703.26 1270943.083 1175366.302 1138128.013 1034257.618 1018354.257 1.107529546 1.183619811 1.08000372 1.166985929 1.155495008 1.248036304 1.154182146 1.11761502 1.015616728 1 19.95780809 1.309848305 2.507237116 0.997968375 1.157969367 0.662603985 0.041905976 0.1658797 1.727499117 0.037646379 0.011170103 20.41024908 -1.309848305 0.160000992 CGESGHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 192.6 3.45E-05 1433370000 1198860 1932260 1968310 1926160 2330930 3139310 2077030 2200860 1941050 1473100 FALSE TRUE 1246191.919 2264110.624 2019605.776 2307148.699 1934719.351 2410252.829 1914226.961 2171361.072 1871191.99 1761725.741 0.707369989 1.285166341 1.146379217 1.309595839 1.09819554 1.368120346 1.086563542 1.232519354 1.062135806 1 20.74855792 4.745670639 24.97241834 1.18821949 0.707369762 0.602330018 0.114004494 495.6650193 1740872.797 0.024036629 0.244469248 55676.33493 -4.745670639 -0.480849728 CGETGHVAINCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 139.48 3.89E-05 339760000 703010 437584 620400 505290 711370 823970 812850 657360 626170 299820 FALSE TRUE 730765.3776 512735.6481 636568.1337 605234.8539 590451.5815 632615.4549 749136.693 648549.1644 603634.264 358563.9886 2.03803338 1.429969725 1.775326452 1.68794099 1.646711885 1.764302816 2.089269187 1.808740378 1.683477101 1 18.45187108 2.686182044 21.73541156 1.760729186 1.701510019 0 0.298421027 641.6555898 266261.9848 0.090399479 0.085229738 485.4919619 -2.686182044 -0.059219168 CGGVEQASSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CGGVEQASSSPR 12 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 CGGVEQASS(0.032)S(0.968)PR;CGGVEQAS(0.001)S(0.033)S(0.966)PR 148.85 7.00E-05 588920000 774500 796910 863390 790990 1133020 1321530 952790 921950 914800 633800 TRUE FALSE 805077.858 933773.0934 885890.6527 947445.4611 940429.6651 1014624.685 878107.8301 909592.7683 881876.5267 757980.9752 1.06213465 1.231921544 1.168750512 1.249959421 1.240703521 1.338588591 1.158482678 1.200020578 1.163454698 1 19.53180211 0.62189995 1.223395251 1.000131246 1.213263231 0.4536787 0.067727619 1.136039025 2.553467325 0.063206952 0.019193562 4.18697097 -0.62189995 0.213131985 CGHTNNLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CGHTNNLRPK 10 1 M0R2S1;P62987 M0R2S1 UBA52 Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40 0 ;; 163.64 3.85E-06 2106150000 1765960 1323098 1568769 1293664 2101170 2137370 1777620 1694870 1730199 1192477 FALSE TRUE 1835681.464 1550329.789 1609652.409 1549546.878 1744013.874 1640998.21 1638285.499 1672153.04 1667929.476 1426120.037 1.287185803 1.087096282 1.128693495 1.086547302 1.222908191 1.150673272 1.148771111 1.172519141 1.169557564 1 20.44366399 -1.494518793 3.012925977 0.995258223 1.158117488 0.419402098 0.056894283 10252782.21 10281427.45 393355.9812 0.012818174 0.032024415 1.494518793 0.162859264 CGLGQENS(ph)DNEHLVENEVSLLLEESDLR ddPTM_MDA-MB-175_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(0.998)DNEHLVENEVS(0.002)LLLEESDLR 128.82 1.85E-05 138918000 33628.1 41294.7 45719.4 43194.9 52840.7 60424.9 43911.5 47543.2 43503.4 37016.4 TRUE FALSE 34955.76335 48386.7435 46910.88512 51738.7223 43858.85669 46392.13272 40469.60189 46905.96117 41937.72113 44269.05486 0.789620729 1.093015056 1.059676681 1.168733384 0.990733975 1.047958509 0.914173614 1.059565453 0.94733717 1 15.43401095 CGLGQENS(ph)DNEHLVENEVSLLLEESDLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CGLGQENSDNEHLVENEVSLLLEESDLRR 29 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 CGLGQENS(1)DNEHLVENEVSLLLEESDLRR 152.87 1.54E-08 17002000 3476.9 3237.7 3838.2 1827.2 3898.7 5655.8 3139.4 5146.3 3661.6 3671.1 TRUE FALSE 3614.170697 3793.749789 3938.226645 2188.614706 3236.000367 4342.326164 2893.325625 5077.322266 3529.819731 4390.381758 0.823201921 0.864104763 0.897012347 0.498502141 0.737065828 0.989054347 0.659014588 1.156464869 0.803989249 1 12.10013068 1.744705373 25 0.994562872 0.784214897 0.282804728 0.149891606 1.56726196 6398.066928 0.068585618 0.03803421 55.55272574 -1.744705373 -0.210347976 CGNQAAIMELDDTLKYSFLQFDPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CGNQAAIMELDDTLKYSFLQFDPAPR 26 1 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 ; 77.693 1.35E-05 0 150707 122046 148108 126183 200084 229520 166366 139134 155972 100274 FALSE TRUE 156657.0287 143006.4511 151967.8162 151141.6208 166073.7931 176217.4584 153325.7982 137269.1363 150358.5982 119920.7704 1.306337744 1.192507775 1.267235155 1.260345645 1.384862627 1.469449018 1.278559149 1.14466523 1.253816146 1 16.87172203 0.923045505 0.942078688 1.008933817 1.30383772 0.531873968 0.08304503 0.565973627 1.051120618 0.086850311 0.029312114 8.376170427 -0.923045505 0.294903903 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 24 CGSGPVHISGQHLVAVEEDAESEDEEEEDVK 31 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.004)GPVHIS(0.004)GQHLVAVEEDAES(0.992)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.002)GPVHIS(0.002)GQHLVAVEEDAES(0.996)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGS(0.014)GPVHIS(0.013)GQHLVAVEEDAES(0.974)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;CGSGPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.999)EDEEEEDVK;CGS(0.002)GPVHIS(0.013)GQHLVAVEEDAES(0.985)EDEEEEDVK;CGS(0.064)GPVHIS(0.052)GQHLVAVEEDAES(0.884)EDEEEEDVK;CGS(0.045)GPVHIS(0.043)GQHLVAVEEDAES(0.912)EDEEEEDVK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 307.28 1.54E-82 24240086000 1053343.1 2513438.3 2987598.6 3255935 3359497.5 4638834.7 3599922.7 4334242.1 3245300.1 2134202.6 TRUE FALSE 1094929.899 2945101.776 3065457.874 3899949.225 2788451.315 3561535.643 3317751.352 4276148.674 3128502.383 2552358.738 0.428987463 1.153874545 1.201029396 1.52797848 1.092499763 1.395389915 1.299876582 1.675371338 1.225729886 1 21.28339969 4.824482868 1.748622471 1.351831564 7.53E-18 0.645965348 0.191006646 0.66888223 1.718436431 0.048698873 1.607233707 66754.85666 -4.824482868 -1.351831564 KLVIIESDLERAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 198.13 4.54E-09 160452000 172120 251590 274216 172326 331160 320170 169265 236356 268754 431030 FALSE TRUE 178915.4305 294798.6254 281362.2942 206411.5685 274869.5415 245815.3697 155997.567 233188.0344 259081.596 515482.0759 0.347083708 0.571889187 0.545823623 0.400424337 0.533228126 0.476865019 0.302624619 0.452368851 0.502600591 1 18.97556274 0.704724865 3.409273723 0.999990082 0.45539278 0.79984321 0.081477849 1.596531743 17.98509634 0.078439305 0.020269372 5.066696203 -0.704724865 -0.544597302 CGYPAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CGYPAKR 7 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 77.72 0.077156 0 139350 149710 143310 137800 173540 178240 159090 142330 151440 145670 FALSE TRUE 144851.6456 175421.5279 147044.7763 165056.4287 144041.7328 136846.4613 146620.1101 140422.2992 145989.704 174211.2475 0.831471261 1.0069472 0.844060177 0.947449898 0.826822234 0.785520242 0.841622526 0.806046115 0.838003895 1 17.41047825 3.224019327 24.87753356 0.834414274 0.910056642 0.112507022 0.072148272 326.5266677 558627.4922 0.019026008 0.022834621 1675.017417 -3.224019327 0.075642368 CHDCS(ph)QPCPWPMIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CHDCSQPCPWPMIEK 15 0 O75509 O75509 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 1 CHDCS(1)QPCPWPMIEK 71.697 0.027662 424450000 35899 194140 216500 185860 225810 249720 207620 203790 235020 224420 TRUE FALSE 37316.32024 227482.0348 222142.1679 222622.5533 187426.8969 191726.3145 191346.2019 201058.5284 226561.6761 268390.8022 0.139037254 0.84757761 0.827681746 0.829471619 0.698335767 0.714355011 0.712938746 0.749126001 0.844148437 1 18.03397571 4.741949496 24.99877035 0.784793303 0.139037013 0.837242533 0.087456335 120.6387291 889877.0717 0.020194565 0.146702687 55201.32421 -4.741949496 -0.645756289 CHEFLIFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CHEFLIFEDR 10 0 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 157.38 9.28E-06 102090000 75662 77370 87505 79647 114130 131070 98058 82424 86417 70022 FALSE TRUE 78649.19418 90657.69564 89785.45219 95400.93888 94730.22337 100630.9789 90371.95773 81319.2411 83306.86905 83741.47025 0.93919051 1.082590207 1.072174299 1.139231716 1.131222357 1.201686316 1.079178064 0.971074915 0.994810203 1 16.35365463 1.808629103 5.215966634 0.987560491 1.099525449 0.356263426 0.063577653 0.231201799 10.72625077 0.031439204 0.017801451 64.36193655 -1.808629103 0.111964958 CHEHIEILTVNGELLFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CHEHIEILTVNGELLFFR 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 183.58 3.62E-14 30976500 19416.2 18639.1 24867.5 17669.7 22589.7 35008.8 23432.5 18539 19812.4 11983.3 FALSE TRUE 20182.76657 21840.22043 25515.56748 21164.71392 18749.91086 26878.53676 21595.79942 18290.51503 19099.35559 14331.1982 1.408309779 1.523963323 1.780421087 1.47682794 1.308328208 1.875526134 1.506908154 1.276272561 1.332711705 1 13.80687161 1.219621942 1.103375839 1.026775511 1.561289051 0.512171541 0.166446668 0.365657139 0.918726471 0.155797524 0.051547914 16.58142849 -1.219621942 0.534513541 CHELS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CHELSPR 7 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 1 CHELS(1)PR;CHELS(1)PR 120.31 0.0029544 502380000 395194 406778 418803 394533 538920 637480 431964 407908 436143 415485 TRUE FALSE 410796.5643 476638.9572 429717.3502 472570.4498 447314.5709 489434.9311 398105.533 402440.6605 420446.2986 496891.3308 0.826733209 0.959241846 0.864811526 0.951053924 0.900226152 0.984993903 0.80119235 0.809916848 0.846153419 1 18.92257085 2.224307247 24.99994248 0.842655447 0.915296153 0.082643531 0.068005429 355.3799134 623320.6886 0.023616326 0.017523396 167.6128253 -2.224307247 0.072640706 CHQPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CHQPLAR 7 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;; 92.692 0.015483 332953000 158996 191002 185242 166039 244848 295259 198155 201375 172665 176518 FALSE TRUE 165273.2849 223805.1077 190069.5587 198881.0186 203228.8244 226689.5719 182623.0933 198675.8975 166450.8204 211103.3225 0.782902339 1.060168571 0.900362706 0.942102741 0.96269837 1.073832327 0.865088674 0.941131078 0.788480344 1 17.68758976 0.705187718 0.0027832 1.137682048 0.73535272 0.001334356 0.09512073 1384591.383 1991.077561 144669.4784 143140.264 5.072098958 -0.705187718 -0.402329328 CHTPPLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CHTPPLYR 8 0 Q02543;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 125.25 0.0012699 1102170000 146407 171438 170141 177640 222615 243160 169928 153390 153216 183858 FALSE TRUE 152187.2614 200881.1429 174575.0142 212776.6618 184774.9818 186689.7751 156608.5993 151334.0579 147701.7861 219881.4549 0.692133229 0.913588383 0.793950605 0.967688075 0.84033909 0.849047389 0.712241055 0.688252941 0.671733713 1 17.74636641 2.245951996 24.34925498 0.735245425 0.849354865 0.067117103 0.110844291 188.5679175 621196.2773 0.03631 0.02979177 176.1781298 -2.245951996 0.11410944 CIACQAAKLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CIACQAAKLSPR 12 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 CIACQAAKLS(1)PR 107.74 0.0010791 132890000 206650 168510 178650 139550 266710 257740 174640 186840 189380 153900 TRUE FALSE 214808.7016 197450.2817 183305.7658 167152.5735 221374.7295 197883.7911 160951.2605 184335.7154 182564.2508 184053.7584 1.16709761 1.072785926 0.99593601 0.908172563 1.202772121 1.075141267 0.874479619 1.001531927 0.991907214 1 17.48976768 4.569503494 2.636962719 1.005330955 1.173793645 0.259782978 0.08423361 0.492482078 5.53515621 0.021861398 0.152257127 37111.07155 -4.569503494 0.16846269 CIALAQLLVEQNFPAIAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CIALAQLLVEQNFPAIAIHR 20 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6UJC5;A0A140T9X9;A0A140TA18;H0Y400;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ; 186.75 3.17E-17 513600000 367850 371920 392400 411340 490320 579150 553400 483670 386220 312700 FALSE TRUE 382373.002 435794.3669 402626.2664 492701.8243 406975.5815 444651.1896 510023.062 477187.1948 372320.0176 373967.578 1.022476344 1.165326602 1.076634152 1.317498771 1.088264346 1.189009999 1.363816256 1.276012208 0.995594376 1 18.51255367 5.491372334 0.875484382 1.197395573 0.574980254 0.069608648 0.123224578 14.52478815 3.338263089 0.038995783 11.85983236 310007.5951 -5.491372334 -0.622415319 CIDHYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CIDHYTK 7 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 111.82 0.006494 635760000 1375310 1332710 1573590 1344130 1896900 1977990 1731150 1604990 1634910 1142460 FALSE TRUE 1429608.301 1561592.575 1614599.048 1609994.902 1574465.616 1518631.799 1595457.939 1583477.734 1576069.908 1366303.163 1.046333156 1.142932709 1.181728251 1.178358468 1.152354512 1.111489631 1.167718836 1.1589505 1.153528698 1 20.3818462 -1.258380484 8.581578237 0.999999936 1.147111177 0.564650207 0.03775026 4.52E-08 3.88E-09 0.036041018 0.008494946 0.055159398 1.258380484 0.14711124 CIESLIAVFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CIESLIAVFQK 11 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 182.65 1.32E-05 476440000 1447330 1137530 1325760 1225470 1822030 1725200 1558940 1526300 1564780 1063520 FALSE TRUE 1504471.706 1332891.929 1360310.395 1467864.308 1512321.991 1324548.446 1436746.209 1505842.445 1508463.873 1271896.382 1.182857132 1.047956381 1.069513535 1.154075387 1.189029243 1.041396504 1.129609479 1.183934845 1.185995884 1 20.27854971 3.732212345 24.65440337 1.136030811 1.094893752 0.014859996 0.067832029 1141.809082 4434394.812 0.017515811 0.02792425 5397.744772 -3.732212345 -0.041137059 CIIPNHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 103.56 0.0047486 3782380000 3351610 2706280 3095730 2849790 3723160 4060100 3856480 3309820 3355650 2136920 FALSE TRUE 3483934.151 3171062.538 3176407.267 3413469.956 3090298.593 3117203.306 3554199.021 3265457.277 3234880.812 2555608.56 1.363250306 1.240824822 1.242916195 1.335677932 1.209222195 1.219749908 1.390744684 1.277761128 1.265796673 1 21.28523545 0.636515652 3.140567054 1.00000396 1.283727139 0.682456952 0.058015986 3.27822857 27.67582801 0.054345606 0.0141426 4.330276741 -0.636515652 0.28372318 CIIPNHEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CIIPNHEKK 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 161.63 4.18E-05 1126300000 2828500 1628780 2329600 1462300 3526800 2978300 2496300 2475100 2771500 1665160 FALSE TRUE 2940171.364 1908510.295 2390311.29 1751538.575 2927315.796 2286634.962 2300633.483 2441925.333 2671754.256 1991416.221 1.476422324 0.958368359 1.200307231 0.879544194 1.469966833 1.148245624 1.155275055 1.226225491 1.341635279 1 20.92536336 4.768716922 23.22058734 1.165742494 1.476423655 0.247721502 0.167673324 6386.247618 4917239.834 0.037732054 3.919637511 58710.65451 -4.768716922 0.31068116 CIIVEEGKEILVGDVGVTITDPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CIIVEEGKEILVGDVGVTITDPFK 24 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;;;; 222.72 7.51E-33 1129206000 1340587 756961 1107699 704674 1612364 1375714 1274003 1088814 1259612 688554 FALSE TRUE 1393514.41 886963.1634 1136566.546 844056.414 1338294.943 1056225.273 1174143.316 1074220.229 1214278.81 823462.9731 1.692261165 1.077113595 1.380227871 1.025008339 1.625203545 1.282662739 1.425860487 1.304515521 1.474600376 1 19.65134426 -1.468170502 5.735413513 0.999686948 1.351462681 0.227736896 0.200344792 0.000718955 6.67E-05 0.173901602 0.040953229 0.034027457 1.468170502 0.351775734 CKDDEFTHLYTLIVRPDNTYEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CKDDEFTHLYTLIVRPDNTYEVK 23 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 300.83 3.99E-62 2151880000 2524320 1262290 1641310 1294790 2921660 2501980 2251420 1862750 1960200 822590 FALSE TRUE 2623982.103 1479078.488 1684083.887 1550895.597 2425037.277 1920933.063 2074947.817 1837782.883 1889652.785 983760.7611 2.667296976 1.503494088 1.711883573 1.576496704 2.465068107 1.952642491 2.109199614 1.868119726 1.92084586 1 19.90794799 0.175323843 1.357342419 0.998994826 1.962565945 0.41636489 0.346591465 8.173253444 12.35421318 0.332179422 0.09358077 1.497351779 -0.175323843 0.963571119 CKELGITALHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CKELGITALHIK 12 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 138.42 4.49E-05 422080000 1168700 741400 992510 686820 1645600 1374300 993990 1030100 1121700 765810 FALSE TRUE 1214841.178 868729.6827 1018375.626 822670.946 1365881.5 1055139.653 916078.4665 1016293.194 1081330.236 915855.8072 1.326454633 0.948544166 1.11193882 0.898253786 1.491371774 1.15208054 1.000243116 1.109665066 1.180677381 1 19.80476095 -1.966015814 4.29603472 0.910004562 1.125955674 0.053646713 0.166431436 0.131389064 0.001039365 0.147589427 0.036196886 0.010813946 1.966015814 0.215951112 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 36 3 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 68.333 0.0032775 495400000 127660 84408 124530 64911 149370 132230 122000 113570 147100 87640 FALSE TRUE 132700.1154 98904.4174 127775.3541 77750.20206 123980.1408 101521.5865 112437.3212 112047.7799 141805.8997 104811.38 1.266084993 0.943641973 1.219098099 0.741810689 1.182888163 0.968612248 1.072758714 1.06904212 1.352962815 1 16.67743584 1.43263816 18.16088239 1.187996059 1.050732711 0.075989476 0.163974178 10.60388849 4329.532484 0.086403475 0.03666572 27.07934532 -1.43263816 -0.137263348 CKQDVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CKQDVLK 7 1 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 59.8 0.092434 196650000 231010 161800 193620 141100 315490 271510 211850 182170 214280 157610 FALSE TRUE 240130.4532 189587.8914 198665.8963 169009.1589 261863.1225 208455.9173 195244.6434 179728.3091 206568.1047 188490.6619 1.273964719 1.005821135 1.053982698 0.896644731 1.389263107 1.105921722 1.035831916 0.953513067 1.095906304 1 17.52413353 2.17911284 4.500908284 1.008480095 1.114828096 0.118776773 0.132200901 0.466875138 19.07152557 0.051364438 0.037817676 151.047256 -2.17911284 0.106348001 CLAFHDISPQAPTHFLVIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLAFHDISPQAPTHFLVIPK 20 0 P49773;D6REP8;D6RE99;D6RD60 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ; 206.98 4.12E-22 3552800000 2627900 2298700 2525800 2333800 3192700 3595100 2714800 2976700 2773200 2115900 FALSE TRUE 2731651.521 2693483.844 2591624.423 2795418.674 2650005.994 2760192.509 2502006.882 2936802.205 2673393.074 2530470.094 1.079503578 1.064420342 1.024167181 1.104703304 1.047238614 1.090782506 0.988751809 1.160575742 1.056480802 1 21.27097399 1.740845963 24.99999998 1.088635122 1.058845771 0 0.048884275 1.003809936 11050.51152 0.020945835 0.011615425 55.0612369 -1.740845963 -0.029789351 CLATHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CLATHGR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 132.72 0.0077741 388047000 132292 134415 139633 149718 164881 211061 143353 137503 133348 119857 FALSE TRUE 137514.9903 157499.7306 143271.9507 179331.7735 136854.5865 162045.2814 132116.6173 135659.9972 128548.8315 143340.6843 0.959357707 1.098778978 0.999520487 1.251087745 0.954750475 1.130490496 0.921696571 0.946416559 0.896806319 1 17.12908862 2.22532117 24.99980889 0.937260541 1.06754979 0.335065708 0.085778229 245.843296 464218.3988 0.029870861 0.022192947 168.0045989 -2.22532117 0.130289249 CLDWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLDWNR 6 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 99.919 0.088987 600070000 885450 1012680 937360 954960 1289280 1430360 984400 1021610 957590 962260 FALSE TRUE 920408.2497 1186599.912 961788.3716 1143848.238 1070128.646 1098180.567 907240.1557 1007916.989 923126.523 1150796.423 0.799801104 1.031111922 0.835758916 0.993962281 0.929902652 0.954278746 0.788358512 0.875842997 0.802163184 1 20.13420121 2.261327211 24.99829096 0.855920016 0.928417398 0.096327129 0.083217424 410.0264914 450218.0545 0.026159841 0.021872886 182.5270398 -2.261327211 0.072497381 CLELFSELAEDKENYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLELFSELAEDKENYK 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 209.66 1.07E-11 560810000 857850 383710 597570 430570 831650 819750 978880 646660 714900 278200 FALSE TRUE 891718.5804 449609.2077 613143.1651 515735.4609 690286.4301 629375.4859 902152.8278 637992.5804 689170.8886 332707.9635 2.68018406 1.351362928 1.842886953 1.550114567 2.074751751 1.891675448 2.71154564 1.917575322 2.071398837 1 18.34389687 CLELFSELAEDKENYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLELFSELAEDKENYKK 17 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 292.8 2.76E-46 6269100000 5938300 1869310 3647800 2225700 5727000 4979800 5620000 3921800 4881600 1512730 FALSE TRUE 6172748.669 2190349.451 3742864.665 2665936.817 4753526.586 3823316.92 5179489.715 3869234.686 4705912.17 1809120.481 3.412016356 1.210726137 2.068886348 1.473609329 2.62753456 2.113356717 2.862987717 2.138737982 2.601215464 1 20.78685706 3.215049665 24.9996447 2.308462603 1.983951288 0.004629046 0.719643468 796.8381298 847291.0389 0.191915389 0.22950575 1640.777397 -3.215049665 -0.324511315 CLELFTELAEDKENYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CLELFTELAEDKENYK 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 169.92 4.97E-09 1074800000 1690800 1054400 1301200 1123000 1734800 1920300 1954200 1461900 1573200 980920 FALSE TRUE 1757554.09 1235484.998 1335110.341 1345126.048 1439919.316 1474339.427 1801024.698 1442305.622 1516580.839 1173112.493 1.498197402 1.053168392 1.138092339 1.14663006 1.227434985 1.25677583 1.53525319 1.229469152 1.292783811 1 20.16190993 2.744885696 3.621767699 1.296898178 1.193997292 0 0.163951137 0.63869151 18.43216359 0.051430579 0.051670741 555.7579648 -2.744885696 -0.102900886 CLELFTELAEDKENYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLELFTELAEDKENYKK 17 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 283.49 2.32E-36 7203300000 3615380 1407750 2125610 1355570 3605090 2876210 3353070 2288790 2896720 933480 FALSE TRUE 3758117.994 1649520.112 2181005.143 1623697.7 2992298.09 2208253.817 3090247.612 2258112.514 2792467.613 1116377.533 3.366350434 1.477564768 1.953644782 1.454434232 2.680363945 1.978052899 2.768102653 2.022714043 2.501364932 1 20.09039357 4.755661252 23.83226331 2.052475366 3.366352458 0.365266387 0.540364727 1956.189468 2726153.145 0.121113907 3.275212123 56971.97202 -4.755661252 1.313877093 CLFTLLGHLDYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CLFTLLGHLDYIR 13 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 150.21 4.35E-05 165600000 325250 219610 241370 176400 534940 398050 294720 256380 280410 295900 FALSE TRUE 338091.1211 257326.3092 247660.3005 211291.3935 444011.0899 305608.92 271619.0763 252943.6455 270318.0989 353875.9397 0.955394485 0.727165315 0.699850633 0.597077591 1.254708332 0.863604687 0.767554518 0.714780569 0.763878152 1 18.43288415 4.76356901 22.14086147 0.809393652 0.955395341 0.045747406 0.177253458 5003.441971 4429391.114 0.042888667 2.272869492 58018.83579 -4.76356901 0.146001689 CLGHPEEFYNLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CLGHPEEFYNLVR 13 0 E9PNM1;P37268;P37268-5;E9PJG4;E9PQ90;E9PNJ2;E9PSH1 E9PNM1 FDFT1 Squalene synthase 0 63.662 0.067355 311080000 162440 166510 208270 180630 282140 258670 184180 197410 227810 194650 FALSE TRUE 168853.2566 195106.7972 213697.6873 216358.0749 234181.9436 198597.8127 169743.4903 194764.0418 219611.1626 232787.9407 0.72535225 0.838131033 0.917992945 0.929421319 1.005988295 0.853127581 0.729176476 0.83665864 0.943395787 1 17.8286568 4.657112162 2.957371684 0.887177553 0.712125025 0.308620958 0.078509848 0.456926409 6.21500844 0.021000524 0.170049469 45405.88684 -4.657112162 -0.175052527 CLIKS(ph)PDRLADINYEGR ddPTM_MDA-MB-175_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 72.145 0.022849 152730000 87212 76520 80891 52751 111930 121260 70553 69612 102270 71146 TRUE FALSE 90655.1971 89661.71476 82999.08591 63184.99035 92904.17858 93099.20271 65022.8715 68678.965 98589.32268 85085.69653 1.065457542 1.053781287 0.975476364 0.742604138 1.091889499 1.09418159 0.764204492 0.807174035 1.158706183 1 16.37662901 2.252791001 24.99993665 0.899306488 0.996996451 0.037043314 0.139895685 588.8261115 1034448.635 0.050383693 0.04197013 178.9744352 -2.252791001 0.097689963 CLKDEDPYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CLKDEDPYVR 10 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ;;; 97.911 0.0052312 2891190000 7231700 5556250 6902500 6410100 8839400 9272700 8199000 7332800 7537700 4945620 FALSE TRUE 7517213.1 6510492.716 7082384.82 7677998.648 7336881.945 7119255.954 7556340.956 7234515.81 7266419.649 5914619.549 1.27095463 1.100745815 1.19743709 1.298139058 1.240465576 1.203670988 1.277570077 1.223158269 1.228552334 1 22.49585394 -0.548029093 8.699787788 0.999994841 1.22602214 0.630528256 0.052068245 0 0 0.050283663 0.011851973 0.283120233 0.548029093 0.226027299 CLLADLPLPPELPGGDDLSKS(ph)PEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CLLADLPLPPELPGGDDLSKSPEEK 25 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61;A0A2R8YD28;A0A2R8YCQ1;A0A2R8Y7Y0;Q9BVE2;A0A087X209 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 CLLADLPLPPELPGGDDLS(0.209)KS(0.791)PEEK 171.15 4.59E-12 104000000 300170 64103 103160 71723 181800 199640 156860 110220 139540 42428 TRUE FALSE 312020.9434 75112.1916 105848.4343 85909.59533 150897.7009 153276.6356 144564.9033 108742.6812 134517.9827 50740.95427 6.149291985 1.480307036 2.086055256 1.693101688 2.973883781 3.020767697 2.849077346 2.143094917 2.651073174 1 15.63086303 8 0.068683825 1.05E-10 8.508619158 0.225859508 1.183322078 498.0535747 2.52813046 55.7020493 411.1687883 100000000 -8 8.508619158 CLS(ph)PGGHPTYRPAYLLENEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CLSPGGHPTYRPAYLLENEEEER 23 1 Q8NFF5-2;Q8NFF5;Q5T190 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 1 CLS(1)PGGHPTYRPAYLLENEEEER;CLS(1)PGGHPTYRPAYLLENEEEER;CLS(1)PGGHPTYRPAYLLENEEEER 195.21 4.64E-19 569348000 151869 234498 209551 232380 292090 348296 246987 244460 229876 213412 TRUE FALSE 157864.9054 274771.2074 215012.0712 278344.0704 242440.6461 267409.5325 227627.5136 241183.4136 221602.8077 255225.9954 0.618529884 1.076580021 0.842437977 1.090578842 0.949905772 1.04773627 0.891866494 0.944979814 0.868261116 1 17.96141575 4.750510256 24.65740513 0.963763147 0.61852963 0.621943381 0.081687747 948.8205983 1957794.194 0.017976707 0.295881725 56300.24123 -4.750510256 -0.345233518 CLSSLKDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 CLSSLKDER 9 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 121.5 0.00055821 3446660000 9001170 7155670 8405530 6941640 12620700 12227800 10274450 9525870 9613380 6791930 FALSE TRUE 9356543.142 8384600.659 8624585.017 8314675.673 10475437.92 9388078.764 9469111.762 9398191.294 9267396.332 8122678.644 1.151903646 1.032245768 1.061790746 1.023637157 1.289653128 1.155786062 1.165762204 1.157031037 1.140928595 1 22.95352414 3.294918762 24.99999998 1.160206732 1.064483412 0.236706332 0.07294666 104.0684355 46162.91206 0.018875835 0.025557992 1972.053814 -3.294918762 -0.09572332 CLTTDEYDGHSTYPSHQYQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CLTTDEYDGHSTYPSHQYQ 19 0 P30043;M0R192;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;; 230.07 6.56E-20 5145790000 2187440 1852562 1689662 1652150 2182753 3412990 1921356 2034691 1892151 1910812 FALSE TRUE 2273801.82 2170725.113 1733695.98 1978940.339 1811729.425 2620374.797 1770755.096 2007419.295 1824052.855 2285199.027 0.995012598 0.94990637 0.758663013 0.865981613 0.792810343 1.146672463 0.774880033 0.878443966 0.79820306 1 21.12388839 -1.308603961 5.341127587 1.000023923 0.882060671 0.084567096 0.113738553 3.09E-05 4.00E-06 0.105118646 0.02477168 0.049135575 1.308603961 -0.117963253 CLVAGLLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CLVAGLLSPR 10 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 CLVAGLLS(1)PR;CLVAGLLS(1)PR;CLVAGLLS(1)PR 134.99 0.00016368 188940000 193751 224509 221250 199369 267110 281406 216022 220599 197768 222721 TRUE FALSE 201400.4391 263066.6743 227015.9568 238803.5931 221706.7376 216053.7212 199089.6312 217642.2312 190650.3683 266358.9157 0.756124264 0.98763983 0.852293441 0.89654815 0.832360866 0.811137561 0.747448722 0.817101356 0.715764921 1 18.02301205 3.021828813 3.10400422 0.802601938 0.879801368 0.063239423 0.088267046 0.480104186 9.544941392 0.025243014 0.029557097 1051.5473 -3.021828813 0.07719943 CMIDQAHQEERPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CMIDQAHQEERPIR 14 1 Q9UBQ5;A0A087WVB9;K7ERF1;Q9UBQ5-2;K7ES31;K7EQM4 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 ;; 207.31 5.78E-09 956280000 435336 559449 602313 542800 560733 748658 585385 597789 511576 487143 FALSE TRUE 452523.4014 655530.0138 618009.7716 650164.2199 465419.8049 574793.5255 539500.9941 589776.6162 493164.4797 582589.3439 0.776745071 1.125200831 1.060798276 1.11599058 0.798881424 0.986618673 0.926039928 1.012336773 0.846504463 1 19.15211979 3.260752369 24.99892798 0.937166467 1.030157327 0.136262858 0.110030734 465.3456781 524206.8613 0.02923921 0.039560359 1822.856027 -3.260752369 0.092990861 CNAEEHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CNAEEHVR 8 0 P11279-2;P11279 P11279-2 LAMP1 Lysosome-associated membrane glycoprotein 1 0 ; 166.09 0.00032049 1243990000 1189400 1347410 1178930 1447820 1514150 2101200 1367040 1362470 1181630 1072400 FALSE TRUE 1236358.43 1578817.186 1209653.884 1734194.475 1256775.324 1613228.144 1259887.833 1344208.318 1139103.367 1282516.248 0.964009955 1.231030943 0.943187961 1.35218129 0.979929359 1.25786176 0.982356235 1.04810237 0.888178508 1 20.29054567 1.855779486 1.99627489 0.965391792 1.120404685 0.184598959 0.134578025 0.502535631 3.77074086 0.077883659 0.03575929 71.74299226 -1.855779486 0.155012893 CNEIINWLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CNEIINWLDK 10 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 112.13 0.0052701 0 289720 250550 274960 225960 409880 410010 307400 295900 348170 269040 FALSE TRUE 301158.3693 293580.0135 282125.6835 270654.2136 340208.744 314791.3913 283305.1848 291933.9445 335639.4297 321753.2369 0.935991731 0.912438415 0.87683868 0.841185674 1.057359196 0.97836278 0.880504537 0.907322479 1.043157896 1 18.29559514 1.294759252 0.247466309 1.019557587 0.893559361 0.173520323 0.063320834 4.498454262 1.144565929 0.226133087 0.17987104 19.71329639 -1.294759252 -0.125998225 CNEIINWLDKNQTAEKEEFEHQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CNEIINWLDKNQTAEKEEFEHQQK 24 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 175.71 7.86E-13 4458800000 918910 356600 534340 343700 791800 786980 785470 539480 629330 207074 FALSE TRUE 955189.2764 417843.276 548265.3394 411682.8342 657210.1188 604215.8218 723902.809 532249.153 606680.5362 247646.1856 3.857072436 1.687259083 2.213905851 1.662383102 2.653826939 2.439834962 2.923133288 2.149232186 2.449787525 1 17.91792087 -0.319868339 1.313038752 0.99125794 2.40644416 0.341356241 0.600888142 57.50253852 54.02241194 3.38912442 0.159503151 0.478775216 0.319868339 1.41518622 CNFYDNKDLECVTNLQEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CNFYDNKDLECVTNLQEVAR 20 1 X6R5C5;X6R8A1;P10619-2;P10619;Q5JZH0 X6R5C5 CTSA Carboxypeptidase;Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain 0 84.159 0.003312 0 44076 43511 38735 34363 51708 61196 40819 43799 46195 38248 FALSE TRUE 45816.15451 50983.67578 39744.46592 41159.89884 42918.69263 46984.15643 37619.50012 43211.94605 44532.45097 45741.9633 1.001621951 1.114593081 0.868884129 0.899827989 0.938278323 1.027156533 0.822428628 0.94468936 0.973557927 1 15.48123067 4.239677725 24.99999998 0.929503261 1.058107521 0.38310003 0.062574702 25.99389438 581652.9033 0.014778363 0.036138025 17365.11744 -4.239677725 0.128604259 CNKEVYFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CNKEVYFAER 10 1 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;; 122.55 0.00044291 727990000 1052180 1335710 1308230 879700 2009600 1815860 943610 1373030 1300920 1775550 FALSE TRUE 1093720.879 1565107.802 1342323.549 1053702.034 1668008.91 1394154.035 869647.3825 1354626.779 1254100.143 2123435.028 0.515071507 0.737064135 0.63214722 0.49622523 0.785523874 0.656556013 0.409547441 0.637941242 0.590599725 1 21.01796854 -0.943755512 4.965533261 1.000001959 0.608297775 0.552247416 0.106222673 0.009421882 68186372.7 369.6513182 0.024114912 0.11382679 0.943755512 -0.391704184 CNREPS(ph)KGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CNREPSKGR 9 2 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 CNREPS(1)KGR;CNREPS(1)KGR;CNREPS(1)KGR 113.38 0.0009444 409828000 447142 251305 352816 264082 495279 523610 398389 367872 378524 192386 TRUE FALSE 464795.5114 294464.6789 362010.6748 316316.6314 411091.6525 402009.5129 367162.2292 362941.2776 364900.9952 230080.3532 2.020144288 1.279834087 1.573409766 1.374809396 1.786730795 1.747257022 1.595800006 1.577454452 1.585971988 1 17.81177827 0.000104266 1.245883648 0.99806208 1.607456037 0.469573366 0.196330362 11.20892637 12.87047195 0.252139113 0.053026279 1.000240111 -0.000104266 0.609393958 CNVWILDGDLYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CNVWILDGDLYHK 13 0 O43237;B4E2E0;Q9Y6G9;C9JGM7;C9JLW1 O43237;Q9Y6G9 DYNC1LI2;DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 2;Cytoplasmic dynein 1 light intermediate chain 1 0 ; 135.02 8.88E-05 606630000 706070 554290 689460 573340 900220 920810 773590 761150 723130 394660 FALSE TRUE 733946.1888 649484.9957 707427.894 686744.9408 747200.926 706965.8325 712953.9944 750948.0292 697104.6926 471986.0708 1.555016629 1.376068143 1.498832143 1.455011034 1.583099528 1.49785317 1.510540328 1.591038541 1.476960308 1 18.84838476 0.949085355 22.82087846 0.999999999 1.509812052 0.867542519 0.059301719 1940.837914 869920.4504 0.058022792 0.014505698 8.893758965 -0.949085355 0.509812052 CPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 362.92 5.44E-112 8038696000 2248240 4247668 4816943 4759111 5790965 6456289 5559235 5691853 5318315 3834626 FALSE TRUE 2337002.251 4977171.937 4942476.492 5700448.951 4806618.838 4956913.726 5123487.634 5615563.021 5126909.882 4585947.546 0.509600737 1.085309391 1.077743791 1.243025328 1.048119018 1.080891937 1.117214618 1.224515319 1.117960864 1 22.12878842 4.745812016 4.004895566 1.126090495 0.449965688 0.866614844 0.070663533 0.079138541 2.642296722 0.016953353 0.156901193 55694.46231 -4.745812016 -0.676124807 CPFPAGAALACCS(ph)EDEEDDEEHEGGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPFPAGAALACCSEDEEDDEEHEGGGSR 28 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 CPFPAGAALACCS(1)EDEEDDEEHEGGGSR;CPFPAGAALACCS(1)EDEEDDEEHEGGGSR 205.89 1.73E-25 420910000 112113 142076 129243 168563 166182 190317 118484 157034 132741 154453 TRUE FALSE 116539.3078 166476.4478 132611.1788 201904.2583 137934.443 146118.761 109196.9145 154929.2161 127963.6773 184715.1082 0.630913784 0.901260592 0.717922752 1.09305763 0.746741533 0.791049322 0.591163958 0.838746855 0.692762377 1 17.49494235 CPGESSHICDFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPGESSHICDFIR 13 0 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2;A0A286YFL6 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 107.37 0.0013003 347790000 293840 295590 288200 296390 404290 390250 360760 310680 302790 262250 FALSE TRUE 305441.0301 346355.2831 295710.7288 355015.0574 335568.9302 299620.3518 332482.6885 306515.8428 291892.647 313632.8664 0.97388081 1.104333507 0.942856315 1.131944689 1.069941853 0.955321919 1.060101552 0.977307788 0.930682586 1 18.25871723 1.610651915 5.249089923 0.962039923 1.035203836 0.191995791 0.060912737 0.216624765 12.8532604 0.031920818 0.01493217 40.79922517 -1.610651915 0.073163913 CPHVTEHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPHVTEHIPR 10 0 P48449-2;P48449;A0A0G2JQD0;P48449-3 P48449-2 LSS Lanosterol synthase 0 82.287 0.010678 28029000 44137 92846 77225 96275 62067 83187 61672 60761 62302 80121 FALSE TRUE 45879.56284 108791.5783 79237.54694 115317.9076 51516.87351 63868.07996 56837.98749 59946.59818 60059.76319 95819.17594 0.478813999 1.135384198 0.826948741 1.203495089 0.537646802 0.666547999 0.593179673 0.625622143 0.62680317 1 16.54802679 3.212874861 24.99994045 0.648625998 0.921161636 0.215667104 0.216871457 275.6725905 268311.3657 0.057804292 0.069112028 1632.581462 -3.212874861 0.272535638 CPLLKPWALTFS(ph)YGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 1 CPLLKPWALT(0.021)FS(0.979)YGR;CPLLKPWALT(0.065)FS(0.935)YGR 100.77 0.0012278 278050000 94456 164565 159689 135164 188188 250690 164417 152190 136967 208594 TRUE FALSE 98185.19582 192827.7586 163850.6265 161899.0358 156199.871 192471.0467 151529.5659 150150.142 132037.5844 249464.0005 0.393584628 0.772968277 0.656810707 0.648987571 0.626141931 0.771538364 0.607420572 0.601891021 0.529285124 1 17.92847211 -1.391551409 3.014663639 1.005399654 0.631060828 0.538495483 0.104423784 24577136.99 30097717.21 1149664.027 0.023485021 0.040592761 1.391551409 -0.374338826 CPLLKPWALTFSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPLLKPWALTFSYGR 15 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ; 162.46 1.45E-06 2121000000 1308090 1227680 1495880 1205900 2008930 2019090 1486080 1666580 1531470 1411220 FALSE TRUE 1359734.403 1438524.49 1534863.862 1444423.421 1667452.796 1550186.947 1369597.166 1644242.221 1476352.694 1687721.54 0.805662766 0.852347059 0.909429563 0.855842262 0.987990469 0.918508718 0.811506599 0.97423786 0.874760829 1 20.68664546 8 0.0856258 1.045911747 0.4862184 0.336568911 0.054799193 207.8012626 1.28594756 1.168596329 13.69363117 100000000 -8 -0.559693347 CPPGVVPACHNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 188.29 6.24E-06 4214680000 862107 5730250 5359150 6796600 5137870 7861440 4121390 6051580 4672650 5842740 FALSE TRUE 896143.6501 6714375.862 5498813.852 8140947.194 4264536.693 6035739.701 3798344.683 5970468.468 4504482.239 6987513.037 0.128249299 0.960910674 0.786948636 1.16507077 0.610308227 0.863789401 0.543590354 0.854448276 0.644647418 1 22.73634764 4.746224966 24.71790599 0.81372837 0.128248912 0.571140505 0.181004232 565.5671261 1823931.121 0.040808962 0.433476044 55747.44479 -4.746224966 -0.685479459 CPQIVIAFYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPQIVIAFYEER 12 0 Q13185;P45973 Q13185;P45973 CBX3;CBX5 Chromobox protein homolog 3;Chromobox protein homolog 5 0 ; 100.55 0.0073708 258290000 194282 245050 245790 221106 266040 288140 237170 212113 211013 204710 FALSE TRUE 201952.4034 287135.4313 252195.4893 264840.1069 220818.6158 221223.8518 218579.9957 209269.9722 203418.6833 244819.0051 0.824904926 1.172847799 1.030130358 1.081779198 0.901966805 0.903622052 0.892822825 0.854794635 0.830894167 1 17.90135603 3.179892989 6.979968597 0.88699869 1.037804487 0.322986149 0.091094324 0.209967153 20.06640835 0.024813126 0.029907325 1513.188349 -3.179892989 0.150805797 CPQVVISFYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPQVVISFYEER 12 0 P83916;J3KS05 P83916 CBX1 Chromobox protein homolog 1 0 103.43 0.0052266 70568000 42601 52189 57427 58652 58726 68349 54465 49205 50778 50391 FALSE TRUE 44282.92038 61152.05478 58923.5948 70253.19054 48743.7755 52475.98059 50195.89098 48545.48746 48950.5097 60264.15166 0.734813636 1.014733521 0.977755319 1.165754244 0.808835338 0.870766105 0.832931181 0.805545023 0.812265806 1 15.87901244 CPS(ph)DEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPSDEDFR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 CPS(1)DEDFR 66.19 0.065376 63090000 361580 251060 226600 285450 299540 402990 328240 256130 231680 163540 TRUE FALSE 375855.4576 294177.602 232505.3822 341911.158 248624.2978 309401.6799 302511.6911 252696.9963 223341.8821 195582.5318 1.92172304 1.504109796 1.188783988 1.748168176 1.271198892 1.581949456 1.546721419 1.292022319 1.141931644 1 17.577418 1.072224198 0.062686895 1.82E-10 2.575024311 0.478515854 0.198355911 31.18785393 1.445260076 30.81842748 26.88114843 11.80930116 -1.072224198 2.575024311 CPS(ph)QSSSRPAAMISQPPTPPTGQPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.994)QS(0.005)S(0.001)SRPAAMISQPPTPPTGQPVR 142.01 1.74E-07 242540000 18783 24156 27722 23067 25738 38986 22384 24030 19930 17227 TRUE FALSE 19524.56734 28304.60509 28444.45809 27629.58375 21363.06395 29932.09234 20629.48359 23707.91716 19212.72319 20602.30082 0.947688684 1.37385651 1.380644732 1.341092143 1.036926125 1.452851922 1.001319405 1.150741238 0.932552309 1 14.33051784 1.825589622 1.398871304 0.989879329 1.257982701 0.285266415 0.163881638 0.508674485 1.871927393 0.119917865 0.049580135 66.92519141 -1.825589622 0.268103372 CPS(ph)QSSSRPAAMISQPPTPPTGQPVREDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.991)QS(0.002)S(0.001)S(0.006)RPAAMISQPPTPPTGQPVREDAK;CPS(0.99)QS(0.001)S(0.004)S(0.004)RPAAMISQPPTPPTGQPVREDAK 189.72 1.43E-18 1348080000 216540 146886 215810 175580 277030 332410 211490 231460 234650 175256 TRUE FALSE 225089.1664 172112.5279 221434.1859 210309.1999 229940.5396 255212.8152 194912.8612 228357.6573 226204.9923 209594.0577 1.073929141 0.821170837 1.056490763 1.003412035 1.097075662 1.217652914 0.929954138 1.089523528 1.079252889 1 17.67723829 4.051311043 24.99523555 1.062285368 0.945369654 0.192887632 0.091208131 142.1681536 69252.70634 0.021493049 0.046430285 11254.10708 -4.051311043 -0.116915714 CPSQS(ph)SSRPAAMISQPPTPPTGQPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVR 26 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.135)QS(0.424)S(0.424)S(0.017)RPAAMISQPPTPPTGQPVR 195.8 4.33E-25 274670000 18684 25994 28094 29960 32267 39529 32277 27705 32727 19075 TRUE FALSE 19421.65875 30458.26729 28826.15272 35885.99858 26782.26687 30348.98882 29747.0444 27333.65979 31549.16166 22812.38104 0.851364823 1.335163885 1.263618764 1.573093073 1.1740233 1.330373571 1.303986829 1.198194075 1.382984162 1 14.47752942 -0.568613042 7.477505311 0.999999972 1.274059596 0.174905094 0.174249516 0 0 0.157746448 0.037181194 0.27001442 0.568613042 0.274059625 CPSQSS(ph)SRPAAMISQPPTPPTGQPVREDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CPSQSSSRPAAMISQPPTPPTGQPVREDAK 30 2 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 CPS(0.303)QS(0.117)S(0.399)S(0.152)RPAAMIS(0.029)QPPTPPTGQPVREDAK 78.901 0.0024312 154500000 23841 15212 21189 15424 32201 32368 25112 23604 26934 15652 TRUE FALSE 24782.26109 17824.54267 21741.20275 18474.82116 26727.48552 24851.02254 23143.65582 23287.62699 25964.6506 18718.70972 1.323929985 0.952231373 1.16146909 0.986970867 1.427848709 1.327603393 1.236391619 1.244082917 1.387096172 1 14.19219337 3.245494956 24.99995732 1.280066663 1.099107475 0.237465184 0.143448845 206.2948233 743737.5117 0.037130385 0.049202277 1759.928225 -3.245494956 -0.180959188 CPSSSGKPNHADILLINLQYVSEVEIINDRTET(ph)PPPLASLNVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSK 44 2 K7ELG9;Q3MHD2 K7ELG9 LSM12 Protein LSM12 homolog 1 CPSSSGKPNHADILLINLQYVSEVEIINDRT(0.006)ET(0.994)PPPLASLNVSK;CPSSSGKPNHADILLINLQYVSEVEIINDRT(0.162)ET(0.838)PPPLASLNVSK 126.03 3.49E-09 94873000 41049 39112 51147 37897 64826 59964 55832 53309 56318 31821 TRUE FALSE 42669.64622 45829.18175 52479.93284 45392.91349 53806.89968 46038.26976 51455.74195 52594.48005 54291.12618 38055.7157 1.12124146 1.204265402 1.379028928 1.192801466 1.413897983 1.209759662 1.352115996 1.382038915 1.42662213 1 15.21582553 4.441054536 4.813084266 1.312075796 1.137470015 0.152749866 0.125306483 0.250175766 13.62278517 0.028109233 0.089106825 27609.24532 -4.441054536 -0.174605782 CPT(ph)PEIQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CPTPEIQKK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 CPT(1)PEIQKK;CPT(1)PEIQKK;CPT(1)PEIQKK 91.62 0.0062289 1920450000 3374700 1655100 2312870 1714690 3497390 3068850 2807320 2396210 2694540 1206600 TRUE FALSE 3507935.762 1939350.55 2373145.292 2053850.564 2902904.897 2356156.096 2587274.923 2364092.724 2597564.032 1443010.168 2.430984784 1.343961805 1.644579743 1.423309835 2.01170093 1.632806302 1.79297068 1.638306352 1.80010099 1 20.46065004 -1.332610908 3.660614189 0.997453608 1.722159577 0.368404175 0.291673649 9047237.266 4943194.905 178755.6323 0.0619184 0.046493163 1.332610908 0.724705969 CPTQFPLILWHPYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CPTQFPLILWHPYAR 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 127.88 7.55E-05 581530000 734410 658130 746700 661510 938070 948090 819150 801100 777290 659810 FALSE TRUE 763405.0739 771158.708 766159.6154 792354.7036 778617.1965 727910.4659 754942.8825 790362.5648 749315.4847 789087.1367 0.967453451 0.977279532 0.970944247 1.004140946 0.986731579 0.92247159 0.956729425 1.001616334 0.949597896 1 19.5898251 CPVTVCGDVHGQFHDLMELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 237.61 4.21E-30 509320000 154630 171194 172677 165458 176854 217536 174637 185010 161197 135648 FALSE TRUE 160734.9118 200595.2378 177177.1045 198185.0986 146792.4203 167016.5608 160948.4956 182530.2436 155395.5515 162225.6285 0.990810844 1.236520023 1.092164698 1.221663312 0.904865783 1.029532524 0.992127429 1.125162807 0.95789767 1 17.30764223 3.246975544 24.99997715 1.016335874 1.139440079 0.374950391 0.083199645 209.0387036 621031.0707 0.022357981 0.029783839 1765.938375 -3.246975544 0.123104205 CQEVINWLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CQEVINWLDR 10 0 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 128.44 0.00076642 265840000 249340 219210 220970 218450 271200 322980 282080 243230 233620 186490 FALSE TRUE 259184.1357 256857.6123 226728.6597 261658.758 225101.5209 247972.7898 259969.8325 239969.8997 225212.0618 223029.1449 1.162108817 1.15167734 1.016587585 1.173204327 1.009291951 1.111840293 1.16563166 1.075957583 1.009787586 1 17.76687272 1.301410602 0.014281805 1.63E-05 2.138213242 0.291384339 0.058745516 732.2877676 9.481215056 714.5479345 702.6734917 20.01753526 -1.301410602 2.138196949 CQEVISWLDANTLAEKDEFEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CQEVISWLDANTLAEKDEFEHK 22 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;; 380.12 5.84E-114 13018090000 5570350 2354960 3600280 2504640 5798110 5432220 5091850 3888330 4762270 1822610 FALSE TRUE 5790271.719 2759406.061 3694106.254 3000050.316 4812549.333 4170669.231 4692737.492 3836213.296 4590876.833 2179715.534 2.656434581 1.265947789 1.694765302 1.376349469 2.207879542 1.913400702 2.152912809 1.759960526 2.106181638 1 21.05570844 3.23264069 24.99176819 1.907439783 1.71008605 0.003060988 0.473254842 539.4597419 2277401.118 0.126163887 0.15460731 1708.601135 -3.23264069 -0.197353733 CQEVISWLDANTLAEKDEFEHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CQEVISWLDANTLAEKDEFEHKR 23 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 174.71 1.42E-12 627960000 817010 434530 555140 428070 911910 799010 768750 665130 735520 342440 FALSE TRUE 849266.1857 509157.1473 569607.4045 512740.9683 756903.8639 613452.0366 708493.3662 656215.0203 709048.7789 409534.5616 2.073735077 1.243258067 1.390865284 1.252009028 1.848205097 1.497924947 1.72999652 1.602343445 1.731352724 1 18.64362568 3.245863302 24.99986459 1.605829391 1.465266208 0.004070457 0.306454007 591.7589633 2025803.853 0.07972604 0.105817476 1761.421538 -3.245863302 -0.140563182 CQHAAEIITDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CQHAAEIITDLLR 13 0 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 74.853 0.032979 282550000 67683 73473 76367 66271 100380 96789 73331 75287 76039 77930 FALSE TRUE 70355.1771 86091.41621 78357.18676 79379.206 83317.44345 74311.2216 67583.12461 74277.90091 73302.37124 93198.89144 0.754892854 0.923738629 0.840752347 0.85171835 0.893974619 0.797340188 0.725149447 0.796982665 0.786515484 1 16.50802517 2.711182024 23.29812149 0.79989688 0.856191096 0.003388135 0.078950927 698.1163692 594068.2365 0.023656437 0.022311001 514.2591462 -2.711182024 0.056294216 CQHGEEECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CQHGEEECK 9 0 P13284 P13284 IFI30 Gamma-interferon-inducible lysosomal thiol reductase 0 81.017 0.021629 0 178820 111560 116990 90024 169730 225600 173830 127560 126450 84386 FALSE TRUE 185879.9517 130719.5622 120038.8555 107830.4785 140879.3552 173207.819 160204.7504 125850.2668 121899.0892 100919.821 1.841857722 1.295281352 1.189447764 1.068476712 1.39595328 1.716291381 1.587445843 1.247032204 1.207880553 1 16.62285003 1.171975438 1.908562781 1.020454212 1.416913595 0.27583476 0.224449764 0.464596464 3.093970404 0.222523492 0.064262148 14.85851605 -1.171975438 0.396459384 CQHLQAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CQHLQAEK 8 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 124.23 0.0030562 2413745000 4062896 3669006 3675056 3412134 6197883 6344334 4538904 4281959 4117310 4152029 FALSE TRUE 4223302.271 4299129.24 3770830.978 4087043.921 5144369.061 4870958.578 4183132.844 4224566.343 3969128.817 4965539.587 0.850522324 0.865792965 0.759400043 0.82308153 1.036014107 0.980952521 0.842432684 0.850776893 0.799334845 1 22.24351907 3.39236484 24.988004 0.906632645 0.822880692 0.263633092 0.075080151 40.02880066 11795.68414 0.022463679 0.030415967 2468.111865 -3.39236484 -0.083751953 CQSLQEELDFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CQSLQEELDFRK 12 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 139.61 9.46E-05 262370000 132154 104673 120195 108944 149154 194691 137602 135939 123047 107101 FALSE TRUE 137371.542 122649.7735 123327.3804 130492.798 123800.8564 149476.9658 126816.3957 134116.9601 118618.5625 128085.3904 1.072499694 0.957562554 0.962852829 1.018795334 0.966549393 1.167010269 0.990092588 1.047090224 0.926089714 1 16.9667464 4.787413644 20.96077477 1.009594159 1.072501876 0.088762508 0.063608721 12612.02293 5410181.401 0.014820346 7.171234964 61293.39032 -4.787413644 0.062907718 CQSLTEDLEFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CQSLTEDLEFRK 12 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 113.8 0.0018068 736390000 442000 420380 418330 367000 641910 577000 476560 482610 489120 374410 FALSE TRUE 459450.5013 492576.9949 429232.0235 439591.5046 532798.3675 443000.4945 439205.9819 476141.4023 471516.6667 447768.471 1.026089444 1.100070744 0.958602607 0.981738405 1.189897016 0.989351692 0.980877419 1.063365184 1.053036775 1 18.77239342 -2.89393605 1.584992 0.00013996 1.038291075 0.029477604 0.06560182 1047421.102 24777.06364 3777828.852 0.015899321 0.001276627 2.89393605 1.038151115 CQYVTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 129.47 0.0085095 1082050000 410180 382880 401740 338220 574470 598290 522890 432950 414940 341010 FALSE TRUE 426374.2231 448636.6616 412209.6744 405118.9065 476821.7946 459346.2147 481904.5155 427147.0134 400006.3905 407824.3805 1.045484879 1.100073176 1.010752898 0.993366081 1.169184133 1.126333384 1.181647147 1.047379789 0.980830008 1 18.6375885 4.807900767 18.95615479 1.07409575 1.045479339 0.001627389 0.070316939 28044.69965 7659941.733 0.017335336 30.1296212 64254.08855 -4.807900767 -0.028616411 CRDDSFFGETSHNYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CRDDSFFGETSHNYHK 16 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 242.42 3.87E-20 1060360000 712270 674590 790770 811890 1032520 1169370 1141340 939980 910910 529520 FALSE TRUE 740390.9696 790445.5849 811378.1158 972479.4188 857012.6192 897801.5395 1051878.788 927381.1056 878126.527 633269.3057 1.16915657 1.248198164 1.281252871 1.535649067 1.353314635 1.417724705 1.661029169 1.464434005 1.386655755 1 19.27245963 3.932199032 4.466722009 1.437483742 1.218308953 0.171485057 0.162954939 0.282155585 10.8799994 0.039782301 0.07724778 8554.586703 -3.932199032 -0.219174789 CRDDSFFGETSHNYHKFDSEYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CRDDSFFGETSHNYHKFDSEYER 23 2 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 299.55 2.54E-62 3181770000 753786 931428 1068954 836174 1378520 1399130 947992 1246455 1186536 900715 FALSE TRUE 783546.0533 1091393.513 1096811.819 1001566.721 1144199.663 1074203.262 873685.9099 1229748.31 1143832.801 1077192.859 0.727396257 1.01318302 1.018213043 0.929793317 1.06220502 0.99722464 0.811076589 1.141623154 1.061864448 1 20.03884514 4.739556764 24.41178429 1.005401726 0.727396132 0.500083224 0.082928008 50.65436535 1241095.861 0.019768545 0.120749619 54898.03054 -4.739556764 -0.278005594 CRS(ph)PGMLEPLGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 CRSPGMLEPLGSSR 14 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR;CRS(1)PGMLEPLGSSR 160.8 2.84E-06 10033610000 1453269 1426930 1545312 1489559 1850567 2237050 1662072 1787750 1607345 1448693 TRUE FALSE 1510645.182 1671994.128 1585584.1 1784189.324 1536008.282 1717529.04 1531794.454 1763788.135 1549496.967 1732536.656 0.871926823 0.965055557 0.915180694 1.029813319 0.886566109 0.991337779 0.884133936 1.01803799 0.894351621 1 20.72445445 5.831345245 0.008243263 1.840756491 8.13E-06 0.091800843 0.055578065 30000.82306 28.73464335 2956.671087 3477.51234 678180.4175 -5.831345245 -1.84074836 CS(ph)LEFLEDAVGCAPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSLEFLEDAVGCAPAQR 17 0 Q9BTV7 Q9BTV7 CABLES2 CDK5 and ABL1 enzyme substrate 2 1 CS(1)LEFLEDAVGCAPAQR 195.23 3.12E-11 18095000 18334 23121 23936 21155 28296 35850 22882 21959 25848 23012 TRUE FALSE 19057.84048 27091.85189 24559.79182 25339.39586 23486.25603 27524.38081 21088.44905 21664.67552 24917.73553 27520.76081 0.692489594 0.984415078 0.892409625 0.920737477 0.853401408 1.000131537 0.766274203 0.787212086 0.90541594 1 14.74823273 2.214552186 24.99992036 0.83770535 0.894623632 0 0.100506215 666.6214938 694146.7121 0.035613802 0.026315447 163.8898984 -2.214552186 0.056918282 CS(ph)LVFY(ph)ILSPLNLNSIPDIEALQLHADVENQSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSLVFYILSPLNLNSIPDIEALQLHADVENQSGK 34 0 Q5T370 Q5T370 ARRDC1 2 CS(0.536)LVFY(0.695)ILS(0.561)PLNLNS(0.208)IPDIEALQLHADVENQSGK 46.773 0.047646 563210000 9500.7 161520 134120 136290 98219 191070 93379 147650 118060 201730 TRUE FALSE 9875.794972 189259.8035 137615.2774 163247.7552 81523.76946 146696.8882 86059.70998 145670.9933 113811.0437 241255.1311 0.040935067 0.78447991 0.570413888 0.676660241 0.337915173 0.60805707 0.356716599 0.603804746 0.471745588 1 17.8802001 -1.975533816 2.304250645 1.429911151 0.510397157 0.362805761 0.19997139 10949709.25 4413760.442 25085745.25 0.043844617 0.010579525 1.975533816 -0.919513994 CS(ph)PTVAFVEFPS(ph)SPQLK ddPTM_MDA-MB-175_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 2 CS(0.993)PT(0.007)VAFVEFPS(0.5)S(0.5)PQLK 121.08 8.98E-05 29193000 69552 44468 55156 47384 75519 85942 71069 67300 66700 38474 TRUE FALSE 72297.96667 52105.03309 56593.41067 56756.41377 62682.30735 65983.27296 65498.42608 66397.95358 64299.48003 46012.24367 1.571276706 1.132416699 1.229964161 1.233506764 1.362296258 1.434037284 1.423499939 1.443049682 1.39744283 1 15.48973019 3.121824428 6.212405985 1.381451557 1.276450544 0 0.163043408 0.537527821 27.20613074 0.044428173 0.053405647 1323.806254 -3.121824428 -0.105001013 CS(ph)PTVAFVEFPSSPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(1)PTVAFVEFPSSPQLK 220.61 4.14E-15 63624000 117772 79398 104156 79513 135536 150657 113993 107136 120714 65130 TRUE FALSE 122421.7295 93033.98887 106870.3909 95240.43408 112497.6391 115669.195 105057.9308 105700.0172 116369.5267 77890.97651 1.571706185 1.194412922 1.372050983 1.222740275 1.444296171 1.485014056 1.348781791 1.357025189 1.494005236 1 16.24916858 -1.754639465 6.783835873 0.991817439 1.377898569 0.516269842 0.112242272 0.013097945 0.000473732 0.102476059 0.024028359 0.017593836 1.754639465 0.386081131 CS(ph)PYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSPYKK 6 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 CS(1)PYKK 55.531 0.095936 117570000 273620 134140 155290 110460 247360 287370 221160 170210 177560 103450 TRUE FALSE 284422.7289 157177.5015 159336.985 132308.6583 205313.8356 220632.6726 203824.9013 167928.6134 171169.6503 123719.0468 2.298940512 1.270438995 1.287893732 1.069428368 1.659516791 1.783336344 1.647481989 1.357338402 1.383535152 1 16.9167081 0.871813224 1.3399965 1.005598936 1.53474806 0.214521428 0.322841257 0.987368032 3.441797301 0.305766915 0.091934768 7.444117585 -0.871813224 0.529149124 CS(ph)SPTVGPPPLPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.553)S(0.446)PTVGPPPLPQK 82.362 0.011461 58662000 154970 116680 148700 117500 183590 204060 167790 157240 175180 116310 TRUE FALSE 161088.3353 136718.8824 152575.2442 140741.1493 152383.4374 156670.1576 154638.1814 155132.455 168875.306 139098.7176 1.158086415 0.982891034 1.096884621 1.01180767 1.095505695 1.126323522 1.111715363 1.115268765 1.21406803 1 17.08574959 3.008279368 23.85351755 1.118985067 1.058506122 0.116170623 0.06527347 189.5440758 546083.0312 0.017401178 0.020759741 1019.246826 -3.008279368 -0.060478945 CSATPSAQVKPIVSAS(ph)PPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 CSATPSAQVKPIVS(0.001)AS(0.999)PPS(0.001)R;CSATPSAQVKPIVS(0.002)AS(0.995)PPS(0.003)R 221.31 4.80E-25 728360000 948050 725020 864490 723060 1108610 1316590 1026020 977590 966390 580270 TRUE FALSE 985479.7461 849536.5451 887019.3196 866079.1099 920168.8682 1010831.926 945597.8714 964487.0051 931609.8127 693962.7966 1.42007576 1.224181684 1.278194341 1.248019511 1.325962822 1.456608237 1.362606001 1.389825232 1.342449217 1 19.4044988 -0.324847161 7.316781088 1.000000161 1.338755241 0.678613698 0.06991734 0 0 0.071704427 0.016900895 0.473317802 0.324847161 0.33875508 CSCSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSCSFR 6 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ; 113.08 0.061517 272650000 233676 221166 225748 212022 318490 340520 263210 227652 224341 191775 FALSE TRUE 242901.7089 259149.5401 231631.1783 253959.3188 264353.1836 261439.3906 242578.9124 224600.6973 216267.0112 229349.6395 1.059089125 1.129932188 1.009947863 1.107302019 1.152620881 1.139916292 1.057681682 0.979293875 0.942957712 1 17.80718911 1.823742969 3.040665545 0.968916868 1.099728656 0.648014804 0.041262781 0.154779834 2.586728035 0.023300629 0.011773884 66.64122453 -1.823742969 0.130811787 CSDAAGYPHATHDLEGPPLDAYSIQGQHTIS(ph)PLDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAK 37 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 CSDAAGYPHATHDLEGPPLDAYSIQGQHT(0.046)IS(0.954)PLDLAK;CSDAAGYPHATHDLEGPPLDAYS(0.002)IQGQHT(0.01)IS(0.988)PLDLAK 267.36 1.44E-62 380420000 296030 279290 339410 265130 466120 495260 410400 429680 438190 274400 TRUE FALSE 307717.493 327255.8849 348255.3034 317571.9227 386889.0889 380243.3707 378231.7756 423920.8424 422419.6275 328163.4263 0.937695881 0.997234484 1.061225217 0.967724911 1.178952491 1.158701245 1.152571388 1.291797953 1.287223358 1 18.32405493 3.201178494 6.538156209 1.197571738 0.996347217 0.54536314 0.082601487 0.132162304 15.58508953 0.023909006 0.029153757 1589.199773 -3.201178494 -0.201224521 CSDVSELSS(ph)SPPGPYHQEPYVCKPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.107)S(0.555)S(0.339)PPGPYHQEPYVCKPEER;CSDVSELS(0.013)S(0.494)S(0.494)PPGPYHQEPYVCKPEER 321.04 1.11E-82 1146380000 462410 355280 429740 369220 585780 605310 522320 461700 484250 329920 TRUE FALSE 480666.3039 416296.5763 440939.3774 442250.614 486209.3248 464735.9261 481379.1936 455511.6667 466821.9371 394561.5073 1.218229085 1.055086643 1.117542815 1.12086609 1.232277645 1.177854194 1.220035874 1.154475686 1.183141103 1 18.58989069 5.08100479 20.26185566 1.15060942 4.179077605 0.087255121 0.068622979 1195.027257 308905.9939 0.015398782 5518.24242 120504.9232 -5.08100479 3.028468185 CSDVSELSSS(ph)PPGPYHQEPYVCKPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 CSDVSELSSSPPGPYHQEPYVCKPEER 27 1 Q9Y478;F5H610;F5H2X8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 CSDVSELS(0.036)S(0.177)S(0.786)PPGPYHQEPYVCKPEER;CSDVSELSS(0.084)S(0.916)PPGPYHQEPYVCKPEER;CSDVSELS(0.062)S(0.423)S(0.515)PPGPYHQEPYVCKPEER;CSDVSELS(0.355)S(0.289)S(0.357)PPGPYHQEPYVCKPEER;CSDVSELS(0.007)S(0.207)S(0.787)PPGPYHQEPYVCKPEER;CSDVSELS(0.001)S(0.249)S(0.75)PPGPYHQEPYVCKPEER;CSDVSELS(0.011)S(0.252)S(0.737)PPGPYHQEPYVCKPEER 181.56 1.01E-17 9796110000 2209330 1767115 2022931 1873580 2904869 2906873 2371324 2279935 2388027 1429253 TRUE FALSE 2296556.054 2070603.255 2075650.244 2244168.532 2411100.405 2231795.8 2185453.429 2249376.201 2302082.375 1709287.761 1.343574855 1.211383655 1.21433634 1.312926111 1.410587767 1.30568758 1.278575486 1.3159728 1.346807967 1 20.70496387 -0.336775934 9.095373079 1.000000004 1.302285387 0.720820106 0.056823367 0 0 0.057761472 0.01361451 0.460494096 0.336775934 0.302285383 CSEKDSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CSEKDSIR 8 1 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ;; 87.308 0.017416 142870000 345750 270715 332710 278743 493060 494960 388410 354780 371870 243867 FALSE TRUE 359400.477 317208.1954 341380.6959 333877.5334 409249.8373 380013.0412 357965.4093 350024.7544 358486.4713 291648.0695 1.232308781 1.087640305 1.170522735 1.144795966 1.403231772 1.302984936 1.227388235 1.200161396 1.229174847 1 18.153869 5.096424529 19.68174065 1.207796425 3.169794872 0 0.105418324 4465.079685 960445.9316 0.024334638 21101.78534 124860.3444 -5.096424529 1.961998447 CSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR ddPTM_MDA-MB-175_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" 0 132.08 5.22E-09 265920000 154690 95159 157670 94158 209850 200170 170060 152810 189140 98072 FALSE TRUE 160797.2806 111501.818 161779.0097 112782.1714 174179.772 153683.5511 156730.2528 150761.8319 182332.8883 117287.3307 1.370968882 0.950672313 1.379339173 0.961588696 1.485068941 1.310316726 1.336293118 1.285405943 1.554582982 1 16.83968766 3.226603204 24.99996871 1.338330621 1.165551294 0.148574068 0.190270935 375.4280514 784925.2457 0.049862924 0.060030829 1685.012799 -3.226603204 -0.172779327 CSGPGLS(ph)PGMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 290.86 4.27E-36 7544500000 3302260 3495110 3641360 3308810 4433420 5684640 3863640 3864400 3580170 2926660 TRUE FALSE 3432635.775 4095367.954 3736256.833 3963282.742 3679828.852 4364468.512 3560797.801 3812604.039 3451320.381 3500082.993 0.980729823 1.170077385 1.06747664 1.132339648 1.051354742 1.246961435 1.017346677 1.08928961 0.986068156 1 21.7389577 1.408648441 1.700303665 0.991504062 1.104061363 0.224922111 0.072841337 0.470829058 2.50479845 0.059805869 0.018791354 25.62408944 -1.408648441 0.112557302 CSGQHWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSGQHWER 8 0 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 ; 89.913 0.013569 236750000 137047 329110 312220 328040 341900 421030 284080 320700 278770 293200 FALSE TRUE 142457.7214 385632.0824 320356.7097 392925.3329 283783.9601 323252.1633 261813.0673 316401.5411 268737.1222 350646.9263 0.406271125 1.099773172 0.913616192 1.120572586 0.809315408 0.921873654 0.746657243 0.902336559 0.766403758 1 18.41965956 CSKQSPSGAHGT(ph)HFGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CSKQSPSGAHGTHFGDDR 18 1 A0A0A0MRP9;Q96C92-3;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 1 CS(0.017)KQS(0.017)PS(0.017)GAHGT(0.949)HFGDDR;CS(0.013)KQS(0.013)PS(0.013)GAHGT(0.96)HFGDDR;CS(0.014)KQS(0.014)PS(0.014)GAHGT(0.958)HFGDDR 66.335 0.046879 669888000 9118.9 333547 150662 337033 79812 283664 79513 183680 107225 361475 TRUE FALSE 9478.921213 390831.1026 154588.3755 403697.1215 66245.58475 217787.335 73280.56329 181218.07 103365.9932 432299.1054 0.021926766 0.904075668 0.357595872 0.933837513 0.153240162 0.50378854 0.169513567 0.419196033 0.239107581 1 18.72167033 -1.20273509 4.485407972 1.000113368 0.423934537 0.270983239 0.288983254 79620968.61 21349966.93 119734.6333 0.06230691 0.06269962 1.20273509 -0.576178832 CSLHSAS(ph)PASVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CSLHSASPASVR 12 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 CSLHS(0.001)AS(0.999)PASVR;CSLHS(0.003)AS(0.992)PAS(0.006)VR;CSLHS(0.027)AS(0.969)PAS(0.003)VR 128.85 0.00015765 577997000 652460 953920 918059 903114 999210 1196980 944172 963152 872161 907455 TRUE FALSE 678219.6246 1117748.34 941984.3717 1081747.254 829364.6411 918999.5354 870165.3315 950242.5228 840772.096 1085253.433 0.624941239 1.029942229 0.867985618 0.996769253 0.76421287 0.846806384 0.801808412 0.87559504 0.774724198 1 20.04960056 3.211993792 24.99995171 0.837634019 0.889774711 0.017499653 0.118417062 778.6865142 732758.3372 0.031743633 0.037950926 1629.272744 -3.211993792 0.052140692 CSLHSASPAS(ph)VR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSLHSASPASVR 12 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 CSLHS(0.004)AS(0.453)PAS(0.543)VR 62.055 0.05184 211850000 504060 350190 398180 358290 512670 503420 477410 408010 438710 308810 TRUE FALSE 523960.678 410332.4084 408556.8979 429158.6926 425526.5365 386508.3344 439989.3567 402541.2933 422920.9128 369315.407 1.418734957 1.111062254 1.106254681 1.162038422 1.152203587 1.046553507 1.191364748 1.089966153 1.145148306 1 18.49449392 4.739297958 24.9186756 1.117434927 1.418735055 0.743584499 0.054006724 26.53789519 896679.2983 0.011541785 0.069655603 54865.32524 -4.739297958 0.301300128 CSPTVAFVEFPSS(ph)PQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 CSPTVAFVEFPS(0.01)S(0.99)PQLK;CSPTVAFVEFPS(0.038)S(0.962)PQLK 299.65 2.79E-46 133894000 325720 192658 272630 243370 371640 446980 374730 312700 356030 171729 TRUE FALSE 338579.6771 225745.5128 279734.9618 291507.8596 308468.7655 343175.669 345357.6834 308508.768 343216.5498 205376.0096 1.648584359 1.099181512 1.362062503 1.419386131 1.501970781 1.670962785 1.681587271 1.502165558 1.671161839 1 17.64790814 3.334404447 2.563364295 1.549455796 1.347166381 0.047932411 0.224663029 0.533924231 7.1282993 0.062095136 0.088217695 2159.754795 -3.334404447 -0.202289415 CSS(ph)PTVGPPPLPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CSSPTVGPPPLPQK 14 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 CS(0.427)S(0.573)PTVGPPPLPQK;CS(0.001)S(0.998)PT(0.001)VGPPPLPQK;CS(0.001)S(0.999)PTVGPPPLPQK 267.23 6.03E-25 955062000 1202472 869230 1115833 875001 1528100 1668820 1340000 1282690 1335300 829759 TRUE FALSE 1249946.523 1018513.491 1144912.525 1048073.586 1268354.108 1281261.846 1234967.299 1265497.639 1287242.814 992334.3894 1.259602143 1.02638133 1.153756775 1.056169772 1.278151923 1.291159371 1.244507206 1.275273388 1.297186541 1 19.92046683 3.229034878 24.97663201 1.250224509 1.119133437 0.199081128 0.100713012 234.3742794 614532.0216 0.026498638 0.032055513 1694.473878 -3.229034878 -0.131091073 CSVCSEPIMPEPGRDETVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CSVCSEPIMPEPGRDETVR 19 1 Q15942;Q15942-2;H0Y2Y8 Q15942 ZYX Zyxin 0 ; 186.05 1.95E-14 585070000 240530 290330 274300 281560 360430 452130 331570 334960 310730 263990 FALSE TRUE 250026.3101 340191.919 281448.4833 337251.7276 299164.2373 347129.6596 305580.677 330470.4091 299546.888 315713.7861 0.791939792 1.07753267 0.891467195 1.068219832 0.947580532 1.099507449 0.967904129 1.046740509 0.948792549 1 18.26825773 4.750695934 24.65693929 1.006432854 0.791939634 0.501662126 0.063788208 1181.681953 2400927.201 0.013449962 0.227816588 56324.31695 -4.750695934 -0.214493221 CSWQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CSWQDLK 7 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 79.474 0.07567 366360000 278400 146120 195970 174480 287430 343800 253860 207530 199400 135780 FALSE TRUE 289391.447 171214.9733 201077.1392 208991.6232 238572.7513 263957.6603 233961.7899 204748.3998 192223.633 162383.4913 1.782148201 1.054386575 1.238285601 1.287025063 1.469193385 1.625520293 1.440797879 1.260894184 1.183763395 1 17.30904544 -0.672642736 4.507705472 0.999999912 1.361496859 0.226305929 0.205255204 34926270.04 97081036.82 247.4456228 0.048624709 0.212499183 0.672642736 0.361496948 CTDKGVESVFDIMEMEDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CTDKGVESVFDIMEMEDEER 20 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 62.94 0.034934 21235000 13443 11371 12716 12061 17473 16704 12482 14734 14982 10597 FALSE TRUE 13973.74002 13323.8808 13047.38941 14446.6298 14502.9457 12824.74915 11503.62822 14536.51483 14442.80075 12673.27926 1.102614385 1.051336479 1.029519601 1.13992831 1.144371982 1.01195191 0.90770731 1.147020793 1.139626173 1 13.62950226 2.721974866 24.74954005 1.047112866 1.090227598 0.112425191 0.072238024 2229.153099 3326376.736 0.025207036 0.02382795 527.1993503 -2.721974866 0.043114733 CTELNQAWSS(ph)LGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CTELNQAWSSLGK 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 CTELNQAWS(0.033)S(0.967)LGK;CTELNQAWS(0.036)S(0.964)LGK 184.44 9.97E-06 113544000 452370 306720 335390 302180 469170 539710 401060 343420 372600 197299 TRUE FALSE 470229.9169 359396.774 344130.5389 361950.3021 389420.651 414370.5319 369623.8692 338817.0166 359190.1988 235955.9615 1.992871525 1.523151912 1.458452402 1.533973966 1.650395474 1.75613504 1.566495149 1.435933275 1.52227643 1 17.8481581 -2.739877179 0.216961151 2.14E-14 1.698465959 0.636655865 0.144447705 32.68111382 0.785122957 15.52125217 0.313178226 0.001820216 2.739877179 1.698465959 CTHWAEGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 CTHWAEGGK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ;;;; 119.75 0.00077709 2067560000 3255610 2481610 2874140 2311520 3838140 4135400 3312760 3034100 3205690 2025650 FALSE TRUE 3384143.997 2907807.213 2949042.45 2768731.757 3185734.334 3175016.023 3053097.215 2993432.852 3090317.843 2422537.334 1.396941937 1.200314716 1.217336223 1.142905712 1.315040346 1.310615931 1.260289025 1.235660153 1.275653341 1 21.20808747 -1.275480894 3.721111421 0.999487821 1.256390806 0.579644037 0.066707878 4961022.64 1700532.472 20480.48278 0.015266034 0.053029692 1.275480894 0.256902984 CTKEEHLCTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 CTKEEHLCTQR 11 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 193.15 6.48E-07 6990510000 5936040 4900880 5890110 4229960 7972140 7869570 5173260 6077380 6052420 4535270 FALSE TRUE 6170399.443 5742568.016 6043611.105 5066633.463 6617038.49 6041981.632 4767766.363 5995922.662 5834594.586 5423869.324 1.137637925 1.058758549 1.114261931 0.934136344 1.219984866 1.113961505 0.879034151 1.105469602 1.075725509 1 22.37089099 CTLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CTLAEK 6 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 122.79 0.04436 300590000 380300 315850 390010 304730 479130 528710 444120 388340 413230 270480 FALSE TRUE 395314.5377 370094.7805 400173.981 365004.6845 397687.6537 405925.1152 409308.7139 383134.9375 398357.933 323475.3773 1.222085405 1.144120407 1.237108012 1.128384755 1.229421717 1.254887214 1.265347357 1.18443308 1.231493835 1 18.30329637 -1.27958063 4.617137724 0.999901128 1.209579755 0.684126036 0.042966065 4.30E-05 6.71E-06 0.040892199 0.00963385 0.052531448 1.27958063 0.209678627 CTLPEHES(ph)PSQDISDACEAESTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CTLPEHESPSQDISDACEAESTER 24 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 CTLPEHES(0.981)PS(0.019)QDISDACEAESTER;CTLPEHES(0.999)PS(0.001)QDISDACEAESTER;CTLPEHES(0.999)PS(0.001)QDISDACEAESTER;CTLPEHES(0.973)PS(0.027)QDISDACEAESTER 303.2 1.45E-62 1256210000 365604 483010 436715 507083 491323 661474 438739 502928 471332 467013 TRUE FALSE 380038.3282 565963.2102 448096.1517 607382.5039 407808.092 507856.6882 404349.4907 496187.0728 454368.8534 558515.2558 0.680443953 1.013335275 0.802298858 1.087494921 0.730164642 0.909297791 0.72397215 0.888403795 0.813529888 1 19.09123716 CTS(ph)PPGLSYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CTSPPGLSYMK 11 0 Q13796;C9IZC6;F5H3B6 Q13796 SHROOM2 Protein Shroom2 1 CTS(0.999)PPGLSYMK 92.112 0.0045852 0 214890 181240 196810 179390 306160 311990 227990 212290 226010 184200 TRUE FALSE 223374.0231 212366.5601 201939.0303 214872.8066 254119.0326 239535.0508 210119.5481 209444.5998 217875.9442 220290.4633 1.0139977 0.96402975 0.916694383 0.975406758 1.153563476 1.087360057 0.953829525 0.950765624 0.989039385 1 17.74904751 5.096281187 17.73113727 0.996966027 1.882149852 0.003726334 0.066898618 1360.178999 301383.7968 0.01723815 9794.995141 124819.1403 -5.096281187 0.885183825 CTVFHGAQVEDAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 230.69 8.17E-13 69680210000 18388335 20002733 20800875 23878049 24545581 31715273 21535753 21654420 20809302 18713964 FALSE TRUE 19114320.66 23438046.79 21342962.89 28601055.82 20373331.91 24349881.5 19847724.41 21364177.92 20060379.29 22380606.95 0.854057297 1.047248042 0.953636465 1.27793924 0.910311859 1.087990221 0.886826906 0.954584385 0.896328653 1 24.41574583 2.232385011 24.99999912 0.93164959 1.026485681 0.127514807 0.111549153 289.4274748 1171644.414 0.039465756 0.029875871 170.7595536 -2.232385011 0.094836091 CVFS(ph)YNSNCQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.348)Y(0.305)NS(0.348)NCQEK;CVFS(0.35)Y(0.3)NS(0.35)NCQEK 64.878 0.040103 2490210000 2275300 1108030 2962900 694290 2749800 1933510 2573100 1626250 2355000 1181460 TRUE FALSE 2365130.601 1298325.533 3040115.608 831618.4898 2282389.978 1484481.605 2371413.698 1604452.779 2270244.01 1412944.467 1.673902023 0.918879378 2.151617194 0.588571249 1.615343017 1.05062983 1.678348834 1.135538457 1.606746807 1 20.43027333 5.077969981 18.48459744 1.322009071 11.39469586 0.059485892 0.435304544 489.9224188 116522.1858 0.088693496 653.6018394 119665.7813 -5.077969981 10.07268679 CVFSYNS(ph)NCQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVFSYNSNCQEK 12 0 Q6NT55 Q6NT55 CYP4F22 Cytochrome P450 4F22 1 CVFS(0.129)Y(0.107)NS(0.764)NCQEK;CVFS(0.129)Y(0.107)NS(0.764)NCQEK 59.57 0.063188 3531200000 2269100 939420 2921000 577720 2474800 1816640 2328000 1518270 1994170 1108300 TRUE FALSE 2358685.82 1100758.077 2997123.66 691991.2917 2054134.38 1394752.891 2145525.277 1497920.074 1922400.211 1325450.165 1.779535649 0.83047866 2.26121188 0.522080203 1.54976357 1.05228618 1.618714406 1.13012176 1.450375323 1 20.338051 -3.842506843 0.049834897 7.10E-17 1.945855317 0.054195372 0.470696087 1621.935711 7.363014641 260.3516044 76.2637286 0.000143712 3.842506843 1.945855317 CVGAELEYDS(ph)EHSDWHGFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 1 CVGAELEYDS(1)EHSDWHGFD;CVGAELEYDS(1)EHSDWHGFD 261.63 2.35E-31 160478000 175817 228942 232680 233033 243691 315470 209570 236006 202183 206013 TRUE FALSE 182758.3909 268261.0076 238743.8319 279126.2319 202268.4909 242206.8735 193143.3558 232842.7256 194906.4733 246377.303 0.741782578 1.088821918 0.96901715 1.132921858 0.820970473 0.983072996 0.783933233 0.945065648 0.791089402 1 17.91050983 3.204427146 24.99931765 0.8860924 0.989676891 0.133455161 0.119074906 328.9660752 240933.5543 0.032042913 0.038300385 1601.132031 -3.204427146 0.103584491 CVGAELEYDSEHSDWHGFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVGAELEYDSEHSDWHGFD 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ; 245.39 1.41E-24 155381000 86802 139610 120335 139867 133872 186405 119186 144012 136101 146107 FALSE TRUE 90229.00999 163586.9315 123471.029 167532.2751 111116.4853 143115.2637 109843.8899 142081.7547 131202.7516 174733.8693 0.516379626 0.936206198 0.706623332 0.958785357 0.635918415 0.819047071 0.628635366 0.81313231 0.750871895 1 17.41479975 -0.1666786 1.378758088 1.000712712 0.758488639 0.242736427 0.131014196 47.00460908 52.64155721 0.288550444 0.032771055 0.681273349 0.1666786 -0.242224073 CVLLSNLSSTSHVPEVDPGSAELQK ddPTM_MDA-MB-175_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 0 209.45 2.52E-36 0 164870 207670 247720 245390 307820 334260 260400 264730 252340 162770 FALSE TRUE 171379.1949 243335.7071 254175.7867 293927.4096 255496.8664 256633.1808 239989.1676 261181.7274 243258.3327 194661.6651 0.880395197 1.250044311 1.305731083 1.509939872 1.312517625 1.318355007 1.232852742 1.341721429 1.24964683 1 17.57060928 4.742520588 3.274382718 1.304496299 0.81945125 0.494072427 0.120309156 0.247360494 4.257208607 0.027282944 0.305656861 55273.96105 -4.742520588 -0.48504505 CVMDDDNEVRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVMDDDNEVRDR 12 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 174.73 2.70E-05 1340570000 333695 413445 401940 375180 476850 531960 329428 383722 365378 466460 FALSE TRUE 346869.5363 484450.9626 412414.8866 449389.4842 395795.2073 408420.3519 303606.5726 378578.8342 352228.1172 557853.9061 0.621792789 0.868419056 0.739288337 0.80556841 0.709496166 0.732127798 0.544240292 0.67863437 0.631398496 1 19.08952782 -1.165790825 4.946732866 1.00002208 0.704465091 0.504862907 0.088101435 2.21E-05 3.73E-06 0.087898579 0.020716347 0.068266742 1.165790825 -0.295556989 CVPASGELS(ph)PELQEWAPYS(ph)PGHSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 2 CVPAS(0.004)GELS(0.996)PELQEWAPYS(0.99)PGHS(0.005)S(0.004)R 165.1 8.33E-12 33589000 7873.7 15853 16162 20657 22025 27699 21335 22859 21864 25174 TRUE FALSE 8184.559756 18575.62943 16583.195 24742.89295 18281.19837 21266.32703 19662.70695 22552.61249 21077.11891 30106.36331 0.271854813 0.617000108 0.550820264 0.821849278 0.607220413 0.706373161 0.653108007 0.749097865 0.700088506 1 14.87778083 4.075203399 0.119249378 1.122122001 8.41E-22 0.631800324 0.108572321 22.08805381 0.551853978 1.235680425 4.514949078 11890.58986 -4.075203399 -1.122122001 CVPASGELS(ph)PELQEWAPYSPGHSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CVPASGELSPELQEWAPYSPGHSSR 25 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 CVPAS(0.002)GELS(0.998)PELQEWAPYSPGHSSR 159.05 1.54E-11 82486000 8851 43591 38968 47050 37008 55639 30978 51542 42007 49710 TRUE FALSE 9200.444314 51077.41516 39983.53809 56356.34957 30717.39338 42717.68547 28549.86341 50851.1638 40495.17628 59449.72274 0.154760088 0.859169947 0.672560548 0.947966567 0.516695318 0.718551467 0.480235434 0.855364188 0.681166781 1 15.85938246 -5 0.096866487 1.982353666 0.445259817 0.230875037 0.211264909 318.0090749 2.111559814 64.60434192 3.737731814 1.00E-05 5 -1.537093849 CVS(ph)VQTDPTDEIPTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CVSVQTDPTDEIPTKK 16 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 CVS(0.999)VQT(0.001)DPTDEIPTKK;CVS(0.99)VQT(0.01)DPTDEIPTKK 149.73 4.95E-07 287370000 498230 346380 463070 337790 758290 682150 581150 507670 614860 329070 TRUE FALSE 517900.5051 405868.0705 475137.9846 404603.8538 629396.1367 523731.0006 535597.9444 500865.514 592731.3087 393544.9661 1.315988133 1.031313079 1.207328325 1.028100697 1.599299168 1.330803455 1.360957427 1.272702124 1.506133631 1 18.58616896 3.264228959 24.99998691 1.352894836 1.141916606 0.256214571 0.165976787 282.0710509 274724.5153 0.042377483 0.057358882 1837.506819 -3.264228959 -0.21097823 CVSSPHFQVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 CVSSPHFQVAER 12 0 Q16537-2;Q16537;Q16537-3;H0YN84;E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H7C5Q9;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;Q15173-2;Q15173 Q16537-2;E9PFR3;H0YJ75;Q15173-2 PPP2R5E;PPP2R5C;PPP2R5D;PPP2R5B Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform 0 ;;; 164.68 5.66E-05 1060750000 477357 786560 776970 813730 887510 1084390 779530 893750 784320 808300 FALSE TRUE 496203.423 921645.5614 797218.4765 974683.3653 736651.3672 832556.8566 718428.4017 881770.7431 756092.4764 966670.9092 0.513311633 0.953422258 0.824705149 1.008288711 0.762049794 0.861261934 0.743198533 0.912172627 0.782161198 1 19.8826653 -3.2600595 0.021419679 1.961957282 2.49E-06 0.166385884 0.128487754 4473.931973 9.886207099 571.8312255 355.8768139 0.000549466 3.2600595 -1.961954796 CYEMASHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 CYEMASHLR 9 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;; 208.72 9.59E-06 15916530000 5826450 7766770 6838870 6781960 10507300 11462450 7230490 7371040 6779020 8448680 FALSE TRUE 6056482.745 9100652.33 7017096.57 8123411.446 8721272.899 8800469.703 6663745.3 7272243.265 6535044.394 10104037.09 0.599412165 0.900694668 0.694484443 0.803976804 0.863147356 0.870985491 0.659513147 0.719736399 0.646775575 1 23.2684285 -2.264081344 2.358867696 2.026281175 0.755502157 0.360328284 0.099376229 3412464.817 661188.6654 18783237.2 0.023642592 0.005444007 2.264081344 -1.270779017 CYEMASHLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CYEMASHLRR 10 1 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 48.64 0.083431 8775400 7623.6 24714 20793 22983 21957 30857 15899 23200 18739 37809 FALSE TRUE 7924.585615 28958.43725 21334.88266 27528.9688 18224.75698 23690.92939 14652.79484 22889.04195 18064.58705 45216.94965 0.175256971 0.640433233 0.471833744 0.60881968 0.403051447 0.523939133 0.324055359 0.50620491 0.399509193 1 15.46457605 -1.433777972 2.988582949 1.010956228 0.459971764 0.618047809 0.129430873 32965501.59 39620376.95 3055131.875 0.03094789 0.036831722 1.433777972 -0.550984465 CYPDRVDYVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 CYPDRVDYVDK 11 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 144.57 3.34E-05 364830000 398580 249990 344310 282510 422640 429370 417730 353030 365770 201420 FALSE TRUE 414316.2462 292923.8378 353283.0015 338389.6348 350799.8038 329655.3247 384987.2311 348298.2103 352606.0091 240884.3926 1.719979621 1.21603494 1.466608101 1.40478024 1.456299431 1.368520896 1.598224057 1.445914393 1.463797656 1 17.8779814 -1.376101467 4.53579545 0.999328259 1.454023435 0.54579475 0.125787701 0.000769913 0.000105902 0.109741376 0.025829371 0.042062834 1.376101467 0.454695177 CYQSEFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CYQSEFGR 8 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ; 176.09 0.00061035 495880000 474350 580260 641400 599120 520440 775960 634520 599150 555240 475770 FALSE TRUE 493077.7043 679915.1412 658115.4109 717624.1478 431975.7947 595755.0498 584784.6644 591119.3743 535257.0209 568988.0223 0.866587142 1.194955104 1.156641942 1.261228918 0.759200155 1.047043218 1.027762697 1.038895989 0.940717554 1 19.11803876 3.26401009 24.99906424 0.983035511 1.127845352 0.258327978 0.123603786 326.4689694 320688.7609 0.033562946 0.045427903 1836.581013 -3.26401009 0.144809841 CYYSNTDAVIYVVDSCDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 CYYSNTDAVIYVVDSCDRDR 20 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;; 215.75 1.07E-24 639730000 234616 222401 254997 262004 295203 356038 262893 266499 293074 233091 FALSE TRUE 243878.8208 260596.6417 261642.4313 313827.6092 245024.4995 273353.5703 242286.7597 262927.0168 282526.324 278760.7187 0.874867959 0.934839898 0.938591465 1.125795667 0.878977858 0.980602904 0.869156748 0.943199666 1.013508379 1 18.08866775 2.800477892 0.006214341 1.90320529 1.99E-05 0.0588793 0.072369633 30368.6868 70.57872433 10613.59686 10998.40287 631.6520233 -2.800477892 -1.903185356 CYYYHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 CYYYHAR 7 0 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 126.68 0.0039289 214536000 111330 114146 106680 102617 234830 201529 152681 118926 114707 153206 FALSE TRUE 115725.3944 133749.6876 109460.1684 122914.3363 194913.6805 154726.944 140713.4643 117331.9915 110578.7175 183223.7824 0.631606841 0.72997995 0.597412448 0.670842697 1.063801205 0.844469762 0.767986898 0.640375338 0.603517273 1 17.48324725 3.439837578 24.99648119 0.795520146 0.656268437 0.242629664 0.136887365 295.1580777 197885.0495 0.040647522 0.055037127 2753.198841 -3.439837578 -0.139251709 DAAAVGNHVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAAAVGNHVAK 11 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 88.441 0.012976 145320000 76051 60201 78319 66087 107970 98224 85280 74116 79289 69573 FALSE TRUE 79053.5522 70540.05345 80360.05748 79158.81135 89617.29797 75412.9646 78595.53076 73122.59625 76435.40438 83204.49729 0.95011153 0.847791354 0.965813869 0.951376595 1.077072765 0.906356832 0.944606762 0.878829854 0.918645108 1 16.34437389 4.681855596 0.00287527 1.865528336 6.63E-05 0.020818638 0.060171134 649513.1191 295.1465799 93777.2561 97740.8146 48067.94951 -4.681855596 -1.865461994 DAADAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAADAVR 7 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 97.473 0.027851 480840000 596550 649370 647120 660630 739870 819970 821200 763870 663720 645160 FALSE TRUE 620102.2546 760894.2461 663984.4788 791300.6422 614107.1617 629544.3943 756832.1982 753631.5721 639832.8469 771566.7497 0.803692299 0.986167751 0.860566476 1.025576391 0.795922274 0.815929917 0.980903076 0.976754859 0.829264412 1 19.55743145 -4.999999956 0.199413087 1.425122372 0.890433352 0.105714629 0.083949108 339.8674401 3.361701316 57.54920405 0.19980148 1.00E-05 4.999999956 -0.534689019 DAADKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAADKPR 7 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ; 97.602 0.010832 514090000 937300 658790 850790 622110 1106600 1023410 1077010 889670 981600 691840 FALSE TRUE 974305.3278 771932.0578 872962.2863 745161.5012 918500.5273 785738.5374 992591.142 877745.4289 946272.4077 827392.8019 1.177560798 0.932969269 1.055075998 0.900613952 1.110114235 0.949655998 1.199661321 1.06085698 1.143679768 1 19.65821288 2.24989949 24.99990519 1.104611967 1.01712475 0.152856372 0.091899336 353.7879931 780029.9784 0.029277926 0.024290163 177.7867907 -2.24989949 -0.087487217 DAAEAIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAAEAIKK 8 1 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 108.98 0.0059437 1297170000 2043440 1344070 1745700 1335660 2698600 2345500 2248500 1782620 2152270 1374430 FALSE TRUE 2124116.589 1574903.567 1791194.376 1599849.561 2239892.936 1800793.171 2072256.695 1758726.895 2074810.223 1643723.243 1.292259264 0.958131835 1.089717739 0.973308352 1.36269469 1.095557405 1.260709005 1.069965337 1.262262508 1 20.64853598 3.288636282 24.99999983 1.173416731 1.070578922 0.11584946 0.130304281 217.9133499 108790.3769 0.033287747 0.045071755 1943.731543 -3.288636282 -0.102837809 DADAGDEDEESEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 ; 356.13 3.24E-82 906020000 403840 418220 455260 416830 543730 589710 506740 481510 460700 374700 FALSE TRUE 419783.915 490046.0317 467124.4496 499277.7299 451306.9688 452758.7896 467020.3947 475056.146 444119.497 448115.2909 0.936776592 1.093571323 1.042420241 1.114172491 1.007122448 1.010362286 1.042188035 1.060120366 0.991083112 1 18.77351043 1.227931548 24.97153175 0.995541517 1.041916023 0.116170641 0.046391036 451.9702221 1061805.361 0.040386119 0.010496483 16.90174512 -1.227931548 0.046374506 DADDAVYELNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 250.72 6.02E-17 348533000 876150 534630 713580 678400 907270 944060 1112730 738650 803010 385108 FALSE TRUE 910741.0785 626448.5437 732176.481 812585.4952 753052.5695 724816.3724 1025511.315 728749.6049 774109.827 460562.5393 1.977453659 1.360181279 1.589743886 1.764332584 1.635071256 1.573763193 2.226649429 1.582303255 1.68079199 1 18.81303755 DADLTDTAQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DADLTDTAQTR 11 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 169.76 3.84E-05 271130000 247080 250060 237760 232640 293440 305500 278520 268550 258930 228380 FALSE TRUE 256834.9092 293005.8598 243956.2209 278655.4976 243561.1736 234552.2549 256688.8746 264950.5265 249611.1599 273126.6884 0.940350834 1.072783702 0.893198033 1.020242655 0.891751645 0.858767249 0.939816157 0.970064581 0.913902487 1 18.05921077 4.226440299 24.99452904 0.935629193 1.006567295 0.202615005 0.056018806 290.8979564 599893.8603 0.013493476 0.029489537 16843.80863 -4.226440299 0.070938102 DADLWSSHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DADLWSSHDK 10 0 P34896-2;P34896;P34896-3;J3KRZ5;J3KRK5 P34896-2 SHMT1 "Serine hydroxymethyltransferase, cytosolic" 0 ; 143.96 3.31E-05 772820000 620080 754040 838080 792320 1100270 1243650 1027250 923680 967820 785380 FALSE TRUE 644561.2372 883540.5044 859921.0533 949038.5312 913246.4984 954831.1352 946731.4608 911299.5804 932988.3473 939260.174 0.686243551 0.940677066 0.915530198 1.010410701 0.972304079 1.0165779 1.007954438 0.970231258 0.993322588 1 19.84116531 5.306230999 1.183864934 0.991612609 2.16E-17 0.924294156 0.025744904 1.171555608 0.54027101 0.006835801 1.985721835 202409.5497 -5.306230999 -0.991612609 DADNLFEHELGALNMAALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DADNLFEHELGALNMAALLR 20 0 Q5T200 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 0 132.14 1.31E-05 16552000 16753 19309 19978 16391 21861 25521 20315 20400 18562 18884 FALSE TRUE 17414.42138 22625.17055 20498.64309 19633.09088 18145.07503 19594.13452 18722.65722 20126.57137 17893.95725 22583.95824 0.771096952 1.001824849 0.907663877 0.869337902 0.803449724 0.867612945 0.829024612 0.891188832 0.792330426 1 14.46301075 5.079483639 10.83659181 0.877225313 5.76E-05 0.19173501 0.068445683 82760.98433 399751.0948 0.015649611 1535873.123 120083.5833 -5.079483639 -0.877167696 DADPILISLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DADPILISLR 10 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 204.07 4.51E-07 755645000 989840 1022415 1062941 946355 1476730 1388720 1150095 1101070 1045170 1137167 FALSE TRUE 1028919.648 1198006.823 1090642.116 1133541.194 1225715.962 1066210.826 1059947.549 1086311.958 1007554.536 1359973.101 0.756573528 0.880904793 0.801958594 0.833502658 0.901279563 0.783994055 0.779388613 0.798774591 0.740863577 1 20.37514669 DADSQNPDAPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DADSQNPDAPEGK 13 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 84.289 0.018695 0 126560 74805 102160 73755 134440 146840 127520 95177 100240 63041 FALSE TRUE 131556.6865 87652.17685 104822.3735 88343.51886 111587.9368 112738.6354 117524.6492 93901.30799 96632.38198 75392.67696 1.744953115 1.16260863 1.39035219 1.171778513 1.480089862 1.495352598 1.558833748 1.245496403 1.281721062 1 16.20213678 0.935097938 1.38885896 1.006162875 1.406117242 0.360961749 0.168470826 0.546525886 2.12297603 0.153026699 0.045808733 8.611879379 -0.935097938 0.399954368 DAEAHPWLSDYDDLTSATYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAEAHPWLSDYDDLTSATYDK 21 0 J3KPV0;B4E0T2;P50542-2;P50542-3;P50542;P50542-4 J3KPV0 PEX5 Peroxisomal targeting signal 1 receptor 0 ; 72.568 0.015565 71887000 27806 39594 42833 33834 39305 53722 37555 36800 37740 43718 FALSE TRUE 28903.80235 46393.9615 43949.26317 40526.26422 32623.95014 41245.87966 34611.34097 36306.75619 36381.74477 52283.70507 0.552826207 0.887350302 0.84059198 0.775122271 0.623979309 0.788885937 0.661990976 0.694418197 0.69585246 1 15.67407376 -0.98658267 4.576693899 1.000005432 0.728000408 0.425570761 0.09592792 1.81165E+11 40121026580 12533185.93 0.022011203 0.103137673 0.98658267 -0.272005025 DAEDAIYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DAEDAIYGR 9 0 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;;;; 255.1 1.41E-14 3384150000 4271629 4380140 4555149 4034893 5498100 5896580 4960908 4595338 4626987 3853017 FALSE TRUE 4440276.211 5132394.972 4673859.925 4832982.792 4563534.926 4527188.659 4572059.068 4533745.011 4460462.642 4607941.911 0.963613756 1.113815033 1.014305305 1.048837613 0.990362946 0.982475202 0.992212827 0.983898039 0.967994547 1 22.1356911 3.198547202 6.926877537 0.985283332 1.03927076 0.311323229 0.035481994 0.204239143 26.35935071 0.009444037 0.011463723 1579.600279 -3.198547202 0.053987428 DAEDALHNLDR ddPTM_MDA-MB-175_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 ;; 166.04 2.09E-05 1554410000 1744320 1581220 1745340 1862980 1993690 2459280 2668740 1982060 1897330 1214120 FALSE TRUE 1813187.101 1852782.235 1790824.994 2231471.884 1654803.286 1888149.491 2459557.185 1955493.728 1829045.464 1452003.568 1.248748378 1.276017687 1.233347516 1.536822589 1.139668884 1.300375242 1.693905745 1.346755456 1.259670089 1 20.46961357 DAEDALHNLDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 198.74 1.17E-07 1729150000 2323620 1483140 1955530 1498250 2560170 2391590 2443130 1917810 2169060 1190180 FALSE TRUE 2415358.312 1737857.758 2006492.718 1794599.378 2124993.218 1836179.467 2251631.087 1892104.894 2090995.954 1423372.984 1.696925781 1.220943335 1.409674584 1.260807532 1.492927885 1.290019895 1.581898148 1.32931067 1.469042885 1 20.44088233 -1.398828738 3.91235903 0.998193665 1.406254146 0.435086245 0.142032669 0.00198997 0.000305777 0.122290224 0.028704251 0.039918229 1.398828738 0.408060481 DAEDAMDAMDGAVLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DAEDAMDAMDGAVLDGR 17 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 314.29 7.45E-58 1119797000 678675 827699 908196 707366 1006512 1097662 878977 841422 896522 731289 FALSE TRUE 705469.6131 969849.8646 931864.3339 847280.8835 835425.4498 842746.6357 810080.486 830144.1144 864256.3483 874571.0782 0.806646401 1.108943445 1.065510119 0.96879591 0.955240198 0.963611371 0.926260319 0.949201426 0.988205956 1 19.73821611 3.501199079 23.28730226 0.958233291 1.007212459 0.018438561 0.075999408 844.6677585 816931.8772 0.019436258 0.029886808 3171.020714 -3.501199079 0.048979168 DAEDAVYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAEDAVYGR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 205.77 3.35E-05 1504260000 1977700 1766280 1914030 2036930 2169500 2459000 2666900 2087300 1928870 1318910 FALSE TRUE 2055781.123 2069624.85 1963911.194 2439828.674 1800729.165 1887934.517 2457861.409 2059323.158 1859450.345 1577325.162 1.303333753 1.312110464 1.245089624 1.546814019 1.141634717 1.196921574 1.558246497 1.305579348 1.178863046 1 20.58904867 1.000453325 2.894859335 1.002291597 1.330227114 0.39626527 0.12689735 0.239852737 4.736061616 0.118478225 0.031388145 10.01044365 -1.000453325 0.327935516 DAEDDGEEEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DAEDDGEEEDD 11 0 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;; 275.21 8.89E-27 682404400 1486890 1295962 1540099 1320696 1890219 2180944 1860966 1513219 1580959 1208112 FALSE TRUE 1545593.565 1518533.392 1580235.245 1581925.727 1568920.25 1674452.809 1715098.622 1492936.774 1524060.594 1444818.416 1.069749353 1.051020236 1.093725847 1.094895877 1.085894416 1.158936507 1.187068633 1.033304087 1.05484577 1 20.46245676 1.604984699 25 1.033044186 1.104598822 0.433965203 0.039960607 0.309383243 2657.39161 0.022132031 0.010945202 40.27028462 -1.604984699 0.071554636 DAEDVDLNHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAEDVDLNHYR 11 0 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;H7C118;C9J177;Q15435-2;Q15435-5;Q15435-4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 95.618 0.0036521 0 86785 164060 126070 159160 121210 177370 128250 127280 117550 224090 FALSE TRUE 90211.33881 192236.0288 129355.4878 190641.373 100606.7675 136178.5056 118197.4299 125574.0198 113319.3985 267996.145 0.336614315 0.717308933 0.482676673 0.711358639 0.375403786 0.508136061 0.44104153 0.468566515 0.422839659 1 18.03185272 -1.638603389 4.272380198 1.014271535 0.50054725 0.61180759 0.120391477 0.015399474 0.001302627 0.10968559 0.025633362 0.022982465 1.638603389 -0.513724285 DAEGILEDLQSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAEGILEDLQSYR 13 0 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8;E5RK61;E5RFS4;E5RHU5 E5RI16 FAM49B Protein FAM49B 0 ;;; 282.94 3.50E-32 198900000 314958 350097 382488 372499 451493 476396 431613 361628 383185 322466 FALSE TRUE 327392.785 410223.4364 392455.9515 446178.1904 374748.3811 365760.2489 397782.0452 356780.9682 369394.2467 385647.0387 0.848944118 1.063727697 1.017655815 1.156959981 0.971739294 0.948432665 1.031466614 0.925148989 0.957855784 1 18.55692151 3.049690585 24.99997103 0.968446668 1.029496575 0.08774698 0.075837079 226.6080161 114007.8348 0.021475945 0.025668661 1121.219352 -3.049690585 0.061049908 DAEGLQELALAPCHEWLSDEDLVPVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAEGLQELALAPCHEWLSDEDLVPVLAR 28 0 X6RJB2;X6RGT4;X6RHD7;A0A0C4DFV0;Q9H469 X6RJB2 FBXL15 F-box/LRR-repeat protein 15 0 179.28 1.60E-17 27572000 26872 28499 30445 26953 32284 42745 30580 32627 29594 29511 FALSE TRUE 27932.92731 33393.48156 31238.42171 32284.22295 26796.37721 32818.12156 28183.05969 32189.68843 28528.91772 35293.11543 0.791455415 0.946175512 0.885113749 0.914745626 0.759252248 0.929873182 0.7985427 0.912067071 0.808342289 1 15.10709917 -1.98990899 6.467586398 1.115928068 0.865273484 0.301093095 0.063350451 0.044742628 6.98E-05 0.025916417 0.012992484 0.010235075 1.98990899 -0.250654584 DAEILRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAEILRK 7 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;; 100.19 0.015998 631090000 898780 864600 968980 674050 1110810 1129460 932880 894990 1018250 848350 FALSE TRUE 934264.5284 1013088.324 994232.4148 807375.0782 921994.913 867160.0321 859758.428 882994.123 981603.3814 1014567.94 0.920849646 0.99854163 0.979956468 0.795782171 0.908756207 0.854708687 0.847413361 0.87031542 0.967508772 1 19.95243405 3.785740764 24.99091964 0.882454847 0.969658544 0.239583883 0.058925941 466.158461 246918.5945 0.014197842 0.025595444 6105.77455 -3.785740764 0.087203698 DAELAWIDGVLDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAELAWIDGVLDMR 14 0 Q9P2I0;H0YJF4 Q9P2I0 CPSF2 Cleavage and polyadenylation specificity factor subunit 2 0 96.229 0.0080358 10788000 13254 16429 16541 16189 19569 24177 20269 18234 16059 15838 FALSE TRUE 13777.27815 19250.55295 16972.07205 19391.13588 16242.66837 18562.25816 18680.26282 17989.60305 15481.03973 18941.15286 0.727372735 1.016334808 0.896042188 1.023756897 0.85753325 0.979996217 0.986226285 0.949762836 0.817322992 1 14.20923652 4.750231848 24.41233243 0.946823572 0.727372551 0.500126459 0.066001391 1009.753759 2112014.022 0.014514471 0.230110529 56264.16109 -4.750231848 -0.219451021 DAELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAELLR 6 0 A0A087WYM3 A0A087WYM3 SIRT2 0 ; 120.86 0.046304 221310000 334760 400840 378290 365610 394570 473400 421980 372540 355840 338620 FALSE TRUE 347976.5833 469681.1519 388148.5482 437926.5668 327501.1323 363460.0244 388904.105 367546.7107 343033.3879 404966.1057 0.859273352 1.159803611 0.958471691 1.081390666 0.808712452 0.897507271 0.96033742 0.907598699 0.84706691 1 18.62744164 3.248936066 24.99942677 0.903212648 1.021078084 0.275158925 0.088174942 251.2249691 605317.6175 0.022721097 0.030432019 1773.928315 -3.248936066 0.117865436 DAELQDQEFGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAELQDQEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 126.83 0.00044976 514540000 445820 317710 434880 317870 558700 507970 517680 378060 457480 240180 FALSE TRUE 463421.3178 372274.2211 446213.3301 380743.7373 463732.3736 390001.6659 477102.8889 372992.7241 441015.3842 287238.6725 1.61336673 1.296044916 1.553458405 1.325530904 1.614449648 1.357761692 1.660998099 1.29854633 1.535362145 1 18.13189047 -2.60711582 0.546168058 3.32E-15 1.466182636 0.521084452 0.135506238 161.5041908 8.344431838 191.5989596 0.051573337 0.002471065 2.60711582 1.466182636 DAELQDQEFGKRDS(ph)LGTYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAELQDQEFGKRDSLGTYSSR 21 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAELQDQEFGKRDS(1)LGTYSSR;DAELQDQEFGKRDS(0.999)LGT(0.001)YSSR;DAELQDQEFGKRDS(0.971)LGT(0.02)YS(0.003)S(0.005)R;DAELQDQEFGKRDS(0.995)LGT(0.001)YS(0.002)S(0.002)R 247.78 1.04E-30 2852220000 2022040 1343239 1770940 1089694 2510680 2324460 1823620 1656240 1955169 1411776 TRUE FALSE 2101871.701 1573929.849 1817092.151 1305232.221 2083915.51 1784639.393 1680679.899 1634040.812 1884802.85 1688386.477 1.24489963 0.932209462 1.076229984 0.773064839 1.234264511 1.057008817 0.995435537 0.96781207 1.116333775 1 20.68721375 2.14725926 0.006456032 6.40E-08 2.054223588 0.01219055 0.132906324 25112.52564 105.6801326 16660.28095 16955.84319 140.365139 -2.14725926 2.054223524 DAEPPS(ph)PTPAGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAEPPSPTPAGPPR 14 0 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 DAEPPS(0.978)PT(0.022)PAGPPR 130.2 6.66E-05 277610000 51819 64971 61404 73529 67934 102320 75419 60580 65221 61747 TRUE FALSE 53864.85413 76129.26385 63004.23868 88072.81674 56386.60295 78557.73067 69507.46171 59768.02419 62873.70895 73845.14243 0.72942989 1.030931234 0.853194084 1.192669062 0.76357904 1.063817173 0.941259769 0.809369746 0.85142647 1 16.1722154 -0.465632841 7.060239607 1.000002328 0.917959278 0.032693529 0.137780618 0 0 0.123519882 0.029113915 0.342268679 0.465632841 -0.082043049 DAEQSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAEQSGSPR 9 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 DAEQS(0.014)GS(0.986)PR;DAEQS(0.008)GS(0.992)PR;DAEQS(0.002)GS(0.998)PR;DAEQS(0.04)GS(0.96)PR 141.39 0.00011207 345706000 398611 419131 491679 413437 520100 553043 530604 454397 476879 463435 TRUE FALSE 414348.4701 491113.4889 504492.5587 495213.6046 431693.5878 424607.1447 489013.872 448306.5515 459716.2179 554236.2153 0.747602662 0.886108622 0.910248275 0.893506399 0.778898195 0.766112233 0.882320315 0.808872714 0.829459002 1 19.08014146 -2.006811125 6.274486553 1.181145306 0.835831145 0.451391415 0.054961009 0.038014938 4.13E-05 0.014525575 0.012679627 0.009844391 2.006811125 -0.34531416 DAESIHQYLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DAESIHQYLLQR 12 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;;;; 267.75 6.67E-22 3088921000 1480252 2564906 2609201 2730413 3097180 3422940 2513706 2599749 2513645 2897690 FALSE TRUE 1538693.492 3005408.653 2677198.922 3270480.542 2570722.45 2628014.06 2316675.155 2564903.617 2423179.407 3465436.876 0.444011404 0.867252459 0.772542977 0.943742639 0.741817711 0.758350002 0.668508831 0.740138606 0.699242114 1 21.72460581 -2.54513375 2.064313233 4.394909687 0.745656543 0.285268557 0.12411637 6480459.146 365642.5496 103066208.8 0.029297021 0.00285014 2.54513375 -3.649253144 DAEVERDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAEVERDEER 10 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 ; 183.33 1.53E-06 607000000 484110 481040 547400 480650 746300 686280 658960 511220 556240 459120 FALSE TRUE 503223.0366 563654.878 561665.6937 575721.1354 619444.1926 526901.8707 607308.9933 504367.9321 536221.0311 549075.7736 0.916491058 1.026552081 1.022929294 1.048527659 1.128157938 0.959615951 1.1060568 0.91857619 0.9765884 1 19.06664573 -1.028388418 7.191164179 0.999999999 1.012549853 0.002372978 0.067720412 1.86E-09 1.33E-10 0.064191093 0.015129984 0.093672386 1.028388418 0.012549854 DAEVIVDWRPLDDALDSSSILYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAEVIVDWRPLDDALDSSSILYAR 24 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5;F8WDJ1;F8WF35 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 90.534 0.0087779 103154000 30937 31169 38096 35859 44477 51705 43870 43549 39937 33251 FALSE TRUE 32158.41665 36522.03329 39088.81306 42951.80317 36916.81543 39697.29735 40431.35477 42965.29689 38499.67517 39765.89682 0.808693358 0.918425993 0.982973256 1.080116547 0.928353649 0.998274917 1.016734388 1.080455876 0.968158102 1 15.27924409 4.557534224 1.756209476 1.015102481 0.779313805 0.670072151 0.04378977 0.358633038 1.466742267 0.011893473 0.125428703 36102.24623 -4.557534224 -0.235788677 DAFADAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAFADAVQR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 88.136 0.030216 257090000 377850 421170 480620 428900 507280 547920 468040 446820 458250 459470 FALSE TRUE 392767.8098 493502.6713 493145.352 513735.1399 421052.7268 420673.8838 431353.8018 440831.1088 441757.672 549494.3494 0.714780434 0.898103269 0.897452999 0.934923426 0.76625488 0.765565441 0.785001342 0.802248666 0.803934877 1 19.06774512 4.758314667 23.12075143 0.838463971 0.714780109 0.207494755 0.076370989 2752.706867 3221706.479 0.018505803 0.624291771 57321.11991 -4.758314667 -0.123683862 DAFDRNPELQNLLLDDFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAFDRNPELQNLLLDDFFK 19 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 211.43 1.18E-16 913732000 1632263 949876 1360223 1114665 1920643 1764535 2001831 1309120 1588844 729734 FALSE TRUE 1696706.004 1113009.814 1395671.529 1335142.41 1594172.789 1354748.488 1844922.255 1291573.388 1531661.815 872711.4057 1.944177643 1.275346932 1.599236036 1.529878493 1.826689532 1.552344199 2.114011852 1.479954747 1.755061072 1 19.73514513 -1.282377254 5.541352558 0.999929981 1.663458371 0.433085845 0.231399165 0.000185928 2.41E-05 0.208114773 0.049047986 0.05219426 1.282377254 0.663528389 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAFEHIVTQFSSVPVSVVSDSYDIYNACEK 30 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 270.21 2.83E-60 232400000 95984 66351 88060 76340 104080 109910 106310 87941 98184 59961 FALSE TRUE 99773.52244 77746.26811 90354.91594 91439.82415 86388.51878 84385.0682 97977.14441 86762.29474 94650.37702 71709.20993 1.391362735 1.084188045 1.260018288 1.275147561 1.204706046 1.176767507 1.366311866 1.209918431 1.319919396 1 16.1298708 -1.336634586 4.424497998 0.999711609 1.248336415 0.432919714 0.087063487 0.000225143 3.38E-05 0.076629532 0.018040962 0.046064399 1.336634586 0.248624806 DAGGPRPES(ph)PVPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAGGPRPESPVPAGR 15 1 Q9BVG9;E9PS47;E9PLE4 Q9BVG9 PTDSS2 Phosphatidylserine synthase 2 1 DAGGPRPES(1)PVPAGR 133.24 2.58E-05 398530000 221730 254990 209050 314410 263820 398450 272430 248490 225970 285580 TRUE FALSE 230484.0716 298782.549 214498.0147 376599.3596 218975.9706 305916.0261 251076.2247 245159.398 217837.3838 341533.9332 0.674849698 0.874825368 0.628043055 1.102670402 0.641154361 0.895711952 0.735142837 0.717818565 0.637820616 1 18.3816694 DAGHPLYPFNDPY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DAGHPLYPFNDPY 13 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;; 117.25 0.0012125 762760000 967990 1091590 1125500 1012970 1291680 1378660 1189880 1154950 1137090 1072110 FALSE TRUE 1006206.993 1279062.091 1154831.455 1213332.443 1072120.695 1058487.109 1096614.096 1139469.784 1096166.353 1282169.428 0.784769135 0.997576501 0.900685533 0.946312099 0.836177085 0.825543868 0.855280178 0.888704534 0.85493097 1 20.29015548 4.845744152 19.53180246 0.892030303 0.784669531 0.240223715 0.060080699 78929.83279 14348942.95 0.014098021 900.2460495 70104.21842 -4.845744152 -0.107360771 DAGLLVEQPPLAGVAAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAGLLVEQPPLAGVAASPR 19 0 Q13469-3;Q13469-4;Q13469-2;Q13469 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 DAGLLVEQPPLAGVAAS(1)PR;DAGLLVEQPPLAGVAAS(1)PR;DAGLLVEQPPLAGVAAS(1)PR;DAGLLVEQPPLAGVAAS(1)PR 214.14 2.16E-18 495147000 400187 385871 416206 472156 512140 634120 582820 529560 508640 541280 TRUE FALSE 415986.6918 452141.3426 427052.6703 565547.0476 425086.6257 486855.2402 537137.0455 522462.1144 490334.1458 647333.4526 0.64261578 0.698467445 0.659710492 0.873656452 0.656673348 0.752093435 0.829768712 0.807098895 0.757467645 1 19.30414954 -4.999999998 0.080687607 1.845170208 0.492898753 0.651317294 0.063425433 148.5163971 0.847927633 22.25674025 2.042312051 1.00E-05 4.999999998 -1.352271456 DAGNFDQNKLEEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAGNFDQNKLEEEMR 15 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 189.59 2.29E-07 206930000 150080 92193 138470 107620 171560 176540 187480 149520 137130 75642 FALSE TRUE 156005.2743 108026.4306 142078.642 128906.9148 142398.2925 135541.2605 172784.8277 147515.929 132194.7181 90462.60165 1.724527832 1.194155691 1.570578774 1.424974657 1.574112284 1.498312651 1.910013913 1.630684131 1.461318995 1 16.46503387 3.223614475 22.76989435 1.575607801 1.464817559 0 0.248737628 295.5277507 450223.1218 0.068146592 0.081864964 1673.456681 -3.223614475 -0.110790242 DAGRPGERGS(ph)GGLFSPSTAHVPDGALGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.987)GGLFS(0.013)PSTAHVPDGALGQR;DAGRPGERGS(0.944)GGLFS(0.051)PS(0.002)T(0.003)AHVPDGALGQR 139.31 6.10E-08 4281800000 409280 807070 814000 688890 1018190 1130370 735690 874120 806830 992300 TRUE FALSE 425438.6904 945677.9944 835213.5087 825150.3859 845118.4275 867858.6984 678024.6954 862403.8512 777792.3459 1186722.186 0.358498978 0.796882375 0.70379868 0.695318917 0.712145132 0.731307385 0.571342394 0.726710818 0.655412324 1 20.17855081 -5 0.343056527 4.619065307 0.65983648 0.439371915 0.115071953 367.9934452 3.074285673 976.8315272 0.083935297 1.00E-05 5 -3.959228827 DAGRPGERGSGGLFS(ph)PSTAHVPDGALGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAGRPGERGSGGLFSPSTAHVPDGALGQR 29 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DAGRPGERGS(0.351)GGLFS(0.649)PSTAHVPDGALGQR 165.48 2.46E-12 2743400000 408970 768970 761380 720490 835590 917620 544310 767260 827290 822450 TRUE FALSE 425116.4514 901034.6157 781222.1883 863000.7716 693556.7103 704516.6617 501645.5599 756976.1347 797515.9945 983593.3307 0.432207538 0.916064178 0.794253238 0.877395916 0.705125471 0.716268238 0.510013177 0.769602753 0.810818831 1 19.90770243 0.902831029 2.36230613 0.998777758 0.721396378 0.277478943 0.140698249 0.552196181 6.543464939 0.130756911 0.035435811 7.99523124 -0.902831029 -0.277381381 DAGTIAGLNVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 168.29 0.00010917 1228650000 711290 786180 870270 678390 973140 1076380 793250 839110 871220 892430 FALSE TRUE 739372.2784 921200.2994 892949.9511 812573.5172 807726.0104 826407.0577 731072.9922 827863.103 839864.9624 1067284.572 0.692760205 0.863125284 0.836655916 0.761346635 0.756804728 0.774308071 0.684984128 0.775672323 0.786917552 1 20.02551347 0.644350541 2.981065987 0.99999424 0.769712549 0.64243471 0.05157305 2.929849023 23.81533025 0.050065799 0.013096475 4.409106008 -0.644350541 -0.230281691 DAHNALLDIQSSGR ddPTM_MDA-MB-175_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 ;; 178.47 2.04E-07 940440000 806580 1567490 1296940 1367830 1138210 1697840 1169040 1311970 1195600 1668270 FALSE TRUE 838424.4012 1836694.214 1330739.322 1638382.691 944737.4708 1303542.391 1077407.59 1294385.188 1152570.59 1995135.566 0.420234302 0.920586173 0.66699193 0.821188655 0.47352044 0.65336031 0.540017234 0.648770545 0.577690363 1 20.92805535 -1.843574835 5.63145908 1.047012807 0.642629988 0.369815677 0.142370503 0.064760422 0.001798851 0.106232352 0.030346552 0.014335907 1.843574835 -0.404382819 DAIAQAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAIAQAVR 8 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 98.457 0.019632 0 125950 119240 121660 118260 249720 160180 127540 109380 108640 180290 FALSE TRUE 130922.6033 139718.5424 124830.5595 141651.475 207272.6836 122980.6226 117543.0815 107913.94 104730.0676 215614.3736 0.607207215 0.648001987 0.578952866 0.656966753 0.961311995 0.570373025 0.545154201 0.500495112 0.485728599 1 17.71809383 DAIHFYNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAIHFYNK 8 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 86.794 0.015781 153520000 285420 219720 253670 235440 391660 324410 330780 266170 273770 265720 FALSE TRUE 296688.602 257455.2008 260280.8486 282009.3293 325085.7731 249070.694 304852.5993 262602.4265 263917.0712 317782.7465 0.933620863 0.810161041 0.819052801 0.88742807 1.022981193 0.783776642 0.959311362 0.826358351 0.83049528 1 18.27768127 -2.39191146 2.276336797 1.986648717 0.873550543 0.211277851 0.072535449 4691185.272 602357.0799 23905592.61 0.01663864 0.004055912 2.39191146 -1.113098173 DAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADR 37 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 ; 297.73 2.00E-92 1125300000 261544 362944 401180 350257 427750 452610 373500 384343 385410 333122 FALSE TRUE 271869.9591 425276.8087 411635.0804 419536.7892 355041.2078 347498.1869 344224.094 379191.5107 371539.1694 398390.8779 0.682420141 1.067486311 1.033244241 1.053078302 0.891188096 0.872254377 0.864036084 0.951807714 0.93259959 1 18.60382509 DAILDALENLTAEELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAILDALENLTAEELKK 17 1 H3BP42;Q9ULZ3-3;Q9ULZ3-2;Q9ULZ3 H3BP42 PYCARD Apoptosis-associated speck-like protein containing a CARD 0 247.78 1.40E-20 171880000 408210 183600 313710 216810 474230 378890 448660 313250 353070 174650 FALSE TRUE 424326.446 215131.8718 321885.5403 259694.3709 393620.554 290898.5396 413492.8568 309051.3961 340363.0797 208869.3236 2.031540289 1.029983092 1.54108576 1.243334188 1.884530228 1.39272984 1.979672504 1.479639953 1.629550351 1 17.6722411 -0.762711843 5.81646436 0.999999964 1.566568621 0.245609473 0.303768032 1.32E-07 2.75E-08 0.268466797 0.063278227 0.172698338 0.762711843 0.566568657 DAKLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 75.109 0.071644 499810000 649720 363820 487950 220500 895560 601860 377980 455520 622010 416970 FALSE TRUE 675371.4473 426303.2549 500666.3779 264114.2419 743333.0311 462087.1363 348352.9399 449414.4995 599623.9816 498667.2881 1.354352819 0.854885141 1.004008865 0.529640199 1.490639247 0.926644172 0.698567859 0.901231162 1.20245301 1 18.92771804 2.513719811 24.9976359 0.914645174 1.025319753 0.024456676 0.271472551 2367.37005 1616964.101 0.08659933 0.081622365 326.3771988 -2.513719811 0.110674579 DALDGPAAEAEPEHSFDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 235.7 1.51E-29 1841120000 600318 656025 619649 638616 714799 841346 785850 625653 601942 467646 FALSE TRUE 624019.0182 768692.1906 635797.562 764932.3387 593297.7213 645956.1422 724253.0236 617267.1449 580278.225 559272.2801 1.115769618 1.374450725 1.1368301 1.367727967 1.060838776 1.154994026 1.294991812 1.103697013 1.037559424 1 19.0931913 1.48657301 3.362028317 1.023108964 1.215780821 0.388534845 0.099912679 0.220385361 5.021591161 0.067575185 0.024750473 30.66006065 -1.48657301 0.192671856 DALDGPAAEAEPEHSFDGLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 222.79 2.47E-25 1807360000 692824 697693 673907 538478 862118 885275 623963 683269 691803 645249 FALSE TRUE 720177.2265 817516.3455 691469.57 644987.3412 715575.4903 679683.2977 575055.1496 674110.8967 666905.1452 771673.1875 0.933267137 1.059407478 0.896065305 0.835829664 0.927303814 0.880791647 0.74520556 0.873570454 0.864232626 1 19.55763045 4.083438913 6.323549395 0.865078805 0.995003412 0.325697739 0.067554897 0.197232176 11.95981644 0.016087319 0.035396527 12118.22223 -4.083438913 0.129924607 DALFPAEGGAADCES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DALFPAEGGAADCESPR 17 0 Q8TF30 Q8TF30 WHAMM "WASP homolog-associated protein with actin, membranes and microtubules" 1 DALFPAEGGAADCES(1)PR 148.15 2.27E-06 0 85354 60464 73580 60055 80394 105370 73609 66834 65785 54493 TRUE FALSE 88723.84183 70848.22166 75497.55525 71933.69975 66728.6566 80899.4144 67839.33424 65938.19955 63417.4107 65169.86002 1.361424465 1.087131714 1.158473491 1.103787851 1.02391898 1.241362409 1.040961792 1.011789799 0.973109512 1 15.99191728 8 0.381665657 1.027535966 4.928529353 0.559147545 0.077169117 54.98475694 0.750735882 0.057659592 158.8212191 100000000 -8 3.900993388 DALGDSLQVPVS(ph)PSSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 DALGDSLQVPVS(0.995)PS(0.002)STT(0.001)S(0.001)S(0.001)R;DALGDSLQVPVS(0.98)PS(0.018)S(0.002)TTSSR 249.14 2.44E-30 477210000 312290 341140 386310 326550 398760 489310 430800 394880 408210 416190 TRUE FALSE 324619.4503 399728.1413 396377.556 391140.6153 330978.9176 375675.1681 397032.7703 389587.2795 393518.6018 497734.4621 0.652194041 0.803095168 0.796363495 0.78584194 0.664970869 0.754770257 0.797679889 0.782721128 0.790619561 1 18.92501675 -0.565943608 0.432072634 1.060933765 0.745581086 0.693341631 0.049465661 5.280085413 0.873377794 0.50638139 0.029248566 0.271679201 0.565943608 -0.315352679 DALQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DALQPGR 7 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 130.77 0.0082156 410540000 369950 405350 434110 442870 484200 554740 470750 414050 429460 402000 FALSE TRUE 384555.9117 474965.7093 445423.2632 530468.3642 401895.857 425910.0422 433851.3849 408500.337 414003.8185 480764.2032 0.799884661 0.987939006 0.926490076 1.103385736 0.835952124 0.885902152 0.902420317 0.849689586 0.861136948 1 18.87496995 DALSDLALHFLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DALSDLALHFLNK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 248.32 2.22E-17 3939700000 2239790 1818300 2464730 1814060 3293100 2948380 3000490 2395750 2532040 1565430 FALSE TRUE 2328218.639 2130578.881 2528962.889 2172875.654 2733340.038 2263663.428 2765303.753 2363638.89 2440912.375 1872146.037 1.243609523 1.138040964 1.350836334 1.160633632 1.460003646 1.209127592 1.477076948 1.262529121 1.303804472 1 20.83626155 4.239309049 24.99999163 1.295791277 1.190825245 0.05001348 0.135230834 43.32401184 1446899.428 0.029964661 0.072869261 17350.38233 -4.239309049 -0.104966033 DALSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DALSEER 7 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 0 100.82 0.022129 39982000 54246 109010 86755 91059 92108 113360 84027 94531 85883 119220 FALSE TRUE 56387.67397 127731.6195 89015.90657 109070.1984 76451.51506 87033.85799 77440.74418 93263.96657 82792.08761 142578.8764 0.395484067 0.895866364 0.624327452 0.76498147 0.536205061 0.610426034 0.543143179 0.654121907 0.580675691 1 17.12140073 -1.428977119 3.823625236 1.002421621 0.630486655 0.437819213 0.12796073 4063.47042 59845494.55 190526.1966 0.027485904 0.037241133 1.428977119 -0.371934965 DALYDVITVGAPAAHFQGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DALYDVITVGAPAAHFQGFK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 251.75 4.63E-36 566620000 785380 636420 809240 674820 1047290 970060 897970 839100 895370 723310 FALSE TRUE 816387.4088 745720.1843 830329.4592 808297.3819 869272.0199 744778.2664 827584.765 827853.237 863145.8086 865028.7459 0.943769109 0.862075611 0.959886551 0.934416788 1.004905356 0.860986724 0.956713599 0.957023961 0.997823266 1 19.72238855 1.471572095 1.845926758 1.000898019 0.929846084 0.300660421 0.040865371 0.405620131 2.636803596 0.03421878 0.011073914 29.61911616 -1.471572095 -0.071051935 DANQVHSTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DANQVHSTTR 10 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;;;; 144.17 3.27E-05 866319000 307193 623871 621023 639436 694848 812686 604863 670843 628722 634059 FALSE TRUE 319321.2168 731015.9912 637207.3696 765914.5323 576737.9852 623951.9929 557452.2575 661851.4469 606094.418 758290.7213 0.421106586 0.964031302 0.840320673 1.010053942 0.760576345 0.822840074 0.735143187 0.872820184 0.7992903 1 19.53239154 -4.999999989 0.02282501 2.058454952 2.00E-12 0.162164585 0.148353121 5770.439995 9.958720424 630.7336407 317.0594282 1.00E-05 4.999999989 -2.058454952 DANSSFFDNSSS(ph)PHLLDQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 DANSSFFDNS(0.008)S(0.061)S(0.931)PHLLDQLK 133.47 6.90E-06 80130000 90597 65699 76798 58009 90821 99927 92674 79881 83106 68666 TRUE FALSE 94173.83952 76982.29218 78799.41897 69483.00706 75383.27886 76720.46866 85409.96972 78810.32585 80115.03129 82119.78801 1.146786199 0.937439003 0.959566761 0.846117711 0.917967285 0.934250691 1.040065638 0.959699577 0.97558741 1 16.32544228 4.740967325 24.76252017 0.950862706 1.146786277 0.58997188 0.048627747 142.2087943 1463079.788 0.012272231 0.082771643 55076.62573 -4.740967325 0.195923571 DAPAPRPLPASEGHLQPPAQTSGPTGS(ph)PPCIQTSPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPR 38 1 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 DAPAPRPLPASEGHLQPPAQT(0.001)S(0.001)GPT(0.184)GS(0.809)PPCIQT(0.004)S(0.001)PDPR;DAPAPRPLPASEGHLQPPAQT(0.001)S(0.001)GPT(0.03)GS(0.968)PPCIQTSPDPR 141.65 2.79E-13 282520000 44672 74805 65964 65508 76164 91953 67192 75098 68350 77584 TRUE FALSE 46435.68505 87652.17685 67683.07603 78465.28688 63217.67049 70598.30931 61925.31547 74091.43415 65890.09685 92785.09936 0.500464895 0.944679452 0.729460619 0.845666895 0.681334297 0.760879816 0.667405822 0.798527292 0.71013662 1 16.50160552 -1.116755979 3.806370923 1.000109311 0.746530977 0.329414371 0.111658459 29744906.45 50460537.78 39906.35483 0.023955569 0.076426509 1.116755979 -0.253578335 DAPHSEGDMHLLSGPLS(ph)PNESFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAPHSEGDMHLLSGPLSPNESFLR 24 0 O95714;A0A0J9YXQ8 O95714 HERC2 E3 ubiquitin-protein ligase HERC2 1 DAPHSEGDMHLLSGPLS(1)PNESFLR 174.86 3.98E-12 57204000 13908 14696 17123 16073 18401 25427 18666 18772 15591 21932 TRUE FALSE 14457.09858 17219.92368 17569.23945 19252.19143 15273.20459 19521.9646 17202.91015 18520.39204 15029.88296 26229.15549 0.551184295 0.656518419 0.669836261 0.733999668 0.582298755 0.744284909 0.655869769 0.706099442 0.573021993 1 14.67888374 -2.214816094 2.441375888 2.137939405 0.659870327 0.728752476 0.063448649 3173487.09 736929.2518 19949275.55 0.014318539 0.006097951 2.214816094 -1.478069078 DAPKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAPKLR 6 1 Q9P2V4 Q9P2V4 LRIT1 "Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1" 0 67.055 0.091002 86960000 245280 198880 233250 227280 282400 313470 308010 261250 268780 190140 FALSE TRUE 254963.8438 233036.0929 239328.6866 272235.3056 234397.7489 240671.3432 283867.3714 257748.3711 259106.6603 227394.2925 1.121241175 1.024810651 1.052483261 1.197194981 1.030798734 1.058387792 1.248348708 1.133486545 1.139459823 1 17.79483652 DAPQDFHPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAPQDFHPDR 10 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 129.74 0.00029506 2883140000 1179680 2050420 1519830 1307990 2284850 2186240 1316030 1528940 1397280 2836720 FALSE TRUE 1226254.677 2402563.685 1559438.018 1566706.518 1896472.013 1678518.893 1212876.13 1508447.06 1346992.166 3392520.972 0.361458245 0.708194203 0.459669382 0.461811889 0.559015561 0.494770381 0.357514704 0.444638979 0.397047558 1 21.6939263 -1.477101244 3.422673363 1.008533349 0.473991489 0.723806957 0.097917181 216873114.9 294442775 17615559.59 0.023185073 0.033334869 1.477101244 -0.53454186 DAPT(ph)SPASVASSSSTPSSK ddPTM_MDA-MB-175_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(0.642)S(0.358)PASVASSSSTPSSK 118.31 0.00091434 200510000 135260 112840 133400 102240 164470 165160 157410 133750 145630 95424 TRUE FALSE 140600.1692 132219.3922 136876.5136 122462.7668 136513.4481 126804.093 145071.7929 131957.3 140388.8047 114120.5058 1.232032475 1.158594516 1.19940332 1.073100456 1.196221899 1.111142052 1.271215825 1.15629789 1.230180359 1 16.80019852 -1.920531503 2.618284005 0.889543904 1.178349919 0.483317865 0.05605877 8523661.367 3717807.205 5747976.662 0.012660774 0.01200794 1.920531503 0.288806015 DAPTS(ph)PASVASSSSTPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.029)S(0.971)PASVASSSSTPSSK;DAPTS(1)PASVASSSSTPSSK 400.26 5.31E-128 788240000 411850 303710 394560 313960 507260 511790 466140 399370 436790 279698 TRUE FALSE 428110.156 355869.83 404842.5577 376060.3509 421036.1264 392934.5288 429602.7288 394017.0984 421070.0132 334499.468 1.279853025 1.063887581 1.210293577 1.124247979 1.258704921 1.174694032 1.284315133 1.177930419 1.258806227 1 18.35164439 3.250317828 24.9932377 1.204970233 1.164930564 0.002633902 0.091033885 785.6077264 1670019.374 0.022816695 0.030632704 1779.581278 -3.250317828 -0.040039669 DAQHYGGWEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DAQHYGGWEHR 11 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 193.15 6.24E-07 4167116000 1037231 1191798 1174012 1253018 1365932 1469811 1173405 1101794 1074871 983658 FALSE TRUE 1078181.681 1396480.036 1204607.717 1500861.221 1133751.367 1128469.67 1081430.45 1087026.254 1036186.603 1176386.952 0.916519585 1.187092422 1.023989356 1.275822737 0.963757176 0.959267415 0.919281235 0.924038006 0.880821231 1 20.16593126 3.026401092 24.99640886 0.933113217 1.103808458 0.417317079 0.092811293 190.8096212 180656.1821 0.024933459 0.029800481 1062.676538 -3.026401092 0.170695241 DAQIGWIQTVEDLHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DAQIGWIQTVEDLHER 16 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ;;;;; 239.18 8.12E-20 631671000 665037 699183 801473 841132 823741 956032 824727 782168 804234 659065 FALSE TRUE 691293.1743 819262.2414 822360.0448 1007505.399 683721.7991 734008.0568 760082.7427 771684.3173 775289.7754 788196.1682 0.877057263 1.039414139 1.043344383 1.27824194 0.867451311 0.931250476 0.964331943 0.97905109 0.983625405 1 19.58819521 DAQIGWIQTVEDLHERVPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAQIGWIQTVEDLHERVPEK 20 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 106.73 0.00014241 40973000 33775 28238 38729 27177 53676 45537 31512 34645 42925 31026 FALSE TRUE 35108.46308 33087.65684 39738.30956 32552.52948 44552.17269 34961.72187 29042.0071 34180.64044 41380.13763 37104.95067 0.946193498 0.891731595 1.070970553 0.877309601 1.200706965 0.942238737 0.782698981 0.921188139 1.115218775 1 15.17932407 4.288766714 0.002109979 1.924143108 4.46E-05 0.001576912 0.117676177 2561645.827 979.5730553 440772.9726 452549.742 19443.15389 -4.288766714 -1.924098497 DAQRLS(ph)PIPEEVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAQRLSPIPEEVPK 14 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK;DAQRLS(1)PIPEEVPK 182.98 8.85E-07 4039640000 7766770 4249440 6121550 5169960 7532140 8101470 8953850 6392910 6488140 3269930 TRUE FALSE 8073408.077 4979248.264 6281082.622 6192562.657 6251829.533 6220026.371 8252023.84 6307223.498 6254633.109 3910610.177 2.064488075 1.273266329 1.606164342 1.583528497 1.598683901 1.590551369 2.110162728 1.612848945 1.599400816 1 21.8989623 DARPS(ph)SPADVASNSSHGYPNDTVSLASSIATQPELITVHIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DARPSSPADVASNSSHGYPNDTVSLASSIATQPELITVHIVK 42 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 DARPS(0.441)S(0.441)PADVAS(0.023)NS(0.023)S(0.023)HGY(0.021)PNDT(0.023)VS(0.005)LASSIATQPELITVHIVK;DARPS(0.378)S(0.378)PADVAS(0.075)NS(0.075)S(0.075)HGY(0.003)PNDT(0.003)VS(0.003)LAS(0.003)S(0.003)IAT(0.003)QPELITVHIVK 85.751 0.00013131 159750000 54804 89244 98684 95684 100581 136991 107116 103163 96130 96366 TRUE FALSE 56967.70424 104570.9628 101255.7861 114610.0096 83484.27755 105176.9164 98719.96802 101780.2687 92670.30008 115247.0727 0.494309338 0.907363288 0.878597467 0.994472198 0.72439391 0.912621153 0.856594148 0.883148408 0.804101119 1 16.81437058 4.741132149 24.92810012 0.879021241 0.494309196 0.695344988 0.077420823 118.1695119 1145451.899 0.016938893 0.115351924 55097.53239 -4.741132149 -0.384712044 DAS(ph)PESPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DASPESPSK 9 0 H0Y7Z6;A2A2S1;O95467 H0Y7Z6 GNAS Neuroendocrine secretory protein 55;LHAL tetrapeptide;GPIPIRRH peptide 1 DAS(0.999)PES(0.001)PSK;DAS(1)PESPSK 155.97 0.0013025 0 918180 526270 684060 577660 1166510 1162510 958090 716840 713690 573640 TRUE FALSE 954430.4554 616652.7787 701887.1656 691919.4239 968227.0469 892534.6705 882992.4023 707231.9323 688004.4363 686033.775 1.391229543 0.898866501 1.023108761 1.008579241 1.411340202 1.301006894 1.287097566 1.030899583 1.002872543 1 19.38792008 1.601021343 6.998205814 1.007148775 1.177050327 0.202910183 0.160576619 0.227845028 24.25408243 0.091378671 0.043867018 39.90445129 -1.601021343 0.169901552 DAS(ph)PSKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DASPSKEER 9 1 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DAS(0.997)PS(0.003)KEER;DAS(0.899)PS(0.101)KEER;DAS(0.724)PS(0.276)KEER;DAS(0.845)PS(0.155)KEER 145.09 5.94E-05 4041750000 5408900 2624840 3636000 2455840 5190000 5548000 5054490 3815750 4148180 2134660 TRUE FALSE 5622447.549 3075635.852 3730757.147 2941597.822 4307805.654 4259561.081 4658305.866 3764606.113 3998887.812 2552905.756 2.202371762 1.204758869 1.461376762 1.152254765 1.687412723 1.668514817 1.824707338 1.474635757 1.566406359 1 21.28370885 0.158161725 1.759179607 0.999919726 1.56630701 0.270272565 0.286016757 27.7465774 55.63215198 0.264948394 0.073563735 1.439334466 -0.158161725 0.566387284 DAS(ph)SPVPPPHVPPPVPPLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DASSPVPPPHVPPPVPPLRPR 21 1 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875;O94875-6 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 DAS(0.526)S(0.474)PVPPPHVPPPVPPLRPR 47.728 0.094898 477790000 65281 62035 70490 70339 78260 95355 79675 72860 72724 61795 TRUE FALSE 67858.34429 72689.02868 72327.02731 84251.84426 64957.39315 73210.24637 73429.86531 71883.43087 70106.67745 73902.54711 0.918213877 0.983579478 0.978681116 1.14003979 0.87896014 0.990632248 0.993603985 0.972678665 0.948636822 1 16.17333647 DASDDLDDLNFFNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 370.98 3.26E-97 301052000 396986 294862 382928 297610 474403 479639 485082 361668 418374 246820 FALSE TRUE 412659.3138 345502.2548 392907.4183 356476.3697 393764.1475 368250.1112 447060.0053 356820.432 403316.8015 295179.6533 1.397993761 1.170481268 1.331078934 1.207659016 1.333981333 1.247545714 1.514535302 1.208824619 1.366343503 1 18.17123375 -1.049563478 4.469978737 0.999982881 1.303331698 0.465742865 0.099042328 1.53E-05 3.26E-06 0.087032315 0.020512556 0.089214721 1.049563478 0.303348817 DASDDLDDLNFFNQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DASDDLDDLNFFNQKK 16 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 146 1.87E-06 168560000 154490 100080 122050 76515 174560 165770 114290 112860 146480 99577 FALSE TRUE 160589.3845 117267.9615 125230.7233 91649.43863 144888.3536 127272.4298 105331.6512 111347.2963 141208.2134 119087.2066 1.348502405 0.984723421 1.051588385 0.769599365 1.216657588 1.068733018 0.884491745 0.935006366 1.185754687 1 16.86165891 4.740350328 23.8899319 1.001779274 1.348502627 0.390116692 0.126253698 84.60650105 1129189.116 0.029351089 0.188529001 54998.43447 -4.740350328 0.346723352 DASIVGFFDDSFSEAHSEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DASIVGFFDDSFSEAHSEFLK 21 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;; 385.41 4.98E-131 2099017900 1589536.5 1474675.7 1697064.8 1780287.5 2099923 2288561 2456725 1850216.1 1779034.6 1071240.2 FALSE TRUE 1652292.628 1727939.78 1741291.703 2132423.054 1742978.839 1757077.391 2264160.475 1825416.98 1715007.492 1281129.207 1.289715838 1.348763084 1.359185079 1.664487112 1.360501992 1.371506778 1.767316257 1.424850023 1.338668639 1 20.28898455 0.852516271 2.756835457 1.000567946 1.456930858 0.468193734 0.143556209 0.513672632 7.309882332 0.138393818 0.036631943 7.120594766 -0.852516271 0.456362913 DASNWSTDKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DASNWSTDKLK 11 1 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 116.24 0.00092641 476210000 903410 446190 577260 358570 1075700 845110 648530 509060 734330 531610 FALSE TRUE 939077.3244 522819.6616 592303.8698 429494.0758 892852.8982 648846.0103 597696.524 502236.8834 707901.6067 635768.8012 1.47707362 0.822342431 0.931634061 0.675550727 1.404367274 1.020569127 0.94011616 0.789967803 1.113457605 1 19.2781427 4.747904384 24.44011363 0.956212662 1.477073998 0.395778163 0.188896947 936.3452811 2449089.275 0.044932851 0.559279323 55963.4377 -4.747904384 0.520861337 DASSGKENRS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DASSGKENRSPSR 13 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 DASSGKENRS(0.994)PS(0.006)R;DAS(0.001)S(0.001)GKENRS(0.998)PS(0.001)R 68.257 0.02657 79610000 59523 47317 58288 38111.7 74395 69147 50342 55366 58813 44763 TRUE FALSE 61873.014 55443.32667 59807.03316 45650.08051 61749.36447 53088.65718 46396.0625 54623.90933 56696.33162 53533.45281 1.15578224 1.035676269 1.117189907 0.852739327 1.153472478 0.991691258 0.866674202 1.020369628 1.059082287 1 15.70815309 6.128863719 0.670890136 0.992722736 2.051369603 0.218216757 0.088365321 25.73018612 2.035313947 0.033114006 31.56821034 1345438.091 -6.128863719 1.058646867 DASSS(ph)PASTASSASSTSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DASSSPASTASSASSTSLK 19 0 Q04724;A0A669KBK8 Q04724 TLE1 Transducin-like enhancer protein 1 1 DASS(0.014)S(0.986)PASTASSASSTSLK;DAS(0.001)S(0.03)S(0.964)PAS(0.005)TASSASSTSLK 214.54 4.48E-19 1011980000 825470 592400 721870 564980 960860 916980 887810 741780 829660 586390 TRUE FALSE 858060.193 694140.0918 740682.5252 676731.3577 797533.3604 704025.292 818221.1323 731837.6524 799800.6987 701281.8934 1.2235596 0.989816076 1.056183729 0.964991916 1.137250752 1.003911977 1.166750689 1.043571293 1.140483886 1 19.41963495 2.273876693 24.99995916 1.088909132 1.057972092 0.019642613 0.082825252 745.2380708 527545.148 0.026750557 0.022380172 187.8783308 -2.273876693 -0.03093704 DASVPLIDVTNLPT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR 231.38 1.56E-14 103649000 69280 66123 55349 53484 64451 73537 56368 52216 53873 69158 TRUE FALSE 72015.2279 77479.11088 56791.44041 64062.97557 53495.64204 56459.14621 51949.72887 51516.12993 51934.12125 82708.18599 0.870714634 0.936776813 0.686648362 0.774566324 0.646799847 0.682630692 0.628108672 0.622866157 0.627919965 1 16.33574251 4.233273121 24.91543461 0.68706482 0.903745752 0.321621524 0.109774118 103.6705032 488520.1571 0.025299992 0.057340543 17110.91056 -4.233273121 0.216680932 DATNRS(ph)PTQIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DATNRSPTQIVK 12 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 DATNRS(0.998)PT(0.002)QIVK;DATNRS(0.98)PT(0.02)QIVK;DATNRS(0.998)PT(0.002)QIVK;DAT(0.001)NRS(0.998)PT(0.001)QIVK 189.32 4.89E-06 2942250000 2086490 1569610 1872400 1357920 2320500 2384490 2039700 1882890 2021130 1367110 TRUE FALSE 2168866.236 1839178.308 1921196.282 1626512.523 1926062.239 1830728.335 1879822.984 1857652.939 1948389.926 1634969.03 1.32654882 1.124901007 1.175065856 0.994827727 1.178042033 1.11973273 1.149760607 1.13620069 1.191698369 1 20.64083188 4.738594033 11.5487018 1.124797423 1.326741813 0.471843195 0.065637652 0.053244159 511.3370736 0.014370053 0.082924691 54776.46892 -4.738594033 0.201944389 DATNVGDEGGFAPNILENKEGLELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DATNVGDEGGFAPNILENKEGLELLK 26 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 230.88 4.41E-35 233550000 296440 208346 275160 148537 471250 322550 226543 238930 311540 241683 FALSE TRUE 308143.6801 244127.8048 282330.8956 177917.1753 391147.0933 247642.6508 208785.9677 235727.5342 300327.7363 289036.1565 1.066107728 0.844627218 0.976801308 0.615553353 1.353280842 0.856787793 0.722352422 0.815564174 1.039066323 1 18.14089045 DATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DATSLLAAGEGGLLDEVEPLRPDELER 27 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 ;;;; 268.31 9.03E-54 257915300 102128.8 112393.1 112453.3 116285 130185 152514 123920.5 127114.6 116556.4 107274.2 FALSE TRUE 106160.9239 131695.7406 115383.9254 139285.8259 108056.2002 117094.9349 114207.2874 125410.8367 112361.5579 128292.5256 0.827491106 1.026526994 0.89938151 1.085689328 0.84226419 0.912718292 0.890209986 0.977538139 0.875823104 1 16.9690776 -1.041325693 4.72584863 1.000001999 0.932185238 0.070874873 0.077434536 1.49E-06 3.02E-07 0.068368209 0.016114066 0.090923115 1.041325693 -0.06781676 DAVAHCHEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAVAHCHEAER 11 0 P49792;O14715;Q99666;J3KQ37;F8W705;Q99666-2;H0YBN8 P49792 RANBP2;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 0 138.45 3.31E-05 91884000 59906 68496 70368 70415 73214 84203 74106 68842 71301 56972 FALSE TRUE 62271.13514 80259.65518 72201.84789 84342.87683 60769.11043 64648.12936 68297.37808 67919.28559 68734.89094 68134.57261 0.913943285 1.177957858 1.059694735 1.237886635 0.891898314 0.948830042 1.002389469 0.996840268 1.008810774 1 16.05609941 3.222804844 24.99989884 0.976855541 1.100435774 0.333456317 0.084825172 265.1870443 420774.8885 0.023417736 0.028076964 1670.339857 -3.222804844 0.123580233 DAVDFDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAVDFDVR 8 0 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ; 103.83 0.010927 402370000 538760 547950 594040 615200 727010 789850 645240 601850 602000 557910 FALSE TRUE 560030.6608 642056.15 609521.1704 736884.7238 603433.0999 606419.3078 594664.4028 593783.1852 580334.1376 667221.7827 0.839347089 0.962282957 0.91352109 1.104407474 0.904396582 0.908872167 0.89125448 0.889933753 0.869776966 1 19.34780686 DAVDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DAVDFLR 7 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ;;; 134.06 0.0074714 744270000 1815380 1862890 1971650 1776570 2476600 2473480 2129720 2009430 2038480 2002620 FALSE TRUE 1887052.604 2182826.866 2023032.819 2127970.243 2055628.417 1899051.756 1962786.981 1982496.878 1965115.503 2394995.047 0.787915034 0.91141185 0.844691859 0.888507159 0.85830174 0.792925129 0.819536969 0.827766588 0.820509214 1 21.19159124 -1.028341025 6.140610717 1.000000173 0.840257119 0.629850149 0.037002252 8.69E-08 1.38E-08 0.035703142 0.008415302 0.093682608 1.028341025 -0.159743053 DAVDWVHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DAVDWVHYK 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;;;;; 129.38 0.00039083 8473280000 8260200 6513700 8190960 6459810 11591130 9944890 9402980 8186240 8743920 7354210 FALSE TRUE 8586319.074 7632377.305 8404423.147 7737541.137 9620873.863 7635340.014 8665949.857 8076516.843 8429228.027 8795126.645 0.976258719 0.86779618 0.955577274 0.879753237 1.093886905 0.868133038 0.985312686 0.918294548 0.958397573 1 23.06827292 DAVFDGSSCIS(ph)PTIVQQFGYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAVFDGSSCISPTIVQQFGYQR 22 0 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 DAVFDGSSCIS(1)PTIVQQFGYQR 217.93 7.87E-26 77692000 27008 31754 30452 37098 36876 51480 36142 29526 35430 46687 TRUE FALSE 28074.29669 37207.50249 31245.60414 44435.87367 30607.83069 39524.55019 33309.0956 29130.25226 34154.88122 55834.42377 0.502813404 0.666390015 0.559611831 0.795850851 0.548189246 0.707888566 0.596569166 0.521725672 0.611717269 1 15.76886725 -1.372068383 5.968003864 1.000069508 0.611371292 0.64921961 0.085490783 7.55E-05 7.94E-06 0.07900256 0.018617769 0.042455271 1.372068383 -0.388698216 DAVFIPAGWDNDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAVFIPAGWDNDKK 14 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 116.58 0.00056677 398460000 261720 114760 183680 104440 250210 212860 232760 186210 209660 104790 FALSE TRUE 272052.9077 134469.1373 188466.8517 125097.9203 207679.3936 163426.4909 214515.663 183714.1595 202114.3776 125321.5942 2.17083823 1.072992553 1.503865738 0.998215201 1.657171655 1.304056911 1.711721467 1.46594177 1.612765772 1 16.9352755 4.754725423 24.60395678 1.402233516 2.170838959 0.461656312 0.257400245 2271.436447 3457212.762 0.057391443 1.495148671 56849.33947 -4.754725423 0.768605444 DAVLLVFANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAVLLVFANK 10 0 P61204;F5H423;P61204-2;P84077;P84085;C9J1Z8 P61204;P84077;P84085 ARF3;ARF1;ARF5 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5 0 ; 169.12 1.10E-05 423390000 1259550 1073000 1317350 1239740 1374230 1718640 1702560 1378600 1505640 903700 FALSE TRUE 1309278.007 1257279.403 1351681.223 1484956.872 1140638.875 1319511.906 1569108.898 1360122.122 1451452.311 1080762.713 1.211438914 1.163326037 1.250673443 1.373989734 1.055401766 1.220908059 1.451853288 1.258483575 1.342988885 1 20.04361838 2.441611863 24.99934823 1.294054627 1.211439161 0.014389288 0.130250897 450.4399037 317116.7501 0.042711133 0.035734836 276.4469883 -2.441611863 -0.082615466 DAVLLVFANKQDLPNAMNAAEITDKLGLHSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAVLLVFANKQDLPNAMNAAEITDKLGLHSLR 32 2 P61204;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 105.21 3.36E-06 574030000 48290 30973 50586 19729 76476 64754 40042 44381 63007 53711 FALSE TRUE 50196.52649 36292.37181 51904.31272 23631.33731 63476.63684 49715.86486 36903.40341 43786.14529 60739.39038 64234.64209 0.781455689 0.564996871 0.808042374 0.367890854 0.988199432 0.773972785 0.574509365 0.681659364 0.945586188 1 15.97106394 1.199922775 5.102747666 0.987947177 0.687253491 0.333800908 0.158712116 0.207441268 12.17711775 0.136689491 0.036650319 15.84611395 -1.199922775 -0.300693686 DAVSGMGVIVHIIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAVSGMGVIVHIIEK 15 0 P49720 P49720 PSMB3 Proteasome subunit beta type-3 0 ; 143.38 4.42E-06 237610000 790640 488540 728130 744390 813620 918340 1222430 821240 921710 366230 FALSE TRUE 821855.0777 572442.9447 747105.666 891628.1202 675321.163 705069.4526 1126612.742 810232.6211 888537.8371 437985.7566 1.876442476 1.306989865 1.705776169 2.035746841 1.54187928 1.609799958 2.572258859 1.849906324 2.02869117 1 18.74052443 3.996873047 24.70510254 1.867543001 1.570382882 0.027087578 0.40489064 271.7928104 2147438.985 0.096665532 0.202529547 9928.257842 -3.996873047 -0.297160118 DAWAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DAWAIR 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;; 116 0.055721 670580000 696360 664600 729400 660990 962630 931100 832790 687430 732380 697690 FALSE TRUE 723852.8305 778739.8801 748408.7632 791731.8491 799002.4964 714866.136 767513.7437 678216.1253 706021.7869 834388.9974 0.867524419 0.933305548 0.896954257 0.948876186 0.957589924 0.85675403 0.919851228 0.81282966 0.846154239 1 19.67036061 2.723757875 24.72887112 0.87325658 0.921771501 0.061666673 0.053481343 1264.486132 2112398.452 0.016657427 0.015765215 529.3682319 -2.723757875 0.048514921 DAWEIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAWEIPR 7 0 J3QRU1;P07947;H0Y3C5;J3KPD6;P07948-2;P08631-3;P08631-2;P07948;P08631-4;P08631;P12931;P12931-2 J3QRU1;P12931 YES1;HCK;LYN;SRC Non-specific protein-tyrosine kinase;Tyrosine-protein kinase Yes;Tyrosine-protein kinase Lyn;Tyrosine-protein kinase HCK;Proto-oncogene tyrosine-protein kinase Src 0 81.784 0.061099 54334000 34651 47460 43327 49293 52534 57764 50936 49054 47485 51804 FALSE TRUE 36019.04824 55610.88581 44456.13721 59043.00828 43604.28944 44349.18642 46943.50322 48396.51137 45776.02413 61954.00195 0.581383722 0.897615716 0.717566837 0.95301363 0.703817156 0.715840543 0.75771543 0.781168445 0.738871141 1 15.91890986 -1.998424266 2.981901001 1.23031403 0.767175722 0.346916822 0.098115279 32688195.18 35550528.93 51712566.32 0.021543606 0.010036349 1.998424266 -0.463138307 DAWWAEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAWWAEIR 8 0 Q86YS7;Q86YS7-5;H0YGU7;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 0 100.45 0.014179 83824000 50610 52793 55567 46920 79033 73319 62170 57022 60770 67305 FALSE TRUE 52608.12188 61859.78708 57015.12167 56200.63596 65598.99889 56291.77341 57296.95295 56257.71336 58582.89957 80492.12612 0.65358097 0.768519731 0.708331664 0.69821284 0.814974111 0.699345093 0.711833017 0.698921945 0.727809071 1 16.29656004 0.924709392 20.77582042 1 0.720394266 0.802657314 0.041641769 3053.165551 842497.9042 0.037890204 0.009472551 8.408323116 -0.924709392 -0.279605734 DAYELEVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DAYELEVLLR 10 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;J3QRL2;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 0 120.99 0.0012259 7796900 14657 19884 15775 15428 20040 21174 17659 18293 16535 21923 FALSE TRUE 15235.66968 23298.92232 16186.10946 18479.61235 16633.60796 16256.6594 16274.84144 18047.81226 15939.90858 26218.39211 0.58110618 0.888648023 0.61735706 0.70483393 0.634425173 0.620047916 0.620741401 0.688364572 0.607966671 1 14.67829159 -1.507332299 4.967534267 1.001189193 0.666883567 0.594595132 0.083509998 0.001033884 0.000102538 0.076008604 0.017855 0.031093363 1.507332299 -0.334305626 DAYELQEVIGSGATAVVQAALCKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAYELQEVIGSGATAVVQAALCKPR 25 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 0 ; 144.4 2.77E-07 177997000 154035 140520 177056 153761 224542 221487 205770 192448 217959 142579 FALSE TRUE 160116.4207 164653.2169 181670.2248 184174.4669 186374.431 170050.0009 189641.2097 189868.5493 210114.6982 170514.6252 0.939018694 0.965625187 1.065423125 1.080109502 1.093011411 0.997275165 1.11216976 1.113503015 1.232238571 1 17.37953596 5.585059993 0.503038893 1.108775137 0.572979483 0.418576477 0.062809442 8.893536657 0.909395646 0.034347552 3.372404377 384644.9125 -5.585059993 -0.535795654 DAYREFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAYREFDR 8 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 135.63 0.00075276 672520000 580330 899140 1052900 927770 1246360 1335790 1036910 1171180 1074510 1080870 FALSE TRUE 603241.8765 1053560.301 1080339.439 1111280.137 1034504.172 1025573.017 955634.2847 1155482.248 1035838.595 1292645.782 0.46667222 0.815041766 0.835758298 0.859694243 0.800299809 0.793390603 0.739285501 0.893889311 0.801332128 1 20.30189556 4.738992923 5.032943773 0.83195288 0.448915804 0.734027318 0.066988708 0.078868571 6.35385879 0.014808347 0.105315484 54826.80301 -4.738992923 -0.383037076 DAYREFDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DAYREFDRK 9 2 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 88.681 0.0070979 749420000 365400 339000 403970 212596 519840 430830 239099 334260 396880 344990 FALSE TRUE 379826.2742 397220.6129 414497.7901 254646.8543 431477.7825 330776.2618 220357.7956 329779.7914 382596.3663 412584.1853 0.920603086 0.962762576 1.004638095 0.617199746 1.045793314 0.801718228 0.534091716 0.799303035 0.927317091 1 18.654329 2.500027855 24.76893907 0.773953067 0.904255132 0.064051917 0.157795689 1390.234357 1503262.106 0.05049092 0.047282774 316.2480489 -2.500027855 0.130302065 DAYSGGAVNLYHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DAYSGGAVNLYHVR 14 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;;; 199.31 2.08E-08 2334980000 1685200 2120000 2079970 1985310 2929550 2991450 2327560 2163150 2210190 2760900 FALSE TRUE 1751732.997 2484093.509 2134175.727 2377998.392 2431586.137 2296731.073 2145119.765 2134156.512 2130645.694 3301845.494 0.530531486 0.752334872 0.646358447 0.720202807 0.736432441 0.695590111 0.649672969 0.646352628 0.645289338 1 21.65484118 -1.741032207 2.85474642 1.059690854 0.672489027 0.731837246 0.060043852 22869583.29 20296587.43 9694400.642 0.013529814 0.01815381 1.741032207 -0.387201827 DCDHADEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 191.45 3.59E-05 1876800000 4607120 2312270 3366820 2679360 3981350 4328280 5322040 3572210 3842880 1616840 FALSE TRUE 4789012.655 2709384.386 3454562.095 3209329.411 3304601.549 3323102.566 4904884.598 3524330.368 3704575.499 1933628.842 2.47669695 1.401191546 1.786569387 1.659744281 1.709015442 1.718583471 2.536621554 1.82265091 1.915866902 1 20.88287947 DCDLQEDACYNCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCDLQEDACYNCGR 14 0 P62633-2;P62633;P62633-7;P62633-3 P62633-2 CNBP Cellular nucleic acid-binding protein 0 ; 352.83 3.59E-55 179680000 345360 292840 361470 340380 364610 415790 501720 360690 369210 205048 FALSE TRUE 358995.0795 343132.992 370890.2052 407706.1481 302633.7224 319229.0739 462393.8754 355855.5405 355922.2042 245223.2297 1.463952171 1.399267893 1.512459507 1.66259187 1.23411523 1.301789697 1.885603888 1.451149391 1.45142124 1 17.90373612 0.661434137 2.844813807 1.000041582 1.493894739 0.416193095 0.172686622 3.38530834 27.28327338 0.165619812 0.043544836 4.586000918 -0.661434137 0.493853157 DCDPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DCDPGSPR 8 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 1 DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR;DCDPGS(1)PR 163.38 0.00035269 5672990000 9301820 9637470 9682970 9268000 11040160 12921690 10758110 10248140 10210340 9013190 TRUE FALSE 9669063.036 11292630.5 9935316.153 11101182.74 9163557.547 9920823.328 9914861.227 10110780.45 9842871.858 10779152.01 0.897015185 1.04763626 0.921715933 1.02987533 0.850118593 0.920371409 0.919818295 0.937994049 0.913139721 1 23.36174035 3.249774471 24.99423872 0.921336818 0.975577144 0.174161436 0.053685811 339.08089 755763.6147 0.013633411 0.018292791 1777.35619 -3.249774471 0.054240325 DCDPGS(ph)PRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DCDPGSPRR 9 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 1 DCDPGS(1)PRR 60.434 0.044257 0 82261 105240 98157 90083 109020 127120 96725 101970 94267 95199 TRUE FALSE 85508.7278 123314.1513 100715.0521 107901.1485 90488.81934 97598.30652 89143.44176 100603.2589 90874.34908 113851.4214 0.751055426 1.083114729 0.884618311 0.947736508 0.79479745 0.857242759 0.782980491 0.88363639 0.798183703 1 16.79679278 3.251441221 24.97596528 0.845060308 0.926236294 0.089790813 0.095767435 423.1205052 820441.4469 0.024252101 0.032628637 1784.190495 -3.251441221 0.081175986 DCEQAENWMAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCEQAENWMAAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 215.56 9.57E-11 504300000 289050 327160 310280 294730 397820 453470 362950 333320 370970 311600 FALSE TRUE 300461.9172 383347.185 318366.1517 353026.7143 330198.6985 348158.4649 334501.0306 328852.3906 357618.8622 372652.0541 0.806280051 1.028700046 0.854325498 0.947336022 0.886077763 0.934272228 0.897622935 0.882464989 0.959658905 1 18.50746969 1.027417062 4.842017404 0.999725446 0.907508306 0.237854285 0.055929953 0.209211609 12.60850142 0.047284866 0.011980682 10.65165428 -1.027417062 -0.09221714 DCEVTNDGHTIQVILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCEVTNDGHTIQVILK 16 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ; 177.74 2.90E-09 399780000 497110 355820 491680 374770 590480 562660 515270 467780 495000 321800 FALSE TRUE 516736.2867 416929.3171 504493.5847 448898.3874 490110.4205 431990.7422 474881.791 461510.1742 477185.0467 384850.5488 1.342693387 1.083353833 1.310881812 1.166422625 1.273508436 1.122489609 1.233938194 1.199193234 1.239922999 1 18.55393878 -1.877893814 2.363981792 0.889646396 1.214521089 0.424090526 0.07644499 4800383.895 2619518.168 2964710.209 0.016579329 0.013246654 1.877893814 0.324874693 DCFGCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DCFGCLR 7 0 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;; 141.55 0.0059305 2442600000 1174370 1372800 1233790 1269370 1891490 1801300 1400000 1331180 1234900 1807940 FALSE TRUE 1220735.034 1608567.721 1265943.581 1520447.597 1569975.205 1382975.374 1290264.342 1313337.709 1190456.19 2162171.228 0.564587586 0.743959452 0.585496451 0.703204065 0.726110488 0.639623429 0.596744756 0.607416144 0.550583679 1 21.04404935 -1.532209901 3.345555134 1.009854765 0.637923042 0.741697068 0.064549494 20266265.18 28494181.11 1828084.476 0.015390531 0.029362302 1.532209901 -0.371931723 DCGATWVVLGHSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DCGATWVVLGHSER 14 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;;; 218.31 5.43E-12 9953720000 4602800 6280510 5203780 4596500 6735140 6658090 4656420 5432560 5300100 7798060 FALSE TRUE 4784522.098 7359138.737 5339394.782 5505673.981 5590303.309 5111849.502 4291437.633 5359745.419 5109350.436 9325940.554 0.513033733 0.789104187 0.572531505 0.590361256 0.599435872 0.548132327 0.460161375 0.574713659 0.547864358 1 23.1528178 -1.676554378 6.688227749 1.002896695 0.578127949 0.711775769 0.080701068 0.003506252 0.000169564 0.078598376 0.018436156 0.021059382 1.676554378 -0.424768746 DCGKT(ph)FQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DCGKTFQDK 9 1 Q5JNZ3 Q5JNZ3 ZNF311 Zinc finger protein 311 1 DCGKT(1)FQDK 66.435 0.093436 96846000 126820 78572 111820 76227 164650 142970 143630 121970 125070 100380 TRUE FALSE 131826.9515 92066.12979 114734.1211 91304.47309 136662.8518 109767.3842 132371.9053 120335.1917 120568.7551 120047.5391 1.098122898 0.766913928 0.955739051 0.760569302 1.138406108 0.914365967 1.102662381 1.002396155 1.004341747 1 16.8732463 3.234163766 24.99996366 1.02549394 0.890477757 0.270067056 0.10592651 135.6031534 771023.7128 0.027647146 0.034139161 1714.603738 -3.234163766 -0.135016182 DCHEEVYAGSHQYPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DCHEEVYAGSHQYPGR 16 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ;;;;; 259.96 5.28E-27 2917170000 354551 435142 433688 417714 487354 527816 449893 368287 442805 473093 FALSE TRUE 368548.9473 509874.2536 444990.2656 500336.5824 404513.7412 405238.7331 414629.2111 363350.7152 426868.5345 565786.5154 0.651392243 0.901177811 0.786498535 0.884320444 0.714958257 0.716239645 0.732836856 0.642204622 0.754469262 1 19.10989827 3.207956759 24.984708 0.731960541 0.811274613 0.001191858 0.109790453 433.0848624 353565.3889 0.02958909 0.03536948 1614.197829 -3.207956759 0.079314072 DCKEPK ddPTM_MDA-MB-175_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 74.415 0.073312 248120000 286020 137640 224900 148100 309890 235460 338000 199190 259370 102470 FALSE TRUE 297312.2905 161278.5993 230761.0788 177393.738 257215.0085 180777.9834 311506.6768 196520.1839 250035.3244 122547.0346 2.426107588 1.316054687 1.883040904 1.447556349 2.098908467 1.475172239 2.541935656 1.603630675 2.040321295 1 16.90297605 3.223036569 24.98500119 1.844411567 1.744097981 0 0.47461917 1738.270686 2797632.41 0.12578397 0.150838005 1671.231331 -3.223036569 -0.100313586 DCQLNAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DCQLNAHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 146.03 0.00055986 1263326000 1697259 1186071 1458621 1445128 2113350 1990774 2008088 1614773 1682727 1245258 FALSE TRUE 1764268.096 1389769.468 1496633.862 1730970.005 1754123.522 1528446.909 1850688.815 1593129.609 1622165.984 1489242.463 1.184674853 0.933205641 1.004963193 1.162315773 1.177862951 1.026325093 1.242704839 1.069758383 1.089255796 1 20.50614723 3.746688877 24.87522818 1.117204222 1.030173667 0.102697236 0.089667158 1006.858649 3081318.572 0.021773563 0.038377628 5580.702565 -3.746688877 -0.087030555 DCQLNAHKDHQYQFLEDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCQLNAHKDHQYQFLEDAVR 20 1 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 252.4 2.88E-36 2523900000 1329240 1197900 1445630 1012330 1860050 1680110 1198230 1403740 1434920 1442570 FALSE TRUE 1381719.422 1403630.007 1483304.305 1212565.852 1543879.365 1289929.915 1104309.602 1384925.161 1383277.509 1725213.972 0.800897422 0.813597635 0.859779905 0.702849543 0.894891527 0.747692713 0.64010008 0.802755591 0.801800549 1 20.71834387 0.646594734 2.543292104 0.999969013 0.780854233 0.465627318 0.069389001 2.604880393 17.66653924 0.066163114 0.017625986 4.431948798 -0.646594734 -0.219114781 DCSCTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCSCTSR 7 0 B1AH88 B1AH88 TSPO Putative peripheral benzodiazepine receptor-related protein 0 ; 83.287 0.05209 81399000 28549 42611 32839 39714 32265 51838 33953 39385 34720 58294 FALSE TRUE 29676.13656 49929.10778 33694.81132 47569.31067 26780.60682 39799.41011 31291.67514 38857.1085 33470.43398 69715.59319 0.425674303 0.716182786 0.483318147 0.682333872 0.384140844 0.570882471 0.448847578 0.557366103 0.48009968 1 16.08919376 -1.30926312 3.133254195 1.003200311 0.531946723 0.658999577 0.101892144 19050015.12 25145635.29 568909.3541 0.023095254 0.049061055 1.30926312 -0.471253588 DCSPS(ph)SPLKLDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.078)PS(0.461)S(0.461)PLKLDAR 60.209 0.056653 86926000 149980 86469 120050 104380 168060 152640 130340 131950 130340 78842 TRUE FALSE 155901.3262 101319.3781 123178.6016 125026.0525 139493.2212 117191.6733 120123.6102 130181.4261 125649.0889 94289.58038 1.653431117 1.074555404 1.306386147 1.325979519 1.479412897 1.242891026 1.273986052 1.380655482 1.33258721 1 16.52481073 -1.140935937 3.278913632 0.99949633 1.333374928 0.336421302 0.143347177 10607681.74 16454752.57 57240.25404 0.032476665 0.072287643 1.140935937 0.333878597 DCSPSS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DCSPSSPLK 9 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCSPS(0.31)S(0.69)PLK;DCS(0.01)PS(0.275)S(0.715)PLK 135.8 0.00022111 199227000 1074870 566240 784400 746090 984090 1173980 1249680 840090 844350 419050 TRUE FALSE 1117306.698 663487.3153 804842.1084 893664.3751 816814.7333 901340.9368 1151726.816 828829.9677 813962.0084 501154.8243 2.229464116 1.323916848 1.605974979 1.783210161 1.629865051 1.798527906 2.298145723 1.653840146 1.624172749 1 18.93489685 2.725101259 22.34258067 1.761437673 1.690577514 0 0.366592508 1628.154105 2702730.507 0.113235418 0.107495563 531.0082382 -2.725101259 -0.070860159 DCSPSS(ph)PLKLDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DCSPSSPLKLDAR 13 1 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 DCS(0.005)PS(0.162)S(0.832)PLKLDAR 113.47 0.00049606 348640000 961250 520930 696460 557840 1028100 958760 900650 708070 836970 431150 TRUE FALSE 999200.8922 610395.6752 714610.3197 668179.087 853343.9292 736102.5201 830054.6996 698579.4798 806847.6132 515625.5876 1.937841946 1.183796324 1.385909344 1.295860995 1.654968158 1.427591139 1.609801219 1.354819265 1.564793588 1 18.97596433 -1.313401194 3.651837147 0.998544721 1.472111719 0.339606822 0.203776835 35678432.56 62352266 578805.7123 0.044976532 0.048595808 1.313401194 0.473566998 DCTSALALVPFSIKPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DCTSALALVPFSIKPLLR 18 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 104.26 0.00046691 154000000 337160 326680 365580 353750 414820 452890 423540 376060 405670 326480 FALSE TRUE 350471.3371 382784.7488 375107.3151 423720.6942 344309.0446 347713.1611 390341.8281 371019.5308 391070.0159 390447.5052 0.897614487 0.980374426 0.960711261 1.085218086 0.881831847 0.890550347 0.999729344 0.950241776 1.001594352 1 18.57476907 1.232523732 24.41853028 1.00079722 0.958201792 0.089511465 0.057008895 313.1141597 1266426.624 0.049305587 0.01360974 17.08141059 -1.232523732 -0.042595428 DCVGPEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DCVGPEVEK 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 122.19 0.0036289 569710000 1263290 818540 1055280 834450 1435870 1400830 1267640 1115890 1249420 727410 FALSE TRUE 1313165.665 959117.8776 1082781.464 999501.7194 1191801.33 1075508.462 1168279.064 1100933.32 1204453.618 869932.0624 1.509503697 1.102520437 1.244673591 1.148942271 1.369993568 1.236313166 1.34295437 1.265539422 1.384537564 1 19.73054321 -1.07126772 4.536143928 0.999988586 1.280434928 0.369100544 0.112973738 7015096.632 1657298.374 1197.670925 0.024278562 0.084865716 1.07126772 0.280446342 DDAT(ph)PVRDEPMDAESITFK ddPTM_MDA-MB-175_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 173.35 1.06E-11 164687000 418530 238290 318030 266590 398300 450860 529770 343790 364830 186362 TRUE FALSE 435053.8876 279214.4539 326318.1231 319320.7063 330597.1083 346154.5978 488245.2431 339182.0574 351699.8396 222876.0658 1.951999135 1.252778996 1.464123669 1.432727669 1.483322613 1.553125934 2.19065803 1.52184155 1.578006316 1 17.76588217 2.466371681 24.97942243 1.657202051 1.497046666 0 0.3182989 706.5521793 1641846.258 0.104422567 0.087444691 292.6656019 -2.466371681 -0.160155385 DDAVANLTQLIGGAQELHAYSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDAVANLTQLIGGAQELHAYSVR 23 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 196.28 3.17E-24 241950000 191070 211170 203100 193260 244830 255780 234950 195880 219810 190450 FALSE TRUE 198613.5911 247436.8048 208392.9528 231486.2512 203213.8841 196378.9714 216534.0051 193254.549 211899.081 227765.0311 0.872010906 1.086368718 0.914947092 1.016337978 0.892208444 0.862199831 0.950690297 0.848482087 0.930340711 1 17.79718674 3.22391718 24.98177515 0.902782016 0.976450709 0.13928054 0.06751041 331.3879305 565348.5146 0.017857504 0.021429839 1674.623493 -3.22391718 0.073668693 DDAYWPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDAYWPEAK 9 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 141.88 0.00024582 277290000 671760 442330 571080 452130 741240 763030 727900 606300 619190 361300 FALSE TRUE 698281.6035 518296.7367 585962.8139 541559.9645 615244.2896 585827.8463 670845.296 598173.5402 596905.4729 432089.8175 1.616056605 1.199511573 1.356113452 1.253350444 1.423880556 1.355801092 1.552559836 1.384373146 1.381438416 1 18.72097171 0.587110677 4.250978329 1.000000073 1.387849182 0.503145432 0.116667708 29.49440009 302.7237517 0.10657161 0.027128195 3.864654523 -0.587110677 0.38784911 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR 304.37 1.24E-55 412980000 755520 278560 388620 315110 571870 737110 698990 412520 458970 147406 TRUE FALSE 785348.513 326400.5131 398747.7565 377437.8175 474663.7417 565927.3735 644201.3373 406990.8441 442451.7594 176287.3834 4.454933176 1.851525088 2.261918855 2.141037039 2.692556509 3.210254543 3.654267962 2.308678229 2.509832245 1 17.4275697 0.661571979 1.543813374 1.003846835 2.786700975 0.352365327 0.740668674 1.445845584 4.999919173 0.691891491 0.199810021 4.587456707 -0.661571979 1.782854139 DDDHNGHIDFITAASNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDDHNGHIDFITAASNLR 18 0 A0AVT1;A0AVT1-2;H0Y9U5 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 94.281 0.0011524 60121000 42091 55055 50058 52961 55388 61731 59915 44224 49212 49141 FALSE TRUE 43752.78518 64510.26798 51362.5526 63436.52773 45973.16754 47394.91079 55218.70574 43631.24962 47440.86973 58769.23809 0.744484472 1.097687669 0.873970027 1.079417222 0.782265842 0.806457806 0.93958519 0.742416459 0.807239829 1 15.84277357 3.213490747 24.99913858 0.832080546 0.954166964 0.147495767 0.117572578 339.3063173 338348.1399 0.031504884 0.037669842 1634.898319 -3.213490747 0.122086417 DDDKNNDGYIDYAEFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDDKNNDGYIDYAEFAK 17 1 Q8NI22-2;Q8NI22-3;Q8NI22 Q8NI22-2 MCFD2 Multiple coagulation factor deficiency protein 2 0 271.31 1.20E-35 249340000 898340 325500 505360 388770 911850 760570 890550 490830 559890 207600 FALSE TRUE 933807.1569 381402.093 518530.0968 465667.5456 756854.0627 583939.144 820746.364 484251.2267 539739.6683 248275.2453 3.761177059 1.536206691 2.08852919 1.875610052 3.048447548 2.351982951 3.305792179 1.950461175 2.173956843 1 17.9215809 4.756575868 24.19677587 2.240952103 3.761179061 0.356895168 0.638785615 2841.199848 3815996.291 0.146071201 4.535485134 57092.08032 -4.756575868 1.520226958 DDDSNFHMDFIVAASNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDDSNFHMDFIVAASNLR 18 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 196.31 1.97E-15 105955000 175233 179503 206482 231164 242475 278309 284187 218991 220490 140063 FALSE TRUE 182151.3341 210331.2439 211863.0905 276887.5492 201259.1861 213675.9526 261911.6804 216055.7838 212554.608 167505.6632 1.087433885 1.255666465 1.264811509 1.653004107 1.201506757 1.275634199 1.563598958 1.289841667 1.268939831 1 17.35385035 0.771728304 2.354622676 1.000326302 1.334072682 0.272210367 0.157743664 1.271563169 10.84756714 0.148773598 0.040135638 5.911916668 -0.771728304 0.33374638 DDDVPLDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDDVPLDWR 9 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 122.19 0.0013792 851507000 2050270 1713870 1913870 1640950 2526790 2717430 2224270 1870470 1940850 1590130 FALSE TRUE 2131216.243 2008213.84 1963747.024 1965525.012 2097287.138 2086348.066 2049925.905 1845399.409 1870999.188 1901685.529 1.120698565 1.056017838 1.032634994 1.033569948 1.102856969 1.097104665 1.077952098 0.970401984 0.983863609 1 20.85884726 1.744826865 7.451759968 0.983788183 1.072536923 0.684903202 0.027811798 0.078129518 13.96298668 0.014487826 0.007716582 55.56826861 -1.744826865 0.088748739 DDDVPLMWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDDVPLMWR 9 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ;;; 167.24 0.00013989 242026000 397965 414548 455523 381128 541246 591651 497453 451412 455140 357946 FALSE TRUE 413676.9655 485743.3943 467394.3036 456513.9808 449245.1982 454249.0218 458461.334 445361.5605 438759.6003 428078.6654 0.966357352 1.134705916 1.091842087 1.066425444 1.049445428 1.061134456 1.070974499 1.040373176 1.024950869 1 18.70751641 1.242779123 1.232899639 1.000336453 1.067255247 0.209272997 0.039739884 0.594064149 1.795504548 0.034958387 0.011201867 17.48956964 -1.242779123 0.066918794 DDDYRGGGDRYEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDDYRGGGDRYEDR 14 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 74.769 0.018066 494190000 230670 262230 253800 196010 340800 296440 174100 234080 235710 270840 FALSE TRUE 239777.0297 307265.9626 260414.2365 234780.193 282870.9377 227596.3026 160453.5871 230942.5405 227226.8431 323905.9125 0.74026753 0.948627212 0.803981115 0.724840714 0.873312054 0.702661773 0.495370973 0.712992667 0.701521134 1 18.30521528 2.653053695 6.816073964 0.68583835 0.819238793 0.086983387 0.130823296 0.412100864 27.98062762 0.040438739 0.03809505 449.8354675 -2.653053695 0.133400443 DDDYRGGGDRYEDRYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDDYRGGGDRYEDRYDR 17 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 115.15 0.00014401 2671600000 2261200 2631700 2605000 1531280 3804500 3454700 1680790 2348700 2799100 3622900 FALSE TRUE 2350473.922 3083674.003 2672888.44 1834162.614 3157812.449 2652398.281 1549045.288 2317219.518 2698360.938 4332737.89 0.542491603 0.711714874 0.616905178 0.423326465 0.728826098 0.61217603 0.357521116 0.534816455 0.622784255 1 22.04684753 0.829399528 4.682979068 0.999990558 0.563521561 0.586843357 0.10857499 1.431543876 38.71876221 0.106767009 0.027058287 6.751488428 -0.829399528 -0.436468997 DDEAAAVALSSLIHALDDLDMVAIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDEAAAVALSSLIHALDDLDMVAIVR 26 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 90.468 0.0079704 586260000 62877.7 77897.3 90947.5 85280.8 94320 130454 99386.2 70211.5 84450.1 94758.5 FALSE TRUE 65360.16015 91275.55532 93317.66656 102149.0877 78287.52009 100158.0355 91596.04995 69270.42969 81410.7574 113324.6138 0.576751669 0.805434515 0.82345453 0.90138483 0.690825386 0.883815371 0.808262626 0.611256702 0.718385483 1 16.79010172 -2.329681365 2.247401911 2.330425542 0.75844899 0.332748443 0.102917282 6584605.646 525406.5165 44887646.49 0.025513296 0.004680784 2.329681365 -1.571976552 DDEDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDEDSFR 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 130.04 0.020343 0 131190 245650 265770 222740 263630 298860 279810 277290 252230 195880 FALSE TRUE 136369.4825 287838.4766 272696.1845 266797.3072 218818.2668 229454.2943 257877.7611 273573.3811 243152.2916 234258.9357 0.582131401 1.228719305 1.164080182 1.138899169 0.934087172 0.97949004 1.100823584 1.167824742 1.037963785 1 17.83774455 2.213477322 23.46185436 1.099272241 1.024909445 0.025909548 0.172794727 450.1737047 421067.6223 0.063835462 0.047171967 163.4847779 -2.213477322 -0.074362796 DDEENYLDLFSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ; 175.15 1.88E-05 261240000 478310 284340 413760 347930 545340 541970 578740 435160 476570 276540 FALSE TRUE 497194.0481 333173.1831 424542.9255 416749.5155 452643.3016 416105.6811 533376.8465 429327.392 459418.3388 330722.7183 1.503356197 1.007409424 1.283682378 1.260117592 1.368648951 1.258170842 1.612761437 1.298149078 1.389134503 1 18.33526263 3.324623319 4.208249391 1.350275524 1.243617596 0.004039062 0.181570604 0.621051169 20.45168664 0.048183842 0.065548398 2111.656719 -3.324623319 -0.106657927 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 DDEKEAEEGEDDRDS(0.998)ANGEDDS(0.002);DDEKEAEEGEDDRDS(0.984)ANGEDDS(0.016);DDEKEAEEGEDDRDS(1)ANGEDDS 233.78 1.59E-30 1888520000 2572050 899207 1048197 1148524 1638970 2334590 2209400 1191287 1119144 502870 TRUE FALSE 2673596.52 1053638.807 1075513.875 1375698.619 1360378.465 1792416.854 2036221.455 1175319.746 1078866.226 601397.7485 4.445637728 1.751983292 1.788357003 2.287502111 2.262027865 2.980418297 3.385814895 1.954313513 1.793931269 1 19.19795994 4.746290092 24.7751491 2.232231059 4.445638941 0.534701028 0.641083719 695.2335317 2228359.745 0.15471448 1.660809608 55755.80524 -4.746290092 2.213407883 DDEVQVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDEVQVVR 8 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 159.46 0.0013342 0 134380 152150 163530 127320 167000 199250 162940 166670 150090 147350 FALSE TRUE 139685.4262 178280.5789 167791.7261 152503.516 138613.3997 152977.2072 150168.337 164436.0613 144688.2902 176220.4113 0.792674499 1.011690857 0.952169643 0.865413461 0.786591057 0.868101521 0.852161994 0.933127213 0.821064309 1 17.42702151 4.939394079 0.004840621 1.753667041 9.02E-07 0.050416884 0.075505874 187995.627 133.1320438 23219.00557 25037.49377 86974.92832 -4.939394079 -1.753666138 DDFTEFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ;; 95.531 0.022298 383374000 923630 673230 762050 707580 986040 1025090 1037650 780380 837170 484930 FALSE TRUE 960095.6256 788852.0155 781909.649 847537.2121 818433.273 787028.3829 956316.2816 769920.2825 807040.4152 579942.749 1.655500698 1.360223948 1.348253169 1.46141531 1.411231151 1.357079443 1.648983944 1.327579807 1.391586353 1 19.14555096 0.504712532 1.25409079 1.000212671 1.444887617 0.592321113 0.111040474 1.337222635 2.68908179 0.100218986 0.030091139 3.1967784 -0.504712532 0.444674946 DDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDGDEEGLLTHSEEELEHSQDTDADDGALQ 30 0 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 DDGDEEGLLT(0.151)HS(0.849)EEELEHSQDTDADDGALQ 148.95 1.83E-08 154860000 46799 40029 35406 30956 44841 59180 43938 40565 34838 24130 TRUE FALSE 48646.66066 46903.66937 36328.70945 37079.00441 37218.94284 45436.34188 40494.02475 40021.29253 33584.18719 28857.8115 1.685736309 1.625337021 1.258886504 1.284886222 1.289735461 1.574490217 1.403225769 1.386844339 1.163781501 1 14.81667427 -2.305985906 0.067491777 1.42E-14 2.032408415 0.549385918 0.136498401 159.3769632 1.388797652 36.38148389 11.17459711 0.004943267 2.305985906 2.032408415 DDGLFSGDPNWFPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 212.24 1.57E-09 1655240000 5712900 4159200 5217100 3470100 6749700 6327100 5352800 4868700 5524300 3984600 FALSE TRUE 5938449.703 4873510.246 5353061.912 4156475.423 5602388.405 4857726.913 4933233.549 4803443.04 5325481.522 4765306.08 1.246184317 1.022706656 1.123340625 0.87223682 1.175661817 1.019394522 1.035239598 1.008003045 1.117552877 1 22.18413745 4.741678002 24.55029833 1.040762017 1.246184415 0.37473066 0.079285887 223.9862587 1763841.425 0.017195 0.121105123 55166.8265 -4.741678002 0.205422398 DDGSWEVIEGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DDGSWEVIEGYR 12 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;; 297.13 5.95E-36 2106380000 1126610 1322360 1134840 1315750 1155520 1798040 1189430 1089490 1079030 1184790 FALSE TRUE 1171089.433 1549465.043 1164414.863 1576001.423 959105.1231 1380472.46 1096199.369 1074887.169 1040195.921 1416926.916 0.826499532 1.093539141 0.821788936 1.112267263 0.676891032 0.974272169 0.773645667 0.758604524 0.734121082 1 20.43433392 3.234463775 24.99999016 0.808357081 0.962686612 0.225020188 0.129855788 138.6767829 846242.2047 0.034312269 0.042439954 1715.788588 -3.234463775 0.154329531 DDGVFVQEVTQNS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 348.12 1.44E-87 582060000 271680 268160 254670 245440 312700 360950 275870 244160 283170 254191 TRUE FALSE 282406.1362 314214.394 261306.9094 293987.2994 259547.3657 277124.8328 254246.5885 240887.4346 272978.767 303994.8597 0.928983261 1.033617458 0.859576737 0.967079837 0.853788666 0.911610259 0.836351604 0.792406276 0.897971654 1 18.2136874 3.572664033 0.97099946 0.861481384 0.971406369 0.120344001 0.067676448 0.841576119 1.564475514 0.025509322 0.065234618 3738.212906 -3.572664033 0.109924986 DDGYSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDGYSTK 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;; 122.13 0.026867 365310000 1080410 838170 1077880 777300 1275540 1318820 1295470 1076630 1148620 772450 FALSE TRUE 1123065.421 982119.1774 1105970.438 931047.62 1058724.166 1012544.042 1193927.676 1062199.536 1107281.391 923796.7881 1.215706133 1.063133354 1.197201 1.007848947 1.146057423 1.096067939 1.292413756 1.149819473 1.198620091 1 19.817216 DDHNWWQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDHNWWQGK 9 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;Q5JS79;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ;;; 127.76 0.00043624 1114360000 4034520 3524830 3704940 3333410 4279950 4746730 4149120 3784650 3870080 3125900 FALSE TRUE 4193805.965 4130192.133 3801493.78 3992748.549 3552445.628 3644373.895 3823901.133 3733922.957 3730796.577 3738360.256 1.121830342 1.104813836 1.016888026 1.068048095 0.950268402 0.974858934 1.022881924 0.998813036 0.997976739 1 21.83397417 4.251414824 1.109890293 0.995815696 1.144541041 0.714670293 0.028166975 0.434340785 0.755349875 0.008703435 0.06282882 17840.82053 -4.251414824 0.148725346 DDILNGSHPVSFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 217.48 5.74E-12 1823510000 2754040 2097910 2705610 2132290 3724480 3491950 3310900 2884990 3135980 1874480 FALSE TRUE 2862771.626 2458209.723 2776120.419 2554050.598 3091394.22 2680997.534 3051383.007 2846321.428 3023116.692 2241748.467 1.277026244 1.096559119 1.238372842 1.139311852 1.379010297 1.195940389 1.36116208 1.269688134 1.348553032 1 21.09619298 3.264198021 24.9978952 1.276134877 1.18491016 0.075669205 0.112698421 432.5289967 421736.6931 0.028112949 0.038051935 1837.375924 -3.264198021 -0.091224717 DDIPVFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DDIPVFLR 8 0 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 ;;;; 139.31 0.0015537 207280500 262816 242924 271731 273006 283664 355161 346741 283515 270500 191383 FALSE TRUE 273192.1786 284644.3073 278812.5331 327005.772 235446.8946 272680.2403 319562.5344 279714.9452 260764.7578 228880.8346 1.193600063 1.243635396 1.218155874 1.428716269 1.028687679 1.191363361 1.396196125 1.22209859 1.139303596 1 17.80423714 0.981145972 2.72355671 1.001434491 1.244073156 0.338695905 0.104866447 0.299012499 5.212826318 0.097785149 0.026084952 9.575158511 -0.981145972 0.242638665 DDIVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDIVDR 6 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 114.19 0.059325 2807850000 2455920 2408010 2640520 2449360 3474330 3622100 2898430 2607120 2718900 2463720 FALSE TRUE 2552881.618 2821566.986 2709334.12 2933836.097 2883764.628 2780922.168 2671243.483 2572175.821 2621047.32 2946438.763 0.866429552 0.957619422 0.9195284 0.995722746 0.978728852 0.943824865 0.906600713 0.872977865 0.889564498 1 21.49054085 -0.383165155 7.880312134 1.000000895 0.925854465 0.225651107 0.041308798 0 0 0.043752523 0.010312568 0.413842267 0.383165155 -0.074146429 DDKEEEEDGT(ph)GSPQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.5)GS(0.5)PQLNNR 172.34 1.78E-11 1140300000 763230 259080 365730 279000 563610 711770 634590 387800 432870 141730 TRUE FALSE 793362.9097 303574.9746 375261.2243 334185.3673 467807.7735 546472.2045 584849.1776 382602.1753 417291.0933 169499.2799 4.680627022 1.791010409 2.213939932 1.971603463 2.759939592 3.224038502 3.450452285 2.257249562 2.461904814 1 17.37091962 0.667714688 1.409659452 1.004905866 2.754060582 0.310556364 0.803259222 1.46368588 4.40842342 0.744837323 0.219243344 4.652803246 -0.667714688 1.749154717 DDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DDKEEEEDGTGSPQLNNR 18 1 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 DDKEEEEDGT(0.019)GS(0.981)PQLNNR;DDKEEEEDGT(0.013)GS(0.987)PQLNNR;DDKEEEEDGT(0.128)GS(0.872)PQLNNR 293.07 1.91E-49 4984400000 3162390 1197140 1693140 1272360 2454450 3107210 2770110 1729660 2003340 725900 TRUE FALSE 3287243.599 1402739.483 1737264.619 1524029.01 2037243.466 2385607.568 2552981.54 1706476.737 1931240.185 868126.2068 3.786596434 1.615824372 2.001165966 1.755538536 2.346713473 2.747996258 2.940795382 1.965701212 2.224607631 1 19.72754527 4.750476456 24.44719522 2.14623203 3.786597791 0.478375686 0.533033217 1222.67223 2508438.698 0.1255872 2.030330507 56295.85975 -4.750476456 1.64036576 DDKHGS(ph)YEDAVHSGALND ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 1 DDKHGS(1)YEDAVHSGALND 134.81 5.88E-06 94536000 165570 102990 138850 101340 180470 189610 157100 134060 147620 81169 TRUE FALSE 172106.8314 120677.7313 142468.5451 121384.7495 149793.7739 145575.9511 144786.0915 132263.145 142307.185 97072.51148 1.772971862 1.243171002 1.467650758 1.250454404 1.54311217 1.499661942 1.491525142 1.362519038 1.465988495 1 16.5667752 -2.746633628 0.4652381 8.96E-09 1.44961753 0.471603201 0.144333401 124.7984327 5.254073303 124.8438783 0.068134597 0.001792117 2.746633628 1.449617521 DDKHGSYEDAVHSGALND ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 269.59 4.28E-32 2145880000 1316006.7 3200080 3709140 2902680 4810655 4783353 3407462 4109126 4003680 3313950 FALSE TRUE 1367963.661 3749668.847 3805803.235 3476821.44 3992941.581 3672491.758 3140376.225 4054049.887 3859588.339 3963255.053 0.345161652 0.946108387 0.960272096 0.877264116 1.007490441 0.92663523 0.792372982 1.022909157 0.973843037 1 21.91825438 4.738782223 24.99999957 0.942299439 0.345161478 0.884362419 0.065086539 5.391777041 607891.3808 0.01519003 0.088582022 54800.21005 -4.738782223 -0.597137961 DDKLTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDKLTPK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 105.78 0.0071582 1158780000 2419620 1246430 1602970 1351280 2398020 2178100 2599110 1678580 1863940 943420 FALSE TRUE 2515148.466 1460494.657 1644744.715 1618559.151 1990405.417 1672269.284 2395384.967 1656081.381 1796857.164 1128265.086 2.22921767 1.294460561 1.457764434 1.434555736 1.764129229 1.482159915 2.1230693 1.467812309 1.592584212 1 20.10567464 0.533058616 1.672703265 1.000416144 1.643298488 0.312882539 0.290295285 3.115192186 9.800009117 0.261521955 0.074159387 3.412389652 -0.533058616 0.642882344 DDLITDLLNEAKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDLITDLLNEAKQR 14 1 P36543;C9J8H1;P36543-2 P36543 ATP6V1E1 V-type proton ATPase subunit E 1 0 59.227 0.093545 203170000 15115 281110 159700 294830 90623 225020 84241 178170 107100 357490 FALSE TRUE 15711.75187 329388.4558 163861.9132 353146.494 75218.93483 172762.5152 77637.9703 175781.9226 103245.4919 427533.3209 0.036749772 0.770439261 0.383272847 0.826009288 0.175937012 0.404091346 0.181595133 0.411153737 0.2414911 1 18.70567734 -1.57917276 3.918288792 1.013620142 0.393117924 0.375017339 0.23920856 0.026705136 0.002868153 0.217320643 0.050863167 0.026352829 1.57917276 -0.620502218 DDLLGFALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDLLGFALR 9 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 137.88 0.000354 139891000 125686 118705 127049 118403 166497 173468 147382 127642 126130 107290 FALSE TRUE 130648.1803 139091.6604 130360.0013 141822.76 138195.8994 133182.6859 135829.8137 125931.1678 121590.6059 128311.4213 1.018211621 1.084016208 1.015965687 1.105301138 1.07703506 1.037964388 1.058594881 0.981449402 0.947621067 1 16.96929007 1.695985185 4.064977467 0.970863665 1.058457397 0.615521993 0.029078473 0.107987027 4.160766093 0.015391032 0.007337878 49.65753819 -1.695985185 0.087593732 DDNMFQIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDNMFQIGK 9 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 107.15 0.0065596 130626000 476710 198007 311887 190901 422601 425300 356591 276146 310066 174548 FALSE TRUE 495530.8789 232013.162 320015.0314 228660.648 350767.433 326530.5205 328640.4656 272444.7146 298906.7852 208747.3387 2.373830881 1.111454467 1.533025683 1.095394315 1.680344455 1.564238004 1.574345655 1.30514102 1.431907047 1 17.67139828 7.999955519 0.039228434 4.97E-08 3.82951424 0.246161691 0.325238302 1340.854764 4.006123271 108.3316361 344.6176887 99989758.34 -7.999955519 3.82951419 DDPDGKQEAKPQQAAGMLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 157.24 3.91E-09 482820000 1815030 310830 579690 280590 967820 1064710 951410 578750 704370 182712 TRUE FALSE 1886688.786 364212.6346 594797.1976 336089.8645 803310.3021 817447.2383 876835.9982 570992.8029 679019.8613 218510.9182 8.634299841 1.666793759 2.722047954 1.53809186 3.676293655 3.74099036 4.012778883 2.613108799 3.107487109 1 17.73734584 4.745455857 24.98915558 2.807710017 8.634302535 0.771959843 0.969234385 376.2991561 1363717.559 0.228278364 2.275903541 55648.80677 -4.745455857 5.826592518 DDREDLVYQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDREDLVYQAK 11 1 P62258;B4DJF2;I3L3T1;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 212.9 3.97E-09 5749500000 7275200 5912800 5997700 4507910 5810300 6883900 5685100 6035800 6111400 3259170 FALSE TRUE 7562430.514 6928277.405 6154004.989 5399561.143 4822667.281 5285218.552 5239487.007 5954899.974 5891451.908 3897741.961 1.940208097 1.777510537 1.578864135 1.385304927 1.23729773 1.355969329 1.344236499 1.527781991 1.511503831 1 21.89420715 4.181103506 1.686925011 1.36451894 1.936081801 0.687131075 0.14188497 0.251465457 1.298697906 0.039139146 0.165831997 15174.11972 -4.181103506 0.571562861 DDREQFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDREQFYK 8 1 P60604-2;P60604 P60604-2 UBE2G2 Ubiquitin-conjugating enzyme E2 G2 0 118.67 0.00168 227200000 163880 219100 198370 166760 254500 253110 209440 173460 208830 239790 FALSE TRUE 170350.1089 256728.7206 203539.6852 199744.6303 211240.1809 194329.0384 193023.5455 171135.0524 201314.2491 286772.2594 0.594025759 0.895235547 0.709760719 0.69652703 0.736613023 0.677642387 0.673090019 0.596762925 0.702000429 1 18.12954595 0.922703117 21.7857882 1 0.695832186 0.567202557 0.079149609 12879.65839 3630080.536 0.077330737 0.019332684 8.369569449 -0.922703117 -0.304167814 DDRGPPQRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DDRGPPQRPK 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 118.28 0.00047591 2369930000 2426400 2041870 2457550 1768380 3157540 2950690 2544870 2338460 2603120 2038450 FALSE TRUE 2522196.146 2392545.289 2521595.772 2118160.286 2620822.479 2265436.966 2345396.44 2307116.769 2509434.22 2437845.249 1.034600595 0.981418033 1.034354323 0.868865769 1.07505695 0.929278414 0.962077655 0.946375398 1.029365675 1 21.21717512 4.847984398 1.133878982 0.972570119 1.069120408 0.071724256 0.056021355 4.918837345 4.48994671 0.015144308 0.598604541 70466.77534 -4.847984398 0.096550289 DDRLEDALLS(ph)LGSVIDIS(ph)GLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDRLEDALLSLGSVIDISGLQR 22 1 F5H5P8;F5H130;O00408-6;O00408-2 F5H5P8 PDE2A 2 DDRLEDALLS(0.909)LGS(0.487)VIDIS(0.604)GLQR 56.327 0.043679 865040000 743080 513250 606600 336970 883810 856500 656200 514660 633060 433990 TRUE FALSE 772417.3722 601396.695 622408.4943 403621.6602 733580.2919 657590.8554 604765.3293 507761.8245 610276.2943 519022.0313 1.488216927 1.158711305 1.199194749 0.777658049 1.413389505 1.266980621 1.165201654 0.978304954 1.175819633 1 18.98543625 4.817888855 2.421116597 1.120134033 1.623127188 0.30528745 0.164588404 0.968266571 5.735275505 0.040997729 1.097844637 65748.95501 -4.817888855 0.502993155 DDRNEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDRNEEKR 8 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 134.25 0.00049764 1226472000 324901 236686 279497 231464 302730 349244 421514 298891 304987 182750 FALSE TRUE 337728.3424 277334.9793 286780.9214 277246.8883 251272.0627 268137.3738 388474.6313 294884.855 294010.5774 218556.3635 1.545268858 1.268940308 1.312160016 1.26853725 1.149689987 1.22685686 1.777457425 1.349239392 1.345239153 1 17.73764586 DDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_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 94.201 0.012945 158590000 350220 52405 64177 62833 131610 308090 193770 78215 95887 31982 TRUE FALSE 364046.956 61405.1511 65849.50534 75261.17986 109238.9792 236540.7666 178581.8011 77166.65586 92436.0456 38248.26057 9.518000312 1.605436435 1.721633987 1.967702027 2.856050905 6.184353566 4.669017582 2.017520659 2.416738545 1 15.22310652 4.745229771 24.73334047 2.855659665 9.51800385 0.649856237 1.494811585 454.2550449 1684606.624 0.382109837 3.711893796 55619.84463 -4.745229771 6.662344184 DDS(ph)HS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR;DDS(1)HS(1)AEDS(1)EDEKEDHKNVR 131.56 1.04E-05 1676661000 3247740 610921 894820 554634 1583630 3101930 1546090 962230 991400 350944 TRUE FALSE 3375963.283 715841.9294 918139.7443 664338.9498 1314445.138 2381553.768 1424903.426 949332.8807 955719.7077 419704.7576 8.043662175 1.705584501 2.187584791 1.582872097 3.131832829 5.674354948 3.395013757 2.261906408 2.277123836 1 18.67901529 4.745175022 24.87825766 2.705080888 8.043664772 0.636149628 1.236434989 493.5588994 1856333.395 0.310358054 2.997788897 55612.83341 -4.745175022 5.338583884 DDS(ph)HSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.69)HS(0.31)AEDS(1)EDEKEDHK 196.1 8.19E-12 357820000 879730 181750 294840 238490 481290 750490 654620 342640 379710 116460 TRUE FALSE 914462.4197 212964.1487 302523.7726 285662.6102 399480.4977 576200.0713 603309.1739 338047.4712 366044.3113 139278.1072 6.565729804 1.529056884 2.172084175 2.051023063 2.868221759 4.137046968 4.331687053 2.427140043 2.628153976 1 17.08760898 DDS(ph)HSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.5)HS(0.5)AEDS(1)EDEKEDHKNVR 93.966 0.00076972 135940000 112550 35142 54600 32918 81395 99531 79531 56675 55423 25331 TRUE FALSE 116993.5609 41177.36513 56022.92085 39429.08215 67559.50697 76416.43366 73297.1524 55915.36433 53428.33706 30294.12446 3.861922501 1.359252524 1.849299884 1.301542225 2.230119146 2.522483651 2.419517108 1.845749475 1.763653448 1 14.88675039 -1.752966695 0.302464153 6.88E-12 2.191903937 0.215650596 0.68412658 45.69697569 2.373356479 33.83168093 0.699327992 0.017661733 1.752966695 2.191903937 DDSFFGETSHNYHKFDSEYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDSFFGETSHNYHKFDSEYER 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 113.51 0.00012853 207030000 144300 136950 181990 153910 232590 213110 188780 181390 197200 140590 FALSE TRUE 149997.0754 160470.0972 186732.8089 184352.9386 193054.4349 163618.4322 173982.9303 178958.7637 190102.8105 168135.9187 0.892117975 0.954406996 1.11060629 1.096451847 1.148204597 0.973131937 1.034775506 1.064369619 1.130649607 1 17.35926843 4.392452703 4.453131727 1.069867961 0.904921168 0.560563919 0.053025015 0.138601597 4.883561293 0.013200973 0.040555369 24686.11243 -4.392452703 -0.164946793 DDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.088)HS(0.913)AEDS(1)EDEKEDHK;DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.01)HS(0.99)AEDS(1)EDEKEDHK;DDS(0.476)HS(0.524)AEDS(1)EDEKEDHK;DDS(0.022)HS(0.978)AEDS(1)EDEKEDHK;DDSHS(1)AEDS(1)EDEKEDHK;DDS(0.087)HS(0.913)AEDS(1)EDEKEDHK;DDS(0.007)HS(0.993)AEDS(1)EDEKEDHK;DDS(0.456)HS(0.544)AEDS(1)EDEKEDHK;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHK 229.97 1.25E-15 23489642000 14828380 2774121 4532086 3172188 7066461 11657763 10217192 4802785 5366240 1288927 TRUE FALSE 15413815.89 3250554.702 4650195.884 3799637.318 5865306.483 8950424.218 9416341.793 4738411.523 5173110.071 1541467.568 9.99944223 2.108740249 3.016732873 2.464947948 3.805014524 5.806430447 6.108686288 3.073961219 3.355964264 1 20.5558731 4.747043834 24.77611489 3.622426219 9.999445874 0.634703014 1.491023365 658.3403963 1922702.782 0.367260456 4.257810827 55852.65644 -4.747043834 6.377019655 DDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DDSHSAEDSEDEKEDHKNVR 20 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 DDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;DDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;DDS(0.477)HS(0.53)AEDS(0.993)EDEKEDHKNVR;DDS(0.043)HS(0.957)AEDS(1)EDEKEDHKNVR;DDS(0.002)HS(0.998)AEDS(1)EDEKEDHKNVR;DDS(0.01)HS(0.99)AEDS(1)EDEKEDHKNVR;DDS(0.374)HS(0.626)AEDS(1)EDEKEDHKNVR;DDS(0.003)HS(0.997)AEDS(1)EDEKEDHKNVR;DDS(0.003)HS(0.997)AEDS(1)EDEKEDHKNVR 234.18 2.91E-29 27289246000 13161703 3178791.9 4935677 2721294.7 8388271 10495482 7800462 5075053 5766631 1989721.7 TRUE FALSE 13681337.2 3724724.681 5064304.797 3259558.669 6962435.692 8058065.366 7189041.406 5007030.216 5559091.077 2379569.572 5.749500818 1.565293457 2.128244056 1.369810199 2.925922307 3.38635418 3.021152015 2.104174753 2.336175056 1 21.1822692 -1.05648604 0.220325557 9.32E-40 3.03334096 0.196189966 1.151163435 35.18061724 1.730611708 26.83976142 2.656930779 0.087803931 1.05648604 3.03334096 DDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DDSHSAEDSEDEKEDHK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(0.999)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK;DDSHSAEDS(1)EDEKEDHK 282.17 3.09E-36 3288410000 2742296 600723 991306 658669 1504973 2231503 1923057 976476 1149293 348515 TRUE FALSE 2850563.964 703892.5023 1017140.249 788951.7623 1249158.227 1713270.247 1772322.767 963387.9364 1107930.169 416799.8415 6.83916758 1.688802231 2.440356611 1.892879228 2.997021838 4.110534785 4.25221555 2.311392281 2.658182799 1 18.6689952 4.747577383 24.79657951 2.725051542 6.839169971 0.632691568 0.965635857 724.1307076 1991349.742 0.235686408 2.875684108 55921.31599 -4.747577383 4.11411843 DDSHSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;DDS(0.002)HS(0.002)AEDS(0.996)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR;DDSHSAEDS(1)EDEKEDHKNVR 329.85 4.03E-80 19461871000 19134662 4981052 8264455 4510548 13423133 14367686 11911934 7977249 8873247 3144103 TRUE FALSE 19890113.23 5836508.934 8479833.487 5402720.932 11141473.65 11031008.67 10978245.49 7870327.025 8553900.574 3760129.785 5.289741144 1.552209436 2.25519702 1.436844269 2.963055608 2.933677639 2.919645362 2.093099833 2.274895033 1 21.84235103 4.746779755 24.68195678 2.249613663 5.28974295 0.67775623 0.644946067 512.9824584 1540437.159 0.150885643 1.697152996 55818.70477 -4.746779755 3.040129286 DDTHKVDVINFAQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDTHKVDVINFAQNK 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ; 212.87 3.94E-10 1046010000 5141300 2658060 3709000 2394880 5458200 4587000 4603400 3814800 4308600 2163050 FALSE TRUE 5344282.494 3114561.128 3805659.587 2868580.116 4530417.114 3521738.767 4242573.479 3763668.846 4153534.328 2586858.233 2.065935591 1.203993743 1.471151197 1.108905034 1.751320213 1.361396122 1.640048699 1.454918865 1.605628895 1 21.30276956 -1.221379857 4.077181357 0.999674524 1.499556433 0.260522986 0.260194784 120.4400222 64070182.76 38387.77969 0.055192472 0.060064815 1.221379857 0.499881909 DDTIPPEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDTIPPEYR 9 0 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;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 85.161 0.034302 0 284410 986520 595970 958660 502420 867140 515050 572380 508120 1635840 FALSE TRUE 295638.7264 1155947.136 611501.4678 1148280.087 417018.8279 665759.8766 474679.0352 564708.1823 489832.8605 1956351.528 0.151117385 0.590868829 0.312572387 0.586949774 0.213161501 0.340306876 0.242634838 0.288653738 0.2503808 1 20.89973419 -1.440099351 4.572514155 1.001830961 0.334982899 0.672793507 0.139990908 0.002474745 0.000303031 0.128375035 0.030186582 0.0362995 1.440099351 -0.666848063 DDWEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DDWEEKR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 143.61 0.0038644 5388370000 5184220 3133430 4151250 2967730 5689230 5521870 5027740 3875440 4448300 2497160 FALSE TRUE 5388897.009 3671572.228 4259434.985 3554738.136 4722176.717 4239499.377 4633652.601 3823496.066 4288206.552 2986430.691 1.804460765 1.229418194 1.426262795 1.190296546 1.581210885 1.419587399 1.551568772 1.28028957 1.435896894 1 21.50999081 -3.103386637 0.320787609 8.68E-13 1.444220314 0.369880716 0.171818675 87.98228239 2.397014546 59.29864618 0.143948009 0.000788158 3.103386637 1.444220314 DDYPSR ddPTM_MDA-MB-175_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 ; 103.02 0.081529 1217979000 345881 334324 402372 368982 498435 556256 454916 400268 438323 342224 FALSE TRUE 359536.649 391741.5463 412858.1449 441965.5383 413711.1967 427073.9741 419258.4952 394903.0622 422547.8409 409276.2405 0.878469389 0.957156824 1.008751801 1.079870988 1.010836095 1.043485871 1.024390018 0.964881474 1.032426999 1 18.64271539 4.551480136 2.200460865 1.019470405 0.868378246 0.715564329 0.028195363 0.250093367 1.838558096 0.0078531 0.063078235 35602.47053 -4.551480136 -0.151092159 DDYSRDDYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DDYSRDDYRR 10 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 55.426 0.073503 104220000 83525 105320 103570 70462 154190 136800 76153 95629 110530 143250 FALSE TRUE 86822.6315 123407.8907 106269.1193 84399.17329 127980.8389 105030.2732 70183.92887 94347.24967 106552.0469 171317.0948 0.506794909 0.720347791 0.620306569 0.492648871 0.747040679 0.613075265 0.409672654 0.550717077 0.621958054 1 17.38630959 0.845297272 6.29835088 0.999999455 0.581926001 0.624553145 0.096503804 3.14403301 127.9280489 0.09431036 0.023691641 7.003211981 -0.845297272 -0.418073454 DDYVHEFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DDYVHEFCR 9 0 Q13564-2;Q13564;Q13564-4;Q13564-3 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ; 137.95 0.0001502 446240000 481100 478060 502520 497960 608680 738300 615140 529010 507450 446390 FALSE TRUE 500094.1995 560163.0862 515616.084 596455.0017 505216.791 566841.014 566923.7194 521919.4862 489186.9736 533851.5738 0.936766367 1.049286194 0.965841648 1.117267478 0.946361902 1.061795154 1.061950076 0.977649054 0.916335172 1 19.02607916 1.541287167 6.110112072 0.954729289 1.021491155 0.167916764 0.057161656 0.201510879 15.34782992 0.029582439 0.013508986 34.77660378 -1.541287167 0.066761866 DEAAYGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DEAAYGELR 9 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;; 134.91 0.0005482 1878870000 2102080 1980110 2234040 2313130 2806490 2822300 2767780 2323480 2350150 1678840 FALSE TRUE 2185071.742 2320178.489 2292260.918 2770660.21 2329443.832 2166863.597 2550834.171 2292337.551 2265568.561 2007776.555 1.088304242 1.155595967 1.141691247 1.379964421 1.160210695 1.079235432 1.270477118 1.141729415 1.128396761 1 20.93716729 0.837267752 1.619074874 1.000619674 1.182717512 0.292158162 0.083814747 0.767387403 3.766544441 0.079127767 0.022793446 6.874921629 -0.837267752 0.182097838 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 33 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 237.49 3.61E-47 292075000 172551 137985 159960 168426 211740 222306 212953 160439 178460 102587 FALSE TRUE 179363.4467 161682.8504 164128.689 201740.1601 175748.5104 170678.8006 196261.1874 158288.5776 172037.2595 122686.9585 1.46196017 1.317848713 1.337784317 1.644348858 1.432495455 1.391173134 1.599690707 1.290182588 1.402245696 1 16.90462237 0.396355841 0.937182887 0.998446224 1.442965669 0.597919467 0.107187958 1.527892832 1.767479802 0.107171668 0.033173381 2.490897412 -0.396355841 0.444519445 DEAEMSSWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEAEMSSWLR 10 0 O15020;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 133.57 0.00045029 51651000 24330 35095 30962 37494 34758 43409 32135 32820 31466 22434 FALSE TRUE 25290.56719 41122.29325 31768.89516 44910.20129 28849.84758 33327.91762 29616.17473 32380.10158 30333.54481 26829.51278 0.942639823 1.532726054 1.184102575 1.673910431 1.075302702 1.242211064 1.103865545 1.206883698 1.13060364 1 14.71153323 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 DEALQNIS(1)ADDLPDSASQAAHPQDSAFSYR;DEALQNIS(1)ADDLPDSASQAAHPQDSAFSYR;DEALQNIS(1)ADDLPDSASQAAHPQDSAFSYR 246.7 3.90E-46 488860000 63685 81861 88514 77936 91251 113959 93089 85615 85491 81588 TRUE FALSE 66199.33298 95919.98996 90820.74756 93351.50818 75740.18761 87493.74932 85792.44094 84467.47096 82414.19561 97573.6065 0.678455326 0.983052625 0.930792156 0.956729094 0.776236426 0.896694838 0.879258685 0.865679501 0.844636153 1 16.57420333 -2.406071603 2.093711788 1.893117691 0.873922119 0.177522449 0.084393788 9133042.674 694108.9538 38756335.68 0.020521787 0.003925802 2.406071603 -1.019195572 DEALQNISADDLPDSAS(ph)QAAHPQDSAFSYR ddPTM_MDA-MB-175_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 DEALQNISADDLPDS(0.191)AS(0.809)QAAHPQDSAFSYR 101.78 0.0002594 105560000 13478 15443 16455 18329 23079 22023 12723 20600 17050 17824 TRUE FALSE 14010.12185 18095.21512 16883.83082 21954.42149 19156.03982 16908.49201 11725.73801 20323.89069 16436.37383 21316.27154 0.657250112 0.848892129 0.792063039 1.029937222 0.898658088 0.793219958 0.550083911 0.953444914 0.771071705 1 14.3796675 -2.444040503 2.00692138 2.415115143 0.81820476 0.156069401 0.131095135 4160830.891 293620.2977 26805508.37 0.035028402 0.003597158 2.444040503 -1.596910383 DEAQNEGPATESEAPLKEDGLLPKPLS(ph)SGGEEEEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEAQNEGPATESEAPLKEDGLLPKPLSSGGEEEEKPR 37 3 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 DEAQNEGPATESEAPLKEDGLLPKPLS(0.5)S(0.5)GGEEEEKPR;DEAQNEGPATESEAPLKEDGLLPKPLS(0.5)S(0.5)GGEEEEKPR 220.44 2.63E-39 202650000 286770 67876 127917 69523 244210 209082 238540 129635 179950 51939 TRUE FALSE 298091.901 79533.175 131250.6221 83274.44189 202699.2714 160525.8742 219842.6115 127897.4549 173473.6347 62115.45262 4.798997487 1.280408846 2.113010798 1.340639702 3.263266432 2.58431465 3.539257982 2.059027979 2.792761339 1 15.9226646 3.187485017 24.99998865 2.625300766 2.285149751 0 1.11736221 540.9364203 264770.0193 0.306598677 0.366455984 1539.873401 -3.187485017 -0.340151016 DEATAAVIDLNDRPIGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEATAAVIDLNDRPIGSR 18 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 243.95 3.71E-24 164070000 120660 129760 139700 129860 159750 149370 142190 126820 137950 115840 FALSE TRUE 125423.75 152045.2706 143340.6968 155545.9204 132595.7521 114681.0812 131044.7763 125120.1853 132985.2064 138536.6301 0.905347199 1.097509521 1.034677231 1.122778288 0.957116915 0.827803312 0.945921495 0.903155976 0.959928117 1 17.07990796 3.027922755 12.57322095 0.918607125 1.043351052 0.380269419 0.067767651 0.905484881 405.4279479 0.018523479 0.022109263 1066.406429 -3.027922755 0.124743927 DEDDADYKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DEDDADYKPK 10 1 P11387 P11387 TOP1 DNA topoisomerase 1 0 ;; 128.01 0.00031082 835500000 2802570 1099590 1765880 1034630 2355140 2151390 2387710 1441320 1809710 643580 FALSE TRUE 2913217.628 1288436.029 1811900.283 1239276.726 1954814.144 1651762.277 2200555.051 1422001.463 1744578.891 769677.1789 3.784986365 1.673995363 2.354104205 1.610125336 2.539784468 2.14604554 2.859062359 1.84752972 2.266637154 1 19.55389395 -1.596498397 0.317262712 1.96E-12 2.408430094 0.322615764 0.598118912 29.35666828 1.746797496 24.11374339 0.534617291 0.02532221 1.596498397 2.408430094 DEDGES(ph)GGQRS(ph)EAEEGEVR ddPTM_MDA-MB-175_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 2 DEDGES(1)GGQRS(1)EAEEGEVR;DEDGES(1)GGQRS(1)EAEEGEVR 125 1.60E-05 400500000 566090 504090 516590 543490 601320 746150 724420 529720 562040 319410 TRUE FALSE 588439.6703 590663.5362 530052.7598 650990.6998 499107.8412 572867.9705 667638.0675 522619.9698 541812.2902 381992.274 1.540449141 1.546270897 1.387600734 1.704198603 1.306591455 1.499684704 1.747778981 1.368142775 1.418385468 1 18.54318393 0.688377528 1.318793394 1.00146511 1.519966259 0.587489446 0.129705155 0.698108973 1.934912832 0.116705663 0.0349015 4.879524786 -0.688377528 0.518501149 DEDGESGGQRS(ph)EAEEGEVR ddPTM_MDA-MB-175_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 DEDGESGGQRS(1)EAEEGEVR;DEDGES(0.021)GGQRS(0.979)EAEEGEVR 230.86 2.86E-20 263890000 157471 153398 144409 147282 154801 191851 200101 140028 139268 98761 TRUE FALSE 163688.0767 179742.9132 148172.4172 176413.94 128487.9813 147296.5128 184416.5608 138151.1537 134255.7719 118111.3271 1.385879583 1.521809277 1.254514879 1.493624231 1.087854861 1.247098957 1.561379127 1.169668965 1.13668837 1 16.8497878 -3.858389788 0.076925867 2.63E-12 1.720230795 0.401448977 0.143474384 211.0993642 1.448886343 39.56737867 6.030842056 0.000138551 3.858389788 1.720230795 DEDGSTLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEDGSTLFR 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 115.49 0.0034126 198640000 215530 178790 176610 139290 255070 229800 206150 152770 204200 160630 FALSE TRUE 224039.2908 209495.7917 181212.6017 166841.1463 211713.2925 176432.4327 189991.4243 150722.368 196850.8819 192102.3731 1.16624947 1.090542446 0.943312666 0.868501225 1.102085774 0.91842922 0.989011334 0.784593993 1.024718637 1 17.55151582 4.35136383 3.212059343 0.94023347 1.154310499 0.417263907 0.083372663 0.215693268 4.229412085 0.02117569 0.073363248 22457.62525 -4.35136383 0.214077029 DEDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DEDLFR 6 0 O75531;A0A0C4DFW4;Q5JUR7 O75531;A0A0C4DFW4 BANF1;TEX30 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed;Testis-expressed sequence 30 protein" 0 ;;;; 132.94 0.034151 1818229000 2958810 3105370 3212810 3040700 3870380 4326340 3568340 3225940 3244910 3144920 FALSE TRUE 3075626.103 3638693.141 3296538.468 3642141.384 3212494.19 3321613.101 3288644.187 3182701.551 3128126.323 3761106.861 0.81774494 0.967452741 0.876480938 0.968369557 0.854135314 0.883147761 0.874382013 0.846214072 0.831703655 1 21.84272587 DEDMLYS(ph)PELAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEDMLYSPELAQR 13 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 DEDMLYS(1)PELAQR;DEDMLYS(1)PELAQR 255.39 8.15E-24 494520000 649480 578830 618000 600190 779300 818060 720780 690600 630620 518650 TRUE FALSE 675121.9719 678239.5498 634105.5877 718905.7906 646834.8644 628077.9628 664283.3802 681343.6366 607924.1094 620269.5373 1.088433223 1.09345939 1.022306513 1.159021598 1.042828682 1.012588762 1.07095922 1.098463806 0.980096672 1 19.24253575 1.232186377 24.99922616 0.990048286 1.073391347 0.410038316 0.040043521 156.966376 615580.271 0.034593588 0.009490596 17.06814709 -1.232186377 0.083343062 DEDRHDINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEDRHDINK 9 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 92.538 0.0060132 76527000 227940 144020 210470 154700 259470 257490 223990 188490 207620 121400 FALSE TRUE 236939.2472 168754.3147 215955.0211 185299.1983 215365.3821 197691.8498 206433.0785 185963.5999 200147.7968 145186.0057 1.631970286 1.162331823 1.487436893 1.276288286 1.483375626 1.361645352 1.421852455 1.280864495 1.378561218 1 17.14754287 -3.409035872 0.276889184 2.70E-09 1.408670255 0.480430527 0.122793658 66.30818777 1.427144451 38.01600589 0.130140631 0.00038991 3.409035872 1.408670252 DEDYKQR ddPTM_MDA-MB-175_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 ;;;;;;; 135.84 0.0027706 6564448000 8337910 6076341 7669600 4691670 10387510 8863680 7063810 7475810 8166190 5501462 FALSE TRUE 8667097.125 7119905.299 7869476.077 5619668.323 8621844.761 6805224.65 6510130.114 7375608.995 7872290.417 6579368.147 1.31731451 1.082156393 1.196083864 0.854134956 1.31043659 1.034327993 0.989476492 1.121020869 1.196511616 1 22.64951761 5.44587884 1.535841173 1.085423727 2.445278148 0.237773312 0.122465953 12.36060497 5.474193982 0.030237389 43.3054169 279176.4884 -5.44587884 1.359854421 DEEPSGWEEPS(ph)PQSISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEEPSGWEEPSPQSISR 17 0 Q9UPQ9-1;Q9UPQ9;H0Y720 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 DEEPSGWEEPS(1)PQSISR;DEEPSGWEEPS(1)PQSISR 427.08 6.47E-128 44336000 192685 178040 188199 187312 212212 229024 239405 183829 179833 125125 TRUE FALSE 200292.3526 208616.985 193103.6205 224361.7545 176140.28 175836.6469 220639.8105 181365.0729 173360.8455 149640.8481 1.338487152 1.394117901 1.290447248 1.499334957 1.177086887 1.175057808 1.474462444 1.21200244 1.15851285 1 17.19114452 0.512299112 0.379603303 0.9554539 1.365909139 0.497501452 0.105432582 2.0882329 0.602077598 0.262031305 0.086934931 3.25311272 -0.512299112 0.410455239 DEESGGGSNPFQHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEESGGGSNPFQHLEK 16 0 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 221.31 1.07E-14 419910000 457340 360300 523520 437080 640250 622580 618900 520450 542020 314670 FALSE TRUE 475396.1363 422178.7223 537163.3613 523533.1194 531420.5337 477995.2303 570389.0008 513474.219 522512.8061 376323.5618 1.263264341 1.121850357 1.427397633 1.391178158 1.412137287 1.270170882 1.515687719 1.364448765 1.388466892 1 18.52161409 4.236153691 24.99983701 1.368886732 1.192557336 0.15487653 0.135486493 78.88782555 819417.314 0.030088157 0.070228579 17224.78031 -4.236153691 -0.176329396 DEESHEFVIEAGALMLADNGVCCIDEFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEESHEFVIEAGALMLADNGVCCIDEFDK 29 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 116.74 6.13E-11 0 12453 7006.3 9358.6 9098.4 14851 13022 13722 8551.7 10627 4779.2 FALSE TRUE 12944.65406 8209.577524 9602.492804 10898.03636 12326.63232 9997.83785 12646.43378 8437.078449 10244.53635 5715.592737 2.264796435 1.436347532 1.680051964 1.906720242 2.156667365 1.749221526 2.212619822 1.47615109 1.79238389 1 12.48068741 0.530357435 0.904308636 1.000123902 1.874126375 0.481965593 0.270117908 1.320662134 1.654681031 0.256888543 0.0832619 3.391231483 -0.530357435 0.874002473 DEEVHAGLGELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DEEVHAGLGELLR 13 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ;;;;; 185.87 8.29E-06 3040990000 2479550 2717210 2498190 3256260 3162430 3764430 3640270 2629700 2527060 1846070 FALSE TRUE 2577444.549 3183869.681 2563294.884 3900338.509 2624881.278 2890198.183 3354936.125 2594453.173 2436111.604 2207772.071 1.167441414 1.442118832 1.16103239 1.766640026 1.188927658 1.309101705 1.519602575 1.17514539 1.10342532 1 21.07415981 1.519131558 4.073839333 1.069104876 1.366781753 0.343863816 0.176899596 0.202918671 7.324515604 0.106656019 0.043409164 33.04696331 -1.519131558 0.297676877 DEEVLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 100.15 0.016044 418570000 522210 246760 335600 268440 519270 453400 455310 340210 363380 227500 FALSE TRUE 542827.254 289139.1105 344346.0117 321536.6308 431004.6709 348104.7213 419621.6125 335650.0414 350302.0248 272074.2692 1.995143663 1.062721261 1.265632405 1.181797278 1.584143448 1.279447418 1.542305392 1.233670653 1.287523534 1 18.053641 -4.078157214 0.170996559 3.94E-14 1.45829055 0.205597701 0.247389513 161.7049658 2.037842081 56.56151351 0.862403381 8.35E-05 4.078157214 1.45829055 DEFEFLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DEFEFLEK 8 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ;;; 163.99 0.00077406 154312000 277384 197653 247732 185097 331714 298272 312960 237746 260356 159857 FALSE TRUE 288335.3345 231598.3652 254188.0994 221708.6341 275329.3728 229002.8484 288429.3774 234559.4037 250985.8384 191177.9185 1.508204173 1.211428428 1.329589219 1.159697918 1.440173504 1.197851981 1.508696086 1.22691682 1.312839058 1 17.54455637 0.222436831 1.216630988 0.999482633 1.319572563 0.389491504 0.120996548 5.254650685 7.284200105 0.109370149 0.031389305 1.66892504 -0.222436831 0.32008993 DEFEGLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DEFEGLFK 8 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 159.04 0.00084097 1164784000 2097350 1389640 1837652 1476060 2475692 2330353 2374085 1881406 2096157 1262715 FALSE TRUE 2180154.998 1628299.86 1885542.721 1768020.262 2054874.758 1789163.833 2187998.014 1856188.83 2020716.719 1510119.828 1.44369669 1.078258712 1.248604704 1.170781437 1.360736228 1.18478269 1.448890329 1.229166584 1.338116805 1 20.5262316 -0.993132628 4.53514722 0.999993868 1.272181062 0.346373953 0.114352806 6659481.334 1468415.568 488.6953592 0.024526891 0.101593839 0.993132628 0.272187195 DEHLDFIQSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEHLDFIQSHLR 12 0 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 138.42 4.32E-05 50441000 20757 18154 21427 25278 24188 29040 29113 21075 23068 16015 FALSE TRUE 21576.50239 21271.80828 21985.40522 30277.91295 20076.5324 22295.90011 26831.04699 20792.5241 22237.78719 19152.83262 1.126543672 1.110635105 1.147893142 1.580858223 1.048227841 1.164104576 1.400891843 1.085610912 1.161070408 1 14.22527016 0.99700929 1.372280875 1.006204746 1.218866269 0.149787257 0.153573181 0.857057703 3.298029254 0.142488949 0.042980731 9.931372916 -0.99700929 0.212661523 DEHLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DEHLLK 6 0 O00505;O00629 O00505;O00629 KPNA3;KPNA4 Importin subunit alpha-4;Importin subunit alpha-3 0 ;;;; 121.68 0.019546 894288000 3859480 2882190 3565690 2918790 4574880 4480380 4513870 3610640 3855900 2648250 FALSE TRUE 4011855.251 3377183.712 3658614.811 3496117.95 3797243.532 3439879.646 4160061.075 3562245.277 3717126.912 3167123.884 1.266718764 1.066325106 1.155185255 1.103877865 1.198956426 1.086120964 1.313513846 1.124757164 1.173660093 1 21.59474187 -0.993510822 4.479438956 0.999994952 1.162777104 0.308414134 0.074232231 3.41E-06 7.66E-07 0.065466975 0.015430235 0.101505407 0.993510822 0.162782152 DEILEWESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DEILEWESR 9 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;;; 182.73 0.00010699 1070280000 882870 881300 962390 925660 1188270 1297010 1153480 1009600 1025730 786830 FALSE TRUE 917726.3893 1032656.419 987470.674 1108752.785 986288.2898 995799.0839 1063067.224 996067.9634 988814.1777 940994.2737 0.975273086 1.097409887 1.049390737 1.17827793 1.04813421 1.058241385 1.129727622 1.058527125 1.050818486 1 19.84382642 0.937371434 1.953716021 1.000639529 1.078714119 0.163522554 0.051055919 0.655553518 5.270734716 0.045867365 0.01284354 8.657080058 -0.937371434 0.07807459 DEILPTT(ph)PISEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 DEILPTTPISEQK 13 0 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 DEILPT(0.001)T(0.999)PISEQK;DEILPT(0.208)T(0.792)PISEQK;DEILPT(0.001)T(0.999)PISEQK;DEILPT(0.209)T(0.791)PISEQK;DEILPT(0.184)T(0.816)PISEQK;DEILPT(0.001)T(0.999)PISEQK;DEILPT(0.133)T(0.867)PISEQK;DEILPT(0.01)T(0.99)PISEQK;DEILPT(0.377)T(0.622)PISEQK;DEILPT(0.239)T(0.761)PISEQK 375.65 1.91E-90 72031490000 19448910 11181670 15299670 11263850 19830820 19492630 19978150 14386980 16227430 7718430 TRUE FALSE 20216767.98 13102034.84 15698391.97 13491805.91 16459984.3 14965762.1 18412210.4 14194146.07 15643407.96 9230708.58 2.190164255 1.419396434 1.700670304 1.461621911 1.783176682 1.621301546 1.994669233 1.537709261 1.694713665 1 23.13800997 0.078705905 1.146066066 0.997219892 1.702907277 0.476307672 0.223815429 6.587664802 7.337303131 0.249619651 0.060007587 1.198687303 -0.078705905 0.705687384 DEKDEHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DEKDEHGR 8 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 134.26 0.00053128 259580000 1153940 582480 941990 615504 1207840 1137180 1285100 890202 1004290 498555 FALSE TRUE 1199498.442 682516.4089 966539.0333 737248.8541 1002531.788 873087.1791 1184370.504 878270.2983 968145.7991 596237.3068 2.011780257 1.144705977 1.621064335 1.236502389 1.681430828 1.464328329 1.986407912 1.473021376 1.623759178 1 19.18552712 DEKPVEAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEKPVEAIR 9 1 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 94.363 0.008001 828650000 844770 730550 757820 744390 1183790 1120470 1049610 878420 915420 550590 FALSE TRUE 878122.1719 856016.2796 777569.4118 891628.1202 982569.7986 860257.8234 967338.8256 866646.2167 882474.213 658467.5688 1.333584543 1.300012818 1.180877311 1.354095725 1.492206823 1.306454356 1.469075884 1.316156266 1.340193891 1 19.32875286 0.270336444 2.107148085 0.999996514 1.34542056 0.607938447 0.082792393 15.11670207 42.36313711 0.081565927 0.022232703 1.863530235 -0.270336444 0.345424046 DELEVIHLIEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DELEVIHLIEEHR 13 0 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;; 262.07 2.48E-24 449257000 338884 333284 366560 348986 443915 475233 466211 372393 388431 257827 FALSE TRUE 352263.402 390522.9344 376112.8547 418014.3892 368458.4869 364867.338 429668.1636 367401.6809 374451.4442 308343.2643 1.142439102 1.266520076 1.219786187 1.355678679 1.19496201 1.183315416 1.393473487 1.191534642 1.214398002 1 18.23417781 0.621840805 1.626727257 1.000271237 1.248910107 0.490936789 0.074062646 1.267945648 4.449829966 0.066859837 0.019093329 4.1864008 -0.621840805 0.24863887 DELHIVEAEAMNYEGS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;DELHIVEAEAMNY(0.001)EGS(0.999)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNYEGS(1)PIK 270 8.32E-33 991117000 1142913 580570 814396 808514 913225 1090130 1464125 861772 919462 322030 TRUE FALSE 1188036.088 680278.3813 835619.8288 968435.656 757995.3407 836963.8286 1349363.057 850221.3559 886370.7422 385125.6129 3.084801551 1.766380523 2.169733201 2.514596858 1.968176915 2.173222971 3.503695967 2.207646876 2.301510761 1 18.55496955 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNY(0.012)EGS(0.988)PIKVTLATLK;DELHIVEAEAMNY(0.012)EGS(0.988)PIKVTLATLK;DELHIVEAEAMNY(0.02)EGS(0.98)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.014)EGS(0.984)PIKVT(0.002)LATLK;DELHIVEAEAMNY(0.009)EGS(0.991)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNYEGS(1)PIKVTLATLK;DELHIVEAEAMNY(0.007)EGS(0.826)PIKVT(0.167)LATLK;DELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK 421.92 4.91E-187 5558036000 5245889 2433771 3593223 2808548 5091767 4968621 5791509 3897569 4365413 1678706 TRUE FALSE 5453000.748 2851752.237 3686865.343 3364070.412 4226270.264 3814734.073 5337555.391 3845328.463 4208302.639 2007616.3 2.716156842 1.420466768 1.836439236 1.675654064 2.105118525 1.900131052 2.658653146 1.915370214 2.096168794 1 20.93705213 3.203432929 24.99515671 2.03194825 1.871646277 0 0.495432571 863.0408597 614095.5415 0.13412122 0.160311315 1597.470803 -3.203432929 -0.160301973 DELHIVEAEAMNYEGSPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;; 260.97 3.92E-31 2661948000 3369895 2538529 3300168 2953928 3916711 4195775 5178725 3567063 3652695 1924709 FALSE TRUE 3502941.057 2974501.609 3386173.089 3538206.142 3250949.863 3221369.844 4772803.002 3519252.355 3521235.22 2301818.878 1.521814375 1.292239645 1.47108581 1.537134905 1.412339561 1.399488846 2.073491989 1.52890064 1.529762074 1 21.13434289 DELHIVEAEAMNYEGSPIKVT(ph)LATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 DELHIVEAEAMNYEGS(0.004)PIKVT(0.996)LATLK 98.74 0.0084152 1851100000 53448 35402 38239 44664 76314 69523 85405 56378 58431 23154 TRUE FALSE 55558.16831 41482.01811 39235.53975 53498.40589 63342.17354 53377.33688 78710.73294 55622.34513 56328.07972 27690.58299 2.006392149 1.498055065 1.416927183 1.932007207 2.287498734 1.927634998 2.842509057 2.008709789 2.034196237 1 14.75710781 3.516374775 5.951967566 2.114667633 1.630155885 0.099043665 0.453838483 0.316538729 30.74722331 0.114913679 0.174748548 3283.785454 -3.516374775 -0.484511748 DELKEALDDVTLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DELKEALDDVTLPR 14 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 138.39 1.43E-05 52676000 75816 43425 63674 50260 86425 80717 93720 58455 73589 39619 FALSE TRUE 78809.27422 50882.90595 65333.39675 60201.27799 71734.50937 61971.70003 86373.98151 57671.50634 70940.54626 47381.5845 1.663289125 1.073896251 1.378877415 1.270562786 1.513974472 1.307927978 1.822944134 1.217171332 1.497217685 1 15.53203882 -0.698979829 5.804708765 0.999999989 1.404449082 0.262300563 0.208559825 2.77E-08 6.20E-09 0.185707745 0.043771734 0.199995475 0.698979829 0.404449094 DELRETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DELRETLK 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 111.46 0.0029459 629460000 260540 212524 265410 185078 400180 336260 279670 245476 294530 239150 FALSE TRUE 270826.3204 249023.3438 272326.8026 221685.876 332157.5465 258168.7111 257748.7346 242185.7957 283929.9228 286006.8637 0.946922451 0.870690097 0.952168767 0.775106839 1.161362151 0.902666138 0.901197724 0.84678316 0.992738143 1 18.12569024 2.998929339 0.006716228 1.846596156 4.24E-05 0.029915113 0.097953286 37392.71326 82.46170695 11081.94377 11587.48711 997.5377494 -2.998929339 -1.846553778 DELTES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DELTESPK 8 0 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELTES(1)PK;DELTES(1)PK;DELTES(1)PK 182.28 0.00024059 1177800000 2386480 838591 984270 1039490 1493720 2303130 1953180 1192660 1169580 561893 TRUE FALSE 2480700.073 982612.4809 1009920.885 1245098.019 1239818.008 1768262.962 1800084.648 1176674.343 1127487.044 671985.1753 3.691599405 1.462253212 1.502891614 1.852865309 1.845007976 2.631401743 2.678756488 1.751042116 1.677845116 1 19.35806988 4.747144895 24.86961604 1.895120509 3.691600382 0.566380082 0.486920731 816.7481151 2366154.683 0.11951822 1.40315929 55865.65505 -4.747144895 1.796479873 DELTES(ph)PKYIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DELTESPKYIQK 12 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 DELT(0.001)ES(0.999)PKYIQK 118.21 0.00039377 507500000 528260 142520 257760 137890 410640 445960 381800 281900 289830 93993 TRUE FALSE 549116.1127 166996.7013 264477.4374 165164.2304 340839.5595 342392.5486 351873.5184 278121.5916 279399.0749 112409.1287 4.884977927 1.485615121 2.352811024 1.469313323 3.032134163 3.04594967 3.130293085 2.474190439 2.485555026 1 16.77839968 DENGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DENGELR 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 134.12 0.007456 312510000 692410 794760 811060 731720 931070 1027410 924050 880920 843170 716890 FALSE TRUE 719746.8815 931253.8476 832196.8899 876452.032 772807.054 788809.598 851620.5464 869112.7083 812824.4764 857350.8698 0.839500964 1.086199222 0.97066081 1.022279282 0.901389479 0.920054584 0.993316245 1.013718816 0.948065145 1 19.70952622 DENQSINHQMAQEDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DENQSINHQMAQEDAQR 17 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 91.065 0.0036477 401530000 696660 186100 226060 198930 595830 2235200 566100 294470 297560 125580 FALSE TRUE 724164.6747 218061.2273 231951.3093 238277.7603 494551.0294 1716108.675 521727.6028 290523.1113 286850.8737 150184.9966 4.821817698 1.451950809 1.544437291 1.586561678 3.292945637 11.42663191 3.47389962 1.934434982 1.909983555 1 17.19638117 5.042013971 17.62807121 3.223159245 13.62188424 0.029366146 2.903896016 141551623.4 1435807223 431.9449442 49337430226 110157.4746 -5.042013971 10.398725 DENWDKEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DENWDKEIEK 10 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 104.24 0.0024692 842510000 1104480 568770 851100 565360 1148020 1088910 1173420 841330 1081390 465810 FALSE TRUE 1148085.723 666451.8231 873280.3652 677186.5206 952879.9705 836027.1551 1081444.274 830053.3475 1042470.985 557076.551 2.060911954 1.196337957 1.56761286 1.215607656 1.710500951 1.500740165 1.94128486 1.49001667 1.871324476 1 19.08751606 DEPCSSTSRPALEEDVIYHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEPCSSTSRPALEEDVIYHVK 21 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 ; 92.31 0.0011336 155546000 111373 112728 122817 102203 138111 155378 164694 126337 137589 97038 FALSE TRUE 115770.092 132088.1571 126017.7119 122418.4484 114634.9416 119293.8143 151784.8539 124643.6592 132637.1988 116050.7382 0.997581694 1.138193166 1.085884621 1.054870053 0.987800193 1.027945329 1.307918039 1.074044518 1.142924214 1 16.82439617 DEPDWESLIFLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DEPDWESLIFLAR 13 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;;; 237.93 2.16E-16 331144000 120500.9 123081 137830.4 137916.2 158757.5 170520.8 177097 138575.9 146042.3 96601.2 FALSE TRUE 125258.3686 144219.2043 141422.3735 165195.6127 131771.9569 130919.9285 163215.6744 136718.5167 140786.2662 115528.3556 1.08422186 1.248344647 1.224135605 1.429913997 1.140602722 1.133227663 1.412775881 1.183419568 1.218629534 1 16.81788747 0.536538173 1.752883871 1.000108148 1.238672212 0.294608333 0.107063701 3.372768835 11.3602533 0.098593027 0.027729852 3.439839454 -0.536538173 0.238564064 DEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEPPPLSPAPLTPATPSSLDPFFSR 25 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DEPPPLS(0.998)PAPLT(0.002)PATPSSLDPFFSR 63.095 0.03662 25746000 6176.5 7562.2 7703.7 9855.3 5470.5 11306 9045.9 7367.5 9504.8 7462.2 TRUE FALSE 6420.352989 8860.949024 7904.464751 11804.64892 4540.626364 8680.352844 8336.858721 7268.750713 9162.724105 8924.275218 0.719425705 0.992904052 0.885726242 1.322757158 0.508794973 0.972667542 0.93417768 0.814491994 1.026719132 1 13.12351929 1.213253465 24.77363825 1.013359788 0.898709067 0.055280199 0.196776759 773.6254329 757293.9284 0.175757407 0.044011163 16.34005317 -1.213253465 -0.114650721 DEPQEPSNKVPEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEPQEPSNKVPEQQR 15 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 133.66 3.64E-05 278270000 171741 126857 146076 124907 198670 208591 177224 155658 163954 124731 FALSE TRUE 178521.4673 148643.7029 149882.8606 149613.2318 164900.1444 160148.9015 163332.7198 153571.6591 158053.3276 149169.6513 1.196768013 0.99647416 1.004781195 1.002973664 1.105453709 1.073602439 1.094946045 1.029510076 1.05955418 1 17.18659452 0.450875312 1.131488666 1.000099925 1.059710439 0.09369087 0.057841606 5.907060857 9.572184657 0.054395102 0.016627587 2.824069055 -0.450875312 0.059610514 DEPSVAAMVYPFTGDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DEPSVAAMVYPFTGDHK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;; 206.95 6.52E-12 2755170000 2505034 1751908 2318360 1736894 3606240 2893820 3355100 2409231 2621411 1591069 FALSE TRUE 2603934.677 2052784.571 2378778.366 2080446.449 2993252.613 2221774.161 3092118.495 2376939.199 2527066.93 1902808.508 1.368469116 1.078818264 1.250140703 1.093355659 1.573070859 1.167628877 1.625028731 1.249174149 1.328072121 1 20.85969895 3.283900497 24.99998639 1.343503229 1.192950846 0.093439898 0.186291034 249.9721709 137830.5509 0.047002955 0.063642057 1922.651171 -3.283900497 -0.150552383 DESETEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DESETEKEK 9 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 116.77 0.0011497 520740000 1330230 440650 752170 447730 1187210 1140470 1194620 768620 997120 394730 FALSE TRUE 1382748.508 516328.2097 771772.1681 536289.6577 985408.4683 875613.1265 1100982.563 758317.9061 961233.846 472069.7859 2.929118848 1.093753985 1.634868808 1.136038937 2.087421177 1.854838315 2.332245349 1.606368229 2.036211329 1 18.84864062 DETALQEEEELQLALALSQSEAEEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DETALQEEEELQLALALSQSEAEEKER 27 1 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 92.198 0.005521 31746000 21601 17294 21974 18616 25204 28284 26812 19686 22263 11345 FALSE TRUE 22453.82416 20264.10997 22546.66049 22298.18924 20919.83308 21715.46965 24710.40538 19422.14137 21461.75898 13567.83554 1.654930449 1.49354036 1.661772833 1.643459576 1.541869595 1.600510972 1.821248888 1.431484139 1.581811551 1 13.72790297 0.190318349 0.914751621 0.994446259 1.614042079 0.771922899 0.098881629 1.705818551 1.560004237 0.115656488 0.029899383 1.549952358 -0.190318349 0.61959582 DETEFYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DETEFYLGK 9 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 190.51 8.60E-05 975587000 2061840 1348682 1935890 1392393 2446670 2293090 2356690 1830880 2106620 1185379 FALSE TRUE 2143243.035 1580307.642 1986340.884 1667804.18 2030785.907 1760554.6 2171966.48 1806340.048 2030803.158 1417631.32 1.511847972 1.114752207 1.401168877 1.176472441 1.432520486 1.241898775 1.532109548 1.274195923 1.432532655 1 20.43505095 -1.419326212 5.677479011 0.999828841 1.33897121 0.37538109 0.133739097 0.000256177 2.62E-05 0.114490171 0.026972109 0.03807797 1.419326212 0.339142369 DETEFYLGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DETEFYLGKR 10 1 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 170.99 6.67E-06 1383890000 929440 832870 1073720 575030 1536810 1155120 863110 988580 1137900 920160 FALSE TRUE 966135.0089 975908.9437 1101702.025 688769.2177 1275583.585 886860.886 795457.1829 975329.7021 1096947.201 1100447.734 0.877947202 0.886828982 1.0011398 0.625899074 1.159149631 0.805909139 0.722848671 0.886302613 0.996818992 1 20.0696592 1.257844706 5.866731609 1.000206636 0.867923214 0.123143146 0.13661205 0.308962048 33.65450025 0.099102948 0.032095508 18.10692514 -1.257844706 -0.132283422 DETNYGIPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 229.61 3.58E-09 822070000 820570 704960 771630 748550 863250 930350 954890 808830 782390 585310 FALSE TRUE 852966.7372 826031.3962 791739.3117 896610.9558 716515.0733 714290.3121 880043.2267 797988.9568 754231.9367 699990.2881 1.218540817 1.180061224 1.131071852 1.280890565 1.023607164 1.020428889 1.257222052 1.140000041 1.077489145 1 19.41697538 -5 0.09607264 0.530396618 1.258398942 0.290587466 0.080917599 281.4959593 1.856931737 26.8594241 1.589322327 1.00E-05 5 0.728002324 DETVSDCSPHIANIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DETVSDCSPHIANIGR 16 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 230.38 2.31E-15 776280000 600470 745150 720190 848860 846760 1020180 940510 849650 797120 584680 FALSE TRUE 624177.0193 873123.716 738958.743 1016761.974 702828.0377 783258.656 866790.3686 838261.8315 768431.8069 699236.8516 0.892654639 1.248680921 1.056807491 1.454102386 1.005135865 1.120162151 1.239623407 1.198823874 1.098957821 1 19.4154217 4.749089997 24.31206463 1.169399542 0.892654409 0.269233731 0.129954041 1255.869803 2899685.969 0.028589681 0.400034902 56116.42517 -4.749089997 -0.276745133 DEVLDNLLAFVCDIRPEIHENYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEVLDNLLAFVCDIRPEIHENYR 23 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 124.86 3.38E-05 115680000 94153 98975 113100 102500 160060 156370 137250 116110 113920 110450 FALSE TRUE 97870.23314 115973.1863 116047.4789 122774.1941 132853.0584 120055.4373 126491.9864 114553.7354 109820.0415 132090.5628 0.74093282 0.877982377 0.878544814 0.929469838 1.005772521 0.908887318 0.957615621 0.867236333 0.831399603 1 17.01116787 5.049916154 1.292995775 0.921734993 0.532237543 0.529898593 0.051982735 2.29086284 1.96965051 0.014720489 1.427095649 112180.1855 -5.049916154 -0.38949745 DEVLYVFPSDFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEVLYVFPSDFCR 13 0 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ; 132.76 0.00026759 62599000 120802 118509 104583 132077 136543 172103 134319 107198 105600 107484 FALSE TRUE 125571.3562 138861.9989 107308.5189 158201.4364 113333.4696 132134.6865 123790.7258 105761.1862 101799.4766 128543.4319 0.976878821 1.080273001 0.834803594 1.230723609 0.881674528 1.027938064 0.963026457 0.822766162 0.791946155 1 16.97189637 1.895323454 4.366517334 0.855812743 1.005110139 0.213843653 0.113249319 0.29680047 9.004929577 0.049520661 0.028484366 78.58206807 -1.895323454 0.149297397 DEVQEVVFVPAGTHT(ph)PGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEVQEVVFVPAGTHTPGSR 19 0 J3KS57;J3KT79;J3QR84;J3QRJ1;J3QL71;Q96FV2-2;Q96FV2 J3KS57 SCRN2 Secernin-2 1 DEVQEVVFVPAGT(0.393)HT(0.597)PGS(0.01)R;DEVQEVVFVPAGT(0.002)HT(0.998)PGSR 156.43 5.89E-08 470860000 273746 289292 353414 337564 403550 424210 398280 330408 351450 271160 TRUE FALSE 284553.7035 338975.6506 362624.2592 404333.1517 334954.7151 325693.6565 367061.7729 325979.4212 338801.3832 324288.6103 0.877470544 1.045290028 1.118214602 1.246831183 1.032890778 1.004332703 1.131898442 1.005213908 1.044752644 1 18.30691883 1.61824036 25 1.018738052 1.06984169 0.055355978 0.090550364 2.411520337 5796.469268 0.044135292 0.02413733 41.51837618 -1.61824036 0.051103638 DEVQEVVYFSAADHEPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DEVQEVVYFSAADHEPESK 19 0 Q12765;Q12765-2;C9K052;B8ZZP4;C9J7U9 Q12765 SCRN1 Secernin-1 0 ;; 232.29 1.39E-20 559900000 1276380 963780 1235230 932350 1737160 1664940 1644310 1243380 1417710 899090 FALSE TRUE 1326772.468 1129301.718 1267421.109 1116766.047 1441878.164 1278282.917 1515424.686 1226714.525 1366686.894 1075249.471 1.233920595 1.050269494 1.178722838 1.03861111 1.340970818 1.188824502 1.409370314 1.140865034 1.27104168 1 20.03623999 3.244468425 24.99937944 1.236739072 1.12382605 0.144075088 0.11712479 235.8018705 997807.9913 0.030035248 0.039630281 1755.773239 -3.244468425 -0.112913022 DEVVS(ph)PLPSALQGPSGSLSAPPAASVISAPPSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEVVSPLPSALQGPSGSLSAPPAASVISAPPSSSSR 36 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DEVVS(0.994)PLPS(0.006)ALQGPSGSLSAPPAASVISAPPSSSSR 199.75 2.80E-30 142190000 39286 40498 47927 37860 49065 48877 42014 40859 45471 46385 TRUE FALSE 40837.04162 47453.21647 49176.01699 45348.595 40724.94883 37526.05749 38720.8329 40311.35194 43834.50759 55473.25266 0.736157331 0.855425168 0.886481586 0.817485776 0.734136667 0.676471195 0.698009059 0.726680878 0.790191768 1 15.7595047 5.060541259 14.32337279 0.781236994 0.404263938 0.009481673 0.094302331 2362310.532 15041178.13 0.022903969 25163121.69 114958.5451 -5.060541259 -0.376973056 DEWLRPEDLPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEWLRPEDLPIK 12 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 172.99 3.13E-05 259840000 502200 358100 453590 385290 563270 566350 582300 462790 478330 279720 FALSE TRUE 522027.2438 419600.8894 465410.928 461499.212 467525.5666 434823.7956 536657.8044 456587.057 461114.9967 334525.7784 1.560499302 1.254315561 1.391255796 1.379562479 1.397577098 1.29982149 1.604234528 1.364878543 1.378413941 1 18.35175786 0.530870872 2.292744454 1.000023478 1.40344577 0.595182581 0.100052072 3.473506525 16.16517098 0.089532257 0.024154663 3.395243073 -0.530870872 0.403422291 DEYLADLYHFVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DEYLADLYHFVTK 13 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 ; 128.9 0.00015992 385300000 447520 316440 424990 398980 539190 540100 645980 459990 486220 253990 FALSE TRUE 465188.4352 370786.1084 436065.5885 477897.0532 447538.6764 414669.9603 595346.3996 453824.5864 468721.0372 303754.4776 1.531461985 1.220677013 1.435585714 1.57330044 1.47335664 1.36514847 1.959959255 1.494050689 1.543091779 1 18.21254615 3.995628811 24.12957602 1.526756396 1.364084978 0.015187086 0.233706961 304.3219893 1679964.243 0.05506584 0.114318468 9899.854478 -3.995628811 -0.162671419 DEYRQDYDAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DEYRQDYDAGR 11 1 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 167.71 1.73E-05 236940000 201760 261680 269150 261280 298730 332080 247510 283810 248780 294190 FALSE TRUE 209725.6406 306621.5044 276164.2701 312960.4042 247951.9813 254959.4527 228109.5195 280005.9912 239826.4564 351830.8979 0.596097847 0.871502492 0.784934671 0.889519386 0.704747601 0.724664759 0.648349877 0.795853897 0.681652629 1 18.42452266 -1.216444538 5.092168386 1.000025499 0.750819387 0.425440192 0.088895181 2.46E-05 3.78E-06 0.082224443 0.019378506 0.060751284 1.216444538 -0.249206111 DFADWYLEQLNSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFADWYLEQLNSDR 14 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 0 114.82 0.0010598 18136000 14358 29782 23150 32714 21077 30886 24804 26695 21526 27339 FALSE TRUE 14924.86493 34896.82683 23753.30802 39184.73156 17494.33907 23713.19458 22859.79767 26337.19719 20751.28346 32695.55361 0.456479958 1.067326378 0.726499643 1.198472796 0.535067834 0.725272765 0.699171451 0.805528406 0.634682126 1 14.99680683 4.773719243 23.74253529 0.806586914 0.456478468 0.233524801 0.196674168 14223.00978 9604409.105 0.044445912 8.587388182 59390.80921 -4.773719243 -0.350108445 DFAKS(ph)SGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFAKSSGLK 9 1 Q8NC26-2;Q8NC26 Q8NC26-2 ZNF114 Zinc finger protein 114 1 DFAKS(0.967)S(0.033)GLK 54.982 0.079625 148260000 123180 120910 157070 107540 164370 195570 166930 148780 161890 123510 TRUE FALSE 128043.2415 141675.352 161163.3732 128811.091 136430.4461 150151.8314 153845.5904 146785.8475 156063.6105 147709.4198 0.866859011 0.959149066 1.091083923 0.87205739 0.923640796 1.016535246 1.041542176 0.99374737 1.05655828 1 17.17240231 2.720247762 19.44441075 1.020657451 0.947814537 0.298589879 0.060352978 67.2819063 71437.52515 0.019870348 0.018814453 525.1069445 -2.720247762 -0.072842915 DFAVSTVPVSGPSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFAVSTVPVSGPSHLR 16 0 O95865;A0A140T971;Q5SSV3;Q5SRR8;H0Y7N1 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ; 124.25 8.35E-05 851940000 352310 501630 509870 472970 544180 651570 495010 524290 494160 507510 FALSE TRUE 366219.4708 587781.0504 523157.6311 566522.0543 451680.478 500252.7421 456209.8227 517262.7501 476375.2781 606946.8676 0.603379786 0.968422578 0.861949635 0.933396455 0.744184544 0.824211754 0.75164705 0.852237284 0.784871467 1 19.2112107 -1.685402828 2.750473731 1.024344141 0.821198067 0.241536898 0.098198571 45296352.32 41177805.3 7719945.769 0.022140427 0.020634653 1.685402828 -0.203146075 DFAYGETDPLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFAYGETDPLIR 12 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;; 157.38 0.0001721 208292000 396704 406023 426119 423603 459983 513438 457480 432470 429634 386253 FALSE TRUE 412366.1802 475754.2918 437224.0112 507390.4091 381795.254 394199.8057 421621.5222 426673.447 414171.5563 461931.8801 0.892699114 1.029923052 0.946511878 1.098409594 0.82651852 0.853372159 0.912735276 0.923671791 0.896607431 1 18.81732059 3.224799375 24.99897418 0.898653202 0.991361876 0.309024214 0.06560904 266.7361334 484557.86 0.018157393 0.021809291 1678.028665 -3.224799375 0.092708674 DFCHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFCHSK 6 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;H0YC07 Q8N573-2 OXR1 Oxidation resistance protein 1 0 ; 115.3 0.024549 132861000 249240 188816 230920 178555 288250 292130 276560 225960 240390 189612 FALSE TRUE 259080.1877 221243.6792 236937.9649 213872.6461 239253.368 224287.2348 254882.5045 222931.3758 231738.4109 226762.8411 1.14251606 0.975661084 1.044871213 0.943155612 1.055081895 0.98908284 1.124004724 0.983103646 1.021941733 1 17.79082472 4.750760205 24.57271996 1.017254883 1.142516158 0.386533429 0.048051524 1500.924531 3023129.785 0.010628219 0.176350246 56332.65301 -4.750760205 0.125261275 DFDFESANAQFNKEEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DFDFESANAQFNKEEIDR 18 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;; 317.46 1.98E-61 2210260000 2081721 1556722 2069723 1569714 2533139 2464317 2388151 2024632 2151130 1283059 FALSE TRUE 2163908.953 1824076.894 2123661.682 1880198.744 2102556.938 1892016.724 2200961.484 1997495.12 2073711.252 1534449.845 1.410218105 1.188749765 1.383988983 1.22532434 1.370235035 1.23302611 1.434365216 1.301766314 1.351436319 1 20.54929006 -1.376444339 3.094885419 0.996274534 1.319572734 0.597269655 0.079328497 6783263.091 9338429.135 231724.7121 0.016666653 0.042029639 1.376444339 0.3232982 DFDFESANAQFNKEEIDREFHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFDFESANAQFNKEEIDREFHNK 23 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 166.69 7.01E-12 99494000 53393 46058 64713 18747 96329 71874 40585 50098 67193 59576 FALSE TRUE 55500.99687 53968.10322 66399.47394 22455.10065 79955.03099 55182.35276 37403.84165 49426.51825 64774.73706 71248.77655 0.778974736 0.757460069 0.931938444 0.315164719 1.122195143 0.774502461 0.524975213 0.693717431 0.909134728 1 16.12057762 1.08520586 4.39448469 0.996275657 0.732741663 0.159664091 0.203817647 0.333774373 10.9922316 0.185592213 0.047393849 12.16762621 -1.08520586 -0.263533994 DFDGEDSDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFDGEDSDSPR 11 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 DFDGEDSDS(1)PR;DFDGEDSDS(1)PR 248.13 3.59E-16 647050000 853560 819970 861620 927450 1040790 1155930 1122810 956510 965410 653160 TRUE FALSE 887259.2079 960793.469 884074.525 1110896.842 863876.8876 887482.7758 1034801.218 943689.548 930665.0827 781134.1965 1.135860153 1.229997961 1.131783155 1.422158762 1.105926346 1.136146362 1.324741924 1.208101697 1.191427909 1 19.57521089 0.708719248 2.974517269 1.000017895 1.215502798 0.314967216 0.093035207 2.869223631 27.92510473 0.084579279 0.022139281 5.113511635 -0.708719248 0.215484903 DFDPAVTEYIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DFDPAVTEYIQR 12 0 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;; 290.68 9.56E-36 9560350000 3444030 3825100 3879130 3662780 5018830 5020770 4397470 4007060 3900310 3961720 FALSE TRUE 3580002.964 4482031.17 3980223.315 4387266.952 4165731.069 3854772.258 4052784.811 3953351.915 3759938.605 4737943.182 0.755602764 0.945986686 0.840074092 0.925985556 0.879227738 0.813596134 0.85538907 0.834402559 0.793580349 1 22.17582947 DFDS(ph)S(ph)EDEKHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 90.561 0.0050023 137820000 1198700 269740 468750 289700 779410 951360 776290 447250 507860 168900 TRUE FALSE 1246025.602 316065.7467 480966.0101 347001.7953 646926.1666 730421.058 715442.3613 441255.3453 489582.2178 201992.7212 6.168665851 1.564738298 2.381105652 1.717892572 3.202720191 3.616076132 3.541921496 2.184511118 2.423761682 1 17.62394378 4.747890254 24.86444189 2.517356941 6.168667924 0.653130499 0.819374696 748.3834275 1994473.992 0.197064384 2.492800451 55961.61683 -4.747890254 3.651310983 DFDTALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFDTALK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 77.674 0.087024 134820000 347720 310140 300700 267360 437740 405370 360160 339980 333050 268030 FALSE TRUE 361448.2541 363404.1324 308536.489 320243.01 363333.1112 311228.9609 331929.7181 335423.1242 321063.5956 320545.3468 1.127604121 1.133705843 0.962536166 0.999056805 1.133484279 0.970935826 1.035515634 1.046413955 1.001616772 1 18.29016894 4.259972514 24.99165287 1.024048788 1.130655108 0.486377757 0.045757367 200.5118643 234030.4929 0.010854251 0.029665323 18195.85694 -4.259972514 0.10660632 DFDWNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 132.29 0.007872 475630000 1570980 1219960 1435100 1222620 1823770 1783580 1738630 1474880 1582920 1068550 FALSE TRUE 1633003.503 1429478.64 1472499.885 1464450.587 1513766.227 1369370.575 1602351.638 1455111.646 1525951.018 1277911.914 1.277868596 1.118604987 1.152270253 1.145971464 1.184562262 1.071568831 1.253882697 1.138663495 1.194097185 1 20.28535696 -1.775580534 2.515133351 0.954481242 1.167025832 0.436107902 0.058131465 48684930.74 33180438.89 13618058.89 0.012897185 0.016765614 1.775580534 0.21254459 DFEPYDFTLDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFEPYDFTLDD 11 0 Q69YN2;Q69YN2-2;Q69YN2-3 Q69YN2 CWF19L1 CWF19-like protein 1 0 107.47 0.0051031 13657000 50710 57432 57087 56934 72076 73116 62103 60516 62112 55467 FALSE TRUE 52712.06996 67295.49924 58574.73412 68195.37527 59824.54726 56135.91708 57235.20458 59704.882 59876.60125 66334.69667 0.794637989 1.014484163 0.883018044 1.028049855 0.901859061 0.846252714 0.862824547 0.900055099 0.902643779 1 16.01747606 3.020911897 24.99957207 0.891390704 0.936748821 0.020061537 0.072327238 608.4956214 727433.5511 0.019408222 0.023195593 1049.329535 -3.020911897 0.045358117 DFEQDILEDMYHAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFEQDILEDMYHAIK 15 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ;;; 197.88 8.20E-09 223154000 291404 179567 268814 265233 321556 332023 422005 281969 293816 123332 FALSE TRUE 302908.8549 210406.2354 275819.5137 317695.2958 266898.026 254915.6901 388927.1454 278189.6668 283241.6196 147496.5441 2.053667473 1.426516375 1.870006619 2.153916878 1.809520539 1.728282461 2.636855988 1.88607583 1.92032716 1 17.17032163 DFESHITSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFESHITSYK 10 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;;; 182.28 1.79E-06 2095320000 4694010 5000700 6333600 5232600 7723300 7676600 7111500 6512300 6679700 4956900 FALSE TRUE 4879333.139 5859531.325 6498658.819 6267592.662 6410496.225 5893825.99 6554082.048 6425013.27 6439298.902 5928109.649 0.823084158 0.988431671 1.096244706 1.057266655 1.081372748 0.994216764 1.10559393 1.083821598 1.08623141 1 22.4991407 4.660588203 2.567870616 1.067030164 0.793096007 0.795862627 0.036772422 0.158449949 1.501234874 0.008754366 0.086593863 45770.76839 -4.660588203 -0.273934157 DFFHGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ;;; 132.09 0.0034023 1078270000 1266955 1426586 1415745 1405655 1768213 1902837 1604938 1526853 1492314 1591696 FALSE TRUE 1316975.362 1671591.048 1452640.478 1683689.364 1467652.786 1460931.945 1479138.766 1506388.033 1438605.911 1903558.356 0.691849219 0.878140165 0.763118437 0.884495796 0.771004882 0.767474209 0.777038834 0.791353744 0.755745631 1 20.86026737 -1.748327562 5.602693989 1.008159576 0.790245524 0.582403911 0.054111843 0.005138255 0.00023081 0.048812988 0.011197049 0.017851406 1.748327562 -0.217914052 DFFLANASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFFLANASR 9 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 82.749 0.040877 48662000 31771 142040 119170 138900 94169 146340 71252 109700 84168 184960 FALSE TRUE 33025.34361 166434.2651 122275.6681 166374.0054 78162.18702 112354.7528 65667.08206 108229.6509 81138.81012 221199.3707 0.149301255 0.752417444 0.552784882 0.752145021 0.353356281 0.507934324 0.296868304 0.489285528 0.366813024 1 17.75498776 -1.512166546 3.493873902 1.010282593 0.479163123 0.436787084 0.180562346 17538402.26 10744392.41 1327237.938 0.040199033 0.030749174 1.512166546 -0.53111947 DFFQSYGNVVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFFQSYGNVVELR 13 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;; 210.93 6.05E-08 150028000 117751.2 103190 122806 126791 129131 161378 152349 124768.5 128392.8 100853 FALSE TRUE 122400.1083 120912.0798 126006.4252 151869.8814 107181.3587 123900.4052 140407.4873 123096.1823 123771.9682 120613.2144 1.014815076 1.002477883 1.044714925 1.259147948 0.888636948 1.027253986 1.164113634 1.020586201 1.026189119 1 16.88002845 1.524937805 20.10916108 1.016530887 1.057502901 0.040529645 0.09318657 0.916904114 361.7260995 0.04993194 0.023121547 33.49174725 -1.524937805 0.040972013 DFIDNLDRPPGSSYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFIDNLDRPPGSSYFR 16 1 Q3YEC7;G3V154;F2Z2T0;Q3YEC7-4;Q3YEC7-6;Q3YEC7-3 Q3YEC7 RABL6 Rab-like protein 6 0 157.58 1.37E-08 0 105080 115190 127330 125100 167680 152200 129690 114830 102910 133390 FALSE TRUE 109228.6395 134972.9864 130648.3244 149844.4066 139177.8135 116853.8566 119524.5589 113290.8917 99206.2892 159525.2166 0.684710805 0.846091855 0.818982272 0.939314861 0.87245024 0.732510252 0.74925182 0.710175445 0.621884686 1 17.28342497 2.728752299 23.82853948 0.7411546 0.838279949 0.075243889 0.108498307 665.3319413 1616367.438 0.033416325 0.031885116 535.4911522 -2.728752299 0.097125349 DFIDNQMLLLVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFIDNQMLLLVAQR 14 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 100.38 0.0065684 0 24089 35018 43173 42253 58248 54246 47422 51828 41584 40925 FALSE TRUE 25040.05232 41032.0691 44298.12385 50610.51729 48347.02577 41648.18861 43704.93973 51133.33043 40087.39996 48943.47019 0.511611707 0.838356351 0.905087516 1.034060664 0.987813606 0.850944742 0.892967735 1.044742644 0.819055122 1 15.57882877 4.801901077 1.840282191 0.948900659 0.322623643 0.765468224 0.071664721 0.462060435 1.410149217 0.0184396 0.525657821 63372.53451 -4.801901077 -0.626277016 DFIHTASISFLTPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFIHTASISFLTPLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 226.19 8.99E-13 434810000 320130 477910 509050 460540 624090 691970 548140 518400 510640 549980 FALSE TRUE 332768.9796 559987.3249 522316.2612 551633.4374 518007.4047 531270.4544 505175.3545 511451.6959 492262.1661 657738.051 0.505929342 0.851383501 0.794109844 0.838682568 0.787558822 0.80772346 0.768049459 0.777591771 0.748416737 1 19.32715361 -5 0.369296854 3.97068787 0.766522484 0.372256381 0.091576537 564.3447961 4.365448478 1337.926998 0.060048902 1.00E-05 5 -3.204165386 DFIIFEAAPQETR ddPTM_MDA-MB-175_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 9.14E-05 102178000 217097 223777 247232 209758 260516 290840 248193 253916 228337 217073 FALSE TRUE 225668.1572 262208.959 253675.069 251247.5063 216233.5834 223296.8177 228738.9841 250512.6713 220119.196 259604.2982 0.86927743 1.010033196 0.977160512 0.967809501 0.832935297 0.860142992 0.881106306 0.964978905 0.847902741 1 17.98595474 5.067113897 17.84978302 0.924379881 4.59E-05 0.068938125 0.062916568 128332372.5 528292799.4 0.015432299 4513831308 116711.5661 -5.067113897 -0.924333963 DFKPGDLIFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFKPGDLIFAK 11 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 132.59 0.0011893 196160000 1447520 897200 1286490 852710 1752650 1542330 1567510 1233910 1464790 828650 FALSE TRUE 1504669.207 1051287.121 1320016.986 1021373.493 1454735.179 1184147.232 1444644.47 1217371.455 1412072.494 991008.102 1.518321802 1.06082596 1.331994142 1.030640911 1.467934698 1.194891575 1.457752431 1.228417257 1.424884914 1 19.91853733 3.219366984 24.9991345 1.307918365 1.229868997 0.022217792 0.183724763 866.4766502 1128557.193 0.048111248 0.057587236 1657.169701 -3.219366984 -0.078049368 DFLDEYIFLAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFLDEYIFLAVGR 13 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 133.81 0.0002394 138760000 126680 122600 130530 116460 182480 178010 173190 119820 153650 115900 FALSE TRUE 131681.4242 143655.5963 133931.719 139495.4404 151462.1148 136669.8753 159614.9153 118214.0089 148120.1665 138608.386 0.950024945 1.036413456 0.966259856 1.006399717 1.092734135 0.986014478 1.151553091 0.852863325 1.068623413 1 17.08065502 6.947487721 18.2113502 1.007367842 0.381325495 0 0.078761406 0 0 0.016528919 0 8861101.707 -6.947487721 -0.626042347 DFLFPHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFLFPHLR 8 0 Q9H2M9;F8WDJ2;Q9H2M9-2 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 148.04 0.00052758 1359870000 965290 1039030 1067870 1135540 1256390 1334040 1147810 1090320 1054110 1012010 FALSE TRUE 1003400.395 1217475.32 1095699.569 1360146.423 1042829.277 1024229.428 1057841.653 1075706.044 1016172.787 1210293.983 0.829055096 1.005933547 0.905316877 1.123814909 0.861633034 0.846264991 0.874036943 0.888797316 0.839608228 1 20.20692609 DFLLKPELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 143.97 3.01E-05 9714790000 8493420 7340460 7759940 6764070 11724730 10437920 9138520 8240950 7476520 7661400 FALSE TRUE 8828746.78 8601126.904 7962170.411 8101982.857 9731764.583 8013871.268 8422218.923 8130493.545 7207441.506 9162504.644 0.963573512 0.938730974 0.868994966 0.884254161 1.062129293 0.874637621 0.919204874 0.887365831 0.786623504 1 23.12731059 DFLLPFLEEPMDTEADLQFRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DFLLPFLEEPMDTEADLQFRPR 22 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;;; 197.84 1.79E-22 811227800 404538.1 473720.6 517678.9 515398.7 585364.9 609321.7 570005.5 537382.7 539562.9 489211.3 FALSE TRUE 420509.5766 555078.428 531170.0374 617343.0245 485864.7834 467815.9695 525326.9795 530179.9639 520144.1366 585062.8877 0.718742524 0.948750023 0.907885372 1.05517379 0.830448818 0.799599461 0.897898312 0.90619312 0.889039704 1 19.15823218 0.038028422 1.065727795 1.000719034 0.887949426 0.142502387 0.084990709 16.51718195 16.15364037 0.119326117 0.025034761 1.091511767 -0.038028422 -0.112769607 DFLMLAQTHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFLMLAQTHSK 11 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 134.49 0.00013977 192860000 257470 237370 262020 247690 375860 390300 301190 252180 298480 299370 FALSE TRUE 267635.1144 278136.451 268848.4565 296682.3427 311971.4515 299658.7401 277581.9408 248799.9396 287737.7631 358025.8197 0.747530205 0.776861432 0.750919184 0.828661863 0.871365791 0.836975222 0.775312633 0.694921779 0.803678805 1 18.44970411 -1.876509018 2.374840115 1.109923246 0.783992709 0.635254249 0.048277612 9267406.62 4981110.083 5727093.751 0.014094144 0.01328896 1.876509018 -0.325930537 DFLRPFEHIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 84.718 0.0094652 469420000 986160 1080300 1261900 1168000 1571200 1567100 1298100 1296200 1305100 1254400 FALSE TRUE 1025094.358 1265833.121 1294786.151 1399026.914 1304127.985 1203164.775 1196351.53 1278826.559 1258129.706 1500175.663 0.683316217 0.843789932 0.863089692 0.932575397 0.869316852 0.802015927 0.797474296 0.85245121 0.838654923 1 20.51670001 DFLSCRPTEIPENDILLCESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFLSCRPTEIPENDILLCESR 21 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 144.92 1.12E-07 127210000 35097 37709 39336 38016 45446 50088 41120 45531 40024 40381 FALSE TRUE 36482.65666 44185.22741 40361.12847 45535.45133 37721.10515 38455.82109 37896.90695 44920.73142 38583.54406 48292.88381 0.755445809 0.914942822 0.835757265 0.942901888 0.781090342 0.796304094 0.784730668 0.930172892 0.798948852 1 15.559523 -1.270004297 3.293888011 1.000612105 0.844289126 0.357016267 0.064774973 21275400.63 27478590.02 127249.7603 0.015221339 0.053702648 1.270004297 -0.156322979 DFLSNEASLGAIGTS(ph)LPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFLSNEASLGAIGTSLPSR 19 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 DFLSNEASLGAIGT(0.2)S(0.785)LPS(0.015)R;DFLSNEASLGAIGT(0.13)S(0.867)LPS(0.003)R 77.39 0.012195 218052000 166822 194532 219736 265730 277360 316840 305490 252120 261410 232989 TRUE FALSE 173408.2614 227941.3578 225462.5007 318290.6009 230214.4463 243258.7118 281544.8956 248740.7438 252001.9052 278638.7337 0.622340832 0.818053379 0.809157068 1.142305654 0.826211213 0.873025471 1.010429856 0.892699807 0.904403712 1 18.0880363 4.607292097 1.508461404 0.936408327 0.557186158 0.538797964 0.09065318 0.656222621 1.691262288 0.023698519 0.344726751 40484.80923 -4.607292097 -0.379222169 DFMHVLEHECQHHHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFMHVLEHECQHHHSK 16 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;; 248.2 6.83E-21 794590000 86888 379080 396670 441980 394490 537830 417230 469320 398110 362080 FALSE TRUE 90318.40533 444184.0412 407007.5461 529402.3248 327434.7307 412927.1334 384526.4224 463029.5331 383782.0989 433022.6436 0.208576634 1.025775552 0.939922085 1.22257423 0.756160759 0.953592473 0.888005346 1.069296352 0.886286444 1 18.72408294 4.740936716 24.97091566 0.97359819 0.208576362 0.790992613 0.117613597 87.77865755 922426.5292 0.02659227 0.179260019 55072.74406 -4.740936716 -0.765021828 DFMIQGGDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFMIQGGDFTR 11 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ;;; 167.12 4.57E-05 1002550000 715976 906500 711062 803160 766030 947980 631192 703252 555006 728070 FALSE TRUE 744243.2853 1062184.323 729592.8599 962022.6508 635820.4942 727826.0118 581717.5217 693826.0572 535031.4425 870721.3768 0.854743326 1.219890027 0.837917707 1.104857049 0.730222676 0.83588853 0.668086873 0.7968405 0.614469171 1 19.73185162 3.229131491 24.99956467 0.762120121 1.007859437 0.384894043 0.141980606 175.7621973 466000.0184 0.03714727 0.044959059 1694.850871 -3.229131491 0.245739316 DFNEECPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFNEECPR 8 0 A0A0A0MTH3;Q13418;Q13418-3;Q13418-2 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 84.498 0.045089 0 56399 165410 188230 134180 204220 199170 197930 163200 188850 117860 FALSE TRUE 58625.67607 193817.8808 193135.4284 160720.4035 169506.7573 152915.786 182415.7294 161012.5709 182053.3254 140952.4104 0.415925318 1.375059002 1.37021728 1.140245868 1.202581473 1.084875282 1.294165377 1.142318677 1.291594268 1 17.10484862 4.74563578 24.99490775 1.214651071 0.415924946 0.807127804 0.116621183 333.6933123 1178831.418 0.026719399 0.27065807 55671.86629 -4.74563578 -0.798726125 DFNGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFNGDFR 7 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 113.91 0.014016 1856160000 2888760 2773890 3183270 3104430 3528870 3836410 3506160 3296780 3163550 2488660 FALSE TRUE 3002810.475 3250284.03 3266228.631 3718476.988 2929033.938 2945461.919 3231338.018 3252592.057 3049694.453 2976265.279 1.008918962 1.092067986 1.097425238 1.249376867 0.984130668 0.989650331 1.085702286 1.092843464 1.024671583 1 21.50507169 DFNHINVELSLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFNHINVELSLLGK 14 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 195.54 2.61E-08 2495932000 5137977 3915030 4850337 4151333 6313697 6114105 5948402 4900787 5325600 3700117 FALSE TRUE 5340828.299 4587405.948 4976740.767 4972454.277 5240497.039 4694196.774 5482150.708 4835099.966 5133932.696 4425084.083 1.206943913 1.03668221 1.124665808 1.123697128 1.184270613 1.060815272 1.238880574 1.092657196 1.160188733 1 22.07727344 -0.963106439 4.26283769 0.999995085 1.133513867 0.315107777 0.060238933 2.61E-06 6.35E-07 0.05242253 0.012355639 0.108866325 0.963106439 0.133518782 DFPLNDLLSATELDKIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFPLNDLLSATELDKIR 17 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 187.39 4.28E-10 384240000 556200 352080 482710 426120 623040 647320 611990 486460 629750 347340 FALSE TRUE 578159.2055 412547.0012 495289.8192 510405.2642 517135.8833 496989.7402 564020.6247 479939.7994 607085.4205 415394.6228 1.391831222 0.99314478 1.192335654 1.228723811 1.244926764 1.196427958 1.357794718 1.155382793 1.461466729 1 18.66412302 3.751497611 4.173556016 1.242882109 1.171066755 0.010793857 0.145096805 0.724557952 30.87137701 0.035348472 0.062537914 5642.838376 -3.751497611 -0.071815354 DFPYEEDSRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ; 207.88 1.96E-08 376560000 209522 226550 242940 224040 279890 306730 261640 235360 235890 219450 FALSE TRUE 217794.0903 265458.2002 249271.216 268354.4433 232314.3978 235496.606 241131.9731 232205.3842 227400.365 262447.0259 0.829859243 1.011473456 0.949796307 1.02250899 0.885185866 0.897311011 0.918783409 0.884770492 0.866461962 1 18.00166672 3.191533203 24.99982608 0.902043178 0.957299417 0.112270529 0.05935583 203.2881369 108067.4465 0.016099284 0.01924238 1554.294116 -3.191533203 0.05525624 DFQDYMEPEEGCQGS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DFQDYMEPEEGCQGSPQR 18 0 O43237;O43237-2;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR;DFQDYMEPEEGCQGS(1)PQR 382.26 3.74E-109 1998250000 1450823 1690310 1703605 1820293 1770213 2229712 1914468 1781184 1782288 1684536 TRUE FALSE 1508102.612 1980607.594 1748002.346 2180341.522 1469312.827 1711895.18 1764406.996 1757310.142 1718143.803 2014588.577 0.748590868 0.983132545 0.867672122 1.082276326 0.729336423 0.849749274 0.87581505 0.872292319 0.852850961 1 20.94205381 -1.563060998 2.792387689 1.007363227 0.877549103 0.132663713 0.096524271 15335460.84 15134352.34 839012.743 0.021934935 0.027348846 1.563060998 -0.129814124 DFQDYMEPEEGCQGS(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR;DFQDYMEPEEGCQGS(1)PQRR 235.76 2.20E-24 8702950000 3304343 3675815 3565012 3617950 4136410 4581685 3561633 3815625 3836423 3760834 TRUE FALSE 3434801.013 4307107.632 3657919.141 4333569.711 3433304.506 3517658.095 3282462.899 3764482.788 3698350.886 4497697.417 0.763679878 0.957625032 0.813287067 0.963508504 0.76334715 0.782101989 0.729809633 0.836980001 0.822276499 1 22.10075518 DFQEYVEPGEDFPAS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFQEYVEPGEDFPASPQR 18 0 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR 257.72 1.30E-30 1140847000 552852 582564 575497 614916 616048 758724 715024 620677 597140 512616 TRUE FALSE 574679.0239 682614.8353 590494.9246 736544.5495 511332.381 582521.8496 658978.5505 612357.84 575649.048 613053.2906 0.93740468 1.11346737 0.963203254 1.201436418 0.834074931 0.950197737 1.074912346 0.998865595 0.938986964 1 19.22565296 3.234545272 24.99765378 0.975038347 1.05165754 0.183262986 0.08949032 199.3735631 1241208.52 0.024965292 0.030896131 1716.110591 -3.234545272 0.076619193 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_MDA-MB-175_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;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR 243.91 1.07E-24 12370040000 2001022 2319681 2263424 2089104 2553867 2841044 2308860 2297877 2334145 2357409 TRUE FALSE 2080023.894 2718068.167 2322410.689 2502322.536 2119761.6 2181254.587 2127885.52 2267077.717 2250139.577 2819298.158 0.737780744 0.964093904 0.823754906 0.887569315 0.751875637 0.77368709 0.754757177 0.8041284 0.798120472 1 21.42690463 5.039000496 16.02143317 0.826533017 0.363662711 0.103296939 0.082203629 10945192.18 125067227.2 0.018888291 146858853.3 109395.7616 -5.039000496 -0.462870306 DFQQLLAELEQEVERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFQQLLAELEQEVERR 16 1 Q6N063 Q6N063 OGFOD2 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 0 ; 177.67 4.67E-09 88820000 34028 42655 45857 39598 51265 50559 42140 39199 47812 49127 FALSE TRUE 35371.45172 49980.66444 47052.07109 47430.36621 42550.99361 38817.43848 38836.95669 38673.60152 46091.25546 58752.49506 0.602041695 0.850698586 0.800852305 0.807291097 0.724241474 0.660694298 0.661026509 0.658246113 0.784498691 1 15.8423625 0.970250866 18.15719929 1.000000004 0.722373542 0.556671207 0.074833536 63.09618863 38511.4568 0.076552758 0.019138182 9.337935414 -0.970250866 -0.277626462 DFQQLLQGISEDVPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFQQLLQGISEDVPHR 16 0 G5E9X1;B3KQH5;Q9UL03-3;Q9UL03 G5E9X1 INTS6 Integrator complex subunit 6 0 68.481 0.048879 14247000 9903.5 13180 13046 12333 13818 17410 13761 13670 12946 13155 FALSE TRUE 10294.49783 15443.56247 13385.98948 14772.43059 11469.2213 13366.79135 12682.37686 13486.77601 12480.07599 15732.47038 0.654347193 0.981636202 0.850851084 0.938977175 0.729015915 0.849630797 0.80612749 0.857257359 0.793268678 1 13.94145761 -1.173698794 4.966151128 1.000012944 0.835716152 0.24509667 0.089330355 1.16E-05 1.93E-06 0.078543311 0.018511378 0.067034937 1.173698794 -0.164296791 DFQYIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFQYIDR 7 0 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;I3L2B2;O95208-3;O95208-2;F6PQP6;O95208;E9PBC1 Q9H201;I3L2B2 EPN3;EPN2 Epsin-3;Epsin-2 0 ; 115.49 0.013186 476910000 592320 649940 663190 667040 774370 871970 715840 670580 642350 570110 FALSE TRUE 615705.251 761562.1392 680473.2762 798978.5211 642742.864 669468.1823 659730.5903 661591.9719 619231.949 681812.1391 0.903042371 1.116967703 0.998036317 1.17184555 0.942697889 0.98189537 0.967613441 0.970343492 0.908214908 1 19.37901476 DFSAFINLVEFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFSAFINLVEFCR 13 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 111.79 0.0022139 67663000 378060 170000 232880 205200 211670 338950 229280 206470 219370 187530 FALSE TRUE 392986.1007 199196.1776 238949.0441 245787.9475 175690.409 260233.9993 211308.4345 203702.6074 211474.9166 224272.913 1.75226734 0.888186517 1.065438714 1.095932381 0.783377746 1.160345205 0.942193293 0.908280026 0.942935612 1 17.77489586 4.742456911 24.99531126 0.974975068 1.75226764 0.833058959 0.104208395 139.5989496 895512.5006 0.023730272 0.180363427 55265.85729 -4.742456911 0.777292572 DFSALESQLQDTQELLQEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFSALESQLQDTQELLQEENR 21 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 264.96 7.33E-37 181187000 118920 116001 127498 125975 139690 166505 135737 136850 134924 139358 FALSE TRUE 123615.0534 135923.2694 130820.7026 150892.479 115945.5437 127836.7372 125097.5793 135015.7496 130068.1116 166662.5319 0.741708721 0.815559849 0.784943689 0.905377335 0.695690521 0.767039452 0.750604097 0.810114595 0.780428031 1 17.34657028 -0.475378819 1.199520442 1.003188519 0.784939763 0.605621485 0.052390935 40.53140157 30.59879665 0.700429185 0.01466659 0.334673389 0.475378819 -0.218248755 DFSAPTLEDHFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSAPTLEDHFNK 13 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 ; 206.32 6.29E-08 877260000 345330 239720 355770 240640 485290 411230 383640 351330 344800 260320 FALSE TRUE 358963.8951 280890.0452 365041.6585 288237.8738 402800.5791 315728.0648 353569.2943 346620.996 332390.7154 311324.7199 1.153020856 0.902241381 1.17254312 0.925843196 1.293827806 1.014143897 1.135692965 1.113374473 1.067665669 1 18.24806061 DFSDKINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSDKINR 8 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 166.52 0.00029002 486170000 524350 517800 619780 382130 761400 666450 520470 554680 600300 547840 FALSE TRUE 545051.7429 606728.1221 635931.976 457714.1735 631977.5 511677.0876 479674.2014 547245.4219 578695.3203 655178.759 0.831913024 0.926049744 0.970623616 0.698609604 0.964587895 0.780973254 0.732127217 0.835261239 0.88326325 1 19.32152906 5.092868071 13.22908925 0.8537107 0.463218607 0 0.098964258 9814637.818 27202843.42 0.022829013 108086030.4 123842.0324 -5.092868071 -0.390492093 DFSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DFSESR 6 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;; 139.92 0.027558 5846770000 4820740 5732480 5655170 5812240 6083580 6904080 6622470 6036870 5583210 4970590 FALSE TRUE 5011066.538 6716988.847 5802548.376 6961883.724 5049495.245 5300712.052 6103383.497 5955955.632 5382271.363 5944481.943 0.842977838 1.129953613 0.976123476 1.171150622 0.84944244 0.891702945 1.026730934 1.001930141 0.905423116 1 22.50311965 3.222684294 24.99995202 0.952832468 1.033335334 0.149828768 0.097266478 476.0711984 749652.9411 0.027353027 0.032790666 1669.876273 -3.222684294 0.080502866 DFSETYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSETYER 8 0 O94992;Q96MH2 O94992;Q96MH2 HEXIM1;HEXIM2 Protein HEXIM1;Protein HEXIM2 0 ; 183.9 0.00051381 1190770000 773210 963230 948200 870960 1066100 1116310 981560 950820 962260 915230 FALSE TRUE 803736.9278 1128657.26 972910.871 1043233.288 884884.7028 857063.9203 904622.7624 938075.8131 927628.4506 1094551.795 0.734306893 1.031159297 0.888866909 0.953114593 0.808444796 0.783027285 0.826477802 0.857041044 0.847496166 1 20.0619088 5.028209382 14.8706738 0.87689364 0.359708813 0.244945166 0.07886843 1509257.09 22988884.45 0.018873789 18799352.32 106711.0472 -5.028209382 -0.517184827 DFSGGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSGGWR 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ; 130.05 0.0083772 497160000 317360 327660 340150 350210 413890 467490 394120 352060 344950 307320 FALSE TRUE 329889.6179 383933.0562 349014.5884 419480.4927 343537.1256 358922.5324 363227.8446 347341.2116 332535.3169 367533.47 0.897577077 1.04462066 0.949613075 1.14133957 0.934709771 0.976571011 0.988285079 0.945060083 0.904775603 1 18.48751611 2.29092163 1.307851921 0.948248177 1.001212575 0.062329257 0.066599884 1.080182771 3.632015058 0.038384792 0.023300256 195.3986822 -2.29092163 0.052964398 DFSHDDTLDVPTQVELLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DFSHDDTLDVPTQVELLIK 19 0 P42345;B1AKP8 P42345 MTOR Serine/threonine-protein kinase mTOR 0 ;; 139.04 7.31E-07 69794000 94760 73088 87404 71618 122037 116864 94725 79834 115284 77963 FALSE TRUE 98501.19797 85640.29545 89681.82004 85783.82664 101293.1943 89724.10709 87300.20698 78763.95581 111134.9514 93238.35716 1.056445019 0.918509271 0.961855429 0.920048672 1.086389737 0.962308966 0.936312154 0.844759155 1.191944547 1 16.50863596 DFSNSPLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 761100000 148427 386530 345150 359570 411660 464270 332880 383890 323250 429350 FALSE TRUE 154287.0126 452913.5207 354144.8925 430691.8728 341686.1802 356450.3286 306787.9958 378744.5825 311616.2956 513472.9121 0.300477414 0.882059229 0.689705112 0.838782071 0.665441491 0.694195001 0.597476495 0.73761356 0.606879717 1 18.96992864 -1.990926769 2.954838436 1.299055 0.681897828 0.300793405 0.150499399 112475346.5 117315749.6 229580185.4 0.032867762 0.010211117 1.990926769 -0.617157172 DFSSMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSSMKK 7 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 106.04 0.012492 2250200000 2195530 1526290 1872790 1171210 2987100 2209110 2130450 1754010 2243500 1615490 FALSE TRUE 2282211.22 1788418.435 1921596.446 1402871.842 2479353.809 1696077.682 1963459.762 1730500.365 2162756.873 1932014.335 1.181259983 0.925675551 0.994607758 0.726118754 1.283299903 0.877880485 1.01627598 0.895697477 1.119431069 1 20.88167437 4.747480643 23.97039518 0.975368397 1.181260173 0.150820872 0.140951156 1158.884409 3114095.452 0.030871255 0.362441427 55908.8608 -4.747480643 0.205891776 DFSVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSVDR 6 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 143.37 0.02654 535650000 606700 605650 651660 619240 781670 832930 735490 691680 692470 611010 FALSE TRUE 630652.9845 709665.6762 668642.7949 741723.8238 648802.0126 639494.6307 677840.372 682409.161 667548.14 730725.711 0.863050218 0.971179289 0.915039371 1.015050945 0.88788721 0.875150034 0.927626279 0.933878678 0.913541333 1 19.47897044 -1.345660112 2.997137919 1.000818686 0.924934806 0.226753077 0.042726091 12682115.73 16781795.72 92566.44702 0.010540615 0.045116966 1.345660112 -0.07588388 DFSWSPGGNIIAFWVPEDKDIPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSWSPGGNIIAFWVPEDKDIPAR 24 1 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 191.42 8.69E-18 642320000 402140 286740 457940 349680 527540 529970 482110 387480 456840 307055 FALSE TRUE 418016.7977 335985.3645 469874.2926 418845.6603 437868.9392 406892.4993 444320.9584 382286.4644 440398.4176 367216.5483 1.138338671 0.914951589 1.279556422 1.140595821 1.192399801 1.108045106 1.209969868 1.041038227 1.199288049 1 18.48627155 -1.827994232 7.961416927 0.994392757 1.131268049 0.151447853 0.095998837 0.009299228 0.000200909 0.090467242 0.02066501 0.014859554 1.827994232 0.136875292 DFSYNYFGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFSYNYFGFK 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 147.95 6.05E-05 118930000 339560 267170 330270 290580 420580 432440 388350 329140 341830 284000 FALSE TRUE 352966.091 313054.3692 338877.1075 348055.8567 349089.9618 332012.3637 357910.1122 324728.4167 329527.6051 339644.3625 1.039222581 0.921712249 0.997741005 1.024765593 1.027810264 0.977529441 1.053779046 0.956083635 0.970213675 1 18.37366538 4.033285824 24.9998576 1.001045375 0.975282233 0.041582672 0.038136863 504.1630329 378653.5901 0.009166132 0.019800661 10796.57048 -4.033285824 -0.025763142 DFT(ph)PVCTTELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 1 DFT(1)PVCTTELGR;DFT(1)PVCTTELGR 155.39 0.0007792 257670000 344490 243290 289510 239760 385100 588510 335530 308000 285950 196017 TRUE FALSE 358090.7312 285073.165 297054.8684 287183.8124 319640.8396 451837.4715 309230.2819 303871.7638 275658.7154 234422.7782 1.527542392 1.216064271 1.267175787 1.225067865 1.363522956 1.927446961 1.31911363 1.296255279 1.17590414 1 17.83875323 1.165247992 1.670756866 1.011099461 1.400644267 0.309479878 0.196451208 0.455358748 2.394958848 0.192964635 0.056880333 14.63012349 -1.165247992 0.389544806 DFTEVLS(ph)PNMYNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFTEVLSPNMYNSK 14 0 B7ZLP8;A2RTX5-2;A2RTX5 B7ZLP8 TARSL2 "Probable threonine--tRNA ligase 2, cytoplasmic" 1 DFTEVLS(0.997)PNMY(0.002)NS(0.001)K;DFTEVLS(1)PNMYNSK 133.66 4.54E-05 76720000 159401 114102 149269 118001 179547 180472 178223 144844 157427 96038 TRUE FALSE 165694.2746 133698.1309 153159.0728 141341.2456 149027.6651 138560.1131 164253.4156 142902.6031 151761.233 114854.8073 1.442641178 1.164062123 1.33350163 1.230608007 1.297530931 1.206393675 1.430096131 1.244202192 1.321331136 1 16.80945172 -1.107031846 4.475933115 0.999970625 1.29163464 0.515804707 0.086115567 0.416392987 22771308.53 1375.401323 0.017868506 0.078157049 1.107031846 0.291664015 DFTNEAPPAPLPDASAS(ph)PLSPHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDAS(0.106)AS(0.447)PLS(0.447)PHRR 57.293 0.041576 419130000 136050 133610 145610 154180 165150 189220 170010 168190 155630 153250 TRUE FALSE 141421.3591 156556.4782 149404.7162 184676.3438 137077.862 145276.5227 156684.172 165935.6882 150028.9067 183276.4034 0.771628843 0.854209682 0.815187954 1.007638411 0.747929682 0.79266354 0.85490641 0.9053849 0.818593687 1 17.48366153 -5 0.25247381 1.953752015 0.832328135 0.315013823 0.070247432 231.136855 2.286976911 113.8002069 0.097777234 1.00E-05 5 -1.12142388 DFTNEAPPAPLPDASASPLS(ph)PHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASAS(0.004)PLS(0.996)PHR;DFTNEAPPAPLPDAS(0.004)AS(0.197)PLS(0.799)PHR 183.07 2.42E-17 364280000 401040 435470 498840 436080 562230 630760 579420 494600 511320 432780 TRUE FALSE 416873.3689 510258.585 511840.1802 522335.3224 466662.3454 484275.5493 534003.5464 487970.696 492917.6931 517574.9549 0.805435744 0.985864135 0.988919915 1.009197446 0.901632393 0.935662641 1.031741473 0.942801987 0.952360017 1 18.98140828 4.741949109 24.55656832 0.970134402 0.805435664 0.644517139 0.03709103 161.535204 1170584.685 0.008843985 0.06393524 55201.27507 -4.741949109 -0.164698738 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 DFTNEAPPAPLPDASAS(0.016)PLS(0.984)PHRR;DFTNEAPPAPLPDAS(0.023)AS(0.045)PLS(0.932)PHRR;DFTNEAPPAPLPDASASPLS(1)PHRR;DFTNEAPPAPLPDASAS(0.002)PLS(0.998)PHRR 279.2 2.27E-52 2082000000 407657 513111 486888 472919 549828 667780 552664 508489 547554 468585 TRUE FALSE 423751.6131 601233.8228 499576.7013 566460.9667 456368.433 512698.2153 509344.7516 501673.5367 527847.6385 560395.2591 0.756165592 1.07287457 0.891472034 1.010823981 0.814368833 0.914886782 0.908902678 0.895213742 0.941920243 1 19.09608523 0.941283895 5.024197336 0.999978348 0.912811737 0.10024475 0.08381318 0.724526873 52.05463032 0.07265433 0.018366649 8.735422099 -0.941283895 -0.087166612 DFTPAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFTPAELR 8 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 ; 95.352 0.022592 178775000 285540 412310 333220 446820 382530 523170 318570 331380 301180 506580 FALSE TRUE 296813.3397 483121.0352 341903.9869 535199.6624 317507.6872 401671.6962 293599.651 326938.3931 290340.5906 605834.6519 0.489924666 0.797447016 0.564351983 0.883408799 0.524083075 0.663005483 0.484620102 0.539649543 0.479240647 1 19.20856457 -1.235024381 5.306961449 1.000034414 0.605154009 0.449283975 0.131885427 5.21E-05 7.51E-06 0.123889296 0.029198447 0.058207054 1.235024381 -0.394880405 DFTPVCTTELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DFTPVCTTELGR 12 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 145.75 0.00014926 5565613000 522570 547138 603827 546664 645543 683715 550882 584085 593199 551516 FALSE TRUE 543201.4671 641104.6954 619563.2277 654792.5076 535813.8314 524932.5531 507702.4294 576256.2959 571849.8839 659575.0008 0.82356285 0.971996656 0.939337038 0.992749129 0.81236225 0.795864841 0.769741771 0.873678195 0.866997511 1 19.33117719 3.227452217 24.99920728 0.840482116 0.935305056 0.210354364 0.072239404 266.6276085 600038.7074 0.020086794 0.024218864 1688.310096 -3.227452217 0.09482294 DFTSEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFTSEPR 7 0 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 ; 83.801 0.051212 350940000 521180 654400 655750 659570 707750 775900 673880 670070 616530 644810 FALSE TRUE 541756.5888 766788.1095 672839.3837 790030.9774 587446.9078 595708.9839 621059.5247 661088.8077 594341.2057 771148.1739 0.702532415 0.99434601 0.872516342 1.024486609 0.761782142 0.772496135 0.805369896 0.857278575 0.770722445 1 19.55664857 3.204425468 24.99979163 0.819395255 0.903465184 0.096796491 0.103138338 352.7048384 258311.835 0.027901703 0.03335049 1601.125847 -3.204425468 0.084069929 DFTVSALHGDMDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DFTVSALHGDMDQK 14 0 Q14240;Q14240-2;E7EQG2 Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;;;; 219.97 4.81E-12 2276960000 1965610 1708260 2244770 1821390 2862560 2734360 2705260 2347090 2455750 1450230 FALSE TRUE 2043213.801 2001640.367 2303270.55 2181655.506 2375983.074 2099346.33 2493214.652 2315631.098 2367368.037 1734374.802 1.178069353 1.154099082 1.328012 1.257891606 1.369936343 1.210434058 1.437529333 1.335138803 1.364969114 1 20.72598427 4.24049464 24.9657003 1.308137899 1.166084169 0.134397124 0.114987825 69.82000054 901220.1381 0.025697705 0.063481119 17397.81225 -4.24049464 -0.14205373 DFTVSAMHGDMDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DFTVSAMHGDMDQK 14 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;;;; 261.98 1.56E-24 7161880000 5342168 5012685 6708623 5611337 8663903 8283197 8147209 7275565 7377786 4569497 FALSE TRUE 5553080.918 5873574.655 6883455.227 6721242.71 7191215.863 6359550.03 7508609.47 7178047.952 7112260.923 5464802.449 1.016154009 1.074800912 1.259598181 1.229915038 1.315915064 1.163729172 1.373994676 1.313505478 1.30146716 1 22.38173791 4.299695359 3.308460155 1.265732577 1.025415438 0.3795847 0.1002178 0.201012724 4.321661527 0.023447104 0.074649558 19938.63204 -4.299695359 -0.240317138 DFTVSAMHGDMDQKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFTVSAMHGDMDQKER 16 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 95.347 0.0022732 52710000 15921 28781 31886 21238 42333 40040 22678 25039 31672 36809 FALSE TRUE 16549.57337 33723.91286 32716.97535 25438.81301 35137.25178 30741.31681 20900.4391 24703.39316 30532.13091 44021.0188 0.375947078 0.766086606 0.743212589 0.577878788 0.798192608 0.698332698 0.474783176 0.561172681 0.693580743 1 15.42590491 0.959563001 16.68833056 1.000000007 0.628799802 0.439901731 0.126605172 67.22949966 27746.79262 0.121183807 0.030296485 9.110936117 -0.959563001 -0.371200205 DFVAEPMGEKPVGSLAGIGEVLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFVAEPMGEKPVGSLAGIGEVLGK 24 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 142.32 2.41E-07 195780000 99979 81002 106930 75980 133220 129750 137630 103060 107660 83953 FALSE TRUE 103926.2481 94913.46339 109716.6836 91008.61722 110575.312 99617.52888 126842.201 101678.6493 103785.3376 100401.983 1.035101549 0.94533455 1.092774071 0.906442428 1.101325977 0.992186867 1.263343584 1.012715549 1.033698086 1 16.61542824 3.19442403 24.99975149 1.074036446 0.998361217 0.139009505 0.086991197 245.4815784 139044.3834 0.024011388 0.028699238 1564.674592 -3.19442403 -0.075675229 DFVDDDDDDDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 ; 388.27 1.06E-107 1720260000 1192260 1211450 1329270 1169270 1567110 1675070 1482320 1262010 1343040 1034820 FALSE TRUE 1239331.345 1419507.114 1363911.868 1400548.116 1300733.202 1286060.378 1366131.885 1245094.82 1294704.253 1237573.166 1.001420667 1.14700864 1.102085845 1.131689143 1.051035395 1.039179269 1.103879692 1.006077745 1.046163805 1 20.23908239 1.853575322 0.671524034 1.004586134 1.09536509 0.284610245 0.043924585 0.806885679 0.722391819 0.038709688 0.020831724 71.37979928 -1.853575322 0.090778956 DFVDHIDLVDPVDGVVLVDPEYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DFVDHIDLVDPVDGVVLVDPEYLK 24 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;;;; 179.58 3.74E-17 2048871000 2060649 1313328.1 1956581 1516522.8 2409766 2319979 2483709 1875358 2289286 1167881.6 FALSE TRUE 2142005.014 1538881.985 2007571.108 1816486.483 2000154.836 1781199.037 2289029.399 1850221.893 2206895.044 1396705.639 1.533612347 1.101794066 1.43736164 1.300550691 1.432051808 1.275285921 1.638877466 1.324704248 1.580071693 1 20.41359657 DFVNYLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFVNYLVR 8 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 98.458 0.017467 594290000 372680 401330 365690 373380 823020 543420 457510 351580 432740 726120 FALSE TRUE 387393.6942 470255.3056 375220.1818 447233.4496 683123.3544 417218.9406 421649.1707 346867.6452 417165.7719 868389.3116 0.446106014 0.541525902 0.432087517 0.515014917 0.786655645 0.480451492 0.485553156 0.399437949 0.480390265 1 19.72798244 -1.195501979 5.28933861 1.000027494 0.50512024 0.680945118 0.101130438 3.43E-05 5.21E-06 0.102379542 0.024129752 0.063752618 1.195501979 -0.494907253 DFVTEALQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFVTEALQSR 10 0 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 110.38 0.0044051 51213000 18958 26880 24285 24755 33072 36930 31767 26162 27966 29279 FALSE TRUE 19706.47648 31496.4309 24917.88705 29651.46511 27450.43325 28353.56718 29277.01953 25811.34118 26959.50912 35015.65947 0.562790385 0.899495579 0.711621241 0.846805845 0.783947344 0.809739631 0.836112185 0.737137086 0.769927213 1 15.09571264 -2.688266933 1.988446752 6.178741396 0.778370821 0.376291109 0.087410341 2554669.194 61741.78045 60210645.99 0.019241067 0.002049902 2.688266933 -5.400370575 DFYELEPEKFQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFYELEPEKFQNK 13 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 172.99 2.05E-05 178710000 156780 88582 115340 90933 174160 155300 144480 109410 135480 78622 FALSE TRUE 162969.7955 103795.2694 118345.8552 108919.276 144556.3454 119233.9286 133155.2801 107943.5379 130604.1013 94026.47559 1.733233054 1.103894076 1.258643955 1.158389436 1.537400445 1.268088885 1.416146668 1.148012166 1.38901411 1 16.52077942 -3.945715192 0.236964141 1.89E-12 1.353324128 0.23153036 0.183837688 146.2227407 2.300699411 70.7202324 0.284752434 0.000113314 3.945715192 1.353324128 DFYFSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DFYFSVK 7 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 77.923 0.085457 74718000 118840 84210 95524 93069 158190 140650 107200 95323 107070 116320 FALSE TRUE 123531.895 98672.41244 98013.43391 111477.7704 131300.9203 107986.1691 98797.38388 94045.3511 103216.5716 139110.6769 0.888011601 0.709308693 0.704571612 0.801360276 0.943859402 0.776260827 0.710207053 0.676046966 0.741974476 1 17.08587363 4.759877735 23.00101301 0.769772005 0.888011958 0.066741915 0.102646603 4252.799519 4588518.104 0.024651593 0.984048622 57527.79596 -4.759877735 0.118239953 DFYLATS(ph)PPDSFLDDHHLTRPHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DFYLATSPPDSFLDDHHLTRPHPER 25 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 DFYLAT(0.004)S(0.996)PPDSFLDDHHLTRPHPER;DFYLAT(0.204)S(0.795)PPDSFLDDHHLTRPHPER;DFYLAT(0.001)S(0.999)PPDSFLDDHHLTRPHPER;DFYLAT(0.083)S(0.917)PPDSFLDDHHLTRPHPER;DFYLAT(0.006)S(0.994)PPDSFLDDHHLTRPHPER;DFYLAT(0.006)S(0.994)PPDSFLDDHHLTRPHPER;DFYLAT(0.187)S(0.81)PPDS(0.003)FLDDHHLTRPHPER;DFYLAT(0.006)S(0.994)PPDSFLDDHHLTRPHPER 153.01 5.62E-08 8027330000 660923.8 921089 1004914 977021 1130349 1296459 1098628 1122772 1089946 1172754 TRUE FALSE 687017.582 1079278.871 1031102.884 1170272.838 938212.6807 995376.0453 1012514.667 1107723.078 1050719.056 1402532.693 0.48984069 0.769521364 0.735172085 0.834399686 0.668941755 0.709698997 0.721918763 0.789801966 0.749158335 1 20.41960297 -5 0.153031969 1.990991792 0.643516999 0.550954092 0.081625664 104.0572414 0.936913168 31.31550049 0.380206453 1.00E-05 5 -1.347474793 DGADFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 143 0.005702 5739910000 6250800 4539270 5899750 4557670 7857170 7149770 7268900 5564060 6180850 4519830 FALSE TRUE 6497586.411 5318854.312 6053502.332 5459163.523 6521611.05 5489344.273 6699144.624 5489482.877 5958402.416 5405404.151 1.202053765 0.983988276 1.119898191 1.009945486 1.206498324 1.015528926 1.239342043 1.015554568 1.102304703 1 22.36597106 0.61754644 1.160255684 1.000821765 1.098625277 0.102542002 0.0880107 2.932360598 6.017321727 0.075234321 0.023148989 4.145209073 -0.61754644 0.097803512 DGAGFLINLIDSPGHVDFSSEVTAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 DGAGFLINLIDSPGHVDFSSEVTAALR 27 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 271.6 9.14E-61 4762368000 823319.1 1092254.6 1222686 1257476.5 1361544.7 1549993.9 1308289.9 1227511.6 1170119.5 1082618.1 FALSE TRUE 855824.3738 1279840.831 1254550.202 1506201.599 1130109.818 1190031.307 1205742.719 1211058.815 1128007.128 1294736.389 0.661002797 0.988495297 0.968961877 1.163326845 0.872849352 0.919130193 0.931265028 0.935370957 0.871225322 1 20.30422696 4.742081893 24.34673406 0.959160822 0.661002631 0.564887362 0.079017142 178.5015022 1234111.972 0.019070736 0.139150171 55218.15521 -4.742081893 -0.298158191 DGAHVVISSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGAHVVISSR 10 0 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 99.788 0.0044566 1165890000 439018 573820 488068 645080 510254 706680 494180 438162 448285 570239 FALSE TRUE 456350.7696 672369.1213 500787.453 772674.8986 423521.2073 542564.2798 455444.8803 432289.1551 432151.3104 681966.4142 0.66916898 0.98592703 0.734328616 1.133010193 0.621029421 0.795587977 0.667840631 0.633886283 0.633684154 1 19.37934116 DGAPWCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGAPWCGR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 149.4 0.0011768 605270000 467836 562950 538708 510497 584600 670090 583080 537450 531970 543560 FALSE TRUE 486306.5265 659632.2834 552747.173 611471.7829 485229.9008 514471.7528 537376.666 530246.3618 512824.5036 650060.1749 0.748094631 1.014724957 0.850301548 0.940638739 0.746438437 0.791421737 0.826656803 0.81568812 0.788887742 1 19.31021375 3.250092775 24.99777696 0.817177528 0.894736143 0.089175513 0.08942392 399.7175141 866446.229 0.02266681 0.030439626 1778.659329 -3.250092775 0.077558615 DGAS(ph)SSPESASR ddPTM_MDA-MB-175_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(0.333)S(0.333)S(0.333)PESASR 70.563 0.049241 97962000 53459 185340 139030 168870 120640 207670 106610 146940 125930 205370 TRUE FALSE 55569.6026 217170.7033 142653.236 202271.982 100133.6559 159441.7898 98253.62963 144970.5096 121397.8039 245608.3195 0.226252933 0.884215583 0.580815977 0.823555091 0.407696515 0.649170965 0.400041944 0.590250811 0.494273989 1 17.9059999 -1.438690478 3.259666457 1.006324851 0.571943486 0.329822316 0.186885511 236567163.3 304645335.5 13744274.58 0.041128028 0.036417449 1.438690478 -0.434381365 DGASS(ph)SPESASR ddPTM_MDA-MB-175_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(0.023)S(0.488)S(0.488)PESASR 79.886 0.022896 92525000 81504 337870 262060 332770 236820 360130 213130 288320 233080 375790 TRUE FALSE 84721.84085 395896.5442 268889.4989 398590.9128 196565.421 276495.2653 196424.3137 284455.542 224691.4963 449418.8556 0.188514211 0.880907731 0.59830489 0.886902959 0.437376889 0.615228449 0.437062912 0.632940827 0.499960101 1 18.77770113 -1.597003266 2.895063676 1.02801246 0.588562895 0.291411442 0.197723675 41967698.38 43271423.3 8965171.878 0.043178796 0.02529279 1.597003266 -0.439449565 DGASSS(ph)PESASR ddPTM_MDA-MB-175_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(0.013)S(0.987)PESASR 229.37 2.50E-06 0 96706 135080 125130 135500 133070 166680 128780 129370 119140 143240 TRUE FALSE 100524.0276 158278.9392 128390.9906 162301.4956 110450.8089 127971.0961 118685.8871 127636.0068 114852.1747 171305.1355 0.586812691 0.923959102 0.749487108 0.947440922 0.644760641 0.747035958 0.692833211 0.745079862 0.670453774 1 17.38620888 -1.187380357 4.951813875 1.000023559 0.75106175 0.332342812 0.108017883 2.62E-05 4.30E-06 0.097590194 0.023000054 0.064956055 1.187380357 -0.248961808 DGATILTHAYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGATILTHAYSR 12 0 F5H0D0;Q14232-2;Q14232 F5H0D0 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 101.39 0.0026989 290980000 78354 83694 82224 87892 96158 119080 98883 97385 99335 82847 FALSE TRUE 81447.47642 98067.79345 84366.82499 105276.7753 79813.09751 91425.47467 91132.29208 96079.71336 95759.95275 99079.28345 0.822043454 0.989791105 0.851508227 1.062550834 0.805547787 0.922750665 0.919791594 0.969725557 0.966498237 1 16.59629581 1.684433744 2.103045901 0.983651372 0.912347033 0.159375359 0.072428834 0.557626506 5.238403416 0.047742914 0.019050991 48.35414893 -1.684433744 -0.071304339 DGAWGAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 206.65 0.00016207 22769986000 7244249 7457253 7200069 6992583 17478840 11536490 8569697 6727393 7232800 16069160 FALSE TRUE 7530257.544 8737978.193 7387708.713 8375695.047 14507793.02 8857315.035 7897981.756 6637223.301 6972492.941 19217604.24 0.391841639 0.454686135 0.384424022 0.435834506 0.754922041 0.460895902 0.410976397 0.345372046 0.362818011 1 24.19592516 -1.125270111 4.92078026 1.000027599 0.443776928 0.696732264 0.10991825 3.54E-05 6.29E-06 0.113147054 0.026667696 0.074942795 1.125270111 -0.556250671 DGDDVIIIGVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGDDVIIIGVFK 12 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 173.32 7.76E-05 40984000 173314 116067 148180 149218 184084 195989 198812 137343 144835 71285 FALSE TRUE 180156.5705 136000.6044 152041.6925 178732.875 152793.4674 150473.525 183228.5959 135502.1417 139622.4166 85251.93092 2.11322569 1.595278874 1.783439869 2.096525828 1.792258143 1.765045359 2.149260362 1.589431938 1.637762513 1 16.37944489 0.791370544 1.139702912 1.004112448 1.876516787 0.67539874 0.183674941 0.433007955 1.039324485 0.165905863 0.051827034 6.185439227 -0.791370544 0.872404338 DGDKEQNSELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGDKEQNSELR 11 1 O60437 O60437 PPL Periplakin 0 137.95 6.18E-05 342840000 629130 398950 495940 367740 694950 724590 643060 495380 609280 344260 FALSE TRUE 653968.5382 467466.5591 508864.6038 440477.8744 576822.6472 556314.9538 592655.2769 488740.2414 587352.1318 411711.1557 1.588415881 1.135423591 1.235974777 1.069871118 1.401037206 1.351226329 1.439492879 1.187094968 1.426612137 1 18.65127301 -1.147059245 4.691458089 0.999970034 1.300721012 0.277093432 0.151065063 4.49E-05 8.17E-06 0.138740816 0.032698269 0.071275579 1.147059245 0.300750977 DGDKPEETQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DGDKPEETQGK 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;; 134.08 0.00013534 1308710000 2577630 914251 1348973 998218 2231900 2041033 2027135 1241373 1485129 511570 FALSE TRUE 2679396.823 1071266.497 1384128.345 1195662.541 1852522.435 1567034.018 1868242.862 1224734.425 1431679.497 611802.3469 4.379513803 1.751000961 2.262378285 1.954328137 3.027975366 2.561340318 3.053670636 2.001846563 2.340101349 1 19.22270612 0.598474964 0.900858196 0.99965949 2.619417183 0.326899881 0.711267356 1.54763779 2.060697808 0.655673585 0.215701005 3.96711659 -0.598474964 1.619757692 DGDLFMSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DGDLFMSYR 9 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;;;; 212.2 9.10E-06 2862460000 2790210 2743230 3093710 2887280 4235710 4179130 4051060 3418440 3190460 2789830 FALSE TRUE 2900369.645 3214358.413 3174334.624 3458375.366 3515725.527 3208590.393 3733527.332 3372621.403 3075635.968 3336443.774 0.869299722 0.963408536 0.951412594 1.036545376 1.053734385 0.961679744 1.119014012 1.010843171 0.921830601 1 21.66987976 4.729219154 1.061879168 1.019420934 0.801958282 0.405804231 0.052056819 1.676540282 1.553941745 0.015528199 0.41167526 53606.70996 -4.729219154 -0.217462653 DGDSVMVLPTIPEEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGDSVMVLPTIPEEEAK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 243.4 4.35E-20 127161000 927620 452900 673980 489580 913080 940940 958310 664140 772680 355352 FALSE TRUE 964243.1539 530682.0519 691544.4725 586417.4627 757874.9877 722420.9451 883195.1581 655238.2896 744871.3977 424976.4208 2.268933303 1.248732932 1.627253746 1.379882351 1.783334206 1.6999083 2.078221555 1.541822693 1.752735826 1 18.69702327 DGDSVMVLPTIPEEEAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGDSVMVLPTIPEEEAKK 18 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 119.68 0.00010713 151800000 480090 176400 289820 193050 417510 417980 465560 295590 365740 100600 FALSE TRUE 499044.3239 206695.3278 297372.9473 231234.7138 346541.7993 320910.4795 429068.1907 291628.0995 352577.0888 120310.6439 4.147964866 1.718013645 2.471709382 1.921980519 2.88039186 2.667349032 3.566336085 2.423959262 2.930556079 1 16.87640476 DGDSYDPYDFS(ph)DTEEEMPQVHT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK;DGDSYDPY(0.004)DFS(0.995)DT(0.007)EEEMPQVHT(0.995)PK;DGDSYDPYDFS(1)DTEEEMPQVHT(1)PK 253.88 1.52E-43 3679352000 2835036 1729192 2356404 1618982 2912841 2905372 2924980 2160536 2585577 1433969 TRUE FALSE 2946965.41 2026167.275 2417813.824 1939211.807 2417717.327 2230643.384 2695712.425 2131577.549 2492522.589 1714927.771 1.718419552 1.181488404 1.409863357 1.130783372 1.409807089 1.300721478 1.571910182 1.242954709 1.453427154 1 20.70971638 -1.421748606 3.028790146 0.993530005 1.365445602 0.308474259 0.169410658 26091891.23 32566904.56 1459327.272 0.036338662 0.037866171 1.421748606 0.371915597 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(0.999)DT(0.001)EEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(1)DTEEEMPQVHTPK;DGDSYDPYDFS(0.996)DT(0.004)EEEMPQVHTPK;DGDSYDPYDFS(0.994)DT(0.006)EEEMPQVHTPK 313.05 1.03E-73 5646340000 4191820 2959080 4024490 2931820 5001820 4983910 4915600 3994910 4457290 2724330 TRUE FALSE 4357316.29 3467278.972 4129371.516 3511725.245 4151612.423 3826472.434 4530302.427 3941364.766 4296873.004 3258110.303 1.337375314 1.064199382 1.26741305 1.077841116 1.274239371 1.174445331 1.390469323 1.209708819 1.318823675 1 21.63560402 DGDSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGDSYR 6 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 127.95 0.039173 68205000 157870 159570 154790 141310 197230 218540 192470 170840 168730 147080 FALSE TRUE 164102.8295 186974.9062 158823.9546 169260.6962 163704.915 167787.397 177383.6985 168550.1692 162657.4403 175897.51 0.932945722 1.062976424 0.902934638 0.962268859 0.930683527 0.953892963 1.008449173 0.958229422 0.924728498 1 17.42437553 DGEDLKDHSTESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGEDLKDHSTESK 13 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 112.42 0.00054193 401280000 379220 275760 247090 276000 355480 428330 390530 234720 282140 280200 FALSE TRUE 394191.8984 323119.6349 253529.3684 330591.9762 295055.6366 328856.8489 359919.2381 231573.9623 271985.8365 335099.8252 1.176341701 0.964248891 0.756578635 0.986547743 0.880500718 0.981369801 1.074065729 0.691059633 0.811656157 1 18.35423141 1.739855246 24.9999997 0.808168121 0.96262405 0.193862271 0.125994396 0.28577961 5534.577353 0.057584632 0.031933671 54.93577384 -1.739855246 0.154455928 DGEEAGAYDGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGEEAGAYDGPR 12 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 218.94 7.70E-11 7703510000 3055840 2958690 3115380 2941440 4123190 4725560 3665000 3005890 2980150 2216750 FALSE TRUE 3176486.923 3466821.992 3196569.362 3523248.053 3422331.637 3628120.307 3377727.723 2965600.961 2872894.984 2651079.72 1.19818612 1.307701902 1.205761312 1.328986083 1.290919926 1.368544401 1.274095116 1.118638922 1.083669782 1 21.33814862 1.597232286 2.339437052 1.042809244 1.287054725 0.790303868 0.051701907 0.115854422 1.400736614 0.038126183 0.014251822 39.55781413 -1.597232286 0.244245481 DGELPVEDDIDLSDVELDDLGKDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGELPVEDDIDLSDVELDDLGKDEL 25 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 255.41 6.64E-45 356467000 847450 498059 566789 498488 907690 938230 796730 574178 664151 342431 FALSE TRUE 880907.9804 583596.7589 581559.987 597087.4386 753401.178 720340.3015 734280.2207 566482.0831 640248.3352 409523.7982 2.15105443 1.425061892 1.420088379 1.458004251 1.839700602 1.758970552 1.793009891 1.383270241 1.563397141 1 18.64358777 0.637049492 0.920603339 1.002279979 1.65973394 0.435678647 0.226710193 1.166223727 1.670449073 0.219332026 0.07216134 4.335602844 -0.637049492 0.657453961 DGFIDKEDLHDMLASLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 222.3 3.47E-19 5868900000 15880500 8290900 13980900 10761400 16330600 16197900 21670400 14247400 15189400 5597100 FALSE TRUE 16507474.4 9714797.581 14345253.74 12889972.8 13554730.45 12436183.21 19971817.42 14056436.91 14642736.46 6693744.582 2.466104615 1.45132481 2.143083526 1.925674433 2.024984712 1.857881348 2.983653944 2.099936252 2.187525425 1 22.67438207 DGFNPADVEAGLYGSHLYVWDWQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGFNPADVEAGLYGSHLYVWDWQR 24 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 231.23 1.34E-33 664520000 464360 502620 564460 479210 615080 579910 607570 669110 632170 449260 FALSE TRUE 482693.2914 588941.0752 579170.2913 573996.3077 510528.9213 445234.6911 559947.0758 660141.6749 609418.3252 537283.8954 0.898395235 1.096145037 1.077959522 1.068329635 0.950203283 0.828676785 1.042181016 1.228664549 1.134257569 1 19.03532507 1.98746065 24.8052928 1.143641627 0.99260933 0.278531428 0.094464906 624.0604556 1234513.713 0.038886409 0.026501271 97.153992 -1.98746065 -0.151032296 DGFQHPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGFQHPAR 8 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;; 131.22 0.0010143 411780000 554760 627760 655670 592910 806940 771390 648660 634250 644690 671260 FALSE TRUE 576662.3532 735572.8967 672757.2988 710185.8283 669776.627 592246.363 597816.3342 625748.9162 621487.7328 802780.545 0.718331251 0.916281419 0.838033885 0.884657498 0.83432095 0.737743792 0.74468214 0.779476932 0.774168902 1 19.61464613 2.97424829 22.67753166 0.787299753 0.846575369 0.003385671 0.085191407 523.8588371 461322.0994 0.023974463 0.025548847 942.4282369 -2.97424829 0.059275616 DGFYEAELCPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGFYEAELCPDR 12 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38;E9PMD5;E9PNV4;E9PRX2;E9PJR1 Q04206 RELA Transcription factor p65 0 ;; 187.42 2.45E-05 616170000 334775 346570 368770 341200 429510 432960 351050 338030 351536 335333 FALSE TRUE 347992.1755 406090.7016 378380.4491 408688.3416 356502.0436 332411.6016 323533.7837 333499.2608 338884.288 401035.081 0.867734999 1.01260643 0.943509601 1.019083768 0.888954759 0.828884098 0.806746838 0.831596228 0.845024049 1 18.61336892 3.038990162 6.010327783 0.846942988 0.962940632 0.334714461 0.063796937 0.166208528 15.78467915 0.017370072 0.020630955 1093.931586 -3.038990162 0.115997645 DGGAWGTEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGGAWGTEQR 10 0 P09382 P09382 LGALS1 Galectin-1 0 ; 169.41 1.08E-05 7362200000 4377300 4397400 4127300 3838600 5302200 5970700 4658800 4793300 4224600 4406000 FALSE TRUE 4550119.184 5152619.243 4234860.829 4597863.623 4400933.938 4584095.412 4293631.082 4729053.654 4072557.471 5269271.342 0.863519619 0.977861816 0.803690027 0.872580538 0.835207309 0.869967613 0.81484342 0.897477724 0.772888167 1 22.32917204 4.235350472 24.99982947 0.854789314 0.920690709 0.129110921 0.064257685 129.0922697 1005373.206 0.014122009 0.032654102 17192.95286 -4.235350472 0.065901395 DGGFCEVCKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 134.75 0.00026041 604970000 1144310 728290 833850 592500 1446230 1233240 1077660 952530 1156350 724030 FALSE TRUE 1189488.242 853368.1422 855580.816 709694.7316 1200400.341 946838.6999 993190.1933 939762.8934 1114733.189 865889.8161 1.373717787 0.985538952 0.988094328 0.81961321 1.386319967 1.093486356 1.147016831 1.085314639 1.287384571 1 19.72382393 3.241806353 24.99956302 1.160266585 1.03389479 0.12067794 0.164021279 184.6056359 1421871.182 0.045006261 0.05851929 1745.043883 -3.241806353 -0.126371796 DGGNPFAEPSELDNPFQDPAVIQHRPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGGNPFAEPSELDNPFQDPAVIQHRPSR 28 1 O14828 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R;DGGNPFAEPSELDNPFQDPAVIQHRPS(1)R 273.01 1.10E-61 740353000 422632 444621 366175 439961 489903 521588 376008 377930 368874 420738 TRUE FALSE 439317.8377 520981.1981 375717.8213 526983.9726 406629.463 400457.0917 346535.5104 372864.4665 355598.2968 503173.5556 0.87309405 1.035390657 0.746696278 1.047320486 0.808129637 0.795862754 0.688699767 0.741025561 0.70671102 1 18.94069658 3.017137015 24.11313715 0.764325149 0.921565173 0.24721434 0.113056593 183.9106709 258774.1902 0.030309932 0.03621792 1040.248301 -3.017137015 0.157240024 DGGQTES(ph)NEEGKENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.001)ES(0.999)NEEGKENR;DGGQT(0.021)ES(0.979)NEEGKENR;DGGQTES(1)NEEGKENR 241.8 4.09E-18 551170000 371390 172486 266211 177944 367890 407880 304446 242558 297564 140447 TRUE FALSE 386052.764 202109.1287 273148.6774 213140.7921 305356.1892 313156.0515 280582.727 239306.9068 286854.7298 167964.9006 2.298413314 1.203281924 1.626224743 1.268960308 1.817976185 1.864413638 1.670484285 1.424743538 1.707825437 1 17.35780026 -2.461661698 0.418872159 1.95E-12 1.64131374 0.296944952 0.299843722 103.4735255 4.981578307 94.79082383 0.166630879 0.003454127 2.461661698 1.64131374 DGGQTESNEEGKENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 225.6 8.91E-13 2718481000 1745772 1153347 1430277 1037655 1914318 1931645 1828421 1487184 1586784 886985 FALSE TRUE 1814696.427 1351425.375 1467551.194 1242900.062 1588922.91 1483049.723 1685104.584 1467250.731 1529675.954 1060772.728 1.710730657 1.274000867 1.383473721 1.171693077 1.497891931 1.398084324 1.588563261 1.383190472 1.442039292 1 20.01668416 -1.466042259 5.331486623 0.99940253 1.419860216 0.443821732 0.143405685 0.000962325 9.64E-05 0.131202388 0.030882431 0.034194617 1.466042259 0.420457687 DGGS(ph)GNSTIIVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 DGGS(0.985)GNS(0.006)T(0.009)IIVSR;DGGS(0.994)GNS(0.005)T(0.002)IIVSR 116.87 0.00057784 101260000 177947 180276 168356 186626 215960 261600 230980 195494 176024 159651 TRUE FALSE 184972.485 211237.0006 172743.4957 223540.0658 179251.1963 200847.3646 212875.184 192873.7227 169688.9306 190931.5567 0.968789487 1.106349334 0.904740414 1.170786378 0.938824359 1.051933834 1.114929285 1.010172053 0.888742194 1 17.54269604 1.44278779 10.65944906 0.945846021 1.038086525 0.165121697 0.081850842 0.462860931 132.4125009 0.043086688 0.018566472 27.71965307 -1.44278779 0.092240503 DGGSEGSGGNNDGEKEPSLTDAIPSHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGGSEGSGGNNDGEKEPSLTDAIPSHPR 28 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;; 200 2.75E-25 306279000 221511 127033 202919 153883 248328 246613 292972 204189 223966 86855 FALSE TRUE 230256.4253 148849.9296 208207.2358 184320.5981 206117.2953 189340.8682 270008.0891 201452.1804 215905.5074 103872.5743 2.216720119 1.433005108 2.004448597 1.774487629 1.984328362 1.822818674 2.599416553 1.939416461 2.078561245 1 16.66445526 2.995457677 2.265635941 2.003192752 1.838415034 0 0.417899983 1.33136997 13.73225996 0.128501339 0.149786995 989.5954204 -2.995457677 -0.164777718 DGGT(ph)SYSPQENSHNHSALHSSNSHSSNPSNNPSK ddPTM_MDA-MB-175_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(0.274)S(0.274)Y(0.002)S(0.274)PQENS(0.053)HNHS(0.053)ALHS(0.014)S(0.014)NS(0.014)HS(0.014)S(0.014)NPSNNPSK 60.312 0.02029 36165000 0 16813 11451 18222 13476 24273 9892.7 24066 13272 18838 TRUE FALSE 0 19700.50196 11749.42247 21826.25721 11185.35433 18635.96361 9117.284324 23743.43463 12794.34331 22528.94542 0 0.874452913 0.52152563 0.968809538 0.496488145 0.827200886 0.404692015 1.053907948 0.567906889 1 14.45949216 4.744972392 24.62179124 0.741199533 4.11E-07 0.503854908 0.222065583 451.0095717 1731858.937 0.047639928 0.44872651 55586.89196 -4.744972392 -0.741199122 DGHADAAQDTEQFVATVLQAASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGHADAAQDTEQFVATVLQAASR 23 0 Q6PJG6;Q6PJG6-3 Q6PJG6 BRAT1 BRCA1-associated ATM activator 1 0 ; 104.63 0.0016182 31430000 27569 26422 27921 29971 32467 36516 28264 27850 30236 24007 FALSE TRUE 28657.44541 30959.77297 28648.6442 35899.17435 26948.27094 28035.71241 26048.59383 27476.7163 29147.81227 28710.71201 0.998144713 1.078335255 0.997838165 1.250375621 0.938613815 0.976489625 0.907277877 0.957019676 1.015224292 1 14.80930149 DGHGEAIMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGHGEAIMFK 10 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;; 100.88 0.0037132 1402620000 2370050 2167070 2590510 2286470 2944570 2957190 2923920 2376520 2466250 2196910 FALSE TRUE 2463621.404 2539247.415 2658020.819 2738726.942 2444053.043 2270427.439 2694735.51 2344666.637 2377490.144 2627352.452 0.937682115 0.966466228 1.011672727 1.042390388 0.930234176 0.864150311 1.025646752 0.892406588 0.904899585 1 21.32517832 3.188606321 24.82660538 0.931165764 0.989483848 0.199019989 0.051820474 148.4535476 73778.77451 0.014802895 0.017692875 1543.854334 -3.188606321 0.058318084 DGHPNVLHDCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGHPNVLHDCQR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 94.023 0.0039572 162880000 61305 83729 82832 90386 94424 114750 87585 85010 69658 105830 FALSE TRUE 63725.36874 98108.80443 84990.66997 108264.081 78373.84221 88101.05155 80719.85884 83870.58 67151.02219 126565.3623 0.5034977 0.775163146 0.671516033 0.855400554 0.619236107 0.696091332 0.637772116 0.662666139 0.530563979 1 16.9495231 -1.484405184 3.147511864 1.007885503 0.669068111 0.514734528 0.098393492 26691582.43 31619944.87 1820453.715 0.022370822 0.032778933 1.484405184 -0.338817392 DGHRYS(ph)RS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGHRYSRSPAR 11 2 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 2 DGHRY(0.064)S(0.94)RS(0.996)PAR;DGHRY(0.014)S(0.987)RS(0.999)PAR 71.279 0.026529 790610000 34548 254690 164159 286620 136368 314440 190243 227675 177785 351360 TRUE FALSE 35911.98172 298431.0263 168437.1184 343312.5805 113188.2161 241416.0754 175331.2566 224623.389 171386.5526 420202.2648 0.085463561 0.710208039 0.400847717 0.817017444 0.26936603 0.574523499 0.41725443 0.534560158 0.407866799 1 18.68072441 -1.684462668 2.471170197 1.085852578 0.48293243 0.390034062 0.198645368 9150997.673 7062338.317 4911166.078 0.044372868 0.020679371 1.684462668 -0.602920148 DGIDDESYGQIFKPIISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGIDDESYGQIFKPIISK 18 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 ; 175.21 3.57E-12 1242520000 964640 552950 783990 602700 1071030 1012880 1004720 854810 906210 436450 FALSE TRUE 1002724.732 647914.8611 804421.4235 721912.2611 888976.7032 777653.9703 925967.4211 843352.6701 873595.6791 521964.0212 1.921061015 1.241301766 1.541143433 1.383069008 1.703137893 1.489861253 1.774006222 1.615729506 1.673670299 1 18.99359084 -1.088200164 7.139469123 0.999999819 1.585771879 0.481336209 0.184712751 4.99E-07 6.35E-08 0.167058266 0.039375999 0.08162061 1.088200164 0.58577206 DGIEPGHIPGTVNIPFTDFLSQEGLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGIEPGHIPGTVNIPFTDFLSQEGLEK 27 0 P25325-2;P25325 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 0 95.366 0.0048966 60778000 61559 41926 61167 50554 70765 67912 72033 60730 65614 38549 FALSE TRUE 63989.39685 49126.46436 62761.06227 60553.43031 58736.39058 52140.46722 66386.86524 59916.01368 63252.56496 46101.93848 1.387997966 1.065605178 1.361354085 1.313468203 1.274054682 1.1309821 1.440001601 1.29964196 1.3720153 1 15.49253979 DGIVLGADTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGIVLGADTR 10 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ;;; 142.43 8.32E-05 877020000 830780 895390 900690 843670 1188900 1183900 1040370 918050 892620 1003950 FALSE TRUE 863579.8359 1049166.267 924162.7213 1010545.408 986811.2027 908957.1672 958823.0809 905745.0414 860494.7806 1200654.781 0.7192574 0.873828418 0.769715605 0.84166192 0.821894202 0.757051221 0.798583487 0.754375909 0.716687923 1 20.19538997 2.775021196 24.14103733 0.786883881 0.809126584 0 0.082138404 2235.184944 1479941.518 0.023029864 0.024426088 595.6912161 -2.775021196 0.022242704 DGKDQGVNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGKDQGVNVR 10 1 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9H201;Q9Y6I3 EPN3;EPN1 Epsin-3;Epsin-1 0 ;; 89.805 0.010272 498820000 1079690 701550 950970 650820 1163080 1193470 1009160 835820 1021920 644820 FALSE TRUE 1122316.995 822035.7552 975753.0594 779550.2535 965380.077 916304.6797 930059.4023 824617.2 985141.2988 771160.1332 1.455361794 1.065972837 1.265305372 1.010879868 1.251854233 1.188215833 1.206052235 1.06932032 1.277479549 1 19.55667094 7.999998811 0.018866219 1.01E-06 2.655872537 0.208602492 0.120920003 5882.904028 8.555802719 454.0699083 794.2014154 99999726.14 -7.999998811 2.655871525 DGKLPLLLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGKLPLLLSR 10 1 P49902-2;P49902;Q5JUV4 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 129.34 0.00027873 1654260000 3557500 3052000 3194900 2514800 6703800 5277200 4400600 3730500 3863100 4477500 FALSE TRUE 3697952.847 3576157.259 3278161.719 3012219.934 5564290.471 4051650.277 4055669.473 3680498.749 3724067.786 5354780.398 0.690589076 0.667843869 0.612193493 0.562529125 1.039125801 0.756641725 0.757392306 0.68732954 0.695466015 1 22.35239598 DGKPMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGKPMLR 7 1 Q9Y3F4 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 67.032 0.060432 324270000 522030 457060 515730 424690 625790 698430 561960 493120 573210 472650 FALSE TRUE 542640.1475 535556.4996 529170.3475 508692.4144 519418.4393 536230.2173 517912.1068 486510.533 552580.2841 565256.7181 0.959988851 0.947457115 0.936159325 0.899931656 0.918907149 0.948648995 0.916242285 0.860689519 0.977574023 1 19.10854671 4.175779435 2.734016678 0.921415333 0.956039909 1.45E-05 0.03787207 0.620948262 9.217966604 0.009689292 0.028529703 14989.23385 -4.175779435 0.034624576 DGKS(ph)PTVPCLQEEAGEPLGGK ddPTM_MDA-MB-175_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(0.985)PT(0.015)VPCLQEEAGEPLGGK;DGKS(0.992)PT(0.008)VPCLQEEAGEPLGGK 139 4.31E-07 701730000 555009 245384 373524 236060 552540 527990 519020 404073 462380 166195 TRUE FALSE 576921.1839 287526.7932 383258.3423 282751.9634 458619.4482 405372.3243 478337.8562 398657.0624 445739.0341 198757.7283 2.902635228 1.446619438 1.928268881 1.422596072 2.307429513 2.039529873 2.406637771 2.005743705 2.242624918 1 17.60065143 DGLAFNALIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGLAFNALIHR 11 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;; 222.74 7.45E-12 2429090000 988039 1146960 1034890 1463330 2478930 2055080 1960910 1188400 1141610 2449760 FALSE TRUE 1027047.543 1343941.458 1061860.084 1752772.306 2057562.364 1577818.815 1807208.75 1172471.442 1100523.679 2929743.569 0.350558852 0.458723239 0.362441305 0.598268164 0.70230118 0.538551849 0.616848781 0.400195927 0.375638227 1 21.48234296 -2.357446435 2.33940089 4.468138832 0.494350869 0.637585 0.115457813 5840132.131 803695.5127 106982718.8 0.030265337 0.0043909 2.357446435 -3.973787964 DGLAPEKT(ph)SPDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.5)S(0.5)PDRDK;DGLAPEKT(0.682)S(0.318)PDRDK;DGLAPEKT(0.836)S(0.164)PDRDK 221.81 6.64E-12 2015700000 1880570 528068 788198 556356 1273493 1450083 1503933 932007 1063883 301905 TRUE FALSE 1954816.356 618759.5712 808739.0874 666401.5562 1057025.115 1113323.199 1386050.802 919514.9706 1025594.059 361057.5044 5.414141326 1.713742447 2.239917679 1.845693686 2.927581069 3.083506604 3.838864404 2.546727209 2.840528298 1 18.4618691 DGLAPEKT(ph)SPDRDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGLAPEKTSPDRDKK 15 3 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.828)S(0.172)PDRDKK 119.38 0.0002234 258800000 293610 67429 125970 63312 198050 190730 218770 142460 162750 47632 TRUE FALSE 305201.9495 79009.40623 129252.8817 75834.92463 164385.5317 146435.848 201622.2358 140550.5567 156892.6593 56964.57843 5.357749639 1.386991854 2.269004445 1.331264563 2.885749992 2.570647446 3.539431719 2.467332518 2.754214349 1 15.79777748 DGLAPEKTS(ph)PDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLAPEKTSPDRDK 14 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 DGLAPEKT(0.085)S(0.915)PDRDK;DGLAPEKT(0.358)S(0.642)PDRDK 223.11 2.87E-12 1454240000 659770 176047 328712 215600 504371 572980 611230 343687 410523 136478 TRUE FALSE 685818.2291 206281.7028 337278.5048 258245.0365 418638.1976 439914.0786 563320.1954 339080.4379 395748.3574 163218.2511 4.201847677 1.263839684 2.066426411 1.58220686 2.564898195 2.695250535 3.451330913 2.077466433 2.424657505 1 17.31644286 DGLGFCALIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLGFCALIHR 11 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V2X9 P12814-3 ACTN1 Alpha-actinin-1 0 ; 125.74 0.000322 895150000 508230 627000 505860 682060 849320 925130 787560 610000 615700 891380 FALSE TRUE 528295.3128 734682.3726 519043.1272 816969.4323 704952.8898 710282.578 725828.9893 601823.9478 593541.0773 1066028.844 0.495573188 0.689176823 0.486894074 0.766367098 0.661288757 0.666288329 0.68087181 0.564547527 0.55677769 1 20.02381504 -1.795300248 2.641469586 1.108713389 0.622390207 0.638163264 0.086106084 10889201.5 8098837.657 7614719.98 0.020114362 0.016021374 1.795300248 -0.486323182 DGLGGLPDIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLGGLPDIVR 11 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 111.06 0.0039813 87735000 104653 101743 104127 106028 158556 150099 120072 116759 112056 129815 FALSE TRUE 108784.7812 119216.5688 106840.6352 127000.0219 131604.7078 115240.782 110660.4429 115194.0366 108023.1264 155249.7638 0.700708192 0.767901773 0.688185493 0.818036813 0.84769667 0.742292801 0.712789767 0.741991703 0.695802195 1 17.24423155 -1.029787046 4.207059378 1.00002007 0.74818038 0.697842908 0.050094186 5696773.655 2789720.634 1021.216974 0.012042022 0.093371203 1.029787046 -0.25183969 DGLILTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGLILTSR 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 163.99 0.00077406 809570000 556740 690020 671610 635730 821690 849580 690380 695510 639100 654950 FALSE TRUE 578720.5251 808525.5674 689112.7083 761475.4965 682019.4273 652277.9205 636266.2116 686187.8261 616098.9158 783274.9127 0.738847263 1.032237283 0.879783965 0.972168882 0.870728037 0.832757324 0.81231532 0.876049794 0.786567916 1 19.57915923 3.015021387 23.84051263 0.851757684 0.914001921 0.045249059 0.088286652 310.1155411 492179.9011 0.023402676 0.027959018 1035.193143 -3.015021387 0.062244237 DGLIPLEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGLIPLEIR 9 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 85.666 0.034107 42499000 67067 62978 71808 71907 74213 77319 88833 72404 68370 56140 FALSE TRUE 69714.85695 73793.9816 73679.37547 86129.98998 61598.30077 59362.83403 81870.03734 71433.54281 65909.37706 67139.55813 1.038357399 1.099113304 1.097406321 1.282850117 0.91746658 0.884170758 1.219400896 1.063956106 0.981677254 1 16.03487542 3.219560422 24.99973888 1.026053551 1.124978762 0.230804537 0.103559484 449.7592766 591774.8364 0.031709488 0.037957659 1657.907981 -3.219560422 0.09892521 DGLLENQTPEFFQDVCKPK ddPTM_MDA-MB-175_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 ;;;;; 287.38 2.15E-40 11914021000 7894604 3538716 6299724 4386794 8419520 7111405 7459517 5428753 6496336 3344353 FALSE TRUE 8206289.062 4146462.946 6463899.983 5254488.76 6988372.998 5459888.963 6874820.566 5355989.446 6262534.136 3999614.939 2.05176978 1.036715536 1.616130573 1.313748658 1.74726145 1.365103653 1.718870609 1.339126273 1.565784265 1 21.93142968 -2.628813297 0.457164322 7.25E-14 1.516285706 0.256652627 0.268340306 161.7057675 7.371537613 159.8432909 0.124294029 0.002350643 2.628813297 1.516285706 DGLLPENTFIVGYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGLLPENTFIVGYAR 15 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 187.51 7.85E-07 796510000 348014 370644 428823 387638 468199 492001 467904 434800 409936 366776 FALSE TRUE 361753.8614 434299.2238 439998.4797 464311.6394 388614.7012 377741.2241 431228.4618 428972.2172 395182.4834 438638.7348 0.824719371 0.990106868 1.00309992 1.058528585 0.885956187 0.861167047 0.983106205 0.977962462 0.900929289 1 18.74267369 -1.222892625 3.838708018 1.000049716 0.949309774 0.050608983 0.069351254 10301130.04 3281619.783 4488.926079 0.016294065 0.059855956 1.222892625 -0.050739942 DGLNDDDFEPYLS(ph)PQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLNDDDFEPYLSPQAR 17 0 Q9Y5A9;S4R3J8 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR 361.23 2.42E-88 661670000 749210 652820 728910 759540 941810 1056740 944480 821930 822120 590100 TRUE FALSE 778789.3893 764936.7568 747905.9934 909774.745 781721.4726 811328.15 870449.1897 810913.3728 792532.0618 705718.7969 1.103540663 1.083911553 1.059779046 1.289146256 1.107695411 1.149647924 1.233422141 1.149060187 1.123013962 1 19.42873391 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGLNQTTIPVSPPSTTKPSR 20 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DGLNQTTIPVS(0.999)PPSTTKPSR;DGLNQTT(0.001)IPVS(0.881)PPS(0.041)T(0.038)T(0.038)KPS(0.002)R;DGLNQTTIPVS(0.998)PPS(0.001)T(0.001)T(0.001)KPSR;DGLNQTTIPVS(0.925)PPS(0.006)T(0.009)T(0.047)KPS(0.013)R;DGLNQTTIPVS(0.684)PPS(0.093)T(0.129)T(0.093)KPS(0.002)R;DGLNQTTIPVS(0.988)PPS(0.003)T(0.004)T(0.004)KPSR 183.24 2.69E-17 8354190000 1951980 1522470 1880270 1425420 2241500 2352910 2157650 1953190 2090630 1343010 TRUE FALSE 2029045.678 1783942.379 1929271.381 1707363.822 1860490.631 1806482.311 1988527.755 1927010.683 2015388.635 1606147.096 1.263300032 1.110696762 1.201179758 1.063018341 1.158356314 1.124730304 1.23807325 1.19977223 1.254797048 1 20.61517259 2.256552778 24.98997169 1.192599649 1.149867991 0 0.082682145 728.5495829 1011906.361 0.026555895 0.022178312 180.5314116 -2.256552778 -0.042731658 DGLPRT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.996)PS(0.004)R;DGLPRT(0.956)PS(0.044)R 84.169 0.02534 1098590000 729290 742250 783530 813520 943230 970880 873310 830390 778990 707600 TRUE FALSE 758082.9323 869725.6636 803949.4355 974431.8279 782900.1015 745407.8338 804857.6802 819259.9803 750954.3021 846240.6722 0.89582427 1.027752142 0.950024576 1.151483094 0.925150642 0.880846145 0.951097846 0.968116999 0.887400389 1 19.6907085 DGLPRTPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGLPRTPSR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.219)PS(0.781)R 91.202 0.0066089 297950000 216600 198210 208510 212030 224820 265210 235760 191940 208240 183340 TRUE FALSE 225151.5353 232251.0256 213943.9419 253968.9012 186605.1767 203618.9968 217280.5152 189367.3583 200745.4831 219261.9627 1.026860895 1.059239928 0.975745812 1.158289828 0.851060414 0.928656271 0.990963104 0.863658046 0.915550881 1 17.74229603 3.22742807 24.99977394 0.919268741 1.049671095 0.518687342 0.061138686 162.8812843 365773.2624 0.016835584 0.020297901 1688.216225 -3.22742807 0.130402354 DGLPRTPS(ph)RR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGLPRTPSRR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DGLPRT(0.079)PS(0.921)RR;DGLPRT(0.119)PS(0.881)RR 77.894 0.016505 1596620000 739120 763290 816320 656740 965330 1065060 814940 830600 815570 775250 TRUE FALSE 768301.0283 894379.1199 837593.9698 786641.2118 801243.5514 817715.9561 751062.8734 819467.1656 786217.795 927145.3944 0.828673726 0.964658969 0.903411671 0.848455071 0.864204855 0.881971653 0.810081005 0.883860472 0.847998383 1 19.82243607 DGMDNQGGYGSVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGMDNQGGYGSVGR 14 0 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 80.287 0.03889 321310000 310740 234610 273840 203690 326540 342180 317500 290750 284150 221110 FALSE TRUE 323008.2551 274902.4425 280976.4954 243979.274 271034.8474 262713.8808 292613.5204 286852.9718 273923.497 264432.2711 1.221516019 1.039594908 1.062565073 0.922653173 1.024968875 0.993501586 1.106572655 1.084788066 1.035892843 1 18.01253873 4.740772693 5.397252959 1.034482215 1.229013734 0.577886622 0.048975293 0.122857081 13.23056677 0.012684932 0.088387524 55051.94821 -4.740772693 0.194531519 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGMEYPFIGEGEPHVDGEPGDLR 23 0 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ;;;;; 226.45 9.98E-33 792822000 448942 592764 583335 599602 672790 719371 618208 560891 551943 506825 FALSE TRUE 466666.5768 694566.6059 598537.1893 718201.486 558429.3961 552307.9874 569751.2416 553373.1736 532078.6792 606127.655 0.769914676 1.145908127 0.987477117 1.184901365 0.921306579 0.911207372 0.939985557 0.912964734 0.877832705 1 19.20926214 3.095292327 22.75100729 0.922366531 1.031516815 0.154331626 0.107482167 12.56749169 2987.866878 0.029032841 0.034700886 1245.352586 -3.095292327 0.109150284 DGMVSFHDNPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGMVSFHDNPEK 12 0 Q9UNS2-2;Q9UNS2;H7C3P9;K7ELN6 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 160.52 6.78E-05 189360000 114470 193430 232770 228000 264920 312180 294140 264490 265550 178230 FALSE TRUE 118989.364 226650.0978 238836.1774 273097.7195 219888.993 239680.9261 271084.5382 260944.9442 255992.9074 213150.7561 0.558240403 1.063332366 1.120503543 1.281242087 1.031612541 1.124466695 1.271797216 1.224227157 1.200994602 1 17.70151465 4.830687808 2.053310358 1.173454407 0.278729281 0.799065545 0.08931593 0.392943445 1.476911624 0.022330196 0.711057323 67715.45614 -4.830687808 -0.894725126 DGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_MDA-MB-175_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 ; 268.28 1.22E-54 13630100000 3737420 2543530 3431150 3124300 3744500 4279200 4355300 3385760 3826600 2252730 FALSE TRUE 3884976.228 2980361.492 3520568.588 3742277.215 3108011.228 3285420.652 4013920.206 3340379.425 3688881.413 2694109.312 1.442026205 1.106251138 1.306765309 1.389059159 1.153632191 1.219483054 1.489887655 1.239882662 1.369239695 1 21.36137696 -1.097409449 4.780010003 0.999985645 1.29606695 0.371263325 0.1176122 1.68E-05 3.18E-06 0.106589529 0.025122175 0.079908053 1.097409449 0.296081304 DGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 215.84 2.90E-39 24692880000 3414340 2123570 2850300 1859390 4366730 3361440 3066200 2827080 3294870 1873640 FALSE TRUE 3549140.78 2488276.628 2924581.16 2227171.792 3624474.794 2580796.503 2825863.232 2789187.617 3176288.272 2240743.885 1.583911844 1.110469003 1.305183149 0.993943041 1.617531936 1.151758807 1.261127276 1.244759669 1.417515091 1 21.09554633 -1.225692929 4.706344058 0.999935457 1.284474319 0.181697367 0.187920443 0.000114562 1.88E-05 0.163777942 0.038594093 0.059471251 1.225692929 0.284538862 DGNDLHMTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGNDLHMTYK 10 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ; 123.8 0.00045244 952720000 1454850 1855240 2221600 1719680 2853300 2700500 2551600 2383010 2329450 1655610 FALSE TRUE 1512288.601 2173863.038 2279496.721 2059827.571 2368297.085 2073349.801 2351598.925 2351069.649 2245613.55 1979995.081 0.763784019 1.097913353 1.15126383 1.04031954 1.196112611 1.047148966 1.187679175 1.187411863 1.134151075 1 20.91706542 4.738043741 4.134409545 1.128805855 0.733662679 0.720316533 0.065626337 0.106049312 4.00999488 0.015005634 0.124681987 54707.10597 -4.738043741 -0.395143176 DGNGYISAAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGNGYISAAELR 12 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;; 173.76 7.49E-05 523548000 291161 341226 353864 446162 305500 452755 527685 394867 344591 276009 FALSE TRUE 302656.2611 399828.9111 363085.9865 534411.5119 253571.2191 347609.5128 486323.6709 389574.4537 332189.2372 330087.679 0.916896571 1.211280931 1.09996831 1.618998666 0.768193529 1.053082362 1.473316642 1.180215072 1.006366667 1 18.33248976 4.74397349 23.00803857 1.174559474 0.916896243 0.084248497 0.230732778 457.4276371 1944149.403 0.053260643 0.442895072 55459.18591 -4.74397349 -0.257663232 DGNLASTLGQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGNLASTLGQHK 12 0 Q9BZK7;A0A0D9SF63;A0A1B0GVH3 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 117.93 0.00022756 0 70839 57667 73763 60428 86279 90585 75902 71149 65676 63111 FALSE TRUE 73635.77842 67570.85866 75685.32438 72380.47804 71613.3264 69548.00658 69952.60291 70195.36403 63312.33359 75476.39212 0.975613385 0.895258196 1.00276818 0.95898169 0.948817563 0.921453777 0.926814345 0.93003073 0.838836248 1 16.20373784 2.798757012 3.020383935 0.919917589 0.956692956 0.122031071 0.04404812 0.543535099 9.830723085 0.013843144 0.014368445 629.154072 -2.798757012 0.036775368 DGNLHEGDIILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 128.9 0.00024376 1514800000 3329710 2605900 3238090 2452800 4326130 4094920 3808400 3269340 3726920 2546000 FALSE TRUE 3461169.522 3053443.054 3322477.286 2937956.519 3590775.968 3143936.889 3509887.657 3225519.845 3592788.877 3044839.954 1.136732825 1.002825469 1.091182898 0.964896863 1.179298755 1.03254586 1.152733053 1.059339701 1.179959844 1 21.53793497 3.234947243 24.99988319 1.100983 1.048637333 0.113142906 0.070955122 196.9267035 1362479.301 0.018373893 0.022794795 1717.699713 -3.234947243 -0.052345667 DGNLKDFPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGNLKDFPVK 10 1 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 73.848 0.03991 387120000 1167000 724930 1071200 744020 1463800 1350900 1192500 1053400 1251400 746920 FALSE TRUE 1213074.061 849431.0883 1099116.352 891184.9353 1214983.799 1037173.948 1099028.734 1039280.896 1206362.358 893264.6734 1.3580231 0.950928783 1.230448695 0.997671756 1.360161031 1.161104854 1.230350608 1.163463559 1.350509423 1 19.76872818 DGNVLLHEMQIQHPTASLIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGNVLLHEMQIQHPTASLIAK 21 0 P40227 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 280.59 3.23E-45 4112200000 2053110 2521900 3165600 2365900 4086400 3993700 3232900 3356600 3519800 2730200 FALSE TRUE 2134168.368 2955016.707 3248098.137 2833867.958 3391795.188 3066223.7 2979496.85 3311610.267 3393123.086 3265130.417 0.653624234 0.905022566 0.994783583 0.867918765 1.038793173 0.93908154 0.912520013 1.01423522 1.039199864 1 21.63870919 4.741966911 2.544828412 0.972547726 0.583130024 0.770766206 0.052617815 0.229646539 1.87809004 0.012795631 0.193494964 55203.53782 -4.741966911 -0.389417702 DGPEETDWWWAALHGQEGYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGPEETDWWWAALHGQEGYVPR 22 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ;; 191.8 1.30E-17 269324000 219474 209730 249096 198213 285236 306530 252860 245372 249544 199390 FALSE TRUE 228139.003 245749.496 255587.6464 237418.9398 236751.6866 235343.053 233040.1725 242083.1897 240562.9602 238456.6529 0.956731549 1.030583517 1.071841122 0.995648211 0.992849995 0.9869427 0.977285262 1.015208369 1.008833082 1 17.86336751 DGPLNMILDDGGDLTNLIHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGPLNMILDDGGDLTNLIHTK 21 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 249.51 1.08E-30 2151788000 897773 632493 854055 685993 1115044 1027123 1033734 884882 918458 555125 FALSE TRUE 933217.7713 741118.7526 876312.3749 821680.3679 925509.2192 788589.2494 952707.2279 873021.6042 885402.876 663891.1152 1.405678958 1.116325758 1.319964004 1.237673391 1.394067789 1.187829196 1.435035364 1.315007211 1.333656763 1 19.34058712 -0.915309923 4.806097143 0.999998141 1.303656848 0.481924 0.094868599 1.74E-06 3.93E-07 0.084598021 0.019939823 0.121531841 0.915309923 0.303658707 DGQAMLWDLNEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 178.15 3.45E-05 212970000 457030 299360 424110 352870 552980 527680 503670 471360 495980 299920 FALSE TRUE 475073.8973 350772.7513 435162.655 422666.6328 458984.6571 405134.3171 464191.0293 465042.1902 478129.7767 358683.5817 1.324493012 0.977944822 1.213221561 1.178382994 1.279636651 1.129503378 1.294151874 1.296524887 1.33301272 1 18.45235218 3.577382028 2.101964427 1.241235403 1.14961345 0.011582422 0.122798878 0.791173606 6.868602989 0.033920937 0.060062943 3779.044688 -3.577382028 -0.091621954 DGQDAIAQS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGQDAIAQSPEK 12 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK 273.23 9.68E-28 1904350000 2949690 1145340 1696450 1339430 2203440 2749220 2884700 1793270 1941850 772000 TRUE FALSE 3066146.039 1342043.235 1740660.881 1604365.256 1828900.056 2110755.32 2658589.676 1769234.149 1871963.198 923258.6192 3.321004511 1.45359405 1.885344848 1.737720312 1.980918475 2.286201586 2.879572008 1.91629313 2.027561031 1 19.8163753 2.810166363 24.97231284 2.135502781 2.011800214 0 0.635853331 1253.201365 437045.5493 0.185809331 0.197080515 645.9016041 -2.810166363 -0.123702567 DGQDAIAQS(ph)PEKESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGQDAIAQSPEKESK 15 1 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 1 DGQDAIAQS(0.989)PEKES(0.011)K;DGQDAIAQS(1)PEKESK 233.12 3.35E-17 191280000 388700 127539 186839 131399 292246 307444 280727 193333 216617 84178 TRUE FALSE 404046.1761 149442.8311 191708.1778 157389.33 242570.1293 236044.7904 258722.8842 190741.6874 208820.9965 100671.0674 4.013528281 1.48446654 1.904302624 1.56340182 2.409531711 2.344713297 2.569982527 1.894702145 2.07429008 1 16.61928959 0.48603991 1.063763829 0.999454027 2.237478479 0.243376214 0.673180098 2.73949217 4.215616763 0.61611028 0.191536228 3.06224483 -0.48603991 1.238024452 DGQPCMDHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGQPCMDHDR 10 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRU9 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 78.903 0.021701 135450000 148350 159090 171100 131680 229150 203990 155630 168350 173150 195110 FALSE TRUE 154206.9726 186412.47 175559.0066 157725.911 190199.1649 156616.414 143431.3139 166093.5436 166918.3653 233338.0689 0.660873613 0.798894372 0.752380473 0.675954471 0.815122735 0.671199581 0.614693156 0.711815026 0.715349905 1 17.83206218 0.650845271 5.824312676 0.999999999 0.712735701 0.680305649 0.059041605 59.4294659 991.6070816 0.05719456 0.014391257 4.475538231 -0.650845271 -0.287264298 DGQS(ph)SPQPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.668)S(0.33)PQPS(0.002)PR 108.72 0.0021248 66222000 82807 80094 85134 79396 92767 112670 81062 76250 78018 60164 TRUE FALSE 86076.2843 93849.52146 87352.66198 95100.29183 76998.49848 86504.10003 74708.14862 75227.99347 75210.14742 71951.98389 1.196301751 1.304335425 1.214041049 1.321718828 1.070137254 1.202247601 1.038305611 1.045530497 1.04528247 1 16.13474685 2.601989497 0.856182755 1.017754481 1.260973848 0.695940975 0.061682025 0.310136917 0.472626873 0.038192056 0.031101333 399.9350777 -2.601989497 0.243219367 DGQSS(ph)PQPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 2 DGQS(0.002)S(0.998)PQPS(1)PR;DGQSS(1)PQPS(1)PR;DGQS(0.29)S(0.71)PQPS(1)PR;DGQS(0.118)S(0.882)PQPS(1)PR;DGQS(0.286)S(0.714)PQPS(1)PR 150.78 4.93E-05 480428000 980289 978200 1070398 1060148 1268446 1552900 1242786 1164776 1160513 1044045 TRUE FALSE 1018991.567 1146198.241 1098293.451 1269842.11 1052836.002 1192262.509 1145373.186 1149164.083 1118746.364 1248605.628 0.816103615 0.9179826 0.87961597 1.017008158 0.843209399 0.954875168 0.917321819 0.920357923 0.895996573 1 20.25188644 1.672682245 0.012744872 1.857087527 7.04E-06 0.256199426 0.05159927 908.3482259 11.51548991 835.0363408 840.7466905 47.06328581 -1.672682245 -1.857080488 DGQSS(ph)PQPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 DGQS(0.037)S(0.963)PQPSPR;DGQS(0.04)S(0.96)PQPSPR;DGQS(0.032)S(0.968)PQPS(0.001)PR 192.91 1.24E-06 1081107000 871698 841881 943830 813732 1026060 1197590 869958 817733 806786 620288 TRUE FALSE 906113.3101 986467.5128 968426.9852 974685.7609 851650.6877 919467.8722 801768.4187 806772.6267 777749.9295 741821.5575 1.221470718 1.329790841 1.305471613 1.31390865 1.148053301 1.239473109 1.080810352 1.08755619 1.048432634 1 19.50071267 2.296914398 0.716961004 1.012542328 1.300810326 0.823963224 0.047915468 0.260405019 0.261110054 0.037825246 0.025290665 198.1136494 -2.296914398 0.288267998 DGQWFTDWDAVPHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGQWFTDWDAVPHSR 15 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;;;;; 199.65 7.31E-09 1548120000 1177220 1385400 1365840 1274170 1501830 1659810 1323840 1425380 1401200 1337500 FALSE TRUE 1223697.555 1623331.673 1401434.912 1526197.023 1246549.473 1274344.282 1220073.962 1406275.113 1350771.086 1599557.517 0.76502254 1.014862958 0.876139118 0.954137008 0.77930894 0.796685501 0.762757168 0.87916508 0.844465467 1 20.60924144 DGQYLLTGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGQYLLTGGDR 11 0 A0A494C1L5;P50851-2;P50851;A0A494BZW2;H0YAC6;A0A3B3IS13 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 130.56 0.00051546 863170000 397770 444880 478120 426470 500410 586490 466140 482970 447520 415560 FALSE TRUE 413474.2667 521284.6793 490580.2 510824.4931 415350.4869 450286.5858 429602.7288 476496.5771 431413.8426 496981.0256 0.831971937 1.048902579 0.987120583 1.027855123 0.835747172 0.906043818 0.86442481 0.958782232 0.868069042 1 18.92283125 3.248521896 24.99953548 0.904492624 0.980255264 0.185224391 0.069816022 308.907513 775251.7514 0.018356601 0.024564879 1772.237393 -3.248521896 0.07576264 DGRHPQGEQMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 0.00010497 1039458000 148316.3 177667.8 183371.9 161456.6 224792.7 238781 173570.3 207615.6 198141.4 163052.8 FALSE TRUE 154171.942 208180.8626 188150.7224 193392.2336 186582.5171 183327.7315 159965.4063 204832.8525 191010.3297 194999.8743 0.790625853 1.067594855 0.964876121 0.991755683 0.956834038 0.940142819 0.820335946 1.050425561 0.979540784 1 17.57311367 1.625409063 25 1.011238898 0.942439346 0.165480353 0.07709488 1.632030894 2320.175387 0.034572955 0.019116578 42.20938871 -1.625409063 -0.068799552 DGS(ph)FGEGLTMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGSFGEGLTMK 11 0 Q9ULT0;Q9ULT0-4;G5E9G4 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 DGS(1)FGEGLTMK;DGS(1)FGEGLTMK 112.44 0.0016007 88295000 286440 123677 174168 142989 232326 270680 241210 170386 184595 84057 TRUE FALSE 297748.8724 144917.5627 178706.9612 171271.7974 192835.3095 207818.6722 222303.3299 168102.2544 177951.462 100526.3598 2.961898481 1.441587689 1.777712448 1.703750119 1.918256166 2.067305259 2.211393414 1.672220647 1.770197015 1 16.61721433 0.655308118 1.131919409 1.002438538 1.956712244 0.364154884 0.388410567 1.230965017 2.534191009 0.349023842 0.108334757 4.521766358 -0.655308118 0.954273706 DGSAFEDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGSAFEDGLR 10 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 86.744 0.031056 272330000 329370 468920 435710 453310 487240 520400 424820 443560 408370 545510 FALSE TRUE 342373.7819 549453.3623 447064.9605 542973.365 404419.1188 399544.9867 391521.4983 437614.8037 393672.8435 652392.2401 0.524797447 0.842213209 0.6852702 0.832280539 0.619901792 0.612430624 0.600132059 0.670784808 0.603429684 1 19.3153801 -1.572497683 8.484420581 1.000077726 0.670638266 0.520388551 0.096177067 0.000136949 6.90E-06 0.090189458 0.021252893 0.026760999 1.572497683 -0.32943946 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGSDEPGTAACPNGSFHCTNTGYKPLYIPSNR 32 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 172.83 1.09E-14 501460000 75021 112769 138344 128035 157234 167529 138711 141687 131722 72113 FALSE TRUE 77982.88701 132136.1985 141949.3583 153359.9409 130507.4208 128622.9287 127838.4694 139787.9175 126981.351 86242.16166 0.90423159 1.532153137 1.645939243 1.778247877 1.513267042 1.491415871 1.482319864 1.620876783 1.472381356 1 16.39610572 -0.218920469 9.718564345 1.000000054 1.515533135 0.311480966 0.217862307 0 0 0.205314785 0.048393159 0.604059239 0.218920469 0.515533081 DGSDVIYPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGSDVIYPAR 10 0 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 159.58 1.78E-05 388920000 489790 519290 536910 508340 631470 689510 559910 532630 546880 508220 FALSE TRUE 509127.2874 608474.018 550902.3157 608888.1348 524132.955 529381.7521 516022.7911 525490.9661 527197.8956 607795.9785 0.837661494 1.001115571 0.906393486 1.001796913 0.862350153 0.870985941 0.84900659 0.864584473 0.867392866 1 19.2132276 3.202338002 24.99958922 0.874950747 0.939172363 0.133805774 0.059822414 246.3376424 170012.9623 0.015815342 0.018903474 1593.44839 -3.202338002 0.064221616 DGSGDSHPDFPEDADIDLKDVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGSGDSHPDFPEDADIDLKDVDK 23 1 Q08752 Q08752 PPID Peptidyl-prolyl cis-trans isomerase D 0 168.14 6.00E-12 76120000 263920 93646 158000 91048 251360 233520 227230 159280 197470 83419 FALSE TRUE 274339.7654 109728.972 162117.6098 109057.0226 208633.917 179288.519 209419.1188 157145.1121 190363.0933 99763.3559 2.749905142 1.099892551 1.625021616 1.093157118 2.09128808 1.797138011 2.099158724 1.575178689 1.908146449 1 16.60622238 DGSYAWEIKDFLVGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGSYAWEIKDFLVGQDR 17 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 136.35 9.67E-06 275280000 383410 255590 361410 286530 507260 405510 432430 314720 435110 239900 FALSE TRUE 398547.3229 299485.5943 370828.6415 343204.7788 421036.1264 311336.4481 398535.0067 310501.6932 419450.4761 286903.8118 1.389132198 1.043853661 1.292519047 1.196236385 1.467516669 1.085159678 1.38908927 1.082250149 1.461989903 1 18.13020761 -1.28200527 5.36416049 0.999964421 1.252716267 0.211578418 0.152536325 5.76E-05 7.71E-06 0.131097299 0.030895586 0.052238985 1.28200527 0.252751845 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DGTAPPPQSPGSPGTGQDEEWS(0.991)DEES(0.009)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.995)DEES(0.005)PRK;DGTAPPPQSPGSPGTGQDEEWS(1)DEESPRK;DGTAPPPQSPGSPGTGQDEEWS(0.983)DEES(0.017)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.995)DEES(0.005)PRK;DGTAPPPQSPGSPGTGQDEEWS(0.994)DEES(0.006)PRK 357.36 1.81E-120 6364570000 1200579 832608 1164050 761998 1413900 1481558 1231971 1132709 1240651 780241 TRUE FALSE 1247978.786 975601.9472 1194386.099 912718.9301 1173565.783 1137488.608 1135405.894 1117526.889 1196000.213 933114.2853 1.337434016 1.045533181 1.279999801 0.978142704 1.257687082 1.219023892 1.216791889 1.197631315 1.281729614 1 19.83169426 DGTGVVEFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 131.22 0.00059503 236990000 259820 246180 277760 266290 292360 348580 288620 264390 271780 236150 FALSE TRUE 270077.8942 288459.5 284998.6538 318961.3672 242664.7516 267627.5778 265997.2102 260846.2845 261998.6909 282419.0711 0.9563019 1.021388176 1.009133883 1.129390327 0.85923642 0.947625728 0.941852861 0.923614271 0.927694755 1 18.10747799 3.226965083 24.99999445 0.930432413 1.027083226 0.455357735 0.051205399 188.7434819 406930.6241 0.01423583 0.017148616 1686.417432 -3.226965083 0.096650813 DGTSLWDLLSSCHFTEEQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGTSLWDLLSSCHFTEEQRR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 146.81 8.39E-08 170700000 54077 148040 152840 120150 148980 170470 106310 139120 135490 158590 FALSE TRUE 56212.00172 173464.7184 156823.136 143915.3114 123656.4328 130880.926 97977.14441 137255.324 130613.7414 189662.6741 0.296378831 0.914595975 0.82685292 0.758796174 0.651980857 0.690072133 0.516586328 0.723681265 0.688663397 1 17.53307626 0.328867535 2.101401922 0.999998386 0.683142134 0.267416113 0.161217708 20.57512977 62.23126988 0.147142647 0.040136845 2.132394408 -0.328867535 -0.316856252 DGVADVSIEDSVISLSGDHCIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGVADVSIEDSVISLSGDHCIIGR 24 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;; 252.55 9.26E-44 317508000 69577 122740 117845 122227 118627 146391 135617 131129 125145 93375 FALSE TRUE 72323.95369 143819.6402 120916.1375 146403.1358 98462.82491 112393.9088 124986.9852 129371.4302 120641.0559 111670.0435 0.647657612 1.28789813 1.082798338 1.311033212 0.881729977 1.00648218 1.119252588 1.158515088 1.080334995 1 16.7688827 2.206355801 24.43522832 1.109301613 1.055284409 0.009110868 0.182823117 858.054846 651038.0672 0.066283547 0.048957864 160.8258297 -2.206355801 -0.054017204 DGVFCLLSDDHGASWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGVFCLLSDDHGASWR 16 0 Q99519;E9PIF4 Q99519 NEU1 Sialidase-1 0 ;; 185.14 1.71E-09 196213000 101313 159521 136551 140324 156201 196389 145308 139448 133026 147403 FALSE TRUE 105312.9155 186917.4908 140109.6312 168079.6684 129650.0098 150780.6311 133918.3793 137578.9277 128238.4202 176283.7956 0.597405536 1.060321456 0.794795862 0.953460684 0.735461869 0.855328934 0.759674925 0.780440012 0.727454386 1 17.42754034 3.221402056 24.99063031 0.7964101 0.862362044 0.01473539 0.13313468 747.1247644 1088149.29 0.035168958 0.042131371 1664.953298 -3.221402056 0.065951944 DGVIEASINHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGVIEASINHEK 12 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 179.67 2.04E-05 1014960000 939020 2022210 2525000 2166500 2519300 2512900 2747400 2461700 2706400 2081200 FALSE TRUE 976093.2347 2369508.837 2590803.574 2595027.234 2091070.286 1929317.058 2532051.609 2428704.938 2608997.193 2488971.293 0.392167333 0.952003281 1.040913401 1.042610351 0.840134353 0.775146368 1.017308482 0.975786641 1.048223095 1 21.24711816 4.738115551 6.764882112 0.963552821 0.382514877 0.799032337 0.086316063 0.05019864 15.85046901 0.021957437 0.134093619 54716.15248 -4.738115551 -0.581037944 DGVLEEQIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGVLEEQIER 10 0 Q09161;X6R941 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 148.56 0.012885 0 103920 85189 112300 97113 114430 143040 114700 114170 104780 97728 FALSE TRUE 108022.8418 99819.54807 115226.6303 116321.6615 94979.22947 109821.1278 105709.5143 112639.7379 101008.9883 116875.9305 0.924252251 0.8540642 0.985888453 0.99525763 0.812650039 0.939638532 0.904459232 0.96375479 0.864241147 1 16.83461833 -2.007206008 3.13096762 1.085255231 0.919060931 0.165930651 0.056112436 0.0480723 0.00011064 0.078213209 0.012280407 0.009835444 2.007206008 -0.1661943 DGVPEGAQLQGPVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGVPEGAQLQGPVHR 15 0 P16989;P16989-3;P16989-2 P16989;P16989-2 YBX3 Y-box-binding protein 3 0 167.55 1.30E-06 151410000 110430 123960 140940 118090 134510 154410 157430 131810 142690 119150 FALSE TRUE 114789.8617 145249.1657 144613.0122 141447.8495 111646.0382 118550.6176 145090.2252 130043.3025 137554.6148 142495.1612 0.805570243 1.019327004 1.014862617 0.992650195 0.783507575 0.831962409 1.018211594 0.912615568 0.965328321 1 17.1205534 -1.156473888 4.987142125 1.000004343 0.930090908 0.058988931 0.086600564 4.20E-06 7.11E-07 0.084255387 0.019857952 0.069747093 1.156473888 -0.069913435 DGVVEITGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DGVVEITGK 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 173.48 0.00012889 6008693000 5580630 3867500 4987760 4060580 6244810 5908920 6433510 5091760 5447790 3208570 FALSE TRUE 5800957.582 4531713.04 5117745.123 4863750.604 5183319.427 4536662.881 5929234.675 5023513.286 5251725.102 3837227.86 1.511757392 1.180986172 1.333708946 1.267516755 1.350797924 1.182276124 1.545187018 1.309151676 1.368624771 1 21.87163301 -0.785566285 5.113200126 0.999999793 1.334887944 0.444335888 0.113612741 2.46E-07 5.81E-08 0.100731557 0.023742641 0.163845197 0.785566285 0.33488815 DGVVEITGKHEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DGVVEITGKHEER 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 196.58 8.46E-08 20917830000 17117470 15914760 18992470 9319980 30333000 23619450 13153820 17504890 21012580 21458320 FALSE TRUE 17793280.93 18647996.23 19487429.37 11163444.23 25177007.49 18134190.69 12122789.22 17270265.58 20256341.35 25662666.96 0.693352759 0.726658545 0.759368829 0.435007174 0.981075254 0.706637027 0.472390077 0.672972361 0.789331108 1 24.61316777 0.92650631 3.31118272 0.999453179 0.678013346 0.318554941 0.142612266 0.373731457 9.88908424 0.133302169 0.034633022 8.443185082 -0.92650631 -0.321439833 DGVVRPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGVVRPLK 8 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 109.11 0.0033574 34518900000 32714900 20120370 30138800 27923100 32829500 33327600 36301200 27872300 29973700 14727900 FALSE TRUE 34006509.51 23575887.03 30924241.89 33446205.84 27249153.32 25587769.98 33455817.09 27498717.41 28894952.39 17613550.02 1.930701617 1.338508535 1.755707501 1.898890672 1.547056288 1.452732127 1.899436346 1.561225158 1.640495661 1 24.07018238 -2.38468872 0.442103108 4.79E-12 1.676152618 0.528937082 0.190273135 65.58156177 3.478135263 63.82349671 0.098586547 0.00412393 2.38468872 1.676152618 DGVYFLYEALHGPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGVYFLYEALHGPPK 15 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 128.96 6.88E-05 806990000 1138280 974150 1299440 1165360 1646920 1534590 1586510 1255980 1483380 931760 FALSE TRUE 1183220.173 1141452.685 1333304.474 1395864.73 1366977.127 1178204.729 1462155.201 1239145.642 1429993.444 1114320.532 1.061831079 1.024348607 1.196517909 1.252659975 1.226736013 1.05733018 1.312149564 1.112019034 1.28328735 1 20.08773285 4.236352779 24.99999268 1.186903283 1.043089811 0.249918846 0.094346013 62.94789993 712814.3734 0.021232136 0.049692949 17232.67824 -4.236352779 -0.143813472 DGVYFLYEALHGPPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGVYFLYEALHGPPKK 16 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 180.49 1.60E-09 1658330000 2998540 1966190 2909610 1937770 3834700 3415400 3328300 2722740 3293000 1823470 FALSE TRUE 3116924.675 2303867.838 2985436.827 2321055.122 3182879.064 2622225.111 3067419.149 2686246.124 3174485.573 2180744.034 1.429294143 1.056459539 1.368999195 1.064340925 1.459538127 1.202445161 1.406592934 1.231802578 1.455689216 1 21.05638901 DGWGGYGSDKR ddPTM_MDA-MB-175_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 ;; 126.76 0.00048209 1341300000 1701810 1364230 1582210 1273950 2285690 2084550 1907760 1656070 1765490 1468220 FALSE TRUE 1768998.773 1598525.89 1623443.692 1525933.508 1897169.23 1600444.854 1758224.786 1633873.09 1701950.36 1755889.598 1.007465831 0.910379498 0.924570482 0.869037273 1.08046043 0.91147237 1.001329917 0.930510148 0.969280962 1 20.74377071 DGWNQNHFITPVST(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGWNQNHFITPVSTLER 17 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 DGWNQNHFITPVS(0.188)T(0.812)LER;DGWNQNHFITPVS(0.194)T(0.806)LER;DGWNQNHFITPVS(0.193)T(0.807)LER 145.04 1.80E-06 275882000 177640 207090 207136 234268 253730 226187 195105 222060 192605 210964 TRUE FALSE 184653.3644 242656.0966 212534.1343 280605.5112 210601.0652 173658.4971 179812.1603 219083.6489 185673.1837 252298.3567 0.731884927 0.961782311 0.842392068 1.112197142 0.83473023 0.688306097 0.712696518 0.86835147 0.735927043 1 17.94477128 3.010499103 24.97983063 0.788940137 0.91849194 0.151461951 0.122316083 334.5624948 795996.3857 0.033866158 0.040439945 1024.469664 -3.010499103 0.129551803 DGWPAMCIHGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DGWPAMCIHGDK 12 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;; 143.86 5.92E-05 3379870000 3692050 2891450 3487840 2786100 4569290 4310940 4024760 3572370 3867900 2770050 FALSE TRUE 3837814.985 3388034.045 3578735.976 3337182.264 3792603.718 3309789.518 3709288.794 3524488.223 3728695.035 3312788.262 1.158484842 1.022713732 1.080279116 1.007363586 1.144837345 0.999094798 1.119687859 1.063903861 1.125545836 1 21.65961457 -0.799218025 9.224264347 1 1.076647582 0.161412569 0.054304551 0 0 0.046384144 0.010932848 0.158774946 0.799218025 0.076647582 DGWPAMGIHGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DGWPAMGIHGDK 12 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 105.65 0.0015223 1237740000 1008190 755320 976510 733160 1175080 1180580 1078790 923840 1028750 770200 FALSE TRUE 1047994.12 885040.3344 1001958.653 878176.8597 975340.3213 906408.1869 994231.6209 911457.4359 991725.4885 921105.9436 1.137756332 0.960845319 1.087777861 0.953393978 1.058879631 0.984043359 1.079388997 0.989525084 1.076668211 1 19.81300758 4.759748149 24.10894762 1.022016424 1.137756522 0.3432382 0.048368588 3541.54533 4029759.845 0.010026448 0.454430814 57510.63315 -4.759748149 0.115740098 DGWPVSLSNSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGWPVSLSNSVR 12 0 Q96RW7-2;Q96RW7 Q96RW7-2 HMCN1 Hemicentin-1 0 49.934 0.096225 1069300000 474600 291970 379500 250940 460510 427170 408560 281390 394050 267190 FALSE TRUE 493337.5745 342113.5763 389390.0818 300575.183 382232.6747 327966.2413 376535.9996 277618.4273 379868.2175 319540.7648 1.54389558 1.070641414 1.21859282 0.940647379 1.196193778 1.026367454 1.178366084 0.868804415 1.18879423 1 18.28564047 7.128485254 1.228268016 1.058422711 199.9977397 0.590688221 0.115180484 402.9842606 1.940556203 0.029903927 224384.0564 13442661.24 -7.128485254 198.9393169 DGWQVEEADDWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DGWQVEEADDWLR 13 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ;; 178.1 3.46E-05 256215000 464750 561794 603983 603850 639531 749430 662990 652219 630430 671133 FALSE TRUE 483098.6889 658277.7493 619723.2932 723289.7277 530823.7491 575386.2402 611023.1114 643477.0711 607740.9474 802628.6617 0.601895636 0.820152308 0.772117073 0.901151133 0.661356583 0.716877265 0.761277463 0.801712052 0.757188195 1 19.61437315 -4.999991294 0.327776195 3.391440332 0.751250279 0.471000659 0.078291978 308.9268728 2.685830435 514.0797886 0.064699994 1.00E-05 4.999991294 -2.640190054 DGWSLWYSEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 167.67 4.41E-05 115511000 110575 94644 101626 128228 113672 138913 163137 114513 114628 69127 FALSE TRUE 114940.5864 110898.3708 104274.457 153591.1157 94350.07404 106652.561 150349.8957 112978.1405 110502.5607 82671.11213 1.390335553 1.341440413 1.261316733 1.857857137 1.141270168 1.290082572 1.818650938 1.366597565 1.336652645 1 16.33509567 0.821329525 2.392542969 1.000819416 1.439100185 0.261797484 0.218709184 0.923865252 9.291156415 0.202135267 0.054486593 6.627191566 -0.821329525 0.438280768 DGYDYDGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGYDYDGYR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 166.68 0.00014089 18378350000 7703000 8310110 8415030 7999850 10190220 10734670 9114100 8863470 8474190 7892770 FALSE TRUE 8007120.388 9737306.749 8634332.595 9582196.453 8458090.044 8241705.578 8399713.027 8744669.682 8169205.557 9439207.165 0.84828315 1.031580998 0.914730702 1.015148443 0.896059372 0.873135363 0.889874846 0.926419934 0.865454631 1 23.17023426 3.145002224 23.3546522 0.90349089 0.955463213 0.112890509 0.059120093 17.83054003 4437.525924 0.015643029 0.018696957 1396.375512 -3.145002224 0.051972324 DGYGGSRDS(ph)YSSSR ddPTM_MDA-MB-175_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 DGYGGSRDS(1)YSSSR 148.41 4.70E-06 819330000 232630 320110 338720 286910 387290 455250 328190 332910 334070 305000 TRUE FALSE 241814.412 375086.4024 347547.3215 343659.9417 321458.5841 349525.0869 302465.6102 328447.886 322046.886 364758.9104 0.662943125 1.0283132 0.952813794 0.942156399 0.881290559 0.958235911 0.829220621 0.900451988 0.88290341 1 18.4765837 -2.336987749 0.008563253 1.902612316 6.11E-07 0.085771029 0.093743725 42430.91082 46.29077648 5549.585706 4759.726797 0.004602696 2.336987749 -1.902611705 DGYGGSRDSYSSS(ph)R ddPTM_MDA-MB-175_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 DGYGGSRDS(0.248)YS(0.159)S(0.159)S(0.434)R 198.38 5.82E-08 250200000 302870 307230 323860 320690 412340 424790 340490 314660 318320 345330 TRUE FALSE 314827.5415 359994.3626 332300.0577 384121.5248 342250.5941 326138.9603 313801.5041 310442.4974 306863.7254 412990.8018 0.762311267 0.871676466 0.804618544 0.930097046 0.828712389 0.789700301 0.75982686 0.751693491 0.74302799 1 18.65575012 2.798473895 4.444100774 0.786039417 0.845356619 0 0.081263501 0.497243092 20.25459772 0.023896711 0.025062128 628.7440598 -2.798473895 0.059317203 DGYNYTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DGYNYTLSK 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 227.08 4.96E-07 7004160000 3679910 2737680 3346200 2715080 4635900 4070660 4164480 3317020 3461370 2696850 FALSE TRUE 3825195.688 3207855.244 3433404.721 3252114.72 3847891.374 3125310.906 3838057.176 3272560.772 3336795.97 3225246.123 1.186016677 0.994607891 1.064540376 1.008330712 1.193053561 0.969014701 1.19000443 1.014670089 1.03458646 1 21.62097783 1.597331247 25 1.018457458 1.080390272 0.139993725 0.078541572 1.685562056 3989.176447 0.038172963 0.017963253 39.56682913 -1.597331247 0.061932814 DGYRDGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGYRDGYR 8 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 89.247 0.015267 0 28651 86091 48378 67114 51845 107630 36958 57090 41897 147060 FALSE TRUE 29782.1636 100876.4596 49638.77042 80388.94888 43032.40542 82634.56365 34061.13539 56324.80193 40389.13515 175873.5914 0.169338463 0.57357366 0.282241183 0.457083683 0.244678039 0.469852028 0.193668277 0.320257302 0.229648663 1 17.42417934 -1.493912493 3.514896652 1.01111662 0.331655504 0.719103825 0.126207911 100750355.7 161560202.9 11151763.12 0.028538446 0.032069154 1.493912493 -0.679461116 DGYSYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DGYSYGSR 8 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ; 110.12 0.0081123 1108530000 651890 781900 740600 758540 893330 918550 748290 766280 672410 802300 FALSE TRUE 677627.1206 916185.2427 759900.6444 908576.948 741482.0857 705230.6833 689637.0745 756009.27 648210.0954 959495.324 0.706232853 0.954861602 0.791979518 0.946932127 0.772783428 0.735001688 0.718749802 0.787923871 0.675574001 1 19.87191625 3.041670488 24.9726083 0.765373303 0.854161052 0.079438952 0.105458373 264.8135644 158697.8038 0.027728049 0.033141327 1100.703856 -3.041670488 0.088787749 DGYWFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DGYWFLK 7 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 93.262 0.035045 543390000 255290 254050 311960 253020 299650 377100 311100 303380 271580 264790 FALSE TRUE 265369.0463 297681.1113 320089.9339 303066.6008 248715.6 289524.24 286715.1691 299313.6873 261805.8889 316670.5308 0.837997289 0.940034144 1.010797983 0.957040745 0.7854081 0.914275917 0.905405275 0.945189584 0.82674535 1 18.27262309 4.748582496 23.14435125 0.918920468 0.837997161 0.121595191 0.066430728 1111.088779 2565774.248 0.015820507 0.200080227 56050.88776 -4.748582496 -0.080923307 DHAGVMGESNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHAGVMGESNR 11 0 P52306-4;P52306;P52306-5;P52306-6;P52306-2;P52306-3 P52306-4 RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 0 ; 94.191 0.0086877 241350000 68197 354780 281790 326850 204967 365080 226980 281710 230210 400300 FALSE TRUE 70889.47022 415710.7052 289133.6789 391499.9545 170126.7826 280295.7028 209188.7145 277934.1382 221924.7871 478731.1208 0.14807784 0.868359476 0.603958394 0.817786723 0.355370218 0.585497142 0.436964938 0.580564175 0.46356875 1 18.86885607 -1.395034865 2.838197417 1.008562678 0.55328535 0.321505647 0.199630964 21838398 25210859.52 1524129.221 0.045937094 0.040268471 1.395034865 -0.455277327 DHAISLSEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DHAISLSEPR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 166.97 6.97E-05 250500000 187254 315241 277974 300290 276569 341214 262420 285317 275598 369710 FALSE TRUE 194646.9325 369381.1895 285218.2308 359686.4657 229557.9002 261972.2196 241850.8347 281492.7923 265679.2818 442147.596 0.44023067 0.835425077 0.645074707 0.813498635 0.519188394 0.592499478 0.546991179 0.636648926 0.600883696 1 18.75416852 -1.325069367 3.965053437 1.000776307 0.630808824 0.48509464 0.115606518 17417588.79 5821150.284 116715.5538 0.025661769 0.047307569 1.325069367 -0.369967483 DHALLEEQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DHALLEEQSK 10 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 193.83 5.30E-07 1097810000 1804140 1556440 1411170 1468590 2031070 2211960 2376580 1632190 1527470 1622760 FALSE TRUE 1875368.84 1823746.463 1447946.249 1759072.719 1685829.447 1698265.813 2190297.45 1610313.163 1472496.653 1940708.752 0.966331933 0.939732178 0.746091472 0.906407371 0.868666895 0.875075052 1.128606983 0.829755192 0.758741697 1 20.88815219 DHASIQMNVAEVDKVTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DHASIQMNVAEVDKVTGR 18 1 Q8WVC2;P63220;Q9BYK1 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;; 243.95 2.44E-24 2027840000 289926 1411750 1579220 1533270 1694610 2256070 1434970 1852450 1599740 1668990 FALSE TRUE 301372.5024 1654207.081 1620375.771 1836546.23 1406560.797 1732131.934 1322493.302 1827620.938 1542165.67 1995996.636 0.150988482 0.828762459 0.811812877 0.920114892 0.704690966 0.867803033 0.662572911 0.915643296 0.772629393 1 20.92867786 4.738772241 24.79511252 0.824690566 0.150988275 0.816570669 0.096718718 5.543494023 649040.1458 0.020701061 0.120640584 54798.95047 -4.738772241 -0.673702291 DHDRFWVLAAHPNLNLFAAGHDGGMIVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHDRFWVLAAHPNLNLFAAGHDGGMIVFK 29 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 38.146 0.065357 133210000 238820 197830 283400 210290 367890 340530 258950 212040 283450 250170 FALSE TRUE 248248.798 231805.7636 290785.6368 251884.7343 305356.1892 261447.0683 238652.8224 209197.9506 273248.6899 299186.0217 0.829747314 0.774788081 0.971922536 0.841900076 1.020623181 0.873861241 0.797673705 0.699223678 0.913307006 1 18.19068325 0.995554641 24.992792 1.000000026 0.846182096 0.21847874 0.087373834 235.6586717 1324933.537 0.091786201 0.02294655 9.898163894 -0.995554641 -0.15381793 DHEDYDPQTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHEDYDPQTVR 11 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 93.345 0.0093188 414270000 130360 113230 149050 129010 146660 194010 138980 119730 134260 113690 FALSE TRUE 135506.7135 132676.3717 152934.3654 154527.7929 121730.7856 148954.1177 128086.3844 118125.2152 129428.0088 135965.3788 0.996626602 0.975809966 1.124803732 1.136523094 0.895307222 1.095529752 0.942051466 0.868788924 0.951918863 1 17.05287982 2.105743024 6.748103277 0.920831182 1.036329549 0.273613777 0.075159456 0.247264744 14.02309396 0.028471743 0.020953792 127.5683753 -2.105743024 0.115498367 DHENIVIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DHENIVIAK 9 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;; 112.71 0.0019183 3360650000 8195910 5826260 7123390 7595370 9048690 9667200 11100780 6804340 7278610 3770480 FALSE TRUE 8519490.855 6826874.833 7309031.395 9097711.516 7510596.906 7422139.308 10230671.86 6713138.952 7016654.248 4509233.366 1.889343523 1.513976829 1.620903334 2.017573893 1.66560395 1.645986957 2.268827321 1.488753943 1.556063676 1 22.10445074 0.884239307 1.554337019 1.007492504 1.77533735 0.524881412 0.22330031 0.406557515 1.927473642 0.205028098 0.05969245 7.66018585 -0.884239307 0.767844847 DHFEEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DHFEEAMR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 217.02 7.62E-06 6023820000 4022460 4166820 4322620 3785127 5965560 5753870 4870560 4297469 4431480 4781910 FALSE TRUE 4181269.827 4882438.922 4435271.028 4533813.823 4951536.242 4417620.893 4488792.78 4239868.457 4271991.9 5718833.709 0.731140306 0.853747315 0.775555166 0.792786441 0.865829729 0.772468849 0.784914024 0.741386911 0.747004043 1 22.44728953 -1.371193254 3.22905008 1.00198771 0.78571456 0.700148972 0.042211379 14374838.98 18242881.54 266101.9099 0.010410982 0.042540907 1.371193254 -0.21627315 DHFGRPPVDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHFGRPPVDIR 11 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ; 96.64 0.0041226 145270000 121524 127820 139372 125546 140425 172502 128503 126371 133603 122295 FALSE TRUE 126321.8614 149772.0907 143004.1488 150378.6241 116555.6087 132441.0248 118430.5991 124677.2034 128794.6541 146256.3638 0.863701641 1.024038113 0.9777636 1.028185169 0.79692675 0.905540254 0.80974664 0.852456606 0.88060889 1 17.15813987 3.243235719 24.99979735 0.863051779 0.977347663 0.332123509 0.067730808 111.8669052 598196.6557 0.01761495 0.023082628 1750.796698 -3.243235719 0.114295885 DHFLGPQESFPEENASS(ph)PFTQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHFLGPQESFPEENASSPFTQAR 23 0 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 1 DHFLGPQESFPEENAS(0.1)S(0.866)PFT(0.033)QAR 165.1 8.71E-12 130920000 62196 78561 68833 71690 94195 91070 74962 67662 67087 64153 TRUE FALSE 64651.54611 92053.24063 70626.84453 85870.06803 78183.76755 69920.37268 69086.28256 66755.10156 64672.55197 76722.55207 0.842666783 1.199819846 0.920548686 1.119228515 1.019045449 0.911340548 0.900469037 0.870084477 0.842940573 1 16.22736309 2.716813272 3.935536243 0.892447244 1.03127798 0.246734851 0.099301845 0.25963191 9.19016804 0.029869157 0.029319373 520.9706684 -2.716813272 0.138830735 DHFNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHFNKK 6 1 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 86.344 0.034849 203360000 366010 308120 386140 361360 487630 480160 519570 396680 446620 306220 FALSE TRUE 380460.3574 361037.2132 396203.1256 432835.9294 404742.8268 368650.1169 478844.7458 391363.1534 430546.2334 366217.9461 1.038890534 0.985853416 1.081877963 1.181908025 1.105196594 1.006641321 1.307540362 1.068661866 1.175655748 1 18.48234296 4.046399428 5.098696805 1.126704103 1.014475519 0.197227822 0.08598314 0.266335108 15.69260465 0.020322962 0.044844998 11127.54677 -4.046399428 -0.112228585 DHGKELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHGKELEK 8 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 61.65 0.050847 44750000 48428 45298 51605 41536 65426 74981 58712 54581 58122 52699 FALSE TRUE 50339.97483 53077.57913 52949.86869 49751.69683 54304.91189 57567.7991 54110.00002 53849.43097 56030.20057 63024.36007 0.798738373 0.842175614 0.840149248 0.789404236 0.861649556 0.913421398 0.858556913 0.854422495 0.889024506 1 15.94362194 -5 0.127194926 1.511675755 0.781981783 0.773569448 0.027150267 72.45729659 0.586354679 9.421472782 0.232975791 1.00E-05 5 -0.729693972 DHGSWS(ph)LSPPPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHGSWSLSPPPER 13 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 DHGS(0.003)WS(0.907)LS(0.09)PPPER 143.88 2.64E-05 107010000 36042 74452 68549 84329 91565 101680 79973 90376 77923 81049 TRUE FALSE 37464.96599 87238.55184 70335.44325 101009.0245 76000.81401 78066.36098 73704.50729 89164.65755 75118.56645 96928.99977 0.38651968 0.900025297 0.725638802 1.042092921 0.784087468 0.805397365 0.760396862 0.919896602 0.77498547 1 16.56464074 4.742246026 24.95060903 0.85103282 0.386519498 0.66069652 0.101056266 197.935606 1339987.953 0.022107216 0.164579573 55239.02773 -4.742246026 -0.464513321 DHGSWSLS(ph)PPPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHGSWSLSPPPER 13 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 DHGS(0.027)WS(0.331)LS(0.642)PPPER 76.378 0.018572 100090000 28204 81722 75704 92740 98306 114300 86867 99765 79706 97859 TRUE FALSE 29317.5157 95757.11779 77676.90843 111083.6952 81595.98123 87755.55723 80058.13756 98427.81336 76837.39663 117032.5974 0.250507263 0.818208943 0.663720281 0.949168844 0.6972073 0.749838585 0.684066998 0.841029043 0.656546965 1 16.8365509 4.74140943 24.84080077 0.775528506 0.250507055 0.665721874 0.113343482 133.0195735 1159824.811 0.024203837 0.168753607 55132.72132 -4.74140943 -0.52502145 DHIIDDALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DHIIDDALVR 10 0 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG77 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ;;; 141.1 3.81E-05 396420000 332423 339421 353010 351488 436556 493428 382620 342094 365286 357315 FALSE TRUE 345547.3167 397713.9164 362209.7306 421011.2773 362350.3671 378836.825 352629.2446 337508.7895 352139.4282 427324.033 0.808630664 0.930708047 0.847623121 0.985227239 0.847952231 0.886532925 0.825203399 0.789819349 0.824057158 1 18.70497093 2.247245596 23.79082233 0.836027842 0.887796987 0 0.070772185 226.0851163 619317.4785 0.023233614 0.019135451 176.7036808 -2.247245596 0.051769145 DHINDIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DHINDIIK 8 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;; 141.2 0.0006374 4077610000 9848790 7024870 9058020 7329780 12577800 11787500 11920400 8677870 9707580 7026340 FALSE TRUE 10237627.83 8231336.777 9294079.442 8779588.607 10439830.05 9050031.766 10986047.9 8561557.347 9358206.092 8403016.796 1.218327665 0.97956924 1.106040803 1.044813883 1.242390715 1.076997939 1.307393305 1.018867099 1.113672187 1 23.00247594 5.07734337 18.9109736 1.106823085 4.454043556 0.110576697 0.099363055 7865915.148 24122216.32 0.022395893 1094374108 119493.249 -5.07734337 3.347220471 DHINLPGFSGQNPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DHINLPGFSGQNPLR 15 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 171.46 1.08E-06 2207860000 795390 765610 924380 857390 1103730 1195830 1044920 849060 917420 835840 FALSE TRUE 826792.6114 897097.5619 948470.1022 1026979.183 916118.3688 918116.6055 963016.44 837679.7395 884402.2334 999606.8449 0.827117797 0.897450399 0.948843145 1.027383104 0.916478687 0.91847771 0.963395204 0.838009207 0.884750077 1 19.93100125 4.644782174 3.060839224 0.929603108 0.820738358 0.288745502 0.051791839 0.439829039 6.525404762 0.013672465 0.101368147 44134.90275 -4.644782174 -0.10886475 DHINLPGFSGQNPLRGPNDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHINLPGFSGQNPLRGPNDER 21 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ; 104.63 0.00024618 1022030000 245060 299640 311250 263120 430540 400910 266230 281700 314720 366050 FALSE TRUE 254735.158 351100.8391 319361.4307 315164.3507 357356.9646 307804.7283 245362.1969 277924.2723 303393.2887 437770.489 0.581892029 0.802020346 0.729517952 0.719930554 0.816311226 0.703118954 0.560481355 0.634862969 0.693041894 1 18.73981518 -1.378541851 7.22452008 1.000009963 0.692286398 0.57479861 0.079087886 1.34E-05 1.16E-06 0.081033722 0.019099214 0.041827138 1.378541851 -0.307723566 DHLDDPLDDTATVFQQLEQLCTVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHLDDPLDDTATVFQQLEQLCTVSR 25 0 H0YBM6;Q8IVM9;Q9H2T7-2;Q9H2T7 H0YBM6 RANBP17 Ran-binding protein 17 0 114.88 0.0016856 7317900 4160.1 5023.1 7104.8 6823.8 6515.1 10019 7448.8 3467.5 6305.6 5493.4 FALSE TRUE 4324.34396 5885.778351 7289.956925 8173.527273 5407.665629 7692.239089 6864.943592 3421.023834 6078.662688 6569.726553 0.658222823 0.895893962 1.109628668 1.244119859 0.823118829 1.170861379 1.044935971 0.520725453 0.925253531 1 12.68161761 1.781513617 25 0.764160982 1.00322958 0.12423107 0.200751338 106.7721409 62166.60279 0.092030724 0.051224097 60.46633102 -1.781513617 0.239068598 DHLKRTPATAEAQHIIY(ph)KMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHLKRTPATAEAQHIIYKMK 20 3 E7ENR6;Q8TBG4-3;Q8TBG4-2;Q8TBG4 E7ENR6 ETNPPL Ethanolamine-phosphate phospho-lyase 1 DHLKRT(0.001)PAT(0.001)AEAQHIIY(0.999)KMK;DHLKRTPATAEAQHIIY(1)KMK 45.704 0.069998 1884100000 3056200 1338660 2148300 1089370 3349000 2680000 2272900 2054770 2545100 1155210 TRUE FALSE 3176861.136 1568564.442 2204286.463 1304844.135 2779738.176 2057610.616 2094744.159 2027229.169 2453502.348 1381551.282 2.299488393 1.135364617 1.595515485 0.944477525 2.012041256 1.489347984 1.516226134 1.467357163 1.775903928 1 20.39785768 -1.115809803 4.530003689 0.999945605 1.550740179 0.176775656 0.371231777 0.000184173 3.59E-05 0.324600124 0.076501452 0.076593197 1.115809803 0.550794574 DHLLSVSLSGYINYLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHLLSVSLSGYINYLDR 17 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 154.49 1.36E-07 196090000 173490 164760 183280 169150 233740 289020 274640 218660 234270 171190 FALSE TRUE 180339.5192 193056.2483 188056.4274 202607.3651 194008.9583 221899.4851 253112.9992 215729.2204 225838.6685 204731.4029 0.880859099 0.942973309 0.91855194 0.989625247 0.947626771 1.083856614 1.236317417 1.053718273 1.103097352 1 17.64337288 2.722174605 4.20468605 1.108516211 0.936919026 0.627597141 0.061289816 0.131260715 5.665204806 0.019513865 0.019216608 527.4418728 -2.722174605 -0.171597185 DHLVTAYNHLFETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHLVTAYNHLFETK 14 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 206.63 6.12E-09 776540000 1592200 1042100 1253200 1227900 1737400 1821800 2099100 1406100 1556800 906440 FALSE TRUE 1655061.285 1221072.569 1285859.422 1470774.955 1442077.369 1398714.56 1934567.057 1387253.529 1500771.072 1084039.563 1.526753581 1.126409598 1.186173886 1.356753946 1.330281124 1.290279993 1.784590824 1.279707472 1.384424631 1 20.04798598 3.164213838 1.829100484 1.389511078 1.271622711 0 0.206740665 1.101238835 7.591177014 0.065985585 0.087684842 1459.53273 -3.164213838 -0.117888368 DHLYGTLDPNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DHLYGTLDPNTR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 184.31 1.45E-05 2456490000 1726105 1759586 1953098 2081150 2115204 2478521 2117898 1816342 1965596 1696731 FALSE TRUE 1794252.958 2061781.208 2003997.338 2492795.258 1755662.38 1902922.06 1951891.621 1791996.906 1894854.584 2029172.954 0.884228698 1.016069726 0.987593164 1.228478457 0.865210812 0.937782093 0.961914862 0.883116889 0.933806347 1 20.95246041 DHNEEEGEETGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHNEEEGEETGLR 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 178.23 5.62E-07 92705000 79744 86670 100752 92878 92581 119790 105052 83431 75846 66121 FALSE TRUE 82892.3547 101554.8983 103377.6799 111248.9912 76844.11469 91970.58794 96817.74974 82312.74391 73116.31728 79076.14399 1.048259949 1.284267203 1.307318171 1.40685908 0.97177367 1.163063641 1.224361038 1.040930169 0.924631799 1 16.2709549 1.601192606 3.352082788 0.965065936 1.206143536 0.407458463 0.119277677 0.199171889 5.244283765 0.078050941 0.032619144 39.92019062 -1.601192606 0.2410776 KLVILEGELERAEER ddPTM_MDA-MB-175_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 ;;; 261.78 3.24E-25 914099000 453056 587571 634777 337914 852130 739562 357863 556442 668558 1021800 FALSE TRUE 470943.0007 688481.7486 651319.8101 404752.3806 707285.247 567809.9337 329812.763 548983.8051 644496.7282 1222002.146 0.385386394 0.563404697 0.532993998 0.331220679 0.578792148 0.464655431 0.269895404 0.449249461 0.527410471 1 20.22081539 0.753055081 3.01946391 0.999937089 0.446993565 0.757257039 0.093403711 0.796611304 9.121828274 0.089695422 0.023451457 5.663111084 -0.753055081 -0.552943523 DHPDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHPDVAK 7 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ; 146.94 0.0021848 501850000 1834960 1278710 1642810 1260140 2010800 2090600 2158100 1650050 1779660 1113070 FALSE TRUE 1907405.638 1498318.496 1685622.978 1509391.931 1669004.934 1605089.833 1988942.483 1627933.779 1715610.384 1331154.755 1.432895484 1.125577991 1.266286261 1.13389666 1.25380233 1.205787552 1.494148201 1.22294855 1.288813624 1 20.34424687 -1.005190597 5.187370617 0.999998165 1.265455956 0.345818949 0.111022118 2.23E-06 4.28E-07 0.101815615 0.023998005 0.098811935 1.005190597 0.265457791 DHPESYHSFMWNNFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHPESYHSFMWNNFFK 16 0 D6RAY7;D6R9P4;D6RFF8;P46926;D6R917;D6RB13 D6RAY7 GNPDA1 Glucosamine-6-phosphate isomerase;Glucosamine-6-phosphate isomerase 1 0 127.32 3.87E-05 307130000 389740 577530 685530 535450 844010 849390 736670 821150 712020 672200 FALSE TRUE 405127.2361 676716.2849 703395.475 641360.4118 700545.4817 652132.0451 678927.8805 810143.8274 686394.5393 803904.72 0.503949319 0.84178668 0.874973685 0.797806501 0.871428497 0.811205643 0.844537746 1.007761004 0.853825736 1 19.616665 4.749946369 3.360715622 0.88122146 0.448982239 0.742309562 0.066517983 0.172733185 3.182623039 0.016895341 0.195164869 56227.18857 -4.749946369 -0.432239221 DHQLDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHQLDTR 7 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 ; 123.72 0.0042162 465530000 1087820 1020750 1182730 1065190 1389290 1470130 1396850 1137990 1145750 1008500 FALSE TRUE 1130767.974 1196055.872 1213552.915 1275881.403 1153138.982 1128714.588 1287361.247 1122737.105 1104514.681 1206096.266 0.937543715 0.991675296 1.006182466 1.057860337 0.956091992 0.935841209 1.06737852 0.930885152 0.915776553 1 20.20191363 1.611622832 25 0.942495468 0.992988863 0.155343188 0.046664016 0.5659622 3739.804101 0.022107542 0.011666271 40.89053867 -1.611622832 0.050493395 DHQPCIIFMDEIDAIGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DHQPCIIFMDEIDAIGGR 18 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;;;;;; 189.44 3.27E-14 781249000 182479.4 210840 221963 214389 236421 280407 243582 215224 217449 205587 FALSE TRUE 189683.8276 247050.1299 227747.5381 256794.5043 196234.2429 215286.7239 224489.4064 212339.2743 209623.053 245867.8364 0.771486952 1.004808654 0.926300656 1.044441225 0.798128969 0.875619711 0.913049098 0.863631768 0.852584283 1 17.90752349 3.22473849 24.99985784 0.877877948 0.940873018 0.087618123 0.081900361 483.1625845 873886.4017 0.022307998 0.02679183 1677.793431 -3.22473849 0.06299507 DHQPCIIFMDEIDAIGGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHQPCIIFMDEIDAIGGRR 19 1 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 85.974 0.0019156 40625000 5446.8 7205.7 6431.4 5776.4 9481.4 10385 6643.2 6254.4 6860.6 11110 FALSE TRUE 5661.84387 8443.222922 6599.007567 6918.954679 7869.755015 7973.241136 6122.488625 6170.569998 6613.688346 13286.79179 0.426125732 0.635459866 0.496659214 0.520739302 0.592299115 0.600087761 0.460795106 0.46441384 0.497764129 1 13.69770517 -1.8825436 2.722500492 1.229054001 0.521680686 0.832661115 0.064340183 5371328.085 3622656.905 7929908.386 0.016059458 0.013105585 1.8825436 -0.707373315 DHQYQFLEDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DHQYQFLEDAVR 12 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 225.13 1.84E-11 3984910000 3126420 3320900 3252660 3600270 3995040 4512870 4098810 3501310 3456900 3076990 FALSE TRUE 3249853.476 3891238.742 3337426.992 4312392.66 3315964.528 3464824.336 3777534.562 3454380.666 3332486.844 3679867.278 0.883144209 1.057439969 0.906942218 1.171888097 0.901109817 0.94156231 1.02654098 0.938724254 0.905599738 1 21.8112223 DHRDNLEFFLAGIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 150.59 1.90E-06 5126346000 3012141 3383275 3573088 3336159 4381930 4625268 3004171 3193838 3584291 3877412 FALSE TRUE 3131062.653 3964326.163 3666205.609 3996041.293 3637091.104 3551119.604 2768696.227 3151029.826 3455293.067 4637116.644 0.675217574 0.854911892 0.790621822 0.861751299 0.784343242 0.765803381 0.597072802 0.67952352 0.745138269 1 22.14479659 2.468818712 24.95215248 0.714089073 0.797898469 0 0.109641099 402.5468562 1209788.273 0.035658208 0.029878431 294.3192795 -2.468818712 0.083809396 DHRPPCAQEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DHRPPCAQEAPR 12 1 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;; 145.29 3.83E-05 206169000 116598 129596 124105 125016 156622 169052 129947 131389 126923 132473 FALSE TRUE 121201.3791 151853.1049 127339.2783 149743.7917 129999.4484 129792.235 119761.4146 129627.9454 122355.066 158428.548 0.765022344 0.958495844 0.803764725 0.945181873 0.820555702 0.819247772 0.755933297 0.818210777 0.772304408 1 17.2734728 3.041285233 24.99396813 0.815815808 0.871587077 0.026799224 0.082671476 337.8185994 204512.4142 0.021741644 0.025986206 1099.727873 -3.041285233 0.055771269 DHS(ph)PPSQGSPGNSAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DHSPPSQGSPGNSAAR 16 0 A0A2R8Y701;Q18PE1-2;Q18PE1;Q18PE1-3;A0A1W2PRA3 A0A2R8Y701 DOK7 Protein Dok-7 1 DHS(1)PPSQGSPGNSAAR;DHS(0.999)PPS(0.001)QGSPGNSAAR;DHS(0.999)PPS(0.001)QGSPGNSAAR;DHS(0.994)PPS(0.006)QGSPGNSAAR 128.66 3.84E-05 734080000 233954 255328 273447 235391 360000 457389 297164 272985 275046 217185 TRUE FALSE 243190.6846 299178.5978 280573.2535 281950.6372 298807.3286 351167.3365 273871.5092 269326.0826 265147.1482 259738.2425 0.936291407 1.151846547 1.080215415 1.085518384 1.15041715 1.352004746 1.054413499 1.036913471 1.020824449 1 17.98669892 2.019108317 24.99620719 1.028926351 1.130970677 0.201791122 0.096528867 394.9714726 516672.6279 0.037053401 0.027362549 104.4980815 -2.019108317 0.102044325 DHS(ph)PTPSVFNS(ph)DEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 DHS(0.964)PT(0.036)PS(0.004)VFNS(0.996)DEER 120.75 6.30E-05 99204000 104730 81249 102980 87720 138560 141980 138710 107630 109410 75714 TRUE FALSE 108864.8213 95202.88372 105663.7434 105070.7542 115007.6207 109007.2967 127837.5477 106187.3959 105472.3555 90548.70867 1.202279114 1.051399684 1.166927115 1.160378273 1.270118839 1.203852582 1.411809728 1.172710218 1.164813469 1 16.46640645 3.415479041 5.453369192 1.223758041 1.13603666 0.053983858 0.103254275 0.393258431 23.1626414 0.027575613 0.037877785 2603.029204 -3.415479041 -0.087721381 DHS(ph)PTPSVFNSDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DHSPTPSVFNSDEER 15 0 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(0.976)PT(0.024)PSVFNSDEER;DHS(0.982)PT(0.018)PSVFNSDEER;DHS(0.992)PT(0.008)PSVFNSDEER;DHS(0.996)PT(0.004)PSVFNSDEER;DHS(0.994)PT(0.006)PSVFNSDEER;DHS(0.942)PT(0.058)PSVFNSDEER 353.92 1.88E-82 5856800000 1657590 1498140 1629840 1434000 2078330 2763500 2010610 1636390 1609520 1199334 TRUE FALSE 1723032.933 1755433.891 1672314.969 1717640.92 1725056.209 2121719.006 1853013.134 1614456.869 1551593.69 1434320.535 1.201288618 1.223878379 1.165928346 1.197529338 1.202699234 1.479250248 1.291910064 1.125590013 1.081762167 1 20.45193604 -0.575340465 7.501108952 0.999998657 1.220295414 0.291975544 0.102227507 0 0 0.105052918 0.02476121 0.265864 0.575340465 0.220296757 DHS(ph)PTPSVFNSDEERYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHSPTPSVFNSDEERYR 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 DHS(1)PTPSVFNSDEERYR;DHS(1)PTPSVFNSDEERYR 237.14 1.99E-20 586610000 156402 156846 182691 119359 246760 270640 126498 161923 176930 172663 TRUE FALSE 162576.8717 183783.0804 187452.0775 142967.8539 204815.8233 207787.9616 116582.7562 159752.687 170562.3239 206493.009 0.787323854 0.890020835 0.907788978 0.692361715 0.99187776 1.006271169 0.564584519 0.773646952 0.825995634 1 17.65573341 2.264691488 24.99999212 0.764934705 0.877680934 0.084624048 0.131279522 426.3845013 407930.2005 0.044583992 0.037290908 183.9464826 -2.264691488 0.11274623 DHSDSKDQSDKHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHSDSKDQSDKHDR 14 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 0 ; 182.57 4.85E-07 115366000 139357 87007 139146 74586 197423 161695 134275 125248 159691 89170 FALSE TRUE 144858.922 101949.7754 142772.2591 89338.88818 163865.109 124143.7868 123750.1746 123569.2554 153943.7521 106641.1542 1.358377289 0.956007802 1.338810144 0.83775245 1.53660292 1.164126436 1.160435439 1.158738916 1.443567947 1 16.70240478 3.242404458 24.99810852 1.236001877 1.126261606 0.077010265 0.204270919 294.3898913 1914525.783 0.053288796 0.069498752 1747.448792 -3.242404458 -0.109740271 DHSVAESLNYVASWNMSMLQTQDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHSVAESLNYVASWNMSMLQTQDLVK 26 0 Q13011 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ; 311.72 9.04E-82 223053000 154472 141185.6 158483 158599 169487 234591 191448 161024 174548 120956.8 FALSE TRUE 160570.6738 165433.1285 162613.1972 189969.4088 140677.6603 180110.7955 176441.8055 158865.7367 168266.0516 144655.9691 1.110017615 1.143631539 1.124137484 1.313249706 0.972498136 1.245097569 1.219734012 1.098231464 1.163215404 1 17.14226633 0.004133192 0.991560762 0.998469366 1.156175925 0.216521119 0.087853455 11.14931734 9.631550116 0.137699801 0.025067908 1.009562457 -0.004133192 0.157706559 DHTLEDEDVIQIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DHTLEDEDVIQIVK 14 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 ;; 107.65 0.00087163 307631000 446956 324850 421094 367794 512821 539809 531330 423290 476040 287680 FALSE TRUE 464602.168 380640.4605 432068.0556 440542.5554 425651.8696 414446.5406 489682.9662 417616.4899 458907.4134 344045.388 1.350409522 1.10636699 1.255846091 1.280478015 1.237196848 1.204627514 1.423309201 1.213841268 1.333857187 1 18.39223938 -1.07584328 5.11662545 0.999995085 1.263107787 0.479178491 0.083505812 4.37E-06 7.89E-07 0.075400142 0.017771652 0.083976297 1.07584328 0.263112702 DHTYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DHTYAK 6 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 103.71 0.034451 1215850000 1611170 1192850 1545680 1215370 1985510 1902120 1957460 1652520 1735770 1293490 FALSE TRUE 1674780.236 1397712.708 1585961.691 1455766.558 1648013.719 1460381.457 1804029.17 1630370.672 1673299.977 1546924.6 1.082651498 0.90354288 1.02523529 0.941071438 1.065348446 0.944054711 1.166203686 1.053943206 1.081694594 1 20.56097145 2.254607613 24.99966204 1.080248908 0.991859589 0.275523167 0.064764593 271.6151582 423149.5937 0.020535895 0.017132451 179.7246361 -2.254607613 -0.088389319 DHYEATAMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DHYEATAMHR 10 0 O75832;B1AJY5;B1AJY7;O75832-2;B1AJY6 O75832 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 ;;;;;;; 195.27 2.15E-07 840355000 797896.2 670785 791057 749784 1102951 1044414 954957 704377 726533 862017 FALSE TRUE 829397.7581 785987.1058 811672.5953 898089.0373 915471.783 801864.6767 880104.975 694935.9784 700385.2193 1030912.727 0.804527616 0.762418666 0.787333956 0.871159133 0.888020643 0.777820135 0.853714337 0.674097778 0.679383619 1 19.97549077 -0.493227434 8.666366333 0.999999533 0.787444337 0.460498731 0.068593582 0 0 0.072030881 0.016977841 0.321197803 0.493227434 -0.212555196 DHYSNGFCTVYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHYSNGFCTVYAK 13 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ; 104.98 0.0014893 236880000 141708 387040 390600 397540 480260 541300 344310 440660 383440 454180 FALSE TRUE 147302.7413 453511.1092 400779.3569 476172.2255 398625.5767 415591.2785 317322.0825 434753.6735 369640.0693 543167.8752 0.271191924 0.834937282 0.737855413 0.876657562 0.733890193 0.765124923 0.584206278 0.800403878 0.680526383 1 19.05103863 -4.999999959 0.036469433 2.10992167 3.85E-11 0.270736999 0.158818199 1614.310528 4.411730834 218.3789626 73.00375859 1.00E-05 4.999999959 -2.10992167 DIAAHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DIAAHIK 7 0 P63167;F8VXL2;F8VRV5 P63167 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 ;;;;;;; 117.17 0.0052914 6762350000 7793121 6190611 7548588 6508860 9579260 9383190 9242578 7828599 8004460 5967076 FALSE TRUE 8100799.435 7253800.283 7745310.405 7796293.081 7950980.807 7204086.326 8518120.585 7723669.435 7716381.048 7136210.296 1.135168261 1.016477932 1.085353442 1.092497664 1.114174117 1.009511495 1.193647641 1.082320884 1.081299559 1 22.7667267 4.021466316 24.99087889 1.089934463 1.069596267 0 0.057585057 1181.094993 1374998.998 0.013352285 0.028840169 10506.69961 -4.021466316 -0.020338197 DIAANEENRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIAANEENRK 10 1 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;; 145.91 4.74E-05 3151650000 1904030 1394480 1488100 1612320 2350080 2476400 2837260 2124010 2197740 1445120 FALSE TRUE 1979202.575 1633971.092 1526881.108 1931232.084 1950614.241 1901293.63 2614868.147 2095541.12 2118643.767 1728263.596 1.145197168 0.945440902 0.883476984 1.117440701 1.128655516 1.10011785 1.513003083 1.212512446 1.225879994 1 20.72089184 3.024328877 1.508712907 1.251481552 0.996570738 0.285623912 0.140322756 0.406535774 1.906245963 0.050700331 0.061693108 1057.618106 -3.024328877 -0.254910814 DIAAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 109.88 0.067884 1590840000 933830 1038130 1054030 1020780 1141420 1272840 1146110 1044340 975210 1043530 FALSE TRUE 970698.3295 1216420.752 1081498.888 1222687.237 947401.8361 977242.2001 1056274.903 1030342.33 940112.3826 1247989.724 0.777809553 0.974704141 0.866592783 0.979725405 0.759142337 0.783053082 0.84638109 0.825601614 0.753301381 1 20.25117462 3.23134807 24.99875003 0.81904852 0.902699471 0.143585347 0.084118628 261.1426532 905121.2955 0.022327421 0.02720783 1703.523268 -3.23134807 0.083650951 DIAWTEDSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIAWTEDSKR 10 1 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ;;; 172.8 5.78E-06 1920870000 1022970 679870 933360 759310 973740 1005980 1165780 898930 974160 570050 FALSE TRUE 1063357.646 796632.3838 957684.1284 909499.2517 808224.0226 772356.3908 1074403.117 886881.3137 939100.1719 681740.3832 1.55976919 1.168527497 1.404763678 1.334084461 1.185530508 1.132918644 1.575971064 1.3009077 1.377504098 1 19.37886292 -2.179595652 2.255754021 0.155440198 1.332277259 0.330432548 0.144055118 3141726.195 873749.1405 13488566.11 0.033047278 0.006613089 2.179595652 1.176837062 DICNDVLSLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DICNDVLSLLEK 12 0 P63104;E7EX29;B0AZS6;E7ESK7 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 193.28 6.99E-06 1053730000 1501282 1040097 1376534 1202647 1769119 1550729 1854567 1457798 1479108 928167 FALSE TRUE 1560553.773 1218725.569 1412407.607 1440526.987 1468404.784 1190595.691 1709201.193 1438258.602 1425875.192 1110023.553 1.405874469 1.097927666 1.272412286 1.297744524 1.322859124 1.072585972 1.539788222 1.295700977 1.284544989 1 20.08215886 2.278984271 24.99999568 1.312091999 1.245416469 0 0.153983509 550.3088821 340336.2019 0.049998004 0.04183094 190.1009431 -2.278984271 -0.06667553 DIDAFWLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIDAFWLQR 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 183.04 0.00010616 349557000 356850 425608 425288 430697 463437 498239 392392 390258 368103 453283 FALSE TRUE 370938.7135 498702.8632 436371.3547 515887.5811 384662.1443 382530.5431 361635.2897 385027.2298 354855.0449 542095.1252 0.684268676 0.919954525 0.804971922 0.951655082 0.709584216 0.705652062 0.667106699 0.710257687 0.654599218 1 19.04818651 3.200929586 24.99205188 0.719252455 0.843391315 0.136359759 0.114217693 233.1511523 154842.9822 0.030291913 0.036206527 1588.289212 -3.200929586 0.124138861 DIDEVSSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;;;; 309.82 1.70E-41 1870303000 1232001 1292643 1365298 1265941 1710431 1746655 1576904 1413467 1357474 1296652 FALSE TRUE 1280641.351 1514644.38 1400878.787 1516340.351 1419692.55 1341020.847 1453302.144 1394521.787 1308618.776 1550706.133 0.825843997 0.976744947 0.903381213 0.977838624 0.915513597 0.864780772 0.937187332 0.89928179 0.843885729 1 20.56449388 2.998513131 24.9838298 0.903484334 0.926556538 0.001211885 0.055988952 226.1389377 3799905.818 0.015187673 0.017938466 996.5822117 -2.998513131 0.023072204 DIDFLKEEEHDCFLEEIMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIDFLKEEEHDCFLEEIMTK 20 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;; 204.31 5.86E-22 863440000 1582330 897120 1341260 897520 1807070 1671570 1615590 1319730 1515350 761890 FALSE TRUE 1644801.61 1051193.381 1376214.337 1075046.777 1499904.887 1283373.2 1488955.834 1302041.178 1460812.85 911167.7582 1.805157827 1.153677105 1.510385245 1.179856034 1.646134725 1.408492771 1.634118219 1.428980741 1.603231497 1 19.79735717 -1.052828901 4.590053027 0.999980108 1.473118821 0.357653477 0.19457494 11684315.64 2681257.505 2500.149077 0.041021754 0.088546439 1.052828901 0.473138713 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(1)PPDYSEYMTGK 322 2.10E-83 1968670000 567775 549465 672213 555059 775744 744890 754231 631574 701718 453376 TRUE FALSE 590191.1954 643831.3395 689731.423 664848.0135 643883.312 571900.5864 695112.4034 623108.7836 676463.3063 542206.3468 1.088499238 1.18742863 1.272082902 1.226190024 1.187524484 1.05476557 1.282007132 1.149209682 1.247612298 1 19.04848248 2.986968 24.61747985 1.161955455 1.199739286 0.047792206 0.088368737 1976.621183 3733849.732 0.025595836 0.028311221 970.4384601 -2.986968 0.03778383 DIDIEDLEELDPDFIMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DIDIEDLEELDPDFIMAK 18 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 215.5 2.20E-18 106020100 418887 333732 425065 341876 561385 536818 528770 431467 490387 300559 FALSE TRUE 435424.9822 391047.8749 436142.5431 409498.0524 465960.9782 412150.1551 487323.6257 425683.8906 472738.0677 359447.7815 1.211372012 1.08791289 1.213368299 1.139242119 1.296324535 1.146620389 1.355756387 1.184271854 1.315178705 1 18.45542267 4.091498949 12.46666592 1.217933387 1.149645287 0.038514113 0.101056486 1.423642532 186.400947 0.022761964 0.049202395 12345.22329 -4.091498949 -0.0682881 DIDIHEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 168.27 0.00030783 12154180000 26790290 26063360 30842230 26397500 31417030 33705560 31501490 29480290 29454930 21431870 FALSE TRUE 27847991.34 30539539.34 31646003.85 31618846.71 26076774.46 25877954.5 29032320.9 29085154.93 28394852.82 25631034.59 1.086495016 1.191506306 1.234675243 1.233615701 1.017390631 1.00963363 1.132701874 1.134763204 1.107830928 1 24.61138838 3.244588785 24.99998573 1.079661601 1.190361314 0.477592981 0.060328053 148.0621519 614038.6606 0.018201404 0.024028367 1756.259897 -3.244588785 0.110699713 DIDISS(ph)PEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 DIDIS(0.009)S(0.991)PEFK;DIDISS(1)PEFK;DIDISS(1)PEFK;DIDIS(0.142)S(0.858)PEFK;DIDISS(1)PEFK;DIDISS(1)PEFK 290.28 4.49E-32 3041910000 12363600 6889430 8648950 7105390 12535420 14244020 12103560 9530530 9898050 5942790 TRUE FALSE 12851724.47 8072636.01 8874348.742 8510814.935 10404653.79 10936062.23 11154851.34 9402788.834 9541821.114 7107165.919 1.808276973 1.135844597 1.248648033 1.197497713 1.463966637 1.538737431 1.569521729 1.323001171 1.342563438 1 22.76084295 0.643172074 1.730278205 1.000430739 1.400388779 0.296166483 0.189062043 2.027280064 8.100229797 0.178907374 0.050544127 4.397158027 -0.643172074 0.39995804 DIDLICSNALEYNPDRDPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIDLICSNALEYNPDRDPGDR 21 1 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 71.073 0.015779 86165000 89609 96801 97056 84393 115760 116880 93482 108380 102360 97168 FALSE TRUE 93146.83251 113425.8187 99585.35909 101085.6835 96083.15655 89736.39133 86154.63657 106927.3434 98676.08359 116206.2092 0.801565021 0.97607365 0.856971067 0.869881947 0.826833241 0.772216837 0.741394433 0.920151721 0.849146395 1 16.82632763 0.515358138 1.28502876 0.999602008 0.845053504 0.33908698 0.064621064 2.410835524 5.094209281 0.063799361 0.019062679 3.276107458 -0.515358138 -0.154548504 DIDPQNDLTFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIDPQNDLTFLR 12 0 Q9NP97;B1AKR6;Q8TF09;H3BQI1 Q9NP97 DYNLRB1;DYNLRB2 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 ; 181.31 4.26E-05 406990000 335450 363830 354990 332030 400610 433730 370210 356230 363360 348750 FALSE TRUE 348693.825 426314.9723 364241.331 397704.543 332514.4553 333002.7807 341191.9728 351455.3195 350282.7446 417080.8853 0.836034058 1.022139799 0.873311014 0.953542963 0.797242135 0.798412952 0.818047494 0.842655063 0.839843678 1 18.66996767 3.243164943 24.99943692 0.837305717 0.925038171 0.184151032 0.071296421 149.4273498 811317.9852 0.018324734 0.024015948 1750.511399 -3.243164943 0.087732453 DIDTHTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIDTHTHR 8 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 158.07 0.00036709 56330000 110310 139920 115140 119850 140320 152890 128510 130160 115180 124260 FALSE TRUE 114665.124 163950.1716 118140.643 143555.9723 116468.4565 117383.6146 118437.0504 128415.4181 111034.6943 148606.3679 0.771603032 1.10325132 0.794990448 0.966014945 0.783737993 0.789896262 0.796985029 0.864131328 0.747173192 1 17.18113641 3.233748112 24.99848704 0.822339706 0.914701501 0.11068434 0.107302043 217.8941008 1131847.297 0.028102551 0.034622783 1712.963513 -3.233748112 0.092361795 DIEDVFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIEDVFYK 8 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 174.27 0.00063491 387910000 714740 550390 663540 573690 853610 831680 846090 687260 726190 433840 FALSE TRUE 742958.4871 644915.2011 680832.3975 687164.1697 708513.6771 638534.9242 779771.255 678048.4038 700054.5638 518842.6416 1.431953405 1.242988046 1.312213652 1.324417298 1.365565627 1.230690913 1.502905105 1.306847875 1.349261814 1 18.98493753 -1.169276024 3.732658301 0.999732831 1.338830114 0.638165414 0.076964262 11347337.55 19406718.44 35988.03939 0.017157581 0.067721096 1.169276024 0.339097283 DIEEHLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIEEHLQR 8 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 144.09 0.000591 944150000 872560 1721950 1490830 1408580 1471760 1971360 1312940 1394110 1233170 2120390 FALSE TRUE 907009.3426 2017681.518 1529682.255 1687192.92 1221590.761 1513541.516 1210028.332 1375424.236 1188788.453 2535839.823 0.357676118 0.795665996 0.603225109 0.665338916 0.481730254 0.596860063 0.477170648 0.542393973 0.468794772 1 21.27403219 -1.578224791 3.122748142 1.021171827 0.56058691 0.57388575 0.115097842 158594554.9 179197554.9 27828062 0.026253459 0.026410414 1.578224791 -0.460584917 DIEIS(ph)TEEEKDTGDLKDSSLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 DIEIS(0.541)T(0.459)EEEKDTGDLKDSSLLK 119.85 2.76E-05 117470000 226960 76979 103240 63451 174660 159410 149610 113850 123570 51687 TRUE FALSE 235920.5561 90199.54444 105930.5192 76001.41842 144971.3556 122389.4434 137883.1773 112324.027 119122.7398 61814.07804 3.816615301 1.459207147 1.713695691 1.229516331 2.34528056 1.97996067 2.23061124 1.817126948 1.927113428 1 15.91564783 8 0.051364347 2.03E-13 5.604525476 0.234149847 0.646446832 890.0398846 3.444475944 86.63535822 391.5954848 100000000 -8 5.604525476 DIELVMSQANVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIELVMSQANVSR 13 0 F8VZJ2;H0YHX9;Q13765;E9PAV3-2;E9PAV3;F8W0W4 F8VZJ2 NACA "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form" 0 138.45 0.00011391 66952000 55602 59005 73468 63302 82927 82009 65347 62524 66272 66822 FALSE TRUE 57797.20989 69138.64975 75382.63643 75822.94666 68831.09816 62963.65261 60224.93139 61685.96805 63886.88367 79914.49152 0.723238161 0.865157851 0.943291198 0.948800965 0.861309343 0.787887796 0.753617151 0.77189965 0.799440533 1 16.28616952 2.826474815 5.104778319 0.800068496 0.878044912 0.030678866 0.087501765 0.436170296 18.97181646 0.026720245 0.028347163 670.6173962 -2.826474815 0.077976416 DIEREDIEFICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIEREDIEFICK 12 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 220.31 2.72E-11 4710060000 4150270 3095770 3818550 3242030 4796710 4923090 4441740 3909830 4636170 2697240 FALSE TRUE 4314125.864 3627444.416 3918064.55 3883293.858 3981366.948 3779776.958 4093584.812 3857425.124 4469315.147 3225712.536 1.337417955 1.124540508 1.214635373 1.203856145 1.234259688 1.171764971 1.269048239 1.195836604 1.385528034 1 21.62118645 -1.019365015 7.249091252 0.999999984 1.229246753 0.481545698 0.07346843 1.89E-08 2.66E-09 0.064715429 0.015253572 0.095638991 1.019365015 0.229246769 DIFQEIYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIFQEIYDK 9 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 150.08 0.00020032 74228000 163052 113415 146796 121583 182909 180132 206005 147050 167081 92356 FALSE TRUE 169489.4189 132893.144 150621.6244 145631.7545 151818.1935 138299.0729 189857.7898 145079.0353 161067.7874 110451.3899 1.534515944 1.203182179 1.363691525 1.318514458 1.374524971 1.252126144 1.718926216 1.313510272 1.458268543 1 16.75305205 DIGKPIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIGKPIEK 8 1 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 76.465 0.032587 788680000 952440 705080 900010 708200 1245000 1150080 1163970 1055210 1015700 764770 FALSE TRUE 990043.0666 826172.0052 923465 848279.8462 1033375.345 882991.3496 1072734.99 1041066.636 979145.1554 914612.0391 1.08247325 0.903303226 1.009679471 0.92747505 1.129851019 0.965427211 1.172885272 1.138260368 1.070557913 1 19.80280038 2.938701634 1.389526791 1.101520856 0.980031535 0.191253319 0.079196355 0.50040236 1.991731703 0.029880592 0.033925437 868.3636467 -2.938701634 -0.121489321 DIGPNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIGPNKR 7 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;; 107.43 0.011993 2609980000 2255620 3906660 3662250 3717040 3766720 4323040 3502180 3798050 3463760 4415770 FALSE TRUE 2344673.619 4577598.465 3757691.244 4452259.418 3126454.28 3319079.476 3227669.98 3747143.352 3339099.954 5280955.586 0.44398662 0.866812529 0.711555169 0.843078368 0.592024346 0.62849979 0.611190518 0.709557824 0.632290861 1 22.33236758 -1.680435545 3.236683039 1.029645488 0.679156628 0.415250954 0.116763799 8782618.372 4810391.854 1835520.753 0.026359059 0.020872019 1.680435545 -0.35048886 DIGRPK ddPTM_MDA-MB-175_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 80.377 0.058982 170860000 347180 295760 356240 303280 448450 459970 418610 372900 385620 282180 FALSE TRUE 360886.9345 346554.4793 365523.9071 363267.8788 372222.6292 353148.9384 385798.2544 367901.8854 371741.6115 337467.7683 1.069396749 1.02692616 1.08313724 1.076452073 1.102987201 1.046467164 1.143215117 1.090183774 1.101561827 1 18.36439019 4.139781069 7.594300828 1.086822158 1.048370043 0.089540817 0.037216982 0.373461122 24.85797181 0.008569625 0.018716203 13796.88579 -4.139781069 -0.038452115 DIHYSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIHYSVK 7 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;; 141.78 0.0025335 1051430000 434748 2376400 2286360 2339480 2905830 3558220 2186350 2873210 2374420 2869110 FALSE TRUE 451912.1867 2784528.214 2345944.42 2802222.161 2411898.055 2731877.33 2014978.174 2834699.32 2288965.088 3431257.172 0.131704551 0.811518366 0.68369822 0.816675061 0.70291964 0.796173878 0.587241956 0.826140151 0.667092256 1 21.71030583 4.741818131 24.93738568 0.753531144 0.131704313 0.753759933 0.108512209 130.5083912 999038.3702 0.022737661 0.163871068 55184.62952 -4.741818131 -0.621826832 DIIFELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIIFELR 7 0 H0YCM7;Q5JVZ5;Q96JJ3-3;Q96JJ3;H7C0N5;H7C0S6;H7C3P3;Q5JVZ8;Q5JVZ4;Q92556 H0YCM7 ELMO2;ELMO1 Engulfment and cell motility protein 2;Engulfment and cell motility protein 1 0 107.66 0.039632 0 39906 51633 50923 49343 63153 69208 60205 51992 48541 55658 FALSE TRUE 41481.51969 60500.5661 52250.09521 59102.89813 52418.27562 53135.49086 55485.97478 51295.13228 46794.01889 66563.11946 0.62319074 0.908920234 0.784970651 0.8879226 0.787497281 0.798272246 0.833584352 0.770623924 0.703002192 1 16.02243543 4.756405266 23.97025298 0.81941116 0.623190449 0.369574957 0.080063505 2265.428357 3043003.329 0.017608557 0.525503989 57069.65743 -4.756405266 -0.196220711 DIIHDPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DIIHDPGR 8 0 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ;;;;; 144.09 0.000591 20233300000 14414510 15779170 16630470 15565650 18791300 20129500 17055990 17308000 16563480 16662480 FALSE TRUE 14983605.99 18489119.7 17063873.71 18644489.11 15597161.54 15454728.69 15719096.94 17076014.57 15967363.59 19927173.93 0.751918262 0.927834512 0.856311776 0.935631373 0.782708155 0.775560485 0.788827206 0.856921038 0.801285905 1 24.24823379 -1.583767186 2.592037173 1.013807979 0.834294049 0.415699465 0.060057566 9104296.474 8339503.75 861190.3571 0.015638558 0.02607551 1.583767186 -0.17951393 DIIHFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIIHFFR 7 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 ; 124.34 0.0041557 529770000 380230 454350 455730 421250 558330 548210 461020 466340 445420 522070 FALSE TRUE 395241.774 532381.0781 467606.6982 504571.9927 463425.266 420896.5357 424884.0477 460089.4751 429389.4212 624359.6209 0.633035451 0.85268339 0.748938084 0.808143217 0.742240931 0.67412517 0.680511733 0.736898191 0.687727724 1 19.25201771 -1.604993748 8.339744219 1.000135684 0.732834876 0.630432854 0.062111538 0.000153452 7.27E-06 0.058894678 0.013874657 0.024831689 1.604993748 -0.267300808 DIILPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIILPFR 7 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 143.37 0.005645 30221000 43256 46154 45057 40746 46948 57063 43016 47552 42286 40129 FALSE TRUE 44963.78028 54080.59047 46231.22243 48805.43719 38967.79573 43810.98305 39644.29352 46914.64322 40764.13512 47991.50923 0.936911154 1.126878303 0.96332087 1.016959832 0.811972708 0.912890296 0.826068906 0.977561322 0.849403067 1 15.55049156 3.269485298 24.54221773 0.896799365 1.015886538 0.371759081 0.072936372 162.6920464 129113.1986 0.018917022 0.025610754 1859.881598 -3.269485298 0.119087173 DIILREDLEELQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIILREDLEELQAR 14 1 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ;; 184.51 1.17E-06 130234000 107324 171969 120218 166836 133810 189250 116604 123740 106512 166944 FALSE TRUE 111561.2344 201503.338 123350.9798 199835.6628 111065.024 145299.5556 107464.2738 122081.4677 102678.6539 199653.4805 0.558774303 1.009265341 0.617825342 1.000912493 0.556288945 0.727758691 0.538253946 0.611466764 0.514284317 1 17.6071387 DIINMLFYHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIINMLFYHDR 11 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 158.2 3.01E-05 434660000 399030 406010 445650 440900 649750 599010 575890 438140 448520 469710 FALSE TRUE 414784.0125 475739.0592 457264.0051 528108.704 539305.7271 459899.0056 530750.237 432267.45 432377.8528 561740.6814 0.738390553 0.84690156 0.814012622 0.940128998 0.960061724 0.8187034 0.944831405 0.769514234 0.769710771 1 19.09954476 4.951802537 1.45244568 0.87126216 0.628004656 0.222789384 0.078034577 3.366516312 4.396547688 0.021226819 1.36799523 89495.77587 -4.951802537 -0.243257504 DIIRQPS(ph)EEEIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 261.15 2.89E-24 7285900000 4301860 3288960 5622690 2346850 7022160 5114000 4156580 4444240 6127580 4244300 TRUE FALSE 4471700.755 3853813.295 5769221.92 2811049.925 5828535.751 3926351.003 3830776.398 4384672.232 5907049.593 5075889.323 0.880968924 0.759239032 1.136593325 0.553804417 1.148278731 0.773529672 0.754700537 0.863823451 1.163746728 1 22.27522918 1.25353232 24.2624031 1.081873271 0.856626361 0.211797201 0.172038609 200.656435 325178.4292 0.105502182 0.038153736 17.92801968 -1.25353232 -0.22524691 DIISDTSGDFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 142.12 9.80E-05 793223000 549217 598360 622330 598810 591510 739500 791200 600160 583190 523258 FALSE TRUE 570900.5112 701123.6754 638548.431 717252.8307 490965.3415 567762.3322 729183.6766 592115.8369 562201.1058 625780.3867 0.912301701 1.12039893 1.020403395 1.146173396 0.784564924 0.907286876 1.165238943 0.946203891 0.89840001 1 19.25529692 3.287762148 24.99999357 0.960258219 1.05275935 0.167099541 0.107411099 226.0570606 114861.0434 0.030050453 0.040688436 1939.823195 -3.287762148 0.092501131 DIISIAEDEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIISIAEDEDLR 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 288.17 1.17E-28 2115950000 891220 777470 829150 879110 968440 1100200 1126950 947190 925980 661550 FALSE TRUE 926406.0538 910994.4246 850758.3302 1052995.334 803824.9147 844695.2237 1038616.714 934494.4673 892654.1607 791168.0564 1.170934603 1.151455013 1.075319363 1.330937625 1.015997686 1.067655875 1.312763712 1.181157985 1.128273764 1 19.59362465 DIISIAEDEDLRVHFEESSKLEDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIISIAEDEDLRVHFEESSKLEDLLR 26 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 184.29 9.62E-18 75602000 82531 79442 111911 52823 145125 119639 70665 91202 108234 92579 FALSE TRUE 85789.38761 93085.54553 114827.4926 63271.23174 120456.7043 91854.6554 65126.09265 89979.58637 104338.6795 110718.0825 0.774845316 0.840743837 1.037115979 0.571462496 1.087958729 0.829626501 0.588215503 0.812690974 0.942381561 1 16.75653134 2.479338384 24.999832 0.798346353 0.865164331 0 0.16732915 372.7666178 4203320.715 0.055449055 0.047094531 301.5354548 -2.479338384 0.066817978 DIKDTTVGTLSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIKDTTVGTLSQR 13 1 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;; 160.04 4.06E-05 1509950000 1248740 1095070 1259210 968390 1758730 1578540 1226290 1271370 1360980 1188150 FALSE TRUE 1298041.219 1283139.754 1292026.047 1159934.652 1459781.703 1211948.008 1130170.185 1254329.365 1311998.596 1420945.244 0.913505446 0.903018438 0.909272227 0.816311998 1.027331425 0.852916756 0.79536505 0.882742928 0.923328046 1 20.43841953 DIKEES(ph)DEEEEDDEESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIKEESDEEEEDDEESGR 18 1 Q96EV2;A8MTF7;Q96EV2-2;H7BXM6;H7C0H2 Q96EV2 RBM33 RNA-binding protein 33 1 DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR 165.62 1.68E-11 1878290000 1072790 442300 605890 492050 851300 1073450 894880 630940 659550 285110 TRUE FALSE 1115144.578 518261.5844 621679.9911 589376.0214 706596.3301 824157.5058 824736.9673 622483.2813 635812.9243 340971.8457 3.270488727 1.519954186 1.823259014 1.728518142 2.072301097 2.417083745 2.418783186 1.825614898 1.864707988 1 18.37929309 0.738516011 1.36775619 1.004198254 2.114615093 0.353022689 0.465721098 1.000327628 3.152625291 0.427283206 0.126973202 5.476662909 -0.738516011 1.110416839 DIKPDNFLMGIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIKPDNFLMGIGR 13 1 P48729-2;A0A5F9W493;U3KPX3;A0A590UJ43;P48729;E7ETM0;P48729-3;D6REM4;A0A590UK94 P48729-2 CSNK1A1 Casein kinase I isoform alpha 0 81.185 0.01437 483280000 456520 385800 509610 458160 684540 629240 509890 578030 579660 388930 FALSE TRUE 474543.7621 452058.1489 522890.8552 548782.6805 568182.1353 483108.5462 469923.4895 570282.4533 558798.1498 465133.387 1.020231562 0.971889272 1.124173989 1.179839366 1.22154666 1.038645171 1.010298342 1.226062178 1.201371833 1 18.82728497 4.214010536 9.37040556 1.134323613 0.996056429 0.281603613 0.081510335 0.292032467 105.3526372 0.020800783 0.046205345 16368.5623 -4.214010536 -0.138267184 DILETHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DILETHLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 167.33 0.00031328 781690000 809060 823330 1095510 1106070 1266410 1173470 1227370 976850 1005830 814580 FALSE TRUE 841002.3135 964730.5229 1124059.891 1324847.345 1051146.081 900949.3766 1131165.532 963756.9236 969630.3748 974181.3549 0.863291326 0.990298693 1.153850754 1.359959661 1.079004515 0.924827161 1.161144716 0.989299291 0.995328406 1 19.89383085 2.986198649 24.56751569 1.021529778 1.105332153 0.072307624 0.130398718 1500.657918 2671296.704 0.041814064 0.046070577 968.7208534 -2.986198649 0.083802375 DILIQYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DILIQYDR 8 0 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;;;;;; 190.26 0.0004359 4878609000 3007730 3347130 3566210 3494880 3788420 4112600 4008680 3631910 3228370 3222540 FALSE TRUE 3126477.503 3921973.54 3659148.362 4186156.833 3144465.722 3157510.977 3694469.187 3583230.187 3112181.594 3853935.014 0.811242922 1.0176543 0.949457723 1.086203275 0.815910416 0.819295335 0.958622596 0.92975885 0.807533491 1 21.87790081 3.216860102 24.99999547 0.889772231 0.968627735 0.157712229 0.087772641 436.194287 502514.5907 0.024954833 0.029850615 1647.631561 -3.216860102 0.078855504 DILKPEIMEEIVMETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DILKPEIMEEIVMETR 16 1 A3KFL2;Q13868-3;Q13868-2;Q13868 A3KFL2 EXOSC2 Exosome complex component RRP4 0 93.152 0.0041303 33760000 16377 16472 18707 17254 18212 20245 22448 18960 19651 14885 FALSE TRUE 17023.57661 19300.93787 19194.51979 20666.7897 15116.33075 15543.40557 20688.4671 18705.87221 18943.76435 17801.43076 0.956303841 1.084235201 1.078257138 1.160962283 0.849163809 0.873154848 1.162180017 1.050807234 1.064170886 1 14.11970558 -0.29151216 6.88028966 1.000009865 1.034826866 0.007007272 0.102150508 0 5.28E-18 0.100933315 0.02379021 0.511078769 0.29151216 0.034817001 DILQDYTHEFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DILQDYTHEFHK 12 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 ; 131.53 0.00011393 107926000 149684 327504 269296 301377 278151 400501 246388 289930 247466 394538 FALSE TRUE 155593.6399 383750.2644 276314.075 360988.4711 230870.9924 307490.7124 227075.4647 286043.9626 238559.747 471840.1672 0.329759208 0.81330563 0.58560948 0.765065156 0.489299149 0.651684053 0.481255053 0.606230632 0.505594402 1 18.84793871 -0.93775009 4.302990379 1.000010663 0.589606414 0.464673205 0.134667456 4700984.787 1820820.859 464.3474447 0.028481991 0.115411719 0.93775009 -0.410404249 DILVDLGHLEGADAGEEDLEQQFHYHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DILVDLGHLEGADAGEEDLEQQFHYHLR 28 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 0 ;; 135.62 3.55E-06 136839000 22604.8 26505.9 25216.1 29763.2 26371.6 33921.8 28881.3 28881.4 28070 24410.3 FALSE TRUE 23497.25496 31058.08214 25873.25228 35650.27213 21888.96485 26043.97604 26617.50824 28494.29207 27059.76618 29193.03092 0.804892614 1.063886865 0.88628181 1.221191188 0.749801037 0.89212991 0.911776112 0.976064875 0.926925548 1 14.83333638 4.774824672 22.50821687 0.954158882 0.804891341 0.132055246 0.117763637 9819.688271 6094406.146 0.02666382 4.681021072 59542.17191 -4.774824672 -0.149267541 DILYIGDHIFGDILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DILYIGDHIFGDILK 15 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 191.09 1.90E-07 874933000 1068556 807231 944467 902831 1180181 1222848 1418562 1041922 1047867 642301 FALSE TRUE 1110743.416 945866.6449 969080.5859 1081408.277 979574.2552 938860.0844 1307371.404 1027956.74 1010154.471 768147.5834 1.446002617 1.231360568 1.261581247 1.407813161 1.275242253 1.222239196 1.701979453 1.338228177 1.315052593 1 19.551024 DIMLATGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 112.94 0.01114 0 471180 356820 424070 398830 629260 600370 507060 386390 452570 408970 FALSE TRUE 489782.5502 418101.0593 435121.6126 477717.3836 522298.61 460943.1662 467315.3122 381211.0741 436282.0941 489099.8413 1.001395848 0.854837855 0.889637607 0.976727742 1.067877284 0.942431641 0.955459955 0.779413612 0.892010296 1 18.89976947 -0.791276474 5.163516863 1.000000045 0.922016989 0.065550474 0.076747815 4.31E-08 1.03E-08 0.081397921 0.019185663 0.161705029 0.791276474 -0.077983055 DIMLATGKLS(ph)PDAIPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIMLATGKLSPDAIPGK 17 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 DIMLATGKLS(1)PDAIPGK;DIMLAT(0.003)GKLS(0.997)PDAIPGK 213.72 2.50E-13 1695110000 6407100 2585000 4504400 3383800 5965400 5601300 5953900 4131200 4931900 1922630 TRUE FALSE 6660057.255 3028953.641 4621788.364 4053105.54 4951403.439 4300482.964 5487217.76 4075828.021 4754401.882 2299332.538 2.89651764 1.317318653 2.010056522 1.762731347 2.153409025 1.87031797 2.3864394 1.772613554 2.067731311 1 21.1327837 -1.65963142 0.965954874 0.532960048 1.996035156 0.373713534 0.396795991 676.9400126 155.9145829 760.3009835 0.109706067 0.021896191 1.65963142 1.463075108 DINAVLIDMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 161.99 5.97E-05 101492100 109672 142801 157722 144398 176352 173179 152931 146802 151319 144365 FALSE TRUE 114001.9352 167325.9609 161832.3649 172959.4934 146375.75 132960.8018 140943.8686 144834.3593 145873.0587 172650.5577 0.660304471 0.96915969 0.937340528 1.00178937 0.847815101 0.770115102 0.816353393 0.838887295 0.84490349 1 17.39749547 3.029445578 24.99648025 0.837522751 0.903867944 0.016672707 0.102831086 529.7848012 449733.372 0.028727954 0.03433606 1070.152272 -3.029445578 0.066345193 DINAYNCEEPTEKLPFPIIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DINAYNCEEPTEKLPFPIIDDR 22 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;; 318.1 1.68E-67 22297771000 4829306 4487958 5146252 3812428 6621768 6043705 4859847 4928270 5366604 4168244 FALSE TRUE 5019970.73 5258729.875 5280367.555 4566514.879 5496202.241 4640146.107 4478919.493 4862214.602 5173460.97 4984931.606 1.007029008 1.054925181 1.059265798 0.916063698 1.10256322 0.930834457 0.898491664 0.97538241 1.03781985 1 22.24914228 2.705743106 24.99822364 0.961876593 1.024988674 0.207964477 0.057149433 988.2383134 752773.3756 0.01831394 0.017267503 507.8589449 -2.705743106 0.063112081 DINTFVGT(ph)PVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DINTFVGTPVEK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 DINTFVGT(1)PVEK;DINTFVGT(1)PVEK;DINTFVGT(1)PVEK 185.26 0.0001483 128982000 661230 363780 435900 425390 484910 568840 641550 470280 488710 336070 TRUE FALSE 687335.871 426256.3852 447259.9121 509530.8723 402485.1714 436735.5309 591263.6346 463976.6658 471121.4226 401916.4821 1.710146017 1.060559604 1.112818041 1.267753116 1.001414944 1.086632548 1.471110693 1.154410646 1.172187366 1 18.61653622 4.745227902 24.68193215 1.162999179 1.710146318 0.614267812 0.133261539 446.5174717 1652931.882 0.031619762 0.306860161 55619.60527 -4.745227902 0.547147138 DINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DINVSVGSQQPDTKDSPVCPHFTTNGNENSSIEK 34 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 DINVSVGSQQPDT(0.014)KDS(0.986)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.009)KDS(0.99)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.164)KDS(0.836)PVCPHFTTNGNENSSIEK;DINVSVGS(0.001)QQPDT(0.026)KDS(0.972)PVCPHFTTNGNENSSIEK;DINVSVGSQQPDT(0.001)KDS(0.998)PVCPHFT(0.001)TNGNENSSIEK;DINVSVGSQQPDT(0.007)KDS(0.993)PVCPHFTTNGNENSSIEK 325.02 1.35E-105 6505770000 1748505 904575 1416357 937561 1952370 1760875 1587085 1358984 1489690 642885 TRUE FALSE 1817537.328 1059928.72 1453268.427 1123007.767 1620506.845 1351938.468 1462685.131 1340769.042 1436076.348 768846.007 2.363980968 1.378596897 1.890194413 1.460640697 2.107713157 1.758399543 1.902442254 1.743872024 1.867833526 1 19.55233514 -1.304658979 5.326728134 0.999839442 1.811941905 0.458832825 0.269882591 0.000454537 5.93E-05 0.230811823 0.054392327 0.049583939 1.304658979 0.812102463 DINWDSSQWQPLIQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DINWDSSQWQPLIQDR 16 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 228.93 8.50E-15 417530000 530490 470110 519720 478250 563970 634070 562500 499980 534430 464590 FALSE TRUE 551434.1548 550847.7356 533264.3302 572846.4226 468106.5808 486816.8519 518409.7802 493278.5859 515195.9687 555617.5154 0.992470791 0.991415354 0.959768753 1.031008575 0.842497884 0.876172616 0.933033545 0.88780244 0.92724933 1 19.08373255 3.247533817 24.999998 0.904340746 0.991083894 0.471790825 0.04238743 154.4366 430269.3275 0.011165209 0.014899322 1768.209898 -3.247533817 0.086743147 DIPCIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIPCIFR 7 0 Q9Y5S2;H0YLY0;Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;H0Y6R0;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q9Y5S2;Q5VT25-2;Q5VT25-3 CDC42BPB;CDC42BPA Serine/threonine-protein kinase MRCK beta;Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 0 99.279 0.024765 46492000 37764 52650 48836 45513 56414 60129 43851 47354 43048 62386 FALSE TRUE 39254.95188 61692.22794 50108.70628 54515.33556 46824.76843 46164.95101 40413.84404 46719.29709 41498.71089 74609.34225 0.5261399 0.826870015 0.671614369 0.73067707 0.627599266 0.618755636 0.541672702 0.626185618 0.556213333 1 16.18706867 -1.148188986 5.106945443 1.000016087 0.639740922 0.614767845 0.086355991 1.57E-05 2.62E-06 0.083162331 0.019600675 0.071090409 1.148188986 -0.360275165 DIPGLTDTTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIPGLTDTTVPR 12 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 113.93 0.0025893 58819000 30576 29051 32637 32816 34442 39848 30381 35879 31260 37181 FALSE TRUE 31783.16409 34040.28326 33487.54703 39306.90685 28587.56114 30593.9059 27999.65783 35398.10069 30134.95871 44465.90508 0.714776052 0.765536723 0.75310616 0.883978563 0.642909688 0.688030657 0.629688247 0.79607287 0.677709329 1 15.44041193 -1.873388372 5.322724861 1.056949237 0.731213922 0.559752792 0.072321424 0.039515349 0.000939951 0.056614562 0.016364577 0.013384792 1.873388372 -0.325735314 DIPRT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DIPRTPSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DIPRT(0.992)PS(0.008)R;DIPRT(1)PSR;DIPRT(0.999)PS(0.001)R;DIPRT(0.998)PS(0.002)R;DIPRT(0.968)PS(0.032)R 154.15 0.00069459 8921430000 3209272 3766724 3503453 3499748 3762915 4314071 3759198 3540719 3359964 3652220 TRUE FALSE 3335976.537 4413629.546 3594755.863 4191987.709 3123296.052 3312193.391 3464542.238 3493261.453 3239039.552 4367802.583 0.763765411 1.010491995 0.82301244 0.959747523 0.715072624 0.758320306 0.793200281 0.799775491 0.741571875 1 22.05847622 3.241239618 24.99999398 0.789608238 0.893182603 0.159546058 0.096482138 103.0318943 961466.6806 0.024704429 0.031987064 1742.768164 -3.241239618 0.103574365 DIPSFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DIPSFER 7 0 K7EJR3;R4GMR5;P48556 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;;; 192.28 0.0011947 1033970000 686967 722407 792186 781066 863515 969214 870051 808302 805358 619939 FALSE TRUE 714088.9876 846474.7827 812831.0179 935558.5236 716735.0287 744128.7371 801854.1292 797468.0338 776373.3229 741404.1776 0.963157491 1.141718388 1.096339949 1.261873822 0.96672645 1.003674864 1.081534409 1.075618479 1.047166102 1 19.49990072 3.175901502 24.99999957 1.038144951 1.116252677 0.23584296 0.075366596 105.5800984 42123.83221 0.02180938 0.026067206 1499.344745 -3.175901502 0.078107726 DIPVTIHNLEEYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIPVTIHNLEEYLR 14 0 Q14669-3;Q14669;Q14669-2;Q14669-4;H7C2Y1 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 0 134.68 3.73E-05 26268000 8504.2 13312 12321 11489 14474 15678 15059 11431 10934 12462 FALSE TRUE 8839.952383 15598.23245 12642.09538 13761.48991 12013.71465 12037.0221 13878.63623 11277.78614 10540.48748 14903.6903 0.593138491 1.046602025 0.84825269 0.923361237 0.806089929 0.8076538 0.931221459 0.756710983 0.707240104 1 13.86338198 3.182672256 24.999809 0.82377327 0.866352999 0 0.131135167 419.2725234 187545.6994 0.035854436 0.042854273 1522.903047 -3.182672256 0.042579729 DIPVVHQLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIPVVHQLLTR 11 0 P30419;P30419-2 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 ; 208.27 2.02E-08 1173760000 1686150 1889140 1732450 1745350 2001090 2320870 1935730 1822650 1846120 1965050 FALSE TRUE 1752720.504 2213585.1 1777599.07 2090575.021 1660945.437 1781883.116 1784002.425 1798220.358 1779678.502 2350063.924 0.745818225 0.941925484 0.756404561 0.889582193 0.706766067 0.758227509 0.759129318 0.765179338 0.757289401 1 21.16426857 DIPVVIDADGLWLVAQQPALIHGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIPVVIDADGLWLVAQQPALIHGYR 25 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 206.34 3.80E-25 188180000 102010 142360 118650 121170 155750 165680 125370 130910 129390 136620 FALSE TRUE 106037.4336 166809.2226 121742.1165 145137.0643 129275.6706 127203.3309 115543.1718 129155.3656 124733.2792 163388.0733 0.648991272 1.020938795 0.745110179 0.888296566 0.791218527 0.778534983 0.707170172 0.790482212 0.763417284 1 17.31794315 3.038296841 24.65858215 0.78627635 0.834723456 0 0.115155962 520.5402634 335162.067 0.030435262 0.036377009 1092.186594 -3.038296841 0.048447106 DIQDLK ddPTM_MDA-MB-175_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 0 107.66 0.072303 622640000 1560800 1140500 1367100 1189800 1663700 1706300 1822100 1380300 1537800 1053700 FALSE TRUE 1622421.589 1336372.003 1402727.749 1425138.889 1380904.868 1310037.684 1679279.041 1361799.336 1482454.878 1260152.341 1.287480519 1.060484483 1.113141407 1.130925875 1.095823754 1.039586756 1.332600025 1.080662466 1.176409257 1 20.26516672 4.753102565 23.67535369 1.122615769 1.287480762 0.258958346 0.086840421 1690.788168 2752627.076 0.019510755 0.396736208 56637.30309 -4.753102565 0.164864993 DIQMPDGIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIQMPDGIRR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 133.91 0.00029599 711790000 237270 291020 291520 268290 346440 354670 256540 292780 277190 300650 FALSE TRUE 246637.6028 341000.4212 299117.2507 321356.9612 287552.2525 272303.2676 236431.7245 288855.763 267213.986 359556.6112 0.685949292 0.948391465 0.831905857 0.893759011 0.799741247 0.757330721 0.65756467 0.803366574 0.743176395 1 18.45585941 3.026577925 8.491636759 0.771768725 0.847254323 0.026791215 0.102861025 0.51012051 142.1856748 0.027802427 0.03302043 1063.10932 -3.026577925 0.075485598 DIREEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIREEAEK 8 1 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;; 169.41 0.0002747 2855470000 4032330 3332640 4200870 3179650 5284480 5559690 4614820 3972730 4372740 3678440 FALSE TRUE 4191529.502 3904994.996 4310348.123 3808575.28 4386225.977 4268536.255 4253098.35 3919482.052 4215365.942 4399159.89 0.952802264 0.887668349 0.979811653 0.865750592 0.997059913 0.970307141 0.966797856 0.89096149 0.958220671 1 22.06879661 3.220503124 24.999664 0.954452202 0.923255573 0.181429953 0.041211606 543.8918453 752987.8123 0.012015513 0.014388836 1661.51063 -3.220503124 -0.03119663 DIRPVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIRPVCR 7 1 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 85.272 0.019091 916090000 107887 180009 109379 186399 158019 172601 145161 120422 110978 185839 FALSE TRUE 112146.4621 210924.1455 112229.5066 223268.1659 131158.9868 132517.0335 133782.9015 118807.9401 106983.9235 222250.5939 0.504594656 0.949037488 0.504968309 1.004578489 0.590140096 0.596250526 0.601946205 0.534567481 0.481366198 1 17.76182775 DIS(ph)ENKR ddPTM_MDA-MB-175_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 122.96 0.0026276 2053640000 3588160 2004800 2617650 1967000 3828970 3974530 3436800 2782800 2914650 1723760 TRUE FALSE 3729823.327 2349108.805 2685868.109 2356066.729 3178123.047 3051505.642 3167414.636 2745501.118 2809752.316 2061497.769 1.809278372 1.13951557 1.302872189 1.142890749 1.541657282 1.480237179 1.536462801 1.331799219 1.36296646 1 20.97526147 0.498102354 1.603551875 1.000140832 1.399679139 0.293216259 0.189790124 3.716067803 10.45154357 0.174988122 0.049971167 3.14849026 -0.498102354 0.399538308 DIS(ph)LDSELHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 DIS(0.992)LDS(0.008)ELHDLR;DIS(0.999)LDS(0.001)ELHDLR 106.13 0.00043749 13603000 44204 48279 49104 43392 49200 59181 49050 43221 48009 51450 TRUE FALSE 45949.20805 56570.54269 50383.69058 51974.80809 40837.00157 45437.10965 45205.33283 42641.69319 46281.16547 61530.64243 0.746769516 0.919388137 0.818839014 0.844697959 0.663685604 0.738446859 0.734680007 0.693015569 0.752164509 1 15.90901744 3.271756839 24.92468424 0.74177195 0.83766516 0.084424287 0.095220956 287.1441785 215594.2619 0.024123626 0.032661587 1869.635042 -3.271756839 0.095893211 DIS(ph)QNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DISQNKR 7 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 1 DIS(1)QNKR;DIS(1)QNKR 85.355 0.022109 211889000 651150 422270 550360 389840 735920 704290 662300 568550 614040 351910 TRUE FALSE 676857.9048 494791.5877 564702.8337 466949.1884 610828.5813 540729.3211 610387.1954 560929.5172 591940.8203 420860.0268 1.608273207 1.175667814 1.34178301 1.109511854 1.451381795 1.284819861 1.450333024 1.332817283 1.406502834 1 18.68298096 -1.128009041 5.104787668 0.999987861 1.343166087 0.37553331 0.135518259 1.71E-05 2.92E-06 0.119874597 0.028253715 0.074471647 1.128009041 0.343178225 DISENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 DISENKR 7 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;; 180.7 0.0010945 49662480000 18271010 14790730 16758000 13471320 22584060 20877120 20066670 16750840 18187050 13819550 FALSE TRUE 18992363.58 17330922.82 17194727.25 16135906.89 18745229.55 16028725.28 18493791.97 16526322.39 17532501.62 16527226.23 1.149156145 1.048628643 1.040387964 0.976322745 1.134202998 0.969837591 1.118989461 0.999945312 1.060825415 1 23.97834128 4.742306227 3.823693015 1.038882881 1.160602119 0.285300479 0.052627447 0.308979277 8.837541951 0.01134278 0.106333446 55246.68537 -4.742306227 0.121719238 DISGPS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DISGPSPSK 9 0 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DISGPS(1)PSK;DISGPS(1)PSK 181.31 5.00E-05 519100000 1123330 700190 923260 733520 1162330 1253050 1175270 936790 942920 604980 TRUE FALSE 1167679.936 820442.1858 947320.9141 878608.0667 964757.5618 962048.1277 1083149.266 924233.8623 908984.4934 723514.248 1.613900402 1.13396825 1.30933277 1.214361803 1.333432706 1.329687882 1.497066947 1.277423167 1.256346362 1 19.4646619 0.781948066 1.970165483 1.000614113 1.33234251 0.390382917 0.127497293 0.805227094 5.229113591 0.114286812 0.031705794 6.052684912 -0.781948066 0.331728397 DISGPS(ph)PSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DISGPSPSKK 10 1 Q96GX9;S4R3D6;Q96GX9-3 Q96GX9 APIP Methylthioribulose-1-phosphate dehydratase 1 DIS(0.001)GPS(0.998)PS(0.002)KK;DISGPS(1)PSKK;DISGPS(0.987)PS(0.012)KK;DISGPS(0.996)PS(0.004)KK;DISGPS(0.899)PS(0.101)KK;DISGPS(0.998)PS(0.002)KK 156 7.17E-06 2348060000 6238870 2232150 3582890 2465310 5430240 5275130 5527980 3658420 4201320 1638410 TRUE FALSE 6485185.405 2615504.399 3676263.057 2952940.96 4507209.744 4050061.003 5094682.483 3609384.864 4050115.314 1959425.07 3.309738915 1.334832568 1.876194764 1.507044594 2.300271551 2.06696396 2.600090486 1.842063225 2.066991678 1 20.90199897 4.754211178 24.43359883 1.912915517 3.309740336 0.484950256 0.448153891 1885.711602 2943898.593 0.102325875 2.478433397 56782.0644 -4.754211178 1.396824819 DISLDSELHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DISLDSELHDLR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ;;; 237.49 4.17E-16 567550000 595570 819690 802300 757530 894560 985120 833990 806920 810340 791130 FALSE TRUE 619083.5635 960465.3812 823208.5971 907367.173 742503.0107 756340.8096 768619.6846 796104.5573 781176.0217 946136.7764 0.654327766 1.015144327 0.870073564 0.959023257 0.784773438 0.799399018 0.812376925 0.841426501 0.825648089 1 19.85168923 3.218501867 24.99912669 0.832381953 0.884351818 0.009961592 0.103814768 750.0392292 934768.2967 0.027904899 0.033393267 1653.871895 -3.218501867 0.051969865 DISLSDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DISLSDYK 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 183.9 0.00051381 2490400000 3324200 2264600 2917200 2080200 4238800 3630400 3628300 2814000 3067000 2330600 FALSE TRUE 3455441.983 2653527.434 2993224.629 2491657.351 3518290.29 2787294.619 3343904.365 2776282.933 2956619.269 2787236.448 1.239737657 0.952028105 1.073904093 0.893952629 1.262286267 1.000020871 1.199720378 0.996070116 1.060770883 1 21.41040396 1.612261055 25 1.021313923 1.080105778 0.067914695 0.115385564 1.314698109 7436.201219 0.051957591 0.027558141 40.95067411 -1.612261055 0.058791855 DISMEIDS(ph)PENMMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR;DISMEIDS(1)PENMMR 295.03 1.43E-43 1004738000 1277760 1419750 1450680 1397070 1622450 1837080 1537070 1460700 1451480 1464570 TRUE FALSE 1328206.951 1663581.018 1488485.913 1673406.276 1346666.529 1410446.011 1416590.437 1441121.706 1399241.518 1751524.451 0.758314822 0.949790349 0.849823085 0.955399895 0.768853971 0.805267669 0.808775713 0.822781381 0.798870674 1 20.7401797 5.037573889 13.81043967 0.851008661 0.452150303 0.130921921 0.075495417 804573.4308 9556811.47 0.017327656 7580163.78 109036.9987 -5.037573889 -0.398858358 DISMEIDSPENMMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 107.85 0.0020007 37632000 25339 33376 30977 27649 30758 38664 33508 31556 29958 32156 FALSE TRUE 26339.40329 39108.06837 31784.28607 33117.88968 25529.76615 29684.87196 30881.5554 31133.04344 28879.81743 38456.35254 0.684916836 1.016946897 0.826502879 0.861181248 0.663863431 0.771910751 0.803028716 0.809568287 0.75097651 1 15.23093431 DISPVLKDPASFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DISPVLKDPASFR 13 1 H3BQB1;P07741-2;P07741;H3BQZ9;H3BQF1;H3BSW3 H3BQB1 APRT Adenine phosphoribosyltransferase 0 ; 113.54 0.00074226 5230400000 6762400 6037600 6927200 5800100 8366500 8437000 7406300 6765100 7471500 5945400 FALSE TRUE 7029384.774 7074510.834 7107728.523 6947342.468 6944365.318 6477634.614 6825774.853 6674424.9 7202602.174 7110287.298 0.988621764 0.994968352 0.99964013 0.977083228 0.976664518 0.911022908 0.959985802 0.938699749 1.012983284 1 22.76147642 3.287832909 2.4684212 0.958123606 0.993494861 0.135820723 0.027722277 0.403560591 5.025065532 0.008162919 0.01132163 1940.139281 -3.287832909 0.035371255 DISQNKR ddPTM_MDA-MB-175_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 ;;;;;; 147.52 0.003441 41849900000 17828240 15398850 17356300 13569720 23219820 20292770 18737370 16833380 17322000 16012100 FALSE TRUE 18532112.68 18043482.7 17808619.44 16253770.11 19272923.29 15580081.71 17268685.98 16607756.07 16698584.6 19149364.42 0.967766463 0.94224969 0.929984883 0.848789012 1.006452374 0.813608293 0.901788989 0.867274532 0.872017694 1 24.19079317 2.735939333 24.99455495 0.882496578 0.933708379 0.138046318 0.057459663 414.173006 3949209.753 0.017038364 0.016767761 544.4265958 -2.735939333 0.0512118 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 242.11 8.34E-38 1752980000 2001660 1088890 1358140 1121190 1801170 2022520 1917450 1505080 1530450 914753 TRUE FALSE 2080687.082 1275898.387 1393534.244 1342958.036 1495007.767 1552820.382 1767155.259 1484906.864 1475369.403 1093981.336 1.901940201 1.166288989 1.273819029 1.227587703 1.366575203 1.419421273 1.615343151 1.357342045 1.348623925 1 20.06115669 0.677133974 2.260380537 1.000146681 1.402528711 0.276225542 0.200261055 2.460312495 15.4589465 0.183988813 0.049825998 4.754818827 -0.677133974 0.402382031 DITDPLSLNTCTDEGHVVLAS(ph)PLKTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DITDPLSLNTCTDEGHVVLASPLKTGR 27 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 DITDPLSLNTCT(0.015)DEGHVVLAS(0.944)PLKT(0.042)GR;DITDPLSLNTCTDEGHVVLAS(0.994)PLKT(0.006)GR 180.23 1.11E-17 130467000 109026 82660 91447 56201 151840 117050 65968 85949 96737 109187 TRUE FALSE 113330.4307 96856.21199 93830.18394 67317.39006 126030.291 89866.91141 60797.25578 84796.99424 93255.45427 130580.1021 0.867899694 0.74173791 0.718564179 0.515525635 0.965156934 0.688212905 0.465593569 0.649386797 0.714162822 1 16.99457555 0.943625942 19.4164689 1.000000002 0.691219123 0.289633884 0.13895752 1266.589026 436244.0505 0.134789833 0.033697458 8.782657396 -0.943625942 -0.308780878 DITDTLVAVTISEGAHHLDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DITDTLVAVTISEGAHHLDLR 21 0 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ; 170.38 4.79E-12 99255000 51733 99066 90471 97960 99682 117314 89577 98495 84407 97945 FALSE TRUE 53775.45879 116079.8149 92828.74858 117336.1956 82738.08925 90069.60141 82555.72067 97174.83563 81369.20856 117135.4475 0.459087833 0.990987932 0.792490664 1.001713812 0.70634544 0.768935479 0.704788537 0.829593754 0.694659134 1 16.8378182 -2.024003453 2.525321778 1.247877978 0.784373564 0.171982171 0.147836741 18012761.74 7242175.958 25868899.84 0.032505607 0.009462296 2.024003453 -0.463504415 DITEEIMSGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DITEEIMSGAR 11 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JHW9;F8WCF2 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 177.06 1.90E-05 73798000 38623 43362 38984 51083 45796 54171 41434 41819 39935 36265 FALSE TRUE 40147.86586 50809.08619 39999.95507 61187.06493 38011.61228 41590.60622 38186.29481 41258.48471 38497.74715 43370.43241 0.925696693 1.171514402 0.922286287 1.410801358 0.876440703 0.958962222 0.88046839 0.951304435 0.887649604 1 15.40442421 DITSDTSGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DITSDTSGDFR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 ; 147.95 8.16E-05 820520000 506930 632520 648970 545870 581500 782120 609650 599860 579270 620830 FALSE TRUE 526943.9878 741150.3897 665882.6913 653841.4567 482656.8377 600484.4831 561864.04 591819.8579 558422.1859 742469.752 0.709717785 0.998223009 0.896848241 0.88063043 0.650069362 0.808766258 0.756750074 0.797096254 0.752114392 1 19.50197273 3.408759377 24.99999753 0.781738054 0.882513503 0.104171558 0.105307083 82.69777524 30241.46564 0.026865119 0.036375549 2563.063563 -3.408759377 0.100775449 DITSSIHFEAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DITSSIHFEAYR 12 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;; 198.49 1.83E-07 1094050000 384106 971120 776470 734610 1633950 1419260 929910 849740 845170 1994140 FALSE TRUE 399270.8015 1137902.306 796705.4461 879913.6654 1356211.763 1089658.374 857021.2243 838350.6252 814752.4968 2384853.553 0.167419421 0.477137183 0.334068918 0.368959203 0.568677167 0.456907877 0.359360105 0.351531281 0.34163628 1 21.18546925 -1.255255703 4.574148889 1.000240715 0.386130862 0.7729298 0.100671877 124.9462601 119390298.2 49282.49306 0.022918315 0.055557705 1.255255703 -0.614109854 DIVEAHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DIVEAHYR 8 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;;; 160.88 0.00035078 3879110000 3607090 3515420 3902770 3631280 5292850 5009140 5034170 4011160 4239600 4282352 FALSE TRUE 3749500.698 4119166.039 4004479.392 4349536.346 4393173.248 3845843.149 4639578.601 3957396.961 4087017.624 5121396.884 0.73212461 0.804305179 0.781911553 0.849287107 0.857807615 0.750936363 0.905920534 0.772718274 0.798027905 1 22.28810593 DIVENYFMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DIVENYFMR 9 0 Q13263;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;;;;; 220.88 1.02E-06 2948100000 1574755 1089508 1153939 1012494 1656880 1716988 1333068 1075212 1209337 1342812 FALSE TRUE 1636927.543 1276622.524 1184011.598 1212762.291 1375244.129 1318243.558 1228578.647 1060800.542 1165813.198 1605910.302 1.01931443 0.794952571 0.737283768 0.755186818 0.856364224 0.820869981 0.76503566 0.66056027 0.725951628 1 20.61495988 2.187984027 4.911777743 0.747733447 0.822692558 0 0.111453784 0.51567639 26.54107043 0.041546583 0.030815346 154.1643753 -2.187984027 0.074959111 DIVHSGLAYTMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIVHSGLAYTMER 13 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 194.12 1.28E-06 247600000 158294 219565 182883 225802 205087 285341 210289 204715 191871 207559 FALSE TRUE 164543.5693 257273.5808 187649.0812 270464.9616 170226.385 219074.8771 193805.9987 201971.1303 184965.6002 248226.2121 0.662877494 1.036448079 0.755959976 1.089590658 0.685771191 0.882561416 0.780763631 0.813657545 0.745149348 1 17.92129594 DIVNGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DIVNGLR 7 0 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;; 105.22 0.018556 497463000 320102 403265 334521 374699 416445 454837 384514 362458 341698 414630 FALSE TRUE 332739.8741 472522.6268 343238.8921 448813.3438 345657.8277 349207.9999 354374.7879 357599.8434 329400.3557 495868.8099 0.671024004 0.95291863 0.692196979 0.905105009 0.697075155 0.704234654 0.714654322 0.72115817 0.664289322 1 18.91959896 DIVNMLMHHDR ddPTM_MDA-MB-175_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 ; 122.45 0.00022587 641420000 621680 631870 642760 734530 840780 822660 904620 707030 665460 599920 FALSE TRUE 646224.4064 740388.7572 659510.8536 879817.8416 697864.5159 631609.6825 833713.5206 697553.4193 641510.2246 717462.8378 0.900707845 1.031954156 0.9192265 1.226290471 0.972683851 0.880337837 1.16203025 0.972250244 0.894137216 1 19.45254458 5.347134808 1.981557313 1.010972312 0.360728948 0.077648441 0.105967623 24.19176775 17.10901517 0.026100607 52.46168497 222400.0129 -5.347134808 -0.650243364 DIVQFVPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIVQFVPYR 9 0 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 89.698 0.027757 48032000 21238 74553 76903 64507 91684 98409 66565 81913 86134 93811 FALSE TRUE 22076.49264 87356.89781 78907.15536 77266.29207 76099.58643 75555.00115 61347.46136 80815.09022 83034.05417 112191.4693 0.196775145 0.778641178 0.703325804 0.688700242 0.678301005 0.673446935 0.546810392 0.720331864 0.74011023 1 16.77560346 -5 0.110083759 2.101151535 0.446706921 0.42174004 0.146023193 177.2516295 1.297841565 44.36159244 1.768177682 1.00E-05 5 -1.654444614 DIVQFVPYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIVQFVPYRR 10 1 Q99829;B0QZ18;F2Z2V0;H0Y524 Q99829 CPNE1 Copine-1 0 109.83 0.0031534 403300000 255270 269460 255550 190710 416420 324820 236030 262880 267040 397100 FALSE TRUE 265348.2567 315737.6589 262209.8429 228431.8688 345637.0771 249385.4777 217529.3519 259356.5236 257429.2826 474904.1421 0.558740666 0.664845031 0.552132146 0.481006267 0.72780388 0.525128032 0.458048967 0.546123945 0.542065777 1 18.85727681 -1.698967289 2.408024987 1.082798627 0.560305066 0.750126198 0.075874579 3897851.08 2856956.999 1954279.69 0.019778184 0.020000125 1.698967289 -0.522493561 DIWAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DIWAELR 7 0 A0A1B0GV75;A0A1B0GTB8;A0A1B0GWC0;A0A1B0GVF3;P23786 A0A1B0GV75 CPT2 "Carnitine O-palmitoyltransferase 2, mitochondrial" 0 ; 79.597 0.074894 26874000 62447 112455 102338 114082 94089 153108 100647 98369 96317 118467 FALSE TRUE 64912.45578 131768.2715 105005.0124 136647.0791 78095.78539 117550.9874 92758.02515 97050.52445 92850.56998 141678.3405 0.458167816 0.930052336 0.741150779 0.96448814 0.551218945 0.829703305 0.65470858 0.685006079 0.655361784 1 17.11225969 -1.016588709 4.522875167 1.000008618 0.725576802 0.24039236 0.149492613 25589950.86 82982826.39 4093.844651 0.03315425 0.096252339 1.016588709 -0.274431816 DIWDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DIWDFLR 7 0 Q8NFF5-2;Q8NFF5;Q8NFF5-3;Q5T190 Q8NFF5-2 FLAD1 FAD synthase;Molybdenum cofactor biosynthesis protein-like region;FAD synthase region 0 80.462 0.069435 49816000 56341 45428 60099 59060 74600 76166 85676 59716 63575 52419 FALSE TRUE 58565.38618 53229.90562 61665.22931 70741.89172 61919.51865 58477.60081 78960.49125 58915.6047 61286.94817 62689.49943 0.934213652 0.849104014 0.983661217 1.128448821 0.987717548 0.932813331 1.259548919 0.93980021 0.977627015 1 15.93593619 4.053881406 5.813998767 1.033852655 0.894551525 0.257639877 0.094389261 0.246482515 17.8281469 0.023078346 0.050697676 11320.91178 -4.053881406 -0.13930113 DIWDIQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DIWDIQMR 8 0 P32456 P32456 GBP2 Interferon-induced guanylate-binding protein 2 0 ;;;; 131.06 0.0023756 272996000 506319 609305 628095 585189 759027 768560 669468 637213 633254 637972 FALSE TRUE 526308.8651 713948.394 644463.6717 700937.6376 630007.8617 590073.5876 616993.3488 628672.202 610463.3122 762970.3987 0.689815576 0.935748484 0.844677163 0.918695717 0.825730412 0.773389883 0.808672722 0.823979807 0.800114019 1 19.54126756 -0.984027094 5.408233855 1.000000548 0.8287131 0.38825005 0.065888012 4.13E-07 7.76E-08 0.060509708 0.014262229 0.103746369 0.984027094 -0.171287448 DIWPTRDEIQAVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DIWPTRDEIQAVER 14 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ;;; 254.18 2.75E-24 1117380000 445233 488253 477489 454378 575250 599720 442664 492140 501440 539530 FALSE TRUE 462811.1426 572106.6547 489932.7556 544252.6122 477469.2105 460444.1188 407966.839 485543.6683 483393.2724 645240.5736 0.717269127 0.886656354 0.759302461 0.843487894 0.73998634 0.713600691 0.632270901 0.752500212 0.749167508 1 19.29947763 -1.294222874 2.990660282 1.001894274 0.754317084 0.553249074 0.066068757 7226188.297 9379167.541 123734.8022 0.017166525 0.050789873 1.294222874 -0.24757719 DIYLS(ph)PDRTGSSFGK ddPTM_MDA-MB-175_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(1)PDRTGSSFGK 216.65 1.32E-12 762160000 780110 649470 799130 615970 1030610 946600 835620 743930 841490 641450 TRUE FALSE 810909.3452 761011.4203 819955.9843 737807.0275 855427.2803 726766.4959 770121.9209 733958.8352 811204.9393 767129.8462 1.057069216 0.992024263 1.068862056 0.961775938 1.115101028 0.94738394 1.00390035 0.956759587 1.057454541 1 19.54911127 2.689224148 24.99988066 0.988569175 1.033731487 0.178285412 0.048099789 625.0806768 316741.2127 0.014309621 0.013491263 488.9046271 -2.689224148 0.045162312 DKADFCIIHYAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKADFCIIHYAGK 13 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 125.53 0.00011963 9522700000 14470300 9098800 13144200 10083500 17811900 15538100 17208200 13981500 15230600 8577400 FALSE TRUE 15041598.62 10661448.12 13486748.65 12077986.2 14784239.6 11929611.76 15859376.32 13794100.86 14682453.68 10257977.31 1.466331828 1.039332395 1.314757115 1.177423759 1.441243157 1.162959461 1.546052974 1.344719378 1.431320546 1 23.29024295 3.249618894 24.99778183 1.346487459 1.239116069 0.025059351 0.17629775 561.9344591 1270272.985 0.044949136 0.060288445 1776.719602 -3.249618894 -0.10737139 DKADKDEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKADKDEQIR 10 2 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;A0A494BZX5;A0A494C122;A0A494C0Y7;H7C0P8 Q92878-2 RAD50 DNA repair protein RAD50 0 ; 54.471 0.076995 210950000 134306 105764 124641 91957 150081 157483 149714 135705 134182 107091 FALSE TRUE 139608.5046 123928.1443 127889.2469 110145.8201 124570.2852 120909.9599 137979.0255 133886.0964 129352.816 128073.4311 1.090066093 0.967633515 0.998561886 0.860020843 0.972647365 0.944067469 1.077343086 1.045385412 1.009989464 1 16.96661169 2.245490888 24.99745806 1.039306356 0.968084321 0.213598991 0.056543975 219.4620184 791598.6093 0.020016332 0.016410816 175.991174 -2.245490888 -0.071222035 DKALQDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKALQDYR 8 1 A0A087X2I1;P62333;H0YJC0;H0YJS8;H0YJT1;H0YJD2;H0YJY8;H0YJE9 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 80.239 0.02368 415730000 649260 595490 615860 499890 1045700 905020 732650 682740 694690 724020 FALSE TRUE 674893.2861 697760.7752 631909.8175 598766.75 867952.2875 694842.8207 675222.9786 673588.987 669688.2426 865877.8568 0.779432435 0.805842036 0.729790943 0.691514104 1.002395754 0.802472098 0.779813196 0.777926103 0.773421144 1 19.723804 -1.849502878 2.655838429 1.082168397 0.793732595 0.3923726 0.077046175 25080081.09 14992171.16 13027881.59 0.018671436 0.014141554 1.849502878 -0.288435802 DKANMQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 151.44 0.00028425 2610952000 2454160 2245322 2418865 2014822 3489029 3209204 2720561 2443951 2588517 2832441 FALSE TRUE 2551052.132 2630938.587 2481902.609 2413347.778 2895965.097 2463915.007 2507316.32 2411193.834 2495356.779 3387403.584 0.753099555 0.776682944 0.732685831 0.712447666 0.854921779 0.727375686 0.740188247 0.711811798 0.736657655 1 21.69174845 -1.36065877 3.545236322 1.001362762 0.748098312 0.782345472 0.039625063 22347562.3 40921044.29 330174.7795 0.009555405 0.043585419 1.36065877 -0.25326445 DKAPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKAPGQR 7 1 Q9Y4G6;H0YMT1;A0A1B0GVU7;H0YN01 Q9Y4G6 TLN2 Talin-2 0 63.486 0.072179 23532000 26143 18222 23566 19475 30334 31645 31059 26648 29858 23317 FALSE TRUE 27175.14583 21351.48675 24180.14932 23327.09687 25177.83752 24295.92833 28624.51442 26290.82715 28783.41641 27885.51972 0.974525349 0.765683658 0.867122061 0.836530827 0.902900063 0.871274001 1.02650102 0.94281288 1.032199389 1 14.76722854 2.251119825 23.85048049 0.991058744 0.864833786 0.578520225 0.054328738 89.64528858 170239.9993 0.017913293 0.014878621 178.2870605 -2.251119825 -0.126224959 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 228 2.53E-34 6754060000 7115220 2709610 4507020 2803190 6064500 5500520 6155930 4574320 5524030 1836450 TRUE FALSE 7396134.38 3174964.44 4624476.644 3357652.615 5033658.456 4223107.591 5673412.121 4513008.722 5325221.239 2196267.217 3.367593125 1.445618464 2.105607464 1.528799679 2.291915309 1.922856909 2.583206669 2.054854113 2.424669093 1 21.06662216 DKAS(ph)PEPEKDFSEK ddPTM_MDA-MB-175_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(1)PEPEKDFSEK;DKAS(1)PEPEKDFSEK;DKAS(0.997)PEPEKDFS(0.003)EK;DKAS(0.983)PEPEKDFS(0.017)EK;DKAS(0.999)PEPEKDFS(0.001)EK 132.01 2.78E-05 3449530000 6606920 1608010 2936100 1611353 4850070 4539990 4823320 2820777 3492980 1051023 TRUE FALSE 6867766.303 1884173.209 3012617.178 1930073.814 4025656.834 3485646.127 4445255.575 2782969.098 3367268.332 1256950.834 5.4638305 1.49900311 2.396766124 1.535520533 3.202716228 2.773096634 3.536538944 2.214063608 2.678918094 1 20.26149679 0.322654742 1.122675353 0.997331134 2.762477106 0.202972233 1.077423231 5.452555074 7.566018618 0.99669103 0.297736085 2.102106628 -0.322654742 1.765145972 DKASDASDKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKASDASDKQR 11 2 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 0 126.76 0.0001691 83395000 93516 49261 74973 40535 127140 95987 68597 78339 97287 64581 FALSE TRUE 97208.08389 57721.19355 76926.85797 48552.70202 105528.7882 73695.47395 63220.1879 77288.99384 93785.65987 77234.41047 1.258611069 0.747350737 0.996017934 0.628640806 1.366344193 0.954179277 0.818549498 1.000706723 1.214298903 1 16.23695614 3.255210888 24.99999781 1.0339095 0.902516654 0.105619171 0.208007856 645.7663007 969597.3847 0.056019891 0.075644542 1799.744637 -3.255210888 -0.131392846 DKAVESLR ddPTM_MDA-MB-175_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 ;;; 119.68 0.0015025 3878600000 2397950 2097380 2466870 2028000 3109650 2927310 2618820 2415000 2343720 2085820 FALSE TRUE 2492622.918 2457588.7 2531158.659 2429132.347 2581072.804 2247486.616 2413550.045 2382630.875 2259369.975 2494496.494 0.999248916 0.985204311 1.014697221 0.973796657 1.034706928 0.900978062 0.967549985 0.955155031 0.905741893 1 21.25031721 2.745156762 24.99954501 0.945971526 0.999814459 0.450046647 0.030727128 483.6980356 1833226.338 0.008837758 0.009179574 556.1049512 -2.745156762 0.053842933 DKDAVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DKDAVDK 7 1 P25815 P25815 S100P Protein S100-P 0 ;;;; 108.74 0.0065522 7581920000 17853700 6301550 9960620 7328030 15752900 13277610 19658200 11210510 12790030 4754170 FALSE TRUE 18558577.86 7383792.193 10220201.94 8777492.462 13075227.68 10194086.3 18117338.92 11060251.45 12329719.32 5685658.587 3.264103459 1.29866964 1.797540563 1.543795205 2.299685689 1.792947316 3.186497859 1.945289412 2.168564842 1 22.43889604 DKDAVDKLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDAVDKLLK 10 2 P25815 P25815 S100P Protein S100-P 0 ; 148.18 1.44E-05 4037300000 6801700 2627490 4245200 2327090 7555100 5428400 5482900 4258300 5402100 2378850 FALSE TRUE 7070236.368 3078740.968 4355833.399 2787381.456 6270886.801 4167736.368 5053135.971 4201224.454 5207679.476 2844940.112 2.485196908 1.082181293 1.531080876 0.979768061 2.204224537 1.464964535 1.776183601 1.476735639 1.830505836 1 21.43996685 -0.921264448 6.259048582 0.999999891 1.61419049 0.161138916 0.437426735 6.02E-07 1.03E-07 0.384724345 0.090680382 0.119876913 0.921264448 0.614190599 DKDAYSSFGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKDAYSSFGSR 11 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 179.67 6.38E-06 3898280000 3652420 3112610 3607480 2857790 4598100 4433200 4105930 3558340 3947850 2830720 FALSE TRUE 3796620.362 3647176.555 3701493.892 3423052.332 3816516.604 3403656.486 3784096.478 3510646.273 3805767.65 3385345.387 1.121486858 1.077342527 1.093387371 1.011138286 1.127364026 1.005408931 1.117787418 1.037012733 1.124188883 1 21.6908716 0.481661367 0.007454613 1.46E-05 2.10440824 0.160193382 0.046153302 8110.190842 25.54495751 3671.264766 3537.962289 3.031526485 -0.481661367 2.104393602 DKDDDEVFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDDDEVFEK 10 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 113.77 0.0013174 656060000 1354380 393550 704510 500840 1014050 1079280 1313980 685080 820540 255171 FALSE TRUE 1407851.968 461139.1511 722870.1094 599904.6571 841682.1432 828633.5766 1210986.814 675897.6232 791008.9257 305166.8719 4.613384013 1.511104886 2.368769929 1.965824971 2.758104567 2.715345776 3.968277443 2.214845992 2.59205372 1 18.21923883 DKDDDEVFEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDDDEVFEKK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 116.84 0.00052602 869060000 1418850 263980 529580 263760 927710 886980 991250 536960 628670 160015 FALSE TRUE 1474867.294 309316.5115 543381.2899 315930.9408 770018.1856 680992.3373 913553.2349 529762.9295 606044.2895 191366.8756 7.707014545 1.61635346 2.839474116 1.650917589 4.02377989 3.558569555 4.773831584 2.768310492 3.166923678 1 17.5459816 4.748971759 24.79164982 2.980845472 7.707017509 0.633563324 1.108618796 864.2957956 2058068.705 0.259717779 3.654842033 56101.14935 -4.748971759 4.726172038 DKDDDGGEDDDANCNLICGDEYGPETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKDDDGGEDDDANCNLICGDEYGPETR 27 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 231.21 3.41E-35 3404840000 2366450 1102572 1510405 1208213 2401740 2469890 2035230 1563171 1856271 1008032 FALSE TRUE 2459879.273 1291930.164 1549767.395 1447193.925 1993493.093 1896295.479 1875703.355 1542219.25 1789464.169 1205536.57 2.040484987 1.071664017 1.285541586 1.200456262 1.653614782 1.572988763 1.555907469 1.279280353 1.484371535 1 20.20124399 -0.461785516 10.28720696 1.000002378 1.437479355 0.214100376 0.261348432 0 0 0.23951332 0.056453831 0.345314237 0.461785516 0.437476977 DKDDELSFMEGAIIYVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKDDELSFMEGAIIYVIK 18 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 131.71 1.49E-05 68311000 471170 218610 352230 257500 459190 479370 511360 317750 363610 157830 FALSE TRUE 489772.1554 256154.567 361409.4032 308432.7314 381137.0478 368043.5824 471278.267 313491.081 350523.7471 188753.7667 2.594767586 1.357083207 1.914713595 1.634048088 2.019228832 1.949860863 2.496788675 1.660846756 1.857042396 1 17.52614591 0.530641342 1.456066891 1.000991612 1.941328773 0.394012206 0.353636622 2.130036769 5.508093113 0.317107038 0.0923247 3.393449124 -0.530641342 0.940337161 DKDDKISWEEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDDKISWEEYK 12 2 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 146.47 3.64E-05 1077780000 1544710 483640 805740 536100 1430000 1146990 1214050 763220 932790 325840 FALSE TRUE 1605696.344 566701.4078 826738.2463 642138.9799 1186929.111 880618.9553 1118889.589 752990.2843 899219.0701 389682.1094 4.120528771 1.454265911 2.121570958 1.647853377 3.045890694 2.259839325 2.871288062 1.93231936 2.307570834 1 18.57193817 0.299730629 0.901964394 0.990392773 2.404855479 0.256447648 0.731203609 3.936023135 3.911518086 0.745344443 0.216904795 1.994025139 -0.299730629 1.414462706 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 DKDDQEWES(0.249)PS(0.751)PPKPTVFISGVIAR;DKDDQEWES(0.048)PS(0.945)PPKPT(0.003)VFIS(0.003)GVIAR;DKDDQEWES(0.026)PS(0.96)PPKPT(0.014)VFISGVIAR;DKDDQEWES(0.028)PS(0.972)PPKPTVFISGVIAR;DKDDQEWES(0.006)PS(0.994)PPKPTVFISGVIAR;DKDDQEWES(0.045)PS(0.955)PPKPTVFISGVIAR 234.07 1.76E-38 17243080000 4452300 1371709 2240120 1446132 3575690 3707500 3531600 2211850 2830300 924733 TRUE FALSE 4628080.242 1607289.35 2298499.367 1732172.593 2967895.491 2846489.313 3254783.964 2182203.769 2728438.056 1105916.726 4.184836102 1.453354771 2.078365679 1.566277598 2.68365187 2.5738731 2.943064235 1.973208033 2.467127941 1 20.07681133 -0.3134343 1.030219248 0.97480468 2.382772146 0.249468099 0.741043773 30.38185545 21.36024467 3.974806064 0.210858976 0.485921036 0.3134343 1.407967467 DKDFAIDIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKDFAIDIIK 10 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 114.82 0.0011904 5653510000 15326490 8876390 13241610 9033170 19044490 15775750 16524650 12703590 13665600 8171890 FALSE TRUE 15931591.66 10400840.93 13586697.23 10819904.06 15807314.39 12112071.15 15229404.75 12533319.15 13173777.73 9773015.385 1.63016132 1.06424072 1.390225708 1.107120335 1.617444951 1.239338185 1.558311755 1.282441361 1.347974725 1 23.22037233 0.275059949 1.637401923 0.999964513 1.354220362 0.248458439 0.187560211 12.07628366 25.5915308 0.162202643 0.045900737 1.883909123 -0.275059949 0.354255849 DKDGLMYWYQLDQDHNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKDGLMYWYQLDQDHNVR 18 1 Q96T23-2;Q96T23;H0YER1;H7C306 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 122.49 2.16E-05 62637000 47286 65472 73235 60120 70102 90709 69880 65707 81439 72947 FALSE TRUE 49152.88779 76716.3067 75143.56426 72011.55656 58186.08708 69643.20946 64402.623 64826.30514 78508.0263 87239.568 0.563424246 0.879375133 0.861347276 0.825446047 0.666968996 0.798298422 0.738227211 0.743083748 0.899913057 1 16.41269501 1.048589109 3.640157435 0.998507147 0.765289669 0.441530278 0.088851279 0.180894007 5.102467176 0.08203126 0.021231955 11.18379271 -1.048589109 -0.233217478 DKDNFWMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDNFWMTR 9 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 181.53 4.32E-05 5568300000 3924100 3262000 4339500 3519800 5493900 4902900 4839500 4325200 4564500 3508900 FALSE TRUE 4079026.498 3822223.125 4452590.935 4216005.934 4560048.84 3764275.779 4460167.344 4267227.769 4400224.537 4196401.773 0.972029543 0.910833455 1.061049722 1.00467166 1.086656876 0.897024637 1.062855176 1.016877792 1.048570841 1 22.00072138 4.242251625 24.99999511 1.021931685 0.941431492 0.283530447 0.051364054 108.2460515 733144.184 0.011741726 0.029692682 17468.33955 -4.242251625 -0.080500193 DKDPILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKDPILR 7 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 112.94 0.005692 1492060000 1818930 2013900 2188770 2034210 2753650 2670870 2853620 2399640 2474950 1702690 FALSE TRUE 1890742.761 2359771.659 2245811.144 2436570.666 2285585.557 2050600.92 2629945.808 2367476.751 2385877.033 2036299.506 0.92851899 1.158852935 1.10288842 1.196567921 1.122421113 1.007023237 1.291531919 1.162636805 1.171672942 1 20.95751834 4.740908945 24.58508537 1.144516958 0.928518894 0.356608302 0.08222216 175.5606966 1837827.205 0.018741303 0.126812933 55069.22255 -4.740908945 -0.215998064 DKDPVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKDPVNK 7 1 P62851;E9PQK3;E9PK60 P62851 RPS25 40S ribosomal protein S25 0 70.919 0.05082 736270000 1098400 624940 860070 571060 1257100 1098100 1134200 938340 1029600 562050 FALSE TRUE 1141765.68 732268.5836 882484.1308 684013.9636 1043418.591 843082.9169 1045298.44 925763.0871 992544.8971 672172.9364 1.698618939 1.089405038 1.312882568 1.017616043 1.552306757 1.254264894 1.555103432 1.377269207 1.476621333 1 19.35847293 DKDTDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKDTDKFK 8 2 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 125.97 0.00069699 6504700000 20392600 6307500 11286000 6509200 20728800 14657300 17824100 11055000 13507000 5017800 FALSE TRUE 21197715.59 7390764.059 11580122.43 7796700.332 17205325.98 11253364.21 16427000.47 10906825.81 13020885.71 6000941.838 3.532398108 1.231600682 1.929717492 1.299246109 2.867104272 1.875266335 2.737403713 1.817519 2.169807017 1 22.51675752 4.756146393 24.36352639 1.953065641 3.532399959 0.41610137 0.581285348 2560.083409 3546685.595 0.130137759 3.895584648 57035.64966 -4.756146393 1.579334319 DKEAPCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKEAPCSR 8 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;H7BZT5;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 59.426 0.090012 325900000 70220 84693 86562 88248 102310 120200 89156 99856 96347 88907 FALSE TRUE 72992.33982 99238.36393 88817.87683 105703.191 84919.38274 92285.37165 82167.71975 98517.59365 92879.49029 106326.6244 0.68649165 0.933335037 0.835330542 0.99413662 0.798665275 0.867942269 0.772785934 0.926556205 0.873529944 1 16.69814337 -5 0.194920119 1.624654948 0.835276601 0.238070931 0.082320287 208.1974873 2.049690871 50.45760695 0.197507599 1.00E-05 5 -0.789378347 DKEDPQEMPHS(ph)PLGSMPEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKEDPQEMPHSPLGSMPEIR 20 1 Q9HB58;Q9HB58-6;G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7 Q9HB58 SP110 Sp110 nuclear body protein 1 DKEDPQEMPHS(1)PLGSMPEIR;DKEDPQEMPHS(1)PLGSMPEIR 211.71 1.48E-22 365200000 273279 200098 256619 218063 336951 320076 315759 263238 291073 157903 TRUE FALSE 284068.2659 234463.275 263306.702 261195.2105 279676.1894 245743.1998 291008.9845 259709.7252 280597.3396 188841.0696 1.504271642 1.241590484 1.394329647 1.383148333 1.481013584 1.301322855 1.541025928 1.375282007 1.485891497 1 17.52681303 -0.588940596 7.866216854 0.999998847 1.407632687 0.657921175 0.089071239 0 0 0.078804914 0.018574496 0.257667358 0.588940596 0.40763384 DKEDQWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKEDQWIR 8 1 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ;; 85.67 0.015119 672840000 765660 560810 675080 536470 685480 799370 741730 688600 731410 450320 FALSE TRUE 795888.848 657124.755 692673.1394 642582.1648 568962.3544 613728.4321 683591.2644 679370.4433 705086.697 538551.5821 1.47783216 1.220170503 1.286177893 1.193167351 1.056467706 1.139590807 1.269314374 1.261477017 1.309227789 1 19.03872501 DKEEIVICDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKEEIVICDR 10 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ;;; 131.69 0.00022199 1095570000 1364630 910290 1171260 964380 1583610 1512850 1546400 1153360 1246190 794790 FALSE TRUE 1418506.646 1066625.226 1201783.998 1155131.486 1314428.538 1161513.515 1425189.127 1137901.096 1201339.865 950513.8833 1.49235763 1.122156388 1.264351862 1.215270504 1.382860956 1.221984797 1.499388018 1.197143057 1.263884606 1 19.85834817 0.588527096 1.435462153 1.000528078 1.296693867 0.366110412 0.118110277 1.702877418 4.69739242 0.10422075 0.030481359 3.877279381 -0.588527096 0.296165789 DKEIS(ph)PSVTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKEISPSVTKK 11 2 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 DKEIS(0.53)PS(0.459)VT(0.011)KK;DKEIS(0.47)PS(0.47)VT(0.059)KK 99.566 0.0024416 317930000 1064380 359940 598410 322430 881500 779000 883270 585850 712140 236960 TRUE FALSE 1106402.544 421756.8951 614005.0562 386205.6916 731662.9449 598089.0559 814036.9894 577997.639 686510.2205 283387.7751 3.904199974 1.48826778 2.166660351 1.36281705 2.581843711 2.110497023 2.87251978 2.039599763 2.422511769 1 18.112418 -1.064589296 4.926996548 0.99996863 2.276794905 0.250744775 0.683432531 0.000215714 4.10E-05 0.604967124 0.142588627 0.086180836 1.064589296 1.276826275 DKELPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKELPR 6 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 74.439 0.073256 198680000 274000 217020 238200 205350 284550 291110 252150 218140 246680 218880 FALSE TRUE 284817.7316 254291.4968 244407.6877 245967.6171 236182.2926 223504.1143 232385.8241 215216.1901 237802.035 261765.3453 1.088065081 0.971448289 0.933690009 0.939649276 0.902267229 0.853833857 0.887763901 0.822172201 0.908454993 1 17.99791459 6.184241765 0.614737844 0.880437743 2.177075876 0.596011043 0.045899547 10.48583388 0.743503291 0.018615566 14.25745114 1528416.667 -6.184241765 1.296638133 DKELTGALIASLINCYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKELTGALIASLINCYIR 18 1 O75694;O75694-2 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 116.98 0.00013214 207682000 560160 506360 581790 505480 801500 747380 774240 653570 676740 504380 FALSE TRUE 582275.5493 593323.3911 596951.9253 605462.4353 665261.3163 573812.3217 713553.0457 644809.9632 652384.2596 603203.6041 0.965305156 0.983620434 0.989635873 1.003744724 1.102880208 0.95127469 1.182938963 1.068975647 1.08153243 1 19.20228552 3.429556651 0.983361464 1.077981799 0.967767728 0.284511637 0.058931912 0.653623215 1.309534226 0.022884104 0.047997533 2688.788557 -3.429556651 -0.11021407 DKENALMPNWLHLPVGYHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKENALMPNWLHLPVGYHGR 20 1 P16930;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 184.7 2.52E-17 1254770000 1027640 853410 1012800 847800 1319450 1323060 1174380 1056710 1123750 765890 FALSE TRUE 1068212.021 999976.5289 1039194.4 1015492.31 1095170.36 1015799.366 1082329.027 1042546.531 1083306.457 915951.4817 1.166232101 1.09173526 1.134551798 1.108674782 1.195664162 1.109010015 1.181644496 1.138211523 1.182711616 1 19.80491165 DKEPEVVFIGDS(ph)LVQLMHQCEIWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 1 DKEPEVVFIGDS(1)LVQLMHQCEIWR 219.24 6.67E-33 25262000 31300 22726 27013 23800 35961 31071 35665 31117 30581 18837 TRUE FALSE 32535.74817 26629.01372 27716.98097 28507.56896 29848.36206 23855.23114 32869.48411 30699.92751 29480.39578 22527.74949 1.44425204 1.182053881 1.230348419 1.265442381 1.324959782 1.058926509 1.459066478 1.362760515 1.30862587 1 14.45941558 DKEPEVVFIGDSLVQLMHQCEIWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKEPEVVFIGDSLVQLMHQCEIWR 24 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;; 209.16 3.36E-25 2859723000 648487 427704 619315 501598 832346 749841 788946 634925 706585 386687 FALSE TRUE 674089.7675 501158.8349 635454.8577 600812.5873 690864.1242 575701.7917 727106.351 626414.8689 681155.1439 462450.9141 1.457646092 1.083701685 1.374102285 1.299192128 1.493918821 1.244892753 1.57228871 1.354554289 1.472924203 1 18.81894072 4.087771431 24.48768236 1.374000617 1.260228319 0.020420896 0.172087314 47.0495578 13116.03191 0.038492627 0.083153605 12239.71854 -4.087771431 -0.113772298 DKEQWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKEQWK 6 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 79.469 0.061166 210680000 575180 285450 439800 362310 541530 553530 648550 423830 470600 186760 FALSE TRUE 597888.5505 334473.817 451261.5493 433973.8366 449480.924 424981.0463 597714.9563 418149.2521 453663.1979 223352.0463 2.676888618 1.497518481 2.020404813 1.94300363 2.012432532 1.902740778 2.676111396 1.872153218 2.031157563 1 17.76895995 0.351006149 1.815518712 1.000023784 2.060838198 0.472294221 0.339554275 6.899754025 18.22775489 0.302922619 0.084494978 2.243913692 -0.351006149 1.060814414 DKEVANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKEVANR 7 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 92.439 0.01429 246050000 369640 263100 380410 302440 441020 442860 425170 346370 418800 292720 FALSE TRUE 384233.6726 308285.3784 390323.7971 362261.7293 366055.5779 340012.4766 391844.0644 341727.4767 403727.4698 350072.8795 1.097581947 0.880631995 1.11497868 1.034818035 1.045655346 0.971261976 1.119321397 0.976160956 1.153266915 1 18.41729577 2.256153329 24.99818402 1.053307967 1.023221297 0.049301294 0.077949439 991.7635115 1409231.373 0.025412781 0.021215869 180.3654414 -2.256153329 -0.030086669 DKEVEFGGPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKEVEFGGPAPR 12 1 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 ; 69.92 0.044393 451750000 613350 604620 623000 514880 744900 734290 600100 679400 652480 611510 FALSE TRUE 637565.5316 708458.7817 639235.8918 616721.7272 618282.1641 563762.2758 553062.5939 670293.7543 628997.3723 731323.6764 0.871796651 0.968734918 0.874080674 0.843295174 0.84542889 0.770879289 0.75624872 0.916548685 0.86008069 1 19.48015054 4.027687751 8.719137019 0.847717185 0.920790458 0.111936876 0.068611962 0.44163911 123.1805074 0.016744346 0.035972641 10658.29535 -4.027687751 0.073073274 DKEVS(ph)DDEAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKEVSDDEAEEK 12 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK;DKEVS(1)DDEAEEK 188.44 2.42E-05 1300770000 3832390 817729 1224164 1044257 2272509 3314320 2868293 1426294 1594964 470083 TRUE FALSE 3983695.716 958167.5947 1256066.72 1250807.918 1886228.732 2544619.409 2643468.7 1407176.862 1537561.557 562186.7636 7.086071702 1.704358154 2.234251677 2.224897488 3.355163896 4.526288369 4.702118355 2.50304161 2.734965774 1 19.10068996 4.749308109 24.55187967 2.929607038 7.086074753 0.573068876 1.108913182 954.5809183 2180617.251 0.275025487 3.970524237 56144.61517 -4.749308109 4.156467715 DKFEEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKFEEDR 7 1 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 108.98 0.0065041 716800000 1650280 1070110 1399300 1271710 1884580 1851270 1817530 1363980 1546570 838780 FALSE TRUE 1715434.329 1253893.068 1435766.908 1523250.442 1564239.765 1421340.599 1675067.249 1345698.079 1490909.248 1003122.882 1.710093908 1.249989499 1.431297136 1.518508321 1.559370037 1.416915739 1.669852498 1.341508706 1.486267809 1 19.93606691 -0.035962897 0.897037549 0.99180628 1.485861122 0.550698751 0.132088657 5.055368275 3.688089453 0.258062065 0.039150194 0.920528211 0.035962897 0.494054842 DKFEPGILQLSQWFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKFEPGILQLSQWFK 15 1 G3V3Y1;Q8N8N7;G3V2R9 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 ; 140.02 4.57E-06 393660000 875100 611370 820730 622030 1201280 1040220 931320 859510 940670 700340 FALSE TRUE 909649.6237 716368.0417 842118.898 745065.6774 997086.8547 798644.6697 858320.7048 847989.6743 906815.4704 837558.2142 1.086073312 0.855305374 1.005445214 0.889568826 1.190468719 0.953539296 1.024789311 1.012454609 1.082689484 1 19.67582994 DKFNECGHVLYADIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKFNECGHVLYADIK 15 1 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 147.24 2.25E-06 4008570000 5933890 3091770 4432560 2941230 6526410 5460780 5380570 4493460 5156920 2690150 FALSE TRUE 6168164.559 3622757.447 4548076.155 3522996.515 5417053.159 4192596.604 4958826.864 4433232.519 4971323.457 3217233.386 1.91722633 1.126047449 1.413660623 1.095039151 1.683761328 1.303168313 1.541332651 1.377964228 1.545216918 1 21.61738917 -1.548247832 5.58238982 0.99871458 1.427467705 0.241156823 0.234911583 0.003378175 0.000273377 0.204455864 0.048059422 0.028297767 1.548247832 0.428753125 DKFPEVIINFPDPAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKFPEVIINFPDPAQK 16 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 98.796 0.003112 0 634340 390630 544120 365770 715450 697550 670660 538390 579230 319260 FALSE TRUE 659384.233 457717.6638 558300.2142 438118.2143 593838.0646 535554.584 618091.9168 531173.7627 558383.6254 381812.8844 1.726982666 1.19880099 1.462235134 1.147468386 1.555311748 1.402662419 1.618834623 1.39118868 1.462453595 1 18.54250626 -1.292913145 5.794530949 0.999965425 1.432514362 0.386242401 0.166360392 6.79E-05 8.28E-06 0.147156605 0.03468238 0.050943274 1.292913145 0.432548937 DKFQETSDEFEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKFQETSDEFEAAR 14 1 G8JLG1;Q14683;V9GY57 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 ; 188.44 7.60E-07 834560000 532040 403880 532620 436450 673410 654640 564380 522900 600630 426970 FALSE TRUE 553045.35 473243.2482 546500.5148 522778.5073 558944.0087 502609.7812 520142.4209 515891.3808 579013.4436 510626.5967 1.083071962 0.926789265 1.070254699 1.023798037 1.094623767 0.984300043 1.018635583 1.010310439 1.133927311 1 18.96190916 DKFS(ph)PFPVQDRPESSLVFK ddPTM_MDA-MB-175_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 152.35 4.46E-08 1393870000 1247010 586590 841530 607470 1155030 1121710 1077810 897210 953830 520890 TRUE FALSE 1296242.918 687332.2695 863460.9631 727625.7529 958698.4132 861209.8522 993328.4359 885184.3675 919501.8446 622948.4225 2.080819007 1.103353415 1.386087406 1.168035309 1.538969164 1.382473767 1.594559678 1.420959321 1.476048115 1 19.24875319 -1.211489993 3.980393096 0.999677437 1.443807567 0.228245951 0.252622212 105.8849886 61156671.21 35816.08939 0.053963701 0.061448319 1.211489993 0.44413013 DKFSFDLGK ddPTM_MDA-MB-175_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 9170300000 16175300 8676800 11805100 10874700 15783600 14868100 19748200 13174400 13432800 6085400 FALSE TRUE 16813913.33 10166972.9 12112750.6 13025683.2 13100709.31 11415209.1 18200284.48 12997818.72 12949356.15 7277717.618 2.3103278 1.397000191 1.664361169 1.789803327 1.800112343 1.56851498 2.50082312 1.785974587 1.779315554 1 22.79505464 DKFSFDLGKGEVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKFSFDLGKGEVIK 14 2 Q02790;F5H1U3 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 155.92 3.21E-06 1637800000 2119900 960500 1902700 1157400 2820900 2070700 2216000 1736900 2346300 976980 FALSE TRUE 2203595.289 1125458.403 1952285.925 1386330.266 2341404.426 1589811.307 2042304.13 1713619.696 2261857.121 1168400.526 1.885993065 0.963247088 1.670904696 1.186519721 2.003939894 1.360673221 1.747948657 1.466637218 1.935857672 1 20.15610348 5.053675076 21.30903262 1.510193795 7.118762776 0.104665766 0.345803009 1148.862083 471939.8895 0.072287573 10245.02553 113155.3458 -5.053675076 5.608568982 DKGETIQGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKGETIQGLR 10 1 F5H0D0;Q14232-2;Q14232;H0YGG4 F5H0D0;H0YGG4 EIF2B1 Translation initiation factor eIF-2B subunit alpha 0 ;; 96.229 0.0062769 922130000 1136760 833300 1012990 884500 1279960 1305810 1284020 1040850 1112590 825420 FALSE TRUE 1181640.163 976412.7928 1039389.352 1059451.46 1062392.856 1002555.417 1183375.157 1026899.108 1072548.103 987145.2454 1.197027659 0.989127788 1.052924437 1.073247797 1.076227497 1.015610845 1.198785247 1.040271544 1.086514987 1 19.91290285 DKGEYTLVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKGEYTLVVK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 141.73 3.38E-05 719690000 1862910 1288060 1717130 1176530 2307460 2146860 2083290 1806620 2037990 1322880 FALSE TRUE 1936459.125 1509274.285 1761879.818 1409244.122 1915238.773 1648284.301 1919996.286 1782405.214 1964643.138 1582073.008 1.224001115 0.953985232 1.113652663 0.890757958 1.210588111 1.041850972 1.213595249 1.126626398 1.241815724 1 20.59338475 DKGFGFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKGFGFIR 8 1 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 93.178 0.010263 595070000 940810 887380 939880 853740 2139500 1586200 1494900 1232800 1323800 1744400 FALSE TRUE 977953.9053 1039780.612 964374.0449 1022607.224 1775828.554 1217829.089 1377725.832 1216276.332 1276156.697 2086181.781 0.468776937 0.498413236 0.462267504 0.490181265 0.851233852 0.583759814 0.660405457 0.583015509 0.611718839 1 20.99243344 -5 0.127835817 2.351826781 0.40237608 0.640861547 0.100569763 98.61749418 0.800647804 34.46089672 0.837139016 1.00E-05 5 -1.949450702 DKGLQTSQDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DKGLQTSQDAR 11 1 P27797 P27797 CALR Calreticulin 0 ;;;;; 164.68 2.05E-05 3010480000 8328390 7750060 7986840 8139510 10468390 11022560 9187130 8281500 8522070 6581570 FALSE TRUE 8657201.268 9081072.518 8194983.612 9749480.784 8688976.807 8462737.489 8467018.745 8170500.038 8215362.365 7871102.63 1.099871476 1.153723048 1.041148108 1.238642315 1.103908463 1.075165436 1.075709356 1.038037543 1.043737168 1 22.90813432 2.109737535 1.024108208 1.020358543 1.129580249 0.446316646 0.048284432 0.493390655 0.964408071 0.035524836 0.018080932 128.7471235 -2.109737535 0.109221706 DKGQKS(ph)PAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKGQKSPAEQK 11 2 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 DKGQKS(1)PAEQK;DKGQKS(1)PAEQK;DKGQKS(1)PAEQK 118.21 0.00039187 577470000 2515600 642290 1246110 549980 2049710 1686420 1742570 1278940 1534070 549500 TRUE FALSE 2614917.83 752598.3112 1278584.65 658764.4025 1701301.026 1294774.513 1605982.81 1261797.901 1478859.12 657164.0042 3.979094737 1.145221446 1.945609684 1.00243531 2.588853034 1.970245638 2.443808242 1.920065453 2.250365374 1 19.32589393 5.923222492 15.28536778 2.022509037 2.029467003 0 0.851659144 0 0 0.170187256 0 837958.4643 -5.923222492 0.006957966 DKGS(ph)PAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKGSPAVK 8 1 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 DKGS(1)PAVK;DKGS(1)PAVK;DKGS(1)PAVK;DKGS(1)PAVK 75.045 0.023865 970330000 2884890 1216330 1777200 1069040 2441910 2421690 2557180 1889850 2202640 962430 TRUE FALSE 2998787.685 1425225.216 1823515.292 1280492.921 2026835.01 1859289.199 2356741.55 1864519.652 2123367.417 1150999.732 2.605376528 1.238249825 1.584288199 1.112504969 1.76093439 1.615368924 2.047560468 1.619913194 1.844802703 1 20.13445607 DKHIEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 ;; 110.53 0.0020473 970450000 1989210 1746340 2078790 1735550 2421620 2504450 2365490 2090080 2082380 1669630 FALSE TRUE 2067745.547 2046260.31 2132964.975 2078836.61 2009993.897 1922829.443 2180076.713 2062065.896 2007435.551 1996762.032 1.035549311 1.024789273 1.068211906 1.041103836 1.006626661 0.962973761 1.091805973 1.032704881 1.005345414 1 20.92923098 3.362445741 8.814876058 1.02188508 1.043275769 0.120329321 0.032381525 0.718489345 52.49451982 0.009387849 0.012715599 2303.805129 -3.362445741 0.02139069 DKHIEEVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DKHIEEVRK 9 2 P16949 P16949 STMN1 Stathmin 0 ;;;; 106.29 0.0017775 2065685000 4778230 3090850 4293190 2818200 5981230 5036420 4971100 4377750 4999120 3065800 FALSE TRUE 4966878.21 3621679.444 4405074.058 3375631.549 4964542.661 3866787.783 4581452.192 4319073.422 4819202.648 3666484.812 1.354670336 0.987779748 1.201443422 0.920672448 1.354033336 1.054630793 1.249548935 1.177987539 1.314393185 1 21.80596613 3.223059134 24.99205826 1.196622857 1.113065689 0.058122982 0.148160011 650.3454261 1048508.992 0.039173442 0.046980049 1671.318169 -3.223059134 -0.083557168 DKHKEEDKNS(ph)ER ddPTM_MDA-MB-175_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 1 DKHKEEDKNS(1)ER 66.797 0.040741 37131000 86941 18348 29206 17441 51664 47505 44511 25231 32456 8698.1 TRUE FALSE 90373.49781 21499.12627 29967.13235 20890.77774 42882.17173 36472.6837 41022.11151 24892.81971 31287.9149 10402.32616 8.687816208 2.066761409 2.880810685 2.008279439 4.122363698 3.506204587 3.943551748 2.393005116 3.007780608 1 13.34461856 4.743516149 24.99687859 2.888287334 8.687818594 0.791039759 0.910655703 221.4157357 1116837.246 0.207922654 1.727983595 55400.81435 -4.743516149 5.79953126 DKHKEEDKNSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKHKEEDKNSER 12 3 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 218.5 2.05E-11 673880000 621280 226325 379530 196066 605630 520551 518740 343093 444514 182755 FALSE TRUE 645808.6141 265194.5582 389420.8636 234847.2696 502685.2289 399660.9193 478079.8033 338494.3995 428516.028 218562.3432 2.954802756 1.213358872 1.781738143 1.074509296 2.299962663 1.828590019 2.187384141 1.548731564 1.960612344 1 17.73768533 -1.260894439 5.483056114 0.999926411 1.830559264 0.200799117 0.516029349 0.000424354 5.72E-05 0.456747237 0.107646914 0.054841025 1.260894439 0.830632853 DKIIVNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DKIIVNDR 8 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;; 132.78 0.00086424 3236560000 4985550 4350290 5207800 4223520 6353070 6213370 5357480 5179070 5416880 4445720 FALSE TRUE 5182383.364 5097418.467 5343519.546 5058919.65 5273177.431 4770408.982 4937546.718 5109653.038 5221927.547 5316773.716 0.974723327 0.95874279 1.005030462 0.951501779 0.991800237 0.897237542 0.928673474 0.961043917 0.982160954 1 22.34211964 4.744879473 21.33862815 0.960875396 0.974723379 0.001389873 0.031731698 568.3068001 1918688.296 0.007617763 0.065221186 55575.00026 -4.744879473 0.013847983 DKITRPGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKITRPGAK 9 2 Q9UBS4;H7C2Y5 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 63.283 0.043353 747700000 125560 76534 97999 87448 147670 204590 174520 150240 144180 128410 FALSE TRUE 130517.2058 89678.11915 100552.9344 104744.9534 122569.1061 157077.0731 160840.6664 148226.2785 138990.99 153569.4809 0.849890258 0.583957949 0.654771598 0.682068812 0.798134534 1.022840425 1.047347854 0.965206613 0.905069087 1 17.22853201 2.937413324 3.083212651 0.988887168 0.683602748 0.790942341 0.071917213 0.109519836 2.053273655 0.022752922 0.025324572 865.7915116 -2.937413324 -0.30528442 DKKS(ph)PLIESTANMDNNQSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKKSPLIESTANMDNNQSQK 20 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 DKKS(0.333)PLIES(0.333)T(0.333)ANMDNNQSQK;DKKS(1)PLIESTANMDNNQSQK 182.02 2.55E-17 326880000 390750 140591 220392 118198 383740 330200 333440 235810 314690 111683 TRUE FALSE 406177.1117 164736.4106 226135.5966 141577.2116 318512.0119 253516.0542 307304.1015 232649.3527 303364.3684 133565.1455 3.041041209 1.233378738 1.693073411 1.059986204 2.38469408 1.898070437 2.300780643 1.741841793 2.271283928 1 17.02718405 3.178400548 24.99999129 1.976991779 1.714856305 0.014410733 0.615924436 267.6189065 111209.277 0.167406715 0.20008938 1507.997243 -3.178400548 -0.262135474 DKLCGPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLCGPYEK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 87.363 0.012323 314410000 365770 291809 321840 247088 729760 571490 510450 425710 517780 433690 FALSE TRUE 380210.882 341924.9258 330227.4148 295961.2689 605715.6559 438770.1085 470439.5952 420004.0538 499145.1989 518663.252 0.733059226 0.659242629 0.636689439 0.57062317 1.16783993 0.845963362 0.907023186 0.809781785 0.962368545 1 18.98443863 3.262947527 24.99998722 0.923176601 0.649626756 0.6782917 0.099920868 145.5004594 149157.2383 0.027729038 0.03752783 1832.09305 -3.262947527 -0.273549846 DKLCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKLCSK 6 1 Q9Y2B0;F8VXJ7;F8W031;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 73.931 0.074476 351540000 780630 687830 798490 633670 1259500 1055600 975910 847640 987440 709180 FALSE TRUE 811449.8752 805959.4519 819299.3054 759008.0347 1045410.64 810452.8978 899415.6241 836278.7723 951902.2273 848130.2429 0.956751492 0.95027793 0.966006474 0.894919196 1.232606252 0.955575991 1.060468757 0.986026355 1.122353831 1 19.6939263 DKLEEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLEEILR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 98.048 0.0071125 534830000 425610 288620 380360 266820 569320 494240 466730 357660 404020 310250 FALSE TRUE 442413.4114 338188.2398 390272.4941 319596.1996 472547.1898 379460.2503 430146.483 352866.1527 389479.3991 371037.5474 1.192368305 0.911466352 1.051840971 0.861358107 1.273583208 1.022700406 1.159307154 0.951025456 1.049703465 1 18.50120566 4.77788488 22.97800045 1.034381256 1.192369549 0.155256351 0.112550191 16008.26684 9353410.639 0.025439149 7.004947338 59963.21081 -4.77788488 0.157988293 DKLESEMEDAYHEHQANLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DKLESEMEDAYHEHQANLLR 20 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 335.29 3.53E-80 4942390000 1940314 1428618 1809328 1372500 2436187 2314800 2298520 1873972 2008177 1277806 FALSE TRUE 2016919.095 1673972.028 1856480.574 1643976.403 2022084.804 1777222.781 2118355.996 1848854.471 1935903.102 1528167.621 1.319828445 1.095411266 1.21484093 1.075782775 1.323208774 1.162976337 1.38620657 1.209850572 1.266813323 1 20.54337137 3.230260216 24.99956325 1.241549041 1.173417312 0.028621781 0.115120115 479.7650866 1444976.297 0.030298576 0.036793347 1699.261493 -3.230260216 -0.068131729 DKLFDQR ddPTM_MDA-MB-175_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 ;;;; 76.679 0.036576 5664710000 18389700 15386700 17982800 14580400 25070900 22884700 20751500 18555900 19904700 16038800 FALSE TRUE 19115739.56 18029246.03 18451446.54 17464359.6 20809357.37 17570075.25 19124943.21 18307188.51 19188333.74 19181295.78 0.996582284 0.939938899 0.961949951 0.910489041 1.084877561 0.916000433 0.997062108 0.954429186 1.000366918 1 24.19319685 DKLGERDDTIPPEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKLGERDDTIPPEYR 15 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;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 60.246 0.055725 149600000 110380 80602 103670 76869 136020 137000 112350 111680 109980 89446 FALSE TRUE 114737.8876 94444.7665 106371.7254 92073.45877 112899.369 105183.8263 103543.7134 110183.1123 106021.8413 106971.2312 1.072605096 0.882898752 0.994395635 0.860731037 1.055418057 0.983290789 0.967958509 1.030025653 0.991124811 1 16.70686332 3.206800618 24.99999783 1.004261154 0.950655849 0.157131712 0.058899507 333.2769988 262339.3073 0.015773702 0.01885479 1609.906366 -3.206800618 -0.053605305 DKLIQDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKLIQDSR 8 1 O00429-3 O00429-3 DNM1L Dynamin-1-like protein 0 63.419 0.066971 176990000 503350 464070 528480 439610 692280 693210 621880 569590 634450 519240 FALSE TRUE 523222.6467 543770.4125 542252.623 526563.5459 574606.4929 532222.4832 573135.4206 561955.5777 611616.2684 620975.1365 0.84258228 0.875671795 0.873227592 0.847962366 0.925329307 0.857075351 0.922960336 0.904956647 0.984928755 1 19.24417598 1.377008071 0.752171501 1.005456606 0.867357077 0.768546472 0.02520214 0.263323503 0.329147909 0.022032616 0.009140872 23.82363743 -1.377008071 -0.138099529 DKLNNLVLFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLNNLVLFDK 11 1 P62851 P62851 RPS25 40S ribosomal protein S25 0 ; 178.58 6.82E-06 6445500000 8150500 5252300 7219900 5425300 10271200 8729300 9019500 7547200 7873900 4892100 FALSE TRUE 8472288.034 6154341.668 7408056.525 6498408.147 8525305.093 6702052.369 8312528.022 7446042.129 7590519.877 5850613.33 1.448102542 1.051913931 1.266201697 1.110722548 1.457164337 1.145529877 1.420796001 1.272694282 1.297388744 1 22.48015644 DKLPLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKLPLEK 7 1 Q92831 Q92831 KAT2B Histone acetyltransferase KAT2B 0 ;; 109.21 0.0064555 2019080000 3078120 1522320 2372870 1448110 3797480 2938590 2971270 2389930 3074460 1563130 FALSE TRUE 3199646.554 1783766.618 2434708.942 1734541.836 3151985.706 2256147.007 2738374.093 2357896.897 2963810.785 1869395.396 1.711594327 0.9541944 1.302404482 0.927862474 1.686098999 1.206885934 1.464844783 1.261315238 1.585438154 1 20.83414031 3.245601099 24.99994469 1.371417752 1.210340541 0.061860114 0.271263361 436.820314 1551088.864 0.069342384 0.091922126 1760.358408 -3.245601099 -0.161077212 DKLPNYEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLPNYEEK 9 1 Q9BV57;Q9BV57-2 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 ; 110.66 0.0020526 221400000 623020 339500 504700 364060 526870 613940 624490 523920 601160 263620 FALSE TRUE 647617.3107 397806.4841 517852.8966 436069.9814 437312.8256 471361.7394 575540.842 516897.7094 579524.369 315271.2917 2.05415884 1.261791018 1.642562803 1.383157912 1.387100054 1.49509883 1.825541548 1.639533072 1.838176784 1 18.26623428 4.75937843 24.27652312 1.534233851 2.0541596 0.305873716 0.246109601 4495.543259 5242316.312 0.056418498 2.374187608 57461.69471 -4.75937843 0.51992575 DKLSELQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLSELQLR 9 1 Q9BVK6 Q9BVK6 TMED9 Transmembrane emp24 domain-containing protein 9 0 ; 154.24 6.95E-05 1457270000 1109790 990010 1140870 1352630 2752700 2108070 1972660 1231620 1327590 1730740 FALSE TRUE 1153605.366 1160036.516 1170602.009 1620176.177 2284797.037 1618502.691 1818037.755 1215112.148 1279810.295 2069845.366 0.557338913 0.560445981 0.565550465 0.782752279 1.103849145 0.781943771 0.878344723 0.587054554 0.618312033 1 20.98109156 3.726691371 5.736776359 0.805675251 0.559754211 0.395693758 0.146843672 0.191519948 24.70333211 0.042114432 0.069792943 5329.560187 -3.726691371 -0.24592104 DKLSGEYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKLSGEYEK 9 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 131.12 0.00031205 5468500000 4745670 2764920 3988960 2826200 5592630 4885350 4876230 4130130 4621970 2501800 FALSE TRUE 4933032.716 3239773.502 4092915.575 3385213.925 4641996.75 3750801.501 4494018.351 4074772.363 4455626.203 2991979.81 1.648752007 1.082819306 1.367962297 1.131429401 1.551479971 1.253618587 1.502021616 1.361898349 1.48918993 1 21.51266901 3.240908945 24.99681793 1.38118281 1.295976527 0.007472935 0.204782286 232.4829981 2474639.093 0.052421844 0.067708733 1741.441721 -3.240908945 -0.085206283 DKLTELQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKLTELQLR 9 1 Q7Z7H5-3;Q7Z7H5;Q7Z7H5-2 Q7Z7H5-3 TMED4 Transmembrane emp24 domain-containing protein 4 0 ; 157.78 6.18E-05 366510000 112969 306880 258850 335080 403860 431310 278770 289850 240660 463550 FALSE TRUE 117429.1034 359584.2528 265595.8436 401357.8239 335212.0215 331144.7891 256919.279 285965.0348 231998.6936 554373.7473 0.211822988 0.648631459 0.479091669 0.723984182 0.604667921 0.597331296 0.463440558 0.515834374 0.418487879 1 19.08049941 -1.765151419 2.703656177 1.109211829 0.528564729 0.532749405 0.135062346 16545856.86 12422260.99 11985255.56 0.032548054 0.017173095 1.765151419 -0.5806471 DKMMNGGHYTYSENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKMMNGGHYTYSENR 15 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 147.1 2.26E-06 89518000 50947 78597 89046 76225 103830 121460 85146 85183 82347 87750 FALSE TRUE 52958.4269 92095.42335 91366.61191 91302.07749 86181.01369 93252.75574 78472.03403 84041.26122 79383.34756 104942.9324 0.504640243 0.877576233 0.870631397 0.87001645 0.821217891 0.88860444 0.747759113 0.800828215 0.756443009 1 16.67924548 -4.745322731 0.021163182 1.97648091 3.32E-06 0.234021845 0.108672403 5436.122809 9.061331798 572.8665483 310.2994655 1.80E-05 4.745322731 -1.976477587 DKNEQAFEEVFQNANFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKNEQAFEEVFQNANFR 17 1 P27694;I3L4R8 P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit;Replication protein A 70 kDa DNA-binding subunit, N-terminally processed" 0 ; 249.18 5.03E-21 404130000 711940 439040 642620 554600 673470 770680 854970 625470 680010 389750 FALSE TRUE 740047.9409 514441.7047 659367.2051 664298.2247 558993.81 591701.2498 787955.2174 617086.5977 655536.5729 466114.0503 1.587697132 1.103682038 1.414604869 1.425183867 1.199264021 1.269434486 1.690477292 1.323896152 1.40638664 1 18.83032348 5.078793257 9.308765582 1.342832161 2.913224632 0.150681267 0.183824806 13781.74654 72837.2627 0.041624902 374046.4619 119892.8425 -5.078793257 1.570392471 DKNESLTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKNESLTMR 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 131.82 0.00029406 690340000 777790 597380 742630 621370 989950 922720 820690 758820 766760 561140 FALSE TRUE 808497.7498 699975.368 761983.5479 744275.1314 821678.6526 708432.264 756362.1733 748649.2591 739164.4574 671084.6393 1.204762712 1.043050797 1.135450736 1.109062982 1.224403904 1.055652629 1.127074186 1.115580979 1.101447439 1 19.35613521 -0.232472691 0.511185119 0.983872214 1.129569504 0.347786156 0.05272401 6.685577028 1.8040499 0.254408826 0.023569628 0.585500552 0.232472691 0.145697289 DKNNMQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DKNNMQHR 8 1 P31942;P31942-3;P31942-2;P31942-4 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;;;;;; 182.69 0.00013653 1207461000 1627752 1441512 1634220 1267174 2048381 1959883 1882128 1699319 1710980 1588018 FALSE TRUE 1692016.906 1689080.473 1676809.116 1517817.235 1700197.929 1504729.876 1734601.889 1676542.408 1649402.164 1899159.723 0.890929228 0.889383053 0.882921587 0.799204626 0.895236935 0.792313494 0.913352294 0.882781152 0.868490493 1 20.85692981 -0.282496176 0.627791131 1.011142484 0.864496231 0.515887536 0.038297236 5.961811636 2.135577207 0.197268897 0.014412663 0.521799699 0.282496176 -0.146646254 DKNSIYSGLEAFGDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKNSIYSGLEAFGDVK 16 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 140.16 1.58E-06 266480000 472580 226790 397790 288560 461860 501310 487530 425090 451410 222170 FALSE TRUE 491237.8233 265739.4183 408156.7342 345636.3067 383353.2022 384888.3499 449316.1247 419392.3639 435163.8423 265699.9578 1.84884419 1.000148515 1.536156564 1.300851944 1.442804904 1.448582654 1.691065849 1.578443472 1.637801699 1 18.01943847 2.463453622 24.37262555 1.54082647 1.405748118 0 0.26760275 548.0775771 977343.6491 0.084875046 0.071049442 290.7057499 -2.463453622 -0.135078352 DKNSVNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKNSVNFK 8 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 138.08 0.00065725 1851480000 2432030 1568550 2087810 1501030 2870530 2320180 2516590 1999930 2297780 1334960 FALSE TRUE 2528048.422 1837936.261 2142220.044 1797929.254 2382598.336 1781353.358 2319333.1 1973124.21 2215083.347 1596519.853 1.583474467 1.15121416 1.341806079 1.126155275 1.492370002 1.115772757 1.452743037 1.235890807 1.387444912 1 20.60649906 -1.006622937 3.848034926 0.999954619 1.309910398 0.278053538 0.154167983 15857807.5 34572144.32 10215.63328 0.032470052 0.098486581 1.006622937 0.309955779 DKPAQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DKPAQIR 7 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;; 144.38 0.0021508 5007810000 5661680 4845800 5543810 4593280 7063300 6982840 6436700 5781450 5997330 4687710 FALSE TRUE 5885207.498 5678028.455 5688286.243 5501817.074 5862682.789 5361181.236 5932174.635 5703959.119 5781487.265 5606177.023 1.04977197 1.012816476 1.014646205 0.981384828 1.045754132 0.956298956 1.058149718 1.01744185 1.031270907 1 22.41858587 DKPEEQWWNAEDSEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKPEEQWWNAEDSEGKR 17 2 P46108-2;P46108 P46108-2 CRK Adapter molecule crk 0 ;;; 209.73 2.26E-12 1415160000 1124810 507547 797580 529343 1098080 949530 1105270 752770 965940 382168 FALSE TRUE 1169218.367 594714.2491 818365.59 634045.4655 911428.7538 729016.0478 1018636.049 742680.3494 931176.0081 457046.5026 2.558204386 1.301211684 1.790552133 1.387266858 1.994170722 1.595058804 2.228736121 1.624955766 2.037376947 1 18.80198144 -0.481373624 10.12572405 0.999974088 1.806287612 0.316295447 0.366192635 0 0 0.317489097 0.074832898 0.330085446 0.481373624 0.806313523 DKPHNIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKPHNIFK 8 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 122.28 0.00083947 2107220000 4044400 2796600 3693300 3078500 5674400 4884900 4907800 3853800 4419800 3145400 FALSE TRUE 4204076.035 3276894.295 3789550.432 3687418.112 4709867.515 3750456.006 4523113.812 3802146.115 4260732.261 3761680.908 1.117605703 0.871125004 1.007408795 0.980258082 1.252064604 0.997015988 1.20241826 1.010757214 1.132667115 1 21.84294604 DKPLELWDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKPLELWDVR 10 1 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 ; 67.153 0.05821 362380000 611130 494590 599530 486300 835250 749740 719070 580860 656400 459960 FALSE TRUE 635257.8843 579531.9851 615154.2443 582488.6885 693274.5033 575624.2474 662707.4145 573074.5218 632776.2922 550080.3555 1.154845611 1.053540595 1.118298878 1.058915634 1.260314964 1.046436655 1.204746557 1.041801468 1.150334285 1 19.06928286 -1.34987322 4.134063462 0.999759554 1.117134283 0.210915606 0.06986352 0.000139675 2.20E-05 0.06102502 0.014354345 0.044681401 1.34987322 0.117374728 DKPLKDVIIADCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKPLKDVIIADCGK 14 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 134.44 2.18E-05 5142500000 3395530 1891040 2380180 1556390 3789320 3029930 2047040 2043870 2915550 1658030 FALSE TRUE 3529588.146 2215811.41 2442209.446 1864239.297 3145212.74 2326274.677 1886587.656 2016475.266 2810619.925 1982889.234 1.780022851 1.117466055 1.231641891 0.940163104 1.58617672 1.173174294 0.951433708 1.016937927 1.417436676 1 20.91917266 4.740572085 24.53951338 1.153057123 1.780023132 0.468258909 0.198309587 122.6890228 1496639.883 0.046808147 0.306531432 55026.52469 -4.740572085 0.626966009 DKPSGDTAAVFEEGGDVDDLLDMI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKPSGDTAAVFEEGGDVDDLLDMI 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 174.7 2.35E-12 65033000 231908 186452 231663 194378 300061 283759 284516 236379 273510 189497 FALSE TRUE 241063.9069 218473.6806 237700.3281 232825.3882 249056.7384 217860.2727 262214.8925 233210.7261 263666.4285 226625.309 1.063711321 0.96403037 1.048869295 1.027358283 1.098980248 0.961323665 1.157041522 1.029058613 1.163446526 1 17.78994946 3.002943201 0.821014741 1.078233866 1.018159816 0.083346852 0.06465436 1.398287616 2.095592745 0.034289403 0.044239435 1006.799986 -3.002943201 -0.06007405 DKPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DKPSLR 6 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ;;;;;; 128.57 0.015113 4083250000 6705360 5687740 6826180 5698230 8448220 8129980 7642560 6762730 6832990 5318890 FALSE TRUE 6970092.79 6664565.101 7004075.859 6825322.886 7012194.582 6241915.356 7043516.177 6672086.666 6587072.025 6361024.659 1.095750003 1.047718797 1.101092392 1.072991106 1.102368715 0.981275139 1.107292701 1.048901242 1.035536313 1 22.60082775 -0.489003232 0.188330124 0.950858708 1.094361084 0.315616673 0.034934317 17.97358466 0.954817112 0.615406563 0.127872329 0.324337204 0.489003232 0.143502375 RRS(ph)FNDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRSFNDFR 8 2 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 RRS(1)FNDFR;RRS(1)FNDFR 77.062 0.036833 264670000 487200 507530 578350 420530 771150 746090 432130 529710 601770 914100 TRUE FALSE 506435.0322 594694.3295 593422.2761 503709.5788 640070.1984 572821.9046 398258.5214 522610.1039 580112.4152 1093200.393 0.463259102 0.543993885 0.54283028 0.460766006 0.585501251 0.523986186 0.364305139 0.478055174 0.530655147 1 20.06012645 0.755559654 4.529964191 0.999998327 0.49439537 0.872011321 0.057690669 1.81820462 33.46781664 0.057871645 0.014686849 5.695864559 -0.755559654 -0.505602957 DKPSVEPVEEYDYEDLKESSNS(ph)VSNHQLSGFDQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.002)S(0.009)NS(0.977)VS(0.013)NHQLSGFDQAR;DKPSVEPVEEY(0.001)DY(0.001)EDLKES(0.073)S(0.308)NS(0.561)VS(0.056)NHQLSGFDQAR 217.41 9.36E-37 202787000 40895 35699 54648 46337 102798 90470 78292 72777 84081 48938 TRUE FALSE 42509.56618 41830.02555 56072.17177 55502.3203 85324.43268 69459.71359 72155.26846 71801.54335 81054.94123 58526.46413 0.726330675 0.714719848 0.958065255 0.948328609 1.457877799 1.186808645 1.232865671 1.226821822 1.38492804 1 15.8368015 3.722311243 1.631213535 1.249841884 0.729110724 0.699947697 0.13295 0.192690286 0.991810067 0.037207945 0.084357754 5276.078434 -3.722311243 -0.52073116 DKPTYDEIFYTLS(ph)PVNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 DKPTYDEIFYT(0.004)LS(0.996)PVNGK;DKPTYDEIFYTLS(1)PVNGK;DKPTYDEIFYT(0.031)LS(0.969)PVNGK 226.56 2.09E-19 529980000 1116360 629880 852970 639050 1225300 1106960 1119420 907520 991740 536357 TRUE FALSE 1160434.755 738056.9902 875199.0989 765452.1826 1017023.944 849885.3161 1031676.935 895356.1788 956047.4711 641445.885 1.809092212 1.150614584 1.36441611 1.193323085 1.585517917 1.32495248 1.608361609 1.395840553 1.49045694 1 19.29096803 -1.031969915 6.176014732 0.999999554 1.424685957 0.323758621 0.188348833 1.06E-06 1.66E-07 0.166906719 0.039340249 0.092903074 1.031969915 0.424686403 DKPVYDELFYTLS(ph)PINGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 1 DKPVYDELFYT(0.001)LS(0.999)PINGK;DKPVYDELFYT(0.001)LS(0.999)PINGK 150.58 3.26E-08 248120000 510720 303393 376715 332999 607030 497110 489550 415125 477410 306097 TRUE FALSE 530883.62 355498.3877 386532.5024 398865.2083 503847.2574 381663.7363 451177.7918 409560.9284 460228.1074 366070.8466 1.450220975 0.971119091 1.055895344 1.08958474 1.376365428 1.042595279 1.232487635 1.118802364 1.257210487 1 18.48176336 -1.286437723 4.355045338 0.999870685 1.165670591 0.113543692 0.145340778 0.00016862 2.76E-05 0.13003278 0.030625168 0.05170854 1.286437723 0.165799906 DKQDEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DKQDEEQR 8 1 P27797;K7EL50 P27797 CALR Calreticulin 0 ;;;;; 136.99 0.00069983 28614410000 27213840 17242360 21693890 17534990 29474560 28592630 27830430 21520530 24458050 14253760 FALSE TRUE 28288263.42 20203601.2 22259250.6 21003358.69 24464484.82 21952425.01 25649008.18 21232082.5 23577809.56 17046511.37 1.659475233 1.185204454 1.305795075 1.232120651 1.435160796 1.287795757 1.504648524 1.245538283 1.383145739 1 24.02297318 -2.760379795 0.600015315 1.11E-10 1.349765296 0.38273814 0.136422993 414.5659077 19.24787617 539.3127037 0.049735262 0.001736282 2.760379795 1.349765296 SQPERDWVLNEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQPERDWVLNEFR 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;; 223.39 1.45E-11 1686020000 896410 1266470 1225630 867510 1434680 1468930 851330 1079480 1257900 1883780 FALSE TRUE 931800.959 1483976.371 1257570.925 1039100.889 1190813.606 1127793.269 784600.5301 1065011.336 1212628.425 2252870.624 0.413606067 0.658704657 0.558208231 0.46123416 0.528576117 0.500602768 0.348267016 0.472735241 0.538259238 1 21.10333304 0.776665965 4.498298609 0.99999669 0.493097729 0.787560183 0.078562232 1.761300341 35.15153707 0.078269166 0.019870412 5.979515078 -0.776665965 -0.50689896 VDNLTYRTSPDT(ph)LRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.056)S(0.033)PDT(0.911)LRR 124.73 0.00015247 845650000 365380 472060 485130 296600 607490 609240 300560 418620 514890 801700 TRUE FALSE 379805.4845 553132.6329 497772.8863 355266.5947 504229.0668 467753.2431 277001.3218 413009.0836 496359.2095 958777.7655 0.396135057 0.576914331 0.519174416 0.370541128 0.525908177 0.487864091 0.288910874 0.43076623 0.517699959 1 19.87083693 0.779410221 3.794180462 0.999981475 0.449148202 0.808792178 0.079796912 0.908311164 15.18669019 0.078770792 0.020195635 6.017418557 -0.779410221 -0.550833273 DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 DKRPLS(0.999)GPDVGT(0.001)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.975)GPDVGT(0.025)PQPAGLASGAK;DKRPLS(1)GPDVGTPQPAGLASGAK;DKRPLS(0.997)GPDVGT(0.003)PQPAGLASGAK 248.66 6.13E-38 8973610000 5080580 2950510 4319920 2998550 6045610 5615530 6062390 4584540 5346950 3029440 TRUE FALSE 5281165.221 3457237.141 4432500.664 3591654.24 5017979.372 4311408.262 5587204.031 4523091.74 5154514.314 3623000.766 1.457677092 0.95424687 1.223433543 0.991347911 1.385034036 1.190010309 1.542148178 1.248437975 1.422719631 1 21.78875368 3.218661618 24.99237669 1.317699 1.146985401 0.114062166 0.18754195 405.2925294 509030.6881 0.049627729 0.059389049 1654.480367 -3.218661618 -0.170713599 DKS(ph)PAPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKSPAPEEK 9 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 DKS(1)PAPEEK;DKS(1)PAPEEK 109.15 0.001512 779850000 2757490 827480 1308820 850900 2280940 2337420 2156330 1336340 1678910 610100 TRUE FALSE 2866357.834 969593.2531 1342928.924 1019205.48 1893226.634 1794589.629 1987311.22 1318428.548 1618486.357 729637.4139 3.928468825 1.328869976 1.840542849 1.396865705 2.594749937 2.459563606 2.723696979 1.806964011 2.218206367 1 19.47682018 4.751365521 24.64021007 2.000089888 3.928470325 0.540918256 0.548932362 1368.390701 2633108.135 0.129595726 2.341993135 56411.2237 -4.751365521 1.928380436 DKS(ph)PSSLLEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.941)PS(0.05)S(0.009)LLEDAK;DKS(0.755)PS(0.122)S(0.122)LLEDAK 97.579 0.0029324 653169000 1506270 513797 894660 555553 1273750 1197490 1245180 862590 978480 372435 TRUE FALSE 1565738.703 602037.638 917975.5746 665439.7252 1057238.43 919391.0956 1147579.538 851028.392 943264.6959 445406.5076 3.515302709 1.351658828 2.060983751 1.494005395 2.373648369 2.064161794 2.57647681 1.910677948 2.117761371 1 18.76476311 0.119028603 1.339410985 0.998465757 2.129835033 0.271292427 0.569614331 13.23583258 18.57468327 0.545609192 0.147501791 1.315311457 -0.119028603 1.131369277 DKS(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 291.24 2.83E-46 32336495000 7183793 3954116 5588599 3899892 7850422 7724505 6989930 5611109 6248616 3514884 TRUE FALSE 7467414.695 4633204.664 5734242.481 4671278.998 6516010.073 5930605.78 6442041.022 5535901.262 6023729.531 4203558.223 1.776450878 1.10221018 1.364140135 1.111267823 1.550117716 1.410853726 1.532520945 1.316956009 1.433007279 1 22.00317963 -1.130514977 4.299698257 0.999929387 1.38673153 0.280609507 0.190988414 0.000118978 2.41E-05 0.170188506 0.040106513 0.074043173 1.130514977 0.386802143 DKSEEVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKSEEVQK 8 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 98.048 0.0071125 128170000 186280 112940 140480 121770 202910 194790 187880 146330 160120 124380 FALSE TRUE 193634.4782 132336.5664 144141.0242 145855.7426 168419.4307 149552.9746 173153.4747 144368.6857 154357.3125 148749.8796 1.301745445 0.88965831 0.969016073 0.980543601 1.132232383 1.005398962 1.164057915 0.970546572 1.037697058 1 17.18252898 1.786761737 0.00561569 3.20E-08 2.067461477 0.027988698 0.112821261 22763.76933 118.2006803 21688.16947 21817.60933 61.20145354 -1.786761737 2.067461445 DKSFLAMVVDIVQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKSFLAMVVDIVQELK 16 1 O00764;F2Z2Y4;O00764-3 O00764 PDXK Pyridoxal kinase 0 123.97 7.75E-05 997530000 424340 379640 518760 403500 437190 481600 513860 519340 487360 245970 FALSE TRUE 441093.2709 444840.2168 532279.3118 483311.0957 362876.6 369755.6987 473582.3105 512379.0968 469820.0088 294163.1121 1.499485329 1.512222976 1.80946995 1.643003748 1.23358975 1.256975071 1.609930991 1.741819676 1.597141142 1 18.16625682 -1.919793776 2.502416659 0.651193125 1.55376731 0.463022079 0.175789106 10215798.09 5806844.778 20904908.13 0.047649128 0.012028355 1.919793776 0.902574185 DKTEDDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKTEDDADR 9 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 111.63 0.0019094 197080000 476690 238620 316990 279600 432270 447400 517010 311650 380860 159120 FALSE TRUE 495510.0893 279601.1288 325251.0198 334904.0455 358792.8998 343498.1304 476485.4052 307472.8415 367152.923 190296.5175 2.603884169 1.469291885 1.709180095 1.759906329 1.885441229 1.805067875 2.503910274 1.615756534 1.929372791 1 17.53788963 0.059027972 1.306534002 0.998272795 1.902338882 0.388493691 0.345406285 12.17108588 15.63051431 0.372890208 0.092294898 1.145586723 -0.059027972 0.904066087 DKTEDDADREAQLLEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKTEDDADREAQLLEMR 17 2 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 211.49 1.36E-12 296240000 442170 297030 439480 297210 570240 586400 496200 392570 427730 279550 FALSE TRUE 459627.213 348042.5919 450933.2098 355997.2509 473310.8085 450217.487 457306.5474 387308.2413 412336.0809 334322.4702 1.374802037 1.041038587 1.348797194 1.064831959 1.415731369 1.346656379 1.367860638 1.158487017 1.233348391 1 18.3508808 0.6544991 1.210897809 1.001423581 1.266175518 0.285740686 0.126188354 1.481756811 3.409709371 0.114775471 0.034996858 4.513350902 -0.6544991 0.264751936 DKTKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKTKLR 6 2 H3BLX4;Q96JM2-2;Q96JM2;Q96JM2-3 H3BLX4 ZNF462 Zinc finger protein 462 0 81.672 0.034455 174940000 694820 646970 701750 574130 887190 875170 794810 710180 809760 696270 FALSE TRUE 722252.0301 758082.0648 720038.1815 687691.2004 736385.7607 671925.0308 732510.7154 700661.1987 780616.8958 832690.7756 0.867371239 0.91040046 0.864712571 0.825866241 0.884344804 0.806932238 0.879691161 0.841442249 0.937463124 1 19.66742132 1.033983366 3.712957545 0.999421106 0.8600407 0.720060308 0.028374998 0.096116385 3.008162227 0.026511067 0.006841689 10.81392533 -1.033983366 -0.139380405 DKTYSYLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKTYSYLNK 9 1 G3V2V8;J3KMY5;H0YIZ1;G3V3E8;E7EMS2;G3V3D1;P61916-2;P61916 G3V2V8 NPC2 Epididymal secretory protein E1 0 ; 121.36 0.00056184 831610000 1096130 833510 906200 728340 1244740 1246480 1138670 899890 995690 737950 FALSE TRUE 1139406.059 976658.8587 929816.3165 872403.4781 1033159.539 957003.9106 1049418.07 887828.4465 959855.3114 882537.1736 1.291057298 1.106648975 1.053571843 0.988517543 1.170669713 1.084378017 1.189092201 1.005995524 1.08760893 1 19.75129752 4.729774153 3.506297511 1.076131464 1.31501426 0.509427154 0.063905033 0.225706918 4.901862893 0.015106132 0.141208499 53675.25948 -4.729774153 0.238882797 DKVADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKVADLR 7 1 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7;Q5T6H2 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ; 86.011 0.018596 1031330000 2518000 2087810 2418160 1950640 3227700 3038600 2811900 2538460 2654200 1931090 FALSE TRUE 2617412.584 2446375.127 2481179.236 2336470.77 2679056.707 2332931.2 2591495.93 2504436.096 2558675.86 2309450.113 1.133348831 1.059289011 1.074359313 1.011700039 1.160040952 1.010167393 1.122126829 1.084429615 1.107915623 1 21.13911795 DKVAGHSLGYGFVNYVTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKVAGHSLGYGFVNYVTAK 19 1 Q15717;Q15717-2;M0QZR9 Q15717 ELAVL1 ELAV-like protein 1 0 103.17 0.00022708 564820000 647540 379310 618630 394110 732870 714910 573580 549380 658260 420270 FALSE TRUE 673105.3792 444453.5419 634752.006 472063.7817 608297.0192 548882.9871 528621.3008 542016.4597 634569.3512 502613.8599 1.339209745 0.884284293 1.262901915 0.939217597 1.210267101 1.092057006 1.051744377 1.07839537 1.262538505 1 18.93909093 -2.486269146 1.956968222 7.56E-05 1.111782792 0.0606168 0.139150729 2860167.696 104062.1785 12856993.38 0.029996482 0.003263855 2.486269146 1.111707204 DKVTLVVGASQDIIPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DKVTLVVGASQDIIPQLK 18 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ; 166.91 2.24E-11 898140000 2010740 1261330 1728280 1321160 2275900 2030280 2143040 1800220 2090300 1264990 FALSE TRUE 2090125.568 1477953.616 1773320.397 1582481.505 1889043.331 1558778.239 1975062.925 1776090.995 2015070.511 1512840.571 1.381590108 0.976939437 1.172179297 1.046033227 1.248673104 1.030365175 1.305532759 1.174010685 1.331978101 1 20.52882853 2.23103273 24.99811104 1.215882663 1.136871185 0.03987926 0.137361139 471.0571819 1564240.208 0.04628489 0.03485097 170.2286794 -2.23103273 -0.079011478 DKVVALAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKVVALAEGR 10 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3;F8VWB3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 123.84 0.00041176 177710000 244510 210710 214940 190250 372490 279190 270680 239790 245680 239610 FALSE TRUE 254163.4436 246897.8034 220541.513 227880.8822 309174.2829 214352.3537 249463.3943 236576.0073 236838.0248 286556.9919 0.886956001 0.861601044 0.769625307 0.795237557 1.078927723 0.748026954 0.870554205 0.825580998 0.826495362 1 18.12846257 -1.711118988 2.55310668 1.02736347 0.850339383 0.208559983 0.086792392 30441997.31 23239600.8 5323912.742 0.02038909 0.019448272 1.711118988 -0.177024087 DKVVEDDEDDFPTTR ddPTM_MDA-MB-175_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 ; 160.97 1.53E-06 480740000 587250 386750 541020 381640 740670 676780 613540 528820 597890 356540 FALSE TRUE 610435.0835 453171.304 555119.4257 457127.2529 614771.178 519608.1017 565449.1316 521732.0329 576372.0557 426397.1866 1.431611424 1.062791496 1.301883415 1.072069111 1.441780568 1.218601149 1.326108964 1.223582259 1.351725747 1 18.70183839 -1.333783664 4.663753044 0.999795165 1.262102979 0.297056516 0.124073701 0.000235674 3.37E-05 0.107140969 0.025233772 0.046367783 1.333783664 0.262307814 DKVVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKVVGK 6 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 68.915 0.086532 240620000 387280 286880 317940 254900 349180 390000 384680 307650 299000 319420 FALSE TRUE 402570.1134 336149.4084 326225.7776 305318.4592 289826.5083 299428.4105 354527.7764 303526.455 288239.0484 382004.2333 1.053836786 0.879962521 0.853984718 0.799254125 0.758699729 0.78383532 0.928072899 0.794563066 0.754544121 1 18.5432291 4.866482135 1.648913926 0.823396435 1.193000261 0.439040449 0.073914327 1.189456439 2.438754183 0.018345273 0.769811426 73532.97461 -4.866482135 0.369603826 DKWLAPDGLIFPDR ddPTM_MDA-MB-175_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 ;;; 138.55 1.35E-05 3217802000 1366525 1136451 1340544 1220799 1753544 1636780 1554382 1424202 1467251 992234 FALSE TRUE 1420476.462 1331627.619 1375479.678 1462269.398 1455477.217 1256662.651 1432545.477 1405112.902 1414444.923 1186643.255 1.197054343 1.122180245 1.159134957 1.232273805 1.226549944 1.059006273 1.207225062 1.184107267 1.191971485 1 20.17845485 -1.543476861 6.33037248 0.999774223 1.175243365 0.532582852 0.049323442 0.00015396 1.11E-05 0.046782446 0.01101266 0.028610348 1.543476861 0.175469142 DKWSPALQIR ddPTM_MDA-MB-175_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 ; 147.91 2.38E-05 2053040000 2296000 2025590 1893950 1473020 5330200 3555000 2485900 2026620 2192220 3999900 FALSE TRUE 2386647.853 2373469.326 1943307.893 1764378.959 4424174.508 2729405.127 2291048.662 1999456.474 2113322.43 4783603.822 0.498922557 0.49616762 0.406243486 0.368838856 0.924862232 0.570575079 0.478937794 0.417981202 0.441784585 1 22.18966648 -1.700695414 2.837528187 1.069384708 0.509527422 0.492841178 0.148622724 31212421.63 27921391.89 15483854.3 0.038405019 0.0199207 1.700695414 -0.559857286 DKYEESRR ddPTM_MDA-MB-175_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 66.435 0.034698 62512000 70794 59672 66707 55096 81605 75226 72651 74736 84931 63238 FALSE TRUE 73589.00178 69920.20182 68445.43922 65993.82435 67733.81125 57755.90156 66956.42478 73734.28616 81874.3499 75628.27534 0.973035567 0.924524611 0.905024462 0.872607818 0.895614913 0.763681326 0.885335868 0.9749566 1.082589145 1 16.2066381 1.564062045 3.419476688 1.039473101 0.88569384 0.573833368 0.053352205 0.144125493 3.836594595 0.036533285 0.014772393 36.64899295 -1.564062045 -0.153779261 DKYGPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKYGPPVR 8 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 82.287 0.018845 617070000 656650 829540 820460 798800 1047200 1079200 795140 900660 811840 889770 FALSE TRUE 682575.049 972007.0421 841841.8616 956800.2558 869197.3181 828572.1554 732814.8491 888588.1259 782622.037 1064103.396 0.641455569 0.913451687 0.791127878 0.899160983 0.816835395 0.778657562 0.688668838 0.835058068 0.735475556 1 20.02120691 2.834069073 6.779932828 0.790873357 0.821937772 0 0.103548622 1.357965882 82.56401124 0.029480815 0.031310677 682.4472262 -2.834069073 0.031064415 DKYVGVSSDSVGGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKYVGVSSDSVGGFR 15 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 212.95 5.62E-10 550210000 515700 280160 358610 259690 462360 411630 384610 311830 394550 270910 FALSE TRUE 536060.2342 328275.3007 367955.6712 311055.9069 383768.2124 316035.1708 354463.2632 307650.4289 380350.2226 323989.6276 1.654559864 1.013227809 1.13570201 0.960079831 1.184507711 0.975448421 1.094057442 0.94956876 1.173958023 1 18.3055881 4.740731728 24.99522627 1.050893994 1.654560073 0.82197888 0.08382593 68.51010086 788679.9669 0.017982876 0.119019346 55046.75571 -4.740731728 0.603666078 DLAALGDKVNSLGETAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLAALGDKVNSLGETAER 18 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 194.19 7.80E-15 724890000 326510 255730 288200 258340 413390 384670 329650 334080 350360 283450 FALSE TRUE 339400.8669 299649.6382 295710.7288 309438.8809 343122.1155 295336.2222 303811.1716 329602.204 337750.612 338986.6005 1.001222073 0.883957176 0.872337515 0.91283514 1.012199641 0.871232732 0.896233571 0.97231632 0.996353872 1 18.37086872 1.573865779 4.294562588 0.994609751 0.919489455 0.31664043 0.046651136 0.20177501 8.315045627 0.02791907 0.012214529 37.48571332 -1.573865779 -0.075120296 DLADELALVDVIEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 255.23 2.37E-24 678437000 850429 365702 609308 482845 807851 761077 995183 612611 678411 236106 FALSE TRUE 884004.5936 428508.4737 625187.067 578350.2999 670532.7756 584328.401 917177.956 604399.9516 653995.1206 282366.4502 3.130699816 1.517561571 2.214098264 2.048225983 2.374689965 2.069397411 3.248183187 2.140480752 2.316121905 1 18.10720916 3.221165937 24.53290316 2.306340595 2.175958258 0 0.635987422 1495.972948 2109868.198 0.172385124 0.206545739 1664.048336 -3.221165937 -0.130382337 DLADVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLADVDLR 8 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 124.98 0.0029812 107046000 350660 401020 399730 421150 436440 508440 448300 399360 402260 353030 FALSE TRUE 364504.3276 469892.0655 410147.2922 504452.213 362254.0847 390362.5155 413161.0746 394007.2324 387782.7412 422199.4693 0.863346248 1.112962236 0.971453832 1.194819628 0.858016438 0.924592625 0.978592122 0.933225314 0.918482304 1 18.68756524 3.200371173 24.99992914 0.934739622 1.036583934 0.236832653 0.088070156 220.1328372 144104.8126 0.023790861 0.028436136 1586.248311 -3.200371173 0.101844313 DLAEDAPWKK ddPTM_MDA-MB-175_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 ;;; 125.74 0.00064307 3041960000 4748250 3145960 3780850 3364500 7086330 6089200 6456410 4316720 4895650 3702060 FALSE TRUE 4935714.576 3686254.158 3879382.057 4029988.058 5881798.158 4675075.583 5950339.714 4258861.429 4719456.513 4427407.777 1.114809122 0.832598745 0.876219732 0.910236477 1.328497047 1.055939687 1.34397824 0.961931144 1.065963821 1 22.07803083 3.300881949 24.99998357 1.124804465 0.922171193 0.320960315 0.136829465 75.14035983 30141.3905 0.036772871 0.049790687 1999.318334 -3.300881949 -0.202633272 DLAGAPPGEVVGCFT(ph)PQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLAGAPPGEVVGCFTPQSR 19 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 1 DLAGAPPGEVVGCFT(1)PQSR;DLAGAPPGEVVGCFT(0.998)PQS(0.002)R 262.38 3.72E-30 306090000 148389 161568 134422 158078 139513 185703 110785 132310 118073 145230 TRUE FALSE 154247.5123 189316.0472 137925.1477 189345.3566 115798.6301 142576.2926 102101.3822 130536.6009 113823.5758 173685.0379 0.888087507 1.089996291 0.794110704 1.090165042 0.666716209 0.820889895 0.587853643 0.751570788 0.655344739 1 17.40611395 3.228460033 24.99998262 0.728578308 0.962227554 0.387072911 0.133478946 180.585194 446966.29 0.034977021 0.042262256 1692.232507 -3.228460033 0.233649246 DLAHTPSQLEGLDPATEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLAHTPSQLEGLDPATEAR 19 0 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 0 ; 168.27 1.64E-11 160470000 74503 102308 98242 101740 99852 99546 94924 88840 90612 92385 FALSE TRUE 77444.43597 119878.6032 100802.2672 121863.8683 82879.19271 76427.95013 87483.60884 87649.24511 87350.89182 110486.0719 0.700942975 1.085010998 0.912352711 1.102979463 0.750132494 0.691742849 0.791806671 0.793305831 0.790605461 1 16.75350499 3.212250803 24.99998682 0.787068021 0.957230245 0.238388985 0.12693818 258.7556035 245872.84 0.034254104 0.04095305 1630.237214 -3.212250803 0.170162224 DLAILQCHGELDPMVPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLAILQCHGELDPMVPVR 18 0 O95372;Q5QPQ1;Q5QPQ0 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ;;;;; 162.33 3.59E-11 1083890000 589220 733413 687720 697270 786763 843110 733127 728666 688505 765926 FALSE TRUE 612482.8606 859370.9776 705642.5482 835187.9249 653029.3063 647310.48 675662.5901 718899.4241 663725.8395 915994.5352 0.6686534 0.93818352 0.770356723 0.91178265 0.712918343 0.706675046 0.737627316 0.784829381 0.724595851 1 19.80497947 -1.526148987 3.214924557 1.006673613 0.777091594 0.400236914 0.083274421 31803572.41 34683508.47 1818738.902 0.019327035 0.029774948 1.526148987 -0.229582019 DLAMMIHDQGDLIDSIEANVESSEVHVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLAMMIHDQGDLIDSIEANVESSEVHVER 29 0 Q86Y82 Q86Y82 STX12 Syntaxin-12 0 ; 254.71 3.74E-58 43757000 27458.9 58420.6 43747.5 58295.5 44209.5 62133 41101.1 44682.6 38564.8 59923 FALSE TRUE 28542.99857 68453.8836 44887.59579 69826.17591 36694.78498 47703.55238 37879.48838 44083.70283 37176.86038 71663.76455 0.398290527 0.95520915 0.62636391 0.97435819 0.51204099 0.665657919 0.528572405 0.615146345 0.518767896 1 16.12895621 -1.1657652 4.984255562 1.000024232 0.651321573 0.265231112 0.177453939 4.48E-05 7.50E-06 0.161104555 0.037970072 0.06827077 1.1657652 -0.348702659 DLANDIMTLMSHTKPYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLANDIMTLMSHTKPYIR 18 1 O14617-5;O14617-2;O14617;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 128.79 1.36E-05 184220000 152450 163240 208470 191190 238820 245190 222820 223080 220770 167790 FALSE TRUE 158468.8437 191275.2002 213902.8995 229006.8114 198225.4617 188248.3384 205354.7862 220089.9775 212824.5308 200665.238 0.789717468 0.953205459 1.065968882 1.141238082 0.98784156 0.938121322 1.023370008 1.096801717 1.060594914 1 17.61443119 4.627752678 2.641874472 1.042416565 0.768417078 0.657469502 0.05488692 0.23468667 2.477972159 0.014914966 0.125428458 42437.78206 -4.627752678 -0.273999487 DLATVAFCDAQSTQEIHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLATVAFCDAQSTQEIHEK 19 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 ;;; 310.3 1.66E-61 654950000 867910 644040 825700 677020 1011670 996810 894190 854110 875460 584970 FALSE TRUE 902175.757 754648.8601 847218.4203 810932.5353 839706.6948 765315.9843 824101.0513 842662.0525 843952.3656 699583.6716 1.2895895 1.078711369 1.211032296 1.159164469 1.200294874 1.093959187 1.17798783 1.204519326 1.206363727 1 19.41613709 -1.071656033 4.193061691 0.999977283 1.1773975 0.470143253 0.057315763 1.10E-05 2.45E-06 0.050371603 0.011871181 0.084789869 1.071656033 0.177420216 DLCNTHLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLCNTHLMR 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 148.32 9.03E-05 170010000 101970 91736 131050 102390 131960 138450 122930 73924 113610 88320 FALSE TRUE 105995.8543 107490.9444 134465.2707 122642.4364 109529.4863 106297.0857 113294.4254 72933.1697 109521.1983 105624.613 1.003514724 1.017669474 1.273048647 1.161116078 1.03696935 1.006366629 1.072613874 0.690494077 1.036890883 1 16.68858653 1.903803289 12.16404343 0.876091888 1.085989074 0.302668453 0.11683501 0.811495474 99.98033125 0.049066971 0.031422905 80.13150302 -1.903803289 0.209897187 DLDADREVTFLEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLDADREVTFLEASR 15 1 A0A087WYT5;P20338 A0A087WYT5 RAB4A Ras-related protein Rab-4A 0 ; 196.95 7.91E-09 203390000 213320 258620 257620 232740 292460 301310 243240 228950 222770 234710 FALSE TRUE 221742.0383 303035.9732 264333.7888 278775.2773 242747.7537 231335.3189 224174.2132 225881.2997 214752.5512 280696.9307 0.789969587 1.079584207 0.941705305 0.993153992 0.864803734 0.824146236 0.798634359 0.804715959 0.765069111 1 18.09865376 3.077769363 4.182534115 0.823047476 0.959189431 0.25150672 0.089666437 0.236877731 7.985596067 0.024744444 0.029739825 1196.105157 -3.077769363 0.136141955 DLDANGDAQVDFSEFIVFVAAITSACHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 DLDANGDAQVDFSEFIVFVAAITSACHK 28 0 P25815 P25815 S100P Protein S100-P 0 ;;;;;;;;; 349.24 8.30E-111 28757870000 17632725 18460041 21893957 22083983 30195318 29847606 31166960 24071762 25876501 17254552 FALSE TRUE 18328878.6 21630409.44 22464531.51 26452128.92 25062728.63 22915951.85 28724012.24 23749119.4 24945210.78 20635251.11 0.88823143 1.048226132 1.088648323 1.281890334 1.214558936 1.110524497 1.391987531 1.150900432 1.208863932 1 24.29860766 4.451744084 1.441308067 1.205371725 0.85466912 0.466510392 0.100398022 0.558038498 1.563920154 0.026043514 0.243119193 28297.2404 -4.451744084 -0.350702605 DLDAPDDVDFF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDAPDDVDFF 11 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 86.011 0.034405 16820000 59673 72327 69485 69288 88913 89193 76392 72222 69005 63629 FALSE TRUE 62028.93612 84748.59962 71295.83618 82992.9596 73799.60002 68479.27748 70404.19543 71253.98222 66521.52353 76095.8843 0.8151418 1.113708059 0.936921055 1.09063664 0.969823805 0.899907769 0.925203723 0.936371039 0.874180307 1 16.21553081 2.992450735 24.80282005 0.925272656 0.998769507 0.109132201 0.082556627 578.7278538 1901397.95 0.022315673 0.025631434 982.7673848 -2.992450735 0.07349685 DLDDFQSWLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLDDFQSWLSR 11 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 229.82 5.25E-12 720210000 524090 599400 508600 518897 624960 701950 566640 537960 540330 595440 FALSE TRUE 544781.4779 702342.2873 521854.5338 621533.2778 518729.5224 538932.7507 522225.2762 530749.5261 520883.6288 712105.0676 0.765029632 0.986290253 0.732833619 0.872811199 0.728445206 0.75681634 0.733354248 0.745324742 0.73147019 1 19.44173059 3.240704019 24.97573242 0.763926897 0.842144143 0.053448724 0.099492816 112.3705608 1309366.407 0.025656627 0.033100039 1740.620199 -3.240704019 0.078217247 DLDEEGS(ph)EK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLDEEGSEK 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EK;DLDEEGS(1)EK;DLDEEGS(1)EK 169.82 6.10E-05 715040000 1580770 469250 585410 646130 949590 1431100 1549040 800410 820120 287169 TRUE FALSE 1643180.02 549840.0372 600666.2655 773932.5855 788179.031 1098748.714 1427622.197 789681.8132 790604.0414 343434.2674 4.784554648 1.601005169 1.748999219 2.253510086 2.294992393 3.199298433 4.156900848 2.299368142 2.302053454 1 18.38967447 2.785097408 24.75192372 2.769814235 2.42514995 0 1.114917696 2007.598416 1067794.379 0.333777892 0.354023773 609.6736253 -2.785097408 -0.344664285 DLDEEGS(ph)EKELHENVLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLDEEGSEKELHENVLDK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 DLDEEGS(1)EKELHENVLDK;DLDEEGS(1)EKELHENVLDK 252.71 1.04E-30 445880000 1570690 352490 568540 505680 877790 1152380 1503470 654970 672320 166186 TRUE FALSE 1632702.054 413027.4155 583356.6195 605701.9947 728583.5693 884757.2095 1385624.093 646191.1985 648123.3345 198746.9649 8.214978554 2.078157097 2.935172468 3.047603746 3.665885262 4.451676583 6.971800016 3.251326121 3.261047709 1 17.6005733 4.751162953 24.45553225 3.637481213 8.214982469 0.476844538 1.493359146 1407.768536 2731785.719 0.360384316 6.349600555 56384.91801 -4.751162953 4.577501256 DLDEEIFDDDDFYHQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 ;;; 205.69 9.35E-16 175886000 174833 194830 210010 202163 225041 259168 253901 210881 211954 180014 FALSE TRUE 181735.5418 228290.5369 215483.0331 242150.238 186788.6112 198980.1597 233999.5762 208054.4851 204325.8169 215284.2967 0.844165341 1.060414254 1.000923135 1.124792852 0.867636953 0.924266947 1.086932859 0.966417376 0.949097635 1 17.71588356 DLDELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDELSR 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 187.63 0.0013526 369360000 641260 614940 644380 670010 741250 844430 893520 734460 627390 462280 FALSE TRUE 666577.44 720551.1614 661173.0722 802535.9782 615252.5898 648323.93 823483.5676 724615.765 604810.3565 552854.9151 1.205700486 1.303327766 1.195925105 1.451621314 1.112864466 1.172683668 1.489511163 1.310679792 1.093976629 1 19.0765414 1.101467369 4.161240699 1.00514545 1.285918158 0.41505155 0.113021641 0.188418071 5.486088188 0.107201229 0.027544865 12.6318619 -1.101467369 0.280772709 DLDELSRYPEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLDELSRYPEDK 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 206.46 8.19E-08 3755020000 6720570 4363565 5832890 4069022 7809830 7309590 6882310 5895100 6468190 3868374 FALSE TRUE 6985903.293 5112973.345 5984899.905 4873862.407 6482317.886 5612048.5 6342856.559 5816085.827 6235401.105 4626307.821 1.51003858 1.105195232 1.293666599 1.053510185 1.401186029 1.213072869 1.371040753 1.257176576 1.34781371 1 22.14142983 -1.471165247 5.750065092 0.999749066 1.275673197 0.299532488 0.12960851 0.000375366 3.45E-05 0.112981247 0.026606013 0.033793623 1.471165247 0.275924131 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDEMDDDDDDDDVGDHDDDHPGMEVVLHEDKK 33 1 Q15029;Q15029-3;K7EIV5;K7EIT3 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 123.89 3.54E-08 171400000 83279 37661 62083 42182 92227 76134 85918 60291 64332 25570 FALSE TRUE 86566.91923 44128.98379 63700.93398 50525.4737 76550.28748 58453.03232 79183.52266 59482.89776 62016.70389 30579.95193 2.830838957 1.443069102 2.083094641 1.652241763 2.503283447 1.911482152 2.5893933 1.94515995 2.028018357 1 14.90029852 4.766543621 23.19654933 1.981303562 2.830842229 0.262241786 0.449654987 4919.083926 4077500.854 0.09816422 8.023327594 58417.58789 -4.766543621 0.849538667 DLDFLHSVFQDQHLHTLLDLYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDFLHSVFQDQHLHTLLDLYDK 23 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 51.834 0.042708 57745000 52021 34483 36080 41378 49342 58403 100790 44931 43189 23539 FALSE TRUE 54074.82925 40405.18701 37020.27444 49562.4449 40954.86446 44839.78836 92889.81643 44328.77344 41634.63633 28151.01637 1.920883727 1.43530118 1.315059959 1.760591669 1.454827205 1.592830176 3.299696722 1.574677548 1.478974534 1 14.78089939 2.434210545 24.99999843 1.97119379 1.560922853 0.025636805 0.580048918 329.718314 192093.8613 0.196599857 0.164487343 271.775651 -2.434210545 -0.410270936 DLDFLHSVFQDQHLHTLLDLYDKINTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDFLHSVFQDQHLHTLLDLYDKINTK 27 1 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 226.39 4.88E-35 99426000 134870 89974 120170 81812 149800 159550 166770 126160 137640 69110 FALSE TRUE 140194.7717 105426.3346 123301.7289 97994.16942 124337.0495 122496.9305 153698.1316 124469.0316 132686.3633 82650.78131 1.696230447 1.275563678 1.491839847 1.185641174 1.504366293 1.482102511 1.859608938 1.505963157 1.605385469 1 16.33474084 3.016343799 24.9827348 1.544998561 1.400327274 0.000672493 0.237216924 635.9197169 972044.6477 0.064154652 0.07666034 1038.350076 -3.016343799 -0.144671288 DLDGFRK ddPTM_MDA-MB-175_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 ;; 101.99 0.013952 1002610000 2174000 1769350 2074700 1611430 2701560 2547320 2162320 2107610 2210160 1789090 FALSE TRUE 2259831.199 2073222.099 2128768.386 1930166.044 2242349.796 1955743.535 1992831.708 2079360.935 2130616.773 2139627.931 1.056179519 0.968963841 0.994924564 0.902103593 1.048009219 0.91405777 0.931391706 0.971832955 0.995788446 1 21.02892851 5.131298823 1.696970815 0.965156473 1.209526182 0.26816842 0.042118429 4.117557897 4.781875416 0.01028712 2.274407952 135300.3198 -5.131298823 0.244369709 DLDIFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDIFDR 7 0 Q14165;F5H1S8;H0YG07 Q14165 MLEC Malectin 0 96.253 0.029935 55620000 132590 170120 154110 246910 233620 314770 218870 177520 165300 239410 FALSE TRUE 137824.7556 199336.7867 158126.2332 295748.061 193909.3558 241669.4379 201714.3975 175140.6348 159350.8853 286317.8057 0.481369837 0.696208139 0.552275234 1.032936322 0.677252172 0.844060108 0.704512236 0.611700115 0.556552482 1 18.12725787 4.873119234 1.362119526 0.738429005 0.32441341 0.207210423 0.158700696 3.029330921 3.980070679 0.042663251 1.877749726 74665.37209 -4.873119234 -0.414015594 DLDIIDNYDYSHTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 320.56 1.41E-56 3806847000 6006734 5113690 5733918 4944133 6871794 7004281 6907234 5975656 6234822 4755437 FALSE TRUE 6243884.497 5991926.479 5883348.614 5922067.751 5703728.91 5377642.889 6365826.95 5895562.106 6010431.974 5687173.832 1.097888808 1.053585956 1.034494248 1.041302398 1.00291095 0.945573856 1.119330469 1.036641798 1.056839856 1 22.43928047 4.750548423 1.750155561 1.032024837 1.121845602 0.197066624 0.042062339 1.682972083 5.009544669 0.011164275 0.254441567 56305.18928 -4.750548423 0.089820765 DLDKADSMIR ddPTM_MDA-MB-175_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 ;;; 167.18 4.85E-06 1271270000 2803930 2307030 2807470 1964230 4022760 3315230 2990320 2634070 2984060 2208320 FALSE TRUE 2914631.322 2703244.456 2880634.975 2352748.831 3338972.692 2545318.075 2755930.905 2598764.6 2876664.264 2640998.023 1.103609808 1.023569284 1.09073727 0.890855961 1.264284434 0.963771291 1.043518731 0.984008537 1.089233781 1 21.33265179 DLDLDAFAEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLDLDAFAEELER 13 0 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 145.91 9.78E-05 11666000 18670 19179 22297 23807 26019 29634 25004 24543 20164 17206 FALSE TRUE 19407.10602 22472.84406 22878.07814 28515.95354 21596.29967 22751.95261 23044.12114 24214.04123 19438.30158 20577.18627 0.943137014 1.092124247 1.111817614 1.385804316 1.049526373 1.105688227 1.11988689 1.176742092 0.944653041 1 14.3287581 -0.596513854 7.732143408 1 1.115410716 0.055502827 0.118625937 0 0 0.111488884 0.026278182 0.253213086 0.596513854 0.115410716 DLDLKKPIYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLDLKKPIYQR 11 2 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 56.225 0.067686 1349260000 2959400 1961320 2693300 1847030 3907100 3184800 2949700 2563300 3060600 1923040 FALSE TRUE 3076239.397 2298161.453 2763489.611 2212367.021 3242972.538 2445178.466 2718494.806 2528943.156 2950449.604 2299822.869 1.337598403 0.99927759 1.201609762 0.96197279 1.410096656 1.063202953 1.182045297 1.099625189 1.282902976 1 21.13309132 -1.144295626 5.017569943 0.999991843 1.160369042 0.117801013 0.137623379 1.12E-05 1.90E-06 0.118350693 0.027894107 0.071730585 1.144295626 0.160377199 DLDLLASVPS(ph)PSSSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DLDLLASVPSPSSSGSR 17 0 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 DLDLLAS(0.033)VPS(0.862)PS(0.08)S(0.017)S(0.004)GS(0.004)R;DLDLLASVPS(0.837)PS(0.146)S(0.013)S(0.003)GS(0.001)R;DLDLLASVPS(0.731)PS(0.249)S(0.02)SGSR;DLDLLAS(0.001)VPS(0.954)PS(0.041)S(0.003)S(0.001)GSR;DLDLLAS(0.001)VPS(0.786)PS(0.192)S(0.017)S(0.003)GS(0.001)R;DLDLLASVPS(0.936)PS(0.057)S(0.006)S(0.001)GSR;DLDLLAS(0.034)VPS(0.952)PS(0.007)S(0.007)SGSR;DLDLLAS(0.002)VPS(0.995)PS(0.002)SSGSR 268.12 7.06E-28 2719736000 1893924 2130330 2142196 2207100 2469010 2665270 2380490 2237113 2109150 1871642 TRUE FALSE 1968697.582 2496197.606 2198023.388 2643657.792 2049328.562 2046301.435 2193900.974 2207128.159 2033242.103 2238354.415 0.879528983 1.115193192 0.98198184 1.18107203 0.915551419 0.91419903 0.980140124 0.986049459 0.908364685 1 21.09400706 DLDNAEEKADALNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLDNAEEKADALNK 14 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ; 137.52 1.61E-05 268030000 573940 248940 371860 252602 592340 486970 508750 381110 432940 220070 FALSE TRUE 596599.5944 291693.5085 381550.9771 302565.9217 491654.2584 373878.5976 468872.8456 376001.8438 417358.574 263188.503 2.266814802 1.108306424 1.449725093 1.149616789 1.868068904 1.420573442 1.781509603 1.428640839 1.585778137 1 18.00573694 -1.316826479 4.925710042 0.999767314 1.539368313 0.207221304 0.327129646 0.00075879 0.000105241 0.28751785 0.067739864 0.04821404 1.316826479 0.539600999 DLDQCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLDQCR 6 0 P60903 P60903 S100A10 Protein S100-A10 0 ; 138.48 0.028581 1435580000 1787070 2371800 1884490 2266300 2363300 2914600 2352900 2035820 1925190 2546500 FALSE TRUE 1857624.904 2779138.2 1933601.358 2714567.376 1961587.11 2237728.321 2168473.55 2008533.163 1855902.788 3045437.919 0.609969716 0.912557824 0.634917345 0.891355348 0.644106747 0.734780475 0.712039978 0.659521953 0.609404242 1 21.53821826 -1.56337838 6.143367934 1.000591081 0.715570652 0.40988247 0.103567396 0.000773227 5.50E-05 0.092477782 0.021753545 0.027328867 1.56337838 -0.285020429 DLDSLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DLDSLHR 7 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;;; 151.29 0.0018911 4248000000 3461380 5449190 4895690 5208080 5696290 6325640 4888690 5033490 4564790 4898910 FALSE TRUE 3598037.955 6385045.994 5023275.703 6238222.679 4728036.66 4856605.976 4505501.704 4966024.3 4400504.1 5858757.619 0.614129853 1.089829348 0.857396061 1.064768861 0.807003288 0.828948096 0.769019986 0.847624125 0.751098507 1 22.48216334 DLEADIIGDTSGHFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLEADIIGDTSGHFQK 16 0 P08133;P08133-2;E5RJF5;E5RK63 P08133 ANXA6 Annexin A6;Annexin 0 ; 178.14 2.84E-09 357060000 146654 307737 303612 328076 252493 404054 313039 255274 259599 347119 FALSE TRUE 152444.0132 360588.4359 311524.3781 392968.4536 209574.33 310218.582 288502.1852 251852.4696 250256.0827 415130.3221 0.367219654 0.868615027 0.750425497 0.946614672 0.504839851 0.747279988 0.694967748 0.606682905 0.602837397 1 18.66320479 -1.179619961 5.117146337 1.000019992 0.684593949 0.267108065 0.160212923 3.44E-05 5.52E-06 0.146226084 0.034463636 0.066127186 1.179619961 -0.315426044 DLEAEHVEVEDTTLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLEAEHVEVEDTTLNR 16 0 Q9H3K6;A0A087WZT3;H3BV85;Q9H3K6-2;H3BTW0;A0A0B4J295;H3BVE0 Q9H3K6 BOLA2;BOLA2B BolA-like protein 2 0 ;;;;; 226.65 5.76E-15 8522940000 4064570 4300880 4760750 4294540 5362360 5801610 5070700 4763610 4866100 4175210 FALSE TRUE 4225042.362 5039522.684 4884819.056 5143987.194 4450867.963 4454274.002 4673245.284 4699761.6 4690970.012 4993262.46 0.846148664 1.009264529 0.978282054 1.030185622 0.891374727 0.892056854 0.935910203 0.941220622 0.939459932 1 22.25155131 3.21723201 24.99981164 0.929501867 0.969942141 0.077368802 0.05354743 517.9665724 607120.3695 0.015089807 0.018052091 1649.043114 -3.21723201 0.040440274 DLEAHIDSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DLEAHIDSANK 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;;; 209.85 1.48E-08 25592058000 22445830.6 17543319 22737670 18452243 29465633 27970552 28556407 23100233 24974406 14591607 FALSE TRUE 23332009.32 20556247.57 23330232.36 22102041.59 24457075.23 21474815.2 26318081.2 22790612.16 24075582.01 17450553.02 1.337035525 1.177971125 1.336933697 1.266552502 1.401507173 1.230609435 1.5081517 1.306010883 1.37964579 1 24.05676942 -0.9902321 4.347471115 0.999987341 1.327057838 0.555971511 0.08771162 5266932.05 1211493.334 665.07653 0.019477457 0.102274626 0.9902321 0.327070498 DLEAHIDSANKNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLEAHIDSANKNR 13 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 180.09 7.93E-06 909670000 639570 842250 950080 438930 1593690 1188390 475660 895610 1112620 1385100 FALSE TRUE 664820.7175 986899.8857 974839.8653 525749.0439 1322795.143 912404.4327 438376.5263 883605.8129 1072577.024 1656483.826 0.401344527 0.595779971 0.588499477 0.317388577 0.798556027 0.550807933 0.264642805 0.533422542 0.647502262 1 20.65969269 0.867798598 2.664975776 0.999309785 0.506741766 0.518126416 0.144173404 0.404066344 5.666297941 0.135249282 0.035974214 7.375621097 -0.867798598 -0.492568018 DLEALMFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLEALMFDR 9 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 ;;; 144.09 0.00023355 175561000 201631 245564 241669 222199 320439 308507 265399 229401 233526 251722 FALSE TRUE 209591.5476 287737.7068 247967.0927 266149.299 265970.8932 236860.9247 244596.3329 226326.2548 225121.4449 301042.1064 0.696220041 0.955805519 0.823695714 0.884093266 0.883500639 0.786803307 0.812498743 0.751809298 0.747807167 1 18.19960576 2.728365644 24.26162743 0.799723715 0.855196669 0 0.091354254 1226.595543 2918999.253 0.027274287 0.025996696 535.0146123 -2.728365644 0.055472954 DLEDKEGEIQAGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLEDKEGEIQAGAK 14 1 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7;E7EQL5 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ; 230.86 6.89E-13 570150000 1264170 521480 803320 519180 1254040 1097710 1140740 781410 943640 457420 FALSE TRUE 1314080.408 611040.1334 824255.1791 621872.2544 1040878.729 842783.4885 1051325.818 770936.4771 909678.5807 547042.6912 2.402153304 1.116988022 1.506747449 1.136789257 1.902737657 1.5406174 1.921835051 1.40928028 1.662902357 1 19.0612939 -1.326793457 3.103066262 0.995167412 1.594721819 0.20298353 0.366259221 31278382.82 41609615.58 1395105.634 0.086490991 0.047120137 1.326793457 0.599554407 DLEDSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLEDSLAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 189.53 0.00044487 3562622000 3359560 3670730 3560810 3887920 4134480 4658100 4430770 3656180 3732940 3125420 FALSE TRUE 3492198.023 4301149.323 3653607.634 4656938.972 3431702.566 3576326.869 4083474.67 3607174.887 3598592.219 3737786.209 0.934295818 1.150721064 0.977479029 1.245908329 0.918110982 0.956803484 1.092484814 0.965056503 0.962760312 1 21.83375262 DLEEAEEYKEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLEEAEEYKEAR 12 1 E5RJD8;O75347;E5RIW3;E5RHG6;E5RIX8 E5RJD8 TBCA Tubulin-specific chaperone A 0 113.24 0.00020779 0 200450 116500 136880 127850 209640 203580 240070 167180 161630 84463 FALSE TRUE 208363.9208 136507.9688 140447.2052 153138.3484 174005.4677 156301.6303 221252.6861 164939.2256 155812.9679 101011.9077 2.06276592 1.351404719 1.390402463 1.516042533 1.722623319 1.547358463 2.190362415 1.632869127 1.542520792 1 16.62416585 3.242738572 24.80072202 1.673739875 1.550261 0 0.329697707 425.9132631 2528238.93 0.088872699 0.116137402 1748.793666 -3.242738572 -0.123478875 DLEEAEGR ddPTM_MDA-MB-175_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 ; 121.67 0.0033111 185460000 264530 312970 314340 344180 281500 461620 308870 265190 295800 312620 FALSE TRUE 274973.8487 366720.1629 322531.9586 412257.7767 233650.7305 354415.7509 284659.9623 261635.5618 285154.2158 373871.9035 0.735476098 0.980871147 0.862680388 1.10267119 0.624948621 0.947960378 0.761383671 0.69980001 0.762705657 1 18.51218453 3.232477048 24.99999287 0.78317871 0.920617711 0.155933338 0.13470546 230.3468965 946594.1432 0.036597802 0.044810185 1707.957454 -3.232477048 0.137439001 DLEEALEMGVDWSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLEEALEMGVDWSLR 15 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;; 190.3 5.17E-07 60639000 47478.4 53688.9 54258.1 52589.7 65319 68699.6 64905.2 52521.7 56693.1 51805.6 FALSE TRUE 49352.88389 62909.55093 55672.11066 62991.7857 54216.09971 52745.15905 59817.76083 51817.73252 54652.72641 61955.91544 0.796580658 1.015392162 0.898576193 1.016719473 0.875075436 0.851333705 0.965489097 0.836364569 0.882122813 1 15.91895441 DLEEDHACIPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DLEEDHACIPIK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 138.99 6.46E-05 2884620000 2655780 1963990 2409600 2155310 2952700 3148150 3435460 2616630 2669480 1698290 FALSE TRUE 2760632.245 2301290.005 2472396.156 2581623.885 2450801.109 2417039.873 3166179.668 2581558.355 2573405.936 2031037.41 1.359222746 1.133061358 1.217307049 1.271086329 1.206674528 1.190051873 1.55889776 1.271054064 1.267040146 1 20.95378538 DLEEDHACIPIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLEEDHACIPIKK 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 196.15 9.36E-08 20601350000 27901700 15780800 23046000 17278800 32182700 27172200 29660900 23755700 27596300 13286250 FALSE TRUE 29003280.66 18491029.64 23646597.69 20696495.07 26712296.15 20861868.35 27336001.15 23437293.7 26603114.55 15889436.31 1.825318413 1.163731002 1.488196135 1.302531737 1.681135544 1.312939487 1.720388353 1.47502361 1.674264212 1 23.92156461 -0.573991665 9.101260909 1 1.504090582 0.370805483 0.201092741 0 0 0.175720694 0.041417765 0.266690985 0.573991665 0.504090582 DLEEWNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 201.49 0.00025906 6353400000 2812010 3233540 3361470 2993670 3786010 4207950 3468500 3104820 3328480 2744710 FALSE TRUE 2923030.326 3788875.342 3449072.67 3585808.991 3142465.373 3230717.385 3196629.907 3063204.966 3208688.655 3282483.374 0.890493566 1.154270992 1.050750995 1.092407358 0.957343881 0.984229626 0.973844965 0.933197405 0.977518631 1 21.64635627 3.226899834 24.93712596 0.966199718 1.054913623 0.246415739 0.064148764 245.1045793 524167.1692 0.017414145 0.020975409 1686.164083 -3.226899834 0.088713905 DLEFTIYDDDDVSPFLEGLEERPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DLEFTIYDDDDVSPFLEGLEERPQR 25 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;;;;; 378.11 3.12E-120 2156162000 292821.4 320645.3 341769 314350 348806 428989 390189 320336 324765 282870 FALSE TRUE 304382.215 375713.636 350675.7809 376527.4918 289516.0807 329362.8061 359604.9666 316042.4199 313076.7711 338292.9606 0.899759234 1.110616181 1.036603837 1.113021953 0.855814677 0.973602305 1.062998668 0.934227006 0.925460496 1 18.36791363 3.255631233 24.99999386 0.961817116 1.044801657 0.221503961 0.074326425 367.0561699 537551.957 0.020073802 0.027111997 1801.487416 -3.255631233 0.082984541 DLEFTIYDDDDVSPFLEGLEERPQRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLEFTIYDDDDVSPFLEGLEERPQRK 26 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ;;; 315.98 3.61E-82 759830000 544621 493763 625707 339277 869738 730633 500902 562607 666530 661972 FALSE TRUE 566123.0576 578562.9543 642013.4384 406384.978 721900.2454 560954.5586 461639.9924 555066.1734 642541.7155 791672.7392 0.715097324 0.730810758 0.810958123 0.513324456 0.911867 0.708568744 0.583119728 0.701130841 0.811625415 1 19.59454465 0.929143514 3.187148242 0.999508859 0.707644108 0.427042636 0.103163879 0.287129154 7.011434277 0.094300659 0.024599654 8.494611362 -0.929143514 -0.291864751 DLEGENIEIVFAKPPDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLEGENIEIVFAKPPDQK 18 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 161.51 3.46E-11 168250000 453590 304350 409050 301930 568830 545780 535060 430730 494190 300950 FALSE TRUE 471498.0834 356619.745 419710.179 361650.8528 472140.4798 419030.8664 493120.5991 424956.7689 476404.1984 359915.3905 1.310024789 0.990843277 1.166135681 1.004821862 1.311809643 1.164248258 1.370101452 1.180712968 1.32365609 1 18.45729827 3.229146802 24.99974824 1.237398541 1.112318261 0.139289381 0.127986566 310.6641784 825012.366 0.033491223 0.040535903 1694.910626 -3.229146802 -0.125080281 DLEGSDIDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLEGSDIDTR 10 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 189.38 2.37E-06 1802550000 1277770 1403510 1532100 1518500 1766010 1887150 1626320 1529610 1484120 1363740 FALSE TRUE 1328217.346 1644551.925 1572027.785 1818854.768 1465824.251 1448888.013 1498844.789 1509108.08 1430706.811 1630938.743 0.814388249 1.008346838 0.963879111 1.115219548 0.898761071 0.888376721 0.919007409 0.925300283 0.87722903 1 20.63727117 DLEGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLEGYR 6 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4;Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 A0A0B4J1W3;Q6N069 NAA15;NAA16 "N-alpha-acetyltransferase 15, NatA auxiliary subunit;N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ; 132.94 0.034151 371150000 511800 614190 607720 551610 678640 742070 660890 609400 593710 504680 FALSE TRUE 532006.2592 719672.3548 623557.6824 660716.8116 563285.0152 569735.4887 609087.7149 601231.9898 572342.4931 603562.3833 0.881443698 1.192374433 1.033128803 1.094695146 0.933267266 0.943954601 1.009154533 0.996138935 0.948273963 1 19.20314337 3.240990466 24.9999455 0.97456371 1.059316393 0.202664911 0.075447387 92.07400348 947309.9868 0.019904844 0.025740362 1741.768638 -3.240990466 0.084752683 DLEHLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLEHLSK 7 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 111.82 0.006494 564950000 429540 1113850 1131380 1352210 1337400 1604380 1493150 1349770 1102040 740270 FALSE TRUE 446498.5709 1305145.073 1160864.692 1619673.102 1110069.226 1231787.06 1376113.001 1331678.541 1062377.796 885311.7332 0.50434051 1.474220915 1.311249641 1.829494676 1.253873844 1.391359691 1.554382428 1.504191677 1.200004197 1 19.75582602 4.740444789 24.91098038 1.424540068 0.504340185 0.600796022 0.215261029 96.63935391 1277584.064 0.047294254 0.30754197 55010.39829 -4.740444789 -0.920199883 DLEIERPILGQNDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLEIERPILGQNDNK 15 1 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ;;; 246.34 3.30E-18 2115670000 1469090 921430 1215060 899810 1620460 1539670 1380900 1151780 1311380 788670 FALSE TRUE 1527090.808 1079678.435 1246725.462 1077789.732 1345014.788 1182104.976 1272661.45 1136342.273 1264183.69 943194.7865 1.619061968 1.144703565 1.321811231 1.142701113 1.426020168 1.253298887 1.34930925 1.204780062 1.340320905 1 19.84719622 -4.046730856 0.239887949 1.35E-10 1.33183632 0.332423642 0.133857738 117.9978874 1.787024594 57.77724894 0.195772701 8.98E-05 4.046730856 1.33183632 DLEKPFLLPVEAVYSVPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLEKPFLLPVEAVYSVPGR 19 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 133.21 1.11E-05 273330000 300150 310980 322890 310140 297670 458840 328710 261020 332880 320330 FALSE TRUE 312000.1538 364388.3959 331304.7787 371484.7663 247072.1597 352281.3638 302944.8513 257521.4538 320899.7138 383092.5304 0.814425051 0.951175935 0.864816597 0.969699842 0.644941209 0.919572521 0.790787675 0.672217372 0.837655888 1 18.54733337 3.267994619 24.99999693 0.79008261 0.901167455 0.126245975 0.106816742 329.884035 280187.3403 0.028231224 0.038219889 1853.508657 -3.267994619 0.111084844 DLELALS(ph)PIHNSSALPTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLELALSPIHNSSALPTTGR 20 0 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR 186.82 2.02E-17 378250000 23897.2 149430 123611 137265 113557 195613 99276 170072 114505 166512 TRUE FALSE 24840.67991 175093.4401 126832.4042 164415.6073 94254.6217 150184.8453 91494.48771 167792.463 110383.9874 199136.8383 0.124741761 0.879261926 0.636910806 0.825641346 0.473315849 0.754179119 0.45945536 0.84259881 0.554312242 1 17.6034006 -5 0.17138918 2.387165371 0.55489249 0.229596535 0.216133317 200.8323554 1.901196922 95.12646817 0.701101979 1.00E-05 5 -1.832272881 DLELPLS(ph)PSLLGGPGPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 DLELPLS(0.854)PS(0.146)LLGGPGPER;DLELPLS(0.769)PS(0.231)LLGGPGPER;DLELPLS(0.998)PS(0.002)LLGGPGPER;DLELPLS(1)PSLLGGPGPER;DLELPLS(0.986)PS(0.014)LLGGPGPER;DLELPLS(0.991)PS(0.009)LLGGPGPER 311.24 3.85E-61 417274000 551601 574754 611395 574288 737505 827951 743611 703410 694127 618173 TRUE FALSE 573378.6334 673463.5285 627328.456 687880.4523 612144.1635 635671.928 685324.8268 693981.9395 669145.5049 739292.1637 0.775577859 0.910957212 0.848552828 0.930458195 0.828013867 0.859838585 0.92700134 0.938711342 0.905116458 1 19.4957851 0.773798272 0.021266722 1.869466516 5.48E-10 0.550647948 0.041131656 293.2493535 3.387223798 154.1258707 142.7766979 5.940161763 -0.773798272 -1.869466515 DLEPESDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLEPESDR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 127.56 0.002724 205880000 82983 83883 96109 75880 101240 118230 93664 99630 99468 76856 FALSE TRUE 86259.23292 98289.25273 98613.67949 90888.83752 84031.26096 90772.87429 86322.37093 98294.62281 95888.16611 91914.4617 0.938472916 1.069355691 1.072885351 0.988841536 0.914233293 0.987579893 0.939159838 1.069414116 1.043232635 1 16.48800425 -0.569049524 4.529795182 1.000000001 1.005130462 0 0.056507316 8.44E-10 3.73E-10 0.056646937 0.013351807 0.269743182 0.569049524 0.00513046 DLEPHSFGGLLEGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLEPHSFGGLLEGIR 15 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 0 ; 176.32 8.06E-07 224080000 168890 183977 183756 173153 245750 237341 203708 188969 196848 208352 FALSE TRUE 175557.9076 215573.6186 188544.8323 207402.1466 203977.5028 182222.1497 187740.8347 186436.1796 189763.4789 249174.5853 0.70455784 0.865150908 0.756677621 0.832356744 0.818612791 0.731303112 0.753450977 0.74821507 0.761568355 1 17.9267974 -1.211004415 6.233032034 1.000002712 0.775569321 0.676061558 0.046792029 1.71E-06 2.16E-07 0.043895022 0.010346031 0.061517062 1.211004415 -0.22443339 DLES(ph)PCQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLESPCQER 9 0 H3BSI0;A0A1B0GVY7;H3BV12;A0A1B0GV12;A0A1W2PRN1;H3BQL2;H3BMP0;A0A0J9YX86;D6RF30;I6L899;A6NCC3-1;P0CJ92;A6NC78;I6L899-2;F8WBI6;A6NCC3;A6NMD2;H3BSY2;H3BSY2-3 H3BSI0 GOLGA8O;GOLGA8Q;GOLGA8T;GOLGA8N;GOLGA8K;GOLGA8R;GOLGA8H;GOLGA8IP;GOLGA8J;GOLGA8M Golgin subfamily A member 8K;Golgin subfamily A member 8R;Golgin subfamily A member 8O;Golgin subfamily A member 8H;Putative golgin subfamily A member 8I;Golgin subfamily A member 8N;Golgin subfamily A member 8J;Golgin subfamily A member 8M 1 DLES(1)PCQER;DLES(1)PCQER 67.385 0.039323 408470000 213766 222670 211080 206444 273080 294340 236390 221497 215560 196532 TRUE FALSE 222205.6467 260911.8404 216580.9182 247278.007 226661.9591 225983.9958 217861.1341 218528.195 207802.0377 235038.6826 0.945400324 1.110080424 0.921469249 1.05207366 0.964360235 0.961475759 0.926916079 0.929754169 0.884118458 1 17.84253869 2.769399113 1.686765941 0.929748651 1.008614331 0.227696347 0.056389873 0.45861609 2.603713701 0.020136897 0.020069161 588.029498 -2.769399113 0.07886568 DLESAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLESAEER 8 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 95.741 0.02195 1285430000 853860 1530100 1194880 1457940 1153760 1678590 1117040 1243630 1078300 1791170 FALSE TRUE 887571.0521 1792882.772 1226019.554 1746316.18 957644.2873 1288762.912 1029483.486 1226961.174 1039492.194 2142115.467 0.414343235 0.836968315 0.572340554 0.815229714 0.4470554 0.601630926 0.480591967 0.572780129 0.485264314 1 21.03060482 -1.850612573 5.17729542 1.069714736 0.586241023 0.458987805 0.136451738 0.071044195 0.002049933 0.085484096 0.029146472 0.014105466 1.850612573 -0.483473713 DLESAEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;; 143.7 0.00016244 706150000 757110 750630 739000 634620 942040 1017380 814460 915880 801530 872620 FALSE TRUE 787001.2874 879544.8634 758258.9471 760145.9418 781912.3773 781108.9135 750620.497 903604.1267 772683.0919 1043593.182 0.754126513 0.842804341 0.726584804 0.728392975 0.749250178 0.748480277 0.719265429 0.865858596 0.74040642 1 19.99312799 -0.342399813 0.546959127 1.029469489 0.757903361 0.685508473 0.047760656 4.317334912 1.197299894 0.306035096 0.021237708 0.45456939 0.342399813 -0.271566129 DLESFNEDFLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLESFNEDFLKR 12 1 Q6N069 Q6N069 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 ; 100.55 0.0050819 256320000 60523 51864 58933 51539 78068 74588 67236 65024 68469 57096 FALSE TRUE 62912.49477 60771.23855 60468.84239 61733.26037 64798.02925 57266.06739 61965.86663 64152.45964 66004.81406 68282.86803 0.921351088 0.889992473 0.885563892 0.904081245 0.948964669 0.838659375 0.907487755 0.939510326 0.966637986 1 16.05923604 1.342905696 1.639096928 0.995403727 0.898282573 0.620875989 0.026774425 0.224921667 1.09634718 0.024047117 0.007402496 22.02448164 -1.342905696 -0.097121154 DLESLFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLESLFHR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 164.53 0.00032954 203122000 201520 337890 272540 349660 318510 418380 372580 328650 264540 324750 FALSE TRUE 209476.1652 395919.9791 279642.6163 418821.7044 264369.784 321217.5856 343376.206 324244.9843 255019.2571 388378.5448 0.539360807 1.019417742 0.720025913 1.078385276 0.680701309 0.827073457 0.88412764 0.834868426 0.656625502 1 18.56710398 4.761008167 24.3014868 0.847741885 0.53936032 0.321908837 0.137298124 4831.000805 5229869.063 0.029725313 1.514976876 57677.73094 -4.761008167 -0.308381565 DLESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLESLR 6 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 160.69 0.020314 1722720000 1304380 1648480 1438930 1507010 1798800 1936970 1457840 1447000 1367440 1440660 FALSE TRUE 1355877.93 1931593.617 1476429.698 1805092.08 1493040.619 1487138.073 1343570.691 1427605.332 1318226.102 1722929.744 0.786960661 1.121109914 0.856929717 1.047687572 0.866570807 0.86314493 0.779817457 0.828591727 0.765107287 1 20.71643244 3.050427996 8.739268215 0.833981643 0.958479297 0.182293399 0.105005348 0.394335408 62.90034669 0.027734317 0.03314604 1123.124745 -3.050427996 0.124497655 DLEWVIFDEVHYINDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLEWVIFDEVHYINDVER 18 0 Q15477 Q15477 SKIV2L Helicase SKI2W 0 ;; 198.38 1.74E-15 53786500 41573.4 41037.3 50194.3 59743.8 67253 66442 66156 48813 51336 44472.8 FALSE TRUE 43214.74993 48085.13705 51502.40469 71560.94532 55821.35908 51011.85244 60970.51985 48158.74158 49488.42739 53186.39368 0.812515137 0.904087187 0.968337974 1.345474667 1.049542096 0.959114708 1.146355593 0.905471085 0.930471573 1 15.6987696 4.252522599 3.106175974 1.044160619 0.840282258 0.279282867 0.121247061 0.329614995 6.402212207 0.032203338 0.098781919 17886.38599 -4.252522599 -0.203878361 DLFAFQES(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLFAFQESPPR 11 0 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 DLFAFQES(1)PPR;DLFAFQES(1)PPR;DLFAFQES(1)PPR;DLFAFQES(1)PPR 225.92 5.37E-12 385892000 503468 613575 554870 612560 692250 778390 589772 610813 589570 591014 TRUE FALSE 523345.3054 718951.7333 569330.368 733722.5397 574581.5923 597620.7191 543544.1296 602626.0508 568351.4909 706811.8777 0.74043083 1.017175512 0.805490663 1.038073302 0.812920114 0.845515954 0.7690082 0.852597516 0.804105744 1 19.43096676 DLFDFSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLFDFSTR 8 0 U3KQC1;A0A0A0MQU0;Q9BV38;K7EIR0 U3KQC1 WDR18 WD repeat-containing protein 18 0 ;;; 147.29 0.0012555 321506000 575225 677952 668112 632556 782893 839834 709407 718711 693606 731899 FALSE TRUE 597935.3272 794384.9823 685523.5476 757673.6888 649817.1275 644795.2813 653801.8256 709077.8546 668643.2555 875300.596 0.683119982 0.907556771 0.783186428 0.865615415 0.742393105 0.736655823 0.746945482 0.810096392 0.763901291 1 19.73941903 -1.00624747 4.846818756 1.000003263 0.786096634 0.524158712 0.06216453 2.07E-06 4.24E-07 0.05673878 0.013373255 0.098571764 1.00624747 -0.21390663 DLFDMKPFEDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLFDMKPFEDALR 13 1 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3 P29353-2 SHC1 SHC-transforming protein 1 0 ; 123.02 0.0002082 441230000 639420 458930 627430 526930 833140 760290 779110 620880 716610 472020 FALSE TRUE 664664.7953 537747.6575 643781.3412 631155.1813 691523.1604 583724.1698 718041.3224 612558.1192 690819.3461 564503.2816 1.177433005 0.952603244 1.140438616 1.118071766 1.225011763 1.034049205 1.271987862 1.08512765 1.223764978 1 19.10662244 4.057783926 24.99983344 1.143301266 1.060393414 0.080744901 0.095666193 153.8248963 66548.91761 0.021214497 0.045828548 11423.0986 -4.057783926 -0.082907852 DLFDYS(ph)PPLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DLFDYSPPLHK 11 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK;DLFDYS(1)PPLHK 124.07 0.00022985 2414337000 1121670 816740 966340 844010 1217890 1201730 1274780 1024170 1042830 686573 TRUE FALSE 1165954.398 957008.7416 991523.6143 1010952.659 1010873.493 922646.4199 1174859.413 1010442.676 1005298.752 821093.8341 1.420001405 1.165529081 1.207564316 1.231226709 1.231130293 1.123679635 1.430846712 1.230605607 1.224340886 1 19.64718758 0.686718787 2.731001857 1.000036682 1.251645148 0.397886693 0.093507466 2.464425564 20.26775697 0.085034077 0.02246645 4.860923512 -0.686718787 0.251608467 DLFEDELVPLFEK ddPTM_MDA-MB-175_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 ;;; 174.84 4.49E-05 162141000 473175 421055 466715 363966 602731 573313 575760 477147 500800 377163 FALSE TRUE 491856.3144 493367.9209 478877.9763 435957.3885 500278.9999 440169.7444 530630.4267 470751.6249 482776.3058 451060.8686 1.090443327 1.093794552 1.061670408 0.96651565 1.109116385 0.975854425 1.176405367 1.043654322 1.070312987 1 18.78296261 DLFEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLFEQR 6 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;E9PN68;E9PLN2;E9PNT0;E9PLH1 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 100.74 0.086812 584220000 546870 713690 742070 642440 729380 814640 665220 692850 776060 715930 FALSE TRUE 568460.8499 836260.7058 761408.9538 769512.7145 605400.2481 625452.206 613078.3182 683563.479 748129.7522 856202.7762 0.6639325 0.976708706 0.88928578 0.898750548 0.707075783 0.730495419 0.716043366 0.798366343 0.873776368 1 19.70759299 4.806510556 21.75483187 0.825502776 0.663923585 0.205630858 0.100421842 46539.92973 14896537.46 0.024706496 89.48074797 64048.73496 -4.806510556 -0.161579191 DLFFELDAMDHLESFIAECDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLFFELDAMDHLESFIAECDRR 22 1 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 ;; 186.3 2.11E-17 111010000 50447.3 74779 81598 74253 89366 99776 83653 78212.8 87460 81419 FALSE TRUE 52438.99836 87621.71155 83724.51091 88940.02178 74175.59924 76604.53612 77096.05927 77164.48535 84312.33168 97371.49419 0.538545688 0.899870258 0.859846217 0.913409233 0.761779408 0.786724459 0.791772376 0.792475108 0.865883105 1 16.57121186 -4.999999999 0.259380088 2.25281476 0.789827609 0.284576855 0.098804294 264.9970418 2.605398409 176.7463258 0.126961793 1.00E-05 4.999999999 -1.462987151 DLFPYEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLFPYEESK 9 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 145.72 0.00022448 1234491000 2528470 1694590 2077070 1688790 2695870 2819980 2900290 2204200 2422650 1318510 FALSE TRUE 2628295.948 1985622.65 2131200.151 2022827.621 2237626.98 2165082.382 2672957.691 2174656.304 2335459.3 1576846.79 1.666804895 1.259236257 1.351558163 1.282830795 1.419051613 1.373045495 1.695128346 1.379117057 1.481094621 1 20.58861106 -0.991703421 5.154623263 0.999997285 1.427772478 0.468446456 0.138606827 4.17E-06 8.17E-07 0.129528231 0.030529903 0.101928722 0.991703421 0.427775193 DLFPYEESKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLFPYEESKEK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 165.58 1.95E-05 3371900000 4188650 2216730 3404040 1670390 5964260 4549200 3417980 3290000 4271270 2470790 FALSE TRUE 4354021.136 2597436.134 3492752.079 2000788.156 4950457.216 3492717.244 3150069.796 3245902.931 4117547.827 2954893.994 1.473494868 0.879028533 1.182022802 0.677109961 1.67534173 1.182011013 1.06605171 1.098483715 1.393467189 1 21.49467494 4.775027464 22.95476727 1.133009497 1.473497204 0.139182192 0.257387559 12937.60665 8143365.592 0.058484201 11.44087125 59569.9813 -4.775027464 0.340487707 DLFQVAFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLFQVAFNR 9 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 128.12 0.00099163 574050000 311560 1454540 1348530 1409530 1047640 1414160 1149980 1076250 1492950 2352200 FALSE TRUE 323860.6294 1704345.93 1383673.8 1688330.827 869562.527 1085742.772 1059841.563 1061824.629 1439219.021 2813068.554 0.115127173 0.605867186 0.491873473 0.600174078 0.309115299 0.385963851 0.376756393 0.377461341 0.511618893 1 21.42371328 0.821507356 3.946592054 0.99997221 0.416702873 0.632019275 0.134841367 0.860459789 18.2913235 0.123838043 0.031672553 6.629905778 -0.821507356 -0.583269336 DLFSLDSEDPSPAS(ph)PPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLFSLDSEDPSPASPPLR 18 0 Q9BTK6;H3BTX0 Q9BTK6 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 DLFSLDSEDPSPAS(1)PPLR;DLFSLDS(0.001)EDPS(0.033)PAS(0.967)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR 252.38 1.85E-30 2757778000 675594 750058 722084 706370 854554 920961 759004 777862 791499 745383 TRUE FALSE 702266.9728 878874.6269 740902.1022 846087.8777 709297.2163 707081.765 699511.2832 767436.0322 763013.1056 891426.5276 0.787801295 0.98591931 0.831142084 0.949139218 0.795687804 0.793202517 0.784709969 0.860907779 0.855946151 1 19.76575637 5.049220534 15.67268285 0.862283331 0.347838711 0.086581965 0.076178908 319869.306 2713753.443 0.017514668 4943409.498 112000.6477 -5.049220534 -0.51444462 DLGEELEALKTELEDTLDSTAAQQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLGEELEALKTELEDTLDSTAAQQELR 27 1 P35579 P35579 MYH9 Myosin-9 0 ; 170.65 4.75E-12 15813600000 81755 51050 70357 49180 107776 100012 86474 67734 76267 46596 FALSE TRUE 84982.75053 59817.44039 72190.56122 58907.65721 89456.27402 76785.7287 79695.94192 66826.13652 73522.16557 55725.59407 1.525021885 1.073428492 1.295465081 1.057102364 1.605299603 1.377925709 1.430149705 1.199200074 1.319360822 1 15.76605247 0.268797981 1.080331268 0.999305624 1.317452339 0.244922008 0.168579873 5.562945981 6.918287955 0.166981959 0.048774148 1.856940469 -0.268797981 0.318146715 DLGEELEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLGEELEALR 10 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 88.496 0.028278 18181000 11266 44381 36996 36982 36060 49643 27137 38674 33241 62875 FALSE TRUE 11710.79038 52003.09151 37960.14615 44296.92922 29930.53408 38114.1656 25009.93103 38155.63829 32044.6629 75194.15244 0.155740706 0.69158425 0.504828433 0.589100718 0.398043373 0.506876723 0.332604733 0.507428265 0.426158975 1 16.19833285 -1.352991316 3.607571689 1.002459842 0.46652805 0.580411523 0.138306238 62223740.49 92428135.5 1614950.357 0.029940026 0.044361751 1.352991316 -0.535931793 DLGEELEALRGELEDTLDSTNAQQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLGEELEALRGELEDTLDSTNAQQELR 27 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;; 190.6 5.36E-18 240446000 84490 103540 109278 88930 114265 123691 111056 100884 112975 103276 FALSE TRUE 87825.73044 121322.1896 112125.8745 106520.0886 94842.27611 94965.63981 102351.1405 99531.81499 108909.0518 123510.9549 0.711076443 0.982278776 0.907821291 0.862434338 0.767885539 0.768884346 0.828680668 0.805854146 0.881776454 1 16.91427948 0.919453914 4.703025064 0.999967664 0.832983174 0.336613466 0.072623209 0.515134794 26.75157199 0.070526902 0.017875491 8.307185598 -0.919453914 -0.16698449 DLGEIHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLGEIHSR 8 0 A0A0D9SEU2;A0A0A0MTN6;G5E931;H3BN57;Q8TDH9-2;Q8TDH9 A0A0D9SEU2 BLOC1S5;BLOC1S5-TXNDC5 Biogenesis of lysosome-related organelles complex 1 subunit 5 0 105.4 0.0075832 0 47068 58035 60606 65699 66081 74346 62245 65776 64070 60388 FALSE TRUE 48926.28098 68002.0598 62185.44215 78694.06611 54848.57522 57080.26822 57366.07425 64894.38031 61764.13322 72219.8724 0.677462856 0.941597618 0.861057214 1.089645599 0.759466521 0.790367891 0.794325334 0.898566809 0.855223516 1 16.14010825 0.209566135 1.345245646 1.0001104 0.856531752 0.147101847 0.106360508 14.58616348 22.62450225 0.102366379 0.029256272 1.620190699 -0.209566135 -0.143578648 DLGGACPPQDHDMQGLAERIS(ph)VL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLGGACPPQDHDMQGLAERISVL 23 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 DLGGACPPQDHDMQGLAERIS(1)VL 55.783 0.056921 57684000 21959 21592 32432 24359 44245 25213 29021 25544 34834 32039 TRUE FALSE 22825.95828 25300.25804 33277.20456 29177.1375 36724.2507 19357.66286 26746.25819 25201.62446 33580.33114 38316.42863 0.59572249 0.660297918 0.868483983 0.761478523 0.958446599 0.505205301 0.698036303 0.657723733 0.876395122 1 15.22567548 1.032526625 4.363405597 0.998837075 0.716470659 0.369788254 0.122577181 0.185217148 8.311793993 0.117864062 0.030035664 10.77771325 -1.032526625 -0.282366417 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_MDA-MB-175_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(1)GDQEDEDDESEDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 446.42 1.24E-231 4258420000 950865 592359 806790 605672 990008 1009854 984601 779842 904736 534012 TRUE FALSE 988405.8844 694092.0503 827815.6102 725472.1138 821726.7938 775330.713 907425.4008 769389.4936 872174.7281 638641.4271 1.547669541 1.08682591 1.296213454 1.135961563 1.28667944 1.214031349 1.420868366 1.204728445 1.36567202 1 19.28464661 -1.079612624 4.292209387 0.999969371 1.273299601 0.298810665 0.129669208 3.39E-05 7.27E-06 0.112043442 0.026405935 0.083250601 1.079612624 0.27333023 DLGLPTEAYISVEEVHDDGTPTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLGLPTEAYISVEEVHDDGTPTSK 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 301.36 3.15E-62 484580000 586520 492680 592420 519700 756330 759730 679270 628110 658760 466340 FALSE TRUE 609676.2625 577293.9575 607858.9519 622495.1089 627769.2968 583294.2213 626027.0425 619691.2128 635051.3563 557710.3944 1.093177155 1.035114216 1.089918635 1.116161928 1.125618785 1.045872961 1.122494845 1.111134415 1.138675848 1 19.08915663 4.016597395 23.26222381 1.100679536 1.063738313 0.059978839 0.04209123 213.0733898 298624.5828 0.009674831 0.020888802 10389.56572 -4.016597395 -0.036941223 DLGLSESGEDVNAAILDESGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLGLSESGEDVNAAILDESGKK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 249.34 4.09E-31 589150000 377830 206243 276540 200139 398580 316400 357440 257270 284730 129846 FALSE TRUE 392747.0201 241663.6309 283746.8596 239725.8968 330829.514 242920.8951 329422.9188 253821.7165 274482.6229 155286.8376 2.529171346 1.556240275 1.827243467 1.543761857 2.13044144 1.564336674 2.121383395 1.634534648 1.767584601 1 17.24457602 -2.173708967 0.293957474 2.55E-11 1.908952727 0.437760802 0.29836798 33.94894682 1.388951979 22.9959305 0.298629631 0.006703337 2.173708967 1.908952727 DLGQPAAAAGHFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLGQPAAAAGHFQR 14 0 P23610 P23610 F8A1 Factor VIII intron 22 protein 0 96.414 0.003381 265360000 57066 71377 72786 66252 77930 95736 71104 70441 70253 79681 FALSE TRUE 59319.00974 83635.44451 74682.86295 79356.44786 64683.48644 73502.76489 65530.68268 69496.85361 67724.60825 95292.96637 0.622490956 0.877666503 0.783718524 0.832762909 0.678785527 0.771334629 0.687675966 0.729296781 0.71069892 1 16.54008211 -1.117027681 5.217408215 1.000006263 0.746731004 0.533104413 0.07187555 5.00E-06 8.47E-07 0.066487539 0.015670876 0.07637871 1.117027681 -0.253275258 DLGTESQIFISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLGTESQIFISR 12 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 174.57 6.98E-05 259100000 93043 194650 151570 166580 172130 232640 143340 168610 147420 196200 FALSE TRUE 96716.40948 228079.6233 155520.0387 199529.0268 142871.4041 178612.8857 132104.6363 166350.0587 142114.383 234641.6335 0.412187761 0.972033905 0.662798142 0.850356451 0.60889196 0.761215659 0.563005952 0.708953719 0.605665673 1 17.84009949 -1.211905782 5.148174958 1.000027007 0.691875473 0.291124081 0.147885479 4.10E-05 6.27E-06 0.127995894 0.030166281 0.061389517 1.211905782 -0.308151534 DLGYIYFYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLGYIYFYQR 10 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 179.68 4.84E-06 626460000 884160 840370 855140 838420 1222540 1156360 997370 839650 890590 1145970 FALSE TRUE 919067.3195 984697.0103 877425.6509 1004256.974 1014733.087 887812.9148 919193.5333 828395.8651 858537.8399 1370500.881 0.67060688 0.718494256 0.64022261 0.732766383 0.740410387 0.647801784 0.670698973 0.604447525 0.626440925 1 20.38627182 -1.372481514 3.284733968 1.002854185 0.670903663 0.837078468 0.043349225 16256886.69 20759077.77 436958.9414 0.011601416 0.042414904 1.372481514 -0.331950523 DLHDQFQHQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLHDQFQHQLK 11 0 B7Z879;A0A087WXL6;A0A0G2JS92 B7Z879 VPS11 0 88.441 0.007504 47871000 49613 63836 75756 63110 76416 85408 55781 64784 70821 72980 FALSE TRUE 51571.75955 74799.33642 77730.26359 75592.96964 63426.83562 65573.28637 51408.73946 63915.67645 68272.16604 87279.03371 0.590883713 0.857013801 0.890594915 0.866106858 0.726713312 0.751306283 0.58901591 0.732314208 0.782228711 1 16.41334751 0.851223755 5.838183997 0.999998837 0.752856503 0.363508632 0.098404936 3.568965433 139.646064 0.099553215 0.025048954 7.099434468 -0.851223755 -0.247142333 DLHEEMNYITAIIEEQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLHEEMNYITAIIEEQPK 18 0 P49354;P49354-2;E9PQP6;H0YCW1;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 ; 125.64 2.93E-05 55656000 66354 44762 58081 47460 77691 72081 74440 60388 63563 39136 FALSE TRUE 68973.70716 52449.5253 59594.63857 56847.44635 64485.11157 55341.28015 68605.19829 59578.59763 61275.38005 46803.9499 1.473672784 1.120621773 1.273282249 1.214586514 1.377770716 1.182406192 1.465799328 1.272939523 1.309192497 1 15.51434267 -1.055019584 4.565804241 0.999985703 1.295014721 0.403544194 0.108930043 1.44E-05 2.99E-06 0.095985673 0.022622944 0.088100914 1.055019584 0.295029018 DLHQGIEAAS(ph)DEEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 DLHQGIEAAS(1)DEEDLR 166.91 4.19E-09 103320000 96827 102950 110230 120590 113670 124750 134100 120410 118900 101570 TRUE FALSE 100649.8047 120630.8617 113102.6844 144442.3421 94348.414 95778.7031 123588.8916 118796.1009 114620.8122 121470.6968 0.828593293 0.993086109 0.931110855 1.189112649 0.776717484 0.78849225 1.017437907 0.977981554 0.943608749 1 16.8902488 DLHQGIEAASDEEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ;;; 241.79 6.41E-20 1845870000 738455 819248 828128 862950 860910 1065990 935180 807200 808260 771620 FALSE TRUE 767609.7736 959947.4711 849709.696 1033638.934 714572.8257 818429.9777 861878.148 796380.8043 779170.8805 922804.1654 0.831823048 1.040250475 0.920790919 1.12010649 0.774349372 0.886894542 0.933977306 0.863000877 0.844351282 1 19.81566499 3.225222353 24.99999778 0.879685614 0.978568197 0.212955558 0.088773833 327.4552999 613750.4561 0.02400398 0.028845029 1679.663764 -3.225222353 0.098882583 DLHQGIEAASDEEDLRWWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLHQGIEAASDEEDLRWWR 19 1 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 ; 247.31 5.85E-25 181179000 12333.1 23104 17480.8 13958.9 25340 26434 13243.7 13806.1 17091.6 28861 FALSE TRUE 12820.02031 27071.93228 17936.36401 16719.92876 21032.71585 20295.10411 12205.62419 13621.05181 16476.47665 34515.76037 0.371425116 0.784335387 0.519657218 0.484414325 0.609365566 0.587995278 0.353624665 0.394632819 0.477360964 1 15.07496765 -1.361457645 3.88689426 1.001624726 0.506978356 0.590947212 0.122488546 2285.486462 65767149.51 157123.5972 0.029713933 0.043505319 1.361457645 -0.494646369 DLIDFDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLIDFDDR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;;; 178.99 0.00057395 1618000000 2965900 3031110 3046630 3241300 3458300 3925580 3710150 3203350 3114210 2598200 FALSE TRUE 3082996.022 3551679.564 3126027.681 3882419.466 2870459.401 3013923.538 3419338.748 3160414.333 3002130.19 3107267.544 0.992188789 1.143023416 1.006037503 1.249464171 0.923788943 0.969959456 1.100432679 1.017104027 0.966164048 1 21.56721504 3.19754223 24.9999995 1.00435081 1.09437299 0.277322575 0.079504456 211.9466994 129177.1727 0.022201998 0.026536729 1575.949258 -3.19754223 0.09002218 DLIDYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLIDYVR 7 0 D6RIC3;A0A0C4DGU5;A0A087X2G6;Q9Y3C1;Q9Y3C1-3;Q9Y3C1-2 D6RIC3 NOP16 Nucleolar protein 16 0 105.12 0.018609 54207000 189930 213870 226100 207100 237120 267380 224610 222870 214210 215250 FALSE TRUE 197428.5831 250600.5088 231992.3517 248063.7619 196814.4271 205285.0472 207004.4813 219882.7922 206500.6239 257424.1163 0.766938956 0.973492742 0.901206752 0.963638393 0.764553181 0.79745849 0.804137873 0.854165474 0.802180568 1 17.97378769 5.041291943 14.03443216 0.863651596 0.399674119 0.127984588 0.079797428 5538160.817 59963951.28 0.01910435 63635231.93 109974.4864 -5.041291943 -0.463977477 DLIEDSSVQKDGLNQTTIPVS(ph)PPSTTKPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLIEDSSVQKDGLNQTTIPVSPPSTTKPSR 30 2 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 DLIEDSSVQKDGLNQT(0.001)T(0.007)IPVS(0.981)PPS(0.008)T(0.001)T(0.001)KPSR 135.11 2.27E-06 368820000 180860 131730 174110 82974 279550 213460 117640 155820 214480 158900 TRUE FALSE 188000.4925 154353.6028 178647.4496 99386.00955 232032.1909 163887.15 108419.0694 153731.4878 206760.9067 190033.4127 0.989302301 0.812244545 0.940084415 0.522992289 1.221007335 0.862412287 0.57052635 0.808970831 1.088023963 1 17.53589358 2.470725052 24.94013068 0.821449564 0.890781692 0 0.207046738 820.6569085 3199878.7 0.070769185 0.059350221 295.6140367 -2.470725052 0.069332128 DLIHDQDEDEEEEEGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLIHDQDEDEEEEEGQR 17 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;R4GNE6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;;; 370.34 9.26E-105 12554790000 3407960 3993120 3992160 3538140 4554880 4993870 4164870 4079130 4069570 3771020 FALSE TRUE 3542508.892 4678907.298 4096198.969 4237973.532 3780643.125 3834119.375 3838416.607 4024455.934 3923106.971 4509879.168 0.785499735 1.037479525 0.908272443 0.939708887 0.838302532 0.850160111 0.85111296 0.89236447 0.869891814 1 22.10465735 5.041516107 15.12734843 0.900803061 0.295876524 0.24744146 0.063290434 1722201.155 18446563.72 0.014908496 28508068.22 110031.2652 -5.041516107 -0.604926536 DLIHDVSFDFHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DLIHDVSFDFHGR 13 0 K7ELV2;Q96EE3;Q96EE3-1;K7EP88;K7ENI5 K7ELV2 SEH1L Nucleoporin SEH1 0 ;;;;; 289.45 9.77E-41 580814000 266446 389908 360388 434862 378484 475895 412465 386757 370127 428612 FALSE TRUE 276965.4938 456871.6659 369780.0073 520876.4057 314149.4249 365375.5985 380134.9155 381573.155 356806.2016 512590.3151 0.540325257 0.89129984 0.721394838 1.016165133 0.612866485 0.712802384 0.741595977 0.744401803 0.696084555 1 18.9674467 -1.199403625 5.361269156 1.000012815 0.748853778 0.272851898 0.125949876 1.78E-05 2.66E-06 0.112691858 0.026560371 0.063182437 1.199403625 -0.251159037 DLILQCLDDKDESIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLILQCLDDKDESIR 15 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ;; 240.63 6.89E-18 738030000 983393 665161 789079 716728 1123520 1171160 1076775 922199 1022506 671926 FALSE TRUE 1022218.115 779397.2275 809643.047 858494.6592 932544.4717 899175.8391 992374.5619 909838.4308 985706.2088 803577.0349 1.272084779 0.969909783 1.007548762 1.068341456 1.160491691 1.118966571 1.234946394 1.132235481 1.226648057 1 19.61607681 3.241512938 22.46964686 1.155538179 1.066507993 0.090503025 0.096193567 37.94447426 288775.5015 0.025615467 0.033161875 1743.865307 -3.241512938 -0.089030186 DLISHDEMFSDIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DLISHDEMFSDIYK 14 0 Q5W0H4;A0A0B4J2C3;P13693 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;;;; 259.27 2.06E-24 14746563000 13125279 10688504 13505685 10037989 17395990 16119960 16080100 13370249 14395400 9798325 FALSE TRUE 13643475.15 12524171.42 13857654.25 12023473.26 14439025.83 12376343.59 14819699.74 13191042.68 13877312.37 11718119.18 1.164305887 1.068786827 1.182583487 1.026058284 1.232196533 1.056171506 1.264682456 1.125696238 1.18426107 1 23.48223769 5.094536973 19.84977533 1.13507433 3.364248929 0.008881013 0.084702216 2644.641928 639508.0086 0.017549542 40330.02846 124318.8467 -5.094536973 2.229174599 DLISLDS(ph)SPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLIS(0.012)LDS(0.566)S(0.422)PAK 89.301 0.012939 42920000 151870 78019 93411 89868 117830 144090 150500 109530 106420 65130 TRUE FALSE 157865.9449 91418.15635 95845.3674 107643.6222 97801.29869 110627.2812 138703.4167 108061.9295 102589.965 77890.97651 2.026755241 1.173668125 1.230506686 1.38197808 1.255617827 1.42028366 1.780737936 1.387348501 1.317096917 1 16.24916858 0.870367802 2.542641326 1.0010471 1.442723257 0.237910593 0.247883349 0.744011103 9.586270494 0.229803845 0.061522006 7.419383196 -0.870367802 0.441676158 DLISLDS(ph)SPAKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.714)S(0.286)PAKER;DLISLDS(0.5)S(0.5)PAKER;DLIS(0.006)LDS(0.72)S(0.274)PAKER 136.6 6.41E-06 572780000 856540 494560 640520 435800 836030 948320 763610 684750 734880 462980 TRUE FALSE 890356.8606 579496.8329 657212.4774 521999.9393 693921.9192 728087.0519 703756.2529 675572.0463 708431.8124 553692.0667 1.608036152 1.046604905 1.186963868 0.942762179 1.25326325 1.314967462 1.271024628 1.220122315 1.279468959 1 19.07872433 -1.918126239 2.345203884 0.855926666 1.224195712 0.151406518 0.165472696 15681294.71 7398742.984 12401259.37 0.039130309 0.012074628 1.918126239 0.368269047 DLISLDSS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.035)S(0.965)PAK;DLISLDS(0.023)S(0.977)PAK 203.88 3.68E-08 147642000 1367720 647760 875640 749930 1077900 1285750 1362160 951400 955680 486280 TRUE FALSE 1421718.642 759007.7411 898459.8977 898263.9157 894678.943 987154.0482 1255390.34 938648.0392 921285.2635 581557.2556 2.444675271 1.305129863 1.544920795 1.5445838 1.538419364 1.697432263 2.158670239 1.614025154 1.584169494 1 19.14956171 4.751889895 24.31049169 1.604719929 2.444676083 0.468691833 0.279820298 1401.776604 2556552.21 0.065450384 1.230255541 56479.3766 -4.751889895 0.839956155 DLISLDSS(ph)PAKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLISLDSSPAKER 13 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLISLDS(0.213)S(0.787)PAKER;DLISLDS(0.231)S(0.769)PAKER 168.05 1.87E-05 749010000 1121750 561900 772570 507140 1034950 1100400 1018560 769660 849010 562580 TRUE FALSE 1166037.556 658401.954 792703.8089 607450.7783 859029.5687 844848.7767 938722.6057 759343.9666 818454.2959 672806.7798 1.733094242 0.978589952 1.178204252 0.902860668 1.276784947 1.255707882 1.395233571 1.128621158 1.21647748 1 19.35983272 -4.999999997 0.022938466 8.20E-08 2.006048105 0.096174648 0.215544403 8583.186326 14.88589003 915.7648085 458.7774926 1.00E-05 4.999999997 2.006048023 DLKDYFSK ddPTM_MDA-MB-175_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 ; 94.309 0.0095311 6761900000 5975500 3971560 5368600 3404370 7265700 6261200 6107500 5198600 6061600 3651360 FALSE TRUE 6211417.354 4653644.536 5508510.126 4077744.225 6030678.909 4807131.189 5628778.191 5128921.27 5843444.2 4366774.082 1.422426999 1.065693908 1.261459838 0.933811584 1.381037534 1.100842658 1.289001465 1.174533231 1.338160411 1 22.05813646 -2.341460413 1.992763904 4.21E-05 1.208710666 0.166930351 0.144977417 1698674.79 238372.0407 7614231.93 0.032299377 0.004555537 2.341460413 1.208668527 DLKDYFTK ddPTM_MDA-MB-175_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 ; 120.45 0.0013671 3483500000 8007800 5218500 7228700 4771400 9699000 8213300 8015300 7331200 8168600 4943000 FALSE TRUE 8323954.127 6114736.781 7417085.86 5715168.679 8050367.444 6305885.549 7387039.842 7232937.255 7874613.682 5911486.211 1.408098375 1.034382313 1.254690546 0.966790495 1.36181785 1.066717459 1.249607895 1.223539563 1.332086958 1 22.49508945 DLKEEFTEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLKEEFTEALR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;; 128.54 0.00024047 331860000 698718 562204 673570 554603 936520 924370 850120 756620 807340 555124 FALSE TRUE 726303.9262 658758.1637 691123.7875 664301.8181 777330.6649 709699.0765 783485.373 746478.7465 778283.9911 663889.9193 1.094012584 0.992270171 1.041021663 1.000620432 1.170872824 1.069001134 1.1801435 1.124401388 1.172308795 1 19.34058452 3.243734024 24.99999745 1.127291037 1.029790449 0.353764688 0.057304209 119.4389021 577173.1739 0.014640563 0.019238555 1752.806699 -3.243734024 -0.097500588 DLKIES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLKIESDVQEPTEPEDDLDIMLGNK 25 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 DLKIES(0.987)DVQEPT(0.013)EPEDDLDIMLGNK 79.365 0.015156 28774000 15631 7759.8 10007 6192.6 16776 16056 11200 8764.2 15176 7296.2 TRUE FALSE 16248.12395 9092.485287 10267.79064 7417.477797 13924.42151 12327.23733 10322.11473 8646.730234 14629.81872 8725.750696 1.86208895 1.042029002 1.176722897 0.850067582 1.595784936 1.412742326 1.182948619 0.990943993 1.676625798 1 13.09106354 7.999999907 0.020921563 3.82E-09 2.878511488 0.053018028 0.313369118 11022.68694 17.76213657 893.1900254 1660.054783 99999978.69 -7.999999907 2.878511484 DLKNPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLKNPDR 7 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 78.516 0.032033 1012990000 2679670 2159890 2428710 2001860 3035320 2806050 2698460 2395640 2720180 2120820 FALSE TRUE 2785465.441 2530834.306 2492004.178 2397821.933 2519377.391 2154387.414 2486947.654 2363530.364 2622281.253 2536354.073 1.098216322 0.997823739 0.982514312 0.945381387 0.993306659 0.849403258 0.980520693 0.931861363 1.033878227 1 21.27432473 5.131179915 1.153854965 0.955612434 1.300577423 0.416653617 0.047288438 3.07865965 1.86442901 0.012799447 1.590472435 135263.2801 -5.131179915 0.344964989 DLKPANILLDEHGHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLKPANILLDEHGHVR 16 1 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 65.943 0.036096 105300000 47298 45139 55431 44231 53564 63007 63898 56291 50117 38200 FALSE TRUE 49165.36156 52891.27212 56875.5774 52979.75978 44459.21041 48374.57913 58889.50779 55536.51122 48313.29896 45684.55862 1.076192111 1.157749439 1.24496283 1.159686366 0.973178066 1.058882489 1.289046224 1.215651697 1.057541113 1 15.479419 3.448022207 24.99527937 1.122806052 1.166592947 0.051910258 0.098216119 863.3448756 741587.1625 0.029943595 0.040544531 2805.577092 -3.448022207 0.043786895 DLKPENILLDEEGHIK ddPTM_MDA-MB-175_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 ; 203.19 1.71E-11 241334000 357730 254820 331360 247760 407870 404200 361880 328760 374550 234746 FALSE TRUE 371853.4566 298583.3528 339995.5138 296766.1885 338540.4031 310330.6757 333514.9 324353.5099 361070.0187 280739.9842 1.324547544 1.063558344 1.211069078 1.057085578 1.205885952 1.105402483 1.187985035 1.155352027 1.286136778 1 18.09887503 -2.350714575 2.19717465 0.000155508 1.169567432 0.286458275 0.083184855 1091837.38 227732.3843 5440301.608 0.01822445 0.004459492 2.350714575 1.169411925 DLKPENLLLASK ddPTM_MDA-MB-175_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 ; 161.76 5.88E-05 876750000 1005470 648970 870920 613910 1186620 980630 1025430 855020 911000 539470 FALSE TRUE 1045166.732 760425.5492 893616.8907 735339.5657 984918.7562 752893.5441 945054.1171 843559.8554 878213.288 645168.8177 1.619989533 1.178645849 1.38509002 1.139763029 1.526606261 1.166971378 1.464816791 1.307502521 1.361214714 1 19.29931719 -1.00040602 4.453539488 0.999989252 1.342079398 0.324817143 0.151018398 1.58E-05 3.55E-06 0.127577757 0.030069303 0.099906554 1.00040602 0.342090146 DLKPQNLLINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLKPQNLLINR 11 1 Q00535 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 100.19 0.0038453 351040000 567940 453260 471370 405980 676790 612360 552400 534280 520740 519740 FALSE TRUE 590362.7097 531103.8791 483654.2894 486281.6323 561749.4775 470148.6704 509101.4446 527118.8505 501998.6691 621573.102 0.949788059 0.854451194 0.778113287 0.782340212 0.903754483 0.75638516 0.81905321 0.848039995 0.807626114 1 19.24556455 -1.351449094 5.293211558 1.000062304 0.831177202 0.440994692 0.056265757 4.00E-05 4.90E-06 0.052712858 0.012419964 0.044519564 1.351449094 -0.168885101 DLLDDLKSELTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLDDLKSELTGK 13 1 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 230.36 3.85E-12 2015110000 3864700 1661550 2604530 1635170 3844200 3296300 2868700 2763140 3110460 1183230 FALSE TRUE 4017281.34 1946908.287 2672406.191 1958601.746 3190764.257 2530784.281 2643843.798 2726104.628 2998515.152 1415061.264 2.838945169 1.375847348 1.888544517 1.384110918 2.254859445 1.788462694 1.868359954 1.926492299 2.119000236 1 20.43243308 -1.547086131 6.849752813 0.999283618 1.906790648 0.327816967 0.400798108 0.003955423 0.000261537 0.350060712 0.082455537 0.028373563 1.547086131 0.907507031 DLLDDLKSELTGKFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLLDDLKSELTGKFEK 16 2 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 99.711 0.0012944 2371200000 211030 96710 140440 69833 257530 182650 139470 129830 178210 86774 FALSE TRUE 219361.6274 113319.1902 144099.9818 83645.75897 213755.1426 140232.3056 128537.977 128089.8412 171796.2569 103775.7039 2.113805246 1.091962626 1.38857147 0.806024491 2.059780223 1.351301897 1.238613395 1.234295084 1.655457399 1 16.66310919 -3.984434545 0.183047334 5.72E-32 1.485522876 0.096433476 0.388850847 238.3317782 3.230948565 91.536741 1.147088246 0.000103649 3.984434545 1.485522876 DLLDQILMLDPAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLDQILMLDPAKR 14 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 74.853 0.051124 194278000 184432 204575 198032 209177 218052 266500 258710 204649 240661 195834 FALSE TRUE 191713.5178 239709.1649 203192.8766 250551.5863 180987.5989 204609.4138 238431.6342 201906.0149 231999.6576 234203.9228 0.818575178 1.023506191 0.867589553 1.06980098 0.772777829 0.87363786 1.018051411 0.862094932 0.990588265 1 17.83740572 1.117733595 8.171471037 0.999417168 0.917130797 0.114329966 0.090964903 0.52152802 33.46515139 0.080277798 0.020105441 13.11395216 -1.117733595 -0.082286371 DLLDTVLPHLYNETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLDTVLPHLYNETK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 260.12 6.88E-25 973990000 2069240 1525060 2104790 1629970 2600400 2462300 2352500 2000690 2285700 1403340 FALSE TRUE 2150935.193 1786977.192 2159642.557 1952373.201 2158384.937 1890468.142 2168104.903 1973874.023 2203438.103 1678297.604 1.281617269 1.06475585 1.286805481 1.163305719 1.286056139 1.126420092 1.291847702 1.176116809 1.312900702 1 20.67856713 -0.74732189 8.121577123 1 1.215969004 0.403678176 0.080398435 0 0 0.068138401 0.016060375 0.178927919 0.74732189 0.215969004 DLLFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLLFGR 6 0 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 138.53 0.028531 1167100000 816070 977520 914080 918820 1006230 1107260 933140 947850 919630 890790 FALSE TRUE 848289.0737 1145401.456 937901.6757 1100559.854 835191.384 850115.6457 859998.0485 935145.6211 886532.6959 1065323.245 0.79627388 1.075167993 0.880391637 1.033075978 0.783979311 0.79798845 0.807264886 0.877804577 0.832172488 1 20.02285982 3.230380703 24.98505367 0.840955747 0.950734868 0.205441673 0.091666622 234.3321084 715752.2155 0.024295076 0.029507305 1699.732988 -3.230380703 0.109779121 DLLHPS(ph)PEEEKRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 1 DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK;DLLHPS(1)PEEEKRK 146.3 2.20E-05 2740470000 6623200 2557240 3945890 2307590 6152300 5735950 5165030 3899040 4614750 2177460 TRUE FALSE 6884689.05 2996426.077 4048723.135 2764024.415 5106534.244 4403862.542 4760181.452 3846779.746 4448666.049 2604091.597 2.643796807 1.150660784 1.554754502 1.061415972 1.960965678 1.691131966 1.827962372 1.477206006 1.708337009 1 21.31234876 -1.375236154 3.08774875 0.992459538 1.641182801 0.185087955 0.419581556 165742865.5 215636374.1 11236699.16 0.096442366 0.042146726 1.375236154 0.648723262 DLLHPSLEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DLLHPSLEEEK 11 0 H0YMV8;Q71UM5;C9JLI6 H0YMV8 RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;;; 218.54 1.05E-11 1367402000 2414350 2915770 3719340 3066390 4835640 4921040 4868850 4257900 4035160 2434340 FALSE TRUE 2509670.402 3416530.816 3816269.056 3672912.79 4013679.64 3778203.039 4487216.815 4200829.815 3889935.38 2911302.315 0.8620439 1.173540377 1.310846021 1.261604737 1.378654364 1.297770767 1.541309122 1.442938369 1.336149585 1 21.47323323 5.255172638 0.933367348 1.367499017 2.89E-10 0.501111828 0.13585153 3.440945964 1.209618488 0.040280029 5.986826898 179958.6134 -5.255172638 -1.367499017 DLLHPSPEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 0 ;;;;;;; 202.65 3.93E-08 4810870000 6893080 5640370 7445090 6204320 9781540 9993170 10412300 8050010 8136010 4470240 FALSE TRUE 7165224.121 6609059.672 7639115.162 7431515.978 8118877.325 7672407.715 9596156.719 7942112.783 7843196.589 5346097.94 1.340271765 1.236239917 1.428914181 1.390082273 1.518654805 1.435141631 1.794983337 1.485590588 1.467088085 1 22.35005484 3.82469914 1.4195637 1.496021657 1.288998844 0.045603677 0.188811244 0.846696306 3.222670878 0.054334435 0.152013602 6678.810782 -3.82469914 -0.207022813 DLLHPSPEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLLHPSPEEEKR 12 1 P42677 P42677 RPS27 40S ribosomal protein S27 0 134.98 8.82E-05 97253000 160550 155020 182010 153770 230350 257180 235220 194370 195550 128020 FALSE TRUE 166888.638 181643.4791 186753.3301 184185.247 191195.1893 197453.8426 216782.8418 191764.7881 188512.1937 153103.0679 1.090041109 1.186413059 1.219788295 1.203014737 1.24880051 1.289679203 1.415927484 1.252520872 1.231276396 1 17.22414367 5.011261349 0.816362027 1.261879936 0.925364544 0.134349785 0.098276237 5.45363911 2.069637221 0.032326328 1.836602815 102626.9327 -5.011261349 -0.336515392 DLLHPSPEEEKRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLHPSPEEEKRK 13 2 P42677 P42677 RPS27 40S ribosomal protein S27 0 ; 173.72 1.27E-05 680990000 671400 561740 792290 407890 1287520 925990 672180 751050 876600 625370 FALSE TRUE 697907.3904 658214.4753 812937.7283 488569.4246 1068667.81 710942.856 619492.7752 740983.4032 845051.3372 747899.2781 0.933156925 0.880084384 1.08696151 0.653255644 1.428892689 0.950586365 0.828310433 0.990752933 1.129899924 1 19.51248447 DLLIAYYDVDYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DLLIAYYDVDYEK 13 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;; 258.01 1.49E-23 920720800 1784532 1448944 1663340 1499698 2297353 2246486 1923522 1678011 1750091 1195710 FALSE TRUE 1854986.701 1697788.861 1706688.007 1796333.788 1906849.758 1724773.672 1772751.319 1655520.007 1687105.567 1429986.481 1.297205761 1.187276162 1.1934994 1.25618935 1.333473975 1.206146838 1.239697957 1.157717243 1.179805256 1 20.44757008 0.736889897 0.723755487 0.999421203 1.246459987 0.722054048 0.045405492 0.566938888 0.587901426 0.046887266 0.017053816 5.456195168 -0.736889897 0.247038785 DLLIDEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLLIDEWK 8 0 Q16539-2;Q16539;B4E0K5 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 111.95 0.0072944 8526600 60077 40414 46473 36996 66003 56448 61233 50217 53351 37023 FALSE TRUE 62448.88635 47354.79012 47684.12456 44313.69838 54783.83364 43338.80748 56433.39746 49543.92325 51430.90793 44276.948 1.410415333 1.069513421 1.076951477 1.000830012 1.237299229 0.978811988 1.274554819 1.118955246 1.161573014 1 15.43426816 4.743397865 24.72571701 1.110546488 1.410415477 0.485327484 0.094902032 365.2321049 1866820.827 0.021162384 0.174377096 55385.72754 -4.743397865 0.299868989 DLLIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLIFR 6 0 H3BPB8;P34949-2;P34949;F5GX71 H3BPB8 MPI Mannose-6-phosphate isomerase 0 ; 148.4 0.035667 138020000 229640 232430 257610 231960 328300 330440 284010 268810 249380 243000 FALSE TRUE 238706.3645 272348.0444 264323.5282 277840.9957 272495.6833 253700.3179 261748.5541 265207.0416 240404.8625 290611.1975 0.821394243 0.937156059 0.909543509 0.956057434 0.937664087 0.872988791 0.900682962 0.912583699 0.827238815 1 18.14873077 2.637776996 0.005931082 1.8144949 1.21E-05 0.120926744 0.049459039 21706.17279 54.23264158 8171.694153 8416.73232 434.2871664 -2.637776996 -1.814482822 DLLPHQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLLPHQELR 9 0 Q15650;H0YL91 Q15650 TRIP4 Activating signal cointegrator 1 0 77.662 0.031966 39095000 13341 16155 16110 12107 15049 18458 13262 15416 13295 21596 FALSE TRUE 13867.71298 18929.49558 16529.83983 14501.72846 12490.97636 14171.40923 12222.48979 15209.37374 12816.51555 25827.32272 0.536939625 0.732925197 0.640013679 0.561487872 0.483634192 0.548698345 0.473238745 0.588886967 0.496238642 1 14.65661048 -1.241834383 4.36975472 1.000211655 0.564861795 0.757229547 0.074313157 0.000160332 2.78E-05 0.075286663 0.017736692 0.057301451 1.241834383 -0.435349861 DLLPSDMAVALLEAQAGTGHIIDPATSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLPSDMAVALLEAQAGTGHIIDPATSAR 29 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 249.09 4.73E-46 443196000 196654 205329 216642 182961 227308 266114 215065 203192 191033 204254.8 FALSE TRUE 204418.0518 240592.6585 222287.8685 219150.1397 188670.2674 204313.0565 198207.6433 200468.5436 184157.7596 244274.6174 0.836837056 0.984926969 0.909991676 0.897146589 0.772369513 0.836407232 0.811413177 0.820668745 0.75389642 1 17.89814444 3.383218986 6.529823087 0.822453904 0.915680964 0.203971583 0.070798336 0.259337411 15.12313701 0.018011475 0.024468276 2416.679099 -3.383218986 0.093227059 DLLPSGSRDEPPPASQSTSQDCSQALKQS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLLPSGSRDEPPPASQSTSQDCSQALKQSP 30 2 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 DLLPSGSRDEPPPASQSTSQDCS(0.014)QALKQS(0.986)P 137.37 1.61E-06 166650000 96647 69150 72420 58079 100340 130200 64486 75240 78177 67636 TRUE FALSE 100462.6982 81025.97459 74307.32469 69566.85285 83284.24264 99963.0232 59431.41882 74231.53087 75363.42504 80887.97923 1.241997873 1.001706006 0.918644839 0.860039446 1.029624469 1.235820503 0.734737341 0.917707817 0.931701172 1 16.3036377 2.225070922 24.9999865 0.886719872 1.030614319 0.240477076 0.12968307 373.2015007 691637.0001 0.049785394 0.036972003 167.9078196 -2.225070922 0.143894447 DLLQFFKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLQFFKPR 9 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 214.93 6.00E-07 721730000 603820 583790 640230 564800 793370 791560 710730 654780 619550 562940 FALSE TRUE 627659.2799 684051.3912 656914.9198 676515.7542 658513.2508 607732.1862 655021.1255 646003.7451 597252.5165 673237.3149 0.932300195 1.0160628 0.975755362 1.004869664 0.978129459 0.902701281 0.972942395 0.959548336 0.887135195 1 19.36075562 2.972635209 24.56421989 0.945304835 0.98511134 0.202216421 0.036581387 860.1875844 772154.8184 0.010527798 0.011196732 938.9343091 -2.972635209 0.039806505 DLLSDLQDIS(ph)DSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.98)DS(0.02)ER;DLLSDLQDIS(1)DSER;DLLSDLQDIS(0.891)DS(0.109)ER 264 1.24E-24 1903360000 1487260 1450620 1534820 1632880 1747770 1994330 1919200 1685470 1476270 1361160 TRUE FALSE 1545978.173 1699752.701 1574818.67 1955858.79 1450684.68 1531177.082 1768768.089 1662879.032 1423139.331 1627853.241 0.949703655 1.044168269 0.967420545 1.201495774 0.891164291 0.940611256 1.086564836 1.021516553 0.874243018 1 20.63453921 DLLSDLQDISDS(ph)ER ddPTM_MDA-MB-175_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(0.468)DS(0.532)ER 263.59 1.32E-24 42073000 91077 100110 96881 98626 106800 121250 125190 98538 94382 78068 TRUE FALSE 94672.79029 117303.1138 99405.79845 118133.9284 88646.17415 93091.52506 115377.2807 97217.25929 90985.21026 93363.9299 1.014018908 1.2564072 1.064713092 1.265305869 0.949469182 0.997082333 1.235780036 1.041272142 0.97452207 1 16.51057767 3.233334235 24.99926129 1.047650473 1.15160396 0.230316581 0.102781326 212.6784556 1017300.681 0.028923557 0.035558706 1711.331856 -3.233334235 0.103953487 DLLVEGLAEILHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLVEGLAEILHQK 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 ; 181.26 1.66E-06 244890000 320530 225410 307210 277030 396110 388720 350860 294460 332140 216900 FALSE TRUE 333184.7719 264122.4141 315216.145 331825.7071 328779.3637 298445.6711 323358.6764 290513.2453 320186.3463 259397.4022 1.284456857 1.01821534 1.215186206 1.279217542 1.267473617 1.150534541 1.246576387 1.119954336 1.234346773 1 17.98480451 -1.224524916 4.760621403 0.999960186 1.195785068 0.362991074 0.079834202 3.25E-05 5.30E-06 0.074518921 0.017560711 0.059631411 1.224524916 0.195824882 DLLVGPGVELLLT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DLLVGPGVELLLTPR 15 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR;DLLVGPGVELLLT(1)PR 179.09 7.65E-06 390657000 161818 159771 166214 176424 181958 207704 225263 193057 195222 152996 TRUE FALSE 168206.6996 187210.4264 170545.6734 211320.1406 151028.8442 159467.8938 207606.2974 190469.3867 188195.9984 182972.6369 0.919299751 1.023160783 0.93208294 1.154927557 0.825417651 0.871539573 1.134630297 1.040971972 1.028547227 1 17.48126839 2.235126656 24.99996249 1.055870955 0.95976699 0.215454159 0.089798354 144.2122659 1049881.372 0.033032414 0.025378145 171.8409463 -2.235126656 -0.096103965 DLLVSSGSNNSLPCGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLVSSGSNNSLPCGSPK 18 0 Q5THK1-4;Q5THK1-2;Q5THK1;Q5THK1-3 Q5THK1-4 PRR14L Protein PRR14L 1 DLLVSSGSNNSLPCGS(1)PK;DLLVSSGSNNSLPCGS(1)PK 232.84 2.67E-21 103163000 191763 87107 110349 83082 144608 189355 150674 122157 132322 74287 TRUE FALSE 199333.9513 102066.9497 113224.7856 99515.37162 120027.5838 145380.171 138863.7782 120519.6852 127559.7571 88842.11534 2.243687586 1.148857715 1.274449456 1.12013735 1.351021229 1.636387995 1.56303998 1.356560284 1.43580279 1 16.43895612 0.110631809 1.36862555 0.999473821 1.437774585 0.166339818 0.3049242 21.02121559 30.01648743 0.305516326 0.082317346 1.290125055 -0.110631809 0.438300764 DLLYFDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLLYFDGLR 9 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 137 0.00041146 238496000 476934 500301 522821 536238 630781 666454 626851 556365 544355 520476 FALSE TRUE 495763.7226 586223.8049 536446.1448 642304.2759 523561.0709 511680.1587 577716.7806 548907.8372 524763.7699 622453.3071 0.796467328 0.941795631 0.86182552 1.031891499 0.841125053 0.822037819 0.928128703 0.881845804 0.843057244 1 19.24760609 -1.027333671 4.66035798 1.000003306 0.887222414 0.220932815 0.065433677 2.12E-06 4.42E-07 0.059752427 0.014083369 0.093900159 1.027333671 -0.112780892 DLLYFDGLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLLYFDGLRK 10 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 107.83 0.0035785 464540000 382510 441140 384240 345410 503310 550470 375250 390260 392970 492730 FALSE TRUE 397611.7902 516902.3634 394253.6101 413731.0671 417757.546 422631.685 345836.9245 385029.203 378827.0865 589271.0096 0.674751996 0.877189536 0.669053124 0.702106603 0.708939587 0.717211059 0.586889426 0.653399195 0.642874128 1 19.16857177 -1.017279452 4.659175946 1.000007397 0.691266 0.624764059 0.07148905 79074667604 16676152170 7217886.286 0.017924585 0.096099372 1.017279452 -0.308741397 DLMHGLITLMLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLMHGLITLMLDSR 14 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 110.77 0.00069006 26349000 81608 105790 106450 103230 135940 146530 128070 117920 122780 116280 FALSE TRUE 84829.94686 123958.6096 109224.1744 123648.5859 112832.9674 112500.6282 118031.5388 116339.4753 118361.1718 139062.8397 0.610011611 0.891385577 0.785430347 0.889156199 0.811381154 0.808991305 0.848764048 0.83659643 0.851134437 1 17.08537743 -5 0.072815809 1.564415121 0.62264474 0.465932024 0.068582866 274.7658608 1.434745364 26.20223165 3.015926209 1.00E-05 5 -0.941770381 DLMLMSHLQDNIQHADPPVQILYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLMLMSHLQDNIQHADPPVQILYNR 25 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 0 178.39 1.69E-17 317370000 73035 81544 90272 88893 98442 104130 95419 102320 96141 86112 FALSE TRUE 75918.4782 95548.54768 92624.56248 106475.7701 81708.864 79947.38561 87939.80945 100948.5678 92680.90419 102983.9977 0.737187135 0.927799948 0.899407331 1.033905971 0.793413208 0.776308819 0.853917224 0.980235474 0.899954423 1 16.65206065 1.750830172 11.20359531 0.954283693 0.865251956 0.230560772 0.082973591 0.207507388 137.7480041 0.040218509 0.021994535 56.34172916 -1.750830172 -0.089031738 DLMPHDLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLMPHDLAR 9 0 P55084-2;P55084;B5MD38;C9JEY0;C9JE81;C9K0M0 P55084-2 HADHB "Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolase" 0 ; 102.06 0.0036456 246260000 190325 267280 207110 261820 199242 348470 207774 206092 186306 267720 FALSE TRUE 197839.178 313183.2609 212507.4567 313607.2145 165374.916 267543.1236 191488.131 203329.6738 179600.8835 320174.6082 0.617910268 0.978163954 0.663723641 0.979488087 0.516514776 0.835616307 0.59807407 0.635058711 0.56094668 1 18.28849937 3.235156132 24.99999926 0.670863925 0.811410373 0.09674977 0.171251387 167.1440254 1227381.752 0.044553243 0.055319997 1718.5261 -3.235156132 0.140546448 DLMSWINGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLMSWINGIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 169.09 1.10E-05 268620000 224890 252300 217630 233130 290360 308960 248790 233710 238710 275330 FALSE TRUE 233768.8309 295630.5624 223301.6166 279242.4182 241004.7109 237208.7223 229289.1897 230577.4997 230118.8737 329275.642 0.709948751 0.897820928 0.678160143 0.848050638 0.731923897 0.720395596 0.696344219 0.700256777 0.698863944 1 18.32893627 -1.098922583 4.85563732 1.000010866 0.742133449 0.560169991 0.068472483 7.84E-06 1.46E-06 0.064550475 0.015214052 0.079630129 1.098922583 -0.257877418 DLMVGDEASELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 ;;; 223.78 5.03E-11 1209480000 1035270 1115650 1209300 1073800 1364830 1442180 1219110 1154370 1246100 1125080 FALSE TRUE 1076143.259 1307254.209 1240815.351 1286194.435 1132836.684 1107255.551 1123552.973 1138897.558 1201253.104 1345517.885 0.799798554 0.97156212 0.922184213 0.955910322 0.841933576 0.822921467 0.835033845 0.846438067 0.892781224 1 20.35973014 4.816680736 21.17210669 0.887584983 0.79978716 0.174810524 0.060251032 63970.15383 17329386.43 0.014933852 120.391212 65566.30892 -4.816680736 -0.087797824 DLNES(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLNESPVK 8 0 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK;DLNES(1)PVK 99.215 0.0073124 1022670000 2005890 1094880 1417740 1194600 1841760 2001400 2063100 1507730 1544040 870960 TRUE FALSE 2085084.086 1282917.123 1454687.469 1430888.314 1528698.293 1536605.182 1901388.831 1487521.345 1488470.302 1041607.936 2.001793586 1.231669881 1.396578711 1.373730234 1.467633108 1.475224149 1.825436198 1.428101009 1.429012059 1 19.99038092 0.708720212 2.055852302 1.000471066 1.513196939 0.349462584 0.214075098 1.440654994 8.518845559 0.195040558 0.053617485 5.113522975 -0.708720212 0.512725872 DLNFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLNFER 6 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4;G3V5H8;G3V4S9;G3V5L7;A0A0U1RR50;G3V2I9 Q9UN36 NDRG2 Protein NDRG2 0 ;;; 126.2 0.040927 635940000 718660 813700 761690 733290 883310 971520 845550 802210 735240 771820 FALSE TRUE 747033.2517 953446.6453 781540.2671 878332.5733 733165.2817 745899.2035 779273.5816 791457.6871 708778.856 923043.3516 0.809315457 1.032938099 0.846699416 0.951561562 0.794291276 0.80808686 0.844243751 0.857443679 0.767871687 1 19.81603888 3.241485426 24.99396999 0.837903339 0.914370079 0.128810711 0.080901303 127.774989 1091890.095 0.020794717 0.026971978 1743.754838 -3.241485426 0.07646674 DLNHVCVISETGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLNHVCVISETGK 13 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ;; 181.26 1.22E-05 859250000 1712820 1315930 1636680 1329440 1942000 2106310 1814830 1694480 1755550 1242180 FALSE TRUE 1780443.456 1541930.741 1679333.225 1592399.264 1611899.534 1617151.424 1672578.882 1671768.267 1692368.098 1485561.388 1.198498743 1.037944816 1.130436776 1.07191751 1.085044042 1.088579332 1.125890115 1.125344453 1.139211151 1 20.50257679 4.762475336 23.99284805 1.096802312 1.198498949 0.35898422 0.042720677 4294.351686 4308262.4 0.009549073 0.528600324 57872.91213 -4.762475336 0.101696636 DLNKDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLNKDGK 7 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 68.016 0.057998 159200000 455830 285500 357800 303870 747460 605130 717000 526640 585230 303870 FALSE TRUE 473826.5204 334532.4041 367124.5619 363974.579 620407.0162 464597.7283 660799.6665 519581.2522 564167.6866 363407.5086 1.303843507 0.920543457 1.010228334 1.001560426 1.707193719 1.278448346 1.81834346 1.429748258 1.552438167 1 18.4712287 3.251968809 24.9619857 1.497220457 1.045664087 0.419604988 0.231389816 185.3636161 345088.7346 0.058782195 0.079145083 1786.359272 -3.251968809 -0.45155637 DLNKDGKLDKDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLNKDGKLDKDEIR 14 3 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ; 73.022 0.016207 1220000000 1361680 575230 880270 402550 1723100 1179990 953260 778660 1040820 471180 FALSE TRUE 1415440.178 674021.2778 903210.5593 482173.1885 1430208.077 905955.2054 878540.9903 768223.3363 1003361.092 563498.6997 2.511878339 1.19613635 1.602861834 0.855677553 2.538085852 1.607732557 1.559082551 1.363309865 1.780591671 1 19.10405276 -2.661730276 0.24961503 4.88E-11 1.70856147 0.141567794 0.497134691 100.1001926 2.808261096 55.129457 0.725713284 0.002179063 2.661730276 1.70856147 DLNYCFSGMSDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 242.91 5.89E-17 15850220000 5379091 5552835 5697980 5210370 6874270 8765790 5616310 6189987 5470363 6088912 FALSE TRUE 5591461.666 6506491.216 5846474.04 6240965.635 5705784.041 6730068.119 5176088.947 6107020.349 5273485.704 7281917.727 0.76785565 0.893513421 0.802875597 0.857049732 0.783555137 0.924216446 0.710813983 0.8386555 0.724189136 1 22.79588701 2.246960977 24.9981879 0.805215823 0.837463236 0.003175905 0.086333719 758.7463222 2257913.981 0.027314015 0.022506902 176.5879141 -2.246960977 0.032247414 DLPAIQES(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLPAIQESPTR 11 0 P49796-1;P49796-4;P49796-6;P49796 P49796-1 RGS3 Regulator of G-protein signaling 3 1 DLPAIQES(0.839)PT(0.161)R 113.76 0.00076705 0 65190 62161 66731 60953 75641 82699 74195 62905 66208 63643 TRUE FALSE 67763.75154 72836.6682 68470.06468 73009.32147 62783.56984 63493.41057 68379.40203 62061.86137 63825.18701 76112.62733 0.890308927 0.956959059 0.899588768 0.959227451 0.824877186 0.834203375 0.898397604 0.815395074 0.838562394 1 16.2158482 3.238408112 24.99999978 0.857027016 0.926771461 0.195803821 0.054602745 5.098053634 835796.4927 0.014290985 0.018137787 1731.442655 -3.238408112 0.069744445 DLPDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLPDEVR 7 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 154.01 0.0039719 527250000 1317440 1328570 1423930 1262720 1641080 1762800 1449340 1355740 1436650 1212280 FALSE TRUE 1369453.548 1556741.563 1461038.786 1512482.247 1362129.808 1353416.415 1335736.944 1337568.523 1384945.247 1449803.055 0.944579019 1.073760713 1.007749832 1.043232901 0.939527478 0.933517425 0.92132303 0.922586359 0.955264401 1 20.4674255 3.228112683 24.84598242 0.938119253 1.020676994 0.463751393 0.037355578 138.3270604 328951.8923 0.010011565 0.012087888 1690.879594 -3.228112683 0.082557742 DLPDGHAAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLPDGHAASPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR;DLPDGHAAS(1)PR 181.44 6.53E-06 3325460000 2008250 2284110 2523710 2317580 2875410 3066850 2633000 2725590 2521850 2531400 TRUE FALSE 2087537.261 2676388.125 2589479.956 2775990.407 2386648.835 2354620.566 2426618.58 2689057.924 2431089.111 3027379.363 0.689552583 0.884061032 0.855353639 0.916961528 0.788354728 0.777775192 0.801557482 0.888246104 0.803034182 1 21.52963804 -4.999999985 0.377662189 3.372703351 0.825155605 0.410551041 0.063330946 592.9247914 4.466233727 1151.172553 0.042067931 1.00E-05 4.999999985 -2.547547746 DLPEHAVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 138.08 0.00014665 9158490000 12638360 10095640 12143480 9424900 17271010 14441100 13791580 11602540 12136480 10610890 FALSE TRUE 13137332.21 11829487.64 12459949.06 11289117.09 14335289.89 11087373.38 12710559.92 11447026.93 11699690.46 12689890.74 1.035259679 0.932197753 0.981879933 0.889614995 1.1296622 0.873717009 1.001628791 0.902058746 0.921969361 1 23.59717631 DLPHWNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLPHWNK 7 0 Q7LG56;A0A0C4DGZ6;H0YAV1;Q7LG56-2;Q7LG56-6 Q7LG56 RRM2B Ribonucleoside-diphosphate reductase subunit M2 B 0 70.268 0.077504 0 96239 111530 106140 111760 125620 136350 166270 117870 128110 90962 FALSE TRUE 100038.59 130684.4099 108906.0956 133865.7944 104267.1573 104684.7789 153237.3229 116290.1454 123499.3461 108784.2623 0.919605354 1.201317241 1.001119953 1.230562138 0.958476484 0.962315473 1.408635033 1.068997877 1.135268498 1 16.73111033 DLPLLLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLPLLLFR 8 0 A0A286YFA2;A0A286YF22;O43175;A0A2C9F2M7 A0A286YFA2 PHGDH D-3-phosphoglycerate dehydrogenase 0 ; 94.262 0.024391 96061000 94972 112268 115984 117846 195763 187008 140559 127480 123294 191281 FALSE TRUE 98721.56789 131549.1557 119006.6383 141155.5871 162487.2752 143578.2261 129541.6183 125771.3391 118856.673 228758.8497 0.431553 0.575056029 0.520227473 0.617049733 0.710299407 0.627640095 0.566280249 0.549798792 0.519571913 1 17.80346803 -1.701701105 2.586656162 1.072249931 0.572961668 0.769892625 0.070716665 7180722.731 5745789.363 3375171.274 0.018194331 0.019874623 1.701701105 -0.499288263 DLPS(ph)PDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLPSPDSR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 DLPS(0.995)PDS(0.005)R;DLPS(0.999)PDS(0.001)R;DLPS(0.984)PDS(0.016)R;DLPS(0.999)PDS(0.001)R 140.17 0.00068587 1010839000 1398500 1466160 1549380 1445800 1824850 1935050 1682380 1614600 1560830 1489830 TRUE FALSE 1453713.86 1717961.575 1589758.116 1731774.925 1514662.649 1485663.963 1550510.66 1592958.928 1504656.033 1781733.664 0.81589852 0.964207844 0.89225351 0.971960602 0.850106096 0.833830551 0.870225832 0.89404997 0.844489872 1 20.76485027 3.192293332 24.99998173 0.875109164 0.913530988 0.045911954 0.059341355 298.0110524 161025.7963 0.015960244 0.019076193 1557.016921 -3.192293332 0.038421825 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.398)QS(0.398)HLRNS(0.204)PEDK 110.9 2.17E-06 302120000 153330 123700 155060 108590 169950 194420 156410 144550 142980 80471 TRUE FALSE 159383.5868 144944.5127 159100.991 130068.7779 141061.9597 149268.9015 144150.1755 142612.5437 137834.1777 96237.75174 1.656144121 1.506108675 1.653207687 1.351535915 1.465765328 1.551043107 1.49785477 1.481877341 1.432225662 1 16.55431532 -2.987626313 0.259296185 3.80E-15 1.563326207 0.79653835 0.07971208 25.43227995 0.638066233 14.01233558 0.108794092 0.001028901 2.987626313 1.563326207 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 33 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 DLPTIPGVTSPSSDEPPMEAS(0.482)QS(0.482)HLRNS(0.035)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.491)QS(0.491)HLRNS(0.019)PEDKR;DLPTIPGVTSPSSDEPPMEAS(0.333)QS(0.333)HLRNS(0.333)PEDKR;DLPTIPGVT(0.001)S(0.023)PS(0.049)S(0.049)DEPPMEAS(0.31)QS(0.31)HLRNS(0.257)PEDKR 212.08 4.58E-28 1111730000 556934 459193 588918 431195 707511 698319 677151 582464 615153 339748 TRUE FALSE 578922.1844 538055.8257 604265.6869 516484.084 587248.5329 536144.9954 624074.1352 574657.0228 593013.7637 406315.1157 1.424810847 1.324232855 1.487184856 1.271141693 1.44530319 1.319530026 1.535936299 1.414313671 1.459492253 1 18.63223951 -0.76489889 5.389053156 0.99999991 1.409247731 0.713221672 0.077824575 4647990.201 862487.3183 4.973231683 0.016886959 0.171830839 0.76489889 0.409247821 DLPVSEQQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLPVSEQQER 10 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 203.97 4.55E-07 616860000 177113 227769 192498 218018 229902 243510 223100 221360 210441 214780 FALSE TRUE 184105.558 266886.554 197514.656 261141.3097 190823.3402 186958.4929 205612.839 218393.0313 202867.2695 256862.0288 0.716748828 1.039026886 0.768952332 1.016659842 0.742902098 0.727855705 0.800479697 0.850234783 0.789790809 1 17.97063411 5.04074338 16.13362699 0.848504805 0.118201938 0.121022862 0.111945989 8579653.714 93027980.38 0.02529615 185549320.5 109835.664 -5.04074338 -0.730302867 DLPWRPAEDGHSHACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLPWRPAEDGHSHACR 16 1 P55268 P55268 LAMB2 Laminin subunit beta-2 0 ; 159.69 5.83E-09 139435000 98396 134212 120837 138490 145588 164299 112572 127926 124839 125791 FALSE TRUE 102280.7501 157261.867 123986.1115 165882.9086 120841.0038 126143.0472 103748.3125 126211.3612 120346.0688 150437.338 0.67988939 1.045364595 0.824171134 1.102671124 0.803264704 0.838508903 0.689644698 0.838963005 0.799974729 1 17.19880316 DLQEQDADAGS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLQEQDADAGSER 13 0 Q6P158-2;Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 DLQEQDADAGS(1)ER;DLQEQDADAGS(1)ER 275.66 3.46E-32 2217300000 1816720 1825400 1793230 1859070 2029360 2192640 1909480 1821710 1705010 1463020 TRUE FALSE 1888445.508 2138898.25 1839963.047 2226788.497 1684410.112 1683432.59 1759809.968 1797292.957 1643647.023 1749670.758 1.07931478 1.222457563 1.051605303 1.272690012 0.962701185 0.962142496 1.005794925 1.027217806 0.939403608 1 20.73865204 3.216281421 24.99974754 0.987757209 1.153733303 0.640622063 0.06363677 140.6335565 157806.2011 0.017029057 0.02036793 1645.437615 -3.216281421 0.165976095 DLQGLTVEHAIDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLQGLTVEHAIDSFR 15 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;; 183.58 5.00E-07 464994000 231332 281488 298346 253695 296793 334639 270775 274715 262119 300294 FALSE TRUE 240465.166 329831.3743 306121.1419 303875.1138 246344.2319 256924.1638 249550.948 271032.8948 252685.3884 359130.8598 0.669575336 0.918415573 0.852394422 0.846140357 0.685945597 0.71540542 0.694874699 0.754691187 0.703602549 1 18.4541501 5.033632004 15.39980507 0.781426388 0.301007572 0.107286183 0.10173627 3151392.161 41950860.31 0.024094568 39989759.33 108051.7995 -5.033632004 -0.480418816 DLQGRDEQSEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLQGRDEQSEEK 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 257.02 3.15E-21 4304180000 2981100 2290480 2818180 1277790 4370520 3662000 2060280 2388710 3078520 2669200 FALSE TRUE 3098796.13 2683852.123 2891624.086 1530533.048 3627620.572 2811555.998 1898789.87 2356693.25 2967724.667 3192178.635 0.970746466 0.840758751 0.905846576 0.479463471 1.136409013 0.880763992 0.594825693 0.738271105 0.929686276 1 21.60610996 DLQHPNEFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLQHPNEFIR 10 0 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 ;; 100.55 0.0039344 520252000 498990 509195 537933 556138 638119 674825 559303 545972 500732 531367 FALSE TRUE 518690.5105 596645.2803 551951.9759 666140.4365 529651.7603 518107.1208 515463.3694 538654.1384 482710.7531 635478.19 0.81622079 0.938891829 0.868561635 1.048250667 0.833469612 0.815302758 0.811142503 0.847635917 0.759602392 1 19.27748309 3.093092453 24.60157584 0.834169241 0.919060638 0.160502807 0.080211214 22.52168186 5940.202793 0.021576203 0.025788498 1239.060331 -3.093092453 0.084891397 DLQSPDFT(ph)TGFHSDKIEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLQSPDFTTGFHSDKIEAK 19 1 E9PDR5;Q9P2D0-2;Q9P2D0;E7EPI0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 DLQS(0.293)PDFT(0.603)T(0.103)GFHSDKIEAK;DLQS(0.378)PDFT(0.526)T(0.096)GFHSDKIEAK 116.45 0.00019108 394890000 347750 176603 279050 201509 329570 321360 348060 266680 290280 174966 TRUE FALSE 361479.4385 206933.1915 286322.2722 241366.8788 273549.8091 246729.0103 320778.1477 263105.5908 279832.8795 209247.2378 1.727523108 0.98894109 1.368344334 1.153500908 1.307304278 1.179126725 1.53301019 1.257390987 1.337331295 1 17.67484905 4.762116966 24.33804683 1.259591726 1.727523878 0.456082 0.159147446 4291.938313 4434260.162 0.035031372 2.03366319 57825.17641 -4.762116966 0.467932152 DLQSS(ph)PPSLPLGFLGEGDAVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLQSSPPSLPLGFLGEGDAVTK 22 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 DLQS(0.203)S(0.782)PPS(0.015)LPLGFLGEGDAVTK;DLQS(0.19)S(0.804)PPS(0.007)LPLGFLGEGDAVTK;DLQS(0.125)S(0.866)PPS(0.009)LPLGFLGEGDAVTK;DLQS(0.159)S(0.835)PPS(0.006)LPLGFLGEGDAVTK 243.97 5.55E-31 562261000 515147 368058 455201 326509 525845 553526 515903 477748 498860 321263 TRUE FALSE 535485.4013 431269.0984 467063.912 391091.5057 436462.0547 424977.9753 475465.1748 471344.5695 480906.126 384208.3339 1.39373708 1.12248762 1.215652735 1.017915207 1.136003611 1.106113371 1.23751916 1.226794236 1.251680621 1 18.55152929 4.743767055 24.57828628 1.157101438 1.393737206 0.429146215 0.084849433 446.123804 2105952.494 0.020342791 0.17163231 55432.83048 -4.743767055 0.236635769 DLQSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DLQSSDR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 219.16 7.26E-05 14620100000 6624410 7019620 7167510 6833800 7718130 8765600 7487220 7172910 6793570 7005930 FALSE TRUE 6885946.822 8225185.13 7354301.199 8185505.243 6406205.019 6729922.244 6900352.132 7076768.874 6549070.743 8378607.847 0.821848563 0.981688758 0.877747394 0.976952901 0.764590626 0.803226785 0.82356786 0.844623475 0.781641874 1 22.99827912 3.239570211 24.99995673 0.827413145 0.916724923 0.205138108 0.074224232 35.43446665 877423.4561 0.019183146 0.024564155 1736.081907 -3.239570211 0.089311778 DLQYITVS(ph)KEELSSGDSLSPDPWKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLQYITVSKEELSSGDSLSPDPWKR 25 2 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 DLQYIT(0.024)VS(0.976)KEELSSGDSLSPDPWKR 134.77 2.44E-05 97957000 82214 40078 66029 37538 82425 90994 65775 62815 71772 43444 TRUE FALSE 85459.8722 46961.08474 67749.76998 44962.90436 68414.42794 69862.02253 60619.38363 61973.06767 69188.93974 51956.02001 1.644850244 0.903862242 1.30398306 0.865403169 1.316775764 1.344637686 1.166744173 1.192798595 1.331682829 1 15.6650033 -1.905822002 2.608750429 0.87898999 1.213305221 0.090057465 0.213494839 27775327.57 17661776.69 20660003.04 0.047046386 0.012421613 1.905822002 0.334315231 DLRDDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLRDDRDR 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 93.649 0.043381 136710000 33587 40043 41940 36932 40641 58529 38269 43263 30770 49051 FALSE TRUE 34913.04069 46920.07376 43032.99085 44237.03937 33732.85734 44936.52677 35269.37578 42683.13025 29662.59371 58661.60431 0.595160005 0.799843003 0.73358019 0.754105516 0.575041507 0.766029625 0.601234422 0.727616143 0.505656026 1 15.84012891 -0.973190133 5.137220221 1.000001692 0.681230309 0.522389245 0.093473353 1.67E-06 3.33E-07 0.08324145 0.019620094 0.106367724 0.973190133 -0.318771383 DLREEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLREEVEK 8 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;; 179.8 0.00022108 717440000 1617410 1186460 1593240 1088010 2034750 1979910 1742680 1438750 1559850 1032960 FALSE TRUE 1681266.596 1390225.276 1634761.143 1303215.131 1688883.922 1520105.908 1606084.188 1419465.91 1503711.303 1235348.735 1.360965166 1.125370704 1.323319559 1.054937034 1.3671313 1.23050752 1.300105908 1.149040647 1.217236284 1 20.23648694 0.432963238 0.825742394 0.998492983 1.242412665 0.353914364 0.097737862 2.02453277 1.999812764 0.09345577 0.029482435 2.70996223 -0.432963238 0.243919682 DLRNPHPSSAFLNLIGFVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLRNPHPSSAFLNLIGFVSR 20 1 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 116.21 5.90E-05 80992000 18672 103150 80633 66437 108140 126310 56491 102490 88263 155680 FALSE TRUE 19409.18498 120865.2101 82734.36222 79578.04031 89758.40143 96976.41675 52063.08781 101116.2892 85086.43187 186182.5153 0.104248162 0.649175944 0.444372352 0.427419514 0.482098984 0.520867476 0.279634678 0.543103035 0.457005491 1 17.50635807 -4.99999993 0.339952449 7.011511993 0.424948028 0.595995979 0.140614334 253.4952781 2.135631431 1105.774478 0.102652111 1.00E-05 4.99999993 -6.586563965 DLRPVDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLRPVDNR 8 1 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 ; 78.334 0.028174 392630000 225150 233220 235880 243360 280620 290280 256560 250630 241160 235060 FALSE TRUE 234039.0959 273273.7208 242027.2266 291495.8816 232920.3126 222866.8692 236450.1568 247270.7148 232480.6987 281115.5065 0.832537126 0.972104756 0.860952957 1.036925658 0.828557327 0.792794649 0.841113889 0.87960539 0.826993507 1 18.10080351 DLS(ph)ENNDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLSENNDQR 9 0 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 1 DLS(1)ENNDQR 140.91 0.00011327 58601000 122520 118990 124570 136880 194240 223000 179230 135740 132090 129490 TRUE FALSE 127357.1842 139425.6069 127816.3965 163954.4555 161223.1542 171211.6296 165181.4843 133920.6273 127336.1067 154861.0863 0.822396299 0.900326933 0.825361617 1.058719523 1.041082418 1.105582001 1.06664294 0.864779078 0.822260193 1 17.24061514 3.748539989 24.63888233 0.991760577 0.854458139 0.371191437 0.086243796 731.1627304 1805220.535 0.025116731 0.044603513 5604.540205 -3.748539989 -0.137302438 DLS(ph)LEEIQK ddPTM_MDA-MB-175_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 144.1 0.00063682 37413000 124351 67859 90195 62815 130384 138607 134856 100558 109557 72835 TRUE FALSE 129260.4735 79513.25538 92545.5558 75239.61952 108221.3743 106417.6249 124285.6343 99210.18449 105614.065 87105.62374 1.483950955 0.91283722 1.062452134 0.863774534 1.242415468 1.221707856 1.426838234 1.138964171 1.212482736 1 16.41047825 DLS(ph)PEPAPDEGPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLSPEPAPDEGPRR 14 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 DLS(1)PEPAPDEGPRR;DLS(1)PEPAPDEGPRR;DLS(1)PEPAPDEGPRR 168.68 2.11E-06 1656700000 1278630 1278880 1345470 1184210 1707340 1999130 1403570 1431240 1463050 1248130 TRUE FALSE 1329111.3 1498517.692 1380534.054 1418443.203 1417126.957 1534862.355 1293554.516 1412056.569 1410395.116 1492677.177 0.890421131 1.003912778 0.924871148 0.950267898 0.949386096 1.028261421 0.866600318 0.945989254 0.944876185 1 20.50947075 2.510023404 0.00319276 1.897600306 1.17E-08 0.056662077 0.046283914 111402.1794 166.0335566 48991.66104 49683.8878 323.6110955 -2.510023404 -1.897600294 DLS(ph)PTLIDNSAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLSPTLIDNSAAK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 DLS(0.999)PT(0.001)LIDNSAAK;DLS(0.971)PT(0.029)LIDNSAAK 214.65 3.20E-11 118517000 376490 224720 281280 224980 399250 393660 411990 290240 346590 194708 TRUE FALSE 391354.1159 263313.9119 288610.3879 269480.3725 331385.6276 302238.431 379697.1473 286349.8075 334116.2936 232857.3047 1.680660679 1.130795155 1.239430252 1.157276869 1.423127473 1.29795555 1.630600113 1.229722245 1.434854251 1 17.82908661 -1.094815699 4.496888953 0.999981584 1.345612746 0.26522674 0.17777543 0.935284737 50202695.56 3074.328954 0.039210175 0.080386719 1.094815699 0.345631161 DLSELGSVR ddPTM_MDA-MB-175_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 95.311 0.018916 140120000 63797 95999 78721 97929 88426 102810 83835 80963 73188 115980 FALSE TRUE 66315.75482 112486.0815 80772.53393 117299.0639 73395.3801 78933.9356 77263.79364 79877.82341 70553.97818 138704.0604 0.478109686 0.810979009 0.582337198 0.84567866 0.529150912 0.56908165 0.557040604 0.575886698 0.508665557 1 17.0816505 -1.604517443 8.35447078 1.000193328 0.610647084 0.504932339 0.116872501 0.000402986 1.91E-05 0.108357628 0.025527816 0.024858937 1.604517443 -0.389546245 DLSGNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLSGNKR 7 1 P17066;P48741;A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2;A0A087WWG9 P17066;A0A087WVR3 HSPA6;HSPA7;UHRF1 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7;E3 ubiquitin-protein ligase UHRF1 0 71.342 0.087507 51679000 85358 74382 88535 68761 114200 109020 96103 88195 100520 92833 FALSE TRUE 88727.99975 87156.52989 90842.29483 82361.72057 94788.32479 83701.75721 88570.19574 87012.89028 96902.30484 111021.849 0.799194038 0.785039438 0.818237993 0.741851458 0.853780816 0.753921485 0.79777266 0.783745642 0.872821933 1 16.7604841 0.938347136 2.759129801 0.999746231 0.79122583 0.824563822 0.029696354 0.108352258 1.922082739 0.02535717 0.006734034 8.676551245 -0.938347136 -0.208520401 DLSHIGDAVVISCAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLSHIGDAVVISCAK 15 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 133.14 4.31E-05 734960000 1856350 1695800 2003870 1685660 2567500 2651400 2309100 2082600 2190500 1807170 FALSE TRUE 1929640.131 1987040.459 2056092.498 2019078.517 2131077.267 2035652.532 2128106.708 2054686.153 2111664.333 2161250.361 0.892835076 0.919393928 0.95134397 0.934217781 0.986039057 0.941886497 0.984664593 0.950693261 0.977056787 1 21.04343477 8 0.33531915 0.977456313 0.064743704 0.706222486 0.017232992 31.21213214 0.444747335 0.013989708 17.74620856 100000000 -8 -0.912712609 DLSLDDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLSLDDFK 8 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 82.426 0.047235 47747000 274500 298390 329220 329970 377020 496800 379630 354960 407760 291100 FALSE TRUE 285337.472 349636.1613 337799.7437 395237.0811 312934.2751 381425.7291 349873.6086 350202.3418 393084.7973 348135.4716 0.819616199 1.004310649 0.97031119 1.135296784 0.898886499 1.095624434 1.004992703 1.005936971 1.129114467 1 18.40928929 5.365640799 1.326550151 1.030871042 0.170210001 0.45315188 0.069146036 5.220045058 2.463148178 0.017299694 9.126973999 232081.6475 -5.365640799 -0.860661041 DLSLENGAHAYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLSLENGAHAYNR 13 0 P26358;P26358-2;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 127.71 0.00017371 293100000 77138 78889 86433 85806 95677 113340 113120 94263 104110 80755 FALSE TRUE 80183.4678 92437.57208 88685.51499 102778.1707 79413.85771 87018.50268 104253.3588 92999.55867 100363.1014 96577.3961 0.830250877 0.957134649 0.918284387 1.064205237 0.822282034 0.901023492 1.07947991 0.962953677 1.039198669 1 16.55939795 2.257595002 24.99896413 1.013715794 0.920065818 0.352744889 0.06919803 296.8609862 389883.8926 0.023645198 0.019753066 180.9651727 -2.257595002 -0.093649976 DLSLEVDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLSLEVDRDR 10 1 E7EMW7;O95071-2;O95071;E5RFK7 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 0 ; 82.417 0.016486 132400000 100245 135976 121862 116288 127333 169171 127995 126858 130053 127627 FALSE TRUE 104202.75 159328.8203 125037.8238 139289.4193 105688.9821 129883.5991 117962.4174 125157.676 125372.4179 152633.0671 0.682701016 1.0438683 0.819205341 0.912576953 0.692438304 0.850953214 0.772849683 0.819990572 0.821397488 1 17.21970802 5.033525951 16.328843 0.844745914 0.111130654 0.209729421 0.099282481 5717710.046 76722355.15 0.022299307 119489844.6 108025.4168 -5.033525951 -0.73361526 DLSSHQLNEFLAQTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLSSHQLNEFLAQTLQR 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 133.47 2.02E-05 1437770000 1091480 887590 1141290 913390 1364870 1443220 1374330 1094810 1183550 870140 FALSE TRUE 1134572.473 1040026.678 1171032.955 1094055.816 1132869.885 1108054.027 1266606.423 1080135.863 1140954.267 1040627.273 1.090277473 0.999422853 1.125314496 1.051342632 1.088641355 1.064794337 1.217156667 1.037966129 1.096410114 1 19.98902199 2.991340947 2.416380971 1.092497218 1.065978456 0.006864328 0.060573184 1.182644694 13.86737239 0.018941346 0.021966094 980.2592454 -2.991340947 -0.026518761 DLSSS(ph)PPGPYGQEMYAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 DLSSSPPGPYGQEMYAFR 18 0 O43741;O43741-2 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 DLS(0.002)S(0.017)S(0.98)PPGPYGQEMYAFR;DLSS(0.049)S(0.95)PPGPYGQEMYAFR;DLSS(0.005)S(0.995)PPGPYGQEMYAFR;DLS(0.005)S(0.05)S(0.946)PPGPYGQEMYAFR;DLS(0.006)S(0.059)S(0.932)PPGPY(0.003)GQEMYAFR;DLSS(0.138)S(0.862)PPGPYGQEMYAFR;DLS(0.009)S(0.107)S(0.883)PPGPYGQEMYAFR;DLSS(0.003)S(0.997)PPGPYGQEMYAFR;DLSS(0.061)S(0.938)PPGPYGQEMYAFR;DLS(0.004)S(0.027)S(0.969)PPGPYGQEMYAFR 303.45 9.66E-50 6036280000 4009500 4301940 4719400 4278210 5121750 5596310 4724690 4766540 4595110 4156440 TRUE FALSE 4167798.156 5040764.731 4842391.441 5124427.169 4251156.764 4296651.815 4354356.452 4702652.328 4429732.889 4970814.838 0.838453713 1.014072118 0.974164518 1.030902847 0.855223319 0.864375752 0.87598444 0.946052605 0.891148239 1 22.24505093 3.230297721 24.99953714 0.901901688 0.968644019 0.174001243 0.0623433 280.9120436 849903.1662 0.017472358 0.021215598 1699.408245 -3.230297721 0.066742331 DLSYCLSGMYDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 DLSYCLSGMYDHR 13 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;;;;;; 220.69 2.04E-11 9278610000 5206960 6819450 6491930 6185350 8671160 8804580 6833410 6661760 6270430 8505850 FALSE TRUE 5412534.801 7990637.49 6661115.029 7408793.769 7197239.32 6759849.73 6297789.468 6572470.004 6044758.449 10172408.45 0.532079972 0.785520708 0.654821821 0.728322482 0.707525593 0.664527949 0.619105052 0.64610756 0.594230804 1 23.27815796 -1.1737892 4.661026696 1.000047442 0.663371413 0.696764014 0.067408111 3.13E-05 5.56E-06 0.061557783 0.014507268 0.067020984 1.1737892 -0.336676029 DLSYKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLSYKDR 7 1 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 ; 101.64 0.0081246 479050000 773550 730910 774740 643120 1072630 1043030 860140 811020 929870 756200 FALSE TRUE 804090.3513 856438.1068 794930.3609 770327.2165 890304.7357 800802.0898 792719.9792 800149.6035 896404.1603 904362.9117 0.889123538 0.947007109 0.878994871 0.851789925 0.984455161 0.88548754 0.87655074 0.884766053 0.991199604 1 19.7865423 1.231375514 24.40688937 0.995599929 0.89950733 0.52566647 0.036410832 102.1130009 346844.8112 0.031781691 0.008623735 17.0363092 -1.231375514 -0.0960926 DLTAHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLTAHFR 7 0 A0A5F9ZHZ6;A0A0A0MRL7;P55210-4;P55210;P55210-3;Q5SVL2 A0A5F9ZHZ6 CASP7 Caspase-7;Caspase-7 subunit p20;Caspase-7 subunit p11 0 100.45 0.02286 0 87881 92366 94768 97788 110600 122280 116090 97133 96897 84739 FALSE TRUE 91350.60974 108229.142 97237.73193 117130.1745 91800.25151 93882.32317 106990.5625 95831.09101 93409.6959 101341.9846 0.901409323 1.067959567 0.959500964 1.155791205 0.905846198 0.926391204 1.055737786 0.945620824 0.921727517 1 16.62887246 DLTDYLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 204.65 0.00019968 19710699000 11686543 8921987 11075313 8772913 15331420 13535010 13594823 10987829 11829749 9020510 FALSE TRUE 12147936.74 10454268.86 11363944.76 10508169.01 12725390.7 10391709.05 12529225.25 10840555.12 11403998.64 10787906.23 1.126069924 0.96907302 1.053396694 0.974069369 1.179597823 0.963273951 1.161413993 1.004880363 1.057109545 1 23.36291155 4.803993677 21.51661234 1.044503072 1.126074833 0.108737369 0.072770893 44616.72648 14667777.07 0.015649096 43.67116542 63678.62495 -4.803993677 0.081571762 DLTEYLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DLTEYLSR 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;;;;;;; 238.31 2.64E-08 3275300000 1644586 1835639 1777916 1663693 2260203 2222480 1927528 1858313 1745092 2027690 FALSE TRUE 1709515.525 2150895.719 1824249.952 1992766.51 1876014.501 1706342.702 1776443.319 1833405.354 1682286.48 2424977.033 0.704961532 0.886975707 0.752275146 0.821767168 0.773621554 0.703653139 0.732560884 0.756050605 0.693732954 1 21.20953965 -1.12537482 4.828164917 1.000014294 0.761223795 0.624115864 0.056210308 8.44E-06 1.53E-06 0.053111239 0.01251769 0.074924729 1.12537482 -0.238790499 DLTNNNIPHLLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLTNNNIPHLLSPK 14 0 A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1;A0A1B0GTX4 A0A096LNR9 CDKL5 Cyclin-dependent kinase-like 5 1 DLTNNNIPHLLS(1)PK 118.72 0.00045365 0 103010 59722 78813 61614 115820 118190 104270 91730 95138 56630 TRUE FALSE 107076.9143 69978.78893 80866.93153 73801.0653 96132.95777 90742.16369 96097.04494 90500.50939 91714.00196 67725.56425 1.581041303 1.033269928 1.194038506 1.089707648 1.419448606 1.339850981 1.418918336 1.336282841 1.354200633 1 16.04741289 3.228382034 24.99991202 1.337047251 1.208677171 0.040704727 0.176404999 445.4854886 1094167.567 0.047435492 0.057305421 1691.928609 -3.228382034 -0.12837008 DLTPEHLPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLTPEHLPLLR 11 0 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 131.43 0.00020344 71142000 105130 131300 123180 117050 133430 158970 126530 121040 114210 114010 FALSE TRUE 109280.6136 153849.7536 126390.172 140202.1406 110749.6163 122051.6267 116612.248 119417.6568 110099.6044 136348.0766 0.801482619 1.128360278 0.926967032 1.028266361 0.812256535 0.895147403 0.855254074 0.875829419 0.807489237 1 17.05693482 3.240830887 24.99999446 0.868433275 0.979325443 0.207992077 0.091704928 77.78359676 856536.9284 0.023487183 0.030332232 1741.12875 -3.240830887 0.110892168 DLTQMADELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DLTQMADELRR 11 1 P41227-2;P41227;C9JN83 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ;;;;;; 197.3 9.23E-08 1763464000 928033 2573290 1814182 2296209 1605114 2539126 1324220 1934645 1468716 2947972 FALSE TRUE 964672.4594 3015232.54 1861461.073 2750392.287 1332277.296 1949452.467 1220424.176 1908714.248 1415857.198 3525570.671 0.273621649 0.85524666 0.527988586 0.780126834 0.377889828 0.552946643 0.346163583 0.541391572 0.401596601 1 21.74942537 -1.667520619 6.382114971 1.003579397 0.526051076 0.404614743 0.175330396 0.00836628 0.000435845 0.159053071 0.037311331 0.021502026 1.667520619 -0.477528322 DLTTGYDDSQPDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLTTGYDDSQPDKK 14 1 Q96G03 Q96G03 PGM2 Phosphoglucomutase-2 0 ;; 167.55 5.82E-06 376550000 689614 297269 513077 289906 636348 593786 610940 445041 549721 212528 FALSE TRUE 716840.4932 348322.6383 526448.2081 347248.5415 528181.7943 455888.2004 563052.9264 439075.9533 529936.6486 254168.7925 2.82033245 1.370438262 2.071254315 1.366212343 2.078074924 1.793643491 2.215271674 1.727497499 2.084979212 1 17.95542738 -1.417165838 3.391660634 0.990444228 1.914010753 0.327578068 0.404707252 86719138.13 127314139.7 8172639.896 0.086583644 0.038267859 1.417165838 0.923566525 DLTVLCHLEQLLLVTHLDLSHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLTVLCHLEQLLLVTHLDLSHNR 23 0 Q92696;H0YKZ8;H0YMG5;H0YLG7 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ;; 269.14 4.11E-45 283809500 157395 149173.3 198047.8 193816.4 205749.9 240601.3 221737.6 187471.7 202798.4 143286 FALSE TRUE 163609.0761 174792.6539 203209.0884 232152.7054 170776.6055 184725.2944 204357.2275 184958.9485 195499.7252 171360.1483 0.954767358 1.020030944 1.185859667 1.354764849 0.996594641 1.077994483 1.192559819 1.079358009 1.140870425 1 17.38667211 4.406640316 4.923063237 1.132946174 0.968806498 0.254157221 0.099073848 0.239112263 10.65014088 0.024243276 0.072666517 25505.88023 -4.406640316 -0.164139677 DLVCFLQLDHVNVYYGQDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLVCFLQLDHVNVYYGQDYR 20 0 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 0 115.46 0.00010915 35591000 34935 41775 42738 47554 46872 53791 44963 48523 50472 37081 FALSE TRUE 36314.26078 48949.53129 43851.78739 56960.03927 38904.71418 41298.85546 41438.68257 47872.62855 48655.52258 44346.31199 0.818878936 1.103801626 0.988848574 1.284436895 0.877293115 0.931280497 0.934433569 1.079517696 1.097171792 1 15.43652651 4.751325544 24.07387762 1.031548674 0.818878707 0.252800981 0.110398739 1801.982361 3398325.977 0.026258024 0.461041483 56406.03127 -4.751325544 -0.212669966 DLVDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLVDDFR 7 0 Q6NUQ1 Q6NUQ1 RINT1 RAD50-interacting protein 1 0 ; 89.55 0.041389 114643000 489970 523850 529490 501520 666560 686910 590620 550620 563410 488020 FALSE TRUE 509314.3939 613817.1625 543288.9444 600719.1591 553258.3693 527385.5627 544325.6611 543239.8395 543132.9842 583638.1753 0.872654352 1.051708385 0.930866018 1.029266392 0.947947534 0.903617318 0.932642319 0.930781883 0.930598798 1 19.15471473 3.01153101 24.8139624 0.933520193 0.975829613 0.069183058 0.051585353 390.9945072 841386.6533 0.013552334 0.016185784 1026.906753 -3.01153101 0.04230942 DLVDEDLSHFQSGS(ph)PPAPNGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLVDEDLSHFQSGSPPAPNGFK 22 0 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 DLVDEDLSHFQS(0.001)GS(0.999)PPAPNGFK;DLVDEDLSHFQS(0.074)GS(0.926)PPAPNGFK;DLVDEDLSHFQS(0.004)GS(0.996)PPAPNGFK 279.27 9.02E-46 275530000 194973 148860 196655 153707 246165 257647 271017 209410 226256 131391 TRUE FALSE 202670.6846 174425.547 201779.9909 184109.7858 204321.9612 197812.3889 249773.9794 206603.2015 218113.0908 157134.5508 1.289790715 1.110039429 1.284122364 1.171669661 1.300299394 1.258872653 1.589554799 1.314817145 1.388065767 1 17.26164091 2.855228388 2.236372749 1.354251658 1.213571597 0.052733061 0.146912313 0.558404389 5.496427949 0.047109797 0.050372901 716.5201165 -2.855228388 -0.140680061 DLVDSPASLASSLGS(ph)PLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLVDSPASLASSLGSPLPR 19 0 K7EMK7;Q04725;Q04725-2;Q04725-3 K7EMK7 TLE2 Transducin-like enhancer protein 2 1 DLVDSPASLASS(0.001)LGS(0.999)PLPR;DLVDSPASLASSLGS(1)PLPR;DLVDSPAS(0.001)LAS(0.127)S(0.127)LGS(0.745)PLPR 348.63 1.15E-90 315532000 190938 213284 229302 215837 260024 292597 245914 224594 252985 219820 TRUE FALSE 198476.3797 249913.8679 235277.7985 258528.9144 215825.2134 224645.7811 226638.6181 221583.6848 243880.1193 262889.5203 0.754980189 0.950642185 0.894968343 0.983412782 0.820973058 0.854525433 0.862105944 0.842877588 0.927690533 1 18.00409711 0.976001022 5.022895601 0.999913325 0.873900741 0.308755499 0.060638706 0.206397427 19.29953347 0.056215151 0.014213647 9.462393891 -0.976001022 -0.126012584 DLVEAVAHILGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 248.15 5.44E-17 12144000000 3297320.6 3310119.9 3623817 3970427 4198097.1 4760833 3912849.1 3492869.5 3385917.4 3087473.4 FALSE TRUE 3427501.363 3878607.244 3718256.648 4755765.61 3484506.054 3655201.687 3606149.763 3446053.298 3264058.894 3692404.699 0.928257231 1.050428531 1.007001385 1.287986014 0.943695596 0.989924449 0.976639902 0.933281582 0.883992726 1 21.81612926 DLVHTEGQLQNEEIVAHDGSATYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLVHTEGQLQNEEIVAHDGSATYLR 25 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 383.83 2.05E-138 260210000 41013 49836 54485 51640 49737 58114 56148 62536 49847 39617 FALSE TRUE 42632.22491 58394.94533 55904.92386 61854.23787 41282.72251 44617.90423 51746.97304 61697.80721 48053.01621 47379.19264 0.89980902 1.232501908 1.179946739 1.305514814 0.871326002 0.941719387 1.092187734 1.30221314 1.01422193 1 15.53196599 -2.602936101 1.439571643 0.191818616 1.109532499 0.022772859 0.152933419 1293861.031 71081.52234 3386479.386 0.044390446 0.002494962 2.602936101 0.917713882 DLVILLYETALLSSGFSLEDPQTHANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 DLVILLYETALLSSGFSLEDPQTHANR 27 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 299.3 8.57E-71 65186524800 19396442.8 22506796 25292713.1 23202478.2 29504988.9 32537141.8 27720281.3 25002871.2 26841609 25079526.7 FALSE TRUE 20162229.34 26372163.13 25951861.98 27791859.14 24489741.43 24980883.72 25547493.22 24667748.61 25875584.74 29993379.78 0.672222653 0.879266136 0.865253005 0.926599781 0.816504896 0.832879919 0.851771071 0.822439778 0.862709869 1 24.83814076 -5 0.318231697 2.495927383 0.832916598 0.39145242 0.062071632 334.2055332 2.972820624 336.4484185 0.053814343 1.00E-05 5 -1.663010785 DLVLPTQALPAS(ph)PALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DLVLPTQALPASPALK 16 0 Q15554;J3KSZ6;U3KQ35;H3BR06 Q15554 TERF2 Telomeric repeat-binding factor 2 1 DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK;DLVLPTQALPAS(1)PALK 233.49 1.24E-19 609870000 1479430 977490 1135750 877770 1559020 1505830 1446380 1301870 1345530 885670 TRUE FALSE 1537839.039 1145366.304 1165348.578 1051390.286 1294018.337 1156123.804 1333008.956 1284420.562 1297104.638 1059200.079 1.451887201 1.081350281 1.10021572 0.992626706 1.221693958 1.09150653 1.25850534 1.212632615 1.224607762 1 20.0145437 2.243892184 24.9890367 1.196290808 1.14607855 0 0.132485844 569.7907479 2670619.86 0.045249792 0.036822923 175.3445146 -2.243892184 -0.050212258 DLVMGS(ph)SPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.5)S(0.5)PQLK;DLVMGS(0.556)S(0.444)PQLK 122.66 0.00040502 258950000 1038140 735230 943890 900780 1167490 1250860 1292320 1002870 992450 566150 TRUE FALSE 1079126.569 861500.0332 968488.5488 1078951.595 969040.4668 960366.722 1191024.582 989428.168 956731.9184 677076.2529 1.593803599 1.272382585 1.430398046 1.593545174 1.431213194 1.418402607 1.759070085 1.461324576 1.413034225 1 19.36895879 0.749058756 2.610674283 1.000177494 1.494636104 0.586979992 0.12403273 0.933053347 8.682418616 0.118084243 0.031397888 5.611238861 -0.749058756 0.49445861 DLVMGS(ph)SPQLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLVMGSSPQLKR 12 1 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.557)S(0.443)PQLKR;DLVMGS(0.5)S(0.5)PQLKR;DLVMGS(0.543)S(0.457)PQLKR;DLVMGS(0.545)S(0.455)PQLKR 100.11 0.0020929 1525870000 889210 767980 895140 693370 1116010 1162080 853100 803170 895670 716470 TRUE FALSE 924316.6974 899874.5909 918468.0838 830516.5165 926311.0188 892204.5315 786231.7928 792404.8199 863435.0117 856848.5789 1.078739838 1.050214254 1.071914112 0.96926871 1.081067346 1.041262778 0.917585455 0.924789793 1.007686811 1 19.70868075 2.278982421 9.947963095 0.951531502 1.047828716 0.516809289 0.04028597 0.287786749 68.4911277 0.013874774 0.011560764 190.1001329 -2.278982421 0.096297214 DLVMGSS(ph)PQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 DLVMGS(0.225)S(0.775)PQLK 148.13 3.67E-05 217790000 903050 639870 835570 746600 1063300 1144100 1129800 938690 999560 560860 TRUE FALSE 938703.1113 749762.695 857345.6406 894275.2516 882560.6458 878400.114 1041243.324 926108.3959 963586.0309 670749.7787 1.399483296 1.117797901 1.278189972 1.333247181 1.315782239 1.309579432 1.552357313 1.380706227 1.436580468 1 19.35541515 3.316868651 1.405339676 1.375285644 1.253312318 0 0.149135095 0.950289973 3.898747377 0.048440988 0.07769941 2074.286069 -3.316868651 -0.121973326 DLVNT(ph)ANWRANYTILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLVNTANWRANYTILK 16 1 Q02487-2;A0A3B3ISU0;Q02487 Q02487-2;A0A3B3ISU0 DSC2 Desmocollin-2 1 DLVNT(0.562)ANWRANY(0.438)TILK 65.472 0.092576 50868000 2006.4 44831 21811 45264 8170.8 34689 11797 22098 15964 67906 TRUE FALSE 2085.614221 52530.37551 22379.41258 54217.0841 6781.930335 26633.00547 10872.32031 21801.81246 15389.45876 81210.88056 0.025681463 0.646839132 0.275571604 0.667608622 0.083510119 0.327948734 0.133877631 0.268459255 0.189499962 1 16.30938541 -1.289340193 3.911969226 1.001163355 0.298067566 0.51865449 0.20480531 22996318.96 15160519.48 212365.5459 0.044933046 0.051364115 1.289340193 -0.703095789 DLVQPDKPAS(ph)PK ddPTM_MDA-MB-175_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 203.99 7.19E-08 8703840000 18212400 3944050 6434500 3904980 10920300 13219500 10479080 6940720 7650970 2537670 TRUE FALSE 18931439.62 4621409.907 6602188.356 4677373.389 9064071.307 10149471.47 9657702.328 6847691.001 7375613.084 3034877.85 6.237957688 1.522766363 2.17543792 1.541206474 2.986634637 3.344276762 3.182237574 2.256331668 2.430283342 1 21.53320702 0.723982589 1.101192134 1.008152485 2.844188523 0.173967956 1.265898467 1.731311803 3.662361446 1.153555266 0.362411194 5.296422103 -0.723982589 1.836036038 DLVSSLTSGLLTIGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLVSSLTSGLLTIGDR 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 151.78 1.42E-06 333240000 51728 47203 55521 46843 85684 72887 67997 62415 67623 57433 FALSE TRUE 53770.26138 55309.74806 56967.92287 56108.40559 71119.46429 55960.09886 62667.21746 61578.42902 65189.26144 68685.89673 0.782842824 0.805256256 0.829397672 0.816883935 1.035430382 0.814724733 0.912373871 0.896522168 0.949092384 1 16.06772628 8 0.146684556 1.008665117 0.168136825 0.506349113 0.05891141 58.7274321 0.567506878 0.212150795 10.46358405 99999999.96 -8 -0.840528292 DLVVLLFETALLSSGFSLEDPQTHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DLVVLLFETALLSSGFSLEDPQTHSNR 27 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 288 5.40E-62 23325050000 3811836 3904530 4848500 4253656 5260810 5975580 5035760 4834430 4797460 4336020 FALSE TRUE 3962330.229 4575102.654 4974855.893 5095016.461 4366579.395 4587842.106 4641043.973 4769632.373 4624800.352 5185580.101 0.764105491 0.88227403 0.959363426 0.982535485 0.842061893 0.884730737 0.894990316 0.919787619 0.891857856 1 22.30607396 -4.73400687 0.013169703 2.029298081 6.32E-07 0.28441174 0.055563427 11497.85018 11.97906002 1115.201333 761.6730626 1.84E-05 4.73400687 -2.02929745 DLYANTVLSGGT(ph)TMYPGIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 1 DLYANT(0.073)VLS(0.341)GGT(0.563)T(0.023)MYPGIADR 145.02 2.06E-08 0 30565 34555 28240 26423 35930 45096 32075 30238 32511 34184 TRUE FALSE 31771.7298 40489.55245 28975.9576 31649.39054 29822.63143 34623.13744 29560.87769 29832.70907 31340.93546 40881.70031 0.777162632 0.990407741 0.708775745 0.774170113 0.729486083 0.846910407 0.723083371 0.72973259 0.766625048 1 15.31916758 4.223844853 24.98441006 0.769862445 0.883785253 0.132438736 0.09530269 302.4390631 513483.0026 0.021433684 0.046613028 16743.44627 -4.223844853 0.113922808 DLYANTVLSGGTTMYPGIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 356.01 3.21E-95 2019896000 700088 817391 741799 766638 915084 1016713 852005 845212 801479 789010 FALSE TRUE 727728.0148 957771.5458 761130.8913 918276.7082 759538.3485 780596.8142 785222.6218 833883.3156 772633.9274 943601.403 0.771223964 1.015017085 0.806623315 0.973161661 0.804935586 0.827252706 0.832154996 0.883724116 0.818813881 1 19.84781804 5.043034075 15.31339553 0.876134102 0.292811381 0.150613396 0.078494164 2893058.953 29653514.2 0.01710257 47397523.26 110416.5249 -5.043034075 -0.58332272 DLYCHK ddPTM_MDA-MB-175_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 80.377 0.064673 64321000 171300 183460 177980 175250 238030 237470 213220 193990 182580 249380 FALSE TRUE 178063.0563 214967.8279 182618.305 209913.9269 197569.7456 182321.1914 196507.2593 191389.8814 176008.9815 298241.2363 0.597043717 0.720785062 0.612317422 0.70383938 0.662449459 0.611321203 0.658886952 0.641728433 0.590156424 1 18.18612022 -1.245494123 3.697947905 1.000566168 0.647193005 0.868077719 0.041587483 10693066.09 18894056.05 70584.1219 0.00923273 0.056820608 1.245494123 -0.353373162 DLYDAGVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLYDAGVKR 9 1 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2 Annexin A2;Annexin 0 ;;; 103.7 0.0054193 2155930000 2179980 2333850 2566880 2320400 2826350 3174970 2930790 2562090 2484520 2145230 FALSE TRUE 2266047.294 2734670.583 2633775.002 2779368.194 2345928.037 2437631.335 2701067.022 2527749.374 2395102.611 2565546.746 0.883260965 1.065921168 1.026594041 1.083343423 0.914396918 0.950141072 1.052823156 0.985267323 0.933564206 1 21.29083488 3.237616426 24.99999867 0.977323743 1.019276703 0.096747202 0.061420796 62.95478166 1666920.472 0.017355849 0.021903127 1728.289241 -3.237616426 0.04195296 DLYDDKDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLYDDKDGLR 10 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;;; 146.11 2.67E-05 1223410000 3751760 2285180 3033330 2367270 4046210 4033970 4221100 3167210 3396680 1690590 FALSE TRUE 3899882.382 2677641.889 3112381.072 2835508.94 3358436.669 3097141.603 3890239.152 3124758.73 3274434.15 2021828.742 1.928888585 1.324366319 1.539389072 1.402447636 1.661088597 1.531851605 1.924119027 1.545511084 1.619540806 1 20.94722937 DLYDDKDGLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DLYDDKDGLRK 11 2 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 64.55 0.038174 238780000 249620 128810 185080 130060 274870 227650 256770 186520 211830 85617 FALSE TRUE 259475.1903 150932.1155 189903.3368 155785.4798 228147.6956 174781.7376 236643.6965 184020.0045 204206.2797 102392.0119 2.53413509 1.47406143 1.854669454 1.521461263 2.228178657 1.706986066 2.311153888 1.797210554 1.994357527 1 16.64374364 -0.889404314 6.803694572 0.999999975 1.916993219 0.426848467 0.324656368 1.10E-07 1.87E-08 0.284018317 0.066943757 0.129001775 0.889404314 0.916993244 DLYEDELVPLFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLYEDELVPLFEK 13 0 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;; 236.37 2.40E-16 226986000 596759 465562 582183 413308 756543 688157 676081 560532 653934 405578 FALSE TRUE 620319.5061 545518.6519 597355.1672 495059.0888 627946.0911 528342.9659 623088.0046 553018.9854 630399.0431 485043.2438 1.278895261 1.124680446 1.23155033 1.020649386 1.294618777 1.089269818 1.284602997 1.140143673 1.299675959 1 18.88775385 -2.337190378 2.140750056 6.00E-05 1.189730345 0.281939988 0.093359932 1703009.701 183991.3191 8295291.004 0.020072981 0.004600549 2.337190378 1.189670361 DLYLASVFHATAFELDTDGNPFDQDIYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DLYLASVFHATAFELDTDGNPFDQDIYGR 29 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;;;;; 414.38 4.80E-175 3292066000 332593.5 791787.1 738396.4 940475 877680 1109508 791730 853060 739343 773367 FALSE TRUE 345724.5482 927770.3752 757639.6168 1126498.148 728492.2671 851841.5818 729672.1338 841626.126 712734.1899 924893.4566 0.373799323 1.00311054 0.819164209 1.217976125 0.787649931 0.921015903 0.788925609 0.909970894 0.770612209 1 19.81892766 4.744904734 24.75439246 0.907629358 0.373799049 0.607141394 0.13009006 408.8815718 1595383.484 0.029220905 0.274415134 55578.2328 -4.744904734 -0.533830309 DLYLASVFHATAFELDTDGNPFDQDIYGREELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DLYLASVFHATAFELDTDGNPFDQDIYGREELR 33 1 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;; 299.36 5.13E-90 263081000 104811.9 128917.6 154970.6 112267.8 183677.2 184042.5 107706.6 126609.5 139079.1 176865.7 FALSE TRUE 108949.9547 151058.195 159009.2611 134474.0358 152455.8152 141301.4186 99264.27525 124912.5067 134073.6704 211519.1476 0.515083178 0.714158489 0.75174878 0.635753487 0.720766025 0.668031335 0.469292149 0.590549405 0.633860678 1 17.69042874 -2.239531703 2.09637767 2.168074286 0.632458327 0.626591002 0.084934168 4551713.058 744319.5041 25185721.84 0.021800907 0.005760608 2.239531703 -1.535615959 DMAEAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DMAEAHK 7 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ;;; 89.142 0.01809 513013000 851013 740210 897623 732480 1010230 1035701 1072228 918140 941948 723453 FALSE TRUE 884611.6504 867335.3095 921015.7928 877362.3578 838511.4654 795175.139 988183.9676 905833.8351 908047.4755 865199.764 1.022436306 1.002468269 1.064512302 1.014057556 0.969153599 0.919065367 1.142145443 1.046964959 1.04952349 1 19.72267375 2.236072162 24.99999364 1.064599038 1.00114873 0.275821321 0.048085949 86.91754926 873192.5857 0.017850301 0.013802246 172.2154705 -2.236072162 -0.063450307 DMDDAYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 126.41 0.0028389 1741460000 1635330 1691920 1637530 1486760 2064280 2445620 1795800 1621160 1468740 1465590 FALSE TRUE 1699894.091 1982494.099 1680205.377 1780836.69 1713394.423 1877661.819 1655040.504 1599431.002 1415880.334 1752744.3 0.969847165 1.131080043 0.958614087 1.01602766 0.977549562 1.071269676 0.944256674 0.91252957 0.807807696 1 20.74118411 2.02323153 3.908264799 0.901759155 1.020739874 0.390865378 0.064777975 0.206399471 6.911212121 0.026548584 0.017261946 105.4949159 -2.02323153 0.11898072 DMDEPS(ph)PVPNVEEVTLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 239.43 2.53E-23 787676000 635698 449663 544126 462450 708525 714606 756546 594923 637253 369373 TRUE FALSE 660795.8479 526889.1224 558306.3706 553921.2297 588090.1736 548649.5865 697245.9477 586949.0303 614318.389 441744.5673 1.495877701 1.192746128 1.263866976 1.253940106 1.33129011 1.242006415 1.578391675 1.328706845 1.390664276 1 18.75285287 DMDLWEQQEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMDLWEQQEEER 12 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 93.959 0.0044888 0 43723 62453 57529 51642 49485 65177 50759 47577 46302 57047 FALSE TRUE 45449.2178 73178.81693 59028.253 61856.63346 41073.55738 50040.62952 46780.37695 46939.30814 44635.60006 68224.26742 0.666173775 1.072621513 0.865209041 0.906666144 0.602037353 0.733472581 0.685685295 0.688014836 0.65424814 1 16.05799738 3.257256894 24.98183809 0.707836917 0.890703067 0.216971366 0.13615355 283.661705 379024.474 0.03447112 0.046593923 1808.243421 -3.257256894 0.18286615 DMDRDVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMDRDVDR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 118.71 0.0016725 258820000 320070 321220 365740 313720 462860 408090 373920 354570 347200 383120 FALSE TRUE 332706.6107 376387.0363 375271.4849 375772.8796 384183.2225 313317.2822 344611.1733 349817.5691 334704.3398 458185.0287 0.726140292 0.821473886 0.819039168 0.820133475 0.838489253 0.68382261 0.752122291 0.763485376 0.730500385 1 18.80557079 -1.024964891 4.414184965 1.000011194 0.774596541 0.664042676 0.048465925 6508231.974 1511198.293 702.4937424 0.011752056 0.09441372 1.024964891 -0.225414653 DMEDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMEDLLR 7 0 M0QZR4;Q92888;Q92888-3;M0QYC1;Q92888-2;Q92888-4;M0R2C7 M0QZR4 ARHGEF1 Rho guanine nucleotide exchange factor 1 0 ; 99.375 0.024601 18964000 113046 132620 146311 130776 166652 165733 152816 135815 134247 134979 FALSE TRUE 117509.1434 155396.4534 150123.9849 156643.1025 138324.5526 127244.0225 140837.8826 133994.6221 129415.4767 161425.5507 0.727946368 0.96265091 0.92998899 0.97037366 0.856893794 0.788252057 0.872463386 0.830070714 0.801703795 1 17.30050942 3.025418062 24.62930251 0.84532436 0.905799226 0.036254858 0.083470061 427.4243164 414157.2129 0.022901738 0.027371941 1060.273879 -3.025418062 0.060474866 DMEESIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DMEESIR 7 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;; 170.73 0.0022429 1059199000 1227389 1434750 1472594 1604280 1669300 1866655 1734061 1480691 1371694 1223649 FALSE TRUE 1275847.265 1681157.152 1510971.009 1921601.796 1385552.982 1433152.666 1598140.768 1460844.759 1322327.001 1463399.593 0.871837925 1.148802528 1.032507468 1.313108056 0.946804269 0.979331054 1.092074082 0.998254179 0.903599404 1 20.48089233 DMES(ph)PTKLDVTLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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(0.998)PT(0.002)KLDVTLAK;DMES(0.938)PT(0.062)KLDVTLAK;DMES(0.992)PT(0.008)KLDVTLAK;DMES(0.572)PT(0.428)KLDVTLAK;DMES(0.992)PT(0.008)KLDVTLAK;DMES(0.767)PT(0.233)KLDVTLAK;DMES(0.998)PT(0.002)KLDVTLAK;DMES(0.974)PT(0.026)KLDVTLAK;DMES(0.975)PT(0.025)KLDVTLAK;DMES(0.977)PT(0.023)KLDVTLAK;DMES(0.543)PT(0.457)KLDVTLAK;DMES(0.997)PT(0.003)KLDVTLAK;DMES(0.885)PT(0.115)KLDVTLAK;DMES(0.575)PT(0.425)KLDVTLAK;DMES(0.973)PT(0.027)KLDVTLAK 279.44 8.43E-33 17026690000 23731700 8223686 13626120 8405993 20730570 19394670 20573920 14183640 16685370 6638998 TRUE FALSE 24668645.84 9636040.099 13981227.88 10068673.33 17206795.12 14890551.82 18961282.39 13993531.51 16084866.79 7939782.547 3.106967438 1.213640303 1.760908161 1.268129608 2.167162012 1.875435723 2.388136234 1.762457778 2.025857345 1 22.92066806 4.754682303 24.41171511 1.777799006 3.10696884 0.489298508 0.421747684 1956.06516 2961837.113 0.096665165 2.46218839 56843.69534 -4.754682303 1.329169833 DMESPT(ph)KLDVTLAK ddPTM_MDA-MB-175_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(0.366)PT(0.634)KLDVTLAK 208.66 4.92E-08 395230000 648860 239730 371680 244630 592660 519860 588810 397620 536550 202080 TRUE FALSE 674477.4938 280901.7627 381366.2861 293017.0839 491919.8649 399130.3936 542657.5336 392290.5543 517239.6703 241673.7069 2.79086005 1.16231826 1.57802142 1.212449164 2.035471178 1.65152593 2.245414036 1.623223971 2.140239734 1 17.882701 DMFCAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DMFCAGR 7 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;;;; 151.14 0.0044232 1735340000 1106250 1347940 1359500 1421410 1512600 1731050 1502860 1396130 1308880 1410210 FALSE TRUE 1149925.604 1579438.209 1394929.687 1702560.656 1255488.792 1329039.872 1385061.906 1377417.161 1261773.664 1686513.649 0.681835931 0.936510778 0.827108448 1.009514898 0.74442848 0.788039796 0.821257454 0.816724585 0.748155027 1 20.68561256 DMFEEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMFEEALR 8 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 142.64 0.0014288 260060000 370780 450860 474640 422220 566940 589580 512390 449600 445860 504270 FALSE TRUE 385418.6807 528291.6978 487009.5083 505733.8558 470571.7413 452658.9802 472227.5329 443573.8474 429813.5857 603072.0517 0.63909226 0.876000963 0.8075478 0.838596076 0.780291078 0.750588556 0.783036673 0.7355238 0.712706856 1 19.20197085 -1.463706639 3.148085207 1.004636034 0.773237254 0.545837434 0.063046991 25994136.13 32910248.98 1064194.779 0.014639889 0.03437901 1.463706639 -0.23139878 DMFQETMEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMFQETMEAMR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 171.92 3.25E-05 103172000 105299 109006 113141 123982 140112 136566 143847 108550 118156 98659 FALSE TRUE 109456.2858 127726.9326 116089.5474 148505.2696 116295.8123 104850.6162 132571.8963 107095.0648 113903.5886 117989.3421 0.927679432 1.082529407 0.983898591 1.258632915 0.985646756 0.888644807 1.12359213 0.907667276 0.965371843 1 16.84829702 3.034070808 24.99987942 0.9742335 1.066808018 0.149097858 0.099036164 324.3430919 237988.7711 0.027656434 0.033055645 1081.610284 -3.034070808 0.092574517 DMGSCEIYPQTIQHNPNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DMGSCEIYPQTIQHNPNGR 19 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;;;; 244.1 1.70E-24 3275230000 1669600 1363278 1541864 1389127 1791000 1974200 1717960 1505890 1593540 1227162 FALSE TRUE 1735517.097 1597410.392 1582046.242 1663892.174 1486566.46 1515721.969 1583301.806 1485706.008 1536188.807 1467600.898 1.182553853 1.088450132 1.077981244 1.133749765 1.012922833 1.032788935 1.078836765 1.012336535 1.046734714 1 20.48502826 8 0.293279551 1.017538229 2.227898786 0.654453738 0.032469509 32.65258193 0.465641975 0.032818488 20.57255969 100000000 -8 1.210360558 DMGYGNWISKPQEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMGYGNWISKPQEEK 15 1 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 196.22 8.25E-09 1276840000 1434310 726510 1119580 760970 1548770 1346400 1317570 1015710 1183430 596830 FALSE TRUE 1490937.666 851282.441 1148757.175 911487.5947 1285510.629 1033719.005 1214295.421 1002096.069 1140838.585 713767.4115 2.088828437 1.192660841 1.609427884 1.277009261 1.801021744 1.448257497 1.701248055 1.403953238 1.598333809 1 19.44509451 -2.599459975 0.419467178 5.48E-13 1.56228921 0.320860589 0.247792851 106.7409786 4.686887945 96.97131093 0.130027912 0.002515012 2.599459975 1.56228921 DMGYHVSMMADSTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMGYHVSMMADSTSR 15 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 105.46 0.0013133 98185000 19283 140980 133840 154970 105150 185340 101390 154330 109020 197830 FALSE TRUE 20044.30773 165192.2183 137327.9804 185622.6035 87276.64056 142297.5939 93442.78687 152261.4588 105096.3915 236591.0008 0.084721345 0.69821852 0.580444649 0.784571699 0.368892478 0.601449731 0.39495495 0.643564034 0.444211281 1 17.85203567 -1.458078932 2.996254685 1.011156613 0.528833489 0.368876739 0.19055035 35841117.3 41621290.61 3352226.449 0.043902227 0.034827401 1.458078932 -0.482323124 DMGYTYLNIDDCWIGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMGYTYLNIDDCWIGGR 17 0 P17050 P17050 NAGA Alpha-N-acetylgalactosaminidase 0 190.1 7.39E-10 26340000 26494 47000 21241 37943 26738 40700 25798 30580 38138 38174 FALSE TRUE 27540.00358 55071.88439 21794.55791 45448.01215 22193.08431 31248.04181 23775.88535 30170.12512 36765.42083 45653.46441 0.603240169 1.206302415 0.477391107 0.995499744 0.486120486 0.684461567 0.520790386 0.660850726 0.805315025 1 15.47843672 4.222477688 24.99997154 0.683022758 0.904771605 0.108459924 0.224228026 374.7833561 582581.0373 0.05064558 0.109943976 16690.82057 -4.222477688 0.221748847 DMHGQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMHGQFK 7 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 111.01 0.0050636 125710000 166820 144020 155200 157890 197560 207140 191930 140900 176010 134790 FALSE TRUE 173406.1824 168754.3147 159244.6395 189120.1707 163978.8218 159034.8742 176886.0251 139011.466 169675.4345 161199.5198 1.075723939 1.046866113 0.987872915 1.173205547 1.017241379 0.986571638 1.097311117 0.862356576 1.052580273 1 17.29848792 1.760063786 25 0.95870355 1.052543805 0.231049925 0.068348241 13.13611784 15284.95795 0.030209337 0.016752862 57.55244597 -1.760063786 0.093840255 DMHSAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DMHSAYK 7 0 P08621;P08621-2 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;;;;; 151.29 0.0018911 2317727000 3803000 6401412 5955590 5949839 6208450 7582710 5647410 5989710 5403470 6752430 FALSE TRUE 3953145.377 7500804.715 6110797.568 7126699.396 5153139.887 5821740.52 5204751.247 5909427.735 5209000.17 8075439.375 0.489526971 0.928841685 0.756713943 0.882515373 0.638125017 0.720919352 0.644516169 0.731777859 0.645042323 1 22.94510933 -1.181692345 5.088460711 1.000018974 0.72325751 0.335985985 0.119591236 2.40E-05 3.85E-06 0.10781655 0.025410863 0.065812389 1.181692345 -0.276761464 DMLGSLRDS(ph)ALFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMLGSLRDSALFVK 14 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DMLGS(0.014)LRDS(0.986)ALFVK 104.89 0.0015643 173790000 318370 291630 337170 342330 559720 480860 426090 386370 423650 386280 TRUE FALSE 330939.4934 341715.1839 345956.9272 410041.8522 464578.9943 369187.5525 392691.9524 381191.3421 408402.9193 461964.1702 0.716374807 0.739700622 0.748882596 0.887605314 1.005660231 0.799169235 0.850048505 0.825153479 0.884057565 1 18.81742144 3.769573823 5.451938851 0.88084665 0.733557477 0.556966758 0.064038137 0.155008777 13.57166044 0.016979854 0.030264979 5882.661018 -3.769573823 -0.147289173 DMLLANKVPAAAR ddPTM_MDA-MB-175_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 ; 191.48 3.22E-06 4016700000 4094600 3719700 4307300 3865900 5851500 5542200 4995200 4538200 4849000 4576500 FALSE TRUE 4256257.97 4358529.54 4419551.776 4630563.481 4856864.12 4255108.043 4603663.171 4477372.852 4674485.437 5473177.553 0.777657573 0.796343531 0.807492857 0.846046641 0.887393854 0.77744747 0.841131706 0.8180573 0.854071587 1 22.38394723 -5 0.240338607 2.017407599 0.804884665 0.756790574 0.030925007 84.59079047 0.84364613 42.04008309 0.049551145 1.00E-05 5 -1.212522934 DMLLELEEQLAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 180.18 4.15E-06 66581000 60559.5 70641.3 71783 74061 79282 86885 84904 73756 70084 50324.7 FALSE TRUE 62950.43582 82773.39376 73653.72395 88710.04475 65805.67396 66707.2755 78249.00262 72767.42146 67561.69053 60184.86144 1.045951329 1.375319171 1.223791535 1.473959441 1.093392464 1.108373001 1.300144268 1.209065199 1.122569512 1 15.87711302 DMMELVQPSISGVDLDKFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMMELVQPSISGVDLDKFR 19 1 O76038 O76038 SCGN Secretagogin 0 172.66 8.25E-15 0 139400 136050 138850 143030 168660 164480 136870 144460 153750 117580 FALSE TRUE 144903.6196 159415.5292 142468.5451 171320.9071 139991.2334 126282.0127 126141.7718 142523.75 148216.5675 140617.5498 1.030480334 1.133681602 1.01316333 1.218346553 0.995545959 0.898053002 0.89705568 1.01355592 1.054040322 1 17.10141714 3.022646433 24.99314034 0.968059337 1.096734609 0.431258587 0.069248548 215.0253668 237305.4077 0.019892401 0.023774659 1053.528851 -3.022646433 0.128675272 DMNQVLDAYENKKPFYLYTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMNQVLDAYENKKPFYLYTGR 21 2 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 205.9 2.53E-22 2497900000 1638960 1297860 1710500 1223820 2170860 1976000 1591900 1723520 1872760 1475710 FALSE TRUE 1703667.406 1520757.359 1755077.035 1465887.943 1801857.993 1517103.947 1467122.718 1700419.034 1805359.733 1764847.12 0.96533427 0.861693538 0.994464061 0.830603357 1.020971149 0.859623437 0.831303007 0.963493673 1.02295531 1 20.75111178 1.49262309 6.06610691 1.006595874 0.909181152 0.298745178 0.063404337 0.163981266 14.13409838 0.034520569 0.015188241 31.09016953 -1.49262309 -0.097414722 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_MDA-MB-175_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 237.13 2.47E-37 2337017000 1061544 1174449 1167930 1173133 1315943 1423527 1197067 1159181 1199688 1243690 TRUE FALSE 1103454.577 1376151.48 1198367.215 1405175.206 1092259.479 1092934.428 1103237.761 1143644.075 1156511.463 1487367.244 0.741884415 0.925226427 0.805696925 0.944739917 0.734357627 0.734811414 0.741738643 0.768904976 0.777556093 1 20.50432947 5.042797965 15.98784536 0.811685845 0.404594858 0.050164944 0.092666026 10450787.65 106645994.6 0.021650632 126225537.9 110356.5118 -5.042797965 -0.407090987 DMPHPLAGSSSEEAVGGDS(ph)TPSPDLLMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMPHPLAGSSSEEAVGGDSTPSPDLLMAR 29 0 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 DMPHPLAGSSSEEAVGGDS(0.394)T(0.319)PS(0.287)PDLLMAR 91.407 0.00097377 44404000 10545 18377 19820 16652 16600 18599 14931 13824 15582 17690 TRUE FALSE 10961.32474 21533.1068 20336.52548 19945.7159 13778.33793 14279.66412 13760.66921 13638.71189 15021.20686 21156.0168 0.51811855 1.017824243 0.961264385 0.942791646 0.651272782 0.674969407 0.650437619 0.644672956 0.710020558 1 14.36878041 3.234393976 24.99995083 0.693473997 0.878506086 0.131676586 0.161511408 150.1584032 900954.9224 0.043978138 0.054375802 1715.512852 -3.234393976 0.185032089 DMPHPLAGSSSEEAVGGDST(ph)PSPDLLMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMPHPLAGSSSEEAVGGDSTPSPDLLMAR 29 0 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 DMPHPLAGSSSEEAVGGDS(0.005)T(0.598)PS(0.398)PDLLMAR 173.25 5.40E-12 158030000 55802 92122 78230 84912 77610 94140 74212 92200 76129 85855 TRUE FALSE 58005.10605 107943.2369 80268.73807 101707.3402 64417.87992 72277.41171 68395.06952 90964.20981 73389.13216 102676.6435 0.564929901 1.051293004 0.781762389 0.990559652 0.627385915 0.703932358 0.666121011 0.885928939 0.714759751 1 16.64774851 4.827537585 21.21464443 0.81126093 0.564876545 0.221627601 0.144062091 103844.4869 24743307.58 0.033110902 805.2477911 67226.04854 -4.827537585 -0.246384385 DMPHPLAGSSSEEAVGGDSTPS(ph)PDLLMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMPHPLAGSSSEEAVGGDSTPSPDLLMAR 29 0 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 DMPHPLAGSSSEEAVGGDS(0.108)T(0.108)PS(0.785)PDLLMAR;DMPHPLAGSSSEEAVGGDS(0.001)T(0.003)PS(0.997)PDLLMAR 167.78 2.42E-12 198027000 39118 66499 58487 59278 59559 75511 65715 60102 70026 47785 TRUE FALSE 40662.40885 77919.68596 60011.21927 71003.01147 49435.18245 57974.71463 60564.08659 59296.431 67505.77794 57147.55585 0.711533647 1.363482389 1.050109989 1.242450537 0.865044563 1.014474088 1.059784372 1.037602223 1.181253982 1 15.80240418 7.225890617 8.518640188 1.060432892 0.082363056 0 0.174890539 0 0 0.035202249 0 16822503.1 -7.225890617 -0.978069836 DMQGLS(ph)LDAASQPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 256.67 9.66E-25 502571000 724596 608694 982090 595956 1606290 901260 941070 878730 1111370 729865 TRUE FALSE 753203.6096 713232.4595 1007684.072 713834.318 1333253.4 691956.0237 867306.4744 866952.0617 1071372.011 872868.0726 0.862906587 0.817113699 1.154451748 0.817803217 1.52743976 0.792738382 0.993628363 0.993222331 1.227415739 1 19.73540409 4.251664438 24.97967547 1.054385946 0.840010014 0.165341441 0.199900491 398.4073986 759465.5844 0.045613144 0.123278999 17851.07761 -4.251664438 -0.214375932 DMQPLS(ph)PISVHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DMQPLSPISVHER 13 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 DMQPLS(0.997)PIS(0.003)VHER;DMQPLS(1)PISVHER 93.753 0.018319 216639000 87126 187620 194107 175546 211691 257117 181171 220877 177442 212492 TRUE FALSE 90565.80176 219842.2755 199165.5879 210268.4748 175707.8394 197405.4734 166970.3436 217916.5051 171055.8971 254125.739 0.356381853 0.865092518 0.783728514 0.827419039 0.69142087 0.776802358 0.6570383 0.857514496 0.673115198 1 17.95518298 -5 0.136144087 1.838781202 0.640582916 0.28198412 0.138734572 194.8795401 1.64531781 45.12071894 0.871023977 1.00E-05 5 -1.198198286 DMS(ph)PLSETEMALGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(0.998)PLS(0.002)ETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(1)PLSETEMALGK;DMS(0.996)PLS(0.004)ETEMALGK;DMS(1)PLSETEMALGK;DMS(0.783)PLS(0.197)ET(0.019)EMALGK;DMS(0.943)PLS(0.049)ET(0.009)EMALGK 329.11 2.38E-68 649803000 1936790 1178946 1643589 1283013 2092549 2151794 2373943 1660898 1850682 934281 TRUE FALSE 2013255.965 1381420.805 1686422.28 1536789.142 1736858.268 1652072.454 2187867.145 1638636.379 1784076.316 1117335.474 1.801836612 1.236352767 1.509324924 1.375405308 1.554464446 1.478582299 1.958111235 1.466557195 1.596723954 1 20.09163098 3.070017903 22.50055116 1.55682682 1.465267417 0 0.257418897 90.38063633 29039.38576 0.069675645 0.083278299 1174.945989 -3.070017903 -0.091559403 DMS(ph)PLSETEMALGKDVTPPPETEVVLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMS(0.973)PLS(0.023)ET(0.005)EMALGKDVTPPPETEVVLIK 114.23 0.00025865 23211000 27914 25759 29771 14914 51576 38555 25193 30418 36849 25015 TRUE FALSE 29016.06627 30182.90787 30546.85672 17863.94469 42809.12994 29601.18556 23218.30683 30010.29646 35522.81169 29916.21031 0.969911161 1.008914818 1.021080424 0.597132608 1.430967676 0.989469764 0.776111232 1.003144989 1.187410147 1 14.86863981 1.459536963 25 1.094229922 0.970011768 0.054346407 0.20277538 18.37722022 26135.47099 0.106862594 0.049463777 28.80958242 -1.459536963 -0.124218154 DMSGHYQNALYLGDVSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DMSGHYQNALYLGDVSER 18 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;; 197.1 1.88E-15 1030510000 400808 646955 608422 633235 662200 761970 594788 660029 567670 628607 FALSE TRUE 416632.2093 758064.4886 624277.9771 758486.993 549639.4805 585014.0153 548166.9624 651182.3908 547239.6676 751770.5062 0.554201323 1.008372212 0.830410307 1.008934225 0.731126688 0.778181653 0.729167955 0.866198375 0.727934473 1 19.51993279 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 DMSPLSETEMALGKDVT(0.994)PPPET(0.006)EVVLIK;DMSPLSETEMALGKDVT(0.996)PPPET(0.004)EVVLIK;DMSPLS(0.012)ET(0.011)EMALGKDVT(0.976)PPPET(0.002)EVVLIK;DMSPLSETEMALGKDVT(0.969)PPPET(0.031)EVVLIK;DMS(0.088)PLS(0.084)ET(0.081)EMALGKDVT(0.682)PPPET(0.065)EVVLIK;DMS(0.005)PLS(0.005)ET(0.018)EMALGKDVT(0.96)PPPET(0.012)EVVLIK 157.15 1.08E-08 751058000 1354975 755050 1118576 704576 1603093 1382480 1290006 1110693 1335079 729102 TRUE FALSE 1408470.459 884723.964 1147727.009 843939.0299 1330599.824 1061419.972 1188891.959 1095805.977 1287029.768 871955.5774 1.615300705 1.014643391 1.316267754 0.967869295 1.525994969 1.217286751 1.36347767 1.256722252 1.476026762 1 19.73389511 4.767817634 23.62054301 1.253803171 1.615301898 0.268071979 0.185503543 6890.644867 5562937.867 0.040640435 3.971010546 58589.20885 -4.767817634 0.361498727 DMVTELFDPLVQGEVQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DMVTELFDPLVQGEVQHR 18 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 ;;;;; 182.15 6.98E-14 366594000 237662 309566 298933 282572 330413 365104 313751 309745 308968 320276 FALSE TRUE 247045.0793 362731.5524 306723.4396 338463.8982 274249.5163 280314.1292 289158.3768 305593.3749 297848.302 383027.9501 0.644979248 0.947010661 0.800786051 0.883653264 0.716003927 0.73183727 0.754927615 0.797835706 0.777615059 1 18.54709015 -1.928101463 7.660483269 1.059625505 0.788061618 0.39302196 0.08043199 0.047208786 0.000443085 0.044886821 0.017367832 0.011800449 1.928101463 -0.271563887 DNAMLEYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNAMLEYLK 9 0 P15311;E7EQR4 P15311 EZR Ezrin 0 114.5 0.0037891 42546000 64930 57738 61821 64734 91524 87744 83608 56107 57666 68655 FALSE TRUE 67493.48654 67654.05236 63432.10605 77538.19199 75966.78317 67366.78577 77054.58649 55354.97744 55590.61192 82106.63277 0.822022342 0.823977918 0.772557635 0.944359662 0.925221028 0.820479217 0.938469694 0.674183992 0.677053851 1 16.32521115 -0.828089791 5.092391896 1.000000106 0.821520445 0.252214731 0.091925932 2.13E-07 4.88E-08 0.094289251 0.022224166 0.148562845 0.828089791 -0.178479661 DNDFIYHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNDFIYHDR 9 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 135.66 0.00021452 1618070000 1899050 2195250 2232800 2307430 2668630 3237170 2735830 2501120 2343160 1931300 FALSE TRUE 1974025.96 2572267.111 2290988.602 2763832.767 2215017.226 2485386.327 2521388.496 2467596.577 2258830.129 2309701.258 0.854667223 1.113679573 0.991898235 1.196619155 0.95900594 1.07606398 1.09165135 1.068361793 0.977975018 1 21.13927483 4.74857048 24.63083721 1.05758041 0.854667087 0.423692215 0.069123946 1001.620235 2464582.585 0.014974385 0.202104957 56049.33698 -4.74857048 -0.202913323 DNDTLKDLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNDTLKDLLK 10 1 Q9H8Y8;Q9H8Y8-3 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 79.82 0.023584 233360000 353590 189150 230470 196260 386050 347440 380270 243610 304460 133430 FALSE TRUE 367550.0062 221635.0411 236476.2375 235079.6422 320429.3589 266752.3255 350463.4437 240344.8064 293502.5441 159573.0538 2.303333786 1.388925234 1.481930889 1.473178814 2.008041779 1.671662722 2.196257046 1.506174136 1.839298911 1 17.28385753 -1.30631241 3.087213018 0.994669033 1.741388067 0.359327323 0.304475126 24379303.45 32216425.78 1202703.264 0.070970533 0.049395523 1.30631241 0.746719034 DNEEKDSAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNEEKDSAFR 10 1 O14787-2;O14787;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ;; 142.1 3.32E-05 945740000 1256640 733090 1042050 761370 1393540 1379480 1377580 994070 1097590 521680 FALSE TRUE 1306253.118 858992.5049 1069206.679 911966.7135 1156666.569 1059116.676 1269601.68 980746.1176 1058087.95 623893.2078 2.093712676 1.376826184 1.713765538 1.461735281 1.853949609 1.697592894 2.034966344 1.571977552 1.695944013 1 19.25093958 0.277128195 1.46468054 0.999790835 1.71708838 0.503814312 0.215249746 5.216802457 9.697855917 0.193281095 0.055597846 1.892902282 -0.277128195 0.717297545 DNFFEVFTPVFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNFFEVFTPVFER 13 0 Q99543;Q99543-2;H7C3L7;C9IZ83 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 ; 164.11 8.75E-05 172911000 126147 148681 147848 138940.8 161912 168223 147080 116817 144002 108505 FALSE TRUE 131127.381 174215.8052 151701.0403 166422.8755 134390.2561 129155.7577 135551.4853 115251.2592 138819.3961 129764.4773 1.010502903 1.342553901 1.169049061 1.282499487 1.035647497 0.995309043 1.044596242 0.888157234 1.069779643 1 16.98553598 3.114664931 5.354530917 0.990463669 1.208105623 0.521355692 0.091849914 0.146510284 6.309782376 0.025330724 0.030536024 1302.161739 -3.114664931 0.217641954 DNFHGLAIFLDTYPNDETTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNFHGLAIFLDTYPNDETTER 21 0 Q12907;D6RBV2;D6RIU4 Q12907 LMAN2 Vesicular integral-membrane protein VIP36 0 ;; 174.7 2.66E-12 272718000 205456 227701 228774 338220 474230 459190 369540 260241 240725 435850 FALSE TRUE 213567.5615 266806.8755 234736.0384 405118.9065 393620.554 352550.0816 340574.4892 256752.8951 232061.3543 521246.4626 0.409724721 0.511863187 0.450335983 0.77721181 0.75515247 0.676359663 0.653384749 0.492574844 0.44520466 1 18.99160616 3.761787976 24.05374012 0.655488115 0.462763425 0.319001346 0.148329478 696.1086132 720870.8899 0.038774675 0.069835832 5778.13888 -3.761787976 -0.192724689 DNFWEMGDTGPCGPCSEIHYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DNFWEMGDTGPCGPCSEIHYDR 22 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;;; 235.76 1.79E-30 3008150000 599989 839220 846197 855835 968978 1108063 875160 851618 917914 806374 FALSE TRUE 623677.029 983349.5068 868249.589 1025116.609 804271.4657 850732.1611 806562.6724 840203.4537 884878.4544 964367.5463 0.646721296 1.019683326 0.900330577 1.062993682 0.833988523 0.882165897 0.836364388 0.871248163 0.917573863 1 19.87922358 -3.166390625 1.072661218 2.959023903 0.890130245 0.092830917 0.106410123 152985.8967 2781.556039 725627.9817 0.029973308 0.000681725 3.166390625 -2.068893658 DNHVVAAGGVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNHVVAAGGVEK 12 0 Q15274 Q15274 QPRT Nicotinate-nucleotide pyrophosphorylase [carboxylating] 0 ; 91.207 0.0045088 0 178593 222321 239860 217020 275410 309350 243770 224605 248290 244490 FALSE TRUE 185643.9895 260502.9023 246110.9486 259945.9083 228595.9066 237508.1507 224662.6704 221594.5374 239354.0914 292393.1345 0.634912273 0.890933718 0.841712474 0.889028769 0.781810103 0.81229045 0.768358227 0.75786505 0.818603665 1 18.15754991 0.954184047 21.76275997 1.000000001 0.800362127 0.429626036 0.069616956 1971.740888 936587.0334 0.064760684 0.016190171 8.998788542 -0.954184047 -0.199637874 DNIACVILTFKEPFGTEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNIACVILTFKEPFGTEGR 19 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 223.51 1.99E-19 7298432000 1530284 1419652 1595666 1245191 1964320 1820488 1633015 1496148 1692882 1352328 FALSE TRUE 1590700.794 1663466.188 1637250.367 1491486.063 1630425.588 1397707.252 1505015.017 1476094.583 1631955.508 1617290.78 0.983558933 1.028551086 1.012341372 0.922212679 1.008121488 0.864227552 0.930577875 0.91269585 1.009067465 1 20.62514766 3.748192293 23.7728597 0.941948624 1.01019054 0.246870551 0.045519029 407.3752733 1005475.248 0.011331829 0.020070624 5600.055004 -3.748192293 0.068241916 DNIPALVEEYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNIPALVEEYLER 13 0 Q9H1I8;B1AH59 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 101.53 0.0044188 9535400 12352 13451 14959 13362 16040 20417 13419 16047 12532 13866 FALSE TRUE 12839.6665 15761.10462 15348.84383 16004.96372 13313.52653 15675.46117 12367.18372 15831.91621 12080.97577 16582.77722 0.774277211 0.950450242 0.925589461 0.965155806 0.802852644 0.94528564 0.745784832 0.954720431 0.728525482 1 14.01739802 3.241266566 24.99998165 0.862830507 0.908746976 0.040783185 0.096270384 237.4286144 2193550.82 0.025019098 0.032390964 1742.876307 -3.241266566 0.045916469 DNIQGITKPAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 ; 111.83 0.0012215 1126810000 906090 623090 1012590 801280 1892400 1275350 1625680 935500 1239430 780580 FALSE TRUE 941863.1329 730100.8605 1038978.927 959770.7924 1570730.524 979169.2906 1498254.954 922961.1527 1194823.156 933519.7059 1.008937601 0.782094749 1.112969465 1.028120549 1.682589574 1.048900505 1.60495268 0.988689523 1.279912088 1 19.83232095 3.776972791 2.208519158 1.259106636 0.913175392 0.240739965 0.236648533 0.402864419 3.825935057 0.062403431 0.129943063 5983.741046 -3.776972791 -0.345931244 DNKDGSCSAEYIPFAPGDYDVNITYGGAHIPGSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 84.226 0.00064538 41051000 113270 96960 120710 83148 153400 141250 105610 104940 107920 104120 FALSE TRUE 117741.9871 113612.1258 123855.8018 99594.42623 127325.1228 108446.8282 97332.01224 103533.4509 104035.9803 124520.3205 0.94556444 0.912398276 0.994663371 0.799824686 1.022524856 0.870916712 0.781655651 0.831458275 0.835493997 1 16.92602167 2.489965403 24.57421035 0.841741848 0.931262744 0.156693882 0.07680206 674.5706662 1290632.733 0.023577829 0.021256033 309.004926 -2.489965403 0.089520896 DNKPLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNKPLVER 8 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 94.804 0.0092111 889180000 1599020 1151260 1480000 1357410 1896580 1830520 1709190 1510720 1534510 1157690 FALSE TRUE 1662150.544 1348979.949 1518570.016 1625901.647 1574200.009 1405409.472 1575219.222 1490471.269 1479283.285 1384517.19 1.200527199 0.974332395 1.096822796 1.174345583 1.137002863 1.01508994 1.137739013 1.076527818 1.068447034 1 20.40095154 0.688090322 0.916702289 0.999581154 1.101818798 0.193609368 0.064483796 1.819893118 2.715243374 0.059903939 0.019873217 4.876298945 -0.688090322 0.102237645 DNLEFFLAGIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 202.31 3.22E-07 9849161000 4663785 4619236 5306794 5165645 6475444 6992985 5812126 4971666 5279948 4939861 FALSE TRUE 4847914.833 5412553.85 5445093.411 6187394.163 5374750.342 5368970.213 5356556.377 4905028.949 5089923.703 5907732.184 0.820605045 0.916181317 0.921689278 1.047338297 0.909782328 0.908803928 0.906702642 0.830272734 0.861569811 1 22.49417299 2.233119743 2.530328476 0.877930162 0.927595866 0 0.066471896 0.708977769 9.289607419 0.029094089 0.02038503 171.0486861 -2.233119743 0.049665704 DNLEWLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DNLEWLAR 8 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 208.72 0.00012332 1970805000 2178240 2334160 2431770 2344370 2828290 2995650 2713200 2519850 2468420 2145070 FALSE TRUE 2264238.597 2735033.823 2495143.924 2808079.389 2347538.276 2299955.687 2500532.294 2486075.532 2379582.046 2565355.397 0.8826218 1.066142269 0.972630898 1.094616127 0.915092809 0.896544662 0.974731336 0.969095953 0.927583776 1 21.29072728 3.174066325 25 0.946842163 1.00620871 0.177516208 0.059847141 97.18886013 37672.38957 0.016483157 0.019701148 1493.022403 -3.174066325 0.059366546 DNLGEVPLT(ph)PTEEASLPLAVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNLGEVPLTPTEEASLPLAVTK 22 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 DNLGEVPLT(0.462)PT(0.462)EEAS(0.077)LPLAVTK;DNLGEVPLT(0.76)PT(0.232)EEAS(0.008)LPLAVTK;DNLGEVPLT(0.81)PT(0.185)EEAS(0.005)LPLAVTK 110.26 0.0013365 126132000 325579 238877 313630 255227 396453 393608 373376 340225 372897 249542 TRUE FALSE 338433.1103 279902.2665 321803.4554 305710.1388 329064.0607 302198.5072 344109.8135 335664.8404 359476.5098 298434.9771 1.134026291 0.93790034 1.078303417 1.024377711 1.102632352 1.012610888 1.153047866 1.124750335 1.204538802 1 18.18705711 2.23384435 24.99988892 1.131100778 1.046034854 0.199622046 0.069547729 153.579475 814080.8882 0.023485779 0.017906842 171.3343142 -2.23384435 -0.085065924 DNLHQIDAVEGPAAFLDILAPPYDPDDGRDCHYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNLHQIDAVEGPAAFLDILAPPYDPDDGRDCHYYR 35 1 Q96SZ5 Q96SZ5 ADO 2-aminoethanethiol dioxygenase 0 ; 101.44 3.14E-05 112464000 24807 30703 33676 33367 48070 49621 37764 30766 34282 51919 FALSE TRUE 25786.39952 35976.00141 34553.62423 39966.89301 39899.07857 38097.27476 34803.959 30353.63209 33048.19752 62091.534 0.415296545 0.579402683 0.556494936 0.643677011 0.642584842 0.613566332 0.560526641 0.488852991 0.532249654 1 15.92210895 -1.511004072 3.08477777 1.013593794 0.561016754 0.799409172 0.066238806 16625291.49 20728950.14 1924713.95 0.017404856 0.03083159 1.511004072 -0.45257704 DNLSSWLEHLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNLSSWLEHLPR 12 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 236.92 4.34E-16 321110000 357120 519060 493820 495330 540550 617180 576810 543320 492610 470350 FALSE TRUE 371219.3734 608204.5173 506689.3549 593304.7956 448667.5041 473849.2985 531598.125 536037.6841 474881.0623 562506.0771 0.659938423 1.081240794 0.900771344 1.054752686 0.797622501 0.842389652 0.945053123 0.952945587 0.844223879 1 19.10150916 -1.803900985 3.459757401 1.019141305 0.908709294 0.057213818 0.117141116 0.018755485 0.00106306 0.122997244 0.02450434 0.015707209 1.803900985 -0.110432011 DNLSYIEHIFEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ;;;;; 261.74 1.60E-24 1272484000 1098418 1243667 1287649 1467476 1458871 1713372 1651066 1410960 1356850 1123692 FALSE TRUE 1141784.391 1457257.133 1321206.191 1757738.373 1210892.629 1315467.319 1521651.133 1392048.389 1308017.234 1343857.933 0.849631767 1.084383324 0.983144243 1.307979311 0.901057023 0.978873798 1.132300592 1.035859785 0.973329994 1 20.3579492 4.745159534 23.98793312 1.048527617 0.849631605 0.227983333 0.107080825 625.1970327 2272563.439 0.024374864 0.231521166 55610.8501 -4.745159534 -0.198896012 DNLTLWTSDQQDDDGGEGNN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 3380510000 4656150 4969620 5010790 4845270 5539930 6271490 5340710 5417720 5265070 4890270 FALSE TRUE 4839978.397 5823113.577 5141375.304 5803649.944 4598254.677 4815031.493 4922091.195 5345104.325 5075581.159 5848424.777 0.827569573 0.995672134 0.879104289 0.992344121 0.78623815 0.823303997 0.84160973 0.913939142 0.867854397 1 22.47961667 5.056021217 15.06672495 0.893102902 0.369996021 0.076259363 0.072116131 2574902.27 18134023.6 0.016816505 39805130.97 113768.2864 -5.056021217 -0.52310688 DNLTLWTSDQQDEEAGEGN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNLTLWTSDQQDEEAGEGN 19 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 ; 297.56 2.17E-49 98819000 188024 200864 215130 182041 230196 252681 216636 207866 211463 203025 FALSE TRUE 195447.3327 235360.8295 220736.4645 218048.1665 191067.3661 193999.6672 199655.5042 205079.8963 203852.4879 242803.8616 0.804959738 0.969345495 0.909114308 0.898042416 0.786920623 0.798997454 0.822291305 0.844631938 0.839576795 1 17.88943184 DNLTLWTSENQGDEGDAGEGEN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 338.92 9.61E-81 5994199000 6575091.1 7025699.1 7406803.2 7124829.1 8230236.4 8979757.2 7646482.7 7635600.5 7876058.4 6888532.2 FALSE TRUE 6834680.774 8232308.268 7599830.576 8534099.03 6831263.756 6894344.68 7047131.406 7533257.765 7592600.597 8238208.196 0.829631955 0.999283834 0.922510138 1.035916892 0.829217179 0.836874295 0.855420407 0.914429156 0.921632522 1 22.97389916 4.824212593 20.76208684 0.915869837 0.829613215 0.139050022 0.067771355 86354.62942 20917849.36 0.016481525 243.3196668 66713.32601 -4.824212593 -0.086256622 DNNLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DNNLLGK 7 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PS65;E9PM13;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;; 101.33 0.026056 167507000 590501 509032 537821 470998 615040 696430 630450 547923 556250 489484 FALSE TRUE 613814.4354 596454.2863 551837.0571 564159.9986 510495.7205 534694.687 581033.6816 540578.9884 536230.6712 585389.0181 1.048558166 1.018902419 0.942684335 0.963735194 0.872062346 0.913400611 0.992559928 0.923452562 0.91602448 1 19.15903616 4.320521721 2.36734897 0.935888602 1.048992711 0.515743843 0.03646109 0.235868484 2.489214203 0.009285033 0.038124572 20918.07524 -4.320521721 0.113104109 DNNLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 153.15 0.0041078 11488680000 4775710 5044110 5249030 4617380 6268500 6513800 5550430 5249060 5310030 4919540 FALSE TRUE 4964258.718 5910396.655 5385824.034 5530683.982 5202982.609 5001068.668 5115372.793 5178704.936 5118923.058 5883429.673 0.843769535 1.004583548 0.915422523 0.940044207 0.884345169 0.850026081 0.869454226 0.88021872 0.870057661 1 22.48822597 3.230068739 23.69666626 0.882593609 0.930818966 0.066880483 0.05340822 168.5999862 470478.9316 0.014136451 0.017177408 1698.512465 -3.230068739 0.048225357 DNPGVVTCLDEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNPGVVTCLDEAR 13 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 196.5 3.29E-07 846070000 135823 148388 147831 142676 180473 196289 160567 138742 146841 142428 FALSE TRUE 141185.3969 173872.4847 151683.5973 170896.887 149796.2639 150703.8545 147981.339 136882.3904 141556.2211 170334.0397 0.828873649 1.020773564 0.890506663 1.003304374 0.879426474 0.884754773 0.868771382 0.803611484 0.831050689 1 17.37800725 3.022830374 23.43845606 0.862046588 0.93902419 0.121295519 0.070192186 169.6038183 174118.6407 0.019128005 0.022860221 1053.975157 -3.022830374 0.076977602 DNPHFENGETSIVISDVLPGGPADGLLQENDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNPHFENGETSIVISDVLPGGPADGLLQENDR 32 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 ; 259.9 2.63E-59 257700000 110370 133484 148528 166482 147900 193935 166795 164010 161369 140628 FALSE TRUE 114727.4928 156408.8386 152398.7617 199411.6427 122760.0108 148896.5354 153721.1721 161811.7142 155561.3612 168181.3641 0.682165313 0.930001011 0.906157246 1.18569405 0.729926359 0.885333141 0.914020248 0.962126304 0.924961942 1 17.35965833 4.739634898 5.896717288 0.935675427 0.674753516 0.340587781 0.106616275 0.15498744 24.84946362 0.024670652 0.162044111 54907.90812 -4.739634898 -0.260921911 DNPS(ph)PGPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNPSPGPSR 9 0 Q9NQS1 Q9NQS1 AVEN Cell death regulator Aven 1 DNPS(0.998)PGPS(0.002)R;DNPS(1)PGPSR 91.694 0.011098 498350000 337060 410340 399480 443130 429920 518840 433130 435680 381790 375360 TRUE FALSE 350367.3891 480812.703 409890.777 530779.7914 356842.352 398347.2731 399180.1388 429840.4222 368049.4525 448904.6053 0.780494085 1.071079907 0.913091049 1.182388831 0.794918002 0.887376223 0.889231552 0.957531772 0.819883441 1 18.77604937 DNPSIFVHSPHALMLQDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNPSIFVHSPHALMLQDVK 19 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 203.77 2.83E-16 850910000 791520 793340 1130120 895360 1346550 1346050 1303210 1166500 1221560 786000 FALSE TRUE 822769.8208 929589.9737 1159571.856 1072459.536 1117663.912 1033450.287 1201060.995 1150864.976 1177596.294 940001.6511 0.875285506 0.988923767 1.233584914 1.140912396 1.189002073 1.099413268 1.277722218 1.224322291 1.252759815 1 19.84230377 4.392133371 3.724156172 1.188533243 0.894163986 0.615620268 0.079082199 0.124078106 3.235374508 0.018662776 0.06253424 24667.96768 -4.392133371 -0.294369256 DNQESS(ph)DAELSSSEYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 DNQES(0.004)S(0.996)DAELSSSEYIK;DNQES(0.012)S(0.988)DAELSSSEYIK 320.76 1.57E-58 529320000 921080 626580 877340 665150 1027740 1144590 1087530 870560 1008170 564890 TRUE FALSE 957444.9496 734190.2409 900204.2011 796714.6847 853045.1219 878776.3189 1002286.557 858891.5671 971886.1586 675569.38 1.417241482 1.086772525 1.332511845 1.179323262 1.262705426 1.30079359 1.483617503 1.271359527 1.438617835 1 19.36574441 2.704094823 4.127583825 1.328362753 1.245689874 0.001430437 0.146461848 0.629570432 24.40214846 0.044085425 0.042795051 505.9351143 -2.704094823 -0.082672879 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNQVVQLHPSTVLDHKPEWVLYNEFVLTTK 30 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 123.89 1.02E-05 441880000 283000 551320 831720 635420 937160 975610 951150 912030 931950 480340 FALSE TRUE 294173.0585 646004.9213 853395.3065 761104.1795 777861.8779 749039.363 876596.3776 899805.7296 898409.3015 574453.4263 0.512092095 1.124555781 1.485577886 1.324918861 1.354090414 1.303916608 1.525965966 1.566368462 1.56393758 1 19.13183041 4.681584159 2.26620652 1.419569002 0.345736768 0.724946639 0.162966812 0.250525369 1.657230702 0.040174982 0.510348781 48037.91605 -4.681584159 -1.073832234 DNS(ph)PLREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNSPLREK 8 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 DNS(1)PLREK 51.066 0.091805 98840000 294940 168050 195110 135590 308330 338030 244040 192830 217960 144470 TRUE FALSE 306584.4589 196911.2803 200194.7269 162409.2973 255920.1767 259527.6554 224911.5071 190245.4293 210115.6622 172776.1305 1.774460732 1.139690302 1.158694354 0.939998464 1.481224149 1.502103645 1.301751038 1.101109446 1.216115106 1 17.39854439 1.757638168 6.012823469 1.119923152 1.312633442 0.170534419 0.222315305 0.355882489 33.11852277 0.111768987 0.059711364 57.23190051 -1.757638168 0.192710289 DNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 126.22 5.25E-05 6615390000 6619600 1620190 2743760 1915430 4512900 5406400 5451500 3235900 3584000 1042760 TRUE FALSE 6880946.919 1898445.029 2815264.64 2294296.337 3745798.87 4150845.535 5024197.185 3192528.053 3455012.54 1247068.857 5.51769606 1.522325747 2.257505368 1.839751128 3.003682474 3.328481431 4.02880495 2.560025483 2.770506633 1 20.2501097 DNSEEFLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNSEEFLKR 9 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;A0A5F9ZH85;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 94.616 0.013792 265330000 255740 246000 292460 209050 328680 322570 297510 270790 306590 216430 FALSE TRUE 265836.8127 288248.5864 300081.7479 250399.466 272811.091 247658.0061 274190.3888 267160.503 295555.8858 258835.3147 1.02705001 1.113637012 1.159353963 0.967408432 1.053994859 0.95681691 1.059323721 1.032164036 1.141868474 1 17.98167494 3.741524149 24.99204076 1.031343722 1.101375992 0.23540922 0.057595901 371.4046872 3132115.402 0.014590236 0.025049228 5514.728659 -3.741524149 0.070032271 DNSEEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNSEEFR 7 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 0 133.79 0.019498 0 206250 285010 280230 262180 314830 343240 274280 285260 244570 226350 FALSE TRUE 214392.9093 333958.2504 287533.024 314038.4215 261315.3091 263527.7119 252781.2169 281436.5563 235767.9735 270698.9488 0.791997569 1.23368876 1.062187442 1.160102109 0.965335515 0.973508442 0.933809378 1.039666233 0.870960063 1 18.04632976 3.20192136 24.78249736 0.969237503 1.074271732 0.147101245 0.11378005 264.6031715 178974.6461 0.030842828 0.036865184 1591.920444 -3.20192136 0.105034229 DNSNLYMVMEYVPGGEMFSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNSNLYMVMEYVPGGEMFSHLR 22 0 P22694-2;P22694-4;A0A0A0MS54;P22694-9;P22694-6;P22694-7;P22694-5;P22694;P22694-3;P22694-10;A0A087WVC4;P22694-8;B1APG3;B1APF9;B1APF8;B1APG2;B1APG1;B1APF7;B1APG0;P17612-2;P17612;Q15136;K7ERP6 P22694-2;P17612-2 PRKACB;PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit beta;cAMP-dependent protein kinase catalytic subunit alpha 0 94.449 0.0017672 57350000 87652 77177 99878 102310 98556 120670 118960 105730 108570 72828 FALSE TRUE 91112.56864 90431.5494 102480.9027 122546.6126 81803.48632 92646.22127 109635.6044 104312.8623 104662.5869 87097.25222 1.046101528 1.038282461 1.176626129 1.407008941 0.939220058 1.063710036 1.258772252 1.197659623 1.201674958 1 16.41033958 2.248959695 24.9886964 1.18556113 1.116999332 0.026564657 0.131729967 692.4744272 1663995.722 0.047004036 0.038938938 177.4024833 -2.248959695 -0.068561798 DNSTMGYMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNSTMGYMAAK 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 79.974 0.042636 0 17263 12746 17882 9855.9 22484 23258 21168 20542 21864 13360 FALSE TRUE 17944.55657 14935.02635 18348.01961 11805.3676 18662.17771 17856.68198 19508.79685 20266.66809 21077.11891 15977.63621 1.123104591 0.934745676 1.148356326 0.738868219 1.16801869 1.117604741 1.221006449 1.268439701 1.319163776 1 13.96376637 3.028185831 24.99863402 1.203343922 0.989075741 0.341082044 0.132496498 215.1206554 190793.8407 0.03658652 0.043728642 1067.052608 -3.028185831 -0.214268181 DNTFFRES(ph)PVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DNTFFRESPVGR 12 1 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;F8VPY7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR;DNTFFRES(1)PVGR 190.1 4.62E-06 10187580000 4092910 4684510 4742850 4203380 5438780 6045940 4726650 4756170 4683180 4606970 TRUE FALSE 4254501.247 5489038.152 4866452.567 5034796.018 4514298.118 4641862.062 4356162.822 4692421.321 4514633.267 5509617.566 0.772195383 0.99626482 0.883265038 0.913819509 0.819348723 0.842501681 0.79064704 0.851678227 0.819409553 1 22.39352075 3.243127122 24.99789434 0.842201066 0.898297441 0.041229765 0.073929804 239.5982399 1311595.611 0.018978706 0.024868188 1750.358961 -3.243127122 0.056096374 DNTIEHLLPLFLAQLKDECPEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNTIEHLLPLFLAQLKDECPEVR 23 1 P30153;B3KQV6 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 166.59 7.09E-12 1433340000 1654330 1250240 1560340 1258330 2061190 2041090 1806330 1660020 1743660 1177350 FALSE TRUE 1719644.226 1464958.994 1601003.742 1507223.918 1710829.66 1567077.781 1664745.135 1637770.147 1680906.017 1408029.191 1.221312908 1.040432261 1.137052948 1.07044934 1.215052693 1.112958304 1.182322885 1.16316491 1.193800546 1 20.42524581 3.254750226 24.99991722 1.154375151 1.113230564 0.021756717 0.071428734 656.4327908 1013653.735 0.017990673 0.024280647 1797.836634 -3.254750226 -0.041144587 DNTINLIHTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DNTINLIHTFR 11 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;;;; 168.31 1.82E-05 5591590000 3760240 3639950 4069760 4017340 4661810 5151250 4729420 4303700 4378760 3194960 FALSE TRUE 3908697.179 4265083.098 4175821.289 4811957.861 3869397.201 3954950.255 4358715.702 4246015.941 4221169.283 3820951.241 1.022964422 1.116235939 1.092874791 1.259361232 1.012679031 1.035069543 1.14074099 1.11124578 1.104743038 1 21.86550042 DNTRPGANS(ph)PEMWSEAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DNTRPGANSPEMWSEAIK 18 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 1 DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNTRPGANS(1)PEMWSEAIK;DNT(0.031)RPGANS(0.969)PEMWSEAIK 258.87 6.81E-31 839500000 736521 539653 706945 527855 850838 861632 833171 677651 768140 437835 TRUE FALSE 765599.4178 632334.2048 725368.5675 632263.1435 706212.8607 661531.0262 767864.8799 668568.1968 740494.7914 523620.3854 1.462126837 1.207619532 1.385294743 1.207483821 1.348711548 1.263379052 1.466453372 1.276818503 1.414182511 1 18.99816174 -1.397180686 3.686494809 0.998030666 1.330567355 0.548589569 0.091519195 924.8340681 20000743.4 54989.6042 0.019055325 0.040069997 1.397180686 0.332536689 DNTVHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNTVHDLR 8 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ;; 132.01 0.0012602 640990000 666310 777570 756760 692990 847110 999260 794040 774150 756750 713930 FALSE TRUE 692616.4333 911111.5988 776481.7873 830061.3536 703118.5448 767197.0089 731801.07 763773.7855 729514.7153 853810.9145 0.811205879 1.067111679 0.909430618 0.972184051 0.823506157 0.898556104 0.85709969 0.894546758 0.854421867 1 19.70355708 3.258233729 24.99920637 0.882043813 0.946881359 0.101024455 0.073525807 431.296684 548058.1572 0.018504871 0.02502022 1812.315185 -3.258233729 0.064837546 DNVKNEDKDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNVKNEDKDQK 11 2 Q8IX12-2;Q8IX12 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ; 95.273 0.0044325 234403000 307650 107828 161496 90930 240567 233957 193884 163809 187371 85590 FALSE TRUE 319796.2596 126346.6202 165704.7184 108915.6826 199675.5073 179624.0324 178686.8655 161613.4083 180627.5543 102359.7218 3.124239242 1.23433923 1.618846901 1.064048248 1.950723427 1.75483119 1.745675568 1.578876979 1.764635065 1 16.64328861 8 0.045098411 1.69E-13 4.584906938 0.209046849 0.505482512 1196.188645 4.08852485 105.3384372 397.408122 99999999.98 -8 4.584906938 DNWEELYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DNWEELYNR 9 0 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 176.38 0.00012376 445780000 339340 314960 398480 421830 409470 475900 503200 380200 408570 252540 FALSE TRUE 352737.4052 369051.93 408864.7162 505266.715 339868.4357 365379.4373 463757.8691 375104.0409 393865.6455 302020.3778 1.167925846 1.221943806 1.353765329 1.672955708 1.125316239 1.209784055 1.535518472 1.241982556 1.304102883 1 18.20428637 0.422117702 1.503908668 1.000061437 1.323419097 0.254922555 0.161543402 5.131506714 11.87608514 0.153643137 0.044328961 2.643124997 -0.422117702 0.32335766 DNYNHPNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DNYNHPNKR 9 1 O14647;O14647-2 O14647 CHD2 Chromodomain-helicase-DNA-binding protein 2 0 76.465 0.022951 16965000 26539 23292 29519 21616 34621 29836 31072 29121 26194 23891 FALSE TRUE 27586.78021 27292.21981 30288.28939 25891.58028 28736.13479 22907.04117 28636.49545 28730.68063 25251.28306 28571.98403 0.965518537 0.955209123 1.06006952 0.906187693 1.005745165 0.801730854 1.002257856 1.005554273 0.883777725 1 14.8023136 3.709408253 24.95645026 0.947711898 0.989760136 0.099035212 0.068022095 1873.250157 1603632.67 0.017944313 0.027803529 5121.630612 -3.709408253 0.042048238 DNYSPGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DNYSPGWK 8 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 99.139 0.016344 462050000 442370 366510 413620 363440 488840 514660 502340 441710 433870 312287 FALSE TRUE 459835.1092 429455.2414 424399.277 435327.3472 405747.1514 395138.0147 462965.2782 435789.5999 418255.1035 373473.6586 1.231238398 1.149894328 1.136356654 1.165617273 1.086414375 1.058007722 1.239619629 1.166854984 1.11990523 1 18.51064697 0.874677475 4.390608266 1.000019525 1.153063424 0.435532381 0.052657512 0.794088333 26.33972641 0.051709497 0.013146721 7.493375133 -0.874677475 0.153043899 DPAQPMS(ph)PGEATQSGARPADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPAQPMSPGEATQSGARPADR 21 1 Q9BQG0;Q9BQG0-2 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 DPAQPMS(0.999)PGEAT(0.001)QSGARPADR 70.391 0.010958 325460000 79476 91417 108110 101080 93591 113170 86218 93726 90847 107680 TRUE FALSE 82613.77385 107117.1586 110927.4354 121073.3223 77682.43525 86887.98261 79460.00787 92469.75627 87577.43422 128777.8343 0.641521689 0.831798105 0.861386092 0.940172064 0.603228309 0.674712252 0.617031714 0.718056463 0.680066058 1 16.97452477 4.774992721 21.49164811 0.752339416 0.641520076 0.067169599 0.129533304 8294.839555 4892609.175 0.031414109 4.7652123 59565.21597 -4.774992721 -0.11081934 DPDAQPGGELMLGGTDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DPDAQPGGELMLGGTDSK 18 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 ;; 198.15 4.11E-15 235770000 268388 189090 236068 208087 317912 365891 333278 245509 266090 192237 FALSE TRUE 278984.1655 221564.7366 242220.126 249245.9875 263873.4318 280918.3604 307154.7995 242218.3534 256513.4729 229902.1596 1.213490843 0.963734908 1.053579168 1.084139392 1.147764042 1.221903965 1.336023986 1.053571458 1.115750602 1 17.81066049 3.266815449 3.832756524 1.159149351 1.0664539 0.082492131 0.102942501 0.440968973 13.85672628 0.029863361 0.039570091 1848.48295 -3.266815449 -0.092695451 DPDASKPEDWDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPDASKPEDWDER 13 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 99.991 0.0023774 153340000 455910 292390 388090 324690 509670 520830 516880 355300 394380 232590 FALSE TRUE 473909.6788 342605.708 398203.9442 388912.7129 423036.4754 399875.1258 476365.595 350537.7847 380186.3408 278161.5573 1.703720972 1.231678854 1.431556352 1.398154068 1.520830123 1.437564305 1.712550072 1.260194932 1.366782472 1 18.08556352 0.81079872 1.246658189 1.004491685 1.466421386 0.481478985 0.146785513 0.593910255 1.71170868 0.131194559 0.040025918 6.468427572 -0.81079872 0.461929701 DPDEGVSPEHLEQLLGQLGQTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPDEGVSPEHLEQLLGQLGQTLR 23 0 Q8IWY9;Q8IWY9-1 Q8IWY9 CDAN1 Codanin-1 0 144.5 1.50E-07 8993000 9471.3 10633 10235 9784.7 11571 12298 13145 9982.9 11075 7724.7 FALSE TRUE 9845.234237 12459.13504 10501.73251 11720.08446 9604.165553 9441.975878 12114.66055 9849.095554 10676.41291 9238.207067 1.065708331 1.348652931 1.136771717 1.268653579 1.039613583 1.022057182 1.311364907 1.066126304 1.155680192 1 13.17339717 -4.999999999 0.110345875 0.480174145 1.251886286 0.164442389 0.109786975 280.4826945 2.057284512 32.82884288 1.29891217 1.00E-05 4.999999999 0.771712141 DPDQTDGLGLSYLSSHIANVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DPDQTDGLGLSYLSSHIANVER 22 0 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;; 308 4.06E-67 651901000 265517 456101 411854 476512 497263 624118 493638 532581 439882 402660 FALSE TRUE 275999.8162 534432.7988 422587.2536 570764.6514 412738.4129 479176.0531 454945.3637 525442.6228 424050.7327 481553.5176 0.573144637 1.10980977 0.877549926 1.185256945 0.857097701 0.995062928 0.944745178 1.09114066 0.880589005 1 18.87733662 4.748119748 24.90361702 0.996579213 0.573144399 0.597310704 0.103508401 771.3493499 2009489.297 0.022227856 0.287415718 55991.1965 -4.748119748 -0.423434814 DPEDRIPS(ph)PLGYAAIPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPEDRIPSPLGYAAIPIK 18 1 Q9Y3A4 Q9Y3A4 RRP7A Ribosomal RNA-processing protein 7 homolog A 1 DPEDRIPS(1)PLGYAAIPIK 95.957 0.0010186 26140000 37812 27592 44456 28541 44684 47144 49190 34956 43079 27744 TRUE FALSE 39304.84696 32330.71136 45614.55988 34186.32461 37088.62964 36195.52047 45334.35927 34487.472 41528.59521 33179.90561 1.184597914 0.974406369 1.374764607 1.030332184 1.117803953 1.090886783 1.366319718 1.039408382 1.251618847 1 15.01802216 DPEEIEKEEQAAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPEEIEKEEQAAAEK 15 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 158.64 1.65E-06 354900000 390120 143936 225870 175345 339990 378820 450710 267940 302130 99938 FALSE TRUE 405522.2388 168655.8883 231756.3578 210027.7176 282198.6212 290844.7961 415382.1725 264348.7026 291256.4003 119518.9377 3.392953843 1.411122719 1.939076453 1.75727564 2.361120562 2.433462025 3.475450674 2.211772525 2.436905866 1 16.8668797 3.041187558 11.64594583 2.460524334 2.060373013 0 0.743656844 2.251017354 629.3379449 0.204359523 0.244186158 1099.480568 -3.041187558 -0.400151321 DPEKRPTAAELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPEKRPTAAELLR 13 2 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 60.657 0.050703 81440000 110890 88179 86045 85987 129050 122090 97861 92004 94444 87205 FALSE TRUE 115268.0228 103323.0573 88287.40339 102994.972 107114.1271 93736.44779 90190.39911 90770.83687 91044.97889 104291.1501 1.105252197 0.990717402 0.846547414 0.987571542 1.027068231 0.898795801 0.864794367 0.870359918 0.87298854 1 16.67025721 2.636284328 6.452772254 0.887548878 0.98292022 0.278439032 0.070222637 0.316248821 17.05662661 0.023211112 0.021844637 432.7970855 -2.636284328 0.095371343 DPEQRPCFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPEQRPCFK 9 1 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 89.247 0.011159 109690000 219860 131680 166230 130380 195160 248590 193170 148420 163160 104160 FALSE TRUE 228540.2426 154295.0157 170562.0904 156168.7749 161986.7729 190858.7399 178028.8306 146430.6727 157287.9035 124568.1577 1.834660211 1.2386393 1.369227044 1.25368134 1.300386679 1.532163142 1.429168046 1.175506448 1.262665406 1 16.92657581 3.096431191 0.041764061 2.92E-10 2.739961865 0.430347469 0.161586303 186.511137 2.435734742 68.01982084 91.3113731 1248.622598 -3.096431191 2.739961865 DPETLVGYSMVGCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 231.92 3.02E-13 234800000 112004 106291 121942 121204 138348 169951 141079 130595 114128 100301 FALSE TRUE 116426.0044 124545.6524 125119.9087 145177.7894 114831.6564 130482.4559 130020.8593 128844.5876 110020.5556 119953.0606 0.970596364 1.038286575 1.043073917 1.210288331 0.957304931 1.087779297 1.083931154 1.074125054 0.917196736 1 16.87211044 1.248563068 24.98947519 0.958598363 1.061561704 0.251579158 0.068498978 227.3513462 568009.3676 0.04507342 0.016029643 17.72405414 -1.248563068 0.102963341 DPFIGEHTEEILEEFGFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPFIGEHTEEILEEFGFSR 19 0 D6RB81;Q9UHK6;Q9UHK6-5 D6RB81 AMACR Alpha-methylacyl-CoA racemase 0 162.15 2.82E-11 9645800 8633.4 8916.4 7750.1 6426.6 10340 12986 8511.3 8195.5 8256.7 8902.9 FALSE TRUE 8974.253298 10447.72234 7952.073973 7697.762299 8582.410493 9970.198305 7844.162066 8085.652728 7959.54298 10647.2528 0.842870313 0.981259912 0.746866269 0.722981077 0.806068068 0.936410405 0.736731081 0.759412111 0.747567765 1 13.37819361 4.232134088 24.99944631 0.794573225 0.912065118 0.160011094 0.092854115 202.4686021 787622.341 0.02213243 0.049693457 17066.09223 -4.232134088 0.117491893 DPGMS(ph)QSHNDLVFLEQPEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPGMSQSHNDLVFLEQPEGSR 21 0 Q9Y426-2;Q9Y426-3;Q9Y426;H7BZB0 Q9Y426-2 C2CD2 C2 domain-containing protein 2 1 DPGMS(0.5)QS(0.5)HNDLVFLEQPEGSR;DPGMS(0.5)QS(0.5)HNDLVFLEQPEGSR 189.08 1.47E-17 152843000 35635 62252 59248 71650 63131 82876 59297 58658 58381 71263 TRUE FALSE 37041.89732 72943.29675 60792.05155 85822.15615 52400.01517 63629.305 54649.1462 57871.78546 56279.87921 85225.62044 0.434633355 0.855884608 0.713307234 1.006999488 0.614838764 0.74659832 0.64122908 0.679042114 0.660363385 1 16.37899958 -1.533614917 2.886478143 1.012909402 0.712660176 0.275031254 0.142876366 32155915.44 32961814.81 3224600.496 0.032079314 0.029267463 1.533614917 -0.300249226 DPGT(ph)PNDDSDIKECNSADHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPGTPNDDSDIKECNSADHIK 21 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 DPGT(1)PNDDSDIKECNSADHIK;DPGT(1)PNDDSDIKECNSADHIK 166.59 1.94E-11 221625000 248410 110177 161847 115111 207445 217247 247645 152699 195824 67584 TRUE FALSE 258217.4186 129099.0427 166064.8658 137879.6122 172183.573 166794.6767 228233.9378 150652.3197 188776.3325 80825.79083 3.194740391 1.597250598 2.054602424 1.705886337 2.130304835 2.063631855 2.823776117 1.863913958 2.335595242 1 16.3025281 4.751917252 24.23201447 2.016904674 3.194741584 0.391585815 0.458193495 1494.55299 2711389.411 0.101534298 1.916551433 56482.93456 -4.751917252 1.17783691 DPGVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DPGVLDR 7 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;; 113.5 0.014228 26306800000 5192420 5896120 5750730 6229430 6195430 6706370 6472490 5960890 5627310 5287800 FALSE TRUE 5397420.751 6908732.745 5900598.748 7461592.661 5142333.022 5148917.204 5965159.321 5880994.02 5424784.212 6323843.169 0.853503259 1.092489576 0.933071645 1.179914249 0.813165805 0.814206973 0.943280717 0.929971516 0.857830289 1 22.59237016 3.207971629 24.99930824 0.892246517 1.014464487 0.271823737 0.097550943 257.1519034 210160.5894 0.026913932 0.032171804 1614.2531 -3.207971629 0.12221797 DPHLACVAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DPHLACVAYER 11 0 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;;;; 113.65 0.0013634 6441420000 735463 3008814 1853541 2575839 1642555 2625566 1318689 2103502 1535720 3169186 FALSE TRUE 764499.6471 3525554.399 1901845.801 3085332.266 1363354.088 2015818.087 1215326.71 2075307.996 1480449.737 3790127.319 0.20170817 0.930194187 0.501789423 0.814044491 0.35971195 0.531860256 0.320655906 0.547556275 0.390606862 1 21.85381488 -1.618647846 6.199293581 1.002068092 0.521718262 0.327593874 0.209700644 0.005560401 0.00034205 0.188355465 0.044243314 0.024063132 1.618647846 -0.48034983 DPILVSLRPGSELLRPHPLPAERPIFNSMAPAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPILVSLRPGSELLRPHPLPAERPIFNSMAPASPR 35 3 Q92828 Q92828 CORO2A Coronin-2A 1 DPILVSLRPGSELLRPHPLPAERPIFNSMAPAS(1)PR 154.27 2.23E-11 661200000 245020 238300 243770 314520 306230 421270 409490 286070 309610 299960 TRUE FALSE 254693.5788 279226.1713 250122.8465 376731.1173 254177.134 323436.4269 377393.1038 282235.6996 298467.1966 358731.4189 0.709984031 0.778371106 0.697242654 1.050175974 0.708544389 0.901611651 1.052021328 0.786760469 0.832007404 1 18.45254458 3.77561146 24.9974847 0.890325164 0.733516408 0.355984097 0.107194344 685.8571707 462732.2798 0.026669209 0.048076903 5965.013896 -3.77561146 -0.156808755 DPLELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DPLELFR 7 0 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;;;; 118.69 0.011517 260398000 356299 383838 381960 439293 437951 473805 433849 386458 363193 339222 FALSE TRUE 370365.9596 449759.1907 391914.1914 526183.8442 363508.2455 363770.9693 399842.7817 381278.1626 350121.7549 405686.0561 0.912937366 1.108638525 0.966052901 1.297022257 0.896033374 0.896680977 0.985596561 0.939835513 0.863036206 1 18.63000419 DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 35 1 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 DPLGGLADMFGQMPGS(0.003)GIGT(0.033)GPGVIQDRFS(0.95)PT(0.014)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.976)PT(0.023)MGR;DPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.993)PT(0.007)MGR 341.65 1.83E-118 3627590000 851820 912660 1039780 1003080 1041510 1208660 866610 955110 909650 918910 TRUE FALSE 885450.5113 1069402.255 1066877.521 1201486.23 864474.5022 927967.0324 798682.8437 942308.3127 876911.8742 1098952.821 0.805722042 0.973110251 0.970812851 1.093301011 0.786634772 0.844410256 0.726767181 0.857460206 0.797952248 1 20.06769802 3.209908006 24.99992168 0.823540222 0.962340244 0.299427838 0.092722048 226.070289 197249.8301 0.025657258 0.030671402 1621.466596 -3.209908006 0.138800022 DPMIVY(ph)VGNLNLVAVNT(ph)VKQNIIVT(ph)TEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPMIVYVGNLNLVAVNTVKQNIIVTTEK 28 1 Q86TM3 Q86TM3 DDX53 Probable ATP-dependent RNA helicase DDX53 3 DPMIVY(1)VGNLNLVAVNT(0.667)VKQNIIVT(0.667)T(0.667)EK 46.307 0.061369 260660000 13555 105670 62053 79495 55273 101130 44750 76200 45172 115050 TRUE FALSE 14090.16187 123818.0005 63670.15216 95218.87373 45877.7152 77644.09014 41242.37807 75178.66364 43546.26854 137591.8447 0.102405502 0.899893455 0.462746555 0.692038645 0.33343339 0.564307356 0.29974435 0.54638895 0.316488733 1 17.07003544 -1.696002246 3.991600308 1.031571667 0.483898586 0.355310016 0.213847523 0.052684246 0.004012399 0.181560123 0.043738455 0.020137138 1.696002246 -0.547673081 DPNDVRPIQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DPNDVRPIQAR 11 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 ;; 113.61 0.0012483 943410000 752580 890670 832900 911040 853560 1021230 949780 918280 847830 794910 FALSE TRUE 782292.4395 1043635.644 854606.0582 1091240.993 708472.1761 784064.8094 875333.7618 905971.9586 817316.7639 950657.395 0.822896286 1.097804161 0.898963247 1.147880402 0.74524448 0.824760648 0.920766794 0.952995226 0.859738501 1 19.85856598 3.233968246 24.99999951 0.886314384 0.992814253 0.194506895 0.107564943 190.9819766 1039669.323 0.029614745 0.03652664 1713.831992 -3.233968246 0.106499868 DPNTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPNTKR 6 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 115.46 0.039143 468730000 815550 581420 825810 623160 866960 847260 1009400 796590 823130 576490 FALSE TRUE 847748.5437 681274.3622 847331.287 746419.1881 719594.4489 650496.7053 930280.5904 785913.014 793505.7121 689442.1779 1.229615145 0.988153008 1.229009936 1.082642188 1.0437343 0.943511619 1.349323584 1.139925927 1.150938741 1 19.39507004 2.251758783 24.99974685 1.174645867 1.086069962 0.082998053 0.116418549 489.7697079 927712.655 0.038754071 0.032242367 178.5495595 -2.251758783 -0.088575905 DPPQECSTFSPTDSGEEPGQLS(ph)PGVQFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPPQECSTFSPTDSGEEPGQLSPGVQFQR 29 0 Q07002;A0A0A0MSJ6;Q07002-3 Q07002 CDK18 Cyclin-dependent kinase 18 1 DPPQECSTFSPTDSGEEPGQLS(1)PGVQFQR 239.98 1.41E-45 85736000 32867 32969 38970 38489 44514 47874 37923 35610 34323 31884 TRUE FALSE 34164.61454 38631.16929 39985.59021 46102.00932 36947.52618 36755.98904 34950.49617 35132.7062 33087.72193 38131.05934 0.895978636 1.013115553 1.048635703 1.209040874 0.96896144 0.963938314 0.916588649 0.921367169 0.867736761 1 15.21867899 3.012353756 24.99977229 0.931004643 1.046254119 0.299783282 0.077675348 275.4821486 557477.282 0.023181586 0.027690392 1028.854014 -3.012353756 0.115249476 DPPSWSVLAGHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPPSWSVLAGHSR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 175.74 1.77E-05 138780000 62163 100070 98624 88021 109340 115580 107580 98413 98443 112240 FALSE TRUE 64617.24324 117256.2441 101194.2225 105431.2911 90754.42586 88738.29663 99147.59849 97093.93471 94900.05566 134231.279 0.481387376 0.873538902 0.753879596 0.785445031 0.676104903 0.661085086 0.738632599 0.723333156 0.706989134 1 17.03436137 -2.001509827 3.108098541 1.284516515 0.718542296 0.448702994 0.095735791 14271.71385 36464839.79 7008.434013 0.020603139 0.009965295 2.001509827 -0.56597422 DPQALSEHLKNPVIAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPQALSEHLKNPVIAQK 17 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 244.88 9.21E-21 1699260000 1444620 1529860 1973960 1474750 2638700 2380300 2215660 2115200 2230510 1440640 FALSE TRUE 1501654.713 1792601.554 2025403.019 1766451.148 2190174.717 1827511.399 2041990.78 2086849.204 2150234.381 1722905.825 0.871582585 1.040452431 1.175573841 1.025274349 1.271209769 1.060714621 1.185201623 1.211238115 1.248027808 1 20.71641241 5.540271021 0.866480087 1.165943285 9.68E-19 0.470991597 0.088668715 6.103272208 1.292412854 0.026683835 9.407389035 346953.2985 -5.540271021 -1.165943285 DPS(ph)KIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;DPS(1)KIK 77.732 0.043388 6411930000 19269900 6072210 10219540 5690160 16699470 15398710 15308720 10184310 11781980 3716530 TRUE FALSE 20030690.53 7115064.832 10485869.61 6815656.665 13860900.05 11822592.97 14108782.52 10047805.98 11357948.84 4444712.896 4.506633162 1.600792897 2.359178164 1.533430128 3.118514149 2.659922755 3.174284336 2.260619801 2.55538414 1 22.0836588 0.216022564 1.283570405 0.998093316 2.600576714 0.26966842 0.808802856 8.366140442 12.32777181 0.753588833 0.215961618 1.644457159 -0.216022564 1.602483398 DPS(ph)PESNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPSPESNK 8 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNK 120.27 0.0016087 370350000 552670 278250 393600 308890 467300 594000 619650 436240 425440 210390 TRUE FALSE 574489.8384 326037.273 403857.5393 369987.5201 387868.5129 456052.5022 571080.2138 430392.9163 410128.4975 251611.8923 2.283238018 1.295794368 1.605081284 1.470469129 1.541534898 1.812523637 2.269686892 1.710542822 1.630004423 1 17.94084059 2.731948461 23.79910358 1.77495338 1.608872103 0 0.380575296 1021.459313 3676522.003 0.116187498 0.112069324 539.4466015 -2.731948461 -0.166081277 DPS(ph)PESNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPSPESNKK 9 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(1)PESNKK 85.813 0.0068566 0 366850 124360 221040 153020 294160 298290 397030 231690 235190 85560 TRUE FALSE 381333.5213 145717.8626 226800.484 183286.8993 244158.7883 229016.6681 365909.7512 228584.5745 226725.5578 102323.8439 3.726731785 1.424085112 2.216496913 1.791243296 2.386137767 2.238155444 3.575996927 2.233932639 2.215764667 1 16.64278284 3.030221138 24.79206895 2.418234011 2.205852236 0 0.809656725 1149.896303 943315.4453 0.222750418 0.266234765 1072.06505 -3.030221138 -0.212381775 DPS(ph)PESNKKGESPSLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPSPESNKKGESPSLESR 18 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 DPS(0.992)PES(0.008)NKKGESPSLESR 89.721 0.0014812 352900000 724110 268620 430250 241880 776890 636230 551420 438730 505960 221800 TRUE FALSE 752698.4219 314753.3954 441462.6685 289723.1421 644834.5153 488475.2247 508198.2595 432849.542 487750.5984 265257.4634 2.837614491 1.186595813 1.664279914 1.092233705 2.430975955 1.841513594 1.915867901 1.631809098 1.838781809 1 18.01703382 -0.629094037 0.862786922 0.947767517 1.79657397 0.20022457 0.491779433 49.37353666 21.8454676 8.734157915 0.14829561 0.234912411 0.629094037 0.848806454 DPSAS(ph)PGDAGEQAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPSASPGDAGEQAIR 15 0 P18206;P18206-2 P18206 VCL Vinculin 1 DPSAS(1)PGDAGEQAIR 249.86 1.26E-18 513860000 204720 208170 181650 230350 207970 260230 259160 219780 177050 203240 TRUE FALSE 212802.5037 243921.5782 186383.9482 275912.5425 172619.3337 199795.5263 238846.362 216834.2086 170678.0051 243060.9867 0.875510737 1.00354064 0.766819681 1.135157666 0.710189389 0.821997512 0.982660217 0.892097952 0.702202387 1 17.89095882 3.211715624 24.99995771 0.856985345 0.936675211 0.113702893 0.126755519 563.7567587 525008.7145 0.035326958 0.042233861 1628.229519 -3.211715624 0.079689866 DPSQQELPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPSQQELPR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 139.02 0.00027975 2126900000 562488 509054 562000 499850 632400 726030 648080 579540 572000 523590 FALSE TRUE 584695.4606 596480.0646 576646.1817 598718.8381 524904.8739 557420.5356 597281.7962 571772.2142 551413.8317 626177.4358 0.933753641 0.952573553 0.920899012 0.956148855 0.838268586 0.89019582 0.953853911 0.913115327 0.880603165 1 19.256212 -0.555595331 6.325076351 1.000000347 0.916385851 0.335864459 0.035631211 0 0 0.034792853 0.008200754 0.278230457 0.555595331 -0.083614497 DPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPSSNDINGGMEPTPSTVSTPSPSADLLGLR 31 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 DPSSNDINGGMEPTPSTVS(0.005)T(0.129)PS(0.683)PS(0.183)ADLLGLR 158.97 1.44E-12 30935000 16029 21565 20431 18225 23280 29988 19957 21019 19874 19618 TRUE FALSE 16661.8373 25268.621 20963.44864 21829.8506 19322.87392 23023.74147 18392.71819 20737.27469 19158.73862 23461.77149 0.710169618 1.077012493 0.893515166 0.930443407 0.823589724 0.981330054 0.783944137 0.88387506 0.816593863 1 14.51802433 3.284259591 24.99595353 0.8743148 0.914567849 0.001916718 0.105011522 526.606397 288033.9713 0.026858884 0.036366965 1924.241563 -3.284259591 0.040253049 DPSVDITQDLVDESEEERFDDMSS(ph)PGLELPSCELSR ddPTM_MDA-MB-175_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 DPSVDITQDLVDESEEERFDDMS(0.154)S(0.846)PGLELPSCELSR 92.49 0.00035416 37673000 23808 35535 29598 27842 32843 34961 28517 31327 32133 32730 TRUE FALSE 24747.95822 41637.85983 30369.3482 33349.0645 27260.35859 26841.83759 26281.76302 30907.11281 30976.53961 39142.81685 0.632247759 1.06374204 0.775860059 0.851984277 0.696433236 0.685741082 0.671432593 0.789598585 0.791372265 1 15.25645996 5.027307952 17.66393205 0.796268127 0.134217363 0.148372521 0.124259947 128392524.3 2089273661 0.029134725 2535332683 106489.7854 -5.027307952 -0.662050765 DPT(ph)RQRPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPTRQRPRR 9 3 M0R1A4;M0QZ32 M0R1A4 OCEL1 1 DPT(1)RQRPRR 48.44 0.095456 0 64598 50334 52258 47594 67876 78054 68436 54810 66947 49759 TRUE FALSE 67148.37892 58978.47296 53619.88641 57007.95115 56338.46176 59927.14142 63071.8075 54075.3616 64537.59055 59508.32336 1.128386335 0.991096197 0.901048515 0.957982815 0.946732467 1.007037975 1.059882113 0.90870249 1.084513677 1 15.86080385 DPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.781)T(0.187)S(0.032)EGLEDAVHSR;DPTSLLGVLQAEADS(0.333)T(0.333)S(0.333)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.333)T(0.333)S(0.333)EGLEDAVHS(0.001)R;DPTSLLGVLQAEADS(0.593)T(0.32)S(0.087)EGLEDAVHSR;DPTSLLGVLQAEADS(0.673)T(0.252)S(0.075)EGLEDAVHSR 143.47 1.19E-07 267938000 63723.4 60370 64802.9 74710.2 69272.8 82154.9 78371 73971.3 73242 64093.7 TRUE FALSE 66239.24904 70738.07789 66491.71681 89487.65457 57497.8342 63075.66954 72228.07624 72979.83572 70606.03473 76651.63337 0.864159655 0.92285154 0.867453359 1.1674592 0.750118839 0.822887482 0.942290113 0.952097594 0.9211289 1 16.22602891 0.939531095 0.995712212 0.996437271 0.908104379 0.065099747 0.102933741 1.969103819 4.072025385 0.096599444 0.031964139 8.700237235 -0.939531095 -0.088332892 DPTSLLGVLQAEADSTS(ph)EGLEDAVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 DPTSLLGVLQAEADS(0.267)T(0.328)S(0.405)EGLEDAVHSR;DPTSLLGVLQAEADS(0.001)T(0.031)S(0.968)EGLEDAVHSR 138.1 4.35E-06 46655000 29388 28337 31587 34294 31549 37193 33470 31571 29216 25763 TRUE FALSE 30548.26093 33203.65932 32410.18317 41077.25084 26186.31225 28555.48942 30846.53394 31147.84238 28164.52187 30810.76659 0.991480067 1.077664174 1.051910964 1.333210932 0.849907846 0.926802303 1.001160872 1.010940195 0.914112987 1 14.91114696 3.200571047 24.99999434 0.957484919 1.106599396 0.414684522 0.094552419 174.9257755 115113.8174 0.027511542 0.032883271 1586.978516 -3.200571047 0.149114477 DPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DPTSLLGVLQAEADSTSEGLEDAVHSR 27 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;; 236.94 4.79E-45 155805000 91764 102379 110033 122778 118040 130019 131873 110919 120852 97816 FALSE TRUE 95386.91358 119961.7969 112900.5504 147063.1219 97975.60296 99824.05771 121536.4497 109432.3122 116502.5601 116981.1724 0.81540398 1.025479523 0.965117275 1.257152061 0.837533091 0.853334393 1.03894026 0.935469443 0.995908638 1 16.83591683 DPTVHDDVLELEMDELNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DPTVHDDVLELEMDELNR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 325.68 1.86E-62 817317000 462310 563107 731380 761140 690451 743651 810249 646460 689133 460629 FALSE TRUE 480562.3558 659816.2469 750440.3636 911691.2202 573088.3856 570949.3254 746739.5662 637795.2611 664331.2379 550880.4333 0.872353285 1.197748562 1.362256341 1.654971143 1.040313562 1.036430577 1.355538373 1.157774396 1.205944517 1 19.0713797 DPTVHDDVLELEMDELNRHECMAPLTALVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DPTVHDDVLELEMDELNRHECMAPLTALVK 30 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 80.359 0.0016391 68038000 33184 29109 38694 29201 51938 41879 38826 38217 46654 34258 FALSE TRUE 34494.12994 34108.24431 39702.39743 34976.87064 43109.59731 32153.23693 35782.71667 37704.76363 44974.93165 40970.19919 0.8419322 0.83251351 0.969055514 0.853714928 1.052218397 0.784795719 0.873384005 0.920297298 1.097747449 1 15.32228729 1.358881016 5.145455397 1.046818568 0.890098599 0.420581846 0.074741455 0.189804996 7.057813727 0.051127127 0.017996136 22.849727 -1.358881016 -0.156719969 DPVQEAWAEDVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DPVQEAWAEDVDLR 14 0 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 226.59 5.46E-12 3550708000 649544 611900 774705 756468 722029 855534 1041391 788609 805664 495825 FALSE TRUE 675188.4987 716989.0651 794894.4487 906095.1126 599298.7685 656849.1942 959764.0523 778038.9863 776668.31 592972.4156 1.138650772 1.209144045 1.340525171 1.528056093 1.010668882 1.107723019 1.618564417 1.312099797 1.309788263 1 19.17760547 DQADFSVLHYAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQADFSVLHYAGK 13 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 136.51 7.14E-05 153250000 364940 304330 363490 324330 472830 470090 437810 386840 413360 312960 FALSE TRUE 379348.113 356596.3101 372962.848 388481.506 392458.5255 360918.7218 403493.3082 381655.0425 398483.2543 374278.52 1.013544974 0.952756546 0.996484778 1.037947638 1.048573467 0.964305196 1.078056278 1.019708645 1.064670381 1 18.51375273 3.871852735 4.373883918 1.031384318 0.981430185 0.260752626 0.033372314 0.267671993 8.245463342 0.00814139 0.015429859 7444.794857 -3.871852735 -0.049954133 DQCCSGKGDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQCCSGKGDMSDEDDENEFFDAPEIITMPENLGHK 35 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 DQCCS(0.019)GKGDMS(0.981)DEDDENEFFDAPEIITMPENLGHK 145.17 6.44E-11 44896000 20900 21808 25493 7942 45785 28451 15458 20687 32661 29703 TRUE FALSE 21725.14814 25553.35436 26157.36852 9512.903895 38002.48205 21843.68643 14246.36157 20409.7246 31485.53699 35522.73415 0.611584346 0.719352127 0.736355721 0.267797627 1.069807349 0.614921316 0.401049128 0.574553876 0.886348918 1 15.11645501 1.110772364 4.395030258 0.992758372 0.621150804 0.294901001 0.200255179 0.243243069 7.520361491 0.185845181 0.047591712 12.90542658 -1.110772364 -0.371607568 DQDEQEELDFLFDEEMEQMDGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDEQEELDFLFDEEMEQMDGRK 23 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 0 107.9 0.0020874 20128000 14700 15222 15865 9368.6 20602 19047 18202 16216 17700 11902 FALSE TRUE 15280.36735 17836.26009 16278.45493 11221.68112 17100.0794 14623.62291 16775.27968 15998.65104 17062.98046 14233.96902 1.073514164 1.253077062 1.143634281 0.788373299 1.201357076 1.027374929 1.178538442 1.123976806 1.198750709 1 13.79705038 2.228917936 24.97500006 1.135929207 1.08401973 0.025238824 0.126889657 840.1625803 2176044.852 0.047250885 0.035353365 169.4017669 -2.228917936 -0.051909477 DQDGYYWITGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DQDGYYWITGR 11 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;;;; 217.14 2.69E-11 1967230000 1148891 1286260 1236183 1238447 1494060 1651400 1402710 1294530 1356930 1218699 FALSE TRUE 1194250.104 1507165.149 1268398.945 1483408.12 1240100.215 1267887.377 1292761.925 1277178.943 1308094.354 1457479.736 0.819393968 1.034089952 0.870268665 1.017789877 0.850852458 0.869917671 0.886984493 0.876292762 0.897504317 1 20.47504439 3.1935558 24.99998258 0.8879901 0.937785727 0.058864938 0.069807434 275.2370665 152892.1087 0.01827107 0.021838177 1561.549659 -3.1935558 0.049795627 DQDLTQEIAMEHFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDLTQEIAMEHFVK 15 0 Q9ULX6;Q9ULX6-2 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 0 174.49 9.10E-07 247930000 153180 123240 157660 121000 185280 198830 181200 160000 146480 111230 FALSE TRUE 159227.6647 144405.5113 161768.7491 144933.4389 153786.1718 152654.7458 166997.0705 157855.4617 141208.2134 133023.3889 1.196989988 1.085564821 1.216092527 1.089533503 1.156083701 1.147578235 1.255396302 1.186674487 1.061529214 1 17.0213204 1.075428695 4.09653712 1.00192192 1.167147897 0.557476959 0.049831678 0.139515851 4.30463481 0.047516617 0.012191262 11.89675986 -1.075428695 0.165225978 DQDMDS(ph)DRAYQYQEFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDMDSDRAYQYQEFTK 17 1 Q9NW75-2;Q9NW75 Q9NW75-2 GPATCH2 G patch domain-containing protein 2 1 DQDMDS(1)DRAYQYQEFTK 141.53 1.10E-05 0 66261 44877 58807 51122 72134 76026 64133 51181 67326 41202 TRUE FALSE 68877.03544 52584.27566 60339.55873 61233.77902 59872.68845 58370.11369 59106.08788 50495.00241 64902.95041 49274.74304 1.397816228 1.067164888 1.224553493 1.242701133 1.215078654 1.184584842 1.199520976 1.024764398 1.317164665 1 15.58856073 -5 0.097243979 0.394665962 1.330412017 0.277242064 0.101485094 248.5860111 1.655689178 30.86584758 1.766774926 1.00E-05 5 0.935746055 DQDS(ph)SDDERALEDWVSSETSALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPR 24 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.5)S(0.5)DDERALEDWVSSETSALPR 49.888 0.084121 26597000 10878 12460 13076 14133 16939 19860 14793 13666 15211 12467 TRUE FALSE 11307.47184 14599.90807 13416.7713 16928.46522 14059.71483 15247.81598 13633.48601 13482.82962 14663.55908 14909.66995 0.758398534 0.979224095 0.899870443 1.135401741 0.942993029 1.022679645 0.91440562 0.904301012 0.983493204 1 13.8639607 4.740093386 24.68241225 0.970012126 0.758398451 0.487802643 0.066598339 99.18081199 1596945.174 0.015923853 0.100756415 54965.90535 -4.740093386 -0.211613676 DQDS(ph)SDDERALEDWVSSETSALPRPR ddPTM_MDA-MB-175_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(0.5)S(0.5)DDERALEDWVSSETSALPRPR;DQDS(0.5)S(0.5)DDERALEDWVSSETSALPRPR 156.26 1.67E-08 334364000 112776 127926 134081 98912 170214 182519 122324 138571 135088 129872 TRUE FALSE 117228.4836 149896.2954 137575.261 118476.4984 141281.0851 140131.7284 112735.9252 136713.6824 130226.2093 155317.9319 0.754764644 0.9650933 0.885765471 0.762799871 0.909625073 0.902225047 0.725839727 0.880218277 0.838449287 1 17.24486488 -1.704424993 6.371444178 1.001966631 0.849698782 0.279852319 0.073436937 0.001957223 9.08E-05 0.067836555 0.015795812 0.01975036 1.704424993 -0.152267849 DQDSSDDERALEDWVSSET(ph)SALPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDSSDDERALEDWVSSETSALPRPR 26 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 DQDS(0.102)S(0.102)DDERALEDWVS(0.18)S(0.18)ET(0.218)S(0.218)ALPRPR 69.782 0.050644 60650000 18387 24049 25544 17755 29488 33890 23001 20797 23922 21499 TRUE FALSE 19112.93296 28179.22867 26209.69762 21266.88601 24475.64029 26019.56111 21198.12152 20518.25023 23061.05189 25711.31743 0.743366535 1.095985406 1.01938369 0.827141047 0.951940342 1.011988638 0.824466563 0.798024072 0.89692222 1 14.65011591 2.225047846 24.9685885 0.854680851 0.947448527 0.053085861 0.107038183 446.1658873 824409.5068 0.038900775 0.028886344 167.898898 -2.225047846 0.092767676 DQDWPALAVDLAHHLQVSEDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQDWPALAVDLAHHLQVSEDVVR 23 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 214.57 1.64E-32 25950000 35923 36511 48484 43367 46980 51342 51155 43416 45295 35727 FALSE TRUE 37341.26778 42781.48023 49747.53287 51944.86316 38994.35638 39418.5986 47145.33743 42834.07953 43664.8418 42727.02162 0.873949701 1.001274571 1.164310804 1.215737985 0.912639236 0.922568368 1.103407999 1.002505626 1.021949112 1 15.38286113 3.181328668 24.99999996 0.99878008 1.066538592 0.105733525 0.098943279 213.3865204 93210.11723 0.030635301 0.036616208 1518.198883 -3.181328668 0.067758512 DQECDKFNQCGTCNEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQECDKFNQCGTCNEFK 17 1 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ; 227 1.73E-15 1555640000 947180 469650 639010 398250 897810 844930 802020 590910 673970 340330 FALSE TRUE 984575.3978 550308.7341 655663.1256 477022.6613 745200.5769 648707.8125 739155.5767 582989.818 649713.9514 407011.1475 2.419037915 1.352072879 1.610921788 1.17201375 1.830909501 1.593833035 1.816057327 1.432368183 1.596305053 1 18.63470878 -2.748204658 0.223084314 4.07E-14 1.723634 0.294101283 0.314435347 65.73950528 1.61326216 32.67177981 0.592872221 0.001785646 2.748204658 1.723634 DQELYFFHELSPGSCFFLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQELYFFHELSPGSCFFLPK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 213.18 9.95E-23 713680000 747800 650060 877380 748730 1013690 1024030 986410 792120 906270 590520 FALSE TRUE 777323.7214 761702.7482 900245.2436 896826.5593 841383.3359 786214.5518 909092.6067 781502.927 873653.5197 706221.0878 1.100680417 1.078561319 1.274735715 1.269894902 1.191388009 1.113269719 1.287263468 1.106598119 1.237082176 1 19.42976038 -0.136671425 7.588268475 1.000000422 1.183435047 0.344496744 0.076293275 4949263.388 652225.6482 0.072916592 0.017684871 0.730009606 0.136671425 0.183434625 DQEPKPS(ph)PEPAAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQEPKPSPEPAAVSR 15 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 DQEPKPS(1)PEPAAVSR 83.213 0.0082171 0 82657 51062 61513 48268 76457 92739 70951 67755 67168 39612 TRUE FALSE 85920.36219 59831.50129 63116.07931 57815.26633 63460.86645 71201.77272 65389.67522 66846.85505 64750.6368 47373.21298 1.813690834 1.262981705 1.332315782 1.22042105 1.339593886 1.502996488 1.380309063 1.411068637 1.366819616 1 15.5317839 0.753379808 4.528236996 1.000000667 1.39468371 0.376715887 0.155697828 5.888643909 107.4090925 0.14203791 0.036047373 5.667347049 -0.753379808 0.394683043 DQETLHSHGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQETLHSHGVR 11 0 B4DML5;G3XAG9;Q9BYM8-4;Q9BYM8-3;Q9BYM8;H0Y4S7 B4DML5 RBCK1 RanBP-type and C3HC4-type zinc finger-containing protein 1 0 ;; 135.5 6.86E-05 188264000 107717 127178 114497 126925 132813 168254 132086 130870 121024 143329 FALSE TRUE 111969.7503 149019.8322 117480.8859 152030.3862 110237.4937 129179.5584 121732.7542 129115.9017 116668.3699 171411.5734 0.653221647 0.869368557 0.685373126 0.886931863 0.643115815 0.75362215 0.710178151 0.753250782 0.680632979 1 17.38710499 -0.840811161 5.575219626 1.000000089 0.74149697 0.495432324 0.079431849 7.84E-08 1.62E-08 0.068299589 0.016098362 0.144274255 0.840811161 -0.258503119 DQEVEHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQEVEHVR 8 0 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 ;; 117.3 0.0021056 484691000 394756 497023 491123 474647 555934 646584 508506 520929 472761 494128 FALSE TRUE 410341.2717 582382.8339 503922.0688 568530.7599 461436.5373 496424.6651 468647.971 513946.7988 455746.424 590942.9209 0.694383937 0.985514528 0.852742373 0.962073899 0.780847897 0.840055185 0.793051163 0.86970633 0.771219026 1 19.17265926 3.213659593 24.99767854 0.834933513 0.880171643 0.0198186 0.095024108 733.8664638 736713.2018 0.025238773 0.030178031 1635.534062 -3.213659593 0.04523813 DQFLDTLQAHGHDVNSFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQFLDTLQAHGHDVNSFVR 19 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 ; 215.06 2.40E-19 148071000 95555 112468 117235 117334 129281 155198 125940 125813 115872 116731 FALSE TRUE 99327.58518 131783.5041 120290.2404 140542.315 107305.8618 119155.6165 116068.4937 124126.6825 111701.7894 139602.2045 0.711504417 0.943993002 0.861664333 1.00673421 0.768654494 0.853536783 0.831423072 0.889145576 0.800143449 1 17.0909622 -1.143788427 4.380454086 1.000025133 0.858471649 0.232014796 0.080044624 1.81E-05 3.54E-06 0.071440985 0.016835813 0.071814406 1.143788427 -0.141553484 DQGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DQGELER 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 147.04 0.0058871 4653500000 3828810 3687570 3972230 3549860 4653000 5078260 4414830 4107480 4042790 3525410 FALSE TRUE 3979974.375 4320881.462 4075749.577 4252011.713 3862084.722 3898911.077 4068784.089 4052425.949 3897290.778 4216146.591 0.94398387 1.024841373 0.966700158 1.008506612 0.916022401 0.924757001 0.96504806 0.961168181 0.924372693 1 22.0074936 3.248039579 24.99984665 0.947697932 0.987402681 0.261848672 0.030744914 253.000724 667260.521 0.008116677 0.010848008 1770.270283 -3.248039579 0.039704749 DQGFRGDGGSTTGLSAT(ph)PPASLPGSLTNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQGFRGDGGSTTGLSATPPASLPGSLTNVK 30 1 P15056;H7C560;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DQGFRGDGGS(0.003)T(0.002)T(0.016)GLS(0.21)AT(0.768)PPASLPGSLTNVK;DQGFRGDGGS(0.001)T(0.001)T(0.001)GLS(0.003)AT(0.88)PPAS(0.108)LPGS(0.006)LT(0.001)NVK 164.11 5.51E-12 539240000 203408 185905 203574 141189 320880 281740 174000 201680 248890 223920 TRUE FALSE 211438.7049 217832.7376 208879.3057 169115.7628 266336.9322 216310.1548 160361.4253 198976.8095 239932.4975 267792.8368 0.78956072 0.813437507 0.780003335 0.631517127 0.994563318 0.807751833 0.598826418 0.743025138 0.89596309 1 18.03075784 1.037106404 3.94831857 0.998355838 0.766787249 0.349893962 0.101866912 0.205733109 7.211341998 0.09905901 0.025430649 10.89196919 -1.037106404 -0.231568589 DQGGELLSLR ddPTM_MDA-MB-175_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 ; 117.52 0.0022026 151351000 278320 286420 301580 275410 358390 376440 323220 308760 309850 311490 FALSE TRUE 289308.2885 335610.407 309439.4226 329885.276 297470.9958 289017.515 297885.1718 304621.5772 298698.559 372520.5017 0.776623802 0.900917951 0.830664141 0.885549317 0.798535905 0.775843245 0.799647725 0.81773104 0.801831195 1 18.5069603 -1.48659092 3.160400554 1.004223332 0.822148409 0.643357578 0.04001203 27965620.47 37882015.83 1052525.636 0.009725193 0.032614376 1.48659092 -0.182074923 DQGGFGDRNEYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DQGGFGDRNEYGSR 14 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 252.01 3.11E-24 8345260000 2369340 2505530 2528420 2355920 2962130 3357190 2585190 2618930 2627680 2640370 FALSE TRUE 2462883.373 2935835.287 2594312.702 2821913.944 2458628.201 2577533.501 2382556.053 2583827.527 2533110.31 3157699.949 0.779961178 0.929738523 0.821583033 0.893661206 0.778613624 0.816269292 0.754522625 0.818262523 0.80220108 1 21.59044266 DQGSCGSCWAFGAVEAISDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQGSCGSCWAFGAVEAISDR 20 0 P07858;E9PKQ7;E9PNL5;E9PHZ5;E9PLY3;E9PSG5;E9PQM1 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 202.5 2.69E-21 138172000 82074 94538 87945 70948 83797 111620 79057 75160 72228 78594 FALSE TRUE 85314.34489 110774.1661 90236.91895 84981.30264 69553.21587 85697.94662 72860.30576 74152.60314 69628.52839 93992.98953 0.907667107 1.17853647 0.960038822 0.90412384 0.739983016 0.911748281 0.775167447 0.788916317 0.740784273 1 16.52026554 3.706180737 2.40441235 0.815285002 1.043567759 0.417314384 0.099355277 0.23282159 2.635703723 0.025754435 0.048754073 5083.70963 -3.706180737 0.228282757 DQGTYEDYVEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DQGTYEDYVEGLR 13 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;; 203.51 1.98E-07 4692500000 2874210 3102170 3126900 3407610 3633790 4077990 4048410 3474520 3175820 2564640 FALSE TRUE 2987686.03 3634943.566 3208389.583 4081625.087 3016119.674 3130938.625 3731085.046 3427949.743 3061522.859 3067132.105 0.974097603 1.185127814 1.046055231 1.330762728 0.983368036 1.020803317 1.216473539 1.117640071 0.998171175 1 21.54845888 DQHDTFFLRDPAEALQLPMDYVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQHDTFFLRDPAEALQLPMDYVQR 24 1 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;; 128.12 4.79E-05 270860000 129030 286205 273752 296768 286700 332922 248924 275695 265048 331560 FALSE TRUE 134124.204 335358.4824 280886.202 355467.8246 237966.8364 255605.911 229412.6864 271999.7595 255508.9743 396522.8339 0.338250896 0.845748224 0.708373334 0.896462434 0.600134005 0.64461839 0.578561099 0.685962412 0.644373924 1 18.59704442 -1.749433593 2.528943609 1.076782464 0.669598281 0.330921621 0.144371689 23244581.21 16918711.72 11144518.86 0.032767161 0.017806002 1.749433593 -0.407184183 DQHFDQNLNFMYIEVDKVTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQHFDQNLNFMYIEVDKVTER 21 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 ; 185.41 2.17E-17 115593000 134002 88614 120453 98960 154303 148133 137629 113287 131427 90253 FALSE TRUE 139292.5024 103832.7652 123592.1041 118533.9926 128074.6312 113731.3557 126841.2794 111768.5731 126696.9679 107936.3474 1.290505987 0.961981462 1.145046198 1.098184213 1.186575554 1.053689128 1.175148895 1.035504497 1.173811891 1 16.71982125 -5 0.272681106 0.196923899 1.1238007 0.145319104 0.088102728 412.0879299 3.988298131 186.7168439 0.095161349 1.00E-05 5 0.926876801 DQHHLGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQHHLGSPSR 10 0 Q9H8M2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2-2 Q9H8M2 BRD9 Bromodomain-containing protein 9 1 DQHHLGS(0.829)PS(0.171)R;DQHHLGS(0.984)PS(0.016)R;DQHHLGS(0.983)PS(0.017)R 103.83 0.001779 1065605000 655764 819749 774494 776667 876856 858275 852164 752567 740558 795470 TRUE FALSE 681654.0691 960534.514 794677.9499 930289.4145 727808.3303 658953.6385 785369.159 742480.0703 713905.4622 951327.1163 0.716529633 1.009678477 0.83533617 0.977885943 0.765045291 0.692667777 0.825551112 0.780467683 0.750431108 1 19.85958198 3.212529771 24.99680853 0.787484184 0.890236149 0.116735949 0.106143688 354.7630562 340669.6818 0.028245598 0.033770135 1631.284729 -3.212529771 0.102751965 DQHLNNSSS(ph)SPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.018)S(0.009)S(0.487)S(0.487)PQR 140.49 4.13E-05 126500000 145840 213530 204810 194630 223020 250250 203960 201820 199540 210510 TRUE FALSE 151597.8758 250202.1165 210147.5169 233127.2331 185111.1401 192133.2301 187973.0822 199114.933 192358.5944 251755.404 0.602163343 0.993830172 0.834728921 0.926006868 0.735281694 0.763174204 0.746649642 0.790906292 0.764069376 1 17.94166322 4.77545351 23.70961852 0.824128622 0.602162289 0.344120031 0.096199768 12440.11853 7994465.96 0.022497951 5.06700346 59628.44857 -4.77545351 -0.221966332 DQHLNNSSSS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQHLNNSSSSPQR 13 0 A0A4W8VX11;A0A5H1ZRS1;E7EV93;E9PGW9 A0A4W8VX11 PCM1 1 DQHLNNS(0.001)S(0.06)S(0.206)S(0.733)PQR 248.18 1.49E-17 579130000 298530 391060 381550 364660 387080 486530 387100 415350 369680 380800 TRUE FALSE 310316.1949 458221.513 391493.5064 436788.6596 321284.2799 373540.7809 356758.0905 409782.9126 356375.289 455410.4691 0.681398905 1.00617255 0.859649773 0.959109834 0.705482859 0.820228796 0.783377008 0.89981004 0.782536444 1 18.79680793 -1.409995051 3.120897931 1.002291742 0.840792585 0.203555292 0.097987969 16753440.22 22835272.86 346729.9457 0.0228032 0.038904958 1.409995051 -0.161499158 DQKLPHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DQKLPHLER 9 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;;; 110.39 0.0013791 416480000 1084770 972160 1158330 860120 1628310 1391160 1159160 1187910 1269060 1162330 FALSE TRUE 1127597.557 1139120.918 1188517.031 1030249.169 1351530.448 1068084.173 1068302.01 1171988.009 1223386.778 1390066.309 0.811182567 0.819472359 0.855007436 0.741151096 0.972277681 0.768369225 0.768525935 0.843116621 0.880092389 1 20.40672227 0.882738457 2.046253634 0.999486566 0.821348411 0.448341456 0.060272452 0.414604794 3.497511221 0.054238563 0.015020034 7.633759213 -0.882738457 -0.178138156 DQLIYNLLKEEQTPQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQLIYNLLKEEQTPQNK 17 1 F5GZQ4;P00338;P00338-3;P00338-4;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2;F5H5J4;F5H6W8;F5GXC7;F5H8H6;F5GXU1;F5GWW2 F5GZQ4;P00338 LDHA L-lactate dehydrogenase A chain 0 ; 176.69 9.80E-10 1185140000 1022780 647470 937800 533830 1250680 1081620 810290 809800 1019460 614310 FALSE TRUE 1063160.144 758667.9359 962239.8384 639419.9807 1038089.86 830430.1471 746777.3525 798945.9556 982769.8337 734672.2828 1.44712162 1.03266171 1.309753833 0.870347222 1.412997175 1.130340924 1.016476829 1.087486182 1.337698259 1 19.48674132 4.750681272 24.0986241 1.134122245 1.447121941 0.251624537 0.162465638 1530.201657 3042295.886 0.035764346 0.580132388 56322.41545 -4.750681272 0.312999696 DQLVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQLVLR 6 0 Q6UVJ0 Q6UVJ0 SASS6 Spindle assembly abnormal protein 6 homolog 0 100.67 0.087001 191210000 191110 177260 190810 175260 250460 265680 201510 200730 195730 159950 FALSE TRUE 198655.1704 207703.0261 195782.6654 209925.9049 207886.8987 203979.8464 185715.1197 198039.5427 188685.7155 191289.1401 1.03850731 1.08580668 1.02349075 1.097427197 1.086767908 1.066343057 0.970860759 1.035289001 0.986390108 1 17.54539545 2.259697728 24.42984999 1.003662331 1.067660087 0.620040615 0.026021089 121.7218263 140683.2259 0.008730182 0.007296259 181.8434776 -2.259697728 0.063997756 DQMEYMLQNHVFPLFSSELGYMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQMEYMLQNHVFPLFSSELGYMR 23 0 O95373 O95373 IPO7 Importin-7 0 87.659 0.006401 58757000 49329 27436 53135 43743 66959 72318 75053 60740 56114 43967 FALSE TRUE 51276.54701 32147.91958 54519.74175 52395.23484 55577.3331 55523.24049 69170.14975 59925.87965 54094.4681 52581.49185 0.97518243 0.611392306 1.036861828 0.996457746 1.056975204 1.055946466 1.315484733 1.139676292 1.028773932 1 15.68226745 3.742213434 1.246548022 1.127307499 0.800184906 0.405067028 0.127803924 0.420857783 1.240641889 0.040253641 0.110690658 5523.488239 -3.742213434 -0.327122593 DQPAFTPSGILT(ph)PHALGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQPAFTPSGILTPHALGSR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 DQPAFTPSGILT(1)PHALGSR 129.72 6.97E-05 159980000 81559 89800 81562 74207 81607 80500 70235 82375 84996 79237 TRUE FALSE 84779.0123 105222.4515 83687.57272 88884.92311 67735.47129 61805.09499 64729.79717 81270.89786 81937.01056 94761.97307 0.894652249 1.110386878 0.883134553 0.937980925 0.714795915 0.6522141 0.683077769 0.857631972 0.864661297 1 16.53202062 3.340953949 5.645716819 0.779390996 0.966523238 0.32802406 0.111707143 0.221910998 10.40612418 0.031463174 0.042718572 2192.57243 -3.340953949 0.187132242 DQPGRQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQPGRQEK 8 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 108.74 0.0034219 162959000 264590 191903 280070 155502 250630 265440 176739 179797 201921 198126 FALSE TRUE 275036.2175 224860.8475 287368.8543 186259.8315 208028.0021 203795.5828 162885.7354 177387.1153 194653.9027 236944.9963 1.160759762 0.949000194 1.212808283 0.7860889 0.877959043 0.860096587 0.687441127 0.748642588 0.821515143 1 17.85419267 3.725708394 24.83059964 0.807155909 1.09167049 0.612654898 0.101593608 417.2168094 806066.3373 0.026215511 0.040901362 5317.510959 -3.725708394 0.284514582 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DQQNLPYGVTPASPSGHSQGR 21 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 DQQNLPYGVTPAS(0.991)PS(0.009)GHS(0.001)QGR;DQQNLPYGVTPAS(0.986)PS(0.014)GHSQGR;DQQNLPYGVTPAS(0.954)PS(0.045)GHSQGR;DQQNLPYGVTPAS(0.99)PS(0.01)GHSQGR 215.46 4.22E-25 1704790000 192760 303706 315883 299541 333254 398785 339029 336070 312576 337100 TRUE FALSE 200370.3136 355865.143 324115.1705 358789.3158 276607.6041 306173.2274 312455.0211 331565.5313 301326.4508 403148.2908 0.497013923 0.882715247 0.803960175 0.88996859 0.686118757 0.759455601 0.775037445 0.822440623 0.747433284 1 18.62095108 -5 0.242391938 2.30837357 0.750377249 0.317531475 0.105603891 213.0513353 2.122605648 137.674529 0.15379947 1.00E-05 5 -1.557996322 DQRPS(ph)SPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DQRPSSPIR 9 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 DQRPS(0.5)S(0.5)PIR;DQRPS(0.5)S(0.5)PIR;DQRPS(0.5)S(0.5)PIR;DQRPS(0.5)S(0.5)PIR 109.24 0.0015031 3794760000 171521 212709 227102 169445 191880 268301 230974 210505 192100 186341 TRUE FALSE 178292.7815 249240.1161 233020.4647 202960.7153 159264.3061 205992.1589 212869.6543 207683.5248 185186.3585 222850.9512 0.80005394 1.118416209 1.0456337 0.910746461 0.714667383 0.924349471 0.955210885 0.931939144 0.830987517 1 17.76571959 3.625609798 6.412071996 0.891557419 1.00040339 0.138991693 0.104737886 0.405594735 20.21697867 0.027720304 0.043168865 4222.890287 -3.625609798 0.108845971 DQS(ph)PFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 DQS(0.996)PFS(0.004)K;DQS(1)PFSK;DQS(1)PFSK;DQS(0.948)PFS(0.052)K;DQS(1)PFSK;DQS(1)PFSK;DQS(0.999)PFS(0.001)K;DQS(0.992)PFS(0.008)K 192.12 0.00054121 12478160000 19485100 11179110 15013000 11373270 20235400 20167500 20280300 15697500 16483900 8157460 TRUE FALSE 20254386.79 13099035.18 15404251.11 13622868.86 16795793.94 15483903.77 18690677.09 15487100.69 15890647.66 9755758.103 2.076146885 1.342697824 1.578990679 1.396392645 1.721628782 1.58715536 1.915861063 1.587483056 1.62884806 1 23.21782256 0.344646845 2.364675927 1.000001626 1.639574433 0.467678463 0.20736891 18.40604486 64.81772674 0.186807085 0.050145786 2.211295818 -0.344646845 0.639572807 DQS(ph)PPPS(ph)PPPSYHPPPPPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQSPPPSPPPSYHPPPPPTK 20 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 2 DQS(0.973)PPPS(0.961)PPPS(0.032)Y(0.033)HPPPPPTK;DQS(0.999)PPPS(0.988)PPPS(0.007)Y(0.005)HPPPPPTK 77.63 0.0051703 367700000 154130 258140 305850 270130 354520 399160 344790 359260 298460 207336 TRUE FALSE 160215.1714 302473.5369 313820.7023 323560.9077 294258.817 306461.1393 317764.4589 354444.7073 287718.4829 247959.5195 0.646134384 1.219850472 1.265612641 1.304894075 1.186721194 1.235932139 1.281517481 1.429445855 1.160344573 1 17.91974509 4.739744027 4.423899632 1.259851658 0.602745603 0.725415788 0.107073905 0.09605535 4.652005409 0.024983913 0.198139662 54921.70707 -4.739744027 -0.657106055 DQS(ph)TPIIEVEGPLLSDTHVTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQSTPIIEVEGPLLSDTHVTFK 22 0 P49116;P49116-2 P49116 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 DQS(0.603)T(0.397)PIIEVEGPLLSDTHVTFK;DQS(0.591)T(0.409)PIIEVEGPLLSDTHVTFK;DQS(0.5)T(0.5)PIIEVEGPLLSDTHVTFK 194.27 2.71E-18 258069000 180351 237508 308119 217204 315022 330615 299410 290653 289291 213159 TRUE FALSE 187471.3967 278298.1514 316148.8343 260166.3029 261474.673 253834.6768 275941.4618 286757.2719 278879.4734 254923.4249 0.735402785 1.091693129 1.240171767 1.020566482 1.025698886 0.995729117 1.082448433 1.124876116 1.093973508 1 17.95970442 4.739676144 24.81216428 1.080691226 0.735402666 0.682947918 0.0693222 50.02538616 1112537.118 0.017103967 0.105406597 54913.12306 -4.739676144 -0.34528856 DQSSWQNSDASQEVGGHQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQSSWQNSDASQEVGGHQER 20 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ;; 318.02 1.56E-66 1029470000 278050 353907 345701 338349 399319 451286 344004 365722 354728 370132 FALSE TRUE 289027.6287 414687.7742 354710.2521 405273.4223 331442.899 346481.6658 317040.0676 360820.0948 341961.4086 442652.2788 0.652945083 0.93682512 0.801329326 0.915557068 0.748765826 0.782740048 0.716228251 0.81513213 0.772528291 1 18.75581432 -1.184734029 4.061910788 1.00009848 0.797876209 0.372171318 0.080262161 6.947992578 40666642.99 7530.697287 0.017581737 0.065353067 1.184734029 -0.202222271 DQTAS(ph)APATPLVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQTASAPATPLVNK 14 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 DQTAS(1)APATPLVNK;DQTAS(0.999)APAT(0.001)PLVNK;DQTAS(0.992)APAT(0.007)PLVNK 197.7 2.42E-08 966640000 2027370 1578650 2079650 1544620 2723300 2482840 2136750 2087730 2278800 1582760 TRUE FALSE 2107412.133 1849770.857 2133847.387 1850141.226 2260394.439 1906238.038 1969265.952 2059747.394 2196786.433 1892871.518 1.113341351 0.977230012 1.12730704 0.977425677 1.194161578 1.007061504 1.040359017 1.088160171 1.160557604 1 20.85214506 DQTASAPAT(ph)PLVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQTASAPATPLVNK 14 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 DQTASAPAT(1)PLVNK 153.22 7.21E-05 88516000 207780 140460 170090 155120 220320 238810 189140 188440 161190 148450 TRUE FALSE 215983.3148 164582.9124 174522.6851 185802.273 182870.0851 183349.9967 174314.7126 185914.27 155388.8034 177535.9353 1.216561112 0.927039994 0.983027379 1.04656149 1.030045466 1.032748646 0.98185594 1.047192332 0.875252681 1 17.43775155 4.750482854 24.86715189 0.998656457 1.216561254 0.619743937 0.052615507 1145.369638 2388940.23 0.012120217 0.200955113 56296.68913 -4.750482854 0.217904797 DQTSSHNSSDDKNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQTSSHNSSDDKNRR 15 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 0 78.932 0.012881 6592700 0 6393.5 5997.9 5367 6377.5 7510.7 3036.6 5382.7 2621.3 6885.8 FALSE TRUE 0 7491.53389 6154.210201 6428.576581 5293.454828 5766.453751 2798.583357 5310.553711 2526.959925 8234.940673 0 0.909725302 0.747329027 0.780646375 0.642804246 0.700242294 0.339842565 0.644880628 0.306858304 1 13.00754254 -2.320783966 2.179089688 3.066988571 0.586658308 0.199005374 0.258966477 15339413.43 1811825.405 156344493.2 0.059035007 0.004777669 2.320783966 -2.480330263 DQVANSAFVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DQVANSAFVER 11 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 286.86 1.40E-27 12167640000 1952105 2134470 2277040 2049790 2362970 2755430 2416010 2270830 2305410 2100430 FALSE TRUE 2029175.613 2501048.619 2336381.533 2455232.344 1961313.203 2115523.141 2226636.823 2240393.238 2222438.744 2511969.043 0.807802794 0.995652644 0.930099652 0.977413456 0.780787171 0.842177234 0.886410933 0.89188728 0.884739703 1 21.26038725 6.628245228 12.32317784 0.896747351 0.430089968 0 0.072576307 0 0 0.015573653 0 4248593.966 -6.628245228 -0.466657383 DQVLHEHIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQVLHEHIQR 10 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 ; 167.2 3.07E-06 1024750000 567900 593840 650420 636680 727080 822560 656990 674500 619680 566550 FALSE TRUE 590321.1305 695827.4006 667370.4795 762613.4037 603491.2013 631532.906 605493.4071 665459.4308 597377.8378 677554.6252 0.871252455 1.026968712 0.984969262 1.125537891 0.890690106 0.93207674 0.893645153 0.982148754 0.881667419 1 19.36997774 DQVTAQEIFQDNHEDGPTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQVTAQEIFQDNHEDGPTAK 20 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 301.34 7.02E-55 577830000 778563 592492 741340 651137 852000 912380 886250 799870 744136 520502 FALSE TRUE 809301.2684 694247.8921 760659.9294 779929.9551 707177.3443 700493.5723 816783.4092 789149.051 717354.6907 622484.4013 1.300114937 1.115285605 1.221974282 1.252930923 1.13605633 1.125319078 1.312134742 1.267741086 1.15240589 1 19.24767816 0.942750739 6.623730639 1.000007842 1.215917836 0.488184466 0.067200045 0.472913554 53.34772375 0.065882994 0.016536523 8.764976164 -0.942750739 0.215909994 DQWEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DQWEDR 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 224.39 1.02E-05 15391080000 7785410 8480670 8594370 8322050 10047910 11252260 9797100 8771130 8891830 7903550 FALSE TRUE 8092783.998 9937159.102 8818346.343 9968126.651 8339969.847 8639093.145 9029177.702 8653567.349 8571814.775 9452099.3 0.856189058 1.051317679 0.93295109 1.054593941 0.882340481 0.91398671 0.955256331 0.915518032 0.906868887 1 23.17220336 3.209126891 24.99990064 0.92534446 0.976387617 0.112898239 0.060786193 380.0140296 322768.7211 0.016152259 0.019308289 1618.552873 -3.209126891 0.051043157 DQWLQDAFHIS(ph)L ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DQWLQDAFHISL 12 0 Q8N5H3-1;Q8N5H3;Q8N5H3-2 Q8N5H3-1 FAM89B Protein FAM89B 1 DQWLQDAFHIS(1)L;DQWLQDAFHIS(1)L;DQWLQDAFHIS(1)L 130.07 0.00023395 41744000 96440 100706 113962 110773 140559 153243 128061 108697 123562 123805 TRUE FALSE 100247.5257 118001.4721 116931.9433 132683.5688 116666.8314 117654.6357 118023.2442 107240.0945 119115.0278 148062.2194 0.677063508 0.796972196 0.789748687 0.896133864 0.787958143 0.794629691 0.797119243 0.724290741 0.804493059 1 17.17584403 -2.307973101 1.951058034 1.855797879 0.785474292 0.592773383 0.053366318 3524502.584 458925.2676 13272117.64 0.013599309 0.0049207 2.307973101 -1.070323587 DQYCFECDCFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DQYCFECDCFR 11 0 Q9H7B4;A8MXR1;Q9H7B4-2;Q9H7B4-3 Q9H7B4 SMYD3 Histone-lysine N-methyltransferase SMYD3 0 122.51 0.0021291 0 26191 25629 25152 22145 30884 33851 24230 24234 26020 28500 FALSE TRUE 27225.0409 30030.58138 25807.48178 26525.2149 25634.34871 25989.61827 22330.78929 23909.18287 25083.54528 34084.02933 0.798762395 0.88107486 0.757172268 0.778230022 0.752092672 0.762516016 0.655168703 0.701477593 0.735932511 1 15.05680828 4.15261161 7.134168563 0.748072227 0.839420043 0.062172026 0.088871377 0.365101157 25.19831436 0.020792266 0.045624777 14210.57367 -4.15261161 0.091347816 DQYSVIFESGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 223.71 5.07E-11 319410000 270880 255390 316580 274360 285280 341630 329420 304360 284600 245050 FALSE TRUE 281574.5516 299251.2458 324830.3349 328627.5891 236788.2075 262291.61 303599.1996 300280.552 274357.3016 293062.8557 0.96079918 1.021116255 1.108398176 1.121355309 0.807977548 0.895001208 1.035952505 1.024628492 0.936172211 1 18.1608506 3.288204503 24.99999018 0.959529699 1.054608542 0.305119278 0.075275709 164.4360528 82806.51551 0.022858769 0.030950871 1941.80003 -3.288204503 0.095078843 DRAEAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRAEAEAR 8 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;;; 186.78 0.00018757 2644202900 2318840.1 2527162.7 2686043.7 2382626.9 3123089.4 3378124 2865637.1 2745637.3 2721179.1 2781043 FALSE TRUE 2410389.698 2961183.235 2756044.205 2853903.389 2592227.779 2593605.897 2641020.976 2708836.523 2623244.396 3325935.13 0.724725409 0.890331026 0.828652423 0.858075482 0.779398178 0.779812533 0.794068697 0.814458616 0.788723861 1 21.6653286 -0.687565895 5.30722802 1.000000021 0.809396053 0.639931032 0.043500617 5352277.804 1008488.56 1.294166117 0.009732936 0.205321347 0.687565895 -0.190603968 DRCPLPCIPTLIGT(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRCPLPCIPTLIGTPVK 17 1 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 DRCPLPCIPTLIGT(1)PVK 88.09 0.007084 253330000 208630 178320 157840 172470 178860 234280 201120 185710 184880 133680 TRUE FALSE 216866.8735 208945.0729 161953.4401 206584.0512 148457.4411 179872.0205 185355.6889 183220.8612 178226.2049 159872.0365 1.356502852 1.306951968 1.013019184 1.292183772 0.928601676 1.125099951 1.159400311 1.146046958 1.11480537 1 17.28655809 4.345769215 6.237321425 1.10996259 1.342762153 0.486557306 0.095976902 0.159207395 8.06244441 0.021812712 0.06116059 22170.17978 -4.345769215 0.232799563 DRDAS(ph)PSKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.982)PS(0.018)KEER;DRDAS(0.996)PS(0.004)KEER;DRDAS(0.969)PS(0.031)KEER;DRDAS(0.978)PS(0.022)KEER;DRDAS(0.999)PS(0.001)KEER 169.98 1.28E-05 3919131000 3640600 2133890 2752240 2003835 3926240 4157520 3532500 2748950 3058180 1705857 TRUE FALSE 3784333.699 2500369.008 2823965.635 2400187.582 3258859.127 3191998.988 3255613.42 2712104.822 2948116.699 2040087.019 1.854986412 1.225618802 1.384237834 1.176512355 1.597411825 1.564638645 1.59582086 1.32940644 1.445093603 1 20.96019926 0.247016889 1.115656517 0.998914233 1.457614215 0.348858186 0.190278724 4.900280287 6.222781989 0.188302154 0.054460102 1.7661065 -0.247016889 0.458699982 DRDASPS(ph)KEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRDASPSKEER 11 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 DRDAS(0.375)PS(0.625)KEER 92.773 0.0076754 216600000 416660 248760 301050 214420 441710 471590 382870 282790 319780 186100 TRUE FALSE 433110.0585 291482.5949 308895.6103 256831.636 366628.292 362070.3695 352859.649 278999.6626 308271.1803 222562.7319 1.9460134 1.309664886 1.387903571 1.153974135 1.647303162 1.626823891 1.585439062 1.253577633 1.385097935 1 17.76385251 0.880771773 1.012667108 1.008160297 1.495623957 0.336869046 0.213421456 0.815635655 1.687686343 0.201347101 0.065817262 7.599268213 -0.880771773 0.487463659 DRDGYSYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;; 171.49 3.65E-06 539548000 221094 234924 251867 220655 281947 323758 254986 241022 230855 263015 FALSE TRUE 229822.9618 275270.3695 258430.8609 264299.9004 234021.7496 248570.1111 234999.531 237791.4943 222546.5736 314547.7535 0.730645695 0.875130617 0.821594998 0.840253658 0.743994344 0.790246022 0.747102875 0.755978994 0.707512838 1 18.26291953 3.247216316 24.99390942 0.774334228 0.821400038 0 0.083139113 526.7815569 1521108.061 0.021181818 0.028249826 1766.91768 -3.247216316 0.04706581 DRDLEVDTTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRDLEVDTTLK 11 1 P02452 P02452 COL1A1 Collagen alpha-1(I) chain 0 66.498 0.057042 131100000 157190 122310 144210 104510 194510 202350 158210 139630 156700 134370 FALSE TRUE 163395.9826 143315.7911 147968.2311 125181.7661 161447.2597 155357.2791 145809.0868 137758.4882 151060.3976 160697.2288 1.016794028 0.891837352 0.92078894 0.778991442 1.004667354 0.96677012 0.907352839 0.857254909 0.94003113 1 17.29398552 4.745356104 23.6033561 0.911131371 1.016794137 0.164674757 0.064359087 605.7457223 2103862.883 0.015069257 0.144114086 55636.02633 -4.745356104 0.105662766 DRDNDSDDVESNLLLPAGIALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DRDNDSDDVESNLLLPAGIALR 22 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5;Q9NZM1-8;Q9NZM1-7 Q9NZM1-6 MYOF Myoferlin 0 ;;;; 222.95 7.40E-26 1415117000 766481 815346 872646 967434 1047012 1175015 977832 888398 902847 797240 FALSE TRUE 796742.2617 955375.333 895387.8716 1158789.558 869041.2742 902135.5738 901186.9728 876490.4779 870353.7128 953443.9139 0.835646702 1.002025729 0.939109117 1.215372547 0.911476031 0.946186305 0.945191384 0.919288975 0.912852555 1 19.86278855 DRDNQDREENDKDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRDNQDREENDKDPER 16 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 153.75 1.85E-07 420970000 514110 292970 373770 306200 498640 543460 556990 368690 397600 169830 FALSE TRUE 534407.4598 343285.3185 383510.7533 366765.4461 413881.3509 417249.6512 513331.6684 363748.3136 383290.4537 203104.9369 2.631188921 1.690186973 1.888239445 1.805792866 2.037771003 2.054355042 2.527420929 1.790937823 1.887154786 1 17.63186578 0.629606437 1.50232347 1.001629982 2.04472739 0.543488556 0.289540215 1.07497483 3.384762604 0.266237179 0.077233147 4.261931219 -0.629606437 1.043097408 DRDPEAQFEMPYVVR ddPTM_MDA-MB-175_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" 0 138.91 7.02E-06 57551000 17537 27721 24837 29333 35488 36018 30597 31107 31503 31447 FALSE TRUE 18229.3743 32481.86611 25484.27262 35134.97985 29455.76244 27653.36536 28198.72719 30690.06155 30369.21318 37608.43756 0.484715013 0.863685604 0.677621148 0.934231309 0.78322218 0.735296842 0.749797892 0.816041919 0.807510632 1 15.19876875 -5 0.031820976 2.149591391 1.65E-16 0.378650484 0.106216118 1515.666937 3.626917622 196.0931952 75.29806749 1.00E-05 5 -2.149591391 DRDS(ph)QRDLVEAVAHILGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR;DRDS(1)QRDLVEAVAHILGIR 311.67 7.95E-62 5705335200 615989.6 698438.4 791269.4 549114.8 1017816 1007804 598545.2 682349.4 778229.5 949071 TRUE FALSE 640309.3451 818389.7621 811890.5306 657728.0685 844807.9999 773756.7944 551629.6632 673203.6224 750221.1723 1135023.291 0.564137626 0.721033452 0.715307375 0.579484204 0.744308955 0.681710059 0.486007351 0.593118773 0.660974253 1 20.11429047 0.944979156 20.09983861 1.000000001 0.634410265 0.663132059 0.077489638 868.045699 317110.0233 0.07766171 0.019415428 8.810065877 -0.944979156 -0.365589736 DRDVSEEHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRDVSEEHKK 10 2 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ; 112.13 0.00099829 105515000 140559 99976 131827 79465 190053 165383 173986 123430 150415 90847 FALSE TRUE 146108.3779 117146.1003 135262.5199 95182.93982 157747.8589 126975.3047 160348.5227 121775.6227 145001.5935 108646.7303 1.344802347 1.078229414 1.244975524 0.876077352 1.451933791 1.168698812 1.475870671 1.120840199 1.334615346 1 16.72928523 DRDVTFSPATIENELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRDVTFSPATIENELIK 17 1 P55145;H7C2D6 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ;;; 231.77 3.28E-16 530516000 445164 342918 416117 338005 563470 556905 512865 386778 452844 290964 FALSE TRUE 462739.4185 401811.499 426961.3509 404861.3802 467691.5707 427572.2537 472665.3012 381593.8736 436546.2329 347972.825 1.329814817 1.154720915 1.226996249 1.163485626 1.344046251 1.228751854 1.358339696 1.096619754 1.254541164 1 18.40861512 -0.978471557 3.754962502 0.999966071 1.232472467 0.431324268 0.08219374 10474244.48 19677346.23 4637.826195 0.018938979 0.105082027 0.978471557 0.232506396 DRDWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRDWER 6 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ;;; 105.04 0.030385 1570320000 1103642 1215790 1406863 1149098 1374180 1535950 1353741 1274660 1195265 1295788 FALSE TRUE 1147214.638 1424592.475 1443527.006 1376386.155 1140597.374 1179248.89 1247631.243 1257575.268 1152247.646 1549672.849 0.740294727 0.919285948 0.931504353 0.888178531 0.736024623 0.760966349 0.80509331 0.811510164 0.743542514 1 20.56353225 4.802690768 21.41547194 0.833570764 0.740289547 0.108067681 0.084739692 43321.68621 14463070.73 0.020478619 48.32391731 63487.87167 -4.802690768 -0.093281216 DRDYSDHPSGGSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 173.19 1.65E-06 5645690000 509825 4324790 3800210 3918280 4022530 5485370 3260810 4743340 3660840 4741080 FALSE TRUE 529953.2847 5067539.04 3899246.595 4693304.089 3338781.787 4211475.949 3005219.192 4679763.286 3529087.084 5670003.853 0.093466124 0.893745255 0.687697345 0.827742663 0.588850003 0.742764213 0.530020661 0.825354516 0.622413525 1 22.43491828 -5 0.046057295 2.219722082 5.18E-11 0.246051242 0.207879468 1040.438533 3.559608148 168.1273853 42.29358974 1.00E-05 5 -2.219722082 DREDRS(ph)KDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREDRSKDR 9 3 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 1 DREDRS(1)KDR 97.214 0.037812 256850000 125010 67440 94810 80827 123280 131920 122500 90868 106560 45922 TRUE FALSE 129945.4913 79022.29539 97280.82649 96814.33936 102324.9096 101283.5793 112898.1299 89650.06309 102724.9264 54919.53667 2.366106839 1.438874036 1.771333707 1.762839696 1.863178676 1.844217657 2.055700699 1.632389283 1.870462364 1 15.74503183 -0.763344865 0.753724567 0.902841433 1.831499349 0.541163694 0.232871592 20.82412198 6.923478475 5.42928639 0.073570411 0.172446798 0.763344865 0.928657916 DREDYVPYTGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DREDYVPYTGEK 12 1 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;;; 195.1 6.14E-07 2175520000 2136900 1529310 2052600 1537680 2611390 2616590 2477000 2044620 2397540 1377749 FALSE TRUE 2221266.462 1791957.096 2106092.442 1841828.514 2167506.861 2008926.627 2282846.268 2017215.213 2311253.004 1647692.538 1.348107375 1.087555509 1.278207186 1.117822938 1.31548017 1.219236345 1.385480734 1.224266765 1.402721048 1 20.65201563 3.212212269 24.99179704 1.272712694 1.204345714 0.028312354 0.125807754 615.1867736 583512.088 0.032924238 0.039361961 1630.092573 -3.212212269 -0.068366981 DREEALHQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DREEALHQFR 10 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A087WVZ1;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ;;; 192.44 4.10E-07 4179430000 2221750 2476990 2478800 2380160 3167670 3147310 2665340 2636550 2547500 2633970 FALSE TRUE 2309466.406 2902393.764 2543399.564 2850948.544 2629230.585 2416394.95 2456423.686 2601211.36 2455815.973 3150045.991 0.733153234 0.921381393 0.807416645 0.905049816 0.83466419 0.767098308 0.779805658 0.825769328 0.779612736 1 21.58694146 2.992959314 24.63390395 0.814637619 0.848094701 0 0.079160717 1036.746619 3627383.199 0.021355455 0.024581167 983.9189241 -2.992959314 0.033457082 DREEDEEDAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 217.68 3.29E-11 599050000 349320 287520 344660 297120 406600 466450 404400 334310 348240 272580 FALSE TRUE 363111.4233 336899.3234 353642.1227 355889.4492 337486.2772 358124.0566 372702.0713 329829.1213 335706.9104 325986.8321 1.113883714 1.033475252 1.084835606 1.091729524 1.035275796 1.098584425 1.143304068 1.011786639 1.029817395 1 18.31445416 1.618077669 12.49233213 1.015409812 1.08238892 0.515463212 0.031840512 0.071780208 45.75067448 0.015415872 0.00808711 41.50282599 -1.618077669 0.066979108 DREEDEEDAYERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREEDEEDAYERR 13 2 P49756 P49756 RBM25 RNA-binding protein 25 0 100.11 0.0014342 102310000 33894 37470 44073 31902 52282 50135 40114 41535 40843 43579 FALSE TRUE 35232.16129 43905.18102 45221.57859 38212.12038 43395.12431 38491.90605 36969.75986 40978.29126 39373.06841 52117.47068 0.676014412 0.842427318 0.867685596 0.73319215 0.832640643 0.738560516 0.709354452 0.786267843 0.755467752 1 15.66947945 -1.68436045 6.7947392 1.001618642 0.774139988 0.579550759 0.058395567 0.001396789 6.49E-05 0.055155822 0.012916125 0.020684239 1.68436045 -0.227478655 DREEILLQELEPVISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DREEILLQELEPVISR 16 1 Q5JU69 Q5JU69 TOR2A Torsin-2A 0 ;;; 225.69 6.06E-15 153379000 82171.5 94678 91416 87186.4 111937 120487 95586.9 98258 90107.1 79408.5 FALSE TRUE 85415.69427 110938.21 93798.37606 104431.6097 92909.98872 92505.72025 88094.54901 96941.01223 86864.16307 94967.07521 0.899424291 1.168175494 0.987693639 1.099661219 0.978338951 0.974082018 0.927632538 1.020785488 0.914676617 1 16.5351398 3.104112544 8.936606317 0.970379417 1.044227385 0.184353193 0.071390364 0.41214716 32.24838588 0.018885534 0.022598852 1270.903407 -3.104112544 0.073847968 DREGFFTNGLTLGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREGFFTNGLTLGAK 15 1 C9J0J7;G5E9Q6;P35080-2;C9J712;C9JQ45;C9J2N0;P35080 C9J0J7 PFN2 Profilin;Profilin-2 0 128.64 6.46E-05 408670000 430200 334430 416790 310270 545920 502350 459370 421690 454770 344730 FALSE TRUE 447184.6282 391865.751 427651.8898 371640.4799 453124.7134 385686.8257 423363.3791 416037.9353 438402.9165 412273.2432 1.08468021 0.950500081 1.037302073 0.901442153 1.099088337 0.935512629 1.026899965 1.009131546 1.063379503 1 18.65324131 1.677877874 2.502384534 1.030430234 1.000518924 0.02294989 0.06122231 0.936668108 13.03749915 0.036994072 0.015415721 47.62970308 -1.677877874 -0.02991131 DREGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 DREGPTDHLESACPLNLPLQNNHT(0.119)AADMY(0.286)LS(0.785)PVRS(0.811)PK 74.164 0.0019092 74416000 18068 12442 18791 12121 24413 26492 17730 18874 19121 14104 TRUE FALSE 18781.33859 14578.81671 19280.7089 14518.49762 20263.28698 20339.63449 16340.27627 18621.0249 18432.83895 16867.40876 1.113469108 0.864318694 1.143074741 0.860742621 1.201327795 1.205854128 0.96874846 1.103964762 1.092807983 1 14.04195074 3.227237158 24.99417751 1.09713625 0.996586327 0.166986849 0.109420488 377.5880778 833445.9128 0.02999153 0.036144906 1687.474265 -3.227237158 -0.100549923 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 37 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 DREGPTDHLESACPLNLPLQNNHTAADMYLS(0.043)PVRS(0.957)PK 299.55 1.21E-92 91960000 51395 30494 42317 26243 52794 54884 51896 50171 39322 28151 TRUE FALSE 53424.11429 35731.10729 43419.81578 31433.78707 43820.09474 42138.02278 47828.25592 49498.53981 37906.8089 33666.64947 1.58685569 1.061320561 1.289698157 0.933677321 1.301587637 1.251625078 1.420641991 1.470254409 1.125945394 1 15.03903253 3.04722065 24.99998705 1.308262676 1.200058807 0 0.204498938 373.6245671 197805.1199 0.057263541 0.068442997 1114.860812 -3.04722065 -0.108203869 DRELALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRELALR 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 150.05 0.001801 405177000 329884 359721 347500 336682 526594 482847 408267 354576 369249 435807 FALSE TRUE 342908.075 421500.2835 356556.1355 403276.6947 437083.74 370713.1019 376265.9657 349823.4887 355959.8006 521195.0376 0.657926592 0.808718912 0.684112683 0.773753903 0.838618384 0.711275195 0.721929294 0.671194972 0.682968515 1 18.99146382 -0.964204774 4.671375668 1.000003231 0.728579328 0.667156406 0.05766953 2.39E-06 5.29E-07 0.056327237 0.013276264 0.108591348 0.964204774 -0.271423903 DRELDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRELDLR 7 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 ;;; 120.87 0.004098 2119360000 3617350 3868350 4031760 3720420 5011000 5277500 4293350 4110300 4055790 3849800 FALSE TRUE 3760165.771 4532709.021 4136830.978 4456307.972 4159232.01 4051880.606 3956826.008 4055208.152 3909822.91 4604094.601 0.816700372 0.984495197 0.89851129 0.967901044 0.903376748 0.880060241 0.859414576 0.880782978 0.849205598 1 22.13448605 2.999736954 24.99851718 0.88414532 0.922319247 0.017432387 0.057400704 22.94707341 2181092.306 0.015346 0.018155676 999.3944986 -2.999736954 0.038173927 DRELWVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRELWVQR 8 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ; 169.09 0.00027639 730650000 591050 611420 637780 521660 929780 852450 697640 676800 663590 721910 FALSE TRUE 614385.1104 716426.6288 654401.0707 624842.791 771736.3277 654481.4065 642957.1539 667728.603 639707.5255 863354.4427 0.711625585 0.829817504 0.757974985 0.723738432 0.893881226 0.758068036 0.744719807 0.773411904 0.740955851 1 19.71959344 -1.576655745 2.964640336 1.012634046 0.772685267 0.64305157 0.051279662 21235155.04 23320959.96 2118241.243 0.012068038 0.026506004 1.576655745 -0.239948778 DRENYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRENYDR 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 130.75 0.0032223 73827000 68768 69330 81129 67423 89696 100810 92665 81255 72028 70485 FALSE TRUE 71483.01374 81236.88819 83243.28839 80759.06816 74449.50596 77398.40529 85401.67517 80165.90963 69435.72635 84295.18623 0.848008255 0.963719185 0.987521258 0.958050771 0.88319997 0.91818298 1.01312636 0.951014088 0.823721133 1 16.36316263 DREPEREER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DREPEREER 9 2 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 0 ; 152.04 4.58E-05 134615000 41876 46969 50160 50045 53418 61686 55554 51454 51369 54423 FALSE TRUE 43529.29682 55035.56038 51467.21081 59943.75163 44338.02744 47360.36136 51199.53232 50764.34329 49520.23972 65086.14486 0.668795132 0.845580277 0.790755251 0.920990969 0.681220674 0.727656577 0.786642571 0.779956217 0.760841494 1 15.99006284 -1.883740888 2.464230641 1.115131301 0.777315988 0.482586319 0.070232212 16374335.92 8989812.221 10973751.52 0.017109418 0.013069504 1.883740888 -0.337815314 DREPHGYS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DREPHGYSPER 11 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 DREPHGY(0.005)S(0.995)PER;DREPHGY(0.001)S(0.999)PER 56.514 0.071772 627000000 277970 292740 309290 301910 307970 390460 316720 299510 303400 286460 TRUE FALSE 288944.4702 343015.8178 317350.3515 361626.8969 255621.3694 299781.5825 291894.6588 295495.5583 292480.6933 342586.3524 0.843420843 1.001253598 0.926336818 1.055578818 0.746151642 0.875054071 0.852032361 0.862543287 0.85374298 1 18.38610815 3.243488748 24.99998817 0.858092451 0.957668592 0.253745499 0.076519269 151.0544967 766280.8924 0.019822382 0.026023959 1751.817046 -3.243488748 0.099576141 DREPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREPSK 6 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 72.138 0.078785 38698000 74774 65384 75036 65793 92782 89627 89025 81674 84459 76644 FALSE TRUE 77726.13526 76613.19338 76991.4998 78806.65903 77010.94878 68812.48756 82046.98788 80579.29362 81419.33709 91660.92436 0.847974595 0.835832651 0.839959888 0.859762866 0.840172072 0.750728711 0.895114122 0.879101909 0.888266594 1 16.48401921 0.853424387 0.819796912 0.998835534 0.834570866 0.679112143 0.033667707 0.467838373 0.653086148 0.03275645 0.011617535 7.135499622 -0.853424387 -0.164264667 DREREPEAAS(ph)SRGSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREREPEAASSRGSPVR 17 3 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 DREREPEAAS(0.489)S(0.489)RGS(0.023)PVR 125.88 0.00025109 113960000 54150 54349 63728 36514 82883 72252 37647 61748 63604 85271 TRUE FALSE 56287.88381 63683.01797 65388.80403 43736.36022 68794.57727 55472.56799 34696.12977 60920.36906 61314.90446 101978.2198 0.551959859 0.624476659 0.641203623 0.428879424 0.674600688 0.543964859 0.340230785 0.597386081 0.601254901 1 16.63790153 0.633084694 2.149729799 0.999877563 0.548155405 0.666470796 0.094910087 1.330958724 7.066661387 0.090143513 0.024573889 4.296202014 -0.633084694 -0.451722158 DREREPEAASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DREREPEAASSR 12 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 54.898 0.0738 72223000 46929 125370 135840 140210 145340 186000 150920 141800 122490 132520 FALSE TRUE 48781.79316 146901.3223 139380.102 167943.1195 120635.1587 142804.3189 139090.496 139899.4029 118081.6088 158484.7568 0.307801167 0.926911365 0.879454307 1.059679953 0.761178306 0.901060277 0.877626965 0.882730969 0.745066032 1 17.27398456 4.740831484 24.99032747 0.888993102 0.307800965 0.79294103 0.089638703 83.95075975 923797.747 0.020065228 0.134507625 55059.40126 -4.740831484 -0.581192137 DREREPEAASSRGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DREREPEAASSRGSPVR 17 3 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 DREREPEAAS(0.192)S(0.005)RGS(0.804)PVR;DREREPEAAS(0.054)S(0.054)RGS(0.891)PVR;DREREPEAAS(0.088)S(0.022)RGS(0.89)PVR 168.81 1.13E-08 2222050000 535565 870610 949012 463055 1159008 983725 479312 804882 833109 1200873 TRUE FALSE 556709.5197 1020130.495 973744.0323 554645.8969 962000.2341 755269.7772 441742.273 794093.8733 803125.5698 1436161.072 0.387637244 0.710317606 0.678018679 0.386200342 0.669841463 0.525894896 0.307585466 0.552928142 0.559216919 1 20.45378613 0.605606126 2.837704318 0.999987559 0.52945641 0.546882467 0.128404961 4.23737239 29.56996326 0.121528508 0.031950049 4.032794818 -0.605606126 -0.470531149 DRES(ph)EKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRESEKDR 8 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 DRES(1)EKDR 60.342 0.073161 119100000 313850 134060 189240 122150 281840 340050 259290 191750 220280 125140 TRUE FALSE 326241.0403 157083.7622 194171.7499 146310.9054 233932.9375 261078.541 238966.1723 189179.9049 212352.1658 149658.787 2.179899001 1.049612691 1.297429664 0.977629903 1.563108602 1.744491895 1.596740004 1.264074824 1.418908773 1 17.19131746 0.504703964 1.18813241 1.000975703 1.441760896 0.145423374 0.330981317 3.977439838 7.384439021 0.310449572 0.094345647 3.19671533 -0.504703964 0.440785194 DRES(ph)RSPFLKPDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRESRSPFLKPDER 14 3 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 DRES(0.956)RS(0.044)PFLKPDER;DRES(0.917)RS(0.083)PFLKPDER 153.68 3.50E-05 1016360000 1941580 1498090 1993180 1022980 2947300 2454100 1711300 1860890 2157600 1740550 TRUE FALSE 2018235.078 1755375.304 2045123.908 1225322.391 2446318.999 1884172.467 1577163.834 1835947.813 2079948.397 2081577.448 0.969570015 0.843290893 0.982487541 0.588650877 1.175223627 0.905165681 0.75767723 0.881998321 0.999217396 1 20.98924581 1.237962304 21.44486685 0.999609044 0.883328856 0.0870416 0.143936773 6.214239074 222098.089 0.107161386 0.032978093 17.29666222 -1.237962304 -0.116280188 DRESEKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRESEKDR 8 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 111.06 0.0018598 99135000 207560 110260 179820 107040 252120 219100 202720 160670 179510 109610 FALSE TRUE 215754.6291 129196.2973 184506.2569 128212.1925 209264.7325 168217.3455 186830.2767 158516.4815 173049.4702 131085.9809 1.645901626 0.985584396 1.407520893 0.978077073 1.596392925 1.283259616 1.425249866 1.209255791 1.32012187 1 17.00015388 -0.047267172 0.987721453 0.996482024 1.30854799 0.167518815 0.210831862 15.1093194 12.42780983 0.376274569 0.058174972 0.896876878 0.047267172 0.312065966 DREVGIPPEQSLETAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DREVGIPPEQSLETAK 16 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ; 149.73 7.36E-07 163420000 295610 192667 256281 178177 312020 325850 296200 232504 252175 168785 FALSE TRUE 307280.9111 225756.0585 262959.8934 213419.8788 258982.9519 250176.2758 272983.07 229387.6642 243099.271 201855.1892 1.522283932 1.118406019 1.302715548 1.057292011 1.283013595 1.239384912 1.352370832 1.136397162 1.204325101 1 17.62296115 -5 0.149180541 0.151461144 1.313423577 0.30461604 0.121557484 173.1497026 1.538847095 43.51393514 0.587013125 1.00E-05 5 1.161962433 DRFGIDDQDYLVSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRFGIDDQDYLVSLTR 16 1 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;;; 254.53 1.27E-26 1210880000 549188 588820 572946 575373 743050 786680 670574 642483 603429 634716 FALSE TRUE 570870.3663 689945.2546 587877.4434 689180.0621 616746.6264 603985.4923 618012.6577 633871.5663 581711.7082 759076.4478 0.752059121 0.908927232 0.774464081 0.907919175 0.812496064 0.795684669 0.814163922 0.835056295 0.766341401 1 19.53388566 -1.245657166 5.330795649 1.000016903 0.822492048 0.529182659 0.0512201 9.22E-06 1.30E-06 0.04444182 0.010474041 0.05679928 1.245657166 -0.177524855 DRFPEAQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRFPEAQWR 9 1 B4DYU2;Q96MW5;H3BQV3;H3BSH5;A0A087X1T3 B4DYU2 COG8 Conserved oligomeric Golgi complex subunit 8 0 138.22 0.0013897 0 74374 92625 77218 98492 103570 120980 71858 81939 70314 110760 FALSE TRUE 77310.34295 108532.6232 79230.36452 117973.4236 85965.20839 92884.22847 66225.58219 80840.74173 67783.41288 132461.3014 0.583644749 0.819353442 0.598139711 0.890625582 0.648983571 0.701217846 0.499961736 0.610297052 0.511722384 1 17.01521141 -1.090324197 4.745742102 1.000016696 0.653495656 0.439143978 0.118118182 2.07E-05 3.97E-06 0.113486678 0.026747778 0.081222397 1.090324197 -0.346521041 DRFQLTDCQIYEVLSVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRFQLTDCQIYEVLSVIR 18 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 125.23 2.75E-05 20901000 25104 24089 23049 23196 29378 29379 30113 29726 26913 22088 FALSE TRUE 26095.1253 28226.09836 23649.67587 27784.09957 24384.33805 22556.17249 27752.66437 29327.57159 25944.40639 26415.7207 0.987863462 1.068534101 0.895287929 1.051801686 0.92309948 0.853891997 1.050611668 1.110231741 0.98215781 1 14.68910915 2.06671617 24.99995668 1.052394203 0.966027371 0.18957995 0.069847246 74.87821257 28057.50374 0.026307509 0.01942938 116.6047306 -2.06671617 -0.086366832 DRGDAYYDTDYRHS(ph)YEYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRGDAYYDTDYRHSYEYQR 19 2 B1AVT0;P49760-3;P49760;P49760-2 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 DRGDAYYDT(0.067)DYRHS(0.933)YEYQR;DRGDAYYDT(0.002)DYRHS(0.998)YEYQR 149.99 4.18E-08 782800000 232980 255510 221644 257740 275450 275460 285170 250260 246910 235340 TRUE FALSE 242178.2303 299391.8549 227420.2247 308720.2027 228629.1074 211488.5896 262817.6302 246905.674 238023.7573 281450.3671 0.860465143 1.063746542 0.80802959 1.096890389 0.812324779 0.751424103 0.933797433 0.877261865 0.845704199 1 18.102521 DRGEEDADGSK ddPTM_MDA-MB-175_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 92.039 0.0093874 118300000 224580 126870 179240 147180 216810 267100 261810 190810 185480 101630 FALSE TRUE 233446.5918 148658.9356 183911.1416 176291.7647 179956.7136 205070.0729 241288.6481 188252.5041 178804.611 121542.4527 1.920700024 1.223102976 1.513143248 1.450454231 1.480607884 1.687230004 1.985221153 1.548862146 1.47112887 1 16.89110078 2.7633186 23.14006833 1.607072996 1.49726251 0 0.282313919 1265.01005 1182338.091 0.0821544 0.087088898 579.8539232 -2.7633186 -0.109810486 DRGFGAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DRGFGAPR 8 1 P17844;P17844-2;J3QRQ7;J3KRX8;J3QR02;X6RLV5;J3QKN9 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 103.87 0.0042765 453565000 546891 658600 632500 603910 803010 845960 669750 685510 598610 822140 FALSE TRUE 568482.679 771709.4268 648983.4696 723361.5955 666514.647 649498.6106 617253.2449 676321.8597 577066.143 983222.5922 0.578183093 0.784877639 0.660057524 0.735704815 0.677887848 0.660581455 0.627785864 0.687862408 0.586913022 1 19.90715854 -1.694524546 2.838955223 1.044554257 0.671666808 0.73854759 0.059434137 11537267.39 11020968.07 3705706.37 0.014076924 0.020205772 1.694524546 -0.372887449 DRGQYQDHAIDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRGQYQDHAIDRR 13 2 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 120.53 0.00015787 78872000 24005 29113 25341 20615 37689 31582 25677 28036 24974 32949 FALSE TRUE 24952.73594 34112.93128 26001.40728 24692.58547 31282.63724 24247.55913 23664.36965 27660.22328 24075.19062 39404.7257 0.633242219 0.865706604 0.659855051 0.626640207 0.793880345 0.615346477 0.600546488 0.70195193 0.610972166 1 15.26608104 -1.814974181 7.292145667 1.01424256 0.681709797 0.574707495 0.082886418 0.018277534 0.000463761 0.076429045 0.018228753 0.015311785 1.814974181 -0.332532762 DRGS(ph)WAQPVDTGVSEASLGDGEPHIPSLLSMSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRGSWAQPVDTGVSEASLGDGEPHIPSLLSMSTR 34 1 Q9NX05;F8W881 Q9NX05 FAM120C Constitutive coactivator of PPAR-gamma-like protein 2 1 DRGS(1)WAQPVDTGVSEASLGDGEPHIPSLLSMSTR;DRGS(1)WAQPVDTGVSEASLGDGEPHIPSLLSMSTR 228.94 5.93E-37 159697000 24281.6 27710 35236 30743 36444 34293 24019.1 25636.6 25529 28900 TRUE FALSE 25240.25632 32468.97695 36154.27911 36823.87364 30249.2619 26328.97047 22136.42018 25292.98331 24610.21628 34562.40168 0.730280741 0.939430577 1.046058068 1.065431563 0.875207174 0.761780698 0.640476909 0.731806301 0.712051683 1 15.07691585 2.845943752 3.42505735 0.73963693 0.953227754 0.298093905 0.122844462 0.254700316 5.584230756 0.038837522 0.041344286 701.3644542 -2.845943752 0.213590824 DRGVAASAGSSGENKK ddPTM_MDA-MB-175_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 83.106 0.0045744 27370000 49246 38318 51696 36676 67442 62300 67748 56736 63570 37660 FALSE TRUE 51190.27011 44898.81843 53043.24023 43930.40333 55978.23293 47831.76917 62437.73473 55975.54672 61282.12812 45038.75596 1.136582684 0.996892953 1.177724364 0.975391136 1.242890301 1.062013551 1.386311265 1.242830658 1.360653216 1 15.45887936 2.256377463 24.97651791 1.269258429 1.098517417 0.253977909 0.122735217 265.3369736 371961.3996 0.038900001 0.032481032 180.4585498 -2.256377463 -0.170741012 DRGYIYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRGYIYWR 8 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 78.264 0.028341 207210000 109760 109040 108540 98906 163700 152920 125020 134780 127540 147450 FALSE TRUE 114093.4096 127766.7718 111368.6416 118469.3116 135874.3325 117406.6475 115220.6057 132973.4946 122949.8603 176340.0044 0.647008091 0.724547854 0.631556305 0.671823231 0.77052472 0.665797009 0.653400266 0.754074465 0.697231809 1 17.42800028 -5 0.282882148 3.299110476 0.673720309 0.828943589 0.042475478 87.00183464 0.829493493 117.5171008 0.046101463 1.00E-05 5 -2.625390167 DRHDDYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRHDDYYR 8 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 119.75 0.0038673 0 36132 49971 41694 44883 66474 59409 32984 38617 39658 69543 FALSE TRUE 37558.51926 58553.13053 42780.57989 53760.72344 55174.77322 45612.1601 30398.62789 38099.40228 38230.71633 83168.61937 0.451594839 0.704029127 0.514383673 0.646406347 0.663408551 0.54842993 0.365505982 0.45809829 0.459677179 1 16.34375166 -1.800902791 2.753141593 1.132047163 0.533465668 0.649121637 0.102644517 24146595.34 18619450.41 21337225.32 0.026527926 0.01581602 1.800902791 -0.598581495 DRHEASGFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRHEASGFAR 10 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 79.82 0.022273 0 8941.1 33751 17332 30770 22862 34655 22209 28046 21623 48709 FALSE TRUE 9294.101532 39547.4717 17783.68616 36856.21416 18975.92541 26606.90145 20468.20055 27670.08924 20844.79245 58252.59596 0.159548281 0.678896297 0.305285728 0.63269651 0.325752442 0.456750485 0.351369758 0.475001822 0.357834567 1 15.83003472 -1.473343799 2.941686423 1.016158052 0.426204118 0.586397425 0.146934835 24699610.4 28498960.69 3269683.884 0.031710145 0.033624528 1.473343799 -0.589953934 DRIELLQDAEPLDFNAETFTDDPLESESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRIELLQDAEPLDFNAETFTDDPLESESGR 30 1 Q68DH5 Q68DH5 LMBRD2 LMBR1 domain-containing protein 2 0 175.46 3.16E-13 44170000 27301 34874 31533 34357 39202 41193 29075 33164 30121 36053 FALSE TRUE 28378.86456 40863.33822 32354.77588 41152.71205 32538.45804 31626.55004 26796.02553 32719.49083 29036.95109 43116.89507 0.658184327 0.947733786 0.750396702 0.954445166 0.7546568 0.733507132 0.621473914 0.75885545 0.673447173 1 15.39596567 3.023314674 24.97213588 0.733968185 0.833719551 0.056118101 0.123709135 447.3533695 479152.7108 0.032724106 0.039110851 1055.151144 -3.023314674 0.099751366 DRISSLPVSRPIS(ph)PSPSAILER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 DRISSLPVS(0.008)RPIS(0.613)PS(0.379)PSAILER;DRISSLPVS(0.003)RPIS(0.982)PS(0.015)PSAILER 130.57 7.01E-06 163031000 106526 160210 133100 111781 176392 190583 110381 176225 132653 195433 TRUE FALSE 110731.7287 187724.8212 136568.6953 133890.9482 146408.9508 146322.9866 101729.0488 173862.9921 127878.8444 233724.3546 0.473770604 0.80318896 0.58431521 0.57285835 0.626417179 0.626049377 0.43525224 0.74388051 0.547135298 1 17.83444855 -1.58651441 2.908594803 1.024441939 0.610111441 0.5620476 0.105298046 25301747.23 26813046.29 4766583.977 0.024211176 0.025911084 1.58651441 -0.414330498 DRLEFWCTDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRLEFWCTDVK 11 1 Q9UNM6;J3KNQ3;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 150.21 3.10E-05 323310000 239870 172128 224641 155517 298330 288430 261610 200705 235761 165341 FALSE TRUE 249340.2528 201689.645 230495.329 186277.7984 247619.9732 221446.5037 241104.3246 198014.8778 227276.0077 197736.4033 1.260972935 1.019992483 1.165669675 0.942051111 1.252273072 1.119907614 1.219321888 1.001408312 1.149388802 1 17.59321897 0.570418374 0.777163508 1.000938427 1.125311015 0.112801909 0.103111958 3.14873479 3.205580666 0.098693758 0.033315876 3.718933173 -0.570418374 0.124372589 DRLGS(ph)YSGPTSVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRLGSYSGPTSVSR 14 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 DRLGS(0.909)YS(0.009)GPT(0.005)S(0.026)VS(0.052)R;DRLGS(0.5)YS(0.5)GPTSVSR 191.83 1.17E-06 380420000 340000 367580 407100 392530 571510 492270 420900 445500 427930 466420 TRUE FALSE 353423.4625 430709.0056 417709.3604 470171.2624 474364.9343 377947.7529 387908.7582 439528.8012 412528.8829 557806.0688 0.633595585 0.772148296 0.748843341 0.842893774 0.850411928 0.677561206 0.695418677 0.787959877 0.739556104 1 19.08940411 -1.127357198 3.776898385 1.000122003 0.754168128 0.568078299 0.065345236 24963126.47 51471925.99 39794.5744 0.015903571 0.074583507 1.127357198 -0.245953875 DRLPQEPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRLPQEPGR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 ; 164.48 9.33E-05 103790000 169470 187612 180738 246334 275370 317900 246523 189360 177679 250317 FALSE TRUE 176160.8065 219832.9016 185448.1808 295058.13 228562.7058 244072.5428 227199.8831 186821.9389 171284.3675 299361.8235 0.588454481 0.734338464 0.619478391 0.985623773 0.763499845 0.815309514 0.758947418 0.624067347 0.572165033 1 18.19153073 4.844382158 1.431985262 0.757198906 0.498744019 0.136019736 0.135740682 3.604741087 5.575160371 0.037027589 1.428760233 69884.70852 -4.844382158 -0.258454887 DRLQYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRLQYFR 7 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 129.68 0.0033167 1165140000 691284 685718 727396 646017 1080070 960770 780630 762280 742950 915070 FALSE TRUE 718576.4261 803484.7324 746352.5373 773797.2344 896480.0872 737645.7281 719442.1808 752062.8834 716211.3746 1094360.446 0.656617688 0.734204836 0.681998824 0.707077122 0.819181733 0.674042753 0.657408794 0.687216799 0.654456561 1 20.06165656 -1.766599249 2.807797059 1.066703376 0.69825766 0.787641007 0.047208347 10890116.46 7943674.659 4979631.571 0.012121446 0.01711594 1.766599249 -0.368445715 DRLSASSLTMESFAFLWAGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 224.97 2.72E-25 1488542000 846278 929004.3 1029287 897648 1202265 1285903 990187 1006353 1103977 963741 FALSE TRUE 879689.7089 1088553.562 1056111.065 1075200.095 997904.4247 987271.5163 912573.5556 992864.4841 1064245.083 1152567.597 0.763243485 0.944459626 0.916311605 0.932873784 0.86580989 0.85658448 0.791774433 0.861437096 0.923368908 1 20.13641994 0.967707285 3.552162352 0.999661222 0.868897711 0.370628422 0.054241962 0.254460769 8.622075035 0.052971492 0.013686851 9.283404736 -0.967707285 -0.130763511 DRNVATPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRNVATPR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 153.05 0.00040799 446327000 191641 276646 217285 261843 301663 345105 233716 272711 234405 307018 FALSE TRUE 199207.1347 324157.7985 222947.6256 313634.7639 250386.431 264959.5939 215396.7292 269055.7551 225968.8098 367172.2989 0.542544019 0.882849277 0.60720165 0.854189613 0.681931703 0.72162196 0.586636655 0.732777924 0.615429896 1 18.48609769 -0.869192981 5.243789213 1.000000355 0.698201169 0.431426664 0.105945214 3.91E-07 8.42E-08 0.091142546 0.021482479 0.13514719 0.869192981 -0.301799186 DRNVATTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRNVATTR 8 1 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 87.308 0.017416 0 9001.3 19766 15953 20076 17084 22743 11355 16132 17289 28346 FALSE TRUE 9356.678275 23160.65674 16368.74829 24046.97288 14180.06778 17461.28292 10464.96543 15915.77693 16666.77227 33899.85598 0.276009381 0.683208116 0.482855983 0.709353246 0.418292862 0.51508428 0.308702357 0.469493939 0.491647288 1 15.04899152 -1.319763446 3.471866675 1.00222784 0.486375701 0.584977293 0.130410283 68069491.04 101134546 1568732.267 0.029663686 0.047889087 1.319763446 -0.515852139 DRNVIPDT(ph)PPSTPLVPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DRNVIPDTPPSTPLVPSR 18 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 DRNVIPDT(1)PPSTPLVPSR;DRNVIPDT(0.778)PPS(0.111)T(0.111)PLVPS(0.001)R;DRNVIPDT(1)PPSTPLVPSR 156.92 1.31E-08 438398000 206768 230338 233923 219725 260180 302589 251896 244994 243241 247664 TRUE FALSE 214931.3603 269896.7597 240019.2255 263185.9492 215954.6965 232317.2905 232151.7333 241710.2562 234486.8039 296189.019 0.725656073 0.911231485 0.810358285 0.888574297 0.729111083 0.78435484 0.783795882 0.816067581 0.791679599 1 18.17615863 -1.409108962 5.157757175 1.000172687 0.807277226 0.520658047 0.056209002 0.000105369 1.21E-05 0.051377919 0.012099102 0.038984416 1.409108962 -0.192895461 DRPFFAGLVK ddPTM_MDA-MB-175_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 ; 162.38 6.19E-06 6085700000 2626300 2157300 2479300 1923940 5678000 3836500 3459900 2622000 2948600 3950100 FALSE TRUE 2729988.352 2527799.494 2543912.595 2304489.59 4712855.588 2945531.018 3188703.997 2586856.379 2842480.462 4724046.466 0.577891935 0.535092005 0.538502873 0.48782111 0.997631082 0.623518638 0.674994207 0.547593339 0.601704594 1 22.17159172 DRPFFPGLVK ddPTM_MDA-MB-175_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 ; 139.86 3.68E-05 17965900000 16542900 13511500 16573900 12738300 27211600 21927700 19626200 15093600 16660800 16796100 FALSE TRUE 17196026.47 15831995.02 17005829.45 15257897.72 22586181.95 16835323.99 18087847.16 14891294.98 16061181.06 20086974.21 0.856078486 0.788172218 0.846609811 0.759591642 1.124419323 0.838121452 0.900476446 0.741340872 0.799581903 1 24.25975693 DRPFMGGQKPNLADLAVYGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRPFMGGQKPNLADLAVYGVLR 22 2 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 108.25 0.0002407 259130000 83708 222980 216810 215990 185710 252390 157800 180720 179430 221750 FALSE TRUE 87012.85648 261275.0805 222460.2467 258712.1773 154143.0805 193776.2475 145431.2237 178297.744 172972.3493 265197.6668 0.328105664 0.98520882 0.838846923 0.975544696 0.581238449 0.730686095 0.548388021 0.672320183 0.652239333 1 18.01670856 3.211282024 24.97023859 0.672212983 0.800512733 0.027291249 0.205975313 545.2464159 499105.4041 0.056267512 0.067267606 1626.604703 -3.211282024 0.12829975 DRPGGSMVVSDVVPGGPAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRPGGSMVVSDVVPGGPAEGR 21 1 O95049;O95049-4;O95049-3;K7ESC0 O95049 TJP3 Tight junction protein ZO-3 0 92.95 0.0016347 186700000 147410 96395 195140 102070 179170 157450 202340 127320 165970 97086 FALSE TRUE 153229.8606 112950.0914 200225.5087 122259.1414 148714.7474 120884.6237 186480.0621 125613.4837 159996.7721 116108.1429 1.319716747 0.972800775 1.724474303 1.052976461 1.28082961 1.041138207 1.606089439 1.081866272 1.377997857 1 16.82510963 -1.245246829 4.727171691 0.999928178 1.265546895 0.106750324 0.236089189 0.000160004 2.55E-05 0.204654452 0.048224502 0.056852972 1.245246829 0.265618717 DRPGS(ph)PES(ph)PLLDAPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 2 DRPGS(1)PES(1)PLLDAPFSR;DRPGS(1)PES(1)PLLDAPFSR 88.836 0.0023886 182009000 65682 75784 69438 67820 85030 106621 86029 82904 85748 71018 TRUE FALSE 68275.17608 88799.31248 71247.61132 81234.59358 70576.63097 81859.88861 79285.82219 81792.80748 82661.94623 84932.61738 0.803874627 1.045526621 0.838872197 0.956459321 0.830972048 0.96382157 0.93351441 0.963031754 0.973265028 1 16.37403109 1.756349576 0.915200778 0.994277581 0.905555368 0.208607572 0.06720792 0.887829632 1.396083122 0.053885682 0.022858029 57.06233981 -1.756349576 -0.088722213 DRPGS(ph)PESPLLDAPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 DRPGS(1)PESPLLDAPFSR;DRPGS(0.994)PES(0.006)PLLDAPFSR;DRPGS(0.997)PES(0.003)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR;DRPGS(0.997)PES(0.003)PLLDAPFSR;DRPGS(1)PESPLLDAPFSR 251.55 6.17E-23 2939790000 1372188 1418626 1460610 1280840 1668170 1825970 1525690 1363600 1464730 1276800 TRUE FALSE 1426363.042 1662263.98 1498674.697 1534186.329 1384615.059 1401916.14 1406102.431 1345323.172 1412014.653 1526964.514 0.934116693 1.088606817 0.981473166 1.004729524 0.906776187 0.918106562 0.920848139 0.881044163 0.924720018 1 20.5422351 3.243062176 24.84412192 0.916203377 1.006918492 0.393044886 0.045902056 85.69718758 472958.8557 0.012004283 0.015718002 1750.097226 -3.243062176 0.090715116 DRPMEESLLLFEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRPMEESLLLFEAMR 15 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3;A0A0U1RQQ5 P47897 QARS Glutamine--tRNA ligase 0 ;;;;; 224.07 1.08E-12 791065000 267074 340495 328696 332945 405454 426500 374957 351142 354772 335688 FALSE TRUE 277618.2877 398972.3676 337262.0878 398800.5273 336535.0739 327451.8387 345566.8906 346435.5158 342003.825 401459.6365 0.691522291 0.993804436 0.840089656 0.993376397 0.838278729 0.815653204 0.860776176 0.862939843 0.851900899 1 18.61489542 -0.996860391 5.191552086 1.000000831 0.865965033 0.203571575 0.081980523 7.15E-07 1.38E-07 0.072022415 0.016975741 0.100725541 0.996860391 -0.134035798 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 281.04 2.57E-53 2114760000 1010031 1024863 1050939 1178478 1205590 1382143 1253669 1102222 1085472 924492 FALSE TRUE 1049907.804 1200875.248 1078327.334 1411577.431 1000664.242 1061161.235 1155403.148 1087448.517 1046406.075 1105628.507 0.94960269 1.086147147 0.975307101 1.276719461 0.905063714 0.959781001 1.045019318 0.983556873 0.946435505 1 20.07643529 DRPVGGS(ph)PGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 DRPVGGS(1)PGGPR;DRPVGGS(1)PGGPR 132.88 0.00018032 3747100000 705790 744850 876140 765990 908590 1081630 977050 828610 854960 777700 TRUE FALSE 733655.1342 872772.1934 898972.9282 917500.5357 754148.1963 830437.8248 900466.268 817503.8383 824190.1566 930075.425 0.788812514 0.938388619 0.966559167 0.98647971 0.810846278 0.892871484 0.968164779 0.878965099 0.886154106 1 19.82698819 -1.723638573 2.782636915 1.016088011 0.905459179 0.179336469 0.062533985 18650470.57 18774878.2 2112669.542 0.015544578 0.018895632 1.723638573 -0.110628832 DRPYDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRPYDYK 7 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 72.879 0.045972 333280000 376630 791540 669040 775230 746240 875610 597440 715110 616170 851150 FALSE TRUE 391499.6432 927480.8377 686475.732 928568.1802 619394.3914 672262.8475 550611.0917 705525.1201 593994.1621 1017916.546 0.384608782 0.911156068 0.67439294 0.912224272 0.608492311 0.660430219 0.540919679 0.693107036 0.583539156 1 19.95718786 -1.137051472 4.654495382 1.000027859 0.672707064 0.308279814 0.150744528 4.58E-05 8.49E-06 0.135597172 0.031957488 0.072937106 1.137051472 -0.327320795 DRQS(ph)PLHGNHITISHTQATGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRQSPLHGNHITISHTQATGSR 22 1 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 DRQS(1)PLHGNHITISHTQATGSR 135.47 3.00E-06 306960000 31205 27641 37309 34273 44911 46810 33348 43408 33960 41418 TRUE FALSE 32436.9975 32388.12673 38281.30319 41052.09711 37277.04426 35939.08691 30734.09662 42826.18676 32737.78623 49533.0641 0.65485546 0.653868831 0.772843431 0.828781701 0.752568914 0.725557515 0.620476386 0.864597972 0.660927944 1 15.59610425 -5 0.306426091 3.301333472 0.720707593 0.523904574 0.077405856 233.8672374 2.135028467 346.856201 0.074736728 1.00E-05 5 -2.580625879 DRRPVHLDQAAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRRPVHLDQAAFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 127.02 0.00010226 150960000 55756 56581 48740 48143 79718 63286 58934 61688 53797 66792 FALSE TRUE 57957.28993 66298.34661 50010.20444 57665.54171 66167.56283 48588.78561 54314.59908 60861.17326 51860.85648 79878.61359 0.725567049 0.829988699 0.626077522 0.721914654 0.828351418 0.608282786 0.679964219 0.761920751 0.649245826 1 16.28552167 -1.579804789 6.193270604 1.000705496 0.717591724 0.578494676 0.073046855 0.000681124 4.62E-05 0.067701115 0.015919157 0.026314505 1.579804789 -0.283113773 DRS(ph)FSEHDLAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRSFSEHDLAQLR 13 1 Q8WWL2-4;Q8WWL2-3;Q8WWL2-2;Q8WWL2 Q8WWL2-4 SPIRE2 Protein spire homolog 2 1 DRS(0.899)FS(0.101)EHDLAQLR;DRS(0.913)FS(0.087)EHDLAQLR 173.37 6.37E-06 176360000 48112 83115 80548 76239 87388 95166 71085 71307 80920 108116 TRUE FALSE 50011.49891 97389.35471 82647.14705 91318.84665 72533.81897 73065.13875 65513.17195 70351.2463 78007.70501 129299.2602 0.386788748 0.753208909 0.63919273 0.706259622 0.560976288 0.565085513 0.50667863 0.544096279 0.603311302 1 16.9803545 -1.360833215 2.207293378 1.016008254 0.587271335 0.62139676 0.097150769 216041.6456 191316.0777 22107.01519 0.024784016 0.043567916 1.360833215 -0.42873692 DRS(ph)PAAET(ph)PPLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR;DRS(1)PAAET(1)PPLQR 133.48 0.00024461 6482160000 1581530 1539030 1669740 1638940 1974960 2269230 1754690 1772610 1725330 1507150 TRUE FALSE 1643970.026 1803346.431 1713254.796 1963117.44 1639257.005 1742235.723 1617152.813 1748851.062 1663235.71 1802447.186 0.912076669 1.000498902 0.950515948 1.089140062 0.909461879 0.966594603 0.897198445 0.970264802 0.922765295 1 20.78152556 DRS(ph)PHRS(ph)SPSDTRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(0.853)PHRS(0.587)S(0.51)PS(0.049)DT(0.001)RPK;DRS(0.996)PHRS(0.653)S(0.346)PS(0.005)DTRPK;DRS(0.971)PHRS(0.563)S(0.462)PS(0.005)DTRPK;DRS(0.996)PHRS(0.53)S(0.471)PS(0.003)DTRPK;DRS(0.735)PHRS(0.662)S(0.601)PS(0.003)DTRPK 126.22 0.00012295 1429887000 270364.1 929344 1048144 916743 1247425 1316034 1068868 1220861 1099746 886273 TRUE FALSE 281038.2834 1088951.603 1075459.494 1098072.029 1035388.144 1010405.048 985087.3332 1204497.355 1060166.356 1059921.226 0.265150161 1.027389184 1.014659833 1.035993999 0.976853863 0.953283153 0.929396741 1.136402712 1.000231273 1 20.01552562 4.739234077 24.9991997 1.012897806 0.265149931 0.946369347 0.053058743 11.99447021 445151.3619 0.013608028 0.081496823 54857.25555 -4.739234077 -0.747747876 DRS(ph)PLRR ddPTM_MDA-MB-175_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 64.82 0.056909 13457080000 854870 943807 985176 922048 1056702 1086522 979667 815138 898810 688538 TRUE FALSE 888620.9277 1105898.51 1010850.496 1104426.342 877084.1715 834193.7319 902878.1407 804212.4084 866462.0037 823443.8382 1.079151833 1.343016316 1.227588876 1.341228498 1.065141459 1.013054799 1.096465962 0.976645123 1.052241772 1 19.65131073 3.130511804 6.113776331 1.029249959 1.252298435 0.663642114 0.074826929 0.115436059 5.828382977 0.020360231 0.024496184 1350.553536 -3.130511804 0.223048476 DRS(ph)PLRRS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRSPLRRSPPR 11 3 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 2 DRS(1)PLRRS(1)PPR 85.734 0.021527 468720000 29086 24360 37835 18873 41612 41369 33975 35055 38995 37591 TRUE FALSE 30234.33774 28543.64051 38821.01118 22606.02307 34538.8071 31761.6767 31311.95072 34585.14506 37591.57757 44956.23673 0.672528217 0.634920594 0.863528934 0.502845094 0.768276209 0.706502123 0.696498484 0.769306943 0.836181591 1 15.45623365 0.968087926 0.946319425 1.000505852 0.687259364 0.555219919 0.086536063 0.43293509 0.825753784 0.07579655 0.025673832 9.291544824 -0.968087926 -0.313246488 DRS(ph)SPPPGYIPDELHQVAR ddPTM_MDA-MB-175_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(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR 183.49 1.63E-14 2222950000 564558 642900 637410 631980 686880 817620 659250 674530 649660 658460 TRUE FALSE 586847.1858 753313.0739 654021.4282 756983.7577 570124.3829 627740.1462 607576.2624 665489.0287 626278.8635 787472.63 0.745228676 0.956621278 0.830532267 0.961282626 0.723992633 0.79715805 0.771552228 0.845094805 0.795302388 1 19.58687026 5.036950593 14.94567407 0.842486591 0.398358784 0.111395054 0.086863649 1985189.44 24094414.98 0.019683956 22986363.27 108880.6219 -5.036950593 -0.444127807 DRS(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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)APNVHINTIEPVNIDDLIR 243.24 6.89E-38 1635948000 415328 433189 493065 402622 612596 586308 480500 485102 482406 509578 TRUE FALSE 431725.4701 507585.841 505914.679 482259.4299 508467.1507 450146.8526 442837.1544 478600.0012 465044.3023 609420.0526 0.708420191 0.832899802 0.830157585 0.791341584 0.834345947 0.738647917 0.726653402 0.785336812 0.763093207 1 19.21707745 -1.655562266 7.171393038 1.000742145 0.780927897 0.704618785 0.042912438 0.000513064 2.46E-05 0.041866222 0.009836124 0.022102313 1.655562266 -0.219814248 DRSFS(ph)EGGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRSFSEGGER 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 DRS(0.207)FS(0.793)EGGER;DRS(0.001)FS(0.999)EGGER 132.24 0.00013855 151433000 51183 69109 69161 67233 93351 106083 74719 95103 79765 99141 TRUE FALSE 53203.74436 80977.93316 70963.39248 80531.48673 77483.23036 81446.83095 68862.32954 93828.29984 76894.27323 118565.7808 0.448727652 0.682978956 0.598514951 0.679213566 0.653504155 0.686933704 0.580794299 0.791360705 0.64853681 1 16.85532817 -5 0.139065719 2.217212482 0.519880945 0.704916118 0.074170917 71.38030461 0.610242719 24.0230095 0.427857394 1.00E-05 5 -1.697331537 DRSFS(ph)ENGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRSFSENGDR 10 1 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 DRS(0.024)FS(0.976)ENGDR;DRS(0.056)FS(0.944)ENGDR 96.707 0.0039709 183672000 132131 198102 193414 186307 213921 262110 205439 222840 202180 252390 TRUE FALSE 137347.6339 232124.4775 198454.5277 223157.9685 177558.7848 201238.9248 189336.1544 219853.1943 194903.5813 301840.9882 0.455033078 0.769029014 0.65748038 0.739322946 0.588252728 0.666705095 0.627271185 0.72837422 0.645716085 1 18.2034292 -5 0.310092475 4.016015956 0.644870906 0.61001909 0.083610285 186.440758 1.688867744 367.1843759 0.07211143 1.00E-05 5 -3.371145049 DRSPAAET(ph)PPLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;DRSPAAET(1)PPLQR;DRS(0.001)PAAET(0.999)PPLQR;DRS(0.001)PAAET(0.999)PPLQR 148.55 7.00E-05 8494570000 1854860 1945310 1997830 1830500 2249140 2531850 2151130 2001880 1986590 1929340 TRUE FALSE 1928091.305 2279401.86 2049895.091 2192567.437 1866831.986 1943866.208 1982518.81 1975048.073 1915093.014 2307357.234 0.835627564 0.987884246 0.88841687 0.950250531 0.809078004 0.842464348 0.859216241 0.855978452 0.829994154 1 21.13780995 3.248299062 24.9999255 0.857337654 0.918774193 0.125720167 0.061039083 316.0514031 811342.2698 0.015437044 0.020647161 1771.328304 -3.248299062 0.06143654 DRSPHRS(ph)S(ph)PSDTRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRSPHRSSPSDTRPK 15 3 A0A0D9SGE8;Q8IWS0-3;Q5JRC6;Q8IWS0-2;Q8IWS0-4;Q8IWS0-5;Q8IWS0 A0A0D9SGE8;Q8IWS0-5 PHF6 PHD finger protein 6 2 DRS(0.549)PHRS(0.73)S(0.696)PS(0.021)DT(0.005)RPK;DRS(0.521)PHRS(0.761)S(0.717)PS(0.001)DTRPK 99.569 0.0035772 861069000 182179 589875 594642 475443 672220 745487 557534 593422 605453 510738 TRUE FALSE 189371.5676 691181.4427 610138.859 569484.2063 557956.2845 572358.9422 513833.0282 585468.1487 583662.8648 610807.3324 0.310034863 1.131586682 0.99890559 0.932346709 0.913473455 0.937053162 0.841235855 0.958515259 0.955559689 1 19.22035786 4.748382518 24.98017384 0.954292648 0.310034511 0.883041951 0.071245347 432.8265812 1100791.246 0.01742467 0.23194908 56025.08421 -4.748382518 -0.644258137 DRSSS(ph)APNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRSSSAPNVHINTIEPVNIDDLIR 24 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 DRS(0.202)S(0.202)S(0.596)APNVHINTIEPVNIDDLIR 92.065 0.0053298 191510000 70891 64172 67572 60515 79307 87439 62301 59274 77287 55672 TRUE FALSE 73689.83142 75193.04181 69332.98183 72484.68638 65826.42447 67132.6174 57417.68483 58479.52898 74505.45597 66579.8625 1.106788579 1.129366133 1.041350631 1.088687835 0.988683695 1.008302133 0.862388156 0.878336584 1.119038898 1 16.02279827 3.134635098 1.441596643 0.946989881 1.100262826 0.362107863 0.071815063 0.377783701 1.637820583 0.026658893 0.035860988 1363.437072 -3.134635098 0.153272945 DRT(ph)PPHLLYSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRTPPHLLYSDR 12 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 DRT(0.988)PPHLLYS(0.011)DR;DRT(1)PPHLLYSDR 102.5 0.0037941 380140000 115984 94724 118100 105701 131728 167394 158649 97796 99132 94560 TRUE FALSE 120563.1379 110992.1101 121177.783 126608.3423 109336.9216 128519.2804 146213.6768 96485.20458 95564.25868 113087.2215 1.066107525 0.981473491 1.071542667 1.119563648 0.966837103 1.136461562 1.292928368 0.853192812 0.845049134 1 16.78707639 1.61573882 24.99995032 0.886837551 1.083111965 0.462830291 0.09389332 0.541589038 1714.614987 0.044917207 0.024336693 41.27991745 -1.61573882 0.196274414 DRT(ph)PPHLLYSDRDR ddPTM_MDA-MB-175_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(0.999)PPHLLYS(0.001)DRDR 128.14 0.0035969 4623260000 1729379 2695634 2459691 2542927 2603890 3201240 2266901 2612740 2606540 2987746 TRUE FALSE 1797656.218 3158588.17 2523792.568 3045910.371 2161281.708 2457800.525 2089215.376 2577720.494 2512731.135 3573137.625 0.503102989 0.883981672 0.706323918 0.852446978 0.604869427 0.687854984 0.584700506 0.721416515 0.703228198 1 21.76876005 -1.534927614 3.838446485 1.004938301 0.698884572 0.414176305 0.108973931 0.004345924 0.000526559 0.099571118 0.02313492 0.029179133 1.534927614 -0.306053728 DRT(ph)PPLLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 89.959 0.019003 1603830000 540344 619270 589450 592340 675820 893260 740310 602380 578150 546680 TRUE FALSE 561677.1984 725624.8052 604811.5512 709503.084 560944.3578 685813.9025 682282.5678 594306.0814 557342.4944 653791.4792 0.859107554 1.109871921 0.925083257 1.085213109 0.857986645 1.048979567 1.04357825 0.909014725 0.852477452 1 19.31847105 1.640517984 7.828382463 0.909949275 0.992729295 0.108182486 0.089477681 0.211718698 26.09759513 0.041282765 0.02109344 43.70367763 -1.640517984 0.082780021 DRTDIQCLIPCAIDQDPYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRTDIQCLIPCAIDQDPYFR 20 1 P23381;P23381-2;H0YJP3 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;; 156.87 1.22E-08 1446860000 1046430 1132340 1119070 1040750 1236690 1408960 1112120 1167880 1193290 1117610 FALSE TRUE 1087743.864 1326810.587 1148233.884 1246607.244 1026477.876 1081750.393 1024949.128 1152226.479 1150343.726 1336584.282 0.813823624 0.992687558 0.859080792 0.932681359 0.767985895 0.809339454 0.766842123 0.862067955 0.860659325 1 20.35011938 DRVDCGYPHVTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRVDCGYPHVTPK 13 1 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;;;; 124.07 0.00012984 5000240000 2760770 2269150 2592280 1892330 3015610 2886400 2437170 2240920 2292620 1897830 FALSE TRUE 2869767.331 2658858.861 2659836.946 2266627.226 2503017.689 2216077.344 2246138.247 2210884.133 2210109.054 2269673.452 1.264396571 1.171471983 1.17190292 0.998657857 1.102809608 0.976385983 0.989630576 0.974097895 0.973756402 1 21.11405332 4.312259293 0.590298955 0.974498655 1.366462146 0.862866522 0.037515091 0.754191772 0.281051132 0.018568623 0.188864382 20523.8718 -4.312259293 0.391963491 DRVEISPEQLSAASTEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRVEISPEQLSAASTEAER 19 1 X6RJS7;P46736-2;P46736-3;P46736;A0A0A0MS96;P46736-5 X6RJS7 BRCC3 Lys-63-specific deubiquitinase BRCC36 0 114.75 0.00013809 107790000 35615 86040 73621 85851 66666 98329 59628 76939 71878 146080 FALSE TRUE 37021.1077 100816.7007 75539.62374 102832.0716 55334.13713 75493.57994 54954.20155 75907.75855 69291.12482 174701.5791 0.21191055 0.577079504 0.432392335 0.588615581 0.316735186 0.432128778 0.314560417 0.434499556 0.396625635 1 17.41453312 -1.144346377 3.630348793 1.000453016 0.417185653 0.723629209 0.10903733 58003484.78 97817526.86 309135.7997 0.025147082 0.071722203 1.144346377 -0.583267363 DRVGQNLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRVGQNLPR 9 1 A2A2Q9;Q9Y312 A2A2Q9 AAR2 Protein AAR2 homolog 0 72.928 0.041372 47499000 54768 46795 54373 45385 52439 61082 50507 51560 56133 55255 FALSE TRUE 56930.28293 54831.67724 55790.00505 54362.01754 43525.43751 46896.63121 46548.12936 50868.92254 54112.78429 66081.15933 0.861520644 0.82976264 0.844264925 0.822655324 0.658666373 0.709682331 0.704408486 0.769794644 0.818883701 1 16.01195138 3.455696949 24.97787716 0.756517067 0.841943998 0.084926716 0.088527059 388.1504273 452530.2878 0.023123574 0.031311972 2855.597207 -3.455696949 0.08542693 DRVGVQDFVLLENFTSEAAFIENLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRVGVQDFVLLENFTSEAAFIENLRR 26 2 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 69.152 0.01816 41257000 10309 8611.4 9847.3 9717 15204 14723 13975 11277 14830 13707 FALSE TRUE 10716.00728 10090.34096 10103.92873 11638.9936 12619.62951 11303.80638 12879.60298 11125.85026 14296.2712 16392.62421 0.653709079 0.615541528 0.616370423 0.710014055 0.769835833 0.689566614 0.785695006 0.678710749 0.872116082 1 14.00075921 -5 0.099974906 2.009849378 0.49026257 0.802277734 0.051366398 78.70084009 0.535710083 16.32754839 0.865104707 1.00E-05 5 -1.519586807 DRVHHEPQLSDK ddPTM_MDA-MB-175_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 ; 111.12 0.00085071 141011000 299800 238720 305380 276240 405240 414210 389650 288880 323280 210991 FALSE TRUE 311636.3355 279718.303 313338.4537 330879.4475 336357.4495 318016.0049 359108.2148 285008.0361 311645.2159 252330.6468 1.235031652 1.108538763 1.241777238 1.311293145 1.333002764 1.260314627 1.423165277 1.129502261 1.235066846 1 17.94495591 -0.923832828 11.46979047 0.999999943 1.251291884 0.432078813 0.087021856 0 0 0.086205824 0.020318907 0.119170064 0.923832828 0.251291941 DRVTSAVEALLSADSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DRVTSAVEALLSADSASR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;; 253.48 1.51E-30 1358382000 757988 870040 898802 824594 1053863 1123315 939926 1000513 960800 937698 FALSE TRUE 787913.9515 1019462.602 922225.5185 987696.232 874727.7437 862442.1153 866252.1441 987102.7597 926220.9957 1121421.97 0.702602564 0.909080283 0.822371546 0.880753417 0.780016593 0.769061191 0.772458689 0.880224203 0.825934412 1 20.09689781 0.375958066 0.941661398 1.000591541 0.814523577 0.471415555 0.059019705 2.0898208 2.385196117 0.05818599 0.017849544 2.376610799 -0.375958066 -0.186067964 DRWSEVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DRWSEVTR 8 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ;; 135.71 0.00074973 515460000 166571 231991 221231 224387 201798 276047 214046 217180 198240 224302 FALSE TRUE 173147.3517 271833.6496 226996.4616 268770.0789 167496.448 211939.2678 197268.5152 214269.0573 191105.3811 268249.6824 0.645470854 1.013360565 0.846213347 1.001939971 0.624405019 0.790082083 0.735391421 0.798767236 0.712416057 1 18.03321694 3.246059839 24.99994223 0.766966941 0.8843234 0.120341012 0.130051498 301.8309727 1006198.693 0.033270512 0.044178099 1762.218835 -3.246059839 0.117356459 DRYDSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRYDSDR 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 106.68 0.0069741 56582000 62934 70699 73192 77676 87088 97281 88602 81312 80570 82850 FALSE TRUE 65418.68292 82841.00329 75099.44365 93040.08096 72284.81287 74688.96206 81657.14372 80222.14564 77670.30144 99082.87124 0.660242099 0.836077944 0.757945775 0.939012766 0.72953894 0.753802964 0.824129768 0.809646962 0.783892316 1 16.59634806 -4.99999998 0.312715029 2.867378258 0.783491304 0.456521981 0.069576201 269.3532498 2.425999008 331.7335839 0.06097469 1.00E-05 4.99999998 -2.083886954 DRYDSDRYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DRYDSDRYR 9 2 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;; 164.66 3.49E-05 1608410000 485358 552115 558809 467834 971998 741548 540347 560276 545285 1001739 FALSE TRUE 504520.3086 646936.4564 573372.0216 560370.1689 806778.1271 569334.7153 497993.1902 552766.4166 525660.2994 1198010.578 0.421131765 0.540008969 0.478603472 0.467750602 0.673431556 0.475233463 0.415683467 0.461403619 0.438777678 1 20.19220922 -1.751972649 2.875437266 1.099312604 0.486892668 0.824796939 0.07109793 49090471.88 40401458.09 34570279.79 0.018505639 0.017702204 1.751972649 -0.612419936 DRYDSFIELQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRYDSFIELQEK 12 1 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 203.87 1.09E-07 644740000 636590 426670 563140 453770 800260 743010 746570 595820 686360 392710 FALSE TRUE 661723.0648 499947.2535 577815.891 543524.3516 664232.091 570457.1879 688051.8926 587834.0075 661658.0377 469654.0056 1.408958631 1.064501202 1.230301209 1.157286737 1.414300917 1.21463286 1.465018683 1.251632053 1.408820174 1 18.84123879 3.259891048 24.99880987 1.309293455 1.205567556 0.053119945 0.147424852 532.5634665 624149.0427 0.036995246 0.05004516 1819.244406 -3.259891048 -0.103725899 DRYGVFPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DRYGVFPLR 9 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 77.379 0.029885 228450000 63216 72543 74344 70464 93772 86288 74740 71410 61948 85195 FALSE TRUE 65711.81649 85001.69594 76281.46571 84401.56889 77832.66893 66248.91971 68881.6835 70452.86575 59718.50358 101887.3291 0.644945913 0.834271511 0.748684516 0.828381406 0.763909209 0.650217454 0.676057407 0.691478189 0.586122967 1 16.63661512 -1.386263843 5.485704499 1.000121282 0.717790316 0.55700111 0.076499879 0.000116708 1.31E-05 0.076182067 0.017948614 0.041090002 1.386263843 -0.282330966 DRYLPDTLLLEECGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DRYLPDTLLLEECGLLR 17 1 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;;;; 303.14 1.38E-46 1492903000 624548.5 751906 772362 682045 900676 942350 723313 782327 758621 807550 FALSE TRUE 649206.157 881040.0065 792490.3882 816951.4653 747579.4152 723503.494 666617.837 771841.1862 731318.3784 965773.961 0.672213358 0.912263161 0.820575435 0.845903388 0.774072863 0.749143716 0.69024209 0.799194446 0.757235552 1 19.88132604 -1.351792549 3.400485141 1.00133805 0.783273329 0.490454901 0.067173212 29630830.23 45403764.9 405320.6351 0.016004987 0.044484371 1.351792549 -0.218064722 DRYSAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRYSAGK 7 1 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 99.136 0.0098044 835830000 1067180 820270 1115660 911870 1267920 1257700 1308230 1073760 1060230 861160 FALSE TRUE 1109313.09 961144.9917 1144735.016 1092235.164 1052399.411 965618.2356 1205687.514 1059368.004 1022072.529 1029887.814 1.077120319 0.933252126 1.111514284 1.060538002 1.0218583 0.937595554 1.170697913 1.028624661 0.992411518 1 19.97405576 DRYVEVFQCSAEEMNFVLMGGTLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DRYVEVFQCSAEEMNFVLMGGTLNR 25 1 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ; 124 0.00014279 31297700 15658.6 18438.8 17600.2 14211.6 13923.6 19216.4 13302 17140.6 16188.1 17849.1 FALSE TRUE 16276.81362 21605.52047 18058.87567 17022.61206 11556.87145 14753.68233 12259.35448 16910.85829 15605.49344 21346.2894 0.762512552 1.012144081 0.84599601 0.797450636 0.541399549 0.691159107 0.574308455 0.792215358 0.731063519 1 14.38169769 3.602678842 3.386752629 0.704048065 0.888219704 0.195395611 0.132033864 0.313628761 6.639508614 0.034408219 0.055848384 4005.70389 -3.602678842 0.184171639 DS(ph)HSPDLQLPTPEVIPSSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 DS(0.544)HS(0.456)PDLQLPTPEVIPSSGSK;DS(0.626)HS(0.374)PDLQLPTPEVIPSSGSK 202.33 4.15E-22 266210000 533970 383170 512560 432870 598230 650920 648860 482640 532880 364550 TRUE FALSE 555051.5479 448976.4669 525917.7347 518490.394 496543.0783 499753.6948 598000.6577 476171.0002 513701.7529 435976.5928 1.273122358 1.029817826 1.206298098 1.189261998 1.138921416 1.14628561 1.37163478 1.092193958 1.178278287 1 18.73389115 0.451068979 1.413908289 1.000186808 1.180078889 0.270774296 0.089003511 3.815610381 8.465871356 0.080309508 0.023466228 2.825328684 -0.451068979 0.179892081 DS(ph)LGTYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DS(0.996)LGT(0.004)YSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(1)LGTYSSR;DS(0.994)LGT(0.006)YSSR;DS(1)LGTYSSR 256.94 5.58E-15 2260292000 1729891 1493448 1736602 1803650 2104190 2476110 2477090 1930450 1827849 1358332 TRUE FALSE 1798188.432 1749936.077 1781859.275 2160406.587 1746520.535 1901070.978 2282929.213 1904575.475 1762065.072 1624471.149 1.106937747 1.077234322 1.096885763 1.329913793 1.075131766 1.170270694 1.405336878 1.17242801 1.084700749 1 20.63153869 3.951842676 24.99578697 1.193736557 1.090829152 0.088974571 0.113250916 709.1039305 368056.5024 0.028401283 0.05120277 8950.404777 -3.951842676 -0.102907405 DS(ph)MVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSMVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 50 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 DS(0.537)MVMHNS(0.463)DPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 180.75 9.68E-30 111320000 32018 30705 37132 22513 47603 43907 31007 31325 44665 43762 TRUE FALSE 33282.09536 35978.3449 38099.69042 26966.00421 39511.45906 33710.26467 28576.59032 30905.13961 43057.51537 52336.32603 0.63592724 0.687444986 0.727977933 0.515244501 0.754952861 0.644108351 0.546018272 0.590510301 0.822708024 1 15.67552503 1.014271837 3.857226996 0.998589446 0.636497684 0.726809651 0.071190622 0.093803425 3.516595118 0.068899888 0.017704304 10.33408042 -1.014271837 -0.362091762 DS(ph)PGIPPSANAHQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSPGIPPSANAHQLFR 16 0 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 DS(1)PGIPPSANAHQLFR 70.555 0.027761 181910000 75152 69648 84818 77470 177000 130860 205230 117760 109470 60123 TRUE FALSE 78119.05899 81609.50221 87028.42676 92793.33478 146913.6032 100469.7482 189143.5363 116181.6198 105530.1961 71902.95073 1.086451365 1.134995176 1.210359601 1.290535838 2.043220782 1.397296595 2.630539281 1.615811572 1.467675457 1 16.13376336 3.381661882 5.894244191 1.764271851 1.15992385 0.268240881 0.408346739 0.237017428 12.07484676 0.109101772 0.148523066 2408.02994 -3.381661882 -0.604348001 DS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSPTREPGALPCACGQLPDLEDELSLLDPLPR 32 1 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 DS(0.957)PT(0.043)REPGALPCACGQLPDLEDELSLLDPLPR 86.891 0.0001061 7561200 2611 1971.5 1950.7 2968 3050.3 5404.6 4075.2 3280.3 2559.6 1538 TRUE FALSE 2714.084296 2310.089789 2001.536845 3555.061541 2531.811096 4149.463558 3755.775175 3236.332944 2467.480496 1839.341653 1.475573769 1.25593295 1.088181111 1.932790211 1.376476791 2.25595041 2.041912751 1.759506146 1.341501994 1 10.84497377 3.739325909 24.99982501 1.739172179 1.271499639 0.188509361 0.361686659 92.49252126 3021415.968 0.091755906 0.154092143 5486.885644 -3.739325909 -0.46767254 DS(ph)QDASAEQSDHDDEVASLASASGGFGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DS(0.333)QDAS(0.333)AEQS(0.333)DHDDEVAS(0.002)LASASGGFGTK 133.15 1.65E-05 39294000 43146 32369 41363 34787 50596 54114 51428 40580 48228 30850 TRUE FALSE 44849.4374 37928.12395 42440.95376 41667.76477 41995.70999 41546.84361 47396.93898 40036.09148 46492.2837 36894.46684 1.215614189 1.028016589 1.150333841 1.129377068 1.138265805 1.12609958 1.284662526 1.085151647 1.260142446 1 15.17111685 DS(ph)QKPTSPLQSAGDHLEEELDLLLNLDAPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSQKPTSPLQSAGDHLEEELDLLLNLDAPIK 31 1 Q9NQS1 Q9NQS1 AVEN Cell death regulator Aven 1 DS(0.25)QKPT(0.25)S(0.25)PLQS(0.25)AGDHLEEELDLLLNLDAPIK 59.573 0.019204 321160000 33957 22422 27598 25771 42468 39649 49800 35348 34696 21999 TRUE FALSE 35297.64858 26272.80408 28317.22655 30868.42688 35249.30453 30441.12064 45896.54587 34874.21788 33447.29774 26309.28285 1.341642369 0.998613464 1.076320731 1.173290319 1.339804841 1.157048666 1.744500073 1.325548023 1.271311648 1 14.6832843 3.222576058 2.025566466 1.354522839 1.122410405 0.105775506 0.197685553 0.500839735 4.226953295 0.061092663 0.083420955 1669.460155 -3.222576058 -0.232112433 DS(ph)RPLSPILHIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.609)RPLS(0.391)PILHIVK;DS(0.5)RPLS(0.5)PILHIVK 106.36 0.00083598 483378000 507237 410406 506293 408138 576477 649117 605805 441772 530067 356115 TRUE FALSE 527263.1084 480890.038 519487.4115 488866.4782 478487.6455 498369.4142 558320.4211 435850.7689 510989.9922 425888.916 1.238029657 1.129144291 1.219772086 1.147873213 1.123503401 1.170186392 1.310953162 1.023390731 1.19981989 1 18.70011766 -4.999999979 0.200011467 0.22341011 1.195247508 0.340379769 0.072955963 159.2127123 1.575692495 49.20104648 0.168114223 1.00E-05 4.999999979 0.971837399 DS(ph)SQEYTDSTGIDLHEFLVNTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSSQEYTDSTGIDLHEFLVNTLK 23 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H0YIX9;Q15032-2;Q15032-4;Q15032;Q15032-3;H7C2F9 A0A0U1RRA6;Q15032-2 R3HDM2;R3HDM1 R3H domain-containing protein 2;R3H domain-containing protein 1 1 DS(0.481)S(0.481)QEY(0.002)T(0.034)DS(0.001)T(0.001)GIDLHEFLVNTLK;DS(0.454)S(0.454)QEY(0.001)T(0.027)DS(0.032)T(0.032)GIDLHEFLVNTLK 96.44 0.0023281 247437000 31857 32146.6 42931 38012 51245 56412 49671 40224 48162 34027 TRUE FALSE 33114.73896 37667.52848 44049.81713 45530.66015 42534.3932 43311.16793 45777.65723 39684.86307 46428.65903 40693.93916 0.81375113 0.92562994 1.082466284 1.118856053 1.045226736 1.064314953 1.124925681 0.975203283 1.140923194 1 15.31252632 4.44258703 2.936616628 1.067093616 0.821586907 0.727409629 0.050867866 0.130940009 2.140485744 0.012395602 0.054588075 27706.84213 -4.44258703 -0.24550671 DSAATTDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSAATTDEER 10 0 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 99.013 0.011407 0 26787 42581 38153 42017 47350 52496 38506 38400 36472 45233 FALSE TRUE 27844.57144 49893.95552 39147.29852 50327.83719 39301.46391 40304.59958 35487.7991 37885.31081 35159.37984 54095.54031 0.514729519 0.922330292 0.723669609 0.930350948 0.726519482 0.745063259 0.65602079 0.700340741 0.649949693 1 15.72322204 -1.108136286 4.721691017 1.000016247 0.735826101 0.323219588 0.116974357 0.411600572 69837015.27 2330.193943 0.025974186 0.077958543 1.108136286 -0.264190147 DSAIPVES(ph)DTDDEGAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 DSAIPVES(0.998)DT(0.002)DDEGAPR 335.98 3.58E-72 328520000 108150 120540 121220 107710 131580 137250 116010 130390 114230 104720 TRUE FALSE 112419.8455 141241.8073 124379.0928 129014.7165 109214.0786 105375.7675 106916.8331 128642.3353 110118.8846 125237.879 0.897650506 1.127788241 0.99314276 1.03015731 0.872053084 0.84140492 0.853710027 1.027183919 0.879277783 1 16.93431146 3.249141315 24.99161341 0.914128134 1.019081985 0.285476146 0.077095803 269.9553339 637630.8643 0.021558897 0.028893848 1774.766877 -3.249141315 0.104953851 DSALAEAPEGLS(ph)PAPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR 302.9 1.09E-49 711950000 681940 724240 743070 682530 879910 934910 746370 756940 722100 717450 TRUE FALSE 708863.5178 848622.5862 762435.0146 817532.3969 730343.2125 717791.3212 687867.5691 746794.4574 696111.7621 858020.5911 0.826161429 0.989046877 0.888597573 0.952812095 0.851195438 0.836566545 0.801691214 0.870368923 0.8112996 1 19.71065274 3.217274117 23.95519131 0.851290454 0.917678445 0.121408916 0.065041189 221.7241466 249520.7988 0.017177918 0.020554058 1649.203002 -3.217274117 0.066387991 DSAPYGEYGSWYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSAPYGEYGSWYK 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 118.87 0.00091618 60701000 31874 25320 26436 25319 28791 38071 29022 31946 28189 27263 FALSE TRUE 33132.41013 29668.51304 27124.94388 30327.02263 23897.1161 29229.58722 26747.17981 31517.81612 27174.4834 32604.66287 1.016186251 0.909946935 0.831934499 0.930143727 0.732935537 0.896484878 0.820348302 0.966665911 0.833453899 1 14.99279068 -0.305030522 6.893274964 1 0.882303684 0.174256814 0.077050711 0 0 0.071396519 0.016828321 0.495415372 0.305030522 -0.117696316 DSASFNPELLTHILDGS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSASFNPELLTHILDGSPEK 20 0 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 1 DSASFNPELLTHILDGS(1)PEK 146.15 8.81E-08 28046000 65466 42564 47901 46304 68831 86091 63148 45263 52511 35587 TRUE FALSE 68050.64823 49874.0359 49149.33941 55462.793 57131.13121 66097.66997 58198.29475 44656.32352 50621.13937 42559.5913 1.598949759 1.171863601 1.154835794 1.303179643 1.342379696 1.553061671 1.367454268 1.049265798 1.189417892 1 15.37719668 1.744319891 7.877836362 1.092428523 1.346257798 0.447758889 0.140033447 0.125616317 26.68410754 0.070047655 0.037436214 55.50343881 -1.744319891 0.253829275 DSASFNPELLTHILDGSPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSASFNPELLTHILDGSPEK 20 0 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 152.32 6.57E-08 34272000 69613 71045 75510 76373 101600 113470 89711 81128 80343 73435 FALSE TRUE 72361.37499 83246.4261 77477.85263 91479.35145 84330.06829 87118.31215 82679.2174 80040.61186 77451.47112 87823.18225 0.823943897 0.947886696 0.882202747 1.041631026 0.960225605 0.991973986 0.941428166 0.911383644 0.881902354 1 16.42231419 5.613606766 1.315518482 0.951452911 0.006915147 0.381378521 0.048533686 13.00770152 3.424650406 0.013467929 28.49488495 410777.6123 -5.613606766 -0.944537764 DSAYISSS(ph)PLGSHQVFDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 DSAYISS(0.202)S(0.797)PLGSHQVFDFR;DSAYIS(0.001)S(0.036)S(0.963)PLGSHQVFDFR;DSAYIS(0.001)S(0.339)S(0.659)PLGSHQVFDFR 231.49 2.10E-20 1772290000 751524 950640 970810 971270 1018430 1289380 1056620 1102640 1037400 1014170 TRUE FALSE 781194.7478 1113905.025 996110.1061 1163384.307 845317.6324 989941.0357 973799.3634 1087860.914 1000064.177 1212877.194 0.644083961 0.918398854 0.821278618 0.959193818 0.696952368 0.816192308 0.802883728 0.896925855 0.824538693 1 20.21000205 -5 0.204870242 1.817762416 0.80025374 0.282383346 0.089062987 190.2756265 1.890730541 63.61719472 0.190992304 1.00E-05 5 -1.017508677 DSAYPEELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSAYPEELSR 10 0 P07686;Q5URX0;H0Y9B6;H0YA83 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ; 146.79 6.52E-05 547200000 242960 313110 309050 319850 357400 453710 293820 301400 306000 283770 FALSE TRUE 252552.2484 366884.2068 317104.0969 383115.3753 296649.2757 348342.7285 270789.6206 297360.226 294987.1198 339369.2984 0.74418119 1.081076599 0.934392411 1.12890405 0.874119365 1.026441491 0.797920206 0.876214282 0.869221586 1 18.37249653 2.245858562 24.99949436 0.872825999 0.97208353 0.101258506 0.111441748 297.6655909 1019670.361 0.036361258 0.029841362 176.140231 -2.245858562 0.09925753 DSCPLDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSCPLDCK 8 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 141.52 0.0014708 381650000 785150 588870 633230 540830 920970 932340 797950 640090 769670 477870 FALSE TRUE 816148.3283 690003.8417 649732.494 647804.5598 764423.8484 715818.1647 735404.5939 631510.6405 741969.727 571499.4771 1.428082371 1.207356908 1.136890793 1.133517327 1.337575762 1.252526369 1.286798367 1.105006506 1.298285925 1 19.12439265 -4.409280395 0.250045323 5.47E-13 1.25368585 0.359872157 0.096316216 153.0096056 1.994488611 77.87127406 0.140032267 3.90E-05 4.409280395 1.25368585 DSDAGSST(ph)PTTSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.087)S(0.292)T(0.62)PT(0.001)TSTR;DSDAGS(0.021)S(0.107)T(0.863)PT(0.006)T(0.001)STR;DSDAGS(0.065)S(0.395)T(0.538)PT(0.002)TSTR 127.03 0.00091636 479910000 722510 882120 897300 826360 1019740 1145640 883070 822890 861560 777690 TRUE FALSE 751035.2527 1033617.248 920684.3751 989811.5416 846404.959 879582.4723 813852.6659 811860.5055 830552.6239 930063.4657 0.807509681 1.111340555 0.989915645 1.064240859 0.910050755 0.945723066 0.875050678 0.872908716 0.893006396 1 19.82696964 3.157504298 9.71824369 0.905685135 1.001360302 0.167489997 0.081512315 0.46354816 51.6170642 0.022279221 0.026657328 1437.157276 -3.157504298 0.095675167 DSDIIDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSDIIDFR 8 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 75.109 0.09129 47469000 170000 161310 177570 150590 170870 198810 168310 181220 189330 120770 FALSE TRUE 176711.7313 189013.7377 182197.6201 180376.2525 141825.5784 152639.3905 155117.4224 178791.0423 182516.0503 144432.5692 1.223489496 1.308664235 1.261471848 1.248861344 0.981950118 1.056821126 1.073978142 1.23788591 1.263676547 1 17.14003658 3.44119062 24.09945644 1.118176933 1.26665623 0.431593448 0.087975505 128.1151689 85929.07042 0.026472272 0.035843777 2761.78979 -3.44119062 0.148479297 DSDKTDTDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSDKTDTDWR 10 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 122.69 0.00043945 5592700000 20112800 12761100 16889900 12807400 22233000 22749200 22401500 17272900 19486400 10373800 FALSE TRUE 20906868.87 14952719.66 17330064.67 15340665.49 18453842.6 17466043.07 20645611.89 17041385.03 18785088.27 12406347.49 1.685175181 1.205247529 1.39687081 1.236517477 1.487451695 1.407831199 1.664116849 1.373602105 1.514151388 1 23.5645751 -1.644630862 7.413885394 0.99899653 1.432694221 0.43956789 0.149180225 0.002333114 0.000111833 0.136194426 0.032036473 0.0226657 1.644630862 0.433697691 DSDPVMAGIGEEIAHFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSDPVMAGIGEEIAHFQK 18 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 182.15 6.98E-14 37701000 78727 65797 84087 59184 115610 100960 96440 83594 93642 59599 FALSE TRUE 81835.20275 77097.12292 86278.3763 70890.41855 95958.65349 77513.57006 88880.7808 82473.55916 90271.84271 71276.28296 1.148140719 1.081665874 1.210478054 0.994586356 1.346291494 1.087508591 1.246989561 1.157096803 1.266506038 1 16.12113448 4.242676532 24.99680953 1.170666116 1.114903305 0.028402996 0.108110864 354.6117815 2153541.564 0.024004854 0.060930421 17485.43867 -4.242676532 -0.05576281 DSDYVYPSLES(ph)DEDNPIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSDYVYPSLESDEDNPIFK 19 0 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 DSDYVY(0.001)PS(0.242)LES(0.758)DEDNPIFK 86.625 0.0018336 23247000 118870 84045 112530 76694 133740 118550 125080 98256 111230 66911 TRUE FALSE 123563.0794 98479.07497 115462.6242 91863.84429 111006.9226 91018.55914 115275.9028 96939.03903 107226.854 80020.92936 1.54413452 1.230666474 1.442905314 1.147997718 1.387223611 1.137434417 1.440571906 1.21142106 1.339985112 1 16.28808976 -4.61036303 0.168525512 2.14E-13 1.387630076 0.379866265 0.126927469 116.7680948 1.237678635 39.76046912 0.426923847 2.45E-05 4.61036303 1.387630076 DSEGTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSEGTWR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 124.34 0.0096679 1623420000 1210250 1228990 1345600 1181090 1499450 1654100 1402410 1245330 1376100 1279890 FALSE TRUE 1258031.605 1440059.472 1380667.441 1414706.077 1244574.025 1269960.343 1292485.44 1228638.388 1326574.43 1530659.941 0.821888371 0.940809539 0.902007954 0.924245836 0.813096359 0.82968157 0.844397508 0.802685401 0.866668288 1 20.54572237 3.243238027 24.99416589 0.844208123 0.9006909 0.052451683 0.060045502 200.5502089 1071651.805 0.015590597 0.020436609 1750.806005 -3.243238027 0.056482777 DSEGYIYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSEGYIYAR 9 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 146.27 0.00022146 331560000 385660 352040 347580 421090 394680 484110 475330 350060 420020 287800 FALSE TRUE 400886.1546 412500.1315 356638.2203 504380.3452 327592.4346 371682.7893 438072.3926 345368.0183 404903.5622 344188.8997 1.164727145 1.198470177 1.036170024 1.465417233 0.95178094 1.079880233 1.272767346 1.003425789 1.176399246 1 18.39284104 DSEHIDDETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSEHIDDETR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 117.67 0.00092646 200178000 155243 222690 215193 210883 233688 296980 229642 215658 207070 198505 FALSE TRUE 161372.1135 260935.2752 220801.1064 252595.028 193965.7972 228010.8958 211642.06 212767.4573 199617.5911 237398.2541 0.679752739 1.099145721 0.930087322 1.06401384 0.81704812 0.96045734 0.891506388 0.896246933 0.840855346 1 17.8569498 3.217869734 24.99929035 0.898030799 0.953445249 0.027839835 0.11535815 778.7832445 940945.1527 0.031034348 0.037131954 1651.466367 -3.217869734 0.05541445 DSEHIDDETRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSEHIDDETRR 11 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 145.55 2.35E-05 392910000 205396 285700 301020 264530 337260 393430 331180 317070 280250 269390 FALSE TRUE 213505.1927 334766.7526 308864.8285 316853.2445 279932.6657 302061.845 305221.2462 312820.1953 270163.8572 322171.8127 0.662705998 1.03909386 0.958696001 0.983491516 0.868892481 0.93757999 0.947386563 0.970973198 0.838570746 1 18.29747075 4.750069119 24.9805733 0.947977231 0.662705828 0.70300163 0.055898315 933.5399759 2026321.448 0.012774375 0.204986191 56243.08307 -4.750069119 -0.285271404 DSENLAS(ph)PSEYPENGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSENLASPSEYPENGER 17 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 DSENLAS(0.999)PS(0.001)EYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(1)PSEYPENGER;DSENLAS(0.938)PS(0.062)EYPENGER 473.57 7.03E-207 4379220000 1593060 1679430 1746270 1511380 2106550 2251610 1939300 1747750 1849730 1563060 TRUE FALSE 1655955.239 1967859.038 1791779.231 1810326.453 1748479.383 1728707.701 1787292.599 1724324.27 1783158.579 1869311.68 0.885863634 1.052718527 0.95852353 0.968445483 0.935360005 0.92478302 0.956123378 0.922438076 0.953911858 1 20.83407571 3.321537924 5.463212253 0.942900658 0.972581973 0.020840477 0.043020775 0.490553813 24.30875226 0.011176133 0.015139942 2096.707864 -3.321537924 0.029681315 DSENLASPS(ph)EYPENGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.108)PS(0.892)EYPENGER 120.53 7.02E-05 1171100000 110420 118010 131040 103180 147390 151810 149210 137140 137080 116860 TRUE FALSE 114779.4669 138277.2995 134455.0101 123588.696 122336.7004 116554.4282 137514.5303 135301.8626 132146.5176 139756.4796 0.821281898 0.989416018 0.962066378 0.884314605 0.875356197 0.833982285 0.983958173 0.968125865 0.945548414 1 17.09255565 2.203800805 24.99517509 0.971799416 0.90047291 0.377387449 0.049934482 226.3554165 162766.9594 0.019408952 0.014335136 159.8824539 -2.203800805 -0.071326506 DSES(ph)PSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(1)PSQK 197.21 0.00012153 0 211810 111610 157690 114080 250060 227380 237310 169690 211480 102460 TRUE FALSE 220172.4224 130778.1493 161799.5309 136644.6835 207554.8905 174574.441 218709.0221 167415.5831 203868.8761 122535.0753 1.796811418 1.067271138 1.320434419 1.115147505 1.693840641 1.424689548 1.784868713 1.36626662 1.663759341 1 16.90283525 3.236614037 24.99979922 1.514451514 1.306192805 0.072577617 0.275093905 107.8433967 1385032.082 0.072163549 0.090481453 1724.304798 -3.236614037 -0.208258709 DSES(ph)PSQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.004)ES(0.963)PS(0.033)QKK;DSES(0.98)PS(0.019)QKK 102.62 0.0021774 296850000 1215090 419090 687790 388440 1114610 976240 1003650 683400 865870 323660 TRUE FALSE 1263062.691 491065.4474 705714.3724 465272.2726 925148.9903 749523.0551 924981.2904 674240.1408 834707.5078 387074.9802 3.263095669 1.268657166 1.82319811 1.202021046 2.390102791 1.936376913 2.389669542 1.741885101 2.156449139 1 18.56225353 4.75295981 24.5492311 1.823999874 3.263096953 0.480581243 0.463097023 1725.663097 2942023.855 0.10468552 2.23560803 56618.68907 -4.75295981 1.43909708 DSFDDRGPSLNPVLDYDHGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 DSFDDRGPSLNPVLDYDHGS(1)R;DSFDDRGPSLNPVLDYDHGS(1)R;DSFDDRGPSLNPVLDYDHGS(1)R;DSFDDRGPSLNPVLDYDHGS(1)R 114.21 0.00011035 227481000 205548 243167 233733 216664 302200 306326 234089 239771 234369 271190 TRUE FALSE 213663.1938 284929.0407 239824.274 259519.4925 250832.1519 235186.4289 215740.4925 236557.2619 225934.1055 324324.4883 0.658794514 0.878530765 0.739457804 0.800184697 0.773398744 0.725157789 0.665199516 0.729384522 0.696629806 1 18.30707843 -1.78463865 6.838262266 1.008663538 0.742727913 0.611784753 0.061937346 0.008167693 0.00025723 0.059874593 0.013906725 0.016419554 1.78463865 -0.265935625 DSFDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSFDDRGPSLNPVLDYDHGSR 21 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 209.75 1.45E-22 6192090000 1308994 5512000 5228010 5456330 5900350 6939620 4885130 6126150 5169540 5536110 FALSE TRUE 1360674.094 6458643.123 5364256.235 6535575.788 4897410.615 5327998.426 4502220.746 6044038.98 4983489.265 6620804.759 0.20551491 0.975507262 0.810212116 0.987127098 0.739700202 0.804735772 0.680011103 0.91288585 0.752701438 1 22.65857516 4.745958318 24.9675084 0.842136737 0.205514604 0.763715268 0.107671181 396.2203626 1337225.363 0.024094034 0.251908621 55713.22747 -4.745958318 -0.636622133 DSFIENSSSNCTSGSSKPNS(ph)PSIS(ph)PSILSNTEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 DS(0.001)FIENS(0.03)S(0.032)S(0.034)NCT(0.075)S(0.082)GS(0.082)S(0.089)KPNS(0.576)PS(0.113)IS(0.855)PS(0.018)ILS(0.006)NT(0.007)EHK;DSFIENSSSNCT(0.001)S(0.001)GS(0.002)S(0.003)KPNS(0.991)PS(0.031)IS(0.884)PS(0.075)ILS(0.006)NT(0.006)EHK 81.078 0.0017121 269930000 122936 85364 113712 76026 148766 153529 152168 123369 151222 93584 TRUE FALSE 127789.6082 100024.603 116675.4281 91063.71589 123478.8085 117874.2165 140240.6745 121715.4403 145779.5498 111919.993 1.141794283 0.893715236 1.042489594 0.813650121 1.103277485 1.053200713 1.253043989 1.087521872 1.302533585 1 16.77210825 2.777646906 2.15831703 1.1576725 0.975115524 0.292872996 0.11798779 0.350374962 3.216437889 0.038701852 0.039352453 599.3036273 -2.777646906 -0.182556976 DSFLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSFLKR 6 1 P46778;M0R181;Q9H553-2;Q9H553 P46778;Q9H553 RPL21;ALG2 "60S ribosomal protein L21;Alpha-1,3/1,6-mannosyltransferase ALG2" 0 ;; 87.989 0.083079 4038900000 5828130 4969080 6149160 4746320 7775160 7180740 6309400 5966830 6026550 4813840 FALSE TRUE 6058229.073 5822480.836 6309412.161 5685127.93 6453541.08 5513121.96 5814852.741 5886854.404 5809655.643 5757019.781 1.05232035 1.01137065 1.0959511 0.987512315 1.120986435 0.957634708 1.010045642 1.022552402 1.009142901 1 22.45689074 2.717662626 24.99141865 1.003865364 1.049958714 0.31878559 0.038886859 1075.465483 1286123.464 0.01171609 0.011059607 521.9905328 -2.717662626 0.046093351 DSFWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSFWAK 6 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 100.82 0.086601 589650000 687400 600930 749260 584530 976930 865670 787970 770550 760240 642630 FALSE TRUE 714539.0828 704135.0529 768786.3311 700148.2894 810871.7876 664631.2619 726206.8524 760222.0376 732879.1109 768541.0446 0.929734447 0.91619707 1.000319159 0.911009626 1.055079352 0.864796053 0.94491616 0.989175585 0.95359788 1 19.55176278 DSGACFSASEPDAVHVVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSGACFSASEPDAVHVVLDR 20 0 H0YER3;Q8NB37-3;Q8NB37 H0YER3 PDDC1 Parkinson disease 7 domain-containing protein 1 0 ;;; 245.03 6.22E-30 453574000 248653 278320 290279 292293 354255 411265 306123 323698 320741 278036 FALSE TRUE 258470.0124 326119.295 297843.9092 350107.683 294038.8616 315754.9365 282128.2794 319359.3578 309197.5941 332511.8309 0.777325762 0.980775012 0.895739284 1.052917973 0.884295939 0.949605118 0.848475913 0.960445097 0.929884489 1 18.34304615 1.537859699 0.010108643 1.881033054 2.89E-07 0.128217655 0.07053819 2409.99532 24.87904776 2313.889858 2311.873392 34.50322566 -1.537859699 -1.881032765 DSGPPTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSGPPTKK 8 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;; 83.456 0.0291 1018470000 2065090 1292870 1812420 1250670 2243480 1949140 2041010 1695260 1900370 1235160 FALSE TRUE 2146621.348 1514910.365 1859653.154 1498048.793 1862134.071 1496481.775 1881030.303 1672537.813 1831976.055 1477165.953 1.453202562 1.02555191 1.258933128 1.014137098 1.260612639 1.01307627 1.273404859 1.13226128 1.240196506 1 20.49440049 4.753107315 24.52963807 1.14535414 1.453202841 0.424709609 0.110428236 1781.190781 3003499.37 0.023061427 0.497451414 56637.92247 -4.753107315 0.307848701 DSGREDEPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSGREDEPGSPR 12 1 Q2TAM9 Q2TAM9 TUSC1 Tumor suppressor candidate gene 1 protein 1 DSGREDEPGS(1)PR;DSGREDEPGS(1)PR 99.451 0.0022946 329060000 534980 512400 571410 533880 623030 725440 615300 579710 519000 500090 TRUE FALSE 556101.4235 600400.7141 586301.414 639479.8705 517127.5831 556967.5541 567071.1782 571939.9357 500321.2914 598073.0607 0.92982189 1.003891921 0.980317377 1.069233698 0.864656205 0.931270092 0.94816372 0.956304461 0.836555472 1 19.18996221 3.231846755 24.99892099 0.925233041 0.995285998 0.307587006 0.053575192 198.646478 739655.3263 0.01488403 0.018176982 1705.480488 -3.231846755 0.070052957 DSGRGDS(ph)VSDSGSDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DSGRGDS(0.989)VS(0.007)DS(0.004)GSDALR;DSGRGDS(0.918)VS(0.082)DSGSDALR;DS(0.004)GRGDS(0.984)VS(0.012)DSGSDALR;DSGRGDS(0.825)VS(0.17)DS(0.004)GSDALR 187.37 1.24E-09 1274270000 608490 662872 754634 746815 1112366 1117901 896665 926477 872086 909331 TRUE FALSE 632513.6551 776715.1096 774300.382 894532.778 923286.4246 858285.4347 826382.0543 914059.0912 840699.7952 1087496.999 0.581623357 0.714222761 0.712002316 0.822561146 0.849001354 0.789230164 0.759893641 0.840516426 0.773059416 1 20.05257999 6.980644361 0.081443618 1.133468965 1.32E-21 0.701003653 0.05664093 94.4922695 0.686454462 1.696238705 12.25607068 9564105.558 -6.980644361 -1.133468965 DSGRGDSVSDS(ph)GSDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 DSGRGDS(0.412)VS(0.127)DS(0.44)GS(0.02)DALR 130.38 8.02E-05 163470000 122250 174680 168190 181180 245780 249120 180960 205750 210230 226080 TRUE FALSE 127076.5244 204679.9312 172573.1696 217016.8632 204002.4034 191265.6555 166775.8823 202992.2578 202663.8634 270376.0474 0.469999194 0.757019466 0.638270924 0.802648257 0.754513594 0.707406064 0.616829353 0.750777518 0.749562934 1 18.04460782 -5 0.18547866 2.263067711 0.640276885 0.556003168 0.086719133 103.3953383 1.005116756 48.17520146 0.242855456 1.00E-05 5 -1.622790826 DSGS(ph)ISLQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 DS(0.002)GS(0.976)IS(0.022)LQETR;DSGS(0.999)IS(0.001)LQETR;DS(0.001)GS(0.997)IS(0.003)LQETR 143.25 3.91E-05 875440000 323660 577850 538890 585140 636510 698250 568450 580420 552500 632870 TRUE FALSE 336438.3467 677091.2425 552933.9161 700878.9455 528316.2576 536092.0196 523893.4036 572640.4193 532615.6329 756868.7595 0.444513454 0.89459531 0.73055455 0.926024409 0.698028887 0.70830248 0.692185266 0.756591433 0.703709363 1 19.52968363 -1.898810112 2.375642343 1.150859041 0.737521596 0.30161302 0.123322146 12813132.8 6525295.067 10804808.52 0.027224387 0.012623794 1.898810112 -0.413337445 DSGSDGHSVSSRDS(ph)AAPS(ph)PIPGADNLSADPVVSPPTSIPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSGSDGHSVSSRDSAAPSPIPGADNLSADPVVSPPTSIPFK 41 1 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 2 DS(0.012)GS(0.014)DGHS(0.094)VS(0.113)S(0.123)RDS(0.655)AAPS(0.985)PIPGADNLS(0.004)ADPVVSPPTSIPFK;DS(0.184)GS(0.195)DGHS(0.232)VS(0.243)S(0.245)RDS(0.243)AAPS(0.466)PIPGADNLS(0.193)ADPVVSPPTSIPFK 118.44 1.69E-06 123448000 16527.4 31576 35696 27644 32047 35223 25573.2 30158 25126 28416 TRUE FALSE 17179.91451 36998.93237 36626.26708 33111.90069 26599.66239 27042.99206 23568.70576 29753.78134 24221.72017 33983.57114 0.505535879 1.088729969 1.077763927 0.97435024 0.782721224 0.795766635 0.693532344 0.875534275 0.712747935 1 15.05254984 3.233208783 24.90966757 0.80026399 0.936116715 0.068683117 0.171800809 262.3738473 1221197.798 0.047732772 0.058644871 1710.837588 -3.233208783 0.135852725 DSGSDQDLDGAGVRAS(ph)DLEDEESAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSGSDQDLDGAGVRASDLEDEESAAR 26 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 DSGSDQDLDGAGVRAS(1)DLEDEESAAR 248.01 8.71E-46 174980000 157190 160790 158100 159170 199960 230100 181680 181440 173640 167500 TRUE FALSE 163395.9826 188404.4317 162220.2159 190653.3509 165970.8706 176662.7622 167439.4469 179008.0936 167390.7303 200318.418 0.815681275 0.940524758 0.809811786 0.951751481 0.82853525 0.881909731 0.83586646 0.893617748 0.835623264 1 17.61193555 -2.31820417 2.286934585 1.700445988 0.868898398 0.412528941 0.047881237 3743723.958 453137.2156 13622783.92 0.010381063 0.004806133 2.31820417 -0.831547591 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.005)VDS(0.991)DDES(0.004)VVKDK;DSGSDTASAIIPSTTPS(0.027)VDS(0.972)DDESVVKDK 172.64 1.04E-12 573080000 930180 298950 494420 336880 770340 742090 843130 510540 611740 211114 TRUE FALSE 966904.2247 350292.337 507304.9914 403513.8585 639397.882 569750.844 777043.2675 503697.0464 589723.5969 252477.7463 3.829661184 1.387418662 2.009305766 1.598215544 2.532492037 2.256637872 3.077670325 1.995015615 2.335744855 1 17.94579671 DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVKDKK 30 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 DSGSDTASAIIPSTTPS(0.113)VDS(0.773)DDES(0.113)VVKDKK 118.01 3.73E-05 210260000 387190 190230 257590 148500 445170 366060 265330 273130 322430 165290 TRUE FALSE 402476.5602 222900.5227 264303.007 177872.8568 369500.1624 281048.1127 244532.7413 269469.1391 310825.8073 197675.4108 2.036047673 1.127608749 1.337055559 0.899822876 1.869226733 1.421765669 1.237041776 1.363189979 1.572405015 1 17.5927739 -1.942159875 2.557909544 0.713445048 1.40309748 0.136578313 0.317745809 18005845.58 9030821.504 30735565.7 0.071528731 0.011424577 1.942159875 0.689652432 DSGSSSVFAES(ph)PGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSGSSSVFAESPGGK 15 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 DSGSSSVFAES(1)PGGK 308 4.64E-56 316090000 469370 277070 331800 262650 529290 492020 440690 359890 414360 278040 TRUE FALSE 487901.09 324654.6172 340446.9806 314601.3861 439321.4749 377755.8116 406147.5663 355066.2632 399447.2645 332516.6146 1.46729838 0.976356076 1.023849533 0.946122306 1.321201575 1.136050937 1.221435406 1.067815103 1.20128513 1 18.3430669 -1.918264777 2.534432583 0.914009534 1.138597629 0.075722949 0.152883307 24545184.44 12139768.47 12513300.01 0.035007766 0.012070777 1.918264777 0.224588095 DSGYIDCWDSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSGYIDCWDSER 12 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 0 ;;; 198.62 4.21E-07 850980000 442154 602400 593620 581570 663760 746130 576910 601330 616760 579520 FALSE TRUE 459610.5813 705857.514 609090.2249 696602.8102 550934.3123 572852.6152 531690.2867 593270.1549 594562.9281 693065.8484 0.663155719 1.018456638 0.878834567 1.005103356 0.794923475 0.826548612 0.767156956 0.856008352 0.857873649 1 19.4026329 DSHGVAQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSHGVAQVR 9 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;;;; 221.94 4.01E-07 7361060000 1701130 1716950 1775900 1610980 2002660 2308750 1929670 1765470 1662300 1813760 FALSE TRUE 1768291.926 2011822.806 1822181.413 1929627.036 1662248.569 1772577.802 1778417.423 1741806.762 1602474.148 2169131.545 0.815207326 0.92747847 0.840051133 0.889585069 0.766319854 0.817183174 0.819875321 0.802997294 0.738763009 1 21.04868612 3.256861064 24.99993915 0.813177506 0.87032112 0.071416837 0.070987476 476.6369044 651121.612 0.017921972 0.024223123 1806.596082 -3.256861064 0.057143614 DSIEKEHVEEISELFYDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSIEKEHVEEISELFYDAK 19 1 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;; 122.17 2.03E-05 99401000 264000 141634 220644 99281 362922 258938 207394 190810 269344 147017 FALSE TRUE 274422.9239 165958.5377 226394.1639 118918.4855 301232.6481 198803.5737 191137.9164 188252.5041 259650.3621 175822.1663 1.560798218 0.943899971 1.287631523 0.676356616 1.713280267 1.130708248 1.087109324 1.070698354 1.476778312 1 17.42375744 -1.869423574 2.478614768 0.909081089 1.191696359 0.041107943 0.292410304 24441295.14 13270426.52 13048338.52 0.066454737 0.013507545 1.869423574 0.28261527 DSIKLDDDSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSIKLDDDSER 11 1 Q86VP6;Q86VP6-2;F5H6I6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;; 193.81 7.19E-07 3516210000 5022090 3207590 4199440 3211420 6109260 5618420 4854170 3928490 4616930 2969070 FALSE TRUE 5220365.991 3758468.631 4308880.856 3846629.291 5070810.167 4313627.103 4473687.471 3875835.017 4450767.591 3550802.42 1.470193318 1.058484305 1.213494964 1.083312681 1.428074437 1.214831633 1.259908872 1.091537787 1.253454027 1 21.75971366 -0.134366441 0.445410562 0.966064145 1.237537649 0.224451584 0.129650552 7.916309267 1.839667206 0.587794555 0.071726773 0.733894374 0.134366441 0.271473505 DSIPVTELSASGPFESHDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSIPVTELSASGPFESHDLLR 21 0 Q9Y244 Q9Y244 POMP Proteasome maturation protein 0 150.23 7.33E-08 62782000 22233 22627 28373 28984 34532 33414 31403 31246 32490 21520 FALSE TRUE 23110.77601 26513.01124 29112.42369 34716.94869 28662.26297 25654.10489 28941.5508 30827.19848 31320.69125 25736.43197 0.897979022 1.030174317 1.131175593 1.348941793 1.113684407 0.996801146 1.124536254 1.197803896 1.216978767 1 14.65152444 4.495100383 2.516873164 1.151011198 0.896663925 0.380049535 0.097387017 0.345430365 3.773072565 0.025335652 0.148248416 31268.02016 -4.495100383 -0.254347273 DSIVAELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSIVAELDR 9 0 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;;;; 155.42 0.00017067 818770000 1651428 1980850 1758770 2011930 1834220 2632070 1840470 1926930 1666740 2290490 FALSE TRUE 1716627.653 2321045.579 1804604.991 2409883.749 1522439.94 2020811.632 1696209.152 1901102.655 1606754.353 2739267.661 0.626673938 0.847323396 0.65879104 0.879754755 0.555783563 0.737719669 0.619219938 0.694018581 0.586563473 1 21.38535881 -1.214023814 5.122745046 1.000028859 0.693355385 0.459494942 0.100939187 3.05E-05 4.68E-06 0.089674444 0.021134483 0.061090853 1.214023814 -0.306673474 DSIVAELDREMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSIVAELDREMSR 13 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ;;; 209.79 3.20E-08 375751000 189726 264697 275845 149687 376215 343332 175561 252673 289097 383005 FALSE TRUE 197216.529 310156.6507 283033.7473 179294.6418 312266.1087 263598.3462 161800.0701 249286.3317 278692.4554 458047.4967 0.430559124 0.677127706 0.617913534 0.391432424 0.681733032 0.575482561 0.35323863 0.544236861 0.608435713 1 18.80513768 0.759151804 2.904152859 0.999916725 0.535319591 0.627431695 0.10719098 0.929432938 10.32942835 0.100758454 0.026456659 5.743171744 -0.759151804 -0.464597133 DSIVHQAGMLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSIVHQAGMLKR 12 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ; 108.35 0.0011137 1103830000 1050360 1137620 1358610 1136810 1801630 1776990 1303930 1375440 1452280 1405200 FALSE TRUE 1091829.024 1332997.386 1394016.493 1361667.625 1495389.576 1364311.003 1201724.559 1357004.477 1400012.726 1680522.036 0.649696345 0.793204348 0.829513962 0.810264665 0.889836339 0.811837616 0.715090034 0.807489844 0.83308204 1 20.68047803 -5 0.27810666 2.477408361 0.781778229 0.51494386 0.061598033 193.8135184 1.861440894 165.1225352 0.073208001 1.00E-05 5 -1.695630132 DSIVQGFQWGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSIVQGFQWGTR 12 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 199.7 0.00026976 0 191926 181435 160170 164364 196904 242880 187238 167616 167878 163628 FALSE TRUE 199503.3867 212595.0499 164344.1618 196874.7086 163434.3284 186474.8009 172561.7963 165369.3817 161836.1036 195687.7738 1.019498474 1.086399246 0.839828461 1.006065452 0.835179047 0.952920038 0.881822063 0.84506752 0.827011828 1 17.5781941 4.242893172 24.99993762 0.893108319 1.052948903 0.468762091 0.065573669 81.9162677 472660.418 0.015219457 0.038781146 17494.16314 -4.242893172 0.159840584 DSKPS(ph)STPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.217)KPS(0.261)S(0.261)T(0.261)PR;DS(0.051)KPS(0.316)S(0.316)T(0.316)PR 97.439 0.0176 498900000 895200 546470 645520 473770 643020 761490 767140 591300 635030 463320 TRUE FALSE 930543.1872 640321.9716 662342.7815 567480.2919 533719.6901 584645.488 707009.5623 583374.5907 612175.3943 554098.6832 1.679381698 1.155609986 1.195351661 1.024150227 0.963221365 1.055128817 1.27596326 1.052835187 1.104812938 1 19.07978341 5.167015123 1.499465547 1.082260321 2.752137642 0.80501881 0.087415009 1.549953114 1.355088661 0.023782102 5.262448626 146897.7429 -5.167015123 1.669877321 DSKPSS(ph)TPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 DS(0.005)KPS(0.04)S(0.477)T(0.477)PR 51.774 0.092354 3004300000 6345100 3616200 4438400 3289300 4357400 4973300 5259100 3982200 4237200 3115900 TRUE FALSE 6595609.447 4237254.22 4554068.35 3939913.722 3616730.704 3818326.446 4846878 3928825.123 4084704 3726400.947 1.769967736 1.137090259 1.222109058 1.057297317 0.970569393 1.024668708 1.300686123 1.05432163 1.096152577 1 21.82935148 5.40733252 1.442210762 1.087729086 4.432272987 0.813635133 0.096696784 2.954766512 1.37730237 0.026020525 22.89577527 255465.6539 -5.40733252 3.344543901 DSKPSSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DSKPSSTPR 9 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 141.95 9.62E-05 26225640000 4927490 4294600 4881430 4026220 5796660 5983380 5834870 5202730 4706010 3582940 FALSE TRUE 5122031.11 5032164.143 5008644.076 4822594.299 4811345.804 4593830.674 5377517.643 5132995.914 4536641.619 4284948.493 1.195354184 1.174381477 1.168892481 1.125473108 1.12284799 1.072085389 1.254978362 1.197913096 1.058738892 1 22.03084643 1.068762584 4.560944129 1.001525806 1.164500547 0.577576392 0.047267231 0.136185351 5.148647476 0.048685518 0.012389288 11.71554737 -1.068762584 0.162974741 DSLDPSFTHAMQLLTAEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSLDPSFTHAMQLLTAEIEK 20 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;; 243.41 7.76E-30 756623000 1441011 1202318 1631949 1378826 1906230 1991352 2203947 1714206 1802861 983795 FALSE TRUE 1497903.227 1408806.764 1674478.932 1651553.667 1582209.705 1528890.677 2031195.875 1691229.872 1737976.385 1176550.794 1.273130947 1.197404116 1.423210064 1.403724918 1.344786569 1.299468484 1.726398796 1.437447393 1.47717922 1 20.16613218 4.232046843 24.65882014 1.418928123 1.235267514 0.093709985 0.172238056 203.199705 769255.5787 0.040815913 0.091662693 17062.66417 -4.232046843 -0.183660609 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.588)S(0.412)PEQLAAGAEEGGGPR;DSLGDFIEHY(0.001)AQLGPS(0.5)S(0.5)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.649)S(0.351)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.582)S(0.418)PEQLAAGAEEGGGPR 205.11 3.35E-27 1408736000 217290.3 232566.9 258957.1 231141.8 274165 318000.9 289784 242368.9 262483.7 233210.9 TRUE FALSE 225869.0888 272508.456 265705.7348 276860.9582 227562.5312 244150.0103 267069.9729 239120.3413 253036.9629 278904.1108 0.809844961 0.977068625 0.952677729 0.992674355 0.815916734 0.875390505 0.957569152 0.857356819 0.907254333 1 18.08940967 3.261214311 24.99997887 0.895254433 0.937610194 0.04122844 0.066531245 614.1992463 677808.3746 0.017685453 0.023929891 1824.795963 -3.261214311 0.042355761 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.604)S(0.396)PEQLAAGAEEGGGPRR 108.92 3.98E-06 508790000 156090 150990 179270 192770 173320 216920 167410 188540 174850 157580 TRUE FALSE 162252.5537 176921.358 183941.9235 230899.3306 143859.1283 166543.6175 154287.9668 186012.9297 168557.1827 188454.7839 0.860962775 0.938800036 0.976053351 1.225224034 0.763361509 0.883732501 0.818700186 0.987042758 0.894417107 1 17.52385889 4.736675712 6.468433615 0.941457235 0.859380362 0.041523888 0.118135146 0.473781719 119.9574474 0.028350533 0.171946314 54535.0496 -4.736675712 -0.082076873 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.167)S(0.833)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.052)S(0.948)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.021)S(0.979)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.169)S(0.831)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.191)S(0.809)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.123)S(0.877)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.187)S(0.813)PEQLAAGAEEGGGPR 365.37 4.35E-148 11647041000 1077614 1272908 1333368 1168055 1428564 1661346 1435722 1397450 1390980 1314667 TRUE FALSE 1120159.033 1491520.047 1368116.665 1399092.793 1185737.202 1275523.569 1323186.358 1378719.469 1340918.902 1572250.828 0.71245568 0.948652735 0.870164379 0.889866151 0.754165417 0.811272315 0.841587318 0.876908089 0.852865763 1 20.58439996 0.271674648 0.857413732 1.001514287 0.839036166 0.367665044 0.063763609 3.232380757 2.903507272 0.072048143 0.020123449 1.869281243 -0.271674648 -0.162478121 DSLGDFIEHYAQLGPSS(ph)PEQLAAGAEEGGGPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 DSLGDFIEHYAQLGPS(0.378)S(0.622)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.052)S(0.948)PEQLAAGAEEGGGPRR;DSLGDFIEHYAQLGPS(0.205)S(0.795)PEQLAAGAEEGGGPRR 297 5.15E-90 848130000 276125 411843 407543 295957 498031 489438 295030 389978 418338 487792 TRUE FALSE 287026.6282 482573.8316 418163.9054 354496.4113 413375.8685 375773.442 271904.7777 384750.9828 403282.0971 583365.5031 0.492018514 0.827223806 0.716812878 0.607674621 0.708605268 0.64414752 0.466096772 0.659536741 0.691302614 1 19.15404055 0.725728279 2.797184807 0.999940928 0.643167755 0.536919753 0.099638022 1.437415523 13.65632845 0.094383667 0.024877977 5.317754446 -0.725728279 -0.356773174 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 0 ;;; 243.24 7.18E-47 433250000 140680 168800 180011 153071 201310 217356 176239 175843 147335 163706 FALSE TRUE 146234.155 197790.0869 184702.2345 183347.9869 167091.3981 166878.3631 162424.9267 173486.1122 142032.4421 195781.0564 0.74692699 1.010261619 0.943412187 0.936495033 0.853460499 0.85237237 0.829625346 0.886123078 0.725465705 1 17.57888165 3.22796355 23.55353661 0.85242084 0.918925801 0.06889224 0.088536919 219.5860352 488060.9376 0.023922226 0.028915006 1690.29906 -3.22796355 0.066504961 DSLHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSLHEK 6 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 76.847 0.073978 168420000 203670 242510 328860 312400 349070 392830 513500 375220 337750 178610 FALSE TRUE 211711.0489 284159.206 337430.3618 374191.7876 289735.2061 301601.1859 473250.5282 370190.7896 325594.4435 213605.2098 0.991132422 1.330300915 1.579691629 1.751791484 1.356405147 1.411956132 2.215538323 1.733060678 1.524281378 1 17.70458731 4.575425206 1.776344985 1.634936802 0.88828468 0.247221512 0.30076132 0.773598776 3.178950789 0.078792145 0.872452009 37620.55568 -4.575425206 -0.746652122 DSLHEKFPDAGEDELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSLHEKFPDAGEDELLK 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 189.9 1.98E-10 1920290000 2454870 1659740 2619070 1887010 3900080 3250410 3731570 2888290 3119070 1171460 FALSE TRUE 2551790.163 1944787.434 2687325.116 2260254.946 3237145.795 2495551.538 3439079.793 2849577.197 3006815.28 1400985.158 1.821425551 1.388157057 1.918168155 1.613332542 2.310621048 1.781283352 2.454758191 2.033981003 2.146214942 1 20.41801024 3.262442274 24.99499275 2.033134109 1.680683817 0.080360997 0.395558359 408.881836 427940.4585 0.09986665 0.135149797 1829.962853 -3.262442274 -0.352450293 DSLITPHVS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSLITPHVSR 10 0 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37;H7BZ48;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5;RGPD6;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 DSLITPHVS(1)R;DSLITPHVS(1)R 122.46 0.00031432 189496000 186871 187124 199106 211170 224680 261100 230830 198248 195698 165345 TRUE FALSE 194248.8114 219261.0914 204294.8659 252938.7957 186488.9739 200463.482 212736.9414 195590.8098 188654.8672 197741.187 0.982338653 1.108828639 1.03314271 1.279140676 0.94309626 1.01376696 1.07583526 0.989125294 0.954049432 1 17.59325387 DSLLDGHFVLATLSDTDSHS(ph)QDLGS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 2 DSLLDGHFVLATLSDT(0.002)DS(0.138)HS(0.859)QDLGS(1)PER;DSLLDGHFVLAT(0.216)LS(0.057)DT(0.064)DS(0.31)HS(0.37)QDLGS(0.983)PER;DSLLDGHFVLAT(0.058)LS(0.051)DT(0.058)DS(0.417)HS(0.447)QDLGS(0.968)PER 123.86 2.23E-05 150639000 123883.5 136791 136449 151089 167274 181232 147632 135890 151867 149829 TRUE FALSE 128774.5162 160283.7902 140004.973 180973.9532 138840.8252 139143.6146 136060.2181 134068.6168 146401.3363 179185.1239 0.718667451 0.894515051 0.781342614 1.009983135 0.774845714 0.776535527 0.759327645 0.748212876 0.817039569 1 17.45109134 DSLLDGHFVLATLSDTDSHS(ph)QDLGSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLAT(0.001)LS(0.004)DT(0.016)DS(0.058)HS(0.897)QDLGS(0.025)PER;DSLLDGHFVLATLS(0.001)DT(0.016)DS(0.226)HS(0.597)QDLGS(0.16)PER 142.37 1.98E-07 1554740000 69880 93768 98871 83985 104845 120301 109861 98179 96071 82533 TRUE FALSE 72638.91636 109871.9246 101447.6595 100596.9823 87023.48435 92362.91593 101249.8078 96863.07109 92613.42348 98703.76116 0.735928555 1.113148307 1.027799329 1.019180841 0.881663306 0.935758829 1.025794829 0.981351369 0.938296802 1 16.59081744 4.757581125 24.5194332 0.988983932 0.735928262 0.617980456 0.060240978 2333.553678 3008133.039 0.014887687 0.524859391 57224.38388 -4.757581125 -0.25305567 DSLLDGHFVLATLSDTDSHSQDLGS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 DSLLDGHFVLAT(0.003)LS(0.134)DT(0.125)DS(0.124)HS(0.083)QDLGS(0.532)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER;DSLLDGHFVLATLSDTDSHSQDLGS(1)PER 312.78 1.67E-82 1514867000 602116 732719 833786 779319 931467 1048938 933400 884629 847324 703881.6 TRUE FALSE 625888.0046 858557.7885 855515.1481 933465.9722 773136.5721 805338.0463 860237.669 872771.9952 816828.9748 841793.7229 0.743517073 1.019914695 1.016300223 1.108901084 0.91843946 0.956692862 1.021910292 1.036800313 0.97034339 1 19.68310723 4.740130367 24.87160908 1.008032557 0.743516979 0.723745852 0.048530258 66.62913562 1055591.796 0.011740423 0.074304202 54970.58599 -4.740130367 -0.264515578 DSLLQDGEFSMDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;;;;;;;;;;;;;; 299.2 2.13E-43 11074286000 2940963.2 3455499.3 3658181.6 3327199.7 4422515.7 4627100.5 3765654.5 3685379.7 3556728.1 3424618.3 FALSE TRUE 3057074.698 4048954.425 3753516.818 3985309.87 3670778.061 3552526.533 3470492.661 3635983.213 3428722.15 4095606.688 0.746427802 0.988609194 0.916473945 0.97306948 0.896272113 0.867399339 0.847369615 0.887776462 0.837170757 1 21.96564575 3.001541625 24.95585959 0.878665772 0.915510368 0 0.074080733 165.5289971 2679483.805 0.020166967 0.023944338 1003.556029 -3.001541625 0.036844596 DSLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSLLQR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 112.66 0.062352 542630000 115950 116190 117780 120410 159330 155750 147700 117310 117330 104180 FALSE TRUE 120527.7955 136144.7287 120849.4436 144226.7386 132247.1435 119579.4229 136122.8881 115737.6513 113107.3162 124592.0764 0.967379299 1.092723812 0.969960908 1.157591581 1.061441043 0.959767478 1.092548515 0.928932679 0.907821103 1 16.9268528 1.679513459 7.440674737 0.939132071 1.04388032 0.323070394 0.064257647 0.132385251 13.89977636 0.030427171 0.015782828 47.80941818 -1.679513459 0.104748248 DSLRDESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSLRDESQR 9 1 Q96MW1;Q86WV7 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 0 ; 66.056 0.059108 756550000 154116 1902939 1136845 1744423 747654 1757203 661340 1229936 944294 2958465 FALSE TRUE 160200.6187 2229753.97 1166472.115 2089464.663 620568.0401 1349119.234 609502.4427 1213450.72 910309.0434 3538119.574 0.045278464 0.630208766 0.329687025 0.590557956 0.175394875 0.381309678 0.172267339 0.34296487 0.257286116 1 21.75455138 -1.68478252 4.237465596 1.030776885 0.333273243 0.580127906 0.17214643 0.044035831 0.003275746 0.146642415 0.0360327 0.020664147 1.68478252 -0.697503642 DSLS(ph)PVLHPSDLILTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 DS(0.005)LS(0.995)PVLHPSDLILTR;DS(0.002)LS(0.998)PVLHPSDLILTR;DS(0.001)LS(0.999)PVLHPSDLILTR;DS(0.006)LS(0.994)PVLHPSDLILTR;DS(0.003)LS(0.997)PVLHPSDLILTR;DS(0.066)LS(0.934)PVLHPSDLILTR 246.18 3.72E-20 955962000 396432 1235748 1216049 1264472 1379594 1707124 1265416 1438350 1226057 1290341 TRUE FALSE 412083.4415 1447978.106 1247740.236 1514580.788 1145091.105 1310670.323 1166229.387 1419071.271 1181931.448 1543158.614 0.267038941 0.938320982 0.808562532 0.981480953 0.742043685 0.849342583 0.755741747 0.919588731 0.765917021 1 20.55745493 4.743463126 24.99922854 0.855794384 0.267038699 0.797726753 0.089873755 201.3621961 1026767.192 0.019378552 0.160457881 55394.0509 -4.743463126 -0.588755684 DSLSVNEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSLSVNEFK 9 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 168.74 0.00013725 291470000 371940 276280 355560 300800 486130 472040 437800 367050 382240 268150 FALSE TRUE 386624.4784 323728.9408 364826.1857 360297.3422 403497.7962 362415.8638 403484.092 362130.2951 368483.2571 320688.8585 1.205606207 1.00947985 1.137632868 1.123510632 1.25822206 1.130116792 1.258179327 1.129226306 1.149036667 1 18.29081471 5.082260913 20.66625107 1.143364347 4.325392836 0.054244374 0.081047977 1913.91358 507587.6889 0.017965524 15812.78484 120853.9676 -5.082260913 3.182028489 DSMVMHNS(ph)DPNLHLLAEGAPIDWGEEYSNSGGGGSPS(ph)PSTPESATLSEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSMVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 50 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 DS(0.002)MVMHNS(0.998)DPNLHLLAEGAPIDWGEEYSNSGGGGS(0.029)PS(0.797)PS(0.132)T(0.029)PES(0.009)AT(0.002)LS(0.002)EKR 167.36 3.55E-22 175680000 22137 34704 36327 23326 39033 40652 26287 35940 36112 35779 TRUE FALSE 23010.98585 40664.14204 37273.71146 27939.81318 32398.1846 31211.18909 24226.55625 35458.28309 34812.33617 42789.21002 0.537775431 0.950336359 0.871100715 0.652963987 0.757157811 0.729417278 0.56618377 0.828673469 0.813577445 1 15.38495942 0.88908198 1.697015221 0.997557409 0.738716619 0.308671022 0.121050574 0.622600599 3.557974898 0.11248983 0.032202219 7.746080028 -0.88908198 -0.25884079 DSMVMHNS(ph)DPNLHLLAEGAPIDWGEEYSNSGGGGSPSPS(ph)TPESATLSEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSMVMHNSDPNLHLLAEGAPIDWGEEYSNSGGGGSPSPSTPESATLSEKR 50 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 2 DS(0.25)MVMHNS(0.75)DPNLHLLAEGAPIDWGEEYSNSGGGGS(0.004)PS(0.36)PS(0.506)T(0.098)PES(0.027)AT(0.004)LS(0.001)EKR 228.01 4.27E-51 88265000 11640 13050 18350 13216 21701 21269 10710 16505 18954 16249 TRUE FALSE 12099.55619 15291.23599 18828.21607 15830.08535 18012.27177 16329.59708 9870.522215 16283.77747 18271.84924 19432.68044 0.62263959 0.786882491 0.968894442 0.81461152 0.926906189 0.840316246 0.50793416 0.837958382 0.940263969 1 14.24619729 1.225706117 3.94499075 0.984741325 0.788300689 0.253431468 0.127704067 0.310628048 9.549193179 0.116796633 0.03310261 16.81535797 -1.225706117 -0.196440636 DSNNLCLHFNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DSNNLCLHFNPR 12 0 P09382 P09382 LGALS1 Galectin-1 0 ;;;;;;; 248.32 9.68E-17 22646334000 4750721.1 6064929.7 5690076.5 5623121.2 7500649 7703466 6136930.7 6019611.7 5696568.3 6831677 FALSE TRUE 4938283.237 7106534.197 5838364.568 6735357.79 6225691.362 5914452.769 5655902.036 5938928.651 5491549.92 8170213.308 0.604425252 0.869810118 0.714591449 0.824379675 0.761998632 0.723904327 0.692258797 0.726900073 0.672142784 1 22.96194231 -1.041910625 4.719972136 1.000007912 0.736709886 0.56055698 0.071017363 5.49E-06 1.11E-06 0.063822992 0.015042772 0.090800737 1.041910625 -0.263298026 DSNPDEIEIDFETLKPTTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSNPDEIEIDFETLKPTTLR 20 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 0 ; 128.01 1.87E-05 86268000 90306 61676 72296 59275 92618 92146 81890 81260 80822 56991 FALSE TRUE 93871.35061 72268.37323 74180.09315 70999.41808 76874.82544 70746.48799 75471.24782 80170.84261 77913.23201 68157.29529 1.377275172 1.060317504 1.088366151 1.041699466 1.127903112 1.037988489 1.1073099 1.17626209 1.143138554 1 16.05658047 4.742965444 24.73936087 1.095486265 1.377275303 0.738738142 0.051565792 208.0438849 1168412.999 0.012757666 0.100531939 55330.60821 -4.742965444 0.281789038 DSNYHLLMSVQESLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSNYHLLMSVQESLER 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 87.16 0.0065639 92514000 53752 76706 76586 82896 76294 94685 75025 69736 59964 63570 FALSE TRUE 55874.17047 89879.65881 78581.89408 99292.58138 63325.57313 72695.84372 69144.34446 68801.30299 57805.90735 76025.32438 0.73494156 1.182233151 1.03362787 1.306046139 0.832953672 0.956205637 0.90949095 0.904978749 0.760350683 1 16.21419245 DSPAFPDS(ph)PWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 DSPAFPDS(1)PWR 95.417 0.0081541 30434000 65565 59327 62720 64771 75211 83540 69421 60101 63715 48631 TRUE FALSE 68153.55683 69515.95075 64354.53473 77582.51048 62426.66108 64139.10106 63979.60062 59295.4444 61421.9096 58159.31335 1.171842529 1.195267735 1.10652157 1.333965379 1.07337342 1.102817371 1.100074897 1.019534808 1.056097572 1 15.82772262 2.486901678 1.042192826 1.027417712 1.190270255 0.522202391 0.06395073 0.411871829 0.902792607 0.038176078 0.027252681 306.8327254 -2.486901678 0.162852543 DSPCQLEALKLESCGVTSDNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSPCQLEALKLESCGVTSDNCR 22 1 P13489 P13489 RNH1 Ribonuclease inhibitor 0 ; 267.57 7.42E-38 1082890000 433370 327920 417510 289520 619800 627740 396920 454550 438220 419480 FALSE TRUE 450479.7822 384237.7091 428390.6536 346786.1919 514446.6174 481956.8985 365808.3732 448457.5007 422448.5478 501669.0746 0.897962033 0.765918668 0.853930759 0.691264839 1.025470063 0.960706814 0.729182626 0.893930927 0.842086087 1 18.93637648 3.246655462 24.99974856 0.892883532 0.803362781 0.224597016 0.094078046 328.3132127 1013941.242 0.026176937 0.034842109 1764.637331 -3.246655462 -0.089520752 DSPDGPTDRFS(ph)REELEWQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSPDGPTDRFSREELEWQNR 20 2 Q6UWE0;Q6UWE0-2 Q6UWE0 LRSAM1 E3 ubiquitin-protein ligase LRSAM1 1 DS(0.001)PDGPT(0.038)DRFS(0.962)REELEWQNR;DS(0.001)PDGPT(0.002)DRFS(0.997)REELEWQNR 55.588 0.050953 96054000 9921.2 15499.6 14288.3 15982.8 19124.6 21171.1 15393.6 14804.7 15009.8 18422.6 TRUE FALSE 10312.89664 18161.53573 14660.66484 19144.15014 15873.80732 16254.43288 14187.00941 14606.26721 14469.60023 22032.15575 0.468083866 0.824319505 0.66542126 0.868918609 0.72048362 0.73775953 0.64392289 0.662952249 0.65674918 1 14.42732304 -1.728040686 2.551371414 1.060771749 0.699611098 0.43899577 0.103520136 13035312.58 9914795.177 5032007.769 0.023389155 0.018705069 1.728040686 -0.361160651 DSPNVEAAHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSPNVEAAHLAR 12 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 127.79 0.00026344 123150000 123780 169290 164460 197210 163890 194950 141560 146330 132820 185110 FALSE TRUE 128666.93 198364.2406 168745.9627 236217.5494 136032.0363 149675.817 130464.1573 144368.6857 128039.8341 221378.7604 0.581207202 0.896040073 0.762250012 1.067028964 0.614476457 0.676107395 0.589325539 0.652134313 0.578374519 1 17.75615729 DSPS(ph)KSSAEAQTPEDTPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSPSKSSAEAQTPEDTPNK 19 1 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 DS(0.008)PS(0.553)KS(0.22)S(0.22)AEAQTPEDTPNK 158.89 2.85E-10 0 488510 249190 360870 328280 699920 604630 664900 353860 431360 251210 TRUE FALSE 507796.752 291986.4441 370274.5687 393212.8042 580947.8484 464213.8458 612783.4006 349117.0855 415835.4379 300429.7898 1.690234355 0.971895777 1.232482867 1.308834269 1.933722514 1.545165831 2.03968921 1.162058815 1.384135169 1 18.19666835 0.997594221 1.623048192 1.019152757 1.494090811 0.181143875 0.317194139 0.722525216 3.907510811 0.309018075 0.089889873 9.94475804 -0.997594221 0.474938055 DSPSVWAAVPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 ; 150.35 0.0001583 201775000 655550 533470 637990 522420 772270 890810 727940 667820 719240 547930 FALSE TRUE 681431.6202 625089.3227 654616.5435 625753.1167 640999.8212 683932.8779 670882.1607 658868.9652 693354.6929 655286.3927 1.039898932 0.953917752 0.998977776 0.954930735 0.978197973 1.043715977 1.023799926 1.005467186 1.058094141 1 19.32176605 2.751497994 24.66702614 1.024588864 0.982533096 0.353161507 0.02760455 689.6678424 1314952.973 0.008008151 0.008436816 564.2843347 -2.751497994 -0.042055768 DSQDAGGFGPEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 269.44 1.06E-24 1042780000 445907 461950 448304 420451 566330 569402 525602 439028 463628 406307 FALSE TRUE 463511.7527 541286.319 459987.1705 503614.9529 470065.4289 437167.0149 484403.9418 433143.5478 446942.1188 485915.0774 0.953894568 1.113952508 0.946641073 1.036425862 0.967381855 0.899677814 0.996890124 0.891397629 0.919794712 1 18.89034467 3.043151644 5.107805155 0.935591431 1.01466122 0.26887904 0.054847633 0.220467638 13.41886465 0.01509816 0.017917934 1104.464203 -3.043151644 0.079069789 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 DSQDAS(0.004)AEQS(0.996)DHDDEVASLASASGGFGTK;DSQDAS(0.001)AEQS(0.999)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDASAEQS(1)DHDDEVASLASASGGFGTK;DSQDAS(0.004)AEQS(0.996)DHDDEVASLASASGGFGTK 405.88 7.76E-175 4561440000 2706268 2101243 2593538 2172899 3346282 3308747 3047303 2636151 2826780 1818679 TRUE FALSE 2813113.55 2462115.14 2661127.731 2602691.937 2777482.181 2540340.654 2808447.428 2600817.708 2725044.74 2175014.329 1.293377019 1.131999503 1.223498942 1.196632087 1.276994888 1.16796502 1.29123169 1.195770378 1.252885879 1 21.05259348 -1.864068604 2.452670571 0.896710101 1.222623061 0.635879399 0.051169227 5842217.379 3186335.025 3511366.299 0.0110929 0.013675128 1.864068604 0.325912961 DSQDGSSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DSQDGSSYR 9 0 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;; 214.05 2.05E-06 2240690000 1813130 1976174 2037898 1883566 2295923 2490892 2207796 2027518 1976649 1903418 FALSE TRUE 1884713.772 2315566.512 2091007.296 2256129.733 1905662.829 1912420.083 2034743.181 2000342.438 1905509.789 2276356.314 0.827952004 1.017224983 0.918576447 0.991114493 0.837154894 0.840123346 0.893859704 0.878747508 0.837087664 1 21.11829497 3.232977682 24.9981717 0.874486412 0.942886087 0.154155314 0.064632296 201.8521755 903813.756 0.017113633 0.021003162 1709.927441 -3.232977682 0.068399675 DSQQTLINIPSLNDSDS(ph)EIEDISEIESNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 DSQQTLINIPSLNDS(0.413)DS(0.587)EIEDISEIESNR;DSQQTLINIPSLNDS(0.342)DS(0.657)EIEDISEIESNR;DSQQTLINIPS(0.105)LNDS(0.388)DS(0.503)EIEDIS(0.004)EIESNR;DSQQTLINIPS(0.011)LNDS(0.389)DS(0.6)EIEDISEIESNR 185.35 4.80E-18 327873000 731374 789059 824486 759470 876556 1013104 847252 857018 904706 746861 TRUE FALSE 760249.2103 924573.7452 845972.7825 909690.8992 727559.3242 777825.9497 780842.1744 845531.0755 872145.8078 893194.1134 0.851157883 1.035131929 0.947132062 1.01846943 0.814559023 0.870836404 0.874213301 0.946637537 0.976434791 1 19.76861422 1.270407485 2.816738652 0.995073755 0.919753728 0.156558858 0.066570155 0.531365045 7.025667515 0.061223926 0.017831297 18.63835095 -1.270407485 -0.075320027 DSRDPMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSRDPMYR 8 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 76.17 0.029755 0 10558 105840 45729 82295 22577 68451 20951 37101 21449 143410 FALSE TRUE 10974.83799 124017.1967 46920.73531 98572.70537 18739.3696 52554.29263 19308.80587 36603.72178 20677.05468 171508.4437 0.063990074 0.723096741 0.273576824 0.574739664 0.109262082 0.306423937 0.112582246 0.213422272 0.120559981 1 17.38792008 -1.411281658 4.971855997 1.000848377 0.282846938 0.529124191 0.204411349 0.001857966 0.000220003 0.191299997 0.04504087 0.038789872 1.411281658 -0.718001439 DSRPLS(ph)PILHIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 DS(0.468)RPLS(0.532)PILHIVK 115.87 0.00038172 245290000 759220 555810 707180 606450 919390 911050 914140 760760 793350 558960 TRUE FALSE 789194.5918 651266.0439 725609.6918 726403.9999 763112.4162 699472.4446 842487.3181 750563.2566 764797.4885 668477.5101 1.180585106 0.974252737 1.085466124 1.086654359 1.141567823 1.046366458 1.260307648 1.122795076 1.144088585 1 19.3505195 3.271625824 1.573882811 1.134550164 1.069775161 0.02318199 0.079857081 0.864304694 4.438047126 0.025360176 0.037795641 1869.071106 -3.271625824 -0.064775003 DSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSRPSQAAGDNQGDEAK 17 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;; 122.31 5.23E-05 925879000 299856 182239 244718 213803 320287 417403 337385 269057 287081 153647 FALSE TRUE 311694.5464 213537.1306 251095.5521 256092.5953 265844.7301 320467.4791 310939.8821 265450.731 276749.0109 183751.1879 1.696285885 1.162099321 1.366497572 1.393692189 1.446764689 1.744029428 1.692178895 1.444620489 1.506107329 1 17.48739405 -1.075475228 5.256437563 0.999993239 1.489436949 0.43629883 0.168596121 1.38E-05 2.42E-06 0.168436219 0.039700249 0.084047495 1.075475228 0.489443709 DSS(ph)QEYTDSTGIDLHEFLVNTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.133)S(0.867)QEYTDSTGIDLHEFLVNTLK 221.5 1.14E-32 62163000 47730 31617 43396 25613 74843 50946 58462 44866 61619 26720 TRUE FALSE 49614.41726 37046.9738 44526.93541 30679.17495 62121.21359 39114.56359 53879.59568 44264.64466 59401.34423 31955.27241 1.552620695 1.159338382 1.393414358 0.960066137 1.944005133 1.224041 1.686094081 1.3852063 1.858890247 1 14.96376637 3.255079088 24.99999931 1.523223237 1.267791 0.142369066 0.300323855 447.771974 677679.6467 0.075575987 0.102047307 1799.198532 -3.255079088 -0.255432237 DSS(ph)TSPGDYVLSVSENSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSSTSPGDYVLSVSENSR 18 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 DS(0.002)S(0.996)T(0.002)SPGDYVLSVSENSR;DSS(0.995)T(0.005)SPGDYVLSVSENSR;DSS(0.999)TSPGDYVLSVSENSR 254.53 1.63E-30 537730000 451330 412150 433820 423250 478000 596010 567600 459440 460870 310069 TRUE FALSE 469148.8569 482933.5564 445125.7056 506967.5867 396749.7307 457595.7101 523110.0289 453281.9583 444283.3787 370821.0839 1.265162304 1.302335755 1.200378632 1.367148764 1.069922256 1.234006722 1.410680383 1.222373748 1.198107114 1 18.50036375 0.808045771 2.160412351 1.000464849 1.260811227 0.43986669 0.088024058 0.653746576 5.300400325 0.081720586 0.022358424 6.42755454 -0.808045771 0.260346378 DSS(ph)VEVR ddPTM_MDA-MB-175_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(0.013)S(0.987)VEVR 154.49 0.0017572 313230000 483140 476360 499510 441010 659340 735300 597440 548070 550390 447030 TRUE FALSE 502214.7403 558171.1244 512527.641 528240.4617 547265.6223 564537.7186 550611.0917 540724.0181 530581.5714 534616.9696 0.939391693 1.044058001 0.958681954 0.988072754 1.02365928 1.055966703 1.029916974 1.011423222 0.992451796 1 19.02814611 3.258475563 7.260136207 1.021373702 0.985084618 0.258248711 0.029894362 0.229918732 51.47057992 0.008145348 0.010740071 1813.324642 -3.258475563 -0.036289085 DSSDSADGRAT(ph)PSENLVPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSSDSADGRATPSENLVPSSAR 22 1 Q8N684-2;Q8N684;Q8N684-3;F5H669;F5H6M0;F5H047 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 DSSDS(0.001)ADGRAT(0.998)PSENLVPSSAR;DSSDSADGRAT(1)PSENLVPSSAR 117.08 0.0002304 1150930000 515080 538530 541960 479540 612610 644520 515640 562160 496530 534480 TRUE FALSE 535415.7561 631018.3383 556083.9228 574391.5807 508478.771 494839.9978 475222.7894 554625.1647 478659.9823 639201.1228 0.83763269 0.98719842 0.869967062 0.898608529 0.795491048 0.774153831 0.743463634 0.867684904 0.74884096 1 19.28591042 3.246729842 23.41414691 0.811248394 0.902670461 0.179368869 0.0783498 113.9963844 326724.5626 0.020248746 0.026906763 1764.939579 -3.246729842 0.091422066 DSSEATGWEEPS(ph)PPSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSSEATGWEEPSPPSIR 17 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 DSSEATGWEEPS(1)PPSIR;DSSEATGWEEPS(1)PPSIR 205.98 2.05E-17 141990000 247795 218835 236872 241238 314779 341140 287096 243135 258293 198079 TRUE FALSE 257578.1379 256418.2089 243045.0789 288954.1564 261272.978 261915.405 264592.6653 239876.173 248997.0854 236888.7876 1.08733782 1.082441307 1.025988108 1.219788236 1.102935182 1.105647117 1.116948877 1.012610919 1.051113849 1 17.85385039 1.734979835 7.529104224 1.024798999 1.106166008 0.406074603 0.04677644 0.126615959 22.05293398 0.022970612 0.012160128 54.32251079 -1.734979835 0.081367008 DSSFFDKFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSSFFDKFFK 10 1 O75363;G3XAF7;O75363-2;H0Y542 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 ; 145.28 2.80E-05 879620000 1624030 1363550 1564930 1183980 2701650 2202890 1941000 1809680 2251510 1620900 FALSE TRUE 1688147.958 1597729.106 1605713.361 1418167.71 2242424.498 1691302.183 1788859.348 1785424.2 2170478.595 1938484.321 0.870859743 0.824215645 0.828334459 0.731585855 1.156792693 0.872486903 0.922813421 0.921041342 1.119678179 1 20.88649764 3.261273451 24.99973091 0.978988636 0.815538386 0.499267322 0.089472405 220.1699891 242336.6665 0.024454689 0.033089055 1825.044471 -3.261273451 -0.16345025 DSSFTEVPRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK;DSSFTEVPRS(1)PK 170.42 2.49E-05 3531900000 6475830 2994390 4144610 2813390 6102090 6606390 5320930 4269190 4615970 2537310 TRUE FALSE 6731500.769 3508653.189 4252621.941 3369870.145 5064858.921 5072156.043 4903861.603 4211968.491 4449842.141 3034447.315 2.218361392 1.156274216 1.4014486 1.11053836 1.669120731 1.671525493 1.616064177 1.388051284 1.46644238 1 21.53300234 0.415304392 1.160631486 0.999830554 1.512000076 0.221539356 0.295486908 3.988158047 6.432460505 0.272873705 0.082666508 2.601982621 -0.415304392 0.512169522 DSSGQHVDVSPTSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSSGQHVDVSPTSQR 15 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 91.457 0.0053763 0 115474 246988 218024 263980 181508 350150 203448 203245 179012 243464 FALSE TRUE 120033.0027 289406.2677 223705.8845 316194.4561 150655.335 268832.9691 187501.2141 200520.8332 172569.3931 291166.1094 0.412249224 0.993955884 0.768310175 1.085958997 0.517420572 0.923297597 0.643966479 0.688681913 0.592683652 1 18.15148292 2.202663074 24.98062747 0.701406052 0.794055941 0.004860966 0.2166281 651.9134356 453654.3507 0.075557176 0.055804651 159.4641545 -2.202663074 0.092649889 DSSGWSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSSGWSSSK 9 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 131.5 0.0026649 0 52907 43186 44360 34859 62087 62293 56363 43077 45900 40883 FALSE TRUE 54995.80921 50602.85956 45516.05804 41754.00616 51533.47392 47826.39481 51945.12078 42499.62327 44248.06797 48893.2411 1.124814146 1.034966356 0.930927405 0.853983193 1.053999955 0.978180087 1.062419255 0.869233095 0.904993553 1 15.57734742 4.510410753 3.098653713 0.954124427 1.121101511 0.383001661 0.067034327 0.28201351 5.014813306 0.0171499 0.086653376 32389.98548 -4.510410753 0.166977084 DSSKGEDS(ph)AEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSSKGEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 45 2 Q12906-7;Q12906-4;Q12906-6 Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 DS(0.066)S(0.066)KGEDS(0.384)AEET(0.384)EAKPAVVAPAPVVEAVS(0.08)T(0.016)PS(0.003)AAFPSDATAENVK 59.899 0.0038851 69759000 222270 55557 95944 50472 173150 152770 159810 98994 112610 34055 TRUE FALSE 231045.3912 65098.48258 98444.37946 60455.21096 143718.0248 117291.4828 147283.6746 97667.14735 108557.1881 40727.42523 5.672968275 1.598394257 2.417152052 1.484385782 3.528777575 2.879914016 3.616326684 2.398068299 2.665456691 1 15.31371299 0.518677106 1.301743642 1.001562949 2.881528696 0.209282634 1.129845549 3.159325453 6.833349434 1.016751036 0.302977268 3.301240057 -0.518677106 1.879965747 DSSLLRDDLIQDVEIQIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSSLLRDDLIQDVEIQIISR 20 1 D6RCC4;D6RCC9;Q8NEC7 D6RCC4 GSTCD Glutathione S-transferase C-terminal domain-containing protein 0 65.47 0.022547 7427200 7555.3 9514.4 10834 11074 11468 12075 12109 12681 12843 7985 FALSE TRUE 7853.589078 11148.42419 11116.34294 13264.40415 9518.673456 9270.764248 11159.86494 12511.03194 12380.78294 9549.507868 0.822407729 1.167434421 1.164074955 1.389014422 0.996771099 0.970810682 1.168632467 1.310123214 1.296483872 1 13.22121067 2.000104149 24.99975323 1.237339845 1.099511579 0.084868638 0.16174843 7.628647871 1830650.598 0.06164839 0.045056468 100.023984 -2.000104149 -0.137828266 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 43 3 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ;; 148.2 6.54E-14 2855110000 1042515 827751 1099228 604810 1606208 1410916 1016010 1070393 1282503 927472 FALSE TRUE 1083674.297 969910.7952 1127874.785 724439.6128 1333185.338 1083252.142 936372.4814 1056046.133 1236345.968 1109192.381 0.976993997 0.874429731 1.016843249 0.653123503 1.201942387 0.976613399 0.844193034 0.952085635 1.114636188 1 20.08107818 1.345610218 7.114829823 1.055765096 0.933602602 0.114941783 0.133974458 0.43912928 25.24933897 0.086809699 0.031459271 22.16206468 -1.345610218 -0.122162494 DSSSLSSCTSGILEERS(ph)PAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSSSLSSCTSGILEERSPAFR 21 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR;DSSSLSSCTSGILEERS(1)PAFR 165.85 8.58E-12 619750000 109663 177078 193497 167765 186681 236869 168248 182064 222082 207526 TRUE FALSE 113992.5799 207489.769 198539.6908 200948.4163 154949.0303 181859.7645 155060.2821 179623.7299 214089.3122 248186.7464 0.459301641 0.836022761 0.799960891 0.809666186 0.624324355 0.732753732 0.624772613 0.723744247 0.862613799 1 17.92106655 1.043842038 2.731641096 0.997878812 0.706911224 0.456793307 0.10566348 0.217482498 3.500134108 0.09677148 0.025960664 11.06221356 -1.043842038 -0.290967587 DSSSLSSCTSGILEERS(ph)PAFRGPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSSSLSSCTSGILEERSPAFRGPDR 25 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR;DSSSLSSCTSGILEERS(1)PAFRGPDR 316.73 5.64E-75 1083720000 268651 345066 338153 257049 418917 431257 246921 328740 330929 461483 TRUE FALSE 279257.5489 404328.4013 346965.545 307892.525 347709.638 331104.0975 227566.6868 324333.778 319018.9299 551901.7582 0.50599141 0.732609373 0.628672657 0.557875601 0.630020892 0.599933036 0.412331875 0.587665781 0.57803572 1 19.07405196 -0.725919985 6.424481597 1.000000003 0.581560635 0.715525307 0.079171311 3.45E-09 5.36E-10 0.077069803 0.018165527 0.18796631 0.725919985 -0.418439368 DSSVPGS(ph)PSSIVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DSSVPGSPSSIVAK 14 0 Q08495;Q08495-2;E5RGQ0;E5RJ61;A0A087WT94 Q08495 DMTN Dematin 1 DSSVPGS(0.996)PS(0.003)S(0.001)IVAK;DSSVPGS(0.996)PS(0.003)S(0.001)IVAK;DSSVPGS(0.859)PS(0.128)S(0.013)IVAK 211.75 3.56E-09 438043000 983800 711530 871480 747610 1197610 1189510 1206120 1003770 1112740 682320 TRUE FALSE 1022641.184 833729.7426 894191.4847 895485.0266 994040.68 913264.3297 1111581.163 990316.105 1072692.705 816007.5402 1.253225164 1.021718185 1.095812772 1.09739798 1.218175851 1.119186141 1.36221923 1.213611463 1.314562246 1 19.63822296 3.233675617 23.61334252 1.221809508 1.108713797 0.122808412 0.108109039 93.17704729 450404.8598 0.029167831 0.035968981 1712.677597 -3.233675617 -0.113095711 DSTEEKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DSTEEKSPR 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 DSTEEKS(1)PR;DSTEEKS(1)PR;DSTEEKS(1)PR;DSTEEKS(1)PR 129.34 0.00023736 1254270000 2228020 1150910 1602800 1128740 2158470 2150610 2073480 1589200 1730060 935370 TRUE FALSE 2315983.95 1348569.84 1644570.285 1352001.403 1791574.04 1651163.42 1910955.22 1567899.373 1667795.479 1118637.843 2.07036081 1.205546414 1.470154345 1.208614041 1.601567524 1.476048241 1.708287657 1.401614815 1.490916376 1 20.09331161 0.202576474 1.363386519 0.999575426 1.502386343 0.297563599 0.236815359 9.337781627 14.61209534 0.215977821 0.061558003 1.594323598 -0.202576474 0.502810917 DSTFDLPADSIAPFHICYYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSTFDLPADSIAPFHICYYGR 21 0 Q8N1G2 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 0 ; 102.37 0.00046342 31353000 46726 47088 52197 45907 52510 62376 57708 53466 54105 48616 FALSE TRUE 48570.77856 55174.99771 53557.2967 54987.26758 43584.36896 47890.11932 53184.69617 52749.37572 52157.77162 58141.37439 0.83539096 0.948979935 0.921156358 0.945751079 0.749627428 0.823683991 0.914747832 0.907260557 0.897085288 1 15.82727755 0.571652605 0.946461582 0.999661021 0.879265743 0.272891478 0.058775991 2.057409647 2.89019958 0.060179628 0.019456809 3.729517117 -0.571652605 -0.120395278 DSTLIMQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 181.55 4.36E-06 3685607000 1390146 1391907 1377016 1731887 2203596 2237292 1885504 1580858 1554335 1591881 FALSE TRUE 1445030.038 1630956.2 1412902.168 2074449.079 1829029.539 1717714.839 1737713.27 1559669.184 1498394.787 1903779.604 0.759032209 0.856693809 0.742156374 1.089647707 0.960735967 0.902265596 0.91277019 0.819248815 0.787063158 1 20.86043504 DSTRHTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSTRHTEK 8 1 H0YFT1;H0YG32;H0YGE2 H0YFT1 NLRC5 0 88.948 0.012999 212540000 139230 164150 153680 217610 430030 418210 347430 200700 192020 286870 FALSE TRUE 144726.9079 192341.4856 157685.027 260652.6085 356933.6542 321087.0655 320197.5288 198009.9448 185109.2377 343076.684 0.421850025 0.560637008 0.459620354 0.759750285 1.0403903 0.935904655 0.933311833 0.577159434 0.53955645 1 18.38817156 3.677987515 4.898379221 0.817440006 0.488158083 0.495311064 0.160389881 0.205601744 10.21494828 0.04776487 0.076499648 4764.172909 -3.677987515 -0.329281923 DSVPKPSVLFLHPDLGVGGAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSVPKPSVLFLHPDLGVGGAER 22 1 Q9H553;A0A0A0MTE0 Q9H553 ALG2 "Alpha-1,3/1,6-mannosyltransferase ALG2" 0 139.36 8.27E-08 274590000 316820 233600 241520 221900 373900 339100 319890 246540 277700 197380 FALSE TRUE 329328.2982 273718.9828 247814.2096 265791.1577 310344.6116 260349.1641 294816.1859 243235.5346 267705.6312 236052.8319 1.395146568 1.159566613 1.049825192 1.125981652 1.314725221 1.102927518 1.248941534 1.030428369 1.134092013 1 17.84875027 8 0.031892827 0.397884325 2.274320303 0.310971223 0.100508113 1608.480123 3.927658347 71.54220564 183.6529854 99999999.98 -8 1.876435977 DSYCSYMGHFDLLNYFAIAENESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSYCSYMGHFDLLNYFAIAENESK 24 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 132.72 4.71E-05 89877000 34487.3 31519.9 40158.8 31158.6 50614.9 48696 46773 43195.6 44004.4 30246.1 FALSE TRUE 35848.88523 36933.19763 41205.37132 37321.67808 42011.39738 37387.092 43106.81004 42616.63364 42420.69024 36172.2442 0.991060578 1.021036943 1.139143347 1.031776681 1.161426345 1.033585082 1.191709583 1.178158408 1.172741454 1 15.14259549 5.235204316 0.542064829 1.139088893 0.785228374 0.253376945 0.067847436 7.576851577 1.145288086 0.033782439 1.898166986 171871.6774 -5.235204316 -0.353860519 DSYDSYATHNE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSYDSYATHNE 11 0 Q14011 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;;;; 224.51 1.43E-11 3989570000 3292730 3851770 4178390 3692250 4556960 4976180 4209500 4014530 3715740 3620810 FALSE TRUE 3422729.523 4513281.535 4287282.276 4422566.03 3782369.567 3820537.61 3879548.391 3960721.792 3582011.243 4330238.395 0.790425194 1.042270915 0.990079964 1.021321606 0.873478368 0.882292673 0.895920279 0.914665991 0.827208785 1 22.04601502 3.223114027 24.9562304 0.895160738 0.968903147 0.135207442 0.075537313 384.1051644 620576.8287 0.020736386 0.024868476 1671.529429 -3.223114027 0.073742409 DSYESYGNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 229.55 3.66E-09 4978784000 1093415 1184047 1173108 1062050 1402021 1430389 1344653 1210807 1128443 1085629 FALSE TRUE 1136583.869 1387397.862 1203680.158 1272120.32 1163705.971 1098202.833 1239255.584 1194578.113 1087830.557 1298337.217 0.875414995 1.068595927 0.927093626 0.979807329 0.896304871 0.84585331 0.954494386 0.920083086 0.837864418 1 20.30823371 3.237465927 24.99995115 0.906436487 0.967744661 0.143877626 0.063418282 48.94596247 1117816.315 0.016952517 0.021382833 1727.690428 -3.237465927 0.061308174 DSYGGPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSYGGPPRR 9 1 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 90.64 0.018107 303300000 146650 200530 168480 175810 224730 233940 191960 204690 168550 222030 FALSE TRUE 152439.8552 234969.4676 172870.7272 210584.6933 186530.4749 179610.9804 176913.6736 201946.4654 162483.9184 265532.5275 0.574091079 0.884898998 0.651034089 0.793065525 0.702476931 0.676417997 0.666259894 0.760533812 0.611917191 1 18.01852908 -2.147818661 2.468028426 1.671141123 0.710297346 0.514408731 0.086458786 13089363.81 2648876.586 49335736.89 0.019497473 0.007115105 2.147818661 -0.960843777 DSYLILETLPTEYDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DSYLILETLPTEYDSR 16 0 P17980;E9PM69;E9PKD5;E9PLG2;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;;;; 213.63 3.30E-12 427346000 411862 442899 476969 471117 556369 609339 520125 488666 473163 441488 FALSE TRUE 428122.6298 518963.458 489399.204 564302.5365 461797.5961 467829.2519 479356.2434 482116.2316 456133.9561 527989.1208 0.810855021 0.982905589 0.92691153 1.068776826 0.874634681 0.886058507 0.90789038 0.913117738 0.863907869 1 19.01014868 DSYS(ph)SSR ddPTM_MDA-MB-175_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" 1 DS(0.006)YS(0.586)S(0.324)S(0.084)R 84.522 0.035964 0 105510 213150 220440 195210 204150 286460 161290 203300 212790 267190 TRUE FALSE 109675.6163 249756.8544 226184.8475 233821.9554 169448.6559 219934.0063 148647.6683 200575.096 205131.7295 319540.7648 0.343228872 0.781611869 0.707843482 0.731743743 0.530288071 0.688281529 0.465191565 0.627697991 0.641957935 1 18.28564047 0.629037094 2.994913126 0.999992396 0.616399061 0.459492148 0.126153296 4.706006106 36.96168996 0.114608277 0.029963364 4.256347659 -0.629037094 -0.383593335 DSYSS(ph)SR ddPTM_MDA-MB-175_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" 1 DS(0.005)YS(0.267)S(0.689)S(0.04)R 80.219 0.032 162920000 82339 329890 278530 279380 274180 389570 192930 275900 265470 482940 TRUE FALSE 85589.8073 386546.0413 285788.7206 334640.5301 227574.9815 299098.2715 177807.6425 272202.0118 255915.7866 577562.8466 0.148191332 0.669270961 0.494818395 0.579401068 0.394026352 0.517862728 0.307858519 0.471294186 0.443095999 1 19.13961841 -1.267265673 3.34541011 1.001918686 0.454801704 0.594973457 0.136676619 53253151.83 79204847.55 1048839.039 0.030666014 0.054042363 1.267265673 -0.547116982 DSYSSS(ph)RSDLYSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DSYSSSRSDLYSSGR 15 1 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 DSYS(0.068)S(0.068)S(0.542)RS(0.319)DLYS(0.001)S(0.001)GR 161.94 4.27E-06 105580000 91674 101880 106730 94395 132140 133320 84612 104560 113680 103530 TRUE FALSE 95293.36031 119377.0975 109511.4715 113066.0493 109678.89 102358.4505 77979.89035 103158.5442 109588.679 123814.7213 0.769644831 0.964159158 0.884478601 0.913187447 0.885830771 0.826706626 0.629811137 0.83316865 0.885102174 1 16.91782333 2.699041525 5.041601697 0.807617804 0.889879396 0.021707791 0.097988314 0.409984373 26.33798714 0.031043854 0.02981774 500.0823478 -2.699041525 0.082261592 DSYSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 187.63 0.0013526 540830000 716470 593860 672310 517610 847120 842960 744360 605960 674400 633250 FALSE TRUE 744756.7888 695850.8354 689830.9509 619991.7131 703126.845 647195.3152 686015.1182 597838.0974 650128.4757 757323.2132 0.983406788 0.918829402 0.910880505 0.818661969 0.928436938 0.854582699 0.905841926 0.789409445 0.858455762 1 19.53054962 4.661946309 1.215770314 0.868290515 1.024424951 0.209107668 0.056810872 1.672927116 2.332393569 0.015612244 0.318357224 45914.12465 -4.661946309 0.156134436 DSYVGDEAQS(ph)KR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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" 1 DSYVGDEAQS(1)KR;DSYVGDEAQS(1)KR;DSYVGDEAQS(1)KR;DSYVGDEAQS(1)KR 144.33 3.86E-05 1096890000 1648660 941250 1197760 852770 1262480 1704990 1387490 1190510 1320390 755020 TRUE FALSE 1713750.37 1102902.366 1228974.61 1021445.361 1047884.101 1309031.912 1278734.908 1174553.161 1272869.422 902951.7133 1.897942431 1.221441135 1.361063489 1.131229218 1.160509566 1.449725265 1.416171972 1.300792881 1.409676069 1 19.78428931 7.999981454 0.027163187 8.05E-08 3.199394195 0.251707126 0.201234743 3005.428179 6.268368949 245.5510543 548.5678887 99995729.71 -7.999981454 3.199394115 DSYVGDEAQSK ddPTM_MDA-MB-175_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 ;;;;;;;;; 334.69 2.99E-57 15632376000 12225320 7767203 10267702 8158849 12631879 12830544 13868308 10501071 11384709 6392720 FALSE TRUE 12707985.07 9101159.695 10535286.75 9772644.98 10484716.72 9850844.605 12781273.78 10360321.32 10974975.55 7645251.088 1.662206372 1.190433066 1.378017102 1.278263443 1.371402535 1.288491966 1.671792546 1.355131597 1.435528463 1 22.86613245 -0.927668249 4.174567289 0.999987399 1.397109088 0.400650706 0.147860747 18814687.75 42169439.29 3754.846188 0.033449834 0.118122261 0.927668249 0.397121689 DSYVGDEAQSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 DSYVGDEAQSKR 12 1 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;; 198.14 3.00E-07 55107307000 40372672 34957551 39062224 25487918 51625214 48206087 36512263 37077829 41561634 31212332 FALSE TRUE 41966616.27 40961238.45 40080217.65 30529352.11 42849978.56 37010953.86 33650336.42 36580861.35 40065838.91 37327790.86 1.124272701 1.09733894 1.073736664 0.817871923 1.147937705 0.991512035 0.90148213 0.979989989 1.073351463 1 25.15374679 3.981429283 24.87758937 0.984631864 1.104488867 0.275744218 0.083672161 838.2696017 1122962.753 0.020780664 0.038322871 9581.406882 -3.981429283 0.119857002 DSYYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DSYYDR 6 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ; 110.61 0.066431 1508860000 1122190 1349280 1484530 1296800 1712190 1793260 1432260 1437090 1340100 1447220 FALSE TRUE 1166494.928 1581008.344 1523218.071 1553303.169 1421152.555 1376802.542 1319995.719 1417828.159 1291870.063 1730775.05 0.673972581 0.913468416 0.880078593 0.897461036 0.821107604 0.795483238 0.762661629 0.819186849 0.746411304 1 20.7229868 3.015847944 24.22123725 0.808988963 0.850441104 0 0.090020353 588.1341598 898866.5704 0.024481371 0.029250608 1037.165217 -3.015847944 0.041452141 DT(ph)HEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_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 72.533 0.0029279 121600000 26716 30701 36985 31422 46895 49822 49990 39628 43750 32288 TRUE FALSE 27770.76831 35973.65793 37948.85948 37637.17781 38923.80465 38251.59556 46071.65318 39096.85148 42175.44605 38614.21541 0.719185098 0.931616959 0.982769146 0.974697464 1.008017494 0.990609162 1.193126746 1.012498922 1.092225897 1 15.23684444 5.577140171 0.654547818 1.057587864 2.42E-12 0.733346577 0.05880337 4.307806014 0.621446207 0.023281427 4.363972398 377694.0743 -5.577140171 -1.057587864 DTAAWTVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTAAWTVGR 9 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 176.44 0.00012365 1380461000 856150 661468 703946 661114 911998 898172 814067 624738 729313 639537 FALSE TRUE 889951.4631 775069.9835 722291.4111 791880.376 756976.9057 689585.1649 750258.3014 616364.409 703065.1676 764842.0305 1.16357552 1.013372635 0.944366787 1.035351542 0.989716668 0.901604694 0.980932364 0.805871519 0.919229252 1 19.54480228 7.999999998 0.426840805 0.908380232 5.507010493 0.53292291 0.060971312 59.67960923 0.755639171 0.0404268 235.4409072 99999999.47 -7.999999998 4.598630261 DTATYWPLNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTATYWPLNWR 11 0 E9PCJ7;Q8N806 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ; 135.55 0.00072136 87466000 198079 119863 186519 126166 238452 202426 177966 176610 178511 150838 FALSE TRUE 205899.3119 140448.5378 191379.8384 151121.2582 197920.0142 155415.6293 164016.5599 174242.8318 172086.424 180391.8181 1.141400503 0.778574878 1.060911966 0.837738983 1.097167356 0.86154478 0.909223941 0.965913164 0.953959142 1 17.46077438 4.781587918 23.37798553 0.94209073 1.141402064 0.293294807 0.093500641 16635.95555 9038317.832 0.019754224 8.496203068 60476.67674 -4.781587918 0.199311334 DTCVQS(ph)PISSFPCTDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DTCVQSPISSFPCTDLK 17 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 DTCVQS(1)PISSFPCTDLK;DTCVQS(1)PISSFPCTDLK;DTCVQS(1)PISSFPCTDLK 213.02 1.10E-12 646450000 1032130 644920 865610 687700 1142040 1195160 1112990 983710 1025880 638740 TRUE FALSE 1072879.289 755679.9932 888168.5077 823725.0074 947916.4487 917602.2028 1025750.936 970524.9765 988958.7792 763888.8736 1.404496552 0.989253829 1.162693342 1.07833094 1.24090883 1.201224726 1.342801252 1.270505449 1.294636973 1 19.54300325 3.13580939 8.761910371 1.247932283 1.1470295 0.038644333 0.13096002 0.550426286 42.47650812 0.035380764 0.042352428 1367.128667 -3.13580939 -0.100902783 DTCYS(ph)PKPSVYLSTPSSASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 DTCYS(1)PKPSVYLSTPSSASK;DTCYS(0.999)PKPSVYLSTPSSASK 228.71 1.73E-25 887330000 2005470 916910 1425180 966440 2016390 1909930 1872100 1503700 1716140 777800 TRUE FALSE 2084647.504 1074382.16 1462321.362 1157598.947 1673644.748 1466377.703 1725359.91 1483545.361 1654376.457 930195.0181 2.241086507 1.155007433 1.572058905 1.24446909 1.799240713 1.576419648 1.854836756 1.594875625 1.778526464 1 19.82717369 DTDAAVGDNIGYITFVLFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTDAAVGDNIGYITFVLFPR 20 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 184.31 1.15E-15 0 33080 27213 27901 31175 43050 29551 40085 31224 40024 31474 FALSE TRUE 34386.02394 31886.62106 28628.12298 37341.32195 35732.37638 22688.2281 36943.03296 30805.49335 38583.54406 37640.72769 0.91353239 0.847130834 0.760562421 0.992045697 0.949300892 0.602757425 0.981464366 0.818408549 1.025047772 1 15.2000069 1.23248202 24.98401943 1.012523991 0.857725446 0.239194892 0.11012486 215.5782516 886017.9426 0.09191535 0.025311603 17.07977006 -1.23248202 -0.154798544 DTDDIES(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTDDIESPKR 10 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9;D6RGH8 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 DTDDIES(1)PKR 63.16 0.049242 363790000 465500 311110 345360 311070 522080 580550 454540 379540 385400 282080 TRUE FALSE 483878.2994 364540.7224 354360.3653 372598.7175 433337.0281 445726.0608 418911.9671 374452.8871 371529.5293 337348.1753 1.434358728 1.080606771 1.050429175 1.104493058 1.284539416 1.321264182 1.241779259 1.109989366 1.101323667 1 18.36387883 1.260959097 1.697755255 1.014990894 1.205286712 0.270811774 0.112883705 0.510224583 2.64668087 0.108969441 0.032618507 18.23723932 -1.260959097 0.190295817 DTDFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DTDFEHR 7 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;;;;; 194.27 0.00048445 4284510000 5500650 5904490 6281610 6053740 7324690 8017490 6859880 6317400 6546790 5566620 FALSE TRUE 5717819.909 6918540.227 6445313.917 7251151.703 6079641.81 6155549.454 6322184.681 6232725.586 6311172.307 6657292.61 0.858880666 1.039242322 0.968158423 1.089204295 0.913230373 0.924632552 0.949663031 0.936225272 0.948008849 1 22.66650415 DTDIVDEAIYYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTDIVDEAIYYFK 13 0 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 ;;; 220.25 4.91E-11 241716000 510267 364238 505154 451874 592756 586850 694948 507969 555311 273389 FALSE TRUE 530412.7352 426793.0431 518318.7282 541253.3285 491999.5468 450562.9813 640476.1599 501160.5064 535325.4656 326954.3402 1.622283818 1.305359772 1.585293922 1.655440109 1.504795888 1.378060866 1.958916219 1.532814968 1.637309556 1 18.31872965 DTDPDSKPFSLQETYEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTDPDSKPFSLQETYEAK 18 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141 D6RGI3;B1AMS2 SEPT11;SEPT6 Septin-11;Septin-6 0 ; 248.35 1.57E-24 408710000 951230 388180 669830 476240 886820 879890 1056830 679190 734380 291390 FALSE TRUE 988785.2949 454846.8954 687286.3201 570438.8506 736078.6532 675548.8824 973992.9031 670086.569 707949.8073 348482.2915 2.837404709 1.305222407 1.97222739 1.636923495 2.112241199 1.938545799 2.794956664 1.92287122 2.031523049 1 18.41072582 DTDSEEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 196.77 6.77E-05 4714600000 3573200 4213200 4207700 5582900 3483500 5147300 6964600 4649900 3872700 2360590 FALSE TRUE 3714272.695 4936784.326 4317356.119 6687180.957 2891375.914 3951917.583 6418696.453 4587575.696 3733322.283 2823102.414 1.315670546 1.748708903 1.529294898 2.368734809 1.024183855 1.399849174 2.273632165 1.62501214 1.322418296 1 21.42885004 1.046079817 3.117116853 1.008330226 1.68039975 0.230307865 0.387075261 0.311133051 6.534571421 0.358625876 0.094488861 11.11936067 -1.046079817 0.672069524 DTDSEEEIREAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;; 301.35 5.38E-41 28151000000 4297030 5132370 5815440 5279270 4929460 6445020 6188800 5302560 5250390 4151350 FALSE TRUE 4466680.062 6013814.623 5966995.144 6323493.849 4091552.15 4948261.78 5703705.685 5231487.856 5061429.49 4964727.55 0.899682816 1.211308085 1.201877663 1.273683961 0.824124206 0.996683449 1.148845657 1.053731107 1.019477794 1 22.24328312 3.26239518 24.99816432 1.021948313 1.155203014 0.240979524 0.119175653 364.5980403 382395.0268 0.033586732 0.045452878 1829.764429 -3.26239518 0.1332547 DTDSEEEIREAFRVFDKDGNGYISAAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTDSEEEIREAFRVFDKDGNGYISAAELR 29 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ; 215.53 1.22E-34 1209010000 308908 156195 218048 162966 313318 262679 263474 205066 236579 177864 FALSE TRUE 321103.9264 183020.2762 223730.51 195200.1884 260060.3183 201675.7832 242822.2194 202317.4257 228064.568 212713.0454 1.509563862 0.860409271 1.051794964 0.917669098 1.222587537 0.948111964 1.141548319 0.951128434 1.072170104 1 17.69854899 4.750478335 24.96206649 1.021369595 1.509564163 0.672179646 0.102886921 1000.247936 2095014.289 0.022333731 0.373835905 56296.10333 -4.750478335 0.488194568 DTDYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTDYKR 6 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 87.989 0.083079 919690000 550920 427560 523200 395520 663810 595520 625530 564200 566450 415590 FALSE TRUE 572670.747 500990.104 536835.0218 473752.6755 550975.8133 457219.5052 576499.3241 556637.8218 546063.5751 497016.9035 1.152215836 1.007994095 1.080114213 0.95319228 1.108565542 0.919927475 1.159918948 1.119957526 1.0986821 1 18.92293539 2.183526465 24.99997804 1.108251945 1.037083239 0.113573186 0.075128556 150.0518974 68161.77775 0.025990532 0.019195294 152.5901377 -2.183526465 -0.071168706 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 149.2 3.94E-08 451810000 421742 146721 203860 95100 386975 271304 227642 199622 248765 122350 TRUE FALSE 438392.6998 171919.1904 209172.7591 113910.4962 321197.1277 208297.7577 209798.8252 196946.3936 239811.9962 146322.14 2.996079062 1.174936277 1.429535948 0.778491185 2.195136893 1.423555982 1.433814632 1.345978084 1.638931718 1 17.15878855 4.743501186 24.97024874 1.400103793 2.996079729 0.644975596 0.359414041 307.3999293 1553586.07 0.080996778 0.671148944 55398.90572 -4.743501186 1.595975936 DTEEQNPETVNWEDRPS(ph)TPTILGYEVMEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPETVNWEDRPS(0.492)T(0.492)PT(0.016)ILGYEVMEER 213.26 8.92E-27 207080000 153590 118320 127700 120850 142820 181470 141530 127680 122860 106830 TRUE FALSE 159653.8518 138640.5396 131027.9669 144753.7693 118543.5074 139326.3427 130436.5088 125968.6584 118438.2926 127761.2931 1.249626142 1.085152915 1.025568572 1.133001755 0.9278515 1.090520762 1.020939172 0.985968875 0.927027973 1 16.96309129 8 0.544619625 0.996468313 11.27591312 0.614743241 0.058029098 85.8461654 0.797827266 0.026418539 1030.072938 100000000 -8 10.27944481 DTEEQNPETVNWEDRPST(ph)PTILGYEVMEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTEEQNPETVNWEDRPSTPTILGYEVMEER 30 1 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6 A0A0C4DGW2 SNX16 Sorting nexin-16 1 DTEEQNPETVNWEDRPS(0.196)T(0.65)PT(0.143)ILGY(0.01)EVMEER;DTEEQNPETVNWEDRPS(0.147)T(0.729)PT(0.123)ILGY(0.001)EVMEER 117.56 0.0001303 337415000 351530 182327 160798 164338 238600 301327 207052 200802 195944 157265 TRUE FALSE 365408.6758 213640.2439 164988.528 196843.5659 198042.8572 231348.3709 190822.7232 198110.5776 188892.0137 188078.0657 1.942856411 1.135912596 0.877234287 1.046605648 1.05298221 1.230065665 1.014593182 1.053342275 1.004327714 1 17.52097208 4.73165212 4.170170221 1.042046471 2.010488587 0.915801693 0.082026837 0.053877352 2.104117136 0.019915445 0.154695681 53907.86352 -4.73165212 0.968442116 DTEQLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTEQLRR 7 1 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 79.116 0.05371 183600000 80122 189450 140040 163870 131340 205260 110730 154080 123130 244290 FALSE TRUE 83285.27843 221986.5638 143689.5574 196282.9969 109014.8737 157591.4757 102050.6933 152014.8096 118698.5754 292153.9483 0.28507326 0.759827362 0.491828224 0.671847832 0.373141881 0.539412446 0.349304515 0.520324338 0.406287767 1 18.15636926 -1.605843819 3.921871585 1.014344886 0.495888007 0.550073507 0.138621149 0.01612334 0.001620429 0.124465445 0.029007975 0.024783131 1.605843819 -0.51845688 DTFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTFEER 6 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 0 107.74 0.072131 184410000 288350 309650 334780 301600 333180 388770 372070 311970 343220 270960 FALSE TRUE 299734.2807 362829.9788 343504.6418 361255.5798 276546.1826 298484.0594 342906.1812 307788.5524 330867.5792 324049.4242 0.924964707 1.119674814 1.06003781 1.114816299 0.853407419 0.921106588 1.058190991 0.949819779 1.021040479 1 18.30585434 3.265334809 24.99964504 0.967892544 1.059870944 0.258950055 0.072406538 294.670217 275137.95 0.019722084 0.026696566 1842.191647 -3.265334809 0.091978399 DTFNHLTTWLEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTFNHLTTWLEDAR 14 0 P61019;P61019-2;E9PKL7;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ;;; 199.58 2.05E-08 1230160000 1473730 1956700 2071210 1999380 2364060 2689960 1974340 2082520 2068270 2046280 FALSE TRUE 1531913.998 2292748.004 2125187.434 2394851.396 1962217.926 2065257.557 1819586.072 2054607.226 1993833.367 2447209.388 0.625984031 0.936882645 0.868412587 0.978605022 0.801818568 0.843923518 0.743535098 0.839571487 0.814737544 1 21.22270612 DTGIFLDLMHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DTGIFLDLMHLK 12 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 144.28 6.29E-05 4012319000 3478244 2812233 3714640 2823263 5039760 4479431 4550949 3541959 3872487 3070126 FALSE TRUE 3615567.759 3295212.142 3811446.57 3381695.995 4183103.395 3439151.037 4194233.726 3494484.833 3733116.949 3671658.409 0.984723347 0.897472416 1.038072213 0.921026854 1.139295362 0.936675108 1.14232678 0.951745627 1.016738632 1 21.80800041 DTGKTPVEPEVAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ; 212.7 4.46E-10 3095700000 4626000 4029900 4942700 3446100 6343300 5684200 4839300 4989800 5448900 4467400 FALSE TRUE 4808638.052 4722003.977 5071510.822 4127728.294 5265068.132 4364130.695 4459983.021 4922919.893 5252795.153 5342701.496 0.900038689 0.883823283 0.949240909 0.772591974 0.985469268 0.816839701 0.834780499 0.921428962 0.983172119 1 22.34913798 1.345379925 2.996087356 0.995918805 0.878373646 0.374904418 0.058391984 0.256745191 3.791464747 0.046013631 0.014269049 22.15031591 -1.345379925 -0.117545158 DTGNIGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTGNIGQER 9 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 125.97 0.0011322 162480000 180043 190155 173368 187434 227360 232017 212088 190437 189076 231620 FALSE TRUE 187151.2367 222812.642 177886.1125 224507.8858 188713.4284 178134.568 195463.9884 187884.5035 182271.1917 277001.5044 0.675632564 0.804373401 0.642184644 0.810493381 0.681272215 0.643081591 0.705642335 0.678279722 0.658015169 1 18.07953429 -1.027275148 6.780062084 1.000000076 0.700902586 0.711251699 0.05736282 6.23E-08 8.87E-09 0.052415482 0.012354444 0.093912813 1.027275148 -0.29909749 DTGQLYAALHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTGQLYAALHHR 12 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EIJ4 Q9H6Z4 RANBP3 Ran-binding protein 3 0 116.74 0.00046804 193760000 109640 130530 123040 121780 146300 171710 132660 131320 129610 129730 FALSE TRUE 113968.6719 152947.5121 126246.5235 145867.7205 121431.9783 131832.9548 122261.7626 129559.8702 124945.3614 155148.1097 0.734579829 0.98581615 0.813716156 0.940183679 0.782684227 0.849723242 0.788032563 0.83507218 0.805329576 1 17.24328659 3.222323271 24.99541324 0.831908106 0.873030017 0.008493169 0.085763439 762.3582052 1173554.5 0.022410776 0.026863373 1668.488707 -3.222323271 0.041121911 DTGSEVPSGSGHGPCT(ph)PPPAPANFEDVAPTGSGEPGATRES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTGSEVPSGSGHGPCTPPPAPANFEDVAPTGSGEPGATRESPK 43 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 2 DTGSEVPSGSGHGPCT(1)PPPAPANFEDVAPT(0.022)GS(0.019)GEPGAT(0.268)RES(0.691)PK 139.93 3.06E-12 103570000 19441 13709 19666 16958 27947 35717 29272 20766 31937 11881 TRUE FALSE 20208.54569 16063.41411 20178.51212 20312.24179 23196.57892 27422.26805 26977.58415 20487.66574 30787.59361 14208.85447 1.42225017 1.130521404 1.420136447 1.429548161 1.632543916 1.929942213 1.898645961 1.441894262 2.166789284 1 13.79450263 3.361667485 2.157717335 1.713861166 1.305860663 0.221304163 0.304526345 0.411086143 3.898174383 0.086965154 0.129521119 2299.680408 -3.361667485 -0.408000503 DTHDQLSEPSEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 213.67 4.07E-09 8457360000 4055860 4594490 4314820 4443320 5254080 5743510 4635610 4464980 4307230 4053150 FALSE TRUE 4215988.485 5383557.917 4427267.754 5322195.434 4360993.358 4409666.846 4272258.775 4405134.246 4152213.634 4847287.14 0.86976248 1.110633177 0.913349597 1.097974038 0.899677125 0.909718512 0.881371095 0.908783433 0.856605667 1 22.20874612 3.16170624 24.99999871 0.903281138 0.999942503 0.241436397 0.076423643 42.1104129 13696.32847 0.019871818 0.023751373 1451.129732 -3.16170624 0.096661365 DTHEDHDT(ph)S(ph)TENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 2 DT(0.301)HEDHDT(0.407)S(0.418)T(0.413)ENT(0.375)DES(0.087)NHDPQFEPIVSLPEQEIK 72.231 0.0078924 28008000 16788 15725 22845 15196 29215 27908 23781 20715 18968 16310 TRUE FALSE 17450.8032 18425.64643 23440.35947 18201.72344 24249.04474 21426.78995 21916.98308 20437.34931 18285.34539 19505.63223 0.89465458 0.944632105 1.20172262 0.933152191 1.243181685 1.098492461 1.123623312 1.047766567 0.937439257 1 14.25160314 4.417735826 9.230377908 1.077801021 0.907022277 0.293545436 0.096422923 0.309482877 44.83925929 0.022183984 0.061071322 26165.90896 -4.417735826 -0.170778744 DTHEDHDT(ph)STENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.002)HEDHDT(0.249)S(0.249)T(0.249)ENT(0.249)DES(0.001)NHDPQFEPIVSLPEQEIK 184.62 1.11E-19 401590000 145560 186190 253570 199050 302310 328210 294320 264330 263240 218880 TRUE FALSE 151306.8212 218166.6841 260178.2425 238421.4959 250923.4542 251988.2016 271250.4293 260787.0887 253766.0438 261765.3453 0.578024647 0.833443724 0.993936926 0.910821467 0.958581641 0.962649205 1.036235064 0.996262849 0.969440945 1 17.99791459 4.73377196 1.732356441 0.981228659 0.43746502 0.933760966 0.032688286 0.213894048 0.639744587 0.009029762 0.192014715 54171.63707 -4.73377196 -0.543763639 DTHEDHDTST(ph)ENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.001)HEDHDT(0.295)S(0.295)T(0.347)ENT(0.049)DES(0.013)NHDPQFEPIVSLPEQEIK;DT(0.011)HEDHDT(0.305)S(0.305)T(0.367)ENT(0.011)DES(0.002)NHDPQFEPIVSLPEQEIK 221.47 5.30E-36 556000000 157372 206049 238547 201104 321830 318120 294410 275824 283850 186380 TRUE FALSE 163585.1681 241436.3129 244763.7308 240881.771 267125.4516 244241.4512 271333.3749 272127.0304 273634.2939 222897.5925 0.733902804 1.08317147 1.098099481 1.080683592 1.198422327 1.095756344 1.217300608 1.220861236 1.227623371 1 17.76602151 5.213354631 1.18243835 1.164110979 3.16E-19 0.736426007 0.072396186 1.987120708 1.085684874 0.02001276 3.734718199 163438.5991 -5.213354631 -1.164110979 DTHEDHDTSTENT(ph)DESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 1 DT(0.001)HEDHDT(0.226)S(0.226)T(0.226)ENT(0.27)DES(0.051)NHDPQFEPIVSLPEQEIK 195.42 4.56E-22 414790000 143420 183180 234930 174290 266570 308450 293670 245650 280850 185460 TRUE FALSE 149082.3323 214639.7401 241052.4688 208764.0418 221258.5266 236817.1621 270651.378 242357.4636 270742.2634 221797.3362 0.672155649 0.967729116 1.086814084 0.941237823 0.997570712 1.067718694 1.220264331 1.09269781 1.220674099 1 17.75888251 5.366382521 0.743254162 1.105565287 1.04E-51 0.665184826 0.086367415 3.951469468 0.853019876 0.032329714 4.516925598 232478.3537 -5.366382521 -1.105565287 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIK 34 0 P43487;P43487-2;C9JJ34 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;; 266.29 2.78E-60 2858820000 969618 1277924 1612968 1235392 2007590 1997603 1806870 1664828 1765113 1163436 FALSE TRUE 1007899.267 1497397.506 1655003.271 1479748.85 1666340.569 1533689.977 1665242.808 1642513.704 1701586.928 1391389.009 0.72438352 1.076188971 1.189461222 1.063504772 1.197609409 1.102272598 1.196820442 1.180484892 1.222941188 1 20.4080944 4.731702967 2.994112359 1.152187659 0.657510273 0.776378548 0.067088977 0.149209703 1.987476778 0.015114304 0.175193323 53914.17533 -4.731702967 -0.494677386 DTHLTITPTVLGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTHLTITPTVLGER 14 0 A0A0B4J2A0;Q9UHJ6 A0A0B4J2A0 TRPV1;SHPK Sedoheptulokinase 0 125.97 0.00040834 0 61606 100010 99425 103560 89697 124820 94025 88584 91017 121080 FALSE TRUE 64038.25245 117185.9395 102016.0972 124043.8589 74450.33598 95832.44667 86655.07481 87396.67637 87741.31595 144803.3078 0.442243022 0.809276676 0.704514964 0.856636915 0.514148034 0.661811171 0.598432979 0.60355442 0.605934473 1 17.14373503 -1.888828783 4.068128504 1.124103449 0.648405034 0.449547752 0.118071377 0.073542201 0.002009714 0.063261923 0.025876947 0.012917284 1.888828783 -0.475698414 DTHPGS(ph)PGSPGPALRPLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTHPGSPGSPGPALRPLPAR 20 1 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 DTHPGS(0.904)PGS(0.096)PGPALRPLPAR;DTHPGS(0.667)PGS(0.333)PGPALRPLPAR 128.12 1.23E-05 445050000 227954 272985 320525 300120 287106 334070 312400 285267 241777 237693 TRUE FALSE 236953.7999 319868.0502 328878.1448 359482.8402 238303.8247 256487.3054 287913.2717 281443.4625 233075.493 284264.3924 0.833568348 1.125248391 1.156944568 1.264607351 0.838317535 0.902284325 1.012836216 0.990076386 0.819925039 1 18.11687387 3.224055846 24.99568959 0.935774928 1.101664254 0.325127405 0.117936767 287.4669265 495383.2562 0.034696941 0.041645275 1675.158269 -3.224055846 0.165889326 DTIEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTIEEHR 7 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;; 166.78 0.0011106 3190180000 2595250 2728900 2719600 2678980 3222360 3516640 3162240 2895640 2881610 2382740 FALSE TRUE 2697712.474 3197567.347 2790475.01 3208874.248 2674624.398 2699953.655 2914375.366 2856828.682 2777901.419 2849592.283 0.946701214 1.122113983 0.979254129 1.126081885 0.938598976 0.947487706 1.022734159 1.002539451 0.974841712 1 21.44232408 3.214646374 24.99944652 0.983933815 1.044558791 0.225163145 0.05663713 339.0053368 354388.0432 0.015351639 0.018357898 1639.254461 -3.214646374 0.060624976 DTIHCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTIHCGK 7 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ; 67.032 0.066262 474100000 1047750 1050530 1153610 1026330 1357660 1553330 1361940 1247820 1253670 1098290 FALSE TRUE 1089115.979 1230950.356 1183674.024 1229335.011 1126885.438 1192592.648 1255187.584 1231095.014 1208550.662 1313478.897 0.829184223 0.937167973 0.901174756 0.935938151 0.857939507 0.907964833 0.95562067 0.937278106 0.920114258 1 20.32496159 -5 0.057733044 1.345528561 0.761109175 0.501903768 0.032406075 364.5061424 1.542363701 17.98946287 3.210261115 1.00E-05 5 -0.584419386 DTIIDVVGAPLT(ph)PNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 DTIIDVVGAPLT(0.976)PNS(0.024)R;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(0.997)PNS(0.003)R;DTIIDVVGAPLT(0.998)PNS(0.002)R 256.98 1.31E-25 745764000 1302490 1353800 1434820 1390390 1555780 1750170 1574920 1488190 1437050 1252420 TRUE FALSE 1353913.311 1586304.619 1472212.588 1665404.992 1291329.071 1343719.542 1451473.655 1468243.247 1385330.851 1497807.72 0.903929986 1.059084285 0.982911604 1.111895052 0.862146091 0.897124193 0.969065412 0.980261503 0.924905669 1 20.514421 3.230154815 24.99987559 0.940994775 1.015389911 0.259900899 0.06238003 259.1115321 770627.8887 0.017707691 0.02148607 1698.849141 -3.230154815 0.074395135 DTILDWEDSLPDRDLALADEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTILDWEDSLPDRDLALADEASR 23 1 M0QZ09;Q8N6T7;M0R1N9;M0QXA0;M0R1F6 M0QZ09;M0R1F6 SIRT6 NAD-dependent protein deacetylase sirtuin-6 0 ; 174.7 2.17E-12 40321000 31591 33910 33866 35174 40388 45220 34710 38221 40330 39874 FALSE TRUE 32838.23707 39733.77872 34748.57578 42131.31222 33522.86219 34718.34032 31989.3395 37708.71001 38878.53118 47686.54687 0.688626861 0.833228265 0.728687189 0.883505202 0.702983638 0.728053143 0.670825245 0.790762018 0.815293489 1 15.5412947 0.790285017 1.836578959 0.999506491 0.753463958 0.587264889 0.062506627 0.509281618 2.963333764 0.057556666 0.0161648 6.169997918 -0.790285017 -0.246042533 DTLRT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DTLRTPPR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DT(0.001)LRT(0.999)PPR;DT(0.028)LRT(0.972)PPR;DT(0.002)LRT(0.998)PPR 89.171 0.022787 2956290000 592340 791210 702710 882890 651900 963800 704480 671320 658510 715010 TRUE FALSE 615726.0406 927094.1627 721023.1999 1057523.007 541090.2709 739972.0565 649261.0168 662322.0535 634810.3537 855102.5198 0.720061076 1.084190657 0.843200883 1.236720723 0.632778244 0.865360631 0.759278568 0.774552803 0.742379234 1 19.70573787 3.213399068 24.99998735 0.784714106 0.969994056 0.232418542 0.155308117 291.3713456 289499.7177 0.041143282 0.049193631 1634.553229 -3.213399068 0.18527995 DTLRT(ph)PPRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTLRTPPRER 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 DTLRT(1)PPRER 126.1 0.018663 1412100000 354350 405240 395300 400380 476000 501230 416200 378180 398750 387130 TRUE FALSE 368340.0116 474836.8177 405601.8427 479573.969 395089.69 384826.9287 383577.1565 373111.1157 384399.0654 462980.7114 0.795583925 1.025608208 0.876066395 1.035840062 0.853361015 0.831194301 0.828494896 0.805889115 0.830270151 1 18.82059256 3.033922213 24.964729 0.841478247 0.936885791 0.149101437 0.082537575 245.9310872 180989.1256 0.021848467 0.026113775 1081.240271 -3.033922213 0.095407545 DTLWHLFNTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTLWHLFNTLQR 12 0 Q7Z434;Q7Z434-5;Q7Z434-2 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 0 78.763 0.024853 73041000 174130 219300 231350 250660 292690 302420 240970 255480 223860 275210 FALSE TRUE 181004.7869 256963.0691 237379.1711 300239.7999 242938.6583 232187.5382 222082.1417 252055.7085 215803.3223 329132.1303 0.549945661 0.780729213 0.721227584 0.912216621 0.738118938 0.70545388 0.67475072 0.765819211 0.655673824 1 18.32830735 -1.265875178 3.844906644 1.000377917 0.730450758 0.465491469 0.088804598 10070753.89 6631371.709 31605.60227 0.020028531 0.054215669 1.265875178 -0.269927158 DTLYEAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DTLYEAVR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 104.75 0.010518 2482390000 1333070 1401300 1374470 1157740 2578030 1955650 1662690 1421180 1409870 2168300 FALSE TRUE 1385700.633 1641962.374 1410289.817 1386737.516 2139817.381 1501479.926 1532364.013 1402131.407 1359129.054 2593136.87 0.534372346 0.633195414 0.543854755 0.534772203 0.825184897 0.5790207 0.590930633 0.5407086 0.52412546 1 21.30626693 -1.047391393 4.592269303 1.000015319 0.590908068 0.676900428 0.085062685 11275992.74 2571795.636 1961.232067 0.019889474 0.089662038 1.047391393 -0.409107251 DTPDEPWAFPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DTPDEPWAFPAR 12 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 178.22 5.18E-05 914287000 477380 526059 586892 530167 577287 663216 649386 578056 541487 518988 FALSE TRUE 496227.331 616405.5411 602186.8877 635032.4502 479159.9619 509194.1351 598485.4285 570308.1048 521998.9886 620673.762 0.799497838 0.993123246 0.970214829 1.023134035 0.771999706 0.820389335 0.964251214 0.918853252 0.841019906 1 19.24347563 6.540031594 9.216003341 0.911310897 0.475044021 0 0.088605864 0 0 0.019378892 0 3467620.755 -6.540031594 -0.436266876 DTPGHGSGWAETPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTPGHGSGWAETPR 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 192.65 3.49E-07 739090000 58170 627610 568110 631150 526000 753260 511900 592550 469270 624810 FALSE TRUE 60466.59652 735397.1354 582915.4133 755989.5862 436590.7079 578326.7808 471775.9404 584607.8365 452381.0644 747229.5568 0.080921045 0.984164945 0.780102189 1.011723344 0.584279227 0.773961329 0.631366808 0.78236712 0.605411095 1 19.511192 4.749136649 24.7379479 0.779798889 0.080920589 0.660469443 0.153217136 779.8820815 1824147.862 0.034704967 0.49755728 56122.45349 -4.749136649 -0.6988783 DTPRPDHPPHDGHS(ph)PASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.999)PAS(0.001)R;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.995)PAS(0.005)R;DTPRPDHPPHDGHS(1)PASR;DTPRPDHPPHDGHS(0.959)PAS(0.041)R;DTPRPDHPPHDGHS(0.745)PAS(0.255)R 157.83 7.77E-10 2830680300 321503 418435 404020 354848 428892 517907 393405 403835 403044 409736 TRUE FALSE 334196.1867 490297.9563 414549.0931 425035.8753 355989.091 397630.9482 362568.8881 398422.2524 388538.5252 490015.9243 0.68201087 1.000575557 0.845991064 0.867391965 0.726484739 0.81146536 0.73991246 0.813080213 0.792909997 1 18.90246911 5.017484485 16.84842302 0.829720515 0.390945739 0.212883662 0.089754495 21387367.37 453553923.6 0.020678629 236188891.8 104108.0914 -5.017484485 -0.438774776 DTPRPDHPPHDGHSPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTPRPDHPPHDGHSPASR 18 1 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 0 83.758 0.0013264 36613000 17600 32950 32139 35878 29769 34527 27867 24103 26948 23756 FALSE TRUE 18294.86159 38608.90618 32976.56874 42974.56131 24708.87601 26508.62751 25682.71172 23779.93871 25978.14674 28410.53336 0.643946432 1.358964497 1.160716285 1.512627756 0.869708277 0.933056313 0.903985553 0.837011344 0.914384338 1 14.7941383 DTQS(ph)PSTCSEGLLGWSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTQSPSTCSEGLLGWSQK 18 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DT(0.004)QS(0.987)PS(0.009)TCSEGLLGWSQK;DTQS(0.996)PS(0.004)TCSEGLLGWSQK;DT(0.002)QS(0.662)PS(0.337)TCSEGLLGWSQK;DTQS(0.987)PS(0.013)TCSEGLLGWSQK;DTQS(0.795)PS(0.205)TCSEGLLGWSQK 390.22 1.33E-126 814537000 1214306 865950 1130758 975440 1263390 1394620 1456890 1202185 1282615 762551 TRUE FALSE 1262247.739 1014670.176 1160226.482 1168379.121 1048639.419 1070740.641 1342695.155 1186071.676 1236453.937 911958.2685 1.384106907 1.11262786 1.272236376 1.281176081 1.149876541 1.174111445 1.47232083 1.300576701 1.355822936 1 19.79860828 DTRPSSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTRPSSEK 8 1 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RCQ8;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 90.15 0.012221 507640000 630240 1046330 1230160 1096420 1449240 1464590 1277710 1287190 1372890 1199310 FALSE TRUE 655122.3619 1226029.038 1262218.98 1313288.604 1202898.702 1124461.169 1177559.752 1269937.323 1323479.957 1434291.832 0.45675667 0.854797476 0.8800294 0.915635559 0.838670817 0.783983526 0.821004293 0.885410692 0.922741054 1 20.45190717 4.738645883 5.393641674 0.870710057 0.440636495 0.829583906 0.057239768 0.057471791 6.206777147 0.013502197 0.091548244 54783.00905 -4.738645883 -0.430073562 DTS(ph)GLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTSGLER 7 0 Q9H307 Q9H307 PNN Pinin 1 DT(0.003)S(0.997)GLER;DT(0.234)S(0.766)GLER;DT(0.002)S(0.998)GLER;DT(0.001)S(0.999)GLER 153.24 0.0018453 1461380000 2589880 2528740 2788110 2387550 3565630 3915190 3209140 2900330 2948630 2446770 TRUE FALSE 2692130.462 2963031.424 2860770.437 2859800.264 2959545.486 3005946.458 2957599.221 2861455.82 2842509.382 2926167.735 0.920019187 1.012597941 0.977650872 0.977319321 1.011406643 1.027263892 1.010741519 0.977885097 0.971410267 1 21.48058104 4.746538036 24.75449946 0.995685071 0.920019145 0.609842728 0.018287671 649.1612816 2014339.665 0.004706855 0.052285524 55787.64599 -4.746538036 -0.075665926 DTS(ph)PSSGSAVSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DTSPSSGSAVSSSK 14 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;Q8NEY8-7;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 DTS(1)PSSGSAVSSSK;DTS(1)PSSGSAVSSSK;DTS(0.999)PS(0.001)SGSAVSSSK;DTS(0.999)PSSGSAVSSSK;DT(0.003)S(0.996)PS(0.001)SGSAVSSSK;DT(0.002)S(0.996)PS(0.001)SGSAVSSSK;DT(0.016)S(0.982)PS(0.002)SGSAVSSSK;DT(0.007)S(0.965)PS(0.025)S(0.004)GSAVSSSK 397.85 1.58E-114 9407994000 12612960 8668770 11019580 8778870 14232640 14196660 13969980 11572150 12239610 7386820 TRUE FALSE 13110929.4 10157563.81 11306759.31 10515304.28 11813380.94 10899700.87 12874976.46 11417044.26 11799108.83 8834125.95 1.484122988 1.149809712 1.279895642 1.190304999 1.337243888 1.233817689 1.457413731 1.292379611 1.335628323 1 23.07465597 -0.885714222 5.34932902 1.000001659 1.302499759 0.456749291 0.100260908 3.70E-07 7.69E-08 0.090534186 0.021339089 0.130102541 0.885714222 0.3024981 DTSEDIEELVEPVAAHGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTSEDIEELVEPVAAHGPK 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;; 270.17 5.98E-33 801669000 1350484 983626 1306296 1007235 1632940 1583540 1481980 1305929 1417250 893442 FALSE TRUE 1403802.151 1152556.114 1340339.147 1206463.077 1355373.442 1215786.834 1365818.535 1288425.158 1366243.449 1068494.854 1.313812739 1.078672592 1.254417971 1.1291239 1.268488507 1.137849967 1.278264027 1.205831879 1.278661703 1 20.02714853 -0.889692214 8.006996044 1.000011094 1.212108293 0.435225781 0.073731783 9.37E-10 2.04E-18 0.06288775 0.014822785 0.128916286 0.889692214 0.212097199 DTSFEQHVLWHTGGK ddPTM_MDA-MB-175_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 ;;;;;;;;;; 235.88 6.26E-18 54768711000 23697130 21433656 27231549 25610553 35020080 34717745 30248720 27159733 28971396 21671440 FALSE TRUE 24632710.99 25114719.69 27941225.54 30676243.94 29067379.31 26655074.88 27877746.29 26795701.2 27928721.12 25917543.74 0.950426137 0.969023914 1.078081543 1.183609228 1.121532951 1.02845683 1.075632265 1.033882742 1.077599073 1 24.62742566 4.259320522 5.62915161 1.077815566 0.957072591 0.47320341 0.048601122 0.143922394 13.59542382 0.012710041 0.033706022 18168.56063 -4.259320522 -0.120742975 DTSFLGSDDIGNIDVREPELEDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DTSFLGSDDIGNIDVREPELEDLTR 25 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 ;; 152.35 1.16E-07 180771000 83630 101346 91943 72657 124500 133880 88235 95577 98669 115313 FALSE TRUE 86931.77698 118751.3871 94339.11011 87028.33774 103337.5345 102788.399 81318.91014 94295.94665 95117.92196 137906.3745 0.630368083 0.861101508 0.684080851 0.631068274 0.749331094 0.745349149 0.589667522 0.68376786 0.689728247 1 17.07332962 -1.304017771 13.05730944 1 0.696062222 0.612064526 0.072594304 7.85E-10 7.84E-11 0.068738806 0.016201892 0.0496572 1.304017771 -0.303937778 DTSGPTPGTPS(ph)PAMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSGPTPGTPSPAMAR 16 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 DTSGPTPGT(0.006)PS(0.994)PAMAR 221.24 4.30E-13 0 179510 177540 167950 183710 183030 207140 142570 164910 136120 143020 TRUE FALSE 186597.1934 208031.1139 172326.915 220047.2897 151918.626 159034.8742 131394.9909 162699.6512 131221.0678 171042.0307 1.09094351 1.216257273 1.007512097 1.286510039 0.888194705 0.929799965 0.76820294 0.951226143 0.767186096 1 17.38399136 3.215797025 24.42403638 0.880636192 1.144816956 0.64340864 0.097032293 101.600162 109010.8077 0.025636914 0.030664113 1643.603379 -3.215797025 0.264180764 DTSLDFRPVVS(ph)PANGVEGVRVDQDDDQDSSSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSLDFRPVVSPANGVEGVRVDQDDDQDSSSLK 33 2 Q8ND24 Q8ND24 RNF214 RING finger protein 214 1 DTSLDFRPVVS(1)PANGVEGVRVDQDDDQDSSSLK 98.735 4.71E-05 140160000 128190 110170 129870 92938 164410 152700 136350 138990 144590 113010 TRUE FALSE 133251.0402 129090.8405 133254.5189 111320.859 136463.6469 117237.7392 125662.5307 137127.0664 139386.2341 135152.1458 0.985933589 0.955151986 0.985959328 0.823670674 1.009703887 0.867450076 0.929785687 1.014612573 1.03132831 1 17.04422489 1.70376217 5.291934073 1.017930399 0.935150415 0.30985643 0.053564595 0.174785657 11.59512193 0.026880111 0.013400135 50.55477368 -1.70376217 -0.082779984 DTSLYRPALEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;;; 257.81 1.31E-24 4387400000 1481210 1670740 1732280 1519360 2029750 2224580 1655970 1693280 1781660 1822940 FALSE TRUE 1539689.315 1957676.598 1777424.64 1819884.873 1684733.82 1707955.009 1526170.744 1670584.351 1717538.405 2180110.191 0.706243804 0.897971399 0.815291194 0.834767381 0.772774618 0.783426001 0.700042939 0.766284364 0.787821832 1 21.05596963 -1.219954792 2.92207779 1.001127799 0.785107676 0.58040475 0.054852062 5132601.026 6644479.464 52480.54191 0.01342115 0.060262231 1.219954792 -0.216020123 DTSNHFHVFVGDLSPEITTEDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSNHFHVFVGDLSPEITTEDIK 23 0 E7ETJ9;Q01085;Q01085-2;A6NKZ9;E7ETC0;C9JTN7;P31483-2;H7BY49 E7ETJ9;C9JTN7 TIAL1;TIA1 Nucleolysin TIAR;Nucleolysin TIA-1 isoform p40 0 86.625 0.0038914 116030000 43974 87575 108310 93121 115510 128800 102960 112150 105030 92411 FALSE TRUE 45710.12748 102615.325 111132.6476 111540.0559 95875.65146 98888.15198 94889.72616 110646.8127 101249.9908 110517.1661 0.413602059 0.928501233 1.005569103 1.009255483 0.867518186 0.894776399 0.858597171 1.00117309 0.916147187 1 16.75391095 4.738011912 6.302344535 0.942278012 0.401817981 0.890941382 0.055522665 0.036918885 8.175519286 0.013705439 0.085586488 54703.09666 -4.738011912 -0.540460031 DTSPDKGELVS(ph)DEEEDT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.991)DEEEDT(0.009);DTSPDKGELVS(0.943)DEEEDT(0.057);DTSPDKGELVS(1)DEEEDT;DTSPDKGELVS(1)DEEEDT;DTSPDKGELVS(0.991)DEEEDT(0.009) 257.6 1.03E-26 1370000000 3118870 2069410 2711460 2019990 3731850 3570630 3336830 2736330 3051980 1852020 TRUE FALSE 3242005.396 2424815.07 2782122.875 2419537.993 3097511.47 2741405.296 3075280.545 2699653.972 2942139.836 2214887.86 1.463733426 1.094780062 1.256101009 1.092397514 1.398495845 1.237717424 1.388458802 1.218867113 1.328347087 1 21.07880223 -1.058315625 4.540281619 0.999985792 1.26794563 0.329654175 0.117394282 1.54E-05 3.20E-06 0.10382936 0.024471518 0.087434811 1.058315625 0.267959838 DTSPDKGELVSDEEEDT(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 DTSPDKGELVS(0.383)DEEEDT(0.617) 266.72 7.03E-27 520660000 1022700 664940 878150 661620 1209500 1259500 1090600 843480 1004200 626840 TRUE FALSE 1063076.986 779138.2725 901035.3104 792486.4613 1003909.622 967000.2129 1005115.922 832174.5303 968059.0382 749657.2964 1.418083958 1.039325938 1.201929621 1.057131659 1.339158075 1.289923032 1.340767211 1.110073275 1.291335445 1 19.5158717 -1.170432204 4.219617048 0.999938902 1.221582971 0.241249285 0.122171897 12492431.07 32791016.58 11937.90679 0.028085199 0.067541048 1.170432204 0.221644069 DTSQSDKDLDDALDKLS(ph)DSLGQR ddPTM_MDA-MB-175_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 1 DTSQSDKDLDDALDKLS(0.655)DS(0.345)LGQR 79.395 0.0064728 98270000 135190 28037 75811 45401 84805 91554 119560 61589 96099 29070 TRUE FALSE 140527.4056 32852.13665 77786.69694 54381.18229 70389.87639 70291.97101 110188.5748 60763.50019 92640.41576 34765.70992 4.042126737 0.944958027 2.237454581 1.564218951 2.024692622 2.021876475 3.169461376 1.747799781 2.664706574 1 15.08537743 DTSQSDKDLDDALDKLSDSLGQR ddPTM_MDA-MB-175_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 82.477 0.00488 51585000 194640 62619 107020 62879 157820 144720 142090 106450 116490 49810 FALSE TRUE 202324.5375 73373.32614 109809.0291 75316.27852 130993.8128 111110.9733 130952.6145 105023.2119 112297.5477 59569.31583 3.396455619 1.231730214 1.843382412 1.264346879 2.199014895 1.865238365 2.198323293 1.763042103 1.885157586 1 15.86228177 0.178880311 1.161472636 0.997462831 1.930364555 0.202254069 0.571161094 9.300443881 11.61342546 0.554087768 0.153469501 1.509664043 -0.178880311 0.932901724 DTSS(ph)SPTTGSTVQSVDLIFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.008)S(0.061)S(0.465)S(0.465)PT(0.001)TGSTVQSVDLIFTR;DT(0.006)S(0.047)S(0.473)S(0.473)PTTGSTVQSVDLIFTR 140.16 1.76E-07 98733000 105743 94029 117996 108387 116777 140920 128365 120990 117730 89042 TRUE FALSE 109917.8153 110177.7493 121071.0727 129825.6251 96927.28725 108193.4657 118303.4159 119368.3269 113492.9203 106488.0751 1.03220774 1.034648708 1.136944889 1.219156464 0.910217291 1.01601485 1.110954591 1.120954875 1.06578056 1 16.70033236 0.964171918 22.16989489 0.999999996 1.076319995 0.068644206 0.078853452 3695.421934 2286680.407 0.077978372 0.019494593 9.208140098 -0.964171918 0.076319998 DTSSDKDLDDALDKLSDSLGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTSSDKDLDDALDKLSDSLGQR 22 2 E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 E7EVY3 CAST 0 ; 211.68 1.69E-23 222570000 653710 234240 370110 251790 574000 510640 524330 375690 428720 177695 FALSE TRUE 679518.9756 274468.8979 379755.3706 301593.3105 476431.685 392051.5988 483231.6445 370654.4901 413290.4509 212510.9331 3.197571841 1.291551893 1.786992157 1.419189621 2.241916113 1.844853783 2.273914276 1.744166687 1.94479618 1 17.69717754 -0.081745047 1.113131205 0.993198636 1.940560277 0.24826612 0.504620727 17.80915977 16.5827101 0.933321553 0.137261724 0.828428351 0.081745047 0.947361641 DTSSS(ph)PTTGSTVQSVDLIFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 DT(0.001)S(0.031)S(0.104)S(0.863)PTTGSTVQSVDLIFTR 201.9 7.00E-22 40966000 41903 35378 41822 39704 49697 50717 50321 48373 44444 29772 TRUE FALSE 43557.3628 41453.8963 42911.91568 47557.3327 41249.52169 38938.74537 46376.70853 47724.63906 42844.46912 35605.25338 1.223340902 1.164263483 1.20521304 1.335683029 1.15852347 1.0936236 1.302524322 1.340381953 1.203318754 1 15.1198025 DTSVLQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTSVLQWR 8 0 O95834;O95834-2;O95834-3 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 132.08 0.0022738 238960000 271820 296910 296520 257340 364740 399660 273190 323340 288130 315890 FALSE TRUE 282551.6635 347901.9829 304247.5548 308241.0839 302741.6251 306845.0219 251776.654 319006.1562 277760.2576 377782.5974 0.747921332 0.920905265 0.8053509 0.815921872 0.801364666 0.81222646 0.666459111 0.844417287 0.735238361 1 18.52719672 5.044699717 17.2394016 0.811668804 0.372064521 0.049724328 0.086928514 53388080.33 498742118.9 0.019123844 777249381.2 110840.8167 -5.044699717 -0.439604283 DTTGTALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTTGTALR 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 A0A0A0MTS7 TTN Titin 0 74.335 0.095951 254070000 248500 275290 251130 243930 220190 383480 225020 229960 236880 286850 FALSE TRUE 258310.9719 322568.916 257674.6541 292178.6259 182762.1824 294422.5817 207382.3444 226877.7623 228354.7351 343052.7654 0.752977378 0.940289508 0.75112251 0.851701707 0.532752395 0.858242846 0.604520253 0.661349463 0.665654844 1 18.38807097 DTTINEIEDTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DTTINEIEDTFR 12 0 Q16864;Q16864-2 Q16864 ATP6V1F V-type proton ATPase subunit F 0 ;; 202.05 3.28E-07 159227000 166886 180160 180465 180939 204139 227325 189207 191014 164600 163184 FALSE TRUE 173474.7881 211101.0785 185168.0662 216728.1942 169439.5257 174532.2139 174376.4609 188453.7698 158676.0782 195156.7805 0.888899621 1.081699944 0.948816975 1.110533765 0.868222592 0.894317961 0.893519869 0.965653201 0.813069768 1 17.57427406 3.213268638 24.99837184 0.906958218 1.008597795 0.305485315 0.075095963 258.9656037 255958.6798 0.020118882 0.024055088 1634.062403 -3.213268638 0.101639577 DTTS(ph)PMELAALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DTTSPMELAALEK 13 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 DTT(0.006)S(0.994)PMELAALEK;DT(0.049)T(0.441)S(0.509)PMELAALEK 184.66 9.77E-06 118247000 599300 420790 521800 416720 682660 677240 695620 565500 596540 400340 TRUE FALSE 622960.8268 493057.4092 535398.5367 499145.9722 566621.697 519961.2737 641095.4867 557920.3975 575070.6419 478778.958 1.301144957 1.029822637 1.118258285 1.042539493 1.18347243 1.0860153 1.339021851 1.165298491 1.20111929 1 18.86900022 DTTVISHS(ph)PNTSYDTALEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DTTVISHSPNTSYDTALEAR 20 0 Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 Q4VCS5 AMOT Angiomotin 1 DTTVIS(0.002)HS(0.996)PNT(0.001)SYDTALEAR 145.81 9.06E-08 87076000 32399 44761 43986 50044 56178 67232 48027 48899 49310 48951 TRUE FALSE 33678.13754 52448.35356 45132.31129 59942.55383 46628.88363 51618.38691 44262.51824 48243.58889 47535.34273 58542.01123 0.575281526 0.895909663 0.770938858 1.023923719 0.796502933 0.88173238 0.756081271 0.824084924 0.81198684 1 15.83718469 -4.61239421 0.019834984 1.98822479 4.59E-06 0.209569819 0.1084178 6214.023333 9.923829979 656.886151 374.2326572 2.44E-05 4.61239421 -1.988220195 DTVTISGPQAPVFEFVEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DTVTISGPQAPVFEFVEQLR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 213.34 1.95E-22 279220000 42356.4 40080 36385.7 41444.5 43448.4 55048.2 41465.3 48739.1 40145.2 34738 FALSE TRUE 44028.66338 46963.42822 37333.94123 49642.0984 36063.05649 42264.08981 38215.14144 48085.83209 38700.38209 41544.246 1.05980172 1.130443629 0.898654924 1.194921155 0.86806381 1.01732716 0.919866049 1.157460701 0.931546142 1 15.34236105 4.290760012 24.99999521 1.010575058 1.095122763 0.115456164 0.102723335 227.5745432 108988.9143 0.02340311 0.064091942 19532.59799 -4.290760012 0.084547705 DTVTISGPQAPVFEFVEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 202.22 1.04E-21 9041632000 665109.7 511444.4 742601.2 555934 841879.8 845189.5 678022 624767.6 736845.9 562927.3 FALSE TRUE 691368.7445 599280.9972 761953.9973 665896.0859 698777.3723 648907.0476 624876.864 616393.6122 710326.96 673222.1265 1.026954875 0.890168302 1.131801774 0.989117944 1.037959605 0.963882532 0.928188245 0.915587275 1.055115291 1 19.36072307 2.659655734 7.342214401 0.959127898 1.013214669 0.075753226 0.066585642 0.580584877 47.51432316 0.021193431 0.019972227 456.7259984 -2.659655734 0.054086772 DTYHPMSEYPTYHTHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DTYHPMSEYPTYHTHGR 17 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ;;;;;; 134.14 6.24E-06 2556846000 561428 980153 703268 1216973 922685 1438402 930936 827824 681723 1070387 FALSE TRUE 583593.611 1148486.653 721595.7418 1457686.627 765847.3333 1104354.935 857966.8038 816728.3733 657187.9224 1280108.839 0.455893744 0.89717891 0.563698742 1.138720852 0.598267358 0.862703937 0.670229576 0.638014791 0.513384411 1 20.28783505 2.105302581 21.89182601 0.67101204 0.761682716 0.000356152 0.215476511 16.07842876 3282.128891 0.07475446 0.055209875 127.4390662 -2.105302581 0.090670676 DVAEAKPELSLLGDGDH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVAEAKPELSLLGDGDH 17 1 H7C5G1;Q2TAA2-2;Q2TAA2 H7C5G1 IAH1 Isoamyl acetate-hydrolyzing esterase 1 homolog 0 ; 229.68 9.42E-16 302880000 394500 328830 408870 368630 644630 585930 578240 430050 454510 373960 FALSE TRUE 410075.1646 385303.9946 419525.4881 441543.9137 535056.0229 449856.6374 532916.0379 424285.8832 438152.2739 447230.3021 0.91692169 0.861533739 0.938052467 0.987285324 1.196376946 1.005872445 1.191591973 0.948696636 0.97970167 1 18.77065842 3.696840804 2.92973694 1.05297178 0.895241136 0.399599067 0.080658033 0.25675267 4.39166452 0.022183001 0.039481268 4975.546663 -3.696840804 -0.157730644 DVAEEIANYRPTLDTLHEQASALPQEHAESPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVAEEIANYRPTLDTLHEQASALPQEHAESPDVR 34 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 146.01 1.38E-10 105490000 37767 74985 54241 41898 73411 72458 48821 53948 48047 74249 FALSE TRUE 39258.07032 87863.09045 55654.56502 50185.29935 60932.62444 55630.72761 44994.28245 53224.9153 46317.79786 88796.66997 0.442111966 0.989486323 0.626764101 0.565170962 0.686203936 0.626495652 0.506711372 0.599402155 0.521616384 1 16.43821795 -1.221640272 5.194440628 1.000034093 0.623460611 0.397092627 0.140995789 5.34E-05 8.01E-06 0.131071922 0.030891156 0.060028809 1.221640272 -0.376573482 DVAFTVGEGEDHDIPIGIDK ddPTM_MDA-MB-175_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 97.384 0.0012932 0 79684 63894 72402 57764 104230 103610 93891 73704 82897 59449 FALSE TRUE 82829.98585 74867.29747 74288.8556 69189.54679 86513.02183 79548.14772 86531.57808 72716.11844 79913.55316 71096.89333 1.165029609 1.053031911 1.044895946 0.973172575 1.21683266 1.118869531 1.217093659 1.022774907 1.124009073 1 16.1174989 4.759213431 22.32016385 1.089658511 1.165029933 0.07965 0.079920249 3151.880649 3406096.995 0.018910114 0.658510165 57439.86777 -4.759213431 0.075371421 DVAIKEPLVDVVDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVAIKEPLVDVVDPK 15 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 165.75 1.28E-06 366080000 1120640 467640 747120 492830 1077040 912450 1060170 781200 922700 386650 FALSE TRUE 1164883.733 547953.5323 766590.561 590310.303 893965.1255 700547.3158 977071.1052 770729.2918 889492.2072 462406.6646 2.519175915 1.185003535 1.657827665 1.276604228 1.933287718 1.515002636 2.113012592 1.666778078 1.923614591 1 18.81880267 DVCIS(ph)TDDDCPPKTFRNVCVQT(ph)DRETFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVCISTDDDCPPKTFRNVCVQTDRETFLK 29 3 Q68DA7-5;A0A5F9ZHS8;H0YM30;Q68DA7 Q68DA7-5 FMN1 Formin-1 2 DVCIS(0.355)T(0.355)DDDCPPKT(0.355)FRNVCVQT(0.468)DRET(0.468)FLK 46.66 0.06701 133130000 194720 28141 49133 23323 77538 97188 73063 30301 56924 20762 TRUE FALSE 202407.696 32973.99784 50413.44634 27936.21979 64358.11846 74617.5599 67336.13115 29894.86466 54875.31636 24829.91639 8.151767118 1.327994719 2.030351031 1.125103257 2.591958726 3.005147449 2.711895203 1.203985716 2.210048375 1 14.59979178 4.74208491 24.99677448 1.954406442 8.151769457 0.881478961 0.686265209 108.9469184 772695.2332 0.166672257 1.22772316 55218.53873 -4.74208491 6.197363015 DVCLYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVCLYPR 7 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 92.467 0.036405 366670000 359790 397560 405310 409330 513230 501390 433330 409330 384440 406790 FALSE TRUE 373994.787 465837.8374 415872.7116 490294.2523 425991.3479 384949.7711 399364.4623 403843.6009 370604.0795 486492.712 0.768757224 0.957543301 0.854838523 1.007814177 0.875637676 0.791275515 0.820905334 0.830112334 0.761787526 1 18.89205867 2.991332 24.75095329 0.829289701 0.903918327 0.083251527 0.0834038 661.4423163 1888716.069 0.022863771 0.026069322 980.2390508 -2.991332 0.074628626 DVCTELLPLIKPQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVCTELLPLIKPQGR 15 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 ; 152 2.65E-06 341860000 311736 277177 329300 296110 364260 387810 319290 324130 352280 291099 FALSE TRUE 324043.578 324779.9936 337881.8285 354679.6742 302343.2153 297747.0048 294263.2155 319785.5675 339601.5116 348134.2756 0.930800558 0.932915879 0.970550308 1.018801362 0.868467245 0.855264838 0.84525781 0.918569615 0.97549002 1 18.40928434 3.223313361 24.98425455 0.900396557 0.961619339 0.182597041 0.052067278 347.827506 569951.1779 0.015408616 0.018480332 1672.296808 -3.223313361 0.061222782 DVDASPS(ph)PLSVQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVDASPSPLSVQDLK 15 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 DVDASPS(0.999)PLS(0.001)VQDLK;DVDASPS(1)PLSVQDLK;DVDASPS(1)PLSVQDLK;DVDAS(0.001)PS(0.998)PLSVQDLK 252.47 1.26E-24 178836000 396738 244882 310354 236952 407765 439189 359132 323389 359718 249168 TRUE FALSE 412401.5226 286938.5786 318442.0802 283820.3984 338453.2509 337194.0107 330982.2954 319054.4994 346771.8194 297987.699 1.383954854 0.962920884 1.068641697 0.95245676 1.135796048 1.131570236 1.110724693 1.070696879 1.16371186 1 18.18489325 5.901232972 0.008224572 2.46E-07 2.255394633 0.064662828 0.114205609 54651.57679 51.40453984 6488.194847 7648.373758 796586.5555 -5.901232972 2.255394386 DVDAVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDAVDK 7 0 P23297;Q5T7Y6 P23297 S100A1 Protein S100-A1;Protein S100 0 ; 87.616 0.044693 556270000 1219380 805580 910690 897600 1353560 1259910 1376760 968680 1016330 715160 FALSE TRUE 1267522.064 943932.0985 934423.3295 1075142.601 1123482.355 967314.9966 1268845.954 955696.429 979752.4818 855281.9094 1.481993305 1.103650256 1.092532555 1.257062249 1.313581338 1.130989661 1.483541204 1.117405172 1.145531632 1 19.7060405 1.129741707 1.882579831 1.012696107 1.248257888 0.256475519 0.136300447 0.440486177 2.964955271 0.122477448 0.035199215 13.48160836 -1.129741707 0.235561781 DVDDDGEEKELMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVDDDGEEKELMER 14 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 163.99 3.82E-06 387110000 386470 212150 268220 208280 424770 374460 366150 272740 299090 140880 FALSE TRUE 401728.134 248585.1122 275210.0335 249477.1623 352567.7471 287497.34 337450.2062 269084.3664 288325.8093 168482.7387 2.384387488 1.47543371 1.633461301 1.480728318 2.092604559 1.706390472 2.002877024 1.597103469 1.711307708 1 17.36224127 0.351387333 1.036118589 0.997900358 1.788485788 0.432772184 0.2733453 2.581560882 3.301586882 0.257126528 0.077895089 2.245884062 -0.351387333 0.79058543 DVDDFFEHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDDFFEHER 10 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ; 183.33 1.68E-06 624870000 847430 804890 881110 890580 1075980 1139420 1112020 984780 940560 751930 FALSE TRUE 880887.1908 943123.5963 904072.4504 1066734.066 893085.3039 874806.9731 1024856.967 971580.6349 906709.4293 899256.2869 0.979573013 1.048781766 1.005355718 1.18624032 0.993137682 0.972811629 1.139671728 1.080426847 1.008288118 1 19.77837282 4.977468487 1.544925219 1.057358361 0.909475846 0.078438843 0.065938359 4.933507754 6.949646918 0.017331499 1.315001466 94944.21038 -4.977468487 -0.147882516 DVDDGSGS(ph)PHS(ph)PHQLSSK ddPTM_MDA-MB-175_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(0.078)GS(0.922)PHS(1)PHQLSSK 185.41 2.81E-14 686540000 577000 487840 654920 466990 812680 751950 712080 595990 623460 408460 TRUE FALSE 599780.4055 571622.7251 671987.7532 559359.2282 674540.9439 577321.0084 656265.3089 588001.7289 601021.7964 488489.9166 1.22782556 1.170183264 1.375643039 1.145078351 1.38086974 1.181848363 1.343457227 1.203713135 1.230366843 1 18.89796926 0.397359637 1.184429743 0.999798319 1.257095725 0.466751983 0.081113034 2.212690422 3.59633934 0.069764439 0.021013111 2.496661341 -0.397359637 0.257297406 DVDDGSGSPHS(ph)PHQLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 DVDDGSGS(0.001)PHS(0.999)PHQLSSK;DVDDGSGSPHS(1)PHQLSSK 261.82 5.37E-31 819020000 446570 490020 627910 509920 807870 777200 724110 620150 699210 467620 TRUE FALSE 464200.9284 574177.1232 644273.8504 610780.654 670548.546 596707.0786 667352.3661 611837.9036 674045.5687 559241.1859 0.830054975 1.026707506 1.152050076 1.092159643 1.199032838 1.066994159 1.193317629 1.094050151 1.205285994 1 19.09311109 4.665348509 2.258935324 1.130026785 0.780041979 0.67331683 0.062551106 0.25282988 1.700625955 0.013905706 0.165093202 46275.22175 -4.665348509 -0.349984807 DVDEIEAWISEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DVDEIEAWISEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;;;; 243.53 5.54E-16 399422100 820654 639588 778773 600194 1034755 964546 952652 758148 882429 566386 FALSE TRUE 853054.0536 749432.2637 799068.4641 718910.5818 858867.7147 740544.8093 877980.6469 747986.2661 850670.5527 677358.4926 1.259383418 1.106404174 1.179683244 1.06134431 1.26796626 1.09328342 1.296183124 1.104269415 1.2558646 1 19.36956006 -1.705272406 5.529998018 0.995904731 1.174632654 0.304210265 0.081455857 0.003689329 0.000196627 0.070749638 0.016337943 0.019711859 1.705272406 0.178727923 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 DVDELPSLQPS(0.001)VGS(0.942)PS(0.057)RPSSSR;DVDELPSLQPS(0.241)VGS(0.722)PS(0.037)RPSSSR 160.43 1.12E-11 865480000 573110 591580 601470 602510 645770 747450 558450 611700 579390 542760 TRUE FALSE 595736.8253 693179.2631 617144.8023 721684.6797 536002.2461 573866.0652 514677.2298 603501.162 558537.8671 649103.4302 0.917784127 1.067902634 0.950764968 1.111817695 0.825757839 0.884090329 0.792904807 0.92974576 0.860475913 1 19.30808885 3.225195403 24.99998806 0.876215263 1.011676865 0.428648561 0.073280404 194.5194453 363853.1711 0.019502396 0.023437714 1679.559537 -3.225195403 0.135461602 DVDFELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDFELIK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 141.39 0.0014757 105263000 355860 263430 333030 273960 460140 441650 474040 356130 357440 240220 FALSE TRUE 369909.6276 308672.0533 341709.0354 328148.4703 381925.5672 339083.4808 436883.5061 351356.6599 344575.8042 287286.5097 1.287598321 1.074439777 1.189436412 1.142234178 1.329423952 1.180297262 1.520724055 1.223018304 1.199415192 1 18.13213072 3.252117924 24.97545857 1.267162068 1.167500146 0.040148655 0.133354037 504.6632256 929691.9685 0.035014669 0.047152701 1786.972728 -3.252117924 -0.099661922 DVDFELIKVEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVDFELIKVEGK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 174.73 2.70E-05 1412280000 2661370 1556550 2192600 1172570 3617680 2673750 2169330 2167530 2667010 1681170 FALSE TRUE 2766442.943 1823875.354 2249740.957 1404500.846 3002748.046 2052812.084 1999292.246 2138477.806 2571024.831 2010563.074 1.375954318 0.907146549 1.118960647 0.698560948 1.493486121 1.021013521 0.994394194 1.063621348 1.278758605 1 20.93916817 4.759245978 23.49950965 1.065014469 1.375955014 0.178685192 0.200635819 3750.273307 4260324.553 0.044897214 1.7634688 57444.17255 -4.759245978 0.310940545 DVDFMYVELIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDFMYVELIQR 12 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 150.94 0.00015946 42732000 28130 41595 48292 44426 50309 58022 45708 41164 51516 42635 FALSE TRUE 29240.59412 48738.61769 49550.52919 53213.3302 41757.49415 44547.26983 42125.28752 40612.26391 49661.94922 50988.51195 0.573474161 0.955874487 0.971797907 1.043633716 0.81895887 0.873672679 0.82617213 0.796498316 0.973983106 1 15.63788461 -3.544178828 0.012916242 1.935508838 5.62E-06 0.107831233 0.123757513 22542.66096 28.39245771 2472.266016 1825.61545 0.000285641 3.544178828 -1.935503219 DVDIIDHHDNTYTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 146 2.29E-06 2773340000 3812430 3182840 3951130 2904680 4991310 4970470 4756040 4127520 4463210 3078010 FALSE TRUE 3962947.68 3729468.011 4054099.694 3479217.034 4142888.909 3816153.671 4383249.157 4072197.346 4302579.944 3681087.127 1.076569922 1.013143097 1.101332175 0.945160197 1.125452554 1.036692026 1.190748549 1.106248563 1.168834041 1 21.81170047 2.655716978 1.861663406 1.122177325 1.042061782 0.144588907 0.068076375 0.506425719 3.489761792 0.024414305 0.022550761 452.6025308 -2.655716978 -0.080115543 DVDKFGNEITQLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVDKFGNEITQLAR 14 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 178.03 1.85E-06 142090000 251180 174110 235740 202470 248660 281700 290710 240750 266280 147270 FALSE TRUE 261096.7804 204012.0381 241883.5781 242517.9617 206392.862 216279.4442 267923.3906 237523.14 256696.6348 176124.7368 1.482453771 1.158338356 1.373365164 1.376967063 1.171856184 1.227990162 1.521213859 1.348607494 1.457470651 1 17.42623803 DVDLEFLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 148.05 0.00021154 464966000 1231110 932117 1164492 929372 1564904 1416780 1369421 1210960 1311066 842521 FALSE TRUE 1279715.173 1092200.844 1194839.618 1113199.008 1298902.177 1087754.317 1262082.204 1194729.062 1263880.991 1007596.859 1.270066656 1.083966106 1.185831027 1.104805953 1.289108998 1.079553104 1.252566632 1.185721304 1.254351857 1 19.9424871 DVDREDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVDREDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 149.65 0.0018257 1024670000 951695 1093017 1069969 1031291 1286338 1346898 1206921 1102409 1088781 1009148 FALSE TRUE 989268.6535 1280734.167 1097853.271 1235277.282 1067686.726 1034101.352 1112319.378 1087633.011 1049595.984 1206871.229 0.81969694 1.061202004 0.909668939 1.023536937 0.884673278 0.856844812 0.921655394 0.901200546 0.869683492 1 20.20284032 3.193161487 24.9993521 0.899750047 0.958085102 0.094365132 0.070651709 236.8653341 130430.8123 0.018687436 0.02233584 1560.13251 -3.193161487 0.058335055 DVDVSEDS(ph)PPPLPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVDVSEDSPPPLPER 15 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVS(0.007)EDS(0.993)PPPLPER;DVDVS(0.004)EDS(0.996)PPPLPER;DVDVS(0.01)EDS(0.99)PPPLPER;DVDVS(0.009)EDS(0.991)PPPLPER;DVDVSEDS(1)PPPLPER 247.38 3.05E-18 3613680000 3441550 3315630 3323720 4034740 3752570 4337260 4531870 3687620 3530620 2470020 TRUE FALSE 3577425.051 3885063.66 3410338.874 4832799.53 3114709.492 3329997.097 4176650.188 3638193.486 3403553.676 2953973.128 1.211055381 1.315199392 1.154492179 1.636033681 1.054413618 1.127294309 1.413909337 1.231627144 1.152195206 1 21.49422527 0.994564218 2.304747496 1.001968955 1.273018888 0.227427451 0.155339826 0.431258447 5.060715224 0.14132429 0.038696128 9.875616522 -0.994564218 0.271049933 DVDVSEDS(ph)PPPLPERTPESFVLASEHNTPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVDVSEDSPPPLPERTPESFVLASEHNTPVR 31 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 DVDVS(0.001)EDS(0.999)PPPLPERTPESFVLASEHNTPVR;DVDVS(0.003)EDS(0.997)PPPLPERTPESFVLASEHNTPVR;DVDVS(0.012)EDS(0.988)PPPLPERTPESFVLASEHNTPVR 211.47 1.26E-26 490294000 105294 296519 276929 225788 338101 353323 180864 295486 277992 360447 TRUE FALSE 109451.0884 347443.8317 284145.9972 270448.1925 280630.7128 271269.0879 166687.4071 291525.4935 267987.1222 431069.6885 0.253905787 0.806003857 0.659164875 0.627388563 0.651010081 0.629292885 0.386683201 0.676283908 0.621679346 1 18.71756159 0.444623047 1.604244418 0.999915197 0.594590734 0.409114045 0.14826475 3.59988491 9.349548594 0.132408528 0.037770875 2.78370396 -0.444623047 -0.405324463 DVDWGEVDYLIVDTPPGTSDEHLSVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVDWGEVDYLIVDTPPGTSDEHLSVVR 27 0 I3L3A0;I3L531;P53384-2;P53384 I3L3A0 NUBP1 Cytosolic Fe-S cluster assembly factor NUBP1 0 103.63 0.002288 49245000 7419 35376 27049 27911 25049 37132 29316 27738 26907 33683 FALSE TRUE 7711.907849 41451.55281 27753.91916 33431.71249 20791.17993 28508.65574 27018.13532 27366.21748 25938.62233 40282.53895 0.191445426 1.029020362 0.688981377 0.829930619 0.516133801 0.70771745 0.670715799 0.679356818 0.643917265 1 15.297867 -1.543847298 2.944027689 1.01465049 0.676330725 0.197269635 0.202730412 41612288.69 46496887.24 4861283.841 0.043785733 0.028585955 1.543847298 -0.338319765 DVDYVCISDNYWLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVDYVCISDNYWLGK 15 0 Q96KP4;Q96KP4-2;J3QKT2;J3QRH4;J3QRA8;J3KRJ8 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 183.66 1.15E-06 49177000 86538 81195 82843 69691 108018 103975 96847 95365 97428 68353 FALSE TRUE 89954.58706 95139.60964 85001.95664 83475.67179 89657.13894 79828.38201 89255.87908 94086.78816 93921.58531 81745.46165 1.100423011 1.163851885 1.039837013 1.021165825 1.0967843 0.976548183 1.09187565 1.15097262 1.148951678 1 16.31885102 -0.717120138 7.046923146 0.999999998 1.088462853 0.174189304 0.057351608 0 6.22E-11 0.058867653 0.013875239 0.191813806 0.717120138 0.088462855 DVEDEETWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVEDEETWIR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;;; 279.79 1.19E-23 3181780000 2005000 2202100 2284800 2058290 2739570 2898290 2519650 2191560 2327330 1996820 FALSE TRUE 2084158.948 2580293.545 2344343.765 2465413.619 2273898.87 2225206.072 2322153.249 2162185.723 2243569.848 2388058.648 0.872741945 1.080498399 0.981694385 1.032392408 0.952195572 0.931805454 0.972402102 0.905415671 0.939495288 1 21.18740684 3.090496333 7.659166473 0.942684931 0.997284291 0.113305692 0.054406783 0.380735824 27.95959815 0.014689892 0.017592691 1231.675587 -3.090496333 0.054599361 DVEDEILWVGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVEDEILWVGER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 283.82 7.08E-28 1037322000 818893 843281 887169 810284 1111807 1222144 1090957 912600 947129 822704 FALSE TRUE 851223.528 988107.9519 910289.353 970555.7567 922822.4433 938319.5778 1005444.94 900368.0897 913042.0123 983897.0972 0.865155035 1.004279771 0.925187558 0.986440309 0.937925771 0.953676538 1.021900504 0.915103919 0.927985269 1 19.90814791 4.756805897 24.05403302 0.9600394 0.865154898 0.400846408 0.035872942 2366.289956 3119560.137 0.008106566 0.254448676 57122.32782 -4.756805897 -0.094884502 DVEDEILWVTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;; 201.75 3.37E-07 132698000 151789 168963 167719 172154 204279 214032 189144 161129 174145 141026 FALSE TRUE 157781.7469 197981.0809 172089.8949 206205.5474 169555.7285 164326.3117 174318.399 158969.3293 167877.5555 168657.3446 0.935516608 1.173865754 1.020352214 1.222630108 1.005326681 0.97432052 1.033565419 0.942557999 0.995376489 1 17.36373562 3.026334016 24.99906001 0.98619253 1.092454336 0.278037663 0.076135285 250.2385418 237551.3255 0.020295474 0.024257148 1062.512423 -3.026334016 0.106261806 DVEDMELS(ph)DVEDDGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 355.2 2.27E-87 786710000 1892260 744864 1106420 1002476 1524240 1808950 2009300 1244880 1342720 477745 TRUE FALSE 1966967.886 872788.5978 1135254.214 1200762.761 1265150.229 1388848.777 1851805.816 1228194.42 1294395.769 571349.9858 3.442667253 1.527590128 1.986968132 2.101623857 2.214317425 2.430819659 3.24110591 2.149635863 2.26550416 1 19.12401523 2.845994573 6.243334419 2.360374525 2.188741495 0 0.688667835 1.592171653 79.71911235 0.201435169 0.214119568 701.4465331 -2.845994573 -0.17163303 DVEDMFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVEDMFSR 8 0 Q15717;Q15717-2;M0QZR9;M0R055 Q15717 ELAVL1 ELAV-like protein 1 0 ;;; 236.1 3.07E-08 1653440000 1891130 2073390 2195980 1932810 2568330 2613760 2301440 2203490 2139550 1975300 FALSE TRUE 1965793.273 2429478.604 2253209.043 2315114.049 2131766.184 2006753.852 2121047.119 2173955.821 2062548.013 2362322.216 0.83214443 1.028428124 0.953811054 0.980016203 0.902402801 0.849483546 0.897865289 0.920262192 0.873101899 1 21.17177433 3.218285508 23.32750236 0.901194692 0.954674169 0.097612467 0.058905007 192.9580902 222006.4869 0.015997546 0.019149868 1653.048164 -3.218285508 0.053479478 DVEPEDPMFLMDPFAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVEPEDPMFLMDPFAIHR 18 0 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 0 ;;; 199.41 1.63E-15 234031000 193247 220843 235846 226551 286760 291382 237737 236734 243320 229066 FALSE TRUE 200876.5408 258771.0673 241992.3405 271362.1116 238016.6376 223712.9464 219102.5527 233560.9679 234562.9607 273947.097 0.733267638 0.944602335 0.88335428 0.990563925 0.868841613 0.816628279 0.799798776 0.852576905 0.856234519 1 18.06353779 3.006269167 24.99408996 0.849616279 0.896420409 0 0.08013231 458.6287977 1828455.028 0.022085758 0.026338751 1014.539983 -3.006269167 0.046804129 DVES(ph)PSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVESPSWR 8 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 DVES(0.993)PS(0.007)WR;DVES(1)PSWR;DVES(0.866)PS(0.134)WR;DVES(0.999)PS(0.001)WR;DVES(0.74)PS(0.26)WR;DVES(0.985)PS(0.015)WR 208.63 9.44E-05 4054370000 1855640 1862760 1975660 1884120 2215010 2515470 2245240 1950750 1978700 1601630 TRUE FALSE 1928902.1 2182674.54 2027147.323 2256793.312 1838503.391 1931290.215 2069252.222 1924603.387 1907486.974 1915438.733 1.007028868 1.13951676 1.058320106 1.178212215 0.959834089 1.00827564 1.080301962 1.004784624 0.995848596 1 20.86924345 3.226032191 24.99972837 1.013082957 1.096219353 0.41359814 0.050894807 224.2102545 447397.6374 0.014081456 0.016941532 1682.79879 -3.226032191 0.083136396 DVESYIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 160.88 0.00035078 366030000 316410 391500 418940 405240 463230 484080 515890 422520 383930 369720 FALSE TRUE 328902.1111 458737.0796 429857.9206 485395.2625 384490.3301 371659.7563 475453.1938 416856.8105 370112.4343 442159.5553 0.743853903 1.037492177 0.97217829 1.097783044 0.869573722 0.840555749 1.075297793 0.942774629 0.837056284 1 18.75420754 7.999547876 0.005254546 1.691526585 0.155514587 0.012819638 0.109401489 445650.3137 181.1323427 24483.56771 28614.39051 99895948.82 -7.999547876 -1.536011997 DVFFYQADDEHYIPR ddPTM_MDA-MB-175_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 ;;; 262.05 5.58E-25 1125310000 780452 927050 950896 844348 963340 1118700 941182 879557 849617 858469 FALSE TRUE 811264.8476 1086263.626 975677.1309 1011357.514 799591.8109 858898.8791 867409.6955 867767.9771 819039.4501 1026669.564 0.790190803 1.058046 0.950332186 0.985085708 0.778820994 0.836587456 0.844877189 0.845226164 0.797763447 1 19.96954049 3.248915853 24.9997905 0.842127015 0.954238746 0.232845838 0.083427816 248.2346976 599288.7742 0.0213883 0.028648471 1773.845756 -3.248915853 0.112111731 DVFHMVVEVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVFHMVVEVPR 11 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 134.98 0.00012963 314490000 273820 278360 285320 329740 293810 344480 367440 295150 278180 223990 FALSE TRUE 284630.625 326166.1647 292755.6736 394961.5878 243868.2811 264479.7406 338639.0927 291193.997 268168.3561 267876.552 1.062544008 1.217598787 1.092875324 1.474416424 0.910375617 0.98731949 1.264161011 1.087045488 1.001089323 1 18.03120878 3.196155163 24.99999904 1.061415992 1.203772884 0.267580044 0.135336847 226.2550958 133387.2464 0.039241903 0.046903356 1570.923956 -3.196155163 0.142356892 DVFHTTVNFINQNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVFHTTVNFINQNLR 15 0 P55957;P55957-2;P55957-4 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ; 295.3 4.86E-44 1447060000 189583 452290 447250 497080 540760 684240 529030 537680 502430 487510 FALSE TRUE 197067.8832 529967.2892 458905.7024 595400.9404 448841.8084 525335.6298 487563.2462 530473.2791 484347.6424 583028.2506 0.338007435 0.908990754 0.787107146 1.021221424 0.769845729 0.901046612 0.836260071 0.909858619 0.830744723 1 19.15320627 4.740454182 24.99436714 0.879514207 0.338007251 0.813517778 0.07852814 60.7109635 801302.0147 0.016564289 0.10790938 55011.58805 -4.740454182 -0.541506956 DVFISAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVFISAAER 9 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 144.5 0.00023128 736031000 384314 528399 557283 594969 969964 835586 679434 551152 546889 840786 FALSE TRUE 399487.0135 619147.4179 571806.2528 712652.0924 805089.8657 641533.8149 626178.1877 543764.7089 527206.5717 1005521.919 0.397293193 0.615747311 0.568666125 0.708738496 0.800668638 0.638010771 0.622739471 0.540778574 0.524311367 1 19.9395131 -2.159861888 2.338681365 1.928470193 0.607465243 0.573539035 0.102887365 10385940.94 2120070.99 51208752.81 0.025967685 0.00692051 2.159861888 -1.32100495 DVFLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVFLYR 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;;; 142.53 0.026789 3473849000 1266310 1264730 1446870 1444270 1669060 1703640 1630410 1421130 1389700 1193320 FALSE TRUE 1316304.897 1481937.539 1484576.621 1729942.295 1385353.777 1307995.429 1502614.204 1402082.077 1339684.968 1427128.207 0.922345232 1.038405332 1.040254557 1.212184222 0.970728328 0.916522722 1.052893634 0.982449979 0.938727833 1 20.44468351 DVFQHSQSR ddPTM_MDA-MB-175_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 ; 135.86 0.00020901 391990000 218740 307610 275170 300000 348670 361430 283120 314820 264140 349460 FALSE TRUE 227376.0241 360439.6246 282341.1563 359339.1046 289403.1979 277493.36 260928.3146 310600.3528 254633.653 417929.9962 0.544052894 0.862440188 0.675570452 0.859806924 0.692468118 0.66397091 0.624334977 0.743187509 0.609273456 1 18.67290178 -0.971267299 4.894492885 1.000002722 0.704834559 0.464612301 0.097195125 2.67E-06 5.61E-07 0.086930516 0.02048953 0.10683971 0.971267299 -0.295168164 DVFRDPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVFRDPALK 9 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;; 145.99 8.74E-05 6829170000 8671250 6171690 8387490 6738910 9998270 9898140 10025930 8815340 8827230 5607480 FALSE TRUE 9013597.646 7231629.748 8606074.88 8071846.284 8298767.637 7599446.993 9240071.409 8697184.786 8509539.717 6706158.344 1.344077665 1.078356546 1.283309227 1.203646838 1.237484594 1.133204228 1.377848678 1.296895233 1.268914225 1 22.67705512 2.259665288 24.99912984 1.268724173 1.211047063 0 0.115001508 738.1354865 874340.8851 0.036827057 0.030781975 181.8298952 -2.259665288 -0.057677111 DVFRDPALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVFRDPALKR 10 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 129.82 0.00016481 4824860000 3797480 3094870 4037550 3235060 5178760 4707500 4377890 4042010 3984600 3136050 FALSE TRUE 3947407.443 3626389.848 4142771.87 3874945.212 4298476.225 3614254.468 4034739.542 3987833.467 3841195.024 3750498.954 1.052501945 0.966908641 1.104592194 1.033181254 1.146107832 0.96367297 1.075787406 1.063280784 1.024182401 1 21.83865111 4.243895309 24.99991836 1.054908654 1.009705319 0.08799626 0.052640258 272.6220183 1277545.599 0.011824985 0.030456454 17534.57764 -4.243895309 -0.045203335 DVGLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVGLKR 6 1 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;E5RJP0 E7ESA6 PTK2 Focal adhesion kinase 1 0 102.81 0.056482 114450000 186060 197000 217280 195580 289360 275490 238300 233010 232560 206890 FALSE TRUE 193405.7925 230833.2176 222942.4953 234265.1403 240174.6906 211511.6226 219621.4233 229886.8821 224190.211 247426.1344 0.781670833 0.932937897 0.901046674 0.946808391 0.97069249 0.854847541 0.887624195 0.929113178 0.906089454 1 17.91663837 -1.858332005 0.012283446 1.944542717 2.99E-06 0.298335061 0.048932547 6736.435822 11.99898246 1044.734396 861.3313934 0.013856961 1.858332005 -1.944539723 DVGPTPMYPPTYLEPGIGRHT(ph)PYGNQTDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVGPTPMYPPTYLEPGIGRHTPYGNQTDYR 30 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 DVGPTPMYPPT(0.133)Y(0.119)LEPGIGRHT(0.499)PY(0.106)GNQT(0.119)DY(0.024)R 71.506 0.0085879 135630000 44230 45755 56453 34586 107820 74312 53727 53178 47077 94005 TRUE FALSE 45976.23455 53613.06533 57924.21156 41427.00757 89492.79491 57054.16421 49515.73735 52465.23589 45382.70797 112423.4799 0.408955803 0.476884948 0.51523233 0.368490707 0.796032955 0.507493312 0.440439465 0.466675075 0.403676421 1 16.77858385 -1.204786217 3.8174826 1.00046643 0.490086783 0.65158114 0.112498974 180830228.3 341992613.9 1040507.99 0.026715263 0.062404195 1.204786217 -0.510379647 DVGRPQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 DVGRPQPGR 9 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;;;; 150.27 7.81E-05 2348720000 1251790 1505691 1261276 1314326 1281743 1643270 1249999 1224252 1049654 1467273 FALSE TRUE 1301211.636 1764281.717 1294145.889 1574295.76 1063872.783 1261645.446 1152020.812 1207842.904 1011877.158 1754757.052 0.741533784 1.005427911 0.737507159 0.897158817 0.606279246 0.718985825 0.656512998 0.688324861 0.576648008 1 20.74283987 3.246297347 24.99235416 0.68931001 0.849129876 0.204278555 0.129940303 222.6974748 719386.8483 0.032840468 0.043645742 1763.182824 -3.246297347 0.159819866 DVHAAS(ph)SPGMGGAAASWAGWAVTGVSSLTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVHAASSPGMGGAAASWAGWAVTGVSSLTSK 31 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;E9PPN3;Q96KG9-5;Q96KG9-6;H0YDH0;A0A0A0MQX4 E9PS17 SCYL1 N-terminal kinase-like protein 1 DVHAAS(0.528)S(0.464)PGMGGAAAS(0.007)WAGWAVTGVSSLTSK 108.71 7.72E-05 127890000 95607 51588 72864 66649 94751 120520 98185 67284 74361 57297 TRUE FALSE 99381.63818 60447.8377 74762.8957 79831.97327 78645.25886 92531.0565 90489.00314 66382.16803 71684.76214 68523.25013 1.450334565 0.882150768 1.091058809 1.165034833 1.147716413 1.350360007 1.320559124 0.968753933 1.0461378 1 16.06430596 1.668667521 9.002560442 1.006627174 1.186490636 0.262726535 0.148824654 0.176887187 23.07280589 0.072987019 0.038765557 46.63022603 -1.668667521 0.179863462 DVHEDSLTVVFENNWQPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVHEDSLTVVFENNWQPER 19 0 B4DXZ6;P51114;C9JAJ4;P51114-2 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 126.88 2.45E-05 57737000 24975 24516 29453 32224 29137 33613 31625 32007 29091 26308 FALSE TRUE 25961.03228 28726.43229 30220.56938 38597.81102 24184.30315 25806.89016 29146.14986 31577.99852 28044.02059 31462.5489 0.825140785 0.913035761 0.960525146 1.226785889 0.768669545 0.820241559 0.926375989 1.00366943 0.891346111 1 14.94134793 -1.262417251 3.257508773 1.000262986 0.933204614 0.029719422 0.120672054 41288370.66 52901126.12 105349.1272 0.029879394 0.054649067 1.262417251 -0.067058372 DVHNIYGLYVHMATADGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVHNIYGLYVHMATADGLR 19 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 179.58 2.05E-14 734475000 159607 350632 253020 356887 292012 365860 213911 222366 225315 466838 FALSE TRUE 165908.4076 410850.3185 259613.9091 427478.1834 242375.9045 280894.5597 197144.0969 219385.5475 217205.9572 558305.9679 0.297163952 0.735887384 0.465002927 0.765670095 0.434127375 0.503119393 0.353111212 0.392948598 0.389044663 1 19.09069645 -1.596450348 6.273668932 1.00151674 0.484002008 0.528776483 0.146746568 0.003081098 0.00019819 0.140623203 0.033063987 0.025325012 1.596450348 -0.517514732 DVHTLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 ; 121.09 0.0014481 223280000 49229 53639 61555 55295 63473 71129 59906 62731 66264 63942 FALSE TRUE 51172.59893 62851.081 63159.17387 66232.18596 52683.88213 54610.36772 55210.41118 61890.19355 63879.17158 76470.21066 0.669183444 0.82190281 0.825931736 0.866117478 0.688946476 0.714139104 0.721985865 0.809337296 0.835347138 1 16.22261023 0.831826646 1.541341121 0.999105637 0.764604261 0.579622265 0.061352826 0.471294116 2.085322227 0.060533253 0.017604481 6.789325735 -0.831826646 -0.234501376 DVIATDKEDVAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVIATDKEDVAFK 13 1 A0A5K1VW95;P40925;P40925-3;C9JF79;C9JRL4;C9JLV6 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 186.56 7.02E-06 953890000 1631800 715820 1179100 874910 1499600 1438000 1790600 1189800 1342600 480070 FALSE TRUE 1696224.724 838756.5167 1209828.315 1047964.587 1244698.528 1104046.293 1650248.093 1173852.677 1294280.088 574130.525 2.954423515 1.460916081 2.107235658 1.82530721 2.167971347 1.922988319 2.874343065 2.04457458 2.254330735 1 19.13101924 DVIEEYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;; 139.19 0.0015663 2035549000 4185340 3154080 4051070 3088990 5311210 4897950 4914880 4056300 4279120 2682410 FALSE TRUE 4350580.455 3695768.705 4156644.212 3699983.002 4408412.421 3760475.342 4529638.863 4001931.933 4125115.307 3207976.882 1.35617575 1.152055903 1.295721374 1.153369597 1.374203301 1.172226447 1.411992365 1.247494007 1.285893091 1 21.61323231 -1.450145795 6.165730352 0.999889939 1.27032488 0.46408568 0.087709045 0.000118257 1.05E-05 0.075682285 0.01783127 0.03546943 1.450145795 0.270434941 DVIKEIEDFDSLEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVIKEIEDFDSLEALR 16 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;;;; 197.45 3.95E-11 345759000 618356 466429 638345 488672 810767 776754 748388 656143 709268 432779 FALSE TRUE 642769.1724 546534.5524 654980.7951 585329.8631 672953.1149 596364.6553 689727.393 647348.4763 683741.5832 517573.759 1.241889028 1.055954911 1.265483004 1.130911011 1.300207175 1.152231242 1.332616619 1.250736663 1.321051486 1 18.98140495 3.246624528 24.99958949 1.243114883 1.171725132 0.041312896 0.106559393 424.9676761 1317467.821 0.027179956 0.036158527 1764.51164 -3.246624528 -0.071389751 DVIRPGMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVIRPGMR 8 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;;; 81.548 0.023692 1036960000 283917 350156 366037 346098 374965 445922 348612 344579 290475 407330 FALSE TRUE 295126.2624 410292.5692 375576.2249 414555.1514 311228.5832 342363.3735 321286.8805 339960.4821 280020.8615 487138.5147 0.605836438 0.842250319 0.77098446 0.851000565 0.63889135 0.702804979 0.659539065 0.697872313 0.574828007 1 18.89397253 -1.520402432 5.588015895 1.000605204 0.710331765 0.500222519 0.088343098 0.000662719 5.69E-05 0.085104902 0.020018815 0.030171546 1.520402432 -0.290273439 DVITLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 116.35 0.055015 580730000 630420 668570 677600 645520 791080 876240 762000 719800 713080 640220 FALSE TRUE 655309.4684 783391.6967 695258.8127 773201.9293 656612.5042 672746.5395 702272.4489 710152.2584 687416.3901 765658.8512 0.855876566 1.023160244 0.908052995 1.009851748 0.857578415 0.878650509 0.917213257 0.927504798 0.897810283 1 19.5463422 DVKPHNVMIDHEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 210.37 3.44E-09 381007000 373109 346538 402667 311980 491030 512128 489999 423041 442055 313408 FALSE TRUE 387839.6314 406053.2058 413160.8328 373688.7128 407564.896 393194.0334 451591.598 417370.8274 426145.5269 374814.297 1.034751434 1.08334503 1.102308093 0.996996955 1.087378201 1.049036914 1.204840908 1.113540307 1.136951099 1 18.51581646 DVKPKPIADAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVKPKPIADAK 11 2 E7EVA0;P27816-4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 83.769 0.0092582 1010770000 2320470 1059310 1646880 1017680 2369240 2173720 2461260 1674810 2150950 869750 FALSE TRUE 2412083.947 1241238.252 1689799.046 1218974.067 1966517.431 1668906.473 2268340.01 1652361.911 2073537.73 1040160.86 2.318952808 1.193313746 1.6245555 1.171909186 1.890589722 1.604469594 2.180758858 1.588563822 1.993477941 1 19.98837523 DVLCVQIAGLCHDLGHGPFSHMFDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVLCVQIAGLCHDLGHGPFSHMFDGR 26 0 Q9Y3Z3-4;Q9Y3Z3;A0A2R8YCS7;Q9Y3Z3-3;A0A2R8YF51;A0A2R8Y5D2;A0A2R8YD90;A0A2R8Y6J9 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 0 156.28 1.10E-08 137400000 6979.9 6526.8 9997.7 3346.1 5911.2 9629.1 7254.9 6238.8 8590.1 6190 FALSE TRUE 7255.471842 7647.727129 10258.24828 4007.948593 4906.416335 7392.887455 6686.241981 6155.179091 8280.943979 7402.811985 0.980096733 1.033084069 1.385723195 0.54140894 0.66277738 0.998659357 0.903202998 0.831465003 1.11862141 1 12.85385767 3.745441391 24.99488588 0.856281116 1.122979575 0.301664946 0.186195007 692.5764608 2515824.119 0.048747522 0.085533459 5564.695323 -3.745441391 0.26669846 DVLDGHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLDGHLR 8 0 P15924 P15924 DSP Desmoplakin 0 ; 152.47 0.00045665 419630000 411570 448080 449830 446880 583190 603240 480140 475510 457800 505310 FALSE TRUE 427819.1014 525034.2544 461552.9393 535271.5302 484059.5721 463146.6522 442505.3722 469136.5662 441323.8674 604315.8198 0.707939603 0.868807728 0.76376114 0.885748002 0.801004303 0.766398358 0.732241913 0.776310252 0.730286802 1 19.20494318 2.989915177 24.04767051 0.781112651 0.812380644 0 0.086580271 1312.16061 3128913.227 0.023601761 0.026687679 977.0463743 -2.989915177 0.031267993 DVLDVYIEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLDVYIEHR 10 0 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 162.36 6.79E-06 201940000 215518 207004 230881 264990 231700 312590 306620 243900 240794 182539 FALSE TRUE 224026.8171 242555.3267 236897.9485 317404.2311 192315.7168 239995.7098 282586.3232 240630.9194 232127.871 218304.0221 1.026214794 1.111089591 1.085174456 1.45395503 0.880953612 1.099364581 1.294462284 1.102274329 1.063323839 1 17.73597919 1.100561193 2.778233778 1.004154901 1.137807459 0.079587315 0.144498987 0.623183343 9.326150156 0.131999553 0.035653219 12.6055324 -1.100561193 0.133652558 DVLEVLDDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLEVLDDSR 10 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 166.19 1.31E-05 36199000 75567 85232 82193 91770 99871 108776 100471 94309 86196 84622 FALSE TRUE 78550.44351 99869.93299 84335.0171 109921.8321 82894.96309 83514.42252 92595.82049 93044.94211 83093.8228 101202.0607 0.776174348 0.986836951 0.833333002 1.086161994 0.819103509 0.825224525 0.914959832 0.919397703 0.821068486 1 16.62687914 -1.014110722 4.378990405 1.000004707 0.893565973 0.122222075 0.089329491 4.12E-06 9.28E-07 0.079773187 0.018801815 0.096803103 1.014110722 -0.106438734 DVLFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLFLK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 103.71 0.080148 1161090000 2476900 2246150 2618800 2200540 3281400 3183700 2892500 2713300 2647300 2148040 FALSE TRUE 2574689.925 2631908.79 2687048.079 2635800.244 2723628.8 2444333.924 2665778.292 2676932.652 2552024.19 2568907.311 1.002251001 1.024524621 1.045988724 1.02603945 1.060228521 0.951507247 1.037709021 1.042051085 0.993427898 1 21.29272341 DVLKDVLLPWYNAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLKDVLLPWYNAYR 15 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 155.56 2.08E-06 294720000 546780 525050 609700 468100 822350 776270 564150 581060 644430 533350 FALSE TRUE 568367.2966 615223.2532 625589.2829 560688.7829 682567.2407 595993.057 519930.4489 573271.8411 621237.0902 637849.7209 0.89106772 0.964526961 0.980778485 0.879029597 1.07010667 0.934378487 0.815130009 0.898756905 0.973955259 1 19.28285704 2.473784107 24.99853241 0.904218272 0.959267428 0.031811133 0.067726632 213.4752931 1599115.067 0.022791065 0.019158114 297.703614 -2.473784107 0.055049156 DVLLPWYNAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVLLPWYNAYR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 176.78 1.92E-05 811680000 832000 814200 920470 855940 1067050 1090680 1001670 851620 855330 830740 FALSE TRUE 864848.0024 954032.5164 944458.2044 1025242.377 885673.2221 837386.0994 923156.488 840205.4269 824546.8404 993507.5975 0.870499636 0.960266956 0.950630077 1.031942161 0.891460945 0.842858275 0.929189158 0.845696026 0.829935113 1 19.92217147 3.028597646 24.98508526 0.879268916 0.954644832 0.206796463 0.059209577 269.5024177 235456.1486 0.016356769 0.019549763 1068.064907 -3.028597646 0.075375916 DVLLQVDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVLLQVDDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 198.25 6.99E-07 982644000 927722 734976 845370 808306 882591 1107140 1055520 817537 886936 618098 FALSE TRUE 964349.1809 861202.4107 867401.0367 968186.5142 732568.4971 850023.5139 972785.5843 806579.2537 855015.3466 739202.4689 1.304580574 1.16504266 1.173428219 1.309771754 0.991025501 1.149919744 1.315993419 1.091147943 1.156672742 1 19.49561005 -5 0.117006133 0.41675245 1.273366606 0.292299624 0.094635463 211.5828592 1.61847588 29.33838296 0.963381714 1.00E-05 5 0.856614156 DVLLQVDDERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DVLLQVDDERR 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 250.48 1.77E-16 9983300000 4209280 4545230 4785890 4697770 5313980 5690770 5289300 4977060 4721900 4211920 FALSE TRUE 4375465.625 5325837.896 4910614.225 5626974.885 4410711.578 4369174.912 4874710.845 4910350.652 4551959.741 5037165.082 0.868636535 1.057308587 0.974876571 1.117091617 0.875633716 0.867387676 0.967748876 0.974824246 0.903674918 1 22.26418058 3.20607274 24.99999804 0.932903663 1.00613786 0.200830256 0.071213115 307.3776584 236531.7489 0.020230347 0.0241816 1607.210421 -3.20607274 0.073234196 DVLLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVLLRPK 7 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YNH0;H0YMV5;A0A0B4J281;H0YMG3;H0YMR9;P36959;H0YN74;H0YKK3 A0A087WWM4 GMPR2;GMPR GMP reductase;GMP reductase 2;GMP reductase 1 0 89.142 0.016498 644900000 258520 237130 238320 203330 376890 345770 333450 249090 286140 252830 FALSE TRUE 268726.5692 277855.2329 244530.815 243548.0671 312826.3724 265470.1577 307313.3177 245751.356 275841.8773 302367.1978 0.888742467 0.918933121 0.808721372 0.805471192 1.03459097 0.877972742 1.016357991 0.81275799 0.912274477 1 18.20594211 3.276638656 24.99998435 0.927103449 0.856661406 0.24911842 0.070970539 287.1517605 188526.4471 0.019803731 0.026813853 1890.769797 -3.276638656 -0.070442043 DVLSVAFSSDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 278.83 1.39E-27 1180000000 429174 466239 475000 468237 579210 590780 527380 499071 520820 454262 FALSE TRUE 446118.1209 546311.9214 487378.8902 560852.8811 480756.0911 453580.2984 486042.5775 492381.7696 502075.7899 543265.9415 0.82117815 1.005606793 0.897127637 1.032372616 0.884936924 0.834913923 0.89466786 0.906336532 0.924180501 1 19.05129908 0.821231124 4.459269094 0.999998126 0.912220897 0.157116952 0.06224045 3.766068325 92.2366569 0.057960469 0.014721924 6.625690181 -0.821231124 -0.087777229 DVMEDAVEDRLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVMEDAVEDRLDR 13 1 Q15833-2;Q15833;Q15833-3;R4GMY7;M0R1A1 Q15833-2 STXBP2 Syntaxin-binding protein 2 0 146 3.84E-05 121910000 31618 83956 63279 80995 55703 85659 55204 65521 62089 100560 FALSE TRUE 32866.30305 98374.78991 64928.10272 97015.56925 46234.62396 65765.99542 50876.96623 64642.79817 59854.42902 120262.8067 0.273287344 0.817998454 0.539885144 0.806696367 0.384446574 0.546852325 0.42304822 0.537512802 0.497696925 1 16.87583101 -1.291219462 5.548243441 1.000053359 0.543236268 0.426487756 0.161111183 9.85E-05 1.26E-05 0.144437401 0.034040261 0.051142333 1.291219462 -0.45681709 DVMQNHLLQMLCLVAMEKPASTNSDDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVMQNHLLQMLCLVAMEKPASTNSDDVR 28 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 236.03 5.35E-45 3703720000 1264333 945902 1354787 1175718 1480640 1597750 1644820 1337196 1476300 940967 FALSE TRUE 1314249.843 1108353.31 1390093.862 1408271.511 1228961.342 1226696.777 1515894.71 1319273.075 1423168.251 1125331.468 1.167877982 0.98491275 1.23527503 1.251428181 1.092088311 1.090075957 1.347065068 1.172341761 1.264665827 1 20.10191858 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVMQNHLLQMLCLVAMEKPASTNSDDVRDEK 31 2 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 250.56 3.82E-47 4872070000 2072087 1143333 1903669 1150936 2745050 2310575 2078393 1702482 2234593 1173046 FALSE TRUE 2153894.595 1339691.549 1953280.178 1378587.706 2278447.382 1773978.973 1915483.126 1679663.013 2154170.434 1402881.904 1.535335646 0.954956753 1.392334003 0.982682649 1.624119161 1.26452481 1.36539157 1.197294661 1.535532269 1 20.41996214 5.063149199 19.74531779 1.270716145 6.207656819 0.123924801 0.219125347 527.2953253 168782.6032 0.046042637 2655.933667 115650.9485 -5.063149199 4.936940674 DVNFEFPEFQL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVNFEFPEFQL 11 0 P62081 P62081 RPS7 40S ribosomal protein S7 0 ;;; 92.866 0.022511 98341000 276383 319626 320026 306941 355177 401851 342972 331449 318527 334840 FALSE TRUE 287294.8143 374519.2792 328366.1405 367653.0137 294804.1404 308527.1954 316088.9584 327006.4683 307063.2755 400445.4871 0.717438012 0.935256586 0.8200021 0.918110019 0.736190443 0.770459914 0.78934329 0.816606701 0.766804185 1 18.61124634 4.83727455 20.79447262 0.827312145 0.717393074 0.153590789 0.081561991 174857.7518 36793822.85 0.018335637 1006.102512 68750.29246 -4.83727455 -0.109919071 DVNQQEFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVNQQEFVR 9 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;; 226.55 5.41E-07 2314460000 1038060 1192180 1155870 1018640 1345530 1475630 1224790 1164340 1182330 1199700 FALSE TRUE 1079043.41 1396927.641 1185992.922 1220123.952 1116817.291 1132937.296 1128787.759 1148733.927 1139778.174 1434758.245 0.752073329 0.973632768 0.826615164 0.850403861 0.778401027 0.789636372 0.786744222 0.800646332 0.794404338 1 20.45237623 5.039855545 17.02646971 0.832054185 0.370502881 0.098280085 0.075994391 16079946.7 176791253.3 0.01729632 234356871.3 109611.3546 -5.039855545 -0.461551305 DVNSSS(ph)PVMLAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVNSSSPVMLAFK 13 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1;Q9NRI2 C4P0D6 DISC1;TSNAX;TRAX Translin-associated protein X 1 DVNS(0.024)S(0.112)S(0.864)PVMLAFK;DVNS(0.019)S(0.097)S(0.884)PVMLAFK;DVNS(0.015)S(0.1)S(0.885)PVMLAFK;DVNSS(0.007)S(0.993)PVMLAFK 161.08 4.09E-05 299230000 1137160 877190 1130470 934870 1398200 1409730 1414230 1175300 1139830 906790 TRUE FALSE 1182055.955 1027840.559 1159930.977 1119784.496 1160534.463 1082341.572 1303378.957 1159547.026 1098807.741 1084458.139 1.08999685 0.947791825 1.069594976 1.032575123 1.070151462 0.998048272 1.201871156 1.069240927 1.013232048 1 20.04854293 DVPIDHSDLVADLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVPIDHSDLVADLLK 15 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 0 112.96 0.00072229 10655000 64178 41195 58542 53523 79298 83661 88044 63026 68645 34844 FALSE TRUE 66711.797 48269.9208 60067.65261 64109.68965 65818.95428 64232.00064 81142.88122 62181.23956 66174.47986 41671.01467 1.600916069 1.158357222 1.441473242 1.538472009 1.57949008 1.541407166 1.947225952 1.492194036 1.588021803 1 15.34675661 5.069256968 21.42537499 1.510315684 4.3616516 0.005969378 0.24348263 5099.865091 1654447.538 0.054883657 33790.342 117288.9149 -5.069256968 2.851335916 DVPLADPGLDNDVGVEVGGSGGCLEERT(ph)PPVPDSGSANGSFFAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVPLADPGLDNDVGVEVGGSGGCLEERTPPVPDSGSANGSFFAPSR 46 1 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 1 DVPLADPGLDNDVGVEVGGSGGCLEERT(1)PPVPDSGSANGSFFAPSR;DVPLADPGLDNDVGVEVGGSGGCLEERT(1)PPVPDSGSANGSFFAPSR 285.8 7.68E-87 138629000 86391 101752 106642 95283 122098 133848 90193 106321 101074 119694 TRUE FALSE 89801.78339 119227.1145 109421.1781 114129.693 101343.8256 102763.8305 83123.43698 104895.9409 97436.36648 143145.7476 0.6273451 0.832907135 0.764403973 0.797297125 0.707976501 0.717896495 0.580690928 0.732791177 0.680679434 1 17.12712529 -0.950024204 4.553105309 1.000004475 0.718040532 0.590291153 0.071014665 9089840.818 1996404.864 422.748309 0.016732847 0.112195592 0.950024204 -0.281963942 DVPLTIKDPAVGFLETISPGYSIHTYLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVPLTIKDPAVGFLETISPGYSIHTYLWR 29 1 P04062-4;P04062-5;P04062-2;P04062 P04062-4 GBA Glucosylceramidase 0 181.62 6.13E-18 247280000 68023 136090 160520 156590 170870 213610 152940 157820 146810 138820 FALSE TRUE 70708.60057 159462.3989 164703.2831 187563.0346 141825.5784 164002.3148 140952.1632 155704.681 141526.3368 166019.1211 0.425906366 0.960506222 0.992074178 1.129767664 0.854272553 0.987851964 0.849011621 0.937871975 0.8524701 1 17.34098989 4.739312508 24.90623516 0.949224789 0.425906196 0.78726814 0.081962319 26.06543083 863245.3654 0.019485027 0.117205347 54867.16339 -4.739312508 -0.523318594 DVPNETLQVEEDDRPELPWWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 ;;; 295.4 6.78E-55 1078140000 644160 685145 825359 652890 904486 966604 850754 814452 773564 614056 FALSE TRUE 669591.9342 802813.3241 846868.5336 782029.6933 750741.7928 742124.87 784069.6784 803535.6031 745723.5827 734368.5164 0.911792811 1.093202263 1.153192865 1.064900899 1.022295722 1.010561936 1.067678776 1.094185801 1.015462355 1 19.48614468 1.053277107 8.216055963 1.000037727 1.057455587 0.077307971 0.060503534 0.513195825 67.49445645 0.057896798 0.014497026 11.30517024 -1.053277107 0.05741786 DVPPDILLDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVPPDILLDSPER 13 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 DVPPDILLDS(1)PER;DVPPDILLDS(1)PER 182.7 1.15E-05 66537000 65418 79434 69685 69228 88474 94759 65300 79798 76462 75847 TRUE FALSE 68000.75315 93076.17159 71501.04835 82921.09178 73435.22108 72752.65834 60181.61537 78728.43833 73710.14756 90707.76747 0.749668469 1.026110268 0.788257173 0.914156462 0.809580294 0.80205544 0.663467055 0.867934914 0.812611198 1 16.46893848 3.213733534 23.90426618 0.81063814 0.8749246 0.02728612 0.104151537 353.1305261 340003.2018 0.028192941 0.033714735 1635.812544 -3.213733534 0.06428646 DVPPDILLDS(ph)PERK ddPTM_MDA-MB-175_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 210.98 2.75E-09 285367000 334144 195944 261133 197685 338005 333113 306694 269319 291046 174460 TRUE FALSE 347336.2631 229595.8578 267938.3405 236786.503 280551.0308 255752.5541 282654.5229 265709.2193 280571.3113 208642.0968 1.664746801 1.10042921 1.284200766 1.134893229 1.344652087 1.225795552 1.354733907 1.273516819 1.344749289 1 17.67067075 -1.48409161 2.801094392 0.989550788 1.291361578 0.274967896 0.146536288 14064470.17 14856736.53 1132734.074 0.034511754 0.032802609 1.48409161 0.30181079 DVPSPGGLSAPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVPSPGGLSAPSSPR 15 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 DVPSPGGLSAPS(0.056)S(0.944)PR;DVPSPGGLSAPS(0.001)S(0.999)PR;DVPSPGGLSAPS(0.001)S(0.999)PR;DVPSPGGLSAPSS(1)PR;DVPSPGGLSAPSS(1)PR 292.63 6.19E-44 3512140000 1798380 1788700 1877100 1953870 2079640 2479320 2108880 2029240 1921630 1754530 TRUE FALSE 1869381.431 2095895.311 1926018.768 2340339.654 1726143.536 1903535.504 1943580.475 2002041.357 1852470.912 2098296.561 0.890904301 0.998855619 0.917896356 1.115352185 0.822640406 0.907181349 0.926265863 0.954126978 0.882845135 1 21.00078716 3.20703683 24.99999241 0.916412667 0.977556048 0.171815197 0.070014899 360.7786668 286115.174 0.019347283 0.023126293 1610.78223 -3.20703683 0.061143381 DVPYPPPLS(ph)PAIEAIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVPYPPPLSPAIEAIQK 17 0 G3V3Y1;Q8N8N7;G3V2R9 G3V3Y1 PTGR2 Prostaglandin reductase 2 1 DVPYPPPLS(1)PAIEAIQK 111.22 0.00054556 40426000 124990 127660 153180 129260 178270 188520 158760 158150 160910 135810 TRUE FALSE 129924.7017 149584.6119 157171.9966 154827.2422 147967.7291 144739.087 146315.9764 156030.2579 155118.8805 162419.3693 0.799933544 0.920977668 0.967692446 0.953256024 0.91102268 0.89114425 0.900853002 0.960662873 0.955051613 1 17.30936417 8 0.057904567 1.105424258 0.562328647 0.391381927 0.041275379 456.6952965 1.978973288 3.877191355 21.12765087 100000000 -8 -0.543095612 DVQAGSHDYPGEGIYLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVQAGSHDYPGEGIYLLK 18 0 Q6PL24 Q6PL24 TMED8 Protein TMED8 0 122.1 0.00010122 0 63545 52517 59209 54216 76005 76064 67401 61810 66046 43718 FALSE TRUE 66053.80567 61536.38622 60752.03518 64939.76298 63085.69725 58399.28876 62117.9335 60981.53805 63669.01736 52283.70507 1.263372701 1.176970648 1.161968822 1.242065054 1.206603418 1.11696921 1.188093564 1.16635839 1.217760242 1 15.67407376 -4.577370875 0.270958865 4.94E-12 1.203865349 0.67923273 0.039862225 95.39872862 1.148957993 53.12265081 0.047814754 2.65E-05 4.577370875 1.203865349 DVQEIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 172.97 0.0020487 825413000 895240 969570 878700 909290 1078070 1239480 1003500 938110 860090 991070 FALSE TRUE 930584.7665 1136086.105 901599.6439 1089144.848 894820.0465 951629.5545 924843.0478 925536.1699 829135.5289 1185251.191 0.78513717 0.958519269 0.760682335 0.918914789 0.754962368 0.802892721 0.780292865 0.780877654 0.699544143 1 20.17676141 3.22322182 24.95908017 0.790056159 0.856354468 0.064141004 0.090786165 490.8182471 798651.0031 0.023877673 0.028638994 1671.944359 -3.22322182 0.06629831 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVQFAVEQVLQEEHFDASHVALMGGSHGGFISCHLIGQYPETYR 44 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;; 121.32 1.45E-09 695426000 59033.5 132116 142112 184934 216775 269569 198875 140278 127965 279284 FALSE TRUE 61364.18816 154805.8953 145815.5555 221513.3932 179927.6629 206965.6851 183286.6578 138397.8029 123359.5646 334004.3526 0.18372272 0.463484664 0.43656783 0.663205109 0.538698557 0.619649665 0.548755297 0.414359279 0.369335201 1 18.34950738 -2.462904972 2.297963772 7.017965746 0.480388108 0.599495417 0.129537209 7029760.827 441384.8053 221540014.1 0.031739605 0.003444253 2.462904972 -6.537577639 DVQIGDIVTVGECRPLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVQIGDIVTVGECRPLSK 18 1 P62280;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;; 264.92 4.83E-31 3791330000 2222870 1803390 2281500 1695320 2689450 2634470 2477290 2215630 2388300 1798590 FALSE TRUE 2310630.624 2113108.204 2340957.764 2030649.236 2232298.25 2022654.268 2283113.537 2185933.104 2302345.55 2150989.274 1.074217641 0.982389001 1.0883168 0.944053632 1.037800735 0.940336752 1.061424882 1.016245469 1.07036589 1 21.0365689 DVQIILESCHNQNILGTILHPNGNITELLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVQIILESCHNQNILGTILHPNGNITELLLK 31 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 284.08 2.37E-72 38525000 8398.1 18495 19112 20447 21552 25343 22837 30227 15790 19211 FALSE TRUE 8729.663473 21671.37238 19610.07442 24491.35557 17888.59874 19457.47233 21046.97627 29821.85651 15221.72098 22975.02763 0.379963133 0.943257729 0.853538665 1.06599896 0.778610543 0.84689658 0.916080564 1.29801178 0.662533305 1 14.48777898 4.739110175 7.008753229 0.949289892 0.371497182 0.498414089 0.164292493 0.090829941 34.11740016 0.040239736 0.247356566 54841.60737 -4.739110175 -0.57779271 DVRPYIVGAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVRPYIVGAVVR 12 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 100.22 0.0030594 268760000 70599 85367 76968 62081 125790 109640 72935 80756 69407 115530 FALSE TRUE 73386.30303 100028.1182 78973.84931 74360.43651 104408.2607 84177.77161 67218.16412 79673.59791 66909.05563 138165.8915 0.531146307 0.723971141 0.571587158 0.53819677 0.755673195 0.609251463 0.486503314 0.576651712 0.484266087 1 17.07604198 -1.35814971 4.589262464 1.000465894 0.588939039 0.674557793 0.086175919 0.000406614 5.69E-05 0.082591948 0.01944555 0.043837955 1.35814971 -0.411526854 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 Q70J99;Q70J99-3;K7EQ37;Q70J99-2;K7EN81;K7EIH3 Q70J99 UNC13D Protein unc-13 homolog D 1 DVSGFSDPYCLLGIEQGVGVPGGS(0.827)PGS(0.173)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.879)PGS(0.121)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.834)PGS(0.166)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.803)PGS(0.197)R 136.02 5.88E-06 208979000 119890.9 134906.5 136308 144569 155266 174218 151941 137563.1 143562 153775.8 TRUE FALSE 124624.2853 158075.6419 139860.2985 173164.3167 128873.9408 133758.5098 140031.4674 135719.2917 138395.2317 183905.2238 0.67765495 0.859549493 0.760502043 0.941595421 0.700762807 0.727323058 0.761432789 0.737984973 0.75253562 1 17.48860293 -1.044186967 4.793537929 1.000006015 0.770412997 0.470485539 0.073559998 4.55E-06 9.07E-07 0.068502397 0.016145747 0.090326053 1.044186967 -0.229593017 DVSLGDWEFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVSLGDWEFGK 11 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 150.1 0.003941 0 54284 28328 32804 28119 42204 48194 47007 37642 36080 20705 FALSE TRUE 56427.17424 33193.11364 33658.89919 33680.85427 35030.17915 37001.67389 43322.46851 37137.47056 34781.48785 24761.74833 2.278804125 1.340499596 1.359310285 1.360196939 1.414689249 1.494307809 1.749572281 1.49979194 1.404645883 1 14.59582556 -2.882826445 0.288457574 1.67E-17 1.572132885 0.288706636 0.266572772 84.75875041 2.41518071 52.43889713 0.289759636 0.001309705 2.882826445 1.572132885 DVSLGDWEFGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVSLGDWEFGKR 12 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 110.08 0.00074354 0 228710 183540 200380 174310 275400 262030 229310 208270 225680 164370 FALSE TRUE 237739.6474 215061.5673 205602.0674 208787.9977 228587.6064 201177.5036 211336.083 205478.4813 217557.8209 196575.1544 1.209408422 1.094042469 1.045920925 1.062128112 1.162850956 1.02341267 1.07509051 1.045292229 1.106741193 1 17.58472146 4.717793463 3.263971108 1.067946059 1.225922168 0.503922269 0.042710856 0.239123415 4.184682643 0.009814656 0.092821775 52214.78128 -4.717793463 0.157976109 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGK 32 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVS(0.044)LGDWEFGKRDS(0.952)LGAY(0.003)AS(0.001)QDANEQGQDLGK;DVSLGDWEFGKRDS(1)LGAYASQDANEQGQDLGK 332.1 2.68E-117 293630000 121679 63618 97607 51341 134560 123016 101998 95248 119533 58413 TRUE FALSE 126482.9809 74543.89662 100150.7186 61496.09656 111687.5393 94447.39833 94003.13024 93971.35635 115231.0307 69857.90897 1.810574962 1.067078842 1.433634646 0.880302567 1.598781597 1.35199292 1.345633324 1.345178488 1.649505867 1 16.09213584 -1.030178332 4.549067466 0.999985835 1.3655899 0.164575119 0.257534629 3.37E-05 7.18E-06 0.226843387 0.053465429 0.093287116 1.030178332 0.365604065 DVSLGDWEFGKRDS(ph)LGAYASQDANEQGQDLGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVSLGDWEFGKRDSLGAYASQDANEQGQDLGKR 33 3 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 DVSLGDWEFGKRDS(0.996)LGAYAS(0.003)QDANEQGQDLGKR;DVSLGDWEFGKRDS(0.998)LGAY(0.002)ASQDANEQGQDLGKR;DVSLGDWEFGKRDS(1)LGAYASQDANEQGQDLGKR 160.07 4.04E-14 858170000 266138 163145 215686 113393 338647 277388 182581 193481 240822 165545 TRUE FALSE 276645.3337 191163.8847 221306.9543 135821.797 281083.9039 212968.8409 168269.8241 190887.7037 232154.8633 197980.3732 1.397337167 0.965569877 1.117822695 0.686036675 1.41975641 1.075706836 0.849931846 0.964174886 1.172615545 1 17.59499789 4.744078527 23.72281735 1.021750052 1.397337505 0.263374028 0.185062127 390.7105393 1679648.153 0.04259772 0.365469543 55472.60073 -4.744078527 0.375587453 DVT(ph)PPPETEVVLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 133.16 0.00051647 886350000 599300 378450 488390 426890 589140 607060 720980 484280 548510 261470 TRUE FALSE 622960.8268 443445.8436 501117.8446 511327.5679 488998.1932 466079.5151 664467.7037 477789.0187 528769.2322 312700.0404 1.992199381 1.41811892 1.602551263 1.635201477 1.563793189 1.490500336 2.124936418 1.527946777 1.690979098 1 18.25441988 -1.576819488 4.282446546 0.989789446 1.662669926 0.476837685 0.210908665 0.019290143 0.001906203 0.191592479 0.044928471 0.026496012 1.576819488 0.67288048 DVTGPDEESFLYFAYGSNLLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVTGPDEESFLYFAYGSNLLTER 23 0 O75223;O75223-3;B8ZZK2;O75223-2;O75223-4;A0A0B4J1Y4 O75223 GGCT Gamma-glutamylcyclotransferase 0 205.68 1.50E-24 10803000 15324 18866 21603 18639 21401 25168 22638 21049 20611 18613 FALSE TRUE 15929.00335 22106.08874 22165.99193 22325.73857 17763.26566 19323.11342 20863.57441 20766.87258 19869.21414 22259.86098 0.715593119 0.99309195 0.995783035 1.002959479 0.797995355 0.868069816 0.937273347 0.932929123 0.892602795 1 14.44215696 -1.513503174 2.911560127 1.003396806 0.911250736 0.092496231 0.087591289 94772948.39 103784906.2 2556536.618 0.020619896 0.030654683 1.513503174 -0.09214607 DVTHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVTHPR 6 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8 P49368 CCT3 T-complex protein 1 subunit gamma 0 103.29 0.080996 56577000 88370 114310 112700 90879 117050 115440 108870 101430 100750 99985 FALSE TRUE 91858.91584 133941.8533 115637.0546 108854.595 97153.88281 88630.80951 100336.4849 100070.4968 97124.02718 119575.1464 0.768210774 1.120147935 0.967065967 0.910344651 0.812492275 0.741214309 0.839108192 0.836883748 0.812242595 1 16.86755803 3.437988625 3.429516596 0.828411868 0.966468796 0.193177933 0.100427151 0.296543397 7.255942094 0.026865913 0.039123287 2741.502369 -3.437988625 0.138056928 DVTNFTVGGFAPMS(ph)PR ddPTM_MDA-MB-175_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 275.85 1.10E-34 7486817000 3802849.8 4322462 3828275 4012140 4559510 5167209 4020557 4294171 3692527 4240323 TRUE FALSE 3952989.247 5064811.224 3928042.991 4805729.317 3784486.119 3967203.02 3705415.237 4236614.662 3559633.675 5071133.106 0.779508083 0.998753359 0.774588817 0.947663809 0.746280178 0.782310962 0.730687828 0.83543748 0.701940493 1 22.27387671 3.226988721 24.99926172 0.788950331 0.876777466 0.116322148 0.099669424 380.4016415 821796.5306 0.026048394 0.031382313 1686.509225 -3.226988721 0.087827135 DVTNNVHYENYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVTNNVHYENYR 12 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;; 283.83 3.03E-28 8944140000 4709260 5290730 5240000 4690820 6304410 6804910 5485120 5401200 5124020 6152940 FALSE TRUE 4895185.221 6199371.721 5376558.705 5618650.195 5232788.64 5224572.782 5055181.962 5328805.749 4939607.521 7358490.788 0.6652431 0.842478696 0.73066052 0.763560132 0.711122537 0.710006023 0.686986246 0.724171016 0.671279976 1 22.81097847 -1.962064011 6.499953567 1.155625443 0.725423876 0.744888448 0.04863967 0.025928682 0.000151329 0.011132017 0.010721421 0.010912795 1.962064011 -0.430201566 DVVEQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVVEQHK 7 0 O75382;O75382-3;O75382-4;E9PMK8;Q9C040;Q9C040-2;A0A0J9YX34;C9J084 O75382 TRIM3;TRIM2 Tripartite motif-containing protein 3;Tripartite motif-containing protein 2 0 110.81 0.0067205 240980000 441690 389350 483520 369670 621340 590890 492410 519140 497370 393340 FALSE TRUE 459128.2623 456217.8338 496120.9284 442789.6226 515724.8487 453664.7525 453813.6175 512181.7774 479469.7509 470407.4421 0.976022531 0.969835494 1.054662159 0.941289578 1.0963365 0.964408111 0.964724571 1.08880458 1.019264807 1 18.84355136 8 0.399503699 1.025052524 0.11669792 0.060818535 0.050729371 180.0461581 2.394650985 0.03471119 128.639716 100000000 -8 -0.908354604 DVVHLDSEKDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVVHLDSEKDFR 12 1 Q14554;Q14554-2 Q14554 PDIA5 Protein disulfide-isomerase A5 0 103.75 0.0013292 75851000 125980 145570 147260 135800 175570 186680 155870 136390 150090 123800 FALSE TRUE 130953.7877 170570.5151 151097.7166 162660.8347 145726.6741 143326.3992 143652.5021 134561.9151 144688.2902 148056.2397 0.884486786 1.152065698 1.020542713 1.098642212 0.984265671 0.968053757 0.970256319 0.908856766 0.977252229 1 17.17578577 3.050086979 6.708297616 0.957502522 1.045719343 0.206715927 0.067520604 0.255366186 26.04613068 0.018440673 0.022015596 1122.243192 -3.050086979 0.088216821 DVVICPDASLEDAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVVICPDASLEDAKK 15 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;; 223.96 1.92E-12 3192700000 2179090 882660 1400730 912030 2047540 1821370 1856470 1330300 1555350 683900 FALSE TRUE 2265122.156 1034249.989 1437234.175 1092426.812 1699499.882 1398384.421 1710955.03 1312469.504 1499373.257 817897.1109 2.769446334 1.264523343 1.75723102 1.3356531 2.077889577 1.709731459 2.091895188 1.604687786 1.833205225 1 19.64155984 -0.502703008 0.889670887 0.962759828 1.801098647 0.268959351 0.40673169 31.21753958 15.75744595 4.418751847 0.118008495 0.314265707 0.502703008 0.838338819 DVVMMENFHHIFATLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVVMMENFHHIFATLSR 17 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 0 67.645 0.022299 31375000 28394 28852 32086 27960 34879 39551 38592 35812 31344 26190 FALSE TRUE 29515.01704 33807.10656 32922.18752 33490.40455 28950.28004 30365.87965 35567.0582 35331.99872 30215.93556 31321.42906 0.942326641 1.079360284 1.051107453 1.069248931 0.92429627 0.969492152 1.135550301 1.128045551 0.964704883 1 14.93486242 2.24820521 24.99695546 1.076627951 1.010523102 0.087501865 0.069367123 367.4384063 952330.3004 0.024992046 0.020669648 177.0945555 -2.24820521 -0.066104849 DVVNVYEPQLQHHVAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DVVNVYEPQLQHHVAQK 17 0 Q16222;Q16222-3;Q16222-2 Q16222 UAP1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase 0 ;; 180.81 4.85E-10 772210000 2040670 1598540 2060060 1623850 2368320 2377980 2170860 1992440 2104020 1521750 FALSE TRUE 2121237.227 1873076.81 2113746.856 1945042.683 1965753.812 1825730.184 2000702.321 1965734.601 2028296.731 1819907.777 1.165574022 1.029215235 1.161458225 1.068758927 1.080139245 1.003199287 1.099342695 1.080128689 1.114505228 1 20.79543391 3.548050654 24.99934974 1.068057058 1.110681333 0.197598128 0.049491864 300.5020183 105911.3018 0.012372883 0.019167981 3532.243658 -3.548050654 0.042624274 DVVVSLYHYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVVVSLYHYSK 11 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 116.84 0.00093537 203270000 1731200 1164800 1681800 1158300 2215700 1944900 1935000 1802400 1814900 1137300 FALSE TRUE 1799549.113 1364845.339 1725629.09 1387408.283 1839076.105 1493226.45 1783329.644 1778241.776 1749582.104 1360132.16 1.323069306 1.003465236 1.268721629 1.020054024 1.352130447 1.09785394 1.311144384 1.307403669 1.286332428 1 20.37531541 3.229313697 24.99971305 1.245348805 1.151294091 0.051708734 0.136229931 442.9635293 1197582.341 0.036234543 0.04388367 1695.562088 -3.229313697 -0.094054714 DVWLEWSDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVWLEWSDAEK 11 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 143.89 8.60E-05 13192000 67250 44431 68763 50305 76938 71029 79120 62215 66272 52088 FALSE TRUE 69905.08193 52061.67862 70555.02027 60255.17885 63860.10624 54533.5912 72918.36766 61381.10969 63886.88367 62293.64631 1.122186388 0.835746207 1.132619849 0.967276479 1.025146384 0.875427823 1.170558668 0.985351048 1.025576242 1 15.9267974 2.246415434 24.99880062 1.042365349 0.992545414 0.062337134 0.099092066 553.8618514 1762730.852 0.032175089 0.026453289 176.3662312 -2.246415434 -0.049819935 DVYDYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DVYDYFR 7 0 P49354;E9PQP6;H0YCW1 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 0 ;;; 110.35 0.015875 460968000 770700 835690 801430 785300 1378390 1168210 972390 835200 838190 1231070 FALSE TRUE 801127.8311 979213.2567 822315.9242 940629.9961 1144091.76 896910.9319 896171.5309 824005.5101 808023.7056 1472274.596 0.544142943 0.665102325 0.558534343 0.638895759 0.777091287 0.609200848 0.608698631 0.559681945 0.548826766 1 20.48961535 -1.511711064 5.861014472 1.000531014 0.613655609 0.750312748 0.067101242 0.000478547 3.99E-05 0.066777395 0.015718791 0.03078144 1.511711064 -0.386875406 DVYEDELVPVFEAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVYEDELVPVFEAVGR 16 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 ; 188.29 2.80E-09 53500000 97152 88746 96660 95897 123608 134553 126742 113815 116109 76800 FALSE TRUE 100987.636 103987.4352 99179.03901 114865.1404 102597.1563 103305.1049 116807.6309 112289.4961 111930.2598 91847.48958 1.099514385 1.13217504 1.079823079 1.250607294 1.11703822 1.124746092 1.27175638 1.222564673 1.218653447 1 16.48695267 3.757120753 24.8473418 1.185458807 1.106671253 0.127887254 0.076390575 1292.568281 1730416.964 0.018993343 0.034168408 5716.37555 -3.757120753 -0.078787554 DVYHHTFFEMLGSWSFGDYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVYHHTFFEMLGSWSFGDYFK 21 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 60.034 0.034695 5487500 4935.4 6773 8267.6 9010.7 10959 9703.5 13183 8566.4 11209 6484.2 FALSE TRUE 5130.253403 7936.210063 8483.060448 10792.98957 9096.193094 7450.009183 12149.68201 8451.58142 10805.59028 7754.654842 0.661570825 1.023412418 1.093931403 1.391807861 1.172997803 0.960714479 1.56675987 1.089872031 1.393432783 1 12.92084685 4.772766621 1.394026085 1.22727233 0.39711548 0.468545192 0.179979247 1.106188929 1.815489504 0.045997397 1.318380532 59260.67867 -4.772766621 -0.83015685 DVYKEHFQDDVFNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DVYKEHFQDDVFNEK 15 1 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 258.23 4.90E-25 2182856000 2456025 1445371 2151059 1296559 3251630 2638775 2345935 2081356 2590912 1524956 FALSE TRUE 2552990.763 1693602.226 2207117.365 1553014.5 2698919.094 2025959.497 2162054.485 2053458.827 2497665.583 1823741.931 1.399864049 0.928641381 1.210213642 0.851553871 1.479879937 1.110880582 1.18550462 1.125959102 1.369527969 1 20.79847016 3.248939622 24.99998545 1.205422387 1.093548262 0.080865152 0.187963058 563.0091103 1356116.425 0.048364602 0.064792077 1773.942839 -3.248939622 -0.111874125 DVYLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 1 DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR;DVYLS(1)PR 135.72 0.0031993 92832679000 71533350 75891760 77177410 75353540 87244920 92461220 87398080 80316770 77232620 66465010 TRUE FALSE 74357541.89 88925579.42 79188716.71 90258245.3 72415059.66 70988502.92 80547590.12 79240255.07 74453033.09 79487556.16 0.935461417 1.118735859 0.996240425 1.135501576 0.911023853 0.893076934 1.013335848 0.996888807 0.936662752 1 26.24422569 3.222773295 24.99981322 0.96173943 1.048056752 0.309540366 0.064250909 293.5367921 464825.5352 0.018092899 0.02169243 1670.21852 -3.222773295 0.086317321 DVYLS(ph)PRDDGYSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.999)PRDDGYS(0.001)TK;DVYLS(1)PRDDGYSTK;DVYLS(0.792)PRDDGYS(0.059)T(0.149)K;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVYLS(1)PRDDGYSTK;DVY(0.001)LS(0.999)PRDDGYSTK 204.07 3.73E-08 13628970000 5349070 4729870 6240380 2787446 8714360 6974590 3724765 5238330 6139870 6215410 TRUE FALSE 5560255.414 5542188.379 6403009.429 3338794.499 7233096.2 5354847.173 3432808.186 5168118.755 5918897.278 7433200.588 0.748029782 0.745599196 0.861406786 0.449173201 0.973079646 0.720395893 0.461821008 0.695275029 0.796278428 1 22.82555211 0.912261194 3.512763204 0.999648039 0.702495421 0.260035862 0.149987112 0.492097656 14.0442057 0.13978302 0.036102775 8.170736296 -0.912261194 -0.297152618 DVYLSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H3BT71;H0Y6E7;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ; 133.81 0.0075265 464400000 190595 310000 232508 248526 436369 409986 320991 244766 285397 539880 FALSE TRUE 198119.8378 363240.0885 238567.3495 297683.701 362195.1532 314772.9649 295830.8867 241485.3121 275125.6177 645659.1494 0.306848959 0.562587998 0.36949426 0.46105395 0.560969598 0.487521884 0.458184302 0.374013614 0.426115882 1 19.30041323 -1.566780939 2.977265477 1.028353598 0.446786375 0.822641618 0.077278962 22087761.52 23998035.05 4976806.156 0.018116757 0.02711559 1.566780939 -0.581567223 DVYLSPRDDGYS(ph)TK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.457)PRDDGYS(0.515)T(0.028)K 182.02 4.13E-06 288880000 479830 454180 554990 251750 801820 699710 359570 517280 600620 629650 TRUE FALSE 498774.0589 532181.882 569453.4953 301545.3986 665526.9228 537212.9567 331385.9638 510346.7077 579003.8035 753017.8621 0.662366836 0.706732083 0.756228403 0.400449198 0.88381293 0.713413298 0.440077162 0.677735195 0.768911114 1 19.52232456 0.911017953 2.698552587 0.999089999 0.652179513 0.381092751 0.134228809 0.382673944 6.162688799 0.124284942 0.033059998 8.147379641 -0.911017953 -0.346910486 DVYVPEASRPHQWQTDEEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DVYVPEASRPHQWQTDEEGVR 21 1 P49757-3;P49757;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;G3V4S6;G3V433;G3V3R1;G3V3M5 P49757-3 NUMB Protein numb homolog 0 136.58 2.83E-06 251960000 72094 86547 99616 78923 86859 110440 89851 90514 85393 97212 FALSE TRUE 74940.32679 101410.774 102212.0748 94533.73384 72094.73821 84791.98373 82808.24384 89300.80788 82319.72261 116258.8302 0.64459901 0.872284487 0.879176873 0.813131645 0.620122687 0.729338009 0.712274876 0.768120647 0.708072862 1 16.82698077 -1.134672215 3.810059067 1.000122885 0.754003637 0.453680075 0.082284209 21554082.23 31317940.22 31004.05558 0.020439218 0.073337784 1.134672215 -0.246119248 DWDAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWDAWK 6 0 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 ; 103.29 0.080996 197358000 497530 329730 376990 383940 394910 576780 486290 360660 394680 295510 FALSE TRUE 517172.8686 386358.5626 386814.6691 459882.1861 327783.3393 442831.5862 448173.3191 355825.9426 380475.5439 353409.5266 1.463381232 1.093231884 1.094522473 1.301272749 0.927488691 1.253026738 1.26814159 1.006837439 1.076585421 1 18.4309814 4.741283539 24.29006251 1.119380512 1.463381417 0.439835821 0.118300118 158.6766475 1415369.038 0.027092897 0.186514453 55116.74208 -4.741283539 0.344000905 DWDDDQND ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 160.26 0.0008244 710730000 1328000 1467080 1465360 1323050 1700060 1905040 1535920 1493440 1491660 1329700 FALSE TRUE 1380430.465 1719039.578 1503548.485 1584745.341 1411084.408 1462623.331 1415530.577 1473422.88 1437975.448 1590229.256 0.868070097 1.081001101 0.945491651 0.996551494 0.887346527 0.919756271 0.890142457 0.926547461 0.904256693 1 20.60080334 3.244647029 24.99777832 0.916158492 0.978559704 0.155362017 0.057374462 212.053286 870928.1385 0.014619642 0.019295487 1756.495449 -3.244647029 0.062401212 DWEDDS(ph)DEDMSNFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 33 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(1)DEDMSNFDR 445.09 3.87E-175 1.60425E+11 12985191 10452084 12206105 12401286 14623044 17198984 17917529 12958463 13391286 7763371 TRUE FALSE 13497856.37 12247148.12 12524206.12 14854223.36 12137424.2 13204780.62 16513106.26 12784776 12909336.23 9284454.909 1.453812475 1.319102547 1.34894361 1.599902579 1.307284523 1.42224619 1.77857574 1.377008788 1.390424786 1 23.14638578 0.688642965 2.16533394 1.000302334 1.454056317 0.496676153 0.135547931 1.321468401 8.042942059 0.129384224 0.035268801 4.882508018 -0.688642965 0.453753982 DWEDDSDEDMSNFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 178.32 4.56E-11 0 94651 102070 109130 93234 165360 138350 119320 115260 117650 82883 FALSE TRUE 98387.89457 119599.7285 111974.0175 111675.4069 137252.1663 106220.3092 109967.3866 113715.1282 113415.7995 99122.33696 0.992590546 1.206587054 1.129654737 1.126642191 1.384674438 1.071608201 1.109410754 1.147220008 1.144200217 1 16.59692258 -0.239825601 0.655302315 0.98935587 1.154391985 0.170186106 0.095901495 12.61217139 4.977251023 0.436333488 0.035004659 0.575671063 0.239825601 0.165036115 DWEQFEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 161.92 0.00096527 982310000 1270420 827471 1153820 871370 1514290 1403190 1402580 1116441 1194520 690253 FALSE TRUE 1320577.163 969582.7074 1183889.497 1043724.385 1256891.527 1077320.388 1292642.115 1101476.935 1151529.459 825494.8597 1.599740019 1.174547238 1.434157322 1.264362065 1.522591585 1.305060081 1.565899653 1.33432319 1.394956546 1 19.65489971 0.073076942 1.588427271 0.999806111 1.394985276 0.463035211 0.128986217 17.36547633 28.3696888 0.117435606 0.031452658 1.183251169 -0.073076942 0.395179165 DWEQFHQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 119.21 0.0008644 822080000 240724 545030 516570 525270 446770 645710 439610 533120 434780 549550 FALSE TRUE 250227.9694 638634.6628 530032.2386 629166.8382 370828.195 495753.6383 405152.2195 525974.3984 419132.3527 657223.8007 0.380734796 0.971715665 0.806471461 0.957309881 0.564234275 0.754314798 0.616460054 0.800297247 0.637731549 1 19.3260252 -1.418212851 5.20819691 1.000247607 0.734646902 0.189051345 0.171257385 0.000455521 5.09E-05 0.15340627 0.036124818 0.038175712 1.418212851 -0.265600705 DWGEHNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DWGEHNQR 8 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 107.15 0.0040577 202230000 197850 236780 227040 234810 256440 294960 236890 221010 207610 252780 FALSE TRUE 205661.2708 277445.1231 232956.8489 281254.7172 212850.4204 226460.0102 218321.9428 218047.7224 200138.1567 302307.4012 0.680305113 0.917758288 0.770595916 0.930360011 0.704086038 0.749105081 0.722185239 0.721278148 0.662035252 1 18.20565677 3.203905519 24.99854598 0.741438523 0.827529743 0.063585564 0.109097155 349.9079094 252406.0643 0.028769454 0.03438741 1599.21008 -3.203905519 0.08609122 DWHRPCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DWHRPCLK 8 1 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;; 146.03 0.00033639 13855120000 7314125 6830750 7622580 7166560 8940820 9217800 8772750 7458980 7897310 6953200 FALSE TRUE 7602892.303 8003878.177 7821230.697 8584084.178 7421062.61 7077105.647 8085118.932 7359004.574 7613087.356 8315546.413 0.914298583 0.962519813 0.940555233 1.03229346 0.892432348 0.851069226 0.972289556 0.884969455 0.915524606 1 22.98737964 DWILPSDYDHAEAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;; 262.23 7.12E-27 1403812000 933097 1114374 1070568 1438209 1182860 1443540 1396222 1106790 1007859 861016 FALSE TRUE 969936.3901 1305759.066 1098467.882 1722682.448 981797.8797 1108299.712 1286782.471 1091955.29 971586.3515 1029715.6 0.941945902 1.268077385 1.066768224 1.672969165 0.953465092 1.076316327 1.249648419 1.060443573 0.943548249 1 19.9738145 DWNDMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWNDMER 7 0 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 129.56 0.0084873 5266800000 5976500 5223300 5945000 5573300 6999300 7567800 7304000 5957700 6322200 4982300 FALSE TRUE 6212456.835 6120361.143 6099931.584 6675682.105 5809561.486 5810293.141 6731493.395 5877846.776 6094665.257 5958486.293 1.042623332 1.02716711 1.02373846 1.120365438 0.975006268 0.975129061 1.129732127 0.986466443 1.022854624 1 22.50651444 DWPELQDDIPHILAQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DWPELQDDIPHILAQAR 17 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 237.01 3.33E-20 204444000 115362 119198 133845 130428 143890 180905 145007 128814 150428 112097 FALSE TRUE 119916.5808 139669.3293 137333.1107 156226.2691 119431.6292 138892.5554 133640.9724 127087.459 145014.1257 134060.2609 0.894497594 1.041839903 1.024413273 1.165343615 0.890880179 1.036045689 0.996872388 0.947987555 1.081708514 1 17.03252212 3.197475423 24.99988672 0.989173178 1.031754305 0.058058083 0.076899483 436.5173755 265614.5984 0.021656166 0.025884362 1575.706851 -3.197475423 0.042581126 DWQSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DWQSGR 6 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ;; 168.74 0.014561 1445493000 279988 316429 292588 282904 305707 373541 294281 314237 301663 326253 FALSE TRUE 291042.1424 370773.2193 300213.0836 338861.5668 253743.0333 286791.7638 271214.4863 310025.167 290806.2076 390176.0289 0.745925226 0.950271651 0.769429851 0.868483817 0.650329632 0.735031736 0.695108018 0.794577688 0.745320538 1 18.57376562 5.101686186 12.26665007 0.788172336 8.87E-05 0.011253224 0.105029128 2730598.756 6710993.195 0.02396452 56354709.9 126382.28 -5.101686186 -0.788083686 DWQSYYYHHPQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 170.56 1.54E-05 4076310000 834022 1230553 1047976 1116926 1090978 1295577 1044960 1086910 1010312 1174735 FALSE TRUE 866949.8326 1441890.905 1075287.115 1337850.629 905533.9492 994698.8764 963053.3047 1072341.749 973951.0685 1404901.832 0.617089261 1.026328583 0.765382386 0.95227339 0.644553184 0.7080202 0.685495088 0.763285893 0.693252045 1 20.42203789 5.024854281 16.97839216 0.787941379 0.165671694 0.141797992 0.132788558 36919581.76 642693972.1 0.030589705 634956760.1 105889.8374 -5.024854281 -0.622269685 DWQSYYYHHPQDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWQSYYYHHPQDRDR 15 1 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 125.5 5.41E-05 401073000 87001 164486 137262 102381 178521 185278 98825 125959 122245 202032 FALSE TRUE 90435.86666 192735.191 140839.1605 122631.6562 148176.0642 142249.9924 91078.83827 124270.7256 117845.4263 241616.3023 0.374295384 0.797691171 0.582904213 0.507547111 0.613270143 0.588743355 0.376956511 0.514330881 0.487737894 1 17.88235827 -1.413978836 3.396224197 1.004684596 0.540884665 0.587905062 0.115978808 49132475.96 67371964.58 2228779.054 0.027433252 0.038549714 1.413978836 -0.463799931 DWTISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DWTISR 6 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 155.73 0.022892 795460000 780774 764881 934020 833779 1131810 1101020 930980 919380 911812 865530 FALSE TRUE 811599.5604 896243.3618 958361.3285 998697.9976 939425.3405 845324.7911 858007.3549 907057.2149 878996.0642 1035114.032 0.784067779 0.865840221 0.925850968 0.964819302 0.907557343 0.816648954 0.828901289 0.876287237 0.849178001 1 19.98135828 -1.75598597 2.422466773 1.032938074 0.871451112 0.372602452 0.050971754 12610394.54 8735617.335 2479627.71 0.013462753 0.017539372 1.75598597 -0.161486963 DWVLNEFR ddPTM_MDA-MB-175_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 ;;;;;; 133.23 0.0021592 2127622000 967063 2006982 1545515 1948921 1992418 2480296 1590704 1785687 1388452 3076723 FALSE TRUE 1005243.394 2351665.546 1585792.391 2334411.757 1653747.5 1904284.843 1466020.464 1761752.787 1338481.884 3679547.964 0.273197524 0.639118057 0.430974784 0.634428951 0.449443115 0.517532279 0.398424067 0.478795984 0.363762586 1 21.81109711 -1.234323981 5.120741321 1.000063255 0.472865425 0.690125735 0.107419112 7.00E-05 1.05E-05 0.093910105 0.022132181 0.058301002 1.234323981 -0.52719783 DWYDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DWYDVK 6 0 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 102.98 0.081604 1754640000 4044600 2803000 3695100 2646440 4464100 4338400 4143400 3761600 3921400 2329340 FALSE TRUE 4204283.931 3284393.446 3791397.342 3169897.933 3705293.877 3330872.349 3818629.481 3711181.905 3780269.58 2785729.575 1.509221846 1.179006561 1.36100696 1.137905833 1.330098194 1.195691204 1.370782547 1.332211833 1.357012401 1 21.40962378 4.753222553 23.99204127 1.270663302 1.509222142 0.290578656 0.117417072 1889.046927 3091046.886 0.025572697 0.542603154 56652.95313 -4.753222553 0.23855884 DWYPHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 DWY(0.008)PHS(0.992)R 66.92 0.042877 117140000 167950 217280 202380 204790 233050 262850 195500 218020 221120 253030 TRUE FALSE 174580.7957 254596.1498 207654.1891 245296.8508 193436.2442 201807.071 180176.1992 215097.7985 213161.9344 302606.3839 0.576923703 0.841344279 0.686218798 0.810613602 0.639233851 0.666896278 0.595414402 0.710817121 0.70441982 1 18.2070829 -1.44272437 3.890179469 1.002073903 0.694725466 0.574795715 0.079338608 0.001361595 0.000195051 0.073294968 0.017165239 0.036080756 1.44272437 -0.307348437 DWYPHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 DWYPHSR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;;;; 182.26 0.0014664 2.37562E+11 11989025 12273266 12625548 13216545 14372111 16532256 15876532 12901221 12681704 11702187 FALSE TRUE 12462360.96 14381103.96 12954580.15 15830738.15 11929144.71 12692890.09 14632087.94 12728301.23 12225291.95 13995006.49 0.890486258 1.027588231 0.925657317 1.131170476 0.852385793 0.9069585 1.045522054 0.90948877 0.873546715 1 23.73840882 DYAFIHFDER ddPTM_MDA-MB-175_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 ;;;;; 149.96 2.24E-05 2595970000 2801480 3085610 3134610 3299780 3361100 3865410 3714670 3334300 3059610 2683340 FALSE TRUE 2912084.594 3615539.515 3216300.512 3952466.635 2789781.423 2967727.108 3423504.459 3289609.162 2949495.234 3209089.097 0.907448969 1.126656009 1.002247184 1.231647522 0.869337478 0.924788006 1.066815023 1.025091253 0.919106682 1 21.61373241 3.212334021 24.99999894 0.977416157 1.066636185 0.206606543 0.094309891 388.336818 370173.6213 0.026933536 0.03220112 1630.549624 -3.212334021 0.089220027 DYAFVHFEDR ddPTM_MDA-MB-175_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 ;;;;; 183.85 1.62E-06 2892070000 2009600 2292350 2392470 2237720 2564240 2759600 2499240 2411520 2278310 2217690 FALSE TRUE 2088940.56 2686043.28 2454819.734 2680334.337 2128371.401 2118724.722 2303343.038 2379197.519 2196314.068 2652203.895 0.787624422 1.012758968 0.925577305 1.01060644 0.80249162 0.798854389 0.868463787 0.897064333 0.828109058 1 21.33876026 5.038786747 14.00019783 0.897641874 0.403493781 0.161560807 0.078593613 1351826.057 15601151.14 0.019033025 16204580.97 109341.933 -5.038786747 -0.494148093 DYAFVHMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DYAFVHMEK 9 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 ;; 123.79 0.00054777 738220000 1308980 1096370 1323190 1212580 1592260 1671180 1661890 1435780 1443230 974740 FALSE TRUE 1360659.541 1284663.019 1357673.418 1452424.705 1321608.214 1283073.772 1531626.719 1416535.718 1391288.434 1165721.64 1.167225085 1.102032401 1.164663476 1.245944704 1.133725384 1.100669086 1.31388718 1.215157777 1.193499705 1 20.1527919 DYAFVHMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYAFVHMER 9 0 Q9BWF3;E9PB51;Q9BQ04;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2;E9PLB0;E9PM61;U3KQD5 Q9BWF3 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 ;;; 148.32 9.03E-05 753890000 760334 875304 819975 887820 928486 1027751 983790 883264 796707 787737 FALSE TRUE 790352.5734 1025630.653 841344.2221 1063428.146 770662.2814 789071.406 906677.9691 871425.2908 768033.6707 942078.983 0.838945128 1.088688604 0.893071852 1.128809967 0.818044235 0.837585192 0.962422457 0.925002369 0.815254012 1 19.84548849 3.208970445 24.99996536 0.894029566 0.987879409 0.186322359 0.096553539 334.975878 283011.5069 0.02625792 0.031388547 1617.969928 -3.208970445 0.093849843 DYALHVGDGS(ph)SDPEVLLNIENQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYALHVGDGSSDPEVLLNIENQR 23 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 DY(0.001)ALHVGDGS(0.866)S(0.132)DPEVLLNIENQR 88.517 0.0039476 28235000 8307.7 7826.6 7639.2 6268.6 7602.5 11274 7363.7 7387.7 9991.7 8339.4 TRUE FALSE 8635.694411 9170.757668 7838.283828 7508.51037 6310.229766 8655.784359 6786.513953 7288.679965 9632.100669 9973.345763 0.865877371 0.919526695 0.785923201 0.752857722 0.632709415 0.867891735 0.680465123 0.730815931 0.965784291 1 13.28386185 1.196506491 7.415682252 0.987165281 0.774545849 0.48520242 0.083712664 0.205211892 28.56527555 0.081987022 0.021122789 15.72195291 -1.196506491 -0.212619432 DYALHWLVLGTHTSDEQNHLVVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYALHWLVLGTHTSDEQNHLVVAR 24 0 Q16576;E9PC52;Q16576-2;C9J7L0 Q16576 RBBP7 Histone-binding protein RBBP7 0 188.32 5.85E-18 27894000 5962.2 32863 29258 31209 27056 42036 25690 37641 25550 36472 FALSE TRUE 6197.59226 38506.96461 30020.48752 37382.04705 22457.03078 32273.77606 23676.35067 37136.48396 24630.46049 43617.9901 0.142087984 0.882822994 0.688259304 0.857032774 0.514857075 0.739918918 0.542811593 0.851402916 0.56468582 1 15.41263567 -5 0.138501906 2.081234463 0.546761458 0.220041335 0.20836205 224.3300852 1.91329801 67.91696046 1.228559028 1.00E-05 5 -1.534473005 DYAPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 148.28 0.0048727 475290000 354926 442038 422440 413017 460710 492456 466310 422265 421375 392635 FALSE TRUE 368938.7525 517954.5879 433449.1334 494710.5299 382398.6788 378090.5572 429759.4037 416605.2284 406209.7961 469564.3108 0.785704416 1.103053567 0.9230879 1.053552237 0.814369129 0.805194408 0.915230127 0.887216551 0.865078088 1 18.84096324 3.231507581 24.99960918 0.87533391 0.97302399 0.16367949 0.093268822 247.3970869 876901.9924 0.025013355 0.030500799 1704.149065 -3.231507581 0.097690079 DYAVSTVPVADGLHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYAVSTVPVADGLHLK 16 0 O94760;B4DYP1;O94760-2 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 ; 160.78 8.66E-09 827530000 278240 269770 277590 235560 327680 351010 302610 285880 288910 265320 FALSE TRUE 289225.13 316100.899 284824.2234 282153.0649 271981.0706 269493.2471 278890.6375 282048.2462 278512.1855 317304.3741 0.911506911 0.99620719 0.897637243 0.889218958 0.857161429 0.849320933 0.878937261 0.888888617 0.877744551 1 18.27550788 4.085877657 7.210201924 0.884187696 0.953440163 0.229704829 0.043670842 0.244544991 17.32209646 0.009939691 0.021714281 12186.46252 -4.085877657 0.069252467 DYDDMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 19 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;DYDDMS(1)PR;DYDDMS(1)PR 206.84 7.15E-05 80133564000 43119934 44185450 45988514 41391878 57080870 61173910 52163416 47296237 49017924 40828476 TRUE FALSE 44822342.29 51773957.32 47187012.45 49579067.93 47378284.11 46967196.5 48074711.15 46662308.3 47253778.49 48828034.16 0.917963278 1.060332619 0.966391813 1.0153812 0.970309064 0.961889974 0.984571916 0.955645852 0.967759184 1 25.54120636 3.171296709 24.47339475 0.970381251 0.993352251 0.042618473 0.035716616 106.0509653 38584.01103 0.009430121 0.011271156 1483.531283 -3.171296709 0.022971001 DYDDMSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 DYDDMSPR 8 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;; 209.37 0.00011101 16196781000 12157110 11593860 12905590 11085260 15236730 16029460 13994940 12730330 12325060 10577850 FALSE TRUE 12637082.09 13585015.27 13241920.28 13277891.34 12646796.08 12306860.84 12897980.03 12559700.75 11881483.5 12650377.18 0.998949036 1.073882231 1.046760906 1.049604383 0.999716917 0.972845368 1.019572764 0.992832116 0.939219703 1 23.59267707 3.16103174 4.489958804 0.987967488 1.044952296 0.518968532 0.026044231 0.16774284 6.304022676 0.007483861 0.009180115 1448.87774 -3.16103174 0.056984808 DYDEEEQGYDS(ph)EKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDEEEQGYDSEKEK 15 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEK 198.14 4.89E-09 416260000 855740 214280 353380 256560 552570 742550 662540 364170 451870 136910 TRUE FALSE 889525.276 251080.9231 362589.3731 307306.8022 458644.3488 570104.016 610608.3836 359288.8968 435607.287 163734.8932 5.432716623 1.533460084 2.214490546 1.876855912 2.801139939 3.481872464 3.729250202 2.194333106 2.660442612 1 17.32100228 4.750580988 24.66189731 2.497929467 5.432718785 0.565194348 0.795919425 1208.26912 2478920.738 0.191720238 3.183619165 56309.41144 -4.750580988 2.934789318 DYDEEEQGYDS(ph)EKEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDEEEQGYDSEKEKK 16 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 DYDEEEQGYDS(1)EKEKK 227.08 2.80E-15 1026800000 2997800 424050 795380 358610 1402000 1878500 1566500 849470 912880 173590 TRUE FALSE 3116155.459 496877.2888 816108.2562 429541.9877 1163688.541 1442246.844 1443713.637 838084.2441 880025.6271 207601.6369 15.01026439 2.393417009 3.931126307 2.069068404 5.605391933 6.947184354 6.954249774 4.036982832 4.239011022 1 17.66345829 4.745222007 24.96248585 4.400173419 15.01026932 0.746974536 1.893761287 392.1911813 1469634.55 0.461432084 4.494331108 55618.85023 -4.745222007 10.6100959 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_MDA-MB-175_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;DYDEEEQGYDS(1)EKEKKEEK;DYDEEEQGY(0.023)DS(0.977)EKEKKEEK 259.53 2.50E-30 3355500000 6252710 517947 1067989 336580 2457040 3595730 1669660 957556 1198795 286186 TRUE FALSE 6499571.819 606900.3682 1095821.671 403154.5194 2039393.218 2760676.201 1538787.686 944721.5281 1155650.602 342258.6673 18.99023294 1.773221327 3.20173534 1.177923477 5.958631331 8.06605198 4.495978724 2.760255965 3.376541524 1 18.38472755 4.743017488 24.98181728 3.719998979 18.9902391 0.831643463 2.084705303 183.1617481 1026628.352 0.52222017 4.152110577 55337.23913 -4.743017488 15.27024012 DYDPVAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDPVAAR 8 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 77.282 0.078204 243120000 847850 832590 787650 916790 877550 1103000 1018800 824340 814360 669920 FALSE TRUE 881323.7727 975580.8558 808176.8061 1098128.326 728384.3645 846844.9661 938943.7939 813291.0706 785051.3427 801177.9976 1.100034918 1.217683035 1.008735647 1.370642141 0.909141747 1.056999779 1.171954044 1.015119079 0.979871321 1 19.61176328 3.213968007 24.99999781 1.034181262 1.165550709 0.324217635 0.106433979 298.0026085 302938.3325 0.029545747 0.03532951 1636.695946 -3.213968007 0.131369447 DYDRDKDDKISWEEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DYDRDKDDKISWEEYK 16 3 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;; 206.8 8.37E-12 1530860000 3959240 1228510 2079840 1012540 3946260 3025030 2586940 1849990 2424160 889660 FALSE TRUE 4115553.852 1439497.036 2134042.339 1212817.39 3275476.135 2322512.627 2384168.883 1825193.91 2336914.955 1063971.843 3.868104102 1.352946551 2.005731968 1.139896133 3.078536481 2.182870385 2.240819527 1.715453206 2.196406765 1 20.02102854 -1.691883045 0.264588004 7.87E-14 2.291952879 0.198480872 0.746982283 44.11352954 2.021829571 30.2677809 1.002298865 0.020329044 1.691883045 2.291952879 DYDS(ph)PERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDSPERER 9 1 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3 P52756 RBM5 RNA-binding protein 5 1 DYDS(1)PERER 92.781 0.0059614 143420000 129330 107750 130110 102020 143730 163110 160480 120960 126200 100120 TRUE FALSE 134436.0483 126255.2243 133500.7735 122199.2515 119298.8259 125230.1745 147901.1583 119338.7291 121658.0867 119736.5971 1.122764898 1.054441394 1.114953796 1.020567266 0.996343882 1.04588052 1.235220992 0.996677139 1.016047638 1 16.86950465 0.853355574 0.008960451 2.07E-05 2.086779501 0.109506681 0.068725243 5735.678381 29.99806531 3541.864301 3440.511239 7.134369105 -0.853355574 2.0867588 DYDSTCVFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDSTCVFCR 10 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 181.55 4.36E-06 139710000 97097 111430 90468 97658 114770 130710 87707 97754 84062 134980 FALSE TRUE 100930.4645 130567.2357 92825.6704 116974.4609 95261.43639 100354.5834 80832.29616 96443.76752 81036.62504 161426.7467 0.625240034 0.808832727 0.575032777 0.724628746 0.590121763 0.621672588 0.500736698 0.597446021 0.502002467 1 17.30052011 -1.031798091 4.610628003 1.000012003 0.616726394 0.629355311 0.088361639 1.20E-05 2.52E-06 0.085908481 0.020248128 0.092939838 1.031798091 -0.383285609 DYDTLSKCS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYDTLSKCSPK 11 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 DYDT(0.003)LS(0.016)KCS(0.981)PK 67.234 0.036657 707080000 1686000 541850 827170 417710 1431300 1250500 877240 795030 979650 488850 TRUE FALSE 1752564.582 634908.5225 848726.7297 500331.7913 1188008.137 960090.3265 808479.6366 784373.9233 944392.5879 584630.7979 2.997728803 1.085999104 1.451731131 0.855808132 2.032065607 1.642216472 1.382889234 1.341656865 1.615365785 1 19.15716631 4.745526426 24.92480643 1.400985122 2.997729572 0.688366488 0.326505756 441.8690524 1581038.521 0.07525145 0.752338365 55657.84994 -4.745526426 1.59674445 DYDVYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 122.98 0.0099764 1027360000 1265830 1631400 1543670 1459210 1767110 1957250 1506560 1632850 1562900 1655830 FALSE TRUE 1315805.946 1911580.259 1583899.308 1747837.383 1466737.273 1502708.35 1388471.891 1610964.317 1506651.534 1980258.186 0.664461814 0.965318701 0.799844848 0.882631061 0.740679818 0.75884466 0.701157001 0.813512262 0.760835908 1 20.91725711 5.019121937 15.95335113 0.810161054 0.370350024 0.195524587 0.093412069 5076196.013 100194748.1 0.021163856 53545288.78 104501.3586 -5.019121937 -0.43981103 DYDWINAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYDWINAER 9 0 O95347-2;O95347;A0A0C4DGE5 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 ;;; 153.05 0.00018384 212456000 328599 338712 338161 359579 366395 456007 397253 343445 356638 276717 FALSE TRUE 341572.3423 396883.1512 346973.7535 430702.653 304115.3088 350106.2851 366115.2718 338841.6815 343802.668 330934.3981 1.032145175 1.199280442 1.048466873 1.301474417 0.918959499 1.057932591 1.106307697 1.023893809 1.038884655 1 18.33618573 3.223178715 24.99964148 1.032502919 1.142274926 0.332483397 0.083474491 287.0809544 466581.1171 0.022687988 0.02721268 1671.77842 -3.223178715 0.109772006 DYEEIGPSICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYEEIGPSICR 11 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 229.48 5.82E-12 905010000 457539 526238 546130 522574 649690 692480 612530 542160 565680 479321 FALSE TRUE 475602.993 616615.2829 560362.5965 625937.5775 539255.9259 531662.0146 564518.2981 534893.232 545321.2873 573234.7728 0.829682733 1.07567669 0.977544669 1.091939302 0.940724379 0.927476908 0.984794232 0.933113721 0.951305317 1 19.1287666 DYEEVGADSADGEDEGEEY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ;;;;;; 435.89 1.90E-169 5234362800 2064004 2127839 2229143 2300572 2576141 2811640 2611356 2348411 2344894 1772267 FALSE TRUE 2145492.472 2493278.796 2287236.298 2755618.275 2138249.473 2158679.221 2406671.093 2316934.392 2260501.723 2119508.787 1.012259296 1.176347469 1.079135087 1.300121185 1.008841995 1.018480902 1.135485311 1.093146868 1.066521515 1 21.01529852 DYEEVGVDSVEGEGEEEGEEY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 28 DYEEVGVDSVEGEGEEEGEEY 21 0 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 349.81 5.75E-95 4330107300 4704349 4897612 5190744 5305255 5771578 6548560 6024722 5401028 5542655 4226351 FALSE TRUE 4890080.331 5738738.763 5326019.053 6354618.604 4790527.233 5027756.184 5552488.547 5328636.054 5343175.929 5054423.56 0.967485268 1.135389366 1.053734217 1.257239036 0.947789036 0.994723953 1.098540413 1.054251982 1.057128645 1 22.26911514 DYEHQFHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYEHQFHLR 9 0 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 182.65 2.67E-05 562660000 405469 419231 439629 410130 510673 547694 436913 421285 420822 408173 FALSE TRUE 421477.2292 491230.6631 451086.0929 491252.4899 423868.9859 420500.3689 402666.6174 415638.3637 405676.6984 488146.6844 0.863423317 1.006317729 0.924078985 1.006362443 0.868322984 0.861422155 0.824888564 0.851462023 0.831054909 1 18.89695521 3.139973201 7.987549539 0.86023798 0.952016403 0.269359057 0.060222232 0.251443475 18.0315307 0.01601041 0.019182604 1380.299088 -3.139973201 0.091778423 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 DYEIESQNPLAS(0.996)PT(0.003)NTLLGSAK;DYEIESQNPLAS(0.996)PT(0.004)NTLLGSAK 294.57 1.11E-55 810370000 805620 574560 813370 535810 985350 984190 901260 797220 862770 576040 TRUE FALSE 837426.4997 673236.2105 834567.0904 641791.6188 817860.559 755626.788 830616.8862 786534.5699 831719.0762 688904.009 1.215592432 0.977256921 1.211441768 0.931612547 1.187190883 1.096853521 1.205707726 1.141718671 1.207307644 1 19.39394345 DYEMNANHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYEMNANHK 9 0 Q9NWH9;H7BXE3;H0YL55 Q9NWH9 SLTM SAFB-like transcription modulator 0 96.331 0.0074403 141020000 66455 73804 75204 69475 91000 96953 96933 91713 88409 58603 FALSE TRUE 69078.69471 86479.26288 77163.87802 83216.94764 75531.8525 74437.13509 89335.13817 90483.73725 85227.17736 70085.13583 0.985639735 1.233917319 1.101002047 1.187369428 1.077715718 1.062095895 1.274665978 1.291054603 1.216052111 1 16.09682088 2.236066402 24.98958647 1.229306258 1.115601133 0.119277629 0.099588172 93.90245229 940794.5182 0.034297512 0.026523415 172.2131864 -2.236066402 -0.113705125 DYENDEDVNKQLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYENDEDVNKQLDK 14 1 A6NKE1;A0A087WWM0;O43617 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ; 250.17 2.48E-18 352500000 675760 249010 393910 221579 651660 566970 559210 427210 543120 173283 FALSE TRUE 702439.5266 291775.5305 404175.6182 265406.6649 540891.066 435299.81 515377.659 421483.9487 523573.2173 207234.4861 3.389587996 1.407948725 1.950329917 1.280707038 2.610043705 2.100518201 2.486929992 2.03385043 2.526477263 1 17.66090458 4.754643932 24.47143663 1.99844224 3.389589414 0.40347251 0.525946693 2383.336418 3626265.478 0.119062563 3.044463576 56838.67327 -4.754643932 1.391147174 DYEVELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYEVELLR 8 0 E9PKP7;P17480-2;P17480 E9PKP7 UBTF Nucleolar transcription factor 1 0 111.04 0.0077015 30226000 33609 34335 36376 38733 41836 47970 39450 38332 38241 40989 FALSE TRUE 34935.90927 40231.76916 37323.98844 46394.27179 34724.73166 36829.69449 36357.80592 37818.22224 36864.71388 49020.00977 0.712686706 0.820721362 0.761403121 0.946435385 0.708378718 0.751319607 0.741693159 0.771485408 0.752033997 1 15.58108315 -2.015178865 5.12800584 1.268235855 0.775777329 0.521086836 0.064973712 0.038486882 0.000113921 0.012151551 0.014268881 0.009656531 2.015178865 -0.492458526 DYEYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYEYNR 6 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 153.61 0.023518 1433020000 952010 1057360 984840 897130 1133430 1260040 1092620 1006060 1010240 930330 FALSE TRUE 989596.0899 1238953.355 1010505.739 1074579.636 940769.9735 967414.8061 1006977.589 992575.4113 973881.6597 1112610.351 0.88943635 1.113555481 0.908229677 0.965818478 0.845552059 0.869500095 0.90505862 0.892114126 0.875312421 1 20.085517 3.768932334 2.007499842 0.894453417 0.99619866 0.180444417 0.068772069 0.417871695 3.267258442 0.017920023 0.038498327 5873.978247 -3.768932334 0.101745244 DYFEEYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 DYFEEYGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 145.63 0.0013173 18779900000 11814503 7811486 9732847 8306881 12110959 11706293 14104941 9958288 10699078 4955824 FALSE TRUE 12280948.7 9153047.956 9986492.988 9949957.268 10052342.52 8987683.861 12999358.87 9824813.438 10314020.27 5926822.828 2.072096477 1.544343103 1.684965669 1.678801199 1.696076095 1.516442135 2.193309847 1.657686373 1.740227534 1 22.4988275 0.315089194 2.23598678 1.000001432 1.749146759 0.550299508 0.204412768 15.13426574 48.07321528 0.185200975 0.050080086 2.065804382 -0.315089194 0.749145326 DYFEEYGKIDTIEIITDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;;;; 272.4 5.07E-39 6949995000 3317416.4 2843779.9 3350525.7 2305015.1 4490515.8 3980353.6 3234929.5 3279091.9 3654796 2873188.5 FALSE TRUE 3448390.561 3332176.976 3437843.152 2760940.207 3727219.528 3055976.799 2981367.273 3235141.037 3523260.606 3436134.776 1.003566736 0.969745715 1.00049718 0.803501721 1.084712845 0.889364649 0.867651436 0.941505863 1.025355766 1 21.71235519 DYFEQYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 DYFEQYGK 8 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;; 174.52 0.00063155 18866707000 6276106 4619639.4 5840201.9 4736537.5 6750230 6572684.7 6767013.3 5578941.8 5801123.2 3682089.1 FALSE TRUE 6523891.511 5413026.531 5992402.359 5673410.48 5602828.316 5046278.288 6236597.115 5504165.21 5592341.909 4403523.961 1.48151607 1.229248797 1.360819746 1.288379609 1.272351045 1.145963627 1.416274141 1.249945557 1.269969678 1 22.07022709 -4.270507188 0.21092106 1.32E-10 1.34288025 0.535353336 0.087573761 80.64668228 1.063283394 34.44032481 0.177591688 5.36E-05 4.270507188 1.34288025 DYFEQYGKIEVIEIMTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 203.63 1.06E-15 217184000 333895 417517 542271 186187 763799 604879 294555 405702 588511 601002 FALSE TRUE 347077.4324 489222.2969 556403.0277 223014.2329 633968.7188 464405.0193 271467.0094 400264.2283 567330.6041 718756.835 0.482885749 0.680650636 0.77411859 0.310277721 0.882035047 0.646122578 0.377689639 0.556884065 0.78932203 1 19.45514424 1.004703686 3.668402938 0.998263539 0.589362111 0.390596155 0.163427379 0.195349071 6.729797666 0.152214204 0.039267578 10.10889501 -1.004703686 -0.408901429 DYFFALAHTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYFFALAHTVR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 199.19 5.11E-08 1194030000 1035540 1104210 967680 892300 2619900 1723740 1229640 1032520 1023110 2324400 FALSE TRUE 1076423.919 1293849.478 992898.5358 1068794.277 2174570.334 1323427.509 1133257.604 1018680.758 986288.471 2779821.677 0.387227687 0.465443337 0.357180658 0.384483036 0.782269723 0.476083599 0.40767277 0.366455434 0.354802784 1 21.40656091 -1.205085804 4.438586992 1.000157837 0.442721255 0.657929512 0.12061735 0.000204721 3.67E-05 0.12131941 0.028586874 0.062361162 1.205085804 -0.557436582 DYFGAHTYELLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 198.49 1.25E-07 2645480000 3883110 2819540 3656480 3324050 4365910 4519560 5212750 3961910 4154440 2309530 FALSE TRUE 4036418.181 3303774.062 3751770.873 3981537.169 3623794.178 3469960.685 4804161.034 3908807.077 4004922.516 2762038.185 1.461391158 1.196136274 1.35833418 1.441521406 1.312000029 1.256304386 1.739353591 1.415189369 1.449988106 1 21.39730183 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYFGAHTYELLAKPGQFIHTNWTGHGGTVSSSSYNA 36 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 148.02 2.15E-13 1028560000 170303 376740 388370 379110 453640 528440 338050 463490 418410 481710 FALSE TRUE 177026.6939 441442.1644 398491.2412 454096.8265 376530.4348 405717.8186 311552.7577 457277.6747 403351.5058 576091.8516 0.307289009 0.766270453 0.691714768 0.78823685 0.653594446 0.704258908 0.540803965 0.793758276 0.700151382 1 19.13593933 -5 0.14007213 2.114271787 0.554382808 0.416727141 0.130612928 142.2187626 1.22093823 44.37716341 0.76876715 1.00E-05 5 -1.559888978 DYGAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYGAALR 7 0 Q9H313-4;Q9H313;Q9H313-2;Q9H313-3 Q9H313-4 TTYH1 Protein tweety homolog 1 0 95.957 0.030441 92793000 182260 220510 187430 161440 279020 261580 201000 205670 187110 262090 FALSE TRUE 189455.7655 258380.8772 192314.5798 193372.3501 231592.2801 200832.0093 185245.0948 202913.3301 180375.9476 313441.5175 0.604437367 0.824335204 0.613558093 0.616932791 0.73886919 0.640731996 0.591003694 0.647372217 0.575469227 1 18.25783676 -2.218190493 2.48114041 2.208106065 0.652708131 0.679165201 0.072088443 8552408.819 1823816.017 57982382.98 0.016723399 0.006050754 2.218190493 -1.555397934 DYGHSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 152.34 0.00045865 251300000 36758.6 149174 120220 153760 111948 171049 110893 155700.9 107531 162331 FALSE TRUE 38209.85791 174793.4741 123353.032 184173.2691 92919.11895 131325.462 102200.9169 153613.9841 103660.9803 194136.6514 0.196819393 0.900363083 0.635392807 0.948678509 0.478627391 0.676458881 0.526438033 0.791267301 0.533958835 1 17.56671299 -2.260718015 2.087359556 2.21850191 0.651982175 0.213054353 0.209024492 7200937.91 1056564.73 41403209.33 0.046027395 0.005486331 2.260718015 -1.566519735 DYGHSSSRDDYPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 166.09 2.32E-06 2170270000 190294 573284 443016 421300 478397 713304 282912 567948 418142 758145 FALSE TRUE 197806.9541 671741.0675 454561.3609 504631.8825 397079.2488 547649.9562 260736.6182 560335.586 403093.1511 906688.9972 0.218164061 0.740872636 0.501342094 0.556565574 0.437944268 0.604010811 0.28757007 0.61800197 0.444577085 1 19.79024825 -1.487406144 2.868324772 1.016843829 0.501228918 0.517027771 0.147540344 37145421.13 41450461.3 4969258.897 0.033011227 0.032553213 1.487406144 -0.515614911 DYGNSPLHR ddPTM_MDA-MB-175_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 ;;;;;;;; 188.91 3.88E-05 14577120000 2127282 5629140 4964690 5194470 5474420 6588920 4686320 5620870 4937570 5573850 FALSE TRUE 2211268.736 6595901.006 5094073.9 6221920.662 4543880.044 5058743.186 4318993.993 5545531.432 4759867.82 6665939.19 0.331726509 0.989493126 0.764194475 0.933389952 0.68165639 0.75889429 0.647919801 0.831920495 0.714058092 1 22.66837673 -2.363564976 1.987573555 2.299881384 0.753862997 0.169599621 0.17035197 8092222.062 800637.8448 47270266.68 0.037729323 0.004329473 2.363564976 -1.546018387 DYHFVTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYHFVTSR 8 0 A0A590UJD9;A0A0C4DFT3;A0A590UJ18;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 Disks large homolog 1 0 ; 120.12 0.0015631 283330000 105461 194587 146041 158295 195912 214198 142706 177729 149660 238134 FALSE TRUE 109624.6817 228005.8036 149846.9484 189605.2785 162610.9482 164453.7607 131520.3308 175346.8335 144273.7658 284791.7979 0.38492921 0.800605232 0.526163146 0.665768045 0.570981852 0.577452588 0.461812214 0.615701838 0.506593824 1 18.11954807 -1.701599 3.020126623 1.053341462 0.575082434 0.589328292 0.108087446 260940207.9 250614905.5 105984021.7 0.023438118 0.019879296 1.701599 -0.478259028 DYIHVVDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYIHVVDLAK 10 0 Q14376;Q14376-2;Q5QPP4;Q5QPP3;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 119.16 0.00072987 143990000 378070 271680 333140 311550 435590 440070 459430 363170 392690 233660 FALSE TRUE 392996.4955 318338.9266 341821.9021 373173.6601 361548.5674 337870.4118 423418.6761 358302.3002 378557.1636 279441.2033 1.4063656 1.139198239 1.223233718 1.335428189 1.293826977 1.209093032 1.515233513 1.282209982 1.354693435 1 18.09218523 3.743369701 24.36892595 1.305875023 1.244559092 0 0.137279316 1074.293264 5443708.887 0.033156761 0.05738925 5538.213586 -3.743369701 -0.061315932 DYINKHPGDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYINKHPGDAEK 12 1 Q8IZD9 Q8IZD9 DOCK3 Dedicator of cytokinesis protein 3 0 64.55 0.057586 772910000 33732 1095500 699360 532790 742100 1085600 194520 674600 677510 2501400 FALSE TRUE 35063.76541 1283643.603 717585.8961 638174.2718 615958.1071 833485.8524 179273.0141 665558.0904 653126.5474 2991501.438 0.011721126 0.42909677 0.239874829 0.213329087 0.205902661 0.278617901 0.059927437 0.222482959 0.218327339 1 21.51243833 0.401041106 3.40670174 0.99999995 0.212050392 0.829568723 0.107579769 28.42107982 160.6430819 0.096521322 0.024931661 2.517915238 -0.401041106 -0.787949558 DYIPVDQEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYIPVDQEELR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 185.77 1.36E-05 326400000 337490 346880 368100 423820 409840 438790 410380 357300 355760 324210 FALSE TRUE 350814.3658 406453.9416 377692.9884 507650.331 340175.5432 336887.6724 378213.3433 352510.9779 342956.2671 387732.7421 0.90478396 1.048283773 0.97410651 1.309278985 0.877345414 0.868865679 0.975448556 0.909159686 0.884517168 1 18.56470304 DYIPVDQEELRDYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYIPVDQEELRDYVK 15 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 140.74 4.46E-06 213650000 52989 50655 58837 31352 88741 74935 32749 48761 56813 71555 FALSE TRUE 55081.04664 59354.60221 60370.34056 37553.33202 73656.83652 57532.4819 30182.04781 48107.43855 54768.31123 85574.83225 0.643659417 0.693598815 0.705468407 0.438836175 0.86073013 0.672306102 0.352697715 0.562168073 0.640004892 1 16.38489894 0.944359696 19.33538354 1.000000002 0.609817791 0.418701488 0.134830001 895.0300171 311031.1835 0.132574797 0.033143699 8.79750852 -0.944359696 -0.390182211 DYIWNTLNSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYIWNTLNSGR 11 0 O75390;B4DJV2;A0A0C4DGI3;H0YIC4 O75390 CS "Citrate synthase, mitochondrial;Citrate synthase" 0 99.343 0.011273 218850000 108030 43535 47506 63646 75615 104170 86342 52385 68368 56713 FALSE TRUE 112295.1078 51011.79759 48744.04539 76234.98884 62761.98931 79978.09621 79574.28843 51682.86476 65907.44903 67824.82651 1.655663768 0.752110993 0.718675563 1.123998287 0.925354218 1.179186152 1.173232465 0.762005115 0.971730448 1 16.04952583 4.748898076 24.8535356 0.953851631 1.655664191 0.625173118 0.162458337 932.1767715 2241111.222 0.040442214 0.567730864 56091.63195 -4.748898076 0.70181256 DYLEDQQGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYLEDQQGGR 10 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 152.97 3.97E-05 755950000 1005900 548980 643970 654830 808500 971260 983390 634390 711720 427950 FALSE TRUE 1045613.709 643263.0445 660752.3872 784353.4195 671071.4588 745699.5846 906309.3222 625887.0397 686105.3362 511798.6089 2.04301788 1.256867513 1.291039826 1.532543086 1.311202194 1.457017607 1.770831937 1.222916649 1.34057679 1 18.9652167 -3.517623042 0.149327114 7.06E-16 1.620570632 0.311357074 0.234984343 107.4861345 1.448978386 34.61291973 1.268008026 0.000303653 3.517623042 1.620570632 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYLGDFIEHYAQLGPSQPPDLAQAQDEPR 29 0 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 ;;; 230.95 3.11E-35 416907000 185195 181864 205574 187878 205456 259586 224950 219765 211143 164318 FALSE TRUE 192506.6416 213097.7273 210931.4273 225039.7076 170532.6625 199301.0856 207317.8312 216819.4096 203544.0047 196512.966 0.979612926 1.084395252 1.073371552 1.145164679 0.867793438 1.014187967 1.054982963 1.103333861 1.035779006 1 17.58426498 -0.401023196 6.629449819 1.000007537 1.044488526 0.022959397 0.072497826 0 0 0.070411115 0.016596059 0.397170336 0.401023196 0.044480989 DYLHLPPEIVPATLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYLHLPPEIVPATLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;; 94.461 0.0044623 2407650000 753134 713582 805494 784200 789865 949586 968764 849714 811557 706613 FALSE TRUE 782868.3119 836134.1576 826485.8354 939312.4194 655604.0294 729059.0426 892829.7463 838324.9737 782349.2221 845060.2884 0.926405279 0.989437285 0.978019967 1.111533026 0.775807405 0.862730213 1.05652787 0.992029782 0.925791015 1 19.68869474 -0.320869351 6.804735192 0.999951725 0.962145547 0.017516032 0.0896208 0 0 0.087323031 0.020582236 0.477672951 0.320869351 -0.037806178 DYLHYHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYLHYHIK 8 0 O15144;H7C3F9 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 131.06 0.00059051 1438180000 2063420 1497220 1920190 1516560 3438240 2524730 2656320 1833920 2063760 2127190 FALSE TRUE 2144885.415 1754355.888 1970231.729 1816531.042 2853809.193 1938399.72 2448110.697 1809339.302 1989485.681 2543972.153 0.843124565 0.689612851 0.774470635 0.714053037 1.121792622 0.761957916 0.962318198 0.711226064 0.782039095 1 21.27865145 DYLHYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DYLHYIR 7 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 ;;;;; 153.15 0.0017657 3636830000 2126130 2073180 2188340 2003860 3463870 2859190 2703490 2199830 2215410 2692270 FALSE TRUE 2210071.254 2429232.538 2245369.938 2400217.527 2875082.615 2195186.454 2491583.39 2170344.877 2135677.827 3219768.76 0.686406826 0.754474224 0.697369937 0.745462704 0.892946925 0.681783885 0.773839234 0.674068556 0.663301618 1 21.61852565 -2.241074869 2.45535009 2.050124093 0.731303602 0.608609311 0.06495748 2860657.929 824185.8154 16666421.12 0.015798074 0.005740175 2.241074869 -1.318820491 DYLIDGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DYLIDGSR 8 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ;;;; 160.11 0.00082654 2173350000 3605060 4015510 3905510 3838290 4584830 5073820 4305330 4064210 3944310 3970720 FALSE TRUE 3747390.553 4705142.606 4007290.799 4597492.306 3805502.234 3895502.199 3967866.985 4009735.913 3802355.054 4748706.56 0.789139212 0.990826143 0.843869957 0.968156749 0.801376582 0.820329104 0.835567946 0.844384858 0.800713838 1 22.17910318 3.22089058 24.99804075 0.840534561 0.900762338 0.077600015 0.075727138 464.2268847 656746.6511 0.019840193 0.023762325 1662.993607 -3.22089058 0.060227778 DYLLCDYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 DYLLCDYNR 9 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 184.49 0.00010223 3393220000 2718670 2965820 2471355 2252373 4706320 3976440 2917180 2545752 2654860 4421470 FALSE TRUE 2826005.191 3475176.514 2535760.542 2697885.657 3906341.407 3052972.074 2688523.809 2511630.358 2559312.107 5287772.392 0.534441534 0.657209928 0.479551757 0.510212138 0.738749915 0.577364502 0.508441667 0.474988364 0.484005724 1 22.33422865 -1.153961858 4.819594119 1.00003289 0.550225507 0.731603824 0.081461772 3.44E-05 6.04E-06 0.082438826 0.019429396 0.070151691 1.153961858 -0.449807384 DYLLS(ph)ES(ph)EDEGDNDGER ddPTM_MDA-MB-175_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 159.8 8.58E-09 108720000 160199 171299 179861 153899 180024 217100 182795 158188 163630 136023 TRUE FALSE 166523.7802 200718.2707 184548.3254 184339.7629 149423.5848 166681.8152 168467.0503 156067.7486 157740.9883 162674.1025 1.02366497 1.233867393 1.134466535 1.133184447 0.918545623 1.024636452 1.035610756 0.959389025 0.969674864 1 17.31162507 3.257131885 24.57813024 0.986367983 1.138848949 0.615961516 0.056593908 122.5860299 162235.1408 0.014987642 0.020254708 1807.723006 -3.257131885 0.152480966 DYNDADMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYNDADMAR 9 0 Q14696;H0YLI4;Q14696-2 Q14696 MESDC2 LDLR chaperone MESD 0 104.39 0.007601 394340000 321830 369650 349550 347650 455290 521270 362810 344300 348460 339400 FALSE TRUE 334536.0969 433134.512 358659.5602 416414.1324 377899.9684 400212.9424 334372.0042 339685.2217 335918.9927 405898.9318 0.824185704 1.067099413 0.883617896 1.025905958 0.931019864 0.985991613 0.823781434 0.836871435 0.827592699 1 18.63076102 2.23939694 24.99999899 0.854914709 0.957322935 0.182688896 0.080322658 27.39072286 818817.5014 0.026163449 0.020712658 173.5389399 -2.23939694 0.102408226 DYNPYNYSDSIS(ph)PFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYNPYNYSDSISPFNK 16 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 DYNPYNYSDSIS(1)PFNK;DYNPYNYSDSIS(1)PFNK 374.74 1.78E-104 180061000 313580 198256 273130 224400 332710 339340 319200 287040 319750 192411 TRUE FALSE 325960.3805 232304.9258 280247.9922 268785.6502 276156.073 260533.4277 294180.2699 283192.6983 308242.26 230110.2515 1.416540021 1.00953749 1.217885732 1.168073341 1.200103304 1.132211303 1.27843183 1.230682668 1.339541624 1 17.81196573 2.234734637 24.99866158 1.2329922 1.183120613 0 0.125155573 393.8920386 2573617.678 0.042019969 0.032190986 171.6859028 -2.234734637 -0.049871587 DYNVTANSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYNVTANSK 9 0 P00338;P00338-3;P00338-2;P00338-5;F5GXY2;F5GYU2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 ;;; 208.66 0.00011253 961390000 908120 687690 863850 710690 1049840 1036480 1005260 825580 853990 574820 FALSE TRUE 943973.2788 805795.408 886362.6407 851262.3608 871388.5718 795773.228 926465.0944 814514.4505 823255.0667 687444.9734 1.373161948 1.172159866 1.289357949 1.238298909 1.267575741 1.157580983 1.34769346 1.184843125 1.197557766 1 19.39088471 -4.612963019 0.210806679 7.57E-10 1.282055132 0.588447979 0.065239411 80.67978919 0.933761109 34.03521319 0.1266503 2.44E-05 4.612963019 1.282055132 DYPFHEEF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYPFHEEF 8 0 P15121 P15121 AKR1B1 Aldose reductase 0 91.906 0.028278 42718000 89502 149590 87910 69657 90045 102600 52777 81255 72919 157820 FALSE TRUE 93035.60807 175280.9189 90201.00682 83434.94669 74739.18306 78772.70492 48640.20083 80165.90963 70294.65943 188741.8074 0.492925279 0.928680939 0.477906872 0.44205864 0.395986369 0.417356949 0.257707614 0.424738487 0.372438202 1 17.5260545 -3.603314817 9.000438116 0.97172293 0.493152512 0 0.232227346 0 0 0 0.050027411 0.000249279 3.603314817 -0.478570418 DYPSSR ddPTM_MDA-MB-175_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 ;;; 139.92 0.027558 1352320000 409982 446482 456251 414441 506596 580270 479192 468502 481550 437440 FALSE TRUE 426168.4059 523161.8104 468141.2759 496416.1928 420484.9929 445511.0866 441631.6789 462222.497 464219.1096 523147.9927 0.814623036 1.000026413 0.894854386 0.948902031 0.803759163 0.851596666 0.844181159 0.883540611 0.887357146 1 18.9968596 DYPVVSIEDPFDQDDWGAWQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DYPVVSIEDPFDQDDWGAWQK 21 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;; 298.76 5.41E-55 758790000 1532140 1262360 1571700 1406570 1941660 1923070 1877350 1465920 1746870 1227420 FALSE TRUE 1592630.07 1479160.51 1612659.793 1684785.348 1611617.327 1476466.137 1730198.401 1446271.74 1684000.49 1467909.449 1.084964792 1.007664684 1.09860986 1.14774474 1.097899689 1.005829166 1.178681971 0.985259507 1.147210062 1 20.48533154 -0.38639039 7.917297072 0.999999998 1.079180924 0.134828924 0.062695321 0 0 0.056612425 0.013343676 0.410780302 0.38639039 0.079180926 DYQASEDKVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYQASEDKVR 10 1 Q96ME1-4;Q96ME1-2;Q96ME1;Q96ME1-3 Q96ME1-4 FBXL18 F-box/LRR-repeat protein 18 0 81.431 0.019179 100560000 70767 74925 85405 65438 113760 117570 91851 69576 84694 69911 FALSE TRUE 73560.9358 87792.78591 87630.72446 78381.44109 94423.11583 90266.14929 84651.47861 68643.44752 81645.87948 83608.72192 0.879823709 1.050043391 1.048105059 0.93747924 1.129345284 1.079625991 1.012471865 0.821008215 0.976523473 1 16.35136583 1.928537934 12.02594797 0.913549697 1.026258871 0.187240064 0.079903858 1.367895555 228.0358928 0.032526067 0.020827422 84.82774727 -1.928537934 0.112709174 DYQDDTLELYNREDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYQDDTLELYNREDR 15 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 152.34 1.43E-08 0 324800 386210 407990 313880 457050 458310 363200 375850 396960 399430 FALSE TRUE 337623.3548 452538.5632 418622.5546 375964.5272 379360.8043 351874.4483 334731.435 370812.3455 382673.4871 477690.661 0.706782406 0.947346474 0.876346533 0.787046007 0.79415579 0.736615716 0.700728447 0.776260404 0.801090577 1 18.86571715 6.248895699 8.811790098 0.802956108 0.710831893 0 0.094978244 0 0 0.020397595 0 1773763.438 -6.248895699 -0.092124215 DYQDNKADVILK ddPTM_MDA-MB-175_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 ;; 157.2 6.73E-05 2048020000 1957530 1579490 1936880 1230920 2577500 2272380 1872070 1921990 2140190 1733680 FALSE TRUE 2034814.796 1850755.121 1987356.684 1474392.302 2139377.471 1744654.183 1725332.262 1896228.868 2063164.98 2073361.403 0.981408641 0.89263508 0.958519186 0.711112062 1.031840116 0.841461687 0.832142558 0.914567458 0.995082178 1 20.98354018 1.286731395 4.085041325 1.00044972 0.890564448 0.193128536 0.084230765 0.317469291 9.664757064 0.063909695 0.0200579 19.35224687 -1.286731395 -0.109885272 DYQGPLKEHEVTIFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ; 197.14 2.65E-11 1712440000 1142700 888010 1189530 828170 1434580 1350450 1098740 1113590 1259950 1007560 FALSE TRUE 1187814.678 1040518.81 1220530.129 991979.5542 1190730.604 1036828.454 1012617.888 1098664.148 1214604.646 1204972.091 0.985761153 0.863521087 1.012911534 0.823238614 0.988181065 0.86045848 0.840366258 0.911775597 1.007994006 1 20.2005683 1.246071353 10.2423691 1.004114408 0.907318592 0.258759353 0.062895675 0.182119099 223.8864543 0.043107512 0.014204484 17.62265556 -1.246071353 -0.096795815 DYRPTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYRPTWK 7 1 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 65.252 0.064833 285630000 277640 226460 244810 227550 270510 304890 250630 256990 271720 190760 FALSE TRUE 288601.4416 265352.7434 251189.9497 272558.7108 224528.8068 234083.9182 230984.9657 253545.4694 261940.8503 228135.7697 1.265042488 1.163135197 1.101054649 1.194721508 0.984189402 1.026072845 1.012489037 1.111379727 1.148179659 1 17.79953314 5.022139603 0.72531475 1.060250107 1.464665962 0.522602546 0.061482242 3.463933732 1.043360784 0.024108232 1.25468862 105230.0079 -5.022139603 0.404415855 DYS(ph)YER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 DYSYER 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 DYS(0.999)Y(0.001)ER;DYS(1)YER;DYS(1)YER 116.25 0.024898 1480600000 1353400 1106890 1242230 1066940 1617350 1790650 1402730 1244990 1264470 1035560 TRUE FALSE 1406833.277 1296989.747 1274603.534 1277977.548 1342433.425 1374798.675 1292780.357 1228302.945 1218961.972 1238458.155 1.135955439 1.047261663 1.02918579 1.031910156 1.083955416 1.110088919 1.043862768 0.991800119 0.984257697 1 20.24011369 1.836879062 3.537124143 0.990846929 1.068966119 0.561646869 0.031747406 0.190067205 4.052957558 0.017204112 0.009121781 68.68771393 -1.836879062 0.078119191 DYSDHPSGGSYR ddPTM_MDA-MB-175_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 ;;;; 122.18 0.00036312 1893482000 1019078 3476900 3044330 3346920 3191270 4128680 2771430 3500070 2800700 3418230 FALSE TRUE 1059311.986 4074030.528 3123667.741 4008930.786 2648819.065 3169856.641 2554198.075 3453157.287 2699903.354 4087966.723 0.259129308 0.996590923 0.76411281 0.980666199 0.647955144 0.775411557 0.62480892 0.84471267 0.660451402 1 21.96295202 -2.425476953 2.173307629 3.131387705 0.746534678 0.137631272 0.19940835 5332780.004 514939.8211 55992679.6 0.0442602 0.003754249 2.425476953 -2.384853027 DYSEADGLS(ph)ER ddPTM_MDA-MB-175_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 226.53 1.12E-11 642700000 804650 964690 905720 994630 1002370 1204830 1099690 987160 869770 825150 TRUE FALSE 836418.2033 1130368.003 929323.8073 1191364.845 831987.5054 925026.4919 1013493.424 973928.7349 838467.1476 986822.344 0.847587419 1.145462514 0.941733649 1.207273885 0.843097555 0.937378949 1.027027236 0.986934214 0.849663724 1 19.91243086 3.205696141 24.99980568 0.948980109 1.036669877 0.153126218 0.108190162 371.6309632 282696.2972 0.029585804 0.03536401 1605.81733 -3.205696141 0.087689768 DYSEADGLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 170.47 3.65E-05 166500000 95226 92455 97822 108870 104210 132860 122200 110450 97339 90746 FALSE TRUE 98985.59601 108333.427 100371.3217 130404.1611 86496.42142 102005.2785 112621.6447 108969.5984 93835.7884 108525.9413 0.912091569 0.9982261 0.924860181 1.20159438 0.797011483 0.939916091 1.037739396 1.004088029 0.864639249 1 16.72768041 DYSNFDQEFLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 186.13 1.88E-05 77819000 123030 98334 128190 100290 164370 155030 140100 130140 140730 108940 FALSE TRUE 127887.3194 115222.0996 131530.7367 120127.0627 136430.4461 119026.632 129118.5959 128395.6862 135665.1548 130284.7072 0.981598855 0.884386986 1.009563897 0.92203502 1.047171606 0.913588667 0.991049515 0.985500823 1.041297614 1 16.99130823 2.542761899 0.427228664 1.014181868 0.941331081 0.159959216 0.047229633 2.166117308 0.835178976 0.044527124 0.059126833 348.9489522 -2.542761899 -0.072850788 DYSSGFGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYSSGFGGK 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 178.83 0.0001175 947120000 1222160 950990 1149090 921210 1391230 1357070 1281960 1156180 1203880 925610 FALSE TRUE 1270411.821 1114315.135 1179036.229 1103422.588 1154749.222 1041911.059 1181476.625 1140683.298 1160552.594 1106965.558 1.147652528 1.006639391 1.065106517 0.996799386 1.043166351 0.941231687 1.067311099 1.030459611 1.048408946 1 20.0781789 4.743584208 24.66608107 1.02414084 1.14765259 0.520259769 0.036115455 347.8704411 1707994.312 0.008100176 0.068162376 55409.49702 -4.743584208 0.12351175 DYSTVSAS(ph)PTALSTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYSTVSASPTALSTLK 16 0 A0A2R8YF49;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 DYSTVS(0.001)AS(0.922)PT(0.077)ALSTLK;DYSTVSAS(0.977)PT(0.023)ALSTLK 243.9 5.28E-20 159720000 347680 246301 296650 285030 392030 409970 397020 340520 369020 243624 TRUE FALSE 361406.6749 288601.2808 304380.9427 341408.0833 325392.8806 314760.6807 365900.535 335955.8864 355739.0423 291357.4583 1.240423626 0.99054022 1.044699334 1.171784258 1.116816719 1.080324775 1.255847498 1.153071173 1.22097112 1 18.15243072 2.290078008 24.99998104 1.171449223 1.102618471 0.060025833 0.089273214 210.4113994 102105.7922 0.029319032 0.024530024 195.0194864 -2.290078008 -0.068830753 DYTQINVGNLELSANHNILQIVDVCMESEKDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYTQINVGNLELSANHNILQIVDVCMESEKDHK 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 64.096 0.0046489 69307000 30650 26597 37494 21153 54167 47753 56740 38144 50885 31088 FALSE TRUE 31860.08567 31164.82785 38471.12444 25337.00026 44959.71269 36663.08945 52292.57054 37632.74207 49053.65879 37179.09838 0.856935403 0.83823517 1.034751409 0.681485065 1.209273883 0.986120994 1.406504536 1.012201578 1.319388068 1 15.18220416 3.221877414 24.98279559 1.155765905 0.864800527 0.488818198 0.151464147 193.5161921 289786.4195 0.040370605 0.048374723 1666.776675 -3.221877414 -0.290965378 DYTYEELLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 DYTYEELLNR 10 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;;; 247.07 2.66E-12 4255380000 2176480 2496980 2551050 2406090 2889450 3030500 2499090 2473050 2466740 2459800 FALSE TRUE 2262409.111 2925816.891 2617532.459 2882007.421 2398302.321 2326712.303 2303204.796 2439902.81 2377962.509 2941750.714 0.769068943 0.994583558 0.889787311 0.979691245 0.815263615 0.79092776 0.782936768 0.82940502 0.808349429 1 21.48824357 3.211393034 24.80695516 0.823613292 0.913126022 0.137582124 0.081568897 281.2648174 256824.4824 0.021747239 0.025999068 1627.020534 -3.211393034 0.08951273 DYVDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DYVDLFR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;; 130.77 0.0082156 442315000 1216540 1130820 1628650 1693500 1581940 1710430 2012310 1539370 1604590 1020340 FALSE TRUE 1264569.939 1325029.538 1671093.957 2028469.245 1313042.404 1313208.554 1854579.884 1518737.263 1546841.119 1220256.087 1.036315206 1.085861855 1.369461684 1.662330773 1.076038397 1.076174557 1.519828422 1.244605357 1.26763647 1 20.21875252 -2.25318423 1.798894347 0.232874025 1.268774613 0.133271083 0.197578916 3512757.355 520749.9593 10928936.85 0.050553394 0.005582333 2.25318423 1.035900588 DYVFIEFCVEDSKDVNVNFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DYVFIEFCVEDSKDVNVNFEK 21 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 236.19 7.31E-30 52171000 97109 46753 79811 47628 96352 90934 91067 67342 81417 44815 FALSE TRUE 100942.9383 54782.46406 81890.94023 57048.67624 79974.12146 69815.95662 83928.93058 66439.39064 78486.81807 53595.64121 1.883416935 1.022144018 1.527940302 1.064427535 1.492175849 1.302642436 1.565965602 1.239641679 1.464425395 1 15.70982805 -1.727775599 2.590568472 0.925904656 1.376270057 0.190632888 0.241688042 29241368.95 22964805.29 14003265.75 0.05451042 0.01871649 1.727775599 0.450365401 DYYINIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DYYINIR 7 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 132.09 0.0079152 594230000 795390 735810 896090 849730 1006500 1039300 963510 895760 854570 665790 FALSE TRUE 826792.6114 862179.6437 919442.8415 1017804.058 835415.4895 797938.3257 887987.5685 883753.8024 823814.1926 796238.8032 1.038372669 1.082815407 1.154732522 1.278264829 1.049202182 1.002134438 1.115227699 1.109910493 1.034632059 1 19.60284165 DYYSSR ddPTM_MDA-MB-175_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 ;;; 149.11 0.024845 3561750000 1551160 2333320 1849360 1758400 2122590 2313100 1878770 1780630 1591170 2632430 FALSE TRUE 1612400.995 2734049.559 1897555.841 2106206.272 1761792.91 1775917.58 1731507.098 1756763.567 1533904.103 3148204.258 0.512165305 0.868447323 0.602742289 0.669018304 0.559618362 0.564104942 0.549998334 0.558020835 0.487231443 1 21.58609772 -0.823013131 9.23593515 1 0.59994506 0.583316849 0.102198395 0 0 0.098595933 0.023239284 0.150309652 0.823013131 -0.40005494 EAAAAALKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAAAALKK 9 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 118.18 0.0016542 2921000000 2538400 1529800 1984500 1464790 3286600 2469000 2847600 2137140 2463100 1533860 FALSE TRUE 2638617.992 1792531.25 2036217.7 1754521.09 2727944.906 1895612.168 2624397.671 2108495.134 2374453.512 1834390.499 1.438416735 0.97718084 1.11002412 0.956459974 1.487112426 1.033374393 1.430664666 1.149425455 1.294410058 1 20.80686936 3.272068573 24.99969751 1.238086875 1.109532356 0.075976426 0.189166381 436.8765752 325943.0392 0.048084875 0.065103611 1870.977533 -3.272068573 -0.128554518 EAAAALVEEETRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 ; 168.89 4.72E-05 326440000 196316 270070 245006 233945 292490 328630 243196 261340 234996 287980 FALSE TRUE 204066.7073 316452.4216 251391.0576 280218.6227 242772.6543 252310.6629 224133.662 257837.1648 226538.5399 344404.1673 0.592521016 0.91884028 0.729930359 0.813633078 0.704906262 0.732600494 0.650786731 0.748647053 0.65776945 1 18.39374307 -1.197652945 5.107591469 1.000021284 0.733239233 0.472223629 0.086173171 1.93E-05 3.03E-06 0.077153631 0.018183836 0.063437645 1.197652945 -0.266782051 EAADGYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAADGYQR 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 125.58 0.0032608 541550000 1863370 2169700 2029270 2051460 2264600 2443500 2115800 2076850 2006040 2071770 FALSE TRUE 1936937.286 2542329.097 2082154.443 2457232.665 1879664.101 1876034.157 1949958.067 2049013.223 1933843.012 2477693.665 0.781750106 1.026086934 0.840359917 0.991741917 0.758634583 0.757169534 0.787005309 0.826984083 0.780501254 1 21.2405664 3.228248215 24.99599554 0.806182818 0.913304542 0.183938736 0.092297376 275.5023921 667782.8983 0.024309538 0.029357742 1691.407355 -3.228248215 0.107121724 EAAEAVVEAMDFHGEVTFDTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAAEAVVEAMDFHGEVTFDTTK 22 0 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 ;; 225.9 5.71E-26 89976000 161607 120680.7 144761.7 125459.3 171081.4 180330 197812 155210.7 160398.4 105011.7 FALSE TRUE 167987.3691 141406.6715 148534.3088 150274.7751 142001.0447 138451.0904 182306.9786 153130.3544 154625.6929 125586.732 1.337620355 1.125968239 1.182722939 1.196581618 1.13070101 1.102434056 1.451642029 1.219319525 1.231226344 1 16.93832453 EAAELEEASAES(ph)EDEMIHPEGVASLLPPDFQSSLERPELELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAAELEEASAESEDEMIHPEGVASLLPPDFQSSLERPELELSR 43 1 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAAELEEAS(0.007)AES(0.993)EDEMIHPEGVASLLPPDFQSSLERPELELSR 220.89 1.54E-44 37199000 6891.1 9202.7 6008 8041.9 8053.2 9904.7 8032.4 8122.2 6506.7 6213 TRUE FALSE 7163.165949 10783.19214 6164.573416 9632.563817 6684.319941 7604.483532 7402.799499 8013.335194 6272.525138 7430.318395 0.964045626 1.45124227 0.829651313 1.296386414 0.899600742 1.023439795 0.996296404 1.078464578 0.844179859 1 12.85920832 3.220157904 24.99984043 0.988181378 1.136062256 0.176528531 0.169322909 430.5674513 584918.7747 0.045165116 0.054078737 1660.190424 -3.220157904 0.147880878 EAAEMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 129.4 0.008525 3738383000 4861100 3645370 4715720 3590500 5710680 5617180 5474910 4701400 4894050 3446220 FALSE TRUE 5053019.982 4271433.94 4838615.537 4300690.183 4739980.653 4312675.074 5045772.248 4638385.423 4717914.097 4121440.827 1.226032398 1.036393368 1.174010677 1.043491916 1.150078541 1.046399853 1.224273855 1.125428125 1.144724453 1 21.97471735 4.77056944 23.67995401 1.114657781 1.22603281 0.208700498 0.068416765 11434.94421 8459205.361 0.014895266 2.093617754 58961.6244 -4.77056944 0.111375029 EAAENSLVAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAENSLVAYK 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ; 143.24 8.67E-05 287350000 240520 222110 229570 199616 300550 297720 268990 257130 241020 218190 FALSE TRUE 250015.9153 260255.6647 235552.7828 239099.449 249462.6184 228579.042 247905.8609 253683.5929 232345.7373 260940.153 0.958135084 0.997376838 0.902708073 0.916299949 0.956014686 0.875982632 0.95004873 0.972190711 0.890417725 1 17.99335943 -1.199069032 4.535890569 1.000014479 0.937818204 0.216454456 0.036590126 5.30E-06 9.37E-07 0.035075248 0.008265391 0.063231134 1.199069032 -0.062196275 EAAEPLSEPKEDQEAAELLS(ph)EPEEESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAAEPLSEPKEDQEAAELLSEPEEESER 28 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 EAAEPLSEPKEDQEAAELLS(0.999)EPEEES(0.001)ER 154.99 1.39E-08 102330000 59538 42068 59952 47487 78061 79256 63660 54489 67696 40917 TRUE FALSE 61888.60621 49292.85176 61514.39837 56879.78687 64792.2191 60849.99514 58670.16286 53758.66408 65259.63418 48933.90275 1.264738816 1.007335385 1.257091606 1.162379939 1.324076263 1.243514041 1.198967578 1.098597518 1.333628232 1 15.57854673 -1.519512723 5.493918103 0.999540913 1.200286959 0.298348769 0.095583896 0.000516786 4.52E-05 0.088985259 0.020926769 0.03023342 1.519512723 0.200746046 EAAEVLQNNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAAEVLQNNRR 11 1 P61081;M0QX69 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 163.46 3.84E-05 1267760000 852560 1024480 1027460 998970 1109820 1260290 962840 1000600 947150 1206340 FALSE TRUE 886219.7271 1200426.471 1054236.452 1196563.284 921173.1928 967606.7474 887370.0849 987188.5937 913062.2565 1442699.226 0.614278923 0.83206981 0.730738904 0.829392061 0.638506749 0.670691943 0.615076288 0.684265005 0.632884693 1 20.46033913 -1.003364402 4.768259411 1.000003907 0.696621932 0.58839822 0.07670263 4.42E-06 9.23E-07 0.074953405 0.017666374 0.099228311 1.003364402 -0.303381975 EAAHLLNDALAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAHLLNDALAIR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 182.25 4.67E-07 247940000 172639 201861 184318 188021 206564 225674 197034 177154 194325 202147 FALSE TRUE 179454.921 236529.0565 189121.4785 225210.9926 171452.3251 173264.6336 181589.9602 174779.5404 187331.2812 241753.8343 0.742304343 0.978388025 0.782289468 0.931571544 0.709202092 0.716698596 0.751135802 0.722964916 0.774884426 1 17.88317925 3.23140999 24.99993348 0.757976005 0.861738405 0.107481489 0.101625415 250.1080218 874424.1109 0.026589168 0.032414406 1703.766167 -3.23140999 0.1037624 EAAIWELEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAIWELEER 10 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 138.66 0.008332 0 133165 178180 143538 170782 181374 209577 147800 159805 142713 154913 FALSE TRUE 138422.457 208781.029 147278.7182 204562.1699 150544.1123 160905.9179 136215.0498 157663.0754 137576.787 185265.2364 0.747158289 1.126930411 0.794961435 1.104158416 0.812586944 0.868516518 0.735243441 0.851012734 0.742593644 1 17.49923267 EAALPPVS(ph)PLK ddPTM_MDA-MB-175_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 190.1 2.54E-06 11828899000 18374310 9812040 12492500 10818350 15846950 17849280 17127520 13845950 13766830 8159550 TRUE FALSE 19099741.95 11497181.54 12818064.81 12958187.34 13153291.1 13704055.23 15785020.23 13660367.69 13271364.48 9758257.598 1.957290198 1.17820025 1.313560816 1.327920196 1.347913904 1.404354731 1.617606429 1.39987775 1.360013747 1 23.21819214 0.729148294 2.466153705 1.000144704 1.42878 0.298682457 0.202247941 1.789151002 14.50799462 0.182463375 0.048861824 5.359796419 -0.729148294 0.428635297 EAALPPVS(ph)PLKAALSEEELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAALPPVSPLKAALSEEELEK 21 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(1)PLKAALSEEELEK 152.35 3.23E-08 191364000 557000 234156 338826 177383 584700 524970 400042 343766 419899 215355 TRUE FALSE 578990.7901 274370.4715 347656.0839 212468.828 485312.9028 403053.6735 368685.6627 339158.3791 404786.917 257549.689 2.248074118 1.065310824 1.349860236 0.824962471 1.884346685 1.564955 1.431512747 1.316865807 1.571684744 1 17.97449127 -1.38707082 3.334295423 0.996085319 1.441710742 0.119088479 0.37741396 65918800.85 81694737.39 2476790.268 0.085528227 0.041013722 1.38707082 0.445625423 EAALPPVS(ph)PLKAALSEEELEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAALPPVSPLKAALSEEELEKK 22 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 EAALPPVS(1)PLKAALSEEELEKK;EAALPPVS(1)PLKAALSEEELEKK 156.2 7.08E-09 2351500000 7003300 1757970 3069800 1368710 5965300 4581900 3676500 2975500 3963400 1496620 TRUE FALSE 7279795.692 2059887.672 3149801.51 1639436.753 4951320.437 3517823.164 3388326.323 2935618.289 3820758.008 1789854.034 4.067256632 1.150869084 1.759809152 0.915961146 2.766326383 1.965424608 1.893074104 1.640143963 2.134675753 1 20.77141051 7.999999999 0.054495374 3.22E-07 5.604179773 0.163863721 0.814026588 934.6324591 3.825380392 86.49939416 427.6870702 99999999.83 -7.999999999 5.604179451 EAALSTALSEKR ddPTM_MDA-MB-175_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 ;;; 250.69 4.32E-17 5733970000 2066830 1662180 1932460 1420620 2519950 2353580 2094450 1900330 2192940 1625850 FALSE TRUE 2148430.044 1947646.485 1982821.495 1701614.396 2091609.799 1806996.714 1930281.536 1874859.185 2114016.518 1944404.179 1.104929761 1.001667506 1.019757886 0.875134097 1.075707315 0.92933184 0.992736776 0.964233262 1.087231009 1 20.89089671 4.86786916 2.040463943 0.987185619 1.16861877 0.234839152 0.059587611 1.507339346 5.081568301 0.013959922 0.569734765 73768.1955 -4.86786916 0.181433151 EAALVQQEEEKAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAALVQQEEEKAEQR 15 1 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 ; 170.09 1.06E-06 566040000 163699 127149 147104 118539 187538 188671 165415 139548 158926 122254 FALSE TRUE 170161.9629 148985.8517 150937.6511 141985.6604 155660.3577 144855.0196 152449.3401 137677.5873 153206.2843 146207.3306 1.163840159 1.019003979 1.032353511 0.971125455 1.064654947 0.99075073 1.042692863 0.941659948 1.04787006 1 17.15765612 4.790457762 2.887331527 1.007534361 1.203331581 0.616271409 0.035780827 0.330512802 3.439240504 0.008391156 0.159800307 61724.52583 -4.790457762 0.19579722 EAARS(ph)PDKPGGSPSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 EAARS(0.63)PDKPGGS(0.235)PS(0.006)AS(0.129)R;EAARS(1)PDKPGGSPSASR 83.905 0.0028254 192323000 151340 104632 132499 100523 145492 186802 152717 130744 133596 91359 TRUE FALSE 157315.0201 122601.7321 135952.0328 120406.1494 120761.3218 143420.0665 140746.6425 128991.5905 128787.9061 109259.0469 1.439835186 1.122119729 1.24430916 1.102024526 1.105275263 1.312660787 1.288192113 1.180603293 1.178739059 1 16.73739322 0.687014166 1.664951222 1.000309837 1.219003954 0.311240867 0.100055977 1.475985808 6.013492235 0.092425829 0.026327243 4.864230715 -0.687014166 0.218694117 EAASGT(ph)TPQK ddPTM_MDA-MB-175_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 EAASGT(0.5)T(0.5)PQK;EAAS(0.001)GT(0.743)T(0.256)PQK 208.63 1.23E-06 1326330000 2830900 2009720 2233700 1799960 2872700 2908500 2715400 2354500 2556600 1854100 TRUE FALSE 2942666.118 2354873.777 2291912.057 2155986.716 2384399.48 2233044.954 2502559.853 2322941.779 2464588.465 2217375.396 1.327094241 1.062009518 1.033614814 0.97231471 1.075325127 1.007066714 1.128613521 1.04760871 1.111489047 1 21.0804216 4.738158979 5.247188386 1.049682065 1.338809678 0.766958236 0.046088914 0.070332234 6.754337995 0.010727593 0.073501596 54721.62412 -4.738158979 0.289127613 EAASGTT(ph)PQK ddPTM_MDA-MB-175_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 EAASGT(0.136)T(0.863)PQK;EAASGT(0.326)T(0.674)PQK 192.6 7.44E-06 1650500000 2019910 1417640 1681200 1254540 1998180 2065380 2033730 1818120 1841380 1356660 TRUE FALSE 2099657.607 1661108.642 1725013.453 1502684.268 1658530.077 1585726.796 1874320.928 1793751.075 1775109.093 1622471.552 1.294110583 1.023813724 1.063201047 0.926169871 1.022224442 0.977352604 1.155225758 1.105567042 1.094077176 1 20.62976175 4.741830558 24.66988892 1.046723503 1.294110695 0.586967109 0.063563222 205.0834391 1547154.767 0.016566188 0.118650355 55186.20853 -4.741830558 0.247387192 EAASS(ph)PAGEPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 EAAS(0.088)S(0.912)PAGEPLR 150.14 7.12E-05 137470000 346000 440420 376320 400520 444510 456870 448920 393730 393140 357180 TRUE FALSE 359660.3472 516058.709 386127.2084 479741.6606 368952.349 350768.8664 413732.4774 388452.6934 378990.9682 427162.5824 0.841975309 1.208108412 0.903934999 1.123089148 0.863728155 0.821160094 0.968559734 0.909379027 0.887228853 1 18.70442575 3.220308975 24.99695494 0.904437031 1.024526248 0.205454111 0.106508684 331.4327879 453920.4776 0.028278662 0.033861945 1660.768025 -3.220308975 0.120089217 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 EAASSSSGTQPAPPAPAS(0.946)PWDS(0.054)KK;EAASSSSGTQPAPPAPAS(0.996)PWDS(0.004)KK;EAASSSSGTQPAPPAPAS(1)PWDSKK 195.97 1.24E-24 1892540000 1630170 758119 1083300 711054 1517370 1425050 1386050 1071990 1298020 621125 TRUE FALSE 1694530.37 888320.0409 1111531.688 851698.3589 1259447.989 1094103.734 1277407.779 1057621.727 1251304.514 742822.5516 2.2812048 1.195871126 1.496362335 1.146570412 1.695489706 1.472900536 1.719667472 1.423787855 1.684526824 1 19.50265809 -2.023169081 2.704587981 0.374296112 1.541536336 0.236264197 0.303164452 6584993.608 5251306.344 25719322.8 0.066651247 0.009480493 2.023169081 1.167240225 EAAVGVPPPAQPAPGEPTPPAPPS(ph)PDWTSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAAVGVPPPAQPAPGEPTPPAPPSPDWTSSSR 32 0 Q8IV56 Q8IV56 PRR15 Proline-rich protein 15 1 EAAVGVPPPAQPAPGEPTPPAPPS(0.911)PDWT(0.054)S(0.01)S(0.013)S(0.013)R;EAAVGVPPPAQPAPGEPT(0.002)PPAPPS(0.701)PDWT(0.056)S(0.069)S(0.086)S(0.086)R 116.3 1.09E-06 1004890000 463860 548890 558550 542294 620290 623140 540821 574230 539410 503700 TRUE FALSE 482173.551 643157.5877 573106.2719 649558.1346 514853.3274 478425.1788 498430.0368 566533.3861 519996.7395 602390.3711 0.800433696 1.067675744 0.95138684 1.078300992 0.85468386 0.794211199 0.827420325 0.940475501 0.863222197 1 19.20033918 3.204421583 24.99969318 0.87393494 0.979461165 0.209194127 0.089283289 250.5245869 183456.1217 0.024860605 0.029715522 1601.111524 -3.204421583 0.105526224 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EAAVSASDILQESAIHS(0.996)PGT(0.004)VEK;EAAVSASDILQESAIHS(0.999)PGT(0.001)VEK;EAAVSASDILQESAIHS(0.967)PGT(0.033)VEK;EAAVSASDILQESAIHS(1)PGTVEK;EAAVSASDILQESAIHS(0.999)PGT(0.001)VEK 307.85 2.77E-73 1609342000 755858 696896 855558 657341 1049073 1040273 986816 897184 938648 677280 TRUE FALSE 785699.8575 816582.4669 877854.5443 787361.0878 870751.9462 798685.3612 909466.7834 885158.716 904866.2418 809980.0487 0.970023717 1.008151334 1.083797738 0.972074669 1.075028882 0.986055598 1.122826155 1.092815456 1.117146334 1 19.62752685 2.237282327 24.99999978 1.092272541 1.01929311 0.3110482 0.04818714 36.20965437 708141.6539 0.016294751 0.012715089 172.6960192 -2.237282327 -0.072979431 EACAVPEPQES(ph)GSEEHLPLSQFTTVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EACAVPEPQESGSEEHLPLSQFTTVDR 27 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 EACAVPEPQES(0.5)GS(0.5)EEHLPLSQFTTVDR 73.317 0.011827 66686000 24619 28174 30502 27248 28741 30688 20576 29568 27172 25076 TRUE FALSE 25590.97713 33012.66534 31296.90718 32637.57307 23855.61509 23561.17708 18963.19935 29171.68932 26194.08503 29989.16209 0.853340852 1.100819864 1.043607257 1.08831227 0.795474546 0.785656398 0.632335085 0.97274106 0.873451714 1 14.87215359 3.23477324 24.9995127 0.83386308 1.028761998 0.362834604 0.115151421 98.42836938 649701.2651 0.033020178 0.040908192 1717.011644 -3.23477324 0.194898918 EACAVPEPQESGS(ph)EEHLPLSQFTTVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EACAVPEPQESGSEEHLPLSQFTTVDR 27 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 EACAVPEPQES(0.007)GS(0.993)EEHLPLSQFTTVDR;EACAVPEPQES(0.281)GS(0.719)EEHLPLSQFTTVDR 219.92 1.87E-34 199995000 156420 176667 185747 184807 202411 213282 174417 199051 168976 179041 TRUE FALSE 162595.5824 207008.183 190587.7194 221361.273 168005.2505 163750.4878 160745.7398 196383.0469 162894.5868 214120.656 0.759364302 0.966782873 0.890094972 1.033815593 0.78462888 0.764758015 0.750725048 0.917160682 0.760760731 1 17.70806445 3.191111376 24.99999201 0.8235385 0.914790767 0.144888266 0.097853565 204.4027222 107694.6466 0.027154499 0.032455913 1552.785174 -3.191111376 0.091252267 EACPELDYFVVFSSVSCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 286.26 9.19E-40 548427000 277955 278057 297019 325132 320653 364640 287020 292284 283375 291912 FALSE TRUE 288928.878 325811.1268 304759.5591 389442.1392 266148.5176 279957.8862 264522.6224 288366.4111 273176.3891 349106.5674 0.827623726 0.933271262 0.872969997 1.115539424 0.762370412 0.801926725 0.757713109 0.826012565 0.782501433 1 18.41330797 EADDIVNWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;;; 218.55 1.57E-08 1084320000 3809470 3105450 3533900 2896950 4452430 4469280 3806950 3409190 3560370 2647370 FALSE TRUE 3959870.817 3638786.88 3625996.337 3469958.063 3695607.539 3431357.453 3508551.311 3363495.384 3432232.979 3166071.465 1.250720605 1.149306616 1.145266738 1.09598223 1.167253355 1.083790272 1.108171862 1.062356116 1.084066806 1 21.59426239 8 0.131135949 0.978041185 1.759414295 0.787953857 0.029692569 35.52289552 0.314411241 0.144747856 5.144711225 100000000 -8 0.78137311 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EADGSDSLEGFVLCHSIAGGTGSGLGSYLLER 32 0 P23258;K7EIS0;Q9NRH3 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ; 347.31 1.59E-131 241944000 72569 89626 82086 95215 97039 109128 91939 80681 85778 88923 FALSE TRUE 75434.08016 105018.5683 84225.22859 114048.2428 80544.34544 83784.67585 84732.58094 79599.60316 82690.86654 106345.7593 0.709328521 0.987520038 0.791994238 1.072428685 0.757381827 0.787851593 0.796765019 0.748498141 0.777566187 1 16.69840298 EADIDGDGQVNYEEFVQMMTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EADIDGDGQVNYEEFVQMMTAK 22 0 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;M0QZ52 P0DP25 CALM2;CALM3 0 114.72 0.00021891 16315000 22123 25583 26349 29913 22665 30128 37153 23813 27513 18866 FALSE TRUE 22996.43312 29976.68124 27035.67659 35829.70212 18812.4114 23131.22859 34240.85078 23493.82569 26522.8125 22562.43149 1.019235588 1.328610405 1.198260773 1.588024861 0.833793619 1.025209921 1.517604643 1.041280755 1.175529885 1 14.46163493 3.234354977 24.99999653 1.122048937 1.280661831 0.150022417 0.210978154 241.2752592 1434236.653 0.060109035 0.074300612 1715.358808 -3.234354977 0.158612893 EADKSHPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EADKSHPEQR 10 1 O14745 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;; 147.91 1.57E-05 3936140000 7887940 6452360 7847030 5995450 9439530 8998040 8711100 7700780 8389400 6377550 FALSE TRUE 8199361.962 7560502.638 8051530.048 7181332.115 7835002.062 6908381.577 8028301.22 7597563.64 8087467.133 7627108.817 1.075028842 0.991267179 1.055646411 0.941553646 1.02725715 0.905766752 1.052600849 0.996126294 1.060358168 1 22.86270485 -0.64716081 6.101082459 1 1.008542334 0.001187461 0.052075351 3.44E-10 1.87E-18 0.046114001 0.010869174 0.225340467 0.64716081 0.008542334 EADLLQESLEHIEMYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EADLLQESLEHIEMYEK 17 0 Q6N069;Q6N069-5;Q6N069-4;Q6N069-3;Q6N069-2 Q6N069 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 100.77 0.0012515 11027000 21332 18871 22339 20235 28851 22905 26095 22142 21696 14388 FALSE TRUE 22174.20383 22111.94745 22921.17269 24237.4226 23946.91733 17585.66088 24049.60571 21845.22271 20915.1652 17207.05313 1.288669458 1.285051385 1.332080079 1.408574869 1.39169195 1.022003056 1.397659758 1.269550489 1.215499542 1 14.07071242 EADPEDGKPVMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EADPEDGKPVMDK 13 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 116.51 0.00052855 1322510000 2557700 1175540 1635520 1163850 2513420 2242720 2471960 1607100 2028980 809450 FALSE TRUE 2658679.971 1377429.851 1678142.995 1394056.056 2086189.766 1721882.269 2278201.316 1585559.453 1955957.406 968046.2296 2.746439054 1.422896767 1.733536006 1.440071779 2.155051796 1.778719049 2.353401363 1.637896419 2.020520659 1 19.88471642 -1.3281423 6.1553452 0.999934919 1.889464366 0.326405025 0.394570554 0.000324014 3.54E-05 0.351143471 0.082759323 0.046974017 1.3281423 0.889529447 EADVDQDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EADVDQDGR 9 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;;; 179.37 0.00011604 1582581000 1218201 1327467 1418916 1397104 1429518 1638836 1594643 1508390 1371690 1158609 FALSE TRUE 1266296.516 1555449.131 1455894.117 1673447.001 1186529.041 1258241.176 1469650.715 1488172.499 1322323.145 1385616.251 0.913886883 1.122568482 1.050719574 1.207727609 0.856318653 0.908073339 1.060647718 1.0740149 0.954321331 1 20.40209632 3.23852 25 0.988373199 1.075571094 0.208163936 0.091745747 2.062678315 1269093.607 0.02712497 0.03446221 1731.888786 -3.23852 0.087197895 EADVDQDGRVNYEEFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EADVDQDGRVNYEEFAR 17 1 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ; 91.475 0.0031406 388500000 171212 319060 256520 276730 257160 308350 169935 253560 212630 364240 FALSE TRUE 177971.582 373856.0731 263205.1219 331466.368 213448.0351 236740.3856 156615.0507 250161.4429 204977.4878 435605.8542 0.408561043 0.858243914 0.604227697 0.760931849 0.490002678 0.543473838 0.359533852 0.574283932 0.470557239 1 18.73266382 -0.853788717 12.98363092 1 0.567815023 0.45199579 0.144173502 0 0 0.138075391 0.032544682 0.140026838 0.853788717 -0.432184977 EAEAAIYHLQLFEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EAEAAIYHLQLFEELR 16 0 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;; 262.36 7.01E-27 5056321000 2937547 2939927 3163198 3615401 3496193 3949407 4074895 3439108 3391236 2524117 FALSE TRUE 3053523.624 3444836.593 3245633.538 4330516.527 2901911.363 3032217.078 3755494.082 3393012.383 3269186.079 3018669.399 1.011546221 1.141177167 1.075186816 1.43457794 0.961321357 1.004487964 1.244089228 1.124009268 1.082989108 1 21.52548133 EAEAAIYHLQLFEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 29 EAEAAIYHLQLFEELRR 17 1 P14618;P14618-3;B4DNK4 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 307.22 1.10E-47 32364046600 8586381.6 9394341.2 9881103.9 9553380.5 11563055.7 11724959.9 10890675.1 10125615 10517626.7 9314925.4 FALSE TRUE 8925378.576 11007746.22 10138613.59 11443010.65 9597571.622 9002015.657 10037035.53 9989897.693 10139099.37 11140006.69 0.801200468 0.988127434 0.910108393 1.027199621 0.861540921 0.808079915 0.900990081 0.89675868 0.910152 1 23.40924676 0.806097927 5.464900217 0.999999879 0.902343264 0.169533884 0.066198082 9.998583153 281.1534182 0.062775496 0.01582207 6.398791019 -0.806097927 -0.097656614 EAEALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEALKR 7 1 Q9BUQ8;F8VVA2;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 92.925 0.04214 0 93784 79082 98396 79142 147430 125890 109340 103230 110600 107350 FALSE TRUE 97486.66474 92663.71833 100960.2806 94796.05138 122369.9013 96653.95538 100769.6451 101846.3707 106619.5276 128383.1772 0.759341425 0.721774615 0.786398053 0.738383747 0.953161496 0.7528553 0.784913159 0.793299971 0.830478961 1 16.97009664 -5 0.196982643 1.936322593 0.754810567 0.548587973 0.059026107 107.0262264 1.056046428 39.38264873 0.145892034 1.00E-05 5 -1.181512026 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(0.708)PS(0.238)S(0.054)K;EAEALLQSMGLTPESPIVPPPMS(0.706)PS(0.172)S(0.123)K;EAEALLQSMGLTPES(0.001)PIVPPPMS(0.762)PS(0.189)S(0.049)K;EAEALLQSMGLTPESPIVPPPMS(0.641)PS(0.149)S(0.21)K;EAEALLQSMGLTPESPIVPPPMS(0.71)PS(0.237)S(0.053)K;EAEALLQSMGLTPESPIVPPPMS(0.498)PS(0.201)S(0.302)K;EAEALLQSMGLTPESPIVPPPMS(0.706)PS(0.238)S(0.056)K;EAEALLQSMGLTPESPIVPPPMS(0.821)PS(0.157)S(0.022)K;EAEALLQSMGLTPESPIVPPPMS(0.792)PS(0.173)S(0.034)K;EAEALLQSMGLTPESPIVPPPMS(0.802)PS(0.161)S(0.037)K 146.57 9.35E-08 4482665000 2572362 2034068 2599129 2057213 3404741 3410591 3126268 2785326 3000305 2037407 TRUE FALSE 2673920.838 2383403.356 2666864.437 2464123.591 2826004.341 2618532.928 2881222.945 2747993.261 2892324.609 2436597.893 1.097399306 0.97816852 1.094503301 1.011296775 1.159815638 1.074667649 1.182477812 1.127799244 1.187034027 1 21.21643675 3.237312393 24.99732589 1.130148438 1.044055392 0.266383082 0.061385269 37.22635399 745516.1975 0.015921696 0.020064644 1727.079755 -3.237312393 -0.086093046 EAEAMALLAEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAEAMALLAEAER 13 0 P54920;M0R0Y2;M0R2M1;M0QZM9;M0QZN5;M0R031 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 153.54 2.93E-06 88034000 120364 150966 164003 141891 168656 195972 162282 154357 145857 152208 FALSE TRUE 125116.0637 176893.2361 168277.0529 169956.6163 139987.9134 150460.473 149561.9128 152288.0969 140607.6351 182030.2434 0.687336683 0.971779375 0.924445574 0.933672411 0.769036566 0.826568543 0.821632219 0.836608764 0.772441065 1 17.47381864 3.247376757 24.99952889 0.8286091 0.889137637 0.036214293 0.093262374 478.1827112 1355952.415 0.024416172 0.032567624 1767.570552 -3.247376757 0.060528538 EAEAYTGLS(ph)PPVPSFNCEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEAYTGLSPPVPSFNCEVR 20 0 O43164-2;O43164 O43164-2 PJA2 E3 ubiquitin-protein ligase Praja-2 1 EAEAYTGLS(1)PPVPSFNCEVR 90.714 0.0019932 0 18592 27661 22699 20416 25480 29223 31572 24600 24001 27263 TRUE FALSE 19326.02652 32411.56158 23290.55459 24454.22386 21148.9187 22436.40113 29097.30414 24270.27724 23137.2087 32604.66287 0.592738118 0.994077495 0.714332017 0.750022289 0.64864706 0.688134738 0.892427695 0.744380561 0.709628828 1 14.99279068 -1.311204034 10.49226753 1.000000014 0.755499249 0.316644557 0.110484384 3.48E-08 2.28E-09 0.100393656 0.02366301 0.048842284 1.311204034 -0.244500766 EAEDGFR ddPTM_MDA-MB-175_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 ; 143 0.005702 416890000 787300 898600 864300 881810 1040910 1120750 971390 939260 897850 785740 FALSE TRUE 818383.2119 1052927.56 886824.368 1056229.386 863976.49 860472.7976 895249.9135 926670.756 865536.5539 939690.7091 0.870906995 1.120504385 0.9437407 1.124018122 0.919426447 0.915697888 0.952706997 0.986144427 0.921086636 1 19.84182646 EAEDGFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEDGFRK 8 1 F6U236;Q9BY11;Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 F6U236;Q9UNF0-2 PACSIN1;PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 1;Protein kinase C and casein kinase substrate in neurons protein 2 0 87.181 0.024863 467530000 659200 839150 944680 795820 1020400 1253600 912700 1036000 1007100 1050400 FALSE TRUE 685225.725 983267.4848 969299.1369 953230.8207 846952.7725 962470.3985 841160.1891 1022114.115 970854.6677 1256205.769 0.545472519 0.782728044 0.77160857 0.75881742 0.674215 0.766172567 0.669603826 0.813651824 0.772846847 1 20.26064137 -5 0.179390833 2.109584341 0.676364608 0.611760335 0.06901549 88.91694658 0.855521457 34.99332161 0.207795082 1.00E-05 5 -1.433219734 EAEDNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEDNIR 7 0 O60925 O60925 PFDN1 Prefoldin subunit 1 0 89.752 0.041043 1571800000 525500 507590 500510 427340 570110 651210 564550 488050 566140 441470 FALSE TRUE 546247.1458 594764.634 513553.7018 511866.5765 473202.9058 499976.3467 520299.0958 481508.488 545764.732 527967.594 1.034622488 1.12651731 0.972699286 0.969503777 0.896272633 0.94698302 0.985475438 0.912003868 1.03370877 1 19.01008986 4.14674 6.308707926 0.956409005 1.079744441 0.528118521 0.043471624 0.127976653 7.150914479 0.010271576 0.022754697 14019.74129 -4.14674 0.123335437 EAEDS(ph)DS(ph)DDNIK ddPTM_MDA-MB-175_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 223.7 3.19E-11 191708000 1162510 597140 839390 644140 1347860 1388850 945600 880220 1020930 576960 TRUE FALSE 1208406.792 699694.1499 861265.193 771548.9694 1118751.239 1066310.636 871481.4011 868422.0906 984186.9287 690004.2654 1.751303366 1.014043224 1.248202708 1.11818 1.621368584 1.54536818 1.263008716 1.25857496 1.42634905 1 19.39624575 -1.30953373 3.084729925 0.997509745 1.342425265 0.194149987 0.217613457 26577086.49 35375158.99 621902.0748 0.053642829 0.049030494 1.30953373 0.34491552 EAEDS(ph)DS(ph)DDNIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;EAEDS(1)DS(1)DDNIKR 165.34 3.05E-07 644600000 3138740 1703720 2158710 1545050 2623360 3267160 3140930 2158240 2221360 1325950 TRUE FALSE 3262659.879 1996320.657 2214967.756 1850656.278 2177442.204 2508411.604 2894735.699 2129312.323 2141413.688 1585744.516 2.057494033 1.258916955 1.396799884 1.167058287 1.373135573 1.581851036 1.825474199 1.342783974 1.35041532 1 20.59672892 0.876385442 1.845537267 1.003495161 1.489137539 0.26765579 0.253068236 0.709760166 4.774927598 0.237662274 0.066958636 7.52290265 -0.876385442 0.485642379 EAEDSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EAEDSLRR 8 1 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776;REV__H7BZ55 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;;; 167.33 0.00050232 4063589000 2650257 2814540 2901070 2719560 3351590 3592100 2924750 2886110 2810980 3015840 FALSE TRUE 2754891.193 3297915.351 2976674.267 3257480.851 2781887.929 2757889.214 2695500.453 2847426.416 2709813.379 3606736.106 0.763818342 0.91437667 0.825309693 0.903165842 0.77130343 0.76464957 0.747351726 0.789474564 0.751320113 1 21.78226244 3.22004769 24.99863947 0.7878028 0.854264155 0.056818735 0.079893509 446.8440474 603387.2109 0.021053223 0.025205241 1659.769156 -3.22004769 0.066461356 EAEDTQVFGDLPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAEDTQVFGDLPRPR 15 1 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 0 ; 155.57 2.08E-06 278450000 119704 148230 142967 111914 183512 179766 135881 139665 152085 147269 FALSE TRUE 124430.0064 173687.3494 146692.8375 134050.2552 152318.6958 138018.0709 125230.2922 137793.0191 146611.4906 176123.5409 0.706492759 0.986167712 0.83289739 0.761114922 0.864840072 0.783643516 0.711036648 0.78236571 0.832435515 1 17.42622823 5.031814302 16.03825636 0.822809575 0.329896703 0.144418632 0.089169735 8061120.641 113405648.3 0.020763873 108981994.5 107600.503 -5.031814302 -0.492912872 EAEEES(ph)DHN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 186.82 4.33E-05 3444460000 3496800 3467380 3920620 3272630 4653180 4621260 4447200 3861380 4045430 3348340 TRUE FALSE 3634856.364 4062875.543 4022794.578 3919946.446 3862234.126 3548042.401 4098616.843 3809624.517 3899835.765 4004383.115 0.907719431 1.014607101 1.004597828 0.978913938 0.964501651 0.886039697 1.023532645 0.951363645 0.973891771 1 21.93314858 0.967943337 21.41750217 1.000000003 0.968532 0.053381838 0.041678123 2146.734797 1434270.222 0.038397145 0.009599286 9.288451911 -0.967943337 -0.031468003 EAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 EAEEGEDDRDS(0.939)ANGEDDS(0.061);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.963)ANGEDDS(0.037);EAEEGEDDRDS(0.969)ANGEDDS(0.031);EAEEGEDDRDS(0.967)ANGEDDS(0.033);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.999)ANGEDDS(0.001);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(1)ANGEDDS;EAEEGEDDRDS(0.905)ANGEDDS(0.095);EAEEGEDDRDS(0.89)ANGEDDS(0.11) 274.68 1.26E-38 14694806000 3377009 3015978 2715880 3790462 3081321 3886018 4125348 2945275 2676947 1869691 TRUE FALSE 3510335.923 3533948.76 2786658.064 4540204.07 2557559.157 2983549.213 3801992.444 2905798.406 2580604.2 2236021.154 1.569902823 1.580463026 1.246257469 2.030483505 1.143799178 1.334311711 1.700338316 1.299539765 1.15410545 1 21.09250241 1.304471883 2.171775353 1.024187461 1.505965156 0.35571395 0.237155001 0.324073225 2.581951621 0.204842497 0.060611693 20.15913453 -1.304471883 0.481777695 EAEEGEDDRDSANGEDDS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEEGEDDRDSANGEDDS 18 1 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 134.04 5.34E-06 0 44202 48751 41291 53010 44955 51511 55069 47937 42555 36821 FALSE TRUE 45947.12909 57123.60502 42367.07738 63495.21978 37313.56516 39548.35091 50752.54788 47294.48292 41023.45386 44035.36997 1.043414172 1.297220963 0.962114714 1.441914076 0.847354415 0.898104204 1.152540513 1.074011254 0.931602344 1 15.42637517 3.21325851 24.99963355 1.001035583 1.178095206 0.308104659 0.1469327 306.0699227 302410.123 0.041395157 0.049494626 1634.024297 -3.21325851 0.177059622 EAEEGPTGASESQDS(ph)PR ddPTM_MDA-MB-175_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;EAEEGPTGASESQDS(1)PR 385.8 9.94E-122 754560000 215310 246229 253005 239714 272501 335190 267995 243163 264385 250094 TRUE FALSE 223810.6051 288516.9154 259598.5181 287128.7137 226181.3774 257347.2024 246988.8516 239903.7977 254869.8355 299095.131 0.748292372 0.964632605 0.86794632 0.959991267 0.756218855 0.86041923 0.825786936 0.80209864 0.852136358 1 18.1902449 4.792238289 22.20228323 0.863417439 0.74828958 0.194027973 0.074195796 24609.90001 10177908.08 0.017164887 17.2053424 61978.1044 -4.792238289 -0.115127859 EAEEVYR ddPTM_MDA-MB-175_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 ; 158.12 0.0033328 536150000 553330 651530 606250 601490 759780 819540 664260 650650 641990 619000 FALSE TRUE 575175.8957 763425.2093 622049.373 720462.9267 630632.867 629214.2552 612193.5655 641929.101 618884.9053 740281.1985 0.776969477 1.03126381 0.840287953 0.973228725 0.851882863 0.849966549 0.826974353 0.867142246 0.83601327 1 19.49771386 EAEGSSAEYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEGSSAEYKK 11 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 150.68 5.42E-05 241090000 544260 291200 471540 304710 646830 539740 569200 479890 564990 290870 FALSE TRUE 565747.8051 341211.3348 483828.7198 364980.7285 536882.0676 414393.5648 524584.6167 473457.8595 544656.1203 347860.4075 1.626364464 0.980885802 1.39087033 1.049216067 1.543383657 1.191263955 1.508031973 1.361057049 1.565731853 1 18.40814896 3.227860957 24.99905412 1.380198134 1.250983262 0.038530945 0.230683568 579.505044 1353972.845 0.0604254 0.072913088 1689.899811 -3.227860957 -0.129214873 EAEILEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEILEVLR 9 0 P36551 P36551 CPOX "Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial" 0 98.033 0.014629 11003000 24606 33683 28768 30532 35885 37489 31281 27858 27294 29142 FALSE TRUE 25577.46388 39467.79323 29517.71771 36571.13847 29785.28052 28782.7479 28829.11348 27484.60908 26311.69427 34851.81694 0.733891835 1.132445786 0.846949178 1.049332336 0.854626333 0.825860756 0.82719112 0.788613378 0.75495904 1 15.08894625 3.020601156 23.63744075 0.824133992 0.948200791 0.139317362 0.117193043 189.4835018 217407.4759 0.030904366 0.036932562 1048.579 -3.020601156 0.124066799 EAEKLESEHPDQAQAILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAEKLESEHPDQAQAILSR 19 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 228.85 5.65E-20 1933930000 2639660 2408720 2929540 2249490 3756600 3779120 3458180 3025890 3331460 2285340 FALSE TRUE 2743875.815 2822398.923 3005886.219 2694432.408 3118054.474 2901476.653 3187118.815 2985332.894 3211561.405 2733108.618 1.003939542 1.032669871 1.099804889 0.985849004 1.140845429 1.061603126 1.166114949 1.092284761 1.175058095 1 21.38211137 3.229008263 24.99995457 1.111327571 1.035661759 0.302962925 0.055474708 228.7939354 598786.8651 0.014767288 0.017861901 1694.370039 -3.229008263 -0.075665812 EAELDKYLECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAELDKYLECR 11 1 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ; 83.617 0.015115 464070000 447400 386310 437240 311070 576380 550720 402940 414150 474990 359620 FALSE TRUE 465063.6975 452655.7374 448634.8336 372598.7175 478407.1335 422823.6262 371356.5099 408598.9967 457895.2027 430080.6537 1.081340659 1.052490349 1.043141164 0.866346148 1.112366086 0.983126357 0.863457835 0.950052027 1.064672867 1 18.71424771 3.976408095 24.49342893 0.971262871 1.062140609 0.210343594 0.072899399 816.0514914 847238.9767 0.018840715 0.034248216 9471.267335 -3.976408095 0.090877738 EAEMEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 113.26 0.0021874 713850000 223382 373908 341015 364875 339590 441261 361612 337064 331043.4 333356.5 FALSE TRUE 232201.2938 438123.7904 349902.131 437046.186 281866.6131 338784.8201 333267.9065 332546.2084 319129.2127 398671.3237 0.582437913 1.098959881 0.877670678 1.096256891 0.707015018 0.849784773 0.835946522 0.834136264 0.800481985 1 18.60484031 3.218825264 24.99973129 0.830506372 0.924472052 0.054988518 0.149809192 600.2670677 760385.8605 0.040189793 0.048098709 1655.103908 -3.218825264 0.09396568 EAEMEEHREHIK ddPTM_MDA-MB-175_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 93.623 0.010155 183850000 113880 91210 116610 81742 140500 171150 114430 121900 129390 90503 FALSE TRUE 118376.0703 106874.608 119648.9524 97910.32362 116617.8602 131403.0063 105460.6776 120266.1299 124733.2792 108235.3301 1.093691591 0.987428115 1.10545191 0.90460595 1.077447263 1.214049112 0.974364632 1.111154092 1.152426653 1 16.72381197 3.020715221 24.9932461 1.094345636 1.021779121 0.131350275 0.082682207 445.3754517 537348.9303 0.022739834 0.027176887 1048.854441 -3.020715221 -0.072566515 EAENPEGEEKEAATLEVERPLPMEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EAENPEGEEKEAATLEVERPLPMEVEK 27 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;; 201.98 2.44E-25 2043736000 1336300 660813 1097245 601534 1540390 1314320 1266090 933771 1212080 548863 FALSE TRUE 1389058.156 774302.4923 1125840.106 720515.6298 1278555.058 1009089.099 1166850.557 921255.3271 1168457.478 656402.1962 2.116169269 1.179615938 1.715168097 1.097674008 1.947822639 1.537303051 1.777645724 1.403492146 1.780093797 1 19.32422054 -1.333040819 4.539502773 0.999444383 1.592159353 0.264177192 0.306471992 0.00152955 0.000224727 0.263369052 0.062020624 0.046447162 1.333040819 0.59271497 EAENQGLDISS(ph)PGMSGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAENQGLDISSPGMSGHR 18 0 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 EAENQGLDIS(0.014)S(0.985)PGMS(0.001)GHR 154.1 1.83E-08 308030000 100280 131930 122390 143080 167110 159960 142180 142470 148270 130760 TRUE FALSE 104239.1318 154587.9512 125579.5839 171380.7969 138704.7019 122811.7142 131035.5601 140560.4227 142933.7917 156379.9184 0.6665762 0.988540938 0.803041626 1.095925862 0.886972594 0.785341976 0.837930863 0.89883934 0.914016282 1 17.25469574 -4.999999986 0.298181215 1.989017951 0.87375271 0.108687167 0.110088064 648.2980279 6.017063544 400.1809237 0.106277231 1.00E-05 4.999999986 -1.115265242 EAEQEAAR ddPTM_MDA-MB-175_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 ;; 140.63 0.0015039 117302000 154682 207298 197108 201058 218283 241078 197533 191068 181174 204083 FALSE TRUE 160788.9648 242899.8189 202244.7964 240826.6723 181179.3336 185091.2881 182049.8473 188507.046 174653.5831 244069.1564 0.658784449 0.995208991 0.828637257 0.986714896 0.742327856 0.758355913 0.745894524 0.772350955 0.715590555 1 17.89693046 3.198678548 24.99923688 0.773256079 0.87370639 0.089577665 0.115075064 270.7607183 169719.862 0.03047438 0.036424335 1580.078079 -3.198678548 0.100450311 EAEQEAARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAEQEAARR 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 ; 162.64 0.00010202 431080000 341720 436940 443450 361670 589680 538780 329640 417080 449390 598130 FALSE TRUE 355211.3695 511981.0461 455006.6713 433207.2465 489446.4042 413656.5103 303801.9554 411489.7248 433216.5417 715322.1216 0.496575401 0.715734954 0.636086397 0.605611421 0.684232165 0.578280047 0.424706501 0.575250943 0.605624415 1 19.44823353 -1.424612494 2.847037232 1.009409368 0.590595519 0.702346294 0.079808859 11855839.98 13567152.07 901310.6105 0.021027279 0.03761729 1.424612494 -0.418813849 EAEREEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAEREEER 8 1 P49756 P49756 RBM25 RNA-binding protein 25 0 129.42 0.00099537 144910000 174710 189470 185840 185880 211780 218910 183740 202180 185330 174450 FALSE TRUE 181607.6857 222009.9986 190683.1431 222646.5092 175781.7112 168071.4701 169337.9787 199470.1078 178660.0095 208630.1375 0.870476758 1.064131967 0.91397698 1.067182872 0.842551864 0.805595357 0.81166595 0.956094408 0.856348041 1 17.67058805 3.218545257 24.999808 0.874095314 0.980386795 0.274044892 0.079694911 292.221169 364992.4805 0.022184364 0.026547308 1654.037142 -3.218545257 0.106291481 EAESAKHS(ph)PEKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAESAKHSPEKGK 13 2 J3KN75;Q0IIM8 J3KN75 TBC1D8B TBC1 domain family member 8B 1 EAES(0.18)AKHS(0.82)PEKGK;EAES(0.228)AKHS(0.772)PEKGK;EAES(0.07)AKHS(0.93)PEKGK 118.31 0.00022844 233819000 923550 254274 459200 254276 801670 693320 689610 459280 557820 189167 TRUE FALSE 960012.4671 297943.5815 471167.1292 304571.0339 665402.4197 532306.9374 635556.5662 453124.1028 537744.1672 226230.6518 4.243511917 1.316990333 2.082684753 1.346285445 2.941256697 2.35293906 2.80933004 2.00292975 2.376973071 1 17.78743489 -1.435997329 5.932606683 0.999402925 2.324449415 0.2084374 0.802217884 0.005825923 0.000553861 0.714289027 0.168294969 0.036643983 1.435997329 1.32504649 EAESSPFVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAESSPFVER 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 182.24 4.19E-06 975590000 523040 629550 622000 670950 789220 808430 654190 654220 667220 562500 FALSE TRUE 543690.0231 737670.3153 638209.831 803661.9074 655068.6663 620684.3844 602912.8784 645451.251 643206.8825 672711.1053 0.808207296 1.096563309 0.948713089 1.194661276 0.973774123 0.922661124 0.896243385 0.959477621 0.956141318 1 19.35962755 3.007470724 24.99626354 0.942153218 1.02238415 0.087409839 0.096338368 359.9968666 1204499.679 0.026546815 0.031669736 1017.350783 -3.007470724 0.080230933 EAETDEIKILLEESRAQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAETDEIKILLEESRAQQK 19 2 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 0 49.559 0.090523 1117300000 22754 1001200 1084700 887470 961830 1168200 850590 1011200 985330 1089400 FALSE TRUE 23652.34549 1173148.312 1112968.173 1063008.917 798338.4802 896903.2542 783918.5332 997646.518 949868.1658 1302847.072 0.018154353 0.900449743 0.85425849 0.815912274 0.612764535 0.688417907 0.601696508 0.765743378 0.729071114 1 20.31323632 -5 0.044289906 2.224788797 3.10E-10 0.221349762 0.225814919 1301.552143 4.289648873 205.9940311 54.59934289 1.00E-05 5 -2.224788797 EAFEETHLTSLDPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAFEETHLTSLDPVK 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 193.96 7.14E-08 543420000 919680 1085370 1298520 1102410 1616460 1611810 1477330 1379200 1414040 993440 FALSE TRUE 955989.6765 1271773.854 1332360.498 1320463.408 1341694.707 1237491.555 1361533.014 1360714.08 1363148.977 1188085.547 0.804647173 1.070439631 1.121434817 1.111421152 1.129291329 1.041584554 1.145989039 1.14529975 1.147349178 1 20.18020729 4.743111224 3.171202714 1.11276264 0.757314673 0.787705156 0.046395333 0.14167215 2.205049669 0.010750861 0.125731894 55349.18415 -4.743111224 -0.355447966 EAFELFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAFELFDR 8 0 P14649;F8W1I5 P14649 MYL6B Myosin light chain 6B 0 ; 83.265 0.042536 87125000 113152 139352 137844 153440 337300 176548 303500 145749 138127 124782 FALSE TRUE 117619.3283 163284.622 141436.3279 183789.974 279965.8665 135547.4026 279710.877 143795.4731 133155.8363 149230.6438 0.788171419 1.094176222 0.947770004 1.231583335 1.876061507 0.908308101 1.874352813 0.963578722 0.892282127 1 17.18718429 3.706231896 5.704305004 1.280003244 0.957492976 0.134731957 0.349901038 0.353530668 35.03967566 0.09091212 0.146426206 5084.308515 -3.706231896 -0.322510268 EAFGFIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAFGFIER 8 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0;E9PNG3 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 101.54 0.012379 275376000 251261 294784 290117 290333 438070 393220 376680 325030 316450 406910 FALSE TRUE 261180.9783 345410.8589 297677.6874 347760.0008 363607.0179 301900.6143 347154.8373 320673.5045 305061.0263 486636.2237 0.536706816 0.709792741 0.611704745 0.714620047 0.747184447 0.620382535 0.713376482 0.65895938 0.626876939 1 18.89248419 -1.515000552 2.955640896 1.012326039 0.664998891 0.740741842 0.060285244 11567927.34 12655340.4 1146210.638 0.014428705 0.030549172 1.515000552 -0.347327148 EAFNMIDQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EAFNMIDQNR 10 0 J3QRS3;P19105;O14950;J3KTJ1;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 194.54 1.05E-06 3115800000 1314431 1491454 1437465 1500611 1605000 1836591 1610228 1513433 1439129 1415270 FALSE TRUE 1366325.751 1747599.623 1474926.519 1797427.377 1332182.673 1410070.574 1484014.122 1493147.906 1387335.028 1692565.06 0.80725154 1.032515479 0.871414963 1.061954675 0.787079153 0.833096823 0.876784094 0.882180509 0.819664225 1 20.69077986 3.218595452 24.99982618 0.861369965 0.944524405 0.159691687 0.085830065 384.267549 481168.1015 0.0228389 0.027330545 1654.228323 -3.218595452 0.083154439 EAFQLFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EAFQLFDR 8 0 P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2 P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;; 232.97 3.69E-08 20703680000 3662700 4280570 4169090 3934380 5193270 5182890 4375470 4219410 4066510 4814710 FALSE TRUE 3807306.224 5015724.599 4277739.91 4712588.621 4310519.82 3979242.345 4032509.228 4162855.711 3920157.099 5758060.241 0.661213337 0.871078868 0.742913365 0.818433365 0.748606239 0.691073413 0.700324251 0.722961472 0.680812103 1 22.45715145 -0.949680402 4.682564053 1.000002161 0.740062349 0.623670046 0.061145484 7720369.382 1648748.402 248.6960486 0.014176221 0.112284445 0.949680402 -0.259939812 EAFSLFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAFSLFDK 8 0 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479;P27482 P0DP25 CALM2;CALM3;CALM1;CALML3 Calmodulin-like protein 3 0 109.71 0.01297 0 171790 133170 172030 167410 173580 188220 231980 178640 183030 128380 FALSE TRUE 178572.4019 156040.9116 176513.2431 200523.1983 144074.9336 144508.7575 213796.8014 176245.623 176442.7861 153533.603 1.16308351 1.016330683 1.149671731 1.306054143 0.93839349 0.941219086 1.392508202 1.147928659 1.149212828 1 17.22819492 2.261066046 24.99998038 1.188216319 1.088850447 0.083369915 0.136522418 547.5479393 608237.6678 0.047610942 0.039806758 182.4173095 -2.261066046 -0.099365873 EAFSLFDKDGDGTITTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;M0QZ52;F8WBR5;G3V479 P0DP25 CALM2;CALM3;CALM1 0 ;;; 261.15 2.57E-27 27324800000 31384190 19179137 27793690 19746580 33510830 29848300 35778530 28183190 31235530 15546180 FALSE TRUE 32623262.06 22473004.59 28518016.39 23652394.59 27814671.09 22916484.68 32974115.33 27805440.44 30111369.38 18592156.32 1.754678774 1.208735781 1.533873527 1.272170596 1.49604331 1.232588855 1.773549811 1.495546829 1.619573806 1 24.14819077 2.267449123 24.99999122 1.520833093 1.409322677 0 0.240438572 691.8127759 598689.5194 0.075834562 0.063438468 185.1182016 -2.267449123 -0.111510417 EAFTNKPNVFTVVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAFTNKPNVFTVVTR 15 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 176.49 7.26E-07 823750000 478170 529790 554980 475520 612950 668420 554010 566220 612210 560530 FALSE TRUE 497048.5208 620777.3113 569443.2347 569576.4367 508760.9779 513189.585 510585.2486 558630.747 590176.6817 670355.1215 0.741470461 0.926042468 0.849465032 0.849663736 0.758942479 0.765548839 0.761663829 0.83333554 0.880394082 1 19.35456604 0.918135354 2.098038544 0.999332058 0.811466064 0.544966816 0.05341754 0.321574245 2.989935249 0.052631789 0.014545359 8.282002439 -0.918135354 -0.187865995 EAFVHVVTLEDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAFVHVVTLEDMR 13 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 155.42 4.67E-05 104630000 141260 174750 157300 158530 186160 219880 165240 166610 159700 182020 FALSE TRUE 146837.0539 204761.9531 161399.3672 189886.7608 154516.5897 168816.2023 152288.057 164376.8655 153952.4282 217683.334 0.674544308 0.940641387 0.741441084 0.872307298 0.709822782 0.775512756 0.699585284 0.755119202 0.70723112 1 17.73187143 EAFVVEEWVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAFVVEEWVK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;; 163.94 1.47E-05 61673000 184073 173179 208358 165240 242982 244058 230385 198975 188137 173273 FALSE TRUE 191340.3442 202921.1461 213787.9806 197923.9788 201680.0064 187379.2282 212326.8217 196308.0656 181365.9861 207222.5268 0.923356872 0.979242697 1.031683109 0.955127716 0.973253292 0.904241595 1.02463195 0.947329755 0.875223311 1 17.66082132 3.546357365 24.99998833 0.954663051 0.980741798 0.050340373 0.047003989 524.8978215 189529.5661 0.012287919 0.019036346 3518.498458 -3.546357365 0.026078746 EAGDEFELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAGDEFELR 9 0 Q5QP56;Q9H1R6;Q5TE64;Q07817-2;Q07817-3;Q07817 Q5QP56 BCL2L1 Bcl-2-like protein 1 0 ; 151.44 0.00019274 1019320000 515280 574620 486120 582200 717300 716950 570630 536850 589960 513670 FALSE TRUE 535623.6523 673306.5151 498788.6866 697357.4223 595373.6022 550449.228 525902.5295 529654.4039 568727.4548 614313.8017 0.871905614 1.096030259 0.811944458 1.135181108 0.969168527 0.896039168 0.856081254 0.862188677 0.925793061 1 19.22861627 2.760960228 5.291216218 0.891917781 0.983740502 0.101202678 0.096262773 0.317186842 27.60435593 0.028229533 0.029006704 576.7136461 -2.760960228 0.091822721 EAGDVCYADVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EAGDVCYADVYR 12 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;; 239.54 8.29E-16 6020280000 1647640 1808840 1765610 1571100 2135610 2147540 1741520 1674820 1649570 1799870 FALSE TRUE 1712690.099 2119494.199 1811623.247 1881858.891 1772599.775 1648806.381 1605015.112 1652371.777 1590202.298 2152520.066 0.795667426 0.984657116 0.841628971 0.874258466 0.823499768 0.765988855 0.745644669 0.767645238 0.738763054 1 21.03759526 3.106431396 2.514524793 0.783033432 0.881685597 0.110055479 0.084069375 0.409688011 5.26730425 0.024370757 0.030231677 1277.707358 -3.106431396 0.098652165 EAGELPTS(ph)PLHLLSPGTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAGELPTSPLHLLSPGTPR 19 0 Q969R5;H7C228;Q969R5-2;Q969R5-3 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 EAGELPT(0.059)S(0.941)PLHLLSPGTPR;EAGELPT(0.203)S(0.797)PLHLLSPGTPR;EAGELPT(0.138)S(0.862)PLHLLSPGTPR 172.81 4.91E-12 218455000 97859 122488 122120 148711 120006 154258 148060 135926 125635 100606 TRUE FALSE 101722.5489 143524.3612 125302.5475 178125.5919 99607.42299 118433.9173 136454.6703 134104.1343 121113.4209 120317.8195 0.84544874 1.192877014 1.041429674 1.480458944 0.82786925 0.984342285 1.134118545 1.114582486 1.006612499 1 16.8764908 EAGEQGDIEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ;;; 138.25 0.00014313 722010000 809810 1040690 961010 882410 1090070 1213590 1008430 999280 982830 940610 FALSE TRUE 841781.9241 1219420.412 986054.7101 1056948.064 904780.2908 931752.1146 929386.6216 985886.2861 947458.1403 1124904.52 0.748314109 1.084021257 0.876567471 0.939589134 0.80431741 0.8282944 0.826191561 0.876417748 0.842256497 1 20.10137112 EAGICYASIAMATDYDCWKEHEEAVSVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAGICYASIAMATDYDCWKEHEEAVSVDR 29 1 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 53.705 0.041774 21174000 3948.5 4062.3 4471.7 4800.8 7370.4 6513.5 5940.2 5300 4742.4 5477.7 FALSE TRUE 4104.389829 4759.968425 4588.236176 5750.383911 6117.582041 5000.838338 5474.591602 5228.962169 4571.72195 6550.950438 0.626533488 0.726607302 0.700392442 0.877793835 0.933846485 0.763375999 0.835694248 0.798199012 0.697871552 1 12.67748852 3.800610799 6.618826536 0.833231664 0.687165987 0.429681237 0.083501743 0.249980643 21.88946279 0.021034839 0.038141297 6318.453584 -3.800610799 -0.146065677 EAGLAHLCEFIEDCEHTVLATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAGLAHLCEFIEDCEHTVLATK 22 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 112.58 0.00016659 65156000 35178 25611 31300 27129 35165 38696 39624 28244 32471 24880 FALSE TRUE 36566.8546 30009.49002 32115.70371 32495.03523 29187.66586 29709.44044 36518.16734 27865.43538 31302.37505 29754.75964 1.228941354 1.008560996 1.07934677 1.09209537 0.980941073 0.998476909 1.227305069 0.936503461 1.052012365 1 14.86083284 4.745177079 24.51354309 1.042905953 1.228941465 0.352304676 0.076150555 640.1467271 2371616.213 0.017394355 0.166129359 55613.09675 -4.745177079 0.186035513 EAGS(ph)PAQEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAGSPAQEFK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK 190.26 9.66E-07 2701480000 3706900 2168370 3058540 2295050 3638240 3754400 3754190 2905180 3301180 1710340 TRUE FALSE 3853251.274 2540770.68 3138248.065 2749004.04 3019813.264 2882497.498 3459926.778 2866240.814 3182371.177 2045448.377 1.883817416 1.242158301 1.534259237 1.343961584 1.476357604 1.409225249 1.69152486 1.401277513 1.555830601 1 20.9639857 -1.611709405 2.804165975 0.960081115 1.490602227 0.431601785 0.172968396 16168578.18 16064476.54 4747115.727 0.038111558 0.02445066 1.611709405 0.530521112 EAGSQKDENLALYVENQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAGSQKDENLALYVENQFR 19 1 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;; 282.62 8.36E-40 297130000 475900 434700 523970 510440 712950 648980 521340 445400 474370 380014 FALSE TRUE 494688.8995 509356.3435 537625.0886 611403.5085 591763.0137 498264.2304 480476.0085 439430.1415 457297.5164 454470.4675 1.08849515 1.120768851 1.182970351 1.345309656 1.302093438 1.096362175 1.05722163 0.966905823 1.006220534 1 18.79382702 2.352285486 2.532544328 0.996527621 1.208346336 0.614938211 0.074477225 0.205261123 2.696135161 0.033715284 0.026043686 225.0533521 -2.352285486 0.211818715 EAGVFVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAGVFVPR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 169.37 0.00070118 162910000 169730 200780 183780 176750 235350 252940 196510 191660 171720 201510 FALSE TRUE 176431.0715 235262.4031 188569.4578 211710.6225 195345.2911 194198.5183 181107.0327 189091.1112 165539.8307 240992.0264 0.732103357 0.976224843 0.782471771 0.878496379 0.810588193 0.805829642 0.751506328 0.78463638 0.686909991 1 17.87862589 2.924414844 2.620845195 0.787013281 0.847593317 0.010958919 0.096060593 0.751974845 10.1724652 0.028820087 0.032035915 840.2622335 -2.924414844 0.060580036 EAHEPLAVADAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAHEPLAVADAK 12 0 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 0 82.543 0.014669 424470000 599940 365510 549550 402980 716620 773410 619360 549560 634730 398860 FALSE TRUE 623626.0945 428283.4992 563871.7245 482688.2412 594809.1884 593797.2486 570812.9448 542194.0471 611886.1913 477008.9804 1.307367618 0.897852067 1.182098761 1.011905983 1.246955954 1.244834527 1.196650311 1.136653752 1.282756125 1 18.8636569 3.230217472 24.99912567 1.191136194 1.091258861 0.098798651 0.123524627 353.6157887 1059562.548 0.032656881 0.03964387 1699.094259 -3.230217472 -0.099877333 EAHEREMAEQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAHEREMAEQFR 12 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 0 ; 66.267 0.053369 2827800000 950500 1388740 1363130 1549990 1300040 1716840 1661920 1509130 1400060 1231380 FALSE TRUE 988026.4739 1627245.292 1398654.288 1856573.396 1079059.665 1318129.929 1531654.368 1488902.581 1349672.114 1472645.335 0.670919502 1.10498112 0.94975637 1.260706398 0.732735601 0.895076294 1.040070091 1.011039485 0.916495019 1 20.48997859 4.751862217 24.65049837 0.989957635 0.670919248 0.348011693 0.131061207 2056.899144 3811759.827 0.030328428 0.572588089 56475.77725 -4.751862217 -0.319038387 EAHLEKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAHLEKEEK 9 1 A0A1W2PRI9;E9PNW5 A0A1W2PRI9 C4orf50 0 ; 55.064 0.078676 313020000 1040920 331100 539710 326830 739380 636260 785030 349240 620220 252165 FALSE TRUE 1082016.325 387963.8494 553775.286 391475.9985 613700.4517 488498.2576 723497.2973 344559.009 597898.4034 301571.9038 3.587921527 1.28647213 1.836296018 1.298118272 2.035005397 1.619840083 2.39908721 1.142543469 1.982606456 1 18.2021425 4.745128561 24.96727226 1.648357532 3.587922417 0.65968956 0.423177541 418.5806443 1591143.101 0.091897373 0.884604126 55606.88417 -4.745128561 1.939564886 EAHLPPGAMAAVGLSWEECK ddPTM_MDA-MB-175_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 ;;;;; 200.99 1.30E-21 6017030000 3934960 2927210 3628020 3394980 4716930 5028960 4144840 3526780 4079010 2832730 FALSE TRUE 4090315.259 3429935.547 3722569.182 4066496.911 3915147.923 3861060.255 3819956.61 3479509.283 3932207.227 3387749.208 1.207384316 1.012452616 1.098832574 1.200353586 1.155678205 1.13971254 1.127579516 1.027085852 1.160713791 1 21.69189565 0.360436656 0.507099471 0.99430114 1.130857218 0.26016827 0.062039469 3.393596176 1.420902341 0.119356887 0.031906318 2.293172137 -0.360436656 0.136556078 EAHQLFLEPEVLDPESVELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAHQLFLEPEVLDPESVELK 20 0 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ;;; 161.8 2.20E-11 212948000 510816 392046 470196 366222 592702 603134 573920 489978 506252 370555 FALSE TRUE 530983.4101 459376.8508 482449.694 438659.6185 491954.7257 463065.2691 528934.6507 483410.6464 488032.0894 443158.1575 1.198180381 1.03659798 1.088662559 0.989848908 1.110110956 1.044921009 1.193557293 1.090830978 1.101259406 1 18.75746214 EAHS(ph)PGPLVKPFETASVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAHSPGPLVKPFETASVK 18 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAHS(1)PGPLVKPFETASVK;EAHS(1)PGPLVKPFETASVK 171.5 7.92E-12 739680000 893330 539220 735950 520620 996390 912310 919950 941990 852500 520290 TRUE FALSE 928599.3582 631826.8405 755129.4616 623597.0821 827023.9837 700439.8287 847841.9152 929364.1648 821818.6915 622230.8639 1.492371099 1.015421891 1.213584066 1.002195677 1.329127229 1.125691233 1.362584154 1.493600235 1.320761697 1 19.24709043 2.227516626 24.88088385 1.353295113 1.186159203 0.025004452 0.180902068 357.5827387 805588.124 0.063353641 0.047234704 168.85605 -2.227516626 -0.16713591 EAIEGTYIDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAIEGTYIDKK 11 1 P62280;M0QZC5 P62280 RPS11 40S ribosomal protein S11 0 ;;; 149.49 5.51E-05 6645900000 6778950 2390820 4209760 2768330 6205750 5481870 5622620 4604100 5080050 2242240 FALSE TRUE 7046588.18 2801424.737 4319469.804 3315897.411 5150898.832 4208788.771 5181904.352 4542389.57 4897219.993 2681563.998 2.627790419 1.044698071 1.61080243 1.236553524 1.9208562 1.569527624 1.932418677 1.693932934 1.826255125 1 21.35464325 EAIESAIGGNAYQHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAIESAIGGNAYQHSK 16 0 P63172 P63172 DYNLT1 Dynein light chain Tctex-type 1 0 ;; 255.21 1.33E-26 993140000 601590 452110 589100 440090 667770 682050 565590 544740 617360 472140 FALSE TRUE 625341.2377 529756.3756 604452.43 527138.4885 554262.6939 523654.2241 521257.5779 537438.6513 595141.3342 564646.7933 1.107490993 0.93820842 1.070496525 0.933572093 0.981609566 0.927401395 0.92315689 0.951813873 1.0540064 1 19.10698917 4.747276691 24.5361366 0.971121914 1.107491084 0.384621918 0.049766759 888.9462337 2502350.401 0.011588535 0.137010169 55882.61116 -4.747276691 0.136369169 EAIHSQLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAIHSQLLEK 10 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;; 157.97 8.23E-06 1468300000 1956890 1644140 1946790 1589020 2507250 2588000 2205250 1985750 2135360 1798010 FALSE TRUE 2034149.528 1926508.255 1997524.947 1903323.413 2081068.541 1986976.222 2032396.743 1959134.269 2058508.811 2150295.635 0.945985982 0.895927157 0.928953635 0.885144992 0.967805778 0.924047926 0.945170845 0.911099961 0.957314324 1 21.03610359 -4.99998647 0.200475813 1.339925854 0.914901551 0.466876966 0.023939772 116.5423048 1.15389041 15.80060932 0.053325279 1.00E-05 4.99998647 -0.425024303 EAILAIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAILAIHK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 98.392 0.0075549 936800000 1517060 1471610 1139890 1430950 1906170 1870000 1871350 1270920 1239000 2246400 FALSE TRUE 1576954.7 1724347.57 1169596.47 1713987.639 1582159.904 1435720.84 1724668.697 1253885.396 1194408.632 2686539.07 0.586983721 0.641847196 0.43535435 0.637990959 0.588921234 0.53441279 0.641966728 0.466728889 0.444590084 1 21.35731739 -1.41508723 4.98506191 1.000542713 0.552907964 0.753237186 0.07671988 0.00045363 5.32E-05 0.072819179 0.01714351 0.038451454 1.41508723 -0.447634749 EAILEYILHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAILEYILHQK 11 0 Q9Y314;A0A075B6F9;M0R3B2;A0A075B797;M0R1K2;M0QX85 Q9Y314 NOSIP Nitric oxide synthase-interacting protein 0 ; 183.33 5.39E-06 184001000 579070 510020 598940 481930 722850 751410 686670 622530 677670 584250 FALSE TRUE 601932.1307 597611.9676 614548.8684 577254.3156 599980.2152 576906.4152 632847.0111 614186.0036 653280.7891 698722.6014 0.861475111 0.855292167 0.879531973 0.826156639 0.858681563 0.825658729 0.905719967 0.879012647 0.934964445 1 19.41436028 1.048015443 0.934047643 1.000103294 0.853287839 0.831949478 0.020608925 0.205256412 0.389990349 0.018419147 0.006340619 11.16902963 -1.048015443 -0.146815454 EAIQHPADEKLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAIQHPADEKLQEK 14 1 E5RI16;Q9NUQ9;E5RGI7;E5RJE1;E5RIR8;E5RJL8 E5RI16 FAM49B Protein FAM49B 0 107.34 0.00053442 95409000 237830 127310 207880 107570 304610 240850 187350 184640 239930 142520 FALSE TRUE 247219.712 149174.5022 213297.5236 128847.0249 252832.501 184916.2376 172665.0175 182165.2028 231294.9662 170444.0653 1.450444823 0.875210891 1.251422414 0.755949025 1.483375209 1.084908631 1.013030387 1.068768235 1.357013902 1 17.37893884 -1.900304723 0.009063355 1.28E-06 2.143640996 0.015508255 0.229472826 66889.65768 86.85645733 11032.31068 9550.687228 0.012580424 1.900304723 2.143639712 EAIVNSCVFVHQTLHQANAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAIVNSCVFVHQTLHQANAR 20 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 168.78 6.79E-12 130600000 45993 81623 93322 72271 86065 81997 57454 71828 81270 80457 FALSE TRUE 47808.83915 95641.11531 95754.04798 86565.98809 71435.70204 62954.43943 52950.60535 70865.26315 78345.10858 96221.00871 0.496864872 0.993973318 0.995146998 0.899657874 0.742412733 0.654269169 0.550301915 0.736484309 0.814220404 1 16.5540643 4.767089128 23.769853 0.797575009 0.496863992 0.291473758 0.147558923 8309.924454 6923572.86 0.038910956 3.648852335 58491.01104 -4.767089128 -0.300711017 EALAAVLTYAKPDEFSALCDLLGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EALAAVLTYAKPDEFSALCDLLGTR 25 1 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;H0YAB3;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 214.57 1.65E-33 260710000 246010 160977 198946 189980 267280 246590 207696 222646 247480 142377 FALSE TRUE 255722.6648 188623.5475 204130.6962 227557.477 221847.8411 189323.2096 191416.2448 219661.7945 238573.2431 170273.0472 1.501838776 1.107771022 1.198843267 1.336426879 1.302894643 1.111880082 1.12417231 1.290056167 1.401121593 1 17.37749056 2.798383775 24.999324 1.205170805 1.277020293 0.112374496 0.138730019 813.8485783 340094.7494 0.042132374 0.04468812 628.6136027 -2.798383775 0.071849488 EALAEAALES(ph)PRPALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 289.35 3.66E-46 26092910000 4551841 4716994 4885758 4741843 5562550 5891980 5245241 5247251 5018439 5438170 TRUE FALSE 4731551.197 5527101.026 5013084.867 5679765.392 4617029.738 4523656.939 4834105.305 5176920.183 4837826.361 6503675.291 0.727519592 0.849842709 0.770807988 0.873316262 0.709910863 0.695553935 0.743288231 0.795999178 0.743860378 1 22.6328238 -1.088378375 4.639961228 1.000012946 0.770407207 0.616910916 0.054861391 7.69E-06 1.51E-06 0.053218072 0.012542881 0.081587124 1.088378375 -0.229605739 EALAEAALESPRPALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EALAEAALESPRPALVR 17 1 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 224.86 2.36E-15 1806080000 606780 744880 711700 696790 820660 839000 765170 766480 726510 786640 FALSE TRUE 630736.1429 872807.3456 730247.4867 834612.9823 681164.5063 644154.9652 705193.976 756206.5893 700363.047 940767.0469 0.670448806 0.927761393 0.776225623 0.887162221 0.72405226 0.684712509 0.749594683 0.803819173 0.744459587 1 19.843478 -1.346700939 9.281091758 1.00000019 0.778848964 0.431454043 0.077582507 2.96E-07 2.09E-08 0.072557223 0.017101887 0.045008969 1.346700939 -0.221151226 EALAPNSLS(ph)PSPQGHR ddPTM_MDA-MB-175_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(0.999)PSPQGHR 130.73 3.12E-05 162460000 24208 52218 54348 54128 54456 72669 51641 57750 53373 60149 TRUE FALSE 25163.75053 61186.0353 55764.35353 64834.35684 45199.58857 55792.72606 47593.24348 56975.95571 51452.11616 71934.04493 0.349816982 0.850585218 0.77521504 0.90130281 0.628347657 0.775609464 0.661623346 0.792058277 0.71526794 1 16.13438711 -5 0.213624419 2.305602187 0.691747292 0.270467605 0.143503761 208.1793832 2.078961304 116.9322116 0.278282391 1.00E-05 5 -1.613854895 EALAPNSLSPS(ph)PQGHR ddPTM_MDA-MB-175_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(0.041)PS(0.959)PQGHR 54.501 0.06443 0 28473 66128 72008 75704 89968 74291 65134 72794 61670 83139 TRUE FALSE 29597.13603 77484.9696 73884.58764 90678.02525 74675.2715 57038.04114 60028.62688 71818.3155 59450.50875 99428.49526 0.297672573 0.779303452 0.743092686 0.911992332 0.751044973 0.573658899 0.603736652 0.722311198 0.597922241 1 16.60137175 -2.166264981 2.34001087 1.788492528 0.678130008 0.28988028 0.156219752 11190465.05 2677535.473 46745822.7 0.03684224 0.006819225 2.166264981 -1.11036252 EALASLPSS(ph)PGLLQSLLER ddPTM_MDA-MB-175_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(0.165)S(0.83)PGLLQS(0.005)LLER 129.32 2.07E-05 51070000 51142 58654 60552 57391 65338 71789 56574 59441 52141 62287 TRUE FALSE 53161.12565 68727.36824 62130.03486 68742.7685 54231.8701 55117.09272 52139.58205 58644.29062 50264.4556 74490.94509 0.713658896 0.922627148 0.834061573 0.922833888 0.728033052 0.739916679 0.699945235 0.787267373 0.674772693 1 16.18477745 3.22242537 24.98865681 0.756718541 0.852588104 0.111921546 0.100323031 386.6355308 598781.0657 0.026548653 0.03182512 1668.880997 -3.22242537 0.095869563 EALEALVPVTIEVEVPFDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EALEALVPVTIEVEVPFDLHR 21 0 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ;;;; 179.87 5.59E-17 1583798000 1510980 1875181 1836399 1847718 2084248 2322513 1892801 1893111 1832628 1947758 FALSE TRUE 1570634.657 2197228.75 1884257.067 2213191.106 1729968.269 1783144.554 1744438.312 1867736.944 1766672.076 2329383.888 0.674270422 0.943266055 0.808907916 0.950118663 0.742672034 0.76550051 0.748883995 0.801815859 0.758428907 1 21.15151699 4.78218745 22.95584775 0.82217195 0.674268943 0.209567502 0.090671636 18218.03274 9585440.209 0.020710485 8.533264181 60560.22076 -4.78218745 -0.147903007 EALEAYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EALEAYRR 8 1 Q9NRF9 Q9NRF9 POLE3 DNA polymerase epsilon subunit 3 0 ; 175.38 0.0004273 279580000 211600 276960 264120 254140 331850 350550 241840 265760 244050 385330 FALSE TRUE 219954.1314 324525.7256 271003.1842 304408.1335 275442.2555 269140.0751 222883.9489 262197.9219 235266.6882 460828.0359 0.477301974 0.704223051 0.588078769 0.660567738 0.597711585 0.58403581 0.483659698 0.56897129 0.510530328 1 18.81386896 -1.892104771 2.546310231 1.224161656 0.577993761 0.775816084 0.068519907 6613022.679 3807897.133 8902870.202 0.016661604 0.012820213 1.892104771 -0.646167895 EALEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EALEHK 6 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 ;; 75.311 0.078026 891920000 849050 620080 774090 618820 971310 925470 937390 797490 862620 610280 FALSE TRUE 882571.1496 726573.9164 794263.4213 741220.749 806207.0731 710543.6181 863914.9224 786800.951 831574.4747 729852.6815 1.209245608 0.995507634 1.0882517 1.015575839 1.104616169 0.973543889 1.183683974 1.078027074 1.139373049 1 19.47724576 2.22959371 24.99996652 1.106440104 1.062007898 0.047640809 0.076010036 519.5818274 1448594.417 0.025817213 0.019351261 169.6655658 -2.22959371 -0.044432206 EALEHLCTYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALEHLCTYEK 11 0 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 132.32 0.0001849 317850000 450200 328590 407560 359300 567690 506120 487970 403280 435200 359050 FALSE TRUE 467974.2436 385022.7764 418181.3484 430368.4676 471194.2566 388581.3003 449721.6363 397874.6912 419537.237 429398.9731 1.089835498 0.896655094 0.973875986 1.002257794 1.097334382 0.904942314 1.04732816 0.926585102 0.977033629 1 18.71195922 -0.069473008 7.483942944 0.999999999 0.986390679 0 0.067440098 0 0 0.060311236 0.014215495 0.852171473 0.069473008 -0.01360932 EALEKTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALEKTEK 8 1 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 64.04 0.063385 685480000 330830 198630 226040 189080 327660 333200 328660 260440 292310 193300 FALSE TRUE 343891.4239 232743.1574 231930.7881 226479.4597 271964.4702 255819.3497 302898.7704 256949.2278 281789.8202 231173.434 1.487590584 1.006790241 1.003276129 0.979695009 1.176452093 1.106612231 1.310266345 1.111499809 1.218954165 1 17.81861609 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EALGLGPPAAQLTPPPAPVGLR 22 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR 146.78 9.27E-07 960028000 448109 448883 474611 455254 496421 559165 486685 489244 479146 434703 TRUE FALSE 465800.6893 525975.1634 486979.7526 545301.8824 412039.5357 429307.403 448537.358 482686.4844 461901.6291 519874.73 0.895986403 1.01173443 0.936725185 1.048910153 0.792574657 0.825790096 0.862779689 0.928466911 0.888486403 1 18.9878045 3.242569024 24.99985812 0.878882738 0.97346628 0.31550079 0.065005181 119.6877358 746469.6013 0.017897898 0.023367634 1748.111072 -3.242569024 0.094583542 EALKEAVILPIKFPHLFTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALKEAVILPIKFPHLFTGK 20 2 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 134.29 5.55E-06 103890000 263930 178270 244510 148810 345580 276920 234890 232810 284760 198950 FALSE TRUE 274350.1602 208886.4858 250882.1315 178244.1738 286838.435 212609.5268 216478.708 229689.5628 274511.5432 237930.4434 1.153068755 0.877930889 1.054434766 0.749144041 1.205555838 0.893578492 0.909840309 0.965364329 1.153747034 1 17.86018035 1.267867408 24.44985518 1.076873534 0.969381304 0.083308732 0.132192145 311.3019714 259711.4219 0.080415696 0.029354866 18.52965818 -1.267867408 -0.107492229 EALLDESRPLFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EALLDESRPLFER 13 1 A0A5F9ZGM7;Q9BU89 A0A5F9ZGM7 DOHH Deoxyhypusine hydroxylase 0 ; 157.52 4.35E-05 199481000 167207 194965 195919 206182 216072 240420 197703 202842 194110 193659 FALSE TRUE 173808.4615 228448.7221 201024.8101 246964.1842 179344.1586 184586.0986 182206.5223 200123.2348 187124.019 231602.7732 0.750459328 0.986381635 0.867972379 1.066326542 0.774361015 0.796994337 0.78671995 0.864079613 0.807952411 1 17.821293 EALLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALLGR 6 0 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 101.33 0.085259 247190000 173910 179050 162330 180020 195290 215770 175180 187360 168730 179340 FALSE TRUE 180776.1011 209800.4447 166560.4532 215627.4187 162094.6756 165660.6875 161448.9339 184848.7457 162657.4403 214478.2393 0.842864533 0.978189887 0.776584392 1.005358023 0.755762804 0.772389255 0.752752048 0.861853148 0.758386682 1 17.71047176 3.213020474 24.99821689 0.807253738 0.897411903 0.160675091 0.092254912 354.4490073 346927.1103 0.024538177 0.029338665 1633.128935 -3.213020474 0.090158164 EALLSSAVDHGSDEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALLSSAVDHGSDEVK 16 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 97.904 0.002915 770920000 292300 224730 279510 262230 353330 380130 332130 327880 304460 210840 FALSE TRUE 303840.2297 263325.6293 286794.2602 314098.3113 293271.0928 291850.5684 306096.7827 323485.3049 293502.5441 252150.0612 1.204997644 1.0443211 1.137395164 1.245680091 1.163081585 1.157447938 1.21394689 1.282907898 1.163999496 1 17.94392305 3.98234788 23.87987331 1.193320958 1.116209075 0.033040865 0.080422666 724.370089 979938.5302 0.0196195 0.036405012 9601.694415 -3.98234788 -0.077111883 EALNIIGDISTSTVSTPVPPPVDDT(ph)WLQSASSHSPTPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALNIIGDISTSTVSTPVPPPVDDTWLQSASSHSPTPQR 39 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7ENE7 P50570-2 DNM2 Dynamin-2 1 EALNIIGDISTSTVSTPVPPPVDDT(0.283)WLQS(0.172)AS(0.172)S(0.172)HS(0.172)PT(0.029)PQR 136.36 5.84E-09 226420000 24618 55440 59341 58043 52758 71581 49751 56636 46697 54108 TRUE FALSE 25589.93765 64961.38874 60887.47521 69523.73216 43790.214 54957.39757 45851.38662 55876.88706 45016.38409 64709.42664 0.395459193 1.003893746 0.940936713 1.074398828 0.676720785 0.849295078 0.708573526 0.863504592 0.695669649 1 15.98168827 EALNSCNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EALNSCNKR 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;;;; 188.91 6.23E-05 6925280000 2650380 2139610 2579390 1976370 3278750 3040750 2910320 2485870 2706940 2397050 FALSE TRUE 2755019.049 2507071.374 2646611.022 2367290.087 2721429.246 2334581.896 2682201.514 2452550.979 2609517.758 2866706.053 0.961039952 0.874547766 0.923223719 0.825787522 0.94932274 0.814377844 0.935638836 0.855529285 0.910284386 1 21.45096255 -1.99254196 6.761325015 1.096981881 0.8910777 0.298363904 0.04832987 0.035811716 3.95E-05 0.02371849 0.009639976 0.010173211 1.99254196 -0.20590418 EALNVINTHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALNVINTHTK 11 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 74.392 0.026879 0 229500 167100 190790 103960 219900 229220 236050 180520 189430 125090 FALSE TRUE 238560.8372 195798.1251 195762.1441 124522.9777 182521.4765 175987.1289 217547.7842 178100.4247 182612.4513 149598.9905 1.594668763 1.308819829 1.308579312 0.832378463 1.220071579 1.176392489 1.454206231 1.190518894 1.220679703 1 17.19074091 4.694882541 1.839096215 1.185887992 1.697234337 0.401709888 0.156859914 0.815603954 3.045408423 0.041179005 0.698539353 49531.62095 -4.694882541 0.511346344 EALPESGELLDVWTELQDIHDAHGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EALPESGELLDVWTELQDIHDAHGLR 26 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 0 ;;; 173.8 1.91E-12 157380000 34000.9 50032.1 50272.3 52059.6 53599.9 59731.7 48705.5 51685.5 53848.7 61020.4 FALSE TRUE 35343.28179 58624.72398 51582.43744 62356.8335 44489.00814 45859.91792 44887.83564 50992.74041 51910.69581 72976.17907 0.484312583 0.803340552 0.706839384 0.854482028 0.609637401 0.628423117 0.615102575 0.698758705 0.711337541 1 16.155138 0.560046753 2.06811278 0.999970584 0.680530812 0.491675484 0.098399631 2.833478701 12.31892844 0.091088232 0.024950365 3.631171431 -0.560046753 -0.319439772 EALPWGLEPQDVQSSDEMRS(ph)PEGYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EALPWGLEPQDVQSSDEMRSPEGYLR 26 1 Q9H5H4 Q9H5H4 ZNF768 Zinc finger protein 768 1 EALPWGLEPQDVQS(0.104)S(0.104)DEMRS(0.79)PEGY(0.001)LR 67.78 0.051585 49921000 23262 30952 27310 21768 33577 34418 28856 26287 30233 32547 TRUE FALSE 24180.40172 36267.76523 28021.72104 26073.64543 27869.59353 26424.94111 26594.19132 25934.66576 29144.92024 38923.9615 0.621221499 0.931759354 0.719909278 0.669861043 0.716000953 0.678886221 0.683234447 0.6662905 0.748765519 1 15.24837093 0.959061248 20.46449156 1.000000001 0.712272037 0.543525271 0.078998673 513.9456978 256912.9267 0.075042609 0.018760652 9.100416052 -0.959061248 -0.287727964 EALTYDGALLGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 204.17 1.86E-07 611934000 1578504 1780013 1666992 1913315 1775159 2120570 2012575 1805676 1685540 1549417 FALSE TRUE 1640824.557 2085716.386 1710435.181 2291762.996 1473418.107 1628099.755 1854824.113 1781473.867 1624877.745 1852995.596 0.885498358 1.125591659 0.923064893 1.236788151 0.795154673 0.878631206 1.00098679 0.961402105 0.876892394 1 20.82142802 3.215278564 24.99995527 0.923764526 1.040106374 0.237735157 0.108425163 346.8925711 372487.6038 0.029879409 0.035733682 1641.642415 -3.215278564 0.116341847 EAMEDGEIDGNKVTLDWAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAMEDGEIDGNKVTLDWAKPK 21 2 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 195.39 1.39E-19 2919590000 3825210 1563250 2935450 1490860 4183190 3093800 3631870 2702870 3574160 1279762 FALSE TRUE 3976232.245 1831726.027 3011950.238 1785747.658 3472132.858 2375311.837 3347194.539 2666642.449 3445526.68 1530506.861 2.597983939 1.196810072 1.967942983 1.166768803 2.268616329 1.551977255 2.186984341 1.74232636 2.251232429 1 20.54557808 3.184821867 24.99999975 1.872347669 1.710918084 0.005047498 0.518986333 457.8174472 212980.7888 0.136410715 0.163042127 1530.459588 -3.184821867 -0.161429585 EAMFDDDADQFPDDLSLDHSDLVAELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAMFDDDADQFPDDLSLDHSDLVAELLK 28 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 209.89 1.39E-25 21819000 13200 11252 14831 12716 14194 18473 18680 16422 16805 9796.5 FALSE TRUE 13721.14619 13184.44347 15217.50804 15231.18685 11781.30895 14182.92571 17215.81279 16201.88995 16200.19133 11715.93661 1.171152307 1.125342677 1.298872514 1.300040053 1.005579779 1.210566955 1.469435467 1.382893275 1.382748292 1 13.51618467 2.399179657 9.120568322 1.34929814 1.182244043 0.132935034 0.141686088 0.430343676 46.14438498 0.047200293 0.039456355 250.7146185 -2.399179657 -0.167054096 EAMNHPGHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAMNHPGHLK 10 0 P00374-2;P00374 P00374-2 DHFR Dihydrofolate reductase 0 71.03 0.03019 65583000 123990 115500 124650 104980 154980 153440 115060 121300 140420 110440 FALSE TRUE 128885.2209 135336.2265 127898.4814 125744.7307 128636.555 117805.8854 106041.2965 119674.1719 135366.3116 132078.6035 0.975822105 1.024664275 0.968351255 0.952044671 0.973939393 0.891937697 0.802865065 0.906082959 1.024892057 1 17.01103725 2.776741063 7.735685636 0.908174337 0.979594347 0.137455642 0.060310866 0.415038831 75.12796494 0.019069303 0.020080633 598.0549142 -2.776741063 0.07142001 EAMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 240.87 5.23E-51 358470000 82247 84297 94568 88527 166575 143241 124351 92412 111007 123621 FALSE TRUE 85494.17507 98774.35401 97032.51977 106037.3764 138260.641 109975.4486 114604.0437 91173.3683 107011.8798 147842.1681 0.578280041 0.668106774 0.65632506 0.71723364 0.935190838 0.743870643 0.775178321 0.616693934 0.723825152 1 17.17369829 3.673424329 3.516500337 0.768548985 0.635111111 0.302123591 0.106077466 0.364852174 8.929955637 0.029693635 0.049874129 4714.377214 -3.673424329 -0.133437874 EAMSAYNSHEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAMSAYNSHEEGR 13 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 109.95 0.00060095 0 25262 157200 101200 140110 56964 162250 70845 98594 75352 155100 FALSE TRUE 26259.36327 184197.8772 103837.3551 167823.3398 47281.27963 124569.8964 65291.98378 97272.5087 72640.09624 185488.8754 0.1415684 0.993040023 0.55980368 0.904762291 0.254900891 0.671576105 0.351999459 0.52441155 0.391614301 1 17.50097314 -0.841214539 12.89111567 1 0.544559476 0.229847313 0.255817886 0 0 0.227402561 0.053599298 0.144140313 0.841214539 -0.455440524 EANELQQWINEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EANELQQWINEK 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 191.23 1.31E-05 62580000 157703 134975 140085 128037 197076 175664 164778 145058 170635 131427 FALSE TRUE 163929.2362 158155.9063 143735.7302 153362.3364 163577.0919 134868.6982 151862.2698 143113.7348 164493.8797 157177.6043 1.042955432 1.006224182 0.914479711 0.97572639 1.040715009 0.858065618 0.966182622 0.910522433 1.046547823 1 17.26203614 EANNFLWPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EANNFLWPFK 10 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 136.33 0.00028073 613030000 776080 786280 821820 753750 1065700 1093300 939120 863460 874250 801850 FALSE TRUE 806720.2377 921317.4736 843237.3043 902839.5003 884552.6947 839397.6441 865509.3205 851886.731 842785.9133 958957.1552 0.841247425 0.960749361 0.879327402 0.94148054 0.922411069 0.875323407 0.902552649 0.88834702 0.878856692 1 19.87110683 -1.02281803 4.654820148 1.000002808 0.900690972 0.454360006 0.033179191 8.86E-07 1.86E-07 0.029431524 0.006936881 0.094881594 1.02281803 -0.099311836 EANQQQQFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EANQQQQFNR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 195.88 7.99E-07 181635000 78147 80668 77330 62166 87266 112421 80279 89955 83957 77633 FALSE TRUE 81232.3039 94522.10149 79345.28333 74462.24925 72432.55649 86312.92651 73986.52221 88749.30036 80935.40397 92843.69998 0.874936091 1.01807771 0.854611388 0.802017253 0.780155859 0.92965841 0.796893297 0.955900081 0.871738244 1 16.5025164 0.606703843 0.886030586 0.99905648 0.871231691 0.21489582 0.071261675 2.0826781 2.720071341 0.071079244 0.023523563 4.04300095 -0.606703843 -0.127824789 EANSSPGLGTPLKS(ph)PSLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EANSSPGLGTPLKSPSLAK 19 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 EANSSPGLGTPLKS(1)PSLAK;EANSSPGLGTPLKS(1)PSLAK 250.71 1.22E-25 470100000 740870 382620 528410 380770 745800 747750 713040 575100 651110 333530 TRUE FALSE 770120.1197 448332.0086 542180.7987 456085.1695 619029.1824 574096.3948 657150.0616 567391.7252 627676.6783 398878.8177 1.930712 1.123980489 1.359261948 1.143417874 1.551922927 1.439275212 1.647493004 1.422466423 1.573602434 1 18.60559099 EANYIAEELDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EANYIAEELDKR 12 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;; 185.95 1.99E-05 1175380000 946920 654292 873072 681882 1095360 1019800 986950 820088 918692 626167 FALSE TRUE 984305.1328 766661.5613 895824.9736 816756.2244 909171.0985 782966.9052 909590.2801 809096.0618 885628.4544 748852.435 1.314418017 1.02378189 1.196263685 1.09067713 1.214085788 1.045555664 1.214645553 1.080447928 1.182647492 1 19.51432193 -5 0.226718927 0.248772933 1.1610717 0.220030811 0.085776414 232.5651952 2.327830734 80.18115645 0.135061902 1.00E-05 5 0.912298768 EAPAPPKAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAPAPPKAEAK 11 1 P62750 P62750 RPL23A 60S ribosomal protein L23a 0 101.39 0.0030271 132900000 251030 162010 224010 147420 335920 260440 240500 224280 255960 180210 FALSE TRUE 260940.8582 189833.9572 229847.8846 176579.236 278820.4384 199956.757 221648.9816 221273.8934 246748.0496 215518.6992 1.210757392 0.880823604 1.066486971 0.819322113 1.293718083 0.927793077 1.028444318 1.026703921 1.144903206 1 17.71745352 EAPCVLIYIPDGHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAPCVLIYIPDGHTK 15 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 179.39 6.72E-07 118010000 214300 193590 207100 203820 254600 274110 232600 231210 247630 208110 FALSE TRUE 222760.7295 226837.5766 212497.1961 244134.9877 211323.1829 210452.1067 214368.2042 228111.0081 238717.8447 248885.17 0.895034162 0.911414596 0.853796135 0.980914161 0.849079047 0.845579135 0.86131369 0.916531138 0.959148529 1 17.92512074 1.190487025 2.138310308 0.997312639 0.886147622 0.497712746 0.038251143 0.243623211 1.970347207 0.035588243 0.010163241 15.50554461 -1.190487025 -0.111165017 EAPGS(ph)PPLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;EAPGS(1)PPLS(1)PR;EAPGS(1)PPLS(1)PR 171.36 0.00049903 1168760000 1537220 1507820 1487130 1526670 1778570 1754060 1664150 1564440 1599680 1464010 TRUE FALSE 1597910.633 1766776.356 1525885.829 1828640.769 1476249.307 1346706.148 1533709.575 1543471.241 1542107.829 1750854.729 0.912646038 1.009093631 0.8715091 1.044427467 0.843159219 0.769170694 0.875977629 0.881553001 0.880774289 1 20.73962796 3.20720261 24.99492433 0.865405617 0.956688074 0.25495226 0.069368684 238.4506718 190064.2433 0.01904256 0.022762226 1611.397218 -3.20720261 0.091282457 EAPGS(ph)PPLSPR ddPTM_MDA-MB-175_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(1)PPLSPR;EAPGS(1)PPLSPR 135.02 0.00013508 631900000 701840 729000 723250 711740 803890 832890 727050 697640 640790 705080 TRUE FALSE 729549.1851 854200.0792 742098.4892 852520.0477 667245.0649 639463.9201 670061.9212 688289.2769 617728.0931 843226.9264 0.865187249 1.013013286 0.880069725 1.011020902 0.791299523 0.758353297 0.794640091 0.816256283 0.732576337 1 19.68556141 3.223744229 24.98907581 0.803196825 0.942925464 0.364603634 0.081029859 210.027385 354228.0706 0.021278532 0.02553138 1673.956736 -3.223744229 0.139728639 EAPIDKK ddPTM_MDA-MB-175_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 ; 75.738 0.068396 3079100000 2548400 1313940 1925390 1356250 2712200 2058950 2424700 2003050 2153970 1098650 FALSE TRUE 2649012.8 1539598.974 1975567.245 1624512.202 2251181.213 1580790.066 2234645.678 1976202.391 2076449.04 1313909.433 2.016130438 1.171769481 1.503579468 1.236395875 1.713345804 1.203119505 1.700760816 1.504062869 1.580359338 1 20.3254344 -1.895823925 2.64877451 0.734720383 1.500779982 0.274859855 0.249772451 14291877.51 6683895.51 23531486.93 0.05359898 0.012710893 1.895823925 0.766059599 EAPPPVLLT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAPPPVLLTPK 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 EAPPPVLLT(1)PK;EAPPPVLLT(1)PK 100.19 0.047132 100181000 198676 122501 135891 130971 206638 221170 179168 162918 162923 117973 TRUE FALSE 206519.8819 143539.5938 139432.4311 156876.6729 171513.7466 169806.6194 165124.344 160734.3507 157059.4331 141087.5506 1.463771119 1.017379586 0.988268848 1.111910103 1.215654718 1.203554946 1.170367926 1.139252542 1.11320547 1 17.10623117 0.78700459 1.729864164 1.000231388 1.155218048 0.139330542 0.122594225 1.611146862 8.348619415 0.114311101 0.032445665 6.123568636 -0.78700459 0.15498666 EAPS(ph)PLMIHS(ph)PQMSQFQSLT(ph)HQSPPQQNVQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 3 EAPS(0.999)PLMIHS(0.993)PQMS(0.19)QFQS(0.134)LT(0.387)HQS(0.297)PPQQNVQPK 65.69 0.0062274 89873000 7436.7 6355 9334.1 9871.5 10545 12951 9319.4 6738.4 10010 9709.2 TRUE FALSE 7730.306658 7446.421815 9577.354314 11824.05324 8752.564667 9943.326524 8588.921076 6648.08277 9649.742055 11611.53185 0.665743914 0.641295388 0.824814025 1.018302614 0.753782083 0.85633202 0.739688888 0.572541406 0.83104815 1 13.50327069 -2.547986205 1.775681525 3.259716398 0.759612623 0.251482656 0.119944235 4252864.16 237581.0231 38616087.24 0.036486022 0.002831482 2.547986205 -2.500103775 EAPS(ph)PTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAPSPTLRR 9 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 EAPS(0.998)PT(0.002)LRR;EAPS(1)PTLRR 135.8 0.00012911 771480000 271900 268570 357990 339380 358430 428370 316820 295930 290470 329270 TRUE FALSE 282634.822 314694.8083 367319.5135 406508.3511 297504.1966 328887.5595 291986.8205 291963.5424 280016.0414 393784.1522 0.717740469 0.799155595 0.932794048 1.032312623 0.755500685 0.835197551 0.741489516 0.741430402 0.711090174 1 18.58704553 EAPSPLMIHS(ph)PQMS(ph)QFQSLTHQSPPQQNVQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPK 32 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 2 EAPS(0.016)PLMIHS(0.983)PQMS(0.545)QFQS(0.359)LT(0.062)HQS(0.034)PPQQNVQPK 111.23 1.65E-06 97566000 24721 61955 68203 54868 82010 85688 61085 61820 74847 69794 TRUE FALSE 25697.00417 72595.28931 69980.42621 65720.72664 68069.96949 65788.26061 56296.99808 60991.40402 72153.27109 83468.79801 0.307863594 0.86972966 0.838402228 0.787368792 0.815513954 0.788177884 0.674467579 0.730709025 0.86443405 1 16.34894938 -5 0.034228757 2.152748882 7.08E-15 0.300764329 0.145636755 1771.410328 4.55159987 237.187847 84.76435299 1.00E-05 5 -2.152748882 EAQLFHPGDLQDLSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAQLFHPGDLQDLSNR 16 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;; 143.67 1.39E-06 468090000 342424 384418 373713 346379 416522 467873 361601 379611 373713 374876 FALSE TRUE 355943.1639 450438.8011 383452.2678 414891.7324 345721.7392 359216.5864 333257.7688 374522.9355 360263.1421 448325.7748 0.793938658 1.004713149 0.855298288 0.92542467 0.771139557 0.801240095 0.74333841 0.835381226 0.803574459 1 18.77418792 3.244777259 24.99791246 0.812214636 0.899866845 0.132129281 0.082023974 221.1218068 889153.7825 0.020971691 0.027701127 1757.022243 -3.244777259 0.087652209 EAQTSFLHLGYLPNQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAQTSFLHLGYLPNQLFR 18 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ; 183.74 6.18E-14 2309700000 1473260 2243510 2242650 2196440 2367020 2816910 2120980 2368530 2232500 2325250 FALSE TRUE 1531425.442 2628815.39 2301095.301 2630889.276 1964674.786 2162725.343 1954732.045 2336783.729 2152152.761 2780838.218 0.550706414 0.945332013 0.827482623 0.94607779 0.706504526 0.777724259 0.702929078 0.840316317 0.773922319 1 21.40708838 -1.230868295 2.788143335 1.00147626 0.793646982 0.245873519 0.111826939 5100083.311 6297511.465 64944.70878 0.026724124 0.058766754 1.230868295 -0.207829278 EARNS(ph)WDSPAFSNDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(1)WDSPAFSNDVIR;EARNS(1)WDSPAFSNDVIR;EARNS(1)WDSPAFSNDVIR 236.38 2.10E-20 737910000 224876 281301 270653 178715 326960 334777 162317 248283 266686 435262 TRUE FALSE 233754.2781 329612.2585 277706.4395 214064.2936 271383.456 257030.1153 149594.1694 244955.1725 257088.023 520543.2553 0.449058317 0.633208202 0.533493493 0.41123248 0.521346599 0.493772828 0.287380862 0.470576018 0.493884073 1 18.98965853 0.672771656 4.212949796 0.999999368 0.473200115 0.776430688 0.084225641 5.702217654 73.0099838 0.084467747 0.021512882 4.707297601 -0.672771656 -0.526799253 EARS(ph)PQPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 81.676 0.01248 14469800000 9563200 7875400 9909800 5227350 12282900 11832000 8040200 8892500 10561200 9522100 TRUE FALSE 9940762.52 9227938.688 10168057.53 6261304.228 10195057.05 9084197.316 7409988.115 8773310.583 10181104.48 11387773.18 0.872932957 0.810337415 0.892892523 0.549826918 0.895263445 0.797714985 0.650696848 0.770414939 0.894038221 1 23.44098233 1.032660696 3.403643967 0.998330803 0.775222522 0.319820706 0.102986646 0.232115804 6.081792612 0.095093042 0.02475833 10.78104097 -1.032660696 -0.223108281 EAS(ph)HVLEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EASHVLEVK 9 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK;EAS(1)HVLEVK 94.887 0.0088301 194652000 57466.6 911944 367299 753136 145657 564546 179782 332572 217962 1708960 TRUE FALSE 59735.42574 1068563.288 376871.1137 902104.0529 120898.2752 433438.7473 165690.2171 328114.4163 210117.5902 2043797.992 0.029227657 0.522832145 0.184397438 0.441386114 0.05915373 0.212075141 0.081069762 0.16054151 0.102807416 1 20.96282118 -1.314402167 4.535258254 1.000619247 0.203424326 0.708651711 0.154005146 0.000919649 0.000139024 0.142213292 0.033495389 0.048483932 1.314402167 -0.797194921 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;EAS(1)PAPLAQGEPGREDLPTR 262.06 1.25E-36 3586570000 1410520 1261060 1395980 1463440 1544990 1843930 1822210 1466060 1390050 1055151 TRUE FALSE 1466208.419 1477637.245 1432360.386 1752904.064 1282373.152 1415705.203 1679380.419 1446409.864 1340022.372 1261887.636 1.16191678 1.170973709 1.135093446 1.389112639 1.016234025 1.12189482 1.330847827 1.146227146 1.061918933 1 20.26715202 1.184133115 3.030684006 1.00738641 1.188385923 0.287533982 0.099702452 0.300563203 4.872261677 0.089811354 0.024712796 15.28034341 -1.184133115 0.180999514 EAS(ph)PAPLAQGEPGREDLPTRLPALGEAHVS(ph)PEVATADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EASPAPLAQGEPGREDLPTRLPALGEAHVSPEVATADK 38 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 2 EAS(0.999)PAPLAQGEPGREDLPT(0.012)RLPALGEAHVS(0.989)PEVATADK 73.719 0.0054034 53606000 35284 22518 24557 20369 41141 41458 43724 34318 34911 24413 TRUE FALSE 36677.03957 26385.29133 25196.97559 24397.9274 34147.86752 31830.0078 40296.79863 33858.02334 33654.55993 29196.25993 1.256223902 0.90372162 0.863020663 0.835652493 1.169597325 1.090208399 1.380204133 1.159669883 1.152701065 1 14.83349595 3.213001497 21.46860296 1.178038408 0.953043021 0.307235821 0.140559319 48.15986537 40451.61363 0.040415821 0.048343569 1633.057575 -3.213001497 -0.224995387 EAS(ph)PLPAESASAGATLRPLLLSGHGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EASPLPAESASAGATLRPLLLSGHGAR 27 1 P35548;D6RIS4 P35548 MSX2 Homeobox protein MSX-2 1 EAS(1)PLPAESASAGATLRPLLLSGHGAR 83.216 0.0056368 130190000 32770 64889 60603 66403 75918 77773 59576 58859 58915 57527 TRUE FALSE 34063.7849 76033.18098 62182.36397 79537.31521 63013.48548 59711.39941 54906.27745 58070.09138 56794.66066 68798.31423 0.495125284 1.105160524 0.903835576 1.156093955 0.915916126 0.867919513 0.798075913 0.844062707 0.825524016 1 16.07008559 2.746499929 4.437506775 0.849950153 0.93936072 0.005948106 0.173028597 0.664992277 34.4193658 0.05320108 0.053630075 557.8275112 -2.746499929 0.089410568 EASDGEVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EASDGEVRR 9 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 85.862 0.023295 310900000 392310 417000 405410 374440 449040 534570 424770 463420 445290 428430 FALSE TRUE 407798.7017 488616.5062 415975.3176 448503.1144 372712.3412 410424.219 391475.4175 457208.6129 429264.0999 512372.6557 0.795902547 0.953635017 0.811860885 0.875345531 0.727424341 0.801026781 0.76404432 0.892336091 0.83779666 1 18.96683396 0.493185536 1.10495322 0.999729875 0.825813398 0.413009405 0.061698635 1.887952525 3.101596859 0.059307989 0.018301842 3.113045983 -0.493185536 -0.173916477 EASELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EASELLR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 106.42 0.040869 0 154970 145173 148562 163039 156174 184497 167398 160434 127096 134549 FALSE TRUE 161088.3353 170105.3335 152433.6478 195287.6276 129627.5993 141650.3678 154276.9073 158283.6446 122521.8398 160911.3005 1.001100201 1.057137274 0.947314746 1.213635258 0.805584188 0.880300932 0.958769875 0.98367016 0.761424707 1 17.29590612 3.221102243 24.99999883 0.906676421 1.047286827 0.394425226 0.094478027 267.8606006 383569.546 0.026723589 0.032011142 1663.804301 -3.221102243 0.140610406 EASEVKPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EASEVKPPR 9 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 87.485 0.012248 125690000 155980 170070 180060 143860 206480 206480 161620 182570 168560 140210 FALSE TRUE 162138.2108 199278.1995 184752.5115 172315.0786 171382.6034 158528.1492 148951.8021 180122.9478 162493.5585 167681.465 0.96694176 1.188433078 1.101806401 1.027633427 1.022072436 0.945412477 0.888302127 1.074197126 0.969060942 1 17.3553637 3.423544818 2.157183129 0.982754139 1.094555319 0.315280371 0.067607233 0.358482327 3.370196367 0.020286071 0.031611102 2651.82474 -3.423544818 0.111801179 EASIDILHSIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EASIDILHSIVK 12 0 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 113.61 0.0011473 298320000 863610 834070 934220 966380 1144910 1152770 1132940 976980 971380 843330 FALSE TRUE 897705.9897 977315.0343 958566.5407 1157527.08 950298.6072 885056.6379 1044137.202 963885.1811 936420.2235 1008564.367 0.890082992 0.969016025 0.950426737 1.147697775 0.942229012 0.877541054 1.035270764 0.955700214 0.928468479 1 19.94387173 4.226302057 0.002528006 1.786467429 0.149111566 0.009093319 0.073659782 1065996.013 494.1116039 157530.016 162522.1742 16838.44788 -4.226302057 -1.637355863 EASIDILHSIVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EASIDILHSIVKR 13 1 O00231;O00231-2;J3QRY4 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 113.07 0.00055245 215910000 134200 145790 157780 126240 197500 189920 128440 141680 168490 192970 FALSE TRUE 139498.3196 170828.2984 161891.8764 151209.8952 163929.0205 145813.9583 118372.5372 139781.0113 162426.0778 230778.7769 0.604467714 0.740225339 0.701502446 0.655215775 0.710329705 0.631834349 0.512926443 0.60569266 0.703817223 1 17.81615103 -1.732995652 4.713218295 1.019424096 0.647798997 0.728464635 0.063738409 0.014242446 0.000806836 0.06756324 0.015764075 0.018492871 1.732995652 -0.371625099 EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EASRPPEEPSAPSPTLPAQFK 21 1 A0A0C4DFX9;Q9H3P2;H0Y3X6;Q9H3P2-7 A0A0C4DFX9 NELFA Negative elongation factor A 1 EASRPPEEPSAPS(0.995)PT(0.005)LPAQFK;EASRPPEEPS(0.001)APS(0.961)PT(0.037)LPAQFK;EASRPPEEPS(0.002)APS(0.962)PT(0.036)LPAQFK;EASRPPEEPSAPS(1)PTLPAQFK 246 1.76E-30 3510620000 2457760 2096320 2439500 2051800 2942210 3002110 2732040 2386200 2656260 2021500 TRUE FALSE 2554794.263 2456346.653 2503075.374 2457639.916 2442094.195 2304915.45 2517895.566 2354216.892 2560661.721 2417574.221 1.056759391 1.016037742 1.035366506 1.016572685 1.010142387 0.953400078 1.041496697 0.973793016 1.059186394 1 21.20512875 5.059827366 0.701855317 1.004129819 1.102664633 0.182142827 0.029362427 6.905608776 1.886405714 0.010810026 0.597203203 114769.7317 -5.059827366 0.098534814 EASSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EASSRPK 7 1 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 66.994 0.060527 76619000 111780 99272 120280 89943 143050 131720 147710 107650 124940 104900 FALSE TRUE 116193.1607 116321.1938 123414.5956 107733.4569 118734.4121 101130.0262 136132.1042 106207.1278 120443.4338 125453.1466 0.926187695 0.92720826 0.9837505 0.858754522 0.946444273 0.806117893 1.085123075 0.846587995 0.960067062 1 16.93678913 2.266282018 24.99996285 0.952455082 0.911888593 0.138253465 0.072066082 616.7921763 556238.6578 0.023953203 0.020036264 184.6213908 -2.266282018 -0.040566489 EATAQKPTGSVGSTVTT(ph)PPPLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 EATAQKPTGSVGST(0.001)VT(0.033)T(0.967)PPPLVR;EATAQKPTGSVGST(0.005)VT(0.033)T(0.962)PPPLVR 151.31 1.20E-07 998440000 1440500 1216930 1477550 1266870 1682240 1828900 1649560 1565160 1570040 1331100 TRUE FALSE 1497372.052 1425928.261 1516056.167 1517453.105 1396293.446 1404165.692 1520263.177 1544181.59 1513534.567 1591903.56 0.940617315 0.895737843 0.952354279 0.953231806 0.877121882 0.88206706 0.954997033 0.970022073 0.950770264 1 20.60232151 2.050809374 8.782470104 0.968354869 0.917361505 0.464858721 0.02774632 0.288069641 46.03280633 0.010855506 0.007998824 112.4111457 -2.050809374 -0.050993363 EATDAIGHLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EATDAIGHLDR 11 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;; 220.29 9.25E-12 7220510000 7371830 8344270 8177640 8176810 8836050 9804900 8522670 8219450 7594550 7242400 FALSE TRUE 7662875.541 9777333.463 8390756.016 9794158.613 7334101.377 7527860.57 7854640.856 8109281.717 7321223.629 8661409.616 0.8847146 1.128838595 0.968751784 1.130781137 0.846756094 0.869126494 0.906854797 0.936254268 0.845269298 1 23.04617041 3.225587253 24.99996705 0.899219416 1.031203496 0.382521591 0.079349091 214.3883624 413130.5413 0.021168743 0.025449159 1681.075634 -3.225587253 0.13198408 EATDLLHDALQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EATDLLHDALQIR 13 0 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 0 ; 100.55 0.0023493 64658000 75421 86390 91711 88015 91699 109248 95824 90044 86062 94514 FALSE TRUE 78398.67932 101226.8105 94101.064 105424.1043 76112.03673 83876.80767 88313.06449 88837.10746 82964.64543 113032.2087 0.693595925 0.895557219 0.832515484 0.932690828 0.673365916 0.742061122 0.781308845 0.785945072 0.73399119 1 16.7863744 4.778090756 22.69914891 0.807346058 0.69359498 0.125726679 0.094853171 15719.10431 9025659.413 0.021813136 5.672737109 59991.64304 -4.778090756 -0.113751078 EATGLS(ph)PQAAQEKDGIVIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EATGLSPQAAQEKDGIVIVK 20 1 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 EAT(0.01)GLS(0.99)PQAAQEKDGIVIVK;EATGLS(1)PQAAQEKDGIVIVK 174.53 1.98E-12 410870000 410750 345930 371250 270110 482760 408780 404160 336650 449510 273640 TRUE FALSE 426966.7272 405340.7865 380925.08 323536.9518 400700.6276 313847.0401 372480.8831 332137.7574 433332.2229 327254.5188 1.304693144 1.238610205 1.164002506 0.988640135 1.224431152 0.959030424 1.138199358 1.014921837 1.324144352 1 18.32005359 4.208553785 2.490448682 1.090707299 1.289638145 0.301324353 0.108721216 0.322027813 3.928894237 0.026066946 0.085073905 16164.18399 -4.208553785 0.198930847 EATNPPVIQEEKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 201.16 1.66E-08 978980000 1318620 609600 794260 539400 1117520 1109950 977860 772040 902740 438508 FALSE TRUE 1370680.136 714294.058 814959.0681 646091.7101 927564.3496 852180.934 901212.778 761692.0666 870250.5637 524425.2469 2.61368068 1.36205124 1.554004261 1.23199963 1.768725581 1.624980756 1.718477101 1.452432108 1.65943682 1 19.00037762 8 0.042660389 1.14E-10 4.28951013 0.303324753 0.339057805 1006.29693 3.260421293 86.20817842 303.0360109 99999999.93 -8 4.28951013 EATNPPVIQEEKPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EATNPPVIQEEKPKK 15 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 198.15 4.54E-09 145300000 224930 107340 163800 108650 250030 216490 201960 144040 192330 77467 FALSE TRUE 233810.4101 125774.81 168068.7626 130140.6457 207529.9899 166213.4784 186129.8475 142109.3794 185408.0809 92645.17545 2.523719222 1.357596976 1.81411241 1.40472124 2.240051777 1.794086714 2.009061417 1.533910198 2.001270762 1 16.49942823 -1.511548285 2.750166326 0.962860722 1.819292475 0.347721312 0.347781694 21729250.46 22596359.8 6057803.452 0.084046197 0.03079298 1.511548285 0.856431753 EATNTTSEPSAPSQDLLDLS(ph)PSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.995)PS(0.005)PR 113.33 0.00093187 111630000 66127 75859 74124 69045 83126 96170 80486 83886 79111 89988 TRUE FALSE 68737.74502 88887.19315 76055.73233 82701.89492 68996.27221 73835.97497 74177.29701 82761.64538 76263.81056 107619.4257 0.638711316 0.825940044 0.706710074 0.768466236 0.641113552 0.686084083 0.689255648 0.769021437 0.708643538 1 16.71557899 -0.503480751 0.800929744 1.017939289 0.715963041 0.701398609 0.055762579 9.760518563 4.256089886 0.588986061 0.017826979 0.313703417 0.503480751 -0.301976248 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EATNTTSEPSAPSQDLLDLSPSPR 24 0 J3KQU4;I3L4I4;O75674;O75674-2;O75674-3;I3NI44 J3KQU4 TOM1L1 TOM1-like protein 1 1 EATNTTSEPSAPSQDLLDLS(0.001)PS(0.999)PR;EATNTTSEPSAPSQDLLDLS(0.003)PS(0.997)PR 135.19 1.91E-05 471220000 469350 563860 552400 534970 651230 705440 539550 524230 507800 568860 TRUE FALSE 487880.3004 660698.5688 566795.9978 640785.4693 540534.1572 541612.251 497258.6611 517203.5543 489524.3772 680317.2255 0.71713648 0.971162487 0.833134862 0.941892172 0.794532517 0.796117209 0.730921756 0.760238805 0.719553113 1 19.37584809 3.0757467 9.646855157 0.780395048 0.8709665 0.078078338 0.097568162 0.589234176 70.07552603 0.026004133 0.031101438 1190.547424 -3.0757467 0.090571452 EATPDGGEDS(ph)DS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EATPDGGEDSDS 12 0 D6RJC6;A0A087WYP9;A6NFV8;Q96EV8-3;Q96EV8 D6RJC6 DTNBP1 Dysbindin 1 EATPDGGEDS(0.976)DS(0.024) 182.93 0.0001182 0 50241 62945 59809 63493 56428 75044 65812 58287 65197 67041 TRUE FALSE 52224.55347 73755.31411 61367.67167 76051.72589 46836.38872 57616.1683 60653.48347 57505.7581 62850.57271 80176.40037 0.651370643 0.919913014 0.765408167 0.948555005 0.584166768 0.718617549 0.756500456 0.717240458 0.783903648 1 16.29089003 0.953918974 20.66800425 1.000000002 0.759815644 0.32678536 0.10364302 1279.84151 574029.8069 0.096044874 0.024011218 8.993297787 -0.953918974 -0.240184358 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EATSDPSRTPEEEPLNLEGLVAHR 24 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 EAT(0.079)S(0.066)DPS(0.427)RT(0.427)PEEEPLNLEGLVAHR;EAT(0.018)S(0.076)DPS(0.465)RT(0.441)PEEEPLNLEGLVAHR 136.89 1.06E-05 157044000 55587 59970 61546 61690 62352 80430 71305 66978 65770 70440 TRUE FALSE 57781.61768 70269.381 63149.93932 73892.09787 51753.42931 61751.35143 65715.92778 66080.26946 63402.95055 84241.36934 0.68590549 0.834143385 0.749630969 0.877147397 0.614346962 0.733028818 0.780090926 0.784415899 0.752634377 1 16.36224127 -0.904686977 0.693227533 1.042126095 0.757834253 0.526579802 0.069130877 24.09765369 6.42282775 2.303856434 0.023930688 0.124541193 0.904686977 -0.284291842 EATTDFTVDSRPLTQVGGDHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 333.36 4.69E-81 4370460000 2697240 2213180 2718490 2024810 3073190 2916360 2700380 2596920 2711980 2331180 FALSE TRUE 2803729.118 2593276.449 2789336.083 2425311.375 2550810.262 2239079.588 2488717.159 2562112.535 2614376.37 2787930.088 1.005666939 0.930179871 1.000504315 0.869932638 0.914947714 0.803133335 0.892675598 0.919001716 0.937748181 1 21.41076295 3.739583866 24.9994947 0.898727549 0.973923326 0.295612927 0.051073065 108.0035439 2638656.829 0.01296104 0.021798831 5490.145643 -3.739583866 0.075195777 EATWVVDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EATWVVDVK 9 0 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ;;; 166.16 0.0001418 396417000 566349 535958 550747 497830 676047 681915 586752 569380 552540 579173 FALSE TRUE 588708.8958 628004.6173 565099.9193 596299.2881 561132.7724 523550.5758 540760.845 561748.3924 532654.1933 692650.8604 0.849935992 0.906668357 0.815851032 0.86089446 0.810123548 0.755865048 0.780712009 0.811012336 0.769008203 1 19.4017688 3.68292543 1.418037967 0.807497933 0.872308952 0.036288125 0.068275125 0.898140334 3.501711808 0.01980799 0.046561155 4818.650526 -3.68292543 0.064811019 EAVAHENNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAVAHENNR 9 0 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 ; 101.65 0.003842 145026000 139751 171445 171441 142141 173272 208328 159715 162747 162649 169117 FALSE TRUE 145268.4774 200889.3451 175908.8933 170256.0656 143819.2873 159946.9792 147196.121 160565.6427 156795.2943 202252.2382 0.718253992 0.993261419 0.869750045 0.84180065 0.711088731 0.790829217 0.72778488 0.793888088 0.775246275 1 17.62579614 3.464763071 24.32215915 0.784026137 0.870717387 0.059891916 0.096752955 288.4403555 567677.1574 0.024624988 0.033367135 2915.835848 -3.464763071 0.08669125 EAVEKEFEPLLNWMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAVEKEFEPLLNWMK 15 1 P14625 P14625 HSP90B1 Endoplasmin 0 ; 188.44 2.73E-07 1102960000 1378890 1103430 1387860 914720 2226400 1772830 1218010 1321200 1590130 1135790 FALSE TRUE 1433329.642 1292935.519 1424028.772 1095648.886 1847957.323 1361117.1 1122539.194 1303491.475 1532901.532 1358326.304 1.055217467 0.951859295 1.048370165 0.806616851 1.360466419 1.002054584 0.826413499 0.959630592 1.128522305 1 20.37339866 -0.751367594 7.828023256 0.999999673 1.006264459 0 0.148974224 0 0 0.139974279 0.032992254 0.177268841 0.751367594 0.006264786 EAVELPLTHFELYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAVELPLTHFELYK 14 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 214.18 6.97E-12 999279000 2613980 2233450 2596980 2109230 3306260 3373830 2989380 2717820 2843700 2230850 FALSE TRUE 2717181.949 2617027.664 2664659.432 2526429.399 2744263.106 2590309.113 2755064.584 2681392.068 2741355.792 2667942.345 1.018456022 0.980916124 0.998769496 0.946958019 1.028606601 0.970901458 1.032655218 1.005041235 1.027516879 1 21.34729606 2.234617127 24.99999462 1.016040761 0.990412428 0.222645501 0.023367202 146.7387022 930251.9556 0.00797061 0.006106343 171.639455 -2.234617127 -0.025628334 EAVFFQSHSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAVFFQSHSAR 11 0 P36954 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 140.24 3.87E-05 87822000 79739 93490 85425 65309 115080 98037 100470 83144 84879 98145 FALSE TRUE 82887.15729 109546.1802 87651.24568 78226.92527 95518.74271 75269.39252 92594.89887 82029.59068 81824.22137 117374.6337 0.706176068 0.933303703 0.746764807 0.666472157 0.813793745 0.641274781 0.78888339 0.698869833 0.697120143 1 16.84076113 -1.16882307 4.516876897 1.000044247 0.744724576 0.476536349 0.080602065 3.52E-05 6.48E-06 0.075315007 0.017748796 0.067791763 1.16882307 -0.255319671 EAVILPIKFPHLFTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAVILPIKFPHLFTGK 16 1 O75351;I3L4J1;Q9UN37 O75351;I3L4J1 VPS4B;VPS4A Vacuolar protein sorting-associated protein 4B;Vacuolar protein sorting-associated protein 4A 0 ; 165.8 4.15E-09 259640000 599020 446750 559520 475460 658200 683360 670010 567950 625700 393280 FALSE TRUE 622669.7721 523475.8373 574101.5509 569504.5689 546319.3991 524659.9964 617492.8655 560337.5592 603181.1792 470335.6862 1.32388375 1.112983455 1.220620862 1.21084703 1.16155209 1.115501145 1.312876917 1.191356675 1.282448253 1 18.84333127 4.763382454 23.31081543 1.190611401 1.323884159 0.193945791 0.085754458 4880.397527 4583119.347 0.018810353 1.125586857 57993.9185 -4.763382454 0.133272758 EAVIT(ph)PVASATQSVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAVITPVASATQSVSR 16 0 P28749;P28749-2;H0YE05 P28749 RBL1 Retinoblastoma-like protein 1 1 EAVIT(0.999)PVAS(0.001)ATQSVSR 141.1 1.83E-05 96929000 98737 109450 108880 104170 124010 126160 119020 103830 96761 124590 TRUE FALSE 102635.213 128247.1861 111717.5022 124774.5151 102930.8245 96861.25197 109690.9014 102438.3287 93278.59051 149001.0251 0.688822194 0.860713448 0.749776736 0.837407092 0.69080615 0.650071044 0.736175482 0.687500832 0.626026502 1 17.18496273 3.224127639 24.9989263 0.711128465 0.787189193 0.033632071 0.107246983 512.9464308 888456.998 0.028312534 0.033986258 1675.435215 -3.224127639 0.076060728 EAVLDVIPTDIHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EAVLDVIPTDIHQR 14 0 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;;;; 162.67 4.40E-06 21445509000 6697198 7768722 7708849 7826851 8982634 9772889 7969448 7741830 7736009 8164129 FALSE TRUE 6961608.548 9102939.571 7909747.938 9374978.767 7455769.081 7503283.639 7344781.841 7638063.432 7457591.547 9763733.766 0.713006798 0.932321568 0.810115078 0.960183777 0.763618638 0.768485071 0.752251343 0.782289195 0.763805295 1 23.21900153 EAVREGS(ph)PANWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAVREGSPANWK 12 1 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EAVREGS(1)PANWK 58.885 0.062348 175270000 141010 131720 147970 85577 194240 193070 96393 128470 162200 182280 TRUE FALSE 146577.1837 154341.8854 151826.2198 102503.8752 161223.1542 148232.4185 88837.46478 126748.0698 156362.4537 217994.276 0.672390057 0.70800889 0.696468836 0.470213609 0.739575172 0.679983077 0.407522007 0.581428431 0.717277795 1 17.73393073 0.894185163 4.048275822 0.999870071 0.614840606 0.558801197 0.101782432 0.391724164 13.15451379 0.100984136 0.025797675 7.837637313 -0.894185163 -0.385029465 EAVTEILGIEPDREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EAVTEILGIEPDREK 15 1 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;;;; 242.26 5.86E-18 1738553000 1079970 761442 1006552 824332 1446779 1222151 1275854 1084998 1105380 754547 FALSE TRUE 1122608.05 892213.7403 1032783.572 987382.4092 1200856.022 938324.9521 1175849.23 1070455.377 1065597.59 902386.038 1.244044126 0.988727333 1.144503049 1.094190699 1.33075643 1.039826541 1.303044573 1.186249932 1.180866663 1 19.78338522 EAVTHIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAVTHIGR 8 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;;; 186.3 0.00020822 1682940000 1666810 1927110 1982830 1980440 2108070 2443390 2113390 2006490 1934530 1981990 FALSE TRUE 1732616.946 2258076.152 2034504.179 2372165.121 1749741.014 1875949.702 1947736.969 1979596.284 1864906.643 2370322.993 0.730962384 0.952644917 0.858323606 1.000777163 0.738186745 0.791432099 0.821717958 0.835158875 0.786773216 1 21.17665223 4.77913157 22.91942615 0.854830507 0.73096131 0.167581594 0.087002762 16327.05769 9222933.256 0.020170298 5.959448464 60135.58912 -4.77913157 -0.123869197 EAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.57)RIS(0.43)EDETERNGDDGTHDK 157.12 2.12E-09 324230000 44579 39119 43163 24542 56277 61683 50099 50794 54850 44047 TRUE FALSE 46339.01334 45837.38395 44287.86324 29396.33435 46711.05564 47358.05806 46172.10947 50113.18951 52875.95921 52677.16632 0.87967931 0.8701566 0.840741185 0.558046995 0.886741997 0.899024404 0.876510881 0.9513266 1.003773796 1 15.68489012 2.008656482 1.039517052 1.000354664 0.803151055 0.414124336 0.090696709 0.55163341 1.098511946 0.075013215 0.035404601 102.0132261 -2.008656482 -0.197203609 EAVVDLHADDSRIS(ph)EDETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.069)RIS(0.931)EDETER;EAVVDLHADDS(0.009)RIS(0.991)EDETER 168.55 7.30E-12 288570000 259880 260030 264920 275640 276370 310090 306590 270250 256790 224210 TRUE FALSE 270140.2631 304688.1297 271824.0328 330160.7693 229392.7261 238076.297 282558.6747 266627.7408 247548.1781 268139.6567 1.007461061 1.13630387 1.013740512 1.231301529 0.855497202 0.88788171 1.053774284 0.994361461 0.923206142 1 18.03262508 3.229690635 24.99997925 0.959027708 1.094033246 0.440306304 0.079711196 190.6694347 537400.0549 0.022939354 0.027802131 1697.03436 -3.229690635 0.135005538 EAVVDLHADDSRISEDET(ph)ERNGDDGTHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 EAVVDLHADDS(0.305)RIS(0.305)EDET(0.39)ERNGDDGTHDK 98.683 0.00089467 113290000 48345 44533 55411 37211 61516 72462 53913 50133 53212 53265 TRUE FALSE 50253.69793 52181.19633 56855.05618 44571.22474 51059.53229 55633.79867 49687.15818 49461.04914 51296.91051 63701.25693 0.788896489 0.819154893 0.892526442 0.699691449 0.8015467 0.873354803 0.780002791 0.776453268 0.805273129 1 15.95903422 -2.202141461 2.114126957 1.527050098 0.803003089 0.576755461 0.050337012 5536924.609 1018900.408 13955924.62 0.012040694 0.006278538 2.202141461 -0.724047009 EAWPHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAWPHIK 7 0 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 84.244 0.021688 752020000 1529320 1328000 1543700 1329310 1880630 1866660 1690760 1590560 1641210 1354630 FALSE TRUE 1589698.734 1556073.67 1583930.09 1592243.55 1560961.184 1433156.505 1558233.813 1569241.145 1582143.173 1620043.813 0.981268977 0.960513325 0.977708182 0.982839808 0.963530228 0.884640584 0.961846711 0.968641177 0.976605176 1 20.6276014 1.032819535 1.728537384 0.999232782 0.958702971 0.183938505 0.026494026 0.646522617 3.947610022 0.026391928 0.007609626 10.78498473 -1.032819535 -0.040529811 EAYALCHCLPVLSTDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAYALCHCLPVLSTDKFK 18 1 Q7L5N1;E7EM64 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 57.52 0.054821 437770000 224290 191650 235990 179510 260560 279800 219590 210160 215900 251970 FALSE TRUE 233145.1424 224564.3967 242140.0933 215016.5422 216270.1043 214820.6904 202377.962 207343.149 208129.8012 301338.6972 0.773697983 0.745222564 0.803547953 0.713537771 0.717697748 0.712887831 0.671596326 0.688073423 0.690683948 1 18.20102643 -1.044014913 4.67943115 1.000009258 0.721425238 0.822874696 0.038382519 4.16E-06 8.49E-07 0.041188062 0.009707793 0.090361844 1.044014913 -0.27858402 EAYPEEAYIADLDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAYPEEAYIADLDAK 15 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;; 230.14 8.57E-13 147335000 158205 110406 148186 104698 181747 177652 176021 144648 155985 101174 FALSE TRUE 164451.0556 129367.3717 152047.8489 125406.9519 150853.7099 136395.0153 162224.0141 142709.2302 150371.1303 120997.1082 1.359132115 1.069177384 1.256623825 1.03644586 1.246754671 1.127258472 1.340726373 1.179443313 1.242766315 1 16.88461304 -2.329254658 2.10995256 5.24E-06 1.201970638 0.272927251 0.100862108 2029877.838 305497.2934 9645932.821 0.023345628 0.004685386 2.329254658 1.201965399 EAYPGDVFYLHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EAYPGDVFYLHSR 13 0 P25705;P25705-2;P25705-3 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;;; 145.81 4.11E-05 2728830000 1875300 2528970 2117410 2453580 1988770 3186040 2038890 1775000 1934420 2552470 FALSE TRUE 1949338.292 2963300.925 2172591.444 2938890.801 1650719.586 2446130.495 1879076.474 1751209.028 1864800.602 3052577.627 0.638587623 0.970753667 0.711723569 0.962757106 0.540762525 0.801332773 0.615570414 0.573682062 0.610893753 1 21.54159655 3.234944436 24.99999804 0.662982656 0.823853073 0.127789758 0.15759616 144.2480162 997241.1632 0.041649088 0.051651671 1717.688609 -3.234944436 0.160870418 EAYSGCSGPVDSECPPPPS(ph)SPVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.566)S(0.434)PVHK 110.61 0.0012473 244650000 97793 81633 99903 84434 108220 123070 121270 100620 121250 79004 TRUE FALSE 101653.9432 95652.83273 102506.5543 101134.7932 89824.80306 94488.85764 111764.5405 99271.35348 116886.2362 94483.32118 1.075892992 1.012377968 1.084916925 1.070398372 0.95069481 1.000058597 1.182902327 1.050675953 1.237109732 1 16.52777206 2.25370862 24.94944026 1.116443235 1.031882137 0.254610306 0.071469765 318.3090738 524268.3667 0.023776818 0.019819738 179.3529896 -2.25370862 -0.084561099 EAYSGCSGPVDSECPPPPSS(ph)PVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EAYSGCSGPVDSECPPPPSSPVHK 24 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 EAYSGCSGPVDSECPPPPS(0.29)S(0.71)PVHK;EAYSGCSGPVDSECPPPPS(0.446)S(0.554)PVHK 119.37 0.00023003 506790000 152460 141214 145464 140126 189066 211378 195241 167122 160401 95365 TRUE FALSE 158479.2385 165466.406 149254.9113 167842.5046 156928.6289 162288.663 179937.5003 164882.0029 154628.1993 114049.9459 1.389559963 1.450824064 1.308680247 1.471657906 1.37596408 1.422961333 1.577707897 1.445699967 1.355793711 1 16.79930624 0.811785492 3.426942251 1.000061964 1.433417994 0.790727946 0.066110519 0.502976362 8.530722929 0.064800258 0.016749057 6.483141371 -0.811785492 0.43335603 EAYVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EAYVHK 6 0 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 74.743 0.079523 1391410000 1820060 1540580 1878440 1507770 2452340 2376550 2071640 1883960 1926390 1560860 FALSE TRUE 1891917.374 1805162.631 1927393.69 1806002.406 2035492.123 1824632.279 1909259.444 1858708.598 1857059.6 1866680.633 1.013519582 0.967044174 1.032524609 0.96749405 1.09043405 0.977474265 1.022809907 0.995729299 0.994845914 1 20.83204369 4.237141324 24.9999745 1.01009589 0.990281886 0.051622201 0.034086467 111.8004261 1969441.071 0.007785375 0.018395678 17263.99591 -4.237141324 -0.019814004 ECADLWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ECADLWPR 8 0 J3KTJ3;P62829 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;; 98.009 0.019897 663080000 1403640 1688540 1689770 1562120 1972900 1948100 1712200 1684150 1606840 1804080 FALSE TRUE 1459056.791 1978533.61 1733806.794 1871102.674 1637547.163 1495683.299 1577993.29 1661576.724 1549010.142 2157554.935 0.676254758 0.917025832 0.803597983 0.867232923 0.758982836 0.693230691 0.731380353 0.77012024 0.717947023 1 21.04096586 3.207250149 24.12076874 0.760481094 0.822354164 0.012462579 0.098649249 331.7896766 255600.6725 0.026261294 0.031392004 1611.573619 -3.207250149 0.06187307 ECFGACLFTCYDLLRPDVVLETAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ECFGACLFTCYDLLRPDVVLETAWR 25 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 265.89 1.97E-45 1747785000 275951 270305 294321 333052 349013 369330 349547 280474 308253 281704 FALSE TRUE 286845.7586 316727.7811 301991.247 398928.6915 289687.8949 283558.7048 322148.5928 276714.7048 297159.0347 336898.5053 0.851430784 0.940128187 0.896386426 1.184121287 0.859866964 0.841673977 0.956218528 0.821359254 0.882043197 1 18.3619545 ECGLWLSLGGFHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ECGLWLSLGGFHER 14 0 Q86X76-2;Q86X76-4;Q86X76;Q86X76-5;Q86X76-3 Q86X76-2 NIT1 Nitrilase homolog 1 0 143.93 8.99E-06 177120000 168910 228140 238800 237610 251210 286060 239040 239230 258390 260810 FALSE TRUE 175578.6972 267321.2703 245023.3242 284608.5488 208509.4139 219626.9003 220303.4202 236023.5132 249090.5944 311910.726 0.562913304 0.857044173 0.785555942 0.912467976 0.668490682 0.70413385 0.706302803 0.756702138 0.798595796 1 18.25077364 0.75381594 2.349682178 0.999914417 0.749422948 0.408598301 0.092065837 1.109588267 8.98125938 0.085472957 0.023055117 5.673041231 -0.75381594 -0.250491469 ECHGLVDALVTSINHALDAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECHGLVDALVTSINHALDAGK 21 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 252.31 1.42E-36 387740000 546220 564010 724500 611220 828890 912200 847650 762700 758360 605030 FALSE TRUE 567785.1874 660874.3301 743381.0652 732117.4917 687995.5739 700355.3745 781208.9781 752477.254 731066.7717 723574.0445 0.784695349 0.913347204 1.027373868 1.011807288 0.950829537 0.967911135 1.079653125 1.039945061 1.010355163 1 19.46478113 4.579320862 2.254663219 1.014187 0.763409723 0.805093112 0.034668419 0.195099329 1.472154459 0.009860842 0.084559541 37959.53308 -4.579320862 -0.250777277 ECHLNADTVSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ECHLNADTVSSK 12 0 P63010;P63010-2;P63010-3;A0A087X253 P63010 AP2B1 AP-2 complex subunit beta 0 ;;; 172.57 3.54E-05 2824440000 3425110 3098060 3643060 3150670 4206720 4508450 3901330 3504280 3693300 3120210 FALSE TRUE 3560335.988 3630127.705 3738001.136 3773863.122 3491663.237 3461430.814 3595533.56 3457310.858 3560378.854 3731555.409 0.954115803 0.972818921 1.001727357 1.011337822 0.935712553 0.927610724 0.963548217 0.926506638 0.954127291 1 21.83134568 3.223837852 24.999753 0.945987083 0.985324717 0.293100366 0.024881556 248.2028526 421455.9555 0.007044584 0.008453816 1674.317636 -3.223837852 0.039337634 ECINAAPDS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ECINAAPDSPSK 12 0 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.689)PS(0.311)K;ECINAAPDS(1)PSK;ECINAAPDS(0.963)PS(0.037)K;ECINAAPDS(0.977)PS(0.023)K;ECINAAPDS(0.965)PS(0.035)K;ECINAAPDS(1)PSK 244.05 2.34E-16 3025750000 6521150 3363810 4422330 3760990 5578180 6645960 6148150 4646320 4930520 2749720 TRUE FALSE 6778610.037 3941518.201 4537579.553 4504902.597 4630002.956 5102536.51 5666241.938 4584043.68 4753071.548 3288474.987 2.061323277 1.198585428 1.37984311 1.369906298 1.407948357 1.551642184 1.723060677 1.393972494 1.445372571 1 21.64898727 0.53670572 1.594220553 1.000289616 1.496227581 0.312537371 0.225622539 2.863092208 8.485376128 0.203867858 0.0583264 3.441166769 -0.53670572 0.495937965 ECINAAPDS(ph)PSKQLPDQISFFSGNPSVEIVHGIMHLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECINAAPDSPSKQLPDQISFFSGNPSVEIVHGIMHLYK 38 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 ECINAAPDS(0.5)PS(0.5)KQLPDQISFFSGNPSVEIVHGIMHLYK;ECINAAPDS(0.5)PS(0.5)KQLPDQISFFSGNPSVEIVHGIMHLYK 197.68 1.60E-30 619450000 917776 429048 631038 366970 1030770 906070 682989 649578 753730 526190 TRUE FALSE 954010.5052 502733.6565 647483.3687 439555.5707 855560.0836 695648.9741 629454.5375 640871.4694 726603.4045 629286.856 1.516018484 0.798894259 1.028916086 0.698497937 1.359570878 1.105456069 1.000266463 1.018409114 1.154645767 1 19.26335828 3.226416473 24.9998795 1.093950959 0.996770678 0.039356363 0.222812425 834.8861829 1718691.132 0.062100524 0.074747816 1684.28846 -3.226416473 -0.097180281 VRHFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_MDA-MB-175_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(0.333)QS(0.333)EET(0.333)GNEVFGALNEEQPLPR 83.362 0.0088186 75944000 28253 24087 34082 19044 60240 46877 24421 35923 47281 70049 TRUE FALSE 29368.45026 28223.75488 34970.20492 22810.84636 50000.42632 35990.52718 22506.81821 35441.51094 45579.36605 83773.76038 0.350568604 0.336904476 0.417436256 0.272291064 0.596850686 0.429615753 0.268661907 0.423062195 0.544076878 1 16.35421081 0.796877938 2.046652399 0.999502462 0.385030807 0.8133312 0.088577287 0.297066033 2.131369838 0.083788334 0.023112761 6.264377749 -0.796877938 -0.614471655 ECLIDPDLTQYAIIMLDEAHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ECLIDPDLTQYAIIMLDEAHER 22 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 0 ;; 132.45 1.06E-05 68424000 62426 98777 87857 96249 96340 119272 91435 96302 90351 98535 FALSE TRUE 64890.62668 115741.1814 90146.6256 115286.7649 79964.16121 91572.88558 84268.08578 95011.22921 87099.28516 117841.0467 0.550662341 0.982180527 0.764984936 0.978324346 0.678576468 0.777088189 0.715099604 0.806265999 0.739125183 1 16.84648262 -1.024543985 4.418845804 1.000009567 0.78462199 0.227407131 0.122616029 14442185.05 3348533.11 1469.401259 0.026085374 0.094505267 1.024543985 -0.215387577 ECLPLIIFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ECLPLIIFLR 10 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 155.75 2.83E-05 176860000 142220 261670 238590 255000 296180 323820 270970 264390 215220 271060 FALSE TRUE 147834.9554 306609.787 244807.8514 305438.2389 245835.4294 248617.7125 249730.6634 260846.2845 207474.2742 324169.0172 0.456042828 0.945833102 0.755185839 0.942219098 0.758355723 0.766938539 0.770371782 0.804661367 0.640018827 1 18.30638668 4.752898152 24.49715652 0.810019501 0.456042505 0.518512872 0.10490348 1469.78705 2511225.584 0.023017021 0.482391707 56610.65132 -4.752898152 -0.353976996 ECLQALEFLHANQVIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ECLQALEFLHANQVIHR 17 0 Q13177;H7C1X3 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 156.17 4.24E-08 354140000 732390 581670 699560 623250 800260 774480 806180 710760 772590 537380 FALSE TRUE 761305.3227 681567.2977 717791.1083 746526.9898 664232.091 594618.7574 742989.505 701233.4248 744784.6368 642669.3222 1.184598823 1.060525645 1.116890263 1.161603587 1.033551888 0.925232832 1.156099224 1.091126339 1.158892468 1 19.29371708 4.746859646 23.11422281 1.082676764 1.184598975 0.158320161 0.072937686 725.8608659 2021506.971 0.017460404 0.188388966 55828.97394 -4.746859646 0.101922211 ECPFLHIDPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ECPFLHIDPESK 12 0 O95639;C9K0K2;B7Z7B0;H7C016;O95639-3;O95639-2 O95639 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 0 73.466 0.039122 74367000 139510 133950 133300 132160 157010 203430 160420 147570 148210 134890 FALSE TRUE 145017.9625 156954.8705 136773.9075 158300.8535 130321.4963 156186.4655 147845.8612 145592.0655 142875.9511 161319.1129 0.898950905 0.972946526 0.847846886 0.981290132 0.807849076 0.968183266 0.916480748 0.902509708 0.885672804 1 17.29955785 ECPGIEPVCVDLGDWEATER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECPGIEPVCVDLGDWEATER 20 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ; 151.99 1.62E-07 89826000 56598 68269 65701 72005 70493 86895 64663 59919 66673 69197 FALSE TRUE 58832.53274 79993.66969 67413.22203 86247.37409 58510.62504 66714.95316 59594.54509 59115.88381 64273.45175 82754.82729 0.710925691 0.966634483 0.814613772 1.042203542 0.707035794 0.80617597 0.720133762 0.714349673 0.776673142 1 16.33655585 3.197057984 24.99989955 0.765697996 0.884599683 0.128508008 0.114647237 218.0859164 131367.5186 0.030640806 0.036623105 1574.193025 -3.197057984 0.118901686 ECPPHAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECPPHAEQR 9 0 J3QT73;A0A087X1P5;J3KQ34;Q9H9Q2-2;Q9H9Q2 J3QT73 COPS7B COP9 signalosome complex subunit 7b 0 ; 161.17 6.47E-05 443520000 282700 327720 305040 309310 360520 404980 340260 322860 294970 355700 FALSE TRUE 293861.2143 384003.3607 312989.593 370490.5948 299238.9392 310929.5325 313589.5321 318532.5898 284354.0873 425392.6047 0.690800007 0.902703424 0.735766418 0.870938025 0.703441799 0.73092369 0.737176737 0.748796726 0.668450942 1 18.69843543 -1.042218627 4.504923144 1.000011724 0.758014544 0.515420051 0.071380864 7.95E-06 1.69E-06 0.065405131 0.015415391 0.090736364 1.042218627 -0.24199718 ECPSDECGAGVFMASHFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 ECPSDECGAGVFMASHFDR 19 0 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;;;;;;;;;;; 336.04 1.85E-75 28669490000 4509342 5934497 5620854 5568559 6311462 7284414 5825810 5913132 5898713 5917069 FALSE TRUE 4687374.304 6953700.696 5767338.073 6670003.35 5238641.944 5592719.245 5369167.789 5833876.137 5686419.471 7076405.381 0.662394825 0.982660026 0.815009565 0.942569425 0.740297038 0.79033336 0.758742257 0.824412371 0.803574578 1 22.75458527 -1.596724278 2.677051314 1.015154042 0.817499834 0.287380936 0.087963911 12220336.31 11234357.96 1302579.087 0.020058481 0.025309043 1.596724278 -0.197654207 ECREPELGLEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ECREPELGLEELLR 14 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;;;;; 176.23 2.06E-06 317648000 228695 290104 266926 233815 297604 321796 245211 275323 269870 329747 FALSE TRUE 237724.0552 339927.1053 273882.3108 280062.9091 247017.3784 247063.7559 225990.7211 271632.7455 260157.4314 394354.6113 0.602817993 0.861983341 0.694507692 0.710180384 0.626383897 0.626501501 0.573064736 0.688803269 0.659704297 1 18.58913399 -1.630073011 5.957802185 1.002043673 0.673138984 0.62906505 0.07565562 0.002086661 0.000129563 0.074428421 0.01744768 0.023438347 1.630073011 -0.328904688 ECS(ph)PTSSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.391)PT(0.391)S(0.2)S(0.018)LER;ECS(0.922)PT(0.071)S(0.006)SLER;ECS(0.991)PT(0.004)S(0.004)SLER;ECS(0.498)PT(0.498)S(0.005)SLER 226.31 3.24E-09 1522690000 1518100 1593120 1586500 1483120 1898410 1972510 1689560 1653080 1598170 1421910 TRUE FALSE 1578035.76 1866725.967 1627845.493 1776476.709 1575718.946 1514424.446 1557127.872 1630923.166 1540652.174 1700506.04 0.927980097 1.097747331 0.957271221 1.04467533 0.926617671 0.890572812 0.915684999 0.959081078 0.905996296 1 20.6975327 3.224017499 24.95450507 0.929802781 1.009860033 0.329411576 0.051484228 231.6329855 397457.866 0.013757839 0.016509173 1675.010367 -3.224017499 0.080057251 ECS(ph)VEKGTGDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECSVEKGTGDSLR 13 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ECS(0.992)VEKGT(0.008)GDSLR;ECS(0.999)VEKGT(0.001)GDSLR 95.197 0.0029109 363390000 523660 323350 425990 233990 641110 585430 404630 398490 457130 318210 TRUE FALSE 544334.5012 378882.8472 437091.6494 280272.5236 532134.3512 449472.7548 372914.0433 393148.8933 440677.9806 380557.157 1.430362013 0.995600372 1.148557165 0.736479445 1.39830336 1.18109132 0.97991599 1.033087635 1.157981061 1 18.53775363 4.746226952 24.08413225 1.07088451 1.430362308 0.305759695 0.162846692 687.581182 2159978.64 0.037473127 0.39063631 55747.69971 -4.746226952 0.359477798 ECSEAMEVETSVISIDS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ECSEAMEVETSVISIDSPQK 20 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVIS(0.067)IDS(0.932)PQK;ECSEAMEVETSVIS(0.211)IDS(0.789)PQK;ECSEAMEVETSVIS(0.003)IDS(0.997)PQK 96.903 0.00065557 96014000 161869 99588 134703 117789 161414 173387 185533 143995 143823 80198 TRUE FALSE 168259.7131 116691.4643 138213.4708 141087.3126 133976.9059 133120.497 170990.4387 142064.9826 138646.8383 95911.26262 1.754326953 1.216660704 1.441055691 1.47101924 1.396883977 1.387954796 1.782798328 1.481212724 1.445574112 1 16.54941262 ECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECSEAMEVETSVISIDSPQKLAILDQELEHK 31 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ECSEAMEVETSVIS(0.007)IDS(0.992)PQKLAILDQELEHK;ECSEAMEVETSVIS(0.001)IDS(0.999)PQKLAILDQELEHK 160.35 1.24E-12 193638000 80935 45946 63303 28102 92240 80570 60560 62421 77825 39108 TRUE FALSE 84130.3763 53836.86809 64952.72818 33660.49172 76561.07775 61858.83855 55813.14896 61584.3486 75024.09345 46770.46383 1.798792858 1.151086897 1.388755271 0.719695487 1.63695357 1.32260477 1.193341788 1.316735896 1.604091286 1 15.51331012 4.746628604 24.39455493 1.269107541 1.798793226 0.283200352 0.257082211 920.7817961 2784005.937 0.057623534 0.629755338 55799.28117 -4.746628604 0.529685685 ECSEFGHSDTCWMPGQS(ph)SPSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECSEFGHSDTCWMPGQSSPSRR 22 1 Q08174-2 Q08174-2 PCDH1 Protocadherin-1 1 ECSEFGHSDTCWMPGQS(0.494)S(0.494)PS(0.012)RR;ECSEFGHSDTCWMPGQS(0.489)S(0.489)PS(0.022)RR 108.44 0.00019833 267050000 103574 185662 140966 177239 162378 223596 150997 151827 153116 191728 TRUE FALSE 107663.1815 217548.0043 144639.6898 212296.3452 134777.0456 171669.2176 139161.4606 149792.0074 147605.3851 229293.4307 0.469543245 0.948775565 0.630806078 0.925871904 0.587792878 0.748687902 0.606914294 0.653276489 0.643740139 1 17.8068355 -1.196605012 5.098232769 1.000024431 0.695325624 0.301445672 0.141133091 3.55E-05 5.59E-06 0.123659847 0.029144571 0.063590902 1.196605012 -0.304698807 ECSPWMSDFKVEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ECSPWMSDFKVEFLR 15 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 125.89 7.99E-05 148710000 144960 133070 205790 153050 230880 196720 161270 145650 189210 160870 FALSE TRUE 150683.1327 155923.7374 211153.0565 183322.8332 191635.1001 151034.7613 148629.236 143697.8 182400.3691 192389.3965 0.78321953 0.810459101 1.097529595 0.952873893 0.996079325 0.785047222 0.772543803 0.746911226 0.948079117 1 17.55366976 2.729678613 24.75356774 0.821324325 0.932297052 0.078022039 0.112288303 1006.249521 2804346.308 0.036973788 0.035348377 536.6345288 -2.729678613 0.110972728 ECYQSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ECYQSHR 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 136.75 0.0029495 342100000 424370 521840 514650 487300 596810 605130 490910 486660 488380 619270 FALSE TRUE 441124.4553 611461.9606 528062.2018 583686.4856 495364.4494 464597.7283 452431.1914 480137.1187 470803.2992 740604.0999 0.595627887 0.825625946 0.713015499 0.788122137 0.668865389 0.627322652 0.610894797 0.6483047 0.635701719 1 19.49834301 -1.008606437 4.580404069 1.00000796 0.680569382 0.641369459 0.071942805 9603900.779 2114782.234 886.6525402 0.017532479 0.098037801 1.008606437 -0.319438578 EDAANNYAR ddPTM_MDA-MB-175_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 ;;;;;;; 221.16 1.00E-06 18102210000 4330362 4765977 4634173 4930567 5200820 5734778 5309925 4892649 4757225 4213135 FALSE TRUE 4501328.036 5584496.476 4754943.355 5905818.436 4316786.474 4402962.721 4893719.204 4827071.043 4586013.402 5038618.138 0.893365584 1.108338898 0.943699885 1.17211074 0.856740153 0.873843304 0.971242327 0.958014859 0.910172844 1 22.26459669 3.207704901 24.99999174 0.928899323 1.028899229 0.262784875 0.08290557 262.6396654 212795.8224 0.022628214 0.027048548 1613.261987 -3.207704901 0.099999905 EDAEHHPDEDVDESES ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDAEHHPDEDVDESES 16 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ; 131.66 4.33E-05 950660000 223550 265550 255250 283740 272420 319720 333540 272540 268460 216299 FALSE TRUE 232375.9266 311156.1468 261902.0247 339862.9251 226114.1457 245469.8754 307396.2633 268887.0471 258798.177 258678.6478 0.898318932 1.202867533 1.012460932 1.313842206 0.874112137 0.948937524 1.188332574 1.039463633 1.000462076 1 17.98080145 3.208852992 24.99979692 1.022001008 1.106986185 0.121044697 0.126723456 503.4213817 423641.5868 0.035844609 0.042847857 1617.532413 -3.208852992 0.084985177 EDAKEDHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDAKEDHER 9 1 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 ; 84.507 0.0092801 171701000 310250 169159 251340 169581 353340 298950 325720 242170 288810 160819 FALSE TRUE 322498.9096 198210.7424 257890.1269 203123.6157 293279.393 229523.3931 300189.2153 238924.1073 278415.7845 192328.404 1.676813736 1.030584866 1.340884246 1.056129056 1.524888612 1.193393115 1.560815819 1.242271564 1.447606171 1 17.55321232 -1.321260427 5.26608825 0.999912551 1.328137336 0.198645831 0.204185154 0.000186774 2.41E-05 0.176140709 0.041505749 0.047724301 1.321260427 0.328224784 EDALDDSVSSSSVHAS(ph)PLAS(ph)SPVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 2 EDALDDSVSSSSVHAS(1)PLAS(0.564)S(0.436)PVRK 174.1 3.65E-12 81983000 28660 34566 45189 41047 56789 56757 61954 58061 49581 34636 TRUE FALSE 29791.51893 40502.44161 46366.66246 49165.97409 47136.02606 43576.04691 57097.88359 57282.78726 47796.5895 41422.26105 0.71921518 0.977794079 1.119365802 1.186945687 1.137939477 1.051995854 1.378434739 1.382898611 1.15388654 1 15.33811869 5.229521756 0.723589468 1.233858651 3.94E-12 0.586306949 0.118754208 3.602326154 0.868628659 0.047116454 4.25490713 169637.4581 -5.229521756 -1.233858651 SAPGGGGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPGGGGKR 9 1 Q14847;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 80.239 0.039566 69609000 57161 43246 51504 33370 72515 100200 99096 107920 103840 127830 FALSE TRUE 59417.76042 50673.16409 52846.23655 39970.4864 60188.9262 76930.06855 91328.59658 106473.5089 100102.8187 152875.841 0.388666777 0.331466135 0.345680758 0.261457181 0.39371117 0.503219266 0.597403723 0.69647047 0.654798155 1 17.22200091 1.56145221 0.507042873 0.988233311 0.302759591 0.931609282 0.055592068 0.198690647 0.127176142 0.06040565 0.03739796 36.4294161 -1.56145221 -0.68547372 EDALDDSVSSSSVHASPLASS(ph)PVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHAS(0.001)PLAS(0.349)S(0.65)PVRK 235.07 1.29E-38 152360000 11233 20501 24408 30015 42748 42142 24076 36718 30222 25327 TRUE FALSE 11676.48751 24021.88727 25044.09253 35951.87741 35481.71023 32355.15917 22188.86021 36225.85527 29134.31612 30289.34074 0.385498239 0.793080559 0.826828578 1.186948165 1.171425636 1.068202819 0.732563327 1.195993521 0.961866961 1 14.88652256 4.692993069 1.328812009 1.043781524 0.152411806 0.672426743 0.138416565 0.712043112 1.178896818 0.038820105 0.840144896 49316.59331 -4.692993069 -0.891369718 EDAMAMVDHCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDAMAMVDHCLK 12 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 176.05 2.60E-05 868780000 978980 765030 1038910 928460 1244720 1273040 1376590 1090090 1116670 696000 FALSE TRUE 1017630.886 896417.9514 1065984.848 1112106.617 1033142.939 977395.7531 1268689.279 1075479.127 1076481.265 832367.8743 1.222573477 1.076949242 1.280665534 1.336075852 1.241209531 1.174235315 1.52419299 1.292071883 1.293275844 1 19.66686176 4.166247986 8.681357976 1.29012389 1.150186712 0.098314455 0.129450365 0.433274922 46.84250227 0.030552477 0.066460389 14663.8492 -4.166247986 -0.139937178 EDAMAMVDHCLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDAMAMVDHCLKK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 220.69 1.32E-11 532120000 1347700 832680 1167600 856290 1681300 1411900 1355000 1118100 1413500 830590 FALSE TRUE 1400908.237 975686.3126 1198028.615 1025661.606 1395513.227 1084007.623 1248791.559 1103113.698 1362628.411 993328.2079 1.410317582 0.982239611 1.206075299 1.032550569 1.404886336 1.091288472 1.257179198 1.110522876 1.371780646 1 19.92191096 4.777335328 23.32330046 1.169601354 1.410319126 0.217893272 0.140538557 14348.30236 8630193.642 0.030286858 8.015630829 59887.38196 -4.777335328 0.240717772 EDCRDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDCRDEK 7 1 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 67.169 0.060092 67252000 50270 34675 51973 32097 110090 73369 102460 46207 48439 28690 FALSE TRUE 52254.69842 40630.16152 53327.45908 38445.6908 91376.94112 56330.16167 94428.91747 45587.67074 46695.68985 34311.2562 1.522960807 1.184164208 1.554226367 1.120497908 2.66317679 1.641739998 2.752126501 1.328650589 1.360943755 1 15.06639433 EDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 270.46 1.06E-61 10431640000 8555880 3989950 5851610 4517160 7666950 7257810 9377740 5616230 6719540 2735420 TRUE FALSE 8893672.749 4675192.875 6004107.764 5410640.766 6363724.578 5572293.621 8642688.235 5540953.623 6477705.068 3271373.176 2.718635958 1.429122458 1.835347862 1.653935664 1.94527626 1.703350037 2.641914502 1.693769963 1.980118048 1 21.64146491 4.755460721 24.26058384 1.823050331 2.71863703 0.329721208 0.400316336 2666.638239 3827941.653 0.088941333 2.434348225 56945.67181 -4.755460721 0.895586699 EDDRETLVSQCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDDRETLVSQCR 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 117.7 0.00021191 0 256680 212850 249910 178220 283350 503170 291280 271490 245550 224580 FALSE TRUE 266813.9246 249405.3318 256422.8599 213471.3841 235186.2682 386316.3931 268448.7125 267851.1206 236712.7035 268582.1512 0.993416441 0.9285998 0.954727851 0.794808527 0.875658592 1.438354676 0.999503174 0.997278186 0.8813419 1 18.03500391 EDDRVAIHEAMEQQTISIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDDRVAIHEAMEQQTISIAK 20 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 135.28 4.48E-06 520740000 409460 283570 391230 266320 472200 464720 372950 385180 402160 352550 FALSE TRUE 425625.797 332270.9416 401425.7752 318997.3011 391935.6127 356795.8229 343717.2045 380017.2921 387686.3402 421625.4225 1.009487982 0.788071411 0.952091012 0.756589342 0.929582496 0.846238874 0.815219354 0.901314939 0.919504184 1 18.68560233 0.966291562 1.799081948 0.998755345 0.868314184 0.217328584 0.073199636 0.517640018 3.494677476 0.06189945 0.017620097 9.253191756 -0.966291562 -0.130441161 EDEEESLNEVGYDDIGGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDEEESLNEVGYDDIGGCR 19 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 341.27 4.40E-69 0 139712 157356 145321 165686 162582 190981 197067 133773 157469 122916 FALSE TRUE 145227.9376 184380.6689 149108.1846 198458.1963 134946.3697 146628.5571 181620.3736 131979.9917 151801.7214 146999.0368 0.987951627 1.254298483 1.014348038 1.350064603 0.91800853 0.997479713 1.235520841 0.897828956 1.032671538 1 17.16544718 3.20282842 24.99978788 1.015448335 1.149189092 0.213703195 0.129691062 270.1437195 189003.4529 0.035597679 0.042548809 1595.248777 -3.20282842 0.133740758 EDEGPPGYPEPLAPGHGS(ph)PFPSLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDEGPPGYPEPLAPGHGSPFPSLSK 25 0 B1AKB5;B0QYS6;B0QYS7;P19484-2;P19484 B1AKB5 TFEB Transcription factor EB 1 EDEGPPGYPEPLAPGHGS(0.978)PFPS(0.011)LS(0.01)K 66.479 0.028989 45419000 41679 28092 29111 36668 48631 44784 53121 38495 48485 22345 TRUE FALSE 43324.5191 32916.58247 29869.65657 43920.82096 40364.71999 34383.59471 48957.23721 37979.03749 46740.03432 26723.07493 1.621240041 1.231766275 1.117747739 1.64355416 1.510481862 1.28666311 1.832021103 1.421207611 1.749051501 1 14.7057984 3.725948879 24.71101303 1.516428214 1.314402827 0.079325868 0.252609787 1307.290534 2561461.336 0.06254127 0.097602413 5320.456281 -3.725948879 -0.202025386 EDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EDEISPPPPNPVVK 14 0 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK 211.51 3.92E-09 1597650000 3044810 1794830 2519170 2215540 3017890 3320550 3886860 2611520 2846170 1365470 TRUE FALSE 3165021.45 2103078.091 2584821.64 2653767.199 2504910.136 2549402.586 3582197.757 2576516.846 2743736.898 1633007.703 1.938154636 1.287855585 1.582859429 1.625079413 1.533924262 1.56116997 2.193619632 1.577773847 1.680173886 1 20.63910017 EDENDAS(ph)DDEDDDEKRR ddPTM_MDA-MB-175_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 207.13 5.01E-12 453790000 293150 119070 173291 119572 247570 328320 283360 170699 183810 73267 TRUE FALSE 304723.7884 139519.3463 177807.1058 143222.9847 205488.1398 252072.6557 261149.5028 168411.0591 177194.714 87622.26587 3.477698109 1.59228188 2.029245695 1.634550115 2.345158936 2.876810514 2.980401159 1.922012144 2.022256698 1 16.4190099 -1.125396473 14.72354696 1.000001307 2.288747916 0.312745492 0.585395626 0 0 0.557635336 0.131435909 0.074920993 1.125396473 1.288746609 EDEVEEWQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDEVEEWQHR 10 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 189.72 9.80E-07 877660000 1017210 1128170 1193730 1172390 1454270 1615390 1528820 1269690 1300490 991110 FALSE TRUE 1057370.236 1321924.422 1224839.584 1404285.243 1207073.705 1240240.154 1408987.094 1252671.882 1253685.619 1185299.029 0.892070449 1.115266603 1.03335914 1.184751872 1.018370619 1.046352122 1.188718677 1.056840386 1.057695644 1 20.17681964 4.744639049 24.64494217 1.082708175 0.892070346 0.443557167 0.062243891 485.9371674 1970159.575 0.013831457 0.127301615 55544.24264 -4.744639049 -0.190637829 EDFATFDYILCMDESNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDFATFDYILCMDESNLR 18 0 P24666;P24666-3;P24666-2 P24666;P24666-2 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;; 148.48 1.61E-07 47849000 44740.9 52842.9 47629.3 49430.8 61484 58603.4 58260.9 52776.5 50270.7 43477.8 FALSE TRUE 46507.30528 61918.25701 48870.55869 59208.0647 51032.97164 44993.64849 53694.25842 52069.11734 48461.46733 51996.44248 0.894432447 1.19081718 0.939882737 1.138694531 0.981470447 0.865321671 1.032652541 1.001397689 0.932015058 1 15.6661253 3.029627447 24.99509781 0.969671257 1.046396634 0.132336743 0.090561795 386.4973398 326064.6169 0.024359864 0.029115284 1070.600513 -3.029627447 0.076725377 EDFLQLFNLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDFLQLFNLRPK 12 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 156.36 6.67E-05 156753000 187992 174710 192137 170361 263180 257900 246740 218939 235640 190653 FALSE TRUE 195414.0693 204715.0834 197144.2481 204057.8973 218444.7576 198006.6335 227399.8741 216004.4808 227159.3624 228007.8051 0.857049912 0.897842437 0.864638156 0.894960141 0.958058245 0.868420419 0.997333727 0.947355643 0.996278888 1 17.79872369 2.489804289 0.465113163 1.004901001 0.861051908 0.670500866 0.0317171 0.623410215 0.284053811 0.028694287 0.033241346 308.8903135 -2.489804289 -0.143849093 EDFLVGRPPELGQGDADVAGYLQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDFLVGRPPELGQGDADVAGYLQSAR 26 1 Q8N0W3-2;Q8N0W3 Q8N0W3-2 FUK L-fucose kinase 0 58.272 0.075131 53116000 16534 25187 24767 24812 23828 27663 22470 22441 21595 21248 FALSE TRUE 17186.77509 29512.67132 25412.44837 29719.73954 19777.72507 21238.68749 20708.74269 22140.2151 20817.80017 25411.13878 0.676348086 1.161406877 1.000051536 1.169555595 0.778309278 0.83580227 0.814947447 0.871279925 0.819239167 1 14.63317341 3.217894862 24.99372383 0.845234427 1.013110417 0.214411847 0.138144193 310.4601374 375478.0143 0.037529913 0.044903647 1651.561923 -3.217894862 0.16787599 EDFPLIETEDEAYLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDFPLIETEDEAYLRR 16 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 191.06 1.86E-12 0 16186 18702 15267 15565 15533 19005 21355 18454 17515 12836 FALSE TRUE 16825.03578 21913.92302 15664.87056 18643.71054 12892.70621 14591.37677 19681.1393 18206.65431 16884.63857 15350.96844 1.096024387 1.427527071 1.02044836 1.214497353 0.839862726 0.950518323 1.282078025 1.186026431 1.09990706 1 13.90604205 4.216456204 24.99898985 1.08910254 1.261775972 0.205055224 0.14539609 346.8817518 392306.8491 0.037342217 0.080768868 16460.99958 -4.216456204 0.172673432 EDFPQKWPDLLTEMVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDFPQKWPDLLTEMVNR 17 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;; 104.03 0.00079381 882170000 598000 676380 1112510 776260 1428020 1164260 1141440 815620 1389980 556610 FALSE TRUE 621609.5018 792543.0035 1141502.925 929801.9111 1185285.67 893878.2595 1051970.95 804687.948 1339954.891 665667.0726 0.933814406 1.19059968 1.714825581 1.396797212 1.780598319 1.342830818 1.580325952 1.208844453 2.012950537 1 19.34444128 4.44904862 5.033385147 1.500370892 0.985186715 0.307921344 0.277238123 0.178223699 11.65930846 0.061943389 0.196071598 28122.15645 -4.44904862 -0.515184177 EDGKVFDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDGKVFDEK 9 1 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 0 ;;; 116.23 0.0012285 1446530000 3086880 1415760 2174090 1283510 3326730 2886440 2637250 2084950 2526260 1214900 FALSE TRUE 3208752.406 1658905.767 2230748.571 1537384.447 2761253.623 2216108.054 2430535.454 2057004.656 2435340.396 1452936.394 2.208460342 1.141760764 1.535338078 1.058122333 1.900464214 1.525261576 1.672843673 1.415756852 1.676150729 1 20.47054012 -1.178305922 4.772804163 0.999934776 1.544780008 0.220057859 0.318907307 0.000200887 3.46E-05 0.280241034 0.066045572 0.066327569 1.178305922 0.544845232 EDGLAQQQTQLNLR ddPTM_MDA-MB-175_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 ;;;;; 434.63 6.01E-153 2907340000 832392 910335 984646 952858 1072120 1203614 916358 942626 964175 934847 FALSE TRUE 865255.4789 1066677.955 1010306.684 1141330.468 889881.4254 924092.8894 844531.4655 929991.6403 929474.5301 1118012.371 0.773922992 0.954084215 0.903663242 1.020856744 0.795949534 0.826549789 0.755386512 0.831825894 0.831363368 1 20.09250472 3.195594408 24.9996364 0.825564494 0.915381279 0.142418299 0.083110989 202.6636633 117917.9788 0.022615327 0.027030663 1568.896911 -3.195594408 0.089816785 EDGNEEDKENQGDETQGQQPPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDGNEEDKENQGDETQGQQPPQR 23 1 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 180.63 4.10E-17 639110000 98346 48263 73989 47906 83845 114220 88316 66525 90485 39588 FALSE TRUE 102228.776 56551.79482 75917.21412 57381.66381 69593.05685 87694.13602 81393.56115 65633.34119 87228.46253 47344.51064 2.159252987 1.194474165 1.603506153 1.212002469 1.469928739 1.852255622 1.719176311 1.386292525 1.842419772 1 15.53090954 -1.064042143 4.359163044 0.999954244 1.574849699 0.277702802 0.288900023 18115207.61 4421801.154 8238.554503 0.063358185 0.086289481 1.064042143 0.574895455 EDGNEEDKENQGDETQGQQPPQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDGNEEDKENQGDETQGQQPPQRR 24 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;; 329.43 4.94E-87 1870640000 1444220 709800 986120 541105 1479960 1463690 1000380 918090 1070200 630730 FALSE TRUE 1501238.921 831702.6285 1011819.097 648133.954 1228396.928 1123770.18 921967.6016 905784.5052 1031683.711 754309.4674 1.990216198 1.102601339 1.341384592 0.859241441 1.62850525 1.489799914 1.222267042 1.200812855 1.367719425 1 19.52479701 7.999879667 0.031716024 1.73E-06 3.248331081 0.168786919 0.282725169 2589.023108 6.287784953 199.9099313 510.5171102 99972296.13 -7.999879667 3.248329349 EDGSGDRGDGPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EDGSGDRGDGPFR 13 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 164.68 3.34E-05 4632630000 2663830 2786560 2963630 2882300 3105890 3489830 3288610 2950350 2828030 2465100 FALSE TRUE 2769000.065 3265130.004 3040864.632 3452410.337 2577951.927 2679369.871 3030840.155 2910805.384 2726249.753 2948089.148 0.939252487 1.107541136 1.031469701 1.171067144 0.87444843 0.908849678 1.028069371 0.987353244 0.924751463 1 21.49134872 3.23061851 24.99999107 0.958625169 1.063357308 0.368831718 0.069312999 198.2618047 624083.227 0.019816776 0.024093055 1700.663967 -3.23061851 0.104732139 EDGVTPYMIFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDGVTPYMIFFK 12 0 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;P13693-2;H0YCX0 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 125.75 0.00069738 43169000 119960 139000 138960 137470 166320 180240 138500 141310 140710 135070 FALSE TRUE 124696.1134 162872.1687 142581.4118 164661.1557 138048.9858 138381.9916 127644.0081 139415.9706 135645.8746 161534.3804 0.771947824 1.008281756 0.882669134 1.019356717 0.854610551 0.856672067 0.790197157 0.863073051 0.839733772 1 17.30148173 3.095187062 20.82922891 0.855050068 0.925736424 0.079695451 0.081610998 8.496925499 1847.350396 0.021749145 0.025995262 1245.050772 -3.095187062 0.070686355 EDGWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDGWIR 6 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 123.34 0.043811 596750000 490130 512350 570810 506250 596470 681140 593310 540990 523760 493920 FALSE TRUE 509480.7109 600342.127 585685.7775 606384.739 495082.2425 522955.5578 546804.8119 533738.9139 504909.9799 590694.1673 0.862511836 1.016333257 0.99152118 1.026562937 0.838136332 0.88532372 0.925698682 0.903579117 0.854773939 1 19.17205184 3.243666219 24.99999919 0.897970678 0.978474428 0.270067135 0.058463396 152.8371501 748374.7274 0.015643735 0.020556198 1752.53306 -3.243666219 0.08050375 EDHLVYADEESSNITDGRIT(ph)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 51 2 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEESSNITDGRIT(1)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR;EDHLVYADEES(0.001)S(0.001)NIT(0.002)DGRIT(0.996)PEPAVSNTEEPSTTSTASNYPDVLTRPSLHR 295.11 3.63E-103 2148720000 38992.8 97816.7 102919 116139.2 84085 114124 101563.6 115057 87496.9 105054 TRUE FALSE 40532.26585 114615.9573 105601.1537 139111.1871 69792.26173 87620.43057 93602.77964 113514.8491 84347.90366 125637.3199 0.322613264 0.912276363 0.840523769 1.107244147 0.555505815 0.69740767 0.74502369 0.903512182 0.671360259 1 16.93890555 -5 0.027940964 2.062751717 3.82E-11 0.120428384 0.20357143 4531.618144 9.546187906 533.2614276 229.9522869 1.00E-05 5 -2.062751717 EDINAIEMEEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDINAIEMEEDKR 13 1 P49756;P49756-2;P49756-3;H0YE46 P49756 RBM25 RNA-binding protein 25 0 ; 187.37 1.13E-05 268730000 196343 251234 226711 232441 221450 306550 214960 214272 218890 350663 FALSE TRUE 204094.7732 294381.4852 232619.2749 278417.136 183808.0081 235358.4083 198110.8735 211400.0343 211012.1917 419368.701 0.486671449 0.701963414 0.554689166 0.66389584 0.438296915 0.56122073 0.472402621 0.504091111 0.503166286 1 18.67785967 -1.560166275 6.313064326 1.000764214 0.54300251 0.750296232 0.07910377 0.000843655 5.88E-05 0.075944007 0.017872505 0.027531744 1.560166275 -0.457761704 EDIQGALHNYR ddPTM_MDA-MB-175_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 ;;; 150.09 3.41E-05 1632840000 963240 1229900 1197650 1109190 1345320 1508020 1203520 1173170 1168480 1300940 FALSE TRUE 1001269.459 1441125.758 1228861.743 1328584.471 1116642.987 1157805.209 1109184.958 1157445.575 1126426.633 1555834.285 0.643557909 0.926272015 0.789841023 0.853937006 0.717713318 0.744170006 0.712919729 0.743938854 0.724001678 1 20.56925697 -1.282396095 3.469462517 1.000751577 0.764728186 0.473116919 0.075349526 21874581.05 33431259.84 174888.684 0.01813516 0.052191996 1.282396095 -0.236023391 EDIQSVMTEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDIQSVMTEIRR 12 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 121.56 0.00059988 186824000 153268 152879 149657 133051 189804 202820 142658 145745 145458 156882 FALSE TRUE 159319.139 179134.779 153557.1844 159368.0907 157541.1839 155718.1288 131476.0932 143791.5267 140222.995 187620.0242 0.849158504 0.954774309 0.818447738 0.849419412 0.839682142 0.829965402 0.700757255 0.766397549 0.747377555 1 17.51745429 3.245151742 1.093485366 0.783617823 0.886944865 0.075778577 0.081971205 0.788191764 2.012716606 0.031436897 0.050502108 1758.53794 -3.245151742 0.103327042 EDITQSAQHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 199.4 1.72E-07 1378000000 460620 1228300 1150300 1198200 1039700 1288900 922150 992200 934130 1125600 FALSE TRUE 478805.6333 1439250.97 1180277.763 1435200.384 862972.1654 989572.5085 849869.4734 978901.1819 900510.8438 1346139.769 0.355687904 1.069169044 0.876786936 1.066160006 0.641071741 0.735118694 0.631338211 0.72719134 0.668957908 1 20.36039678 3.186814062 24.99975937 0.714142646 0.860673489 0.052494538 0.209171684 227.6372908 109974.9929 0.057015852 0.068147054 1537.496239 -3.186814062 0.146530844 EDKHECPFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDKHECPFAR 10 1 F8W9E7;Q96BJ8-2;Q96BJ8;Q96BJ8-3 F8W9E7 ELMO3 Engulfment and cell motility protein 3 0 69.672 0.033814 70904000 57512 44777 60297 71567 62560 78207 78307 59346 61614 44509 FALSE TRUE 59782.61817 52467.10143 61868.38935 85722.73899 51926.07355 60044.60949 72169.09272 58550.56394 59396.52418 53229.68637 1.123106714 0.985673691 1.162291074 1.610431036 0.975509665 1.128028617 1.355805334 1.099960716 1.115853356 1 15.69994345 1.046981435 1.802619329 1.005299299 1.187004267 0.094810522 0.175176185 0.855840396 5.657718409 0.165626542 0.047463776 11.14246902 -1.046981435 0.181704968 EDKIEAEAEVELYYMILER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDKIEAEAEVELYYMILER 19 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 88.755 0.0022854 4551700 17577 9249.3 13759 12413 15633 15043 18432 10857 16258 7581.6 FALSE TRUE 18270.95353 10837.79533 14117.57084 14868.25435 12975.70824 11549.49123 16987.25168 10711.47967 15672.87776 9067.069361 2.015089198 1.195291984 1.557015865 1.639808163 1.43108073 1.273784369 1.873510723 1.181360729 1.72854945 1 13.14642061 -2.925562351 0.294282415 2.79E-15 1.553781407 0.260821383 0.269017902 86.9929483 2.462257189 54.88796912 0.261518305 0.001186964 2.925562351 1.553781407 EDKLECSEELGDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDKLECSEELGDLVK 15 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;; 171.71 9.74E-07 789690000 1536550 564794 968881 647504 1386770 1327930 1568650 1019890 1181530 458393 FALSE TRUE 1597214.18 661792.976 994130.8348 775578.3586 1151047.331 1019538.382 1445695.114 1006220.043 1139006.966 548206.3319 2.913527421 1.207196885 1.813424576 1.414756294 2.099660773 1.859771263 2.637136841 1.835476871 2.077697575 1 19.06435947 EDKNGHDGDTHQEDDGEKS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EDKNGHDGDTHQEDDGEKSD 20 2 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D;EDKNGHDGDTHQEDDGEKS(1)D 267.47 3.70E-37 3588854000 3533063 774526 1195385 650447 2150818 1951505 1756740 1317701 1489932 569685 TRUE FALSE 3672551.055 907544.8155 1226537.715 779103.4752 1785222.725 1498297.539 1619042.128 1300039.373 1436309.638 681303.8685 5.390474391 1.332070545 1.800279981 1.143547705 2.620303226 2.199161943 2.376387693 1.908163792 2.108177723 1 19.37793887 4.744287588 24.84166119 1.898898853 5.390476041 0.814165361 0.509122451 232.2515446 1007396.331 0.118755196 1.05457797 55499.31057 -4.744287588 3.491577188 EDKS(ph)PSEESAPTTSPESVSGSVPSSGSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKS(0.75)PS(0.25)EESAPTTSPESVSGSVPSSGSSGR;EDKS(0.933)PS(0.066)EES(0.001)APTTSPESVSGSVPSSGSSGR;EDKS(0.848)PS(0.15)EES(0.002)APTTSPESVSGSVPSSGSSGR;EDKS(0.813)PS(0.178)EES(0.009)APTTSPESVSGSVPSSGSSGR 298.01 2.61E-81 3495990000 941674 510342 676083 465835 913662 1015302 990407 704803 771485 309711 TRUE FALSE 978852.0167 597989.2686 693702.2784 557975.7726 758358.0596 779513.4976 912776.3114 695356.2686 743719.4056 370392.9407 2.642739397 1.61447264 1.872882019 1.506442784 2.04744199 2.104558192 2.464345864 1.87734752 2.007920033 1 18.49869708 EDKSPSEESAPTT(ph)SPESVSGSVPSSGSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKSPSEESAPT(0.027)T(0.822)S(0.15)PESVSGSVPSSGSSGR 220.64 2.08E-34 519220000 106110 66236 89457 86506 119640 117810 122630 99952 107130 54612 TRUE FALSE 110299.3047 77611.51776 91788.32291 103616.6286 99303.63553 90450.41293 113017.9402 98612.30693 103274.4122 65312.17579 1.688801566 1.188316218 1.405378428 1.586482572 1.520445986 1.38489358 1.730426812 1.509860998 1.581242869 1 15.99506435 -0.62457698 5.859611338 0.999999996 1.506759905 0.513967705 0.148930312 8.37E-09 2.14E-09 0.140495592 0.033115128 0.237368464 0.62457698 0.50675991 EDKSPSEESAPTTS(ph)PESVSGSVPSSGSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725;A0A494C0B4;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 1 EDKSPSEES(0.003)APT(0.054)T(0.22)S(0.718)PES(0.004)VSGSVPSSGSSGR 98.114 0.00037275 372020000 145550 85657 114380 84354 145460 164790 153830 123860 129750 57526 TRUE FALSE 151296.4264 100367.9234 117360.8368 101038.9694 120734.7612 126520.0199 141772.4026 122199.8593 125080.3228 68797.1183 2.199168078 1.458897203 1.705897568 1.468651187 1.75493922 1.839030806 2.060731701 1.776235144 1.8181041 1 16.07006052 3.018724653 24.9168686 1.780398108 1.680389237 0 0.324985981 1216.977927 1619419.266 0.087719705 0.104830827 1044.058067 -3.018724653 -0.100008871 EDKYEEEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 101.93 0.0033445 3214800000 5671770 1859400 2935590 2099540 4206730 4620930 5597030 3151440 3578860 1162880 FALSE TRUE 5895695.859 2178737.486 3012093.887 2514822.745 3491671.537 3547789.038 5158320.163 3109200.102 3450057.528 1390724.071 4.239299499 1.566620964 2.165845799 1.808283036 2.510686059 2.551037342 3.709089581 2.235670012 2.480763509 1 20.40740478 3.02311245 24.74538437 2.557211094 2.336974151 0 0.915537352 1417.297572 1517420.531 0.253265169 0.302692619 1054.659939 -3.02311245 -0.220236943 EDLAAFVEELDKVESQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDLAAFVEELDKVESQER 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 214.19 9.29E-19 106725000 79064 57209 73420 66041 87151 103287 118918 77312 81244 32426.9 FALSE TRUE 82185.50777 67034.20073 75333.38552 79103.71269 72337.10415 79300.15958 109596.8964 76275.7591 78320.04431 38780.3302 2.119257555 1.728561886 1.942566892 2.03978956 1.865303977 2.044855192 2.826094978 1.96686719 2.019581677 1 15.24303747 2.488339542 24.88254638 2.102424724 1.935375831 0 0.430897461 2171.468599 4816405.651 0.136103621 0.121427687 307.8502721 -2.488339542 -0.167048893 EDLAAFVEELDKVESQEREDVLAGMSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDLAAFVEELDKVESQEREDVLAGMSGK 28 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 ; 162.27 4.88E-12 71838000 106090 60354 87313 54849 137139 116694 113697 82810 107851 45648 FALSE TRUE 110278.5151 70719.33001 89588.44851 65697.96849 113828.1618 89593.58701 104785.132 81700.0674 103969.4636 54591.85162 2.020054493 1.29541915 1.641058983 1.203439095 2.08507604 1.641153109 1.919428064 1.496561574 1.904486851 1 15.73639801 -0.757574404 8.382821256 1 1.669631236 0.346099558 0.283177814 0 0 0.253124824 0.059662094 0.174753385 0.757574404 0.669631236 EDLAYMNHIMVS(ph)VSPPEEHAMPIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.5)VS(0.5)PPEEHAMPIGR;EDLAYMNHIMVS(0.651)VS(0.349)PPEEHAMPIGR 156.03 2.88E-08 85925000 29636 32779 38220 39335 37378 45802 39524 31703 32681 30501 TRUE FALSE 30806.05216 38408.53826 39216.0446 47115.3456 31024.50091 35165.17964 36426.0056 31278.07314 31504.81719 36477.08697 0.844531587 1.052949713 1.075087071 1.29164222 0.850520244 0.964034756 0.998599631 0.857471792 0.86368786 1 15.1547029 EDLAYMNHIMVSVS(ph)PPEEHAMPIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDLAYMNHIMVSVSPPEEHAMPIGR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 EDLAYMNHIMVS(0.005)VS(0.995)PPEEHAMPIGR;EDLAYMNHIMVS(0.316)VS(0.684)PPEEHAMPIGR;EDLAYMNHIMVS(0.006)VS(0.994)PPEEHAMPIGR 274.79 8.40E-53 272043000 118731 156882 146363 148881 147767 175852 156568 147341 137102 123704 TRUE FALSE 123418.5916 183825.2631 150177.34 178329.2174 122649.6181 135013.0381 144295.791 145366.1349 132167.7258 147941.4303 0.834239545 1.242554318 1.015113479 1.205404173 0.829041722 0.912611415 0.97535755 0.982592466 0.893378721 1 17.1746666 3.234847501 24.99998326 0.936867036 1.082114446 0.272435441 0.113373918 118.7847091 799764.4087 0.030312639 0.037586429 1717.305264 -3.234847501 0.145247411 EDLDVLGLTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDLDVLGLTFR 11 0 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 140.17 9.01E-05 137229000 108148 120645 113899 117474 133860 154361 156540 125838 120709 108201 FALSE TRUE 112417.7665 141364.8403 116867.3015 140710.0066 111106.525 118512.9971 144269.9858 124151.3474 116364.7067 129400.9143 0.868755581 1.092456271 0.903141235 1.087395768 0.858622411 0.91585904 1.114907004 0.959431764 0.899257222 1 16.98148829 EDLPAENGETKTEESPASDEAGEKEAKS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDLPAENGETKTEESPASDEAGEKEAKSD 29 3 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 EDLPAENGETKTEESPASDEAGEKEAKS(1)D 107.14 0.0024951 178590000 247020 31922 72680 24290 123900 176540 111010 62751 87884 21971 TRUE FALSE 256772.5403 37404.35518 74574.10051 29094.4895 102839.5223 135541.2605 102308.7461 61909.92548 84721.07201 26275.79679 9.772207572 1.423528865 2.838128986 1.107273349 3.913849809 5.158407244 3.893649618 2.356157873 3.224300777 1 14.68144689 4.746163746 24.86712866 2.89689463 9.772211123 0.727067629 1.285183506 466.9158425 1527076.268 0.313157241 3.328398594 55739.58698 -4.746163746 6.875316492 EDLQELNDR ddPTM_MDA-MB-175_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 ; 166.19 0.00014175 466650000 670740 614410 660430 756740 708620 821670 879210 689660 698170 461900 FALSE TRUE 697221.3331 719930.1381 677641.3483 906420.9134 588169.0255 630849.595 810295.2228 680416.2358 673042.9981 552400.4614 1.262166457 1.303275773 1.226721185 1.64087646 1.064751148 1.142014968 1.466861959 1.23174451 1.218396879 1 19.075355 0.810475488 1.735891943 1.000858162 1.29694437 0.250852542 0.153086579 0.934596928 5.063710908 0.141228918 0.040100228 6.463615115 -0.810475488 0.296086208 EDLRLPEGDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EDLRLPEGDLGK 12 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;;; 194.86 8.95E-07 21669645000 30718405 21118849 28009486 23258426 34382970 35386490 36957504 28786658 31311024 16996806 FALSE TRUE 31931191.35 24745847.03 28739436.22 27858873.24 28538565.04 27168513.98 34060678.27 28400819.93 30184146.36 20327004.71 1.570875385 1.217387775 1.413854949 1.370535091 1.403972963 1.336572425 1.675636856 1.397196505 1.484928389 1 24.27689431 EDLRPSAPQQEGEASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDLRPSAPQQEGEASK 16 1 O76070 O76070 SNCG Gamma-synuclein 0 ;;; 163.18 7.13E-09 1774320000 1285500 898500 1240190 1045890 1443180 1580160 1618250 1280720 1397920 767830 FALSE TRUE 1336252.533 1052810.386 1272510.37 1252763.92 1197868.779 1213191.788 1491407.336 1263554.043 1347609.132 918271.5875 1.455182269 1.14651308 1.385766899 1.364262967 1.304482024 1.321168818 1.624146229 1.376013437 1.467549634 1 19.80856138 EDLRPSAPQQEGEASKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDLRPSAPQQEGEASKEK 18 2 O76070 O76070 SNCG Gamma-synuclein 0 125.28 1.69E-05 125230000 320860 175480 234630 170570 362920 316340 304610 249960 304180 145690 FALSE TRUE 333527.8006 205617.325 240744.6506 204308.2369 301230.988 242874.8292 280733.8722 246609.6951 293232.6212 174235.1661 1.91423929 1.180113806 1.381722507 1.172600466 1.728875948 1.39394839 1.611235427 1.415384165 1.682970366 1 17.41067631 -1.022933948 5.374428648 0.999997312 1.479329049 0.299407074 0.226893737 6.73E-06 1.22E-06 0.20232163 0.047687398 0.094856272 1.022933948 0.479331737 EDLRPSAPQQEGEASKEKEEVAEEAQSGGD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDLRPSAPQQEGEASKEKEEVAEEAQSGGD 30 3 O76070 O76070 SNCG Gamma-synuclein 0 78.159 0.0041151 284900000 192320 94519 141500 73249 257190 211610 132500 134740 178940 82623 FALSE TRUE 199912.9421 110751.903 145187.6062 87737.43357 213472.9357 162466.7845 122114.3038 132934.0307 172499.9844 98811.39494 2.023177005 1.120841408 1.469340721 0.887928296 2.160408076 1.64421102 1.235832202 1.345330979 1.745749915 1 16.5923898 -1.185211128 3.569074915 0.999414852 1.483285114 0.139926319 0.375637804 262385294.9 436825733.1 1777214.761 0.086472705 0.065281312 1.185211128 0.483870262 EDLRVECSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDLRVECSK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 113.63 0.0016136 171320000 610900 490290 630020 486700 803230 854720 747710 687680 767630 542470 FALSE TRUE 635018.8037 574493.4936 646438.8388 582967.8073 666697.2515 656224.2334 689102.5364 678462.7744 740003.1462 648756.6103 0.978824406 0.885530081 0.996427364 0.898592474 1.027653886 1.01151067 1.062189619 1.045789382 1.140648333 1 19.30731781 2.85051117 1.304887211 1.064571634 0.938679651 0.540791427 0.048045744 0.300972876 1.05752889 0.019009609 0.019914803 708.7795366 -2.85051117 -0.125891983 EDLSKS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.014)KS(0.986)PK;EDLS(0.003)KS(0.997)PK;EDLS(0.017)KS(0.983)PK 68.893 0.033508 1445440000 5231300 1449150 2198100 1085110 3986300 4336900 2776800 2218910 2691300 1166090 TRUE FALSE 5437835.763 1698030.24 2255384.292 1299741.519 3308710.15 3329720.701 2559147.16 2189169.141 2594440.639 1394563.009 3.899311632 1.2176074 1.617269551 0.932006306 2.372578455 2.387644502 1.835088944 1.569788619 1.860396856 1 20.41138169 7.999999996 0.055014047 2.13E-08 5.463987347 0.180962722 0.749370676 885.0702883 3.655026793 79.19899615 397.4398497 99999999.07 -7.999999996 5.463987326 EDLTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EDLTEIR 7 0 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;Q8NHW5;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;; 112.17 0.014922 2492810000 3700270 3492710 3927580 3814590 4439200 4761570 4748940 4054520 3959500 3087330 FALSE TRUE 3846359.517 4092555.773 4029935.961 4569104.517 3684626.37 3655767.53 4376705.674 4000175.791 3816998.368 3692233.203 1.041743385 1.108422883 1.091463009 1.237490772 0.997939774 0.990123681 1.185381701 1.0834028 1.033791247 1 21.81606225 EDLTEIRDMLLANK ddPTM_MDA-MB-175_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 0 117.92 0.00025145 131710000 146820 124330 148590 86069 188640 190490 118690 141380 167170 131730 FALSE TRUE 152616.567 145682.7103 152462.3775 103093.1913 156575.0402 146251.5844 109386.7677 139485.0324 161153.5844 157539.9714 0.968748221 0.924734904 0.967769488 0.654393868 0.993875007 0.928345887 0.694342945 0.885394552 1.022937753 1 17.26535839 1.259239566 8.17843189 1.011745174 0.871429185 0.194206667 0.108956347 0.249983434 80.97039491 0.076903353 0.02643422 18.16517414 -1.259239566 -0.140315989 EDLTEIRDMLLANKVPAAAR ddPTM_MDA-MB-175_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 85.146 0.0015124 162330000 136250 157990 160670 107180 216800 196020 117370 148620 158180 190420 FALSE TRUE 141629.2552 185123.5535 164857.1922 128379.8841 179948.4134 150497.3257 108170.2327 146627.992 152487.1327 227729.1532 0.621919738 0.812911087 0.72391782 0.563739347 0.790186109 0.660861043 0.474995104 0.643870097 0.669598646 1 17.79695947 0.90527534 15.95783409 1.000000001 0.659428844 0.533647495 0.094676519 637.4715627 107394.5189 0.09363518 0.023408651 8.040357144 -0.90527534 -0.340571156 EDLVGPEVGAS(ph)PQSGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDLVGPEVGASPQSGRK 17 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 EDLVGPEVGAS(0.999)PQS(0.001)GRK;EDLVGPEVGAS(0.997)PQS(0.003)GRK;EDLVGPEVGAS(0.981)PQS(0.019)GRK;EDLVGPEVGAS(0.999)PQS(0.001)GRK 159.04 2.00E-09 1010760000 710640 459493 593340 455540 790730 793910 773360 615410 658560 435580 TRUE FALSE 738696.6159 538407.3484 608802.9278 545644.4523 656321.997 609536.4343 712742.0224 607161.4356 634858.5542 520923.5613 1.418051843 1.033563057 1.168699159 1.04745589 1.259919969 1.170107247 1.368227654 1.165548039 1.218717296 1 18.99071217 EDLYEAADKWVAAVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDLYEAADKWVAAVGK 16 1 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 112.34 0.00068102 307860000 555880 331120 515700 391160 620300 593830 605950 448520 525460 287180 FALSE TRUE 577826.5716 387987.2842 529139.5657 468530.2805 514861.6276 455921.9821 558454.0556 442508.323 506548.7972 343447.4226 1.682430945 1.129684658 1.540671238 1.364197981 1.499098825 1.327486981 1.626024884 1.288431049 1.474894741 1 18.38972973 -2.004674422 0.617157959 0.569109528 1.428072431 0.408523522 0.157177698 139.9412936 13.65073164 85.66541039 0.054121154 0.009892945 2.004674422 0.858962903 EDLYLKPIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 141.93 3.34E-05 9916030000 14763570 9221130 11697070 9706650 15176530 16051510 14386220 11453390 13317060 8375720 FALSE TRUE 15346447.14 10804787.35 12001905.25 11626596.4 12596828.85 12323790.07 13258590.49 11299876.04 12837781.61 10016781.97 1.532073593 1.078668516 1.198179744 1.160711737 1.257572431 1.230314297 1.323637723 1.128094439 1.281627338 1 23.25591576 -3.906892467 0.325930769 2.94E-10 1.241304823 0.269771252 0.119099765 208.6238076 3.607574838 141.4385472 0.095505192 0.00012391 3.906892467 1.241304823 EDMAALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 2066110000 3258130 2457600 2899930 2779380 3946310 3839710 4294300 2946240 3140060 1849390 FALSE TRUE 3386763.488 2879673.683 2975504.558 3329133.068 3275517.636 2947995.544 3957701.545 2906750.472 3027049.854 2211742.562 1.53126478 1.301993158 1.345321381 1.505208213 1.48096695 1.33288367 1.789404252 1.314235446 1.368626669 1 21.07675204 0.739908699 1.680344307 1.001449463 1.45301851 0.493940794 0.137176091 0.75551294 3.42964957 0.125803786 0.035835522 5.494253565 -0.739908699 0.451569048 EDMAALEKDYEEVGADSADGEDEGEEY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDMAALEKDYEEVGADSADGEDEGEEY 27 1 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 330.28 3.02E-95 71109000 279140 232010 328600 194930 466830 411360 261190 284650 360220 311660 FALSE TRUE 290160.6627 271855.9127 337163.5859 233486.5722 387478.4033 315827.8742 240717.2453 280834.7323 347255.7526 372723.8099 0.778487059 0.729376298 0.904593635 0.626433209 1.039585862 0.847350949 0.645832756 0.753466038 0.931670431 1 18.50774746 1.090694092 4.510146664 0.996964788 0.788690415 0.279365172 0.114785535 0.244086434 8.168682969 0.107700213 0.027464341 12.32236567 -1.090694092 -0.208274373 EDMAALEKDYEEVGVDSVEGEGEEEGEEY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDMAALEKDYEEVGVDSVEGEGEEEGEEY 29 1 P68363;P68363-2 P68363 TUBA1B Tubulin alpha-1B chain 0 ;;; 280.92 2.08E-71 288885000 1060560 1001230 1296270 727120 1774190 1590130 1024540 1171920 1389530 1167500 FALSE TRUE 1102431.728 1173183.464 1330051.861 870942.1658 1472613.818 1220846.406 944233.8777 1156212.329 1339521.087 1396249.272 0.789566555 0.840239266 0.952589117 0.623772691 1.054692631 0.87437568 0.676264544 0.828084464 0.959371019 1 20.4131251 1.175952896 4.647249116 0.9924631 0.828619053 0.211770216 0.116467745 0.309973149 12.37763168 0.104854711 0.027453573 14.99522189 -1.175952896 -0.163844048 EDNS(ph)EGEEILEEVGGDLEEEDDHHMEFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 91.967 0.0024469 32250000 21402 23163 19058 23891 17005 22468 27749 17093 20352 16475 TRUE FALSE 22246.96749 27141.06507 19554.66714 28616.56849 14114.49617 17250.14751 25573.96087 16863.89629 19619.5355 19702.96082 1.129117989 1.377512005 0.992473533 1.452399401 0.716364221 0.87551042 1.297975523 0.855906706 0.995765848 1 14.26612482 3.241766549 24.99999992 0.963036767 1.230320982 0.362474172 0.182319569 95.14107252 741907.5478 0.049591555 0.064452302 1744.883956 -3.241766549 0.267284215 EDPDGEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDPDGEHAR 9 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 132.01 0.00031705 434120000 1060710 1069190 1093450 1208220 1125880 1387880 1457990 1116890 1051720 813440 FALSE TRUE 1102587.65 1252815.065 1121946.205 1447202.31 934503.3198 1065565.904 1343708.934 1101919.916 1013868.803 972817.9938 1.133395617 1.287820613 1.153295079 1.487639331 0.960614756 1.095339427 1.381254194 1.132709226 1.042197831 1 19.89181039 1.338247244 3.50124871 1.015794462 1.213276128 0.227372286 0.140912623 0.344955653 6.861941607 0.110773077 0.035284751 21.78949898 -1.338247244 0.197481665 EDQDKVAVLSQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDQDKVAVLSQNR 13 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 163.8 3.48E-05 2682940000 2553390 1875850 2351120 1654610 3352290 3102020 2470580 2445580 2766430 2174870 FALSE TRUE 2654199.809 2198012.645 2412392.119 1981886.919 2782468.943 2381622.867 2276929.484 2412801 2666866.725 2600994.136 1.020455899 0.845066359 0.927488488 0.761972852 1.069771325 0.915658684 0.875407388 0.92764569 1.025325927 1 21.31063172 1.292726243 5.576848839 1.012760248 0.913484711 0.179092177 0.080976228 0.282678979 17.63237248 0.055758492 0.019107495 19.62123067 -1.292726243 -0.099275537 EDQEAAELLS(ph)EPEEESER ddPTM_MDA-MB-175_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 293.63 3.18E-49 613430000 610610 533340 634740 704770 700380 809610 810150 659920 706250 455630 TRUE FALSE 634717.3543 624936.9962 651281.8458 844171.4025 581329.6578 621590.3473 746648.3261 651074.8518 680832.2005 544901.9749 1.164828508 1.146879668 1.195227538 1.549216999 1.066851809 1.140737923 1.370243384 1.194847664 1.249458126 1 19.05563719 -1.242138041 7.252784903 0.999999258 1.232674251 0.219902692 0.13044252 1.52E-06 1.58E-07 0.122411814 0.028852649 0.0572614 1.242138041 0.232674992 EDQIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EDQIYR 6 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 187.93 0.0039122 19414270000 8959760 9737640 10037340 10105360 11774350 12906130 11347300 9952360 9962980 9045350 FALSE TRUE 9313498.243 11410003.92 10298921.33 12104170.05 9772950.193 9908876.902 10457868.98 9818964.893 9604414.296 10817613.15 0.860956859 1.05476169 0.952051177 1.118931679 0.90342944 0.915994755 0.966744589 0.907683124 0.887849673 1 23.36687888 EDQKMS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 99.539 0.010642 1344960000 5463950 1349548 2098543 1438587 3420420 4535470 3623820 2383920 2677330 868069 TRUE FALSE 5679670.965 1581322.371 2153232.755 1723135.215 2839018.23 3482175.828 3339775.519 2351967.452 2580973.416 1038150.5 5.470951431 1.523211105 2.074104625 1.659812536 2.734688496 3.354211 3.217043693 2.265536115 2.486126448 1 19.98558418 0.578913723 1.293520909 1.002930066 2.720720643 0.200482019 1.065898725 2.629566474 6.104519557 0.978561647 0.292702603 3.79239638 -0.578913723 1.717790577 EDQSILCTGESGAGKTENTKK ddPTM_MDA-MB-175_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 ; 139.83 9.61E-08 259790000 338280 202717 255254 133793 449260 327660 241829 274090 337130 168843 FALSE TRUE 351635.5556 237532.0678 261906.1289 160256.8561 372894.9457 251565.9307 222873.8111 270416.2719 324996.7572 201924.5532 1.741420496 1.176340688 1.297049442 0.793647199 1.846704325 1.245841215 1.103747947 1.339194603 1.609495983 1 17.62345682 -1.516471946 3.305829781 0.991789428 1.328431027 0.107026683 0.297606193 32925820.19 61854117.62 2595930.267 0.067621341 0.030445847 1.516471946 0.336641599 EDQTEYLEER ddPTM_MDA-MB-175_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 ;;;;;; 247.08 2.65E-12 38524170000 9862360 9323080 11083040 11171950 11225030 13093230 13521690 11606190 10641180 7968700 FALSE TRUE 10251733.59 10924246.47 11371873.13 13381728.37 9317003.41 10052525.76 12461824.61 11450628.01 10258206.01 9530014.195 1.075731198 1.146299076 1.193269275 1.404166677 0.977648429 1.054827995 1.307639669 1.201533153 1.07641036 1 23.18404693 3.205451228 24.9999195 1.130650137 1.199855827 0.121926577 0.120657094 584.4908922 441330.263 0.036942288 0.044157254 1604.912013 -3.205451228 0.06920569 EDQTEYLEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 218.06 1.75E-11 4126220000 2220890 2699630 2619340 1697930 3188270 3004740 1843180 2206860 2512530 2910560 FALSE TRUE 2308572.452 3163270.452 2687602.152 2033775.486 2646329.004 2306934.672 1698706.735 2177280.651 2422104.536 3480828.506 0.66322499 0.908769406 0.772115646 0.58427914 0.760258369 0.662754476 0.488017934 0.625506441 0.695841387 1 21.73099931 3.894742451 6.694147216 0.660722408 0.798974673 0.061821117 0.13917678 0.417877687 22.85383208 0.033791781 0.061697946 7847.701057 -3.894742451 0.138252265 EDS(ph)CHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSCHRLSPVKGEFHQEFQPEPSLLGDSTNSGEER 35 2 Q9Y2L9-2;Q9Y2L9;Q9Y2L9-3 Q9Y2L9-2 LRCH1 Leucine-rich repeat and calponin homology domain-containing protein 1 1 EDS(0.5)CHRLS(0.5)PVKGEFHQEFQPEPSLLGDSTNSGEER 191.99 4.20E-21 71920000 42808 39421 57587 56569 61931 67364 65325 62215 63033 33867 TRUE FALSE 44498.09289 46191.2501 59087.76453 67758.17936 51403.99074 51719.73191 60204.6558 61381.10969 60764.45464 40502.59023 1.098648078 1.140451755 1.458863845 1.672934471 1.269153169 1.276948749 1.486439644 1.51548603 1.500260954 1 15.30572655 4.260707904 7.913342489 1.425994256 1.117212452 0.275366625 0.175598998 0.201362069 53.62944891 0.041219623 0.10872359 18226.69408 -4.260707904 -0.308781804 EDS(ph)FESLDSLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EDSFESLDSLGSR 13 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EDS(0.998)FES(0.002)LDSLGSR;EDS(0.943)FES(0.057)LDSLGSR;EDS(1)FESLDSLGSR;EDS(1)FESLDSLGSR;EDS(0.929)FES(0.071)LDSLGSR 246.73 7.30E-12 136659000 555208 458506 590230 462456 751397 782286 641855 579268 575962 405391 TRUE FALSE 577128.0406 537250.8388 605611.8787 553928.4165 623674.8063 600611.9322 591544.7279 571503.86 555233.2401 484819.6048 1.19039749 1.108145862 1.249148906 1.142545415 1.286405913 1.238835902 1.220133679 1.178796926 1.145236774 1 18.88708851 0.791794209 1.554205559 1.000377643 1.204336081 0.613106275 0.048698576 0.479716273 2.050053679 0.046038898 0.013341531 6.191476211 -0.791794209 0.203958438 EDS(ph)GTFSLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDSGTFSLGK 10 0 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 EDS(0.549)GT(0.451)FSLGK;EDS(0.98)GT(0.02)FSLGK;EDS(0.999)GT(0.001)FSLGK;EDS(0.883)GT(0.117)FSLGK 232.56 1.68E-10 1666200000 3486800 1793690 3064890 2051700 3686980 3309770 4180940 2787120 3280350 1210250 TRUE FALSE 3624461.556 2101742.305 3144763.551 2457520.136 3060268.457 2541126.078 3853226.998 2749763.215 3162290.844 1447375.316 2.50416151 1.452105948 2.172735376 1.697914915 2.114357225 1.755678745 2.66221688 1.899827353 2.184845084 1 20.46500764 EDS(ph)LPEESSAPDFANLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSLPEESSAPDFANLK 17 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 EDS(1)LPEESSAPDFANLK 157.8 1.26E-08 26046000 54925 29266 53375 28225 78102 58606 59530 45445 58948 28734 TRUE FALSE 57093.48141 34292.20784 54765.99635 33807.82076 64826.24994 44995.64468 54863.88305 44835.88411 56826.47299 34363.87715 1.661438875 0.9979144 1.593708303 0.983818578 1.886464954 1.309387892 1.596556838 1.304738808 1.653668844 1 15.0686052 -1.218568071 3.419733232 0.999096765 1.427529691 0.182226918 0.279847002 84855139.07 145748207.4 845881.6498 0.060026126 0.060454959 1.218568071 0.428432926 EDS(ph)PGPEVQPMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSPGPEVQPMDK 13 0 O75382;O75382-3;O75382-2;E9PMK8;E9PMW5 O75382 TRIM3 Tripartite motif-containing protein 3 1 EDS(1)PGPEVQPMDK 216.27 2.91E-11 246120000 369160 173160 292430 190660 403930 415520 372010 289190 313890 148430 TRUE FALSE 383734.7219 202898.883 300050.966 228371.9789 335270.1229 319021.7773 342850.8841 285313.8811 302593.1602 177512.0166 2.161739409 1.143014917 1.690313545 1.286515602 1.888717898 1.797184119 1.931423521 1.607293334 1.704634796 1 17.43755717 3.219560629 24.99098939 1.70455963 1.548433999 0.000315476 0.350580265 839.6048873 1104343.126 0.093484971 0.111906494 1657.908771 -3.219560629 -0.156125631 EDSARPGAHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EDSARPGAHAK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;;;;; 122.33 0.0002362 5042600000 7070970 6374890 7462030 5728270 8961540 8804150 7972210 7628970 7823500 5948500 FALSE TRUE 7350137.356 7469727.768 7656496.632 6861304.709 7438260.632 6759519.591 7347327.349 7526716.136 7541933.763 7113994.684 1.033194103 1.050004688 1.076258413 0.964479876 1.045581416 0.950172145 1.032799106 1.058015429 1.06015454 1 22.76222847 -0.528162646 6.24492865 1 1.030353137 0.05091044 0.038937175 0 0 0.03757354 0.008856168 0.296372125 0.528162646 0.030353137 EDSEKDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSEKDEK 8 1 P29374;P29374-3;P29374-2;H7C485 P29374 ARID4A AT-rich interactive domain-containing protein 4A 0 58.596 0.062457 1892400000 0 2415500 1308900 2290800 628770 2024600 699710 1495700 782600 2410500 FALSE TRUE 0 2830343.335 1343011.009 2743913.403 521891.9 1554417.333 644864.9018 1475652.588 754434.3789 2882791.323 0 0.981806526 0.46587174 0.951825191 0.181037003 0.539205637 0.223694617 0.511883249 0.261702737 1 21.45903498 -1.220276334 5.0632686 1.000059228 0.474613229 0.223664909 0.301720018 0.00018515 2.85E-05 0.268127874 0.063191253 0.060217631 1.220276334 -0.525445999 EDSGLFS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDSGLFSPIR 10 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 EDSGLFS(1)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR;EDSGLFS(1)PIR 171.26 4.28E-06 1524410000 1259900 1341570 1335170 1280960 1692080 1772670 1530760 1401530 1442470 1505980 TRUE FALSE 1309641.825 1571974.212 1369965.627 1534330.065 1404460.846 1360994.258 1410775.031 1382744.783 1390555.786 1801047.947 0.727155447 0.872810862 0.76064917 0.851909616 0.77980203 0.755667976 0.78330787 0.767744571 0.772081492 1 20.78040516 -1.748946787 7.789226192 1.00236083 0.786904166 0.702622153 0.041821978 0.001602305 5.16E-05 0.037841678 0.00883744 0.017825972 1.748946787 -0.215456664 EDSGSSS(ph)PPGVFLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDSGSSSPPGVFLEK 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 EDS(0.005)GS(0.006)S(0.022)S(0.967)PPGVFLEK;EDS(0.012)GS(0.059)S(0.186)S(0.743)PPGVFLEK 90.966 0.0060946 155385000 302470 233910 272850 264810 338030 367850 388560 301330 299900 196250 TRUE FALSE 314411.7492 274082.2229 279960.6951 317188.6276 280571.7813 282422.4123 358103.6519 297291.1642 289106.6576 234701.4301 1.339624343 1.167791022 1.19283762 1.35145588 1.195441294 1.203326338 1.525783851 1.266678112 1.231806119 1 17.84046711 0.797193714 3.118400451 1.000098062 1.28127568 0.406453994 0.101218235 1.157935058 16.27012387 0.097813403 0.025502485 6.268934237 -0.797193714 0.281177618 EDSHPFDLGLYNEAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDSHPFDLGLYNEAVK 16 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 ;;; 218.98 1.28E-14 1056110000 1226460 860290 1070380 885300 1409630 1394600 1342490 1153400 1183250 848920 FALSE TRUE 1274881.588 1008038.115 1098274.982 1060409.698 1170021.596 1070725.285 1237262.126 1137940.56 1140665.064 1015249.62 1.255732149 0.992896816 1.081778274 1.044481747 1.152447214 1.054642389 1.218677753 1.120848052 1.123531633 1 19.95340306 3.227602375 24.99562589 1.122510006 1.085667283 0 0.083067918 766.9428849 1749385.444 0.022529851 0.02718437 1688.893931 -3.227602375 -0.036842723 EDSLDEEFFHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSLDEEFFHHK 12 0 Q5JRA6-2;Q5JRA6;A0A0A0MRH6 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 134.13 8.73E-05 41889000 69519 67570 61479 93667 84467 113310 85234 73110 71919 64025 FALSE TRUE 72263.6638 79174.62188 63081.19325 112194.053 70109.32951 86995.46973 78553.13636 72130.08003 69330.64924 76569.47292 0.943765982 1.034023337 0.823842595 1.465258265 0.915630301 1.136163884 1.025906714 0.942021373 0.905460709 1 16.22448171 1.813045628 3.998055547 0.942882327 1.055893738 0.074126139 0.162941823 0.577955221 15.99126464 0.079435137 0.0425987 65.01979988 -1.813045628 0.113011411 EDSQRPGAHLTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EDSQRPGAHLTVK 13 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646;F8VYN5 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;;;;;;;; 101.53 0.0011412 28194477000 17860939 22875510 27977189 23687952 30911448 33141745 29790685 28977180 28233696 21728453 FALSE TRUE 18566102.66 26804200.9 28706297.53 28373358.2 25657131.11 25445076.99 27455613.27 28588788.3 27217570.8 25985727.35 0.71447308 1.031497042 1.104694787 1.091882395 0.987354742 0.979194334 1.056565125 1.100172718 1.047404617 1 24.63121611 4.73632889 5.070240968 1.050880523 0.699066796 0.838653738 0.043394922 0.062710728 5.220311254 0.011267453 0.077286923 54491.5159 -4.73632889 -0.351813728 EDSQRPGAHLTVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDSQRPGAHLTVKK 14 2 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 86.291 0.004443 1743200000 234240 330490 440060 273300 606820 455620 302200 372280 418560 417300 FALSE TRUE 243487.9761 387249.0866 451528.3251 327357.9243 503672.9532 349809.16 278512.7743 367290.1955 403496.1074 499061.9453 0.48789129 0.775953948 0.904754068 0.655946476 1.00923935 0.700933348 0.558072554 0.735961135 0.808509066 1 18.92885937 0.881780101 3.20632666 0.999741961 0.734279491 0.247041358 0.143334635 0.712838096 14.91078232 0.135297129 0.035226522 7.6169324 -0.881780101 -0.26546247 EDSVKPGAHLTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EDSVKPGAHLTVK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 154.47 2.78E-05 6593440000 5893530 6170880 8299440 6181070 11064780 10516110 10355430 9124940 9784110 5936450 FALSE TRUE 6126211.115 7230680.637 8515730.224 7403667.197 9183992.648 8073902.826 9543744.338 9002635.105 9431981.792 7099583.717 0.862897229 1.018465438 1.19946895 1.04283117 1.293595937 1.13723609 1.34426816 1.268051123 1.328526033 1 22.759303 5.596243279 0.58963389 1.248335824 2.51E-09 0.496577977 0.110030875 6.526907319 0.810583204 0.046240704 6.94334588 394678.3274 -5.596243279 -1.248335821 EDTDDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDTDDTER 8 0 P40818 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 ; 86.011 0.038005 44711000 108649 127868 134014 140568 148173 168603 181725 139218 137849 108377 FALSE TRUE 112938.5464 149828.3343 137506.5149 168371.9308 122986.6064 129447.5085 167480.9197 137352.0104 132887.8414 129611.3981 0.871362766 1.15598116 1.060913754 1.299051883 0.948887275 0.99873553 1.292177401 1.059721694 1.025278975 1 16.98383307 4.747470707 24.07429382 1.100511818 0.871362565 0.250282352 0.114705523 944.399431 2551589.579 0.026294151 0.311759685 55907.58174 -4.747470707 -0.229149253 EDTEEHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 EDTEEHHLR 9 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;A0A2R8Y4L2;F8VYN5;P22626;P22626-2;A0A087WUI2 F8W6I7;P22626 HNRNPA1;HNRNPA1L2;HNRNPA2B1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoproteins A2/B1" 0 ;;;;;;;;;;; 231.3 1.36E-07 2837515600 3377106.7 3342510 3589017 3615390 3923153.2 4551976 4454416 3765460 3551387.4 2743272 FALSE TRUE 3510437.48 3916560.091 3682549.731 4330503.351 3256297.02 3494848.56 4105267.234 3714990.168 3423573.661 3280763.625 1.070006218 1.193795268 1.122467252 1.319968107 0.992542405 1.065254605 1.251314542 1.132355327 1.043529511 1 21.64560022 1.165051372 3.560674801 1.004744412 1.147941482 0.234284819 0.089587997 0.312186234 7.04999547 0.081574548 0.021818431 14.62350143 -1.165051372 0.14319707 EDTEEHHLRDYFEQYGK ddPTM_MDA-MB-175_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 74.786 0.015104 192670000 132120 177330 220330 60767 377720 247530 84950 163590 220600 320830 FALSE TRUE 137336.1996 207785.0481 226071.9808 72786.53123 313515.2893 190044.9089 78291.39702 161397.3436 212660.6491 383690.4958 0.357934849 0.54154338 0.589204015 0.189701158 0.817104653 0.495307835 0.204048309 0.420644622 0.5542505 1 18.5495835 0.841752253 3.960617507 0.999937641 0.451584254 0.470363776 0.173853448 0.920353031 21.84745435 0.163548772 0.041823804 6.946279488 -0.841752253 -0.548353387 EDTEEYNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDTEEYNLR 9 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 268.28 1.88E-15 2796210000 2421540 1740300 1928850 2011550 2153840 2700840 2672990 2067710 2077230 1443750 FALSE TRUE 2517144.269 2039182.987 1979117.416 2409428.586 1787731.046 2073610.842 2463474.059 2039995.73 2002470.898 1726625.17 1.457840597 1.181022391 1.146234545 1.395455498 1.035390354 1.200961782 1.426756717 1.181493103 1.159760052 1 20.71952349 -4.662041305 0.212677833 7.68E-14 1.274684463 0.267810725 0.128350312 180.3604052 2.053036718 76.93405174 0.260639714 2.18E-05 4.662041305 1.274684463 EDTHHLVNYIPQGSIDSLFEGTWYLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EDTHHLVNYIPQGSIDSLFEGTWYLVR 27 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;;; 258.1 3.49E-53 1755563000 488218 524405 546866 564857 552210 715675 656129 560301 621493 484413 FALSE TRUE 507493.2236 614467.4794 561117.7772 676584.0287 458345.5414 549470.3274 604699.8945 552791.0816 599125.5883 579324.4527 0.876008636 1.060662081 0.968572576 1.167884465 0.791172441 0.948467348 1.043801779 0.954199463 1.034179699 1 19.14401204 1.229960175 24.84305764 1.017089839 0.980189598 0.026090871 0.097331251 978.6116523 2826681.079 0.08341175 0.022196725 16.98087931 -1.229960175 -0.036900241 EDTLLLIGHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDTLLLIGHLER 12 0 Q92621 Q92621 NUP205 Nuclear pore complex protein Nup205 0 131.13 0.00020417 56355000 35136 34925 40142 47081 45300 48410 50116 41421 39939 28204 FALSE TRUE 36523.19641 40923.09707 41188.1335 56393.48128 37599.92218 37167.51116 46187.77697 40865.81925 38501.60319 33730.0338 1.082809363 1.21325396 1.221111539 1.671907049 1.114731233 1.101911471 1.369336812 1.211555834 1.141463522 1 15.04174614 EDVETGLDPLS(ph)LLATECTGGKTPDSEDKLFSPVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDVETGLDPLSLLATECTGGKTPDSEDKLFSPVIAR 36 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 EDVET(0.001)GLDPLS(0.258)LLAT(0.246)ECT(0.246)GGKT(0.246)PDS(0.002)EDKLFS(0.001)PVIAR 46.05 0.044541 77278000 15595 4721 5825.6 5623.9 10777 9603.3 9844.4 6200.6 6699 4178.5 TRUE FALSE 16210.70264 5531.795026 5977.419922 6736.290634 8945.129389 7373.079114 9072.770204 6117.491099 6457.904299 4997.197073 3.243959045 1.106979562 1.196154531 1.348013804 1.790029342 1.475442935 1.815571824 1.22418448 1.292305307 1 12.2869034 4.743965138 24.96738684 1.392338368 3.24395984 0.828595052 0.256570735 227.5288326 1051087.642 0.061862743 0.534724522 55458.11931 -4.743965138 1.851621472 EDVETGLDPLSLLATECTGGKT(ph)PDSEDKLFSPVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDVETGLDPLSLLATECTGGKTPDSEDKLFSPVIAR 36 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 EDVETGLDPLSLLATECT(0.032)GGKT(0.968)PDSEDKLFSPVIAR 237.13 6.25E-48 81489000 135990 38004 73242 41576 106200 107120 123500 71806 82664 28853 TRUE FALSE 141358.9902 44530.89137 75150.74669 49799.60871 88148.16193 82243.00342 113819.7473 70843.55802 79688.93879 34506.19293 4.09662667 1.29051882 2.17789157 1.443207856 2.55456063 2.383427334 3.298531007 2.053067928 2.309409762 1 15.07456769 EDVEVAES(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLR;EDVEVAES(1)PLR;EDVEVAES(1)PLR 263.7 8.53E-21 1148790000 839090 787660 785900 743835 953430 1043140 951600 850390 770910 688473 TRUE FALSE 872217.9211 922934.4779 806381.1996 890963.3429 791366.3092 800886.5439 877011.1055 838991.913 743165.0997 823366.1027 1.059331831 1.120928436 0.979371384 1.082098643 0.961135401 0.972697979 1.065153281 1.018977962 0.902593752 1 19.65117453 4.038180546 1.112335028 0.997548199 1.093193161 0.275841708 0.053160305 0.935886541 1.896946668 0.016897827 0.080028676 10918.94167 -4.038180546 0.095644962 EDVEVAES(ph)PLRVLAETPDSFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDVEVAESPLRVLAETPDSFEK 22 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 EDVEVAES(1)PLRVLAETPDSFEK 106.04 0.00030246 12636000 44198 37225 46326 30163 67529 58905 38392 44695 54314 47718 TRUE FALSE 45942.97117 43618.10418 47533.29362 36129.15137 56050.4447 45225.20646 35382.73472 44095.93663 52359.24975 57067.42848 0.805064682 0.764325734 0.83293211 0.633095836 0.98217926 0.792487197 0.62001628 0.772698855 0.917497969 1 15.80037993 1.099782154 3.631885964 0.995931058 0.771931312 0.381856324 0.095965257 0.211703303 5.062452721 0.089721225 0.023375066 12.58294082 -1.099782154 -0.223999746 EDVFVHQTAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 169.52 1.68E-05 305110000 227350 284720 357210 377260 412700 470140 523030 390000 385480 242440 FALSE TRUE 236325.9536 333618.4452 366519.1861 451880.902 342549.4014 360957.11 482033.5419 384772.6879 371606.6501 289941.4762 0.81508157 1.150640638 1.264114368 1.558524527 1.181443255 1.244930925 1.662520134 1.327070183 1.281660889 1 18.1454022 4.66957433 1.758848713 1.347937761 0.683964699 0.421810941 0.176490838 0.666438004 2.313727038 0.044355349 0.706451481 46727.69196 -4.66957433 -0.663973062 EDVRPEEIADQELAEALQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDVRPEEIADQELAEALQK 19 1 Q5TDH0;Q5TDH0-3 Q5TDH0 DDI2 Protein DDI1 homolog 2 0 ; 213.15 4.45E-17 78075000 137689 104368 132175 94431 159926 151812 149423 130258 141369 93562 FALSE TRUE 143125.068 122292.3921 135619.5891 113109.17 132741.8356 116555.9637 137710.8348 128512.1046 136281.1573 111893.6825 1.279116611 1.09293384 1.212039733 1.010862878 1.186321092 1.041667064 1.230729311 1.148519752 1.217952204 1 16.77176906 4.749643279 23.5917317 1.135040052 1.279116799 0.227285812 0.083017165 1066.703809 2270599.456 0.018029206 0.255932747 56187.96186 -4.749643279 0.144076747 EDVSLHGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDVSLHGYK 9 0 Q12792;Q12792-3;Q12792-4;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 122.13 0.0017752 0 272690 387770 424710 467520 524150 551960 567850 446460 406970 403150 FALSE TRUE 283456.0118 454366.4811 435778.2915 559994.0606 435055.1702 423775.655 523340.4332 440475.934 392323.2292 482139.5237 0.58791283 0.942396254 0.903842705 1.161477193 0.902342888 0.878948176 1.085454329 0.913586031 0.813713064 1 18.87909117 4.745385082 4.386239317 0.959341809 0.559264231 0.563185664 0.097237229 0.155140651 7.203956396 0.022880075 0.194369578 55639.73868 -4.745385082 -0.400077579 EDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 34 1 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR;EDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR 202.7 4.55E-27 235730000 190323 150869 171717 144134 231952 225110 201060 180659 196824 145185 TRUE FALSE 197837.099 176779.5772 176192.0861 172643.275 192524.8819 172831.6141 185300.3918 178237.5616 189740.3427 173631.221 1.139409709 1.018132431 1.014748874 0.99431009 1.108814882 0.995394797 1.067206639 1.026529449 1.092777794 1 17.40566686 EDYDSVEQDGDEPGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EDYDSVEQDGDEPGPQR 17 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 145.6 1.24E-05 0 98337 52621 71018 68343 78897 110450 88098 70999 75230 45560 FALSE TRUE 102219.4207 61658.24742 72868.78742 81861.04142 65486.11612 84799.66139 81192.64856 70047.37454 72522.487 54486.6097 1.876046633 1.131622022 1.337370554 1.502406589 1.201875405 1.556339472 1.490139486 1.285588788 1.331014857 1 15.73361411 0.666703446 1.012374399 1.000959561 1.419207895 0.300188817 0.196980648 1.357896163 2.347102798 0.175244082 0.056214741 4.64198194 -0.666703446 0.418248334 EEADEYIDIGALNGIFVLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;; 237.3 3.15E-29 100223000 63040 59064 66470 59830 78385 84448 79089 69068 70018 61765.8 FALSE TRUE 65528.86788 69207.78255 68202.26281 71664.19543 65061.1457 64836.23182 72889.79752 68142.25643 67498.06586 73867.62593 0.887112142 0.936916297 0.923303842 0.970170552 0.880780245 0.877735422 0.986762423 0.922491492 0.913770613 1 16.17265459 -4.999999989 0.283168212 1.566791744 0.919319619 0.317910659 0.034193654 291.3219893 2.776258533 97.18146868 0.037845707 1.00E-05 4.999999989 -0.647472124 EEADKLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 108.81 0.0034105 459300000 689500 678570 654620 487190 1060000 1023100 773450 717810 786670 816980 FALSE TRUE 716721.9924 795109.119 671679.935 583554.7279 879821.5786 785500.5302 712824.968 708188.9311 758357.9004 977051.589 0.733555936 0.813784173 0.687455957 0.597260917 0.900486309 0.803949903 0.72956738 0.724822455 0.776169763 1 19.89807521 -4.999995715 0.469484327 7.46120982 0.747604556 0.486839948 0.076566281 1456.493956 7.779231703 9828.94711 0.039257837 1.00E-05 4.999995715 -6.713605264 EEAEKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEAEKPER 8 1 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 90.629 0.011911 2388600000 1883970 1409320 1644100 1668900 2067750 2348020 2088460 1603470 1698350 1028120 FALSE TRUE 1958350.59 1651359.747 1686946.597 1999003.439 1716274.594 1802727.94 1924761.048 1581978.107 1637226.715 1229560.429 1.59272415 1.343048871 1.371991613 1.625787063 1.395844037 1.466156438 1.565405817 1.286620868 1.331554494 1 20.22971121 0.855780494 0.986024775 1.00339196 1.47108643 0.674002701 0.099123857 0.408487212 0.79288718 0.090730817 0.029873021 7.174315881 -0.855780494 0.46769447 EEAIEHNYGGHDDDLSVR ddPTM_MDA-MB-175_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 ;;; 204.29 6.30E-16 1005722000 512179 501057 541897 542298 549779 675845 636668 553928 537583 498305 FALSE TRUE 532400.2224 587109.6421 556019.281 649562.9258 456327.762 518890.2413 586764.2985 546503.5012 518235.4928 595938.3241 0.893381414 0.985185242 0.933014808 1.089983476 0.765729847 0.870711314 0.984605747 0.917047082 0.869612629 1 19.1848035 3.248866779 24.99998018 0.902879873 0.973063861 0.182097836 0.07683371 391.3915026 949405.1724 0.021126113 0.028292734 1773.645328 -3.248866779 0.070183988 EEALGLYQWIYHTHEDAQEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEALGLYQWIYHTHEDAQEAR 21 0 Q8TCU6;Q8TCU6-3;Q8TCU6-2;H0YDZ4 Q8TCU6 PREX1 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein" 0 98.132 0.0005951 39597000 11759 18153 17966 15655 18411 23917 17704 15680 17050 12244 FALSE TRUE 12223.2544 21270.63654 18434.20872 18751.51227 15281.5048 18362.63922 16316.31422 15469.83525 16436.37383 14642.97737 0.834751983 1.452616909 1.258911234 1.280580567 1.043606393 1.254023601 1.114275724 1.056467879 1.12247485 1 13.83792131 1.849569272 0.788102874 1.025344218 1.211825658 0.109138909 0.156411421 1.178670642 1.388193611 0.13163814 0.063030737 70.72440009 -1.849569272 0.18648144 EEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 EEAPAS(1)PLRPLY(0.001)PQIS(0.999)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK;EEAPAS(0.999)PLRPLY(0.001)PQIS(1)PLK;EEAPAS(1)PLRPLYPQIS(1)PLK 116.24 6.96E-05 364264000 1141430 614860 835990 714750 961880 1166910 1249360 908300 944870 513534 TRUE FALSE 1186494.538 720457.4221 857776.5862 856125.4167 798379.9812 895912.8372 1151431.899 896125.7242 910864.3133 614151.1551 1.931925924 1.17309463 1.396686433 1.393997894 1.2999731 1.458782304 1.874834703 1.45912894 1.483127249 1 19.22823425 2.470238189 24.98937792 1.523133025 1.415478378 0 0.272522143 712.4196556 2586456.393 0.088839231 0.074484336 295.282826 -2.470238189 -0.107654647 EEAPAS(ph)PLRPLYPQISPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EEAPASPLRPLYPQISPLK 19 1 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK;EEAPAS(1)PLRPLYPQISPLK 189.39 8.54E-15 1888690000 2224190 1732775 2114629 1822100 2553530 2610250 2797480 2345500 2429200 1615505 TRUE FALSE 2312002.739 2030365.627 2169737.969 2182505.942 2119481.883 2004058.996 2578206.208 2314062.409 2341773.567 1932032.274 1.196668798 1.05089633 1.123034019 1.12964259 1.097021986 1.037280289 1.334452971 1.197734862 1.212077872 1 20.88168776 2.262142218 24.99999971 1.206740186 1.104737608 0.153194592 0.087222117 309.9182672 328558.3272 0.028102885 0.023499995 182.869896 -2.262142218 -0.102002578 EEAQAEIEQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEAQAEIEQYR 11 0 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 202.03 8.12E-05 483440000 543510 611100 704440 611880 800820 936010 692830 731520 668290 552010 FALSE TRUE 564968.1945 716051.6713 722798.2851 732908.0377 664696.9024 718635.8629 638524.1742 721715.1709 644238.3734 660165.7906 0.855797441 1.084654312 1.094873887 1.110187847 1.006863597 1.08856877 0.967217907 1.093233217 0.97587361 1 19.33246886 4.744585988 24.71533029 1.051435985 0.85579734 0.547360258 0.051964085 405.3453256 1662620.959 0.011644313 0.10618214 55537.4567 -4.744585988 -0.195638644 EEAS(ph)DDDMEGDEAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 418.75 7.31E-141 1359090000 1035450 952110 1045870 1062800 1027380 1291130 1576250 1102950 1010900 712510 TRUE FALSE 1076330.366 1115627.486 1073126.231 1273018.668 852746.3146 991284.6248 1452699.406 1088166.759 974517.9065 852112.6927 1.263131479 1.30924876 1.259371255 1.493955763 1.000743589 1.163325735 1.704820758 1.277022122 1.143649091 1 19.70068472 1.065889175 3.217260097 1.005806863 1.315947721 0.242437123 0.176882344 0.308721949 6.530003541 0.169116345 0.044483361 11.63829002 -1.065889175 0.310140858 EEASDYLELDTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEASDYLELDTIK 13 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;; 248.05 5.59E-17 86682000 256564 170939 225855 207967 284414 290757 304545 204306 233544 116736 FALSE TRUE 266693.3448 200296.4435 231740.9668 249102.2519 236069.4099 223233.0932 280673.9671 201567.6122 225138.7971 139608.1842 1.910298787 1.434704167 1.659938264 1.784295479 1.690942485 1.598997183 2.01044064 1.443809426 1.612647557 1 17.09102399 0.529623571 1.044255348 1.000403167 1.699280572 0.604218903 0.168845826 1.046222794 1.642548776 0.152849981 0.047968176 3.385505868 -0.529623571 0.698877405 EEASLLSHS(ph)PGTSNQSQPCS(ph)PKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 2 EEASLLSHS(1)PGTS(0.004)NQS(0.432)QPCS(0.563)PKPIR 167.34 1.69E-11 477600000 115880 96466 125150 101820 158960 173330 150310 143620 161100 97463 TRUE FALSE 120455.0319 113033.2851 128411.5118 121959.6921 131940.036 133076.7343 138528.3094 141695.0088 155302.0425 116559.0088 1.033425328 0.969751598 1.101686718 1.046334328 1.131959145 1.141711273 1.188482219 1.215650427 1.332389869 1 16.83070099 3.102791329 0.947201372 1.204005555 1.015185838 0.384544704 0.082147322 0.490681731 0.965355818 0.037241623 0.052440751 1267.042928 -3.102791329 -0.188819718 EEASLLSHS(ph)PGTSNQSQPCSPKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.968)PGT(0.007)S(0.025)NQSQPCSPKPIR;EEASLLSHS(1)PGTSNQSQPCSPKPIR 299.97 2.17E-63 2927790000 528440 697980 796790 677390 955280 1003980 843620 892980 864850 654250 TRUE FALSE 549303.2192 817852.6355 817555.002 811375.7202 792901.8468 770820.8605 777494.86 881011.0637 833724.2174 782437.7611 0.702040784 1.045262225 1.044881833 1.036984359 1.013373697 0.98515294 0.993682691 1.125982292 1.065547011 1 19.57761647 4.739230227 24.97908293 1.038778645 0.702040679 0.865314115 0.039321856 20.2635818 755755.2046 0.010470161 0.062958168 54856.76934 -4.739230227 -0.336737966 EEASLLSHSPGTSNQS(ph)QPCSPKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHS(0.015)PGT(0.028)S(0.013)NQS(0.597)QPCS(0.348)PKPIR 184.3 1.15E-17 611490000 351320 430490 501180 449620 609110 611220 513210 566820 545310 372670 TRUE FALSE 365190.3849 504423.3088 514241.1625 538553.494 505573.6998 469273.4181 472983.2592 559222.705 525684.3996 445687.5513 0.81938655 1.131786848 1.153815405 1.208365575 1.134368008 1.052920183 1.061244044 1.254741586 1.179490874 1 18.76567314 4.738455124 5.760106174 1.142043441 0.809338565 0.617731831 0.073039446 0.088919481 12.86429585 0.017814652 0.116356265 54758.95158 -4.738455124 -0.332704876 EEASLLSHSPGTSNQSQPCS(ph)PKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEASLLSHSPGTSNQSQPCSPKPIR 25 1 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 EEASLLSHSPGT(0.001)SNQS(0.124)QPCS(0.875)PKPIR;EEASLLSHSPGT(0.052)S(0.052)NQS(0.191)QPCS(0.705)PKPIR;EEASLLSHSPGTSNQS(0.047)QPCS(0.953)PKPIR 173.96 2.28E-12 2477920000 618792 642640 848430 636330 1023200 1052320 916300 967650 932880 658697 TRUE FALSE 643222.386 753008.421 870540.7828 762194.1747 849276.8295 807934.6281 844478.0117 954680.2345 899305.831 787756.0656 0.816524828 0.95589035 1.105089279 0.967551007 1.078096211 1.025615242 1.072004455 1.211898297 1.141604451 1 19.58738943 5.925625286 0.528493205 1.110484552 6.79E-12 0.573738366 0.068658741 9.49226717 0.772247602 0.036854416 8.564366843 842607.434 -5.925625286 -1.110484552 EEASNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEASNFR 7 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;; 200.12 0.0008406 2093350000 1394816 1590826 1594348 1535545 1901907 1968018 1716594 1609705 1506643 1534314 FALSE TRUE 1449884.413 1864037.991 1635898.019 1839271.218 1578621.527 1510975.645 1582042.877 1588129.537 1452419.213 1834933.452 0.790156401 1.015861359 0.89152989 1.002363991 0.860315411 0.823449833 0.862179974 0.865497076 0.791537814 1 20.80729631 3.062602398 24.99779575 0.858438305 0.929363182 0.111959333 0.077087189 111.0625241 44347.14324 0.02041331 0.024398571 1155.054292 -3.062602398 0.070924877 EEATS(ph)PGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEATSPGAK 9 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 EEAT(0.041)S(0.959)PGAK;EEAT(0.068)S(0.932)PGAK;EEAT(0.015)S(0.985)PGAK;EEAT(0.041)S(0.959)PGAK 169.21 6.15E-05 1456590000 5812370 3417600 4580290 3319910 5977600 5966700 6103310 4825700 5100030 2902000 TRUE FALSE 6041846.856 4004546.215 4699656.12 3976578.289 4961529.687 4581024.351 5624916.614 4761019.385 4916480.917 3470591.338 1.740869572 1.153851268 1.354136994 1.14579272 1.429592022 1.319954989 1.620737237 1.371817918 1.416611879 1 21.72675007 -1.055126106 4.707069858 0.9999862 1.38677979 0.317068667 0.173471591 2.36E-05 4.73E-06 0.157521626 0.03712688 0.088079308 1.055126106 0.38679359 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGK;EEAT(0.003)YGVWAERDS(0.993)DDERPS(0.004)FGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(1)DDERPSFGGK;EEATYGVWAERDS(0.86)DDERPS(0.14)FGGK;EEATYGVWAERDS(1)DDERPSFGGK 227.96 3.98E-33 8435491000 3629726 2766519 3463863 2834052 4228554 4164359 4138830 3512510 3890030 2433040 TRUE FALSE 3773030.385 3241647.118 3554134.115 3394619.027 3509785.901 3197249.734 3814417.69 3465430.549 3750028.58 2909747.605 1.296686482 1.114064709 1.221457871 1.166636935 1.206216613 1.098806552 1.310910157 1.190972902 1.288781396 1 21.47246259 4.772098891 22.35629637 1.189131092 1.296687346 0.131837327 0.087275826 7061.01813 4706459.053 0.018891773 2.448470461 59169.63513 -4.772098891 0.107556253 EEATYGVWAERDS(ph)DDERPSFGGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEATYGVWAERDSDDERPSFGGKR 24 3 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 EEATYGVWAERDS(1)DDERPSFGGKR 132.85 3.30E-05 207530000 76837 74974 80012 31987 109500 92007 46638 81601 89931 104620 TRUE FALSE 79870.58409 87850.20128 82097.17845 38313.93313 90887.22911 70639.76863 42982.39169 80507.27207 86694.40088 125118.2859 0.6383606 0.702137187 0.656156515 0.306221691 0.72641044 0.56458389 0.343534052 0.643449289 0.692899525 1 16.93293313 0.858018103 2.017312771 0.998525251 0.56640475 0.484940924 0.133764432 0.451404371 3.555632172 0.126282858 0.035008841 7.211375388 -0.858018103 -0.432120501 EEAYHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEAYHSR 7 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 72.485 0.051478 26673000 37346 43853 39015 42752 42795 63903 40807 42913 43129 47459 FALSE TRUE 38820.44892 51384.41162 40031.76295 51208.218 35520.72119 49062.49671 37608.44071 42337.82143 41576.79571 56757.68239 0.683968183 0.90532963 0.705310035 0.902225317 0.625831071 0.864420368 0.662614101 0.745939926 0.732531597 1 15.79252806 -0.961131763 4.632591506 1.000003566 0.759622169 0.369400389 0.094580148 0.018213759 52143582.22 461.501567 0.019766541 0.109362451 0.961131763 -0.240381398 EEDACHLIIPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEDACHLIIPLR 12 0 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 0 107.85 0.0017698 76058000 130870 118000 150420 145140 151730 162340 161000 142870 144480 113490 FALSE TRUE 136036.8487 138265.5821 154340.0688 173848.2588 125938.9888 124638.9953 148380.3993 140955.0613 139280.193 135726.1926 1.002288844 1.018709649 1.137142845 1.280874793 0.927890088 0.918312029 1.093233343 1.038525126 1.026185074 1 17.05033964 EEDAFHFVSYVPVNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEDAFHFVSYVPVNGR 16 0 Q5LJB0;Q5LJA5;Q5LJA9;Q9Y5K5-2;Q9Y5K5-4;Q9Y5K5-3;Q9Y5K5;H0Y4E0;H0Y6Y4 Q5LJB0 UCHL5 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L5 0 ; 106.52 0.001199 249890000 227200 248800 249480 269800 259940 321930 310010 262240 240580 207460 FALSE TRUE 236170.0314 291529.4646 255981.6538 323165.6347 215755.4916 247166.6364 285710.6061 258725.1017 231921.5728 248107.8149 0.951884694 1.175011213 1.031735553 1.302520982 0.869603772 0.996206574 1.15155827 1.042793037 0.934761256 1 17.92060765 3.221922156 24.99999145 1.014331665 1.113586113 0.205482413 0.109439073 441.5183439 663398.5229 0.031174275 0.03735755 1666.948398 -3.221922156 0.099254448 EEDCHS(ph)PTSKPPKPDQPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEDCHSPTSKPPKPDQPLK 19 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 EEDCHS(0.944)PT(0.028)S(0.028)KPPKPDQPLK;EEDCHS(0.89)PT(0.096)S(0.013)KPPKPDQPLK;EEDCHS(0.875)PT(0.111)S(0.014)KPPKPDQPLK;EEDCHS(0.998)PT(0.001)SKPPKPDQPLK 172.61 4.18E-12 984875000 1597960 721260 1119170 888070 1609240 1455950 2152880 1208010 1423630 424503 TRUE FALSE 1661048.695 845130.7944 1148336.49 1063727.595 1335701.96 1117827.678 1984131.64 1191818.602 1372393.834 507676.2352 3.271866161 1.664704266 2.261946512 2.095287353 2.631011394 2.201851495 3.908261806 2.347595808 2.703285557 1 18.9535492 3.221041366 24.18701403 2.604966108 2.27200455 0 0.76898953 605.0957477 835390.3883 0.209449652 0.250942295 1663.571095 -3.221041366 -0.332961558 EEDEENDNDNES(ph)DHDEADS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 EEDEENDNDNES(0.958)DHDEADS(0.042);EEDEENDNDNES(0.999)DHDEADS(0.001);EEDEENDNDNES(1)DHDEADS;EEDEENDNDNES(1)DHDEADS 211.06 3.98E-25 241261000 494487.9 487757.2 531882.4 491597 582579.6 718024 630141.9 529918 519614.8 418524.2 TRUE FALSE 514010.6641 571525.7049 545743.6923 588833.4193 483552.9277 551273.8078 580749.7313 522815.316 500913.9648 500526.0039 1.026940978 1.141850175 1.090340338 1.176429226 0.966089522 1.101388946 1.16027884 1.044531776 1.000775107 1 18.9330855 1.491470502 5.238059964 1.005750245 1.095389194 0.296420985 0.058729892 0.196395096 12.02457831 0.034555451 0.014631009 31.00776771 -1.491470502 0.08963895 EEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEK;EEDEEPES(1)PPEK;EEDEEPES(1)PPEK 284.24 2.93E-28 591280000 2522730 1210280 1578420 1505520 2125320 2495270 2919610 1724430 1868730 731810 TRUE FALSE 2622329.328 1418136.175 1619554.922 1803307.362 1764058.866 1915781.359 2690763.339 1701316.836 1801474.772 875194.1582 2.996282944 1.620367506 1.850509292 2.060465493 2.015620019 2.188978686 3.074475891 1.94393075 2.058371569 1 19.73924358 2.723079782 20.75306111 2.181600696 2.064504363 0 0.581274631 710.282296 952168.64 0.179867853 0.170569155 528.5423386 -2.723079782 -0.117096333 EEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 EEDEEPESPPEKK 13 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK;EEDEEPES(1)PPEKK 169.92 1.70E-05 32809110000 30470090 9045480 14679180 10394740 21943680 23557080 27992240 15124700 17153940 5225703 TRUE FALSE 31673072.68 10598970.83 15061731.49 12450788.55 18213701.11 18086305.18 25798135.08 14921978.14 16536573.05 6249579.451 5.068032646 1.695949449 2.410039205 1.992260222 2.914388281 2.89400356 4.127979377 2.387677163 2.646029734 1 22.57532768 EEDEPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEDEPEER 8 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 150.05 0.0011524 547220000 429070 522810 534390 530990 580110 675460 548800 521600 518610 460820 FALSE TRUE 446010.0149 612598.5506 548316.6424 636018.2372 481503.1094 518594.6517 505783.622 514608.8052 499945.3274 551108.8561 0.809295677 1.111574499 0.994933463 1.154070072 0.873698733 0.94100221 0.917756295 0.933769798 0.907162572 1 19.07197779 3.198396083 24.99999835 0.926010467 1.022581454 0.188504108 0.08965694 222.1276895 138260.396 0.024260524 0.028997282 1579.050732 -3.198396083 0.096570988 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK;EEDEPEERS(1)GDETPGSEVPGDK 295.01 1.01E-55 6724760000 4653520 2540160 3333790 2378650 4828510 4524850 4854560 3337570 3584790 1861770 TRUE FALSE 4837244.563 2976412.72 3420671.306 2849139.87 4007761.595 3474022.162 4474046.902 3292835.333 3455774.108 2226548.186 2.172530823 1.33678343 1.536311376 1.279621923 1.799988709 1.560272616 2.009409422 1.478896956 1.552076946 1 21.0863774 0.620835844 1.638957411 1.000775728 1.635158137 0.345570111 0.266150821 1.809861571 6.41191876 0.240287802 0.068521838 4.176724632 -0.620835844 0.634382409 EEDFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEDFKR 6 1 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 110.36 0.046126 236580000 255870 216510 201430 300170 279620 375220 273040 208050 232940 227530 FALSE TRUE 265971.9452 253693.9083 206679.4313 359542.7301 232090.2923 288080.8415 251638.4113 205261.4301 224556.5349 272110.1472 0.977442216 0.932320646 0.759543271 1.321313203 0.852927738 1.058692021 0.924766731 0.754332142 0.825241312 1 18.05383123 1.990863426 22.14966388 0.83430833 0.981511725 0.114704791 0.149530643 166.2716829 403089.4839 0.056053792 0.039129728 97.91820109 -1.990863426 0.147203395 EEDGADAS(ph)EEDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEDGADASEEDLTR 14 0 E5RHA3;Q86X53 E5RHA3 ERICH1 Glutamate-rich protein 1 1 EEDGADAS(1)EEDLTR;EEDGADAS(1)EEDLTR 250.6 1.99E-18 397580000 511930 514600 525280 497430 544620 659600 653680 525970 499200 464660 TRUE FALSE 532141.3917 602978.547 538969.2283 595820.1693 452045.6869 506417.8963 602442.8535 518920.2325 481233.8895 555701.2305 0.957603407 1.085076861 0.969890291 1.072195159 0.813468933 0.911313253 1.084112866 0.933811559 0.865993925 1 19.08394991 3.301637263 25 0.940816278 1.022090189 0.227381902 0.077545721 106.5322801 42221.98781 0.021574996 0.029212676 2002.798524 -3.301637263 0.08127391 EEDLEDKNNFGAEPPHQNGECYPNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEDLEDKNNFGAEPPHQNGECYPNEK 26 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 216.74 2.33E-34 481070000 444510 198920 269660 213980 403250 397250 419060 280100 355960 134240 FALSE TRUE 462059.598 233082.9626 276687.5611 256304.6053 334705.709 304994.7079 386212.9822 276345.7177 343149.0691 160541.7578 2.878127188 1.451852563 1.723461639 1.596498063 2.084851403 1.899784281 2.40568552 1.721332328 2.137444325 1 17.29258907 4.752210316 24.20572504 1.831740739 2.878128279 0.429938032 0.3750898 1407.66588 2496219.255 0.083960255 1.614535443 56521.06232 -4.752210316 1.04638754 EEDRPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEDRPPLR 8 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 160.56 0.00032161 1322780000 1175780 1237150 1242440 1315940 1387930 1606420 1315930 1261780 1260430 1132640 FALSE TRUE 1222200.702 1449620.889 1274819.007 1576229.004 1152010.154 1233353.301 1212783.968 1244867.903 1215067.371 1354559.122 0.902286716 1.070179119 0.941132053 1.163647255 0.850468714 0.910520095 0.895334835 0.919020722 0.897020551 1 20.36939193 3.199194495 24.99999476 0.907644051 1.017361271 0.331342524 0.074460199 163.5115497 103839.7581 0.019759387 0.023617369 1581.956344 -3.199194495 0.10971722 EEEADMSS(ph)PTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEEADMSSPTQR 12 0 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 EEEADMS(0.034)S(0.966)PTQR;EEEADMS(0.002)S(0.987)PT(0.011)QR;EEEADMS(0.007)S(0.991)PT(0.002)QR 169.6 0.00010315 532677000 931630 1011060 1028810 1243940 1170420 1373250 1568140 1213250 1181950 845930 TRUE FALSE 968411.4718 1184701.69 1055621.634 1489987.619 971472.4265 1054333.499 1445225.089 1196988.368 1139411.85 1011673.787 0.957236892 1.17103132 1.043440729 1.472794529 0.960262526 1.042167458 1.428548518 1.183176221 1.126264083 1 19.94831274 5.4166088 1.372544545 1.179016445 0.13099884 0.109260195 0.163798122 14.72602872 6.408534578 0.042974021 33.79307825 260980.9455 -5.4166088 -1.048017605 EEEEGISQES(ph)S(ph)EEEQ ddPTM_MDA-MB-175_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 218.83 2.76E-12 382320000 225250 248870 244150 240380 281350 288820 273080 255270 226090 184328 TRUE FALSE 234143.0439 291611.4866 250512.7496 287926.4465 233526.2275 221745.9321 251675.276 251848.5232 217953.0651 220443.5424 1.06214517 1.322839777 1.136403212 1.306123297 1.059347101 1.005908042 1.141676791 1.142462693 0.988702425 1 17.75004969 3.21432705 24.99807203 1.07222137 1.21012697 0.410810121 0.08704352 233.8551021 241231.9739 0.024214721 0.028954793 1638.049608 -3.21432705 0.137905599 EEEEISELQEDDRDQFSDQLASVGMLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEEEISELQEDDRDQFSDQLASVGMLGR 28 1 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 0 ; 119.14 0.00012559 75805000 20104.6 30614 28742 26840 26011 36257 26434.5 28286 27874 27672 FALSE TRUE 20898.34513 35871.71636 29491.04013 32148.87189 21589.65951 27836.86123 24362.49482 27906.87244 26870.82018 33093.79859 0.631488255 1.083940735 0.891134937 0.971447016 0.6523778 0.841150379 0.736164957 0.843265918 0.81195938 1 15.01427328 5.010028137 15.47157806 0.854953948 0.312109226 0.252416746 0.120696565 6114117.503 146619825.8 0.028396453 68487268.68 102335.9292 -5.010028137 -0.542844721 EEEEQQEGGFAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEEEQQEGGFASPR 14 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2;A0A087WWG9 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 EEEEQQEGGFAS(1)PR 231.21 2.36E-09 0 89511 73087 72827 85678 84454 106480 79663 81453 81191 68981 TRUE FALSE 93044.9634 85639.12371 74724.93145 102624.8527 70098.53925 81751.63372 73418.8059 80361.25577 78268.95177 82496.50623 1.127865502 1.038093946 0.905795104 1.24399029 0.849715248 0.99097086 0.889962609 0.97411708 0.948754745 1 16.3320454 3.206737547 24.99929018 0.941898643 1.06365221 0.353525018 0.089599908 228.072375 179166.5189 0.024529874 0.029321124 1609.672582 -3.206737547 0.121753567 EEEERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEEERER 7 1 Q9H3P7;E9PEW5;A0A0A0MQX1;Q9HD67-3;Q9HD67 Q9H3P7;E9PEW5 ACBD3;MYO10 Golgi resident protein GCP60;Unconventional myosin-X 0 ; 167.24 0.0009973 384380000 338850 388750 381780 319290 424680 465990 435850 372670 375790 376830 FALSE TRUE 352228.0596 455514.7884 391729.5004 382444.609 352493.0453 357770.8846 401686.9381 367674.9682 362265.3913 450662.6237 0.78157815 1.010766734 0.869230062 0.848627308 0.782166141 0.793877428 0.891325167 0.815854142 0.803850535 1 18.78168828 4.003636193 24.98949932 0.838486644 0.90712892 0.043685164 0.078967696 217.5019215 1494713.427 0.018044347 0.03868915 10084.07793 -4.003636193 0.068642276 EEEGTGVVHQAPYFGAEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEEGTGVVHQAPYFGAEDYR 20 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 134.86 8.22E-06 195520000 150280 146280 159270 175650 153650 202160 211500 159540 153070 117300 FALSE TRUE 156213.1704 171402.4521 163420.707 210393.0457 127532.6279 155211.4038 194922.0773 157401.6273 147561.0406 140282.6892 1.113559851 1.221836088 1.164938511 1.499779103 0.909111656 1.106418794 1.389494873 1.122031722 1.051883461 1 17.09797747 1.328179454 3.527772017 1.019827115 1.199984451 0.171794795 0.151907519 0.408626701 8.304369239 0.120964663 0.038257034 21.2901859 -1.328179454 0.180157336 EEEHDCFLEEIMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEEHDCFLEEIMTK 14 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 148.68 7.69E-06 46302000 69914 60975 66337 76776 83738 91218 102220 71502 77888 42581 FALSE TRUE 72674.25871 71446.98193 68065.79672 91962.06365 69504.24467 70034.00192 94207.7293 70543.63264 75084.82609 50923.93169 1.427114056 1.403013859 1.336617077 1.80587124 1.36486407 1.375266984 1.849969674 1.38527467 1.474450688 1 15.63605619 0.444618755 1.753018319 1.000095683 1.498837943 0.417655746 0.17430553 4.298950581 12.48509433 0.160677979 0.045129562 2.783676446 -0.444618755 0.498742259 EEEKLELQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEEKLELQK 9 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 72.848 0.041579 141290000 93565 71505 71008 77841 109270 108490 100310 70550 96437 79812 FALSE TRUE 97259.01845 83785.42752 72858.52681 93237.71747 90696.32443 83294.84168 92447.44009 69604.39265 92966.25121 95449.63331 1.018956439 0.87779727 0.763319086 0.976826356 0.950200868 0.872657535 0.968546833 0.729226402 0.973982277 1 16.54245203 -0.359211914 7.930540274 0.999978146 0.891978516 0.079752039 0.091058016 0 0 0.086437632 0.020373545 0.437308668 0.359211914 -0.10799963 EEELKAMMHDLQITCSEMQQKVELLRY(ph)ESEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEELKAMMHDLQITCSEMQQKVELLRYESEK 31 3 H0YDJ4;H9KV85;E9PN67;C9J066;Q8N4C6-4;Q8N4C6-9;Q8N4C6-2;Q8N4C6;Q8N4C6-5;Q8N4C6-10;Q8N4C6-7 H0YDJ4 NIN Ninein 1 EEELKAMMHDLQIT(0.217)CS(0.217)EMQQKVELLRY(0.564)ES(0.002)EK 44.264 0.038236 25762000 33371 6849.8 12940 3928.6 24071 18535 11876 11925 15111 5986.9 TRUE FALSE 34688.51285 8026.199866 13277.22703 4705.665354 19979.42002 14230.52715 10945.12809 11765.16488 14567.15806 7159.918429 4.844819559 1.120990406 1.854382443 0.657223319 2.790453581 1.987526435 1.52866659 1.643198173 2.034542461 1 12.80572744 4.744538916 24.99261033 1.662986199 4.844820953 0.737705873 0.575716839 324.8482075 1358007.675 0.130544925 1.191189656 55531.43755 -4.744538916 3.181834753 EEEMMIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEEMMIR 7 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 120.65 0.02809 0 664660 669370 645710 615570 942090 936410 788370 743650 732510 661860 FALSE TRUE 690901.29 784329.0905 662537.7331 737327.9087 781953.8783 718942.9689 726575.4994 733682.5881 706147.1082 791538.7949 0.872858405 0.990891534 0.837024966 0.931512029 0.987890781 0.908285195 0.917927844 0.926906669 0.892119392 1 19.59430054 EEEMRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEEMRR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 114.54 0.040403 210960000 177980 234700 220800 197010 251410 277350 226700 217250 214170 258810 FALSE TRUE 185006.7878 275007.8993 226554.2294 235977.99 208675.418 212939.6658 208930.6616 214338.1191 206462.0635 309518.8643 0.597723787 0.888501255 0.731956128 0.76240261 0.674192891 0.687969912 0.675017538 0.692488064 0.667041939 1 18.23966781 -0.966421272 9.168360327 0.999999996 0.711684755 0.590653248 0.072738173 0 0 0.067878831 0.015999194 0.108038545 0.966421272 -0.288315241 EEEPVKK ddPTM_MDA-MB-175_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 ;;;;; 114.6 0.009409 4708710000 5564680 2803050 3953010 3171090 5210290 4874830 6607540 4230510 4482130 1902990 FALSE TRUE 5784377.863 3284452.033 4056028.688 3798322.137 4324646.767 3742724.611 6089623.749 4173806.933 4320819.017 2275844.456 2.541640247 1.443179487 1.782208216 1.668972644 1.900238286 1.644543239 2.675764477 1.833959664 1.898556383 1 21.11797053 EEEWDPEYT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEEWDPEYTPK 11 0 Q9NYF8;Q9NYF8-2;H0YF14;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 EEEWDPEYT(1)PK 157.5 0.00034164 154460000 569430 292660 316010 283960 454500 463180 525070 338280 357160 191560 TRUE FALSE 591911.5361 342922.0784 324245.4802 340126.4405 377244.2523 355613.4646 483913.6414 333745.9099 344305.8814 229092.5144 2.583722728 1.4968716 1.415347337 1.484668504 1.646689563 1.552270119 2.112306649 1.456817176 1.502911967 1 17.80557079 -2.614769623 0.178123753 3.40E-30 1.859619951 0.313518925 0.339222436 68.30089521 1.431482025 28.78917695 1.209218699 0.002427898 2.614769623 1.859619951 EEFASTCPDDEEIELAYEQVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEFASTCPDDEEIELAYEQVAK 22 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 111.18 0.00033339 15251000 12684 9866.8 11125 9958.2 13735 13907 14369 12039 13734 10004 FALSE TRUE 13184.77411 11561.34615 11414.92664 11927.90224 11400.32961 10677.31001 13242.72023 11877.6369 13239.71602 11964.09226 1.10202879 0.966337094 0.954098848 0.996975113 0.952878777 0.892446312 1.106872126 0.992773763 1.106621023 1 13.54642332 2.226858019 24.99994447 1.046726493 0.975662928 0.262468485 0.0605952 318.7445802 680920.4552 0.021965333 0.016359306 168.6001741 -2.226858019 -0.071063565 EEFEHQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEFEHQQK 8 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 82.452 0.020235 357170000 261800 280940 277590 292950 295080 328380 301530 265930 286010 286920 FALSE TRUE 272136.0662 329189.2596 284824.2234 350894.6356 244922.407 252118.7216 277895.2907 262365.6433 275716.556 343136.4806 0.79308404 0.959353721 0.830061039 1.022609531 0.713775483 0.734747647 0.809868103 0.764610172 0.803518633 1 18.38842299 3.222726652 24.99999203 0.788210712 0.900338598 0.189759016 0.094546002 314.3349693 496297.4389 0.025163873 0.030169384 1670.039148 -3.222726652 0.112127886 EEFLIPIYHQVAVQFADLHDTPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEFLIPIYHQVAVQFADLHDTPGR 24 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 196.19 1.16E-24 433390000 131045 159958 180555 156652 218960 206261 167812 174553 184523 168250 FALSE TRUE 136218.7578 187429.5422 185260.4116 187637.298 181741.2574 158360.0087 154658.4569 172213.4025 177882.0533 201215.3662 0.676979897 0.931487221 0.920707077 0.932519726 0.903217587 0.787017471 0.768621502 0.85586606 0.884038116 1 17.61838096 0.825945162 2.979940135 0.999919794 0.851616014 0.253073516 0.078701221 1.193947802 17.56801287 0.076263416 0.019988813 6.698000284 -0.825945162 -0.14830378 EEFTAFLHPEEFEHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEFTAFLHPEEFEHMK 16 0 Q15293;Q15293-2;E9PP27 Q15293 RCN1 Reticulocalbin-1 0 ;;;; 228.51 2.34E-15 1332140000 1095820 987280 1161550 1021540 1610170 1464050 1313030 1152670 1175710 800510 FALSE TRUE 1139083.82 1156837.66 1191820.947 1223597.563 1336473.879 1124046.575 1210111.278 1137220.344 1133396.427 957354.6078 1.189824346 1.208369031 1.24491065 1.278102756 1.396007151 1.174117267 1.264015724 1.187877861 1.183883608 1 19.86869388 0.687796782 0.858069387 0.999893683 1.254565579 0.615588414 0.058906876 0.718168965 0.957644351 0.058197402 0.019732651 4.873004161 -0.687796782 0.254671896 EEFTAFLHPEEYDYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EEFTAFLHPEEYDYMK 16 0 O43852;O43852-3;O43852-15;O43852-6;H0Y875;O43852-10;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;;;;;; 192.32 5.55E-10 1153684000 2371552 1817813.8 2196615 2379620 2832426 2898258 3215577 2273634 2403066 1285723.9 FALSE TRUE 2465182.704 2130009.18 2253860.591 2850301.734 2350971.24 2225181.503 2963531.672 2243159.655 2316580.124 1537636.882 1.603228131 1.385248497 1.46579509 1.853689755 1.528950865 1.447143685 1.927328687 1.458835751 1.506584651 1 20.55228342 0.628551739 1.683834848 1.000604512 1.587972849 0.521651252 0.16727439 1.261620487 4.715415584 0.156358487 0.044375117 4.251593544 -0.628551739 0.587368337 EEGAQTLEEDRAQT(ph)PHEDGGPQPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGAQTLEEDRAQTPHEDGGPQPHR 25 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EEGAQTLEEDRAQT(1)PHEDGGPQPHR 178.72 1.59E-17 168740000 65940 75929 76803 69857 89923 90591 63952 76813 62859 92203 TRUE FALSE 68543.36212 88969.2151 78804.54927 83674.5061 74637.92058 69552.61317 58939.27513 75783.44738 60596.71687 110268.4125 0.621604688 0.806842259 0.714661139 0.758825707 0.676874899 0.630757364 0.534507333 0.68726343 0.549538308 1 16.75066005 -1.082612089 4.548981773 1.000020974 0.66806962 0.606815306 0.080963553 1.88E-05 3.79E-06 0.080448274 0.018960568 0.082677609 1.082612089 -0.331951354 EEGFPIRPHYFWPLLVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGFPIRPHYFWPLLVGR 18 1 P42704;B8ZZ38;A0A0C4DG06 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 110.37 0.00020167 86283000 105740 107490 103460 121370 105430 164300 126970 96584 101730 94213 FALSE TRUE 109914.6968 125950.5713 106156.2526 145376.6237 87509.04626 126143.815 117017.7596 95289.44946 98068.75717 112672.2335 0.975526032 1.117849246 0.942168707 1.290261311 0.776669136 1.119564342 1.038567853 0.845722557 0.87038975 1 16.7817725 1.753600178 20.09752992 0.893586156 1.039551378 0.17311357 0.131237079 1.814389611 2436.757489 0.056259005 0.031171972 56.7022351 -1.753600178 0.145965222 EEGGFEYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEGGFEYKR 9 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 76.465 0.056689 591370000 235820 204154 255490 222199 280600 298660 299290 253180 254380 170477 FALSE TRUE 245130.3557 239215.8614 262148.2793 266149.299 232903.7122 229300.7412 275830.8678 249786.5362 245224.9135 203878.7042 1.202334283 1.173324415 1.285805108 1.305429618 1.142364099 1.124691969 1.352916524 1.225172277 1.202798078 1 17.63735156 0.736188121 3.28974612 1.000014455 1.228764603 0.494241126 0.068283567 2.079508825 24.95911926 0.066598925 0.017265855 5.447385627 -0.736188121 0.228750148 EEGINKSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGINKSEK 9 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 64.374 0.063779 84260000 126650 72997 110080 75732 147180 144460 119930 103160 120510 95028 FALSE TRUE 131650.2398 85533.66691 112948.7752 90711.56356 122162.3962 110911.3543 110529.5732 101777.3089 116172.8686 113646.9172 1.158414527 0.752626372 0.993856921 0.798187631 1.074929256 0.975929282 0.972569921 0.895557147 1.022226309 1 16.79419902 3.224713913 24.99991228 0.977150543 0.918267074 0.065655281 0.111371059 695.1040044 1254991.965 0.030098192 0.036152064 1677.698488 -3.224713913 -0.058883469 EEGLGFPSFLDPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEGLGFPSFLDPDR 14 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 ;; 107.06 0.0021075 59465000 54338 53234 52526 67462 56035 69333 80438 57885 59216 37880.5 FALSE TRUE 56483.3062 62376.5254 53894.87071 80805.78225 46510.19072 53231.4615 74133.05937 57109.14626 57084.82773 45302.45871 1.24680443 1.376890508 1.189667675 1.78369529 1.026659304 1.175023675 1.636402559 1.260619134 1.26008233 1 15.46730173 0.823101355 2.038587888 1.001139965 1.343810267 0.187005444 0.21171335 1.047025596 7.884468804 0.192168602 0.053098089 6.654284351 -0.823101355 0.342670303 EEGS(ph)DIEDEDMEELLNDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGSDIEDEDMEELLNDTR 19 0 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 EEGS(1)DIEDEDMEELLNDTR 142.94 1.58E-07 52663000 37246 41106 49231 44969 48971 59805 55996 43970 48545 47440 TRUE FALSE 38716.50084 48165.63574 50514.0003 53863.73398 40646.92691 45916.1951 51606.8872 43380.65407 46797.87493 56734.95971 0.682409947 0.848958667 0.89035051 0.949392302 0.716435283 0.809310438 0.909613534 0.764619457 0.824850765 1 15.79195037 -2.297507322 2.069852203 1.725108603 0.824395515 0.310133221 0.07965926 3040134.141 439274.8665 10291449.54 0.019779592 0.005040721 2.297507322 -0.900713087 EEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.353)LS(0.294)DT(0.353)EADAVSGQLPDPTTNPSAGK 127.38 2.10E-05 120950000 62571 45645 55132 58108 63810 68321 80631 51788 60275 25078 TRUE FALSE 65041.3514 53484.17368 56568.78521 69601.58896 52963.59899 52454.48316 74310.93153 51093.86657 58105.71452 29991.55395 2.168655599 1.783307853 1.886157193 2.320706325 1.765950476 1.74897517 2.477728618 1.703608511 1.937402597 1 14.87226865 0.237848395 1.061315211 0.996383359 1.987467033 0.584287829 0.24831024 2.767931897 3.255843073 0.246815683 0.070510189 1.729212613 -0.237848395 0.991083675 EEGSLSDT(ph)EADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 EEGS(0.311)LS(0.311)DT(0.378)EADAVSGQLPDPTTNPSAGK 126.68 0.00013567 63894000 129590 73800 103060 118440 114550 134150 178080 125760 121400 54867 TRUE FALSE 134706.3133 86474.57592 105745.8283 141867.0785 95078.83192 102995.6956 164121.6243 124074.3929 117030.8377 65617.13816 2.052913569 1.317865703 1.611558066 2.162043065 1.448993885 1.569646261 2.501200584 1.890883943 1.783540718 1 16.00178505 EEGVIDSSDKEIVAEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGVIDSSDKEIVAEAER 18 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 139.11 2.35E-06 0 140080 94323 109520 98411 121260 150410 174050 115800 119930 53912 FALSE TRUE 145610.4666 110522.2415 112374.1812 117876.4021 100648.2685 115479.557 160407.5062 114247.8904 115613.7427 64475.02419 2.258401116 1.714186895 1.74291026 1.828249055 1.561042741 1.791074272 2.48790145 1.771971269 1.793155476 1 15.97645279 0.646169112 2.323951345 1.000233185 1.888536114 0.511309989 0.260865293 1.999673096 12.10235175 0.250475334 0.067532033 4.42760748 -0.646169112 0.888302929 EEGVIDSSDKEIVAEAERLDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEGVIDSSDKEIVAEAERLDVK 22 2 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 197.4 1.13E-22 62141000 116750 53919 79134 45598 123180 99488 102520 86708 96072 44590 FALSE TRUE 121359.3802 63179.16882 81196.29705 54617.1483 102241.9076 76383.41976 94484.21451 85545.82109 92614.38749 53326.55677 2.275777539 1.184759952 1.522624035 1.024201666 1.917279378 1.432371118 1.771804148 1.604187974 1.736740436 1 15.70256656 EEHDKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEHDKEER 8 1 Q9Y6I3 Q9Y6I3 EPN1 Epsin-1 0 ;;;; 180.8 0.00014251 854239000 946926 625266 845278 579692 1045611 1033035 993905 808845 959806 639656 FALSE TRUE 984311.3697 732650.5716 867306.6391 694353.3474 867878.4157 793128.277 916000.129 798003.7558 925262.7695 764984.3462 1.286707858 0.957732763 1.133757368 0.907670008 1.134504804 1.036790205 1.197410291 1.04316351 1.209518566 1 19.5450707 EEHGGLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEHGGLIR 8 0 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 98.904 0.0071921 372380000 1450620 1411380 1418890 1346320 1705600 1694380 1617550 1542470 1533380 1413000 FALSE TRUE 1507891.598 1653773.536 1455867.439 1612618.078 1415682.721 1300885.924 1490762.204 1521795.713 1478193.953 1689850.296 0.892322593 0.978650913 0.86153634 0.954296414 0.837756294 0.769823177 0.882185959 0.900550608 0.874748465 1 20.68846401 4.221632937 24.99921931 0.879307434 0.935486779 0.089789626 0.061988542 445.6413327 658136.6172 0.015199474 0.032964436 16658.38662 -4.221632937 0.056179345 EEHGGLIRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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;EEHGGLIRS(1)PR 131.48 0.00012263 44999490000 8186578 8662797 8404550 8590574 9345001 10375779 9378489 9272408 8405375 8132301 TRUE FALSE 8509790.421 10150565 8623579.477 10289763.9 7756541.068 7966161.574 8643378.526 9148126.537 8102867.196 9725669.679 0.874982464 1.043688027 0.886682333 1.058000553 0.797532851 0.819086175 0.888718084 0.94061662 0.83314234 1 23.21336616 3.234265777 24.99999389 0.87913606 0.96574503 0.228414008 0.077417853 159.2784847 927151.4638 0.021245961 0.026250657 1715.006525 -3.234265777 0.086608969 EEHLCTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EEHLCTQR 8 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;;;; 172.21 0.00028488 11925680000 2764741 2998380 3015194 3166660 3247490 3763290 3561200 3098488 2860310 2592351 FALSE TRUE 2873895.11 3513328.441 3093772.433 3793015.896 2695482.81 2889322.931 3282063.839 3056957.836 2757368.002 3100272.545 0.92698144 1.133232124 0.997903374 1.223445952 0.869434145 0.931957719 1.058637198 0.986028742 0.889395355 1 21.56396362 3.216423833 24.99998247 0.963242985 1.069701881 0.281641821 0.089106808 321.4695276 363048.0433 0.024949656 0.029843191 1645.977268 -3.216423833 0.106458896 EEHS(ph)KTPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.595)KT(0.405)PEER 62.891 0.049607 79294000 15874 13267 15860 9789.7 16821 21158 19652 10497 23254 17030 TRUE FALSE 16500.71778 15545.50405 16273.32463 11726.07344 13961.77243 16244.37515 18111.62489 10356.30488 22417.09308 20366.70244 0.810181119 0.763280364 0.799016172 0.575747275 0.685519537 0.79759476 0.889276256 0.508491982 1.100673668 1 14.31392479 1.218938364 24.99988354 1.050337195 0.725160386 0.575181157 0.11055574 194.4706539 247760.3756 0.10567779 0.026571194 16.55534991 -1.218938364 -0.325176809 EEHSKT(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EEHS(0.022)KT(0.978)PEER;EEHS(0.001)KT(0.999)PEER 155.09 1.95E-05 1118890000 1355490 906920 1009320 794360 1317730 1489660 1285050 956770 1081020 635520 TRUE FALSE 1409005.792 1062676.455 1035623.708 951482.0371 1093742.725 1143709.041 1184324.423 943946.0631 1042114.301 760037.9762 1.853862354 1.398188628 1.362594687 1.251887494 1.439063257 1.504805124 1.558243746 1.241972234 1.371134514 1 19.53571198 -3.786904223 0.124139968 1.81E-17 1.644292601 0.478056984 0.153707487 101.1853464 1.085985768 27.60770612 1.470359761 0.000163341 3.786904223 1.644292601 EEHSKTPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEHSKTPEER 10 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 103.91 0.0016535 99270000 36562 46350 41116 29749 38818 57101 33115 42787 42080 48518 FALSE TRUE 38005.49599 54310.25195 42187.51674 35633.26341 32219.73023 43840.15812 30519.35977 42213.51025 40565.54902 58024.17317 0.654994185 0.935993552 0.727067952 0.614110662 0.555281161 0.755549898 0.525976642 0.727515929 0.699114641 1 15.82436644 -1.453644576 4.881227975 1.000670974 0.688404774 0.421999255 0.109402273 0.000805993 9.02E-05 0.106876231 0.025138285 0.035184827 1.453644576 -0.312266199 EEIDSILNKVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEIDSILNKVEER 13 1 P52788;H7C2R7 P52788 SMS Spermine synthase 0 ; 170.56 2.43E-05 131845000 261580 179702 223440 200166 320780 298280 317150 240330 287200 146560 FALSE TRUE 271907.3804 210564.4206 229263.03 239758.2374 266253.9302 229008.9905 292290.9543 237108.7695 276863.7281 175275.6259 1.551313133 1.201333154 1.308014327 1.367892632 1.519058504 1.306564956 1.667607534 1.352776624 1.579590583 1 17.41926586 3.463217359 23.81569476 1.431402669 1.338268469 0.001019044 0.189305398 422.5629247 723794.9171 0.047843248 0.064818012 2905.476449 -3.463217359 -0.093134199 EEIFRES(ph)PIPIEIPPAAVPSYVPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEIFRESPIPIEIPPAAVPSYVPESR 26 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 EEIFRES(1)PIPIEIPPAAVPSYVPESR;EEIFRES(1)PIPIEIPPAAVPSYVPESR 95.099 0.0047472 91156000 39703 38008 39604 37646 40594 47245 34896 38734 39393 35646 TRUE FALSE 41270.5051 44535.57834 40636.11278 45092.26644 33693.84638 36273.06475 32160.76034 38214.83409 37975.25363 42630.15122 0.968105998 1.044696701 0.953224692 1.057755254 0.790375953 0.850878163 0.754413471 0.896427364 0.890807387 1 15.37958655 3.240878209 24.99999861 0.85328517 1.004947817 0.504628834 0.068508847 45.21066704 487684.69 0.018273104 0.023609396 1741.31848 -3.240878209 0.151662647 EEILQPPEPHPVPPILTPS(ph)PPSAFPTVTTVWQDNDRYHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEILQPPEPHPVPPILTPSPPSAFPTVTTVWQDNDRYHPK 40 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 EEILQPPEPHPVPPILT(0.005)PS(0.477)PPS(0.477)AFPT(0.025)VT(0.006)T(0.006)VWQDNDRY(0.004)HPK 64.318 0.0021953 161810000 46269 28542 42781 41825 42502 52406 56447 40806 44928 18931 TRUE FALSE 48095.73585 33443.86647 43895.908 50097.86016 35277.52522 40235.50072 52022.53664 40259.06232 43311.05006 22640.16699 2.124354289 1.477191687 1.938850893 2.212786689 1.558183084 1.777173319 2.297798274 1.778214018 1.913018136 1 14.46659698 -1.070919691 3.239197844 0.999193321 1.891364688 0.5333921 0.251773775 10105363.52 15824324.36 95247.03992 0.059354144 0.084933752 1.070919691 0.892171367 EEIQETQTPTHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEIQETQTPTHSR 13 0 Q9BYG3;H7BZL0 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 109.84 0.0011058 98128000 70992 93881 96825 97438 111800 128470 111850 106190 107100 115720 FALSE TRUE 73794.81898 110004.3315 99348.33904 116710.9456 92796.27593 98634.78948 103082.9047 104766.6967 103245.4919 138393.1184 0.533226072 0.794868507 0.717870514 0.843329111 0.670526663 0.712714553 0.744855712 0.757022444 0.746030533 1 17.07841268 -5 0.235330896 2.501336102 0.701235021 0.557469603 0.075556347 121.3863397 1.213047661 86.97094767 0.116858491 1.00E-05 5 -1.800101081 EEIQPGDIVIIDQFIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEIQPGDIVIIDQFIDR 17 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2;J3QSB7;Q13126-7;Q13126-6;Q13126-5;F2Z2F3;A0A2R8Y4K0 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase;Purine nucleoside phosphorylase 0 ; 240.59 5.84E-20 43890000 42944 37703 45647 45179 45057 54455 52346 44836 49776 41697 FALSE TRUE 44639.46228 44178.19696 46836.59832 54115.27135 37398.22723 41808.65152 48242.98374 44235.04676 47984.57148 49866.72881 0.895175267 0.885925306 0.939235427 1.085197939 0.749963515 0.838407742 0.967438308 0.88706534 0.96225625 1 15.60578995 1.045675234 4.1512022 0.999675021 0.907180137 0.126234391 0.081766543 0.393676709 14.53042146 0.078091968 0.019977931 11.10900685 -1.045675234 -0.092494884 EEIVDKYDLFVGSQATDFGEALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 205.53 8.79E-25 1168080000 1703768 1445070 1615790 1593598 2119903 2055919 1969141 1632757 1644370 1148313 FALSE TRUE 1771034.076 1693249.531 1657898.815 1908806.928 1759562.645 1578462.97 1814794.583 1610872.563 1585189.445 1373302.947 1.289616454 1.232975969 1.207234586 1.389938711 1.281263285 1.149391672 1.321481606 1.172991412 1.154289699 1 20.38921848 0.931396963 0.855527365 0.999428693 1.269950026 0.631177239 0.06311964 0.444970268 0.698315607 0.059409321 0.020920836 8.538802399 -0.931396963 0.270521333 EEIVELMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEIVELMR 8 0 P42574;A8MVM1;C9JXR7 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ;;; 143.89 0.0013825 280411000 346692 381981 402438 397100 471620 480890 421756 421243 416816 418122 FALSE TRUE 360379.6679 447583.2654 412925.8649 475645.1948 391454.2009 369210.5855 388697.6627 415596.9266 401814.8736 500045.0005 0.720694473 0.895085972 0.825777409 0.95120478 0.782837946 0.738354718 0.777325365 0.831119052 0.803557426 1 18.93169841 -1.112034093 4.706130071 1.000012116 0.817081053 0.42063096 0.065399416 8.25E-06 1.56E-06 0.062823371 0.01480663 0.077261993 1.112034093 -0.182931063 EEIVYLPCIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEIVYLPCIYR 11 0 Q13228;Q13228-4;Q13228-3;H0Y532;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 172.23 3.16E-05 262900000 277590 357670 334610 344610 404470 419230 335160 328750 317930 339820 FALSE TRUE 288549.4675 419097.0402 343330.2115 412772.8294 335718.3339 321870.186 308889.2834 324343.644 306487.7614 406401.2228 0.710011317 1.031239614 0.844806049 1.015678119 0.826076092 0.792001027 0.760059926 0.798087274 0.754150687 1 18.63254522 3.022290199 24.87774144 0.803314075 0.907687861 0.104095883 0.106341754 356.1770084 397520.6357 0.02809399 0.03357656 1052.665038 -3.022290199 0.104373786 EEKDGELNVLDDILTEVPEQDDELYNPESEQDKNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEKDGELNVLDDILTEVPEQDDELYNPESEQDKNEK 36 2 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 142.37 2.93E-13 43081000 143137 35293 66862 33183 105000 96679 103169 67405 86289 23463 FALSE TRUE 148788.1593 41354.29821 68604.47865 39746.49836 87152.13751 74226.76743 95082.3442 66501.54623 83183.47575 28060.12562 5.302476592 1.473774521 2.44490989 1.416476137 3.10590689 2.645275664 3.388521686 2.369966091 2.964472678 1 14.77623385 -1.066306054 5.011353498 1.000026127 2.706371703 0.20711588 1.039217196 0.000380596 7.09E-05 0.923259611 0.21760986 0.085840837 1.066306054 1.706345576 EEKDKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEKDKDDQEWESPSPPKPTVFISGVIAR 28 3 P51397 P51397 DAP Death-associated protein 1 1 EEKDKDDQEWES(0.012)PS(0.983)PPKPT(0.005)VFISGVIAR;EEKDKDDQEWES(0.002)PS(0.998)PPKPTVFISGVIAR 162.81 4.62E-11 908800000 1931090 386770 636960 338150 1178600 1333480 1066630 668410 705240 235920 TRUE FALSE 2007330.924 453194.7388 653559.7009 405035.0607 978261.993 1023799.479 983024.7535 659451.0572 679858.5502 282144.007 7.114561622 1.606253287 2.316404689 1.435561453 3.467243566 3.628641593 3.484124167 2.337285361 2.40961542 1 18.10607218 0.942081324 1.202558437 1.027351161 3.118624685 0.172103556 1.502789052 1.021916598 3.003684202 1.366449069 0.424860509 8.751476361 -0.942081324 2.091273523 EEKESEDKPEIEDVGS(ph)DEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEKESEDKPEIEDVGSDEEEEK 22 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 EEKESEDKPEIEDVGS(1)DEEEEK;EEKESEDKPEIEDVGS(1)DEEEEK 196.15 1.13E-22 254588000 794650 150211 208870 183484 381590 467170 501750 247570 270330 92482 TRUE FALSE 826023.3956 176008.5708 214313.3238 219776.5876 316727.4681 358676.8475 462421.5239 244251.7291 260600.8761 110602.0772 7.468425696 1.591367678 1.937697095 1.987092766 2.863666543 3.242948564 4.180947913 2.208382837 2.356202367 1 16.75501896 4.744974403 24.97859677 2.497902957 7.468427951 0.761652325 0.852390533 362.0556583 1409993.792 0.208680026 1.984525211 55587.14934 -4.744974403 4.970524995 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 36 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 267.66 6.11E-63 160074000 295710 211975 271330 279180 295050 348140 430530 293130 315100 160045 FALSE TRUE 307384.8591 248380.0573 278401.0827 334400.9707 244897.5064 267289.7611 396783.9336 289201.0718 303759.6126 191402.7535 1.605958397 1.29768278 1.454530186 1.747106374 1.279487896 1.39647814 2.073031481 1.51095565 1.587017987 1 17.54625206 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 EELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 37 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;; 363.58 6.20E-147 26595839000 581086 474360 564774.3 466015.6 696199 708694 723163.2 566053.6 616962.4 404212.3 FALSE TRUE 604027.724 555827.64 579492.7822 558192.0948 577859.3427 544110.5589 666479.7787 558466.5774 594758.0437 483409.9611 1.249514434 1.14980593 1.198760532 1.15469713 1.195381538 1.125567536 1.3787051 1.155264935 1.230338825 1 18.88288768 -0.978205431 5.24154571 0.999999107 1.202626126 0.442280809 0.068779364 6.70E-07 1.31E-07 0.062230308 0.01466776 0.105146439 0.978205431 0.202627019 EELEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EELEALRR 8 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 131.06 0.0016373 360640000 348371 392096 338529 372741 445790 481050 409556 376059 383106 378791 FALSE TRUE 362124.9561 459435.4379 347351.3438 446468.0573 370014.775 369333.4279 377453.9305 371018.5442 369318.0899 453007.8441 0.799378997 1.014188703 0.766766731 0.985563635 0.816795514 0.815291463 0.833217207 0.819011302 0.815257605 1 18.78917651 EELEEVIKDI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;;; 156.92 8.23E-05 271321000 1140477 822173 1045554 852174 1314120 1303500 1359970 1089838 1176265 731508 FALSE TRUE 1185503.913 963374.8171 1072801.996 1020731.474 1090746.352 1000781.88 1253371.998 1075230.504 1133931.452 874832.987 1.355120269 1.101209981 1.226293489 1.16677296 1.246805239 1.143969071 1.432698602 1.229069457 1.296169062 1 19.7386481 EELEFEVPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EELEFEVPFR 10 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;; 193.41 1.34E-06 176385000 264792 275776 287813 314779 306512 339557 359448 309372 295772 222808 FALSE TRUE 275246.1926 323138.3828 295313.6432 377041.3467 254411.1997 260700.0328 331273.5265 305225.3744 285127.2235 266462.9617 1.032962296 1.212695306 1.108272765 1.414985949 0.954771343 0.978372496 1.243225416 1.145470171 1.070044488 1 18.02357549 EELEQASQAHGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EELEQASQAHGAR 13 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 206.49 6.15E-08 1876950000 1506070 1767530 1768260 1815470 1908190 2226390 2020310 1961930 1693950 1534050 FALSE TRUE 1565530.807 2071089.528 1814342.308 2174564.547 1583836.545 1709344.664 1861952.823 1935633.537 1632985.07 1834617.726 0.853328072 1.128894319 0.988948424 1.185295725 0.86330603 0.931717076 1.014899614 1.055060959 0.890095548 1 20.80704805 3.219282095 24.99769344 0.970770807 1.041946005 0.131221954 0.097971207 547.7782505 710281.0271 0.0277834 0.033256943 1656.845814 -3.219282095 0.071175198 EELFQGDAFHQSDTHIFIIMGASGDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EELFQGDAFHQSDTHIFIIMGASGDLAK 28 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;; 209.89 8.02E-26 1524506000 257364 1031533 1114009 1158163 1263818 1594860 1203283 1445723 1234705 951384 FALSE TRUE 267524.9294 1208690.769 1143040.99 1387244.185 1048994.668 1224477.935 1108966.534 1426345.448 1190268.208 1137789.479 0.235126914 1.062314945 1.004615538 1.219245045 0.921958488 1.076190242 0.974667594 1.253611036 1.046123408 1 20.11780222 4.738909822 6.800807949 1.074195351 0.221044356 0.863077851 0.098718071 0.036505443 11.75941896 0.023154072 0.142993994 54816.31311 -4.738909822 -0.853150995 EELGDEWLKPELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EELGDEWLKPELFR 14 1 G3V158;E9PPM8;Q9Y315 G3V158 DERA Deoxyribose-phosphate aldolase 0 ; 143.93 8.20E-06 207398000 269271 177838 243527 199206 305700 269006 298623 237038 260981 150010 FALSE TRUE 279902.027 208380.2931 249873.5137 238608.3522 253737.2232 206533.4333 275216.149 233860.8933 251588.3448 179401.5874 1.560198163 1.161529818 1.392816626 1.33002364 1.414353278 1.151235261 1.534078672 1.303560892 1.402375243 1 17.45283313 -1.057242739 4.781792587 0.999991756 1.354458156 0.416824371 0.127928023 1.33E-05 2.61E-06 0.109394911 0.025783828 0.087651078 1.057242739 0.354466399 EELGLIEQAYDNPHEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 279.54 1.36E-39 565139000 515749 593053 604829 600612 663371 695500 645514 646126 602511 591469 FALSE TRUE 536111.1688 694905.2394 620591.3406 719411.261 550611.4344 533980.6654 594916.9259 637465.7378 580826.7468 707356.0262 0.757908534 0.982398133 0.877339441 1.017042669 0.77840778 0.754896609 0.84104313 0.901195034 0.821123628 1 19.43207701 4.791352414 21.56657808 0.878311102 0.757904749 0.158958394 0.086766634 17280.39438 7058219.268 0.020655299 16.1855024 61851.81014 -4.791352414 -0.120406353 EELMS(ph)SDLEETAGSTSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.5)S(0.5)DLEETAGSTSIPK;EELMS(0.5)S(0.5)DLEETAGSTSIPK 152.68 3.44E-08 205470000 339130 230720 316840 288890 380670 359470 452700 315220 326250 161213 TRUE FALSE 352519.1143 270344.3652 325097.1107 346031.5797 315963.8494 275988.5403 417216.1911 310994.9915 314508.3262 192799.6007 1.828422429 1.402203968 1.686191825 1.794773321 1.63882004 1.431478796 2.163988875 1.613047902 1.63127063 1 17.55674254 0.623511596 2.394190893 1.000111569 1.695144566 0.510383493 0.203063599 2.407158205 14.34552504 0.1869259 0.050178951 4.202537491 -0.623511596 0.695032997 EELMSS(ph)DLEETAGSTSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.146)S(0.854)DLEETAGSTSIPK;EELMS(0.074)S(0.926)DLEETAGSTSIPK 246.95 1.11E-24 355710000 283580 189301 224910 223030 292670 309760 331990 271970 275710 152482 TRUE FALSE 294775.9574 221811.9742 230771.3394 267144.6683 242922.0579 237822.9345 305967.7563 268324.687 265787.251 182357.9285 1.616469105 1.216354979 1.265485638 1.464946825 1.332116788 1.304154618 1.677841808 1.471417718 1.457503127 1 17.4764134 EELMSS(ph)DLEETAGSTSIPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 EELMS(0.147)S(0.853)DLEETAGSTSIPKR;EELMS(0.166)S(0.834)DLEETAGSTSIPKR;EELMS(0.135)S(0.865)DLEETAGSTSIPKR;EELMS(0.176)S(0.824)DLEETAGSTSIPKR 202.73 6.93E-22 569320000 520530 422945 466808 340041 653910 555010 460718 479543 498880 365256 TRUE FALSE 541080.9263 495582.5137 478973.4 407300.0949 542758.6118 426117.3388 424605.7193 473115.5105 480925.4063 436820.92 1.23867906 1.134521015 1.096498309 0.93241893 1.242519731 0.975496638 0.972036136 1.083088032 1.100966974 1 18.73668242 4.551054317 1.711862515 1.049018744 1.26463862 0.34040667 0.083610953 0.724981995 2.799844692 0.021443367 0.227429278 35567.57997 -4.551054317 0.215619876 EELRSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EELRSPK 7 1 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 ;; 96.492 0.011575 736520000 878480 813300 808860 769920 1342020 1152180 909800 795160 908060 809110 FALSE TRUE 913163.0687 952977.9484 829939.5561 922207.878 1113903.92 884603.6565 838487.4987 784502.1808 875379.098 967639.6132 0.943701618 0.984848011 0.857694895 0.953048909 1.151155766 0.914187105 0.866528703 0.810737975 0.904654053 1 19.88411031 2.484909138 24.78478478 0.874161683 0.97661411 0.172518293 0.081950481 472.8036015 1504695.063 0.028392324 0.024764534 305.4282037 -2.484909138 0.102452427 EELSHS(ph)PEPCTK ddPTM_MDA-MB-175_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(0.001)HS(0.999)PEPCTK;EELS(0.002)HS(0.998)PEPCTK 143.46 4.01E-05 683170000 1146530 861840 1118230 923150 1402450 1351430 1301930 1052820 1071440 743560 TRUE FALSE 1191795.89 1009854.316 1147371.992 1105746.315 1164062.05 1037580.864 1199881.325 1038708.67 1032879.084 889246.3457 1.340231417 1.135629425 1.290274622 1.243464559 1.309043389 1.166809252 1.349323875 1.168077524 1.161521876 1 19.76222362 0.944411647 1.306363544 1.002166151 1.255150231 0.572192062 0.068266412 0.336408655 1.161464126 0.058106409 0.017668835 8.798560956 -0.944411647 0.25298408 EELSNVLAAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EELSNVLAAMR 11 0 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 95.483 0.01797 20436000 15138 22125 23123 19503 25501 24377 20281 24930 22814 22189 FALSE TRUE 15735.65993 25924.79664 23725.60438 23360.63519 21166.34913 18715.81119 18691.32223 24595.85413 21992.9286 26536.50972 0.592981522 0.976948247 0.894074037 0.880320564 0.797631239 0.705285337 0.704362496 0.926868469 0.828780003 1 14.69569101 0.777978158 1.195739002 0.997035317 0.811441511 0.212808979 0.110487009 1.309662751 3.386546251 0.104471254 0.032169362 5.997609118 -0.777978158 -0.185593806 EELSSGDSLS(ph)PDPWKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EELSSGDSLSPDPWKR 16 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 EELSSGDS(0.034)LS(0.966)PDPWKR;EELSSGDS(0.028)LS(0.972)PDPWKR;EELSSGDSLS(1)PDPWKR;EELSSGDS(0.001)LS(0.999)PDPWKR 136.04 1.20E-05 586891000 812234 529375 673444 546623 887930 847132 846384 715502 735851 426654 TRUE FALSE 844301.6255 620291.0383 690994.5039 654743.3979 736999.9758 650398.4314 780042.2105 705911.866 709367.8663 510248.6825 1.654686537 1.215664164 1.354230844 1.283184887 1.444393687 1.274669497 1.528749093 1.383466318 1.390239486 1 18.96084103 -1.390545084 4.679164821 0.999456324 1.386438501 0.481117088 0.122043527 0.000631112 8.22E-05 0.107741182 0.025360046 0.040686929 1.390545084 0.386982178 EELTLEGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EELTLEGIR 9 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 132.76 0.0027373 0 46014 52382 52511 55050 68992 72547 68411 62099 59427 48868 FALSE TRUE 47830.66825 61378.20102 53879.4798 65938.72569 57264.76448 55699.05871 63048.76706 61266.66448 57288.23388 58442.74897 0.818419207 1.050227823 0.921918985 1.128261878 0.979843787 0.953053368 1.078812482 1.048319348 0.980245366 1 15.83473642 4.744136677 24.50071788 1.01894542 0.818419092 0.50279114 0.058751192 363.7638066 1598282.181 0.013387557 0.116796404 55480.02864 -4.744136677 -0.200526328 EELYQNLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EELYQNLTR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 125.71 0.0011489 121260000 76226 96053 90655 90802 93377 118230 109310 91603 83607 95464 FALSE TRUE 79235.46134 112549.3556 93017.54377 108762.3646 77504.81089 90772.87429 100741.9966 90375.21162 80598.0004 114168.343 0.694023047 0.985819296 0.814740245 0.952649059 0.678864288 0.795079195 0.882398692 0.79159607 0.705957521 1 16.80080315 5.061345736 11.30435188 0.834595324 5.31E-05 0.149751611 0.105382081 118534.3354 829688.8037 0.023753283 2059839.526 115171.689 -5.061345736 -0.83454224 EEMAAEAGEAVASPMDDGFVSLDS(ph)PSYVLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEMAAEAGEAVASPMDDGFVSLDSPSYVLYR 31 0 P49354;P49354-2;E9PN85 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 EEMAAEAGEAVASPMDDGFVS(0.038)LDS(0.689)PS(0.136)Y(0.136)VLY(0.001)R 119.14 1.45E-05 21501000 47487 57139 51880 67829 59163 69205 77863 62074 58426 49210 TRUE FALSE 49361.82343 66952.17877 53232.03542 81245.37375 49106.49439 53133.18756 71759.8946 61241.99956 56323.25967 58851.75732 0.838748504 1.137641114 0.904510551 1.380508883 0.834409993 0.902830943 1.219333082 1.040614628 0.957036157 1 15.84479787 EENEGVYNGSWGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 277.15 9.25E-33 969950000 657650 796190 802290 778490 783060 1008790 885040 823110 763650 678180 FALSE TRUE 683614.5298 932929.439 823198.3365 932472.9984 649955.7409 774513.8109 815668.2522 812077.5568 736166.3857 811056.3865 0.842869301 1.150264587 1.014970537 1.149701814 0.801369364 0.95494447 1.005686245 1.001259062 0.907663632 1 19.62944269 3.258744244 24.99969625 0.953608544 1.045618059 0.177412304 0.098109654 427.7174588 529772.7693 0.02614224 0.035352957 1814.44682 -3.258744244 0.092009515 EENKGGEDKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EENKGGEDKLK 11 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 71.607 0.027317 3614600000 3913800 969750 1734550 1139810 2737850 2427030 3126310 1878080 2109410 444480 FALSE TRUE 4068319.846 1136297.019 1779753.798 1365261.016 2272471.235 1863389.064 2881261.653 1852907.41 2033492.746 531567.3459 7.653441991 2.137635104 3.34812477 2.568368856 4.275039188 3.505461874 5.420313485 3.485743479 3.825465883 1 19.01989296 0.383833035 1.80312637 1.000122434 3.946028953 0.271999753 1.481524326 8.894998987 24.41953178 1.320347337 0.368839021 2.420098456 -0.383833035 2.945906518 EENSGLLQELEELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EENSGLLQELEELRK 15 1 A0A3B3ISJ8;J3KP58;P30622-2;P30622-1;P30622;F5H0N7;A0A3B3ITA2 A0A3B3ISJ8;J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 0 ;;; 205.68 6.86E-09 200962000 235167 178727 225270 168029 266315 269064 279580 213466 263557 181363 FALSE TRUE 244451.5747 209421.9719 231140.7213 201264.6347 221046.8714 206577.9637 257665.7891 210604.8374 254071.6351 216897.6074 1.127036751 0.965533804 1.065667455 0.927924642 1.019130059 0.952421588 1.187960495 0.97098737 1.171389754 1 17.72665461 2.297007353 24.99998363 1.072325721 1.006881895 0.153988009 0.082242669 151.6317037 64857.89297 0.026402982 0.022090308 198.1560577 -2.297007353 -0.065443826 EENVGLHQTLDQTLNELNCI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EENVGLHQTLDQTLNELNCI 20 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ; 247.38 9.30E-30 134111000 157019 240020 206271 229870 236040 300280 216840 231910 232780 253120 FALSE TRUE 163218.2314 281241.5679 211646.5917 275337.5999 195918.0051 230544.5208 199843.5142 228801.6258 224402.2933 302714.0177 0.539182931 0.92906688 0.699163499 0.909563429 0.647204932 0.761591824 0.660172646 0.755834261 0.741301295 1 18.20759596 -2.045076861 2.162294549 1.3214222 0.74321333 0.334388645 0.110633074 6154795.363 1965159.277 9783804.136 0.025261156 0.009014116 2.045076861 -0.57820887 EENWSFLDWDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EENWSFLDWDSR 12 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 0 ; 122.42 0.00083474 26326000 44044 57680 52655 51147 57389 60910 47622 52491 45158 54141 FALSE TRUE 45782.89113 67586.09131 54027.23256 61263.72394 47634.03828 46764.5756 43889.2632 51787.444 43532.7724 64748.89236 0.707083773 1.043818494 0.834411688 0.946174084 0.735673408 0.722245183 0.677838054 0.799819767 0.67233231 1 15.98256789 3.228707648 24.97854232 0.752830793 0.890906737 0.176616907 0.118344171 265.9338486 674175.5992 0.031148618 0.037657317 1693.197613 -3.228707648 0.138075944 EEPCLLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEPCLLKR 8 1 Q60FE5;P21333-2;P21333;H0Y5F3;H7C2E7 Q60FE5 FLNA Filamin-A 0 78.516 0.048781 212680000 156100 168010 168800 145240 220170 211530 190940 191600 186700 155620 FALSE TRUE 162262.9485 196864.4106 173199.0667 173968.0385 182745.582 162405.3633 175973.6239 189031.9154 179980.7035 186110.7595 0.871862266 1.057780921 0.930623609 0.934755406 0.981918415 0.872627481 0.945531706 1.015695793 0.967062323 1 17.50580194 1.755109809 25 0.994459749 0.944730945 0.177447215 0.051189268 10.79041967 16319.19161 0.022730285 0.012605201 56.89967799 -1.755109809 -0.049728804 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 135.32 1.85E-05 104511000 67102 74524 78500 96882 80052 103754 101185 84876 76336 63656 TRUE FALSE 69751.23877 87322.91728 80545.77449 116044.9704 66444.78963 79658.70591 93253.8553 83738.37605 73588.68227 76128.17443 0.916234223 1.147051245 1.058028451 1.524336703 0.872801563 1.046376148 1.224958512 1.099965639 0.966641888 1 16.21614286 EEPFFPPPEEFVFIHAVPVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEPFFPPPEEFVFIHAVPVEER 22 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;; 202.43 1.41E-22 572864000 360663 410031 395895 454666 452582 514959 519433 417193 430867 339112 FALSE TRUE 374902.2537 480450.6347 406212.3489 544597.5778 375652.2733 395367.5765 478718.4842 411601.2102 415360.1808 405554.5037 0.924418914 1.18467587 1.001622088 1.342846825 0.926268282 0.974881484 1.180404803 1.014909726 1.024178445 1 18.62953629 EEPGPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEPGPRPR 8 1 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 136.8 0.00070734 1945470000 4129600 4882350 4739500 4596880 5203450 5589210 4761270 4763900 4465000 4308650 FALSE TRUE 4292639.797 5720855.633 4863015.264 5506129.144 4318969.428 4291200.683 4388069.216 4700047.713 4304305.522 5152847.473 0.833061685 1.110231899 0.943753 1.068560475 0.838171409 0.832782399 0.851581429 0.912126302 0.835325622 1 22.29693846 3.226804957 24.99996765 0.872746891 0.994343298 0.293502109 0.08360297 236.4969301 502941.2176 0.022242152 0.026788279 1685.795758 -3.226804957 0.121596407 EEPLDPEEAEGPLSLVTTANHS(ph)PDFDHDRDYEDEPVNEDME ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 EEPLDPEEAEGPLSLVT(0.135)T(0.168)ANHS(0.697)PDFDHDRDYEDEPVNEDME;EEPLDPEEAEGPLSLVT(0.158)T(0.158)ANHS(0.685)PDFDHDRDYEDEPVNEDME 244.75 5.66E-55 350318000 213770 257037 279880 264757 329300 361120 297860 288900 309000 264730 TRUE FALSE 222209.8047 301181.1053 287173.9027 317125.1444 273325.7036 277255.3528 274512.9549 285027.768 297879.1504 316598.7749 0.701865649 0.951302182 0.907059425 1.001662576 0.863318892 0.875730972 0.867068911 0.900280704 0.940872719 1 18.27229615 -4.999994681 0.014075326 2.051871104 6.16E-07 0.239616073 0.071352544 11847.32492 12.65391017 1138.704051 744.7093202 1.00E-05 4.999994681 -2.051870489 EEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 EEPLS(1)EEEPCT(0.172)S(0.157)T(0.143)AIAS(0.528)PEKK 81.292 0.019002 201200000 185410 53661 78437 60268 123130 151120 156560 84673 94054 39627 TRUE FALSE 192730.13 62876.85933 80481.13266 72188.83052 102200.4066 116024.6702 144288.4181 83538.09693 90669.01491 47391.15195 4.066795637 1.326763684 1.698231196 1.523255451 2.156529276 2.44823486 3.044627788 1.762736154 1.91320555 1 15.53233011 EEPLS(ph)EEEPCTSTAIASPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK;EEPLS(1)EEEPCTSTAIASPEKK 223.97 2.05E-25 1213310000 1620720 821200 1149390 870090 1648370 1458240 1686350 1161750 1378090 544501 TRUE FALSE 1684707.277 962234.712 1179344.048 1042191.205 1368180.656 1119585.86 1554169.481 1146178.641 1328492.81 651185.5458 2.587138624 1.477665956 1.811072213 1.600451994 2.101061157 1.719303917 2.38667687 1.760141405 2.040114094 1 19.31270915 -1.440224751 16.02451337 1.000000007 1.920577854 0.422899029 0.329440244 9.02E-09 5.40E-10 0.290580655 0.068490517 0.036289021 1.440224751 0.920577847 EEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEPVLTPIDEGHLPMINQDEFR 22 0 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 EEPVLT(1)PIDEGHLPMINQDEFR 68.895 0.070573 22120000 29553 26923 27164 34709 30936 32664 32891 29711 32672 27931 TRUE FALSE 30719.77526 31546.81582 27871.91616 41574.3366 25677.50977 25078.28103 30312.91748 29312.77264 31496.1411 33403.54468 0.919656149 0.944415215 0.834399954 1.244608529 0.768706136 0.75076706 0.907476071 0.877534792 0.942898169 1 15.02771358 EEPVSS(ph)GPEEAVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEPVSSGPEEAVGK 14 0 O00567 O00567 NOP56 Nucleolar protein 56 1 EEPVS(0.015)S(0.985)GPEEAVGK;EEPVS(0.182)S(0.818)GPEEAVGK 253.16 9.94E-18 314270000 1047340 732350 916360 733540 1200490 1100830 1078780 865560 961820 566630 TRUE FALSE 1088689.792 858125.4156 940241.0944 878632.0226 996431.1386 845178.9157 994222.4047 853958.584 927204.2861 677650.2997 1.606565794 1.266324852 1.387501924 1.296586193 1.470420863 1.247219866 1.467161462 1.260175911 1.36826367 1 19.37018144 -3.700828064 0.230439544 3.95E-14 1.41365643 0.5425977 0.105880897 59.58988789 1.023847984 28.19928949 0.168655499 0.000199146 3.700828064 1.41365643 EEQNGEDEDGGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEQNGEDEDGGWR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9IYH5;C9JH78;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 ; 282.05 4.01E-32 291480000 217210 233860 236914 246370 255270 290980 272370 245160 252920 190672 FALSE TRUE 225785.6185 274023.6358 243088.1735 295101.2507 211879.2966 223404.3048 251020.9277 241874.0312 243817.4586 228030.5278 0.990155225 1.201697152 1.066033464 1.294130455 0.92917075 0.979712265 1.100821588 1.060708992 1.069231655 1 17.79886745 3.218930634 24.99999863 1.031893352 1.13741294 0.288678411 0.087601578 328.1394615 417904.9102 0.02466715 0.029521676 1655.505524 -3.218930634 0.105519588 EEQRS(ph)PFNDRFPLK ddPTM_MDA-MB-175_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 195.27 2.52E-08 495540000 960560 748010 884450 759190 1082660 1111120 1106250 970620 982210 668580 TRUE FALSE 998483.6505 876474.8988 907499.4936 909355.516 898629.8399 853079.2192 1019539.234 957610.4265 946860.454 799575.4503 1.248767268 1.09617535 1.134976685 1.137297944 1.123883731 1.066915222 1.275100723 1.19764861 1.184204009 1 19.60887465 2.255040566 24.9999912 1.185895183 1.132562857 0.003151021 0.07867425 560.9605917 850972.2039 0.025625581 0.021383781 179.9038948 -2.255040566 -0.053332326 EEQTDTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEQTDTSDGESVTHHIR 17 0 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 EEQT(0.006)DT(0.071)S(0.922)DGESVTHHIR;EEQTDT(0.011)S(0.893)DGES(0.04)VT(0.056)HHIR 96.55 0.003834 1214140000 464350 419280 469790 450460 553040 635350 597580 445480 484570 358480 TRUE FALSE 482682.8966 491288.0785 482033.1133 539559.6435 459034.4583 487799.5913 550740.1181 439509.0693 467130.4204 428717.2925 1.125876901 1.145948827 1.124361256 1.258544157 1.070715986 1.137811793 1.284623055 1.025172245 1.089600136 1 18.70966708 1.61487821 25 1.043036358 1.160394458 0.448275537 0.063763463 0.542314502 1927.040693 0.029192123 0.015749034 41.19819701 -1.61487821 0.1173581 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 40 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 453.68 2.31E-245 1430171000 477403 610807 717069 672795 843725 846956 972185 823475 908054 500344 FALSE TRUE 496251.2391 715708.3508 735756.4072 805871.8429 700308.9259 650263.3047 895982.5994 812437.6646 875373.3139 598376.8271 0.829328972 1.196083001 1.229587066 1.34676312 1.170347671 1.086712044 1.497355109 1.357735841 1.462913125 1 19.19069478 5.197106989 1.273074676 1.29577292 4.32E-15 0.428159612 0.149880127 3.595177557 2.276389701 0.041285019 8.077277495 157437.0664 -5.197106989 -1.29577292 EERLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EERLSPR 7 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EERLS(1)PR;EERLS(1)PR;EERLS(1)PR;EERLS(1)PR 112.71 0.003811 1349270000 1184500 1330970 1402460 1289040 1587270 1754330 1466920 1416810 1377280 1404840 TRUE FALSE 1231264.975 1559553.744 1439009.26 1544008.265 1317466.412 1346913.445 1351938.977 1397819.979 1327711.962 1680091.501 0.732855903 0.928255243 0.856506481 0.919002485 0.784163489 0.801690529 0.804681755 0.831990388 0.790261698 1 20.68010838 -1.104112269 5.101011706 1.000004543 0.831245576 0.447030002 0.057364523 2.86E-06 5.02E-07 0.053614776 0.012636784 0.078684236 1.104112269 -0.168758967 EERS(ph)PQTLAPVGEDAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EERSPQTLAPVGEDAMK 17 1 Q92797 Q92797 SYMPK Symplekin 1 EERS(0.958)PQT(0.042)LAPVGEDAMK 140.17 4.06E-07 192440000 240930 159880 210650 197870 261980 283740 313380 211700 263300 123870 TRUE FALSE 250442.1024 187338.1463 216139.7121 237008.0954 217448.7332 217845.6851 288816.4567 208862.5078 253823.8844 148139.9549 1.690577688 1.264602426 1.459023747 1.599893126 1.467860128 1.470539702 1.949618906 1.409899901 1.713405979 1 17.17660128 -1.067702061 6.819457819 0.999999759 1.549648946 0.458107559 0.181966933 6.34E-07 8.68E-08 0.167641925 0.039513564 0.085565351 1.067702061 0.549649187 EES(ph)DGEYDEFGR ddPTM_MDA-MB-175_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 313.82 2.35E-46 1789530000 1229290 1125010 1151770 1314800 1343540 1611710 1640840 1244750 1317890 703830 TRUE FALSE 1277823.318 1318221.716 1181786.072 1574863.516 1115165.551 1237414.778 1512226.673 1228066.162 1270459.396 841732.0129 1.51808806 1.56608243 1.40399326 1.870979708 1.324846309 1.47008164 1.796565475 1.458975236 1.509339525 1 19.68300146 0.450654845 1.545358379 1.00008707 1.555580743 0.519486743 0.158402127 2.552871779 6.372232217 0.142336535 0.04088732 2.822635797 -0.450654845 0.555493673 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESEEEEDEDDEEEEEEEKEK 21 1 H0Y993;A0A494C028;P35659;B4DFG0;H0Y8X0;A0A494C198;D6R9L5 H0Y993 DEK Protein DEK 1 EES(1)EEEEDEDDEEEEEEEKEK 240.49 3.50E-30 4879100000 4102200 768190 1250200 834140 2533400 3423300 2723000 1423300 1645500 409300 TRUE FALSE 4264158.024 900120.6568 1282781.239 999130.4023 2102773.573 2628290.456 2509564.145 1404222.992 1586278.776 489494.4985 8.711350254 1.838877985 2.620624426 2.041147358 4.295806346 5.369397335 5.126848519 2.868720682 3.240646792 1 18.90093312 4.748560199 24.83015702 3.33515466 8.711353481 0.599360023 1.35552413 941.8695993 2338723.207 0.335794282 4.523784357 56048.01024 -4.748560199 5.376198821 EES(ph)EES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_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 231.58 2.70E-15 365623800 847519 736763 808069 845454 1007875 1200940 1020569 907944 888081 606148.2 TRUE FALSE 880979.7045 863296.314 829127.942 1012682.278 836556.7675 922039.8854 940574.135 895774.4958 856119.1383 724911.3344 1.215293047 1.19089918 1.143764627 1.396973988 1.154012536 1.271934707 1.297502316 1.235702152 1.180998417 1 19.46744502 -0.577183867 8.384418693 1 1.234842623 0.483444107 0.071854362 0 0 0.065854905 0.01552215 0.264737908 0.577183867 0.234842622 EES(ph)EES(ph)EAEPVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 EES(1)EES(1)EAEPVQR 326.19 3.44E-52 578550000 522430 434270 513880 483740 610890 749440 586420 540680 523120 364910 TRUE FALSE 543055.9398 508852.4943 527272.135 579422.3282 507051.136 575393.9179 540454.8681 533433.069 504293.0134 436407.1279 1.244379171 1.166004086 1.208211556 1.327710505 1.161876385 1.318479651 1.238418975 1.222328956 1.155556317 1 18.73531514 0.866876591 1.850757958 1.000288486 1.237378247 0.663594392 0.051473169 0.297880289 1.991707147 0.046806608 0.013173995 7.35997926 -0.866876591 0.23708976 EES(ph)EESEAEPVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EES(0.969)EES(0.031)EAEPVQR;EES(1)EESEAEPVQR 294.52 1.28E-40 293990000 304590 277980 299770 270770 332630 499770 370660 351130 330890 251070 TRUE FALSE 316615.4484 325720.9026 307582.2525 324327.4978 276089.6714 383705.9916 341606.7007 346423.6767 318981.3335 300262.3595 1.054462667 1.084787661 1.024378324 1.080147037 0.919494777 1.277902406 1.137694053 1.15373661 1.06234206 1 18.19586411 2.746142544 24.99779643 1.138106 1.037729144 0.250902239 0.079405529 763.8321298 2518373.343 0.023291112 0.024293306 557.3686582 -2.746142544 -0.100376856 EES(ph)KTCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESKTCK 7 1 Q9BTE3 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 EES(0.5)KT(0.5)CK 58.64 0.065612 1413700000 10806 73972 35361 53073 21655 45935 16814 44679 20822 126760 TRUE FALSE 11232.62922 86676.11558 36282.53671 63570.68099 17974.09083 35267.2924 15496.07474 44080.15109 20072.62029 151596.195 0.07409572 0.571756538 0.239336724 0.419342194 0.11856558 0.232639694 0.102219417 0.290773466 0.13240847 1 17.20987402 -1.623708849 3.506625835 1.035929191 0.250147693 0.70285309 0.147711319 79487191.3 117462133.8 26519686.35 0.033962653 0.023784343 1.623708849 -0.785781499 EES(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 155.88 0.010303 5663630000 3113210 3267670 3127990 3368270 3839930 4194670 4306280 3414890 3258460 2355620 TRUE FALSE 3236121.935 3828866.904 3209507.989 4034503.753 3187220.07 3220521.463 3968742.521 3369118.985 3141188.661 2817158.638 1.14871839 1.35912364 1.139271302 1.432118056 1.131359813 1.143180728 1.408774951 1.195928032 1.115020155 1 21.42580938 1.093188864 2.411250808 1.004799178 1.252183978 0.346979409 0.109538657 0.273803741 3.1383117 0.096147544 0.026471858 12.39335427 -1.093188864 0.247384799 EES(ph)WESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 EES(1)WESGR;EES(1)WESGR 174.8 0.00028303 419610000 504270 525520 567530 603950 682160 765570 704780 593540 573960 451190 TRUE FALSE 524178.969 615773.972 582320.298 723409.5074 566206.6869 587777.9698 649537.502 585584.5671 553303.2917 539592.0419 0.971435693 1.14118431 1.079186224 1.340660075 1.049323642 1.089300664 1.203756637 1.085235737 1.0254104 1 19.04150955 1.31063772 3.146333265 1.006497026 1.128620727 0.185144361 0.092843236 0.39576064 6.465801474 0.076612635 0.023296824 20.44738246 -1.31063772 0.1221237 EESAEQPEFYYDEFGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESAEQPEFYYDEFGFR 17 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 218.16 1.10E-14 19408000 15941 19864 15805 15893 19077 23553 19651 16304 15309 15526 FALSE TRUE 16570.36299 23275.48748 16216.89128 19036.58796 15834.29835 18083.1727 18110.70327 16085.47155 14758.03208 18568.02244 0.89241399 1.253525385 0.873377407 1.02523508 0.85277247 0.973887917 0.975370605 0.866299661 0.79480904 1 14.18053255 4.191329235 24.99991377 0.91886517 1.07297341 0.246765456 0.106728243 128.9672997 68263.07951 0.024574883 0.05308805 15535.64308 -4.191329235 0.154108241 EESEES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.08)EES(0.92)DEDMGFGLFD;EES(0.001)EES(0.999)DEDMGFGLFD 179.46 1.03E-08 160004000 198426 217228 215982 203718 248450 253900 238220 218651 226818 194080 TRUE FALSE 206260.0117 254535.2192 221610.6684 244012.8124 206218.5577 194935.5729 219547.6939 215720.341 218654.8645 232106.2601 0.88864476 1.096632288 0.954781091 1.051297851 0.88846616 0.83985487 0.945893031 0.929403373 0.94204639 1 17.82442591 3.230482707 24.98037576 0.919054285 1.001820099 0.234839791 0.064478824 222.2851166 687400.4194 0.017555153 0.021324203 1700.132254 -3.230482707 0.082765814 EESEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EESEKPR 7 1 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ; 114.6 0.0053517 767890000 975730 660150 887050 692610 1176420 1129850 1231380 934280 937010 669950 FALSE TRUE 1014252.574 773525.6272 910167.2517 829606.1908 976452.5486 867459.4605 1134861.218 921757.5048 903287.1931 801213.8755 1.265894919 0.965442126 1.135985384 1.035436624 1.218716473 1.082681525 1.416427314 1.15045125 1.12739834 1 19.61182788 3.229054456 24.99736792 1.185021608 1.093550329 0.048044976 0.124578613 435.1501428 1144268.358 0.034081814 0.041236288 1694.550265 -3.229054456 -0.091471279 EESELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESELQR 7 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 88.942 0.042427 71150000 50549 72528 58143 78031 78046 92000 71107 65244 73063 86743 FALSE TRUE 52544.71355 84984.11981 59658.25435 93465.2989 64779.7688 70634.39427 65533.44754 64369.5109 70433.4769 103738.6301 0.506510579 0.819213824 0.575082342 0.900969088 0.624451747 0.680888057 0.631716917 0.620497021 0.678951292 1 16.6625937 0.916992236 20.23003281 1 0.672245992 0.453466572 0.108398495 7163.097061 1745741.746 0.09535557 0.023838893 8.260231827 -0.916992236 -0.327754009 EESGKPGAHVTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EESGKPGAHVTVK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 151.74 2.47E-05 15980330000 17178810 15279480 20852360 15547390 25751220 24024720 25479820 21485880 22467210 12946680 FALSE TRUE 17857042.68 17903611.83 21395789.63 18622617.34 21374036.82 18445342.88 23482645.13 21197896.92 21658619.5 15483334.07 1.153307331 1.156315026 1.381859329 1.202752408 1.380454412 1.191303036 1.516640087 1.369078315 1.398834347 1 23.88421283 4.618164923 0.927009707 1.335110319 1.04519039 0.095606015 0.141650654 3.031706489 2.344402341 0.043377952 0.85351301 41511.16512 -4.618164923 -0.289919929 EESHSNDQSPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESHSNDQSPQIR 13 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 150.26 4.42E-05 30586000 107350 87218 94957 82504 94457 201770 88468 88587 84122 80332 FALSE TRUE 111588.2609 102197.013 97431.65743 98823.04495 78401.23288 154911.9754 81533.64699 87399.63616 81094.46565 96071.51735 1.161512423 1.063759747 1.014157579 1.02864041 0.816071558 1.612465168 0.848676582 0.909735149 0.844105182 1 16.55182115 EESLADDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESLADDLFR 10 0 O60934;A0A0C4DG07;A0A087X1V5 O60934 NBN Nibrin 0 120.99 0.0012259 21883000 29763 38354 37632 37880 43500 49267 42947 39154 35667 38974 FALSE TRUE 30938.06622 44941.00115 38612.72084 45372.55094 36105.88554 37825.4859 39580.70192 38629.20467 34383.35164 46610.2091 0.663761584 0.964187933 0.82841767 0.973446629 0.774634704 0.811527917 0.849185247 0.828771323 0.737678554 1 15.50835836 EESQDTLTHSS(ph)PSFNLDTLLVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 EES(0.001)QDT(0.019)LT(0.016)HS(0.109)S(0.812)PS(0.042)FNLDT(0.001)LLVPK;EESQDT(0.003)LT(0.003)HS(0.219)S(0.773)PS(0.003)FNLDTLLVPK 141.49 1.18E-07 81504000 35553 35209 47995 39191 67560 55335 61633 47299 51885 34438 TRUE FALSE 36956.65989 41255.87186 49245.78913 46942.86283 56076.17533 42484.28486 56802.04441 46665.03427 50017.66899 41185.46674 0.897322838 1.001709465 1.195707929 1.139791935 1.361552503 1.031535836 1.379176902 1.133046144 1.214449488 1 15.32984772 4.382113972 2.578001858 1.195138916 0.901021851 0.399855281 0.115985785 0.253422477 3.141863511 0.026630161 0.114900366 24105.37941 -4.382113972 -0.294117065 EESQIPVDEVFFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EESQIPVDEVFFHR 14 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 99.927 0.0019869 44995000 75793 85870 93150 81073 91134 101780 88274 90432 88487 84017 FALSE TRUE 78785.36616 100617.5045 95577.56552 97108.99742 75643.07523 78143.13749 81354.85322 89219.90696 85302.37015 100478.5225 0.784101559 1.001383201 0.951223835 0.96646522 0.752828299 0.777709858 0.809674059 0.887950028 0.848961231 1 16.61652763 EESYS(ph)PSKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EESYSPSKDR 10 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 EES(0.01)YS(0.876)PS(0.114)KDR;EES(0.011)YS(0.964)PS(0.025)KDR;EES(0.002)YS(0.849)PS(0.149)KDR 89.189 0.0070751 1751490000 4446760 2106910 3073110 2332670 3977850 3936270 4079980 2848350 3170320 1672960 TRUE FALSE 4622321.518 2468755.403 3153197.771 2794065.164 3301696.478 3022130.947 3760180.507 2810172.527 3056220.802 2000744.481 2.310300771 1.233918387 1.57601223 1.396512743 1.650233955 1.510503203 1.879390668 1.404563428 1.527541788 1 20.9321055 -2.72744067 0.268614144 6.20E-12 1.649769566 0.313835984 0.280473168 63.38638281 1.838335133 36.93136668 0.337283014 0.001873093 2.72744067 1.649769566 EETEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EETEELKR 8 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 98.582 0.011898 661580000 118500 105300 118040 115580 139320 152240 157080 126040 132530 92419 FALSE TRUE 123178.4715 123384.4559 121116.2194 138441.379 115638.4362 116884.5672 144767.6591 124350.64 127760.2712 110526.7336 1.114467672 1.116331333 1.095809271 1.252560123 1.046248563 1.057523039 1.309797679 1.125072966 1.155921894 1 16.75403584 EETKEDAEEKQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EETKEDAEEKQ 11 2 P43487;F6WQW2;P43487-2 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 154.28 0.00012744 4986500000 12258190 3982960 6249870 4121090 9626420 10373880 11534640 7129580 8479970 2493785 FALSE TRUE 12742152.81 4667002.397 6412746.747 4936229.302 7990124.567 7964703.588 10630524.78 7034019.642 8174777.536 2982394.424 4.272457292 1.564850832 2.150200756 1.655122898 2.679097205 2.670573524 3.564426184 2.358514214 2.741011541 1 21.50803964 EETNGPSNQKPVKS(ph)PDNSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EETNGPSNQKPVKSPDNSIK 20 2 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 EETNGPSNQKPVKS(1)PDNSIK 150.53 4.51E-08 443260000 1305000 355050 636850 411080 904190 908220 1140900 639280 780630 215590 TRUE FALSE 1356522.408 416027.0756 653446.8342 492390.397 750496.1068 697299.6692 1051473.277 630711.4973 752535.2788 257830.7328 5.261290588 1.613566665 2.534402424 1.909742845 2.910809346 2.704486241 4.07815339 2.446223111 2.918718303 1 17.97606471 EETPGQRPAVTETHQLAELNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EETPGQRPAVTETHQLAELNEK 22 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1;I3L1C0 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 270.77 1.58E-45 421540000 573590 392750 476280 368810 622180 575220 581260 469510 513820 333690 FALSE TRUE 596235.7761 460201.7573 488692.2481 441759.5172 516422.0658 441633.8725 535699.3224 463216.9864 495327.7186 399070.1666 1.494062513 1.153185068 1.224577252 1.106972042 1.294063323 1.106657198 1.342368754 1.160740705 1.24120458 1 18.60628291 -5 0.192031845 0.036606641 1.267560092 0.30170332 0.111318605 174.6923284 1.713892989 64.69880094 0.27359406 1.00E-05 5 1.230953451 EETVNDPEEAGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EETVNDPEEAGHR 13 0 O00567 O00567 NOP56 Nucleolar protein 56 0 ; 94.728 0.005022 280860000 179120 197980 214849 224959 222560 257140 244160 202519 203552 175360 FALSE TRUE 186191.7959 231981.5249 220448.1414 269455.2188 184729.3307 197423.132 225022.1012 199804.5641 196226.2033 209718.4345 0.887817975 1.10615705 1.05116244 1.284842791 0.880844505 0.941372333 1.072972444 0.952727711 0.93566502 1 17.67809416 3.154358905 24.8805634 0.967427888 1.082170401 0.24814744 0.100990014 35.5282904 10493.50842 0.028777111 0.034395236 1426.786214 -3.154358905 0.114742514 EEVFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EEVFWR 6 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;;;; 154.29 0.023318 1018021000 1091142 1155960 1173819 1283147 1240633 1430350 1398900 1209105 1128147 1037252 FALSE TRUE 1134221.129 1354487.138 1204409.687 1536949.647 1029750.646 1098172.89 1289250.563 1192898.925 1087545.21 1240481.67 0.914339289 1.091904194 0.970920987 1.238994242 0.830121614 0.885279417 1.039314481 0.961641719 0.876712035 1 20.24246899 3.207540978 24.99999973 0.937616581 1.050807795 0.271749049 0.097428869 281.1201806 226565.606 0.027528588 0.03290597 1612.653182 -3.207540978 0.113191214 EEVGEEAIVELVENGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EEVGEEAIVELVENGKK 17 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 149.09 5.42E-07 171062000 394630 193368 287280 263230 429160 391880 540360 337130 380750 154672 FALSE TRUE 410210.2971 226577.4498 294766.7528 315296.1083 356211.5365 300871.809 498005.1712 332611.3238 367046.8819 184977.017 2.217628458 1.224895143 1.593531767 1.704515044 1.925707 1.626536171 2.692254309 1.798122432 1.984283711 1 17.4969865 3.291719948 2.55056685 1.925850483 1.632668601 0.001080564 0.45444895 0.759958598 10.09232775 0.129497321 0.179307668 1957.581932 -3.291719948 -0.293181882 EEVNDRPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEVNDRPVR 9 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 105.86 0.0035474 0 112430 97668 104310 115590 90467 123110 126550 114250 102160 80679 FALSE TRUE 116868.8232 114441.7192 107028.4043 138453.357 75089.45165 94519.56825 116630.6803 112718.6656 98483.28156 96486.50536 1.21124527 1.186090416 1.109257755 1.434950478 0.778237862 0.979614381 1.208777123 1.16823244 1.020694875 1 16.55803956 3.252220541 24.99988654 1.053637726 1.222855598 0.35492129 0.134856354 342.1781459 626237.8751 0.039636398 0.053387064 1787.395008 -3.252220541 0.169217872 EEVNDRPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEVNDRPVRR 10 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;;; 156.48 6.11E-06 310918000 286670 330714 334869 294921 391000 412997 313310 336329 358444 357861 FALSE TRUE 297987.953 387511.5569 343595.9612 353255.4935 324537.9597 317084.7058 288751.9435 331821.0599 345543.6705 427977.0113 0.696270933 0.905449467 0.802837424 0.825407637 0.758306991 0.740891911 0.674690313 0.775324494 0.807388391 1 18.70717378 0.768286318 3.164925465 0.999970782 0.773727261 0.548212075 0.061645117 1.243620618 15.96502716 0.060650193 0.015784713 5.865247156 -0.768286318 -0.226243521 EEVTELLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EEVTELLAR 9 0 P19388;A0A087WVZ9;A0A0A0MQR7;A0A087WWX0 P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" 0 101.43 0.0092776 37462000 24895 37330 36620 35013 42738 41718 33504 32768 33988 41080 FALSE TRUE 25877.87382 43741.13711 37574.34728 41938.4669 35473.41003 32029.62674 30877.86893 32328.79856 32764.77852 49128.83948 0.526734889 0.890335241 0.764812434 0.853642531 0.722048605 0.651951625 0.628508006 0.658041161 0.666915377 1 15.58428254 -0.974801142 4.636722646 1.000004268 0.709989582 0.424929862 0.102203547 0.042195669 63998181.55 772.7259316 0.024238767 0.105973885 0.974801142 -0.290014686 EEWYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EEWYAR 6 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 177.42 0.0085408 1694750000 1077440 1441270 1335170 1417580 1430340 1758730 1377360 1308910 1330290 1606460 FALSE TRUE 1119978.163 1688796.911 1369965.627 1697973.093 1187211.318 1350291.611 1269398.924 1291366.202 1282413.123 1921215.079 0.582953036 0.87902543 0.713072493 0.883801669 0.617948157 0.702832091 0.660727129 0.672161184 0.667501071 1 20.87358761 -1.007731221 4.672519898 1.000006387 0.711340008 0.460862896 0.09442487 11636830.31 2509737.421 796.5912714 0.021222134 0.098235572 1.007731221 -0.288666379 EEYLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EEYLLLR 7 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;; 151.17 0.0044183 1761870000 1551411 1722029 1849217 1887831 2138858 2220018 2187307 1929205 1842263 1650960 FALSE TRUE 1612661.904 2017774.085 1897409.114 2261238.337 1775295.681 1704452.464 2015860.162 1903347.163 1775960.314 1974434.002 0.816771744 1.021950636 0.960988877 1.145259013 0.899141566 0.8632613 1.020981283 0.963996345 0.899478186 1 20.91300771 EFADFEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EFADFEYR 8 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A0G2JQ95;A0A096LP11;A0A140TA66 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;;; 155.75 0.00093967 1736525000 2621310 3061620 3044740 2923030 3407570 3513750 3197440 3119860 2988200 3102410 FALSE TRUE 2724801.343 3587429.419 3124088.426 3501196.61 2828352.469 2697734.814 2946816.298 3078043.38 2880655.266 3710267.84 0.734394782 0.966892304 0.842011564 0.943650637 0.762304122 0.727099749 0.794232768 0.829601396 0.776400893 1 21.82309191 5.042108245 15.04350538 0.838008659 0.288903842 0.121188857 0.088228641 2146446.624 22622648.17 0.020669933 32145843.22 110181.3894 -5.042108245 -0.549104817 EFAFPPPVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFAFPPPVSPR 11 0 Q13191 Q13191 CBLB E3 ubiquitin-protein ligase CBL-B 1 EFAFPPPVS(1)PR;EFAFPPPVS(1)PR 112.08 0.0016505 105848000 94683 101006 106077 110492 131264 133970 130586 123082 121999 133269 TRUE FALSE 98421.15795 118352.9948 108841.4538 132346.9878 108951.7922 102857.4978 120350.3281 121432.2871 117608.2798 159380.509 0.617523175 0.742581358 0.682903163 0.830383769 0.683595459 0.645358071 0.755113212 0.76190174 0.737908798 1 17.28211568 -5 0.239813305 2.605381366 0.692693636 0.702036934 0.056347864 93.37374124 0.931470034 72.97842267 0.087205954 1.00E-05 5 -1.91268773 EFAGEDTSDLFLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 122.39 0.00025398 41039000 52457 75512 87625 71397 78282 93606 79074 69452 72954 77216 FALSE TRUE 54528.04287 88480.5986 89908.57948 85519.1135 64975.6536 71867.42511 72875.97326 68521.10954 70328.39979 92344.99681 0.590481832 0.958152598 0.973616142 0.926082803 0.703618559 0.778249257 0.789170781 0.742012149 0.761583217 1 16.49474618 3.248161782 24.99054853 0.779133527 0.876912056 0.048649995 0.125173406 426.2453048 1109453.213 0.033522314 0.044815073 1770.768478 -3.248161782 0.097778529 EFALHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFALHK 6 0 A0A087WW66;Q99460-2;Q99460;C9J9M4;F8WCE3 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 74.743 0.079523 950800000 1780550 1427770 1665560 1459710 2343700 2050430 2179610 1757560 1777220 1613630 FALSE TRUE 1850847.489 1672978.391 1708965.862 1748436.281 1945318.711 1574248.707 2008766.473 1734002.783 1713258.199 1929789.904 0.959092741 0.866922553 0.885570941 0.906024162 1.00804689 0.815761708 1.040924957 0.898544852 0.887795193 1 20.88001236 3.450149002 24.99108109 0.937116793 0.899439613 0.068446484 0.065739773 597.0733873 553215.4221 0.017067672 0.023110211 2819.350058 -3.450149002 -0.03767718 EFCENLSADCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFCENLSADCR 11 0 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 172.8 3.01E-05 188910000 178531 197386 180950 207551 198132 233542 208445 193028 166915 172045 FALSE TRUE 185579.5417 231285.5101 185665.7057 248603.9683 164453.5934 179305.4099 192106.5362 190440.7754 160907.7618 205753.9237 0.90194898 1.124087968 0.902367752 1.208258699 0.799273182 0.871455604 0.933671313 0.925575425 0.782039821 1 17.65056042 3.213439258 24.99989823 0.887361257 1.03117492 0.328225307 0.104249601 255.4715844 254235.6188 0.027970226 0.033442929 1634.704498 -3.213439258 0.143813664 EFDEDS(ph)DEKEEEEDTYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFDEDSDEKEEEEDTYEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK;EFDEDS(1)DEKEEEEDTYEK 273.56 3.13E-39 675054000 1587390 272453 381828 328828 610990 1185140 1106450 470330 552640 137259 TRUE FALSE 1650061.383 319244.6834 391778.7514 393869.1969 507134.138 909909.196 1019723.558 464025.9957 532750.5944 164152.2731 10.05201666 1.94480818 2.386678808 2.399413603 3.089412827 5.543080086 6.212058711 2.826802133 3.245465837 1 17.3246752 4.746196671 24.7457931 3.374907019 10.05202036 0.649241752 1.508729191 543.2826739 1760541.533 0.377764013 4.008536535 55743.81281 -4.746196671 6.677113341 EFDEDSEDRLVNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFDEDSEDRLVNEK 14 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;; 244 1.32E-17 1756220000 1631080 1174960 1439210 1342700 1851010 1920150 1981560 1500550 1717720 915490 FALSE TRUE 1695476.298 1376750.24 1476716.995 1608282.052 1536375.981 1474224.263 1826240.149 1480437.582 1655899.593 1094862.737 1.548574301 1.257463783 1.348769069 1.46893487 1.403258992 1.346492316 1.668008315 1.352167291 1.51242666 1 20.06231858 -1.548421839 6.405022687 0.99945101 1.428489903 0.566986781 0.113693094 0.000842013 5.94E-05 0.10399453 0.024481992 0.028286431 1.548421839 0.429038893 EFDKHFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFDKHFGK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 56.563 0.070185 817630000 1337100 941060 1540000 936190 1970500 1570500 1207400 1275400 1474900 1055000 FALSE TRUE 1389889.74 1102679.735 1580133.665 1121365.588 1635555.114 1205775.176 1112760.833 1258305.349 1421818.637 1261707.051 1.101594653 0.873958605 1.252377613 0.888768583 1.296303379 0.955669682 0.881948652 0.997303889 1.126900762 1 20.26694555 EFDLTKEEDLAALR ddPTM_MDA-MB-175_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 63.709 0.061039 32091000 55840 45840 48121 49651 66110 71321 51192 42623 45785 43011 FALSE TRUE 58044.60632 53712.66341 49375.07279 59471.81961 54872.64581 54757.77863 47179.43727 42051.7084 44137.20679 51438.18195 1.128434251 1.044217765 0.959891484 1.156180435 1.066768765 1.064535653 0.917206547 0.817519337 0.858063118 1 15.65055203 2.172173976 3.881380836 0.870867194 1.068497146 0.615435583 0.066025369 0.132123583 3.969943095 0.025579051 0.01855909 148.653102 -2.172173976 0.197629952 EFDRHS(ph)GSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFDRHSGSDR 10 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 EFDRHS(0.962)GS(0.038)DR;EFDRHS(0.895)GS(0.105)DR 97.297 0.0037275 2855600000 1060320 1338220 1379010 1275730 1535590 1756210 1480290 1512490 1447950 1618840 TRUE FALSE 1102182.252 1568048.875 1414948.133 1528065.586 1274570.96 1348356.843 1364261.002 1492217.545 1395838.562 1936020.703 0.569302927 0.809933939 0.730853823 0.789281635 0.658345728 0.696457864 0.704672734 0.770765283 0.720983283 1 20.88466295 -4.99999633 0.336630221 3.942440497 0.712337681 0.633633954 0.064910387 233.8149352 1.987302567 493.57613 0.049779133 1.00E-05 4.99999633 -3.230102816 EFDSDS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFDSDSLR 8 0 Q12955;D6RFK6;B1AQT1;A0A087WZ26;Q12955-4;Q12955-5;Q12955-6;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 EFDS(0.014)DS(0.986)LR;EFDSDS(1)LR 117.02 0.0022646 403410000 384210 338190 380150 357230 491710 552550 462400 430300 395310 365600 TRUE FALSE 399378.9075 396271.5017 390057.0213 427889.0278 408129.3098 424228.6365 426155.8797 424532.5323 381082.8703 437232.3202 0.913424944 0.906317954 0.892104731 0.978630829 0.933438108 0.970259098 0.974666922 0.970954142 0.871579828 1 18.73804052 3.744626832 24.95712624 0.957371913 0.904186082 0.348317272 0.033298257 527.4454545 2169964.96 0.008290232 0.014474232 5554.268013 -3.744626832 -0.053185831 EFDSLHWFQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFDSLHWFQSVR 12 0 Q2M389;A0A087X256 Q2M389 KIAA1033 WASH complex subunit 7 0 74.46 0.036444 15386000 30810 43057 44179 43479 56714 60714 45192 47669 46066 58002 FALSE TRUE 32026.40259 50451.70481 45330.34103 52079.01643 47073.77454 46614.09363 41649.73295 47030.07503 44408.09366 69366.38138 0.461699197 0.727322138 0.653491506 0.750781796 0.678625201 0.671998347 0.600431104 0.67799522 0.640196198 1 16.08194901 -1.525474097 2.868652297 1.01490912 0.657374327 0.658519372 0.075199592 15206074.28 16602102.35 1768263.599 0.016971853 0.029821254 1.525474097 -0.357534793 EFEDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFEDRDR 7 1 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 ;;; 142.36 0.0022749 1670980000 1374920 1429530 1495820 1419440 1739840 1914560 1612750 1574770 1635360 1527850 FALSE TRUE 1429202.903 1675040.657 1534802.298 1700200.995 1444102.618 1469932.455 1486338.441 1553662.784 1576503.713 1827202.955 0.782180709 0.916723921 0.83997363 0.930493786 0.790335093 0.804471365 0.813450108 0.850295683 0.862796171 1 20.80120546 0.634962375 2.141010303 0.99997454 0.84252206 0.505989585 0.046855316 1.818162538 9.641443802 0.043797656 0.011947228 4.314816939 -0.634962375 -0.15745248 EFEPLLNWMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFEPLLNWMK 10 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 183.47 3.87E-06 268600000 546350 498650 508430 519660 855360 735430 670280 512750 560910 526400 FALSE TRUE 567920.3199 584289.2585 521680.1035 622447.197 709966.2127 564637.528 617741.7021 505877.4249 540722.9587 629538.0015 0.90212238 0.92812389 0.828671347 0.988736495 1.127757516 0.896907775 0.981261974 0.803569322 0.858920283 1 19.26393394 -3.223241046 9.167656029 0.999170628 0.926294318 0 0.09139067 0 0 0 0.021154562 0.00059808 3.223241046 -0.07287631 EFESVLVDAFSHVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EFESVLVDAFSHVAR 15 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;;;; 220.99 1.60E-12 948006000 1076587 1221473 1212966 1171226 1457585 1549591 1386600 1325307 1289482 1285255 FALSE TRUE 1119091.486 1431251.486 1244576.89 1402891.007 1209825.222 1189721.975 1277914.669 1307543.427 1243073.795 1537076.11 0.72806511 0.931151995 0.809704141 0.912701068 0.787095196 0.774016307 0.831393228 0.85066928 0.808726248 1 20.55175717 -1.758594209 2.967228523 1.032621364 0.830249985 0.445347241 0.058094204 32032478.66 21277103 7514262.376 0.012957676 0.017434351 1.758594209 -0.202371379 EFETAETLLNSEVHMLLEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EFETAETLLNSEVHMLLEHR 20 0 O15514;E9PHV4 O15514 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 ;;;;;;; 244.46 3.91E-30 185127400 51831.4 64755.9 70132.1 65316.1 77145.3 81957.7 73220.2 74287.4 70044.1 69844.8 FALSE TRUE 53877.74369 75877.22209 71959.80014 78235.42963 64032.16946 62924.26626 67481.0094 73291.69891 67523.22652 83529.5513 0.645014164 0.908387761 0.861489126 0.936619776 0.76658103 0.753317422 0.80786989 0.877434366 0.808375305 1 16.34999907 -0.651070295 0.677944101 1.021502437 0.822925245 0.310744021 0.080624746 22.41761813 6.914185643 1.21965916 0.02893589 0.223321072 0.651070295 -0.198577192 EFFNGKEPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFFNGKEPSR 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 142.1 3.32E-05 3373800000 3960000 4326500 4056000 4075900 5729300 5665400 4703200 4257100 4321800 4129520 FALSE TRUE 4116343.858 5069542.72 4161702.692 4882100.855 4755435.632 4349696.71 4334550.894 4200040.538 4166259.262 4938620.38 0.833500764 1.026509902 0.842685279 0.988555604 0.962907708 0.880751379 0.877684568 0.850448144 0.843607919 1 22.23567665 2.676851993 9.099118452 0.877680284 0.934431343 0.062531359 0.069062571 0.866753156 122.7715408 0.020707836 0.019528026 475.1732598 -2.676851993 0.056751059 EFFVTS(ph)APWSVIDQQAIHPELNGATYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFFVTSAPWSVIDQQAIHPELNGATYR 27 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 EFFVT(0.068)S(0.93)APWS(0.001)VIDQQAIHPELNGATYR;EFFVT(0.005)S(0.901)APWS(0.094)VIDQQAIHPELNGATYR 170.6 3.38E-12 252760000 52071 72916 64269 66978 81675 81515 67074 70975 61574 77054 TRUE FALSE 54126.80329 85438.75579 65943.90294 80226.04849 67791.91267 62584.37662 61816.56461 70023.69622 59357.96377 92151.25601 0.587369132 0.9271578 0.715605037 0.870590939 0.735659128 0.679148384 0.6708163 0.759877827 0.644136242 1 16.49171621 -1.084721004 4.53469553 1.000014723 0.739032297 0.405603116 0.096922708 12413874.25 2969458.727 2276.333287 0.021247513 0.082277104 1.084721004 -0.260982426 EFFVTSAPWSVIDQQAIHPELNGATYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFFVTSAPWSVIDQQAIHPELNGATYR 27 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 263.55 3.34E-53 509820000 153050 172870 181690 181650 174580 206390 150800 182120 135530 170880 FALSE TRUE 159092.5322 202559.0778 186424.9907 217579.8278 144904.954 158459.0504 138979.902 179678.9793 130652.3018 204360.6643 0.778489015 0.991184279 0.912235196 1.06468546 0.709064802 0.775389192 0.680071688 0.879224874 0.639322162 1 17.640758 3.225175603 24.99992972 0.774671681 0.938800116 0.296527396 0.117590087 259.7849059 485213.6428 0.031598331 0.037969675 1679.482963 -3.225175603 0.164128435 EFGIADPDEIMWFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFGIADPDEIMWFK 14 0 Q15067-2;Q15067;Q15067-3;I3L0T4;I3L4S5;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;; 136.53 6.17E-05 120663000 266704 256273 261964 284192 335395 372897 322516 262545 294374 229146 FALSE TRUE 277233.6799 300285.8942 268790.997 340404.3294 278384.6777 286297.3231 297236.3532 259026.0137 283779.5372 274042.7714 1.011643834 1.095762872 0.980835932 1.242157666 1.0158439 1.044717661 1.084634897 0.945202869 1.035530095 1 18.06404155 1.752343421 25 0.990230292 1.069465793 0.189040157 0.070431187 6.568394442 11931.10141 0.031045432 0.017216383 56.53838783 -1.752343421 0.079235501 EFGSVDDENKPIWMHAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFGSVDDENKPIWMHAEER 19 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8 Q07866-6 KLC1 Kinesin light chain 1 0 ;; 224.97 1.11E-19 724470000 569500 445250 567290 492380 693260 732400 714000 622710 679360 386070 FALSE TRUE 591984.2997 521718.2239 582074.0434 589771.2944 575419.9128 562311.1996 658034.8143 614363.591 654909.9663 461713.0247 1.282147715 1.129962111 1.260683611 1.277354683 1.246271779 1.217880306 1.425203057 1.330617847 1.418435113 1 18.81663691 2.290753595 24.99905931 1.325852057 1.234416832 0.026625259 0.118651259 199.5027585 95555.53146 0.037916463 0.03172315 195.3230941 -2.290753595 -0.091435225 EFGVTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFGVTTGR 8 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 173.68 0.00064297 435866000 372586 466932 460870 453430 471700 559810 468190 443258 408708 436915 FALSE TRUE 387295.983 547123.9388 472880.6508 543117.1006 391520.6025 429802.6115 431492.0444 437316.8515 393998.6789 522520.129 0.741207776 1.047086817 0.904999874 1.039418523 0.749292861 0.822557042 0.825790281 0.836937808 0.754035408 1 18.99512709 3.230680105 24.99850199 0.823610336 0.939301837 0.189981536 0.101842739 243.3196659 771856.5297 0.026983515 0.032814411 1700.905185 -3.230680105 0.115691502 EFHGNIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFHGNIIK 8 0 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;; 109.71 0.0035651 726160000 1269990 1760560 1668950 1723040 2119290 2360480 1897140 1855300 1825870 2057770 FALSE TRUE 1320130.186 2062922.485 1712444.208 2063852.169 1759053.843 1812294.293 1748437.21 1830432.738 1760157.295 2460950.633 0.536430991 0.838262441 0.695846631 0.838640215 0.714786318 0.736420418 0.710472281 0.743790921 0.715234703 1 21.23078429 -1.837041113 2.569885691 1.102311885 0.731633235 0.515607769 0.079609121 19163321.9 12901744.76 12097041.29 0.017029037 0.014553213 1.837041113 -0.37067865 EFHLNESGDPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 EFHLNESGDPSSK 13 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;;;;;; 193.97 1.42E-06 32137160000 17069120 15660760 19162360 16014340 22179910 23319800 21688210 19646830 20415200 15427170 FALSE TRUE 17743022.04 18350373.71 19661746.84 19181928.65 18409776.82 17904129.86 19988231.43 19383496.38 19680460.94 18449828.59 0.961690346 0.994609441 1.065687236 1.039680589 0.997829152 0.970422559 1.083383042 1.05060577 1.06670156 1 24.13710408 2.231173132 24.99999539 1.055019786 1.008525653 0.279778258 0.034898639 226.7631682 767382.2242 0.0133321 0.010050005 170.283721 -2.231173132 -0.046494133 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.049)EWHS(0.951)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK;EFITGDVEPTDAESEWHS(1)ENEEEEK 397.66 4.76E-139 13167000000 9640592 5420844 6527378 6144981 8411709 9155845 11045551 7351529 7875290 3748186 TRUE FALSE 10021210.02 6351831.789 6697486.833 7360439.901 6981889.709 7029538.757 10179771.85 7252993.778 7591859.851 4482571.283 2.235594123 1.417006309 1.494117195 1.642012906 1.557563565 1.568193412 2.270967087 1.618043154 1.693639514 1 22.09589509 0.465108777 2.464856195 1.000016667 1.714247005 0.375920843 0.279060147 11.48342118 51.37237371 0.260530692 0.069594457 2.918157825 -0.465108777 0.714230338 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK;EFITGDVEPTDAES(0.001)EWHS(0.999)ENEEEEKLAGDMK 419.08 1.40E-176 29981630000 5848733 2794147 4060158 2458506 5907116 4667980 5126624 3924137 4584801 2401729 TRUE FALSE 6079645.495 3274020.012 4165969.053 2944791.149 4903026.532 3583912.389 4724785.815 3871540.362 4419794.908 2872301.814 2.116645774 1.139859327 1.450393908 1.025237367 1.707002554 1.247749234 1.644947544 1.347887727 1.538764097 1 21.45377592 -2.008181266 2.99966888 0.527871158 1.446190156 0.17903999 0.297608458 133036.513 53365310.71 40799.82872 0.062484111 0.009813383 2.008181266 0.918318998 EFKEEGEEIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFKEEGEEIPR 11 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 124.07 0.00032544 475010000 968070 815050 918800 763890 1290170 1218960 1178690 1062640 1120950 844820 FALSE TRUE 1006290.151 955028.4973 942744.6828 914985.162 1070867.364 935875.0135 1086301.198 1048397.049 1080607.228 1010346.304 0.995985384 0.945248667 0.933090643 0.90561539 1.059901303 0.926291322 1.075177089 1.037661092 1.069541428 1 19.94641844 2.516310734 1.212095761 1.048402327 0.951901744 0.360530129 0.048682116 0.447973697 1.334586919 0.025234341 0.018914332 328.3301267 -2.516310734 -0.096500583 EFKEEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFKEEISR 8 1 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 111.46 0.0029459 703350000 635990 652980 651330 705830 885290 1015490 947270 794260 758710 841600 FALSE TRUE 661099.3763 765124.2355 668304.1949 845441.0673 734808.722 779657.8374 873020.5022 783614.2438 731404.1753 1006495.407 0.656832979 0.760186515 0.663991301 0.839985023 0.730066642 0.774626324 0.867386474 0.778557198 0.726684067 1 19.94090916 -5 0.131010542 1.774483929 0.663966109 0.617749219 0.059949936 94.2369438 0.777101972 19.31113895 0.429613172 1.00E-05 5 -1.110517821 EFKEEISRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFKEEISRR 9 2 Q9NRR5;Q9NRR5-2 Q9NRR5 UBQLN4 Ubiquilin-4 0 ; 105.86 0.0017036 136933000 436920 367270 420440 305310 558540 509490 415770 453460 448850 410200 FALSE TRUE 454169.939 430345.7655 431397.0118 365699.4067 463599.5703 391168.6689 383180.861 447382.1104 432695.9762 490570.8362 0.925798897 0.877234711 0.879377615 0.745456884 0.94502065 0.797374487 0.781091807 0.911962305 0.882025478 1 18.90410194 0.783228452 1.350406532 0.99881161 0.852809147 0.327853496 0.061445686 0.860973838 2.798887193 0.056446222 0.01685825 6.070555747 -0.783228452 -0.146002464 EFLEDYDDDRDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFLEDYDDDRDDPK 14 1 P49756 P49756 RBM25 RNA-binding protein 25 0 101.3 0.0013138 173420000 250200 103390 144680 131280 169880 196340 226170 143440 149280 78514 FALSE TRUE 260078.0892 121146.4282 148450.4797 157246.7922 141003.8583 150743.0106 208442.2044 141517.4214 143907.442 93897.31506 2.769813908 1.290201197 1.580987482 1.67466761 1.501681472 1.605402779 2.219895258 1.507150884 1.53260444 1 16.51879628 -2.4460239 0.225524636 4.46E-20 1.840869117 0.263536146 0.401689754 61.44153556 1.71761243 31.92397397 0.756704928 0.003580767 2.4460239 1.840869117 EFLEKEELPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFLEKEELPR 10 1 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;; 121.08 0.00047845 468070000 526389 478124 554340 421704 669480 648370 547290 548235 587340 463971 FALSE TRUE 547171.2442 560238.0777 568786.5558 505115.7925 555682.0287 497795.8936 504391.9797 540886.8066 566201.7481 554877.2342 0.986112261 1.009661315 1.025067386 0.910319908 1.001450401 0.897127982 0.909015452 0.974786445 1.020409044 1 19.08180909 3.758768231 24.96432715 0.955322896 1.007218422 0.21698128 0.041309985 1182.65486 1461037.286 0.010625869 0.019128289 5738.101567 -3.758768231 0.051895526 EFLHAQEEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;; 135.6 7.57E-05 2108077000 1336513 1078338 1315982 1054342 1618935 1653438 1543767 1453310 1505707 1233247 FALSE TRUE 1389279.565 1263534.163 1350277.572 1262887.701 1343749.007 1269452.083 1422762.509 1433830.757 1451516.899 1474878.138 0.941962275 0.856704111 0.91551806 0.856265795 0.911091549 0.860716591 0.964664451 0.972168968 0.984160564 1 20.49216433 2.140703299 5.693977718 0.978768688 0.889551273 0.722449909 0.027373754 0.103152196 4.981881923 0.009491543 0.006972177 138.2621477 -2.140703299 -0.089217415 EFLHNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFLHNQGK 8 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 133.55 0.0009147 508960000 871580 704500 802000 753470 1008170 1021090 950890 771140 850480 690600 FALSE TRUE 905990.6514 825492.3948 822900.7789 902504.1171 836801.6235 783957.3223 876356.7571 760804.1296 819871.3909 825909.8477 1.096960708 0.999494554 0.996356662 1.092739262 1.013187609 0.949204474 1.061080407 0.921170914 0.992688722 1 19.65562479 2.997810091 24.98479448 0.981468673 1.04115198 0.282177092 0.045827884 111.8855551 1276541.549 0.012992893 0.015297301 994.9702401 -2.997810091 0.059683307 EFLLIFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFLLIFHK 8 0 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2;C9JTV4 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 ; 112.94 0.0029442 278250000 417280 386980 387400 391600 523330 521140 490710 383990 395490 461540 FALSE TRUE 433754.5366 453440.8047 397495.9623 469057.3112 434374.5535 400113.133 452246.868 378843.2421 381256.3922 551969.9263 0.785830017 0.821495489 0.720140615 0.849787803 0.786953297 0.724882125 0.819332443 0.686347614 0.690719501 1 19.07423014 2.977016104 23.59917912 0.761027404 0.794383681 0 0.090401326 1625.944748 1669473.986 0.025770512 0.027540838 948.4536321 -2.977016104 0.033356277 EFLLSLDDSVDETEAVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFLLSLDDSVDETEAVKR 18 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;A0A286YEP7;H7C0U8 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 292.8 5.14E-49 170264000 293760 215460 271980 217630 328560 333650 343010 279080 294250 217280 FALSE TRUE 305357.8716 252463.579 279068.0222 260676.5644 272711.4886 256164.844 316123.9799 275339.3891 283660 259851.8559 1.17512292 0.97156735 1.073950468 1.003173764 1.049488323 0.9858111 1.216554636 1.059601395 1.09162199 1 17.98732984 EFLSELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFLSELQR 8 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 A0A087X142 8-Sep Septin-8 0 ;; 127.02 0.0027782 209873000 231972 260505 237979 245770 326030 324600 272228 257908 236745 334042 FALSE TRUE 241130.4337 305244.7073 244180.9282 294382.5724 270611.5371 249216.5694 250890.058 254451.1651 228224.5937 399491.1343 0.603593955 0.764083808 0.611229905 0.736893881 0.677390595 0.623835044 0.628024095 0.636938203 0.571288257 1 18.60780396 -1.338203533 4.095147484 1.000676375 0.652990225 0.771500108 0.057067603 8833796.534 2886855.351 53365.02683 0.012830521 0.045898286 1.338203533 -0.34768615 EFMTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFMTPR 6 0 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 111.69 0.064292 87555000 80176 97063 93514 90578 102860 112060 100150 95154 92320 104700 FALSE TRUE 83341.41039 113732.8152 95951.05166 108494.0581 85375.89394 86035.76329 92299.98131 93878.61627 88997.42123 125213.9604 0.665592 0.908307786 0.766296756 0.866469343 0.681840057 0.687109992 0.737138104 0.749745603 0.710762769 1 16.9340359 -1.115628065 3.857607523 1.000088801 0.755830065 0.49389655 0.07507157 16507274.79 27717529.23 19000.28237 0.018361879 0.076625255 1.115628065 -0.244258736 EFNAEVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EFNAEVHR 8 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 226.64 3.01E-06 8020040000 4034010 4695790 4658240 4815750 5348700 5866990 5009710 4767670 4409880 5496280 FALSE TRUE 4193275.83 5502255.404 4779637.561 5768290.976 4439529.885 4504470.488 4617035.84 4703767.182 4251169.28 6573170.833 0.637938057 0.837077804 0.727143365 0.877550747 0.675401568 0.685281214 0.702406184 0.715600933 0.646745595 1 22.64815805 -1.159413178 5.050821454 1.000015524 0.726680631 0.559829387 0.073668079 1.25E-05 2.07E-06 0.069035457 0.016270889 0.069276641 1.159413178 -0.273334893 EFNAEVHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EFNAEVHRK 9 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 152.37 5.23E-05 3887790000 4422990 4142130 4642230 3339110 6069670 5509070 4315960 4617800 4742560 4993500 FALSE TRUE 4597613.06 4853508.606 4763210.327 3999575.992 5037949.661 4229671.983 3977663.778 4555905.944 4571876.192 5971880.719 0.769876908 0.812726984 0.797606408 0.669734742 0.843611904 0.708264646 0.66606551 0.762892991 0.765567232 1 22.50975392 0.56108422 2.732131364 0.999996001 0.752455565 0.638268607 0.055357113 4.522689274 27.35125061 0.052813888 0.013940632 3.639856151 -0.56108422 -0.247540436 EFNKYDTDGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFNKYDTDGSK 11 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 138.42 5.28E-05 6166400000 4353460 2668900 3842600 2721420 5366030 4908540 5359700 4117940 4693450 2533370 FALSE TRUE 4525337.962 3127262.814 3942741.313 3259708.753 4453914.137 3768605.975 4939592.709 4062745.75 4524533.651 3029735.347 1.49364134 1.032190094 1.301348422 1.075905444 1.470067061 1.243872993 1.63037102 1.340957306 1.493375867 1 21.53076035 3.225643368 24.96141586 1.389897975 1.217342432 0.094802729 0.197074846 395.6446606 764546.0777 0.052020858 0.062543768 1681.292856 -3.225643368 -0.172555543 EFNSYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFNSYGSR 8 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ; 164.71 0.00076423 234802000 158874 228491 228127 227925 256990 258990 211968 204706 215372 249480 FALSE TRUE 165146.4682 267732.5518 234072.177 273007.8847 213306.9316 198843.4975 195353.3943 201962.2509 207620.8038 298360.8294 0.553512566 0.897344844 0.78452717 0.915025894 0.71492941 0.666453093 0.654755501 0.676906051 0.69587152 1 18.18669862 3.040494961 24.99780267 0.706886766 0.797691246 0.009423947 0.132205476 349.9587583 216029.6687 0.035651878 0.042612102 1097.728555 -3.040494961 0.09080448 EFRPEDQPWLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 ;;; 190.85 5.58E-06 756990000 298024 338680 319278 318036 375927 379920 331889 356091 316798 356677 FALSE TRUE 309790.2176 396845.6554 327598.647 380942.5716 312027.0628 291689.3377 305874.6729 351318.1826 305396.5019 426561.0292 0.726250633 0.930337345 0.767999476 0.893055262 0.731494538 0.68381619 0.717071303 0.823605905 0.715950312 1 18.70239264 5.048423338 15.47026882 0.796043704 0.334632751 0.045673728 0.100001775 1108608.646 9662226.636 0.022695655 15043619.7 111795.2464 -5.048423338 -0.461410953 EFS(ph)GGSYSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFSGGSYSAK 10 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 EFS(0.955)GGS(0.043)YS(0.002)AK;EFS(0.896)GGS(0.104)YSAK;EFS(0.998)GGS(0.002)YSAK;EFS(1)GGSYSAK 233.45 4.81E-12 1958320000 3020680 2056810 2852810 2149280 3820850 3659020 3593230 2605760 3288610 1864700 TRUE FALSE 3139938.779 2410051.118 2927156.572 2574401.169 3171383.282 2809268.058 3311583.243 2570834.049 3170253.568 2230052.263 1.408011297 1.080715083 1.312595503 1.154412931 1.42211164 1.259731937 1.484980105 1.152813363 1.421605054 1 21.08864609 -1.042915602 4.470438582 0.999984747 1.289722261 0.320837804 0.130075827 0.186407483 35313649.24 1187.165687 0.027744464 0.090590863 1.042915602 0.289737514 EFS(ph)IPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFSIPR 6 0 Q8NFJ5 Q8NFJ5 GPRC5A Retinoic acid-induced protein 3 1 EFS(1)IPR;EFS(1)IPR 96.253 0.044496 234947000 229640 310930 268420 396620 367820 467000 407500 324900 280070 308740 TRUE FALSE 238706.3645 364329.8088 275415.2457 475070.2522 305298.0878 358546.3275 375559.0852 320545.2469 269990.3354 369231.6918 0.646494789 0.9867241 0.745914427 1.286645385 0.826846922 0.971060544 1.017136648 0.868141208 0.731221998 1 18.49416686 4.744922161 24.10742712 0.936105853 0.646494572 0.24670419 0.152321155 612.2129917 2319907.827 0.034291072 0.317736056 55580.46312 -4.744922161 -0.289611281 EFSDFIQAVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFSDFIQAVER 11 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 0 78.342 0.070129 11368000 17219 20177 23953 21557 27579 27549 23873 25338 20545 22469 FALSE TRUE 17898.81942 23642.24279 24577.23486 25820.91026 22891.13143 21151.16226 22001.77188 24998.38555 19805.58946 26871.37036 0.666092543 0.879830187 0.914625288 0.960907833 0.851878082 0.787126298 0.818781163 0.930298129 0.73705171 1 14.71378228 -2.378470566 2.299219392 2.115140888 0.849668293 0.228982488 0.086751088 2761675.682 617138.9308 16049897.14 0.020942261 0.0041834 2.378470566 -1.265472595 EFSDIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFSDIFR 7 0 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;;; 128.57 0.0087129 470645000 921820 1000800 951260 1153500 1117950 1292120 1296960 1045750 981780 932820 FALSE TRUE 958214.1654 1172679.615 976050.6171 1381658.857 927921.2583 992044.7123 1195300.886 1031733.432 946445.9296 1115588.219 0.858931772 1.051176048 0.874920155 1.238502553 0.83177757 0.889257071 1.071453486 0.924833567 0.848382865 1 20.08937317 EFSGGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFSGGWR 7 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 107.67 0.039617 0 98916 107450 113090 105060 115480 125290 105170 106440 103030 114310 FALSE TRUE 102821.2801 125903.7017 116037.2183 125840.5544 95850.75085 96193.29629 96926.50059 105013.3459 99321.97043 136706.8559 0.752129653 0.920975768 0.848803211 0.920513851 0.701140775 0.703646468 0.7090098 0.768164444 0.726532475 1 17.06072607 3.236418685 24.99702158 0.75059337 0.864074746 0.173890899 0.094158456 74.1620334 865496.6512 0.024707494 0.0309362 1723.529355 -3.236418685 0.113481376 EFSIDVGYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFSIDVGYER 10 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 ;;; 262.84 4.54E-17 842770000 1356230 1530270 1365230 1464980 1615150 1777610 1526050 1548350 1482440 1478710 FALSE TRUE 1409775.008 1793081.969 1400809.015 1754748.671 1340607.38 1364787.017 1406434.213 1527596.901 1429087.274 1768434.913 0.797187953 1.013937214 0.792117937 0.992260817 0.758075613 0.771748515 0.795298828 0.863812906 0.808108494 1 20.75404169 5.077593757 14.46535557 0.857330312 6.48E-05 0.037921294 0.095303574 1876311.363 7091553.705 0.021612751 48807298.22 119562.1614 -5.077593757 -0.857265559 EFSITDVVPYPISLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFSITDVVPYPISLR 15 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 158.01 4.30E-06 216722000 337950 316480 354440 302780 287510 513390 262660 411950 434700 321520 FALSE TRUE 351292.527 370832.9781 363676.9976 362668.9803 238639.1529 394162.953 242072.0229 406428.4841 419055.2319 384515.6881 0.913597384 0.96441573 0.945805357 0.943183832 0.62062267 1.025089392 0.629550446 1.056988041 1.089826098 1 18.55268294 1.603502476 25 1.055088699 0.868298522 0.297902182 0.130414163 0.499214932 2844.653481 0.064108748 0.031279469 40.13307863 -1.603502476 -0.186790177 EFTGS(ph)PPSSATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFTGSPPSSATK 12 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFTGS(1)PPSSATK;EFTGS(0.998)PPS(0.001)S(0.001)ATK;EFT(0.004)GS(0.996)PPSSATK;EFTGS(0.988)PPS(0.011)SATK 253.83 4.50E-21 1354170000 3405060 2590490 3352380 2971970 4068260 4207060 4632600 3613210 3765540 2565090 TRUE FALSE 3539494.398 3035386.506 3439745.777 3559816.796 3376738.618 3230034.074 4269484.707 3564780.83 3630018.951 3067670.274 1.153805358 0.989476129 1.121289275 1.160430059 1.100750184 1.052927396 1.3917678 1.162048236 1.183314576 1 21.54871199 EFTGS(ph)PPSSATKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EFTGSPPSSATKK 13 1 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 EFT(0.001)GS(0.999)PPSSATKK;EFT(0.043)GS(0.945)PPS(0.009)S(0.002)AT(0.002)KK;EFT(0.044)GS(0.942)PPS(0.012)S(0.002)ATKK;EFT(0.002)GS(0.996)PPS(0.001)SATKK 123.36 0.00013738 2887290000 5148190 3067960 4426470 2805830 6101800 5357320 5349900 4488640 5265240 2976660 TRUE FALSE 5351444.516 3594858.265 4541827.445 3360814.799 5064618.216 4113163.621 4930560.859 4428477.123 5075745.041 3559879.535 1.50326562 1.009825818 1.275837398 0.944081047 1.422693708 1.155422137 1.385035873 1.243996343 1.425819326 1 21.76339699 EFTKLEEVLTNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFTKLEEVLTNKK 13 2 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 125.28 0.00011362 339260000 1368100 670260 1102800 579110 1583600 1288300 1082200 1004200 1328500 602050 FALSE TRUE 1422113.644 785371.9411 1131539.874 693656.2295 1314420.238 989111.8494 997374.3362 990740.3415 1280687.545 720010.1706 1.975129939 1.090778955 1.571560959 0.963397821 1.825557876 1.373747052 1.385222566 1.376008815 1.778707575 1 19.45765776 -1.516003063 4.918142927 0.998106808 1.454534256 0.180562763 0.303066301 0.005643024 0.000555333 0.263205207 0.061809378 0.030478735 1.516003063 0.456427449 EFVEAVLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EFVEAVLELR 10 0 O75367-2;O75367-3;O75367;B4DJC3 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 ;;;; 140.11 9.28E-05 235343500 250371.2 375332.3 230852.6 345318.4 270478.4 375931.1 265899.4 246949.5 203188.8 324924.4 FALSE TRUE 260256.0483 439792.7028 236868.8084 413621.3488 224502.5782 288626.7993 245057.5102 243639.5459 195876.0748 388587.1151 0.669749557 1.131773766 0.609564237 1.064423736 0.577740665 0.742759572 0.630637251 0.626988226 0.50407249 1 18.56787854 3.217434787 24.96604369 0.659217292 0.869133814 0.182538127 0.192334227 328.8413371 388616.5671 0.050540171 0.060463468 1649.81325 -3.217434787 0.209916522 EFVISDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFVISDRK 8 1 Q14019;H3BT58 Q14019 COTL1 Coactosin-like protein 0 ; 109.71 0.0057164 594830000 403760 393550 420680 387220 566700 525680 440170 447870 445630 460550 FALSE TRUE 419700.7566 461139.1511 431643.2664 463810.9603 470372.5364 403598.7868 405668.3252 441867.0352 429591.8633 550785.9547 0.762003375 0.837238399 0.783686045 0.842089302 0.854002417 0.732768843 0.736526271 0.80224819 0.779961543 1 19.07113225 -1.738788658 7.070610612 1.002943249 0.793104668 0.705472394 0.040261259 0.001939553 7.17E-05 0.040476412 0.009428143 0.018247835 1.738788658 -0.209838581 EFVTHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFVTHPK 7 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 81.297 0.027584 304440000 1042880 1183930 1383930 1041380 1517940 1591940 1376890 1342910 1336030 1202000 FALSE TRUE 1084053.708 1387260.768 1419996.353 1247361.856 1259921.101 1222236.061 1268965.764 1324910.488 1287946.541 1437508.886 0.754119657 0.965045003 0.987817443 0.867724623 0.876461435 0.850245917 0.882753335 0.921671164 0.895957273 1 20.45513944 0.256060206 0.918065781 1.000741632 0.8908079 0.232142878 0.060759498 5.093515191 4.980679465 0.06741586 0.018924055 1.803267711 -0.256060206 -0.109933732 EFWEIVHSFTDEQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFWEIVHSFTDEQKR 15 1 A0A1B0GVL3;Q05086-2;Q05086-3;Q05086;A0A0D9SG63;S4R306 A0A1B0GVL3 UBE3A Ubiquitin-protein ligase E3A 0 ; 164.15 9.72E-07 151826000 269229 196098 267375 229922 330109 301361 277141 253484 278042 204085 FALSE TRUE 279858.3688 229776.3061 274343.0122 275399.8854 273997.1901 231374.4749 255417.9642 250086.4616 268035.3227 244071.5483 1.146624302 0.941430116 1.124027008 1.128357186 1.12261012 0.947978068 1.046488073 1.024644058 1.0981834 1 17.8969446 2.770403141 24.95305656 1.026845681 1.087942247 0.221354372 0.064395083 1164.390455 912459.9322 0.019527521 0.020710748 589.3905126 -2.770403141 0.061096565 EFWGDIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EFWGDIAK 8 0 Q9NR19;Q9NR19-2;F8WCJ4;C9IYL0;B4DEH9;C9JY31 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 92.439 0.027398 74657000 82376 108820 115360 100210 179980 142540 120250 121230 136680 141630 FALSE TRUE 85628.26809 127508.9885 118366.3764 120031.2389 149387.0639 109437.2452 110824.4908 119605.1101 131760.9135 169379.6868 0.505540361 0.752799765 0.698822737 0.708651912 0.88196564 0.646106078 0.654296231 0.706136092 0.777902687 1 17.36990134 -5 0.256464808 2.862438058 0.680934325 0.515394414 0.089108928 158.079757 1.558627115 154.7558642 0.119885344 1.00E-05 5 -2.181503734 EFWPQEVWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EFWPQEVWSR 10 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ;; 169.76 1.05E-05 763099000 361067 464822 391111 474723 444979 545001 383895 360289 313380 447380 FALSE TRUE 375322.204 544651.5627 401303.674 568621.7925 369341.6285 418432.7773 353804.3068 355459.9153 302101.515 535035.5454 0.701490223 1.01797267 0.750050492 1.062773861 0.69031232 0.78206538 0.661272526 0.664366916 0.564638214 1 19.02927522 3.182226814 24.99992695 0.705584063 0.883207594 0.203620876 0.147461622 108.2104618 48021.26569 0.039295692 0.046967363 1521.341855 -3.182226814 0.177623531 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EFYHEVHRPSHFLNFALLQEGEVYSADREDLYA 33 2 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 122.63 4.03E-08 110281000 27979.7 42429 44258 46432 49127 55965 43843 49693 45881 51691 FALSE TRUE 29084.36016 49715.8507 45411.39984 55616.11101 40776.41009 42967.97691 40406.4711 49026.94662 44229.75177 61818.86177 0.470477122 0.804218151 0.734588094 0.899662489 0.659611143 0.69506257 0.653626902 0.793074237 0.715473409 1 15.91575947 -5 0.312583791 3.504465615 0.709919391 0.39342918 0.107122463 312.8724198 2.818782355 516.4416095 0.095240214 1.00E-05 5 -2.794546224 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSR 39 1 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 114.61 3.77E-06 91639000 27362 27047 29448 25908 35638 43439 26617 26976 31180 27906 FALSE TRUE 28442.27289 31692.11185 30215.43907 31032.52507 29580.26549 33350.95057 24530.68999 26614.43084 30057.83789 33373.64641 0.852237497 0.949614899 0.905368227 0.929851197 0.886336037 0.999319947 0.735031758 0.797468473 0.900645903 1 15.0264217 2.246065975 24.99813905 0.832901816 0.919970611 0.10588215 0.075199857 238.8190074 795437.3429 0.025165571 0.020672367 176.2243733 -2.246065975 0.087068795 EGAGEQKTEHMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGAGEQKTEHMTR 13 1 Q12906;Q12906-5;Q12906-2;Q12906-3;K7EKJ9;K7ER69;K7EM82;K7EJ09;K7EKY0;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 68.972 0.029427 71784000 43200 70154 76776 72551 90636 100880 74880 73743 75823 74658 FALSE TRUE 44905.56936 82202.40378 78776.84563 86901.37126 75229.72509 77452.14885 69010.70994 72754.5957 73094.14504 89285.80569 0.502941862 0.92066598 0.882299768 0.973294362 0.842572059 0.867463179 0.77291916 0.814850638 0.818653586 1 16.44614322 4.743851556 24.966142 0.865890911 0.502941707 0.727204844 0.068422787 304.961138 1438962.639 0.016742507 0.143280497 55443.61718 -4.743851556 -0.362949204 EGALCEENMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 EGALCEENMR 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;; 219.97 1.41E-08 5827520000 1414793 1846417 1714528 1685585 1892170 2076703 1759782 1807235 1719898 1800996 FALSE TRUE 1470650.12 2163524.757 1759210.008 2018988.682 1570539.619 1594420.201 1621845.689 1783011.971 1657999.207 2153866.684 0.682795333 1.004484062 0.81676829 0.937378667 0.729172159 0.740259466 0.752992607 0.827819096 0.769778009 1 21.03849752 5.027251699 15.30961497 0.82905241 0.30057088 0.177035992 0.099521426 557352.6031 8776880.932 0.022979756 7299342.716 106475.9931 -5.027251699 -0.52848153 EGALTAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGALTAFR 8 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 122.74 0.0032044 51291000 107120 131740 119500 119540 148170 140480 131490 110090 102720 136660 FALSE TRUE 111349.1803 154365.3202 122614.2682 143184.6552 122984.1163 107855.649 121183.4702 108614.4236 99023.12727 163435.9105 0.681301802 0.944500629 0.75022844 0.876090541 0.752491395 0.659926259 0.741473951 0.664568902 0.605883535 1 17.31836548 3.02086859 9.024729868 0.71005713 0.817632269 0.071146866 0.119637635 0.424019703 163.6673541 0.031862442 0.037754127 1049.224903 -3.02086859 0.107575139 EGASGRPGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGASGRPGSPK 11 1 E7EMV7;A0A0A0MRZ4;Q15025-7;Q15025-8;Q15025-5;Q15025-6;Q15025-4;Q15025-3;Q15025-2;Q15025;E7EW15 E7EMV7 TNIP1 TNFAIP3-interacting protein 1 1 EGAS(0.003)GRPGS(0.997)PK;EGASGRPGS(1)PK;EGAS(0.055)GRPGS(0.945)PK;EGAS(0.019)GRPGS(0.981)PK;EGASGRPGS(1)PK 103.11 0.0027564 831541000 1770000 925720 1189862 922695 1810590 2195590 1720620 1274780 1340110 761779 TRUE FALSE 1839880.967 1084705.209 1220870.781 1105201.317 1502826.559 1685697.497 1585753.308 1257693.659 1291879.703 911035.0099 2.019550233 1.190629556 1.340092058 1.213127163 1.649581566 1.850310338 1.740606334 1.380510788 1.418035189 1 19.79714697 0.790403565 1.540882357 1.003075394 1.539955634 0.292748872 0.258331554 0.999602243 4.195208522 0.251041364 0.07287128 6.171682339 -0.790403565 0.536880241 EGATVYATGTHAQVEDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 153.11 3.56E-08 474340000 109024 176448 165231 176582 136320 223760 154393 130122 127589 195490 FALSE TRUE 113328.3517 206751.5714 169537.0556 211509.3926 113148.3751 171795.1311 142291.2732 128377.9274 122997.0968 233792.5226 0.484738992 0.884337827 0.725160299 0.90468844 0.483969178 0.734818758 0.608622002 0.549110493 0.526095084 1 17.83486926 3.236725326 24.99978643 0.624017043 0.757591038 0.059878059 0.173750622 101.0040667 1375855.866 0.045964575 0.057676535 1724.746715 -3.236725326 0.133573995 EGCEAIVDTGTSLMVGPVDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGCEAIVDTGTSLMVGPVDEVR 22 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 203.2 3.06E-22 118811000 141734 166646 157454 158849 168852 200494 164566 153072 145165 182828 FALSE TRUE 147329.7678 195266.1542 161557.3806 190268.8581 140150.5974 153932.307 151666.8869 151020.3202 139940.54 218649.6461 0.67381663 0.893054975 0.738886998 0.870199707 0.640982502 0.70401352 0.693652561 0.69069547 0.6400218 1 17.73826149 4.030977701 24.94746414 0.729999816 0.791569608 0 0.116740104 649.311253 522905.5148 0.027126791 0.058599738 10739.34269 -4.030977701 0.061569792 EGDELEDNGKNFYES(ph)DDDQKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGDELEDNGKNFYESDDDQKEK 22 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK;EGDELEDNGKNFYES(1)DDDQKEK 253.35 3.97E-37 1402080000 2387900 315139 588450 312388 1153590 1403900 975060 578564 647329 146038 TRUE FALSE 2482176.136 369261.6718 603785.4904 374177.414 957503.1839 1077865.501 898632.2494 570809.2959 624031.7557 174651.35 14.21217835 2.114278943 3.457090313 2.142424974 5.48236921 6.17152688 5.145292316 3.26827875 3.573014212 1 17.41411827 4.744236219 24.99947863 3.800143279 14.21218281 0.807172797 1.553895148 266.9354117 1175743.177 0.376664843 3.334191918 55492.74639 -4.744236219 10.41203953 EGDIIPPLTGAT(ph)PPLIGHLK ddPTM_MDA-MB-175_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;EGDIIPPLT(0.001)GAT(0.999)PPLIGHLK 149.85 3.46E-07 114876000 259620 178296 236620 179583 281430 278370 277790 239280 248140 188646 TRUE FALSE 269869.9981 208916.951 242786.5116 215103.9814 233592.6291 213722.7862 256016.0939 236072.843 239209.4899 225607.5719 1.196192113 0.926019235 1.076145227 0.953443094 1.035393569 0.947320981 1.134785024 1.046387056 1.060290166 1 17.78345596 2.238066661 24.99997638 1.064839048 1.017933817 0.049487642 0.079070015 35.41620996 1792334.64 0.026259579 0.020600935 173.0081892 -2.238066661 -0.046905231 EGDIVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGDIVKR 7 1 P25705;P25705-2;P25705-3;K7EK77;K7ERX7;K7EJP1;K7EQH4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 105.2 0.012796 404400000 892590 771560 770660 739880 883480 1234200 883210 682080 833960 791510 FALSE TRUE 927830.1424 904069.4281 790744.0327 886226.0557 733306.3852 947575.7545 813981.6924 672937.8333 803945.9425 946591.2301 0.98018037 0.955079024 0.835359559 0.936228889 0.774681153 1.001040073 0.859908339 0.710906474 0.84930635 1 19.85238203 5.61953879 0.564937774 0.844466359 1.308115665 0.104201725 0.089716834 16.31069298 1.879084309 0.043475294 6.168941744 416426.9134 -5.61953879 0.463649306 EGDKHTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 EGDKHTLSK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;; 134.68 0.00014553 1.19352E+11 103052830 66811500 96800050 60075640 120142860 102778750 105888610 90501580 98710760 55455130 FALSE TRUE 107121435.3 78285855.4 99322738.83 71958422.28 99721019.57 78909942.94 97588784.06 89288554.35 95158179.03 66320500.97 1.615208476 1.18041713 1.497617439 1.085010234 1.503622833 1.189827305 1.47147236 1.346319057 1.434822983 1 25.98295157 -1.056320297 4.519417371 0.999985085 1.361179294 0.320079563 0.16110585 2.77E-05 5.78E-06 0.135478757 0.031930916 0.087837447 1.056320297 0.361194208 EGDKHTLSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGDKHTLSKK 10 2 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;; 134.75 9.75E-05 8159600000 8020900 5099720 7703400 3575550 12042800 8088100 7389400 7182180 8996000 5276100 FALSE TRUE 8337571.325 5975557.24 7904156.932 4282783.118 9995769.158 6209761.351 6810199.519 7085914.625 8672235.717 6309850.778 1.321357924 0.947020373 1.252669391 0.678745547 1.584153019 0.984137592 1.079296446 1.122992425 1.374396324 1 22.58917446 3.247938272 24.99940824 1.174795063 1.057076601 0.077076075 0.234407728 638.6606243 1702563.009 0.061278647 0.081867664 1769.857382 -3.247938272 -0.117718462 EGDLIAAQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGDLIAAQAR 10 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 145.72 6.96E-05 503600000 950580 1118430 1112730 1114340 1281770 1373030 1147400 1090610 1001740 1048300 FALSE TRUE 988109.6324 1310511.652 1141728.658 1334753.126 1063895.193 1054164.591 1057463.79 1075992.157 965687.5731 1253694.314 0.788158342 1.04531993 0.910691422 1.064655962 0.848608135 0.840846592 0.843478173 0.858257188 0.770273553 1 20.25775419 EGDNVNYDWIHWDPEHSYEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGDNVNYDWIHWDPEHSYEFK 21 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 ; 241.43 3.06E-30 167113000 101865 85104 117448 100948 136284 145386 125521 113406 119920 87757 FALSE TRUE 105886.7089 99719.94998 120508.7914 120915.2131 113118.4944 111622.3048 115682.336 111885.9781 115604.1026 104951.3039 1.008912752 0.950154464 1.148235294 1.152107773 1.077818856 1.063562821 1.102247725 1.066075159 1.101502299 1 16.67936057 4.247201313 24.99994412 1.091556626 0.979533579 0.503633453 0.043385156 140.6167899 406834.5567 0.010321486 0.027355907 17668.5664 -4.247201313 -0.112023046 EGDSIAVILFSGVHFYTGQHFNIPAITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGDSIAVILFSGVHFYTGQHFNIPAITK 28 0 A0A087WYM2;A0A087X297;Q16719-2;Q16719;A0A087WYQ7 A0A087WYM2 KYNU Kynureninase 0 45.862 0.069645 2757200 4470.8 3200.7 4805.4 2960 6345.1 6119.4 7873.4 4699.8 6272.1 4268.9 FALSE TRUE 4647.310636 3750.395327 4930.632672 3545.479165 5266.562168 4698.26209 7256.262335 4636.806868 6046.368346 5105.309222 0.910289746 0.734606889 0.965785314 0.694469034 1.031585344 0.920269838 1.421316911 0.908232326 1.184329505 1 12.31778263 2.863464388 2.076920842 1.103017119 0.83363358 0.37269217 0.157414981 0.327533648 2.79191998 0.051254227 0.055059417 730.2379307 -2.863464388 -0.269383539 EGDVLRRS(ph)EEHS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGDVLRRSEEHSPPR 15 2 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 EGDVLRRS(1)EEHS(1)PPR;EGDVLRRS(1)EEHS(1)PPR 108.18 0.00058947 713470000 223397 211669 249390 144237 257110 310810 179605 231270 239114 350930 TRUE FALSE 232216.8861 248021.5042 255889.3083 172766.6481 213406.534 238629.0879 165527.0908 228170.2039 230508.3338 419688.0145 0.553308358 0.590966374 0.609713166 0.411654949 0.508488512 0.568586854 0.394405094 0.543666238 0.549237352 1 18.67895774 0.508058472 2.296845649 0.999987904 0.520386292 0.819768701 0.066845587 2.483343424 11.09056041 0.064572826 0.017413698 3.221502494 -0.508058472 -0.479601613 EGDVLTLLESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;; 265.69 2.80E-21 2860350000 904124 1010820 1035910 933322 1212370 1243820 1078800 1094700 1032480 960370 FALSE TRUE 939819.5137 1184420.472 1062906.666 1117930.306 1006291.78 954961.6553 994240.8371 1080027.337 995321.2465 1148536.114 0.818275979 1.031243561 0.925444705 0.973352333 0.876151623 0.831459841 0.865659186 0.940351221 0.866599869 1 20.13136479 5.038252416 16.22981137 0.917669299 0.403146748 0.20323018 0.061499521 14858674.82 173285586.3 0.014705141 224175539.5 109207.4877 -5.038252416 -0.514522551 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGEEPTVYSDEEEPKDESAR 20 1 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 EGEEPTVYS(1)DEEEPKDESAR;EGEEPT(0.007)VYS(0.993)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPT(0.001)VYS(0.999)DEEEPKDESAR 306.46 8.49E-56 7875920000 5729800 2600430 3234230 3513920 4832530 6665530 5203610 3161540 3575080 2210480 TRUE FALSE 5956016.928 3047033.624 3318516.691 4208962.888 4011098.277 5117561.675 4795737.451 3119164.728 3446413.569 2643581.234 2.253010746 1.152615847 1.255311034 1.592144336 1.517297152 1.935844304 1.81410633 1.179901222 1.303691192 1 21.33406223 1.655178303 6.73590176 1.177215965 1.614969474 0.337269803 0.308491621 0.168226634 15.2158079 0.15980561 0.080482083 45.20414957 -1.655178303 0.437753509 EGEIIHLISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGEIIHLISK 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ; 104.52 0.004312 0 241820 199672 235220 205820 315520 294480 301310 255850 270160 167487 FALSE TRUE 251367.2403 233964.1128 241350.0264 246530.5817 261888.0231 226091.4829 277692.5349 252420.7492 260436.9944 200302.8709 1.254935784 1.168051719 1.204925448 1.230789057 1.307460157 1.12874809 1.386363229 1.260195364 1.300215984 1 17.61182357 3.478993131 24.67423334 1.251915791 1.207292082 0 0.102961123 227.2587639 2995619.698 0.026331451 0.036241491 3012.95837 -3.478993131 -0.04462371 EGENNKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGENNKPR 8 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ; 103.56 0.0043308 362700000 403510 288120 390630 275361 479680 470590 477610 394590 398310 276080 FALSE TRUE 419440.8864 337602.3687 400810.1387 329826.5839 398144.1649 361302.6044 440173.6802 389301.1665 383974.9009 330172.5901 1.270368586 1.022502712 1.213941286 0.998952044 1.205866801 1.094284066 1.333162393 1.179083843 1.162952081 1 18.33286083 EGEQHVDDVSSALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGEQHVDDVSSALKR 15 1 Q96P48-3;Q96P48;E7EU13;Q96P48-7;Q96P48-2;Q96P48-4;Q96P48-1;A0A0A0MSJ2;Q96P48-5 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 0 69.594 0.031935 66053000 135470 103860 129640 106850 152670 142840 138040 119540 134190 93527 FALSE TRUE 140818.4602 121697.1471 133018.5249 127984.6111 126719.2079 109667.5748 127220.0641 117937.7618 129360.5281 111851.825 1.258973291 1.088021113 1.189238753 1.144233553 1.132920343 0.980471931 1.137398197 1.054410707 1.156534801 1 16.77122927 8 0.222421768 1.043656693 1.957397697 0.400968431 0.062571118 52.88172095 0.6807094 0.0907449 17.41874554 100000000 -8 0.913741004 EGERPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGERPSLR 8 1 Q7L2H7;J3KNJ2;E9PN86;E7ESM3 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 136.57 0.00071634 3300790000 1454100 1422570 1545500 1653320 1831490 2180160 1811130 1497800 1710380 1317090 FALSE TRUE 1511508.991 1666885.331 1585777 1980341.761 1520173.984 1673850.881 1669168.898 1477724.441 1648823.758 1575148.568 0.95959773 1.05824007 1.006747574 1.257241254 0.965098794 1.062662224 1.059689817 0.938149246 1.046773486 1 20.58705648 1.769341486 25 0.989185453 1.056070121 0.093074357 0.081599351 54.52010796 44304.25278 0.036611046 0.020307686 58.79514775 -1.769341486 0.066884668 EGES(ph)LEDLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGESLEDLMK 10 0 P13796 P13796 LCP1 Plastin-2 1 EGES(1)LEDLMK 148.18 2.68E-05 74941000 191020 85321 96748 166230 402660 364050 453910 128680 139960 119780 TRUE FALSE 198561.6171 99974.21804 99269.33236 199109.7979 334215.997 279504.9047 418331.3481 126955.2551 134922.8669 143248.5977 1.38613306 0.697907133 0.692986416 1.38995984 2.333118805 1.95118772 2.920317231 0.886258275 0.941879147 1 17.12816149 3.499980946 7.623067857 1.7237406 0.92312904 0.2151207 0.633228772 0.302497198 79.02470033 0.179184329 0.267580962 3162.138926 -3.499980946 -0.80061156 EGESLEDLMKLS(ph)PEELLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGESLEDLMKLSPEELLLR 19 1 P13796 P13796 LCP1 Plastin-2 1 EGESLEDLMKLS(1)PEELLLR;EGES(0.001)LEDLMKLS(0.999)PEELLLR 105.16 0.00020536 49271000 101360 67772 80724 84631 190658 159754 191100 90924 99338 81929 TRUE FALSE 105361.7711 79411.31381 82827.73376 101370.7592 158250.0213 122653.5546 176121.0827 89705.3125 95762.84478 97981.41892 1.075323997 0.810473197 0.845341236 1.034591664 1.615102363 1.251804229 1.797494715 0.915533919 0.977357195 1 16.58022056 3.466179232 24.85233904 1.273268892 0.906985065 0.259225903 0.269033454 261.2612241 593393.7546 0.076117882 0.103158117 2925.359418 -3.466179232 -0.366283827 EGFES(ph)DTDSEFTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGFESDTDSEFTFK 14 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EGFES(0.883)DT(0.116)DS(0.001)EFTFK;EGFES(0.915)DT(0.083)DS(0.001)EFTFK;EGFES(0.86)DT(0.139)DS(0.001)EFTFK;EGFES(0.998)DT(0.002)DSEFTFK 351.2 6.67E-82 931490000 2097970 1352950 1701690 1476200 2250500 2218040 2324510 1854000 1868340 1037790 TRUE FALSE 2180799.476 1585308.638 1746037.439 1768187.954 1867960.814 1702933.825 2142308.832 1829150.163 1801098.808 1241125.081 1.757114983 1.27731577 1.40681827 1.424665395 1.50505444 1.372088802 1.72610228 1.4737839 1.451182348 1 20.24321709 0.665327448 3.189973372 1.000011508 1.487134888 0.521426789 0.140745786 3.577371899 33.2321585 0.128434099 0.033378062 4.627297776 -0.665327448 0.48712338 EGFHFEETLTGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGFHFEETLTGFK 13 0 Q96G03-2;H0Y921;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 176.51 1.64E-05 66544000 178490 155510 193940 154800 236700 229730 237530 189800 206050 149200 FALSE TRUE 185536.923 182217.6328 198994.2357 185418.978 196465.8185 176378.6891 218911.7779 187256.0415 198634.3007 178432.8834 1.039813511 1.021211053 1.115232977 1.039152506 1.101062847 0.98848758 1.226857818 1.04944805 1.113215776 1 17.44502199 EGFTFEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGFTFEYR 8 0 O75175;H7C5J4;A0A0G2JPP0 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 0 88.294 0.034238 94254000 111820 123130 106380 117030 144050 141250 110560 117320 125640 127660 FALSE TRUE 116234.7399 144276.6197 109152.3502 140178.1847 119564.4325 108446.8282 101894.0183 115747.5173 121118.2409 152672.5328 0.761333672 0.945007049 0.714944255 0.918162436 0.783143046 0.710323109 0.667402423 0.758142379 0.79332044 1 17.22008101 5.098739669 13.7894096 0.794463672 6.66E-05 0 0.105454307 1612483.916 3502557.259 0.02445197 38370346.61 125527.7282 -5.098739669 -0.794397113 EGGDGEEQDVGDAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 240.37 1.80E-17 322230000 268710 291940 302740 270820 337820 391690 314270 303270 304650 264770 FALSE TRUE 279318.8783 342078.424 310629.6531 324387.3877 280397.4771 300725.9336 289636.6962 299205.1617 293685.706 316646.6122 0.88211548 1.080316071 0.980997873 1.024446102 0.885521797 0.949720989 0.914700126 0.944918247 0.927487283 1 18.27251412 3.250942848 24.99996271 0.934141456 0.997495752 0.197761765 0.053528168 303.1308851 612023.3881 0.013603358 0.018287626 1782.144225 -3.250942848 0.063354297 EGGFLLLHTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 210.91 3.80E-08 10264792000 6400851 4757949 5819609 7867437 7626331 8108562 9028358 6056536 6130179 4714070 FALSE TRUE 6653561.54 5575089.729 5971272.791 9423592.557 6330009.981 6225471.362 8320691.709 5975358.041 5909555.055 5637701.76 1.180190408 0.98889405 1.05916791 1.671530875 1.122799724 1.104256952 1.475901362 1.059892541 1.048220588 1 22.42667573 1.572967283 11.18771045 1.03640135 1.224541757 0.173403944 0.193439929 0.218217385 51.04664753 0.105552546 0.049327083 37.40824062 -1.572967283 0.188140408 EGGGVHAVPPDPEDEGLEETGSKDKDQPPSPS(ph)PPPQSEALSSTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGGGVHAVPPDPEDEGLEETGSKDKDQPPSPSPPPQSEALSSTSR 45 2 H3BU99;H3BPL8;H3BR21;H3BUX9;Q7L1V2 H3BU99 MON1B Vacuolar fusion protein MON1 homolog B 1 EGGGVHAVPPDPEDEGLEET(0.007)GS(0.007)KDKDQPPS(0.197)PS(0.688)PPPQS(0.02)EALS(0.02)S(0.02)T(0.02)S(0.02)R 54.593 0.0075862 398980000 136560 64041 107570 60285 145520 131850 122550 93303 108510 61394 TRUE FALSE 141951.4942 75039.54358 110373.3626 72209.19307 120784.5624 101229.8357 112944.2108 92052.4259 104604.7463 73422.97884 1.933338806 1.02201715 1.503253672 0.983468584 1.64505124 1.378721448 1.53826789 1.253727748 1.424686766 1 16.16394403 -0.585746703 0.700480923 0.959678338 1.395652576 0.171801822 0.267349695 28.5496273 9.676346159 3.143150885 0.086524282 0.259569283 0.585746703 0.435974237 EGGVIVDYHGCDFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGGVIVDYHGCDFFPER 17 0 A0A087WVD7;D6RDH4;Q9Y3D8-2;Q9Y3D8 A0A087WVD7 TAF9;AK6 Adenylate kinase isoenzyme 6 0 ; 155.92 8.24E-08 182898000 244710 220660 245650 267640 281100 335290 325840 286510 278140 196053 FALSE TRUE 254371.3398 258556.6385 252051.8408 320578.3932 233318.7224 257423.9789 300299.8094 282669.8021 268129.7957 234465.8317 1.084897266 1.102747623 1.075004571 1.36727126 0.995107563 1.097916814 1.280782821 1.205590597 1.14357727 1 17.83901817 EGHDAFELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGHDAFELK 9 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 0 ; 85.533 0.014751 212170000 526680 462920 494720 432070 605050 649480 574470 517590 543890 469060 FALSE TRUE 547473.7331 542422.909 507612.8096 517532.1564 502203.8171 498648.113 529441.5403 510652.5527 524315.5051 560963.3263 0.975952807 0.966948967 0.904894823 0.922577524 0.895252494 0.888913926 0.94380776 0.910313614 0.934669845 1 19.09754693 -0.722802154 5.990926231 1.000000002 0.925002186 0.384318136 0.027597024 6.19E-10 1.38E-10 0.027673274 0.006522653 0.189320589 0.722802154 -0.074997816 EGHGSSS(ph)FDRELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGHGSSSFDRELER 14 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EGHGS(0.013)S(0.053)S(0.933)FDRELER 81.854 0.0074756 562320000 60126 96539 80413 95284 140920 147840 87260 113410 112170 135110 TRUE FALSE 62499.82091 113118.8223 82508.62884 114130.8908 116966.4687 113506.4005 80420.33319 111889.9245 108133.0236 161582.2177 0.386798881 0.700069747 0.510629388 0.706333237 0.723882061 0.702468392 0.497705344 0.692464345 0.669213637 1 17.30190891 -5 0.195166677 2.644079837 0.561948306 0.564800582 0.104235121 102.828184 1.012619431 65.84631336 0.256051083 1.00E-05 5 -2.082131531 EGHILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EGHILK 6 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 0 ;;;;; 106.84 0.03178 1933160000 6788110 5963330 6937980 5989180 8845000 8727100 8110960 7262110 7483250 6408560 FALSE TRUE 7056109.824 6987485.539 7118789.458 7173821.928 7341530.059 6700363.285 7475201.761 7164773.294 7213929.294 7664194.633 0.920659008 0.911705127 0.928837249 0.936017712 0.957899742 0.874242319 0.975340805 0.934837075 0.941250795 1 22.86970277 -5 0.158387558 1.259797709 0.912065388 0.440298887 0.024586007 118.6942351 1.086587547 9.631032887 0.101033489 1.00E-05 5 -0.347732321 EGHLS(ph)PDIVAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 1 EGHLS(1)PDIVAEQK;EGHLS(1)PDIVAEQK;EGHLS(1)PDIVAEQK;EGHLS(1)PDIVAEQK 183.23 6.78E-06 1316880000 2794920 2108600 2538210 2085780 3223530 3461790 3198700 2640770 2862650 2012490 TRUE FALSE 2905265.6 2470735.647 2604357.838 2498341.059 2675595.522 2657841.736 2947977.536 2605374.798 2759623.786 2406798.884 1.207107756 1.026565063 1.082083698 1.038034825 1.111682218 1.104305704 1.224854123 1.082506235 1.146595091 1 21.19868416 3.018839568 24.62004011 1.121715919 1.082483731 0.013095227 0.06967471 584.1646998 763396.1263 0.019009071 0.022715639 1044.334363 -3.018839568 -0.039232188 FMKPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMKPGK 6 1 P61353;K7EQQ9;K7ERY7 P61353 RPL27 60S ribosomal protein L27 0 65.619 0.094454 656890000 977330 1061100 791570 1103900 2583300 2696900 2805700 2460000 2644700 1748300 FALSE TRUE 1015915.743 1243335.671 812198.9645 1322248.125 2144191.589 2070585.847 2585781.903 2427027.724 2549517.764 2090845.912 0.485887428 0.594656767 0.388454721 0.632398647 1.025513921 0.990310111 1.23671567 1.160787464 1.219371427 1 20.99565531 3.219090671 2.045987055 1.144225864 0.491786938 0.910607219 0.09010543 0.081619702 0.702607158 0.028160491 0.038303668 1656.115689 -3.219090671 -0.652438926 down EGHPVYPQLRPGYIPIPVLHEGAENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGHPVYPQLRPGYIPIPVLHEGAENR 26 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 ; 130.25 4.71E-05 289632000 183331 172936 187472 177702 216803 224370 193814 188994 202396 159120 FALSE TRUE 190569.0494 202636.4127 192357.6743 212850.9252 179950.9035 172263.4679 178622.3522 186460.8446 195111.8075 190296.5175 1.001432144 1.064845618 1.010831291 1.118522441 0.945634244 0.905237101 0.938652765 0.979843704 1.025304142 1 17.53788963 3.211873938 24.99959841 0.961220039 1.047326567 0.468563434 0.043194648 186.9234501 175105.9604 0.012610042 0.015075969 1628.823166 -3.211873938 0.086106529 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.899)DEDDNS(0.101)FLK 347.34 6.04E-111 4269980000 1328113 1048065 1201984 1059408 1448917 1476277 1630082 1300820 1393662 772489 TRUE FALSE 1380547.927 1228062.011 1233308.69 1268955.74 1202630.606 1133434.04 1502311.913 1283384.636 1343504.377 923843.4294 1.494352704 1.329296688 1.334975875 1.373561472 1.301768858 1.226868108 1.626154244 1.389179806 1.454255488 1 19.81728884 -1.09785367 4.61990666 0.999973445 1.390830322 0.552529635 0.105895977 2.88E-05 5.62E-06 0.101787324 0.023989874 0.079826361 1.09785367 0.390856878 EGHSLEMENENLVENGADS(ph)DEDDNSFLKQQS(ph)PQEPK ddPTM_MDA-MB-175_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(0.983)DEDDNS(0.019)FLKQQS(0.999)PQEPK 98.631 0.00083165 109880000 24560 18669 17277 10774 28103 26466 20048 19702 20719 17158 TRUE FALSE 25529.64776 21875.25553 17727.25281 12905.06504 23326.0621 20319.6726 18476.58537 19437.92692 19973.32724 20519.78159 1.244148124 1.066056938 0.863910404 0.628908499 1.136759765 0.990247996 0.900427974 0.947277476 0.973369387 1 14.32472775 4.537351042 3.286401151 0.927269008 1.23721687 0.387631083 0.122788509 0.269300003 5.269406131 0.030706521 0.15957855 34462.83824 -4.537351042 0.309947862 EGIDPTPYYWYTDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 181.66 1.35E-06 917300000 182622 252870 252960 229117 244980 294560 281300 267170 222452 192095 FALSE TRUE 189832.0576 296298.4554 259552.3454 274435.6588 203338.3871 226152.9041 259250.971 263589.0232 214445.996 229732.3374 0.826318401 1.289755107 1.129803267 1.19458872 0.885109991 0.984419114 1.128491417 1.147374489 0.93346021 1 17.80959442 0.525874858 0.389969496 0.987021102 1.087337911 0.018563351 0.139388649 10.6952743 3.260180945 0.327214943 0.109680144 3.356408854 -0.525874858 0.100316809 EGILPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGILPER 7 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7;O43768-8 A6NMQ3 ENSA Alpha-endosulfine 0 ; 84.568 0.049902 218580000 274800 310610 299950 355550 290280 329130 357540 331490 257580 227916 FALSE TRUE 285649.3162 363954.8513 307766.9434 425876.7288 240938.3093 252694.5455 329515.0805 327046.9188 248309.7461 272571.7765 1.047978334 1.335262425 1.129122565 1.562438835 0.883944451 0.927075242 1.208911226 1.199856137 0.910988472 1 18.05627666 3.213379654 24.9996945 1.051473204 1.26348552 0.341473345 0.164849184 299.8915483 297731.9228 0.048459444 0.057941348 1634.480161 -3.213379654 0.212012315 EGILPERAEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 156.81 5.39E-05 1290940000 2260670 1463288 1883153 1238096 2573770 2238176 1852244 1852580 2052835 1378874 FALSE TRUE 2349922.997 1714596.331 1932229.514 1482987.693 2136281.495 1718393.544 1707060.275 1827749.195 1978953.869 1649037.96 1.425026624 1.039755526 1.171731374 0.899304764 1.295471388 1.042058209 1.035185555 1.108373027 1.200065685 1 20.65319318 4.744080562 24.56377857 1.091415092 1.425026807 0.473162092 0.106635773 386.3956313 1719394.711 0.023289766 0.200867766 55472.86067 -4.744080562 0.333611715 EGIPALDNFLDKL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGIPALDNFLDKL 13 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 185.25 0.00018073 237920000 518320 436590 459730 422670 632460 666870 621380 510410 476470 406760 FALSE TRUE 538783.6738 511570.9363 471710.9415 506272.8645 524954.6751 511999.549 572674.6119 503568.7888 459321.9378 486456.8341 1.107567283 1.051626579 0.969687151 1.040735434 1.079139275 1.05250767 1.177236235 1.035176718 0.944219313 1 18.89195227 1.466430815 25 0.97797212 1.066101068 0.355183525 0.051184272 2.855610268 6681.379069 0.028809052 0.013336526 29.27054544 -1.466430815 0.088128948 EGIREETVSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;; 232.42 3.17E-13 3010240000 1771860 1943250 1938310 1837770 2149340 2293980 2095200 2077300 1879830 1947810 FALSE TRUE 1841814.401 2276988.071 1988823.951 2201275.421 1783995.955 1761237.911 1930972.749 2049457.191 1812175.286 2329446.076 0.790666253 0.977480481 0.853775484 0.944978054 0.765845568 0.756075845 0.828940738 0.879804522 0.777942578 1 21.1515555 5.08176604 13.0874725 0.857952897 7.41E-05 0.061858907 0.082848415 903388.8247 3452708.434 0.019257412 21009181.14 120716.3346 -5.08176604 -0.857878811 EGIVALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGIVALR 7 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 86.086 0.047307 71027000 140630 176480 168600 181070 170840 221100 189550 144520 154180 183380 FALSE TRUE 146182.181 206789.0672 172993.8545 216885.1056 141800.6778 169752.8758 174692.5757 142582.9458 148631.0919 219309.8 0.666555626 0.942908466 0.788810416 0.988943976 0.646577024 0.774032332 0.796556176 0.650143978 0.677722071 1 17.74261076 3.222502287 24.99966339 0.737696447 0.849526796 0.095614206 0.125886978 425.4137612 662284.3658 0.033979881 0.04073343 1669.176598 -3.222502287 0.11183035 EGIVALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGIVALRR 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;; 130.27 0.0016916 682600000 689822 872578 780135 668960 1087160 1029511 705687 773494 783852 1177647 FALSE TRUE 717056.7052 1022436.484 800465.959 801278.2914 902364.9315 790422.6726 650373.409 763126.5781 755641.3196 1408384.382 0.509134235 0.725964088 0.568357594 0.568934377 0.640709271 0.561226525 0.461786865 0.541845385 0.536530601 1 20.4256097 -1.568131589 2.903134938 1.024069581 0.5682209 0.782207154 0.068342013 12717112.76 13841332.64 2377176.585 0.017218574 0.027031392 1.568131589 -0.455848681 EGLDWDLIYVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGLDWDLIYVGR 12 0 Q8NBJ5;M0QX72 Q8NBJ5 COLGALT1 Procollagen galactosyltransferase 1 0 ;;; 173.32 7.76E-05 119436000 211351 271636 237713 288447 281872 321765 260862 228739 220527 226123 FALSE TRUE 219695.3007 318287.37 243907.9961 345500.9557 233959.4981 247039.9551 240414.9548 225673.1278 212590.2763 270427.4725 0.812400082 1.176978681 0.901934977 1.277610416 0.865146932 0.913516489 0.889018237 0.834505185 0.786126773 1 18.0448822 3.107158065 20.21089353 0.872551533 1.045560897 0.262120661 0.131640693 3.229088734 594.847743 0.035047727 0.041890188 1279.84703 -3.107158065 0.173009365 EGLELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGLELLK 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 119.21 0.011243 800140000 1838200 1397320 1686060 1477970 2282240 2070620 2105170 1700510 1870890 1277350 FALSE TRUE 1910773.555 1637298.84 1730000.109 1770308.055 1894305.66 1589749.886 1940161.275 1677717.445 1803557.034 1527622.276 1.250815457 1.071795604 1.132478974 1.158865043 1.240035374 1.040669484 1.270053013 1.098254111 1.180630227 1 20.54285643 -2.01852237 2.486010862 0.826253428 1.156259754 0.298965796 0.073439929 6656407.158 2654496.635 6601554.942 0.016385528 0.009582474 2.01852237 0.330006326 EGLELPEDEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLELPEDEEEK 12 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;Q58FG0 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AA5P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 171.92 8.64E-05 504840000 826850 397290 496850 496440 734130 830070 926720 579580 660530 284220 FALSE TRUE 859494.6765 465521.467 509798.3192 594634.3503 609342.8448 637298.8223 854081.2649 571811.6781 636757.6543 339907.4673 2.528613694 1.369553516 1.499815003 1.749400668 1.792672723 1.87491857 2.512687561 1.682256888 1.873326466 1 18.37478253 2.945097107 3.58720274 1.87642133 1.738782185 0 0.450343355 1.344945216 34.69592911 0.135441258 0.150258964 881.2458949 -2.945097107 -0.137639145 EGLELPEDEEEKK ddPTM_MDA-MB-175_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 ;;;;; 173.68 1.18E-06 3829220000 4939520 1235888 1902160 1291960 3018120 3202620 3466570 1976490 2323440 805389 FALSE TRUE 5134536.064 1448142.15 1951731.852 1547505.832 2505101.04 2458860.041 3194851.185 1949998.384 2239819.848 963189.5544 5.330763856 1.503486145 2.026321655 1.606647232 2.600839086 2.552830883 3.316949577 2.024521939 2.325419579 1 19.87746022 4.746402484 24.91996889 2.196894591 5.330765445 0.705165086 0.623014914 516.775179 1642173.762 0.146603207 1.59754377 55770.23618 -4.746402484 3.133870854 EGLELPEDEEEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 171.26 1.71E-06 10096410000 11947900 2136970 4172760 2233930 7126030 6908610 7469620 4319550 5207120 1289350 FALSE TRUE 12419612.32 2503977.974 4281505.554 2675794.686 5914749.966 5304190.028 6884131.666 4261653.498 5019716.768 1541973.446 8.054361991 1.62387879 2.776640262 1.735305295 3.835831272 3.439871186 4.464494303 2.763765814 3.255384702 1 20.55634649 0.407236611 1.127117891 0.998064637 3.474133516 0.167006761 1.716660668 4.689128557 7.187300831 1.563081447 0.475406054 2.554092436 -0.407236611 2.476068879 EGLELPEDEEEKKKQEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 219.79 8.72E-19 15058059000 16015100 1339504 2973102 1341585 7172810 9405220 6514660 3069140 4083910 716012 FALSE TRUE 16647388.51 1569553.392 3050583.481 1606946.509 5953578.318 7221000.192 6004023.926 3028003.198 3936930.877 856300.8425 19.44105119 1.83294622 3.562513697 1.87661442 6.952671331 8.432784173 7.011582411 3.536144131 4.59760248 1 19.70775822 4.74504852 24.99325526 4.576202703 19.44105788 0.78526274 2.369897012 351.5471457 1354223.963 0.590025998 5.667690428 55596.63674 -4.74504852 14.86485518 EGLEQALPSGKPS(ph)SPVELDLFGDPSPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.015)GKPS(0.492)S(0.492)PVELDLFGDPSPSSK;EGLEQALPS(0.118)GKPS(0.441)S(0.441)PVELDLFGDPSPSSK;EGLEQALPS(0.11)GKPS(0.445)S(0.445)PVELDLFGDPSPSSK 231 1.84E-35 2582480000 1527700 738295 1113290 775040 1546939 1455601 1579476 1183025 1362054 605430 TRUE FALSE 1588014.776 865091.4231 1142303.252 928340.5987 1283990.861 1117559.728 1455672.544 1167168.485 1313033.943 724052.4168 2.193231786 1.194791155 1.577652702 1.28214557 1.773339653 1.543479038 2.010451882 1.61199446 1.813451502 1 19.46573462 EGLEQALPSGKPSS(ph)PVELDLFGDPS(ph)PSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 2 EGLEQALPS(0.027)GKPS(0.459)S(0.514)PVELDLFGDPS(0.807)PS(0.151)S(0.042)K 89.111 0.0009718 121160000 497670 200190 288450 219480 452550 425370 505680 337720 375530 159290 TRUE FALSE 517318.3959 234571.0752 295967.244 262892.4889 375625.7126 326584.264 466043.4803 333193.4158 362014.7487 190499.8257 2.715584615 1.231345354 1.553635248 1.380014328 1.971790322 1.714354661 2.446424707 1.749048402 1.900341627 1 17.53943015 3.166677513 24.99999984 1.868295028 1.673276714 0 0.501981532 179.7641726 62515.70236 0.137468338 0.164306143 1467.835926 -3.166677513 -0.195018315 EGLEQALPSGKPSS(ph)PVELDLFGDPSPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGLEQALPSGKPSSPVELDLFGDPSPSSK 29 1 Q9H201 Q9H201 EPN3 Epsin-3 1 EGLEQALPS(0.052)GKPS(0.158)S(0.79)PVELDLFGDPSPSSK;EGLEQALPS(0.001)GKPS(0.21)S(0.788)PVELDLFGDPSPSSK 278.9 1.72E-71 724030000 1807960 840960 1344600 880290 1824840 1701960 1893340 1448410 1611310 702280 TRUE FALSE 1879339.657 985388.3382 1379641.381 1054408.735 1514654.349 1306705.583 1744935.063 1428996.433 1553319.268 839878.32 2.237633252 1.173251309 1.642668167 1.255430352 1.803421177 1.555827258 2.077604603 1.701432694 1.849457512 1 19.6798208 EGLGQGQS(ph)LEQLEALVQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLGQGQSLEQLEALVQTK 19 0 Q9NSC5-2;Q9NSC5;M0QYF9;Q9NSC5-5 Q9NSC5-2 HOMER3 Homer protein homolog 3 1 EGLGQGQS(1)LEQLEALVQTK 176.57 4.08E-13 11691000 16210 15519 17477 15993 18563 16780 23887 17163 18846 13936 TRUE FALSE 16849.98332 18184.26753 17932.46498 19156.36767 15407.66789 12883.0993 22014.67452 16932.95806 18167.73614 16666.49238 1.011009571 1.091067461 1.07595915 1.149394079 0.924469741 0.772994042 1.320894284 1.015988108 1.090075568 1 14.02466289 -0.901675111 8.528074195 1 1.052520894 0.01202352 0.135071991 0 0 0.127499885 0.030052011 0.125407898 0.901675111 0.052520894 EGLHNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGLHNAK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 107.32 0.0075045 550230000 1979230 1486590 1804060 1532600 1968130 2081980 2033930 1729500 1631950 1247420 FALSE TRUE 2057371.529 1741900.268 1851075.286 1835743.706 1633587.966 1598471.698 1874505.252 1706318.881 1573216.438 1491828.066 1.379094264 1.167628032 1.240810069 1.230533027 1.095024288 1.071485203 1.25651561 1.143777169 1.054556134 1 20.50864984 8 0.118248576 0.962803361 2.010725316 0.580183591 0.070312997 78.92991697 0.642641812 0.512562514 13.61059058 100000000 -8 1.047921954 EGLLFEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGLLFEGR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 142.08 0.0014499 1458340000 1607270 1833720 1739230 1791740 1885180 2205570 1678170 1681580 1443040 1492870 FALSE TRUE 1670726.261 2148647.146 1784555.763 2146140.824 1564737.777 1693359.793 1546630.65 1659041.171 1391105.272 1785369.294 0.935787496 1.203474907 0.999544335 1.202071096 0.876422476 0.948464723 0.866280526 0.929242581 0.779169485 1 20.76779109 3.219995043 24.99828869 0.898624111 1.087546634 0.48678438 0.093186682 182.3720297 245560.8436 0.024479425 0.029307178 1659.567964 -3.219995043 0.188922523 EGLLLWCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 160.75 0.00015136 793751000 443004 458354 410055 592685 911910 768519 608949 444005 406777 1014534 FALSE TRUE 460494.14 537072.734 420741.3702 709916.324 756903.8639 590042.1093 561217.9862 438053.8392 392137.1752 1213312.513 0.37953465 0.442649959 0.346770816 0.585105912 0.623832571 0.486306787 0.462550234 0.361039579 0.323195526 1 20.21051976 -1.305916245 3.606452233 1.001731256 0.447612457 0.755519834 0.094594426 61743019.63 97228178.85 1157998.69 0.025249566 0.049440603 1.305916245 -0.5541188 EGLMLDSHEELYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLMLDSHEELYK 13 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 141.38 3.98E-05 126190000 207190 174400 214110 169780 243670 279830 267130 210410 238150 153470 FALSE TRUE 215370.0212 204351.8434 219689.8825 203361.9773 202251.0604 214843.7234 246191.6526 207589.7981 229579.028 183539.5081 1.173425947 1.113394306 1.196962358 1.108001102 1.101948362 1.170558457 1.341355085 1.131036038 1.250842559 1 17.48573112 2.479303357 24.99682278 1.198742624 1.138603034 0.036140854 0.086411515 204.4544233 2342145.835 0.027589564 0.02344519 301.511136 -2.479303357 -0.06013959 EGLQNMEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLQNMEAR 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 85.29 0.034699 135080000 115280 165390 159070 134030 162800 210510 140080 155740 150550 124130 FALSE TRUE 119831.3434 193794.4459 163215.4949 160540.734 135127.3142 161622.2428 129100.1636 153652.56 145131.7349 148450.8969 0.807211987 1.305444763 1.099457789 1.081439973 0.910249227 1.08872527 0.86964893 1.035039621 0.977641348 1 17.17962628 3.358894255 8.071710214 0.98309992 1.093445967 0.108064778 0.126205809 0.446410209 29.64298988 0.032592926 0.044157923 2285.04236 -3.358894255 0.110346047 EGLSGDALSSPSAPEPVVGT(ph)PDDKLDADYIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGLSGDALSSPSAPEPVVGTPDDKLDADYIKR 32 2 K7EJ08;Q92503-3;Q92503;Q92503-2 K7EJ08 SEC14L1 SEC14-like protein 1 1 EGLSGDALSSPSAPEPVVGT(1)PDDKLDADYIKR 160.6 3.57E-12 327330000 125800 53846 86388 52527 133170 123710 110650 85171 106300 55743 TRUE FALSE 130766.6811 63093.63164 88639.34225 62916.68382 110533.811 94980.22734 101976.9639 84029.42206 102474.2838 66664.77359 1.961555918 0.94643135 1.32962789 0.943777057 1.658054247 1.424743867 1.529697896 1.260477124 1.537157906 1 16.02463701 -1.366355593 5.27878648 0.999830217 1.375637329 0.138416221 0.293495268 0.000540406 6.49E-05 0.261863486 0.061694197 0.043017425 1.366355593 0.375807112 EGMNIVEAMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 243.77 1.80E-15 6084450000 1785636 2548326 2244453 2174919 2685330 2818064 2151155 2344898 2146196 2863811 FALSE TRUE 1856134.288 2985981.167 2302945.289 2605111.487 2228878.566 2163611.344 1982541.85 2313468.478 2068954.825 3424919.934 0.541949687 0.8718397 0.672408504 0.760634274 0.650782678 0.631726109 0.578857868 0.67548104 0.604088523 1 21.70763883 -1.261071409 8.872271978 1.000000092 0.669657939 0.557627957 0.089355543 1.55E-07 1.30E-08 0.082949544 0.01955139 0.054818682 1.261071409 -0.330342153 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER 404.51 1.06E-157 50133750000 9150515 10686835 10439696 10222328 11392009 12553357 10396541 10683618 10667576 10676279 TRUE FALSE 9511784.398 12522215.78 10711763.05 12244273.97 9455599.379 9638030.085 9581632.95 10540421.58 10283652.02 12768091.46 0.744965246 0.980742957 0.838947864 0.958974488 0.740564822 0.754852839 0.750435802 0.825528358 0.805418105 1 23.60603956 5.034471863 16.91348123 0.838192349 0.388044014 0.090972889 0.09300733 15286559.6 200008766.2 0.021947321 206820628.1 108260.9574 -5.034471863 -0.450148334 EGNASGVSLLEALDTILPPTRPTDKPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGNASGVSLLEALDTILPPTRPTDKPLR 28 2 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 238.23 1.92E-45 1938960000 1060290 892080 1013000 1010240 1170720 1309820 1303080 1064750 1167550 743480 FALSE TRUE 1102151.068 1045287.801 1039399.612 1210062.457 971721.4326 1005634.156 1200941.185 1050478.768 1125530.104 889150.6712 1.239554896 1.175602555 1.168980293 1.360919466 1.092864757 1.131005338 1.350661056 1.181440673 1.265848568 1 19.76206839 -1.524478325 5.684809758 0.999570389 1.216933291 0.381793257 0.083404817 0.000431933 3.61E-05 0.076808202 0.018068659 0.029889708 1.524478325 0.217362903 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYK 36 3 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 278.59 1.27E-76 1637900000 1993600 1393700 1991100 1303900 2894900 2367100 2200400 1949600 2446800 1759300 FALSE TRUE 2072308.867 1633057.134 2042989.702 1561807.528 2402825.932 1817376.899 2027926.898 1923468.801 2358740.146 2104001.151 0.984937136 0.776167414 0.971002179 0.742303552 1.142026909 0.863771818 0.963843056 0.914195698 1.1210736 1 21.00470406 2.211648664 0.507681422 1.02583206 0.880569167 0.142555593 0.11435942 1.844197016 1.005179028 0.102901236 0.089119906 162.7978494 -2.211648664 -0.145262893 EGNDKDFTLNDFGFMIFHSPYCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGNDKDFTLNDFGFMIFHSPYCK 23 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 227.87 4.67E-33 1288850000 1451360 937820 1373410 1007350 1791840 1601110 1665980 1439160 1672910 915610 FALSE TRUE 1508660.813 1098883.29 1409202.193 1206600.823 1487263.677 1229276.468 1535396.134 1419870.414 1612702.296 1095006.249 1.37776457 1.003540656 1.286935297 1.101912272 1.358223917 1.122620504 1.402180248 1.29667791 1.47277908 1 20.06250767 2.239075427 24.99991595 1.318406892 1.20470927 0.054355321 0.158352294 30.08962095 1461306.751 0.051809186 0.040907792 173.4105147 -2.239075427 -0.113697623 EGNTTEDDFPSS(ph)PGNGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 EGNTTEDDFPSS(1)PGNGNK;EGNTTEDDFPS(0.001)S(0.999)PGNGNK;EGNTTEDDFPS(0.002)S(0.998)PGNGNK;EGNTTEDDFPS(0.001)S(0.999)PGNGNK 469 1.66E-214 1815190000 4396360 2667340 3435370 2484440 4675500 4533740 4414490 3567420 3894160 2379570 TRUE FALSE 4569931.688 3125434.896 3524898.564 2975854.817 3880760.18 3480847.594 4068470.739 3519604.57 3754009.942 2845801.182 1.605850653 1.098261859 1.238631352 1.045700183 1.363679306 1.223152066 1.429639837 1.236771069 1.31913992 1 21.44040344 -1.340034111 3.4485172 0.998550773 1.274674748 0.236402234 0.152489961 40951082.88 73166217.2 633732.4299 0.034085069 0.045705229 1.340034111 0.276123975 EGPAHEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGPAHEPK 8 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 64.711 0.066151 392780000 1021130 821590 928790 798630 1331550 1360400 1169160 960150 1030450 742290 FALSE TRUE 1061445.001 962691.6914 952995.0304 956596.6303 1105213.607 1044467.717 1077518.184 947280.7597 993364.3058 887727.5135 1.195687849 1.084445032 1.073522017 1.077579117 1.244991948 1.176563417 1.213793836 1.067085052 1.118996866 1 19.75975739 -1.553185277 7.460667277 0.999936807 1.136208342 0.312734568 0.061757908 6.74E-05 4.03E-06 0.062055764 0.014619918 0.027977875 1.553185277 0.136271535 EGPDLDRPGS(ph)DR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGPDLDRPGSDR 12 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WZ99 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR;EGPDLDRPGS(1)DR 138.19 4.78E-05 336200000 810910 849330 832240 957640 960850 1097400 1157610 961580 916310 687640 TRUE FALSE 842925.353 995195.8206 853928.8581 1147058.334 797525.0602 842545.4813 1066873.503 948691.5929 883332.1821 822369.8923 1.024995395 1.210155953 1.038375634 1.394820438 0.969788738 1.024533472 1.297315859 1.153606913 1.074130012 1 19.64942792 EGPDLDRPGS(ph)DRQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 135.04 2.47E-05 1822550000 1267580 1312510 1479580 1125190 1635420 1758150 1325490 1365970 1474410 1408410 TRUE FALSE 1317625.037 1537923.383 1518139.07 1347749.224 1357431.893 1349846.308 1221594.63 1347661.406 1421346.272 1684360.974 0.782269987 0.913060446 0.90131456 0.800154625 0.805903196 0.801399657 0.725257026 0.800102488 0.84384897 1 20.68376992 5.043591752 15.97902743 0.829593648 0.54697488 0.028801136 0.074384668 1275539.622 12685152.24 0.017648655 10743118.86 110558.4018 -5.043591752 -0.282618768 EGPDLDRPGSDR ddPTM_MDA-MB-175_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 ;;; 114.72 0.00093677 2497460000 2617700 3115300 3111060 2996940 3690130 3883470 3453820 3244070 3086910 2848940 FALSE TRUE 2721048.817 3650328.541 3192136.779 3589725.787 3062883.021 2981592.947 3183100.564 3200588.548 2975812.712 3407135.247 0.798632464 1.071377646 0.936897584 1.053590635 0.898961385 0.87510261 0.934245439 0.939378192 0.873406101 1 21.70012779 EGPEPPEEVPPPTT(ph)PPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGPEPPEEVPPPTTPPVPK 19 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 EGPEPPEEVPPPT(0.03)T(0.97)PPVPK;EGPEPPEEVPPPT(0.168)T(0.832)PPVPK 112.34 0.0022199 132171000 252190 155334 208755 176644 271650 277840 283070 218330 244000 137562 TRUE FALSE 262146.6559 182011.4062 214195.3268 211583.656 225475.03 213315.8707 260882.2337 215403.6435 235218.4877 164514.6401 1.593454879 1.106353854 1.301983378 1.286108372 1.3705469 1.296637616 1.585769106 1.309328114 1.429772375 1 17.32785645 -1.128576536 5.020552618 0.999984945 1.357040773 0.384559006 0.138026184 2.18E-05 3.78E-06 0.125215787 0.029512401 0.074374398 1.128576536 0.357055829 EGPET(ph)PPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGPETPPRPR 10 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 EGPET(1)PPRPR 113.61 0.0023692 211140000 167860 165230 176640 141550 202950 223700 178580 168570 163760 153570 TRUE FALSE 174487.2424 193606.9672 181243.3835 169548.1675 168452.6315 171749.0652 164582.433 166310.5949 157866.3096 183659.1012 0.950060418 1.054164841 0.98684673 0.923167795 0.917202743 0.935151398 0.896130014 0.905539632 0.859561593 1 17.48667087 3.765031845 3.510738452 0.913475651 1.005749473 0.427152687 0.04094152 0.185583484 4.862063813 0.010227011 0.018741428 5821.459019 -3.765031845 0.092273822 EGPLGWSSDGSLGSVLLDSPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 EGPLGWSSDGSLGSVLLDS(0.001)PS(0.18)S(0.819)PR;EGPLGWSSDGSLGSVLLDSPS(0.148)S(0.852)PR;EGPLGWSSDGSLGSVLLDSPS(0.017)S(0.983)PR;EGPLGWSSDGSLGSVLLDSPS(0.042)S(0.958)PR 263.92 2.14E-44 404905000 164249 188950 197373 189756 231671 247296 212061 228165 219581 224302 TRUE FALSE 170733.6773 221400.6927 202516.7025 227289.1704 192291.6462 189865.2518 195439.1047 225106.8214 211678.3227 268249.6824 0.63647299 0.825353047 0.754955983 0.847304528 0.7168383 0.707793016 0.728571616 0.839169014 0.789109313 1 18.03321694 0.507354144 0.820933069 1.001133755 0.752693408 0.596332412 0.060754205 1.111276014 1.166906748 0.060632952 0.019816549 3.216282177 -0.507354144 -0.248440347 EGPLSVFGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGPLSVFGDR 10 0 P17987;E7ERF2;F5GZ03;F5GZI8;F5GYL4 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;; 129.38 0.00070858 275776000 143608 310068 239593 261876 186227 293953 184089 239631 217769 292063 FALSE TRUE 149277.7547 363319.767 245836.9904 313674.2912 154572.2011 225686.8707 169659.6232 236419.1384 209931.5362 349287.153 0.427378315 1.040175008 0.703824885 0.898041306 0.442536176 0.646135619 0.485731072 0.676861821 0.601028507 1 18.41405405 5.003808115 20.10470515 0.696162503 0.106793582 0.162320456 0.192875342 2686.386943 16971.03254 0.043248861 39916.63856 100880.7065 -5.003808115 -0.589368921 EGPPAPPPVKPPPS(ph)PVNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 177.6 2.41E-14 12559800000 9151220 7417970 8657680 7333990 10583010 10867250 10099870 9162840 9800400 7585710 TRUE FALSE 9512517.232 8691948.644 8883306.253 8784631.332 8784113.74 8343495.882 9308215.798 9040027.117 9447685.518 9071984.637 1.048559672 0.958108836 0.979202083 0.968325199 0.968268145 0.919699075 1.026039634 0.99647734 1.041413307 1 23.11298677 EGPSCPS(ph)PGPFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGPSCPSPGPFCR 13 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 EGPSCPS(1)PGPFCR;EGPSCPS(1)PGPFCR 276.28 3.30E-32 211648000 299720 313130 294370 321580 380500 414550 343410 334640 323240 308870 TRUE FALSE 311553.177 366907.6417 302041.524 385187.5642 315822.7459 318277.0451 316492.6269 330154.6982 311606.6555 369387.1628 0.843432605 0.993287473 0.817682785 1.042774636 0.854991125 0.861635371 0.856804618 0.893790395 0.843577381 1 18.4947742 EGPTDHLESACPLNLPLQNNHTAADMYLS(ph)PVRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGPTDHLESACPLNLPLQNNHTAADMYLSPVRSPK 35 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 EGPTDHLESACPLNLPLQNNHT(0.048)AADMY(0.445)LS(0.813)PVRS(0.693)PK;EGPTDHLESACPLNLPLQNNHTAADMY(0.031)LS(0.97)PVRS(1)PK;EGPTDHLESACPLNLPLQNNHT(0.022)AADMY(0.354)LS(0.768)PVRS(0.857)PK 225.96 4.03E-37 239763000 142382 84800 105024 93650 131523 168790 135687 114233 111569 85175 TRUE FALSE 148003.3513 99363.74035 107761.0117 112173.6905 109166.7674 129591.0805 125051.4984 112701.8935 107553.6535 101863.4105 1.452958924 0.975460569 1.057897151 1.101216717 1.07169755 1.272204415 1.22763903 1.106402122 1.055861501 1 16.6362764 1.201389624 2.481099423 1.006490098 1.152273421 0.155539468 0.126759407 0.541400072 5.762282418 0.11442078 0.032285915 15.8997254 -1.201389624 0.145783323 EGPYSISVLYGDEEVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 200.13 2.95E-11 123964000 62091 71138 59635 61524 86011 88248 76480 68610 70321 68297 FALSE TRUE 64542.40062 83355.39812 61189.13709 73693.26357 71390.88094 67753.73941 70485.29776 67690.39517 67790.16095 81678.48952 0.790200713 1.020530602 0.749146286 0.902235876 0.874047517 0.829517536 0.862960348 0.828742005 0.82996345 1 16.31766857 EGPYSISVLYGDEEVPRS(ph)PFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGPYSISVLYGDEEVPRSPFK 21 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 EGPYSISVLYGDEEVPRS(1)PFK 146.34 6.65E-08 141640000 46185 28397 37565 27018 47057 39618 33377 39698 34795 24754 TRUE FALSE 48008.41946 33273.96385 38543.97476 32362.07976 39058.26795 30417.31992 30760.82353 39165.91324 33542.73475 29604.07236 1.621682952 1.123965766 1.301982183 1.093163108 1.319354563 1.0274708 1.039074056 1.322990728 1.133044614 1 14.85350803 4.741966143 24.4530719 1.167388112 1.621683188 0.587770818 0.117497239 167.93605 1205774.554 0.026739692 0.193749501 55203.44013 -4.741966143 0.454295076 EGQEKEESKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGQEKEESKK 10 2 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;; 89.805 0.0063346 477220000 2716100 802710 1499870 774350 2447620 1872010 2420610 1602120 1978000 632780 FALSE TRUE 2823333.725 940569.1983 1538957.844 927514.1188 2031574.427 1437264.048 2230876.263 1580646.202 1906812.166 756761.1257 3.730812312 1.242887837 2.033611125 1.225636581 2.684564994 1.899230813 2.947926614 2.088698994 2.51970153 1 19.52947845 EGQEKEESKKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGQEKEESKKDR 12 3 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 82.543 0.006426 307670000 965620 382920 619650 308060 1059360 738370 572870 562350 707470 335210 FALSE TRUE 1003743.423 448683.5313 635798.588 368993.3485 879290.3656 566894.7576 527966.9525 554812.6181 682008.2929 400887.9815 2.503800237 1.119224202 1.585975677 0.920440037 2.193356763 1.414097663 1.316993716 1.38395922 1.701244049 1 18.61283964 7.999999989 0.040507291 1.87E-10 3.968401865 0.161470378 0.441021006 1593.58818 4.911403132 130.7235643 431.6329982 99999997.43 -7.999999989 3.968401864 EGQHYPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGQHYPER 8 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 91.265 0.01261 1189078000 533653 664131 616356 615318 702508 776955 653673 701315 627453 642134 FALSE TRUE 554722.0325 778190.333 632418.7437 737026.0639 583095.9411 596518.9761 602436.4022 691915.0195 604871.0891 767947.8629 0.722343351 1.013337455 0.823517812 0.959734507 0.759291053 0.776770149 0.784475654 0.900992181 0.787646035 1 19.55064884 -1.655614995 2.876377 1.016015064 0.842949153 0.231119423 0.088780204 21539483.9 23337174.31 2583109.053 0.020744364 0.02209963 1.655614995 -0.173065912 EGQLLHVYPVLFNVGINEQQTLAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGQLLHVYPVLFNVGINEQQTLAER 25 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 253.43 8.24E-45 405760000 265540 286570 283090 284380 323640 357780 304740 329190 321940 298450 FALSE TRUE 276023.7242 335786.1683 290467.558 340629.5152 268627.7884 274691.0172 280853.6825 324777.7465 310353.4423 356925.5633 0.773336944 0.940773659 0.813804299 0.954343287 0.752615716 0.769603092 0.78686906 0.909931313 0.869518673 1 18.44526371 0.85403857 1.216581431 0.997426605 0.834922055 0.342612785 0.068902787 0.749793334 2.141110486 0.064689057 0.019918705 7.145597834 -0.85403857 -0.16250455 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEK;EGQPSPADEKGNDS(0.956)DGEGES(0.044)DDPEK;EGQPSPADEKGNDS(0.992)DGEGES(0.008)DDPEK;EGQPSPADEKGNDS(1)DGEGESDDPEK 229.65 1.94E-34 1229540000 3410560 877396 1337650 901453 2061780 2407850 2352240 1396700 1635310 544074 TRUE FALSE 3545211.542 1028081.938 1372510.258 1079757.713 1711319.372 1848663.329 2167865.282 1377979.521 1576455.513 650674.8834 5.448514508 1.580024009 2.109364128 1.659442742 2.630068281 2.841147516 3.331718094 2.117769652 2.422800623 1 19.31157734 0.58940987 1.207566776 1.003342207 2.652546058 0.193618336 1.048161797 2.459590592 5.198990052 0.952344005 0.289669599 3.885168603 -0.58940987 1.649203851 EGQPSPADEKGNDS(ph)DGEGESDDPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGQPSPADEKGNDSDGEGESDDPEKK 26 2 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKK;EGQPSPADEKGNDS(1)DGEGESDDPEKK 196.06 3.68E-25 358370000 728860 105564 160344 95252 352482 417830 349466 197932 241377 47124 TRUE FALSE 757635.9556 123693.7958 164522.6964 114092.5613 292567.2355 320795.3148 322073.9418 195279.0453 232689.8889 56357.04556 13.44350024 2.194823994 2.919292428 2.024459589 5.191316057 5.692195388 5.714883358 3.465033402 4.128851799 1 15.78230836 4.744390556 24.9531489 3.795727596 13.44350452 0.785618512 1.540528064 290.955174 1245302.023 0.376873712 3.37916154 55512.47055 -4.744390556 9.647776921 EGQPSPADEKGNDS(ph)DGEGESDDPEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGQPSPADEKGNDSDGEGESDDPEKKK 27 3 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 EGQPSPADEKGNDS(1)DGEGESDDPEKKK 185.7 8.41E-18 644320000 989270 97045 205010 78583 445200 562360 322620 164460 270560 45719 TRUE FALSE 1028327.143 113711.7238 210352.729 94126.48285 369525.063 431760.4126 297332.2014 162255.6827 260822.5985 54676.76271 18.80738896 2.079708421 3.847205259 1.721507971 6.758356653 7.896597956 5.437999374 2.9675437 4.770264104 1 15.73864021 4.743763526 24.97161527 4.242266862 18.80739513 0.813918902 2.114653313 230.8482267 1107932.208 0.518212095 4.394354499 55432.38009 -4.743763526 14.56512827 EGRGES(ph)ENAGTNQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(0.569)ENAGT(0.06)NQET(0.371)R;EGRGES(1)ENAGTNQETR;EGRGES(0.999)ENAGT(0.001)NQETR 147.17 2.77E-06 177189000 122888 148092 155353 123162 167055 174531 131534 141775 160807 163790 TRUE FALSE 127739.7131 173525.649 159401.6268 147523.076 138659.0508 133998.8203 121224.0214 139874.738 155019.5875 195881.5146 0.652127453 0.885870468 0.813765542 0.753124032 0.707872058 0.684080989 0.618864019 0.714078295 0.791394675 1 17.57962173 0.862333614 3.744180792 0.999933485 0.729759974 0.555033803 0.072910321 0.582160722 14.32333709 0.075298301 0.01933406 7.283390807 -0.862333614 -0.270173511 EGRGESENAGT(ph)NQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 EGRGES(0.065)ENAGT(0.935)NQETR 258.48 6.64E-26 109280000 105620 121230 126610 101860 142910 149260 101230 112460 121830 123330 TRUE FALSE 109789.9592 142050.3095 129909.5606 122007.604 118618.2092 114596.6271 93295.32808 110952.6576 117445.3621 147494.1522 0.744368217 0.963091128 0.880777703 0.827202992 0.804223133 0.776957088 0.632535776 0.752251232 0.796271312 1 17.17029823 3.22737128 1.959603963 0.763038117 0.870332399 0.046789653 0.099895077 0.55187243 4.363288789 0.030543455 0.042060637 1687.995483 -3.22737128 0.107294282 EGRPPEPTPAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ; 69.03 0.028726 280370000 243820 182552 196787 162470 309410 279600 248270 215880 250010 165974 FALSE TRUE 253446.2019 213903.8859 201915.4309 194606.0811 256816.5987 214667.1374 228809.9487 212986.4817 241012.1889 198493.4275 1.27684934 1.077637122 1.017239882 0.980415742 1.293829231 1.081482344 1.152733123 1.073015285 1.214207402 1 17.59873171 4.743488218 24.31832871 1.101655454 1.276849447 0.247994784 0.092828128 514.1033921 2537038.548 0.021461049 0.177415359 55397.25144 -4.743488218 0.175193993 EGRPSGEAFVELESEDEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 177.73 3.60E-14 304210000 417240 247100 325600 247850 411470 429110 395380 330010 370180 257430 FALSE TRUE 433712.9574 289537.5028 334085.4035 296873.9902 341528.4764 329455.7057 364389.0825 325586.7557 356857.2941 307868.4797 1.408760513 0.940458416 1.085156245 0.964288356 1.10933239 1.070118338 1.183586845 1.057551446 1.15912254 1 18.23195464 EGS(ph)GGPQESSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGSGGPQESSR 11 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 EGS(1)GGPQESSR;EGS(0.975)GGPQES(0.025)SR 116.71 0.00099856 172434000 157516 147230 157856 150634 230364 323590 213712 185131 194498 138360 TRUE FALSE 163734.8533 172515.6072 161969.857 180428.9556 191206.8096 248441.1266 196960.695 182649.6218 187498.055 165468.9929 0.989519851 1.042585708 0.978853223 1.090409462 1.15554465 1.501436143 1.190317845 1.103829899 1.133131058 1 17.33620137 3.384175903 2.973060574 1.195800455 1.009750004 0.296158332 0.121671531 0.324200644 5.764350067 0.036967621 0.053049867 2422.009836 -3.384175903 -0.186050451 EGS(ph)PANWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGSPANWK 8 0 O96019-2;O96019 O96019-2 ACTL6A Actin-like protein 6A 1 EGS(1)PANWK;EGS(1)PANWK;EGS(1)PANWK 141.1 0.0006703 1045680000 3535810 1678320 2314530 1802080 3283280 3298920 3292370 2325110 2475700 1244980 TRUE FALSE 3675406.509 1966558.404 2374848.553 2158526.045 2725189.238 2532795.826 3034305.436 2293945.704 2386600.041 1488909.994 2.468521618 1.320804086 1.595024926 1.449735749 1.830325035 1.701107411 2.037937449 1.540687961 1.602917604 1 20.50582511 0.655609929 1.413941998 1.001512224 1.728373583 0.345659798 0.307338452 1.366114367 4.063114034 0.274636165 0.080752129 4.524909827 -0.655609929 0.72686136 EGS(ph)PAPLEPEPGAAQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGSPAPLEPEPGAAQPK 17 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK;EGS(1)PAPLEPEPGAAQPK 277.34 9.14E-36 1214270000 1792400 680220 1025030 770730 1456620 1709380 1515290 1098450 1199840 550020 TRUE FALSE 1863165.336 797042.4936 1051743.124 923178.0936 1209024.253 1312402.401 1396517.61 1083727.074 1156657.993 657785.8882 2.832479944 1.211705067 1.598914088 1.403462905 1.838020964 1.995181752 2.123058027 1.647537738 1.758411078 1 19.32725853 0.397653094 1.552568828 1.000080739 1.802652259 0.255703688 0.421210962 6.152046739 14.33991515 0.38312916 0.10982955 2.498348932 -0.397653094 0.80257152 EGS(ph)PIPHDPEFGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 211.45 4.02E-09 4944080000 12657080 5742574 8296980 6102690 12560410 13823720 12227120 9128370 9723810 4586605 TRUE FALSE 13156791.29 6728816.413 8513206.115 7309783.867 10425395.99 10613370.53 11268726.38 9006019.131 9373851.978 5485262.434 2.39857098 1.226708201 1.552014369 1.332622451 1.900619363 1.934888377 2.054364129 1.641857475 1.708915861 1 22.38712922 3.206227863 24.99599651 1.765591458 1.593461333 0 0.398421969 707.9181425 547279.7586 0.109265294 0.130605983 1607.784593 -3.206227863 -0.172130125 EGS(ph)PRDNPTAQQIMQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGSPRDNPTAQQIMQLLR 18 1 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 1 EGS(1)PRDNPTAQQIMQLLR 91.238 0.0015488 20435000 22014 25336 26381 20550 33897 44567 23324 25171 28167 28537 TRUE FALSE 22883.12972 29687.26091 27068.51053 24614.72866 28135.20005 34216.98967 21495.80393 24833.62392 27153.27517 34128.27878 0.670503481 0.869872785 0.79314022 0.721241432 0.824395518 1.002599337 0.629853151 0.727655329 0.795623927 1 15.05868004 4.761675942 22.70581008 0.799954101 0.670502976 0.115805853 0.112690627 4105.67902 4032714.178 0.02655396 1.222627646 57766.48495 -4.761675942 -0.129451125 EGS(ph)PYKAPIYIPDDIPIPAEFELR ddPTM_MDA-MB-175_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(0.998)PY(0.002)KAPIYIPDDIPIPAEFELR 84.097 0.0079272 57904000 39654 39063 37941 32500 49846 55756 44943 37959 37483 30712 TRUE FALSE 41219.57054 45771.76638 38929.77363 38928.403 41373.19472 42807.51399 41420.25022 37450.22169 36133.99415 36729.42838 1.122249171 1.246187823 1.059906874 1.059869557 1.126431762 1.165482717 1.127712901 1.019624409 0.983788633 1 15.16464882 1.674220948 3.615385229 0.994526516 1.130558918 0.585558161 0.049873053 0.141611181 4.337731577 0.030571782 0.013974277 47.23032656 -1.674220948 0.136032402 EGS(ph)SPEGSTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGSSPEGSTRR 11 1 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 EGS(0.587)S(0.413)PEGSTRR;EGS(0.543)S(0.457)PEGSTRR 87.498 0.0083787 562800000 266836 815668 823920 656414 771140 1013250 611960 804937 776735 1038968 TRUE FALSE 277370.8913 955752.634 845392.0321 786250.73 640061.8982 777938.0435 563992.9761 794148.1361 748780.4591 1242533.887 0.223230042 0.769196433 0.680377445 0.63278011 0.515126311 0.626090002 0.453905509 0.639135998 0.602623773 1 20.24485377 0.286717618 1.335077874 1.000297712 0.576331765 0.453239239 0.141626908 4.537513646 7.601496045 0.128048996 0.037321449 1.935163296 -0.286717618 -0.423965947 EGSALSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGSALSHVR 9 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 0 158.76 6.66E-05 73128000 108170 113540 96189 100570 146420 157770 104410 104490 103440 148120 FALSE TRUE 112440.6351 133039.6118 98695.76436 120462.4458 121531.5807 121130.3085 96226.07138 103089.4825 99717.21461 177141.2781 0.634751179 0.751036761 0.557158475 0.680035998 0.686071491 0.683806224 0.543216536 0.581961944 0.562924778 1 17.43454091 -1.115036589 4.987038654 1.000014294 0.629742466 0.740596042 0.065471701 1.08E-05 1.91E-06 0.065738525 0.015494121 0.076729684 1.115036589 -0.370271828 EGSEFSFS(ph)DGEVAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGSEFSFSDGEVAEK 15 0 Q9BVS4-2;Q9BVS4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 EGSEFS(0.03)FS(0.97)DGEVAEK 166.92 1.41E-06 27821000 33944 23661 29982 24740 37641 37585 37834 31253 32194 23835 TRUE FALSE 35284.13533 27724.59269 30763.35555 29633.49816 31242.79627 28856.45336 34868.47222 30834.10465 31035.34423 28505.0119 1.237822157 0.972621685 1.079226196 1.039589047 1.096045719 1.012329111 1.223240051 1.081708184 1.08876798 1 14.79892798 EGSGSSGTGEQKEDQKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGSGSSGTGEQKEDQKEEK 19 2 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 69.148 0.013122 168160000 448830 147765 176436 164478 241583 353780 338040 185209 212625 102848 FALSE TRUE 466550.155 173142.4893 181034.0671 197011.2575 200518.808 271619.9566 311543.5415 182726.5763 204972.6678 122999.0965 3.793118555 1.407672855 1.471832496 1.601729307 1.630246187 2.208308552 2.532892927 1.485592834 1.666456695 1 16.90828819 4.74383644 24.88275601 1.718812739 3.793119485 0.709514586 0.406880482 299.3787506 1411935.083 0.098903792 0.844045381 55441.68749 -4.74383644 2.074306747 EGSGSSGTGEQKEDQKEEKQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGSGSSGTGEQKEDQKEEKQ 20 3 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 152.32 8.04E-08 373410000 744430 198229 299110 195831 440370 522050 403510 256830 364650 132103 FALSE TRUE 773820.6712 232273.2887 306905.0523 234565.7873 365516.0647 400811.7992 371881.8318 253387.6139 351526.3177 157986.0536 4.898031527 1.470213879 1.942608511 1.484724645 2.313597032 2.537007477 2.353890254 1.603860646 2.225046514 1 17.26943768 4.743991178 24.96215202 1.929743263 4.898032811 0.79065139 0.46510377 249.2635966 1145731.334 0.10789739 0.937782135 55461.44469 -4.743991178 2.968289548 EGSLS(ph)PASVGSDTLSDLGISSLQDGLALHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGSLSPASVGSDTLSDLGISSLQDGLALHIR 31 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 EGS(0.028)LS(0.968)PAS(0.004)VGSDTLSDLGISSLQDGLALHIR;EGS(0.039)LS(0.955)PAS(0.005)VGSDTLSDLGISSLQDGLALHIR;EGS(0.183)LS(0.797)PAS(0.009)VGS(0.01)DT(0.001)LSDLGISSLQDGLALHIR;EGS(0.036)LS(0.963)PASVGSDTLSDLGISSLQDGLALHIR;EGS(0.014)LS(0.985)PAS(0.001)VGSDTLSDLGISSLQDGLALHIR 272.72 8.70E-72 1132173000 114499.2 143391.7 142102.4 165198.7 156450.7 172661.7 156074.4 140593.1 134464.6 118788.4 TRUE FALSE 119019.7168 168018.109 145805.7053 197874.5098 129857.2659 132563.6369 143840.8807 138708.6795 129625.2453 142062.7126 0.837797017 1.182703793 1.026347467 1.39286732 0.914084093 0.933134631 1.012516782 0.976390475 0.912450867 1 17.11616841 EGSQGELT(ph)PANSQSR ddPTM_MDA-MB-175_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 195.77 3.87E-11 0 67508 79364 81331 82157 72956 84302 88749 70744 70795 58755 TRUE FALSE 70173.26797 92994.14963 83450.55267 98407.40939 60554.96518 64724.13811 81792.62148 69795.79239 68247.10178 70266.91732 0.998667234 1.323441431 1.187622225 1.400479958 0.861784855 0.921118224 1.164027463 0.99329521 0.9712551 1 16.10055799 3.233244674 24.99993996 0.994765463 1.231549729 0.490930726 0.120617257 111.6425368 525035.1466 0.033992027 0.041764723 1710.97898 -3.233244674 0.236784266 EGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGSVIDHIHLISVGDMIEAINGQSLLGCR 29 0 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 258.46 2.84E-58 471870000 195699 306450 309740 351530 379460 399360 394970 377990 385510 313180 FALSE TRUE 203425.3476 359080.4036 317812.0789 421061.5848 314959.5247 306614.6924 364011.2193 372923.6623 371635.5704 374541.6248 0.543131482 0.958719619 0.848536071 1.124205047 0.840919951 0.818639831 0.971884552 0.995680153 0.992241038 1 18.51476654 4.739488337 24.80704605 0.947994327 0.54313134 0.660011055 0.087613781 42.4215066 1134152.12 0.020745362 0.126421042 54889.38142 -4.739488337 -0.404862987 EGTETFADHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 145.89 2.96E-05 2350850000 1466915 1636728 1657616 1565061 1833352 2083297 1781203 1641264 1681403 1545099 FALSE TRUE 1524829.937 1917823.302 1700814.835 1874625.395 1521719.482 1599482.844 1641587.655 1619265.541 1620889.634 1847831.566 0.825199637 1.037877768 0.92043824 1.014500146 0.823516336 0.865599914 0.888385979 0.876305812 0.87718473 1 20.81740183 3.236993112 24.99999383 0.880996447 0.953740236 0.155748322 0.067968093 61.46425545 980298.5557 0.01772428 0.022282167 1725.810521 -3.236993112 0.072743789 EGTGQQERES(ph)PRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 2 EGT(0.003)GQQERES(0.997)PRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;EGT(0.46)GQQERES(0.54)PRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR 329.29 1.05E-138 388790000 93192 85119 98046 80104 104901 112319 83252 95957 101662 95284 TRUE FALSE 96871.29212 99737.52612 100601.1593 95948.33211 87069.96549 86234.61446 76726.4907 94670.85337 98003.20448 113953.0755 0.850098093 0.87525085 0.882829699 0.841998618 0.764086139 0.756755481 0.673316542 0.83078805 0.860031237 1 16.79808034 3.436398711 5.624793371 0.795565737 0.869014162 0.058960402 0.080769504 0.349008398 27.47391476 0.021816665 0.03016862 2731.484312 -3.436398711 0.073448425 EGTINVHDVETQFNQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGTINVHDVETQFNQYK 17 0 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;P15941-13 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 ;;; 286.68 1.75E-36 1692930000 1457980 1272900 1049430 1298280 2266990 2186600 1676450 1305540 1261470 1915190 FALSE TRUE 1515542.176 1491510.673 1076779.008 1555075.909 1881647.85 1678795.288 1545045.468 1288041.372 1216069.941 2290434.812 0.661683174 0.65119106 0.47011991 0.678943535 0.821524297 0.732959209 0.674564262 0.562356704 0.530934098 1 21.12719007 3.509709877 24.24887963 0.692424229 0.595769723 0.131143186 0.133952362 1111.557001 827095.1888 0.035959829 0.055651458 3233.775576 -3.509709877 -0.096654506 EGTPGS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGTPGSPGR 9 0 Q99856 Q99856 ARID3A AT-rich interactive domain-containing protein 3A 1 EGT(0.001)PGS(0.999)PGR;EGT(0.002)PGS(0.998)PGR;EGT(0.026)PGS(0.974)PGR;EGT(0.01)PGS(0.99)PGR;EGT(0.007)PGS(0.993)PGR 153.33 8.22E-05 2047600000 1814620 2061300 2030550 1884430 2267180 2543610 2231060 2157370 2137380 1896230 TRUE FALSE 1886262.599 2415312.24 2083467.801 2257164.63 1881805.553 1952895.126 2056183.687 2128453.984 2060456.111 2267759.963 0.831773481 1.06506521 0.918733832 0.995327842 0.829808086 0.861156012 0.906702526 0.938571109 0.90858651 1 21.11283651 7.039880259 9.664930953 0.92483496 0.254842425 0 0.072696499 0 0 0.015343848 0 10961759.24 -7.039880259 -0.669992535 EGTVSDHIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGTVSDHIER 10 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 0 120.06 0.0031033 0 139770 216570 194740 199420 221280 233120 167040 211000 163400 197620 FALSE TRUE 145288.2275 253764.2128 199815.0844 238864.6808 183666.9046 178981.413 153946.9683 208171.8901 157519.2659 236339.8553 0.614742813 1.073725853 0.845456574 1.010683029 0.777130478 0.757305249 0.651379633 0.880815848 0.666494721 1 17.85050341 3.173634741 24.99546929 0.778899168 0.896643856 0.091586949 0.14665924 114.3028663 44003.67658 0.039213769 0.046869435 1491.539436 -3.173634741 0.117744688 EGVFVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGVFVNR 7 0 P49902-2 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 99.139 0.025003 236520000 216870 164680 226810 177270 280740 238940 254470 230040 259590 196290 FALSE TRUE 225432.1951 192962.509 232720.8549 212333.4769 233019.9151 183449.8062 234523.9765 226956.6901 250247.4066 234749.2673 0.960310538 0.821994084 0.991359239 0.904511777 0.992633194 0.781471262 0.999040292 0.966804679 1.066019969 1 17.84076113 1.779472631 2.212368434 1.021341435 0.913053867 0.297334687 0.06968786 0.346805192 3.356914356 0.041880656 0.018588639 60.18283352 -1.779472631 -0.108287567 EGVHGGLINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;; 154.81 1.38E-05 5833600000 6810620 5985160 6684670 5772340 7855660 8070080 7792820 6853970 6777350 5211880 FALSE TRUE 7079508.537 7013064.672 6858877.992 6914091.623 6520357.719 6195926.223 7181998.406 6762103.743 6533434.497 6233048.099 1.135802006 1.125142075 1.100405112 1.109263319 1.046094562 0.994044346 1.152244984 1.084879121 1.048192537 1 22.57150641 7.999999975 0.011670129 2.11E-07 2.336035447 0.391091366 0.041006592 10914.54657 9.841692065 827.5903292 1169.849186 99999994.26 -7.999999975 2.336035235 EGVHGGLINKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 ;;; 149.96 2.21E-05 32166670000 46560670 34233860 43991520 32861700 58395780 51741200 50461140 44440240 49542580 32071390 FALSE TRUE 48398921.2 40113259.15 45137975.15 39361646.18 48469686.17 39725090.45 46505863.99 43844591.27 47759552.22 38355164.83 1.261861901 1.045837225 1.176842163 1.02624109 1.263706893 1.035716849 1.212505909 1.143120919 1.245192204 1 25.19291753 3.24998502 24.99281201 1.155136668 1.125359104 0.01019462 0.09954558 1150.297648 2516452.827 0.025158969 0.033781161 1778.218072 -3.24998502 -0.029777565 EGVIEAGAFQGSPAPPLPSVMS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGVIEAGAFQGSPAPPLPSVMSPSR 25 0 P53367 P53367 ARFIP1 Arfaptin-1 1 EGVIEAGAFQGSPAPPLPS(0.003)VMS(0.741)PS(0.256)R 125.71 8.96E-05 65869000 26372 28825 31487 31885 26419 33980 30463 34270 29105 35220 TRUE FALSE 27413.18692 33775.46952 32307.57709 38191.75783 21928.30782 26088.65997 28075.23046 33810.6667 28057.51674 42120.68467 0.650824818 0.801873706 0.767024025 0.906722152 0.520606633 0.61937882 0.666542595 0.802709333 0.666122048 1 15.36224127 -1.188248531 4.660914521 1.000046518 0.717433471 0.402800546 0.10521717 5.16E-05 8.98E-06 0.103312993 0.024347104 0.064826335 1.188248531 -0.282613047 EGVKFDESEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 149.38 2.14E-05 2102200000 6113200 2869630 4071320 3061820 6496900 5743000 5791480 3951490 4748510 2142720 FALSE TRUE 6354553.856 3362466.63 4177421.944 3667438.857 5392559.259 4409275.286 5337528.664 3898526.74 4577612.053 2562544.959 2.479782387 1.312159078 1.63018484 1.431170542 2.104376448 1.720662605 2.082901471 1.521349597 1.78635385 1 21.28914589 -0.003396179 0.958601687 0.990958396 1.771063142 0.329928382 0.335026209 8.291780347 6.803549749 0.55695227 0.097006956 0.992210506 0.003396179 0.780104746 EGVKTENDHINLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EGVKTENDHINLK 13 1 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ;; 121.04 0.00015097 676890000 851070 541592 724850 427064 1073840 889080 737400 710980 853730 586832 FALSE TRUE 884670.9008 634606.213 743740.1865 511535.9845 891309.0604 682604.6441 679600.6612 701450.476 823004.4241 701810.4948 1.260555246 0.904241555 1.059745034 0.7288805 1.270013867 0.972633851 0.968353517 0.999487014 1.172687542 1 19.420722 3.214010502 24.9999611 1.048791144 0.987446161 0.049808536 0.153286159 923.5149012 940434.622 0.042650003 0.050998287 1636.856105 -3.214010502 -0.061344983 EGVVGAVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EGVVGAVEK 9 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 ;;;; 172.21 0.00013112 700231000 1268210 1088930 1294190 1083983 1670280 1656440 1491870 1320360 1359800 1130200 FALSE TRUE 1318279.91 1275945.257 1327917.655 1298391.602 1386366.402 1271756.914 1374933.331 1302662.734 1310861.064 1351641.051 0.975318047 0.943997118 0.982448449 0.960603853 1.025691252 0.940898408 1.017232593 0.963763814 0.969829277 1 20.36628064 3.909850475 2.11110118 0.982575287 0.960843286 0.094284174 0.025940187 0.736637048 6.382772067 0.006615678 0.016112362 8125.507118 -3.909850475 -0.021732002 EGVVGPELHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGVVGPELHHK 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 57.836 0.063689 87129000 151820 149330 168090 133240 211690 197850 187570 165800 174720 134490 FALSE TRUE 157813.9708 174976.2659 172470.5635 159594.4743 175707.0094 151902.3359 172867.7733 163577.7222 168431.8613 160840.7405 0.981181573 1.087885229 1.07230645 0.992251551 1.092428503 0.944426987 1.074776034 1.017016719 1.047196505 1 17.29527336 EGYAWAEDKEHCEEYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGYAWAEDKEHCEEYGR 17 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 213.99 1.02E-13 753250000 691600 566970 653200 502130 820590 800440 741050 683240 689440 562470 FALSE TRUE 718904.902 664342.6871 670222.9286 601449.8153 681106.4049 614549.9408 682964.5646 674082.2854 664627.1891 672675.2274 1.068725104 0.987612833 0.996354409 0.894116196 1.012533801 0.913590862 1.015296144 1.002091735 0.988035774 1 19.3595506 0.085543981 7.182516227 1 0.985207006 0.00661755 0.04740985 664103.5964 82187.67684 0.043939777 0.010656961 1.217710304 -0.085543981 -0.014792994 EGYGGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EGYGGFR 7 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 122.98 0.0099764 259570000 248360 307540 250320 271740 280550 345630 264780 260800 258490 292240 FALSE TRUE 258165.4446 360357.6027 256843.5448 325489.3609 232862.2112 265362.6706 244025.8517 257304.4026 249186.9954 349498.8327 0.738673267 1.031069546 0.734890995 0.931303142 0.666274646 0.759266257 0.6982165 0.736209619 0.71298377 1 18.41492811 3.241128284 24.9999986 0.743907612 0.862412237 0.127708908 0.118200499 105.2773988 1025020.205 0.030092625 0.03893823 1742.321452 -3.241128284 0.118504625 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK 34 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ; 192.64 8.92E-21 513030000 165428 297874 321100 276058 378250 400030 352100 327500 342540 284060 FALSE TRUE 171959.2252 349031.5424 329468.1298 330661.4484 313955.2001 307129.095 324501.482 323110.3982 330212.0523 339716.1183 0.506185064 1.027421201 0.96983367 0.973346364 0.924169279 0.904075722 0.955213675 0.951118833 0.972023506 1 18.37397015 4.743830659 24.99997947 0.959224985 0.506184875 0.944201591 0.0333785 120.0891427 569660.2729 0.008154205 0.069467397 55440.94943 -4.743830659 -0.45304011 EHAFFRYIDWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHAFFRYIDWEK 12 1 P05771;P05771-2;I3L148 P05771 PRKCB Protein kinase C beta type 0 64.121 0.060044 130640000 58594 252070 136230 219430 134990 232670 103500 176980 117370 308680 FALSE TRUE 60907.33636 295361.0617 139780.2657 262832.5991 112044.448 178635.9186 95387.39955 174607.8726 113145.8766 369159.936 0.164989021 0.800089698 0.378644192 0.711974874 0.303511939 0.483898444 0.258390443 0.472987059 0.306495547 1 18.49388646 -1.064992027 4.742313879 1.000016993 0.441419892 0.449299505 0.188606129 2.153270674 216724074.6 9592.013701 0.04012738 0.086100956 1.064992027 -0.558597101 EHALLAYTLGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 178.71 2.16E-05 19504311000 12367860.9 10450639.3 12921124.4 10687623 17536070 15906449.5 15742973.8 13438372.5 14741338.4 11142672 FALSE TRUE 12856153.6 12245455.31 13257859.52 12801602.93 14555295.09 12212417.67 14508998.38 13258253.1 14210800.51 13325865.24 0.964751884 0.918923844 0.994896712 0.960658291 1.092258913 0.916444632 1.088784714 0.994926248 1.066407341 1 23.66772587 3.713152244 1.629271613 1.022754194 0.945455554 0.247145745 0.052921445 0.505595047 2.598919489 0.014548547 0.032676833 5165.974328 -3.713152244 -0.07729864 EHALTSGTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHALTSGTIK 10 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ; 128.03 0.00034028 307390000 637530 627260 684560 582990 967020 858200 828210 727180 734540 708830 FALSE TRUE 662700.1767 734987.0256 702400.196 698303.6819 802646.2858 658896.0561 763292.7361 717433.3415 708104.0489 847711.6671 0.781751865 0.867024785 0.828583849 0.823751411 0.946838786 0.777264348 0.900415514 0.846317645 0.835312378 1 19.69321412 -5 0.295994786 2.226271786 0.839579989 0.481097916 0.048260153 213.4284727 1.989134919 162.1488404 0.045523468 1.00E-05 5 -1.386691798 EHAMLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 0.035077 876901000 1529830 1452870 1639630 1440360 2234700 2075110 1925120 1665590 1772730 1631910 FALSE TRUE 1590228.87 1702389.121 1682360.105 1725258.909 1854846.492 1593197.151 1774224.064 1643265.49 1708929.794 1951651.52 0.814811893 0.872281298 0.862018699 0.88399947 0.950398405 0.816332801 0.909088557 0.841987145 0.875632651 1 20.89626404 -2.402487321 1.906746618 1.758899638 0.870368979 0.504817154 0.038733475 2957770.769 269146.019 9666003.957 0.009153505 0.003958336 2.402487321 -0.888530659 EHAPSIIFMDEIDSIGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHAPSIIFMDEIDSIGSSR 19 0 P62195-2;P62195;J3QSA9;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ;;; 338.5 1.35E-75 920410000 329609 427980 450314 451568 476922 507041 454261 450566 435593 498064 FALSE TRUE 342622.2178 501482.2358 462049.5528 540886.8026 395854.9688 389288.412 418654.8358 444526.8997 419916.093 595650.1048 0.575207181 0.841907408 0.775706323 0.90806129 0.664576344 0.653552159 0.702853626 0.746288628 0.704971072 1 19.18410559 -1.943489762 4.382340517 1.149465981 0.735643823 0.442041093 0.090710312 0.062408164 0.000804753 0.041378736 0.020331678 0.011389646 1.943489762 -0.413822158 EHASGSGAQSEAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHASGSGAQSEAAGR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 122.16 0.00088895 0 2589.5 12881.4 11567.3 15155.3 6159.2 12707 9444.4 15065.5 8604.5 14178.8 FALSE TRUE 2691.73546 15093.68025 11868.75334 18152.97311 5112.261384 9755.991826 8704.12325 14863.57161 8294.825726 16956.86439 0.158740165 0.89012213 0.699937976 1.070538319 0.301486246 0.575341738 0.513309716 0.876551895 0.489172145 1 14.0495818 -1.548145809 2.996860123 1.015689121 0.645121436 0.151121862 0.26434549 58079440.95 67150062.92 7387194.002 0.059309184 0.028304415 1.548145809 -0.370567685 EHDPVGQMVNNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHDPVGQMVNNPK 13 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 134.18 9.85E-05 165850000 178570 145970 177630 149500 214350 228790 198260 178990 196530 138170 FALSE TRUE 185620.0815 171039.212 182259.1837 179070.6538 177914.8636 175656.9898 182719.8631 176590.9318 189456.9237 165241.7661 1.123324241 1.035084628 1.102984966 1.083688816 1.076694275 1.063030213 1.105772877 1.068682186 1.146543808 1 17.33421886 -0.067440348 14.29784155 1.000000456 1.086368492 0.435690754 0.030377162 0 0 0.026413879 0.006225811 0.856169302 0.067440348 0.086368036 EHDQLIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHDQLIEK 8 0 O14980 O14980 XPO1 Exportin-1 0 ;;; 124.74 0.0012917 817980000 3243230 2264770 3263130 2551790 3949610 3954430 4014650 3105740 3463570 1897810 FALSE TRUE 3371275.225 2653726.63 3348169.848 3056526.446 3278256.703 3036073.562 3699971.243 3064112.635 3338916.792 2269649.534 1.485372598 1.169223085 1.475192447 1.346695338 1.444388948 1.337683866 1.630194965 1.350037788 1.471115581 1 21.11403811 -0.698646695 5.603474594 0.999999984 1.408980124 0.532474582 0.115840699 2.78E-08 6.62E-09 0.103674562 0.024436327 0.200148945 0.698646695 0.408980139 EHDYRDEHFDFIQSHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EHDYRDEHFDFIQSHIR 17 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;;; 214.5 1.99E-15 4370453000 861696 873770.1 1081115 985898.6 1054975.8 1298329 1234463 1015580.6 977579 743309.5 FALSE TRUE 895716.4235 1023833.318 1109289.745 1180906.4 875651.3903 996811.7661 1137702.564 1001968.403 942396.1227 888946.765 1.00761537 1.151737492 1.247869714 1.328433205 0.985043677 1.121340226 1.279832054 1.127141065 1.060126613 1 19.7617375 1.158720603 2.810416707 1.005312419 1.163952971 0.204348419 0.103270532 0.388227223 5.502004202 0.097666168 0.026780034 14.41187885 -1.158720603 0.158640552 EHDYRDEHLDFIQSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EHDYRDEHLDFIQSHLR 17 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;;;; 183.77 2.26E-10 4449708000 835414.7 859903 954377 1008484 1034436 1148426 1159299 918339 1011865 783061 FALSE TRUE 868397.5174 1007584.651 979248.8486 1207959.125 858602.9382 881721.4661 1068430.115 906030.1678 975448.1763 936486.8103 0.927292844 1.075919746 1.04566219 1.289883757 0.916833989 0.941520432 1.140891792 0.967477767 1.041603753 1 19.83689915 EHDYRDEHLDFIQSHLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHDYRDEHLDFIQSHLRR 18 2 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;; 149.34 2.02E-08 897820000 245544 319851 332054 215294 417228 367350 208865 281626 311162 466837 FALSE TRUE 255238.2667 374782.9212 340707.6 257878.5106 346307.7336 282038.5297 192493.6155 277851.2641 299963.3404 558304.772 0.45716655 0.671287333 0.610253784 0.461895587 0.620284388 0.505169477 0.344782322 0.497669513 0.537275258 1 19.09069336 0.914430122 16.62341468 1 0.519795197 0.719817392 0.089352323 442.1383638 85894.55527 0.089949261 0.022487849 8.211644164 -0.914430122 -0.480204804 EHEEAVSVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHEEAVSVDR 10 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 115.57 0.0012049 524290000 366290 406830 419890 401240 483130 541400 472990 468840 488910 397390 FALSE TRUE 380751.412 476699.8878 430832.6783 480604.0744 401007.7352 415668.055 435915.8079 462555.9667 471314.2246 475250.962 0.801158635 1.003048759 0.906537204 1.011263759 0.843781007 0.87462854 0.917232878 0.973287807 0.991716508 1 18.85833002 1.656246371 3.119909618 0.992916582 0.911613462 0.272978577 0.060463238 0.297207325 6.783318958 0.036451158 0.015797115 45.31545768 -1.656246371 -0.08130312 EHELLEQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHELLEQQKR 10 1 Q13435;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 82.379 0.011807 96991000 124650 84381 115850 89976 145860 157680 148620 112490 123420 86960 FALSE TRUE 129571.2783 98872.78036 118869.1462 107772.9842 121066.7693 121061.2097 136970.7761 110982.2555 118978.1383 103998.1471 1.245899873 0.95071675 1.142992924 1.036297158 1.164124292 1.164070833 1.317050158 1.067156086 1.144040944 1 16.6661983 3.213909663 24.89880174 1.153493801 1.087244965 0.042978155 0.103727684 543.6016991 549065.9679 0.028444508 0.034012593 1636.476086 -3.213909663 -0.066248836 EHENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHENLK 6 0 Q8IWJ2;U3KQE0;U3KPU4;B8ZZW2 Q8IWJ2 GCC2 GRIP and coiled-coil domain-containing protein 2 0 103.29 0.034815 842070000 742590 533320 732860 560170 922500 887740 991080 720470 758650 472170 FALSE TRUE 771908.0266 624913.5613 751958.9337 670969.9541 765693.7795 681575.8388 913396.5599 710813.2781 731346.3347 564682.6713 1.366976651 1.106663252 1.33164868 1.1882248 1.355971802 1.207006826 1.617539561 1.258783586 1.295145702 1 19.10708083 4.128222875 18.25485126 1.302918239 1.232300854 0 0.158961926 5.819527837 926.3568803 0.037107079 0.080162646 13434.54231 -4.128222875 -0.070617385 EHEVFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;;; 172.03 0.0009156 2038930000 1177580 1286090 1369500 1266550 1497630 1603860 1462000 1237340 1376930 1166950 FALSE TRUE 1224071.768 1506965.953 1405190.295 1517069.81 1243063.388 1231387.822 1347404.62 1220755.481 1327374.558 1395591.51 0.877098892 1.079804472 1.006877933 1.08704431 0.890707187 0.882341153 0.965472067 0.874722634 0.951119686 1 20.4124453 3.222713732 24.99499981 0.918656537 1.017082815 0.285290826 0.065131211 250.4134969 394971.744 0.017689202 0.021209922 1669.989469 -3.222713732 0.098426278 EHEVTIFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EHEVTIFVR 9 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 182.76 4.59E-05 2598480000 989351 866218 911667 1047580 1028588 1184720 1239466 949113 926476 698213 FALSE TRUE 1028411.341 1014984.203 935425.791 1254788.197 853748.9792 909586.7346 1142313.416 936391.6927 893132.3097 835014.4693 1.231609007 1.215528881 1.120250996 1.502714316 1.02243615 1.089306555 1.368016314 1.121407745 1.069600998 1 19.67144167 1.343177165 2.87751786 1.023419418 1.216409969 0.245640333 0.131064042 0.373720624 5.105366252 0.108182481 0.033264652 22.03825303 -1.343177165 0.19299055 EHEWFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHEWFK 6 0 Q13131-2;Q13131;A0A087WXX9;P54646 Q13131-2;A0A087WXX9 PRKAA1;PRKAA2 5-AMP-activated protein kinase catalytic subunit alpha-1;5-AMP-activated protein kinase catalytic subunit alpha-2 0 ; 119.7 0.020787 481900000 891200 726180 842800 681280 1131950 1056790 993450 837610 943080 660930 FALSE TRUE 926385.2642 850895.7661 864764.0604 816035.1506 939541.5433 811366.5383 915580.7931 826383.208 909138.735 790426.5792 1.172006722 1.076501965 1.094047294 1.032398419 1.188651252 1.026491972 1.158337557 1.045490156 1.150187454 1 19.59227193 -1.382324092 3.247317145 0.99901855 1.100046139 0.229737423 0.0570038 1655372.551 1071201.061 10714.66256 0.011812517 0.04146445 1.382324092 0.101027589 EHFGTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHFGTVK 7 0 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 ;; 127.12 0.003886 812630000 1129570 954000 1154950 971380 1596820 1547910 1378260 1129970 1236940 1178420 FALSE TRUE 1174166.296 1117842.079 1185048.946 1163516.065 1325393.107 1188431.361 1270228.38 1114824.6 1192422.771 1409308.837 0.833150453 0.793184609 0.84087243 0.825593393 0.94045611 0.843272482 0.901313003 0.791043504 0.846104658 1 20.42655637 -2.614554248 2.059220544 3.85781122 0.844942471 0.536291536 0.04291691 1604316.388 110696.9695 21350725.43 0.011123286 0.002429102 2.614554248 -3.012868748 EHFQDDVFNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHFQDDVFNEK 11 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 116.06 0.0010395 336690000 243140 461720 394180 435700 399010 577590 422050 424060 375670 517550 FALSE TRUE 252739.3549 541016.8183 404452.6546 521880.1596 331186.4227 443453.476 388968.6182 418376.1693 362149.7101 618954.0134 0.408333009 0.874082414 0.653445403 0.843164675 0.53507436 0.716456257 0.628428946 0.675940636 0.585099543 1 19.2394727 -1.867285251 2.40179807 1.159792836 0.667077603 0.382159149 0.130056927 8541645.969 4776230.312 7781593.06 0.028870003 0.013574216 1.867285251 -0.492715232 EHFQSYDLDHMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHFQSYDLDHMEK 13 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 ;;; 194.48 5.70E-07 548328000 553758 506206 620750 550720 776929 795062 728041 658762 686501 449417 FALSE TRUE 575620.7934 593142.9428 636927.255 659650.7723 644866.8861 610420.8998 670975.244 649932.3729 661793.9631 537471.6565 1.070978881 1.103579948 1.185043429 1.22732197 1.199815615 1.135726679 1.248391866 1.209240273 1.231309512 1 19.03582915 4.299876586 3.38403345 1.192929755 1.077501964 0.214590496 0.068275428 0.274581677 6.178164207 0.015641289 0.049302354 19946.95399 -4.299876586 -0.115427791 EHGAFDAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHGAFDAVK 9 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 99.688 0.0052152 0 1997190 1958840 2108260 1690570 3363900 2816700 2643100 2031350 2216900 2199000 FALSE TRUE 2076040.603 2295255.532 2163202.988 2024959.7 2792105.48 2162564.113 2435926.916 2004123.076 2137114.202 2629851.948 0.78941349 0.872769866 0.822556946 0.76999 1.061696831 0.822314014 0.926260095 0.762066883 0.812636698 1 21.32655015 6.292105131 0.82050428 0.866793389 4.23E-07 0.06302557 0.093055565 97.3207134 6.35980835 0.030281951 132.6806264 1959318.916 -6.292105131 -0.866792966 EHGAVAVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHGAVAVER 9 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;; 101.38 0.0040217 2562290000 303756 515913 473421 455839 469725 549532 408585 433244 442055 544809 FALSE TRUE 315748.5214 604517.0445 485758.7402 546002.5937 389881.3123 421911.5212 376559.0401 427437.0728 426145.5269 651553.8926 0.484608449 0.9278082 0.745538851 0.838000663 0.598386897 0.647546621 0.577939975 0.656027195 0.654044941 1 19.31352499 -1.089825579 4.349529481 1.00003465 0.684832349 0.381252648 0.121794626 4.02E-05 8.41E-06 0.115843496 0.027301576 0.081315703 1.089825579 -0.315202302 EHGLIFMETSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHGLIFMETSAK 12 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 144.57 5.98E-05 270340000 658360 590130 654710 624710 871860 944380 751060 643080 664250 590280 FALSE TRUE 684352.5612 691480.2369 671772.2805 748275.7734 723661.5486 725062.0572 692189.9547 634460.5645 640343.7723 705934.0644 0.969428443 0.979525244 0.951607685 1.059979694 1.025112096 1.027096005 0.980530604 0.898753292 0.907087226 1 19.42917391 1.920816393 5.517340028 0.926394198 1.002621463 0.363292308 0.038997538 0.215071483 11.07448622 0.017770949 0.010731642 83.33288027 -1.920816393 0.076227265 EHGTVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHGTVLLR 8 0 O75382;O75382-3;O75382-4;E9PMK8 O75382 TRIM3 Tripartite motif-containing protein 3 0 127.56 0.0011709 256770000 17366 42935 47150 45566 45216 53607 34089 41124 34600 59279 FALSE TRUE 18051.62309 50308.75226 48378.76773 54578.8188 37530.20047 41157.58667 31417.0151 40572.80005 33354.75276 70893.58508 0.254629852 0.709637581 0.682413898 0.76986964 0.52938782 0.580554455 0.443157375 0.572305661 0.470490422 1 16.11336747 -1.143900167 4.164077977 1.000117372 0.566797326 0.469500862 0.14093912 19494900.92 5355391.416 20808.15129 0.032187158 0.071795931 1.143900167 -0.433320046 EHGVLGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHGVLGGK 8 0 O95865;A0A140T971;Q5SSV3;Q5SRR8 O95865 DDAH2 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 ;; 74.301 0.041332 574400000 1651970 1604000 1780280 1528630 2232990 2351070 1981470 1859280 1915160 1687210 FALSE TRUE 1717191.051 1879474.523 1826675.559 1830988.451 1853427.157 1805069.623 1826157.204 1834359.393 1846233.766 2017786.496 0.85102713 0.931453613 0.905286839 0.907424277 0.918544733 0.894579098 0.905029946 0.90909489 0.914979741 1 20.9443421 -5 0.299903967 1.788733598 0.900385871 0.692190072 0.019448322 141.8160907 1.311855601 70.28628054 0.017867157 1.00E-05 5 -0.888347727 EHHFGSSGMTLHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EHHFGSSGMTLHER 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;;; 130.61 2.12E-05 494806000 250085 379703 377692 366795 396589 491847 402397 386421 358566 441119 FALSE TRUE 259958.5489 444914.0366 387534.9638 439345.9562 329176.9434 377622.9883 370856.0717 381241.6586 345661.2797 527547.8223 0.492767741 0.843362474 0.734596841 0.832807828 0.623975552 0.71580807 0.702980954 0.722667486 0.655222645 1 19.00894235 -1.212981637 4.143254598 1.000158401 0.71067388 0.463557801 0.095602921 0.000128052 2.43E-05 0.084578273 0.019924409 0.061237628 1.212981637 -0.289484521 EHIEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EHIEELLR 8 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ;;;; 172.21 0.00028488 1356090000 1297185 1436531 1471920 1407664 1667704 1725017 1469141 1397327 1437878 1443278 FALSE TRUE 1348398.865 1683244.025 1510279.444 1686095.738 1384228.27 1324407.945 1353985.89 1378598.117 1386129.052 1726060.691 0.781200147 0.975193997 0.874986292 0.976846148 0.801958052 0.767300913 0.784437011 0.798696201 0.803059278 1 20.71905176 3.210341809 24.82032571 0.809411379 0.905347165 0.15794438 0.080781625 255.2226886 224484.6303 0.021468076 0.0256642 1623.087036 -3.210341809 0.095935786 EHIKNPDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EHIKNPDWR 9 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 126.39 0.00028535 3266020000 2185410 2299920 2601140 2349490 3137980 3123840 2599050 2435790 2596280 2492300 FALSE TRUE 2271691.674 2694913.369 2668927.845 2814212.109 2604587.28 2398375.502 2395329.67 2403142.219 2502840.39 2980618.467 0.762154465 0.9041457 0.895427535 0.944170527 0.873841221 0.804656996 0.803635117 0.806256234 0.839705054 1 21.50718028 2.889755513 6.913519905 0.832657547 0.883276377 0 0.070247227 0.582462754 32.26191677 0.020545193 0.021853902 775.8102504 -2.889755513 0.050618829 EHIYDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;; 149.4 0.0020189 1558050000 2648250 2994790 2685160 2792430 3306350 3481960 2669420 2632840 2667910 3164860 FALSE TRUE 2752804.955 3509121.886 2755137.475 3344764.319 2744337.808 2673327.56 2460183.885 2597551.086 2571892.44 3784953.722 0.727302143 0.927124119 0.727918405 0.883700189 0.725065089 0.706303896 0.64999048 0.686283447 0.679504329 1 21.85184423 3.125305733 7.993585871 0.714503599 0.817849428 0.072621824 0.109701773 0.401871144 26.64306559 0.029099137 0.034855679 1334.460529 -3.125305733 0.103345829 EHKLDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHKLDGK 7 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;; 103.74 0.0049921 799660000 1928640 1082300 1561700 943390 2252300 1887450 1620910 1482910 1771530 1147140 FALSE TRUE 2004784.196 1268176.606 1602399.185 1129989.726 1869454.851 1449118.342 1493858.839 1463034.017 1707772.981 1371900.12 1.461319354 0.924394267 1.168014465 0.823667634 1.362675623 1.056285601 1.088897666 1.066428959 1.244823116 1 20.38774402 3.297868248 0.01151516 8.49E-07 2.241431859 0.041444095 0.180966106 12657.5879 40.32401802 3743.58561 4105.562153 1985.492488 -3.297868248 2.241431009 EHLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHLASK 6 0 Q96TA1;Q96TA1-2;Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q96TA1;Q9P0K7-3 FAM129B;RAI14 Niban-like protein 1;Ankycorbin 0 ;;; 111.81 0.027528 1054580000 4345790 3755550 4852300 3815030 5805100 5651000 5557400 4715300 5245300 3933370 FALSE TRUE 4517365.145 4400536.498 4978754.924 4569631.547 4818351.176 4338640.892 5121796.466 4652099.116 5056522.678 4704038.543 0.960316355 0.935480536 1.058400113 0.971427318 1.024300956 0.922322564 1.088808355 0.988958546 1.074932238 1 22.16546845 2.235267069 24.99993797 1.033921269 0.982106933 0.276794166 0.046695678 126.9012659 963240.6215 0.016276554 0.01251742 171.8965138 -2.235267069 -0.051814336 EHLELFWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 200.86 2.24E-05 4204150000 2940150 3158750 3392910 3369270 4719870 4469930 3707190 3146690 3088970 4085190 FALSE TRUE 3056229.392 3701240.741 3481332.022 4035701.55 3917588.183 3431856.5 3416610.761 3104513.767 2977798.573 4885604.765 0.625558051 0.757580877 0.712569311 0.826039302 0.80186351 0.702442515 0.699321972 0.635441039 0.609504599 1 22.22010573 -2.175624185 2.473562422 1.789419897 0.709695683 0.619749455 0.068646462 12013966.36 3654961.935 52869993.9 0.017967559 0.00667384 2.175624185 -1.079724214 EHLIDELDYILLPTEGWNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHLIDELDYILLPTEGWNK 19 0 Q9Y4E8;F8W0H4;H0YI31;Q9Y4E8-4;F8VZG8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 95.015 0.0014697 0 40483 30928 36854 34933 45392 47128 46421 35203 39779 32402 FALSE TRUE 42081.3001 36239.64341 37814.44552 41842.64314 37676.28405 36183.23623 42782.40072 34731.16137 38347.36156 38750.55153 1.085953579 0.935203294 0.975842769 1.079794777 0.972277363 0.933747645 1.10404624 0.896275279 0.989595246 1 15.24192922 1.704253046 25 0.955377693 1.006072063 0.108895638 0.063544654 1.468494213 1062.481034 0.028000158 0.015527481 50.61194719 -1.704253046 0.050694369 EHLIQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHLIQLR 7 0 B5MD46;Q9BXI6;Q9BXI6-2;H0Y2U5;H7C1Q1 B5MD46 TBC1D10A TBC1 domain family member 10A 0 91.041 0.016695 32285000 44351 53987 41600 50594 62378 57020 48404 45829 48380 56474 FALSE TRUE 46102.01173 63258.84729 42684.13017 60601.34219 51775.00984 43777.96915 44609.968 45214.73722 46638.81325 67538.99904 0.682598386 0.936626959 0.631992342 0.897279247 0.766594273 0.648188006 0.660506798 0.669461168 0.690546409 1 16.04343318 4.224971994 24.9884581 0.729006003 0.809612768 0.026392572 0.126921977 589.4485596 1083956.967 0.02999406 0.065359589 16786.95761 -4.224971994 0.080606765 EHLLSYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHLLSYLEK 9 0 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 88.496 0.012745 364570000 268280 214130 238670 244040 535770 358300 291940 243570 251530 460120 FALSE TRUE 278871.9016 250905.1618 244889.9363 292310.3836 444700.0068 275090.2551 269056.98 240305.3426 242477.4844 550271.7045 0.506789463 0.455965952 0.445034579 0.531211002 0.808146236 0.499917137 0.488952962 0.43670307 0.440650469 1 19.06978462 -0.926223072 4.194703717 1.000014691 0.511265962 0.666088458 0.103524522 29381849.09 62181617.19 6689.835277 0.026571625 0.118515984 0.926223072 -0.488748729 EHLLVSIPLLINHLQAESIVVHTYAAHALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHLLVSIPLLINHLQAESIVVHTYAAHALER 31 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 ;; 238.36 2.49E-46 3684518000 242040 277841 369282 326471 423491 436614 378343 341251 369089 361126 FALSE TRUE 251595.9261 325558.0304 378905.7923 391045.9894 351506.1511 335217.0154 348687.487 336677.0885 355805.559 431881.7255 0.582557472 0.753812934 0.877336942 0.905446946 0.813894477 0.776177818 0.807368005 0.779558543 0.823849536 1 18.72027675 -5 0.172163611 1.76889992 0.749558158 0.411097686 0.07933443 154.4193725 1.46432889 40.93302043 0.295430333 1.00E-05 5 -1.019341763 EHMGDILYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHMGDILYK 9 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 107.21 0.0028113 819530000 1627500 1655670 1789280 1592560 2004010 2231280 1965480 1714910 1818570 1910560 FALSE TRUE 1691754.957 1940018.443 1835910.107 1907563.615 1663369.096 1713099.035 1811420.542 1691924.436 1753120.021 2284897.652 0.740407324 0.849061419 0.803497743 0.834857357 0.727984072 0.749748696 0.792779729 0.740481498 0.767264135 1 21.12369811 -1.276386999 9.119039882 1.000000056 0.778438015 0.741686502 0.039223776 4.55E-08 3.61E-09 0.038804985 0.00914642 0.052919167 1.276386999 -0.221562041 EHMQPTHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 EHMQPTHPIR 10 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;;;;;;;;;;;; 124.42 0.00030517 4658580000 1754339 2062597 1946620 2087256 2147802 2363642 2226050 2066332 1976995 2010429 FALSE TRUE 1823601.658 2416831.99 1997350.516 2500109.007 1782719.383 1814721.967 2051566.384 2038636.199 1905843.336 2404334.071 0.758464342 1.005198079 0.830729199 1.039834288 0.741460767 0.75477114 0.853278423 0.847900558 0.792669937 1 21.19720593 EHNGQVTGIDWAPESNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EHNGQVTGIDWAPESNR 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;;; 180.31 8.67E-10 4029660000 2397030 2445560 2453140 2322292 2636610 3230620 2819940 2492290 2493102 2390910 FALSE TRUE 2491666.595 2865565.906 2517070.844 2781634.426 2188439.974 2480357.466 2598905.734 2458884.929 2403375.746 2859363.038 0.871406171 1.002169318 0.880290754 0.97281611 0.765359258 0.867451049 0.908910726 0.859941496 0.840528367 1 21.44726237 EHNSMWASLS(ph)SPDAEAVEPDFSSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWAS(0.127)LS(0.509)S(0.364)PDAEAVEPDFSSIER 135.88 9.36E-05 142140000 48927 55395 71957 58918 87938 99695 63078 69227 56334 62376 TRUE FALSE 50858.67574 64908.66034 73832.25853 70571.80455 72990.33017 76542.34714 58133.78154 68299.1253 54306.55034 74597.38294 0.681775603 0.870119806 0.989743281 0.94603593 0.978456982 1.026072821 0.77930055 0.915569992 0.727995383 1 16.1868374 7.999889014 0.008989147 1.696447893 4.52E-06 0.046699359 0.113197087 86619.95205 60.19766736 4968.074532 6486.249908 99974447.84 -7.999889014 -1.696443372 EHNSMWASLSS(ph)PDAEAVEPDFSSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EHNSMWASLSSPDAEAVEPDFSSIER 26 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 EHNSMWAS(0.001)LS(0.029)S(0.971)PDAEAVEPDFSSIER;EHNSMWASLS(0.183)S(0.817)PDAEAVEPDFSSIER;EHNSMWASLS(0.22)S(0.78)PDAEAVEPDFSSIER;EHNSMWAS(0.001)LS(0.097)S(0.902)PDAEAVEPDFSSIER;EHNSMWAS(0.001)LS(0.048)S(0.951)PDAEAVEPDFSSIER;EHNSMWASLS(0.033)S(0.967)PDAEAVEPDFSSIER;EHNS(0.001)MWAS(0.01)LS(0.193)S(0.796)PDAEAVEPDFSSIER 245.51 1.57E-45 2152030000 131198.4 651557 536193 636873 533794 906086 428726 752767 499200 778325 TRUE FALSE 136378.2141 763456.8463 550166.6301 762844.5785 443059.8865 695661.2584 395121.3359 742677.3896 481233.8895 930822.8818 0.146513603 0.820195615 0.591054046 0.819537845 0.475987317 0.747361579 0.424486058 0.797871866 0.516998345 1 19.82814715 -5 0.231470841 3.072754054 0.570484207 0.26413711 0.203865521 218.1456427 2.182204511 212.3200896 0.315667817 1.00E-05 5 -2.502269847 EHPDAWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHPDAWTR 8 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;H7BZC5 O14980 XPO1 Exportin-1 0 ; 97.635 0.0080918 1169330000 1249230 1263500 1386610 1307430 1357150 1544960 1369690 1350300 1305100 1139450 FALSE TRUE 1298550.565 1480496.296 1422746.196 1566035.752 1126462.128 1186166.454 1262330.119 1332201.437 1258129.706 1362703.411 0.95292237 1.086440589 1.044061521 1.149212469 0.826637784 0.870450932 0.926342525 0.977616572 0.923260113 1 20.37804017 3.239824811 24.99999547 0.921678637 1.059172346 0.523163387 0.064275044 27.58025306 545402.7162 0.018452414 0.023668585 1737.099963 -3.239824811 0.137493709 EHPDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHPDYK 6 0 P48431;O95416;Q9Y651;O00570 P48431 SOX2;SOX14;SOX21;SOX1 Transcription factor SOX-2;Transcription factor SOX-14;Transcription factor SOX-21;Transcription factor SOX-1 0 91.584 0.047726 107660000 385090 296120 341550 287650 457340 429720 339400 344400 336100 248410 FALSE TRUE 400293.6506 346976.3065 350451.0736 344546.3115 379601.5102 329924.0425 312796.9411 339783.8813 324003.8267 297081.1834 1.347421758 1.167951139 1.179647494 1.159771573 1.277770291 1.110551798 1.052900549 1.143740837 1.090623859 1 18.1804977 8 0.107151433 0.928587778 1.969668717 0.639761203 0.058053289 76.20711151 0.57185945 0.575556034 11.71429487 100000000 -8 1.041080939 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQR 34 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 0 166.88 1.30E-14 29702000 20450 20506 27509 22641 31023 33089 28008 27155 26664 23812 FALSE TRUE 21257.38179 24027.74599 28225.90714 27119.32222 25749.72154 25404.58122 25812.65977 26791.03164 25704.36785 28477.50549 0.746462214 0.843744758 0.991165014 0.952306803 0.904212679 0.892092927 0.906422783 0.940778737 0.902620065 1 14.79753516 4.50208018 3.878953223 0.93090436 0.757679581 0.732431616 0.036186717 0.109498774 3.484449032 0.008852247 0.037575238 31774.6064 -4.50208018 -0.173224779 EHPHS(ph)RS(ph)PS(ph)PEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHPHSRSPSPEPR 13 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 3 EHPHS(1)RS(1)PS(1)PEPR 94.325 0.023456 334040000 154620 151880 125600 154040 145330 168360 150900 143060 121090 125480 TRUE FALSE 160724.517 177964.2085 128873.2392 184508.6522 120626.8585 129260.9415 139072.0637 141142.5147 116731.9946 150065.4035 1.071029786 1.185910972 0.858780479 1.229521581 0.803828569 0.861364035 0.926743009 0.94054 0.777874126 1 17.19523189 3.22543079 24.98694657 0.887903536 1.077172877 0.447604328 0.109312084 211.0035867 401553.3306 0.029901956 0.035939855 1680.470101 -3.22543079 0.189269342 EHPVIESHPDNALEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHPVIESHPDNALEDLR 17 0 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 171.98 9.59E-10 97825000 65195 69707 76852 86678 69940 87898 95162 79211 72572 57036 FALSE TRUE 67768.94894 81678.635 78854.82625 103822.6497 58051.62378 67485.02161 87702.95378 78149.30611 69960.1479 68211.11218 0.993517724 1.197438839 1.156040764 1.522078242 0.851058162 0.989355245 1.285757569 1.145697579 1.025641507 1 16.05771917 3.212696686 24.99971896 1.076125876 1.21147965 0.193812594 0.162038243 463.4131473 447927.5515 0.048444323 0.057920338 1631.911812 -3.212696686 0.135353774 EHPWEVMPDLYFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHPWEVMPDLYFYR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 146.96 8.16E-06 216990000 304370 298330 309440 401590 348850 423990 491300 349510 335130 254710 FALSE TRUE 316386.7626 349565.8568 317504.2606 481023.3034 289552.6016 325524.7481 452790.6222 344825.3901 323068.7368 304615.5478 1.038642856 1.147564067 1.042311408 1.579116059 0.950550961 1.068641278 1.486433065 1.132001937 1.060578618 1 18.21663005 EHPWEVMPDLYFYRDPEEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHPWEVMPDLYFYRDPEEIEK 21 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;; 166.25 8.20E-12 165684000 250459 169537 229061 219830 265973 308065 368237 258105 259112 121389 FALSE TRUE 260347.3147 198653.6609 235030.5178 263311.7179 220763.0045 236521.5725 339373.6217 254645.5246 249786.6097 145172.8504 1.793360907 1.368394024 1.618970194 1.813780725 1.520690706 1.629241086 2.337721005 1.754085037 1.720615177 1 17.14741215 2.433239642 24.99999582 1.809893395 1.614830372 0 0.329648169 367.0880568 209133.4809 0.107631208 0.090050768 271.1687518 -2.433239642 -0.195063023 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EHPWEVMPDLYFYRDPEEIEKEEQAAAEK 29 2 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ;;;;;; 236.6 1.90E-45 1837150000 1681048 767355 1187016 781964 1805892 1688888 1655390 1180933 1453207 672140 FALSE TRUE 1747417.073 899142.2521 1217950.612 936634.1453 1498927.123 1296669.357 1525636.206 1165104.525 1400906.364 803832.9641 2.173855952 1.118568524 1.515178733 1.165209922 1.864724625 1.613107966 1.897951781 1.44943611 1.742782924 1 19.61653622 3.223499652 24.99955593 1.626710639 1.468013197 0.01233035 0.358093972 841.6122792 1396981.827 0.096132072 0.115323527 1673.014296 -3.223499652 -0.158697442 EHPYLFSQCQAIHCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHPYLFSQCQAIHCR 15 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 180.06 3.73E-07 1025030000 91298 109841 94475 108541 132865 177429 101307 129536 109654 149249 FALSE TRUE 94902.51554 128705.3373 96937.09611 130010.0858 110280.6548 136223.8037 93366.29262 127799.7818 105707.574 178491.484 0.53169212 0.721072706 0.543090874 0.72838257 0.617848271 0.763194975 0.523085419 0.715999323 0.592227548 1 17.44549572 -2.222549201 2.384589377 2.210695653 0.643277699 0.617353092 0.08552847 4977559.007 950000.1994 32534211.72 0.018176748 0.005990331 2.222549201 -1.567417953 EHQEDPEMLIDLMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHQEDPEMLIDLMYR 15 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0;K7ESB7;Q96HP0 Q96N67-2;K7ESB7;Q96HP0 DOCK7;DOCK6 Dedicator of cytokinesis protein 7;Dedicator of cytokinesis protein 6 0 122.1 0.00011096 15424000 52475 34254 41962 39281 49499 60359 51227 40803 45300 28119 FALSE TRUE 54546.75352 40136.85804 43055.56419 47050.66456 41085.17766 46341.537 47211.69388 40256.10253 43669.66185 33628.37968 1.62204525 1.193541242 1.280334188 1.399135641 1.221741221 1.378048465 1.403924136 1.19708719 1.29859548 1 15.03739165 -4.331785869 0.174241069 1.97E-10 1.40078523 0.452493698 0.116728946 94.39660967 1.110954352 33.10521162 0.383597301 4.66E-05 4.331785869 1.40078523 EHQIPEFDNLYLDMNGIIHQCSHPNDDDVHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHQIPEFDNLYLDMNGIIHQCSHPNDDDVHFR 32 0 Q8IZH2-2;Q8IZH2;Q8IZH2-3;F8WDA0 Q8IZH2-2 XRN1 5-3 exoribonuclease 1 0 139.93 2.10E-10 53647000 11886 14323 15724 16137 17135 18724 13183 15317 14936 16571 FALSE TRUE 12355.26846 16782.86383 16133.78036 19328.85044 14222.39882 14375.63476 12149.68201 15111.70067 14398.45628 19817.77018 0.623443927 0.846859343 0.814106744 0.975329225 0.717658884 0.725391133 0.613070083 0.762532845 0.726542701 1 14.27450702 EHQISPGDFPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHQISPGDFPSLR 13 0 A0A024R571;Q9H4M9;C9JC03;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 98.943 0.0030876 624300000 194350 243560 263840 238500 267200 291910 223010 247400 226470 274430 FALSE TRUE 202023.0881 285389.5354 270715.8871 285674.5881 221781.4394 224118.3264 205529.8935 244084.0077 218319.3889 328199.3042 0.615550019 0.869561671 0.824852106 0.870430207 0.675752314 0.682872643 0.626235007 0.743706658 0.665203692 1 18.32421265 3.225870224 24.99972975 0.711945577 0.802542566 0.045987879 0.118420713 466.8619964 919703.9662 0.031868477 0.038326747 1682.17132 -3.225870224 0.090596989 EHQMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHQMAK 6 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;B7Z4S1;S4R3M9;O75764 A0A1W2PRL9;S4R3M9 TCEA1;TCEA3 Transcription elongation factor A protein 1;Transcription elongation factor A protein 3 0 ;; 83.843 0.056526 173740000 274526 243591 269608 207522 323899 294544 329533 261695 293083 254928 FALSE TRUE 285364.4985 285425.8594 276634.206 248569.2322 268842.7637 226140.6199 303703.3424 258187.4066 282535.0001 304876.2607 0.936001044 0.936202309 0.907365517 0.815311863 0.881809437 0.741745583 0.996152805 0.84685966 0.926720235 1 18.21786429 -0.132843568 6.5658606 1 0.88495329 0.19514026 0.068310934 939330.2807 158958.642 0.06296532 0.015271333 0.736472326 0.132843568 -0.115046711 EHQTSAYS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EHQTSAYSPPR 11 0 H3BRF9;Q96K21-2;Q96K21;Q96K21-4;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 EHQTS(0.001)AY(0.005)S(0.994)PPR;EHQTS(0.002)AY(0.001)S(0.997)PPR;EHQT(0.001)S(0.001)AYS(0.998)PPR;EHQTSAY(0.001)S(0.999)PPR;EHQTS(0.008)AY(0.007)S(0.985)PPR 153.79 2.08E-05 2826120000 666212 869717 915771 966076 942245 1201610 1003130 953736 905522 907288 TRUE FALSE 692514.5642 1019084.129 939636.7446 1157162.949 782082.5315 922554.2881 924502.0494 940952.7289 872932.4401 1085053.713 0.638230676 0.939201551 0.865981779 1.066456836 0.720777711 0.850238359 0.852033442 0.867194608 0.804506201 1 20.04933503 -2.389858573 2.162157373 2.025233878 0.85284879 0.150114095 0.109229882 4003162.19 416449.0064 20132197.39 0.026206998 0.00407513 2.389858573 -1.172385088 EHQTSAYS(ph)PPRAGQEH ddPTM_MDA-MB-175_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(0.001)AYS(0.999)PPRAGQEH;EHQTSAYS(1)PPRAGQEH;EHQT(0.001)S(0.003)AYS(0.996)PPRAGQEH 201.32 2.02E-11 802941000 136027 290394 255017 160184 338112 368288 166577 261853 269192 356189 TRUE FALSE 141397.451 340266.9105 261662.9525 191867.9171 280639.843 282758.6935 153520.2595 258343.2888 259503.8325 425977.4149 0.331936497 0.798790966 0.614264849 0.450418051 0.658813902 0.663787993 0.360395303 0.606471798 0.609196224 1 18.70041742 0.612500927 2.262628862 0.999933824 0.565937538 0.479053303 0.136590155 2.42296236 13.13125659 0.123240474 0.0333376 4.097329846 -0.612500927 -0.433996286 EHS(ph)AFGDRPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHSAFGDRPEKR 12 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 EHS(1)AFGDRPEKR;EHS(1)AFGDRPEKR 73.833 0.019897 155193000 107450 73992 73287 66572 138509 133432 86166 85468 85563 74030 TRUE FALSE 111692.209 86699.55042 75196.91943 79739.7429 114965.2897 102444.4402 79412.08377 84322.44126 82483.60434 88534.76111 1.26156334 0.979271298 0.849349097 0.900660282 1.298532782 1.157109805 0.896959372 0.952421853 0.931652193 1 16.43395639 2.222967745 24.99030419 0.940902463 1.0621488 0.171608718 0.137307644 507.0684904 812660.7898 0.055457228 0.04110005 167.0966507 -2.222967745 0.121246337 EHS(ph)PSKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHSPSKEK 8 1 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 EHS(0.997)PS(0.003)KEK 94.767 0.0061323 71789000 130420 45577 71833 42197 121090 111250 112790 75083 99232 37710 TRUE FALSE 135569.0823 53404.49521 73705.02699 50543.44065 100507.1651 85413.87351 103949.2251 74076.6352 95660.6597 45098.5525 3.006062829 1.184173155 1.634310258 1.120733102 2.228611773 1.893938248 2.304934844 1.642550173 2.121147008 1 15.46079351 EHS(ph)PYGPS(ph)PLGWPSSETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 2 EHS(0.998)PY(0.002)GPS(1)PLGWPSSETR 115.34 0.00028083 50559000 33841 32130 34853 41572 40546 59724 35888 32006 31943 37201 TRUE FALSE 35177.06881 37648.07756 35761.29781 49794.81752 33654.0054 45854.00613 33075.00478 31577.01192 30793.37767 44489.82369 0.790676741 0.846217729 0.803808486 1.119240612 0.756442768 1.030662797 0.743428542 0.709758082 0.692144295 1 15.44118776 2.169076063 24.99983529 0.755863527 0.889406251 0.114391182 0.132415849 79.16150366 28479.95554 0.04683042 0.034586566 147.5965015 -2.169076063 0.133542723 EHSAFGDRPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHSAFGDRPEKR 12 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 216.06 2.40E-11 1096740000 763110 649560 776040 609813 965470 949300 765050 739970 805750 707920 FALSE TRUE 793238.172 761116.8771 796264.2399 730432.1913 801359.7543 728839.4618 705083.3819 730051.9125 776751.2149 846623.3701 0.936943392 0.899002914 0.940517671 0.862759306 0.946536302 0.860878033 0.832818236 0.862310135 0.917469612 1 19.69136079 2.724037577 24.75754412 0.879190597 0.914419927 0.000895618 0.04894615 1594.614347 2718347.639 0.014971778 0.014175471 529.7092744 -2.724037577 0.035229329 EHSLQVS(ph)PSLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 EHSLQVS(1)PSLEK;EHSLQVS(0.999)PS(0.001)LEK 248.25 6.37E-17 548060000 646320 444320 505000 411420 637220 678580 605670 517570 544130 455990 TRUE FALSE 671837.2127 520628.5037 518160.7149 492797.648 528905.572 520990.079 558196.0028 510632.8207 524546.8676 545332.51 1.231977189 0.954699186 0.950173894 0.903664533 0.969877208 0.955362223 1.023588347 0.936369667 0.961884461 1 19.05677664 4.739170558 24.97503603 0.959477734 1.231977273 0.871997038 0.03105092 15.58350851 637946.6469 0.007276015 0.043290665 54849.23289 -4.739170558 0.272499539 EHSNPNYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHSNPNYDK 9 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 160.53 6.52E-05 474660000 751280 537820 698300 607390 875600 901390 868760 680860 724680 499400 FALSE TRUE 780941.1145 630186.4013 716498.2717 727529.9291 726765.8248 692055.8332 800664.3211 671734.1854 698598.9084 597247.8684 1.307566181 1.055150524 1.19966652 1.218137339 1.216857963 1.158741403 1.340589667 1.124715919 1.16969678 1 19.18797027 0.703658343 1.390990016 1.000879634 1.202643846 0.386570195 0.077080643 1.009653606 3.128395208 0.068614491 0.02028319 5.054268891 -0.703658343 0.201764211 EHSNPS(ph)PSQDTDGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHSNPSPSQDTDGTK 15 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EHS(0.002)NPS(0.998)PSQDTDGTK;EHSNPS(0.998)PS(0.002)QDTDGTK;EHS(0.03)NPS(0.969)PS(0.001)QDTDGTK;EHS(0.009)NPS(0.959)PS(0.031)QDTDGTK 229.59 2.84E-13 965648000 1399645 940358 1252008 988834 1609660 1759260 1393810 1243781 1264992 858249 TRUE FALSE 1454904.065 1101857.172 1284636.357 1184422.414 1336050.568 1350698.527 1284559.53 1227110.15 1219465.185 1026406.459 1.417473606 1.073509584 1.251586392 1.153950663 1.301677865 1.315948974 1.251511541 1.195540167 1.188091885 1 19.96917072 0.676702726 1.189088463 1.00055468 1.243687966 0.417535145 0.087832043 1.025358802 2.35024719 0.078691772 0.024134114 4.750099708 -0.676702726 0.243133286 EHSPYGPS(ph)PLGWPSSETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHSPYGPSPLGWPSSETR 18 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 EHS(0.002)PYGPS(0.998)PLGWPSSETR;EHSPYGPS(1)PLGWPSSETR 184.68 3.67E-14 924890000 206203 261470 265580 340110 284320 422630 289510 270990 267960 319780 TRUE FALSE 214344.0537 306375.4385 272501.233 407382.7429 235991.388 324480.5875 266817.4497 267357.8223 258316.1719 382434.7684 0.560472194 0.801118161 0.712543041 1.065234588 0.617076185 0.848459958 0.697680943 0.699093922 0.675451589 1 18.54485416 -2.218786074 2.281179761 1.80042224 0.746391108 0.252282764 0.133097812 10957614.74 2017941.142 45267207.62 0.03053564 0.006042462 2.218786074 -1.054031132 EHTALLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EHTALLK 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ;;;;; 122.79 0.0043066 3251170000 5467960 4666050 5917640 4532840 7024320 6917530 6733360 5916990 6409700 4501590 FALSE TRUE 5683839.283 5467407.791 6071858.56 5429422.223 5830328.595 5311038.494 6205581.649 5837682.427 6179016.149 5383590.372 1.055771129 1.015569056 1.127845571 1.00851325 1.082981466 0.986523514 1.152684588 1.084347438 1.147750056 1 22.36013721 2.230620972 24.996326 1.102968351 1.048478239 0.16398719 0.054302646 281.9738838 887729.4706 0.018417377 0.013850816 170.0673607 -2.230620972 -0.054490112 EHTEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHTEPK 6 0 P20810-6;P20810-10;P20810;P20810-8;B7Z574;E7ES10;E9PDE4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;F8W7E0;A0A0C4DGB5;H0Y944;E7EN75;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;; 109.7 0.029331 682836000 2399520 1875490 2439540 1641870 2960650 3027100 2947990 2407350 2672780 1964340 FALSE TRUE 2494254.902 2197590.818 2503116.417 1966626.986 2457399.771 2324101.901 2716918.841 2375083.411 2576587.17 2349214.813 1.061739815 0.935457586 1.065511933 0.837142255 1.046051539 0.989310083 1.156522096 1.011011593 1.096786533 1 21.16374721 2.424879367 24.99990074 1.065286606 0.985558797 0.198728179 0.075443557 149.5891095 71583.57043 0.024357682 0.020379102 265.99861 -2.424879367 -0.079727809 EHTLAWK ddPTM_MDA-MB-175_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 234800000 548930 474270 586340 415150 880280 758150 696920 600570 640520 514860 FALSE TRUE 570602.1803 555722.1832 601620.5021 497265.4309 730650.32 582081.1524 642293.5893 592520.3415 617467.8103 615736.9594 0.926697954 0.902531795 0.977073883 0.80759393 1.186627356 0.945340609 1.043129829 0.962294584 1.002811023 1 19.23195464 3.266040397 24.99995934 1.015290307 0.908664256 0.388651278 0.073130354 242.5102362 220624.0567 0.01908215 0.025831667 1845.187046 -3.266040397 -0.106626051 EHVEEISELFYDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 ;; 151.99 6.79E-06 535058000 992360 715477 888430 757020 1111390 1081810 1150700 916170 949820 605295 FALSE TRUE 1031539.139 838354.6091 911583.2157 906756.2965 922476.3248 830576.0225 1060505.127 903890.2397 915636.1637 723890.9662 1.424992419 1.158122767 1.259282486 1.252614467 1.274330483 1.147377245 1.465006716 1.248655228 1.264881324 1 19.46541289 0.519223067 2.615100281 1.000006311 1.275991612 0.435299118 0.094824471 7.882505606 41.65664601 0.084831726 0.022502158 3.305392724 -0.519223067 0.275985301 EHVIEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EHVIEALR 8 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 123.72 0.0013355 4368550000 4508400 4775920 4865790 5214340 4634500 5667610 5608020 5062150 4868890 4135040 FALSE TRUE 4686395.113 5596147.108 4992596.485 6245720.889 3846729.345 4351393.471 5168448.739 4994300.159 4693659.6 4945221.918 0.947661236 1.131627094 1.009579867 1.262980912 0.777867891 0.879918746 1.0451399 1.009924376 0.949130227 1 22.23760383 3.237851031 24.99999212 0.952653794 1.085482418 0.313491111 0.104076511 25.90893357 912842.5 0.029854708 0.037753994 1729.22311 -3.237851031 0.132828624 EHVMNEVDTNKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EHVMNEVDTNKDR 13 1 P80303-2;P80303;E9PKG6;H0YD18 P80303-2 NUCB2 Nucleobindin-2;Nesfatin-1 0 ;;; 171.87 1.46E-05 1207533000 1737698 1430740 1620800 1788309 2899200 2673660 2400150 1710720 1828414 1574430 FALSE TRUE 1806303.659 1676458.465 1663039.38 2142031.183 2406395.02 2052742.985 2212019.971 1687790.597 1762609.737 1882909.414 0.95931522 0.890355347 0.883228565 1.137617756 1.278019538 1.09019742 1.174788311 0.896373763 0.936109684 1 20.84453216 3.746905116 24.77838348 1.073486664 0.908905262 0.3235488 0.107551865 730.3331337 2168664.217 0.031238875 0.05509998 5583.481942 -3.746905116 -0.164581401 EHVVAASK ddPTM_MDA-MB-175_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 ;; 117.89 0.001992 362960000 1415630 1269110 1533350 1363550 1992900 2015130 1735940 1469670 1652500 1400370 FALSE TRUE 1471520.166 1487069.77 1573310.361 1633256.12 1654147.57 1547146.597 1599872.487 1449971.478 1593026.848 1674745.69 0.878652905 0.887937661 0.939432399 0.975226346 0.987700748 0.923809869 0.955292793 0.865786063 0.951205223 1 20.67551061 4.25211963 4.791865553 0.94288069 0.881471128 0.343789054 0.03586106 0.234614098 13.76887115 0.009704482 0.025890356 17869.79745 -4.25211963 -0.061409562 EHVYDLFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHVYDLFEK 9 0 A0A499FI31;Q15020-4;Q15020;Q15020-2;A0A494C0L2;F8W667;F8VVK9;F8VZM2 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 152.97 7.92E-05 144230000 141220 114100 139450 142650 185600 185290 190300 155230 168190 113910 FALSE TRUE 146795.4746 133695.7874 143084.1816 170865.7442 154051.7783 142259.2056 175383.7887 153149.3958 162136.8748 136228.4836 1.077568147 0.981408469 1.050324997 1.254258579 1.130833833 1.044269171 1.287423776 1.124209796 1.190183363 1 17.05566886 3.943125953 11.13470524 1.154151978 1.026080808 0.266177075 0.084264492 0.965779529 187.7580806 0.020249863 0.036594618 8772.552038 -3.943125953 -0.12807117 EHWDAVYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHWDAVYER 9 0 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 0 ; 102.06 0.0036456 201951000 107240 134903 136230 140398 173622 165621 140775 135095 136976 165958 FALSE TRUE 111473.918 158071.5409 139780.2657 168168.3054 144109.7945 127158.0328 129740.6877 133284.2725 132046.2605 198474.2926 0.56165419 0.796433325 0.704273908 0.847305226 0.726087961 0.640677596 0.653690138 0.671544263 0.665306619 1 17.59859263 -1.39245775 3.674939797 1.001759229 0.699308154 0.586435459 0.076467213 12378880.02 4691835.448 172776.4778 0.017853863 0.040508135 1.39245775 -0.302451074 EHWSHDPFEAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHWSHDPFEAFK 12 0 A0A1B0GW23;Q03154;Q03154-2;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5;F8WC59 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 77.64 0.016121 86434000 26578 68725 64510 82492 75215 105262 74275 84080 72683 61803 FALSE TRUE 27627.31996 80527.98414 66191.1836 98808.67139 62429.98117 80816.49576 68453.13142 82953.04513 70067.15303 73912.11456 0.373786085 1.089509949 0.895539033 1.336840002 0.844651537 1.09341339 0.926142241 1.12232001 0.947979278 1 16.17352323 4.741527423 24.97832243 1.033371879 0.373785842 0.680192381 0.13463959 142.4705953 1199436.864 0.028829418 0.202506167 55147.70239 -4.741527423 -0.659586037 EHYLDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHYLDSK 7 0 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 ; 109.86 0.0069328 417860000 706210 538290 637930 576520 864790 864050 775430 615830 686200 499450 FALSE TRUE 734091.7161 630737.1202 654554.9799 690553.9353 717793.3047 663387.4823 714649.7704 607575.8061 661503.796 597307.665 1.229000998 1.055966895 1.095842257 1.156110956 1.201714538 1.110629448 1.196451699 1.017190707 1.10747582 1 19.18811471 1.715296786 9.765881817 1.047945505 1.144465736 0.433764514 0.056067989 0.108782159 26.37795517 0.025946573 0.013998426 51.9154695 -1.715296786 0.096520232 EHYLEDILAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHYLEDILAK 10 0 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 72.434 0.047998 88186000 73194 53433 64658 61702 82184 85865 82874 67445 75338 56307 FALSE TRUE 76083.75564 62609.7021 66343.0406 73906.47144 68214.39304 65924.15505 76378.11933 66541.01009 72626.6001 67339.27859 1.129857005 0.929764966 0.985205693 1.097523956 1.012995602 0.978985169 1.134228357 0.988145574 1.078517644 1 16.03916065 EHYPNGVCTVYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EHYPNGVCTVYGK 13 0 P47755;F8W9N7;A0A0D9SET8 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ; 148.52 3.90E-05 529150000 1153940 952340 1202690 1086160 1451860 1476900 1456810 1267050 1302430 1022890 FALSE TRUE 1199498.442 1115896.987 1234033.089 1300999.206 1205073.356 1133912.358 1342621.426 1250067.267 1255555.799 1223305.711 0.980538578 0.91219797 1.008769172 1.063511103 0.985095831 0.926924764 1.097535484 1.021876425 1.026363065 1 20.22235356 4.128135845 6.821458072 1.019503619 0.946984131 0.275394204 0.04536015 0.250617198 13.96501269 0.011384273 0.025003348 13431.85038 -4.128135845 -0.072519488 EHYPVSSPS(ph)SPS(ph)PPAQPGGVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 EHYPVSS(0.014)PS(0.545)S(0.44)PS(1)PPAQPGGVSR 148.1 3.87E-08 328410000 61580 92489 87198 93041 80714 99320 99885 79917 91460 93290 TRUE FALSE 64011.22595 108373.2663 89470.45151 111444.2321 66994.26311 76254.43521 92055.7527 78845.84333 88168.37247 111568.3894 0.573739805 0.971361753 0.801933702 0.998887165 0.600477102 0.683477064 0.825106047 0.706704146 0.790263021 1 16.7675688 -1.172181775 2.416172551 1.002229498 0.775455613 0.208904385 0.132732787 562248.8843 613555.7306 9644.953777 0.032645163 0.067269504 1.172181775 -0.226773884 EHYPVSSPSS(ph)PS(ph)PPAQPGGVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 EHYPVSSPS(0.032)S(0.968)PS(1)PPAQPGGVSR 183.25 2.28E-17 255860000 57787 71792 80775 69335 80689 90172 77014 83261 78199 73916 TRUE FALSE 60068.47538 84121.71754 82880.06286 83049.25606 66973.5126 69230.91957 70977.44144 82145.02248 75384.63327 88398.42499 0.679519747 0.951620094 0.937573977 0.939487961 0.757632419 0.783169152 0.802926539 0.929258892 0.852782539 1 16.43173304 0.565717965 0.995396525 0.999165668 0.849013224 0.215252649 0.087371267 2.418114337 3.660298793 0.085667873 0.027321323 3.678899846 -0.565717965 -0.150152444 EHYPVSSPSSPS(ph)PPAQPGGVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 EHYPVSSPS(0.003)S(0.054)PS(0.944)PPAQPGGVSR 156.7 6.34E-09 126490000 30866 40397 37207 41924 38207 52578 31386 37876 36429 33665 TRUE FALSE 32084.61351 47334.8705 38176.64499 50216.44207 31712.58779 40367.55633 28925.88331 37368.33417 35117.92741 40261.01219 0.796915223 1.175699962 0.948228644 1.24727222 0.787674876 1.002646335 0.718458919 0.92815188 0.872256446 1 15.29709582 3.210365231 24.99974541 0.878558189 1.044877236 0.231911283 0.139800353 275.3244001 244118.6109 0.03706404 0.044308283 1623.174574 -3.210365231 0.166319048 EHYVDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 23041360000 21578210 15099750 19460380 16060500 22650670 23733750 24532170 18877860 19983270 11310450 FALSE TRUE 22430134.39 17693014.6 19967533.49 19237218.96 18800517.2 18221946.25 22609274.41 18624833.16 19264076.02 13526516.13 1.658234403 1.308024508 1.47617711 1.422185786 1.38990092 1.347127825 1.671478022 1.376912798 1.424171297 1 23.68928697 0.422689531 1.67380335 1.000043295 1.452069853 0.582607581 0.115318201 3.042624032 8.074480731 0.102248698 0.02893799 2.646607455 -0.422689531 0.452026558 EIAATCSGTEWGQSSGAAS(ph)PGLFQAGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EIAATCSGTEWGQSSGAASPGLFQAGHR 28 0 P49757-3;P49757;G3V3Z8 P49757-3 NUMB Protein numb homolog 1 EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSSGAAS(1)PGLFQAGHR;EIAATCSGTEWGQSS(0.001)GAAS(0.999)PGLFQAGHR 363.3 2.12E-112 2618760000 775331 868801 840873 1004597 879018 1118537 973965 958003 856359 790171 TRUE FALSE 805941.6666 1018010.813 862786.8412 1203303.288 729602.8343 858773.7333 897623.0783 945162.5368 825538.8069 944989.8787 0.852857459 1.077271658 0.913011727 1.273350451 0.772074761 0.908765007 0.949875865 1.000182709 0.873595396 1 19.84993935 3.171102374 24.99999885 0.924888108 1.024322563 0.169352718 0.120328202 103.797808 38466.07217 0.033430492 0.039957095 1482.867593 -3.171102374 0.099434455 EIADYLAAGKDER ddPTM_MDA-MB-175_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 ;;; 204.13 7.32E-08 1914860000 1997090 1550170 1903460 1500690 2534610 2279210 2100460 1849280 2051780 1607010 FALSE TRUE 2075936.655 1816399.639 1953065.731 1797522.003 2103777.898 1749898.019 1935820.457 1824493.426 1977936.839 1921872.841 1.080163375 0.945119573 1.016230465 0.935297052 1.094649892 0.910517065 1.007257304 0.949330979 1.029171543 1 20.87408145 2.70394602 24.9997398 0.976280253 1.006168343 0.078744432 0.056147974 1813.401934 1309692.229 0.01679518 0.01583496 505.7617954 -2.70394602 0.02988809 EIAIVHS(ph)DAEKEQEEEEQKQEMEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIAIVHSDAEKEQEEEEQKQEMEVK 25 2 Q9H307 Q9H307 PNN Pinin 1 EIAIVHS(1)DAEKEQEEEEQKQEMEVK 70.632 0.020123 71828000 79967 34911 42188 43129 64495 78502 61272 40288 49213 28963 TRUE FALSE 83124.15891 40906.69268 43287.45394 51659.78747 53532.16294 60271.10021 56469.34054 39748.00526 47441.83374 34637.74532 2.399814368 1.180986011 1.249719159 1.491430432 1.54548636 1.740041093 1.630283381 1.147534428 1.369657098 1 15.0800574 8 0.044552253 8.51E-14 3.99882513 0.288914511 0.319552679 929.4307483 3.139801037 72.01262896 267.4158344 100000000 -8 3.99882513 EIAKS(ph)PHSTVPEHHPHPISPYEHLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIAKSPHSTVPEHHPHPISPYEHLLR 26 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 EIAKS(0.933)PHS(0.064)T(0.003)VPEHHPHPISPYEHLLR 182.56 6.61E-18 131690000 100080 132250 157690 132860 173610 166230 141430 150460 151950 150910 TRUE FALSE 104031.2357 154962.9087 161799.5309 159139.3115 144099.8342 127625.6017 130344.347 148443.3298 146481.3492 180477.9252 0.576420831 0.858625278 0.896505934 0.881766074 0.798434679 0.707153529 0.722217672 0.82250131 0.811630281 1 17.46146286 0.545150181 1.654284383 0.999899409 0.788617255 0.336586493 0.090761948 2.937743723 9.286073461 0.087761236 0.024941903 3.508731863 -0.545150181 -0.211282155 EIAVHIGDRDNAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIAVHIGDRDNAVR 14 1 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 ; 121.79 6.76E-05 213467000 116065 187922 190075 177123 204901 221032 144695 177599 185103 220835 FALSE TRUE 120647.3358 220196.1417 195028.5106 212157.4007 170072.0012 169700.6678 133353.4278 175218.5759 178441.1792 264103.3901 0.456818581 0.833749773 0.738455158 0.803311918 0.643959932 0.642553917 0.504928876 0.663446902 0.675648954 1 18.01074329 -1.853739981 5.625753009 1.050264437 0.665740647 0.45416904 0.110934502 0.055976369 0.00145529 0.085970113 0.025075386 0.014004255 1.853739981 -0.38452379 EIDCLS(ph)PEAQK ddPTM_MDA-MB-175_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 210176000 619760 406250 436790 398450 599720 645410 564270 488730 516490 406200 TRUE FALSE 644228.6034 476020.2773 448173.1062 477262.2207 497779.8086 495523.3088 520041.043 482179.3738 497901.6258 485787.1128 1.326154166 0.979894824 0.922571008 0.982451383 1.024687143 1.020042104 1.070512225 0.992573415 1.024937905 1 18.88996469 4.741008248 24.99820474 1.002645983 1.326154279 0.876419842 0.036519987 77.31476924 789585.7939 0.009500424 0.064232893 55081.81577 -4.741008248 0.323508297 EIDNFYPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIDNFYPER 9 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 215.14 1.51E-06 1158590000 1177570 1389620 1263880 1310890 1535190 1599660 1323780 1283360 1318400 1424060 FALSE TRUE 1224061.373 1628276.425 1296817.751 1570180.129 1274238.952 1228163.208 1220018.665 1266158.658 1270951.042 1703077.292 0.718735068 0.956078995 0.761455606 0.921966453 0.748197958 0.721143552 0.716361301 0.743453433 0.746267388 1 20.69971248 5.054477082 15.98695076 0.797375899 0.134622807 0.05335027 0.10167064 11974242.24 85142664.36 0.023561608 251235860.3 113364.5013 -5.054477082 -0.662753092 EIEAWIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIEAWIYR 8 0 A0A0A0MRB5;Q8WXG6-6;Q8WXG6-8;Q8WXG6-5;Q8WXG6-4;Q8WXG6-7;Q8WXG6-3;Q8WXG6-2;Q8WXG6;C9J6B0 A0A0A0MRB5 MADD MAP kinase-activating death domain protein 0 78.324 0.071936 63231000 36446 30728 27500 31510 38568 40187 38147 34133 26950 35237 FALSE TRUE 37884.91622 36005.29497 28216.67259 37742.58395 32012.22514 30854.17829 35156.93846 33675.50297 25980.07476 42141.0155 0.8990034 0.854400269 0.669577424 0.895625877 0.759645318 0.73216504 0.834268896 0.799114653 0.616503292 1 15.36293746 4.464104517 24.9231133 0.783790787 0.887852689 0.110252555 0.103169147 349.5930647 669365.8389 0.022883146 0.062741872 29114.17695 -4.464104517 0.104061902 EIEDFDSLEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;;; 193.52 6.28E-06 285930000 399829 429890 424475 502030 450140 542830 584210 482490 424010 337025 FALSE TRUE 415614.5577 503720.2634 435537.1672 601330.0356 373625.3636 416765.9592 538418.0937 476023.0107 408749.9629 403058.596 1.031151703 1.2497445 1.080580272 1.491917159 0.926975302 1.034008363 1.335830817 1.181026817 1.014120445 1 18.62063007 EIEDFDSLEALRLEGNTVGVEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIEDFDSLEALRLEGNTVGVEAAR 24 1 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 148.95 1.39E-07 26097000 24845 29241 36529 20275 31055 31887 19116 29594 32040 41577 FALSE TRUE 25825.89978 34262.91429 37480.97575 24285.33449 25776.28219 24481.7275 17617.63797 29197.34084 30886.88666 49723.21711 0.519393179 0.689072757 0.753792251 0.488410362 0.518395303 0.492360087 0.354314121 0.58719734 0.621176353 1 15.60163202 0.717027943 2.334975908 0.999815866 0.549276366 0.622502545 0.104575303 1.016562587 7.387099725 0.108008886 0.029136274 5.212282467 -0.717027943 -0.450539501 EIEELKELLPEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIEELKELLPEIR 13 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 ; 119.32 0.00032681 56583000 160449 126616 159253 113357 202582 197656 172798 154571 182211 124276 FALSE TRUE 166783.6504 148361.3131 163403.264 135778.6763 168147.184 151753.3895 159253.6412 152499.2286 175653.2617 148625.5028 1.122173835 0.998222447 1.099429512 0.913562435 1.131348126 1.021045424 1.071509521 1.026063668 1.181851421 1 17.18132216 EIEENSR ddPTM_MDA-MB-175_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 ; 139.68 0.0062246 492470000 371460 736340 524330 691740 546170 694690 476970 564530 445540 705700 FALSE TRUE 386125.5276 862800.6671 537994.4705 828564.1074 453332.2185 533358.7756 439583.8451 556963.3987 429505.1024 843968.4036 0.457511829 1.022313944 0.637458071 0.981747781 0.53714359 0.631965336 0.520853439 0.659933946 0.508911353 1 19.68682946 3.207394808 24.99912937 0.619977436 0.782633782 0.087182778 0.199763233 369.7431851 296582.3024 0.052225877 0.062427622 1612.110506 -3.207394808 0.162656346 EIEGEEIEIVLAKPPDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIEGEEIEIVLAKPPDKK 18 2 O43390;O43390-3;B4DT28;A0A286YEZ8;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 164.68 1.69E-11 80830000 168310 64425 115600 76699 150780 140230 165180 109480 150350 46931 FALSE TRUE 174955.0088 75489.49259 118612.631 91869.83328 125150.4695 107663.7077 152232.76 108012.5997 144938.9329 56126.2309 3.117170099 1.344994869 2.113319014 1.636843091 2.22980356 1.918242255 2.71232822 1.924458456 2.58237424 1 15.77638756 EIEHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIEHLSR 7 0 O95347-2;O95347;Q5T821 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 84.498 0.040077 0 36047 66180 57553 77225 65585 79961 62871 67966 64225 60841 FALSE TRUE 37470.16339 77545.90019 59052.87846 92499.87451 54436.88513 61391.26957 57943.00674 67055.02694 61913.5548 72761.62908 0.514971474 1.065752666 0.811593682 1.271272725 0.748153743 0.843731378 0.796340152 0.92157127 0.850909409 1 16.15089022 7.999975252 0.014033741 1.633655668 1.40E-13 0.040118572 0.187980781 37010.80651 40.10598439 1892.893009 2869.761572 99994301.7 -7.999975252 -1.633655668 EIEIDIEPTDKVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIEIDIEPTDKVER 14 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 ; 224.16 2.97E-12 5311200000 7317200 4794700 6418700 4905400 8208600 7451500 7427100 6387100 6668800 4646200 FALSE TRUE 7606088.706 5618152.427 6585976.595 5875673.479 6813305.104 5721002.054 6844944.495 6301491.372 6428791.191 5556533.933 1.368854901 1.011089376 1.185267052 1.057435003 1.226178979 1.029599049 1.231873066 1.134068728 1.156978661 1 22.40575381 -2.277888982 2.031051261 0.45005455 1.149905158 0.170989212 0.102137568 3301198.53 440388.0727 8337606.969 0.022743629 0.005273647 2.277888982 0.699850607 EIELTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIELTHR 7 0 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 98.299 0.023905 0 48051 66103 59346 58523 67327 71288 57227 58458 55961 73065 FALSE TRUE 49948.09058 77455.67604 60892.60551 70098.67473 55882.78059 54732.44238 52741.39821 57674.46613 53946.97454 87380.68784 0.571614756 0.886416415 0.696865715 0.802221595 0.639532395 0.626367722 0.603581861 0.66003676 0.617378689 1 16.41502684 -1.055163283 4.429135926 1.000018908 0.681081007 0.524846211 0.091813116 0.521023046 54078264.32 2451.595134 0.021441622 0.088071768 1.055163283 -0.3189379 EIENGNSFDSS(ph)GDELDVHQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIENGNSFDSSGDELDVHQLLR 22 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 EIENGNSFDS(0.013)S(0.987)GDELDVHQLLR 268.68 3.12E-38 42719000 30589 36037 31251 34318 35670 38687 32224 26525 30973 30197 TRUE FALSE 31796.67734 42226.07442 32065.42673 41105.99797 29606.82614 29702.53056 29698.19868 26169.47576 29858.28778 36113.52399 0.880464541 1.169259318 0.887906335 1.138243888 0.81982656 0.822476659 0.822356707 0.724644755 0.826789648 1 15.14025159 3.21282498 23.33792154 0.814359174 1.020341906 0.400533771 0.107706822 85.85443599 77855.10834 0.028710409 0.034331888 1632.393964 -3.21282498 0.205982732 EIENMILNDPDFQHEDLNFLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 EIENMILNDPDFQHEDLNFLTR 22 0 Q15067-2;Q15067;I3L0T4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;;;;;;;;;;; 306.49 1.64E-56 2166549000 928541 1174182 998762 1257568 1152493 1366638 1127565 1033788 1037249 1072540 FALSE TRUE 965200.5157 1375838.625 1024790.558 1506311.197 956592.6515 1049257.036 1039183.509 1019931.763 999918.6111 1282683.678 0.752485225 1.072625035 0.798942542 1.174343467 0.745774401 0.818016986 0.810163509 0.79515455 0.779551988 1 20.290734 EIENYPHFFLDFENAQPTEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIENYPHFFLDFENAQPTEGER 22 0 Q9H0Q0;C9JPE5;C9IYV6 Q9H0Q0 FAM49A Protein FAM49A 0 ;;; 184.26 3.97E-17 158045000 96154.6 107233.9 111857.6 120803.2 130147.6 142621.2 115773 115637.1 114693.8 121330 FALSE TRUE 99950.85786 125650.4882 114772.7009 144697.7124 108025.1574 109499.5877 106698.4097 114087.1738 110565.9925 145102.2905 0.688830325 0.865944209 0.790977872 0.997211773 0.744475894 0.754637211 0.73533236 0.786253431 0.761986542 1 17.14671077 -1.155765136 5.315267477 1.000006694 0.794411887 0.370945055 0.08129447 6.34E-06 1.01E-06 0.077354095 0.018231941 0.069861011 1.155765136 -0.205594807 EIEQEAAVELSQLRDPQHDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIEQEAAVELSQLRDPQHDLDR 22 1 P47985 P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial;Cytochrome b-c1 complex subunit 11" 0 ;; 208.39 4.17E-23 120203000 27168.8 38321 29119.8 42678 31098.4 56937 30220.3 30826.3 33108.9 52250 FALSE TRUE 28241.4452 44902.33365 29878.68591 51119.58102 25812.30508 43714.24464 27851.55392 30413.12387 31917.31716 62487.38711 0.45195433 0.718582353 0.478155469 0.81807839 0.413080243 0.699569092 0.445714811 0.486708203 0.510780153 1 15.9312774 -2.007727073 3.06504641 1.467002087 0.557796594 0.505404491 0.131153598 44510398.39 49527131.59 146416879.2 0.029199268 0.009823651 2.007727073 -0.909205493 EIES(ph)SPQYR ddPTM_MDA-MB-175_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(0.5)S(0.5)PQYR 85.813 0.015274 149430000 183530 179600 159430 153510 183130 218430 164570 154120 150430 181080 TRUE FALSE 190775.9061 210444.9029 163584.8768 183873.8198 152001.628 167702.9428 151670.5734 152054.2735 145016.0537 216559.159 0.880941296 0.971766347 0.755381936 0.849069698 0.701894248 0.77439783 0.700365545 0.702137348 0.66963713 1 17.72440166 4.007951345 1.284096733 0.740658877 0.934026958 0.224526838 0.099329268 0.613096201 1.775769237 0.027937163 0.110997891 10184.7728 -4.007951345 0.193368081 EIETFDMESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIETFDMESLR 11 0 Q9H2K8;G3V1Q8;F5GWV8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 0 95.573 0.017814 22458000 15841 17951 18215 22683 23453 21829 20254 17040 16189 19676 FALSE TRUE 16466.41491 21033.94461 18689.69786 27169.6297 19466.46744 16759.54557 18666.43856 16811.60667 15606.36105 23531.13548 0.69977137 0.893877162 0.794253974 1.154624677 0.827264262 0.71222851 0.793265526 0.714440945 0.663221758 1 14.52228332 2.999311692 24.99999955 0.758248167 0.89360008 0.11497247 0.137226163 43.88489696 1594048.35 0.038649376 0.045678409 998.4163673 -2.999311692 0.135351913 EIEVGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIEVGGGR 8 0 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;;; 205.38 0.00018589 1789070000 1245440 1372130 1339420 1391100 1374690 1690850 1470830 1398510 1303580 1303280 FALSE TRUE 1294610.933 1607782.654 1374326.386 1666255.428 1141020.685 1298175.713 1355542.501 1379765.261 1256664.41 1558632.763 0.830606775 1.031533978 0.881751249 1.069049405 0.732065123 0.832893895 0.869699735 0.885240766 0.806260743 1 20.57184962 3.239893586 24.99998033 0.851319384 0.95372208 0.226622975 0.089374547 49.90048085 935875.9088 0.023491163 0.030140131 1737.37507 -3.239893586 0.102402696 EIEVGGGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIEVGGGRK 9 1 P62081;B5MCP9 P62081 RPS7 40S ribosomal protein S7 0 ;; 114.89 0.0025079 4426310000 1785000 1480660 1908180 1380880 2198260 2063680 1787870 1724750 1791180 1491820 FALSE TRUE 1855473.178 1734951.837 1957908.738 1654013.942 1824600.55 1584421.595 1647732.078 1701632.547 1726715.782 1784113.566 1.039997236 0.972444731 1.097412617 0.927078844 1.022693053 0.888072164 0.923557843 0.953769188 0.967828402 1 20.76677602 3.717281535 24.99740165 0.951135515 1.03020086 0.397160474 0.045890315 758.9664816 891588.8255 0.011678885 0.01811547 5215.326889 -3.717281535 0.079065345 EIFAPLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIFAPLDER 9 0 F8VZZ2;Q8NFX7-2;Q8NFX7 F8VZZ2 STXBP6 Syntaxin-binding protein 6 0 95.502 0.018616 31796000 61245 71247 64010 51516 73331 74278 67792 61263 64019 62897 FALSE TRUE 63662.99989 83483.11803 65678.15318 61705.71104 60866.22281 57028.06019 62478.2859 60441.86969 61714.9687 75220.46291 0.846352142 1.109845842 0.873142103 0.820331445 0.809171075 0.758145563 0.830602252 0.803529616 0.820454519 1 16.19883756 4.013506133 24.72181399 0.822936457 0.981447828 0.304789366 0.084216432 186.3817003 341149.705 0.018818812 0.040619857 10315.87648 -4.013506133 0.15851137 EIFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EIFDSR 6 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 148.07 0.025152 24535300000 20832000 24727800 23554200 24895700 28719200 27596400 23966600 23118200 22394900 26401800 FALSE TRUE 21654463.45 28974607.29 24168041.8 29819995.15 23837520.64 21187554.33 22088035.27 22808338.34 21588911.92 31574727.22 0.685816327 0.917651864 0.765423614 0.944426058 0.754955711 0.671028895 0.699547936 0.722360582 0.683740251 1 24.91226693 5.050870457 15.09334387 0.779776358 0.135427215 0.063828306 0.112348481 1046151.825 8566162.757 0.026540043 19459101.87 112426.9573 -5.050870457 -0.644349143 EIFDSRGNPTVEVDLFTSKGLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIFDSRGNPTVEVDLFTSKGLFR 23 2 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 143.74 8.89E-08 282970000 225170 253420 322740 326370 75177 235490 212880 168140 281990 116290 FALSE TRUE 234059.8855 296942.9137 331150.8695 390925.0119 62398.44039 180801.0164 196193.9093 165886.3583 271841.235 139074.799 1.68297842 2.135130993 2.381099034 2.810897551 0.448668205 1.300027163 1.41070784 1.192785174 1.954640502 1 17.08550149 3.246800466 24.999967 1.241751722 2.253324794 0.575030117 0.435483311 136.1056104 412946.2642 0.12128273 0.161490474 1765.226611 -3.246800466 1.011573072 EIFVDFAPFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIFVDFAPFLSR 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 178.08 5.22E-05 326630000 133910 165780 198890 169030 239980 232810 173290 202160 166340 201680 FALSE TRUE 139196.8702 194251.4254 204073.2368 202463.6295 199188.2853 178743.4058 159707.077 199450.3759 160353.4559 241195.3346 0.577112615 0.805369746 0.846091145 0.839417685 0.825838052 0.74107323 0.662148284 0.826924684 0.664828182 1 17.87984248 -1.539955357 2.852231592 1.011500169 0.763464857 0.408748131 0.088029716 24753731.08 25709777.98 2187557.371 0.021517285 0.02884328 1.539955357 -0.248035312 EIGDLWGHLHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIGDLWGHLHDR 12 0 O75146;O75146-2 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ; 112.44 0.00073664 246290000 262089 239714 269194 311620 290775 320370 292435 257486 248185 236632 FALSE TRUE 272436.4761 280883.0148 276209.4168 373257.5059 241349.1694 245968.9228 269513.1806 254034.8213 239252.8703 282995.5098 0.962688335 0.992535235 0.976020492 1.318952043 0.852837451 0.869161927 0.952358505 0.897663788 0.845429917 1 18.11041964 EIGDVENWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIGDVENWAR 10 0 G8JLQ3;P78537-2;P78537 G8JLQ3 BLOC1S1 Biogenesis of lysosome-related organelles complex 1 subunit 1 0 ;; 107.79 0.0052054 182173000 178828 204180 208691 193678 216890 268216 209046 208357 212356 220350 FALSE TRUE 185888.2675 239246.3267 214129.6589 231986.9303 180023.1153 205926.8989 192660.4283 205564.3152 204713.349 263523.3636 0.705395776 0.907875201 0.812564229 0.880327752 0.683139107 0.78143697 0.731094297 0.780061063 0.776831876 1 18.00757135 -1.326395835 3.022439159 1.001958593 0.785786559 0.483647663 0.066845363 20086734.09 25740155.8 354371.4319 0.016370748 0.047163298 1.326395835 -0.216172034 EIGDYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIGDYIR 7 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 134.85 0.0072917 300210000 864390 894620 861170 810630 1079120 1125660 953610 925090 913590 929290 FALSE TRUE 898516.7847 1048264.026 883612.7977 970970.1945 895691.5679 864242.5245 878863.5564 912690.6817 880710.0744 1111366.583 0.808479217 0.943220753 0.795068712 0.873672296 0.805937106 0.777639473 0.790795377 0.821232792 0.792456861 1 20.08390334 5.079081933 15.03459659 0.834537733 0.405985144 0.005558382 0.070848925 5633255.783 19066571.55 0.015746116 77096357.58 119972.5619 -5.079081933 -0.42855259 EIGEATEHLTQLEADLTDVQDENFNANHALSGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIGEATEHLTQLEADLTDVQDENFNANHALSGLER 35 0 P55268 P55268 LAMB2 Laminin subunit beta-2 0 ; 337.93 3.60E-118 79852000 12769.6 27158 23353.9 25612 29068 31738 21635 23929.2 19541.2 24967 FALSE TRUE 13273.75367 31822.17524 23962.52182 30677.97716 24127.03174 24367.33049 19939.19217 23608.46821 18837.91603 29858.80563 0.444550724 1.065755129 0.802527808 1.027434839 0.808037403 0.816085238 0.667782644 0.790670213 0.630899851 1 14.86586884 2.591151861 3.109833303 0.7552067 0.852527782 0.008330879 0.182239069 0.821887137 15.15254595 0.059377244 0.054598335 390.0783629 -2.591151861 0.097321082 EIGTHKPLPGITVGDIGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIGTHKPLPGITVGDIGPK 19 1 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 113.53 0.0001053 660980000 2047620 1510610 1701700 1593300 2419100 2307700 2045680 1684220 2001500 1099930 FALSE TRUE 2128461.619 1770045.517 1746047.7 1908449.984 2007902.246 1771771.649 1885334.256 1661645.786 1929466.406 1315440.224 1.618060311 1.345591753 1.32734857 1.450807075 1.526410862 1.346903961 1.433234458 1.263186084 1.466783797 1 20.32711426 -3.465855761 0.234808422 2.65E-10 1.4606185 0.631043967 0.097288832 47.05126253 0.899606185 22.89247106 0.161020804 0.000342093 3.465855761 1.460618499 EIHQDWANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EIHQDWANR 9 0 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ;;;;; 186.78 4.13E-05 2877360000 829997 935622 899749 1043881 1189093 1258091 1089653 937681 879425 1227836 FALSE TRUE 862765.9225 1096307.8 923197.1981 1250357.546 986971.3966 965918.4318 1004243.151 925112.9199 847774.666 1468406.956 0.587552326 0.746596709 0.628706636 0.851506145 0.672137511 0.657800229 0.68389975 0.630011262 0.577343129 1 20.48582042 -1.585285907 2.988760413 1.018754487 0.674007947 0.627326715 0.076121847 23549437.61 24516897.24 3482029.942 0.018336928 0.025984484 1.585285907 -0.34474654 EIHQFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EIHQFNR 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 158.12 0.0014326 2301505000 1719305 2224800 1937492 2009010 2081840 2567130 1911039 1877683 1813435 2145560 FALSE TRUE 1787184.489 2606892.093 1987984.633 2406386.182 1727969.58 1970952.963 1761246.77 1852515.731 1748169.829 2565941.403 0.696502456 1.015959324 0.774758391 0.937818057 0.673425191 0.7681208 0.686393995 0.721963381 0.681297643 1 21.29105679 3.234895368 24.99828877 0.736191969 0.861845171 0.13311393 0.120289187 139.0204003 948169.802 0.031094941 0.038561574 1717.49455 -3.234895368 0.125653202 EIIDAS(ph)DKEGMS(ph)PAKR ddPTM_MDA-MB-175_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 125.11 4.23E-05 576780000 1156770 291600 512290 306220 767600 834110 763210 512350 562620 232344 TRUE FALSE 1202440.173 341680.0317 525640.6983 366789.402 637123.6262 640400.5936 703387.6059 505482.7863 542371.4161 277867.3583 4.327389083 1.229651564 1.891696461 1.320016155 2.292905615 2.304698895 2.531379037 1.819151373 1.951907627 1 18.08403684 0.653831155 1.191802658 1.003121104 2.167500532 0.1685915 0.812262472 2.13335224 4.777336767 0.727860068 0.222835202 4.506414701 -0.653831155 1.164379427 EIIDASDKEGMS(ph)PAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 117.37 0.0003148 799030000 1367260 488278 727590 450327 1074990 985690 1089310 742420 851850 379787 TRUE FALSE 1421240.481 572135.9482 746551.5931 539400.3365 892263.5838 756778.4358 1003927.036 732469.0743 821192.0849 454198.9912 3.129114129 1.259659223 1.643666339 1.187585941 1.964477247 1.666182555 2.210324231 1.612661165 1.80800068 1 18.79296498 0.002062745 1.345623758 0.998431231 1.796043635 0.183878064 0.520501405 27.97324901 35.26420531 0.613969041 0.136507169 1.004760942 -0.002062745 0.797612404 EIIDLVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 175.51 0.00012529 5634065000 2511695 2592381 2590107 3036151 3182385 3456029 3638760 2911221 2657735 2402405 FALSE TRUE 2610858.658 3037602.271 2657607.316 3636692.606 2641444.334 2653418.641 3353544.483 2872200.844 2562083.637 2873110.263 0.908722053 1.057252243 0.924993151 1.265768548 0.919367547 0.923535263 1.167217467 0.999683472 0.89174567 1 21.45418193 1.465966314 24.99999996 0.945819348 1.028051235 0.06716079 0.114098694 6.729051811 15088.34903 0.059104807 0.027361399 29.23925573 -1.465966314 0.082231888 EIIDLVLDRIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIIDLVLDRIR 11 1 P68363;F8VQQ4;F8VVB9;F8VS66;F8VRZ4;Q9BQE3;F5H5D3;A0A1W2PQM2 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 138.75 0.0014065 0 71355 77758 85361 78194 117950 111510 84975 86634 89407 100510 FALSE TRUE 74172.1505 91112.33163 87585.57778 93660.53981 97900.90113 85613.49245 78314.43746 85472.81293 86189.25953 120203.0101 0.617057347 0.757987105 0.728647125 0.779186309 0.814462974 0.712240836 0.651518106 0.711070487 0.717030792 1 16.8751135 -1.444041498 3.547734898 1.002954731 0.722641138 0.704333872 0.054216197 9389987.959 4015651.586 211520.8173 0.013036655 0.035971496 1.444041498 -0.280313593 EIIELLFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIIELLFHK 9 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 73.721 0.043119 57259000 59254 46682 59942 52265 71244 66664 70690 53822 61347 41768 FALSE TRUE 61593.39367 54699.27036 61504.13776 62602.861 59133.97033 51182.2963 65149.13309 53100.60413 59139.13345 49951.6399 1.233060492 1.095044536 1.231273646 1.253269385 1.183824404 1.024636957 1.304244129 1.063040257 1.183927766 1 15.60824442 -2.856858541 0.203808236 0.69274647 1.206455249 0.299742589 0.083064219 63.86919232 1.389599206 8.681028084 0.194489582 0.001390405 2.856858541 0.513708779 EIIKQEESVDPDYWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 176.21 2.96E-09 396970000 1013090 604340 919640 554150 1179300 974600 1074650 894200 1046130 478530 FALSE TRUE 1053087.575 708130.6939 943606.5739 663759.216 978843.0072 748263.9202 990416.1249 882214.7116 1008479.986 572288.7915 1.840133148 1.237366002 1.648829381 1.159832633 1.710400451 1.307493579 1.730622965 1.541555111 1.762187205 1 19.12638383 2.240043556 24.99997563 1.558735332 1.475845214 0 0.280382302 209.0063734 3523588.078 0.091023722 0.072314623 173.7975126 -2.240043556 -0.082890118 EIILDDDECPLQIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIILDDDECPLQIFR 15 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;H0Y7R8;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 176.29 1.88E-06 18843000 15077 22088 22877 18122 22689 27889 21188 23160 21151 22228 FALSE TRUE 15672.2516 25881.44218 23473.19341 21706.47751 18832.33188 21412.20241 19527.2292 22849.57808 20389.77964 26583.15102 0.589555828 0.973603248 0.883010197 0.816550209 0.708431136 0.805480223 0.734571653 0.859551152 0.767018915 1 14.6982245 -1.923697782 2.811938063 1.121163908 0.801420224 0.276650442 0.099556113 36153892.03 19524446.38 28752113.75 0.022666751 0.011920713 1.923697782 -0.319743684 EIIQDVTLHDLDVANAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIIQDVTLHDLDVANAR 17 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;H7C4I3 Q9Y265 RUVBL1 RuvB-like 1 0 77.505 0.017641 69706000 23658 24367 20339 18769 24508 33411 23450 25507 19832 20724 FALSE TRUE 24592.03611 28551.8427 20869.05105 22481.45218 20342.13891 25651.8016 21611.92772 25165.12039 19118.25019 24784.47102 0.992235666 1.15200533 0.842021241 0.907078153 0.820761472 1.03499492 0.871994714 1.015358382 0.771380199 1 14.59714885 4.236682966 24.99977198 0.913332993 1.0721205 0.346096113 0.090021455 47.72875799 635518.263 0.020765798 0.048797706 17245.78495 -4.236682966 0.158787507 EIKCS(ph)PSESPLMEKKNS(ph)LK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIKCSPSESPLMEKKNSLK 19 3 Q8WUM9 Q8WUM9 SLC20A1 Sodium-dependent phosphate transporter 1 2 EIKCS(0.471)PS(0.471)ES(0.174)PLMEKKNS(0.884)LK 56.407 0.053595 35347000 100080 13442 24658 14760 42572 45757 46951 16346 33831 9673.4 TRUE FALSE 104031.2357 15750.55894 25300.60774 17679.48395 35335.62665 35130.6302 43270.85794 16126.90861 32613.42892 11568.71752 8.992460529 1.361478393 2.186984658 1.52821468 3.054411743 3.036691849 3.740333175 1.39401006 2.819104958 1 13.49794132 4.743480726 24.9805356 2.301926907 8.992463306 0.846245393 0.863609511 184.6647073 937554.5766 0.202892041 1.685616141 55396.29583 -4.743480726 6.690536399 EIKDILIQYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIKDILIQYDR 11 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;; 145.6 3.30E-05 2768030000 3322980 2762190 3418210 2309970 4669420 3921690 3419440 3164880 3566410 3154800 FALSE TRUE 3454173.816 3236574.646 3507291.361 2766875.171 3875713.656 3010936.931 3151415.358 3122459.96 3438055.601 3772922.658 0.915516731 0.857842829 0.929595351 0.73335062 1.027244396 0.798038339 0.835271656 0.827597129 0.911244654 1 21.8472511 0.955704749 5.951244372 0.99998145 0.863131963 0.22753043 0.075663344 0.388099697 46.06988378 0.06673141 0.016784712 9.030353441 -0.955704749 -0.136849488 EIKDSLAEVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIKDSLAEVEEK 12 1 Q32MZ4-2;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 158.81 6.30E-05 496490000 656860 306990 478160 268590 708970 564920 560710 466720 517630 305870 FALSE TRUE 682793.34 359713.1444 490621.2424 321716.3003 588459.5326 433725.8914 516760.0851 460464.3818 499000.5974 365799.3703 1.866578774 0.983361847 1.341230418 0.879488393 1.608694767 1.185693379 1.412687192 1.258789433 1.364137388 1 18.48069307 -1.679351498 2.415547588 0.948813201 1.304623839 0.111166215 0.269259493 17625020.83 13275997.05 5520166.408 0.064827821 0.020924183 1.679351498 0.355810639 EILDESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EILDESLR 8 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 160.75 0.00081788 410804000 389155 427669 397950 425160 474441 515949 484404 447456 413836 410597 FALSE TRUE 404519.1399 501117.8239 408320.9039 509255.379 393795.6883 396127.664 446435.1487 441458.5842 398942.1232 491045.6208 0.82379136 1.020511746 0.831533541 1.037083638 0.801953366 0.806702366 0.909152082 0.899017455 0.812433929 1 18.90549754 EILDHQDGNVEDDGLTGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EILDHQDGNVEDDGLTGLLR 20 0 Q70CQ2-3;Q70CQ2-2;Q70CQ2;A0A0C4DG73 Q70CQ2-3 USP34 Ubiquitin carboxyl-terminal hydrolase 34;Ubiquitin carboxyl-terminal hydrolase 0 152.81 6.01E-08 33832000 16229 18038 16986 17265 19835 21213 19513 17768 19506 20310 FALSE TRUE 16869.73345 21135.88618 17428.66911 20679.96547 16463.45378 16286.60224 17983.52007 17529.84902 18803.98287 24289.35564 0.694531946 0.870170724 0.717543494 0.851400332 0.677805292 0.670524261 0.740386873 0.721709101 0.774165571 1 14.5680366 -1.724517753 5.064819412 1.010221577 0.746028054 0.580824352 0.06461274 0.007376788 0.000401233 0.061882761 0.014220827 0.018857419 1.724517753 -0.264193523 EILDKFTEEVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EILDKFTEEVVK 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;; 167.98 4.35E-05 872204000 1251293 790023 1032500 757511 1434502 1255098 1324989 940713 1146202 797965 FALSE TRUE 1300695.014 925703.3047 1059407.798 907344.4149 1190665.862 963620.5107 1221132.9 928104.2809 1104950.414 954310.9638 1.362967694 0.970022707 1.110128499 0.950784859 1.247670736 1.009755255 1.279596427 0.972538634 1.157851535 1 19.86409992 -0.209793799 0.012624883 4.10E-07 2.113342195 0.067827176 0.136485295 7741.858243 26.69159671 2348.640994 2119.594712 0.616887828 0.209793799 2.113341786 EILEVLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EILEVLDGR 9 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ; 128.12 0.00099163 49798000 94109 114221 115450 122890 132458 142097 126705 119206 115699 114448 FALSE TRUE 97824.49599 133837.5682 118458.7218 147197.2752 109942.8365 109097.1253 116773.531 117608.2386 111535.0156 136871.8944 0.714715731 0.977830904 0.865471486 1.075438284 0.80325356 0.797074708 0.85315931 0.859257769 0.814886183 1 17.0624667 EILFYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EILFYDR 7 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ;; 124.08 0.0097275 346708000 315591 354520 352740 330593 440910 443600 369560 360830 341090 429140 FALSE TRUE 328050.7764 415406.0522 361932.6942 395983.3087 365964.2757 340580.6228 340592.9215 355993.664 328814.2375 513221.7666 0.639198876 0.809408484 0.70521696 0.771563746 0.713072398 0.663612974 0.663636938 0.693644906 0.640686461 1 18.96922283 -1.937744394 4.952878013 1.146230654 0.702571318 0.748120458 0.052202039 0.03294488 0.000414103 0.01975496 0.011769018 0.011541323 1.937744394 -0.443659335 EILHNTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EILHNTEK 8 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;;; 112.84 0.0029633 1284360000 1599240 1824470 2078300 1744270 2442580 2533970 2214310 2166210 2126870 1670630 FALSE TRUE 1662379.23 2137808.53 2132462.205 2089281.4 2027391.124 1945493.87 2040746.596 2137175.498 2050324.364 1997957.962 0.832039143 1.069996752 1.067320857 1.045708388 1.014731622 0.973741143 1.021416183 1.069679912 1.026209962 1 20.9300948 4.744712932 24.98043728 1.034536487 0.832039053 0.796040326 0.030355673 317.2235732 1287996.803 0.007827373 0.072782898 55553.69272 -4.744712932 -0.202497434 EILKEQENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EILKEQENR 9 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;; 121.61 0.00055552 3351330000 4903530 4406080 4841200 3503530 6500410 5879650 4386420 4685440 5286430 4640630 FALSE TRUE 5097125.151 5162789.965 4967365.649 4196517.777 5395472.63 4514190.394 4042600.939 4622639.341 5096172.417 5549872.598 0.918422011 0.93025378 0.895041384 0.756146687 0.972179547 0.81338631 0.728413286 0.832927109 0.918250343 1 22.40402322 3.988504056 23.76765257 0.845557195 0.921415363 0.071742463 0.082564272 553.1753067 1143696.773 0.020386033 0.039688412 9738.768812 -3.988504056 0.075858168 EILKEQENRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EILKEQENRK 10 2 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 71.066 0.029303 384140000 722760 475190 627460 372110 1042670 781710 609950 602040 793600 585350 FALSE TRUE 751295.1229 556800.186 643812.1231 445712.2474 865437.3258 600169.6994 562140.5252 593970.6385 765038.491 700038.1253 1.073220294 0.795385517 0.919681514 0.636697104 1.236271704 0.85733859 0.803014157 0.848483271 1.092852608 1 19.41707397 1.239965745 24.99573433 1.046426332 0.888528027 0.128104954 0.155660399 67.58451968 1202450.954 0.112128038 0.03588432 17.37663764 -1.239965745 -0.157898305 EILSEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EILSEVER 8 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;; 188.98 0.00045163 2074630000 2534620 2109580 2205810 2001820 2548330 2756160 2225180 2358260 2235820 1967930 FALSE TRUE 2634688.755 2471883.955 2263295.221 2397774.021 2115165.777 2116083.61 2050764.577 2326651.382 2155353.275 2353508.205 1.119472942 1.050297572 0.961668719 1.018808439 0.898728873 0.899118858 0.871364957 0.9885886 0.915804445 1 21.16638145 4.621465666 0.913630928 0.931483458 1.203054881 0.640185617 0.044566492 1.126117092 0.839073015 0.01477041 0.293905847 41827.86191 -4.621465666 0.271571423 EILSPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EILSPLR 7 0 A0A140T9S5;Q9Y334-2;Q9Y334 A0A140T9S5 VWA7 von Willebrand factor A domain-containing protein 7 0 ; 99.919 0.02367 232410000 475560 558350 565320 506870 575350 645770 531310 547070 517810 590160 FALSE TRUE 494335.476 654242.2691 580052.7036 607127.3731 477552.2125 495799.7042 489664.5339 539737.4215 499174.1192 705790.5527 0.700399678 0.926963767 0.821848212 0.860208982 0.676620296 0.702474271 0.69378165 0.764727467 0.707255314 1 19.42888059 5.044174777 15.98348286 0.780629245 0.292661965 0.054499961 0.103766288 17827544.63 174790086.5 0.024343426 260274607.6 110706.9222 -5.044174777 -0.48796728 EIPFNEDPNPNTHSS(ph)GPST(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNT(0.005)HS(0.124)S(0.777)GPS(0.173)T(0.921)PLK;EIPFNEDPNPNT(0.001)HS(0.466)S(0.533)GPS(0.276)T(0.724)PLK 112.9 0.0004926 294380000 289060 309170 339720 326320 400790 455740 461980 396700 364350 248760 TRUE FALSE 300472.312 362267.5425 348573.3823 390865.122 332663.859 349901.2918 425768.8004 391382.8854 351237.1147 297499.7592 1.009991782 1.217707011 1.171676183 1.313833406 1.11819875 1.176139748 1.43115679 1.315573789 1.180629912 1 18.18252898 5.55089612 1.174083862 1.242560922 5.69E-14 0.188558492 0.115422022 12.82419756 3.6161391 0.032407658 30.89714036 355546.2644 -5.55089612 -1.242560922 EIPFNEDPNPNTHSS(ph)GPST(ph)PLKNQTYSFSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLKNQTYSFSPSK 32 1 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNTHS(0.026)S(0.974)GPS(0.151)T(0.849)PLKNQTYSFSPSK 221.68 9.00E-35 105120000 52006 45051 55324 36880 76462 63010 52791 57017 62851 36169 TRUE FALSE 54059.23704 52788.1588 56765.78889 44174.75392 63465.01655 48376.88243 48653.10348 56252.78038 60589.00479 43255.62305 1.249762071 1.220376799 1.312333169 1.021248818 1.467208471 1.118395228 1.124781012 1.300473243 1.400719733 1 15.40060007 EIPFNEDPNPNTHSS(ph)GPSTPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 EIPFNEDPNPNTHS(0.182)S(0.367)GPS(0.367)T(0.084)PLK;EIPFNEDPNPNT(0.009)HS(0.058)S(0.772)GPS(0.126)T(0.035)PLK 129.72 7.54E-07 0 343750 330310 397670 305570 396870 444990 365540 330400 375330 267270 TRUE FALSE 357321.5154 387038.173 408033.6069 366010.834 329410.1792 341647.8164 336888.0196 325971.5284 361821.9466 319636.4393 1.117899812 1.210869993 1.276555351 1.145084818 1.030577677 1.068863791 1.053972508 1.019819671 1.131979656 1 18.28607236 3.406668542 4.340979612 1.051228471 1.204217844 0.663473605 0.048834918 0.118855629 4.371174231 0.013461324 0.018745094 2550.753796 -3.406668542 0.152989374 EIPFNEDPNPNTHSSGPS(ph)T(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 EIPFNEDPNPNT(0.007)HS(0.278)S(0.198)GPS(0.554)T(0.963)PLK 100.29 0.0015575 114820000 158580 143470 193040 172690 228780 236620 256670 194500 197890 144390 TRUE FALSE 164840.8609 168109.8565 198070.781 206847.5666 189892.0573 181668.591 236551.5347 191893.0456 190767.9776 172680.456 0.954600565 0.97353146 1.147036472 1.197863217 1.099673129 1.052050679 1.369880183 1.111260939 1.104745621 1 17.39774528 4.249540065 6.008148259 1.148014243 0.96120468 0.340712303 0.094061019 0.14871744 19.24464611 0.022529206 0.058018892 17763.97137 -4.249540065 -0.186809563 EIPFNEDPNPNTHSSGPS(ph)TPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIPFNEDPNPNTHSSGPSTPLK 22 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 EIPFNEDPNPNT(0.008)HS(0.127)S(0.307)GPS(0.432)T(0.127)PLK;EIPFNEDPNPNTHS(0.03)S(0.253)GPS(0.613)T(0.103)PLK 138.23 1.15E-06 277872000 297160 275142 316247 245286 366060 387080 310660 304320 338870 229308 TRUE FALSE 308892.1063 322395.4982 324488.6566 293802.8387 303837.252 297186.5363 286309.6574 300241.0882 326674.1349 274236.5122 1.126371189 1.175611138 1.183243814 1.071348364 1.107938726 1.083686975 1.044024572 1.09482536 1.191213133 1 18.06506114 3.73671804 24.98967063 1.087455282 1.163128958 0.350684602 0.047915983 180.8918587 2453324.161 0.012171418 0.019992189 5454.036498 -3.73671804 0.075673676 EIPSATQS(ph)PISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIPSATQSPISK 12 0 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 EIPSAT(0.058)QS(0.942)PISK 164.15 6.09E-05 276020000 374950 330320 332840 286210 439600 433590 405530 316060 385740 296540 TRUE FALSE 389753.3155 387049.8905 341514.0838 342821.4837 364876.949 332895.2936 373743.4989 311823.7327 371857.2928 354641.3354 1.099007015 1.091384032 0.962984429 0.96667097 1.028861874 0.938681593 1.053863331 0.879265053 1.0485447 1 18.43600117 4.244320365 24.93989172 0.978326261 1.095195593 0.429255169 0.05044321 107.0545855 463535.4843 0.011614769 0.030039 17551.74759 -4.244320365 0.116869332 EIPSHVLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIPSHVLSK 9 0 E5RHG8;Q15369-2;Q15369 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;;; 144.65 9.91E-05 1579790000 2699590 2470840 2952660 2632820 3642410 3669930 3495380 3175710 3158190 2382100 FALSE TRUE 2806171.898 2895187.55 3029608.745 3153583.938 3023274.449 2817644.376 3221402.982 3133144.802 3044527.359 2848826.887 0.985027174 1.016273598 1.063458352 1.106976332 1.061234876 0.989054263 1.130782287 1.099801752 1.068695108 1 21.44193653 4.3465305 2.771417086 1.072617028 0.988933764 0.273348845 0.042139338 0.322276008 4.721973072 0.010827034 0.041146154 22209.07652 -4.3465305 -0.083683264 EIPYTFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIPYTFEDR 9 0 P34897-3;P34897-2;P34897;H0YIZ0;G3V2Y4 P34897-3 SHMT2 "Serine hydroxymethyltransferase, mitochondrial;Serine hydroxymethyltransferase" 0 88.37 0.029849 45968000 34343 44794 42320 42140 32678 71660 42956 43157 39126 40412 FALSE TRUE 35698.88816 52487.02105 43422.89397 50475.16622 27123.40523 55018.05102 39588.99648 42578.55101 37717.8629 48329.95767 0.738649274 1.086014215 0.898467453 1.044386725 0.561213097 1.13838401 0.819139896 0.880997068 0.780424083 1 15.56063011 EIQGHQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EIQGHQPR 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 220.51 5.94E-06 1415897000 1062855 1390670 1261850 1320380 1290150 1535370 1221790 1264220 1256320 1404250 FALSE TRUE 1104817.336 1629506.755 1294734.848 1581547.223 1070850.764 1178803.586 1126022.907 1247275.199 1211105.289 1679385.902 0.657869841 0.970299175 0.770957316 0.941741396 0.63764425 0.70192538 0.67049682 0.742697195 0.721159614 1 20.67950235 5.038204711 16.56352204 0.778158279 0.141522848 0.084987217 0.124336695 10085993.85 117809259.5 0.02894 193278507.7 109195.4924 -5.038204711 -0.636635431 EIQNGNLHES(ph)DSESVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 EIQNGNLHES(1)DSESVPR;EIQNGNLHES(1)DSESVPR;EIQNGNLHES(0.999)DS(0.001)ESVPR 252.32 3.56E-27 980860000 284348 346126 271382 438470 365549 482066 335436 294014 299296 426323 TRUE FALSE 295574.2786 405570.448 278454.4379 525198.0573 303413.1116 370113.4773 309143.6498 290073.2232 288524.3954 509852.8294 0.5797247 0.79546572 0.546146695 1.030097367 0.595099397 0.72592218 0.60633899 0.568935203 0.56589741 1 18.95972134 EIQSSNLETAMSVIGDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIQSSNLETAMSVIGDRR 18 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 71.842 0.03664 1126400000 15837 1326600 1143700 1230700 847220 1387600 730690 1085000 851320 1585500 FALSE TRUE 16462.25699 1554433.23 1173505.762 1474128.787 703209.847 1065350.929 673416.6085 1070457.35 820681.1595 1896148.369 0.008681946 0.819784599 0.618889208 0.777433249 0.370862248 0.561849983 0.355149744 0.564543032 0.432814844 1 20.85464043 -1.361921029 2.986371777 1.005995716 0.517303554 0.312649264 0.220742167 31871719.35 40242013.56 1669573.242 0.053303975 0.043458924 1.361921029 -0.488692162 EIQSTLEGDRGS(ph)GNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 188.86 6.73E-10 6638660000 960953 1081618 1174768 1182071 1182520 1503540 1100580 1078650 1105760 1161400 TRUE FALSE 998892.1665 1267377.478 1205383.419 1415881.116 981515.6728 1154365.621 1014313.664 1064192.461 1065963.914 1388954.094 0.719168597 0.912468946 0.867835319 1.019386546 0.706658109 0.831104229 0.730271554 0.766182602 0.767457988 1 20.40556749 3.213030469 24.99999415 0.783954191 0.881206091 0.114339103 0.102396089 372.1999308 364469.9065 0.027760247 0.033191312 1633.166523 -3.213030469 0.0972519 EIQTAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 200.66 0.00081247 12642260000 3495130 3877940 3696120 3498270 4089530 4216370 3680200 3909780 3260220 3941150 FALSE TRUE 3633120.431 4543946.029 3792443.924 4190217.365 3394393.151 3237181.967 3391736.308 3857375.794 3142885.319 4713342.885 0.770816068 0.964060146 0.804618721 0.889011784 0.720166819 0.686812321 0.719603133 0.818394903 0.666806001 1 22.16831921 3.241412526 24.99928588 0.756706989 0.861014224 0.149922232 0.100694945 115.4697954 1012175.496 0.026224749 0.034001323 1743.462162 -3.241412526 0.104307235 EIQVQHPAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIQVQHPAAK 10 0 P49368;B4DUR8;Q5SZX6;E9PRC8;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 98.353 0.0054345 2960410000 2942020 2541470 3080510 2536390 3439310 3761320 3275580 3056440 3313520 2671810 FALSE TRUE 3058173.221 2977947.703 3160790.621 3038080.372 2854697.315 2887810.433 3018831.48 3015473.421 3194267.062 3195300.015 0.957084846 0.931977495 0.989199952 0.950796594 0.893405095 0.903768166 0.944772468 0.943721531 0.999676728 1 21.60751997 1.254775369 4.285185661 1.001889588 0.938367697 0.478255964 0.025298087 0.181997729 6.979689877 0.022861343 0.006887829 17.9794072 -1.254775369 -0.063521891 EIRPALELLEPIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIRPALELLEPIEQK 15 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 172.82 9.16E-07 378370000 744570 491510 642940 590760 796520 911270 978250 694640 738590 436160 FALSE TRUE 773966.1985 575923.0191 659695.5446 707610.5648 661127.8149 699641.3529 901572.2088 685329.487 712008.2902 521617.2012 1.48378197 1.104110481 1.264712021 1.35657061 1.267457847 1.341292717 1.728417327 1.313855228 1.365001554 1 18.99263192 2.474643494 24.99937818 1.402523651 1.2882021 0 0.188493911 216.5955105 2185294.536 0.06178771 0.051982228 298.2932968 -2.474643494 -0.114321552 EIRPVCR ddPTM_MDA-MB-175_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 ;;;;; 161.68 0.0011857 3138730000 1013848 1167690 1101516 1127110 1235040 1359920 1124340 1145930 1035547 1206300 FALSE TRUE 1053875.502 1368231.674 1130222.412 1350048.994 1025108.342 1044099.19 1036211.293 1130570.683 998277.8658 1442651.389 0.730512936 0.948414624 0.783434183 0.935810969 0.710572457 0.723736308 0.718268669 0.783675593 0.691974425 1 20.46029129 3.223930741 24.99759334 0.756591396 0.851883374 0.113058379 0.102274491 388.6835012 664129.5314 0.026835946 0.032204231 1674.675785 -3.223930741 0.095291978 EIS(ph)DDEAEEEK ddPTM_MDA-MB-175_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 281.26 2.25E-27 361560000 1038990 476090 572150 622200 810290 1062150 1298190 615100 856230 250410 TRUE FALSE 1080010.127 557854.754 587060.699 745269.3029 672557.1952 815481.7595 1196434.476 606855.5906 825414.4496 299473.0451 3.606368403 1.862787864 1.960312317 2.48860228 2.245802105 2.723055623 3.995132434 2.026411393 2.756222849 1 18.19206663 2.731365947 23.75897914 2.642288556 2.377962301 0 0.830941191 1466.559766 4843009.366 0.255765264 0.246016933 538.7235326 -2.731365947 -0.264326255 EIS(ph)DDEAEEEKGEK ddPTM_MDA-MB-175_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 228.39 1.01E-12 1044670000 1480100 363558 553730 525070 879410 1101820 1404500 646580 749890 177244 TRUE FALSE 1538535.491 425996.2584 568160.6587 628927.2788 729928.2023 845939.0032 1294411.62 637913.6527 722901.6054 211971.5683 7.258216295 2.009685836 2.680362576 2.967036023 3.443519375 3.990813533 6.106534148 3.009430264 3.410370605 1 17.69351124 2.761920926 21.28411678 3.790823538 3.485196857 0 1.768539572 1153.998876 1051424.969 0.52329428 0.554373021 577.9908002 -2.761920926 -0.305626681 EIS(ph)LSAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EISLSAVR 8 0 B1APY4;Q01974 B1APY4 ROR2 Tyrosine-protein kinase transmembrane receptor ROR2 1 EIS(0.5)LS(0.5)AVR 81.191 0.015137 538300000 218180 230650 229740 200970 325110 264420 305190 206100 242520 262720 TRUE FALSE 226793.9149 270262.3433 235727.2131 240721.2662 269847.9183 203012.4623 281268.4103 203337.5666 233791.7526 314194.9539 0.721825453 0.860174041 0.750257794 0.766152553 0.858855036 0.646135337 0.895203461 0.647170058 0.744097732 1 18.26130049 -1.09796389 5.217629433 1.000004635 0.764219986 0.430732252 0.080848744 4.02E-06 6.95E-07 0.072154842 0.017006725 0.079806104 1.09796389 -0.235784648 EIS(ph)SS(ph)PTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 EIS(0.998)S(0.002)S(0.999)PT(0.001)SK;EIS(0.993)S(0.008)S(0.999)PTSK;EIS(0.977)S(0.023)S(0.992)PT(0.008)SK;EIS(0.999)S(0.009)S(0.978)PT(0.011)S(0.002)K 202.65 2.85E-05 6011520000 16676200 10139900 12677900 9934200 16969100 17337500 16249100 13293700 13774000 8302400 TRUE FALSE 17334589.25 11881348.95 13008296.49 11899155.11 14084698.44 13311128.38 14975453.08 13115519.7 13278276.43 9929096.321 1.745837556 1.196619366 1.310118874 1.198412698 1.418527728 1.340618315 1.50823928 1.320917762 1.337309661 1 23.24323099 0.498652132 1.750360397 1.00006787 1.369749432 0.358267597 0.151273058 3.656981392 11.54436978 0.135584538 0.038120415 3.152478492 -0.498652132 0.369681562 EIS(ph)TPTHWSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EISTPTHWSK 10 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 1 EIS(0.499)T(0.499)PT(0.001)HWSK 91.961 0.0063075 220330000 88679 160860 148500 165200 180810 208470 176460 176580 157360 145710 TRUE FALSE 92180.1154 188486.4537 152370.032 197876.0669 150075.9808 160056.0019 162628.6041 174213.2339 151696.6443 174259.0847 0.528983126 1.08164492 0.874387882 1.135527983 0.861223282 0.918494448 0.933257536 0.999736882 0.870523592 1 17.41087435 4.748493145 24.76428072 0.962154461 0.528982857 0.69070332 0.087297544 636.530107 1586992.377 0.01907613 0.256303351 56039.35716 -4.748493145 -0.433171604 EISEVFPDQFIHLGGDEVEFK ddPTM_MDA-MB-175_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 ;;; 306.06 1.01E-55 988687000 1080400 806180 918010 761524 1180710 1221120 1047300 905650 976120 715071 FALSE TRUE 1123055.026 944635.1438 941934.0948 912151.1743 980013.3359 937533.3863 965209.8894 893511.2431 940989.6319 855175.4716 1.313245133 1.104609727 1.101451253 1.066624575 1.145979239 1.096305282 1.128668819 1.04482796 1.100346845 1 19.70586095 4.743908657 4.082133771 1.089446745 1.333535815 0.747220974 0.039448453 0.109499108 3.925985574 0.008897984 0.079311842 55450.9074 -4.743908657 0.24408907 EISLWFKPEELVDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ;; 215.23 2.16E-12 12761881000 9476110 4531712 7623830 5086890 8879840 7829300 8743640 6400970 7614580 3602393 FALSE TRUE 9850234.14 5309998.284 7822513.273 6093061.659 7370447.969 6011063.729 8058290.65 6315175.467 7340532.753 4308212.936 2.286385164 1.232529209 1.815721133 1.414289811 1.710790083 1.395256877 1.870448552 1.465845714 1.703846319 1 22.03865813 -2.5472337 0.344937185 5.73E-18 1.662928624 0.322190538 0.28545811 67.83625921 2.647214311 51.32319602 0.201627913 0.002836392 2.5472337 1.662928624 EISNFEYLMFLNTIAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EISNFEYLMFLNTIAGR 17 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3IU76;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9;Q8NFP9-3 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 166.6 5.41E-09 55443000 23547 26422 25722 28540 32409 32004 28200 25304 30259 24919 FALSE TRUE 24476.65374 30959.77297 26392.33645 34185.12682 26900.12976 24571.55603 25989.61031 24964.84127 29169.9845 29801.40095 0.821325608 1.038869717 0.88560724 1.14709798 0.902646483 0.824510098 0.872093576 0.837706969 0.978812525 1 14.86309253 3.023821707 24.99989617 0.883446615 0.978307685 0.096534528 0.096834155 380.7981721 399629.07 0.026383174 0.031532639 1056.383737 -3.023821707 0.09486107 EISS(ph)PARPCSFEEAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EISSPARPCSFEEAMK 16 1 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 1 EIS(0.133)S(0.867)PARPCSFEEAMK 95.5 0.0022599 236610000 159460 126540 152370 140360 175960 199260 163690 152070 185950 123450 TRUE FALSE 165755.6039 148272.2607 156340.8874 168122.7891 146050.3821 152984.8848 150859.5501 150031.7504 179257.6958 147637.6639 1.122718956 1.004298339 1.058949886 1.138752705 0.989248801 1.036218542 1.021822928 1.01621596 1.214173207 1 17.17170129 -1.685323102 2.654983708 0.991456014 1.058553903 0.068614586 0.06793668 9777492.621 7992933.182 558903.8846 0.01547347 0.020638441 1.685323102 0.067097889 EISSS(ph)PTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 EISS(0.003)S(0.997)PTSK;EISS(0.001)S(0.999)PTSK;EISS(0.002)S(0.998)PTSK;EISSS(0.999)PTSK 202.68 2.04E-05 1904490000 6278400 4547000 5362130 4246240 6420100 6797300 6318300 5500210 5789300 4139230 TRUE FALSE 6526276.08 5327911.879 5501871.513 5086133.598 5328813.695 5218730.089 5823055.136 5426488.681 5580944.224 4950232.868 1.31837759 1.076295201 1.111436908 1.027453401 1.076477377 1.054239311 1.176319436 1.09620877 1.127410442 1 22.23906496 4.740428737 24.90470503 1.088592074 1.318377672 0.684731618 0.047798998 88.66462421 1181929.606 0.011070095 0.071602265 55008.36507 -4.740428737 0.229785598 EITALAPS(ph)TMK ddPTM_MDA-MB-175_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(1)TMK;EITALAPS(0.987)T(0.013)MK;EITALAPS(0.991)T(0.009)MK 224.8 6.23E-12 440570000 1707390 1506210 1895500 1221500 2145640 2128660 1801610 1752460 1917320 1633280 TRUE FALSE 1774799.076 1764889.851 1944898.287 1463109.054 1780924.879 1634310.975 1660395.101 1728971.14 1848316.028 1953289.945 0.908620392 0.903547297 0.995703834 0.749048577 0.911756539 0.836696559 0.850050503 0.885158471 0.946257893 1 20.89747469 1.061683471 2.766827838 0.999006349 0.878242922 0.299573967 0.059776849 0.290594265 4.637540653 0.054933407 0.014744848 11.52612886 -1.061683471 -0.120763427 EITALAPSTMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P68133;P68032;P63267;P62736;A6NL76 P60709;P63261;P68133 ACTB;ACTG2;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 ; 110.14 0.0029169 410520000 1332020 1024620 1406720 1022813 1725720 1734780 1491680 1458390 1305600 1074270 FALSE TRUE 1384609.178 1200590.515 1443380.279 1225122.359 1432382.731 1331903.636 1374758.224 1438842.667 1258611.711 1284752.638 1.077724331 0.934491573 1.123469402 0.953586178 1.114909351 1.036700448 1.070056743 1.119937507 0.979652949 1 20.29305918 3.221311247 24.99966934 1.063881812 1.023269632 0.037552943 0.065909821 614.9409259 891237.8772 0.017747574 0.021258991 1664.605201 -3.221311247 -0.04061218 EIVHLQAGQCGNQIGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EIVHLQAGQCGNQIGAK 17 0 P68371;M0R2D3;M0QY85;M0R0X0;M0QY37;M0QX14;M0QZL7;M0R2T4;P04350;M0QYM7;M0R042;M0R278 P68371;P04350 TUBB4B;TUBB4A Tubulin beta-4B chain;Tubulin beta-4A chain 0 ;;;;; 288.42 4.47E-37 6832960000 2361920 2101390 2221710 2068380 2691480 2869920 2449500 2338580 2428110 1900350 FALSE TRUE 2455170.425 2462287.386 2279609.588 2477499.391 2233983.191 2203424.574 2257501.789 2307235.16 2340722.795 2272687.198 1.080294036 1.083425554 1.003045905 1.090118954 0.982969937 0.969523908 0.993318302 1.015201371 1.029936191 1 21.1159677 3.919288059 0.931954185 1.001162656 1.088210187 0.457239767 0.03107031 0.744126045 1.063678034 0.011531525 0.051031339 8304.013744 -3.919288059 0.087047531 EIVLADVIDNDSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;; 317.55 1.35E-55 956270000 699090 763960 795350 808400 838170 883440 838590 831270 773290 707590 FALSE TRUE 726690.613 895164.1872 816077.4744 968299.1072 695698.1628 678274.4487 772859.1246 820128.1853 745459.444 846228.7129 0.858740199 1.057827717 0.964369871 1.144252248 0.822115998 0.801526158 0.913298158 0.969156651 0.880919582 1 19.69068811 EIVQQLIDEYHAATRPDYISWGTQEQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIVQQLIDEYHAATRPDYISWGTQEQ 26 1 P23258 P23258 TUBG1 Tubulin gamma-1 chain 0 183.31 1.59E-17 294010000 212810 279300 255530 266790 302520 346830 272450 280800 294440 307730 FALSE TRUE 221211.9031 327267.6023 262189.3217 319560.2657 251097.7585 266283.9888 251094.6571 277036.3353 283843.1619 368023.8017 0.601080425 0.889256621 0.712424904 0.868314126 0.682286736 0.723550997 0.682278309 0.752767441 0.771263056 1 18.48943955 -1.670408264 2.816504612 1.030041771 0.745301035 0.471097737 0.081781024 27601352.21 24744247.77 5940952.51 0.017775987 0.021359532 1.670408264 -0.284740735 EIVVIHQDPEALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EIVVIHQDPEALK 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 117.7 0.00048545 290650000 758990 526340 641290 636500 764410 856490 848420 655940 681740 417510 FALSE TRUE 788955.5113 616734.8006 658002.5442 762397.8002 634475.8612 657583.1777 781918.6235 647148.1972 657204.3106 499313.0908 1.580081768 1.235166496 1.317815528 1.526893275 1.27069743 1.316975641 1.565988631 1.296076969 1.316216864 1 18.92958521 0.667629001 1.474456842 1.000660799 1.386967035 0.491307406 0.119021759 0.974999978 3.160570429 0.106976778 0.031189214 4.651885332 -0.667629001 0.386306236 EIVWLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EIVWLER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 109.86 0.016129 496900000 388890 501960 425510 464290 535320 552400 494880 469660 471390 558770 FALSE TRUE 404243.6775 588167.7253 436599.1402 556125.1762 444326.4976 424113.4717 456090.0125 463364.9759 454424.766 668250.2832 0.604928554 0.880160832 0.653346734 0.83221091 0.664910302 0.634662614 0.682513759 0.693400343 0.680021808 1 19.35002902 -1.648833217 7.35414719 1.00076989 0.705584179 0.540826532 0.082091412 0.000965913 4.61E-05 0.074090207 0.017420646 0.022447438 1.648833217 -0.295185711 EIYDDSFIRPVTFWIVGDFDSPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIYDDSFIRPVTFWIVGDFDSPSGR 25 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 119.32 0.0004808 184130000 185720 260870 220010 241660 262700 303180 211230 218490 237030 242080 FALSE TRUE 193052.369 305672.3932 225743.6413 289459.6267 218046.3478 232771.0397 194673.2407 215561.4989 228499.3366 289510.9411 0.66682236 1.055823286 0.779741313 0.999822755 0.753154085 0.804014656 0.672421014 0.744571166 0.789259762 1 18.14325835 3.185977335 24.99942869 0.771106039 0.881586449 0.071492432 0.128609689 174.716367 83063.82744 0.034083641 0.040737783 1534.536896 -3.185977335 0.11048041 EIYENMAPGENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EIYENMAPGENKR 13 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 92.935 0.009372 250920000 215290 160570 189710 176990 247170 213710 216890 167220 190230 105170 FALSE TRUE 223789.8154 188146.6484 194653.9984 211998.0937 205156.1317 164079.0913 199889.5951 164978.6894 183383.6595 125776.0479 1.77927212 1.495886153 1.547623746 1.685520393 1.63112242 1.304533685 1.589250087 1.311686066 1.458017345 1 16.94049768 -2.66268358 0.125251342 6.60E-09 1.837315279 0.714955129 0.114682256 36.76386059 0.539443145 11.17663972 1.095033512 0.002174285 2.66268358 1.837315273 EKADFTVVAGDEGSSTTGGS(ph)SEENKGPSGSAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKADFTVVAGDEGSSTTGGSSEENKGPSGSAVSR 34 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 EKADFTVVAGDEGS(0.002)S(0.008)T(0.037)T(0.037)GGS(0.774)S(0.127)EENKGPS(0.005)GS(0.005)AVS(0.005)R 98.561 7.48E-05 86877000 108690 51127 68933 42413 102120 79441 74725 63834 84950 42273 TRUE FALSE 112981.1651 59907.66454 70729.45061 50802.16481 84761.67888 60992.03169 68867.85924 62978.40964 81892.66609 50555.58498 2.234790976 1.184986081 1.399043264 1.0048774 1.676603661 1.206435089 1.362220599 1.245726059 1.619853991 1 15.62558286 4.743332771 24.78176162 1.310113048 2.234791405 0.630302722 0.214655334 259.9264145 1349744.346 0.046007022 0.375550263 55377.42677 -4.743332771 0.924678356 EKADS(ph)IERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKADSIERR 9 2 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 EKADS(1)IERR;EKADS(1)IERR 95.401 0.0063556 680030000 864300 511960 595920 516750 889030 913390 637310 607610 637810 425480 TRUE FALSE 898423.2314 599885.1475 611450.1648 618961.6077 737912.9982 701269.0151 587355.9769 599465.9818 614855.3427 508844.6597 1.765613954 1.178916072 1.201644064 1.216405824 1.450173416 1.37815933 1.154293291 1.178092312 1.208336043 1 18.95686577 8 0.089072052 0.836823085 2.53587491 0.40273713 0.155350445 182.8556036 1.17141611 2.958712306 37.98463401 100000000 -8 1.699051825 EKAEGDVAALNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKAEGDVAALNR 12 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 176.51 2.26E-05 8927080000 7880550 6357010 7870300 6401940 9921090 9745240 9579180 8082450 8468300 6140610 FALSE TRUE 8191680.199 7448777.017 8075406.484 7668224.624 8234706.666 7482055.701 8828338.841 7974117.978 8163527.537 7343744.96 1.115463601 1.014302247 1.099630574 1.044184495 1.121322528 1.018833816 1.202157603 1.085838087 1.111630045 1 22.80808453 EKAEGDVAALNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKAEGDVAALNRR 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;; 190.27 2.56E-06 4579630000 4292290 3906390 4813860 3018140 6388600 5457600 4051290 4359630 4920180 5103930 FALSE TRUE 4461752.924 4577282.095 4939313.146 3615119.084 5302668.054 4190155.111 3733739.304 4301196.291 4743103.683 6103947.363 0.730961894 0.749888854 0.809199826 0.592259217 0.868727684 0.686466455 0.611692579 0.704658156 0.777055142 1 22.54131109 0.845175283 3.6076153 0.999940768 0.717534124 0.53840062 0.077822458 0.630425095 13.42914483 0.072447283 0.018652087 7.001245124 -0.845175283 -0.282406644 EKAGS(ph)PAPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKAGSPAPSNR 11 1 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 EKAGS(1)PAPSNR 70.529 0.0312 99419000 120120 92358 108870 75277 152600 137360 122320 113280 119150 96020 TRUE FALSE 124862.4304 108219.7681 111707.2416 90166.56592 126661.1065 105460.2217 112732.2388 111761.6669 114861.8148 114833.2806 1.087336613 0.942407702 0.972777587 0.785195419 1.102999983 0.918376808 0.981703546 0.973251538 1.000248484 1 16.80918129 1.374847802 1.742652624 1.001965285 0.964860273 0.017086377 0.083298581 1.682414295 9.228747857 0.071543263 0.022103812 23.70542806 -1.374847802 -0.037105011 EKAPSIIFIDELDAIGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKAPSIIFIDELDAIGTK 18 1 P17980;E9PM69;E9PKD5;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 151.23 4.49E-08 156310000 399560 232630 317040 232600 407170 402420 380390 299700 361120 230230 FALSE TRUE 415334.9373 272582.3929 325302.3229 278607.5858 337959.3888 308964.0537 350574.0378 295683.0117 348123.3617 275339.1605 1.508448477 0.989987739 1.18146043 1.011870543 1.22742943 1.122121725 1.273244377 1.073886516 1.264343805 1 18.07085029 -5 0.017952142 1.37E-07 2.005928428 0.112974546 0.144425501 11192.84685 15.22614568 1112.239578 647.2650606 1.00E-05 5 2.00592829 EKASATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKASATR 7 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 60.91 0.086332 44589000 79019 68104 93318 63876 112300 96386 100990 84855 98302 86525 FALSE TRUE 82138.73114 79800.33222 95749.94374 76510.48215 93211.28611 74001.81224 93074.13991 83717.65752 94764.13022 103477.9171 0.793780291 0.771182243 0.925317656 0.739389469 0.900784329 0.715145939 0.899458962 0.809038874 0.915790855 1 16.65896339 1.003827306 2.031766462 1.00091765 0.819009393 0.428696748 0.067141413 0.282917877 2.484261212 0.056879233 0.015906377 10.08851645 -1.003827306 -0.181908257 EKAWQTFIIDLLLHCHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKAWQTFIIDLLLHCHSK 18 1 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 121.26 2.49E-05 51926000 35754 16561 29971 19476 35686 39342 35824 29870 39581 19038 FALSE TRUE 37165.59553 19405.22292 30752.06888 23328.29467 29620.10647 30205.41673 33016.02127 29469.64151 38156.48754 22768.1316 1.632351578 0.852297556 1.350662822 1.024602944 1.300945857 1.326653292 1.450097964 1.294337279 1.675872585 1 14.47472829 3.009403417 24.30121665 1.36397366 1.194265845 0.058295422 0.246073999 336.8106221 870408.0987 0.065170584 0.077788961 1021.888277 -3.009403417 -0.169707815 EKDAESVECPDADS(ph)LNIPDVDEEGYSIKPETNQNDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDAESVECPDADSLNIPDVDEEGYSIKPETNQNDTK 37 2 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 EKDAESVECPDADS(1)LNIPDVDEEGYSIKPETNQNDTK;EKDAESVECPDADS(1)LNIPDVDEEGYSIKPETNQNDTK 194.9 9.59E-25 346530000 346341 113118 177104 123998 344130 266952 275233 202103 261595 89816 TRUE FALSE 360014.8101 132545.1366 181719.4757 148524.4343 285634.9055 204956.4437 253659.5183 199394.1399 252180.247 107413.7256 3.351664866 1.233968339 1.691771464 1.38273236 2.65920304 1.908102923 2.361518669 1.856319002 2.347746954 1 16.71281883 -1.41337137 6.374837329 0.999810614 2.03994268 0.227070893 0.596330084 0.00148631 0.000136773 0.534658774 0.125998318 0.038603673 1.41337137 1.040132066 EKDDANFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDDANFK 8 1 Q5VTR2;H3BP71;O75150-4;O75150;O75150-3 Q5VTR2;H3BP71 RNF20;RNF40 E3 ubiquitin-protein ligase BRE1A;E3 ubiquitin-protein ligase BRE1B 0 104.01 0.0042517 186740000 754090 331150 469040 335220 742770 649930 681430 528890 579220 292850 FALSE TRUE 783862.0555 388022.4365 481263.5677 401525.5155 616514.2207 498993.6073 628017.736 521801.0946 558373.9853 350228.3505 2.238145639 1.107912697 1.374142233 1.146467768 1.760320716 1.42476646 1.793166473 1.489888222 1.594314065 1 18.41793635 EKDDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDDLQR 7 1 A0A087X0P0;Q02224-3;Q02224 A0A087X0P0 CENPE Kinesin-like protein;Centromere-associated protein E 0 71.223 0.050068 256370000 254860 278790 254690 350590 678120 631390 544340 257320 252130 612670 FALSE TRUE 264922.0696 326670.0138 261327.4306 419935.6556 562853.4046 484759.2413 501673.2084 253871.0463 243055.8906 732710.9562 0.361564226 0.44583749 0.356658282 0.57312594 0.768179321 0.661596824 0.684680916 0.346481848 0.331721381 1 19.48288466 3.696865246 6.885745995 0.59364304 0.393854301 0.242967366 0.185378275 0.381972674 51.602473 0.051079255 0.080430356 4975.826694 -3.696865246 -0.199788739 EKDDLS(ph)PQPLMTDFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDDLSPQPLMTDFER 16 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 EKDDLS(1)PQPLMTDFER 66.868 0.032322 118450000 124330 83239 100120 98859 152860 138000 142820 94256 108640 86526 TRUE FALSE 129238.6444 97534.65074 102729.2094 118413.0151 126876.9118 105951.5914 131625.3952 92992.65249 104730.0676 103479.1131 1.248934597 0.942553988 0.992753092 1.144318033 1.226111319 1.023893502 1.271999646 0.89866109 1.012088957 1 16.65898007 1.677102782 11.84493146 0.967570969 1.110673173 0.286768062 0.108246788 0.158342299 28.00423379 0.050313924 0.027458358 47.54477345 -1.677102782 0.143102204 EKDECT(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDECTPTR 9 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.977)PT(0.023)R;EKDECT(0.974)PT(0.026)R 100.38 0.0076013 1536400000 2718710 1901100 2213750 1994620 3205850 3544490 3147760 2619680 2880040 1829720 TRUE FALSE 2826046.77 2227599.136 2271442.144 2389149.883 2660920.762 2721335.915 2901030.346 2584567.475 2776387.923 2188218.602 1.291482838 1.017996618 1.038032554 1.091824135 1.216021452 1.243630738 1.325749787 1.181128555 1.268789106 1 21.06132544 3.227387987 8.513793253 1.222468628 1.098048118 0.151177054 0.105813574 0.205807422 105.0126383 0.028671238 0.035611129 1688.060418 -3.227387987 -0.12442051 EKDECT(ph)PTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKDECTPTRK 10 2 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 EKDECT(0.957)PT(0.043)RK;EKDECT(0.97)PT(0.03)RK;EKDECT(0.997)PT(0.003)RK;EKDECT(0.996)PT(0.004)RK 147.7 4.25E-05 6169470000 8018130 3451460 5175170 3167440 7795210 6842070 7027300 5229080 5947340 2696790 TRUE FALSE 8334691.964 4044221.406 5310039.182 3793950.178 6470182.989 5253102.935 6476481.864 5158992.736 5733296.395 3225174.367 2.584260885 1.253954343 1.646434759 1.176355057 2.006149824 1.628781063 2.008102858 1.599601184 1.77767021 1 21.62094573 -1.016166111 5.020801462 0.999991784 1.715743412 0.251392222 0.381839175 3.21E-05 6.29E-06 0.337405672 0.079526365 0.096346044 1.016166111 0.715751628 EKDFIILSCVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDFIILSCVR 11 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 120.14 0.00092237 0 269070 180440 221460 220770 394050 357520 306670 254400 272150 296980 FALSE TRUE 279693.0914 211429.1664 227231.4295 264437.6471 327069.5218 274491.3983 282632.4041 250990.1841 262355.3747 355167.545 0.787496198 0.595294163 0.639786582 0.744543388 0.920887976 0.772850454 0.795772046 0.70668108 0.738680598 1 18.43814023 -5 0.198421902 2.124821049 0.700531651 0.455742718 0.08403775 138.9772832 1.373330389 62.26180677 0.221954447 1.00E-05 5 -1.424289397 EKDHSSS(ph)RPSSPRPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDHSSSRPSSPRPQK 16 3 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 EKDHS(0.004)S(0.084)S(0.304)RPS(0.304)S(0.304)PRPQK 50.957 0.069988 11562000 4579.3 31933 28509 25324 23414 33462 20759 28182 23427 46491 TRUE FALSE 4760.0943 37417.24435 29251.96796 30333.01162 19434.09664 25690.95762 19131.85534 27804.26639 22583.86685 55600.02133 0.085613174 0.672971762 0.52611433 0.545557554 0.349533978 0.462067406 0.344097986 0.500076542 0.4061845 1 15.76279782 -1.339381479 2.950500187 1.006206565 0.444423192 0.565413062 0.148936432 14598133.9 18128189.14 791587.0123 0.033760386 0.045773964 1.339381479 -0.561783373 GLEWLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLEWLGR 7 0 A0A0B4J1U7 A0A0B4J1U7 IGHV6-1 0 79.454 0.097538 0 115890 92486 49698 42437 49773 45028 36944 31440 31535 36613 FALSE TRUE 120465.4267 108369.7511 50993.17071 50830.91194 41312.60324 34570.92941 34048.23274 31018.59823 30400.06151 43786.61635 2.75119287 2.474951483 1.164583495 1.160877825 0.943498418 0.789531877 0.777594516 0.708403636 0.694277477 1 15.41820235 4.256326314 1.567940176 0.817216376 2.947294432 0.953832617 0.151369939 0.089774144 0.372908362 0.042476182 0.224380469 18043.72974 -4.256326314 2.130078057 up EKDIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKDIQR 6 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 97.602 0.037288 3998340000 2606910 2248930 2464710 2263130 3516570 3519420 3444210 3081700 3171400 2547610 FALSE TRUE 2709832.82 2635166.233 2528942.367 2710770.359 2918824.687 2702088.042 3174243.82 3040394.852 3057261.933 3046765.403 0.889413021 0.864906182 0.830041711 0.889720737 0.958007691 0.886871053 1.041840576 0.997909077 1.003445139 1 21.53884699 2.703966531 0.997100043 1.012924479 0.862456891 0.737921307 0.035160345 0.254671639 0.532426187 0.01946472 0.017371783 505.7856817 -2.703966531 -0.150467588 EKDLDLEPLS(ph)DLEEGLEETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDLDLEPLSDLEEGLEETR 20 1 P29375;P29375-2 P29375 KDM5A Lysine-specific demethylase 5A 1 EKDLDLEPLS(0.999)DLEEGLEET(0.001)R;EKDLDLEPLS(0.996)DLEEGLEET(0.004)R 64.722 0.015528 39362000 90985 58818 74462 58513 108743 96377 103820 78959 81069 44639 TRUE FALSE 94577.15806 68919.53396 76402.54089 70086.69676 90258.9037 73994.90236 95682.31712 77900.68376 78151.34253 53385.15738 1.771600248 1.290986809 1.431156985 1.312849867 1.690711578 1.386057586 1.792301864 1.459219895 1.463915185 1 15.70415107 0.613240897 2.338540677 1.000073277 1.511377187 0.449018121 0.170705532 2.755993085 15.58734391 0.154112675 0.041497883 4.104317001 -0.613240897 0.51130391 EKDLEDLFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDLEDLFYK 10 1 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 101.47 0.0030202 1350400000 5962500 3193600 4644000 2929200 6438300 5576800 5989100 4834300 5272800 2624900 FALSE TRUE 6197904.104 3742075.957 4765026.455 3508587.017 5343920.066 4281672.717 5519658.692 4769504.116 5083032.958 3139198.898 1.974358524 1.19204806 1.51791161 1.117669549 1.702319681 1.363938016 1.758301679 1.519337981 1.619213412 1 21.58196501 EKDLLPS(ph)PAGPVPSKDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDLLPSPAGPVPSKDPK 18 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 EKDLLPS(1)PAGPVPSKDPK;EKDLLPS(1)PAGPVPSKDPK 128.88 1.17E-05 1474040000 2717500 1083300 1735960 981000 2657700 2193540 2256170 1634040 1985000 751870 TRUE FALSE 2824788.998 1269348.348 1781200.544 1175038.872 2205945.103 1684123.578 2079325.5 1612138.367 1913560.238 899184.5311 3.141500883 1.411666131 1.980906568 1.306782792 2.453272968 1.872945452 2.31245693 1.792889347 2.128106269 1 19.77825769 -1.309954083 3.899022375 0.997950545 2.004946242 0.278691696 0.500486589 3523.111724 58820870.16 191476.956 0.105971623 0.04898306 1.309954083 1.006995696 EKDNIDITLQWLIQHSK ddPTM_MDA-MB-175_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 ; 228.46 8.57E-16 960690000 1223160 868750 1150470 893310 1388620 1382550 1293190 1135880 1287270 730130 FALSE TRUE 1271451.301 1017951.055 1180452.193 1070004.052 1152582.868 1061473.715 1191826.389 1120655.387 1240941.404 873184.9943 1.456107594 1.165790825 1.351892441 1.225403619 1.319975579 1.215634398 1.364918541 1.283411183 1.421166663 1 19.73592781 -1.247678518 4.444487822 0.999862175 1.304097365 0.531348473 0.087534594 0.00010571 1.79E-05 0.074945566 0.017656873 0.056535532 1.247678518 0.304235191 EKDPFEVDLSHVYLAYTEESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDPFEVDLSHVYLAYTEESLR 22 1 J3KPF9;A0A087X011;E9PES4;Q9Y496;H7C2F6 J3KPF9 KIF3A Kinesin-like protein;Kinesin-like protein KIF3A 0 115.66 0.00011338 19734000 54358 37122 51572 48364 67439 66048 70717 57304 59401 39588 FALSE TRUE 56504.09581 43497.41473 52916.00869 57930.25485 55975.74287 50709.35297 65174.01676 56535.93361 57263.16961 47344.51064 1.193466677 0.918742514 1.117679916 1.223589685 1.182306927 1.071071435 1.376590778 1.194139148 1.209499662 1 15.53090954 3.998883202 24.99809075 1.193445539 1.046631238 0.156801282 0.11186863 57.54913652 1288291.543 0.026190307 0.05544062 9974.3178 -3.998883202 -0.146814301 EKDQADFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKDQADFR 8 1 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;;; 83.948 0.016233 2384090000 8152090 6615950 7623800 6226370 9745490 9798690 8949130 7737920 8150310 6202070 FALSE TRUE 8473940.808 7752187.948 7822482.491 7457927.402 8088955.091 7523092.748 8247673.806 7634205.839 7856981.935 7417246.871 1.142464442 1.045157062 1.054634237 1.005484586 1.090560316 1.014270238 1.111958918 1.029250606 1.059285483 1 22.82245236 5.35962377 0.007248315 1.79E-07 2.159819099 0.214097088 0.039717351 24984.17819 23.61978287 3301.33075 3748.000706 228888.3929 -5.35962377 2.159818921 EKDQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDQFK 6 1 H3BPK3;Q16775-2;Q16775;H3BV79 H3BPK3 HAGH "Hydroxyacylglutathione hydrolase, mitochondrial" 0 64.803 0.096415 201390000 423080 242310 322150 224540 467390 420020 409440 327680 384980 230200 FALSE TRUE 439783.5251 283924.8576 330545.4936 268953.3418 387943.2147 322476.7205 377347.0229 323287.9856 371124.645 275303.2826 1.597451077 1.031316645 1.200659471 0.976934744 1.409148526 1.171350801 1.370659367 1.174297606 1.348057464 1 18.07066229 -1.176541187 5.046153394 0.999983253 1.239465843 0.153658147 0.175667493 3.01E-05 4.92E-06 0.154865568 0.036499613 0.066597636 1.176541187 0.23948259 EKDRDPEAQFEMPYVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDRDPEAQFEMPYVVR 17 2 O14744-2;O14744;O14744-4;O14744-3;O14744-5;H0YJD3;H7BZ44 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 160.45 1.74E-09 483000000 212100 195010 259100 196020 284850 249210 251480 205670 240700 161140 FALSE TRUE 220473.8718 228501.4505 265852.3589 234792.1709 236431.2987 191334.7543 231768.3405 202913.3301 232037.254 192712.2978 1.144057096 1.185712864 1.379529806 1.218355931 1.2268615 0.992851813 1.202665025 1.052933997 1.20406044 1 17.55608911 2.872066685 8.67727834 1.099775649 1.237069139 0.387730252 0.087743123 0.331893242 21.7987606 0.025855201 0.02744934 744.8463356 -2.872066685 0.13729349 EKDRQS(ph)PLHGNHITISHTQATGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDRQSPLHGNHITISHTQATGSR 24 2 Q86VQ1;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 EKDRQS(1)PLHGNHITISHTQATGSR;EKDRQS(1)PLHGNHITISHTQATGSR 171.14 4.40E-12 723110000 232760 215405 303970 231820 392780 384640 280230 293960 306390 216547 TRUE FALSE 241949.5445 252399.1331 311891.7079 277673.3041 326015.3959 295313.1893 258264.8404 290019.947 295363.0838 258975.2386 0.934257444 0.974607204 1.204330227 1.072200206 1.258867055 1.140314382 0.997256887 1.1198752 1.140507044 1 17.98245464 4.365161164 6.469635636 1.118592482 0.944727842 0.418914762 0.076918734 0.177843497 9.192068427 0.018403793 0.051521429 23182.5478 -4.365161164 -0.17386464 EKDS(ph)PHMQDPNQADEEAMTQIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDSPHMQDPNQADEEAMTQIIR 23 1 P23511-2;P23511 P23511-2 NFYA Nuclear transcription factor Y subunit alpha 1 EKDS(1)PHMQDPNQADEEAMTQIIR;EKDS(1)PHMQDPNQADEEAMTQIIR 243.97 1.22E-37 275780000 255130 177408 234210 171312 290020 294530 264750 228060 265570 158279 TRUE FALSE 265202.7294 207876.444 240313.705 205197.0023 240722.504 226129.8711 243998.2032 225003.2287 256012.1876 189290.7396 1.401033827 1.09818602 1.269548133 1.084030855 1.271707768 1.19461666 1.289012889 1.188664745 1.35248131 1 17.53024431 -1.793040453 2.84344184 0.940739323 1.229753257 0.352999042 0.096292538 44437943.12 34622200.14 18213899.12 0.020704406 0.016104956 1.793040453 0.289013934 EKDTAGVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDTAGVTR 9 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 67.726 0.054798 40850000 94696 119090 128510 103050 142660 155560 129750 104670 119340 119590 FALSE TRUE 98434.6712 139542.7811 131859.0762 123432.9824 118410.7042 119433.5475 119579.856 103267.0699 115044.9767 143021.3708 0.688251487 0.975677833 0.921953659 0.863038731 0.827923152 0.835074834 0.836097817 0.722039436 0.804390114 1 17.12587121 3.183429777 2.679083165 0.814875162 0.875783904 0 0.095480902 0.760042701 11.13375646 0.028398551 0.036653443 1525.561701 -3.183429777 0.060908742 EKDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKDVER 6 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 69.344 0.0855 983390000 1714070 1740200 1848020 1411170 2305360 2305950 2040420 2008060 2047640 2095990 FALSE TRUE 1781742.807 2039065.813 1896180.919 1690295.214 1913495.731 1770428.06 1880486.549 1981145.24 1973945.836 2506659.11 0.710803794 0.813459558 0.756457434 0.674321932 0.76336496 0.706289919 0.750196363 0.790352877 0.787480766 1 21.25733438 0.387619745 0.805509242 1.002673393 0.739882353 0.813261493 0.036811906 0.862522326 0.785490982 0.040343581 0.012337121 2.441292096 -0.387619745 -0.26279104 EKEAAYQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEAAYQER 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 96.229 0.0068484 191920000 308240 267240 334650 273200 427940 398060 388330 310330 341880 298370 FALSE TRUE 320409.5532 313136.3912 343371.2539 327238.1446 355198.9117 305616.5977 357891.6799 306170.5339 329575.8056 356829.8889 0.897933618 0.877550903 0.96228277 0.917070444 0.995429258 0.856477014 1.002975622 0.858029396 0.923621636 1 18.44487694 4.255364304 24.87496131 0.932205738 0.88774224 0.128175755 0.051238408 490.5136394 726107.1722 0.011575916 0.031514224 18003.80514 -4.255364304 -0.044463498 EKEDDVPQFTSAGENFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEDDVPQFTSAGENFDK 18 1 P28838-2;P28838;H0Y983 P28838-2 LAP3 Cytosol aminopeptidase 0 ; 198.88 1.54E-15 1347360000 1982660 896180 1351700 875510 1980600 1823250 1804760 1218720 1566310 685840 FALSE TRUE 2060936.948 1050091.944 1386926.412 1048683.265 1643938.319 1399827.819 1663298.195 1202385.052 1509938.809 820217.2168 2.512672138 1.280260792 1.69092575 1.278543346 2.0042719 1.706655006 2.027875252 1.46593491 1.84090114 1 19.6456465 -1.561139868 2.633272732 0.949372968 1.724761888 0.284980648 0.356293536 15734587.41 14938333.86 5596143.819 0.084631262 0.027470093 1.561139868 0.77538892 EKEDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKEDFEK 7 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 69.423 0.054518 157250000 630470 279100 399260 311600 579660 551130 629610 394680 461720 187210 FALSE TRUE 655361.4424 327033.2539 409665.0436 373233.55 481129.6002 423138.41 580259.523 389389.9602 445102.7874 223890.2151 2.927155356 1.460685782 1.829758586 1.667038239 2.148953227 1.889937038 2.591714527 1.739200438 1.988040375 1 17.77243195 0.2832114 1.394519516 0.999629071 2.009365076 0.353148305 0.416789752 6.252635302 11.01934575 0.376185209 0.108999189 1.91960291 -0.2832114 1.009736005 EKEEEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKEEEEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 116.3 0.0020949 1956960000 3621400 2492170 3144420 2248470 4223190 4183610 3984530 3158660 3499410 2138150 FALSE TRUE 3764375.668 2920180.811 3226366.168 2693210.655 3505333.672 3212029.981 3672212.127 3116323.329 3373466.918 2557079.555 1.472138659 1.14199842 1.261738674 1.053236944 1.370834812 1.256132205 1.436096159 1.218704097 1.319265531 1 21.28606562 -1.236389994 5.249755174 0.999973118 1.27431339 0.325379107 0.12108208 3.56E-05 5.18E-06 0.109553532 0.025819487 0.058024313 1.236389994 0.274340272 EKEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKEELDR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 95.099 0.012508 7831570000 9987200 6763240 8690680 6219290 10453620 10309960 10177220 8481590 9038630 5614480 FALSE TRUE 10381502.37 7924773.859 8917166.26 7449446.999 8676717.406 7915628.039 9379502.903 8367908.159 8713331.472 6714529.86 1.546124983 1.180242552 1.328040302 1.109451764 1.292230072 1.178880458 1.396896447 1.246238878 1.297683033 1 22.67885496 -1.707191758 2.379125645 0.944021332 1.278532022 0.346815578 0.117406915 6606980.275 4764656.988 2206800.203 0.028660771 0.019624936 1.707191758 0.334510689 EKEELEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKEELEEIR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 73.885 0.038901 222250000 525940 372950 470010 377930 624760 608490 656670 502940 486280 357570 FALSE TRUE 546704.5173 437001.2614 482258.8467 452683.426 518563.5184 467177.4193 605198.4895 496198.9119 468778.8778 427628.9954 1.27845521 1.021916816 1.127750578 1.058589176 1.212648169 1.092483027 1.415241941 1.160349081 1.096227999 1 18.70600015 3.223767171 24.99288375 1.183957695 1.114985897 0.008325048 0.119793602 670.1603914 1132205.455 0.033440685 0.040121911 1674.045164 -3.223767171 -0.068971799 EKEELEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEELEQR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 116.52 0.0020575 1709300000 2326300 1540790 2166500 1499580 2691700 2733400 2472500 2105030 2268000 1467100 FALSE TRUE 2418144.12 1805408.697 2222960.77 1796192.448 2234165.795 2098609.275 2278698.989 2076815.516 2186375.123 1754550.156 1.378213163 1.028986656 1.266969065 1.023733886 1.273355332 1.196095346 1.298736877 1.183674066 1.246117198 1 20.74266976 -0.970545996 4.507955777 0.999996092 1.205113209 0.259198539 0.106467567 4.49E-06 1.03E-06 0.092201196 0.021731533 0.107017303 0.970545996 0.205117117 EKEELMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 EKEELMLR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;; 156.92 0.00035135 6993550000 7175520 6238920 7200610 5833770 9897250 8962080 9028400 7056110 7687280 6314140 FALSE TRUE 7458815.07 7310405.978 7388263.812 6987672.294 8214918.98 6880772.742 8320730.417 6961534.387 7410616.294 7551274.841 0.98775574 0.968102225 0.97841278 0.925363259 1.087885046 0.911206768 1.10189744 0.921901869 0.981372874 1 22.8482888 EKEES(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKEESPQPR 9 1 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 EKEES(1)PQPR;EKEES(1)PQPR;EKEES(1)PQPR;EKEES(1)PQPR 139.89 6.69E-05 2431410000 3511450 1818140 2595180 1803200 3405190 3689790 3020620 2559860 2802330 1538790 TRUE FALSE 3650084.757 2130391.402 2662812.523 2159867.578 2826377.02 2832892.192 2783855.911 2525549.264 2701474.691 1840286.439 1.983432949 1.1576412 1.446955467 1.173658368 1.535835379 1.539375682 1.512729678 1.372367481 1.467964244 1 20.81149891 -0.882078285 0.798733181 0.942363448 1.450552 0.289902175 0.217293031 55.44204321 18.41328289 8.6048794 0.06688194 0.131196339 0.882078285 0.508188552 EKEEVAEEAQS(ph)GGD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 1 EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD;EKEEVAEEAQS(1)GGD 269.91 1.95E-25 13481280000 8267760 5628554 8191029 5948332 9015950 9151850 10052600 7427179 8348375 4709208 TRUE FALSE 8594177.549 6595214.365 8404493.945 7124894.316 7483422.039 7026471.535 9264650.944 7327629.814 8047918.615 5631887.144 1.525985399 1.171048744 1.492305106 1.265098915 1.328759232 1.247622929 1.645034907 1.301096706 1.428991457 1 22.42518699 -1.75588908 6.790322709 0.991785168 1.373415534 0.403752297 0.137844422 0.015675278 0.000563523 0.122041805 0.028610902 0.017543285 1.75588908 0.381630367 EKEEVAEEAQSGGD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EKEEVAEEAQSGGD 14 1 O76070 O76070 SNCG Gamma-synuclein 0 ;;;;;;; 211.22 3.38E-08 9294240000 11116900 7735400 9795140 7698350 12281920 12250670 12298530 9933170 10963150 6712800 FALSE TRUE 11555803.8 9063894.777 10050409.4 9221060.653 10194243.63 9405637.553 11334539.08 9800032.104 10568588.37 8028044.636 1.43942944 1.129028946 1.251912496 1.148606052 1.269828967 1.171597566 1.41186797 1.220724666 1.316458596 1 22.93661721 -1.813824305 2.570819113 0.914969326 1.256081994 0.386108377 0.098903272 15499597.69 10675514.84 8192571.779 0.023180906 0.015352379 1.813824305 0.341112668 EKEHASGSGAQSEAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKEHASGSGAQSEAAGR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 192.16 1.21E-10 227046000 29512.7 257164 236762 249087 236710 330368 196717 294574 219601 260245 FALSE TRUE 30677.88418 301329.9165 242932.2122 298355.6651 196474.1188 253645.0388 181297.8075 290625.7174 211697.6029 311235.0251 0.098568226 0.968174827 0.780542653 0.958618539 0.631272521 0.814963029 0.582510942 0.933782171 0.680185666 1 18.2476449 4.746668087 24.77490627 0.807169696 0.098567828 0.698074616 0.141555554 469.7237916 1435350.572 0.031069101 0.347091019 55804.35424 -4.746668087 -0.708601868 EKEHNKEPDSSVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKEHNKEPDSSVSK 14 2 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 113.72 0.00031168 55979000 103630 39817 69680 37863 103650 78895 102010 63375 84398 37731 FALSE TRUE 107721.3924 46655.26002 71495.91804 45352.18839 86031.61002 60572.83192 94014.18965 62525.56179 81360.53247 45123.66705 2.387248189 1.033942121 1.584443879 1.005064335 1.906573992 1.342373878 2.083478489 1.385648948 1.80305675 1 15.46159669 EKEHQVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEHQVVR 8 1 Q9H307 Q9H307 PNN Pinin 0 ; 92.439 0.0070761 191147000 112358 116795 124368 106675 160766 152590 144146 127448 136537 121914 FALSE TRUE 116793.9806 136853.6327 127609.1322 127774.9966 133439.0527 117153.285 132847.4599 125739.768 131623.06 145800.7141 0.801052185 0.938634859 0.875229816 0.876367426 0.915215358 0.803516538 0.911157813 0.862408451 0.902760051 1 17.15363826 0.860031723 3.939293344 0.999990939 0.875755796 0.449467852 0.042135879 0.690782661 18.04093924 0.036424875 0.009319212 7.244888788 -0.860031723 -0.124235144 EKEIAETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKEIAETR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 113.62 0.0025657 615030000 1396680 1295260 1408540 1242660 1758900 1824770 1665650 1496100 1462730 1192700 FALSE TRUE 1451822.005 1517710.829 1445247.71 1488454.439 1459922.806 1400994.822 1535092.001 1476047.227 1410086.633 1426386.729 1.017831963 1.064024782 1.013222908 1.043513942 1.023511209 0.982198441 1.076210237 1.034815591 0.988572457 1 20.44393376 3.146474706 9.334129496 1.022654197 1.035197983 0.0636372 0.028306368 1.15975126 106.8032819 0.008270935 0.009897454 1401.117979 -3.146474706 0.012543786 EKEIS(ph)DDEAEEEKGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKEISDDEAEEEKGEK 16 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK;EKEIS(1)DDEAEEEKGEK 171.29 2.59E-09 3863060000 5919800 1421860 1931200 1761456 3063030 4249590 4382100 2215940 2479330 823827 TRUE FALSE 6153518.275 1666053.394 1981528.658 2109866.739 2542377.255 3262687.126 4038619.552 2186238.949 2390099.398 985240.1275 6.245704071 1.691012524 2.011213919 2.141474632 2.580464583 3.311565409 4.099122071 2.218990973 2.425905453 1 19.91011586 4.746342452 24.694285 2.505297866 6.245706228 0.668293378 0.811771995 506.5904805 1607530.826 0.197394047 2.123800161 55762.52766 -4.746342452 3.740408362 EKELAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKELAK 6 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 66.682 0.091899 423300000 261620 178080 248130 151670 324480 269030 308980 243120 306670 169590 FALSE TRUE 271948.9596 208663.8547 254596.4716 181669.8733 269325.0055 206551.8597 284761.3402 239861.3741 295633.0066 202817.9135 1.340852763 1.028823594 1.255295784 0.895728933 1.327915276 1.018410337 1.404024602 1.182643929 1.457627689 1 17.62982556 2.241330005 24.99997113 1.270822186 1.141311091 0.094169212 0.175914312 152.7838197 1379234.424 0.056848701 0.045599774 174.3130912 -2.241330005 -0.129511095 EKELETGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKELETGPK 9 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 141.95 9.62E-05 3787220000 3977150 2344460 3120420 2267060 4208600 3872780 4057340 3006500 3409400 1959120 FALSE TRUE 4134170.953 2747102.768 3201740.709 2715477.702 3493223.675 2973385.538 3739315.089 2966202.785 3286696.36 2342972.054 1.764498618 1.172486357 1.366529619 1.158988515 1.490936978 1.269065729 1.595970845 1.26600007 1.402789399 1 21.15990832 -0.771393194 1.085603166 0.982614595 1.375032877 0.290885387 0.180474629 127.0715014 69.26675909 8.922252956 0.048674748 0.169280451 0.771393194 0.392418283 EKELGNDAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKELGNDAYK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 85.845 0.012734 1107470000 463510 377190 492920 323090 566380 643140 527130 496760 515240 483740 FALSE TRUE 481809.7327 441969.4484 505765.9001 386996.2377 470106.9299 493780.4819 485812.1732 490101.7447 496696.613 578519.5912 0.832832181 0.76396626 0.874241612 0.66894232 0.812603302 0.853524218 0.839750599 0.847165337 0.858564897 1 19.14200629 0.444793535 0.427236502 1.017647477 0.788024509 0.560715165 0.052590663 1.699545801 0.568416148 0.112825763 0.03377359 2.784796952 -0.444793535 -0.229622968 EKELS(ph)PPPGLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;EKELS(1)PPPGLPSK 97.095 0.0023834 1856160000 3149890 1571640 2243190 1379160 3104870 2761120 2928910 2294270 2600290 1218170 TRUE FALSE 3274250.089 1841556.944 2301649.374 1651953.732 2577105.306 2119891.725 2699334.381 2263519.063 2506706.071 1456847.088 2.247490568 1.264070169 1.579883979 1.1339239 1.768960742 1.455123013 1.85286047 1.553710806 1.720637733 1 20.47441803 -1.678324521 2.693529859 0.918516641 1.599875381 0.279902925 0.296637878 27525209.77 23632108.14 15352499.25 0.065827734 0.020973721 1.678324521 0.68135874 EKENLSYDLVPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKENLSYDLVPLK 13 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;R4GN69 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 155.42 4.26E-05 244750000 522500 311360 420140 332460 653110 544700 538910 448830 527160 312530 FALSE TRUE 543128.7035 364833.658 431089.1935 398219.5957 542094.5955 418201.68 496668.826 442814.168 508187.6146 373764.2698 1.453131686 0.976106299 1.153371867 1.065429812 1.450364948 1.118891542 1.328829067 1.184741838 1.359647392 1 18.51176913 EKEPEYTLLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKEPEYTLLTER 12 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 75.316 0.031134 309050000 248420 195610 284770 184570 313410 301730 336440 266640 300050 185820 FALSE TRUE 258227.8134 229204.4959 292191.3401 221077.3951 260136.6801 231657.7803 310068.9537 263066.1269 289251.2591 222227.8713 1.161995622 1.031394013 1.314827607 0.994822989 1.170585304 1.042433512 1.395274823 1.183767479 1.301597579 1 17.76168024 2.269197887 24.99979477 1.235641511 1.120900353 0.127769965 0.126443696 341.4154894 278591.4908 0.040117091 0.033560914 185.8651161 -2.269197887 -0.114741159 EKEPIAASTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKEPIAASTNR 11 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 170 1.48E-05 1379880000 1315988 1099819 1239733 1032789 1695370 1614835 1503048 1276912 1368809 1218915 FALSE TRUE 1367944.222 1288704.358 1272041.46 1237071.582 1407191.613 1239814.044 1385235.17 1259797.083 1319545.831 1457738.057 0.938401941 0.884043846 0.872613193 0.848624056 0.965325428 0.850505369 0.950263433 0.86421362 0.905200921 1 20.47530007 -1.66021462 1.645819613 1.028780846 0.895683243 0.374750682 0.039570306 47219.21524 22026.73488 5645.968911 0.009821238 0.021866807 1.66021462 -0.133097603 EKEPIVGSTDYGKDEDSAEALLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKEPIVGSTDYGKDEDSAEALLK 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 202.44 1.17E-24 997600000 2028520 712850 1170080 709000 1934270 1583170 1731900 1125910 1434730 554560 FALSE TRUE 2108607.536 835276.4423 1200573.246 849238.0838 1605483.476 1215502.761 1596149.153 1110819.018 1383094.348 663215.4143 3.179370519 1.259434603 1.810231216 1.280486047 2.42075718 1.832742024 2.406682833 1.674899277 2.085437578 1 19.33911801 -0.735831373 6.502352625 0.999999994 1.951417982 0.225898129 0.547069008 4.32E-08 7.74E-09 0.482640803 0.113759527 0.183725157 0.735831373 0.951417988 EKEPS(ph)RER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 86.114 0.012808 1997410000 2770580 1593410 2254160 1590020 2890370 2874040 2711950 2177160 2461920 1525710 TRUE FALSE 2879964.638 1867065.772 2312905.261 1904521.21 2399065.94 2206587.766 2499380.273 2147978.731 2373315.98 1824643.663 1.578370997 1.023249531 1.26759285 1.043777067 1.314813401 1.209325312 1.369790893 1.1772045 1.300701078 1 20.79918332 -1.375327324 3.714720319 0.998843397 1.241970351 0.196963249 0.15208389 11080896.96 4185424.353 102681.9107 0.031894443 0.042137879 1.375327324 0.243126954 EKEQEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EKEQEDR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;;;; 121.09 0.0040782 4672168000 11391475 7475666 10159196 6811375 12480111 11427474 12652663 10025081 11667292 7249255 FALSE TRUE 11841219.23 8759553.483 10423952.99 8158644.645 10358746.19 8773616.349 11660914.21 9890711.187 11247388.44 8669607.722 1.365831028 1.010374836 1.202355784 0.941062722 1.194834475 1.011996924 1.345033661 1.140848756 1.297335335 1 23.04753529 2.253581611 24.99710618 1.205306628 1.114908906 0.059360883 0.142490815 580.8582617 966631.502 0.045299283 0.037763108 179.3005457 -2.253581611 -0.090397721 EKEQEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKEQEDRR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 ;;;;; 203.29 5.45E-05 4789520000 8741880 6547350 8374050 5985470 10247360 9493760 9427770 8153770 9201680 6185440 FALSE TRUE 9087016.173 7671806.431 8592284.622 7169378.101 8505517.407 7288978.119 8688796.753 8044482.05 8870513.334 7397358.541 1.228413646 1.037100796 1.161534158 0.969180831 1.149804672 0.985348767 1.174580995 1.087480349 1.199146058 1 22.81857877 4.753150422 23.54102105 1.089381492 1.228413868 0.222434552 0.080100644 1670.751734 2695693.969 0.017240061 0.355529406 56643.54458 -4.753150422 0.139032376 EKEQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EKEQFR 6 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 138.62 0.011151 40628500000 18267500 15488190 18066250 15708580 21409420 21151870 21008110 18747980 18068420 13282970 FALSE TRUE 18988715.01 18148166.15 18537071.32 18815690.24 17770254.44 16239668.75 19361439.44 18496693.99 17418141.09 15885513.65 1.195347876 1.14243496 1.166916709 1.184455892 1.118645253 1.022294218 1.218811042 1.164374939 1.096479565 1 23.9212084 -5 0.245211095 0.128750843 1.1617877 0.434437822 0.051866607 178.0556499 1.771051421 77.53197356 0.080471792 1.00E-05 5 1.033036857 EKEQFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEQFRK 7 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 111.01 0.0037546 1871640000 1649310 1251350 1672020 1111010 2203800 1757160 1629210 1537750 1667870 1270090 FALSE TRUE 1714426.032 1466259.628 1715594.215 1330764.462 1829198.863 1349086.22 1501508.263 1517138.977 1607843.685 1518939.818 1.128699118 0.96531779 1.129468195 0.876114015 1.204260262 0.888176216 0.988523867 0.998814409 1.05853021 1 20.53463328 EKEQMMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKEQMMR 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;; 113.41 0.0055956 1627310000 1714199 1806480 1917487 1742186 2551400 2489050 2144598 1969547 2191228 1853513 FALSE TRUE 1781876.9 2116728.888 1967458.286 2086785.191 2117713.939 1911005.859 1976498.805 1943148.444 2112366.132 2216673.385 0.803851804 0.954912394 0.887572477 0.941404 0.955356776 0.862105294 0.891650894 0.876605664 0.952944239 1 21.07996478 1.01708029 4.531499628 0.99972212 0.899463195 0.367540239 0.04388531 0.169551024 9.434281194 0.039998856 0.010166667 10.40112438 -1.01708029 -0.100258925 EKETLAVNYEKEEEFLTNELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKETLAVNYEKEEEFLTNELSR 22 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;;; 254.25 2.69E-37 906760000 1012215 583123 852936 551479 1264177 1199000 1142566 1017343 1106758 720489 FALSE TRUE 1052178.03 683269.8392 875164.2129 660559.9002 1049292.645 920550.421 1053008.691 1003707.181 1066925.996 861655.025 1.221112858 0.792973777 1.015678186 0.766617592 1.217764203 1.06835148 1.222076888 1.164859662 1.238228717 1 19.71675086 3.217220355 24.99952488 1.161248159 0.942699873 0.347858393 0.135545794 228.5302961 267716.2744 0.03609661 0.043182146 1648.99886 -3.217220355 -0.218548286 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 EKEVDGLLTSEPMGSPVSSK 20 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.999)PVS(0.001)SK;EKEVDGLLTSEPMGS(0.997)PVS(0.003)SK;EKEVDGLLTSEPMGS(0.999)PVSSK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.971)PVS(0.029)SK;EKEVDGLLTSEPMGS(1)PVSSK;EKEVDGLLTSEPMGS(0.996)PVS(0.003)S(0.001)K;EKEVDGLLTSEPMGS(0.997)PVS(0.002)SK 218.86 5.82E-25 7995044000 9000950 4908302 7189460 4792788 9752990 8717100 9468070 7119074 8472235 3972760 TRUE FALSE 9356314.456 5751264.687 7376823.234 5740787.161 8095180.243 6692685.634 8725937.933 7023654.457 8167320.917 4751146.259 1.969275191 1.210500451 1.552640738 1.208295188 1.703837306 1.408646518 1.836596362 1.478307355 1.719021152 1 22.17984419 EKEWQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKEWQR 6 1 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-4;C9JMV9;A0A1B0GV31 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 100.74 0.034032 518000000 901420 860120 954990 788540 1024510 1080250 980790 889150 979780 769720 FALSE TRUE 937008.7576 1007838.919 979877.8239 944510.8584 850364.1561 829378.3088 903913.117 877232.3986 944517.9092 920531.8968 1.017899283 1.094844103 1.06446917 1.026049029 0.923774786 0.900977263 0.981946546 0.952962523 1.026056688 1 19.81210819 3.42411717 4.839062496 0.959958764 1.060487446 0.564137979 0.037909224 0.135100009 6.73116746 0.010713456 0.014893222 2655.321852 -3.42411717 0.100528682 EKFENSIESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKFENSIESLR 11 1 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 90.731 0.010277 729060000 292550 229720 263970 284080 308970 310880 266350 225510 231250 199990 FALSE TRUE 304100.0999 269172.623 270849.2751 340270.1761 256451.3898 238682.8314 245472.791 222487.4073 222927.3577 239174.2115 1.271458566 1.125424942 1.132435112 1.422687563 1.072236794 0.997945514 1.026334694 0.930231591 0.932071047 1 17.86770232 3.008786664 24.98120175 0.979750579 1.225550227 0.691359843 0.082038311 116.2548384 330519.0141 0.024193261 0.028876913 1020.438097 -3.008786664 0.245799649 EKFEPTVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKFEPTVFR 9 1 E7ETZ4;Q9Y6E2;Q75MG1;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;; 118.6 0.00087858 1346060000 1751800 1513920 1766760 1549710 2410500 2223780 2012280 1768140 1879190 1703510 FALSE TRUE 1820962.417 1773923.983 1812803.217 1856238.013 2000764.071 1707340.797 1854552.235 1744440.975 1811558.319 2037280.169 0.893820322 0.870731483 0.889815375 0.911135366 0.982076055 0.838049093 0.910307902 0.856259734 0.889204316 1 20.95821296 -2.455509029 2.179875644 2.059912812 0.89228104 0.430953378 0.036694054 1927076.248 196303.437 10107059.25 0.009161593 0.00350341 2.455509029 -1.167631773 EKFEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKFEVK 6 1 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 67.757 0.089314 174550000 34408 25480 29417 22083 40165 33530 41152 32172 33552 23089 FALSE TRUE 35766.45441 29855.99179 30183.63119 26450.95149 33337.76765 25743.16565 37926.39871 31740.78696 32344.47007 27612.84748 1.29528309 1.08123553 1.093101 0.957921906 1.207328135 0.932289423 1.37350553 1.149493437 1.171355837 1 14.75305205 2.247504228 24.99995112 1.188825071 1.092775675 0.076437374 0.130315074 415.9446705 1162685.518 0.042976558 0.035459991 176.8089432 -2.247504228 -0.096049396 EKFPEFCSS(ph)PSPPVEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.072)S(0.901)PS(0.027)PPVEVK;EKFPEFCS(0.023)S(0.958)PS(0.019)PPVEVK 142.53 3.53E-07 1079230000 760840 400340 566780 420930 725720 640650 735360 566270 631270 311950 TRUE FALSE 790878.5507 469095.2808 581550.7524 504188.6976 602362.3736 491868.7466 677720.5617 558680.0769 608550.716 373070.6299 2.119916411 1.257390004 1.558822126 1.35145642 1.614606794 1.318433313 1.816601221 1.49751825 1.631194383 1 18.50908926 4.751667111 24.6714216 1.483825993 2.119916905 0.447846631 0.220365526 1620.050053 3049487.568 0.047640181 0.889530615 56450.41137 -4.751667111 0.636090912 EKFPEFCSSPS(ph)PPVEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 EKFPEFCS(0.001)S(0.01)PS(0.989)PPVEVK 169.56 1.19E-09 914170000 616580 316940 498080 341390 633490 579820 602760 452440 526360 242920 TRUE FALSE 640923.0545 371371.9795 511060.374 408915.9231 525809.5961 445165.5923 555514.0962 446375.7818 507416.4064 290515.523 2.206157688 1.278320606 1.759149971 1.407552749 1.809919107 1.532329796 1.912166656 1.536495459 1.746606863 1 18.14825573 -1.184769141 4.692387634 0.999900077 1.66841271 0.397832221 0.252803832 0.000230911 4.01E-05 0.213876852 0.050403784 0.065347783 1.184769141 0.668512633 EKFS(ph)FEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKFSFEPK 8 1 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 EKFS(1)FEPK;EKFS(1)FEPK 97.214 0.0050813 684850000 1987090 821400 1360450 956080 2462600 2035990 2231700 1715460 1958380 886010 TRUE FALSE 2065541.848 962469.0604 1395904.445 1145189.77 2044008.132 1563162.178 2056773.523 1692467.065 1887898.286 1059606.696 1.949347674 0.908326707 1.317379788 1.080768718 1.929025307 1.475228672 1.941072599 1.597259692 1.781697203 1 20.01509743 3.244440217 24.99996699 1.661492603 1.285226815 0.14371146 0.355883123 213.8102753 909111.5651 0.091114453 0.12017413 1755.6592 -3.244440217 -0.376265787 EKGSFS(ph)DTGLGDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKGSFSDTGLGDGK 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 EKGS(0.206)FS(0.786)DT(0.008)GLGDGK 90.654 0.0034316 118980000 137030 68596 109490 69789 153700 141760 154940 110350 118690 53697 TRUE FALSE 142440.0502 80376.8294 112343.3993 83593.0559 127574.1289 108838.3884 142795.3979 108870.9387 114418.3701 64217.89906 2.218073968 1.25162658 1.749409448 1.301709603 1.986582102 1.694829479 2.223607437 1.695336352 1.781720856 1 15.97068785 3.212278406 24.99967516 1.791582168 1.611677636 0.000131662 0.385019299 733.0884535 697312.6606 0.102626367 0.122696894 1630.340835 -3.212278406 -0.179904531 EKGTWVQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKGTWVQLK 9 1 P46778 P46778 RPL21 60S ribosomal protein L21 0 ; 133.23 0.000258 1030750000 1784520 1353390 1508250 1236940 3765200 2825300 2497200 1880930 2238430 2774400 FALSE TRUE 1854974.228 1585824.205 1547556.234 1481603.04 3125192.649 2169166.893 2301462.939 1855719.21 2157869.342 3317990.561 0.559065553 0.477947172 0.466413694 0.446536243 0.94189317 0.653759211 0.693631551 0.559290081 0.650354274 1 21.66187835 3.285027858 24.99996435 0.708601538 0.485303168 0.468744558 0.132518472 125.1195546 67315.01532 0.036332393 0.049194137 1927.64856 -3.285027858 -0.22329837 EKHLDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKHLDLEK 8 1 P55263-3;P55263-2;P55263;P55263-4;A0A5K1VW54;A0A5K1VW94;A0A5F9ZHJ1;A0A5F9ZH72;A0A5F9ZH31;A0A5F9ZGZ8 P55263-3 ADK Adenosine kinase 0 66.435 0.037067 161060000 515140 441110 462060 373750 697240 630160 518270 473000 509130 433710 FALSE TRUE 535478.125 516867.2111 474101.6632 447676.6345 578723.3938 483814.8902 477646.6432 466660.2087 490806.5108 518687.1706 1.032372026 0.996491219 0.914041623 0.863095638 1.115746497 0.932768184 0.920876147 0.899694913 0.946247639 1 18.98450516 2.520737422 24.99829271 0.928985735 0.979369193 0.084597379 0.067641098 1056.40476 605469.4801 0.022153822 0.02088549 331.6938523 -2.520737422 0.050383458 EKHPDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EKHPDGK 7 1 P53396;P53396-2;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;;; 75.854 0.02544 2644963000 4543300 2333702 3593142 2449070 4724620 3854810 4955620 3828900 4361840 2133955 FALSE TRUE 4722672.992 2734497.165 3686782.232 2933488.736 3921530.78 2959588.798 4567185.555 3777579.858 4204858.23 2552062.625 1.85053178 1.071485134 1.444628433 1.149457975 1.536612284 1.15968502 1.789605596 1.480206567 1.647631288 1 21.2832323 2.253458162 24.99771591 1.52483222 1.356335784 0.024314107 0.284562788 617.6021577 1036319.623 0.090133948 0.07512512 179.2495862 -2.253458162 -0.168496436 EKHPNS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.532)S(0.468)PR 71.241 0.030364 65091000 150750 140580 155610 135780 185780 198730 183890 168860 184010 150790 TRUE FALSE 156701.7264 164723.5214 159665.3244 162636.8787 154201.182 152577.9693 169476.2213 166596.7079 177387.516 180334.4135 0.868950764 0.91343365 0.885384666 0.901862687 0.855084612 0.846083487 0.939788574 0.923820943 0.983658707 1 17.46031521 1.477559201 1.290303253 0.999265177 0.882256435 0.758411487 0.024100013 0.201242861 0.641911841 0.021923673 0.007414437 30.03026751 -1.477559201 -0.117008742 EKHPNSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKHPNSSPR 9 1 P29374 P29374 ARID4A AT-rich interactive domain-containing protein 4A 1 EKHPNS(0.118)S(0.882)PR 75.849 0.022466 21260000 57521 52653 70040 47709 74828 77618 74750 62688 69962 55210 TRUE FALSE 59791.9735 61695.74317 71865.29994 57145.6978 62108.76329 59592.39581 68890.89968 61847.7699 67444.08129 66027.34244 0.905563836 0.934396886 1.088417272 0.865485353 0.940652175 0.902541184 1.043369264 0.936699367 1.021456851 1 16.01077596 2.247936349 24.99998389 0.990572112 0.942732817 0.185864379 0.060823041 425.7574368 1135265.067 0.021169526 0.017488086 176.9849546 -2.247936349 -0.047839295 EKHQTLEVS(ph)LSRDSPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKHQTLEVSLSRDSPLK 17 2 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 EKHQT(0.005)LEVS(0.744)LS(0.125)RDS(0.125)PLK 69.922 0.017599 94111000 69779 70135 94608 69459 116190 118330 118030 100190 84352 77338 TRUE FALSE 72533.9288 82180.14068 97073.5622 83197.78289 96440.0653 90849.65081 108778.5002 98847.11693 81316.188 92490.90037 0.78422773 0.888521361 1.049547164 0.899523981 1.042697875 0.982255016 1.176099484 1.068722615 0.879180413 1 16.49702381 5.717235316 0.676682799 1.035841538 1.30E-13 0.427774683 0.082432967 9.025571078 1.16228487 0.032241149 9.732579674 521477.1887 -5.717235316 -1.035841538 EKIDLENTLEQEQEALVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKIDLENTLEQEQEALVNR 19 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 275.68 1.74E-39 1227370000 593756 449291 581222 430468 713326 710618 626854 562556 609236 444926 FALSE TRUE 617197.9454 526453.2343 596369.1228 515613.2856 592075.1013 545587.739 577719.5455 555015.857 587309.7154 532100.7311 1.159926888 0.989386414 1.120782378 0.969014428 1.112712437 1.025346719 1.085733418 1.043065391 1.103756641 1 19.02133986 0.382732764 0.005438401 1.60E-05 2.090404727 0.078130415 0.058700758 28231.76749 60.52462615 11801.05109 11460.13775 2.413974977 -0.382732764 2.090388758 EKIEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKIEDAK 7 1 P49321;P49321-3;P49321-4;P49321-2;Q5T624;H0YF33;E9PRH9;H0YDS9 P49321 NASP Nuclear autoantigenic sperm protein 0 59.35 0.094907 2161200000 861430 410540 556510 401530 883530 801350 902420 563870 689470 377410 FALSE TRUE 895439.9216 481047.0514 571013.1078 480951.4356 733347.8862 615248.6071 831685.9624 556312.245 664656.1094 451356.2635 1.983887217 1.065781269 1.265105093 1.065569428 1.624765059 1.363110821 1.842637467 1.232534674 1.472575354 1 18.7839071 3.214819599 24.9968561 1.4461487 1.319422144 0.008270032 0.318530956 926.8821214 975909.2348 0.087618098 0.104778423 1639.908432 -3.214819599 -0.126726557 EKIETELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKIETELR 8 1 P63104;E7EX29;B0AZS6;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 132.01 0.00089427 30875850000 23428100 17616690 21887200 18848740 27175200 25770000 28519500 23118300 23243900 14390490 FALSE TRUE 24353059.48 20642219.47 22457598.41 22576964.51 22555969.21 19785308.05 26284067.07 22808437 22407356.58 17210030.99 1.415050298 1.199429535 1.304913304 1.311849149 1.310629203 1.149638142 1.527252745 1.325299008 1.30199397 1 24.03674636 0.756576759 5.208407436 1.00000032 1.318150925 0.484688535 0.097942776 8.177250734 174.6515909 0.090822032 0.022923999 5.709219747 -0.756576759 0.318150605 EKINIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKINIR 6 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;;; 111.28 0.025523 1891580000 2363060 2951290 3020350 2663790 5730230 4112710 3175800 3138180 3117450 4290120 FALSE TRUE 2456355.433 3458151.1 3099062.802 3190679.711 4756207.551 3157595.431 2926872.498 3096117.83 3005253.583 5130686.875 0.478757619 0.674013282 0.604024934 0.62188159 0.927011854 0.615433276 0.570464066 0.603450942 0.585740985 1 22.29072055 -2.103604092 2.412878876 1.649595706 0.63469511 0.504159057 0.109674836 8673501.636 2520596.01 30919396.28 0.026550058 0.007877636 2.103604092 -1.014900595 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 43 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 104.43 1.69E-06 559990000 63181 66734 89872 42218 118120 83974 94121 76227 99313 64683 FALSE TRUE 65675.43467 78195.04538 92214.13815 50568.59439 98042.00459 64472.31114 86743.55008 75205.30175 95738.74453 77356.39542 0.848998125 1.010841379 1.192068706 0.653709291 1.26740658 0.833445131 1.121349432 0.972192426 1.237631924 1 16.23923295 1.702041076 1.643396499 1.097074522 0.98270615 0.062439159 0.180901264 1.094600929 5.870470057 0.12931297 0.049664847 50.35482325 -1.702041076 -0.114368372 EKKEESHSNDQSPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKKEESHSNDQSPQIR 16 2 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ;; 229.54 1.85E-15 342968000 513666 290769 478082 242604 637410 521880 408917 375450 508292 290466 FALSE TRUE 533945.9303 340706.3139 490541.2097 290590.3471 529063.2759 400681.2792 376865.017 370417.7069 489998.6702 347377.2514 1.537077999 0.980796274 1.412128191 0.836526704 1.523022229 1.153447088 1.084886864 1.066326898 1.410566375 1 18.40614375 5.421042769 0.021528653 4.98E-07 2.554211479 0.07676755 0.227530593 4600.217427 12.71885887 620.8717184 910.1638033 263659.1025 -5.421042769 2.554210981 EKKEEWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKKEEWDR 8 2 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 0 ;; 94.692 0.0057251 859810000 1383920 732540 1076360 630730 1487780 1267340 1242850 996910 1186010 623700 FALSE TRUE 1438558.23 858348.0466 1104410.826 755486.5115 1234887.687 973019.4917 1145432.169 983548.0521 1143325.732 745902.0735 1.928615406 1.150751656 1.480637828 1.012849459 1.655562749 1.304486911 1.535633443 1.318602115 1.532809429 1 19.50862671 -2.046804961 2.585471617 0.450759808 1.415669196 0.215877845 0.246419454 13658366.33 4996510.745 44404309.26 0.053950948 0.008978319 2.046804961 0.964909388 EKLCYVALDFEQEMATAASSSSLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 328.27 8.04E-88 3984266000 3712427 2689269.3 3597236 2863829 4586625 4485405 4703460 3844052 4431506 3024223 FALSE TRUE 3858996.485 3151130.383 3690982.925 3430285.829 3806992.121 3443737.666 4334790.515 3792528.771 4272016.965 3616761.595 1.066975631 0.871257422 1.020521488 0.948441234 1.052596922 0.952160538 1.198528131 1.048597944 1.181171845 1 21.78626707 2.256838625 24.99971355 1.107546642 0.983121656 0.385449212 0.075280504 225.8571968 308915.1086 0.023872479 0.019937385 180.6502741 -2.256838625 -0.124424987 EKLDSVIEFSIPDSLLIR ddPTM_MDA-MB-175_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 ; 145.75 8.10E-08 787820000 1532990 1396040 1540270 1411330 1922560 2032530 1610120 1397750 1542520 1239300 FALSE TRUE 1593513.629 1635799.01 1580410.702 1690486.862 1595763.938 1560505.711 1483914.587 1379015.448 1487005.007 1482117.107 1.075160405 1.103690796 1.066319722 1.140589265 1.076678712 1.052889615 1.001212779 0.930436226 1.003297917 1 20.49922801 2.325417127 2.129099505 0.969267064 1.093927595 0.77935536 0.027316271 0.126926798 1.178767015 0.011811245 0.008563162 211.551996 -2.325417127 0.124660531 EKLEAEMEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKLEAEMEAAR 11 1 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;;;; 152.4 3.01E-05 1707446000 2516030 1986809 2353580 1993982 3270810 3046770 2912310 2552030 2715250 2051225 FALSE TRUE 2615364.807 2328027.991 2414916.228 2388385.688 2714838.885 2339203.842 2684035.532 2517824.212 2617528.683 2453123.266 1.066136726 0.949005712 0.984425146 0.973610141 1.106686697 0.953561476 1.094129908 1.026374927 1.067018816 1 21.2261883 3.30684226 24.99999999 1.041095389 0.989497276 0.178712933 0.050145791 79.69874648 29178.6311 0.012773725 0.017295702 2026.946381 -3.30684226 -0.051598112 EKLEAYQHLFYLLQTNPTYLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKLEAYQHLFYLLQTNPTYLAK 22 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 231.76 5.55E-27 4762500000 3416300 2282090 3310830 2361990 4005100 3702980 3990200 3505770 3857550 2308020 FALSE TRUE 3551178.162 2674021.205 3397112.95 2829184.572 3324314.533 2843019.014 3677437.698 3458780.887 3718717.529 2760232.329 1.286550456 0.968766715 1.230734425 1.024980594 1.204360407 1.029992651 1.332292814 1.253076 1.347248016 1 21.39635827 2.234509557 24.99590418 1.2569062 1.121136269 0.135481795 0.129201285 153.4400203 946744.7592 0.042663006 0.032653126 171.5969472 -2.234509557 -0.135769932 EKLEDFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKLEDFFK 8 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 63.397 0.067095 403360000 647070 365610 548500 388190 794530 642260 692660 555930 570450 345890 FALSE TRUE 672616.8232 428400.6734 562794.3606 464972.8234 659476.0744 493104.8485 638367.4993 548478.6677 549919.6159 413660.523 1.626011635 1.035633447 1.360522286 1.12404447 1.594244647 1.192051987 1.543215907 1.32591494 1.329398348 1 18.65808776 0.575463202 3.079539386 1.00000322 1.343596757 0.237930888 0.186823222 13.40643856 95.46889007 0.162013117 0.042232099 3.762384721 -0.575463202 0.343593538 EKLEMEMEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 159.5 2.61E-05 3947330000 3916153 3459289 4343560 3397647 5396570 5255330 4719000 4347180 4491080 3729754 FALSE TRUE 4070765.744 4053394.976 4456756.742 4069691.436 4479262.959 4034859.253 4349112.449 4288913.163 4329446.908 4460527.886 0.912619728 0.908725398 0.999154552 0.91237888 1.004200192 0.904569898 0.975021917 0.961525916 0.970613124 1 22.08878303 8 0.095801364 1.021380328 0.740836934 0.266810689 0.033579945 188.3590877 1.285290154 0.453883027 6.943068084 99999999.94 -8 -0.280543394 EKLQEEGGGS(ph)DEEETGSPSEDGMQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKLQEEGGGSDEEETGSPSEDGMQSAR 27 1 Q13610;Q13610-2 Q13610 PWP1 Periodic tryptophan protein 1 homolog 1 EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR;EKLQEEGGGS(1)DEEETGSPSEDGMQSAR 222.42 1.42E-34 2206600000 690585 803198 1000482 851080 1136725 1239262 1208903 1057452 1154628 681550 TRUE FALSE 717849.829 941141.0085 1026555.383 1019421.084 943504.8905 951462.1817 1114146.024 1043278.586 1113073.164 815086.6734 0.880703675 1.154651449 1.259443218 1.250690408 1.157551609 1.167314118 1.366904969 1.279960303 1.365588716 1 19.63659395 4.7289716 2.373645456 1.245675333 0.798348081 0.507589078 0.102479238 0.411243781 2.842861372 0.024688 0.375571573 53576.16206 -4.7289716 -0.447327252 EKLQSFDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKLQSFDSPER 11 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 EKLQSFDS(1)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER;EKLQSFDS(1)PER 179.79 4.21E-06 1497500000 2169140 1867960 2161130 1786770 2755690 2670380 2529590 2291690 2394530 1927730 TRUE FALSE 2254779.322 2188767.599 2217450.823 2140187.773 2287278.798 2050224.715 2331314.126 2260973.644 2308351.333 2305431.785 0.978029078 0.94939595 0.961837534 0.928324051 0.992125993 0.889301834 1.011226678 0.980715916 1.001266378 1 21.13660555 EKMLRAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EKMLRAAR 8 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 0 ;;;;;; 87.323 0.02478 42558610000 23184050 18010240 20536340 14100540 35086750 26543660 21407460 22077330 23401550 30129410 FALSE TRUE 24099374.2 21103358.62 21071533.89 16889584.73 29122716.77 20379297.24 19729487.35 21781419.5 22559332.79 36032691.03 0.668819716 0.585672566 0.584789348 0.468729485 0.808230413 0.565577998 0.547544099 0.604490502 0.6260796 1 25.10280306 0.582647577 2.779459724 0.999996273 0.601602087 0.667215571 0.083447184 3.59159091 23.21827689 0.076462168 0.020145808 3.825142129 -0.582647577 -0.398394186 EKNGS(ph)EEDDDEKPGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKNGSEEDDDEKPGKR 16 3 Q6ZU65;Q6ZU65-2;H7C4P8 Q6ZU65 UBN2 Ubinuclein-2 1 EKNGS(1)EEDDDEKPGKR 101.17 0.0099813 54710000 123460 16927 34929 18294 73172 84686 63895 37522 43327 8908.4 TRUE FALSE 128334.2961 19834.08058 35839.27843 21912.4986 60734.24958 65018.95993 58886.74294 37019.07896 41767.66973 10653.83042 12.0458362 1.861685403 3.363980562 2.056771859 5.700696106 6.102871679 5.527283674 3.474720125 3.920436885 1 13.3790846 4.747406138 24.92843242 3.889040729 12.04584056 0.698105005 1.647096211 648.1290959 1826515.471 0.399630013 4.803029582 55899.27021 -4.747406138 8.156799828 EKNPDMVAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKNPDMVAGEK 11 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 79.646 0.024238 378688000 436040 275887 374281 281071 532412 445031 450344 352083 458585 263222 FALSE TRUE 453255.1959 323268.4461 384035.0703 336666.0049 441912.7984 341679.2948 415044.8605 347363.9033 442080.6154 314795.3112 1.439841001 1.026916331 1.219951685 1.069475919 1.403809976 1.085401474 1.318459474 1.103459584 1.404343075 1 18.26405453 -1.504396194 3.26410518 0.994811095 1.215468587 0.173127627 0.147799031 7078734.78 6535013.877 237691.5892 0.030589937 0.031304286 1.504396194 0.220657491 EKPEEESLAAPTWLVHLQQVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKPEEESLAAPTWLVHLQQVER 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ;; 268.36 3.48E-38 625150000 525870 364610 486280 370876 622530 613560 546240 489110 484520 332453 FALSE TRUE 546631.7537 427228.9312 498952.8563 444234.1658 516712.573 471069.9886 503424.2815 482554.2805 467082.2198 397590.8002 1.374860166 1.074544308 1.254940648 1.117315002 1.299608977 1.184811088 1.266186947 1.21369579 1.174781257 1 18.60092485 0.76976657 2.455652582 1.000075438 1.218982817 0.400991389 0.081678378 0.960787514 8.698078172 0.069349375 0.018597756 5.885272419 -0.76976657 0.218907379 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.845)S(0.155)DPEAAFLSR;EKPELSEPSHLNGPS(0.986)S(0.014)DPEAAFLSR;EKPELSEPS(0.001)HLNGPS(0.499)S(0.499)DPEAAFLS(0.001)R 283.98 1.08E-53 1799320000 835616 930652 1156776 1075203 1162787 1353416 1354650 1189518 1137084 801503 TRUE FALSE 868606.7649 1090484.242 1186922.533 1287874.944 965136.8811 1039105.645 1248468.993 1173574.457 1096160.569 958542.1671 0.906174809 1.137648691 1.238258027 1.343576723 1.006879941 1.084047923 1.302466429 1.224332635 1.143570525 1 19.87048237 4.718815032 3.606214526 1.182880393 0.880262389 0.32777063 0.109918825 0.280229464 6.665785791 0.026582865 0.222015685 52337.74802 -4.718815032 -0.302618004 EKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKPELSEPSHLNGPSSDPEAAFLSR 25 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 EKPELSEPSHLNGPS(0.176)S(0.824)DPEAAFLSR;EKPELSEPSHLNGPS(0.068)S(0.932)DPEAAFLSR;EKPELSEPSHLNGPS(0.225)S(0.775)DPEAAFLSR 193.05 2.49E-18 4339740000 858920 913470 1170180 1018030 1225610 1343170 1297060 1121830 1061270 684090 TRUE FALSE 892830.8248 1070351.367 1200675.852 1219393.295 1017281.25 1031239.123 1195393.048 1106793.704 1023075.1 818124.3378 1.091314344 1.308299139 1.467595812 1.490474295 1.243431106 1.260491927 1.461138598 1.352842903 1.250512976 1 19.64196059 0.872647548 3.189869003 1.000210692 1.343662103 0.430978816 0.115245295 0.501494076 9.99868626 0.112237579 0.029232279 7.458432232 -0.872647548 0.343451411 EKPEVTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKPEVTDR 8 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ;;; 110.38 0.0031343 981560000 1128962 979084 1166364 912025 1345759 1354110 1239977 1183193 1142880 873244 FALSE TRUE 1173534.292 1147234.061 1196760.404 1092420.823 1117007.366 1039638.474 1142784.363 1167334.233 1101747.972 1044339.443 1.123709633 1.098526029 1.145949636 1.046039993 1.069582667 0.99549862 1.094265251 1.11777281 1.05497114 1 19.99415928 1.043862629 0.010612167 6.96E-06 2.117843275 0.347678329 0.039047804 1705.17189 12.77034531 1289.170738 1257.27824 11.06273805 -1.043862629 2.117836319 EKPGVESMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKPGVESMR 9 1 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 94.465 0.0079376 162700000 107340 100330 122400 110960 145060 165220 134960 137320 123460 88131 FALSE TRUE 111577.8661 117560.897 125589.8446 132907.5568 120402.753 126850.1589 124381.4825 135479.45 119016.6987 105398.5821 1.058627772 1.115393535 1.191570532 1.260999476 1.142356478 1.203528135 1.180105843 1.285401068 1.129205881 1 16.68549593 4.415764311 2.93042886 1.19246731 1.064066984 0.160329043 0.075696168 0.347087483 5.659435667 0.017742121 0.073603504 26047.39591 -4.415764311 -0.128400326 EKPPITVVGDVGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKPPITVVGDVGGR 14 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;I3L4G9;C9J168;B4DP31;Q14558;Q14558-2 O60256;C9J168 PRPSAP2;PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 2;Phosphoribosyl pyrophosphate synthase-associated protein 1 0 ; 146.3 7.61E-06 465400000 783220 631050 696230 669050 903070 890230 806280 727330 751120 631630 FALSE TRUE 814142.1304 739427.9286 714374.3258 801386.0931 749566.484 683487.5741 743081.6668 717581.331 724087.3379 755385.8052 1.0777832 0.978874535 0.945707903 1.060896416 0.992296226 0.904819192 0.983711451 0.949953423 0.958566249 1 19.52685415 2.988350013 24.80774935 0.956935852 1.010472578 0.283921357 0.041958545 677.2383308 1442132.302 0.012164853 0.013602978 973.5315109 -2.988350013 0.053536726 EKPQGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKPQGQR 7 1 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 89.298 0.016394 298820000 292020 258200 304800 223600 330160 324070 346410 283160 328210 253830 FALSE TRUE 303549.1751 302543.8415 312743.3384 267827.4126 274039.5211 248809.6538 319257.479 279364.7034 316397.7862 303563.1286 0.999954034 0.996642256 1.030241518 0.882279129 0.902743104 0.819630681 1.05170045 0.920285361 1.042280028 1 18.21163704 -0.293794513 6.89888667 0.999999851 0.956863068 0.022999735 0.07333225 9494264.73 1376202.457 0.07018915 0.017023369 0.508399936 0.293794513 -0.043136783 EKPSEDMESNTFFDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKPSEDMESNTFFDPR 16 1 O43395;O43395-3 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 71.697 0.036406 140680000 234350 229080 298550 248770 322210 331560 295860 293910 292320 242940 FALSE TRUE 243602.319 268422.708 306330.4583 297975.9635 267440.8593 254560.2148 272669.7201 289970.6172 281799.4603 290539.4416 0.838448362 0.923877001 1.054350681 1.025595567 0.920497602 0.876164053 0.938494679 0.998042178 0.96991809 1 18.1483745 4.61265242 3.854317638 0.970010957 0.839326524 0.404725468 0.049512948 0.254303665 5.96806243 0.013138658 0.07031111 40987.59344 -4.61265242 -0.130684434 EKPYFPIPEEYTFIQNVPLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKPYFPIPEEYTFIQNVPLEDR 22 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 255.2 4.10E-37 8439450000 5646980 5281530 6343610 5443690 6727230 7068750 6300220 6340710 6341820 5484890 FALSE TRUE 5869927.131 6188591.693 6508929.688 6520435.634 5583737.848 5427139.94 5806392.294 6255723.154 6113579.137 6559549.181 0.894867463 0.943447716 0.992283084 0.994037159 0.851238049 0.827364776 0.885181608 0.953681874 0.932012089 1 22.64516524 0.821828475 1.4492729 0.998926848 0.917035966 0.18487261 0.05228634 1.299709148 5.04299961 0.055322956 0.016291625 6.634809757 -0.821828475 -0.081890881 EKQDETQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKQDETQTK 9 1 P35221-2;P35221;P35221-3;E5RGY7 P35221-2 CTNNA1 Catenin alpha-1 0 ;;; 96.113 0.00692 205032000 585783 301084 410125 281617 557764 531544 553566 426913 476703 285915 FALSE TRUE 608910.1652 352792.8349 420813.1944 337320.0021 462955.4745 408100.9616 510176.0504 421190.9295 459546.5521 341934.5701 1.78077977 1.031755388 1.230683386 0.986504529 1.353930006 1.193506002 1.492028286 1.231788086 1.343960489 1 18.38336076 -2.289705198 1.912934566 3.66E-05 1.279130594 0.13998268 0.215759077 3973330.694 548183.0439 17136170.15 0.048880084 0.005132096 2.289705198 1.279094006 EKQEEELSFLQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKQEEELSFLQDK 13 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 146 3.84E-05 137130000 369220 185680 242400 160090 353550 319360 328150 234910 304930 148870 FALSE TRUE 383797.0907 217569.0956 248717.1431 191755.3242 293453.6973 245193.4799 302428.7455 231761.4157 293955.6289 178038.2262 2.155700486 1.222035853 1.396987312 1.077045802 1.648262306 1.377195702 1.698673099 1.301750869 1.651081541 1 17.44182751 -2.159145548 2.029861435 4.78E-05 1.47528094 0.207748975 0.290222499 3534731.108 756995.1477 16244098.28 0.066161713 0.006931935 2.159145548 1.475233109 EKQLAAENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EKQLAAENR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 169.65 5.32E-05 6654417500 9439378 9210479 9482443 7722108 15313708 13149442 10044897 10116474 10691584 12252706 FALSE TRUE 9812051.932 10792307.12 9729563.254 9249517.914 12710689.38 10095683.38 9257551.726 9980879.213 10306795.98 14653389.15 0.669609729 0.73650587 0.663980405 0.631220383 0.867423178 0.688965759 0.631768639 0.68113111 0.703372843 1 23.80473105 0.913939147 18.43976039 1 0.695698944 0.666460508 0.064298722 1718.799983 368279.8937 0.061610183 0.015402546 8.20236606 -0.913939147 -0.304301056 EKQPMVPESLADYITAAYVEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKQPMVPESLADYITAAYVEMR 22 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 152.13 3.97E-08 70001000 79627 79108 101870 76088 96063 111370 96493 94137 97197 75265 FALSE TRUE 82770.73545 92694.18363 104524.8159 91137.9793 79734.24557 85506.00533 88929.62652 92875.24749 93698.89896 90011.73571 0.919554931 1.029801091 1.161235422 1.012512186 0.885820554 0.949942856 0.987978132 1.031812649 1.040963139 1 16.45782549 6.886545166 9.120054503 1.004201921 0.344042879 0 0.072042912 0 0 0.016860052 0 7700965.297 -6.886545166 -0.660159043 EKQPVAGSEGAQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EKQPVAGSEGAQYR 14 1 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;; 117 0.00030016 929070000 442045 467700 483650 411982 538730 579090 459220 452750 475710 450530 FALSE TRUE 459497.2779 548023.8368 496254.3163 493470.81 447156.867 444605.1237 423225.1365 446681.6268 458589.29 538802.7276 0.852811715 1.017114073 0.921031559 0.915865464 0.829908321 0.82517237 0.785491822 0.829026291 0.851126519 1 19.03939763 3.330412138 3.846975041 0.837928609 0.936326175 0.208001052 0.065827254 0.254302599 7.164702724 0.01754678 0.023995377 2139.991943 -3.330412138 0.098397566 EKQSDS(ph)KGKDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKQSDSKGKDQER 13 3 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 EKQS(0.005)DS(0.995)KGKDQER 82.59 0.065962 142110000 266230 47207 74030 45112 140480 157770 141630 89933 100960 29610 TRUE FALSE 276740.966 55314.43503 75959.28262 54035.01895 116601.2598 121130.3085 130528.6705 88727.59524 97326.46932 35411.51258 7.814999863 1.562046662 2.145044848 1.525916715 3.292750049 3.420647685 3.686051823 2.505614383 2.748441459 1 15.11193085 0.600554215 1.054190803 1.001942206 3.142366027 0.137436707 1.691941792 2.826985715 4.871684008 1.548996027 0.488334019 3.986155305 -0.600554215 2.140423821 EKS(ph)PSLGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKSPSLGKK 9 2 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 EKS(0.974)PS(0.026)LGKK 48.004 0.092463 121510000 386660 138670 218180 126670 306610 282000 298830 216770 269570 117590 TRUE FALSE 401925.6354 162485.4938 223865.95 151724.9479 254492.5417 216509.7738 275406.9238 213864.5527 259868.2284 140629.5091 2.858046209 1.155415352 1.591884601 1.078898368 1.809666715 1.539575692 1.95838644 1.520765834 1.847892594 1 17.10153983 -2.028329943 2.723448525 0.203814237 1.666570289 0.164603584 0.46986467 19321981.82 9274094.895 96784112.21 0.106134553 0.0093685 2.028329943 1.462756052 EKS(ph)PVREPVDNLSPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 245.36 7.42E-21 735630000 376140 253782 306390 226307 409490 392390 387990 324910 337330 220470 TRUE FALSE 390990.2976 297367.0844 314374.7751 271069.8491 339885.0361 301263.3692 357578.33 320555.1129 325189.5592 263666.8753 1.482895025 1.127813587 1.192318052 1.028076996 1.289069913 1.142590888 1.356174641 1.215757999 1.233334899 1 18.00835681 -1.520554023 2.588109851 0.987152214 1.223822849 0.246638058 0.120072267 7247439.482 6963742.802 653913.4538 0.028646574 0.030161017 1.520554023 0.236670635 EKSTFREES(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.002)T(0.001)FREES(0.997)PLR;EKS(0.001)TFREES(0.999)PLR;EKSTFREES(1)PLR;EKS(0.001)TFREES(0.999)PLR;EKS(0.002)T(0.005)FREES(0.994)PLR;EKS(0.05)T(0.013)FREES(0.937)PLR 147.51 5.17E-05 13605970000 6894510 6629280 7892370 5025100 10389830 9048310 6176600 7238330 8284900 8495390 TRUE FALSE 7166710.579 7767807.271 8098051.646 6019049.782 8623770.408 6946977.131 5692461.952 7141312.026 7986728.067 10159899.02 0.705391911 0.764555559 0.79706025 0.592432048 0.848804737 0.683764388 0.560287257 0.702892028 0.786103096 1 23.27638273 0.875833632 3.173785995 0.999767202 0.705254851 0.539293415 0.081750368 0.392993138 7.869627675 0.078261867 0.020395295 7.513350202 -0.875833632 -0.29451235 EKT(ph)PELPEPSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(1)PELPEPSVK;EKT(1)PELPEPSVK 157.74 0.00010846 25351600000 10916900 3363650 5619380 3283820 8718500 8957800 8293900 5858660 6469300 2468050 TRUE FALSE 11347907.64 3941330.722 5765825.659 3933349.795 7236532.484 6877486.707 7643802.446 5780134.246 6236471.157 2951617.144 3.844640781 1.335312315 1.953446324 1.332608398 2.451717866 2.330074116 2.58969984 1.958294035 2.112899761 1 21.49307417 0.358600162 1.451214637 0.999895766 2.177934577 0.224213356 0.675670544 6.902234942 14.025839 0.609623697 0.176630278 2.283495511 -0.358600162 1.178038811 EKT(ph)PPRPQGQRPEPENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKTPPRPQGQRPEPENR 17 3 A9X3U0;Q96GF1 A9X3U0 RNF185 E3 ubiquitin-protein ligase RNF185 1 EKT(1)PPRPQGQRPEPENR 90.22 0.0039661 56930000 30979 20644 24907 26471 32619 38724 34592 26681 31273 20661 TRUE FALSE 32202.07484 24189.44641 25556.09688 31706.88479 27074.43403 29730.93787 31880.58865 26323.38484 30147.49084 24709.12737 1.303246139 0.978968057 1.034277597 1.283205364 1.09572603 1.203237064 1.290235311 1.065330412 1.220095327 1 14.59275644 4.828262992 21.15399504 1.139069182 1.303277329 0.182534865 0.108433902 120084.8055 28299442.86 0.025130267 651.3720038 67338.43086 -4.828262992 0.164208148 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 EKT(1)PS(1)PKEEDEEPES(1)PPEK 95.212 0.0096459 59426000 238820 20833 30919 19971 75086 175180 69126 37063 42620 9687.1 TRUE FALSE 248248.798 24410.90569 31724.77454 23921.20419 62322.90854 134497.0999 63707.72349 36566.23111 41086.11453 11585.10177 21.42827943 2.107094626 2.73841138 2.064824691 5.379573676 11.60948799 5.499107797 3.156315052 3.54646125 1 13.4999831 4.74319357 24.88991477 4.359869768 21.42828678 0.768015033 2.850699902 225.7773079 1212913.682 0.722689315 5.819412196 55359.67984 -4.74319357 17.06841701 EKT(ph)PS(ph)PKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK;EKT(1)PS(1)PKEEDEEPES(1)PPEKK 137.7 3.67E-05 2695510000 8032860 374859 849420 354887 1788679 5470270 1726356 971856 986534 153737 TRUE FALSE 8350003.516 439238.1173 871556.583 425082.5894 1484639.982 4199882.695 1591039.706 958829.86 951028.834 183858.8217 45.41529984 2.388996695 4.740357711 2.312005404 8.074891207 22.84297624 8.653594596 5.215033204 5.172603769 1 17.48823887 4.742941183 24.98888101 7.182046224 45.4153151 0.795062088 5.890709619 204.081055 1164135.601 1.47836887 11.70289452 55327.51736 -4.742941183 38.23326887 EKT(ph)PSPKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 EKT(0.816)PS(0.483)PKEEDEEPES(0.701)PPEKK;EKT(0.678)PS(0.322)PKEEDEEPES(1)PPEKK 191.13 2.98E-17 437320000 1979890 155135 370340 128296 654330 1302660 621530 353160 409570 92802 TRUE FALSE 2058057.586 181778.2295 379991.3646 153672.5659 543107.2203 1000136.957 572812.8545 348426.4679 394829.6557 110984.7751 18.5436028 1.637866359 3.423815242 1.384627448 4.893529043 9.011478882 5.161184082 3.139407793 3.557511878 1 16.76000226 4.744003036 24.97938726 3.909764865 18.54360907 0.800044391 2.225299864 262.947462 1206828.489 0.555553714 4.824313623 55462.95898 -4.744003036 14.6338442 EKTPS(ph)PKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 EKT(0.01)PS(0.99)PKEEDEEPES(1)PPEKK 155.95 3.45E-08 268180000 1220100 104500 207810 93105 421030 822760 385580 206590 250660 58931 TRUE FALSE 1268270.49 122447.0621 213225.6993 111520.8911 349463.471 631686.459 355357.2321 203820.999 241638.7956 70477.40115 17.99542079 1.737394684 3.025447815 1.58236384 4.958518125 8.962964706 5.042144379 2.892005035 3.428599688 1 16.10487311 4.743735578 24.97422726 3.829730451 17.99542678 0.793667622 2.195842015 252.4560117 1218307.279 0.553221462 4.695160025 55428.81296 -4.743735578 14.16569633 EKTPSPKEEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EKTPSPKEEDEEPES(1)PPEK;EKT(0.003)PSPKEEDEEPES(0.997)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK;EKTPSPKEEDEEPES(1)PPEK 205.73 2.08E-16 3395880000 3885470 1068700 1868060 1016280 3027750 2927860 2866720 1853250 2148920 743640 TRUE FALSE 4038871.356 1252240.912 1916743.178 1217297.151 2513094.136 2247908.887 2642018.996 1828410.215 2071580.789 889342.0202 4.541415186 1.408053239 2.155237394 1.368761537 2.825790393 2.527608992 2.970756959 2.055913443 2.329340953 1 19.76237883 0.38752762 1.232722141 0.999584128 2.428301514 0.210233546 0.853924406 4.831067196 8.202775673 0.773061077 0.230984951 2.440774289 -0.38752762 1.428717386 EKTPSPKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_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 192.18 6.59E-17 63203080000 22302080 3617203 7369320 3111986 13579580 12374980 12043580 7535490 9068900 2315636 TRUE FALSE 23182583.34 4238429.477 7561370.533 3727527.542 11271327.84 9501078.44 11099572.73 7434489.082 8742512.061 2769340.539 8.371156604 1.530483311 2.730386685 1.345998259 4.070040389 3.430808998 4.008020167 2.684570199 3.156893108 1 21.40111104 8 0.073799244 3.04E-08 11.02977445 0.198246418 1.785116504 483.5452379 2.620370124 64.59682309 549.3943583 100000000 -8 11.02977442 EKVESELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKVESELR 8 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 129.38 0.00099688 7860620000 13653500 9306680 12456000 10173500 15986500 14819200 16304600 12830900 13489400 8345360 FALSE TRUE 14192550.72 10905029.89 12780613.59 12185787.94 13269120.44 11377665.39 15026602.85 12658922.77 13003919.13 9980473.51 1.422031801 1.092636525 1.280561847 1.220962905 1.329508107 1.139992544 1.505600193 1.268368957 1.30293609 1 23.25067683 -1.751433528 7.650465944 0.996453264 1.282799487 0.355527109 0.114980762 0.00650785 0.000211443 0.104160882 0.024341509 0.017724193 1.751433528 0.286346222 EKVEVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKVEVFR 7 1 Q9BW83-2;Q9BW83 Q9BW83-2 IFT27 Intraflagellar transport protein 27 homolog 0 83.005 0.020932 99512000 206510 201020 218380 189500 274860 268970 226450 218050 222490 229890 FALSE TRUE 214663.1743 235543.6213 224071.1622 226982.5344 228139.3954 206505.7938 208700.2573 215127.3964 214482.6284 274932.544 0.780784883 0.856732411 0.815004142 0.825593548 0.829801347 0.751114403 0.759096229 0.782473378 0.780128192 1 18.06871816 -1.309088248 3.249432005 1.001142202 0.79764609 0.784863013 0.031749322 28584202.64 42446119.37 323831.7693 0.008312257 0.049080813 1.309088248 -0.203496112 EKVFDVIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKVFDVIIR 9 1 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 103.22 0.0031534 641650000 747500 641610 786200 642650 984310 873440 811350 762480 792770 649060 FALSE TRUE 777011.8772 751801.5265 806689.0179 769764.2519 816997.3378 670596.7971 747754.2669 752260.2028 764238.3626 776230.88 1.00100614 0.968528238 1.039238503 0.991669195 1.052518469 0.863914094 0.963314249 0.96911914 0.984550322 1 19.5661263 EKVGEVTYVELLMDAEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKVGEVTYVELLMDAEGK 18 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 139.11 5.38E-07 90980000 264810 139980 218750 132660 276440 221000 260010 199290 235090 125210 FALSE TRUE 275264.9033 164020.4761 224450.8047 158899.752 229450.8275 169676.0993 239629.7368 196618.8435 226629.1568 149742.5022 1.838254999 1.095350176 1.498911808 1.061153311 1.532302614 1.133119166 1.6002787 1.313046334 1.513459128 1 17.19212424 4.756413026 23.94336904 1.327981905 1.838255767 0.357767742 0.21227178 2172.000212 2912967.354 0.044879666 1.329404363 57070.67721 -4.756413026 0.510273863 EKVLATVTKPVGGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 161.19 9.37E-07 1591140000 2302000 1161160 1714260 1080530 2690700 2168600 2430500 1846610 2187700 1215490 FALSE TRUE 2392884.738 1360580.197 1758935.024 1294255.609 2233335.775 1664975.515 2239991.059 1821859.213 2108965.104 1453641.994 1.646130717 0.935980251 1.210019408 0.890353756 1.536372632 1.145382097 1.540950983 1.253306675 1.450814653 1 20.47124057 EKVMYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKVMYEK 7 1 E5RJD8;O75347;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 64.091 0.068854 72024000 157970 137640 167030 113250 193200 181950 164040 155990 171070 117530 FALSE TRUE 164206.7776 161278.5993 171382.939 135650.512 160359.933 139694.87 151182.1162 153899.2092 164913.2241 140557.7533 1.168251297 1.147418734 1.219306193 0.965087367 1.140882871 0.993861006 1.075587171 1.094917965 1.173277321 1 17.10080351 3.761368938 24.99859765 1.069856168 1.175234742 0.402002782 0.063873406 834.2171438 914323.6416 0.015605503 0.028109589 5772.566407 -3.761368938 0.105378574 EKVS(ph)SIDLEIDSLSSLLDDMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 1 EKVS(0.5)S(0.5)IDLEIDS(0.001)LSSLLDDMTK;EKVS(0.493)S(0.493)IDLEIDS(0.01)LS(0.002)S(0.002)LLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.658)S(0.342)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK;EKVS(0.653)S(0.347)IDLEIDSLSSLLDDMTK;EKVS(0.5)S(0.5)IDLEIDSLSSLLDDMTK 292.37 3.05E-55 10632859000 4284504.6 1719806 2992601.4 1857980.9 4823058.7 4125976.1 5050601 3299219.4 4086509.3 1603559 TRUE FALSE 4453660.15 2015169.302 3070591.051 2225483.977 4003236.905 3167780.681 4654721.696 3254998.76 3939436.629 1917745.684 2.322341376 1.050801115 1.601146115 1.160468771 2.087470168 1.651825217 2.427184029 1.697304699 2.054201796 1 20.87097998 3.225606247 24.99732445 1.876810009 1.504015599 0.071967758 0.472537079 449.829543 868009.4216 0.125543898 0.150936328 1681.149156 -3.225606247 -0.37279441 EKYDTDFYILDKYPLAVRPFYTMPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKYDTDFYILDKYPLAVRPFYTMPDPR 27 3 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 56.303 0.032588 598090000 662030 459420 645520 466440 800800 728890 705680 594490 655340 483860 FALSE TRUE 688167.4556 538321.8112 662342.7815 558700.4398 664680.302 559616.3439 650366.9576 586521.8339 631754.4414 578663.1029 1.189236798 0.930285357 1.14460863 0.965502098 1.148648149 0.967084891 1.123912954 1.01358084 1.09174827 1 19.14236413 2.22151112 0.006155906 3.72E-05 2.104030231 0.046152248 0.085640294 18105.1111 67.48539226 11421.02457 11638.48596 166.537147 -2.22151112 2.10399305 EKYEITEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EKYEITEQR 9 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 154.35 6.92E-05 10034550000 13003310 9934310 12545880 11126710 13893400 14929530 16095020 13076740 13097320 8742710 FALSE TRUE 13516690.72 11640450.46 12872835.94 13327540.03 11531804.83 11462372.92 14833450.28 12901467.69 12625950.01 10455676.64 1.292760975 1.113313932 1.231181528 1.274670257 1.102922865 1.09628227 1.418698263 1.233919921 1.207568908 1 23.31778309 EKYIDQEELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 9975010000 16280660 8196860 11858260 8099890 16965300 14367210 15686820 12359840 14702080 7289900 FALSE TRUE 16923433.03 9604606.942 12167296 9702024.066 14081544.37 11030643.21 14457246.06 12194176.56 14172955.01 8718216.331 1.941157731 1.101671096 1.395617582 1.11284507 1.61518639 1.265240824 1.658280262 1.398700846 1.625671407 1 23.05560157 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVR 36 1 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5;C9J1B2;C9JAY7;C9JK97 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 ELAEAAKEPLPVEQDDDIEVIVDETSDHTEET(0.305)S(0.695)PVR 152.35 1.14E-13 46049000 12615 17401 17793 12569 26222 22033 15766 16370 18038 17888 TRUE FALSE 13113.04994 20389.48639 18256.7002 15055.11069 21764.79381 16916.16966 14530.21972 16150.58693 17388.8159 21392.81111 0.612965256 0.953099912 0.853403515 0.703746254 1.01738821 0.790740851 0.679210397 0.754953935 0.812834546 1 14.38483845 2.498768939 24.9037991 0.777371093 0.837009397 0 0.132361804 2659.168834 3059144.035 0.040840377 0.038175646 315.3326488 -2.498768939 0.059638304 ELAEDGYSGVEVR ddPTM_MDA-MB-175_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 ; 155.97 9.81E-05 172715000 103506 101354 116824 99543 126341 129590 116921 111650 127272 112168 FALSE TRUE 107592.4968 118760.7611 119868.5294 119232.3083 104865.6019 99494.68646 107756.4265 110153.5144 122691.5056 134145.172 0.80206015 0.88531521 0.893573191 0.88883041 0.781732211 0.741694129 0.803282182 0.821151538 0.914617379 1 17.03343561 1.016320917 3.1529262 0.999235995 0.827495316 0.578074022 0.047256701 0.175050424 4.076227147 0.050632782 0.013284319 10.38295369 -1.016320917 -0.171740678 ELAEEEPHLVEQFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ELAEEEPHLVEQFQK 15 0 Q5QNY5;P40855;E9PS71;P40855-5;B7Z8B3 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 0 ;;;; 189.1 2.72E-07 761546000 1050274 914389 1072272 910574 1298211 1257439 1145942 1117156 1204242 958963 FALSE TRUE 1091739.629 1071428.198 1100216.289 1090682.819 1077541.558 965417.8489 1056120.072 1102182.351 1160901.566 1146853.439 0.951943458 0.934232885 0.95933469 0.951021972 0.939563436 0.841797056 0.92088495 0.961049 1.012249278 1 20.12924961 1.450264064 3.181307784 1.005353205 0.928121892 0.490701434 0.031452631 0.217669176 4.107625145 0.025865909 0.008935643 28.20097112 -1.450264064 -0.077231313 ELAGHTGYLSCCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 133.15 0.00011056 196470000 114610 215330 128140 196270 187410 239980 126850 129780 122270 325010 FALSE TRUE 119134.8913 252311.2525 131479.4337 235091.6202 155554.1151 184248.2819 116907.1655 128040.5114 117869.5266 388689.4868 0.306504023 0.649133205 0.338263416 0.604831435 0.400201499 0.474024352 0.300772646 0.329415937 0.303248559 1 18.56825856 -1.342208212 4.121027434 1.0011417 0.412787165 0.682268194 0.120414061 0.001240564 0.000198016 0.114388164 0.026912417 0.045476998 1.342208212 -0.588354535 ELAILLGMLDPAEKDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELAILLGMLDPAEKDEK 17 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;; 167.05 2.38E-09 3057650000 1769970 791778 1177490 755690 1813850 1747380 1645660 1156260 1327770 605351 FALSE TRUE 1839849.782 927759.7123 1208176.357 905163.2265 1505532.425 1341577.477 1516668.869 1140762.226 1279983.817 723957.9383 2.541376626 1.281510518 1.668848828 1.250298089 2.079585491 1.853115224 2.094968214 1.575729978 1.768036165 1 19.46554635 0.183068717 1.273711616 0.998922356 1.773322199 0.291846107 0.368597149 8.889969523 12.52918431 0.353621851 0.099622296 1.524293918 -0.183068717 0.774399843 ELALGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELALGQDR 8 0 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ;;; 133.98 0.0020852 1558580000 849650 1036150 940640 981740 1331370 1173160 1068320 946350 971040 1300030 FALSE TRUE 883194.8381 1214100.702 965153.8511 1175925.242 1105064.203 900711.3694 984582.2869 933665.7262 936092.4601 1554745.988 0.568063751 0.780899717 0.620779123 0.756345571 0.710768326 0.579330242 0.633275335 0.600526217 0.602087072 1 20.56824746 -2.202593262 2.386859514 2.061052986 0.651543821 0.688807561 0.070524176 5036944.723 1109305.62 28845028.2 0.017054506 0.00627201 2.202593262 -1.409509166 ELANDELILTFGADDVVCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELANDELILTFGADDVVCTR 20 0 P29762 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 72.417 0.020749 0 9164.5 11067 11947 12042 10490 14882 12485 12435 11397 13183 FALSE TRUE 9526.321537 12967.67116 12258.34863 14423.87166 8706.913547 11425.88104 11506.39308 12268.32916 10986.8242 15765.95645 0.604233658 0.822510909 0.777520138 0.914874509 0.552260408 0.724718546 0.729825248 0.778153181 0.696870135 1 13.94452507 -1.491098645 2.739955204 1.010473366 0.739858485 0.398133153 0.098036694 12775258.94 13215299.99 1007953.549 0.02245368 0.032277609 1.491098645 -0.270614881 ELAPEPWVERAT(ph)PT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELAPEPWVERATPT 14 1 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 1 ELAPEPWVERAT(0.5)PT(0.5);ELAPEPWVERAT(0.993)PT(0.007) 150.05 4.66E-05 135183000 337520 401880 398290 348410 437860 492830 308310 406970 403990 554020 TRUE FALSE 350845.5502 470899.7638 408669.7646 417324.4581 363432.7136 378377.7014 284143.8566 401515.2328 389450.4788 662569.6116 0.52952255 0.710717418 0.616795213 0.629857529 0.548520046 0.571076148 0.428851326 0.605997054 0.587788018 1 19.33771251 0.3640298 2.495211753 0.999999179 0.58037471 0.766863171 0.069319911 11.180142 42.94858757 0.068279701 0.018205728 2.312223442 -0.3640298 -0.419624469 ELAPLFEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELAPLFEELR 10 0 Q9UHA4;Q9UHA4-2 Q9UHA4 LAMTOR3 Ragulator complex protein LAMTOR3 0 95.502 0.017166 14579000 12468 18005 16663 22135 19606 19163 17592 18370 17899 18209 FALSE TRUE 12960.24627 21097.21869 17097.25147 26513.23693 16273.37912 14712.68367 16213.09307 18123.7802 17254.81849 21776.70492 0.595142668 0.968797565 0.785116552 1.217504532 0.747283815 0.675615697 0.744515441 0.832255397 0.792352128 1 14.41049805 4.756940021 23.734893 0.850389866 0.595142225 0.214012094 0.1521581 3303.273606 4265659.451 0.036419134 1.12564772 57139.97177 -4.756940021 -0.255247641 ELAPYDENWFYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELAPYDENWFYTR 13 0 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;;;; 263.29 8.51E-24 4251430000 472704 484395 578762 504524 554232 633453 631238 509003 545365 516009 FALSE TRUE 491366.7189 567586.0732 593845.0132 604317.3413 460023.8426 486343.1408 581759.9161 502180.6473 525737.4202 617111.084 0.796237066 0.919747008 0.962298407 0.979268331 0.745447383 0.78809659 0.942715066 0.813760537 0.851933199 1 19.23517068 4.757863775 22.80460804 0.88039365 0.796236817 0.094050589 0.082584581 3493.3952 4126845.435 0.020099383 0.634012651 57261.63908 -4.757863775 -0.084156832 ELAQIAGRPTEDEDEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELAQIAGRPTEDEDEKEK 18 2 O15355 O15355 PPM1G Protein phosphatase 1G 0 ; 185.55 2.96E-14 395690000 523260 125329 213407 156357 285580 344500 381180 191307 254980 67248 FALSE TRUE 543918.7088 146853.2808 218968.5617 187283.9479 237037.2136 264495.0959 351302.1156 188742.8426 245803.3196 80423.95806 6.76314275 1.825989225 2.722678254 2.328708415 2.947345783 3.288759996 4.368127658 2.346848466 3.056344472 1 16.29533772 4.747019272 24.92382442 2.775329756 6.763144833 0.67214919 0.857208153 609.9358525 1797163.091 0.196394405 2.276248655 55849.49778 -4.747019272 3.987815077 ELAQIAGRPTEDEDEKEKVADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELAQIAGRPTEDEDEKEKVADEDDVDNEEAALLHEEATMTIEELLTR 47 3 O15355 O15355 PPM1G Protein phosphatase 1G 0 103.14 1.03E-07 18531000 27779 6129.6 12341 6302.8 20213 20850 18371 14926 17946 9057.9 FALSE TRUE 28875.73637 7182.311118 12662.6166 7549.475028 16777.20148 16007.90348 16931.03302 14725.94138 17300.12697 10832.62208 2.665627597 0.663026095 1.168933662 0.696920374 1.548766435 1.47774965 1.562967201 1.359406917 1.597039649 1 13.40309488 ELAQPSGGHLPQAS(ph)PISVYLFPGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELAQPSGGHLPQASPISVYLFPGER 25 0 H7C3T2;Q2TAZ0-3;Q2TAZ0 H7C3T2;Q2TAZ0 ATG2A Autophagy-related protein 2 homolog A 1 ELAQPSGGHLPQAS(0.991)PIS(0.009)VYLFPGER 90.485 0.0087785 37484000 39638 46836 53603 48126 56853 60652 46237 49436 48819 59229 TRUE FALSE 41202.93885 54879.71867 54999.93822 57645.17916 47189.14737 46566.49219 42612.82312 48773.39128 47062.01373 70833.78854 0.58168481 0.77476752 0.776464726 0.813809064 0.666195446 0.657405077 0.601588931 0.688561099 0.66440063 1 16.11215009 -1.880428487 7.211908327 1.042001228 0.694084997 0.622524575 0.07200985 0.038920719 0.000645295 0.055802403 0.017185499 0.013169568 1.880428487 -0.347916231 ELCGER ddPTM_MDA-MB-175_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 97.068 0.09653 316880000 127300 168940 141730 179790 148390 188240 145220 157940 132620 169520 FALSE TRUE 132325.9023 197954.1308 145423.6002 215351.9254 123166.7208 144524.1128 133837.2769 155823.0726 127847.0321 202734.1983 0.652706368 0.976421997 0.71731164 1.062237783 0.607528092 0.712874858 0.660161325 0.768607733 0.630614041 1 17.62922995 3.204375507 24.99999653 0.716545266 0.851412756 0.134818529 0.149352169 308.996128 225971.8936 0.039233793 0.046895524 1600.941665 -3.204375507 0.13486749 ELCQQIHAECKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELCQQIHAECKR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 89.43 0.0061198 111180000 109210 105860 122970 96332 136180 147880 101570 131320 114990 113340 FALSE TRUE 113521.6951 124040.6315 126174.6992 115386.1821 113032.1722 113537.1111 93608.678 129559.8702 110851.5324 135546.803 0.837509204 0.915112926 0.930857065 0.851264505 0.833897737 0.837622937 0.690600412 0.955831251 0.81781001 1 17.04843156 5.098688229 13.02506979 0.864742947 0.313080136 0.010037471 0.08239944 60198474.23 145019123.9 0.018973595 929627150.4 125512.8608 -5.098688229 -0.551662811 ELCWLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELCWLLR 7 0 O94964-2;H0YDM2;O94964;X6R3R3;O94964-4 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 65.263 0.07106 137060000 2134.2 169890 115590 175910 60698 175820 67181 130360 80013 193810 FALSE TRUE 2218.459864 199067.2859 118602.3704 210704.473 50380.57564 134988.4696 61915.17768 128612.7374 77133.34776 231783.3588 0.009571265 0.85885064 0.511694933 0.909057812 0.217360625 0.582390687 0.267125207 0.554883397 0.332782078 1 17.82241746 -1.25621529 4.055309097 1.000491761 0.48884447 0.26100436 0.265337367 58638865.06 36330067.74 238954.6768 0.056719365 0.055435084 1.25621529 -0.511647291 ELDAFFLHMLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELDAFFLHMLMK 12 0 O76038 O76038 SCGN Secretagogin 0 125.22 0.00030917 67982000 65888 68688 73912 63649 109400 89000 70511 71802 73052 84146 FALSE TRUE 68489.30912 80484.62968 75838.20744 76238.58223 90804.22708 68331.09881 64984.16357 70839.61163 70422.87279 100632.7976 0.680586357 0.799785275 0.753613228 0.757591799 0.902332333 0.679014202 0.645755311 0.703941591 0.699800408 1 16.61874105 -1.091412235 5.406545595 1.000003233 0.735780147 0.560195166 0.070222138 2.86E-06 4.80E-07 0.071032622 0.016742345 0.081019165 1.091412235 -0.264223086 ELDALDANDELTPLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 272.5 8.22E-35 163416000 293623 312144 326248 306131 384340 395580 372683 344689 365338 327208 FALSE TRUE 305215.4628 365752.3039 334750.2909 366682.7981 319010.0241 303712.5401 343471.1326 340069.0078 352189.5567 391318.1428 0.779967575 0.934667381 0.855442808 0.937045227 0.8152191 0.776126908 0.877728618 0.869034605 0.90000825 1 18.57798247 0.781912028 1.438637538 0.999767134 0.856511302 0.417374372 0.052030066 0.752028618 2.745398428 0.048567939 0.014298005 6.052182674 -0.781912028 -0.143255832 ELDALGHELPVLAPQWEGYDELQTDGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 271 2.04E-61 1984013000 731450 866941 865383 821317 973072 1088631 893564 904005 928279 916652 FALSE TRUE 760328.2108 1015831.373 887935.5919 983771.0512 807669.569 835812.9486 823524.1188 891888.2916 894870.4201 1096252.409 0.69357039 0.926640037 0.809973674 0.897394654 0.736755114 0.762427468 0.751217614 0.813579322 0.816299616 1 20.06414858 0.531104362 2.205272761 0.999989771 0.80187044 0.443951479 0.067058362 4.396525742 19.55210922 0.061973585 0.016810853 3.397068949 -0.531104362 -0.198119331 ELDALGHELPVLAPQWEGYDELQTDGNRS(ph)SHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELDALGHELPVLAPQWEGYDELQTDGNRSSHSR 33 1 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 1 ELDALGHELPVLAPQWEGY(0.009)DELQT(0.075)DGNRS(0.305)S(0.305)HS(0.305)R 55.3 0.024895 20122000 5586.7 6308.1 5558.3 7115.7 6667.5 9419.9 6392.7 5915.6 6647.1 10017 TRUE FALSE 5807.26723 7391.467105 5703.153864 8523.164222 5534.160732 7232.270985 5891.62347 5836.311058 6407.872169 11979.63936 0.48476144 0.617002472 0.47607058 0.711470852 0.461963884 0.603713582 0.491803074 0.487185873 0.534896918 1 13.54829686 -0.944746572 5.522733115 1.000000684 0.539791575 0.766501401 0.076000897 5.91E-07 1.13E-07 0.067902512 0.016004752 0.113567333 0.944746572 -0.460209109 ELDDLEQWIQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELDDLEQWIQER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;;; 240.21 7.83E-16 226869000 202119 236094 210517 236093 260150 294786 225871 221400 215825 245729 FALSE TRUE 210098.8142 276641.3079 216003.246 282791.4907 215929.7959 226326.419 208166.6408 218432.4951 208057.5004 293874.8928 0.714926043 0.94135741 0.735017694 0.962285305 0.734767757 0.770145475 0.708351227 0.743283964 0.707979843 1 18.16484258 ELDDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELDDLKR 7 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 90.777 0.027081 361840000 881760 695810 716530 635020 957610 908310 884050 781920 847790 678340 FALSE TRUE 916572.5657 815309.9548 735203.3604 760625.0607 794835.7942 697368.7681 814755.851 771439.6414 817278.2035 811247.7354 1.129830662 1.005007372 0.90626245 0.937598994 0.979769508 0.859624918 1.004324346 0.950929793 1.007433572 1 19.62978302 4.66087816 3.136823795 0.953293427 1.142451851 0.578489908 0.044676024 0.190134402 2.98478093 0.010372985 0.078817181 45801.33747 -4.66087816 0.189158424 ELDDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELDDTR 6 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 127.66 0.039465 6582200000 13246500 15161800 14926700 14694900 16926000 17949300 15398200 15430600 15102400 14264000 FALSE TRUE 13769482.05 17765721.21 15315702.06 17601507.36 14048924.57 13780847.1 14191248.85 15223778.05 14558867.57 17058757.7 0.807179649 1.041442848 0.897820482 1.031816482 0.823560825 0.807845878 0.831904005 0.892431812 0.853454151 1 24.02400925 3.217706712 24.99723969 0.859744154 0.948145883 0.175114228 0.079791437 337.0204718 403979.9628 0.021438854 0.025649709 1650.84657 -3.217706712 0.088401729 ELDEEGS(ph)DPPLPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR 201.06 1.93E-08 1843620000 2260610 2209270 2538300 2124060 2732500 2920280 2556760 2556850 2450680 2258080 TRUE FALSE 2349860.628 2588694.937 2604450.183 2544192.728 2268030.626 2242089.227 2356354.47 2522579.608 2362480.506 2700507.542 0.870155181 0.958595707 0.964429887 0.942116505 0.839853468 0.830247349 0.872559855 0.93411315 0.874828331 1 21.36479915 6.170437723 13.16599437 0.906316678 0.59434447 0 0.055302507 0 0 0.012480972 0 1480599.924 -6.170437723 -0.311972207 ELDEETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELDEETER 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 176.09 0.00061035 181550000 179090 215390 212640 189350 250300 271690 222480 197350 183890 235700 FALSE TRUE 186160.6115 252381.557 218181.5731 226802.8648 207754.0954 208594.115 205041.4363 194704.846 177271.8348 281880.9023 0.66042293 0.895348195 0.774020416 0.804605289 0.737027921 0.740007973 0.727404498 0.690734436 0.628889128 1 18.10472621 3.222295996 16.77593851 0.733187103 0.790896759 0 0.106004902 14.92778643 15395.08578 0.028375992 0.034227571 1668.383924 -3.222295996 0.057709656 ELDEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELDEGR 6 0 O15541 O15541 RNF113A RING finger protein 113A 0 ;; 122.5 0.044655 4557800000 6593700 7641400 7187500 6935200 8203000 8569500 7916600 7588500 7426500 7064400 FALSE TRUE 6854024.367 8953751.008 7374812.155 8306961.86 6808656.99 6579363.497 7296076.206 7486788.57 7159221.716 8448533.924 0.811267899 1.059799379 0.872910285 0.983243002 0.805898047 0.778758014 0.863590804 0.886164231 0.847392196 1 23.01026958 3.240171484 24.99932739 0.856134759 0.936740808 0.137270814 0.082076525 70.69757095 1097154.155 0.021717577 0.027922638 1738.487148 -3.240171484 0.080606049 ELDFLREENHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELDFLREENHK 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 94.767 0.0049619 429690000 175231 155361 163392 110143 222881 198653 152223 147145 185568 176907 FALSE TRUE 182149.2552 182043.0432 167650.1297 131928.9567 184995.7672 152518.8514 140291.3635 145172.762 178889.4439 211568.5396 0.860946791 0.860444769 0.792415215 0.623575494 0.874401117 0.720895704 0.663101252 0.686173673 0.845538965 1 17.69076559 4.105586696 4.407892252 0.74919824 0.859654434 0.060514009 0.10775485 0.381697914 12.8882035 0.025701159 0.059463845 12752.24641 -4.105586696 0.110456194 ELDFVSHHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELDFVSHHVR 10 0 Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 Q02818 NUCB1 Nucleobindin-1 0 ; 120.09 0.00035035 249760000 53087 130961 121854 144452 206046 219871 143975 119054 113249 244092 FALSE TRUE 55182.91575 153452.533 125029.6153 173024.1745 171022.3745 168809.2924 132689.8633 117458.2759 109173.1906 291917.154 0.189036221 0.525671516 0.428305133 0.592716708 0.585859283 0.578278084 0.454546304 0.402368529 0.373986897 1 18.15519947 -1.450444976 2.994472627 1.012035572 0.466413263 0.656757773 0.117226548 35623708.48 41983586.99 3604562.16 0.02806274 0.035445004 1.450444976 -0.545622309 ELDGERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ELDGERER 8 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A590UJB9;A0A590UK79;A0A5F9UKJ4 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;; 134.26 0.00080641 3050060000 2552680 3276370 3164650 2417800 3913690 3834090 2758890 3119960 3125640 3962270 FALSE TRUE 2653461.777 3839061.061 3247123.379 2896033.624 3248442.372 2943680.704 2542640.993 3078142.039 3013148.827 4738600.944 0.559967342 0.810167622 0.685249384 0.611157947 0.685527735 0.621213041 0.536580527 0.649588787 0.63587309 1 22.17602974 -1.517444101 4.351235411 1.002819925 0.64522597 0.689631653 0.071657855 0.001960673 0.00021744 0.069396796 0.016241078 0.030377771 1.517444101 -0.357593955 ELDGHVLK ddPTM_MDA-MB-175_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 86.011 0.016336 169320000 285200 249940 300360 228020 385690 354940 308290 279280 304570 252660 FALSE TRUE 296459.9162 292865.2507 308187.6283 273121.6754 320130.5516 272510.5642 284125.4242 275536.7084 293608.5852 302163.8895 0.981122915 0.969226505 1.019935337 0.903885887 1.059459991 0.901863438 0.940302379 0.911878348 0.971686543 1 18.20497173 2.687750426 24.99956097 0.937074548 0.982997044 0.159421727 0.045503236 550.7708126 270988.8063 0.013562513 0.012786863 487.2484052 -2.687750426 0.045922496 ELDLFLAYYVQEQDSGQS(ph)GSPSHNDPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELDLFLAYYVQEQDSGQSGSPSHNDPAK 28 0 A0A1B0GW37;O00712;O00712-4;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A1B0GWJ4;Q5VW27;O00712-5;Q5VW26;A0A2R8Y7V8;Q5VW30;A0A1B0GWI9 A0A1B0GW37 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 ELDLFLAYYVQEQDS(0.158)GQS(0.443)GS(0.332)PS(0.067)HNDPAK 153.25 2.33E-08 27629000 29273 19710 30438 21736 31876 27383 34398 25805 28894 16321 TRUE FALSE 30428.72064 23095.03918 31231.23929 26035.31592 26457.72891 21023.71324 31701.79488 25459.12618 27854.11058 19518.78747 1.558945231 1.183220998 1.600060421 1.333859287 1.35550064 1.077101397 1.62416825 1.304339536 1.427041031 1 14.25257581 -1.624735064 2.532833079 0.957581314 1.378876515 0.321038822 0.167723873 9547435.041 8126906.235 2662186.942 0.038970491 0.023728208 1.624735064 0.421295201 ELDRYS(ph)LDSEDLYSR ddPTM_MDA-MB-175_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(1)LDSEDLYSR;ELDRYS(0.884)LDS(0.116)EDLYSR 296.63 2.63E-44 497740000 416910 437420 545610 419340 684530 574960 549530 565050 555370 567120 TRUE FALSE 433369.9287 512543.4823 559829.0448 502284.2004 568173.8351 441434.2536 506456.4027 557476.429 535382.3422 678236.3058 0.638965984 0.755700451 0.82541887 0.740574039 0.837722532 0.650856125 0.746725586 0.821950144 0.789374349 1 19.37142849 0.397249316 0.734144564 1.00384537 0.747158953 0.593816834 0.062268297 1.433755961 1.138525043 0.072110751 0.021885396 2.496027214 -0.397249316 -0.256686417 ELDTVTLEDIKEHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELDTVTLEDIKEHVK 15 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 269.26 4.28E-26 1516297000 2860220 1507410 2265970 1541150 3173790 2747080 2734970 2212820 2631480 1555510 FALSE TRUE 2973143.694 1766295.941 2325023.04 1845984.87 2634310.309 2109112.302 2520595.905 2183160.767 2536773.549 1860282.402 1.598221695 0.949477315 1.249822627 0.992314322 1.416080863 1.133759208 1.354953367 1.173564167 1.363649705 1 20.82709022 -1.075407905 4.376277773 0.999979017 1.233425683 0.132224237 0.187273423 11262892.16 2767695.512 2257.762061 0.039005385 0.084060524 1.075407905 0.233446667 ELDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELDYER 6 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 123.1 0.044052 2706030000 3081560 3988750 3499660 3518710 4482360 4635690 3944310 3691010 3494050 4650660 FALSE TRUE 3203222.368 4673786.784 3590864.015 4214700.336 3720450.048 3559121.252 3635144.676 3641538.048 3368299.823 5561867.785 0.575925659 0.840326841 0.645621966 0.757785064 0.66892098 0.639914753 0.653583439 0.65473294 0.605605878 1 22.40713802 -1.976426943 3.890249355 1.263201604 0.674917491 0.652012002 0.071981043 0.042662505 0.000258515 0.018095254 0.015372918 0.010557791 1.976426943 -0.588284113 ELEAENYHDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEAENYHDIKR 12 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 135.1 8.68E-05 115140000 144800 183430 142590 117380 239000 223340 134510 163670 138230 205310 FALSE TRUE 150516.8158 214932.6756 146306.0125 140597.4137 198374.8654 171472.6698 123966.7547 161476.2714 133255.1293 245536.5636 0.61301182 0.875359142 0.595862426 0.57261294 0.80792393 0.698359003 0.504881036 0.657646539 0.542709922 1 17.90557835 -1.038512849 4.825435949 1.000007926 0.654351545 0.473744903 0.109996719 9.21E-06 1.83E-06 0.104535118 0.024638599 0.091513918 1.038512849 -0.345656381 ELEAIFGRPVVDGEEGEPHSIS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 ELEAIFGRPVVDGEEGEPHS(0.025)IS(0.975)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.002)IS(0.998)PR;ELEAIFGRPVVDGEEGEPHSIS(1)PR;ELEAIFGRPVVDGEEGEPHS(0.002)IS(0.998)PR;ELEAIFGRPVVDGEEGEPHS(0.008)IS(0.992)PR;ELEAIFGRPVVDGEEGEPHS(0.027)IS(0.973)PR 293.21 4.35E-62 6161700000 2589304 2848417 2802895 3340381 3216204 3575149 3709812 3250745 3094487 2886438 TRUE FALSE 2691531.721 3337610.462 2875940.746 4001098.392 2669514.793 2744874.827 3419027.242 3207174.08 2983117.017 3451980.262 0.779706579 0.966868351 0.833127807 1.159073369 0.773328522 0.795159479 0.990453879 0.929082392 0.864175572 1 21.71899278 -5 0.337628581 1.997708242 0.902351451 0.063194855 0.113310339 1245.047938 10.55438127 894.8479021 0.088028107 1.00E-05 5 -1.095356791 ELEAIFGRPVVDGEEGEPHSISPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;;;;; 257.51 4.01E-44 1832510000 829720 1143346 1123212 1141345 1291413 1441141 1154186 1079372 1099306 1177296 FALSE TRUE 862477.9863 1339706.782 1152483.827 1367099.634 1071899.08 1106457.843 1063717.885 1064904.784 1059742.192 1407964.611 0.612570785 0.95152021 0.818546019 0.97097585 0.761311095 0.785856289 0.755500442 0.756343431 0.752676725 1 20.42517964 ELEALDEVFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEALDEVFTK 11 0 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 155.15 7.37E-05 57583000 70989 67619 75320 67742 93690 96885 77211 72346 77632 65893 FALSE TRUE 73791.70054 79232.03725 77282.90108 81141.16541 77764.60727 74384.92706 71159.00007 71376.3202 74838.03948 78803.47175 0.936401644 1.005438409 0.980704268 1.029664856 0.986817021 0.943929568 0.902993212 0.90575096 0.949679472 1 16.26597157 2.66930277 3.754605976 0.927710281 0.99099724 0.298914721 0.034123599 0.221032006 6.134264663 0.011081971 0.010565597 466.9848269 -2.66930277 0.063286959 ELEAMGLGT(ph)PSEAIEIR ddPTM_MDA-MB-175_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(0.969)PS(0.031)EAIEIR 180.62 9.50E-09 25786000 50012 58628 54425 62014 71092 80661 64280 67216 68954 69914 TRUE FALSE 51986.51238 68696.90294 55843.36021 74280.18411 59007.80723 61928.70518 59241.56564 66315.07946 66472.35901 83612.30972 0.621756683 0.82161231 0.667884435 0.888388138 0.705731099 0.740664926 0.708526841 0.793125793 0.79500685 1 16.35142774 0.551250217 1.048181186 1.000218067 0.742687334 0.538025004 0.071844948 1.095852157 1.772420884 0.062728884 0.019714193 3.558362735 -0.551250217 -0.257530734 ELEAVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEAVLSR 8 0 Q96DP5 Q96DP5 MTFMT "Methionyl-tRNA formyltransferase, mitochondrial" 0 77.072 0.034161 626280000 43501 1284000 738990 1117000 433160 1163000 414900 818410 446110 1447800 FALSE TRUE 45218.45307 1504517.012 758248.6865 1337939.266 359531.6179 892910.8754 382379.0539 807440.5526 430054.5882 1731468.69 0.026115663 0.868925335 0.437922263 0.772719295 0.207645463 0.515695652 0.220840871 0.466332748 0.248375608 1 20.72356487 -1.134786639 5.282600524 1.000015236 0.433158886 0.331954289 0.246757669 4.04E-05 6.62E-06 0.218240263 0.051438342 0.073318465 1.134786639 -0.566856351 ELEDATETADAMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEDATETADAMNR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 320.94 8.37E-56 1837130000 432040 583760 575020 533890 638070 771940 567630 612860 597780 588580 FALSE TRUE 449097.2728 684016.239 590005.4936 639491.8485 529611.0893 592668.6339 523137.6774 604645.6141 576266.0146 703900.982 0.638011999 0.971750653 0.838193878 0.908496884 0.752394304 0.84197728 0.743197823 0.858992429 0.818674827 1 19.42501297 -0.278908938 1.439705604 1.000583264 0.824455061 0.274719255 0.087779124 83.20219429 89.56211956 0.376011459 0.022340312 0.526127572 0.278908938 -0.176128203 ELEDDEQFVSLYGTEEYLHPDMYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEDDEQFVSLYGTEEYLHPDMYER 25 0 A0A494C0X2;A0A494C167;A0A494C045;Q9UHD2;A0A494C1I2;A0A494C079;A0A494C0R4;A0A494C0A8;A0A494C1M6;A0A494C148 A0A494C0X2 TBK1 Serine/threonine-protein kinase TBK1 0 ; 163.15 1.84E-11 52524000 17820.1 20308.1 17948.9 20581.6 27200 27557 21557.3 23138.2 24466.3 19085.1 FALSE TRUE 18523.65131 23795.8582 18416.66308 24652.57905 22576.55372 21157.30438 19867.5825 22828.07028 23585.76264 22824.45994 0.811570191 1.042559529 0.806882753 1.080094737 0.989138572 0.926957502 0.870451373 1.000158178 1.033354686 1 14.4782931 4.757981909 24.08036024 0.966409941 0.811569956 0.269225292 0.078868173 3698.963748 4586202.909 0.017943822 0.640121069 57277.21717 -4.757981909 -0.154839985 ELEDYIDNLLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 126.19 0.00067891 36849000 49979 63875 63293 69861 75472 82012 67703 61418 61835 57378 FALSE TRUE 51952.20951 74845.03437 64942.46758 83679.29729 62643.2964 62965.9559 62396.26195 60594.79217 59609.57043 68620.12053 0.75709878 1.090715577 0.946405618 1.21945716 0.91289983 0.917601943 0.909299801 0.883047009 0.868689387 1 16.06634404 3.048857025 24.99999962 0.906897573 1.013156843 0.121461818 0.113760172 195.563745 100068.0618 0.031259974 0.037362809 1119.069411 -3.048857025 0.106259269 ELEEEEENS(ph)DEDELDSHTMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;ELEEEEENS(1)DEDELDSHTMVK 305.17 9.96E-56 2893420000 1526228 1352229 1667175 1275501 1965965 1877714 1938671 1546615 1721997 1171970 TRUE FALSE 1586484.66 1584463.812 1710622.95 1527791.291 1631790.972 1441643.381 1786712.901 1525885.156 1660022.664 1401595.083 1.131913689 1.130471868 1.220482985 1.090037565 1.164238511 1.028573372 1.274771097 1.088677589 1.184381056 1 20.41863819 -1.056599235 5.02288148 0.999997359 1.144674948 0.300481803 0.066780443 1.76E-06 3.31E-07 0.057767281 0.01361563 0.087781049 1.056599235 0.144677589 ELEEER ddPTM_MDA-MB-175_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 ; 132.96 0.034132 679510000 1348290 1491890 1513740 1485610 1597290 1806190 1476690 1443210 1379790 1445050 FALSE TRUE 1401521.53 1748110.502 1553189.308 1779459.224 1325783.216 1386729.746 1360943.179 1423866.131 1330131.627 1728179.88 0.810981279 1.011532724 0.898742848 1.029672457 0.767155799 0.80242211 0.787500882 0.823910836 0.769671978 1 20.72082196 3.226236043 24.99999779 0.813428875 0.940218833 0.293405316 0.084426413 230.191348 466934.9525 0.022219796 0.026738379 1683.588857 -3.226236043 0.126789959 ELEELKEIEADLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEELKEIEADLER 14 1 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 ; 87.148 0.0064367 85475000 175284 109321 147936 110140 191732 193497 175575 155209 162009 99861 FALSE TRUE 182204.3477 128096.0314 151791.3337 131925.3633 159141.4631 148560.2542 161812.9727 153128.6772 156178.3277 119426.851 1.525656468 1.072589876 1.270998376 1.104654122 1.332543409 1.243943493 1.35491283 1.28219639 1.307732109 1 16.86576771 -1.082296442 5.169499089 0.999995118 1.270785298 0.321886668 0.120394194 6.19E-06 1.10E-06 0.106467203 0.025094108 0.082737722 1.082296442 0.270790179 ELEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEELKR 7 1 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 0 ; 115.78 0.0089856 3627000000 3607600 2774140 3336400 2590650 3993900 3638400 3579000 3413300 3511400 2779140 FALSE TRUE 3750030.834 3250576.965 3423349.325 3103072.838 3315018.305 2793436.74 3298468.628 3367550.297 3385025.4 3323659.273 1.128283776 0.978011492 1.029994065 0.933631453 0.997400164 0.84047025 0.99242081 1.013205633 1.018463423 1 21.66434106 7.195282097 1.250462447 0.973848753 86.94677447 0.417402298 0.052776809 851.3603237 3.13805946 0.01474309 209067.6627 15677690.87 -7.195282097 85.97292571 ELEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEELR 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;P06727;Q9BT92;F5GWH6;A0A499FI31;Q15020-4;Q15020;P61129;O94964-2 Q14980;A0A499FI31;P61129;O94964-2 NUMA1;APOA4;TCHP;SART3;ZC3H6;SOGA1 Nuclear mitotic apparatus protein 1;Apolipoprotein A-IV;Trichoplein keratin filament-binding protein;Squamous cell carcinoma antigen recognized by T-cells 3;Zinc finger CCCH domain-containing protein 6;Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 101.21 0.08557 150200000 343170 385260 405560 366310 444930 461340 401450 374250 382900 347680 FALSE TRUE 356718.6166 451425.4081 416129.2268 438765.0247 369300.9575 354200.7767 369983.3 369233.7909 369119.5038 415801.2393 0.857906574 1.085675956 1.000788808 1.055227795 0.888167044 0.851851181 0.889808074 0.888005508 0.887730649 1 18.66553453 3.223950406 24.99352648 0.89196654 1.006090151 0.341702204 0.066383801 215.4752025 368610.3341 0.017875656 0.021454343 1674.751618 -3.223950406 0.114123611 ELEELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELEELRK 7 1 P61129 P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6 0 ;;; 104.76 0.012953 1466870000 1841290 1508050 1668770 1406930 2142900 2083710 2044070 1798870 1721140 1468740 FALSE TRUE 1913985.551 1767045.856 1712259.517 1685216.555 1778650.623 1599799.931 1883850.452 1774759.09 1659196.508 1756511.482 1.089651602 1.005997327 0.974806902 0.959411067 1.01260404 0.910782507 1.072495381 1.01038855 0.944597587 1 20.74428158 4.721881772 3.381677027 0.989102036 1.100919311 0.356263123 0.041589891 0.328232895 6.387019638 0.010013435 0.09276772 52708.63535 -4.721881772 0.111817274 ELEEQLENETLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEEQLENETLHK 13 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 138.87 4.41E-05 52720000 58893 40825 50385 51276 60258 70469 68954 50051 46937 34090 FALSE TRUE 61218.14112 47836.37618 51698.07449 61418.23976 50015.36668 54103.64272 63549.2053 49380.14821 45247.74654 40769.28281 1.50157513 1.173343578 1.26806436 1.506483203 1.226790447 1.327068788 1.558752103 1.211209637 1.10984897 1 15.31519496 1.311992533 2.67420785 1.028438843 1.354060001 0.505482515 0.123023203 0.219930374 2.593908203 0.104926503 0.031294406 20.51126912 -1.311992533 0.325621158 ELEEWYAR ddPTM_MDA-MB-175_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 ;;;;; 194.25 0.00038703 8516790000 3774480 4415250 4087120 4270540 4645770 5364860 4564240 4380280 4199910 4112240 FALSE TRUE 3923499.385 5173534.842 4193633.705 5115240.066 3856083.675 4118952.57 4206482.942 4321569.511 4048756.06 4917954.694 0.797790876 1.051968788 0.85271906 1.040115329 0.784082798 0.837533655 0.85533178 0.878733087 0.823260138 1 22.22962701 3.225473225 24.99999092 0.857008583 0.938033598 0.136649177 0.088377738 385.3888539 736181.6661 0.023218661 0.027908376 1680.634307 -3.225473225 0.081025015 ELEFYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ELEFYLR 7 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;;;;;;; 216.54 8.65E-05 5530651000 2466203 2904104 2872464 2646134 3617546 3568137 3224736 2817781 2676447 3611833 FALSE TRUE 2563570.599 3402861.271 2947322.772 3169531.407 3002636.823 2739491.257 2971972.766 2780013.255 2580122.195 4319502.524 0.593487464 0.787790088 0.682329216 0.733772324 0.69513487 0.634214529 0.688035891 0.643595701 0.597319293 1 22.04243374 -1.241317696 3.402549417 1.000847109 0.67614784 0.749331818 0.056735649 11279810.34 17238102.32 100529.794 0.013135415 0.057369664 1.241317696 -0.324699269 ELEIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELEIEER 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 89.142 0.042085 532390000 487150 839360 662080 779770 610450 937800 602150 708740 602070 1089330 FALSE TRUE 506383.0582 983513.5507 679334.3487 934006.1786 506685.927 720010.1625 554951.9096 699240.4996 580401.6183 1302763.357 0.388699187 0.754944131 0.521456445 0.716942316 0.388931669 0.552679164 0.425980595 0.536736389 0.445515769 1 20.31314362 -1.449076787 5.835167177 1.000286129 0.53087285 0.583894079 0.120032169 0.00041597 3.93E-05 0.108201091 0.025488076 0.035556845 1.449076787 -0.469413279 ELEKPIQSKPQS(ph)PVIQAAAVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 2 ELEKPIQS(0.132)KPQS(0.868)PVIQAAAVS(1)PK 93.505 0.0024381 316250000 595640 126700 241020 152240 359080 366630 334880 224340 267940 92983 TRUE FALSE 619156.3271 148459.7394 247301.1792 182352.6176 298043.7099 281485.7388 308631.2306 221333.0892 258296.8917 111201.2386 5.567890565 1.335054729 2.223906697 1.639843404 2.680219336 2.531318378 2.775429793 1.990383309 2.322787903 1 16.76281333 4.746859948 24.98614426 2.13856533 5.56789228 0.780393409 0.557414051 458.7214122 1381005.448 0.12624173 1.442003797 55829.0128 -4.746859948 3.429326949 ELELAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELELAHR 7 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 107.32 0.019524 0 71394 80156 82778 86983 94406 100550 93418 92653 89594 87676 FALSE TRUE 74212.69025 93922.16947 84935.26268 104187.9778 78358.90184 77198.78635 86095.65306 91411.13808 86369.52944 104854.4335 0.707768739 0.895738657 0.810030247 0.993643991 0.747311289 0.736247231 0.821096926 0.871790872 0.823708894 1 16.67802834 0.034565427 0.878851033 1.002700139 0.824534268 0.307021314 0.079707318 7.138982239 5.373189959 0.136843293 0.025081283 1.082842834 -0.034565427 -0.178165871 ELELELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELELELDR 8 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 103.56 0.011047 81501000 92895 101104 99702 95850 118256 136211 115939 101546 93123 107099 FALSE TRUE 96562.56633 118467.8255 102300.316 114808.8439 98154.88736 104578.0595 106851.3982 100184.942 89771.52142 128082.9985 0.753906197 0.924930138 0.798703319 0.896362868 0.766338144 0.816486659 0.834235609 0.782187668 0.700885539 1 16.96671946 3.228890893 24.99847852 0.805623196 0.846095793 0.013289734 0.084420467 657.6731349 1700236.842 0.02247037 0.027176011 1693.912188 -3.228890893 0.040472597 ELELLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELELLDR 7 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 0 110.81 0.015635 27002000 31449 31915 35649 40504 36106 42722 46830 36960 41174 26883 FALSE TRUE 32690.6308 37396.15299 36578.04223 48515.57031 29968.71502 32800.46296 43159.34223 36464.61165 39692.15578 32150.20914 1.016809274 1.16316982 1.137723306 1.50902814 0.932146814 1.020225493 1.34242804 1.134195162 1.234584684 1 14.9725405 -1.02607794 5.034835585 0.999997891 1.168954326 0.088343204 0.159252595 3.62E-06 7.01E-07 0.148182912 0.034926611 0.094172058 1.02607794 0.168956435 ELELVEDVWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELELVEDVWR 10 0 A0A1B0GVV3;Q5EBL4-2;Q5EBL4 A0A1B0GVV3 RILPL1 RILP-like protein 1 0 ; 144.77 7.35E-05 39175000 65737 70416 73233 73072 83822 100582 75091 73990 74607 82827 FALSE TRUE 68332.34752 82509.40024 75141.51214 87525.4235 69573.96638 77223.35483 69205.17121 72998.28507 71921.90864 99055.36483 0.689839946 0.832962459 0.758580944 0.883601041 0.702374541 0.779597904 0.698651419 0.736944286 0.726077873 1 16.59594749 -0.865457824 5.034736231 1.00000047 0.757592944 0.606736295 0.058802219 2.99E-07 6.74E-08 0.054850243 0.012928301 0.136314538 0.865457824 -0.242407527 ELELVQNAFFTDPNDQSAWFYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELELVQNAFFTDPNDQSAWFYHR 23 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 173.43 2.09E-19 0 75812 85052 81043 86869 98137 95172 79927 81475 87381 86539 FALSE TRUE 78805.1163 99659.01939 83155.04716 104051.4289 81455.70779 73069.74535 73662.11289 80382.96089 84236.17488 103494.6602 0.761441375 0.962938757 0.803471861 1.005379686 0.787052276 0.706024303 0.711747957 0.776687036 0.813918078 1 16.65919681 3.038488674 24.99863443 0.776377307 0.884908706 0.119113032 0.10149931 238.4493326 154872.8253 0.027220159 0.032534262 1092.66913 -3.038488674 0.108531398 ELENAEFIPMPDS(ph)PSPLSAAFSESEKDTLPYEELQGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELENAEFIPMPDSPSPLSAAFSESEKDTLPYEELQGLK 38 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 ELENAEFIPMPDS(0.162)PS(0.162)PLS(0.162)AAFS(0.162)ES(0.162)EKDT(0.162)LPY(0.03)EELQGLK 44.968 0.045269 14626000 39382 17175 32096 23689 48308 39312 38862 29401 39302 21239 TRUE FALSE 40936.83177 20124.67265 32932.44813 28374.6135 40096.62342 30182.38378 35815.89489 29006.92769 37887.5287 25400.3754 1.61166247 0.792298237 1.296533913 1.117094257 1.57858389 1.188265264 1.410053762 1.141988149 1.491612942 1 14.6325622 5.055538062 20.79168552 1.238993826 6.934882582 0.211976859 0.222532738 597.1038269 230021.1152 0.047697002 4414.202161 113641.7891 -5.055538062 5.695888756 ELENAEFIPMPDSPS(ph)PLSAAFSESEKDTLPYEELQGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELENAEFIPMPDSPSPLSAAFSESEKDTLPYEELQGLK 38 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 ELENAEFIPMPDS(0.42)PS(0.49)PLS(0.063)AAFS(0.009)ES(0.009)EKDT(0.009)LPY(0.001)EELQGLK 86.194 0.00040917 20761000 28665 13953 26412 18536 35582 31360 30898 23976 28524 14250 TRUE FALSE 29796.71633 16349.31921 27100.31842 22202.36548 29533.78435 24077.11527 28476.13402 23654.64094 27497.42681 17042.01467 1.748426868 0.959353664 1.590206261 1.302801688 1.732998412 1.412809209 1.670937068 1.388019046 1.613507989 1 14.05680828 -1.060632031 4.374237405 0.999964184 1.478661196 0.293813357 0.22764364 1.81640776 60122962.59 4842.776703 0.048274961 0.086969699 1.060632031 0.478697012 ELENFFQELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELENFFQELEK 11 0 P22676;A6NER6;H3BN14 P22676 CALB2 Calretinin 0 ; 161.94 5.98E-05 22452000 50390 40088 50144 41597 63447 60951 64177 47410 59018 42395 FALSE TRUE 52379.43611 46972.80216 51450.79383 49824.76245 52662.3016 46796.05397 59146.63904 46774.5465 56893.95371 50701.48855 1.033094641 0.926458049 1.014778763 0.98270808 1.038673678 0.922971994 1.166566125 0.922547796 1.122135766 1 15.62974048 ELEQHIQTS(ph)DPENFQSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELEQHIQTSDPENFQSEER 19 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 ELEQHIQT(0.041)S(0.959)DPENFQSEER 172.32 5.53E-12 121480000 86490 98658 97037 100460 99489 123110 100560 99918 89981 91895 TRUE FALSE 89904.69198 115601.744 99565.86394 120330.6882 82577.89532 94519.56825 92677.84444 98578.76264 86742.60139 109900.0658 0.818058582 1.051880572 0.905967282 1.094910065 0.751390772 0.860050151 0.843291983 0.896985474 0.789286164 1 16.74583272 3.231566539 24.99998988 0.854112084 0.969306956 0.25177161 0.093546995 206.3935043 737743.1569 0.024764913 0.03020809 1704.380432 -3.231566539 0.115194872 ELESQISELQEDLESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 317.77 5.32E-58 712374000 419048 456577 523855 583916 490083 582109 561398 496447 533085 420532 FALSE TRUE 435592.3386 534990.5481 537507.0917 699412.842 406778.8667 446923.0067 517394.1578 489792.94 513899.375 502927.1938 0.866114109 1.063753471 1.068757264 1.39068408 0.808822573 0.88864355 1.028765523 0.973884383 1.021816639 1 18.93999004 ELEVQHPAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELEVQHPAAK 10 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 115.57 0.0012049 2673200000 4889280 3824140 4712530 3904270 5569750 5631960 5240770 4744760 4900360 3603990 FALSE TRUE 5082312.55 4480906.297 4835342.403 4676522.953 4623005.884 4324022.643 4829984.753 4681164.253 4723997.001 4310122.838 1.17915724 1.039623803 1.121857215 1.085009205 1.072592605 1.003224921 1.120614176 1.086086042 1.096023751 1 22.03929756 0.017733126 0.009572511 8.37E-08 2.103704101 0.2747892 0.044682558 5448.86094 16.15846351 1835.429501 1715.084416 1.041677122 -0.017733126 2.103704018 ELFALKPMNCPGHCLMFDHRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELFALKPMNCPGHCLMFDHRPR 22 2 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 101.29 0.00023374 443980000 367590 332140 378870 412440 460440 495080 482570 419280 426970 292110 FALSE TRUE 382102.737 389182.4613 388743.6634 494019.401 382174.5733 380105.173 444744.9024 413660.2374 411603.4331 349343.3617 1.093774146 1.11403995 1.112783886 1.414137079 1.093979778 1.088056092 1.273088174 1.184107909 1.178220279 1 18.4142862 -2.431166115 1.747728393 2.13E-05 1.176374014 0.218438626 0.097616074 1401701.354 124244.1453 5517885.68 0.025599973 0.00370539 2.431166115 1.17635274 ELFDDPS(ph)YVNVQNLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.996)Y(0.004)VNVQNLDK;ELFDDPS(0.995)Y(0.005)VNVQNLDK;ELFDDPS(0.569)Y(0.431)VNVQNLDK;ELFDDPS(0.678)Y(0.322)VNVQNLDK 352.06 3.09E-87 460727000 767131 546556 729957 627415 985221 1027901 901726 809561 873360 633331 TRUE FALSE 797417.9242 640422.7414 748980.2791 751515.8144 817753.4863 789186.5707 831046.3599 798710.159 841927.9442 757420.0836 1.052808001 0.845531767 0.988857168 0.992204763 1.07965646 1.041940381 1.09720666 1.054514102 1.111573303 1 19.53073415 3.478656791 2.116534319 1.067786017 0.948960417 0.40212607 0.056197235 0.264923719 2.374669317 0.015407037 0.025156233 3010.625885 -3.478656791 -0.1188256 ELFDDPSY(ph)VNVQNLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELFDDPSYVNVQNLDK 16 0 P29353-2;P29353-7;P29353;P29353-6;H0Y539;X6R6D0;P29353-5;P29353-3;Q5T188 P29353-2 SHC1 SHC-transforming protein 1 1 ELFDDPS(0.02)Y(0.98)VNVQNLDK;ELFDDPS(0.028)Y(0.972)VNVQNLDK 223.03 9.38E-14 307290000 690170 455100 636630 581690 951940 927010 875470 742740 779890 604990 TRUE FALSE 717418.4445 533259.8848 653221.1008 696746.5458 790129.5788 711725.9765 806848.3738 732784.7852 751821.9112 723526.2073 0.991558339 0.737029121 0.90282991 0.962987296 1.092053848 0.983690666 1.115161228 1.012796465 1.039108057 1 19.46468575 3.620208889 2.625176807 1.041210508 0.859256011 0.522230622 0.069493876 0.189221902 2.528230481 0.018017246 0.031025328 4170.699399 -3.620208889 -0.181954497 ELFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELFEER 6 0 Q9H307 Q9H307 PNN Pinin 0 ;;; 122.78 0.044374 583637000 722283 882570 815385 839570 959790 1053930 881270 862916 773390 899360 FALSE TRUE 750799.2906 1034144.532 836634.6029 1005634.44 796645.2386 809170.73 812193.7546 851350.0225 745555.845 1075572.373 0.698046277 0.961482982 0.777850588 0.934976079 0.740670976 0.752316395 0.755127014 0.791532066 0.693171249 1 20.03667317 3.205077473 24.99368939 0.775558648 0.846886056 0.052595799 0.103635457 411.5029685 307167.6415 0.02717574 0.032483041 1603.531417 -3.205077473 0.071327408 ELFEMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELFEMAR 7 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 100.19 0.023212 305661000 254077 1239070 771290 1191680 678050 1211130 644060 915100 647120 1323180 FALSE TRUE 264108.1562 1451870.634 791390.451 1427390.747 562795.3032 929863.4124 593576.8943 902834.5813 623830.2776 1582431.787 0.166900184 0.917493345 0.50011031 0.902023556 0.355652173 0.587616743 0.375104254 0.570536176 0.394222539 1 20.59371188 -1.27434257 4.033865891 1.000520106 0.543357522 0.282593619 0.223761178 31423841.55 9927506.542 148640.9537 0.047625773 0.05316887 1.27434257 -0.457162584 ELFGKDEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELFGKDEQQR 10 1 G3XA94;Q9NPL8 G3XA94 TIMMDC1 "Complex I assembly factor TIMMDC1, mitochondrial" 0 ;;;;; 52.79 0.088821 42793770000 221812.9 19840340 15789110 16827480 11161340 20376010 9108280 17529650 12828630 24452900 FALSE TRUE 230570.2446 23247764.06 16200587.18 20155905.32 9264139.414 15643990.48 8394349.214 17294693.71 12366930.11 29243977.58 0.007884367 0.79495903 0.55398029 0.68923269 0.31678794 0.534947424 0.287045399 0.591393345 0.4228881 1 24.80163621 -1.329637341 2.95038089 1.005432753 0.483230956 0.357996756 0.213255239 19061291.69 23841650.73 904328.9207 0.049480403 0.046812589 1.329637341 -0.522201797 ELFLAEHS(ph)DLEEGGLDLTVSLKPVSFYISDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELFLAEHSDLEEGGLDLTVSLKPVSFYISDKK 32 2 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 ELFLAEHS(1)DLEEGGLDLTVSLKPVSFYISDKK 182.79 6.97E-20 690150000 183960 97774 156980 91651 219130 162420 175090 153530 198770 106410 TRUE FALSE 191222.8828 114565.9239 161071.0278 109779.2942 181882.3609 124700.4165 161365.9883 151472.1815 191616.3065 127259.0022 1.502627552 0.900257915 1.265694568 0.862644625 1.429229821 0.979894659 1.268012365 1.190266927 1.505719071 1 16.95740819 ELFS(ph)PLHALNFGIGGDTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 ELFS(1)PLHALNFGIGGDTTR 56.766 0.059495 17664000 5905.9 10643 6226 10192 9243.5 13329 8012.3 10108 8978.7 10343 TRUE FALSE 6139.069492 12470.85246 6388.254675 12207.94718 7672.293172 10233.54175 7384.27499 9972.518793 8655.558341 12369.51282 0.49630649 1.008192694 0.516451599 0.986938399 0.620258314 0.827319709 0.596973793 0.806217588 0.699749333 1 13.59450106 -1.522816857 2.624063609 1.014655519 0.737371917 0.184277621 0.170358057 17689317.69 17304725.73 1849759.121 0.037899179 0.030004275 1.522816857 -0.277283603 ELFSPLHALNFGIGGDGTQHVLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELFSPLHALNFGIGGDGTQHVLWR 24 0 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;; 283.72 1.16E-52 4230220000 971670 2079040 1979632 1990188 1938364 2257452 1742706 2083155 1838987 2083615 FALSE TRUE 1010032.282 2436098.947 2031222.836 2383841.246 1608881.58 1733192.985 1606108.15 2055233.715 1772802.217 2491859.466 0.405332763 0.977622928 0.815143416 0.95665156 0.645655023 0.695542027 0.644542027 0.824779143 0.711437479 1 21.24879128 -1.772073484 3.411975322 1.041019079 0.754152637 0.189695495 0.158232132 27034292.65 15622948.92 8375767.983 0.034831907 0.016901549 1.772073484 -0.286866442 ELFSPLHALNFGIGGDTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELFSPLHALNFGIGGDTTR 19 0 P68402;P68402-3;P68402-2;P68402-4 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ; 255.69 6.14E-31 1112100000 812500 1538930 1374950 1316970 1485020 1753910 1352300 1385130 1293010 1508650 FALSE TRUE 844578.1274 1803229.256 1410782.327 1577462.735 1232596.831 1346590.983 1246303.192 1366564.598 1246474.823 1804241.083 0.468107137 0.999439196 0.78192562 0.874308179 0.68316637 0.74634759 0.690763116 0.757417959 0.690858242 1 20.78296069 -1.224029412 5.166652649 1.000024228 0.752552132 0.255791487 0.130403255 3.33E-05 5.00E-06 0.115544637 0.027231468 0.059699486 1.224029412 -0.247472096 ELGDVLFQMAEVHR ddPTM_MDA-MB-175_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 ; 156.5 5.55E-06 57342000 103709 112217 126984 140459 131835 157124 149608 126382 109603 109434 FALSE TRUE 107803.5114 131489.3968 130293.3074 168241.371 109425.7338 120634.3322 137881.334 124688.056 105658.4094 130875.4971 0.823710426 1.004690716 0.995551576 1.285507026 0.836105583 0.921748799 1.053530547 0.952722693 0.807320024 1 16.99783549 ELGELSPHWDNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELGELSPHWDNLR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;;; 225.13 1.30E-11 1449620000 993530 1442420 1381590 1479490 1460580 1631350 1508620 1360620 1321730 1355770 FALSE TRUE 1032755.332 1690144.415 1417595.37 1772128.706 1212311.133 1252493.686 1390370.422 1342383.114 1274161.195 1621407.174 0.63695002 1.042393571 0.874299432 1.092957238 0.747690742 0.77247326 0.857508493 0.827912406 0.785836659 1 20.628815 3.15301751 20.71592923 0.822857222 0.918757647 0.07923439 0.130076154 13.5969239 3285.808429 0.035217974 0.042093622 1422.386134 -3.15301751 0.095900425 ELGENLDQILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELGENLDQILR 11 0 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 227.27 9.61E-12 140579000 174233 170970 186932 197738 186177 229229 218214 205139 189325 135066 FALSE TRUE 181111.8534 200332.7675 191803.6015 236849.9862 154530.7 175994.0387 201109.8165 202389.4472 182511.2302 161529.5967 1.121230146 1.240223288 1.187420791 1.466294667 0.956671119 1.089546698 1.245033855 1.252955814 1.129893431 1 17.30143901 3.227287051 24.99989678 1.141445052 1.248082242 0.224819787 0.121486657 432.7571003 959666.1384 0.036425665 0.043911942 1687.668136 -3.227287051 0.10663719 ELGIIPTIIRDEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELGIIPTIIRDEELK 15 1 Q8NDH3-3;Q8NDH3-2;Q8NDH3;Q8NDH3-5;Q8NDH3-4;H0YEP3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 ; 218.78 1.73E-12 187727000 194149 132002 159733 105196 220530 211622 176864 159083 170743 135233 FALSE TRUE 201814.1524 154672.3167 163895.7732 126003.4548 183044.3894 162475.9977 163000.9375 156950.7526 164597.9928 161729.3172 1.247851385 0.95636536 1.013395568 0.779100889 1.131794733 1.004616853 1.007862646 0.970453319 1.017737512 1 17.3032217 4.742497342 24.70819302 0.985612231 1.247851505 0.474260805 0.082443099 281.8445333 1768867.173 0.018733931 0.142583819 55271.00252 -4.742497342 0.262239274 ELGITALHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ; 168.83 4.82E-06 1529690000 2015970 1645580 1943370 1628130 2663600 2400510 2547500 2058900 2132860 2034960 FALSE TRUE 2095562.052 1928195.564 1994015.819 1950169.255 2210842.223 1843027.933 2347820.293 2031303.813 2056098.785 2433671.45 0.861070237 0.792299044 0.819344706 0.801328073 0.908439068 0.75730351 0.964723604 0.83466641 0.844854709 1 21.21470298 -5 0.171431603 1.624199912 0.805511728 0.433973531 0.055278548 115.5844388 1.094293693 24.47015244 0.180143309 1.00E-05 5 -0.818688184 ELGLREENEGVYNGSWGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELGLREENEGVYNGSWGGR 19 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9;P49419-4;A0A1B0GUY0;A0A0J9YWF7;H0YHM6;F8WDY6;A0A0J9YWM6;F8VVF2;F8WD33;A0A1B0GW65 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 127.32 1.25E-05 0 61390 57299 61500 48944 77745 77287 59370 66123 61151 51741 FALSE TRUE 63813.7246 67139.65753 63102.74052 58624.97712 64529.93267 59338.26555 54716.42427 65236.72934 58950.18746 61878.65831 1.03127195 1.085021223 1.019781977 0.947418362 1.042846345 0.958945575 0.884253566 1.054268646 0.952673976 1 15.9171543 3.997037431 6.086793431 0.980291326 1.05739799 0.319062097 0.047697628 0.169447659 26.91103672 0.01193669 0.024299143 9932.016476 -3.997037431 0.077106663 ELGPQDLLWMLDHQEDGGEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELGPQDLLWMLDHQEDGGEALR 22 0 Q8N0W3-2;Q8N0W3 Q8N0W3-2 FUK L-fucose kinase 0 ; 165.46 1.28E-11 66870000 40591.1 50112.9 52882 51536.5 69694 62254 56514 47674 60705 49694.8 FALSE TRUE 42193.66797 58719.40075 54260.14836 61730.26588 57847.43877 47796.45197 52084.28501 47035.00801 58520.23891 59431.5446 0.709954087 0.98801741 0.912985667 1.038678471 0.973345707 0.804226986 0.876374413 0.791414868 0.984666296 1 15.85894126 2.754020055 24.81841317 0.870174799 0.933812529 0.000953475 0.103246227 1996.956661 3205890.132 0.030711614 0.032466743 567.5708137 -2.754020055 0.06363773 ELGTVMR ddPTM_MDA-MB-175_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 ;; 125.62 0.023984 0 1451560 1883560 1692220 1770600 1769330 2028220 1924820 1738020 1639570 1869700 FALSE TRUE 1508868.71 2207046.778 1736320.643 2120819.395 1468579.919 1557196.643 1773947.579 1714724.685 1580562.196 2236031.917 0.674797483 0.987037243 0.77651872 0.948474563 0.656779497 0.69641074 0.793346269 0.766860558 0.706860302 1 21.09250935 5.042788731 15.52163351 0.801224227 0.091387496 0.10356466 0.11761332 4171668.469 42855247.37 0.026888832 84520623.92 110354.1655 -5.042788731 -0.709836731 ELHCPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELHCPDR 7 0 Q17RN3;Q17RN3-2;K7EQL1;K7EQT7 Q17RN3 FAM98C Protein FAM98C 0 97.798 0.024149 0 140790 232160 182850 200590 198430 248210 172780 193020 179830 214250 FALSE TRUE 146348.4979 272031.674 187615.2212 240266.1033 164700.9395 190566.9892 159237.0521 190432.8826 173357.9534 256228.1854 0.571164713 1.061677401 0.732219295 0.937703644 0.642790094 0.74373937 0.621465792 0.743215983 0.67657644 1 17.96706966 ELHEVCHLLEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELHEVCHLLEQER 13 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 216.34 1.60E-11 427120000 89938 114604 104139 99333 109639 128569 94856 102147 103384 125668 FALSE TRUE 93488.82169 134286.3455 106852.9479 118980.7709 91002.60194 98710.79823 87420.93886 100777.8865 99663.23003 150290.2385 0.622055182 0.893513423 0.710977299 0.791673312 0.605512393 0.656801128 0.581680751 0.670555104 0.663138411 1 17.19739178 -1.104709336 3.828631052 1.000113635 0.688752985 0.528752456 0.088240352 31087662.94 62439602.13 46763.4879 0.021766506 0.078576135 1.104709336 -0.31136065 ELHINLIPNK ddPTM_MDA-MB-175_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 ; 121.9 0.00050283 2514700000 7411500 5847400 6640300 6327300 8906000 8887400 9552600 7306100 7236200 6183600 FALSE TRUE 7704111.743 6851645.464 6813351.673 7578821.055 7392161.301 6823436.04 8803842.251 7208173.68 6975770.576 7395158.028 1.041777838 0.926504266 0.921326042 1.024835578 0.999594772 0.922689686 1.190487373 0.974715301 0.943288913 1 22.81814955 ELHINLIPNKQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELHINLIPNKQDR 13 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 164.88 2.18E-05 59890420000 28230220 25269760 27250680 24783140 33332150 31884020 29949920 28077300 29788400 25129820 FALSE TRUE 29344770.88 29609644.71 27960855.11 29685171.12 27666363.05 24479439.56 27602367.01 27700969.72 28716321.3 30053527.09 0.976416871 0.985230273 0.930368506 0.987743337 0.920569588 0.814528008 0.918440186 0.921721089 0.955505862 1 24.84103098 3.157383249 6.86429491 0.912688125 0.968058477 0.191983883 0.046267644 0.31474461 21.93373278 0.013396035 0.016103771 1436.756759 -3.157383249 0.055370352 ELHIQGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELHIQGNR 8 0 Q15404;Q15404-2 Q15404 RSU1 Ras suppressor protein 1 0 126.41 0.0012203 193000000 88680 127830 127610 117700 123450 140610 127150 126500 114560 139640 FALSE TRUE 92181.15488 149783.8081 130935.6214 140980.7087 102466.0131 107955.4585 117183.6508 124804.4744 110437.008 166999.7844 0.551983676 0.896910188 0.784046649 0.84419695 0.613569733 0.646440705 0.701699413 0.747333147 0.661300303 1 17.34948671 -1.38333242 5.523535924 1.000108493 0.723569125 0.416747771 0.100332633 0.000130612 1.46E-05 0.094656024 0.022301929 0.041368291 1.38333242 -0.276539368 ELHSEFSEVMNEIWASDQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 120.11 4.11E-05 77263000 28207 37562 32769 39081 27483 47759 33341 24875 28955 43872 FALSE TRUE 29320.63414 44012.98131 33622.98706 46811.10515 22811.44948 36667.69604 30727.6453 24541.59131 27912.91521 52467.87842 0.558830184 0.838855746 0.640829934 0.892185973 0.434769809 0.698859896 0.585646804 0.467745067 0.532000074 1 15.67914683 -1.201193206 4.730292076 1.000062425 0.625069575 0.385952707 0.140825368 9.35E-05 1.58E-05 0.137572639 0.032420799 0.062922619 1.201193206 -0.37499285 ELHYLPFPS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ELHYLPFPSP 10 0 Q8N565 Q8N565 MREG Melanoregulin 1 ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P;ELHYLPFPS(1)P 94.692 0.0083189 352430000 257093 335114 290158 340145 368068 434873 322423 312827 291687 422665 TRUE FALSE 267243.2302 392667.2227 297719.7558 407424.6658 305503.9328 333880.3363 297150.6428 308634.0657 281189.2418 505478.1143 0.528693968 0.776823391 0.588986442 0.80601841 0.604386074 0.660523823 0.587860551 0.610578494 0.556283712 1 18.9472891 -0.889520879 6.004947175 1.000000077 0.639039994 0.619047871 0.085725202 8.23E-08 1.53E-08 0.07724559 0.018206956 0.128967156 0.889520879 -0.360960083 ELIDWLIEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELIDWLIEHK 10 0 Q8TB45 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 0 104.52 0.004312 0 136130 114870 138930 111760 211440 159900 170480 138320 148670 99981 FALSE TRUE 141504.5175 134598.0289 142550.6299 133865.7944 175499.5043 122765.6483 157117.3321 136466.0466 143319.3957 119570.3627 1.183441401 1.125680527 1.192190328 1.119556648 1.467750874 1.026723057 1.314015686 1.141303276 1.198619729 1 16.86750031 0.043983774 1.061238453 0.998708406 1.198712712 0.210650267 0.114182291 11.31203639 11.06191001 0.147358249 0.031297887 1.10658244 -0.043983774 0.200004306 ELIESIKDVIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELIESIKDVIGR 12 1 Q5VZK9;Q5VZK9-2;Q5VZK9-3 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 0 101.39 0.0024614 51057000 128440 111780 131650 116780 163210 165890 136320 132420 139380 110040 FALSE TRUE 133510.9104 130977.3455 135080.9072 139878.7354 135467.6225 127364.5616 125634.8822 130645.1265 134363.741 131600.2312 1.014518814 0.995266834 1.026448859 1.062906457 1.029387421 0.967814118 0.95467068 0.992742379 1.020999278 1 17.0058025 2.750435143 24.67987576 0.98458563 1.026122631 0.410576807 0.022927759 638.2825255 1326598.076 0.007654727 0.008057999 562.9050481 -2.750435143 0.041537001 ELIFEETAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELIFEETAR 9 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 120.15 0.0016539 44920000 49335 66417 63673 60692 59887 74009 69012 66229 63174 61218 FALSE TRUE 51282.78389 77823.6031 65332.37069 72696.69645 49707.42913 56821.53137 63602.65911 65341.30858 60900.38008 73212.49501 0.700464912 1.062982529 0.892366401 0.992954774 0.678947345 0.776117948 0.868740494 0.892488483 0.831830415 1 16.15980227 3.925785274 0.005725546 1.723850528 4.26E-05 0.033158527 0.118721054 126382.1928 149.6346903 21827.40848 23233.74398 8429.178956 -3.925785274 -1.723807879 ELIIGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELIIGDR 7 0 P25705;P25705-2;P25705-3;K7EK77;K7ENJ4 P25705 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 ;; 126.67 0.0091423 996480000 638020 861690 752370 864470 689580 1059700 696600 698690 670760 894570 FALSE TRUE 663209.5223 1009678.554 771977.3803 1035459.586 572365.4379 813600.7349 641998.6718 689325.2034 646619.4786 1069843.864 0.619912442 0.943762533 0.721579481 0.967860471 0.534999038 0.76048549 0.600086324 0.644323183 0.604405466 1 20.02896883 3.234201052 24.99831357 0.668378267 0.816049048 0.124460176 0.152424831 176.3465897 1011194.684 0.039569855 0.048868109 1714.75095 -3.234201052 0.147670781 ELIKPPTILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELIKPPTILR 10 1 Q9Y2T2;H0YBA0;E7ER80;E5RJ52;P53677-2;P53677 Q9Y2T2 AP3M1;AP3M2 AP-3 complex subunit mu-1;AP-3 complex subunit mu-2 0 113.22 0.0023618 0 338520 323410 381150 356480 425670 399640 395210 365580 348300 330790 FALSE TRUE 351885.031 378953.1517 391083.0821 426990.68 353314.7654 306829.6666 364232.4075 360679.9981 335764.751 395601.9671 0.889492622 0.957915236 0.988577193 1.079344178 0.893106695 0.775601974 0.920704237 0.911724481 0.848743886 1 18.59369007 3.040951152 24.99901754 0.884969911 0.9790583 0.27689524 0.068640547 185.1698565 113037.5459 0.019838664 0.02371171 1098.882234 -3.040951152 0.094088389 ELILGSETPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 ELILGSETPSS(1)PR 221.85 1.93E-11 180740000 387030 429510 450940 430500 458770 517080 442260 426720 442320 457260 TRUE FALSE 402310.2433 503275.0014 462691.8669 515651.6151 380788.4393 396996.0064 407594.5056 421000.5164 426400.9896 546851.3422 0.735684842 0.920314101 0.84610173 0.942946602 0.696328984 0.72596696 0.745347911 0.76986282 0.779738398 1 19.06078917 5.046733139 14.52663907 0.810829606 0.376972672 0.054053724 0.096807113 1983783.029 18513741.16 0.023118233 23088029.31 111361.0043 -5.046733139 -0.433856935 ELIPQES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELIPQESPR 9 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 ELIPQES(1)PR;ELIPQES(1)PR 94.191 0.0058109 440510000 359460 414000 429040 399300 530210 579700 408110 428960 426400 488100 TRUE FALSE 373651.7584 485101.2795 440221.1349 478280.3482 440085.0936 445073.4604 376121.2718 423210.4928 411053.9473 583733.8498 0.640106375 0.831031608 0.754147006 0.819346605 0.753913952 0.762459571 0.644336922 0.725005913 0.70418042 1 19.1549512 -1.012587701 4.662748365 1.000005901 0.738986223 0.632691958 0.060063663 4.02E-06 8.51E-07 0.057654866 0.013589044 0.097143176 1.012587701 -0.261019678 ELISDNQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELISDNQYR 9 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 108.98 0.0058716 77228000 92117 109720 97226 105540 106810 131700 105340 118590 92301 117100 FALSE TRUE 95753.85029 128563.5565 99759.78943 126415.497 88654.47435 101114.6709 97083.17555 117000.495 88979.10504 140043.503 0.68374361 0.918025855 0.712348572 0.902687339 0.633049534 0.722023291 0.693235841 0.835458215 0.635367605 1 17.09551553 -1.351636239 9.288850467 1.000000231 0.756234819 0.370100378 0.09798204 4.34E-07 3.03E-08 0.087636168 0.020656023 0.044500384 1.351636239 -0.243765412 ELISNASDALDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELISNASDALDK 12 0 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ; 178.95 4.96E-05 262780000 428430 297030 334480 304440 451190 443650 499610 385150 389150 225160 FALSE TRUE 445344.7472 348042.5919 343196.8236 364657.3233 374496.885 340619.0111 460449.2627 379987.6942 375144.5675 269275.7911 1.653861067 1.292513488 1.274517929 1.35421503 1.390755862 1.264944798 1.709954173 1.411146887 1.393161138 1 18.03872501 0.69442505 4.020016851 1.000002237 1.415486424 0.431971251 0.143378942 7.290580894 95.06179001 0.135985783 0.034727393 4.94794713 -0.69442505 0.415484187 ELISNASDALDKIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELISNASDALDKIR 14 1 P08238;P14625;Q96GW1;A0A1W2PRR1;F8W026 P08238;P14625 HSP90AB1;HSP90B1 Heat shock protein HSP 90-beta;Endoplasmin 0 ;; 247.17 7.71E-18 8587800000 3504358 3089634 3737801 2487879 5184590 4221648 3116689 3655854 4122831 4017841 FALSE TRUE 3642712.76 3620254.605 3835211.165 2979974.041 4303315.244 3241234.232 2872394.772 3606853.257 3974451.118 4805060.018 0.758099326 0.753425471 0.798160928 0.620174156 0.895579915 0.674546045 0.59778541 0.750636463 0.827138704 1 22.19612302 0.928983423 2.555788034 0.999090358 0.728243472 0.50734072 0.081455366 0.274581187 4.033209284 0.075915508 0.020365565 8.491480627 -0.928983423 -0.270846886 ELISNSSDALDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELISNSSDALDK 12 0 P07900;P07900-2;G3V2J8;Q14568 P07900 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 155.99 0.00016937 263620000 382300 248530 292650 261870 392400 354080 420930 331650 323250 196930 FALSE TRUE 397393.4992 291213.0942 300276.6994 313667.1044 325699.9882 271850.2861 387936.4067 327204.7742 311616.2956 235514.663 1.687340797 1.23649666 1.27498091 1.331836839 1.382928706 1.154281787 1.647185792 1.389318058 1.323129064 1 17.84545736 -2.366930124 1.123360478 0.023420227 1.378004497 0.339255525 0.159410325 14125.93552 1397.051589 34532.0089 0.044892114 0.004296055 2.366930124 1.35458427 ELISNSSDALDKIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELISNSSDALDKIR 14 1 P07900;P07900-2;G3V2J8 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 222.75 3.44E-12 8387060000 5587268 4843558 5616210 3695300 8146140 6689590 5020982 5661775 6112120 5916700 FALSE TRUE 5807857.655 5675401.409 5762573.046 4426219.311 6761462.033 5136034.104 4627424.311 5585888.167 5892145.995 7075964.083 0.820786763 0.802067583 0.814386984 0.625528798 0.95555347 0.725842308 0.653963793 0.789417258 0.832698686 1 22.75449529 0.850970237 2.505561805 0.999651535 0.770484165 0.378790577 0.087499678 0.577435966 6.8593764 0.080507349 0.021581477 7.095291403 -0.850970237 -0.22916737 ELIVVFGGGNEGIVDELHVYNTATNQWFIPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELIVVFGGGNEGIVDELHVYNTATNQWFIPAVR 33 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 0 111.79 6.42E-06 15101000 6670.2 7480.2 7730.4 7451.2 9567.7 9012.2 8899.1 8111.2 6989 8526.1 FALSE TRUE 6933.544647 8764.866162 7931.860575 8925.02512 7941.385771 6919.253131 8201.565289 8002.482631 6737.467255 10196.62605 0.679984204 0.859584937 0.7778907 0.875291991 0.778824852 0.678582611 0.804341088 0.784816722 0.660754569 1 13.31580424 -1.087223892 4.321495938 1.00002228 0.773303987 0.496220791 0.070243441 13419119.54 38876630.57 5117.22389 0.016256241 0.081804295 1.087223892 -0.226718292 ELKDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELKDDLK 7 1 P12429;D6RA82;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ; 95.099 0.023733 161620000 504760 218764 317540 255480 494360 470800 507990 335090 410170 169026 FALSE TRUE 524688.3146 256335.0153 325815.3533 306013.1815 410328.8638 361463.835 468172.4164 330598.6666 395408.0618 202143.4085 2.595624158 1.268084956 1.611803005 1.513841998 2.029889903 1.788155437 2.316040973 1.635465975 1.956076949 1 17.62501964 3.238093733 24.99999631 1.842171318 1.703425058 0 0.453601063 66.11805205 3540507.845 0.12039627 0.152503683 1730.189741 -3.238093733 -0.13874626 ELKENGELLPILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELKENGELLPILR 13 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 128.22 0.00015304 547990000 947910 594020 649110 595280 930320 938460 748740 676490 703130 653340 FALSE TRUE 985334.2187 696038.3142 666026.3398 713024.6073 772184.5387 720516.8875 690051.8023 667422.7581 677824.4886 781349.4641 1.261067248 0.890815629 0.852405192 0.912555316 0.988270389 0.922144214 0.883153869 0.85419238 0.8675049 1 19.57560842 4.739588821 24.94612148 0.901432716 1.261067366 0.823121266 0.049032902 33.44574951 811343.0286 0.012059456 0.073876784 54902.08286 -4.739588821 0.35963465 ELKIDIIPNPQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELKIDIIPNPQER 13 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;; 116.96 0.00049616 1760430000 2165990 1986940 2330170 1420510 3327280 2782740 1869630 2245580 2620650 2599300 FALSE TRUE 2251504.958 2328181.489 2390896.144 1701482.638 2761710.134 2136490.808 1723083.515 2215481.673 2526333.318 3108583.068 0.724286567 0.748952638 0.769127314 0.547349902 0.888414455 0.687287668 0.554298688 0.712698237 0.812696094 1 21.5678257 0.937395076 2.837113729 0.999157946 0.701454871 0.485017106 0.093843191 0.259618582 4.909785391 0.087632263 0.023185978 8.657551339 -0.937395076 -0.297703075 ELKTDS(ph)SPNQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.014)DS(0.785)S(0.201)PNQAR;ELKT(0.002)DS(0.499)S(0.499)PNQAR 140.49 3.62E-05 2424600000 1089400 912240 899130 636600 1421160 1258050 820100 868910 1071330 1057430 TRUE FALSE 1132410.353 1068910.124 922562.0664 762517.5799 1179591.731 965886.9534 755818.4191 857263.6827 1032773.043 1264613.163 0.895459882 0.845246717 0.729521164 0.602965082 0.932768823 0.763780563 0.597667683 0.677886098 0.816671116 1 20.27026471 4.35755027 4.024441294 0.741922941 0.884567796 0.085330583 0.124002813 0.39127421 11.23016771 0.029981202 0.093282625 22779.81907 -4.35755027 0.142644855 ELKTDSS(ph)PNQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 ELKT(0.064)DS(0.279)S(0.657)PNQAR;ELKT(0.001)DS(0.094)S(0.905)PNQAR 178.85 1.30E-05 1184320000 850810 676130 776720 464231 1038390 1028220 607016 745750 833330 811480 TRUE FALSE 884400.6358 792250.0679 796961.9613 556054.5062 861884.8387 789431.4878 559436.4998 735754.4411 803338.6161 970473.9693 0.911307942 0.816353754 0.821209004 0.572972098 0.888107117 0.81344942 0.576456986 0.758139285 0.827779664 1 19.88832999 0.886751483 3.515061289 0.999825126 0.762848796 0.288672256 0.108359141 0.616665697 15.59690509 0.103441915 0.026703089 7.704624596 -0.886751483 -0.23697633 ELKTDSSPNQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;; 108.32 0.001567 473910000 666247 653192 719600 446451 984010 865370 527850 657530 766560 894290 FALSE TRUE 692550.946 765372.6449 738353.3672 534757.6753 816748.3317 664400.9323 486475.7377 648716.8859 738971.6553 1069509.003 0.647541015 0.715629922 0.690366668 0.500002967 0.763666626 0.621220514 0.454858946 0.606555797 0.690944773 1 20.0285172 0.829128852 3.737169603 0.999951298 0.622083641 0.618777121 0.087904304 0.738175737 15.21896685 0.086304546 0.022157108 6.747281856 -0.829128852 -0.377867656 ELLDLAMQNAWFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLDLAMQNAWFR 13 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 204.69 1.76E-07 199093000 174583 198936 186237 177798 233600 267910 225710 206707 201820 212167 FALSE TRUE 181475.6716 233101.7105 191090.4892 212965.9137 193892.7554 205691.9627 208018.2604 203936.4308 194556.5376 253737.0615 0.715211529 0.918674273 0.753104368 0.839317333 0.764148344 0.810650055 0.819818198 0.803731349 0.766764368 1 17.95297473 -2.193103542 2.41356881 1.576932181 0.802755819 0.563619057 0.052956038 7520088.076 1737815.478 23678935.9 0.01175397 0.006410567 2.193103542 -0.774176362 ELLDT(ph)SFEDLSKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 ELLDT(0.559)S(0.441)FEDLSKPK;ELLDT(0.665)S(0.335)FEDLSKPK 144.05 1.45E-05 123499000 201793 78006 124537 91218 172232 165566 196509 115667 140919 67749 TRUE FALSE 209759.9435 91402.9237 127782.5365 109260.6481 142956.0662 127115.8057 181106.1111 114116.6731 135847.3527 81023.11942 2.588889998 1.128109166 1.577112032 1.348511992 1.764386106 1.568883136 2.235239922 1.40844581 1.676649254 1 16.30604601 0.342019401 1.333188985 0.999987842 1.680328734 0.209384932 0.406463192 6.438898442 11.49350037 0.362689818 0.106474467 2.197958059 -0.342019401 0.680340892 ELLELGIDNEDS(ph)EHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLELGIDNEDSEHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR 46 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 ELLELGIDNEDS(1)EHENDDDTNQSATLNDKDDDSLPAETGQNHPFFR 87.348 1.72E-05 88080000 22098 18901 18356 13758 25464 26383 27589 21241 22652 18892 TRUE FALSE 22970.4461 22147.09972 18834.37244 16479.29134 21135.63838 20255.94809 25426.50209 20956.29914 21836.75894 22593.52569 1.016682674 0.980240978 0.833618121 0.729381132 0.935473226 0.896537723 1.125388859 0.927535588 0.96650515 1 14.4636218 2.418601796 24.99998352 0.997609603 0.893070754 0.256821844 0.087872942 117.8329462 50338.21644 0.032243507 0.026976856 262.1813502 -2.418601796 -0.104538849 ELLFHPALFEVPSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLFHPALFEVPSLK 15 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 0 123.29 0.00010365 209830000 592080 457160 567470 411280 773190 694220 719890 584680 683670 445120 FALSE TRUE 615455.7756 535673.6738 582258.7344 492629.9565 641763.44 532997.926 663463.1407 576843.3209 659064.8502 532332.7417 1.156148641 1.006276022 1.093787191 0.925417353 1.205568228 1.001249565 1.246331643 1.083614206 1.238069348 1 19.02196878 3.217175399 24.99630797 1.132012768 1.046067807 0.147270438 0.098555019 419.8857851 490786.3735 0.026142318 0.03127249 1648.82817 -3.217175399 -0.085944961 ELLGPDFGYVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLGPDFGYVTR 12 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 188.28 2.19E-05 177244000 225750 306390 282850 311300 287490 354580 278470 288170 274460 276990 FALSE TRUE 234662.7843 359010.0991 290221.3034 372874.2109 238622.5525 272234.1687 256642.7938 284307.5525 264582.2382 331260.8872 0.70839267 1.083768453 0.876110989 1.125620999 0.720346294 0.821811989 0.774745235 0.858258743 0.798712581 1 18.33760835 3.217213442 24.99991805 0.820509178 0.952968629 0.175232905 0.126050688 350.2208983 410146.7439 0.033500353 0.040076436 1648.97261 -3.217213442 0.132459451 ELLHSVHPES(ph)PNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELLHSVHPESPNLK 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK;ELLHSVHPES(1)PNLK 264.52 1.81E-24 3818890000 954289 1280405 1567393 1462238 2016910 1949498 1666743 1701497 1692414 1395051 TRUE FALSE 991965.0666 1500304.599 1608240.549 1751464.312 1674076.359 1496756.634 1536099.328 1678691.216 1631504.351 1668384.534 0.594566209 0.899255878 0.963950766 1.049796541 1.003411579 0.897129291 0.920710602 1.006177642 0.977894675 1 20.67002041 4.762874834 2.351434587 0.976731435 0.488366217 0.884865042 0.041349346 0.205335026 1.291112825 0.011209974 0.210059789 57926.17265 -4.762874834 -0.488365218 ELLIHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLIHER 7 0 Q96BN8 Q96BN8 OTULIN Ubiquitin thioesterase otulin 0 105.57 0.020374 0 26591 27489 28542 32080 29741 31568 31912 27520 27380 33405 FALSE TRUE 27640.83321 32210.02192 29285.82797 38425.32825 24685.63544 24236.81042 29410.65405 27151.13941 26394.59915 39950.07017 0.691884472 0.806256955 0.733060739 0.961833811 0.617912192 0.606677543 0.736185291 0.679626827 0.660689682 1 15.28591042 -1.131256423 3.808477991 1.000134163 0.722540799 0.422017365 0.097747021 37754322.44 50383487.1 58669.11839 0.023905755 0.073916871 1.131256423 -0.277593364 ELLNPVVEFVSHPSTTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLNPVVEFVSHPSTTCR 18 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 174.19 6.44E-12 508720000 124615 300160 337320 390110 314220 392200 257390 331130 292670 313740 FALSE TRUE 129534.8964 351710.1451 346110.8363 467272.5936 260808.9966 301117.4938 237215.0992 326691.744 282136.8639 375211.3461 0.345231821 0.937365431 0.922442351 1.245358379 0.695098907 0.802527687 0.632217287 0.870687274 0.751941184 1 18.51734393 ELLQHPFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLQHPFLK 9 0 Q13177;A0A087X294;O75914-2;O75914;O75914-4;O75914-3 Q13177 PAK2;PAK3 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34;Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 3 0 ; 86.624 0.014012 762170000 1414180 1255580 1482330 1213170 1726880 1701270 1460930 1472580 1527910 1373580 FALSE TRUE 1470012.918 1471216.098 1520960.738 1453131.405 1433345.554 1306175.825 1346418.489 1452842.474 1472920.818 1642706.702 0.894872418 0.895604855 0.925886974 0.884595773 0.872551109 0.795136359 0.819634136 0.884419886 0.896642606 1 20.64764349 0.761960074 2.179847361 0.999872811 0.870202299 0.533785092 0.035941747 0.84253198 6.196825927 0.038500806 0.010503224 5.780429039 -0.761960074 -0.129670513 ELLQTELSGFLDAQKDVDAVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLQTELSGFLDAQKDVDAVDK 22 1 P23297;Q5T7Y6 P23297 S100A1 Protein S100-A1;Protein S100 0 ; 166.79 1.03E-11 210751000 231061 155572 176736 93971 270427 226605 194608 176326 200639 142516 FALSE TRUE 240183.4667 182290.2808 181341.8854 112558.1833 224459.9151 173979.423 179354.1164 173962.6384 193418.0416 170439.2816 1.409202529 1.069532089 1.06396767 0.66040048 1.316949432 1.02077069 1.052305048 1.020672211 1.134820798 1 17.37889835 4.751603576 3.360962984 1.032406345 1.464748361 0.350139373 0.152504423 0.366319037 6.727039569 0.035400844 0.414765614 56442.15354 -4.751603576 0.432342015 ELLS(ph)PLS(ph)EPDDRYPLIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 ELLS(1)PLS(1)EPDDRYPLIVK 77.847 0.0073395 13887000 80331 68254 78667 66557 98686 94352 91466 78210 91306 62146 TRUE FALSE 83502.52991 79976.09356 80717.12665 79721.77595 81911.38897 72440.17792 84296.65592 77161.72288 88019.9149 74322.31884 1.1235189 1.076071021 1.086041554 1.072649201 1.102110244 0.974675966 1.134203793 1.038203921 1.184299902 1 16.18150789 7.366419619 1.167421983 1.073249322 29.99426592 0.061124082 0.057763559 2801.944092 8.611032566 0.014899245 216162.4374 23249821.29 -7.366419619 28.9210166 ELLS(ph)PLSEPDDRYPLIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.975)PLS(0.025)EPDDRYPLIVK;ELLS(0.988)PLS(0.012)EPDDRYPLIVK 213.45 4.87E-17 84186000 154866 150446 173836 137731 211561 200619 205355 183495 188955 143950 TRUE FALSE 160980.2293 176283.9302 178366.309 164973.7807 175599.9368 154028.2777 189258.7385 181035.5497 182154.5465 172154.2464 0.935092991 1.023988277 1.036084283 0.958290511 1.020015134 0.894710882 1.099355621 1.05158922 1.058089186 1 17.39334224 2.212193345 24.99978633 1.057553768 0.983769218 0.372932487 0.046598132 231.7327592 219712.9712 0.016711304 0.012345783 163.0021546 -2.212193345 -0.073784551 ELLSPLS(ph)EPDDRYPLIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 ELLS(0.166)PLS(0.834)EPDDRYPLIVK;ELLS(0.004)PLS(0.996)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK;ELLSPLS(1)EPDDRYPLIVK 235.68 5.12E-24 1613470000 755843 687321 783227 668622 913351 889876 870965 799167 778436 609584 TRUE FALSE 785684.2653 805363.0351 803638.539 800873.436 758099.9233 683215.7852 802696.4875 788455.4735 750420.2404 729020.3136 1.077726163 1.104719608 1.10235411 1.098561207 1.039888614 0.93716975 1.101061894 1.08152744 1.029354363 1 19.47559949 7.999999994 0.11421937 0.991540488 1.334896237 0.239726061 0.045889833 176.1665831 1.394064608 0.396537944 9.575520854 99999998.72 -7.999999994 0.343355749 ELLTLDEKDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;; 69.721 0.049001 5824200000 7088080 4869030 6521720 4973410 8129100 7739300 7727900 7017010 6946790 4609950 FALSE TRUE 7367922.872 5705248.027 6691681.381 5957135.654 6747318.486 5941964.865 7122167.005 6922958.458 6696776.385 5513181.44 1.336419444 1.034837705 1.213760413 1.080525957 1.223852064 1.077774227 1.291843391 1.255710253 1.214684562 1 22.39445365 2.2347443 24.998859 1.219422262 1.157022076 0 0.110299607 273.5132557 1791623.106 0.037023672 0.028378911 171.6897231 -2.2347443 -0.062400186 ELLTMQLVDWHQLQADSFIQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLTMQLVDWHQLQADSFIQDER 23 0 P52948-6;P52948-5;P52948;P52948-2;H7C3P6;H0YDF4 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 97.509 0.0032752 21245000 12252 12805 14758 13618 16544 17212 17774 15997 13024 11567 FALSE TRUE 12735.71842 15004.15914 15142.6056 16311.59975 13731.85679 13214.77385 16380.82744 15782.58638 12555.26878 13833.33219 0.92065442 1.0846381 1.094646279 1.179151887 0.992664429 0.955284936 1.184156298 1.140909953 0.907609867 1 13.7558611 2.249888087 24.99968482 1.081598694 1.046919164 0 0.099717424 1080.798928 2385318.517 0.035769087 0.029680064 177.7821225 -2.249888087 -0.034679529 ELLTTMGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELLTTMGDR 9 0 J3QRS3;P19105;O14950;P24844-2;P24844 J3QRS3;P24844 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 ;;;;; 195.88 7.11E-05 2099870000 997180 1104960 1118900 1227640 1112400 1334740 1206950 1175690 1099270 1055900 FALSE TRUE 1036549.436 1294728.285 1148059.453 1470463.528 923314.6453 1024766.863 1112346.105 1159931.799 1059707.487 1262783.389 0.820845005 1.02529721 0.909149949 1.164462204 0.731174209 0.811514368 0.880868497 0.918551676 0.839183899 1 20.26817576 ELLTTMGDRFTDEEVDELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;;;;;; 352.97 3.18E-95 4170204000 2376464 3682634 3276577 2564423 3940872 3950102 2301094 2949422 3298745 5078275 FALSE TRUE 2470288.634 4315097.743 3361967.288 3071658.215 3271003.985 3032750.675 2120728.239 2909889.822 3180023.812 6073265.757 0.406747989 0.710506985 0.553568282 0.505767134 0.538590623 0.499360772 0.349190752 0.479130988 0.523610186 1 22.53404107 0.92039727 17.78816033 1 0.50534137 0.73131175 0.089638653 689.2875827 154031.0032 0.088938124 0.022234531 8.325249743 -0.92039727 -0.494658631 ELLVHLDDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELLVHLDDPER 11 0 Q86Y56;H0Y650;Q86Y56-2;E9PGY2;Q86Y56-3 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 ;; 130.01 0.00023316 125039000 130451 158891 154151 184297 163999 193832 172903 156354 156477 141938 FALSE TRUE 135601.3062 186179.2932 158168.3017 220750.3965 136122.5086 148817.4556 159350.4111 154258.3304 150845.4233 169748.0335 0.798838746 1.096797939 0.931782822 1.300459227 0.801909193 0.876696198 0.938746728 0.908748851 0.888643127 1 17.37303534 ELLVSALQELESST(ph)SNSPSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLVSALQELESSTSNSPSNK 21 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 1 ELLVSALQELES(0.001)S(0.078)T(0.557)S(0.058)NS(0.297)PS(0.009)NK 122.73 0.00010149 38148000 82882 44977 60040 56194 77780 82224 83377 66872 72448 31731 TRUE FALSE 86154.24536 52701.44988 61604.69172 67309.00548 64558.98338 63128.72212 76841.69287 65975.69022 69840.61063 37948.08192 2.270318841 1.388777699 1.623394085 1.77371298 1.701244967 1.663555018 2.024916385 1.738577732 1.840425315 1 15.21173935 -1.677941054 6.950655762 0.995571755 1.766924242 0.51989845 0.224680387 0.014314217 0.00066325 0.201973505 0.047570521 0.020992248 1.677941054 0.771352487 ELLVSALQELESSTSNS(ph)PSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLVSALQELESSTSNSPSNK 21 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 1 ELLVSALQELES(0.002)S(0.092)T(0.092)S(0.092)NS(0.718)PS(0.004)NK 124.81 1.56E-05 41935000 58805 36667 54944 46461 57037 62670 64620 48321 54030 24969 TRUE FALSE 61126.66681 42964.27202 56375.88578 55650.84713 47341.87111 48115.84227 59554.91555 47673.33603 52085.47085 29861.19749 2.047026641 1.438799366 1.887931179 1.863650885 1.585397609 1.611316569 1.994391403 1.596497798 1.744252583 1 14.8659844 -2.276395344 0.436118592 1.23E-08 1.758936913 0.598147202 0.185443117 47.95930847 2.707604681 46.5867016 0.095760363 0.005291815 2.276395344 1.758936901 ELLVSQHTVQLVGGLS(ph)PLS(ph)SPSDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 2 ELLVSQHTVQLVGGLS(0.986)PLS(0.591)S(0.36)PS(0.06)DT(0.002)K 81.242 0.011682 30446000 23542 23840 27916 23004 31323 34093 36831 24702 30001 24089 TRUE FALSE 24471.45634 27934.33455 28643.51389 27554.12254 25998.72765 26175.41743 33944.08998 24370.91009 28921.26987 28808.77834 0.849444432 0.96964662 0.9942634 0.956448837 0.902458526 0.908591719 1.178255099 0.845954306 1.003904766 1 14.81422086 ELLVSQHTVQLVGGLS(ph)PLSSPSDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELLVSQHTVQLVGGLSPLSSPSDTK 25 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 ELLVSQHTVQLVGGLS(1)PLSSPSDTK;ELLVSQHTVQLVGGLS(1)PLSSPSDTK;ELLVSQHTVQLVGGLS(0.998)PLS(0.002)SPSDTK 235.67 1.31E-38 1612880000 747766 1119093 1297250 1386510 1456188 1707930 1848810 1522620 1419550 971455 TRUE FALSE 777288.3791 1311288.517 1331057.401 1660757.54 1208665.684 1311289.141 1703895.441 1502211.769 1368460.673 1161793.008 0.669042053 1.128676545 1.145692384 1.429477995 1.040345118 1.128677082 1.466608449 1.293011543 1.177886821 1 20.14792162 4.913605739 1.706119394 1.238152169 0.260497613 0.548931677 0.145030092 1.113485403 2.228446342 0.037352296 2.037038316 81960.71511 -4.913605739 -0.977654556 ELMETMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELMETMHR 8 0 E9PM90;Q9UK41;Q9UK41-2 E9PM90 VPS28 Vacuolar protein sorting-associated protein 28 homolog 0 ; 150.28 0.00049174 161020000 112676 152613 138521 148900 162370 186982 148411 140206 142531 158123 FALSE TRUE 117124.5355 178823.0956 142130.9711 178351.9756 134770.4054 143558.2642 136778.158 138326.7679 137401.3372 189104.1744 0.619365151 0.945632724 0.751601447 0.943141399 0.712678109 0.759149102 0.723295287 0.731484476 0.726590714 1 17.52882169 ELMWLNEKEEEEVGFDWSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 229.1 2.36E-25 148192000 123683 92387 110015 99546 149857 148739 140780 119665 131987 70260 FALSE TRUE 128566.1003 108253.7486 112882.0813 119235.9017 124384.3607 114196.6214 129745.2957 118061.0864 127236.8137 84026.10179 1.530073365 1.288334771 1.343416853 1.419034076 1.480306215 1.359061279 1.544107045 1.405052524 1.51425344 1 16.35854993 -0.799036827 5.844155417 0.999999959 1.42694066 0.716689185 0.081346637 4.16E-08 8.47E-09 0.075540096 0.01780497 0.158841205 0.799036827 0.426940701 ELNDIRFEFTPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 103.14 0.0014905 344390000 668120 845870 789340 694410 1003200 1045900 634490 813840 844490 1050000 FALSE TRUE 694497.8935 991141.5925 809910.8489 831762.2254 832676.4223 803005.5758 584757.0159 802931.806 814096.9699 1255727.397 0.55306422 0.789296782 0.644973464 0.662374834 0.663102855 0.639474442 0.465671942 0.639415695 0.648307086 1 20.26009188 0.624732199 3.527504577 0.999998464 0.632610314 0.665203576 0.077978512 6.03979984 56.08861198 0.075449839 0.019439257 4.214365511 -0.624732199 -0.36738815 ELNEDKLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNEDKLEK 9 1 O00567;A0A494C128;Q5JXT2 O00567 NOP56 Nucleolar protein 56 0 ; 105.46 0.002822 363500000 1100410 511760 754480 548570 1044460 953720 1117890 783470 862490 407772 FALSE TRUE 1143855.037 599650.7991 774142.3686 657075.5087 866923.0623 732232.9838 1030266.861 772968.8661 831449.1534 487667.1161 2.34556524 1.229631401 1.587440168 1.34738531 1.77769432 1.501501659 2.1126437 1.585033808 1.704952263 1 18.89553717 ELNEYLEQFVGDQEAWHELAELYINEHDYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELNEYLEQFVGDQEAWHELAELYINEHDYAK 31 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 188.54 8.94E-19 64583000 79033 127050 109600 103970 128930 154700 108440 119200 115260 150730 FALSE TRUE 82153.28387 148869.8492 112456.266 124534.9557 107014.5247 118773.2695 99940.18944 117602.319 111111.8151 180262.6576 0.45574211 0.825849631 0.623846711 0.690852766 0.593658865 0.658890039 0.554414268 0.652394237 0.616388422 1 17.45974104 -1.896940238 2.530311123 1.20004054 0.635328225 0.601853564 0.090140395 11639634.55 6208239.44 13860042.78 0.019687894 0.012678263 1.896940238 -0.564712315 ELNFVTDSVEQELPSS(ph)PKQPICFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNFVTDSVEQELPSSPKQPICFDR 25 1 B4DP81;Q8TAP6-2;Q8TAP6 B4DP81 CEP76 Centrosomal protein of 76 kDa 1 ELNFVTDSVEQELPS(0.164)S(0.836)PKQPICFDR;ELNFVTDSVEQELPS(0.051)S(0.949)PKQPICFDR 242.63 5.02E-39 167302000 129026 73795 90900 80565 136374 139671 122465 118974 106871 78835 TRUE FALSE 134120.0461 86468.7172 93268.92868 96500.51654 113193.1962 107234.527 112865.8733 117379.3481 103024.7336 94281.20886 1.422553314 0.91713628 0.989263182 1.023539237 1.200591269 1.137390242 1.197119497 1.244991972 1.092738785 1 16.52468264 3.23453244 24.97228388 1.166547489 1.068848249 0.018476821 0.140994184 241.3998734 1496535.398 0.038978757 0.048230245 1716.059888 -3.23453244 -0.09769924 ELNHMLSDTGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ELNHMLSDTGNR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;; 201.09 1.52E-07 11176260000 4937593 7154970 6207020 6627220 6192820 7656170 6260350 6038410 5384980 6870830 FALSE TRUE 5132532.984 8383780.44 6368780.04 7938064.336 5140166.668 5878140.548 5769647.409 5957474.991 5191175.622 8217037.589 0.624620848 1.020292332 0.775070087 0.966049413 0.625549855 0.715360066 0.702156628 0.725014937 0.631757561 1 22.97018694 3.2333093 24.99991457 0.717302259 0.853818603 0.129487685 0.139638575 204.8710276 975328.3091 0.036328625 0.044650172 1711.233604 -3.2333093 0.136516344 ELNHMLSDTGNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ELNHMLSDTGNRK 13 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;; 145.71 2.72E-05 5692680000 5130737 5252312 5674009 5280297 6479119 7304310 6547428 5740509 5747510 5381386 FALSE TRUE 5333302.459 6154355.729 5821878.336 6324723.986 5377800.667 5607994.7 6034223.485 5663566.866 5540658.238 6435765.554 0.828697443 0.956274071 0.904613179 0.982746176 0.835611649 0.871379582 0.937607723 0.880014478 0.86091673 1 22.61768034 -1.352856588 5.430963665 1.000031165 0.898073765 0.295980905 0.048266285 1.73E-05 2.06E-06 0.044359113 0.010452349 0.044375516 1.352856588 -0.101957401 ELNLVLSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELNLVLSVR 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 0 135.55 0.0028983 0 273480 254750 260450 231820 345480 342300 286890 244630 272240 234930 FALSE TRUE 284277.2016 298501.3308 267237.541 277673.3041 286755.433 262806.0126 264402.8122 241351.135 262442.1356 280960.0355 1.011806541 1.062433418 0.951158554 0.988301783 1.020627124 0.935385747 0.941069116 0.859023009 0.934090627 1 18.10000541 2.602619887 3.080681709 0.916791418 1.006031753 0.399424815 0.04250597 0.226412492 4.096392752 0.014885973 0.013758034 400.5160159 -2.602619887 0.089240335 ELNNYEIRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELNNYEIRPGR 11 1 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7 B7Z8Z7 RBM47 RNA-binding protein 47 0 ;; 191.79 1.53E-06 1794400000 851320 952750 930790 947270 1013570 1146080 950450 1012620 976670 852400 FALSE TRUE 884930.771 1116377.401 955047.1521 1134637.179 841283.7334 879920.289 875951.2455 999047.4852 941519.8375 1019411.46 0.86808007 1.095119532 0.936861306 1.11303161 0.825264152 0.863164996 0.859271531 0.980023793 0.923591577 1 19.95930505 3.229074403 24.99999772 0.907094558 1.005089896 0.239427301 0.082655269 272.2578238 717508.111 0.022911105 0.02772102 1694.628098 -3.229074403 0.097995338 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR 198.82 9.44E-27 1346350000 308688 241033 295604 273287 355573 370116 419997 320252 315680 190350 TRUE FALSE 320875.2406 282428.5428 303307.6831 327342.3529 295132.8285 284162.1682 387076.5377 315959.5458 304318.7385 227645.438 1.409539516 1.240651011 1.332368818 1.437948222 1.296458348 1.248266474 1.700348318 1.387945871 1.336810178 1 17.79642902 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.001)NHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK;ELNS(0.099)NHDGADET(0.45)S(0.45)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 191.44 1.79E-28 1809930000 561421 369618 510366 381971 735740 695540 709370 604672 610275 300188 TRUE FALSE 583586.3346 433097.0163 523666.5572 457523.7237 610679.1776 534011.376 653767.7258 596567.3609 588311.322 359004.0912 1.625570151 1.206384626 1.458664595 1.274424819 1.70103682 1.487479918 1.821059263 1.661728586 1.638731526 1 18.45364076 3.236661621 24.99992696 1.604704485 1.382870126 0.075330643 0.233979428 83.98937615 1105711.271 0.061323073 0.076886296 1724.493736 -3.236661621 -0.221834359 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.212)S(0.788)EKEQQEAIEHIDEVQNEIDR;ELNSNHDGADET(0.063)S(0.937)EKEQQEAIEHIDEVQNEIDR 364.89 3.07E-148 1402290000 226470 196995 235450 222010 290690 308240 305470 283730 263320 142596 TRUE FALSE 235411.2105 230827.3588 241586.0204 265922.9154 241278.6176 236655.9314 281526.4632 279927.0634 253843.1646 170534.956 1.380427896 1.353548646 1.416636366 1.559345495 1.414833787 1.387726815 1.650843145 1.641464424 1.488511039 1 17.37970797 3.96700532 5.7727433 1.492756263 1.370374063 0 0.176602818 0.468056007 46.31130181 0.043698341 0.084142982 9268.411763 -3.96700532 -0.122382199 ELNSNHDGADETS(ph)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 1 ELNSNHDGADET(0.433)S(0.567)EKEQQEAIEHIDEVQNEIDRLNEQASEEILK 170.93 9.66E-21 515890000 161520 103790 153530 115440 224610 214680 196970 178160 180360 87403 TRUE FALSE 167896.9343 121615.1251 157531.1179 138273.6874 186430.8724 164823.8235 181530.9767 175772.0566 173868.8788 104527.9444 1.606239702 1.163469977 1.507071806 1.32283944 1.783550547 1.576839805 1.736674128 1.681579577 1.663372219 1 16.67352916 3.25319816 24.96142912 1.62326587 1.390671725 0.094384831 0.234609856 370.0167324 630986.5546 0.05905651 0.079624378 1791.423057 -3.25319816 -0.232594145 ELNSNHDGADETSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNSNHDGADETSEK 15 0 Q01105-2 Q01105-2 SET Protein SET 0 ; 218.28 1.96E-12 455690000 390736 533085 615307 657580 760730 827680 856110 766850 702290 422958 FALSE TRUE 406162.559 624638.2019 631342.4059 787647.3613 631421.3863 635463.8636 789005.8612 756571.6301 677014.7201 505828.5221 0.80296492 1.234881338 1.248135244 1.557143037 1.248291385 1.256283179 1.55982873 1.495707729 1.338427334 1 18.94828886 5.047942156 1.303272264 1.381303261 0.134416093 0.479369998 0.163792284 2.102746369 1.841915854 0.043644998 4.220946004 111671.4501 -5.047942156 -1.246887168 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 0 ; 221.01 2.95E-36 806110000 154660 171404 201895 183143 214060 277100 264620 217080 227540 130849 FALSE TRUE 160766.0962 200841.3037 207156.5496 219368.1388 177674.1577 212747.7245 243878.3929 214170.3977 219350.8798 156486.3563 1.027348965 1.283442905 1.323799432 1.401835559 1.135397116 1.359528904 1.558464257 1.36862026 1.401725269 1 17.25567735 4.816527281 2.077130242 1.344023445 0.89413641 0.245882401 0.146883423 1.144741262 4.58289629 0.035854623 1.037323094 65543.14571 -4.816527281 -0.449887034 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDRLNEQASEEILK 44 2 Q01105-2 Q01105-2 SET Protein SET 0 ; 88.012 3.76E-05 243540000 178940 177299 228684 173943 329980 289456 305093 259289 269731 134044 FALSE TRUE 186004.6894 207748.7241 234643.6929 208348.4062 273890.1175 222234.2307 281179.0134 255813.6551 260023.434 160307.3554 1.160300405 1.295940062 1.463711334 1.29968089 1.708531195 1.386300898 1.753999452 1.595769916 1.622030589 1 17.2904811 4.458868331 0.841121888 1.547339604 1.041839459 0.174004848 0.211690313 2.185388891 1.585799996 0.069802159 0.948655655 28765.26183 -4.458868331 -0.505500145 ELNYFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELNYFAK 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 117.02 0.012389 1712778000 2129010 2075125 2163400 1943553 2675110 2696550 2301480 2258710 2269770 2130670 FALSE TRUE 2213064.959 2431511.577 2219779.981 2327981.982 2220395.758 2070317.129 2121083.984 2228435.687 2188081.421 2548133.992 0.868504155 0.954232228 0.871139425 0.913602656 0.871381083 0.81248362 0.832406769 0.874536305 0.858699514 1 21.28100971 4.101570493 24.82026424 0.871164152 0.911701421 0.039566021 0.05214108 24.8489536 6036.322335 0.012287361 0.02654374 12634.86173 -4.101570493 0.040537269 ELPALGNPAAAAPPGPHPS(ph)PAAPEPLAYDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELPALGNPAAAAPPGPHPSPAAPEPLAYDYR 31 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0G2JP16;Q6ZUM4-4 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 ELPALGNPAAAAPPGPHPS(1)PAAPEPLAYDYR;ELPALGNPAAAAPPGPHPS(1)PAAPEPLAYDYR;ELPALGNPAAAAPPGPHPS(1)PAAPEPLAYDYR 187.96 1.08E-18 298518000 70950 63740 64348 64806 82725 86451 78944 70111 71497 74506 TRUE FALSE 73751.16079 74686.84917 66024.96174 77624.43337 68663.43405 66374.06543 72756.163 69171.27672 68923.83694 89104.0242 0.827697306 0.838198385 0.740987428 0.871166416 0.770598575 0.744905362 0.816530607 0.776298011 0.773521034 1 16.44320297 -1.379773476 5.764886338 1.000054543 0.794752958 0.70110556 0.040045532 2.67E-05 2.87E-06 0.036857195 0.008685021 0.041708688 1.379773476 -0.205301586 ELPDLEDLMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELPDLEDLMKR 11 1 Q9HC38-2;F6TLX2;Q9HC38 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;; 151.1 5.38E-05 468802000 911144 644041 752435 536246 1012590 966719 766805 727520 845154 736915 FALSE TRUE 947116.6687 754650.0318 772044.0742 642313.8583 840470.3135 742213.163 706700.8204 717768.7844 814737.0726 881299.3852 1.074682094 0.856292475 0.87602929 0.728825946 0.953671735 0.842180507 0.801885071 0.814443759 0.92447253 1 19.74927267 4.738884115 7.083702477 0.853728143 1.077809125 0.398030851 0.075399854 0.095546926 38.06980413 0.016735221 0.102212481 54813.06846 -4.738884115 0.224080982 ELPDVLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPDVLER 8 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 83.265 0.042536 101361000 159385 192276 177531 205373 194844 242250 191016 200877 199627 197458 FALSE TRUE 165677.6429 225297.9073 182157.6037 245995.1664 161724.4865 185991.1088 176043.6668 198184.5724 192442.4633 236146.1145 0.701589536 0.954061462 0.771376671 1.041707448 0.684849237 0.787610286 0.745486188 0.839245536 0.814929619 1 17.84932027 -1.313245838 2.455966145 1.003695739 0.818847657 0.219081641 0.104257807 1513775.961 1559146.892 41087.56546 0.024903947 0.048613195 1.313245838 -0.184848082 ELPDVQGESDSIS(ph)PLLLHLEDDDFSENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELPDVQGESDSISPLLLHLEDDDFSENEK 29 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 ELPDVQGES(0.001)DS(0.022)IS(0.977)PLLLHLEDDDFSENEK 119.89 3.37E-05 36398000 32074 22746 31472 24721 38395 41196 38539 33047 34359 21085 TRUE FALSE 33340.30629 26652.44856 32292.18617 29610.74002 31868.63161 31628.85333 35518.21248 32604.05902 33122.4263 25216.20205 1.322177948 1.056957289 1.280612604 1.174274379 1.263815683 1.254306785 1.408547267 1.292980559 1.313537472 1 14.62206338 3.044679529 3.026440618 1.285490045 1.202754689 0 0.118815531 0.617951989 11.58357659 0.03420553 0.04062745 1108.356645 -3.044679529 -0.082735356 ELPFGDKDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELPFGDKDTK 10 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 64.64 0.080325 0 440090 237430 333620 253740 552220 458970 495150 390640 455370 247010 FALSE TRUE 457465.093 278206.7556 342314.4113 303929.0147 458353.8416 352381.1733 456338.8492 385404.1098 438981.3227 295406.8802 1.548593224 0.9417748 1.158789569 1.028848802 1.551601782 1.192867184 1.544780707 1.304655157 1.486022676 1 18.1723439 3.249371486 24.99984104 1.364157227 1.152470275 0.134663178 0.215576223 344.5065032 796657.3578 0.054823237 0.073503095 1775.707731 -3.249371486 -0.211686952 ELPGFLQSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPGFLQSGK 10 0 P25815 P25815 S100P Protein S100-P 0 ; 164.97 1.39E-05 525480000 591660 461450 504340 489110 647930 709460 704920 557610 576100 447260 FALSE TRUE 615019.1937 540700.4479 517483.5147 585854.4982 537795.09 544698.667 649666.5284 550136.15 555366.2735 534892.0337 1.149800623 1.01085904 0.967454144 1.09527617 1.005427369 1.018333856 1.214575068 1.028499427 1.038277332 1 19.02888819 ELPGFLQSGKDKDAVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELPGFLQSGKDKDAVDK 17 2 P25815 P25815 S100P Protein S100-P 0 103.88 0.00049354 654570000 700450 291870 406410 218140 673420 600950 593970 369290 520580 298910 FALSE TRUE 728104.3069 341996.4021 417001.3785 261287.4409 558952.3089 461388.47 547413.0793 364340.2716 501844.4275 357475.6915 2.036793897 0.956698344 1.16651674 0.73092366 1.563609281 1.29068488 1.531329521 1.019202928 1.403856093 1 18.44748562 7.999999978 0.02183835 2.10E-08 2.894002194 0.064193184 0.348265265 10599.40612 17.82135041 851.3032792 1625.607127 99999995 -7.999999978 2.894002173 ELPGHTGYLSCCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPGHTGYLSCCR 13 0 P62879;E7EP32;C9JZN1;C9JIS1;C9JXA5;P62879-2;Q9HAV0;H7C5J5 P62879 GNB2;GNB4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2;Guanine nucleotide-binding protein subunit beta-4 0 ; 138.2 5.18E-05 574420000 160033 297900 197506 258940 306720 364880 237830 242350 189630 421090 FALSE TRUE 166351.2264 349062.0077 202653.1686 310157.5591 254583.844 280142.1498 219188.2631 239101.6947 182805.2533 503594.5232 0.330327712 0.693140993 0.402413369 0.615887475 0.505533385 0.55628514 0.435247512 0.474790101 0.363000877 1 18.94190307 -1.585204621 6.0207835 1.00161337 0.492860738 0.67428949 0.107022491 0.002103165 0.000144895 0.094030867 0.022104102 0.025989348 1.585204621 -0.508752632 ELPPAAAIGATSLVAAPHS(ph)SSSSPSKDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPPAAAIGATSLVAAPHSSSSSPSKDSSR 30 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 ELPPAAAIGATS(0.001)LVAAPHS(0.125)S(0.125)S(0.125)S(0.125)S(0.125)PS(0.125)KDS(0.125)S(0.125)R;ELPPAAAIGATSLVAAPHS(0.258)S(0.174)S(0.174)S(0.174)S(0.174)PS(0.04)KDS(0.003)S(0.003)R 164.14 2.05E-12 255131000 30168.7 178924 191673 176830 202999 238043 179898 236171 175929 196551 TRUE FALSE 31359.78357 209652.8052 196668.1558 211806.4462 168493.3025 182761.1208 165797.1247 233005.514 169597.3497 235061.4053 0.133411027 0.891906542 0.836667149 0.901068578 0.716805476 0.777503736 0.705335376 0.991253812 0.721502322 1 17.84267816 4.741381794 24.9672577 0.835126817 0.13341077 0.807918338 0.103058311 102.6997159 908838.1446 0.023558011 0.163871949 55129.21313 -4.741381794 -0.701716047 ELPPAAAIGATSLVAAPHSS(ph)SSSPSKDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.079)S(0.216)S(0.216)S(0.216)S(0.216)PS(0.052)KDS(0.003)S(0.003)R 141.13 3.19E-08 267970000 21557 161340 163000 170240 193790 233110 162120 219990 164380 165450 TRUE FALSE 22408.08701 189048.8899 167247.9139 203912.9639 160849.645 178973.7353 149412.6108 217041.3939 158463.9959 197866.7598 0.113248365 0.955435315 0.845255232 1.030556947 0.812918982 0.904516431 0.755117287 1.096906798 0.800862136 1 17.59416974 4.740364519 24.9962426 0.913908772 0.113248096 0.839924614 0.104511236 54.88318718 760443.4831 0.023367583 0.15102693 55000.2317 -4.740364519 -0.800660676 ELPPS(ph)PEKK ddPTM_MDA-MB-175_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 64.121 0.043849 159970000 627230 220770 341790 236570 429080 565030 541890 363260 374650 180940 TRUE FALSE 651993.5247 258685.5301 350697.3282 283362.8399 356145.1349 433810.3456 499415.2458 358391.0939 361166.4197 216391.7287 3.013024244 1.195450176 1.62065958 1.309490162 1.64583525 2.004745506 2.307922067 1.656214385 1.669039856 1 17.72328583 0.17775274 16.08503367 0.999999587 1.795715095 0.196427271 0.497316738 0 0 0.455565233 0.107377755 1.505749542 -0.17775274 0.795715508 ELPQLVASVIESESEILHHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPQLVASVIESESEILHHEK 21 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 199.33 4.67E-22 56916000 55774 56030 64319 63495 83155 86495 75400 67344 66471 58349 FALSE TRUE 57976.00059 65652.71665 65995.20598 76054.12149 69020.3428 66407.84709 69489.95098 66441.36383 64078.72169 69781.36939 0.830823486 0.940834455 0.945742489 1.089891502 0.989094129 0.951655831 0.995823836 0.952136142 0.918278364 1 16.09055429 4.742896736 1.888574723 0.98117066 0.783558798 0.518327281 0.043734986 0.689778397 2.529107455 0.011670227 0.241023149 55321.85522 -4.742896736 -0.197611862 ELPSFLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPSFLGK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 144.38 0.0013642 722740000 1548790 1538360 1727660 1463870 1876550 1967570 1808270 1623990 1724420 1563590 FALSE TRUE 1609937.425 1802561.363 1772684.239 1753419.117 1557574.701 1510631.686 1666533.072 1602223.07 1662358.461 1869945.524 0.860954185 0.96396464 0.947987102 0.937684598 0.832951913 0.807847965 0.891220119 0.856828742 0.888987642 1 20.83456481 5.114292138 12.29872691 0.89479803 8.75E-05 0.028561687 0.057786933 2646160.53 4628612.863 0.01431833 63462520.29 130104.4461 -5.114292138 -0.894710571 KSGVS(ph)SDNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSGVSSDNEDDDDEEDGNYLHPSLFASK 28 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 KS(0.335)GVS(0.412)S(0.253)DNEDDDDEEDGNYLHPSLFASK 230.21 2.60E-35 135480000 32063 53712 94535 67579 114820 114010 102530 103860 104800 60283 TRUE FALSE 33328.872 62936.61818 96998.65976 80945.9245 95302.93741 87532.90534 94493.43069 102467.9266 101028.2685 72094.29966 0.462295523 0.872976345 1.34544146 1.122778429 1.321920566 1.21414461 1.310692123 1.42130414 1.401335042 1 16.13759757 4.529190242 2.22078068 1.28943788 0.405666007 0.800476016 0.126916616 0.160908928 1.243730857 0.031641189 0.234220177 33821.29576 -4.529190242 -0.883771873 down ELPSLS(ph)PAPDTGLSPSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPS(0.008)LS(0.992)PAPDTGLSPSKR 193.63 6.98E-15 140940000 158970 147380 177600 141990 193330 231150 173570 166490 176220 141910 TRUE FALSE 165246.2584 172691.3685 182228.4019 170075.1982 160467.8357 177468.9156 159965.1299 164258.4739 169877.8766 169714.5475 0.973671738 1.017540164 1.073734719 1.002125043 0.945516092 1.045690651 0.942554025 0.967851468 1.000962376 1 17.37275071 3.47742114 24.9996914 0.980604803 1.024019984 0.179386667 0.035940211 15.45623498 1288548.552 0.009772705 0.013380058 3002.072246 -3.47742114 0.043415181 ELPSLSPAPDT(ph)GLSPSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 ELPSLSPAPDT(0.681)GLS(0.128)PS(0.191)KR;ELPSLSPAPDT(0.746)GLS(0.218)PS(0.036)KR 132.13 9.06E-06 501320000 284031 198461 239240 196223 296377 325510 264358 254887 234704 196655 TRUE FALSE 295244.7632 232545.1329 245474.7909 235035.3237 245998.9434 249915.2357 243636.9292 251470.6567 226257.0489 235185.7821 1.255368248 0.988772072 1.043748431 0.999360258 1.045977105 1.062629014 1.03593392 1.069242598 0.962035404 1 17.84344132 4.744889294 24.99586684 1.029465251 1.255368348 0.811737904 0.033433219 293.4358235 1158929.275 0.007688059 0.072681677 55576.257 -4.744889294 0.225903097 ELPTAFDYVEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELPTAFDYVEFTR 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 155.48 9.15E-05 304338000 178057 195820 181850 168131 219178 225782 209662 203656 193941 180693 FALSE TRUE 185086.8278 229450.5617 186589.1604 201386.81 181922.2018 173347.5523 193228.1446 200926.3244 186961.1013 216096.3338 0.856501471 1.061797568 0.863453614 0.931930711 0.841856956 0.802177201 0.89417595 0.929799784 0.865174795 1 17.72131507 5.098112547 12.67574149 0.905404683 0.000108023 0.043160285 0.072735419 1277183.579 3277425.601 0.017083919 31290990.87 125346.5967 -5.098112547 -0.90529666 ELQAHGADELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELQAHGADELLK 12 0 O15144;C9JTV5;G5E9J0 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;; 144.27 6.13E-05 786670000 2096120 1228750 1735500 1601200 2013840 2107610 2594600 1813150 1995480 953820 FALSE TRUE 2178876.436 1439778.254 1780728.556 1917912.581 1671528.196 1618149.519 2391228.472 1788847.69 1923663.065 1140702.767 1.910117604 1.262185291 1.561080246 1.681342972 1.465349471 1.418554917 2.09627656 1.568197905 1.686384149 1 20.12149149 ELQELVQYPVEHPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;; 208.2 3.01E-09 9968246000 6223725 4562678 5815437 5084797 6660447 6933868 7573895 6092784 6291702 3782283 FALSE TRUE 6469442.469 5346282.454 5966992.066 6090554.67 5528306.598 5323582.241 6980233.319 6011120.196 6065264.874 4523348.938 1.4302329 1.181930142 1.319153607 1.346470227 1.222171156 1.17691169 1.543156059 1.328909239 1.340879282 1 22.10895986 -1.445357549 5.966126974 0.999842483 1.320919081 0.452511576 0.105954812 0.00021823 2.03E-05 0.100851047 0.02375927 0.035862656 1.445357549 0.321076598 ELQELVQYPVEHPDKFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQELVQYPVEHPDKFLK 18 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 197.09 1.13E-15 1261550000 3460900 2544200 3583900 2210120 4800400 4022400 3203400 3502900 4103100 2998100 FALSE TRUE 3597539.004 2981146.559 3677299.378 2647275.139 3984429.723 3088258.56 2952309.137 3455949.355 3955430.232 3585520.293 1.003352013 0.831440437 1.025597146 0.738323848 1.111255661 0.861313926 0.823397693 0.963862724 1.103167716 1 21.77375105 1.440429778 6.18876349 1.048307514 0.912341548 0.208810102 0.106488983 0.258078635 20.68680934 0.06226936 0.024669314 27.5695564 -1.440429778 -0.135965965 ELQEMDKDDESLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ELQEMDKDDESLIK 14 1 P52566;F5H3P3;H0YGX7;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;;;;;; 248.23 5.87E-18 11049313000 22609610 8731853 13955507 8640449 20720950 19396490 20362540 13485430 16403830 6799302 FALSE TRUE 23502254.86 10231480.83 14319198.98 10349504.02 17198810.32 14891949.15 18766470.91 13304679.87 15813459.36 8131495.046 2.890274756 1.258253343 1.76095526 1.272767672 2.115085876 1.831391284 2.307874604 1.636191105 1.944717333 1 22.9550892 4.753976057 24.54117684 1.732770574 2.89027585 0.46025681 0.389281549 2045.033874 3255596.309 0.087804104 2.109086991 56751.33174 -4.753976057 1.157505276 ELQEVIALTSQELEESREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQEVIALTSQELEESREK 19 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 ; 220.28 2.68E-19 35481000 83483 63046 80094 50114 117337 92987 70441 73969 87427 81832 FALSE TRUE 86778.9733 73873.66007 82181.31544 60026.39962 97392.09865 71392.17848 64919.65036 72977.56654 84280.51935 97865.41363 0.886717484 0.754849516 0.839738089 0.613356623 0.995163613 0.729493453 0.663356419 0.745693129 0.861187995 1 16.57851147 0.955174829 4.034809433 0.999716192 0.77350212 0.301516287 0.103578138 0.269957017 12.62929042 0.094677045 0.02420932 9.019341452 -0.955174829 -0.226214071 ELQHAALGGTATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQHAALGGTATR 13 0 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 0 ; 111.43 0.00098001 513610000 573460 411690 411850 447750 466280 560050 432660 353960 422230 414750 FALSE TRUE 596100.6436 482394.555 422583.1493 536313.6136 387021.8922 429986.8751 398746.9787 349215.7452 407034.0248 496012.3216 1.201785959 0.972545507 0.851960992 1.081250586 0.78026669 0.866887487 0.80390539 0.704046512 0.820612729 1 18.92001643 7.999999774 0.48262785 0.80892031 11.46821637 0.496224215 0.10289747 75.23270804 0.837075252 0.055661335 805.5827565 99999947.96 -7.999999774 10.65929606 ELQNAGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 148.27 0.001219 807318000 585469 784749 710261 770903 754796 926207 751552 828977 678353 795321 FALSE TRUE 608583.7682 919523.5363 728770.9851 923385.3125 626496.0455 711109.4611 692643.3904 817865.9192 653939.208 951148.9226 0.639840675 0.966750332 0.766200716 0.970810449 0.658672928 0.747632094 0.728217605 0.859871572 0.687525573 1 19.85931172 -1.331130635 3.440086748 1.001039413 0.78968438 0.253715001 0.11190927 31092351.11 47591540.34 334917.9569 0.024999194 0.046651903 1.331130635 -0.211355033 ELQNTVANLHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQNTVANLHVR 12 0 H3BV04;H3BN93;H3BUB6;H3BPL9;O15127 H3BV04 SCAMP2 Secretory carrier-associated membrane protein 2 0 ; 171.29 3.89E-05 263800000 246390 304880 290680 395460 341700 394930 298110 293570 248940 324050 FALSE TRUE 256117.6675 357240.7684 298255.3596 473680.8077 283617.9561 303213.4927 274743.3592 289635.1743 239980.698 387541.3932 0.660878223 0.921813191 0.76960904 1.22227152 0.73183913 0.782402856 0.708939391 0.747365777 0.619238879 1 18.56399089 ELQQAELPNRS(ph)PGFGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELQQAELPNRSPGFGIK 17 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK;ELQQAELPNRS(1)PGFGIK 233.26 2.53E-20 2262630000 2506660 1835750 2232000 1864790 2555450 2837390 2646270 2348110 2546430 1682830 TRUE FALSE 2605624.872 2151025.782 2290167.754 2233639.896 2121075.522 2178449.174 2438848.443 2316637.426 2454784.482 2012548.319 1.294689349 1.068807026 1.137944233 1.109856531 1.053925266 1.082433228 1.211821063 1.15109655 1.219739401 1 20.94059199 2.253094357 24.99322403 1.159401658 1.118795464 0.001488683 0.084427926 788.1636468 1355381.117 0.027781978 0.023155077 179.0994934 -2.253094357 -0.040606194 ELQQAVLHMEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQQAVLHMEQR 12 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 ; 138.77 6.86E-05 275660000 160010 185832 161445 214263 295630 276260 201413 174090 158445 295580 FALSE TRUE 166327.3184 217747.2004 165652.3893 256643.5819 245378.9182 212102.8018 185625.7228 171756.6083 152742.5954 353493.2418 0.470524748 0.615986884 0.468615435 0.726021184 0.694154482 0.600019397 0.525118166 0.485883711 0.432094811 1 18.43132311 -2.118559643 2.447042921 1.858049116 0.560067787 0.662449752 0.094723904 13262286.04 4721581.271 63018115.89 0.027142536 0.007610976 2.118559643 -1.297981329 ELQQELQEYEVVTESEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELQQELQEYEVVTESEKR 18 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 261.19 1.44E-30 179963000 161720 114324 148175 159795 174169 209950 245170 169131 185096 98934 FALSE TRUE 168104.8305 133958.2577 152036.5622 191401.9741 144563.8156 161192.2943 225952.9348 166864.0756 178434.4311 118318.2231 1.420785624 1.132186186 1.284980101 1.617688037 1.221822064 1.362362366 1.909705275 1.410299033 1.508089172 1 16.85231277 3.895910698 8.500888022 1.463770271 1.259801956 0.070969885 0.235265713 0.621532748 45.79357196 0.058283906 0.105526802 7868.8397 -3.895910698 -0.203968315 ELQTLHNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 187.97 3.99E-05 1714620000 815611 977512 882758 847361 1299310 1234800 1005443 864971 874305 1307180 FALSE TRUE 847811.9521 1145392.082 905763.3987 1014966.477 1078453.75 948036.4136 926633.7504 853377.4786 842838.9338 1563296.894 0.542323058 0.732677258 0.579393078 0.649247421 0.689858564 0.606434016 0.592743294 0.545883179 0.539141949 1 20.57616036 -1.133737468 4.131620706 1.000102409 0.609570519 0.784264577 0.061577471 20710022.72 47437412.96 29635.49184 0.015122225 0.073495802 1.133737468 -0.39053189 ELRAPS(ph)PPVEHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELRAPSPPVEHPR 13 1 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 ELRAPS(1)PPVEHPR;ELRAPS(1)PPVEHPR 132.79 6.93E-05 187944000 108584 153280 127674 118347 163979 174314 104661 127863 126984 169412 TRUE FALSE 112870.9802 179604.6476 131001.2893 141755.6834 136105.9082 133832.2153 96457.39734 126149.2056 122413.8706 202605.0378 0.557098586 0.886476711 0.64658456 0.699665146 0.671779486 0.660557194 0.476085878 0.622636076 0.60419954 1 17.62831052 -1.003388808 4.541173217 1.000010116 0.647528657 0.526711447 0.100319689 12929403.63 2856798.722 1351.119124 0.023733636 0.099222735 1.003388808 -0.352481459 ELS(ph)APAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSAPAR 7 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 ELS(1)APAR;ELS(1)APAR 72.879 0.052876 842300000 914040 912590 910470 908540 1115720 1311200 1019930 948100 916660 950130 TRUE FALSE 950127.005 1069320.234 934197.5962 1088246.5 926070.3129 1006693.671 939985.2215 935392.2703 883669.5857 1136289.782 0.836166108 0.941062967 0.822147317 0.957719164 0.814994843 0.88594801 0.827240759 0.823198699 0.777679778 1 20.11589937 3.184175479 24.99980608 0.844181498 0.88818073 0.044149802 0.068354645 218.3684177 100378.7236 0.018190753 0.021742127 1528.183403 -3.184175479 0.043999232 ELS(ph)PAALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 158.3 7.02E-05 974690000 2407440 1746540 2055660 1658290 2530140 2659250 2493340 2030650 2006610 1606660 TRUE FALSE 2502487.59 2046494.659 2109232.188 1986294.812 2100067.707 2041679.489 2297905.496 2003432.458 1934392.498 1921454.266 1.302392482 1.065075914 1.09772698 1.033745558 1.092957425 1.062569911 1.195919953 1.04266466 1.006733563 1 20.87376721 4.739767501 24.64957034 1.072933036 1.302392571 0.636056798 0.053351718 53.67532551 1096111.97 0.012317697 0.076545421 54924.67568 -4.739767501 0.229459535 ELS(ph)PAGSISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSPAGSISK 10 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 ELS(1)PAGSISK;ELS(1)PAGSISK 208.63 1.16E-07 1390920000 3530700 2690100 3294100 2591600 4441000 3895400 3795900 3377700 3403000 2479800 TRUE FALSE 3670094.762 3152103.749 3379946.952 3104210.745 3686120.406 2990752.385 3498367.439 3332427.456 3280526.695 2965669.331 1.237526626 1.062864196 1.139691103 1.046715058 1.242930345 1.008457805 1.179621545 1.123667909 1.106167387 1 21.49992632 -4.602857904 0.340507858 5.66E-09 1.130287464 0.220993034 0.072928865 426.0945284 4.691555072 306.5789353 0.052231051 2.50E-05 4.602857904 1.130287458 ELS(ph)PQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELSPQHK 7 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHK;ELS(1)PQHK;ELS(1)PQHK 84.213 0.013984 586448000 680730 558520 683170 624080 804530 893940 938220 729560 728690 489290 TRUE FALSE 707605.746 654441.4653 700973.9714 747521.1613 667776.278 686335.9828 864679.8648 719781.4415 702464.5892 585157.0075 1.209257921 1.118403193 1.197924595 1.277471092 1.141191628 1.172909106 1.477688644 1.230065491 1.200471976 1 19.15846425 3.999215334 24.12746219 1.235020964 1.162413879 0.007095129 0.115730632 55.1239772 1695383.117 0.028303663 0.059880528 9981.948716 -3.999215334 -0.072607085 ELS(ph)PQHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSPQHKR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 ELS(1)PQHKR;ELS(1)PQHKR 83.775 0.010978 1119640000 1814870 1470260 1709120 1263220 2282980 2167100 1732020 1756040 1870990 1548430 TRUE FALSE 1886522.469 1722765.718 1753661.071 1513081.146 1894919.875 1663823.868 1596259.747 1732503.156 1803653.435 1851815.212 1.01874229 0.930311894 0.946995715 0.817079985 1.023276979 0.898482666 0.861997318 0.935570215 0.973992126 1 20.82050871 1.143901429 3.301703139 0.997626728 0.924974087 0.136988275 0.059459759 0.42018319 8.202939536 0.053701612 0.01434619 13.92840637 -1.143901429 -0.072652641 ELSAALQDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELSAALQDKK 10 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 73.632 0.057866 0 185430 114330 132390 93872 213330 191310 178150 115750 148910 108270 FALSE TRUE 192750.9196 133965.2881 135840.1922 112439.6014 177068.2428 146881.1518 164186.1375 114198.5606 143550.7582 129483.4335 1.488614522 1.034613344 1.049093219 0.868370558 1.367497277 1.134362503 1.268008833 0.881954992 1.108641888 1 16.982408 4.742380808 24.33033896 1.078348587 1.488614756 0.412137628 0.14669751 262.6089519 1672422.465 0.035009916 0.26286178 55256.17367 -4.742380808 0.41026617 ELSDDCFQQWGVRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSDDCFQQWGVRPR 15 1 P42785;P42785-2 P42785 PRCP Lysosomal Pro-X carboxypeptidase 0 ; 168.5 1.14E-06 289940000 95109 115475 102061 97657 122429 143992 109404 110933 107770 93842 FALSE TRUE 98863.97676 135306.933 104720.7935 116973.2631 101618.5623 110552.0402 100828.6286 109446.1246 103891.3788 112228.5432 0.880916512 1.205637435 0.933103028 1.042277301 0.905460941 0.985061706 0.898422324 0.975207567 0.92571262 1 16.77608012 3.249308594 24.96862647 0.947286797 1.023181673 0.128810163 0.084614464 369.4720069 858315.3333 0.021496101 0.028817051 1775.450605 -3.249308594 0.075894876 ELSDFISYLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 227.88 8.56E-12 8452714000 2569426 3667987 3382677 3867870 4781284 5003892 3759955 3497999 3270860 5161841 FALSE TRUE 2670868.923 4297935.234 3470832.342 4632923.142 3968563.054 3841813.918 3465239.902 3451114.045 3153142.388 6173204.915 0.432655154 0.696224294 0.562241557 0.750489123 0.642869159 0.622337015 0.561335635 0.559047382 0.510778831 1 22.55758825 -1.491018255 3.387221095 1.007585838 0.597992153 0.666077071 0.086366941 163715341 177228569.5 11264925.72 0.020202815 0.032283584 1.491018255 -0.409593685 ELSDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ELSDFLR 7 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ;;;; 158.38 0.0033101 539043000 1090212 1285489 1180180 1191794 1691744 1625449 1357385 1185364 1148753 1659220 FALSE TRUE 1133254.412 1506261.736 1210936.46 1427527.296 1404181.959 1247963.104 1250989.617 1169476.134 1107409.604 1984312.391 0.571106856 0.759084982 0.610254951 0.719406532 0.707641582 0.628914635 0.630439855 0.589360899 0.55808229 1 20.92020774 -1.405288714 3.309982427 1.003819716 0.643534513 0.741972959 0.063398391 22532504.17 31571593.71 823399.0952 0.015834363 0.039328853 1.405288714 -0.360285203 ELSDIAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 ELSDIAHR 8 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;;;;;;; 210.05 4.23E-05 88630732700 34336197.9 47235946.8 42731727.4 44347481.9 50894988.6 54638927 46937212.5 44706099.8 41139170.7 50728317.2 FALSE TRUE 35691817.51 55348353.22 43845351.32 53119281.46 42243876.62 41949864.27 43258151.14 44106887.66 39658579.98 60667559.7 0.588318002 0.912322063 0.722714933 0.875579663 0.696317386 0.6914711 0.713035951 0.727025908 0.653703234 1 25.85442195 -1.2256551 5.150969891 1.000027012 0.736860793 0.436543131 0.091421096 2.65E-05 3.98E-06 0.082559815 0.01945754 0.059476431 1.2256551 -0.263166219 ELSDLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELSDLAR 7 0 P61077-3;P61077-2;P61077;A0A087WY85;D6RA11;D6RGD0;D6R933;D6RIZ3;D6R980;D6R9F6 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ;; 135.87 0.0070624 406750000 724570 841500 843150 862720 1020000 1023420 866110 855400 779750 995420 FALSE TRUE 753176.5831 986021.079 865123.1817 1033363.441 846620.7643 785746.2151 798222.035 843934.7622 751686.9498 1190453.491 0.632680394 0.8282735 0.72671733 0.868041842 0.711175003 0.660039406 0.670519295 0.708918718 0.631429078 1 20.18307983 -1.177071583 5.079065871 1.000018575 0.719047404 0.56824904 0.074381603 1.56E-05 2.53E-06 0.071946887 0.016956924 0.066516351 1.177071583 -0.280971171 ELSDQATAS(ph)PIVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELSDQATASPIVAR 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 ELSDQATAS(1)PIVAR;ELSDQATAS(1)PIVAR;ELSDQAT(0.069)AS(0.931)PIVAR;ELSDQAT(0.004)AS(0.996)PIVAR 332.36 1.90E-68 1410950000 1156270 1180450 1190160 1188900 1211020 1430930 1230430 1146400 1029090 1091180 TRUE FALSE 1201920.432 1383183.105 1221176.547 1424060.871 1005171.253 1098618.193 1133985.681 1131034.383 992053.2519 1304975.829 0.921028885 1.059930057 0.935784802 1.091254596 0.770260437 0.841868615 0.86897064 0.866709067 0.760208143 1 20.31559165 3.235624533 24.99996972 0.847097635 1.001407848 0.475435426 0.077451763 60.70961195 516927.3684 0.020347281 0.02534472 1720.380585 -3.235624533 0.154310212 ELSEALGQIFDSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELSEALGQIFDSQR 14 0 Q08380;K7ESM3;K7EKQ5;K7EP36;K7EJY8 Q08380 LGALS3BP Galectin-3-binding protein 0 106.49 0.0021835 14254000 10599 11992 12637 12440 18067 16020 10433 11540 12597 20449 FALSE TRUE 11017.4567 14051.53272 12966.3306 14900.59487 14995.97779 12299.59779 9615.234198 11385.32518 12143.63643 24455.59003 0.450508726 0.574573449 0.53019905 0.60929198 0.61319223 0.502936047 0.393171221 0.465551032 0.496558718 1 14.57787665 -1.372819891 3.649306148 1.002489302 0.513660404 0.82699499 0.066530953 5159808.157 2913090.714 97924.19574 0.017406421 0.042381869 1.372819891 -0.488828898 ELSEALTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSEALTR 8 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 150.4 0.0011395 220720000 249840 293450 274110 274010 322190 364630 286880 293840 285900 315340 FALSE TRUE 259703.8761 343847.7548 281253.5318 328208.3602 267424.2589 279950.2085 264393.596 289901.5554 275610.5148 377124.8355 0.688641669 0.9117611 0.745783638 0.870291026 0.709113359 0.742327692 0.701077127 0.7687151 0.730820378 1 18.52468264 -1.164590447 4.61114674 1.000027018 0.765507598 0.513653128 0.06910098 2.22E-05 4.02E-06 0.063372482 0.01493494 0.06845569 1.164590447 -0.23451942 ELSEDIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELSEDIRR 8 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 70.816 0.087794 0 38248 69217 49607 60332 58938 82816 60057 51210 52144 71127 FALSE TRUE 39758.06057 81104.48132 50899.79917 72265.48953 48919.73981 63583.23909 55349.57541 50523.61371 50267.34763 85062.97384 0.46739561 0.953463977 0.598377847 0.849552823 0.575100277 0.747484319 0.6506894 0.593955412 0.590942749 1 16.37624367 -1.031154575 4.873950833 1.000006181 0.674049698 0.344723254 0.136512645 8.33E-06 1.66E-06 0.12013642 0.028315889 0.093077653 1.031154575 -0.325956483 ELSEPMEFQYLPDTDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELSEPMEFQYLPDTDDR 17 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ;; 275.44 2.36E-35 228808000 128475 154293 140820 149209 161240 179425 152135 157869 143034 137013 FALSE TRUE 133547.2922 180791.6225 144489.8849 178722.0949 133832.4824 137756.263 140210.2612 155753.0243 137886.2343 163858.0741 0.815018076 1.103342777 0.881798994 1.090712776 0.816758546 0.840704761 0.855681125 0.950536159 0.841497955 1 17.32208724 3.21801827 24.99881153 0.882550131 0.975554345 0.170816076 0.095423646 383.3476692 466510.2754 0.025598983 0.030629093 1652.031296 -3.21801827 0.093004214 ELSEQIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELSEQIQR 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 176.84 0.00060031 1216120000 1007960 1274060 1161950 1149180 1351040 1573100 1205130 1174530 1115150 1494310 FALSE TRUE 1047755.039 1492869.894 1192231.372 1376484.374 1121390.703 1207771.366 1110668.762 1158787.346 1075015.969 1787091.434 0.586290673 0.835362906 0.667135071 0.77023724 0.627494868 0.675830762 0.621495207 0.64842085 0.601545029 1 20.76918202 -1.402643827 8.44015139 1.000002969 0.6730776 0.644810209 0.073358553 3.94E-06 2.79E-07 0.068265694 0.016090232 0.0395691 1.402643827 -0.326925369 ELSESVQQQSTPVPLIS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;ELSESVQQQST(0.003)PVPLIS(0.997)PKR 194.21 2.78E-18 441570000 373650 268410 355090 235280 460550 483730 328810 356760 448700 346900 TRUE FALSE 388401.9905 314507.3296 364343.9371 281817.6818 382265.8755 371391.0385 303037.013 351978.2157 432551.3746 414868.4132 0.93620526 0.758089359 0.87821566 0.67929414 0.921414751 0.895202013 0.730441276 0.84840929 1.04262306 1 18.66229429 1.275747949 6.310783591 1.021843343 0.825484829 0.470317832 0.080799172 0.129440364 13.86039878 0.054816848 0.018822199 18.86895935 -1.275747949 -0.196358514 ELSEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSEYVR 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 138.07 0.0065628 564820000 655460 865990 812010 893460 874700 1012580 760760 823510 732010 996380 FALSE TRUE 681338.0669 1014717.046 833171.6477 1070183.721 726018.8064 777423.6408 701129.6433 812472.1954 705665.1031 1191601.584 0.571783452 0.851557315 0.699203206 0.898105319 0.609279826 0.652419106 0.588392675 0.681832087 0.592198863 1 20.18447052 -1.079772604 4.584329716 1.00001892 0.687001377 0.448816062 0.105376503 2.00E-05 4.01E-06 0.099995542 0.023567752 0.08321994 1.079772604 -0.313017543 ELSFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ELSFGR 6 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;; 185.89 0.0048112 1668360000 871740 1218350 935560 1051510 1101230 1261220 872990 960220 864280 1111400 FALSE TRUE 906156.9683 1427592.135 959941.4622 1259495.54 914043.3179 968320.769 804562.7627 947349.8215 833174.7316 1329157.551 0.681752865 1.074057875 0.722217965 0.94758935 0.687686209 0.728522189 0.605317829 0.712744566 0.626844223 1 20.34208069 3.222448025 24.9831619 0.704622942 0.862366432 0.151361923 0.144368183 334.3237621 518380.1519 0.037888112 0.045417927 1668.96806 -3.222448025 0.157743489 ELSLAGNELGDEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSLAGNELGDEGAR 15 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 302.87 4.42E-44 135054000 108061 117406 127518 125602 133966 152671 127764 124136 122899 122128 FALSE TRUE 112327.3317 137569.5672 130841.2238 150445.7007 111194.5072 117215.474 117749.5238 122472.16 118475.889 146056.6433 0.769066912 0.941891886 0.895825215 1.030050378 0.761310849 0.802534355 0.806190812 0.83852509 0.811163986 1 17.15616845 3.211720985 24.99965542 0.82578678 0.91058736 0.143365501 0.084442622 345.0980917 321439.0935 0.023029572 0.027532783 1628.249619 -3.211720985 0.08480058 ELSLKAS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSLKASPLR 10 1 Q86W50 Q86W50 METTL16 Methyltransferase-like protein 16 1 ELS(0.058)LKAS(0.942)PLR;ELS(0.022)LKAS(0.978)PLR 65.809 0.041094 391360000 781910 548020 629580 560130 850220 854840 853700 707310 719640 463230 TRUE FALSE 812780.4106 642138.172 645987.372 670922.0422 705699.9081 656316.3652 786784.7633 697829.6664 693740.297 553991.0494 1.467136358 1.1591129 1.166061027 1.211070184 1.27384713 1.18470572 1.420212049 1.259640688 1.252259035 1 19.07950314 0.65851613 3.905117513 1.000000852 1.263417434 0.40029974 0.097725113 10.53222778 119.4498727 0.090954327 0.023268083 4.555291047 -0.65851613 0.263416582 ELSNS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.01)NS(0.99)PLR;ELSNS(1)PLR;ELS(0.001)NS(0.999)PLR;ELS(0.004)NS(0.996)PLR;ELS(0.036)NS(0.964)PLR;ELS(0.004)NS(0.996)PLR 153.66 0.00045884 8961890000 4607920 4624850 4704370 5341120 4653600 5583430 5969470 4963930 4441090 3797850 TRUE FALSE 4789844.24 5419132.011 4826969.747 6397577.594 3862582.734 4286763 5501567.343 4897396.638 4281256.038 4541965.993 1.0545751 1.193124744 1.062748984 1.408548105 0.850420884 0.943812218 1.211274446 1.078254801 0.942599756 1 22.11488547 3.222973254 24.99999164 1.024338571 1.172347572 0.302748607 0.128047723 356.341076 571521.0869 0.037693088 0.045198133 1670.987705 -3.222973254 0.148009001 ELSNS(ph)PLRENS(ph)FGSPLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.026)NS(0.974)PLRENS(1)FGSPLEFR;ELS(0.106)NS(0.894)PLRENS(0.997)FGS(0.003)PLEFR 166.85 1.09E-11 222481000 229079 252350 241929 243660 275910 309250 269200 288510 256330 263188 TRUE FALSE 238123.2158 295689.1495 248233.8685 291855.2207 229010.9168 237431.3742 248099.4006 284642.9954 247104.7334 314754.6496 0.756535975 0.939427424 0.788658305 0.927246734 0.727585493 0.754337941 0.78823109 0.904332933 0.785070955 1 18.26386816 -1.526256265 4.766372764 1.000966859 0.824853206 0.353831408 0.072981672 0.000727463 7.23E-05 0.068555828 0.016071866 0.029767594 1.526256265 -0.176113653 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 ELS(0.011)NS(0.989)PLRENSFGS(1)PLEFR;ELS(0.028)NS(0.972)PLRENSFGS(1)PLEFR;ELS(0.004)NS(0.996)PLRENSFGS(1)PLEFR;ELS(0.031)NS(0.969)PLRENS(0.004)FGS(0.996)PLEFR;ELS(0.013)NS(0.987)PLRENSFGS(1)PLEFR;ELS(0.023)NS(0.977)PLRENSFGS(1)PLEFR;ELS(0.031)NS(0.969)PLRENS(0.464)FGS(0.536)PLEFR 273.79 1.24E-39 3118075000 2070775 2302331 2242985 2070283 2349977 2605318 2163447 2241441 2223516 2468309 TRUE FALSE 2152530.796 2697738.44 2301439.032 2479778.798 1950528.749 2000272.378 1993870.371 2211398.15 2143492.094 2951926.89 0.729195158 0.913890669 0.779639577 0.840054273 0.660764586 0.677615826 0.675447071 0.749137168 0.726133191 1 21.49322556 5.092185276 14.14418273 0.765422459 0.000164556 0.003210287 0.105550542 2359929.296 5924542.431 0.024608344 55116468.29 123647.4819 -5.092185276 -0.765257903 ELSNS(ph)PLRENSFGSPLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ELS(0.015)NS(0.985)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.004)NS(0.996)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELSNS(1)PLRENSFGSPLEFR;ELS(0.002)NS(0.997)PLRENSFGSPLEFR;ELS(0.038)NS(0.962)PLRENSFGSPLEFR 301.69 3.36E-50 18609228000 3324753 3924983 4085354 3587067 3849791 4418722 3618111 3700603 3702939 4448399 TRUE FALSE 3456016.816 4599068.298 4191821.681 4296578.146 3195404.901 3392540.782 3334514.006 3651002.47 3569670.949 5319977.614 0.649629955 0.86449016 0.787939722 0.807630869 0.600642546 0.637698319 0.626790984 0.686281547 0.670993603 1 22.34298874 -1.368102614 3.464135331 1.001899707 0.704182919 0.534246556 0.083032181 33643313.14 41374095.82 626096.0384 0.021582384 0.042844728 1.368102614 -0.297716788 ELSPEEAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELSPEEAHR 9 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 143.03 0.00010291 521160000 447280 778120 626230 602620 620820 877810 565430 657600 648720 1015060 FALSE TRUE 464938.9598 911756.0571 642550.0683 721816.4374 515293.2382 673951.9308 521110.1191 648785.9476 625372.6939 1213941.573 0.382999454 0.751070791 0.529308892 0.594605584 0.424479439 0.55517658 0.42927117 0.534445778 0.515158808 1 20.21126756 -1.179860136 3.357983757 1.000830866 0.52733922 0.678422394 0.098280053 13587830.21 21102821.39 120663.6421 0.021868207 0.066090626 1.179860136 -0.473491646 ELSSTEAQLHDAQELLQEETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELSSTEAQLHDAQELLQEETR 21 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ;;; 278.58 6.91E-45 547250000 347012 435153 462365 423772 458610 564400 417274 442950 468100 500700 FALSE TRUE 360712.3017 509887.1427 474414.6117 507592.8368 380655.636 433326.6536 384566.9735 437012.9798 451253.1724 598802.5785 0.602389359 0.851511268 0.792272159 0.847679778 0.635694718 0.72365529 0.642226649 0.729811453 0.753592567 1 19.19172091 0.709260444 3.522263251 0.999995604 0.731107946 0.500670623 0.080907272 3.351099992 39.73137263 0.077169762 0.019888965 5.119887801 -0.709260444 -0.268887658 ELST(ph)PDKVLIPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELSTPDKVLIPER 13 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 ELS(0.077)T(0.923)PDKVLIPER 186.85 1.21E-05 171890000 329760 193740 260140 220270 303870 308530 357730 274290 293250 164720 TRUE FALSE 342779.1794 227013.3379 266919.4621 263838.7486 252218.2859 236878.5833 329690.1878 270613.5912 282695.9898 196993.7302 1.740051214 1.152388645 1.354964251 1.339325613 1.280336616 1.202467627 1.673607518 1.373716772 1.435050696 1 17.58779019 -2.195875405 2.104797244 0.00015498 1.386942041 0.308469149 0.176933118 3214864.378 569608.9314 15324554.87 0.044201786 0.006369782 2.195875405 1.386787061 ELSVEEQIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELSVEEQIKR 10 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 95.822 0.011481 300270000 373920 319280 365390 282500 460730 474470 432140 370850 395410 353500 FALSE TRUE 388682.6503 374113.8563 374912.3636 338377.6568 382415.2792 364281.5332 398267.7376 365879.3623 381179.2713 422761.5568 0.91938977 0.884928751 0.886817539 0.80039836 0.904564933 0.861671378 0.942062331 0.865450882 0.90164128 1 18.68948467 0.906509992 7.651285874 0.999999864 0.882702927 0.485555766 0.035893551 2.267231503 185.5818138 0.033194742 0.008316435 8.063247523 -0.906509992 -0.117296938 ELSVQDQPSLS(ph)PTSLQNSSSHTTTAK ddPTM_MDA-MB-175_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(0.895)PT(0.101)S(0.004)LQNSSSHTTTAK;ELSVQDQPSLS(0.459)PT(0.459)S(0.082)LQNSSSHTTTAK 276.1 7.92E-61 959730000 238940 837760 899680 855790 1010680 1223740 918980 1099650 991570 969450 TRUE FALSE 248373.5357 981638.7631 923126.3999 1025062.708 838884.9746 939544.931 846947.9463 1084910.99 955883.5894 1159395.166 0.214226817 0.84668178 0.796213773 0.884135744 0.723553969 0.810375063 0.730508433 0.935756006 0.824467461 1 20.14494095 4.739358942 24.98731821 0.832485536 0.214226623 0.842274296 0.081073662 23.03105432 720740.1116 0.018239316 0.110056627 54873.02996 -4.739358942 -0.618258913 ELTDEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 166.16 0.0001418 502530000 369780 456670 448390 447100 445910 557960 492190 448110 422770 371010 FALSE TRUE 384379.1999 535099.5201 460075.4118 535535.0455 370114.3775 428382.246 453610.8617 442103.8184 407554.5903 443702.3061 0.866299757 1.205987692 1.036901106 1.206969263 0.834150223 0.96547221 1.02233154 0.996397387 0.918531603 1 18.75923253 3.240749928 24.9999993 0.963664185 1.085097279 0.255301231 0.102132396 79.61885284 909165.4582 0.027261634 0.035196233 1740.804207 -3.240749928 0.121433094 ELTDEEAERLQLEIDQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELTDEEAERLQLEIDQKK 18 2 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 48.907 0.090458 48074000 32131 25896 31014 25410 46980 40839 37247 32571 33038 27784 FALSE TRUE 33399.55669 30343.43656 31822.25032 30436.02216 38994.35638 31354.76117 34327.48281 32134.43902 31848.96883 33227.74284 1.005170795 0.913195841 0.957701234 0.915982235 1.173548157 0.943631992 1.033097041 0.967096657 0.958505336 1 15.02010067 ELTHIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELTHIYR 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 162.31 0.0012769 2157210000 1408237 1774304 1645895 1700110 1920880 1989433 1650145 1687251 1599899 1883493 FALSE TRUE 1463835.284 2079026.91 1688788.376 2036386.684 1594369.504 1527417.336 1520802.323 1664636.16 1542318.948 2252527.392 0.649863478 0.922975196 0.74973045 0.904045248 0.707813592 0.67809046 0.675153753 0.739008176 0.684705968 1 21.10311322 ELTIGS(ph)KLQDAEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELTIGSKLQDAEIAR 15 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 1 ELT(0.065)IGS(0.935)KLQDAEIAR;ELT(0.069)IGS(0.931)KLQDAEIAR 56.081 0.080694 257990000 386090 241130 293080 249630 370620 391870 347470 281380 301100 235750 TRUE FALSE 401333.1313 282542.2018 300717.9056 299006.0689 307622.1448 300864.1313 320234.3935 277608.5613 290263.4698 281940.6988 1.42346647 1.002133438 1.066599845 1.060528225 1.091088112 1.067118485 1.135821805 0.984634579 1.02951958 1 18.10503222 4.743240692 24.98085021 1.051852528 1.423466622 0.867549655 0.043924669 160.9231938 858930.677 0.010499139 0.085156539 55365.68684 -4.743240692 0.371614094 ELTIGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELTIGSK 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;; 130.04 0.0083798 7117980000 8855800 6702000 8196900 7201800 9549800 9613800 10193500 7738400 8275700 5862420 FALSE TRUE 9205433.822 7853016.366 8410517.948 8626294.545 7926528.407 7381140.649 9394506.834 7634679.405 7977859.174 7011048.956 1.312989523 1.120091503 1.199609074 1.230385724 1.130576674 1.052786922 1.339957386 1.088949664 1.137898084 1 22.74119888 -5 0.132625841 0.39475617 1.248628352 0.333740988 0.084585258 170.330075 1.415338379 27.23276519 0.579367196 1.00E-05 5 0.853872182 ELTNDGELILTMTADDVVCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELTNDGELILTMTADDVVCTR 21 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;; 184.99 8.74E-17 64731000 89672 106935 100071 100213 117330 131923 107858 105547 111871 119256 FALSE TRUE 93212.3198 125300.2544 102678.9325 120034.8323 97386.28851 101285.8826 99403.80813 104132.3151 107844.7846 142621.9299 0.653562323 0.878548302 0.719937898 0.841629561 0.68282829 0.710170467 0.696974218 0.730128355 0.7561585 1 17.12183631 0.793242211 5.854854122 0.9999999 0.741176244 0.581748288 0.065978409 6.264969474 177.3228117 0.060046255 0.015107157 6.21215397 -0.793242211 -0.258823656 ELTNRHS(ph)LPFSLPSQMEPRPDVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELTNRHSLPFSLPSQMEPRPDVPR 24 2 P22681;A0A0U1RR39;A0A1B0GW38;A0A0U1RQX8 P22681 CBL E3 ubiquitin-protein ligase CBL 1 ELT(0.04)NRHS(0.959)LPFSLPSQMEPRPDVPR;ELT(0.016)NRHS(0.984)LPFSLPSQMEPRPDVPR 114.98 0.00059896 132895000 49984 57254 52604 65414 76150 75877 62578 68438 62512 81176 TRUE FALSE 51957.40692 67086.92913 53974.90345 78352.69396 63206.0502 58255.71668 57672.97284 67520.70055 60262.20533 97080.88299 0.535197099 0.691041604 0.555978703 0.807086746 0.651065877 0.60007403 0.594071367 0.695509749 0.620742246 1 16.56689961 ELTPAS(ph)PTCTNSVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ELTPASPTCTNSVSK 15 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 ELTPAS(1)PTCTNSVSK;ELTPAS(0.999)PT(0.001)CTNSVSK;ELTPAS(0.99)PT(0.01)CTNSVSK;ELTPAS(0.998)PT(0.002)CTNSVSK;ELTPAS(0.997)PT(0.003)CTNSVSK;ELTPAS(0.71)PT(0.18)CT(0.088)NS(0.021)VSK 315.47 2.76E-56 2180900000 3003390 2365960 2758120 2382040 3328820 3470550 3178860 2886960 3011600 2248810 TRUE FALSE 3121966.156 2772295.225 2829998.873 2853200.402 2762988.365 2664567.359 2929692.647 2848265.023 2903213.104 2689421.263 1.16083196 1.030814794 1.05227058 1.06089754 1.02735425 0.990758642 1.089339438 1.059062432 1.079493623 1 21.35886432 4.743471146 24.52200452 1.046556474 1.160832022 0.572532299 0.030343672 293.4810314 1465511.147 0.007208525 0.058447646 55395.07391 -4.743471146 0.114275548 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(ph)SPQRDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLK 42 2 O00139-1;O00139-5;O00139;O00139-4;O00139-2;H0Y8H2 O00139-1 KIF2A Kinesin-like protein KIF2A 1 ELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGS(0.853)S(0.147)PQRDDLK;ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.1)QWGVGS(0.45)S(0.45)PQRDDLK;ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.002)QWGVGS(0.499)S(0.499)PQRDDLK;ELTVDPTAAGDVRPIMHHPPNQIDDLET(0.129)QWGVGS(0.436)S(0.436)PQRDDLK 219.31 1.93E-44 992610000 483602 309736 418388 288220 469183 485740 472503 398045 448182 313739 TRUE FALSE 502694.9804 362930.7486 429291.535 345229.0557 389431.4412 372934.2465 435466.9802 392709.8578 432052.0174 375210.1502 1.339769141 0.967273269 1.144136252 0.920095194 1.037902203 0.993934323 1.160594883 1.04663975 1.151493416 1 18.51733933 4.748916902 24.86500089 1.050581398 1.339769314 0.558415241 0.078070022 987.603966 2371144.584 0.017573691 0.245553684 56094.06349 -4.748916902 0.289187915 ELVEFAQDDDRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;;;;;; 255.45 7.06E-24 3027870000 1587453 1846210 1671006 1757548 1808273 2028128 1634440 1636734 1499222 1794991 FALSE TRUE 1650126.87 2163282.206 1714553.789 2105185.749 1500903.401 1557126.009 1506328.322 1614796.258 1445265.293 2146685.119 0.768686034 1.007731496 0.798698316 0.980668161 0.699172593 0.725363023 0.701699708 0.752227816 0.673254442 1 21.03367916 3.227149556 24.96171136 0.741528848 0.890984425 0.244685921 0.10971402 239.485721 523874.5206 0.028577153 0.034438413 1687.133915 -3.227149556 0.149455577 ELVGPPLAETVFT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 ELVGPPLAETVFT(1)PK;ELVGPPLAETVFT(1)PK 119.45 0.0023671 74420000 98287 45406 54200 54204 82316 75805 89537 54762 58876 39716 TRUE FALSE 102167.4467 53204.12729 55612.49653 64925.38942 68323.95572 58200.43759 82518.85598 54028.00496 56757.06426 47497.58979 2.151002758 1.120143728 1.170848811 1.366919663 1.438472058 1.225334545 1.737327227 1.137489401 1.194946196 1 15.53556669 8 0.057412859 0.509616849 3.047843741 0.242205444 0.287629966 642.3877565 2.76146006 25.69105998 138.0512956 100000000 -8 2.538226892 ELVGPPLAETVFT(ph)PKT(ph)SPENVQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 ELVGPPLAETVFT(1)PKT(0.903)S(0.097)PENVQDR;ELVGPPLAET(0.025)VFT(0.975)PKT(0.64)S(0.36)PENVQDR 121.5 0.00062436 184492000 155420 98295 109429 82316 136850 152735 117391 103211 111810 88494 TRUE FALSE 161556.1016 115176.4016 112280.8096 98597.85911 113588.2859 117264.611 108189.5867 101827.6254 107785.9799 105832.705 1.526523409 1.088287422 1.060927335 0.931638846 1.073281514 1.108018651 1.022269881 0.962156503 1.018456251 1 16.691426 4.794442733 2.482620678 1.019470894 1.685221937 0.904132878 0.048961477 0.191865821 1.296167426 0.01295976 0.286266832 62293.5001 -4.794442733 0.665751042 ELVLDNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELVLDNSR 8 0 P39687;H0YN26;H7BZ09 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 114.28 0.0062496 191400000 322350 400050 359700 340470 462740 476620 415170 369440 373800 456080 FALSE TRUE 335076.6269 468755.4755 369074.0775 407813.9498 384083.6201 365932.2282 382627.8906 364488.2611 360347.011 545440.1438 0.614323369 0.859407729 0.676653674 0.747678649 0.704171896 0.670893465 0.701502988 0.668246122 0.66065363 1 19.05706136 -0.789545969 5.907165468 1.000000021 0.70256305 0.674119161 0.062477143 1.60E-08 3.28E-09 0.056609767 0.013343049 0.16235065 0.789545969 -0.297436971 ELVVNCCTEFIHLISSEANEICNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ELVVNCCTEFIHLISSEANEICNK 24 0 Q01658 Q01658 DR1 Protein Dr1 0 192.45 7.09E-18 87299000 48170 37242 54500 35273 53787 57580 49010 48533 54078 46274 FALSE TRUE 50071.7888 43638.0238 55920.31477 42249.89412 44644.30495 44207.91763 45168.46814 47882.49452 52131.74334 55340.50433 0.904794588 0.788536793 1.010477144 0.763453363 0.80672024 0.798834744 0.816191841 0.865234155 0.942017858 1 15.75604817 1.139398495 2.339141811 0.99828088 0.839748393 0.379896947 0.067283428 0.27505734 2.784988181 0.061037355 0.017032068 13.78473732 -1.139398495 -0.158532487 ELWAVLNGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELWAVLNGWR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ; 145.17 7.19E-05 615560000 426520 490230 483830 511580 658380 636270 528220 511890 532830 652590 FALSE TRUE 443359.3389 574423.189 496439.0073 612768.9971 546468.8028 488505.9353 486816.7362 505028.9518 513653.5524 780452.5159 0.568079838 0.736012989 0.636091238 0.785145777 0.700194812 0.62592653 0.623762146 0.647097602 0.658148372 1 19.57395133 -1.2956195 6.38535381 1.000010616 0.666059347 0.745591097 0.05878794 8.69E-06 9.58E-07 0.055650811 0.013116605 0.050626803 1.2956195 -0.333951269 ELYDHAEATIVVMLVGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELYDHAEATIVVMLVGNK 18 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 ;; 128.9 2.23E-05 59256400 124925 91269 121158 112748 130176 142530 156195 116606 120062 75823 FALSE TRUE 129857.1355 106943.7408 124315.477 135049.2179 108048.73 109429.5676 143952.0278 115043.0873 115740.9921 90679.06513 1.432051988 1.179365277 1.370939112 1.489309773 1.191550992 1.206778736 1.587489103 1.268684091 1.276380517 1 16.4684819 0.742895216 1.958494674 1.000563905 1.340952417 0.391122374 0.12762247 1.015698328 6.00601891 0.118158819 0.032769282 5.532166158 -0.742895216 0.340388511 ELYLLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ELYLLFR 7 0 H0YBU9;B4E3T4;Q93062-4;Q93062-5;Q93062;Q93062-2;Q6ZRY4;Q93062-3 H0YBU9 RBPMS;RBPMS2 RNA-binding protein with multiple splicing;RNA-binding protein with multiple splicing 2 0 ;; 64.776 0.072379 1364150000 808210 1226560 1187550 1323860 1304940 1532050 1346260 1364030 1367200 1246540 FALSE TRUE 840118.7549 1437212.139 1218498.529 1585715.557 1083126.765 1176254.606 1240736.623 1345747.409 1317994.739 1490775.647 0.563544727 0.964070041 0.817358756 1.063684908 0.726552495 0.789021882 0.832275887 0.902716255 0.884099993 1 20.50763173 -4.999999998 0.02146406 2.102781831 1.35E-08 0.18404296 0.123630909 5637.378934 9.155159263 617.4415632 323.3250721 1.00E-05 4.999999998 -2.102781818 ELYLLFRPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ELYLLFRPFK 10 1 H0YBU9;B4E3T4;Q93062-4;Q93062-5;Q93062;Q93062-2;Q6ZRY4;Q93062-3 H0YBU9 RBPMS;RBPMS2 RNA-binding protein with multiple splicing;RNA-binding protein with multiple splicing 2 0 ; 119.68 0.0028631 0 358700 199215 230640 166681 376450 328310 293770 214090 268340 264860 FALSE TRUE 372861.753 233428.6266 236650.6679 199650.0043 312461.1635 252064.9781 270743.5398 211220.4737 258682.4958 316754.2459 1.177132612 0.736939219 0.747111273 0.630299378 0.986446646 0.795774583 0.854743206 0.6668276 0.81666623 1 18.27300443 4.743230109 24.89387483 0.788624706 1.17713278 0.480486134 0.115463565 366.3141596 1952813.295 0.026321686 0.213436514 55364.33769 -4.743230109 0.388508074 ELYVAADEASIAPILAEAQAHFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 142.99 2.53E-07 31104000 402343.7 83673.9 117599.9 105729.4 146398 255227 142443.2 148739.5 123303.3 111599 FALSE TRUE 418228.54 98044.24143 120664.65 126642.3597 121513.3203 195954.3973 131278.1298 146745.8903 118865.6383 133464.6874 3.133626941 0.734608108 0.904094202 0.948882901 0.910452964 1.468211563 0.983616958 1.099510988 0.890614894 1 17.02609855 4.743056412 24.99914622 1.008112404 3.133627792 0.925193759 0.182533994 113.4618138 630889.2577 0.044116222 0.352002437 55342.19909 -4.743056412 2.125515388 EMDEAATAEER ddPTM_MDA-MB-175_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 ; 121.73 0.0014409 277420000 173438 141205 174986 155572 273760 324150 237800 197843 161494 174101 FALSE TRUE 180285.4662 165455.8603 179546.2789 186343.6773 227226.373 248871.075 219160.6146 195191.2382 155681.8625 208212.7576 0.865871372 0.794648043 0.862321219 0.894967626 1.091318206 1.195272941 1.052580145 0.937460511 0.747705685 1 17.66769894 3.425205109 5.576608772 1.008516782 0.842392189 0.316511254 0.109624351 0.246110893 16.72335161 0.033534223 0.046154826 2661.981963 -3.425205109 -0.166124594 EMDEEDKAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 ; 124.1 0.00040532 1499560000 2660600 1805940 2153100 1572760 2907900 3035300 2567000 2008200 2320800 1664720 FALSE TRUE 2765642.542 2116096.147 2209211.555 1883847.234 2413616.197 2330397.575 2365791.832 1981283.364 2237274.861 1990890.011 1.389148837 1.062889529 1.109660274 0.946233706 1.212330256 1.170530548 1.188308656 0.995174697 1.123756134 1 20.92498209 4.742085813 24.42681821 1.092229582 1.389148994 0.530881736 0.084371643 198.1552386 1372973.63 0.020043325 0.146910174 55218.65364 -4.742085813 0.296919412 EMDEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EMDEQIR 7 0 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ;;; 152.31 0.0042389 2738030000 2659860 3453690 3116970 3324270 3440830 4103260 3375570 3356020 2944920 3408780 FALSE TRUE 2764873.327 4046834.392 3198200.799 3981800.684 2855958.946 3150340.051 3110984.003 3311038.041 2838932.904 4076665.176 0.67821938 0.992682552 0.784513974 0.976729879 0.700562549 0.772773803 0.763119822 0.812192785 0.696386086 1 21.95895804 5.028204887 16.31365969 0.82159852 0.264619465 0.142542044 0.110796108 15843805.54 247940903.4 0.024787192 239498316.7 106709.9427 -5.028204887 -0.556979054 EMDRETLIDVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EMDRETLIDVAR 12 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;;;;;;; 227.06 1.26E-11 6602800000 6172190 7507340 7540370 6961890 8389660 8685100 6929240 7623990 7488010 7960190 FALSE TRUE 6415872.827 8796667.246 7736878.237 8338931.063 6963588.59 6668117.149 6386108.063 7521802.884 7218517.983 9519836.823 0.673947773 0.924035507 0.812711224 0.875953151 0.731481928 0.70044448 0.670821169 0.790118888 0.758260684 1 23.18250541 5.030048332 15.06191834 0.791433834 0.340870194 0.125038815 0.098082714 3083773.443 44993389.34 0.023003775 34586097.93 107163.856 -5.030048332 -0.45056364 EMDT(ph)ARTPLSEAEFEEIMNR ddPTM_MDA-MB-175_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(0.5)ART(0.5)PLSEAEFEEIMNR;EMDT(0.5)ART(0.5)PLSEAEFEEIMNR 84.249 0.0077815 155128000 109207 140104 133538 132610 166499 177643 157289 138078 146948 142805 TRUE FALSE 113518.5767 164165.7721 137018.11 158839.8622 138197.5595 136388.1055 144960.2772 136227.2903 141659.3702 170784.9056 0.664687411 0.961242866 0.80228466 0.930057968 0.809190713 0.798595783 0.848788578 0.797654159 0.829460717 1 17.38182095 -1.851521702 8.575637946 1.00903893 0.830404967 0.315871234 0.076272977 0.012032541 0.000208331 0.067415247 0.015565513 0.014075969 1.851521702 -0.178633962 EMDTART(ph)PLSEAEFEEIMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EMDTARTPLSEAEFEEIMNR 20 1 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 1 EMDT(0.055)ART(0.945)PLSEAEFEEIMNR;EMDT(0.053)ART(0.946)PLSEAEFEEIMNR;EMDT(0.112)ART(0.888)PLSEAEFEEIMNR;EMDTART(1)PLSEAEFEEIMNR 301.97 1.02E-54 517213000 264694 244740 257652 246583 299264 373307 269712 277598 259200 235280 TRUE FALSE 275144.3235 286772.1912 264366.6228 295356.3814 248395.2122 286612.1068 248571.2687 273877.2529 249871.4426 281378.6113 0.977843775 1.019168408 0.939540577 1.049676022 0.882779295 1.018599479 0.883404988 0.973340694 0.888025716 1 18.10215314 3.240720283 24.9999543 0.94161406 0.994099654 0.214406859 0.051982615 88.15884457 1020503.054 0.0132355 0.017076934 1740.685387 -3.240720283 0.052485595 EMEADERDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMEADERDR 9 1 P49756 P49756 RBM25 RNA-binding protein 25 0 112.75 0.0020067 123350000 130300 159390 173080 141950 180710 202120 157780 164300 175820 182650 FALSE TRUE 135444.3446 186763.9926 177590.607 170027.2863 149992.9787 155180.6932 145412.7913 162097.8272 169492.2725 218436.7705 0.620062018 0.855002536 0.813006925 0.778382165 0.686665429 0.710414702 0.665697405 0.74208123 0.775932881 1 17.73685621 -1.499827269 4.175619217 1.002120757 0.739971023 0.57769042 0.067044327 0.00133508 0.000159921 0.065475612 0.015314329 0.031635356 1.499827269 -0.262149734 EMEAELEDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EMEAELEDER 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 247.5 2.41E-12 6077190000 3060120 3787240 3622100 3453590 4104890 4441530 3723990 3771970 3655380 3678140 FALSE TRUE 3180935.901 4437669.009 3716494.902 4136699.794 3407142.264 3410051.97 3432093.933 3721412.912 3523823.588 4398801.111 0.723137014 1.008836021 0.844888143 0.940415284 0.774561563 0.77522304 0.780233943 0.846006177 0.801087273 1 22.06867894 5.034305045 16.30173614 0.851838816 0.256757588 0.182233262 0.086065504 9432441.911 123681733.3 0.019980008 160574756.2 108219.3808 -5.034305045 -0.595081228 EMEAELEDERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 EMEAELEDERK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 211.46 1.48E-08 7981415000 4998866 2952132 3750215 2789073 5111927 4598830 4936159 3930411 4400851 2720118 FALSE TRUE 5196225.09 3459137.707 3847948.684 3340743.315 4243003.474 3530821.428 4549249.959 3877730.269 4242465.232 3253073.042 1.597328133 1.063344616 1.18286575 1.026949986 1.304306242 1.08538031 1.398446915 1.192020658 1.304140785 1 21.63337179 -1.922612155 2.616146079 0.857119331 1.22791442 0.15813944 0.163797936 19258073.95 11989901.21 16881943.56 0.036615919 0.011950549 1.922612155 0.370795089 EMEHNTVCAAGTS(ph)PVGEIGEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.207)S(0.793)PVGEIGEEK;EMEHNTVCAAGT(0.1)S(0.9)PVGEIGEEK;EMEHNTVCAAGT(0.205)S(0.795)PVGEIGEEK;EMEHNTVCAAGT(0.005)S(0.995)PVGEIGEEK;EMEHNTVCAAGT(0.003)S(0.997)PVGEIGEEK;EMEHNTVCAAGT(0.006)S(0.994)PVGEIGEEK;EMEHNTVCAAGT(0.002)S(0.998)PVGEIGEEK;EMEHNTVCAAGT(0.045)S(0.955)PVGEIGEEK;EMEHNTVCAAGT(0.007)S(0.993)PVGEIGEEK 258.25 2.31E-37 11702490000 4255954 4781111 5429840 4584080 7128010 7449410 6215000 5881480 5950090 4341680 TRUE FALSE 4423982.35 5602229.622 5571346.091 5490797.342 5916393.406 5719397.424 5727852.06 5802648.381 5735947.423 5192349.07 0.852019441 1.078939329 1.072991437 1.057478468 1.139444465 1.1015048 1.103133087 1.11753819 1.104692182 1 22.30795594 4.745971824 4.071223036 1.093834308 0.829470848 0.784386302 0.036713986 0.097524514 3.449694657 0.008381695 0.076501709 55714.96016 -4.745971824 -0.26436346 EMEKGS(ph)PSLRH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMEKGSPSLRH 11 2 F5GXK4;B9A071;Q9P2M4-2;Q9P2M4 F5GXK4 TBC1D14 TBC1 domain family member 14 1 EMEKGS(0.993)PS(0.007)LRH 79.652 0.013859 94957000 81629 116840 106470 78964 120290 144270 94782 105730 113300 116710 TRUE FALSE 84851.77595 136906.3611 109244.6957 94582.84352 99843.14877 110765.4789 87352.73917 104312.8623 109222.3551 139577.09 0.607920512 0.980865564 0.782683574 0.677638741 0.715326196 0.793579225 0.625838662 0.747349456 0.782523516 1 17.09070263 0.766417361 3.125464949 0.999964519 0.744357891 0.378287451 0.098892889 1.660528957 20.83487424 0.092115723 0.02400305 5.8400607 -0.766417361 -0.255606628 EMEKS(ph)FDEQNVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMEKSFDEQNVPK 13 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 EMEKS(1)FDEQNVPK 119.68 0.00019959 329930000 539260 252010 433440 194950 740550 452550 510610 401430 486840 189920 TRUE FALSE 560550.4012 295290.7571 444735.8025 233510.5281 614671.5755 347452.121 470587.054 396049.4875 469318.7235 227131.1878 2.467958745 1.300088993 1.958056958 1.028086589 2.706240308 1.529742016 2.071873346 1.743703678 2.066289214 1 17.79316629 -0.545743347 8.031826618 1.000003657 1.8501501 0.227894851 0.481086997 0 0 0.414195065 0.097626713 0.284614258 0.545743347 0.850146444 EMFEDTVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EMFEDTVEER 10 0 Q16576;E9PC52 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;;;; 185.81 3.28E-06 1643689000 884503 1095870 1077640 1081092 1195238 1298873 1124226 1083459 1042371 1126423 FALSE TRUE 919423.8614 1284077.148 1105724.184 1294928.771 992071.8717 997229.4304 1036106.229 1068937.004 1004856.271 1347124.02 0.682508698 0.95319891 0.820803554 0.96125431 0.736436926 0.740265496 0.769124604 0.793495616 0.745927069 1 20.36145124 4.806367977 21.88028347 0.822285439 0.682501326 0.175475399 0.095717352 55627.19976 17945799.2 0.022221478 87.55829079 64027.71107 -4.806367977 -0.139784112 EMFEVTGLHDVDQGWMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMFEVTGLHDVDQGWMR 17 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ; 231.71 3.78E-16 174680000 91303 127541 121833 130880 156038 168161 127594 122994 109603 132566 FALSE TRUE 94907.71294 149445.1746 125008.0681 156767.6734 129514.7165 129108.1563 117592.8489 121345.4666 105658.4094 158539.7696 0.598636627 0.942635246 0.788496592 0.988822387 0.816922573 0.814358168 0.741724611 0.765394493 0.666447351 1 17.27448526 2.499288344 3.321816889 0.771965467 0.839635277 0 0.125832301 0.770308301 17.63053209 0.0421067 0.036932915 315.7100041 -2.499288344 0.06766981 EMFPYEAS(ph)TPTGISASCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMFPYEASTPTGISASCR 18 0 P42167;G5E972;H0YJH7;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 EMFPYEAS(0.656)T(0.307)PT(0.037)GISASCR 112.34 0.00029237 39895000 50018 49789 41282 61673 44765 68360 49491 43711 46769 86796 TRUE FALSE 51992.74926 58339.87345 42357.84283 73871.73532 37155.86129 52484.42601 45611.7661 43125.12554 45085.79283 103802.0144 0.500883818 0.562030263 0.408063785 0.71165994 0.357949328 0.505620496 0.439411185 0.415455575 0.434344103 1 16.66347492 -1.635289934 4.148586871 1.015983901 0.479148194 0.72979312 0.094599003 0.013352159 0.001173813 0.087448583 0.020467441 0.023158481 1.635289934 -0.536835707 EMGTPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMGTPDVR 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 89.142 0.032838 191750000 232570 295850 300860 273370 325380 368450 275930 266920 271740 338580 FALSE TRUE 241752.0432 346659.9361 308700.6588 327441.7701 270072.0238 282883.0714 254301.8856 263342.374 261960.1305 404918.2685 0.597039111 0.85612323 0.762377701 0.808661391 0.666979104 0.698617705 0.628032631 0.65035933 0.646945695 1 18.62727121 -1.058736321 4.599261245 1.000013922 0.702947614 0.562781556 0.078875343 1.17E-05 2.39E-06 0.079367087 0.018706125 0.087350155 1.058736321 -0.297066309 EMIDIYSTREPQLAFHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMIDIYSTREPQLAFHQR 18 1 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 141.13 7.34E-08 25493000 41710 53814 45514 38279 61990 59860 34044 52353 54822 73966 FALSE TRUE 43356.74301 63056.13589 46700.13223 45850.47195 51452.96194 45958.42219 31375.54232 51651.29367 52848.96693 88458.22154 0.490138082 0.712835221 0.527934334 0.518329118 0.581663988 0.519549471 0.354693343 0.583906083 0.597445506 1 16.43270862 0.645358694 2.063950544 0.999841315 0.535560245 0.73006034 0.084198096 0.999130614 5.159084189 0.081045707 0.022235597 4.419353018 -0.645358694 -0.46428107 EMIPFAVVGSDHEYQVNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMIPFAVVGSDHEYQVNGK 19 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ; 265.22 2.14E-31 648140000 312690 391770 490970 413810 567890 655930 492420 511830 509690 442950 FALSE TRUE 325035.2426 459053.45 503765.0815 495660.3829 471360.2606 503600.1982 453822.8337 504969.756 491346.3565 529737.5717 0.613577854 0.866567664 0.950971025 0.935671565 0.889799565 0.95065977 0.856693687 0.953245122 0.92752786 1 19.01491831 4.727829324 2.876332614 0.927711724 0.5623199 0.869890663 0.036936604 0.118242618 1.407729941 0.008358155 0.099531973 53435.43186 -4.727829324 -0.365391824 EMKPVIFLDVFLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMKPVIFLDVFLPR 14 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 165.75 3.57E-06 258620000 151040 156560 234090 190020 245710 220780 212230 177790 219310 152130 FALSE TRUE 157003.1758 183447.9621 240190.5777 227605.3888 203944.302 169507.191 195594.858 175407.0159 211417.0759 181936.9608 0.862953713 1.008305082 1.320185721 1.251012372 1.120961354 0.931680898 1.075069393 0.96410875 1.162034779 1 17.47307913 2.886696309 11.10498445 1.023479116 1.126701074 0.093098459 0.130703022 1.167775534 107.8335607 0.042219864 0.044793791 770.3645846 -2.886696309 0.103221958 EMLMEDVGS(ph)EEEQEEEDEAPFQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EMLMEDVGSEEEQEEEDEAPFQEK 24 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK 122.09 5.69E-05 136025000 240524 196797 229712 238487 272870 300213 348042 254737 261885 153764 TRUE FALSE 250020.0732 230595.3539 235698.4834 285659.0168 226487.6549 230493.0805 320761.5586 251322.6672 252459.81 183891.1118 1.35960934 1.253977702 1.281728525 1.553413941 1.231640032 1.25342154 1.744301589 1.366692847 1.372876631 1 17.48849222 0.614119487 3.647621673 1.000001665 1.385951791 0.363277617 0.150722615 14.22528778 133.1907129 0.145227177 0.037322851 4.112628561 -0.614119487 0.385950126 EMLQQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 128.61 0.0087036 272153000 546490 367490 434200 378730 595120 542390 461530 434950 437240 427370 FALSE TRUE 568065.8472 430603.5488 445515.6087 453641.6636 493961.715 416428.1425 425354.0726 429120.2067 421503.8178 511104.969 1.111446536 0.842495329 0.871671449 0.887570443 0.966458448 0.814760505 0.832224491 0.839593103 0.824691293 1 18.96326009 2.734964981 24.99072281 0.848951537 0.924481324 0.142262079 0.085165528 578.8821486 4023384.683 0.025857721 0.025279083 543.2065288 -2.734964981 0.075529787 EMLRDPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMLRDPELR 9 1 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 87.258 0.012388 168180000 61340 74593 71975 71324 86277 86504 69346 75984 71031 83674 FALSE TRUE 63761.75056 87403.7675 73850.72763 85431.67432 71611.66636 66414.75698 63910.47932 74965.55876 68474.60819 100068.3183 0.637182194 0.873440955 0.738003085 0.853733487 0.715627759 0.663694145 0.638668466 0.749143786 0.684278595 1 16.61062576 -1.059215148 4.365857074 1.000018518 0.731574417 0.525102673 0.077485026 0.429329484 44856390.12 2037.153233 0.018042992 0.087253901 1.059215148 -0.268444101 EMNDAAMFYTNR ddPTM_MDA-MB-175_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 ; 240.8 7.43E-16 810560000 374480 518480 460670 419150 543300 586220 439140 420680 431870 527910 FALSE TRUE 389264.7596 607524.9068 472675.4386 502056.619 450950.0601 450079.2893 404719.0593 415041.4727 416327.0831 631343.8571 0.616565371 0.962272619 0.748681457 0.795218981 0.714270132 0.712890898 0.641043791 0.657393698 0.659430005 1 19.26806645 3.19128946 4.050992865 0.701974273 0.792058158 0.003357147 0.125768094 0.498708655 17.06236921 0.034311849 0.043022987 1553.422031 -3.19128946 0.090083885 EMNPALGIDCLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EMNPALGIDCLHK 13 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 157.68 4.76E-05 2111750000 1445893 1227492 1504147 1155628 1740679 1739254 1502021 1450602 1538736 1253128 FALSE TRUE 1502977.972 1438304.202 1543346.306 1384207.769 1444799.005 1335338.617 1384288.669 1431159.053 1483357.192 1498654.439 1.002884943 0.959730385 1.029821329 0.923633716 0.964064142 0.89102503 0.923687698 0.954962676 0.989792679 1 20.51523633 3.727681126 24.98581887 0.94498174 0.993704037 0.280443871 0.034441611 857.8850342 1970217.251 0.008959836 0.014033021 5341.720083 -3.727681126 0.048722298 EMPQDLRS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EMPQDLRSPAR 11 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR;EMPQDLRS(1)PAR 119.54 0.00034634 3706220000 2151120 2557690 2323750 2666810 2490060 2948960 2453700 2601950 2420940 2647050 TRUE FALSE 2236047.879 2996953.361 2384308.834 3194297.058 2066800.491 2264108.732 2261372.582 2567075.116 2333810.842 3165688.767 0.706338507 0.946698675 0.753172219 1.009036988 0.652875454 0.715202567 0.714338253 0.810905716 0.737220559 1 21.59408799 5.042280039 14.80078134 0.802790837 0.298899169 0.05935125 0.12121712 2149271.385 22597105.79 0.027476802 28947826.28 110224.9825 -5.042280039 -0.503891668 EMPQDLRS(ph)PART(ph)PPSEEDSAEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EMPQDLRSPARTPPSEEDSAEAER 24 2 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 EMPQDLRS(1)PART(1)PPSEEDSAEAER;EMPQDLRS(1)PART(1)PPSEEDSAEAER;EMPQDLRS(0.985)PART(0.799)PPS(0.136)EEDS(0.08)AEAER;EMPQDLRS(1)PART(0.891)PPS(0.104)EEDS(0.005)AEAER;EMPQDLRS(1)PART(0.999)PPS(0.001)EEDSAEAER;EMPQDLRS(1)PART(0.97)PPS(0.03)EEDSAEAER 141.75 5.17E-07 2387100000 1078738 1373100 1321006 1236433 1448460 1537920 1209399 1348541 1275606 1412530 TRUE FALSE 1121327.409 1608919.244 1355432.502 1480995.757 1202251.287 1180761.387 1114603.146 1330466.014 1229697.189 1689288.209 0.663786915 0.952424361 0.802369006 0.876698096 0.711691043 0.698969768 0.659806385 0.787589712 0.727938065 1 20.68798406 5.031126814 17.4101433 0.786585816 0.236131796 0.116465602 0.106872241 17379440.13 251396671 0.024968715 290250458.2 107430.3063 -5.031126814 -0.55045402 EMQPTHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 22 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 ;;;;;;;;;;;;;;;;;;;;; 159.93 6.57E-05 36353326000 5820102.7 6061637 6596647 6975683 6577729 7392282 7261301 6584418 6314141 5376472 FALSE TRUE 6049884.849 7102676.002 6768561.04 8355452.277 5459648.974 5675536.537 6692141.254 6496164.647 6086896.299 6429888.75 0.940900393 1.104634353 1.052671563 1.299470738 0.849104734 0.882680363 1.040786476 1.010307472 0.94665655 1 22.61636235 3.210337758 24.99999943 0.961738035 1.096453058 0.340072076 0.098301675 265.1777863 234895.6193 0.028913419 0.034564136 1623.071897 -3.210337758 0.134715023 EMSGSNETS(ph)SPVSEKPSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EMSGSNETSSPVSEKPSASR 20 1 A0A087X165;Q9C0H9 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 EMSGSNET(0.055)S(0.644)S(0.301)PVSEKPSASR 155.44 1.81E-08 391500000 119780 96744 123200 104100 134590 142280 144680 128150 140430 116030 TRUE FALSE 124509.0069 113359.0294 126410.6932 124690.6693 111712.4399 109237.6263 133339.6035 126432.3589 135375.9517 138763.857 0.897272601 0.816920428 0.91097708 0.898581749 0.805054301 0.787219588 0.960910186 0.911133213 0.975585103 1 17.08227232 1.690552122 1.406751017 0.984591342 0.856952431 0.522155575 0.047982448 0.332161127 1.266132997 0.039960087 0.015023768 49.04018748 -1.690552122 -0.127638911 EMSLWESLGESWMRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMSLWESLGESWMRPR 16 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 171.46 4.48E-09 1004760000 458290 597660 666720 597130 677560 688810 623610 612900 633460 651430 FALSE TRUE 476383.6431 700303.4559 684095.2709 715240.5317 562388.5932 528844.3165 574729.8187 604685.078 610661.8983 779065.2361 0.611481069 0.898902201 0.878097545 0.918075276 0.721876124 0.678819041 0.737717192 0.77616745 0.783839235 1 19.57138461 -1.085106912 2.852193268 1.000534243 0.782158038 0.336948614 0.093147341 2530956.489 3430838.288 12768.47482 0.024482129 0.082204026 1.085106912 -0.218376205 EMTLDEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EMTLDEWK 8 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 155.75 0.00093967 392202000 1037416 795642 925979 694443 1257446 1199353 1099589 908242 1039354 763686 FALSE TRUE 1078373.985 932287.3243 950110.7734 831801.7527 1043705.778 920821.4421 1013400.341 896068.5016 1001947.853 913315.65 1.180724303 1.020772308 1.040287411 0.910749479 1.142765678 1.00821818 1.1095839 0.981115895 1.097044436 1 19.80075403 4.741778584 24.08821411 1.033847004 1.180724396 0.316524673 0.064452871 208.8826792 1563470.656 0.014135042 0.100622651 55179.60464 -4.741778584 0.146877392 EMTNHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EMTNHQK 7 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 101.28 0.014036 273940000 351055 320161 385374 305175 419097 417922 446940 388978 402628 333952 FALSE TRUE 364914.9225 375146.1612 395417.163 365537.7041 347859.0416 320865.9492 411907.6749 383764.3861 388137.4969 399383.5005 0.913695538 0.939313118 0.99006885 0.915254896 0.870990016 0.803403117 1.031358768 0.960891939 0.971841592 1 18.60741521 2.200379122 24.99999963 0.986441841 0.909717992 0.427772936 0.048216913 191.8439363 125612.0799 0.019576166 0.01445825 158.6277345 -2.200379122 -0.076723849 EMVELPLRHPALFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMVELPLRHPALFK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 161.76 2.73E-06 2443400000 3248800 3531300 3752800 2883300 5241000 4607700 3484700 3915500 4236800 4226100 FALSE TRUE 3377065.133 4137773.305 3850601.051 3453608.134 4350136.692 3537631.505 3211560.108 3863019.127 4084318.396 5054123.381 0.668180192 0.818692579 0.76187318 0.683324856 0.860710427 0.699949574 0.635433658 0.764330198 0.808116084 1 22.26902945 0.832902687 2.200407745 0.999561548 0.737149158 0.599534236 0.065136386 0.415099494 3.688703561 0.060826637 0.016610355 6.806168349 -0.832902687 -0.26241239 EMVQNLMVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EMVQNLMVLR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 107.79 0.0052054 376160000 305920 212775 224060 196209 293950 392610 244720 248120 215780 280630 FALSE TRUE 317997.9578 249317.4511 229899.1877 235018.5546 243984.484 301432.2776 225538.2069 244794.3572 208014.12 335614.0755 0.94751079 0.742869472 0.685010566 0.700264297 0.726979295 0.898151477 0.672016531 0.729392404 0.619801537 1 18.3564437 ENAEVDGDDDAEEMEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 229.54 2.50E-15 165490000 114700 78212 99473 81618 134540 121850 126220 96025 106330 60343 FALSE TRUE 119228.4446 91644.3026 102065.3481 97761.79679 111670.9389 93552.18415 116326.5466 94737.94194 102503.2041 72166.05551 1.652140244 1.269908712 1.414312413 1.354678402 1.547416414 1.296346094 1.611928846 1.312777057 1.420379753 1 16.13903278 -0.009942804 0.900095147 0.993182162 1.430654523 0.514661548 0.125925917 4.907533026 3.676320035 0.218422842 0.03589771 0.977365931 0.009942804 0.437472361 ENALSSGTLQEEQRT(ph)PPPGQDTQQFHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ENALSSGTLQEEQRTPPPGQDTQQFHEK 28 1 Q12802-2;Q12802;Q12802-4;H0YMW2 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ENALSSGT(0.001)LQEEQRT(0.999)PPPGQDTQQFHEK;ENALSSGTLQEEQRT(1)PPPGQDTQQFHEK;ENALSSGTLQEEQRT(1)PPPGQDTQQFHEK 261.81 1.33E-53 995430000 651308 564594 675065 590748 771660 852210 700780 651630 710260 523799 TRUE FALSE 677022.1428 661558.6276 692657.7485 707596.1912 640493.5088 654297.1429 645851.0325 642895.9657 684697.8813 626427.3853 1.080767155 1.056081907 1.10572712 1.129574166 1.022454516 1.044490005 1.031007021 1.026289688 1.093020352 1 19.25678776 3.222176375 24.99852899 1.036750426 1.091304298 0.493267615 0.028191916 209.2147668 319212.3458 0.008142037 0.00975631 1667.924451 -3.222176375 0.054553872 ENALVQMADGNQAQLAMSHLNGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENALVQMADGNQAQLAMSHLNGHK 24 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 258.48 3.57E-44 1162300000 596680 650640 757010 630250 881890 809740 745900 771820 828680 611750 FALSE TRUE 620237.3871 762382.3587 776738.3025 754911.5689 731986.6528 621690.1567 687434.409 761475.0153 798855.9687 731610.6998 0.847769705 1.042060154 1.061682535 1.031848726 1.00051387 0.849755419 0.939617763 1.040819955 1.091914004 1 19.48071665 1.620754591 6.10895128 1.052215832 0.973496452 0.183996483 0.072947631 0.241598195 19.12214347 0.041106939 0.019812938 41.75943274 -1.620754591 -0.078719381 ENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.977)PAPGT(0.011)T(0.011)AEEAMSR;ENAS(0.996)PAPGT(0.002)T(0.003)AEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR;ENAS(1)PAPGTTAEEAMSR 326.51 7.26E-72 3580970000 2302204 2411845 2366254 2729320 2595990 3087120 3077330 2580066 2408524 1876717 TRUE FALSE 2393096.792 2826060.617 2427920.523 3269171.35 2154724.547 2370183.166 2836120.833 2545484.435 2321841.692 2244423.764 1.066241068 1.25914752 1.081756735 1.456574913 0.960034634 1.056031933 1.263629836 1.134137179 1.034493454 1 21.09791366 ENDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENDFDR 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 156.16 0.022768 6041100000 4976100 4986500 5315600 5066900 6450800 6458500 5874600 5245900 5219100 4356390 FALSE TRUE 5172560.27 5842892.585 5454128.903 6069117.697 5354295.32 4958611.255 5414133.502 5175587.291 5031265.61 5209941.212 0.992825074 1.121489158 1.046869567 1.164910975 1.027707435 0.951759541 1.03919282 0.993406083 0.965704872 1 22.31283566 3.008663469 24.84962176 0.993598062 1.083703855 0.454039575 0.047208515 156.182195 447976.8405 0.012789308 0.015263165 1020.148673 -3.008663469 0.090105793 ENDPMDS(ph)HQSQESPNLENIANPLEENVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDS(0.446)HQS(0.303)QES(0.251)PNLENIANPLEENVTK;ENDPMDS(0.412)HQS(0.294)QES(0.294)PNLENIANPLEENVTK 86.507 0.0012434 109454000 22913 45334 44048 46667 53088 70600 48696 54075 50997 43217 TRUE FALSE 23817.62293 53119.76185 45195.92707 55897.59331 44064.12072 54204.21995 44879.08028 53350.21307 49161.62793 51684.54371 0.460826801 1.027768807 0.87445731 1.081514691 0.852558958 1.048751059 0.868326913 1.032227611 0.951186262 1 15.65744529 4.742588078 24.98697259 0.969138717 0.460826602 0.794898321 0.077702852 151.0348857 937006.9293 0.016149438 0.124241564 55282.55134 -4.742588078 -0.508312115 VVSVLTVLHQDWLNGK ddPTM_MDA-MB-175_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 ; 307.01 6.85E-47 875040000 5126500 2235850 785800 191817 189231 862420 70495 48990 63006 62611 FALSE TRUE 5328898.179 2619839.845 806278.5935 229757.8301 157065.5822 662136.0251 64969.4177 48333.36918 60738.42637 74878.42669 71.16733636 34.98791255 10.76783567 3.06841156 2.097607938 8.842814337 0.867665369 0.645491249 0.811160558 1 16.1922625 4.668867858 1.369185094 2.176083288 95.09352563 0.988369554 2.337331058 0.108480446 0.200294074 0.691208483 13.47306198 46651.7412 -4.668867858 92.91744235 up ENDWYLAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENDWYLAYK 9 0 A0A2R8YFH0;E9PHA6;A0A2R8Y6P0;A0A2R8YG02;P43246;P43246-2;A0A2R8Y7S8 A0A2R8YFH0 MSH2 DNA mismatch repair protein Msh2 0 112.75 0.0046461 0 62008 61546 71288 61988 79229 87844 81284 67328 65342 64140 FALSE TRUE 64456.12372 72116.04674 73145.82384 74249.04138 65761.68288 67443.56229 74912.74768 66425.57829 62990.35418 76707.00497 0.840289929 0.940149427 0.953574238 0.967956465 0.857310006 0.879236027 0.976608951 0.865964957 0.82118125 1 16.22707071 3.237694298 24.99999595 0.895907524 0.928545268 0.038080945 0.059749145 71.86186195 2073784.192 0.016736235 0.021121509 1728.59916 -3.237694298 0.032637744 ENEFSFEDNAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 113.61 0.00045713 50166000 197339 250326 273829 246209 307663 337773 256407 285029 286981 261409 FALSE TRUE 205130.0961 293317.5432 280965.2087 294908.4053 255366.5532 259330.3397 236309.1493 281208.6525 276652.6099 312627.0886 0.656149462 0.938234574 0.898723172 0.943323263 0.816840774 0.829519735 0.755881873 0.899501875 0.884928466 1 18.25408327 0.846204529 1.575060119 0.998766002 0.845672319 0.253650284 0.082628768 0.857195331 4.024113947 0.07621914 0.022085475 7.017857239 -0.846204529 -0.153093682 ENFMTVDQDGSGTVEHHELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENFMTVDQDGSGTVEHHELR 20 0 H7C2Z6;H7BXD5;P28676;C9JIZ3 H7C2Z6 GCA Grancalcin 0 ; 161.22 1.32E-11 251030000 39146.1 38766.8 43755 43901 41128 47421 44389 47574 38142.3 40115.7 FALSE TRUE 40691.61826 45424.69634 44895.29125 52584.48677 34137.07725 36408.19142 40909.67419 46936.34835 36769.56607 47975.60335 0.848173142 0.946829079 0.935794198 1.096067232 0.711550765 0.758889704 0.852718285 0.978337844 0.766422171 1 15.55001333 5.154283656 8.253853515 0.893406822 0.000126409 0.013996998 0.115431642 53255.78526 82061.24097 0.027984973 833663.2068 142653.9021 -5.154283656 -0.893280413 ENFQNWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENFQNWLK 8 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ; 134.91 0.0019923 874710000 587650 640470 589180 560920 719100 829810 591800 551150 574640 746880 FALSE TRUE 610850.8758 750465.7403 604534.5148 671868.3018 596867.6389 637099.2034 545413.1696 543762.7357 553958.8186 893216.8361 0.683877476 0.840183156 0.676806001 0.752189474 0.668222558 0.713263765 0.610616759 0.608769018 0.620184032 1 19.76865092 -1.0902591 4.650023239 1.000014567 0.683634704 0.661729107 0.067328864 1.41E-05 2.76E-06 0.070737243 0.016671948 0.081234573 1.0902591 -0.316379863 ENFS(ph)PER ddPTM_MDA-MB-175_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 128.51 0.0039339 2742610000 1936170 2169530 2245740 2232820 2692440 2853340 2686470 2307150 2421670 1968470 TRUE FALSE 2012611.487 2542129.901 2304265.829 2674465.132 2234780.011 2190695.028 2475897.462 2276226.428 2334514.57 2354154.008 0.854919211 1.079848596 0.978808447 1.136062094 0.949292189 0.930565724 1.051714312 0.966897841 0.991657539 1 21.16677727 ENFSCLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENFSCLTR 8 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;C9JF79;C9JRL4 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 ;;; 150.17 0.0011479 842790000 587660 636110 695770 622670 801090 872670 662170 639410 655220 765700 FALSE TRUE 610861.2706 745356.9443 713902.3378 745832.2675 664921.0079 670005.6179 610267.3851 630839.7548 631638.7602 915724.2548 0.667079929 0.81395348 0.77960405 0.814472548 0.726114881 0.731667436 0.666431387 0.688897069 0.689769608 1 19.80455371 -1.226083077 5.380564983 1.000018424 0.731157592 0.699774834 0.052880653 1.27E-05 1.82E-06 0.055482534 0.013076463 0.059417849 1.226083077 -0.268860832 ENFTAGS(ph)DCVTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ENFTAGSDCVTLK 13 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 ENFTAGS(0.997)DCVT(0.002)LK;ENFT(0.001)AGS(0.999)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK;ENFTAGS(1)DCVTLK 261.64 4.74E-24 2065570000 4649490 3614690 4478570 3556900 6436550 5440050 4437200 4182310 4987560 3614090 TRUE FALSE 4833055.455 4235484.889 4595285.213 4260444.204 5342467.53 4176680.832 4089400.67 4126252.975 4808058.69 4322201.74 1.118192937 0.97993688 1.063181566 0.985711556 1.23605233 0.966331764 0.946138315 0.954664595 1.112409596 1 22.04333498 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENGAFTVLVDNYVKEEEGTGVVHQAPYFGAEDYR 34 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 94.807 0.00016948 34072000 25242 12911 21948 15409 22679 25242 25295 18886 20220 13984 FALSE TRUE 26238.57365 15128.36382 22519.98291 18456.85421 18824.03168 19379.92805 23312.3118 18632.86406 19492.28615 16723.89706 1.568927 0.904595607 1.346575073 1.103621611 1.125576868 1.158816511 1.393952123 1.114146063 1.165534928 1 14.02962345 -4.999999569 0.218035455 9.19E-08 1.225564926 0.126328057 0.173904367 332.6726185 3.326992295 145.9625558 0.309118612 1.00E-05 4.999999569 1.225564835 ENGEEGCHQNGLALPVVEEGEVLS(ph)HSLEAEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENGEEGCHQNGLALPVVEEGEVLSHSLEAEHR 32 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 ENGEEGCHQNGLALPVVEEGEVLS(0.5)HS(0.5)LEAEHR 94.389 4.13E-05 36144000 23757 21504 24846 27851 28030 34510 24372 29986 29552 25793 TRUE FALSE 24694.9447 25197.14472 25493.50717 33359.84467 23265.47061 26495.5755 22461.65896 29584.08672 28488.42929 30846.64451 0.800571508 0.816852047 0.826459655 1.081474021 0.754230192 0.858945144 0.728171874 0.95906985 0.923550349 1 14.91282594 1.608754401 25 0.955995736 0.843756648 0.27182715 0.091652578 0.13783495 3558.226787 0.045040822 0.023143488 40.62135452 -1.608754401 -0.112239087 ENGKGDIKS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENGKGDIKSK 10 2 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 ENGKGDIKS(1)K;ENGKGDIKS(1)K 59.607 0.054002 620430000 2583460 449070 768620 405190 1452950 1692360 1424200 898260 1034680 227059 TRUE FALSE 2685456.996 526194.2792 788650.8686 485335.3726 1205978.078 1299335.038 1312567.483 886220.294 997442.0689 271546.8637 9.88947896 1.937765997 2.904290102 1.787298759 4.441141619 4.784938482 4.833668356 3.263599814 3.673185745 1 18.05084168 4.746319239 24.75927449 3.358965798 9.889482586 0.718625498 1.254929435 459.3053474 1465693.415 0.302535948 3.2517353 55759.54729 -4.746319239 6.530516788 ENGSGHEASLQLRPPPEPST(ph)PVSGQDDLIQHQDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENGSGHEASLQLRPPPEPSTPVSGQDDLIQHQDMR 35 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 ENGSGHEASLQLRPPPEPS(0.244)T(0.749)PVS(0.007)GQDDLIQHQDMR 93.955 0.00031618 43736000 9439.4 18938 15508 14367 17082 23334 14628 14614 17724 14210 TRUE FALSE 9812.074801 22190.45418 15912.15122 17208.74972 14178.40774 17915.03213 13481.41914 14418.12323 17086.1167 16994.17743 0.577378625 1.305768065 0.936329592 1.012626224 0.834309739 1.054186482 0.793296362 0.848415482 1.005410045 1 14.05275291 3.26143725 24.81653085 0.907819234 0.981314651 0 0.182463968 868.3840511 942014.5414 0.047300192 0.064000638 1825.732934 -3.26143725 0.073495417 ENGVTHPIDYHTTDYVDEIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENGVTHPIDYHTTDYVDEIKK 21 1 Q99536-3;Q99536;K7ENX2;K7EM19;Q99536-2 Q99536-3 VAT1 Synaptic vesicle membrane protein VAT-1 homolog 0 167.16 5.07E-12 58033000 58704 41389 59020 47115 88323 72353 78546 58297 77043 33761 FALSE TRUE 61021.67925 48497.23879 60558.10969 56434.20638 73309.88801 55550.11227 72389.35928 57515.62407 74270.23748 40375.82156 1.511342108 1.20114556 1.499860742 1.3977228 1.815687834 1.375826178 1.792888825 1.424506595 1.839473096 1 15.301204 3.408403866 24.9997688 1.566041426 1.394627771 0.063321205 0.250458857 111.4513854 40544.9887 0.06252934 0.084665117 2560.966313 -3.408403866 -0.171413655 ENHGQADHS(ph)PSMTATHFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 ENHGQADHSPSMTATHFPR 19 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ENHGQADHS(0.995)PS(0.005)MTATHFPR;ENHGQADHS(0.992)PS(0.008)MTATHFPR;ENHGQADHS(0.998)PS(0.002)MTATHFPR;ENHGQADHS(0.999)PS(0.001)MTATHFPR;ENHGQADHS(0.999)PS(0.001)MTATHFPR;ENHGQADHS(0.99)PS(0.01)MTATHFPR;ENHGQADHS(0.751)PS(0.249)MTATHFPR;ENHGQADHS(0.946)PS(0.053)MTATHFPR;ENHGQADHS(0.669)PS(0.312)MT(0.019)ATHFPR 326.81 6.20E-75 15492050000 1520275 2227055 2033838 2128053 2233619 2582734 2145250 2278484 2083433 2298353 TRUE FALSE 1580296.631 2609534.372 2086841.489 2548975.532 1853949.24 1982933.17 1977099.699 2247944.649 2008450.653 2748671.266 0.574931113 0.949380308 0.759218287 0.927348266 0.674489257 0.721415178 0.71929289 0.817829573 0.730698748 1 21.39030294 -1.934847951 3.432861058 1.136444158 0.771643762 0.304866531 0.10639388 0.075740306 0.00143747 0.070226363 0.02233165 0.011618553 1.934847951 -0.364800397 ENIKPNETS(ph)PSFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENIKPNETSPSFSK 14 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 ENIKPNET(0.058)S(0.938)PS(0.004)FSK;ENIKPNET(0.113)S(0.88)PS(0.006)FSK;ENIKPNET(0.13)S(0.868)PS(0.001)FSK;ENIKPNET(0.059)S(0.919)PS(0.019)FS(0.003)K 137.69 1.20E-05 764720000 1953140 959649 1430220 1174136 1746560 1898350 2435220 1441240 1746490 709793 TRUE FALSE 2030251.475 1124461.251 1467492.708 1406376.596 1449680.355 1457486.982 2244341.093 1421922.535 1683634.166 848863.3485 2.391729457 1.324666983 1.72877379 1.656776204 1.70779002 1.716986585 2.643936856 1.675090034 1.983398351 1 19.6951728 ENISEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENISEWR 7 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 91.853 0.037453 296620000 360540 404110 427460 394950 453780 498840 465270 410680 428650 365730 FALSE TRUE 374774.3976 473512.749 438599.9588 473069.9312 376646.6377 382991.97 428800.9216 405175.5063 413222.9702 437387.7912 0.856846956 1.082592515 1.00277138 1.081580101 0.86112746 0.875634798 0.980367834 0.926353032 0.944751954 1 18.73855343 3.237290444 24.99997502 0.92848975 1.011195475 0.210868444 0.070250544 47.70416354 938936.6591 0.019198305 0.024176112 1726.99247 -3.237290444 0.082705725 ENIVEAIIHSPELIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ENIVEAIIHSPELIR 15 0 O95373;E9PLB2 O95373 IPO7 Importin-7 0 ;;;;; 148.52 3.52E-06 584681000 613856 654426 685476 698676 809248 876478 802160 747502 697699 561683 FALSE TRUE 638091.5089 766818.5748 703340.0677 836872.0275 671692.314 672929.2677 739284.6031 737482.9584 672588.9493 671734.0298 0.949916903 1.141550883 1.047051417 1.245838368 0.999937898 1.001779332 1.100561488 1.097879407 1.001272705 1 19.35753059 ENLATVEGNFASIDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENLATVEGNFASIDER 16 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ; 220.21 2.72E-14 122973000 28351 29000 31031 35822 41033 42483 31520 32328 31206 37143 FALSE TRUE 29470.31937 33980.52441 31839.69335 42907.48468 34058.22532 32616.96709 29049.38004 31894.69604 30082.90216 44420.4597 0.663440216 0.764974623 0.716779915 0.965939681 0.766723837 0.734278017 0.653963967 0.718018144 0.677230771 1 15.4389367 -2.186566713 2.308864098 1.695917878 0.741909301 0.462215153 0.084067228 6178807.085 1321058.8 22474189.06 0.021542715 0.006507786 2.186566713 -0.954008577 ENLPSHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENLPSHFK 8 0 Q8TBX8;F8VNT5;Q8TBX8-2;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 126.07 0.001235 154520000 466930 468290 513410 424250 699670 661280 559140 496520 537140 547690 FALSE TRUE 485364.7569 548715.1647 526789.8864 508165.3837 580740.3433 507707.7418 515313.1458 489864.9615 517808.4363 654999.3693 0.74101561 0.837733882 0.804260143 0.77582576 0.886627332 0.77512707 0.786738385 0.747886158 0.790547992 1 19.32113399 -0.885827123 4.69555215 1.000001211 0.793519004 0.701117765 0.040354144 0.001024045 25178849.98 78.22663059 0.009416796 0.130068723 0.885827123 -0.206482207 ENLSDEDKLNNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENLSDEDKLNNAK 13 1 Q14651 Q14651 PLS1 Plastin-1 0 ; 135.37 5.55E-06 335950000 642510 303690 413420 269190 621150 554660 551500 435180 508660 236970 FALSE TRUE 667876.7909 355846.3951 424194.0648 322434.9785 515567.1449 425848.621 508271.9889 429347.1239 490353.426 283399.7344 2.356659904 1.255634187 1.496804737 1.13773917 1.819222399 1.502642978 1.793480823 1.514987743 1.730253654 1 18.11247888 -1.215031005 4.925640678 0.999918747 1.597555857 0.249070769 0.321821202 0.000264129 4.21E-05 0.286569997 0.067536071 0.060949338 1.215031005 0.59763711 ENLVRPGIDHLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENLVRPGIDHLGR 13 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 0 ; 91.441 0.0039238 141729000 64467 60236 67249 63374 67849 78810 70043 66924 68726 62627 FALSE TRUE 67012.20694 70581.06443 69001.56419 75909.18805 56316.05122 60507.57188 64552.84664 66026.99325 66252.56468 74897.56158 0.894718139 0.942367988 0.921279181 1.013506801 0.751907673 0.807871052 0.861881819 0.88156399 0.884575723 1 16.19263113 3.253329602 24.99999545 0.857636546 0.941375934 0.251071516 0.065592325 316.0776882 535032.7423 0.017796797 0.023997345 1791.965328 -3.253329602 0.083739388 ENPDKEEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENPDKEEFR 9 1 G3XAH6;P51003 G3XAH6 PAPOLA Poly(A) polymerase alpha 0 ; 92.611 0.0090825 374900000 558170 446350 598200 502420 679130 717090 650000 579730 655870 400360 FALSE TRUE 580206.9826 523007.1404 613789.5834 601797.1764 563691.7252 550556.7151 599051.3015 571959.6676 632265.3668 478802.8766 1.211786752 1.092322469 1.28192543 1.256878782 1.17729394 1.149860918 1.251143907 1.194561887 1.320512883 1 18.86907229 2.228725838 24.99323269 1.207902309 1.196301154 0 0.090842073 2570.248486 6531784.141 0.032104441 0.023999363 169.3268536 -2.228725838 -0.011601155 ENPEDVLS(ph)PTSVATYLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENPEDVLSPTSVATYLSSK 19 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 ENPEDVLS(0.788)PT(0.115)S(0.096)VAT(0.001)YLSSK;ENPEDVLS(0.881)PT(0.095)S(0.024)VATYLSSK;ENPEDVLS(0.494)PT(0.413)S(0.092)VATYLSSK;ENPEDVLS(0.964)PT(0.015)S(0.021)VATYLSSK 170.91 1.18E-11 95742000 189671 156007 194077 165136 225722 232993 235525 205820 213421 140618 TRUE FALSE 197159.3575 182799.9887 199134.8061 197799.4079 187353.8551 178883.9068 217063.9351 203061.3196 205740.0199 168169.4048 1.172385416 1.086999082 1.184132193 1.176191401 1.114078124 1.063712552 1.290745694 1.207480753 1.223409336 1 17.35955573 2.248076474 24.99999525 1.202070158 1.134268067 0.053397707 0.079055272 369.4051267 970499.3743 0.026003269 0.021490243 177.0420682 -2.248076474 -0.067802091 ENPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENPEKR 6 1 Q1KMD3;H3BQZ7;Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q1KMD3;Q7Z6E9 HNRNPUL2;HNRNPUL2-BSCL2;RBBP6 Heterogeneous nuclear ribonucleoprotein U-like protein 2;E3 ubiquitin-protein ligase RBBP6 0 ; 129.39 0.025998 202850000 394130 304150 351980 263860 442620 407420 453970 359790 410240 304310 FALSE TRUE 409690.5567 356385.3965 361152.888 316050.7205 367383.6105 312802.8795 418386.6452 354967.6035 395475.5425 363933.7181 1.125728495 0.979259076 0.992358965 0.868429345 1.009479452 0.85950508 1.149623199 0.975363331 1.086669146 1 18.4733162 2.234967473 24.99994304 1.046299038 0.970627647 0.183211674 0.082696036 169.0025389 1175847.928 0.029224026 0.022432518 171.7779729 -2.234967473 -0.075671391 ENPSATLEDLEKPGVDEEPQHVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENPSATLEDLEKPGVDEEPQHVLLR 25 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 211.72 7.14E-26 156390000 135470 114070 133480 104130 216270 175560 156330 137900 137410 147710 FALSE TRUE 140818.4602 133660.6352 136958.5985 124726.6032 179508.5026 134788.8506 144076.4461 136051.6761 132464.6409 176650.9464 0.797156557 0.75663696 0.775306338 0.706062468 1.016176286 0.763023654 0.815599628 0.770172359 0.749866579 1 17.43054195 -2.087298606 2.461926926 1.336498133 0.794889959 0.377173217 0.07924161 7506704.033 2898663.481 14129785.52 0.01866127 0.008179022 2.087298606 -0.541608174 ENPVYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENPVYEK 7 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ;;; 107.9 0.017157 579260000 738860 635980 738890 579570 897240 941390 817650 783990 768270 590490 FALSE TRUE 768030.7633 745204.6178 758146.0804 694207.2162 744727.4653 722766.4394 753560.4565 773481.8964 740620.1128 706185.2099 1.087576959 1.055253788 1.073579664 0.983038453 1.054578112 1.023480001 1.06708615 1.095296086 1.048761858 1 19.42968708 ENPYYDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 169.44 0.00070028 8714250000 8286850 7877660 8641310 7314560 10440590 11484240 9116400 8702120 9286530 7964780 FALSE TRUE 8614021.237 9230586.825 8866509.638 8761358.136 8665902.241 8817199.305 8401832.747 8585482.315 8952309.599 9525326.146 0.90432822 0.969057299 0.930835281 0.919796131 0.909774858 0.92565852 0.882051976 0.90133211 0.939842842 1 23.18333706 3.825376098 3.961394386 0.917152263 0.939212022 0 0.033352082 0.622592468 18.0624367 0.008231499 0.015542754 6689.229521 -3.825376098 0.022059759 ENQELNAHNQELNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENQELNAHNQELNNR 15 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 0 91.14 0.0055055 0 43367 60334 61223 45699 63506 69142 60788 49169 64100 53622 FALSE TRUE 45079.16265 70695.89517 62818.52168 54738.1258 52711.2728 53084.81836 56023.27772 48509.96998 61793.05352 64128.20424 0.702953765 1.102415014 0.979577121 0.853573345 0.82196708 0.827792061 0.873613699 0.756452961 0.963586214 1 15.96867139 3.722428797 21.56602502 0.851625659 0.945725251 0.025181592 0.114095803 261.7435696 349915.6544 0.028614091 0.044575993 5277.506742 -3.722428797 0.094099593 ENQPENSQT(ph)PTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 ENQPENS(0.001)QT(0.977)PT(0.022)KK;ENQPENSQT(1)PTKK 155.03 3.82E-06 147440000 507200 235916 349270 219674 480410 452080 445150 333310 409990 210878 TRUE FALSE 527224.6476 276432.7378 358372.2631 263124.8615 398750.0798 347091.2713 410257.9798 328842.5246 395234.54 252195.5066 2.090539418 1.096104929 1.421009708 1.043336835 1.581114926 1.376278571 1.626745795 1.303919047 1.567175186 1 17.94418305 -1.511941214 4.163254705 0.995990083 1.431567626 0.186016114 0.282101582 0.009575141 0.001122494 0.249092464 0.058258159 0.030765132 1.511941214 0.435577542 ENQRS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ENQRSPVR 8 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR;ENQRS(1)PVR 111.52 0.0019481 4060830000 1842691 1912982 1879945 1865332 1998882 2348881 2148414 1950616 1847151 1861883 TRUE FALSE 1915441.864 2241521.778 1928937.911 2234289.102 1659112.752 1803388.985 1980015.697 1924471.183 1780672.396 2226683.326 0.860221946 1.006663925 0.866283 1.003415742 0.745104943 0.809899174 0.889221953 0.864276999 0.799697189 1 21.08646497 3.252184708 24.99961035 0.846773863 0.934478601 0.214875009 0.077218362 333.0057258 611047.2696 0.02006226 0.02701876 1787.247541 -3.252184708 0.087704738 ENREDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ENREDYR 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 136.75 0.0026899 942231000 1143237 1509346 1437889 1102624 1785431 1654310 1070412 1320601 1365819 1722430 FALSE TRUE 1188372.88 1768564.434 1475361.569 1320719.736 1481944.076 1270121.574 986510.3104 1302900.504 1316663.441 2059907.181 0.576906033 0.85856511 0.716227208 0.641154975 0.719422744 0.616591653 0.478910079 0.632504472 0.639185811 1 20.9741479 -0.99917328 4.448913239 1.000010818 0.652499785 0.549091544 0.094258029 12565249.37 2824341.163 1497.846528 0.023180921 0.100190541 0.99917328 -0.347511033 ENS(ph)REALAEAALESPRPALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENSREALAEAALESPRPALVR 21 2 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 ENS(0.984)REALAEAALES(0.016)PRPALVR;ENS(0.993)REALAEAALES(0.007)PRPALVR 142.45 1.15E-07 692910000 180170 228690 229920 204243 283200 306770 265950 246620 278370 215128 TRUE FALSE 187283.2507 267965.7285 235911.9041 244641.6558 235061.7652 235527.3166 245104.1441 243314.4623 268351.5181 257278.2127 0.727940577 1.041540695 0.916952514 0.950883688 0.913648158 0.915457684 0.952681307 0.945725095 1.043040199 1 17.97296976 4.752074946 25 0.95676661 0.727940427 0.695341678 0.046715001 1290.71606 2387638.965 0.010666627 0.212910017 56503.44741 -4.752074946 -0.228826183 ENS(ph)SPENKNWLLAMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENSSPENKNWLLAMAAK 17 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 ENS(0.632)S(0.368)PENKNWLLAMAAK 144.57 3.07E-07 286920000 437650 404140 463250 356060 479960 532230 522380 409520 471860 338120 TRUE FALSE 454928.7599 473547.9012 475322.6756 426487.6053 398376.5706 408627.6485 481434.4906 404031.0542 454877.8508 404368.1403 1.125036111 1.171081136 1.175470143 1.054701305 0.985182884 1.010533738 1.190584625 0.999166388 1.124910213 1 18.62530981 3.731955707 23.52524739 1.052874875 1.158584334 0.380069859 0.061464232 229.7949025 818481.7509 0.015944117 0.025395007 5394.55601 -3.731955707 0.105709459 ENS(ph)SPSVTSANLDHTKPCWYWDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ENSSPSVTSANLDHTKPCWYWDKK 24 2 O75909;G3V5E1;O75909-1;O75909-4;G3V2Q3;O75909-2;G3V235 O75909 CCNK Cyclin-K 1 ENS(0.493)S(0.493)PS(0.014)VTSANLDHTKPCWYWDKK;ENS(0.487)S(0.487)PS(0.023)VT(0.001)S(0.002)ANLDHTKPCWYWDKK;ENS(0.491)S(0.491)PS(0.016)VTS(0.001)ANLDHTKPCWYWDKK 135.41 1.33E-05 2743790000 1750320 1071240 1591570 998250 2006170 1785240 1912820 1511630 1881550 808890 TRUE FALSE 1819423.985 1255217.137 1633047.622 1195700.871 1665161.94 1370645.066 1762888.17 1491369.072 1813833.383 967376.5084 1.88078165 1.297547673 1.68811999 1.236024299 1.721317321 1.416868255 1.822339239 1.541663519 1.875002512 1 19.88371798 ENSFGS(ph)PLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 ENS(0.012)FGS(0.988)PLEFR;ENS(0.002)FGS(0.998)PLEFR;ENS(0.002)FGS(0.998)PLEFR;ENS(0.002)FGS(0.998)PLEFR;ENS(0.001)FGS(0.999)PLEFR 230.54 1.81E-12 1869730000 2571090 2412530 2412820 2803990 2448590 3000160 3163190 2535980 2434590 2048130 TRUE FALSE 2672598.619 2826863.261 2475700.071 3358610.853 2032379.546 2303418.308 2915250.902 2501989.336 2346969.581 2449421.86 1.091114055 1.154094077 1.010728332 1.371185139 0.82973847 0.940392648 1.190179181 1.021461177 0.958172873 1 21.22400984 3.225673191 24.99999777 1.004506756 1.146156292 0.311681378 0.119856135 327.5965612 635495.0386 0.034780917 0.04181731 1681.408315 -3.225673191 0.141649536 ENSQLDT(ph)SPPCLGGNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENSQLDTSPPCLGGNKK 17 1 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 ENS(0.024)QLDT(0.488)S(0.488)PPCLGGNKK 57.496 0.05984 289470000 296840 179080 243340 157420 280760 286580 245020 206520 240940 163130 TRUE FALSE 308559.4724 209835.597 249681.6403 188557.2061 233036.5155 220026.1382 225814.6922 203751.9372 232268.6165 195092.2002 1.58160845 1.075571431 1.279813545 0.966503048 1.194494271 1.127805919 1.157476782 1.04438792 1.190558189 1 17.57379657 4.741788356 24.95314724 1.118401027 1.581608626 0.702019426 0.091142926 150.7152773 1165101.102 0.019670022 0.140946338 55180.84619 -4.741788356 0.463207599 ENSQLDTS(ph)PPCLGGNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENSQLDTSPPCLGGNKK 17 1 Q9Y3E2 Q9Y3E2 BOLA1 BolA-like protein 1 1 ENS(0.001)QLDT(0.264)S(0.734)PPCLGGNKK 53.625 0.08186 179830000 280380 251880 295190 257270 387490 383730 291770 288840 311530 284680 TRUE FALSE 291449.6189 295138.4306 302882.8939 308157.2381 321624.5882 294614.523 268900.305 284968.5722 300318.0962 340457.5955 0.856052627 0.866887491 0.889634709 0.905126636 0.944683251 0.865348657 0.789820255 0.837016345 0.882101325 1 18.37711559 2.493519119 24.33470224 0.854339608 0.892941746 0 0.055970285 1245.563137 1848438.135 0.017817931 0.016376887 311.5438046 -2.493519119 0.038602138 ENTEGEYSGIEHVIVDGVVQSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENTEGEYSGIEHVIVDGVVQSIK 23 0 H0YL72;P50213;P50213-2;H0YLI6;H0YMU3 H0YL72 IDH3A "Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial" 0 100.19 0.0024238 26350000 18906 17899 18785 21153 22058 28823 22822 17252 22762 19846 FALSE TRUE 19652.42348 20973.01402 19274.55253 25337.00026 18308.58904 22129.29507 21033.15201 17020.76516 21942.80007 23734.44373 0.828012812 0.883653068 0.812092028 1.067520291 0.771393223 0.932370496 0.886186854 0.717133519 0.924512928 1 14.53469462 ENVEYIEREES(ph)DGEYDEFGR ddPTM_MDA-MB-175_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 283.43 4.08E-45 17862300000 3865586 4350800 4504970 4018900 5067380 5525470 4429280 4543250 4387320 4760700 TRUE FALSE 4018202.32 5098016.055 4622373.219 4813826.425 4206028.558 4242263.332 4082101.46 4482355.165 4229421.21 5693468.016 0.705756546 0.895414893 0.811873046 0.845499863 0.738746322 0.745110593 0.716979783 0.787280293 0.742855005 1 22.44087627 -1.381682263 3.164200001 1.002422781 0.779135115 0.580484034 0.056935272 10915784.15 14701126.16 245010.0213 0.014225057 0.041525774 1.381682263 -0.223287666 ENVEYIEREES(ph)DGEYDEFGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 183.31 2.27E-17 2195360000 1668900 1178990 1438150 994049 1940480 1774430 1634450 1430420 1632030 1074890 TRUE FALSE 1734789.461 1381472.361 1475629.37 1190668.925 1610637.903 1362345.524 1506337.538 1411247.56 1573293.559 1285494.115 1.349511787 1.074662532 1.147908304 0.926234442 1.252932925 1.059783555 1.171796526 1.097824986 1.22388235 1 20.29389158 4.743868978 24.6498768 1.11041745 1.349511909 0.375296221 0.094060658 469.647874 2180770.724 0.020371712 0.172522036 55445.84135 -4.743868978 0.239094459 ENVFQEHQTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ENVFQEHQTLK 11 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 164.11 2.32E-05 6662780000 4558590 5108790 5899180 4955900 6913580 6963170 6695440 6242340 6199250 4761060 FALSE TRUE 4738566.653 5986184.942 6052917.477 5936162.228 5738412.141 5346079.295 6170633.918 6158671.643 5976140.203 5693898.551 0.832218314 1.051333263 1.063053271 1.042547944 1.00781777 0.938913689 1.083727408 1.081626514 1.04956914 1 22.44098536 2.213795784 24.99425597 1.063621382 0.998745654 0.166612171 0.067221043 408.2769517 412056.6014 0.025120633 0.018561043 163.6047031 -2.213795784 -0.064875728 ENVKDYYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENVKDYYQK 9 1 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 94.616 0.0059403 0 281360 200600 250290 185740 315610 284980 263720 253470 274210 153840 FALSE TRUE 292468.3101 235051.4895 256812.763 222478.8176 261962.7249 218797.7139 243048.9373 250072.6492 264341.2357 183982.0026 1.589657173 1.27757871 1.39585807 1.209242287 1.423849731 1.189234332 1.321047352 1.359223434 1.436777685 1 17.48920512 -2.095277341 2.436791966 0.408182358 1.34674442 0.475680936 0.111707745 4513050.484 1195642.602 14846881.28 0.02475744 0.008030132 2.095277341 0.938562062 ENVPENSRPATGYPLPPQIFNESQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENVPENSRPATGYPLPPQIFNESQYR 26 1 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 130.78 6.27E-05 208580000 161480 166450 212410 176290 233560 280950 232760 206640 220130 205340 FALSE TRUE 167855.3551 195036.4927 217945.5791 211159.6358 193859.5546 215703.6203 214515.663 203870.3288 212207.5643 245572.4415 0.683526841 0.794211645 0.887500152 0.859866989 0.789419014 0.878370631 0.873533128 0.830184069 0.864134277 1 17.90578914 -4.999999999 0.023849979 2.121690857 9.75E-11 0.608653441 0.048576524 1756.905007 3.166584197 200.8207979 97.89191651 1.00E-05 4.999999999 -2.121690856 ENVPENSRPATGYPLPPQIFNESQYRGDYDAFFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENVPENSRPATGYPLPPQIFNESQYRGDYDAFFEAR 36 2 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ; 146.01 2.25E-13 164727000 25858 38681 35520 30854 45440 46751 28881 39705 42635 48884 FALSE TRUE 26878.89381 45324.16085 36445.68038 36956.82911 37716.12503 35893.78877 26617.23175 39172.81942 41100.57468 58461.88386 0.459767836 0.775277118 0.623409271 0.632152553 0.645140432 0.613969075 0.455292064 0.670057426 0.703031992 1 15.8352087 0.778250052 1.89269504 0.999328285 0.611242397 0.638985448 0.088560135 0.486713564 2.922036867 0.080580996 0.022503417 6.001365156 -0.778250052 -0.388085888 ENYSHHTQDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ENYSHHTQDDR 11 0 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 219.43 5.71E-12 823257000 294805.6 936822 890824 1045913 778942 1208834 884501 1058518 788021 809283 FALSE TRUE 306444.7527 1097713.891 914039.6053 1252791.47 646537.7171 928100.6236 815171.5004 1044330.298 759660.2781 967846.5092 0.316625363 1.134181795 0.94440554 1.294411312 0.668016789 0.958933689 0.84225287 1.079024709 0.784897472 1 19.88441874 4.74759669 24.88534695 0.968972969 0.316625002 0.569979351 0.169557929 781.8790329 2153246.145 0.038084657 0.467889119 55923.80214 -4.74759669 -0.652347967 ENYSHHTQDDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ENYSHHTQDDRR 12 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;; 156.81 4.77E-05 329844000 33478.7 217255.1 151308.8 173756.1 115375.3 173099 108691.1 136422.2 114701.1 225053.1 FALSE TRUE 34800.46493 254566.9734 155252.0316 208124.538 95763.84772 132899.3806 100171.6076 134593.6836 110573.0298 269147.946 0.129298646 0.945825436 0.576827852 0.773271879 0.355803747 0.493778171 0.372180464 0.500073233 0.410826207 1 18.03803989 -1.494697553 5.873558418 1.000519557 0.517433827 0.320465541 0.215080923 0.001380928 0.000118801 0.19652624 0.04627416 0.032011236 1.494697553 -0.48308573 ENYVWNVLLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ENYVWNVLLHR 11 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 ; 156.71 3.09E-05 330610000 622500 657820 693540 737740 945360 921980 705260 655220 679890 863880 FALSE TRUE 647076.7807 770795.4679 711614.2221 883662.7701 784668.0449 707864.1177 649979.8783 646437.8476 655420.8917 1033140.746 0.626320066 0.746070147 0.688787297 0.855316929 0.759497724 0.685157487 0.629130039 0.625701629 0.634396518 1 19.97860538 2.681335693 7.425020422 0.679271849 0.739850233 0 0.118129257 0.896783852 103.2421624 0.036275546 0.034261752 480.1044074 -2.681335693 0.060578384 EPAAAISRPR ddPTM_MDA-MB-175_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 ;;; 169.58 4.19E-06 789340000 461501 570980 542030 568450 581780 658800 548230 541760 501950 587990 FALSE TRUE 479721.4158 669041.3734 556155.7471 680887.7133 482889.2434 505803.6842 505258.3001 534498.5933 483884.9176 703195.3828 0.68220217 0.951430271 0.790897894 0.968276712 0.686707074 0.719293239 0.718517659 0.760099691 0.688123002 1 19.42356607 5.047600537 15.00783852 0.795191522 0.096907331 0.087805033 0.115081445 1125845.499 10152213.67 0.026724419 22120343.86 111583.6433 -5.047600537 -0.698284191 EPAESAAVAHERPPGGTGSADPERPPGATCPES(ph)PGPGPPHPLGVVESGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPAESAAVAHERPPGGTGSADPERPPGATCPESPGPGPPHPLGVVESGK 49 2 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 EPAESAAVAHERPPGGTGSADPERPPGAT(0.001)CPES(0.999)PGPGPPHPLGVVESGK;EPAESAAVAHERPPGGTGSADPERPPGAT(0.05)CPES(0.95)PGPGPPHPLGVVESGK 203.19 5.07E-39 638250000 286040 214253 264150 245548 295848 349560 361340 279291 303090 189352 TRUE FALSE 297333.0801 251049.2861 271033.966 294116.6615 245559.8626 268379.9876 333017.2266 275547.561 292181.8501 226451.899 1.313007669 1.108620803 1.196872127 1.298804129 1.08437979 1.185152294 1.470587034 1.216803931 1.290260101 1 17.78884511 EPAHLMSLFGGKPMIIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPAHLMSLFGGKPMIIYK 18 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ; 231.4 4.88E-20 914310000 1964940 2007420 2454820 1997530 2867900 2933450 2755010 2402210 2726570 2144980 FALSE TRUE 2042517.348 2352178.769 2518794.626 2392635.472 2380415.382 2252200.694 2539065.117 2370012.304 2628441.278 2565247.763 0.796226149 0.916940189 0.981891364 0.93271126 0.927947552 0.877966147 0.989793327 0.923892163 1.024634469 1 21.29066674 4.703752418 3.197188257 0.950375542 0.779670752 0.569976367 0.041695108 0.214131161 3.542886956 0.009681899 0.086791893 50553.63843 -4.703752418 -0.170704789 EPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EPAITSQNSPEAR 13 0 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITS(0.002)QNS(0.998)PEAR 289.2 1.80E-40 4719940000 1560280 1713770 1508270 1717970 1682440 1967440 1805860 1691580 1564320 1618480 TRUE FALSE 1621881.059 2008096.666 1547576.755 2057779.338 1396459.45 1510531.877 1664311.974 1668907.137 1508020.429 1935590.168 0.837925861 1.037459633 0.799537413 1.063127604 0.721464426 0.78039861 0.859847297 0.862221334 0.7791011 1 20.88434209 3.230517738 24.99997733 0.828855532 0.932224905 0.190819236 0.101207126 276.1213368 858277.5448 0.02703929 0.032858238 1700.269396 -3.230517738 0.103369373 EPALPLEPDSGGNTS(ph)PGVTANGEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPALPLEPDSGGNTSPGVTANGEAR 25 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 EPALPLEPDS(0.002)GGNT(0.121)S(0.811)PGVT(0.065)ANGEAR;EPALPLEPDSGGNT(0.132)S(0.864)PGVT(0.004)ANGEAR;EPALPLEPDS(0.003)GGNT(0.15)S(0.827)PGVT(0.02)ANGEAR 102.07 0.0032361 401420000 460780 547860 526310 489290 518340 629620 524270 553380 553370 546090 TRUE FALSE 478971.9502 641950.6932 540026.071 586070.1016 430232.7519 483400.297 483176.3475 545962.8462 533454.3218 653085.88 0.73339811 0.982949889 0.826883703 0.897385963 0.65876903 0.74017876 0.739835851 0.835974047 0.816821092 1 19.31691319 7.036810922 10.87932388 0.815853825 0.254969786 0 0.105823363 0 0 0.022593482 0 10884561.1 -7.036810922 -0.560884039 EPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPAPAEALPQQYPEPAPAALCGPPPRAPSR 30 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 EPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 103.94 0.00021493 76698000 9032.8 13353 12497 12495 10952 15666 11927 13136 10166 12390 TRUE FALSE 9389.421919 15646.27388 12822.68209 14966.47371 9090.382952 12027.80892 10992.13057 12959.93341 9800.127646 14817.58328 0.633667565 1.055926164 0.865369328 1.010048226 0.613486206 0.811725414 0.741830187 0.874632061 0.661385022 1 13.85502255 3.258098984 24.99996717 0.782737536 0.90116632 0.114913411 0.14497473 475.1960942 608024.7951 0.037152995 0.0502347 1811.752979 -3.258098984 0.118428784 EPCHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPCHSK 6 0 B1AN48;Q9UBC9 B1AN48 SPRR3 Small proline-rich protein 3 0 ;; 82.263 0.059704 411319000 714407 559614 740410 527841 902610 811070 877790 726090 800820 641770 FALSE TRUE 742612.34 655723.3513 759705.6929 632246.3744 749184.6746 622711.2844 808986.5261 716357.9512 771998.6446 767512.5441 0.967557268 0.854348709 0.989828373 0.823760314 0.97612043 0.811336947 1.054036878 0.933350154 1.005844987 1 19.5498308 2.226275038 24.99994726 0.988577827 0.90513244 0.334394692 0.064707956 274.5873452 558754.3216 0.021859529 0.016259141 168.3740035 -2.226275038 -0.083445387 EPDCFKDIVNMLMHHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPDCFKDIVNMLMHHDR 17 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 211.06 1.81E-12 1452110000 1180660 1028650 1261730 1057820 1579820 1496260 1179000 1193710 1345350 1135160 FALSE TRUE 1227273.368 1205312.636 1294611.72 1267053.639 1311282.761 1148776.291 1086586.899 1177710.27 1296931.116 1357572.868 0.904020254 0.887843787 0.95362227 0.933322747 0.965902304 0.846198623 0.800389375 0.867511644 0.955330757 1 20.37259821 2.733628985 24.98596631 0.876536355 0.928273494 0.045863517 0.057060303 778.3273026 3943358.015 0.018198357 0.017671668 541.5380606 -2.733628985 0.051737139 EPEAASS(ph)RGSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAAS(0.122)S(0.848)RGS(0.03)PVR 136.32 0.00019386 385100000 301460 403360 388720 305210 455730 426960 288560 368770 394960 475160 TRUE FALSE 313361.8736 472633.9423 398850.3625 365579.627 378265.1774 327805.0106 265941.9132 363827.2413 380745.4668 568258.5045 0.55144247 0.831723482 0.701881907 0.643333314 0.66565687 0.576858961 0.467994603 0.640249532 0.67002159 1 19.11618784 -1.496961498 5.58641991 1.000560367 0.63804329 0.584215039 0.09141397 0.000664581 5.98E-05 0.09219897 0.021699049 0.031844798 1.496961498 -0.362517076 EPEAASSRGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EPEAASSRGSPVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EPEAASS(0.001)RGS(0.999)PVR;EPEAAS(0.115)S(0.066)RGS(0.818)PVR;EPEAAS(0.052)S(0.052)RGS(0.896)PVR;EPEAAS(0.006)S(0.029)RGS(0.966)PVR 168.67 1.81E-05 1857085000 1363932 1837094 1718377 1163114 1888606 1982534 1320531 1621819 1634250 1943168 TRUE FALSE 1417781.089 2152600.604 1763159.316 1393174.478 1567581.427 1522120.524 1217024.33 1600081.169 1575433.662 2323894.565 0.610088388 0.926290132 0.758708825 0.599499865 0.674549289 0.654986912 0.523700321 0.688534322 0.677928201 1 21.14811318 -0.906192296 3.637043229 1.00003252 0.679549452 0.472295846 0.101676238 18921911.24 36062104.18 8398.834418 0.025494679 0.124110265 0.906192296 -0.320483068 EPELGLEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPELGLEELLR 11 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 77.662 0.074451 14008000 18207 19764 18500 19279 23510 25107 19076 19723 18293 15945 FALSE TRUE 18925.82642 23158.31326 18982.1252 23092.32866 19513.7786 19276.27975 17580.77327 19458.64545 17634.6385 19069.11746 0.992485701 1.214440747 0.995438055 1.210980461 1.023318391 1.010863758 0.921950022 1.020427164 0.924774759 1 14.21895046 3.011365829 24.45570323 0.980111098 1.105263316 0.387311996 0.075688642 162.8270416 350349.231 0.019903396 0.023768901 1026.51625 -3.011365829 0.125152218 EPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPEQLR 6 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 103.02 0.081529 746080000 300340 336640 339950 348660 332360 422190 424300 327080 334560 322860 FALSE TRUE 312197.6551 394455.3013 348809.3763 417623.9074 275865.5659 324142.7709 391042.2573 322696.0276 322519.251 386118.2355 0.808554547 1.021592002 0.903374522 1.081595918 0.714458786 0.839490967 1.012752627 0.835744075 0.835286245 1 18.55868317 3.251497138 24.99995383 0.870962616 0.955022608 0.12521041 0.10455854 477.2777267 922338.5434 0.027970506 0.037638569 1784.420228 -3.251497138 0.084059992 EPEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPEQLRK 7 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646;P51991;P51991-2 F8W6I7;P51991;P51991-2 HNRNPA1;HNRNPA1L2;HNRNPA3 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2;Heterogeneous nuclear ribonucleoprotein A3" 0 82.716 0.038057 1029500000 759500 624460 763640 635300 728270 798760 842690 762140 700760 521830 FALSE TRUE 789485.6465 731706.1474 783541.0857 760960.4438 604478.9255 613260.0953 776637.7558 751924.7599 675539.7845 624072.5975 1.265054177 1.172469598 1.255528746 1.219346029 0.968603537 0.982674288 1.244467004 1.204867451 1.082469872 1 19.25135434 3.430473402 24.99204664 1.104114008 1.2272089 0.381288315 0.089162648 164.6114471 88191.68707 0.027511999 0.037251436 2694.47031 -3.430473402 0.123094891 EPES(ph)PPASAPIPLFGADTIGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPESPPASAPIPLFGADTIGQR 22 0 Q96AY4 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 EPES(0.994)PPAS(0.006)APIPLFGADTIGQR 58.997 0.019329 0 7971.3 8337.6 9316.9 8774.7 10501 11272 8934.7 7914.5 9952.1 7728.4 TRUE FALSE 8286.013079 9769.517942 9559.706068 10510.30947 8716.043771 8654.248829 8234.374868 7808.419073 9593.925865 9242.632011 0.896499295 1.057006049 1.034305602 1.137155462 0.94302616 0.9363403 0.890912335 0.844826351 1.038007989 1 13.17408803 3.026823266 24.45310458 0.922903067 1.034149611 0.232882629 0.075215208 198.6119626 181060.4875 0.021735738 0.025978532 1063.710059 -3.026823266 0.111246544 EPFFHGHDNYDQLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPFFHGHDNYDQLVR 15 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;; 246.5 2.03E-18 608300000 172578 221180 206319 220960 196855 242714 232020 209006 209785 194555 FALSE TRUE 179391.5127 259165.9445 211695.8426 264665.2285 163393.6574 186347.3519 213833.6661 206204.6164 202234.8788 232674.3273 0.770998308 1.11385707 0.909837562 1.137492183 0.702241882 0.800893481 0.919025612 0.88623708 0.869175732 1 17.82795251 3.240694482 24.99998417 0.860352103 0.98716068 0.193820466 0.119826054 87.21709796 1021807.874 0.032004899 0.04129376 1740.581974 -3.240694482 0.126808577 EPFGTEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPFGTEGR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 122.18 0.0032608 862820000 577920 582310 548360 645000 571850 729870 705300 631760 609710 533090 FALSE TRUE 600736.7279 682317.2128 562650.7121 772579.0749 474647.1413 560368.7538 650016.743 623292.2906 587766.6562 637538.7789 0.942274804 1.070236408 0.882535668 1.211815031 0.744499248 0.878956343 1.019572087 0.977653927 0.921930831 1 19.28215357 3.236256961 24.99986045 0.930922154 1.019525525 0.176058934 0.107995381 124.5243848 1351375.416 0.030281269 0.037884489 1722.887661 -3.236256961 0.088603371 EPFHSILSVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPFHSILSVLK 11 0 Q8NCW5-2;Q8NCW5;Q5T3I4 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ; 145.91 3.60E-05 789730000 1825380 1727920 2043960 1781540 3401050 2892540 2594400 2106520 2216750 2315390 FALSE TRUE 1897447.412 2024676.819 2097227.277 2133923.295 2822940.736 2220791.422 2391044.149 2078285.545 2136969.601 2769046.34 0.68523498 0.731181992 0.757382513 0.770634736 1.019463162 0.802005871 0.863490117 0.750541988 0.771734864 1 21.40095777 -5 0.025473831 2.072905089 2.25E-12 0.357298823 0.085494973 2659.296142 5.114783219 303.8306274 141.0652174 1.00E-05 5 -2.072905089 EPGFEAGPEAS(ph)DDDLWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPGFEAGPEASDDDLWTR 18 0 H9KVB4;O15417;O15417-2;H7C177 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 EPGFEAGPEAS(1)DDDLWTR 236.16 8.60E-24 115130000 21170 24064 33211 28965 35825 34519 25942 23609 26795 24456 TRUE FALSE 22005.80795 28196.80481 34076.50594 34694.19055 29735.4793 26502.48539 23908.59825 23292.55997 25830.65318 29247.68496 0.752394864 0.96406963 1.165100964 1.186220058 1.016678049 0.906139594 0.817452673 0.796389868 0.883169154 1 14.83603482 2.636603326 3.350249472 0.850644723 1.032183229 0.222983255 0.123344892 0.326642714 6.931723403 0.044729578 0.042059745 433.1151008 -2.636603326 0.181538505 EPHCMVVFDHCNEFSVNITEDFIEHLSEGALAIEVYGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPHCMVVFDHCNEFSVNITEDFIEHLSEGALAIEVYGHK 39 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 90.246 0.00012535 57407000 20948 47979 50565 46748 64457 71028 47050 57118 58781 43832 FALSE TRUE 21775.04322 56219.02003 51882.76544 55994.61487 53500.62216 54532.82344 43362.09806 56352.42664 56665.48329 52420.04119 0.415395385 1.072471878 0.989750566 1.068190974 1.02061389 1.040304857 0.827204578 1.075016833 1.080988912 1 15.67783087 4.741788918 24.98321091 1.016789321 0.41539516 0.866039299 0.071258461 100.770236 779805.2088 0.016714508 0.120253434 55180.91756 -4.741788918 -0.60139416 EPLGPALAHELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPLGPALAHELR 12 0 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 162.32 6.30E-05 133133000 106905 122580 118032 130934 129688 141928 135462 129846 109675 102111 FALSE TRUE 111125.6919 143632.1615 121108.0109 156832.3544 107643.6801 108967.3729 124844.1345 128105.6268 105727.8182 122117.6954 0.909988447 1.17617812 0.991731874 1.284272143 0.881474873 0.892314358 1.022326323 1.0490341 0.865786222 1 16.89791274 3.18858968 24.99999222 0.96278174 1.089605499 0.273775163 0.109811961 152.1265284 76106.84799 0.030831691 0.036850981 1543.795176 -3.18858968 0.126823759 EPLIPAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK;EPLIPAS(1)PK 103.88 0.0035146 1363301000 4330450 1726961 2396800 1965061 3480730 3736790 3270040 2545310 2695150 1537853 TRUE FALSE 4501419.51 2023553.118 2459262.577 2353744.201 2889076.758 2868977.154 3013725.72 2511194.283 2598152.078 1839165.851 2.447533215 1.100255921 1.33716194 1.279788986 1.570862549 1.559933897 1.638637276 1.365398493 1.412679599 1 20.81062015 -3.520384386 0.141174252 4.31E-39 1.689396562 0.214007774 0.335012544 153.1789797 1.968539102 48.51250985 2.100114689 0.000301728 3.520384386 1.689396562 EPNEDCKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 98.048 0.0057254 294550000 427520 391530 358860 368140 482300 508430 467370 418750 369720 308110 FALSE TRUE 444398.8197 458772.2318 368212.1864 440956.9932 400318.8183 390354.8378 430736.3182 413137.3412 356413.8494 368478.2554 1.206038113 1.245045603 0.999277925 1.196697463 1.086410968 1.059370077 1.168959937 1.121198701 0.967258839 1 18.49121996 7.999999998 0.098489677 0.934996578 1.690616255 0.373653057 0.073472498 154.6760044 1.080785385 0.963906213 15.79526303 99999999.5 -7.999999998 0.755619676 EPPAAAPSAGGAAPCS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPPAAAPSAGGAAPCSPR 18 0 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 EPPAAAPSAGGAAPCS(1)PR;EPPAAAPSAGGAAPCS(1)PR 160.05 1.10E-09 101610000 114959 199119 181429 179864 183416 227828 142896 158936 165901 255918 TRUE FALSE 119497.6701 233316.1393 186157.1888 215440.5624 152239.0138 174918.3998 131695.4381 156805.7229 159930.2554 306060.2323 0.390438409 0.76232099 0.608237102 0.703915568 0.497415207 0.571516262 0.430292551 0.512336156 0.522545037 1 18.22345608 -1.454235847 6.094908093 1.000208747 0.557409339 0.602916976 0.108221857 0.000305028 2.73E-05 0.104120864 0.024530166 0.035136957 1.454235847 -0.442799408 EPPSS(ph)PLQPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPPSSPLQPQK 11 0 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EPPS(0.026)S(0.974)PLQPQK;EPPS(0.157)S(0.843)PLQPQK 157.22 3.22E-05 431360000 622550 468340 569710 534570 595650 749090 789890 564290 593810 375890 TRUE FALSE 647128.7547 548773.7518 584557.1106 640306.3505 494401.6258 575125.2001 727976.3578 556726.6155 572438.8941 449538.4487 1.439540392 1.220749312 1.30034953 1.424363928 1.099798309 1.279368209 1.619386195 1.238440488 1.273392511 1 18.77808499 0.727335362 1.944013522 1.000636897 1.327461501 0.348472857 0.134373176 1.227312831 6.934496513 0.125800018 0.034914901 5.337468958 -0.727335362 0.326824604 EPQLAFHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPQLAFHQR 9 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 111.06 0.0021866 391010000 355820 370490 398100 349060 478940 492850 459460 371770 406370 438840 FALSE TRUE 369868.0484 434118.7755 408474.813 418103.0262 397529.9499 378393.0567 423446.3246 366787.0312 391744.8231 524822.2959 0.704749115 0.82717289 0.778310709 0.796656372 0.757456291 0.720992724 0.806837529 0.698878523 0.746433271 1 19.00146949 -1.332612076 6.974777357 1.000005319 0.759736219 0.754743346 0.041091134 3.33E-06 3.19E-07 0.039031136 0.009199523 0.046493038 1.332612076 -0.2402691 EPRPNS(ph)SPSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.874)S(0.081)PS(0.045)PSPGQASETPHPRPS;EPRPNS(0.417)S(0.417)PS(0.166)PSPGQASETPHPRPS 172.1 3.06E-12 236620000 48786 80883 68125 83639 80801 93558 81003 81821 71165 80050 TRUE FALSE 50712.10895 94774.02607 69900.39347 100182.5446 67066.47488 71830.57239 74653.7732 80724.32333 68603.78555 95734.26485 0.529717432 0.989969748 0.730150209 1.046464865 0.700548283 0.750312049 0.779802021 0.843212443 0.716606386 1 16.54674776 -1.187788148 4.725982548 1.000029188 0.798764711 0.167710647 0.140031576 3.87E-05 6.65E-06 0.121895851 0.028726964 0.064895092 1.187788148 -0.201264477 EPRPNSS(ph)PSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.087)S(0.701)PS(0.212)PSPGQASETPHPRPS 254.09 4.41E-44 92770000 23879 27823 26439 25009 31995 33984 27657 33791 29048 28111 TRUE FALSE 24821.76136 32601.38382 27128.02206 29955.70556 26556.50133 26091.73103 25489.17207 33338.08692 28002.56815 33618.81223 0.738329516 0.969736337 0.806929819 0.891039973 0.789929791 0.776105082 0.758181815 0.991649755 0.832943412 1 15.03698113 1.735286687 20.03150781 0.93409675 0.824019287 0.346905185 0.076837619 0.151445757 829.9119829 0.034286321 0.018995759 54.36090607 -1.735286687 -0.110077463 EPRPNSSPS(ph)PSPGQASETPHPRPS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 EPRPNS(0.001)S(0.005)PS(0.75)PS(0.244)PGQASETPHPRPS;EPRPNS(0.034)S(0.034)PS(0.772)PS(0.161)PGQASETPHPRPS;EPRPNS(0.051)S(0.051)PS(0.891)PS(0.007)PGQASETPHPRPS;EPRPNS(0.002)S(0.003)PS(0.88)PS(0.116)PGQASETPHPRPS;EPRPNS(0.006)S(0.064)PS(0.914)PS(0.016)PGQASETPHPRPS;EPRPNS(0.006)S(0.085)PS(0.908)PS(0.001)PGQASETPHPRPS 274.96 2.77E-52 10218940000 616712 1043520 940143 1117130 1066040 1254570 899721 1046870 930604 967890 TRUE FALSE 641060.266 1222736.443 964643.8989 1338094.98 884834.9016 963215.1307 829198.517 1032838.42 897111.7438 1157529.514 0.553817642 1.056332843 0.833364409 1.155992105 0.764416709 0.832130083 0.716351943 0.892278259 0.775022782 1 20.14261755 EPRPNSSPSPSPGQASETPHPRPS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPRPNSSPSPSPGQASETPHPRPS 24 2 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 181.81 1.81E-17 409870000 80157 126684 129503 129817 135385 162283 122343 139367 129368 128278 FALSE TRUE 83321.66025 148440.9915 132877.9546 155494.4151 112372.3061 124595.2327 112753.436 137499.0133 124712.071 153411.6181 0.543124838 0.967599413 0.866153139 1.013576528 0.732488891 0.812162952 0.734973253 0.8962751 0.812924552 1 17.22704822 -0.257082554 1.022178425 1.002809581 0.828574635 0.150902056 0.126361883 34.53365207 25.08673961 0.52781907 0.036067526 0.553244934 0.257082554 -0.174234945 EPS(ph)PALGPNLDGSGLLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EPSPALGPNLDGSGLLPR 18 0 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR;EPS(1)PALGPNLDGSGLLPR 211.13 3.53E-16 588398000 87020 74492 84446 90120 93085 112140 124230 95555 89466 68082 TRUE FALSE 90455.61679 87285.42153 86646.73213 107945.467 77262.44495 86097.1845 114492.528 94274.24152 86246.13614 81421.36439 1.11095678 1.072021111 1.064176863 1.325763426 0.94892103 1.057427435 1.406173046 1.157856322 1.059256828 1 16.31311978 EPS(ph)PALGPNLDGSGLLPRPIFYCSFPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPSPALGPNLDGSGLLPRPIFYCSFPTR 28 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR;EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR;EPS(1)PALGPNLDGSGLLPRPIFYCSFPTR 152.62 2.48E-08 571662000 28426 27985.8 34773.4 24884.7 33859.2 36322 35468.6 23671.5 35327.6 26285.3 TRUE FALSE 29548.28043 32792.14345 35679.62337 29806.81939 28103.82528 27886.76597 32688.47845 23354.22226 34056.16658 31435.40127 0.939968292 1.04315969 1.13501409 0.948192744 0.89401834 0.887113408 1.039861975 0.742927442 1.08336987 1 14.94010256 3.501704222 21.06919072 0.920346181 1.040066239 0.147756298 0.099762079 149.104004 127789.9151 0.025743313 0.039538605 3174.711187 -3.501704222 0.119720057 EPS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EPSPEK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK;EPS(1)PEK 101.43 0.038321 5414740000 13013400 6183810 8311250 7179260 10861720 14272500 15203200 9403230 9597070 4098900 TRUE FALSE 13527179.08 7245831.264 8527848.003 8599296.2 9015448.714 10957928.18 14011533.46 9277195.082 9251673.325 4902000.977 2.759521906 1.478137458 1.739666729 1.754242041 1.839136458 2.235399019 2.858329389 1.892532279 1.887325884 1 22.22493934 2.759718433 23.09468788 2.091088044 1.87134219 0 0.534458864 1220.662216 1332401.897 0.157365233 0.166694282 575.0669823 -2.759718433 -0.219745853 EPS(ph)PEKNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EPSPEKNSK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(1)PEKNSK;EPS(0.996)PEKNS(0.004)K 126.83 0.00028006 5912043000 6263900 2283579 3641720 2026927 5590758 5166359 4720133 3558518 4257706 1641234 TRUE FALSE 6511203.609 2675765.929 3736626.215 2427847.111 4640442.952 3966550.419 4350156.642 3510821.887 4104471.993 1962802.379 3.317299632 1.363237562 1.903720036 1.236928963 2.364192647 2.020860817 2.216298843 1.788678231 2.091128499 1 20.90448349 -1.492654854 2.694691825 0.957672434 1.988669997 0.240862064 0.545262911 18713749.43 19193644.48 5880423.415 0.122474582 0.032162155 1.492654854 1.030997564 EPS(ph)PHPGVGLTSGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPSPHPGVGLTSGSSR 16 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EPS(1)PHPGVGLTSGSSR 103.9 0.00090374 314280000 319020 310840 339590 392510 369790 457870 443540 391330 355220 315710 TRUE FALSE 331615.1559 364224.352 348439.9944 470147.3065 306933.2279 351536.6316 408774.1758 386084.8614 342435.7016 377567.3299 0.878294094 0.964660666 0.922855255 1.245201238 0.812923163 0.931056804 1.0826524 1.022558974 0.90695268 1 18.52637441 4.605323486 1.863887258 0.998137509 0.863951716 0.086464399 0.110004612 1.542591392 6.878381246 0.028084349 0.328359725 40301.71113 -4.605323486 -0.134185793 EPS(ph)PLPELALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPSPLPELALR 11 0 Q13207 Q13207 TBX2 T-box transcription factor TBX2 1 EPS(1)PLPELALR;EPS(1)PLPELALR 135.08 0.00013365 66347000 45788 50337 53565 58177 63678 79751 76704 64759 69003 59601 TRUE FALSE 47595.7456 58981.98818 54960.9479 69684.23696 52854.03631 61230.03889 70691.74005 63891.01153 66519.59551 71278.67482 0.667741729 0.827484354 0.771071404 0.977630927 0.741512611 0.85902325 0.991765633 0.89635521 0.933232775 1 16.12118289 7.13093468 0.202649908 0.994649859 8.70E-14 0.55995239 0.071759511 28.21274955 0.465882924 0.127543121 8.332626752 13518692.22 -7.13093468 -0.994649859 EPSAT(ph)PPISNLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPSATPPISNLTK 13 0 J3KP58;P30622-2;P30622-1;P30622;F5H6A0;F5H1T5 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 EPSAT(0.999)PPIS(0.001)NLTK 113.53 0.0091086 73446000 344360 270680 303960 283620 385490 399650 392450 328550 375450 248200 TRUE FALSE 357955.5987 317167.1844 311881.4473 339719.1895 319964.5475 306837.3443 361688.7435 324146.3246 361937.6278 296830.0379 1.205927814 1.068514449 1.050707164 1.144490604 1.077938573 1.033713927 1.218504522 1.092026693 1.219342996 1 18.17927757 2.255702695 24.99803898 1.137781595 1.094796772 0.04948046 0.074642684 657.148716 958308.708 0.024216046 0.020210077 180.1783872 -2.255702695 -0.042984823 EPSIDLLQAFVEHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPSIDLLQAFVEHWK 15 0 Q86V87 Q86V87 FAM160B2 Protein FAM160B2 0 130.06 6.21E-05 39155000 85817 86582 90571 96184 108920 110950 102590 105280 103620 68239 FALSE TRUE 89205.12143 101451.785 92931.35466 115208.9081 90405.81731 85183.54396 94548.72773 103868.8938 99890.73644 81609.12554 1.093077776 1.243142655 1.138737293 1.411715998 1.107790541 1.043799249 1.158555825 1.272760774 1.224014297 1 16.31644286 EPSVPASCAVSATYERS(ph)PS(ph)PAHLPDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPSVPASCAVSATYERSPSPAHLPDDPK 28 1 Q92615;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 2 EPSVPASCAVSAT(0.005)YERS(0.995)PS(1)PAHLPDDPK;EPSVPASCAVS(0.004)AT(0.018)Y(0.009)ERS(0.97)PS(1)PAHLPDDPK;EPSVPASCAVS(0.002)AT(0.018)Y(0.006)ERS(0.974)PS(1)PAHLPDDPK 204.51 4.15E-25 644290000 432570 281909 351060 292563 437810 534180 470110 377400 387120 259536 TRUE FALSE 449648.1976 330324.6778 360208.912 350431.0882 363391.2126 410124.7906 433261.5498 372341.5703 373187.6268 310387.1101 1.448669043 1.064234522 1.160515048 1.129013019 1.170767731 1.321333191 1.395874815 1.199603844 1.202329654 1 18.24370912 0.684948415 2.400157886 1.000086253 1.230984247 0.27520633 0.114208563 2.690214636 18.67642925 0.109844384 0.029501259 4.841148617 -0.684948415 0.230897995 EPTEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EPTEEER 7 0 Q15056;Q15056-2 Q15056;Q15056-2;REV__B4E135 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 173.85 0.001973 1560160000 1791800 1937360 1957810 2088810 1888150 2300050 2343690 2062770 1809090 1813760 FALSE TRUE 1862541.648 2270086.509 2008832.137 2501970.384 1567202.937 1765898.245 2159985.454 2035121.942 1743981.204 2169131.545 0.858657766 1.046541651 0.926099729 1.153443363 0.722502488 0.814103805 0.995783524 0.938219697 0.803999743 1 21.04868612 3.239880388 24.99999024 0.885325295 0.994776313 0.217581075 0.108372704 59.86546368 1133993.473 0.03047217 0.039107156 1737.322276 -3.239880388 0.109451018 EPTGVEENKTDSLFVLPSRDDAT(ph)PVRDEPMDAESITFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EPTGVEENKTDSLFVLPSRDDATPVRDEPMDAESITFK 38 3 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 EPTGVEENKTDSLFVLPS(0.002)RDDAT(0.997)PVRDEPMDAESITFK;EPTGVEENKTDSLFVLPS(0.001)RDDAT(0.999)PVRDEPMDAESITFK;EPT(0.006)GVEENKT(0.005)DS(0.019)LFVLPS(0.2)RDDAT(0.763)PVRDEPMDAES(0.006)IT(0.002)FK 151.44 9.85E-14 607460000 295386 195423 260564 175845 342563 313064 312629 261988 296710 165607 TRUE FALSE 307048.0674 228985.3801 267354.5119 210626.6162 284334.2636 240359.6305 288124.3221 258476.4794 286031.4651 198054.5209 1.550320921 1.156173457 1.349903606 1.063477951 1.43563632 1.213603352 1.45477276 1.305077401 1.444205685 1 17.59553811 -1.572233329 2.822551658 0.98005709 1.321754492 0.322658285 0.143105157 18050522.6 17772938.69 2690102.692 0.031016658 0.026777293 1.572233329 0.341697402 EPTPSIAS(ph)DISLPIATQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-2;A0FGR8;A0FGR8-6;A0FGR8-5 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 EPTPS(0.001)IAS(0.999)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR;EPTPSIAS(1)DISLPIATQELR 250.47 1.12E-30 276618000 114207 136057 137709 188096 141289 215758 140882 122526 131986 146859 TRUE FALSE 118715.9805 159423.7314 141297.8097 225300.8274 117272.7462 165651.4743 129839.3007 120883.7394 127235.8496 175633.2093 0.675931283 0.907708354 0.804505083 1.282791724 0.667713963 0.943167155 0.739263954 0.688273817 0.724440726 1 17.42220613 2.227019248 24.76700611 0.75330368 0.886735083 0.045104352 0.180492035 442.3646343 949277.611 0.064755785 0.048242429 168.6627774 -2.227019248 0.133431403 EPVQTLYSQSPALELDKFLEDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EPVQTLYSQSPALELDKFLEDVR 23 1 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 0 93.633 0.0041087 61388000 86321 80968 89291 66866 109590 109610 123580 116380 105800 65948 FALSE TRUE 89729.01973 94873.62416 91617.99681 80091.89522 90961.93094 84154.73866 113893.4767 114820.1165 101992.2787 78869.24795 1.13769336 1.202922896 1.161644103 1.015502205 1.153325704 1.067015863 1.444079659 1.455828722 1.293181833 1 16.26717527 2.243667845 24.99986514 1.35292017 1.124895772 0.265585284 0.130671098 118.9070625 582051.8266 0.044362245 0.03606226 175.2539619 -2.243667845 -0.228024397 EPWLLPSQHNDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EPWLLPSQHNDIIR 14 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 117.08 0.00032416 296710000 162230 373390 339630 412740 372860 441780 309740 339740 299880 349570 FALSE TRUE 168634.9657 437516.8279 348481.0368 494378.7401 309481.3904 339183.2902 285461.7694 335186.341 289087.3774 418061.5486 0.403373537 1.046536878 0.833563952 1.182550134 0.740277099 0.811323814 0.682822351 0.801763143 0.691494777 1 18.67335583 EQAAEHYK ddPTM_MDA-MB-175_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 ;; 85.676 0.016574 1036710000 1392330 1156260 1268170 1075980 1627610 1641290 1409720 1235800 1339530 1102790 FALSE TRUE 1447300.264 1354838.661 1301219.552 1288805.633 1350949.434 1260125.271 1299222.463 1219236.122 1291320.577 1318860.586 1.097386849 1.027279664 0.986624034 0.977211425 1.024330735 0.955465107 0.985109781 0.924461717 0.979118332 1 20.33086064 8 0.590042581 0.966848606 8.690514871 0.682207787 0.025008773 88.23933231 0.705138091 0.011010911 876.0064094 100000000 -8 7.723666265 EQADYCVSHMKPYVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQADYCVSHMKPYVDGK 17 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 121.77 7.95E-05 428720000 312420 256088 327500 229192 439920 397980 329370 329280 419390 259307 FALSE TRUE 324754.5828 300069.1219 336034.919 274525.4935 365142.5555 305555.1764 303553.1188 324866.5402 404296.2358 310113.2419 1.047212885 0.967611444 1.083587779 0.885242732 1.177449093 0.985301932 0.97884604 1.047573906 1.303705167 1 18.24243561 1.437531968 14.73857949 1.159819606 1.018691085 0.218115941 0.099797151 1.557510326 578.0744777 0.051774246 0.022394925 27.38621211 -1.437531968 -0.141128521 EQAEAEVASLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQAEAEVASLNR 12 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ; 213.63 1.48E-08 632690000 309870 360920 362910 390180 416700 470970 428530 407610 342300 356690 FALSE TRUE 322103.9069 422905.2024 372367.7327 467356.4394 345869.4828 361594.3551 394940.6988 402146.6547 329980.6899 426576.5763 0.755090469 0.9913934 0.87292119 1.09559799 0.810802801 0.847665754 0.925837753 0.942730279 0.773555578 1 18.70244522 EQAEAEVASLNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQAEAEVASLNRR 13 1 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4 P06753-2;P06753-3 TPM3 Tropomyosin alpha-3 chain 0 ;; 240.59 1.20E-16 2818240000 1574940 1892210 1819650 1505260 2058830 2203440 1542280 1889470 1764590 2362720 FALSE TRUE 1637119.847 2217182.348 1867071.574 1802995.935 1708870.812 1691724.453 1421392.064 1864144.745 1701082.751 2825649.747 0.579378194 0.784662837 0.660758318 0.638081891 0.604770925 0.598702813 0.503031936 0.659722511 0.602014723 1 21.43015122 -1.375990892 4.927526594 1.000313684 0.627338984 0.729480518 0.068377551 0.000239898 3.04E-05 0.067404494 0.015874234 0.042073545 1.375990892 -0.3729747 EQAEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQAEEER 7 0 Q9UII2;A0A0B4J230;Q9UII2-3;Q9UII2-2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 ; 147.16 0.0050496 244020000 380770 514650 410380 488530 359520 590620 382720 388860 389920 524630 FALSE TRUE 395803.0936 603037.1341 421074.8399 585159.7759 298408.9188 453457.4559 352721.4063 383647.9677 375886.8554 627421.2039 0.630841118 0.961136044 0.671119875 0.932642653 0.475611785 0.722732119 0.56217642 0.611467967 0.599098107 1 19.25907476 3.244931283 24.99997519 0.636723902 0.80139104 0.136262082 0.161783297 232.6645205 913023.2216 0.040721432 0.05382709 1757.645486 -3.244931283 0.164667138 EQAIGEYEDLRAENQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQAIGEYEDLRAENQK 16 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;; 141.13 1.49E-06 851021000 593547 534347 607714 487714 711973 749374 699929 645711 665676 487748 FALSE TRUE 616980.6939 626116.9406 623551.5261 584182.3735 590952.0838 575343.2454 645066.7361 637056.3002 641718.4508 583312.8821 1.057718272 1.073380959 1.068982951 1.001490609 1.013096233 0.986337287 1.105867461 1.092134804 1.100127342 1 19.15391041 2.217878342 24.99998802 1.084118541 1.03454406 0.196658643 0.038700536 331.8576848 401135.3319 0.014798592 0.010940815 165.1499102 -2.217878342 -0.049574481 EQALQEAMEQLEQLELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQALQEAMEQLEQLELER 18 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 150.59 1.25E-07 8165600 5455.5 8670.8 8241.9 10283 10548 9984.4 11990 9827.4 7137.3 11029 FALSE TRUE 5670.887353 10159.94245 8456.690685 12316.94671 8755.054728 7665.674415 11050.19247 9695.679777 6880.429967 13189.92139 0.429940952 0.770280743 0.641147922 0.93381502 0.66376853 0.581176657 0.837775461 0.735082454 0.521642985 1 13.68714835 -2.180161538 2.481357991 1.853214645 0.695234733 0.308914894 0.142090745 17527811.84 1404734.63 85243274.17 0.034885189 0.006604477 2.180161538 -1.157979912 EQCCYNCGKPGHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQCCYNCGKPGHLAR 15 1 P62633-2;P62633;P62633-7;P62633-3;P62633-5;P62633-6;P62633-8;P62633-4 P62633-2;P62633-8 CNBP Cellular nucleic acid-binding protein 0 ;;; 192.4 8.15E-08 3561260000 1764940 1616300 1760180 1671570 1981760 2174230 1911160 1863850 1957290 1598170 FALSE TRUE 1834621.194 1893886.952 1806051.737 2002201.557 1644901.143 1669298.033 1761358.285 1838868.139 1886847.515 1911300.813 0.959880926 0.990889 0.944933275 1.047559622 0.860618659 0.873383207 0.921549488 0.962102944 0.98720594 1 20.86612343 3.242401545 24.9999965 0.930706618 0.983257893 0.211915246 0.048445686 162.0657849 1054852.701 0.014045207 0.018336195 1747.437073 -3.242401545 0.052551274 EQDDLLVLLADQDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQDDLLVLLADQDQK 15 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 179.39 4.27E-11 0 19662 13274 16854 13605 20629 22288 21484 18315 19744 12236 FALSE TRUE 20438.27094 15553.70624 17293.22909 16296.02839 17122.48995 17111.94978 19800.02794 18069.51738 19033.4173 14633.40993 1.396685465 1.06289008 1.181763456 1.113617979 1.170095694 1.169375413 1.353069998 1.234812492 1.300682301 1 13.83697837 EQDFFFELDAMDHLQSFIADCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQDFFFELDAMDHLQSFIADCDR 23 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 99.366 0.0026858 15588000 12249 14640 13578 14721 18046 18400 15422 15742 14002 11603 FALSE TRUE 12732.59998 17154.30612 13931.85383 17632.76986 14978.54737 14126.87885 14213.18334 15531.00424 13498.07076 13876.3857 0.917573225 1.236222925 1.003997304 1.270703355 1.079427143 1.018051758 1.02427128 1.119239878 0.972736781 1 13.76034423 3.000059585 24.99999999 1.041744221 1.117240059 0.11175205 0.101870257 4.696542933 1968771.486 0.027621177 0.032705893 1000.137208 -3.000059585 0.075495837 EQDFFFELDAMDHLQSFIADCDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EQDFFFELDAMDHLQSFIADCDRR 24 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;;;;; 242.05 8.46E-38 1155858000 770209 925336 891090 865004 1039278 1133793 864810 912445 925136 1006036 FALSE TRUE 800617.4461 1084255.26 914312.5374 1036099.209 862621.8968 870486.7585 797023.9324 900215.1672 891840.5361 1203149.492 0.66543472 0.901180831 0.759932613 0.861155838 0.716969838 0.723506733 0.662447965 0.748215557 0.741254966 1 20.19838448 -1.042634353 3.840995833 1.000049606 0.754645942 0.513249292 0.07205116 13551959.68 27996158.15 9344.72267 0.016936909 0.090649549 1.042634353 -0.245403664 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EQDLPLAEAVRPKTPPVVIK 20 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK;EQDLPLAEAVRPKT(1)PPVVIK 137.62 5.25E-06 16860570000 9045790 4292300 6501090 3715080 9420910 7779830 7480090 6318390 7188530 3773200 TRUE FALSE 9402924.774 5029469.136 6670513.746 4449911.736 7819547.083 5973082.387 6893781 6233702.317 6929816.21 4512486.298 2.08375697 1.114567182 1.478234682 0.986133019 1.732868881 1.323678787 1.52771234 1.381434071 1.535698006 1 22.10549112 -1.742292647 2.432583653 0.895937705 1.440913563 0.181957442 0.291033618 13084045.32 9190542.371 8196064.993 0.067090894 0.018101199 1.742292647 0.544975858 EQDLQLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQDLQLEELR 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ; 104.07 0.0063525 91072000 184517 503237 331838 507664 291547 475365 280706 339472 310395 625208 FALSE TRUE 191801.8736 589664.0401 340485.9709 608078.424 241989.9451 364968.683 258703.5302 334921.9331 299223.9446 747705.5373 0.256520601 0.788631367 0.455374414 0.813259223 0.323643377 0.488118203 0.345996542 0.447932931 0.400189553 1 19.51211069 -1.136528117 5.076225187 1.000021304 0.485190343 0.441986293 0.17520806 3.98E-05 6.77E-06 0.159725985 0.03764622 0.073025053 1.136528117 -0.514830961 EQDRVHS(ph)PCPTSGSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQDRVHSPCPTSGSEK 16 1 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 EQDRVHS(0.999)PCPT(0.001)S(0.001)GSEK;EQDRVHS(0.992)PCPT(0.006)S(0.002)GSEK;EQDRVHS(0.997)PCPT(0.003)SGSEK 102.19 0.00093017 378090000 257476 214011 254395 180795 317091 309113 263151 260358 267951 213342 TRUE FALSE 267641.3513 250765.7245 261024.7427 216555.7114 263191.9851 237326.1904 242524.537 256868.3269 258307.4959 255142.2802 1.048988631 0.982846607 1.023055616 0.848764506 1.031549866 0.930171942 0.950546247 1.006765036 1.012405688 1 17.96094247 -0.424907539 6.560834076 1.000002153 0.979566748 0.008216658 0.056243299 0 0 0.05136402 0.012106616 0.375917428 0.424907539 -0.020435405 EQDRVHS(ph)PCPTSGSEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQDRVHSPCPTSGSEKK 17 2 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 EQDRVHS(1)PCPTSGSEKK 103.31 0.00047234 42425000 64328 36998 55354 25767 78789 61020 56287 47911 66343 30926 TRUE FALSE 66867.71911 43352.1187 56796.57071 30863.63569 65396.47392 46849.02977 51875.07786 47268.83141 63955.32839 36985.35759 1.807951132 1.172142749 1.535650171 0.834482555 1.768172006 1.266691275 1.402584191 1.278041758 1.729206707 1 15.1746666 -2.024830179 2.930903583 0.531568812 1.396135752 0.155879414 0.2889246 1421679.978 24298964.47 5144955.366 0.060703169 0.009444301 2.024830179 0.86456694 EQDVVTGVS(ph)PLLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 EQDVVT(0.001)GVS(0.999)PLLFR;EQDVVTGVS(1)PLLFR 172.2 3.04E-06 81107000 274380 291730 294240 277830 321210 356150 258530 284470 273020 265950 TRUE FALSE 285212.7343 341832.3582 301908.1361 332783.9448 266610.8389 273439.56 238265.7431 280657.1449 263194.0635 318057.8106 0.89673237 1.074749139 0.949224091 1.046300181 0.838246476 0.859716539 0.749127156 0.882409221 0.827503852 1 18.27892949 3.228381914 24.99192341 0.848201798 0.994642184 0.42626237 0.074446996 162.5484421 399107.0889 0.019728815 0.023833754 1691.928142 -3.228381914 0.146440387 EQDYLCHVYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQDYLCHVYVR 11 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 ; 164.13 2.31E-05 450730000 557410 581420 657260 623920 694580 709610 619810 631660 610330 568910 FALSE TRUE 579416.9772 681274.3622 674388.7355 747329.5138 576515.5397 544813.8317 571227.6726 623193.6309 588364.3425 680377.0221 0.851611619 1.001318887 0.991198576 1.098404987 0.847347163 0.800752839 0.839575197 0.915953377 0.864762218 1 19.37597489 3.204370646 24.99999136 0.870689565 0.987151571 0.328128532 0.074949843 195.6844945 143085.5911 0.021464962 0.025656713 1600.923743 -3.204370646 0.116462006 EQEAGLLQFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQEAGLLQFLR 11 0 Q9NZL4;Q9NZL4-3;K7EN20 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 ;; 175.15 2.36E-05 62168000 68450 80248 76650 78314 90952 103912 88976 87973 85562 90921 FALSE TRUE 71152.45885 94029.96976 78647.56197 93804.27546 75492.01153 79780.0128 82001.82862 86793.86583 82482.64033 108735.2292 0.654364362 0.864760855 0.723294213 0.862685223 0.694273715 0.733708968 0.754142234 0.79821293 0.758564092 1 16.73045991 -0.783223821 0.700824323 1.033364588 0.762115931 0.559708723 0.063706884 17.22892061 5.08297769 1.404200464 0.020820116 0.16473132 0.783223821 -0.271248657 EQEEEEQKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQEEEEQKER 10 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 90.793 0.0096572 177920000 91671 76790 94268 73735 117270 129320 87680 102470 92169 72204 FALSE TRUE 95290.24187 89978.08516 96724.70152 88319.56292 97336.48729 99287.38986 80807.41249 101096.5573 88851.85569 86350.99137 1.103522268 1.042004078 1.120134233 1.022797324 1.127219106 1.149811812 0.935801792 1.170763134 1.028961617 1 16.39792512 1.010987534 24.98912951 0.999999934 1.083461768 0.159703546 0.065489112 276.9703404 629916.0282 0.057679016 0.014419754 10.25622487 -1.010987534 0.083461834 EQEEELRR ddPTM_MDA-MB-175_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 ; 176.38 0.00041792 945560000 562640 860680 912530 825400 1021420 1103890 916360 873180 823610 858060 FALSE TRUE 584853.4617 1008495.095 936311.2815 988661.6564 847799.3932 847528.2771 844533.3087 861476.4503 793968.437 1026180.428 0.569932388 0.982765863 0.91242364 0.963438426 0.826169911 0.825905712 0.822987152 0.839498032 0.773712317 1 19.96885298 EQEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQEELER 7 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 103.87 0.019259 156760000 198370 278970 252460 253960 249840 331800 239590 258320 251070 325940 FALSE TRUE 206201.8008 326880.9274 259039.315 304192.53 207372.286 254744.4785 220810.3097 254857.6429 242034.0397 389801.7025 0.528991535 0.838582606 0.664541261 0.780377633 0.531994306 0.653523258 0.566468305 0.653813571 0.62091581 1 18.57238087 -1.523128528 5.153438933 1.00121364 0.651968897 0.554067406 0.094482455 0.001253044 0.00011595 0.087008843 0.020441182 0.029982751 1.523128528 -0.349244743 EQEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQEELRR 7 1 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 103.56 0.013385 161170000 122140 166770 131860 153190 139790 181710 133520 145270 115570 160380 FALSE TRUE 126962.1815 195411.4502 135296.3799 183490.5248 116028.5457 139510.6063 123054.3535 143322.8933 111410.6583 191803.3903 0.661939194 1.018811241 0.705390972 0.956659444 0.604934801 0.727362567 0.641565059 0.747238581 0.580858649 1 17.5492687 3.233636727 24.99999567 0.70289481 0.839471766 0.131835479 0.146450674 201.7582248 1024383.724 0.037775049 0.046507499 1712.524239 -3.233636727 0.136576956 EQEKGEGS(ph)DSKESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQEKGEGSDSKESPK 15 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 1 EQEKGEGS(0.966)DS(0.034)KESPK 149.94 1.71E-06 269160000 512710 92405 198320 87984 322040 341500 307850 171770 229490 61990 TRUE FALSE 532952.1867 108274.8399 203488.3821 105386.9726 267299.7558 262191.8005 283719.9126 169467.7041 221230.6997 74135.75363 7.188868536 1.460494224 2.744807629 1.42154045 3.605544461 3.536644435 3.82703215 2.285910587 2.984129639 1 16.17788186 -0.89786555 0.240225649 1.37E-56 3.527091371 0.178983663 1.524884521 30.40709369 1.803648155 28.24763462 2.797400792 0.126512795 0.89786555 3.527091371 EQELQQTLQQEQSVLDQLRGEAEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 235.68 5.82E-45 455576000 119679 141377 120511 101098 147781 163576 92722 116676 134570 160819 FALSE TRUE 124404.0193 165657.4 123651.6157 121094.8827 122661.2384 125587.953 85454.20736 115112.1491 129726.852 192328.404 0.646831236 0.861325715 0.642919159 0.629625579 0.637769751 0.652987029 0.444314025 0.598518714 0.674506985 1 17.55321232 0.894699585 8.740500023 0.999999955 0.635413006 0.563672072 0.094578746 6.152136902 511.0378744 0.097799976 0.024477618 7.846926513 -0.894699585 -0.364586949 EQELSEEDKQLQDELEMLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQELSEEDKQLQDELEMLVER 21 1 Q13200;C9JPC0 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 120.75 2.81E-05 17266000 21345 15969 19253 14798 23665 26155 27705 20049 22875 12035 FALSE TRUE 22187.71708 18711.55153 19754.749 17725.00023 19642.43175 20080.89763 25533.40971 19780.27595 22051.73322 14393.02783 1.541560077 1.300042754 1.372522115 1.23149906 1.364718528 1.395182298 1.774012391 1.374295679 1.532112179 1 13.8130825 2.466238354 24.99446926 1.470825004 1.354749569 0 0.194979419 594.0524217 1364335.017 0.062873276 0.052647985 292.5757683 -2.466238354 -0.116075435 EQEVAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQEVAEER 8 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 133.32 0.0037741 309240000 494470 592700 540700 579630 600640 689380 592130 585100 579100 580010 FALSE TRUE 513992.0574 694491.6144 554791.0862 694279.084 498543.4273 529281.9427 545717.3034 577257.6915 558258.3041 693651.8545 0.740994281 1.001210636 0.799812013 1.000904242 0.718722835 0.763036874 0.786730836 0.832200891 0.804810512 1 19.40385223 EQEVAEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQEVAEERR 9 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;; 128.01 0.00068823 619080000 320396 432730 361420 394840 472670 508970 312345 348370 368260 486400 FALSE TRUE 333045.4815 507048.0113 370838.9021 472938.1735 392325.7222 390769.431 287862.5827 343700.67 355006.3945 581700.7673 0.572537463 0.871664677 0.637508016 0.81302656 0.674445942 0.671770527 0.494863681 0.590854765 0.610290401 1 19.14991768 -1.291522653 5.27880851 1.000062191 0.658298174 0.483688815 0.105479721 7.98E-05 1.07E-05 0.105612039 0.024888481 0.051106642 1.291522653 -0.341764018 EQEVNILKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQEVNILKK 9 1 P35579 P35579 MYH9 Myosin-9 0 78.655 0.037481 0 297660 413890 421870 398240 490980 517220 370790 410990 415810 464280 FALSE TRUE 309411.8466 484972.3879 432864.2788 477010.6834 407523.395 397103.4935 341726.5109 405481.3513 400845.0793 555246.7768 0.557251045 0.873435755 0.779588999 0.859096718 0.733950042 0.715183789 0.615449788 0.730272319 0.721922388 1 19.08276959 -1.030823096 5.21724637 1.000002325 0.73523787 0.437677588 0.091126818 2.42E-06 4.50E-07 0.086683458 0.020431308 0.093148723 1.030823096 -0.264764455 EQFAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EQFAWR 6 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435;Q9NQ39 P46783 RPS10;RPS10-NUDT3;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ;;;; 137.59 0.029481 7211160000 3794420 3681900 4024580 4184800 4595860 4894950 4596000 4090070 4120230 3411800 FALSE TRUE 3944226.632 4314237.684 4129463.861 5012540.95 3814657.359 3758172.046 4235753.511 4035249.302 3971943.727 4080276.887 0.966656612 1.057339441 1.012054813 1.228480588 0.934901592 0.921058092 1.03810443 0.988964576 0.973449557 1 21.96023563 EQFLDGDGWTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;; 318.28 3.37E-46 31528300000 15077400 19619120 17871290 19618900 19312560 22943870 17699450 17236080 16431850 18240570 FALSE TRUE 15672667.39 22988551.24 18337030.5 23499459.86 16029817.95 17615503.91 16312120.86 17005058.54 15840470.93 21814460.45 0.71845313 1.053821674 0.840590604 1.077242314 0.734825323 0.807514994 0.747766414 0.779531475 0.726145437 1 24.37878146 3.207274124 24.99994963 0.784788354 0.926052789 0.196398737 0.11989611 255.9919193 204553.5733 0.031489719 0.037640847 1611.662585 -3.207274124 0.141264435 EQFNEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQFNEFR 7 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 ;;; 184.89 0.0014457 2076440000 3230260 4100690 3547720 4152480 4231920 4811110 3668840 3627790 3460160 3882600 FALSE TRUE 3357793.159 4804951.609 3640176.498 4973828.15 3512579.75 3693802.616 3381266.734 3579165.409 3335629.518 4643321.133 0.72314472 1.034809239 0.783959669 1.071179013 0.756480039 0.795508755 0.728200061 0.770820132 0.718371489 1 22.14672563 EQFVEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQFVEFR 7 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 127.46 0.0089627 361610000 782190 1026580 878690 984130 1088730 1182770 890870 933420 810620 973090 FALSE TRUE 813071.4652 1202887.129 901589.3833 1178787.977 903668.0635 908089.5926 821041.2815 920909.0317 781445.9445 1163748.355 0.698666049 1.033631648 0.774728815 1.012923431 0.776515009 0.780314394 0.705514451 0.79133004 0.671490483 1 20.1503477 3.05505679 24.99966406 0.7719681 0.884853345 0.110877977 0.123403802 149.9277294 68076.54853 0.032277515 0.038579005 1135.159243 -3.05505679 0.112885245 EQGDGAEDEEWDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQGDGAEDEEWDD 13 0 Q7Z6K5;H0YMP5 Q7Z6K5 ARPIN Arpin 0 ; 229.68 1.25E-11 1279640000 2321500 2489800 2506500 2348600 2859600 3263200 2690100 2548000 2662200 2477700 FALSE TRUE 2413154.613 2917403.782 2571821.449 2813146.07 2373526.213 2505371.254 2479242.933 2513848.228 2566387.942 2963157.877 0.814386109 0.984559009 0.867932644 0.949374346 0.801012404 0.845507178 0.83668945 0.848367968 0.866098956 1 21.49870406 EQGVEEHETLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQGVEEHETLLLR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 164.88 9.49E-07 0 67465 126700 122930 114220 118300 145150 108380 111910 106660 132050 FALSE TRUE 70128.57029 148459.7394 126133.6568 136812.3751 98191.40826 111441.1123 99884.8924 110410.0295 102821.3274 157922.6693 0.444069054 0.940078711 0.798705198 0.866325118 0.621768925 0.705668875 0.632492427 0.699139839 0.65108656 1 17.26885875 -1.105271664 4.604867291 1.000021683 0.7140872 0.306990565 0.131818927 2.80E-05 5.44E-06 0.121856128 0.028719589 0.07847446 1.105271664 -0.285934484 EQGVTFPS(ph)GDIQEQLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 153.21 1.93E-07 87544000 140602 143747 160701 172334 138602 206567 162061 139447 146657 136438 TRUE FALSE 146153.0755 168434.4291 164889.0001 206421.1508 115042.4815 158594.9448 149358.2354 137577.9411 141378.8432 163170.4138 0.895708187 1.032260844 1.010532462 1.265064824 0.705044982 0.971958954 0.915351208 0.843154943 0.866449008 1 17.31601997 3.229284698 24.9999966 0.879943242 1.046678039 0.343018898 0.113251186 218.1181065 587860.3451 0.031561083 0.038214407 1695.448873 -3.229284698 0.166734797 EQGVTFPSGDIQEQLIR ddPTM_MDA-MB-175_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 0 ;;; 314.45 7.36E-58 688120000 481646 456444 512639 571703 482024 593900 472021 480499 454486 467389 FALSE TRUE 500661.756 534834.7064 525998.7935 684784.147 400089.7327 455975.7256 435022.7606 474058.6968 438129.1376 558964.9258 0.895694404 0.95683053 0.941022896 1.225093231 0.71576894 0.815750156 0.778264862 0.848100972 0.783822235 1 19.09239823 3.207672236 24.99999987 0.814932808 0.996698826 0.404952177 0.107028956 189.3872627 153283.057 0.02969113 0.035491156 1613.140655 -3.207672236 0.181766017 EQHDAQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQHDAQVR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 108.98 0.0037068 172426000 71266 95212 88014 94221 106938 100248 76114 79168 68833 115950 FALSE TRUE 74079.63671 111563.9204 90307.71714 112857.6326 88760.71696 76966.92127 70147.98579 78106.88245 66355.71378 138668.1825 0.534222309 0.804538708 0.651250456 0.813868261 0.640094327 0.555043846 0.505869368 0.56326463 0.478521551 1 17.08127727 -1.058145661 4.803389981 1.000011408 0.6186606 0.523041881 0.10990207 1.42E-05 2.78E-06 0.11246517 0.026507502 0.087469036 1.058145661 -0.381350808 EQHGVAASCLEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQHGVAASCLEDLR 14 0 O00273;O00273-2;K7ERT1 O00273 DFFA DNA fragmentation factor subunit alpha 0 ;; 182.18 1.55E-06 500630000 216830 276980 253303 243359 276831 322312 239564 252884 261594 277038 FALSE TRUE 225390.6158 324549.1604 259904.2843 291494.6838 229775.3655 247459.9227 220786.3477 249494.5036 252179.283 331318.2919 0.68028425 0.979569098 0.784454981 0.879802567 0.693518502 0.74689484 0.666387438 0.753035705 0.761139029 1 18.33785833 5.041991247 16.62978653 0.790030779 0.132479074 0.092089236 0.108059375 11680412.39 121371331.6 0.025117314 238589221.3 110151.711 -5.041991247 -0.657551704 EQHLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQHLTK 6 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 77.058 0.073422 177970000 326700 385660 422380 392500 540170 519980 498490 455600 451680 383070 FALSE TRUE 339598.3683 451894.105 433387.5698 470135.3285 448352.0963 399222.5254 459417.0512 449493.4272 435424.125 458125.2322 0.741278464 0.986398638 0.946002401 1.026215749 0.978667109 0.871426626 1.002819795 0.981158416 0.950447813 1 18.8053825 4.740918994 24.98555632 0.970848451 0.741278383 0.745647799 0.040329847 103.8062544 1099695.371 0.009458774 0.063471064 55070.49682 -4.740918994 -0.229570069 EQHVQDIIPINSHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQHVQDIIPINSHFR 15 0 Q01968-2;Q01968;A0A2R8YF88 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 201.75 3.62E-09 126350000 38378 47855 44184 53306 51760 50914 46107 49711 44029 44197 FALSE TRUE 39893.19307 56073.72399 45335.47134 63849.7677 42961.85369 39089.99511 42493.01286 49044.70536 42444.40489 52856.55595 0.754744466 1.060866017 0.85770763 1.207981991 0.812800852 0.73954866 0.803930792 0.927883107 0.803011171 1 15.6897948 EQIKLDEGWVPLEIMIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQIKLDEGWVPLEIMIK 17 1 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 147.06 3.77E-07 140340000 501150 256540 377660 288380 542410 501470 498900 420470 505280 249390 FALSE TRUE 520935.789 300598.7494 387502.1299 345420.7033 450211.3419 385011.1924 459794.9144 414834.2874 487095.0715 298253.1956 1.746622657 1.007864304 1.29923882 1.158145858 1.509493774 1.290887065 1.541626112 1.390879607 1.633159606 1 18.18617807 3.230421321 24.99894258 1.417211976 1.281622711 0.025853991 0.238342388 495.9994291 1523405.128 0.06331148 0.076906119 1699.891963 -3.230421321 -0.135589265 EQISDIDDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ; 239.36 2.81E-15 2983200000 1245610 1514700 1466150 1424170 1529410 1788200 1571570 1477150 1491330 1424600 FALSE TRUE 1294787.645 1774837.942 1504359.073 1705866.575 1269441.434 1372917.65 1448386.237 1457351.22 1437657.325 1703723.094 0.759975403 1.041740849 0.88298332 1.001258116 0.745098449 0.805833797 0.850130072 0.855392068 0.843832739 1 20.70025944 EQIVPKPEEEVAQKK ddPTM_MDA-MB-175_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 79.022 0.011913 150500000 131750 54619 77758 47970 92517 89465 63409 69363 75635 41696 FALSE TRUE 136951.5917 63999.38837 79784.43736 57458.32282 76790.99339 68688.10961 58438.83689 68433.30244 72912.91112 49865.53288 2.746417893 1.283439375 1.599991673 1.152265292 1.539961351 1.377466672 1.171928455 1.372356786 1.462190553 1 15.60575535 4.740094141 24.98710226 1.345213808 2.746418357 0.85409507 0.175654364 42.421403 691146.8044 0.038063974 0.241452047 54966.00095 -4.740094141 1.40120455 EQIVVDLSHPGVSEDDQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EQIVVDLSHPGVSEDDQVSR 20 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;;; 273.51 1.87E-44 4684570000 3059500 3760810 3572860 3596200 3929900 4618040 3837170 3878460 3772600 4150310 FALSE TRUE 3180291.422 4406699.862 3665971.667 4307517.626 3261897.002 3545570.197 3536402.589 3826475.588 3636824.863 4963483.782 0.640737748 0.887823967 0.738588425 0.867841584 0.657178938 0.714330973 0.712483962 0.770925373 0.732716177 1 22.24292165 -1.683953906 4.314518769 1.01078744 0.750824575 0.502001986 0.075520788 0.007536866 0.000552089 0.070327358 0.016071155 0.020703611 1.683953906 -0.259962865 EQIYDVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EQIYDVYR 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;;;;; 164.71 0.00076423 2006410000 1661560 1878070 1753310 1728690 2865590 2489850 2087170 1774370 1789540 2694540 FALSE TRUE 1727159.672 2200613.913 1799002.699 2070619.722 2378498.035 1911620.072 1923572.162 1750587.472 1725134.805 3222483.523 0.535971607 0.682893767 0.558265911 0.642554014 0.738094708 0.593213296 0.596922264 0.543241714 0.535343251 1 21.61974155 -0.99060344 4.430171578 1.000013132 0.604111416 0.775865311 0.064019913 23395.03247 38759384.24 1206.670671 0.015366329 0.102187214 0.99060344 -0.395901716 EQLEEEEEAKHNLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 306.77 2.28E-45 15920880000 7540165 3687199 5706193 3664413 7859103 6404560 7359599 5354893 6679759 3185702 FALSE TRUE 7837856.536 4320446.746 5854901.077 4389222.954 6523215.479 4917198.002 6782734.4 5283119.418 6439355.778 3809879.313 2.057245359 1.134011445 1.536768122 1.152063515 1.712184283 1.290644033 1.780301643 1.386689442 1.690173165 1 21.86131387 -1.153791567 5.969409625 0.999995522 1.505085847 0.239104709 0.279481428 1.48E-05 2.09E-06 0.239143403 0.05636614 0.070179203 1.153791567 0.505090325 EQLEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EQLEWER 7 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;;;; 121.85 0.010232 1795545000 1205623 1385764 1300907 1276429 1532120 1679840 1497421 1365172 1395975 1427295 FALSE TRUE 1253221.927 1623758.187 1334809.705 1528902.846 1271690.79 1289722.618 1380049.229 1346874.102 1345734.132 1706946.128 0.734189502 0.951265046 0.781987014 0.895694844 0.745009329 0.755573124 0.808490207 0.789054839 0.788386997 1 20.7029861 EQLLELPEQQEGHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQLLELPEQQEGHLK 15 0 P07476 P07476 IVL Involucrin 0 ;;; 202.41 5.92E-09 871310000 1016040 851740 1065900 833260 1282030 1291130 1204400 1055460 1196430 905880 FALSE TRUE 1056154.044 998019.7194 1093678.23 998076.341 1064110.999 991284.6248 1109995.981 1041313.285 1153370.718 1083369.842 0.974878571 0.921217927 1.009515114 0.921270191 0.982223205 0.915001126 1.024577146 0.961179871 1.064614016 1 20.04709441 1.692037685 1.411682727 1.02261908 0.956839644 0.298981309 0.039152849 0.466995679 1.793394778 0.029001697 0.010915128 49.20822336 -1.692037685 -0.065779436 EQLLEREEEIAELKAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQLLEREEEIAELKAER 17 2 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;O75145-2;O75145;R4GN36;R4GNF1 Q13136-2;O75145-2 PPFIA1;PPFIA3 Liprin-alpha-1;Liprin-alpha-3 0 146.76 2.39E-07 39522000 25938 29695 33436 18255 47042 45423 25613 30605 36487 38045 FALSE TRUE 26962.05227 34794.88525 34307.36963 21865.78451 39045.81764 34874.19664 23605.38613 30194.79003 35173.84 45499.18933 0.592583135 0.764736378 0.754021558 0.480575255 0.858165128 0.766479516 0.518808939 0.663633583 0.773065202 1 15.47355322 0.898942944 3.393098549 0.99972309 0.675621875 0.436766127 0.112011833 0.38857514 9.748854816 0.105138187 0.027233079 7.923972222 -0.898942944 -0.324101215 EQLQLLEEQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 207.47 2.29E-08 2043100000 1816050 2188440 2003000 2099670 2197470 2503860 2117070 2170240 1974220 2127270 FALSE TRUE 1887749.056 2564287.546 2055199.825 2514978.459 1823944.834 1922376.461 1951128.521 2141151.483 1903168.208 2544067.827 0.74201994 1.007947791 0.807840028 0.988565805 0.716940333 0.755630978 0.766932587 0.841625156 0.748080765 1 21.2787057 3.230876896 24.99994687 0.795351023 0.889636326 0.126108911 0.103468071 297.1759679 966898.0413 0.027294188 0.033206173 1701.676089 -3.230876896 0.094285303 EQLRQEQALLEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQLRQEQALLEEIER 15 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 314.51 2.61E-56 701880000 350220 463560 432930 399270 510340 534710 379890 435850 447690 514760 FALSE TRUE 364046.956 543172.824 444212.5115 478244.4143 423592.5891 410531.7061 350113.2291 430008.1437 431577.7244 615617.3663 0.591352642 0.882322127 0.721572418 0.776853352 0.688077712 0.666861802 0.568718896 0.698499047 0.701048651 1 19.2316744 0.782322936 12.71815048 1 0.70055405 0.537599379 0.083608309 5487.680994 320645.7905 0.080805035 0.020202866 6.057911661 -0.782322936 -0.29944595 EQLSAQELMESGLQIQKS(ph)PEPEVLSTQEDLFDQSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNK 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 EQLSAQELMES(0.002)GLQIQKS(0.998)PEPEVLSTQEDLFDQSNK 137.46 1.68E-09 107030000 41104 21025 27467 19359 42494 41464 36450 32559 28960 15751 TRUE FALSE 42726.81766 24635.8802 28182.81258 23188.15242 35270.88506 31834.61439 33592.95376 32122.59986 27917.73526 18837.10688 2.26822611 1.307837788 1.496132754 1.230982686 1.87241519 1.689994891 1.78333934 1.705283092 1.482060671 1 14.20128978 0.882515186 3.756608498 1.000197106 1.65162254 0.345503067 0.277560308 0.628530743 17.40598193 0.256043203 0.065740681 7.629835701 -0.882515186 0.651425434 EQLVDQGIMPPLKS(ph)PAAFHEQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQLVDQGIMPPLKSPAAFHEQIK 23 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5;I3L2S3;Q9ULH7-2;Q9ULH7-3 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2;Phosphatase and actin regulator 1 EQLVDQGIMPPLKS(1)PAAFHEQIK 119.18 0.00012733 391110000 212490 166670 219150 161700 415210 317530 314550 276490 330390 204630 TRUE FALSE 220879.2693 195294.276 224861.229 193683.7774 344632.7525 243788.4697 289894.7491 272784.1038 318499.3284 244723.3306 0.902567273 0.798020669 0.918838545 0.791439774 1.408254585 0.996179927 1.184581578 1.114663253 1.301466957 1 17.90079212 3.262340284 24.99999267 1.162506854 0.853532609 0.612848988 0.122538912 146.1186659 153616.1263 0.031160138 0.042168678 1829.533154 -3.262340284 -0.308974245 EQMMNSSISSGS(ph)GSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 EQMMNSSISS(0.003)GS(0.95)GS(0.047)LR 182.63 2.22E-09 329220000 161070 341950 320560 299090 298510 401850 259140 265530 269760 342880 TRUE FALSE 167429.168 400677.2525 328914.0569 358249.1093 247769.3768 308526.4276 238827.9297 261971.0047 260051.3903 410060.7712 0.408303305 0.977116761 0.802110516 0.873648821 0.604225993 0.752391961 0.582420818 0.638858977 0.634177684 1 18.64547821 3.232231108 24.99901976 0.675427141 0.783054678 0.012887891 0.177397519 394.5867392 1558459.118 0.047602389 0.058226104 1706.990516 -3.232231108 0.107627537 EQMMNSSISSGSGS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 256.14 1.31E-26 388740000 188770 229790 237290 257040 282640 270890 221140 212340 215140 254610 TRUE FALSE 196222.7854 269254.645 243473.9723 307881.7448 234596.9538 207979.9029 203806.469 209493.9296 207397.1534 304495.9547 0.644418365 0.884263455 0.799596739 1.011119327 0.770443581 0.683030102 0.669324061 0.688002341 0.681116285 1 18.21606354 3.005276517 24.99683381 0.717094186 0.842726045 0.084358626 0.125254348 236.1117914 1118536.547 0.034176841 0.040724475 1012.223736 -3.005276517 0.125631859 EQMQPTHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EQMQPTHPIR 10 0 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 ;;;;;;;; 129.84 0.00029251 2091989000 612985 741369 751468 836901 843985 923285 816542 824695 789196 713893 FALSE TRUE 637186.1211 868693.3587 771051.8734 1002437.52 700524.7312 708866.0513 752539.3044 813641.3125 760792.9901 853766.665 0.746323495 1.017483341 0.903117801 1.17413523 0.820510755 0.830280778 0.881434396 0.953001969 0.891101774 1 19.70348231 -0.78832016 4.081467196 1.000000869 0.919509807 0.048606736 0.112176747 32370211.88 74026262.23 465.673422 0.026006582 0.162809536 0.78832016 -0.080491062 EQNDKPYCQNCFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQNDKPYCQNCFLK 14 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 0 151.56 3.24E-07 0 160600 120880 132150 106020 173440 164480 177390 138280 161070 93398 FALSE TRUE 166940.612 141640.1997 135593.9376 126990.4396 143958.7308 126282.0127 163485.7083 136426.5828 155273.1222 111697.5499 1.494577206 1.268068994 1.213938333 1.136913385 1.288826218 1.130571018 1.463646324 1.221392796 1.390121111 1 16.76923801 -2.062068015 2.807231091 0.580480672 1.280873211 0.344300969 0.119403136 1307087.176 8830737.592 4073912.594 0.026549585 0.008668261 2.062068015 0.700392539 EQNFYGSQESIIALCTHLQQLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQNFYGSQESIIALCTHLQQLIR 23 0 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ; 149.18 9.79E-08 349972000 87002 71806 92486 97241 86820 115794 117289 91000 95662 76726 FALSE TRUE 90436.90614 84138.12193 94896.26114 116474.9796 72062.36741 88902.59838 108095.5817 89780.29385 92219.14331 91758.99069 0.985591771 0.916946899 1.034190333 1.26935768 0.785343941 0.968870709 1.178038042 0.978435935 1.005014796 1 16.4855619 EQNSELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQNSELR 7 0 O60437 O60437 PPL Periplakin 0 79.116 0.077928 31815000 3870.6 6323.7 5381.6 6738.5 7212.1 7713.8 5521.3 6858.7 4415.9 8089.4 FALSE TRUE 4023.414277 7409.746283 5521.848917 8071.355188 5986.189818 5922.386854 5088.526079 6766.770345 4256.972622 9674.363049 0.415884152 0.765915673 0.570771315 0.834303524 0.618768366 0.61217331 0.525980476 0.699453836 0.440026139 1 13.23995096 -1.10447537 4.701448398 1.000023298 0.621926885 0.46046711 0.126220537 2.81E-05 5.36E-06 0.111566847 0.026294939 0.078618478 1.10447537 -0.378096412 EQPFGEGVPLDGDDPEHIQWIFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQPFGEGVPLDGDDPEHIQWIFQK 24 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 211.35 3.14E-25 722370000 449062 408631 468702 428480 526528 581249 515870 479053 473522 410406 FALSE TRUE 466791.3145 478810.1955 480916.7592 513232.0651 437028.9586 446262.7287 475434.7614 472632.0781 456480.0357 490817.198 0.951049222 0.975536712 0.979828664 1.045668463 0.89041085 0.909223903 0.96865954 0.962949302 0.930040833 1 18.90482628 5.112063619 11.21076399 0.961084845 0.770061939 0.005548217 0.042353181 937456.1642 2063410.881 0.010292765 4283499.976 129438.5439 -5.112063619 -0.191022906 EQQAQVEKEDFSDMVAEHAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQQAQVEKEDFSDMVAEHAAK 21 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 163.72 1.02E-11 549530000 358860 207630 315510 232110 449110 362380 373680 308380 372890 204461 FALSE TRUE 373028.0699 243288.8374 323732.4498 278020.6652 372770.4426 278222.7369 344389.9852 304246.6705 359469.7617 244521.2183 1.525544787 0.994960025 1.323944204 1.137000164 1.524491188 1.137826561 1.40842577 1.244254681 1.470096396 1 17.89960013 5.065508463 18.36002253 1.266389744 5.659119541 0.175769329 0.176067376 202.7986923 59223.15614 0.036693558 1486.880034 116280.9211 -5.065508463 4.392729798 EQQDVGS(ph)PDKAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQQDVGSPDKAR 12 1 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;A6PVV2;Q9Y3S1-3 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 1 EQQDVGS(1)PDKAR 55.851 0.075372 364720000 332660 326380 361290 306940 431550 499440 392570 382640 385980 388050 TRUE FALSE 345793.6737 382433.2261 370705.5142 367651.8159 358195.2851 383452.6291 361799.3376 377511.3367 372088.6552 464080.9678 0.745114964 0.82406574 0.798794908 0.79221481 0.771837912 0.826262346 0.779603911 0.81346007 0.801775296 1 18.82401701 -5 0.350490283 3.363762819 0.78986955 0.881260458 0.022698741 123.9110373 1.013906347 220.0896536 0.015721452 1.00E-05 5 -2.573893269 EQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQQEAIEHIDEVQNEIDR 18 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ; 251.13 2.50E-25 2349900000 1090420 1180250 1152590 1484890 1076720 1359610 1543570 1241790 1090600 893860 FALSE TRUE 1133470.624 1382948.756 1182627.442 1778596.81 893699.519 1043861.183 1422580.95 1225145.836 1051349.519 1068994.753 1.060314487 1.293690874 1.106298641 1.663803124 0.836018621 0.976488593 1.330765138 1.146072825 0.98349362 1 20.02782334 3.200540831 24.9999971 1.075288217 1.269453664 0.252000167 0.194381944 275.8863694 181408.924 0.056549781 0.067591324 1586.868105 -3.200540831 0.194165447 EQQEAIEHIDEVQNEIDRLNEQAS(ph)EEILK ddPTM_MDA-MB-175_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 217.1 1.53E-34 21368000 17812 10828 12462 11839 17493 15519 16825 14379 15687 8456.6 TRUE FALSE 18515.23151 12687.62477 12786.76996 14180.71886 14519.54611 11914.94744 15506.21254 14186.27302 15122.42793 10113.50886 1.830742601 1.254522535 1.264325778 1.402156172 1.435658614 1.178122016 1.533217873 1.402705354 1.495270153 1 13.303996 4.74592673 24.50185334 1.352493771 1.830742903 0.482932809 0.153941415 570.1719102 1896497.552 0.034279433 0.351849918 55709.17542 -4.74592673 0.478249132 EQQEAIEHIDEVQNEIDRLNEQASEEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQQEAIEHIDEVQNEIDRLNEQASEEILK 29 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;;; 284.08 8.35E-72 959180000 176275.6 123166.6 173155.9 172402 197770.7 212447.4 211740 175913.4 181266.5 126141.9 FALSE TRUE 183235.0968 144319.5054 177668.485 206502.601 164153.7071 163109.711 195143.2655 173555.5686 174742.7541 150856.9902 1.214627818 0.956664357 1.177727892 1.368863324 1.088141205 1.08122077 1.293564622 1.150464214 1.158333822 1 17.20282202 0.565215307 2.777047669 1.000004505 1.166205559 0.174142436 0.108273857 13.41646513 83.36676632 0.103149162 0.027177599 3.674644303 -0.565215307 0.166201055 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQQEAIEHIDEVQNEIDRLNEQASEEILKVEQK 33 2 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ; 164.17 2.56E-14 290250000 163638 86382 120406 65029 186743 147024 126899 116228 152388 79739 FALSE TRUE 170098.5546 101217.4365 123543.8793 77891.54211 155000.4916 112879.9042 116952.3248 114670.1538 146903.5856 95362.33035 1.783708032 1.061398523 1.295520766 0.816795708 1.625384898 1.183694901 1.22639961 1.202468033 1.540478144 1 16.54113187 4.749177828 24.51598234 1.224223164 1.783708447 0.3610049 0.226039139 1249.500367 2885120.97 0.049841241 0.717366149 56127.77525 -4.749177828 0.559485283 EQQEVADRLETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQQEVADRLETK 12 1 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 ;;; 140.31 5.43E-05 1220570000 1211380 1014770 1129030 942330 1369580 1470130 1141800 1133320 1200860 885280 FALSE TRUE 1259206.218 1189048.854 1158453.449 1128720.061 1136779.281 1128714.588 1052302.732 1118129.699 1157641.283 1058733.666 1.189351258 1.123085901 1.094187789 1.066103872 1.073716003 1.066098702 0.993925825 1.056101015 1.093420678 1 20.01390828 8 0.428350655 1.03832768 4.048632097 0.735816645 0.027587106 40.28220425 0.508502676 0.017503993 104.507825 100000000 -8 3.010304417 EQQHFLQDCHELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQQHFLQDCHELK 13 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 128.71 9.38E-05 352520000 295130 216380 269550 215050 360780 368030 266130 254640 294690 219310 FALSE TRUE 306781.9603 253541.5818 276574.6944 257586.2481 299454.7445 282560.61 245270.0352 251226.9673 284084.1645 262279.5956 1.169675284 0.966684356 1.054503282 0.982105556 1.141738624 1.077325933 0.935147222 0.957859367 1.083134827 1 18.00074605 2.254768521 24.97276932 0.985046154 1.060051415 0.199856336 0.068473636 361.3624299 556777.8644 0.023427299 0.019544779 179.7912372 -2.254768521 0.07500526 EQQHVMEELFQSSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQQHVMEELFQSSFR 15 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 189.42 2.59E-07 215890000 208880 217440 300400 300080 285670 304460 303580 298360 305080 245330 FALSE TRUE 217126.7437 254783.6286 308228.6708 359434.9284 237111.9154 233753.7791 279784.6063 294360.9722 294100.2304 293397.7164 0.740042378 0.868389951 1.050548977 1.225077457 0.808158695 0.796713015 0.953601854 1.003283106 1.002394409 1 18.16249812 4.511908034 3.870402405 0.976089511 0.754034721 0.30170801 0.11456633 0.298953253 9.218381151 0.030070176 0.131599253 32501.84641 -4.511908034 -0.222054791 EQQTRPIWTAEDQLDGS(ph)LEDNLDLPHHGLADSSADLSCDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQT(0.003)RPIWT(0.003)AEDQLDGS(0.995)LEDNLDLPHHGLADSSADLSCDSR 109.03 4.07E-06 82094000 19468 31919 26878 29188 34922 46611 28657 38677 29967 43878 TRUE FALSE 20236.61167 37400.83995 27578.46276 34961.29928 28985.97091 35786.30165 26410.78946 38158.59808 28888.49352 52475.054 0.385642513 0.712735616 0.525553776 0.666246085 0.5523762 0.681967886 0.503301806 0.727175966 0.550518605 1 15.67934413 -5 0.250067277 3.429072397 0.563685519 0.59849156 0.101425979 113.9534199 1.129661253 141.4514344 0.129378902 1.00E-05 5 -2.865386878 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(ph)SADLSCDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.572)S(0.418)ADLS(0.01)CDSR;EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.519)S(0.397)ADLS(0.082)CDS(0.002)R;EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.832)S(0.16)ADLS(0.008)CDSR;EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.571)S(0.405)ADLS(0.023)CDS(0.001)R 232.93 1.54E-54 932560000 175395 287570 233836 299492 264174 345555 239701 271885 259459 295884 TRUE FALSE 182319.73 336957.9105 239929.9583 358730.6237 219269.7978 265305.0882 220912.6093 268240.8263 250121.1213 353856.8048 0.515235902 0.952243693 0.678042516 1.013773422 0.619656864 0.749752681 0.624299452 0.758049083 0.706842762 1 18.43280614 -1.072659564 4.412448225 1.000016431 0.741631394 0.235150663 0.14279622 17509005.93 4256413.239 3529.975176 0.030359117 0.08459417 1.072659564 -0.258385036 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLS(ph)CDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADSSADLSCDSR 41 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 EQQTRPIWTAEDQLDGSLEDNLDLPHHGLADS(0.034)S(0.034)ADLS(0.929)CDS(0.004)R 152.77 5.23E-14 232840000 40742 74746 58250 70584 60128 77562 51701 65238 63195 85016 TRUE FALSE 42350.52562 87583.04406 59768.04285 84545.30453 49907.46404 59549.40096 47648.54052 64363.59132 60920.62429 101673.2575 0.416535544 0.861416721 0.58784428 0.831539253 0.490861268 0.585693844 0.468643788 0.633043466 0.599180412 1 16.63358074 -0.639634727 6.087020052 1.000000002 0.612977929 0.425992482 0.136306434 3.67E-09 7.54E-10 0.12325364 0.029051161 0.229279525 0.639634727 -0.387022073 EQRERERWQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQRERERWQR 10 3 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 51.727 0.090741 32784000 8233.6 6072.4 6483.9 5620.8 7973.1 8678.4 6041.2 7224.1 6350.9 6773.4 FALSE TRUE 8558.668886 7115.287463 6652.875761 6732.577464 6617.83531 6662.973122 5567.674958 7127.272756 6122.33235 8100.518045 1.056558215 0.878374374 0.82129016 0.831129247 0.816964455 0.822536668 0.68732332 0.879853945 0.755795162 1 12.98379846 4.797086873 1.909742505 0.817375034 1.155473115 0.44544335 0.076299789 0.767577611 2.596268287 0.017787002 0.482876193 62673.92198 -4.797086873 0.338098081 EQS(ph)PSQHGKDPASLLASELVQLHMQLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQSPSQHGKDPASLLASELVQLHMQLEEK 29 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 EQS(0.966)PS(0.031)QHGKDPAS(0.001)LLAS(0.001)ELVQLHMQLEEK;EQS(0.497)PS(0.497)QHGKDPAS(0.007)LLASELVQLHMQLEEK;EQS(0.787)PS(0.199)QHGKDPAS(0.014)LLASELVQLHMQLEEK;EQS(0.955)PS(0.043)QHGKDPAS(0.002)LLASELVQLHMQLEEK 86.195 0.0009813 113385000 41855.7 49653.4 68804.9 48902.9 97211 84620 77316 73556 81444 49981.6 TRUE FALSE 43508.19536 58180.9852 70598.01222 58575.74766 80687.10894 64968.28743 71255.76989 72570.10213 78512.84635 59774.53756 0.727871718 0.973340616 1.181071659 0.979944807 1.349857518 1.086889001 1.192075636 1.214063799 1.313483124 1 15.86724344 5.221400943 0.887980385 1.189141348 4.33E-10 0.589029383 0.113803455 2.916086513 0.991064461 0.033815075 4.116722166 166494.903 -5.221400943 -1.189141348 EQSEVSVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 174.89 3.11E-06 6481100000 2496939 2799930 2631380 2577090 3066490 3092960 2695990 2911520 2786630 2589590 TRUE FALSE 2595520.08 3280796.197 2699955.925 3086830.71 2545249.125 2374666.914 2484671.259 2872495.837 2686339.731 3096970.58 0.838083544 1.059356591 0.871805481 0.996725875 0.821851244 0.766770899 0.802290882 0.927517961 0.867408863 1 21.56242625 EQSLDALQTHYDELQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQSLDALQTHYDELQAR 17 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 151.57 2.45E-07 333680000 191980 231670 239410 197130 211790 243760 216980 206020 200810 226550 FALSE TRUE 199559.5186 271457.5204 245649.2213 236121.7256 175790.0114 187150.4342 199972.5406 203258.6389 193582.8873 270938.1349 0.73655013 1.001916989 0.906661668 0.87149683 0.648819744 0.690749696 0.738074545 0.750203137 0.714491105 1 18.04760394 3.366854981 7.445505759 0.741211115 0.892826135 0.227158343 0.107437153 0.261180091 16.18404342 0.027699345 0.037549576 2327.313996 -3.366854981 0.151615021 EQSSDLTPSGDVS(ph)PVKPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQSSDLTPSGDVSPVKPLSR 20 1 Q8WYQ5-3;Q8WYQ5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPS(0.001)GDVS(0.999)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR;EQSSDLTPSGDVS(1)PVKPLSR 258.83 1.73E-36 2474810000 2502810 1702260 2168740 1672640 2760540 2672140 2659210 2320790 2504060 1583930 TRUE FALSE 2601622.871 1994609.913 2225259.146 2003483.2 2291304.397 2051575.982 2450774.172 2289683.606 2413939.37 1894270.757 1.373416583 1.052969807 1.174731298 1.057654082 1.209597091 1.083042629 1.293782403 1.208741463 1.274337029 1 20.85321113 2.24441781 24.99117175 1.214237679 1.152235776 0.009037509 0.114965972 408.8010898 1744259.08 0.037273128 0.03043776 175.5568623 -2.24441781 -0.062001903 EQST(ph)PPKS(ph)PQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 2 EQST(1)PPKS(1)PQ;EQS(0.001)T(0.999)PPKS(1)PQ;EQST(1)PPKS(1)PQ 132.79 0.0053743 1332028000 3614520 1742480 2175780 1638670 2996330 3433900 2793700 2349760 2440420 1461010 TRUE FALSE 3757224.041 2041737.385 2232482.614 1962794.035 2487014.897 2636428.766 2574722.494 2318265.311 2352589.761 1747266.937 2.150343466 1.168532033 1.277699799 1.123350985 1.423374325 1.508887229 1.473571347 1.326795158 1.346439809 1 20.7366686 7.999986186 0.031712879 1.27E-07 3.415204123 0.236050026 0.26076472 2311.821618 5.613929943 187.6812974 479.2510856 99996819.27 -7.999986186 3.415203995 EQSTCNFQAIVISLKEEFYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQSTCNFQAIVISLKEEFYTK 21 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 110.38 0.00016416 0 7977.2 5875.5 7124.5 5900.7 8467.9 9466.2 5252.3 5657.4 8418.6 6239.2 FALSE TRUE 8292.146016 6884.57142 7310.170323 7067.840848 7028.529383 7267.818512 4840.611002 5581.571807 8115.61623 7461.651783 1.11130166 0.922660507 0.979698669 0.947222016 0.94195355 0.97402274 0.648731828 0.748034345 1.087643389 1 12.86527932 2.383767555 24.50847476 0.829398447 0.973798759 0.117280476 0.125830931 21.46822501 5624.422192 0.043480695 0.036378557 241.9733602 -2.383767555 0.144400312 EQSTPPKS(ph)PQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EQSTPPKSPQ 10 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 EQST(0.001)PPKS(0.999)PQ;EQST(0.051)PPKS(0.949)PQ;EQST(0.001)PPKS(0.999)PQ;EQSTPPKS(1)PQ;EQST(0.021)PPKS(0.979)PQ;EQST(0.021)PPKS(0.979)PQ;EQS(0.014)T(0.082)PPKS(0.904)PQ 173.76 8.72E-06 3682050000 7444394 4678852 5773383 4527197 7118338 7790576 7158424 6033659 6527768 4162691 TRUE FALSE 7738304.423 5482408.435 5923842.104 5422663.054 5908365.449 5981332.791 6597328.022 5952787.67 6292834.905 4978290.602 1.554409946 1.101263239 1.189934975 1.089262056 1.186826146 1.201483254 1.325219548 1.195749334 1.264055357 1 22.24721902 4.746664588 24.90269272 1.185473259 1.554410137 0.627958495 0.087656198 632.4657689 1943457.096 0.020242234 0.227317677 55803.9046 -4.746664588 0.368936879 EQTLS(ph)PTITSGLHNIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.02)LS(0.789)PT(0.139)IT(0.051)S(0.001)GLHNIAR;EQT(0.002)LS(0.454)PT(0.454)IT(0.088)S(0.002)GLHNIAR;EQT(0.001)LS(0.496)PT(0.496)IT(0.007)S(0.001)GLHNIAR;EQT(0.003)LS(0.559)PT(0.431)IT(0.006)SGLHNIAR;EQTLS(0.914)PT(0.086)ITSGLHNIAR;EQT(0.136)LS(0.71)PT(0.062)IT(0.082)S(0.009)GLHNIAR 249.59 2.95E-21 6941098000 1111145 1948850 1716658 1857114 1865422 2273754 1667736 1813935 1825688 1883965 TRUE FALSE 1155013.863 2283549.828 1761395.518 2224445.606 1548338.235 1745709.093 1537014.495 1789622.168 1759981.846 2253091.871 0.512635049 1.013518293 0.781768174 0.987285798 0.687205992 0.774805997 0.682180125 0.794296136 0.781140737 1 21.10347471 -1.085451719 4.812839646 1.000008486 0.786058436 0.187694668 0.137036624 0.135948323 80884095.5 1445.524321 0.029513155 0.082138786 1.085451719 -0.213950051 EQTLSPT(ph)ITSGLHNIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 EQTLS(0.342)PT(0.655)IT(0.002)SGLHNIAR;EQT(0.001)LS(0.098)PT(0.3)IT(0.3)S(0.3)GLHNIAR 258.06 4.21E-26 5157780000 438830 720950 635560 609350 654330 846130 611380 701980 592650 646890 TRUE FALSE 456155.3473 844767.5543 652123.2157 729877.6113 543107.2203 649629.1307 563458.4381 692571.1063 571320.6423 773635.71 0.589625506 1.091944882 0.842933188 0.943438367 0.702019327 0.839709339 0.728325271 0.895216052 0.738487941 1 19.56129486 4.795460718 23.02454331 0.853083849 0.589620366 0.322683368 0.118480946 36471.17027 14756599.1 0.026656298 45.69342734 62439.68708 -4.795460718 -0.263463483 EQTLSPTIT(ph)SGLHNIAR ddPTM_MDA-MB-175_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(0.023)PT(0.092)IT(0.442)S(0.442)GLHNIAR 279.1 8.27E-35 439120000 149720 230190 212140 210230 236880 265910 220010 230690 213440 235370 TRUE FALSE 155631.0612 269723.3419 217668.5427 251812.8665 196615.2222 204156.4324 202765.0413 227597.9779 205758.3361 281486.2451 0.552890466 0.958211446 0.773283052 0.894583202 0.698489627 0.725280315 0.720337298 0.80855808 0.730971192 1 18.1027049 -1.487899474 5.707069046 1.000274225 0.770543412 0.311797966 0.105241483 0.000336843 3.02E-05 0.093474166 0.02200606 0.032516255 1.487899474 -0.229730814 EQTLSPTITSGLHNIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;O94979-7;H7BXG7;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 0 ; 176.11 1.15E-09 686770000 555580 698580 672010 674310 737070 816910 695370 691390 651380 707000 FALSE TRUE 577514.7274 818555.6808 689523.1327 807686.5054 611783.1047 627195.0329 640865.0824 682123.0479 627936.961 845523.1137 0.683026541 0.968105623 0.815498857 0.955250652 0.723555743 0.741783427 0.757950992 0.806746778 0.742660905 1 19.68948467 5.017490196 15.52544285 0.821547469 0.424172894 0.163860482 0.098837781 1945227.976 39338156.03 0.022778921 17590458.09 104109.4606 -5.017490196 -0.397374575 EQVANSAFVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;; 267.85 7.03E-21 2731040000 1128610 1095710 1122460 994830 1359670 1476800 1240980 1160180 1121000 1012480 FALSE TRUE 1173168.394 1283889.669 1151712.23 1191604.405 1128553.779 1133835.581 1143708.745 1144629.685 1080655.429 1210856.071 0.968875181 1.060315672 0.95115535 0.984100781 0.932029666 0.936391705 0.944545576 0.945306145 0.892472239 1 20.20759596 3.775546243 1.490000943 0.940297669 1.010979266 0.314203565 0.035842207 0.423184394 1.797219822 0.010005883 0.02546308 5964.11821 -3.775546243 0.070681597 EQVEPTPEDEDDDIELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQVEPTPEDEDDDIELR 17 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 326.89 1.58E-71 1036230000 309760 326000 337910 318490 368620 404810 338990 337340 337690 331330 FALSE TRUE 321989.564 381987.9641 346716.2122 381486.3714 305962.1041 310799.0125 312419.078 332818.5091 325536.6029 396247.7698 0.812596533 0.964012906 0.87499852 0.96274705 0.772148457 0.784355235 0.788443751 0.839925255 0.821548101 1 18.59604329 5.098155191 12.79243345 0.857719076 2.76E-05 0.028914337 0.078740276 1041552.32 2635390.286 0.018880573 24445814.18 125358.9053 -5.098155191 -0.857691432 EQWDTIEELIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EQWDTIEELIR 11 0 Q16698-2;Q16698 Q16698-2 DECR1 "2,4-dienoyl-CoA reductase, mitochondrial" 0 ;;;;; 178.53 1.75E-05 208404000 192800 200829 184323 216670 177424 275510 200596 159891 183516 188943 FALSE TRUE 200411.8929 235319.8185 189126.6088 259526.6793 147265.5319 211526.9779 184872.7614 157747.9227 176911.295 225962.7633 0.88692442 1.041409722 0.836981306 1.148537376 0.651724778 0.936114317 0.818155871 0.698114682 0.782922338 1 17.78572552 3.232767686 24.9999985 0.798624149 0.972853533 0.291029873 0.123764032 159.7765792 689532.4747 0.033453311 0.041011547 1709.100835 -3.232767686 0.174229384 EQWEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQWEER 6 0 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4 A0A2R8Y5S7 RDX Radixin 0 101.28 0.085378 158270000 262020 314740 271590 229890 300250 389470 298510 274120 335120 269360 FALSE TRUE 272364.7519 368794.1467 278667.8585 275361.5558 249213.6122 299021.495 275112.0062 270445.8698 323059.0967 322135.9348 0.845496334 1.144840134 0.865062939 0.854799251 0.773628724 0.928246317 0.854024579 0.839539587 1.002865753 1 18.29731008 EQWIQDAEECDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQWIQDAEECDR 12 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 ; 213.84 9.03E-09 464200000 305170 332230 318340 343280 358390 438540 308260 307890 307590 333340 FALSE TRUE 317218.3472 389287.9181 326636.2019 411179.7594 297470.9958 336695.7311 284097.7757 303763.2382 296519.896 398651.5908 0.795728286 0.976511638 0.819352561 1.03142636 0.746192923 0.844586448 0.712646788 0.761976736 0.743807131 1 18.6047689 3.205701439 24.99339638 0.783914908 0.904637433 0.195887014 0.099670421 240.2839792 182764.4962 0.026410155 0.031568102 1605.836922 -3.205701439 0.120722524 EQWWLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EQWWLSLR 8 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 135.83 0.0019006 456270000 320180 321900 316030 393850 450160 476660 396850 329740 383170 347800 FALSE TRUE 332820.9536 377183.821 324266.0014 471752.3545 373641.964 365962.9389 365743.86 325320.3746 369379.7865 415944.751 0.800156638 0.906812311 0.779589118 1.134170712 0.898297101 0.879835454 0.879308752 0.782124005 0.888050121 1 18.66603239 0.947140661 22.31270696 1.000000001 0.880644432 0.118192142 0.095745038 10848.41981 4579286.367 0.092432598 0.023108149 8.854023319 -0.947140661 -0.119355569 EQYELVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EQYELVHR 8 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 136.57 0.0016562 0 159950 173770 176050 185240 201720 204540 180400 188280 169580 178020 FALSE TRUE 166264.9495 203613.6458 180638.0076 221879.9191 167431.7065 157038.6848 166259.7766 185756.4146 163476.8489 212899.6106 0.780954691 0.956383364 0.848465655 1.042180953 0.786435006 0.737618469 0.780930393 0.872507066 0.767858844 1 17.69981379 EQYVPPRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EQYVPPRSPK 10 1 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK;EQYVPPRS(1)PK 80.96 0.013592 2868950000 4429130 2296803 2915688 2288393 3938380 4407860 3825840 3108635 3240472 2124626 TRUE FALSE 4603995.472 2691261.049 2991673.225 2741030.305 3268935.574 3384201.317 3525960.664 3066968.833 3123848.046 2540905.786 1.811950485 1.059173883 1.177404231 1.078761094 1.286523724 1.33188776 1.387678631 1.207037604 1.229423012 1 21.27691145 -4.281880934 0.233073109 6.03E-23 1.302750086 0.16750391 0.199497693 225.3157555 3.060402957 106.7303605 0.326762585 5.23E-05 4.281880934 1.302750086 ERAS(ph)LDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERASLDK 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK;ERAS(1)LDK 113.93 0.0036457 3851010000 3283630 1995310 2584740 2046860 3318780 3336790 3552730 2638070 2682690 1521730 TRUE FALSE 3413270.248 2337988.971 2652100.448 2451722.799 2754654.961 2561871.092 3274257.739 2602710.987 2586140.511 1819883.858 1.875542899 1.284691306 1.457291044 1.347186408 1.513643274 1.407711311 1.799157526 1.430152246 1.421047008 1 20.79541495 0.713163287 2.081707595 1.00042277 1.506170261 0.430134934 0.177100602 1.176227697 7.160042382 0.159263829 0.043701245 5.166105688 -0.713163287 0.505747491 ERASS(ph)PPDRIDIFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERASSPPDRIDIFGR 15 2 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 ERAS(0.125)S(0.875)PPDRIDIFGR;ERAS(0.044)S(0.956)PPDRIDIFGR;ERAS(0.144)S(0.856)PPDRIDIFGR;ERAS(0.159)S(0.841)PPDRIDIFGR 114.4 0.00031785 420963000 160127 168840.9 164129 159909 197383 202147 176157 179113 186421 186316 TRUE FALSE 166448.9376 197838.0112 168406.3366 191538.5229 163831.9082 155201.4228 162349.354 176712.2832 179711.7446 222821.053 0.74700723 0.88787845 0.755791853 0.859606937 0.735262247 0.696529438 0.728608683 0.793068163 0.806529465 1 17.76552602 0.630343494 1.974396315 0.999935292 0.775718824 0.590135537 0.055853087 1.42124699 6.691409933 0.054486595 0.01504935 4.269170443 -0.630343494 -0.224216468 ERAVELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERAVELLR 8 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ;; 185.81 0.00019224 762990000 338586 117375 174211 148036 613840 310680 576794 324454 250882 307511 FALSE TRUE 351953.6367 137533.2432 178751.0818 177317.079 509499.6961 238529.2784 531583.3791 320105.2248 241852.8058 367761.8928 0.95701497 0.373973611 0.486051125 0.482151855 1.385406444 0.648597049 1.445455306 0.870414339 0.657634221 1 18.48841247 3.268718229 24.99648303 1.000697365 0.554113988 0.3495389 0.284436835 213.5182457 176975.6277 0.074880757 0.101376704 1856.599499 -3.268718229 -0.446583377 ERDAEQSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERDAEQSGSPR 11 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5 P08651-3 NFIC Nuclear factor 1 C-type 1 ERDAEQSGS(1)PR;ERDAEQS(0.008)GS(0.992)PR;ERDAEQS(0.007)GS(0.993)PR;ERDAEQS(0.008)GS(0.992)PR 225.32 1.46E-11 2146910000 2346280 2415580 2519990 2268690 2749060 2855010 2666530 2604220 2479920 2222930 TRUE FALSE 2438912.946 2830437.074 2585663.01 2717430.111 2281775.763 2191977.196 2457520.411 2569314.691 2390668.164 2658470.573 0.917412053 1.064686254 0.972612989 1.022177991 0.858303939 0.824525657 0.924411365 0.966463468 0.899264482 1 21.34216507 3.25041347 24.9985925 0.911191274 0.997711946 0.323201185 0.058076857 262.5876398 553814.4959 0.016396732 0.022027155 1779.973227 -3.25041347 0.086520671 ERDEDSLHQTDLFDSHMLWFLMHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERDEDSLHQTDLFDSHMLWFLMHHLR 26 1 Q5TAQ9;V9GY98 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 0 ; 174.99 6.63E-13 266540000 194755 141837 163987 133921 198247 227180 181212 139696 173873 130309 FALSE TRUE 202444.0778 166196.4014 168260.6359 160410.1741 164549.0458 174420.8879 167008.1299 137823.6036 167615.3447 155840.5536 1.299046192 1.066451559 1.07969737 1.029322409 1.055880783 1.119226568 1.071660271 0.884388565 1.075556656 1 17.24971118 7.967206878 0.967180939 1.02571272 199.9968987 0.614812597 0.060871598 933.5027021 1.56937133 0.020497933 411065.3817 92727142.88 -7.967206878 198.971186 ERDFYFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 152.34 0.0004183 1032760000 1812200 1679500 1827360 1599630 2270310 2333950 2150930 1967180 1979450 1745090 FALSE TRUE 1883747.055 1967941.06 1874982.503 1916032.04 1884403.517 1791925.484 1982334.486 1940813.17 1908209.981 2087006.974 0.902606977 0.942948962 0.898407397 0.918076491 0.902921524 0.858610204 0.949845646 0.929950496 0.914328512 1 20.99300399 0.045812119 0.58675387 1.005332715 0.909520877 0.541759901 0.024171503 3.082635214 1.276238975 0.063821744 0.010210811 1.111250882 -0.045812119 -0.095811838 ERDHS(ph)PTPS(ph)VFNSDEERYR ddPTM_MDA-MB-175_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(0.095)PS(0.556)VFNS(0.347)DEERY(0.002)R 79.237 0.0048287 722350000 114500 128990 141080 95466 133720 163560 153180 146210 114530 123560 TRUE FALSE 119020.5484 151143.0291 144756.6607 114348.8899 110990.3222 125575.6688 141173.3513 144250.2941 110408.0877 147769.2163 0.805448871 1.022831635 0.979613104 0.773834312 0.751105846 0.849809398 0.955363741 0.976186365 0.747165685 1 17.17298623 -0.436481243 8.93127259 0.999999976 0.884299513 0.119995878 0.098957031 0 0 0.099804396 0.023524122 0.366031749 0.436481243 -0.115700463 ERDHS(ph)PTPSVFNS(ph)DEERYR ddPTM_MDA-MB-175_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(0.102)PS(0.381)VFNS(0.517)DEERYR 109.97 0.00013136 652750000 127030 189880 168220 125680 195450 220740 171320 189340 196110 175110 TRUE FALSE 132045.2425 222490.4129 172603.9514 150539.1289 162227.4788 169476.4803 157891.4907 186802.207 189052.0394 209419.4518 0.630529979 1.06241522 0.824202097 0.718840239 0.774653345 0.809268093 0.753948544 0.892000267 0.902743455 1 17.67603593 1.19436176 1.504410753 0.992501776 0.805204733 0.27244598 0.105519095 0.503228849 2.169768074 0.095375164 0.028824598 15.6445026 -1.19436176 -0.187297044 ERDHS(ph)PTPSVFNSDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.752)PT(0.194)PS(0.054)VFNSDEER;ERDHS(0.975)PT(0.025)PSVFNSDEER;ERDHS(0.333)PT(0.333)PS(0.333)VFNSDEER 250.41 1.64E-21 2271570000 947730 1005150 1087090 1037790 1201900 1372680 1173550 1107620 1025940 1004230 TRUE FALSE 985147.1122 1177776.694 1115420.458 1243061.765 997601.4673 1053895.873 1081564.084 1092774.166 989016.6198 1200989.641 0.820279441 0.980671817 0.928751107 1.035031212 0.830649518 0.877522867 0.90056071 0.909894747 0.823501374 1 20.19579228 3.212855564 24.99998706 0.887704051 0.943116128 0.118036243 0.067751761 434.9254148 422994.6995 0.018551172 0.022180122 1632.508924 -3.212855564 0.055412076 ERDHS(ph)PTPSVFNSDEERYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERDHSPTPSVFNSDEERYR 19 2 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.984)PT(0.015)PS(0.001)VFNSDEERYR;ERDHS(0.91)PT(0.08)PS(0.01)VFNSDEERYR;ERDHS(0.999)PT(0.001)PSVFNSDEERYR;ERDHS(0.988)PT(0.012)PSVFNSDEERYR 201.15 3.20E-16 2033420000 233281 760823 755312 594531 611991 905029 347371 679678 552477 988812 TRUE FALSE 242491.114 891488.4319 774996.0512 712127.4573 507964.9884 694849.7306 320143.1533 670568.0281 532593.4607 1182550.779 0.205057676 0.753869049 0.655359638 0.602196091 0.429550255 0.587585533 0.270722542 0.567052206 0.450376821 1 20.1734707 -1.557890028 3.656949557 1.011803209 0.511599565 0.461723955 0.160899981 0.014873059 0.00179809 0.149645423 0.03478409 0.027676424 1.557890028 -0.500203644 ERDHSPT(ph)PSVFNSDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDHSPTPSVFNSDEER 17 1 Q6UN15;Q6UN15-5;Q6UN15-3 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 ERDHS(0.337)PT(0.654)PS(0.009)VFNSDEER 171.56 2.51E-09 202820000 101740 110120 109290 108990 107710 131800 111730 114440 108350 104680 TRUE FALSE 105756.7738 129032.2534 112138.1872 130547.8967 89401.49267 101191.4474 102972.3106 112906.119 104450.5047 125190.0418 0.844769858 1.030691032 0.895743668 1.042797772 0.714126231 0.808302689 0.822527968 0.901877796 0.834335568 1 16.93376028 3.251773084 24.99975996 0.842740884 0.954888661 0.264641059 0.086909658 295.0783975 558324.552 0.022893847 0.030816056 1785.554392 -3.251773084 0.112147778 ERDLFFELDAMDHLESFIAECDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDLFFELDAMDHLESFIAECDRR 24 2 Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 84.762 0.0076463 16448000 10262 13333 14015 9674.4 15927 16164 11156 13673 12544 15771 FALSE TRUE 10667.15168 15622.83903 14380.24241 11587.96744 13219.73423 12410.15597 10281.56357 13489.7358 12092.54389 18861.0255 0.565565838 0.82831334 0.76243163 0.614386924 0.700902198 0.657978855 0.545122192 0.715217516 0.641139258 1 14.2031205 -1.572374751 4.758629092 1.003008485 0.673969814 0.592345363 0.082043252 0.00257794 0.000231662 0.078203714 0.018284221 0.026768575 1.572374751 -0.329038671 ERDLS(ph)RDR ddPTM_MDA-MB-175_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 77.744 0.025533 2332230000 920920 1178970 1099900 949620 1327900 1346890 1102260 1091280 1094210 1213170 TRUE FALSE 957278.6327 1381448.926 1128564.298 1137452.002 1102184.032 1034095.21 1015861.981 1076653.177 1054829.596 1450867.434 0.65979745 0.95215379 0.777854869 0.783980655 0.75967246 0.712742726 0.700175603 0.7420755 0.727033753 1 20.46848428 4.01315159 24.99444235 0.757740874 0.820732768 0 0.104441528 667.2448126 1268071.025 0.023673742 0.051099652 10307.45838 -4.01315159 0.062991894 ERDLS(ph)RDRS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDLSRDRSR 10 3 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 2 ERDLS(1)RDRS(1)R 73.022 0.012748 0 274040 363900 365980 240960 437220 460260 246730 373280 380680 452520 TRUE FALSE 284859.3108 426396.9943 375517.7395 288621.1688 362901.5006 353371.5903 227390.6579 368276.7922 366979.4012 541182.63 0.526364475 0.787898522 0.693883578 0.533315655 0.670571228 0.652961811 0.420173607 0.680503719 0.678106393 1 19.04575601 0.673647905 1.973846109 0.999729926 0.621379804 0.570871469 0.098316009 1.094801932 5.641455541 0.092412836 0.02554896 4.716804812 -0.673647905 -0.378350122 ERDPQQEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDPQQEQER 10 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 0 99.439 0.0042812 74576000 72642 128020 119870 121350 87370 143810 102100 124100 104660 139320 FALSE TRUE 75509.96225 150006.4391 122993.9107 145352.6678 72518.87861 110412.307 94097.13521 122436.6425 100893.307 166617.0866 0.45319459 0.900306459 0.738183059 0.872375522 0.435242748 0.662670974 0.564750814 0.734838455 0.605539979 1 17.34617683 -1.415618268 4.881347498 1.000460488 0.672064137 0.315099946 0.148509134 0.000707844 8.47E-05 0.136761213 0.032190599 0.038404466 1.415618268 -0.328396352 ERDQGGFGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERDQGGFGDR 10 1 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ; 84.605 0.013504 555420000 298300 349190 349350 349910 400170 418490 380300 382590 375230 317400 FALSE TRUE 310077.1143 409160.6662 358454.348 419121.1536 332149.2463 321302.0398 350491.0923 377462.0068 361725.5456 379588.453 0.816877099 1.077905987 0.944323636 1.104146215 0.875024632 0.846448403 0.923344979 0.994398022 0.952941384 1 18.53407658 1.716776849 11.51779557 0.9799197 0.946626741 0.042245645 0.087140515 0.506502291 183.0796301 0.041334449 0.022561255 52.0926977 -1.716776849 -0.033292959 ERDQGGFGDRNEYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERDQGGFGDRNEYGSR 16 2 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;; 267.62 1.33E-27 1094600000 304326 367160 364370 302944 427810 444710 277548 334320 359160 424840 FALSE TRUE 316341.0255 430216.8739 373865.7815 362865.419 355091.009 341432.8421 255793.0625 329838.9872 346233.9018 508079.2639 0.622621406 0.84675149 0.735841448 0.71419057 0.698889001 0.67200704 0.503451096 0.649188051 0.68145647 1 18.95469406 0.896038217 19.03243428 1 0.678120703 0.57470088 0.082440587 9028.067331 1652788.55 0.085636517 0.021409129 7.871150513 -0.896038217 -0.321879297 ERDQRPS(ph)SPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.9)S(0.1)PIR 119.96 0.0004061 1010300000 439230 495620 463580 405920 472520 565850 462980 481680 446830 415820 TRUE FALSE 456571.1396 580738.8796 475661.2756 486209.7644 392201.2192 434439.913 426690.4178 475223.8675 430748.6756 497291.9676 0.918114849 1.167802654 0.956503034 0.977714896 0.788673947 0.873611362 0.858027971 0.955623453 0.866188685 1 18.9237336 3.711664687 2.375190406 0.891271716 1.039214567 0.309516528 0.081942277 0.30580622 3.376753842 0.021717904 0.041475155 5148.309965 -3.711664687 0.147942851 ERDQRPSS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDQRPSSPIR 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 ERDQRPS(0.032)S(0.968)PIR 90.707 0.005889 332290000 40502 54431 51517 45399 51123 74968 51675 55007 38558 55350 TRUE FALSE 42101.05023 63779.10084 52859.57534 54378.7867 42433.13072 57557.81815 47624.57847 54269.72114 37170.30511 66194.77276 0.636017747 0.963506606 0.798546065 0.82149669 0.641034465 0.869522105 0.719461318 0.819849044 0.561529311 1 16.01442967 ERDSASFNPELLTHILDGSPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERDSASFNPELLTHILDGSPEK 22 1 Q15067-2;Q15067;I3L0T4;I3L2U4;K7ELT1 Q15067-2;K7ELT1 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;; 196.32 1.29E-22 296067000 508450 482452 511075 481117 718470 737292 620751 539266 554392 467962 FALSE TRUE 528523.9986 565309.378 524394.0344 576280.5066 596344.726 566067.1068 572094.9146 532038.0213 534439.5402 559650.1942 0.944382766 1.010112002 0.937003221 1.029715548 1.065566906 1.011465935 1.022236605 0.950661729 0.954952836 1 19.09416584 6.125940329 1.126579822 0.998847803 7.06E-07 0.144626906 0.038008916 75.4814578 5.97160851 0.011756476 171.7468016 1336411.886 -6.125940329 -0.998847097 ERDTSPDKGELVS(ph)DEEEDT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERDTSPDKGELVSDEEEDT 19 2 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 ERDTSPDKGELVS(0.999)DEEEDT(0.001) 76.959 0.0096385 113410000 150200 89850 120320 81755 150860 160020 136880 110160 138140 89092 TRUE FALSE 156130.012 105281.0386 123455.638 97925.89499 125216.8711 122857.7801 126150.9879 108683.4854 133168.3684 106547.8716 1.465350829 0.988110198 1.15868704 0.919078847 1.17521701 1.153075873 1.183984119 1.020043702 1.249845411 1 16.70114225 4.749205547 24.66243458 1.096360907 1.465351081 0.546546545 0.101396075 919.9400035 2131289.314 0.022512664 0.321627743 56131.35767 -4.749205547 0.368990175 ERDVIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERDVIMR 7 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QL52;Q14240;Q14240-2;E7EQG2 P60842;Q14240 EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed" 0 ;; 138.54 0.0025311 1681260000 470068 456078 545322 515270 611442 646026 644006 621052 607445 485461 FALSE TRUE 488626.6476 534405.8487 559533.5393 617188.8681 507509.3072 495996.2521 593527.1269 612727.8138 585583.1731 580577.7882 0.841621325 0.920472432 0.963752921 1.063059732 0.874145235 0.854314895 1.022304227 1.055375914 1.008621385 1 19.14712985 2.132001271 8.829090626 1.030156027 0.926177781 0.396581115 0.0610136 0.287975094 21.87009647 0.024345766 0.017973647 135.5193378 -2.132001271 -0.103978247 ERDVYEELLTQAEIQGNINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERDVYEELLTQAEIQGNINK 20 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 266.83 7.91E-37 717360000 944070 713660 952370 845500 1005260 1121330 1226340 915760 971280 545300 FALSE TRUE 981342.6126 836225.5535 977189.5446 1012737.376 834386.2643 860918.1014 1130216.266 903485.7351 936323.8225 652141.0946 1.504801063 1.282277042 1.498432705 1.552942124 1.279456656 1.320140854 1.733085487 1.38541451 1.435768778 1 19.31482461 0.382154072 2.232040109 1.000006662 1.445161278 0.504517331 0.13192594 10.91934918 38.18134832 0.123709864 0.033469188 2.410760525 -0.382154072 0.445154616 ERECSPS(ph)SPLPPLPEDEEGSEVTNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERECSPSSPLPPLPEDEEGSEVTNSK 26 1 Q96GY3 Q96GY3 LIN37 Protein lin-37 homolog 1 ERECS(0.054)PS(0.523)S(0.423)PLPPLPEDEEGSEVTNSK 71.44 0.017818 133430000 25920 22377 27953 24267 38875 37885 31672 32200 35723 24449 TRUE FALSE 26943.34161 26220.07568 28681.47814 29066.94017 32267.04139 29086.7829 29189.46588 31768.41167 34437.33621 29239.31345 0.921476548 0.89674047 0.980921737 0.994104743 1.103549899 0.994783375 0.998295187 1.086496498 1.17777513 1 14.83562182 3.828467332 1.331048436 1.05983851 0.902322207 0.524062655 0.055487076 0.386360861 1.280545602 0.017680788 0.05207836 6737.012173 -3.828467332 -0.157516303 EREDEIATMECINNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EREDEIATMECINNGK 16 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 314.34 8.34E-58 1484860000 763191 488806 702704 585417 893540 873740 844103 710588 794470 410015 FALSE TRUE 793322.37 572754.6281 721017.0435 701210.7353 741656.39 670827.1267 777940.0012 701063.7301 765877.1799 490349.589 1.61787098 1.168053652 1.470414291 1.430022072 1.512505377 1.368058915 1.586500771 1.429722275 1.56190032 1 18.90345114 -1.032451089 6.019671015 0.99999932 1.453840475 0.559338471 0.122506955 1.03E-06 1.65E-07 0.108900338 0.025668017 0.0928002 1.032451089 0.453841155 EREDLYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EREDLYAK 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 123.86 0.0012125 454700000 525990 464620 550100 444650 686960 653920 616090 536300 565840 461260 FALSE TRUE 546756.4914 544414.8708 564436.0579 532600.4429 570190.7846 502056.9903 567799.2559 529111.7757 545475.5289 551635.0656 0.991156156 0.986911284 1.023205545 0.965494175 1.033637671 0.910125229 1.029302326 0.959169945 0.988834037 1 19.07335464 EREEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EREEIEK 7 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;; 122.19 0.0039811 5655820000 3401450 2449730 3181500 2305240 4142260 3868430 3720380 3070110 3470840 2230880 FALSE TRUE 3535741.872 2870452.071 3264412.504 2761209.592 3438160.125 2970045.759 3428766.894 3028960.197 3345925.146 2667978.223 1.325251399 1.075890368 1.223552904 1.034944576 1.288676232 1.113219641 1.285155503 1.135301694 1.254105119 1 21.34731546 -1.662114536 5.748093508 0.99787059 1.186404542 0.272095504 0.094113816 0.002269009 0.000133377 0.080507708 0.018776412 0.021771355 1.662114536 0.188533952 EREELWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EREELWK 7 1 Q16537-2;Q16537;Q16537-3 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 0 98.933 0.0099397 175340000 222630 194140 227320 199950 292400 279490 248250 216170 248150 205010 FALSE TRUE 231419.6043 227482.0348 233244.1459 239499.5132 242697.9524 214582.6832 228791.5163 213272.5947 239219.13 245177.7843 0.943884883 0.927824825 0.951326592 0.976840189 0.989885577 0.875212588 0.933165772 0.869869166 0.975696598 1 17.90346874 2.74838399 24.99717018 0.918680773 0.956959876 0.061541204 0.041080851 1232.062893 3135182.999 0.01223519 0.012838336 560.2527416 -2.74838399 0.038279102 EREEQETTSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EREEQETTSSK 11 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 91.64 0.0096589 225890000 462640 348840 454090 321670 602680 749550 588420 418130 512700 387850 FALSE TRUE 480905.3844 408750.5564 465923.9584 385295.3659 500236.6689 575478.372 542298.1029 412525.6513 494248.0272 463841.7817 1.03678755 0.881228411 1.004488981 0.830661189 1.078464012 1.240678168 1.169144575 0.889367167 1.065553054 1 18.82327325 3.203412744 24.75107883 1.070337999 0.938943924 0.294510062 0.102708861 227.3837119 160122.5533 0.03215325 0.03843203 1597.396558 -3.203412744 -0.131394074 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_MDA-MB-175_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 296.18 1.29E-70 4008750000 2429260 1461475 2080518 1565868 2580300 2741690 2665560 2040743 2315400 1180939 TRUE FALSE 2525169.061 1712471.963 2134738.008 1875592.017 2141701.528 2104974.048 2456626.442 2013390.178 2232069.206 1412321.387 1.787956399 1.212522857 1.511510077 1.328020686 1.516440626 1.490435582 1.739424514 1.425589244 1.580425835 1 20.42963699 -1.519598436 6.352619984 0.999556021 1.500250477 0.468404313 0.162762656 0.000944242 7.14E-05 0.145390363 0.0342399 0.030227454 1.519598436 0.500694456 EREKEPS(ph)RER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EREKEPSRER 10 3 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 EREKEPS(1)RER 118.76 0.0043206 742620000 581130 325430 428210 334430 636510 582340 551200 490430 493680 272590 TRUE FALSE 604073.4611 381320.071 439369.5044 400579.2558 528316.2576 447100.3604 507995.5037 483856.588 475912.5532 325998.7914 1.852992947 1.169697806 1.347764212 1.228775279 1.620608025 1.371478583 1.558274193 1.484228165 1.45985987 1 18.31450709 -1.456133354 6.923278023 0.999923387 1.446315079 0.347061675 0.186835243 0.000205907 1.62E-05 0.16859425 0.039731285 0.034983773 1.456133354 0.446391692 ERELEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERELEEAR 8 1 Q9Y490;Q9Y4G6;H0YMT1;A0A1B0GVU7 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 ; 166.19 0.00029177 226056000 154946 199657 192462 189685 228884 249089 211058 217403 198048 215711 FALSE TRUE 161063.3877 233946.5366 197477.7178 227204.1268 189978.3794 191241.8547 194514.7225 214489.0684 190920.2912 257975.4404 0.624336129 0.906855847 0.76549038 0.880719988 0.736420409 0.741318067 0.754004808 0.831432124 0.740071578 1 17.9768742 -2.000186822 2.582879669 1.217393812 0.782842783 0.430633088 0.076997351 8119764.563 3912712.02 10497864.61 0.017251488 0.009995699 2.000186822 -0.434551029 ERENMDTDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERENMDTDDER 11 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ; 90.653 0.011886 297620000 254101 308450 291973 299080 321270 367040 312780 305990 291850 270294 FALSE TRUE 264133.1037 361423.8881 299582.0562 358237.1313 266660.6402 281800.5225 288263.4863 301888.7045 281346.3755 323252.9342 0.817109686 1.118083859 0.926772891 1.108225459 0.824928754 0.871764778 0.891758298 0.933908629 0.870359851 1 18.30230394 3.22395357 24.99996292 0.896469775 0.996816637 0.202125288 0.0910335 333.6069812 570967.372 0.024236314 0.02908618 1674.76382 -3.22395357 0.100346862 EREPEAASS(ph)RGSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.217)S(0.42)RGS(0.363)PVR 141.7 3.72E-06 722570000 217860 269980 285200 149880 353680 327620 199330 245050 262800 359320 TRUE FALSE 226461.281 316346.9648 292632.5463 179525.8167 293561.5999 251535.2201 183705.9937 241765.5056 253341.8793 429721.8744 0.526995004 0.736166771 0.680981267 0.417772116 0.683143255 0.585344231 0.42749975 0.56260926 0.589548483 1 18.71304369 0.885449758 13.08419782 1 0.576536601 0.619977106 0.098944185 154.5876389 17659.00941 0.095548419 0.023889459 7.681565848 -0.885449758 -0.4234634 EREPEAASSRGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EREPEAASSRGSPVR 15 2 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EREPEAAS(0.005)S(0.022)RGS(0.973)PVR;EREPEAAS(0.003)S(0.01)RGS(0.987)PVR 108.45 0.00056256 632607000 161200 244687 220583 155318 261121 283113 113234 191687 179899 292557 TRUE FALSE 167564.3005 286710.0888 226331.5742 186039.4368 216735.7457 217364.2964 104358.4232 189117.7493 173424.4701 349877.9428 0.478922161 0.819457456 0.646887233 0.53172668 0.619461015 0.621257501 0.298270941 0.540524926 0.495671344 1 18.41649219 -1.160600468 5.485784754 1.000010908 0.560945733 0.515840196 0.127488517 1.75E-05 2.68E-06 0.127334485 0.030012281 0.069087509 1.160600468 -0.439065175 EREQPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 172.15 0.00083115 323890000 149735 164555 160449 154937 194093 209910 175873 164836 166296 162280 FALSE TRUE 155646.6534 192816.0412 164630.4328 185583.0762 161101.1412 161161.5837 162087.6147 162626.643 160311.0394 194075.659 0.801989566 0.993509656 0.848279654 0.956240866 0.830094521 0.830405959 0.835177454 0.837954867 0.826023419 1 17.56625966 3.212072969 24.99914455 0.848046719 0.902989231 0.057430258 0.06978505 426.1464056 402197.4751 0.018274498 0.021848358 1629.569807 -3.212072969 0.054942512 ERESLQQMAEVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERESLQQMAEVTR 13 1 K7ELL7;P14314-2;P14314;K7EPW7;K7EKX1;K7EJ70 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 155.57 4.26E-05 570750000 239340 381760 351900 381490 384360 423980 290500 329600 320730 388240 FALSE TRUE 248789.328 447324.3103 361070.8031 456947.5834 319026.6245 325517.0705 267729.8509 325182.2511 309186.99 464308.1947 0.535827993 0.963421097 0.777653307 0.984147143 0.687100999 0.701079744 0.57662099 0.70035863 0.665908966 1 18.82472322 4.79377651 21.9264538 0.762784736 0.535821205 0.201809836 0.142556248 23222.16303 9220213.481 0.034440686 37.89053093 62198.01284 -4.79377651 -0.22696353 ERESSANNSVS(ph)PSESLR ddPTM_MDA-MB-175_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 ERESSANNS(0.022)VS(0.953)PS(0.025)ESLR 110.18 0.0012412 0 30469 36862 32220 41427 24415 40788 34484 27044 32273 34739 TRUE FALSE 31671.93965 43192.76175 33059.67967 49621.13695 20264.94702 31315.60515 31781.05397 26681.51942 31111.50103 41545.44193 0.762344512 1.039651036 0.795747455 1.194382215 0.487777866 0.75376753 0.764970897 0.642224951 0.748854738 1 15.34240258 3.234794326 24.99999995 0.713617042 0.943698134 0.28675809 0.164448955 108.7284566 721721.5282 0.043275959 0.053632422 1717.095008 -3.234794326 0.230081092 EREVDEDS(ph)EPER ddPTM_MDA-MB-175_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 220.64 1.76E-11 1294600000 410470 399270 399530 445410 425820 483520 492340 407550 425280 337620 TRUE FALSE 426675.6726 467841.5166 409942.08 533510.7686 353439.2685 371229.8078 453749.1043 402087.4589 409974.2559 403770.1749 1.056729048 1.158682701 1.015285689 1.321322876 0.875347637 0.919408691 1.123780637 0.995832491 1.015365377 1 18.62317482 3.218356995 24.99999917 0.994721196 1.130716529 0.364607973 0.096408031 281.5277736 348362.1353 0.027368733 0.032749244 1653.320288 -3.218356995 0.135995333 EREVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EREVEER 7 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 172.21 0.00082886 1990555000 1566621 1824387 1741275 1806267 2019389 2286009 1900251 1894292 1771387 1875304 FALSE TRUE 1628472.407 2137711.275 1786654.057 2163541.221 1676133.979 1755118.055 1751304.361 1868902.114 1707635.128 2242733.914 0.726110394 0.953172047 0.79664112 0.964689216 0.747361945 0.782579709 0.780879243 0.833314243 0.761407814 1 21.09682703 EREWQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EREWQK 6 1 O75937;S4R3J5 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 109.11 0.027215 132880000 152520 184060 175560 167950 260280 270260 246210 250300 253070 223420 FALSE TRUE 158541.6074 215670.8732 180135.2378 201170.0087 216037.6986 207496.2108 226911.4168 246945.1379 243962.0601 267194.8714 0.593355728 0.807166964 0.674171764 0.75289622 0.80853984 0.776572581 0.849235675 0.924213615 0.913049187 1 18.02753279 2.425427042 0.343265958 1.017370857 0.634964228 0.807462002 0.050236494 0.664437749 0.180788978 0.058829848 0.091435483 266.3342637 -2.425427042 -0.382406628 ERFS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ERFSPPR 7 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR;ERFS(1)PPR 95.822 0.0098849 3008100000 1605719 1767730 1635123 1972221 1635045 2038236 2139502 1836001 1656236 1360900 TRUE FALSE 1669114.026 2071323.876 1677735.649 2362320.427 1357120.635 1564886.579 1971802.243 1811392.41 1596628.39 1627542.299 1.02554264 1.272669766 1.030839966 1.451464843 0.833846614 0.961502862 1.21152135 1.112961802 0.981005772 1 20.63426361 2.31306257 0.277592558 0.996500968 1.182947098 0.06484555 0.164408686 7.155215805 1.487922595 0.282373114 0.476213358 205.6186815 -2.31306257 0.186446131 ERFS(ph)PPRHELS(ph)PPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 78.987 0.011414 196250000 129010 91682 110070 94853 145040 131990 132650 116440 107200 81696 TRUE FALSE 134103.4144 107427.6703 112938.5146 113614.6403 120386.1526 101337.3228 122252.5464 114879.3123 103341.8929 97702.76704 1.372565164 1.099535597 1.155939776 1.162860006 1.232167279 1.037200132 1.251270052 1.175804082 1.057717157 1 16.5761118 -5 0.108971867 0.441130049 1.27385762 0.35048006 0.085857778 208.1464973 1.512705828 25.93171849 1.066363532 1.00E-05 5 0.832727571 ERFS(ph)PPRHELS(ph)PPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 2 ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR;ERFS(1)PPRHELS(1)PPQKR 85.884 0.010045 11105400000 771320 613865 758900 535139 910040 868420 718400 729480 795550 658205 TRUE FALSE 801772.3092 719291.5385 778677.5574 640987.897 755351.7259 666742.616 662089.9308 719702.5138 766918.3109 787167.6677 1.018553406 0.913771701 0.989214356 0.814296526 0.959581747 0.847014738 0.841104072 0.914293795 0.974275675 1 19.58631144 5.805428464 0.97115733 0.903801874 1.693003017 0.176576245 0.062666379 19.80644656 3.031669557 0.017976121 26.51714922 638893.4922 -5.805428464 0.789201142 ERFS(ph)PPRHELSPPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERFSPPRHELSPPQK 15 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQK;ERFS(1)PPRHELSPPQK 123.55 5.32E-05 547460000 407380 316000 411270 357530 453200 477500 459250 403010 377290 266070 TRUE FALSE 423463.677 370270.5419 421988.0341 428248.3669 376165.2259 366607.8616 423252.785 397608.3101 363711.4066 318201.3223 1.330804265 1.163636088 1.326166815 1.345840941 1.182161102 1.152125513 1.330141503 1.249549522 1.143022926 1 18.27958031 0.984353969 2.647290765 1.000991264 1.259337924 0.578861955 0.069856652 0.192600789 3.134552839 0.066083966 0.017704124 9.64614906 -0.984353969 0.25834666 ERFS(ph)PPRHELSPPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERFSPPRHELSPPQKR 16 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR;ERFS(1)PPRHELSPPQKR 178.32 2.00E-09 2132850000 585487 607890 706190 536871 787150 824086 676113 686726 712342 583102 TRUE FALSE 608602.4789 712290.3788 724593.8915 643062.4814 653350.5242 632704.5156 623117.4964 677521.5612 686704.9506 697349.6727 0.872736452 1.021424985 1.039068232 0.922152123 0.936905185 0.907298792 0.893550998 0.971566472 0.98473546 1 19.41152272 1.501323196 8.379329962 0.987774732 0.945495363 0.143258823 0.049749289 0.254298617 42.0831914 0.028846453 0.013304997 31.71927087 -1.501323196 -0.042279369 ERFTEHEVQIYVGEIVLALEHLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERFTEHEVQIYVGEIVLALEHLHK 24 1 O75582-3;O75582;O75582-2;A0A3B3ISL8;G3V2D1 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 0 ; 155.97 1.17E-08 114737000 224303 123605 198544 156244 274140 251530 275630 216439 246740 139179 FALSE TRUE 233158.6556 144833.1972 203718.2197 187148.5969 227541.7807 193115.9695 254025.4004 213537.9892 237859.8756 166448.4603 1.400785896 0.870138402 1.22391171 1.124363641 1.367040466 1.160214814 1.526150497 1.282907567 1.429030194 1 17.344716 3.24576699 24.89148815 1.316033644 1.139403467 0.114022325 0.182473403 259.5990213 896672.8901 0.046869568 0.062158395 1761.030956 -3.24576699 -0.176630177 ERGDYVLAVK ddPTM_MDA-MB-175_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 ; 100.72 0.0034837 779350000 1298560 1146270 1267410 1062640 1794230 1699260 1587780 1283690 1492330 1313310 FALSE TRUE 1349828.152 1343132.956 1300439.746 1272827.02 1489247.425 1304632.618 1463325.655 1266484.235 1438621.335 1570627.95 0.859419414 0.855156663 0.827974407 0.810393716 0.948185995 0.830643959 0.931681914 0.806355341 0.91595297 1 20.58291004 -4.999999993 0.237438057 1.782100329 0.847412648 0.448850319 0.046626105 148.580106 1.483688787 55.96643061 0.071163215 1.00E-05 4.999999993 -0.934687681 ERGT(ph)PPVDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERGTPPVDPK 10 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERGT(1)PPVDPK 68.809 0.095163 292050000 517360 346920 408070 303130 497350 534350 483490 397450 437020 296050 TRUE FALSE 537785.7723 406500.8113 418704.6394 363088.2092 412810.6246 410255.3107 445592.7904 392122.8328 421291.7356 354055.3293 1.518931443 1.148127927 1.182596631 1.025512623 1.165949473 1.1587322 1.25853999 1.107518516 1.18990367 1 18.43361531 4.738890637 7.087471876 1.143805452 1.524229054 0.709470309 0.073142045 0.055015911 21.98042367 0.016366581 0.09995916 54813.89166 -4.738890637 0.380423602 ERGTGDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERGTGDVK 8 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 93.598 0.0099914 276610000 314130 280270 369080 283120 370350 409260 427260 377610 351630 224400 FALSE TRUE 326532.095 328404.1923 378698.528 339120.291 307398.0393 314215.5674 393770.2448 372548.7556 338974.905 268366.8836 1.216737664 1.223713552 1.411122427 1.263644331 1.145439538 1.170843299 1.467283293 1.388206885 1.263102587 1 18.03384713 2.28094472 24.99990858 1.325711244 1.242655634 0 0.133572553 377.8683568 222880.9242 0.045696481 0.038232177 190.9610176 -2.28094472 -0.083055609 ERGVGQADWT(ph)PDLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERGVGQADWTPDLGLR 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 ERGVGQADWT(1)PDLGLR 85.808 0.011354 53121000 64352 41528 43743 37040 76513 71928 52524 53656 51333 65239 TRUE FALSE 66892.66665 48660.11096 44882.97852 44366.40145 63507.34759 55223.81208 48407.03163 52936.82908 49485.53536 78021.33297 0.857363802 0.623677001 0.575265467 0.568644494 0.813974142 0.707804007 0.620433281 0.678491729 0.634256472 1 16.25158103 -0.998653039 4.546815518 1.00000921 0.67099932 0.534435971 0.090759068 11352733.41 2496853.905 1041.615657 0.020901108 0.100310631 0.998653039 -0.329009889 ERHAS(ph)EMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERHASEMR 8 1 P49754-2;P49754-3;P49754 P49754-2 VPS41 Vacuolar protein sorting-associated protein 41 homolog 1 ERHAS(1)EMR 66.92 0.0366 284690000 97018 97422 97231 93892 116300 145130 103050 98789 102850 98336 TRUE FALSE 100848.3456 114153.4707 99764.91974 112463.5574 96531.36754 111425.757 94972.67173 97464.89504 99148.44859 117603.0564 0.857531671 0.97066755 0.848319106 0.956297912 0.820823629 0.947473308 0.807569757 0.828761581 0.843077141 1 16.84356603 2.895529494 1.336048669 0.858945482 0.905538503 0 0.068860015 1.155603827 4.258295471 0.026644142 0.029108365 786.1935822 -2.895529494 0.046593021 ERHPGSFDVVHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ERHPGSFDVVHVK 13 1 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;;;;; 220.85 1.30E-11 2943380000 2118863 2529880 2886646 2564061 3406110 3620810 3199159 3122379 3086957 2821497 FALSE TRUE 2202517.347 2964367.21 2961874.366 3071224.613 2827140.639 2779931.751 2948400.558 3080528.617 2975858.021 3374315.316 0.652730151 0.878509248 0.877770477 0.910177125 0.837841273 0.823850616 0.873777428 0.912934426 0.881914623 1 21.68616336 8 0.092105592 1.057210968 0.285100445 0.492959069 0.059899167 143.6798839 0.947669338 1.008195052 14.01456839 100000000 -8 -0.772110523 ERHPS(ph)WR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 126.39 0.0023964 1.21073E+11 12938980 15518703 14551018 15058037 17284503 18065267 16090084 16164480 14541299 17236001 TRUE FALSE 13449820.92 18183919.52 14930229.48 18036471.77 14346489.35 13869882.52 14828901.17 15947821.59 14017960.49 20613065.39 0.652490091 0.88215504 0.724309034 0.875001919 0.695990096 0.672868506 0.719393302 0.773675399 0.680052201 1 24.29705573 -1.951421964 7.402321044 1.110549923 0.746983606 0.506867189 0.076256174 0.041631137 0.000273206 0.022094093 0.01644985 0.011183508 1.951421964 -0.363566317 ERHPS(ph)WRS(ph)EETQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.966)EET(0.034)QER;ERHPS(1)WRS(0.699)EET(0.301)QER 145.88 4.54E-06 1327080000 349000 530150 497150 496840 537660 662980 478890 529340 520820 645500 TRUE FALSE 362778.7895 621199.1385 510106.1374 595113.4691 446268.7452 509012.9426 441353.3505 522245.0631 502075.7899 771973.3662 0.469936924 0.804689858 0.660782042 0.770898965 0.578088267 0.659365938 0.571720955 0.676506582 0.650379679 1 19.55819155 -1.73146658 1.852592259 1.109982421 0.654160214 0.570032569 0.091319833 171589.1586 85544.05139 86326.49801 0.022398705 0.018558096 1.73146658 -0.455822207 ERHPS(ph)WRSEET(ph)QER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERHPSWRSEETQER 14 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 ERHPS(1)WRS(0.27)EET(0.73)QER 112.57 0.00064674 553530000 308760 339190 349490 340730 451910 527530 358850 420630 401140 483300 TRUE FALSE 320950.0832 397443.244 358597.9965 408125.377 375094.4996 405019.1523 330722.3993 414992.1429 386703.0498 577993.3817 0.555283319 0.687625943 0.620418863 0.706107353 0.648959852 0.700733201 0.572190634 0.717987707 0.669044079 1 19.14069345 -5 0.301090837 3.88793697 0.638457911 0.808745523 0.051039833 103.1070739 0.951556093 187.9464134 0.046359141 1.00E-05 5 -3.249479059 ERHPSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERHPSWR 7 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 98.629 0.010143 306240000 157740 176360 178490 197680 218600 238360 193870 188890 157050 218260 FALSE TRUE 163967.697 206648.4581 183141.596 236780.514 181442.4501 183004.5024 178673.9628 186358.2385 151397.8012 261023.8682 0.628171279 0.791684146 0.701627776 0.907122079 0.695118233 0.701102561 0.684511972 0.713950949 0.580015162 1 17.99382221 -1.237192796 5.134581847 1.000034263 0.717172572 0.514473337 0.083922314 3.18E-05 4.72E-06 0.078461263 0.01849126 0.057917153 1.237192796 -0.282861691 ERKS(ph)ESDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERKSESDKDVK 11 3 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 ERKS(0.998)ES(0.002)DKDVK 87.647 0.074978 627610000 1437600 347910 699320 337410 1144500 1055200 1028000 662560 792630 245480 TRUE FALSE 1494357.558 407660.8361 717544.8537 404148.6909 949958.2988 810145.7917 947422.6738 653679.4669 764103.4011 293577.106 5.090170615 1.388598865 2.444144448 1.376635585 3.235805107 2.759567334 3.227168108 2.226602325 2.602734973 1 18.16337994 4.751448899 24.81396503 2.353152384 5.090172544 0.565129583 0.742274149 1414.617035 2723525.482 0.169346323 3.129290305 56422.05492 -4.751448899 2.737020159 ERLDQPMTEIVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERLDQPMTEIVSR 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 194.59 8.07E-07 348030000 70023 108310 108034 104047 113908 133305 87457 101644 109476 127700 FALSE TRUE 72787.56211 126911.4 110849.4548 124627.1861 94545.95885 102346.934 80601.89181 100281.6284 105535.9801 152720.37 0.476606769 0.831005058 0.725832806 0.81604822 0.619078901 0.670159023 0.527774336 0.656635578 0.691040626 1 17.22053298 -1.853681377 4.876696586 1.063724565 0.670497734 0.470937505 0.105466284 0.056408939 0.001692473 0.078831463 0.023531804 0.014006145 1.853681377 -0.393226831 ERLEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERLEIER 7 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 96.948 0.01127 232110000 143860 118340 143380 121370 148110 158250 151340 144240 135630 112400 FALSE TRUE 149539.7039 138663.9744 147116.6006 145376.6237 122934.3151 121498.8358 139477.5753 142306.6987 130748.7028 134422.628 1.112459309 1.031552325 1.094433302 1.081489225 0.914535871 0.903857019 1.037604884 1.058651366 0.972668849 1 17.03641649 3.277393295 24.9833197 0.989493007 1.07755641 0.488290053 0.049069409 173.8459184 111844.0133 0.015459624 0.020932038 1894.058094 -3.277393295 0.088063404 ERLEQEQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;A0A075B6E5;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 177.04 2.16E-06 819900000 784729 691863 839806 750590 953494 970768 830371 812160 707926 765748 FALSE TRUE 815710.7069 810685.0883 861692.0343 899054.4617 791419.4305 745321.8441 765284.3512 801274.3236 682447.8815 915781.6595 0.890726188 0.885238397 0.940936112 0.981734513 0.864201005 0.813864131 0.835662457 0.874962187 0.745208068 1 19.80464415 3.025290378 20.51954898 0.846402737 0.923001379 0.210613322 0.064854609 41.72115288 33848.72457 0.017726362 0.021184056 1059.962201 -3.025290378 0.076598642 ERLNS(ph)SENGEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 ERLNS(0.956)S(0.044)ENGEDR;ERLNS(0.964)S(0.036)ENGEDR;ERLNS(0.975)S(0.025)ENGEDR;ERLNS(0.982)S(0.018)ENGEDR 220.97 1.71E-11 1448290000 1481651 1378730 1469320 1380460 1624020 1881700 1585560 1581380 1485700 1470440 TRUE FALSE 1540147.726 1615516.152 1507611.686 1653510.868 1347969.66 1444703.692 1461279.664 1560184.188 1432229.947 1758544.565 0.875808186 0.918666598 0.8573065 0.940272371 0.766525732 0.82153374 0.8309597 0.887201962 0.814440519 1 20.74595047 3.273530645 24.99999226 0.847634456 0.896580953 0.107603311 0.061474666 365.6124775 261373.2323 0.015953462 0.021600199 1877.286882 -3.273530645 0.048946497 ERMT(ph)ELY(ph)DYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERMTELYDYPK 11 1 P48147 P48147 PREP Prolyl endopeptidase 2 ERMT(0.999)ELY(0.952)DY(0.049)PK 43.897 0.07339 0 195050 78899 122330 77775 160430 127500 153760 98256 127810 74721 TRUE FALSE 202750.7246 92449.2895 125518.0203 93158.66286 133160.1659 97890.05728 141707.8894 96939.03903 123210.1431 89361.14933 2.268891192 1.034557973 1.404615107 1.042496248 1.490134884 1.095443132 1.585788572 1.084800719 1.378788702 1 16.44736012 4.745986032 24.99862822 1.249213233 2.268891674 0.698746425 0.203435143 445.3817777 1499400.096 0.042582653 0.444245312 55716.7829 -4.745986032 1.01967844 ERNEEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERNEEEAKR 9 2 Q96IZ7-2;Q96IZ7;C9J713;H7C5Q0 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 0 83.397 0.0091099 25416000 56097 44960 51447 39106 59733 70680 50805 51948 53834 47338 FALSE TRUE 58311.75288 52681.53026 52787.75108 46841.05008 49579.606 54265.64117 46822.77135 51251.72203 51896.52486 56612.97476 1.030006869 0.930555769 0.932432032 0.827390722 0.875764014 0.95853718 0.827067851 0.905299929 0.916689594 1 15.78884511 4.813399767 1.630667311 0.89589763 1.094970343 0.340414411 0.051138253 1.225856068 2.721404199 0.012672248 0.407180242 65072.84081 -4.813399767 0.199072713 ERNHKPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERNHKPSR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 ERNHKPS(1)R;ERNHKPS(1)R 67.385 0.030906 312060000 185908 94563 130781 125396 187672 166237 278970 165250 181963 116277 TRUE FALSE 193247.7914 110803.4597 134189.2603 150198.9545 155771.5805 127630.9761 257103.6024 163035.094 175414.1872 139059.2519 1.389679498 0.796807535 0.964979018 1.080107598 1.12018135 0.917817221 1.848878079 1.172414577 1.261434854 1 17.08534021 ERNS(ph)YLGLVSLPAASVAGR ddPTM_MDA-MB-175_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(0.952)Y(0.048)LGLVSLPAASVAGR 74.763 0.0093 41797000 30796 32450 36959 37086 38615 45110 38739 35606 33797 34542 TRUE FALSE 32011.84986 38023.03507 37922.1819 44421.50011 32051.23609 34633.88615 35702.53595 35128.75981 32580.65257 41309.84355 0.774920627 0.920435223 0.91799384 1.075324821 0.775874061 0.83839306 0.864262192 0.850372618 0.788689808 1 15.33419798 ERPAEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPAEAER 8 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 96.143 0.008345 121740000 49489 42148 36005 47596 55339 51141 51013 50185 44704 45862 FALSE TRUE 51442.86393 49386.59113 36943.31988 57010.34674 45932.49655 39264.2778 47014.46776 49512.35216 43095.11177 54847.78082 0.937920608 0.90043007 0.673560887 1.039428504 0.837454057 0.715877237 0.857180857 0.90272298 0.785722068 1 15.74314563 -1.129795998 4.460636083 1.000019479 0.851672814 0.164850792 0.101203053 13703323.21 3470796.641 2606.126324 0.022666433 0.074165854 1.129795998 -0.148346665 ERPAS(ph)SEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPASSEK 8 1 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 ERPAS(0.947)S(0.053)EK;ERPAS(0.597)S(0.403)EK 77.867 0.028108 334260000 246429 165898 200939 138004 272290 278260 240370 238870 227290 152671 TRUE FALSE 256158.2072 194389.691 206175.6354 165300.7793 226006.2431 213638.3321 221529.1713 235668.3384 219109.8773 182583.9594 1.402961181 1.064659194 1.129210014 0.905341191 1.237820912 1.170082699 1.213300292 1.290739554 1.200049983 1 17.4782005 ERPAYAVHGNMLHYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPAYAVHGNMLHYVK 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 115.31 0.00033251 759110000 236580 226470 277490 254880 354570 339090 276140 267600 284120 277280 FALSE TRUE 245920.3611 265364.4608 284721.6174 305294.5033 294300.318 260341.4865 254495.4252 264013.2597 273894.5767 331607.7072 0.741600258 0.800236108 0.858609771 0.920649601 0.88749541 0.785088769 0.767459319 0.79616141 0.825959623 1 18.33911801 -2.54634622 1.906623159 2.974339067 0.820651441 0.51549114 0.052246054 1943687.652 88592.95933 16633487.3 0.014786281 0.002842194 2.54634622 -2.153687625 ERPDLEAPAPGS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR 232.6 2.31E-14 47779390000 4531970 5064300 4451250 4464370 4853550 5288090 4246800 4320080 3719630 3920450 TRUE FALSE 4710895.675 5934054.13 4567253.232 5347409.061 4028545.305 4060011.239 3913924.719 4262176.394 3585761.243 4688587.116 1.004758056 1.265638023 0.97412144 1.140516093 0.859223729 0.865934905 0.834777007 0.909053471 0.764785031 1 22.16072181 3.233679595 24.9469447 0.867820721 1.099632892 0.585972711 0.092163294 73.84954855 377445.7476 0.024261379 0.029883152 1712.693286 -3.233679595 0.231812172 ERPDLEAPAPGSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERPDLEAPAPGSPFR 15 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 ;;; 265.43 3.00E-25 1004450000 309582 354190 382170 345752 464119 474021 410059 440813 397812 374662 FALSE TRUE 321804.5364 415019.3773 392129.6642 414140.7136 385228.2182 363936.8066 377917.5041 434904.6228 383494.8238 448069.8456 0.718201726 0.926238133 0.875152988 0.924277136 0.859750376 0.812232312 0.843434361 0.970617923 0.855881795 1 18.77336411 -5 0.100500881 1.412251388 0.785055524 0.326339534 0.063477416 232.3447039 1.58802487 20.00406541 1.044266317 1.00E-05 5 -0.627195865 ERPDLPPIQYEPVLCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPDLPPIQYEPVLCSR 17 1 F5H365;Q15436;G3V4V1;G3V1W4;G3V3G5;G3V2R6;G3V5X8;G3V4Q2 F5H365 SEC23A Protein transport protein Sec23A 0 ; 174.19 1.26E-09 568340000 284821 313988 352536 344907 359654 457330 348704 317182 347091 351397 FALSE TRUE 296065.953 367912.9965 361723.3778 413128.5752 298520.1415 351122.0384 321371.6693 312930.6941 334599.2627 420246.5142 0.704505434 0.875469478 0.860740935 0.983062467 0.710345313 0.835514458 0.764721796 0.744636025 0.796197592 1 18.68087633 3.210301768 24.99998726 0.790837908 0.85768211 0.03556867 0.097251407 493.7770346 436832.5383 0.026734197 0.031959093 1622.937399 -3.210301768 0.066844202 ERPEIS(ph)PPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.785)PPS(0.214)DFEHT(0.001)IHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.967)PPS(0.032)DFEHTIHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.99)PPS(0.01)DFEHTIHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.459)PPS(0.459)DFEHT(0.081)IHVGFDAVT(0.001)GEFTGMPEQWAR;ERPEIS(0.472)PPS(0.472)DFEHT(0.056)IHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.494)PPS(0.494)DFEHT(0.012)IHVGFDAVTGEFTGMPEQWAR;ERPEIS(0.955)PPS(0.045)DFEHTIHVGFDAVTGEFTGMPEQWAR 242.84 1.00E-47 388070000 87978.9 112825 108460 105394.2 117080 128300 121121.6 109788 111312.7 119733 TRUE FALSE 91452.37491 132201.8161 111286.5567 126240.8582 97178.78342 98504.26941 111627.7725 108316.4714 107306.5777 143192.3889 0.638667848 0.92324611 0.777182066 0.881617097 0.67865886 0.687915539 0.779564985 0.756440145 0.749387439 1 17.12759529 -1.956946627 6.329719617 1.124181594 0.767419661 0.421668364 0.082938456 0.049977389 0.000339935 0.027613163 0.018082084 0.011042143 1.956946627 -0.356761934 ERPEISPPS(ph)DFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 ERPEIS(0.394)PPS(0.528)DFEHT(0.079)IHVGFDAVTGEFTGMPEQWAR 155.15 1.20E-11 54047000 12306 14699 16010 14842 14927 15797 17373 13423 14792 13770 TRUE FALSE 12791.85038 17223.43891 16427.23375 17777.7033 12389.71387 12128.38616 16011.25886 13243.08664 14259.63881 16467.96786 0.776771639 1.045875184 0.997526464 1.079532305 0.752352323 0.736483473 0.972266828 0.804172485 0.865901545 1 14.00737492 3.23731682 24.99996049 0.845402046 0.981608452 0.2210682 0.108888781 44.32172035 890861.5219 0.030030305 0.037833606 1727.097358 -3.23731682 0.136206405 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWAR 35 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 147.5 5.63E-11 55980000 12027 14855 14439 13931 15463 19432 13612 11844 13835 16270 FALSE TRUE 12501.83525 17406.23069 14815.2922 16686.51022 12834.60478 14919.21249 12545.05587 11685.25055 13337.08105 19457.79499 0.64251038 0.894563372 0.761406532 0.857574572 0.659612499 0.766747337 0.644731629 0.60054341 0.685436405 1 14.24806061 3.228870813 24.98801607 0.695746232 0.794581038 0.024857088 0.122016485 394.3245153 1016880.904 0.033176826 0.040129271 1693.833871 -3.228870813 0.098834807 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHR 33 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.997)PMVPS(0.003)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.982)PMVPS(0.018)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHR;ERPES(0.989)PMVPS(0.011)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR;ERPES(0.996)PMVPS(0.004)EQVVEEAVPLPPQALTTSQDGHR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHR 209.24 1.25E-27 3442479000 544963.4 1019859.9 937338.9 1023684.7 998572.7 1193560 914977.8 1029441.1 942412 1041077.3 TRUE FALSE 566478.9758 1195012.904 961766.7218 1226166.478 828835.6691 916373.7786 843259.4492 1015643.126 908494.7762 1245056.464 0.454982559 0.959806192 0.772468357 0.984828009 0.66570127 0.736009815 0.67728611 0.815740615 0.729681587 1 20.24777974 -1.903097785 3.631404045 1.104222902 0.765655775 0.205477009 0.14310022 0.091276854 0.002435677 0.104738711 0.029995352 0.012499776 1.903097785 -0.338567127 ERPES(ph)PMVPSEQVVEEAVPLPPQALTTSQDGHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ERPESPMVPSEQVVEEAVPLPPQALTTSQDGHRR 34 2 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 ERPES(0.971)PMVPS(0.029)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.915)PMVPS(0.085)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(1)PMVPSEQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHRR;ERPES(0.999)PMVPS(0.001)EQVVEEAVPLPPQALTTSQDGHRR 153.04 4.63E-11 847908000 87299 238539 210069 228080 238445 278968 179981 255112 220475 254732 TRUE FALSE 90745.63193 279506.2177 215543.5707 273193.5432 197914.2041 214181.9098 165873.6189 251692.6409 212540.1478 304641.8583 0.297876439 0.917491179 0.70753104 0.896769554 0.649661886 0.703061329 0.544487287 0.826191917 0.697672175 1 18.21675466 -4.999999947 0.297011919 3.392517589 0.691315946 0.228914398 0.169965092 395.7011426 3.680837267 588.3929632 0.160975005 1.00E-05 4.999999947 -2.701201643 ERPFYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPFYGR 7 1 Q13232 Q13232 NME3 Nucleoside diphosphate kinase 3 0 ; 100.45 0.0089232 192361000 72055 130221 113388 154921 105298 158179 98124 130377 102126 155755 FALSE TRUE 74899.78704 152585.4438 116342.9844 185563.9114 87399.48357 121444.3245 90432.78448 128629.5096 98450.50521 186272.2101 0.402098558 0.819153022 0.624585838 0.996197507 0.46920302 0.651972317 0.485487258 0.690545892 0.52853029 1 17.50705293 -1.855754435 4.227816829 1.088544353 0.639417456 0.301506377 0.168485097 0.093359976 0.003185275 0.108309855 0.035703468 0.013939448 1.855754435 -0.449126896 ERPGEQSEVAQLIQQTLEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPGEQSEVAQLIQQTLEQER 21 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 64.87 0.022352 60350000 14573 12866 12532 12558 12568 17592 12916 16186 8779.7 16190 FALSE TRUE 15148.35329 15075.63542 12858.59422 15041.93492 10431.69585 13506.52461 11903.61017 15969.05314 8463.720312 19362.12052 0.782370571 0.778614894 0.664110845 0.776874356 0.538768253 0.697574658 0.614788559 0.82475745 0.437127757 1 14.24094934 -1.851917611 8.492059061 1.017217619 0.688471708 0.404584577 0.116198989 0.033350956 0.000581565 0.099061838 0.024633012 0.014063143 1.851917611 -0.328745911 ERPGLGSENMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPGLGSENMDR 12 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ; 121.45 0.00034298 867950000 367620 414930 408300 413950 422170 513960 428220 405960 383270 437780 FALSE TRUE 382133.9215 486190.9998 418940.6334 495828.0745 350409.6942 394600.5791 394654.9975 400518.7702 369476.1876 523554.6092 0.729883597 0.928634743 0.800185169 0.947041752 0.669289675 0.753695168 0.753799108 0.764999034 0.705707067 1 18.9979805 3.237747771 25 0.760880081 0.853289679 0.114067295 0.100620796 37.009535 1138289.534 0.02598971 0.032831268 1728.812011 -3.237747771 0.092409598 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPGSEEPPAEPVSFYTQPFSHYGQALCVSFPQPCR 36 1 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 306.32 3.46E-93 251250000 46412 50653 52372 46235 59124 57151 49522 50152 54159 56143 FALSE TRUE 48244.3816 59352.25872 53736.85734 55380.145 49074.1236 43878.54638 45640.33624 49479.79447 52209.82817 67143.14593 0.718530253 0.883966009 0.800332731 0.824807123 0.730888059 0.653507454 0.679746765 0.73692994 0.777589841 1 16.03495251 0.826332023 5.540823658 0.999999281 0.753420568 0.563887525 0.064612993 3.185534409 101.3319903 0.068446095 0.0172448 6.703969397 -0.826332023 -0.246578712 ERPIS(ph)LGIFPLPAGDGLLT(ph)PDAQK ddPTM_MDA-MB-175_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 169.75 2.02E-11 186148000 154219 105442 144165 120591 249881 225966 214010 181729 212686 153940 TRUE FALSE 160307.6852 123550.8433 147922.0583 144443.5399 207406.3169 173488.821 197235.337 179293.22 205031.4724 184101.5956 0.870756631 0.671101426 0.803480588 0.784586029 1.126586199 0.942353707 1.071339639 0.973881945 1.113686558 1 17.49014261 3.253798366 24.9738579 1.030345995 0.776025324 0.755440625 0.071098628 105.5086494 172921.9785 0.018159322 0.024494511 1793.900563 -3.253798366 -0.254320671 ERPIS(ph)LGIFPLPAGDGLLTPDAQK ddPTM_MDA-MB-175_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 209.36 3.25E-25 936450000 1135800 868830 1214030 857380 1583570 1431580 1358060 1362040 1336840 953570 TRUE FALSE 1180642.261 1018044.794 1245668.619 1026967.205 1314395.337 1099117.241 1251611.709 1343784.082 1288727.39 1140403.784 1.035284412 0.892705556 1.09230488 0.900529461 1.152570129 0.963796557 1.097516271 1.178340602 1.130062358 1 20.1211133 2.625322612 1.029882644 1.121046683 0.987419058 0.179035354 0.088013193 0.67399867 1.480114231 0.047890713 0.039368407 422.009873 -2.625322612 -0.133627625 ERPISLGIFPLPAGDGLLT(ph)PDAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 229.28 4.72E-33 4342890000 3873770 2554470 3496280 2840280 4352430 4726070 4906770 3876900 4219150 2686650 TRUE FALSE 4026709.431 2993180.351 3587395.929 3402078.907 3612605.503 3628511.867 4522164.546 3824936.497 4067303.616 3213047.628 1.25323677 0.931570489 1.116508793 1.058832392 1.124354794 1.129305347 1.407437757 1.190438779 1.265870938 1 21.61551094 2.459137396 24.99736617 1.237987613 1.090704047 0.172170795 0.1195593 313.9934888 436445.0658 0.038229521 0.031990832 287.8308871 -2.459137396 -0.147283567 ERPKDDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPKDDIK 8 2 Q9HAU5 Q9HAU5 UPF2 Regulator of nonsense transcripts 2 0 54.539 0.072901 43552000 61055 38379 53882 39737 76069 64314 58336 47628 50481 36610 FALSE TRUE 63465.49854 44970.2947 55286.20918 47596.86 63138.81855 49378.04819 53763.47189 46989.62456 48664.19867 43783.02856 1.449545649 1.02711704 1.262731497 1.087107529 1.44208431 1.12778969 1.227952329 1.073238333 1.111485438 1 15.41808413 1.562313945 1.136516645 1.021849013 1.230952117 0.26576163 0.130992718 0.614385113 1.520526917 0.107725441 0.038939266 36.50177172 -1.562313945 0.209103105 ERPLLLEEQPLLLQDLLDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPLLLEEQPLLLQDLLDQER 21 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 123.53 2.40E-05 10025000 15113 22536 20428 19387 19313 25931 18974 20792 19359 21532 FALSE TRUE 15709.67291 26406.38269 20960.37046 23221.69074 16030.18316 19908.91824 17486.7683 20513.31725 18662.27337 25750.78314 0.610065831 1.025459402 0.813970214 0.901785806 0.622512452 0.77313836 0.679077145 0.796609452 0.724726439 1 14.65232869 5.025839771 15.95651469 0.799137224 0.121491297 0.187414639 0.124158915 8706538.115 144277703 0.02855638 152096191.5 106130.3927 -5.025839771 -0.677645928 ERPLQQVS(ph)PVASVPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPLQQVSPVASVPWR 16 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 ERPLQQVS(1)PVASVPWR;ERPLQQVS(1)PVASVPWR 132.76 2.26E-05 1028330000 515230 552270 569000 581420 568600 705070 558880 611250 544960 593550 TRUE FALSE 535571.6782 647118.0764 583828.6074 696423.1406 471949.5751 541328.1779 515073.5252 603057.1936 525346.9961 709844.7583 0.754491277 0.911633239 0.822473647 0.981092179 0.664863084 0.762600796 0.725614325 0.849562086 0.740087167 1 19.43714402 5.053236299 14.26682804 0.818980052 0.383904265 0.035855798 0.105096408 1697268.332 13334768.66 0.023986693 20057503.36 113041.0802 -5.053236299 -0.435075787 ERPPLDVDEMLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERPPLDVDEMLER 13 1 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-5;A0A0G2JMG8;F5H5B1;K7ELX1;K7EPE6;F5GYZ4 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 89.541 0.006751 369284000 164580 182388 177512 192639 227998 229521 199862 189961 186708 201363 FALSE TRUE 171077.7455 213711.7202 182138.1085 230742.4192 189242.9814 176218.2262 184196.2942 187414.8835 179988.4156 240816.2245 0.710407888 0.88744735 0.756336534 0.958168079 0.785839832 0.731753961 0.764883241 0.778248575 0.747409839 1 17.87757307 -1.124431738 5.198418888 1.000005793 0.79372161 0.433173757 0.071612802 4.65E-06 7.83E-07 0.067008968 0.015793722 0.075087607 1.124431738 -0.206284183 ERPQDRPEDLDVPPALADFIHQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPQDRPEDLDVPPALADFIHQQR 24 2 Q01780;Q01780-2 Q01780 EXOSC10 Exosome component 10 0 108.4 0.0014021 60301000 12161 15845 14282 17544 18776 20668 14545 15910 15443 14795 FALSE TRUE 12641.12567 18566.25549 14654.20065 21014.15084 15584.46223 15868.17023 13404.92489 15696.75247 14887.20945 17693.79698 0.714438268 1.049308722 0.82821119 1.187656378 0.880786766 0.896821086 0.757605895 0.887133072 0.841380144 1 14.11095605 3.025923439 24.99857154 0.864033325 0.955300368 0.054655989 0.129972548 511.0773164 492840.0562 0.035344828 0.042244066 1061.50841 -3.025923439 0.091267043 ERPQLAECEEPSIYS(ph)PAFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERPQLAECEEPSIYSPAFPR 20 1 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 ERPQLAECEEPSIYS(1)PAFPR;ERPQLAECEEPSIYS(1)PAFPR;ERPQLAECEEPS(0.001)IYS(0.999)PAFPR 168.79 7.11E-12 420200000 230852 245746 238229 264702 239324 296220 249910 247872 232249 255143 TRUE FALSE 239966.2152 287950.9639 244437.4434 317059.2655 198643.792 227427.3943 230321.4012 244549.6813 223890.4039 305133.3858 0.786430546 0.943688817 0.801083902 1.039084152 0.651006416 0.745337629 0.754822028 0.801451734 0.733746008 1 18.21908051 3.229541194 24.99999342 0.770013274 0.889688225 0.203304543 0.106746445 268.9487037 745469.8419 0.028357972 0.034358149 1696.450507 -3.229541194 0.119674951 ERPS(ph)SAIYPSDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ERPSSAIYPSDSFR 14 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ERPS(0.623)S(0.377)AIYPSDSFR;ERPS(0.887)S(0.113)AIYPSDSFR;ERPS(0.499)S(0.499)AIYPS(0.002)DSFR;ERPS(0.562)S(0.391)AIYPS(0.014)DS(0.033)FR 176.17 5.97E-06 2103270000 860264 1055499 992730 981754 1155620 1216450 992192 993627 999301 1130070 TRUE FALSE 894227.887 1236772.743 1018601.359 1175942.011 959188.1252 933947.923 914421.3984 980309.0553 963336.3522 1351485.58 0.661662914 0.915120931 0.753690142 0.870110661 0.709728716 0.691052821 0.676604628 0.725356652 0.712798099 1 20.36611469 4.045595143 24.99981162 0.750350758 0.799895242 0 0.110314146 498.5888159 273369.8579 0.025828063 0.055794976 11106.95835 -4.045595143 0.049544484 ERPS(ph)SREDT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 ERPS(0.9)S(0.101)REDT(0.616)PS(0.383)R 88.19 0.011175 279180000 260320 355760 308350 297630 350130 346060 284380 285170 324430 307450 TRUE FALSE 270597.6346 416859.0126 316385.8543 356500.3257 290615.0277 265692.8096 262089.5525 281347.7626 312753.8277 367688.941 0.735941728 1.13372736 0.860471499 0.969570433 0.790382835 0.722602124 0.712802381 0.765178745 0.850593512 1 18.48812626 3.227984786 23.02724526 0.783155879 0.935237984 0.168150189 0.121015192 100.6675357 219187.4929 0.032443211 0.039234015 1690.381713 -3.227984786 0.152082105 ERPS(ph)SREDTPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERPSSREDTPSR 12 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 ERPS(0.761)S(0.239)REDTPSR;ERPS(0.765)S(0.235)REDTPSR;ERPS(0.751)S(0.246)REDT(0.002)PS(0.002)R 110.56 0.0011631 1799681000 626336 730112 663194 670432 826977 875463 699369 755283 767198 755081 TRUE FALSE 651064.2289 855503.0565 680477.3805 803041.4486 686407.7449 672149.986 644550.6303 745159.6668 739586.6938 903024.6651 0.720981668 0.947375071 0.753553482 0.889279639 0.760120705 0.744331813 0.713768577 0.825181964 0.819010513 1 19.78440587 -1.658135676 6.794100364 1.000958143 0.798585522 0.419994989 0.071523051 0.000988913 4.98E-05 0.065975127 0.015480339 0.021971734 1.658135676 -0.202372621 ERPSQPEGLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERPSQPEGLRK 11 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 112.5 0.00085368 1378160000 825760 718060 753520 632360 995800 989270 854790 774590 795310 737810 FALSE TRUE 858361.6424 841381.2193 773157.3502 757438.9206 826534.2717 759527.035 787789.3262 764207.888 766686.9485 882369.7433 0.972791337 0.953547224 0.876228311 0.85841443 0.936721004 0.860780915 0.892810902 0.866085781 0.868895329 1 19.7510238 4.315381833 4.998974908 0.888031548 0.967312039 0.288301694 0.041988254 0.199877384 8.812998 0.009361167 0.026792353 20671.96844 -4.315381833 0.079280492 ERPSS(ph)AIYPSDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPSSAIYPSDSFR 14 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ERPS(0.175)S(0.825)AIYPSDSFR;ERPS(0.315)S(0.685)AIYPSDSFR 203.82 8.78E-09 2430900000 392430 537010 495850 528340 629140 677590 557170 501230 552250 628090 TRUE FALSE 407923.4394 629237.2901 508772.2583 632844.0751 522199.0075 520229.9915 513497.5595 494511.8317 532374.6304 751152.21 0.543063621 0.837696118 0.677322454 0.842497788 0.695197326 0.692575998 0.683613191 0.658337718 0.708744011 1 19.51874575 -0.723417403 5.154188556 1.000000077 0.706491623 0.54202026 0.081510949 9725026.075 1886820.193 8.484325846 0.017721171 0.189052575 0.723417403 -0.293508454 ERPSS(ph)REDTPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.443)S(0.474)REDT(0.042)PS(0.042)R;ERPS(0.147)S(0.851)REDTPS(0.002)R;ERPS(0.131)S(0.864)REDT(0.002)PS(0.003)R;ERPS(0.197)S(0.803)REDTPSR;ERPS(0.299)S(0.616)REDT(0.014)PS(0.071)R;ERPS(0.143)S(0.857)REDTPSR 118.64 0.00047532 13242140000 2809603 3284988 3409468 3082295 3733503 4087267 3348036 3443726 3328036 3299280 TRUE FALSE 2920528.296 3849159.135 3498321.537 3691963.751 3098883.494 3138061.182 3085608.19 3397568.486 3208260.634 3945710.747 0.740178002 0.975529982 0.886613784 0.935690421 0.785380301 0.795309485 0.782015811 0.861078955 0.813100818 1 21.91185377 4.821041738 21.60308965 0.85979038 0.740163588 0.198764412 0.075802249 108553.6313 28419382.46 0.017956027 278.5947656 66228.01494 -4.821041738 -0.119626792 ERPT(ph)SPAPHRPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.863)S(0.137)PAPHRPPKR;ERPT(0.853)S(0.147)PAPHRPPKR;ERPT(0.881)S(0.119)PAPHRPPKR;ERPT(0.5)S(0.5)PAPHRPPKR;ERPT(0.5)S(0.5)PAPHRPPKR 110.38 0.00037751 4532596000 115879 105167 113785 86179 139525 140533 125560 109439 109858 99368 TRUE FALSE 120453.9924 123228.6142 116750.3306 103224.949 115808.5903 107896.3405 115718.2791 107972.1492 105904.232 118837.2571 1.013604617 1.036952696 0.982438786 0.868624466 0.974514165 0.907933616 0.973754208 0.908571536 0.891170283 1 16.85862769 3.985683432 6.838883994 0.929879089 1.022009701 0.481719466 0.039142072 0.108116915 25.64754312 0.009208968 0.018086531 9675.723121 -3.985683432 0.092130613 ERPTPSLNNNCTTSEDSLVLYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERPTPSLNNNCTTSEDSLVLYNR 23 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 257.42 1.19E-43 1041660000 146568 155781 146580 161219 174138 193639 167252 149294 160054 172340 FALSE TRUE 152354.6178 182535.1749 150399.9952 193107.637 144538.085 148669.2769 154142.3512 147292.9581 154293.6878 206106.7234 0.739202561 0.885634258 0.729719015 0.936930314 0.701277875 0.72132182 0.747876385 0.714644121 0.748610648 1 17.65303204 4.203666672 24.99898009 0.77230321 0.812419258 0 0.101788385 725.5766638 519823.0045 0.023948177 0.05173783 15983.30815 -4.203666672 0.040116048 ERPTS(ph)PAPHRPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPTSPAPHRPPKR 14 3 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 ERPT(0.134)S(0.866)PAPHRPPKR 125.52 6.48E-05 64795000 34613 34914 41529 32780 47007 46271 37248 39191 41629 38588 TRUE FALSE 35979.54797 40910.20791 42611.27986 39263.78616 39016.76693 35525.26149 34328.40443 38665.70875 40130.78042 46148.57979 0.779645834 0.88648899 0.923349755 0.850812448 0.845459754 0.769801837 0.743866975 0.837852626 0.869599468 1 15.49399863 0.827449517 2.78227905 0.999875226 0.830318562 0.499817903 0.051197965 0.674581061 8.944473636 0.053712453 0.014191709 6.721241763 -0.827449517 -0.169556663 ERPVQSLKTS(ph)RDT(ph)SPSSGSAVSSSK ddPTM_MDA-MB-175_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(0.056)LKT(0.433)S(0.511)RDT(0.575)S(0.354)PS(0.069)S(0.001)GS(0.001)AVSSSK 137.44 3.71E-05 89453000 112070 64399 85128 32898 117150 104010 59015 62489 85962 67378 TRUE FALSE 116494.6101 75459.0273 87346.50561 39405.12621 97236.88484 79855.25379 54389.25009 61651.43717 82868.24441 80579.42907 1.445711536 0.936455224 1.0839802 0.489022157 1.206720946 0.991012901 0.674976861 0.765101439 1.028404462 1 16.29812396 5.365356489 1.326065807 0.873326578 3.198189206 0.386224352 0.201413966 6.000148895 2.831855206 0.053822633 28.32084374 231929.7658 -5.365356489 2.324862628 ERPVS(ph)EMFSLEDSIIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERPVSEMFSLEDSIIER 17 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ERPVS(1)EMFSLEDSIIER 102.48 0.00057271 51810000 8181.7 15069 11553 15248 18716 14545 11160 16396 14118 19036 TRUE FALSE 8504.719834 17656.98353 11854.08067 18264.00889 15534.66101 11167.14418 10285.25004 16176.23844 13609.89594 22765.73973 0.373575378 0.775594544 0.520698243 0.80225853 0.68237014 0.490524108 0.451786332 0.710551848 0.597823576 1 14.47457672 0.000403939 1.181346957 1.001647071 0.606335671 0.439073687 0.135194335 10.46400868 11.26449675 0.185100854 0.037572607 1.000930536 -0.000403939 -0.395311399 ERQELGS(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;ERQELGS(1)PEER 121.62 0.00024698 1503660000 703110 659930 801350 640770 859850 1135660 838850 767990 754110 814350 TRUE FALSE 730869.3257 773267.844 822233.8393 767512.3935 713693.0041 871920.1761 773098.7451 757696.3502 726969.7284 973906.2908 0.750451386 0.793985881 0.844263814 0.788076225 0.732814862 0.895281388 0.793812251 0.777997182 0.746447307 1 19.89342344 -1.854575313 2.463275246 1.090585725 0.79332012 0.65117772 0.045771186 7458384.936 4323470.486 3963130.972 0.011082082 0.013977345 1.854575313 -0.297265604 ERQEQEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERQEQEEAR 9 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 166.66 5.52E-05 1060340000 563470 674780 635540 648780 625380 822240 675240 664030 644790 662240 FALSE TRUE 585716.2307 790668.2159 652102.6945 777106.7476 519078.131 631287.2212 622312.9244 655129.764 621584.1339 791993.2486 0.739547 0.998326965 0.823369007 0.981203753 0.655407268 0.797086619 0.78575534 0.827191097 0.784835142 1 19.59512861 5.06328493 13.77413299 0.838919786 8.81E-05 0.080251998 0.106376721 74778297.77 453238949.5 0.024259953 1704940629 115687.0987 -5.06328493 -0.838831701 ERQEQEEARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ERQEQEEARR 10 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;; 147.62 1.49E-05 1221321000 378899 465895 452591 377991 503308 515507 412449 453931 463577 503697 FALSE TRUE 393858.2251 545908.8421 464385.8933 452756.4916 417755.8859 395788.3118 380120.1696 447846.7974 446892.9543 602386.7833 0.65382946 0.90624306 0.770909831 0.751604292 0.693501082 0.657033525 0.631023422 0.74345389 0.741870451 1 19.20033059 -1.611564926 9.124626529 1.000077471 0.728690797 0.544811168 0.074659326 0.000121595 5.18E-06 0.074703983 0.017602918 0.024458796 1.611564926 -0.271386674 ERQEQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERQEQLER 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;A0A0U1RQP7;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ;; 152.11 0.00042164 1628250000 519711 578692 546685 488581 610079 701072 564133 533625 534473 556371 FALSE TRUE 540229.5916 678077.8494 560932.0602 585220.8635 506377.9895 538258.6528 519914.7814 526472.6297 515237.4211 665381.2451 0.811909857 1.019081699 0.843023551 0.87952714 0.761034359 0.808947738 0.781378774 0.79123455 0.774349179 1 19.34382168 3.379519895 5.59949464 0.805153717 0.897501511 0.131217584 0.081714871 0.297579237 14.08823129 0.020969119 0.028580901 2396.182518 -3.379519895 0.092347794 ERRPDS(ph)PTRPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERRPDSPTRPTLR 13 3 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 ERRPDS(0.997)PT(0.003)RPTLR;ERRPDS(0.993)PT(0.007)RPTLR 117.4 0.0028149 305040000 35270 40793 45817 42408 55651 66799 37102 48785 53788 60309 TRUE FALSE 36662.48683 47798.88042 47011.02866 50796.17582 46191.4629 51285.9446 34193.84829 48131.11687 51852.18039 72125.39386 0.508315932 0.66271916 0.651795798 0.704275888 0.64043273 0.711066406 0.474088895 0.667325533 0.718917119 1 16.13821967 0.801068118 2.169799254 0.999544434 0.629044381 0.700697267 0.073356669 0.399871664 3.213207291 0.067871621 0.018552201 6.32511051 -0.801068118 -0.370500053 ERRT(ph)PPGR ddPTM_MDA-MB-175_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 94.791 0.016253 5361280000 240201 292468 289204 257229 302610 333504 272445 310677 246936 321567 TRUE FALSE 249684.321 342697.1039 296740.8938 308108.1284 251172.4603 256052.7503 251090.049 306512.883 238048.8216 384571.8969 0.649252644 0.891113227 0.771613569 0.801171721 0.653122244 0.665812433 0.65290795 0.797023614 0.618996925 1 18.55289381 -1.125221511 4.069392943 1.000068504 0.729383254 0.489216281 0.084841208 9647036.53 5334977.308 5938.885352 0.019660551 0.074951182 1.125221511 -0.27068525 ERRT(ph)PS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_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 123.64 3.70E-05 347090000 513220 360500 505200 366680 586570 583080 560900 495970 560570 401470 TRUE FALSE 533482.3219 422413.0707 518365.927 439208.2096 486865.0409 447668.5067 516935.1924 489322.3334 540395.1952 480130.3599 1.111119743 0.879788295 1.079635804 0.914768668 1.014026776 0.932389501 1.076655916 1.019144745 1.125517652 1 18.87306664 2.222000952 24.9969945 1.053581774 0.98560935 0.163715203 0.073630392 408.5465139 616701.2294 0.02487523 0.018422101 166.7250868 -2.222000952 -0.067972424 ERS(ph)AEKTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSAEKTEK 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(0.904)AEKT(0.096)EK 58.32 0.086318 137960000 297260 85964 157890 77850 249300 198520 189640 131390 175810 73128 TRUE FALSE 308996.0543 100727.6483 162004.7431 93248.49764 206924.075 152416.7386 174775.5213 129628.932 169482.6324 87456.03148 3.533158881 1.151751876 1.852413611 1.066232895 2.366035499 1.742781327 1.998438739 1.482218319 1.93791817 1 16.41627026 8 0.052554709 1.35E-09 5.206493341 0.200493753 0.637710106 851.9871318 3.369615921 75.57992063 353.4972708 99999999.9 -8 5.20649334 ERS(ph)HERPDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 76.311 0.025959 3050140000 781620 503208 615200 416024 942000 861000 731500 669764 654330 544102 TRUE FALSE 812478.9611 589630.0596 631232.6174 498312.3055 781879.1765 661045.7986 674163.1186 660786.9091 630780.7911 650708.3694 1.248606902 0.906135663 0.970069922 0.765799748 1.201581558 1.015886424 1.036044948 1.015488566 0.969375562 1 19.31165158 4.750857463 24.08932205 0.990802168 1.24860717 0.366415661 0.103189894 1291.788938 2530515.227 0.024295477 0.404363675 56345.26986 -4.750857463 0.257805002 ERS(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSKDASPINRWSPTR 16 3 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 ERS(1)KDAS(0.999)PINRWS(0.934)PT(0.067)R 95.122 0.0075264 244610000 269560 116020 167830 94599 215940 271840 207340 167140 167280 98385 TRUE FALSE 280202.4369 135945.5325 172203.7877 113310.3999 179234.5959 208709.2798 191088.149 164899.7617 161259.6255 117661.6571 2.381425215 1.155393659 1.463550591 0.963018903 1.523305046 1.773808775 1.624047747 1.401474072 1.370536754 1 16.84428473 -3.06977624 0.251674841 5.34E-16 1.551805238 0.173990159 0.35676493 119.9391098 2.839721864 64.05359115 0.514018594 0.000851577 3.06977624 1.551805238 ERS(ph)KDAS(ph)PINRWSPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSKDASPINRWSPTR 16 3 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 ERS(1)KDAS(0.971)PINRWS(0.08)PT(0.95)R 95.666 0.0062243 272430000 315320 125600 173660 105730 273170 318260 202210 200130 210330 110640 TRUE FALSE 327769.0771 147170.823 178185.7223 126643.0784 226736.661 244348.9383 186360.2518 197447.5847 202760.2644 132317.7897 2.477135372 1.112252731 1.346649779 0.957113014 1.713576546 1.846682437 1.4084293 1.492222514 1.532373424 1 17.01364751 -1.41008124 2.749324917 0.98786575 1.513299446 0.139330034 0.39874736 19466602.89 21535162.11 1868955.519 0.093621518 0.038897238 1.41008124 0.525433696 ERS(ph)MSETGTAAAPGVSSELLSVAAQTLLSSDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSMSETGTAAAPGVSSELLSVAAQTLLSSDTK 33 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 ERS(0.377)MS(0.377)ET(0.101)GT(0.101)AAAPGVS(0.014)S(0.014)ELLS(0.016)VAAQTLLSSDTK 69.143 0.0025233 36511000 34389 17192 24686 19117 49102 40207 46781 33653 38702 27976 TRUE FALSE 35746.70427 20144.59226 25329.33744 22898.28554 40755.65958 30869.53359 43114.18298 33201.93658 37309.12258 33457.36157 1.06842568 0.602097455 0.757063207 0.684402011 1.218137285 0.922652957 1.288630692 0.992365657 1.11512447 1 15.03003606 3.243965682 24.99998925 1.088511203 0.763937518 0.505047329 0.150806066 99.14992659 458593.8711 0.039101066 0.05145632 1753.741916 -3.243965682 -0.324573685 ERS(ph)PALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 107.58 0.0045093 32585422000 15809889 10429013 13402243 11469647 15575307 17299149 18550524 13774279 14299776 7978251 TRUE FALSE 16434075.63 12220114.86 13751516.46 13738308.94 12927821.88 13281683.82 17096485.46 13589657.32 13785129.86 9541436.531 1.72239008 1.280741618 1.441241727 1.439857499 1.354913575 1.392000437 1.791814618 1.424277914 1.444764613 1 23.18577506 0.577800422 2.484571922 1.000034674 1.476172255 0.477343147 0.150110917 4.06685176 22.87912735 0.139259354 0.037186272 3.782687132 -0.577800422 0.476137581 ERS(ph)PALKS(ph)PLQSVVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 ERS(1)PALKS(0.903)PLQS(0.097)VVVR;ERS(1)PALKS(0.999)PLQS(0.001)VVVR;ERS(1)PALKS(0.944)PLQS(0.056)VVVR;ERS(1)PALKS(0.987)PLQS(0.013)VVVR;ERS(0.996)PALKS(0.677)PLQS(0.327)VVVR 133.65 3.41E-05 1628110000 2404960 1455770 1907930 1402910 2605820 2634440 2447010 2019440 2122190 1409200 TRUE FALSE 2499909.678 1705787.173 1957652.223 1680401.411 2162883.647 2022631.235 2255206.962 1992372.71 2045812.796 1685305.759 1.483356752 1.012152937 1.161600625 0.997089935 1.283377592 1.200156841 1.338158936 1.182202517 1.213911948 1 20.68457893 ERS(ph)PALKSPLQSVVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 ERS(0.998)PALKS(0.001)PLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR;ERS(1)PALKSPLQSVVVR 208.46 7.73E-12 27862100000 9500720 8450130 9992250 6305760 13635860 12037250 8555990 9420230 10956380 9444590 TRUE FALSE 9875815.762 9901374.095 10252656.24 7553020.507 11318041.39 9241781.114 7885349.147 9293967.225 10562062.02 11295076.58 0.87434695 0.876609735 0.907710202 0.668700248 1.002033169 0.818213232 0.698122681 0.822833485 0.935103179 1 23.42919072 1.079000057 3.822622753 0.997574447 0.830283179 0.268002819 0.091388912 0.258353685 7.057007298 0.085382654 0.022053879 11.9949946 -1.079000057 -0.167291268 ERS(ph)PAPPPPAVFPAARPEPGDGLS(ph)SPAGGSYETGDRDDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSPAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR 40 3 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 2 ERS(1)PAPPPPAVFPAARPEPGDGLS(0.457)S(0.422)PAGGS(0.067)YET(0.054)GDRDDGR 88.245 0.00051616 143030000 35269 26022 30958 35549 35981 38019 28393 24772 26274 30411 TRUE FALSE 36661.44735 30491.07608 31764.79091 42580.4861 29864.96247 29189.66343 26167.48247 24439.97186 25328.40387 36369.4532 1.008028555 0.838370484 0.87339204 1.170776087 0.821155114 0.80258736 0.719490676 0.671991732 0.696419705 1 15.15043962 3.012411839 24.99668141 0.75272129 0.960962234 0.363963521 0.119732684 226.1391985 455427.1118 0.034364552 0.041048848 1028.991623 -3.012411839 0.208240945 ERS(ph)PAPPPPAVFPAARPEPGDGLSSPAGGSYETGDRDDGR ddPTM_MDA-MB-175_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 143.34 2.45E-13 1925510000 145960 138508 145269 157501 148058 194242 179105 148097 153170 103566 TRUE FALSE 151722.6135 162295.6716 149054.8295 188654.2277 122891.154 149132.2393 165066.2821 146112.002 147657.4416 123857.7748 1.224974482 1.31033899 1.20343539 1.523152083 0.99219572 1.204060379 1.332708281 1.179675658 1.192153192 1 16.91832491 -4.999972966 0.169700148 0.029105335 1.301668117 0.267964362 0.125709496 174.413769 1.644787336 56.63601191 0.436956435 1.00E-05 4.999972966 1.272562782 ERS(ph)PQR ddPTM_MDA-MB-175_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 78.334 0.042427 51836000 6835.5 8308.2 6187.9 5980.2 10430 9832.1 7575.1 7039 9028.4 8942.4 TRUE FALSE 7105.370818 9735.068721 6349.161757 7163.065711 8657.112326 7548.743782 6981.343868 6944.653718 8703.469648 10694.49207 0.664395352 0.910288087 0.593685209 0.669790175 0.809492613 0.705853418 0.652798078 0.649367326 0.813827304 1 13.38458034 0.951052997 4.792150167 0.999867735 0.707198957 0.522391801 0.086160271 0.191320004 13.57414556 0.081371501 0.020610733 8.934145004 -0.951052997 -0.292668778 ERS(ph)PS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 100.93 0.0032742 6073200000 350080 304390 297480 351400 374290 404580 449660 342860 294840 242110 TRUE FALSE 363901.4287 356666.6147 305232.5732 420905.8712 310668.3195 310622.4265 414414.4742 338264.5225 284228.766 289546.819 1.2567965 1.231809819 1.054173464 1.453671198 1.072946754 1.072788254 1.431252036 1.168255012 0.981633184 1 18.14343712 1.301040386 4.940579973 0.989480244 1.221584825 0.328119354 0.131326457 0.213320059 9.423621454 0.094324571 0.031691828 20.00047851 -1.301040386 0.23210458 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ERSPSPLRGNVVPSPLPTR 19 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 ERS(1)PS(1)PLRGNVVPS(0.973)PLPT(0.027)R;ERS(1)PS(1)PLRGNVVPS(0.899)PLPT(0.101)R;ERS(1)PS(1)PLRGNVVPS(0.955)PLPT(0.045)R;ERS(1)PS(0.999)PLRGNVVPS(0.977)PLPT(0.024)R;ERS(1)PS(1)PLRGNVVPS(0.875)PLPT(0.126)R;ERS(0.997)PS(0.997)PLRGNVVPS(0.979)PLPT(0.026)R 133.15 8.10E-06 12904330000 2907780 2973940 3176310 2995250 3426310 4004990 3102270 3268100 3023410 2939650 TRUE FALSE 3022581.4 3484691.061 3259087.248 3587701.51 2843907.05 3074891.769 2859105.971 3224296.465 2914598.065 3515618.135 0.859758166 0.991202949 0.927031072 1.020503756 0.808935141 0.874637589 0.813258398 0.917135008 0.829042846 1 21.74534694 3.234506315 24.99999063 0.868926809 0.950980129 0.240005708 0.065705376 130.5866083 805234.4132 0.017351299 0.021463782 1715.956663 -3.234506315 0.08205332 ERS(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;ERS(1)PS(1)PLRGNVVPS(0.995)PLPT(0.005)RR 84.948 0.0052984 2943600000 311170 284670 307880 224278 423230 377850 305870 284360 350540 297790 TRUE FALSE 323455.2319 333559.8581 315903.6057 268639.519 351289.5158 290100.0639 281895.1102 280548.6193 337924.1339 356136.249 0.908234511 0.936607433 0.887030193 0.754316697 0.986390789 0.814576064 0.791537258 0.787756428 0.948861945 1 18.44206976 ERS(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 157.55 2.39E-08 4270270000 2076970 1981880 2047150 1846990 2014170 2500900 2247120 2039010 2111680 1839680 TRUE FALSE 2158970.379 2322252.473 2100500.411 2212319.109 1671802.103 1920103.877 2070984.863 2011680.406 2035681.049 2200130.073 0.981292154 1.0555069 0.954716467 1.005540143 0.75986512 0.87272289 0.941301102 0.914346125 0.925254863 1 21.06915739 ERS(ph)PS(ph)PPTIQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(0.999)PS(0.97)PPT(0.032)IQSK;ERS(1)PS(0.999)PPT(0.001)IQSK;ERS(1)PS(0.995)PPT(0.005)IQSK 111.77 0.00076592 1096290000 1104220 824320 1017490 790080 1249900 1266110 1143970 978890 1035290 761960 TRUE FALSE 1147815.458 965890.5477 1044006.625 946355.4658 1037442.444 972075.1406 1054302.642 965769.5807 998030.1151 911251.4734 1.259603405 1.059960478 1.14568443 1.038522838 1.138480951 1.066747401 1.156983196 1.05982773 1.09523018 1 19.79748972 8 0.013991108 5.88E-12 2.412192101 0.34882487 0.057270341 7419.990828 8.016035516 560.6934685 848.9864733 100000000 -8 2.412192101 ERS(ph)PS(ph)PSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 ERS(1)PS(0.989)PS(0.011)FR 74.78 0.02283 712810000 561130 687850 587640 605460 598980 750790 663470 641810 664570 484470 TRUE FALSE 583283.8457 805982.8868 602954.3812 725218.1809 497165.5936 576430.4008 611465.4877 633207.5867 640652.2555 579392.6208 1.006716042 1.391082416 1.040666311 1.251686947 0.858080645 0.99488737 1.055356016 1.09288169 1.105730782 1 19.14418178 3.265542021 24.99669066 1.028678727 1.17872884 0.286530062 0.118703607 287.3703927 266229.9138 0.03155589 0.042715481 1843.07081 -3.265542021 0.150050112 ERS(ph)PSPSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERSPSPSFR 9 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 ERS(0.99)PS(0.009)PS(0.001)FR;ERS(0.462)PS(0.462)PS(0.077)FR;ERS(1)PSPSFR 101.56 0.002364 1035600000 816148 764391 918012 766386 1117001 1071518 953177 900435 905465 704562 TRUE FALSE 848370.1532 895669.2081 941936.1469 917974.8634 927133.569 822674.1835 878464.4961 888366.1416 872877.4915 842607.4342 1.00683915 1.062973304 1.11788255 1.089445483 1.100314964 0.976343372 1.042554884 1.054306081 1.03592427 1 19.68450112 2.764206106 24.99028473 1.029276841 1.077925983 0.364573874 0.034660437 955.9087792 931484.9463 0.011047434 0.011712906 581.0401002 -2.764206106 0.048649142 ERSDS(ph)GGS(ph)SSEPFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 2 ERS(0.099)DS(0.914)GGS(0.94)S(0.042)S(0.006)EPFDR 109.36 0.012029 213460000 286630 367040 350420 352250 412900 443210 365630 378970 347420 409800 TRUE FALSE 297946.3737 430076.2648 359552.2331 421923.9986 342715.4055 340281.1944 336970.9652 373890.527 334916.4221 490092.4639 0.607939105 0.877541069 0.733641628 0.86090693 0.699287238 0.694320398 0.687566102 0.762897932 0.683373948 1 18.90269444 -1.969448295 5.157200676 1.181145722 0.739630953 0.508550486 0.078232532 0.046118544 0.00027321 0.021439654 0.01669195 0.010728814 1.969448295 -0.44151477 ERSDS(ph)GGSSSEPFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 ERS(0.001)DS(0.8)GGS(0.147)S(0.026)S(0.026)EPFDR;ERSDS(0.696)GGS(0.165)S(0.135)S(0.003)EPFDR 202.84 1.50E-08 421280000 272640 353860 358270 320960 389040 421600 355340 359770 375510 379380 TRUE FALSE 283404.0377 414632.7024 367606.8105 384444.93 322911.1198 323689.7894 327487.5223 354947.8716 361995.4685 453712.2473 0.624633872 0.913867115 0.810220162 0.847332053 0.711709066 0.713425285 0.721795641 0.782319353 0.797852539 1 18.79141808 -1.762678256 4.07499309 1.024557713 0.772347522 0.446267195 0.077044417 0.017478984 0.001017951 0.075855251 0.016993663 0.017271169 1.762678256 -0.252210191 ERSDYDRS(ph)R ddPTM_MDA-MB-175_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(1)R 155.47 5.77E-05 1602122000 367225 539585 533183 426018 602954 668111 514183 589137 469807 687329 TRUE FALSE 381723.3266 632254.5264 547078.187 510283.0889 500464.0944 512952.3456 473879.9929 581240.5821 452898.7378 821997.9578 0.464384763 0.769168001 0.665546893 0.620783889 0.60883861 0.624031168 0.576497774 0.707107088 0.550973069 1 19.64877528 -1.328203234 3.831010622 1.000985009 0.630079909 0.668818565 0.0798089 11584867.44 4016879.74 94759.2269 0.017158556 0.046967427 1.328203234 -0.3709051 ERSPS(ph)PPT(ph)IQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERSPSPPTIQSK 12 1 Q14687;Q14687-2;Q14687-3;H0Y613;H7C3B5 Q14687 GSE1 Genetic suppressor element 1 2 ERS(0.099)PS(0.903)PPT(0.997)IQS(0.001)K 164.7 0.0014194 210830000 555220 468690 547300 476530 688710 729320 655040 566280 611140 420710 TRUE FALSE 577140.5143 549183.8616 561563.0876 570786.2117 571643.3202 559946.483 603696.2532 558689.9428 589145.1908 503140.0695 1.147077224 1.091512871 1.116116806 1.134447933 1.136151451 1.112903775 1.199857236 1.110406379 1.170936736 1 18.94060056 3.748566239 19.38759876 1.131498752 1.115563309 0 0.050904835 175.5203866 340073.1093 0.011931474 0.021018455 5604.878969 -3.748566239 -0.015935443 ERT(ph)SSLTQFPPSQSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERTSSLTQFPPSQSEER 17 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ERT(0.333)S(0.333)S(0.333)LT(0.002)QFPPSQSEER 127.01 6.74E-05 190750000 22491 35803 45210 30921 51481 54422 45755 53705 51963 65974 TRUE FALSE 23378.96205 41951.88674 46388.20974 37037.08151 42730.27801 41783.31527 42168.60354 52985.17232 50092.86178 78900.34215 0.296310021 0.531707285 0.587934203 0.469415981 0.541572785 0.529570774 0.534454001 0.671545533 0.634887764 1 16.26774394 -5 0.127247947 2.598645494 0.329694902 0.840049676 0.067988353 54.23147276 0.438982058 21.93738073 0.541673742 1.00E-05 5 -2.268950592 ERTESEVPPRPAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ERTESEVPPRPASPK 15 2 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 ERTESEVPPRPAS(1)PK;ERTESEVPPRPAS(1)PK;ERTESEVPPRPAS(1)PK 130.02 3.25E-05 717220000 612490 352030 458740 325264 612650 767960 610030 469150 542920 324417 TRUE FALSE 636671.5781 412488.4141 470695.1413 389600.2484 508511.9718 589612.9285 562214.2546 462861.8116 523380.4153 387980.2998 1.640989448 1.06316845 1.213193406 1.004175337 1.310664413 1.519698111 1.449079386 1.193003387 1.348987089 1 18.56562387 -0.963167723 4.533748713 0.999996781 1.291552898 0.188451891 0.187944728 0.034547633 41108404.46 569.9129678 0.045037275 0.108850963 0.963167723 0.291556117 ERTSSLT(ph)QFPPSQSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERTSSLTQFPPSQSEER 17 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 ERT(0.215)S(0.215)S(0.215)LT(0.354)QFPPSQSEER 63.857 0.053343 0 17677 38696 29415 39580 47435 45292 33372 45644 37104 51307 TRUE FALSE 18374.90161 45341.73699 30181.57906 47408.80587 39372.01564 34773.61941 30756.21544 45032.21684 35768.63429 61359.62432 0.29946242 0.738950694 0.491880115 0.772638464 0.641659985 0.566718258 0.501245172 0.733906332 0.582934376 1 15.90500203 -5 0.224814472 3.064424525 0.556312738 0.468483697 0.132657715 135.5185502 1.356498327 126.9554386 0.224844643 1.00E-05 5 -2.508111787 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 ERVDDS(0.007)T(0.007)GT(0.007)VIS(0.98)DVEEDAGELSR 93.667 0.0027218 18569000 9003.3 10281 11611 10556 12526 14819 10619 12204 10649 8511 TRUE FALSE 9358.757236 12046.68177 11913.5922 12643.94529 10396.83499 11377.51183 9786.655032 12040.42534 10265.74457 10178.5675 0.919457206 1.183534105 1.170458633 1.242212649 1.021443833 1.117791068 0.961496304 1.182919438 1.008564768 1 13.31324691 3.189110385 24.99996928 1.063362767 1.135786239 0.124697963 0.09900245 246.7977404 124769.672 0.028005388 0.033472896 1545.647249 -3.189110385 0.072423472 ERVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERVEEK 6 1 Q15843;F8VSA6;E9PS38;S4R3E9;E9PL57 Q15843 NEDD8;NEDD8-MDP1 NEDD8 0 64.757 0.096525 380330000 295520 283570 264970 251630 370110 408670 310530 337800 332670 262140 FALSE TRUE 307187.3578 332270.9416 271875.3359 301401.663 307198.8344 313762.586 286189.8472 333272.3435 320697.2717 313501.314 0.979859873 1.059870969 0.867222317 0.961404784 0.979896481 1.0008334 0.912882449 1.063065221 1.022953517 1 18.25811196 1.709830549 12.01595744 1.031696239 0.967523549 0.246182259 0.050100016 0.159139414 50.58879186 0.023229554 0.012705941 51.26613169 -1.709830549 -0.06417269 ERVNEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERVNEAR 7 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 78.77 0.031404 31897000 16298 17433 16322 19481 20745 22665 18875 17687 18079 18037 FALSE TRUE 16941.45762 20426.98214 16747.36473 23334.28366 17218.77231 17401.39724 17395.52818 17449.9347 17428.34032 21571.00481 0.785381014 0.946964795 0.776383153 1.081743009 0.798236914 0.806703137 0.806431056 0.808953261 0.807952178 1 14.39680576 ERVPS(ph)VAEAPQLRPAGTAAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ERVPSVAEAPQLRPAGTAAAK 21 2 Q63ZY3-3;Q63ZY3;Q63ZY3-2 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 ERVPS(1)VAEAPQLRPAGTAAAK;ERVPS(1)VAEAPQLRPAGTAAAK 105.63 0.00020147 1391950000 627180 605160 665310 662270 1009490 918260 766600 923450 845690 874620 TRUE FALSE 651941.5507 709091.5225 682648.5252 793265.0293 837897.2504 705008.0314 706511.8889 911072.6632 815253.7821 1045985.043 0.623279993 0.677917459 0.652636985 0.758390413 0.801060451 0.674013492 0.675451235 0.871018825 0.779412466 1 19.99643079 -5 0.08575698 1.947195754 0.470657028 0.739361093 0.056559441 117.0945616 0.703931345 20.27458849 1.609049903 1.00E-05 5 -1.476538726 ERWET(ph)FQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ERWETFQK 8 1 A0A0M3HER2;Q7Z7K6-3;Q7Z7K6 A0A0M3HER2 CENPV Centromere protein V 1 ERWET(1)FQK 88.417 0.093179 7194500 22201 20457 29974 20863 27892 26132 24551 22527 20082 21140 TRUE FALSE 23077.51262 23970.33062 30755.14706 24989.63913 23150.9278 20063.23903 22626.62847 22225.06241 19359.25274 25281.97825 0.91280486 0.948119264 1.21648499 0.988436857 0.915708714 0.793578684 0.894970648 0.879087158 0.765733304 1 14.62582173 3.192944219 3.330711967 0.863324841 1.028585582 0.354641217 0.095258901 0.248963532 5.658286498 0.028267593 0.036035985 1559.352204 -3.192944219 0.16526074 ES(ph)EELLK ddPTM_MDA-MB-175_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 144.09 0.0024941 3559420000 3575660 1867780 3440400 1874820 4176930 3678840 4534330 2929400 3872160 1476900 TRUE FALSE 3716829.818 2188556.686 3530059.65 2245653.8 3466936.931 2824485.163 4178917.366 2890136.185 3732801.718 1766270.278 2.104338087 1.239083685 1.998595399 1.27141006 1.962857539 1.599123984 2.365955776 1.636293279 2.113380814 1 20.75227469 ES(ph)GGSGFRSPHLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.366)GGS(0.366)GFRS(0.269)PHLWK;ES(0.367)GGS(0.367)GFRS(0.266)PHLWK 62.165 0.047834 364770000 262886 516380 460200 432150 443910 614550 388350 456230 406080 563720 TRUE FALSE 273264.9423 605064.2481 472193.1901 517627.9802 368454.3368 471830.0761 357910.1122 450114.9831 391465.2601 674170.1409 0.405335279 0.897494878 0.700406561 0.767800216 0.546530192 0.699867952 0.53088989 0.667657844 0.580662412 1 19.36275321 -1.187341118 6.548133071 1.000001661 0.651875415 0.399914015 0.130485081 2.93E-06 3.63E-07 0.116823112 0.02753534 0.064961925 1.187341118 -0.348126246 ES(ph)KGSPVFLPR ddPTM_MDA-MB-175_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(0.767)KGS(0.233)PVFLPR 81.431 0.018944 0 128440 103700 131460 96163 156500 169550 141690 129180 137520 99654 TRUE FALSE 133510.9104 121509.6683 134885.9556 115183.7544 129898.1859 130174.5821 130583.9676 127448.5534 132570.6821 119179.2933 1.120252576 1.019553523 1.131790195 0.966474554 1.089939219 1.092258382 1.095693421 1.06938504 1.112363384 1 16.86277407 ES(ph)KS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESKSSPR 7 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 2 ES(0.906)KS(0.941)S(0.153)PR 56.729 0.068197 163100000 3653.2 119460 118880 103340 71103 129630 74981 88735 82351 135670 TRUE FALSE 3797.431157 139976.3257 121978.1105 123780.3436 59016.93746 99525.39706 69103.79329 87545.65247 79387.2036 162251.9389 0.023404535 0.862709726 0.751782144 0.762889765 0.363736408 0.613400356 0.425904268 0.53956614 0.489283543 1 17.30787619 -1.481513492 3.183269649 1.01003381 0.551120022 0.269059346 0.227884 37007095.3 50058348.02 3318546.86 0.05270478 0.032997916 1.481513492 -0.458913788 ES(ph)PSLASR ddPTM_MDA-MB-175_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(0.951)PS(0.049)LASR 134.51 0.0015942 0 155550 149010 160250 172320 179140 211160 234060 165720 160460 130900 TRUE FALSE 161691.2341 174601.3084 164426.2466 206404.3817 148689.8468 162121.2902 215713.7656 163498.7945 154685.0759 156547.3488 1.032858336 1.115325873 1.050329168 1.318478935 0.949807505 1.035605467 1.377945825 1.044404749 0.988104092 1 17.25623955 1.488325576 24.99999928 1.001451713 1.126292628 0.159543045 0.124272691 1.372288952 3054.428654 0.065699641 0.030415323 30.78403723 -1.488325576 0.124840914 ES(ph)PSPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESPSPAPKPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 ES(0.991)PS(0.009)PAPKPR 86.772 0.014469 0 146210 105500 120850 89697 165950 151340 153250 120950 143760 80768 TRUE FALSE 151982.4837 123618.8043 123999.4503 107438.7989 137741.8783 116193.5786 141237.8646 119328.8631 138586.1057 96592.9432 1.573432579 1.279791258 1.28373198 1.112284141 1.426003533 1.202919952 1.462196511 1.235378684 1.434743586 1 16.55963017 -1.472822224 3.091640341 0.992436676 1.322719973 0.362161397 0.132345768 17409047.36 23454055.37 1152148.366 0.030285803 0.033664935 1.472822224 0.330283297 ES(ph)RSPQQSAALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESRSPQQSAALPR 13 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 ES(0.561)RS(0.439)PQQSAALPR 87.088 0.0051647 447030000 99772 276640 216540 246520 164190 294850 165800 153790 196730 526860 TRUE FALSE 103711.0756 324150.768 222183.2103 295280.9202 136281.0424 226375.556 152804.1628 151728.6966 189649.7257 630088.1297 0.16459773 0.514453063 0.352622435 0.468634317 0.216288859 0.359276021 0.242512365 0.240805515 0.300989206 1 19.26519411 -1.087558637 3.67698802 1.000297173 0.318266543 0.791985648 0.104886933 201487894.6 350276812.3 735008.8612 0.025142427 0.081741267 1.087558637 -0.682030631 ES(ph)SPEKEAEEGCPEKESEEGCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.5)S(0.5)PEKEAEEGCPEKESEEGCPK;ES(0.561)S(0.439)PEKEAEEGCPEKESEEGCPK 239.15 1.72E-37 720630000 1093270 199215 329950 187136 644950 785940 583140 342940 398400 107798 TRUE FALSE 1136433.144 233428.6266 338548.7681 224150.9423 535321.6294 603417.346 537431.963 338343.4502 384061.6618 128918.9542 8.815097446 1.810661807 2.626058908 1.738696561 4.152388861 4.680594486 4.168758321 2.624466297 2.979093837 1 16.97610486 4.745886875 24.86280209 3.010417606 8.8151004 0.711705857 1.132761396 461.3234351 1565532.044 0.276273906 2.855829085 55704.06324 -4.745886875 5.804682794 ES(ph)SPSHGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESSPSHGLLK 10 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 ES(0.499)S(0.499)PS(0.002)HGLLK;ES(0.499)S(0.499)PS(0.002)HGLLK;ES(0.499)S(0.499)PS(0.002)HGLLK;ES(0.633)S(0.343)PS(0.023)HGLLK 208.74 6.97E-08 746770000 784339 803381 916355 810103 1267950 1209990 1141260 989019 1002048 754112 TRUE FALSE 815305.3094 941355.4373 940235.9641 970338.9555 1052424.312 928988.1601 1051805.059 975762.818 965984.4882 901865.8081 0.904020645 1.043786591 1.042545305 1.075923876 1.166941137 1.030073601 1.166254502 1.081937922 1.071095588 1 19.78255326 5.568634574 0.974559805 1.092116019 0.233382273 0.520107249 0.050407091 5.906789778 1.359930549 0.014129984 7.842570418 370368.9535 -5.568634574 -0.858733745 ESAAHDYTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESAAHDYTLR 10 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ;;; 171.85 3.89E-06 1329300000 592310 1108480 971090 1026680 1083790 1238870 839504 1013070 854904 1198590 FALSE TRUE 615694.8562 1298852.817 996397.4032 1229754.24 899567.7629 951161.2178 773701.4828 999491.4537 824136.172 1433430.762 0.429525354 0.906114792 0.69511373 0.857909759 0.627562758 0.663555745 0.539755043 0.697272223 0.574939644 1 20.45104079 -1.097068921 4.885279432 1.000012636 0.674397696 0.358635592 0.133647282 1.72E-05 3.19E-06 0.12129556 0.028588529 0.079970733 1.097068921 -0.32561494 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(ph)PAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(0.999)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR;ESAAPAAAPTAEAPPPSVVTRPEPQALPS(1)PAIR 286.35 1.63E-74 2308990000 484237 547388 483386 535059 640245 643660 536818 562448 540991 645564 TRUE FALSE 503355.0507 641397.6309 495983.4363 640892.0732 531416.3836 494179.7198 494740.8024 554909.3045 521520.8396 772049.9057 0.651972168 0.830772242 0.642424062 0.830117417 0.688318695 0.640087792 0.640814536 0.718747973 0.675501461 1 19.55833458 -1.319070607 5.806445207 1.000032918 0.704057805 0.625372115 0.069159284 2.80E-05 3.28E-06 0.063597529 0.014988417 0.047965546 1.319070607 -0.295975113 ESADPLGAWLQDAR ddPTM_MDA-MB-175_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 ;;; 289.71 4.49E-43 313842000 291144 364862 361692 320149 379891 436286 321028 360817 330246 349431 FALSE TRUE 302638.5899 427524.2103 371117.9907 383473.5167 315317.2635 334965.1885 295864.9865 355980.8383 318360.511 417895.3142 0.724197137 1.023041407 0.888064494 0.917630573 0.75453649 0.80155287 0.707988284 0.851842139 0.76181881 1 18.67278206 3.24848933 24.9889766 0.801198018 0.897850495 0.109525568 0.100408436 337.038082 848265.4116 0.025727674 0.034421023 1772.104506 -3.24848933 0.096652478 ESAGADTRPTVRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESAGADTRPTVRPR 14 2 O75489;E9PS48;O75489-2;G3V194 O75489 NDUFS3 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial" 0 86.291 0.0041609 140780000 76951 157950 125740 150610 92875 184090 104280 126590 109110 212590 FALSE TRUE 79989.0849 185076.6838 129016.8877 180400.2085 77088.14067 141337.8874 96106.26111 124893.2681 105183.1524 254242.9402 0.31461674 0.727952106 0.507455143 0.709558379 0.303206613 0.555916665 0.378009557 0.491235934 0.413711202 1 17.95584819 -1.225545387 5.306004642 1.000039302 0.494560558 0.547751467 0.139195703 6.00E-05 8.76E-06 0.124938244 0.029445944 0.059491458 1.225545387 -0.505478744 ESAS(ph)PTIPNLDLLEAHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 ES(0.022)AS(0.824)PT(0.155)IPNLDLLEAHTK;ES(0.001)AS(0.944)PT(0.054)IPNLDLLEAHTK;ESAS(1)PTIPNLDLLEAHTK;ES(0.004)AS(0.99)PT(0.006)IPNLDLLEAHTK 331.01 4.31E-75 1096590000 2105550 1645360 2125340 1612940 2453360 2277380 2337500 2049430 2162560 1441030 TRUE FALSE 2188678.74 1927937.781 2180728.106 1931974.718 2036338.744 1748493.009 2154280.642 2021960.743 2084729.888 1723372.238 1.269997677 1.11870073 1.265384261 1.121043194 1.181601222 1.01457652 1.250037916 1.173258277 1.209680556 1 20.71680292 -2.422487468 1.788020312 4.93E-05 1.175620887 0.33811692 0.074738024 867286.6537 75499.52749 3497799.539 0.017086932 0.00378018 2.422487468 1.175571635 ESAWS(ph)PPPIEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESAWSPPPIEIR 12 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 ES(0.001)AWS(0.999)PPPIEIR;ESAWS(1)PPPIEIR 117.48 0.00076489 44594000 83428 76225 85548 73841 82581 101103 91862 71249 78727 74017 TRUE FALSE 86721.80186 89316.0508 87777.45116 88446.52941 68543.91112 77623.36048 84661.6164 70294.02369 75893.63065 88519.21401 0.979694667 1.009001851 0.991620318 0.999178883 0.774339355 0.876909735 0.956420788 0.794110346 0.857369007 1 16.43370302 3.268254354 24.9712825 0.867012021 0.995650772 0.451129725 0.063431152 167.6453229 140982.0774 0.016923841 0.022911831 1854.617503 -3.268254354 0.128638751 ESCFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESCFYR 6 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 109.7 0.068236 64002000 87911 104910 99719 91828 126360 119760 110170 96914 99988 116640 FALSE TRUE 91381.79416 122927.4764 102317.7591 109991.3043 104881.3723 91947.55498 101534.5875 95615.02635 96389.45141 139493.3748 0.655097737 0.8812424 0.733495474 0.788505579 0.751873503 0.659153563 0.727881074 0.685444929 0.690996627 1 17.08983708 -1.065813668 4.60430856 1.000010584 0.731688253 0.614985823 0.063985544 8557038.534 1980798.584 1159.210826 0.014854744 0.085938216 1.065813668 -0.268322331 ESCSS(ph)PSTVGSSLTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESCSSPSTVGSSLTTR 16 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;H0YEP9 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 ESCS(0.012)S(0.978)PS(0.005)T(0.005)VGSSLTTR 242.35 6.35E-20 189900000 92024 98031 100830 90082 107540 119780 95754 94949 99585 103650 TRUE FALSE 95657.17858 114867.0617 103457.7126 107899.9507 89260.38921 91962.91028 88248.55127 93676.36396 96000.9553 123958.233 0.771688788 0.926659399 0.834617517 0.870454089 0.720084395 0.741886263 0.711921662 0.755709094 0.774462115 1 16.91949457 3.249929393 24.97326005 0.764146912 0.855109752 0.101038562 0.085850217 322.854352 709194.9795 0.021846181 0.029319829 1777.990322 -3.249929393 0.090962841 ESCSSPST(ph)VGSSLTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESCSSPSTVGSSLTTR 16 0 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;H0YEP9 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 ESCSS(0.142)PS(0.231)T(0.627)VGSSLTTR 247.38 3.09E-19 231880000 186540 219180 220720 201720 246670 274180 220400 221830 239750 218490 TRUE FALSE 193904.7432 256822.46 226472.1445 241619.6139 204741.1215 210505.8502 203124.4721 218856.7317 231121.4443 261298.9323 0.742080121 0.982868387 0.866716686 0.924686572 0.783551313 0.805613128 0.77736434 0.837572239 0.884509716 1 17.9953417 5.015698693 16.82313393 0.859837628 0.525768803 0.199278369 0.07463308 128682047.4 2857463628 0.017596435 1055916552 103680.8845 -5.015698693 -0.334068825 ESDFYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESDFYLR 7 0 P61326;P61326-2 P61326 MAGOH Protein mago nashi homolog 0 ; 168.74 0.0024144 420400000 468270 510410 513510 489140 566940 621470 575420 517140 494660 473690 FALSE TRUE 486757.6612 598068.9471 526892.4925 585890.4321 470571.7413 477143.011 530317.0768 510208.5842 476857.2832 566500.4862 0.859236087 1.055725391 0.930083037 1.034227589 0.83066432 0.84226408 0.936128194 0.900632209 0.841759707 1 19.11171767 3.23731188 24.99996061 0.88874466 0.973116048 0.231988326 0.069199025 43.97857914 880464.1328 0.018432823 0.023217101 1727.077713 -3.23731188 0.084371389 ESDGFREEK ddPTM_MDA-MB-175_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 ; 71.349 0.045447 1729100000 1523290 1127280 1332910 1041870 1770510 1687750 1586280 1427760 1441760 982490 FALSE TRUE 1583430.665 1320881.571 1367646.73 1247948.776 1469559.343 1295795.641 1461943.229 1408623.213 1389871.339 1174990.105 1.347611915 1.124163996 1.163964466 1.06209301 1.250699335 1.102814088 1.244217481 1.198838362 1.182879187 1 20.16421718 -2.415820815 1.771966577 1.64E-05 1.18330572 0.339931831 0.077803194 1330136.365 113631.2232 5318586.827 0.017783562 0.003838656 2.415820815 1.183289303 ESDHIHIIALAQALSVSIQVEYMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDHIHIIALAQALSVSIQVEYMDR 25 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 147.41 1.37E-07 15262000 18157 12723 16668 15675 17553 18779 19775 16630 18611 12548 FALSE TRUE 18873.85238 14908.07628 17102.38177 18775.46821 14569.34733 14417.86185 18224.98383 16407.10205 17941.19375 15006.54035 1.257708435 0.993438589 1.139661865 1.251152349 0.970866501 0.960771871 1.214469385 1.093330086 1.195558291 1 13.87330379 -2.510227835 1.848818669 7.37E-05 1.113938693 0.098074715 0.10761132 3415997.918 189177.865 14323737.67 0.025644614 0.003088675 2.510227835 1.113864956 ESDLSHVQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDLSHVQNK 10 0 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 137.05 0.00010158 569780000 761140 1213500 1083500 1150200 1129900 1453900 1102700 1111400 1183300 1302200 FALSE TRUE 791190.3949 1421909.185 1111736.9 1377706.127 937840.0016 1116253.759 1016267.493 1096503.501 1140713.264 1557341.158 0.508039225 0.913036413 0.713868567 0.884652743 0.602205879 0.716768932 0.652565745 0.704086895 0.732474871 1 20.57065359 -1.932823278 3.507567244 1.16384051 0.71813045 0.364353881 0.113144407 0.07664477 0.001467896 0.057921464 0.023668288 0.011672845 1.932823278 -0.44571006 ESDQTLAALLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ESDQTLAALLSPK 13 0 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2 P18583-7 SON Protein SON 1 ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK 258.14 6.65E-24 4946377000 6042290 2187685 3000580 2495212 4173511 4443986 4527846 3363709 3487894 1672563 TRUE FALSE 6280844.275 2563402.881 3078777.58 2988757.486 3464099.091 3411937.601 4172941.599 3318623.983 3362365.376 2000269.697 3.139998714 1.281528628 1.539181234 1.494177256 1.731816013 1.705738784 2.08618948 1.659088266 1.680956014 1 20.9317631 7.999999888 0.043214259 2.80E-10 4.682318409 0.242570497 0.472616793 1248.711929 4.09645655 115.741578 413.4444466 99999974.3 -7.999999888 4.682318409 ESDRLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDRLEEK 8 1 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 0 64.711 0.060331 196610000 228990 203900 267370 228580 402080 334670 269020 272520 312240 298600 FALSE TRUE 238030.702 238918.2389 274337.8818 273792.4418 333734.5852 256947.9645 247933.5094 268867.3152 301002.5434 357104.953 0.666556708 0.669042075 0.768227602 0.766700208 0.934556025 0.719530666 0.694287512 0.75290839 0.84289658 1 18.44598862 -5 0.19153006 2.060867279 0.711150012 0.528113629 0.073169756 120.9060352 1.185443653 48.92543691 0.209690973 1.00E-05 5 -1.349717268 ESDSAEGDEAES(ph)PEQQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESDSAEGDEAESPEQQVR 18 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 ESDSAEGDEAES(1)PEQQVR;ESDSAEGDEAES(1)PEQQVR 476.24 4.52E-195 402280000 216960 310270 287440 313110 300450 402140 296340 283210 292680 276930 TRUE FALSE 225525.7483 363556.4589 294930.9225 375042.2235 249379.6163 308749.0795 273112.0965 279414.0332 282146.504 331189.1314 0.680957577 1.097730645 0.890521139 1.132411024 0.752982489 0.932243997 0.824640879 0.84366909 0.851919575 1 18.3372958 3.207418083 24.9997504 0.858852176 0.956651489 0.085693052 0.130054488 407.8618846 327411.137 0.034626227 0.041390161 1612.196905 -3.207418083 0.097799313 ESDTKNEVNGTSEDIKS(ph)EGDT(ph)QSN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 2 ESDTKNEVNGTSEDIKS(1)EGDT(0.627)QS(0.373)N 109.45 0.0023675 257050000 580510 172670 274080 166820 419300 469320 333800 291540 344000 136710 TRUE FALSE 603428.9831 202324.7293 281222.75 199816.4981 348027.5358 360327.5426 307635.8838 287632.3832 331619.5072 163495.707 3.690794052 1.237492611 1.720061982 1.222151344 2.128664673 2.203896048 1.881614443 1.759265661 2.028307123 1 17.31889323 8 0.046978273 1.26E-14 5.210860547 0.194006295 0.642852748 1201.982457 4.272328 116.7262569 464.9779955 100000000 -8 5.210860547 ESDTKNEVNGTSEDIKS(ph)EGDTQS(ph)N ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 2 ESDTKNEVNGTS(0.001)EDIKS(0.998)EGDT(0.214)QS(0.786)N 113.7 0.0067898 162050000 214810 67517 98362 63550 162100 185900 142680 98332 121990 50231 TRUE FALSE 223290.8647 79112.51954 100925.3945 76120.00032 134546.2999 142727.5423 131496.3688 97014.02038 117599.6037 60072.80272 3.717004277 1.316944041 1.68005137 1.267129165 2.239720702 2.375909494 2.188950121 1.614940805 1.957618064 1 15.87442435 -1.927564896 0.259276411 6.71E-22 2.115460386 0.195305243 0.659040015 54.5559856 2.194110992 35.00555499 0.934688821 0.011815037 1.927564896 2.115460386 ESDTKNEVNGTSEDIKSEGDTQS(ph)N ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESDTKNEVNGTSEDIKSEGDTQSN 24 2 O95232 O95232 LUC7L3 Luc7-like protein 3 1 ESDTKNEVNGTSEDIKSEGDT(0.017)QS(0.983)N 157.96 9.46E-10 643710000 284340 120950 191700 120200 256810 245680 260770 200510 202210 120770 TRUE FALSE 295565.9628 141722.2216 196695.8595 143975.2012 213157.5279 188624.5433 240330.166 197822.4914 194932.5016 144432.5692 2.046394136 0.981234512 1.361852528 0.996833346 1.475827295 1.305969591 1.663961026 1.369652929 1.349643662 1 17.14003658 0.707039697 3.386618272 1.000014668 1.382817007 0.142160514 0.290652298 7.152547236 80.56549513 0.25844631 0.066822793 5.093774286 -0.707039697 0.382802339 ESDVPLKTEEFEVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESDVPLKTEEFEVTK 15 1 Q969H8;M0QXF7;M0QYN0 Q969H8 MYDGF Myeloid-derived growth factor 0 ;;; 217.37 1.90E-12 1494370000 3353490 1754280 2630960 1732640 3858270 3260290 3349310 2459680 3052100 1411370 FALSE TRUE 3485888.375 2055563.944 2699524.979 2075351.021 3202442.644 2503137.058 3086782.33 2426712.013 2942255.517 1687900.929 2.065220958 1.217822627 1.599338523 1.229545517 1.897293015 1.482988139 1.828769851 1.437709981 1.743144675 1 20.6867988 -1.259795588 3.827614197 0.999135494 1.590831039 0.320956676 0.265252727 27442062.07 60770706.54 279195.9993 0.05738016 0.054979959 1.259795588 0.591695545 ESEDAELLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESEDAELLWR 10 0 E5RH53;Q96DB5-3;Q96DB5-2;Q96DB5;H0YB83;E5RGC8 E5RH53 RMDN1 Regulator of microtubule dynamics protein 1 0 ;;; 172.25 8.78E-06 699702000 1329781 855070 1057952 874488 1286801 1335987 1081439 931612 1049396 769130 FALSE TRUE 1382281.781 1001921.621 1085523.098 1047459.116 1068071.026 1025724.266 996672.9854 919125.2649 1011628.443 919826.2976 1.502763929 1.089250898 1.18013923 1.138757523 1.161166003 1.115128225 1.083544782 0.999237864 1.099803784 1 19.81100192 7.088646695 1.285509722 1.088886843 199.9999941 0.799062091 0.060303699 328.7121598 1.463096531 0.017673564 191804.0038 12264410.96 -7.088646695 198.9111073 ESEDDPES(ph)EPDDHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESEDDPESEPDDHEK 15 0 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 ESEDDPES(1)EPDDHEK 119.68 0.00054345 0 402550 298530 365310 300240 458250 459360 465490 378230 372840 230630 TRUE FALSE 418442.9848 349800.2053 374830.2787 359626.5759 380356.8287 352680.6017 429003.6775 373160.4455 359421.5612 275817.5328 1.517100746 1.268230492 1.358979159 1.303856837 1.379016137 1.278673615 1.555389438 1.352925036 1.303113539 1 18.07335464 0.77593236 2.611294268 1.000173599 1.374234168 0.61620504 0.088981696 0.673275424 6.811005759 0.080901739 0.02152176 5.969423079 -0.77593236 0.37406057 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ESEDKPEIEDVGSDEEEEK 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK 337.2 9.75E-76 7789430000 14247670 2880400 4738540 3834230 7183740 10172630 12684870 5443760 6393270 1292226 TRUE FALSE 14810179.01 3375086.294 4862030.245 4592629.25 5962650.441 7810190.85 11690596.74 5370795.301 6163177.462 1545412.944 9.583314981 2.183938156 3.14610426 2.971781276 3.85828944 5.053788945 7.564707409 3.475314041 3.988045711 1 20.55956096 4.749905114 24.54437074 3.935035837 9.583319289 0.524058272 1.669647365 1131.22912 2447409.4 0.404693693 6.252722711 56221.8476 -4.749905114 5.648283452 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 285.77 3.09E-45 13009540000 21398600 2326530 4590020 3178820 8180700 12694380 13409230 5145720 6048140 885776 TRUE FALSE 22243433.25 2726093.43 4709639.692 3807581.108 6790147.536 9746302.63 12358179.51 5076750.04 5830468.623 1059326.848 20.99770557 2.573420503 4.445879665 3.594340232 6.409870144 9.200467871 11.66606844 4.792430259 5.503937367 1 20.01471636 4.746314819 24.83845447 5.873234662 20.99771358 0.709973287 2.967959106 503.404923 1612477.718 0.732793172 7.901277443 55758.97983 -4.746314819 15.12447892 ESEDKPEIEDVGS(ph)DEEEEKKDGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 ESEDKPEIEDVGSDEEEEKKDGDK 24 3 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK;ESEDKPEIEDVGS(1)DEEEEKKDGDK 294.72 3.56E-61 99447967000 36052490 1913355 3962970 2366068 9207801 19054500 13248240 4875477 5583703 631292 TRUE FALSE 37475870.14 2241958.837 4066248.254 2834069.188 7642662.275 14629381.15 12209808.33 4810129.205 5382746.62 754981.5806 49.6381251 2.969554351 5.385890674 3.753825605 10.12297846 19.37713651 16.17232611 6.371187495 7.12963966 1 19.52608192 4.743425175 24.99124948 8.666879297 49.63814195 0.835095611 5.540203143 206.9224767 1063011.286 1.410237005 11.61004634 55389.21057 -4.743425175 40.97126265 ESEDSETQPFDTHLEAYGPCLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESEDSETQPFDTHLEAYGPCLSPPR 25 0 Q14676;Q14676-3 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 ESEDSETQPFDTHLEAYGPCLS(1)PPR;ESEDSETQPFDTHLEAYGPCLS(1)PPR 231.41 9.45E-35 407390000 146467 182147 171529 185743 222555 243490 192495 206238 191446 174235 TRUE FALSE 152249.6303 213429.3303 175999.1867 222482.411 184725.1806 186943.1376 177406.7389 203473.7169 184555.8959 208373.0123 0.730659065 1.024265705 0.844635227 1.067712217 0.886512023 0.897156189 0.851390192 0.97648786 0.885699611 1 17.66880891 0.126467503 0.010795973 1.898121698 1.81E-06 0.091570562 0.091027367 7655.485233 27.35604509 2489.517268 2318.71457 1.338035089 -0.126467503 -1.898119883 ESEEGNPVRGSEEDS(ph)PKKESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESEEGNPVRGSEEDSPKKESK 21 3 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ESEEGNPVRGS(0.038)EEDS(0.961)PKKES(0.001)K;ESEEGNPVRGSEEDS(1)PKKESK;ESEEGNPVRGSEEDS(1)PKKESK;ESEEGNPVRGS(0.009)EEDS(0.953)PKKES(0.038)K 195.73 7.16E-22 1534380000 2206070 397329 739790 255191 1448420 1370340 821360 679760 922830 320399 TRUE FALSE 2293167.347 465567.165 759069.5351 305667.0181 1202218.086 1052099.303 756979.657 670648.9291 889617.5286 383175.0496 5.984646832 1.21502474 1.980999378 0.797721612 3.137516618 2.745740631 1.97554527 1.750241645 2.321700041 1 18.5476441 4.744808226 24.96370679 1.934540277 5.984648664 0.752540743 0.705430553 336.9823896 1346450.596 0.166025575 1.546387493 55565.88376 -4.744808226 4.050108387 ESEEQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESEEQKR 7 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 112.17 0.010285 624900000 595000 362100 417330 386750 470960 632550 571510 386600 437770 382020 FALSE TRUE 618491.0594 424287.8583 428205.9626 463247.9957 390906.3874 485649.8489 526713.5528 381418.2594 422014.7432 456869.5048 1.353758684 0.928685005 0.937260986 1.013961297 0.855619347 1.062994671 1.152875268 0.834851649 0.923709591 1 18.80142262 4.741840038 24.94973397 0.96518093 1.353758832 0.622694804 0.090116259 204.7825898 1557905.286 0.021840035 0.158223166 55187.41323 -4.741840038 0.388577902 ESEIIDFFLGASLKDEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESEIIDFFLGASLKDEVLK 19 1 P15880;E9PQD7;E9PPT0;E9PMM9;I3L404 P15880 RPS2 40S ribosomal protein S2 0 224.89 1.70E-19 356910000 410130 233000 347010 231380 460840 369720 393010 317000 398760 176150 FALSE TRUE 426322.2491 273015.9375 356053.3657 277146.2734 382506.5814 283858.1332 362204.8493 312751.1335 384408.7055 210663.2199 2.023714673 1.295982933 1.690154389 1.315589278 1.815725505 1.347449893 1.719354947 1.484602455 1.824754723 1 17.68457893 -1.112103688 4.607989734 0.999964932 1.591872971 0.37716983 0.234920244 0.000100464 1.94E-05 0.197466055 0.046539437 0.077249613 1.112103688 0.591908038 ESEITDEDIDGILER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESEITDEDIDGILER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ; 257.79 1.97E-24 104518000 148888 181186 179639 182790 210320 213340 201767 171513 176804 170862 FALSE TRUE 154766.2132 212303.2861 184320.5399 218945.3164 174569.8815 163795.0182 185951.9753 169214.1488 170440.8586 204339.1375 0.757398779 1.03897515 0.902032484 1.071480085 0.854314468 0.801584171 0.910016444 0.828104448 0.834107752 1 17.64060603 ESEKQQDS(ph)QPEEVMDVLEMVENVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESEKQQDSQPEEVMDVLEMVENVK 24 1 Q9H307 Q9H307 PNN Pinin 1 ES(0.003)EKQQDS(0.997)QPEEVMDVLEMVENVK;ES(0.171)EKQQDS(0.829)QPEEVMDVLEMVENVK;ES(0.156)EKQQDS(0.844)QPEEVMDVLEMVENVK 123.89 6.65E-05 70321000 72595 41759.6 65747 30860.2 88387 75609 61322 59756 76756 38187.5 TRUE FALSE 75461.10666 48931.48646 67460.42083 36964.25545 73363.00931 58049.95562 56515.4214 58955.06856 73993.56655 45669.60948 1.652326515 1.07142336 1.477140304 0.809384093 1.606385738 1.271085001 1.237484227 1.290903715 1.620192671 1 15.47894683 -1.913598448 2.801163873 0.818185991 1.317441139 0.133677908 0.253119034 39549599.55 42719126.68 47879418.08 0.055116225 0.012201172 1.913598448 0.499255148 ESESVDKVMDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 182.33 1.55E-05 3317770000 6587120 3555080 5403730 2977710 7842630 6107810 5737850 4965150 6120490 3251910 FALSE TRUE 6847184.584 4165637.335 5544555.643 3566692.15 6509542.554 4689363.692 5288102.324 4898600.286 5900214.76 3889059.503 1.760627365 1.071116894 1.425680332 0.917109175 1.673808937 1.205783478 1.359738086 1.259584813 1.517131521 1 21.89098988 -1.406032839 3.823288729 0.998205622 1.334828049 0.153470731 0.245900179 18030411.75 6632989.832 268543.3779 0.051132899 0.039261525 1.406032839 0.336622427 ESEVAHVDQLFDDASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESEVAHVDQLFDDASR 16 0 E9PRF4;Q15047-3;Q15047;E9PAP1;X6RHV1;B0QZE6;E9PS59;X6R732;E9PQM8;Q15047-2 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 0 140.22 1.72E-06 46880000 68152 106870 101060 98399 113180 134210 102680 116190 103380 107010 FALSE TRUE 70842.69358 125224.0912 103693.7066 117862.0285 93941.70403 103041.7615 94631.6733 114632.6631 99659.37399 127976.5607 0.553559911 0.978492394 0.810255457 0.920965745 0.734053983 0.805161202 0.739445355 0.895731707 0.77873146 1 16.96552007 -4.99999992 0.347482969 3.134091008 0.806083561 0.216689065 0.112058 648.5731063 5.3522895 1029.942915 0.079274682 1.00E-05 4.99999992 -2.328007447 ESFDGSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESFDGSVR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 122.18 0.0032608 314870000 596690 641520 663660 698880 656650 842660 817090 664380 599780 514200 FALSE TRUE 620247.7819 751696.0697 680955.5248 837116.3781 545032.8675 646964.9856 753044.3507 655475.0728 578194.035 614947.645 1.008618843 1.222374093 1.107339024 1.361280728 0.886307756 1.052065149 1.224566606 1.065903867 0.940232944 1 19.23010406 3.231271607 24.99951201 1.048222934 1.173467945 0.259077469 0.118676913 268.1491251 919684.0802 0.034126399 0.041571745 1703.223367 -3.231271607 0.125245011 ESGADGASTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESGADGASTSPR 12 0 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 ESGADGAST(0.001)S(0.999)PR;ESGADGAST(0.001)S(0.999)PR 143.58 6.54E-05 145956000 229082 264164 249351 227407 247617 280790 249834 256628 229213 241350 TRUE FALSE 238126.3342 309532.1121 255849.2919 272387.4259 205527.1508 215580.7779 230251.3583 253188.3214 220963.6689 288637.9116 0.825000198 1.072388968 0.886402242 0.943699407 0.712058751 0.746890028 0.797716963 0.877183181 0.765539314 1 18.13890128 3.271235368 24.74480176 0.810663086 0.938661824 0.259735513 0.094776229 209.1407997 158382.1872 0.025011619 0.033863293 1867.391458 -3.271235368 0.127998738 ESGGS(ph)GFRSPHLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.024)GGS(0.863)GFRS(0.113)PHLWK 109.42 0.00046551 195190000 149130 138520 176600 142070 210760 206160 160360 152820 177300 138630 TRUE FALSE 155017.7676 162309.7325 181202.3411 170171.022 174935.0905 158282.4644 147790.5642 150771.6979 170919.0076 165791.8943 0.935014153 0.978996791 1.092950544 1.0264134 1.055148632 0.954705687 0.891422134 0.909403313 1.030924994 1 17.33901395 2.615183336 6.118532973 0.941572026 1.019962282 0.207852105 0.055213938 0.30077506 13.82365122 0.018657336 0.017536145 412.2715216 -2.615183336 0.078390256 ESGGSGFRS(ph)PHLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGGSGFRSPHLWK 14 1 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 ES(0.158)GGS(0.158)GFRS(0.684)PHLWK 58.158 0.067267 359990000 82885 77053 94210 68652 102110 115120 85796 96480 85265 78489 TRUE FALSE 86157.3638 90286.25336 96665.18999 82231.16069 84753.37867 88385.12466 79071.08533 95186.84341 82196.32931 93867.41679 0.917862308 0.961848706 1.029805584 0.876035194 0.902905199 0.941595366 0.842369888 1.014056279 0.875664124 1 16.51833684 -1.879570814 2.686382299 1.031676503 0.933258709 0.117664763 0.057225225 15794357.75 10553852.21 3181816.652 0.013580334 0.013195601 1.879570814 -0.098417794 ESGLQAAHPNSIFLIDHAWTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESGLQAAHPNSIFLIDHAWTCR 22 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 267.57 4.70E-38 1593210000 409740 536420 546540 629790 561770 672280 546360 583390 595480 565250 FALSE TRUE 425916.8516 628545.9622 560783.2814 754360.5823 466280.5361 516153.1585 503534.8756 575570.6113 574048.7911 675999.9151 0.630054593 0.929801836 0.829561171 1.115918161 0.689764193 0.763540271 0.74487417 0.851435922 0.849184709 1 19.36666354 0.65935721 1.967659944 0.999881772 0.8245764 0.15114871 0.12755048 3.298013758 16.41317639 0.11869738 0.03282192 4.564121637 -0.65935721 -0.175305372 ESGLVYTEDEWQKEWNELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGLVYTEDEWQKEWNELIK 20 1 Q6GQQ9;Q6GQQ9-2;Q5SZ59 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 0 73.809 0.013207 20381000 23181 15156 20537 11810 25972 21055 20752 19325 20463 15864 FALSE TRUE 24096.20378 17758.9251 21072.21109 14145.98275 21557.28872 16165.29534 19125.40401 19065.97998 19726.54063 18972.24707 1.270076428 0.936047535 1.110686099 0.745614513 1.136253847 0.85204959 1.008072684 1.004940528 1.039757735 1 14.21160294 4.744203597 24.41633747 0.981450939 1.270076602 0.384280491 0.109587819 427.5946518 1850061.195 0.02345441 0.205056246 55488.57821 -4.744203597 0.288625663 ESGNQVLKNGNFS(ph)LAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGNQVLKNGNFSLAIR 17 1 A0A2R8YEM9;A0A096LPF5;A0A2R8Y8A3 A0A2R8YEM9 TRANK1 1 ES(0.001)GNQVLKNGNFS(0.999)LAIR 47.548 0.091839 305960000 287690 293510 339510 98815 565760 367190 157570 310810 349460 508700 TRUE FALSE 299048.2233 343918.0593 348357.9095 118360.3121 469592.3173 281915.6873 145219.2517 306644.1003 336883.0029 608370.0254 0.491556472 0.565310658 0.572608602 0.194553162 0.77188602 0.463395098 0.238702181 0.504042092 0.553746879 1 19.21458955 0.728515623 2.545421531 0.999850275 0.472273968 0.50385555 0.155392685 1.213344138 10.25987589 0.143913242 0.038376922 5.351994065 -0.728515623 -0.527576307 ESGPPHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESGPPHMK 8 0 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28;E7EVI1;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;E5RJN7 O95793-2;E7EPX0 STAU1;STAU2 Double-stranded RNA-binding protein Staufen homolog 1;Double-stranded RNA-binding protein Staufen homolog 2 0 ;;; 121.99 0.0014096 557810000 1295180 1253800 1450700 1201980 1691520 1734480 1619060 1442460 1509220 1178230 FALSE TRUE 1346314.706 1469130.397 1488506.434 1439728.056 1403996.035 1331673.306 1492153.847 1423126.183 1454903.467 1409081.61 0.955455452 1.042615549 1.056366376 1.021749235 0.996390858 0.945064712 1.05895488 1.009967182 1.032518952 1 20.42632374 -0.932321736 3.856684313 0.999998972 1.014799627 0.009888579 0.036824452 1.02127E+11 28251210675 1102640.382 0.008655753 0.116863332 0.932321736 0.014800655 ESGS(ph)PYSVLVDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGSPYSVLVDTK 13 0 Q9Y2D9;D6RF85 Q9Y2D9 ZNF652 Zinc finger protein 652 1 ES(0.066)GS(0.916)PYS(0.018)VLVDTK 87.447 0.006079 0 47728 45085 50176 44235 62426 63908 50794 48831 47782 42810 TRUE FALSE 49612.33829 52827.99804 51483.62778 52984.55097 51814.85082 49066.33554 46812.63355 48176.50032 46062.33515 51197.79985 0.969032623 1.031841177 1.005582817 1.034898982 1.012052295 0.958368049 0.91434854 0.940987708 0.899693645 1 15.64379419 2.624726077 3.388020224 0.934050875 1.013153974 0.568836256 0.029760987 0.157186499 3.36838292 0.00942736 0.00882058 421.4306104 -2.624726077 0.079103099 ESGSDSDLFHS(ph)PSDDMDSIIFPKPEEEHLACDITGSSSSTDDTASLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESGSDSDLFHSPSDDMDSIIFPKPEEEHLACDITGSSSSTDDTASLDR 48 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 ES(0.005)GS(0.005)DS(0.028)DLFHS(0.93)PS(0.032)DDMDSIIFPKPEEEHLACDITGSSSSTDDTASLDR 173.54 4.15E-22 23228000 7751.8 7121 9560.4 8814.5 13131 10675 8221.6 9266.1 9949.9 9177.2 TRUE FALSE 8057.84705 8343.976356 9809.551878 10557.98179 10898.99731 8195.893031 7577.169509 9141.903086 9591.805043 10975.29663 0.734180343 0.760250646 0.89378467 0.961976896 0.993048086 0.746758225 0.690384029 0.832952711 0.873944948 1 13.42197231 -2.927340395 0.949854065 2.280823928 0.831503724 0.219539098 0.095096454 18877.1845 652.5088831 51100.23048 0.032201292 0.001182115 2.927340395 -1.449320204 ESGYSDDEIMELWSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESGYSDDEIMELWSTR 16 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 0 ; 183.79 4.48E-09 57100000 46153 48036 55760 52568 55009 67292 58213 54112 52892 46594 FALSE TRUE 47975.15608 56285.80933 57213.15141 62965.7935 45658.58983 51664.45282 53650.11295 53386.71715 50988.42725 55723.2022 0.860954758 1.010096461 1.026738399 1.129974427 0.819382017 0.927162309 0.96279666 0.958069799 0.915030458 1 15.76599055 3.234745008 24.99993587 0.932448 1.008580487 0.199916428 0.074911887 166.3242083 1089759.659 0.021565617 0.026719735 1716.900031 -3.234745008 0.076132486 ESHPHGVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESHPHGVKR 9 1 E9PM92;O00193;E9PQA1;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ; 57.598 0.074219 65922000 52567 51056 56936 40249 75625 75252 43044 53132 53408 66343 FALSE TRUE 54642.38575 59824.47084 58419.79893 48210.13207 62770.28951 57775.86346 39670.09881 52419.85245 51485.85651 79341.64064 0.688697452 0.754011013 0.736306919 0.607627113 0.791139293 0.728190935 0.499990906 0.66068526 0.648913434 1 16.27579061 -1.096931568 5.536151782 1.000003235 0.676823938 0.596686885 0.07901974 3.25E-06 5.31E-07 0.078905835 0.018598098 0.07999603 1.096931568 -0.323179298 ESIESEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 172.28 9.03E-05 10975210000 5138110 5645980 5395070 4870480 6533190 6531460 5314830 5302440 5678600 5753790 FALSE TRUE 5340966.55 6615633.145 5535669.956 5833846.407 5422680.697 5014627.4 4898239.737 5231369.465 5474228.295 6881134.988 0.776175233 0.961415981 0.804470479 0.84780293 0.78805033 0.72875004 0.711836019 0.760248051 0.795541478 1 22.71421511 5.100241426 13.91188629 0.80748246 3.89E-05 0 0.089717147 1711496.564 3462585.525 0.021400393 41932191.77 125962.5448 -5.100241426 -0.807443519 ESIWLPFMETELHCDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESIWLPFMETELHCDEK 17 0 O75884;O75884-2 O75884 RBBP9 Putative hydrolase RBBP9 0 ;; 227.29 1.80E-15 154677000 337010 239979 318904 265792 406307 428627 354617 326752 363760 207204 FALSE TRUE 350315.415 281193.5265 327214.9002 318364.8643 337243.0813 329084.8752 326821.1929 322372.4239 350668.3487 247801.6566 1.413692789 1.134752408 1.320470995 1.284756804 1.360939575 1.328017252 1.318882195 1.300929252 1.415117047 1 17.91882631 -1.032775185 4.623658681 0.999989424 1.313673845 0.621547226 0.074712197 0.05705614 21510441.33 506.7062656 0.016339828 0.092730973 1.032775185 0.313684421 ESKGS(ph)PVFLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESKGSPVFLPR 11 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ES(0.001)KGS(0.999)PVFLPR;ESKGS(1)PVFLPR;ES(0.031)KGS(0.969)PVFLPR 150.12 2.06E-05 2507340000 2840290 2108970 2618200 2057120 3400900 3230640 2773690 2693690 2748040 2080560 TRUE FALSE 2952426.842 2471169.192 2686432.443 2464012.196 2822816.233 2480372.821 2556280.93 2657585.492 2649138.577 2488205.897 1.186568541 0.993153016 1.079666456 0.990276648 1.134478556 0.996851918 1.027359083 1.068072982 1.064678201 1 21.24667444 4.751574502 24.47449096 1.043414861 1.186568665 0.487667786 0.045086138 1323.8779 2489684.522 0.009797588 0.181425523 56438.37521 -4.751574502 0.143153805 ESKKEDLVFIFWAPESAPLK ddPTM_MDA-MB-175_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 94.384 0.00077379 407910000 1711700 452830 878100 299710 1665100 1005700 788730 801290 1222700 561670 FALSE TRUE 1779279.238 530600.03 900984.0074 358991.7435 1382066.897 772141.4165 726907.2816 790550.0182 1178695.266 671718.4827 2.648846628 0.789914292 1.34131192 0.534437793 2.057509109 1.14950152 1.082160608 1.176906753 1.754745918 1 19.3574972 4.749242934 24.84622142 1.214933293 2.648847514 0.518560764 0.416001318 1099.162554 2556510.9 0.092894536 1.350169576 56136.19007 -4.749242934 1.43391422 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLASPK 38 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLAS(1)PK;ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLS(0.006)LAS(0.994)PK;ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLS(0.001)LAS(0.999)PK;ESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLS(0.019)LAS(0.98)PK 243.17 6.83E-50 1339530000 201681 205552 211226 222124 336736 355518 304227 317404 304743 210278 TRUE FALSE 209643.5216 240853.957 216730.7231 266059.4642 279497.735 272954.3324 280380.8928 313149.7185 293775.359 251477.9481 0.833645746 0.957753787 0.861827944 1.057983279 1.111420453 1.085400666 1.114932323 1.24523729 1.168195308 1 17.94007237 3.534718951 1.240810353 1.14983263 0.871572759 0.687519115 0.069418709 0.250929673 0.774455919 0.023729937 0.050627833 3425.460394 -3.534718951 -0.278259872 ESLCDS(ph)PHQNLSRPLLENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;ES(0.001)LCDS(0.999)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK;ESLCDS(1)PHQNLSRPLLENK 257.34 3.29E-31 2948870000 2226010 1797270 1959260 1511660 2460170 2525690 2026080 1907620 2211400 1666610 TRUE FALSE 2313894.594 2105937.142 2010319.925 1810661.836 2041991.182 1939136.775 1867270.555 1882051.474 2131812.146 1993150.32 1.160923273 1.056587213 1.008614305 0.908442187 1.024504354 0.972900415 0.936843818 0.944259675 1.069569176 1 20.92661909 4.577654713 1.733907985 0.973966577 1.190491235 0.611060875 0.044161653 0.4060661 1.562543929 0.01144499 0.131041784 37814.18228 -4.577654713 0.216524658 ESLIDGIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESLIDGIKR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;; 170.69 9.22E-05 2186125000 1787740 1377451 1714840 1475046 2342000 2084470 1808890 1780690 1916190 1417036 FALSE TRUE 1858321.356 1614017.494 1759530.139 1766805.696 1943907.677 1600383.433 1667104.475 1756822.763 1847226.696 1694677.073 1.096563696 0.95240416 1.038268687 1.042561869 1.147066723 0.944358933 0.983729881 1.03667111 1.090016927 1 20.69257896 2.130059394 0.002418872 3.65E-05 2.059426079 0.014383626 0.061443799 226645.2377 357.8742772 151849.5743 152826.6133 134.9147379 -2.130059394 2.059389592 ESLKEEDES(ph)DDDNM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 25 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 210.31 1.92E-08 75165630000 42521460 21512540 28709600 20708490 40494050 43581240 37712610 28310300 31505480 17773510 TRUE FALSE 44200240.07 25207151.4 29457795.76 24804567.51 33610885.85 33460157.49 34756597.08 27930846.73 30371603.93 21255888.99 2.079435026 1.185890245 1.385865149 1.16695037 1.581250535 1.574159401 1.635151421 1.314028632 1.428855972 1 24.34135926 0.515874635 1.08358854 1.000511524 1.479811268 0.25899803 0.248942009 2.429719861 3.97691104 0.228805338 0.071081275 3.280005979 -0.515874635 0.479299743 ESLKELSLAGNELGDEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESLKELSLAGNELGDEGAR 19 1 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 202.53 5.00E-16 479280000 332650 340260 414950 258140 531660 457720 322390 357790 412490 394920 FALSE TRUE 345783.2789 398697.0081 425763.9379 309199.3215 441288.6231 351421.4668 297120.2294 352994.4103 397644.5655 472297.0128 0.732130989 0.844165848 0.901474975 0.654671347 0.934345573 0.74406879 0.629096144 0.747399202 0.841937498 1 18.84933489 0.918190977 4.226977294 0.999890985 0.772660029 0.355924472 0.092483961 0.424671586 18.09022731 0.088873826 0.022648902 8.283063228 -0.918190977 -0.227230957 ESLLGDMEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESLLGDMEWR 10 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4;Q63HN8-5 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 90.906 0.024455 30750000 49523 62293 61163 59682 85348 71021 68283 58943 62119 72387 FALSE TRUE 51478.20628 72991.33818 62756.95803 71486.92147 70840.57745 54527.44908 62930.80004 58152.9655 59883.34932 86569.84672 0.594643611 0.843149676 0.724928603 0.825771607 0.818305451 0.629866531 0.726936716 0.671746199 0.691734496 1 16.40157698 -0.870737791 4.295496028 1.000003688 0.727584475 0.519269142 0.079283669 20842342.58 46156313.41 1249.279106 0.018755298 0.134667317 0.870737791 -0.272419213 ESLLVSVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ESLLVSVQR 9 0 J3QRZ1;A6NIZ0;Q9GZM8-3;Q9GZM8;Q9GZM8-2 J3QRZ1 NDEL1 Nuclear distribution protein nudE-like 1 0 ;;;; 110.87 0.0022166 1722695000 36837.3 2964640 1596191 2661660 952825 2515450 806914 1704360 1017380 3217530 FALSE TRUE 38291.66505 3473793.858 1637789.049 3188128.404 790864.1468 1931274.86 743665.9722 1681515.842 980764.6925 3847943.4 0.009951203 0.90276636 0.425627115 0.828527884 0.205529049 0.501897938 0.19326323 0.436990794 0.254880228 1 21.87565615 -1.259252132 4.858749679 1.000120267 0.4312506 0.302021136 0.26483955 0.00037882 5.78E-05 0.236536154 0.055738223 0.055048802 1.259252132 -0.568869667 ESMAGNKPANAVLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESMAGNKPANAVLHK 15 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y795 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 62.377 0.049025 539830000 651360 487170 650420 513800 859810 779640 795650 677970 678140 452750 FALSE TRUE 677076.1958 570837.6578 667370.4795 615428.1065 713659.8033 598580.4256 733284.874 668882.9211 653733.8739 541457.6941 1.250469248 1.054260867 1.232544088 1.136613466 1.318034282 1.105498051 1.354279165 1.235337365 1.207359099 1 19.04648909 ESNCYDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ESNCYDPER 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 157.34 0.00015997 3440610000 3899200 4339820 4342920 4526000 4905570 5434560 4183400 4292190 4282440 4198350 FALSE TRUE 4053143.427 5085150.326 4456100.063 5421229.291 4071722.964 4172465.802 3855494.177 4234660.214 4128315.821 5020936.3 0.807248526 1.012789253 0.887503803 1.07972477 0.810948939 0.831013491 0.767883507 0.843400505 0.822220314 1 22.25952499 3.168878071 24.9999998 0.832624172 0.947302532 0.230773828 0.088271327 57.43933647 20606.53394 0.023475504 0.028058603 1475.292284 -3.168878071 0.11467836 ESNEEEQVWHFLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESNEEEQVWHFLGK 14 0 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4;H0YAK2 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 0 113.35 0.00054083 67667000 20353 22994 19626 25140 22898 30919 25841 18690 25514 19152 FALSE TRUE 21156.55216 26943.04063 20137.46968 30112.61696 19005.80614 23738.53083 23815.5149 18439.49112 24595.75612 22904.46771 0.923686698 1.176322496 0.879193961 1.314704945 0.829785978 1.036414866 1.03977596 0.805060888 1.073840983 1 14.48334142 ESNRLS(ph)APSYLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESNRLSAPSYLAR 13 1 H0YJH0;Q9H4B6 H0YJH0 SAV1 Protein salvador homolog 1 1 ESNRLS(1)APSYLAR;ESNRLS(1)APSYLAR 144.5 2.50E-05 760770000 314610 391060 392010 387370 482140 524100 330730 392510 371070 459000 TRUE FALSE 327031.0457 458221.513 402226.1026 463990.6298 400186.015 402385.7178 304806.5184 387249.0455 357715.2632 548932.2619 0.595758472 0.83475056 0.732742691 0.845260266 0.729026226 0.733033465 0.555271642 0.70545871 0.651656476 1 19.06626861 -1.001655003 4.925142235 1.000003491 0.711673416 0.50102623 0.087024801 3.34E-06 6.78E-07 0.084528079 0.019923218 0.099619647 1.001655003 -0.288330075 ESNTAGNDVFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESNTAGNDVFHK 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 141.58 6.06E-05 455350000 373770 614090 525630 620280 489240 658210 550480 549350 529590 782240 FALSE TRUE 388526.7282 719555.1805 539328.3496 742969.5326 406079.1596 505350.7028 507331.9392 541986.8618 510530.1593 935504.9511 0.415312316 0.769162343 0.576510417 0.794190915 0.434074837 0.540190303 0.542308128 0.579352211 0.545726838 1 19.83538576 -1.246965598 3.76942801 1.000603018 0.582401568 0.544176556 0.115944929 24906379.45 39928026.6 171039.7971 0.026306996 0.056628414 1.246965598 -0.41820145 ESNYFGLS(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESNYFGLSPEER 12 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 ESNYFGLS(1)PEER 116.43 0.0008837 39547000 61922 83484 80024 80076 102720 106340 92874 97250 87686 87024 TRUE FALSE 64366.72837 97821.72758 82109.49118 95914.7938 85259.69109 81644.1466 85594.2932 95946.52282 84530.19799 104074.6866 0.618466704 0.939918541 0.788947763 0.921595797 0.819216409 0.784476507 0.822431429 0.921900665 0.812207086 1 16.66725969 -5 0.106505693 1.513072743 0.735725963 0.305342665 0.085462692 221.5274799 1.582739573 25.133947 1.107736214 1.00E-05 5 -0.77734678 ESPFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESPFFR 6 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 ; 141.59 0.027066 173617000 146824 276010 232070 257590 209711 277000 184133 222540 193134 294620 FALSE TRUE 152620.7249 323412.5704 238117.9348 308540.5332 174064.3991 212670.948 169700.1743 219557.2153 186183.1451 352345.1482 0.43315688 0.917885693 0.675808752 0.875676974 0.494016733 0.603586992 0.481630513 0.623131087 0.528411264 1 18.42662982 -1.214465707 4.364866399 1.000137168 0.631865647 0.347559481 0.153564092 22549959.03 6274243.252 29530.99308 0.035131583 0.061028724 1.214465707 -0.368271521 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 337 1.97E-130 9116340000 1868230 2232410 2146310 2125950 2186220 2717050 2279030 2444330 2274400 2210740 TRUE FALSE 1941989.163 2615809.052 2202244.602 2546456.565 1814607.105 2086056.315 2100393.673 2411567.754 2192544.788 2643892.176 0.734519048 0.989378113 0.832955527 0.963146904 0.6863393 0.789009603 0.794432425 0.912127876 0.829286765 1 21.33423191 0.221789756 0.94450972 1.00091051 0.838376563 0.223444662 0.090786942 5.760702251 5.677137382 0.101176266 0.027613429 1.666440287 -0.221789756 -0.162533947 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGRR 41 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR 109.66 3.32E-06 372730000 58165 102800 143550 75766 154250 134940 83798 107710 119480 181570 TRUE FALSE 60461.39911 120455.1003 147291.0309 90752.28866 128030.6401 103602.23 77229.69379 106266.3236 115179.9381 217145.1651 0.278437694 0.55472154 0.678306749 0.417933729 0.589608523 0.477110462 0.355659283 0.489379184 0.530428288 1 17.72830031 0.669854136 3.009285146 0.999986221 0.485244147 0.671995569 0.108246707 2.158529663 19.00598009 0.101840735 0.026618191 4.675780723 -0.669854136 -0.514742074 ESPSTRPST(ph)PSLEGSQSSAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESPSTRPSTPSLEGSQSSAEGR 22 1 Q3KR16-2;Q3KR16;Q3KR16-3 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 ESPST(0.001)RPS(0.053)T(0.698)PS(0.247)LEGSQSSAEGR;ESPS(0.001)T(0.006)RPS(0.147)T(0.842)PS(0.004)LEGSQSSAEGR 129.37 2.46E-05 551050000 163505 167778 185708 173232 212271 237857 242889 206129 189355 168044 TRUE FALSE 169960.3037 196592.5664 190547.703 207496.7726 176189.2512 182618.3165 223850.7255 203366.1779 182540.1505 200969.0044 0.845704063 0.978223318 0.948144733 1.032481467 0.876698632 0.908688964 1.113856966 1.011928076 0.908300019 1 17.61661349 2.299260716 24.99997316 1.013504959 0.936607738 0.236370743 0.067091279 104.2111842 42919.676 0.023365282 0.019548789 199.1868739 -2.299260716 -0.076897221 ESQAKDVIEEYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESQAKDVIEEYFK 13 1 P25398 P25398 RPS12 40S ribosomal protein S12 0 92.063 0.0056955 211840000 190990 119050 182960 91372 313900 212390 114860 177180 225570 178840 FALSE TRUE 198530.4327 139495.9114 187728.0879 109445.1089 260543.3901 163065.6413 105856.9731 174805.1919 217451.7798 213880.2739 0.928231618 0.652214947 0.877725115 0.511712029 1.218174006 0.762415525 0.494935653 0.817303946 1.016698622 1 17.7064439 1.279681718 5.672215118 1.009992263 0.772874841 0.171444374 0.198641543 0.282994213 21.39999924 0.141618698 0.047858524 19.04064771 -1.279681718 -0.237117422 ESQFLKEELVAAVEDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESQFLKEELVAAVEDVR 17 1 P35221-2;P35221;G3XAM7;E5RIB1;E5RJL0;E5RHV7;E5RG03;E5RIE0;E5RGY6 P35221-2 CTNNA1 Catenin alpha-1 0 ;;; 217.36 4.56E-15 167055000 469047 415031 458757 404089 518385 574353 529634 465654 468501 395182 FALSE TRUE 487565.3377 486309.3458 470712.5843 484016.5981 430270.1029 440968.2202 488119.9031 459412.6698 451639.7405 472610.3467 1.031643385 1.028985821 0.995984509 1.024134578 0.910411941 0.933048172 1.032816794 0.97207493 0.955628127 1 18.85029169 ESQLAHIKDEPPPLS(ph)PAPLT(ph)PATPSSLDPFFSR ddPTM_MDA-MB-175_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(0.015)QLAHIKDEPPPLS(0.985)PAPLT(0.999)PAT(0.001)PSSLDPFFSR 154.04 1.68E-09 164385000 112489 106101 132984 94869 178378 181502 129319 137117 155977 134256 TRUE FALSE 116930.1526 124323.0214 136449.6723 113633.805 148057.3713 139350.9112 119182.6389 135279.1709 150363.4182 160560.8927 0.728260479 0.774304498 0.849831301 0.707730277 0.922125985 0.8679007 0.742289339 0.842541223 0.936488429 1 17.29276102 -4.999999987 0.087057295 1.634112319 0.648044215 0.520894667 0.064301151 188.1217587 1.145220211 22.06616465 1.687387407 1.00E-05 4.999999987 -0.986068104 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 ES(0.07)QLAHIKDEPPPLS(0.93)PAPLTPATPSSLDPFFSR;ES(0.018)QLAHIKDEPPPLS(0.982)PAPLTPATPSSLDPFFSR;ES(0.068)QLAHIKDEPPPLS(0.932)PAPLTPATPSSLDPFFSR;ES(0.001)QLAHIKDEPPPLS(0.999)PAPLTPATPSSLDPFFSR;ES(0.004)QLAHIKDEPPPLS(0.996)PAPLTPATPSSLDPFFSR 217.35 3.62E-36 7794460000 1144091 1023744 1323697 1006033 1596988 1643303 1170801 1301747 1485207 1156106 TRUE FALSE 1189260.596 1199564.068 1358193.631 1205023.325 1325532.55 1261670.783 1079030.558 1284299.211 1431754.69 1382622.836 0.860148238 0.867600359 0.982331259 0.871548837 0.958708706 0.91251985 0.780422925 0.928886156 1.035535255 1 20.39897623 1.355252879 5.115050998 1.015787714 0.892977213 0.468089053 0.053307202 0.180019266 6.649276892 0.038157998 0.013394133 22.65963337 -1.355252879 -0.122810501 ESQSHPGDFVLSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESQSHPGDFVLSVR 14 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 164.7 4.08E-06 1210090000 450730 821540 797560 804830 826940 999110 755720 801380 722630 811100 FALSE TRUE 468525.1684 962633.1043 818345.0688 964022.9718 686377.0342 767081.8442 696484.6917 790638.8119 696622.6875 970019.5156 0.48300592 0.992385296 0.843637737 0.993818121 0.707590954 0.790790115 0.71801101 0.81507516 0.71815327 1 19.88765425 ESRPSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESRPSEER 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 150.27 0.00044863 651100000 448198 536045 529819 521050 523482 656160 574310 511641 497861 468063 FALSE TRUE 465893.2031 628106.5589 543626.5184 624112.1348 434500.7166 503776.7842 529294.0815 504783.2893 479943.0799 559770.9832 0.832292522 1.122077738 0.971158804 1.11494192 0.776211575 0.899969451 0.945554695 0.901767516 0.857391852 1 19.09447718 3.244546785 24.99995556 0.896154799 1.015332082 0.263212093 0.092698838 181.6870416 758772.0621 0.024187088 0.031910885 1756.090062 -3.244546785 0.119177284 ESRPSEEREWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESRPSEEREWDR 12 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 73.927 0.021306 82375000 15738 18345 21304 21899 17597 29462 21524 15671 19602 20227 FALSE TRUE 16359.34839 21495.61105 21859.19974 26230.55684 14605.86823 22619.897 19836.89264 15460.95588 18896.52785 24190.09338 0.676282978 0.888612157 0.903642636 1.084351202 0.603795446 0.93508928 0.820042003 0.639144117 0.781168041 1 14.56212872 3.231813963 24.99992252 0.777305917 0.88935155 0.079034285 0.144620903 342.8937925 1270601.756 0.041089918 0.050160199 1705.351719 -3.231813963 0.112045632 ESRPSEEREWDREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESRPSEEREWDREK 14 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 90.707 0.0024731 106020000 49932 93626 113970 83293 145730 149030 85109 113350 114400 146780 FALSE TRUE 51903.35392 109705.5372 116940.1518 99768.1068 120958.8667 114420.0411 78437.93419 111830.7287 110282.7663 175538.7307 0.295680353 0.624964854 0.666178634 0.568353812 0.689072242 0.651822197 0.446841184 0.637071535 0.628253183 1 17.42142986 -5 0.266131032 3.781357178 0.553553531 0.573478166 0.111317813 149.788938 1.461794244 228.4712088 0.137842846 1.00E-05 5 -3.227803647 ESRS(ph)PQQSAALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESRSPQQSAALPR 13 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 ES(0.061)RS(0.939)PQQSAALPR 162.77 2.42E-05 558710000 72079 261850 221230 251520 157930 262570 159980 164120 222340 607880 TRUE FALSE 74924.73458 306820.7006 226995.4355 301269.9053 131085.115 201592.0968 147440.3496 161920.2398 214338.0268 726982.4474 0.103062646 0.422046917 0.312243351 0.414411526 0.180314003 0.277299813 0.20281143 0.222729229 0.294832465 1 19.47156101 0.928770012 20.30226978 1 0.269616021 0.844473652 0.094049534 1544.615643 440254.2654 0.087994242 0.02199856 8.487308959 -0.928770012 -0.730383979 ESS(ph)KVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESSKVPR 7 1 E5RJ29;Q9NYI0-2;Q9NYI0 E5RJ29 PSD3 PH and SEC7 domain-containing protein 3 1 ES(0.065)S(0.935)KVPR 70.856 0.03385 107560000 556380 83422 81126 76881 166520 475870 153440 107190 121390 61836 TRUE FALSE 578346.312 97749.07957 83240.21021 92087.83233 138214.9899 365356.4044 141412.9719 105753.2934 117021.1976 73951.58028 7.820607888 1.321798388 1.125604211 1.245244956 1.868993054 4.940481366 1.912237322 1.43003426 1.582402934 1 16.17429336 4.741832303 24.99715238 1.879533902 7.820610089 0.733963261 1.082418569 169.7715861 1297071.543 0.271892066 1.961007259 55186.43032 -4.741832303 5.941076187 ESS(ph)PEKEAEEGCPEKESEEGCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESSPEKEAEEGCPEKESEEGCPK 23 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 ES(0.099)S(0.901)PEKEAEEGCPEKESEEGCPK;ES(0.027)S(0.973)PEKEAEEGCPEKESEEGCPK 243.97 1.06E-37 1409010000 4237800 733890 1312050 735680 2683200 3195010 2414400 1467910 1796620 472638 TRUE FALSE 4405111.616 859929.8986 1346243.101 881195.3082 2227110.622 2453017.348 2225153.019 1448235.067 1731959.997 565242.3669 7.793314646 1.521347211 2.381709475 1.558968966 3.940098536 4.339762007 3.936635237 2.562148827 3.064101523 1 19.10851008 4.7481568 24.60695722 2.836622922 7.793317965 0.663448665 1.084282149 668.311221 1713669.06 0.265098433 3.413770258 55995.97354 -4.7481568 4.956695043 ESS(ph)PIPS(ph)PTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESSPIPSPTSDR 12 0 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 ES(0.008)S(0.992)PIPS(0.988)PT(0.011)SDR;ESS(1)PIPS(0.982)PT(0.017)S(0.001)DR 161.21 9.65E-05 250510000 378010 408580 444900 455570 530360 589430 559940 474050 463350 408080 TRUE FALSE 392934.1267 478750.4367 456494.4595 545680.3863 440209.5966 452543.8154 516050.4397 467696.1351 446674.124 488035.4628 0.805134374 0.98097469 0.935371493 1.11811626 0.902003297 0.927276499 1.057403568 0.958324078 0.915249317 1 18.89662646 4.739194334 24.31702475 0.977907083 0.805134304 0.394306342 0.063968288 35.79234426 1372968.904 0.01465633 0.087488405 54852.23573 -4.739194334 -0.172772779 ESS(ph)PIPS(ph)PTSDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESSPIPSPTSDRK 13 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 ES(0.406)S(0.594)PIPS(0.93)PT(0.039)S(0.031)DRK 127.79 2.49E-05 0 296710 182210 220820 182970 317680 353150 313570 248390 268740 155850 TRUE FALSE 308424.3399 213503.1501 226574.7506 219160.9199 263680.8671 271136.2645 288991.564 245060.7383 259068.0999 186385.8236 1.654762868 1.145490285 1.215622231 1.175845436 1.41470452 1.45470433 1.550501849 1.314803528 1.389956033 1 17.50793261 -1.45334128 5.999927193 0.99981091 1.360230601 0.337372763 0.154536465 0.000390758 3.56E-05 0.14958179 0.035238511 0.035209408 1.45334128 0.36041969 ESS(ph)PLS(ph)SRK ddPTM_MDA-MB-175_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(0.999)PLS(0.615)S(0.386)RK;ES(0.003)S(0.78)PLS(0.677)S(0.54)RK 79.16 0.018532 5936280000 340545 2770300 2288852 2508940 2255042 2769940 2294946 2569090 2467877 2493490 TRUE FALSE 353989.9796 3246077.475 2348501.363 3005200.844 1871730.766 2126663.414 2115062.136 2534655.551 2379058.589 2982041.625 0.118707256 1.088541973 0.78754815 1.007766229 0.627667552 0.713156851 0.70926647 0.84997323 0.797795232 1 21.50786896 4.752135827 25 0.825591721 0.118706789 0.700016863 0.14174281 1289.310733 2374343.406 0.032800393 0.65569821 56511.36884 -4.752135827 -0.706884932 ESSANNSVS(ph)PSESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ESSANNSVSPSESLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 ESSANNSVS(1)PSESLR;ESSANNSVS(1)PSESLR;ESSANNS(0.003)VS(0.988)PS(0.009)ESLR;ESSANNSVS(1)PSESLR;ESSANNS(0.009)VS(0.991)PSESLR;ESSANNS(0.005)VS(0.995)PSESLR 408.52 5.29E-133 3647860000 1910050 2137740 2038200 2056460 2303110 2675000 2162300 2219310 2108100 2060720 TRUE FALSE 1985460.249 2504880.216 2091317.166 2463221.65 1911628.185 2053771.79 1992813.276 2189563.78 2032229.893 2464478.629 0.805630946 1.016393563 0.848584014 0.999489961 0.775672453 0.833349401 0.808614549 0.888449084 0.824608446 1 21.23285104 ESSIIAPAPAEDVDT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESSIIAPAPAEDVDTPPR 18 0 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 ESSIIAPAPAEDVDT(1)PPR;ESSIIAPAPAEDVDT(1)PPR 250.86 4.41E-24 409140000 325380 339180 335190 336220 379980 455870 429270 384920 338940 361870 TRUE FALSE 338226.2536 397431.5265 343925.3268 402723.3125 315391.1353 350001.1013 395622.6957 379760.777 326741.6156 432771.4981 0.781535418 0.918340344 0.794704199 0.930568012 0.728770579 0.80874342 0.9141607 0.877508752 0.754998 1 18.72324596 -1.182628471 4.46165269 1.000035868 0.840947993 0.338941945 0.068843855 0.96666599 38861185.45 2623.317498 0.015295863 0.065670682 1.182628471 -0.159087875 ESSRDT(ph)SPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESSRDTSPVR 10 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 ESSRDT(0.642)S(0.358)PVR 92.039 0.015746 63140000 26046 40482 42369 35913 52223 48486 30038 36568 35988 45783 TRUE FALSE 27074.31619 47434.46859 43473.17095 43016.48421 43346.15311 37225.86131 27683.54307 36077.86577 34692.79891 54753.30228 0.494478234 0.866330735 0.79398263 0.785641823 0.791662809 0.6798834 0.505604994 0.658916709 0.63362021 1 15.74065836 -1.096586916 4.841945139 1.000012961 0.693154592 0.38508854 0.117453767 16923497.91 3832775.47 2342.24948 0.028492079 0.080059539 1.096586916 -0.30685837 ESSSCGKDT(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESSSCGKDTPSK 12 1 O43148;O43148-2;K7EPP5 O43148 RNMT mRNA cap guanine-N7 methyltransferase 1 ESSS(0.001)CGKDT(0.999)PSK 88.311 0.016259 168830000 499020 170510 254850 157440 353880 386190 370160 293170 300670 134530 TRUE FALSE 518721.6949 199793.7661 261491.6004 188581.1621 293727.604 296503.2253 341145.892 289240.5357 289848.9454 160888.5778 3.224105167 1.241814484 1.625296239 1.172122749 1.825658528 1.842910351 2.120386026 1.797769237 1.801550797 1 17.29570238 ESSTSEGADQKMS(ph)S(ph)PEDDSDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 2 ESSTS(0.002)EGADQKMS(0.953)S(0.92)PEDDS(0.122)DT(0.003)KR;ES(0.023)S(0.023)T(0.023)S(0.023)EGADQKMS(0.954)S(0.953)PEDDS(0.003)DTKR;ESSTSEGADQKMS(1)S(1)PEDDSDTKR 106.81 0.00075501 1477390000 1788710 506338 793990 480632 1246150 1441840 1187030 819552 949680 406577 TRUE FALSE 1859329.652 593297.6127 814682.0317 575699.5751 1034329.868 1106994.511 1093987.487 808567.246 915501.2023 486237.9788 3.82390873 1.220179498 1.675480047 1.183987266 2.127209131 2.27665168 2.249901354 1.662904342 1.88282537 1 18.89130306 0.484507493 1.047664036 1.000075106 1.986920701 0.159348981 0.704740661 3.609230823 5.418022236 0.651021234 0.202993855 3.051458677 -0.484507493 0.986845595 ESSTVFELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 176.95 3.82E-06 980510000 1254550 1024640 1196520 919490 1702460 1502180 1253700 1272160 1344720 1247470 FALSE TRUE 1304080.603 1200613.949 1227702.294 1101362.378 1413076.457 1153321.461 1155431.718 1255108.776 1296323.79 1491887.862 0.874114359 0.804761524 0.822918616 0.738234022 0.947173372 0.773061763 0.774476251 0.841288952 0.868915032 1 20.50870767 0.812751817 1.85754537 0.999665731 0.818956591 0.486138642 0.055317479 0.536117373 3.318139971 0.049785803 0.013967613 6.497582724 -0.812751817 -0.18070914 ESSYACYYDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESSYACYYDEKR 12 1 Q99538-3;Q99538-2;Q99538 Q99538-3 LGMN Legumain 0 ; 113.69 0.0018248 921030000 459060 417880 470980 341910 626680 541640 464780 458310 497320 349100 FALSE TRUE 477184.0433 489647.6393 483254.1257 409538.7775 520157.1574 415852.3186 428349.3291 452167.1041 479421.5503 417499.4611 1.142957268 1.172810231 1.157496406 0.98093247 1.245887015 0.996054744 1.025987741 1.083036378 1.148316573 1 18.67141481 3.936852369 24.99880457 1.073842367 1.159701632 0.221075543 0.076228886 309.4416065 122501.1749 0.018680233 0.033676322 8646.739368 -3.936852369 0.085859265 ESSYDIYRVPS(ph)SQS(ph)MEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ESSYDIYRVPSSQSMEDR 18 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 ESSYDIYRVPS(0.607)S(0.548)QS(0.845)MEDR;ESSYDIYRVPS(0.606)S(0.441)QS(0.953)MEDR;ESSYDIY(0.012)RVPS(0.944)S(0.185)QS(0.858)MEDR;ES(0.014)S(0.017)Y(0.002)DIY(0.006)RVPS(0.85)S(0.133)QS(0.978)MEDR;ESSYDIYRVPS(0.98)S(0.037)QS(0.984)MEDR 124.31 1.83E-05 1145610000 1456930 1780110 1715950 1564100 1970790 2109720 1512640 1706940 1695480 1944710 TRUE FALSE 1514450.721 2085830.045 1760669.067 1873474.312 1635795.82 1619769.503 1394075.324 1684061.261 1634460.006 2325738.691 0.651169767 0.896846259 0.757036495 0.80553947 0.70334463 0.69645378 0.599411847 0.724097367 0.702770269 1 21.14925758 -1.273091332 3.551321871 1.000712131 0.727183096 0.52893992 0.077484273 40548215.2 76144743.22 328033.2267 0.01920517 0.053322275 1.273091332 -0.273529035 ESSYDIYRVPS(ph)SQSMEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESSYDIYRVPSSQSMEDR 18 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 ESSYDIYRVPS(0.792)S(0.199)QS(0.009)MEDR;ESSYDIYRVPS(0.814)S(0.184)QS(0.002)MEDR;ESSYDIYRVPS(0.95)S(0.05)QS(0.001)MEDR 195.97 1.21E-15 478990000 310600 384782 372798 333675 393597 433023 320422 368694 372046 400487 TRUE FALSE 322862.7278 450865.3153 382513.4221 399674.9191 326693.5225 332459.9708 295306.4864 363752.26 358656.1371 478954.7599 0.674098589 0.941352614 0.798642073 0.834473217 0.682096828 0.694136479 0.616564467 0.75947102 0.748830928 1 18.86952987 5.048103457 15.91387177 0.768750976 0.122560861 0.064084176 0.111892918 7197970.973 62342174.55 0.026416838 141665828.9 111712.9336 -5.048103457 -0.646190114 ESSYDIYRVPSS(ph)QS(ph)MEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESSYDIYRVPSSQSMEDR 18 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 ESSYDIYRVPS(0.266)S(0.736)QS(0.998)MEDR 102.66 0.00036611 394490000 232700 253390 251790 235670 273120 302230 228060 242560 244720 269840 TRUE FALSE 241887.1757 296907.7614 258351.8542 282284.8226 226695.16 232041.6628 210184.0613 239308.8799 235912.575 322709.9816 0.749549718 0.920045175 0.800569765 0.874732232 0.702473344 0.71904086 0.651309452 0.741560204 0.731035879 1 18.29987868 3.237956784 24.99999331 0.735734758 0.839664692 0.110875718 0.097849203 24.03797168 995247.423 0.025438852 0.032187185 1729.644236 -3.237956784 0.103929933 ESSYGPEIDSHDFVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ESSYGPEIDSHDFVLR 16 0 E5RGL4;E5RHV6;Q11201 E5RGL4 ST3GAL1 "CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1" 0 ;; 220.14 1.18E-14 320638000 200138 219837 228326 282739 371553 379256 300148 240296 227955 380249 FALSE TRUE 208039.6028 257592.2947 234276.3631 338663.9303 308396.5538 291179.5417 276621.6155 237075.2252 219750.9441 454751.5112 0.457479739 0.566446264 0.515174458 0.744723045 0.678164989 0.640304726 0.6082918 0.521329164 0.483233015 1 18.79471891 -2.316310636 2.402694417 3.396915257 0.583500436 0.683738474 0.085764081 3705285.718 585318.75 48416846.16 0.021859946 0.004827134 2.316310636 -2.813414821 ESTAEKDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESTAEKDEL 9 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 95.502 0.065259 312310000 469880 341570 350830 367540 527940 496020 502890 363600 366890 209500 FALSE TRUE 488431.2252 400231.9905 359972.918 440238.315 438200.9474 380826.8723 463472.1677 358726.5367 353685.7006 250547.5139 1.949455485 1.597429503 1.43674512 1.757105102 1.748973441 1.519978651 1.849837424 1.43177049 1.411651208 1 17.9347247 0.976691916 1.151047989 1.005699583 1.679054398 0.659332269 0.152137775 0.312294199 0.85482574 0.138130479 0.043645708 9.477459044 -0.976691916 0.673354816 ESTESSNT(ph)TIEDEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESTESSNTTIEDEDVK 16 0 E9PF82;E9PBG7;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 ESTESSNT(0.676)T(0.324)IEDEDVK 212.9 3.48E-12 0 151340 72305 96516 88329 134710 147450 150170 105550 124690 55395 TRUE FALSE 157315.0201 84722.8213 99031.28625 105800.2126 111812.0423 113206.9721 138399.283 104135.2749 120202.4313 66248.58965 2.374616892 1.278862263 1.494843691 1.597018338 1.68776487 1.708820863 2.089090254 1.571886669 1.814414947 1 16.01560212 3.029239134 18.31332764 1.700628921 1.64340636 0 0.369209424 118.0856547 73946.32708 0.100948154 0.120640416 1069.643691 -3.029239134 -0.057222561 ESTLHLVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 138.98 0.00012151 1064750000 763840 1268030 1132440 1237160 1199280 1463840 1112920 1184890 1053060 1292510 FALSE TRUE 793996.993 1485804.289 1161952.317 1481866.555 995426.814 1123885.345 1025686.422 1169008.488 1015160.576 1545752.588 0.5136637 0.961217403 0.751706532 0.95866995 0.643975512 0.727079711 0.663551483 0.756271409 0.656741955 1 20.55987799 -1.154599709 4.868754525 1.000019505 0.745202439 0.264910027 0.130794998 2.57E-05 4.47E-06 0.117680263 0.027735382 0.070048734 1.154599709 -0.254817066 ESTQLSPADLTEGKPTDPSKLES(ph)PSFTGTGDTEIAHATEDLENNGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESTQLSPADLTEGKPTDPSKLESPSFTGTGDTEIAHATEDLENNGSK 47 2 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 EST(0.002)QLS(0.057)PADLT(0.072)EGKPT(0.028)DPS(0.091)KLES(0.185)PS(0.185)FT(0.185)GT(0.185)GDT(0.013)EIAHATEDLENNGSK 98.041 3.54E-06 302550000 70839 30824 45572 28372 74300 60990 71777 48233 57275 20173 TRUE FALSE 73635.77842 36117.78222 46759.64376 33983.89692 61670.51254 46825.99681 66150.93119 47586.51553 55213.68394 24125.51311 3.052195328 1.497078303 1.938182352 1.408628979 2.556236307 1.940932679 2.741949192 1.972456101 2.288601435 1 14.55827201 3.214879785 24.99031762 2.158432628 1.937393099 0 0.60463187 985.513254 1040006.716 0.162644509 0.194500026 1640.135712 -3.214879785 -0.221039529 ESTSSKS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ESTSSKSPPR 10 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 ES(0.001)T(0.006)S(0.018)S(0.079)KS(0.897)PPR;ESTS(0.004)S(0.046)KS(0.95)PPR;ESTSS(0.027)KS(0.973)PPR;ESTS(0.002)S(0.084)KS(0.914)PPR;ESTS(0.001)S(0.01)KS(0.989)PPR;ES(0.001)T(0.01)S(0.009)S(0.49)KS(0.49)PPR;ESTSS(0.002)KS(0.998)PPR;ES(0.003)T(0.003)S(0.003)S(0.014)KS(0.977)PPR 95.183 0.0046 19835831000 4674370 3112380 3961054 2869365 4999800 5546980 4430840 3914610 4284700 2830943 TRUE FALSE 4858917.737 3646907.054 4064282.321 3436916.833 4149935.782 4258777.96 4083539.183 3862141.056 4130494.484 3385612.079 1.435166706 1.077178061 1.200457178 1.01515376 1.225756432 1.257904881 1.20614503 1.140751204 1.220014103 1 21.69098525 -1.911960778 2.583274006 0.888557852 1.188142443 0.232620807 0.106432257 14929556.62 8803496.105 10092076.73 0.023780982 0.012247268 1.911960778 0.299584591 ESTSSKS(ph)PPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ESTSSKSPPRK 11 2 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 EST(0.001)S(0.056)S(0.056)KS(0.886)PPRK;ES(0.001)T(0.001)S(0.002)S(0.035)KS(0.962)PPRK;ESTSS(0.002)KS(0.998)PPRK;ES(0.002)T(0.002)S(0.009)S(0.077)KS(0.91)PPRK;ESTSS(0.002)KS(0.997)PPRK 97.273 0.003334 4333810000 4926980 2624690 3587880 2509860 5064550 4634360 4679970 3752150 4394990 1997930 TRUE FALSE 5121500.975 3075460.09 3681383.1 3006302.817 4203679.6 3558100.124 4313141.723 3701858.567 4236815.168 2389386.131 2.143437977 1.287133984 1.54072339 1.258190452 1.759313635 1.489127303 1.805125453 1.549292732 1.773181452 1 21.18820859 -0.55501902 8.257016306 1.00000113 1.603666331 0.356407 0.249896872 0 0 0.22132631 0.052167112 0.278599915 0.55501902 0.6036652 ESVDHLTIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESVDHLTIPSR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 121.36 0.00041322 1014760000 522220 717990 665890 717690 845340 872880 733740 747080 721920 805790 FALSE TRUE 542837.6488 841299.1973 683243.6404 859646.9399 701649.4087 670166.8486 676227.5415 737066.6146 695938.2402 963669.1227 0.563302939 0.873016658 0.709002317 0.892056121 0.728101993 0.695432522 0.701721707 0.764854448 0.72217551 1 19.87817835 -1.342843719 3.152481238 1.002162048 0.744758914 0.439653569 0.088220128 24623077.12 33493914.65 496402.7927 0.019632337 0.0454105 1.342843719 -0.257403134 ESVFTVEGGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESVFTVEGGHR 11 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H0C5;F5H3X6;F5H2D2;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ;;; 172.8 1.29E-05 515315000 309811 443117 351224 500796 335336 552028 358445 319685 317976 401860 FALSE TRUE 322042.5775 519218.8978 360377.186 599851.9541 278335.7065 423827.8631 330349.1443 315400.1455 306532.1059 480596.7729 0.67008893 1.080362847 0.749853529 1.248139788 0.579146016 0.881878296 0.687372789 0.656267714 0.637815573 1 18.87446744 3.199587217 24.999989 0.721865897 0.93396989 0.201533502 0.189619387 218.9449437 140444.4118 0.050533572 0.060400103 1583.387516 -3.199587217 0.212103993 ESVGNSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESVGNSTR 8 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;Q5T948;Q5T949;A6PVN6;A6PVN8;C9IZ76 Q15257 PPP2R4 Serine/threonine-protein phosphatase 2A activator 0 98.033 0.018168 132720000 63564 93247 92631 77537 104410 110690 88518 104230 77690 114490 FALSE TRUE 66073.5558 109261.4469 95045.03996 92873.58718 86662.42549 84983.92502 81579.72786 102832.9673 74893.95208 136922.1235 0.482563038 0.797982416 0.694154002 0.678294967 0.632932234 0.620673437 0.59581115 0.751032519 0.546982111 1 17.06299605 -1.911229484 2.781748859 1.19511528 0.655461464 0.589660853 0.08854496 25790847.88 17596830.68 32926351.48 0.020452726 0.012267908 1.911229484 -0.539653817 ESVPEFPLS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 205.96 1.00E-07 984724000 1311633 581260 756527 686396 974418 1352520 1312440 954538 948612 491842 TRUE FALSE 1363417.284 681086.8834 776242.7151 822163.0801 808786.7764 1038417.728 1209567.523 941743.9794 914471.6394 588209.023 2.317912902 1.157899415 1.319671553 1.39773966 1.374998929 1.765388981 2.056356628 1.601036269 1.55467122 1 19.16596939 2.737822155 24.76269976 1.667749155 1.476665451 0 0.383952731 194.7397921 6530072.78 0.116510747 0.115943346 546.7920033 -2.737822155 -0.191083704 ESVPS(ph)ASPTGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESVPSASPTGIPK 13 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 ES(0.001)VPS(0.564)AS(0.419)PT(0.017)GIPK 82.85 0.011777 148890000 201450 133590 159490 154410 225310 224530 234680 183320 178020 100480 TRUE FALSE 209403.4016 156533.0433 163646.4404 184951.8371 187011.8867 172386.3103 216285.1684 180862.8953 171613.095 120167.1322 1.742601306 1.302627769 1.361823632 1.53912167 1.556264873 1.434554584 1.799869602 1.505094546 1.428120084 1 16.87468282 0.786936214 2.823462957 1.000198752 1.526385487 0.546690298 0.144420781 0.819758419 9.64149141 0.137116665 0.036134641 6.122604615 -0.786936214 0.526186734 ESVPSAS(ph)PTGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESVPSASPTGIPK 13 0 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 ESVPS(0.002)AS(0.563)PT(0.435)GIPK;ESVPS(0.182)AS(0.806)PT(0.012)GIPK 109.6 0.0011797 261770000 437140 379800 410700 482050 517320 623800 577900 437370 420210 415480 TRUE FALSE 454398.6247 445027.6956 421403.1794 577398.0512 429386.1312 478931.9038 532602.6879 431507.7705 405086.7242 496885.3512 0.914493904 0.895634565 0.84808936 1.162034763 0.864155343 0.963868028 1.071882451 0.86842522 0.815251895 1 18.92255348 ESVQVPDDQDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESVQVPDDQDFR 12 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5H1Z6;F5GWK5;F5H3G8;F5H5A8 Q9Y365 STARD10 PCTP-like protein 0 ;;; 280.38 1.17E-27 3088540000 2042200 2342570 2275660 2248680 2563250 2852020 2400320 2377510 2352810 2391190 FALSE TRUE 2122827.633 2744888.175 2334965.569 2693462.192 2127549.681 2189681.578 2212176.646 2345643.367 2268132.828 2859697.898 0.742325836 0.959852499 0.816507775 0.941869487 0.743977076 0.765703811 0.77357005 0.820241666 0.793137215 1 21.44743132 5.044918291 14.86926065 0.834049917 0.315386328 0.102273463 0.085793441 1153268.533 11252526.91 0.019594088 16361064.12 110896.6152 -5.044918291 -0.518663589 ESVS(ph)PEDSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESVSPEDSEK 10 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 ESVS(0.998)PEDS(0.002)EK 122.18 0.00051968 298420000 501200 268040 450670 256480 509160 551770 545800 422740 431880 270900 TRUE FALSE 520987.763 314073.7849 462414.8304 307210.9785 422613.1651 423629.7797 503018.7698 417073.8618 416336.7232 323977.6683 1.608097761 0.969430352 1.427304644 0.94824739 1.30445153 1.307589446 1.552634083 1.287353736 1.28507846 1 18.30553485 3.026598959 24.99895108 1.322867401 1.219292213 0 0.221425811 747.0919987 702147.2929 0.059369749 0.070958407 1063.160809 -3.026598959 -0.103575188 ESVSTEDLSPPS(ph)PPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 ESVSTEDLSPPS(1)PPLPK;ESVSTEDLSPPS(1)PPLPK 309.33 4.73E-58 231630000 412550 323080 406810 293620 472720 428060 412510 374890 382360 262720 TRUE FALSE 428837.7926 378566.4768 417411.8028 351697.1596 392367.2233 328649.5523 380176.3883 369865.2127 368598.9383 314194.9539 1.364878039 1.204877647 1.328512115 1.119359669 1.248801798 1.046005189 1.210001572 1.177183809 1.17315359 1 18.26130049 8 0.07115179 0.837754706 2.03253222 0.53358909 0.073569613 195.9778055 1.027374987 2.958456821 23.38771394 100000000 -8 1.194777513 GGQS(ph)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGQSDDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 37 0 A0A669KBG8;A0A669KB10;Q92538 A0A669KBG8 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR;GGQS(1)DDDEDEGVPASYHTVSLQVSQDLLDLMHTLHTR 170.49 2.46E-18 1439640000 33733 58533 86580 74432 80817 94640 93946 73330 84978 62519 TRUE FALSE 35064.80489 68585.58743 88836.34593 89154.42744 67079.75521 72661.29428 86582.26704 72347.13129 81919.65838 74768.40105 0.468978932 0.917307131 1.188153614 1.192407838 0.897167176 0.971818218 1.158006134 0.967616403 1.09564545 1 16.19014106 4.693098948 3.235095654 1.054432038 0.41410028 0.769925834 0.096617183 0.133025495 2.275031325 0.023948436 0.19996073 49328.61797 -4.693098948 -0.640331758 down ESYELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESYELR 6 0 P35268;K7ERI7;K7EMH1 P35268 RPL22 60S ribosomal protein L22 0 ; 122.98 0.044171 5102700000 5442400 6754700 6611000 6381600 6991800 8178400 6646400 6636700 6449300 7048900 FALSE TRUE 5657270.154 7914767.181 6783288.091 7643861.433 5803336.333 6279090.545 6125437.801 6547745.892 6217190.953 8429996.996 0.671088039 0.938881376 0.804660796 0.906745452 0.688414994 0.744850864 0.72662396 0.776719837 0.737508086 1 23.00710069 5.020859693 15.22921558 0.798878615 0.405524965 0.144933232 0.098142025 803127.9681 14808811.55 0.022437593 7290185.125 104920.3409 -5.020859693 -0.39335365 ESYPHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESYPHIK 7 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 96.964 0.012345 264990000 506380 439590 564000 528270 632520 609390 606830 594180 515230 455620 FALSE TRUE 526372.2734 515086.163 578698.3033 632760.2293 525004.4763 467868.4079 559265.0789 586215.989 496686.9729 544890.0156 0.966015633 0.945302994 1.062046077 1.161262294 0.963505407 0.858647423 1.026381587 1.07584278 0.911536198 1 19.05560553 ESYPVFYLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ESYPVFYLFR 10 0 P30040;F8VY02 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 105.57 0.0083393 0 211900 393270 341900 351880 411710 569910 261130 344600 281390 549610 FALSE TRUE 220265.9756 460811.0633 350810.1949 421480.8137 341727.6813 437557.0396 240661.9483 339981.2007 271262.8289 657295.5566 0.335109485 0.70107132 0.533717582 0.641234844 0.519899576 0.665692983 0.366139624 0.517242506 0.412695364 1 19.32618271 -1.08672855 4.389399425 1.000038682 0.527287274 0.597639946 0.117715794 2.954350702 64755060 6309.104023 0.025907323 0.081897652 1.08672855 -0.472751408 ESYSIYVYK ddPTM_MDA-MB-175_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 ; 175.44 0.00012542 2037040000 1155890 1057610 1159730 1038430 1398790 1449450 1359990 1199630 1219780 1054550 FALSE TRUE 1201525.43 1239246.29 1189953.517 1243828.355 1161024.175 1112837.204 1253390.43 1183550.922 1175880.356 1261168.882 0.952707799 0.982617244 0.943532253 0.986250432 0.920593738 0.882385555 0.993832347 0.938455538 0.93237343 1 20.26633005 -1.698630851 2.355358497 1.010019243 0.948625321 0.191986768 0.031934944 6943899.327 4892062.69 411377.6098 0.008336828 0.020015625 1.698630851 -0.061393922 ESYSVYVYK ddPTM_MDA-MB-175_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 ;;;;;;; 188.76 9.07E-05 10801590000 6139040 5487910 6399340 5152910 7515880 7450280 6889570 6144480 6085090 5395830 FALSE TRUE 6381414.04 6430415.852 6566112.058 6172140.218 6238333.402 5720065.38 6349547.501 6062123.296 5866088.8 6453039.579 0.988900496 0.996494098 1.017522359 0.956470225 0.9667279 0.886414117 0.983962274 0.939421372 0.909042743 1 22.62154744 3.558463258 3.138956687 0.944435023 1.000389845 0.351653745 0.032148237 0.261170934 4.965789801 0.008545054 0.013680049 3617.955808 -3.558463258 0.055954822 ESYTEEIVS(ph)EAESHVSGISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR 294.08 9.65E-55 289433000 152358 339616 350030 424943 320264 441762 399791 439538 383443 336939 TRUE FALSE 158373.2115 397942.4062 359152.0694 508995.4571 265825.6397 339169.4705 368454.3368 433646.712 369642.9613 402955.746 0.393028796 0.987558585 0.891294076 1.263154731 0.659689413 0.841704018 0.914379161 1.076164607 0.917328925 1 18.62026188 4.740801532 24.60767574 0.952107156 0.393028554 0.55969958 0.148229394 119.9702226 1317294.267 0.034911794 0.232314125 55055.60412 -4.740801532 -0.559078603 ET(ph)ERASPIKMDLAPSK ddPTM_MDA-MB-175_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(0.657)ERAS(0.343)PIKMDLAPSK 107.45 0.0015124 563740000 152380 74655 108840 65891 167360 140890 138850 110740 135610 77648 TRUE FALSE 158396.0801 87476.41551 111676.4598 78924.04313 138912.207 108170.4327 127966.5742 109255.7114 130729.4226 92861.63894 1.705721349 0.942008094 1.202611338 0.849910082 1.495905183 1.164855951 1.378034845 1.176543002 1.407787156 1 16.50279512 3.20220099 24.99996306 1.274665357 1.160381511 0.032731613 0.248543697 585.7010703 402711.5453 0.067127057 0.080234376 1592.945765 -3.20220099 -0.114283846 ET(ph)LS(ph)LT(ph)LAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETLSLTLAEEK 11 0 H7BZ55 H7BZ55 Putative ciliary rootlet coiled-coil protein-like 3 protein 3 ET(1)LS(1)LT(1)LAEEK;ET(1)LS(1)LT(1)LAEEK 110.29 0.0019391 192260000 83966 548210 570200 695170 476540 721620 642870 611860 637160 508230 TRUE FALSE 87281.04252 642360.803 585059.8804 832672.5511 395537.901 554034.6913 592480.1696 603659.0175 614228.7361 607807.9378 0.143599708 1.056848328 0.962573609 1.369959981 0.650761328 0.911529213 0.974781889 0.993173962 1.01056386 1 19.21325599 4.741360895 24.89468877 0.989132609 0.143599385 0.704654326 0.16481426 131.0658301 1165119.818 0.0381581 0.264469558 55126.56025 -4.741360895 -0.845533225 ET(ph)RHSWDSPAFNNDVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETRHSWDSPAFNNDVVQR 18 1 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PRJ5 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 ET(0.473)RHS(0.263)WDS(0.263)PAFNNDVVQR 199.41 2.38E-15 99272000 64473 96798 95747 93289 106890 126700 85790 113350 104030 126550 TRUE FALSE 67018.44382 113422.3035 98242.24548 111741.2858 88720.87598 97275.84516 79065.55563 111830.7287 100285.9806 151345.0496 0.44281887 0.749428566 0.649127578 0.738321379 0.58621591 0.642742167 0.522419173 0.738912366 0.66263139 1 17.20748196 0.296820803 0.96087468 1.001861062 0.634112003 0.586132561 0.092371145 2.036286149 2.211589549 0.0911743 0.026770476 1.980709584 -0.296820803 -0.367749058 ET(ph)TMSPLLFQAQPLSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETTMSPLLFQAQPLSHR 17 0 Q5VVP1 Q5VVP1 SPATA31A6 Spermatogenesis-associated protein 31A6 1 ET(0.333)T(0.333)MS(0.333)PLLFQAQPLSHR;ET(0.333)T(0.333)MS(0.333)PLLFQAQPLSHR 68.944 0.066831 861550000 930410 635280 847030 678550 987070 1080580 1021340 841890 889280 481120 TRUE FALSE 967143.3052 744384.3982 869104.2976 812765.1647 819288.194 829631.6713 941284.702 830605.8416 857274.9865 575386.2524 1.680859251 1.293712519 1.510471086 1.412555759 1.423892543 1.441869123 1.635917956 1.443562195 1.489912181 1 19.13417123 -1.268907955 4.151971504 0.999561141 1.476209481 0.652228385 0.105398791 11230749.89 26784434.09 62378.29654 0.023314375 0.053838388 1.268907955 0.476648339 ETAAVIFLHGLGDTGHSWADALSTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETAAVIFLHGLGDTGHSWADALSTIR 26 0 O95372;Q5QPQ3;Q5QPQ2;Q5QPN5;Q5QPN9 O95372 LYPLA2 Acyl-protein thioesterase 2 0 ; 294.1 1.45E-70 891180000 195733 256410 253310 243280 272310 336130 252140 290000 262350 247160 FALSE TRUE 203460.69 300446.4229 259911.4667 291400.0579 226022.8435 258068.9016 232376.608 286113.0243 252908.0747 295586.2698 0.688329299 1.016442418 0.879308321 0.985837597 0.76465948 0.873074726 0.786154946 0.967950996 0.855615096 1 18.17321973 0.350100178 0.838463355 1.00055472 0.871794726 0.135267835 0.098154773 4.892426627 4.574568934 0.101043954 0.030208726 2.239237601 -0.350100178 -0.128759994 ETAEADVASLNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETAEADVASLNRR 13 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5 H7BYY1 TPM1 Tropomyosin alpha-1 chain 0 162.49 6.47E-05 162460000 189660 215970 197920 163970 246040 251750 155120 181530 209290 262210 FALSE TRUE 197147.9232 253061.1675 203077.9578 196402.7766 204218.2087 193284.8778 142961.2891 179096.8873 201757.6938 313585.0292 0.628690482 0.806993778 0.647600934 0.626314263 0.651237112 0.61637151 0.455893221 0.571127033 0.643390707 1 18.25849716 0.942074102 20.76225158 1.000000001 0.621066196 0.654213001 0.081281724 1712.091932 613663.3118 0.086648774 0.021662193 8.751330839 -0.942074102 -0.378933805 ETAIELGYLTAEQFDEWVKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 251.13 2.23E-31 615360000 489880 366670 464520 373250 605190 586810 599290 467660 526370 340710 FALSE TRUE 509220.8407 429642.7202 476625.7728 447077.736 502320.02 450532.2707 552316.0838 461391.7826 507426.0465 407465.6012 1.24972719 1.054426972 1.16973254 1.097215899 1.232791231 1.105694001 1.355491316 1.132345359 1.245322415 1 18.63631874 3.23950057 24.99997758 1.190214876 1.138390528 0.021287985 0.100480674 77.77455173 2068539.654 0.026026304 0.033295631 1735.803541 -3.23950057 -0.051824348 ETAIQTEDSAIS(ph)ESPEEPLPNLKPKPNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETAIQTEDSAISESPEEPLPNLKPKPNLR 29 2 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 ETAIQT(0.001)EDS(0.001)AIS(0.499)ES(0.499)PEEPLPNLKPKPNLR 73.696 0.0033576 178200000 18195 13832 19120 11524 29924 27727 21245 20139 27146 17984 TRUE FALSE 18913.35265 16207.5384 19618.28291 13803.4128 24837.52917 21287.82446 19579.76139 19869.06965 26169.02076 21507.62048 0.879379133 0.753571899 0.91215497 0.641791723 1.154824598 0.989780552 0.910363906 0.923815336 1.216732497 1 14.3925603 3.235785997 24.99999639 1.011427961 0.801887155 0.506569056 0.112840914 66.41496759 598415.8693 0.03188237 0.039756463 1721.020314 -3.235785997 -0.209540806 ETAIQTEDSAISES(ph)PEEPLPNLKPKPNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETAIQTEDSAISESPEEPLPNLKPKPNLR 29 2 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR;ETAIQTEDSAISES(1)PEEPLPNLKPKPNLR;ETAIQTEDSAIS(0.003)ES(0.997)PEEPLPNLKPKPNLR 260.21 2.19E-58 742430000 419736 307264 405683 281866 486348 480304 448867 396539 449587 267417 TRUE FALSE 436307.5014 360034.2018 416255.4323 337618.2535 403678.7407 368760.6751 413683.6316 391224.0433 433406.4517 319812.2411 1.364261417 1.125767421 1.301561913 1.055676457 1.262236677 1.15305366 1.293520317 1.223292898 1.355190315 1 18.28686563 4.760355741 23.46930956 1.208292369 1.364261793 0.170303107 0.108266355 4239.826308 4565337.665 0.023354949 1.02252386 57591.14867 -4.760355741 0.155969425 ETAVPGPLGIEDISPNLS(ph)PDDKSFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 ETAVPGPLGIEDISPNLS(0.999)PDDKS(0.001)FS(0.001)R 185.3 8.82E-18 308930000 138880 80153 117620 96079 151990 176870 133880 127570 135810 87960 TRUE FALSE 144363.0896 93918.65425 120685.2738 115083.1394 126154.7941 135794.623 123386.1358 125860.1328 130922.2246 105194.0779 1.37234997 0.892813133 1.147263004 1.094007778 1.199257569 1.290896082 1.172938042 1.196456448 1.244577901 1 16.68269396 3.231858826 24.27098752 1.197901036 1.111384126 0.033510127 0.129647365 258.375074 935722.3456 0.034466814 0.042132063 1705.52789 -3.231858826 -0.08651691 ETCAWFTDNYEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ETCAWFTDNYEQAR 14 0 Q13630 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;;; 355.39 9.91E-82 2732970000 1122593 1100456 1128786 1149530 1177454 1395270 1102447 1113412 1106178 1132470 FALSE TRUE 1166913.838 1289450.758 1158203.09 1376903.603 977310.7897 1071239.688 1016034.323 1098488.533 1066366.87 1354355.814 0.861600642 0.952076806 0.855168988 1.01664835 0.721605637 0.790958828 0.750197483 0.811078242 0.787360942 1 20.36917538 3.232024425 24.99984896 0.79670701 0.918837869 0.29732675 0.082133979 161.133032 616306.7493 0.021541266 0.026319438 1706.178341 -3.232024425 0.122130859 ETCSTLAES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETCSTLAESPR 11 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR;ETCSTLAES(1)PR 255.58 1.90E-20 2950930000 1593050 1562330 1620780 1604480 1643430 1867380 1603150 1601280 1493680 1542770 TRUE FALSE 1655944.844 1830648.024 1663018.858 1921841.355 1364080.356 1433709.295 1477490.914 1579817.461 1439922.749 1845046.243 0.897508586 0.992196283 0.901342643 1.041622324 0.739320416 0.777058733 0.800788012 0.856248165 0.780426373 1 20.81522555 3.236784268 24.99969929 0.817290287 0.956539171 0.413122835 0.076988048 41.65862273 586291.4929 0.020414523 0.025623672 1724.980809 -3.236784268 0.139248883 ETDGDHLSS(ph)LLNKT(ph)T(ph)VHNIPGFDS(ph)IK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETDGDHLSSLLNKTTVHNIPGFDSIK 26 1 Q9NVR5-2;Q9NVR5 Q9NVR5-2 DNAAF2 Protein kintoun 4 ET(0.421)DGDHLS(0.535)S(0.548)LLNKT(0.748)T(0.748)VHNIPGFDS(1)IK 49.001 0.069331 596850000 29202 159830 150690 163320 149600 204480 171290 171690 159530 114260 TRUE FALSE 30354.91751 187279.5592 154617.1052 195624.2085 124171.0454 156992.6189 157863.8422 169388.7764 153788.5465 136647.0594 0.222141023 1.370534866 1.131507007 1.431602037 0.908698994 1.148891309 1.155267028 1.239607915 1.125443513 1 17.06009489 4.745763991 24.92638806 1.176096406 0.222140555 0.788832348 0.146752328 338.3293361 1170716.845 0.03270475 0.335816898 55688.30393 -4.745763991 -0.95395585 ETDKQILQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETDKQILQNR 10 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4 Q9UM54-1 MYO6 Unconventional myosin-VI 0 70.488 0.049093 313020000 263660 220970 272290 198230 334460 291200 252080 252780 254270 260670 FALSE TRUE 274069.5004 258919.8786 279386.1011 237439.3023 277608.6087 223573.2132 232321.3109 249391.8976 245118.8724 311743.2957 0.879151225 0.830554762 0.896205644 0.761650068 0.890503862 0.717170878 0.745232742 0.799991214 0.786284343 1 18.24999901 3.742986401 24.91162414 0.80107697 0.864828964 0.073246147 0.078654421 742.3690877 4178590.76 0.018980154 0.032801136 5533.327829 -3.742986401 0.063751994 ETDLHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETDLHTK 7 0 Q9NQT8;E7ERX9;F2Z2F9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ; 89.55 0.017791 777570000 1697180 1521490 1654100 1309200 2141140 1987320 1825210 1633010 1799210 1531780 FALSE TRUE 1764185.977 1782794.072 1697207.205 1568155.852 1777189.788 1525795.048 1682145.271 1611122.172 1734456.784 1831902.963 0.963034622 0.973192417 0.92647222 0.85602561 0.970133147 0.832901676 0.918250205 0.879480084 0.946806036 1 20.80491165 4.113188488 4.517140758 0.906341566 0.967629506 0.14180665 0.04834947 0.294230591 10.16932598 0.011085782 0.025600497 12977.42382 -4.113188488 0.061287939 ETDLLILFKDDYFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETDLLILFKDDYFAK 15 1 P05455 P05455 SSB Lupus La protein 0 121.79 0.00010295 103650000 142200 128170 144710 113230 197930 169230 144750 142900 131080 116070 FALSE TRUE 147814.1658 150182.2005 148481.2615 135626.556 164285.9293 129928.8972 133404.1168 140984.6592 126362.4564 138811.6942 1.064853841 1.081913173 1.069659601 0.977054252 1.183516491 0.936008295 0.961043791 1.015654049 0.910315641 1 17.08276959 2.700700928 24.99994788 0.969431443 1.069978919 0.508165348 0.054265726 488.5038153 322574.0375 0.016750565 0.015792757 501.996776 -2.700700928 0.100547476 ETDLLLDDSLVSIFGNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ETDLLLDDSLVSIFGNRR 18 1 P30044-2;P30044;P30044-3;P30044-4 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 ;;;;; 261.74 1.35E-30 1778333000 1440101 1601026 1636208 1414127 1884259 1979280 1401984 1667525 1618075 1759715 FALSE TRUE 1496957.299 1875989.761 1678848.925 1693837.1 1563973.328 1519622.216 1292092.831 1645174.555 1559840.797 2104497.462 0.711313426 0.891419351 0.797743383 0.804865356 0.743157621 0.722083178 0.613967398 0.781742237 0.741193955 1 21.00504434 -1.413312573 2.851367282 1.005153318 0.757139812 0.532756732 0.068439601 8782207.42 10079612.34 367606.4151 0.017501092 0.0386089 1.413312573 -0.248013506 ETDLQELFRPFGS(ph)ISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 ETDLQELFRPFGS(0.968)IS(0.032)R 73.783 0.020655 35826000 5547.4 5790.6 6567.3 7873.1 6648.3 7451.7 6638.4 7728.6 6373.1 7010.9 TRUE FALSE 5766.415636 6785.090505 6738.449233 9430.375681 5518.224341 5721.155607 6118.064862 7625.010758 6143.733376 8384.551623 0.687742875 0.809237132 0.803674369 1.124732258 0.658141853 0.682344848 0.72968301 0.909411869 0.732744415 1 13.03351792 -1.164274971 3.920236662 1.000100384 0.801647848 0.178936767 0.131828094 13649817313 22982226349 17580930.9 0.031765612 0.068505435 1.164274971 -0.198452536 ETDLQELFRPFGSISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETDLQELFRPFGSISR 16 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ;; 247.5 2.44E-20 2372585000 1390501 1558260 1380950 1584631 1829352 1964547 1619689 1645170 1584507 1584935 FALSE TRUE 1445399.053 1825879.033 1416938.691 1898066.282 1518399.4 1508310.732 1492733.544 1623119.187 1527480.903 1895472.668 0.762553361 0.963284285 0.747538445 1.001368321 0.801066365 0.795743857 0.787525755 0.856313686 0.80585752 1 20.85412622 -1.321769471 3.740725379 1.000468207 0.838745247 0.27648 0.079600645 11367049.75 4016591.425 42904.44764 0.016988025 0.047668395 1.321769471 -0.16172296 ETDPS(ph)PEER ddPTM_MDA-MB-175_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;ETDPS(1)PEER 157.97 7.06E-05 1345930000 1619580 1926920 1702400 1700880 2001460 2371200 2048310 1850390 1839130 1895290 TRUE FALSE 1683522.269 2257853.521 1746765.943 2037308.987 1661252.544 1820524.736 1887758.11 1825588.549 1772940.071 2266635.788 0.742740531 0.996125418 0.770642532 0.898825033 0.732915519 0.803183619 0.832845806 0.805417685 0.782190099 1 21.11212116 5.048609992 18.59738555 0.835380119 4.34E-05 0.100828676 0.087420779 445.3775208 86019.80513 0.018537768 21315.42013 111843.3049 -5.048609992 -0.83533668 ETDPVKS(ph)PPLPEHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETDPVKSPPLPEHQK 15 1 Q96JM3;A0A2R8Y4S6;S4R3K0;A0A2R8Y735 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 ETDPVKS(1)PPLPEHQK;ET(0.005)DPVKS(0.995)PPLPEHQK;ET(0.18)DPVKS(0.82)PPLPEHQK;ET(0.023)DPVKS(0.977)PPLPEHQK 132.14 2.97E-05 1572100000 1595140 755230 1080760 748940 1581330 1566240 1550230 1103060 1316880 550234 TRUE FALSE 1658117.359 884934.8776 1108925.493 897078.0966 1312536.091 1202504.497 1428718.922 1088275.285 1269485.746 658041.8174 2.519775058 1.344800367 1.685190005 1.363253934 1.994608939 1.827398297 2.17116737 1.653808704 1.92918704 1 19.32781974 ETEAAPTS(ph)PPIVPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETEAAPTSPPIVPLK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A3B3IT55;Q7Z3B3-4;Q7Z3B3-2 A0A1W2PRB5;Q7Z3B3-4 KANSL1 KAT8 regulatory NSL complex subunit 1 1 ETEAAPT(0.145)S(0.855)PPIVPLK;ETEAAPT(0.023)S(0.977)PPIVPLK;ETEAAPT(0.138)S(0.862)PPIVPLK;ETEAAPT(0.264)S(0.736)PPIVPLK 172.09 1.10E-06 354485000 2292370 724940 863810 680490 1219410 1408370 1039560 897000 996410 651620 TRUE FALSE 2382874.538 849442.8057 886321.5982 815088.8909 1012135.124 1081297.412 958076.5708 884977.1822 960549.3987 779292.463 3.057741029 1.090017992 1.137341422 1.045934524 1.298787261 1.387537366 1.2294185 1.135616247 1.23259167 1 19.57180534 4.74028678 24.9985116 1.183073619 3.057741655 0.962325901 0.11185755 26.25579572 380208.7127 0.0274123 0.176456321 54990.38745 -4.74028678 1.874668035 ETEDGHESPLFDFIESCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETEDGHESPLFDFIESCLR 19 0 Q9UBF2;Q9UBF2-2 Q9UBF2 COPG2 Coatomer subunit gamma-2 0 ;; 211.13 1.44E-16 83378000 34398.1 88797 86581 116769 84692 130840 100905 100042 86148 83479 FALSE TRUE 35756.16355 104047.194 88837.37199 139865.5597 70296.08409 100454.3929 92995.80243 98701.10063 83047.55031 99835.11175 0.358152186 1.04219039 0.889840963 1.400965625 0.704121855 1.00620304 0.931493948 0.988641159 0.831847121 1 16.60725968 4.7422162 24.64507 0.978114348 0.358151895 0.542659147 0.170504948 211.1978936 1423771.471 0.037889109 0.280243546 55235.23427 -4.7422162 -0.619962453 ETEEILADVLKVEVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETEEILADVLKVEVFR 16 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 69.431 0.042164 18064000 18499 15644 20115 17733 23679 23976 23241 18988 19001 15634 FALSE TRUE 19229.3548 18330.73531 20639.21342 21240.53447 19654.05204 18407.93736 21419.30969 18733.49692 18317.15772 18697.18297 1.028462675 0.980400916 1.103867543 1.136028594 1.051177178 0.98452999 1.145590206 1.001942215 0.979674732 1 14.1905333 1.566461135 9.80368343 0.990832771 1.06044171 0.254293561 0.0532399 0.163780917 27.37006684 0.029311311 0.013697906 36.85200612 -1.566461135 0.069608939 ETEFKDDSLPIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETEFKDDSLPIKR 13 2 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 77.776 0.014078 232600000 228570 153700 210400 150210 259960 254900 234270 203000 269810 142250 FALSE TRUE 237594.1201 180096.7794 215883.1968 179921.0897 215772.0921 195703.338 215907.3052 200279.117 260099.5908 170121.164 1.396617061 1.058638297 1.268996707 1.057605565 1.268343615 1.150376199 1.26913842 1.177273376 1.528907896 1 17.37620311 ETELELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETELELR 7 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 93.262 0.035045 210160000 358280 289550 396020 273080 305770 334020 266370 318590 393180 245350 FALSE TRUE 372425.1711 339277.9601 406340.6065 327094.4089 253795.3246 256448.9171 245491.2234 314319.8222 379029.5286 293421.635 1.269249185 1.156281336 1.384835193 1.114759002 0.864950959 0.873994575 0.836650042 1.07122238 1.291757265 1 18.16261572 3.482062954 7.449246176 0.983085074 1.257827488 0.470290005 0.133128439 0.118602753 45.9205362 0.038380449 0.055187022 3034.330998 -3.482062954 0.274742414 ETERAS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETERASPIK 9 1 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.001)ERAS(0.999)PIK;ETERAS(1)PIK;ETERAS(1)PIK;ETERAS(1)PIK 84.365 0.009412 1830970000 3534520 2133020 2769040 2436330 3305810 3765310 4129160 2918000 2980870 1561480 TRUE FALSE 3674065.579 2499349.592 2841203.457 2918228.802 2743889.597 2890873.816 3805505.65 2878888.983 2873589.071 1867422.11 1.967453186 1.338395631 1.521457544 1.562704429 1.469346209 1.548055901 2.037839024 1.541638052 1.538799962 1 20.83261664 0.685224959 2.409319284 1.000203213 1.616452751 0.450711645 0.205276319 1.768763077 12.35008521 0.191791356 0.051483534 4.844232275 -0.685224959 0.616249537 ETERAS(ph)PIKMDLAPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ETERASPIKMDLAPSK 16 2 E7EVA0;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 ET(0.143)ERAS(0.857)PIKMDLAPSK;ET(0.017)ERAS(0.983)PIKMDLAPSK;ET(0.024)ERAS(0.976)PIKMDLAPSK;ET(0.058)ERAS(0.942)PIKMDLAPSK;ET(0.006)ERAS(0.994)PIKMDLAPSK;ET(0.346)ERAS(0.654)PIKMDLAPSK;ET(0.001)ERAS(0.999)PIKMDLAPSK 150.36 6.62E-07 7201680000 15319610 7329510 10600420 6515210 15699540 13857560 13371060 10651230 12587950 6335390 TRUE FALSE 15924440.03 8588296.327 10876675.65 7803899.092 13030937.8 10639351.7 12323001.38 10508467.68 12134912.14 7576688.372 2.10176785 1.133515846 1.435544808 1.029988131 1.719872477 1.404221895 1.62643635 1.386947327 1.60161162 1 22.85313598 -1.074212987 5.235287805 0.9999933 1.470830136 0.206876844 0.28675115 2.04E-05 3.61E-06 0.252604432 0.059538589 0.084292127 1.074212987 0.470836837 ETES(ph)APGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 2 ET(0.002)ES(0.998)APGS(1)PR;ET(0.001)ES(0.999)APGS(1)PR;ET(0.001)ES(0.999)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR;ETES(1)APGS(1)PR 222.48 7.14E-09 6020820000 5151750 5567540 5407530 4925250 6293660 6655110 5273210 5247080 5232460 5149930 TRUE FALSE 5355145.068 6523721.686 5548454.674 5899449.75 5223865.921 5109561.562 4859882.021 5176751.475 5044144.787 6158960.182 0.869488503 1.059224527 0.900875231 0.957864571 0.848173355 0.82961432 0.789075084 0.840523615 0.81899292 1 22.55425537 3.219382163 6.652345075 0.840230855 0.951817251 0.279013384 0.070498604 0.161155325 27.4645924 0.018701998 0.023178933 1657.227619 -3.219382163 0.111586396 ETESAPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETESAPGSPR 10 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR 177.41 2.44E-06 4858800000 2770710 3009950 2830670 2671950 2937860 3732830 3351300 3130020 3097490 3009980 TRUE FALSE 2880099.77 3526885.498 2904439.586 3200453.735 2438483.607 2865936.804 3088616.349 3088067.202 2986011.94 3599727.951 0.800088176 0.979764456 0.806849747 0.889082113 0.677407748 0.796153721 0.858013825 0.857861273 0.829510446 1 21.77945645 -0.366527575 8.014770789 1 0.835142395 0.320259342 0.073024386 0 0 0.069961065 0.016489981 0.43000393 0.366527575 -0.164857605 ETFAS(ph)DTNEALASLDESQEGHAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 ET(0.011)FAS(0.986)DT(0.003)NEALASLDESQEGHAEAK 151.67 9.14E-08 38108000 22466 19882 24250 18986 27432 34791 34968 26240 22455 13519 TRUE FALSE 23352.97503 23296.57884 24881.97492 22741.37413 22769.11844 26711.31751 32227.11679 25888.29572 21646.84894 16167.78921 1.444413625 1.440925443 1.538984372 1.406585269 1.408301292 1.652131727 1.993291499 1.601226697 1.33888738 1 13.9808348 2.741703043 24.50308693 1.597200882 1.450229171 0 0.243917354 586.584643 4573904.863 0.074367764 0.07580181 551.700075 -2.741703043 -0.146971711 ETFLTSPEELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETFLTSPEELYR 12 0 O95433;O95433-2;G3V438;H0YJ63;H0YJG7 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;; 241.13 7.20E-16 599843000 479635 527638 508791 537355 586896 670128 527221 525850 512059 551633 FALSE TRUE 498571.3602 618255.722 522050.5114 643642.2152 487135.6276 514500.9279 485896.0404 518801.8409 493630.0966 659714.9247 0.755737579 0.937155882 0.791327423 0.975636887 0.738403224 0.779883717 0.73652425 0.786403068 0.748247581 1 19.33148322 3.199499215 24.99824397 0.782684706 0.864861789 0.095593193 0.093454905 273.0180572 174723.381 0.024486689 0.029267683 1583.066704 -3.199499215 0.082177083 ETFS(ph)SAEGTVDKDTTIMELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.01)FS(0.919)S(0.065)AEGT(0.005)VDKDTTIMELR;ET(0.193)FS(0.758)S(0.047)AEGT(0.001)VDKDTTIMELR;ET(0.143)FS(0.833)S(0.023)AEGTVDKDTTIMELR 73.546 0.0089653 133409000 119301 120831 147590 121471 187402 176072 157255 146982 156551 131827 TRUE FALSE 124011.0956 141582.7843 151436.3166 145497.6012 155547.475 135181.9464 144928.9422 145011.9467 150916.7601 157655.9767 0.78659305 0.89804895 0.960549164 0.922880339 0.986625932 0.857448917 0.919273378 0.919799869 0.957253656 1 17.26642034 4.694827892 3.011340268 0.933856612 0.769872398 0.586908951 0.038597917 0.225278215 3.16077197 0.009004673 0.083715626 49525.38856 -4.694827892 -0.163984214 ETGANLAICQWGFDDEANHLLLQNNLPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETGANLAICQWGFDDEANHLLLQNNLPAVR 30 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 383.8 8.58E-155 1026340000 384690 502480 532200 480900 527100 629650 545400 528750 528970 556920 FALSE TRUE 399877.8582 588777.0312 546069.5692 576020.5847 437503.7303 483423.3299 502650.1229 521662.9711 509932.473 666037.8111 0.600383119 0.883999409 0.819877731 0.864846672 0.656875215 0.725819648 0.754687068 0.783233268 0.765620907 1 19.34524456 -1.409795208 2.673474875 1.006145758 0.766876704 0.427748881 0.082491682 7416191.968 7882789.048 347266.5123 0.019103718 0.038922864 1.409795208 -0.239269054 ETGEAGWWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETGEAGWWR 9 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 0 ;; 167.9 0.00013873 366170000 394474 439569 457577 430289 516207 552276 470136 429863 449151 503917 FALSE TRUE 410048.1381 515061.5564 469501.8325 515398.8799 428462.3185 424018.2688 433285.5118 424101.3896 432986.1432 602649.8881 0.680408553 0.854661333 0.779062341 0.855221066 0.710963906 0.703589725 0.718967215 0.70372765 0.718470462 1 19.20096058 -1.085866503 4.616171305 1.000011819 0.747680141 0.618805654 0.05951625 0.19783709 38219562.83 1223.697808 0.014539777 0.082060375 1.085866503 -0.252331678 ETGEHLVHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 ;;;; 150.61 1.23E-05 2134670000 1568340 1479940 1660740 1527590 1922310 2103430 2067300 1745230 1846380 1487090 FALSE TRUE 1630259.274 1734108.183 1704020.249 1829742.743 1595556.433 1614940.26 1905259.624 1721838.046 1779929.144 1778456.813 0.916670712 0.97506342 0.958145419 1.028837321 0.897157817 0.908057057 1.071299348 0.968164104 1.00082787 1 20.76219451 2.254316828 24.99979423 1.005495304 0.950499975 0.336301671 0.042855048 319.0031321 506149.7297 0.015061949 0.012561181 179.6043405 -2.254316828 -0.054995329 ETGENVLHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETGENVLHVR 10 0 Q9Y223-5;Q9Y223-3;Q9Y223;Q9Y223-2;Q9Y223-4 Q9Y223-5 GNE Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase;UDP-N-acetylglucosamine 2-epimerase (hydrolyzing);N-acetylmannosamine kinase 0 ; 109.42 0.0020212 200149000 88153 113027 106691 121738 130521 136141 109257 110706 112123 131774 FALSE TRUE 91633.34851 132438.508 109471.4551 145817.413 108335.087 104524.316 100693.1508 109222.1671 108087.7151 157592.5923 0.581457207 0.840385364 0.694648482 0.925280883 0.687437686 0.66325653 0.638945964 0.693066632 0.685867994 1 17.2658402 -0.927206795 5.094420792 1.000000977 0.714809297 0.45626654 0.094196261 1.02E-06 2.15E-07 0.089010648 0.020979939 0.118247837 0.927206795 -0.28519168 ETGEPYRLS(ph)PEPTPLAEPILEVEVTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETGEPYRLSPEPTPLAEPILEVEVTLSK 28 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 ET(0.002)GEPYRLS(0.998)PEPTPLAEPILEVEVTLSK;ETGEPYRLS(0.996)PEPT(0.004)PLAEPILEVEVTLSK;ET(0.185)GEPY(0.009)RLS(0.751)PEPT(0.054)PLAEPILEVEVTLSK 214.41 2.32E-34 834690000 329316 206246 257487 257562 308806 339178 373539 281268 286407 172091 TRUE FALSE 342317.65 241667.1461 264197.3227 308506.9949 256315.2664 260409.0498 344260.0371 277498.0625 276099.268 205808.9366 1.663278843 1.174230576 1.283701899 1.49899708 1.245403969 1.265295153 1.672716661 1.348328538 1.34153197 1 17.6509461 0.693935325 2.597617739 1.000090877 1.388224937 0.344401007 0.162032363 2.352988488 18.54046603 0.148572086 0.039496401 4.942370803 -0.693935325 0.388134059 ETGKTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETGKTAR 7 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 63.48 0.072214 25999000 27263 61383 68139 59522 69193 79312 53608 54386 61019 80675 FALSE TRUE 28339.36429 71925.05276 69914.75832 71295.27394 57431.59858 60892.98998 49406.06488 53657.04463 58822.93811 96481.72163 0.293727805 0.745478538 0.724642524 0.738951096 0.595258849 0.631134986 0.512076941 0.55613689 0.609679607 1 16.55796803 0.891426103 18.4003372 1 0.605759648 0.471173984 0.126787768 8205.140106 1390557.235 0.119748816 0.029937204 7.788002877 -0.891426103 -0.394240353 ETGLMYSIMVHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETGLMYSIMVHALR 14 0 P78527;P78527-2;H0YG84 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 144.27 8.90E-06 113250000 103400 125940 177860 169070 191960 207230 194930 166790 182000 137720 FALSE TRUE 107482.3118 147569.2153 182495.1777 202511.5414 159330.7078 159103.9731 179650.8772 164554.4529 175449.8556 164703.5972 0.652580233 0.895968381 1.108021809 1.229551417 0.967378433 0.966001811 1.090752602 0.999094468 1.065246045 1 17.32951254 4.590932637 2.836559066 1.051723935 0.636800723 0.723793101 0.076256954 0.169599494 2.204538548 0.019727254 0.135518112 38988.15077 -4.590932637 -0.414923212 ETGLSHLCEFIEDCEFTVLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ETGLSHLCEFIEDCEFTVLATR 22 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;;;;; 286.55 3.55E-46 1281641000 506024.4 638482.8 590236.3 761055.1 657878.6 798864.8 690744.7 637746.7 615190.2 535910 FALSE TRUE 526002.634 748137.2542 605618.3429 911589.5273 546052.6306 613340.5571 636602.3255 629198.7486 593049.6249 640911.3039 0.820710496 1.167302324 0.944933159 1.422333358 0.85199407 0.956981962 0.993276795 0.981725154 0.925322461 1 19.28976519 ETHADLWPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETHADLWPAK 10 0 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;; 129.85 0.00029216 1958040000 1400000 1098000 1322270 1056290 1721830 1592410 1438690 1251650 1350180 1231930 FALSE TRUE 1455273.081 1286572.959 1356729.442 1265221.009 1429153.952 1222596.911 1325921.718 1234873.679 1301587.286 1473303.097 0.987762182 0.873257486 0.920875986 0.858764915 0.970033902 0.829833938 0.899965337 0.838166757 0.883448415 1 20.49062283 2.732775208 24.98758376 0.877756017 0.915832322 0.045567409 0.057043445 1137.746941 4913995.878 0.01683639 0.016304412 540.4744996 -2.732775208 0.038076305 ETHPDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETHPDSLR 8 0 P56597 P56597 NME5 Nucleoside diphosphate kinase homolog 5 0 84.568 0.01736 129830000 108820 141630 145590 136660 163810 165110 130300 130560 136400 148660 FALSE TRUE 113116.2976 165953.8508 149384.195 163690.9401 135965.6347 126765.7048 120086.7455 128810.0568 131490.9906 177787.0807 0.63624588 0.933441564 0.840242128 0.920713358 0.764766676 0.713019778 0.675452598 0.724518656 0.73959812 1 17.43979097 3.023843722 22.7551542 0.743001459 0.840693431 0.041279396 0.113431744 155.4194471 148320.9313 0.030640529 0.036619056 1056.43729 -3.023843722 0.097691972 ETHQQVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETHQQVVSR 9 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;; 128.03 0.00042867 2085680000 935400 1085110 1000190 1156510 1086750 1299270 1142340 1090570 1041700 1005580 FALSE TRUE 972330.3143 1271469.202 1026255.773 1385264.226 902024.6232 997534.2331 1052800.406 1075952.693 1004209.42 1202604.148 0.808520672 1.057263276 0.853361245 1.151887118 0.750059464 0.829478457 0.875433872 0.894685666 0.835029068 1 20.19773041 3.207380635 24.99998719 0.860609307 0.96598069 0.182591138 0.107250242 314.543907 252199.2481 0.028766508 0.034385634 1612.057894 -3.207380635 0.105371383 ETHVMDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 ETHVMDYR 8 0 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;;;; 143.73 0.00045261 11697960000 6471590 7259690 6818380 7008010 8591950 8690100 7203160 6673040 6706350 7791630 FALSE TRUE 6727093.37 8506485.285 6996072.584 8394173.461 7131493.408 6671955.975 6638557.497 6583598.814 6464989.774 9318250.719 0.721926633 0.912884354 0.750792482 0.900831467 0.765325341 0.716009493 0.712425293 0.706527331 0.69379865 1 23.15162772 3.015067515 24.51850377 0.740128661 0.824321177 0.039596417 0.100869329 360.4513943 586536.6288 0.026609011 0.031792458 1035.303102 -3.015067515 0.084192516 ETIEDVEEMLNNLPGVTSVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ETIEDVEEMLNNLPGVTSVHSR 22 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;; 208.98 6.24E-23 568980000 203359 608447 614991 663313 612758 762756 599547 684770 592829 625235 FALSE TRUE 211387.7703 712943.0392 631018.1707 794514.3316 508601.614 585617.4787 552552.9395 675591.7782 571493.2001 747737.8274 0.282703058 0.953466594 0.843902966 1.06255736 0.680187086 0.783185573 0.738966145 0.903514244 0.764296227 1 19.51217299 4.744963803 24.78588372 0.850802838 0.28270277 0.689744755 0.115818139 358.7106603 1388478.971 0.026683224 0.250432819 55585.79262 -4.744963803 -0.568100068 ETIFELEDEVEQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETIFELEDEVEQHR 14 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 0 ; 220.32 4.68E-12 127765000 139012 163922 169228 176670 178857 209439 201195 177827 172893 147996 FALSE TRUE 144500.3011 192074.3284 173638.2207 211614.7987 148454.951 160799.9663 185424.8102 175443.5199 166670.6147 176992.9826 0.81641825 1.085208721 0.981045791 1.195611236 0.83876179 0.908510405 1.047639332 0.991245626 0.941679225 1 17.43333264 ETIFELEDQVEQHR ddPTM_MDA-MB-175_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 86.944 0.0071387 21881000 16763 18973 22394 18770 22607 29797 26497 23837 17469 24401 FALSE TRUE 17424.81618 22231.46516 22977.60604 22482.64998 18764.27022 22877.09833 24420.0959 23517.504 16840.2941 29181.90876 0.597110228 0.761823544 0.787392155 0.770431097 0.643010379 0.783947977 0.836823119 0.805893274 0.577079938 1 14.83278663 -2.176906234 2.562261055 1.733088324 0.741864115 0.459031847 0.087209419 6126846.21 3325204.225 25644072.46 0.020654082 0.006654168 2.176906234 -0.991224209 ETKPEPMEEDLPENKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETKPEPMEEDLPENKK 16 2 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 174.49 2.17E-09 603240000 1050660 348770 701040 349770 853260 679040 720500 456650 628700 181219 FALSE TRUE 1092140.868 408668.5344 719309.6783 418953.462 708223.17 521343.251 664025.3273 450529.3537 606073.2098 216725.3934 5.03928428 1.885651368 3.318991222 1.933107401 3.267836587 2.405547605 3.06390182 2.078802796 2.796502986 1 17.72550868 8 0.070731871 9.63E-15 9.005626858 0.378604248 0.824090475 284.9369051 1.485693676 32.64015023 255.0468771 100000000 -8 9.005626858 ETLAVNYEKEEEFLTNELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETLAVNYEKEEEFLTNELSR 20 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 195.34 4.09E-19 164970000 118699 83099 107192 92937 134858 143923 134156 112344 118833 87006 FALSE TRUE 123385.3282 97370.60683 109985.5116 111319.6612 111934.8853 110499.0644 123640.5022 110838.2124 114556.2235 104053.1599 1.185791266 0.93577751 1.057012701 1.069834509 1.075747103 1.061948187 1.188243609 1.065207559 1.100939401 1 16.66696125 3.146439234 1.69816613 1.093386122 1.050106916 0.004826613 0.071511922 1.076597845 6.411086758 0.022986948 0.030452781 1401.003544 -3.146439234 -0.043279206 ETLEQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETLEQQKR 8 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 110.38 0.0055123 1355120000 774550 674290 795160 605730 1006930 964620 847450 769070 874260 658360 FALSE TRUE 805129.8321 790094.0623 815882.5228 725541.5861 835772.3983 740601.624 781024.6546 758761.8746 842795.5534 787353.0369 1.022577922 1.003481317 1.036234681 0.921494618 1.06149638 0.940622045 0.991962459 0.963686985 1.070416337 1 19.58665114 ETLIAEIEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETLIAEIEELDR 12 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 90.685 0.020289 3911400 12303 12722 11723 13684 14837 14634 19993 16547 12425 9261.2 FALSE TRUE 12788.73194 14906.90454 12028.51101 16390.65436 12315.01204 11235.47528 18425.89642 16325.21453 11977.82668 11075.75482 1.154660079 1.345904164 1.086021784 1.479867929 1.111889188 1.014420729 1.66362444 1.473959544 1.081445632 1 13.4351174 2.263701676 24.99980269 1.369557626 1.209180783 0.019637633 0.217820871 509.4821114 506617.783 0.074446468 0.062263004 183.5277226 -2.263701676 -0.160376843 ETLPLLLQHLWQVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETLPLLLQHLWQVNR 15 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;H0Y746 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 0 ; 173.44 9.70E-07 224000000 216970 256950 252800 259940 295360 306640 269200 247680 271280 241480 FALSE TRUE 225536.1431 301079.1637 259388.1757 311355.3562 245154.8127 235427.5072 248099.4006 244360.2547 261516.6858 288793.3826 0.780960218 1.042541768 0.898179083 1.078124967 0.848893456 0.815210879 0.859089631 0.846142154 0.90554944 1 18.13967816 ETLQQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ETLQQHK 7 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 145.04 0.0023131 4482980000 6849930 6224820 6316870 5949130 9926110 8964620 7223420 5964540 6354880 6202700 FALSE TRUE 7120370.526 7293884.413 6481492.822 7125850.158 8238873.368 6882722.865 6657229.466 5884595.097 6126169.11 7418000.307 0.959877357 0.983268281 0.873752029 0.96061605 1.110659615 0.927840736 0.897442598 0.793285906 0.825851828 1 22.8225989 2.221666902 3.091467128 0.850927068 0.973882199 0.247952556 0.075534266 0.28177389 5.5795927 0.030809804 0.022409937 166.5968947 -2.221666902 0.122955131 ETLVYLTHLDYVDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 ;;;;; 249.19 1.57E-20 1693990000 1030138 1108220 1245040 1196690 1294460 1402300 1250190 1212260 1187450 1170980 FALSE TRUE 1070808.644 1298548.164 1277486.765 1433391.71 1074428.152 1076637.077 1152196.841 1196011.638 1144713.906 1400411.111 0.76463878 0.927262112 0.912222672 1.023550655 0.767223384 0.768800725 0.822756141 0.854043236 0.817412756 1 20.41741898 4.763188138 22.80562517 0.86826043 0.764638364 0.129380814 0.084760381 4897.932428 4535349.009 0.020705672 1.128395549 57967.97618 -4.763188138 -0.103622066 ETMQSLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 280.85 4.79E-21 30265070000 8237222 9005473 8615659 9202749 9657836 11279804 10247053 8907451 8626639 8501570 FALSE TRUE 8562433.885 10552092.93 8840190.151 11023025.28 8016200.486 8660240.468 9443862.21 8788061.189 8316167.948 10167289.87 0.842154989 1.037847162 0.869473603 1.084165537 0.788430407 0.851774719 0.928847543 0.864346478 0.817933594 1 23.27743184 3.219184641 24.99984554 0.870905051 0.957731851 0.183101516 0.085785424 371.0939191 478802.7061 0.022920645 0.027433975 1656.474067 -3.219184641 0.0868268 ETNGNEDEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETNGNEDEEGR 11 0 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ; 130.09 0.00053828 65655000 54383 67148 65108 71765 65766 73052 76011 68125 57653 59571 FALSE TRUE 56530.08283 78680.14666 66804.76797 85959.9028 54587.11881 56086.78011 70053.0592 67211.89581 55578.07979 71242.79689 0.79348489 1.10439441 0.937705577 1.206576757 0.766212462 0.787262468 0.983300239 0.94342023 0.780122093 1 16.12045654 3.21416039 24.99992874 0.881896228 1.012042037 0.210688019 0.126640726 365.0961762 374068.4378 0.035704138 0.042693113 1637.421127 -3.21416039 0.130145809 ETPEHPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETPEHPLK 8 0 Q8N163-2;Q8N163;H0YB24;G3V119;E5RHJ4 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ; 94.302 0.010456 880520000 2011930 1731410 2059400 1803200 2498500 2466900 2301200 2133140 2225380 1607240 FALSE TRUE 2091362.55 2028766.199 2113069.656 2159867.578 2073805.862 1893999.861 2120825.931 2104548.747 2145289.009 1922147.906 1.088034143 1.055468309 1.099327294 1.123673975 1.078900253 0.985355943 1.103362507 1.09489428 1.116089455 1 20.87428792 3.00154902 24.99121701 1.067782112 1.091055062 0.096822606 0.042580615 165.0151258 2662200.531 0.012773673 0.015145525 1003.573119 -3.00154902 0.02327295 ETPGTLSSDTNDSGVELGEES(ph)RSSPLKLEFDFTEDTGNIEAR ddPTM_MDA-MB-175_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 ETPGTLSSDTNDS(0.014)GVELGEES(0.329)RS(0.329)S(0.329)PLKLEFDFTEDTGNIEAR 106.08 3.42E-06 33275000 14748 15475 16301 12439 16917 21347 18189 14828 15375 13541 TRUE FALSE 15330.26243 18132.71087 16725.81745 14899.39707 14041.45438 16389.48277 16763.29865 14629.25491 14821.65675 16194.09969 0.946657284 1.119710957 1.032834043 0.920050967 0.867072245 1.012065078 1.03514854 0.903369449 0.915250433 1 13.98318064 3.795251634 7.141822006 0.948095472 1.042476574 0.260051239 0.063255201 0.328132113 35.59204044 0.016413411 0.029681589 6240.963376 -3.795251634 0.094381102 ETPHS(ph)PGVEDAPIAK ddPTM_MDA-MB-175_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 ETPHS(1)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.08)PHS(0.92)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.152)PHS(0.848)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.04)PHS(0.96)PGVEDAPIAK;ET(0.039)PHS(0.961)PGVEDAPIAK;ET(0.057)PHS(0.943)PGVEDAPIAK;ET(0.021)PHS(0.979)PGVEDAPIAK;ET(0.149)PHS(0.851)PGVEDAPIAK;ET(0.017)PHS(0.983)PGVEDAPIAK;ET(0.019)PHS(0.981)PGVEDAPIAK;ET(0.02)PHS(0.98)PGVEDAPIAK 311.26 3.82E-56 87461333000 21275721 17800061 21192861 16783514 24861320 25108696 23987996 21045392 21915231 16659089 TRUE FALSE 22115702.89 20857083.01 21745164.37 20103242.98 20635401.71 19277581.88 22107754.19 20763312.94 21126506.12 19923118.53 1.110052267 1.046878428 1.091453847 1.009040976 1.03575159 0.967598614 1.109653298 1.042171832 1.060401567 1 24.24794015 5.473325481 0.932851645 1.038890865 1.29533809 0.236528907 0.039232285 11.11164147 2.834154393 0.011935383 4.002505927 297389.3973 -5.473325481 0.256447225 ETPPNGNLS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETPPNGNLSPAPR 13 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR 212.46 1.44E-08 1281010000 775915 848777 901274 787965 861332 1080130 838680 891782 831190 892007 TRUE FALSE 806548.7233 994547.8472 924761.9408 943822.1252 714923.0943 829286.177 772942.0701 879829.121 801275.6343 1066778.693 0.756060023 0.932290693 0.866873276 0.884740323 0.670170016 0.777374147 0.724557094 0.824753181 0.751117021 1 20.02482948 5.085521672 12.97775546 0.814774328 8.92E-05 0.035099635 0.095041227 974348.5915 3404730.501 0.022212446 21504292.83 121764.7753 -5.085521672 -0.814685165 ETPQGELRPEVVEDEVPRS(ph)PVAEEPGGGGSSSSEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETPQGELRPEVVEDEVPRSPVAEEPGGGGSSSSEAK 36 2 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 ETPQGELRPEVVEDEVPRS(1)PVAEEPGGGGSSSSEAK;ETPQGELRPEVVEDEVPRS(1)PVAEEPGGGGSSSSEAK 193.05 5.38E-24 428180000 154610 91248 146620 114375 174520 156213 167352 137954 149669 115039 TRUE FALSE 160714.1222 106919.1342 150441.0376 136998.0336 144855.1527 119934.8982 154234.5129 136104.9523 144282.4419 137578.6895 1.168161456 0.777148951 1.093490847 0.995779464 1.052889465 0.871754911 1.121063978 0.989288041 1.048726677 1 17.06989749 2.204504512 24.99989495 1.036499006 0.990771591 0.042120996 0.107964617 694.1693098 509571.7893 0.037365217 0.027597501 160.1417287 -2.204504512 -0.045727415 ETQS(ph)PEQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;ET(0.002)QS(0.998)PEQVK;ETQS(1)PEQVK;ETQS(1)PEQVK 242.97 1.88E-10 11809907000 11413193 7880480 9658115 8306736 11731531 12546206 12938208 10096476 10475979 6156847 TRUE FALSE 11863794.67 9233891.138 9909813.411 9949783.588 9737409.551 9632539.796 11924077.45 9961149.254 10098950.56 7363163.29 1.611236123 1.254065783 1.345863594 1.351291992 1.32244922 1.308206734 1.619423199 1.352835576 1.371550537 1 22.81189427 0.52504488 2.464951589 1.000014151 1.39091319 0.506161369 0.116619796 5.544276231 27.7321051 0.107160869 0.028633833 3.350000563 -0.52504488 0.390899038 ETQS(ph)PEQVKSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;ET(0.14)QS(0.86)PEQVKSEK;ET(0.053)QS(0.947)PEQVKSEK;ET(0.004)QS(0.996)PEQVKSEK;ET(0.001)QS(0.999)PEQVKSEK 179.14 1.28E-05 8985770000 6200030 3359360 4769360 2634160 6931200 5902680 4629580 4485430 5413790 3426970 TRUE FALSE 6444811.972 3936303.948 4893653.44 3155188.986 5753037.1 4531872.026 4266701.422 4425310.148 5218948.755 4098419.158 1.572511674 0.960444453 1.194034395 0.769855123 1.403721015 1.10576099 1.041060286 1.079760263 1.273405319 1 21.96663611 4.748869995 24.31765044 1.094661417 1.572512067 0.432088102 0.165237608 903.2780258 2130579.76 0.036553074 0.500295755 56088.00529 -4.748869995 0.47785065 ETRHS(ph)WDSPAFNNDVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETRHSWDSPAFNNDVVQR 18 1 A0A1W2PR28;Q5JU85-3;Q5JU85;A0A1W2PRJ5 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 ET(0.01)RHS(0.99)WDSPAFNNDVVQR;ET(0.004)RHS(0.995)WDS(0.001)PAFNNDVVQR 188.08 2.40E-14 466510000 106521 125390 156711 124538 147936 180510 145058 133583 146756 159034 TRUE FALSE 110726.5313 146924.7571 160795.0174 149171.2447 122789.8916 138589.2882 133687.9749 131792.5384 141474.2802 190193.6674 0.582177802 0.772500784 0.845427819 0.784312363 0.645604521 0.728674567 0.702904449 0.692938625 0.743843274 1 17.53710969 ETSFGS(ph)SENITMTSLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.927)S(0.073)ENITMTSLSK;ETSFGS(0.994)S(0.006)ENITMTSLSK;ETSFGS(0.914)S(0.086)ENITMTSLSK;ETSFGS(0.772)S(0.228)ENITMTSLSK;ETSFGS(0.918)S(0.082)ENITMTSLSK;ETSFGS(0.915)S(0.085)ENITMTSLSK;ETSFGS(0.973)S(0.027)ENITMTSLSK 380.03 2.02E-105 2106972000 1876250 1660660 1933300 1656360 2331710 2305670 2182490 1947620 2083470 1524389 TRUE FALSE 1950325.799 1945865.437 1983683.386 1983983.064 1935366.767 1770213.085 2011420.731 1921515.34 2008486.322 1823063.838 1.06980664 1.06736001 1.088104182 1.088268563 1.061601205 0.971009927 1.103318868 1.054003321 1.101709265 1 20.79793365 3.007165421 23.89619526 1.050636102 1.077872024 0.131432408 0.038324875 248.1364167 827504.6042 0.010972645 0.013085633 1016.635852 -3.007165421 0.027235922 ETSSALTHAGAHLDLSAFSSWEELASLGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETSSALTHAGAHLDLSAFSSWEELASLGLDR 31 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 132.69 1.82E-06 37338000 23165 29767 36783 35075 44393 47035 35430 39127 38641 38135 FALSE TRUE 24079.57209 34879.25069 37741.5952 42012.73031 36847.09372 36111.83407 32652.90402 38602.56656 37250.31796 45606.82311 0.52798179 0.764781415 0.827542736 0.921193967 0.807929411 0.791807708 0.715965327 0.846420863 0.816770725 1 15.47696206 -0.883037123 0.033172742 1.845089965 2.73E-27 0.427021111 0.089649402 507.227099 3.400330314 112.843264 77.86836263 0.130907002 0.883037123 -1.845089965 ETTLITPFPVLLFGGDIEVQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETTLITPFPVLLFGGDIEVQHR 22 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 119.01 8.03E-05 62175000 79560 72911 77572 77685 78439 93693 105770 61041 103010 62968 FALSE TRUE 82701.09023 85432.89708 79593.59005 93050.86113 65105.9668 71934.22068 97479.47102 60222.84524 99302.69022 75305.374 1.098209674 1.13448606 1.056944356 1.235647022 0.864559371 0.955233562 1.294455705 0.799715107 1.318666716 1 16.2004652 3.259277777 24.99998155 1.027004282 1.126235049 0.070642821 0.160671091 640.3073051 772671.7917 0.042305581 0.057219098 1816.677249 -3.259277777 0.099230768 ETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETTSGTSTEPVKNSSPAPPQPAPGK 25 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 ETTSGTSTEPVKNS(0.151)S(0.849)PAPPQPAPGK 168.72 6.59E-12 282320000 118350 63791 89162 60533 120410 111110 101750 83760 103610 53079 TRUE FALSE 123022.5494 74746.60802 91485.63497 72506.24673 99942.75121 85306.38639 93774.56913 82637.3342 99881.09634 63478.81379 1.938009582 1.177504801 1.441199504 1.142211746 1.574426887 1.343856025 1.477257742 1.301809679 1.57345562 1 15.95398755 -1.799826056 2.585312311 0.872956613 1.418300127 0.263698721 0.218143584 25972265.68 18576599 20729562.38 0.047416745 0.015855281 1.799826056 0.545343515 ETVAYLQAHALTTEGIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETVAYLQAHALTTEGIFR 18 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 194.49 7.00E-15 1268800000 655990 847500 858330 764300 947210 993570 718790 772010 856450 900060 FALSE TRUE 681888.9917 993051.5324 880698.7849 915476.2588 786203.5825 762828.4252 662449.3616 761662.4687 825626.5318 1076409.524 0.633484725 0.922559221 0.818181895 0.850490671 0.730394487 0.708678628 0.615425028 0.707595438 0.767018977 1 20.03779563 3.220267393 22.29600693 0.726733635 0.815349289 0.009105806 0.116277388 142.6331247 173841.6016 0.031630372 0.037910401 1660.609021 -3.220267393 0.088615654 ETVQTTEDQILKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ETVQTTEDQILKR 13 1 P18206;P18206-2 P18206 VCL Vinculin 0 ;; 189.09 8.91E-06 871930000 391526 365257 402839 349768 459648 510092 442535 423030 434328 343531 FALSE TRUE 406983.7488 427987.0484 413337.3153 418951.0664 381517.1971 391630.8635 407847.9503 417359.9748 418696.6201 410839.3222 0.990615374 1.041738279 1.006080219 1.019744323 0.928628728 0.953245813 0.992718877 1.01587154 1.01912499 1 18.64821475 -0.876081687 5.653084745 1.000000001 0.996708304 0.001067773 0.031769141 4.92E-10 1.30E-10 0.032988399 0.007775437 0.133020419 0.876081687 -0.003291697 ETVRDYEHQFHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ETVRDYEHQFHLR 13 1 Q15276-2;Q15276;A0A087WZZ3 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 131.53 8.34E-05 42962000 25664 35855 39217 23156 45117 40286 20575 33739 32340 50652 FALSE TRUE 26677.23454 42012.81734 40239.02724 27736.18769 37448.02846 30930.18704 18962.27774 33286.78389 31176.08972 60576.28961 0.440390699 0.693552174 0.664270253 0.457872013 0.618196141 0.510598903 0.31303135 0.549501861 0.514658292 1 15.88646559 -1.058328092 5.923126695 1.000000481 0.529833506 0.636720204 0.10670227 1.78E-06 2.83E-07 0.104849346 0.024713162 0.087432301 1.058328092 -0.470166975 ETVVEEPVDITPYLDQLDESLRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETVVEEPVDITPYLDQLDESLRDK 24 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 0 ; 128.55 7.00E-05 49680000 51645 38134 41649 39694 59989 57525 49613 44114 50188 32000 FALSE TRUE 53683.98448 44683.21786 42734.40716 47545.35473 49792.09121 44165.69055 45724.20342 43522.72399 48381.74368 38269.78732 1.402777184 1.167584692 1.116661736 1.242373111 1.301080949 1.154061562 1.19478593 1.13726067 1.264228183 1 15.22391826 -4.999999999 0.16407355 0.213693734 1.264548162 0.408912398 0.081106059 137.2156463 1.276144391 35.21207466 0.31644883 1.00E-05 4.999999999 1.050854428 ETVVEVPQVTWEDIGGLEDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 213.72 8.90E-24 2140410000 2565090 1819250 2338690 1748580 2757720 2604490 2624940 2418150 2614670 1723830 FALSE TRUE 2666361.734 2131692.036 2399638.183 2094443.905 2288963.739 1999636.669 2419190.344 2385738.655 2520568.537 2061581.484 1.293357432 1.03400814 1.163979305 1.015940394 1.110295061 0.969952769 1.173463364 1.157237137 1.222638328 1 20.97532005 -0.275939751 6.90096572 0.999999988 1.121391093 0.139720288 0.093512544 0 0 0.086184268 0.020313827 0.529736928 0.275939751 0.121391105 ETVYCLNDDDETEVLKEDIIQGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ETVYCLNDDDETEVLKEDIIQGFR 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;; 372.63 7.40E-119 3385821100 973106 770768.6 905133.5 775500.5 1167762 1134682.7 1047667.9 940913.4 1018227.1 701028.1 FALSE TRUE 1011524.976 903142.1113 928722.0226 928892.1843 969266.2324 871169.8392 965548.9524 928301.9949 981581.3056 838381.1342 1.206521634 1.07724527 1.107756347 1.107959312 1.156116464 1.039109545 1.151682586 1.107255348 1.170805575 1 19.67724673 -2.44608348 2.055874062 1.59E-05 1.121033489 0.397095291 0.045958317 858656.9286 117308.4012 3962584.022 0.010141793 0.003580276 2.44608348 1.121017596 ETWYLSWALDTNQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ETWYLSWALDTNQEER 16 0 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1;H3BSV8 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ;;; 251.3 4.57E-21 271954000 218477 231534 249299 254958 253362 293951 272320 234247 268650 231889 FALSE TRUE 227102.6407 271298.1634 255795.9367 305387.9314 210295.6177 225685.3351 250974.8468 231107.3021 258981.339 277323.2098 0.818909607 0.97827428 0.922374788 1.101198604 0.758305148 0.813798944 0.904990415 0.833350019 0.933861032 1 18.08120884 4.789590351 21.25738515 0.905146981 0.818906717 0.076968416 0.094320755 19206.94444 7999514.431 0.022723109 13.98478317 61601.36715 -4.789590351 -0.086240264 ETYVEQEQGENANDRNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ETYVEQEQGENANDRNDR 18 1 Q9Y2L1;F2Z2C0 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 ; 178.22 8.20E-14 344664000 79167 99552 92576 86301 96765 113365 91642 107977 77511 94967 FALSE TRUE 82292.57429 116649.2816 94988.60661 103371.0802 80316.91986 87037.69681 84458.86058 106529.7449 74721.39425 113573.9654 0.72457252 1.027077651 0.836358987 0.910165282 0.707177209 0.76635254 0.743646313 0.937976803 0.65790953 1 16.79327264 3.28316507 24.99998536 0.802997331 0.882711471 0.08028422 0.118692337 319.9443715 179320.7194 0.031045246 0.042035251 1919.398143 -3.28316507 0.07971414 EVAATEEDVTRLPS(ph)PT(ph)SPFSSLSQDQAATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVTRLPS(0.997)PT(0.601)S(0.401)PFS(0.001)SLSQDQAATSK;EVAATEEDVTRLPS(0.966)PT(0.554)S(0.478)PFS(0.002)SLSQDQAATSK;EVAATEEDVT(0.001)RLPS(0.909)PT(0.613)S(0.473)PFS(0.004)S(0.001)LSQDQAATSK 158.6 5.21E-12 1377830000 304938 283606 333209 276876 406911 409674 384108 345826 378173 293738 TRUE FALSE 316977.1877 332313.1244 341892.7003 331641.2464 337744.4136 314533.4222 354000.6113 341190.7681 364562.6276 351290.3371 0.902322535 0.945978552 0.973248234 0.944065952 0.961439521 0.895365995 1.007715197 0.97125008 1.037781542 1 18.42230437 2.213254544 24.99898015 0.998730258 0.940545199 0.588922845 0.027226129 180.3106164 178121.3386 0.01006738 0.007438051 163.4009374 -2.213254544 -0.058185059 EVAATEEDVTRLPS(ph)PTS(ph)PFSSLSQDQAATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 EVAATEEDVT(0.002)RLPS(0.968)PT(0.067)S(0.944)PFS(0.018)S(0.002)LSQDQAATSK;EVAATEEDVTRLPS(0.998)PT(0.104)S(0.898)PFSSLSQDQAATSK;EVAATEEDVTRLPS(0.794)PT(0.224)S(0.981)PFS(0.001)SLSQDQAATSK 222.95 2.87E-35 1838760000 700120 529539 665010 543230 789160 806870 745690 717320 740300 578720 TRUE FALSE 727761.2782 620483.204 682340.7069 650679.2726 655018.8651 619486.6707 687240.8693 707705.4987 713656.7476 692109.1037 1.051512362 0.896510681 0.985886045 0.94013974 0.946409838 0.895070831 0.992966088 1.02253459 1.031133305 1 19.40063996 2.009948636 24.78846157 1.017232448 0.950148812 0.32728015 0.042538003 192.3323127 479221.134 0.014936357 0.011018566 102.3171974 -2.009948636 -0.067083636 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 EVAATEEDVTRLPS(0.986)PT(0.014)SPFSSLSQDQAATSK;EVAATEEDVT(0.015)RLPS(0.973)PT(0.01)S(0.001)PFSSLSQDQAATSK;EVAATEEDVTRLPS(0.496)PT(0.496)S(0.008)PFSSLSQDQAATSK;EVAAT(0.007)EEDVT(0.085)RLPS(0.476)PT(0.17)S(0.199)PFS(0.02)S(0.02)LS(0.023)QDQAATSK 358.88 4.00E-121 3912120000 650178 498549 632420 510914 765000 747554 710179 654913 685695 511816 TRUE FALSE 675847.5295 584170.9126 648901.3847 611971.2643 634965.5733 573945.9128 654513.3143 646134.9625 661016.9709 612096.5459 1.104151843 0.954377077 1.06012914 0.999795324 1.037361798 0.937672197 1.069297513 1.055609555 1.079922727 1 19.2233997 EVADEVTRPRPSGEEVLQDIQVMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVADEVTRPRPSGEEVLQDIQVMLK 25 2 P33992;B1AHA9 P33992 MCM5 DNA replication licensing factor MCM5 0 113.54 0.0011442 37014000 26484 23184 30636 26720 31809 33003 31892 26772 31570 25293 FALSE TRUE 27529.60877 27165.67165 31434.39933 32005.13625 26402.11754 25338.55342 29392.22171 26413.16513 30433.80187 30248.67909 0.910109453 0.898077948 1.039199075 1.058067235 0.872835388 0.837674708 0.971686123 0.873200613 1.006120029 1 14.88458452 EVADIFNAPS(ph)DDEEFVGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVADIFNAPSDDEEFVGFR 19 0 Q96GN5-5;Q96GN5-2;Q96GN5 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR 130.11 1.91E-05 35703000 42828 45807 53519 59061 43472 56215 64997 51458 44814 38240 TRUE FALSE 44518.88251 53673.99592 54913.74911 70743.08952 36082.64497 43159.9182 59902.3653 50768.28968 43201.15289 45732.39585 0.973464908 1.173653707 1.200762569 1.546892268 0.788995291 0.943749336 1.309845334 1.110116554 0.944650987 1 15.48092888 3.223027759 24.99999807 1.044358339 1.218481344 0.228566934 0.182279925 443.0143131 713026.2088 0.055190944 0.066179205 1671.197428 -3.223027759 0.174123005 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVAETSMHNLLETDIEQVSQLSALVDAQLDYHR 33 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 ;;; 359.22 2.29E-132 387516600 37341.6 84866.7 81022.7 68872.7 77064.3 91539.7 75700.8 85763.2 69405.1 66496.8 FALSE TRUE 38815.8752 99441.89555 83134.21812 82495.5145 63964.93781 70280.99197 69767.17349 84613.68458 66907.22401 79525.5748 0.488092985 1.250439193 1.045377142 1.037345718 0.804331663 0.883753335 0.877292288 1.063980799 0.84132965 1 16.27913127 7.999709604 0.00971761 1.549240434 0.261941756 0.00901785 0.192571973 144998.494 108.9198388 6241.351703 8326.479898 99933156.28 -7.999709604 -1.287298678 EVCFACVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVCFACVDGK 10 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 112.71 0.0050998 0 62228 55765 64663 44914 91808 83903 70384 65441 79067 49799 FALSE TRUE 64684.80949 65342.20496 66348.1709 53797.85515 76202.50895 64417.79981 64867.11817 64563.87043 76221.39411 59556.16059 1.086114498 1.097152743 1.114043791 0.903313018 1.279506741 1.081631173 1.08917562 1.084083826 1.27982384 1 15.86196313 3.23584865 24.9998663 1.130375778 1.058076359 0.149942824 0.098583081 159.6588058 1471791.03 0.027161567 0.033884027 1721.268616 -3.23584865 -0.072299419 EVCGFAPYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EVCGFAPYER 10 0 Q9Y3U8;J3QSB5 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;;;;; 204.86 4.17E-07 3991100000 1817640 2074680 2034180 1880630 2786360 2610830 2103120 2021540 2083660 2701070 FALSE TRUE 1889401.831 2430990.151 2087192.402 2252613.001 2312735.522 2004504.3 1938271.959 1994444.563 2008669.484 3230292.951 0.584901078 0.752560275 0.646130996 0.697340159 0.715952255 0.620533286 0.600029777 0.617419099 0.6218227 1 21.62323358 -1.676720396 2.950902997 1.038767389 0.651282729 0.805070268 0.051556447 10116667.1 11057483.29 2980810.494 0.013544494 0.021051333 1.676720396 -0.38748466 EVDDFFEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVDDFFEQEK 10 0 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 128.17 0.00078358 57728000 58238 33470 49797 36384 54912 68063 64850 48021 51579 24332 FALSE TRUE 60537.28121 39218.21214 51094.75073 43580.6466 45578.07785 52256.39975 59766.88755 47377.35704 49722.68187 29099.38954 2.080362584 1.347733157 1.755870193 1.49764814 1.566289829 1.795790241 2.05388802 1.628122026 1.708719071 1 14.82870127 2.75136937 23.86442085 1.70614974 1.630275747 0 0.308798712 2750.155506 5123896.868 0.088253507 0.093032557 564.1172372 -2.75136937 -0.075873993 EVDDFFEQEKNFLINYYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVDDFFEQEKNFLINYYNR 19 1 Q9Y5X3;Q5QPE5;A0A087WUY5;Q5QPE4 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 228.3 9.75E-20 431790000 398620 369710 453790 298190 546420 529800 400350 425140 494570 416900 FALSE TRUE 414357.8254 433204.8166 465616.1402 357171.092 453539.7236 406761.9792 368969.5209 419441.6937 476770.5223 498583.573 0.831069951 0.868871018 0.93387782 0.71637156 0.909656371 0.8158351 0.740035454 0.841266573 0.956249961 1 18.92747582 1.17425926 3.822255747 0.994829694 0.830186405 0.466897621 0.063235218 0.184720098 4.870612017 0.057559626 0.015369419 14.93685825 -1.17425926 -0.164643289 EVDDKDAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVDDKDAPR 9 1 Q8WXA9-2;Q8WXA9 Q8WXA9-2 SREK1 Splicing regulatory glutamine/lysine-rich protein 1 0 68.893 0.051785 106070000 184600 156510 182190 174880 214000 263100 218630 189900 189090 146290 FALSE TRUE 191888.1505 183389.375 186938.0211 209470.742 177624.3564 201999.0123 201493.2093 187354.7011 182284.6878 174952.7246 1.096800013 1.048222458 1.068505915 1.197299113 1.015270593 1.154591978 1.151700894 1.070887587 1.041908254 1 17.41660561 1.176868521 2.267939894 1.003783548 1.103029114 0.303574757 0.051313172 0.342875371 3.136924021 0.046604424 0.013172971 15.02686973 -1.176868521 0.099245566 EVDDLEQWIAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EVDDLEQWIAER 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;;; 315.5 4.51E-46 1056381000 544236 651923 618234 611924 727943 771250 672665 681030 673899 664965 FALSE TRUE 565722.8575 763885.704 634345.6859 732960.7408 604207.5089 592138.8759 619939.7596 671901.9068 649645.5066 795252.1602 0.711375443 0.960557848 0.797666096 0.921670858 0.75976846 0.744592603 0.77955118 0.844891646 0.816905051 1 19.60105286 -0.008178852 1.427992341 1.000255248 0.818096084 0.362662019 0.073383676 22.50972661 30.11841538 0.087124207 0.019569104 0.981343721 0.008178852 -0.182159164 EVDEDS(ph)EPER ddPTM_MDA-MB-175_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 191.23 8.54E-07 941780000 619020 651280 649120 739240 690230 797430 837500 722220 680830 530940 TRUE FALSE 643459.3876 763132.2737 666036.6005 885459.4656 572904.9511 612238.9677 771854.5616 712539.8222 656327.0613 634967.5275 1.013373692 1.201844568 1.048930176 1.394495667 0.902258661 0.964205162 1.215581157 1.122167341 1.033638781 1 19.27632329 3.201748428 24.99999872 1.059388762 1.15905215 0.182589771 0.125256249 361.4328505 245456.275 0.036623154 0.043774195 1591.286682 -3.201748428 0.099663387 EVDEDS(ph)EPEREVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVDEDSEPEREVR 13 1 Q53GS9;B9A018;Q53GS9-3;F8WC91 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR 210.1 1.98E-08 1825050000 932210 1106960 1184970 894040 1449840 1347270 1025800 1224460 1175610 1301200 TRUE FALSE 969014.3706 1297071.769 1215851.292 1070878.444 1203396.715 1034386.961 945395.1156 1208048.117 1133300.026 1556145.227 0.622701759 0.833515887 0.781322508 0.688160992 0.773319028 0.664711071 0.607523706 0.776308082 0.728273946 1 20.56954528 0.278769821 1.472202297 1.000075282 0.720355441 0.59268798 0.069827331 4.630554432 8.679014068 0.066520866 0.019124472 1.900070963 -0.278769821 -0.279719841 EVDEKPASTPWGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVDEKPASTPWGSK 14 1 A0A1W2PNV4;E9PF58;Q92747;Q92747-2 A0A1W2PNV4;Q92747 ARPC1A Actin-related protein 2/3 complex subunit 1A 0 127.75 0.0002601 0 93786 59285 86509 65066 115350 96484 105810 81184 101460 52393 FALSE TRUE 97488.7437 69466.73758 88763.49561 77935.8606 95742.8482 74077.05323 97516.33572 80095.86127 97808.47442 62658.40523 1.555876556 1.108657926 1.416625516 1.243821325 1.528012848 1.182236493 1.556316912 1.278293965 1.560979314 1 15.93522043 -0.848282452 5.243420502 0.999999662 1.369500749 0.331826172 0.161514075 5.59E-07 1.23E-07 0.136860617 0.032258327 0.141813491 0.848282452 0.369501086 EVDEQMLNVQNK ddPTM_MDA-MB-175_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 ;;;;; 256.9 8.12E-21 1769829000 1509663 1141585 1549379 1199092 1759430 1805742 1668427 1449884 1614499 1067436 FALSE TRUE 1569265.661 1337643.343 1589757.09 1436268.819 1460362.717 1386385.787 1537651.332 1430450.677 1556393.496 1276579.647 1.229273602 1.047833832 1.245325424 1.125091429 1.14396522 1.086015894 1.204508732 1.120533826 1.219190279 1 20.28385212 -1.463576003 3.009967732 0.996280705 1.153376227 0.364627124 0.062293596 13913293.45 20091260.01 451410.0001 0.013734979 0.034389352 1.463576003 0.157095522 EVDETRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVDETRK 7 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 94.006 0.023278 320610000 719600 564090 645280 544920 719340 771600 791010 750080 723390 556690 FALSE TRUE 748010.3637 660968.0695 662096.5269 652703.5496 597066.8437 592407.5937 729008.5693 740026.4045 697355.3352 665762.747 1.123538929 0.992798219 0.994493203 0.980384608 0.89681624 0.889817876 1.094997539 1.11154673 1.047453223 1 19.34464862 2.208599795 24.98450495 1.077739918 0.977183569 0.264969034 0.066683416 244.4266877 203827.4084 0.026129907 0.019300773 161.6589653 -2.208599795 -0.100556348 EVDGEGKPYYEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVDGEGKPYYEVR 13 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;E9PQ14 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;; 125.47 0.00018224 1830160000 2174010 1590370 2076580 1659000 2609900 2462910 2293340 2050030 2226860 1476550 FALSE TRUE 2259841.594 1863503.676 2130697.381 1987145.248 2166270.13 1890936.478 2113582.018 2022552.701 2146715.744 1765851.702 1.279745967 1.055300212 1.206611732 1.125318307 1.226756543 1.07083538 1.19691932 1.145369511 1.215682914 1 20.75193276 -1.105338344 4.083048912 0.999964086 1.164201239 0.360857837 0.067250554 1.94E-05 4.26E-06 0.05657685 0.013332329 0.078462412 1.105338344 0.164237152 EVDGLLTSEPMGS(ph)PVSSK ddPTM_MDA-MB-175_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 EVDGLLTS(0.068)EPMGS(0.932)PVSSK;EVDGLLTS(0.008)EPMGS(0.991)PVS(0.001)SK;EVDGLLTSEPMGS(0.929)PVS(0.071)SK;EVDGLLTSEPMGS(0.996)PVS(0.003)S(0.001)K;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.997)PVS(0.003)SK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(1)PVSSK;EVDGLLTSEPMGS(0.999)PVS(0.001)SK 371.19 1.28E-107 3547403000 4986178 3714618 4652447 4076801 5782985 5742404 5405642 4840771 5188262 3545995 TRUE FALSE 5183036.158 4352574.746 4773693.591 4883180.07 4799995.275 4408817.698 4981933.655 4775888.383 5001537.464 4240764.828 1.222193724 1.026365508 1.125668077 1.151485703 1.131870186 1.039627963 1.174772442 1.126185624 1.179395148 1 22.01589305 4.782587061 22.70594374 1.114481966 1.222194962 0.240720813 0.060213079 14768.57171 7616071.662 0.013426757 5.716025751 60615.97028 -4.782587061 0.107712996 EVDILNHVFDDVESFVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVDILNHVFDDVESFVSR 18 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 0 ; 105.38 0.00047963 1305010000 69231 88649 71379 86250 97584 102311 86339 90143 79812 99865 FALSE TRUE 71964.29334 103873.7762 73239.19538 103309.9926 80996.70654 78550.82079 79571.52358 88934.78053 76939.58171 119431.6347 0.602556379 0.869734191 0.613231122 0.865013636 0.678184693 0.657705314 0.666251649 0.744650115 0.644214424 1 16.8658255 -1.632977595 6.467102602 1.001225833 0.710263786 0.489279937 0.090370358 0.001439205 8.17E-05 0.078843485 0.018511471 0.023282114 1.632977595 -0.290962047 EVDRNEGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVDRNEGLK 9 1 H0Y6T8;Q9NP72;Q9NP72-2;Q5W0J0;A0A087X163;Q9NP72-3 H0Y6T8 RAB18 Ras-related protein Rab-18 0 146.11 8.72E-05 162710000 228780 186790 215920 191290 286300 285010 246000 206360 223270 176450 FALSE TRUE 237812.4111 218869.7295 221547.0526 229126.5911 237634.8283 218820.7469 226717.8772 203594.0817 215234.5563 211021.9992 1.12695554 1.037189157 1.04987657 1.085794808 1.126114003 1.036957036 1.074380293 0.96480027 1.019962645 1 17.68703388 1.751863744 24.99999947 0.993864217 1.074912858 0.571983256 0.032407909 2.856111462 5375.351175 0.014707391 0.008156054 56.47597584 -1.751863744 0.081048641 EVDRPGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EVDRPGSK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;;;; 116.37 0.0020832 8562930000 7415380 5595920 6670110 5221790 7803990 7871500 8086300 7044190 6936390 4971900 FALSE TRUE 7708144.928 6556975.73 6843938.546 6254644.477 6477470.567 6043463.419 7452474.676 6949774.155 6686750.679 5946048.612 1.296347445 1.102745059 1.151006154 1.051899317 1.089373967 1.016383116 1.2533491 1.168805472 1.124570469 1 22.50349983 4.741436928 24.43463506 1.117208758 1.296347536 0.378648623 0.071795455 227.1010442 1929110.978 0.017497268 0.121996012 55136.2123 -4.741436928 0.179138778 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNR 36 1 Q96EK6;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 268.87 3.33E-63 1417220000 24577.6 21315.3 23743.7 29674 32756 34993 29434 19280.6 28875 33170 FALSE TRUE 25547.94263 24976.03696 24362.48033 35543.42863 27188.14682 26866.40607 27126.88617 19022.17509 27835.79439 39669.02642 0.644027468 0.629610535 0.614143641 0.89599952 0.685374693 0.677264065 0.683830399 0.479522106 0.701700972 1 15.27572537 -1.746826487 2.372503185 1.085260364 0.660037865 0.510031429 0.097361628 6635597.955 4487600.428 3313792.674 0.02600699 0.017913214 1.746826487 -0.425222499 EVDYSGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVDYSGLR 8 0 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 157.33 0.0014403 296910000 355480 376540 356910 363430 479940 432570 364340 387140 372470 413940 FALSE TRUE 369514.6249 441207.8159 366211.3678 435315.3693 398359.9702 332112.1732 335782.0788 381951.0215 359064.8775 495043.6176 0.746428419 0.891250387 0.73975576 0.879347503 0.80469671 0.670874568 0.678287866 0.771550239 0.725319678 1 18.91719612 2.973984024 24.40162109 0.747998779 0.817837293 0.024571717 0.097852095 1209.532029 1134478.462 0.027504876 0.029279891 941.8549494 -2.973984024 0.069838514 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_MDA-MB-175_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 288.93 6.80E-47 5076110000 6902110 1416010 2361970 1480660 3936170 5197820 3941400 2457560 2958620 917200 TRUE FALSE 7174610.632 1659198.702 2423524.879 1773530.129 3267101.229 3990705.079 3632462.769 2424620.428 2852139.844 1096907.779 6.540760097 1.512614583 2.209415344 1.616845247 2.978464819 3.638140922 3.311548006 2.210414106 2.60016375 1 20.06501081 4.746635882 24.96181863 2.446148344 6.540762148 0.716514359 0.789875495 551.0189116 1703240.04 0.191392397 2.127664897 55800.21627 -4.746635882 4.094613805 EVEEDEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVEEDEYK 8 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 198.07 0.00032315 2003010000 2608800 1521040 1874960 1639290 2753400 2801100 2318800 1728820 1973030 998970 FALSE TRUE 2711797.438 1782266.788 1923822.998 1963536.669 2285378.051 2150586.976 2137046.397 1705647.996 1902021.036 1194699.045 2.269858212 1.491812348 1.610299268 1.643540838 1.912932015 1.800107722 1.788773839 1.427680053 1.592050352 1 20.18821581 0.746861347 0.692618098 0.996838774 1.777129618 0.549538395 0.211915424 0.809243548 0.783523502 0.212188588 0.078642118 5.582919256 -0.746861347 0.780290843 EVEEEPGIHSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVEEEPGIHSLK 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 151.98 6.71E-05 698320000 480140 461390 488850 447310 635410 659180 528970 478710 527560 435350 FALSE TRUE 499096.2979 540630.1434 501589.8326 535786.5829 527403.2352 506095.435 487507.9492 472293.6755 508573.2187 520648.4972 0.958605087 1.038378381 0.963394373 1.029075443 1.012973701 0.972048201 0.936347558 0.907125783 0.976807234 1 18.98995018 2.476502426 3.758960756 0.943016325 1.001811764 0.262694691 0.033613247 0.221328732 6.922855308 0.011419651 0.009915221 299.5728328 -2.476502426 0.058795439 EVEELEQLTQQLMQDMEHPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 ;;;;;;;; 216.04 6.33E-25 3675726000 1203011.7 1267038 1387860 1299550.3 1490620 1686765 1369647 1306920 1322937 1491293.3 FALSE TRUE 1250507.531 1484641.92 1424028.772 1556597.471 1237244.945 1295039.392 1262290.489 1289402.875 1275324.756 1783483.67 0.701160068 0.832439313 0.798453496 0.872784818 0.693723731 0.7261291 0.707766777 0.722968703 0.715075096 1 20.76626658 -1.196585964 4.374690823 1.000075544 0.752891825 0.618716936 0.058337851 3.80970184 35824153.85 5006.442093 0.01438078 0.063593692 1.196585964 -0.247183719 EVEEQHEVNEQLQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVEEQHEVNEQLQAR 15 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 88.427 0.0066133 0 59978 107290 120620 97845 119560 143150 101280 116120 127330 107890 FALSE TRUE 62345.97775 125716.2229 123763.4563 117198.449 99237.23391 109905.582 93341.40895 114563.6013 122747.4182 129028.9798 0.483193604 0.974325482 0.959191156 0.908311056 0.769108103 0.851789901 0.723414299 0.887890468 0.95131666 1 16.9773356 -4.999999978 0.022234161 2.106529209 6.50E-10 0.18808602 0.134282755 5689.513901 9.567649397 631.1114323 322.9255369 1.00E-05 4.999999978 -2.106529209 EVEERPAPTPWGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVEERPAPTPWGSK 14 1 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ;;; 192.32 3.54E-07 2957230000 1898730 1501920 1782660 1586520 2112860 2176350 2191590 1804650 2083670 1376040 FALSE TRUE 1973693.327 1759863.077 1829117.584 1900328.921 1753716.812 1670925.695 2019807.449 1780461.619 2008679.124 1645648.692 1.199340622 1.069403868 1.111487277 1.154759779 1.06566901 1.015359902 1.227362473 1.081920842 1.220600201 1 20.65022496 4.756592808 23.40492309 1.109788586 1.199340807 0.127184846 0.073111225 3327.366527 4318591.976 0.016215738 0.471181209 57094.30733 -4.756592808 0.089552221 EVEERS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;EVEERS(1)R 109.44 0.0042562 835544000 716312 933458 917408 612808 1198270 1191210 601730 888587 995817 1388490 TRUE FALSE 744592.5509 1093772.15 941316.4061 734019.5934 994588.4934 914569.5305 554564.8303 876676.9447 959977.7407 1660538.031 0.448404395 0.658685396 0.566874343 0.442037207 0.598955564 0.550766988 0.333966955 0.527947526 0.578112469 1 20.66321933 0.719980616 2.865378417 0.999948449 0.516179317 0.737009598 0.086222747 1.034558 9.955631422 0.083026604 0.021823289 5.247840365 -0.719980616 -0.483769132 EVEEYKNFRPDDPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVEEYKNFRPDDPTR 15 2 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ;; 99.796 0.0013522 683000000 847180 786630 877570 591600 1229980 1036600 802280 854330 968580 823620 FALSE TRUE 880627.3206 921727.5834 900440.1951 708616.7143 1020908.439 795865.3598 739395.1972 842879.1038 933720.995 984992.5698 0.894044633 0.935771103 0.914159378 0.719413258 1.036463086 0.807991232 0.750660685 0.855721281 0.947947247 1 19.90975332 3.951426998 24.99826657 0.860639711 0.917423089 0.022942866 0.096787038 1070.887469 551136.3216 0.024001747 0.043271152 8941.842137 -3.951426998 0.056783378 EVEGERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 139.68 0.0042901 1473144000 1657589 1901342 1912193 1658102 2091062 2248300 1612163 1864560 1864431 2405020 FALSE TRUE 1723031.894 2227882.698 1962026.32 1986069.627 1735624.028 1726166.398 1485797.451 1839568.623 1797330.493 2876237.622 0.599057561 0.774582281 0.682150287 0.690509578 0.603435549 0.600147354 0.516576739 0.639574633 0.624889431 1 21.45575144 -1.407735065 5.443400435 1.000216998 0.636594361 0.736833895 0.065122867 0.000182535 1.99E-05 0.067112662 0.015809284 0.03910794 1.407735065 -0.363622638 EVEGLKDLLVGPGVELLLT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVEGLKDLLVGPGVELLLTPR 21 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 EVEGLKDLLVGPGVELLLT(1)PR;EVEGLKDLLVGPGVELLLT(1)PR 134.67 1.27E-05 388730000 491140 393580 503340 359500 710790 650110 520210 540990 637980 549850 TRUE FALSE 510530.5864 461174.3034 516457.4539 430608.027 589970.1697 499131.805 479434.5809 533738.9139 615019.2244 657582.58 0.776374865 0.701317701 0.78538798 0.654834906 0.897180351 0.759040492 0.729086499 0.811668268 0.935272988 1 19.32681256 1.218466878 2.24625287 0.998166303 0.757918647 0.66542894 0.059528637 0.161641604 1.403447267 0.052647079 0.015072062 16.53738656 -1.218466878 -0.240247656 EVEPEPTEDKDLEADEEDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;; 250.83 6.63E-31 2570090000 3150730 1906970 2500400 2034370 3192020 3420210 3477800 2493850 2841400 1435450 FALSE TRUE 3275123.253 2234477.263 2565562.478 2436762.314 2649441.581 2625918.061 3205200.948 2460424.02 2739138.569 1716698.944 1.907802917 1.301612767 1.494474315 1.419446504 1.543335009 1.529632246 1.867072243 1.433229762 1.5955847 1 20.71120563 -1.289716487 4.917132702 0.999852788 1.554132083 0.46845169 0.180425157 0.000329363 4.76E-05 0.163198154 0.038453963 0.05131963 1.289716487 0.554279295 EVESPYEVHDYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 155.08 1.36E-06 228200000 206262 984050 628990 821770 488310 919490 413910 698450 500190 1047910 FALSE TRUE 214405.383 1153052.933 645381.9961 984313.6533 405307.2406 705952.3825 381466.6526 689088.4202 482188.2596 1253227.901 0.171082516 0.920066439 0.514975764 0.785422709 0.323410642 0.563307266 0.304387296 0.549850845 0.384757042 1 20.25721736 -1.386456767 5.598280372 1.000178728 0.513615901 0.327115442 0.2137179 0.000437787 4.80E-05 0.190021218 0.044772219 0.041071752 1.386456767 -0.486562827 EVESRLS(ph)PGESAYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVESRLSPGESAYQK 15 1 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 EVES(0.465)RLS(0.535)PGESAYQK 60.938 0.081762 0 53678 78780 57141 52165 78227 81298 61516 71831 69003 76480 TRUE FALSE 55797.24889 92309.85218 58630.1414 62483.0813 64930.00248 62417.77158 56694.21518 70868.22294 66519.59551 91464.7917 0.610040736 1.009239189 0.641013228 0.68313807 0.709890672 0.682424028 0.61984742 0.774814239 0.727269961 1 16.48092888 0.25475778 1.365305874 1.000172931 0.718402138 0.379620372 0.108486169 6.40320641 10.63619049 0.100872723 0.029161281 1.797867905 -0.25475778 -0.281770793 EVFDNDGKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVFDNDGKPR 10 1 Q08209-3;Q08209-2;Q08209;Q08209-4 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 ; 114.86 0.0011849 354850000 561560 477850 497650 467950 660770 635760 635330 541080 496040 416640 FALSE TRUE 583730.8224 559917.0203 510619.1678 560509.1133 548452.5514 488114.375 585531.1745 533827.7076 478187.6173 498272.6309 1.171508901 1.123716186 1.024778678 1.124904477 1.10070776 0.979613057 1.175122088 1.071356672 0.959690715 1 18.92657581 7.99999981 0.083871218 0.928554574 1.490518986 0.308592377 0.061881143 249.8433362 1.518130177 1.449991478 16.21315547 99999956.31 -7.99999981 0.561964412 EVFEDAAEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVFEDAAEIR 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 182.39 4.15E-06 4156470000 2850220 2883720 2909740 2743970 3143220 3430430 3157110 2983340 3013500 2785750 FALSE TRUE 2962748.886 3378976.478 2985570.215 3286719.076 2608936.587 2633764.621 2909647.469 2943353.207 2905044.724 3331564.376 0.889296604 1.014231183 0.896146638 0.986539267 0.783096555 0.790548921 0.87335772 0.883474811 0.871976164 1 21.66776834 3.254628256 24.99965445 0.859847033 0.947787064 0.255568054 0.065748073 300.7867267 467991.381 0.017527096 0.023659257 1797.331791 -3.254628256 0.087940031 EVFEFRPELVNDDDEEADDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 ; 221.48 3.91E-25 345940000 289430 330260 317220 358120 338720 373640 401220 339860 330950 270970 FALSE TRUE 300856.9199 386979.5859 325487.0138 428955.0671 281144.4954 286867.7726 369771.328 335304.7326 319039.1741 324061.3835 0.928394851 1.194155199 1.00439926 1.323684613 0.867565559 0.885226649 1.141053352 1.034695122 0.98450229 1 18.30590759 3.205905936 24.99999918 0.99648526 1.110747693 0.204161665 0.121809831 336.9372798 257953.9175 0.034757232 0.041545328 1606.593242 -3.205905936 0.114262433 EVFQIASNDHDAAINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVFQIASNDHDAAINR 16 0 Q9UKG1;C9JAB0 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 178.22 2.82E-09 343570000 256510 275990 273940 282670 333750 355830 294650 310430 296540 299030 FALSE TRUE 266637.2129 323389.1356 281079.1014 338581.2823 277019.2942 273193.8752 271554.5631 306269.1936 285867.5833 357619.2032 0.745589752 0.904283474 0.785973177 0.946764825 0.774620858 0.763923952 0.759339992 0.856411487 0.799363068 1 18.44806468 -1.735718016 2.635832573 1.036503416 0.81845602 0.431504475 0.063552546 11691748.75 9247290.164 2795407.633 0.014625213 0.018377312 1.735718016 -0.218047396 EVGVYEALKDDSWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVGVYEALKDDSWLK 15 1 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;; 152.68 2.54E-06 3233440000 2618910 1745688 2417502 1722351 2992710 2839760 3174510 2196228 2425760 1531135 FALSE TRUE 2722306.589 2045496.334 2480504.088 2063026.887 2484010.223 2180268.777 2925683.611 2166791.156 2338457.371 1831131.588 1.486679934 1.117066817 1.354629074 1.126640434 1.356543811 1.190667449 1.597746241 1.18330718 1.277055885 1 20.80430404 0.569532852 1.608191368 1.000419715 1.298970905 0.271823871 0.14773004 2.599551059 8.221932819 0.129132442 0.036910338 3.71135803 -0.569532852 0.29855119 EVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVHDELEDLPSPPPPLSPPPTTSPHK 26 0 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 EVHDELEDLPS(0.982)PPPPLS(0.654)PPPT(0.13)T(0.121)S(0.113)PHK;EVHDELEDLPS(1)PPPPLS(0.996)PPPT(0.003)T(0.001)SPHK;EVHDELEDLPS(1)PPPPLS(0.991)PPPT(0.003)T(0.003)S(0.003)PHK;EVHDELEDLPS(1)PPPPLS(0.997)PPPT(0.001)T(0.001)S(0.001)PHK 119.61 0.00016642 578643000 322225 374371 396883 360045 464497 520502 454751 427950 433885 364028 TRUE FALSE 334946.6918 438666.307 407226.097 431260.8264 385541.9659 399623.2988 419106.4283 422214.0302 418269.5636 435352.3169 0.769369264 1.007612203 0.935394349 0.990601886 0.885586112 0.917930796 0.962683353 0.969821485 0.960761083 1 18.73182388 4.748584579 24.88278824 0.955566638 0.769369156 0.71402467 0.035933298 713.4315725 1770935.238 0.008420944 0.115305252 56051.1566 -4.748584579 -0.186197482 EVHELYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVHELYK 7 0 P10155-3;P10155-5;P10155-4;P10155;D6RE09;H0Y9N5 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;; 102.71 0.0085387 629560000 1415380 1406400 1553940 1432830 1776060 1883510 1745370 1513080 1590790 1340730 FALSE TRUE 1471260.295 1647938.26 1594436.953 1716239.497 1474165.956 1446093.347 1608563.339 1492799.637 1533537.779 1603420.374 0.917576151 1.027764326 0.994397339 1.070361538 0.919388315 0.901880362 1.003207496 0.931009523 0.956416548 1 20.61272128 3.209882974 24.99977346 0.94863283 1.003747235 0.219356163 0.046428832 287.6229367 250734.8573 0.012966017 0.015499978 1621.373138 -3.209882974 0.055114405 EVHNRS(ph)PVSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVHNRSPVSFR 11 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 EVHNRS(1)PVSFR 88.282 0.0079304 142680000 79367 52031 62494 61180 63054 94244 77517 67439 62506 61298 TRUE FALSE 82500.47044 60966.91951 64122.64498 73281.2214 52336.1036 72357.25928 71441.01499 66535.09051 60256.42127 73308.16948 1.125392586 0.83165246 0.874699852 0.9996324 0.713919117 0.987028592 0.974530063 0.907608129 0.821960522 1 16.16168636 4.749942797 24.45566896 0.901152612 1.125392766 0.363687357 0.088953627 1349.113507 2898621.245 0.020109887 0.309809668 56226.72618 -4.749942797 0.224240154 EVIEIEDAS(ph)PTKCPITTK ddPTM_MDA-MB-175_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(0.968)PT(0.032)KCPITTK;EVIEIEDAS(0.989)PT(0.011)KCPITTK 135.86 4.54E-06 295120000 446740 228598 309640 219124 403970 395930 409600 311710 356400 188755 TRUE FALSE 464377.6402 267857.9283 317709.4728 262466.0732 335303.3237 303981.2579 377494.4817 307532.0373 343573.2336 225737.9283 2.057153814 1.18658805 1.407426192 1.162702587 1.485365469 1.346611357 1.672268743 1.36234101 1.522000473 1 17.78428931 4.748518951 24.74497542 1.37506685 2.057154243 0.562911989 0.185849686 870.2857445 2162479.841 0.041375206 0.555925825 56042.6872 -4.748518951 0.682087393 EVIELPVKHPELFEALGIAQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVIELPVKHPELFEALGIAQPK 22 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0;J3QRR3 P62195-2 PSMC5 26S protease regulatory subunit 8 0 70.99 0.010141 374990000 544720 378870 537790 370150 656700 576940 587930 507390 589660 383710 FALSE TRUE 566225.9662 443937.9753 551805.2492 443364.5652 545074.3686 442954.4286 541846.5103 500589.267 568438.2518 458890.6279 1.233901788 0.96741565 1.202476616 0.966166093 1.187808893 0.965272336 1.180774846 1.090868361 1.238722731 1 18.80779082 EVIITPNSAWGGEGSLGCGIGYGYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVIITPNSAWGGEGSLGCGIGYGYLHR 27 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ; 238.72 4.21E-45 1369940000 521170 654030 596040 581760 660990 714130 533010 597520 652910 766590 FALSE TRUE 541746.194 766354.5649 611573.2921 696830.3916 548635.1559 548284.1302 491231.2834 589511.2217 629411.8966 916788.6332 0.590917224 0.83591194 0.667082106 0.760077477 0.598431455 0.598048569 0.53581738 0.643017595 0.686539813 1 19.80622963 -1.682214596 6.002349035 1.004256151 0.656065341 0.602308145 0.083531485 0.004927542 0.000260882 0.08376766 0.019570474 0.020786693 1.682214596 -0.34819081 EVIKPYDWTYTTDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVIKPYDWTYTTDYK 15 1 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 183.7 4.51E-07 1148760000 1089420 615280 870670 698980 1107850 988690 1151840 977740 1025780 568540 FALSE TRUE 1132431.143 720949.5538 893360.3755 837236.1578 919538.0527 759081.7312 1061555.771 964634.9946 988862.3782 679934.5276 1.665500275 1.060322023 1.313891763 1.231348202 1.352392054 1.116404154 1.561261751 1.418717473 1.454349409 1 19.37503631 2.237041699 24.99930789 1.402172136 1.280796811 0.007496848 0.205510434 109.3836713 1800252.135 0.068640913 0.053443346 172.6003605 -2.237041699 -0.121375325 EVIKS(ph)PTASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVIKSPTASR 10 1 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 EVIKS(0.974)PT(0.026)ASR;EVIKS(0.965)PT(0.035)ASR 144.57 1.94E-05 497550000 494580 369870 464250 381950 593860 572480 474690 439290 463900 382180 TRUE FALSE 514106.4003 433392.2953 476348.7364 457498.57 492915.8893 439530.196 437482.5574 433402.0361 447204.3296 457060.8537 1.124809522 0.948215739 1.042199813 1.000957676 1.078446962 0.961644806 0.957164793 0.948237051 0.978434985 1 18.80202673 2.709905765 23.6063805 0.963488017 1.031959019 0.362960131 0.045490383 378.1282556 311507.8861 0.013702426 0.01292159 512.750113 -2.709905765 0.068471002 EVLAELEALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVLAELEALER 11 0 Q16822;Q16822-3;H0YML5 Q16822 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 0 ; 120.09 0.0011599 20741900 35001 45882 45936 51639 57282 67804 45769 48751 48212 59286 FALSE TRUE 36382.86651 53761.87659 47133.1299 61853.04007 47545.2261 52057.54858 42181.50618 48097.57259 46476.85954 70901.9566 0.513143336 0.758256601 0.664764869 0.872374234 0.670577067 0.734218787 0.594927252 0.678367352 0.655508843 1 16.11353782 -1.389921806 3.435473415 1.002499251 0.68652544 0.524402714 0.090646472 21624462.99 32393815.97 541690.9084 0.020696796 0.040745363 1.389921806 -0.315973811 EVLAGRPLFPHVLCHNCAVEFNFGQK ddPTM_MDA-MB-175_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 55.051 0.061629 1656200000 387940 307730 343690 272510 422030 393670 302600 333100 320790 267630 FALSE TRUE 403256.1708 360580.2337 352646.8437 326411.6646 350293.4913 302246.1086 278881.4213 328635.3393 309244.8306 320066.9744 1.25991184 1.126577443 1.101790787 1.019823008 1.0944381 0.944321448 0.871322078 1.026770537 0.966187877 1 18.2880143 5.233888363 0.509528598 0.963389388 1.619139855 0.753051153 0.051610711 3.445187501 0.472885582 0.029842906 1.499572969 171351.6786 -5.233888363 0.655750468 EVLAS(ph)PDRLWGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVLASPDRLWGSR 13 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 EVLAS(1)PDRLWGSR;EVLAS(1)PDRLWGSR 191.51 2.12E-06 264310000 132483 165582 148627 143145 154225 185748 160196 172257 147746 161138 TRUE FALSE 137713.5311 194019.4205 152500.3417 171458.6538 128009.8896 142610.842 147639.4189 169948.1767 142428.6503 192709.9059 0.714615735 1.006795263 0.791346667 0.889724132 0.664262114 0.740028601 0.766122625 0.881886044 0.739083181 1 17.55607121 -1.187362163 7.160393495 1.000000294 0.806323581 0.279704991 0.096022259 4.37E-07 4.96E-08 0.090179544 0.02125549 0.064958777 1.187362163 -0.193676713 EVLASHDSSVVPLDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVLASHDSSVVPLDAR 16 0 Q9Y2V7;Q9Y2V7-2 Q9Y2V7 COG6 Conserved oligomeric Golgi complex subunit 6 0 113.59 0.0018403 0 20314 66031 51564 65407 55731 83281 46666 64381 51745 73193 FALSE TRUE 21116.01241 77371.3106 52907.8002 78344.30938 46257.86453 63940.24989 43008.19698 63518.078 49882.70756 87533.76699 0.241232762 0.883902444 0.60442732 0.895018141 0.528457373 0.730463821 0.491332642 0.725640861 0.569868169 1 16.41755204 -1.379681562 2.958554039 1.005155838 0.644566688 0.262478708 0.184605043 37382874.56 45280149.57 1658460.284 0.039214233 0.041717516 1.379681562 -0.36058915 EVLDEDT(ph)DEEKETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK 298.34 5.94E-44 961110000 2063370 518460 855440 537780 1402580 1627480 1342970 906750 1033090 405377 TRUE FALSE 2144833.441 607501.4719 877733.4692 644151.2789 1164169.953 1249522.435 1237704.502 894596.4994 995909.2927 484802.8617 4.424135273 1.253089699 1.810495644 1.328687039 2.401326486 2.577382547 2.553005768 1.845278916 2.054256217 1 18.88703869 -1.716723142 0.331261886 3.24E-13 2.273687742 0.173347064 0.842786341 53.10923347 3.12330794 43.72500491 0.712738999 0.019198923 1.716723142 2.273687742 EVLDEDTDEEKETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ; 121.82 0.0001028 76299000 328700 148364 184852 131000 247870 279860 255690 171018 210070 120974 FALSE TRUE 341677.3298 173844.3629 189669.395 156911.409 205737.1459 214866.7563 235648.3497 168725.7834 202509.6217 144676.5391 2.361663694 1.201607143 1.310989302 1.084567062 1.422049126 1.485152725 1.62879449 1.166227672 1.399740573 1 17.14247147 4.742396482 24.97788678 1.316438326 2.361664101 0.75199482 0.182702084 182.4856164 1188237.855 0.042868053 0.32393121 55258.16797 -4.742396482 1.045225774 EVLEALGEVMVSRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVLEALGEVMVSRPR 15 1 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 220.21 1.55E-12 142000000 97587 102810 101870 110680 113580 140540 102020 96842 105750 110090 FALSE TRUE 101439.8101 120466.8177 104524.8159 132572.1737 94273.71217 107901.7149 94023.40582 95543.99139 101944.0782 131660.0277 0.770467787 0.914983992 0.793899392 1.00692804 0.716038982 0.819548019 0.714137825 0.725687159 0.774297864 1 17.00645788 3.195577926 24.99999952 0.770641027 0.869124101 0.112817418 0.099845216 218.1022639 126854.008 0.026694909 0.031906735 1568.837372 -3.195577926 0.098483074 EVLEGLDYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVLEGLDYLHR 11 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 0 ;;; 222.74 7.45E-12 1260340000 1266450 1290170 1312990 1495390 1352180 1642290 1652080 1367690 1331670 1046050 FALSE TRUE 1316450.424 1511746.661 1347207.598 1791173.679 1122336.927 1260893.037 1522585.653 1349358.353 1283743.457 1251003.47 1.052315566 1.208427233 1.076901568 1.431789537 0.897149332 1.007905307 1.217091471 1.078620792 1.02617098 1 20.25465436 3.209716402 24.99999968 1.05504139 1.185259951 0.271386394 0.121885414 327.5812625 283921.988 0.035019851 0.041863486 1620.751387 -3.209716402 0.130218562 EVLEGLEYLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVLEGLEYLHK 11 0 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 0 ; 168.22 1.83E-05 321710000 351870 298940 350470 302900 431200 424850 392050 350930 376890 296920 FALSE TRUE 365762.0993 350280.6196 359603.5361 362812.7159 357904.778 326185.0262 361320.0966 346226.3574 363325.8025 355095.7891 1.030037839 0.986439801 1.012694454 1.021731958 1.00791051 0.9185832 1.017528531 0.975022425 1.023176883 1 18.43784873 2.966771798 24.999427 0.984663788 1.011343091 0.155639401 0.028874853 1125.638413 846880.2769 0.008435885 0.008952113 926.3429438 -2.966771798 0.026679303 EVLHGNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EVLHGNQR 8 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 136.27 0.00079823 7530580000 3504160 3921570 3993570 3664100 4675730 4626990 4040060 4018540 3899770 4558850 FALSE TRUE 3642506.943 4595069.142 4097645.715 4388848.044 3880951.085 3552441.695 3723389.54 3964678.044 3759418.039 5452069.373 0.668096221 0.842811936 0.751576224 0.804987564 0.711830833 0.65157676 0.682931431 0.727187747 0.689539656 1 22.37837249 -0.944767073 4.322111389 1.000007008 0.727687915 0.673336107 0.057318091 5313267.74 3688338.414 328.8007597 0.013825982 0.113561973 0.944767073 -0.272319092 EVLTPESDISIAHVLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVLTPESDISIAHVLAAR 18 0 Q17RN3 Q17RN3 FAM98C Protein FAM98C 0 ; 162.59 3.52E-11 127841000 26160 33257 39164 33479 39762 42016 31921 41864 30716 41543 FALSE TRUE 27192.817 38968.63105 40184.64601 40101.04628 33003.26944 32258.42076 29418.94861 41302.88156 29610.53716 49682.55546 0.547331287 0.784352389 0.808828081 0.807145404 0.664282848 0.649290691 0.592138394 0.831335691 0.595994648 1 15.60045176 -1.673163976 2.701738517 1.038097492 0.708959569 0.451759724 0.099177881 23252772.99 19711041.46 6076122.426 0.02342617 0.021224429 1.673163976 -0.329137923 EVLYDS(ph)EGLS(ph)GEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 EVLYDS(1)EGLS(1)GEER 171.14 4.48E-06 553680000 452230 487910 490950 482360 505210 568150 484520 478490 459760 458360 TRUE FALSE 470084.3896 571704.7471 503744.5603 577769.3683 419334.5847 436205.7729 446542.0563 472076.6242 443213.3274 548166.8662 0.857557103 1.042939262 0.918962074 1.054002721 0.764976161 0.795753629 0.814609718 0.861191461 0.808537244 1 19.0642556 3.234329881 24.9999725 0.83208416 0.970163201 0.378325008 0.079594801 97.49850306 576131.3094 0.021018678 0.025972415 1715.259689 -3.234329881 0.138079041 EVMDWEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVMDWEER 8 0 P45984-3;P45984-2;P45984-4;P45984;J3KNK1 P45984-3 MAPK9 Mitogen-activated protein kinase 9 0 83.005 0.048721 0 155120 234330 225390 221790 257980 292690 216850 217400 210260 223670 FALSE TRUE 161244.2574 274574.3547 231263.8486 265659.4 214128.6517 224717.1833 199852.7304 214486.1086 202692.7837 267493.8541 0.60279612 1.026469769 0.864557615 0.99314207 0.800499333 0.840083538 0.747130176 0.801835651 0.757747442 1 18.02914622 EVMNADDPDLQRPDEEAIKEITEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVMNADDPDLQRPDEEAIKEITEK 24 2 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 217.7 6.91E-33 99957000 264450 110920 185520 115810 281550 207420 232530 184940 217980 112670 FALSE TRUE 274890.6902 129969.6472 190354.8036 138716.8723 233692.2316 159249.8485 214303.691 182461.1818 210134.9424 134745.5293 2.040072807 0.964556285 1.412698474 1.029472911 1.73432271 1.181856269 1.590432663 1.354116777 1.559494727 1 17.03987788 -1.528400524 3.017306933 0.984661496 1.408192179 0.144884021 0.309217044 29537146.23 31899948.25 3691713.253 0.070827048 0.029620984 1.528400524 0.423530683 EVMSLHEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVMSLHEASR 10 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 123.79 0.00045266 190930000 54682 125620 135790 139810 126130 165500 127200 125240 104390 165790 FALSE TRUE 56840.88758 147194.2578 139328.799 167464.0007 104690.4677 127065.1332 117229.7316 123561.3627 100633.0243 198273.3763 0.286679375 0.742380347 0.702710579 0.844611636 0.528010717 0.640858271 0.591253016 0.623186859 0.507546834 1 17.59713144 -1.914473048 2.430520138 1.235673979 0.619586973 0.400427088 0.143408079 15039482.06 7478308.18 20184844.01 0.032857562 0.012176626 1.914473048 -0.616087006 EVMVDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVMVDDR 7 0 P51149;C9J592;C9J8S3;C9IZZ0;C9J4V0;C9J7D1 P51149 RAB7A Ras-related protein Rab-7a 0 79.116 0.077928 193490000 433400 503270 514130 612660 569630 649050 517130 491840 493870 578690 FALSE TRUE 450510.9667 589702.7076 527528.6502 733842.3194 472804.4961 498317.9739 476595.9993 485247.6893 476095.7152 692073.2258 0.650958526 0.852081378 0.76224398 1.060353575 0.6831712 0.720036487 0.688649671 0.70115079 0.687926794 1 19.40056517 EVNAVDSEHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVNAVDSEHEK 11 0 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 102.73 0.0028291 402910000 276520 659600 586460 689600 518500 822410 555230 568800 543640 601830 FALSE TRUE 287437.2231 772881.169 601743.6294 826000.8217 430365.5552 631417.7412 511709.6218 561176.1664 524074.5026 719747.0658 0.399358659 1.0738233 0.836048743 1.147626522 0.597939993 0.87727727 0.710957566 0.779685244 0.728137046 1 19.45713048 EVNKFQMAYSNLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVNKFQMAYSNLLR 14 1 P37108 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ; 201.3 1.65E-08 1270220000 631300 771840 671340 719350 1177300 1071460 858370 824210 1022340 1048140 FALSE TRUE 656224.2115 904397.5159 688835.6719 861635.283 977182.9665 822629.6531 791088.7165 813162.8131 985546.1831 1253502.965 0.523512293 0.721496112 0.549528554 0.687381926 0.779561751 0.656264625 0.631102389 0.648712317 0.786233627 1 20.25753398 -5 0.207956874 2.621147059 0.612592776 0.680582951 0.073132421 84.82629786 0.844661347 57.14464237 0.158049654 1.00E-05 5 -2.008554283 EVPAESVTVWIDPLDATQEYTEDLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVPAESVTVWIDPLDATQEYTEDLRK 26 1 Q9NX62;H0YB38 Q9NX62 IMPAD1 Inositol monophosphatase 3 0 229.66 1.24E-34 16649000 25201 21155 25074 28476 52047 40977 38572 24108 26513 35000 FALSE TRUE 26195.95494 24788.20669 25727.44904 34108.46781 43200.06953 31460.71276 35548.62585 23784.87169 25558.80231 41857.57988 0.625835393 0.592203533 0.614642536 0.814869562 1.032072797 0.751613276 0.849275709 0.568233323 0.610613475 1 15.35320128 3.747004353 22.48372609 0.783008356 0.609024716 0.281257788 0.138548203 247.1750042 658160.2219 0.038680068 0.06808297 5584.757926 -3.747004353 -0.17398364 EVPAHSTEVGR ddPTM_MDA-MB-175_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 ;;; 208.17 2.05E-08 2147780000 459341 830680 760450 789880 777660 899340 755210 779350 639220 815880 FALSE TRUE 477476.1374 973342.8282 780267.9517 946115.9064 645473.631 690481.9146 696014.6668 768904.088 616214.5971 975736.065 0.489349686 0.99754725 0.79967112 0.969643268 0.661524826 0.707652345 0.713322682 0.788024667 0.631538199 1 19.89613143 3.204091343 24.99995542 0.738813065 0.82613292 0.031882299 0.159324791 516.5325293 374630.391 0.042818091 0.051179736 1599.894491 -3.204091343 0.087319855 EVPENETPVDTNLIELDTNDDDIVFEDFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EVPENETPVDTNLIELDTNDDDIVFEDFAR 30 0 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 246.69 6.06E-46 94890600 54979.7 68479.2 69400.6 74357.4 68669.1 76630.4 66452.5 67252.8 65024 73668.8 FALSE TRUE 57150.34101 80239.96991 71209.23665 89065.07179 56996.75091 58834.15094 61243.77941 66351.38622 62683.79894 88102.79089 0.648677987 0.910754008 0.80825177 1.010922252 0.646934681 0.667789866 0.695140061 0.75311333 0.711484827 1 16.4269001 4.806219346 21.263708 0.784487163 0.648667801 0.102715588 0.12691029 49367.64406 15510483.03 0.030246188 96.08969789 64005.80238 -4.806219346 -0.135819362 EVPIPEHIDIYHLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVPIPEHIDIYHLTR 15 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;; 151.9 1.69E-06 1167270000 273290 384825 358843 356772 354783 430885 364673 389283 358197 406092 FALSE TRUE 284079.7002 450915.7002 368194.7434 427340.4367 294477.1124 330818.4889 336088.9774 384065.2981 345305.5599 485657.9523 0.584937812 0.928463537 0.75813593 0.8799206 0.606346732 0.681175892 0.692028156 0.790814392 0.711005674 1 18.88958106 -1.633571 4.402006369 1.006251568 0.743544641 0.366774189 0.103355078 0.006165251 0.000513204 0.097296089 0.022477339 0.023250324 1.633571 -0.262706927 EVPTADPTGVDRDDGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVPTADPTGVDRDDGPR 17 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ; 111.22 0.00047433 2091000000 1145250 1437030 1341750 1298720 1521420 1619420 1307220 1406780 1371340 1511110 FALSE TRUE 1190465.354 1683828.724 1376717.107 1555602.94 1262809.572 1243334.248 1204756.681 1387924.415 1321985.741 1807183.073 0.658740873 0.931742196 0.76180279 0.860788795 0.698772355 0.687995736 0.666648941 0.768004325 0.731517333 1 20.78531123 -1.277422498 3.14139971 1.001315749 0.754420169 0.44930648 0.082394271 12993415.66 17822723.56 163058.2724 0.0195186 0.052793141 1.277422498 -0.24689558 EVPVY(ph)IGEDS(ph)T(ph)IARESY(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVPVYIGEDSTIARESYR 18 1 H0YL34;A0A075B7B1;O15061-2;O15061 H0YL34 SYNM Synemin 4 EVPVY(0.816)IGEDS(0.816)T(0.835)IARES(0.717)Y(0.816)R 57.009 0.038761 364620000 10477 7123.7 13245 7627.2 20820 12767 12332 13446 14050 11495 TRUE FALSE 10890.64005 8347.14006 13590.17558 9135.837395 17281.02384 9802.057736 11365.38562 13265.77836 13544.34324 13747.22516 0.792206421 0.607187266 0.988575907 0.66455865 1.257055415 0.713020818 0.826740341 0.96497862 0.985241973 1 13.74685282 4.235311893 24.99945203 0.916256909 0.69969683 0.233054318 0.162882033 106.5121245 819655.3111 0.037824263 0.087438584 17191.42563 -4.235311893 -0.216560079 EVPWS(ph)PSAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVPWSPSAEK 10 0 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWS(0.998)PS(0.002)AEK;EVPWS(0.999)PS(0.001)AEK;EVPWS(0.999)PS(0.001)AEK 206.36 1.59E-07 1281330000 2173170 1657000 2033160 1686710 2502230 2603690 2356930 2002560 2148720 1517950 TRUE FALSE 2258968.43 1941576.86 2086145.82 2020336.204 2076901.838 1999022.457 2172187.668 1975718.959 2071387.987 1815363.24 1.244361668 1.069525271 1.149161652 1.112910166 1.144069569 1.101169404 1.196558144 1.08833258 1.141032242 1 20.79182682 -5 0.271617296 0.064498196 1.144155624 0.426805699 0.048673923 193.3892065 1.874336051 101.5133765 0.053172345 1.00E-05 5 1.079657428 EVPWS(ph)PSAEKAS(ph)PQENGPAVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 2 EVPWS(0.992)PS(0.288)AEKAS(0.72)PQENGPAVHK 75.71 0.015522 96674000 77471 101850 78825 89080 92469 139990 86507 89625 95059 112210 TRUE FALSE 80529.6149 119341.9452 80879.24426 106699.7581 76751.15241 107479.4441 79726.3553 88423.72347 91637.84516 134195.4011 0.600092211 0.889314717 0.602697586 0.795107412 0.571935787 0.800917492 0.594106464 0.658917688 0.682868745 1 17.03397571 -1.116726401 12.30973884 0.999999944 0.688508347 0.459141047 0.101445337 0 0 0.08788046 0.020713623 0.076431714 1.116726401 -0.311491596 EVPWSPSAEKAS(ph)PQENGPAVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVPWSPSAEKASPQENGPAVHK 22 1 Q5JSZ5;Q5JT00;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 EVPWSPSAEKAS(1)PQENGPAVHK 224.83 3.98E-26 174970000 92521 50224 66952 53906 92390 89047 83713 67058 89381 46759 TRUE FALSE 96173.80052 58849.58131 68696.82412 64568.44591 76685.5808 68367.18377 77151.35632 66159.19719 86164.19527 55920.53079 1.719829894 1.052378804 1.228472319 1.154646513 1.371331418 1.222577518 1.379660658 1.183093155 1.540832929 1 15.77109043 -2.177110359 2.502443862 0.181635934 1.294863888 0.195183683 0.188340236 7724342.104 1994187.123 36356375.58 0.043071161 0.006651041 2.177110359 1.113227954 EVQAEQPSSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSS(0.007)S(0.993)PR;EVQAEQPSSSS(1)PR;EVQAEQPSSSS(1)PR 287.03 5.16E-33 2093540000 2467600 3048830 2792660 2916970 2910290 3477490 2877810 2935000 2775280 2944780 TRUE FALSE 2565022.753 3572442.836 2865439.014 3493937.96 2415599.945 2669895.649 2652239.732 2895661.126 2675398.215 3521753.26 0.728336872 1.014393279 0.813639912 0.99210186 0.685908344 0.758115476 0.753102088 0.822221465 0.759677927 1 21.7478624 3.238041225 24.99999564 0.785472654 0.890960626 0.138529471 0.108460748 22.52228459 1084099.03 0.028151092 0.035654278 1729.980569 -3.238041225 0.105487972 EVQDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVQDEEK 7 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 128.69 0.0086857 2811810000 4168370 2446400 3207940 2260790 4439850 4048700 4153550 3514940 3909240 2401530 FALSE TRUE 4332940.466 2866550.17 3291541.552 2707967.514 3685165.883 3108450.784 3827983.898 3467827.979 3768547.216 2872063.823 1.50865048 0.998080247 1.146054459 0.942864672 1.283107239 1.082305608 1.332833855 1.207434163 1.312139092 1 21.45365638 2.254385322 24.98420021 1.231587446 1.147877052 0.015199844 0.169756394 766.2833676 1209813.867 0.055358275 0.0461745 179.6326688 -2.254385322 -0.083710395 EVQDLFEAQGNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVQDLFEAQGNDR 13 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 107.65 0.0029749 133530000 52439 56440 58062 56966 63089 73580 56244 56805 53893 61050 FALSE TRUE 54509.33221 66133.13096 59575.14342 68233.70477 52365.15431 56492.16012 51835.44831 56043.62189 51953.40146 73011.57863 0.746584764 0.905789632 0.815968433 0.934560053 0.717217122 0.773742483 0.709962026 0.767599098 0.711577567 1 16.15583765 3.223558285 24.99839927 0.763544466 0.852176217 0.107686221 0.09266693 380.7963499 634520.2111 0.024359819 0.029225165 1673.240181 -3.223558285 0.088631751 EVQQGEEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVQQGEEFER 10 0 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;; 187.99 2.72E-06 1044400000 341137 394694 381150 377558 394043 493188 390147 404855 372532 376783 FALSE TRUE 354605.3522 462479.6242 391083.0821 452237.8455 327063.7116 378652.5613 359566.2587 399428.5809 359124.6461 450606.4149 0.786951407 1.026349401 0.867903938 1.003620522 0.725830128 0.840317734 0.797960807 0.886424533 0.796980767 1 18.78150833 3.251515279 24.99986103 0.836175536 0.924909194 0.153704856 0.091280261 374.8049491 723292.9976 0.023183788 0.03119629 1784.494767 -3.251515279 0.088733658 EVQQGEEFERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EVQQGEEFERR 11 1 P00568;Q5T9B7;H0YID2 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;;;; 199.4 9.27E-07 2136470000 1249690 1609870 1570393 1511190 1705980 1893130 1257966 1549560 1473197 2068710 FALSE TRUE 1299028.726 1886352.649 1611318.732 1810098.872 1415998.129 1453479.248 1159363.338 1528790.683 1420176.928 2474034.117 0.525065001 0.762460241 0.651292042 0.731638606 0.572343817 0.587493616 0.46861251 0.617934358 0.574032879 1 21.23843396 -1.448845843 5.217347194 1.000516973 0.611822283 0.660678674 0.083819629 0.000513376 5.42E-05 0.082661271 0.019458293 0.035575758 1.448845843 -0.38869469 EVRPDTQYTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVRPDTQYTGR 11 1 O43709;O43709-3;H7C0G4 O43709 WBSCR22 Probable 18S rRNA (guanine-N(7))-methyltransferase 0 ; 142.97 0.00032437 222560000 99136 133735 129902 126475 129128 162643 120003 130137 121740 131652 FALSE TRUE 103049.9658 156702.9459 133287.3528 151491.3775 107178.8687 124871.6281 110596.8513 128392.7264 117358.6012 157446.6888 0.654507037 0.995276224 0.846555452 0.962175697 0.68073117 0.793104187 0.702439995 0.815467936 0.745386277 1 17.26450389 5.011287444 16.61626027 0.823558761 0.394147334 0.188261983 0.110695644 84827367.09 2087271814 0.025751726 830880184.4 102633.0994 -5.011287444 -0.429411427 EVS(ph)DSEAGGGPQGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.914)DS(0.086)EAGGGPQGER 282.29 8.58E-34 181800000 134280 140790 133730 159380 132610 173260 174960 148630 133650 99723 TRUE FALSE 139581.4781 164969.5873 137215.1137 190904.8883 110068.9996 133022.9908 161246.178 146637.858 128839.9626 119261.8125 1.170378641 1.383255745 1.15053688 1.600721004 0.922919057 1.115386291 1.352035279 1.229545777 1.080311961 1 16.86377264 -1.877736453 0.174480338 0.698891527 1.314891492 0.163393813 0.173479216 64.89432002 1.729886141 8.648366444 0.683413455 0.013251454 1.877736453 0.615999966 EVS(ph)PAPAVAGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSPAPAVAGQSK 13 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK;EVS(1)PAPAVAGQSK 235.93 1.11E-16 2925620000 3397940 2645730 3119250 2579820 3791580 3987790 3698240 3177650 3342160 2468780 TRUE FALSE 3532093.295 3100113.547 3200540.217 3090100.696 3147088.586 3061686.208 3408362.285 3135058.799 3221876.314 2952490.173 1.196309924 1.049999615 1.084013842 1.046608292 1.065909927 1.036984385 1.154402584 1.061835473 1.091240318 1 21.49350083 0.158718841 0.008709432 1.81E-06 2.106868359 0.229173372 0.048075372 7144.503006 21.03336733 2614.73447 2472.285491 1.441182039 -0.158718841 2.106866553 EVS(ph)PEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSPEVVR 8 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR;EVS(1)PEVVR 171.7 0.00030198 3599230000 2546060 2669540 2653820 2470260 2960370 3222050 2691980 2643470 2627220 2559710 TRUE FALSE 2646580.415 3128012.729 2722980.729 2958870.055 2457167.365 2473777.718 2480975.573 2608038.608 2532666.865 3061236.166 0.864546305 1.021813594 0.889503646 0.966560531 0.802671611 0.808097639 0.810448929 0.851956029 0.827334687 1 21.54568292 3.241396209 24.99999682 0.83887217 0.938470684 0.271755074 0.067029538 79.08692168 697262.7803 0.017250723 0.022365228 1743.396657 -3.241396209 0.099598514 EVS(ph)PLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSPLLPK 8 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK;EVS(1)PLLPK 150.61 0.00051025 470150000 2001560 1399460 1721090 1507080 2148390 2138390 2245990 1753620 1845860 1087300 TRUE FALSE 2080583.134 1639806.369 1765943.019 1805175.926 1783207.435 1641781.33 2069943.435 1730115.592 1779427.859 1300335.617 1.600035488 1.261063949 1.358067099 1.388238468 1.371343991 1.262582758 1.591853216 1.330514653 1.368437375 1 20.3104526 0.433538551 1.792329565 1.000035293 1.390824117 0.532490026 0.110602558 3.741130562 10.97744321 0.097923472 0.027397955 2.713554518 -0.433538551 0.390788824 EVS(ph)PPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVSPPGAR 8 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 EVS(1)PPGAR;EVS(1)PPGAR 100.57 0.0080645 0 236533 281430 346440 318550 353820 420690 358240 367170 379520 289179 TRUE FALSE 245871.5055 329763.4133 355468.511 381558.2392 293677.8028 322991.1231 330160.2127 362248.6867 365861.1493 345838.0884 0.710943976 0.953519651 1.027846622 1.103285763 0.849177152 0.933937394 0.954667007 1.04745168 1.057897212 1 18.39973724 4.728305098 3.486579468 0.995258097 0.679299464 0.611070662 0.067995845 0.196979251 4.20533799 0.017398002 0.162032889 53494.00306 -4.728305098 -0.315958633 EVS(ph)PSDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVSPSDVR 8 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 EVS(0.999)PS(0.001)DVR;EVS(0.977)PS(0.023)DVR;EVS(0.994)PS(0.006)DVR 150.08 0.00051922 317937000 827790 993820 1012480 1118100 1009410 1121490 1144760 957720 923180 737940 TRUE FALSE 860471.7884 1164500.854 1038866.061 1339256.843 837830.8488 861040.9438 1055030.72 944883.3299 889954.9321 882525.2143 0.975010996 1.31951001 1.177151705 1.517528135 0.949356274 0.975655913 1.195468076 1.070658735 1.008418703 1 19.75127797 3.19366532 24.99999877 1.04746264 1.247450077 0.354155618 0.140819794 149.7953117 83413.18245 0.03977745 0.047543351 1561.943501 -3.19366532 0.199987437 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.5)S(0.5)RPS(0.547)T(0.453)PGLSVVSGISATSEDIPNK 189.31 4.23E-18 363790000 227110 143240 190910 207920 213610 234060 283060 211930 210250 117200 TRUE FALSE 236076.4782 167840.3557 195885.2714 249045.9554 177300.6485 179703.1122 260873.0176 209089.425 202683.1436 140163.0961 1.684298398 1.197464671 1.397552401 1.776829725 1.264959561 1.282100048 1.861210439 1.491758037 1.44605213 1 17.09674702 EVS(ph)SRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_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(0.598)T(0.402)PGLSVVSGISATSEDIPNKIEDLR 156.26 3.60E-11 460120000 69377 52221 66259 53064 79286 82415 68043 60803 67533 45921 TRUE FALSE 72116.05753 61189.55053 67985.76397 63559.90082 65808.99404 63275.36526 62709.61186 59988.03524 65102.50052 54918.34074 1.313150699 1.114191538 1.23794279 1.157352898 1.198306306 1.152171832 1.141870111 1.092313322 1.18544187 1 15.74500042 -5 0.050304167 0.296795428 1.518262991 0.5806903 0.051931231 365.3273668 1.358957211 34.3149336 7.615785791 1.00E-05 5 1.221467563 EVSAYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSAYIK 7 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 79.116 0.077928 48951000 50865 44769 53997 43391 63956 66452 64816 51581 51031 51968 FALSE TRUE 52873.18948 52457.7275 55404.20618 51973.61029 53084.78196 51019.53009 59735.55255 50889.64106 49194.40428 62150.13461 0.850733306 0.844048494 0.891457541 0.836259014 0.854137844 0.820907797 0.961149206 0.818817874 0.791541395 1 15.9234699 -1.471878687 3.216307896 1.002918484 0.853964905 0.501409231 0.044205498 11460680.28 12871473.41 291509.2154 0.010260137 0.033738154 1.471878687 -0.148953579 EVSDS(ph)EAGGGPQGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 EVS(0.095)DS(0.905)EAGGGPQGER 193.54 9.31E-08 202060000 107510 110520 114240 159420 116380 138820 162940 128860 119770 79228 TRUE FALSE 111754.5778 129500.9503 117217.1882 190952.8002 96597.76917 106581.1588 150168.337 127132.8425 115459.5011 94751.20969 1.179452781 1.366747197 1.237104926 2.015307254 1.019488506 1.124852751 1.584869866 1.341754294 1.218554375 1 16.53185674 EVSEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVSEDR 6 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 129.96 0.037149 168319000 357610 423050 411030 405010 434400 463580 466240 439370 417820 460770 FALSE TRUE 371728.7189 495705.5466 421741.7795 485119.7692 360560.8432 355920.5706 429694.8905 433480.9638 402782.7398 551049.0595 0.67458371 0.899566995 0.765343434 0.880356768 0.654317137 0.64589634 0.779776107 0.786646772 0.730938077 1 19.07182124 -1.884497592 4.376914772 1.074289846 0.762056605 0.438432462 0.082191463 0.049582759 0.001308439 0.066224307 0.018538923 0.013046752 1.884497592 -0.312233241 EVSEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSEDRR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 180.18 0.0011068 1075820000 1149390 1425630 1387980 1339130 1477010 1680670 1571110 1510190 1328400 1481320 FALSE TRUE 1194768.805 1670470.863 1424151.899 1604005.917 1225948.368 1290359.863 1447962.293 1489948.373 1280591.143 1771556.292 0.674417635 0.942939759 0.803898756 0.90542193 0.692017732 0.728376439 0.817339138 0.841039249 0.722862236 1 20.75658588 -1.654613079 6.100420907 1.001566232 0.799616668 0.347858465 0.084854732 0.001732976 9.81E-05 0.078770016 0.018431194 0.022150673 1.654613079 -0.201949563 EVSGHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSGHSVR 8 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 71.692 0.048085 24250000 15190 37922 29787 33717 32575 42733 29007 33688 31293 43684 FALSE TRUE 15789.71293 44434.80851 30563.27369 40386.12196 27037.91314 32808.90837 26733.35554 33236.46746 30166.77104 52243.04342 0.302235703 0.850540198 0.585020927 0.773043056 0.517540927 0.628005304 0.511711298 0.636189343 0.577431349 1 15.67295132 -1.916219903 2.370848968 1.248599671 0.607148468 0.420382398 0.141251984 14901296.07 7460751.859 20583406.35 0.032141534 0.012127746 1.916219903 -0.641451203 EVSHLNALEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVSHLNALEER 11 0 A0A087WYJ2;M0R2B7;P28340;M0R3H8 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 167.71 1.89E-05 69642000 53248 68699 54807 75817 59634 66333 55776 55731 57377 79327 FALSE TRUE 55350.27216 80497.51885 56235.31544 90813.37631 49497.43398 50928.16604 51404.13138 54984.0171 55312.01298 94869.60684 0.583435243 0.84850693 0.592764293 0.957244152 0.521741742 0.53682278 0.541839827 0.579574628 0.583031962 1 16.53365835 -1.27667017 3.52505054 1.001017284 0.637601691 0.381698292 0.138091262 62687901.53 108713015.7 704609.1265 0.033417373 0.052884674 1.27667017 -0.363415593 EVSQVDTICECLLEHEEQVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSQVDTICECLLEHEEQVLR 21 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 0 ;;; 249.34 1.18E-30 207592000 118771 146480 124953 155031 160468 175636 147661 146422 141451 148131 FALSE TRUE 123460.1708 171636.8005 128209.3778 185695.6691 133191.7067 134847.2008 136086.945 144459.4526 136360.2061 177154.4333 0.696907035 0.968854108 0.723715322 1.048213503 0.751839535 0.761184455 0.768182554 0.815443621 0.769725056 1 17.43464804 5.01208935 14.19934686 0.832309965 0.495884869 0.127672967 0.111812068 683725.7118 14670140.92 0.024752004 4411852.065 102822.782 -5.01208935 -0.336425096 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.468)S(0.532)RPS(0.531)T(0.468)PGLS(0.001)VVSGISATSEDIPNK;EVS(0.46)S(0.54)RPS(0.536)T(0.456)PGLS(0.008)VVSGISATSEDIPNK;EVS(0.459)S(0.541)RPS(0.541)T(0.459)PGLSVVSGISATSEDIPNK 195.55 3.77E-25 407375000 406807 300522 328213 364291 404414 422871 498693 381093 375477 236793 TRUE FALSE 422868.0545 352134.3158 336766.5004 436346.6725 335671.8527 324665.6189 459604.1396 375985.0717 361963.6561 283188.0547 1.493241143 1.243464581 1.189197407 1.540837141 1.185331963 1.146466504 1.622964429 1.327686904 1.278174168 1 18.11140089 0.807676097 3.135525897 1.000128963 1.342083221 0.307978444 0.154069055 1.264200149 18.65801991 0.143718851 0.037455671 6.422085705 -0.807676097 0.341954257 EVSS(ph)RPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.48)S(0.519)RPS(0.52)T(0.481)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.108)S(0.89)RPS(0.601)T(0.402)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.498)S(0.502)RPS(0.501)T(0.498)PGLS(0.001)VVSGISATSEDIPNKIEDLR;EVS(0.099)S(0.901)RPS(0.537)T(0.463)PGLSVVSGISATSEDIPNKIEDLR 184.54 6.78E-20 4085976000 226082 165227 201443 182288 259940 262160 225644 209059 212091 162222 TRUE FALSE 235007.8919 193603.452 206692.7701 218344.0223 215755.4916 201277.3131 207957.4337 206256.9061 204457.8863 194006.295 1.21134158 0.997923557 1.06539208 1.125448132 1.112105624 1.037478259 1.071910753 1.063145431 1.053872434 1 17.56574394 0.384990148 0.01192429 3.03E-07 2.083562496 0.28195289 0.050955689 2521.324936 11.85203224 1068.07941 1001.578443 2.426555046 -0.384990148 2.083562193 EVSS(ph)RPST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 EVS(0.466)S(0.534)RPS(0.152)T(0.848)PGLSVVSGISATSEDIPNKIEDLR;EVS(0.116)S(0.884)RPS(0.183)T(0.817)PGLSVVSGISATSEDIPNKIEDLR 213.34 9.05E-28 1435250000 463040 314520 453980 369580 541400 558740 485350 435700 463140 323340 TRUE FALSE 481321.1767 368536.3634 465811.0917 442681.8209 449373.0214 428981.1028 447306.9988 429860.1542 446471.6819 386692.2823 1.244713688 0.953048148 1.204604056 1.144790939 1.162094621 1.109360394 1.156751813 1.111633653 1.154591654 1 18.56082645 -1.514758139 5.507413721 0.999715767 1.133691025 0.242600895 0.072776133 0.000227261 2.00E-05 0.063050098 0.014829715 0.030566229 1.514758139 0.133975258 EVSSRPS(ph)TPGLSVVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_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(0.001)S(0.007)RPS(0.496)T(0.496)PGLSVVSGISATSEDIPNKIEDLR 143.39 2.88E-10 266870000 175290 119330 169040 138630 193690 209720 200640 156740 189240 126170 TRUE FALSE 182210.5846 139823.9992 173445.3213 166050.6002 160766.643 161015.7083 184913.3125 154639.1567 182429.2894 150890.5958 1.207567533 0.926658142 1.149477344 1.100470174 1.065451708 1.067102343 1.225479371 1.024842906 1.209016959 1 17.20314337 EVSSRPSTPGLS(ph)VVSGISATSEDIPNKIEDLR ddPTM_MDA-MB-175_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(0.048)S(0.228)RPS(0.228)T(0.228)PGLS(0.267)VVSGISATSEDIPNKIEDLR 67.752 0.0021422 62867000 11778 13738 15548 10779 18578 20156 15880 16044 13774 9375.3 TRUE FALSE 12243.00453 16097.39463 15953.19365 12911.05403 15420.1182 15475.07447 14635.28411 15828.95642 13278.27643 11212.21053 1.091934949 1.435702138 1.422841072 1.151517267 1.375296883 1.380198349 1.305298724 1.411760542 1.184269274 1 13.45278312 0.980786374 4.949893828 1.0002604 1.32939241 0.455728453 0.109683958 0.133089192 11.93941003 0.099143857 0.025083326 9.567233511 -0.980786374 0.32913201 EVSTYIKK ddPTM_MDA-MB-175_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 ; 135.83 0.00131 8029900000 6141700 4616900 6255600 3983300 8343600 7031400 5501100 5911000 6891000 5743600 FALSE TRUE 6384179.058 5409816.661 6418626.075 4771184.851 6925357.852 5398463.912 5069909.408 5831772.713 6642994.256 6868948.452 0.929425967 0.787575667 0.934440857 0.69460193 1.008212232 0.785922904 0.738091055 0.849005165 0.96710498 1 22.71165783 1.207321094 4.317652984 0.993901712 0.835948647 0.284926348 0.090911407 0.237260303 9.120539883 0.076122348 0.020916807 16.11836899 -1.207321094 -0.157953065 EVTDEIVKEFMTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVTDEIVKEFMTPR 14 1 P23381;P23381-2 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 130.06 5.86E-05 30659000 42202 50661 46316 28536 65097 61666 35889 38520 51191 57283 FALSE TRUE 43868.16755 59361.63266 47523.03301 34180.33563 54031.83519 47345.00606 33075.9264 38003.70241 49348.64591 68506.5071 0.640350376 0.866510864 0.693701008 0.498935606 0.788710992 0.691102321 0.482814375 0.554745878 0.720349759 1 16.06395341 0.97320097 21.83790646 1.000000005 0.647676769 0.454692799 0.113919442 473.3224469 385701.1346 0.116149957 0.029037489 9.401582696 -0.97320097 -0.352323236 EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPTLPS(ph)PTSVITQAPPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPTLPSPTSVITQAPPSNR 50 2 P17544;K7ELQ4;P17544-1 P17544 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPT(0.042)LPS(0.85)PT(0.053)S(0.053)VIT(0.003)QAPPSNR;EVTPKPVLISTPTPTIVRPGSLPLHLGYDPLHPT(0.033)LPS(0.765)PT(0.094)S(0.094)VIT(0.013)QAPPS(0.001)NR 151.38 3.82E-16 395420000 117870 148624 151972 156149 184046 221941 148566 183316 185042 206423 TRUE FALSE 122523.5986 174149.0159 155932.5152 187034.8061 152761.9267 170398.5663 136921.0087 180858.9489 178382.3746 246867.6346 0.496312928 0.705434781 0.631644223 0.757631945 0.618800949 0.690242634 0.554633291 0.732615068 0.722583075 1 17.91337818 0.628756317 1.112286557 0.999739021 0.64638416 0.676199571 0.073775908 0.671896752 1.303905405 0.065255984 0.020317895 4.253596769 -0.628756317 -0.353354861 EVTSLFNKDDEQHLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVTSLFNKDDEQHLLER 17 1 Q86YL5;Q86YL5-2 Q86YL5 TDRP Testis development-related protein 0 ;;; 229.6 6.35E-16 749470000 833520 749740 883020 700110 1121470 1085060 976460 910480 1029400 761300 FALSE TRUE 866428.0132 878502.0128 906032.2266 838589.6684 930842.93 833071.2592 899922.5137 898276.5048 992352.0951 910462.159 0.951635392 0.964896788 0.995134413 0.921059332 1.022385083 0.914998225 0.988423851 0.986615969 1.089943261 1 19.79623953 1.442390633 4.077908239 1.045137549 0.966282187 0.412067309 0.036961498 0.179708118 5.512290205 0.023522968 0.008594356 27.69431536 -1.442390633 -0.078855362 EVTWEVLEGEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVTWEVLEGEVEK 13 0 P05455 P05455 SSB Lupus La protein 0 136.38 0.00016994 16099000 32293 25501 26778 26251 27989 32982 39856 24936 26226 16748 FALSE TRUE 33567.95258 29880.59838 27475.85668 31443.36945 23231.43978 25322.43035 36731.98258 24601.77371 25282.13138 20029.44994 1.675929827 1.491833199 1.371772902 1.569856863 1.159864092 1.264259898 1.833898718 1.228280047 1.262247913 1 14.28983518 -3.66545981 0.126137713 9.45E-12 1.643335873 0.369553088 0.192048389 115.172251 1.292936562 31.81408229 1.736740237 0.000216043 3.66545981 1.643335873 EVTYELDHPGFQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVTYELDHPGFQIR 14 0 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ;;; 160.84 4.69E-06 542510000 313885 351108 402363 366147 398902 448587 350046 373964 354251 372972 FALSE TRUE 326277.4222 411408.0678 412848.9103 438569.7838 331096.7805 344409.4677 322608.4798 368951.6243 341501.5757 446048.7224 0.731483817 0.922338855 0.92556909 0.983232911 0.742288373 0.772134187 0.723258388 0.827155433 0.765614962 1 18.76684178 3.225039049 24.99877307 0.791648383 0.895413015 0.155549954 0.094373106 338.2136111 625290.8169 0.025971765 0.031203014 1678.954971 -3.225039049 0.103764632 EVVAGSHELGQDYEHVTMLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVAGSHELGQDYEHVTMLQER 22 0 Q01082;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 245.92 3.71E-31 325020000 62757 110190 111480 109710 106160 135430 95816 117390 100790 115560 FALSE TRUE 65234.69482 129114.2753 114385.2604 131410.3105 88114.96112 103978.435 88305.69155 115816.5791 97162.58759 138201.7695 0.472025033 0.934244734 0.827668566 0.950858379 0.637582004 0.752366886 0.638962091 0.838025298 0.703048796 1 17.07641656 -1.940630151 3.250579735 1.152816197 0.761682564 0.220869389 0.139152796 17555859.48 320646.8114 20086896.82 0.030598957 0.011464889 1.940630151 -0.391133633 EVVEEAENGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;; 280.94 1.04E-23 14289720000 7663000 7354520 7563910 7381640 8162740 9404890 8551140 8127140 7293540 7126490 FALSE TRUE 7965541.157 8617601.6 7761031.708 8841706.36 6775240.37 7220746.83 7880879.303 8018208.982 7031046.92 8522789.271 0.934616697 1.011124566 0.910621096 1.037419333 0.794955754 0.847228132 0.924683112 0.940796343 0.824970171 1 23.02289423 3.251721521 24.99999138 0.890188357 0.971649315 0.290531337 0.064774823 311.2932111 591317.8982 0.017607953 0.023699563 1785.342408 -3.251721521 0.081460958 EVVEFYRDPQLEGSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVVEFYRDPQLEGSLSR 17 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 124.46 4.58E-05 521290000 232300 244990 258480 257630 285080 330510 273750 270760 276440 254340 FALSE TRUE 241471.3834 287065.1267 265216.2011 308588.4451 236622.2034 253754.0614 252292.7597 267130.9051 266490.9784 304173.0534 0.793861852 0.943755943 0.871925367 1.014516051 0.777919677 0.834242411 0.829438232 0.878220152 0.876116327 1 18.21453283 0.481606705 2.346747078 0.999997252 0.870020136 0.262320274 0.066024172 11.23923563 49.0117461 0.061604132 0.016562343 3.031144949 -0.481606705 -0.129977116 EVVESCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVVESCR 7 0 O60701-2;O60701;E7ER95;E7ER83;E7ETF4;E7EV97 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;; 111.04 0.015516 961840000 581282 600110 600289 593203 689200 845270 591946 616757 605914 584529 FALSE TRUE 604231.4622 703174.2243 615933.0245 710536.7829 572050.0302 648968.8527 545547.7258 608490.3812 584107.2735 699056.2661 0.864353117 1.005890739 0.881092202 1.016422879 0.818317577 0.928349954 0.780406031 0.8704455 0.835565464 1 19.41504906 3.224747481 24.99597152 0.862469384 0.942161428 0.175842535 0.072170583 322.8543247 584229.6105 0.018947179 0.022757923 1677.828169 -3.224747481 0.079692045 EVVETPLLHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVVETPLLHPER 12 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;;; 201.04 1.53E-07 1606610000 682710 897780 818930 902310 931280 1034680 877710 875180 805520 927180 FALSE TRUE 709663.918 1051966.731 840271.9886 1080784.225 772981.3582 794391.2507 808912.7967 863449.6436 776529.4925 1108843.169 0.640003869 0.948706508 0.757791554 0.9746953 0.697106119 0.716414433 0.729510556 0.778694109 0.700305971 1 20.0806239 EVVKGPCAPAASS(ph)PTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVKGPCAPAASSPTQK 17 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVKGPCAPAAS(0.047)S(0.887)PT(0.066)QK 177.91 6.07E-10 227950000 500070 264320 373760 245250 508180 489440 421140 369440 451690 285970 TRUE FALSE 519813.1497 309714.9039 383500.4926 293759.718 421799.7451 375774.9775 388129.9464 364488.2611 435433.7651 342000.3463 1.519919952 0.905598217 1.121345334 0.858945674 1.233331339 1.098756132 1.134881735 1.06575407 1.273196855 1 18.38363826 EVVKGPGAPAAS(ph)SPTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVVKGPGAPAASSPTQK 17 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVKGPGAPAAS(0.628)S(0.355)PT(0.017)QK;EVVKGPGAPAAS(0.496)S(0.496)PT(0.008)QK;EVVKGPGAPAAS(0.5)S(0.5)PT(0.001)QK;EVVKGPGAPAAS(0.492)S(0.492)PT(0.017)QK 202.66 6.29E-12 2956790000 3823730 2056850 2938390 1875050 4241880 3719310 3216000 2932650 3452490 2152800 TRUE FALSE 3974693.813 2410097.987 3014966.857 2245929.294 3520846.753 2855556.619 2963921.517 2893342.624 3328235.559 2574599.942 1.543810263 0.936105819 1.171042851 0.87234108 1.36753159 1.109126343 1.151216338 1.1238028 1.292719504 1 21.29591684 -4.999595158 0.012700481 1.74E-05 2.069264077 0.049273316 0.187672467 39456.65556 38.04281948 3748.782951 2555.410612 1.00E-05 4.999595158 2.069246721 EVVKGPGAPAAS(ph)SPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVVKGPGAPAASSPTRK 17 2 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVKGPGAPAAS(0.498)S(0.498)PT(0.005)RK;EVVKGPGAPAAS(0.487)S(0.487)PT(0.027)RK 92.098 0.0026718 537120000 973342 428262 686697 376493 996080 825248 748142 642350 811040 446198 TRUE FALSE 1011770.294 501812.6671 704592.8879 450962.1917 826766.6774 633596.6588 689500.6751 633740.3489 781850.8288 533621.9551 1.896043227 0.940389844 1.320397111 0.845096772 1.549349065 1.187351181 1.292114518 1.187620455 1.4651774 1 19.0254585 7.999999999 0.019485062 1.62E-09 2.856252499 0.076757182 0.286129222 11852.73054 17.79888832 974.4820569 1735.907323 99999999.8 -7.999999999 2.856252497 EVVKGPGAPAASS(ph)PTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVKGPGAPAASSPTRK 17 2 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVKGPGAPAAS(0.423)S(0.573)PT(0.004)RK 73.405 0.013744 163310000 230210 121650 162650 125580 243150 226590 196640 180220 216080 123800 TRUE FALSE 239298.8686 142542.4412 166888.7926 150419.3492 201819.4499 173967.9065 181226.843 177804.4457 208303.323 148056.2397 1.616270068 0.962758756 1.127198644 1.015960891 1.363126946 1.175012325 1.224040563 1.200925041 1.406920258 1 17.17578577 3.231193559 24.99170896 1.23288456 1.161180175 0.010189884 0.193560545 726.1198306 2463258.226 0.052632616 0.064118653 1702.917306 -3.231193559 -0.071704385 EVVKPVPITS(ph)PAVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 EVVKPVPIT(0.155)S(0.845)PAVSK;EVVKPVPIT(0.032)S(0.968)PAVSK 123.19 6.31E-05 784060000 974860 556970 760500 541360 1162730 950230 767850 756410 881310 617500 TRUE FALSE 1013348.226 652625.2649 780319.2548 648439.3922 965089.5699 729553.4834 707663.9106 746271.5612 849591.8253 738487.3022 1.372194515 0.883732547 1.056645459 0.878064376 1.306846532 0.987902542 0.958261447 1.010540816 1.150448793 1 19.49421359 EVVNKDVLDVYIEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVVNKDVLDVYIEHR 15 1 P33993;P33993-2 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 123.97 5.98E-05 96773000 318100 278730 343530 280790 429370 417600 358530 358720 356240 316680 FALSE TRUE 330658.8336 326599.7093 352482.674 336329.4239 356385.8408 320618.7288 330427.4818 353911.9451 343418.992 378727.3828 0.87307876 0.86236096 0.930702901 0.888051509 0.941008908 0.846568649 0.872467893 0.93447678 0.906770959 1 18.53080021 0.569488956 0.851544169 1.000174145 0.890499919 0.537622413 0.029987313 1.09701101 1.295984185 0.029739607 0.009857029 3.71098292 -0.569488956 -0.109674226 EVVQGSGAPAALS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVQGSGAPAALSPK 15 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGSGAPAALS(1)PK 223.18 1.37E-12 267950000 255300 123540 161330 124620 231820 258420 215520 173470 176890 116790 TRUE FALSE 265379.4411 144757.034 165534.3923 149269.464 192415.3192 198405.8714 198626.9792 171144.9184 170523.7635 139672.7644 1.900008511 1.036401296 1.185158703 1.068708453 1.377615171 1.42050508 1.422088122 1.22532778 1.220880564 1 17.0916912 0.879737811 1.539011022 1.002561363 1.316555101 0.162390359 0.22997322 1.0359377 4.794687699 0.209555828 0.061118868 7.58119751 -0.879737811 0.313993738 EVVQGSSASAAS(ph)SPTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVQGSSASAASSPTWK 17 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGS(0.097)S(0.333)AS(0.036)AAS(0.413)S(0.121)PTWK 304.29 1.19E-46 395160000 705210 537260 593450 478370 771790 745900 675990 637180 645970 467320 TRUE FALSE 733052.2353 629530.2257 608915.7945 572990.1582 640601.4115 572676.0292 623004.1374 628639.6443 622721.6659 558882.4066 1.311639491 1.126409095 1.089523999 1.025242791 1.146218603 1.024680724 1.114732062 1.124815591 1.11422664 1 19.09218523 4.750144721 2.678381296 1.086875043 1.35988496 0.687142258 0.046606909 0.267953084 2.491613511 0.010989128 0.165026677 56252.87472 -4.750144721 0.273009917 EVVQGSSASAASS(ph)PTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EVVQGSSASAASSPTWK 17 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 EVVQGSSAS(0.013)AAS(0.009)S(0.729)PT(0.249)WK;EVVQGS(0.003)S(0.003)AS(0.014)AAS(0.167)S(0.799)PT(0.014)WK;EVVQGSSAS(0.066)AAS(0.062)S(0.708)PT(0.164)WK;EVVQGS(0.001)SAS(0.391)AAS(0.11)S(0.472)PT(0.026)WK 296.22 3.97E-46 864882000 1364950 985958 1217680 955357 1418180 1562530 1400930 1256288 1358610 932772 TRUE FALSE 1418839.28 1155288.617 1249413.741 1144323.763 1177118.27 1199656.088 1291121.446 1239449.514 1309713.891 1115530.814 1.271896089 1.035640255 1.120017238 1.025810985 1.055209103 1.075412774 1.157405452 1.111084964 1.174072356 1 20.08929894 2.271702032 24.91780596 1.120293212 1.09039259 0 0.07827949 759.77559 571244.5877 0.025741514 0.021535752 186.9399112 -2.271702032 -0.029900622 EVVSFS(ph)PDPLPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVVSFSPDPLPVR 13 0 J3QLG5;F8W925;Q8NFI3-2;Q8NFI3-3;Q8NFI3 J3QLG5 ENGASE Cytosolic endo-beta-N-acetylglucosaminidase 1 EVVS(0.151)FS(0.849)PDPLPVR;EVVS(0.017)FS(0.983)PDPLPVR 92.151 0.0029172 27182000 107686 204752 161258 187499 169068 215853 159489 180369 169679 223822 TRUE FALSE 111937.5264 239916.5633 165460.516 224585.7426 140329.8817 165724.412 146987.8354 177951.4486 163572.2859 267675.6356 0.418183471 0.896295857 0.618138127 0.839021983 0.524253474 0.619124007 0.549126689 0.664802563 0.611083955 1 18.0301263 -1.401619472 4.060226373 1.001322081 0.64451723 0.396798745 0.133747607 0.001470027 0.000216647 0.118932694 0.027933183 0.03966254 1.401619472 -0.356804852 EVVTEHLINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVVTEHLINK 10 0 Q13618;Q13618-2;A0A087X1R9;H7C1L6 Q13618 CUL3 Cullin-3 0 85.377 0.014281 237900000 154540 151810 160980 145900 205600 222730 192110 182900 177350 172970 FALSE TRUE 160641.3585 177882.1866 165175.271 174758.5845 170652.1854 171004.333 177051.9162 180448.5247 170967.2081 206860.1598 0.776569827 0.859915156 0.798487593 0.84481509 0.824964003 0.826666349 0.855901477 0.872321306 0.82648688 1 17.65829629 -5 0.196374714 1.741673777 0.806522033 0.810280775 0.024986809 52.68944007 0.519559811 15.28118626 0.057535319 1.00E-05 5 -0.935151744 EVWALVQAGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 125.48 0.0022583 104450000 241281 240223 232436 300624 303911 322503 326080 224273 284162 205121 FALSE TRUE 250806.9602 281479.4316 238493.4731 360086.5299 252252.3168 247606.5658 300520.9975 221266.9873 273935.0651 245310.5327 1.022405999 1.14744128 0.97221049 1.467880429 1.028297946 1.009359701 1.225063573 0.901987309 1.116686928 1 17.90424965 1.738537323 24.99999963 1.002146612 1.124738041 0.123963543 0.144164036 0.077056086 7242.825107 0.064519836 0.035779541 54.76931675 -1.738537323 0.122591429 EVWEELDGLDPNRFNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVWEELDGLDPNRFNPK 17 1 Q02818;H7BZI1 Q02818 NUCB1 Nucleobindin-1 0 171.46 1.57E-09 129680000 120300 96125 123090 117260 242890 203700 150680 133270 163190 147420 FALSE TRUE 125049.5369 112633.721 126297.8265 140453.678 201603.6446 156393.7621 138869.3079 131483.7336 157316.8238 176304.1265 0.709283097 0.638860379 0.716363417 0.796655647 1.143499296 0.887068075 0.787669073 0.745777971 0.892303697 1 17.42770672 3.648823212 3.691985236 0.882492557 0.681271292 0.444606136 0.107560433 0.259132724 6.599103952 0.032333172 0.05300779 4454.74872 -3.648823212 -0.201221265 EVWEMELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVWEMELDR 9 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 0 ; 105.78 0.0078283 20731000 33095 35404 38140 32311 46776 48163 39077 36371 36891 45415 FALSE TRUE 34401.61615 41484.3616 39133.95973 38702.01936 38825.03223 36977.87317 36014.04263 35883.50624 35563.30012 54313.19973 0.633393288 0.763798889 0.720523923 0.712571153 0.714836033 0.680826638 0.66308085 0.660677449 0.6547819 1 15.72901524 -1.419826562 3.787520454 1.001965452 0.690342831 0.864381527 0.036908461 0.000640927 9.82E-05 0.037391732 0.008760353 0.038034126 1.419826562 -0.311622621 EVWYFGLHYVDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVWYFGLHYVDNK 13 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 218.5 2.40E-11 4306636000 4390230 2819910 4005900 3390440 4935830 4894460 5860760 3952710 4683730 2085708 FALSE TRUE 4563559.67 3304207.607 4110297.045 4061058.913 4096839.38 3757795.841 5401378.317 3899730.388 4515163.472 2494362.549 1.829549466 1.324670148 1.647834653 1.628094887 1.64243942 1.506515499 2.165434339 1.563417631 1.810147235 1 21.25023974 EVYELLDS(ph)PGKVLLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EVYELLDSPGKVLLQSK 17 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK;EVYELLDS(1)PGKVLLQSK 141.31 1.12E-05 22367000 692460 338290 442392 316422 627430 600342 535818 435735 505246 325867 TRUE FALSE 719798.8555 396388.676 453921.0989 379009.3272 520779.6727 460921.6688 493819.1851 429894.685 487062.2952 389714.3995 1.846990659 1.017126071 1.164753213 0.972530981 1.336311087 1.182716547 1.26713097 1.103101875 1.249792914 1 18.57205771 4.745457167 24.93561774 1.152798643 1.84699099 0.768435288 0.115721773 349.7296552 1264471.949 0.026068512 0.259373688 55648.97473 -4.745457167 0.694192347 EVYFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EVYFAER 7 0 P50238 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;;; 148.98 0.0047622 16716140000 7738870 8860660 8062190 8530600 10766370 10582810 8926000 8615510 8088420 10502680 FALSE TRUE 8044406.563 10382409.43 8272297.295 10217927.22 8936306.273 8125112.762 8226356.796 8500033.181 7797319.344 12560479.06 0.640453802 0.826593427 0.658597276 0.813498209 0.711462217 0.646879209 0.654939733 0.676728423 0.620782003 1 23.58238815 -1.091103589 4.660866395 1.000017605 0.696696219 0.647431368 0.067628236 1.21E-05 2.36E-06 0.063969924 0.015076981 0.081076765 1.091103589 -0.303321386 EVYPHVSTIINICLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EVYPHVSTIINICLK 15 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 146 3.96E-06 362660000 92361 170370 191630 181830 216370 257730 158310 206400 191150 189290 FALSE TRUE 96007.4836 199629.7222 196624.0352 217795.4313 179591.5047 197876.1134 145901.2485 203633.5456 184270.5488 226377.7513 0.424103001 0.881843384 0.868566076 0.9620885 0.793326657 0.874097001 0.64450348 0.899529854 0.813995844 1 17.78837265 4.74112838 24.64566305 0.850809138 0.424102814 0.664051113 0.092766892 113.7433756 1091643.683 0.021082595 0.14407628 55097.0542 -4.74112838 -0.426706324 EVYQQQQYGSGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ; 331.48 4.46E-62 698860000 231560 270020 233650 243300 249120 295150 245930 254520 243460 260380 FALSE TRUE 240702.1676 316393.8345 239739.1109 291424.0138 206774.6714 226605.8855 226653.364 251108.5757 234697.9222 311396.4757 0.772976531 1.016048219 0.769883829 0.935861632 0.664023801 0.727708575 0.727861044 0.806395047 0.753694857 1 18.24839309 3.253211769 24.99679739 0.767024424 0.876445895 0.148770564 0.107132834 370.4009579 631949.0196 0.0273608 0.036889993 1791.479196 -3.253211769 0.10942147 EWAHATIIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWAHATIIPK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 123.63 0.00045709 1389390000 2779100 3429200 4014500 4136200 4712800 5159900 4967600 4356000 4184400 3015300 FALSE TRUE 2888821.014 4018138.425 4119121.168 4954328.015 3911719.939 3961591.424 4578226.532 4297614.945 4033804.261 3606090.304 0.801095028 1.114264504 1.142267892 1.373877967 1.084753739 1.098583532 1.269581776 1.191765758 1.118608776 1 21.78200409 4.772572903 2.491858075 1.175433201 0.698965378 0.535556915 0.098831308 0.424567733 3.062027198 0.02359215 0.444880753 59234.2513 -4.772572903 -0.476467824 EWAMNVGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWAMNVGDK 9 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 109.42 0.005705 96545000 189544 154794 179963 159914 229518 243140 254004 179453 213386 144571 FALSE TRUE 197027.3435 181378.6654 184652.9836 191544.5119 190504.6123 186674.4198 234094.5028 177047.7261 205706.2795 172896.9195 1.139565379 1.049056663 1.067994642 1.107853815 1.101839252 1.079686211 1.353954157 1.024007406 1.189762549 1 17.39955264 EWAMNVGDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EWAMNVGDKK 10 1 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;; 88.803 0.019154 7929000000 1997660 1367710 1755240 1369940 2598270 2286470 2460700 1816920 1943480 1382950 FALSE TRUE 2076529.159 1602603.553 1800982.996 1640910.043 2156616.993 1755471.994 2267823.904 1792567.159 1873534.534 1653912.574 1.255525347 0.968977187 1.08892273 0.99213832 1.303948605 1.061405555 1.371187292 1.083834289 1.132789341 1 20.65745155 3.262683984 24.99922712 1.167603173 1.069613667 0.089922023 0.125976487 475.7161706 492984.8612 0.032374135 0.043812975 1830.981619 -3.262683984 -0.097989506 EWDFDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWDFDLK 7 0 Q96EY4;H0Y9X1 Q96EY4 TMA16 Translation machinery-associated protein 16 0 ; 105.12 0.018609 100020000 364570 248420 300690 260010 371330 381210 369780 300860 315320 232700 FALSE TRUE 378963.5051 291084.2026 308526.2284 311439.2019 308211.4592 292679.7548 340795.6774 296827.4638 303971.6948 278293.1097 1.361742321 1.045962665 1.108637683 1.119104969 1.107506613 1.051696016 1.224592581 1.066600119 1.092271724 1 18.08624566 4.745582178 24.8596683 1.098219163 1.361742453 0.670923526 0.056726141 430.9733714 1525809.236 0.01253144 0.12513522 55664.99542 -4.745582178 0.263523291 EWDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWDRDK 6 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 88.029 0.047213 509880000 451770 311848 370200 273988 611620 475080 454480 382790 384350 355750 FALSE TRUE 469606.2284 365405.4682 379847.7161 328182.0086 507657.0509 364749.8699 418856.67 377659.3262 370517.3186 425452.4013 1.103780886 0.858863335 0.892808961 0.771371857 1.193217031 0.857322391 0.984497135 0.887665283 0.870878428 1 18.69863821 -0.689257429 0.001798908 0.644643678 1.221393376 0 0.121898107 4937328.106 2279.059752 368028.4524 362662.9531 0.204523196 0.689257429 0.576749698 EWEEAER ddPTM_MDA-MB-175_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 ; 116.9 0.012449 195101000 341930 403400 361440 390630 450790 480990 425210 393350 389700 412260 FALSE TRUE 355429.6604 472680.812 370859.4233 467895.4481 374164.8768 369287.362 391880.9291 388077.7866 375674.7731 493034.4538 0.720902277 0.958717608 0.752197783 0.949011665 0.758902089 0.749009241 0.794834775 0.787121029 0.761964545 1 18.91132894 5.035299182 16.92773386 0.821779976 0.321619343 0.105276962 0.092896855 14287999.31 181967476.1 0.02051029 216464438.8 108467.3879 -5.035299182 -0.500160632 EWEKMKS(ph)LEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWEKMKSLEK 10 2 Q7RTT5 Q7RTT5 SSX7 Protein SSX7 1 EWEKMKS(1)LEK 58.978 0.074332 166780000 534070 254890 241630 121070 334370 338070 381450 556940 192200 191650 TRUE FALSE 555155.496 298665.3747 247927.0763 145017.2846 277533.9068 259558.366 351550.9523 549475.1303 185282.7595 229200.1481 2.422142832 1.303076709 1.081705567 0.632710257 1.210880137 1.132452872 1.533816427 2.397359403 0.808388481 1 17.80624845 2.077114549 6.658469771 1.656220185 1.256843069 0 0.591412845 0.557437863 38.89300048 0.2266935 0.166455812 119.430307 -2.077114549 -0.399377116 EWHGPPSQGPSYHDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWHGPPSQGPSYHDTR 16 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 100.58 0.0011607 51948000 29421 27844 37043 33362 40290 40526 35461 39633 38475 30960 FALSE TRUE 30582.5638 32625.9904 38008.37101 39960.90402 33441.52019 31114.45068 32681.47416 39101.78446 37090.29227 37026.01923 0.825974934 0.88116387 1.026531391 1.079265469 0.903189727 0.840340153 0.882662377 1.056062339 1.001735888 1 15.17625183 4.418859861 5.391763982 0.971614124 0.838108093 0.312797884 0.073148884 0.2273753 13.23828735 0.019897403 0.058614783 26233.7189 -4.418859861 -0.133506032 EWHHFLVVNMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWHHFLVVNMK 11 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 81.475 0.012475 356070000 413210 491530 414130 380360 594280 621520 390100 486630 396220 643350 FALSE TRUE 429523.8499 575946.4539 424922.568 455594.0727 493264.4979 477181.3992 359522.9427 480107.5208 381960.1196 769402.1148 0.558256654 0.748563648 0.552276319 0.592140396 0.641101042 0.62019767 0.46727574 0.624000781 0.496437574 1 19.55337827 -1.949400541 2.608569582 1.300984163 0.592109558 0.73022929 0.074935546 7360046.259 3271393.294 13417922.39 0.01733783 0.011235683 1.949400541 -0.708874605 EWLEVLEDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWLEVLEDTKR 11 1 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 106.01 0.0038311 27917000 45348 38125 43204 39618 55859 57417 52979 42711 46070 38075 FALSE TRUE 47138.37406 44672.67218 44329.93173 47454.32215 46364.10713 44082.77191 48826.36755 42138.52891 44411.9497 45535.06726 1.035210375 0.981060859 0.973533903 1.042148942 1.018206625 0.968106002 1.072280563 0.925408294 0.975335107 1 15.47469039 1.717798423 24.99999912 0.962631997 1.009796355 0.257155223 0.035340763 1.149033598 1377.98347 0.015551746 0.00862421 52.21537759 -1.717798423 0.047164358 EWLKDTCGANAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWLKDTCGANAK 12 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 97.551 0.0016889 0 189840 155500 196140 131050 288760 199470 168730 185330 220390 166430 FALSE TRUE 197335.0298 182205.9154 201251.5695 156971.2989 239676.6783 153146.1155 155504.5017 182845.9545 212458.207 199038.772 0.991440149 0.915429258 1.01111742 0.788646841 1.204170805 0.769428559 0.781277437 0.918644908 1.067421211 1 17.60268996 EWLTNFMEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 130.98 0.00060998 50411000 30278.7 72681 68626 86289 76320 91341 67266 71969 66615 69804 FALSE TRUE 31474.12646 85163.39637 70414.44994 103356.7067 63347.15366 70128.43704 61993.51515 71004.37327 64217.53916 83480.75732 0.377022531 1.020156011 0.843481207 1.23809019 0.758823419 0.840055113 0.742608442 0.850547786 0.7692496 1 16.34915607 7.999550561 0.017145488 1.536586406 4.35E-06 0.047957841 0.207424762 24479.05295 32.37702658 1122.663115 1866.158453 99896566.49 -7.999550561 -1.536582059 EWNGVVSESDS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWNGVVSESDSPVK 14 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSESDS(1)PVK;EWNGVVS(0.001)ES(0.01)DS(0.988)PVK 231.21 6.55E-13 171298000 354570 191349 236110 213630 291850 345700 351990 259480 263090 144485 TRUE FALSE 368568.6974 224211.7023 242263.2206 255885.3764 242241.4412 265416.4141 324400.104 256002.095 253621.4423 172794.0694 2.132993908 1.297565958 1.402034349 1.480868974 1.401908307 1.536027336 1.87737985 1.481544453 1.467767054 1 17.39869418 0.714962533 2.115475095 1.000442015 1.561917582 0.34627637 0.236518604 1.452255404 9.094476416 0.21667547 0.059308795 5.18755283 -0.714962533 0.561475567 EWNGVVSESDS(ph)PVKRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EWNGVVSESDSPVKRPGR 18 2 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR;EWNGVVSESDS(1)PVKRPGR 247.85 1.04E-24 2958100000 2339000 1566540 1899790 1572170 2237360 2441940 2394500 1876850 2012040 1298250 TRUE FALSE 2431345.526 1835581.059 1949300.088 1883140.534 1857054.346 1874836.443 2206812.833 1851693.896 1939627.073 1552617.231 1.565965827 1.182249573 1.255493015 1.212881382 1.196079954 1.207532936 1.421350214 1.192627429 1.24926288 1 20.56627077 -4.64296281 0.198378449 1.23E-16 1.312812813 0.362969823 0.114462801 138.0479768 1.551517339 55.13157966 0.271772174 2.28E-05 4.64296281 1.312812813 EWQELDDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWQELDDAEK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 80.979 0.046019 0 356570 146760 187260 157490 280880 263370 252210 187210 234160 123940 FALSE TRUE 370647.6589 171964.8884 192140.1494 188641.0519 233136.1179 202206.3089 232441.1212 184700.7562 225732.6273 148223.67 2.500596962 1.160171573 1.296285198 1.272678324 1.572866991 1.364197155 1.568178154 1.246094879 1.522918892 1 17.17741633 4.744448703 24.94121869 1.352461923 2.500597477 0.799596479 0.175027271 255.9200881 1084014.654 0.038860561 0.352800396 55519.9036 -4.744448703 1.148135554 EWSGLLEELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EWSGLLEELAR 11 0 Q01813;Q01813-2;Q5VSR5;V9GYV7 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;;; 142 8.81E-05 226860000 169683 202939 203919 206174 223737 246654 232567 206092 213602 222667 FALSE TRUE 176382.2159 237792.1946 209233.2967 246954.6018 185706.2647 189372.3466 214337.7908 203329.6738 205914.5057 266294.3354 0.662358122 0.892967529 0.785721921 0.927374596 0.697372193 0.711139222 0.804890538 0.763552381 0.773259053 1 18.02266221 -1.16406869 5.456197184 1.000005964 0.782963858 0.41666939 0.078067342 5.39E-06 8.25E-07 0.071902334 0.016947077 0.068537981 1.16406869 -0.217042106 EWSLESS(ph)PAQNWTPPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EWSLESSPAQNWTPPQPR 18 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 EWSLES(0.071)S(0.815)PAQNWT(0.114)PPQPR 183.41 6.65E-14 250470000 85618 98388 91881 92112 106050 112040 82867 94777 86991 93825 TRUE FALSE 88998.26475 115285.3736 94275.49434 110331.4787 88023.65888 86020.40798 76371.66801 93506.66934 83860.2109 112208.2124 0.793152862 1.027423673 0.840183551 0.983274542 0.784467171 0.766614191 0.680624585 0.83333178 0.747362507 1 16.77581874 3.218246329 24.83909666 0.786730922 0.914265069 0.215163843 0.099296021 267.8172197 327470.0647 0.026330458 0.03150718 1652.899045 -3.218246329 0.127534147 EWSLESSPAQNWT(ph)PPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWSLESSPAQNWTPPQPR 18 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;F8W1U7;E5RHT6;E5RHC5;Q8N6T3-3 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 EWSLES(0.001)S(0.001)PAQNWT(0.997)PPQPR;EWSLESSPAQNWT(1)PPQPR 189.45 3.65E-13 306949000 261760 283080 302130 284510 314780 362290 266780 290960 257430 289020 TRUE FALSE 272094.4869 331696.7879 310003.756 340785.2288 261273.808 278153.6381 245869.0865 287060.1571 248165.1446 345647.9354 0.78720125 0.959637695 0.89687721 0.98593162 0.755895758 0.804731085 0.711328092 0.830498689 0.717970858 1 18.39894378 3.226367899 24.97309829 0.791329237 0.910389882 0.234489312 0.090434767 260.2895264 533123.5338 0.02394921 0.028824373 1684.100089 -3.226367899 0.119060645 EWSQHINGASHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWSQHINGASHSR 13 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 230.23 2.56E-12 1016950000 332785 619240 626920 670740 620900 790740 595430 689910 541300 556830 FALSE TRUE 345923.6088 725589.653 643258.0502 803410.37 515359.6398 607102.6188 548758.6407 680662.8849 521818.7187 665930.1773 0.519459277 1.089588185 0.965954198 1.20644836 0.773894407 0.911661071 0.824048315 1.022123502 0.783593741 1 19.34501139 EWTDGLFTHVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 208.95 6.09E-08 1565779000 953152 1121112 1164489 1217018 1348140 1433448 1134573 1175378 1157555 1213287 FALSE TRUE 990783.177 1313654.265 1194836.54 1457740.528 1118983.644 1100551.426 1045642.204 1159623.98 1115894.822 1451007.358 0.682824364 0.905339492 0.823453123 1.004640342 0.771177099 0.758474049 0.72063191 0.799185458 0.769048355 1 20.4686234 EWVESMGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EWVESMGGK 9 0 P50502;Q3KNR6;Q8NFI4 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ; 85.862 0.051627 102540000 207081 143827 177088 155781 253515 220192 216821 190150 205374 166187 FALSE TRUE 215256.7178 168528.1684 181703.0588 186594.0168 210422.6109 169055.745 199826.0035 187601.3503 197982.6299 198748.1608 1.083062691 0.847948317 0.914237687 0.938846508 1.058739915 0.850602815 1.005423158 0.9439149 0.996148236 1 17.60058198 1.223456159 1.451426861 1.002318744 0.949536154 0.041670316 0.073932026 1.231868768 4.94297185 0.064573481 0.019765853 16.72846756 -1.223456159 -0.052782591 EYAENIGDGRS(ph)PEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYAENIGDGRSPEFR 15 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 1 EYAENIGDGRS(1)PEFR;EYAENIGDGRS(1)PEFR 169.62 7.19E-07 643100000 322800 348310 352170 357610 368860 385810 403270 352030 363700 290040 TRUE FALSE 335544.3933 408129.533 361347.8395 428344.1906 306161.309 296211.4745 371660.6436 347311.6137 350610.508 346867.7848 0.967355309 1.176614119 1.04174517 1.234891821 0.882645556 0.853960752 1.071476395 1.001279533 1.010790057 1 18.40402633 3.228270197 24.99925591 0.973855972 1.105727055 0.353521554 0.089427424 237.6748856 577399.7122 0.025776306 0.031137514 1691.492968 -3.228270197 0.131871083 EYATEVDVDFVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYATEVDVDFVRK 13 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1;K7EJ01;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 145.83 6.73E-05 515350000 518680 348620 482140 382600 582310 535410 496200 434540 481550 354200 FALSE TRUE 539157.8869 408492.7731 494704.9645 458277.1381 483329.1542 411069.1417 457306.5474 428715.7021 464219.1096 423598.7084 1.272803425 0.964339043 1.167862306 1.081866231 1.141007148 0.97042114 1.079574933 1.012079814 1.095893591 1 18.69233866 2.757096215 24.83160262 1.034637238 1.116539005 0.253689187 0.079763648 1144.395805 1533111.386 0.022280038 0.023590457 571.6052576 -2.757096215 0.081901766 EYCIQAFESFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYCIQAFESFVR 12 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 120.57 0.00091861 84326000 101525 100067 107552 114570 110483 130900 120039 99403 107802 89934 FALSE TRUE 105533.2854 117252.7288 110354.8935 137231.604 91703.13912 100500.4588 110630.0295 98070.66538 103922.2271 107554.8454 0.98120438 1.090166867 1.026033677 1.275922098 0.85261746 0.934411262 1.028591777 0.911820058 0.966225433 1 16.71471299 3.211051526 24.99999819 0.947174897 1.088298998 0.413873779 0.084076396 209.0310545 189964.9381 0.023519725 0.028117785 1625.741626 -3.211051526 0.141124101 EYEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYEEEER 7 0 Q16543;K7EKQ2;K7EQA9;K7EL68;K7EIU0 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 153.73 0.004017 938750000 696330 705140 764600 723850 781700 889940 923500 768090 704470 568520 FALSE TRUE 723821.6461 826242.3098 784526.1041 867025.3695 648826.9132 683264.9222 851113.6569 757795.0099 679116.2623 679910.609 1.064583544 1.21522197 1.153866543 1.275204943 0.954282673 1.004933462 1.251802289 1.114550942 0.998831689 1 19.37498556 0.462368243 0.241463644 0.954259428 1.169969338 0.157152175 0.101312367 9.570686375 1.298357028 0.636172805 0.242730215 2.899801316 -0.462368243 0.215709909 EYELFEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EYELFEFR 8 0 A0A2R8YE10;Q9NRW7;B7Z7G7;A0A2R8YF01;A0A087WU65;A0A1B0GXI6;A0A2R8YD95;Q9NRW7-2 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;;; 145.63 0.0013173 376124000 420663 481363 456305 485403 589439 578256 540094 473241 441349 460732 FALSE TRUE 437271.1001 564033.3508 468196.6832 581414.2646 489246.3693 443964.8076 497760.021 466897.9785 425464.9357 551003.6142 0.793590258 1.02364728 0.849716175 1.055191381 0.887918621 0.805738467 0.903369793 0.847359194 0.772163603 1 19.07170226 3.008195787 24.99614094 0.857650136 0.936431793 0.097888663 0.090606913 352.2323858 1074255.516 0.024116093 0.028778508 1019.05069 -3.008195787 0.078781657 EYELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYELRK 6 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;; 91.14 0.077336 1580410000 2084750 1877000 2155500 1577430 2744300 2456790 2123560 2020870 2227850 2045930 FALSE TRUE 2167057.54 2199360.149 2211674.101 1889440.946 2277824.866 1886237.756 1957109.818 1993783.543 2147670.114 2446790.812 0.885673401 0.898875432 0.903908127 0.772211885 0.930943853 0.770902746 0.799868059 0.81485656 0.877749787 1 21.22245933 3.854804808 19.86558763 0.839785532 0.896435474 0.058319527 0.068647228 9.114392608 1531.910231 0.016378371 0.029526748 7158.216144 -3.854804808 0.056649942 EYFLIGHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYFLIGHDR 9 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7;A0A494C040 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 0 ; 81.338 0.021566 179940000 714605 525581 624679 470167 790899 705277 637591 619066 667827 591305 FALSE TRUE 742818.1572 615845.4483 640958.6479 563164.6293 656462.2705 541487.1053 587614.9514 610768.4329 643792.0367 707159.8935 1.050424613 0.870871572 0.906384332 0.796375239 0.928308119 0.765720893 0.830950619 0.863692127 0.910391048 1 19.43167693 4.747036588 4.491250425 0.864593614 1.064166942 0.391165786 0.064669061 0.191466349 9.668882322 0.014334405 0.121823737 55851.72459 -4.747036588 0.199573327 EYFSWEGAFQHVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 259.48 2.02E-24 11202800000 3782800 3384600 3835300 3046600 4354900 4320600 3922800 4087400 3920100 3307600 FALSE TRUE 3932147.865 3965878.721 3935251.069 3649208.387 3614655.654 3317206.129 3615320.686 4032615.089 3779016.367 3955660.892 0.994055854 1.00258309 0.994840351 0.922528115 0.913793106 0.838597195 0.913961228 1.019454195 0.955343865 1 21.91548732 3.750345487 21.71227443 0.937038492 0.997702152 0.251482719 0.047022382 204.6866771 377104.2584 0.01372227 0.024393336 5627.888529 -3.750345487 0.06066366 EYGEQIDPSTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYGEQIDPSTHR 12 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ; 108.72 0.0016758 391900000 370680 499170 483460 565040 527570 571050 474880 480460 473080 427720 FALSE TRUE 385314.7326 584898.5645 496059.3648 676803.2255 437893.8398 438432.2918 437657.6647 474020.2196 456053.9432 511523.5448 0.753268811 1.143444071 0.969768391 1.323112557 0.856058033 0.857110677 0.855596324 0.926683091 0.891560023 1 18.96444112 EYGS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EYGSPLK 7 0 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;Q9UQ88-5;Q9UQ88-10 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK;EYGS(1)PLK 139.02 0.0028627 6392930000 8070480 4722080 6302060 5069650 7779900 9455510 9092410 6661830 6812480 3585753 TRUE FALSE 8389108.782 5533060.507 6466296.861 6072411.639 6457475.377 7259611.102 8379723.146 6572539.065 6567300.176 4288312.647 1.956272658 1.290265184 1.507888392 1.416037528 1.505831293 1.692882889 1.954084004 1.532663219 1.531441552 1 22.03197866 2.786590251 24.09280693 1.605333374 1.513504179 0 0.276030996 1274.191457 639161.9459 0.080073086 0.084930038 611.7729226 -2.786590251 -0.091829195 EYGS(ph)PLKAYT(ph)PVVVTLWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYGSPLKAYTPVVVTLWYR 19 1 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;A0A0D9SER5;A0A0D9SEI3;A0A0D9SEN2;P21127-10;P21127-5;P21127-4;P21127-12 P21127-2 CDK11B Cyclin-dependent kinase 11B 2 EYGS(0.999)PLKAYT(0.999)PVVVT(0.001)LWYR;EYGS(1)PLKAYT(0.999)PVVVTLWYR 145.19 2.93E-07 1366160000 2285560 1414460 1858510 1275600 2675560 2379810 1951160 1810070 2077950 1459150 TRUE FALSE 2375795.674 1657382.502 1906944.297 1527909.873 2220769.267 1827135.194 1798222.981 1785808.972 2003164.985 1745042.505 1.361454329 0.949766265 1.092778137 0.875571723 1.272616145 1.047043375 1.030475175 1.023361303 1.147917589 1 20.73483075 4.750339949 24.71539952 1.050315134 1.361454549 0.455651731 0.102496284 1341.767387 2815235.485 0.022857743 0.367084505 56278.16771 -4.750339949 0.311139415 EYGS(ph)TSSIDKQGTSGESFFDLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYGSTSSIDKQGTSGESFFDLLK 23 1 O43166-3;O43166-2;O43166 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 EY(0.001)GS(0.706)T(0.132)S(0.143)S(0.018)IDKQGTSGESFFDLLK;EYGS(0.963)T(0.031)S(0.005)S(0.001)IDKQGTSGESFFDLLK 122.78 3.89E-05 80072000 94381 68554 90277 45398 129335 102926 86859 75951 107706 70469 TRUE FALSE 98107.23476 80327.61622 92629.69278 54377.5889 107350.6829 79022.99636 80050.76462 74933.00108 103829.6821 84276.05134 1.164117602 0.953148788 1.099122364 0.645231807 1.273798205 0.937668473 0.949863732 0.889137541 1.232018829 1 16.3628351 4.745705356 23.15977081 0.986571455 1.164117844 0.076629161 0.169249465 739.9486518 2398374.688 0.037339102 0.362234654 55680.78586 -4.745705356 0.177546389 EYGS(ph)TSSIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYGSTSSIDR 10 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 EYGS(0.768)T(0.197)S(0.034)S(0.002)IDR;EYGS(0.94)T(0.055)S(0.004)SIDR 150.09 2.33E-05 855290000 410620 397440 460970 447550 513240 587300 481390 489460 466880 482450 TRUE FALSE 426831.5947 465697.2283 472983.2569 536074.0542 425999.6481 450908.4756 443657.3939 482899.5893 450077.08 576976.8404 0.739772491 0.807133312 0.819761252 0.929108444 0.738330585 0.781501863 0.768934492 0.83694796 0.780060911 1 19.13815389 -1.978107312 2.831477564 1.170341228 0.803507251 0.563945141 0.052640899 7298039.42 6532935.654 8112151.913 0.012525332 0.01051702 1.978107312 -0.366833978 EYGSCSHHYQQLLQSLEQGAQEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EYGSCSHHYQQLLQSLEQGAQEESR 25 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 254.68 4.41E-45 1232390000 161012 466623 454968 515725 453156 607738 459731 511136 456720 527051 FALSE TRUE 167368.8781 546761.8704 466824.8398 617733.8657 376128.705 466600.0599 423696.0829 504285.058 440282.7364 630316.5524 0.265531466 0.867440127 0.740619674 0.980037512 0.596729855 0.74026306 0.672195711 0.800050476 0.69851051 1 19.26571702 -4.999999971 0.035959126 2.123268457 4.50E-13 0.231497344 0.174643857 1816.906296 4.897921054 245.6421662 83.37474427 1.00E-05 4.999999971 -2.123268457 EYHPDKNPNAGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYHPDKNPNAGDK 13 1 O60884;I3L320 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;; 121.76 0.00014595 328290000 358426 207976 273394 221612 334213 341299 425279 302723 304169 200997 FALSE TRUE 372576.9352 243694.2602 280518.8722 265446.1922 277403.5936 262037.4797 391944.5207 298665.4933 293222.0171 240378.5138 1.549959392 1.013793855 1.16698813 1.104284189 1.154028242 1.090103585 1.630530593 1.24247999 1.219834554 1 17.87494842 EYHTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYHTMR 6 0 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 67.035 0.075729 19557000 8172.5 15142 9475.2 11978 13102 15631 11266 14068 10665 16760 FALSE TRUE 8495.156611 17742.52071 9722.131496 14347.21265 10874.92672 12000.93714 10382.94148 13879.44147 10281.16873 20043.80111 0.42382962 0.885187426 0.485044301 0.715793006 0.542558104 0.598735593 0.518012598 0.692455557 0.51293508 1 14.29086851 -1.663581537 3.054388786 1.036862243 0.607198057 0.466513245 0.128831211 43991484.88 45636356.06 12700083.03 0.028056196 0.021697938 1.663581537 -0.429664185 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.001)QS(0.998)S(0.001)DS(0.603)S(0.397)PT(0.001)R;EYIPGQPPLSQS(0.998)S(0.001)DS(0.788)S(0.212)PTR 225.69 2.45E-19 906650000 772940 812090 777430 830550 763270 985230 761870 763570 731420 717240 TRUE FALSE 803456.268 951560.1403 797690.4645 994830.3111 633529.638 756425.2638 702152.6386 753335.5931 705096.3371 857769.4456 0.936680914 1.109342546 0.929959057 1.159787535 0.738577996 0.88185149 0.81857968 0.878249507 0.822011487 1 19.7102304 3.235592571 24.99999945 0.851052519 1.031900835 0.484239965 0.089573027 59.44171453 500681.8585 0.023101148 0.028763864 1720.25398 -3.235592571 0.180848315 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLSQS(1)SDS(0.295)S(0.703)PT(0.002)R 252.41 1.10E-30 310750000 240050 269200 235240 247280 227540 273550 231830 231310 204100 202110 TRUE FALSE 249527.3594 315433.0059 241370.5477 296191.2459 188862.8321 210022.1582 213658.5588 228209.6678 196754.4809 241709.5849 1.032343668 1.305008265 0.998597336 1.225401327 0.78136261 0.868902896 0.883947399 0.944148193 0.81401191 1 17.88291516 3.241049345 24.99999939 0.883286972 1.141975543 0.61826027 0.099416829 40.41631134 405989.2232 0.025942722 0.033550096 1742.004791 -3.241049345 0.258688571 EYIPGQPPLSQSS(ph)DS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 EYIPGQPPLS(0.309)QS(0.309)S(0.381)DS(0.517)S(0.42)PT(0.063)R;EYIPGQPPLS(0.266)QS(0.287)S(0.471)DS(0.52)S(0.438)PT(0.018)R;EYIPGQPPLS(0.067)QS(0.347)S(0.586)DS(0.512)S(0.429)PT(0.059)R 90.385 0.0032819 290500000 161207 168644 168334 177853 173468 199223 165550 157193 160447 160004 TRUE FALSE 167571.5768 197607.2951 172720.9223 213031.7926 143981.9713 152956.4775 152573.7584 155086.085 154672.5438 191353.7203 0.875716325 1.032680707 0.902626414 1.113287958 0.75243884 0.799338927 0.797338866 0.810468094 0.808306959 1 17.54588242 3.222295593 24.99998503 0.814781472 0.979160131 0.420027491 0.087297526 196.7813861 302460.1895 0.023039519 0.027615069 1668.382373 -3.222295593 0.164378659 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.498)S(0.498)PT(0.003)R;EYIPGQPPLSQSSDS(0.498)S(0.498)PT(0.003)R 218.14 3.60E-19 4777230000 616000 686740 670140 713300 687830 828330 650610 666850 593490 623720 TRUE FALSE 640320.1557 804682.2529 687604.3989 854388.611 570912.9023 635962.911 599613.4881 657911.9665 572130.4108 745925.9922 0.858423171 1.078769558 0.921813164 1.145406676 0.765374727 0.852581781 0.803851179 0.882007027 0.767006937 1 19.50867297 3.222402857 24.99977007 0.83981096 1.000987218 0.384357874 0.096560143 221.2004433 342247.2397 0.025429324 0.030481322 1668.79449 -3.222402857 0.161176258 EYIPGQPPLSQSSDSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 EYIPGQPPLSQSSDS(0.362)S(0.638)PTR;EYIPGQPPLSQSS(0.001)DS(0.261)S(0.725)PT(0.013)R;EYIPGQPPLSQSS(0.002)DS(0.113)S(0.885)PTR;EYIPGQPPLSQSS(0.001)DS(0.212)S(0.78)PT(0.007)R;EYIPGQPPLSQSSDS(0.212)S(0.688)PT(0.099)R 318.84 8.22E-62 19735600000 1636650 1883330 1762140 1995420 1940040 2330500 1820620 1793560 1669040 1869020 TRUE FALSE 1701266.206 2206777.277 1808062.816 2390108.12 1610272.694 1789276.694 1677915.047 1769520.262 1608971.576 2235218.684 0.761118461 0.987275783 0.808897505 1.069294981 0.720409464 0.800492903 0.750671538 0.791654201 0.719827365 1 21.09198455 3.197802711 24.99999761 0.784309201 0.905424874 0.188001583 0.109501596 205.6303159 126128.4418 0.028718248 0.034325227 1576.894764 -3.197802711 0.121115673 EYKDVDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYKDVDKK 8 2 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 53.683 0.07595 536200000 2265300 758040 1435500 753770 2334100 1759200 1840800 1323300 1743200 759550 FALSE TRUE 2354735.793 888227.4733 1472910.309 902863.4562 1937350.516 1350652.461 1696513.286 1305563.328 1680462.573 908369.28 2.592267093 0.977826411 1.621488465 0.993938782 2.13277855 1.486897995 1.867647138 1.437260547 1.849977327 1 19.79291939 -1.352338241 3.736974719 0.997675717 1.624661089 0.149416286 0.466322613 24787108.01 17948049.65 442629.3638 0.098113409 0.044428511 1.352338241 0.626985372 EYKPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYKPKPR 7 2 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 56.547 0.068028 288090000 258470 219120 251760 160230 387960 319290 311500 269650 290640 219860 FALSE TRUE 268674.5952 256752.1555 258321.0724 191923.0158 322014.6978 245139.7364 287083.816 266035.7828 280179.9232 262937.3575 1.021819789 0.976476519 0.982443403 0.729919162 1.224682186 0.932312315 1.091833503 1.011783891 1.065576705 1 18.00435961 3.229367187 24.99999996 1.049003954 0.935064019 0.268404695 0.101954111 282.2780967 767607.2318 0.028023271 0.033932617 1695.770934 -3.229367187 -0.113939935 EYLSEEVQAVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYLSEEVQAVHK 12 0 Q53GS9;B9A018;A0A087X1B2;Q53GS9-2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 150.06 0.0003643 0 144060 135520 166650 134460 186980 190960 168840 163790 181070 148260 FALSE TRUE 149747.6 158794.5058 170993.0359 161055.7867 155197.2064 146612.434 155605.8796 161594.663 174553.3261 177308.7084 0.844558631 0.895582102 0.964380359 0.908335457 0.875293762 0.826876668 0.87759863 0.911374655 0.984459972 1 17.43590387 1.273863121 2.784812952 1.000174822 0.886802137 0.597321731 0.034899678 0.198083837 2.553857932 0.034092055 0.009946687 18.78724596 -1.273863121 -0.113372685 EYNEFAEVFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYNEFAEVFLK 11 0 O95373 O95373 IPO7 Importin-7 0 122.51 0.0009056 23803000 49724 40053 49384 44300 60680 65426 59514 51065 55386 43026 FALSE TRUE 51687.14192 46931.79118 50670.98761 53062.40778 50365.63527 50231.80304 54849.13717 50380.5572 53392.66868 51456.12092 1.00448967 0.912074022 0.984741693 1.031216633 0.978807465 0.976206565 1.065939993 0.979097458 1.037634935 1 15.65105508 4.00379063 24.93378812 1.008011971 0.955813339 0.265283937 0.034378588 127.3397754 837577.1619 0.007957181 0.01706794 10087.66449 -4.00379063 -0.052198632 EYRPCDPQLVSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYRPCDPQLVSER 13 1 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ;; 93.243 0.0052014 340849000 294312 351646 325138 381067 493234 444982 464033 359281 373480 335080 FALSE TRUE 305931.665 412038.4651 333611.3634 456440.9152 409394.2609 341641.6743 427660.8809 354465.4259 360038.5278 400732.5105 0.763431109 1.02821322 0.832503864 1.139016434 1.021614793 0.852542944 1.067197868 0.884543721 0.898451007 1 18.61228003 4.750120902 24.06365769 0.965590755 0.763430904 0.296562273 0.094980543 1304.094856 2714490.388 0.021671419 0.331634609 56249.78958 -4.750120902 -0.20215985 EYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(1)PPYAPSHQQYPPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK;EY(0.074)S(0.847)PPY(0.074)APS(0.002)HQQY(0.002)PPSHATPLPK;EYS(1)PPYAPSHQQYPPSHATPLPK 220.98 3.08E-32 3035150000 1109490 1237270 1571100 1283790 1975680 1961280 1781210 1676590 1715790 1092170 TRUE FALSE 1153293.522 1449761.498 1612044.157 1537719.83 1639854.619 1505802.443 1641594.106 1654118.053 1654039.053 1306159.801 0.882965102 1.109941905 1.234186013 1.177283078 1.25547779 1.152847027 1.256809546 1.266397919 1.266337436 1 20.31689998 4.695615959 2.181331504 1.215968672 0.812344371 0.596211104 0.078297241 0.34124285 1.992534994 0.018215693 0.258344433 49615.33857 -4.695615959 -0.403624301 EYSPPYAPS(ph)HQQYPPSHATPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYSPPYAPSHQQYPPSHATPLPK 23 0 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 EYS(0.461)PPYAPS(0.537)HQQYPPS(0.002)HATPLPK 116.94 0.00027533 222550000 46683 60354 73923 52829 84971 87175 83614 74356 77685 49357 TRUE FALSE 48526.08089 70719.33001 75849.49411 63278.41852 70527.65977 66929.9274 77060.1162 73359.37944 74889.13202 59027.55915 0.822091945 1.198073087 1.284984424 1.072014825 1.194825956 1.133875911 1.305493863 1.242798796 1.2687147 1 15.84910107 4.738295675 8.187964617 1.20173189 0.81936281 0.581767842 0.092760974 0.058036509 52.92138412 0.021038628 0.12366433 54738.85077 -4.738295675 -0.38236908 EYSSELNAPSQESDSHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYSSELNAPSQESDSHPR 18 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 172.93 9.58E-12 495540000 110860 174670 188160 199690 201140 235000 188890 231010 208290 209140 FALSE TRUE 115236.8384 204668.2138 193063.6042 239188.086 166950.2946 180424.8115 174084.3082 227913.6888 200793.6836 250116.9788 0.46073177 0.818289965 0.771893236 0.956304874 0.66748885 0.72136171 0.696011559 0.911228378 0.802799093 1 17.93224347 -4.999999966 0.035024024 2.225214436 5.90E-09 0.351066457 0.120521565 1332.086365 3.500167781 186.3691015 65.04333986 1.00E-05 4.999999966 -2.22521443 EYTAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYTAGR 6 0 P07237;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 ;; 159.87 0.020901 3144750000 1419550 1927780 1562100 1716140 1751700 1944970 1549010 1667970 1293880 1737800 FALSE TRUE 1475594.93 2258861.219 1602809.609 2055587.37 1453946.66 1493280.194 1427594.549 1645613.59 1247313.512 2078288.638 0.71000481 1.086885228 0.771216077 0.989076942 0.699588418 0.718514342 0.686908701 0.791811859 0.600163754 1 20.9869646 3.225550737 24.99846163 0.737243997 0.894975043 0.194217173 0.137958959 306.2757915 588507.4408 0.036094349 0.043389452 1680.934291 -3.225550737 0.157731046 EYTINIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;;; 164.72 0.00032843 4177333300 4008308 3404062.4 4120223 3729453.5 4333636 4758711 4830469 4285991 4216496 3292343.2 FALSE TRUE 4166559.095 3988683.637 4227599.396 4467128.271 3597006.101 3653572.489 4451844.218 4228544.301 4064745.133 3937414.814 1.058196632 1.013020935 1.073699266 1.134533312 0.913545123 0.927911501 1.130651564 1.073939247 1.032338558 1 21.90881728 -0.349213354 6.723422297 0.999997011 1.042140112 0.027143603 0.070117474 0 0 0.070302746 0.016570516 0.447493412 0.349213354 0.0421431 EYTINIHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 ; 168.83 3.83E-05 1364680000 2141100 2211100 2375100 1754630 3053800 2845200 2117400 2420200 2659700 2809600 FALSE TRUE 2225632.281 2590839.225 2436997.057 2101690.577 2534716.167 2184445.419 1951432.655 2387761.178 2563977.917 3360087.327 0.662373345 0.771063063 0.725277893 0.625486891 0.754360206 0.650115669 0.580768434 0.710624738 0.763068833 1 21.6800673 0.808910437 2.204003229 0.999635662 0.684099291 0.7475601 0.055152387 0.354844196 2.987662444 0.053555271 0.014607649 6.44036435 -0.808910437 -0.315536371 EYVAYSHTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EYVAYSHTGR 10 0 Q969X5;Q969X5-2 Q969X5 ERGIC1 Endoplasmic reticulum-Golgi intermediate compartment protein 1 0 ; 175.86 2.67E-06 702220000 213659 293190 248010 398130 723550 579470 418140 262130 252350 697250 FALSE TRUE 222094.4223 343543.1018 254473.3443 476878.9257 600561.2294 444896.8745 385365.0942 258616.5761 243267.9728 833862.7878 0.266344086 0.411989966 0.305174122 0.571891362 0.720215889 0.533537269 0.462144492 0.310142843 0.291736214 1 19.66945048 -1.403196964 3.469889439 1.004792884 0.434191977 0.602719635 0.138713703 1003757992 1310485145 47201294.11 0.036555542 0.039518735 1.403196964 -0.570600907 EYVDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYVDLER 7 0 Q13951-2;A0A494C0A9;Q13951 Q13951-2 CBFB Core-binding factor subunit beta 0 79.809 0.073554 255380000 579420 584530 573250 632570 717030 780680 625440 678840 587110 670870 FALSE TRUE 602295.949 684918.4805 588189.3659 757690.458 595149.4967 599378.9013 576416.3785 669741.2602 565980.0258 802314.1319 0.750698417 0.853678694 0.733116048 0.944381294 0.741791118 0.747062625 0.71844226 0.834761889 0.705434447 1 19.61380768 -1.106927712 4.708322234 1.000013392 0.78535273 0.459505632 0.071103494 9.35E-06 1.77E-06 0.064426468 0.015184517 0.078175792 1.106927712 -0.214660662 EYVEPELHINDLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;;; 133.14 4.63E-05 228433000 210261 245892 237914 239585 246956 268149 254146 236782 240039 234472 FALSE TRUE 218562.2666 288122.0382 244114.2343 286974.1979 204978.5073 205875.4586 234225.3724 233608.3246 231400.0433 280412.2992 0.779431813 1.027494297 0.870554662 1.023400895 0.730989717 0.734188405 0.835289226 0.833088724 0.825213601 1 18.0971901 3.235463886 24.99999443 0.815734239 0.928620991 0.196086567 0.096409012 110.4315193 891519.1855 0.025830704 0.032142985 1719.744329 -3.235463886 0.112886752 EYVESQLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EYVESQLQR 9 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;;; 203.02 4.40E-05 666416000 411560 535759 491414 517924 602595 684362 461983 522056 500190 569453 FALSE TRUE 427808.7066 627771.4406 504220.6525 620367.8214 500166.1171 525429.2971 425771.5653 515058.6932 482188.2596 681026.4125 0.628182254 0.921801899 0.740383403 0.910930633 0.734429837 0.771525579 0.625190973 0.756297676 0.708031657 1 19.37735123 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;EYVSNDAAQS(1)DDEEKLQSQPTDTDGGR 318.13 1.70E-82 3256320000 1631570 809470 1113410 866940 1447010 1601860 1423540 1141850 1248530 672490 TRUE FALSE 1695985.643 948490.1757 1142426.379 1038418.144 1201047.757 1229852.291 1311959.215 1126545.368 1203595.649 804251.5399 2.108775127 1.179345178 1.420483919 1.291160903 1.493373276 1.529188606 1.631279705 1.400737596 1.496541305 1 19.61728727 -0.217781511 1.133434325 0.995348903 1.489123432 0.29125203 0.235300975 26.42441851 22.52537238 0.781634674 0.063996255 0.605645493 0.217781511 0.493774528 EYVTCHTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 EYVTCHTCR 9 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ;;;; 211.27 5.43E-06 1963430000 1312012 1424010 1373490 1403129 2019270 1805830 1650328 1470860 1353588 2075870 FALSE TRUE 1363811.247 1668572.64 1409284.278 1680663.728 1676035.207 1386453.35 1520970.979 1451145.528 1304872.632 2482596.982 0.549348628 0.672107737 0.567665347 0.676978076 0.675113689 0.558468958 0.612653198 0.584527226 0.525607919 1 21.24341865 -1.530388297 5.80399934 1.000742027 0.605501222 0.835112618 0.052973545 0.0004925 3.98E-05 0.049664196 0.011685142 0.029485718 1.530388297 -0.395240804 EYWDYESHVVEWGNQDDYQLVR ddPTM_MDA-MB-175_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 ;;; 314.9 2.54E-67 891350000 794244 770653 871780 868870 813206 958410 887510 882424 860720 716400 FALSE TRUE 825601.3664 903006.6579 894499.303 1040729.893 674977.5346 735833.8023 817944.6471 870596.5496 829742.8553 856764.8637 0.963626546 1.053972561 1.044042935 1.214720557 0.787821213 0.858851516 0.954689766 1.016144086 0.968460415 1 19.70853979 3.238440747 25 0.935870352 1.066221639 0.384313687 0.085465148 3.867858653 806703.1134 0.025754842 0.032692703 1731.572768 -3.238440747 0.130351287 EYWMDPEGEMKPGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 EYWMDPEGEMKPGRK 15 2 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 ;; 67.115 0.027288 995880000 1493280 1017730 1322290 866837 1964180 1548860 1449320 1377700 1583620 1032001 FALSE TRUE 1552235.847 1192517.211 1356749.964 1038294.771 1630309.385 1189160.738 1335718.511 1359234.185 1526625.826 1234201.837 1.257683955 0.966225438 1.099293424 0.841268211 1.320942277 0.963505889 1.082252895 1.10130624 1.236933684 1 20.23514692 1.591518212 4.269185348 1.132179268 1.068971056 0.010221299 0.142274539 0.670449055 27.49895297 0.077643609 0.034411199 39.04075534 -1.591518212 -0.063208212 EYYDHLPELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 EYYDHLPELK 10 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;; 143.96 3.31E-05 2509940000 4309000 3228890 4031770 3315240 5168600 5012530 4663710 3965940 4335620 2962470 FALSE TRUE 4479122.647 3783426.74 4136841.238 3970984.577 4290043.218 3848445.873 4298156.224 3912783.061 4179581.883 3542909.277 1.264249886 1.067886995 1.167639619 1.120825928 1.210881477 1.086238899 1.213171405 1.104398322 1.179703333 1 21.75650309 -1.803097318 2.354841638 0.947674103 1.152200376 0.383222717 0.059531396 5537329.148 3443084.77 1652743.245 0.012553653 0.015736302 1.803097318 0.204526273 EYYSEADASHCIQQILESVNHCHLNGIVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EYYSEADASHCIQQILESVNHCHLNGIVHR 30 0 Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5 Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 0 154.69 3.22E-09 329480000 10520 14044 11003 16291 10228 14418 8824.7 12374 9439.4 12650 FALSE TRUE 10935.33772 16455.94775 11289.74722 19513.31118 8489.448213 11069.63801 8132.996955 12208.14677 9099.677838 15128.5253 0.72282906 1.087743017 0.746255633 1.289835644 0.56115504 0.731706349 0.537593506 0.806962115 0.601491398 1 13.88498374 3.202963615 24.99999549 0.694192158 0.955286092 0.286967356 0.196381545 202.1610832 141978.4176 0.051770225 0.06187932 1595.745452 -3.202963615 0.261093934 FAAFFGNVPIFHIPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAAFFGNVPIFHIPGR 16 0 Q92620;J3KTG2 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 0 68.277 0.040278 0 31625 34177 46176 32216 36379 52788 55388 43726 40089 32837 FALSE TRUE 32873.57942 40046.63389 47379.38449 38588.22864 30195.31057 40528.78701 51046.54383 43139.92449 38646.20472 39270.78145 0.837100211 1.019756481 1.206479289 0.982619322 0.768900171 1.032034136 1.299860658 1.098524728 0.984095638 1 15.26116869 2.470829892 24.98770355 1.117223753 0.972717782 0.168341787 0.134929338 274.7533307 1091239.501 0.04864053 0.040793547 295.6854072 -2.470829892 -0.144505972 FAAGHDAEGSHSHVHFDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAAGHDAEGSHSHVHFDEK 19 0 Q9GZN8-2;Q9GZN8;H7BYU9 Q9GZN8-2 C20orf27 UPF0687 protein C20orf27 0 ; 90.654 0.00067745 206663000 73352 224870 164118 192158 178337 236058 130067 153363 146017 394820 FALSE TRUE 76247.9936 263489.6733 168395.0499 230166.2789 148023.3404 181237.107 119872.0087 151307.4198 140761.8767 472177.4197 0.16148166 0.558031075 0.356635118 0.487457191 0.313490934 0.383832643 0.253870693 0.320446115 0.298112258 1 18.84896953 -1.389513392 3.269523571 1.006529419 0.352262259 0.77158959 0.10637675 63780481.55 84776666.27 3917835.815 0.025272626 0.040783699 1.389513392 -0.654267159 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAAQAAHQGTASQYFMLLLLTDGAVTDVEATR 32 0 Q99829;B0QZ18;A6PVH9;H0Y524 Q99829 CPNE1 Copine-1 0 ;;; 291.93 2.20E-89 666229000 352652 568058 604479 591127 673424 753980 652102 673783 643990 610507 FALSE TRUE 366574.9733 665617.5426 620232.2193 708050.1563 558955.629 578879.5717 600988.5413 664752.041 620812.9257 730124.1578 0.502072106 0.9116498 0.849488697 0.969766784 0.765562436 0.792850867 0.823131977 0.910464383 0.85028405 1 19.47778229 4.742763357 24.84401152 0.867886023 0.502071948 0.712356957 0.070932075 205.6778606 1215791.265 0.01636253 0.127093762 55304.86757 -4.742763357 -0.365814076 FACNGTVIEHPEYGEVIQLQGDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FACNGTVIEHPEYGEVIQLQGDQR 24 0 K7EM18;P41567;O60739;K7EQP2 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 ;;;;; 332.25 7.20E-87 2925350000 1233204 1445525 1520693 1424204 1504612 1902751 1516414 1443518 1519103 1382791 FALSE TRUE 1281891.846 1693782.674 1560323.509 1705907.3 1248858.59 1460865.917 1397553.508 1424170.002 1464430.78 1653722.421 0.775155389 1.024224291 0.943522014 1.031556009 0.755180297 0.883380365 0.84509558 0.861190478 0.885536025 1 20.65728567 3.249429733 24.99999724 0.863415815 0.949365641 0.137529069 0.086221291 346.754025 797561.9549 0.022333328 0.029948348 1775.945905 -3.249429733 0.085949826 FADDQLIIDFDNFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FADDQLIIDFDNFVR 15 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 104.87 0.0031641 15507000 23590 21706 27956 24119 24367 29584 30313 24991 24415 16186 FALSE TRUE 24521.35142 25433.83665 28684.55633 28889.66621 20225.10604 22713.56435 27936.98785 24656.03652 23536.30892 19357.3368 1.26677299 1.313911976 1.481844151 1.492440128 1.044828958 1.173382712 1.443224765 1.273730822 1.215885696 1 14.24059286 -4.301909257 0.191257456 2.63E-10 1.366533431 0.345060422 0.131038598 123.929452 1.546683627 47.57852237 0.377282911 4.99E-05 4.301909257 1.366533431 FADQDDIGNVS(ph)FDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FADQDDIGNVSFDR 14 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR 174.78 2.47E-07 190314000 284171 331797 335465 367028 330414 439366 377655 356735 338431 288707 TRUE FALSE 295390.2905 388780.5537 344207.4935 439625.0429 274250.3463 337329.9052 348053.4143 351953.5508 326250.9344 345273.609 0.85552525 1.126007154 0.996912259 1.273265698 0.794298606 0.976993018 1.008051022 1.019346807 0.944905507 1 18.39738054 3.223964268 24.99898995 0.966737409 1.062717982 0.166441716 0.11467044 460.2196402 788211.1697 0.032002842 0.038406844 1674.805073 -3.223964268 0.095980573 FADQDDIGNVSFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FADQDDIGNVSFDR 14 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 374.42 6.41E-97 307330000 404780 411250 414180 446170 476880 527440 495110 473570 435410 403500 FALSE TRUE 420761.027 481878.9884 424973.8711 534421.0943 395820.1079 404950.0534 456301.9845 467222.5688 419739.6792 482558.0995 0.871938586 0.998592685 0.880668818 1.107475131 0.820253786 0.839173674 0.945589733 0.968220343 0.869822058 1 18.88034313 -1.159024975 3.866383691 1.00003869 0.927508444 0.071478186 0.082061953 11138121.15 3338872.789 3765.228378 0.018392658 0.069338593 1.159024975 -0.072530246 FADQHVPGS(ph)PFSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FADQHVPGSPFSVK 14 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 FADQHVPGS(0.887)PFS(0.113)VK 78.661 0.013691 158220000 347540 234720 317320 243210 400690 419870 358420 324860 374900 250120 TRUE FALSE 361261.1476 275031.3341 325589.6199 291316.2121 332580.8569 322361.5557 330326.1038 320505.7831 361407.4222 299126.2252 1.207721414 0.919449085 1.088468989 0.973890577 1.111841186 1.077677343 1.104303388 1.071473365 1.20821042 1 18.19039488 3.178518539 24.99999567 1.096969759 1.041176853 0.069540856 0.085084435 170.6054035 71034.58299 0.022603965 0.027016916 1508.407001 -3.178518539 -0.055792907 FAEAFEAIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAEAFEAIPR 10 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;; 149.72 5.31E-05 327813000 370028 412897 400190 382494 472143 509518 408383 416160 398085 395023 FALSE TRUE 384636.9912 483808.8479 410619.2802 458150.1716 391888.3015 391190.1663 376372.8733 410582.0559 383757.9986 472420.1937 0.81418406 1.024107044 0.86918232 0.969793793 0.829533341 0.828055556 0.796690909 0.869103526 0.812323444 1 18.84971111 3.224125625 24.99907963 0.845589584 0.923220792 0.13837185 0.074575263 347.030022 600998.9938 0.019600279 0.023523283 1675.427445 -3.224125625 0.077631208 FAEEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAEEDKK 7 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 117.17 0.0084845 2167250000 3291300 1301950 1536150 1265790 2609400 2782200 2687000 1776590 1966630 966860 FALSE TRUE 3421243.065 1525549.785 1576183.331 1516159.484 2165855.12 2136076.215 2476385.919 1752777.717 1895851.37 1156297.705 2.958790846 1.319339974 1.363129343 1.311218968 1.873094714 1.847341048 2.141650811 1.515853321 1.639587592 1 20.14108146 0.678042095 1.386263294 1.002587674 1.764340155 0.203793443 0.469481298 1.865108968 5.544564691 0.433752723 0.128193849 4.764771677 -0.678042095 0.761752481 FAEFEDFPETSEPVWILGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAEFEDFPETSEPVWILGR 19 0 Q9Y4P1;H0Y2Y0;F2Z2K8;C9JIK8;Q9Y4P1-6;Q9Y4P1-2 Q9Y4P1 ATG4B Cysteine protease ATG4B 0 124.86 6.62E-05 15452000 21747 28450 28164 30322 34062 33380 28335 30635 29341 27902 FALSE TRUE 22605.58835 33336.06619 28897.97698 36319.6011 28272.15341 25628.00088 26114.02866 30224.38793 28285.02314 33368.86268 0.677445575 0.999017153 0.866016239 1.088427899 0.847261523 0.768021407 0.782586716 0.905766199 0.847647204 1 15.0262149 FAELETILGDIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAELETILGDIDR 13 0 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 ;;; 168.3 7.08E-05 117716000 92529 110803.8 118915 99924 134452 141163 120301.6 120618 96776 107626.7 FALSE TRUE 96182.11637 129833.4907 122014.0226 119688.669 111597.8971 108380.0326 110872.0462 119001.313 93293.05066 128714.0912 0.747253975 1.008696791 0.947946114 0.929880076 0.867021598 0.842021503 0.861382349 0.9245399 0.72480837 1 16.97381048 3.231165535 23.9726193 0.868398439 0.918426698 0.037646753 0.089603111 293.0360085 949932.4085 0.024396493 0.029739879 1702.807425 -3.231165535 0.050028258 FAELPEFRPEEVLPS(ph)PTLQS(ph)LATSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.984)PT(0.167)LQS(0.724)LAT(0.065)S(0.06)PR 81.862 0.0093101 112410000 48222 61889 57037 57828 63802 78837 70330 71028 67382 74259 TRUE FALSE 50125.8418 72517.95432 58523.43108 69266.2058 52956.95883 60528.30154 64817.35083 70075.98584 64956.93498 88808.62928 0.564425352 0.816564279 0.65898361 0.779949047 0.596304202 0.681558786 0.729854197 0.789067306 0.731425938 1 16.43841225 0.066043889 0.482612005 1.030615276 0.6860335 0.602954831 0.074243246 2.482167297 0.760866166 0.219404314 0.036792924 1.164243679 -0.066043889 -0.344581776 FAELPEFRPEEVLPS(ph)PTLQSLAT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.999)PT(0.001)LQS(0.004)LAT(0.616)S(0.38)PR 122.09 0.00031706 77645000 65351 62195 61278 62278 82728 89340 70483 74813 69388 74880 TRUE FALSE 67931.10794 72876.50744 62874.95502 74596.40252 68665.92411 68592.13896 64958.35829 73810.2541 66890.73943 89551.30234 0.758571971 0.813796176 0.702111007 0.833001872 0.766777504 0.765953561 0.72537592 0.824223123 0.746954401 1 16.45042679 -1.592604745 2.921598156 1.014621724 0.773348845 0.744966202 0.040214163 11800092.29 11922878.82 1324125.029 0.009354565 0.025550256 1.592604745 -0.241272879 FAELPEFRPEEVLPS(ph)PTLQSLATS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 2 FAELPEFRPEEVLPS(0.997)PT(0.003)LQS(0.006)LAT(0.19)S(0.804)PR;FAELPEFRPEEVLPS(0.999)PT(0.001)LQS(0.002)LAT(0.245)S(0.752)PR 162.29 9.21E-12 1832840000 246214 263448 251096 250808 302240 342940 284220 297260 291530 304410 TRUE FALSE 255934.7188 308693.1447 257639.768 300417.0738 250865.3528 263297.3823 261942.0937 293275.7159 281037.8922 364053.3112 0.703014396 0.847933902 0.707697912 0.825200773 0.689089606 0.723238532 0.719515757 0.805584531 0.771969059 1 18.47379021 0.271055205 0.960578241 1.001389581 0.750794578 0.670065275 0.052036883 1.823251014 1.929784731 0.052670732 0.015163244 1.866616951 -0.271055205 -0.250595002 FAELPEFRPEEVLPSPTLQS(ph)LATSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPS(0.004)PT(0.029)LQS(0.322)LAT(0.322)S(0.322)PR 77.276 0.013389 140920000 31203 36961 30169 27820 33911 32454 28277 26626 27432 25972 TRUE FALSE 32434.91853 43308.76423 30955.22892 33322.71297 28146.82033 24917.05035 26060.57485 26269.12202 26444.72768 31060.71614 1.044242457 1.394326005 0.996603838 1.072825006 0.906187102 0.802204632 0.839020412 0.84573459 0.851388215 1 14.92280347 3.547707992 1.350453665 0.853826622 1.20105603 0.577876732 0.108008904 0.26503618 0.964584869 0.032876491 0.068126116 3529.457789 -3.547707992 0.347229407 FAELPEFRPEEVLPSPTLQSLAT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPS(0.022)PT(0.022)LQS(0.078)LAT(0.44)S(0.44)PR 95.244 0.012538 175070000 25192 30955 30530 32677 29610 36506 26376 27486 30207 25076 TRUE FALSE 26186.59961 36271.28045 31325.63688 39140.41307 24576.90278 28028.03475 24308.5802 27117.59513 29119.85597 29989.16209 0.87320211 1.209479623 1.044565259 1.30515194 0.819526158 0.934605464 0.810578839 0.904246509 0.971012657 1 14.87215359 3.217228656 24.99999795 0.896863572 1.110803079 0.40978886 0.11806382 206.6456438 242177.9047 0.031931547 0.038198996 1649.030379 -3.217228656 0.213939508 FAELPEFRPEEVLPSPTLQSLATS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAELPEFRPEEVLPSPTLQSLATSPR 26 1 I3L2J0;A0A0A0MQR4;Q96RK0;I3L135;I3L1Q4;I3L373 I3L2J0 CIC Protein capicua homolog 1 FAELPEFRPEEVLPSPTLQSLAT(0.152)S(0.848)PR;FAELPEFRPEEVLPSPTLQSLAT(0.287)S(0.713)PR 217.94 2.18E-34 590660000 257320 311690 323920 259520 288000 297920 281990 271410 248870 180393 TRUE FALSE 267479.1923 365220.3329 332361.6213 310852.2814 239045.8629 228732.595 259886.887 267772.1929 239913.2173 215737.5545 1.239836026 1.692891781 1.540583057 1.44088164 1.108040106 1.060235412 1.204643705 1.241194161 1.112060521 1 17.71891781 3.31046328 4.657429889 1.142891271 1.507095131 0.667645953 0.122970056 0.123846468 5.067390207 0.034279377 0.046342975 2043.917113 -3.31046328 0.364203859 FAEQTLR ddPTM_MDA-MB-175_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 ; 119.29 0.011201 295250000 784590 325260 465250 391960 618600 603330 733550 490150 545020 324940 FALSE TRUE 815566.219 381120.8748 477374.7972 469488.5181 513450.593 463215.7511 676052.4342 483580.341 525404.8367 388605.7716 2.098698163 0.9807391 1.228429509 1.208135731 1.321263425 1.191994007 1.739687065 1.244398247 1.352025304 1 18.5679478 4.751779005 25 1.278540181 2.098698693 0.613678712 0.20056813 1524.611541 2883454.661 0.046812271 0.906545731 56464.95737 -4.751779005 0.820158512 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPR 39 1 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 67.209 0.0024417 22034000 12162 10933 11103 10083 14115 19109 11092 12415 12317 6673.4 FALSE TRUE 12642.16515 12810.6577 11392.3533 12077.38731 11715.73734 14671.22435 10222.58006 12248.59723 11873.71358 7980.92496 1.584047615 1.605159523 1.42744774 1.513281652 1.46796736 1.838286217 1.280876604 1.534734043 1.487761586 1 12.96234024 -2.786487361 0.327614886 2.70E-11 1.553051091 0.589023194 0.133185482 45.14749628 1.482811812 31.5840698 0.109992812 0.001634981 2.786487361 1.553051091 FAGDKGYLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAGDKGYLTK 10 1 P60903 P60903 S100A10 Protein S100-A10 0 116.55 0.00098122 671720000 395510 375240 391900 299660 558480 537190 374230 379910 416710 437360 FALSE TRUE 411125.0402 439684.551 402113.2359 358931.8536 463549.7691 412435.7637 344896.8747 374817.9279 401712.6885 523052.3182 0.786011314 0.840612948 0.768782055 0.686225529 0.886239775 0.788517227 0.659392689 0.716597393 0.768016266 1 18.99659573 2.442296837 24.985714 0.750069939 0.793699783 0 0.097532096 652.6020439 468223.5447 0.032197852 0.026938754 276.8833473 -2.442296837 0.043629843 FAGHSEAGGGSGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FAGHSEAGGGSGDR 14 0 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;; 182.33 1.54E-06 853260000 434800 428889 510360 456750 488013 715130 451410 433430 427520 405580 FALSE TRUE 451966.2397 502547.3495 523660.4009 547093.7867 405060.7246 549051.8954 416027.3047 427620.5798 412133.6387 485045.6357 0.931801477 1.036082613 1.079610582 1.127922295 0.835098174 1.131959253 0.857707552 0.881608963 0.84968013 1 18.88776096 2.215034864 24.99803279 0.885704677 1.023006249 0.308087197 0.092218639 258.6697214 274855.9681 0.033045538 0.024419655 164.0721479 -2.215034864 0.137301572 FAGVDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FAGVDIR 7 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 128.75 0.0086702 1795480000 4614740 4885750 5197590 5039600 5658260 6144410 5707950 5499580 5303250 4726630 FALSE TRUE 4796933.499 5724839.557 5333043.465 6036417.838 4696470.986 4717463.897 5260545.964 5425867.126 5112387.068 5652722.652 0.848605848 1.012757906 0.943446865 1.067877943 0.830833436 0.834547206 0.930621629 0.959867919 0.904411446 1 22.43051448 4.783134203 22.30871532 0.938982365 0.84860464 0.135372588 0.070784275 17773.43378 8894617.897 0.017192218 7.026901502 60692.38484 -4.783134203 -0.090377724 FAHIDGDHLTLLNVYHAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAHIDGDHLTLLNVYHAFK 19 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 319.16 2.61E-62 2387700000 879850 1070660 1269350 1072080 1544180 1527480 1313410 1337190 1255820 946920 FALSE TRUE 914587.1574 1254537.526 1302430.304 1284134.224 1281700.835 1172745.919 1210461.492 1319267.155 1210623.284 1132450.844 0.807617533 1.107807489 1.150098753 1.133942573 1.131793792 1.035582185 1.068886565 1.164966375 1.069029433 1 20.111017 4.738949163 24.78968049 1.104514258 0.807617437 0.743432826 0.050553749 13.19030587 841221.7883 0.011756005 0.069292948 54821.27891 -4.738949163 -0.296896821 FAHTNVESLVNEYDDNGEGIILFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAHTNVESLVNEYDDNGEGIILFR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 378.82 3.07E-119 2240080000 740848 995587 872055 1208692 919702 1247788 1086977 1004377 874416 641420 FALSE TRUE 770097.2511 1166571.323 894781.4697 1447767.67 763371.3825 958008.1474 1001776.902 990914.9691 842945.939 767093.9683 1.003915143 1.520767169 1.166456141 1.887340704 0.995147158 1.248879781 1.305937661 1.291777814 1.098882241 1 19.54904379 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAHTNVESLVNEYDDNGEGIILFRPSHLTNK 31 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 210.21 1.83E-26 1882540000 244132 369970 393615 365020 432840 524050 438200 408990 414670 324333 FALSE TRUE 253770.5199 433509.4695 403872.9303 437219.8665 359266.0114 402347.3296 403852.739 403508.158 399746.1077 387879.8416 0.654250344 1.117638565 1.04123207 1.127204406 0.926230169 1.037298891 1.041180014 1.040291644 1.030592634 1 18.56525027 4.74558615 24.99841748 1.040572644 0.654250167 0.825808383 0.053174967 310.6778454 1105433.641 0.012139727 0.12243939 55665.50457 -4.74558615 -0.386322477 FAKPVYPGQTLQTEMWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FAKPVYPGQTLQTEMWK 17 1 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 167.82 1.98E-09 279630000 206580 171650 208100 190840 272820 288440 230450 188490 236670 167830 FALSE TRUE 214735.9379 201129.5522 213523.257 228587.5824 226446.1538 221454.1814 212386.7268 185963.5999 228152.2929 200713.0752 1.069865218 1.002074987 1.063823355 1.138877386 1.128208283 1.103337095 1.058160893 0.926514626 1.136708671 1 17.61477508 -1.205051397 5.906996527 0.999998756 1.061737793 0.087485102 0.062966762 1.13E-06 1.53E-07 0.06700325 0.015792499 0.062366102 1.205051397 0.061739037 FAMEPEEFDSDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAMEPEEFDSDTLR 14 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;; 302.33 1.35E-43 786770000 438341 673986 538128 687830 605485 730105 568557 563405 508492 626180 FALSE TRUE 455647.0412 789737.8526 552152.0578 823880.721 502564.876 560549.1786 523992.0167 555853.4775 490191.4722 748867.9821 0.608447753 1.054575535 0.737315616 1.100168175 0.67109943 0.748528702 0.699712138 0.742258303 0.65457662 1 19.51435188 FAPPLS(ph)PLSSDMLIMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAPPLSPLSSDMLIMPK 17 0 Q5H9M0 Q5H9M0 MUM1L1 PWWP domain-containing protein MUM1L1 1 FAPPLS(0.996)PLS(0.004)S(0.001)DMLIMPK;FAPPLS(1)PLSSDMLIMPK 212.39 1.69E-12 188099000 198530 170706 206976 164221 258948 243817 230408 211682 202148 168139 TRUE FALSE 206368.1177 200023.4276 212369.9646 196703.4236 214932.1115 187194.1968 212348.0189 208844.749 194872.733 201082.6178 1.026285215 0.994732562 1.056132881 0.978221916 1.068874644 0.930931767 1.056023744 1.038601702 0.969117744 1 17.61742885 1.23477543 24.99201846 0.984558872 1.019382663 0.103422945 0.040201835 216.2622493 1427787.709 0.031124229 0.00895354 17.17020301 -1.23477543 0.034823791 FAQFFLCPLFDESCKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAQFFLCPLFDESCKDR 17 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 202.03 9.99E-12 709690000 757350 634510 758010 570540 1004100 969510 853760 810970 967740 613840 FALSE TRUE 787250.7628 743482.1567 777764.3633 683391.1091 833423.4407 744355.9956 786840.0603 800100.2736 932911.2264 734110.1953 1.072387726 1.012766423 1.059465416 0.9309108 1.135283839 1.013956761 1.07182827 1.089891243 1.270805435 1 19.48563711 1.606302689 3.35018691 1.145381175 1.039724205 0.174253051 0.079000208 0.267336017 7.048817232 0.04581535 0.019244149 40.39268184 -1.606302689 -0.10565697 FAQHGTFEYEYSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FAQHGTFEYEYSQR 14 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 221.91 4.09E-12 2410200000 730200 1096740 1213400 1138750 1291520 1389160 1143140 1184170 1076530 1176640 FALSE TRUE 759028.8598 1285096.564 1245022.201 1363991.351 1071987.892 1066548.643 1053537.7 1168298.138 1037785.896 1407180.08 0.539397104 0.913242436 0.884763946 0.969308314 0.761798655 0.757933301 0.74868719 0.830240674 0.737493311 1 20.42437553 -2.136513521 2.461296999 1.426710695 0.803174275 0.226989336 0.113015442 42948967.84 8403913.121 102746951.1 0.026472706 0.007302751 2.136513521 -0.623536419 FAQPGSFEYEYAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAQPGSFEYEYAMR 14 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 134.99 0.00012624 923650000 463096 438196 515135 422771 562775 678444 523206 469209 535613 477012 FALSE TRUE 481379.3877 513452.7543 528559.8413 506393.842 467114.7065 520885.6629 482195.7466 462920.0208 516336.3928 570473.3685 0.84382447 0.900046843 0.926528512 0.887673062 0.818819479 0.913076213 0.84525549 0.811466488 0.90510166 1 19.12180001 3.455481939 24.87666146 0.866553176 0.893787356 0 0.055527046 737.5226953 847856.6557 0.014751457 0.019974906 2854.183814 -3.455481939 0.027234179 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167;Q01167-2 Q01167 FOXK2 Forkhead box protein K2 1 FAQSAPGS(0.944)PLS(0.028)S(0.028)QPVLITVQR;FAQSAPGS(0.942)PLS(0.055)S(0.003)QPVLITVQR;FAQSAPGS(0.878)PLS(0.015)S(0.107)QPVLITVQR;FAQSAPGS(0.998)PLS(0.002)SQPVLITVQR 283.86 3.58E-45 874970000 692520 790700 768950 728200 869510 1031510 787830 774630 746500 726680 TRUE FALSE 719861.2243 926496.5742 788989.4687 872235.7865 721711.0008 791957.4352 726077.826 764247.3519 719633.6108 869059.0329 0.828322585 1.066091645 0.907866369 1.003655395 0.830451067 0.911281519 0.835475841 0.879396362 0.828060677 1 19.72909465 3.23686405 24.99999758 0.873499209 0.956554713 0.171683791 0.074738994 63.03482905 928862.8778 0.019237849 0.024161182 1725.297726 -3.23686405 0.083055504 FARPDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FARPDFR 7 1 F8WF90;C9JQU6;F8WF33;O75915 F8WF90 ARL6IP5 PRA1 family protein 3 0 ; 91.9 0.014651 108540000 359180 543640 443370 606350 596130 778210 496630 428710 427360 732840 FALSE TRUE 373360.7037 637005.9411 454924.5864 726284.2202 494800.0355 597482.5214 457702.8429 422963.8437 411979.3971 876425.9669 0.426003699 0.726822305 0.5190679 0.828688614 0.564565695 0.681726174 0.522237885 0.482600767 0.470067539 1 19.7412727 -1.812216053 2.676656744 1.131129471 0.582668643 0.519964691 0.120987456 39194802.75 26942361.26 33211448.56 0.02847901 0.015409337 1.812216053 -0.548460828 FAS(ph)AENIPDLPYDYSSSLESVADETSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FASAENIPDLPYDYSSSLESVADETSPER 29 0 P50747 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 FAS(1)AENIPDLPYDYSSSLESVADETSPER;FAS(1)AENIPDLPYDYSSSLESVADETSPER;FAS(1)AENIPDLPYDYSSSLESVADETSPER 242.09 1.15E-45 199759000 273707 264671 288868 274213 364572 396874 316538 317389 314569 234988 TRUE FALSE 284513.1637 310126.1854 296396.1374 328451.513 302602.1817 304706.0282 291726.9244 313134.9196 303247.7231 281029.3995 1.01239644 1.103536448 1.054680179 1.168744315 1.076763435 1.084249651 1.038065501 1.114242567 1.079060496 1 18.10036154 0.947311848 22.29717379 1 1.084346315 0.261544984 0.040793819 6093.355799 2578661.476 0.036948149 0.009237037 8.85751401 -0.947311848 0.084346316 FAS(ph)DDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 267.18 5.03E-37 8703440000 4741860 2711191 3737970 3132420 4833850 5053260 5977980 3893620 4200010 1837386 TRUE FALSE 4929072.294 3176816.964 3835384.569 3752003.327 4012193.904 3879716.948 5509410.307 3841432.393 4048852.461 2197386.608 2.243152059 1.445725096 1.745430028 1.707484388 1.825893491 1.765605076 2.507255795 1.748182308 1.842576289 1 21.06735729 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 FASDDEHDEHDENGATGPVKR 21 1 P05455 P05455 SSB Lupus La protein 1 FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR 209.76 1.13E-22 51400802000 7715970 4776504 6610216 4606711 8726640 8536670 7796190 6453525 6740220 3926413 TRUE FALSE 8020602.454 5596831.406 6782483.659 5517904.686 7243288.85 6554157.767 7185104.256 6367026.053 6497640.799 4695718.452 1.708067154 1.191900976 1.444397429 1.175092745 1.542530483 1.395773157 1.530139494 1.355921595 1.383737306 1 22.16291448 0.369302335 1.53629293 0.999972099 1.410279717 0.405609603 0.150845619 4.605950783 10.19737802 0.131528794 0.037745652 2.34046599 -0.369302335 0.410307618 FAS(ph)ENDLPEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FASENDLPEWK 11 0 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6;C9JDM3;C9JIC6 P43487 RANBP1 Ran-specific GTPase-activating protein 1 FAS(1)ENDLPEWK;FAS(1)ENDLPEWK;FAS(1)ENDLPEWK;FAS(1)ENDLPEWK;FAS(1)ENDLPEWK 248.61 3.09E-16 540530000 1778860 1136376 1401285 861634 1610000 1901650 1779400 1354011 1739170 837393 TRUE FALSE 1849090.766 1331539.738 1437803.638 1032062.633 1336332.775 1460020.607 1639925.978 1335862.697 1676577.611 1001464.125 1.846387423 1.329593047 1.435701591 1.030553773 1.334379077 1.457886079 1.637528431 1.333909686 1.67412648 1 19.93367931 4.742098767 23.72996109 1.375018281 1.846387799 0.327641211 0.20823695 202.3919297 1357290.98 0.047926476 0.349335815 55220.30067 -4.742098767 0.471369518 FASEAEDKIR ddPTM_MDA-MB-175_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 93.442 0.0080101 183080000 269820 269700 276100 262530 369750 367940 307880 303700 299260 281610 FALSE TRUE 280472.7019 316018.877 283295.3928 314457.6504 306900.0271 282491.5112 283747.5611 299629.3983 288489.6911 336786.0878 0.832791829 0.938337088 0.841173086 0.933701426 0.911261 0.838786166 0.842515684 0.88967273 0.856596224 1 18.36147302 -0.878001261 4.789664587 1.000000516 0.877936662 0.485022189 0.03826043 8.07175E+11 1.89043E+11 4846675.506 0.008514842 0.132433769 0.878001261 -0.122063854 FATHAAALSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FATHAAALSVR 11 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 118.9 0.00065773 830230000 236490 394720 328360 310700 684710 527590 329040 307350 326220 713790 FALSE TRUE 245826.8078 462510.0895 336917.3314 372155.5327 568323.2388 405065.2182 303248.985 303230.476 314479.4059 853643.4842 0.287973624 0.541807087 0.394681548 0.435961311 0.665761819 0.474513337 0.355240789 0.355219107 0.368396657 1 19.70327414 -1.344944109 3.152739269 1.004876063 0.432563884 0.732266357 0.103202025 34412855.96 45529746.97 1555166.982 0.027150692 0.04519141 1.344944109 -0.572312178 FATHGAALTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FATHGAALTVK 11 0 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 121.29 0.001014 0 381280 323270 371790 317890 540310 487830 443460 397430 420310 389490 FALSE TRUE 396333.2288 378789.1078 381479.1528 380767.6932 448468.2992 374538.8756 408700.4464 392103.1009 405183.1252 465803.1083 0.850859992 0.81319575 0.818970818 0.817443436 0.962785115 0.804071224 0.877410303 0.841778627 0.869859213 1 18.82936074 -5 0.232397706 1.820703314 0.833140308 0.528007134 0.043165238 126.0741409 1.260920451 48.69851767 0.07066319 1.00E-05 5 -0.987563007 FATLAELVQYYMEHHGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FATLAELVQYYMEHHGQLK 19 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 199.56 3.98E-16 785430000 317110 261350 317340 287070 374810 395010 424620 340340 326720 215050 FALSE TRUE 329629.7477 306234.8295 325610.1411 343851.5892 311099.9301 303274.9139 391337.1749 335778.299 314961.411 257184.9301 1.281683758 1.190718404 1.266054512 1.336981871 1.209635144 1.179209504 1.521617828 1.305590879 1.224649558 1 17.97244658 0.869164021 4.001525961 1.000071468 1.289791021 0.463031263 0.092390224 0.671668059 18.92835921 0.091538082 0.023397355 7.398846567 -0.869164021 0.289719553 FATVEVTDKPVDEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FATVEVTDKPVDEALR 16 1 Q9NRV9;A0A3B3IRV5;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ;;; 272.16 3.29E-35 2133020000 2803110 2165250 2557490 2129940 3324130 3199650 3037360 2682150 2759460 1912130 FALSE TRUE 2913778.947 2537114.844 2624140.29 2551235.775 2759095.57 2456579.779 2799283.787 2646200.166 2660147.574 2286775.264 1.27418684 1.109472752 1.14752872 1.115647793 1.206544261 1.074255008 1.224118448 1.157175438 1.163274597 1 21.12488316 -1.301967913 3.089535943 0.998882145 1.161088233 0.434238958 0.055949356 5885004.673 7936273.923 61301.68217 0.012103841 0.049892135 1.301967913 0.162206088 FAVLHGEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FAVLHGEAPR 10 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 161.17 7.15E-06 943240000 866250 1143830 1102780 1147080 1446280 1477310 1190990 1106350 1111660 1285390 FALSE TRUE 900450.2189 1340273.905 1131519.353 1373969 1200441.842 1134227.141 1097637.092 1091521.188 1071651.574 1537237.56 0.585758664 0.871871687 0.736073189 0.893790938 0.780908477 0.737834653 0.714032184 0.710053681 0.697128148 1 20.5519087 -1.862176793 2.385709304 1.116567903 0.75136156 0.451442144 0.083405014 9864839.168 5555165.037 6524098.311 0.019354528 0.013734827 1.862176793 -0.365206342 FAVQDVNDVLDLEWDQHLEQK ddPTM_MDA-MB-175_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 ; 211.75 1.32E-22 69144000 72229 52416 63968 56731 85712 76842 72557 65912 71338 63547 FALSE TRUE 75080.65669 61418.04026 65635.05863 67952.22247 71142.70486 58996.61005 66869.79275 65028.55745 68770.55932 75997.81797 0.987931742 0.808155312 0.863643989 0.894133862 0.936115099 0.776293473 0.879890957 0.855663481 0.904901761 1 16.21367038 0.893483511 4.225269129 0.999978851 0.871681775 0.305509913 0.056309171 0.630711407 22.55611357 0.050263889 0.012807289 7.824984954 -0.893483511 -0.128297076 FCDS(ph)PTSDLEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FCDSPTSDLEMR 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 FCDS(0.544)PT(0.337)S(0.119)DLEMR;FCDS(0.649)PT(0.253)S(0.099)DLEMR;FCDS(0.498)PT(0.498)S(0.005)DLEMR 225.63 1.81E-11 284908000 526370 837546 859336 830290 853905 1051228 753531 816627 798574 919522 TRUE FALSE 547151.494 981388.0103 881731.0021 994518.8838 708758.5331 807096.2285 694467.2712 805681.4508 769833.4777 1099684.731 0.497553052 0.892426696 0.801803442 0.904367276 0.644510661 0.733934196 0.631514881 0.732647666 0.700049256 1 20.06865855 -0.873774697 4.231767322 1.000004365 0.732565421 0.33306053 0.1158103 29706344.01 63856170.67 2082.473569 0.026828288 0.13372891 0.873774697 -0.267438945 FCFSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FCFSNR 6 0 Q15363;E7EQ72;F5GX39 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 119.03 0.049697 848420000 370180 265840 303940 313240 634340 526780 475840 315130 366820 503010 FALSE TRUE 384794.9922 311495.9521 311860.9261 375197.9371 526515.1134 404443.3284 438542.4174 310906.1978 353618.2199 601565.1788 0.639656359 0.517809147 0.518415854 0.623702884 0.875242005 0.672318383 0.729002331 0.516828781 0.587830267 1 19.19836153 3.475679663 24.99965356 0.695854332 0.557297644 0.230793707 0.134130792 81.20219161 1408163.039 0.037484203 0.051132291 2990.058349 -3.475679663 -0.138556688 FCFTPHTEEGCLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 309.23 4.13E-56 1.20018E+11 15006274 19895188 18326165 21228136 21502126 24017200 17032305 18682694 17548100 18884776 FALSE TRUE 15598733.28 23312031.78 18803759.92 25426997.94 17847202.3 18439569.28 15697268.43 18432283.05 16916547.31 22584886.29 0.690671323 1.03219611 0.832581563 1.125841309 0.79022768 0.816456149 0.695034202 0.816133533 0.749020699 1 24.42885431 FCIWTESAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FCIWTESAFR 10 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 219.56 1.45E-08 3023937900 1117254 1235790 1143906 983757 2420394 1836072 1385820 1137170 1164916 2480623 FALSE TRUE 1161364.051 1448027.319 1173717.13 1178341.198 2008976.292 1409672.104 1277195.807 1121928.096 1122990.901 2966653.582 0.391472755 0.488101249 0.395636733 0.397195414 0.677186007 0.475172468 0.430517339 0.378179678 0.378537928 1 21.50040504 -1.018627942 4.278064152 1.000033407 0.446125439 0.790298595 0.085646464 48583836.38 101590145.4 24764.77448 0.021455562 0.095801445 1.018627942 -0.553907969 FCLDNGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FCLDNGAK 8 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 101.43 0.012562 241410000 208290 313390 319520 314890 333870 430190 298410 304840 284850 336320 FALSE TRUE 216513.45 367212.2947 327846.9537 377174.3021 277118.8967 330284.8921 275019.8445 300754.1184 274598.3041 402215.4648 0.538302151 0.912974082 0.815102805 0.93774192 0.688981208 0.82116408 0.683762482 0.747743796 0.682714436 1 18.61760903 FCLESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FCLESER 7 0 Q9H074;Q9H074-3;Q9H074-2 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 81.613 0.062176 132370000 106200 431670 499260 416310 574720 601660 486980 482600 484070 436650 FALSE TRUE 110392.858 505805.9646 512271.1257 498654.8754 477029.2997 461933.5832 448809.2351 476131.5364 466648.4153 522203.2073 0.211398276 0.968599881 0.980980428 0.954905808 0.913493623 0.884585879 0.859453234 0.911774439 0.89361461 1 18.99425179 4.740755202 24.99917891 0.923670755 0.211398031 0.960855836 0.043479661 36.22816432 412658.961 0.011063378 0.073335807 55049.73109 -4.740755202 -0.712272725 FCLSS(ph)PTEALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FCLSSPTEALK 11 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 FCLS(0.03)S(0.964)PT(0.006)EALK;FCLS(0.156)S(0.844)PT(0.001)EALK;FCLS(0.001)S(0.848)PT(0.151)EALK;FCLS(0.046)S(0.907)PT(0.046)EALK 175.54 1.02E-05 200064000 742170 526199 631575 550769 720970 777460 798670 647910 662500 453421 TRUE FALSE 771471.4447 616569.585 648034.3633 659709.4643 598419.7769 596906.6975 736068.1585 639225.8262 638656.7544 542260.1637 1.422696145 1.137036475 1.195061719 1.216592161 1.10356581 1.10077549 1.357407768 1.178817603 1.177768159 1 19.04862566 -4.158129337 0.310500484 2.29E-17 1.2164328 0.299476432 0.098146172 216.5364353 3.23372454 139.529711 0.089904135 6.95E-05 4.158129337 1.2164328 FCNVDDDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FCNVDDDELR 10 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 285.74 4.23E-24 2333980000 1628070 1647150 1634710 2076040 1800390 2002710 2170080 1711620 1677670 1016400 FALSE TRUE 1692347.461 1930035.199 1677311.886 2486674.516 1494360.351 1537610.954 1999983.459 1688678.534 1617290.984 1215544.12 1.392255068 1.587795266 1.379885648 2.045729542 1.229375657 1.264956926 1.64534008 1.389236726 1.330507843 1 20.21317083 FCNVDDDELREYCIQAFESFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FCNVDDDELREYCIQAFESFVR 22 1 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 233.68 1.85E-30 195733000 94831 121896 123544 103047 148691 147822 90795 116237 126490 147475 FALSE TRUE 98575.00111 142830.6898 126763.6581 123429.389 123416.5569 113492.5808 83678.25065 114679.0331 121937.6496 176369.9027 0.55891056 0.809835962 0.718737473 0.699832495 0.699759738 0.64349177 0.47444745 0.650218838 0.691374479 1 17.42824486 -1.933833836 6.945359993 1.118122267 0.659686167 0.579780207 0.086645704 0.048524855 0.00046228 0.025687508 0.020497013 0.011645715 1.933833836 -0.458436101 FCPFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FCPFAER 7 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 76.847 0.092244 92286000 86359 96683 96731 93654 134640 128880 113080 108040 104030 91452 FALSE TRUE 89768.52 113287.5532 99251.88933 112178.4817 111753.9409 98949.5732 104216.4941 106591.9005 100285.9806 109370.2684 0.820776261 1.035816724 0.907485103 1.025676203 1.021794519 0.90472095 0.952877739 0.97459668 0.916940061 1 16.73886108 4.755724814 24.59233047 0.968976735 0.820776112 0.476008047 0.047268575 2466.238676 3533477.761 0.010717514 0.312349559 56980.31082 -4.755724814 -0.148200623 FCQLLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FCQLLWR 7 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 97.071 0.028538 94554000 135300 164840 137180 142310 247410 223630 181120 148600 157720 231780 FALSE TRUE 140641.7485 193149.9877 140755.0235 170458.4932 205355.3366 171695.3216 166923.3411 146608.2601 152043.688 277192.8533 0.507378696 0.696807242 0.507787347 0.614945484 0.740839218 0.619407462 0.602192081 0.528903463 0.548512295 1 18.08053054 -1.752147134 2.840715089 1.079546268 0.59737926 0.729117197 0.073815574 16588764.58 14018120.31 9267713.38 0.018273047 0.017695094 1.752147134 -0.482167008 FCSNSGRLS(ph)GPAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FCSNSGRLSGPAELR 15 1 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5 Q96PC5 MIA2 Melanoma inhibitory activity protein 2 1 FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR;FCSNSGRLS(1)GPAELR 193.85 4.61E-08 4165150000 2193300 2653020 2340930 3104550 2620720 3752790 2397210 2413160 2296950 2872430 TRUE FALSE 2279893.178 3108655.547 2401936.559 3718620.724 2175250.95 2881261.397 2209310.416 2380815.537 2214283.218 3435227.663 0.663680373 0.90493436 0.699207387 1.082496151 0.633218862 0.838739577 0.643133624 0.693059026 0.644581214 1 21.71197428 FDASFFGVHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 105.17 0.0025024 25737610000 602550 630600 788680 706370 931790 976140 809400 688090 682950 655300 FALSE TRUE 626339.1393 738900.6446 809233.6487 846087.8777 773404.6686 749446.2785 745957.113 678867.279 658370.7629 783693.4885 0.799214423 0.942843925 1.032589476 1.079615807 0.986871372 0.956300249 0.951848043 0.866240806 0.840087065 1 19.57992998 1.907981173 4.127116382 0.889372195 0.973189321 0.107311086 0.078602619 0.416451521 11.97799674 0.038892578 0.022297272 80.90608255 -1.907981173 0.083817126 FDCHHCNESLFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDCHHCNESLFGK 13 0 Q14192;C9J3S8;F8WDA8;U3KQT4;Q14192-2 Q14192 FHL2 Four and a half LIM domains protein 2 0 59.898 0.055461 70459000 136280 134440 141030 131740 180960 199880 172590 167050 159560 117180 FALSE TRUE 141660.4396 157529.0242 144705.3577 157797.7788 150200.4838 153460.8992 159061.9448 164810.968 153817.4668 140139.1775 1.010855367 1.12408983 1.032583181 1.126007599 1.071795101 1.095060653 1.135028389 1.176052058 1.097605035 1 17.09650081 7.019833413 0.542331892 1.113930314 1.85E-08 0.115430909 0.051403257 69.97304238 1.973236273 0.024140693 81.47462391 10467269.66 -7.019833413 -1.113930296 FDDDKVSIVTPEDILR ddPTM_MDA-MB-175_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 ;; 230.33 2.16E-15 283027000 646551 391957 540712 435130 645437 730099 821773 558412 610930 280213 FALSE TRUE 672077.3327 459272.5657 554803.3989 521197.4153 535725.8493 560544.572 757360.285 550927.4005 588942.7486 335115.3723 2.005510305 1.370490893 1.655559383 1.55527755 1.598631079 1.672691312 2.259998638 1.643993221 1.757432804 1 18.35429834 2.468235365 24.99368724 1.759809048 1.620452823 0 0.325211481 754.3237208 2121699.111 0.10505835 0.088020494 293.9242139 -2.468235365 -0.139356225 FDDDVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDDDVVSR 8 0 Q93009;A0A669KBL1;Q93009-3;H3BND8;F5H2X1 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 122.52 0.0032269 233680000 450430 433800 476190 409950 554830 591890 477080 450530 469710 389730 FALSE TRUE 468213.3242 508301.7755 488599.9026 491036.8864 460520.1948 454432.5177 439685.223 444491.3823 452805.2289 466090.1317 1.004555326 1.09056541 1.048294888 1.053523456 0.988049657 0.974988499 0.943348063 0.953659715 0.971497138 1 18.83024944 3.113890306 2.554739013 0.962983022 1.053328371 0.707439758 0.024355922 0.132300029 1.755332233 0.007253464 0.00902774 1299.841223 -3.113890306 0.090345349 FDDGAGGDNEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FDDGAGGDNEVQR 13 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 196.24 3.34E-07 509400000 491190 663650 669150 588030 773100 873150 683420 705730 657020 579510 FALSE TRUE 510582.5605 777626.725 686588.5987 704340.5789 641688.7381 670374.1452 629851.7546 696270.8437 633373.9785 693053.8891 0.736714083 1.122029235 0.990671302 1.016285443 0.925885776 0.967275642 0.90880632 1.004641709 0.913888499 1 19.40260801 3.226498806 24.96682446 0.954708339 0.97927149 0 0.094879118 1344.799504 2783606.697 0.025761305 0.031023866 1684.607794 -3.226498806 0.024563151 FDDKPDYSYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDDKPDYSYLR 11 1 P48730-2;H7BYT1;P48730;H0Y645;B0QY35;B0QY34;A0A669KBC0;P49674 P48730-2;P49674 CSNK1D;CSNK1E Casein kinase I isoform delta;Casein kinase I isoform epsilon 0 ; 117.86 0.00072785 1057410000 643640 465680 607270 476410 922380 813480 691670 639570 656440 481440 FALSE TRUE 669051.4042 545656.9175 623095.9551 570642.4761 765594.1771 624561.5984 637455.0981 630997.6103 632814.8526 575768.9503 1.162013693 0.947701187 1.082197911 0.9910963 1.329689933 1.084743452 1.107136982 1.095921567 1.099077768 1 19.13513046 5.073680538 21.10006905 1.089184637 3.774069859 0.052317659 0.097964111 2360.085037 680718.0708 0.022120835 2151.872619 118489.6832 -5.073680538 2.684885222 FDDMS(ph)SPGLELPSCELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDDMSSPGLELPSCELSR 18 0 Q6IN85-2;Q6IN85;G3V5Z3;G3V231;H0YIY8;Q6IN85-5 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 FDDMS(0.5)S(0.5)PGLELPSCELSR 86.39 0.0034446 0 13662 16218 17493 16616 15630 22192 17027 16679 14425 14734 TRUE FALSE 14201.38631 19003.31534 17948.88195 19902.59521 12973.21818 17038.24432 15692.37925 16455.44529 13905.84707 17620.8452 0.805942402 1.078456517 1.018616403 1.129491519 0.736242674 0.966936837 0.890557693 0.933862428 0.789170265 1 14.10499551 3.249764732 24.99999771 0.890351762 1.013899488 0.236461883 0.107035575 308.172512 687628.2044 0.028158772 0.037788915 1777.316334 -3.249764732 0.123547726 FDDPGLMLMGFKPLVLLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDDPGLMLMGFKPLVLLKK 19 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 162.4 1.56E-11 145245000 258680 219480 280980 174549 467210 355780 248020 279830 357100 276620 FALSE TRUE 268892.8861 257173.9827 288302.5696 209074.2712 387793.8111 273155.4869 228579.5443 276079.3366 344248.0408 330818.3928 0.812811174 0.777387196 0.871482892 0.631991074 1.172225667 0.825696191 0.690951741 0.834534423 1.040595228 1 18.33567992 -4.999999997 0.117024445 1.565240217 0.754216837 0.13461793 0.144397377 345.5360822 2.64342312 45.37053595 1.489066665 1.00E-05 4.999999997 -0.81102338 FDDTNPEKEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDDTNPEKEEAK 12 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;A0A0U1RR66 P47897 QARS Glutamine--tRNA ligase 0 ; 113.65 0.0010424 561080000 626010 198848 322340 251753 535740 531520 550880 319720 401370 121563 FALSE TRUE 650725.3582 232998.5972 330740.4452 301548.992 444675.1062 408082.5353 507700.5861 315434.6764 386924.7721 145380.9424 4.476001789 1.602676344 2.274991755 2.074198908 3.058689116 2.806987825 3.492208661 2.16971132 2.66145456 1 17.14947864 0.285439241 1.176638759 0.997771601 2.704271142 0.312404059 0.772534736 4.981107801 7.072324643 0.723415177 0.213037199 1.929475377 -0.285439241 1.706499541 FDDTNPEKEKEDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDDTNPEKEKEDFEK 15 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 133.45 2.32E-05 530160000 1294950 271960 517750 282170 954920 885100 861990 530100 650040 218959 FALSE TRUE 1346075.626 318667.0144 531242.9903 337982.3838 792603.0395 679548.9388 794424.9714 522994.8766 626645.1874 261859.8238 5.140443487 1.216937405 2.02873042 1.290699653 3.026821862 2.595086672 3.033779523 1.997232217 2.393055866 1 17.9984352 -1.588845679 0.422016133 4.29E-07 2.496088038 0.159961838 1.054027602 61.91470177 5.245910926 65.58823961 0.587676561 0.025772368 1.588845679 2.496087609 FDEDDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FDEDDDK 7 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;; 99.139 0.025003 6771160000 9263700 3156570 5119400 3182430 7210100 7615500 7499900 4961300 5614800 2279190 FALSE TRUE 9629438.029 3698686.343 5252815.77 3811905.155 5984529.777 5846915.539 6912038.241 4894801.889 5412724.445 2725753.643 3.532761684 1.356940805 1.927105842 1.398477506 2.195550502 2.145063826 2.535826471 1.795760927 1.9857717 1 21.37822374 0.450574585 1.321915995 1.000376137 2.074530339 0.242185037 0.585050877 3.793028766 7.668760684 0.524910875 0.155453222 2.822114204 -0.450574585 1.074154202 FDEDDDKSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDEDDDKSFR 10 1 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 112.15 0.0015133 82849000 88995 82665 100320 85060 118610 131620 101160 95942 95781 82729 FALSE TRUE 92508.59132 96862.07071 102934.4216 101884.6141 98448.71457 101053.2497 93230.81487 94656.05442 92333.86052 98938.16361 0.935014235 0.979016258 1.040391471 1.029780728 0.99505298 1.021377859 0.942313981 0.956719338 0.933248174 1 16.5942395 2.23319855 24.99989993 0.954271411 1.002097366 0.286280888 0.032201099 158.4676464 738826.5867 0.012171635 0.009253862 171.0797274 -2.23319855 0.047825955 FDEFDEAIDEAIEDDIKEADGGGVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FDEFDEAIDEAIEDDIKEADGGGVGR 26 1 Q96T23-2;Q96T23;Q96T23-3;H0YDG9 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 ;;;; 219.07 3.03E-34 97178300 153394 81560.9 120145 84242.7 169026 160134 142254 112361.9 133075.2 71360.1 FALSE TRUE 159450.1136 95568.35012 123276.0774 100905.6546 140295.0209 122945.3054 131103.7598 110855.8725 128285.8495 85341.74532 1.868371838 1.119831212 1.444499136 1.182371584 1.643920222 1.440623283 1.536220747 1.298964207 1.503201617 1 16.38096399 -1.70383985 2.381836028 0.915179857 1.430472196 0.293259655 0.207227988 9520961.496 6863704.505 4826315.864 0.046756242 0.019776988 1.70383985 0.515292339 FDEILEASDGIMVAR ddPTM_MDA-MB-175_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 ;;; 220.23 3.95E-12 251126000 311617 344034 340326 364357 405649 462602 444682 382001 347433 283626 FALSE TRUE 323919.8798 403119.1633 349195.1751 436425.7271 336696.9279 355169.6963 409826.6629 376880.9014 334928.9542 339197.0844 0.954960684 1.188451145 1.029475757 1.28664351 0.992629192 1.047089473 1.208225783 1.111097114 0.987416961 1 18.37176424 1.239742986 24.99999938 0.993708432 1.108718489 0.16306319 0.097568884 48.52814245 1026275.454 0.069265152 0.022059741 17.36772707 -1.239742986 0.115010057 FDENGLPTHDMEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDENGLPTHDMEGK 14 0 P49589-3;P49589 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ; 127.75 7.77E-05 94980000 448040 303720 381780 331220 512520 519070 533040 431770 455410 238791 FALSE TRUE 465728.9652 355881.5474 391729.5004 396734.3274 425402.0335 398523.8591 491258.932 425982.8294 439019.8831 285577.5245 1.630831999 1.246181918 1.37170984 1.389235123 1.489620145 1.395501483 1.720229674 1.491653904 1.537305444 1 18.12352292 -1.102528047 6.228058862 0.999998784 1.472737121 0.550554639 0.128658541 2.19E-06 3.16E-07 0.125587048 0.029601075 0.078971785 1.102528047 0.472738338 FDEVLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDEVLIR 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 111.04 0.015516 40800000 43593 39145 45248 51260 60342 67310 60728 49195 46561 40160 FALSE TRUE 45314.0853 45867.84924 46427.20005 61399.075 50085.08839 51678.27259 55967.98068 48535.62149 44885.27871 48028.58309 0.943481618 0.955011501 0.966657708 1.278386141 1.042818363 1.075989947 1.16530568 1.010557014 0.934553464 1 15.55160563 3.964693202 24.97005624 1.077179827 0.952143362 0.26550019 0.089584111 716.752925 506910.8099 0.023025063 0.041531896 9219.199265 -3.964693202 -0.125036465 FDFLCQYHKPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDFLCQYHKPASK 13 1 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 147.68 2.58E-05 1852440000 2970700 2058430 2690700 2261140 3471100 3431800 3516400 2913300 3203100 1745290 FALSE TRUE 3087985.53 2411949.34 2760821.852 2708386.743 2881083.662 2634816.459 3240775.38 2874251.979 3087821.057 2087246.16 1.479454407 1.15556535 1.322710232 1.297588562 1.380327686 1.262341026 1.552656051 1.377054625 1.479375608 1 20.99316932 3.239834153 24.86294311 1.372237579 1.303159366 0 0.157490733 116.5557835 2275446.543 0.041359646 0.053045131 1737.13733 -3.239834153 -0.069078213 FDGILGMAYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 191.85 3.84E-06 1435840000 916920 1028860 942330 855830 1496150 1458270 1057080 917630 920380 1378240 FALSE TRUE 953120.7096 1205558.702 966887.8939 1025110.62 1241834.957 1119608.893 974223.3074 905330.6708 887255.7036 1648279.74 0.57825179 0.731404186 0.586604246 0.621927574 0.753412741 0.679259027 0.591054591 0.549257901 0.538291943 1 20.65252968 -1.371762346 4.645319023 1.000451856 0.625575734 0.721063328 0.069878523 0.000347914 4.71E-05 0.071984822 0.016946937 0.042485199 1.371762346 -0.374876122 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 FDIYDPFHPT(0.009)DEAY(0.107)S(0.885)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPTDEAYS(1)PPPAPEQK;FDIYDPFHPT(0.047)DEAY(0.003)S(0.949)PPPAPEQK 247.51 6.98E-38 8084866000 2777397 1995866 2510135 1933788 3241298 3295971 2985026 2547841 2857837 1848694 TRUE FALSE 2887050.778 2338640.46 2575551.18 2316285.495 2690343.324 2530531.686 2751051.862 2513691.359 2754984.005 2210910.194 1.305820013 1.057772707 1.164927995 1.047661502 1.216848758 1.14456557 1.244307376 1.136948649 1.246085894 1 21.07620899 FDKEEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDKEEEIR 8 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 89.247 0.012805 99844000 129510 94573 125040 118030 159050 173340 148820 120710 141830 79841 FALSE TRUE 134623.1548 110815.1771 128298.6451 141375.9817 132014.7378 133084.412 137155.0995 119092.0799 136725.566 95484.3153 1.409898101 1.160558954 1.34366199 1.480619945 1.382580347 1.393782964 1.436414966 1.24724233 1.431916494 1 16.54297615 -1.095495864 6.773707244 0.999999733 1.358165576 0.591277736 0.090918023 3.67E-07 4.91E-08 0.088067407 0.020757672 0.08026092 1.095495864 0.358165844 FDLGQDVIDFTGHALALYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDLGQDVIDFTGHALALYR 19 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ; 231.21 3.91E-20 1447980000 977150 1080770 1164730 1229540 1350270 1648460 1531300 1220570 1231350 1098820 FALSE TRUE 1015728.637 1266383.84 1195083.821 1472739.342 1120751.588 1265630.148 1411272.705 1204210.256 1187033.954 1314112.741 0.772938733 0.963679752 0.909422596 1.12071004 0.852858018 0.963106215 1.07393579 0.916367537 0.903296892 1 20.32565762 4.741696303 5.643962615 0.966789579 0.766134929 0.364415463 0.076903656 0.157471847 20.51731597 0.017553722 0.121108291 55169.15129 -4.741696303 -0.20065465 FDLLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDLLKR 6 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;H0Y9G8;O15519-11;C9JV51;F8WBH9;C9J408;O15519-5;E9PAP3;O15519-14;O15519-8;O15519-6;O15519-10;O15519-12;O15519-9;O15519-2;O15519-13;O15519 D6RGI3 SEPT11;CFLAR Septin-11;CASP8 and FADD-like apoptosis regulator;CASP8 and FADD-like apoptosis regulator subunit p43;CASP8 and FADD-like apoptosis regulator subunit p12 0 ; 129.16 0.026159 509640000 954650 829020 896640 675610 1527440 1267080 1006090 953500 989340 1006370 FALSE TRUE 992340.3192 971397.7361 920007.175 809243.6415 1267806.294 972819.8728 927230.0369 940719.8921 953733.8467 1203548.933 0.824511818 0.807111127 0.76441194 0.672381171 1.053389903 0.808292746 0.770413243 0.781621641 0.792434624 1 20.19886337 -2.296357131 2.178674386 1.85534776 0.806637928 0.284435564 0.091190277 4052438.114 622600.9109 17040162.53 0.021893353 0.005054089 2.296357131 -1.048709832 FDLLWLIQDRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDLLWLIQDRPDR 13 1 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 195.94 1.33E-07 850650000 704080 743270 815540 847630 806060 1100430 1019830 901630 826010 648360 FALSE TRUE 731877.6221 870920.8407 836793.6424 1015288.684 669046.2091 844871.8097 939893.0598 889545.1246 796282.0615 775393.7284 0.943878697 1.123198201 1.079185466 1.3093847 0.862847073 1.089603615 1.212149422 1.147217332 1.026939002 1 19.56456954 2.468079073 24.98009559 1.120924266 1.070985069 0 0.12311562 842.2591521 2326823.959 0.042015719 0.035196844 293.8184564 -2.468079073 -0.049939196 FDLLWLIQDRPDRDNDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDLLWLIQDRPDRDNDLR 18 2 P33993;P33993-3 P33993 MCM7 DNA replication licensing factor MCM7 0 ; 142.3 6.40E-08 680250000 555130 696790 644950 532460 758210 862330 570570 682460 637730 749520 FALSE TRUE 577046.9611 816458.2622 661757.9268 637778.9988 629329.735 662066.9262 525847.2325 673312.74 614778.2219 896374.0936 0.643756848 0.910845447 0.73826088 0.711509852 0.702083806 0.738605601 0.586638142 0.751151494 0.685850056 1 19.77374143 -0.96073319 4.366190505 1.000007672 0.721256887 0.529257414 0.079543913 22547699.03 45101073.9 2638.266997 0.018665944 0.109462865 0.96073319 -0.278750786 FDLSQNHPLGMAIFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDLSQNHPLGMAIFLK 16 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 230.38 2.31E-15 7009400000 4842700 4280600 5850300 6621800 6904600 7553900 7648200 5960600 6060300 3922200 FALSE TRUE 5033893.535 5015759.752 6002763.624 7931572.276 5730958.558 5799621.205 7048714.099 5880707.907 5842190.987 4690679.995 1.073169251 1.069303333 1.279721412 1.690921633 1.221775641 1.236413742 1.50270624 1.253700511 1.245489139 1 22.16136565 4.195888098 5.059949243 1.329607631 1.068954237 0.214853244 0.174100609 0.228750542 13.27006623 0.041898483 0.099340599 15699.58232 -4.195888098 -0.260653394 FDMGAY(ph)KSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDMGAYKSSK 10 1 P01583 P01583 IL1A Interleukin-1 alpha 1 FDMGAY(0.991)KS(0.009)SK 49.715 0.058362 0 777650 67308 95980 65972 172610 206400 109550 113750 103720 58857 TRUE FALSE 808352.2225 78867.62542 98481.31765 79021.06469 143269.8139 158466.728 100963.1847 112225.3673 99987.13746 70388.90226 11.48408622 1.120455397 1.399102905 1.122635276 2.035403441 2.251302733 1.434362257 1.594361664 1.420495763 1 16.10306037 4.739997368 24.99998302 1.531771927 11.48408947 0.984304803 0.378697309 13.68365898 238077.3588 0.092554342 0.583413822 54953.75433 -4.739997368 9.952317539 FDMIWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDMIWDR 7 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 0 92.925 0.035623 11837000 26533 31194 30191 33689 53781 47371 35264 30105 31382 43684 FALSE TRUE 27580.54333 36551.32684 30977.80226 40352.58365 44639.32483 36369.80316 32499.91553 29701.49172 30252.56795 52243.04342 0.527927577 0.699640076 0.592955545 0.772401089 0.854454907 0.696165476 0.622090778 0.568525296 0.579073614 1 15.67295132 5.348454056 1.478618839 0.69238712 3.53E-17 0.134026601 0.130747319 14.55277801 8.056903262 0.035050353 23.12907955 223076.6201 -5.348454056 -0.69238712 FDNLYGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDNLYGCR 8 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 91.069 0.02966 130950000 100300 124350 110430 123540 154280 168870 122030 121680 117030 158090 FALSE TRUE 104259.9214 145706.1452 113307.8965 147975.8433 128055.5407 129652.5017 112464.9697 120049.0786 112818.1132 189064.7087 0.551450994 0.770668128 0.599307493 0.782673003 0.67731065 0.685757287 0.594849089 0.634962915 0.596716933 1 17.52852057 -1.153793359 4.1024154 1.000113616 0.657680193 0.671407585 0.072412368 7971777.45 4484088.677 7694.62505 0.01597236 0.070178914 1.153793359 -0.342433422 FDPFGPIGT(ph)SPPGPNPDHLPPPGYDDMYL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.527)S(0.473)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.529)S(0.471)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.561)S(0.439)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.531)S(0.469)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.604)S(0.396)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.532)S(0.468)PPGPNPDHLPPPGYDDMYL 223.42 4.32E-34 1320256000 174076 201165 212059 219813 273488 276413 240617 245798 254581 259538 TRUE FALSE 180948.6549 235713.5239 217585.4317 263291.3553 227000.6074 212220.2698 221756.8108 242503.4799 245418.6795 310389.5019 0.582972858 0.759412037 0.701007703 0.848261148 0.731341125 0.683722447 0.714446879 0.781287635 0.790679704 1 18.24372024 -5 0.191608452 2.165053676 0.687357341 0.65196055 0.061962434 86.39875569 0.847196154 38.29807403 0.163798678 1.00E-05 5 -1.477696335 FDPFGPIGT(ph)SPPGPRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.581)S(0.419)PPGPRPDR;FDPFGPIGT(0.5)S(0.5)PPGPRPDR;FDPFGPIGT(0.546)S(0.454)PPGPRPDR;FDPFGPIGT(0.519)S(0.481)PPGPRPDR 122.53 5.81E-05 500055000 265716 303169 298860 313809 348517 421042 368993 368126 351887 340978 TRUE FALSE 276206.6729 355235.9174 306648.5371 375879.4836 289276.2048 323261.3765 340070.3645 363191.8731 339222.6556 407786.1107 0.677332223 0.87113295 0.751983771 0.921756464 0.709382191 0.792722871 0.83394298 0.890643069 0.831864173 1 18.63745311 -5 0.120444168 1.639370407 0.719792795 0.461266315 0.068855043 134.7873378 1.051890612 20.73438285 0.618587181 1.00E-05 5 -0.919577612 FDPFGPIGTS(ph)PPGPNPDHLPPPGYDDMYL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FDPFGPIGTSPPGPNPDHLPPPGYDDMYL 29 0 Q92530 Q92530 PSMF1 Proteasome inhibitor PI31 subunit 1 FDPFGPIGT(0.399)S(0.601)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.193)S(0.807)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.469)S(0.531)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.286)S(0.714)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.148)S(0.852)PPGPNPDHLPPPGYDDMYL;FDPFGPIGT(0.245)S(0.755)PPGPNPDHLPPPGYDDMYL 206.32 6.57E-25 1533741000 185916 234185 257294 254992 297527 321627 284266 289271 292537 296221 TRUE FALSE 193256.1072 274404.452 263999.293 305428.6565 246953.4668 246934.0036 261984.4881 285393.7954 282008.6505 354259.8335 0.545520799 0.774585279 0.745213733 0.862159996 0.697096999 0.697042058 0.739526368 0.805605853 0.796050311 1 18.43444837 -5 0.150500858 1.928683054 0.664918408 0.572768402 0.073309773 101.9124822 0.909880792 28.16542477 0.36646921 1.00E-05 5 -1.263764646 FDPFGPIGTS(ph)PPGPRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDPFGPIGTSPPGPRPDR 18 1 Q5QPM7 Q5QPM7 PSMF1 1 FDPFGPIGT(0.098)S(0.902)PPGPRPDR;FDPFGPIGT(0.007)S(0.993)PPGPRPDR 162.43 2.16E-11 368430000 209573 241800 238577 248450 267590 314310 241960 237980 257600 263590 TRUE FALSE 217847.1039 283327.2691 244794.5126 297592.6685 222105.1474 241316.2659 222994.543 234790.2674 248329.0263 315235.4138 0.691061646 0.898779949 0.77654509 0.944033111 0.70456915 0.765511283 0.707390519 0.744809298 0.787757389 1 18.26607009 3.194574352 24.99993559 0.764487949 0.829043201 0.017349218 0.10155148 325.1188756 184782.7382 0.026995636 0.032266118 1565.216262 -3.194574352 0.064555252 FDQLFDDES(ph)DPFEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDQLFDDESDPFEVLK 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK 117.18 0.00038851 103652000 255720 160667 210486 154531 251180 265850 278220 215513 229870 120298 TRUE FALSE 265816.0231 188260.3074 215971.4381 185096.7706 208484.5133 204110.3665 256412.3894 212624.4007 221597.0236 143868.0899 1.847637119 1.308561945 1.501176795 1.286572796 1.449136591 1.41873272 1.782274232 1.477912169 1.540279181 1 17.13438711 -1.821423429 2.318177146 0.80548423 1.50470066 0.445792064 0.171223948 4404138.93 2554255.89 4777689.241 0.04266812 0.015086086 1.821423429 0.69921643 FDREVDIGIPDATGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 224.67 1.00E-12 309910000 280160 328850 333820 291410 410930 414000 310670 344850 345430 357770 FALSE TRUE 291220.9331 385327.4294 342519.6234 349050.0282 341080.2654 317854.7742 286318.8736 340227.8498 332998.0418 427868.1816 0.680632367 0.900575098 0.800526046 0.815788701 0.797162023 0.742880139 0.669175428 0.795169785 0.778272506 1 18.70680687 0.271443492 2.570128098 1.000000086 0.77725566 0.530171506 0.063363571 41.64608439 144.6714913 0.060517452 0.016075983 1.86828657 -0.271443492 -0.222744426 FDRPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FDRPPAR 7 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;; 126.28 0.0036185 940080000 923966 1004577 1062260 1010584 1275422 1406128 1194904 1098697 1018555 1094201 FALSE TRUE 960444.8911 1177105.285 1089943.368 1210474.499 1058626.224 1079576.082 1101244.302 1083970.764 981897.4045 1308588.736 0.733954729 0.899522709 0.832915138 0.925022863 0.808983139 0.824992645 0.841551109 0.828350981 0.750348354 1 20.31958033 -1.098311965 4.692877111 1.000008209 0.832265712 0.468519601 0.054954378 5.29E-06 1.02E-06 0.049712353 0.011716627 0.079742167 1.098311965 -0.167742497 FDSEYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FDSEYER 7 0 P43243;A0A0R4J2E8;D6REM6;D6R991;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 163.34 0.0028812 2002990000 2499450 2436530 2492390 2537430 2905260 3513440 3189210 2640930 2427390 1951520 FALSE TRUE 2598130.216 2854985.074 2557343.731 3039326.081 2411424.943 2697496.807 2939231.387 2605532.653 2340028.708 2333882.98 1.113222145 1.223276873 1.095746339 1.302261556 1.033224443 1.155797797 1.259373933 1.11639387 1.002633263 1 21.1543008 1.333968618 3.74976201 0.998873805 1.168694589 0.436630113 0.075022353 0.196142394 4.456855871 0.055653966 0.017958959 21.57588495 -1.333968618 0.169820784 FDSLTDLVEHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDSLTDLVEHYK 12 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4;H0YF12 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 206.58 8.85E-08 546170000 1429040 1084210 1431910 1276300 1703120 1826140 1823820 1434350 1575150 989600 FALSE TRUE 1485459.603 1270414.634 1469226.751 1528748.331 1413624.271 1402046.66 1680864.223 1415124.884 1518460.659 1183493.173 1.255148434 1.073444835 1.241432384 1.291725517 1.194450718 1.184668144 1.420256797 1.195718671 1.283032884 1 20.17461995 4.103171508 22.48992022 1.240836919 1.162566836 0.036620782 0.108821574 13.0659417 2818.160719 0.024897789 0.053785395 12681.52574 -4.103171508 -0.078270083 FDSPDLLLEAGDPAT(ph)SPCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FDSPDLLLEAGDPATSPCR 19 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 FDSPDLLLEAGDPAT(0.5)S(0.5)PCR 84.874 0.034954 28989000 45546 62662 54881 54905 66195 75348 57308 64769 63185 55854 TRUE FALSE 47344.19125 73423.71106 56311.24395 65765.04512 54943.19754 57849.56891 52816.04921 63900.8775 60910.98419 66797.52191 0.708771671 1.099198128 0.843013967 0.984543187 0.822533471 0.866043638 0.790688752 0.956635451 0.911874909 1 16.02750696 0.979818071 1.487612169 0.996275551 0.885988975 0.107745263 0.103071815 1.005077621 4.539895795 0.089809586 0.026559164 9.545926161 -0.979818071 -0.110286576 FDSPDLLLEAGDPATS(ph)PCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDSPDLLLEAGDPATSPCR 19 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 FDSPDLLLEAGDPAT(0.214)S(0.786)PCR;FDSPDLLLEAGDPAT(0.102)S(0.898)PCR 185.96 2.26E-14 64231000 133278 143801 139233 151176 165117 202270 147013 166202 147555 151607 TRUE FALSE 138539.9184 168497.7031 142861.5264 181078.1616 137050.4713 155295.8579 135489.7369 163974.334 142244.5244 181311.489 0.76409895 0.929327226 0.787934219 0.998713113 0.755884098 0.856514161 0.74727607 0.904379171 0.784531224 1 17.46811082 -1.467258632 4.541714375 1.000602979 0.841561376 0.268440056 0.080578053 0.000441062 5.17E-05 0.069945817 0.016424537 0.034098978 1.467258632 -0.159041602 FDSSLDR ddPTM_MDA-MB-175_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 ;; 197.65 0.00097132 1103650000 1312700 1001650 1031320 1090100 1131460 1422730 1277350 1019210 956110 961070 FALSE TRUE 1364526.41 1173675.596 1058197.046 1305718.526 939134.8333 1092322.519 1177227.969 1005549.157 921699.7879 1149373.266 1.187191707 1.021143984 0.920673099 1.136026533 0.817084285 0.950363604 1.024234689 0.874867362 0.801915109 1 20.13241597 7.999999999 0.528910618 0.91771369 10.79451446 0.400580987 0.093095635 121.392237 1.184585708 0.044432402 1350.250964 99999999.88 -7.999999999 9.876800768 FDSSLDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 157.91 0.00059218 9343420000 8183030 5555980 6650770 5863380 9438220 8754330 9731170 7376690 7697800 4838470 FALSE TRUE 8506102.343 6510176.345 6824094.53 7023139.064 7833914.736 6721269.531 8968415.468 7277817.536 7420757.682 5786475.558 1.469997109 1.125067631 1.179317956 1.213716189 1.35383182 1.161548072 1.549892569 1.2577289 1.282431353 1 22.46425346 3.267978707 24.96075762 1.293045843 1.233477292 0 0.156592046 877.9349603 744907.1735 0.040951933 0.055441762 1853.44075 -3.267978707 -0.059568551 FDTQYPYGEKQDEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDTQYPYGEKQDEFKR 16 2 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 186.75 8.16E-10 1624920000 1399800 870326 1110486 668511 1744920 1357600 993310 1027947 1170010 737618 FALSE TRUE 1455065.185 1019797.72 1139426.177 800740.4805 1448319.122 1042317.975 915451.7667 1014169.052 1127901.569 882140.1246 1.649471716 1.15604958 1.291661206 0.907724814 1.641824333 1.181578692 1.037762302 1.149668883 1.278596832 1 19.75064831 4.741006257 24.53698506 1.187888365 1.649471929 0.349828736 0.190761746 190.9681725 1915821.661 0.043333555 0.292860636 55081.56317 -4.741006257 0.461583565 FDVHDVTLHADAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDVHDVTLHADAIHR 15 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 104.41 0.00048514 92567000 70011 86173 83268 81158 110139 108782 84632 86610 81811 88962 FALSE TRUE 72775.08834 100972.5424 85438.03249 97210.81017 91417.61212 83519.02911 77998.3227 85449.13462 78866.63809 106392.4006 0.684025249 0.949057845 0.803046383 0.913700693 0.859249454 0.785009349 0.733119304 0.803150734 0.741280746 1 16.69903558 2.738262685 24.4103399 0.794179789 0.849613543 0.001748534 0.096296621 53.39019433 4374226.116 0.027852274 0.027812579 547.3469283 -2.738262685 0.055433755 FDVNTSAVQVLIEHIGNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDVNTSAVQVLIEHIGNLDR 20 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 228.15 3.25E-25 390890000 267331 294352 358180 391680 332790 431460 391450 334700 354480 268748 FALSE TRUE 277885.4343 344904.6663 367514.465 469153.135 276222.4747 331259.9538 360767.1261 330213.894 341722.334 321404.0251 0.864598488 1.07311869 1.143465658 1.459699003 0.859424441 1.030665231 1.122472334 1.027410574 1.063217344 1 18.29402847 FDVPGDENAEMDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FDVPGDENAEMDAR 14 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 234.63 7.53E-17 604560000 137546 135419 161192 174399 183739 222130 221479 163315 171467 120639 FALSE TRUE 142976.4223 158676.1598 165392.7959 208894.6017 152507.1104 170543.6739 204118.8973 161126.0296 165295.9362 144275.9023 0.990993091 1.099810553 1.146364662 1.44788283 1.057051857 1.182066244 1.414781637 1.116791003 1.145693311 1 17.13847083 4.421743104 2.362524025 1.205370964 0.997722873 0.171491562 0.134675985 0.528689207 5.257838031 0.033179638 0.170109841 26408.46166 -4.421743104 -0.207648091 FEAAETLEEAAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEAAETLEEAAMR 13 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 0 117.67 0.001135 10107000 7062.1 11827 13969 9431.3 9719.9 16074 11397 11604 9657.1 13899 FALSE TRUE 7340.917161 13858.19525 14333.04362 11296.78299 8067.71487 12341.0571 10503.67336 11448.46736 9309.542857 16622.24294 0.441632167 0.833713916 0.862280961 0.679618451 0.485356573 0.74244235 0.631904695 0.688743836 0.560065383 1 14.02082745 -1.01640366 4.896142829 1.000005073 0.668066774 0.381513519 0.129953253 7.01E-06 1.41E-06 0.122583364 0.028892735 0.09629336 1.01640366 -0.331938298 FEAELKAEQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEAELKAEQDER 12 1 Q9BUP0;A0A087X1Z2;Q9BUP0-2;Q8WYH2 Q9BUP0 EFHD1;PP1187 EF-hand domain-containing protein D1 0 87.498 0.0095892 97705000 321460 237820 329250 187470 473960 399010 271690 320050 373910 304770 FALSE TRUE 334151.489 278663.735 337830.5255 224551.0065 393396.4485 306345.9746 250394.2279 315760.2532 360453.0521 364483.8463 0.916779968 0.764543444 0.926873794 0.616079447 1.079324783 0.840492597 0.686983059 0.866321667 0.98894109 1 18.47549535 1.274964391 4.601198418 0.998364218 0.831177664 0.211629276 0.122467572 0.27536093 12.04422592 0.091523596 0.029098991 18.83494651 -1.274964391 -0.167186554 FEDEDSDDVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 0 ; 174.86 2.44E-05 221680000 481010 495440 527200 595380 541070 648490 740020 560080 552120 383270 FALSE TRUE 500000.6462 580527.966 540939.2651 713144.387 449099.1147 497888.0255 682015.2987 552573.0437 532249.3091 458364.4184 1.090836518 1.266520574 1.180151084 1.555845869 0.979786163 1.086227476 1.487932465 1.205532152 1.161192466 1 18.80613553 0.912857491 2.71287912 1.00090022 1.239103146 0.149495947 0.16733347 0.685388786 11.21042977 0.15499848 0.041204064 8.181962625 -0.912857491 0.238202926 FEDENFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 246.51 2.46E-10 3574887000 3089404 2881297 3116798 2696877 3798439 3776728 3338475 3372062 3052112 2306985 FALSE TRUE 3211376.055 3376137.346 3198024.316 3230311.221 3152781.696 2899640.159 3076796.606 3326865.024 2942267.085 2758994.541 1.163966078 1.223683953 1.159126729 1.170829146 1.142728501 1.050977128 1.115187638 1.205825157 1.066427295 1 21.39571117 -5 0.105262486 0.525659687 1.241999724 0.549553939 0.045402176 150.1466605 1.063302216 15.50226493 0.707563627 1.00E-05 5 0.716340037 FEDHEGLPTVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEDHEGLPTVVK 12 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 96.64 0.0019084 0 283000 224020 279510 229000 340710 327170 308800 277160 292450 216680 FALSE TRUE 294173.0585 262493.6924 286794.2602 274295.5165 282796.2359 251189.7258 284595.4491 273445.1235 281924.7816 259134.2974 1.13521468 1.012963915 1.106739876 1.058507188 1.091311489 0.969341875 1.098254658 1.055225519 1.087948544 1 17.98334045 4.762315353 23.75301834 1.057418396 1.135214857 0.234331127 0.043837863 4906.074573 4905566.057 0.009596882 0.522528765 57851.59706 -4.762315353 0.077796461 FEDKTVAYTEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FEDKTVAYTEQK 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 162.48 5.71E-05 1418320000 1627770 1078130 1321840 888280 2175900 1795820 1299620 1261790 1491480 921180 FALSE TRUE 1692035.617 1263290.441 1356288.236 1063979.133 1806041.295 1378768.021 1197752.388 1244877.769 1437801.926 1101667.584 1.535885816 1.146707464 1.231122941 0.965789634 1.639370461 1.251528175 1.087217602 1.129994008 1.305114126 1 20.07125754 -4.999999932 0.079028472 0.213155736 1.483414813 0.164654056 0.188926044 504.1189267 2.827270292 69.6462178 6.702669003 1.00E-05 4.999999932 1.270259077 FEDRFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FEDRFDK 7 1 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ;; 107.66 0.006773 924650000 819199 626657 626404 955520 1680990 1409330 1463700 768025 716215 884551 FALSE TRUE 851541.6091 734280.465 642728.6028 1144519.004 1395255.92 1082034.466 1348971.369 757730.8811 690438.5621 1057861.833 0.804964867 0.694117551 0.607573298 1.081917287 1.318939655 1.022850464 1.275186728 0.716285301 0.652673667 1 20.01271978 3.736133249 24.99251097 1.009570879 0.701408464 0.329095208 0.201180758 271.1455151 2791757.102 0.057979789 0.094694707 5446.697412 -3.736133249 -0.308162415 FEDYLNAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FEDYLNAESR 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ;;; 237.44 8.31E-12 2140500000 2163850 2177250 2302270 2432810 2547730 2925870 2841730 2407060 2326240 1898570 FALSE TRUE 2249280.469 2551175.751 2362269.048 2914012.557 2114667.765 2246381.034 2618987.777 2374797.298 2242519.077 2270558.441 0.990628749 1.123589556 1.040391212 1.283390246 0.931342584 0.98935178 1.153455348 1.045908907 0.987650895 1 21.11461574 FEDYLREPAQGDLGCGSPPHRPPAPS(ph)SPEGPDTGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEDYLREPAQGDLGCGSPPHRPPAPSSPEGPDTGQK 36 2 Q8N573-2 Q8N573-2 OXR1 Oxidation resistance protein 1 1 FEDYLREPAQGDLGCGSPPHRPPAPS(0.5)S(0.5)PEGPDTGQK 108.14 1.09E-05 53908000 57563 46953 57998 41889 74535 76991 64133 60184 62515 40829 TRUE FALSE 59835.63169 55016.81251 59509.47553 50174.51917 61865.56732 59111.00706 59106.08788 59377.33192 60265.09736 48828.66083 1.225420289 1.126731956 1.218740685 1.027562876 1.266992915 1.21058014 1.210479396 1.216034413 1.23421565 1 15.57544059 FEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FEEAKR 6 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 95.957 0.068555 597390000 670850 496700 656740 477880 752680 784300 759440 595720 701650 458740 FALSE TRUE 697335.676 582004.3612 673855.1839 572403.2377 624739.7225 602158.2112 699913.1084 587735.3478 676397.7536 548621.3199 1.271069225 1.060848968 1.228270137 1.043348512 1.138744886 1.097584416 1.275767242 1.071295129 1.232904608 1 19.06545116 -1.224787941 3.806582798 0.999841242 1.150560694 0.234017729 0.084729003 5579616.106 1795276.656 7703.702084 0.017656725 0.059595307 1.224787941 0.150719452 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 425.77 4.51E-188 22940050000 9372050 6774188 8429740 5653305 8447150 9804920 9963730 7558240 8312570 6121557 TRUE FALSE 9742065.771 7937602.093 8649425.95 6771511.856 7011306.46 7527875.925 9182746.807 7456934.156 8013402.229 7320958.89 1.330708985 1.084229841 1.1814608 0.924948761 0.957703296 1.028263652 1.254309298 1.018573423 1.094583695 1 22.80360119 5.330049839 1.279855974 1.054719789 2.056716767 0.435232112 0.093577866 5.459816142 2.66370784 0.026385678 10.40282963 213820.7452 -5.330049839 1.001996978 FEELCSDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 297.46 5.86E-32 4573588800 1781893 1951852 1909043 2065415 2385607 2559920 2357516 2033934 1975906 2030946 FALSE TRUE 1852243.512 2287067.398 1958794.229 2473947.922 1980102.374 1965417.376 2172727.736 2006672.442 1904793.529 2428870.984 0.762594442 0.941617489 0.806462855 1.018558803 0.815235715 0.809189697 0.894542259 0.826174982 0.784230015 1 21.21185443 FEELNADLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 342.72 1.70E-53 5690131800 2925285 3237795 3179565 3317690 3984951 4217876 3876179 3318121 3112185 3328619 FALSE TRUE 3040777.511 3793861.105 3262427.076 3973919.18 3307590.452 3238338.222 3572353.961 3273647.015 3000178.07 3980798.163 0.763861263 0.953040307 0.819540942 0.998271959 0.830886249 0.813489679 0.897396405 0.822359457 0.753662443 1 21.92462629 FEELNMDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FEELNMDLFR 10 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 185.29 3.41E-06 129648000 176589 231467 207196 246601 279859 304329 243367 198898 189719 237141 FALSE TRUE 183560.8701 271219.6567 212595.698 295377.9418 232288.6671 233653.2019 224291.2586 196232.0976 182891.0502 283604.2386 0.647243042 0.956331464 0.749621018 1.041514553 0.819059222 0.823870627 0.790860037 0.691922302 0.64488123 1 18.11351957 2.209720566 2.5743987 0.745154789 0.851922213 0.021089135 0.133722069 0.613433257 8.292131731 0.055080358 0.037972863 162.0766926 -2.209720566 0.106767424 FEENQKEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEENQKEFER 10 1 Q5JY65;Q9BZJ0-2;Q9BZJ0-3;Q9BZJ0 Q5JY65 CRNKL1 Crooked neck-like protein 1 0 82.171 0.019594 0 84391 68321 73578 61441 107650 103150 95492 78710 92618 63769 FALSE TRUE 87722.82184 80054.60029 75495.50312 73593.84642 89351.69145 79194.97575 88007.08752 77655.02119 89284.69627 76263.31462 1.150262381 1.049713098 0.989932099 0.964996693 1.171620876 1.038441302 1.153989804 1.018248703 1.170742404 1 16.21870162 3.245681753 24.99825837 1.08973532 1.036025599 0.112458021 0.073209969 378.1805551 1327569.991 0.019726091 0.026146318 1760.68536 -3.245681753 -0.053709721 FEEPAPLSYDSRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEEPAPLSYDSRPR 14 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 159.52 4.47E-06 171490000 87934 101180 116360 118070 125020 145350 107210 96731 102620 104270 FALSE TRUE 91405.70222 118556.8779 119392.4372 141423.8936 103769.1451 111594.6653 98806.60006 95434.47917 98926.72625 124699.7101 0.733006533 0.950739002 0.957439573 1.134115656 0.832152256 0.894907175 0.792356293 0.765314363 0.793319617 1 16.92809859 3.059375005 24.99996975 0.828325254 0.950022024 0.145759644 0.110198289 115.7208793 48723.4204 0.031927425 0.038160569 1146.502497 -3.059375005 0.12169677 FEGGDRDLEHLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FEGGDRDLEHLSK 13 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 208.27 2.84E-08 2675080000 1698250 3386380 3686360 3764610 4438920 4903540 3945360 3986440 3638540 2708320 FALSE TRUE 1765298.221 3967964.423 3782429.57 4509238.622 3684393.964 3764767.149 3636112.374 3933008.292 3507589.656 3238963.45 0.545019494 1.225072306 1.167790137 1.392185707 1.13752255 1.162337028 1.122616056 1.214279924 1.082935856 1 21.62710076 4.741079137 24.97472905 1.179225831 0.545019267 0.784336515 0.097691406 94.00562118 932145.5384 0.022044185 0.150190039 55090.80733 -4.741079137 -0.634206564 FEGLS(ph)PLQR ddPTM_MDA-MB-175_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 115 0.001622 1119420000 1303460 1409010 1368510 1284800 1535000 1749240 1329470 1319700 1252530 1226220 TRUE FALSE 1354921.607 1650996.507 1404174.495 1538929.605 1274081.248 1343005.52 1225262.667 1302011.58 1207451.69 1466474.332 0.923931349 1.125827075 0.957517267 1.049407802 0.868805693 0.915805678 0.835515932 0.887851599 0.823370491 1 20.48392039 3.233692605 24.99947947 0.881034383 1.018099637 0.44846419 0.06788095 93.36750875 479485.1308 0.01771624 0.021821582 1712.744592 -3.233692605 0.137065255 FEHCNFNDVTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FEHCNFNDVTTR 12 0 E9PNW4;A0A2U3TZL5;P13987;P13987-2 E9PNW4 CD59 CD59 glycoprotein 0 ;;; 194.98 8.36E-07 1675230000 951610 1213710 1036090 1149240 1175520 1431240 1097730 1127610 1021940 1242190 FALSE TRUE 989180.2976 1422155.251 1063091.357 1376556.242 975705.5303 1098856.201 1011687.054 1112496.232 985160.579 1485573.347 0.665857596 0.957310693 0.715610144 0.926616141 0.656787181 0.739684919 0.681007812 0.74886658 0.663151759 1 20.50258841 5.032394245 17.40209983 0.772851523 0.274045446 0.071320358 0.121719878 25092814.54 350183448 0.027030979 383720306.8 107744.2855 -5.032394245 -0.498806077 FEHLLED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 113.08 0.014445 759522000 1223577 1432000 1448760 1452390 1713160 1860680 1547020 1462850 1475530 1408800 FALSE TRUE 1271884.765 1677934.861 1486515.876 1739668.407 1421957.675 1428565.269 1425760.53 1443242.888 1422425.964 1684827.387 0.754905087 0.995909061 0.882295651 1.032549934 0.843978253 0.847900076 0.846235372 0.856611722 0.844256198 1 20.68416936 FEHQEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FEHQEWK 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 143.61 0.0024101 742240000 1619830 1260910 1539080 1336270 1988490 1975000 1820800 1437040 1528860 1060660 FALSE TRUE 1683782.139 1477461.484 1579189.689 1600580.218 1650487.18 1516336.181 1678080.938 1417778.829 1473836.627 1268476.019 1.327405574 1.164753185 1.24495037 1.261813541 1.301157574 1.195399959 1.322911046 1.117702509 1.161895538 1 20.27466481 1.088844886 1.011051534 1.005671497 1.255215585 0.649074075 0.058024517 0.299976481 0.658078159 0.050847433 0.017034279 12.27000914 -1.088844886 0.249544088 FEIGEGENLDLPYGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;;;; 324.94 9.23E-59 2402690000 1251348 1499101 1524524 1462501 1769265 1977010 1574491 1621087 1599786 1452038 FALSE TRUE 1300752.185 1756559.935 1564254.348 1751779.333 1468525.967 1517879.389 1451078.281 1599358.98 1542210.014 1736537.045 0.749049488 1.011530356 0.900789506 1.008777404 0.845663484 0.874084082 0.835616082 0.921004815 0.888095085 1 20.72778176 -1.055287951 4.418410721 1.000006882 0.897239219 0.155805672 0.07424155 4.67E-06 9.98E-07 0.066686711 0.015717156 0.08804649 1.055287951 -0.102767662 FEIINAIYEPTEEECEWKPDEEDEISEELKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEIINAIYEPTEEECEWKPDEEDEISEELKEK 32 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8VV59;F8W543;F8W118;H0YH88;F8VRJ2 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 309.43 3.17E-104 184460000 257730 48059 73862 42130 143720 130950 126220 86044 103100 27608 FALSE TRUE 267905.3794 56312.7594 75786.9044 50463.18825 119290.5257 100538.8471 116326.5466 84890.72092 99389.45114 33017.25901 8.114101153 1.705555249 2.29537238 1.528388175 3.612974829 3.045039173 3.523204229 2.571101401 3.0102272 1 15.01093274 4.744200721 24.8805972 2.590291799 8.114103687 0.806684863 0.826203433 239.8972202 1058242.46 0.193202237 1.708272884 55488.21078 -4.744200721 5.523811888 FEIWDTAGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 200.68 1.07E-07 255327000 366591 381396 397886 513076 425476 525699 481474 424214 358538 321271 FALSE TRUE 381064.2957 446897.7962 408255.236 614560.9014 353153.7415 403613.3743 443734.8098 418528.1052 345634.2874 384217.9013 0.991792143 1.163136321 1.062561725 1.599511369 0.919149629 1.050480399 1.154904049 1.089298816 0.899578823 1 18.55156521 FEKEAAEMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 129.84 0.00026678 806550000 1010320 676180 932290 520190 1513020 1156070 884680 873910 1093140 719940 FALSE TRUE 1050208.214 792308.655 956586.2433 623082.0294 1255837.401 887590.2629 815336.4699 862196.6659 1053798.105 860998.4589 1.219756206 0.920220759 1.111019693 0.723673803 1.458582635 1.030884845 0.946966236 1.001391648 1.223925657 1 19.71565113 4.772535956 22.41763349 1.044061344 1.219757604 0.073654726 0.184393697 10272.03601 6777215.211 0.041591096 5.703673586 59229.21219 -4.772535956 0.17569626 FELAVDAVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 117.02 0.0010127 109810000 68787 88012 76611 81985 88809 97255 79636 83293 76490 79260 FALSE TRUE 71502.76388 103127.3764 78607.5456 98201.3883 73713.2779 74669.00016 73393.92223 82176.59357 73737.13984 94789.47948 0.754332277 1.08796226 0.82928555 1.035994594 0.777652523 0.787735101 0.774283419 0.866937914 0.77790426 1 16.53243933 3.216921497 24.98916197 0.821365663 0.931426624 0.154156745 0.108796901 356.9148221 412169.3079 0.02860882 0.034222801 1647.864497 -3.216921497 0.110060961 FELPFDIPEEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FELPFDIPEEEAR 13 0 O14795;O14795-2;A0A1B0GUS7;A0A0U1RRL2;B1AM27 O14795 UNC13B Protein unc-13 homolog B 0 103.22 0.0037868 5487300 12834 16355 11713 12651 17262 22940 11998 11624 13658 14283 FALSE TRUE 13340.69623 19163.84403 12018.2504 15153.33004 14327.81141 17612.53266 11057.56541 11468.19929 13166.45125 17081.48039 0.781003515 1.12190768 0.703583655 0.887120419 0.838792135 1.031089359 0.647342336 0.671382049 0.770802703 1 14.06014539 2.226780767 24.99923471 0.733621981 0.892813385 0.124738938 0.143708806 327.5772697 695180.6564 0.050627738 0.037688548 168.5701863 -2.226780767 0.159191405 FELSENCSERPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FELSENCSERPGLR 14 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;; 265.95 7.43E-25 562797000 296039 354293 344674 348343 376159 421462 351480 344762 321516 298269 FALSE TRUE 307726.8483 415140.0667 353656.4876 417244.2057 312219.6275 323583.8378 323930.0792 340141.0293 309944.702 356709.0998 0.862682921 1.163805653 0.991442292 1.169704406 0.875278 0.907136482 0.908107136 0.953552992 0.868900463 1 18.44438849 3.216147447 24.99972949 0.917822935 1.051296762 0.33417429 0.088474967 240.8490963 268643.3181 0.023502537 0.028110132 1644.930097 -3.216147447 0.133473827 FENLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FENLCK 6 0 P08238;Q58FF7;P07900;P07900-2;Q58FG0;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA5P;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5;Putative heat shock protein HSP 90-beta 2 0 ;; 99.919 0.088987 2313260000 1831560 1461070 1715350 1471970 2119740 2140030 2064640 1777650 1744910 1218010 FALSE TRUE 1903871.403 1711997.407 1760053.43 1763121.273 1759427.352 1643040.465 1902808.122 1753823.509 1682111.03 1456655.739 1.307015345 1.175293078 1.20828373 1.210389816 1.207853925 1.127953861 1.306285398 1.204006865 1.15477596 1 20.47422853 0.859601016 2.500349601 1.000292263 1.216746356 0.626846403 0.051066935 0.328244918 3.976890805 0.046086074 0.012361815 7.237707305 -0.859601016 0.216454093 FEPES(ph)PGFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FEPESPGFESR 11 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(1)PGFESR 284.12 1.42E-27 2286910000 1195638 1368619 1350810 1202791 1467908 1538320 1349609 1326065 1319825 1277990 TRUE FALSE 1242842.711 1603668.667 1386013.218 1440699.47 1218393.522 1181068.493 1243823.12 1308291.268 1272324.756 1528387.672 0.813172426 1.04925517 0.906846636 0.942626989 0.797175707 0.772754528 0.813813892 0.855994387 0.832462064 1 20.5435791 3.249010889 24.92329927 0.834093776 0.935128988 0.198314434 0.078929211 255.0518375 608280.0325 0.020474805 0.027431571 1774.233965 -3.249010889 0.101035212 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIK 34 2 P63279;H3BQQ9;B0QYN7 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 129.62 3.14E-08 451320000 202280 108380 179750 120690 230260 205310 200060 165180 188090 96607 FALSE TRUE 210266.1706 126993.4219 184434.4327 144562.1218 191120.4874 157629.864 184378.7744 162966.0323 181320.6776 115535.292 1.81993023 1.099174285 1.596347138 1.251237776 1.654217375 1.364343841 1.595865395 1.410530319 1.569396455 1 16.81797409 -1.157339904 4.186700098 0.999860242 1.471349243 0.34523479 0.199450198 0.00022522 4.53E-05 0.167164288 0.039389396 0.069608151 1.157339904 0.471489001 FEPYANPTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FEPYANPTKR 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 116.77 0.0016784 1213390000 1894630 1932210 2342150 2238820 2736340 3057400 2850860 2687480 2833760 2737390 FALSE TRUE 1969431.455 2264052.037 2403188.353 2681651.914 2271217.904 2347365.185 2627402.144 2651458.726 2731773.531 3273729.16 0.601586557 0.691581962 0.734082826 0.819142874 0.693770863 0.717030967 0.802571629 0.809920002 0.834453126 1 21.64250354 -5 0.057066617 2.017143705 0.299720567 0.818791081 0.043938828 185.4697184 0.776391958 26.67720951 4.854389998 1.00E-05 5 -1.717423138 FES(ph)PEVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 FES(1)PEVAER 96.171 0.005405 0 93305 74656 88043 84976 107310 132320 111260 91659 98742 71587 TRUE FALSE 96988.75345 87477.58726 90337.47291 101783.9992 89069.48453 101590.6853 102539.1505 90430.46103 95188.29471 85613.10203 1.132872786 1.021778036 1.055182802 1.188883439 1.040372121 1.186625445 1.19770395 1.056268946 1.111842609 1 16.38554398 FESDPATHNEPGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FESDPATHNEPGVR 14 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;D6R9Y6;D6RDP1 D6RGI3 11-Sep Septin-11 0 89.992 0.0059291 360140000 321480 431960 456900 467620 492390 556750 506810 517170 462070 422870 FALSE TRUE 334172.2786 506145.7698 468807.1893 560113.8403 408693.7237 427453.2501 467084.9079 510238.1821 445440.191 505723.2802 0.660780889 1.000835417 0.927003379 1.107550042 0.808137058 0.845231507 0.923597798 1.008927613 0.880798271 1 18.94798867 4.745630663 24.89957754 0.944172971 0.66078075 0.508027047 0.083810617 663.8517431 2337918.344 0.019990803 0.201349874 55671.21033 -4.745630663 -0.283392221 FESPATGILS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FESPATGILSPR 12 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR;FESPATGILS(1)PR 200.05 1.73E-07 2085259000 1573027 1753836 1695214 1629183 1889580 2178405 1725625 1739854 1631558 1640676 TRUE FALSE 1635131.321 2055043.69 1739392.669 1951430.535 1568389.867 1672503.453 1590366.003 1716534.103 1572838.546 1962135.05 0.833342904 1.047350788 0.886479588 0.994544456 0.799328195 0.852389571 0.810528309 0.874829744 0.801595459 1 20.90399291 3.238209456 24.99996426 0.848694102 0.944213112 0.220112376 0.07648406 11.7132214 833924.5164 0.019589749 0.024837042 1730.650833 -3.238209456 0.09551901 FESPEVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 166.3 0.00014156 1096750000 1076920 806170 931980 753950 1203940 1123330 947010 898040 1073940 801710 FALSE TRUE 1119437.633 944623.4264 956268.1644 903079.0597 999294.7088 862453.6317 872780.8816 886003.2427 1035289.109 958789.7248 1.167552806 0.985224812 0.997370059 0.941894804 1.042245951 0.899523232 0.910294363 0.924085042 1.079787447 1 19.87085492 FEVGDIMLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FEVGDIMLIR 10 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 80.239 0.057241 260830000 171220 243660 239320 226930 303810 297270 253910 267250 233780 249560 FALSE TRUE 177979.8978 285506.7096 245556.8758 271816.0767 252168.4847 228233.5477 234007.8707 263667.9509 225366.3035 298456.5039 0.596334459 0.956610782 0.822755988 0.910739331 0.84490866 0.76471293 0.784060215 0.883438449 0.755106022 1 18.18716117 -1.900441744 2.302956318 1.104161462 0.823344848 0.251645013 0.095207897 9179122.919 4476511.807 5177847.363 0.02167796 0.012576455 1.900441744 -0.280816614 FEWELPLDEAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FEWELPLDEAQR 12 0 Q9BSJ8-2;Q9BSJ8 Q9BSJ8-2 ESYT1 Extended synaptotagmin-1 0 ; 110.38 0.0034802 29578000 45774 55117 43613 71128 54659 73309 52556 51376 49269 62064 FALSE TRUE 47581.19287 64582.916 44749.59061 85196.9061 45368.0827 56284.09576 48436.52339 50687.38875 47495.81831 74224.25251 0.64104644 0.870105307 0.602897154 1.147831109 0.611229904 0.758297913 0.652570039 0.68289524 0.639896216 1 16.17960304 FFDANYDGKDYDPVAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFDANYDGKDYDPVAAR 17 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 164.2 2.39E-09 2789500000 4470100 3420000 4283700 3182800 4928300 5066500 5070200 4140500 4495700 3013910 FALSE TRUE 4646583 4007358.396 4395336.741 3812348.34 4090589.326 3889882.159 4672784.475 4085003.37 4333900.635 3604427.96 1.289131882 1.111787624 1.219426991 1.05768471 1.134878924 1.079195424 1.296401129 1.133329176 1.202382371 1 21.78133888 -1.327798731 3.621382498 0.999391619 1.165376472 0.297469267 0.07786356 5668821.494 2078577.962 26800.67981 0.01701086 0.047011193 1.327798731 0.165984853 FFDEESYSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 179.8 1.62E-05 125838000 94092 143462 106041 162887 144697 185690 118589 103055 86890 171735 FALSE TRUE 97806.82481 168100.4825 108804.5156 195105.5624 120101.4556 142566.3117 109293.6843 101673.7163 83762.84587 205383.1852 0.476216321 0.818472468 0.529763503 0.949958792 0.584767714 0.694147924 0.53214524 0.495044013 0.407836921 1 17.64795855 2.242811879 24.83876921 0.557768649 0.683770134 0 0.197064955 245.7752791 1435994.848 0.064454827 0.052155547 174.908888 -2.242811879 0.126001485 FFDQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFDQYR 6 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 104.11 0.079355 95752000 117510 149070 122590 124500 176480 180860 129300 134870 115740 201240 FALSE TRUE 122149.3855 174671.6129 125784.7961 149125.7284 146481.9926 138858.006 119165.1281 133062.2883 111574.54 240669.125 0.507540739 0.725774911 0.522646169 0.619629661 0.608644722 0.57696643 0.495140904 0.552884747 0.463601386 1 17.87669155 -2.02337057 2.745180531 1.502416632 0.566585392 0.769366151 0.071656407 16825399.77 7763773.681 53231455.64 0.016635219 0.009476096 2.02337057 -0.93583124 FFDS(ph)EDEDFEILSL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FFDSEDEDFEILSL 14 0 Q9Y4P1;Q9Y4P1-4 Q9Y4P1 ATG4B Cysteine protease ATG4B 1 FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL;FFDS(1)EDEDFEILSL 220.23 4.95E-12 350643000 892935 1070110 1033950 1056353 1210309 1374189 1097105 1021530 999513 1011818 TRUE FALSE 928188.7633 1253893.068 1060895.586 1265296.471 1004581.108 1055054.431 1011111.043 1007838.061 963540.7224 1210064.365 0.767057349 1.036220142 0.876726575 1.04564394 0.83018816 0.871899431 0.835584513 0.832879713 0.79627229 1 20.20665236 FFEDLEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FFEDLEQR 8 0 Q5VV41;Q5VV41-2;B0QZD3 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 ;; 116.37 0.0053142 157934000 415080 524930 478300 489610 584340 624030 518260 536840 508320 484360 FALSE TRUE 431467.6789 615082.6441 490764.8909 586453.3967 485014.0955 479108.4898 477637.427 529644.5379 490025.6625 579261.0684 0.744858756 1.061840123 0.847225746 1.012416385 0.837297934 0.827102866 0.824563315 0.914345132 0.845949589 1 19.14385418 5.022178673 14.71336799 0.899048196 0.417991095 0.249515968 0.083559005 3265400.112 57342969.75 0.018890553 35203572.53 105239.475 -5.022178673 -0.481057101 FFEEVLLFEDELHDHGVSSLSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFEEVLLFEDELHDHGVSSLSVK 23 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 248.89 4.15E-38 59776000 56662 56264 76400 70251 77040 93865 91998 75305 77987 41019.4 FALSE TRUE 58899.05951 65926.90433 78391.04676 84146.43812 63944.76832 72066.27629 84786.95637 74295.65965 75180.2631 49056.36607 1.200640492 1.3439011 1.597979081 1.715301089 1.303495824 1.469050443 1.72835787 1.514495785 1.532528174 1 15.58215275 2.467005654 24.98514607 1.510873212 1.445683981 0 0.222549724 1236.95086 3055198.168 0.07564411 0.063350791 293.0931402 -2.467005654 -0.065189231 FFEHFIEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FFEHFIEGGR 10 0 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;;;;; 223.31 4.50E-09 3416920000 1946762 2171326 2250388 2262495 2695920 2789879 2328023 2320033 2190566 2355802 FALSE TRUE 2023621.667 2544234.35 2309034.96 2710009.758 2237668.481 2141971.883 2145546.474 2288936.752 2111727.958 2817376.297 0.718264603 0.903050953 0.819569243 0.961891303 0.794238414 0.760271848 0.761540614 0.812435582 0.749537064 1 21.42592084 FFEHHPIPQEEASLAETALTS(ph)GSSPSAPASDSIGPQILTSPSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEAS(0.005)LAET(0.005)ALT(0.063)S(0.325)GS(0.325)S(0.266)PS(0.01)APASDSIGPQILTSPSPSK 109.45 1.47E-06 204900000 38082 31951 43346 44449 48853 52572 46691 39480 34178 32662 TRUE FALSE 39585.50677 37438.33571 44475.63237 53240.87953 40548.98451 40362.94974 43031.23742 38950.83518 32947.94046 39061.49355 1.013415084 0.958446089 1.138605525 1.363001634 1.03808075 1.033318137 1.101628061 0.997167073 0.843489008 1 15.25345949 1.556730278 3.566326715 0.919978087 1.094819914 0.285414099 0.109093322 0.254548921 7.312449238 0.074784554 0.030419494 36.03547723 -1.556730278 0.174841827 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTS(ph)PSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSK 45 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILT(0.035)S(0.842)PS(0.116)PS(0.007)K;FFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILT(0.189)S(0.81)PS(0.001)PSK 162.14 3.73E-20 175744000 25750.1 21794 26976 26785 35858 37408 33905 27556 30398 23873 TRUE FALSE 26766.73383 25536.94997 27679.01672 32082.99305 29762.86997 28720.55892 31247.43751 27186.65689 29303.98192 28550.45727 0.937523822 0.894449771 0.969477177 1.123729569 1.042465614 1.005957931 1.094463644 0.952231925 1.026392735 1 14.80122623 3.992912463 14.36894637 1.032130578 0.919968822 0.520701148 0.046342314 1.007866331 2050.166315 0.011895838 0.023783652 9838.127866 -3.992912463 -0.112161756 FFEVILIDPFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFEVILIDPFHK 12 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 188.06 9.69E-06 2663800000 2327400 1784560 2487800 2149580 2810200 2952500 3195500 2685600 2688000 1779370 FALSE TRUE 2419287.549 2091044.298 2552634.112 2574760.508 2332523.208 2266826.621 2945028.36 2649603.925 2591259.405 2128003.483 1.136881386 0.98263199 1.199544142 1.209941867 1.096108736 1.06523633 1.383939633 1.245112588 1.217695096 1 21.02106908 2.27367548 24.99686025 1.238928518 1.116329994 0.143891464 0.107521637 254.9089497 181458.4945 0.036165264 0.030256843 187.7913049 -2.27367548 -0.122598524 FFGNS(ph)WAETYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 1 FFGNS(1)WAETYR 154.47 3.36E-05 28279000 24418 56930 48417 55861 39897 57786 32266 46611 36458 84641 TRUE FALSE 25382.04149 66707.28465 49678.7868 66910.13907 33115.32219 44366.07726 29736.90661 45986.25579 35145.8837 101224.7834 0.250749279 0.659001505 0.490776914 0.661005505 0.327146387 0.438292637 0.293771008 0.454298387 0.347206312 1 16.62720303 -1.481881116 5.837549822 1.000527145 0.442204701 0.616015115 0.133546365 0.000884204 7.85E-05 0.124789001 0.029386765 0.032969995 1.481881116 -0.558322444 FFGNSWAETYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFGNSWAETYR 11 0 O43488;H3BLU7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 138.76 0.00011814 384050000 264760 304900 342350 297800 402740 399710 373460 317380 357260 299410 FALSE TRUE 275212.9292 357264.2032 351271.9222 356703.9512 334282.3987 306883.4102 344187.2293 313126.0402 344402.2824 358073.6569 0.768593064 0.997739421 0.981004649 0.996174793 0.933557641 0.857039897 0.961219075 0.874473824 0.961819658 1 18.44989686 2.997668518 24.99316524 0.919113404 0.946188265 0 0.073412244 425.5146122 4561538.602 0.020653995 0.024308301 994.6459486 -2.997668518 0.027074861 FFGQHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFGQHDR 7 0 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 0 109.36 0.018532 0 63502 75959 74860 77394 95747 99621 75511 85254 91757 81714 FALSE TRUE 66009.10799 89004.36737 76810.9131 92702.3022 79471.95914 76485.53252 69592.25051 84111.30958 88454.68349 97724.29379 0.675462625 0.910770126 0.785996093 0.948610613 0.813226231 0.782666516 0.712128457 0.860700101 0.905145282 1 16.57642963 1.069421704 2.157083889 0.996555746 0.812237215 0.384761233 0.077418047 0.300293799 2.829592563 0.070610276 0.019699334 11.73334132 -1.069421704 -0.184318531 FFHLAFEEEFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;; 193.73 2.43E-06 2938976000 1683091 2124671 1997093 2034832 2283641 2668061 2396163 2170160 2112627 2460554 FALSE TRUE 1749540.732 2489566.717 2049138.884 2437315.696 1895468.519 2048444.268 2208345.483 2141072.555 2036593.967 2942652.446 0.594545487 0.84602812 0.696357766 0.828271684 0.644136048 0.696121715 0.750460859 0.727599536 0.692094634 1 21.48868573 -2.153032307 2.442245858 1.651424061 0.724512583 0.574775561 0.072260855 9169717.601 2720937.017 32976577.64 0.016226432 0.0070302 2.153032307 -0.926911478 FFHPEEWADLFQAAGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFHPEEWADLFQAAGAK 17 0 P04066 P04066 FUCA1 Tissue alpha-L-fucosidase 0 159.4 3.22E-09 146400000 334760 200410 219250 199090 288640 313760 250970 228750 233520 195380 FALSE TRUE 347976.5833 234828.8585 224963.8351 238469.4078 239577.0759 240893.9951 231298.3156 225683.9804 225115.6608 233660.9702 1.48923709 1.004998217 0.962778828 1.020578694 1.025319186 1.030955212 0.989888535 0.965860838 0.963428597 1 17.83405725 4.738347247 6.503177705 0.994415286 1.49906749 0.974190038 0.024091057 0.017864728 4.610043627 0.006414334 0.03980945 54745.35131 -4.738347247 0.504652203 FFLSHPAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFLSHPAYR 9 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4;E5RIK2 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 131.06 0.00034369 172780000 90872 113190 106520 106920 122190 146160 102560 109120 101190 133020 FALSE TRUE 94459.69673 132629.502 109295.9987 128068.4569 101420.1874 112216.5551 94521.07921 107657.4249 97548.19167 159082.7222 0.593777221 0.833714059 0.687038776 0.805043157 0.637531129 0.705397504 0.594163074 0.676738639 0.613191617 1 17.27941763 -1.039742261 4.983842963 1.000005144 0.685877815 0.596919802 0.078125939 4.28E-06 8.25E-07 0.072504632 0.017089226 0.091255225 1.039742261 -0.314127329 FFMPAWNLEIIGTYAQTEMGHGTHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFMPAWNLEIIGTYAQTEMGHGTHLR 26 0 Q15067-2;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 138.35 4.71E-06 15673000 5682.5 10214 8342.6 9753.4 9086.6 14277 9014.3 8336.7 8051.8 11031 FALSE TRUE 5906.849488 11968.17505 8560.01501 11682.59341 7542.062978 10961.38312 8307.735612 8224.960173 7762.017291 13192.31325 0.447749335 0.907208222 0.648863838 0.885560643 0.571701326 0.830891665 0.629740627 0.623466106 0.588374241 1 13.68740994 FFMT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFMTPPR 7 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 FFMT(1)PPR;FFMT(1)PPR 104.44 0.091122 132355000 246750 303520 270760 278880 308800 343270 301640 293330 281100 320480 TRUE FALSE 256491.8805 355647.1989 277816.228 334041.6316 256310.2863 263550.7448 277996.6686 289398.3911 270983.2659 383271.92 0.669216468 0.927923963 0.724854114 0.871552582 0.668742668 0.687633847 0.725324904 0.755073294 0.707026139 1 18.54800878 -1.129062674 4.237672943 1.000048507 0.751900603 0.460064499 0.081636087 10955991.05 2919056.252 5109.903847 0.018250378 0.074291192 1.129062674 -0.248147904 FFPASADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FFPASADR 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;; 130.77 0.0024052 1013590000 565052 707090 612630 572463 1183840 936790 657851 535387 609555 1106470 FALSE TRUE 587360.6893 828527.2071 628595.6411 685694.4728 982611.2997 719234.7197 606286.9196 528211.013 587617.2346 1323261.612 0.443873444 0.626125023 0.475035046 0.518185117 0.742567676 0.543531765 0.458176157 0.399173533 0.444067318 1 20.33566688 -0.998582953 8.078495801 1.000000003 0.515079109 0.692562718 0.096586718 6.74E-09 9.27E-10 0.100529601 0.023695054 0.10032682 0.998582953 -0.484920894 FFQEENTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFQEENTEK 9 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 115.78 0.0043193 0 60985 50227 68984 58437 82839 102940 75081 64940 63560 56567 FALSE TRUE 63392.73489 58853.09654 70781.77971 69995.66418 68758.05637 79033.74507 69195.95503 64069.58552 61272.48802 67650.22061 0.937066196 0.869961635 1.046290449 1.034670154 1.016375937 1.168270323 1.022848919 0.947071346 0.905724881 1 16.04580702 7.24359714 7.676688778 0.996904204 0.125591751 0 0.080489416 0 0 0.018976846 0 17522543.23 -7.24359714 -0.871312453 FFQGS(ph)QEFLASASASAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FFQGSQEFLASASASAER 18 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(1)QEFLASASASAER;FFQGS(0.999)QEFLAS(0.001)ASASAER 155.88 1.64E-08 219444000 167558.3 180581 190698 190726 209301 247805 184038 188733 193090 186498 TRUE FALSE 174173.6311 211594.382 195667.7465 228451.0335 173724.0908 190256.0443 169612.6207 186203.3428 186140.7286 223038.7124 0.780912108 0.94868904 0.877281547 1.024266286 0.778896582 0.853018035 0.760462697 0.834847641 0.834566908 1 17.76693461 FFQTSGLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FFQTSGLSK 9 0 P0CE72;P0CE71 P0CE72 OCM;OCM2 Oncomodulin-1;Putative oncomodulin-2 0 ;; 63.816 0.042555 3949300000 139873.1 15075990 10073260 13899830 6191630 15536590 5435850 11059310 7204490 18209400 FALSE TRUE 145395.398 17665174.01 10335777.43 16649174.89 5139178.944 11928452.43 5009773.873 10911078.04 6945201.812 21777183.29 0.006676502 0.811178093 0.474614981 0.764523798 0.235989149 0.547750013 0.230046917 0.501032567 0.318921034 1 24.37631403 -1.361356098 4.537228613 1.000699507 0.44733075 0.343997496 0.234361136 0.001506884 0.000212103 0.206196379 0.048542159 0.043515492 1.361356098 -0.553368757 FFSDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 1655273000 3303410 2811780 3065580 2632490 4106770 4266320 3635150 3360890 3421600 2984910 FALSE TRUE 3433831.178 3294681.342 3145471.533 3153188.665 3408702.702 3275531.837 3350217.444 3315842.767 3298457.284 3569745.965 0.961925922 0.922945603 0.881147164 0.883308979 0.954886632 0.917581214 0.938503041 0.928873595 0.924003365 1 21.76738998 -1.857434635 0.331326076 1.073884002 0.91731167 0.460419562 0.024803193 28.7971125 1.572128772 1.68409662 0.022273968 0.013885623 1.857434635 -0.156572333 FFSGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFSGYGR 7 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 121.29 0.010358 802000000 199080 341920 305630 309560 280970 383180 265200 309070 241690 361650 FALSE TRUE 206939.8321 400642.1002 313594.9689 370790.0441 233210.8198 294192.2521 244412.931 304927.4222 232991.6241 432508.3933 0.478464315 0.92632214 0.725061002 0.857301384 0.539205304 0.680200099 0.565105637 0.70502082 0.538698503 1 18.7223686 -1.059145892 4.30825022 1.000027641 0.677345501 0.343380865 0.137069889 40153583.42 102660156.7 17475.05418 0.031384566 0.087267816 1.059145892 -0.322682139 FFSLSSVDKLEQIYECTDTEDVCIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFSLSSVDKLEQIYECTDTEDVCIVER 27 1 Q9Y4P8-4;Q9Y4P8;Q9Y4P8-2;Q9Y4P8-6 Q9Y4P8-4;Q9Y4P8-2 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 102.23 0.0022518 32918000 18016 15507 17227 18835 22809 26912 22773 22534 22588 13422 FALSE TRUE 18727.28559 18170.20662 17675.94977 22560.50678 18931.93433 20662.09586 20987.99275 22231.96859 21775.06229 16051.78392 1.166679397 1.131974285 1.101182888 1.405482836 1.17942868 1.287214926 1.307517772 1.385015441 1.356550923 1 13.97044602 3.757353114 24.82204418 1.294388104 1.133148383 0.235758351 0.11254819 891.8944103 1178053.707 0.027243878 0.049010014 5719.434806 -3.757353114 -0.161239721 FFT(ph)TPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FFTTPSK 7 0 O76021;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 1 FFT(0.825)T(0.175)PSK;FFT(0.82)T(0.18)PSK;FFT(0.861)T(0.139)PSK 116.73 0.060253 302534000 2386520 1604870 1945850 1406790 2132970 2247240 2085780 1788640 1933650 1394070 TRUE FALSE 2480741.652 1880493.938 1996560.45 1685048.863 1770408.521 1725352.567 1922291.113 1764666.206 1864058.314 1667211.325 1.487958734 1.127927762 1.197544918 1.010699026 1.06189809 1.034873349 1.152997874 1.058453826 1.118069609 1 20.66900555 FFTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FFTESR 6 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 137.5 0.029562 1536630000 1471670 1714950 1699990 1762480 1902230 2026630 1767780 1821460 1622340 1683580 FALSE TRUE 1529772.668 2009479.322 1744293.136 2111093.284 1578889.624 1555975.896 1629216.784 1797046.308 1563952.3 2013445.267 0.759778621 0.998030269 0.866322599 1.048497974 0.784173104 0.772792746 0.809168648 0.892523049 0.776754316 1 20.94123482 3.185156139 24.99999445 0.83291316 0.92016361 0.137280564 0.096090765 164.1379767 76836.38395 0.026091763 0.031185645 1531.638022 -3.185156139 0.08725045 FFTGDVFGYHGYTFANLGEHEFVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFTGDVFGYHGYTFANLGEHEFVEEK 26 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 64.028 0.023625 34700000 20234 21215 31474 18481 29862 31495 25712 23954 30851 23497 FALSE TRUE 21032.85394 24858.51122 32294.2383 22136.48664 24786.06791 24180.76356 23696.62625 23632.93581 29740.67854 28100.78727 0.74847917 0.884619743 1.149228952 0.787753255 0.882041762 0.860501285 0.843272682 0.841006182 1.058357485 1 14.77832293 1.236873314 24.98765309 1.029178798 0.877539757 0.270110693 0.10154099 60.67240582 898375.2377 0.081895998 0.024565058 17.25334529 -1.236873314 -0.151639041 FFTNFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FFTNFESR 8 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4;J3QQV6;A0A286YFL3 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ; 129.42 0.0025391 826520000 613230 831530 657900 653590 1200820 956710 767040 734200 713000 1129720 FALSE TRUE 637440.7939 974338.8091 675045.4145 782868.1512 996705.0453 734528.6016 706917.4005 724359.2499 687339.2693 1351067.004 0.471805463 0.721162463 0.499638739 0.579444357 0.737716962 0.543665562 0.523228973 0.536138658 0.508738106 1 20.36566779 -1.262445353 5.157034544 1.000067364 0.571428779 0.694543603 0.085723002 6.40E-05 9.16E-06 0.080058071 0.018866915 0.054645531 1.262445353 -0.428638585 FFTVEPQHIPCVLMAFLDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFTVEPQHIPCVLMAFLDHR 20 0 O43592 O43592 XPOT Exportin-T 0 106.86 0.00013597 41382000 38323 45390 53533 52364 55615 62333 52035 46934 50479 47597 FALSE TRUE 39836.02163 53185.37941 54928.11396 62721.44291 46161.58217 47857.10542 47956.36073 46304.9265 48662.27065 56922.72085 0.699826379 0.934343591 0.964959389 1.101870079 0.810951786 0.840738192 0.842481877 0.813470013 0.854883075 1 15.796717 FFWEMAEEEGWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FFWEMAEEEGWIR 13 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 118.4 0.00053614 0 42002 60639 64247 58826 55427 73598 44291 69222 46163 72689 FALSE TRUE 43660.27139 71053.27654 65921.3296 70461.60722 46005.53834 56505.97989 40819.35569 68294.19231 44501.60265 86931.01784 0.502240426 0.817352406 0.758317701 0.810546212 0.529218908 0.650009413 0.46956031 0.785613628 0.511918574 1 16.40758342 -1.222860116 5.048792453 1.00004061 0.659393109 0.389107428 0.131541502 5.76E-05 8.87E-06 0.122057656 0.028765842 0.059860437 1.222860116 -0.340647502 FGAVFLWDSGSSVGEITGHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGAVFLWDSGSSVGEITGHNK 21 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 278.07 7.25E-45 316020000 614180 632060 734720 623200 820300 895090 808350 723310 740950 634930 FALSE TRUE 638428.3007 740611.3883 753867.4068 746467.0999 680865.699 687218.9127 744989.4148 713615.2125 714283.3542 759332.377 0.840775818 0.975345462 0.992802927 0.98305712 0.896663595 0.905030437 0.981111088 0.939792947 0.940672854 1 19.534372 -4.999999998 0.311227802 1.511783787 0.940011872 0.13910669 0.045286984 658.8933716 5.953897416 221.2004972 0.042213683 1.00E-05 4.999999998 -0.571771915 FGAVWTGDNTAEWDHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGAVWTGDNTAEWDHLK 17 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 256.45 4.26E-27 1218130000 1000520 847120 1028760 948160 1275600 1315070 1114740 950860 1098700 654430 FALSE TRUE 1040021.302 992606.2703 1055570.331 1135703.218 1058773.968 1009664.923 1027363.766 938115.277 1059158.002 782653.0287 1.328840832 1.26825839 1.34870791 1.451094133 1.352801214 1.290054322 1.31266823 1.198634954 1.353291897 1 19.57801334 -0.730053299 0.347745894 0.875283397 1.35103519 0.717767038 0.061103365 5.974405431 0.646243625 0.866953821 0.054389087 0.186185863 0.730053299 0.475751792 FGCRDPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGCRDPVR 8 1 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 69.812 0.048292 97875000 112300 120000 105160 76971 338090 220450 115460 90799 101920 362490 FALSE TRUE 116733.6907 140609.0665 107900.556 92195.63406 280621.5826 169253.8285 106409.9435 89581.98792 98251.91911 433512.9752 0.26927381 0.324348 0.2488981 0.212670991 0.647319916 0.390423905 0.245459651 0.206641999 0.226641242 1 18.72571565 -1.492567209 5.821621546 1.000771166 0.306208006 0.732852252 0.125343954 0.001326444 0.000115618 0.128316298 0.030214113 0.032168647 1.492567209 -0.694563159 FGDES(ph)PLLTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGDESPLLTMR 11 0 H0YJ41;Q9P203-5;Q9P203 H0YJ41 BTBD7 BTB/POZ domain-containing protein 7 1 FGDES(1)PLLTMR 135.1 0.00013333 31010000 28865 33816 35652 29854 41600 47688 35673 36689 36686 32415 TRUE FALSE 30004.61249 39623.63495 36581.12041 35759.03209 34528.84686 36613.18472 32876.85705 36197.24397 35365.67803 38766.09863 0.773991027 1.02212078 0.943636881 0.922430509 0.890696977 0.944464004 0.848082686 0.933734506 0.912283652 1 15.24250793 0.098143011 1.770032899 1.000015389 0.913803239 0.156670629 0.06200051 52.69900851 99.69139635 0.055891512 0.015297091 1.253553896 -0.098143011 -0.08621215 FGDILHVINASDDEWWQAR ddPTM_MDA-MB-175_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 ; 244.7 1.57E-24 579410000 1074170 1109230 1199630 1089410 1398730 1490950 1234770 1213000 1214620 1120690 FALSE TRUE 1116579.061 1299731.624 1230893.343 1304892.046 1160974.374 1144699.458 1137985.501 1196741.719 1170906.063 1340267.749 0.833101492 0.969755204 0.918393615 0.973605496 0.866225704 0.854082671 0.849073256 0.89291242 0.873635932 1 20.35408981 4.811862491 21.36886088 0.90327208 0.833095972 0.155855204 0.051640019 58421.23053 17024918.67 0.012393245 68.6363642 64842.90921 -4.811862491 -0.070176108 FGDRFPAMSDAYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FGDRFPAMSDAYDR 14 1 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 216.39 5.61E-12 1254460000 705091 932309 900660 671407 1433820 1301170 655303 919404 902110 1414810 FALSE TRUE 732928.5371 1092425.818 924131.9395 804209.3007 1190099.789 998992.9869 603938.6385 907080.8932 869643.2373 1692014.931 0.433169072 0.645636039 0.546172449 0.475296811 0.703362462 0.590416177 0.35693458 0.536095088 0.513969009 1 20.69031087 -1.196280614 5.060664549 1.000039868 0.534435516 0.685547246 0.094791325 4.21E-05 6.69E-06 0.090653019 0.021365297 0.06363842 1.196280614 -0.465604352 FGDYNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FGDYNK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 113.08 0.061517 1363920000 2455020 1951090 2275460 1938590 2994830 2896190 2937670 2324450 2456260 1667490 FALSE TRUE 2551946.085 2286174.53 2334760.357 2322037.316 2485769.866 2223593.765 2707407.749 2293294.55 2367859.682 1994202.739 1.279682369 1.146410285 1.170773819 1.164393805 1.24649807 1.115028939 1.357639169 1.149980644 1.187371592 1 20.92738066 0.523634443 1.691711423 1.000107946 1.20297879 0.437078965 0.069138399 2.469803836 7.767429671 0.061130319 0.017296752 3.339138579 -0.523634443 0.202870844 FGEEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGEEIAR 7 0 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 146.94 0.0050827 308270000 473860 493680 535460 444020 612220 641410 563470 505660 509100 411310 FALSE TRUE 492568.3587 578465.6997 549414.5275 531845.8307 508155.0631 492452.2482 519303.749 498882.4548 490777.5904 491898.3195 1.00136215 1.17598633 1.116927027 1.081210912 1.033048992 1.001126104 1.055713607 1.014198331 0.997721625 1 18.9080006 3.28344362 2.792139407 1.017947891 1.105228079 0.438386109 0.042961091 0.229287216 3.648164916 0.012234181 0.01669077 1920.629612 -3.28344362 0.087280188 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 280.36 7.54E-46 1051640000 1771570 376825 656520 363484 1082010 1516910 1102490 683200 808770 244617 TRUE FALSE 1841512.952 441541.7625 673629.4505 435380.0503 898090.3267 1164630.641 1016073.953 674042.8215 779662.5257 292545.0177 6.294801963 1.509312194 2.302652275 1.488249753 3.069921798 3.981030512 3.473222552 2.304065292 2.665102731 1 18.15829912 4.748337645 24.86771056 2.5350742 6.294804145 0.629287014 0.88801744 859.6215188 2186385.451 0.216884716 2.862235374 56019.2958 -4.748337645 3.759729944 FGEVVDCTLKLDPITGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 130.56 2.73E-05 525920000 837230 774480 942820 459350 1375950 1116790 666930 891730 1009220 992030 FALSE TRUE 870284.4869 907490.9154 967390.6637 550208.059 1142066.51 857432.4476 614654.2839 879777.8179 972898.3693 1186399.285 0.733551089 0.764911887 0.815400579 0.463762973 0.962632501 0.722718277 0.518083829 0.74155289 0.82004295 1 20.1781582 0.942862674 2.65070264 0.998751997 0.712118131 0.303387873 0.132950291 0.379775992 6.163246764 0.122154075 0.032626916 8.767235533 -0.942862674 -0.286633867 FGEYHKDDPSSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FGEYHKDDPSSFR 13 1 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 178.67 8.65E-06 1540490000 2754860 2100800 2831160 2228950 3456780 3504640 2928610 2604790 2945740 1937460 FALSE TRUE 2863624 2461596.058 2904942.355 2669829.657 2869197.77 2690740.473 2699057.896 2569877.051 2839723.393 2317068.192 1.235882487 1.062375318 1.253714658 1.152244749 1.238288014 1.161269436 1.164859068 1.109107215 1.225567466 1 21.14386907 -4.368968759 0.314614803 6.42E-08 1.18066857 0.443785611 0.059089416 176.6920705 2.327810617 115.7209418 0.050402943 4.28E-05 4.368968759 1.180668506 FGGEHVPNS(ph)PFQVTALAGDQPSVQPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FGGEHVPNSPFQVTALAGDQPSVQPPLR 28 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 1 FGGEHVPNS(0.999)PFQVT(0.001)ALAGDQPSVQPPLR;FGGEHVPNS(1)PFQVTALAGDQPSVQPPLR;FGGEHVPNS(1)PFQVTALAGDQPSVQPPLR 280.49 6.24E-62 1002160000 347234 441668 422417 381728 409727 514050 380283 398264 408613 422404 TRUE FALSE 360943.0664 517521.0433 433425.534 457232.6591 340081.7509 394669.678 350475.4248 392925.9225 393907.0979 505165.9764 0.714503912 1.024457441 0.857986393 0.905113726 0.673207949 0.781267339 0.693782719 0.777815492 0.779757775 1 18.94639795 3.264342644 24.99710945 0.767453334 0.884902068 0.131312811 0.10884913 328.7192926 318709.2905 0.027600398 0.037358514 1837.987885 -3.264342644 0.117448734 FGGPVHHQAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGGPVHHQAQR 11 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 150.27 1.96E-05 43553000 40698 55547 40409 45675 115970 80277 49240 47850 37943 142590 FALSE TRUE 42304.78847 65086.76515 41462.09174 54709.37867 96257.46082 61633.88336 45380.44014 47208.64902 36577.43884 170527.7804 0.248081505 0.381678369 0.243139808 0.320823848 0.564467916 0.361430162 0.266117579 0.276838465 0.214495484 1 17.37964726 -1.16231144 4.660088674 1.000084623 0.322056446 0.818574039 0.096079766 29117743.22 7262508.116 25254.06207 0.023365188 0.068815863 1.16231144 -0.678028178 FGGSGS(ph)QVDSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGGSGSQVDSAR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 FGGS(0.354)GS(0.645)QVDSAR;FGGS(0.124)GS(0.876)QVDSAR 92.65 0.0079887 609820000 439160 351040 403570 314890 456760 504770 408890 375900 386650 334970 TRUE FALSE 456498.3759 411328.3893 414087.3657 377174.3021 379120.0984 387544.8174 376840.1334 370861.6753 372734.542 400600.9581 1.139533909 1.026778346 1.03366544 0.941521218 0.946378411 0.967408613 0.94068705 0.925763326 0.930438469 1 18.61180635 5.191827102 0.713896837 0.94222364 1.396265715 0.832657661 0.025988364 1.769942705 0.434568668 0.009382674 0.748899083 155534.6306 -5.191827102 0.454042075 FGHEFLEFEFRPDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FGHEFLEFEFRPDGK 15 1 P61326;Q96A72;F5H6N1;P61326-2 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 ;; 220.85 9.70E-13 1182247000 2384940 1747142 2456797 1935470 2717192 2925701 3099451 2452219 2651718 1555375 FALSE TRUE 2479099.273 2047200.048 2520823.148 2318300.189 2255324.674 2246251.282 2856507.932 2419351.015 2556283.187 1860120.952 1.332762405 1.100573619 1.355193137 1.246316906 1.212461304 1.207583453 1.535657092 1.300641774 1.374256435 1 20.826965 FGIDDQDYLVSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGIDDQDYLVSLTR 14 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ; 153.75 1.47E-05 107241000 265488 369750 319411 324485 387545 446000 357764 319036 309262 396460 FALSE TRUE 275969.6712 433251.6862 327735.1131 388667.1645 321670.2393 342423.2592 329721.5228 314759.8443 298131.721 474138.7463 0.582044124 0.913765622 0.691221959 0.819732974 0.678430611 0.722200541 0.695411471 0.663855985 0.628785821 1 18.85494977 -0.976807296 4.687876395 1.000004564 0.71429045 0.483186108 0.089715833 4.03E-06 8.78E-07 0.081717205 0.019260622 0.105485485 0.976807296 -0.285714114 FGINIPS(ph)PEHSNTIDVCNTVDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGINIPSPEHSNTIDVCNTVDIK 23 0 C9IZ03;Q9HCI7-2;Q9HCI7 C9IZ03 MSL2 E3 ubiquitin-protein ligase MSL2 1 FGINIPS(0.999)PEHS(0.001)NTIDVCNTVDIK;FGINIPS(0.999)PEHS(0.001)NTIDVCNTVDIK 228.55 4.33E-33 284360000 631660 431230 533230 444770 686400 689490 626110 553670 612590 377850 TRUE FALSE 656598.4245 505290.398 547126.4119 532744.1785 569725.9732 529366.3968 577033.8622 546248.9593 590543.0056 451882.4731 1.453029191 1.118189857 1.210771482 1.178944106 1.260783516 1.171469195 1.276955617 1.208829711 1.306850875 1 18.78558808 -1.300839623 3.362531421 0.998958947 1.234309348 0.404068864 0.08793259 17842965.78 28265652.25 191515.5445 0.019118662 0.050021922 1.300839623 0.235350401 FGKPNKR ddPTM_MDA-MB-175_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 ; 95.62 0.0074985 5887200000 5757800 4610700 5317600 4322100 8990000 7621600 6553300 5513600 6372500 5156200 FALSE TRUE 5985122.39 5402551.859 5456181.024 5176998.48 7461883.011 5851598.906 6039635.222 5439699.21 6143154.97 6166458.669 0.970593125 0.876119042 0.884815956 0.839541584 1.210075898 0.948939938 0.979433342 0.88214314 0.996220894 1 22.55601077 FGLGS(ph)PLPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FGLGSPLPSPR 11 0 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR;FGLGS(1)PLPS(1)PR 177.93 1.14E-05 447756000 982740 991600 949510 1064110 1121450 1386760 1095950 1107610 1037120 1114640 TRUE FALSE 1021539.334 1161899.586 974255.0106 1274587.782 930826.3296 1064706.007 1010046.575 1092764.3 999794.2538 1333032.367 0.76632748 0.871621436 0.73085623 0.956156665 0.698277366 0.798709794 0.757705964 0.819758264 0.750014987 1 20.34628038 -1.464252655 5.643953476 1.00019226 0.796940574 0.430638727 0.070873738 0.000153874 1.46E-05 0.061585065 0.014502099 0.034335814 1.464252655 -0.203251687 FGLGS(ph)PLPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FGLGSPLPSPR 11 0 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 FGLGS(1)PLPSPR;FGLGS(0.984)PLPS(0.016)PR;FGLGS(0.999)PLPS(0.001)PR 140.78 4.03E-05 186887000 155142 828400 916340 809100 1090810 1230290 715793 960390 1086710 1066810 TRUE FALSE 161267.126 970671.2559 940220.5732 969137.5651 905394.5058 944573.7927 659687.2743 947517.5429 1047599.519 1275830.994 0.126401637 0.76081492 0.736947587 0.759612809 0.709650816 0.740359653 0.517064782 0.742666973 0.821111514 1 20.2830058 3.919016932 0.090982292 1.218571293 3.12E-24 0.389422171 0.170941495 66.77323674 1.314240308 5.133901949 13.37209012 8298.831225 -3.919016932 -1.218571293 FGLSVGHHLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGLSVGHHLGK 11 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 148.56 2.01E-05 34621000000 8611400 27309700 27206100 25820000 32720800 36703500 29670000 34317100 28651600 27921400 FALSE TRUE 8951384.721 31999928.54 27915113.32 30927118.93 27158930.1 28179668.37 27344387.87 33857135.41 27620434.51 33392063.74 0.268069227 0.958309399 0.835980475 0.926181717 0.813334878 0.843903168 0.818888826 1.013927611 0.82715566 1 24.99300192 4.74232806 24.99002684 0.891046997 0.268068988 0.868314871 0.073015095 118.5908394 786599.1043 0.016877535 0.126783031 55249.46285 -4.74232806 -0.622978009 FGNDVQHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGNDVQHFK 9 0 P62993;J3KT38 P62993 GRB2 Growth factor receptor-bound protein 2 0 ; 88.496 0.012745 408250000 1730740 1749720 2023820 1665120 2253210 2351730 2041640 1856700 2135730 1446880 FALSE TRUE 1799070.952 2050220.799 2076562.412 1994475.766 1870210.169 1805576.348 1881610.922 1831813.973 2058865.494 1730368.434 1.039703982 1.184846394 1.200069518 1.152630692 1.080816162 1.043463527 1.087404789 1.058626555 1.189842264 1 20.72264782 3.230285411 7.728455527 1.077222684 1.15130195 0.229455579 0.060169746 0.181550971 69.18673736 0.016671245 0.020887122 1699.360075 -3.230285411 0.074079266 FGNQADHFLGSLAFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGNQADHFLGSLAFAK 16 0 Q9H488;Q9H488-2 Q9H488 POFUT1 GDP-fucose protein O-fucosyltransferase 1 0 ; 164.01 7.53E-09 272440000 442760 448700 486730 427040 686710 661680 497740 494700 499660 443540 FALSE TRUE 460240.5067 525760.7346 499414.5837 511507.2374 569983.2795 508014.8479 458725.8382 488069.3557 481677.3342 530443.1709 0.867652808 0.991172596 0.941504408 0.964301674 1.074541649 0.957717765 0.864797331 0.920116202 0.90806586 1 19.01683867 -0.487637214 10.16866003 1 0.944342652 0.078478562 0.058173749 0 0 0.058630079 0.013819242 0.325358971 0.487637214 -0.055657348 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 201.85 1.54E-21 1242618000 1043924 1002943 982689 967045 1049267 1210614 1011015 1026792 954524 1146791 TRUE FALSE 1085138.926 1175190.658 1008298.683 1158323.615 870912.9701 929467.2455 931769.0025 1013029.533 920170.8677 1371482.74 0.791215882 0.85687601 0.735188751 0.84457761 0.635015626 0.677709765 0.679388063 0.738638193 0.670931424 1 20.38730504 3.256059758 24.99966821 0.715838007 0.805402823 0.097475704 0.100952747 433.8478093 619801.1096 0.025578041 0.034555692 1803.26585 -3.256059758 0.089564816 FGQYNKEDPTSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGQYNKEDPTSFR 13 1 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 166.86 3.00E-05 1166110000 3073810 2970590 3463660 2579290 4461800 4262400 3255150 3266490 3726200 3227810 FALSE TRUE 3195166.392 3480765.725 3553925.825 3089465.864 3703384.83 3272522.197 3000002.837 3222708.044 3592094.79 3860237.569 0.827712371 0.901697282 0.92064951 0.8003305 0.959367076 0.847751502 0.777154976 0.834847075 0.930537234 1 21.88025821 1.010534211 4.265698976 0.999516742 0.858454371 0.426315188 0.052537523 0.163419681 8.095438681 0.051239816 0.01306865 10.24552485 -1.010534211 -0.141062371 FGTVLTEHVAAAELGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FGTVLTEHVAAAELGAR 17 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;; 183.7 6.77E-10 1040635000 759540 721560 750260 708260 886330 1043520 825110 806100 791800 747180 FALSE TRUE 789527.2257 845482.317 769812.3919 848351.7141 735671.9432 801178.2947 760435.7222 795295.548 763303.2727 893575.6154 0.883559502 0.946178815 0.861496642 0.949389956 0.823290084 0.896598207 0.851003216 0.890014828 0.85421229 1 19.76923029 5.101432421 20.40133986 0.891072417 0.000573926 0 0.051737707 20776.51342 2016192.546 0.010827072 445986.6172 126308.4545 -5.101432421 -0.890498491 FGVEQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FGVEQDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 151.29 0.0043996 7889450000 5471540 5673610 5844650 5444590 6386040 7345750 6205630 6035880 5580690 5199380 FALSE TRUE 5687560.624 6648008.383 5996966.38 6521513.652 5300543.202 5639810.888 5719216.505 5954978.901 5379842.057 6218098.963 0.91467837 1.069138401 0.964437269 1.04879541 0.852437897 0.906999217 0.919769296 0.957684806 0.865190807 1 22.56804215 3.246162685 24.99992078 0.917595964 1.001765996 0.341638418 0.055888233 186.4425095 613125.3032 0.014562613 0.019347401 1762.636199 -3.246162685 0.084170032 FGVLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGVLFR 6 0 Q9P1F3 Q9P1F3 ABRACL Costars family protein ABRACL 0 98.352 0.093134 450920000 301420 368360 306050 350710 414820 459670 346950 350550 295660 390310 FALSE TRUE 313320.2943 431622.9646 314025.9144 420079.3912 344309.0446 352918.6089 319755.1524 345851.4506 285019.2544 466783.7716 0.671232192 0.924674316 0.672743856 0.899944293 0.737619998 0.756064436 0.685017715 0.740924325 0.610602321 1 18.83239488 3.084519888 22.12400373 0.737502652 0.796298567 0.009421402 0.120933885 32.6167952 8528.203434 0.031808197 0.038018207 1214.84225 -3.084519888 0.058795915 FGVQMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FGVQMDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;;; 149.48 0.0046838 3681848000 2657590 2866480 2683680 2470440 3094280 3488760 2767850 2769070 2620500 2837990 FALSE TRUE 2762513.705 3358775.642 2753618.905 2959085.658 2568315.391 2678548.363 2550898.685 2731955.146 2526188.717 3394039.804 0.813930851 0.989609974 0.811310139 0.871847659 0.756713397 0.789191794 0.751581841 0.804927256 0.744301441 1 21.69457205 3.264531268 18.59715966 0.794047078 0.875788332 0.110515547 0.083177502 20.97679841 15018.67756 0.021086835 0.02850936 1838.786336 -3.264531268 0.081741253 FGVQSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FGVQSER 7 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;;;; 137.18 0.0067653 2588170000 1845810 2417060 2300590 2145370 2661200 2889930 2292150 2296640 2226620 2558400 FALSE TRUE 1918684.004 2832171.253 2360545.265 2569717.783 2208850.175 2218787.555 2112485.294 2265857.297 2146484.381 3059669.496 0.627088647 0.925646138 0.77150335 0.839867765 0.721924436 0.725172296 0.690429243 0.740556227 0.701541256 1 21.54494439 -1.197038508 4.378103197 1.000075427 0.75284268 0.476591809 0.078737867 5.60E-05 1.03E-05 0.073598977 0.017342163 0.06352746 1.197038508 -0.247232746 FGVQTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FGVQTDR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 158.03 0.0033409 4596770000 3173240 3831380 3603520 3546400 4137640 4657910 3817180 3712990 3580620 3682060 FALSE TRUE 3298521.965 4489389.711 3697430.692 4247867.335 3434325.431 3576180.994 3517979.457 3663223.442 3451754.186 4403489.16 0.749070077 1.019507383 0.839659315 0.964659428 0.779910045 0.8121244 0.79890726 0.8318911 0.783867988 1 22.07021568 3.227608008 24.99632345 0.823196161 0.898418245 0.084638004 0.089596935 388.9441648 887656.6499 0.02342081 0.028246449 1688.915835 -3.227608008 0.075222085 FGWDCHGLPVEYEIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FGWDCHGLPVEYEIDK 16 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 180.74 2.42E-09 339400000 848610 592350 731900 611350 1010460 917830 898660 725910 795580 548480 FALSE TRUE 882113.7781 694081.5047 750973.9153 732273.2053 838702.3701 704677.8923 828220.681 716180.3638 766947.2312 655944.1547 1.34480012 1.058141154 1.144874773 1.116365166 1.278618559 1.074295559 1.262639014 1.091831307 1.169226413 1 19.32321347 -4.99999991 0.244744066 0.02336333 1.180792568 0.25337265 0.090042774 242.536333 2.413110245 118.0117203 0.123987106 1.00E-05 4.99999991 1.157429238 FGYDEIDNGYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGYDEIDNGYLK 12 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 120.96 0.00089511 37721000 76545 87251 75101 81195 119580 121800 88306 76644 80964 70503 FALSE TRUE 79567.05571 102235.6805 77058.19376 97255.12866 99253.83431 93513.7959 81384.34498 75616.71254 78050.12146 84316.71299 0.943668851 1.212519759 0.913913636 1.15345019 1.177154929 1.109077816 0.965221984 0.896817604 0.925677943 1 16.36353101 2.148475206 4.661464228 0.93019683 1.090187406 0.346309027 0.092576026 0.209966675 8.017413041 0.034345632 0.025043859 140.7586866 -2.148475206 0.159990576 FGYTVSEENYMCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FGYTVSEENYMCR 13 0 Q96EK6;G3V5E4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 218.07 4.59E-07 0 32880 37543 36011 35830 42705 51130 36850 28904 32941 48829 FALSE TRUE 34178.12779 43990.71821 36949.47624 42917.06706 35446.01935 39255.83238 33961.60071 28516.58916 31755.45984 58396.10766 0.585280923 0.753315931 0.632738683 0.734930268 0.606992842 0.672233715 0.58157302 0.488330307 0.543794118 1 15.83358459 -1.091573497 5.646869175 1.000002824 0.619193504 0.681919608 0.077398336 3.07E-06 4.93E-07 0.083467996 0.01967345 0.080989087 1.091573497 -0.38080932 FGYVDFESAEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 ;;; 308.55 2.72E-55 265321000 510794 316403 397534 330971 520891 517301 495885 403856 433609 291941 FALSE TRUE 530960.5415 370742.754 407894.0626 396436.076 432350.1339 397165.6825 457016.2379 398442.9709 418003.4968 349141.2494 1.520761418 1.061870388 1.168278063 1.135460438 1.238324416 1.137550155 1.308972339 1.141208527 1.197233204 1 18.41345129 -5 0.204165509 0.070398973 1.233993233 0.235902642 0.119544916 218.0179456 2.165256375 82.96549821 0.253792763 1.00E-05 5 1.16359426 FHCPHCDTVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHCPHCDTVIAR 12 0 A0A2R8Y595;A0A2R8YFL0;P49711-2;P49711 A0A2R8Y595 CTCF Transcriptional repressor CTCF 0 98.105 0.002629 37698000 28433 32869 29124 26817 27684 32174 33282 25621 30599 26441 FALSE TRUE 29555.5568 38513.99506 29882.99537 32121.32256 22978.28357 24702.0761 30673.26987 25277.5924 29497.74797 31621.60771 0.934663318 1.217964482 0.945018218 1.015802955 0.726663988 0.781177109 0.970009816 0.799377206 0.932835175 1 14.9486231 3.378650544 8.328861905 0.857656031 1.039398453 0.342481187 0.108045183 0.248469552 18.69312179 0.028710562 0.038901494 2391.390744 -3.378650544 0.181742422 FHDEVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHDEVGK 7 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;B0QYR8;B0QYR9;B0QYS0;B0QYS1;B0QYS2;B0QYS3;B0QYR5;B0QYS5 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 72.138 0.052417 211150000 234060 152440 212780 198450 280330 272990 257120 194560 210190 153060 FALSE TRUE 243300.8695 178620.3842 218325.2216 237702.8177 232679.6067 209592.2097 236966.2625 191952.2414 202625.303 183049.1765 1.329155772 0.975805451 1.192713487 1.298573543 1.271131677 1.145004931 1.294549733 1.048637558 1.10694463 1 17.48187176 1.656075267 7.666197417 1.057941851 1.207506405 0.359513648 0.099288811 0.145346382 15.96301855 0.049201525 0.025357199 45.29760773 -1.656075267 0.149564554 FHDFDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FHDFDHR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 117.93 0.0051196 467400000 859520 833110 835840 784290 1133010 1100250 965410 735010 755010 916910 FALSE TRUE 893454.5133 976190.1618 857622.6771 939420.2211 940421.3649 844733.612 889738.6416 725158.3932 727837.3376 1096560.959 0.8147787 0.890228814 0.782102144 0.85669676 0.857609745 0.770348064 0.811390041 0.661302399 0.663745441 1 20.06455458 2.406962301 1.996826759 0.744048097 0.839850583 0.028103424 0.094997055 0.580095159 4.72404027 0.038873035 0.029786843 255.2479722 -2.406962301 0.095802486 FHDFLGDSWGILFSHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FHDFLGDSWGILFSHPR 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;; 261.64 1.54E-27 29929523000 974572 1356070 1570410 1379657 1786909 2061100 1599872 1383780 1395610 1616772 FALSE TRUE 1013048.855 1588964.474 1611336.175 1652549.037 1483170.846 1582440.761 1474469.852 1365232.693 1345382.269 1933547.518 0.523932743 0.821787134 0.833357422 0.854672058 0.767072354 0.818413174 0.762572338 0.706076618 0.695810295 1 20.88281879 4.742317757 24.83300839 0.792995568 0.52393263 0.506850681 0.082677919 287.1488733 1897838.913 0.019332162 0.144845645 55248.15221 -4.742317757 -0.269062939 FHDIISDAEIEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHDIISDAEIEIVK 14 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 123.02 0.00010534 39372000 117810 106290 106900 112170 163970 157720 130340 106870 120530 87817 FALSE TRUE 122461.2298 124544.4807 109685.9018 134356.8912 136098.438 121091.9203 120123.6102 105437.5825 116192.1488 105023.0598 1.166041344 1.185877472 1.044398269 1.279308482 1.295891 1.153003164 1.143783189 1.003946968 1.106348921 1 16.68034661 1.955637117 2.924766979 1.039194441 1.189605824 0.472756679 0.070777375 0.245290318 3.894316234 0.037586009 0.020891778 90.28947267 -1.955637117 0.150411383 FHDTS(ph)SPLMVTPPSAEAHWAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDTS(0.5)S(0.5)PLMVTPPSAEAHWAVR;FHDT(0.098)S(0.492)S(0.41)PLMVTPPSAEAHWAVR 194.68 4.65E-18 2186320000 92424 202275 169617 184549 176678 210214 164820 152574 148804 179635 TRUE FALSE 96072.97089 237014.1578 174037.3584 221052.2414 146646.3367 161394.9843 151900.9777 150528.9951 143448.5731 214831.0389 0.447202468 1.103258444 0.810112725 1.028958583 0.682612426 0.751264739 0.707071839 0.700685505 0.66772741 1 17.71284292 3.189147577 24.99999345 0.731439584 0.862999916 0.051743335 0.184784177 239.6356775 121240.1307 0.049341293 0.058974232 1545.77962 -3.189147577 0.131560331 FHDTSS(ph)PLMVTPPSAEAHWAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 FHDTSSPLMVTPPSAEAHWAVR 22 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 FHDT(0.049)S(0.175)S(0.776)PLMVTPPSAEAHWAVR;FHDT(0.001)S(0.179)S(0.82)PLMVTPPSAEAHWAVR;FHDTS(0.003)S(0.997)PLMVTPPSAEAHWAVR;FHDT(0.018)S(0.138)S(0.844)PLMVTPPSAEAHWAVR;FHDT(0.041)S(0.271)S(0.689)PLMVTPPSAEAHWAVR;FHDTS(0.031)S(0.969)PLMVTPPSAEAHWAVR;FHDTS(0.025)S(0.975)PLMVTPPSAEAHWAVR;FHDT(0.059)S(0.401)S(0.54)PLMVTPPSAEAHWAVR;FHDTS(0.028)S(0.971)PLMVTPPSAEAHWAVR 264.97 2.65E-37 7661420000 603954 1045264 899083 944462 960370 1295065 854958 925221 858414 960952 TRUE FALSE 627798.5703 1224779.961 922513.8416 1131273.765 797126.6504 994305.7806 787944.1579 912819.9259 827519.8478 1149232.146 0.546276549 1.065737645 0.802721926 0.984373583 0.693616736 0.86519141 0.685626625 0.794286802 0.720063262 1 20.13223882 3.222023184 24.99764311 0.779804706 0.861842111 0.025058582 0.153465867 694.960769 1050486.411 0.040554275 0.048600472 1667.336218 -3.222023184 0.082037404 FHFPPLDT(ph)HSPTNDVQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.955)HS(0.045)PTNDVQPGR 195.13 3.00E-15 122610000 104890 131960 124120 123980 141690 164810 124430 139230 119330 143730 TRUE FALSE 109031.1382 154623.1035 127354.6692 148502.874 117605.5844 126535.3752 114676.8515 137363.8496 115035.3366 171891.1416 0.634303415 0.899540849 0.740903039 0.863935585 0.684186418 0.736136685 0.667148117 0.799132802 0.669233653 1 17.39113567 -1.245321085 9.00301756 1.00000004 0.750189401 0.459078117 0.083161809 6.16E-08 5.15E-09 0.074117685 0.017469703 0.056843252 1.245321085 -0.249810639 FHFPPLDTHS(ph)PTNDVQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FHFPPLDTHSPTNDVQPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 1 FHFPPLDT(0.093)HS(0.902)PT(0.006)NDVQPGR;FHFPPLDTHS(0.8)PT(0.2)NDVQPGR;FHFPPLDT(0.014)HS(0.982)PT(0.004)NDVQPGR 209.71 1.35E-16 615440000 272143 324485 311823 308935 330149 408540 313025 337704 314714 323475 TRUE FALSE 282887.4158 380212.7746 319949.3635 370041.4209 274030.3909 313662.7765 288489.2826 333177.6303 303387.5046 386853.7329 0.731251612 0.982833413 0.827055128 0.956540908 0.70835659 0.810804575 0.745732193 0.861249619 0.784243446 1 18.56142867 5.04858211 15.24229821 0.842195422 0.120932285 0.120247527 0.09482105 2543706.093 22153272.91 0.021360856 52975058.24 111836.1248 -5.04858211 -0.721263137 FHGILDQGEGVLIIFDEPPVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHGILDQGEGVLIIFDEPPVDK 22 0 O00231 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 82.037 0.0047419 22936000 29315 22095 27154 20602 33470 35716 38748 27299 28281 16414 FALSE TRUE 30472.37884 25889.64437 27861.65555 24677.01411 27780.78136 27421.50028 35710.83051 26933.10156 27263.17233 19630.00903 1.552336465 1.31888092 1.419339925 1.25710661 1.415219998 1.396917354 1.819195827 1.372037145 1.388851747 1 14.26077322 2.449595575 24.99518951 1.456003448 1.384805418 0 0.200560439 992.2150954 900993.2029 0.06612755 0.055326976 281.5759613 -2.449595575 -0.07119803 FHGTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 FHGTVK 6 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;; 120.06 0.020482 29249290000 9395778 21218340 21331250 20393310 18479580 22706020 19383630 19144480 18308990 19081400 FALSE TRUE 9766730.571 24862424.84 21887159.9 24427045.85 15338427.59 17432890.97 17864290.43 18887879.56 17650053.03 22820034.99 0.42798929 1.089499856 0.959120348 1.070421051 0.672147418 0.763929195 0.782833612 0.827688457 0.773445485 1 24.44379767 4.758355318 24.21806946 0.86842193 0.42798866 0.5017147 0.13515385 2750.469266 3365012.038 0.033623711 1.261079787 57326.48563 -4.758355318 -0.44043327 FHHTIGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHHTIGGSR 9 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 96.331 0.0074403 640500000 229120 361770 401740 383490 448380 541560 367280 372580 361020 408260 FALSE TRUE 238165.8345 423901.1833 412209.6744 459343.1774 372164.5278 415790.8974 338491.6339 367586.1745 348026.9607 488250.7304 0.487794118 0.86820389 0.844258183 0.940793631 0.762240596 0.851592986 0.693274199 0.752863543 0.712803769 1 18.89726268 -2.440325013 2.084361602 2.855005082 0.775850947 0.25378798 0.118589985 4658254.073 348403.1731 40852314.88 0.028251247 0.003628064 2.440325013 -2.079154134 FHKPGENYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHKPGENYK 9 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQJ6 P47897 QARS Glutamine--tRNA ligase 0 ; 166.19 3.66E-05 1080030000 1382770 943820 1312850 931150 1767220 1580430 1533320 1173780 1365710 863840 FALSE TRUE 1437362.827 1105913.743 1347063.95 1115328.691 1466828.576 1213399.084 1413134.372 1158047.399 1316558.364 1033092.909 1.391320001 1.070488176 1.303913654 1.079601536 1.419841878 1.174530455 1.367867652 1.120951842 1.274385249 1 19.97853857 -1.499785773 2.775738553 0.990359117 1.236423838 0.261890804 0.122556466 13000254.62 13710296.67 955495.6208 0.025898956 0.031638379 1.499785773 0.24606472 FHMYEGYPLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHMYEGYPLWK 11 0 P00491;G3V5M2;G3V393 P00491 PNP Purine nucleoside phosphorylase 0 ; 130.94 0.0002137 1720500000 3518800 3206400 3940600 3504900 5966900 5421600 5047400 4045000 4567100 3986000 FALSE TRUE 3657724.941 3757074.258 4043295.273 4198158.759 4952648.469 4162515.565 4651771.599 3990783.391 4402730.963 4766980.383 0.767304383 0.788145525 0.84818794 0.880674645 1.038948783 0.873197544 0.975831916 0.837172187 0.923589067 1 22.18464426 3.952263028 1.916058913 0.926626726 0.773367251 0.551748492 0.05720687 0.276963908 1.968025194 0.015934489 0.04306199 8959.072033 -3.952263028 -0.153259475 FHNLEGFLEEFADIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHNLEGFLEEFADIAK 16 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 161.32 8.47E-09 90196000 207150 107890 145550 122770 202700 187790 236430 155420 157730 95034 FALSE TRUE 215328.442 126419.2682 149343.1526 147053.5396 168245.1264 144178.6185 217897.9988 153336.8491 152053.3281 113654.0928 1.894594701 1.112316021 1.314014735 1.293869283 1.480326157 1.268573924 1.917203274 1.349153782 1.337860559 1 16.79429011 0.836064802 2.370491628 1.001212918 1.444797356 0.233160557 0.248241972 0.914450778 9.410376557 0.226000691 0.061033353 6.855905171 -0.836064802 0.443584437 FHPEPYGLEDDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 155.08 3.95E-05 2816440000 1345490 1676340 1475590 1583540 1630800 1920130 1576280 1571090 1466740 1534860 FALSE TRUE 1398610.984 1964238.355 1514045.088 1896759.486 1353597.199 1474208.907 1452727.055 1550032.108 1413952.314 1835586.43 0.76194232 1.070087642 0.824829091 1.033326164 0.737419484 0.803126937 0.791423945 0.844434281 0.770300047 1 20.80780962 3.229191325 24.99997446 0.815521041 0.92610518 0.166231858 0.106386636 291.2005472 777006.314 0.02773731 0.033573758 1695.08439 -3.229191325 0.110584139 FHPEPYGLEDDQRS(ph)MGYDDLDYGMMSDYGTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FHPEPYGLEDDQRSMGYDDLDYGMMSDYGTAR 32 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 FHPEPY(0.003)GLEDDQRS(0.813)MGY(0.184)DDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(1)MGYDDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(1)MGYDDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(0.999)MGY(0.001)DDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(1)MGYDDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(1)MGYDDLDYGMMSDYGTAR;FHPEPYGLEDDQRS(1)MGYDDLDYGMMSDYGTAR 319.11 1.47E-104 877525000 141517.6 222839 205394 112229.9 257355 244375 114629.1 194202 178680.4 390290 TRUE FALSE 147104.8241 261109.8648 210746.7364 134428.6392 213609.889 187622.6098 105644.1716 191599.0398 172249.7273 466759.8529 0.31516169 0.559409433 0.45150999 0.28800386 0.457644092 0.401968183 0.226335172 0.410487403 0.369032868 1 18.83232095 -1.297598738 3.469835555 1.002229646 0.387858747 0.807416696 0.089867895 31651883.61 47284480.74 736525.6353 0.022046637 0.050396603 1.297598738 -0.6143709 FHPLQEHVVKEELLNALYCEFINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHPLQEHVVKEELLNALYCEFINR 24 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 136.34 1.39E-05 212869000 231682 221867 258790 190199 323720 315700 221623 255170 276930 259020 FALSE TRUE 240828.9843 259970.9314 265534.28 227819.7945 268694.19 242383.4595 204251.6102 251749.8635 266963.3434 309770.0098 0.77744448 0.839238542 0.857198152 0.735448195 0.867398978 0.78246264 0.659365348 0.812699279 0.861811457 1 18.24083795 0.915238623 2.543501292 0.999283269 0.790102743 0.548636237 0.057937716 0.284990731 4.057535592 0.056166453 0.015066699 8.226945554 -0.915238623 -0.209180526 FHQLDIDDLQSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FHQLDIDDLQSIR 13 0 O75828;P16152;E9PQ63;A8MTM1;P16152-2 O75828;P16152 CBR3;CBR1 Carbonyl reductase [NADPH] 3;Carbonyl reductase [NADPH] 1 0 ;;;; 249.33 1.54E-17 3148140000 1647260 1900530 1860270 1867630 2106410 2418550 2069560 1919710 1857980 2151840 FALSE TRUE 1712295.097 2226931.243 1908750.164 2237041.64 1748363.181 1856878.416 1907342.479 1893979.427 1791111.663 2573451.849 0.665369005 0.865347935 0.741708132 0.869276665 0.679384455 0.721551646 0.74116113 0.735968473 0.695995794 1 21.29527336 -1.07347134 9.06380556 1.000000001 0.749339484 0.569770378 0.066112976 1.26E-09 1.49E-10 0.060424242 0.01424213 0.084436196 1.07347134 -0.250660517 FHQLLDDESDPFDILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHQLLDDESDPFDILR 16 0 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 0 189.42 1.02E-09 46160000 19747 22933 22551 20128 28742 29524 23053 23383 22497 27608 FALSE TRUE 20526.62681 26871.56436 23138.69759 24109.25832 23856.44511 22667.49844 21246.04562 23069.58913 21687.33736 33017.25901 0.621693848 0.813864178 0.700806132 0.73020169 0.722544688 0.686534834 0.643483022 0.698713031 0.656848509 1 15.01093274 -1.665083106 6.808873925 1.0015744 0.699723012 0.762097649 0.050738364 0.001164825 5.73E-05 0.047190501 0.011071642 0.021623047 1.665083106 -0.301851388 FHS(ph)PSTTWS(ph)PNKDTPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 FHS(0.752)PS(0.213)T(0.079)T(0.031)WS(0.923)PNKDT(0.002)PQEK;FHS(0.979)PS(0.008)T(0.014)TWS(0.999)PNKDTPQEK 165.85 3.60E-11 596420000 614100 264970 400250 270680 569820 545220 561280 391290 449950 178890 TRUE FALSE 638345.1422 310476.5363 410680.8438 324219.6961 472962.1999 418600.9179 517285.407 386045.3976 433756.3874 213940.0704 2.98375681 1.451231346 1.919606939 1.515469708 2.210722839 1.956626998 2.417898647 1.804455784 2.027466788 1 17.7068472 -0.140449425 1.309033539 0.996326576 2.005165717 0.349819298 0.420477963 28.07094233 30.25380778 0.874893153 0.11023642 0.723686672 0.140449425 1.008839141 FHS(ph)PSTTWSPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHSPSTTWSPNK 12 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.93)PS(0.069)T(0.002)TWSPNK;FHS(0.677)PS(0.13)T(0.168)T(0.026)WSPNK 148.28 4.27E-05 438490000 652340 558360 693700 668970 924400 939210 932670 726600 786890 481070 TRUE FALSE 678094.8869 654253.9866 711778.3919 801290.2693 767270.8182 721092.7114 859564.8883 716861.1155 758569.9826 575326.4559 1.178626291 1.137187383 1.23717306 1.392757557 1.333626866 1.253362685 1.494047214 1.246007563 1.318503564 1 19.13402129 4.015031519 5.096809786 1.310515211 1.161810076 0.14835888 0.120784808 0.251208869 18.90319332 0.028058697 0.059795492 10352.17296 -4.015031519 -0.148705135 FHS(ph)PSTTWSPNKDTPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FHSPSTTWSPNKDTPQEK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 FHS(0.803)PS(0.122)T(0.068)T(0.006)WSPNKDTPQEK;FHS(0.982)PS(0.018)TTWSPNKDTPQEK;FHS(0.747)PS(0.249)T(0.003)TWSPNKDTPQEK 206.09 5.38E-16 655570000 853450 520228 741600 475400 1121540 954560 877200 728320 861600 452040 TRUE FALSE 887144.865 609573.1122 760926.7052 569432.7011 930901.0314 732877.9065 808442.7719 718558.0617 830591.1843 540608.5832 1.641011432 1.127568321 1.407537225 1.053317907 1.721950151 1.355653479 1.495430885 1.3291651 1.536400291 1 19.04422489 -1.259509939 5.022763784 0.999924534 1.395449737 0.274458605 0.19791526 0.000152753 2.25E-05 0.175004505 0.041241118 0.055016133 1.259509939 0.395525203 FHSEDYIDFLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHSEDYIDFLQR 12 0 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 0 ; 195.25 4.90E-07 157464000 149202 189273 163229 159102 191629 216400 162124 158431 158280 189599 FALSE TRUE 155092.6102 221779.1654 167482.8818 190571.9007 159055.971 166144.3796 149416.2972 156307.4916 152583.5337 226747.294 0.683988803 0.97808958 0.738632329 0.840459427 0.701468001 0.732729272 0.658955151 0.689346668 0.672923284 1 17.79072581 3.236407575 25 0.718672529 0.817159458 0.051370566 0.116833314 105.8985862 1229641.573 0.030512903 0.038195842 1723.485267 -3.236407575 0.098486929 FHSGWEPPVDVLQEAPWEVEGLAS(ph)APIEEVSPVSRQSIR ddPTM_MDA-MB-175_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(0.25)APIEEVS(0.25)PVS(0.25)RQS(0.25)IR 58.672 0.012345 50022000 8636.9 11355 16859 7845.4 23749 18119 7367.3 11444 16628 30239 TRUE FALSE 8977.891481 13305.13292 17298.35939 9397.196704 19712.15346 13911.13685 6789.831775 11290.6119 16029.56153 36163.75309 0.24825663 0.367913499 0.478334186 0.259851257 0.545080413 0.384670717 0.187752409 0.312207969 0.443249391 1 15.14225679 0.81357557 4.09687785 0.999975671 0.348944103 0.787020629 0.101169604 0.752876441 16.08566151 0.098296813 0.025081137 6.509918775 -0.81357557 -0.651031568 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVSPVSR 35 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.904)PVS(0.096)R;FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(0.85)PVS(0.15)R 104.48 3.79E-05 29388300 28285 28549 33140 33319 31752 46569 34923 31558 31309 36111 TRUE FALSE 29401.71364 33452.06867 34003.65562 39909.39875 26354.80638 35754.05551 32185.64401 31135.01663 30182.19521 43186.25906 0.680811774 0.774599824 0.787372103 0.924122617 0.610259072 0.827903511 0.745275111 0.720947294 0.698884225 1 15.39828473 -1.005404865 4.423759953 1.00000959 0.754307351 0.454816675 0.08134887 14238375.39 45662581.39 2247.88291 0.018652389 0.098763196 1.005404865 -0.245702239 FHSGWEPPVDVLQEAPWEVEGLASAPIEEVS(ph)PVSRQSIR ddPTM_MDA-MB-175_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(0.029)APIEEVS(0.402)PVS(0.284)RQS(0.284)IR 231.02 1.36E-40 66852000 20496 32449 49849 21524 78285 49390 21568 31521 49570 78086 TRUE FALSE 21305.19791 38021.86333 51148.10589 25781.38296 64978.14366 37919.92101 19877.4438 31098.51255 47785.98538 93385.45665 0.228142568 0.407149729 0.547709544 0.276074925 0.695805814 0.406058099 0.212853741 0.333012373 0.511706931 1 16.51091027 0.865050342 4.445581623 0.999953865 0.390734697 0.63466511 0.138891639 0.623013931 19.69206462 0.134051084 0.034058516 7.329094844 -0.865050342 -0.609219168 FHSMNQR ddPTM_MDA-MB-175_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 ; 81.635 0.020229 40817500 76728.3 25538.3 27832.3 21298.5 50643.9 46230 34408.6 32128.1 31977.7 37343.3 FALSE TRUE 79757.59253 29924.30436 28557.6326 25511.27973 42035.46797 35493.78312 31711.56402 31697.47537 30826.82882 44660.00465 1.785884107 0.67004705 0.639445357 0.571233253 0.941232951 0.794755473 0.710066295 0.70975083 0.690255835 1 15.44669578 4.740692705 24.92690738 0.734308948 1.785884484 0.858347078 0.126458276 60.20103208 703779.3043 0.029149896 0.192466818 55041.80976 -4.740692705 1.051575536 FHSQLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHSQLMR 7 0 P49458 P49458 SRP9 Signal recognition particle 9 kDa protein 0 94.539 0.014126 409290000 203110 238530 206470 213390 282760 273270 231540 212300 203960 303570 FALSE TRUE 211128.9396 279495.672 211850.7778 255597.9051 234696.5562 209807.1839 213391.2898 209454.4658 196619.5194 363048.7293 0.581544356 0.769857183 0.583532624 0.704031951 0.646460206 0.577903645 0.587775889 0.5769321 0.541578867 1 18.46980368 -1.874513472 4.371617828 1.107491691 0.619850838 0.748886059 0.066211562 0.041129359 0.001180611 0.038011862 0.015147989 0.013350162 1.874513472 -0.487640853 FHTEALTALLSDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FHTEALTALLSDDSK 15 0 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 180.11 8.64E-09 525770000 1052470 506930 836190 753540 977890 1048850 1500090 891160 962670 334020 FALSE TRUE 1094022.328 593991.2841 857981.7983 902587.9629 811668.6071 805270.483 1382509.026 879215.4578 928023.6947 399464.8238 2.738720065 1.486967685 2.147828162 2.259492974 2.031890066 2.015873326 3.460903047 2.200983429 2.323167497 1 18.60770894 FHTVSGSK ddPTM_MDA-MB-175_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 ; 97.635 0.0080918 1504000000 5151000 2551300 2986800 2408500 5064200 5317600 4152700 3582800 4412200 3020300 FALSE TRUE 5354365.457 2989465.929 3064638.462 2884894.111 4203389.093 4082667.989 3827200.523 3534778.426 4253405.784 3612069.958 1.482353753 0.827632345 0.848443828 0.798681683 1.163706446 1.130284861 1.059558804 0.978601873 1.177553545 1 21.7843944 3.204544913 24.99933564 1.077056506 0.96767156 0.051453455 0.190698725 534.4207476 392763.1162 0.054832908 0.065540967 1601.566268 -3.204544913 -0.109384946 FHVDISLTDFIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHVDISLTDFIQK 13 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 192.15 2.96E-06 277580000 262340 180590 240560 219780 278240 287050 297540 235330 268630 184530 FALSE TRUE 272697.3858 211604.9277 246829.1912 263251.828 230944.8642 220386.9878 274218.0373 232175.7863 258962.0588 220685.1205 1.23568542 0.958854531 1.118467755 1.192884357 1.046490419 0.998649059 1.242576014 1.052068149 1.173445941 1 17.75162983 5.200854858 8.202317829 1.094257524 7.516888608 0.197256542 0.088885123 26940.32571 18187.1998 0.019741241 3143096.835 158801.5941 -5.200854858 6.422631084 FHVEEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;; 189.14 0.00019329 4432110000 7485830 4567950 5611580 5096540 7403980 7897240 8204210 6189250 6408730 3436260 FALSE TRUE 7781376.349 5352459.879 5757822.385 6104620.4 6145454.124 6063225.694 7561142.582 6106293.227 6178081.059 4109529.356 1.893495745 1.30245082 1.401090462 1.485479205 1.495415555 1.475406347 1.83990475 1.485886265 1.503354892 1 21.97054175 0.563121916 2.40518136 1.000036571 1.539085357 0.467987817 0.173963974 4.230160388 22.21048893 0.160748477 0.043100705 3.656974364 -0.563121916 0.539048786 FHVEEEGKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;;;; 182.64 1.06E-06 4738700000 15054970 7852270 12083690 6586720 18813860 14663640 12176580 11204440 13615940 7463810 FALSE TRUE 15649351.84 9200836.29 12398600.89 7889553.557 15615886.8 11258231.84 11222147.84 11054262.81 13125904.98 8926200.666 1.753192923 1.030767359 1.389012117 0.883864687 1.749443843 1.261256862 1.257214381 1.238406263 1.470491811 1 23.08961481 -1.246935376 3.333415483 0.999051866 1.316587023 0.125125755 0.262404666 230253074.2 333802041.2 2293589.232 0.057320997 0.056632355 1.246935376 0.317535157 FHVLVASQDFVESVLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FHVLVASQDFVESVLVR 17 0 O60784;O60784-4;O60784-2;O60784-3;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01;H7BYN7 O60784 TOM1 Target of Myb protein 1 0 206.43 6.98E-12 98315000 64441 61864 71719 77538 80022 89290 77718 71460 73444 63133 FALSE TRUE 66985.18044 72488.66076 73588.05606 92874.78497 66419.88902 68553.7507 71626.26008 70502.19558 70800.76479 75502.7026 0.887189175 0.960080345 0.974641351 1.23008557 0.87970214 0.907964197 0.948658228 0.93377049 0.937724907 1 16.20424067 FICEQDHQNFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FICEQDHQNFLR 12 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;; 308.6 3.16E-46 7791760000 3842020 3980200 3911610 3860440 4665220 5217060 4209610 4237850 4049630 4401390 FALSE TRUE 3993705.916 4663768.388 4013549.77 4624023.51 3872227.571 4005476.88 3879649.768 4181048.552 3903884.607 5263758.101 0.758717601 0.886014953 0.762487503 0.878464288 0.735639347 0.760953829 0.737049404 0.794308643 0.741653498 1 22.32766176 -1.272836532 3.649693336 1.000475057 0.785577023 0.604897733 0.052374514 26391972 53026260.05 147410.155 0.012148977 0.053353568 1.272836532 -0.214898034 FICVTPTTCSNTIDLPMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 230.05 6.51E-25 746259000 429455 472606 478104 530916 554140 608241 502084 526974 504865 562429 TRUE FALSE 446410.215 553772.4041 490563.783 635929.6002 459947.4807 466986.2457 462729.3441 519910.7755 486695.0073 672626.1942 0.663682472 0.823298898 0.729326017 0.945442812 0.683808458 0.694273059 0.687944282 0.77295648 0.72357427 1 19.35944544 -1.45544574 6.017113816 1.000132023 0.750371586 0.472901729 0.080020079 0.000137059 1.24E-05 0.074929875 0.017651865 0.035039206 1.45544574 -0.249760437 FIDFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIDFFK 6 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 121.68 0.045473 82433000 277140 262110 296520 272280 383820 369000 357030 307590 321940 280270 FALSE TRUE 288081.7012 307125.3536 304247.5548 326136.1713 318578.4135 283305.3422 329045.0557 303467.2592 310353.4423 335183.5404 0.859474486 0.916290082 0.907704341 0.973007717 0.950459599 0.845224506 0.981686199 0.905376376 0.925920891 1 18.35459178 -5 0.178747911 1.316834957 0.903206064 0.28103483 0.040829686 184.5729008 1.773773844 20.86375068 0.126057164 1.00E-05 5 -0.413628892 FIDFFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FIDFFKR 7 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 107.66 0.029728 0 507900 519590 526020 376910 1248330 755730 519810 497940 550430 1098890 FALSE TRUE 527952.2842 608825.5407 539728.5133 451461.673 1036139.312 580223.1607 479065.9339 491265.9288 530620.1318 1314196.456 0.401730108 0.463268287 0.410690891 0.343526777 0.788420413 0.441504128 0.364531446 0.373814681 0.40376013 1 20.32574953 -1.063479967 5.142478666 1.000008527 0.441735693 0.657983876 0.120365743 1.19E-05 2.17E-06 0.118071848 0.027829377 0.086401251 1.063479967 -0.558272834 FIEEHATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FIEEHATK 8 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 143.12 0.00060653 7014710000 5328770 5628480 5815840 5759490 7692020 7680160 6364090 5814160 5723760 4923790 FALSE TRUE 5539153.954 6595127.657 5967405.568 6898699.932 6384533.188 5896559.234 5865255.996 5736230.695 5517762.996 5888512.379 0.940671191 1.119998946 1.013397813 1.171552251 1.084235334 1.001366534 0.99605055 0.974139193 0.937038532 1 22.48947178 2.583399687 3.393697679 0.97678901 1.071652103 0.335285814 0.059683895 0.2744806 5.911893963 0.019992585 0.018390271 383.1772245 -2.583399687 0.094863093 FIEIAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FIEIAAR 7 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PPE9;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 114.94 0.013473 634250000 348684 517010 464360 477500 471890 539160 404620 459190 437060 572590 FALSE TRUE 362450.3136 605802.4457 476461.6031 571948.0748 391678.3064 413948.261 372904.8271 453035.3091 421330.296 684778.0476 0.529296047 0.884669781 0.695789833 0.835231323 0.571978479 0.6044999 0.544563057 0.661579779 0.615280086 1 19.38527693 -1.092972564 4.597434892 1.000017756 0.663656339 0.451951424 0.112161609 2.60E-05 5.12E-06 0.107893023 0.025428912 0.080728603 1.092972564 -0.336361417 FIESDKFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FIESDKFTR 9 1 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 ; 146.11 8.72E-05 782320000 673040 619030 725200 678250 1010260 952660 811350 912930 757010 613360 FALSE TRUE 699612.1389 725343.5871 744099.3078 812405.8256 838536.3661 731419.1527 747754.2669 900693.6666 729765.358 733536.1485 0.953752777 0.988831414 1.014400325 1.107519823 1.143142526 0.997113986 1.019382983 1.227879046 0.994859435 1 19.48450854 3.987255798 2.825152373 1.084705809 0.970921686 0.216023153 0.07241569 0.348646315 5.588665245 0.019705417 0.045972011 9710.817637 -3.987255798 -0.113784123 FIGEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIGEGAR 7 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 81.1 0.092484 0 200180 103510 126030 99352 172560 196720 180840 140260 142760 91446 FALSE TRUE 208083.261 121287.0373 129314.4453 119003.5291 143228.3128 151034.7613 166665.2883 138380.0441 137622.0955 109363.0929 1.902682665 1.10903079 1.182432226 1.088150728 1.309658579 1.381039594 1.523962828 1.265326725 1.258396154 1 16.73876642 0.777977082 1.97718389 1.000707386 1.330025723 0.175937053 0.223856995 1.505366623 9.754505617 0.206922494 0.057363083 5.997594254 -0.777977082 0.329318337 FIGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FIGSPR 6 0 P23443-5;P23443;P23443-3;P23443-2;P23443-4;K7ERJ3 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 FIGS(1)PR;FIGS(1)PR;FIGS(1)PR;FIGS(1)PR 98.523 0.041788 1209100000 1313160 1489960 1457130 1712520 1599800 1742830 1729700 1574720 1465710 1460850 TRUE FALSE 1365004.571 1745849.04 1495104.005 2051251.345 1327866.567 1338084.145 1594121.594 1553613.454 1412959.383 1747075.588 0.78130825 0.999297942 0.855775225 1.174105665 0.760051011 0.7658994 0.912451416 0.889265161 0.80875687 1 20.7365106 FIHQQPQSS(ph)SPVYGSSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.034)S(0.903)S(0.062)PVYGSSAK 166.27 1.68E-11 1315600000 901830 875680 954410 843710 1139700 1288400 1063400 979220 1089300 899000 TRUE FALSE 937434.9448 1026071.228 979282.7087 1010593.32 945974.2011 989188.6259 980047.9293 966095.1576 1050096.306 1075141.838 0.871917464 0.954358943 0.910840481 0.939962789 0.879859911 0.920054072 0.91155222 0.89857461 0.976704904 1 20.03609557 1.124092279 4.506410626 0.998426158 0.911995035 0.638703886 0.02353023 0.116975504 3.728308772 0.020762444 0.005318228 13.30737144 -1.124092279 -0.086431123 FIHQQPQSSS(ph)PVYGSSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FIHQQPQSSSPVYGSSAK 18 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 FIHQQPQS(0.026)S(0.146)S(0.828)PVYGSSAK;FIHQQPQS(0.003)S(0.13)S(0.867)PVYGSSAK;FIHQQPQS(0.031)S(0.197)S(0.772)PVYGSSAK;FIHQQPQSSS(1)PVYGSSAK;FIHQQPQSS(0.037)S(0.963)PVYGSSAK;FIHQQPQSSS(1)PVYGSSAK;FIHQQPQSS(0.001)S(0.999)PVYGSSAK 271.19 3.85E-39 14863670000 8396500 7908860 9592480 7908560 10674850 12018310 10527370 10057960 10230310 8167740 TRUE FALSE 8728000.304 9267145.183 9842467.909 9472849.563 8860342.81 9227239.642 9702207.231 9923149.498 9862123.141 9768052.272 0.893525143 0.94871986 1.007618268 0.969778754 0.907073648 0.944634548 0.993259143 1.015878009 1.009630463 1 23.21963949 2.139041078 3.990252913 1.009020915 0.947564513 0.49328474 0.029715478 0.209585371 6.225582159 0.01269494 0.009088222 137.7339738 -2.139041078 -0.061456402 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FIIGSVSEDNSEDEISNLVK 20 0 Q13085;Q13085-4;A0A0C4DGT1;A0A087X2F8;A0A087X126;A0A087WYK6 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 FIIGSVS(0.002)EDNS(0.994)EDEIS(0.004)NLVK;FIIGSVS(0.011)EDNS(0.989)EDEISNLVK;FIIGSVSEDNS(1)EDEISNLVK;FIIGSVSEDNS(1)EDEISNLVK 193.54 4.50E-18 444916000 643100 427744 578437 535351 715237 702198 608272 586377 619157 453686 TRUE FALSE 668490.0846 501205.7046 593511.5434 641241.8299 593661.2702 539123.1564 560594.0512 578517.5754 596873.6605 542577.0854 1.23206472 0.923750225 1.093875063 1.181844658 1.094151018 0.993634215 1.033206279 1.066240339 1.100071633 1 19.04946859 2.956964976 22.9830179 1.044132602 1.099264036 0.144849587 0.07970245 448.6522384 239603.6175 0.024011297 0.025471136 905.6595603 -2.956964976 0.055131434 FIIHAPPGEFNEVFNDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FIIHAPPGEFNEVFNDVR 18 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 ;;;;; 253.71 1.63E-30 2632927000 1513029 1829187 1709460 1714394 1982693 2204934 1751287 1831400 1740267 1882562 FALSE TRUE 1572764.553 2143335.638 1754009.932 2053496.016 1645675.552 1692871.495 1614016.549 1806853.079 1677635.131 2251413.98 0.698567463 0.951995349 0.779070374 0.912091705 0.730952 0.751914801 0.716890169 0.802541467 0.745147337 1 21.10239993 5.023074082 17.66398918 0.80772489 0.419552413 0.11599437 0.095236445 29742364.3 551633716.2 0.021399383 329349863.5 105456.6769 -5.023074082 -0.388172476 FIIVSAFDHFASVHSVSAEGTVVSNLSS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIIVSAFDHFASVHSVSAEGTVVSNLSS 28 0 Q9Y547 Q9Y547 HSPB11 Intraflagellar transport protein 25 homolog 0 72.532 0.010432 13841000 7380.8 9164.7 13730 12600 10696 17031 11356 9841.1 11553 12485 FALSE TRUE 7672.199683 10738.66593 14087.81508 15092.24239 8877.897741 13075.80836 10465.88705 9709.196151 11137.20979 14931.19671 0.51383689 0.719209996 0.94351547 1.010785852 0.594587153 0.875737465 0.700940939 0.650262423 0.74590202 1 13.86604218 FIKDNWEELYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FIKDNWEELYNR 12 1 E9PLK3;P55786;P55786-2;H0YDG0 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 199.8 1.53E-07 5451400000 2606600 2551400 3262900 2759670 3751400 3578400 2968800 2938200 3120900 2526470 FALSE TRUE 2709510.581 2989583.103 3347933.855 3305524.489 3113738.368 2747370.831 2736097.698 2898818.235 3008579.419 3021483.424 0.896748451 0.989442166 1.108043098 1.094007156 1.030532997 0.909278803 0.90554781 0.959402329 0.995729248 1 21.5268256 2.757581229 23.35721823 0.948150122 1.030434132 0.236439567 0.061661679 479.1958481 588448.6803 0.020160406 0.021341792 572.2439757 -2.757581229 0.08228401 FIKIDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 212070000 340360 297850 309930 171200 488130 398730 268020 324260 376720 382370 FALSE TRUE 353797.6756 349003.4205 318007.0304 205062.849 405157.837 306131.0003 247011.8921 319913.8251 363161.9208 457288.0806 0.773686634 0.763202531 0.695419461 0.448432526 0.886001307 0.669448895 0.540166916 0.699589249 0.794164415 1 18.80274379 0.922656037 2.601844667 0.999122973 0.679571827 0.414429335 0.114880513 0.339560069 5.148347914 0.10783547 0.028845283 8.368662189 -0.922656037 -0.319551146 FIMLNLMHETTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIMLNLMHETTDK 13 0 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 148.68 4.34E-05 165070000 373750 335880 392340 401790 551200 592010 527840 396290 389110 286430 FALSE TRUE 388505.9386 393564.7772 402564.7027 481262.8628 457507.2209 454524.6495 486466.5215 390978.3807 375106.0071 342550.4745 1.134156767 1.148924922 1.175198205 1.404939998 1.335590679 1.326883725 1.420130923 1.141374512 1.095038644 1 18.38595706 1.512327652 4.624736386 1.064180993 1.278723068 0.480478631 0.097673895 0.16448629 7.69470291 0.066151689 0.027786066 32.53326512 -1.512327652 0.214542075 FIMLNLMHETTDKNLSPDGQYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIMLNLMHETTDKNLSPDGQYVPR 24 1 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 201.87 8.24E-25 462070000 420840 493100 549450 497870 734130 683240 485440 536890 548620 536400 FALSE TRUE 437455.0882 577786.0892 563769.1184 596347.2 609342.8448 524567.8646 447389.9443 529693.8677 528875.2734 641497.31 0.681928172 0.900683573 0.878833176 0.929617616 0.949875916 0.817724184 0.697415153 0.82571487 0.824438801 1 19.29108369 2.513931661 24.71550804 0.810677518 0.874977504 0.004162592 0.09778849 1255.383046 842896.8441 0.030787417 0.029017971 326.5364453 -2.513931661 0.064299986 FINDQYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 183.65 0.00051691 433290000 621120 546910 619190 531110 790710 813170 727020 620040 691980 527080 FALSE TRUE 645642.2972 640837.5381 635326.6001 636161.9728 656305.3966 624323.5912 670034.2727 611729.378 667075.775 630351.2344 1.024258004 1.016635652 1.007893005 1.009218255 1.041174128 0.990437643 1.062953852 0.970457968 1.05826044 1 19.2657964 FINYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FINYVK 6 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 106.75 0.074111 385170000 643830 602170 630900 558660 736220 779810 696810 585540 636360 632000 FALSE TRUE 669248.9055 705588.0133 647341.7723 669161.2806 611077.5874 598710.9456 642192.2114 577691.7941 613457.5279 755828.2996 0.885450976 0.933529498 0.856466704 0.885335044 0.808487308 0.7921256 0.849653568 0.764316174 0.811636093 1 19.52769901 3.493229306 1.868093526 0.821023113 0.900006529 0.095524543 0.06390657 0.50673073 3.536027879 0.018094803 0.031011302 3113.359744 -3.493229306 0.078983416 FIPHENGVHTIDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 2363960000 2802050 2769160 3167450 2843170 3872540 4273130 3519730 3345460 3569990 3011000 FALSE TRUE 2912677.098 3244741.689 3249996.349 3405540.54 3214287.034 3280760.317 3243844.365 3300619.581 3441506.757 3600947.801 0.808864015 0.901079901 0.902539145 0.945734492 0.892622502 0.911082442 0.90083071 0.916597452 0.955722479 1 21.77994526 7.999766075 0.019064147 1.630884282 4.96E-08 0.638721293 0.028281326 2395.955243 3.520962716 113.2179437 199.1843088 99946151.3 -7.999766075 -1.630884233 FIQAWQSLPEFGITHFIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIQAWQSLPEFGITHFIAR 19 0 A0A0U1RRM8;H0YJ34;Q96AC1-2;Q96AC1;Q96AC1-3;H0YJB6 A0A0U1RRM8 FERMT2 Fermitin family homolog 2 0 179.46 4.77E-15 0 88687 93368 104630 91264 127220 128290 103430 94256 106480 98178 FALSE TRUE 92188.43124 109403.2277 107356.7438 109315.7468 105595.1898 98496.59175 95322.88634 92992.65249 102647.8056 117414.0994 0.785156397 0.93177249 0.914342863 0.931027427 0.899339946 0.838882147 0.811852127 0.792005841 0.874237474 1 16.84124614 2.739376172 23.89305016 0.841595863 0.897892232 0 0.066885328 78.31267226 2294307.42 0.020127274 0.02023099 548.7520712 -2.739376172 0.056296369 FIQENIFGICPHMTEDNKDLIQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FIQENIFGICPHMTEDNKDLIQGK 24 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 264.63 1.78E-44 3755940000 2964740 2272260 2875500 1950014 4200920 3814730 3084870 2828490 3108140 1985776 FALSE TRUE 3081790.224 2662502.979 2950437.892 2335720.949 3486849.119 2928816.77 2843069.829 2790578.718 2996278.649 2374850.787 1.297677412 1.121124322 1.242367692 0.983523243 1.468239242 1.23326349 1.197157246 1.175054337 1.261670276 1 21.17940544 -0.977411124 5.991571515 0.99999984 1.214503375 0.238027889 0.117720632 2.36E-07 4.02E-08 0.106664706 0.025141094 0.105338924 0.977411124 0.214503535 FIQENVFVAANHNGS(ph)PLSIK ddPTM_MDA-MB-175_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 237.2 8.78E-30 830400000 928540 720230 765770 686090 1043880 1071960 971310 837780 896630 701990 TRUE FALSE 965199.4762 843923.8999 785726.5953 821796.5542 866441.6505 823013.5357 895176.1842 826550.9294 864360.4614 839531.5001 1.14968822 1.005231965 0.935910797 0.978875187 1.032053771 0.980324783 1.066280639 0.984538316 1.029574782 1 19.67922493 4.736790246 6.591661503 1.000595798 1.152415601 0.633112571 0.033870699 0.071092978 19.79660171 0.008061746 0.048648867 54549.43372 -4.736790246 0.151819803 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;; 370.46 8.13E-127 16589940000 3472649 3272070 3940999 3088985 5525306 4472698 4123522 3894116 4224576 2675592 FALSE TRUE 3609751.864 3834022.569 4043704.672 3699977.013 4586116.46 3433981.674 3800309.571 3841921.745 4072534.335 3199823.025 1.128109847 1.198198319 1.2637276 1.156306766 1.433240659 1.073178625 1.187662424 1.200666948 1.272737368 1 21.60956068 FISETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FISETLR 7 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 104.76 0.018793 59199000 66287 171230 90535 172560 113320 161270 94123 104440 74305 180600 FALSE TRUE 68904.06194 200637.4205 92894.41648 206691.853 94057.90688 123817.4866 86745.39332 103040.1526 71630.77756 215985.1122 0.319022275 0.928940974 0.430096387 0.956972686 0.435483288 0.573268617 0.401626725 0.477070626 0.331646829 1 17.72057235 -1.183064106 5.247557798 1.000023412 0.546729551 0.290568724 0.215658695 5.55E-05 8.64E-06 0.196229911 0.046249448 0.065604842 1.183064106 -0.453293861 FITHAPPGEFNEVFNDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 ;;;;; 233.49 9.62E-24 4098360000 1871790 2210090 2141800 2081670 2261100 2608890 2093800 2191710 2109620 2287980 FALSE TRUE 1945689.715 2589655.765 2197617.068 2493418.113 1876759.03 2003014.836 1929682.485 2162333.712 2033695.188 2736265.875 0.711074802 0.94641964 0.803144566 0.911248478 0.685883286 0.73202493 0.705224775 0.790249856 0.74323742 1 21.38377699 FITIFGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FITIFGTR 8 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 177.78 0.00058879 554740000 449070 356050 414200 399150 508580 495650 422620 374810 408540 355920 FALSE TRUE 466799.6304 417198.8178 424994.3923 478100.6787 422131.7533 380542.7991 389493.9401 369786.285 393836.7252 425655.7095 1.096660094 0.980132084 0.998446356 1.123209834 0.991721111 0.894015493 0.915044557 0.868745037 0.925247134 1 18.69932746 2.910672905 4.286359689 0.909278335 1.042782932 0.581499891 0.050929905 0.15133792 4.93358002 0.015475787 0.016737532 814.0909086 -2.910672905 0.133504597 FITLLLPGGAQTAVRPGS(ph)PSTSTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FITLLLPGGAQTAVRPGSPSTSTMR 25 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 FITLLLPGGAQTAVRPGS(0.849)PS(0.125)T(0.019)S(0.003)T(0.004)MR;FITLLLPGGAQT(0.001)AVRPGS(0.959)PS(0.031)T(0.007)S(0.001)T(0.001)MR 162.58 1.16E-11 543770000 536980 502390 584060 578730 643180 649610 607330 612450 621340 476100 TRUE FALSE 558180.385 588671.5744 599281.0834 693201.0667 533852.4933 498747.9224 559725.8876 604241.1095 598978.0948 569382.6795 0.980325544 1.033876856 1.05251021 1.217460755 0.937598758 0.87594502 0.983039892 1.061221444 1.051978074 1 19.11903908 4.746998164 20.55143906 1.025059448 0.980325251 0.022756334 0.08494702 481.7582121 1173057.457 0.021576429 0.217384028 55846.7834 -4.746998164 -0.044734197 FIVLNSLNQNAKPEGPEQAELGRLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FIVLNSLNQNAKPEGPEQAELGRLSPR 27 2 P41182-2;P41182 P41182-2 BCL6 B-cell lymphoma 6 protein 1 FIVLNSLNQNAKPEGPEQAELGRLS(1)PR 68.326 0.01196 546870000 367740 317800 318590 262100 424680 364570 355720 306870 371420 295750 TRUE FALSE 382258.6592 372379.6779 326892.7171 313942.5977 352493.0453 279904.1426 327837.7369 302756.9096 358052.6668 353696.55 1.080753146 1.052822477 0.924217997 0.887604354 0.996597352 0.791368032 0.926889835 0.855979256 1.012315972 1 18.43215262 4.256982697 3.960673101 0.912047774 1.074264083 0.421530595 0.065971851 0.165493729 5.648885801 0.015492886 0.043556301 18071.02128 -4.256982697 0.162216309 FKAEAPLPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FKAEAPLPSPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK;FKAEAPLPS(1)PK 116.78 0.0005711 4019140000 13529260 4598880 6950330 5306710 10658200 12308090 11657010 8457400 9040700 4654940 TRUE FALSE 14063405.63 5388701.866 7131461.31 6356361.399 8846522.971 9449722.628 10743303.1 8344042.387 8715326.973 5566986.369 2.526215209 0.967974683 1.281027263 1.141795754 1.589104479 1.697457476 1.929823855 1.498843689 1.565537689 1 22.40846512 3.047269807 24.99926494 1.600171159 1.420683675 0 0.448802347 488.3644744 258274.6836 0.124377755 0.148659815 1114.987008 -3.047269807 -0.179487484 FKAESDLFLAEHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKAESDLFLAEHHK 14 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 87.566 0.0044464 144890000 376460 191920 301190 235040 484870 388550 398710 296470 376590 220980 FALSE TRUE 391322.9315 224880.7671 309039.2588 281530.2105 402451.9706 298315.151 367458.0684 292496.3046 363036.5995 264276.8001 1.480731307 0.850928901 1.169377179 1.065285376 1.522842605 1.128798105 1.390428779 1.106780105 1.373698332 1 18.01169026 5.057317178 20.55175228 1.191527019 5.8378006 0.18184353 0.19046063 590.7376372 223776.9121 0.041577749 6877.993672 114108.2849 -5.057317178 4.646273581 FKDIFQEIFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKDIFQEIFDK 11 1 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 179.93 6.28E-06 1191920000 2589200 1667000 2108000 1927880 2491700 3289500 2732600 2011720 2328600 1617240 FALSE TRUE 2691423.615 1953294.283 2162936.212 2309208.91 2068161.724 2525563.478 2518411.672 1984756.184 2244794.141 1934107.214 1.391558646 1.009920375 1.118312468 1.193940487 1.069310796 1.305803246 1.302105516 1.026187261 1.160635835 1 20.88323634 1.674721615 10.74482675 1.070966479 1.187154369 0.219794038 0.115898993 0.204898036 32.44131933 0.054177273 0.029352462 47.28480639 -1.674721615 0.11618789 FKDIFQEIFDKHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKDIFQEIFDKHYK 14 2 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 210.1 3.43E-09 315580000 940740 759450 858760 471820 1302410 1318320 656970 725710 930810 937540 FALSE TRUE 977881.1416 889879.6298 881139.9911 565144.5878 1081026.813 1012160.159 605474.9747 715983.0445 897310.3299 1121233.013 0.872148011 0.793661638 0.785866971 0.504038484 0.964141085 0.902720619 0.540008159 0.638567574 0.800288896 1 20.0966547 2.260501198 24.99965984 0.700215319 0.796156249 0.00038068 0.161290713 669.2811169 762593.939 0.055852869 0.046692917 182.1802097 -2.260501198 0.09594093 FKDIFQEIYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 203.39 3.35E-08 3637600000 3272500 1871770 2899000 2123110 4170800 3489100 3982300 2980100 3320400 1824990 FALSE TRUE 3401700.827 2193231.937 2974550.322 2543054.821 3461848.906 2678809.403 3670156.92 2940156.634 3200899.453 2182561.849 1.55858164 1.004888791 1.362871033 1.165169648 1.586140117 1.227369297 1.681582092 1.347112631 1.466579036 1 21.05759111 3.259092053 24.9931053 1.41108524 1.260163833 0.049278124 0.220798269 550.6308713 670283.7263 0.055445726 0.074990987 1815.90052 -3.259092053 -0.150921407 FKDLEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKDLEDK 7 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 80.438 0.02728 359730000 2167660 1075440 1409790 1013190 2351460 2062040 2148850 1635160 1901720 867460 FALSE TRUE 2253240.891 1260138.454 1446530.286 1213595.958 1951759.669 1583162.461 1980417.522 1613243.355 1833277.469 1037422.178 2.171961365 1.214682393 1.394350647 1.16981879 1.881355257 1.526054188 1.908979356 1.555049996 1.767146979 1 19.98457169 3.227721276 24.99920284 1.645132 1.461533709 0.017597191 0.351290268 646.0972298 1490117.31 0.094944066 0.114539159 1689.356379 -3.227721276 -0.183598291 FKDPNAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 78.264 0.028341 4767900000 17687500 10515800 14742700 10050400 18908400 16933100 18760200 14887900 16081000 9056300 FALSE TRUE 18385816.16 12321806.85 15126906.87 12038339.12 15694356.92 13000644.15 17289726.5 14688352.05 15502247.95 10830708.59 1.697563553 1.137673195 1.396668255 1.111500602 1.449060954 1.200350285 1.596361527 1.356176461 1.431323521 1 23.3686243 4.758057471 24.14823124 1.322938474 1.697564103 0.310172502 0.175300186 3452.078436 4275533.093 0.038723891 1.394204016 57287.18349 -4.758057471 0.374625628 FKDPNCVGTVLASRPHTLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKDPNCVGTVLASRPHTLDGR 21 2 K7EQ55;K7EK33;Q96EP5;Q96EP5-2;K7EQ02 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 156.92 6.31E-09 3770300000 1985730 1873850 2110440 1818520 2601100 2455300 2253000 2266900 2502800 1917360 FALSE TRUE 2064128.154 2195669.161 2165439.8 2178217.828 2158965.951 1885093.785 2076403.973 2236515.913 2412724.717 2293029.982 0.900174952 0.957540537 0.944357386 0.949929938 0.941534113 0.822097312 0.905528488 0.975353978 1.052199376 1 21.12882379 1.523600111 3.732413475 1.024489492 0.918818603 0.561343692 0.038791466 0.151684866 4.59410222 0.02721117 0.010814272 33.38874622 -1.523600111 -0.105670889 FKEANNFLWPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKEANNFLWPFK 12 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 145.31 5.82E-05 1594110000 5439600 4540100 5844600 3968700 8537200 7248400 6146400 5818400 6666000 5661700 FALSE TRUE 5654359.608 5319826.858 5996915.077 4753697.015 7086049.793 5565068.951 5664629.107 5740413.865 6426091.962 6771001.715 0.835084652 0.785677966 0.885676201 0.702067023 1.046529021 0.821897436 0.83660134 0.847793887 0.949060749 1 22.69093785 -5 0.11408853 1.503187773 0.769665615 0.268623803 0.083355659 215.4414892 1.618820226 24.86714014 0.885950923 1.00E-05 5 -0.733522157 FKEIAEAYDVLSDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKEIAEAYDVLSDPR 15 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 72.583 0.023734 0 382060 334640 363920 310710 399940 416710 357400 328650 346510 257140 FALSE TRUE 397144.0238 392111.8169 373404.0542 372167.5106 331958.3417 319935.4178 329386.0541 324244.9843 334039.1728 307521.6598 1.291434314 1.275070566 1.214236599 1.210215602 1.079463287 1.040367101 1.071098713 1.054380965 1.086229741 1 18.2303285 3.406223453 1.413466261 1.051876676 1.275573538 0.923675881 0.027512997 0.100010097 0.409675956 0.008941816 0.015637113 2548.140982 -3.406223453 0.223696863 FKEMELPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKEMELPAK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 104.79 0.0029205 1087080000 990410 633940 843230 610970 1156140 1026810 1072460 844180 954940 539080 FALSE TRUE 1029512.152 742814.2636 865205.2665 731818.0424 959619.7358 788348.939 988397.7828 832865.1479 920571.8959 644702.4047 1.596879652 1.152181624 1.342022707 1.135125349 1.488469298 1.222810607 1.533107021 1.291859844 1.427902067 1 19.29827384 -1.000411298 5.258877153 1.000011984 1.345583173 0.33292217 0.150058852 3.02E-06 5.73E-07 0.130174525 0.03068226 0.09990534 1.000411298 0.345571189 FKEYCPQVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKEYCPQVFR 10 1 Q8TBX8;F8VNT5;Q8TBX8-2;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 122.51 0.0004438 684420000 251590 235390 253080 220250 388030 361420 289310 261840 266100 343370 FALSE TRUE 261522.9675 275816.4014 259675.4727 263814.7926 322072.7992 277485.6824 266633.1262 258330.4631 256523.113 410646.7773 0.636856252 0.671663378 0.632357264 0.642437265 0.784306165 0.675728382 0.649300423 0.62908192 0.624680692 1 18.64753845 -1.349332384 5.517201006 1.000087189 0.660899531 0.839842504 0.044449131 4.98E-05 5.87E-06 0.04496382 0.010595363 0.044737078 1.349332384 -0.339187658 FKFPGR ddPTM_MDA-MB-175_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 ; 90.285 0.044874 7921200000 8519400 6793000 7938100 6502900 9892200 9752300 9215100 7948700 7489500 7134800 FALSE TRUE 8855752.49 7959644.908 8144973.407 7789154.211 8210727.377 7487476.123 8492796.383 7842160.678 7219954.358 8532727.456 1.037857184 0.93283712 0.954556846 0.912856323 0.962262936 0.877500912 0.995320245 0.919068459 0.846148479 1 23.02457554 4.738863446 8.044072826 0.932288598 1.038695615 0.319174328 0.045745412 0.104923834 84.70532686 0.010093706 0.06013902 54810.45982 -4.738863446 0.106407017 FKGPEFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKGPEFVR 8 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 93.111 0.010306 248730000 240690 235930 230490 214120 341900 301120 289610 236590 281620 214110 FALSE TRUE 250192.6271 276449.1422 236496.7587 256472.2969 283783.9601 231189.4435 266909.6114 233418.898 271484.5512 256060.7551 0.977083064 1.079623241 0.923596272 1.001607204 1.108268075 0.902869491 1.04236829 0.911576231 1.060234908 1 17.96612663 2.720078278 24.9584193 0.977424446 1.015297811 0.059041569 0.066571442 2303.801746 3111034.429 0.020442388 0.019302153 524.9020611 -2.720078278 0.037873365 FKGPGDTSNFDDYEEEEIRVS(ph)INEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;FKGPGDTSNFDDYEEEEIRVS(1)INEK 260.92 2.39E-45 3218110000 1475100 787479 1194010 805691 1634260 1337940 1318200 1081880 1323110 756392 TRUE FALSE 1533338.087 922722.3925 1225126.881 965054.2751 1356469.069 1027223.712 1214876.04 1067379.168 1275491.53 904592.5304 1.695059417 1.020042021 1.354341143 1.066838651 1.499536005 1.135565105 1.343009144 1.179955762 1.410017756 1 19.78690856 -2.050744691 2.447864763 0.624490982 1.282050584 0.167014987 0.197494225 6745637.457 2919574.618 14157239.36 0.041776286 0.00889724 2.050744691 0.657559603 FKGQILMPNIGYGSNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKGQILMPNIGYGSNKK 17 2 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 120.24 4.55E-05 1387300000 2418300 1458690 2240800 1395260 3070400 2580100 2229600 2242100 2654400 1421020 FALSE TRUE 2513776.351 1709208.66 2299197.089 1671238.264 2548494.505 1980910.877 2054838.126 2212048.317 2558868.663 1699441.662 1.479177784 1.005747181 1.352913219 0.983404315 1.499606937 1.165624523 1.209125428 1.301632393 1.505711387 1 20.69662941 3.236911512 24.99995982 1.28538611 1.2015992 0.033575333 0.195503042 163.1496464 2473313.443 0.051472918 0.064697812 1725.486284 -3.236911512 -0.08378691 FKIPGS(ph)PPESMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 1 FKIPGS(0.994)PPES(0.006)MGR 52.52 0.091977 83588000 90871 87767 98875 68693 123970 126580 108480 92404 100600 69833 TRUE FALSE 94458.65725 102840.2995 101451.7637 82280.27037 102897.6237 97183.71334 99977.05414 91165.47552 96979.42565 83515.43932 1.131032274 1.231392667 1.21476657 0.985210292 1.232079057 1.163661643 1.197108642 1.091600263 1.161215536 1 16.34975531 -4.999999929 0.229281144 0.156994489 1.173407555 0.306058869 0.071012623 195.6496685 1.95788407 76.33434173 0.120207325 1.00E-05 4.999999929 1.016413066 FKIPGSPPESMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKIPGSPPESMGR 13 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 136.33 6.71E-05 4605100000 1426230 2567300 2362140 2170150 2265500 3081400 1929420 2649100 2195120 3736100 FALSE TRUE 1482538.662 3008213.804 2423699.309 2599399.193 1880411.119 2365791.549 1778187.019 2613593.148 2116118.06 4468117.263 0.331803884 0.673262054 0.542443084 0.581766109 0.420850888 0.529482869 0.397972326 0.584942828 0.473603967 1 22.09123562 -1.390307679 3.549231479 1.003327873 0.511541794 0.704578651 0.096237851 34215370.61 41986864.49 1128777.702 0.021376901 0.040709177 1.390307679 -0.491786079 FKLDLDFPNLPYLLDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKLDLDFPNLPYLLDGK 17 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 184.8 5.61E-10 2539300000 8136000 4341200 7668500 5195200 9657600 8496200 9982400 7378300 8707200 4169400 FALSE TRUE 8457215.562 5086767.33 7868347.41 6222795.054 8016004.602 6523086.311 9199953.404 7279405.957 8393829.573 4986314.102 1.696085603 1.020145788 1.57798872 1.247974942 1.607601214 1.308198035 1.845040889 1.459877137 1.68337361 1 22.24954233 3.229473348 24.99649063 1.519896575 1.373194253 0.01964221 0.273014558 555.8011951 1528848.107 0.071825569 0.087013057 1696.185506 -3.229473348 -0.146702322 FKNEEEVFAWNNEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKNEEEVFAWNNEVK 15 1 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GTY9;P49419-4 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 156.57 1.06E-08 245500000 1605050 905940 1276430 978880 1676880 1570220 1646380 1220100 1440570 922470 FALSE TRUE 1668418.613 1061528.148 1309694.814 1172499.542 1391844.537 1205560.202 1517332.434 1203746.555 1388724.167 1103210.335 1.512330478 0.962217371 1.187166919 1.062806888 1.261631162 1.092774572 1.375379097 1.091130601 1.258802717 1 20.07327645 -2.012891587 2.418501015 0.797959761 1.18806143 0.128538856 0.153566068 28294553.25 8939325.492 31782949.02 0.03288371 0.009707523 2.012891587 0.39010167 FKNELER ddPTM_MDA-MB-175_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 ;;;; 131.06 0.0031944 1941170000 2225170 1835220 2203750 1940940 3040270 2900350 3107930 2662380 2776910 1870400 FALSE TRUE 2313021.43 2150404.759 2261181.535 2324852.139 2523485.991 2226787.668 2864322.326 2626695.151 2676969.552 2236869.069 1.034044174 0.961345833 1.010868972 1.039333134 1.12813308 0.995493075 1.280505133 1.174273089 1.196748432 1 21.09304938 2.917165361 1.096431905 1.170038809 0.999512922 0.320656328 0.082898462 0.466662425 1.195472404 0.037101551 0.041495897 826.3525293 -2.917165361 -0.170525888 FKNWDDVLTVDYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKNWDDVLTVDYTR 14 1 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 163.7 3.87E-06 396580000 774550 734070 782770 618490 979240 994200 781700 824020 896190 820960 FALSE TRUE 805129.8321 860140.8122 803169.6293 740825.476 812789.1346 763312.1172 720428.3114 812975.3597 863936.297 981811.3938 0.820045313 0.876075403 0.818048797 0.754549683 0.827846509 0.777452902 0.73377465 0.828036184 0.879941201 1 19.90508638 0.947862037 2.167660131 0.999060622 0.802139205 0.715827874 0.038239152 0.195328728 1.996303302 0.038432567 0.010586261 8.868742317 -0.947862037 -0.196921417 FKPNQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKPNQTR 7 1 Q9NZJ9;A0A024RBG1;Q9NZJ9-2 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ; 105.57 0.0072026 2670000000 1499100 1433620 1537450 1186270 1892820 1866110 1646660 1527100 1448970 1513900 FALSE TRUE 1558285.626 1679833.083 1577517.21 1420910.665 1571079.132 1432734.234 1517590.486 1506631.722 1396821.853 1810519.72 0.86068415 0.927818164 0.871306285 0.784808169 0.867750357 0.791338652 0.838207102 0.832154274 0.771503253 1 20.78797246 3.991439725 23.78761782 0.832506611 0.89557894 0.097939735 0.062671479 350.8474816 974968.6887 0.014144407 0.028330486 9804.822253 -3.991439725 0.063072329 FKPPPPNSDIGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKPPPPNSDIGWR 13 1 E1CEI4;P48506;A0A2R8YEL6;B4E2I4;A0A2R8Y648 E1CEI4 GCLC Glutamate--cysteine ligase catalytic subunit 0 66.285 0.062739 0 155700 118710 138620 108220 188030 189160 148600 143400 154130 137060 FALSE TRUE 161847.1562 139097.5191 142232.5511 129625.593 156068.7278 145230.4567 136952.3437 141477.9576 148582.8914 163914.2828 0.987388978 0.848599138 0.867725183 0.790813288 0.952136233 0.886014655 0.83551196 0.863121597 0.906467019 1 17.32258204 0.886263998 4.051794325 0.999969813 0.874861386 0.316181392 0.053161872 0.656728168 20.97944594 0.048773066 0.012458199 7.695981205 -0.886263998 -0.125108427 FKVAS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKVASFR 7 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 FKVAS(1)FR 78.934 0.045513 0 539970 450470 594360 462860 815710 707550 650440 636220 640100 439380 TRUE FALSE 561288.4325 527834.7183 609849.5099 554412.3265 677055.9056 543232.2355 599456.8132 627692.5115 617062.926 525468.0986 1.068168428 1.004503831 1.160583319 1.05508275 1.288481465 1.033806309 1.140805341 1.194539713 1.17431092 1 19.00324365 4.234596952 24.99629767 1.140591915 1.036336118 0.168889423 0.081747189 131.8946757 831796.6726 0.018933951 0.043467924 17163.14817 -4.234596952 -0.104255796 FKVASFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FKVASFR 7 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 76.774 0.036341 237820000 526260 432110 461630 416860 668030 610290 537380 516540 548110 511690 FALSE TRUE 547037.1512 506321.5312 473660.457 499313.6638 554478.4992 468559.3965 495258.7514 509616.6262 528383.6282 611945.8586 0.893930637 0.82739596 0.77402347 0.815944183 0.906090778 0.765687667 0.809317923 0.832780579 0.863448328 1 19.22304449 0.745908275 2.04398095 0.999920343 0.825484008 0.597869841 0.042181939 0.674958523 4.307051115 0.039570751 0.010899249 5.570680813 -0.745908275 -0.174436335 FKYDDAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FKYDDAER 8 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;;; 134.25 0.00080692 2906380000 4563270 3654360 4065630 3431430 5398790 5451030 5084770 4308390 4509220 3500590 FALSE TRUE 4743431.423 4281967.903 4171583.658 4110156.612 4481105.604 4185110.894 4686212.441 4250643.079 4346934.053 4186463.588 1.133040172 1.022812647 0.996445704 0.981772927 1.070379692 0.999676889 1.119372555 1.01533024 1.038330792 1 21.99730065 FKYDDAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FKYDDAERR 9 2 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ; 157.24 3.88E-05 494630000 1597720 1318190 1577270 1128230 2002760 1784860 1352040 1493510 1678930 1658590 FALSE TRUE 1660799.219 1544578.878 1618374.952 1351390.527 1662331.571 1370353.315 1246063.572 1473491.941 1618505.637 1983558.955 0.837282509 0.778690684 0.815894556 0.681295871 0.838055036 0.690855854 0.628195884 0.742852607 0.81596044 1 20.91965985 0.876038809 3.255311111 0.999824234 0.747476563 0.560370752 0.06619305 0.387217315 8.123012514 0.065045574 0.01690771 7.516900635 -0.876038809 -0.252347672 FLAAGTHLGGTNLDFQMEQYIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FLAAGTHLGGTNLDFQMEQYIYK 23 0 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ;; 280.2 6.47E-52 3140260000 1210960 1080555 1287620 1100427 1446970 1568510 1515860 1382239 1362820 941491 FALSE TRUE 1258769.636 1266131.916 1321176.435 1318088.176 1201014.556 1204247.323 1397042.932 1363712.347 1313772.374 1125958.136 1.117954208 1.124492888 1.173379714 1.170636931 1.066660046 1.069531171 1.240759215 1.211157239 1.166803927 1 20.10272176 2.243893983 24.99999414 1.17888813 1.122869757 0.00897935 0.069195827 269.7289653 1264352.943 0.023892647 0.019453611 175.3452408 -2.243893983 -0.056018373 FLAAGTHLGGTNLDFQMEQYIYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLAAGTHLGGTNLDFQMEQYIYKR 24 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 203.64 7.63E-25 936790000 269870 309550 348870 267574 461310 457300 310270 336110 375200 404450 FALSE TRUE 280524.676 362712.8045 357961.8388 320499.3386 382896.691 351099.0054 285950.2267 331604.9952 361696.6253 483694.2338 0.579962828 0.749880357 0.740058106 0.662607317 0.791608963 0.725869735 0.59117973 0.685567394 0.747779485 1 18.88373581 0.808113359 3.376706542 0.99995522 0.693215021 0.678566487 0.063579088 0.672492372 11.00651586 0.060459429 0.015646697 6.428554922 -0.808113359 -0.306740199 FLATEGAPDFLCPEELEHVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FLATEGAPDFLCPEELEHVSR 21 0 A0A494C1T9;Q6ZRV2 A0A494C1T9 FAM83H Protein FAM83H 0 ;; 189.55 2.12E-17 267658000 110527 315156 283489 326097 284368 360791 255999 328796 260566 349025 FALSE TRUE 114890.6913 369281.5914 290876.9562 390598.0133 236031.2289 277002.7581 235933.1295 324389.0274 251188.2806 417409.7663 0.275246773 0.884698014 0.696861884 0.93576635 0.565466474 0.663623088 0.565231455 0.77714767 0.601778638 1 18.67110483 -1.893073139 2.673458242 1.166323668 0.6787387 0.242078822 0.176965191 40378908.9 23885656.94 42317188.31 0.038742055 0.012791659 1.893073139 -0.487584968 FLCADYAEQDELDYHR ddPTM_MDA-MB-175_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 ;;; 250.95 4.27E-21 671211000 687543 827999 790295 809134 890777 1008950 794751 824063 802767 863968 FALSE TRUE 714687.7285 970201.3873 810890.7369 969178.2902 739363.0437 774636.6533 732456.3399 813017.7834 773875.5725 1033245.988 0.691691753 0.938983939 0.784799309 0.937993761 0.715573109 0.749711746 0.708888637 0.786857915 0.748975154 1 19.97875233 5.025400602 16.47168353 0.804572099 0.395888291 0.114868719 0.098965411 12983439.89 220168010.7 0.022532183 141853516.2 106023.1253 -5.025400602 -0.408683808 FLDAGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FLDAGHK 7 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 134.44 0.0031745 6115520000 10447250 8492730 9269960 9095690 11841600 11995660 11435240 9886900 9782490 7252300 FALSE TRUE 10859715.5 9951290.313 9511542.773 10894790.33 9828769.062 9209849.761 10538916.01 9754382.277 9430420.096 8673249.331 1.252093083 1.147354346 1.096652755 1.256137108 1.133228008 1.061868443 1.215105851 1.124651432 1.08729955 1 23.04814115 -5 0.121299354 0.479056073 1.228578106 0.453289829 0.0583724 145.4309215 1.140431527 18.38294463 0.535524026 1.00E-05 5 0.749522033 FLDAGHKLNFAVASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLDAGHKLNFAVASR 15 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 133.71 2.38E-05 560080000 303900 516060 414740 351480 724740 612970 295250 396110 389640 849600 FALSE TRUE 315898.2067 604689.2906 425548.4651 421001.6949 601548.9537 470617.0072 272107.5335 390800.7934 375616.9325 1016062.853 0.310904198 0.595129808 0.418821005 0.414346114 0.592039116 0.463177062 0.267805808 0.384622656 0.369678836 1 19.95455822 -1.258487103 3.569125302 1.001283561 0.424898674 0.747442708 0.10043525 146880962.1 232320909.8 2081182.81 0.024624112 0.055145858 1.258487103 -0.576384888 FLDEQAIDREHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLDEQAIDREHER 13 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A6I8PUD8 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 87.498 0.0050109 88927000 61610 89287 82880 66638 91345 94891 64153 83502 78478 108200 FALSE TRUE 64042.41037 104621.3477 85039.92089 79818.79751 75818.20953 72854.00334 59124.52023 82382.79227 75653.59211 129399.7184 0.494919241 0.808512947 0.657187836 0.616839036 0.585922523 0.563015161 0.456913825 0.636653567 0.584650361 1 16.98147495 -1.667995075 6.646986523 1.002463331 0.603397935 0.637118039 0.090423987 0.003316256 0.000165641 0.087959909 0.020633713 0.021478548 1.667995075 -0.399065396 FLDFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLDFWR 6 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 126.68 0.040453 406030000 669350 835570 806670 739980 1168000 1075000 940280 822820 771610 1186700 FALSE TRUE 695776.4549 979072.6477 827692.4829 886345.8354 969463.7772 825347.5418 866578.3966 811791.4438 743839.9068 1419211.144 0.490255772 0.689871026 0.58320602 0.624534157 0.683100454 0.581553735 0.610605688 0.572001881 0.524122087 1 20.43665781 -1.151820675 4.790015587 1.000034649 0.599609197 0.808383478 0.0590541 2.06E-05 3.64E-06 0.053804823 0.012680823 0.07049841 1.151820675 -0.400425452 FLDGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLDGDR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 122.98 0.044171 410760000 659680 752560 737290 838630 801040 893180 952880 805230 754930 670040 FALSE TRUE 685724.6758 881806.3259 756504.3831 1004508.511 664879.5069 685752.4813 878190.7757 794437.2089 727760.2168 801321.5093 0.855742256 1.100440105 0.944070981 1.253564892 0.829728766 0.855776955 1.095928121 0.991408816 0.908200027 1 19.61202168 FLDGDRLTLADCSLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLDGDRLTLADCSLLPK 17 1 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 105.38 0.00073384 229480000 190780 146590 188440 142750 268850 198720 170010 153130 215700 174010 FALSE TRUE 198312.1417 171765.6922 193350.9012 170985.5239 223150.973 152570.2916 156684.172 151077.5428 207936.9991 208103.9279 0.952947615 0.825384191 0.929107409 0.821635255 1.072305436 0.733144699 0.752913093 0.725971606 0.999197859 1 17.66694467 2.694371804 24.99996689 0.809887826 0.910015206 0.067029038 0.114750944 850.0355359 480909.6104 0.035814125 0.033766009 494.7340522 -2.694371804 0.10012738 FLDGIYVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLDGIYVSEK 10 0 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 123.63 0.0010634 21004000 163700 162910 174378 133150 238400 217249 212246 173861 170531 148132 FALSE TRUE 170163.0024 190888.5252 178922.4339 159486.6726 197876.8532 166796.2122 195609.6039 171530.6777 164393.6226 177155.6292 0.96052834 1.077518824 1.009973178 0.900263081 1.116966218 0.941523636 1.104168153 0.96824853 0.927961608 1 17.43465778 1.552840782 10.96216094 0.959109351 1.016025389 0.102496127 0.068156609 0.236379279 39.52402183 0.033986127 0.015807865 35.71418811 -1.552840782 0.056916037 FLDGKDGDFDYSTVDDNPDFDNLDIVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLDGKDGDFDYSTVDDNPDFDNLDIVAR 28 1 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 0 90.55 0.0027259 30501000 25276 21022 29031 19950 33062 26260 21468 23092 24598 24086 FALSE TRUE 26273.916 24632.36497 29787.57171 23896.05046 27442.13305 20161.51297 19785.28206 22782.48951 23712.72278 28805.19055 0.91212436 0.855136332 1.034104311 0.829574462 0.952680143 0.699926388 0.686865169 0.790916119 0.823210065 1 14.81404118 2.749273047 24.92609919 0.778352292 0.914981888 0.254751243 0.096080017 788.00189 1833552.677 0.027998494 0.029425236 561.4008256 -2.749273047 0.136629596 FLEDTFGNDGRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLEDTFGNDGRPR 13 1 O00754;O00754-2;M0R2P5 O00754;M0R2P5 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 124.48 0.00019266 134330000 240600 241200 228010 221020 241210 324380 213900 225170 229440 253750 FALSE TRUE 250099.0738 282624.2237 233952.1279 264737.0963 200209.2104 249047.661 197133.9591 222151.9645 221182.4992 303467.4542 0.824138043 0.931316422 0.77092988 0.872373932 0.659738656 0.820673379 0.649604946 0.732045435 0.728850808 1 18.21118228 3.262869867 24.99239982 0.745360612 0.849894401 0.127270245 0.100745745 350.0832046 359918.8535 0.025535641 0.034559023 1831.765465 -3.262869867 0.104533789 FLEEHPGGEEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLEEHPGGEEVLR 13 0 P00167-2;P00167;P00167-3 P00167-2 CYB5A Cytochrome b5 0 ; 156.81 4.74E-05 457790000 381360 541980 414800 633050 508020 711330 476280 469670 442250 678980 FALSE TRUE 396416.3873 635060.849 425610.0288 758265.4005 421666.9419 546134.3878 438947.9291 463374.8419 426333.5089 812013.1311 0.488189627 0.782081994 0.524141806 0.933809284 0.519285866 0.672568419 0.540567526 0.570649444 0.525032777 1 19.63114353 -0.61795563 6.507201916 1 0.620509514 0.419775853 0.134909826 0 1.39E-10 0.121071999 0.028536944 0.241015165 0.61795563 -0.379490487 FLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FLEELR 6 0 Q5T508;D6R9F0;Q92535;Q9HBX8-1;O75473-3;O75473-2;O75473;Q9HBX8-2;Q9HBX8 REV__Q8IYE1 LGR6;PIGC;LGR5 Phosphatidylinositol N-acetylglucosaminyltransferase subunit C;Leucine-rich repeat-containing G-protein coupled receptor 6;Leucine-rich repeat-containing G-protein coupled receptor 5 0 ;;; 113.08 0.061517 199566000 477552 554830 573010 619380 603880 697620 579070 567210 538965 532550 FALSE TRUE 496406.1217 650117.7365 587943.1113 741891.5153 501232.6933 535608.3275 533680.9803 559607.4777 519567.7549 636892.9762 0.779418427 1.020764494 0.923142715 1.16486057 0.786996736 0.840970693 0.837944522 0.878652299 0.815785029 1 19.28069144 FLEESVSMS(ph)PEER ddPTM_MDA-MB-175_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;FLEESVSMS(1)PEER;FLEESVSMS(1)PEER;FLEESVSMS(1)PEER;FLEES(0.434)VS(0.042)MS(0.524)PEER 388.9 4.53E-108 1331390000 867567 1004369 926400 1009827 1151614 1190885 1054371 1018522 968899 1046704 TRUE FALSE 901819.2151 1176861.563 950542.745 1209567.767 955863.0636 914320.0068 971726.6459 1004870.379 934028.5143 1251785.608 0.720426253 0.940146264 0.759349475 0.966273904 0.763599659 0.730412621 0.776272422 0.802749586 0.746156936 1 20.25555606 5.036868748 16.10736707 0.819621855 0.331183739 0.097638854 0.095320358 7245359.942 88107487.77 0.02130774 101691990.3 108860.1049 -5.036868748 -0.488438115 FLEFQYLTGGLVDPEVHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLEFQYLTGGLVDPEVHGR 19 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 208.17 2.83E-16 326360000 211500 277260 252810 283530 308240 366280 260100 249170 274830 253950 FALSE TRUE 219850.1833 324877.2482 259398.4363 339611.3877 255845.4749 281217.021 239712.6824 245830.2837 264938.922 303706.6403 0.723889945 1.069707425 0.854108544 1.118221806 0.842409882 0.925949531 0.789290225 0.809433351 0.87235143 1 18.21231893 FLEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FLEGVR 6 0 F8VWS0;P05388;F8VU65;F8VW21;Q8NHW5;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 ;;;;; 136.44 0.030638 2376940000 2202500 3007920 2547500 2818830 2951520 3366350 2615250 2716560 2298750 2941180 FALSE TRUE 2289456.401 3524506.862 2613889.943 3376386.161 2449821.685 2584566.23 2410259.871 2680148.957 2216018.437 3517447.909 0.650885659 1.002006839 0.743121152 0.959896564 0.696477033 0.734784508 0.685229727 0.761958393 0.630007464 1 21.74609763 3.207696583 24.99985382 0.736040735 0.843775811 0.08962875 0.130995043 368.6524754 298607.36 0.034222111 0.040907279 1613.231088 -3.207696583 0.107735076 FLEIGKFDLSQNHPLGMAIFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 261.46 1.58E-37 5097659000 7224180 6320210 8908450 6591440 12700330 11024160 8063690 8296970 10174230 7310550 FALSE TRUE 7509396.205 7405656.903 9140611.525 7895207.159 10541532.44 8463965.913 7431636.907 8185762.688 9808061.45 8742912.304 0.858912447 0.847046916 1.045488186 0.903040873 1.205723228 0.968094568 0.850018466 0.936274139 1.121830016 1 23.0596825 4.250777364 24.72548488 0.992799336 0.852979572 0.26726712 0.098555698 282.7477359 572240.8614 0.024517497 0.066054011 17814.65287 -4.250777364 -0.139819765 FLELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FLELGK 6 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ;; 102.98 0.081604 1986651000 4023448 2655618 3457828 3560008 3875878 4434890 4701036 3447858 3571941 1859927 FALSE TRUE 4182296.834 3111699.734 3547941.838 4264166.957 3217057.642 3404954.009 4332556.514 3401645.103 3443387.541 2224344.085 1.880238252 1.398929129 1.595050812 1.917044663 1.446294961 1.530767668 1.947790606 1.529280081 1.54804626 1 21.08494855 0.640080154 1.606347177 1.000663696 1.65394767 0.52739636 0.186036259 1.102486698 3.915337495 0.16910046 0.048428785 4.365964037 -0.640080154 0.653283974 FLELGKEEDFHPELES(ph)LDGDLDPGLPSTEDVILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLELGKEEDFHPELESLDGDLDPGLPSTEDVILK 34 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 FLELGKEEDFHPELES(1)LDGDLDPGLPSTEDVILK;FLELGKEEDFHPELES(0.936)LDGDLDPGLPS(0.032)T(0.032)EDVILK 84.969 0.00038998 52746000 54298 27312 40115 29403 59744 53887 55539 43683 50088 28849 TRUE FALSE 56441.72697 32002.62354 41160.42985 35218.82564 49588.73622 41372.56092 51185.70806 43097.50084 48285.34266 34501.4092 1.635925264 0.927574388 1.193007208 1.02079383 1.437295965 1.199155683 1.483583113 1.249151899 1.399517984 1 15.07436767 3.23116004 24.99939925 1.311523796 1.175177401 0.043399888 0.215517532 420.2974123 1419778.425 0.057221958 0.069695842 1702.785881 -3.23116004 -0.136346395 FLEMCNDLLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLEMCNDLLAR 11 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 111.27 0.0039162 148250000 84234 101590 88626 105660 116370 127890 101240 113110 109780 94022 FALSE TRUE 87559.62336 119037.2922 90935.66637 126559.2326 96589.46897 98189.48569 93304.54426 111593.9455 105829.0392 112443.8107 0.778696691 1.058638012 0.808720958 1.125533116 0.859002095 0.873231573 0.829788173 0.992441867 0.941172649 1 16.77884473 1.616944646 25 0.975105864 0.912431195 0.090216297 0.104270395 1.913515817 5254.877408 0.046253198 0.02518702 41.39469108 -1.616944646 -0.062674669 FLENGS(ph)QEDLLHGNPGSTYLASNSTSAPNWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FLENGSQEDLLHGNPGSTYLASNSTSAPNWK 31 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK;FLENGS(1)QEDLLHGNPGSTYLASNSTSAPNWK 362 1.59E-121 2398010000 1102880 1100250 1253390 1106220 1342300 1443800 1209160 1209940 1315050 999240 TRUE FALSE 1146422.554 1289209.379 1286054.373 1325027.014 1114136.325 1108499.331 1114382.88 1193722.733 1267721.607 1195021.946 0.959331799 1.078816488 1.076176364 1.108788854 0.932314531 0.927597467 0.932520849 0.998912812 1.060835419 1 20.18860568 3.234392081 24.99997156 0.971827455 1.058880955 0.358150906 0.052544938 113.5611109 681060.8814 0.015657308 0.019360251 1715.505366 -3.234392081 0.0870535 FLENHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLENHEK 7 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ; 100.15 0.010006 231670000 393260 365748 376590 345529 482950 458310 433200 373428 416374 321437 FALSE TRUE 408786.2085 428562.3739 386404.2448 413873.6049 400858.3315 351874.4483 399244.652 368422.8085 401388.7811 384416.4259 1.063394228 1.11483887 1.005171004 1.076628305 1.04277108 0.915347068 1.038573342 0.958395073 1.044150963 1 18.55231046 2.983202904 24.34030732 0.989068253 1.063719166 0.404593619 0.042647253 475.2805473 688720.4447 0.012045057 0.013084556 962.0616527 -2.983202904 0.074650912 FLEPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLEPTLR 7 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 154.09 0.0039591 35877000 70733 82587 81830 86794 92446 109140 89636 82202 80762 81182 FALSE TRUE 73525.59346 96770.67481 83962.55702 103961.5941 76732.06194 83793.88903 82610.0961 81100.21665 77855.3914 97088.05858 0.757308309 0.99673097 0.864808281 1.070796921 0.790334703 0.863071013 0.850878031 0.835326381 0.801904915 1 16.56700624 FLESAAADFS(ph)DEDEDDDVDGREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FLESAAADFSDEDEDDDVDGREK 23 1 O43815-2;O43815 O43815-2 STRN Striatin 1 FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK 316.38 1.41E-73 2236200000 1171020 775710 947760 646972 1443680 1239980 939770 927430 1041830 903140 TRUE FALSE 1217252.774 908932.1583 972459.4042 774941.1306 1198283.789 952013.4371 866108.3718 914999.3178 1004334.742 1080092.991 1.126988864 0.841531392 0.900347852 0.717476307 1.109426502 0.88141803 0.801883151 0.847148648 0.929859512 1 20.0427241 2.503374394 24.64814382 0.871174209 0.926875624 0.017698583 0.122729008 2273.467421 2134476.499 0.038850856 0.03651041 318.6943716 -2.503374394 0.055701415 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL 40 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 229.31 7.25E-41 85980000 75455 46172 58059 32470 114170 99607 59396 58217 75205 40809 FALSE TRUE 78434.02166 54101.68183 59572.06524 38892.46909 94763.42418 76474.78381 54740.38632 57436.69634 72498.38674 48804.74221 1.60709837 1.108533298 1.220620426 0.796899386 1.94168476 1.566953954 1.121620233 1.176867118 1.485478325 1 15.57473372 -1.490097363 3.310726992 0.993562458 1.314904377 0.093464937 0.307746022 66565541.94 67754812.59 3740515.764 0.073962607 0.032352112 1.490097363 0.321341919 FLEVDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLEVDER 7 0 Q92696;H0YLH3 Q92696 RABGGTA Geranylgeranyl transferase type-2 subunit alpha 0 ; 94.407 0.033089 211880000 401900 448930 464550 500140 532850 578160 507060 475640 448970 426680 FALSE TRUE 417767.3223 526030.2353 476656.5546 599066.1992 442276.3473 443891.1021 467315.3122 469264.8238 432811.6574 510279.7767 0.818702487 1.030866319 0.934108261 1.173995574 0.86673305 0.8698975 0.915802141 0.919622617 0.84818501 1 18.96092894 FLEVQYLTGGLIEPDTPGRVPLDEALQR ddPTM_MDA-MB-175_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 0 206 2.41E-25 196190000 19806 23171 34621 29116 38411 41777 25125 29549 29252 31763 FALSE TRUE 20587.95617 27150.439 35523.2517 34875.0579 31881.91194 32074.92489 23155.63685 29152.94399 28199.22623 37986.35171 0.541982982 0.714741948 0.93515829 0.918094429 0.83929913 0.844380243 0.609577804 0.767458381 0.742351528 1 15.21319354 4.602296745 3.560894032 0.814012745 0.541832364 0.408362078 0.105872427 0.270631554 5.56834799 0.02701973 0.152079913 40021.81174 -4.602296745 -0.272180382 FLFAGFPGTFSLQDKESVPSAS(ph)PTGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLFAGFPGTFSLQDKESVPSASPTGIPK 28 1 Q5THJ4-2;Q5THJ4;H3BLS7;A0A2R8YD87 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 FLFAGFPGTFSLQDKESVPSAS(0.996)PT(0.004)GIPK 221.31 1.45E-34 279100000 159930 97290 146210 94920 221620 182990 153610 132650 153440 111160 TRUE FALSE 166244.1599 113998.8007 150020.3527 113694.8927 183949.1116 140493.3457 141569.6468 130872.0437 147917.7244 132939.6737 1.250523303 0.857522796 1.128484436 0.855236736 1.383703649 1.056820299 1.064916461 0.984446855 1.112668026 1 17.02041219 -1.951419811 3.739145262 0.955695964 1.067311873 0.0186972 0.153440278 0.075645352 0.000982809 0.198312884 0.032150829 0.011183563 1.951419811 0.111615909 FLGDIEVWDQAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 199.43 2.74E-07 67510000 141349 120970 159570 133238 197673 196019 182019 147503 139169 126485 FALSE TRUE 146929.5677 141745.6565 163728.5253 159592.0787 164072.6141 150496.5579 167751.8752 145525.9636 134160.3349 151267.314 0.971323968 0.937054098 1.082378743 1.055033467 1.08465345 0.994904675 1.108976359 0.962045003 0.886908951 1 17.20674076 1.559016352 7.110166105 0.937791341 1.033281747 0.315439521 0.056845452 0.139397633 13.41657531 0.031254365 0.014543909 36.22566377 -1.559016352 0.095490407 FLGEVHCGTNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FLGEVHCGTNVR 12 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;;;;; 193.73 2.43E-06 2911780000 2468610 2831860 2671410 2686490 3011070 3317920 2557740 2664180 2459750 2710450 FALSE TRUE 2566072.629 3318209.926 2741029.139 3217869.704 2499249.397 2547383.364 2357257.655 2628471.025 2371224.078 3241510.783 0.791628596 1.023661542 0.845602351 0.992706771 0.771013754 0.785862992 0.727209568 0.810878384 0.731518183 1 21.62823494 3.22161206 24.99782411 0.790150975 0.916432984 0.232092423 0.094952132 276.9423242 408467.9419 0.024831395 0.029750522 1665.758583 -3.22161206 0.126282009 FLGMHPCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FLGMHPCER 9 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;;; 93.551 0.0093226 1693340000 1396679 1490407 1462346 1443839 1868004 1906977 1563025 1531410 1525419 1516627 FALSE TRUE 1451820.965 1746372.808 1500455.938 1729426.045 1550481.347 1464110.492 1440511.016 1510883.954 1470519.468 1813781.023 0.800438943 0.962835528 0.82725308 0.953492193 0.854833813 0.807214583 0.794203378 0.833002405 0.810748072 1 20.79056886 3.008473506 24.90434827 0.833568234 0.889404619 0.035367848 0.071931732 379.1771629 1114423.619 0.018948221 0.022613607 1019.702551 -3.008473506 0.055836385 FLHKHDLDLICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 168.31 2.82E-05 1220670000 1136160 1043170 1068390 793170 1691080 1397030 854000 1041200 1134020 1293650 FALSE TRUE 1181016.474 1222326.333 1096233.121 950056.6586 1403630.826 1072590.955 787061.2485 1027244.417 1093206.842 1547115.949 0.763366492 0.790067696 0.708565587 0.614082389 0.907256387 0.693284143 0.50872803 0.663973775 0.706609509 1 20.56114989 0.916160697 19.42402247 1 0.699731363 0.434927005 0.100246174 4968.600052 1151137.995 0.100845081 0.02521127 8.244431181 -0.916160697 -0.300268637 FLHNPDAAQGFVGCALSSTIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLHNPDAAQGFVGCALSSTIQR 22 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 253.13 5.11E-37 921840000 324960 316830 310991 314446 265704 396950 327230 331910 339630 301356 FALSE TRUE 337789.6717 371243.0879 319095.6809 376642.4803 220539.729 304764.3783 301580.8575 327461.2893 327406.7826 360400.9384 0.9372608 1.030083577 0.885390816 1.045065204 0.611928842 0.845625929 0.836792653 0.908602766 0.908451527 1 18.45924324 FLIDGFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FLIDGFPR 8 0 P30085;P30085-3;A0A494BXC7;P30085-2;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ;;; 100.19 0.014613 511023300 879390 1061298 1035357 933284 1363381 1369904 1106855 1025707 1045117 1223849 FALSE TRUE 914108.9962 1243567.676 1062339.254 1117884.79 1131633.985 1051764.557 1020096.813 1011959.075 1007503.443 1463638.78 0.624545488 0.849641109 0.725820652 0.763770956 0.7731648 0.718595716 0.696959405 0.691399469 0.688355254 1 20.48112812 -0.930503056 5.134286021 1.000000004 0.72782471 0.673529125 0.057253981 5.56E-07 1.16E-07 0.053492908 0.012608358 0.117353742 0.930503056 -0.272175294 FLISYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLISYDR 7 0 Q8TBX8;Q8TBX8-3;F8VNT5;F8VU68 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 81.119 0.065295 373510000 136960 152180 154350 152240 206090 214020 191970 173860 160230 221360 FALSE TRUE 142367.2866 178315.7312 158372.4878 182352.6176 171058.8954 164317.0985 176922.8898 171529.6911 154463.3536 264731.2538 0.537780426 0.673572646 0.598238725 0.688821645 0.646160561 0.620693991 0.668311305 0.647938952 0.5834723 1 18.014169 -1.948324593 2.542430964 1.27001409 0.634577042 0.864041632 0.044054906 3564417.705 1902405.949 5694952.754 0.009920728 0.011263553 1.948324593 -0.635437047 FLKNEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLKNEVER 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 101.46 0.0049058 1615430000 1760630 1829150 2047510 1473090 2560600 2491400 1884640 2056370 2124450 1919150 FALSE TRUE 1830141.032 2143292.284 2100869.793 1764462.805 2125350.127 1912810.108 1736916.992 2028807.724 2047991.459 2295170.698 0.797387764 0.933826963 0.915343593 0.768771929 0.926009612 0.833406469 0.756770289 0.883946334 0.892304638 1 21.13017002 0.847880064 2.028840384 0.999434065 0.852205409 0.357582072 0.060264089 0.621059032 4.861001387 0.05616658 0.015548621 7.044984858 -0.847880064 -0.147228656 FLKPDVRLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLKPDVRLSR 10 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 1 FLKPDVRLS(1)R;FLKPDVRLS(1)R 98.974 0.0039468 2242200000 3241200 3565600 3977700 2479700 5645000 4955900 2692100 3888700 4294900 5386400 TRUE FALSE 3369165.079 4177964.063 4081362.13 2970177.259 4685464.916 3804967.332 2481086.168 3836578.337 4140327.388 6441761.951 0.523019184 0.648574737 0.63357854 0.461081499 0.727357663 0.590671832 0.38515645 0.59557903 0.642732131 1 22.61902392 0.744285689 2.525315167 0.999849406 0.570170002 0.661535458 0.0917486 0.781245944 6.839698078 0.086940246 0.023214792 5.549906791 -0.744285689 -0.429679405 FLKPVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLKPVELR 8 1 A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 69.598 0.048796 250430000 254720 257520 261500 261440 375490 411380 326780 338570 359120 323720 FALSE TRUE 264776.5423 301747.0568 268314.9048 313152.0517 311664.3439 315843.2295 301166.1297 334032.0229 346195.3414 387146.736 0.683917796 0.779412633 0.693057386 0.808871734 0.805028985 0.815823046 0.777912098 0.862804699 0.89422255 1 18.56252095 -4.999999929 0.034615157 2.246566938 0.019902973 0.853098608 0.033749045 369.0175487 0.958604782 51.37616971 18.1501842 1.00E-05 4.999999929 -2.226663965 FLLDHQGELFPSPDPSGL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLLDHQGELFPSPDPSGL 18 0 Q07960 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 104.24 0.0011919 98492000 81917 109962 99678 98006 110673 122869 101036 108064 103094 103095 FALSE TRUE 85151.14641 128847.1181 102275.6906 117391.2943 91860.84299 94334.53685 93116.53431 106615.5788 99383.66708 123294.4914 0.690632205 1.045035481 0.829523602 0.952121161 0.745052289 0.765115585 0.755236777 0.864722971 0.806067376 1 16.91174882 5.008105461 17.79750622 0.850299415 0.468062115 0.200521836 0.100332628 16087539.51 451200976.2 0.023218957 144860699.7 101883.8764 -5.008105461 -0.3822373 FLLESFNNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLLESFNNDR 10 0 Q13618;Q13618-2;Q13618-3 Q13618 CUL3 Cullin-3 0 ; 145.9 6.89E-05 537420000 501460 425090 502740 435500 575040 626950 561380 510820 519430 410470 FALSE TRUE 521258.028 498095.9008 515841.8174 521640.6002 477294.9062 481350.364 517377.5687 503973.2934 500735.8158 490893.7376 1.061855119 1.014671532 1.050821752 1.062634457 0.97229781 0.980559187 1.053950232 1.026644373 1.020049305 1 18.90505124 3.270862374 24.99999559 1.013118034 1.0453887 0.352348986 0.025176089 281.4417347 217820.0925 0.007507077 0.010164059 1865.788338 -3.270862374 0.032270666 FLLSLPEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLLSLPEHR 9 0 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 134.66 0.00024271 2725100000 1918520 2547700 2224200 2320200 2661200 2936900 2283300 2385900 2229900 2546300 FALSE TRUE 1994264.651 2985247.657 2282164.479 2779128.635 2208850.175 2254849.484 2104328.98 2353920.913 2149646.335 3045198.733 0.654888178 0.980312918 0.749430392 0.91262636 0.725355016 0.740460535 0.69103174 0.772994185 0.705913316 1 21.53810495 5.027424719 17.89710089 0.793513498 0.225701581 0.138312129 0.109416376 22838499.31 371833372.9 0.024626856 393862037.7 106518.4208 -5.027424719 -0.567811917 FLMECRNS(ph)PVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FLMECRNSPVTK 12 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 FLMECRNS(0.905)PVT(0.095)K;FLMECRNS(0.996)PVT(0.004)K;FLMECRNS(1)PVTK;FLMECRNS(0.994)PVT(0.006)K;FLMECRNS(0.981)PVT(0.019)K;FLMECRNS(0.998)PVT(0.002)K;FLMECRNS(1)PVTK 168.47 2.81E-05 5829000000 3280630 2457870 2898590 2174620 4501360 4104910 2674150 3111180 3661130 3496830 TRUE FALSE 3410151.806 2879990.053 2974129.637 2604753.345 3736220.435 3151606.863 2464543.135 3069479.721 3529366.646 4181966.888 0.815442087 0.688668784 0.711179623 0.622853651 0.893412247 0.753618321 0.589326315 0.73397992 0.84394897 1 21.99575021 0.98378222 2.833638479 0.998656785 0.721159746 0.519080061 0.082455547 0.200120245 3.826375868 0.07819808 0.020750443 9.63345825 -0.98378222 -0.277497039 FLMPEAYPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;FLMPEAYPS(0.751)S(0.249)PR 162.32 6.61E-05 264342000 489744 578687 578112 550315 602088 685974 603277 578742 527461 566880 TRUE FALSE 509079.4713 678071.9907 593178.0736 659165.6645 499745.2968 526666.9345 555990.5724 570984.9101 508477.7816 677949.2824 0.750910849 1.000180999 0.874959365 0.972293476 0.7371426 0.776853001 0.82010644 0.842223637 0.750023335 1 19.37081782 3.241915077 24.99999598 0.813255402 0.905012449 0.143993005 0.092255372 139.7157785 1041259.506 0.023990021 0.031199256 1745.480805 -3.241915077 0.091757047 FLMPEAYPSS(ph)PR ddPTM_MDA-MB-175_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(0.039)S(0.961)PR;FLMPEAYPS(0.101)S(0.899)PR 176.86 2.52E-05 176586000 310830 392800 355600 369070 398990 415910 364690 376670 353890 377320 TRUE FALSE 323101.8084 460260.3444 364867.2281 442070.9444 331169.8223 319321.2057 336104.6449 371621.3548 341153.568 451248.6298 0.716017262 1.019970619 0.80857249 0.979661577 0.733896572 0.70763917 0.7448325 0.823540129 0.756021283 1 18.78356303 5.059367969 13.47133248 0.829564033 8.39E-05 0.093536858 0.111765469 1844761.602 12610368.87 0.026243564 39734131.53 114648.3924 -5.059367969 -0.829480178 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLNEHPGGEEVLLEQAGVDASESFEDVGHSSDAR 34 0 D6RFH4;H3BUX2;O43169 D6RFH4 CYB5B Cytochrome b5 type B 0 155.17 2.95E-11 15607000 3896.9 17958 11775 20935 14805 24243 13882 15695 12698 19143 FALSE TRUE 4050.752621 21042.14681 12081.86617 25075.88052 12288.45139 18612.93066 12793.89257 15484.6342 12241.00146 22893.70434 0.176937404 0.919123725 0.527737495 1.095317741 0.536761164 0.813015246 0.558838901 0.676370847 0.534688545 1 14.4826633 -2.252645958 2.261249576 2.248932365 0.664930948 0.159311016 0.239481201 6973036.414 1012634.635 44675149.25 0.052675223 0.005589257 2.252645958 -1.584001416 FLPEEEKLTEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLPEEEKLTEQER 13 1 A0A1B0GUA3;Q96EK5;A0A1B0GUH6;A0A1B0GTE6;A0A0D9SFK7;A0A1B0GV79;A0A1B0GW21 A0A1B0GUA3 KIAA1279;KIF1BP KIF1-binding protein 0 ; 122.34 0.0002154 175608000 188396 142128 178748 145904 243314 241536 212547 166536 221017 165292 FALSE TRUE 195834.0196 166537.3784 183406.3197 174763.3757 201955.5732 185442.9245 195887.0108 164303.8573 213062.6413 197677.8027 0.990672786 0.842468786 0.927804322 0.884081942 1.021640116 0.93810697 0.990940855 0.83116999 1.077827851 1 17.59279135 0.56827371 0.240650815 1.02530079 0.90820957 0.101874669 0.072151437 10.74649269 1.571526912 0.400836638 0.169117441 3.700613344 -0.56827371 -0.11709122 FLPLFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLPLFDR 7 0 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 133.47 0.0076042 876410000 949500 1408000 1025580 1327050 1179420 1800460 1074850 956920 1018800 1608350 FALSE TRUE 986986.9932 1649813.047 1052307.457 1589536.529 978942.6097 1382330.451 990600.4484 944094.0526 982133.587 1923475.389 0.513126915 0.857725062 0.54708652 0.826387766 0.508944703 0.718662926 0.515005523 0.490827207 0.510603667 1 20.87528394 -1.117985361 5.173486669 1.000010693 0.608985949 0.436790786 0.132915523 1.60E-05 2.73E-06 0.12552952 0.029586783 0.07621047 1.117985361 -0.391024744 FLPLNIRNS(ph)PFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLPLNIRNSPFTR 13 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 FLPLNIRNS(0.828)PFT(0.172)R;FLPLNIRNS(1)PFTR 194.37 6.49E-07 1330970000 717760 811340 756620 651230 844490 919610 637040 716770 698060 902190 TRUE FALSE 746097.719 950681.3337 776338.1388 780041.3503 700943.8914 706044.5143 587107.1402 707162.8705 672936.957 1078956.857 0.691499122 0.881111536 0.719526581 0.722958796 0.649649601 0.654376966 0.544143296 0.655413482 0.623692182 1 20.04120575 3.649470673 1.922265045 0.659397249 0.783420682 0.041995486 0.12321472 0.624825953 4.506039372 0.033324464 0.064915621 4461.394963 -3.649470673 0.124023433 FLPS(ph)PVVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLPSPVVIK 9 0 Q13618;Q13618-2;Q13618-3;A0A087WTG3;H7C399 Q13618 CUL3 Cullin-3 1 FLPS(1)PVVIK 87.298 0.014219 53626000 367630 327480 375740 348660 505020 487940 398050 421660 427890 315230 TRUE FALSE 382144.3163 383722.1426 385532.0931 417623.9074 419176.8808 374623.3298 366849.8009 416008.3374 412490.3225 376993.2831 1.013663462 1.017848752 1.022649767 1.107775459 1.111894826 0.99371354 0.973093732 1.103490052 1.094158281 1 18.52417929 3.968290156 24.58128166 1.057384896 1.01687936 0.107754786 0.048427119 1152.523385 893431.9804 0.013208484 0.023841027 9295.872443 -3.968290156 -0.040505536 FLPSELRDEH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLPSELRDEH 10 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 169.58 4.19E-06 161930000 178700 225420 210740 162540 245960 250280 167900 199890 210650 268470 FALSE TRUE 185755.214 264134.1315 216232.0575 194689.9269 204151.8071 192156.263 154739.5593 197210.8015 203068.7476 321071.5563 0.578547711 0.822664376 0.673469989 0.606375504 0.635845197 0.59848423 0.481947268 0.614226946 0.632471932 1 18.29253534 -1.554334155 6.149562818 1.000679983 0.625761862 0.656877924 0.080844376 0.000793641 5.75E-05 0.082426451 0.01939467 0.02790396 1.554334155 -0.374918121 FLQDYFDGNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLQDYFDGNLK 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 135.8 0.00026192 171980000 369630 313730 365540 344180 421570 509320 447630 372580 376890 236130 FALSE TRUE 384223.2778 367610.687 375066.2727 412257.7767 349911.682 391038.1488 412543.5909 367586.1745 363325.8025 282395.1525 1.36058737 1.301759905 1.328161158 1.459861379 1.239085299 1.384719764 1.460873486 1.301673103 1.286586541 1 18.1073558 0.686553296 1.611099087 1.000421183 1.357269526 0.729076868 0.064896737 0.574721938 2.218590871 0.059992578 0.017194892 4.859071567 -0.686553296 0.356848343 FLQDYFDGNLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 211.22 5.53E-08 22692000000 2837700 3004500 3137000 2845100 4381400 4030300 3379000 3358000 3379700 2919700 FALSE TRUE 2949734.587 3520499.503 3218752.797 3407852.288 3636651.193 3094323.905 3114145.151 3312991.503 3258065.257 3491759.314 0.844770307 1.008230862 0.921814051 0.975969986 1.04149538 0.886179037 0.891855615 0.94880294 0.93307269 1 21.73552269 3.788746343 0.003478407 1.880829294 0.000101706 0.0476009 0.057170046 235721.1592 179.376462 47628.93762 49363.63318 6148.176737 -3.788746343 -1.880727588 FLQEHGSDS(ph)FLAEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 FLQEHGS(0.111)DS(0.889)FLAEHK;FLQEHGS(0.024)DS(0.976)FLAEHK 167.16 2.22E-06 293940000 169875 240987 261543 218834 309870 343010 300350 291540 274860 204809 TRUE FALSE 176581.7962 282374.6426 268359.0254 262118.712 257198.4081 263351.1259 276807.7822 287632.3832 264967.8423 244937.4022 0.720926223 1.152844115 1.095622894 1.070145717 1.050057712 1.075177263 1.130116428 1.174309765 1.081777792 1 17.90205357 4.743399583 24.99116758 1.100356111 0.720926066 0.839402968 0.04860586 189.1766198 976982.8481 0.01206983 0.098935132 55385.9467 -4.743399583 -0.379430045 FLQEHGSDSFLAEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FLQEHGSDSFLAEHK 15 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ;;;; 262.23 3.16E-25 1946310000 444036 1289130 1308320 1224520 1684990 1811530 1367340 1621720 1369210 1402310 FALSE TRUE 461566.8842 1510528.049 1342415.894 1466726.401 1398576.002 1390829.612 1260164.318 1599983.496 1319932.4 1677065.796 0.275222884 0.900696951 0.800455115 0.874578925 0.833942237 0.829323223 0.751410184 0.954037403 0.787048667 1 20.67750786 4.741352702 24.99983543 0.854264312 0.275222676 0.853099646 0.072656477 84.52729909 756802.6614 0.015858565 0.110245061 55125.52036 -4.741352702 -0.579041636 FLQHGTLVGLLPVPHPILIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLQHGTLVGLLPVPHPILIR 20 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 ; 259.38 1.58E-36 340620000 185974 266230 293700 280920 329150 374430 285310 325380 288940 297920 FALSE TRUE 193316.3971 311952.9315 301354.0633 336485.1375 273201.2006 287474.307 262946.6567 321018.8133 278541.1058 356291.72 0.542578978 0.875554817 0.845807091 0.944409086 0.766790765 0.806850934 0.738009451 0.900999926 0.781778218 1 18.44269943 -5 0.151451761 1.649675375 0.75464892 0.265530633 0.103673673 198.6098867 1.778922031 39.18374879 0.496739194 1.00E-05 5 -0.895026455 FLQPVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLQPVHK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 86.866 0.019762 427790000 1307990 1097780 1366010 1133710 1643250 1630150 1427750 1282990 1419340 1123800 FALSE TRUE 1359630.455 1286315.175 1401609.343 1357954.454 1363930.952 1251572.368 1315839.224 1265793.618 1368258.231 1343987.094 1.011639518 0.957088935 1.042874109 1.010392481 1.014839323 0.931238383 0.979056444 0.941819772 1.018059055 1 20.35808785 2.773665921 24.89206093 0.968536377 1.006714373 0.215878143 0.030874029 758.2822149 537672.4756 0.009103095 0.009654841 593.8351773 -2.773665921 0.038177996 FLRPHYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLRPHYGK 8 1 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 117.18 0.0012794 1887290000 3105800 2756800 3138400 2422800 3742200 3638800 3299200 3183100 3141900 2993900 FALSE TRUE 3228419.382 3230258.955 3220189.282 2902022.609 3106102.181 2793743.847 3040600.083 3140435.751 3028823.633 3580497.383 0.901667851 0.902181627 0.89936926 0.810508233 0.867505782 0.780266971 0.849211648 0.877094832 0.845922594 1 21.77172858 -1.262250498 3.300740315 1.000516339 0.859099245 0.550766502 0.038120029 12243968.08 17378414.43 63369.07353 0.009720422 0.054670054 1.262250498 -0.141417094 FLRT(ph)AEADGGLAR ddPTM_MDA-MB-175_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 78.692 0.036437 306228000 6211.2 12322.5 12385.1 8173.2 10717.1 19068.5 7846.7 11172.1 15050.8 10982.1 TRUE FALSE 6456.422972 14438.79352 12707.86588 9789.834565 8895.41117 14640.12986 7231.65515 11022.35627 14509.12465 13133.83223 0.491587136 1.09935876 0.967567246 0.74539056 0.677289843 1.114688356 0.550612725 0.839233826 1.104713719 1 13.68100031 1.270854111 9.27052075 1.052207176 0.81684585 0.189515874 0.199608773 0.431622705 118.382775 0.130104595 0.046571065 18.65752837 -1.270854111 -0.235361326 FLSAIVSSVDKIPYGMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSAIVSSVDKIPYGMR 17 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 248.25 6.96E-21 1094360000 428180 459730 507540 467660 666570 646820 598940 545630 591800 400910 FALSE TRUE 445084.877 538685.0513 520766.9093 560161.7522 553266.6695 496605.8577 551993.5178 538316.7223 570501.2336 479460.6386 0.928303267 1.123522992 1.086151537 1.168316452 1.153935537 1.035759388 1.151280154 1.122754777 1.18988127 1 18.87105286 4.739251356 24.51575803 1.119787545 0.928303195 0.492167976 0.056559687 33.53183256 1189795.309 0.012420269 0.074465823 54859.43823 -4.739251356 -0.191484349 FLSAQSHSTS(ph)PQGLDSPLPLEGSGAHQVLHNESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESK 34 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHS(0.001)T(0.042)S(0.957)PQGLDSPLPLEGSGAHQVLHNESK;FLSAQSHST(0.151)S(0.849)PQGLDSPLPLEGSGAHQVLHNESK 292.63 1.66E-89 670140000 137137 246110 253000 213320 278550 378520 276100 300210 290820 234190 TRUE FALSE 142551.2747 288377.478 259593.3878 255514.0593 231202.1705 290614.4665 254458.5605 296186.176 280353.445 280075.0467 0.508975278 1.029643595 0.926870819 0.912305692 0.825500784 1.037630699 0.908537064 1.05752433 1.000994013 1 18.09545393 4.74353182 24.98927843 0.96488075 0.508975089 0.798937697 0.068860318 228.3721946 1147945.603 0.016780376 0.139957669 55402.81349 -4.74353182 -0.455905661 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGS(ph)PTSAYPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNESKGSPTSAYPER 44 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 FLSAQSHSTSPQGLDSPLPLEGSGAHQVLHNES(0.176)KGS(0.793)PT(0.026)S(0.006)AYPER 299.87 2.44E-97 780220000 62347 201770 227690 183180 251230 269130 186400 246090 227200 238710 TRUE FALSE 64808.5077 236422.4279 233623.7884 219412.4573 208526.0143 206628.6362 171789.4809 242791.5661 219023.1164 285480.6541 0.22701541 0.828155689 0.818352435 0.76857207 0.730438337 0.723792079 0.601755245 0.850465916 0.767208262 1 18.12303346 4.753477946 0.07578355 1.245236176 3.23E-23 0.339848394 0.157795879 140.1150812 1.673975446 7.639782467 22.73300685 56686.27842 -4.753477946 -1.245236176 FLSCTVEADGIHLVTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FLSCTVEADGIHLVTER 17 0 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 0 ;; 165.45 2.47E-09 143340000 55304 72395 71720 73638 77227 107550 71486 75401 74495 73458 FALSE TRUE 57487.44462 84828.2781 73589.08212 88203.37661 64099.98212 82573.14244 65882.74053 74390.37293 71813.9395 87850.68866 0.65437671 0.965596052 0.837660845 1.004014629 0.729646894 0.939925955 0.749939944 0.846781898 0.817454486 1 16.42276598 -2.131348775 2.390161926 1.323122174 0.843191701 0.177260818 0.103995026 8678703.279 3037316.001 15147032.78 0.022639237 0.007390115 2.131348775 -0.479930473 FLSDPQVHTVLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FLSDPQVHTVLVER 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 171.91 2.94E-06 698090000 922937 1392420 1380390 1634110 1537080 1772040 1371040 1465270 1275730 1506550 FALSE TRUE 959375.2654 1631557.303 1416364.097 1957332.081 1275807.691 1360510.566 1263574.302 1445630.452 1229816.727 1801729.628 0.532474601 0.905550577 0.786113563 1.086362821 0.708101632 0.755113611 0.70131183 0.802357041 0.682575625 1 20.7809511 FLSHS(ph)TDSLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FLSHSTDSLNK 11 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;A0A087WY36 Q12802-2 AKAP13 A-kinase anchor protein 13 1 FLS(0.003)HS(0.97)T(0.027)DSLNK;FLS(0.003)HS(0.995)T(0.002)DSLNK;FLS(0.002)HS(0.992)T(0.006)DSLNK;FLSHS(0.997)T(0.003)DSLNK;FLS(0.002)HS(0.99)T(0.008)DSLNK;FLS(0.013)HS(0.945)T(0.042)DSLNK 184.21 3.23E-06 2572600000 2118750 2679740 3033920 2593790 3774490 3686340 3209260 3069690 3036550 2394500 TRUE FALSE 2202399.886 3139964.5 3112986.448 3106833.92 3132903.538 2830243.402 2957709.815 3028545.827 2927265.159 2863656.43 0.769086635 1.096487856 1.087067015 1.084918529 1.094022141 0.98833204 1.032843809 1.057580021 1.022212416 1 21.44942698 4.74377329 24.99632056 1.054057266 0.769086516 0.835137981 0.037627278 210.8247162 1010936.085 0.009173384 0.077494005 55433.62637 -4.74377329 -0.28497075 FLSLYGDQIDMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSLYGDQIDMHR 13 0 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ; 172.57 2.32E-05 685920000 721860 626710 645090 768080 701630 869950 896110 688170 651020 571110 FALSE TRUE 750359.5902 734342.5674 661901.5753 920003.9315 582367.1832 667917.2967 825870.5567 678946.2068 627589.9174 683008.0699 1.098610138 1.07515943 0.969097738 1.346988377 0.852650516 0.977905425 1.209166616 0.994052979 0.918861643 1 19.3815431 3.196539721 24.99999837 1.00612294 1.108133266 0.20442337 0.122855789 290.5528377 172861.278 0.035636265 0.042593846 1572.315591 -3.196539721 0.102010326 FLSNGHVTIPGQQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLSNGHVTIPGQQDK 15 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 66.335 0.058878 441830000 220780 296990 362410 315320 381830 447140 425520 354540 361520 240010 FALSE TRUE 229496.5649 347995.7222 371854.7023 377689.3549 316926.673 343298.5115 392166.6305 349787.9712 348508.9658 287035.3642 0.799541079 1.212379259 1.295501352 1.315828647 1.10413807 1.196014688 1.366265901 1.21862326 1.214167344 1 18.13086897 4.737316002 5.656659547 1.229613458 0.785540664 0.602715837 0.100206928 0.085288569 11.39491937 0.022585884 0.146644959 54615.51108 -4.737316002 -0.444072795 FLSNGHVTIPGQQDKDMFQETMEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSNGHVTIPGQQDKDMFQETMEAMR 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 175.46 8.68E-13 3372200000 1558680 3057700 3321400 2647900 3659900 4206300 3397300 3412300 3412200 2921100 FALSE TRUE 1620217.89 3582836.189 3407958.413 3171646.717 3037791.505 3229450.572 3131010.749 3366563.7 3289395.589 3493433.617 0.463789517 1.025591605 0.975532609 0.907888074 0.869571842 0.924434504 0.896255974 0.963683318 0.941593844 1 21.7362143 4.744914041 24.99981345 0.939549255 0.463789305 0.9085713 0.045761406 202.0694203 795092.9392 0.011223117 0.105584511 55579.42389 -4.744914041 -0.47575995 FLSPQDTFEALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLSPQDTFEALKR 13 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 190.27 7.30E-06 201850000 260060 218040 283350 208340 343420 351390 315510 260450 282090 269250 FALSE TRUE 270327.3696 255486.6739 290734.3338 249549.0302 285045.5911 269784.9979 290779.5018 256959.0938 271937.636 322004.3824 0.839514567 0.793426077 0.902889369 0.774986441 0.885222707 0.837830205 0.903029641 0.797998747 0.844515326 1 18.2967208 0.925127507 21.93662145 1 0.840973675 0.553114999 0.042563384 11285.75722 3306577.139 0.037363123 0.009340781 8.416422086 -0.925127507 -0.159026326 FLSPVVPNYDNVHPNYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSPVVPNYDNVHPNYHK 18 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 123.97 1.90E-05 787680000 1314660 1084950 1403520 1499740 1629670 1779740 1781860 1520140 1498840 1066400 FALSE TRUE 1366563.792 1271281.723 1440096.884 1796384.096 1352659.276 1366422.357 1642193.157 1499765.01 1444897.041 1275340.663 1.071528441 0.996817368 1.129186049 1.408552357 1.060625851 1.071417541 1.28765059 1.175972079 1.132949873 1 20.28245123 4.054594688 6.900682637 1.176620965 1.039039658 0.159864657 0.112538585 0.320590605 31.91591602 0.027331505 0.059587795 11339.52043 -4.054594688 -0.137581307 FLSPVVPNYDNVHPNYHKEPFLQQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLSPVVPNYDNVHPNYHKEPFLQQLK 26 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 89.946 0.0069729 335110000 229540 170230 223030 189100 283750 260560 229750 215480 268610 209470 FALSE TRUE 238602.4164 199465.6783 228842.345 226503.4156 235518.2764 200048.8888 211741.5947 212591.8431 258942.7786 250511.636 0.952460414 0.796233187 0.913499863 0.904163253 0.940149049 0.798561265 0.845236565 0.848630612 1.033655693 1 17.93451809 1.237098182 24.99991076 1.016827914 0.871569057 0.544893662 0.051825447 27.62906037 472230.5468 0.040647164 0.012258513 17.262281 -1.237098182 -0.145258857 FLSQIESDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FLSQIESDR 9 0 P19367-4;P19367-2;P19367;P19367-3;Q2TB90 P19367-4;Q2TB90 HK1;HKDC1 Hexokinase-1;Putative hexokinase HKDC1 0 ;;;;; 177.91 0.00011997 1248288000 1033070 1161980 1102670 1255330 1114320 1311110 1161870 1073640 909915 798402 FALSE TRUE 1073856.401 1361541.026 1131406.486 1503630.527 924908.2844 1006624.573 1070799.593 1059249.612 877167.3369 954833.5856 1.124652942 1.425945889 1.184925314 1.574756638 0.968659145 1.054240852 1.121451538 1.109355209 0.918659911 1 19.86488979 3.213344164 24.99983492 1.046677507 1.324408285 0.560418885 0.129063213 165.9554881 164529.4308 0.035158027 0.042037196 1634.3466 -3.213344164 0.277730778 FLSQIESDRLALLQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSQIESDRLALLQVR 16 1 P19367-4;P19367-2;P19367;P19367-3;Q2TB90 P19367-4;Q2TB90 HK1;HKDC1 Hexokinase-1;Putative hexokinase HKDC1 0 ; 141.55 1.45E-06 355160000 315380 291280 334360 181691 423690 386230 238220 313240 313740 391020 FALSE TRUE 327831.4459 341305.0742 343073.6963 217628.9375 351671.3251 296533.9359 219547.6939 309041.5302 302448.5587 467632.8825 0.701044469 0.729856875 0.733638949 0.465384163 0.752024373 0.634116947 0.469487288 0.660863557 0.646764952 1 18.83501685 -1.283517752 5.344969159 1.000053255 0.640304329 0.550593705 0.096529774 6.03E-05 8.09E-06 0.092042476 0.021691417 0.052057373 1.283517752 -0.359748926 FLSQLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLSQLLER 8 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ; 80.755 0.057296 61978000 115149 163854 154777 148045 183667 201296 139462 160960 140668 202086 FALSE TRUE 119695.1714 191994.6499 158810.6158 177327.8591 152447.3489 154548.0547 128530.604 158802.5945 135605.3862 241680.8825 0.495261231 0.794413889 0.657108722 0.733727291 0.630779511 0.639471575 0.531819491 0.657075532 0.56109273 1 17.88274383 -1.9675618 2.886514608 1.291117162 0.638838027 0.626158055 0.084882968 39165580.31 36151996.93 76556240.13 0.02006645 0.010775519 1.9675618 -0.652279135 FLSQPFQVAEVFTGHMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLSQPFQVAEVFTGHMGK 18 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 269.16 1.13E-31 371630000 663190 808210 708060 769550 674790 1031000 822550 650600 687850 687510 FALSE TRUE 689373.2533 947013.7805 726512.6253 921764.6931 560089.4368 791565.875 758076.3817 641879.7712 663094.4129 822214.4213 0.838434884 1.151784444 0.883604819 1.121075804 0.681196319 0.962724387 0.921993536 0.780671993 0.806473829 1 19.64915515 3.251159396 24.99973984 0.85257156 1.001434895 0.234155015 0.12358163 303.8608514 602947.0626 0.031885511 0.04288937 1783.033063 -3.251159396 0.148863334 FLTAFLVQISAHSDQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLTAFLVQISAHSDQNK 17 0 Q07960 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 125.45 4.69E-05 143454000 121096 83852 127940 104763 140502 159829 147000 134248 142412 93569 FALSE TRUE 125876.9636 98252.92872 131274.2215 125484.8087 116619.5202 122711.137 135477.7559 132448.6251 137286.6199 111902.0541 1.124885192 0.878026141 1.173117175 1.121380745 1.042157101 1.096594142 1.210681582 1.183612099 1.226846291 1 16.77187699 2.395408961 5.329912852 1.172850362 1.066412733 0.151290319 0.093974889 0.308577707 14.97599321 0.031879729 0.026544929 248.5472491 -2.395408961 -0.106437629 FLVHNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLVHNVK 7 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 99.919 0.010175 3298900000 5882100 4534000 5389200 4452200 6526700 6769700 6047700 5410000 6207700 4755100 FALSE TRUE 6114329.85 5312679.23 5529646.979 5332831.872 5417293.865 5197539.771 5573665.471 5337487.799 5984286.09 5686770.803 1.075184857 0.934217224 0.972370291 0.937760999 0.952613364 0.913970327 0.980110798 0.938579729 1.052317088 1 22.43917823 1.24130573 24.99998454 1.026158552 0.959480959 0.24761187 0.043603805 83.20900228 757848.958 0.030072002 0.009880957 17.43033485 -1.24130573 -0.066677592 FLVYVANFDEKDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLVYVANFDEKDPR 14 1 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 98.105 0.0024715 6699100000 6985300 4825500 6335500 5452300 7873700 7822400 7886500 6536400 6937300 4216800 FALSE TRUE 7261085.038 5654242.088 6500608.335 6530748.667 6535331.286 6005766.15 7268335.522 6448790.249 6687627.928 5043001.224 1.439834082 1.121205773 1.289035645 1.29501231 1.295921019 1.190911103 1.441271814 1.278760397 1.326120623 1 22.26585114 -1.49549955 3.022421284 0.991220956 1.294030913 0.484311068 0.092050583 32230139.71 37455866.89 2351512.914 0.020508441 0.031952177 1.49549955 0.302809957 FLYDDNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FLYDDNQR 8 0 Q02880;Q02880-2;E9PCY5;P11388;P11388-2;P11388-3;P11388-4 Q02880;P11388 TOP2B;TOP2A DNA topoisomerase 2-beta;DNA topoisomerase 2;DNA topoisomerase 2-alpha 0 ; 130.64 0.0024179 619910000 518060 625400 632330 596590 772800 760110 759540 584360 554420 572670 FALSE TRUE 538513.4088 732807.5851 648809.0393 714593.7214 641439.732 583585.9721 700005.2701 576527.61 534466.5325 684873.7221 0.786295913 1.069989345 0.94734112 1.04339486 0.936581024 0.852107408 1.022093924 0.84180133 0.780386975 1 19.38547848 2.997110206 24.93624115 0.895775074 0.97114813 0.080971682 0.09730366 246.4525595 2126687.361 0.027197118 0.031939792 993.3680916 -2.997110206 0.075373057 FLYQLHETEKEDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FLYQLHETEKEDLIR 15 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 124.7 5.71E-05 124960000 173810 160710 167600 168470 217740 215470 176670 189130 169870 132440 FALSE TRUE 180672.153 188310.6923 171967.7937 201792.8632 180728.6326 165430.358 162822.1438 186595.0217 163756.4119 158389.0823 1.140685648 1.188912074 1.085730097 1.274032656 1.141042236 1.044455562 1.027988428 1.178080074 1.033886992 1 17.27311337 2.921469334 5.884311528 1.075351963 1.171977408 0.416813313 0.063506672 0.261925613 15.29419246 0.019481052 0.020853125 834.5826156 -2.921469334 0.096625445 FMADCPHTIGVEFGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMADCPHTIGVEFGTR 16 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 69.805 0.034277 109690000 95998 95563 104970 115070 108390 141920 118640 108800 118690 89725 FALSE TRUE 99788.07517 111975.2019 107705.6044 137830.5026 89965.90652 108961.2308 109340.6868 107341.714 114418.3701 107304.8959 0.929948949 1.043523699 1.003734299 1.284475433 0.838413809 1.015435782 1.018972023 1.000343117 1.066292168 1 16.71135638 FMEQS(ph)RSPS(ph)VSPSKQPVSTSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMEQSRSPSVSPSKQPVSTSSK 22 2 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 FMEQS(0.563)RS(0.437)PS(0.878)VS(0.108)PS(0.013)KQPVSTSSK 105.46 0.00036287 87636000 130600 61107 104800 47075 122310 115200 106200 92192 95846 53919 TRUE FALSE 135756.1888 71601.6519 107531.1741 56386.2945 101519.7899 88446.54587 97875.7665 90956.31704 92396.52118 64483.39571 2.10528908 1.110388979 1.667579272 0.874431222 1.574355519 1.371617374 1.517844484 1.410538574 1.43287307 1 15.9766401 -2.872138089 0.409365747 1.06E-53 1.443931139 0.161980154 0.308406446 210.0398022 7.532079678 183.8271477 0.168934023 0.001342338 2.872138089 1.443931139 FMEQSRS(ph)PS(ph)VSPSKQPVSTSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMEQSRSPSVSPSKQPVSTSSK 22 2 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 2 FMEQS(0.111)RS(0.888)PS(0.888)VS(0.112)PSKQPVSTSSK 104.3 0.00038906 81095000 188690 86434 156700 76378 204910 199300 162200 143200 175860 90067 TRUE FALSE 196139.6269 101278.3671 160783.7307 91485.34043 170079.4714 153015.5954 149486.3402 141280.6382 169530.833 107713.9042 1.820931368 0.940253423 1.492692442 0.849336407 1.578992727 1.42057422 1.387809134 1.311628608 1.573899249 1 16.71684497 -1.63721627 6.705776778 0.998690335 1.354749644 0.137774719 0.277344553 0.004898436 0.000265007 0.242224194 0.056906092 0.023055988 1.63721627 0.356059309 FMEQSRS(ph)PSVSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FMEQSRSPSVSPSK 14 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 FMEQS(0.001)RS(0.997)PS(0.003)VSPSK;FMEQS(0.038)RS(0.934)PS(0.027)VSPSK 167.14 2.24E-06 638910000 609030 494280 651320 556650 778710 806010 735960 660020 719510 495220 TRUE FALSE 633074.9747 579168.745 668293.9343 666753.7086 646345.1523 618826.3927 678273.5321 651173.5115 693614.9756 592248.8774 1.068934022 0.977914467 1.128400508 1.125799869 1.091340443 1.044875586 1.145250853 1.099493028 1.171154564 1 19.17584403 4.228928784 24.99648464 1.10491898 1.023424237 0.266590253 0.050961277 199.1764395 516906.4997 0.011762086 0.025925862 16940.59985 -4.228928784 -0.081494743 FMERDPDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FMERDPDELR 10 1 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 ;;; 186.87 1.18E-06 1688020000 1174227 1565520 1476600 1364154 1594760 1784870 1392250 1483860 1397040 1651880 FALSE TRUE 1220586.389 1834385.882 1515081.409 1633979.59 1323683.265 1370360.992 1283121.807 1463971.284 1346760.803 1975534.259 0.617851289 0.928551795 0.766922367 0.827107696 0.670038122 0.693666023 0.649506229 0.741050821 0.681719792 1 20.91381143 -1.151126125 3.547829169 1.000244535 0.734511522 0.459012401 0.087616526 22386092.32 36469095.95 65648.94017 0.020842847 0.070611246 1.151126125 -0.265733013 FMFNIADGGFTELHSLWQNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 266.18 1.23E-37 34907000 18237 21774 21462 23013 27234 30578 19247 25337 22638 22989 FALSE TRUE 18957.01084 25513.51512 22021.31735 27564.90271 22604.77441 23476.72291 17738.36985 24997.39896 21823.2628 27493.2544 0.689514983 0.927991818 0.80097165 1.002606032 0.822193476 0.853908474 0.645189892 0.909219352 0.7937679 1 14.74679007 FMGVQMETFMLHYQDLLQLQYEGVAVMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMGVQMETFMLHYQDLLQLQYEGVAVMK 28 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 131.7 1.59E-05 12470000 5087.6 6416.5 7956.6 5887.4 7258.7 8881.9 10752 7001.6 9486.8 5152.5 FALSE TRUE 5288.462376 7518.483962 8163.955532 7051.910148 6024.868767 6819.213331 9909.230145 6907.755004 9145.371921 6162.033724 0.858233274 1.220130285 1.324880047 1.14441278 0.97774031 1.106649791 1.60811034 1.121018695 1.484148307 1 12.58919086 DHNVGSPPKS(ph)PTHASPQHTQTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 DHNVGSPPKSPTHASPQHTQTEK 23 1 A0A0C4DGH6;A0JNW5;F8W665;A0JNW5-2 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 DHNVGSPPKS(0.97)PT(0.03)HASPQHTQTEK;DHNVGSPPKS(0.998)PT(0.002)HASPQHTQTEK 291.25 7.96E-62 387270000 31304 101365 135113 126255 163034 203900 201780 175907 153492 93911 TRUE FALSE 32539.90609 118773.6502 138634.1558 151227.8622 135321.5389 156547.3151 185963.9563 173549.2544 147967.8529 112311.0624 0.289730196 1.057541864 1.234376675 1.346509052 1.204881656 1.393872623 1.65579376 1.54525521 1.317482443 1 16.77714051 4.704961909 1.556642504 1.393755262 4.79E-25 0.764100473 0.174423797 0.47072758 1.130305044 0.048142066 0.983385958 50694.62428 -4.704961909 -1.393755262 down FMLQDVLDLR ddPTM_MDA-MB-175_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 ; 134.68 0.00038235 332260000 445550 531450 593490 561470 634280 733830 580170 547010 585520 585850 FALSE TRUE 463140.658 622722.4034 608956.837 672527.0902 526465.3122 563409.1038 534694.7594 539678.2257 564447.2496 700636.0907 0.661028834 0.888795784 0.869148542 0.959880741 0.751410496 0.804139426 0.763156175 0.77026895 0.805621145 1 19.41830578 FMQASEDLLKEHYVDLK ddPTM_MDA-MB-175_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 ; 183.56 4.11E-10 1019720000 1621020 1043490 1504790 741420 2604750 1839190 1099860 1339600 1898900 1394030 FALSE TRUE 1685019.121 1222701.29 1544006.064 888070.6631 2161995.525 1412065.996 1013650.099 1321644.853 1830558.96 1667163.488 1.010710187 0.733402152 0.926127566 0.532683609 1.296810745 0.846987117 0.608008816 0.792750599 1.098008068 1 20.66896416 1.239855299 24.9980645 1.04900409 0.833737262 0.139449594 0.203126685 61.18530222 1181587.853 0.149847311 0.047876782 17.37221915 -1.239855299 -0.215266829 FMQDPMEIFVDDETKLTLHGLQQYYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FMQDPMEIFVDDETKLTLHGLQQYYVK 27 1 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;H0YCC6 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 206.46 1.65E-25 82050000 125760 87194 122180 85908 164930 133860 130190 105130 120630 87886 FALSE TRUE 130725.1019 102168.8912 125364.1112 102900.346 136895.2575 102773.0437 119985.3676 103720.9043 116288.5499 105105.579 1.243750362 0.972059639 1.192744594 0.979018877 1.30245472 0.977807692 1.141569922 0.986825869 1.1063975 1 16.68147972 FMSVQRPGPYDRPGTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FMSVQRPGPYDRPGTAR 17 2 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 225.13 1.40E-15 7450800000 1749780 2022910 2112680 1937790 2315480 2367230 1939410 2096850 1838640 2152710 FALSE TRUE 1818862.666 2370329.056 2167738.176 2321079.078 1921895.537 1817476.708 1787393.976 2068745.156 1772467.706 2574492.308 0.706493727 0.920697665 0.84200608 0.901567688 0.746514383 0.705955385 0.694270467 0.803554607 0.688472714 1 21.29585653 5.038022616 15.09129483 0.799518498 0.35784032 0.077973366 0.1010369 1546734.102 18243657.13 0.023806665 18182469.29 109149.7175 -5.038022616 -0.441678178 FNADEFEDMVAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FNADEFEDMVAEK 13 0 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;; 186.58 1.79E-05 511492000 711519 515623 680997 604123 841671 823970 942443 731842 764577 464550 FALSE TRUE 739610.3195 604177.2393 698744.3413 723616.7263 698604.0641 632615.4549 868571.855 722032.855 737060.0231 555569.6782 1.331264734 1.087491386 1.257707842 1.302476997 1.25745535 1.138678873 1.563389597 1.299626102 1.326674317 1 19.08360834 4.008369465 24.75578104 1.293406167 1.200183442 0.007324462 0.146738124 489.3650772 1447446.288 0.034771983 0.074923869 10194.58297 -4.008369465 -0.093222725 FNADEFEDMVAEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 FNADEFEDMVAEKR 14 1 P27635;X1WI28;A0A087WV22;F8W7C6 P27635;F8W7C6 RPL10 60S ribosomal protein L10 0 ;;;;;;;;; 231.23 9.92E-13 5724658000 2690488 2434255 2894501 2068440 3705096 3439296 3017508 2775755 3146345 2542663 FALSE TRUE 2796710.544 2852319.36 2969934.074 2477571.258 3075305.105 2640571.627 2780987.838 2738550.544 3033108.658 3040849.133 0.919713679 0.938000945 0.976679192 0.814762966 1.011331037 0.868366536 0.914543181 0.900587443 0.997454502 1 21.53604281 1.230504272 24.75598001 0.998727339 0.917618485 0.286248235 0.050988049 204.6521023 628838.01 0.041850647 0.011202299 17.00216678 -1.230504272 -0.081108853 FNAHGDANTIVCNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FNAHGDANTIVCNSK 15 0 P09382 P09382 LGALS1 Galectin-1 0 ;;; 222.42 1.40E-12 3340890000 3461150 3131680 3351720 3115800 4430300 4704050 4126350 3731640 3757140 3048750 FALSE TRUE 3597798.875 3669521.679 3439068.577 3732095.94 3677239.188 3611605.678 3802915.905 3681623.47 3621921.265 3646094.191 0.986754232 1.006425366 0.943219894 1.023587364 1.008542017 0.99054097 1.043010878 1.009744476 0.993370186 1 21.7979204 3.691339819 24.9994124 1.011321085 0.981562221 0.322709781 0.020401957 456.0260231 241426.867 0.005266309 0.008158541 4912.921439 -3.691339819 -0.029758864 FNAHHGDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNAHHGDTK 9 0 P53602 P53602 MVD Diphosphomevalonate decarboxylase 0 ; 142.36 6.04E-05 213811000 404130 277551 352550 285914 433650 440680 437140 332842 379960 241394 FALSE TRUE 420085.3645 325218.2252 361737.7426 342466.9358 359938.3279 338338.7486 402875.8245 328380.7974 366285.3138 288690.5325 1.455140772 1.12652889 1.253029462 1.18627699 1.246796439 1.171977292 1.395528357 1.137483777 1.26878187 1 18.13916427 -3.772576334 0.341003148 1.58E-08 1.249931395 0.353813898 0.100885388 167.4670189 3.149780906 119.099824 0.07345731 0.00016882 3.772576334 1.249931379 FNDEHIPESPYLVPVIAPSDDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;;;;;;; 168.65 9.40E-12 6048850000 4410340 5241620 5153550 5058130 5930040 6781160 5780000 5686250 5448910 4928780 FALSE TRUE 4584463.629 6141827.461 5287855.747 6058613.017 4922053.919 5206338.359 5326948.497 5610035.12 5252804.793 5894480.074 0.777755387 1.041962545 0.897086033 1.027845194 0.835027663 0.883256588 0.903718128 0.951743843 0.89113963 1 22.49093313 -1.553505378 5.769723878 1.000217549 0.918019996 0.103133264 0.075958106 0.000193985 1.50E-05 0.067118437 0.015778227 0.027957261 1.553505378 -0.082197553 FNDEHIPESPYLVPVIAPSDDARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNDEHIPESPYLVPVIAPSDDARR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ; 139.46 2.02E-07 166935000 118021 113248 109488 74637 143277 142737 81890 100432 113691 122642 FALSE TRUE 122680.5602 132697.4631 112341.3472 89399.97583 118922.8267 109588.495 75471.24782 99085.87331 109599.2831 146671.3518 0.836431646 0.904726529 0.765939264 0.609525819 0.810811554 0.747170416 0.514560253 0.67556392 0.74724397 1 17.16222758 4.059831733 5.012225696 0.703898371 0.867505323 0.148718041 0.122864978 0.275943635 14.04600072 0.029626623 0.066009709 11477.08858 -4.059831733 0.163606952 FNDFDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FNDFDHR 7 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;;; 141.39 0.0025601 737180000 1295140 1527930 1500240 1388790 1701700 1835480 1563960 1552950 1504760 1345260 FALSE TRUE 1346273.127 1790340.092 1539337.487 1663488.517 1412445.642 1409217.587 1441372.729 1532135.245 1450603.982 1608837.94 0.83679847 1.112815683 0.956800836 1.033968975 0.877929098 0.875922647 0.89590921 0.952324163 0.901647049 1 20.61758758 3.236095009 24.99983256 0.914172426 0.992197744 0.166897623 0.073337844 97.60415276 989652.4458 0.019505593 0.024371586 1722.245303 -3.236095009 0.078025318 FNDILGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 152.47 0.0042143 181553000 339480 389830 393000 367410 445020 490510 392770 400400 391540 378730 FALSE TRUE 352882.9325 456780.27 403241.9029 440082.6014 369375.6594 376596.4863 361983.6611 395033.2929 377448.5519 452934.8923 0.779102998 1.008489913 0.890286683 0.971624419 0.815516017 0.831458324 0.799195794 0.872163526 0.833339534 1 18.78894416 3.22765763 24.9992863 0.84844002 0.91766348 0.095642733 0.076595269 367.1442522 841817.7729 0.020322895 0.024510973 1689.108822 -3.22765763 0.06922346 FNDS(ph)EGDDT(ph)EETEDYR ddPTM_MDA-MB-175_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 271.43 2.00E-34 605570000 617080 555310 614680 564260 632120 831940 679720 612480 630520 482690 TRUE FALSE 641442.7949 650680.1728 630699.0658 675868.9439 524672.4682 638734.5432 626441.7703 604270.7074 607827.7084 577263.8638 1.111177808 1.127179811 1.092566338 1.170814572 0.908895396 1.106486276 1.085191382 1.046784227 1.052946055 1 19.13887139 8 0.136390185 0.99428709 1.459777262 0.216619172 0.061882829 120.8158674 1.103128427 0.274248333 10.91975948 100000000 -8 0.465490171 FNDS(ph)EGDDTEETEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.961)EGDDT(0.039)EETEDYR;FNDS(0.999)EGDDT(0.001)EETEDYR;FNDS(1)EGDDTEETEDYR;FNDS(0.993)EGDDT(0.007)EETEDYR 439.63 7.03E-182 6498910000 1413914 1344905 1462916 1289401 1691057 1843520 1659552 1477128 1407377 1081780 TRUE FALSE 1469736.416 1575881.972 1501040.793 1544440.669 1403611.735 1415390.419 1529471.978 1457329.515 1356725.777 1293734.079 1.136042128 1.218088012 1.160239045 1.193785256 1.084930634 1.094035043 1.182215111 1.126452135 1.048689834 1 20.30310968 -0.030454512 0.204192747 0.91811771 1.202351633 0.60176138 0.040919733 6.664555494 0.509987473 0.499750412 0.139021776 0.932278113 0.030454512 0.284233923 FNDS(ph)EGDDTEETEDYRQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 246.32 7.26E-25 274600000 83529 120110 125180 59336 156250 144930 67728 90551 115030 203170 TRUE FALSE 86826.78942 140737.9582 128442.2936 71072.4837 129690.6808 111272.2039 62419.30239 89337.31196 110890.0928 242977.2716 0.357345314 0.579222728 0.528618553 0.292506716 0.533756429 0.457953138 0.256893585 0.367677649 0.456380517 1 17.89046184 0.941451546 20.02029072 1.000000001 0.419849824 0.74675121 0.100526957 837.353974 286329.4637 0.099730607 0.024932605 8.738794893 -0.941451546 -0.580150177 FNEEHIPDSPFVVPVAS(ph)PSGDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDSPFVVPVAS(0.742)PS(0.258)GDAR;FNEEHIPDSPFVVPVAS(0.831)PS(0.169)GDAR;FNEEHIPDSPFVVPVAS(0.935)PS(0.065)GDAR;FNEEHIPDSPFVVPVAS(0.882)PS(0.118)GDAR;FNEEHIPDSPFVVPVAS(0.942)PS(0.058)GDAR 178.11 3.39E-17 1779150000 970358 1105241 1150936 1069915 1237068 1400406 1233934 1190072 1154558 1022405 TRUE FALSE 1008668.483 1295057.544 1180930.338 1281540.994 1026791.623 1075182.93 1137215.029 1174121.031 1113005.683 1222725.685 0.824934403 1.059156244 0.965817887 1.048101802 0.839756322 0.879332906 0.930065544 0.960248931 0.910266053 1 20.22166934 4.78998229 22.49843231 0.950204891 0.824932051 0.256163521 0.065955163 21742.87882 9512139.247 0.015966842 13.50969737 61656.98582 -4.78998229 -0.12527284 FNEEHIPDSPFVVPVAS(ph)PSGDARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FNEEHIPDSPFVVPVASPSGDARR 24 1 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 FNEEHIPDS(0.001)PFVVPVAS(0.807)PS(0.192)GDARR 75.174 0.011598 43647000 11321 14957 14289 10605 14157 17619 11095 13997 14636 17292 TRUE FALSE 11767.96182 17525.7484 14661.38308 12702.63735 11750.5982 13527.25427 10225.34491 13809.39311 14109.25322 20680.03632 0.569049379 0.847471838 0.70896312 0.614246375 0.568209746 0.654121398 0.494454881 0.667764451 0.682264431 1 14.3359511 0.649046139 2.361401437 0.999941542 0.641360715 0.587489072 0.089840613 1.765608495 10.98093062 0.088223594 0.023734887 4.457035967 -0.649046139 -0.358580827 FNEEHIPDSPFVVPVASPSGDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 ;;;;; 177.6 5.41E-17 2163270000 1054900 1281030 1232590 1147630 1419630 1626990 1347580 1301160 1318860 1247110 FALSE TRUE 1096548.267 1501036.937 1264712.308 1374627.789 1178321.8 1249146.23 1241953.158 1283720.078 1271394.486 1491457.327 0.735219337 1.006422987 0.84797083 0.921667529 0.790047277 0.837534006 0.832711158 0.860715258 0.852451132 1 20.50829127 -1.134689689 3.976406599 1.000046938 0.857186557 0.289547478 0.068496764 62750.8363 33319926.8 3465.457184 0.014721335 0.073334834 1.134689689 -0.142860381 FNEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FNEGER 6 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 139.27 0.02779 14201980000 5888710 6817920 6819070 6555970 7540830 8368790 7109050 6956190 6571760 6028680 FALSE TRUE 6121200.818 7988844.724 6996780.566 7852721.298 6259042.41 6425265.353 6551824.085 6862953.651 6335243.641 7209884.42 0.849001241 1.108040609 0.97044282 1.089160497 0.86811966 0.891174529 0.908728033 0.95188123 0.878688655 1 22.7815447 3.225799111 24.99999447 0.914988456 1.009172795 0.246769776 0.074857557 283.6450485 555664.1662 0.02007164 0.024139568 1681.895897 -3.225799111 0.094184339 FNENNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FNENNRR 7 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;;; 133.55 0.0054568 3398700000 1081749 1624390 1367327 1362745 1530011 1878660 1258141 1303868 1353866 1837530 FALSE TRUE 1124457.286 1903366.346 1402960.665 1632291.894 1269940.277 1442369.686 1159524.621 1286391.782 1305140.627 2197558.822 0.511684727 0.866127599 0.638417798 0.742775064 0.577886819 0.656350889 0.527642132 0.585373083 0.593904752 1 21.06747035 -0.938751082 4.565374969 1.000004829 0.634359518 0.548377396 0.099816629 10973150.92 4807119.677 541.2615266 0.022968372 0.115146017 0.938751082 -0.365645311 FNEVAAQYSEDKAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNEVAAQYSEDKAR 14 1 Q9Y237;Q9Y237-2;H0Y4T6;J3KMW3;H0Y610;H0Y8P6;A0A494C021;Q9Y237-3 Q9Y237 PIN4 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 0 ; 169.37 3.05E-06 527050000 238310 188429 227708 164737 345540 289460 243440 242660 284420 233767 FALSE TRUE 247718.6628 220790.215 233642.2575 197321.4869 286805.2342 222237.3018 224358.5367 239407.5396 274183.7798 279569.1679 0.886072898 0.789751662 0.835722549 0.705805609 1.02588292 0.794927794 0.802515307 0.856344573 0.980736831 1 18.09284574 1.245961326 3.664963193 0.999616568 0.833383433 0.386823212 0.077764222 0.21554181 5.379889972 0.064621768 0.018771906 17.6181915 -1.245961326 -0.166233135 FNEYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNEYWR 6 0 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 116.11 0.05549 1900910000 1139280 1763900 1550010 1887350 1685870 2093110 1887280 1599010 1457970 1471800 FALSE TRUE 1184259.654 2066836.104 1590404.534 2260662.197 1399306.42 1607016.924 1739350.062 1577577.886 1405497.944 1760171.031 0.672809422 1.174224588 0.903551136 1.284342349 0.794983212 0.912989077 0.988171054 0.896263976 0.798500782 1 20.74728419 FNFESFPES(ph)PGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FNFESFPESPGEK 13 0 H0YBR0;Q96Q05-3;Q96Q05;Q96Q05-2 H0YBR0 TRAPPC9 Trafficking protein particle complex subunit 9 1 FNFESFPES(1)PGEK 187 3.18E-07 0 115950 65179 78268 81435 100360 126520 145860 80332 93402 47179 TRUE FALSE 120527.7955 76372.98623 80307.72838 97542.59994 83300.84305 97137.64743 134427.1121 79255.28094 90040.48027 56422.82175 2.136153276 1.353583246 1.42331996 1.728779187 1.476367903 1.721602082 2.382495378 1.404667092 1.595816683 1 15.7839912 FNFLNPNDPYHAYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNFLNPNDPYHAYYR 15 0 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 ; 176.75 7.81E-07 1796170000 695990 834220 840360 795920 919230 1010620 917870 813930 736720 837440 FALSE TRUE 723468.2226 977490.7957 862260.472 953350.6004 762979.6129 775918.8211 845924.951 803020.5997 710205.5911 1001520.334 0.722369979 0.976006939 0.860951538 0.951903389 0.76182139 0.774740956 0.844640815 0.801801593 0.70912748 1 19.93376028 3.22725535 24.99766819 0.805572862 0.883618153 0.086624734 0.095510355 416.2980062 920496.7831 0.025537925 0.030784886 1687.544953 -3.22725535 0.078045291 FNGGHS(ph)PTHSPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.776)PT(0.222)HS(0.003)PEK;FNGGHS(0.948)PT(0.052)HSPEK 129.36 9.96E-05 2076810000 734800 570020 753860 604490 1022320 970000 864870 825490 793530 617560 TRUE FALSE 763810.4714 667916.5009 773506.2109 724056.3178 848546.4116 744732.2005 797079.2295 814425.6568 764971.0103 738559.0581 1.034190107 0.904350835 1.047318021 0.980363466 1.148921542 1.00835836 1.079235602 1.102722454 1.035761463 1 19.49435376 3.289760915 24.99999492 1.068591956 0.989309544 0.284152102 0.054606865 115.1563769 56227.44536 0.014146415 0.019154315 1948.77148 -3.289760915 -0.079282412 FNGGHSPT(ph)HSPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 FNGGHS(0.131)PT(0.863)HS(0.005)PEK;FNGGHS(0.126)PT(0.874)HSPEK 152.68 0.00016682 1954210000 1264730 1083180 1374830 1035180 1744300 1793320 1510690 1421790 1433730 1095350 TRUE FALSE 1314662.517 1269207.739 1410659.199 1239935.514 1447804.509 1376848.608 1392278.17 1402733.231 1382130.337 1309962.861 1.003587626 0.968888338 1.076869613 0.946542495 1.105225615 1.05105927 1.062837896 1.070819084 1.055091239 1 20.32109448 3.231236666 24.99999977 1.061702864 1.002387296 0.339048365 0.039664541 177.5581881 606087.3913 0.010533127 0.012833311 1703.08634 -3.231236666 -0.059315568 FNGS(ph)TEALDKLDADAVSPTVSQLSAVFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.838)T(0.162)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.5)T(0.5)EALDKLDADAVSPTVSQLSAVFEK;FNGS(0.964)T(0.036)EALDKLDADAVSPTVSQLSAVFEK 193.13 1.04E-18 2279325000 1877312 919079 1463833 849964 2003898 1739520 1798326 1421095 1637227 774578 TRUE FALSE 1951429.727 1076923.669 1501981.691 1018084.342 1663276.134 1335542.843 1657368.509 1402047.546 1578303.52 926341.7289 2.106598101 1.162555497 1.621412103 1.099037548 1.79553191 1.441738832 1.789154539 1.513531672 1.70380268 1 19.82118498 -1.494111297 4.268418813 0.996095277 1.563553487 0.269614936 0.28575167 0.009564786 0.001133608 0.249231014 0.058427143 0.032054478 1.494111297 0.56745821 FNGST(ph)EALDKLDADAVSPTVSQLSAVFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FNGSTEALDKLDADAVSPTVSQLSAVFEK 29 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 FNGS(0.375)T(0.625)EALDKLDADAVSPTVSQLSAVFEK 299.13 9.64E-81 1811800000 707540 339910 510520 307960 659480 582380 619810 456140 551170 251980 TRUE FALSE 735474.2255 398286.8984 523824.5706 368873.5688 547381.8252 447131.0711 571227.6726 450026.1894 531333.4994 301350.6566 2.440592743 1.321672575 1.738255946 1.22406758 1.816428182 1.483756751 1.895558082 1.493363892 1.763173525 1 18.20108368 -1.988554605 2.577628193 0.385291059 1.658098213 0.280255803 0.327156919 5115320.13 2177162.228 18688507.29 0.070618986 0.010267043 1.988554605 1.272807154 FNHDGEEEEEDDDYGSR ddPTM_MDA-MB-175_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 ; 255.19 4.64E-27 496860000 178523 199882 201318 201642 232900 258610 205644 207460 202805 182951 FALSE TRUE 185571.2259 234210.1786 206564.5125 241526.1858 193311.7412 198551.7468 189525.0859 204679.338 195506.0877 218796.7456 0.84814436 1.070446354 0.944093167 1.103883813 0.883522013 0.907471207 0.866215287 0.935477068 0.893551168 1 17.73923175 FNHPEIVQLVSELEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNHPEIVQLVSELEAER 17 0 Q7Z4H3-2;Q7Z4H3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 ; 132.79 2.24E-05 73294000 112017 128487 115394 122552 137939 151350 133528 132779 120737 117137 FALSE TRUE 116439.5177 150553.6428 118401.2624 146792.4198 114492.1781 116201.2562 123061.7264 130999.3147 116391.699 140087.7524 0.831189848 1.074709531 0.845193533 1.047860482 0.817288993 0.829489047 0.878461709 0.935123253 0.8308485 1 17.0959713 5.076605204 13.12522982 0.913282949 7.91E-05 0.074850876 0.090026045 730265.2007 3207269.275 0.020299377 17872852.74 119290.3201 -5.076605204 -0.913203851 FNHWELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 126.67 0.0039297 3344600000 6267300 5008200 6019500 5099800 7463500 7569600 6814000 5967300 6215000 4219700 FALSE TRUE 6514737.843 5868319.392 6176373.115 6108525.219 6194856.936 5811675.118 6279900.875 5887318.104 5991323.364 5046469.424 1.290949632 1.162856425 1.223899839 1.210455212 1.227562562 1.15163189 1.244414728 1.166621178 1.187230688 1 22.26684298 -4.814060695 0.228226771 3.27E-16 1.229368371 0.746315504 0.037310871 65.65396852 0.710664862 30.21030271 0.059379212 1.53E-05 4.814060695 1.229368371 FNIDMPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FNIDMPHR 8 0 Q05655;Q05655-2;A0A494C1T7 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ;;; 93.551 0.0083352 493760000 415488 587123 539791 565397 698627 744656 593713 536609 552424 622303 FALSE TRUE 431891.7871 687956.8081 553858.3969 677230.8391 579874.6321 571720.9294 547176.2237 529416.6341 532542.3682 744231.3581 0.580319255 0.924385677 0.744201908 0.909973534 0.779159096 0.768203225 0.735223285 0.711360289 0.715560239 1 19.50539165 3.004083659 24.96739361 0.760981943 0.802147566 0 0.118955799 550.9808646 3368638.286 0.032020912 0.038131974 1009.447318 -3.004083659 0.041165623 FNLTYVSHDGDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNLTYVSHDGDDK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 119.77 0.00032223 1055060000 378200 241813 290510 274350 433710 435880 396290 341860 352090 186809 FALSE TRUE 393131.628 283342.5017 298080.9293 328615.6111 359988.1291 334653.4758 365227.7543 337277.9259 339418.3497 223410.6469 1.759681705 1.268258723 1.334228845 1.470903987 1.611329335 1.497929846 1.634782225 1.509677048 1.519257719 1 17.76933842 -1.232017208 6.311248409 0.999992797 1.506310139 0.567408668 0.133983024 1.34E-05 1.63E-06 0.127843385 0.030132547 0.058611494 1.232017208 0.506317341 FNNDSHS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNNDSHSPK 9 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 FNNDSHS(1)PK;FNNDSHS(1)PK 117.2 0.00076662 756750000 1867860 944500 1123600 869300 1753860 1978790 1654390 1221820 1344750 670880 TRUE FALSE 1941604.555 1106710.528 1152881.939 1041244.945 1455739.504 1519246.011 1524714.589 1205443.501 1296352.71 802326.0912 2.419969357 1.379377462 1.436924402 1.29778273 1.814398808 1.893551796 1.9003677 1.502435873 1.615742931 1 19.61382919 0.514515205 1.255206118 1.000729559 1.69010553 0.312749746 0.3128649 2.459184602 5.014314944 0.296016273 0.08890506 3.269754941 -0.514515205 0.689375971 FNPFVTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FNPFVTSDR 9 0 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;J3KSS0;E5RHH1;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 ;;; 156.35 0.00016551 1952060000 1205580 1402400 1307080 1363860 1536660 1695480 1442600 1351750 1308470 1368900 FALSE TRUE 1253177.229 1643251.291 1341143.579 1633627.437 1275459.082 1301730.465 1329525.242 1333632.002 1261378.42 1637109.746 0.765481503 1.003751456 0.819214217 0.997872892 0.779091985 0.795139403 0.812117359 0.814625901 0.770491058 1 20.64271961 3.204680026 24.99999384 0.816558058 0.898709261 0.110047482 0.090882049 309.5906674 228441.6106 0.023759577 0.02839958 1602.064608 -3.204680026 0.082151203 FNQTYQLAHGTAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNQTYQLAHGTAEEK 15 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 233.78 1.23E-17 481750000 410710 342690 434460 376060 566650 584440 533960 414820 473160 271500 FALSE TRUE 426925.1479 401544.3417 445782.3845 450443.5456 470331.0354 448712.6673 492106.82 409260.0164 456131.064 324695.2268 1.314848857 1.236680766 1.372925586 1.387281082 1.448530796 1.381950304 1.515596102 1.260443587 1.404797565 1 18.30872665 -1.206490171 1.001535836 0.941025914 1.367625098 0.664230766 0.078715566 153.3733381 55.14529839 26.78554896 0.024519425 0.062159832 1.206490171 0.426599184 FNSLNELVDYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FNSLNELVDYHR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 ;; 145.81 6.42E-05 627819000 702330 814710 835440 792410 940960 955130 853530 814980 813630 957190 FALSE TRUE 730058.5307 954630.1049 857212.2527 949146.3329 781015.9553 733315.5326 786628.0883 804056.5261 784347.6152 1144733.054 0.63775439 0.833932506 0.748831572 0.829142069 0.682269069 0.640599597 0.687171638 0.702396531 0.685179494 1 20.12657978 -1.052701884 4.636817822 1.000009864 0.718426506 0.628714419 0.065372478 0.125257309 41340782.99 1028.540705 0.015657144 0.088572339 1.052701884 -0.281583359 FNVLHWHIVDDQSFPYQSITFPELSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNVLHWHIVDDQSFPYQSITFPELSNK 27 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ; 175.48 6.24E-13 522060000 211781 227588 245549 214101 270105 331980 277390 227212 225014 247474 FALSE TRUE 220142.2774 266674.4686 251948.2087 256449.5388 224192.6486 254882.6762 255647.447 224166.5948 216915.7901 295961.7921 0.743819923 0.901043566 0.851286265 0.866495425 0.757505376 0.861201287 0.863785305 0.757417345 0.732918221 1 18.17505141 FNVWDTAGQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNVWDTAGQEK 11 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 196.88 8.97E-05 244270000 719710 489430 624250 511200 772460 788410 772460 627530 645770 464270 FALSE TRUE 748124.7065 573485.7953 640518.4678 612313.8342 641157.5251 605313.726 711912.5668 619118.9868 622528.8638 555234.8175 1.347402366 1.032870737 1.153599248 1.10280158 1.154750215 1.090194107 1.282182861 1.115057931 1.121199255 1 19.08273851 0.793461675 1.924675019 1.000484803 1.155562287 0.233185056 0.087371079 1.068026515 6.81035304 0.076314074 0.021263482 6.215293972 -0.793461675 0.155077484 KFDHES(ph)SPGTDEDKSG ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFDHESSPGTDEDKSG 16 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KFDHES(0.499)S(0.499)PGT(0.003)DEDKSG 54.281 0.075377 88308000 23637 38971 54590 41420 63598 65790 55703 59736 61532 43897 TRUE FALSE 24570.20701 45663.9661 56012.66025 49612.75237 52787.63468 50511.26956 51336.85331 58935.33663 59317.47534 52497.77669 0.468023763 0.869826666 1.066952998 0.945044829 1.005521338 0.962160166 0.977886237 1.122625382 1.129904523 1 15.6799687 4.71191025 2.317194248 1.027674585 0.349336654 0.884226721 0.060949758 0.178679736 1.19302767 0.016764603 0.239755507 51512.21801 -4.71191025 -0.678337931 down FPAMSDAYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPAMSDAYDR 10 0 P00491;G3V5M2 P00491 PNP Purine nucleoside phosphorylase 0 81.296 0.049866 201540000 89562 105410 90505 111280 127700 125460 112220 113460 99422 101000 FALSE TRUE 93097.97692 123513.3475 92863.63465 133290.8519 105993.5996 96323.81636 103423.9032 111939.2543 95843.82164 120789.0162 0.770748697 1.022554462 0.768808602 1.103501428 0.877510248 0.797455095 0.856235992 0.926733719 0.793481267 1 16.88212975 3.031064866 24.99995035 0.869893331 0.923075818 0.030291058 0.10994659 656.6238778 528424.4637 0.02967082 0.035463104 1074.149836 -3.031064866 0.053182488 FPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSER 40 3 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 242.42 3.39E-51 255713000 395911 70167 144586 69084 245107 267818 246280 140543 167120 44774 FALSE TRUE 411541.872 82217.63643 148354.0299 82748.609 203443.7997 205621.3283 226975.9301 138659.251 161105.3838 53546.60805 7.685675843 1.535440608 2.770558871 1.545356691 3.799377908 3.840043951 4.238847956 2.589505779 3.008694476 1 15.70850757 4.748213794 24.99450105 2.846201545 7.685678429 0.673292425 1.036942827 797.7691106 2065582.631 0.245437726 3.217126615 56003.32259 -4.748213794 4.839476884 FPDSVEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FPDSVEELR 9 0 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 ; 137.42 0.00038401 251070000 198989 268900 282630 240920 261590 320290 263940 244640 254750 268060 FALSE TRUE 206845.2394 315081.4832 289995.57 288573.2569 217125.0252 245907.5015 243251.6931 241361.001 245581.5973 320581.2247 0.645219443 0.982844468 0.904593119 0.900156449 0.677285532 0.767067696 0.758783342 0.752885641 0.766051092 1 18.29033041 4.816281091 21.50587631 0.817602721 0.645204325 0.216301514 0.103684302 70638.45761 19538701.9 0.025390317 226.9772372 65506.0016 -4.816281091 -0.172398396 FPEFCSSPS(ph)PPVEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FPEFCSSPSPPVEVK 15 0 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 FPEFCS(0.002)S(0.008)PS(0.99)PPVEVK;FPEFCSSPS(1)PPVEVK;FPEFCS(0.036)S(0.098)PS(0.867)PPVEVK 195.38 1.36E-11 165061000 394870 272342 338205 302217 444490 448700 388104 348770 360730 273815 TRUE FALSE 410459.7725 319114.62 347018.9001 361994.6206 368935.7486 344496.2251 357683.3944 344095.3086 347747.3978 327463.8067 1.253450806 0.974503482 1.059716808 1.105449253 1.12664588 1.052013132 1.092283749 1.050788825 1.061941474 1 18.32097593 0.694454923 0.011857992 2.09E-06 2.097302391 0.206829332 0.064781258 2492.870832 14.92488732 1349.766272 1287.740157 4.948287476 -0.694454923 2.097300303 FPEHELTFDPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FPEHELTFDPQR 12 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;; 178.32 2.21E-05 1093610000 678460 867180 773090 833500 986470 1074950 773290 746610 725820 880540 FALSE TRUE 705246.1247 1016111.419 793237.3605 998363.8123 818790.1818 825309.1535 712677.5092 736602.9142 699697.88 1053064.954 0.669708095 0.964908589 0.753265368 0.948055301 0.777530558 0.783721033 0.676765005 0.699484786 0.664439432 1 20.006163 2.746131017 2.513795476 0.731393215 0.837607638 0.031082624 0.121487215 0.560934131 7.022187732 0.038770637 0.038803962 557.3538649 -2.746131017 0.106214423 FPGDQVVNGAGPELSTGPSPGS(ph)PTLDIDQSIEQLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPGDQVVNGAGPELSTGPSPGSPTLDIDQSIEQLNR 36 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 FPGDQVVNGAGPELSTGPS(0.075)PGS(0.453)PT(0.453)LDIDQS(0.02)IEQLNR 236.31 2.31E-49 115120000 23409 25646 27843 23468 27226 35456 22213 27278 20235 28244 TRUE FALSE 24333.2054 30050.501 28568.61145 28109.90036 22598.13424 27221.88134 20471.88702 26912.38303 19506.7463 33777.87104 0.72038896 0.889650534 0.845778925 0.8321987 0.669021864 0.805908736 0.606073929 0.796745982 0.577500763 1 15.04379078 3.26238898 24.75376242 0.730574475 0.828534406 0.09098963 0.118788101 394.7925205 410121.6218 0.02985847 0.040406566 1829.738304 -3.26238898 0.097959931 FPGDQVVNGAGPELSTGPSPGSPT(ph)LDIDQSIEQLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPGDQVVNGAGPELSTGPSPGSPTLDIDQSIEQLNR 36 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 FPGDQVVNGAGPELS(0.005)T(0.013)GPS(0.292)PGS(0.292)PT(0.393)LDIDQS(0.006)IEQLNR 129.25 2.81E-08 66171000 34047 37400 39795 45602 51968 46380 39743 41118 43955 49841 TRUE FALSE 35391.20185 43823.15907 40832.09039 54621.93949 43134.49792 35608.9479 36627.83981 40566.88047 42373.06814 59606.38969 0.593748456 0.735209082 0.685028746 0.91637725 0.723655604 0.597401522 0.614495191 0.680579392 0.710881306 1 15.86317937 -1.87981253 1.633569216 1.193486502 0.695915499 0.516396438 0.088468498 93386.69225 31513.84995 69652.47383 0.025180621 0.013188259 1.87981253 -0.497571003 FPGLALRPS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.626)S(0.374)R;FPGLALRPS(0.5)S(0.5)R 83.204 0.010224 984260000 362247 396389 388565 368001 433331 541135 445970 370802 388302 411299 TRUE FALSE 376548.7913 464465.7273 398691.3231 440790.4994 359673.5514 415464.5972 411013.7061 365832.0057 374327.0869 491885.1643 0.765521749 0.944256426 0.810537402 0.89612481 0.731214473 0.844637382 0.835588743 0.743734579 0.761005035 1 18.90796202 3.266314813 24.99870018 0.804813441 0.85743676 0.021697474 0.084486586 555.9771374 500774.7915 0.021711557 0.029391124 1846.353326 -3.266314813 0.052623318 FPGLALRPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPGLALRPSSR 11 1 B4DF95;Q15735;B5MCL8;B5MBZ3;A0A087WVS7;Q15735-3;Q15735-2 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 FPGLALRPS(0.048)S(0.952)R 90.861 0.0067658 880330000 345890 362130 375180 398640 397020 476550 403280 349310 354810 385200 TRUE FALSE 359546.0043 424323.0105 384957.499 477489.8022 329534.6822 365878.4847 371669.8598 344628.0708 342040.4574 460672.5649 0.78048061 0.921094597 0.835642338 1.036505836 0.715333856 0.794226773 0.806798338 0.748097666 0.742480633 1 18.81338216 3.207892821 24.99684136 0.786158221 0.891279427 0.171757131 0.095887157 284.8222614 232153.3966 0.025720622 0.030745282 1613.9602 -3.207892821 0.105121206 FPGQLNADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 140.11 9.28E-05 1071810000 596355 690160 506926 581693 1104050 932800 674670 585357 578649 1154700 FALSE TRUE 619899.5559 808689.6113 520136.908 696750.1392 916383.9754 716171.3367 621787.6025 577511.2469 557823.5355 1380941.357 0.448896365 0.585607497 0.376653871 0.504547232 0.663593693 0.51861097 0.450263582 0.418201138 0.403944406 1 20.39722062 -1.709139292 7.019459021 1.004673404 0.48557966 0.775844453 0.082950164 0.006322878 0.000261997 0.083707059 0.01966402 0.019537127 1.709139292 -0.519093744 FPGQLNADLRK ddPTM_MDA-MB-175_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 ; 93.839 0.014351 5543500000 761690 610060 686660 496780 1061050 914160 710900 675940 691490 774000 FALSE TRUE 791762.1094 714833.0594 704554.9237 595041.6013 880693.1 701860.1942 655177.8004 666880.1299 666603.41 925650.4809 0.85535753 0.772249433 0.761145744 0.642836161 0.95143158 0.75823457 0.707802582 0.720444859 0.720145912 1 19.82010802 4.73760684 4.707024259 0.766701445 0.860505469 0.025574601 0.105723805 0.567242949 34.94500818 0.02380894 0.175171507 54652.09814 -4.73760684 0.093804024 FPHHDNELAQSEAYFENDCWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FPHHDNELAQSEAYFENDCWVR 22 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;;; 235.84 1.03E-30 399582000 151387 201728 202858 225713 169885 252639 205210 190388 198848 221648 FALSE TRUE 157363.8757 236373.2148 208144.6461 270358.3577 141008.0084 193967.421 189125.104 187836.1603 191691.4993 265075.6819 0.593656402 0.891719727 0.78522724 1.019928934 0.53195377 0.731743552 0.713475875 0.708613325 0.72315762 1 18.0160448 -1.262616632 3.47132342 1.000687003 0.747243047 0.256696152 0.130408992 37660076.15 57332436.94 277176.6289 0.030343691 0.054623984 1.262616632 -0.253443957 FPLDYYSIPFPTPT(ph)TPLTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.01)PT(0.494)T(0.494)PLT(0.001)GR 109.35 0.0022209 10501000 10776 10817 13080 12956 15184 15403 16167 14681 12786 16749 TRUE FALSE 11201.4448 12674.73561 13420.87555 15518.65813 12603.0291 11825.88668 14899.7883 14484.22521 12325.83436 20030.64587 0.559215358 0.632767195 0.670017114 0.774745769 0.629187355 0.590389684 0.743849619 0.723103254 0.615348823 1 14.28992132 -5 0.258565965 3.123508206 0.63969882 0.705271574 0.065844395 108.9441108 1.07199073 122.8244104 0.090107526 1.00E-05 5 -2.483809386 FPLDYYSIPFPTPTT(ph)PLTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPLDYYSIPFPTPTTPLTGR 20 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;H0Y5H6;H7C2T8 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 FPLDYYSIPFPTPT(0.026)T(0.972)PLT(0.001)GR 221.47 8.74E-24 1185800000 198270 208420 192820 198300 262040 291450 224770 249530 237300 278080 TRUE FALSE 206097.8527 244214.5137 197845.0476 237523.1481 217498.5344 223765.1545 207151.9401 246185.4585 228759.6194 332564.4518 0.619723039 0.734337396 0.594907383 0.714216889 0.654004158 0.672847483 0.622892612 0.740263901 0.687865519 1 18.34327444 -0.393102468 0.565195547 1.041670144 0.661510046 0.829763246 0.045059791 2.923352087 0.822692632 0.290857888 0.017418745 0.404480447 0.393102468 -0.380160098 FPPEDFRHS(ph)PEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR 161.35 2.78E-06 1766984000 1767562 2013263 1874923 1991678 2227647 2382636 1972082 2043303 2019960 1944975 TRUE FALSE 1837346.713 2359025.259 1923785.034 2385625.964 1848992.359 1829304.898 1817505.06 2015915.865 1947262.034 2326055.612 0.789898016 1.014174058 0.827058916 1.025610029 0.794904623 0.78644074 0.781367844 0.866667097 0.837151968 1 21.14945416 3.190497699 24.99982751 0.832943498 0.915105484 0.118752732 0.089881829 195.6982542 101791.3123 0.023930365 0.028602327 1550.592572 -3.190497699 0.082161986 FPQGPPSQMGS(ph)PMGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FPQGPPSQMGSPMGSR 16 0 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 1 FPQGPPS(0.004)QMGS(0.995)PMGSR;FPQGPPSQMGS(1)PMGSR;FPQGPPSQMGS(1)PMGSR;FPQGPPSQMGS(1)PMGSR 250.26 3.76E-17 427958000 234871 232169 237404 285085 235266 288043 300619 250155 250841 213717 TRUE FALSE 244143.8884 272042.2197 243590.9433 341473.9621 195275.5694 221149.3786 277055.6973 246802.0814 241813.2814 255590.7543 0.955214085 1.064366434 0.953050684 1.336018445 0.764016562 0.865247959 1.083981688 0.965614277 0.946095574 1 17.96347612 3.207235801 24.99998018 0.944551268 1.067384272 0.224173252 0.126361103 340.5503132 271788.4393 0.03644966 0.043569623 1611.520377 -3.207235801 0.122833004 FPQLDS(ph)TSFANSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.662)T(0.279)S(0.059)FANSR 140.96 4.16E-05 71483000 61219 88510 67378 65189 78574 89014 66103 69322 65451 73570 TRUE FALSE 63635.97339 103710.904 69133.92603 78083.18963 65218.01955 68341.84752 60921.67413 68392.85198 63095.4313 87984.63292 0.723262362 1.178738838 0.785750008 0.887463947 0.741243299 0.776747544 0.692412665 0.777327241 0.717118765 1 16.42496395 3.673350927 1.76235905 0.769251995 0.939361766 0.112755912 0.137242605 0.545082786 3.296371725 0.037237925 0.077101038 4713.580489 -3.673350927 0.170109771 FPQLDSTSFANSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 182.08 9.63E-07 216570000 107439 101500 124755 117853 138406 152581 116109 116501 124255 120029 FALSE TRUE 111680.7747 118931.8354 128006.2178 141163.9716 114879.7976 117146.3751 107008.0732 114939.4947 119783.0868 143546.3845 0.778011756 0.828525469 0.891741149 0.983403185 0.800297395 0.816087257 0.745459898 0.800713268 0.834455617 1 17.13115747 FPQS(ph)PHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPQSPHSGR 9 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 FPQS(1)PHSGR 78.964 0.011654 0 23601 56254 40480 70265 27567 57481 38783 48096 29290 48337 TRUE FALSE 24532.7857 65915.1869 41534.94205 84163.20728 22881.17119 44131.90888 35743.08712 47451.35179 28235.85862 57807.70968 0.424386052 1.140249065 0.718501776 1.455916654 0.395815218 0.763426005 0.618310037 0.820848154 0.488444513 1 15.81897429 3.180149422 25 0.68198018 0.9340306 0.150469442 0.295218656 141.22313 60442.63958 0.079100996 0.094543822 1514.082089 -3.180149422 0.252050421 FPS(ph)SPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPSSPLR 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 FPS(0.642)S(0.358)PLR 87.696 0.02009 88381000 171260 164750 179230 186980 209490 245620 262660 189730 191160 175050 TRUE FALSE 178021.477 193044.5309 183900.881 223964.0859 173880.9646 188578.4774 242072.0229 187186.9797 184280.1889 209347.696 0.850362724 0.922123982 0.878447122 1.069818729 0.830584563 0.900790795 1.156315677 0.894143969 0.880258978 1 17.67554151 FPSLLTHNENMVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPSLLTHNENMVAK 14 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 178.67 1.96E-06 524870000 343820 296980 401460 371210 450900 479380 527920 441510 427000 289720 FALSE TRUE 357394.2791 347984.0048 411922.3774 444634.23 374256.1791 368051.2601 486540.2509 435592.2806 411632.3534 346485.087 1.031485315 1.004326067 1.188860337 1.283270902 1.080150902 1.062242717 1.404217005 1.257174687 1.188023291 1 18.40243373 4.219002418 7.289072034 1.202581015 1.017411563 0.242686833 0.1125189 0.175816327 41.41189735 0.028490437 0.065587681 16557.79184 -4.219002418 -0.185169452 FPSS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FPSSPLR 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 FPS(0.025)S(0.975)PLR 111.74 0.0068301 168050000 180660 169930 176190 199430 223240 253640 248730 206520 177440 175380 TRUE FALSE 187792.5963 199114.1556 180781.6561 238876.6588 185293.7445 194735.954 229233.8927 203751.9372 171053.9691 209742.3531 0.895348953 0.949327366 0.861922513 1.13890521 0.883435042 0.928453176 1.092930871 0.971439169 0.815543292 1 17.67825869 FPTTATKIS(ph)PK ddPTM_MDA-MB-175_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 FPTTAT(0.01)KIS(0.989)PK;FPTTATKIS(1)PK 84.753 0.0095241 1025170000 1467410 627050 801630 573110 1233480 1323290 1037360 859090 1008890 521430 TRUE FALSE 1525344.48 734740.9597 822521.1363 686469.4474 1023813.51 1015975.952 956049.0126 847575.3037 972580.246 623594.2251 2.446052927 1.17823567 1.319000567 1.10082714 1.641794406 1.629226044 1.53312679 1.359177602 1.55963639 1 19.25024804 7.999999999 0.034444008 1.36E-09 3.712745736 0.194352801 0.34722634 2216.909819 5.83634756 187.3767193 518.338219 99999999.78 -7.999999999 3.712745735 FPVIQHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FPVIQHFK 8 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;Q68CR8;B7ZBQ0 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 113.7 0.002799 659900000 945170 1090990 987130 1123380 1429630 1373620 1346020 1185520 1111620 1107380 FALSE TRUE 982486.0414 1278359.046 1012855.419 1345581.211 1186622.003 1054617.572 1240515.435 1169630.044 1071613.013 1324349.909 0.741862883 0.965272876 0.764794419 1.01603149 0.896003386 0.796328497 0.936697641 0.883172971 0.809161541 1 20.33685292 -2.578966896 2.126140493 3.13772438 0.874427409 0.174336117 0.085250238 2842724.419 242144.1339 29334447.35 0.018999037 0.002636532 2.578966896 -2.26329697 FQAPS(ph)PSTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQAPSPSTLLR 11 0 Q6P9B9 Q6P9B9 INTS5 Integrator complex subunit 5 1 FQAPS(0.998)PS(0.002)TLLR 150.49 3.55E-05 45207000 57431 61223 72151 59683 63881 76392 58634 59958 63584 61098 TRUE FALSE 59698.42023 71737.574 74031.31433 71488.11926 53022.53044 58651.11573 54038.11387 59154.36108 61295.62426 73068.98331 0.817014519 0.981778735 1.013170171 0.978364773 0.725650311 0.802681426 0.739549278 0.80956869 0.83887337 1 16.15697151 3.251724687 24.99185326 0.80385892 0.954709569 0.339103899 0.085821644 215.7524355 409601.433 0.022656656 0.030496013 1785.355421 -3.251724687 0.150850649 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQDADPLEQDELHTFTDTMLPGCFHLLDELPDTVYR 36 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 317.05 5.31E-110 165059000 46705 56117 59957 57958 60450 63067 60538 54510 56801 49941 FALSE TRUE 48548.94946 65754.65822 61519.52868 69421.91941 50174.73059 48420.64504 55792.87337 53779.38261 54756.74311 59725.98277 0.812861458 1.100938907 1.030029575 1.162340345 0.840082126 0.810713241 0.934147431 0.90043529 0.916799365 1 15.86607107 3.216958399 24.99999969 0.894070674 1.032105742 0.289219036 0.096446351 270.7570583 313343.3392 0.027077979 0.0323921 1648.004523 -3.216958399 0.138035068 FQDIEETHLIHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQDIEETHLIHIK 13 0 Q0JRZ9;H0YAE2;H7BXJ4;Q0JRZ9-2 Q0JRZ9 FCHO2 F-BAR domain only protein 2 0 119.32 0.00020722 42435000 58247 49581 53607 46146 66040 67910 67370 58596 66944 46363 FALSE TRUE 60546.63654 58096.15106 55004.04246 55273.54107 54814.54439 52138.93169 62089.36336 57810.61646 64534.69852 55446.94218 1.091974312 1.04777917 0.992012189 0.996872666 0.988594542 0.940339172 1.119797791 1.04262948 1.163900045 1 15.75882028 2.222950263 24.99876478 1.081818176 1.008998837 0.290531394 0.055104256 312.2308454 500010.3971 0.020374088 0.015097194 167.0899245 -2.222950263 -0.072819338 FQDLGAAYEVLSDSEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQDLGAAYEVLSDSEKR 17 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 159.06 5.23E-09 64947000 85749 78017 85547 74027 105530 115760 80756 81243 84583 85480 FALSE TRUE 89134.43673 91415.81286 87776.4251 88669.31965 87592.04829 88876.49436 74426.1337 80154.07047 81538.87435 102228.1694 0.871916589 0.8942331 0.858632465 0.867366795 0.856828884 0.869393386 0.728039386 0.784070291 0.797616497 1 16.64143327 2.389069272 24.99999995 0.80317418 0.869681966 0.040738781 0.067588393 34.34623636 9744.190483 0.021721365 0.018173394 244.9453911 -2.389069272 0.066507785 FQDNFEFVQWFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQDNFEFVQWFK 12 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 205.56 2.33E-07 1046190000 492010 466480 518050 470970 582460 618920 612780 530910 493430 379930 FALSE TRUE 511434.9347 546594.3113 531550.8086 564126.4603 483453.6572 475185.2098 564748.7024 523794.0198 475671.5507 454370.0093 1.125591312 1.202971807 1.169863322 1.241557428 1.064008732 1.045811123 1.24292689 1.152791798 1.046881486 1 18.79350809 1.144966352 3.706013695 1.003932989 1.158340323 0.42635948 0.062408225 0.207668555 4.98503902 0.060092619 0.015826149 13.96260178 -1.144966352 0.154407334 FQEAEERPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQEAEERPK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 89.827 0.010502 429410000 967790 657130 839750 606380 1057170 1098870 982890 810020 882330 707450 FALSE TRUE 1005999.096 769986.9657 861634.5749 726320.1541 877472.621 843674.096 905848.5135 799163.0068 850575.1157 846061.2826 1.189038096 0.910084153 1.018406814 0.858472275 1.037126552 0.997178471 1.070665367 0.944568701 1.005335114 1 19.69040264 4.751573975 24.42570943 0.982474009 1.18903828 0.522182845 0.059291933 1193.180244 2239511.23 0.01341764 0.243277745 56438.30663 -4.751573975 0.206564271 FQEHCPDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQEHCPDLER 10 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 118.77 0.00078145 551600000 257850 328740 291440 287500 346510 404210 307960 290610 308800 327080 FALSE TRUE 268030.1171 385198.5378 299035.1658 344366.6419 287610.354 310338.3534 283821.2905 286714.8483 297686.3483 391165.0637 0.685209754 0.984746782 0.764473092 0.880361448 0.735265955 0.793369302 0.725579345 0.732976625 0.761024887 1 18.577418 5.036325351 16.12297189 0.802712258 0.232619504 0.123878264 0.098355136 821279.8633 10148713.21 0.022391128 13415198.75 108723.9824 -5.036325351 -0.570092754 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FQEHLQLQNLGINPANIGFSTLTMESDKFICIR 33 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 330.59 2.52E-117 3504349700 1271713.7 993903.8 1253278.4 1151089.2 1701400 1750010.4 1415679.8 1330372.4 1485105.5 970803.3 FALSE TRUE 1321921.939 1164599.046 1285939.865 1378771.208 1412196.636 1343597.006 1304715.118 1312540.934 1431656.843 1161013.619 1.138592965 1.003088187 1.107601016 1.187558169 1.216348036 1.157262054 1.123772449 1.130512952 1.233109431 1 20.14695347 3.99748637 24.8171787 1.154514275 1.066966573 0.180362402 0.067606682 125.4526907 1238659.294 0.01576703 0.033136067 9942.288708 -3.99748637 -0.087547702 FQEKPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FQEKPDR 7 1 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;; 123.72 0.0038452 1926730000 3359450 2766330 3161160 2664230 3933850 3864270 3689210 3315990 3425950 2478030 FALSE TRUE 3492083.68 3241425.658 3243542.427 3191206.742 3265175.582 2966851.856 3400040.08 3271544.578 3302650.729 2963552.534 1.178343775 1.093763523 1.09447779 1.07681801 1.101777527 1.0011133 1.14728524 1.103926636 1.114422873 1 21.4988962 -1.934073629 2.284320874 0.929620423 1.099568908 0.326565062 0.043586201 11139898.73 5222147.57 4180039.576 0.010345238 0.011639287 1.934073629 0.169948485 FQEKPDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FQEKPDRR 8 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;; 109.66 0.0020106 561220000 1054070 1141540 1216320 1081820 1506760 1469270 1233000 1294380 1355800 1210760 FALSE TRUE 1095685.498 1337590.615 1248018.298 1295800.767 1250641.473 1128054.31 1136354.238 1277030.953 1307005.023 1447985.241 0.756696592 0.923759841 0.861899875 0.894899154 0.863711479 0.779050972 0.784783026 0.881936443 0.902636979 1 20.46561547 0.955985858 1.826743823 0.998542202 0.843798821 0.480472565 0.050884347 0.348542627 2.429526061 0.048707415 0.01381678 9.036200486 -0.955985858 -0.154743381 FQELIFEDFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FQELIFEDFAR 11 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;;;;; 196.88 1.37E-07 681086000 925297 899919 972076 968992 1089727 1218850 1192504 1019420 1058978 853000 FALSE TRUE 961828.44 1054473.088 997409.0991 1160655.725 904495.5938 935790.5594 1099032.42 1005756.342 1020865.589 1020129.018 0.942849799 1.033666398 0.977728387 1.137753857 0.886648235 0.917325694 1.077346493 0.985910923 1.000722036 1 19.96032019 2.229551654 24.99942953 1.013956318 0.987441541 0.050687114 0.068602925 878.3972796 2437492.63 0.025829537 0.019338013 169.6491367 -2.229551654 -0.026514778 FQESEERPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FQESEERPK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;;;; 194.06 3.00E-05 5399690000 5065120 3746940 4471440 3548910 6000890 5738680 5335080 4565330 4891320 3309720 FALSE TRUE 5265094.849 4390447.798 4587969.4 4250873.806 4980860.861 4405958.541 4916902.489 4504139.219 4715282.349 3958196.266 1.330175286 1.109204169 1.159106091 1.073942149 1.258366318 1.113122808 1.242207854 1.137927206 1.191270476 1 21.91641172 -1.808556062 2.504949124 0.942291226 1.174106624 0.339542229 0.074758105 9398517.085 5776768.186 3274961.436 0.016194971 0.015539747 1.808556062 0.231815398 FQETEFLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 FQETEFLS(1)PPR 172.33 1.41E-05 101650000 147210 148710 143570 131120 140880 165930 145660 142480 145730 157310 TRUE FALSE 153021.9645 174249.7857 147311.5521 157055.1446 116933.2679 127395.2722 134242.7886 140570.2887 140485.2058 188131.8826 0.813376034 0.926210822 0.783022793 0.834814081 0.621549449 0.677159397 0.713556824 0.747190145 0.746737894 1 17.52138484 3.432475262 24.94177389 0.732933823 0.842656548 0.144887151 0.099501619 182.0310023 101692.2239 0.02578243 0.034909593 2706.919011 -3.432475262 0.109722725 FQGEDTVVIASKPYAFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FQGEDTVVIASKPYAFDR 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 214.74 9.02E-19 2410510000 1284860 1281930 1416360 1170960 1629440 1734040 1470420 1395200 1409690 1318790 FALSE TRUE 1335587.265 1502091.505 1453271.505 1402572.393 1352468.371 1331335.49 1355164.638 1376499.626 1358955.532 1577181.651 0.846818922 0.952389666 0.921435717 0.889290332 0.857522258 0.844123116 0.859231806 0.872759092 0.861635394 1 20.5889174 FQGIKHECQANGPEDLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FQGIKHECQANGPEDLNR 18 1 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;; 287.01 4.06E-40 5787950000 2917430 3038940 3450010 2243420 4586420 4460360 2417200 3484350 3791190 4121000 FALSE TRUE 3032612.389 3560854.305 3539920.095 2687161.78 3806821.967 3424508.987 2227733.548 3437647.987 3654745.812 4928431.049 0.615330185 0.722512757 0.718265115 0.545236761 0.772420661 0.694847702 0.452016783 0.697513662 0.74156375 1 22.23269701 0.832205169 2.247516305 0.99932097 0.650798302 0.579490136 0.089455456 0.436724509 4.031719933 0.084124756 0.022897064 6.795245777 -0.832205169 -0.348522669 FQIPPNAELKYELHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQIPPNAELKYELHLK 16 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 179.03 1.62E-09 1054810000 1046970 839400 1072890 643510 1699730 1314530 969580 1021050 1232820 979100 FALSE TRUE 1088305.184 983560.4204 1100850.395 770794.3573 1410810.502 1009250.329 893581.7861 1007364.495 1188451.049 1170935.899 0.929431906 0.839978022 0.940145738 0.658272035 1.20485716 0.861917659 0.763134674 0.860307123 1.014958248 1 20.15923067 1.235636819 24.92299587 1.007479201 0.878577067 0.123736225 0.133007505 151.8742739 1294482.805 0.105336265 0.030825096 17.20429257 -1.235636819 -0.128902134 FQNDRTEDEQFNDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQNDRTEDEQFNDEK 15 1 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 ; 149.22 3.10E-06 611330000 212903 135793 180368 135798 227470 255981 226666 160704 207926 127788 FALSE TRUE 221308.5748 159114.3914 185068.5383 162658.4391 188804.7307 196533.2922 208899.3266 158550.0257 200442.7839 152825.612 1.448111819 1.041150036 1.210978552 1.064340178 1.235425975 1.28599709 1.366913072 1.037457163 1.31157848 1 17.22152682 -1.11158858 6.330463541 0.999999506 1.207993373 0.193265648 0.133433051 8.72E-07 1.23E-07 0.121151221 0.028555549 0.077341291 1.11158858 0.207993868 FQNVADLHLYLYSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FQNVADLHLYLYSAK 15 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;; 130.29 6.06E-05 1106405000 1543419 1236381 1500864 1243551 1867620 1947330 1804560 1600053 1705629 1083081 FALSE TRUE 1604354.374 1448719.819 1539977.749 1489521.676 1550162.619 1495092.12 1663113.872 1578606.907 1644243.745 1295289.985 1.238606329 1.118452112 1.188905779 1.149952283 1.196768783 1.154252821 1.283970301 1.218728566 1.269402037 1 20.30484369 FQPGETLTEILETPATSEQEAEHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FQPGETLTEILETPATSEQEAEHQR 25 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 252.84 8.53E-45 1996528000 607357 605664 583008 614136 745164 775171 679638 638530 640853 652646 FALSE TRUE 631335.9233 709682.0806 598201.6674 735610.2678 618501.2894 595149.2831 626366.1977 629971.5498 617788.8257 780519.488 0.808866317 0.909243256 0.766414775 0.942462397 0.792422609 0.762504066 0.802499114 0.807118284 0.791509802 1 19.57407513 FQPGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQPGYR 6 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 101.23 0.085526 130030000 114260 193890 172670 166300 195430 233210 163720 171010 143790 210330 FALSE TRUE 118771.073 227189.0992 177169.922 199193.6436 162210.8784 179050.5118 150887.1986 168717.8907 138615.026 251540.1365 0.472175434 0.90319224 0.704340566 0.791896062 0.644870758 0.711816867 0.59985337 0.670739442 0.551065241 1 17.94042909 -1.012058126 4.679181771 1.000007626 0.680072086 0.422322875 0.114677353 8.51E-06 1.80E-06 0.103629004 0.024425009 0.097261704 1.012058126 -0.31993554 FQPISEHQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQPISEHQTR 10 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;A0A6I8PUD8 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 98.182 0.0055511 177495000 254495 309876 319653 311100 357800 442360 412650 357000 330491 275178 FALSE TRUE 264542.6591 363094.7925 327983.4198 372634.6515 296981.2838 339628.594 380305.4147 352214.9989 318596.6935 329093.8605 0.8038517 1.103316823 0.996625763 1.132305084 0.902421222 1.032011334 1.155613824 1.070256973 0.968102817 1 18.32813959 2.477643072 24.99995124 1.063937207 0.999112098 0.065691199 0.098892702 49.5416311 2373701.658 0.032783645 0.027723226 300.3606749 -2.477643072 -0.064825109 FQPLDQVVVDNVFPNCILLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 100.35 0.00040593 534110000 89488 1132400 491000 1202600 282930 958640 286830 621150 259300 1622800 FALSE TRUE 93021.05534 1326880.891 503795.8634 1440470.691 234837.6597 736010.3883 264347.5151 612824.5002 249967.8437 1940756.59 0.047930305 0.683692586 0.259587352 0.742221203 0.121003149 0.379238897 0.136208485 0.315765771 0.128799173 1 20.88818776 -1.377380546 4.072761095 1.001970657 0.322855864 0.457936539 0.224081787 68356342 23128543.25 1198719.705 0.048562363 0.041939134 1.377380546 -0.679114793 FQPQLNPDVVAPLPTHTAHEDFTFGES(ph)RPELGSEGLGSAAHGSQPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPT(0.004)HT(0.016)AHEDFT(0.06)FGES(0.237)RPELGS(0.237)EGLGS(0.237)AAHGS(0.208)QPDLR 75.34 0.00011092 366780000 28801 57259 47538 52177 50148 62676 56446 54545 40461 48110 TRUE FALSE 29938.08572 67092.78784 48776.87933 62497.45487 41623.86087 48120.44886 52021.61503 53813.91349 39004.81651 57536.23338 0.520334474 1.166096282 0.847759342 1.086227777 0.723437362 0.836350349 0.904153991 0.935304769 0.677917448 1 15.81218316 3.216756177 24.9994487 0.852833489 0.919650873 0.021290631 0.182156311 1018.463542 1167696.434 0.049337197 0.059014802 1647.237334 -3.216756177 0.066817384 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGS(ph)AAHGSQPDLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLRR 49 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPTHTAHEDFT(0.004)FGES(0.119)RPELGS(0.119)EGLGS(0.379)AAHGS(0.379)QPDLRR 75.779 0.00013152 2094100000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(ph)QPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGSQPDLR 48 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 FQPQLNPDVVAPLPTHTAHEDFTFGESRPELGSEGLGSAAHGS(1)QPDLR;FQPQLNPDVVAPLPTHTAHEDFTFGES(0.001)RPELGS(0.004)EGLGS(0.003)AAHGS(0.991)QPDLR 180.03 3.22E-29 1656480000 67232 92515 86973 108194 96703 103520 86405 93354 74143 89959 TRUE FALSE 69886.37127 108403.7316 89239.58783 129594.4503 80265.4586 79479.04886 79632.35032 92102.74233 71474.60791 107584.7437 0.649593696 1.007612491 0.829481809 1.204580183 0.746067294 0.738757617 0.740182554 0.856094825 0.664356353 1 16.71511398 FQPVHDLTIGVEFGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQPVHDLTIGVEFGAR 16 0 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 156.22 1.65E-08 367340000 765250 783260 868280 855450 814510 957920 801940 767800 766460 672930 FALSE TRUE 795462.6609 917778.8121 890908.0901 1024655.457 676059.8811 735457.5974 739081.8473 757508.8969 738875.2543 804777.7495 0.988425266 1.140412757 1.10702376 1.27321544 0.840057869 0.913864229 0.918367646 0.941264712 0.918110938 1 19.61823089 3.226970627 24.99999334 0.919980616 1.126762031 0.650081724 0.073789549 128.6725862 277550.7176 0.020703081 0.02494322 1686.438961 -3.226970627 0.206781415 FQQDDAHIFCAMEQIEDEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FQQDDAHIFCAMEQIEDEIK 20 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ;; 192.94 9.18E-18 176078800 181577.8 78817 124502.1 119905.8 146835 163924.5 213307.5 132265.5 153155 61720.9 FALSE TRUE 188746.6318 92353.20664 127746.727 143622.8094 121876.0391 125855.5192 196587.9008 130492.6973 147642.9815 73813.92864 2.557059829 1.251162326 1.730658825 1.945741299 1.65112522 1.705037538 2.663290038 1.767860074 2.000204896 1 16.17160546 FQSGDFHVINGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQSGDFHVINGVLR 14 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ; 179.27 1.89E-06 2429400000 1906480 2383500 2558000 2471600 3204900 3330400 2502900 2463540 2243510 2892500 FALSE TRUE 1981749.303 2792847.584 2624663.581 2960475.103 2660132.243 2556965.073 2306716.158 2430520.276 2162766.513 3459229.995 0.572887407 0.807361057 0.758742144 0.855819101 0.768995484 0.739171745 0.66682937 0.702618872 0.625216166 1 21.72201951 -2.418435678 2.401767426 3.759708823 0.727216801 0.518742201 0.080198052 2331581.36 688097.6674 34660631.88 0.019381532 0.003815613 2.418435678 -3.032492022 FQSPQIQATIS(ph)PPLQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQSPQIQATISPPLQPK 17 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 1 FQSPQIQATIS(1)PPLQPK;FQSPQIQAT(0.007)IS(0.993)PPLQPK 239.43 5.23E-21 721380000 985460 732010 966930 701720 985740 1031890 957540 880200 923140 639970 TRUE FALSE 1024366.722 857727.0233 992128.9901 840518.1216 818184.2669 792249.1859 882485.5127 868402.3587 889916.3717 765359.8685 1.338411855 1.120684607 1.296290844 1.098199888 1.069019033 1.035132907 1.153033428 1.134632732 1.162742402 1 19.54577873 3.723490011 24.25375834 1.101098646 1.238684649 0.506942285 0.071006783 460.151735 740541.8143 0.018194093 0.02832048 5290.418287 -3.723490011 0.137586003 FQSSHHPTDITSLDQYVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FQSSHHPTDITSLDQYVER 19 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 236.16 2.03E-24 3024690000 249113 1446470 1085680 1532190 1200510 1887080 930540 1368160 960380 1445430 FALSE TRUE 258948.1736 1694889.971 1113973.713 1835252.609 996447.739 1448834.269 857601.8433 1349822.053 925816.1114 1728634.334 0.149799277 0.980479178 0.644424151 1.061677749 0.576436392 0.838138084 0.496115243 0.780860374 0.535576607 1 20.72120129 4.752660225 24.65050949 0.751709511 0.149798779 0.478348472 0.193043111 1676.250335 2930546.827 0.042012206 0.865647487 56579.64583 -4.752660225 -0.601910732 FQVWDLGGQTSIRPYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQVWDLGGQTSIRPYWR 17 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 168.05 1.96E-09 1131850000 918570 895260 908010 830800 1075220 1227990 977240 1054770 922410 847720 FALSE TRUE 954835.8529 1049013.941 931673.4865 995129.7603 892454.4885 942807.9329 900641.3753 1040632.533 889212.6443 1013814.503 0.941825008 1.034719801 0.918978258 0.98156986 0.880293669 0.929960984 0.888368999 1.0264526 0.877095999 1 19.95136228 5.103957416 19.85251149 0.949954239 0.00026225 0.000783202 0.056439549 12834.72703 1659264.982 0.012509139 178446.994 127044.9528 -5.103957416 -0.94969199 FQVWDYEEGEVEALLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FQVWDYEEGEVEALLDR 17 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ;;;;; 206.63 1.58E-11 908490000 200502.1 248810.6 252722 251127.9 276656.4 312527.7 277551.9 260649.6 251860.2 249161.3 FALSE TRUE 208418.0777 291541.8851 259308.1429 300800.2491 229630.4439 239947.8781 255796.6568 257156.0184 242795.8006 297979.6863 0.699437201 0.978395168 0.870220874 1.009465621 0.770624491 0.805249113 0.85843656 0.862998487 0.814806552 1 18.18485446 -1.294265 3.189748699 1.000790729 0.858000237 0.205097285 0.086623526 18365094.19 23810067.2 138131.6093 0.020387153 0.050784947 1.294265 -0.142790493 FQWDLNAWTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FQWDLNAWTK 10 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 198.25 6.99E-07 314290000 1163420 973790 1156240 918160 1736180 1564420 1344910 1072410 1250000 1394490 FALSE TRUE 1209352.72 1141030.857 1186372.564 1099769.308 1441064.744 1201107.164 1239492.44 1058036.098 1205012.744 1667713.616 0.725156111 0.684188728 0.711376673 0.65944734 0.864096047 0.720211883 0.74322859 0.634423133 0.72255376 1 20.66944014 -1.722392025 2.377375265 1.062383138 0.714840774 0.678668511 0.058107424 4353495.489 3037321.179 1607893.088 0.015069086 0.018949946 1.722392025 -0.347542364 FRAESVVPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRAESVVPAR 10 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 0 103.21 0.0025939 201640000 99438 115330 117930 113720 144100 163170 129460 113670 118910 145420 FALSE TRUE 103363.889 135137.0304 121003.3527 136213.4766 119605.9335 125276.2404 119312.5869 112146.4396 114630.4523 173912.2648 0.594345023 0.777041404 0.695772393 0.783230997 0.687737197 0.720341607 0.686050447 0.644844915 0.659128052 1 17.40800015 -1.43298737 3.302678936 1.004060426 0.695855213 0.74199251 0.054076432 81319272.3 104963914.7 3080134.768 0.012762735 0.036898833 1.43298737 -0.308205213 FRALCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRALCSR 7 1 H3BVG3;Q96S16-2;Q96S16 H3BVG3 JMJD8 JmjC domain-containing protein 8 0 60.358 0.089365 248870000 38010 53296 49154 39421 56562 60156 41099 47206 39550 57122 FALSE TRUE 39510.66415 62449.17341 50434.99362 47218.35614 46947.61144 46185.68067 37877.55299 46573.28078 38126.60323 68313.96223 0.578368797 0.914149485 0.738282365 0.691196274 0.687233033 0.676079665 0.554462832 0.68175347 0.558108503 1 16.05989285 -1.098858976 4.361521886 1.00003756 0.680053389 0.487643006 0.099684145 3.63E-05 7.50E-06 0.096261514 0.022686397 0.079641792 1.098858976 -0.319984171 FRAPELLFQPDLVGDESEGLHEVVAFAIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRAPELLFQPDLVGDESEGLHEVVAFAIHK 30 1 P42025 P42025 ACTR1B Beta-centractin 0 231.07 1.23E-35 149160000 94173 76234 96892 78106 121370 134950 112130 117340 105970 95733 FALSE TRUE 97891.02276 89326.59648 99417.08512 93555.13368 100739.5708 103609.9077 103340.9576 115767.2492 102156.1604 114490.0484 0.855017743 0.780212758 0.868346957 0.817146424 0.879898053 0.904968677 0.902619564 1.011155562 0.892271091 1 16.80486268 2.527974013 0.837345321 0.974503255 0.822695003 0.664552209 0.039413577 0.333999903 0.478256202 0.026145873 0.019884291 337.2671268 -2.527974013 -0.151808253 FRAPELLFRPDLIGEESEGIHEVLVFAIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FRAPELLFRPDLIGEESEGIHEVLVFAIQK 30 2 P61163;R4GMT0 P61163 ACTR1A Alpha-centractin 0 ;; 189.94 1.58E-18 2391250000 1109110 1055540 1391090 1112290 1928140 1775090 1655240 1511360 1657330 1343310 FALSE TRUE 1152898.519 1236820.784 1427342.948 1332297.642 1600395.452 1362852.249 1525497.964 1491102.691 1597683.017 1606505.875 0.717643513 0.769882515 0.888476644 0.829313893 0.996196451 0.848333187 0.949575092 0.928165103 0.994508045 1 20.61549483 6.378036738 0.328248943 0.976364027 4.78E-16 0.748368461 0.047273774 9.540203259 0.353770027 0.041295341 4.587438578 2388013.28 -6.378036738 -0.976364027 FRCPEALFQPSFLGMESCGIHETTFNSIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 301.68 1.61E-81 890882000 458952 398960 610630 310685 1982423 1061074 762414 1052873 906835 1659180 FALSE TRUE 477071.7793 467478.2765 626543.5194 372137.5657 1645451.447 814655.6442 702653.9985 1038760.96 874198.1855 1984264.554 0.240427507 0.235592716 0.315756041 0.18754433 0.829250033 0.410557979 0.354113063 0.523499227 0.440565339 1 20.92017296 -5 0.117032527 2.927894567 0.09044843 0.597744234 0.160353727 110.9566465 0.848882458 50.97554892 1.672646003 1.00E-05 5 -2.837446137 FRDGPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FRDGPPLR 8 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;;;; 143.7 0.00054464 5951460000 2471640 3197960 2858400 3010940 3330030 3786850 2904310 3112630 2700320 3199040 FALSE TRUE 2569222.256 3747184.753 2932892.252 3606494.945 2763992.69 2907411.478 2676662.593 3070910.286 2603136.011 3825830.639 0.67154626 0.979443448 0.76660274 0.942669785 0.722455579 0.759942546 0.699629138 0.802678052 0.680410676 1 21.86734158 5.028535333 16.12301244 0.804453126 0.288181064 0.124044407 0.111570259 10923802.84 168646128.9 0.025005472 151223433.5 106791.1672 -5.028535333 -0.516272062 FRDQDLASCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FRDQDLASCDR 11 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;;; 236.08 1.40E-15 2318440000 1032860 1324440 1219430 1303390 1341040 1590980 1263330 1265180 1130610 1509830 FALSE TRUE 1073638.11 1551902.267 1251209.348 1561196.652 1113090.5 1221499.007 1164306.894 1248222.332 1089919.567 1805652.281 0.594598485 0.859469059 0.692940363 0.864616443 0.616447868 0.676486287 0.644812352 0.691286105 0.603615424 1 20.78408867 -1.256731526 5.206440484 1.000040721 0.698283638 0.502173801 0.091361335 4.12E-05 5.88E-06 0.084303505 0.01986785 0.055369229 1.256731526 -0.301757083 FRDQDLASCDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FRDQDLASCDRDR 13 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ;; 242.07 3.63E-17 977950000 249224 334577 286447 258462 363920 380820 273828 289553 295998 345810 FALSE TRUE 259063.556 392037.9971 293912.0441 309585.0122 302061.0084 292380.3264 252364.6458 285672.0156 285345.0898 413564.8486 0.626415801 0.947948063 0.710679462 0.748576706 0.730383662 0.706975768 0.610217833 0.690755069 0.689964562 1 18.65775404 -1.142323174 4.418499646 1.000045662 0.718681357 0.486061827 0.086992385 3.88E-05 7.53E-06 0.083493532 0.019676425 0.072057108 1.142323174 -0.281364304 FRDQDLASCDRDRSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FRDQDLASCDRDRSSR 16 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 1 FRDQDLASCDRDRS(0.009)S(0.991)R;FRDQDLASCDRDRS(0.001)S(0.999)R;FRDQDLASCDRDRS(0.002)S(0.998)R;FRDQDLASCDRDRS(0.009)S(0.991)R;FRDQDLASCDRDRS(0.011)S(0.989)R;FRDQDLASCDRDRS(0.046)S(0.954)R 168.81 3.23E-08 9987130000 1477890 2245900 2096740 1385510 2596670 2351680 1272550 1970560 2091550 2861290 TRUE FALSE 1536238.238 2631615.854 2151382.767 1659559.743 2155288.961 1805537.96 1172804.206 1944147.866 2016275.524 3421904.993 0.4489424 0.769049947 0.628709088 0.484981245 0.629850614 0.527641172 0.342734298 0.568147821 0.589226039 1 21.70636827 0.662424296 2.941630272 0.999980269 0.55100467 0.602637733 0.108978996 2.595804358 21.81109102 0.106268668 0.027839756 4.596468586 -0.662424296 -0.448975598 FRDSILR ddPTM_MDA-MB-175_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 ;;;;;; 150.35 0.0017827 7513744000 1730592 1679644 1842010 1759155 2585905 2441614 1779055 1918403 1822183 2225131 FALSE TRUE 1798917.108 1968109.791 1890014.294 2107110.608 2146353.792 1874586.152 1639608.02 1892689.946 1756602.99 2661102.817 0.676004361 0.739584273 0.71023723 0.791818563 0.806565525 0.70443958 0.616138546 0.711242697 0.66010339 1 21.34359282 -1.468027878 3.00088396 1.007242857 0.713982284 0.716713045 0.054145041 15231751.41 18645709.57 927768.3509 0.013813183 0.034038634 1.468027878 -0.293260573 FREFLESQEDYDPCWSLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 98.132 0.00076882 109890000 32556 29442 33359 29195 44117 45477 34263 35174 41214 30134 FALSE TRUE 33841.33602 34498.43447 34228.36294 34969.68386 36618.0081 34915.65596 31577.37653 34702.55006 39730.71619 36038.18035 0.939041197 0.957274594 0.949780555 0.970350987 1.016089263 0.968851802 0.87622006 0.962938465 1.102461773 1 15.13723855 1.319931945 8.503711324 1.05065701 0.954151277 0.481972846 0.039918423 0.200753228 18.34569317 0.027010895 0.009838131 20.88968757 -1.319931945 -0.096505732 FRELAEEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 214.26 7.97E-09 2322460000 873910 1071318 1033449 827773 1402155 1380307 976492 1022385 996175 1210980 FALSE TRUE 908412.6416 1255308.533 1060381.53 991504.0287 1163817.194 1059751.618 899952.0055 1008681.601 960322.8563 1448248.345 0.627249218 0.866777122 0.73218211 0.684622932 0.803603331 0.731747163 0.621407239 0.696483862 0.663092666 1 20.46587759 -1.551185688 6.148763324 1.000494039 0.715937503 0.586168433 0.072045074 0.000481843 3.52E-05 0.068887541 0.016209555 0.028106988 1.551185688 -0.284556536 FRIDELEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FRIDELEPR 9 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 166.55 5.53E-05 2096303000 1316165 1683734 1452544 1676091 1870881 2023002 1469960 1461210 1391156 1484014 FALSE TRUE 1368128.211 1972902.217 1490398.49 2007616.797 1552869.316 1553190.444 1354740.694 1441624.87 1341088.567 1774778.13 0.770872813 1.111633158 0.839766089 1.131193113 0.874965321 0.875146261 0.763329608 0.812284559 0.755637307 1 20.75920725 2.859544704 2.960374781 0.820053523 0.966896926 0.163365829 0.121543306 0.366363977 6.167177199 0.036178804 0.038770348 723.6768904 -2.859544704 0.146843403 FRKVQHELDEAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FRKVQHELDEAEER 14 2 P13533;P12883 P13533 MYH6;MYH7 Myosin-6;Myosin-7 0 ; 59.898 0.054689 787800000 27748.6 305217 161193 225089 109253 255855 91516 184380 119992 337206 FALSE TRUE 28844.13615 357635.6455 165393.822 269610.9324 90682.21408 196436.5538 84342.73679 181908.6877 115673.5114 403275.0595 0.071524721 0.886828077 0.410126583 0.66855345 0.224864424 0.487103155 0.209144441 0.451078447 0.286835272 1 18.62140466 -1.013720602 4.433076621 1.000023352 0.422418449 0.380245027 0.225263832 113902438.7 244985661.8 41851.69813 0.049931107 0.096890099 1.013720602 -0.577604902 FRLS(ph)LFSDLPEDTELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FRLSLFSDLPEDTELQR 17 1 Q9BST9 Q9BST9 RTKN Rhotekin 1 FRLS(0.999)LFS(0.001)DLPEDTELQR;FRLS(0.9)LFS(0.1)DLPEDTELQR;FRLS(1)LFSDLPEDTELQR;FRLS(1)LFSDLPEDTELQR 129.51 2.02E-05 121758000 89788 101107 93556 110206 126959 134052 113578 106429 112164 140211 TRUE FALSE 93332.89957 118471.3407 95994.14622 132004.4179 105378.5545 102920.4546 104675.4596 105002.4933 108127.2396 167682.6609 0.556604356 0.706521116 0.572475089 0.787227595 0.628440376 0.613781139 0.624247367 0.62619768 0.64483256 1 17.35537399 0.887179451 17.66093109 1 0.641224344 0.749874869 0.06236842 2976.754352 465984.946 0.055588132 0.013897033 7.712220732 -0.887179451 -0.358775656 FRNS(ph)VEGLNQEIEIIIK ddPTM_MDA-MB-175_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 272.24 7.58E-36 283026000 369854 285690 337658 290740 417681 419579 384002 369612 380400 287388 TRUE FALSE 384456.1215 334755.0351 346457.6449 348247.5042 346683.7328 322138.136 353902.9198 364657.9557 366709.4783 343696.1762 1.118592955 0.973985334 1.008034621 1.0132423 1.008692435 0.93727588 1.029696995 1.060989272 1.066958272 1 18.39077428 2.003909783 24.99990168 1.048405117 1.006266592 0.086706328 0.046176094 212.6770405 1359889.179 0.016752647 0.012317211 100.9043254 -2.003909783 -0.042138525 FRPAGAAPRPPPKPM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FRPAGAAPRPPPKPM 15 3 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 ; 105.19 0.0016319 1495330000 603920 573170 692800 590570 760680 841230 721260 681050 739970 611630 FALSE TRUE 627763.2279 671607.4889 710854.9371 707382.9833 631379.8853 645867.0815 664725.7565 671921.6387 713338.6242 731467.1881 0.858224727 0.918164888 0.971820676 0.967074115 0.863169115 0.882974783 0.908756766 0.918594367 0.975216163 1 19.48043362 1.159399545 2.924296066 0.999310555 0.91196221 0.431233572 0.035764642 0.251208224 3.847882683 0.035684091 0.009741088 14.43442689 -1.159399545 -0.087348344 FRPAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRPAIK 6 1 Q96CN7;D6RGE2 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 81.716 0.055765 301210000 262320 401980 364770 398170 405490 485770 378620 373610 431480 614140 FALSE TRUE 272676.5962 471016.938 374276.2059 476926.8376 336564.9546 372957.2794 348942.7751 368602.3691 415951.1191 734468.9746 0.371256793 0.641302702 0.509587496 0.649349195 0.458242576 0.507791741 0.475095323 0.501862409 0.566329053 1 19.48634202 0.74557502 3.729069692 0.999993794 0.518395718 0.777690265 0.077390912 1.316116413 18.87401493 0.069179783 0.017755926 5.566407796 -0.74557502 -0.481598076 FRPDMEEEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FRPDMEEEEAK 11 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;;;;;;; 182.71 5.17E-06 3141960000 2757061 1784897 2311671 1842180 3060410 3287370 3267420 2537110 2634040 1574339 FALSE TRUE 2865911.897 2091439.175 2371915.045 2206557.706 2540202.601 2523928.138 3011311.083 2503104.19 2539241.415 1882800.585 1.522153711 1.110812899 1.259780279 1.171955078 1.349161787 1.340518034 1.599378664 1.329457942 1.348651278 1 20.84444878 3.091304723 9.027157687 1.363329199 1.254747995 0.00433468 0.169917489 0.726208979 64.88195677 0.046418401 0.055537839 1233.970347 -3.091304723 -0.108581205 FRPFTFSQS(ph)TPIGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRPFTFSQSTPIGLDR 16 1 A0A0A0MRY4;Q96N96-6;J3KQJ8;Q96N96-5;Q96N96-4;Q96N96 A0A0A0MRY4 SPATA13 Spermatogenesis-associated protein 13 1 FRPFTFSQS(0.976)T(0.024)PIGLDR 166.69 3.99E-09 405700000 95703 153230 138620 113000 195490 166240 113630 127650 121120 197590 TRUE FALSE 99481.42834 179546.0605 142232.5511 135351.0627 162260.6796 127633.2794 104723.3837 125939.0605 116760.9149 236303.9774 0.420989225 0.759809727 0.601905024 0.572783684 0.686660806 0.54012328 0.443172328 0.532953622 0.494113202 1 17.85028439 -1.842907532 2.837497338 1.156096605 0.56433216 0.642281759 0.098176989 21388580.84 13473367.16 22556421.14 0.025185756 0.014357951 1.842907532 -0.591764446 FRPLNESEVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRPLNESEVNR 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 84.289 0.014658 517600000 119490 131120 129440 148140 140720 174130 155720 150140 127600 150160 FALSE TRUE 124207.5575 153638.84 132813.3127 177441.6498 116800.4647 133690.9465 143514.2595 148127.6189 123007.7009 179580.977 0.691652087 0.855540729 0.739573394 0.988087117 0.650405553 0.744460514 0.799161815 0.824851392 0.684970663 1 17.45427501 -0.982288667 7.830382278 1.000000002 0.782640231 0.337482802 0.093911815 3.77E-09 4.82E-10 0.084348518 0.019881136 0.104162485 0.982288667 -0.217359772 FRPLNESEVNRGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FRPLNESEVNRGDK 14 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 221.59 2.37E-12 2714400000 1439960 1159670 1412930 1178890 1836190 1738600 1432650 1481500 1646080 1152960 FALSE TRUE 1496810.733 1358834.302 1449752.117 1412070.923 1524075.08 1334836.499 1320355.149 1461642.916 1586837.902 1378860.437 1.085541866 0.985476314 1.051413238 1.024085459 1.105314968 0.96807223 0.957569826 1.06003688 1.150832861 1 20.39504501 1.497565995 9.2321756 1.08528469 1.024678847 0.116811595 0.056337207 0.170588848 37.27669081 0.029485236 0.013638243 31.44604235 -1.497565995 -0.060605844 FRPPETTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FRPPETTER 9 1 Q96P70 Q96P70 IPO9 Importin-9 0 ;;; 117.02 0.0011117 1597350000 713489 840200 893820 898270 930600 1077040 898380 907780 917330 861070 FALSE TRUE 741658.0967 984497.8142 917113.6835 1075945.125 772416.9444 826913.7827 827962.6281 895612.6939 884315.4725 1029780.18 0.72021011 0.956027153 0.890591702 1.044829902 0.750079443 0.803000289 0.804018803 0.869712499 0.858741981 1 19.97390498 4.759013774 23.85056553 0.876465177 0.720209825 0.237055981 0.087815622 4126.870715 4812225.89 0.020980065 0.81328249 57413.46717 -4.759013774 -0.156255352 FRPSDEHHPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FRPSDEHHPEVK 12 1 Q9H008 Q9H008 LHPP Phospholysine phosphohistidine inorganic pyrophosphate phosphatase 0 ; 100.55 0.0020447 107790000 73961 85055 91747 123448 229340 228141 209266 108628 103514 164326 FALSE TRUE 76881.03739 99662.53461 94138.00219 147865.6459 190356.8687 175158.7103 192863.1841 107172.0193 99788.55136 196522.5335 0.391207237 0.507130317 0.479018871 0.752410644 0.968626169 0.891290719 0.981379492 0.545342142 0.50777155 1 17.58433522 3.722524277 4.232220822 0.796207147 0.459190969 0.487515503 0.163695711 0.203087932 8.958118101 0.047835383 0.081481748 5278.667132 -3.722524277 -0.337016178 FRPSLEER ddPTM_MDA-MB-175_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 ;;; 155.58 0.00037084 986840000 792190 1148050 726350 787120 1429010 1405400 843520 779810 711230 1732380 FALSE TRUE 823466.2729 1345218.657 745279.2777 942809.9867 1186107.391 1079017.149 777402.6983 769357.9225 685632.9712 2071806.693 0.397462889 0.64929738 0.359724332 0.45506658 0.572499063 0.520809761 0.37522936 0.371346383 0.330934818 1 20.98245797 -1.712631477 2.996067799 1.075952737 0.448492189 0.739484036 0.098283193 43526852.01 43363946.56 24981749.61 0.024371079 0.019380658 1.712631477 -0.627460548 FRQDLMNIAGTTLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FRQDLMNIAGTTLSSK 16 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 135.27 2.17E-05 854150000 1049880 939140 1073810 837450 1356230 1422870 1174110 1085500 1143600 1043390 FALSE TRUE 1091330.073 1100429.99 1101794.371 1003095.11 1125698.509 1092430.006 1082080.19 1070950.648 1102442.059 1247822.294 0.874587735 0.881880373 0.882973783 0.803876574 0.902130467 0.875469217 0.867174914 0.858255742 0.883492838 1 20.25098106 0.822621342 4.929171512 0.999999088 0.868017414 0.723573747 0.02426904 1.324148049 36.47485578 0.022454279 0.005678803 6.646933621 -0.822621342 -0.131981673 FRQS(ph)LPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FRQSLPLSR 9 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 FRQS(1)LPLSR;FRQS(1)LPLSR 166.24 3.69E-05 1052600000 255050 282280 281330 243070 332020 323530 306000 287460 299670 300940 TRUE FALSE 265119.5709 330759.3942 288661.6909 291148.5205 275583.359 248395.0606 282014.9204 283607.0689 288884.9352 359903.4312 0.736640854 0.91902262 0.802053179 0.808962892 0.765714731 0.690171416 0.783584973 0.788008794 0.802673468 1 18.45725033 0.563735806 2.568800364 0.999998132 0.788362564 0.569784422 0.055262296 4.367403952 24.77649703 0.054113969 0.01438844 3.662147277 -0.563735806 -0.211635568 FRREEDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FRREEDAEK 9 2 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 105.98 0.0016934 246500000 150610 123140 152020 83065 244710 222180 125130 150020 173070 169080 FALSE TRUE 156556.1991 144288.3371 155981.7661 99495.00908 203114.2816 170582.0622 115321.9836 148009.2273 166841.2445 202207.9888 0.774233501 0.713563979 0.771392698 0.492042919 1.004481983 0.843597047 0.570313687 0.731965281 0.825097196 1 17.62548047 0.922600487 3.247810601 0.999557074 0.734517267 0.269035694 0.131911102 0.438573616 10.97719074 0.124114725 0.032306005 8.367591829 -0.922600487 -0.265039807 FRRS(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FRRSETPPHWR 11 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR;FRRS(1)ET(1)PPHWR 103.39 0.0051812 4835030000 519155 633666 608985 567030 639895 707767 545577 571935 547936 641194 TRUE FALSE 539651.6403 742493.2063 624855.6494 679186.8416 531125.8765 543398.8406 502813.2491 564269.1468 528215.8904 766823.6879 0.703749309 0.968271088 0.814862216 0.885714477 0.692631024 0.70863596 0.655709072 0.735852525 0.688836168 1 19.54853538 3.237982628 24.99987264 0.726219318 0.850066049 0.138700451 0.109884649 21.53601391 931527.0649 0.028434878 0.035993974 1729.747167 -3.237982628 0.12384673 FRYS(ph)GR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;FRY(0.001)S(0.999)GR 94.302 0.027032 1080560000 465976 533408 531149 532347 580654 665035 544277 557168 563931 557211 TRUE FALSE 484373.0923 625016.6747 544991.1793 637643.6477 481954.6405 510590.7 501615.1465 549700.0743 543635.2335 666385.827 0.726865838 0.93792012 0.817831288 0.956868562 0.723236631 0.766208823 0.752739819 0.824897607 0.815796512 1 19.34599819 5.033706894 14.28108911 0.830745364 0.412164894 0.120940131 0.08847204 21616248.49 283833231.2 0.020279685 216762192.7 108070.4335 -5.033706894 -0.41858047 FS(ph)GGFGAR ddPTM_MDA-MB-175_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 145.84 0.00059051 1827630000 1262229 1309014 1442035 1361651 1839907 2169486 1894699 1661670 1513980 1363702 TRUE FALSE 1312062.776 1533826.972 1479615.617 1630981.504 1527160.265 1665655.755 1746187.542 1639398.032 1459492.156 1630893.297 0.804505591 0.940482725 0.907242441 1.000054085 0.936394961 1.02131498 1.070693922 1.005214771 0.894903522 1 20.63723096 6.052589032 0.615670212 0.999677418 7.72E-11 0.558783763 0.048522384 11.11620142 0.91056501 0.020784637 11.29589037 1128727.306 -6.052589032 -0.999677418 FS(ph)LCSDNLEGISEGPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FS(0.5)LCS(0.5)DNLEGISEGPSNR;FS(0.647)LCS(0.324)DNLEGIS(0.029)EGPSNR 219.17 7.84E-19 117740000 76133 74242 86534 96021 98467 118382 97780 102196 88626 70078 TRUE FALSE 79138.78963 86992.48598 88789.14713 115013.6672 81729.61451 90889.5746 90115.7481 100826.2298 85436.36757 83808.44238 0.944281833 1.03799192 1.05942963 1.372339873 0.975195484 1.084491872 1.075258596 1.203055765 1.019424358 1 16.35480796 4.452154022 2.365423817 1.114328764 0.948617492 0.150989027 0.109887427 0.571319702 5.573120279 0.0271863 0.150485538 28323.96324 -4.452154022 -0.165711272 FS(ph)MPDLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSMPDLSK 8 0 A0A1X7SBR1;Q7Z3G6 A0A1X7SBR1 PRICKLE2 Prickle-like protein 2 1 FS(0.999)MPDLS(0.001)K 81.865 0.022591 0 120220 80528 102820 86201 136040 143370 124460 102500 107630 55479 TRUE FALSE 124966.3784 94358.05758 105499.5737 103251.3005 112915.9694 110074.4903 114704.5 101126.1552 103756.4173 66349.04784 1.883469055 1.422146371 1.590069143 1.556183606 1.701847624 1.659021401 1.72880401 1.524153827 1.563796629 1 16.01778814 0.332169411 1.079618363 0.998458018 1.631799601 0.721816951 0.117675873 1.540728848 2.046117328 0.110173249 0.033087126 2.148668472 -0.332169411 0.633341582 FS(ph)PDSQYIDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSPDSQYIDNR 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 FS(0.997)PDS(0.002)QYIDNR 80.96 0.024108 123770000 96090 84675 96081 99440 126170 138120 110820 110030 120250 88790 TRUE FALSE 99883.7074 99217.27257 98584.94979 119108.9352 104723.6685 106043.7232 102133.6388 108555.2278 115922.226 106186.7005 0.940642349 0.934366282 0.928411461 1.121693532 0.986222078 0.998653529 0.961830797 1.02230531 1.091683096 1 16.69624356 FS(ph)PGAPGGSGSQPNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK 334.14 1.23E-71 1093446000 1470500 948846 1222050 1114160 1423890 1639120 1903900 1357370 1438770 700516 TRUE FALSE 1528556.475 1111802.92 1253897.627 1334537.523 1181857.686 1258459.221 1754667.343 1339176.675 1386988.949 837768.698 1.824556681 1.327100096 1.496711001 1.592966562 1.41072075 1.502155934 2.094453215 1.598504072 1.655575044 1 19.67619246 FS(ph)PTMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FSPTMGR 7 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.886)PT(0.114)MGR;FS(0.998)PT(0.002)MGR;FS(0.989)PT(0.011)MGR;FS(0.847)PT(0.153)MGR;FS(0.995)PT(0.005)MGR 154.71 0.0017417 2667960000 1955180 1862060 2073060 2310720 2238090 2685170 2646060 2110660 1923400 1422850 TRUE FALSE 2032372.016 2181854.32 2127085.647 2767773.519 1857660.261 2061579.962 2438654.903 2082370.055 1854177.21 1701630.215 1.194367612 1.282214138 1.250028136 1.626542297 1.091694449 1.211532296 1.433128585 1.223750046 1.089647559 1 20.69848613 1.212573683 2.641967772 1.008835321 1.298834358 0.349278948 0.13830441 0.285479602 3.415129623 0.12451553 0.035126461 16.31449678 -1.212573683 0.289999037 FS(ph)PVLGR ddPTM_MDA-MB-175_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 182.73 0.00068499 3460295000 3128522 3122752 3438004 3384030 4094860 4616460 3849430 3383350 3171854 2838681 TRUE FALSE 3252038.464 3659060.364 3527601.209 4053381.034 3398817.16 3544357.128 3547701.618 3338001.727 3057699.594 3394866.192 0.957928319 1.077821675 1.039098748 1.193973725 1.001163807 1.044034412 1.045019573 0.983249866 0.900683391 1 21.69492328 1.645391081 2.987443953 0.947926309 1.055963512 0.316609014 0.061412884 0.236865807 4.953585229 0.038186418 0.01616441 44.19682599 -1.645391081 0.108037203 FS(ph)PVTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FS(0.999)PVT(0.001)PK;FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK;FS(1)PVTPK 106.68 0.0080214 5055983000 7916750 4717840 6336550 5528690 8171490 8986710 9829940 6908390 7388910 3503760 TRUE FALSE 8229309.403 5528092.32 6501685.699 6622248.381 6782503.049 6899682.797 9059443.617 6815794.332 7122984.572 4190254.688 1.963916281 1.319273584 1.551620649 1.58039281 1.618637423 1.64660225 2.162026963 1.626582353 1.69989299 1 21.9986065 2.674299754 4.367679676 1.70882499 1.585627657 0 0.305463327 0.919377466 35.24067541 0.095210765 0.09063807 472.3889764 -2.674299754 -0.123197333 FSALQQAVPTESTDNRR ddPTM_MDA-MB-175_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 ;;;; 206.8 1.07E-11 2980910000 1113860 1407680 1255050 1171060 1365520 1587960 1255810 1479900 1325500 1279250 FALSE TRUE 1157836.053 1649438.09 1287757.634 1402692.173 1133409.398 1219180.356 1157376.331 1460064.361 1277795.514 1529894.545 0.756807753 1.078138422 0.841729672 0.916855464 0.740841519 0.796904832 0.75650726 0.954356211 0.835218034 1 20.54500078 0.239355993 1.033702498 1.000320273 0.856114541 0.158577038 0.10015233 7.671317782 8.718085836 0.104937971 0.029871579 1.735225787 -0.239355993 -0.144205731 FSAS(ph)SGGGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSASSGGGGSR 11 0 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5;H0YD77;H0YEC5;H0YD99;H0YEN8;H0YDC0;H0YCF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 FS(0.004)AS(0.677)S(0.319)GGGGSR 67.385 0.063061 166670000 254510 254760 274400 294550 327250 356150 269200 284950 268520 283840 TRUE FALSE 264558.2513 298513.0482 281551.0894 352811.1109 271624.1619 273439.56 248099.4006 281130.7113 258856.0177 339453.0136 0.779366336 0.879394309 0.829425806 1.03935183 0.800181913 0.805529923 0.730879947 0.828187408 0.762568035 1 18.37285237 FSAVKDELPQS(ph)PGLIHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FSAVKDELPQSPGLIHGR 18 1 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 FSAVKDELPQS(1)PGLIHGR;FSAVKDELPQS(1)PGLIHGR;FSAVKDELPQS(1)PGLIHGR 190.8 1.56E-14 1219560000 1654590 1321650 1551780 1340900 2114490 2222920 1958190 1846170 2064630 1629170 TRUE FALSE 1719914.491 1548633.106 1592220.662 1606126.018 1755069.745 1706680.519 1804701.951 1821425.111 1990324.37 1948374.669 0.8827432 0.79483332 0.817204559 0.824341459 0.900786575 0.875950886 0.926260221 0.934843354 1.021530613 1 20.8938397 2.043948472 0.685765985 1.011645807 0.825550545 0.823449482 0.030048892 0.271077033 0.245938626 0.026054966 0.015220345 110.6492494 -2.043948472 -0.186095262 FSCPETDSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSCPETDSHR 10 0 P50416 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 ; 106.62 0.0023926 456480000 365180 559350 426680 688750 507600 756050 434890 486380 464280 632830 FALSE TRUE 379597.5884 655414.0114 437799.6313 824982.6943 421318.3333 580468.8455 400802.1854 479860.8717 447570.6535 756820.9222 0.501568571 0.866009372 0.578471893 1.090063277 0.556694881 0.766983085 0.529586556 0.634048105 0.591382506 1 19.52959245 FSDAGQPMSFVLEFHFEPNEYFTNEVLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 108.32 0.00041476 22801000 16703 15425 18658 13810 20355 25794 21444 18674 20615 14262 FALSE TRUE 17362.44734 18074.12376 19144.24281 16541.57678 16895.06437 19803.73441 19763.16325 18423.70557 19873.07018 17056.36584 1.017945294 1.059670268 1.122410424 0.969818362 0.990543034 1.161075847 1.158697195 1.080165948 1.165140943 1 14.05802267 2.737689399 24.99972292 1.118538914 1.035170067 0.310711072 0.059906627 95.15649904 2730514.055 0.0187081 0.018613296 546.6248844 -2.737689399 -0.083368847 FSDFLGLHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSDFLGLHSK 10 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 86.344 0.013622 7288700000 71492 4399700 1358900 3339500 519670 2685200 448230 1592030 387630 5046300 FALSE TRUE 74314.55936 5155314.25 1394314.05 4000043.133 431336.679 2061602.995 413096.5614 1570691.442 373679.272 6035025.868 0.012313876 0.854232337 0.231036963 0.662804638 0.071472217 0.341606323 0.068449841 0.260262586 0.061918421 1 22.52492852 -1.261478263 4.603355584 1.00028102 0.294632648 0.399344484 0.262859983 0.000712476 0.000114302 0.23918869 0.056355375 0.054767351 1.261478263 -0.705648372 FSDHVALLSVFQAWDDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FSDHVALLSVFQAWDDAR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;; 300.54 1.54E-49 1665312000 853232.3 1820462 1822490.5 1859432.6 1915963 2423172 1749253 2057116 1848978.9 1855849.1 FALSE TRUE 886918.57 2133112.187 1869986.1 2227222.818 1590288.294 1860427.027 1612141.979 2029543.725 1782434.511 2219467.199 0.399608776 0.961092008 0.842538291 1.003494361 0.716518043 0.838231368 0.726364409 0.914428348 0.803091171 1 21.08178196 4.746461514 24.95751575 0.858637458 0.399608548 0.671374895 0.097995682 544.0627049 1718555.848 0.021986087 0.239949798 55777.81706 -4.746461514 -0.45902891 FSDIQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 157.9 0.0033611 304602000 769350 867290 860720 881560 1030790 1125850 917960 945170 887390 856690 FALSE TRUE 799724.5321 1016240.311 883151.0703 1055929.937 855576.684 864388.3999 846007.8966 932501.5421 855453.0072 1024542.003 0.780567834 0.991897167 0.861995963 1.030636063 0.835082097 0.843682736 0.825742521 0.910164287 0.834961382 1 19.9665477 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSDPGQPMSFVLEFHFEPNDYFTNSVLTK 29 0 Q99733;Q99733-2;C9JZI7;E9PP22;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 149.98 3.92E-08 168700000 87132 77479 109020 91670 135480 131460 125110 96616 110530 79399 FALSE TRUE 90572.03864 90785.41555 111861.1508 109802.0524 112451.158 100930.4073 115303.5513 95321.02055 106552.0469 94955.71386 0.953834529 0.95608165 1.178034962 1.156350133 1.184248461 1.062920842 1.214287657 1.003847127 1.122123594 1 16.5349672 4.252820148 24.82901967 1.116666898 0.954957937 0.457577589 0.069784162 182.8550281 318385.124 0.016525451 0.044786882 17898.64475 -4.252820148 -0.161708961 FSEAEHWLDYFPPLAIQDLK ddPTM_MDA-MB-175_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" 0 139.17 4.85E-07 127370000 90279 67933 78697 79668 119300 114540 114590 81405 98700 53545 FALSE TRUE 93843.28463 79599.9643 80747.90847 95426.09261 99021.42861 87939.82087 105608.1364 80313.89913 95147.80628 64036.11757 1.465474301 1.243047944 1.260974455 1.490191727 1.546337167 1.373284706 1.649196428 1.254196884 1.485845955 1 15.96659822 -1.145882311 3.8426677 0.999822162 1.41191032 0.48592216 0.129035048 4055621.685 1814086.54 6951.847365 0.029836007 0.071468997 1.145882311 0.412088158 FSEAEHWLDYFPPLAIQDLKR ddPTM_MDA-MB-175_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 ; 134.06 5.76E-06 324510000 316180 304220 348600 286510 462830 448030 333220 375720 407500 276260 FALSE TRUE 328663.0305 356467.4185 357684.8024 343180.8229 384158.3219 343981.8225 307101.3457 370684.088 392834.1546 330387.8577 0.994779387 1.078936196 1.082620908 1.038721051 1.162749517 1.041145473 0.929517652 1.121966438 1.189009055 1 18.33380114 4.741773259 23.15430846 1.072306719 0.994779309 0.092460909 0.072202324 280.7927517 2023445.546 0.017161015 0.12037457 55178.92807 -4.741773259 -0.07752741 FSEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FSEEQR 6 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 125.86 0.041275 3706050000 4084410 4532840 4673250 4700940 4896290 5653510 5076680 4679420 4341260 3795460 FALSE TRUE 4245665.661 5311320.009 4795038.734 5630771.901 4064020.375 4340567.982 4678756.556 4616700.029 4185018.901 4539107.719 0.93535248 1.170124249 1.056383552 1.240501933 0.89533464 0.956260184 1.030765702 1.017094177 0.921991537 1 22.11397729 3.221853531 24.99994083 0.977703785 1.10239966 0.369824922 0.083002303 261.4583799 391237.2714 0.023156522 0.027747642 1666.685018 -3.221853531 0.124695875 FSEGTSADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FSEGTSADR 9 0 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;; 125.31 0.0011749 495030000 329325 382170 391900 380997 425930 505480 404020 413690 394876 388550 FALSE TRUE 342327.0053 447804.7246 402113.2359 456357.0694 353530.5707 388089.9306 372351.8567 408145.1622 380664.4899 464678.9333 0.736695772 0.963686306 0.865357147 0.982091153 0.760806108 0.835178664 0.801309958 0.878337994 0.819198941 1 18.82587471 -1.558644923 3.069460308 1.006462642 0.853692095 0.266214526 0.074780277 22793034.31 25286460.7 1203869.538 0.01701198 0.027628358 1.558644923 -0.152770547 FSEGVLQS(ph)PSQDQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.672)PS(0.328)QDQEK;FSEGVLQS(0.981)PS(0.019)QDQEK;FSEGVLQS(0.535)PS(0.465)QDQEK 233.14 1.33E-17 328674000 687320 414165 552550 401497 649220 729820 635130 589170 643390 392970 TRUE FALSE 714455.9243 485294.617 566949.9069 480911.9083 538865.8163 560330.3655 585346.851 581273.1398 620234.5196 469964.9476 1.520232366 1.03261875 1.206366368 1.023293143 1.146608527 1.192281187 1.245511722 1.236843605 1.31974634 1 18.84219363 2.4575482 6.673585081 1.222680443 1.169365273 0 0.149921436 0.75235843 134.2213449 0.048957548 0.041664849 286.7795639 -2.4575482 -0.05331517 FSEGVLQSPS(ph)QDQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 FSEGVLQS(0.007)PS(0.993)QDQEK 191.37 1.87E-07 108260000 390330 222510 309870 215370 357240 384340 348580 321610 343950 219490 TRUE FALSE 405740.5298 260724.3616 317945.4668 257969.5432 296516.4724 295082.8597 321257.3888 317299.344 331571.3067 262494.8631 1.545708457 0.9932551 1.211244529 0.982760349 1.129608667 1.124147178 1.223861621 1.208783061 1.263153506 1 18.00192966 4.751659286 24.79138542 1.138704497 1.545708752 0.615761031 0.098954567 1343.622443 2542975.805 0.023284642 0.444326217 56449.39424 -4.751659286 0.407004255 FSELSEELLWEYVHSGEPMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSELSEELLWEYVHSGEPMDK 21 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 94.176 0.0012226 66365000 15180 53418 38292 55120 34059 58576 32556 39475 41698 62184 FALSE TRUE 15779.31812 62592.12597 39289.92098 66022.57148 28269.66335 44972.61173 30004.17565 38945.90219 40197.29713 74367.76422 0.212179542 0.841656686 0.528319244 0.887784811 0.380133296 0.604732604 0.403456739 0.523693331 0.540520447 1 16.18238978 -1.300180297 2.996992376 1.003553769 0.55345764 0.333663215 0.191874968 25350992.21 32700769.66 812314.976 0.047548012 0.050097921 1.300180297 -0.450096128 FSESES(ph)RSPLEDETDNTWMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSESESRSPLEDETDNTWMFK 21 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 FSESES(0.538)RS(0.461)PLEDETDNTWMFK;FSES(0.004)ES(0.573)RS(0.423)PLEDETDNTWMFK 131.57 7.87E-06 127159000 63424 49137 62377 47224 80138 81815 58001 47727 63265 50839 TRUE FALSE 65928.02849 57575.89752 64002.59586 56564.76625 66516.17138 62814.70617 53454.73006 47087.29763 60988.10501 60799.92868 1.084343846 0.946973109 1.052675509 0.930342642 1.09401726 1.033137827 0.879190671 0.774463041 1.003095009 1 15.89178201 2.23602045 24.93899145 0.881857053 1.020385422 0.275382748 0.080256873 63.34743107 621923.7509 0.028515118 0.022043447 172.1949655 -2.23602045 0.138528369 FSESESRS(ph)PLEDETDNTWMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSESESRSPLEDETDNTWMFK 21 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 FSES(0.001)ES(0.384)RS(0.615)PLEDETDNTWMFK 144.26 7.83E-08 50264000 67311 58683 55722 48437 72968 82035 77332 64995 67547 45356 TRUE FALSE 69968.49026 68761.34876 57174.1611 58017.69403 60564.92542 62983.6145 71270.51577 64123.84834 65115.99666 54242.63981 1.289916761 1.267662286 1.054044591 1.069595695 1.11655564 1.16114582 1.313920488 1.182166808 1.200457738 1 15.72713977 2.450370971 24.98391356 1.198567387 1.153116349 0 0.10147444 851.6280969 795388.7134 0.035891002 0.030029152 282.0791402 -2.450370971 -0.045451038 FSFHS(ph)PSAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSFHSPSAQQR 11 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 FSFHS(1)PSAQQR 147.52 2.27E-05 174520000 63932 129560 117020 123100 140450 165300 117950 131820 97627 137570 TRUE FALSE 66456.08473 151810.9222 120069.6373 147448.8126 116576.3592 126911.5801 108704.7708 130053.1685 94113.42334 164524.2076 0.403928915 0.922726962 0.729799214 0.89621348 0.708566605 0.771385452 0.660722045 0.790480443 0.572033895 1 17.32794035 4.754069232 24.50795262 0.77144215 0.403928559 0.463221975 0.121969754 1930.315248 3050371.247 0.02653058 0.642696481 56763.50863 -4.754069232 -0.367513591 FSFSGNTLVSSSADPEGHFETPIWIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSFSGNTLVSSSADPEGHFETPIWIER 27 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 199.04 5.38E-25 1034890000 200626 316650 260178 335560 339130 386580 283570 289158 310940 273070 FALSE TRUE 208546.8694 371032.1743 266958.4524 401932.7665 281484.8037 296802.6537 261343.0424 285282.31 299749.3301 326572.8383 0.638592207 1.136139112 0.81745455 1.230759939 0.861935748 0.908840598 0.80025958 0.873564107 0.917863628 1 18.31704528 FSFSPEPTLEDIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 ; 162.48 7.11E-06 467840000 195922 506760 379200 449280 374370 527550 282440 418110 342550 657230 FALSE TRUE 203657.1518 593792.088 389082.2635 538146.243 310734.7211 405034.5076 260301.6148 412505.9193 330221.6924 786001.6351 0.259105252 0.7554591 0.495014573 0.684663007 0.395335973 0.515310006 0.331171849 0.5248156 0.420128506 1 19.58417279 -1.553493479 3.656313193 1.011782677 0.494377529 0.538091225 0.142495083 31602767.55 27125325.21 2806429.473 0.03089062 0.027958027 1.553493479 -0.517405149 FSFWDKDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSFWDKDAR 9 1 P78406;E9PQ57 P78406 RAE1 mRNA export factor 0 78.098 0.02803 282880000 892660 880940 813550 693600 2264300 1463300 1057000 866610 1014100 1881500 FALSE TRUE 927902.9061 1032234.592 834751.7813 830792.0098 1879415.095 1123470.752 974149.578 854994.5104 977602.7391 2250143.902 0.412374918 0.458741591 0.370977065 0.36921728 0.835242179 0.499288401 0.43292768 0.379973259 0.43446232 1 21.10158584 -1.954480713 2.547991088 1.410132083 0.464233478 0.604018794 0.129725392 28633663.92 13031964.34 69464901.21 0.03233426 0.011105019 1.954480713 -0.945898605 FSGDLDDQTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FSGDLDDQTCR 11 0 P05455 P05455 SSB Lupus La protein 0 ;;; 297.13 2.82E-35 2864670000 2634880 2599050 2558080 2871240 3011340 3439270 2951300 2816850 2605410 2273390 FALSE TRUE 2738907.097 3045416.62 2624745.666 3439162.702 2499473.502 2640551.665 2719969.394 2779094.733 2511641.803 2718817.244 1.007389189 1.120125535 0.965399816 1.264948098 0.919323838 0.971213373 1.000423769 1.022170482 0.923799424 1 21.37454775 FSGEEGEIEDDES(ph)GTENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSGEEGEIEDDESGTENR 18 0 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(1)GTENR;FSGEEGEIEDDES(1)GTENR 415.75 1.07E-147 795400000 521220 484950 464250 634080 447210 628410 759200 521830 502100 281900 TRUE FALSE 541798.1681 568236.3901 476348.7364 759499.1315 371193.4039 482471.3011 699691.9202 514835.7224 484029.5191 337132.9077 1.607075891 1.685496661 1.412940492 2.252818144 1.101029877 1.431101177 2.075418638 1.527100175 1.435723147 1 18.36295793 0.898834834 2.188764028 1.002842118 1.644411757 0.282089813 0.310407916 0.541498439 5.401574903 0.282510618 0.077455491 7.921999925 -0.898834834 0.641569639 FSGEEGEIEDDES(ph)GTENREEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.999)GT(0.001)ENREEK;FSGEEGEIEDDES(0.996)GT(0.004)ENREEK 227.03 1.33E-25 243606000 311760 160280 229710 214410 256460 266730 357530 239850 244380 107889 TRUE FALSE 324068.5255 187806.8432 235696.4313 256819.658 212867.0208 204785.9998 329505.8644 236635.2031 235584.8115 129027.7839 2.511618163 1.455553506 1.826710684 1.990421367 1.649776617 1.587146533 2.553759 1.833986417 1.8258456 1 16.97732223 0.663784142 2.699066803 1.000106808 1.913896343 0.393756501 0.342445458 2.955346763 22.51326914 0.312582815 0.082682171 4.610883424 -0.663784142 0.913789535 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 FSGEEGEIEDDES(0.994)GT(0.006)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.806)GT(0.194)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.964)GT(0.036)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.983)GT(0.017)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.969)GT(0.031)ENREEKDNIQPTTE 210.21 7.79E-26 2614150000 1120694 689702 845065 700921 1118843 1161340 1130568 885556 951419 566243 TRUE FALSE 1164939.864 808152.9534 867088.0881 839561.0818 928662.4665 891636.3853 1041951.126 873686.5703 917177.616 677187.4745 1.720261978 1.193396192 1.280425467 1.239776448 1.371352102 1.316675838 1.538645006 1.290169419 1.35439247 1 19.36919576 0.212255002 1.557049393 0.999896614 1.359045334 0.357510301 0.147377543 11.34756982 21.03870801 0.133967699 0.037946404 1.630252978 -0.212255002 0.35914872 FSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSGFSAKPNNSGEAPSSPTPK 21 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 FSGFSAKPNNSGEAPS(0.008)S(0.992)PTPK 204.61 3.15E-22 383170000 902860 377160 557840 385210 828430 739030 748440 622160 679360 289800 TRUE FALSE 938505.61 441934.2961 572377.7687 461403.3883 687613.7645 567401.4826 689775.3171 613820.9628 654909.9663 346580.7614 2.707898748 1.27512645 1.651498965 1.331301213 1.983992884 1.637140735 1.990229678 1.771076272 1.889631622 1 18.40283205 -0.803641276 7.440933977 0.999999999 1.777938476 0.28383822 0.381181094 1.01E-08 6.77E-10 0.337846592 0.079631206 0.157166045 0.803641276 0.777938477 FSGWYDADLS(ph)PAGHEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 1 FSGWYDADLS(1)PAGHEEAK;FSGWYDADLS(1)PAGHEEAK 209.71 3.17E-16 209990000 437800 280070 378980 294350 427430 464260 478470 354470 371690 237642 TRUE FALSE 455084.6821 328169.8439 388856.5301 352571.5515 354775.6013 356442.6509 440966.2712 349718.9094 358312.9495 284203.4 1.601264032 1.154700626 1.36823321 1.240560639 1.248315824 1.254181516 1.551586896 1.230523314 1.260762361 1 18.11656429 0.752785449 1.659530774 1.001085526 1.326506676 0.351934604 0.135590268 0.936795842 4.252911809 0.120048218 0.034292125 5.659596237 -0.752785449 0.325421151 FSGWYDADLSPAGHEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 267.62 2.64E-31 2193500000 640820 577080 806180 637420 938220 970640 934220 792120 888550 450400 FALSE TRUE 666120.0684 676189.0009 827189.7131 763499.7735 778741.6995 745223.5702 860993.3953 781502.927 856571.2591 538647.2566 1.236653599 1.255346598 1.535679803 1.417439269 1.445735943 1.383509451 1.598436425 1.450862169 1.590226718 1 19.03898128 4.257650848 22.45243289 1.451238755 1.245999179 0.1582068 0.160519882 104.1274409 122458.7942 0.034874538 0.094999122 18098.84449 -4.257650848 -0.205239576 FSGWYDADLSPAGHEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FSGWYDADLSPAGHEEAKR 19 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;; 173.87 3.63E-12 6501770000 2830010 2946060 3791380 3022860 4615110 4404370 4196360 3987070 4200890 2798740 FALSE TRUE 2941740.98 3452022.888 3890186.477 3620772.686 3830635.251 3381521.816 3867438.338 3933629.848 4049700.789 3347099.518 0.878892595 1.03134755 1.162255994 1.081764276 1.144464104 1.010284217 1.15545962 1.175235402 1.209913469 1 21.67448002 4.616293743 2.607614526 1.124129672 0.859024212 0.54700895 0.066079137 0.262499693 2.718325535 0.016236977 0.133287833 41332.69684 -4.616293743 -0.26510546 FSHEEIAMATVTALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FSHEEIAMATVTALR 15 0 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;;; 218.68 1.91E-12 7502000000 1887493.6 2495055 2327644.3 2422306.4 3169000 3190402 2990625 2379098 2252334.1 2624756.6 FALSE TRUE 1962013.305 2923561.287 2388304.623 2901431.376 2630334.512 2449479.487 2756211.998 2347210.083 2171273.036 3139027.402 0.625038604 0.931358957 0.760842235 0.924309031 0.8379457 0.780330712 0.878046492 0.747750746 0.691702479 1 21.58188619 -2.472581202 2.192050684 3.126277545 0.804255783 0.294150504 0.093586911 4748234.258 229111.7766 50779758.45 0.022637399 0.003368362 2.472581202 -2.322021762 FSHEEIAMATVTALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FSHEEIAMATVTALRR 16 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;; 261.61 4.98E-27 8648670000 1607146 1819520 1893242 1334002 2241199 2146237 1480682 1773289 1906688 1930699 FALSE TRUE 1670597.365 2132008.406 1942581.442 1597863.614 1860240.795 1647805.983 1364622.276 1749520.961 1838066.671 2308982.504 0.723521015 0.923354076 0.841314925 0.692020668 0.805653915 0.713650268 0.591005897 0.75770213 0.796050498 1 21.13882581 5.056245228 15.18810433 0.773403751 0.367006628 0.010186519 0.111222767 5812099.113 40373543.21 0.026353932 70603602.11 113826.9837 -5.056245228 -0.406397123 FSHQGVQLIDFSPCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FSHQGVQLIDFSPCER 16 0 P55884;P55884-2;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 178.22 2.82E-09 1051140000 762161 843233 873880 922930 1050560 1181920 929460 985920 902500 918940 FALSE TRUE 792251.7048 988051.7083 896654.0307 1105482.799 871986.1865 907436.9922 856606.4965 972705.355 870019.2013 1098988.699 0.720891585 0.899055386 0.815890128 1.00590916 0.79344418 0.825701841 0.779449777 0.885091317 0.791654366 1 20.06774512 -1.189177912 4.860730861 1.000018215 0.840921302 0.300205854 0.075017956 1.38E-05 2.30E-06 0.067687208 0.015952202 0.064687756 1.189177912 -0.159096913 FSHVDSPNSECKGEDATDDQFES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSHVDSPNSECKGEDATDDQFESPK 25 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 FSHVDSPNSECKGEDATDDQFES(1)PK;FSHVDSPNSECKGEDATDDQFES(1)PK 179.67 1.63E-17 340510000 272168 59835 90997 71923 152416 189776 167964 110767 116169 45624 TRUE FALSE 282913.4028 70111.1958 93368.45657 86149.15473 126508.3828 145703.4001 154798.5428 109282.3495 111988.1004 54563.14928 5.185063666 1.284955079 1.711199918 1.578888973 2.318568199 2.670362727 2.837052935 2.002860007 2.052449352 1 15.7356393 4.746877023 24.99887473 2.026787078 5.185065235 0.754522418 0.553344638 543.015986 1632253.904 0.135847065 1.557023798 55831.20782 -4.746877023 3.158278157 FSLCS(ph)DNLEGISEGPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSLCSDNLEGISEGPSNR 18 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-5;Q14C86;C9IZ08;H0Y7I9;B4DGD8;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 FSLCS(1)DNLEGISEGPSNR;FS(0.047)LCS(0.953)DNLEGISEGPSNR 317.58 2.24E-61 160570000 146676 154860 163560 176293 186573 210137 191836 177087 184529 159286 TRUE FALSE 152466.8817 181456.0004 167822.508 211163.2292 154859.3881 161335.8664 176799.393 174713.4384 177887.8373 190495.042 0.800371916 0.952549728 0.880980976 1.108497245 0.812931331 0.846929478 0.928104959 0.917154781 0.933818726 1 17.53939392 0.747798601 1.360110464 0.999798687 0.908299034 0.107719253 0.082271333 2.079393413 6.564758543 0.075676612 0.022526581 5.59498081 -0.747798601 -0.091499653 FSLDVCEAMEYLEGNNFVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSLDVCEAMEYLEGNNFVHR 20 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 ; 279.54 1.14E-44 445320000 324140 372380 376520 357410 408640 502530 395490 390500 372850 345350 FALSE TRUE 336937.2975 436333.3683 386332.4205 428104.6312 339179.5188 385825.0234 364490.4604 385265.9862 359431.2013 413014.7204 0.81579973 1.056459605 0.93539625 1.036536012 0.821228644 0.934167729 0.882512033 0.932814176 0.870262447 1 18.65583368 3.246331908 24.99980101 0.905133012 0.966030734 0.11018001 0.074855085 341.0399033 1097099.088 0.019089277 0.025374225 1763.323145 -3.246331908 0.060897722 FSLQDPPNKKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSLQDPPNKKPK 12 2 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 51.286 0.088198 589440000 2380900 1234900 1884400 1193700 2586500 2204800 2372000 1862900 2157200 1099300 FALSE TRUE 2474899.77 1446984.469 1933509.012 1429810.297 2146847.654 1692768.614 2186076.442 1837930.873 2079562.793 1314686.788 1.88250144 1.10063057 1.470699356 1.087567252 1.632972716 1.287583195 1.662811601 1.397999044 1.581793331 1 20.3262877 -1.277594316 5.500296464 0.999953102 1.441176212 0.245952953 0.238282732 0.000122676 1.61E-05 0.206532764 0.048675083 0.052772259 1.277594316 0.44122311 FSLYFLAYEDKNDIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSLYFLAYEDKNDIPK 16 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 226.25 5.58E-15 833790000 1425450 753290 1105960 687550 1436140 1385250 1151830 1135420 1174940 720480 FALSE TRUE 1481727.867 882661.6977 1134782.226 823545.3379 1192025.436 1063546.681 1061546.555 1120201.552 1132654.139 861644.2616 1.719651523 1.024392243 1.316996209 0.955783465 1.383431062 1.234322247 1.232000957 1.300074291 1.314526411 1 19.71673284 -2.350060255 1.658527115 8.45E-05 1.262684917 0.148613622 0.195742581 1267068.127 142104.435 4724121.601 0.047480349 0.004466216 2.350060255 1.262600439 FSPDGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSPDGNR 7 0 O75083;O75083-3;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 95.62 0.051608 0 621760 702900 653160 646400 721730 875270 684670 672240 644470 636930 FALSE TRUE 646307.5649 823617.6072 670181.8862 774255.9907 599050.5924 672001.8073 631003.7763 663229.7224 621275.6506 761724.2387 0.848479715 1.081254298 0.879822188 1.016451822 0.786440239 0.8822114 0.828388732 0.87069531 0.815617541 1 19.53890928 3.243287707 24.99999822 0.856890566 0.959935749 0.235963257 0.080959253 145.0587994 767161.5751 0.020401077 0.026741224 1751.006295 -3.243287707 0.103045184 FSPFLQTAEDNTQDEVAGAPADHHGPS(ph)DEEQGSPPEDK ddPTM_MDA-MB-175_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 236.36 1.23E-49 94289000 49593 43161 49977 42937 56558 53257 61551 54562 54346 34976 TRUE FALSE 51550.96993 50573.566 51279.44168 51429.81045 46944.29136 40888.86887 56726.47179 53830.68564 52390.09808 41828.87754 1.232425371 1.209058645 1.225933964 1.22952882 1.122293834 0.977527279 1.356155726 1.286926372 1.252486348 1 15.35221166 FSPPS(ph)PLPQAVFSTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR;FSPPS(1)PLPQAVFSTSSR 255.08 4.91E-27 1631580000 733766 665366 712172 633259 937644 972512 771373 751206 813534 721807 TRUE FALSE 762735.6483 779637.4347 730731.7874 758515.7401 778263.6078 746660.8266 710910.7687 741137.3123 784255.0703 863231.2618 0.88358205 0.903161724 0.846507558 0.878693548 0.901570231 0.864960364 0.823546134 0.858561715 0.908510969 1 19.71938759 0.906260536 3.720897117 0.999922868 0.869052879 0.746735412 0.02292228 0.209301154 6.507104649 0.02367578 0.006085176 8.058617375 -0.906260536 -0.130869989 FSPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSPSPR 6 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 FSPS(1)PR 110.12 0.030394 221830000 189780 197860 195310 213450 223660 256350 196990 217320 192450 192620 TRUE FALSE 197272.6609 231840.9159 200399.939 255669.7729 185642.3531 196816.5975 181549.4091 214407.1809 185523.7621 230360.2011 0.856366074 1.006427824 0.869941674 1.109869551 0.805878586 0.85438629 0.788111003 0.930747498 0.805363779 1 17.81353196 3.154106319 24.16402675 0.859858513 0.95760347 0.219144406 0.089011468 27.24551106 7790.911701 0.023807831 0.028455815 1425.956638 -3.154106319 0.097744956 FSPVT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSPVTPK 7 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FSPVT(1)PK 86.882 0.091822 0 484040 276650 397440 317210 581500 652430 557470 432740 526110 350690 TRUE FALSE 503150.273 324162.4855 407797.6129 379953.1912 482656.8377 500913.0202 513774.0447 426939.8281 507175.4039 419400.9911 1.199687849 0.772917786 0.972333451 0.905942521 1.150824266 1.194353449 1.225018671 1.017975248 1.209285182 1 18.67797075 3.233255656 24.99905784 1.134963204 0.94984971 0.321172184 0.120611421 137.6217865 648527.6744 0.032814223 0.040323879 1711.022246 -3.233255656 -0.185113495 FSQTVLGADSEALT(ph)DSWEALSLDTEYWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSQTVLGADSEALTDSWEALSLDTEYWK 28 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 1 FSQTVLGADS(0.003)EALT(0.378)DS(0.303)WEALS(0.303)LDT(0.013)EYWK 75.226 2.76E-05 0 9664.2 7562.3 10581 9419.3 10406 11756 11139 9205.9 7558.8 4811.6 TRUE FALSE 10045.75008 8861.066198 10856.74955 11282.40943 8637.191837 9025.847164 10265.89607 9082.509968 7286.760265 5754.340896 1.745769022 1.539892467 1.88670601 1.96067797 1.500987166 1.568528408 1.7840264 1.578375375 1.266306671 1 12.49043498 1.13320755 1.925040406 1.00242374 1.71019887 0.739660101 0.139806481 0.159090361 1.113712524 0.135500035 0.03882664 13.5896274 -1.13320755 0.70777513 FSS(ph)PIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSSPIVK 7 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 FS(0.003)S(0.997)PIVK;FS(0.025)S(0.975)PIVK 86.136 0.021292 201804000 684060 468770 546940 428290 678310 737470 637330 557700 614220 429180 TRUE FALSE 711067.217 549277.601 561193.7057 513004.4837 563011.1085 566203.769 587374.4092 550224.9437 592114.3422 513269.6039 1.385367868 1.070154158 1.093370232 0.999483468 1.096911066 1.103131307 1.144377935 1.07199986 1.153612717 1 18.9693573 4.74027659 24.96465596 1.084958374 1.385367971 0.777929415 0.048681577 64.75351104 941978.9613 0.011109083 0.071512365 54989.09728 -4.74027659 0.300409596 FSS(ph)PTEELDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSSPTEELDYR 11 0 O95359-3;E9PBC6;E7EMZ9;O95359;O95359-5;D6RAA5;O95359-1;O95359-6;Q4VXL8;E9PGB3;O95359-2;Q4VXL4;H0Y911 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 FS(0.053)S(0.945)PT(0.001)EELDYR;FS(0.001)S(0.998)PTEELDYR 208.33 2.09E-08 1293660000 590830 627740 675770 605750 790270 863130 740580 681270 691030 632140 TRUE FALSE 614156.4246 735549.4619 693381.1214 725565.542 655940.1877 662681.1384 682531.4045 672138.69 666159.9653 755995.7299 0.812380812 0.972954519 0.917175976 0.959748201 0.867650652 0.876567303 0.902824417 0.889077363 0.881168952 1 19.52801856 -1.363473921 5.910881333 1.000017235 0.900268647 0.330480241 0.043535555 9.36E-06 1.01E-06 0.039898405 0.00940252 0.043303807 1.363473921 -0.099748588 FSS(ph)VSSPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.039)S(0.438)VS(0.135)S(0.388)PQPR 94.363 0.0085544 322860000 533720 771120 689190 686250 755930 1019100 667220 756860 620320 814850 TRUE FALSE 554791.6777 903553.8615 707150.8576 821988.2017 627437.2886 782429.4696 614921.5529 746715.5297 597994.8044 974504.2563 0.569306572 0.927193345 0.725651892 0.843493701 0.643852794 0.802900002 0.631009612 0.766251686 0.613640013 1 19.89430896 -1.020121053 4.954201517 1.000003737 0.732642617 0.369603387 0.107380479 3.98E-06 7.86E-07 0.093265877 0.021982671 0.095472643 1.020121053 -0.26736112 FSSDELQILTYQLCHTYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSSDELQILTYQLCHTYVR 19 0 Q9UKV8-2;Q9UKV8 Q9UKV8-2 AGO2 Protein argonaute-2 0 114.4 0.00015824 48500000 82610 73763 90446 59763 108740 117290 104790 74525 105460 50199 FALSE TRUE 85871.50659 86431.22145 92803.09706 71583.94303 90256.41364 90051.17505 96576.28598 73526.11427 101664.5152 60034.53293 1.430368529 1.439691745 1.545828584 1.192379444 1.503408276 1.4999896 1.608678893 1.224730346 1.693433933 1 15.87350498 -1.345834555 4.594304485 0.999559117 1.446435275 0.46473219 0.147419606 0.000622666 8.87E-05 0.13350469 0.031437009 0.045098848 1.345834555 0.446876158 FSSETWQNLGTLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSSETWQNLGTLHR 14 0 F8W9U3;Q96IU4;B4DQI4 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 268.93 2.58E-25 2451200000 1237360 1274140 1460770 1549010 1659620 1784430 1616650 1442870 1479660 1247690 FALSE TRUE 1286211.928 1492963.634 1498838.866 1855399.555 1377518.385 1370023.176 1489932.749 1423530.688 1426407.326 1492150.967 0.861985119 1.000544628 1.004482053 1.243439569 0.923176284 0.918153194 0.998513409 0.954012509 0.955940355 1 20.50896208 FSSVSS(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FSSVSSPQPR 10 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 FS(0.001)S(0.18)VS(0.042)S(0.778)PQPR;FSS(0.024)VS(0.05)S(0.926)PQPR;FS(0.015)S(0.14)VS(0.036)S(0.809)PQPR 120.03 0.00064342 1263030000 2200640 2618670 2348000 2358510 2717090 3202730 2516700 2507090 2347230 2378190 TRUE FALSE 2287522.966 3068406.202 2409190.809 2825016.239 2255240.012 2458944.495 2319434.478 2473486.559 2262753.651 2844150.797 0.804290324 1.078847931 0.847068591 0.993272312 0.792939676 0.864561927 0.815510373 0.8696749 0.795581462 1 21.43956653 3.237832873 24.99986074 0.848946356 0.935453853 0.139609706 0.089170584 31.12295196 1069170.086 0.022823495 0.028842054 1729.150814 -3.237832873 0.086507497 FSTELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSTELER 7 0 Q9UH65;E7EMB1 Q9UH65 SWAP70 Switch-associated protein 70 0 127.31 0.022596 0 52697 79826 69569 73106 77337 91724 75845 77190 63956 90468 FALSE TRUE 54777.51825 93535.49454 71382.02529 87566.1486 64191.28436 70422.49109 69900.07072 76155.39431 61654.23605 108193.4725 0.506292265 0.864520681 0.659762772 0.809347797 0.593300898 0.650894083 0.646065508 0.703881598 0.569851717 1 16.72325394 -1.009232334 5.408813517 1.00000142 0.675510568 0.491037916 0.101350962 1.58E-06 2.89E-07 0.089348635 0.021059583 0.097896613 1.009232334 -0.324490852 FSTLTDDPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;FSTLTDDPS(1)PR 138.42 6.07E-05 540610000 763900 807680 848740 862190 963040 1033260 922010 869720 849050 808810 TRUE FALSE 794059.3619 946392.7571 870858.8616 1032728.609 799342.8048 793301.0242 849740.447 858062.826 818492.8564 967280.8339 0.820919152 0.978405365 0.900316466 1.067661606 0.826381312 0.820135163 0.878483701 0.887087592 0.846179132 1 19.88357529 FSTYS(ph)QSPPDTPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSTYSQSPPDTPSLR 15 0 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 FSTYS(0.681)QS(0.319)PPDTPSLR 138.98 7.56E-06 416330000 264410 297270 311430 266430 308110 376130 299110 317070 304340 238880 TRUE FALSE 274849.111 348323.8101 319546.1216 319129.0588 255737.5723 288779.5078 275664.9766 312820.1953 293386.8628 285683.9624 0.962073995 1.219262738 1.118530137 1.117070262 0.89517651 1.010835559 0.964929828 1.094986896 1.026963013 1 18.12406052 3.351534786 22.03488822 1.007748423 1.113495682 0.313092678 0.07530593 4.400193895 837.5618801 0.020602316 0.027895677 2246.646719 -3.351534786 0.105747259 FSTYSQS(ph)PPDTPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSTYSQSPPDTPSLR 15 0 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 FST(0.001)YS(0.063)QS(0.936)PPDTPSLR;FSTYS(0.071)QS(0.928)PPDTPSLR 185.91 1.09E-11 130090000 234710 276380 259410 256530 274130 323300 267350 267400 247050 245110 TRUE FALSE 243976.532 323846.1151 266170.4377 307270.8683 227533.4805 248218.4747 246394.4084 263815.9404 238158.7188 293134.6116 0.832302029 1.104769284 0.908014363 1.048224455 0.77620817 0.846773001 0.840550377 0.899982226 0.812455129 1 18.1612038 3.242071979 24.99949284 0.85843004 0.978050996 0.271782736 0.088446653 106.1174128 755507.0443 0.022701345 0.029559884 1746.111526 -3.242071979 0.119620956 FSVCVLGDQQHCDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ;;;;; 250.41 7.80E-21 5022460000 4192010 2830450 4065090 2780320 5054840 5055690 4495350 3965100 4504480 2537580 FALSE TRUE 4357513.792 3316557.77 4171029.585 3330258.998 4195620.102 3881582.617 4142992.721 3911954.32 4342364.645 3034770.216 1.435862843 1.092853011 1.374413642 1.097367761 1.382516568 1.279036744 1.365175096 1.289044653 1.430870984 1 21.53315585 FSWFAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FSWFAGEK 8 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 113.7 0.0065106 1246930000 1072530 820970 998700 867130 1673180 1400880 1463080 1063350 1122280 849430 FALSE TRUE 1114874.313 961965.2112 1024726.942 1038645.726 1388773.461 1075546.851 1348399.967 1049097.533 1081889.362 1015859.545 1.097468954 0.946947062 1.00872896 1.022430444 1.367092004 1.05875547 1.327348818 1.032719078 1.064998963 1 19.95426952 3.43466175 24.99998762 1.14891012 1.011460679 0.201798586 0.119102528 196.3449524 115606.4681 0.031531974 0.042694525 2720.581557 -3.43466175 -0.137449441 FSWMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FSWMGR 6 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 124.86 0.042275 163120000 152560 263930 220010 233240 244310 274440 191820 240690 183390 273660 FALSE TRUE 158583.1866 309257.9244 225743.6413 279374.1758 202782.2735 210705.4692 176784.6472 237463.9442 176789.8297 327278.4375 0.484551282 0.944938282 0.689760203 0.853628421 0.619601692 0.643811034 0.540165886 0.725571614 0.540181721 1 18.32015903 -1.063502328 4.292141181 1.000029592 0.680626331 0.342803763 0.135967886 14632618.23 7251310.965 3937.619974 0.030095966 0.086396803 1.063502328 -0.319403262 FSWNVWPSSR ddPTM_MDA-MB-175_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 ; 99.53 0.010776 1369370000 623810 702210 750590 681450 880440 937040 756520 699760 706270 877640 FALSE TRUE 648438.5005 822809.1051 770150.992 816238.7761 730783.1233 719426.661 697221.9856 690380.8618 680851.4807 1049596.755 0.617797738 0.783928782 0.73375893 0.777668921 0.696251318 0.685431484 0.664276049 0.65775819 0.648679102 1 20.00140373 -1.558535455 5.924988511 1.000732611 0.697625015 0.756185071 0.051750565 0.000522477 3.89E-05 0.052274559 0.012292684 0.027635323 1.558535455 -0.303107596 FT(ph)DTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTDTRK 6 1 P13639 P13639 EEF2 Elongation factor 2 1 FT(1)DTRK 55.531 0.091784 154640000 113590 80528 125170 71601 407340 147210 119870 135920 169900 133290 TRUE FALSE 118074.6209 94358.05758 128432.033 85763.46409 338100.4923 113022.7085 110474.2762 134098.2147 163785.3322 159405.6235 0.740718039 0.591936818 0.805693238 0.538020317 2.121007307 0.709025855 0.693038763 0.841238921 1.027475246 1 17.282343 FT(ph)GSFDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.5)GS(0.5)FDDDPDPHRDPYGEEVDRR;FT(0.554)GS(0.446)FDDDPDPHRDPYGEEVDRR;FT(0.59)GS(0.41)FDDDPDPHRDPYGEEVDRR;FT(0.5)GS(0.5)FDDDPDPHRDPYGEEVDRR 163.71 7.21E-10 2021650000 193333 218578 261487 183391 368101 289902 237079 278010 290243 261410 TRUE FALSE 200965.9361 256117.0712 268301.566 219665.1924 305531.3235 222576.654 218496.1285 274283.7307 279797.2111 312628.2845 0.642827108 0.819238322 0.858212706 0.702640175 0.977299044 0.711953029 0.698900705 0.877347778 0.894983675 1 18.25408878 -5 0.136439931 1.720500542 0.720321858 0.346714935 0.095289185 166.6366339 1.408695729 32.29012219 0.618270704 1.00E-05 5 -1.000178684 FT(ph)SPADLDASGAGPGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTSPADLDASGAGPGPK 17 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 FT(0.5)S(0.5)PADLDASGAGPGPK 95.57 0.028346 37635000 140650 96684 121120 91652 160560 174490 164000 127560 134130 96628 TRUE FALSE 146202.9706 113288.7249 124276.4867 109780.492 133268.0686 133967.3419 151145.2515 125850.2668 129302.6875 115560.4065 1.265164904 0.980342042 1.07542445 0.949983609 1.15323295 1.1592841 1.307932846 1.08904313 1.118918593 1 16.81828766 FTDALELLRPWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTDALELLRPWAK 13 1 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 0 ; 144.47 3.77E-05 184186000 277770 231020 275690 249450 349860 371010 353140 310170 313060 220921 FALSE TRUE 288736.5741 270695.8879 282874.7079 298790.4655 290390.9222 284848.5502 325459.964 306012.6785 301793.0318 264206.2402 1.0928454 1.02456281 1.070658693 1.130898594 1.099106978 1.078129533 1.231840565 1.158234106 1.142263073 1 18.01130502 3.463849905 1.055948954 1.141545335 1.05516579 0.103365614 0.060271682 0.811443727 1.853643431 0.022588869 0.047936194 2909.711327 -3.463849905 -0.086379545 FTDCGHFQNTEFHELITVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTDCGHFQNTEFHELITVVK 20 0 O75884 O75884 RBBP9 Putative hydrolase RBBP9 0 96.143 0.00065103 14666000 23526 19985 24740 20232 28624 30977 24323 20979 25525 19594 FALSE TRUE 24454.82465 23417.26829 25384.74472 24233.82921 23758.5027 23783.06121 22416.4997 20697.81082 24606.36024 23433.06915 1.043603144 0.999325702 1.083287237 1.034172223 1.01388779 1.014935818 0.956618169 0.883273577 1.050069885 1 14.5162583 2.334915116 3.379263099 0.953706886 1.034074914 0.262092167 0.045299806 0.246040419 5.564529113 0.017122946 0.013663861 216.2295858 -2.334915116 0.080368028 FTDDDKTDHLSWEWNLTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FTDDDKTDHLSWEWNLTIK 19 1 P52565;J3KRE2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;; 245.95 7.71E-25 1732320000 2050500 2110620 3174800 2392780 4006970 3724800 3916230 3379880 3669870 1752230 FALSE TRUE 2131455.323 2473102.567 3257537.896 2866064.742 3325866.671 2859771.65 3609265.659 3334578.237 3537792.096 2095545.92 1.017136061 1.18017102 1.554505614 1.367693599 1.587112284 1.364690519 1.722351023 1.591269466 1.688243651 1 20.99889471 4.366675647 3.258814954 1.518138515 1.038773373 0.373933704 0.200033839 0.210851205 4.241256681 0.046543052 0.163318502 23263.53171 -4.366675647 -0.479365142 FTDEEVDELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;;; 323.61 5.54E-46 26231400000 9784150 10280470 10674500 11417320 11509490 13602620 12777230 11203230 10711730 9346370 FALSE TRUE 10170435.8 12046060.75 10952686.24 13675631.82 9553111.001 10443617.65 11775717.33 11053069.03 10326216.93 11177612.25 0.909893416 1.07769535 0.979877096 1.223484185 0.854664734 0.934333507 1.053509198 0.988857797 0.923830304 1 23.4141087 3.19508425 24.9999928 0.966015112 1.045032734 0.187987784 0.08940585 254.0230094 146068.6403 0.025375022 0.030329146 1567.055037 -3.19508425 0.079017622 FTDFDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTDFDEVR 8 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 ; 128.61 0.0026201 176846000 294780 309860 289610 358260 357410 423150 409130 358350 304410 267820 FALSE TRUE 306418.142 363076.0446 297157.4745 429122.7587 296657.5759 324879.8254 377061.3215 353546.9044 293454.3436 320294.2013 0.956677145 1.133570459 0.927764141 1.339776858 0.926203393 1.014316913 1.177234305 1.103819248 0.916202486 1 18.28903815 1.243295712 24.97171925 0.95810123 1.078165614 0.120957121 0.122492085 205.1712214 1082069.906 0.082485119 0.027935643 17.51038569 -1.243295712 0.120064384 FTDFDEVRQEIEAETDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FTDFDEVRQEIEAETDR 17 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ;; 166.76 2.10E-09 90871000 144961 174821 169744 138572 198688 202811 132563 176679 175711 192139 FALSE TRUE 150684.1722 204845.1468 174167.6681 165981.128 164915.0847 155711.2189 122172.3657 174310.907 169387.1954 229784.9583 0.655761688 0.89146456 0.757959395 0.722332433 0.717693125 0.677638867 0.531681301 0.758582756 0.737155281 1 17.80992484 -0.997311368 13.13901396 1 0.71699654 0.494224202 0.085978056 0 0 0.08509417 0.020056888 0.100621001 0.997311368 -0.28300346 FTDFDEVRQEIEAETDRVTGTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTDFDEVRQEIEAETDRVTGTNK 23 2 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 101.29 0.0011681 35217000 34451 30520 35593 20149 52216 39119 20762 32078 39061 41222 FALSE TRUE 35811.15208 35761.57259 36520.58282 24134.41206 43340.34297 30034.2051 19134.62019 31648.04688 37655.20224 49298.66166 0.726412257 0.72540656 0.740802723 0.489555117 0.879138328 0.609229624 0.388136707 0.64196564 0.763817941 1 15.58926086 -1.798989773 7.307239671 1.011773903 0.653462395 0.360073419 0.134382284 0.025648183 0.000705539 0.129469361 0.030671675 0.015885842 1.798989773 -0.358311509 FTDKDQQPS(ph)GSEGEDDDAEAALKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTDKDQQPSGSEGEDDDAEAALKK 24 2 Q9NXG2;H3BNW0 Q9NXG2 THUMPD1 THUMP domain-containing protein 1 1 FTDKDQQPS(0.997)GS(0.003)EGEDDDAEAALKK 214.74 7.66E-33 214150000 363540 111050 198980 99161 275540 243150 291150 170830 218980 73951 TRUE FALSE 377892.8399 130121.9737 204165.5823 118774.7498 228703.8092 186682.0975 268328.9022 168540.3033 211098.9526 88440.28257 4.272858803 1.471297579 2.308513455 1.342993785 2.585968775 2.110826561 3.034012267 1.905696119 2.386909522 1 16.43241601 -1.753070354 0.505361693 7.20E-10 2.3394092 0.21286815 0.792074075 87.98375927 8.335629043 107.5947828 0.342551551 0.017657518 1.753070354 2.3394092 FTDLFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTDLFEK 7 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 119.21 0.011243 289490000 662480 571050 712400 552560 805980 832380 731900 676570 703900 514700 FALSE TRUE 688635.2219 669123.3953 730965.7292 661854.7188 668979.8075 639072.3598 674531.7655 667501.6858 678566.7765 615545.6105 1.118739554 1.087041129 1.187508638 1.075232619 1.08680786 1.038220968 1.095827432 1.08440654 1.10238261 1 19.23150624 3.54335509 24.9998902 1.07408127 1.127470962 0.3663699 0.036921221 219.300775 82774.13283 0.009244495 0.014321507 3494.258979 -3.54335509 0.053389692 FTDLLQLVEFHQLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTDLLQLVEFHQLNR 15 0 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 0 ; 261.39 6.02E-25 365500000 268980 304350 312130 292960 366750 426910 337440 333290 331620 303680 FALSE TRUE 279599.5381 356619.745 320264.3642 350906.6136 304409.966 327766.6224 310990.5711 328822.7927 319685.061 363180.2817 0.769864313 0.981935868 0.881833019 0.966205026 0.838178671 0.902490138 0.856298061 0.905398253 0.880237934 1 18.47032635 -2.536926375 1.911804425 2.1617278 0.890719687 0.255705531 0.057543639 2311527.884 138083.662 11628184.34 0.012705778 0.002904515 2.536926375 -1.271008113 FTENDSEKVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTENDSEKVDR 11 1 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 113.24 0.00078581 0 251710 176550 207610 182410 334220 311910 263590 227390 275430 142020 FALSE TRUE 261647.7052 206871.0891 213020.4872 218490.1536 277409.4038 239473.6295 242929.127 224342.209 265517.3281 169846.0999 1.540498754 1.217991401 1.254197107 1.28640077 1.633298639 1.409944825 1.430289699 1.320855817 1.563281867 1 17.37386856 -1.06810683 4.615423891 0.999980256 1.394991207 0.455549642 0.132738114 2.67E-05 5.39E-06 0.127257577 0.029993401 0.08548564 1.06810683 0.395010951 FTFPALEEDVIYDDVPCES(ph)PDAHQPGAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTFPALEEDVIYDDVPCESPDAHQPGAER 29 0 Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6 Q9HCE6-5 ARHGEF10L Rho guanine nucleotide exchange factor 10-like protein 1 FTFPALEEDVIYDDVPCES(1)PDAHQPGAER;FTFPALEEDVIYDDVPCES(1)PDAHQPGAER 109.11 0.0002511 110695000 28966 43688 36184 39456 48451 57413 40175 45149 43356 56441 TRUE FALSE 30109.60005 51191.07415 37126.98477 47260.27904 40215.31633 44079.70085 37025.97852 44543.8515 41795.62603 67499.53332 0.446071233 0.758391527 0.550033207 0.700157123 0.595786583 0.65303712 0.548536808 0.659913474 0.619198741 1 16.04258991 -0.751373577 0.832907725 1.034858643 0.617741235 0.659975555 0.082986663 19.74326434 7.630727803 2.083636029 0.023727729 0.177266399 0.751373577 -0.417117408 FTFPDPPPLS(ph)PPVLGLHGVTFGYQGQKPLFK ddPTM_MDA-MB-175_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 213.27 4.18E-27 3624300000 2274900 1670000 2224900 1740500 2889600 2524300 2532900 2318400 2659000 1643500 TRUE FALSE 2364714.809 1956809.509 2282882.722 2084765.705 2398426.824 1938069.581 2334364.679 2287325.64 2563303.109 1965512.358 1.203103506 0.995572224 1.161469533 1.060672906 1.220255275 0.986037851 1.187662174 1.163729971 1.30413991 1 20.906474 FTGS(ph)FDDDPDPHRDPYGEEVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 FT(0.133)GS(0.867)FDDDPDPHRDPYGEEVDR;FT(0.064)GS(0.936)FDDDPDPHRDPYGEEVDR 174.86 1.30E-12 235740000 65454 64103 67813 68557 101070 83889 84609 75181 71049 61133 TRUE FALSE 68038.17446 75112.1916 69580.26249 82117.36998 83890.1575 64407.0511 77977.1255 74173.32167 68491.96037 73110.84089 0.930616768 1.027374199 0.951709236 1.123190063 1.147438006 0.880950763 1.06656037 1.014532466 0.936823589 1 16.15779772 5.512507364 1.486657631 1.021847798 0.404321139 0.092900658 0.077951411 25.1272562 9.093487604 0.020529332 39.95649112 325467.3018 -5.512507364 -0.617526659 FTGS(ph)FDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_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(0.169)GS(0.831)FDDDPDPHRDPYGEEVDRR;FT(0.163)GS(0.837)FDDDPDPHRDPYGEEVDRR;FTGS(1)FDDDPDPHRDPYGEEVDRR;FT(0.039)GS(0.961)FDDDPDPHRDPYGEEVDRR;FT(0.026)GS(0.974)FDDDPDPHRDPYGEEVDRR 216.51 1.32E-32 16552320000 1158484 1319880 1432414 1231805 1939957 1573020 1471883 1494761 1420659 1526902 TRUE FALSE 1204221.843 1546559.123 1469743.886 1475452.352 1610203.802 1207709.944 1356512.964 1474726.174 1369529.76 1826069.213 0.659461227 0.846933463 0.804867568 0.807993663 0.881786841 0.661371396 0.742859556 0.80759599 0.74998787 1 20.80031002 -2.056103068 2.497479642 1.305884666 0.778466804 0.49022346 0.069088818 5891287.701 2376787.524 10274041.99 0.016471684 0.008788139 2.056103068 -0.527417862 FTGSFDDDPDPHRDPYGEEVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FTGSFDDDPDPHRDPYGEEVDRR 23 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;; 223.97 8.30E-33 3072490000 858650 938050 941900 880460 957680 1144090 867550 943720 1014320 958410 FALSE TRUE 892550.165 1099152.79 966446.6878 1054612.36 794893.8957 878392.4364 799549.1641 931070.977 977814.8213 1146192.09 0.77870906 0.95896037 0.843180385 0.920100889 0.693508447 0.766357092 0.697569955 0.812316701 0.85309856 1 20.12841741 5.038230668 16.09602816 0.824256637 0.590874173 0.014515202 0.098003283 13051342.65 152484737.3 0.023405223 88339175.23 109202.019 -5.038230668 -0.233382463 FTISDHPQPIDPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTISDHPQPIDPLLK 15 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 83.386 0.0087339 432960000 263070 414270 440910 392930 456470 567930 443620 435360 452640 468310 FALSE TRUE 273456.2067 485417.6499 452400.4768 470650.3812 378879.3924 436036.8646 408847.9052 429524.7113 436349.5748 560066.3782 0.488256781 0.866714498 0.807762248 0.840347501 0.676490158 0.778544975 0.729999016 0.766917508 0.77910332 1 19.0952383 -4.999999982 0.307991404 3.150327373 0.742852011 0.371338368 0.099790009 309.617023 2.817283628 431.4092521 0.089346112 1.00E-05 4.999999982 -2.407475362 FTLDCTHPVEDGIMDAANFEQFLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 FTLDCTHPVEDGIMDAANFEQFLQER 26 0 P35268 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;; 334.08 4.48E-95 6876407000 1706950 2084752 2044427 1976305 2210110 2525372 1978805 2159652 2057037 2078604 FALSE TRUE 1774341.704 2442791.939 2097706.447 2367212.23 1834436.292 1938892.625 1823701.093 2130705.397 1983004.64 2485866.657 0.713771875 0.982672153 0.843853166 0.952268387 0.737946376 0.779966464 0.733627883 0.857127792 0.797711589 1 21.24531748 5.026138365 15.34388905 0.841924828 0.391081166 0.16072803 0.092488656 3186023.962 51696349.84 0.021465566 35319522.28 106203.3865 -5.026138365 -0.450843662 FTLRDEGK ddPTM_MDA-MB-175_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 ;;; 133.57 0.00083321 2124730000 1480870 1150745 1375797 1008464 1814310 1881950 1487720 1339190 1413086 1234641 FALSE TRUE 1539335.891 1348376.502 1411651.4 1207935.169 1505914.234 1444895.634 1371108.619 1321240.349 1362229.311 1476545.265 1.042525365 0.913196862 0.956050203 0.818082044 1.019890328 0.978565079 0.928592337 0.894818723 0.922578767 1 20.49379415 2.025575301 24.3956892 0.923510632 0.949971113 0.000321477 0.063032806 674.184828 643085.4674 0.023303016 0.017209691 106.0657827 -2.025575301 0.026460481 FTLTQSEADADILFNFSHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTLTQSEADADILFNFSHFK 20 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 213.15 1.03E-22 872840000 586050 529750 611370 486880 705310 782780 697370 628860 688110 458010 FALSE TRUE 609187.7065 620730.4416 627302.8044 583183.4108 585421.6581 600991.2081 642708.3172 620431.1603 663345.0555 547748.2904 1.112167244 1.133240309 1.145239183 1.064692343 1.068778613 1.097203257 1.173364351 1.132693924 1.211039938 1 19.06315355 2.269385927 24.96857552 1.140693716 1.10345059 0.032911135 0.055971201 473.9559559 383903.9467 0.018485808 0.015464904 185.9456087 -2.269385927 -0.037243125 FTMDCVAPTIHVYEHHENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTMDCVAPTIHVYEHHENR 19 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 81.317 0.0021025 113230000 16444 17779 18919 16633 22434 25420 16957 21521 16060 19466 FALSE TRUE 17093.22182 20832.40495 19412.04468 19922.95776 18620.67669 19516.59024 15627.86603 21232.5462 15482.00374 23279.99 0.734245239 0.89486314 0.833851075 0.855797522 0.79985759 0.838341865 0.671300376 0.912051345 0.66503481 1 14.50680282 3.22007879 24.59076215 0.808417215 0.834641806 0.002384712 0.100958685 1193.901436 1588525.795 0.026922107 0.032239365 1659.888017 -3.22007879 0.02622459 FTPGTFTNQIQAAFREPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTPGTFTNQIQAAFREPR 18 1 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 111.66 0.00027208 1790760000 368130 535780 444610 355410 574690 603310 313980 440270 413100 728410 FALSE TRUE 382664.0567 627796.0472 456196.9019 425709.0372 477004.3991 463200.3958 289369.4272 434368.9008 398232.6117 871127.9932 0.439274205 0.720670271 0.523685274 0.488687128 0.547570969 0.531724843 0.332177854 0.498628105 0.457145924 1 19.73252518 -1.350910274 5.710573924 1.000097282 0.504885257 0.719519638 0.092829025 0.000115996 1.32E-05 0.09068197 0.021369782 0.044574833 1.350910274 -0.495212025 FTPVASKFS(ph)PGAPGGSGSQPNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 FTPVAS(0.003)KFS(0.997)PGAPGGSGSQPNQK 265.78 2.78E-44 2587300000 2305000 1339900 1789500 1247700 2402000 2329000 2097500 1801600 2195100 1364200 TRUE FALSE 2396003.18 1570017.402 1836135.84 1494491.336 1993708.898 1788125.046 1933092.469 1777452.499 2116098.78 1631488.871 1.468599157 0.962321858 1.125435713 0.916029133 1.22201808 1.096008118 1.184864024 1.089466518 1.297035375 1 20.63775772 FTRPLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTRPLFK 7 1 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 81.784 0.023952 1210940000 1042900 1184340 1186810 1098590 1498260 1515640 1207690 1252670 1237260 1330630 FALSE TRUE 1084074.497 1387741.182 1217739.244 1315887.823 1243586.3 1163655.58 1113028.102 1235880.008 1192731.254 1591341.472 0.681233108 0.872057447 0.76522812 0.826904751 0.781470427 0.731241911 0.699427572 0.776627788 0.749513084 1 20.60181201 -1.931958151 6.325961004 1.086412674 0.767186837 0.63606627 0.053333689 0.033302971 0.000358206 0.026458383 0.011730845 0.011696121 1.931958151 -0.319225838 FTSGAFLS(ph)PSVSVQECR ddPTM_MDA-MB-175_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(1)PSVSVQECR;FTSGAFLS(0.997)PS(0.003)VSVQECR 183.36 7.30E-10 170505000 170405 187311 169371 183943 195938 244820 168386 183323 179955 185721 TRUE FALSE 177132.721 219480.2072 173784.9474 220326.3764 162632.5287 187964.2653 155187.4653 180865.855 173478.4547 222109.4741 0.79750187 0.988162293 0.782429242 0.991971987 0.732217882 0.846268562 0.69869809 0.814309501 0.781049324 1 17.76091141 3.22359911 24.99967891 0.797623629 0.889342013 0.119514358 0.099047048 390.5307065 652549.3914 0.025872614 0.031041219 1673.397476 -3.22359911 0.091718384 FTSGAFLSPSVSVQECRT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTSGAFLSPSVSVQECRTPR 20 1 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 FTSGAFLSPSVSVQECRT(1)PR 184.47 6.46E-17 124000000 123580 149830 133610 136430 165900 184970 97900 130770 120250 178360 TRUE FALSE 128459.0338 175562.137 137091.9864 163415.4468 137700.3773 142013.5207 90226.34219 129017.242 115922.226 213306.2271 0.60222824 0.823052095 0.642700348 0.766107249 0.645552543 0.665772972 0.422989724 0.604845174 0.543454486 1 17.70256656 -1.096837531 4.78170045 1.000017551 0.634441423 0.52357469 0.104396972 15191031.61 3484554.079 2808.487663 0.025601706 0.080013353 1.096837531 -0.365576128 FTVHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 74.335 0.080597 450520000 561240 575570 568620 561520 714310 787330 717090 705450 701250 571190 FALSE TRUE 583398.1886 674419.6702 583438.7043 672586.98 592891.8413 604484.5396 660882.612 695994.5966 676012.1495 683103.7444 0.85404039 0.987287327 0.854099702 0.98460444 0.86793821 0.884908836 0.96747034 1.018871002 0.989618568 1 19.38174517 2.050882903 4.512807666 1.002794934 0.909075642 0.486914687 0.045444657 0.165390394 7.204828842 0.017021593 0.011854728 112.4301793 -2.050882903 -0.093719291 FTVTSLPPAGPARS(ph)PDPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTVTSLPPAGPARSPDPESR 20 1 A0A0D9SGD0;A0A0D9SF89;Q9H2X9 A0A0D9SGD0 SLC12A5 Solute carrier family 12 member 5 1 FTVTSLPPAGPARS(0.999)PDPESR 83.826 0.0017421 137080000 55442 62536 56020 58487 68340 75132 56527 58346 58586 63096 TRUE FALSE 57630.89297 73276.07154 57479.92722 70055.55403 56723.59121 57683.73164 52096.26603 57563.9673 56477.5013 75458.45315 0.763743366 0.971078368 0.761742718 0.928399021 0.751719507 0.764443601 0.690396687 0.762856445 0.748458243 1 16.20339491 3.213719627 24.99293023 0.766400121 0.857693707 0.08808026 0.098380811 373.8936991 376179.6164 0.025928741 0.031002849 1635.760161 -3.213719627 0.091293586 FTVWLHGVLDK ddPTM_MDA-MB-175_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 0 109.6 0.0019071 38239000 110150 98174 100310 87001 240660 166970 142220 101770 112810 172880 FALSE TRUE 114498.8071 115034.6208 102924.161 104209.5381 199752.6992 128193.748 131072.4248 100405.9396 108749.9901 206752.526 0.553796412 0.556387982 0.497813318 0.504030302 0.966143936 0.620034736 0.633958033 0.485633436 0.525991108 1 17.65754543 FTYFSSLS(ph)PMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FTYFSSLSPMAR 12 0 Q9H425 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 FTYFS(0.001)S(0.006)LS(0.994)PMAR 135.1 0.00014028 100310000 143530 122910 124410 123460 126080 173540 119220 115580 123630 143500 TRUE FALSE 149196.6752 144018.8364 127652.2268 147880.0195 104648.9666 133237.965 109875.2249 114030.8392 119180.5804 171616.0775 0.869363042 0.839191983 0.743824405 0.861690942 0.609785331 0.776372278 0.640238528 0.664453126 0.694460462 1 17.38882519 3.938120242 1.037890141 0.711444534 0.869260643 0.091761825 0.111158787 1.130519981 2.053939056 0.035152995 0.148390474 8672.019418 -3.938120242 0.157816109 FTYHNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FTYHNVR 7 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 84.097 0.021795 409820000 1514960 1876430 1430260 1268330 2016140 2140150 1389950 1582070 1458100 2523000 FALSE TRUE 1574771.791 2198692.256 1467533.751 1519201.888 1673437.243 1643132.597 1281002.087 1560864.939 1405623.266 3017333.544 0.521908423 0.728687175 0.486367758 0.503491532 0.554607974 0.544564455 0.424547723 0.517299436 0.465849481 1 21.52484275 -1.270377057 3.756258463 1.000852641 0.527493359 0.775100648 0.076358273 4488515.374 3054747.976 28923.16557 0.01807134 0.053656575 1.270377057 -0.473359282 FVADSKDKEPEVVFIGDSLVQLMHQCEIWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVADSKDKEPEVVFIGDSLVQLMHQCEIWR 30 2 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 106.39 0.00018349 139290000 65529 56496 74111 43172 103800 79791 64228 58816 71416 78676 FALSE TRUE 68116.13552 66198.74852 76042.39354 51711.29274 86156.11308 61260.74949 59193.64153 58027.66772 68845.75211 94091.05586 0.723938475 0.703560481 0.808178767 0.549587761 0.915667406 0.651079414 0.629110185 0.616718212 0.731692842 1 16.52176997 0.960760828 22.09757564 1.000000002 0.695257337 0.454660005 0.097948227 1363.59344 767910.8186 0.090845817 0.022711454 9.136099648 -0.960760828 -0.304742666 FVAFSGEGQS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVAFSGEGQSLR 12 0 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 FVAFSGEGQS(1)LR 125.47 0.00031963 105310000 51215 80590 101070 74138 138440 96269 76769 93502 96104 132210 TRUE FALSE 53237.00775 94430.7056 103703.9672 88802.27512 114908.0182 73911.98372 70751.64518 92248.75863 92645.23581 158114.0182 0.336700113 0.597231711 0.655880917 0.561634421 0.726741497 0.46746003 0.447472311 0.583431878 0.585939418 1 17.27060576 0.494225436 2.002340036 0.99997393 0.552782691 0.626261328 0.104314951 3.0610937 11.34019744 0.098676373 0.027142191 3.120508973 -0.494225436 -0.447191238 FVDGEWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FVDGEWYR 8 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;;;; 179.16 0.00057191 4183730000 4321260 5176340 5091000 4923340 5807580 6160430 5120960 5127040 4887520 5928150 FALSE TRUE 4491866.682 6065336.129 5223675.642 5897161.957 4820409.626 4729763.495 4719565.774 5058320.415 4711619.11 7089657.491 0.63358021 0.855518921 0.736802257 0.831797864 0.679921369 0.667135683 0.665697289 0.713478813 0.664576408 1 22.7572845 -1.044833342 4.520333321 1.000012723 0.719415153 0.595681721 0.070032205 9233342.883 2134202.172 1234.164611 0.016348197 0.090191718 1.044833342 -0.28059757 FVDGLMIHSGDPVNYYVDTAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 FVDGLMIHSGDPVNYYVDTAVR 22 0 P23396;P23396-2;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ;;;;;;; 253.83 4.90E-37 7623980000 5089117 5722730 6081733 5896354 6283465 7053791 6578925 6239200 5741422 5521094 FALSE TRUE 5290039.269 6705564.361 6240227.958 7062635.222 5215403.864 5415654.941 6063251.668 6155573.729 5534789.344 6602846.662 0.801175544 1.015556578 0.945081459 1.069634899 0.789872025 0.820200017 0.91827843 0.932260591 0.838242901 1 22.65465671 4.779986468 22.26472342 0.921183467 0.801174032 0.1598922 0.084957582 12096.34353 6500714.217 0.020486596 5.93315807 60254.08113 -4.779986468 -0.120009435 FVDILGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVDILGLR 8 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 91.906 0.028278 18452000 65093 120120 102820 125510 97778 133500 84203 107600 92550 144050 FALSE TRUE 67662.9219 140749.6756 105499.5737 150335.5034 81157.73049 102496.6482 77602.94884 106157.798 89219.14358 172273.8395 0.392763766 0.817011312 0.612394627 0.87265428 0.471097241 0.59496351 0.450462758 0.61621543 0.517891421 1 17.39434411 -1.574088513 5.343391794 1.002116522 0.600575464 0.412707586 0.145123376 0.003482594 0.000277591 0.133735675 0.031377024 0.026663152 1.574088513 -0.401541058 FVDILTNWYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVDILTNWYVR 11 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 77.358 0.076386 308140000 272350 150120 182950 147900 258860 278580 354930 180050 237350 136740 FALSE TRUE 283102.5883 175901.9422 187717.8273 177154.1786 214859.0697 213884.0169 327109.6592 177636.7243 228807.8199 163531.585 1.731179872 1.075645064 1.147899516 1.083302523 1.313868937 1.307906463 2.000284283 1.086253303 1.399165916 1 17.31920978 2.756474109 3.65203014 1.396155499 1.238540378 0.012355826 0.304759153 0.78994114 23.08773394 0.097226453 0.098572039 570.7870475 -2.756474109 -0.157615121 FVDIPQLGVSDKENNSAHNEQNSQIPT(ph)PTDGPSFTVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVDIPQLGVSDKENNSAHNEQNSQIPTPTDGPSFTVMR 38 1 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 FVDIPQLGVSDKENNSAHNEQNSQIPT(0.991)PT(0.009)DGPSFTVMR 127.76 2.77E-08 54945000 28088 30100 41847 33014 38475 46385 35144 40904 35997 36271 TRUE FALSE 29196.93593 35269.44085 42937.5672 39544.07066 31935.03324 35612.78672 32389.32145 40355.74879 34701.475 43377.608 0.673087735 0.813079432 0.989855577 0.91162405 0.736210103 0.82099471 0.746682976 0.930335965 0.799985905 1 15.40466288 -4.999999391 0.304936832 2.442176674 0.824185614 0.245315987 0.091660494 440.6602715 4.035314258 407.022885 0.091070394 1.00E-05 4.999999391 -1.61799106 FVDKYSISLS(ph)PPEQQKK ddPTM_MDA-MB-175_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(0.021)IS(0.396)LS(0.583)PPEQQKK;FVDKYS(0.004)IS(0.139)LS(0.856)PPEQQKK 72.086 0.015204 530820000 1147070 609160 851070 462140 1340800 1017480 853580 796030 910220 513330 TRUE FALSE 1192357.209 713778.4914 873249.5834 553549.9126 1112891.295 781185.6901 786674.1692 785360.5199 877461.36 613907.1852 1.94224345 1.162681442 1.422445615 0.901683391 1.812800569 1.272481751 1.281421994 1.279282176 1.429306223 1 19.22766103 7.999974373 0.031432711 1.17E-07 3.328895266 0.179598152 0.27928599 2482.164231 5.975414409 197.2891748 499.6612562 99994099.24 -7.999974373 3.328895149 FVEGLPINDFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FVEGLPINDFSR 12 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic" 0 ;;;; 249.83 1.21E-16 414216000 523510 598679 574471 564620 692645 719042 562170 581859 543096 656195 FALSE TRUE 544178.579 701497.4612 589442.1862 676300.1508 574909.4503 552055.3927 518105.6464 574060.1318 523550.081 784763.8466 0.693429726 0.893896252 0.751107723 0.861788108 0.732589113 0.703466903 0.660205804 0.731506853 0.667143477 1 19.58189905 3.120372591 9.565265121 0.72714148 0.803168641 0.029239709 0.104659357 0.620618827 49.14328297 0.027597405 0.033015051 1319.388187 -3.120372591 0.076027161 FVEKPQVFVSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVEKPQVFVSNK 12 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 147.68 6.00E-05 693770000 377890 251840 338240 225680 494970 479230 389710 366000 422830 342650 FALSE TRUE 392809.389 295091.561 347054.8123 270318.8304 410835.1762 367936.0953 359163.5119 361094.3687 407612.4309 409785.7071 0.958572694 0.720111892 0.846917807 0.659659002 1.002561019 0.897874399 0.876466665 0.881178534 0.994696554 1 18.64451014 3.222007206 24.99992982 0.926084182 0.794486655 0.39847792 0.086416171 254.2194711 383936.3928 0.023797181 0.028516957 1667.274878 -3.222007206 -0.131597527 FVEVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FVEVGR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;;;; 154.91 0.023134 1444410000 1286220 1356930 1470180 1381640 1543280 1618340 1480350 1560380 1485010 1465950 FALSE TRUE 1337000.959 1589972.172 1508494.099 1654924.268 1280953.817 1242505.061 1364316.299 1539465.658 1431564.78 1753174.835 0.762617015 0.906910218 0.860435633 0.943958489 0.730648074 0.708717143 0.778197514 0.878101617 0.816555629 1 20.74153845 -1.999129054 6.643701825 1.173461104 0.82421233 0.35033414 0.073114736 0.04886166 6.41E-06 0.018413667 0.017447403 0.010020074 1.999129054 -0.349248775 FVEVLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FVEVLDER 8 0 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 ;;; 115.49 0.0057067 206722000 490460 601520 586050 580010 655560 683830 573780 585960 562880 629270 FALSE TRUE 509823.7395 704826.3808 601322.9444 694734.2468 544128.1454 525020.846 528805.6243 578106.1646 542622.0588 752563.4084 0.677449546 0.936567435 0.799032929 0.923157091 0.723032955 0.697643335 0.702672517 0.768182665 0.72103168 1 19.52145362 5.031604994 15.09500181 0.792926113 0.331066182 0.109261135 0.104115535 2484365.852 34820647.16 0.024368778 29032827 107548.6576 -5.031604994 -0.461859931 FVFDRPLPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVFDRPLPVSR 11 1 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ; 213.84 1.04E-09 4215800000 1835580 2024810 1918840 2119960 2526060 2537520 2159600 2103020 2036470 2396040 FALSE TRUE 1908050.116 2372555.367 1968846.547 2539281.761 2096681.223 1948219.436 1990324.909 2074832.457 1963177.843 2865498.163 0.665870298 0.827973089 0.687087004 0.886157176 0.73169868 0.679888566 0.694582511 0.724073909 0.685108742 1 21.45035454 -1.078072398 4.643812072 1.000013937 0.733671749 0.586312668 0.06766587 9.40E-06 1.87E-06 0.063068611 0.014864637 0.083546373 1.078072398 -0.266342187 FVFLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVFLLDR 7 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 110.63 0.015726 143101000 290410 357230 311310 317900 530050 454210 349210 328350 305880 549740 FALSE TRUE 301875.611 418581.4736 319422.9943 380779.6712 439952.2903 348726.6111 321838.0077 323949.0053 294871.4386 657451.0276 0.459160604 0.636673237 0.485850628 0.579175718 0.669178801 0.530422186 0.489523925 0.492734807 0.448507077 1 19.32652391 -1.725860465 2.786491969 1.080154904 0.534475122 0.798055726 0.070564931 14415625.84 12100969.14 8026707.114 0.017248341 0.018799207 1.725860465 -0.545679782 FVFSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVFSFK 6 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 100.82 0.086601 52497000 149940 148520 170320 143230 224720 214130 210500 185830 177490 162330 FALSE TRUE 155859.747 174027.1547 174758.6791 171560.4665 186522.1747 164401.5527 194000.46 183339.2528 171102.1696 194135.4555 0.802840195 0.896421286 0.9001894 0.88371527 0.960783666 0.8468394 0.999304632 0.9443883 0.881354563 1 17.5667041 8 0.274819036 0.958093783 1.89E-13 0.426447282 0.046114242 49.79647246 0.700858328 0.049457153 22.766506 100000000 -8 -0.958093783 FVGHTK ddPTM_MDA-MB-175_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 71.995 0.086763 1271800000 1844200 1254900 1735400 1386800 1979200 1951700 2185100 1928600 1701300 1260300 FALSE TRUE 1917010.44 1470419.313 1780625.95 1661104.901 1642776.291 1498447.253 2013826.152 1902750.272 1640070.545 1507231.655 1.271875119 0.975576188 1.181388371 1.102089977 1.089929531 0.99417183 1.336109247 1.262413953 1.088134355 1 20.52346974 2.246732632 24.99938773 1.206004448 1.099730801 0.04596318 0.118068141 326.5330383 998912.3374 0.03952775 0.032556113 176.4950918 -2.246732632 -0.106273647 FVHFIDAPSLALIMPIVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVHFIDAPSLALIMPIVQR 19 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 182.18 2.98E-14 258650000 178152 246030 292810 284520 253440 350120 230150 247890 287610 268900 FALSE TRUE 185185.5785 288283.7387 300440.8691 340797.2068 210360.3593 268809.9361 212110.2416 244567.44 277258.9723 321585.8066 0.575851218 0.896444223 0.934247914 1.059739577 0.654134464 0.835888682 0.659575881 0.760504459 0.86216172 1 18.29484421 4.747446837 24.02100321 0.834197834 0.575850985 0.289247433 0.127033568 960.9143632 2597418.438 0.031367084 0.368915782 55904.50898 -4.747446837 -0.258346849 FVHLLDQSDQDFQEELDLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 FVHLLDQSDQDFQEELDLMK 20 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;; 261.63 1.64E-36 985399000 582441.2 426848 542094 471842 636773 611329 668754 543579 590120 378577 FALSE TRUE 605436.4283 500155.8236 556221.415 565170.9393 528534.5529 469357.1045 616335.314 536293.2126 568881.6965 452751.9149 1.337236593 1.10470173 1.228534649 1.248301599 1.167382259 1.036676134 1.361309127 1.184518928 1.256497605 1 18.78836122 -2.347280484 1.950952152 2.44E-05 1.210120392 0.321483065 0.093081855 2258726.698 239506.8078 9956873.084 0.021306352 0.004494895 2.347280484 1.210095949 FVHSENQHLVSPEALDFLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVHSENQHLVSPEALDFLDK 20 0 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A087WY74 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 107.89 0.0001273 945410000 538470 560200 646970 514230 804580 830020 716270 734650 681200 600520 FALSE TRUE 559729.2114 656409.9922 663830.5697 615943.1592 667817.779 637260.4341 660126.8858 724803.2184 656683.7451 718180.3964 0.779371331 0.913990406 0.924322876 0.857644071 0.929874698 0.887326412 0.919165838 1.009221669 0.914371582 1 19.45398675 8 0.151476788 1.014721126 0.343380017 0.539918802 0.042282563 52.77869648 0.522748727 0.143890799 7.812668366 99999999.95 -8 -0.671341109 FVIKPIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVIKPIDK 8 1 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 95.502 0.0097348 0 3302900 2266000 2765700 2208000 3657900 3372500 3659100 2889200 3033700 1854000 FALSE TRUE 3433301.042 2655167.873 2837776.414 2644735.81 3036131.465 2589287.986 3372290.181 2850475 2924517.73 2217255.803 1.548446074 1.197501826 1.27985973 1.192796883 1.369319436 1.167789473 1.52092969 1.285586893 1.318980753 1 21.08034379 -0.869655105 5.542358107 0.999999829 1.315173927 0.376526782 0.123436252 2.40E-07 4.90E-08 0.109770523 0.025873146 0.135003459 0.869655105 0.315174099 FVIKPIDKK ddPTM_MDA-MB-175_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 ; 79.148 0.015614 3969100000 2358170 1441500 1845950 1469060 3237590 2486140 2706230 2115970 2702240 1370930 FALSE TRUE 2451272.373 1689066.412 1894056.973 1759635.683 2687265.608 1908771.663 2494108.621 2087608.883 2604986.91 1639537.485 1.495099926 1.030209084 1.15523859 1.073251267 1.639038834 1.164213493 1.521226958 1.273291341 1.588854743 1 20.64485746 3.280621276 24.99995027 1.372235718 1.174774617 0.135755124 0.215899376 247.9624688 147381.8862 0.054574759 0.073894008 1908.188508 -3.280621276 -0.197461101 FVINYDYPNSSEDYIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FVINYDYPNSSEDYIHR 17 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;; 214.22 6.01E-15 4313490000 1671035 2112140 1944860 2063480 2194620 2406540 2122340 2079250 2024530 2238010 FALSE TRUE 1737008.752 2474883.615 1995544.649 2471630.185 1821579.276 1847657.556 1955985.445 2051381.055 1951667.561 2676505.21 0.648983886 0.924669829 0.745578466 0.923454278 0.680581255 0.690324663 0.730798295 0.76644015 0.729185041 1 21.35191903 -1.079751753 3.792434517 1.000071314 0.763804275 0.394091196 0.089163844 88252063.2 175769825.3 87358.94025 0.02052218 0.083223935 1.079751753 -0.236267039 FVINYDYPNSSEDYVHR ddPTM_MDA-MB-175_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 ;;; 297.16 8.10E-46 900327000 663805 861272 791942 817163 889747 933743 817946 836497 757954 913572 FALSE TRUE 690012.534 1009188.766 812580.6591 978795.4024 738508.1227 716895.3393 753833.2552 825285.1259 730675.3836 1092568.942 0.631550566 0.923684289 0.74373399 0.895866032 0.67593732 0.6561557 0.689964016 0.755362059 0.668768217 1 20.05929289 -1.294933471 3.471498631 1.000905026 0.742827641 0.409249481 0.094305938 27469155.2 41747786.78 263114.1256 0.022203266 0.050706838 1.294933471 -0.258077385 FVKDFQDYMEPEEGCQGS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FVKDFQDYMEPEEGCQGSPQR 21 1 O43237;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 FVKDFQDYMEPEEGCQGS(1)PQR;FVKDFQDYMEPEEGCQGS(1)PQR;FVKDFQDYMEPEEGCQGS(1)PQR 104.51 0.00024986 382240000 310130 351079 349500 281641 431781 441466 247890 348025 376047 441761 TRUE FALSE 322374.1719 411374.0872 358608.2571 337348.7492 358387.0198 338942.212 228459.7341 343360.2941 362513.1419 528315.6099 0.610192404 0.778652153 0.678776569 0.638536403 0.678357809 0.641552522 0.432430407 0.649915103 0.686167766 1 19.01104051 0.743840054 3.017431794 0.999948606 0.637187877 0.636818599 0.081399047 1.214372995 13.46488047 0.082001563 0.021439305 5.544214876 -0.743840054 -0.362760729 FVKDFQDYMEPEEGCQGS(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVKDFQDYMEPEEGCQGSPQRR 22 2 O43237;B4E2E0;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 FVKDFQDYMEPEEGCQGS(1)PQRR 193.11 4.34E-18 204370000 132840 148740 172770 126290 216460 209890 123910 160780 190830 227770 TRUE FALSE 138084.6258 174284.938 177272.5281 151269.7851 179666.2065 161146.2284 114197.6104 158625.0071 183962.0656 272397.1706 0.506923862 0.639819193 0.650786966 0.555328033 0.659574423 0.591585544 0.419231999 0.582329863 0.675344994 1 18.05535219 0.829821022 2.841609207 0.999766258 0.57613641 0.776480505 0.068384404 0.339297574 4.696421402 0.067619284 0.017821671 6.758044104 -0.829821022 -0.423629848 FVKWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVKWPR 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 81.297 0.056772 255860000 182140 242640 231000 130670 397950 271590 173090 207870 235810 425180 FALSE TRUE 189331.0278 284311.5325 237020.0498 156516.136 330306.6011 208517.3385 159522.7535 205083.8427 227323.2442 508485.8804 0.372342744 0.559133584 0.466129068 0.307808224 0.649588541 0.410074982 0.313721107 0.403322591 0.447059108 1 18.95584819 0.913552664 18.91760396 1 0.434266002 0.742985027 0.099433795 2009.846408 439824.8368 0.094250987 0.023562747 8.195069939 -0.913552664 -0.565733999 FVLDHEDGLNLNEDLENFLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 207.56 3.60E-22 177852000 127304 95558 128186 98819 127337 144235 135545 112899 119995 98813 FALSE TRUE 132330.0602 111969.3432 131526.6325 118365.1033 105692.3022 110738.6072 124920.6287 111385.7736 115676.4034 118173.5155 1.119794564 0.947499469 1.112995852 1.001621241 0.894382314 0.937084817 1.057094969 0.942561226 0.978869106 1 16.85054722 3.482975051 24.94558322 0.966879632 1.050248858 0.318222539 0.059536306 307.7546498 1311479.633 0.015652392 0.021872267 3040.710338 -3.482975051 0.083369226 FVLHAVQLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVLHAVQLVK 10 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 93.649 0.0069836 0 179730 151260 174480 170170 240390 230240 213960 187010 198910 156100 FALSE TRUE 186825.8792 177237.7284 179027.0921 203829.1181 199528.5937 176770.2493 197189.2561 184503.4368 191751.268 186684.8063 1.000755674 0.949395572 0.958980517 1.091835603 1.068799318 0.946891463 1.05626837 0.988315228 1.027139122 1 17.51024499 FVLMAT(ph)PNLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.995)PNLS(0.005)R;FVLMAT(1)PNLSR;FVLMAT(1)PNLSR 175.21 0.00011279 1204924000 1213630 1514310 1253540 1582900 1532680 1696300 1057590 1240150 1006120 1593780 TRUE FALSE 1261545.05 1774380.963 1286208.282 1895992.896 1272155.601 1302360.033 974693.3323 1223527.818 969909.9377 1906050.676 0.661863331 0.93092014 0.674802773 0.994723235 0.667430104 0.683276709 0.511368005 0.64191778 0.508858421 1 20.86215505 3.028167091 24.92395719 0.637940754 0.815925396 0.155374559 0.159588266 289.1033241 255814.2327 0.042219001 0.050460451 1067.006565 -3.028167091 0.177984642 FVMEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FVMEEGR 7 0 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;; 202.71 0.00070408 3836890000 2838700 3737970 3318920 3250570 4297470 4315760 3524690 3298140 3290670 4213790 FALSE TRUE 2950774.068 4379937.27 3405413.782 3893523.044 3566987.584 3313490.146 3248415.588 3253933.828 3172239.429 5039401.473 0.585540581 0.869138388 0.675757588 0.772616166 0.707819689 0.657516605 0.644603452 0.645698471 0.62948734 1 22.26482097 -1.00690697 4.994637375 1.000003401 0.689681518 0.597807606 0.076860646 2.84E-06 5.65E-07 0.072703026 0.01713608 0.098422191 1.00690697 -0.310321884 FVMEEGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FVMEEGRK 8 1 P09467 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;; 117.04 0.0034575 1944620000 1588260 1279760 1445550 1100541 2036360 1694790 1589340 1432870 1578500 1469310 FALSE TRUE 1650965.731 1499548.825 1483222.221 1318224.725 1690220.255 1301200.707 1464763.378 1413664.721 1521690.093 1757193.163 0.939547095 0.853377339 0.844086041 0.750187716 0.961886428 0.740499528 0.83358131 0.804501606 0.8659777 1 20.74484136 0.965774698 19.46589262 1.000000002 0.837077661 0.3357358 0.066590264 247.3327909 140673.9472 0.059795069 0.014948739 9.242185864 -0.965774698 -0.162922342 FVMQEEFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 FVMQEEFSR 9 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;;;;;;;;; 282.57 3.78E-21 5979943000 1513602 2045826 1669856 1743327 2113174 2319050 1691977 1655611 1566103 2019543 FALSE TRUE 1573360.176 2397180.701 1713373.819 2088151.877 1753977.438 1780485.783 1559355.422 1633420.243 1509739.259 2415233.784 0.651431835 0.992525327 0.709402887 0.864575467 0.726214352 0.73718983 0.645633326 0.67629902 0.62509032 1 21.20373141 FVNDYDKDNDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FVNDYDKDNDGR 12 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 153.39 6.44E-05 562820000 1919620 1199600 1382860 1435700 1815600 1862710 2062140 1502200 1485750 816910 FALSE TRUE 1995408.08 1405621.968 1418898.468 1719677.175 1506984.961 1430123.832 1900504.078 1482065.466 1432278.148 976967.8738 2.042450047 1.438759663 1.452349157 1.760218755 1.542512298 1.46383916 1.945308673 1.517005324 1.466044264 1 19.8979516 0.820545759 1.813668313 1.001823863 1.639253222 0.492264501 0.199177341 0.526349238 3.153264852 0.179378082 0.050554207 6.615242341 -0.820545759 0.637429359 FVNLFPEVKPTIQDVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVNLFPEVKPTIQDVLR 17 1 O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O94973-3 AP2A2 AP-2 complex subunit alpha-2 0 ; 142.3 5.40E-07 340530000 377920 288230 313690 270800 406190 438940 430760 330880 325320 284030 FALSE TRUE 392840.5734 337731.2604 321865.0191 324363.4317 337145.9689 337002.8372 396995.9056 326445.0948 313611.7967 339680.2404 1.156501105 0.99426231 0.947552965 0.954908155 0.992539244 0.992117872 1.168734175 0.961036457 0.923255931 1 18.37381777 4.738822394 24.91787247 0.995471526 1.156501155 0.373382751 0.0635643 23.37981756 2224211.092 0.015630193 0.092301569 54805.27918 -4.738822394 0.161029629 FVPDKEFSGSDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVPDKEFSGSDRR 13 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ; 98.253 0.0019147 163412000 271220 262640 286810 225465 352340 358380 293570 296230 292520 291070 FALSE TRUE 281927.975 307746.3769 294284.5042 270061.3041 292449.3727 275151.6763 270559.2163 292259.5214 281992.2623 348099.5936 0.809906073 0.884075657 0.845403182 0.7758162 0.840131324 0.790439522 0.777246573 0.839585931 0.810090754 1 18.4091406 -1.172762414 4.099528771 1.000073126 0.819966284 0.73893533 0.032238756 4712292.973 1348058.422 3064.978724 0.007633754 0.067179627 1.172762414 -0.180106842 FVPYLIAGIQHSCQDIGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVPYLIAGIQHSCQDIGAK 19 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 236.43 3.44E-24 357390000 288900 316420 278190 287970 452450 480070 319660 307070 318140 394230 FALSE TRUE 300305.9951 370762.6736 285439.8599 344929.6065 375542.7106 368581.018 294604.2139 302954.2289 306690.2035 471471.8205 0.636954282 0.786394133 0.605422949 0.731601745 0.796532675 0.781766803 0.624860705 0.642571233 0.6504953 1 18.84681202 -1.367511141 3.020757031 1.003715734 0.694867691 0.63257205 0.069694218 11883687.42 15044784.73 391912.3473 0.017547877 0.042903118 1.367511141 -0.308848042 FVS(ph)EGDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;FVS(1)EGDGGR 199.59 2.57E-05 11044220000 5025560 5994120 6088710 6887680 7837710 8738260 7089160 7544360 6776680 7702040 TRUE FALSE 5223972.989 7023563.482 6247386.785 8250042.546 6505458.854 6708931.545 6533493.115 7443240.194 6532788.611 9211107.274 0.567138438 0.762510225 0.678244927 0.895662411 0.706262413 0.728352341 0.709305941 0.808072252 0.709229457 1 23.13494316 -5 0.213172265 2.27417214 0.700539592 0.516289334 0.079637389 118.8130007 1.186290965 64.882954 0.156272295 1.00E-05 5 -1.573632548 FVSEDDRNS(ph)FTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 1 FVSEDDRNS(0.999)FT(0.001)LK;FVSEDDRNS(1)FTLK 171.78 1.48E-05 1053580000 1704850 1153060 1402710 1074690 1731860 1707050 1616540 1399620 1447060 973500 TRUE FALSE 1772158.794 1351089.085 1439265.775 1287260.474 1437479.056 1310613.508 1489831.371 1380860.383 1394980.593 1164238.686 1.522161061 1.160491488 1.236229127 1.105667154 1.23469446 1.125725784 1.279661455 1.186062961 1.198191238 1 20.15095543 7.999999982 0.022689802 3.76E-12 2.803766905 0.3884432 0.101537755 2843.372708 4.965125862 218.3332866 427.5284778 99999995.96 -7.999999982 2.803766905 FVSEDDRNSFTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FVSEDDRNSFTLK 13 1 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;; 180.28 1.19E-05 3493970000 4170330 3741110 4174400 3483040 5656100 5388320 4530140 4354850 4421010 4032170 FALSE TRUE 4334977.849 4383616.541 4283188.293 4171974.916 4694678.142 4136964.341 4175055.789 4296480.359 4261898.714 4822196.511 0.898963333 0.909049752 0.888223506 0.865160701 0.973555958 0.857900405 0.865799596 0.89097994 0.883808593 1 22.20125901 -1.244034513 4.217602293 1.000069844 0.892232359 0.518447696 0.031049165 1.96E-05 3.52E-06 0.028937697 0.006816266 0.057011896 1.244034513 -0.107837485 FVSEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FVSEEHR 7 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ;; 138.55 0.0027748 742230000 2046240 2380730 2346390 2408760 3388170 3600990 3484110 3255790 2998910 3388650 FALSE TRUE 2127027.135 2789601.858 2407538.851 2885205.539 2812250.074 2764714.646 3211016.354 3212151.46 2890979.815 4052591.088 0.524856096 0.688350193 0.594073964 0.711940947 0.69393877 0.682209131 0.792336627 0.792616721 0.713365783 1 21.95041318 -5 0.047766161 2.330781851 0.012700951 0.822994998 0.050845896 220.8705028 0.782300018 38.10762696 9.114490502 1.00E-05 5 -2.3180809 FVSISDLLVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVSISDLLVPK 11 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 111.61 0.0020174 0 135090 94648 163250 104560 199470 170780 167050 158970 164220 135020 FALSE TRUE 140423.4575 110903.0577 167504.4291 125241.6559 165564.1606 131118.9332 153956.1845 156839.2672 158309.7543 161474.5839 0.869631952 0.686814328 1.03734238 0.775612192 1.025326442 0.81200973 0.953439116 0.971293831 0.980400447 1 17.30094758 5.979521141 0.196731384 1.019750789 0.475357862 0.236260487 0.098604534 31.27076298 0.740214435 0.185759755 4.489988729 953940.1789 -5.979521141 -0.544392926 FVSSFS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVSSFSR 7 0 A1L390-3;A1L390;A1L390-2;G3V311;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 FVSSFS(1)R 86.205 0.033697 0 61583 87170 84654 77392 115930 102450 66760 79541 76276 117720 TRUE FALSE 64014.34439 102140.7694 86860.15278 92699.90661 96224.26001 78657.54014 61527.17676 78474.883 73530.84166 140784.9801 0.454695837 0.725508995 0.61697031 0.658450259 0.683483848 0.558706902 0.43702941 0.557409483 0.522291807 1 17.1031339 -1.878635638 2.67144344 1.198342639 0.581550796 0.665860707 0.089374083 16021932.51 10594989.1 20132135.45 0.022348662 0.013224046 1.878635638 -0.616791843 FVSSSSSGAYGGGYGGVLTAS(ph)DGLLAGNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FVSSSSSGAYGGGYGGVLTASDGLLAGNEK 30 0 P08727;C9JM50 P08727 KRT19 "Keratin, type I cytoskeletal 19" 1 FVSSSSSGAYGGGYGGVLT(0.008)AS(0.992)DGLLAGNEK 255.37 2.64E-58 48127000 130570 114500 126190 117250 165770 162440 147280 140450 147640 108170 TRUE FALSE 135725.0044 134164.4843 129478.6151 140441.7 137592.4746 124715.7718 135735.8088 138567.4975 142326.4652 129363.8405 1.049172659 1.037109627 1.000887223 1.085633354 1.063608456 0.9640698 1.049256178 1.071145515 1.100202844 1 16.98107489 2.001462648 24.99974854 1.063816102 1.033417005 0.064300282 0.039009459 106.8740481 1826673.615 0.014566091 0.010682672 100.3373549 -2.001462648 -0.030399097 FWAWDPEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 143.86 7.73E-05 315780000 659900 830140 773420 798960 863640 953900 797610 794460 805130 868420 FALSE TRUE 685953.3616 972710.0874 793575.9606 956991.9033 716838.7813 732371.1815 735091.244 783811.5632 776153.5286 1038570.272 0.660478525 0.936585721 0.764104252 0.921451277 0.690216927 0.705172487 0.707791532 0.754702483 0.747328851 1 19.9861674 5.029432533 14.96958039 0.786348611 0.31334054 0.124014237 0.105589652 2224708.928 32904813.46 0.024126772 25845623.05 107012.0129 -5.029432533 -0.473008071 FWAWDPEEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FWAWDPEEERR 11 1 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 91.752 0.016847 42226000 27116 33562 33544 30989 34423 36678 28269 38924 33914 42776 FALSE TRUE 28186.56062 39326.01242 34418.1842 37118.53171 28571.79076 28160.09036 26053.20191 38402.28745 32693.44176 51157.1382 0.550980012 0.768729718 0.672793385 0.725578737 0.558510342 0.550462582 0.509277939 0.750673099 0.639078786 1 15.64264794 0.23128413 1.09456317 1.001008375 0.635082798 0.609057336 0.087503647 3.061695911 3.729384791 0.093391311 0.026679777 1.703272483 -0.23128413 -0.365925576 FWEGDFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FWEGDFHR 8 0 P49589-3;P49589;B4DKY1;P49589-2 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 ;;;;; 136.27 0.00079823 1234730000 855880 1067420 981540 994430 1193270 1299420 1016960 971700 992250 1204480 FALSE TRUE 889670.8033 1250741.082 1007119.739 1191125.286 990438.3916 997649.3979 937248.0179 958675.9509 956539.1163 1440474.795 0.617623305 0.868283906 0.699158182 0.826897694 0.687577731 0.692583724 0.650652147 0.665527751 0.664044327 1 20.45811299 -1.1558894 5.223578155 1.000011332 0.709204032 0.579034947 0.074676251 9.72E-06 1.57E-06 0.071310476 0.016807386 0.069841024 1.1558894 -0.2908073 FWETLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FWETLDR 7 0 A0A1B0GUB2;Q6P1J9 A0A1B0GUB2 CDC73 Parafibromin 0 ;; 170.06 0.0023005 199048000 287576 330880 351630 346153 404640 444010 362500 368990 369990 338448 FALSE TRUE 298929.7225 387706.0661 360793.7667 414621.0302 335859.4373 340895.4065 334086.3028 364044.2926 356674.1322 404760.4056 0.738534991 0.957865593 0.891376137 1.024361633 0.829773448 0.8422153 0.825392746 0.899406878 0.881198179 1 18.62670864 0.241905747 1.822622805 1.00000624 0.880184245 0.199865321 0.073731779 25.07735405 57.70423175 0.068486319 0.01905156 1.745443304 -0.241905747 -0.119821995 FWEVISDEHGIDPSGNYVGDSDLQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FWEVISDEHGIDPSGNYVGDSDLQLER 27 0 Q13509;G3V5W4;G3V2R8;G3V3R4;G3V2N6;G3V3J6;G3V3W7 Q13509 TUBB3 Tubulin beta-3 chain 0 ; 178.15 2.09E-17 122230000 52324 60364 62280 66230 70588 65600 64569 72491 59053 69150 FALSE TRUE 54389.79192 70731.04743 63903.06796 79330.09632 58589.47697 50365.39418 59507.91306 71519.37672 56927.69407 82698.61854 0.657686826 0.855286928 0.772722315 0.959267491 0.708469839 0.609023404 0.71957566 0.864819485 0.688375393 1 16.33557561 -1.69043302 3.896852891 1.014419493 0.768107339 0.332275644 0.10162999 19357816.5 8557786.985 2416627.865 0.023966579 0.020397032 1.69043302 -0.246312154 FWEVISDEHGIDPT(ph)GSYHGDSDLQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 1 FWEVISDEHGIDPT(0.456)GS(0.456)Y(0.072)HGDS(0.017)DLQLER 61.014 0.087242 9266900 9581.1 14689 13554 12411 16019 17283 14703 13612 14205 13621 TRUE FALSE 9959.369226 17211.72149 13907.22837 14865.85876 13296.0961 13269.28518 13550.54044 13429.5534 13693.76482 16289.77416 0.611387802 1.056596692 0.85373979 0.912588389 0.816223477 0.814577602 0.831843358 0.824416181 0.840635646 1 13.99167898 -0.940290465 4.360495497 1.000003433 0.845793285 0.175761897 0.103167686 10315098.03 4731158.665 339.7357494 0.021925331 0.114738597 0.940290465 -0.154210148 FWEVISDEHGIDPTGSYHGDSDLQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FWEVISDEHGIDPTGSYHGDSDLQLER 27 0 Q13885;Q9BVA1 Q13885;Q9BVA1 TUBB2A;TUBB2B Tubulin beta-2A chain;Tubulin beta-2B chain 0 ;; 311.64 2.90E-82 917350000 163258 440440 411482 443571 439327 531048 366755 452017 388431 439035 FALSE TRUE 169703.5519 516082.1439 422205.559 531308.0199 364650.3535 407720.1501 338007.7848 445958.4515 374451.4442 525055.5024 0.323210691 0.982909695 0.804116054 1.011908298 0.69449868 0.776527716 0.643756295 0.849354877 0.713165451 1 19.00211041 -1.802291191 2.401132564 1.076682707 0.771036812 0.133153132 0.183336589 29717217.58 18859803.73 13265098.94 0.042360632 0.015765538 1.802291191 -0.305645895 FWEVISDEHGIDPTGTYHGDS(ph)DLQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 1 FWEVISDEHGIDPT(0.081)GT(0.081)Y(0.001)HGDS(0.836)DLQLDR 77.925 0.023653 21168000 12674 16648 15173 15176 15366 18440 15327 14832 17099 15099 TRUE FALSE 13174.37931 19507.1645 15568.42084 18177.7675 12754.09281 14157.58946 14125.62969 14633.2013 16483.61033 18057.35996 0.729585019 1.080288843 0.862164839 1.006668059 0.706309939 0.784034294 0.782264391 0.81037324 0.912847192 1 14.14029936 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 ;;;;;;;;;;;;;; 340.81 5.61E-96 50269608000 1339229 2147097 2018747 2118858 2274223 2611757 1935342 2141763 1958063 2137842 FALSE TRUE 1392102.795 2515844.208 2071357.205 2537961.788 1887651.387 2005216.018 1783644.837 2113056.17 1887592.695 2556711.208 0.544489652 0.984015793 0.810164714 0.992666587 0.738312321 0.784295079 0.697632502 0.826474325 0.738289365 1 21.28585778 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 19 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 ;;;;;;;;;;;;;;;;;; 349.21 2.23E-110 65033117000 3124814.1 4923986.5 4618775.8 4881783 4855591.4 5502577.7 4257680.3 4779901.9 4655298.8 5028387.5 FALSE TRUE 3248184.174 5769642.878 4739144.892 5847385.107 4030239.708 4224687.422 3923952.193 4715835.133 4487755.506 6013603.756 0.540139375 0.959431834 0.788070695 0.972359561 0.670187108 0.702521748 0.652512595 0.784194524 0.746267245 1 22.51979838 -1.245739232 3.512523096 1.000528413 0.763302227 0.250136724 0.125679211 46572594.35 75879262.24 269535.8205 0.029044746 0.056788548 1.245739232 -0.237226186 FWLADCHQVLETVGLATQLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FWLADCHQVLETVGLATQLYR 21 0 Q12955;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 0 71.535 0.016766 10707000 16723 15347 16241 16758 19212 20712 22566 18840 21160 20200 FALSE TRUE 17383.23695 17982.72787 16664.2538 20072.68238 15946.3511 15901.95189 20797.21795 18587.48062 20398.45573 24157.80325 0.719570268 0.74438589 0.689808325 0.830898496 0.660091108 0.658253225 0.860890278 0.769419323 0.844383718 1 14.56020165 0.859121157 0.693304575 1.001316059 0.723640231 0.660003248 0.059462978 0.535257535 0.558677783 0.0584745 0.022430398 7.229714652 -0.859121157 -0.277675828 FWQIYIEGQDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FWQIYIEGQDEPR 13 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ; 146.16 9.64E-05 46035000 47088 47972 49615 57734 56704 67483 48616 52825 42797 45090 FALSE TRUE 48947.0706 56210.81783 50908.00766 69153.61288 47065.47433 51811.09596 44805.35089 52116.96728 41256.74433 53924.5222 0.907695954 1.042398069 0.944060431 1.28241494 0.872802807 0.960807697 0.830890086 0.966479908 0.765083169 1 15.71865387 FWTHWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FWTHWNR 7 0 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 169.37 0.0010144 807330000 373280 441110 393230 382820 836860 641720 506040 433990 424560 850720 FALSE TRUE 388017.3826 516867.2111 403477.8968 458540.6534 694610.8361 492690.2554 466375.2625 428173.0739 409280.1685 1017402.296 0.381380487 0.508026386 0.396576554 0.450697482 0.682729771 0.484262968 0.458398083 0.420849329 0.40227958 1 19.95645882 -1.062642242 4.58960644 1.000024916 0.467155987 0.79239466 0.082143061 1.657346566 102870847.1 5900.942939 0.019680717 0.086568075 1.062642242 -0.53286893 FYAFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FYAFGR 6 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;; 164.54 0.017566 10743983000 6866027 8791610 8003409 8622020 9193291 9968370 8512795 8275734 7594678 10080330 FALSE TRUE 7137103.048 10301500.63 8211984.413 10327429.82 7630618.68 7653367.14 7845539.884 8164811.322 7321347.022 12055377.66 0.5920265 0.854514965 0.681188482 0.856665806 0.632963885 0.634850882 0.650791713 0.677275449 0.607309636 1 23.52317351 -1.02808983 4.562134672 1.000010021 0.691453394 0.524854885 0.089126157 0.159436364 52567555.97 1336.217039 0.020235022 0.09373681 1.02808983 -0.308556627 FYAGGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYAGGSER 8 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 107.32 0.0093669 1027010000 457130 851740 659380 690410 664010 839010 591690 658830 577080 939410 FALSE TRUE 475177.8454 998019.7194 676563.9845 826971.0373 551141.8174 644162.6428 545311.7917 649999.4615 556311.0035 1123469.403 0.422955751 0.888337249 0.602209533 0.736086835 0.490571275 0.573369102 0.48538197 0.578564454 0.495172367 1 20.0995294 -1.756368198 6.110460608 1.013268264 0.591194547 0.477356159 0.129896902 0.022466704 0.000895776 0.120347062 0.028432595 0.017523942 1.756368198 -0.422073718 FYALSASFEPFSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYALSASFEPFSNK 14 0 P27797 P27797 CALR Calreticulin 0 ; 262.93 5.17E-17 230100000 830170 761720 822720 851200 1136880 1115080 943500 806820 828930 773030 FALSE TRUE 862945.7526 892539.4846 844160.7591 1019564.819 943633.5437 856119.5692 869546.0046 796005.8976 799096.9712 924490.4279 0.933428542 0.965439401 0.913109248 1.102839779 1.020706667 0.926044817 0.940567883 0.861021243 0.864364786 1 19.81829886 2.413988045 2.490582778 0.899487863 0.987162205 0.213313197 0.061814386 0.38103929 4.831035198 0.02496617 0.020119356 259.4107953 -2.413988045 0.087674342 FYCDYCDTYLTHDSPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FYCDYCDTYLTHDSPSVR 18 0 A0A0A0MRR7;P09234 A0A0A0MRR7 SNRPC U1 small nuclear ribonucleoprotein C 0 ;;; 320.73 1.38E-61 2486840000 143591 1381110 1002280 1476720 938480 1747800 888920 1408730 951100 1346240 FALSE TRUE 149260.0836 1618304.899 1028400.24 1768810.808 778957.5048 1341899.938 819244.1276 1389848.279 916870.0968 1610009.953 0.092707553 1.005152109 0.638753965 1.098633462 0.483821546 0.83347307 0.508844139 0.863254464 0.569481012 1 20.61863818 -4.999999988 0.03530522 2.050857243 5.95E-11 0.107485848 0.276802848 3008.365518 7.966431857 389.3946283 134.7657501 1.00E-05 4.999999988 -2.050857243 FYEAFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYEAFSK 7 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 112.17 0.014922 4176100000 4503800 4024900 4946900 4139800 5914500 5791800 5270000 4982700 5186300 4159400 FALSE TRUE 4681613.502 4716145.266 5075820.278 4958640.084 4909155.403 4446742.226 4856923.629 4915915.057 4999646.076 4974354.793 0.941149897 0.948091855 1.020397718 0.996840855 0.986892895 0.893933467 0.976392684 0.988251796 1.005084334 1 22.24607798 1.63510398 3.102169526 1.000741802 0.966754568 0.173361619 0.032558561 0.423243167 9.602763972 0.022071976 0.009340262 43.16224042 -1.63510398 -0.033987234 FYEDDENGWQAFGDFSPTDVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYEDDENGWQAFGDFSPTDVHK 22 0 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 0 147.93 7.44E-08 47409000 39849 41348 41146 38685 54549 47216 47504 43774 44015 36140 FALSE TRUE 41422.26929 48449.19736 42218.29856 46336.77754 45276.78046 36250.79957 43780.51235 43187.28113 42430.90875 43220.94106 0.958384253 1.120965814 0.976801928 1.072090899 1.047565818 0.838732306 1.012946763 0.999221213 0.981721076 1 15.39944286 FYEEEENGGVWEGFGDFSPTDVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYEEEENGGVWEGFGDFSPTDVHR 24 0 P19838;P19838-2;P19838-3;A0A494C1E9;D6RF93 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 ; 209.24 5.50E-25 96845000 39323 54164 47840 46722 53339 60994 43082 46545 45314 52934 FALSE TRUE 40875.5024 63466.24566 49086.7497 55963.47215 44272.45583 46829.06787 39705.12027 45921.14041 43683.15799 63305.40382 0.645687413 1.002540729 0.775395886 0.884023618 0.699347183 0.739732551 0.627199542 0.72539053 0.690038375 1 15.95004103 3.231237139 24.97098853 0.724506025 0.835777113 0.070906941 0.125434019 289.6675408 987683.5675 0.032962355 0.040156244 1703.088196 -3.231237139 0.111271089 FYEEVHDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 235.01 4.19E-12 24439310000 12118030 15617660 15093300 14334010 17131000 18487290 15882710 15338280 14974110 18024960 FALSE TRUE 12596459.18 18299871.62 15486643.8 17169234.4 14219078.74 14193897.08 14637781.69 15132695.44 14435194.71 21556605.8 0.584343347 0.848921754 0.718417544 0.796472068 0.659615844 0.65844768 0.679039262 0.70199806 0.669641354 1 24.3616267 -1.482077384 6.639187522 1.000107193 0.705725546 0.614843626 0.070727811 0.00010679 8.33E-06 0.065167791 0.015354644 0.032955099 1.482077384 -0.294381647 FYEQFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FYEQFSK 7 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 144.38 0.0079173 3434030000 6138560 5167480 6232070 5043130 7731500 7158280 6985500 6304950 6180800 5180920 FALSE TRUE 6380915.089 6054954.493 6394482.864 6040646.062 6417302.392 5495877.955 6437958.257 6220442.458 5958354.215 6196022.079 1.029840599 0.977232556 1.032030355 0.974923263 1.035713287 0.887001028 1.039047017 1.0039413 0.961641863 1 22.56291085 4.754705831 22.48647494 0.992137758 1.029840715 0.069860175 0.042888342 2162.657004 3011860.994 0.009578672 0.21195923 56846.77493 -4.754705831 0.037702957 FYETKEESYS(ph)PSKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYETKEESYSPSKDR 15 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 FYETKEES(0.022)YS(0.95)PS(0.028)KDR 70.114 0.024863 383130000 360050 157690 219900 103550 368200 292080 181680 228470 257890 170830 TRUE FALSE 374265.052 184772.0308 225630.7746 124031.8809 305613.4955 224248.8465 167439.4469 225407.7334 248608.5893 204300.8678 1.8319308 0.904411385 1.104404387 0.607104034 1.495899155 1.097640206 0.819572862 1.103312658 1.216874857 1 17.64033581 4.744665569 24.47668204 1.039421976 1.831931273 0.527768228 0.225070985 391.7552221 1570610.972 0.051442779 0.469455667 55547.63443 -4.744665569 0.792509298 FYFHDGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ;;; 182.39 0.00022882 2457320000 1502130 1615780 1635000 1602420 2066500 2270250 1704270 1619910 1568980 1781210 FALSE TRUE 1561435.252 1893277.646 1677609.443 1919373.893 1715237.068 1743018.843 1570684.864 1598197.756 1512512.716 2130203.996 0.732997992 0.888777624 0.787534643 0.90102821 0.805198503 0.818240341 0.737340117 0.750255731 0.710031865 1 21.02256016 2.391906613 7.864591698 0.774153942 0.827400259 0 0.08788057 0.64394546 51.74967736 0.028126719 0.023492528 246.5509121 -2.391906613 0.053246317 FYGDEEKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;; 166.33 5.55E-05 11019700000 17950500 6928270 9120790 6953460 16397080 15531210 16538360 10646980 11379610 5204922 FALSE TRUE 18659199.6 8118146.478 9358485.28 8328833.634 13609910.2 11924321.86 15242040.13 10504274.65 10970060.06 6224726.812 2.997593335 1.304177151 1.503437109 1.338023962 2.186426908 1.915637781 2.448627962 1.687507736 1.762335985 1 22.56957909 4.751517373 24.50926351 1.743345914 2.997594395 0.473343805 0.411604328 1511.759723 2859608.164 0.098424427 1.796204345 56430.95148 -4.751517373 1.254248481 FYGDEEKDKGLQTSQDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 FYGDEEKDKGLQTSQDAR 18 2 P27797 P27797 CALR Calreticulin 0 ;;;;; 173.21 4.99E-12 6051440000 13614850 7534310 10220830 5523180 17780200 13451960 10031110 9342370 11506700 6669550 FALSE TRUE 14152374.79 8828269.134 10487193.23 6615648.519 14757927.95 10327946.16 9244845.387 9217150.811 11092576.11 7976320.626 1.774298634 1.106809712 1.314790831 0.829411057 1.850217493 1.294825853 1.15903633 1.155564231 1.390688343 1 22.92729197 -5 0.063892942 0.025563151 1.692903024 0.118204439 0.285463561 883.7724679 4.104371111 134.2005076 20.00784213 1.00E-05 5 1.667339873 FYHDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYHDAK 6 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 124.12 0.018491 362980000 1232590 1121930 1265470 1087260 1638790 1703160 1502840 1369680 1438300 1138970 FALSE TRUE 1281253.605 1314612.75 1298449.188 1302316.783 1360229.061 1307626.902 1385043.474 1351321.68 1386535.864 1362129.365 0.940625493 0.965115931 0.953249538 0.956088912 0.998604902 0.959987308 1.016822271 0.992065596 1.017917901 1 20.3774323 2.921894673 0.676413856 1.007945441 0.948032592 0.66592024 0.015449991 0.433857962 0.437761829 0.010066695 0.012680976 835.4003887 -2.921894673 -0.059912849 FYHDWNDKEIEVLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 303.3 1.04E-44 1623300000 2455500 1390600 1867900 1277300 2762300 2507200 2393100 1823900 2205600 1146800 FALSE TRUE 2552445.036 1629424.733 1916579.008 1529946.128 2292765.233 1924940.797 2205522.569 1799453.604 2126220.887 1371493.503 1.861069724 1.188065951 1.397439364 1.115532902 1.671728832 1.403536213 1.608117402 1.312039466 1.550295996 1 20.38731636 -1.307902684 5.103572951 0.999871185 1.438668211 0.286393781 0.214499631 0.000287719 3.90E-05 0.190068738 0.044786584 0.04921498 1.307902684 0.438797026 FYIGEMVLAIDSIHQLHYVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FYIGEMVLAIDSIHQLHYVHR 21 0 Q9Y5S2;A0A0U1RRC3 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 0 ;; 168.09 3.91E-12 252543000 34565.83 51709 48525 56419 53864.96 67553 53323 50273 60362 53121 FALSE TRUE 35930.51566 60589.61851 49789.60136 67578.50981 44709.01334 51864.83953 49143.40393 49599.17267 58189.58341 63529.04289 0.565576216 0.953731014 0.783729757 1.063741979 0.703757074 0.816395733 0.773558072 0.780732251 0.915952465 1 15.95512866 1.03044506 4.140099447 0.999141451 0.812236811 0.201876191 0.126248482 0.276828488 11.19196299 0.112087446 0.028662557 10.72617949 -1.03044506 -0.18690464 FYNELTEILVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYNELTEILVR 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 106.29 0.00547 133900000 205710 73224 86875 92004 91263 146770 101770 99306 73723 81944 FALSE TRUE 213831.5896 85799.6524 89139.03387 110202.1166 75750.14786 112684.8918 93793.00147 97974.9655 71069.72363 97999.35789 2.181969293 0.875512394 0.909587938 1.124518762 0.772965757 1.149853369 0.957077715 0.999751096 0.725206013 1 16.58048468 4.740783786 24.99989391 0.953980552 2.181969717 0.89285548 0.12841492 54.95739144 617964.4954 0.02834589 0.189283792 55053.35445 -4.740783786 1.227989165 FYQHKFPEVEDVVMVNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYQHKFPEVEDVVMVNVR 18 1 P05198;G3V4T5 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 156.11 8.39E-09 536400000 769410 528010 676270 525270 805510 781260 735320 674800 748820 499540 FALSE TRUE 799786.9009 618691.6102 693894.1518 629166.8382 668589.6979 599824.2051 677683.697 665755.4098 721870.1145 597415.2987 1.338745262 1.035613938 1.161493777 1.053148186 1.119137222 1.004032214 1.134359462 1.114392971 1.20832211 1 19.18837466 4.747852858 24.55478678 1.097553902 1.338745426 0.561305086 0.065217674 687.0271988 1815422.963 0.01445178 0.179731669 55956.79833 -4.747852858 0.241191524 FYQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYQLER 6 0 Q9Y3P9;A0A0U1RQX4;Q5R372-4;Q5R372;Q5R372-3 Q9Y3P9;Q5R372-4 RABGAP1;RABGAP1L Rab GTPase-activating protein 1;Rab GTPase-activating protein 1-like 0 ; 103.29 0.080996 298310000 202288 285010 229048 249770 259190 298960 243390 233100 209682 248320 FALSE TRUE 210274.4864 333958.2504 235017.179 299173.7605 215132.9764 229531.0708 224312.4558 229975.6758 202135.5858 296973.5496 0.708057962 1.124538703 0.791374112 1.007408777 0.724417971 0.772900722 0.755328062 0.774397841 0.680651816 1 18.17997492 3.227131252 24.99774391 0.771135296 0.915003686 0.168407515 0.1317448 304.7409862 666513.2527 0.034362729 0.041410154 1687.062809 -3.227131252 0.143868391 FYQNNKDFIDSLGLLHEQNMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYQNNKDFIDSLGLLHEQNMAK 22 1 Q7L2H7;Q7L2H7-2;H0YCQ8 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 190.79 9.95E-18 290870000 396450 206760 359810 253180 406820 357140 426460 341380 406130 177070 FALSE TRUE 412102.1521 242269.4216 369186.9442 303258.2483 337668.8817 274199.6475 393032.9509 336804.3595 391513.4606 211763.4763 1.94604924 1.144056689 1.743392915 1.432061154 1.594556756 1.294839187 1.855999711 1.590474266 1.848824299 1 17.69209426 4.826394086 21.00779288 1.539342763 1.9461338 0.178112554 0.276004162 93151.57764 22264589.84 0.060011821 1228.841795 67049.27494 -4.826394086 0.406791037 FYS(ph)TSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 77.674 0.039238 229814000 31579 713780 380130 736860 207840 634260 218580 421980 281790 1040720 TRUE FALSE 32825.7633 836366.1626 390036.5001 882608.7087 172511.431 486962.7273 201447.1284 416324.0483 271648.4329 1244629.158 0.026373931 0.67198021 0.313375673 0.709133884 0.138604684 0.391251261 0.161853133 0.334496461 0.218256523 1 20.24728452 -1.244197876 4.290068376 1.000376818 0.338870662 0.48136358 0.208593702 58998196.84 17110914.85 209210.4735 0.045138532 0.056990455 1.244197876 -0.661506156 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYTEDGNWDLVGNNTPIFFIRDPILFPSFIHSQK 34 1 P04040 P04040 CAT Catalase 0 176.13 8.19E-16 137460000 36818 52667 47782 48676 59469 73554 56646 43808 49015 51576 FALSE TRUE 38271.60307 61712.14756 49027.23817 58303.96752 49360.48062 56472.19822 52205.9385 43220.82542 47250.95972 61681.32972 0.620473055 1.00049963 0.794847297 0.945244984 0.800249944 0.915547678 0.846381535 0.700711635 0.766049629 1 15.91254625 -1.695189155 8.357413512 1.000500258 0.823548808 0.198455943 0.107753506 0.000961875 3.51E-05 0.099916335 0.0234861 0.020174875 1.695189155 -0.176951451 FYTLIPHDFGMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 FYTLIPHDFGMK 12 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 174.24 3.09E-05 780280000 1824440 1657160 1911350 1620160 2731340 2514570 2263160 2062470 2143130 1903690 FALSE TRUE 1896470.3 1941764.339 1961161.351 1940622.812 2267067.802 1930599.226 2085767.606 2034825.963 2065999.17 2276681.607 0.832997594 0.852892356 0.861412217 0.852390956 0.995777273 0.847988239 0.916143741 0.89376835 0.907460737 1 21.11850111 -4.450709274 0.016820496 2.066586432 5.82E-07 0.497185469 0.040452128 3525.727957 4.908626501 379.5732564 238.4679013 3.54E-05 4.450709274 -2.06658585 FYTQQWEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 FYTQQWEDYR 10 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJA0 A0A590UJ56 CUL1 Cullin-1 0 ;;; 154.84 3.20E-05 457320000 432879 497416 483290 516920 510020 663960 558290 466111 478165 473445 FALSE TRUE 449969.3972 582843.3286 495884.9344 619165.2331 423326.9826 509765.3524 514529.771 459863.5444 460955.9351 566207.4831 0.794707613 1.029381183 0.875800743 1.093530643 0.747653458 0.900315463 0.908730079 0.812182033 0.814111344 1 19.11097129 3.224400599 24.99997375 0.85649289 0.948960227 0.147315848 0.098672934 392.4139119 692818.5038 0.026500745 0.031817328 1676.488579 -3.224400599 0.092467337 FYVHNDMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 FYVHNDMFR 9 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 152.34 0.0016752 0 153420 251620 164490 119010 603770 355430 203790 172020 181560 834080 FALSE TRUE 159477.1401 294833.7777 168776.7445 142549.8228 501141.3911 272886.7691 187816.4073 169714.3533 175025.6911 997502.0066 0.159876511 0.295572115 0.169199404 0.142906803 0.502396374 0.273570146 0.188286746 0.17013936 0.175463999 1 19.92796022 -1.847501612 2.705734329 1.297290587 0.231212713 0.83543022 0.102415729 34730384.27 23250344.62 66753243.93 0.025523879 0.014206869 1.847501612 -1.066077874 FYWGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FYWGHK 6 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 128.65 0.016535 5604400000 4330300 4192700 4305000 3890400 5435700 5375200 4800900 4762900 4973200 3943600 FALSE TRUE 4501263.588 4912763.61 4417191.837 4659909.508 4511741.656 4126891.262 4424592.913 4699061.116 4794215.503 4716272.915 0.954411178 1.041662283 0.93658529 0.988049163 0.956632862 0.875032327 0.938154554 0.996350551 1.01652631 1 22.16921577 1.602214435 5.231623474 1.007509651 0.956649019 0.240895108 0.039726656 0.228935435 13.46574199 0.023498544 0.010921706 40.0142273 -1.602214435 -0.050860632 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.02)S(0.919)S(0.061)PESQHGGTQSPGGGQPLLQPTK 332.05 2.43E-117 986530000 125410 240100 254780 306280 279550 338250 308560 305940 285010 246820 TRUE FALSE 130361.2836 281335.3073 261419.7761 366861.2698 232032.1909 259696.5637 284374.2609 301839.3747 274752.5458 295179.6533 0.441633704 0.953098576 0.885629389 1.242840642 0.786071087 0.879791547 0.963393844 1.022561587 0.930797711 1 18.17123375 4.740258989 5.669098647 0.965393415 0.423915029 0.655408416 0.113360451 0.085050171 11.37907952 0.026365396 0.177886621 54986.86875 -4.740258989 -0.541478386 GAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTKVDAAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTKVDAAEGR 40 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLS(0.077)S(0.461)S(0.461)PESQHGGTQSPGGGQPLLQPTKVDAAEGR;GAAAADLLS(0.032)S(0.824)S(0.144)PESQHGGTQSPGGGQPLLQPTKVDAAEGR 288.28 1.16E-78 1950770000 310860 712180 718910 612500 912230 989650 548780 800180 799180 960110 TRUE FALSE 323132.9928 834491.375 737645.3852 733650.6719 757169.4704 759818.7858 505765.1896 789454.8959 770417.6679 1148225.172 0.281419534 0.726766313 0.642422238 0.638943205 0.659425946 0.66173326 0.440475616 0.687543624 0.670963925 1 20.13097416 -4.999999997 0.243736312 3.30021681 0.570122265 0.494499934 0.125098011 147.1616899 1.465055921 167.929195 0.181130627 1.00E-05 4.999999997 -2.730094546 GAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 33 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 GAAAADLLSS(0.026)S(0.974)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLSS(0.037)S(0.963)PESQHGGTQSPGGGQPLLQPTK;GAAAADLLS(0.001)S(0.025)S(0.975)PESQHGGTQSPGGGQPLLQPTK 383.37 1.07E-148 2221590000 372826 786010 835400 923260 910980 1151670 972400 950600 919670 776070 TRUE FALSE 387545.4584 921001.1032 857171.2103 1105878.072 756131.945 884212.0962 896180.7471 937858.7619 886571.2563 928126.0577 0.41755692 0.99232329 0.92355042 1.191517104 0.814686689 0.952685348 0.965580849 1.010486403 0.955227201 1 19.82396124 4.73941465 24.72920311 0.978682326 0.417556715 0.783405452 0.08847734 25.70193309 744077.4877 0.019943819 0.120578493 54880.06916 -4.73941465 -0.561125611 GAAAHPDSEEQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GAAAHPDSEEQQQR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;; 246.51 9.72E-18 1822634000 1277413 1789252 1589830 1728317 1657623 1936355 1524580 1684106 1547360 1924843 FALSE TRUE 1327846.252 2096542.113 1631262.276 2070172.944 1375860.835 1486665.897 1405079.436 1661533.314 1491670.816 2301979.133 0.576828101 0.91075635 0.708634693 0.899301351 0.597686059 0.645820753 0.610378876 0.721784698 0.647994934 1 21.13444332 -1.192223798 4.632853841 1.000044267 0.706660742 0.390891744 0.111419669 5.91E-05 1.03E-05 0.10426877 0.024571945 0.064235662 1.192223798 -0.293383525 GAAEEAELEDS(ph)DDEEKPVKQDDFPK ddPTM_MDA-MB-175_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 333.38 3.21E-88 1455150000 3634920 645721 1205030 582383 1993550 2426490 1971190 1177530 1400820 420674 TRUE FALSE 3778429.448 756618.5587 1236434.072 697576.6192 1654687.083 1862974.471 1816682.977 1161747.136 1350404.762 503097.016 7.510339613 1.503921778 2.457645409 1.386564811 3.289001983 3.703012365 3.610999309 2.309191069 2.684183604 1 18.94047711 0.735952675 0.986216767 1.010212045 3.154608685 0.150010962 1.622656678 1.891378281 3.340949627 1.482733981 0.482638496 5.444433223 -0.735952675 2.14439664 GAAS(ph)PVLQEDHCDSLPSVLQVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAASPVLQEDHCDSLPSVLQVEEK 24 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 GAAS(1)PVLQEDHCDSLPSVLQVEEK 179.41 2.44E-17 131300000 81977 60299 61015 64369 85809 100170 103980 77284 79064 49077 TRUE FALSE 85213.51526 70654.88419 62605.10102 77100.99608 71223.21683 76907.03559 95829.7759 76248.13439 76218.50208 58692.69851 1.451858875 1.203810456 1.066659101 1.31363863 1.213493648 1.310333952 1.632737603 1.299107663 1.298602791 1 15.84089342 2.483880765 24.89801472 1.356159568 1.242815881 0 0.170891782 759.9674777 2799280.725 0.056126706 0.048667893 304.7058311 -2.483880765 -0.113343687 KPAPAPPKPGNPPPGHPGGQSSSGTSQHPPS(ph)LSPKPPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPAPAPPKPGNPPPGHPGGQSSSGTSQHPPSLSPKPPTR 39 3 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;I3L460;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 KPAPAPPKPGNPPPGHPGGQS(0.021)S(0.019)S(0.019)GT(0.019)S(0.027)QHPPS(0.443)LS(0.443)PKPPT(0.009)R 50.214 0.017693 285280000 33538 58895 80227 61865 86117 110640 73452 83888 79983 62757 TRUE FALSE 34862.10614 69009.75811 82317.78153 74101.71235 71478.8631 84945.53677 67694.64031 82763.61857 77104.42745 75053.03259 0.464499634 0.919479943 1.096794875 0.987324693 0.95237808 1.131806855 0.901957429 1.102735169 1.027332605 1 16.19562275 4.720619357 3.105380758 1.02592803 0.389830709 0.859731068 0.067627319 0.103223201 1.553428947 0.015272753 0.157150941 52555.64339 -4.720619357 -0.636097321 down GACS(ph)TPDMPQFEPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GACSTPDMPQFEPVK 15 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 GACS(0.5)T(0.5)PDMPQFEPVK 68.034 0.056466 25568000 40912 35172 38240 36866 39208 49769 46724 38615 33687 26253 TRUE FALSE 42527.23735 41212.5174 39236.56581 44157.98477 32543.43816 38210.90401 43061.65079 38097.42909 32474.61145 31396.77271 1.354509833 1.312635467 1.249700604 1.406449802 1.036521762 1.217032858 1.371531119 1.213418635 1.034329603 1 14.93832865 -5 0.072840952 0.05545402 1.567450109 0.450138522 0.105356776 283.2877382 1.479695086 43.38466021 4.990031879 1.00E-05 5 1.511996089 GACST(ph)PDMPQFEPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GACSTPDMPQFEPVK 15 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 GACS(0.074)T(0.926)PDMPQFEPVK 220.19 1.90E-11 120060000 157980 128230 121250 175280 139730 194160 226200 155080 167070 99652 TRUE FALSE 164217.1724 150252.505 124409.8746 209949.8608 115978.7445 149069.2825 208469.8529 153001.4063 161057.1833 119176.9014 1.377927857 1.260751901 1.04390929 1.761665711 0.973164624 1.250823614 1.749247131 1.283817622 1.351412743 1 16.86274512 GADDDRPSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GADDDRPSWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 140.49 3.58E-05 3784160000 4844500 5571800 5359200 6227300 5173200 6319400 5825900 5410600 4986100 5380400 FALSE TRUE 5035764.601 6528713.307 5498865.155 7459041.353 4293861.312 4851815.121 5369250.735 5338079.757 4806651.235 6434586.366 0.782608907 1.014628282 0.854579431 1.159210698 0.667309609 0.754021291 0.834436035 0.829591749 0.747002365 1 22.61741598 3.218920089 24.99999016 0.798942676 0.950163698 0.257182184 0.122365694 308.3164271 392448.2198 0.033240023 0.039781505 1655.465327 -3.218920089 0.151221022 GADFLVTEVENGGSLGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GADFLVTEVENGGSLGSK 18 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 120.14 0.00012485 47260000 42498 29398 42517 34379 50318 51438 45958 38396 45360 33058 FALSE TRUE 44175.85386 34446.87782 43625.02795 41179.06359 41764.96433 39492.30405 42355.69187 37881.36442 43727.50246 39535.08217 1.117383636 0.871299007 1.103451051 1.041582851 1.056402619 0.998917971 1.071344476 0.958170879 1.10604304 1 15.2708458 1.742230036 0.003894612 0.672538893 1.379721092 5.83E-05 0.073145086 120482.7336 447.5632393 40564.52893 40694.13122 55.23699398 -1.742230036 0.707182199 GADILRGS(ph)PSYTQASLGLLTPVSGTQEQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GADILRGSPSYTQASLGLLTPVSGTQEQTK 30 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GADILRGS(0.987)PS(0.012)YT(0.001)QASLGLLTPVSGTQEQTK 195.74 1.81E-25 273900000 114440 120740 122060 78262 169760 156760 95775 127600 131610 152720 TRUE FALSE 118958.1796 141476.1558 125240.9839 93741.99001 140904.2558 120354.8657 88267.90524 125889.7307 126873.3818 182642.56 0.651316865 0.774606728 0.685716319 0.513253811 0.771475476 0.658963966 0.483282238 0.689268321 0.694653983 1 17.47866346 0.649933126 2.201548528 0.999898953 0.651831013 0.57371898 0.089119896 1.515011852 8.619828763 0.084846465 0.023054869 4.466148155 -0.649933126 -0.34806794 GADNDGS(ph)GS(ph)ESGYTTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 GADNDGS(1)GS(0.998)ES(0.002)GYTTPK;GADNDGS(1)GS(0.998)ES(0.002)GYTTPK;GADNDGS(0.999)GS(0.965)ES(0.035)GYTTPK;GADNDGS(0.997)GS(0.986)ES(0.012)GY(0.004)T(0.001)TPK 195.02 6.07E-11 945210000 1731650 1327000 1555480 1222950 1938740 1964880 1593490 1529560 1588420 1218370 TRUE FALSE 1800016.879 1554901.927 1596017.087 1464845.86 1609193.667 1508566.398 1468588.09 1509058.75 1531253.074 1457086.274 1.235353672 1.067130996 1.095348378 1.005325413 1.10439148 1.035330869 1.007893709 1.03566877 1.050900761 1 20.47465487 7.999999994 0.915062723 1.036473991 109.3350049 0.762797126 0.032477647 454.9489568 0.915707305 0.009502743 102978.8691 99999998.55 -7.999999994 108.2985309 GADNDGS(ph)GSESGYTTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 GADNDGS(0.991)GS(0.009)ESGYTTPK;GADNDGS(0.498)GS(0.498)ES(0.004)GYTTPK;GADNDGS(0.999)GS(0.001)ESGYTTPK;GADNDGS(1)GSESGYTTPK;GADNDGS(0.913)GS(0.087)ES(0.001)GYTTPK 295.52 4.21E-46 2793220000 2517135 1982479 2169577 1870652 2785460 2901930 2777910 2377514 2477156 1873079 TRUE FALSE 2616513.433 2322954.347 2226117.959 2240661.382 2311988.504 2228000.737 2560170.155 2345647.314 2388003.639 2240072.968 1.168048305 1.03699941 0.993770288 1.000262676 1.032104104 0.994610787 1.142895875 1.047129869 1.066038327 1 21.0951143 GADQKPTSADCAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GADQKPTSADCAVR 14 1 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 0 65.472 0.052962 96953000 83971 72409 76586 72991 99227 99633 86645 77281 79247 67748 FALSE TRUE 87286.23992 84844.68249 78581.89408 87428.40194 82360.42998 76494.7457 79853.5385 76245.1746 76394.91595 81021.92349 1.077316313 1.047181785 0.969884331 1.079070925 1.0165203 0.94412404 0.985579397 0.941043749 0.942891907 1 16.30602472 2.878777919 4.502202707 0.959825244 1.03936717 0.566258529 0.033388632 0.167457876 5.412578135 0.010164824 0.010887318 756.4459799 -2.878777919 0.079541926 GADS(ph)GEEKEEGINR ddPTM_MDA-MB-175_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 240.61 1.27E-17 5058860000 6329580 3117933 3971796 3557136 5037630 6129290 6252940 4487403 4543510 2366648 TRUE FALSE 6579476.706 3653413.739 4075304.267 4260726.884 4181335.452 4705855.288 5762818.224 4427256.703 4379989.963 2830347.363 2.324618098 1.290800481 1.43986011 1.505372428 1.477322362 1.662642313 2.036081613 1.564209666 1.547509687 1 21.43254769 0.709526814 2.289327805 1.000345837 1.645287438 0.318269498 0.289120533 1.802062886 12.49010026 0.267202495 0.072272775 5.123029001 -0.709526814 0.6449416 GADS(ph)GEEKEEGINREDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDK;GADS(1)GEEKEEGINREDK 135.21 1.13E-05 936560000 1170380 384840 474610 331630 797440 871650 861780 518380 576770 217099 TRUE FALSE 1216587.506 450933.2764 486978.7265 397225.4242 661891.4336 669222.4975 794231.4318 511431.964 556012.1604 259635.3924 4.685753721 1.736794326 1.87562536 1.529935578 2.549311276 2.577547272 3.059026061 1.96980835 2.141511429 1 17.98612753 4.743944071 24.89891018 2.128357585 4.685754866 0.665351486 0.558473243 339.2237882 1568886.955 0.132982599 1.147011144 55455.42917 -4.743944071 2.557397281 GADS(ph)GEEKEEGINREDKTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GADSGEEKEEGINREDKTDK 20 3 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK;GADS(1)GEEKEEGINREDKTDK 162.01 1.20E-10 1539680000 2052800 389950 725010 361655 1234810 1308340 1084560 674190 906940 270118 TRUE FALSE 2133846.129 456920.8791 743904.3562 433189.2796 1024917.437 1004497.863 999549.3532 665153.5858 874299.4066 323042.4504 6.605466639 1.414429833 2.302806815 1.340967043 3.172702027 3.109491839 3.094173388 2.059028419 2.706453612 1 18.30136423 4.746148061 24.99547067 2.332792864 6.605468681 0.749169378 0.755468392 457.0331448 1505577.857 0.176846211 1.886580621 55737.57384 -4.746148061 4.272675817 GADSLEDFLYHEGYACTSIHGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 271.54 7.42E-52 673321000 134301.4 346393 293629 382401 323975.3 396285 307748.8 340678.3 291396 349637.2 FALSE TRUE 139603.723 405883.3032 301281.213 458038.7764 268906.0942 304253.8145 283626.6449 336112.0646 280908.7149 418141.9151 0.333866847 0.970683131 0.720523827 1.095414642 0.643097677 0.7276329 0.678302353 0.803822943 0.671802335 1 18.67363314 -2.435774803 2.211794949 3.269919502 0.753327861 0.139072664 0.19207453 6984036.706 567687.7751 79791847.48 0.043020562 0.003666276 2.435774803 -2.516591642 GAEDDELEEEADWIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ;; 287.45 7.84E-36 201540000 161866 189005 178732 208414 190447 230771 185682 184480 183846 190491 FALSE TRUE 168256.5947 221465.1385 183389.9027 249637.6671 158074.887 177177.9326 171127.7597 182007.3473 177229.4184 227814.0643 0.73856983 0.972131107 0.804998161 1.095795679 0.693876769 0.777730441 0.751172937 0.798929372 0.77795644 1 17.79749729 GAEDDRGPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAEDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 105.86 0.0022734 445260000 649620 760700 708670 861570 707360 863310 809220 737330 678180 697410 FALSE TRUE 675267.4992 891344.3076 727138.5224 1031985.974 587123.1999 662819.3361 745791.2219 727447.2974 653772.4343 834054.1368 0.809620706 1.068688792 0.871812141 1.237312938 0.703938958 0.79469582 0.894176036 0.87218235 0.78384892 1 19.6697815 3.207857419 24.99995208 0.839224717 0.993058151 0.257268342 0.129242658 266.5810085 217061.7678 0.035202164 0.042078927 1613.828643 -3.207857419 0.153833434 GAEEEPPPPLQAVLVADSFDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAEEEPPPPLQAVLVADSFDRR 22 1 Q13144;A0A3B3IUB1;A0A3B3IRP4;A0A3B3ISX3;A0A3B3ISM8;A0A3B3IUF2;A0A3B3ITQ2;A0A3B3IS56;A0A3B3ISS1;C9JRD9;A0A3B3IT53;H7C2X0 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 0 116.69 0.00024872 44759000 20684 39506 29548 29314 27018 37308 25739 25569 29974 37015 FALSE TRUE 21500.62029 46290.84819 30318.04515 35112.22171 22425.49001 28643.78241 23721.50992 25226.28938 28895.2416 44267.38056 0.485698951 1.045710128 0.684884553 0.793184988 0.506591755 0.647062963 0.535868841 0.569861805 0.652743425 1 15.43395639 5.016117195 17.96847618 0.686092282 0.095332309 0.113665619 0.176143645 38366616.54 876239400.1 0.041464128 606970859.1 103780.8433 -5.016117195 -0.590759974 GAEEMETVIPVDVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GAEEMETVIPVDVMR 15 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;; 247.13 7.15E-18 190302000 192480 241540 219973 235577 242804 267683 215064 221901 219586 264000 FALSE TRUE 200079.259 283022.6161 225705.6771 282173.4275 201532.2628 205517.68 198206.7217 218926.7801 211683.1428 315725.7454 0.633712207 0.896419187 0.714878911 0.893729547 0.638314315 0.65093735 0.627781309 0.693408071 0.670465256 1 18.26831238 -1.293593451 3.697804281 1.000694156 0.714678053 0.447013705 0.095654227 6494813.798 3408243.536 34675.7806 0.022489889 0.050863536 1.293593451 -0.286016103 GAEETSWS(ph)GEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAEETSWSGEER 12 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GAEETS(0.001)WS(0.999)GEER;GAEETSWS(1)GEER 243.3 2.57E-16 1759530000 751790 923460 895290 870740 838290 930280 827550 917700 816750 899800 TRUE FALSE 781471.2497 1082057.071 918621.9929 1042969.773 695797.7652 714236.5685 762684.4686 905399.7326 787355.327 1076098.582 0.726207861 1.005537122 0.8536597 0.969213964 0.646592958 0.663727822 0.708749627 0.84137248 0.731675833 1 20.03737882 3.247072063 24.99924699 0.754847251 0.894503761 0.205271872 0.117546569 259.9095336 763384.0831 0.031285631 0.041691448 1766.330885 -3.247072063 0.139656509 GAEFLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAEFLLR 7 0 Q9BXT2 Q9BXT2 CACNG6 Voltage-dependent calcium channel gamma-6 subunit 0 142.11 0.020032 0 79710 94161 81745 99052 95158 115230 87817 84342 81791 83284 FALSE TRUE 82857.01235 110332.4193 83875.34185 118644.19 78983.07715 88469.57883 80933.67407 83211.53345 78847.35789 99601.90523 0.831881801 1.107734024 0.842105798 1.191183941 0.792987614 0.888231793 0.812571546 0.835441182 0.791624997 1 16.60388572 GAEILEVLHSLPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAEILEVLHSLPAVR 15 0 Q15008;Q15008-4;Q15008-3;Q15008-2;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 220.21 1.70E-12 1040270000 719640 739160 793870 827940 799000 934710 852670 819590 845450 668670 FALSE TRUE 748051.9429 866104.9801 814558.9044 991704.0608 663186.2654 717637.7682 785835.4974 808604.7366 815022.4196 799683.084 0.935435497 1.083060274 1.018602145 1.240121344 0.829311359 0.897402712 0.982683657 1.011156485 1.019181768 1 19.60906884 GAELVEGCDGILGDNFRPTQPLSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GAELVEGCDGILGDNFRPTQPLSDR 25 1 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ;;;; 255.67 6.52E-45 2361422000 731326 850431 730286 887490 852163 898399 689991 799349 759848 858262 FALSE TRUE 760199.3152 996485.9088 749317.8531 1063032.873 707312.6376 689759.4476 635907.7025 788635.0341 732501.2189 1026422.006 0.740630375 0.970834513 0.730029022 1.035668435 0.689105098 0.67200376 0.619538259 0.768334105 0.713645279 1 19.96919258 5.084497711 14.38651874 0.785718784 0.00010169 0.006670337 0.141823322 3401327.011 10504359.55 0.033515583 81925662.97 121478.0218 -5.084497711 -0.785617094 GAEQDNPNQYSWGENYAGSSGLMSAS(ph)PELGPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAEQDNPNQYSWGENYAGSSGLMSASPELGPAQR 34 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 GAEQDNPNQYSWGENYAGSSGLMSAS(1)PELGPAQR 371.11 1.37E-148 103250000 63787 81540 74759 79305 68307 92873 69849 81510 73833 87754 TRUE FALSE 66305.36001 95543.86071 76707.28096 94991.2923 56696.20054 71304.65325 64374.05286 80417.49177 71175.76475 104947.7161 0.631794216 0.910394854 0.730909483 0.905129676 0.540232819 0.679430252 0.613391651 0.766262428 0.678202131 1 16.67931125 -1.14890438 3.605228721 1.000234134 0.721363421 0.359787958 0.113013316 28189293.59 51548715.87 79687.22952 0.027102877 0.070973402 1.14890438 -0.278870713 GAES(ph)ENEEESPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAESENEEESPR 12 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 GAES(1)ENEEESPR;GAES(1)ENEEESPR 123.81 0.00035043 138816000 233870 171297 166850 184847 213960 237280 233990 179622 175364 120094 TRUE FALSE 243103.3682 200715.9272 171198.2481 221409.1849 177591.1556 182175.316 215649.2524 177214.4609 169052.6839 143624.12 1.692636085 1.397508492 1.191988143 1.541587757 1.236499522 1.268417283 1.501483542 1.23387674 1.177049398 1 17.13193853 5.690109674 0.038715402 1.23E-12 3.080128774 0.512761809 0.136607223 461.7573473 2.148381879 58.54965237 121.8480838 489902.5209 -5.690109674 3.080128774 GAFFMDEDEEVYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAFFMDEDEEVYKR 14 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 113.24 0.00087713 79752000 54530 48179 55412 41918 61251 72499 64628 55051 61172 49941 FALSE TRUE 56682.88651 56453.36847 56856.08224 50209.25529 50839.5769 55662.20598 59562.28849 54313.13139 58970.43167 59725.98277 0.949049038 0.945206187 0.951948877 0.840660178 0.851213735 0.93195965 0.997259245 0.909371916 0.987349708 1 15.86607107 2.47438027 24.92616852 0.961451315 0.906761133 0.324418975 0.04349054 124.0758592 1128308.925 0.016132609 0.01357106 298.1125574 -2.47438027 -0.054690182 GAFGKPQGTVAR ddPTM_MDA-MB-175_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 ; 99.732 0.0033113 3087300000 5186900 5132400 5184700 4625000 6390200 6355100 5592900 5297900 5611400 5514300 FALSE TRUE 5391682.817 6013849.775 5319817.541 5539811.196 5303996.087 4879224.337 5154513.884 5226890.316 5409446.81 6594721.507 0.817575513 0.911918687 0.806678119 0.840037171 0.80427901 0.73986814 0.781612063 0.792586967 0.820269181 1 22.65288031 4.199632373 24.61471805 0.809802021 0.864747199 0.027290847 0.06904445 263.9012942 166867.094 0.015850954 0.034243006 15835.52159 -4.199632373 0.054945178 GAGATS(ph)GSPPAGRN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGAT(0.249)S(0.499)GS(0.252)PPAGRN;GAGAT(0.01)S(0.576)GS(0.414)PPAGRN;GAGAT(0.056)S(0.472)GS(0.472)PPAGRN;GAGAT(0.044)S(0.608)GS(0.348)PPAGRN 99.844 0.0021395 1789820000 734797 888010 756953 737086 792680 995690 717360 821920 787423 987080 TRUE FALSE 763807.3529 1040518.81 776679.817 882879.4108 657940.5367 764456.0873 661131.4487 810903.5068 759083.8 1180479.427 0.647031482 0.881437478 0.657935919 0.747899023 0.557350278 0.647581033 0.560053342 0.686927267 0.643030097 1 20.17094147 -1.740591403 6.464528395 1.006933066 0.670481658 0.557770168 0.088172966 0.008899388 0.000357115 0.086234727 0.020118995 0.018172246 1.740591403 -0.336451409 GAGATSGS(ph)PPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAGATSGSPPAGR 13 0 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 GAGATSGS(1)PPAGR;GAGATS(0.002)GS(0.998)PPAGR 192.91 2.43E-06 785770000 570090 668520 590990 689570 590410 758690 740070 627920 581360 567730 TRUE FALSE 592597.5934 783333.1096 606391.6849 825964.8878 490052.3191 582495.7456 682061.3796 619503.7595 560436.9672 678965.8237 0.872794436 1.15371508 0.893110763 1.216504365 0.721762866 0.85791615 1.004559222 0.912422596 0.82542736 1 19.37297943 3.235027636 24.99999187 0.891458031 1.032514252 0.253002262 0.123604277 129.4045101 915690.4636 0.033461263 0.041525908 1718.017709 -3.235027636 0.14105622 GAGDGS(ph)DEEVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 1 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK 209.39 4.01E-08 3279500000 5041930 2784290 3724130 3470740 4469490 4872510 5500400 3532030 4000920 2243390 TRUE FALSE 5240989.29 3262470.149 3821183.887 4157242.013 3709767.686 3740943.396 5069264.275 3484688.915 3856927.671 2682939.318 1.953450551 1.21600594 1.424252819 1.549510265 1.382725156 1.394345139 1.889444253 1.29883255 1.43757544 1 21.35538299 0.667049842 1.351180092 1.001932365 1.507923742 0.321424922 0.224812929 1.336899548 3.750724652 0.199926859 0.059404416 4.645685884 -0.667049842 0.505991377 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE 234.71 3.53E-37 14302840000 13273510 4943540 8103480 4953810 12479140 11671640 10709670 7471890 9153350 4117680 TRUE FALSE 13797558.42 5792554.54 8314663.346 5933658.832 10357940.24 8961078.495 9870218.081 7371741.536 8823922.722 4924460.558 2.801841595 1.176282046 1.688441454 1.204935802 2.103365459 1.819707639 2.00432473 1.496964276 1.7918557 1 22.23153426 -0.163078087 0.786757824 0.972985574 1.765728785 0.217356103 0.446044403 12.12749973 6.645550345 1.436657285 0.139975616 0.686944914 0.163078087 0.792743212 GAGGEENKENERPSAGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GAGGEENKENERPSAGSK 18 2 Q9UHB9;Q9UHB9-4;Q9UHB9-2;K7EN53;K7EQC2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 242.26 2.79E-24 704880000 1621410 758340 1109430 767490 1463270 1273980 1256380 955300 1130240 611237 FALSE TRUE 1685424.519 888578.9959 1138342.657 919297.2313 1214543.888 978117.4524 1157901.653 942495.7661 1089562.883 730997.1873 2.305651168 1.215571019 1.557246289 1.257593391 1.66148914 1.338059119 1.584002884 1.289328854 1.490515835 1 19.47950633 GAGGS(ph)PVGVEEGLVNVGTGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAGGSPVGVEEGLVNVGTGQK 21 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK 287.39 1.13E-45 246600000 297660 255040 295700 258290 322570 364960 326350 296900 308830 242430 TRUE FALSE 309411.8466 298841.1361 303406.1849 309378.9911 267739.6666 280203.571 300769.8342 292920.5411 297715.2686 289929.5169 1.067196779 1.030737192 1.046482566 1.067083457 0.923464673 0.966454102 1.037389492 1.010316384 1.026853946 1 18.14534269 GAGHPCYLDKPEEWHTGLLDFLQGLQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAGHPCYLDKPEEWHTGLLDFLQGLQ 26 1 F8W9U3;Q96IU4;Q96IU4-2 F8W9U3 ABHD14B Alpha/beta hydrolase domain-containing protein 14B 0 ; 169.6 4.81E-12 1423960000 1822590 1428720 1595310 1467520 2090700 2104900 1872100 1635940 1805500 1484460 FALSE TRUE 1894547.261 1674091.546 1636885.089 1757791.076 1735323.561 1616068.875 1725359.91 1614012.9 1740520.408 1775311.515 1.06716328 0.942984672 0.922026965 0.990131062 0.977475528 0.910301579 0.971863189 0.909143486 0.980402815 1 20.75964077 4.741061654 24.90834387 0.951281661 1.067163324 0.516340035 0.031969021 161.1596126 1604922.017 0.007265971 0.04923809 55088.58972 -4.741061654 0.115881663 GAGSVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAGSVFR 7 0 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 99.139 0.025003 569740000 279590 364320 381550 363220 457140 462530 432740 411510 383510 444230 FALSE TRUE 290628.4291 426889.126 391493.5064 435063.8319 379435.5061 355114.4172 398820.708 405994.3815 369707.55 531268.3632 0.547046369 0.803528227 0.736903481 0.818915377 0.714206854 0.668427563 0.750695384 0.764198303 0.69589604 1 19.01908128 -4.999999997 0.485350742 8.782286026 0.727429551 0.56205938 0.07325681 1453.288702 7.256825141 12252.69608 0.033615214 1.00E-05 4.999999997 -8.054856475 GAGTDDHTLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 209.85 1.48E-08 8368740000 6593880 7342450 7037270 7448110 7209550 8350300 6288230 7393490 6635470 7179840 FALSE TRUE 6854211.474 8603458.671 7220667.037 8921323.928 5984073.266 6411069.375 5795342.101 7294392.36 6396660.731 8586592.182 0.798245838 1.001964282 0.840923487 1.038983073 0.696908988 0.746637227 0.674929236 0.849509585 0.744959187 1 23.03365424 3.228327445 24.99996297 0.773710811 0.920231284 0.268435667 0.107759323 238.5596184 582807.7154 0.028793035 0.034779708 1691.715955 -3.228327445 0.146520474 GAGYTFGQDISETFNHANGLTLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAGYTFGQDISETFNHANGLTLVSR 25 0 P67775;P62714;H0YC23 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 0 ; 371.63 8.36E-120 338396000 149227 205991 180187 212257 190951 242087 178226 202206 194651 208584 FALSE TRUE 155118.5972 241368.3519 184882.8212 254240.8011 158493.2172 185865.9631 164256.1804 199495.7593 187645.5485 249452.0412 0.621837354 0.967594214 0.741155776 1.019197116 0.635365485 0.745096982 0.658467975 0.799735927 0.75223096 1 17.92840295 GAHGIIVVYDVTDQESYANVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAHGIIVVYDVTDQESYANVK 21 0 Q9H0U4 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ; 246.95 2.42E-30 299930000 169710 125336 156147 139979 178104 190114 160720 157474 149947 121211 FALSE TRUE 176410.2818 146861.483 160216.3191 167666.4284 147829.9457 145962.9047 148122.3464 155363.3186 144550.4368 144959.9747 1.216958558 1.013117471 1.10524522 1.15663947 1.019798368 1.006918668 1.021815482 1.071767009 0.99717482 1 17.14529508 3.223161594 24.9950497 1.025976457 1.113874631 0.484416984 0.051673371 230.7373193 374522.4759 0.014564753 0.017465517 1671.712517 -3.223161594 0.087898174 GAHNGQGLGNAFLSHISACDGIFHLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAHNGQGLGNAFLSHISACDGIFHLTR 27 0 J3KQ32;Q9NTK5;Q9NTK5-3 J3KQ32 OLA1 Obg-like ATPase 1 0 381.07 3.25E-128 705270000 54266 112480 106050 98790 108600 148950 88989 121600 108840 163140 FALSE TRUE 56408.46358 131797.565 108813.7501 118330.3671 90140.21079 114358.6199 82013.80965 119970.1509 104922.8697 195104.1595 0.289119739 0.675524117 0.557721324 0.606498434 0.462010708 0.586141373 0.420359104 0.614903092 0.537778743 1 17.57388501 -0.385679433 0.796685285 1.024280683 0.529890271 0.641675262 0.105993274 7.96038436 3.752838906 0.700593016 0.032289963 0.411453316 0.385679433 -0.494390411 GAHSVGLMWWMLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAHSVGLMWWMLAR 14 0 C9J9K3;A0A0C4DG17;P08865 C9J9K3 RPSA 40S ribosomal protein SA 0 185.57 1.16E-06 125510000 59948 132580 95411 81446 139160 139740 101140 97763 83048 227160 FALSE TRUE 62314.79333 155349.5837 97897.48904 97555.77571 115505.6329 107287.5028 93212.38252 96452.64689 80059.1187 271667.6528 0.229378775 0.571836883 0.360357547 0.359099711 0.425172566 0.39492189 0.343111819 0.355039129 0.294695073 1 18.05148327 -1.384133078 3.660045672 1.003478214 0.37540262 0.833480035 0.084398251 50736355.68 76526040.53 1862227.059 0.018891143 0.041292095 1.384133078 -0.628075594 GAHVTINAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GAHVTINAR 9 0 Q9UJU6-2;Q9UJU6-3;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;; 163.32 6.31E-05 397291000 276818 412844 367669 400456 465172 493232 370107 383427 334713 546039 FALSE TRUE 287746.9884 483746.7455 377250.7562 479665.0016 386102.2296 378686.343 341097.0462 378287.7882 322666.7445 653024.8875 0.440637093 0.740778422 0.577697364 0.734527904 0.591251937 0.579895729 0.522333915 0.579285408 0.494110945 1 19.31677845 -1.656862873 2.99598658 1.038401189 0.589928386 0.659542729 0.089480678 27926661.6 25407774.6 8173151.241 0.021159419 0.022036221 1.656862873 -0.448472803 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 GAILSEEELAAMS(0.982)PT(0.018)AAAVAK;GAILSEEELAAMS(1)PTAAAVAK;GAILSEEELAAMS(0.998)PT(0.002)AAAVAK;GAILSEEELAAMS(0.987)PT(0.013)AAAVAK 323.47 3.17E-67 323165000 772450 571324 678880 606034 743330 786810 778350 665050 733320 586955 TRUE FALSE 802946.9225 669444.4527 696572.1705 725905.7164 616979.0321 604085.3017 717340.8932 656136.0926 706927.9564 701957.5943 1.143868132 0.953682186 0.992327993 1.034116195 0.878940604 0.860572357 1.021914855 0.934723262 1.007080716 1 19.42102435 7.059253036 1.415551362 0.958374473 153.5965214 0.460228544 0.056893761 1034.944594 3.268345307 0.015195834 512012.9104 11461805.53 -7.059253036 152.6381469 GAKEEHGGLIRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 153.04 3.39E-06 61345560000 23079460 22803100 25350860 16791200 32136000 29319610 20421080 23441880 25996140 27682770 TRUE FALSE 23990654.9 26719355.04 26011524.24 20112449.24 26673534.2 22510574.92 18820422.39 23127679.94 25060544 33106678.76 0.724646984 0.807068424 0.785688121 0.607504286 0.805684387 0.679940597 0.568478117 0.698580492 0.756963396 1 24.98061895 -1.026929915 9.248598315 1 0.71079774 0.556187057 0.076307926 5.48E-10 6.09E-11 0.075536712 0.017804174 0.093987497 1.026929915 -0.289202261 GALALEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GALALEEKR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 161.28 0.00010366 2325300000 1614210 1480260 1497860 1226260 2625120 2123510 1487660 1637780 1826700 2288980 FALSE TRUE 1677940.257 1734483.14 1536895.462 1468810.568 2178903.04 1630356.985 1371053.322 1615828.238 1760957.424 2737461.806 0.612954765 0.633609987 0.561430833 0.536559292 0.795957421 0.595572505 0.500848384 0.590265126 0.643281093 1 21.38440741 0.758201803 3.823284718 0.999992512 0.601759916 0.717267639 0.074231031 1.540719844 23.84380389 0.0724093 0.018553451 5.730622529 -0.758201803 -0.398232597 GALHTVS(ph)HEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GALHTVSHEDIR 12 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHT(0.002)VS(0.998)HEDIR;GALHT(0.003)VS(0.997)HEDIR;GALHT(0.004)VS(0.996)HEDIR;GALHT(0.001)VS(0.999)HEDIR;GALHT(0.007)VS(0.993)HEDIR;GALHT(0.001)VS(0.999)HEDIR 230.36 3.87E-12 14969020000 10761260 12576390 11514880 12159240 11660800 13024710 11604000 11636970 10311900 12276550 TRUE FALSE 11186122.85 14736287.15 11814967.23 14564301.38 9678701.381 9999918.494 10694448.16 11480995.45 9940776.733 14681904.92 0.761898603 1.003704031 0.804729856 0.991989899 0.65922654 0.681104976 0.728410122 0.781982686 0.677076768 1 23.80753583 3.234580854 24.9999981 0.741458192 0.892528645 0.249518792 0.11411892 120.0977144 754428.2541 0.029951273 0.037069337 1716.251202 -3.234580854 0.151070453 GALHTVS(ph)HEDIRDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GALHTVSHEDIRDIR 15 1 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2;H0YD72 Q13136-2 PPFIA1 Liprin-alpha-1 1 GALHTVS(1)HEDIRDIR;GALHT(0.017)VS(0.983)HEDIRDIR;GALHT(0.012)VS(0.988)HEDIRDIR;GALHT(0.002)VS(0.998)HEDIRDIR 191.37 1.08E-07 1787180000 902400 1565360 1272140 647136 1688820 1558830 456458 1089300 1184610 2995550 TRUE FALSE 938027.4488 1834198.403 1305293.013 775137.5693 1401754.98 1196815.357 420679.6292 1074699.715 1141976.118 3582470.669 0.261838138 0.511992581 0.364355534 0.216369551 0.391281635 0.33407541 0.117427236 0.29998842 0.318767751 1 21.77252346 0.867446706 14.4236537 1 0.310439259 0.810728873 0.099598646 554.4275289 60331.8054 0.098389739 0.024598539 7.369647345 -0.867446706 -0.689560741 GALKEEVASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GALKEEVASR 10 1 Q9P2M7;Q9P2M7-2 Q9P2M7 CGN Cingulin 0 ;;; 119.16 0.00043854 409168000 11798.4 967560 791950 885300 663100 1088230 502791 831210 677720 1260830 FALSE TRUE 12264.20994 1133730.903 812588.8676 1060409.698 550386.4989 835505.0748 463380.9276 820068.9895 653328.9896 1507865.498 0.008133491 0.751878005 0.5389001 0.703252179 0.36501034 0.554097879 0.307309192 0.543860835 0.433280681 1 20.52407632 -1.714234942 2.753950253 1.084538739 0.481970068 0.384824552 0.201287791 56633303.61 49032069.32 33107013.63 0.046692306 0.019309235 1.714234942 -0.602568671 GALQNIIPAS(ph)TGAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 GALQNIIPAS(0.918)T(0.082)GAAK;GALQNIIPAS(0.92)T(0.08)GAAK;GALQNIIPAS(0.625)T(0.375)GAAK;GALQNIIPAS(0.912)T(0.088)GAAK;GALQNIIPAS(0.5)T(0.5)GAAK;GALQNIIPAS(0.933)T(0.067)GAAK 319.28 1.80E-56 6407280000 6160310 5072700 6037940 4269940 7154230 7085150 6009260 5659050 6063260 5587200 TRUE FALSE 6403523.796 5943896.765 6195293.677 5114521.388 5938156.54 5439731.289 5538238.499 5583199.691 5845044.457 6681904.867 0.958338067 0.889551241 0.92717478 0.765428645 0.888692171 0.814098883 0.828841267 0.835570066 0.87475721 1 22.67182801 3.858278178 18.09371841 0.84817202 0.921507844 0.191927182 0.060292975 3.410528255 502.6314721 0.013998883 0.025237368 7215.695171 -3.858278178 0.073335824 GALQNIIPASTGAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GALQNIIPASTGAAK 15 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 259.48 1.70E-24 1669540000 1402790 1133710 1267240 1125110 1510250 1444590 1370190 1342620 1278740 1102000 FALSE TRUE 1458173.232 1328415.873 1300265.315 1347653.4 1253538.244 1109105.865 1262790.927 1324624.375 1232718.397 1317915.801 1.106423666 1.00796718 0.986607274 1.022564111 0.951151996 0.841560489 0.958172689 1.00509029 0.935354441 1 20.32982677 6.054051132 0.713579846 0.954537826 1.946376661 0.486800546 0.046479265 14.87578387 1.333415539 0.01833528 18.16082548 1132533.696 -6.054051132 0.991838835 GANDFMCDEMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GANDFMCDEMER 12 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 297.2 5.91E-36 1837878000 995186 1212212 1207112 1236247 1335830 1455770 1239590 1288364 1211910 1271244 FALSE TRUE 1034476.712 1420399.981 1238570.33 1480772.967 1108766.094 1117689.48 1142427.697 1271095.588 1168293.596 1520319.922 0.68043357 0.93427703 0.814677432 0.973987741 0.729297878 0.735167292 0.75143901 0.836071125 0.768452468 1 20.53594351 -1.602645972 2.596411831 1.017855633 0.807670952 0.311896385 0.087655364 11915621.53 10809494.77 1450239.619 0.020364736 0.024966291 1.602645972 -0.210184681 GANLKDYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GANLKDYYSR 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 127.87 0.00031437 943670000 529450 714950 632900 495440 1013860 860300 534280 702930 731090 1103190 FALSE TRUE 550353.0948 837737.101 649393.8939 593436.5533 841524.4393 660508.363 492401.7375 693508.3731 704778.2137 1319338.959 0.417143063 0.634967303 0.492211565 0.4497984 0.637837937 0.500635836 0.373218523 0.52564837 0.534190406 1 20.33138383 0.533182176 2.474443011 0.99999001 0.505449687 0.776176164 0.07952676 2.884217888 14.72440075 0.074063366 0.019781321 3.413360636 -0.533182176 -0.494540324 GAPGS(ph)PTQERPAGGLGEAPNGAPSVCAEEGSLGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAPGSPTQERPAGGLGEAPNGAPSVCAEEGSLGPR 35 1 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 GAPGS(0.496)PT(0.496)QERPAGGLGEAPNGAPS(0.006)VCAEEGS(0.002)LGPR 44.148 0.065924 306860000 22866 43800 35592 41932 37679 51057 33390 38563 37763 61926 TRUE FALSE 23768.76734 51322.30928 36519.55676 50226.02445 31274.33704 39199.78553 30772.80455 38046.12606 36403.91701 74059.21406 0.320942743 0.692990196 0.49311294 0.678187381 0.422288265 0.529303288 0.415516218 0.51372576 0.49155149 1 16.17639162 -1.300022257 3.081142904 1.003400017 0.511009043 0.655339522 0.107341567 21402188.79 28229418.63 672611.9791 0.025350872 0.050116155 1.300022257 -0.492390974 GAPHS(ph)SPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAPHSSPAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 GAPHS(0.5)S(0.5)PAR 102.42 0.0037626 129950000 257850 308690 236760 208760 339990 367180 262090 238000 232020 438560 TRUE FALSE 268030.1171 361705.1062 242930.1601 250052.1049 282198.6212 281908.0097 241546.701 234809.9993 223669.6455 524487.4353 0.511032484 0.689635408 0.46317632 0.476755186 0.538046486 0.537492399 0.460538584 0.447694232 0.426453773 1 19.00054869 -1.528047166 3.136451401 1.016370571 0.504656218 0.813997503 0.070892023 30342580.35 35837169.88 4229509.872 0.01847436 0.029645094 1.528047166 -0.511714353 GAPHSS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GAPHSSPAR 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 GAPHS(0.01)S(0.99)PAR;GAPHS(0.001)S(0.999)PAR;GAPHS(0.079)S(0.921)PAR 165.63 3.95E-05 770210000 410183 480901 333477 344950 554594 557495 406930 361733 384433 800770 TRUE FALSE 426377.3416 563492.0059 342167.6846 413180.0804 460324.31 428025.2352 375033.7633 356884.5608 370597.3314 957665.5498 0.445225728 0.588401667 0.357293509 0.43144507 0.480673352 0.446946468 0.391612462 0.372660958 0.386979913 1 19.86916238 -1.265322071 3.477954467 1.001578759 0.431320792 0.878321479 0.063254629 34574346.74 52572256.16 579306.355 0.016322266 0.054284761 1.265322071 -0.570257967 GAPS(ph)PGVLGPHASEPQLAPPACTPAAPAVPGPPGPR ddPTM_MDA-MB-175_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 220.08 3.20E-39 494290000 13569 66810 52990 77387 49081 79999 43500 54535 44990 85225 TRUE FALSE 14104.7146 78284.09779 54370.96293 92693.91762 40738.22915 61420.44465 40090.35633 53804.04753 43370.81869 101923.207 0.138385702 0.768069413 0.533450276 0.909448597 0.399695323 0.602614914 0.393338843 0.527888094 0.42552447 1 16.63712305 -1.177641532 4.346242118 1.000122473 0.533840387 0.334492958 0.201633978 0.000224615 4.25E-05 0.180612295 0.042559449 0.066429115 1.177641532 -0.466282086 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPRS(ph)PQREPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAPSPGVLGPHASEPQLAPPACTPAAPAVPGPPGPRSPQREPQR 44 2 O96013;O96013-4;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 GAPSPGVLGPHASEPQLAPPACT(0.002)PAAPAVPGPPGPRS(0.998)PQREPQR 90.698 4.52E-05 991970000 10169 102210 73012 68187 79588 135610 40983 74811 77723 174060 TRUE FALSE 10570.47997 119763.7724 74914.7527 81674.18508 66059.66019 104116.6327 37770.64537 73808.28091 74925.76441 208163.7244 0.050779645 0.575334501 0.359883803 0.392355514 0.317344726 0.500167034 0.181446818 0.354568411 0.359936702 1 17.66735915 0.535513803 3.722900596 0.999999825 0.348654154 0.666431072 0.139311748 18.06581208 143.9431034 0.121633216 0.031211962 3.431735468 -0.535513803 -0.65134567 GAPSS(ph)PATGVLPSPQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5;Q5SRE5-2 Q5SRE5 NUP188 Nucleoporin NUP188 homolog 1 GAPS(0.015)S(0.985)PATGVLPSPQGK;GAPS(0.017)S(0.983)PATGVLPSPQGK 245.96 1.35E-20 328000000 463940 392370 476500 429630 511840 549370 508790 447230 460500 426910 TRUE FALSE 482256.7094 459756.4953 488917.9814 514609.5317 424837.6196 421787.1433 468909.7103 441235.6134 443926.695 510554.8408 0.944573767 0.900503645 0.957620891 1.007941734 0.832109669 0.826134843 0.918431622 0.864227656 0.869498552 1 18.96170641 3.231893111 24.99993879 0.877070843 0.949288905 0.276475062 0.052509417 187.8291219 704268.0891 0.014594931 0.017824557 1705.662536 -3.231893111 0.072218062 GAPVGGHILSYLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAPVGGHILSYLLEK 15 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 155.98 2.21E-06 768180000 710210 764360 809770 785730 994340 1081580 940230 815700 856890 821890 FALSE TRUE 738249.6392 895632.8841 830873.2714 941145.0488 825322.442 830399.4365 866532.3158 804766.8757 826050.6963 982923.6095 0.751075294 0.911192768 0.845308082 0.957495618 0.839660818 0.844826015 0.881586633 0.818748139 0.840401724 1 19.90671977 -1.015408661 4.109600229 1.000012451 0.856628302 0.411751537 0.052124272 5331895.112 2634831.859 573.2945804 0.01147319 0.096514228 1.015408661 -0.143384149 GAPVNIS(ph)SSDLTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNIS(0.966)S(0.033)S(0.001)DLTGR;GAPVNIS(0.807)S(0.184)S(0.01)DLTGR;GAPVNIS(0.495)S(0.495)S(0.01)DLTGR;GAPVNIS(0.493)S(0.493)S(0.014)DLTGR;GAPVNIS(0.482)S(0.482)S(0.036)DLTGR;GAPVNIS(0.913)S(0.085)S(0.002)DLTGR;GAPVNIS(0.848)S(0.112)S(0.04)DLTGR 328 2.55E-68 4378093000 2107927 2459815 2073283 2233796 2331570 2342387 1973135 2111775 2054853 2256557 TRUE FALSE 2191149.586 2882269.092 2127314.458 2675634.182 1935250.564 1798403.118 1818475.523 2083470.11 1980899.242 2698686.14 0.811931982 1.068026789 0.788277832 0.991458081 0.717108424 0.666399509 0.673837352 0.772031278 0.734023573 1 21.36382577 3.228203991 24.99562607 0.740792438 0.916813479 0.289192897 0.116080714 213.756199 515897.9463 0.030875515 0.037287744 1691.235128 -3.228203991 0.176021041 GAPVNISSS(ph)DLTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GAPVNISSSDLTGR 14 0 P48730-2;H7BYT1;P48730;J3KRM8 P48730-2 CSNK1D Casein kinase I isoform delta 1 GAPVNISS(0.01)S(0.99)DLTGR;GAPVNISS(0.035)S(0.965)DLTGR;GAPVNISS(0.003)S(0.997)DLTGR;GAPVNISS(0.003)S(0.996)DLTGR 246.8 9.60E-18 686920000 991950 1138580 1151350 1227620 1151990 1298430 1038800 1039050 1055840 1179030 TRUE FALSE 1031112.952 1334122.258 1181355.127 1470439.572 956175.1513 996889.3104 957376.1416 1025123.234 1017840.525 1410038.355 0.73126589 0.946160261 0.837817725 1.042836578 0.678119959 0.706994464 0.678971702 0.727017979 0.721853077 1 20.42730298 3.212802947 24.99920753 0.730994005 0.889872943 0.242609669 0.115314234 251.38092 243978.0691 0.030780268 0.036801283 1632.311148 -3.212802947 0.158878938 GAQASSGS(ph)PALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.032)S(0.37)GS(0.598)PALPR;GAQAS(0.016)S(0.014)GS(0.969)PALPR;GAQAS(0.005)S(0.117)GS(0.879)PALPR;GAQAS(0.009)S(0.262)GS(0.728)PALPR;GAQAS(0.067)S(0.399)GS(0.534)PALPR;GAQAS(0.074)S(0.137)GS(0.788)PALPR 187.01 1.35E-06 2087896000 965086 1232700 1051824 1122420 1141850 1231140 1067621 1096380 959660 1121610 TRUE FALSE 1003188.34 1444406.636 1079235.398 1344431.326 947758.7449 945226.3931 983938.0763 1081684.819 925122.0241 1341368.005 0.747884501 1.076816079 0.804578157 1.002283729 0.706561318 0.70467343 0.733533283 0.80640422 0.689685471 1 20.35527366 3.230338909 24.99904899 0.761070771 0.912577265 0.226098751 0.120398344 223.7669935 680388.5798 0.03161699 0.038394306 1699.569422 -3.230338909 0.151506493 GAQEVGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAQEVGER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 110.38 0.0079978 362230000 349690 539890 485140 505520 448180 540370 454950 440000 457700 640520 FALSE TRUE 363496.0312 632611.9077 497783.1469 605510.3472 371998.5237 414877.2569 419289.8302 434102.5197 441227.4664 766017.6305 0.474526978 0.825845101 0.649832494 0.790465288 0.485626582 0.541602752 0.547363159 0.566700429 0.576001712 1 19.54701807 -1.751039715 6.443341299 1.009741472 0.608473931 0.524940035 0.112303437 0.015771216 0.000609374 0.109122342 0.02562055 0.017740272 1.751039715 -0.401267541 GAQGGDYFYSFGGCHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAQGGDYFYSFGGCHR 16 0 Q9BYN0 Q9BYN0 SRXN1 Sulfiredoxin-1 0 137.19 1.34E-05 198120000 182050 236710 198310 203510 220060 251870 228060 229800 206220 294650 FALSE TRUE 189237.4746 277363.1012 203478.1215 243763.6706 182654.2798 193377.0096 210184.0613 226719.9069 198798.1825 352381.0261 0.537025153 0.787111339 0.577437792 0.691761623 0.518343118 0.54877248 0.596468157 0.643394196 0.564156886 1 18.42677672 -1.308061928 4.091855583 1.000569152 0.611667397 0.69769924 0.077523441 11693668.54 3738325.145 59681.52961 0.01730355 0.049196938 1.308061928 -0.388901754 GAQPGRHS(ph)VTGYGDCAVGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GAQPGRHSVTGYGDCAVGAR 20 1 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 GAQPGRHS(0.5)VT(0.5)GYGDCAVGAR;GAQPGRHS(0.887)VT(0.107)GY(0.006)GDCAVGAR 172.66 3.64E-12 278300000 137930 169700 152855 159404 176886 179751 149113 154619 145847 176643 TRUE FALSE 143375.5829 198844.6549 156838.5269 190933.6354 146818.9809 138006.5544 137425.1334 152546.5852 140597.995 211252.8138 0.678691944 0.941263935 0.742421008 0.903815821 0.694991836 0.653276763 0.650524511 0.722104395 0.665543774 1 17.68861103 -0.894406907 7.986588386 0.999996014 0.740964419 0.39292707 0.09723498 1.43E-09 0 0.096127862 0.022657554 0.127524343 0.894406907 -0.259031596 GAS(ph)PEAASGGLPQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GASPEAASGGLPQAR 15 0 P17861-2;B1AHH2;P17861 P17861-2 XBP1 "X-box-binding protein 1;X-box-binding protein 1, cytoplasmic form;X-box-binding protein 1, luminal form" 1 GAS(1)PEAASGGLPQAR;GAS(1)PEAASGGLPQAR 224.67 1.16E-12 758560000 137843 194567 169697 185909 189334 204484 180410 172515 172183 185414 TRUE FALSE 143285.1481 227982.3687 174119.4432 222681.2453 157151.0743 156995.69 166268.9928 170202.7186 165986.1675 221742.3233 0.646178618 1.028140976 0.785233241 1.004234293 0.708710326 0.708009583 0.749829759 0.767569835 0.74855429 1 17.75852463 5.024070833 16.14741194 0.817362445 0.227270859 0.163749184 0.122178272 7813788.165 136413674.2 0.028487183 118536991.8 105698.989 -5.024070833 -0.590091586 GAS(ph)PPISAIEEFSIIPEAPMR ddPTM_MDA-MB-175_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(1)PPISAIEEFSIIPEAPMR;GAS(1)PPISAIEEFSIIPEAPMR;GAS(0.983)PPIS(0.017)AIEEFSIIPEAPMR;GAS(0.999)PPIS(0.001)AIEEFSIIPEAPMR;GAS(0.998)PPIS(0.002)AIEEFSIIPEAPMR;GAS(0.987)PPIS(0.013)AIEEFSIIPEAPMR 311.1 1.63E-66 753518000 190019.9 233778.2 217749.3 214167.9 230725.7 250981.5 222650.6 218084 210910.1 243801.1 TRUE FALSE 197522.0324 273927.7873 223424.0256 256529.6714 191507.0279 192694.8503 205198.6642 215160.9407 203319.4867 291569.2577 0.677444645 0.939494752 0.766281148 0.87982414 0.656814883 0.660888778 0.703773319 0.737941107 0.697328272 1 18.15347909 GAS(ph)TVSSSSSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GASTVSSSSSTK 12 0 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 1 GAS(0.983)T(0.017)VSSSSSTK;GAS(0.992)T(0.008)VSSSSSTK;GAS(0.88)T(0.12)VSSSSSTK;GAS(0.976)T(0.024)VSSSSSTK;GAS(0.904)T(0.096)VSSSSSTK 237.32 4.43E-16 458340000 887459 736159 799080 826654 1375310 1298330 1145300 1096117 1031534 1093006 TRUE FALSE 922496.5666 862588.5817 819904.6813 990163.6939 1141535.297 996812.5339 1055528.393 1081425.345 994409.2928 1307159.599 0.705726039 0.659895381 0.627241449 0.757492578 0.873294507 0.762579057 0.807497718 0.82730934 0.760740535 1 20.31800387 -1.519922605 0.041662026 1.919735801 3.36E-13 0.697506622 0.056229419 197.4142796 1.328413982 40.46425869 22.51700061 0.030204899 1.519922605 -1.919735801 GASDEEIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GASDEEIKR 9 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ;; 152.97 0.00012698 1564900000 3032280 2125450 2052190 1864760 2606990 2522530 2590770 2179240 2171490 1840880 FALSE TRUE 3151996.756 2490479.504 2105671.757 2233603.962 2163854.771 1936710.637 2387698.678 2150030.852 2093338.499 2201565.19 1.43170721 1.131231323 0.956443065 1.014552725 0.982871087 0.879697156 1.08454598 0.976591955 0.950841024 1 21.07009813 4.679713504 2.216940279 0.982245295 1.516222158 0.882505931 0.050131196 0.159325368 0.997145774 0.012289804 0.158971039 47831.44536 -4.679713504 0.533976864 GASFLFPPAESLS(ph)PEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GASFLFPPAESLSPEEPR 18 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 GASFLFPPAES(0.309)LS(0.691)PEEPR;GASFLFPPAES(0.006)LS(0.994)PEEPR;GASFLFPPAES(0.249)LS(0.751)PEEPR 233.49 1.01E-23 145573000 186622 230522 215459 224603 230581 244675 203723 207507 173122 201923 TRUE FALSE 193989.9807 270112.3603 221074.0385 269028.803 191386.924 187852.9393 187754.6589 204725.7081 166891.373 241485.9458 0.803317891 1.118542776 0.915473726 1.114055736 0.792538561 0.777904233 0.777497251 0.847774836 0.691101805 1 17.8815797 3.215293294 24.98634896 0.805637997 0.992013358 0.360959548 0.112592923 214.0013403 229811.5178 0.02966337 0.035474737 1641.698096 -3.215293294 0.186375361 GASFLFPPAESLSPEEPRS(ph)PGGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GASFLFPPAESLSPEEPRSPGGWR 24 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 GASFLFPPAESLSPEEPRS(1)PGGWR;GASFLFPPAESLSPEEPRS(1)PGGWR;GASFLFPPAESLSPEEPRS(1)PGGWR 280.77 1.89E-52 184174000 143320 157432 165775 153318 188808 213960 164287 185477 182480 272842 TRUE FALSE 148978.3843 184469.7213 170095.2327 183643.8428 156714.4836 164271.0326 151409.7557 182990.9842 175912.5804 326300.166 0.456568521 0.565337504 0.521284542 0.562806464 0.480277058 0.503435333 0.464019855 0.560805673 0.539112752 1 18.3158402 0.016795635 1.075253202 1.003258581 0.513726987 0.938301359 0.037238107 1.775956281 1.723865936 0.053588605 0.010686011 1.039430929 -0.016795635 -0.489531594 GASIVEDKLVEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GASIVEDKLVEDLR 14 1 P00367 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ; 110.98 0.00061822 323060000 1120990 1111650 989020 855020 1205440 1521130 901550 911660 1052670 1237770 FALSE TRUE 1165247.551 1302567.24 1014794.674 1024140.404 1000539.739 1167870.61 830884.1552 899440.6889 1014784.612 1480287.333 0.787176601 0.879942165 0.685538984 0.691852441 0.675909141 0.788948594 0.56129924 0.607612231 0.685532187 1 20.49744581 4.227481125 24.85715332 0.68692558 0.833559375 0.120815492 0.116167597 257.6108369 577961.5117 0.02734218 0.059964407 16884.22476 -4.227481125 0.146633795 GATKES(ph)SEKDR ddPTM_MDA-MB-175_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(0.169)KES(0.795)S(0.037)EKDR;GAT(0.024)KES(0.789)S(0.187)EKDR 137.8 3.70E-05 476150000 1479590 499190 734250 493130 1106540 1091870 1117860 818760 877530 404590 TRUE FALSE 1538005.356 584921.9993 753385.1582 590669.6422 918450.726 838299.7399 1030239.212 807785.8614 845947.8667 483861.6642 3.178605518 1.208862042 1.557025931 1.220740732 1.898167997 1.732519441 2.129201978 1.669456213 1.748325874 1 18.88423511 0.385116524 1.772370552 1.000029634 1.78378233 0.174890213 0.528384577 11.37840206 30.66067891 0.473915633 0.132763311 2.427261256 -0.385116524 0.783752696 GATQQILDEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GATQQILDEAER 12 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 249.83 1.21E-16 453810000 1521070 777760 807950 784460 878040 1363650 845570 732500 744640 853190 FALSE TRUE 1581123.018 911334.2299 829005.8407 939623.8466 728791.0744 1046962.954 779292.0139 722682.0356 717840.5519 1020356.245 1.5495794 0.893152989 0.812467062 0.920878224 0.714251594 1.026075901 0.763745033 0.708264431 0.703519536 1 19.96064151 4.743800913 3.572186326 0.818391776 1.638894065 0.784289548 0.112198476 0.124175238 2.819972131 0.026912504 0.275409785 55437.15228 -4.743800913 0.820502289 GATYGKPVHHGVNQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GATYGKPVHHGVNQLK 16 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 120.7 6.63E-05 1447200000 1435100 1065700 1580800 1217600 1684600 1579200 1568100 1497900 1581900 1257600 FALSE TRUE 1491758.856 1248725.685 1621996.947 1458437.646 1398252.294 1212454.733 1445188.225 1477823.101 1524967.728 1504002.642 0.991859199 0.830268279 1.078453522 0.969704178 0.929687392 0.806151997 0.960894738 0.982593421 1.013939528 1 20.52037567 1.708163301 3.188605814 1.002630287 0.934588654 0.132985955 0.072989824 0.452095254 10.25233932 0.043555784 0.02002967 51.06969934 -1.708163301 -0.068041633 GAVAAEGAS(ph)DTEREEPTESQGLAAR ddPTM_MDA-MB-175_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(0.977)DT(0.023)EREEPTESQGLAAR;GAVAAEGAS(1)DTEREEPTESQGLAAR;GAVAAEGAS(0.99)DT(0.01)EREEPTESQGLAAR;GAVAAEGAS(0.985)DT(0.015)EREEPTESQGLAAR;GAVAAEGAS(1)DTEREEPTESQGLAAR;GAVAAEGAS(0.97)DT(0.03)EREEPTESQGLAAR 341.67 1.10E-88 10335090000 2689420 3313430 3012040 3160650 3077290 3373880 2920620 3254290 2932580 3375750 TRUE FALSE 2795600.378 3882485.828 3090536.237 3785817.136 2554213.345 2590347.502 2691694.173 3210671.565 2827037.019 4037163.58 0.692466461 0.961686528 0.765521678 0.937741823 0.632675217 0.641625599 0.666729034 0.795279037 0.700253275 1 21.94491061 GAVAEDGDELRTEPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 157.03 3.72E-08 1015890000 498670 477910 519340 458290 589330 595670 505120 527660 508490 481470 FALSE TRUE 518357.8767 559987.3249 532874.427 548938.3941 489155.8971 457334.67 465527.3745 520587.5808 490189.5442 575804.8282 0.900231904 0.972529749 0.925442791 0.953341075 0.849516838 0.794252927 0.808481193 0.90410423 0.851311973 1 19.13522036 3.236521292 24.99997818 0.858647119 0.939472085 0.260248823 0.056452776 62.40281626 764996.0419 0.015530463 0.019453798 1723.936607 -3.236521292 0.080824966 GAVDGGLSIPHSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GAVDGGLSIPHSTK 14 0 P46777;A0A2R8Y6J3;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 173.06 2.76E-06 3252600000 2802270 3696630 4112620 3638390 4745390 4972100 4328570 4482480 4319490 4058940 FALSE TRUE 2912905.783 4331497.447 4219798.256 4358052.682 3938770.303 3817405.128 3989285.373 4422399.687 4164032.399 4854211.58 0.600078043 0.892317398 0.869306619 0.897787954 0.811412984 0.786410947 0.821819426 0.911043867 0.85781848 1 22.21080556 -4.999999985 0.02404612 2.135021268 6.71E-12 0.390391927 0.077784801 2590.059168 4.706109276 298.7365498 144.7671108 1.00E-05 4.999999985 -2.135021268 GAVEALAAALAHISGATSVDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GAVEALAAALAHISGATSVDQR 22 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 140.2 1.31E-07 171070000 31093 75036 82463 76315 72507 98014 58145 66015 66710 89183 FALSE TRUE 32320.57565 87922.8493 84612.05352 91409.87922 60182.28604 75251.73392 53587.44297 65130.1769 64309.12013 106656.7013 0.303033708 0.824353727 0.793312117 0.857047687 0.564261648 0.705550922 0.502429217 0.610652459 0.602954332 1 16.70261509 -1.214566542 4.65533081 1.000068099 0.647655237 0.316930062 0.158054375 0.000124421 2.10E-05 0.149357301 0.035196115 0.061014556 1.214566542 -0.352412862 GAVEKGEELSCEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GAVEKGEELSCEER 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;;;; 201.16 1.66E-08 4324180000 3571510 3113840 3898730 2637360 4847770 4478780 3473470 3416550 4060180 3941920 FALSE TRUE 3712515.973 3648617.798 4000334.107 3159021.936 4023747.787 3438651.222 3201210.345 3370756.736 3914054.915 4714263.751 0.787507057 0.773952836 0.848559673 0.670098684 0.853526234 0.729414263 0.679047782 0.715012336 0.830257941 1 22.16860105 -1.766095729 8.311426984 1.002734937 0.759549573 0.551334855 0.063337873 0.003175348 8.94E-05 0.060667012 0.014177251 0.017135796 1.766095729 -0.243185364 GAVIVVSHDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;H0YGW7;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;;; 169.37 1.70E-05 785460000 704260 742240 698180 775870 810800 887150 801930 751820 735080 745860 FALSE TRUE 732064.7286 869713.9462 716375.1444 929334.7703 672980.5056 681122.8574 739072.6311 741743.0826 708624.6144 891996.9866 0.820703141 0.975018929 0.803113861 1.041858643 0.754464999 0.763593227 0.82855956 0.83155335 0.794424897 1 19.76667931 3.200650573 24.99999913 0.818322951 0.907159078 0.156536861 0.090542675 257.5380133 169834.2076 0.024077638 0.028778842 1587.269143 -3.200650573 0.088836126 GCALQCAILS(ph)PAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GCALQCAILSPAFK 14 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;P34932;A0A087WYC1;A0A087WTS8;O95757;E9PDE8;D6RJ96 Q92598-2;P34932;O95757 HSPH1;HSPA4;HSPA4L Heat shock protein 105 kDa;Heat shock 70 kDa protein 4;Heat shock 70 kDa protein 4L 1 GCALQCAILS(1)PAFK 118.13 0.00087926 0 33223 26112 28220 19055 36573 32576 28467 30854 33229 23196 TRUE FALSE 34534.66969 30596.53288 28955.43638 22824.02213 30356.33452 25010.71769 26235.68216 30440.4526 32033.09478 27740.81209 1.244904785 1.102942941 1.043784742 0.822759696 1.094284278 0.901585636 0.945743119 1.097316564 1.154728084 1 14.7597224 4.570009639 2.139529745 1.005138257 1.26554213 0.385255289 0.093492419 0.497231956 3.324250151 0.024516217 0.21629835 37154.34756 -4.570009639 0.260403873 GCCFDDTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GCCFDDTVR 9 0 P04155 P04155 TFF1 Trefoil factor 1 0 77.318 0.053189 0 176250 229130 183230 191040 193170 244100 162410 185880 165100 214990 FALSE TRUE 183208.4861 268481.2951 188005.1243 228827.1418 160335.0324 187411.4744 149679.8798 183388.5826 159158.0833 257113.1743 0.712559699 1.044214463 0.731215446 0.889986063 0.62359711 0.72890654 0.582155622 0.713260155 0.619019557 1 17.97204401 3.244553588 24.96979186 0.690277603 0.850668368 0.172424179 0.138387763 193.418233 805874.1302 0.035107387 0.046323995 1756.117571 -3.244553588 0.160390765 GCCFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GCCFDSR 7 0 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;; 109.63 0.016251 5103700000 8173300 8924500 7749600 7322800 8173500 8410100 6825900 7076100 6747400 8862600 FALSE TRUE 8495988.195 10457213.45 7951560.942 8771227.984 6784171.39 6456981.731 6290868.122 6981256.454 6504562.392 10599056.79 0.801579647 0.986617363 0.750214015 0.827547975 0.640073124 0.609203428 0.593530939 0.658667709 0.613692569 1 23.33743255 3.491929673 1.776014586 0.658825755 0.871529088 0.238400295 0.126597542 0.383697851 2.423691299 0.035817393 0.062372501 3104.056895 -3.491929673 0.212703333 GCGDLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GCGDLCR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 128.82 0.0086565 367680000 570830 663850 597340 645250 790640 775150 689840 609690 565970 818820 FALSE TRUE 593366.8092 777861.0735 612907.1711 772878.5241 656247.2952 595133.16 635768.5382 601518.1028 545600.8503 979252.1017 0.605938765 0.794342 0.625893138 0.789253883 0.670151531 0.60774254 0.64923888 0.614262764 0.557160765 1 19.90132079 -1.098358207 4.961068408 1.000011458 0.659412531 0.660233631 0.073776876 9.24E-06 1.68E-06 0.070627001 0.016646384 0.079733677 1.098358207 -0.340598927 GCHLLVATPGR ddPTM_MDA-MB-175_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 ;; 120.09 0.00049858 1012590000 625054 657670 615940 616260 714200 778860 633533 625596 638927 764080 FALSE TRUE 649731.6146 770619.7065 631991.9024 738154.3886 592800.5391 597981.5687 583875.028 617210.9089 615932.1421 913786.8468 0.711031918 0.843325453 0.691618515 0.807797126 0.64872956 0.654399405 0.638961953 0.675442978 0.674043563 1 19.80149815 -1.146764429 4.424760275 1.000047115 0.703582551 0.651605883 0.064695772 3.32E-05 6.40E-06 0.06553714 0.015444665 0.07132398 1.146764429 -0.296464564 GCLDEETSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GCLDEETSR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 194.9 7.42E-05 658610000 530760 838300 801240 798010 1002740 1014670 939020 832160 857680 832600 FALSE TRUE 551714.8146 982271.5039 822120.9726 955853.9962 832294.613 779028.27 865417.1587 821006.2563 826812.2643 995732.0289 0.55407961 0.98648178 0.825644801 0.959951039 0.835862048 0.782367391 0.869126566 0.824525307 0.830356201 1 19.92539801 GCQLLVYPGAFNLTTGPAHWELLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GCQLLVYPGAFNLTTGPAHWELLQR 25 0 Q9NQR4 Q9NQR4 NIT2 Omega-amidase NIT2 0 ; 252.21 8.84E-45 1060440000 958100 1092320 1072830 1118250 1107800 1282380 1119240 1133210 1088420 1224330 FALSE TRUE 995926.5278 1279917.463 1100788.831 1339436.512 919496.5517 984566.6797 1031511.044 1118021.174 1049247.977 1464214.022 0.680178248 0.874132773 0.751795034 0.914781918 0.627979611 0.672419923 0.704481058 0.763564039 0.716594679 1 20.48169502 -1.14669678 4.258089512 1.000056279 0.747903411 0.449338219 0.084601772 4.64E-05 9.31E-06 0.080781901 0.019036056 0.071335091 1.14669678 -0.252152868 GCRLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GCRLSPR 7 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 GCRLS(1)PR;GCRLS(1)PR 64.841 0.043728 2994520000 311853 380770 302525 301319 436360 429140 295175 306817 290335 504260 TRUE FALSE 324165.1972 446164.2855 310409.05 360918.9989 362187.6831 329478.7387 272038.4122 302704.62 279885.9001 603060.0924 0.537533823 0.739833876 0.514723249 0.598479328 0.600583072 0.546344789 0.451096691 0.501947689 0.46410947 1 19.20194224 -1.586242786 5.091845721 1.003520035 0.549873182 0.746247395 0.07863104 0.00330297 0.000268395 0.080032535 0.018749536 0.025927295 1.586242786 -0.453646853 GCTSSSSLS(ph)PPRGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GCTSSSSLSPPRGDR 15 1 Q96LT9-2;Q96LT9;X6RLP6 Q96LT9-2 RNPC3 RNA-binding protein 40 1 GCTSS(0.002)S(0.006)S(0.008)LS(0.984)PPRGDR 75.017 0.011849 0 42763 52842 42953 68265 50513 57622 36274 46417 53779 49238 TRUE FALSE 44451.31626 61917.20245 44072.39047 81767.61325 41926.8183 44240.16377 33430.7491 45794.85604 51843.5043 58885.24338 0.754880403 1.051489285 0.748445416 1.388592601 0.712008916 0.751294573 0.567727111 0.777696642 0.880415896 1 15.84561852 GCWDSIHVVEVQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GCWDSIHVVEVQEK 14 0 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 233.59 3.44E-17 1558150000 2103600 2381450 2929390 2641320 3418350 3627230 3469120 3135200 3232120 2371590 FALSE TRUE 2186651.752 2790445.512 3005732.31 3163765.212 2837300.088 2784860.804 3197201.31 3093177.772 3115796.633 2836257.654 0.77096372 0.98384768 1.059752913 1.115471723 1.000367539 0.981878639 1.127260531 1.090584196 1.098559092 1 21.43555717 4.731509479 2.137766562 1.06478598 0.693407294 0.761283981 0.0485734 0.313492131 1.62563978 0.012837365 0.222271787 53890.16077 -4.731509479 -0.371378686 GCWVLYEEPEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GCWVLYEEPEFR 12 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 0 177.06 5.53E-05 19516000 32991 33171 31745 34545 35446 40143 32479 31432 27259 42404 FALSE TRUE 34293.51015 38867.86122 32572.30078 41377.89789 29420.90158 30820.39662 29933.21111 31010.70545 26277.95391 50712.25193 0.676237178 0.766439267 0.642296478 0.815934933 0.58015372 0.607750503 0.590256003 0.611503222 0.518177618 1 15.63004672 -1.06396139 4.581932439 1.000018207 0.645915659 0.615304242 0.084110296 11641236.19 2703188.444 2130.04284 0.020250464 0.086305527 1.06396139 -0.354102548 GDAAVRDELMAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDAAVRDELMAAVR 14 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 222.75 3.44E-12 1587140000 845920 1149780 1033210 968590 1247590 1196060 957030 1052770 980220 1351100 FALSE TRUE 879317.5748 1347245.771 1060136.301 1160174.211 1035525.097 918293.1915 882015.4879 1038659.34 944942.0737 1615822.177 0.544192045 0.833783439 0.656097135 0.718008595 0.640865754 0.568313274 0.545861729 0.642805474 0.584805734 1 20.62383701 -1.184433707 5.511996001 1.000011499 0.640196501 0.627947541 0.083750791 1.18E-05 1.75E-06 0.081108167 0.019116768 0.065398275 1.184433707 -0.359814999 GDAPVDKVELSEDS(ph)PNSEQDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDAPVDKVELSEDSPNSEQDLEK 23 1 Q5T5P2;Q5T5P2-3;Q5T5P2-7;Q5T5P2-9;Q5T5P2-2;Q5T5P2-8;Q5T5P2-6;Q5T5P2-4 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 GDAPVDKVELSEDS(0.751)PNS(0.249)EQDLEK;GDAPVDKVELS(0.001)EDS(0.998)PNSEQDLEK 185.68 1.79E-17 169863000 301170 129550 175765 112619 261165 223252 224422 176894 218307 109705 TRUE FALSE 313060.4242 151799.2047 180345.5803 134894.7021 216772.2666 171405.1064 206831.2172 174523.0253 210450.1737 131199.5943 2.38613866 1.157009711 1.374589466 1.028164018 1.65223275 1.306445399 1.576462323 1.330210098 1.604045918 1 17.00140373 8 0.03353169 5.01E-08 3.594603577 0.173845588 0.347681287 2405.708181 6.169514725 199.7314776 537.9509101 99999999.95 -8 3.594603526 GDDALEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDDALEKR 8 1 Q9Y617 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 97.635 0.012975 421380000 602430 517500 496750 484840 749180 625680 590810 563320 577900 555690 FALSE TRUE 626214.4016 606376.5994 509695.7131 580739.9049 621834.6512 480375.3023 544500.7684 555769.6168 557101.4919 664566.8162 0.942289603 0.912438877 0.766959319 0.873862328 0.93569922 0.722839736 0.819331864 0.836288547 0.838292672 1 19.34205473 4.454285446 22.07108769 0.840979268 0.934826997 0.148378294 0.07438426 78.8533399 76212.58325 0.017018654 0.046622289 28463.31282 -4.454285446 0.093847729 GDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDDDEESDEEAVKK 14 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK 152.32 4.10E-06 702860000 952590 365696 586760 466200 838250 791420 1028450 642500 709380 255092 TRUE FALSE 990198.9888 428501.4433 602051.4476 558412.9685 695764.5644 607624.6991 947837.4016 633888.3384 683849.5524 305072.3934 3.245783658 1.404589378 1.973470759 1.83042773 2.280653968 1.991739378 3.106926167 2.077829237 2.241597625 1 18.21879211 3.167758045 24.99996833 2.224679472 2.052889642 0 0.65242101 276.9231588 97774.63027 0.1779644 0.212708214 1471.492472 -3.167758045 -0.17178983 GDDGIFDDNFIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;;;;;; 324.11 3.55E-56 3101066000 1710458 2146695 1960150 2101454 1953314 2298729 2144298 2005777 1895187 2044626 FALSE TRUE 1777988.203 2515373.167 2011233.119 2517115.329 1621290.384 1764884.027 1976222.32 1978892.84 1826979.59 2445231.318 0.727124747 1.028685159 0.822512416 1.029397632 0.663041722 0.721765673 0.808194425 0.809286559 0.747160228 1 21.22153952 3.23713488 24.99992811 0.782073629 0.90531123 0.172736205 0.117117047 57.54091329 1008970.425 0.030882669 0.038862158 1726.373974 -3.23713488 0.123237601 GDDLLPAGTEDYIHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDDLLPAGTEDYIHIR 16 0 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 184.99 1.73E-09 648380000 1048000 1117700 1176900 1363200 1124000 1358200 1348400 1266100 1105900 1069600 FALSE TRUE 1089375.849 1309656.281 1207570.981 1632836.891 932942.8815 1042778.634 1242708.885 1249130 1066098.875 1279167.641 0.85162868 1.023834749 0.944028712 1.276483894 0.729335899 0.815200917 0.971498062 0.976517823 0.83343171 1 20.28677392 3.204723151 24.99999054 0.895077242 1.018272044 0.215064835 0.126932578 321.8096647 237760.3904 0.036975799 0.044196745 1602.223699 -3.204723151 0.123194801 GDDQLELIKDDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDDQLELIKDDEKEAEEGEDDRDSANGEDDS 31 3 P07910;G3V2Q1;P07910-3;P07910-2;G3V4C1;G3V2D6;P07910-4 P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 GDDQLELIKDDEKEAEEGEDDRDS(1)ANGEDDS 183.92 1.42E-17 571690000 1220300 465730 508480 565910 719230 953770 928070 496920 573860 454860 TRUE FALSE 1268478.386 545715.5046 521731.4065 677845.3089 596975.5415 732271.372 855325.4483 490259.6002 553206.8907 543981.1082 2.331842719 1.003188339 0.959098393 1.246082444 1.097419621 1.346133829 1.572344031 0.901243798 1.016959748 1 19.05319702 4.742497685 24.99372337 1.137875591 2.331843182 0.772166764 0.196266826 188.9203716 1199277.838 0.048689672 0.371621928 55271.04612 -4.742497685 1.193967591 GDDSFGDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDDSFGDKYR 10 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 137.89 7.21E-05 252870000 299870 270370 286140 264850 382520 377140 359180 302760 329750 302670 FALSE TRUE 311709.0992 316803.9443 293597.0435 317236.5395 317499.387 289554.9506 331026.5331 298701.9974 317882.3619 361972.3915 0.861140536 0.875215767 0.811103417 0.876410873 0.877137026 0.799936563 0.914507683 0.825206575 0.878195048 1 18.46552014 0.966274954 21.43410216 1.000000001 0.855139754 0.634421252 0.032836769 399.5887607 253961.4033 0.028589 0.00714725 9.252837903 -0.966274954 -0.144860247 GDDWNDREWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDDWNDREWDR 11 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 172.09 1.26E-05 297210000 237250 245010 230430 243970 257830 254780 217340 232010 248160 255310 FALSE TRUE 246616.8132 287088.5616 236435.1951 292226.5378 214004.1487 195611.2062 200304.3229 228900.2854 239228.7701 305333.1063 0.807697587 0.94024708 0.774351651 0.957074525 0.700887471 0.640648532 0.656019013 0.749673981 0.783500921 1 18.2200245 3.222660316 24.99749352 0.731411427 0.868050818 0.196107447 0.107517389 299.342547 470607.2593 0.029227693 0.035040484 1669.78408 -3.222660316 0.136639391 GDEASEEGQNGSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDEASEEGQNGSSPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5 P35611 ADD1 Alpha-adducin 1 GDEASEEGQNGS(0.001)S(0.999)PK 282.87 1.86E-27 0 538490 237680 280780 243530 401740 440250 385920 299280 300360 171140 TRUE FALSE 559750.001 278499.6911 288097.3575 291699.5071 333452.3783 338008.6096 355670.582 295268.6411 289550.1023 204671.6063 2.734868852 1.360714835 1.407607839 1.425207494 1.629206827 1.651468006 1.737762205 1.442645838 1.414705769 1 17.64295145 4.74207498 24.94738092 1.486314826 2.734869336 0.794562368 0.194977117 141.1652703 1002043.821 0.044688223 0.330380209 55217.27628 -4.74207498 1.24855451 GDEELDSLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 223.55 1.02E-08 582914000 1836280 1332610 1678920 1417440 2007810 1949170 2127690 1757330 1784050 1224030 FALSE TRUE 1908777.752 1561475.401 1722674.034 1697805.401 1666523.173 1496504.807 1960916.098 1733775.866 1719842.389 1463855.243 1.303938871 1.06668703 1.176806274 1.159817823 1.138448068 1.02230382 1.339556017 1.184390242 1.174871899 1 20.48134147 2.256038127 24.99999334 1.194800682 1.142989373 0.004950468 0.103511441 765.0920573 1094392.56 0.033785299 0.028209168 180.3176036 -2.256038127 -0.051811309 GDEGIFEESFIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ;;; 241.31 4.57E-17 187184000 309519 321318 297639 318988 307103 393889 367315 311430 291939 321174 FALSE TRUE 321739.0491 376501.867 305395.7169 382082.8743 254901.7418 302414.2492 338523.8905 307255.7902 281432.1724 384101.8961 0.837639836 0.980213508 0.795090365 0.994743526 0.663630522 0.787328186 0.881338764 0.799933021 0.732701857 1 18.55112956 3.256996363 24.9995031 0.804725666 0.8998832 0.164798728 0.099864821 412.7698951 559726.7383 0.025857322 0.034945461 1807.158991 -3.256996363 0.095157534 GDFCIQVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 187.78 9.34E-05 10493670000 5449710 6118620 5869830 5834340 7112950 7163020 5969980 6306800 6079810 6575380 FALSE TRUE 5664868.759 7169445.389 6022802.592 6988355.038 5903893.3 5499517.162 5502037.368 6222267.662 5860998.826 7863699.818 0.720382122 0.911714022 0.765899352 0.888685377 0.750778061 0.699354921 0.699675407 0.791264647 0.745323316 1 22.90677682 GDFDENLNYPEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDFDENLNYPEQK 13 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 222.25 1.97E-07 0 79692 60097 65483 52654 84382 85892 79461 65231 82374 55390 FALSE TRUE 82838.3017 70418.19226 67189.54077 63068.80404 70038.77778 65944.88471 73232.63919 64356.68514 79409.37583 66242.60999 1.250528953 1.063034688 1.014294889 0.952088151 1.057307038 0.995505532 1.105521645 0.971530034 1.198765807 1 16.0154719 4.73206525 3.46161405 1.032706612 1.276037978 0.464685563 0.068227841 0.233822419 4.865423825 0.015345741 0.148263896 53959.16865 -4.73206525 0.243331366 GDFIALDLGGSSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDFIALDLGGSSFR 14 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 153.74 1.47E-05 95430000 141620 150380 164620 162470 140580 177160 170970 133430 139610 135960 FALSE TRUE 147211.267 176206.5952 168910.1324 194606.0811 116684.2618 136017.2749 157568.9247 131641.5891 134585.4634 162598.7589 0.905365256 1.083689669 1.038815632 1.196848502 0.717620864 0.836520991 0.969065974 0.809610049 0.827715195 1 17.31095672 3.238009486 24.99999717 0.854352021 1.056904452 0.480168627 0.099845172 12.14849644 551084.3785 0.027481075 0.034789778 1729.854142 -3.238009486 0.202552431 GDFIHVMDNSDPNWWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDFIHVMDNSDPNWWK 16 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 199.41 3.82E-11 249510000 560930 497180 579330 529460 607120 692940 721130 550210 658280 479860 FALSE TRUE 583075.9495 582566.7975 594427.8157 634185.6077 503921.9593 532015.1866 664605.9463 542835.3349 634588.6314 573879.3795 1.016025267 1.015138056 1.035806194 1.105085198 0.878097345 0.927050536 1.158093443 0.945904931 1.105787477 1 19.13038801 -0.254731989 6.868980109 1.000007965 1.017334588 0.004108549 0.082659115 0 0 0.076287625 0.017981166 0.556247422 0.254731989 0.017326622 GDFVTSFYWPWQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDFVTSFYWPWQTK 14 0 G3V3Y1;Q8N8N7;Q8N8N7-2 G3V3Y1 PTGR2 Prostaglandin reductase 2 0 ; 192.05 9.72E-07 110899000 169419 190313 214032 179035 242200 233680 189067 202682 226760 209040 FALSE TRUE 176107.7929 222997.7773 219609.8497 214447.5886 201030.9305 179411.3615 174247.4345 199965.3793 218598.9519 249997.3857 0.704438538 0.892000437 0.878448585 0.857799325 0.804132131 0.71765295 0.696997027 0.799869882 0.874404951 1 17.93155348 0.947245477 2.953443979 0.999403147 0.795525866 0.478884349 0.066530408 0.273808159 5.76460542 0.068783095 0.018115268 8.856160457 -0.947245477 -0.20387728 GDGGITHSEEINGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDGGITHSEEINGK 14 0 O75363;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 228.62 1.59E-12 167290000 283150 234900 278640 254470 302810 347790 339390 307710 324190 267940 FALSE TRUE 294328.9806 275242.2477 285901.5873 304803.4065 251338.4644 267021.0433 312787.725 303585.6508 312522.4652 320437.713 0.918521662 0.858957097 0.892222032 0.95120953 0.784359812 0.833300927 0.976126443 0.947409242 0.975298639 1 18.28968443 2.226624533 24.99983167 0.968077832 0.872839166 0.554695198 0.044443473 186.8207273 391288.6959 0.017175925 0.012782388 168.5095557 -2.226624533 -0.095238666 GDGPVQGIINFEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDGPVQGIINFEQK 14 0 P00441 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ; 150.11 1.70E-05 135088000 313960 249450 309010 243290 354870 352110 351030 288110 330970 231360 FALSE TRUE 326355.3832 292291.097 317063.0545 291412.0359 294549.3242 270337.7888 323515.3514 284248.3567 319058.4544 276690.5623 1.179495898 1.056382605 1.145912068 1.05320555 1.064544167 0.977040151 1.169231609 1.02731497 1.153123734 1 18.07791391 7.999999045 1.013258661 1.069563094 113.1461716 0.202525084 0.062367544 2874.462033 3.691167671 0.016928214 748236.3705 99999780.05 -7.999999045 112.0766085 GDHNRT(ph)LDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDHNRTLDR 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;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 GDHNRT(1)LDR;GDHNRT(1)LDR 74.611 0.06564 461820000 368530 550030 387340 449900 569230 577730 325380 430550 353560 634840 TRUE FALSE 383079.849 644493.3739 397434.3986 538888.8772 472472.4879 443560.9631 299875.8654 424779.1815 340835.4447 759224.7433 0.504567129 0.848883522 0.523473981 0.709788349 0.622309128 0.584228803 0.394976413 0.559490698 0.448925628 1 19.53416749 -1.05493743 4.783189101 1.00001268 0.579716836 0.514440926 0.123149893 1.65E-05 3.26E-06 0.118286751 0.027879614 0.088117582 1.05493743 -0.420295844 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDHRYPSSNPESPVVIFYSEIGSEEFSNFHR 31 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;; 137.44 5.87E-07 309026000 62209.2 100924 83603 99241 100462 110109 81697 84125 87194 102251 FALSE TRUE 64665.26725 118256.9119 85781.76286 118870.5736 83385.50512 84537.85347 75293.37566 82997.44198 84055.90497 122285.1257 0.528807301 0.967058841 0.701489755 0.972077126 0.681894095 0.69131755 0.61571982 0.678720666 0.687376363 1 16.89988941 GDHSPVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDHSPVTR 8 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-3;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 ; 102.51 0.0049505 166527000 94915 114463 102018 116085 103780 125990 105791 102068 104065 125813 FALSE TRUE 98662.31749 134121.1299 104676.6729 139046.2665 86139.51267 96730.7319 97498.82499 100699.9454 100319.721 150463.6485 0.655721953 0.891385602 0.695694102 0.924118668 0.572493845 0.642884397 0.647989238 0.66926428 0.666737262 1 17.19905545 GDHWTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDHWTTR 7 0 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 98.299 0.011364 47543000 49141 79347 78955 91812 62034 76253 72801 79345 66258 75512 FALSE TRUE 51081.12463 92974.23002 81012.63216 109972.1396 51489.48284 58544.39638 67094.66739 78281.51006 63873.38752 90307.13064 0.565637777 1.029533652 0.897079019 1.21775699 0.570159659 0.648280994 0.742960904 0.866836423 0.707290632 1 16.46255229 4.768866076 23.42218984 0.842779512 0.56563679 0.175934141 0.185527069 9813.907548 7584573.666 0.045102251 4.885458462 58730.82153 -4.768866076 -0.277142722 GDIFLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDIFLVR 7 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 124.37 0.009661 71422000 111460 140440 113530 141680 148160 163370 114470 121040 115800 194320 FALSE TRUE 115860.5269 164559.4775 116488.6851 169703.8811 122975.8161 125429.7934 105497.5423 119417.6568 111632.3806 232393.2835 0.498553681 0.708107717 0.501256677 0.730244345 0.529171129 0.539730716 0.453961236 0.51386019 0.480359755 1 17.82620885 -1.02152771 4.83963055 1.000008255 0.551106646 0.698593491 0.088558859 7.80E-06 1.58E-06 0.084760428 0.019977857 0.095163913 1.02152771 -0.448901609 GDIYFCTGYDPPMKPYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDIYFCTGYDPPMKPYGR 18 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 132.59 1.32E-05 1642590000 1467990 1473640 1595060 1499660 1800850 1885920 1573370 1527780 1666200 1662860 FALSE TRUE 1525947.379 1726726.207 1636628.574 1796288.272 1494742.16 1447943.661 1450045.148 1507302.608 1606233.787 1988665.58 0.767322266 0.86828385 0.822978278 0.903263118 0.751630729 0.728098116 0.729154848 0.757946748 0.807694267 1 20.92336926 5.068072321 13.8622658 0.80381491 0.446932991 0.005285853 0.083097111 4553351.903 23973733.56 0.01954727 45362727.62 116969.4158 -5.068072321 -0.356881919 GDKEEVAYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDKEEVAYEER 11 1 Q9NRV9;F5GWX2 Q9NRV9 HEBP1 Heme-binding protein 1 0 ;;; 144.27 3.36E-05 5058420000 8449900 7222900 8000500 6921000 10373900 9943600 9123200 8172300 8612900 6781800 FALSE TRUE 8783508.577 8463376.889 8208999.602 8289953.143 8610548.183 7634349.597 8408099.745 8062763.686 8302923.411 8110563.865 1.082971384 1.043500431 1.012136732 1.022117979 1.061646062 0.94128469 1.036684981 0.99410643 1.023717161 1 22.95137079 8 0.569628285 1.006256128 4.944116318 0.374534071 0.029426264 148.9550787 1.276211765 0.012504063 722.9077269 100000000 -8 3.937860189 GDKSELNEIKENQRS(ph)PVR ddPTM_MDA-MB-175_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 252.84 1.22E-30 3485650000 3008720 1617050 2293290 1412030 3077110 2636030 2361480 2139980 2564650 1630190 TRUE FALSE 3127506.589 1894765.759 2353055.021 1691325.32 2554063.941 2023851.982 2176381.027 2111297.068 2472348.747 1949594.519 1.604183105 0.971876839 1.206945854 0.86752671 1.310048791 1.038088671 1.116324962 1.082941631 1.268134847 1 20.89474267 4.747653094 24.74555962 1.099709308 1.604183408 0.5795751 0.129867527 681.1172952 1853644.03 0.027736904 0.339012203 55931.06566 -4.747653094 0.504474101 GDLAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDLAGR 6 0 P12532;P12532-2;F8WCN3;C9JSQ1;P17540;H0YD98 P12532 CKMT1A;CKMT1B;CKMT2;JAM3 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 116.87 0.053984 158930000 197870 238610 210980 221510 201730 248550 182710 172880 158450 206530 FALSE TRUE 205682.0604 279589.4114 216478.3121 265324.0169 167440.0067 190828.0293 168388.7128 170562.8264 152747.4155 246995.5992 0.832735729 1.131961105 0.876446029 1.074205442 0.677906842 0.77259688 0.681747826 0.690550062 0.618421607 1 17.91412581 3.231933579 24.9965724 0.720239221 0.982460868 0.456272058 0.126472736 116.549536 439613.6327 0.033112562 0.040449327 1705.821481 -3.231933579 0.262221647 GDLGIEIPAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 185.08 1.08E-05 1218930000 2827320 2371749 2551221 2155833 3328512 3151490 2966712 2717659 3014889 2467694 FALSE TRUE 2938944.777 2779078.441 2617707.915 2582250.333 2762732.719 2419604.209 2734173.361 2681233.226 2906383.734 2951191.392 0.995850281 0.94168018 0.88700039 0.874985723 0.936141494 0.819873701 0.926464264 0.9085257 0.984817095 1 21.49286606 1.194717542 3.986383634 0.999246739 0.908380629 0.352960386 0.043934216 0.229014877 6.922218965 0.040270268 0.010924308 15.65732413 -1.194717542 -0.09086611 GDLGPAS(ph)PSQELGSQPVPGGDGAPALGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDLGPASPSQELGSQPVPGGDGAPALGK 28 0 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 GDLGPAS(0.5)PS(0.5)QELGSQPVPGGDGAPALGK;GDLGPAS(0.5)PS(0.5)QELGSQPVPGGDGAPALGK;GDLGPAS(0.871)PS(0.129)QELGSQPVPGGDGAPALGK 184.66 6.89E-18 408696000 264124 262178 288890 262577 349237 358340 324058 299994 330451 265392 TRUE FALSE 274551.8195 307205.032 296418.7107 314513.9469 289873.8195 275120.9657 298657.4872 295973.0711 318558.1331 317390.4812 0.865028524 0.967908776 0.933924388 0.990936923 0.913303444 0.866821729 0.940978085 0.932520314 1.003678913 1 18.27589934 1.252556746 5.484256391 1.003048565 0.92832637 0.398130124 0.037034301 0.164219402 14.54733909 0.029135053 0.009159307 17.88779242 -1.252556746 -0.074722196 GDLPFVVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDLPFVVPR 9 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 106.36 0.0068607 96074000 122712 140154 138314 139275 147073 159715 143438 142338 137614 140643 FALSE TRUE 127556.7645 164224.3593 141918.5765 166823.1793 122073.584 122623.6118 132194.9548 140430.1919 132661.299 168199.3031 0.758366784 0.976367656 0.843752464 0.991818493 0.725767478 0.729037573 0.785942345 0.83490353 0.788714915 1 17.3598122 5.047399452 14.81372873 0.842228157 0.335995395 0.066996201 0.098856239 2566527.277 23370023.8 0.023418995 35899111.81 111531.9903 -5.047399452 -0.506232762 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK 248.95 2.08E-39 327510000 146233 98896 144033 85009 188391 164070 155950 131316 167679 87236 TRUE FALSE 152006.3918 115880.6187 147786.6183 101823.5265 156368.3651 125967.229 143726.2315 129555.9238 161644.2655 104328.224 1.457001624 1.110731251 1.41655453 0.975992139 1.498811723 1.207412762 1.377635179 1.241810882 1.549381935 1 16.67076998 GDLSGHFEHLMVALVTPPAVFDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDLSGHFEHLMVALVTPPAVFDAK 24 0 P12429;D6RA82;D6RFG5;D6RCA8;D6RAZ8 P12429 ANXA3 Annexin A3;Annexin 0 ; 153.21 4.69E-08 282660000 70044 172648 141161 188109 140538 179101 147267 148782 130756 155182 FALSE TRUE 72809.39121 202298.951 144839.7716 225316.3988 116649.401 137507.5071 135723.8277 146787.8206 126050.1171 185586.9418 0.392319581 1.090049489 0.78044161 1.214074636 0.62854315 0.740933094 0.731322077 0.790938302 0.679197124 1 17.50173568 GDLSSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 195.98 0.0010591 3841840000 3321050 3572620 3421300 3938120 4802790 4447590 3667310 3304330 3152500 5029700 FALSE TRUE 3452167.618 4186189.694 3510461.889 4717068.382 3986413.471 3414704.626 3379856.659 3260040.861 3039042.141 6015173.416 0.573909907 0.695938322 0.583601111 0.784194911 0.662726275 0.567681826 0.561888482 0.541969555 0.505229348 1 22.5201749 -1.363933179 4.313403247 1.000705643 0.608981063 0.689136832 0.078868518 13907043.36 4397822.134 92921.52866 0.019696364 0.043258038 1.363933179 -0.39172458 GDLSYLDQGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDLSYLDQGHR 11 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 ; 192.3 0.00095715 0 273900 342850 311090 341750 339350 394760 307870 322680 297340 383360 FALSE TRUE 284713.7835 401731.8205 319197.261 409347.13 281667.4082 303082.9726 283738.3449 318355.0024 286638.7915 458472.0521 0.621005756 0.876240588 0.69621967 0.892850781 0.61436113 0.661071861 0.618878171 0.694382571 0.625204503 1 18.80647427 -1.15366081 4.638312935 1.000028718 0.702935078 0.458289131 0.097795148 3.49E-05 6.36E-06 0.092602402 0.021824008 0.070200336 1.15366081 -0.29709364 GDMEQNDSDNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 GDMEQNDSDNRR 12 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ;;;;;;;;;;; 208.28 1.10E-07 3807534000 1627314.2 2221807.3 1870010.3 1953568.7 1979140.6 2273736.9 1829608.9 1915350.6 1788013.8 2138299.9 FALSE TRUE 1691561.821 2603385.421 1918744.305 2339978.758 1642726.988 1745695.964 1686199.374 1889678.458 1723663.533 2557258.825 0.661474625 1.018037515 0.750312908 0.915033995 0.64237807 0.682643441 0.659377673 0.738946891 0.674027797 1 21.28616676 3.238506618 25 0.714145401 0.843066251 0.120357866 0.130557595 2.296758122 1063313.249 0.033594287 0.042696394 1731.835421 -3.238506618 0.12892085 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 31 GDMSDEDDENEFFDAPEIITMPENLGHK 28 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK 319.48 3.29E-83 9847472000 3589146.7 2997335.5 3880993.3 3342338.1 4528879.8 4788745.8 4826622.1 3970466.8 4202000.5 2701540.3 TRUE FALSE 3730848.983 3512104.556 3982135.174 4003442.6 3759062.429 3676632.162 4448298.848 3917249.187 4050771.323 3230855.398 1.154755792 1.087050989 1.232532776 1.239127756 1.163488292 1.137974842 1.376817685 1.212449554 1.253776732 1 21.62348475 4.232105358 24.9993851 1.216181481 1.120903384 0.094066318 0.092706245 247.2321179 957473.5122 0.021761448 0.048830445 17064.96326 -4.232105358 -0.095278097 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 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 239.57 1.38E-45 3010170000 998882 1170346 1335970 832694 1712563 1486848 995439 1264620 1363915 1430335 TRUE FALSE 1038318.633 1371343.821 1370786.476 997398.3879 1421462.153 1141550.085 917413.8901 1247669.837 1314827.966 1710581.758 0.606997373 0.801682711 0.801356889 0.583075543 0.830981709 0.667346112 0.536316891 0.729383341 0.768643743 1 20.70605563 0.813814858 2.319271547 0.999577966 0.695492445 0.489126797 0.093986708 0.602385962 5.620030973 0.088185369 0.023873043 6.513506612 -0.813814858 -0.304085521 GDNRLDLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDNRLDLLK 9 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 135.86 0.00019061 577150000 1169780 986200 994660 852560 1676280 1376560 1222760 967390 1115210 1091880 FALSE TRUE 1215963.818 1155572.178 1020581.657 1021193.823 1391346.524 1056874.802 1126916.876 954423.7194 1075073.81 1305812.981 0.931192932 0.884944625 0.781568013 0.782036814 1.065502139 0.809361538 0.86300021 0.730903838 0.823298455 1 20.31651686 GDPESPWWEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDPESPWWEGR 11 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 ;; 147.95 8.16E-05 347570000 182505 253271 239528 249187 274892 317156 253283 255964 243178 281709 FALSE TRUE 189710.4383 296768.3241 245770.2965 298475.4449 228165.956 243501.3255 233430.0166 252533.2213 234426.0713 336904.4849 0.563098584 0.880867835 0.729495473 0.885934911 0.677242264 0.722760712 0.69286705 0.749569188 0.69582354 1 18.36198011 -1.65965439 6.726451916 1.001340884 0.738958428 0.440885512 0.089958586 0.001662483 8.41E-05 0.080050503 0.018779764 0.021895033 1.65965439 -0.262382456 GDPQQQSITHIAIPQEAYNAVHVSGS(ph)PTALAAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDPQQQSITHIAIPQEAYNAVHVSGSPTALAAVK 34 0 Q2TAL8 Q2TAL8 QRICH1 Glutamine-rich protein 1 1 GDPQQQSITHIAIPQEAYNAVHVS(0.092)GS(0.692)PT(0.216)ALAAVK 128.47 9.77E-08 914670000 33508 182170 193800 196230 172650 264940 187040 234920 193020 194440 TRUE FALSE 34830.92171 213456.2804 198850.5872 235043.7083 143303.0147 203411.7002 172379.3161 231771.2817 186073.2479 232536.7952 0.149786711 0.917946255 0.85513601 1.010780716 0.616259524 0.874750596 0.741299096 0.99670799 0.800188408 1 17.82709949 4.741153714 24.99350524 0.864701515 0.149786457 0.76678801 0.118832465 106.0699232 1022294.887 0.026785369 0.183751635 55100.2683 -4.741153714 -0.714915059 GDQCCYSHS(ph)PPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDQCCYSHSPPTPR 14 0 Q9NXH9-2;Q9NXH9 Q9NXH9-2 TRMT1 tRNA (guanine(26)-N(2))-dimethyltransferase 1 GDQCCYS(0.005)HS(0.991)PPT(0.004)PR;GDQCCYSHS(0.998)PPT(0.001)PR;GDQCCYSHS(0.923)PPT(0.077)PR;GDQCCYS(0.001)HS(0.995)PPT(0.004)PR 157.98 3.32E-06 1186570000 344480 358292 342185 330413 351341 395749 321429 358228 345813 349688 TRUE FALSE 358080.3364 419825.8639 351102.6222 395767.7052 291620.1823 303842.2924 296234.5551 353426.5396 333367.2577 418202.6684 0.856236374 1.003881361 0.839551368 0.94635385 0.697317842 0.72654317 0.708351662 0.845108284 0.797142828 1 18.67384274 3.253364044 24.99610875 0.782965116 0.912964419 0.267779858 0.092326218 278.1061363 469589.1524 0.024365329 0.032855662 1792.107444 -3.253364044 0.129999303 GDQENVHPDVMLVQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDQENVHPDVMLVQPR 16 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 186.68 1.46E-09 1198540000 1397500 1403650 1432020 1813630 1491940 1778930 1857690 1522100 1461740 1297800 FALSE TRUE 1452674.379 1644715.969 1469339.618 2172360.601 1238340.572 1365800.467 1712079.404 1501698.739 1409132.263 1552079.062 0.935953853 1.059685688 0.946691218 1.399645581 0.797859208 0.879981246 1.103087752 0.967540105 0.907899795 1 20.56577062 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDQPAASGDSDDDEPPPLPR 20 0 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 GDQPAAS(0.001)GDS(0.999)DDDEPPPLPR;GDQPAASGDS(1)DDDEPPPLPR 224.36 6.13E-25 175195000 88406 102216 93574 136776 140113 147669 180334 105712 116680 100983 TRUE FALSE 91896.33714 119770.8029 96012.61531 163829.8846 116296.6423 113375.1127 166198.9499 104295.1035 112480.7096 120768.6854 0.760928521 0.991737241 0.795012507 1.35655931 0.962970176 0.938779058 1.376175863 0.863593929 0.931373139 1 16.8818869 GDQVLNFS(ph)DAEDLIDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GDQVLNFSDAEDLIDDSK 18 0 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK;GDQVLNFS(1)DAEDLIDDSK 210.38 4.40E-16 269806000 420404 235753 306405 249842 363982 379875 392259 308957 313275 221956 TRUE FALSE 437001.8745 276241.7438 314390.166 299260.0019 302112.4697 291654.7883 361512.7146 304815.9368 302000.2939 265444.0286 1.646305162 1.040677936 1.184393439 1.127393988 1.138140011 1.098743075 1.361916923 1.148324709 1.137717415 1 18.01804816 4.746545484 24.97797641 1.152184709 1.646305406 0.732202948 0.091929872 500.4156128 1565346.097 0.021100255 0.232607619 55788.60266 -4.746545484 0.494120696 GDQVLNFS(ph)DAEDLIDDSKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDQVLNFSDAEDLIDDSKLK 20 1 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 GDQVLNFS(1)DAEDLIDDSKLK;GDQVLNFS(1)DAEDLIDDSKLK 89.946 0.0012152 126469000 59293 37678 44295 25386 76463 61118 48150 42595 57132 32995 TRUE FALSE 61633.93342 44148.90341 45449.36409 30407.27503 63465.84657 46924.27075 44375.87718 42024.0837 55075.83048 39459.73852 1.561944801 1.11883416 1.151790807 0.770589876 1.608369669 1.189168315 1.124586195 1.06498637 1.395747477 1 15.26809378 7.999999901 0.018153418 6.44E-09 2.673194003 0.063248103 0.235769779 13534.44524 18.94532002 1063.113366 1820.693163 99999977.12 -7.999999901 2.673193997 GDRDES(ph)DDGGVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDRDESDDGGVAQR 14 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 GDRDES(1)DDGGVAQR 102.33 0.0007148 94858000 50818 70312 66094 61281 68462 79147 65833 65588 60135 69495 TRUE FALSE 52824.33388 82387.53905 67816.46394 73402.19889 56824.85369 60766.30873 60672.83744 64708.90014 57970.7531 83111.21469 0.635586113 0.991292684 0.81597248 0.883180437 0.68372065 0.731144515 0.730019862 0.778582053 0.697508192 1 16.34275554 5.025170489 15.51038265 0.797685543 0.237318485 0.181049685 0.108836322 4386693.933 73255680.71 0.025156692 60704572.16 105966.9634 -5.025170489 -0.560367058 GDRDESDDGGVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDRDESDDGGVAQR 14 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 0 ; 186.69 9.43E-07 178261000 83703 122118 103019 119819 106656 132299 99916 116539 100067 113358 FALSE TRUE 87007.65907 143090.8166 105703.7598 143518.8406 88526.65122 101574.5623 92084.32284 114976.9853 96465.60822 135568.3297 0.6417993 1.055488526 0.779708358 1.058645783 0.653003924 0.749249935 0.679246569 0.848110953 0.711564481 1 17.04866066 5.022661252 16.75168171 0.824503238 0.203919254 0.135240024 0.145075736 566424.9258 10408209.44 0.033108575 9329136.132 105356.4799 -5.022661252 -0.620583984 GDREEEVERPVS(ph)SPGDPEQK ddPTM_MDA-MB-175_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 64.069 0.015235 618350000 310730 256970 262480 238080 394160 394490 312730 289270 290180 256320 TRUE FALSE 322997.8603 301102.5986 269320.4444 285171.5134 327160.824 302875.6761 288217.4054 285392.8088 279736.4785 306540.9965 1.053685687 0.982258824 0.878578877 0.930288336 1.067266133 0.988042968 0.940224664 0.931010247 0.91255813 1 18.22572051 4.663453183 3.980803015 0.954465634 1.056354499 0.253813023 0.049963765 0.302301592 8.214150638 0.012733298 0.073202905 46073.70981 -4.663453183 0.101888865 GDRSEDFGVNEDLADSDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GDRSEDFGVNEDLADSDAR 19 1 P04083 P04083 ANXA1 Annexin A1 0 ;;; 292.97 1.24E-49 2712530000 1076830 1337690 1190790 1049682 1273010 1426100 1028270 1095785 1108700 1594530 FALSE TRUE 1119344.08 1567427.852 1221822.966 1257305.967 1056624.215 1094909.888 947671.5105 1081097.794 1068798.104 1906947.624 0.586982078 0.821956425 0.640721827 0.659329051 0.554091891 0.574168831 0.496957283 0.566925793 0.560475857 1 20.86283379 -1.010723937 9.28447678 0.999998938 0.60549571 0.664414908 0.083818641 1.29E-09 0 0.087473423 0.020617683 0.09756096 1.010723937 -0.394503228 GDRYDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDRYDALR 8 1 A0AVT1 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ; 111.82 0.0028818 550470000 315280 396390 316810 333130 498200 465990 296080 313930 270730 570240 FALSE TRUE 327727.4978 464466.899 325066.3289 399022.1197 413516.142 357770.8846 272872.4759 309722.2818 260986.4802 681967.6101 0.480561676 0.681068854 0.476659484 0.58510421 0.606357451 0.524615655 0.400125273 0.454159812 0.382696299 1 19.37934369 -1.646451572 3.339028293 1.032291738 0.51065109 0.7352024 0.088193339 76419346.09 41441995.21 19956645.17 0.022427773 0.022570877 1.646451572 -0.521640648 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_MDA-MB-175_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 268.55 2.53E-31 641760000 388840 357470 342510 407800 352790 452060 488520 343710 326540 271278 TRUE FALSE 404191.7034 418862.6918 351436.092 488461.6228 292822.8818 347075.916 450228.5259 339103.1296 314787.8892 324429.7302 1.245852848 1.291073699 1.083242562 1.505600681 0.902577213 1.069803054 1.3877536 1.045228282 0.970280649 1 18.30754651 2.053293158 0.321904574 0.968218311 1.287419597 0.200932196 0.167222606 2.681272664 0.79225917 0.239086127 0.306038117 113.0558808 -2.053293158 0.319201285 GDS(ph)LILEHQWELEK ddPTM_MDA-MB-175_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 306.11 1.12E-44 524956000 1178269 930501 1092316 1009162 1222062 1311982 1538690 1155827 1244479 733051 TRUE FALSE 1224787.97 1090307.308 1120782.652 1208771.232 1014336.338 1007294.064 1418083.457 1140335.03 1199690.444 876678.3083 1.397077991 1.243680034 1.278442322 1.37880819 1.157022283 1.148989378 1.617564212 1.300745118 1.368450015 1 19.74168803 GDS(ph)LILEHQWELEKLELLHEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;GDS(1)LILEHQWELEKLELLHEVEK 292.37 8.93E-62 286860000 231391 189058 251010 134410 320980 264290 219140 211860 258160 179457 TRUE FALSE 240526.4954 221527.2408 257551.5268 160995.8968 266419.9343 202912.6529 201963.2342 209020.3632 248868.872 214618.1632 1.120718264 1.032192418 1.200045341 0.750150381 1.241367134 0.945458901 0.941035144 0.973917399 1.15958905 1 17.71141265 GDS(ph)PENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;GDS(1)PENR;GDS(1)PENR;GDS(1)PENR 154.75 0.0017385 1040621000 2474751 2779439 2798902 2649155 2968361 3234861 2991964 2852654 2846219 3043585 TRUE FALSE 2572456.08 3256786.027 2871843.685 3173149.952 2463800.057 2483613.558 2757446.044 2814418.839 2743784.134 3639917.208 0.706734778 0.894741787 0.788985991 0.871764321 0.676883543 0.682326937 0.757557353 0.773209576 0.753803995 1 21.79547421 -1.459640031 9.306610511 1.000002156 0.769502427 0.508541743 0.068587515 3.10E-06 1.80E-07 0.067119304 0.015820024 0.034702437 1.459640031 -0.230499729 GDS(ph)RS(ph)PSHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDSRSPSHKR 10 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GDS(0.996)RS(0.98)PS(0.024)HKR;GDS(0.997)RS(0.971)PS(0.032)HKR;GDS(1)RS(0.988)PS(0.013)HKR 58.487 0.059414 3994650000 837260 765409 754591 607433 875174 949151 1050609 841725 934625 824781 TRUE FALSE 870315.6713 896862.0417 774256.2614 727581.4344 726412.2361 728725.0648 968259.5213 830443.0532 900988.0288 986381.0456 0.882332112 0.909245008 0.784946411 0.737627145 0.736441803 0.738786565 0.981628272 0.841908973 0.913427963 1 19.91178555 1.35672686 0.880271281 0.986886498 0.806108354 0.383949312 0.074677567 0.598565659 0.983240386 0.074478064 0.028004721 22.73667007 -1.35672686 -0.180778145 GDS(ph)VSDSGSDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDSVSDSGSDALR 13 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 GDS(0.977)VS(0.023)DSGSDALR;GDS(0.829)VS(0.171)DSGSDALR 271.07 4.65E-32 274530000 189214 246580 240860 290840 300940 334190 314370 294930 268870 291310 TRUE FALSE 196684.3148 288928.1969 247137.0095 348367.2839 249786.3263 256579.4372 289728.8579 290976.9458 259193.4212 348386.617 0.564557607 0.829332077 0.709375726 0.999944507 0.716980257 0.736479028 0.831630274 0.835212754 0.743982141 1 18.41032968 -5 0.12189072 1.657865894 0.686126241 0.310646951 0.10524638 196.6374211 1.547062388 32.40535837 0.928601235 1.00E-05 5 -0.971739653 GDSFFIR ddPTM_MDA-MB-175_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 ; 86.086 0.047307 157513000 273700 308240 296400 274590 444250 394920 310410 331600 324880 400410 FALSE TRUE 284505.8873 361177.8222 304124.4275 328903.0824 368736.5437 303205.8151 286079.2531 327155.4444 313187.6323 478862.6732 0.594128345 0.754240918 0.635097377 0.68684218 0.770025655 0.633179055 0.597413975 0.68319262 0.654023898 1 18.86925246 -1.281431823 5.633794057 1.000029559 0.669664438 0.759971617 0.056035849 1.99E-05 2.54E-06 0.051951437 0.012243977 0.052308007 1.281431823 -0.330365121 GDSGAAPDVDDKLCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDSGAAPDVDDKLCLR 16 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 0 ; 144.05 1.23E-06 460680000 358500 245980 298700 239820 371480 386550 372540 305920 314080 256120 FALSE TRUE 372653.8568 288225.1515 306484.3674 287255.6802 308335.9623 296779.6207 343339.3413 301819.6428 302776.3222 306301.8103 1.216623096 0.94098416 1.000596004 0.937819074 1.006641005 0.968912395 1.12091842 0.985366827 0.988490149 1 18.22459437 4.747685349 24.99744646 0.997292567 1.21662321 0.657384824 0.048085201 745.7925555 2043075.134 0.011421583 0.140174599 55935.21978 -4.747685349 0.219330643 GDTHPLTLDEILDETQHLDIGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDTHPLTLDEILDETQHLDIGLK 23 0 P29084;E5RH41;E5RIW4 P29084 GTF2E2 Transcription initiation factor IIE subunit beta 0 330.89 8.95E-87 45785000 34366 27723 38942 33297 43888 40694 39837 39993 39012 34265 FALSE TRUE 35722.79622 32484.20959 39956.86051 39883.04722 36427.93344 31243.43522 36714.47185 39456.95925 37607.96574 40978.57071 0.871743343 0.792712118 0.975067208 0.973265942 0.888950805 0.762433503 0.895943202 0.962868118 0.917747132 1 15.32258204 1.808326058 5.058895567 0.954895154 0.879022042 0.24031627 0.065501445 0.359711199 15.75578144 0.033366139 0.018768706 64.31704138 -1.808326058 -0.075873112 GDTPGHAT(ph)PGHGGATSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GDT(0.011)PGHAT(0.989)PGHGGATSSAR;GDT(0.004)PGHAT(0.996)PGHGGATSSAR 208.72 9.46E-16 683770000 178770 288730 294010 323500 252350 300960 302510 287720 224510 258710 TRUE FALSE 185827.9776 338317.1315 301672.1421 387487.3344 209455.6371 231066.6011 278798.4757 283863.584 216429.929 309399.2712 0.60060897 1.093464539 0.975025381 1.252386061 0.676975212 0.746823353 0.901096097 0.91746688 0.699516609 1 18.23911027 3.207908347 24.99999536 0.828080512 0.988068233 0.154725414 0.178915941 369.7825596 301593.6952 0.050705356 0.06061086 1614.017901 -3.207908347 0.159987721 GDTPGHATPGHGGATSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 90.718 0.0012674 221310000 18230 96362 67784 83196 58488 98892 56330 75753 70354 73542 FALSE TRUE 18949.73448 112911.4239 69550.50673 99651.92048 48546.23065 75925.83172 51914.70741 74737.65494 67821.97328 87951.14685 0.215457503 1.283797062 0.790785672 1.133037192 0.551968137 0.863272788 0.590267544 0.849763279 0.771132335 1 16.42441477 4.768658432 24.33244681 0.848557203 0.215456009 0.454887115 0.213898656 8109.165696 6555655.84 0.048423347 5.87237811 58702.74797 -4.768658432 -0.633101194 GDTSGDYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GDTSGDYKK 9 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;; 120.09 0.0011567 4420100000 12192340 7032770 9973300 6138320 12160860 10257260 9557900 9539080 10179880 6497430 FALSE TRUE 12673703 8240593.54 10233212.39 7352461.375 10093761.36 7875166.815 8808726.823 9411224.235 9813508.107 7770477.008 1.631007078 1.060500344 1.316934904 0.946204637 1.29898864 1.013472765 1.133614682 1.211151417 1.262922224 1 22.88957173 4.744953816 24.91941446 1.148096185 1.631007304 0.580780399 0.125353474 462.5887786 1803028.383 0.027060124 0.255092002 55584.51441 -4.744953816 0.482911119 GDVAEGDLIEHFSQFGTVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GDVAEGDLIEHFSQFGTVEK 20 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ;; 305.98 1.93E-55 779980000 414810 1347560 1347930 1354480 1508690 1877970 1372870 1687500 1398930 1542050 FALSE TRUE 431187.0191 1578992.947 1383058.163 1622392.101 1252243.413 1441839.928 1265260.862 1664881.823 1348582.783 1844185.173 0.233808961 0.856200869 0.749956232 0.879733838 0.679022601 0.781830344 0.686081246 0.902773673 0.731262133 1 20.81455209 4.742073649 24.9489501 0.799328884 0.233808741 0.756083147 0.097644603 147.0189009 1044056.411 0.021191914 0.155634077 55217.10703 -4.742073649 -0.565520143 GDVEEDETIPDSEQDIRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GDVEEDETIPDSEQDIRPR 19 1 Q92973-2;Q92973;Q92973-3 Q92973-2 TNPO1 Transportin-1 0 ;;;;; 265.43 1.87E-31 3085760000 694508 863073 828062 851046 882691 1032718 833281 837795 802413 854564 FALSE TRUE 721927.7121 1011299.074 849641.976 1019380.359 732651.4991 792884.8955 767966.2578 826565.7284 773534.3129 1021999.454 0.706387571 0.989529955 0.831352671 0.997437283 0.716880519 0.775817338 0.751435096 0.80877316 0.756883294 1 19.962963 3.223185891 24.99929672 0.788830522 0.885357545 0.112837307 0.105411588 402.0362566 653709.4369 0.027843337 0.033393676 1671.806045 -3.223185891 0.096527024 GDVEGSQS(ph)QDEGEGSGESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDVEGSQSQDEGEGSGESER 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 GDVEGSQS(1)QDEGEGSGESER;GDVEGSQS(1)QDEGEGSGESER 333.08 7.03E-80 243110000 111865 139744 126539 133104 126793 150948 126480 125451 114324 135278 TRUE FALSE 116281.5166 163743.9449 129836.7103 159431.5739 105240.7711 115892.6146 116566.1671 123769.5345 110209.5016 161783.134 0.718749314 1.012119996 0.802535512 0.985464739 0.650505207 0.716345467 0.720508771 0.765033607 0.681217497 1 17.30370169 3.23588855 24.99999911 0.741387474 0.883661723 0.201993117 0.118754208 90.94465347 850885.3941 0.03075919 0.03837476 1721.42676 -3.23588855 0.142274249 GDVEHTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDVEHTIR 8 0 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YK13;H0YK71;H0YMW6;H0YN22 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 101.64 0.0052489 162440000 171490 150090 151210 170580 158270 186330 168590 146440 149180 153160 FALSE TRUE 178260.5576 175866.79 155150.6568 204320.2149 131367.3219 143057.6814 155375.4753 144477.2113 143811.0409 183168.7696 0.973203882 0.960135237 0.847036627 1.115475173 0.717192796 0.781015681 0.848264012 0.788765528 0.785128607 1 17.48281402 3.22434165 24.99988971 0.808473894 0.963908941 0.39555294 0.09220483 219.4499065 385837.7407 0.024875895 0.029865307 1676.261036 -3.22434165 0.155435047 GDVIHVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDVIHVTR 8 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E7EUY6;E7EU80;C9JAD7;C9JDI6;B1ANY6;E7ENL8 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 78.334 0.029348 0 168310 243310 219850 252980 226500 271570 229560 230400 220760 254690 FALSE TRUE 174955.0088 285096.5998 225579.4716 303018.6889 187999.6109 208501.9832 211566.4874 227311.8649 212814.8907 304591.6292 0.574392045 0.935996175 0.740596425 0.994835905 0.617218574 0.684529591 0.694590616 0.746284018 0.69868923 1 18.21651677 -1.299220577 3.542259506 1.000827588 0.748393621 0.27900731 0.123661275 41242739.78 60088322.12 357467.2186 0.028376893 0.050208752 1.299220577 -0.252433966 GDVPTKRPPVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDVPTKRPPVLR 12 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 117.23 0.00042508 1840820000 1383700 1476890 1792080 1228640 2099980 2084690 1437680 1716590 1870930 2264410 FALSE TRUE 1438329.544 1730534.369 1838783.077 1471661.325 1743026.15 1600552.341 1324990.885 1693581.919 1803595.595 2708077.785 0.531125639 0.639026832 0.678999358 0.543433919 0.643639618 0.59102894 0.48927357 0.625381563 0.666005831 1 21.36883775 0.696987191 1.987896623 0.999807972 0.592983818 0.832521032 0.054647843 0.497870562 2.726599671 0.051691226 0.014282451 4.977224055 -0.696987191 -0.406824155 GDVTAEEAAGAS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK 159.35 1.86E-06 805270000 1184790 700240 854890 840500 1055550 1216130 1214940 956930 938070 643330 TRUE FALSE 1231566.424 820500.7729 877169.1357 1006748.391 876127.988 933702.2381 1119709.828 944103.9186 904309.0439 769378.1962 1.600729563 1.066446615 1.14010137 1.308522124 1.138748138 1.213580321 1.455343853 1.227099914 1.17537649 1 19.55333342 0.906485808 2.537339917 1.000907616 1.26059495 0.230156005 0.150351603 0.589010604 8.211881788 0.136550948 0.036626264 8.062798537 -0.906485808 0.259687334 GDVVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GDVVPK 6 0 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A0A1W2PQM2;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ; 100.82 0.086601 483720000 1319110 1020020 1227080 1104170 1530390 1492730 1458370 1259650 1288450 983840 FALSE TRUE 1371189.481 1195200.5 1259058.713 1322571.53 1270254.854 1146066.08 1344059.149 1242766.452 1242078.936 1176604.611 1.1653783 1.015804705 1.070078003 1.124057749 1.079593639 0.974045205 1.142320144 1.056231159 1.055646837 1 20.16619816 1.449714132 0.008885926 1.02E-07 2.114331646 0.18868287 0.053099766 2479.959868 22.00894048 2622.504023 2611.053182 28.1652838 -1.449714132 2.114331544 GDY(ph)PQAMKHY(ph)T(ph)EAIKRNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDYPQAMKHYTEAIKRNPK 19 3 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 3 GDY(1)PQAMKHY(1)T(1)EAIKRNPK 47.392 0.061102 512950000 9801.5 178310 123120 182460 85236 210910 80451 139170 101390 160320 TRUE FALSE 10188.47079 208933.3554 126328.6083 218550.0434 70747.61517 161929.3489 74145.0404 137304.6538 97740.99371 191731.6345 0.053139227 1.089717698 0.658882446 1.139874721 0.368992917 0.844562502 0.386712608 0.716129366 0.509780214 1 17.54872887 -1.359680841 2.927966817 1.004444149 0.660438826 0.101001047 0.316626296 72962095.72 88327631.33 2817424.642 0.074666889 0.043683674 1.359680841 -0.344005322 GDYDAFFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GDYDAFFEAR 10 0 O75368 O75368 SH3BGRL SH3 domain-binding glutamic acid-rich-like protein 0 ;;;;; 234.47 1.01E-11 6183160000 1856400 2228470 2067510 2304340 2193550 2407500 2178680 2033220 1855810 2206820 FALSE TRUE 1929692.105 2611192.387 2121391.009 2760131.574 1820691.155 1848394.611 2007909.369 2005968.012 1789019.761 2639204.127 0.731164401 0.989386293 0.80379952 1.045819664 0.689863712 0.70036061 0.760801087 0.760065503 0.677863354 1 21.33167151 3.211878648 24.99997227 0.750390395 0.893121278 0.212157991 0.118627918 280.2372762 262570.7106 0.031350387 0.037480838 1628.840833 -3.211878648 0.142730883 GDYGPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDYGPPGR 8 0 Q16630-2;F8WJN3;Q16630-3;Q16630 Q16630-2 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 83.753 0.046902 0 51839 64788 52177 56368 53494 79478 57664 59290 49715 67416 FALSE TRUE 53885.64375 75914.83502 53536.77548 67517.42216 44401.10899 61020.439 53144.145 58495.31453 47925.76686 80624.87444 0.668350111 0.941580815 0.664023056 0.837426695 0.550712287 0.756843833 0.659153213 0.725524411 0.594429042 1 16.29893739 -1.135635728 4.141585438 1.000071094 0.715201609 0.389537485 0.108455351 14218095.15 3898649.673 9579.026809 0.023639616 0.07317526 1.135635728 -0.284869485 GDYPLEAVR ddPTM_MDA-MB-175_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 ;;;;;;; 212.2 9.10E-06 5809890000 5789450 4752360 4280180 4449520 6171330 6405380 5299730 4462400 4328420 5483060 FALSE TRUE 6018021.956 5568540.862 4391725.007 5329621.776 5122329.531 4917827.569 4884323.314 4402588.827 4172641.01 6557360.627 0.917750647 0.849204608 0.669739741 0.812769356 0.78115721 0.749970583 0.744861171 0.671396478 0.636329348 1 22.64468381 4.429269574 5.815515296 0.744807492 0.90239728 0.214106832 0.097054981 0.204984882 15.7799154 0.022258822 0.064928606 26870.11799 -4.429269574 0.157589788 GDYYEAHQMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GDYYEAHQMYR 11 0 Q7L5D6 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 133.07 0.00016936 144990000 104900 131020 125040 136140 162800 150100 135820 144840 128090 141000 FALSE TRUE 109041.533 153521.6658 128298.6451 163068.0857 135127.3142 115241.5498 125174.0735 142898.6567 123480.0659 168626.2504 0.646646253 0.910425663 0.76084622 0.967038556 0.801342103 0.683414056 0.742316651 0.8474283 0.732270721 1 17.36346962 -1.391889927 2.863986363 1.003703062 0.795286051 0.312185535 0.093852795 11943854.31 13891389.84 364450.4818 0.021974394 0.040561133 1.391889927 -0.208417011 GEAAAERPGEAAVASS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEAAAERPGEAAVAS(0.24)S(0.748)PS(0.012)K;GEAAAERPGEAAVAS(0.038)S(0.959)PS(0.003)K 186.82 1.19E-14 914530000 759380 429400 487420 475900 560220 721990 801550 556290 599860 352920 TRUE FALSE 789360.9088 503146.1097 500122.5656 570031.5996 464994.0045 554318.7644 738722.4165 548833.8425 578271.1558 422067.9169 1.870222486 1.192097503 1.184933859 1.35056842 1.101704218 1.313340205 1.750245368 1.300344851 1.370090293 1 18.68711564 0.332261205 2.405587688 1.000002411 1.37068399 0.193660054 0.232593656 43.27212532 152.4627987 0.217695958 0.058307104 2.149122666 -0.332261205 0.370681579 GEADRDTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEADRDTYR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;; 197.79 2.50E-05 13352910000 7024258 7739905 7025602 7472190 7601882 8221538 8230907 6950311 6472494 7593214 FALSE TRUE 7301581.13 9069173.476 7208694.96 8950166.88 6309716.813 6312210.398 7585747.002 6857153.449 6239550.205 9080958.902 0.804053978 0.998702183 0.793825304 0.985597113 0.694829355 0.695103949 0.835346474 0.755113367 0.687102571 1 23.11441322 3.23334837 24.99999966 0.765381559 0.895647373 0.221259361 0.106564006 165.7692888 795095.3228 0.028177248 0.034641577 1711.387559 -3.23334837 0.130265814 GEADRDTYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GEADRDTYRR 10 2 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;;;; 186.24 7.66E-07 8209272000 2499828 3650166 2965172 2765951 3552171 3492087 2491920 3015543 2899556 4072157 FALSE TRUE 2598523.14 4277053.616 3042446.818 3313047.852 2948374.242 2681102.717 2296596.799 2975124.579 2795201.546 4870018.198 0.533575653 0.878241814 0.624730072 0.680294758 0.605413393 0.550532382 0.471578689 0.610906255 0.573961212 1 22.21549573 -1.186203164 9.338128653 1.00000001 0.615598577 0.556140639 0.103350362 2.05E-08 1.79E-09 0.101820861 0.023999407 0.065132363 1.186203164 -0.384401433 GEAEAPHHGTGHPESAGEHALEPPAPAGASAS(ph)TPPPPAPEAQLPPFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGTGHPESAGEHALEPPAPAGAS(0.014)AS(0.52)T(0.466)PPPPAPEAQLPPFPR 153.07 7.59E-16 289470000 24039 45654 35308 52673 31770 44930 39279 42705 32035 36789 TRUE FALSE 24988.07828 53494.71936 36228.15549 63091.56219 26369.74675 34495.68842 36200.20934 42132.60933 30882.06661 43997.10018 0.567948301 1.215869208 0.823421438 1.433993648 0.599351926 0.784044591 0.822786256 0.957622415 0.70191141 1 15.42512082 GEAEAPHHGTGHPESAGEHALEPPAPAGASAST(ph)PPPPAPEAQLPPFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEAEAPHHGTGHPESAGEHALEPPAPAGASASTPPPPAPEAQLPPFPR 48 0 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GEAEAPHHGTGHPESAGEHALEPPAPAGAS(0.032)AS(0.171)T(0.797)PPPPAPEAQLPPFPR 105.95 3.90E-08 508700000 24357 77030 102980 97037 69964 113370 64009 96507 85769 83740 TRUE FALSE 25318.63317 90259.30329 105663.7434 116230.629 58071.54427 87041.53564 58991.80732 95213.48152 82682.19044 100147.2497 0.252814064 0.901265922 1.055083826 1.160597314 0.579861598 0.869135557 0.589050698 0.950734861 0.825606202 1 16.61176328 4.740106505 24.58322784 0.874091169 0.252813811 0.53583635 0.175358017 85.27954629 1355982.831 0.042211727 0.267221562 54967.56576 -4.740106505 -0.621277358 GEAGVPAEFSIWTR ddPTM_MDA-MB-175_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 ;;; 221.8 9.61E-12 697850000 576830 774920 632916 682680 696881 762700 671962 670120 647646 785320 FALSE TRUE 599603.6938 908006.482 649410.3109 817712.0664 578425.4165 585574.4838 619291.8626 661138.1375 624337.347 939188.4181 0.638427479 0.966799062 0.691459028 0.870658167 0.615877928 0.62348989 0.659390438 0.703946221 0.664762613 1 19.84105509 5.044457027 16.29404718 0.737355995 0.114006653 0.04924986 0.134792079 41984253.59 403716481.2 0.030771821 804393157.1 110778.8946 -5.044457027 -0.623349342 GEAHLAVNDFELAR ddPTM_MDA-MB-175_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 ;;;;; 264.58 1.07E-24 4846470000 2685800 3078920 2983970 3707060 3078170 3576140 3803010 3358110 2916530 2885210 FALSE TRUE 2791837.458 3607700.559 3061734.71 4440305.404 2554943.763 2745635.682 3504920.139 3313100.028 2811564.655 3450511.659 0.809108252 1.045555244 0.887327739 1.286854195 0.740453595 0.795718419 1.015768235 0.960176448 0.814825433 1 21.71837888 GEAVLRPGLDAEPELS(ph)PEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 GEAVLRPGLDAEPELS(1)PEEQR;GEAVLRPGLDAEPELS(1)PEEQR;GEAVLRPGLDAEPELS(1)PEEQR;GEAVLRPGLDAEPELS(1)PEEQR 187.21 1.79E-17 704530000 452647 466862 463823 484618 477128 522032 478219 497518 469906 457802 TRUE FALSE 470517.8531 547041.9168 475910.6084 580473.994 396025.953 400797.9795 440734.9452 490849.585 452994.1749 547499.5368 0.859394066 0.999164164 0.869243856 1.06022737 0.723335686 0.732051723 0.804996015 0.896529681 0.827387321 1 19.06249822 3.234484181 24.99964256 0.824262342 0.945178307 0.27599136 0.091897786 132.1673609 810546.4326 0.025780467 0.031892486 1715.869211 -3.234484181 0.120915965 GEAVLRPGLDAEPELSPEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 0 225.08 2.68E-25 93383000 26686 42712 36144 42333 37383 43581 35290 38554 33084 38623 FALSE TRUE 27739.58389 50047.45375 37085.94233 50706.34105 31028.65101 33459.97323 32523.87759 38037.24669 31893.3133 46190.43737 0.600548197 1.083502487 0.80289221 1.097767069 0.671754865 0.724391782 0.704125777 0.823487476 0.690474373 1 15.49530659 3.204824857 24.99997909 0.758272844 0.902895231 0.131306731 0.158384133 312.8089243 231807.0775 0.042053118 0.050265765 1602.59896 -3.204824857 0.144622387 GECEESWIHFI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GECEESWIHFI 11 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ;;;;; 157.86 7.07E-05 658332000 946120 1338280 1235130 1235340 1295480 1432020 1189750 1275450 1136060 1479510 FALSE TRUE 983473.5482 1568119.18 1267318.502 1479686.565 1075274.772 1099455.057 1096494.286 1258354.679 1095173.423 1769391.658 0.555825808 0.886247639 0.716245325 0.836268532 0.607708739 0.621374614 0.619701286 0.711179277 0.618954779 1 20.754822 -1.035863577 4.406247028 1.000016366 0.691551749 0.467830981 0.100326104 0.392989675 57522336.07 2223.998622 0.022925644 0.092073875 1.035863577 -0.308464617 GEDIFLDMFEDEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEDIFLDMFEDEYR 14 0 Q2KHT3;Q2KHT3-2 Q2KHT3 CLEC16A Protein CLEC16A 0 ; 156.51 1.29E-05 25597000 25165 29900 28493 31057 43037 43448 36482 31029 25593 38002 FALSE TRUE 26158.53363 35035.09241 29235.55099 37199.9819 35721.58611 33357.86046 33622.44551 30613.10701 24671.91293 45447.76431 0.575573607 0.770887038 0.643278089 0.818521713 0.785992153 0.733982429 0.739804169 0.673588844 0.542863072 1 15.47192171 4.747720635 23.73791339 0.732417802 0.575573438 0.157489361 0.11434988 1129.574263 2927126.552 0.025407768 0.301378479 55939.76464 -4.747720635 -0.156844363 GEDLTEEEDGGIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEDLTEEEDGGIIR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 178.1 4.70E-06 178172000 274970 229000 204073 264690 262900 279560 324980 244470 245740 153383 FALSE TRUE 285826.0279 268328.9686 209391.31 317044.892 218212.3519 214636.4268 299507.2184 241193.2795 236895.8654 183435.4622 1.55818305 1.462797681 1.141498528 1.728372956 1.189586514 1.170092327 1.632766178 1.314867238 1.291439848 1 17.48491305 -3.629056665 0.221154606 6.86E-14 1.444531404 0.295088013 0.189217522 100.9523722 1.743700915 45.9715367 0.356773373 0.000234933 3.629056665 1.444531404 GEDSVPDTVHHVVVPVNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEDSVPDTVHHVVVPVNPK 19 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 72.184 0.010999 245520000 318860 233260 244640 256400 299870 306700 361400 256040 289180 226680 FALSE TRUE 331448.839 273320.5905 251015.5194 307115.1547 248898.2045 235473.5731 333072.5237 252608.2026 278772.4683 271093.6059 1.222636137 1.008214818 0.925936702 1.132874948 0.91812643 0.868606149 1.228625524 0.931811732 1.028325501 1 18.04843156 4.737741448 7.308314264 1.004117256 1.225274952 0.289949153 0.102315934 0.12454509 59.58842798 0.023125871 0.137510342 54669.04003 -4.737741448 0.221157696 GEDVDQLVACIESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GEDVDQLVACIESK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;; 147.18 7.96E-06 10425000 83439 77025 84254 79828 96335 105027 92144 82158 91135 77126 FALSE TRUE 86733.23615 90253.44458 86449.72846 95617.74014 79960.01111 80636.07095 84921.51251 81056.80639 87855.06915 92237.36303 0.940326493 0.978491162 0.937252818 1.036648675 0.866893941 0.874223507 0.920684522 0.878784949 0.952488951 1 16.49306365 3.223479307 24.99996084 0.905974564 0.970992979 0.261526205 0.045761551 265.2059957 439625.5216 0.012431431 0.014912509 1672.935922 -3.223479307 0.065018415 GEDVPS(ph)EEEEEEENGFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR 347.33 1.25E-90 1803910000 126228 125062 122545 140166 140978 154386 169310 137543 135192 118647 TRUE FALSE 131211.5789 146540.4257 125738.6234 167890.4164 117014.6099 118532.1912 156039.0398 135699.4611 130326.4663 141893.608 0.924718039 1.032748604 0.8861472 1.183213386 0.82466442 0.835359625 1.099690409 0.95634654 0.918480178 1 17.11445008 -1.554350105 2.949045018 1.00163122 0.966295567 0.009613432 0.108168794 48341229.45 38824000.28 594767.5321 0.024764607 0.027902936 1.554350105 -0.035335654 GEEAAGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEEAAGGDR 9 0 O43598;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 148.99 0.00020636 388680000 264386 327510 289296 284926 309827 322290 305707 302230 280769 341385 FALSE TRUE 274824.1634 383757.2948 296835.2914 341283.5124 257162.7172 247443.0319 281744.8865 298179.1012 270664.1785 408272.8545 0.673138467 0.939953001 0.727051255 0.835920166 0.629879539 0.606072701 0.690089687 0.730342706 0.66294924 1 18.63917412 5.064588174 15.2551726 0.742771663 6.17E-05 0.027598264 0.124379821 5873024.059 31449811.55 0.028638065 135707615.3 116034.7775 -5.064588174 -0.742709973 GEEDTGQEEGGSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEEDTGQEEGGSRR 14 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 96.591 0.0057977 0 49575 55605 56962 63086 55213 72980 62054 55733 55533 55084 FALSE TRUE 51532.25928 65154.7262 58446.47651 75564.22251 45827.91398 56031.50102 57190.04533 54985.9903 53534.37818 65876.65515 0.782253731 0.989041202 0.887210748 1.147056151 0.69566243 0.8505517 0.868138268 0.834680968 0.812645664 1 16.00747968 3.219586172 24.99981456 0.837477272 0.949495683 0.186312175 0.109865345 375.7103623 495016.7717 0.029930512 0.035829218 1658.006281 -3.219586172 0.11201841 GEEDWLYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 ;;;; 215.88 1.45E-06 4361260000 2553630 3165990 2804700 2935950 3008510 3417940 3049800 2862980 2638430 3079660 FALSE TRUE 2654449.284 3709724.155 2877792.786 3516672.147 2497124.545 2624175.234 2810748.707 2824606.436 2543473.42 3683060.413 0.720718366 1.007239561 0.781359104 0.954823368 0.678002602 0.712498558 0.763155743 0.766918301 0.69058694 1 21.81247363 3.236190724 24.99995896 0.754909749 0.870072842 0.14432347 0.113272487 95.7839122 1010427.272 0.029372631 0.03671584 1722.624915 -3.236190724 0.115163093 GEEGHDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEEGHDPK 8 0 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 99.442 0.0068105 545180000 1419770 907790 1175550 1091040 1318520 1563270 1892690 1191100 1287760 705980 FALSE TRUE 1475823.616 1063695.871 1206185.799 1306844.456 1094398.441 1200224.234 1744336.012 1175135.253 1241413.769 844303.2642 1.7479781 1.259850478 1.428616766 1.547837739 1.296214865 1.421555838 2.066006477 1.391840234 1.470341075 1 19.68740177 GEEGHDPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GEEGHDPKEPEQLR 14 1 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 174.59 1.51E-06 2439760000 3123520 2155050 2698180 2090740 3364600 3384740 3184250 2602000 2970500 1962960 FALSE TRUE 3246838.981 2525163.074 2768496.787 2504282.132 2792686.494 2598685.431 2934660.165 2567124.446 2863592.285 2347564.429 1.383067038 1.075652298 1.179305988 1.066757573 1.189610159 1.106970867 1.250087166 1.093526727 1.21981414 1 21.16273332 GEEGHDPKEPEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEEGHDPKEPEQLRK 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 154.6 1.47E-06 225790000 488280 244530 357780 236090 509370 465720 445070 352220 436580 255640 FALSE TRUE 507557.6714 286526.1253 367104.0407 282787.8973 422787.4693 357563.5881 410184.2504 347499.067 420867.5711 305727.7635 1.660162184 0.937193672 1.200754673 0.924966363 1.3828887 1.169548961 1.341665035 1.136629082 1.376608936 1 18.22188805 -2.249472957 2.317322759 0.173432608 1.218352095 0.097841832 0.209049056 5364736.134 1347507 23164534.52 0.046985748 0.005630242 2.249472957 1.044919487 GEEGRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 76.478 0.032557 244740000 441220 367260 490420 397930 534660 512920 525940 452130 464200 383510 FALSE TRUE 458639.7063 430334.0481 503200.7481 476639.3663 443778.6842 393802.1034 484715.4485 446069.9369 447493.5327 458651.4418 0.999974413 0.938259447 1.097131072 1.039219161 0.967572853 0.858608668 1.056827482 0.972568483 0.975672356 1 18.80703865 5.140307188 19.49232252 0.989861302 6.501500429 0.00245633 0.062783288 8248.527444 1222309.081 0.014652107 135746.8443 138136.0993 -5.140307188 5.511639128 GEEGRPGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 64.711 0.038592 223750000 342390 249100 339670 231843 416710 371460 415890 379000 377680 305540 FALSE TRUE 355907.8216 291880.9873 348522.0792 277700.8534 345877.783 285194.0445 383291.4551 373920.1249 364087.3706 365404.7131 0.974009937 0.798788239 0.953797438 0.759981586 0.946560815 0.780488139 1.048950496 1.023304056 0.99639484 1 18.47913572 2.224274278 24.99573555 1.020620286 0.868182111 0.509528832 0.071209365 171.7519876 300499.6152 0.023951687 0.017772197 167.6001019 -2.224274278 -0.152438176 GEEGS(ph)DDDETENGPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GEEGSDDDETENGPKPK 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(1)DDDETENGPKPK 307.34 7.95E-48 7699120000 9028250 3009980 4704000 3104360 6632140 6514800 7532780 4893020 5404580 2229523 TRUE FALSE 9384692.281 3526920.651 4826590.104 3718393.142 5504811.212 5001836.433 6942341.02 4827437.07 5210070.222 2666355.345 3.519670512 1.322749669 1.81018262 1.394560237 2.064545231 1.875907666 2.603681851 1.810500269 1.954004455 1 21.34643763 0.443139604 1.757279344 1.000163177 2.008353983 0.212841096 0.598539907 7.18070601 20.86972729 0.535256247 0.150272664 2.774211735 -0.443139604 1.008190806 GEEGVGEERPVKGHS(ph)PFTLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEEGVGEERPVKGHSPFTLRPK 22 3 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 GEEGVGEERPVKGHS(0.968)PFT(0.032)LRPK 61.801 0.031876 102420000 34855 29862 32451 17791 55326 38898 32184 31064 42217 31107 TRUE FALSE 36231.10231 34990.56621 33296.69972 21310.0067 45921.70628 29864.529 29661.33398 30647.63789 40697.61842 37201.82107 0.973906687 0.940560575 0.895028758 0.572821601 1.234394042 0.802770621 0.797308657 0.823820905 1.093968447 1 15.18308562 1.237718796 24.99961511 1.046984267 0.874972042 0.149068673 0.159137491 40.11640379 1190990.612 0.121242001 0.037028167 17.28696672 -1.237718796 -0.172012225 GEEHCGHLIEAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEEHCGHLIEAHK 13 0 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ; 184.21 3.37E-06 427330000 553900 420990 467730 488570 489510 540010 621920 467470 429440 320220 FALSE TRUE 575768.3997 493291.7577 479919.428 585207.6878 406303.265 414600.8614 573172.2853 461204.3293 413984.5383 382960.978 1.503464929 1.288099274 1.253181017 1.528113101 1.060952129 1.082619079 1.496685872 1.204311551 1.081009717 1 18.54683787 4.852690328 0.034548483 1.73E-06 2.76432651 0.355100172 0.152540024 648.8577445 3.375312377 103.0326144 173.6800135 71234.49145 -4.852690328 2.764324779 GEEHCGHLIEAHKECMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEEHCGHLIEAHKECMR 17 1 H7C4E5;C9J8T6;Q14061 H7C4E5 COX17 Cytochrome c oxidase copper chaperone 0 ;;; 175.51 4.10E-10 694105000 296652 361062 341037 302462 384782 434362 280991 324308 310383 390763 FALSE TRUE 308364.05 423071.5898 349924.7044 362288.0808 319376.8931 333488.0083 258966.1912 319961.1817 299212.3765 467325.5282 0.659848503 0.905303828 0.748781488 0.775237086 0.683414181 0.713609654 0.554145185 0.684664463 0.640265422 1 18.83406832 3.252385044 6.089073781 0.685465534 0.780736207 0.024725655 0.12255183 0.334236646 44.13264653 0.03212477 0.041889341 1788.072171 -3.252385044 0.095270673 GEEKPAGHRTS(ph)PVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEEKPAGHRTSPVAK 15 2 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 GEEKPAGHRT(0.248)S(0.752)PVAK;GEEKPAGHRT(0.111)S(0.889)PVAK 154.55 1.28E-06 845050000 1763070 1073560 1507130 1155800 1947490 1907220 2197300 1612780 1788530 889060 TRUE FALSE 1832677.365 1257935.579 1546407.046 1384413.79 1616456.345 1464297.059 2025069.884 1591163.322 1724161.155 1063254.285 1.723649169 1.183099468 1.454409418 1.302053337 1.5202914 1.377184254 1.904596025 1.496503089 1.62158872 1 20.02005524 GEFGDVMLGDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEFGDVMLGDYR 12 0 P41240 P41240 CSK Tyrosine-protein kinase CSK 0 150.04 0.00015769 43755000 47614 63459 57827 61810 70002 70907 57067 61530 57567 75452 FALSE TRUE 49493.83749 74357.58961 59334.01913 74035.83352 58103.08504 54439.92386 52593.93942 60705.29099 55495.17492 90235.37478 0.548497057 0.824040348 0.657547212 0.820474605 0.643905843 0.60331022 0.582852784 0.672743823 0.615004648 1 16.4614055 -1.943330134 5.873257723 1.154760511 0.666959627 0.570594347 0.087608582 0.047042933 0.000453908 0.022477057 0.019408453 0.011393833 1.943330134 -0.487800884 GEFKDEEETVTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEFKDEEETVTTK 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 195.54 1.36E-07 711260000 796700 391940 504100 352380 708910 662720 742210 502090 567640 307200 FALSE TRUE 828154.3312 459252.6461 517237.2601 422079.7123 588409.7314 508813.3236 684033.6408 495360.3048 547210.7473 367389.9583 2.254156142 1.250041368 1.40786989 1.148860231 1.601594486 1.384940748 1.861873536 1.348322929 1.489454828 1 18.48695267 -2.706534267 0.404644625 1.89E-09 1.519440244 0.212781105 0.305330296 152.8574283 6.091918233 133.0082077 0.177607301 0.001965467 2.706534267 1.519440242 GEFSAS(ph)PMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GEFSASPMLK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEFS(0.002)AS(0.998)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.001)AS(0.999)PMLK;GEFSAS(1)PMLK;GEFSAS(1)PMLK;GEFS(0.015)AS(0.985)PMLK;GEFS(0.067)AS(0.933)PMLK;GEFS(0.087)AS(0.913)PMLK 244.64 1.84E-12 15186600000 18657330 15240850 16951020 14424810 20765050 22183380 20166010 18030860 18074330 14421990 TRUE FALSE 19393935.79 17858347.43 17392777.51 17277994.36 17235414.22 17031626.19 18585345.44 17789185.81 17423838.39 17247702.81 1.124435874 1.035404403 1.008411247 1.001756266 0.999287523 0.98747215 1.077554828 1.0313945 1.010212118 1 24.03990089 4.728948696 3.196929576 1.017795464 1.138772609 0.650640466 0.02398013 0.221661576 3.609677358 0.006322718 0.066102463 53573.33671 -4.728948696 0.120977145 GEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_MDA-MB-175_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 GEGDAPFSEPGTTSTQRPS(0.608)S(0.39)PET(0.002)ATK;GEGDAPFSEPGT(0.001)T(0.001)S(0.003)T(0.003)QRPS(0.566)S(0.41)PET(0.017)AT(0.001)K 149.16 9.65E-08 4741230000 843830 594350 676400 649460 852700 854960 939340 706200 768530 483810 TRUE FALSE 877145.06 696424.9891 694027.5397 777921.2496 707758.3586 656408.497 865712.0763 696734.5441 740870.7554 578603.3064 1.515969664 1.203631195 1.199487684 1.344481169 1.223218656 1.134470698 1.49621004 1.204166199 1.280446806 1 19.14221504 -3.248256729 0.434140579 2.27E-09 1.28750479 0.337917914 0.121655302 226.7035372 6.301035576 208.8533543 0.063862777 0.000564603 3.248256729 1.287504788 GEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GEGDAPFSEPGTTSTQRPS(0.217)S(0.783)PETATK;GEGDAPFSEPGTTSTQRPS(0.199)S(0.795)PET(0.006)ATK;GEGDAPFSEPGTTST(0.002)QRPS(0.061)S(0.936)PET(0.001)ATK;GEGDAPFSEPGTTSTQRPS(0.01)S(0.985)PET(0.004)ATK;GEGDAPFSEPGT(0.044)T(0.044)S(0.044)T(0.044)QRPS(0.219)S(0.604)PETATK 220.78 1.76E-34 11001100000 5187170 3629800 4474930 3933170 5143710 5290820 5867200 4725310 4921160 3127010 TRUE FALSE 5391963.477 4253189.914 4591550.352 4711139.287 4269384.011 4062107.238 5407313.533 4661974.948 4744048.413 3739687.739 1.441821845 1.137311511 1.227789771 1.259768092 1.141641845 1.08621562 1.445926481 1.246621449 1.268568058 1 21.83448638 4.75243801 24.01879676 1.218893742 1.441822108 0.267783879 0.116048076 1943.080688 3362954.242 0.026919939 0.522373262 56550.70326 -4.75243801 0.222928366 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 278.1 4.64E-81 1578790000 641000 448700 569710 555900 586930 669690 835950 623030 620780 382510 TRUE FALSE 666307.175 525760.7346 584557.1106 665855.3608 487163.8482 514164.6468 770426.0547 614679.3019 598438.2491 457455.5109 1.456550766 1.149315555 1.277844723 1.455563098 1.064942572 1.12396645 1.68415515 1.343691982 1.30818896 1 18.80327192 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSRR 43 2 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 GEGDIHENVDT(0.001)DLPGS(0.118)LGQS(0.118)EEKPVPAAPVPS(0.635)PVAPAPVPS(0.128)RR;GEGDIHENVDTDLPGS(0.004)LGQS(0.014)EEKPVPAAPVPS(0.931)PVAPAPVPS(0.051)RR 87.564 8.38E-05 152728000 47010 33358 41643 32724 53019 50118 38409 44389 48772 43850 TRUE FALSE 48865.9911 39086.97701 42728.25079 39196.70953 44006.84932 38478.85405 35398.40222 43794.03806 47016.70525 52441.56794 0.931817888 0.745343409 0.814778285 0.747435881 0.839159679 0.733747208 0.675006557 0.835101615 0.896554148 1 15.6784232 1.089637392 2.223501601 0.995797389 0.781867477 0.508134029 0.066774761 0.213644575 2.088519363 0.060642975 0.016888914 12.29242004 -1.089637392 -0.213929912 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 120.15 1.31E-07 93287000 40177 29656 32075 30362 32792 42138 45584 38865 39423 20459 FALSE TRUE 41763.21898 34749.18731 32910.90085 36367.51298 27218.02755 32352.08811 42011.00697 38344.07825 38004.17393 24467.54934 1.706881977 1.420215275 1.345083661 1.48635699 1.11241331 1.322244727 1.717009186 1.567140122 1.553248076 1 14.57858199 GEGERPAQNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEGERPAQNEK 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 188.29 2.93E-06 7043340000 5268310 4595620 5230800 4426210 6074280 5914740 5671910 5339760 5267730 4631660 FALSE TRUE 5476306.947 5384881.986 5367118.945 5301701.127 5041776.055 4541131.274 5227330.873 5268189.251 5078145.426 5539145.099 0.988655623 0.972150375 0.968943555 0.957133462 0.910208338 0.819825297 0.943707157 0.951083454 0.91677422 1 22.4012319 3.407562132 3.894599384 0.920088403 0.974728139 0.238025174 0.042814256 0.32695296 9.883059392 0.012579949 0.017712737 2556.007546 -3.407562132 0.054639736 GEGLY(ph)ADPYGLLHEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEGLYADPYGLLHEGR 16 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR;GEGLY(1)ADPYGLLHEGR 200.77 2.01E-10 435506000 529094 648260 572178 650531 606013 698660 512194 585098 510965 707310 TRUE FALSE 549983.0397 759593.6122 587089.4287 779204.0902 503003.1267 536406.8033 472046.8959 577255.7183 492575.4695 845893.8522 0.650179734 0.897977459 0.694046218 0.921160602 0.594640953 0.634130159 0.558045072 0.682420988 0.582313571 1 19.69011711 4.050842056 24.99985864 0.689472124 0.779562192 0.017828603 0.148906191 310.7289722 152786.2667 0.035492286 0.07667209 11241.96053 -4.050842056 0.090090068 GEGMPQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEGMPQYR 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 89.296 0.032585 114120000 195900 163540 215420 144390 222800 253470 239410 194380 186810 182670 FALSE TRUE 203634.2833 191626.7228 221034.0222 172949.911 184928.5356 194605.4339 220644.4186 191774.654 180086.7446 218460.6891 0.932132386 0.877167987 1.011779387 0.791675206 0.846507151 0.890802985 1.009995984 0.877845139 0.824343937 1 17.73701417 -0.031410588 8.356459795 0.999999998 0.897619168 0.171939312 0.068493657 8855649.041 1059736.543 0.065039004 0.015774275 0.930228009 0.031410588 -0.102380831 GEGPAIPGDT(ph)PPPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;GEGPAIPGDT(1)PPPTPR 293.77 1.47E-44 4787768000 2423340 2927180 2555540 2720860 2748920 3220620 2425660 2662600 2476880 2916100 TRUE FALSE 2519015.334 3429900.395 2622139.472 3259037.987 2281659.56 2472679.814 2235530.431 2626912.202 2387737.573 3487453.963 0.722307839 0.983496967 0.751877874 0.934503515 0.654247937 0.709021493 0.641020772 0.753246417 0.684664973 1 21.73374274 3.234211121 24.99995146 0.721830615 0.850852387 0.153498045 0.119130164 157.3414437 904364.8254 0.030907936 0.038166296 1714.790704 -3.234211121 0.129021772 GEGPGEAGGPLT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GEGPGEAGGPLTPR 14 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR 226.14 2.81E-11 3880490000 1283230 1424930 1396330 1479870 1590910 1864760 1621910 1648490 1543910 1980930 TRUE FALSE 1333892.911 1669650.643 1432719.507 1772583.869 1320487.686 1431697.751 1494780.456 1626394.688 1488344.981 2369055.306 0.563048447 0.704774869 0.604764061 0.748223929 0.557389979 0.604332768 0.630960557 0.686516133 0.628244084 1 21.17588045 -1.525062881 0.575283237 1.193768747 0.636441247 0.779978915 0.057901663 24.26871331 3.185767323 6.909962576 0.022515413 0.029849504 1.525062881 -0.5573275 GEGQLGPAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GEGQLGPAER 10 0 P13639 P13639 EEF2 Elongation factor 2 0 ;; 200.09 6.20E-07 1623380000 980370 990630 951630 952850 1074520 1304830 1028210 936990 916730 985500 FALSE TRUE 1019075.765 1160762.996 976430.2596 1141320.886 891873.4742 1001803.007 947616.2135 924431.1817 883737.0664 1178589.856 0.864656826 0.984874416 0.828473327 0.968378338 0.756729298 0.850001382 0.804025428 0.784353587 0.749825787 1 20.16863032 3.237591706 24.99998291 0.811442271 0.910892603 0.218024372 0.07894831 32.44970559 837284.1584 0.020523062 0.025909317 1728.190868 -3.237591706 0.099450331 GEGS(ph)PSEATRLPTQGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEGSPSEATRLPTQGAR 17 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 GEGS(0.978)PS(0.022)EATRLPTQGAR;GEGS(0.866)PS(0.133)EAT(0.002)RLPTQGAR 164.94 1.53E-09 283730000 231200 371300 306741 262891 359880 379300 280080 304506 269357 404950 TRUE FALSE 240327.9545 435067.8867 314734.9225 314890.0551 298707.7261 291213.3233 258126.5977 300424.5951 259662.8942 484292.1993 0.496245768 0.898358238 0.649886418 0.650206746 0.616792355 0.601317394 0.532997637 0.620337465 0.536169888 1 18.88551824 -0.911693974 13.02135058 1 0.627051028 0.538667848 0.104734528 0 0 0.098817862 0.023291594 0.122547943 0.911693974 -0.372948972 GEGYAKPNEGAIVEVALEGYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEGYAKPNEGAIVEVALEGYYK 22 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 241.71 1.02E-30 766767000 2780140 1817523 2472555 1961124 3115620 2920000 3250210 2642539 2946340 1701626 FALSE TRUE 2889902.074 2129668.437 2536991.815 2349028.474 2586028.025 2241874.253 2995450.047 2607120.087 2840301.799 2035027.035 1.420080433 1.046506214 1.246662462 1.154298411 1.27075856 1.101643474 1.47194607 1.281123072 1.395707158 1 20.95661653 2.25886698 24.99981429 1.313222242 1.201730687 0.054164898 0.148982504 491.438402 605024.1155 0.046961435 0.039248351 181.4959672 -2.25886698 -0.111491555 GEGYAKPNEGAIVEVALEGYYKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GEGYAKPNEGAIVEVALEGYYKDK 24 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 228.63 1.94E-33 1313876000 1138991 595119 904090 460313 1552495 1028587 889195 850802 1153748 648698 FALSE TRUE 1183959.244 697326.0589 927651.3281 551361.5375 1288602.454 789713.2576 819497.5724 839398.3908 1112224.835 775797.953 1.526118031 0.898850089 1.195738303 0.710702491 1.661002648 1.017936764 1.056328609 1.081980672 1.433652706 1 19.56532144 4.76120818 23.19450195 1.118923592 1.526119221 0.189398792 0.253674112 3579.51807 3665805.275 0.056256543 2.608843836 57704.30042 -4.76120818 0.407195629 GEHLTIEFENLVESDEGES(ph)PGSSHRPLTEEEIVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEHLTIEFENLVESDEGESPGSSHRPLTEEEIVDLR 36 1 Q63HQ0;Q63HQ0-2 Q63HQ0 AP1AR AP-1 complex-associated regulatory protein 1 GEHLTIEFENLVES(0.332)DEGES(0.38)PGS(0.096)S(0.096)HRPLT(0.096)EEEIVDLR 56.638 0.020102 32751000 10562 18272 16986 19248 21404 20743 15086 16869 14518 19460 TRUE FALSE 10978.99592 21410.07386 17428.66911 23055.19695 17765.75573 15925.75261 13903.5199 16642.89865 13995.50002 23272.81442 0.471751964 0.919960667 0.748885322 0.990649285 0.763369458 0.68430712 0.597414634 0.715121874 0.60136689 1 14.50635807 2.864668281 5.049849474 0.693841951 0.799434504 0.015392868 0.165386059 0.591163363 21.88806001 0.048011457 0.0512032 732.2650076 -2.864668281 0.105592553 GEHSIVYLKPSYAFGSVGK ddPTM_MDA-MB-175_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 ; 265.43 1.23E-31 5907100000 5018700 3783400 5007600 4226500 5509900 5559700 5649000 4770600 5218600 4051200 FALSE TRUE 5216842.151 4433169.519 5138102.17 5062489.085 4573329.166 4268543.933 5206216.619 4706657.91 5030783.605 4844955.075 1.07675759 0.915007353 1.060505637 1.044899077 0.943936341 0.881028589 1.074564478 0.971455429 1.038355057 1 22.20805186 -1.797499275 8.757396891 1.000044284 0.997371971 0 0.066356466 5.52E-05 1.28E-06 0.061853134 0.01433723 0.015940455 1.797499275 -0.002672314 GEILVIIEKPEEQWWSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEILVIIEKPEEQWWSAR 18 1 P46109 P46109 CRKL Crk-like protein 0 101.05 0.0010476 0 64318 56262 71042 56106 86499 81235 75567 75347 60411 67311 FALSE TRUE 66857.3243 65924.56084 72893.41288 67203.59934 71795.93088 62369.40238 69643.86108 74337.09671 58236.81991 80499.3017 0.830532972 0.818945748 0.905516089 0.834834563 0.891882654 0.774781906 0.865148636 0.923450206 0.723445032 1 16.29668865 -1.900675488 4.688169832 1.051928425 0.848275635 0.399806131 0.057839148 0.030469099 0.000645524 0.054354487 0.012522739 0.012569688 1.900675488 -0.20365279 GEIPS(ph)PQLTRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEIPSPQLTRPK 12 1 Q8IWZ3-6;H7C0V5 Q8IWZ3-6 ANKHD1;ANKHD1-EIF4EBP3 Ankyrin repeat and KH domain-containing protein 1 1 GEIPS(0.991)PQLT(0.009)RPK;GEIPS(1)PQLTRPK 110.57 0.00040576 301540000 672420 495200 558160 495820 620370 677230 628880 544010 532700 377600 TRUE FALSE 698967.6608 580246.7479 572706.1081 593891.7161 514919.729 519953.596 579586.7423 536718.4358 513528.2311 451583.4904 1.547814913 1.284915769 1.268217551 1.315131595 1.140253663 1.151400809 1.283454233 1.188525372 1.137172288 1 18.78463322 8 0.450751209 1.157653232 9.229086606 0.697767868 0.076380191 51.72271164 0.622308224 0.044582055 384.3496574 100000000 -8 8.071433375 GEKPNPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEKPNPLR 8 1 P68402;J3KNE3 P68402 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 0 ;;; 83.005 0.017149 1481980000 2511520 2432860 2642360 2440930 3012940 3097570 2853280 2693810 2680090 2566990 FALSE TRUE 2610676.749 2850684.78 2711222.072 2923738.669 2500801.535 2378206.312 2629632.458 2657703.883 2583634.084 3069942.543 0.850399222 0.928579197 0.883150754 0.952375697 0.81460858 0.774674535 0.856573835 0.865717793 0.841590371 1 21.54978022 GELS(ph)EEELPYYVELPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GELSEEELPYYVELPDR 17 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 GELS(1)EEELPYYVELPDR;GELS(1)EEELPYYVELPDR 258.2 3.90E-27 77703000 66939 70040 78189 84070 80942 90096 94722 75069 77923 61242 TRUE FALSE 69581.80341 82068.82516 80226.66957 100698.7951 67183.50775 69172.56942 87297.44213 74062.82284 75118.56645 73241.19735 0.950036399 1.120528174 1.09537627 1.374892802 0.917291227 0.944448916 1.19191719 1.011218078 1.025632693 1 16.16036776 GELS(ph)PSFLNPPLPPSIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GELSPSFLNPPLPPSIDDR 19 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 GELS(0.981)PS(0.019)FLNPPLPPSIDDR;GELS(0.983)PS(0.017)FLNPPLPPSIDDR;GELS(0.956)PS(0.044)FLNPPLPPSIDDR;GELS(0.959)PS(0.041)FLNPPLPPSIDDR 88.551 0.0026628 242348000 63737.9 81885 76334 87041 72420 95155 77433 76478 70943 77471.9 TRUE FALSE 66254.32151 95948.11177 78323.32675 104257.45 60110.07427 73056.69334 71363.59913 75452.9375 68389.77529 92651.03552 0.715095316 1.035585962 0.845358353 1.125270208 0.648779303 0.788514591 0.770240707 0.814377703 0.738143669 1 16.49951948 3.224168244 24.99999954 0.784544939 0.931776767 0.206965522 0.130672037 324.4685021 563610.8582 0.03475433 0.041717889 1675.591869 -3.224168244 0.147231827 GELS(ph)PSFLNPPLPPSIDDRDLSTEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GELSPSFLNPPLPPSIDDRDLSTEEVR 27 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 GELS(0.959)PS(0.04)FLNPPLPPS(0.001)IDDRDLSTEEVR;GELS(0.645)PS(0.355)FLNPPLPPSIDDRDLSTEEVR;GELS(0.992)PS(0.008)FLNPPLPPSIDDRDLSTEEVR 121.52 5.75E-05 154800000 54625.7 60599 56933.8 50529.3 66588.2 66588.9 48332.8 57446.6 50296.3 79551 TRUE FALSE 56782.36482 71006.40686 58417.5416 60523.84473 55269.56155 51124.63714 44544.34884 56676.62229 48486.14599 95137.49535 0.596845278 0.746355647 0.614032789 0.636172358 0.580944047 0.53737632 0.468210233 0.595733807 0.509642868 1 16.53772642 -1.464295735 6.007564242 1.000249334 0.587846418 0.749241352 0.071633075 0.000254636 2.27E-05 0.073828797 0.017391302 0.034332408 1.464295735 -0.412402916 GEMMDLQHGSLFLQTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEMMDLQHGSLFLQTPK 17 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 245.97 1.28E-20 927580000 346380 1219750 1182520 1305720 1314970 1599610 1244010 1537360 1230450 1123890 FALSE TRUE 360055.3499 1429232.574 1213337.443 1563987.519 1091451.869 1228124.82 1146501.246 1516754.204 1186166.345 1344094.727 0.267879445 1.063342148 0.90271721 1.163599177 0.812034931 0.913718948 0.852991402 1.128457818 0.882502044 1 20.35820339 4.743095283 24.9633531 0.972082151 0.267879157 0.777819862 0.112374382 198.1115352 1090566.115 0.025763086 0.206143561 55347.15259 -4.743095283 -0.704202994 GEMMDLQHGSLFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 216.15 6.24E-12 5314140000 991457 6006870 4942980 7299170 4482530 7239630 4992760 6238690 4350880 5475230 FALSE TRUE 1030600.488 7038503.196 5071798.12 8742924.04 3720591.152 5558335.65 4601414.425 6155070.565 4194292.679 6547996.489 0.157391729 1.074909433 0.774557245 1.335205976 0.568202985 0.848860512 0.702720967 0.939992954 0.640545957 1 22.64262212 4.749039285 24.49857132 0.8701729 0.157391196 0.501689982 0.214814774 901.5379264 2107692.792 0.047832569 0.670758722 56109.87288 -4.749039285 -0.712781704 GENHPHFEGGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GENHPHFEGGVK 12 0 F6WE04;Q5SRH9-5;Q5SRH9-6;Q5SRH9-4;Q5SRH9;A0A0A0MRQ0;A0A0A0MSH8;E9PAZ4;A0A0A0MSW9;Q5SRH9-3 F6WE04 TTC39A Tetratricopeptide repeat protein 39A 0 59.227 0.058132 63549000 53640 69650 63480 63501 68001 77526 67285 64942 71823 67778 FALSE TRUE 55757.74862 81611.8457 65134.34095 76061.30827 56442.21431 59521.76142 62011.02588 64071.55871 69238.10426 81057.80141 0.6878764 1.006835175 0.803554252 0.938358886 0.696320568 0.734312557 0.765022303 0.79044284 0.854181868 1 16.30666342 5.032850769 16.1851191 0.826611137 0.215954047 0.152476057 0.103401991 20670531.26 282911437.1 0.023987923 353443482.8 107857.6041 -5.032850769 -0.61065709 GENLEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GENLEHLR 8 0 C9JXZ5;Q9BV40;B8ZZT4 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ;;; 164.71 0.0003285 1449210000 839439 1119520 948190 1098990 1192750 1314060 949470 955210 894760 1392640 FALSE TRUE 872580.6999 1311788.851 972900.6103 1316366.942 990006.781 1008889.48 875048.0604 942406.9724 862557.7624 1665501.144 0.523914801 0.787624107 0.584148869 0.790372883 0.594419754 0.605757302 0.525396253 0.565839883 0.51789683 1 20.66752491 -1.131902445 5.021633546 1.000016942 0.612531362 0.602417952 0.09489245 1.78E-05 3.08E-06 0.091040933 0.021457616 0.073807 1.131902445 -0.38748558 GEPAAAAAPEAGAS(ph)PVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEPAAAAAPEAGASPVEK 18 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK 343.12 1.01E-75 2126810000 2749980 1591650 2035490 2147100 2272900 2721450 3462830 2361630 2199610 1243410 TRUE FALSE 2858551.334 1865003.506 2088536.542 2571789.972 1886553.27 2089434.481 3191404.336 2329976.213 2120446.466 1487032.383 1.922319491 1.254178139 1.404499704 1.729478121 1.26866993 1.405103551 2.146156582 1.566863129 1.4259585 1 20.50400463 GEPGRPALYFCGSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEPGRPALYFCGSIR 15 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 117.4 0.00034009 1411580000 1178160 1003090 994100 912050 1331740 1473270 1279990 1104560 1214400 1341300 FALSE TRUE 1224674.667 1175362.905 1020007.063 1092450.768 1105371.31 1131125.37 1179661.039 1089755.18 1170693.981 1604102.054 0.763464309 0.732723271 0.63587417 0.681035702 0.68909039 0.705145516 0.735402736 0.679355267 0.729812656 1 20.6133345 0.829047139 5.692254795 0.999999528 0.701129792 0.873656859 0.033702095 1.353761027 44.97532531 0.033078517 0.008328101 6.746012463 -0.829047139 -0.298869736 GEPNVS(ph)YICSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.808)Y(0.191)ICS(0.001)R;GEPNVS(0.999)Y(0.001)ICSR;GEPNVS(0.999)Y(0.001)ICSR;GEPNVS(0.995)Y(0.005)ICSR;GEPNVS(0.989)Y(0.011)ICSR 294 1.64E-35 26587130000 1272184 1504779 1395670 1368197 1472918 1602645 1328356 1397979 1316649 1474896 TRUE FALSE 1322410.807 1763213.088 1432042.307 1638822.283 1222551.924 1230454.987 1224235.986 1379241.378 1269263.06 1763873.633 0.749719698 0.999625515 0.811873527 0.929104133 0.693106298 0.697586814 0.69406105 0.781938883 0.719588431 1 20.75031578 3.239350618 24.99999995 0.747834999 0.877319122 0.190321338 0.105908068 27.4120165 867446.7849 0.027447808 0.035084889 1735.204313 -3.239350618 0.129484123 GEPNVSY(ph)ICSR ddPTM_MDA-MB-175_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(0.452)Y(0.548)ICSR;GEPNVS(0.237)Y(0.763)ICSR;GEPNVS(0.484)Y(0.516)ICSR;GEPNVS(0.337)Y(0.663)ICSR 175.49 0.00010065 1109117000 659414 530147 560928 465826 731571 791649 594878 562196 566264 555552 TRUE FALSE 685448.1739 621195.6233 575546.2445 557964.9924 607218.8227 607800.5173 548249.9079 554660.6822 545884.2693 664401.7777 1.031677212 0.934969839 0.866262349 0.839800571 0.91393317 0.914808686 0.825178268 0.83482721 0.821617713 1 19.34169641 4.603629379 2.189414747 0.867865358 1.050856992 0.44110879 0.052702903 0.396785013 2.689448498 0.013047038 0.126155941 40144.80742 -4.603629379 0.182991634 GEPPHSELHPMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEPPHSELHPMK 12 0 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98 B4DR80 STK24 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit 0 ;;; 125.82 0.00017262 436019000 378434 453246 496025 459875 572037 606298 521861 490911 502834 501458 FALSE TRUE 393374.8665 531087.4747 508951.819 550836.9024 474802.3551 465494.478 480956.1712 484331.141 484737.1026 599709.0941 0.655942807 0.885575156 0.848664501 0.918506836 0.791721119 0.776200466 0.801982454 0.807610133 0.808287063 1 19.19390332 -2.181639258 2.20869455 1.466972786 0.814614959 0.420042002 0.06664352 6499916.812 1255474.307 15192707.33 0.016748022 0.006582043 2.181639258 -0.652357827 GEQVSQNGLPAEQGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEQVSQNGLPAEQGSPR 17 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR 367.76 1.18E-104 2338840000 1066053 1169930 1058815 1293160 1125210 1361480 1350910 1148490 1101310 1101659 TRUE FALSE 1108141.596 1370856.377 1086408.589 1548943.188 933947.2061 1045296.903 1245022.144 1133096.37 1061674.068 1317507.989 0.84108909 1.04049189 0.824593549 1.175661326 0.708874037 0.793389423 0.944982615 0.860029981 0.805819834 1 20.32938028 3.21426208 24.99973109 0.850010352 0.965042675 0.190728761 0.119096017 376.6542411 387522.516 0.032540662 0.038910624 1637.804575 -3.21426208 0.115032323 GERDS(ph)QTQAILTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GERDSQTQAILTK 13 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 GERDS(0.997)QT(0.003)QAILTK 89.468 0.0045031 122330000 95980 88379 96924 84191 109510 103990 96709 88155 99480 82608 TRUE FALSE 99769.36451 103557.4058 99449.91906 100843.7285 90895.52932 79839.89848 89128.69588 86973.42642 95899.73423 98793.45597 1.009878271 1.048221309 1.006644803 1.020753121 0.920056176 0.808149666 0.902172062 0.880356149 0.970709378 1 16.59212786 3.201687912 4.644718071 0.898913975 1.023017948 0.517416793 0.050134763 0.137180495 6.701534908 0.014127567 0.017637339 1591.064964 -3.201687912 0.124103973 GES(ph)ENAGTNQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 GES(1)ENAGTNQETR;GES(1)ENAGTNQETR 329.77 2.26E-62 352500000 283060 305690 325860 342450 358190 409390 392480 344490 347620 272150 TRUE FALSE 294235.4274 358189.8796 334352.1793 410185.5879 297304.9917 314315.3769 361716.392 339872.675 335109.2241 325472.5819 0.904025235 1.100522439 1.027282167 1.260276935 0.913456335 0.965719985 1.111357491 1.044243644 1.029608154 1 18.31217649 0.93988054 3.41444325 1.000132323 1.046095399 0.013178865 0.098838529 1.567802199 46.26317982 0.090846046 0.023540441 8.707240498 -0.93988054 0.045963076 GES(ph)LDNLDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GESLDNLDSPR 11 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 GES(1)LDNLDSPR;GES(1)LDNLDSPR;GES(1)LDNLDSPR;GES(1)LDNLDSPR 217.68 1.17E-11 1545760000 962860 1107720 1126880 1071360 1224380 1290400 1179860 1214000 1153490 1083410 TRUE FALSE 1000874.456 1297962.293 1156247.419 1283271.81 1016260.325 990724.1562 1087379.49 1197728.316 1111976.12 1295683.446 0.772468352 1.001758799 0.892384187 0.990420781 0.784343064 0.764634417 0.839232371 0.924398872 0.858215889 1 20.30528186 -0.295502364 1.08978084 1.001735038 0.873992844 0.188642145 0.080376365 43.59525001 33.34714847 0.426946443 0.024170368 0.506404592 0.295502364 -0.127742193 GESAEDKEHEEGRDS(ph)EEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 248.58 1.49E-30 1593343000 1117660 674786 756989 701791 954946 1014100 1184765 785283 875850 475140 TRUE FALSE 1161786.08 790675.2464 776716.7552 840603.1652 792624.62 778590.6438 1091900.023 774757.5658 844328.3296 568234.5859 2.04455362 1.391459207 1.366894544 1.479324184 1.394889786 1.370192282 1.921565583 1.363446691 1.485879865 1 19.11612712 0.520752769 1.468465141 1.000475978 1.530678227 0.328136323 0.231493583 2.658520355 6.857576627 0.211289932 0.06139595 3.317055736 -0.520752769 0.53020225 GESDPAYQQYQDAANNLREDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GESDPAYQQYQDAANNLREDYK 22 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 123.99 2.13E-05 547520000 406400 291419 345650 278895 505620 489820 364950 372160 396450 291049 FALSE TRUE 422444.9858 341467.9463 354657.923 334059.5986 419674.893 376066.7283 336344.2654 367171.8039 382181.8419 348074.4791 1.213662625 0.981019773 1.018913894 0.959735972 1.205704291 1.080420286 0.966299702 1.054865628 1.097988692 1 18.40903651 0.224177824 0.006714383 0.000151649 2.06983844 0.050247736 0.085539524 27723.44172 65.5903254 10315.87041 9899.165279 1.675628829 -0.224177824 2.069686791 GESEDDFWWCIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 332.56 4.10E-62 972345000 592527 708153 638017 735794 692371 821273 712792 705668 691371 681226 FALSE TRUE 615920.4235 829772.7691 654644.2472 881331.8571 574682.0247 630544.7923 656921.5005 696209.6747 666488.6928 814699.1918 0.756009616 1.018502016 0.803541054 1.081788059 0.705391672 0.773960253 0.806336261 0.854560409 0.818079482 1 19.63590795 5.040244542 15.67892544 0.863099757 0.298181166 0.079606981 0.115066452 5678836.477 62797205.19 0.026244555 91200168.9 109709.5774 -5.040244542 -0.56491859 GESFYQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GESFYQDR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 153.08 0.0010393 906470000 770060 908440 801240 802540 932120 981560 803640 832310 688240 914820 FALSE TRUE 800462.5634 1064457.503 822120.9726 961280.0167 773678.5753 753607.5657 740648.5969 821154.2458 663470.3768 1094061.464 0.731643139 0.972941227 0.751439476 0.878634381 0.707161893 0.688816479 0.676971652 0.750555863 0.606428797 1 20.06126236 3.230442004 24.96804445 0.72138488 0.837739672 0.13038375 0.115578462 271.8717556 836115.7746 0.03025861 0.036763226 1699.972925 -3.230442004 0.116354792 GESLSLPGPS(ph)PPPDGTEQVIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GESLSLPGPSPPPDGTEQVIISR 23 0 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 GESLSLPGPS(1)PPPDGTEQVIISR 112.11 0.00057633 57093000 106120 137190 132820 123570 131930 160170 118340 116890 117640 131650 TRUE FALSE 110309.6995 160751.3153 136281.3983 148011.7772 109504.5857 122972.9449 109064.2016 115323.2807 113406.1594 157444.2969 0.700626836 1.021004371 0.865584851 0.940089797 0.695513193 0.781056839 0.692716114 0.732470359 0.720293854 1 17.26448197 3.240002359 24.99871693 0.750793542 0.890607634 0.176675115 0.112643362 48.79910134 846126.6849 0.029096943 0.037361249 1737.810267 -3.240002359 0.139814092 GETEERKDS(ph)DDEKSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GETEERKDSDDEKSDR 16 3 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 GETEERKDS(0.99)DDEKS(0.01)DR 90.729 0.029575 455840000 1000900 557270 527820 416420 700320 968760 437690 468530 519270 769400 TRUE FALSE 1040416.305 652976.7875 541575.4228 498786.6331 581279.8565 743780.1717 403382.7141 462250.1217 500581.5741 920149.1989 1.130703919 0.709642293 0.588573487 0.542071475 0.631723483 0.80832562 0.438388377 0.502364315 0.544022181 1 19.81150828 4.738212404 2.625043028 0.602447544 1.238870304 0.465834574 0.156769762 0.377363168 3.393134525 0.037079565 0.528150552 54728.35613 -4.738212404 0.63642276 GEVPAELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEVPAELRR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 88.267 0.020684 66565000 45142 64040 48381 57776 57678 61913 46061 55963 46563 63116 FALSE TRUE 46924.24102 75038.37184 49641.84861 69203.92036 47873.91416 47534.64405 42450.61846 55212.90752 44887.20673 75482.37177 0.621658275 0.994117833 0.657661484 0.916822282 0.634239665 0.629744971 0.562391158 0.731467576 0.594671387 1 16.20385213 GEVPPKET(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK 94.688 0.012769 1157280000 4194720 1151230 1659360 1087460 2554290 2896080 2507170 1744360 1861580 861050 TRUE FALSE 4360330.785 1348944.797 1702604.285 1302556.342 2120112.698 2223509.311 2310651.464 1720979.707 1794582.099 1029756.262 4.234332868 1.309965132 1.653405129 1.264917137 2.058849047 2.159257868 2.243881926 1.671249568 1.742725115 1 19.97387147 4.744537889 24.96124486 1.735092009 4.234333983 0.796321413 0.386854925 287.8665872 1202103.78 0.092563132 0.846134898 55531.3062 -4.744537889 2.499241974 GEVQFGSWFDHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEVQFGSWFDHIK 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 156.24 4.71E-05 473990000 192280 176450 202580 186780 242170 249990 239280 198770 214020 169700 FALSE TRUE 199871.3629 206753.9149 207859.4012 223724.5265 201006.0299 191933.6111 220524.6084 196105.8133 206317.462 202949.4659 0.984833155 1.018745795 1.024192896 1.102365683 0.99042404 0.945721194 1.086598614 0.966279031 1.016595245 1 17.63076102 GEVQVSDKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GEVQVSDKER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;;;; 199.7 2.50E-07 2922550000 2941170 2395708 2699890 2105047 3768560 3277730 3079660 2659481 2843477 2865054 FALSE TRUE 3057289.663 2807152.213 2770251.351 2521419.014 3127981.517 2516526.882 2838268.202 2623835.007 2741140.818 3426406.477 0.892272906 0.819270052 0.808500501 0.735878545 0.912904391 0.734450772 0.828351283 0.765768751 0.800004564 1 21.70826488 -1.079225495 3.623859746 1.000087972 0.807226621 0.507444211 0.055813408 5957656.58 10787370.11 6421.127571 0.013185408 0.083324843 1.079225495 -0.192861351 GEVWGPGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEVWGPGYR 9 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 95.531 0.01857 128370000 62151 77798 70740 68294 83768 94991 59831 76040 68533 67967 FALSE TRUE 64604.76947 91159.20132 72583.54251 81802.34936 69529.14528 72930.77985 55141.28988 75020.80818 66066.51072 81283.83234 0.794804669 1.121492414 0.892964079 1.006379092 0.855387145 0.897235991 0.678379553 0.92294871 0.812787842 1 16.3106808 3.220108601 22.5456541 0.851017823 0.961526901 0.140845214 0.109949219 119.8432541 146429.8196 0.029491595 0.035339806 1660.001959 -3.220108601 0.110509078 GEWFLLGSPGS(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GEWFLLGSPGS 11 0 Q96T76-5;Q96T76;Q96T76-8;Q96T76-9;H0Y746;H0Y7V3 Q96T76-5 MMS19 MMS19 nucleotide excision repair protein homolog 1 GEWFLLGS(0.414)PGS(0.586) 76.927 0.035679 5403200 12502 17381 16500 20740 17229 20585 16214 15968 15605 19692 TRUE FALSE 12995.58861 20366.05154 16930.00355 24842.3101 14300.42073 15804.44572 14943.10431 15753.97508 15043.3791 23550.27037 0.55182333 0.864790562 0.718887864 1.054863053 0.607229578 0.671094024 0.634519438 0.668950922 0.638777341 1 14.523456 GEWKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GEWKPR 6 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;; 122.98 0.017316 16457800000 15244910 14286250 14303450 14294570 19502390 18139450 16335360 13968750 13678350 14259010 FALSE TRUE 15846790.82 16739802.31 14676209.66 17121993.28 16187380.71 13926837.64 15054951.8 13781521.75 13186068.86 17052790 0.929278483 0.981645954 0.860633929 1.004058179 0.949251161 0.816689682 0.88284391 0.80816815 0.77324994 1 24.02350446 2.747050323 23.95096221 0.843752293 0.945607853 0.295527583 0.067176168 377.4119905 1064745.077 0.019420673 0.02028455 558.5349107 -2.747050323 0.101855559 GEYNVYSTFQSHEPEFDYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GEYNVYSTFQSHEPEFDYLK 20 0 P63151;P63151-2;E5RIY1;Q00005-3;Q00005-5;Q00005-4;Q66LE6;Q00005-2;Q00005;Q00005-6;Q00005-7;H0YB06 P63151 PPP2R2A;PPP2R2B;PPP2R2D Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform 0 ; 256 3.57E-36 314500000 506560 472370 539910 426360 672450 697080 597110 571020 595960 509050 FALSE TRUE 526559.3799 553495.873 553980.4981 510692.7354 558147.1892 535193.7343 550306.9579 563366.4109 574511.516 608788.6011 0.864929762 0.909175816 0.909971864 0.838867112 0.916816097 0.879112607 0.903937684 0.925389224 0.943696244 1 19.21558182 1.089975893 0.845430871 0.999631846 0.886239068 0.72284055 0.022082968 0.29877946 0.478195486 0.019903527 0.007230104 12.30200484 -1.089975893 -0.113392777 GEYWECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GEYWECK 7 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 ;; 117.17 0.01231 1034750000 402442 338269 389902 351694 494410 477260 422423 375995 438030 353070 FALSE TRUE 418330.7209 396364.0694 400063.1664 421258.0235 410370.3648 366423.5979 389312.3815 370955.402 422265.3859 422247.3066 0.990724427 0.938701238 0.947461737 0.9976571 0.971872072 0.867793808 0.922000864 0.87852639 1.000042817 1 18.68772869 GFAFVEFSHLQDATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFAFVEFSHLQDATR 15 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 0 73.593 0.020126 0 109940 152920 153950 114280 172940 172370 118060 144610 166570 171370 FALSE TRUE 114280.5161 179182.8204 157962.0635 136884.2429 143543.7206 132339.6798 108806.1487 142671.7395 160575.1782 204946.6704 0.557610991 0.87428998 0.770747157 0.667901765 0.700395475 0.645727396 0.530899812 0.696140802 0.783497375 1 17.64488903 0.89624188 2.756737362 0.999429819 0.682542765 0.526734083 0.092310568 0.337940723 5.500412017 0.090484881 0.023986428 7.874842565 -0.89624188 -0.316887053 GFAFVEYESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFAFVEYESHR 11 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;F8W9F8;Q5T0W7;Q8TBY0-2;Q8TBY0-3;Q8TBY0;Q9NQ94-6;Q9NQ94-3;Q9NQ94-2;Q9NQ94;Q9NQ94-4;Q9NQ94-5 B7Z8Z7 RBM47;A1CF;RBM46 RNA-binding protein 47;Probable RNA-binding protein 46;APOBEC1 complementation factor 0 131.83 0.00019525 330390000 124990 156330 131740 148660 194760 201730 155690 148550 143010 197550 FALSE TRUE 129924.7017 183178.4614 135173.2526 178064.5043 161654.7648 154881.2647 143486.611 146558.9302 137863.098 236256.1402 0.549931535 0.775338416 0.572147046 0.753692599 0.684235189 0.655565035 0.60733495 0.620339138 0.583532339 1 17.8499923 -1.267539563 4.574502445 1.000157234 0.647477147 0.691449269 0.071185231 0.000106378 1.70E-05 0.064231609 0.015132828 0.054008291 1.267539563 -0.352680087 GFAFVQYVNER ddPTM_MDA-MB-175_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 ; 175.93 2.15E-05 1612920000 500630 560300 407180 495470 810530 714460 510060 423400 409090 1025920 FALSE TRUE 520395.259 656527.1665 417791.4453 593472.4872 672756.4001 548537.4927 470080.1644 417725.0155 394366.9308 1226929.382 0.424144427 0.535097762 0.340517924 0.483705498 0.548325283 0.447081553 0.383135469 0.34046378 0.321425941 1 20.22662078 -1.640128344 3.111624652 1.043733506 0.423674544 0.83683151 0.076185309 56942468.84 61847524.22 20083436.2 0.020311317 0.022901907 1.640128344 -0.620058963 GFAFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFAFVR 6 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ; 105.82 0.075953 1244920000 919300 1201520 981380 1049440 1663430 1497370 1165740 1140290 1029220 1964800 FALSE TRUE 955594.6739 1407871.713 1006955.569 1257016.1 1380680.763 1149628.51 1074366.253 1125006.278 992178.5732 2349764.942 0.406676709 0.599154276 0.428534596 0.534953977 0.587582502 0.489252559 0.457222862 0.478773965 0.422245883 1 21.16408501 -1.776815273 2.920856339 1.113083469 0.492651086 0.854118812 0.063295444 20381103.37 18863282.77 16592271.06 0.015314821 0.016718016 1.776815273 -0.620432383 GFAFVTFDDHDSVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 279.29 1.18E-33 12916035000 3461963.8 7597463 8549186 8913081 8758283 9812228 10805178 9210085 8651233 6541407 FALSE TRUE 3598644.804 8902268.17 8771984.81 10676061.82 7269553.184 7533486.753 9958239.914 9086638.875 8339876.814 7823070.459 0.460004141 1.137950657 1.12129692 1.364689462 0.929245521 0.96298337 1.272932408 1.16151822 1.066061831 1 22.89930353 4.73925247 24.93793413 1.124748381 0.460003928 0.69929903 0.128243528 30.21708228 1088954.763 0.030534664 0.183544438 54859.57891 -4.73925247 -0.664744453 GFAFVTFDDHDSVDKIVIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 210.75 2.04E-22 400203000 46427 72908 95065 59269 122303 108566 81407 97612 102940 83868 FALSE TRUE 48259.97381 85429.38185 97542.472 70992.2313 101513.9797 83353.19183 75026.10662 96303.6708 99235.20951 100300.3289 0.481154692 0.85173581 0.97250401 0.707796596 1.012100169 0.831036077 0.748014563 0.960153091 0.989380699 1 16.61396681 4.732192919 4.267645472 0.892345455 0.45191 0.598889949 0.102530734 0.134972432 5.732002749 0.023552122 0.179525712 53975.03336 -4.732192919 -0.440435455 GFAFVTFDDHDTVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;;;; 292.76 5.85E-44 6570860200 5675552 4491643.5 5463581.6 4911622.7 6357806.9 6740287.8 7361635.8 5753857.6 5815636.3 3825961.3 FALSE TRUE 5899627.175 5263048.331 5605967.025 5883127.01 5277109.154 5174958.108 6784611.55 5676736.55 5606332.686 4575585.164 1.289371078 1.150245956 1.225191276 1.285764946 1.153318967 1.130993725 1.482785547 1.240658046 1.225271191 1 22.12552483 GFAFVTFDDHDTVDKIVVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFAFVTFDDHDTVDKIVVQK 20 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 290.16 1.16E-54 2351854000 2351340 1805507 2695192 1414893 3412785 2930559 2251803 2452531 2927911 2121819 FALSE TRUE 2444172.719 2115588.782 2765430.918 1694754.612 2832681.025 2249981.085 2075300.797 2419658.833 2822536.055 2537548.808 0.963202249 0.833713533 1.08980403 0.667870745 1.116306025 0.886674998 0.8178368 0.95354179 1.112308085 1 21.27500414 1.41071717 6.193430982 1.052695539 0.910549807 0.172648838 0.125538098 0.332080359 20.7132579 0.07711314 0.02872982 25.74643897 -1.41071717 -0.142145732 GFAFVTFES(ph)PADAK ddPTM_MDA-MB-175_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 161.04 4.89E-06 80254000 271840 140644 187960 176109 232160 253900 245160 195883 211150 144829 TRUE FALSE 282572.4531 164798.5129 192858.392 210942.8346 192697.5261 194935.5729 225943.7186 193257.5088 203550.7527 173205.4696 1.631429156 0.951462522 1.113465946 1.217876289 1.112537188 1.125458528 1.304483739 1.115770242 1.17519818 1 17.40212496 7.999999731 0.018706056 1.08E-06 2.645478377 0.151184693 0.165111827 8486.291365 12.2380245 654.065918 1138.605969 99999938.13 -7.999999731 2.645477296 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFAVLEYETAEMAEEAQQQADGLSLGGSHLR 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 0 ;; 202.85 8.71E-26 144422000 39992.9 72181.8 68080.4 70169.2 68445.8 77257.7 68807.4 66909.4 62457.8 83605.9 FALSE TRUE 41571.85057 84578.46265 69854.63115 84048.45833 56811.40736 59315.77003 63414.09619 66012.58893 60209.95598 99986.87537 0.415773074 0.845895647 0.698638005 0.840594908 0.568188646 0.59323556 0.634224201 0.66021254 0.602178593 1 16.60945111 -1.818404289 2.53692324 1.118025479 0.659034552 0.429132934 0.120439961 16486695.72 10886679.03 11904147.93 0.029899129 0.015191327 1.818404289 -0.458990927 GFAYVQFEDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 157.66 7.09E-05 357695000 319787 408866 340000 345700 454987 476070 381228 346810 332794 495517 FALSE TRUE 332412.4377 479085.555 348860.6793 414078.4282 377648.4723 365509.9574 351346.3532 342161.5792 320816.8089 592604.0689 0.560935125 0.808441218 0.588690996 0.698743816 0.637269455 0.616786108 0.592885489 0.577386483 0.541367881 1 19.17670901 -1.906876079 4.729015735 1.13552748 0.626395715 0.697164708 0.074193465 0.044639783 0.000879048 0.030248806 0.016597745 0.012391501 1.906876079 -0.509131764 GFAYVQFEDVRDAEDALHNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 286.38 2.28E-46 781346000 257754 378692 339333 292093 401917 387977 252322 324608 325342 482526 FALSE TRUE 267930.3269 443729.4052 348176.2967 349868.1236 333599.2919 297875.2216 232544.3423 320257.1607 313633.005 577067.7312 0.464296152 0.76893817 0.6033543 0.606286064 0.578093825 0.516187625 0.40297582 0.554973261 0.543494269 1 19.13838113 -1.492619583 6.284163525 1.000284726 0.560570981 0.674760384 0.091674492 0.000376299 3.04E-05 0.091336138 0.021514561 0.032164768 1.492619583 -0.439713745 GFAYVQFEDVRDAEDALHNLDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 169.84 4.82E-12 212315000 145126 137398 165009 91446 233144 183584 106525 141392 176708 216182 FALSE TRUE 150855.6865 160995.0377 169309.2701 109533.7459 193514.2662 140949.3982 98175.29215 139496.8715 170348.3136 258538.7238 0.583493584 0.622711504 0.654870062 0.423664758 0.748492386 0.545177125 0.37973148 0.539558908 0.658888971 1 17.98002086 0.854988634 3.574230119 0.99987821 0.55929805 0.630600723 0.100447103 0.471279966 10.41056346 0.097104444 0.025021503 7.161246678 -0.854988634 -0.44058016 GFCFITFKEEEPVKK ddPTM_MDA-MB-175_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 ; 188.31 1.71E-07 3186700000 1585650 633080 1017620 552010 1665940 1132620 1212830 1027810 1240280 577670 FALSE TRUE 1648252.686 741806.5653 1044140.013 661195.9304 1382764.114 869586.17 1117765.215 1014033.888 1195642.565 690853.3763 2.38582128 1.073753984 1.511377159 0.957071288 2.001530515 1.258713064 1.617948546 1.46779899 1.730674852 1 19.39802003 -1.817529304 2.517609408 0.817694205 1.525359316 0.142817358 0.402413797 45405291.26 29874695.72 50295698.3 0.087901989 0.015221964 1.817529304 0.707665111 GFCFITYTDEEPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFCFITYTDEEPVKK 15 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 218.16 3.17E-12 953600000 361350 207600 292540 180330 408760 349060 323960 306960 363170 226590 FALSE TRUE 375616.377 243253.6851 300163.8327 215998.7358 339279.1212 267996.1051 298567.1687 302845.7033 350099.5826 270985.9722 1.386110041 0.89766154 1.107672956 0.797084565 1.252017285 0.988966709 1.101780901 1.117569669 1.291947254 1 18.04785865 1.711403653 2.996536837 1.157995748 1.061414397 0.021703996 0.17041606 0.718386091 14.20307894 0.095129939 0.043219861 51.45216493 -1.711403653 -0.096581351 GFCFLEYEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 247.31 4.23E-16 11928990000 8110769.3 5940032.8 7044692.1 5866713.7 8771822.1 8127267.6 8393677.5 7175764.3 7675581 5737795.2 FALSE TRUE 8430988.735 6960187.226 7228282.563 7027132.159 7280790.913 6239832.87 7735759.125 7079584.917 7399338.339 6862006.313 1.228647767 1.014307902 1.053377428 1.024063785 1.061029469 0.90933068 1.127331974 1.031707724 1.078305382 1 22.71019902 4.742468952 24.84187272 1.0357774 1.228647849 0.541661692 0.05387189 263.6900409 1675973.47 0.012010609 0.091241631 55267.38955 -4.742468952 0.192870449 GFCYVEFDEVDSLKEALTYDGALLGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GFCYVEFDEVDSLKEALTYDGALLGDR 27 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;; 356.21 1.83E-110 4322466500 2139488.9 1998810 2375336.3 1762366 2996236 2868015 2262424.4 2385195 2688411 2508527 FALSE TRUE 2223957.574 2342090.069 2437239.515 2110956.735 2486936.875 2201961.981 2085089.664 2353225.362 2591655.613 3000024.837 0.741313054 0.780690226 0.812406446 0.703646419 0.828972095 0.733981251 0.695024134 0.78440196 0.863878052 1 21.51654301 0.979099239 2.232789101 0.998838048 0.758473006 0.773970307 0.040755488 0.139129735 1.527220391 0.037794996 0.010386559 9.530139095 -0.979099239 -0.240365042 GFDEYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFDEYMK 7 0 Q01469 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 ; 105.95 0.018175 289005000 334490 316920 347160 284620 444660 406060 377840 337740 364980 332180 FALSE TRUE 347695.9235 371348.5447 356207.2748 340916.9865 369076.852 311758.7189 348223.9135 333213.1477 351844.4411 397264.311 0.875225672 0.934764424 0.89665058 0.858161624 0.929046083 0.784763973 0.876554737 0.8387694 0.885668386 1 18.59973967 3.912336289 5.549034095 0.871099543 0.907481481 0.002821775 0.055384996 0.571062849 27.86518782 0.013262342 0.024644977 8172.149234 -3.912336289 0.036381938 GFDILGIKPVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFDILGIKPVQR 12 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 137.16 0.00026095 0 1192500 993240 1115100 945610 1441900 1309000 1237000 1157000 1106000 911030 FALSE TRUE 1239580.821 1163821.244 1144160.422 1132648.836 1196806.353 1005004.588 1140040.708 1141492.307 1066195.276 1089528.886 1.137721851 1.068187598 1.050142348 1.039576693 1.098462252 0.922421242 1.046361159 1.047693478 0.978583762 1 20.05527302 8 0.423043581 1.011918671 3.289190433 0.446006862 0.042853987 77.89435295 0.993639392 0.027493651 150.4133305 99999999.99 -8 2.277271762 GFDPLLNLVLDGTIEYMRDPDDQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFDPLLNLVLDGTIEYMRDPDDQYK 25 1 Q9UK45 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 95.195 2.57E-05 0 56479 42178 53361 42715 62844 63036 67144 44956 54385 33704 FALSE TRUE 58708.83453 49421.7434 54751.6315 51163.89951 52161.79933 48396.84432 61881.07783 44353.43835 52427.69447 40307.6535 1.45651829 1.226113135 1.358343311 1.269334607 1.294091687 1.200686225 1.535219058 1.100372622 1.300688329 1 15.29876618 -4.39950849 0.187150294 1.63E-10 1.357775065 0.404596011 0.115147997 102.0049581 1.218589501 38.17637251 0.306947355 3.99E-05 4.39950849 1.357775065 GFDQTINLILDESHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 ;;;;; 254.72 1.37E-26 1880100000 1134520 1354180 1283560 1332440 1341980 1484660 1284860 1288260 1256880 1452630 FALSE TRUE 1179311.726 1586749.881 1317010.628 1595992.655 1113870.719 1139870.215 1184149.316 1270992.982 1211645.134 1737245.036 0.678840176 0.913371371 0.758102974 0.918691734 0.641170759 0.656136694 0.681624809 0.73161411 0.697452063 1 20.72836983 5.041858099 15.17555372 0.76145252 0.322201865 0.04345473 0.119011598 5529466.911 58541556.95 0.027606834 66897027.02 110117.9453 -5.041858099 -0.439250655 GFEGSFEELCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GFEGSFEELCR 11 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ;;;; 244.61 1.60E-15 537313000 568151 592667 553585 659265 687278 784272 550828 568286 580258 625935 FALSE TRUE 590582.0402 694452.9469 568011.8799 789665.6493 570454.731 602136.7138 507652.662 560669.0557 559374.6279 748574.979 0.788941732 0.927699918 0.758790897 1.054891856 0.762054232 0.804377291 0.678158737 0.748981827 0.747252638 1 19.5137873 GFEKPTENSSAVLLQWHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFEKPTENSSAVLLQWHEK 19 1 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 174.74 2.34E-12 750830000 1306600 671470 868080 662330 1207900 1130500 1155200 938150 1133100 718710 FALSE TRUE 1358185.577 786789.7492 890702.8779 793336.8971 1002581.589 867958.5079 1064652.405 925575.6338 1092319.952 859527.464 1.580153787 0.915374764 1.036270411 0.922991912 1.166433455 1.009808929 1.238648502 1.076842419 1.270837755 1 19.71318421 2.246003932 24.99647656 1.147886882 1.087916852 0.006330951 0.19091195 872.4986342 2930066.821 0.063824177 0.052442162 176.1991999 -2.246003932 -0.05997003 GFENVIHDKLPLQES(ph)EEEEREER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFENVIHDKLPLQESEEEEREER 23 2 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 GFENVIHDKLPLQES(1)EEEEREER;GFENVIHDKLPLQES(1)EEEEREER 80.847 0.0055562 246700000 97334 81772 82433 74256 105966 108049 90421 86415 106228 85983 TRUE FALSE 101176.8215 95815.7049 84581.2717 88943.61517 87953.93717 82956.25725 83333.56575 85256.74827 102404.875 102829.7226 0.983925843 0.931789977 0.822537196 0.864960178 0.855335743 0.806734232 0.810403487 0.829106081 0.995868436 1 16.64989781 1.230751517 24.99059477 0.997934349 0.857968745 0.504571252 0.053249408 159.9491772 511846.9382 0.051216673 0.013748851 17.0118489 -1.230751517 -0.139965604 GFESPSDNSSAMLLQWHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ; 303.86 3.55E-50 940590000 873110 840460 960850 840460 1103340 1124690 971060 984180 930210 873680 FALSE TRUE 907581.057 984802.4671 985890.5403 1006700.479 915794.6609 863497.7923 894945.7798 970988.6769 896731.9238 1044860.868 0.868614267 0.942520193 0.94356155 0.963478019 0.876475221 0.826423707 0.856521482 0.929299495 0.858230939 1 19.99487942 4.838991557 18.30337866 0.906102929 0.868574492 0.048814313 0.052299746 54702.07136 9939715.756 0.012694035 253.7018291 69022.63849 -4.838991557 -0.037528438 GFFDPNTEENLTYLQLMER ddPTM_MDA-MB-175_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 0 160.78 7.17E-11 49989000 9693.5 8158.9 5869.4 8226.9 9573.2 13493 11196 7376.2 7660.8 10708 FALSE TRUE 10076.20687 9560.127608 6022.361386 9854.156265 7945.950883 10359.45524 10318.42826 7277.334104 7385.089304 12806.02758 0.786833138 0.746533423 0.470275528 0.7694936 0.620485223 0.808951501 0.805747778 0.568274124 0.576688536 1 13.6445354 -1.330673523 15.84193715 1 0.680691522 0.414773463 0.112663516 0 0 0.108079068 0.025474481 0.046701032 1.330673523 -0.319308478 GFFDPNTHENLTYLQLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 295.65 1.11E-49 3972618000 3284570 4222600 3949600 4045300 4129800 4733460 4041900 3891320 3628720 4409540 FALSE TRUE 3414247.36 4947798.703 4052529.821 4845448.266 3427818.071 3634185.651 3725085.316 3839163.22 3498123.076 5273504.937 0.647434183 0.938237237 0.768469902 0.91882881 0.650007559 0.689140466 0.706377516 0.72800979 0.6633393 1 22.33033071 5.018095317 17.67203651 0.768859639 0.393872691 0.093927614 0.11907719 24784208.99 529983730.6 0.027418198 250119669.4 104254.6217 -5.018095317 -0.374986948 GFFDPNTHENLTYLQLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFFDPNTHENLTYLQLLQR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 227.04 1.36E-19 429130000 475950 538440 514930 512120 616910 656520 497790 512920 531840 615600 FALSE TRUE 494740.8735 630912.8815 528349.4988 613415.8075 512047.8586 504053.1797 458771.9191 506045.1464 512699.1823 736215.0336 0.672005937 0.856968213 0.717656493 0.833201958 0.695513994 0.684654831 0.623149349 0.687360517 0.696398686 1 19.48976768 -1.072262131 4.373159181 1.000023952 0.717829187 0.604098713 0.068352563 36455247967 7733654136 9489819.837 0.016665082 0.08467162 1.072262131 -0.282194765 GFFDPNTHENLTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFFDPNTHENLTYR 14 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 195.1 6.71E-08 3182620000 3236610 4102320 3580940 3907540 3869650 4465040 3664270 3692250 3560580 4377790 FALSE TRUE 3364393.862 4806861.548 3674262.238 4680439.749 3211888.275 3428102.128 3377054.943 3642761.428 3432435.421 5235534.133 0.642607569 0.918122474 0.701793197 0.893975596 0.613478624 0.654776006 0.645025867 0.695776464 0.655603676 1 22.3199053 GFFDPNTHENLTYVQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 237.3 7.60E-24 2249028000 1568098 1998629 1857249 1805935 1956081 2343815 1913536 1891300 1781328 2132417 FALSE TRUE 1630007.72 2341877.984 1905650.435 2163143.553 1623587.05 1799499.487 1763548.048 1865950.217 1717218.353 2550223.284 0.639162747 0.918303114 0.747248465 0.848217318 0.636645058 0.705624287 0.691526918 0.731681116 0.673360001 1 21.28219214 -1.104522329 3.875551731 1.000082247 0.736051069 0.471665948 0.084881573 4572875.861 2608131.255 3165.207285 0.019262855 0.078609977 1.104522329 -0.264031178 GFFNIYHPLDPVAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFFNIYHPLDPVAYR 15 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 109.83 0.00096944 983200000 625780 738030 675180 724720 868280 904560 711760 756310 714700 913310 FALSE TRUE 650486.2776 864780.9114 692775.7455 868067.4529 720690.0757 694489.6487 655970.3914 746172.9015 688978.0866 1092255.608 0.595544003 0.791738587 0.63426156 0.794747536 0.659818151 0.635830701 0.60056491 0.683148611 0.630784664 1 20.05887908 -1.958787135 2.580362778 1.256482343 0.672345321 0.685357696 0.067136089 5760590.348 2802582.708 8844905.706 0.015490835 0.010995446 1.958787135 -0.584137022 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GFGDGYNGYGGGPGGGNFGGSPGYGGGR 28 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR 297.91 1.39E-71 2399460000 1333756 1472223 1341687 1357726 1443193 1683669 1354343 1371636 1282110 1553778 TRUE FALSE 1386413.717 1725065.848 1376652.465 1626280.15 1197879.569 1292662.391 1248186.057 1353251.463 1235967.112 1858211.05 0.74610132 0.928347643 0.740848283 0.875185922 0.64464129 0.695648856 0.671713827 0.728254986 0.665138178 1 20.82548294 3.245004337 24.99602082 0.715456748 0.824331814 0.123959363 0.108386444 238.5742922 925454.6122 0.027417497 0.036254247 1757.94117 -3.245004337 0.108875066 GFGDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGDLK 6 0 P24534;C9JZW3;F2Z2G2;F8WF65;F8WFC9 P24534 EEF1B2 Elongation factor 1-beta 0 102.98 0.081604 174790000 743910 590270 694940 578940 831780 847180 855170 731050 738340 627590 FALSE TRUE 773280.1412 691644.2808 713050.7073 693452.604 690394.3327 650435.2841 788139.5408 721251.4705 711767.2876 750554.2446 1.03027882 0.921511384 0.950032209 0.923920701 0.919846017 0.866606629 1.050076722 0.960958486 0.948322247 1 19.51759682 2.236147214 24.99879898 0.986107623 0.934177169 0.252715884 0.045682556 95.6035479 990274.8608 0.016480957 0.012741472 172.245234 -2.236147214 -0.051930454 GFGDSFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFGDSFGR 8 0 A0A0A0MQW0;A0A0A0MR39;A0A087WUT0;H0YN19;A0A0C4DGV1 A0A0A0MQW0 MYEF2 0 ;;; 194.25 0.00038703 888160000 1431470 1767100 1616750 1641220 1773520 1949110 1589030 1661870 1483920 1903350 FALSE TRUE 1487985.541 2070585.679 1658883.833 1965848.417 1472057.704 1496458.742 1464477.676 1639595.351 1430514.009 2276274.991 0.653693226 0.909637758 0.728771278 0.863625188 0.6466959 0.657415623 0.643365886 0.720297573 0.628445164 1 21.11824343 4.032812331 24.99628493 0.719351212 0.791050265 0.006382146 0.124764602 580.640127 442321.8502 0.029014024 0.062676912 10784.80584 -4.032812331 0.071699053 GFGEYSRS(ph)PTF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFGEYSRSPTF 11 1 D6REL5;Q6UWZ7-2;Q6UWZ7 D6REL5 FAM175A BRCA1-A complex subunit Abraxas 1 GFGEYS(0.016)RS(0.93)PT(0.054)F;GFGEYS(0.001)RS(0.999)PTF;GFGEYS(0.003)RS(0.997)PTF 138 0.00017541 420485000 637766 862438 738411 579513 875442 930799 605406 737258 696943 1007856 TRUE FALSE 662945.4941 1010555.018 757654.5973 694138.9417 726634.6815 714635.0386 557952.6958 727376.2624 671860.1576 1205326.087 0.550013396 0.838407987 0.628588899 0.575893071 0.602853194 0.592897679 0.462906015 0.603468448 0.557409455 1 20.20099207 -1.506677029 6.190868228 1.000351216 0.602194039 0.637245944 0.090223928 0.000446682 3.56E-05 0.08921903 0.021011107 0.031140313 1.506677029 -0.398157177 GFGFGQGAGALVHS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 244.57 5.08E-18 12522310000 5252820 6204940 5978120 6023480 6136030 6744140 5806570 5967670 5595630 6290060 TRUE FALSE 5460205.39 7270590.177 6133914.718 7214906.366 5093029.812 5177915.693 5351435.871 5887683.145 5394244.369 7522476.827 0.725852072 0.966515464 0.81541158 0.959113139 0.677041609 0.688325908 0.711392802 0.782678801 0.717083548 1 22.84277633 3.233253359 24.99997561 0.747349101 0.870185986 0.173299698 0.108044606 180.3725356 849649.9291 0.028557704 0.035089748 1711.013195 -3.233253359 0.122836885 GFGFGQGAGALVHSE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGFGQGAGALVHSE 15 0 P21291;E9PP21 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 117.71 0.00081155 126397000 209580 231435 218072 213410 273690 280960 203349 223265 230749 304010 FALSE TRUE 217854.3802 271182.1609 223755.1355 255621.861 227168.2716 215711.298 187409.974 220272.4979 222444.3886 363574.9389 0.599200761 0.745876935 0.61543058 0.703078881 0.62481829 0.59330629 0.5154645 0.605851708 0.611825417 1 18.47189323 -1.479642947 4.780324412 1.001228245 0.62263603 0.784316978 0.059169096 0.000816203 8.88E-05 0.060372638 0.014186421 0.033140347 1.479642947 -0.378592215 GFGFVDFNSEEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 280.21 6.87E-33 378970000 927890 566860 728200 527270 930400 904680 879090 686570 773690 531490 FALSE TRUE 964523.8137 664213.7954 747177.4902 631562.4323 772250.9403 694581.7806 810184.6287 677367.6522 745845.048 635625.2895 1.517440904 1.04497698 1.175499941 0.993608094 1.214946845 1.092753533 1.274626171 1.065671337 1.173403671 1 19.277817 4.74550019 24.82665292 1.122334873 1.517441105 0.648256594 0.088775355 423.5010768 1515053.218 0.019124771 0.188999157 55654.48772 -4.74550019 0.395106233 GFGFVEFEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGFVEFEDPR 11 0 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 85.064 0.036048 159950000 175660 217260 190120 254840 177840 216960 242010 199540 176410 167880 FALSE TRUE 182595.1924 254572.715 195074.6834 305246.5914 147610.8203 166574.3281 223040.6238 196865.4927 170061.0386 200772.8717 0.909461477 1.267963708 0.971618734 1.520357749 0.735212975 0.829665515 1.110910164 0.980538312 0.847031957 1 17.61520482 3.207328921 24.99999936 0.929884354 1.160557279 0.307983161 0.18297477 255.1222557 204216.6995 0.051177812 0.061174721 1611.865951 -3.207328921 0.230672925 GFGFVEFEDPRDADDAVYELDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGFVEFEDPRDADDAVYELDGK 23 1 Q13243;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ; 193.87 4.39E-18 538320000 975890 779850 908080 628610 1208770 1070620 971510 931790 974160 772890 FALSE TRUE 1014418.891 913783.1711 931745.3108 752947.1818 1003303.707 821984.7304 895360.5076 919300.8792 939100.1719 924322.9976 1.097472305 0.988597247 1.008029999 0.814593149 1.085447089 0.889283002 0.968666267 0.994566706 1.015987024 1 19.81803755 4.832999253 2.036084747 0.968899774 1.156120891 0.221970933 0.070017264 1.431336327 5.238754667 0.016636007 0.539649235 68076.81877 -4.832999253 0.187221117 GFGFVR ddPTM_MDA-MB-175_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 ; 110.43 0.066786 644240000 815300 982960 846370 899680 1253270 1240620 960870 895490 870450 1195900 FALSE TRUE 847488.6735 1151775.734 868427.0975 1077634.019 1040239.613 952504.8068 885554.4986 883487.4213 839122.6745 1430213.708 0.592560866 0.805317224 0.607200933 0.753477618 0.727331592 0.665987748 0.619176347 0.617731054 0.586711391 1 20.44779931 -1.009844008 4.869768248 1.000005041 0.665524766 0.66816422 0.071040338 3.84E-06 7.80E-07 0.067843075 0.015990525 0.097758829 1.009844008 -0.334480275 GFGFVSFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 167.9 0.00013873 2600204000 926979 1284971 1101434 1079476 1459214 1379720 1206518 1180600 1079545 1736284 FALSE TRUE 963576.8467 1505654.774 1130138.275 1292993.131 1211177.325 1059300.94 1111947.967 1164775.988 1040692.386 2076475.607 0.464044385 0.725101113 0.544257911 0.622686405 0.583285121 0.510143696 0.535497727 0.560938922 0.501182091 1 20.98570549 -1.665696208 2.798141261 1.050474659 0.564791117 0.783724693 0.06918822 16912639.6 15363966.72 6099070.111 0.01568906 0.021592543 1.665696208 -0.485683542 GFGFVTFDDHDPVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;;; 242.07 6.56E-18 44620123000 46080680 28570240 36307270 31176370 43824750 40939490 47352870 37676670 38175540 24638891 FALSE TRUE 47899980.83 33476956.47 37253467.28 37342962.93 36375434.65 31431913.89 43641228.32 37171675.87 36801609.77 29466409.95 1.625579122 1.136105706 1.264268954 1.267306163 1.234471207 1.066703204 1.481050063 1.261493203 1.248934289 1 24.81256796 4.74796429 24.8384583 1.237913412 1.625579347 0.480841834 0.1255563 1019.939109 2693962.077 0.028370521 0.363521383 55971.15773 -4.74796429 0.387665935 GFGFVTFDDHDPVDKIVLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 284.38 3.36E-45 7516300000 7088700 5288000 6855600 3814100 9692800 7611100 5221400 5959400 7352600 6064500 FALSE TRUE 7368567.35 6196172.865 7034262.568 4568517.596 8045221.318 5843537.372 4812133.024 5879523.991 7087981.362 7252722.663 1.015972579 0.854323701 0.969878885 0.629903804 1.109269124 0.805702581 0.663493318 0.81066439 0.977285592 1 22.79009125 GFGFVTFENIDDAKDAMMAMNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGFVTFENIDDAKDAMMAMNGK 23 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;K7ENX8;K7ELV6;K7EJV5;K7ELT6;K7ER40 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 326.67 1.83E-86 895710000 1116280 741090 1047120 647220 1274920 1080590 1160990 946410 1056490 701220 FALSE TRUE 1160351.596 868366.4426 1074408.807 775238.1842 1058209.554 829639.349 1069988.57 933724.922 1018467.131 838610.6333 1.383659532 1.03548227 1.281177181 0.924431618 1.261860405 0.989302205 1.275906276 1.113418892 1.214469613 1 19.6776416 0.006255031 0.014864518 9.58E-07 2.196839915 0.102045451 0.139893499 4090.959735 18.72874845 1456.74877 1310.198737 1.01450696 -0.006255031 2.196838957 GFGFVTFSSMAEVDAAMAARPHS(ph)IDGR ddPTM_MDA-MB-175_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 161.04 8.11E-12 149466000 44005.8 60659.8 54775.2 55125.5 63295.1 67664.1 55004.5 58587.8 55307.3 65655.7 TRUE FALSE 45743.18296 71077.64878 56202.68671 66029.15937 52536.22151 51950.13823 50693.10356 57802.52637 53316.80108 78519.67736 0.582569676 0.905220846 0.71577837 0.840924996 0.669083512 0.661619354 0.645610187 0.736153386 0.679024709 1 16.26076662 -1.218592299 9.098681169 1.000000022 0.719705026 0.47266255 0.090157578 3.80E-08 3.19E-09 0.082920159 0.019544467 0.060451586 1.218592299 -0.280294996 GFGFVTFSSMAEVDAAMAARPHSIDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GFGFVTFSSMAEVDAAMAARPHSIDGR 27 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 246.31 1.04E-45 2438957500 509161.2 732339.7 613034.1 610947.8 764757.7 831163.9 556717.62 686434.2 632454.8 847041.73 FALSE TRUE 529263.2773 858113.3467 629010.2723 731791.4513 634764.4593 638138.6806 513080.6382 677233.6723 609692.8753 1013003.339 0.52246943 0.847098241 0.62093603 0.722397867 0.626616354 0.629947263 0.506494518 0.668540414 0.6018666 1 19.9502075 -1.599286675 4.747368761 1.004480993 0.642144131 0.582184287 0.091830498 0.004147289 0.000350062 0.084668388 0.019757272 0.025160156 1.599286675 -0.362336862 GFGFVTYATVEEVDAAMNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGFVTYATVEEVDAAMNAR 20 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;A0A2R8Y4L2;F8W646;F8VYN5 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 99.531 0.0014988 9646200 9610.6 9996.6 9543.2 12198 10551 11566 12408 10004 11927 10382 FALSE TRUE 9990.033909 11713.43829 9791.903632 14610.72799 8757.544789 8879.971784 11435.42854 9869.912743 11497.7496 12416.15412 0.804599702 0.9434031 0.788642242 1.1767515 0.705334736 0.715195035 0.921012128 0.794925115 0.926031482 1 13.59993075 GFGFVTYATVEEVDAAMNARPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 337.41 7.67E-87 6449600000 1696445 1787893 2049232 1760072 2284843 2397777 2135558 2104999 2175167 1966531 FALSE TRUE 1763421.959 2094949.715 2102636.669 2108208.988 1896466.203 1840929.63 1968167.384 2076784.931 2096883.165 2351835.098 0.749806804 0.890772366 0.894040858 0.896410208 0.806377201 0.782763057 0.836864534 0.883048702 0.891594469 1 21.16535548 0.862474663 1.238365445 0.99879129 0.841556789 0.518863665 0.047034343 0.536233229 1.593812084 0.046149841 0.014149703 7.285756679 -0.862474663 -0.157234501 GFGFVTYATVEEVDAAMNARPHKVDGR ddPTM_MDA-MB-175_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 ;; 208.39 1.23E-25 869474000 323116.6 431267 403067 220245 687622 523818 226303.4 393715 500889 721814 FALSE TRUE 335873.4929 505333.7525 413571.2571 263808.8036 570740.2581 402169.208 208565.1482 388437.8944 482862.1027 863239.6333 0.389084884 0.585392205 0.479092063 0.305603211 0.66116086 0.465883623 0.241607475 0.4499769 0.559360442 1 19.71940158 0.809279848 2.966423306 0.999817223 0.446820748 0.674669608 0.114909368 0.541692332 7.425719702 0.109996856 0.028836277 6.445844847 -0.809279848 -0.552996475 GFGFVTYSCVEEVDAAMCARPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFGFVTYSCVEEVDAAMCARPHK 23 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 241.8 1.56E-37 1386354000 1077003 1248009 1171341 1082404 1667588 1600699 1124658 1346818 1358796 1502685 FALSE TRUE 1119523.91 1462344.838 1201867.109 1296500.281 1384131.987 1228960.916 1036504.367 1328766.108 1309893.197 1797107.355 0.622958838 0.813721469 0.668778693 0.721437301 0.770199946 0.683855037 0.576762631 0.739391614 0.728889787 1 20.77724516 0.548344602 1.904273277 0.999932685 0.700805956 0.656359274 0.064864844 1.798208915 6.889004131 0.060074166 0.016666696 3.53463523 -0.548344602 -0.299126729 GFGFVYFQNHDAADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 ; 256.57 9.27E-25 2755700000 3272600 2269060 2751100 2274550 3507900 3568600 3422900 2856400 3076300 2020360 FALSE TRUE 3401804.775 2658753.404 2822795.926 2724449.201 2911628.411 2739846.733 3154604.154 2818114.63 2965584.564 2416210.86 1.4079089 1.100381365 1.168273834 1.127570961 1.205039038 1.133943555 1.305599692 1.166336381 1.227369934 1 21.20431493 -1.343965821 3.35332166 0.998753329 1.198242229 0.326564448 0.08775075 2652304.372 1608495.049 22581.77969 0.018837592 0.045293322 1.343965821 0.1994889 GFGHIGIAVPDVYSACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGHIGIAVPDVYSACK 17 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 101.39 0.0011002 1028100000 327020 718040 638020 527060 644350 791490 426200 539400 605900 1338800 FALSE TRUE 339931.0021 841357.7844 654647.3253 631310.8949 534823.6172 607678.4426 392793.3303 532170.2253 584093.7774 1601112.227 0.212309291 0.52548333 0.408870355 0.394295218 0.334032561 0.379535196 0.245325296 0.332375343 0.36480502 1 20.610643 0.900501619 18.65461218 1 0.355959638 0.847239771 0.08214356 2445.83924 458564.581 0.077747817 0.019436954 7.952462302 -0.900501619 -0.644040362 GFGS(ph)EEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 1 GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR;GFGS(1)EEGSR 195.27 3.30E-05 2971060000 2673800 3129400 2888720 2942820 3219540 3537260 2928430 3059810 2765450 3041930 TRUE FALSE 2779363.689 3666850.107 2964002.416 3524901.013 2672283.741 2715784.973 2698892.005 3018798.252 2665921.995 3637937.942 0.763994255 1.007947405 0.814747932 0.968928296 0.734560013 0.746517675 0.741874119 0.829810266 0.73281129 1 21.7946895 3.230070126 24.99981307 0.785935211 0.892110648 0.162895744 0.099208555 268.080848 789349.4429 0.026081365 0.03164537 1698.517891 -3.230070126 0.106175437 GFGS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 GFGS(1)FR 79.307 0.070799 94484000 94129 116320 124130 116770 121630 129360 122910 116170 105990 111360 TRUE FALSE 97845.2856 136297.0552 127364.9298 139866.7575 100955.376 99318.10047 113275.993 114612.9312 102175.4406 133178.8599 0.734690819 1.02341359 0.956344948 1.050217411 0.758043552 0.745749743 0.850555359 0.860594026 0.76720465 1 17.02300557 3.228059406 24.99467703 0.823614088 0.948125643 0.210977668 0.10414545 284.699975 677633.6608 0.028892933 0.034881552 1690.672177 -3.228059406 0.124511555 GFGS(ph)VEELCTNSSLGMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGSVEELCTNSSLGMEK 18 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 GFGS(1)VEELCTNSSLGMEK;GFGS(1)VEELCTNSSLGMEK 254.59 1.62E-30 122722000 112027 113307 127409 109454 145092 151472 141518 125215 122177 106792 TRUE FALSE 116449.9125 132766.5958 130729.3832 131103.6745 120429.3137 116294.9236 130425.4494 123536.6977 117779.8736 127715.8477 0.911789058 1.039546761 1.023595627 1.026526283 0.942947299 0.910575513 1.021215861 0.967277749 0.922202497 1 16.96257803 3.236037232 24.99584687 0.961511383 1.004822541 0.154212405 0.04499779 116.7079367 1156075.141 0.012751047 0.015920187 1722.016198 -3.236037232 0.043311158 GFGSDKEAILDIITSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFGSDKEAILDIITSR 16 1 E5RK69;P08133;P08133-2;E7EMC6;E5RFF0;E5RJF5;E5RK63;E5RIU8;E5RJR0;E5RI05 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 174.78 3.42E-09 177550000 220710 301830 327780 312000 288940 437070 375290 325370 314170 380170 FALSE TRUE 229423.8012 353666.9546 336322.2161 373712.6688 239826.082 335567.1164 345873.7892 321008.9473 302863.0831 454657.0327 0.504608495 0.777876353 0.739727293 0.821966102 0.527487897 0.738066481 0.760735597 0.70604637 0.666135265 1 18.79441914 -2.347812753 2.160086596 2.686134631 0.701091466 0.46423809 0.098444985 4111527.62 435038.6646 33912437.74 0.02244751 0.004489389 2.347812753 -1.985043164 GFGSEEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 190.52 8.60E-05 1642300000 1194580 1331140 1326400 1214700 1397510 1502780 1335060 1304500 1167150 1428870 FALSE TRUE 1241742.941 1559752.94 1360967.074 1454964.034 1159961.749 1153782.12 1230414.509 1287015.311 1125144.499 1708829.719 0.726662772 0.912760893 0.796432236 0.851438864 0.678804761 0.675188468 0.720033421 0.753155974 0.658429852 1 20.70457721 3.249069606 24.98684007 0.731589359 0.826505541 0.101274059 0.101438243 353.8860196 841417.0767 0.025781901 0.034545382 1774.47386 -3.249069606 0.094916182 GFGSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GFGSFR 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 105.42 0.076756 2984500000 1191860 1565760 1304220 1320880 1737160 1741290 1429050 1465340 1349770 1798430 FALSE TRUE 1238915.553 1834667.1 1338209.045 1582146.122 1441878.164 1336901.787 1317037.327 1445699.514 1301192.041 2150797.925 0.576026013 0.853016956 0.622191899 0.735608912 0.670392205 0.621584097 0.612348241 0.672168918 0.604981075 1 21.03644055 -0.978680025 6.472223113 1.000000082 0.666852602 0.635443988 0.076496722 8.45E-08 1.32E-08 0.069122531 0.016292333 0.105031598 0.978680025 -0.33314748 GFGSSAPEGLEPDS(ph)MASAASALHLLSPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;GFGSSAPEGLEPDS(0.25)MAS(0.25)AAS(0.25)ALHLLS(0.25)PRPR 107.17 0.00036522 198656000 110346 150611 146940 161623 155330 189880 163774 156493 145988 151447 TRUE FALSE 114702.5453 176477.2677 150769.3771 193591.547 128927.0621 145783.2477 150936.9659 154395.4673 140733.9204 181120.14 0.633295366 0.974365786 0.832427454 1.068857097 0.711831727 0.804898051 0.833352745 0.852447813 0.77701972 1 17.46658745 -1.045238096 4.508760486 1.000007932 0.839972668 0.155269795 0.116204512 8.58E-06 1.82E-06 0.104231885 0.024566473 0.0901077 1.045238096 -0.160035264 GFGSSAPEGLEPDSMAS(ph)AASALHLLSPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.085)MAS(0.305)AAS(0.305)ALHLLS(0.305)PRPR;GFGSSAPEGLEPDS(0.013)MAS(0.329)AAS(0.329)ALHLLS(0.329)PRPR;GFGSSAPEGLEPDS(0.061)MAS(0.313)AAS(0.313)ALHLLS(0.313)PRPR;GFGSSAPEGLEPDS(0.003)MAS(0.332)AAS(0.332)ALHLLS(0.332)PRPR;GFGSSAPEGLEPDS(0.015)MAS(0.328)AAS(0.328)ALHLLS(0.328)PRPR 123.65 2.02E-05 1476263000 392305 514706 480282 573056 498964 627955 474553 539520 469011 508744 TRUE FALSE 407793.5043 603102.7516 492798.5435 686404.7664 414150.2775 482121.968 437356.2958 532288.6169 452131.3857 608422.6463 0.670247084 0.991256251 0.809960882 1.128170969 0.68069504 0.792412924 0.71883632 0.874866542 0.743120573 1 19.21471433 GFGSSAPEGLEPDSMASAAS(ph)ALHLLSPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDS(0.012)MAS(0.072)AAS(0.458)ALHLLS(0.458)PRPR;GFGSSAPEGLEPDSMAS(0.061)AAS(0.469)ALHLLS(0.469)PRPR 162.03 2.40E-12 1329290000 96351 137348 129327 145721 138617 152474 135002 125790 122407 141365 TRUE FALSE 100155.0119 160936.4506 132697.3679 174544.1789 115054.9319 117064.2243 124420.1905 124103.9908 118001.596 169062.7652 0.592413189 0.95193315 0.784900021 1.032422359 0.680545664 0.692430555 0.735940823 0.734070513 0.697975074 1 17.36719943 4.77751611 22.58181864 0.795883532 0.592411277 0.201219986 0.127707348 10650.58543 6173510.47 0.030085499 7.155278499 59912.31629 -4.77751611 -0.203472255 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDS(0.001)MAS(0.001)AASALHLLS(0.998)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR;GFGSSAPEGLEPDSMASAASALHLLS(1)PR 308.39 8.51E-83 3934239000 949242 1311903 1198511 1581164 1268982 1546492 1418382 1393078 1268316 1315125 TRUE FALSE 986718.8071 1537212.135 1229745.181 1893913.52 1053280.893 1187342.67 1307205.513 1374406.068 1222669.555 1572798.564 0.627365023 0.977373816 0.781883459 1.204167885 0.669685818 0.754923547 0.83113346 0.8738602 0.77738471 1 20.58490248 -1.06731719 4.339817149 1.000011365 0.842019971 0.091523559 0.15548627 1.99E-05 4.28E-06 0.140632407 0.033144407 0.085641213 1.06731719 -0.157991394 GFGSSAPEGLEPDSMASAASALHLLS(ph)PRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFGSSAPEGLEPDSMASAASALHLLSPRPR 30 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GFGSSAPEGLEPDSMASAASALHLLS(1)PRPR;GFGSSAPEGLEPDSMASAASALHLLS(1)PRPR;GFGSSAPEGLEPDSMAS(0.001)AASALHLLS(0.999)PRPR 206.64 7.39E-26 1255170000 329336 398811 388028 452380 422017 514550 433589 441189 420287 424010 TRUE FALSE 342338.4396 467303.6869 398140.3284 541859.4138 350282.7011 395053.5606 399603.1612 435275.5831 405160.953 507086.6413 0.675108377 0.921546041 0.785152469 1.068573631 0.690774855 0.77906521 0.788037248 0.858385032 0.798997489 1 18.95187274 -1.49262742 2.901771905 1.005917354 0.824168103 0.202238066 0.107654714 26193951.84 28335619.28 1233159.181 0.024368716 0.032164187 1.49262742 -0.181749251 GFHLDVEDYLSGVLILASELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFHLDVEDYLSGVLILASELSR 22 0 E9PGT1;Q15631;H7C1D4 E9PGT1 TSN Translin 0 ;;; 215.75 1.40E-25 859695100 181669.9 245370 336804 248221 345089 313649 304136 265648 326014 346783 FALSE TRUE 188842.3679 287510.3888 345581.3889 297318.3729 286430.895 240808.7731 280297.0256 262087.4231 314280.8198 414728.4893 0.455339753 0.693249671 0.8332714 0.71689884 0.690646778 0.580641985 0.675856694 0.631949407 0.757798965 1 18.66180763 0.890951137 3.793192908 0.999908918 0.66648957 0.554121334 0.092214164 0.386048274 11.40433455 0.089225007 0.02289481 7.779490184 -0.890951137 -0.333419348 GFIYVHKPPVHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 129.84 9.62E-05 496780000 210350 215200 241240 221980 235010 281880 260020 261670 253650 255040 FALSE TRUE 218654.7804 252158.926 247526.9126 265886.9815 195063.0841 216417.6419 239638.953 258162.7417 244521.186 305010.205 0.716876934 0.826722916 0.811536495 0.871731428 0.639529698 0.709542299 0.785675197 0.846406899 0.801681983 1 18.21849799 0.561323802 0.857285751 0.999918379 0.770261217 0.517430121 0.065604296 1.22716196 1.454332279 0.068344795 0.022571246 3.641864656 -0.561323802 -0.229657163 GFKDQIYDIFQK ddPTM_MDA-MB-175_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 ; 203.87 1.09E-07 3738200000 5186500 3804000 5079200 3935300 6831400 6151300 5635400 4734100 5729000 4754000 FALSE TRUE 5391267.025 4457307.409 5211568.125 4713690.594 5670201.068 4722753.799 5193682.623 4670647.133 5522814.409 5685455.279 0.94825599 0.783984253 0.916649216 0.829078827 0.997316976 0.830672931 0.913503381 0.821508024 0.971393519 1 22.43884445 1.090878978 6.179056579 0.999086813 0.877855511 0.319427183 0.06217286 0.199625838 10.14209714 0.053795728 0.013529171 12.32761261 -1.090878978 -0.121231302 GFKDQIYEIFQK ddPTM_MDA-MB-175_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 ; 158.11 6.57E-05 1417160000 1865620 1299860 1769710 1319520 2409700 2029780 2016790 1755240 1986640 1476750 FALSE TRUE 1939276.118 1523100.843 1815830.096 1580517.118 2000100.055 1558394.357 1858708.73 1731713.879 1915141.214 1766090.888 1.098061335 0.862413624 1.028163448 0.894923997 1.132501202 0.882397597 1.052442285 0.980534971 1.084395615 1 20.75212816 1.681583274 1.773013734 1.033448166 0.984114797 0.034471097 0.088976003 1.144178368 7.313427129 0.06172939 0.023599681 48.03781817 -1.681583274 -0.049333369 GFLTERDDILCPDCGKDI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFLTERDDILCPDCGKDI 18 2 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 ;;; 211.89 1.00E-15 415709000 466588 436378 453606 352447 611350 568420 452285 445513 520630 495386 FALSE TRUE 485009.2545 511322.527 465427.345 422159.9647 507432.9454 436413.0695 416833.7199 439541.6269 501892.628 592447.402 0.818653695 0.863068224 0.785601124 0.712569526 0.856502946 0.736627535 0.703579286 0.74190827 0.84715137 1 19.17632755 0.928506664 4.415759384 0.999907422 0.774840825 0.620212334 0.052959481 0.229814472 11.47203726 0.05399831 0.013728909 8.482163977 -0.928506664 -0.225066597 GFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 188.8 4.87E-18 409030000 404780 348040 352009 339796 436070 480550 411670 405180 410840 335142 TRUE FALSE 420761.027 407813.1626 361182.6437 407006.6346 361946.9772 368949.5453 379402.2297 399749.2248 396053.9487 400806.6582 1.049785522 1.017481008 0.901139331 1.015468746 0.903046319 0.920517506 0.946596624 0.997361737 0.988142139 1 18.61254695 -0.830564094 5.812155994 1.000000005 0.969154694 0.02915946 0.048998739 3.19E-09 6.09E-10 0.047499643 0.011195771 0.147718846 0.830564094 -0.030845311 GFPTDATLDDIKEWLEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFPTDATLDDIKEWLEDK 18 1 P05455;E7ERC4;E9PGX9 P05455 SSB Lupus La protein 0 ; 180.14 7.30E-14 517160000 961880 407730 602280 483900 814370 765160 1022710 664900 689960 269030 FALSE TRUE 999855.7651 477754.4558 617975.9116 579613.9757 675943.6783 587463.1861 942547.3178 655988.1031 665128.4744 321741.2776 3.107639071 1.484902588 1.920723123 1.801490875 2.100892006 1.825886907 2.92951941 2.038868335 2.067277408 1 18.29554151 GFPTIYFSPANKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 178.58 2.32E-05 2181200000 2501090 2076570 2285710 1854940 3354500 3050800 2533840 2236770 2526500 2108330 FALSE TRUE 2599834.964 2433204.744 2345277.48 2221841.596 2784303.288 2342297.935 2335231 2206789.757 2435571.759 2521416.897 1.031100794 0.965014848 0.930142684 0.881187716 1.104261374 0.928960989 0.926158226 0.87521812 0.965953612 1 21.26580325 2.522959669 24.9999788 0.925514312 0.977234481 0.0814526 0.063516081 885.0458902 482697.1145 0.020539911 0.019364483 333.3954505 -2.522959669 0.051720169 GFQFVSS(ph)SLPDICYR ddPTM_MDA-MB-175_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(0.143)S(0.563)S(0.294)LPDICYR 118.2 0.00032497 40229000 78136 82142 90181 104200 102070 108720 115360 103190 106510 104240 TRUE FALSE 81220.86961 96249.24952 92531.19094 124810.449 84720.17786 83471.42767 106317.7818 101806.9068 102676.7259 124663.8322 0.651519115 0.772070358 0.74224568 1.001176097 0.679589071 0.66957213 0.852835822 0.81665151 0.823628827 1 16.92768344 -5 0.156552953 1.81746953 0.718960635 0.360620968 0.095205138 154.9732385 1.410932359 39.13692577 0.431618387 1.00E-05 5 -1.098508895 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFQQILAGEYDHLPEQAFYMVGPIEEAVAK 30 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 190 2.60E-18 47687000 76750 75311 78729 79344 82970 114420 80960 72765 77202 83055 FALSE TRUE 79780.14926 88245.07841 80780.74242 95038.00638 68866.78904 87847.68905 74614.14365 71789.70419 74423.5151 99328.03707 0.80319869 0.888420642 0.813272313 0.956809469 0.693326789 0.884419864 0.751189149 0.722753679 0.749269967 1 16.59991338 3.236824645 24.99937973 0.7827712 0.863342579 0.08821547 0.09313017 85.84364146 1236222.17 0.024850961 0.031199771 1725.141191 -3.236824645 0.080571379 GFRDDFLGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFRDDFLGGR 10 1 Q15056-2 Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 166.69 4.99E-06 1031410000 249642 298595 310635 251026 348329 347105 270557 279894 308506 366959 FALSE TRUE 259498.0589 349876.3685 318730.4033 300678.1936 289120.161 266495.1242 249350.0354 276142.4787 297402.9293 438857.5902 0.591303568 0.797243517 0.726272965 0.685138415 0.658801779 0.607247385 0.56817984 0.629230267 0.677675255 1 18.74339333 -1.816720226 6.29601458 1.023924671 0.658981346 0.716830186 0.06408198 0.022088601 0.000643009 0.063685524 0.015713685 0.015250349 1.816720226 -0.364943325 GFS(ph)IAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFSIAK 6 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 1 GFS(1)IAK 84.498 0.058514 483710000 551750 400030 730110 438780 1018900 610440 626060 516780 627710 460870 TRUE FALSE 573533.516 468732.0407 749137.2664 525569.3744 845707.7419 468674.5613 576987.7813 509853.4094 605118.8397 551168.6526 1.040577169 0.850433054 1.359179741 0.953554546 1.534390133 0.850328768 1.046844334 0.925040651 1.097883265 1 19.07213431 GFS(ph)LEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 1 GFS(1)LEELR;GFS(1)LEELR;GFS(1)LEELR 144.77 0.00060847 151939000 243353 316645 294998 277597 278707 351015 363736 316833 407654 301872 TRUE FALSE 252960.7643 371026.3156 302685.8902 332504.8581 231332.4837 269497.0859 335225.4219 312586.3719 392982.6122 361018.0387 0.700687326 1.027722373 0.838423175 0.921020067 0.640778185 0.746492023 0.928555878 0.865846962 1.088540101 1 18.4617114 1.404043568 2.401211029 1.04365627 0.829775103 0.356664303 0.111344707 0.323323135 3.294961869 0.094628574 0.029670623 25.35382967 -1.404043568 -0.213881167 GFSDEDNTWEPEENLDCPDLIAEFLQSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFSDEDNTWEPEENLDCPDLIAEFLQSQK 29 0 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 207.86 1.58E-25 31677000 52161 41719 49972 48477 54392 58902 56335 52507 48952 46452 FALSE TRUE 54220.35656 48883.91372 51274.31137 58065.60591 45146.46727 45222.90317 51919.3155 51803.22955 47190.22708 55553.38002 0.976004638 0.879944905 0.922973748 1.045221837 0.812668235 0.814044135 0.934584277 0.932494648 0.849457352 1 15.76158707 4.756376501 22.49408016 0.908887897 0.976004865 0.070932055 0.071363579 2583.546172 3261731.033 0.016940337 0.442253775 57065.8777 -4.756376501 0.067116969 GFSEEHNTWEPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFSEEHNTWEPEK 13 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 0 ;; 154.07 4.60E-05 744380000 831170 854010 1078570 1055970 1171700 1433490 1592870 1151970 1149360 733980 FALSE TRUE 863985.2334 1000679.574 1106678.42 1264837.714 972534.8525 1100583.672 1468016.687 1136529.726 1107994.758 877789.3281 0.984274023 1.139999704 1.260756294 1.440935397 1.107936519 1.253813002 1.672402068 1.294763664 1.2622559 1 19.7435152 4.46271978 1.915463798 1.317519076 0.965162015 0.227884507 0.171711271 0.615465074 3.530857581 0.044427027 0.317247768 29021.49498 -4.46271978 -0.352357061 GFSESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFSESER 7 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 92.822 0.035798 251700000 303230 373810 423510 523960 350030 482520 455570 475310 306020 418240 FALSE TRUE 315201.7545 438008.9597 434547.0185 627597.7241 290532.0256 370462.0427 419861.233 468939.2469 295006.4 500186.1203 0.630168935 0.875691951 0.868770645 1.254728387 0.580847836 0.740648386 0.839410003 0.937529507 0.589793255 1 18.9321055 GFSIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFSIAK 6 0 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 102.98 0.081604 322840000 517490 476560 492260 470850 707260 675000 624810 537770 556810 546100 FALSE TRUE 537920.9048 558405.4729 505088.7 563982.7247 587040.1978 518241.4797 575835.7596 530562.0728 536770.5169 653097.8393 0.823645207 0.855010443 0.773373712 0.863550131 0.898854907 0.793512776 0.881699073 0.812377627 0.821883774 1 19.31693961 -1.126958037 4.274126257 1.000029201 0.836375489 0.636952397 0.037145701 1.01E-05 2.07E-06 0.033923289 0.007994313 0.074652089 1.126958037 -0.163653712 GFSLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GFSLEELR 8 0 P26373;P26373-2;J3QSB4 P26373 RPL13 60S ribosomal protein L13 0 ;;;;;;;; 208.67 0.00012422 2548428000 3164283 4131231 3004014 2896061 6543210 5069039 3492630 3274715 3111365 7815060 FALSE TRUE 3289211.336 4840737.788 3082301.073 3468893.222 5430997.501 3891831.514 3218868.534 3230822.802 2999387.581 9346271.379 0.351927651 0.517932509 0.329789383 0.371152632 0.581087075 0.41640472 0.344401356 0.345680397 0.320918092 1 23.1559595 -1.434457922 3.904689416 1.003725265 0.398195855 0.829110856 0.082032146 28199540.43 10374950.87 894234.257 0.019594516 0.036774102 1.434457922 -0.605529409 GFSLLATEDKEALKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFSLLATEDKEALKK 15 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 166.04 7.82E-07 2206000000 1548290 650150 1107530 555900 1762440 1376170 1364000 1137690 1290870 645210 FALSE TRUE 1609417.685 761808.205 1136393.142 665855.3608 1462861.078 1056575.374 1257086.116 1122441.126 1244411.841 771626.5462 2.08574691 0.987275786 1.47272427 0.862924382 1.895814867 1.369283339 1.629137984 1.454642964 1.612712584 1 19.55754325 -1.602560083 6.548778153 0.998836626 1.466086841 0.146199202 0.34919056 0.005403001 0.000327904 0.307991019 0.072435785 0.024971229 1.602560083 0.467250215 GFSNLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 98.392 0.018113 1381000000 1214450 1281480 1133280 1211550 2674090 2233640 2099730 1996060 2381920 1616320 FALSE TRUE 1262397.424 1501564.221 1162814.208 1451190.974 2219549.137 1714910.961 1935147.676 1969306.081 2296195.164 1933006.958 0.653074433 0.776802285 0.601557177 0.750742758 1.148236497 0.887172679 1.001107455 1.018778579 1.187887687 1 20.8824154 3.350653278 5.729782134 1.029388978 0.686074262 0.785418647 0.088672746 0.092580222 4.307420256 0.024029039 0.032647274 2242.091222 -3.350653278 -0.343314717 GFSQYGVSGS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 GFSQYGVS(0.001)GS(0.701)PT(0.298)K;GFSQYGVSGS(1)PTK;GFSQYGVS(0.011)GS(0.988)PT(0.001)K;GFSQYGVS(0.003)GS(0.976)PT(0.021)K 211.9 1.91E-08 821500000 2450170 1596660 1904150 1555660 2306810 2367760 2229700 1897470 1950190 1538370 TRUE FALSE 2546904.604 1870873.935 1953773.713 1863364.905 1914699.26 1817883.624 2054930.288 1872037.518 1880003.043 1839784.148 1.384349684 1.016898606 1.061958119 1.012817132 1.040719512 0.988096145 1.116940969 1.017531062 1.02186066 1 20.81110508 4.740250045 24.9935931 1.033920485 1.384349801 0.902661497 0.034820048 38.67730532 572147.9065 0.007726682 0.049870115 54985.73631 -4.740250045 0.350429317 GFSVVADT(ph)PELQR ddPTM_MDA-MB-175_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 280.87 2.25E-31 2856110000 4871050 4978580 4004960 4547400 4321760 5070360 3657540 3879510 3582690 4930010 TRUE FALSE 5063362.815 5833612.387 4109332.548 5446862.147 3587148.779 3892845.732 3370852.458 3827511.514 3453749.687 5895951.069 0.858786438 0.989426866 0.696975348 0.923830962 0.608408845 0.660257469 0.571723276 0.649176268 0.585783302 1 22.49129312 3.236020424 24.99998107 0.653037738 0.863818659 0.308559054 0.134468489 67.14763648 660852.9228 0.035310674 0.044094211 1721.949551 -3.236020424 0.210780921 GFTDADNTWEPEENLDCPELIEAFLNSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFTDADNTWEPEENLDCPELIEAFLNSQK 29 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 0 ; 155.16 1.40E-08 42118200 72199 58155 67590 68922 65900 80239 78755 63783 75445 56208 FALSE TRUE 75049.47227 68142.66887 69351.45093 82554.56589 54698.34154 61604.70828 72581.97731 62928.09321 72729.74919 67220.88143 1.116460699 1.013712814 1.031695054 1.228108947 0.813710567 0.916451956 1.07975343 0.936139067 1.081951733 1 16.03662184 3.243364002 24.99999999 0.970929553 1.086809987 0.312231522 0.091178472 163.3675195 850266.7943 0.02546961 0.03341479 1751.31393 -3.243364002 0.115880434 GFTECEMTKSS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFTECEMTKSSPLK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 GFTECEMT(0.002)KS(0.042)S(0.956)PLK;GFTECEMT(0.003)KS(0.094)S(0.903)PLK;GFTECEMTKS(0.096)S(0.904)PLK 181.51 1.02E-07 496580000 1436290 701780 916120 579610 1310810 1256930 1104600 981490 1061630 604860 TRUE FALSE 1492995.838 822305.2559 939994.8398 694255.128 1087998.984 965027.0565 1018018.566 968334.7319 1023422.144 723370.7363 2.063942821 1.136768761 1.299464842 0.959750088 1.504068287 1.334069804 1.407326167 1.338642391 1.414796165 1 19.46437571 4.745343714 24.96578039 1.286459049 2.063943183 0.658786449 0.171696492 468.0694966 1722725.561 0.039379075 0.388071911 55634.43906 -4.745343714 0.777484134 GFTGIDSDYEKPETPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFTGIDSDYEKPETPER 17 1 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 145.62 4.26E-07 1285750000 720960 600560 657570 505030 849760 786410 783130 628900 718270 544600 FALSE TRUE 749424.0575 703701.5083 674706.8144 604923.4266 705318.0987 603778.1957 721746.2243 620470.6242 692419.603 651303.943 1.150651805 1.08045025 1.035932335 0.928788215 1.082932333 0.927029849 1.108155773 0.952659094 1.063128222 1 19.31297144 4.458288814 2.095978441 1.008320434 1.154108786 0.360073445 0.059210024 0.398152104 2.874352389 0.013804066 0.088253346 28726.90338 -4.458288814 0.145788352 GFTIPEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GFTIPEAFR 9 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;; 173.23 0.00012932 2515880000 1536810 1739540 1584600 1564920 1863420 1942060 1719850 1599680 1530010 1826960 FALSE TRUE 1597484.445 2038292.463 1625895.978 1874456.505 1546676.534 1491045.997 1585043.663 1578238.906 1474945.239 2184917.833 0.731141657 0.932892044 0.744145136 0.857907092 0.707887734 0.682426577 0.725447721 0.722333299 0.675057532 1 21.0591476 3.233092404 24.98177244 0.73254045 0.819663929 0.066735755 0.102924722 242.999655 1110154.874 0.026859428 0.032974339 1710.379191 -3.233092404 0.087123479 GFTSLGMEEERIETAQQFFSWFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFTSLGMEEERIETAQQFFSWFAK 24 1 Q96JB2;Q96JB2-2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 121.35 0.00011657 98022000 27490 27239 27769 25477 34122 34758 25809 30270 32069 25005 FALSE TRUE 28575.32643 31917.08636 28492.68295 30516.27456 28321.95463 26685.98126 23786.02314 29864.28016 30914.84295 29904.251 0.95556068 1.067309339 0.952797077 1.020466106 0.947087912 0.892380861 0.795406083 0.998663373 1.033794257 1 14.86806296 5.129268157 16.55854313 0.962474436 0.00068764 0 0.074372747 3127.056357 392965.2253 0.018180498 2158.660127 134669.1619 -5.129268157 -0.961786796 GFVEFAAKPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFVEFAAKPPAR 12 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 136.38 0.00010127 1784910000 1449300 1507640 1519890 1300430 1850160 1726440 1688180 1488160 1620340 1536390 FALSE TRUE 1506519.483 1766565.442 1559499.582 1557651.173 1535670.464 1325500.474 1555856.04 1468213.649 1562024.28 1837416.205 0.819911939 0.961440004 0.848745961 0.847739978 0.835777142 0.7213937 0.846762991 0.799064276 0.850120009 1 20.80924703 GFVEPDHYVVVGAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GFVEPDHYVVVGAQR 15 0 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ; 192.18 1.45E-07 920100000 457130 592920 484180 708210 572160 662000 510630 484750 414730 565490 FALSE TRUE 475177.8454 694749.3977 496798.1286 848291.8242 474904.4476 508260.5327 470605.4863 478252.7191 399803.9483 676286.9385 0.702627566 1.027299742 0.734596663 1.25433714 0.702223303 0.751545688 0.695866591 0.707174266 0.591175026 1 19.36727596 GFVLHK ddPTM_MDA-MB-175_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 ; 105.82 0.032648 1741840000 2286900 2126720 2251200 2009660 2842100 2654200 2517800 2255300 2300500 2441700 FALSE TRUE 2377188.578 2491967.616 2309868.121 2407164.75 2359000.857 2037802.275 2320448.257 2225071.392 2217705.454 2920104.366 0.814076581 0.853383066 0.791022454 0.824342026 0.807848132 0.697852549 0.794645659 0.761983516 0.759461025 1 21.4775885 2.987193258 24.41928091 0.782222816 0.820316767 0 0.075917046 1422.434389 2712237.545 0.020816509 0.023098782 970.9419339 -2.987193258 0.038093952 GFVQVDDGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GFVQVDDGRK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 105.46 0.0040826 685860000 651210 624500 582920 591500 758460 706200 645500 560700 627220 655020 FALSE TRUE 676920.2736 731753.0171 598111.3741 708496.9345 629537.2401 542195.7526 594904.0233 553184.7336 604646.4747 783358.6279 0.864125637 0.934122624 0.76352178 0.904434967 0.803638612 0.692142441 0.759427422 0.706170474 0.771864192 1 19.57931341 4.234051532 24.9996511 0.78361276 0.899124143 0.144619458 0.089310142 152.8577287 847506.6052 0.021734932 0.049607538 17141.60693 -4.234051532 0.115511383 GFWYDAEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GFWYDAEISR 10 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 117.81 0.0021127 27305000 32015 46791 42579 38698 57236 53386 39718 40239 40637 60228 FALSE TRUE 33278.97692 54826.99027 43688.64372 46352.3489 47507.04516 40987.91057 36604.79938 39699.66202 39174.48231 72028.52347 0.462024977 0.761184426 0.606546429 0.643527684 0.659558781 0.569051101 0.508198664 0.551165845 0.543874571 1 16.13628071 -1.93061002 2.484510695 1.27460454 0.591541066 0.70172171 0.080287905 11162476.05 5618553.273 17782875.63 0.020827662 0.011732484 1.93061002 -0.683063474 GGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 380.7 3.59E-177 713143000 243807 382113.9 363608 403233.1 362196.7 422969.6 371696.4 382391.8 357865.8 395528.5 FALSE TRUE 253432.6886 447738.9899 373083.9232 482991.4036 300630.6343 324741.3206 342561.8649 377266.4634 344986.2798 473024.7367 0.535770477 0.946544557 0.788719689 1.021070076 0.635549499 0.6865208 0.724194399 0.797561806 0.729319744 1 18.85155611 -1.146115436 4.264513612 1.000049772 0.770954274 0.218365184 0.133831325 18167918.89 4882747.03 8828.402589 0.029848235 0.071430644 1.146115436 -0.229095498 GGAARPNGPAAGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGAARPNGPAAGNK 14 1 P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;F8VWU4;F8VSF8 P51148 RAB5C Ras-related protein Rab-5C 0 67.519 0.054813 0 12830 43579 28137 46589 28691 42396 23758 35676 34943 80147 FALSE TRUE 13336.53831 51063.35425 28870.27333 55804.16515 23814.11407 32550.17152 21895.78588 35197.82157 33685.40826 95850.27014 0.139139288 0.532740849 0.301201794 0.582201438 0.248451194 0.339593947 0.228437394 0.367216718 0.351437802 1 16.54849488 0.198481153 2.549338159 1.000001493 0.347786053 0.708722905 0.126259108 42.45330028 133.1746299 0.111821028 0.029728763 1.579360067 -0.198481153 -0.65221544 GGAAVDPDSGLEHSAHVLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GGAAVDPDSGLEHSAHVLEK 20 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 214.26 7.38E-25 3281490000 3435990 4318730 5047040 4479680 6098340 6183250 5462370 5563860 5344640 4740010 FALSE TRUE 3571645.538 5060438.282 5178570.009 5365747.333 5061746.345 4747283.896 5034215.166 5489285.557 5152287.45 5668724.207 0.630061617 0.892694387 0.913533596 0.946552899 0.892925138 0.837451907 0.888068458 0.968345849 0.908897181 1 22.43459265 4.742208276 3.937442287 0.916103375 0.602317414 0.802826698 0.042741195 0.10567647 3.345350037 0.010535532 0.095705893 55234.22639 -4.742208276 -0.313785961 GGAEQFMEETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGAEQFMEETER 12 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 186.81 2.62E-05 1936400000 944350 978190 936900 949720 1071090 1140520 1000050 961750 955940 941190 FALSE TRUE 981633.6672 1146186.523 961316.3837 1137571.781 889026.5044 875651.5147 921663.4679 948859.3144 921535.9061 1125598.16 0.872099566 1.018291042 0.854049356 1.010637563 0.789825833 0.777943271 0.81882105 0.84298229 0.818707722 1 20.10226045 3.227949284 24.99955415 0.8299305 0.938398077 0.279089522 0.075343259 226.7053104 534101.1288 0.019934847 0.024058114 1690.243536 -3.227949284 0.108467577 GGAESHTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GGAESHTFK 9 0 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 ;;;;;;; 130.75 0.0003525 6333621000 9914930 8879840 9740380 8259440 13245860 12295700 11419200 9731030 9944530 11007690 FALSE TRUE 10306379.09 10404883.44 9994222.305 9893132.58 10994333.45 9440210.018 10524133.27 9600601.46 9586628.308 13164436.1 0.782895599 0.79037821 0.759183472 0.75150447 0.835154151 0.71709946 0.799436693 0.729283152 0.728221721 1 23.65014239 -1.162333348 4.782840371 1.000023113 0.76542093 0.801614397 0.034936059 8.18E-06 1.43E-06 0.032128803 0.007572086 0.068812392 1.162333348 -0.234602184 GGAGGS(ph)PGSSSGSGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGAGGSPGSSSGSGSSR 17 0 Q8TAE6 Q8TAE6 PPP1R14C Protein phosphatase 1 regulatory subunit 14C 1 GGAGGS(1)PGSSSGSGSSR;GGAGGS(1)PGSSSGSGSSR;GGAGGS(0.999)PGS(0.001)SSGSGSSR;GGAGGS(0.998)PGS(0.002)SSGSGSSR 384.29 1.09E-121 581789000 689988 753870 709421 765026 726636 795270 724864 736071 639951 704131 TRUE FALSE 717229.259 883341.3082 727909.0941 916345.8594 603122.6723 610580.5949 668047.2656 726205.1722 616919.2885 842091.988 0.851723172 1.04898434 0.864405676 1.088177862 0.716219464 0.725075887 0.793318634 0.862382237 0.732603204 1 19.68361831 3.229052464 24.9999739 0.798173082 0.962375951 0.360294357 0.103154696 198.0189117 520654.2782 0.027853562 0.033702399 1694.542492 -3.229052464 0.16420287 GGAPDPSPGATATPGAPAQPS(ph)SPDARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDARR 27 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDARR 133.23 2.00E-05 434740000 101390 152210 118600 93783 126040 140390 76961 105470 103760 197860 TRUE FALSE 105392.9555 178350.8835 121690.8134 112332.9975 104615.7658 107786.5501 70928.59572 104056.3472 100025.6979 236626.8787 0.445397226 0.753721996 0.514272994 0.474726278 0.442112774 0.455512707 0.299748685 0.439748636 0.42271486 1 17.85225443 -1.0904173 4.517223478 1.000038306 0.47036694 0.683456862 0.107795202 5.13650652 138723446.2 11978.49421 0.026965116 0.081204987 1.0904173 -0.529671366 GGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGAPDPSPGATATPGAPAQPSSPDAR 26 0 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 GGAPDPSPGATATPGAPAQPS(0.173)S(0.827)PDAR 151.06 8.06E-08 386620000 64396 99350 82228 98632 78336 100260 90976 90359 77442 86145 TRUE FALSE 66938.4038 116412.5897 84370.92923 118141.1152 65020.4747 76976.13445 83845.0634 89147.8854 74654.87755 103023.4634 0.649739405 1.129961912 0.818948679 1.146739891 0.631122975 0.747170906 0.813844348 0.865316331 0.724639563 1 16.65261342 3.22846905 24.9999985 0.794432343 0.941791473 0.151909535 0.161006495 353.0275952 874559.582 0.043143349 0.052128837 1692.267642 -3.22846905 0.14735913 GGAVERPLT(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;GGAVERPLT(1)PAPR;GGAVERPLT(1)PAPR 117.48 0.00081281 2374380000 1257551 1690700 1450367 1463538 1500664 1639560 1391224 1468567 1243603 1676760 TRUE FALSE 1307200.085 1981064.573 1488164.756 1753021.448 1245581.669 1258797.038 1282176.228 1448883.261 1198845.971 2005289.018 0.65187615 0.987919724 0.742119835 0.874198897 0.621148202 0.627738459 0.639397222 0.722530891 0.597841987 1 20.93537875 3.24073234 24.99996981 0.682687807 0.821313103 0.132673411 0.135531953 88.55851783 1019437.208 0.034809605 0.044940327 1740.733711 -3.24073234 0.138625296 GGCGS(ph)PGLQCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGCGSPGLQCK 11 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GGCGS(1)PGLQCK;GGCGS(1)PGLQCK 160.56 2.87E-05 440040000 845240 647070 730430 627750 849540 938290 790050 740250 743890 627410 TRUE FALSE 878610.7279 758199.239 749465.6059 751917.0764 705135.4942 720386.3674 728123.8166 730328.1596 717117.5442 750338.977 1.170951736 1.010475615 0.998836031 1.002103182 0.939755918 0.960081229 0.970393167 0.973330964 0.955724767 1 19.51718298 GGCVS(ph)PERGPTFNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGCVSPERGPTFNPK 15 1 Q9ULD5 Q9ULD5 ZNF777 Zinc finger protein 777 1 GGCVS(1)PERGPTFNPK 69.605 0.038725 0 45267 31225 38116 30820 43982 47962 44221 31058 43088 33045 TRUE FALSE 47054.17611 36587.65085 39109.33427 36916.10401 36505.95535 36823.55237 40754.84247 30641.71831 41537.2713 39519.53507 1.190656116 0.925811774 0.989620303 0.934122933 0.923744555 0.931781012 1.031258146 0.775356245 1.051056679 1 15.27027835 4.740570295 24.10330416 0.939788276 1.190656261 0.480197874 0.073785452 86.62531744 1038820.173 0.017003054 0.110723745 55026.29793 -4.740570295 0.250867984 GGCWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGCWPR 6 0 Q9Y4W6 Q9Y4W6 AFG3L2 AFG3-like protein 2 0 ;;; 128.65 0.038468 2448820000 1932710 1444590 1852340 1372850 2536570 2641080 2134620 1960510 1901170 1379580 FALSE TRUE 2009014.883 1692687.095 1900613.502 1644395.632 2105404.737 2027729.196 1967302.907 1934232.57 1832747.263 1649882.287 1.217671648 1.025944159 1.151969154 0.996674517 1.276093909 1.229014465 1.192389858 1.1723458 1.110835165 1 20.65393167 4.053101638 24.9993253 1.153760253 1.113595155 0 0.095468167 417.4846426 196538.271 0.023192216 0.050100913 11300.60351 -4.053101638 -0.040165098 GGDAKS(ph)PVLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGDAKSPVLQEK 12 1 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK;GGDAKS(1)PVLQEK 123.4 0.00020681 3670340000 7876720 3709520 5480490 3320470 6947340 6259650 6516130 5122160 6181380 3253450 TRUE FALSE 8187698.988 4346601.204 5623316.072 3977249.055 5766433.628 4805941.153 6005378.704 5053505.823 5958913.341 3890901.236 2.104319408 1.117119387 1.445247702 1.022192241 1.482030326 1.235174285 1.543441568 1.298800847 1.531499511 1 21.89167293 4.74763336 24.8260343 1.316862548 2.104319859 0.608259782 0.193726424 689.7407974 1887315.179 0.04168613 0.513657137 55928.52426 -4.74763336 0.787457311 GGDEYDNHCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGDEYDNHCGK 11 0 P20645;F5GX30;F5H4U1;H0YGE9 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;; 157.68 3.05E-05 1969160000 2775470 2509310 2794950 2947940 3906500 3966360 3535780 2746890 2842810 2902020 FALSE TRUE 2885047.699 2940264.473 2867788.693 3531033.733 3242474.525 3045233.001 3258636.325 2710072.433 2740497.823 3470615.256 0.831278458 0.847188252 0.826305563 1.017408578 0.934265047 0.877433186 0.9389218 0.780862248 0.789628818 1 21.72676001 -0.533349866 7.422603371 0.999999999 0.872028189 0.232806347 0.069987042 0 0 0.071813765 0.016926667 0.292853308 0.533349866 -0.127971809 GGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 31 0 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ; 236.79 9.04E-46 86959000 77698 93751 79460 86461 90111 106188 76416 90256 100180 98548 FALSE TRUE 80765.57704 109852.005 81530.79288 103562.7277 74793.96441 81527.44629 70426.31424 89046.26595 96574.54137 117856.5938 0.685286877 0.93208196 0.691779647 0.878718147 0.634618412 0.691751252 0.59755939 0.755547595 0.819424169 1 16.84667295 0.896991175 2.539873531 0.999339505 0.733148632 0.410688514 0.097437943 0.411614185 5.641951051 0.092099504 0.024688509 7.88844088 -0.896991175 -0.266190873 GGDISVCEWYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GGDISVCEWYQR 12 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ;;;;; 312.69 5.67E-46 4015720000 1119466 1541880 1056151 1396531 1111573 1466686 935614 964397 825209 1319443 FALSE TRUE 1163663.382 1806685.896 1083675.163 1672760.664 922628.2185 1126070.404 862278.1299 951470.8357 795509.8893 1577962.594 0.737446747 1.144948494 0.686755926 1.060076247 0.584695874 0.713623003 0.546450298 0.602974265 0.504137356 1 20.58963158 3.224752167 24.9999544 0.631653439 0.908527629 0.306241533 0.180626383 233.97689 423610.2043 0.04753434 0.057091365 1677.84627 -3.224752167 0.27687419 GGDLMAYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GGDLMAYDR 9 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;; 185.58 9.93E-05 2837070000 2340030 2780910 2453730 2589670 3459930 3272490 2867280 2505720 2318220 3519650 FALSE TRUE 2432416.191 3258509.66 2517676.22 3101898.997 2871812.334 2512503.793 2642535.101 2472134.922 2234787.715 4209258.03 0.577872911 0.774129226 0.598128269 0.736922986 0.682260939 0.596899448 0.627791189 0.587308952 0.530922006 1 22.00513452 -1.265112867 3.610565291 1.000802834 0.63708355 0.700770289 0.071597999 24185476.05 34247248.81 208321.8077 0.017140209 0.054310917 1.265112867 -0.363719284 GGDLMAYDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 GGDLMAYDRR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;;;;;; 144.65 5.10E-05 11683460000 3014011 3766187 3262349 2864441 5190235 4217772 3182553 3065118 3126705 6254735 FALSE TRUE 3133006.482 4413000.32 3347368.495 3431018.88 4308000.709 3238258.374 2933096.18 3024035.107 3014175.498 7480230.569 0.418838223 0.58995512 0.447495363 0.458678225 0.575918171 0.432908898 0.392113071 0.404270307 0.402952218 1 22.83465131 -1.373880566 3.626507235 1.00289096 0.457588609 0.857677591 0.066220498 45080956.42 67167288.97 1374309.507 0.016734198 0.042278487 1.373880566 -0.545302351 GGDS(ph)PEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;GGDS(1)PEAK 163.65 0.00035105 3315280000 8439675 5123268 6486434 4737732 9041535 8514093 8544051 6529320 7362581 5063065 TRUE FALSE 8772879.886 6003149.426 6655475.799 5674841.249 7504658.11 6536823.933 7874345.957 6441805.145 7097603.148 6055075.649 1.44884728 0.991424348 1.099156507 0.937204022 1.239399563 1.079561068 1.30045377 1.063868648 1.172174149 1 22.52971355 0.429651352 0.011108392 6.79E-07 2.198209518 0.07179476 0.144676972 8051.236534 36.43293097 3706.48546 3499.020361 2.689374927 -0.429651352 2.198208839 GGDSIGET(ph)PTPGASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 GGDSIGET(0.999)PT(0.001)PGASK;GGDSIGET(0.983)PT(0.016)PGASK 151.18 3.41E-05 557670000 373250 262519 321760 276060 353140 432220 394650 322720 326300 235000 TRUE FALSE 387986.1982 307604.5961 330145.3299 330663.844 293113.3889 331843.4554 363716.3018 318394.4663 314556.5267 281043.7507 1.38051886 1.094507867 1.174711514 1.176556473 1.042945763 1.180753725 1.294162567 1.132900004 1.119243983 1 18.10043521 -5 0.192370974 0.24327818 1.20481872 0.2890071 0.08984552 191.0379846 1.875055579 55.39938502 0.232152342 1.00E-05 5 0.96154054 GGDVAVELPFTLMHPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGDVAVELPFTLMHPKPK 18 1 P49407-2;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ; 146.58 4.97E-08 980930000 2820200 1766500 2565000 1920400 3287000 3047800 3007100 2554700 3142300 1809260 FALSE TRUE 2931543.674 2069882.634 2631846.007 2300249.388 2728276.914 2339994.64 2771395.644 2520458.425 3029209.237 2163749.857 1.354844075 0.956618265 1.216335613 1.06308471 1.260902181 1.0814534 1.280829961 1.164856657 1.399981254 1 21.04510229 2.234496888 24.99905227 1.220682861 1.14984798 0.034287936 0.139965547 323.4439753 1989718.261 0.046736721 0.035778777 171.5919413 -2.234496888 -0.070834881 GGDVCPKPVFAFHHANFPQYVMDVLMDQHFTEPTPIQCQGFPLALSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGDVCPKPVFAFHHANFPQYVMDVLMDQHFTEPTPIQCQGFPLALSGR 48 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 210.05 2.85E-39 143980000 29446 37934 43195 34203 49054 48124 40354 45309 46763 47977 FALSE TRUE 30608.55082 44448.86941 44320.69719 40968.25131 40715.8186 36947.93033 37190.94803 44701.70697 45080.00876 57377.17457 0.533462148 0.774678602 0.772444749 0.714016534 0.709617002 0.643948236 0.648183678 0.77908519 0.785678436 1 15.80818931 0.825029138 1.206148357 0.998317715 0.694611403 0.648269724 0.068967153 0.432422486 1.186802237 0.064446253 0.019853904 6.683887608 -0.825029138 -0.303706312 GGDVS(ph)PSPYSSSSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(0.939)PS(0.061)PYSSSSWR;GGDVS(0.976)PS(0.024)PYSSSSWR;GGDVS(0.711)PS(0.289)PYSSSSWR;GGDVS(0.996)PS(0.004)PYSSSSWR;GGDVS(0.965)PS(0.035)PYSSSSWR 358.52 1.01E-82 3378600000 1725790 1955140 1770880 1870440 1959480 2170410 1881670 1870180 1735340 1913850 TRUE FALSE 1793925.522 2290920.086 1817030.588 2240407.449 1626408.29 1666365.17 1734179.789 1845113.296 1672885.452 2288832.265 0.783773258 1.000912178 0.793867954 0.978843004 0.710584307 0.728041629 0.757670108 0.806137402 0.730890366 1 21.12618031 3.231598179 24.99987603 0.776357357 0.890497811 0.187733168 0.100351159 220.9344369 793303.744 0.026332772 0.032127109 1704.504605 -3.231598179 0.114140454 GGDVSPS(ph)PYSSSSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGDVSPSPYSSSSWR 15 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YFE7 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 GGDVS(0.344)PS(0.656)PYSSSSWR 294.18 5.56E-44 1233100000 382670 531260 442050 526990 526550 533290 489560 445930 445190 550410 TRUE FALSE 397778.1071 622499.7724 453570.1861 631227.0491 437047.2191 409441.4796 451187.008 439953.0377 429167.6989 658252.3013 0.60429429 0.945685676 0.689052185 0.958943931 0.663950917 0.622012986 0.685431721 0.668365362 0.651980552 1 19.32828113 GGEFDEFVNDDT(ph)DDDLPISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGEFDEFVNDDTDDDLPISK 20 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GGEFDEFVNDDT(1)DDDLPISK;GGEFDEFVNDDT(1)DDDLPISK 164.83 6.46E-11 146721000 432240 365900 415810 352570 477860 509200 487560 439250 459110 366110 TRUE FALSE 449305.169 428740.4787 426646.3502 422307.2937 396633.5279 390946.017 449343.7732 433362.5722 442586.7208 437842.2449 1.026180489 0.979212225 0.974429387 0.964519296 0.905882273 0.892892409 1.026268658 0.989768752 1.01083604 1 18.74005163 -0.681145119 6.516998455 1.000000107 0.973353381 0.030404409 0.042901034 0 0 0.0439618 0.010361896 0.208379447 0.681145119 -0.026646725 GGEFDEFVNDDT(ph)DDDLPISKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGEFDEFVNDDTDDDLPISKK 21 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 GGEFDEFVNDDT(1)DDDLPISKK 69.152 0.011447 261580000 60566 32833 39887 34386 58114 54532 40998 43340 51759 33973 TRUE FALSE 62957.19245 38471.81234 40926.48799 41187.44817 48235.80304 41867.76944 37784.46963 42759.09819 49896.2037 40629.3589 1.549549246 0.94689686 1.007313162 1.013736108 1.187215461 1.030480681 0.929979469 1.052418727 1.228082477 1 15.31023498 4.745238667 24.89641192 1.042739124 1.549549491 0.738849903 0.090162542 370.2846839 1380419.127 0.021491537 0.209260618 55620.98388 -4.745238667 0.506810367 GGEHGPQVPLSQPPEDELDRLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGEHGPQVPLSQPPEDELDRLTK 23 1 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 118.35 0.00017521 71803000 41931 41159 50509 29379 49945 53093 43766 50232 50769 46562 FALSE TRUE 43586.46826 48227.73808 51825.30603 35190.07851 41455.36674 40762.95538 40335.50656 49558.7222 48941.83361 55684.93242 0.782733612 0.866082367 0.930688137 0.631949739 0.744462908 0.732028461 0.724352258 0.889984419 0.878906223 1 15.76499939 1.23464697 1.496586422 0.98600515 0.776674488 0.432547648 0.080589412 0.370268823 1.560035869 0.079025355 0.024078868 17.16512499 -1.23464697 -0.209330662 GGEQISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGEQISR 7 0 Q96AE4;E9PEB5;Q96AE4-2;C9JSZ1;Q96I24;Q96I24-2 Q96AE4;C9JSZ1;Q96I24 FUBP1;FUBP3 Far upstream element-binding protein 1;Far upstream element-binding protein 3 0 77.282 0.089494 132810000 104710 200790 173580 197060 149980 215580 140370 174840 161250 215970 FALSE TRUE 108844.0317 235274.1206 178103.6374 236037.8798 124486.4532 165514.8121 129367.4326 172496.5558 155446.644 258285.1865 0.421410276 0.910908302 0.689561952 0.91386534 0.481972872 0.640821932 0.500870508 0.667853074 0.601841113 1 17.97860538 -1.041805596 4.273717207 1.000026688 0.654038471 0.312456623 0.156533379 16760155.95 8171259.51 4083.263864 0.034967068 0.090822699 1.041805596 -0.345988217 GGET(ph)PGSEQWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGETPGSEQWK 11 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(1)PGSEQWK;GGET(0.996)PGS(0.004)EQWK 287.62 4.33E-27 1600440000 2960480 2264870 2436780 2387830 3452430 3607100 3215270 2799510 2924070 2397440 TRUE FALSE 3077362.036 2653843.804 2500284.489 2860135.647 2865587.182 2769405.691 2963248.736 2761987.148 2818833.292 2867172.466 1.073309008 0.925596153 0.8720384 0.997545729 0.999447091 0.965901327 1.033509065 0.96331392 0.983140472 1 21.45119726 GGEVTDHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGEVTDHSVR 10 0 A0A2R8YFN3;A1Z1Q3-5;A1Z1Q3-4;A1Z1Q3;A1Z1Q3-1 A0A2R8YFN3 MACROD2 O-acetyl-ADP-ribose deacetylase MACROD2 0 ; 180.67 1.97E-06 454982000 274295 346250 314340 324831 354397 371450 295489 303892 309649 377470 FALSE TRUE 285124.3784 405715.744 322531.9586 389081.6023 294156.7245 285186.3669 272327.8001 299818.8248 298504.793 451428.0194 0.631605408 0.898738507 0.714470402 0.861890679 0.651613794 0.631742724 0.603258523 0.664156437 0.661245603 1 18.78413644 4.027140471 24.99701526 0.701668504 0.775530087 0 0.130647707 690.7629547 636199.8887 0.031005703 0.066977743 10644.87267 -4.027140471 0.073861583 GGFCNFMHLKPISR ddPTM_MDA-MB-175_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 ; 204.18 8.41E-09 1511000000 1688790 1903470 1991320 1725030 2498300 2437800 2071700 2077500 2039900 2474000 FALSE TRUE 1755464.733 2230376.166 2043215.435 2066235.785 2073639.858 1871657.895 1909314.741 2049654.511 1966484.397 2958732.932 0.593316387 0.753828148 0.690571093 0.698351569 0.700854016 0.632587644 0.645314999 0.692747388 0.664637344 1 21.49654805 -1.921598886 2.588779454 1.202050916 0.677573866 0.844538369 0.041855261 13155562.72 6526734.041 16082345.03 0.009945014 0.011978463 1.921598886 -0.52447705 GGFDGEYQDDSLDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGFDGEYQDDSLDLLR 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 116.01 0.0010725 19232000 32118 33400 35908 25355 35523 41558 37459 34750 34706 34303 FALSE TRUE 33386.04344 39136.19018 36843.79198 30370.14332 29484.81315 31906.78432 34522.8657 34284.23309 33456.93784 41024.01608 0.813817043 0.953982421 0.898103002 0.740301565 0.718720788 0.777758673 0.841528183 0.835711282 0.815545162 1 15.32418111 -0.328513426 16.47101394 0.999999981 0.822967796 0.398254911 0.065727358 0 0 0.069523029 0.016386735 0.469338925 0.328513426 -0.177032185 GGFDS(ph)PFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;GGFDS(1)PFYR;GGFDS(1)PFYR 148.56 9.41E-05 2476630000 4113350 4202590 4016240 4183210 4771950 4932230 4353740 4123130 3995520 4114630 TRUE FALSE 4275748.234 4924352.141 4120906.514 5010636.452 3960815.643 3786794.331 4012482.482 4067866.186 3851722.016 4920812.969 0.868910942 1.000719225 0.837444247 1.018253789 0.804910828 0.769546487 0.815410484 0.826665474 0.78274099 1 22.23046525 3.210446913 24.99915055 0.820779449 0.929582053 0.264617913 0.078486041 234.8107916 208796.8063 0.0206442 0.024679104 1623.47989 -3.210446913 0.108802604 GGFGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGFGFR 6 0 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 123.06 0.044092 3914770000 2104550 2563870 2302180 2325550 2511200 2619160 2339520 2492220 2078450 2490290 FALSE TRUE 2187639.259 3004194.728 2362176.702 2785536.849 2084347.121 2010899.784 2156142.309 2458815.867 2003646.991 2978214.646 0.73454721 1.008723375 0.793151933 0.935304261 0.69986464 0.675203107 0.723971428 0.825600623 0.672767825 1 21.5060163 3.236429588 24.99972497 0.755335667 0.872646832 0.156022784 0.113987271 87.32446225 1024431.995 0.030139869 0.037734319 1723.572626 -3.236429588 0.117311165 GGFNTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGFNTFR 7 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 95.541 0.051686 0 55691 61270 60445 62279 54478 71773 55704 57919 55882 68032 FALSE TRUE 57889.72368 71792.64589 62020.24636 74597.60032 45217.84902 55104.80848 51337.77492 57142.69054 53870.81774 81361.56785 0.711511899 0.882390148 0.762279391 0.916865325 0.555764229 0.677283021 0.630983108 0.702330253 0.662116269 1 16.31205986 3.246738395 24.99998742 0.684773357 0.818843536 0.16148448 0.121716215 260.3080526 795773.3341 0.030861056 0.041087462 1764.974338 -3.246738395 0.134070179 GGGAPWPGGAQTYS(ph)PSSTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGGAPWPGGAQTYSPSSTCR 20 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GGGAPWPGGAQTYS(1)PSSTCR;GGGAPWPGGAQTYS(0.936)PS(0.063)STCR;GGGAPWPGGAQTYS(0.977)PS(0.001)S(0.018)T(0.005)CR;GGGAPWPGGAQTYS(0.999)PSSTCR 317.83 1.67E-66 941426000 394648 594481 500183 527326 474838 617311 455709 494745 462713 562116 TRUE FALSE 410229.0078 696578.4873 513218.1799 631629.5089 394125.2064 473949.8757 419989.3378 488113.7525 446060.0495 672251.8678 0.610231116 1.036186764 0.763431393 0.939572709 0.586276105 0.70501831 0.624749975 0.726087611 0.663531142 1 19.35864233 3.243125845 24.99934904 0.698834171 0.846277423 0.127807306 0.147728433 180.7414129 989739.5637 0.037522275 0.049160075 1750.353814 -3.243125845 0.147443252 GGGDRYEDRYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGDRYEDRYDR 12 2 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 204.48 6.35E-08 3388200000 1720670 2452100 2120520 1857660 2467400 2567300 1790770 2132680 2169770 3133100 FALSE TRUE 1788603.38 2873229.1 2175782.493 2225099.603 2047992.229 1971083.483 1650404.768 2104094.913 2091680.402 3746970.958 0.477346475 0.766813816 0.580677704 0.593839565 0.546572752 0.526047174 0.44046372 0.561545562 0.55823235 1 21.83729337 -1.220311425 6.638061526 1.000002923 0.562031329 0.721708978 0.081727609 3.56E-06 4.18E-07 0.079635223 0.018770077 0.060212766 1.220311425 -0.437971594 GGGEAAQS(ph)PGPLPQSKPDGGETLYVTADLTLEDNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGGEAAQSPGPLPQSKPDGGETLYVTADLTLEDNRR 36 2 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 GGGEAAQS(1)PGPLPQSKPDGGETLYVTADLTLEDNRR 64.083 0.0043075 88402000 93786 108990 129430 111000 131820 147690 122970 121630 131530 131700 TRUE FALSE 97488.7437 127708.1847 132803.0521 132955.4687 109413.2835 113391.2358 113331.2901 119999.7488 126796.261 157504.0935 0.618960064 0.810824544 0.843172068 0.844139767 0.69466946 0.719925643 0.719545045 0.761883365 0.805034702 1 17.2650298 0.756542539 2.304714719 0.999914633 0.755318845 0.559666179 0.065976881 0.821233589 6.501969974 0.064442373 0.017432084 5.708769901 -0.756542539 -0.244595788 GGGEYGETWHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGEYGETWHK 11 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ; 97.597 0.0061481 735380000 831480 713190 988750 802320 1086710 1116990 1001910 905730 1015210 782320 FALSE TRUE 864307.4724 835674.8347 1014517.637 961016.5013 901991.4224 857586.0006 923377.6762 893590.1708 978672.7904 935600.6256 0.923799588 0.893196105 1.084349037 1.027165304 0.964077404 0.916615463 0.986935719 0.955097877 1.046036913 1 19.8355333 4.304291753 24.99999984 0.990563457 0.908497032 0.366953151 0.046055374 67.70500057 25748.91896 0.011690789 0.032016537 20150.77497 -4.304291753 -0.082066424 GGGFGDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGGFGDRDR 9 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 104.89 0.0029066 3573130000 2232690 3097200 2574510 2388230 3386200 3250600 2261560 2644020 2448400 4009260 FALSE TRUE 2320838.325 3629120.007 2641603.846 2860614.766 2810614.934 2495697.413 2084293.018 2608581.237 2360282.562 4794797.735 0.484032581 0.756886986 0.550931237 0.596608016 0.586180083 0.520501083 0.434698841 0.544044062 0.492259047 1 22.19303853 -1.795417392 6.907188247 1.017252311 0.553380323 0.726185083 0.082561396 0.021318434 0.000631426 0.077694624 0.01895961 0.016017053 1.795417392 -0.463871988 GGGGEGGGEAS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGGGEGGGEASPDR 14 0 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR;GGGGEGGGEAS(1)PDR 186.62 1.09E-06 445010000 575988 647122 601709 706688 596883 696142 706213 645692 561545 555870 TRUE FALSE 598728.451 758260.1696 617390.0308 846468.7771 495425.0409 534473.5706 650858.1797 637037.5549 541335.1051 664782.0837 0.900638669 1.140614629 0.928710394 1.273302632 0.745244273 0.803983115 0.979054935 0.958265228 0.814304595 1 19.34252198 3.22261836 24.99999309 0.889581179 1.057080376 0.328922961 0.123864911 290.930216 456224.0056 0.034808784 0.041728323 1669.622776 -3.22261836 0.167499198 GGGGEGGGEAS(ph)PDRQGSLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGGGEGGGEASPDRQGSLPSR 21 1 A0A0D9SGD0;A0A0D9SGA5 A0A0D9SGD0 SLC12A5 1 GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR;GGGGEGGGEAS(1)PDRQGSLPSR 278.61 4.17E-45 2726640000 769444 906396 886594 780622 996057 956621 737561 836475 844893 1113066 TRUE FALSE 799822.2433 1062062.462 909699.368 935026.7017 826747.5869 734460.2705 679749.0416 825263.4208 814485.466 1331149.972 0.600850588 0.797853348 0.683393597 0.702420254 0.621077718 0.551748703 0.510647978 0.619962768 0.611866043 1 20.34424169 -1.468145389 9.079936543 1.000005445 0.632550986 0.676355459 0.07609454 9.17E-06 5.37E-07 0.080555252 0.018986774 0.034029425 1.468145389 -0.367454459 GGGGGQDNGLEGLGNDS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 326.37 1.91E-63 1808180000 1436120 1619370 1434420 1820530 1656110 1849810 1698190 1608470 1585400 1365380 TRUE FALSE 1492819.127 1897484.201 1471802.164 2180625.4 1374605.014 1420219.662 1565081.43 1586911.091 1528341.764 1632900.069 0.914213401 1.162033266 0.901342459 1.335431017 0.84181821 0.869752956 0.958467367 0.971836012 0.935967725 1 20.63900507 GGGGNFGPGPGSNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 245.46 9.83E-18 455400000 362280 338500 326360 322380 355870 388200 330880 344370 336210 370670 FALSE TRUE 376583.0941 396634.7418 334865.2097 386145.8018 295379.3445 298046.4332 304944.761 339754.2834 324109.8678 443295.6896 0.849507683 0.894740804 0.755399201 0.871079532 0.666325776 0.672342277 0.687903736 0.766428123 0.731136971 1 18.75790981 3.252170127 24.97562351 0.73603085 0.840165845 0.153664264 0.096470548 346.3920914 635680.9809 0.025036678 0.033717607 1787.187538 -3.252170127 0.104134995 GGGGSSS(ph)SSSELSTPEKPPHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGGGSSSSSSELSTPEKPPHQR 22 1 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1 A0A2R8YFV7 TSC1 Hamartin 1 GGGGS(0.011)S(0.07)S(0.458)S(0.458)S(0.003)SELSTPEKPPHQR 120.63 1.72E-05 97417000 94993 72458 97691 76004 118630 113180 92052 76383 92111 69574 TRUE FALSE 98743.39699 84902.09786 100236.9077 91037.36435 98465.31497 86895.66026 84836.72371 75359.21082 88795.9431 83205.69323 1.186738469 1.020388084 1.204688091 1.094124222 1.183396366 1.044347531 1.01960239 0.90569777 1.067185906 1 16.34439463 2.431195959 2.6671666 0.980717562 1.132323379 0.514598566 0.063359583 0.199242719 2.896568 0.022964492 0.018907847 269.895696 -2.431195959 0.151605816 GGGGYTCQS(ph)GSGWDEFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGGYTCQSGSGWDEFTK 18 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GGGGYTCQS(0.999)GS(0.001)GWDEFTK;GGGGYTCQS(0.999)GS(0.001)GWDEFTK 318.82 1.93E-61 323350000 680020 548240 645380 589900 812630 770720 705540 659430 695860 556430 TRUE FALSE 706867.7147 642395.9553 662199.133 706580.4593 674499.4429 591731.9604 650237.9312 650591.4195 670816.1345 665451.805 1.062237279 0.965353089 0.995112085 1.061805609 1.013596233 0.889218356 0.977137527 0.977668728 1.008061184 1 19.34397466 2.959909464 24.99997363 0.9684475 1.01808701 0.271976185 0.040214282 713.6274426 445008.8602 0.012294654 0.013042372 911.8207356 -2.959909464 0.04963951 GGGHVAQIYAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGGHVAQIYAIR 12 0 P62249;M0R210;M0R3H0;M0R1M5;M0QX76 P62249 RPS16 40S ribosomal protein S16 0 ;;;; 141.93 6.09E-05 2612600000 1315335 1408780 1377530 1445732 1644450 1496760 1722770 1477500 1325683 1332610 FALSE TRUE 1367265.441 1650727.006 1413429.563 1731693.475 1364926.976 1149160.174 1587734.786 1457696.529 1277971.928 1593709.415 0.857913888 1.035776654 0.88688035 1.086580438 0.856446579 0.721060039 0.996251117 0.914656408 0.801885159 1 20.60395717 GGGPGKS(ph)PTQGST ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGPGKSPTQGST 13 1 Q6P582 Q6P582 MZT2A Mitotic-spindle organizing protein 2A 1 GGGPGKS(0.631)PT(0.367)QGS(0.001)T(0.001);GGGPGKS(0.915)PT(0.082)QGS(0.001)T(0.002) 112.96 0.0022604 203344000 499770 402930 437050 376420 535640 561000 471640 441370 461850 409420 TRUE FALSE 519501.3055 472130.0931 448439.882 450874.7525 444592.1041 430716.252 434671.6244 435454.1571 445228.1087 489638.0102 1.060990558 0.964243142 0.915860029 0.920832826 0.908001615 0.879662614 0.88774077 0.889338957 0.909300543 1 18.90135603 4.931897676 1.22504607 0.903961277 1.192176575 0.65132768 0.032487998 1.150916737 1.089777635 0.008430082 0.468527137 85486.52738 -4.931897676 0.288215298 GGGPGKS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.637)PT(0.363)R;GGGPGKS(0.954)PT(0.046)R;GGGPGKS(0.877)PT(0.123)R;GGGPGKS(0.5)PT(0.5)R;GGGPGKS(0.842)PT(0.158)R 87.216 0.012493 4149840000 3006540 2229550 2554210 2130480 3018230 3140710 2888200 2510540 2665780 2218760 TRUE FALSE 3125240.521 2612457.869 2620774.811 2551882.585 2505192.343 2411327.7 2661815.337 2476890.318 2569839.099 2653483.541 1.177787792 0.984538938 0.987673287 0.96171035 0.944114521 0.908740402 1.003139946 0.933448533 0.968477497 1 21.33945617 5.290595734 1.420329194 0.957091303 1.75472287 0.832372336 0.028557144 1.785698975 1.084695257 0.007245539 2.986757507 195252.1094 -5.290595734 0.797631567 GGGPGKS(ph)PTRGST ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGPGKSPTRGST 13 2 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.9)PT(0.093)RGS(0.002)T(0.005);GGGPGKS(0.941)PT(0.058)RGS(0.001)T(0.001) 58.246 0.0854 239450000 327220 414640 387800 190055 633820 485770 189663 340960 401920 712920 TRUE FALSE 340138.8983 485851.1945 397906.3866 227647.3117 526083.5028 372957.2794 174796.7185 336389.9889 387454.9777 852603.0243 0.398941698 0.569844559 0.46669596 0.267002703 0.61703218 0.437433681 0.205015363 0.394544682 0.454437724 1 19.70151465 0.780010517 5.266722952 0.999999251 0.416785098 0.690518104 0.115992859 4.000578607 95.56218294 0.113268572 0.028579753 6.025741781 -0.780010517 -0.583214152 GGGPGKSPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGGPGKSPTR 10 1 H7BZ50;H7C173;A0A494C0V9;B8ZZ87;Q6NZ67 H7BZ50 MZT2B Mitotic-spindle organizing protein 2B 1 GGGPGKS(0.263)PT(0.737)R 76.357 0.058587 595330000 1242000 930050 1103400 1004100 1310000 1393000 1242900 1096100 1187900 914610 TRUE FALSE 1291035.119 1089778.853 1132155.51 1202707.983 1087326.668 1069496.861 1145478.25 1081408.572 1145147.711 1093810.318 1.180309874 0.996314292 1.035056528 1.099558089 0.994072418 0.977771779 1.047236647 0.988661886 1.046934457 1 20.06093115 4.743944689 24.91183913 1.020758434 1.180309945 0.648876234 0.035240198 344.7508001 1595094.638 0.008389767 0.072522371 55455.50816 -4.743944689 0.159551511 GGGPQAQSHGEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGPQAQSHGEAR 13 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 0 ; 115.34 0.00067172 296910000 53811 67995 60868 70082 58077 89179 48588 47937 57847 62648 FALSE TRUE 55935.49983 79672.61232 62454.27008 83944.01043 48205.09228 68468.52877 44779.5456 47294.48292 55765.09777 74922.67613 0.746576373 1.063397845 0.833583013 1.120408597 0.643397897 0.913855889 0.597676804 0.631243909 0.744302001 1 16.19311481 3.222058548 24.99924676 0.726359555 0.942062789 0.245775568 0.154711709 276.4766223 418837.9148 0.042411446 0.050825504 1667.471993 -3.222058548 0.215703234 GGGPVTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GGGPVTLQDYRLPDS(1)DDDEDEETAIQR;GGGPVTLQDYRLPDS(1)DDDEDEETAIQR;GGGPVT(0.005)LQDY(0.016)RLPDS(0.978)DDDEDEETAIQR;GGGPVTLQDYRLPDS(1)DDDEDEETAIQR 189.31 4.50E-18 793841000 127922 166111 168581 138679 160692 184989 108406 147247 144972 220609 TRUE FALSE 132972.4593 194639.2721 172974.3594 166109.2923 133377.6312 142028.1083 99908.85445 145273.3948 139754.486 263833.1097 0.504002168 0.737736337 0.655620364 0.629599873 0.505537881 0.538325567 0.378682018 0.550626094 0.529707913 1 18.0092661 -0.994205884 4.878530621 1.000005474 0.55835897 0.670609854 0.092747959 5.92E-06 1.22E-06 0.096343178 0.022708023 0.101343084 0.994205884 -0.441646503 GGGQEERPFVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGGQEERPFVAR 12 1 Q9HA64;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 ;; 187.58 9.40E-06 1436130000 913260 1135040 1031050 1082080 1114630 1293630 1085590 1114810 996610 1114920 FALSE TRUE 949316.21 1329974.291 1057920.01 1296112.194 925165.5907 993204.0377 1000498.619 1099867.795 960742.2008 1333367.228 0.711969059 0.997455362 0.793419838 0.972059435 0.693856555 0.744884093 0.75035489 0.824879878 0.720538334 1 20.34664274 3.233152211 24.99938421 0.778916258 0.872541874 0.107171439 0.110072176 243.4796243 1125440.041 0.028870691 0.035457392 1710.614742 -3.233152211 0.093625616 GGGSQHYPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGGSQHYPEER 11 0 Q9NWH9;Q9NWH9-3;H7C3F4;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 72.958 0.034684 0 104930 215070 187190 198890 201900 223710 172340 192830 167910 244520 FALSE TRUE 109072.7174 252006.5995 192068.3252 238229.8484 167581.1101 171756.7429 158831.5405 190245.4293 161866.9519 292429.0124 0.372988701 0.861770169 0.656803248 0.814658732 0.573065951 0.587345084 0.543145631 0.650569612 0.553525625 1 18.15772693 -1.858440592 3.799329612 1.106467048 0.632677887 0.421555333 0.131844861 0.076906547 0.002865465 0.082570446 0.028156977 0.013853497 1.858440592 -0.473789161 GGGT(ph)PDANSLAPPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGGTPDANSLAPPGK 15 0 Q9BRQ0;Q5T171 Q9BRQ0 PYGO2 Pygopus homolog 2 1 GGGT(1)PDANSLAPPGK;GGGT(1)PDANSLAPPGK;GGGT(0.958)PDANS(0.042)LAPPGK;GGGT(1)PDANSLAPPGK 229.92 4.45E-12 4548200000 6473270 5209500 6106480 5081970 6897380 6976950 6211090 5986090 6234890 5847800 TRUE FALSE 6728839.698 6104191.101 6265619.885 6087168.498 5724965.811 5356659.099 5724248.536 5905856.255 6010497.527 6993564.447 0.962147378 0.872829749 0.895912225 0.870395711 0.818604855 0.765941193 0.818502293 0.844470127 0.859432636 1 22.73759652 5.129921684 0.866704357 0.841530651 1.103163076 0.196306543 0.058751957 5.497414455 2.017866203 0.0184005 1.600960038 134871.9646 -5.129921684 0.261632425 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 GGGTSSGGSSTNS(0.999)LT(0.001)GSRPPK;GGGTSSGGSST(0.001)NS(0.993)LT(0.005)GSRPPK;GGGTSSGGSSTNS(1)LTGSRPPK;GGGTSSGGSSTNS(1)LTGSRPPK;GGGTSSGGSS(0.001)T(0.004)NS(0.995)LTGSRPPK;GGGTSSGGSS(0.004)T(0.003)NS(0.988)LT(0.005)GSRPPK 307.26 1.74E-56 1725960000 690222 635526 705120 631424 881580 800675 821499 758312 749881 726608 TRUE FALSE 717472.4975 744672.6468 723496.0065 756317.7826 731729.3465 614730.3656 757107.7618 748148.068 722892.9293 868972.9258 0.825655755 0.856957248 0.832587512 0.870358282 0.842062307 0.70742177 0.871267377 0.860956706 0.831893501 1 19.7289517 -0.159967853 0.78207714 1.006009615 0.831666164 0.553755128 0.044886665 5.952382643 3.241819395 0.15653234 0.015396278 0.691882183 0.159967853 -0.17434345 GGGYGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGGYGGDR 8 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ; 103.91 0.010893 258960000 338910 415510 327330 341060 384840 429970 312480 338010 311990 430830 FALSE TRUE 352290.4285 486870.6103 335860.4887 408520.65 319425.0343 330115.9838 287987.0011 333479.5288 300761.5408 515242.8898 0.683736613 0.944934166 0.651848857 0.792870039 0.619950397 0.640699737 0.55893445 0.647227813 0.583727688 1 18.97489317 3.240646122 24.996456 0.647672322 0.772639446 0.079150394 0.137660553 95.98744678 1150472.538 0.03554459 0.045857471 1740.388168 -3.240646122 0.124967125 GGHMDDGGYSMNFNMSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 226.32 1.53E-19 1272960000 484794 715260 688280 696640 737510 854090 661790 676260 631860 863600 FALSE TRUE 503934.0415 838100.341 706217.1422 834433.3127 612148.3136 655740.5414 609917.1705 667195.8408 609119.482 1032805.885 0.487927159 0.811479052 0.683784971 0.807928503 0.59270413 0.634911701 0.590543856 0.646003136 0.589771506 1 19.9781377 -1.901149104 3.63927612 1.15084639 0.654633167 0.55257869 0.094527195 0.061352154 0.001666462 0.048536022 0.02064127 0.012555988 1.901149104 -0.496213223 GGHSGQLGPSSVAPSFRPEDELEHLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGHSGQLGPSSVAPSFRPEDELEHLTK 27 1 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ; 294.36 8.76E-71 529330000 263900 401960 439960 429640 512920 601190 501700 497570 490900 403770 FALSE TRUE 274318.9758 470993.5032 451425.719 514621.5097 425734.0416 461572.7336 462375.4431 490900.888 473232.6049 482881.0009 0.568088153 0.975382138 0.934859144 1.065731534 0.881654157 0.955872633 0.957534967 1.016608413 0.980019102 1 18.88130818 4.738673611 24.52704436 0.974086103 0.568088009 0.872940125 0.0464796 2.172140964 470735.6114 0.010711935 0.061975083 54786.50689 -4.738673611 -0.405998093 GGIDNPAITS(ph)DQELDDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGIDNPAITSDQELDDKK 18 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GGIDNPAIT(0.023)S(0.977)DQELDDKK;GGIDNPAIT(0.105)S(0.895)DQELDDKK;GGIDNPAIT(0.024)S(0.976)DQELDDKK 232.02 2.91E-20 1607380000 3103020 807670 1345180 800280 2068630 2032510 2086470 1408990 1822570 697210 TRUE FALSE 3225529.626 946381.0397 1380236.496 958572.9954 1717005.011 1560490.355 1922927.029 1390104.794 1756976.062 833814.9506 3.868399845 1.135001284 1.655327114 1.14962318 2.059215909 1.871506807 2.3061796 1.667162231 2.107153464 1 19.66936771 8 0.043620593 2.37E-11 5.050571157 0.147290154 0.725798946 1711.187645 5.664431746 169.9723917 614.3652358 99999999.99 -8 5.050571157 GGISNVWFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGISNVWFDR 10 0 Q5VWZ2 Q5VWZ2 LYPLAL1 Lysophospholipase-like protein 1 0 123.42 0.0069263 0 124980 143440 130440 121930 143850 174240 134330 132880 99351 157960 FALSE TRUE 129914.3069 168074.7042 133839.3736 146047.3901 119398.4284 133775.4006 123800.8636 131098.9609 95775.37692 188909.2377 0.687707539 0.88971141 0.708485065 0.773108779 0.632041238 0.708146421 0.655345737 0.693978561 0.506991495 1 17.52733373 3.26013162 24.31731949 0.682528266 0.769659692 0.049926147 0.126712074 400.5285926 451517.8185 0.032071317 0.043381129 1820.252432 -3.26013162 0.087131426 GGKNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGKNIR 6 1 Q9NYT6 Q9NYT6 ZNF226 Zinc finger protein 226 0 ; 80.498 0.058693 874840000 1266830 1261140 1435510 1141190 1811530 1836710 1917150 1871480 1900870 1677990 FALSE TRUE 1316845.427 1477730.985 1472920.57 1366913.976 1503606.778 1410161.938 1766878.773 1846395.872 1832458.06 2006760.013 0.656204737 0.736376535 0.73397943 0.681154681 0.749270848 0.702705819 0.880463414 0.920088032 0.913142602 1 20.93643667 2.136871181 2.948283838 0.932097477 0.711235892 0.903238341 0.035312902 0.073576068 1.277617361 0.014739572 0.009891805 137.0475201 -2.136871181 -0.220861585 GGLDNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGLDNAR 7 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;; 111.73 0.015154 644510000 987580 1177850 1149620 1076840 1268670 1361320 1325480 1146670 1112880 1308930 FALSE TRUE 1026570.421 1380136.575 1179580.042 1289835.738 1053021.927 1045174.061 1221585.414 1131300.764 1072827.666 1565389.773 0.655792212 0.881656824 0.753537593 0.823970976 0.672689924 0.667676562 0.780371404 0.722695896 0.685342197 1 20.57809049 -1.661919446 8.720260841 1.00029084 0.741889708 0.556001703 0.07011683 0.000384442 1.49E-05 0.065831108 0.015499605 0.021781137 1.661919446 -0.258401133 GGLLTSEEDSGFSTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFST(0.023)S(0.977)PK;GGLLTSEEDSGFS(0.003)T(0.336)S(0.661)PK;GGLLTSEEDSGFST(0.004)S(0.996)PK;GGLLTSEEDSGFST(0.001)S(0.999)PK 270.45 1.45E-35 312580000 1335730 574700 712920 625340 868480 1035200 1001010 764750 746840 401516 TRUE FALSE 1388465.652 673400.2545 731499.2809 749030.3855 720856.0798 794790.4886 922548.2205 754499.7771 719961.3743 480185.3727 2.891520089 1.402375609 1.523368521 1.559877556 1.501203745 1.655174301 1.921233492 1.571267723 1.499340495 1 18.87323193 8 0.049281681 3.38E-19 4.685147748 0.343014966 0.377919253 699.5151549 2.602641625 58.85895356 250.5742339 100000000 -8 4.685147748 GGLLTSEEDSGFSTS(ph)PKDNSLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGLLTSEEDSGFSTSPKDNSLPK 23 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 GGLLTSEEDSGFS(0.002)T(0.125)S(0.872)PKDNSLPK 125.78 3.19E-05 149980000 115330 50841 70228 38686 107580 97860 93282 64404 77910 43718 TRUE FALSE 119883.3175 59572.54626 72058.19937 46337.97533 89293.59003 75133.49808 85970.31309 63540.76972 75106.03432 52283.70507 2.292938446 1.139409424 1.378215245 0.886279488 1.707866531 1.437034693 1.644304148 1.215307325 1.43650941 1 15.67407376 7.999999983 0.034299222 1.61E-10 3.549362317 0.168889757 0.350602556 2333.802022 6.118857623 189.0088913 520.6433405 99999996.1 -7.999999983 3.549362316 GGLRPGS(ph)LDAEIDLLSSTLAELNGGR ddPTM_MDA-MB-175_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(1)LDAEIDLLSSTLAELNGGR 140.24 1.93E-07 23577560000 1068272 1218021 1195936 1386490 1471870 1571982 1299724 1245980 1297778 1700450 TRUE FALSE 1110448.203 1427206.632 1227103.075 1660733.584 1221682.063 1206913.004 1197848.237 1229279.676 1251071.223 2033620.62 0.546044917 0.701805744 0.603408061 0.81663884 0.600742366 0.59347992 0.589022468 0.604478369 0.61519401 1 20.95561913 -1.980391156 2.402904571 1.330872858 0.631201348 0.701105967 0.072454259 5566942.897 2223696.048 10224508.01 0.017087304 0.010461859 1.980391156 -0.69967151 GGLS(ph)PANDTGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGLSPANDTGAK 12 0 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK;GGLS(1)PANDTGAK 242.57 2.80E-16 8509800000 17119900 12046000 14155700 11929000 17502200 17924200 17862000 14940800 15502800 10623600 TRUE FALSE 17795806.87 14114806.8 14524609.17 14288520.6 14527182.3 13761576.19 16461929.77 14740543.01 14944857.26 12705091.02 1.400683147 1.110956763 1.143211737 1.124629534 1.143414264 1.083154475 1.29569554 1.160207589 1.176288878 1 23.59890338 -1.229628199 0.01661241 8.78E-06 2.173916087 0.250515869 0.091693279 3729.680364 10.96408741 796.2138858 643.5162452 0.058934798 1.229628199 2.173907303 GGLS(ph)PANDTGAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGLSPANDTGAKK 13 1 P30419;B7Z8J4;K7EN42 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 GGLS(1)PANDTGAKK;GGLS(0.999)PANDT(0.001)GAKK 104.2 0.00047017 380750000 1225790 647670 878490 514300 1258520 1080430 904450 803410 1028700 647480 TRUE FALSE 1274185.136 758902.2843 901384.1711 616027.005 1044597.22 829516.5066 833556.8457 792641.6031 991677.2879 774341.3092 1.645508409 0.980061732 1.164065717 0.795549711 1.349013939 1.071254364 1.076472139 1.023633369 1.280672071 1 19.56261008 4.744910526 24.91439674 1.081642482 1.645508674 0.564514066 0.148400407 473.3692546 1857251.201 0.032616696 0.306905045 55578.97408 -4.744910526 0.563866191 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGLWDDDDAPRPSQFEEDLALMEEMEAEHR 30 1 A0A087WYJ2;M0R2B7;P28340;M0QZR8;A0A2R8Y7K6;M0R2J2 A0A087WYJ2 POLD1 DNA polymerase;DNA polymerase delta catalytic subunit 0 ;; 225.84 4.45E-35 121472000 88327 117249 118383 125434 127173 142249 113140 116009 116225 143756 FALSE TRUE 91814.21816 137385.6037 121468.1582 150244.4708 105556.1789 109213.8256 104271.7912 114454.0891 112042.085 171922.2358 0.534045045 0.799114803 0.706529657 0.873909475 0.613976304 0.63525131 0.606505556 0.665731739 0.651702116 1 17.39139662 -1.919447763 5.441995067 1.116793647 0.679532424 0.521222487 0.093023729 0.056490854 0.000836176 0.0385998 0.020911313 0.012037942 1.919447763 -0.437261224 GGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 35 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 479.09 1.77E-283 1015590000 438810 458340 520330 334840 660520 643610 369350 489320 537340 733920 FALSE TRUE 456134.5576 537056.3296 533890.2273 401070.3526 548245.0463 494141.3315 340399.3819 482761.4658 518001.2384 877717.5723 0.519682609 0.611878293 0.608271093 0.456946933 0.624625806 0.562984435 0.387823364 0.550019142 0.590168472 1 19.74339727 0.690187722 2.826375774 0.999968097 0.539338879 0.796226278 0.069339664 1.114318031 9.651029443 0.066936831 0.017615984 4.899905697 -0.690187722 -0.460629218 GGMRAVEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGMRAVEFK 9 1 P55072;C9IZA5 P55072 VCP Transitional endoplasmic reticulum ATPase 0 67.563 0.063538 461870000 348700 285740 324430 323550 457340 449050 373970 322700 367690 316690 FALSE TRUE 362466.9453 334813.6223 332884.9123 387547.2243 379601.5102 344764.9429 344657.2542 318374.7343 354456.9087 378739.3421 0.957035367 0.884021238 0.878928792 1.023255789 1.002276415 0.910296092 0.910011757 0.840617013 0.935886161 1 18.53084577 -0.266850927 7.932262064 0.999999999 0.92200901 0.139437329 0.05321461 0 0 0.056440412 0.013303133 0.540939971 0.266850927 -0.077990989 GGNFGFGDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GGNFGFGDSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;;;; 222.07 1.18E-08 26179900000 11865610 14668850 13042180 13519420 14235660 15439710 13192940 13673710 12534030 15027690 FALSE TRUE 12334073.45 17188110.88 13382069.93 16193520.92 11815887.6 11854071.34 12158842.89 13490436.28 12082932.71 17972078.13 0.686290887 0.956378598 0.744603369 0.901037754 0.657458059 0.659582674 0.676540732 0.750633076 0.672316947 1 24.0992539 5.055161289 15.69282669 0.765344495 0.106208979 0.038375438 0.122467055 9309896.79 65225048.22 0.028241877 190339883 113543.2417 -5.055161289 -0.659135515 GGNFGGR ddPTM_MDA-MB-175_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 ;;;;; 153.61 0.0040348 3781160000 2451680 3114260 2670560 2776270 2959100 3307840 2773760 2831350 2725860 3175480 FALSE TRUE 2548474.22 3649109.929 2740156.987 3325407.92 2456113.239 2539644.291 2556345.443 2793400.384 2627756.831 3797654.508 0.671065315 0.960885178 0.721539303 0.875647828 0.646744783 0.668740215 0.673137969 0.735559377 0.691942046 1 21.85667723 5.046438026 16.57833683 0.758772795 0.15489713 0.047665584 0.121276858 12858092.71 115489963.7 0.027625389 246986747.5 111285.3576 -5.046438026 -0.603875665 GGNIGDGGGAADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGNIGDGGGAADR 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 157.22 0.00011065 1779300000 1617880 1939190 1674100 1825830 1907610 2000960 1731940 1740380 1616790 1992240 FALSE TRUE 1681755.152 2272230.798 1717728.421 2186973.724 1583355.134 1536267.365 1596186.017 1717053.053 1558602.044 2382581.284 0.705854261 0.953684482 0.720952705 0.917900992 0.664554508 0.644791166 0.669939795 0.720669244 0.654165318 1 21.184094 3.223024429 24.99936696 0.705169723 0.826415342 0.125046723 0.121048472 365.3646661 587909.017 0.031791656 0.038124323 1671.184615 -3.223024429 0.121245618 GGNRFEPYANPTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGNRFEPYANPTKR 14 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 151.54 3.89E-06 1208200000 1340150 1305750 1418700 1016520 1899080 1664900 1165930 1312520 1424980 1713060 FALSE TRUE 1393060.157 1530002.405 1455672.487 1217584.622 1576275.06 1278252.207 1074541.36 1294927.816 1373695.248 2048701.308 0.679972308 0.74681575 0.710534269 0.594320225 0.769402086 0.623932928 0.524498791 0.632072529 0.670520023 1 20.96627823 -1.785089185 7.717609379 1.00751845 0.657448375 0.684815273 0.068879927 0.009407395 0.000261966 0.070411318 0.016529574 0.016402529 1.785089185 -0.350070075 GGNVFAALIQDQS(ph)EEEEEEEKHPPKPAKPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGNVFAALIQDQSEEEEEEEKHPPKPAKPEK 31 3 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 GGNVFAALIQDQS(1)EEEEEEEKHPPKPAKPEK;GGNVFAALIQDQS(1)EEEEEEEKHPPKPAKPEK 147.76 6.04E-09 7753200000 12353800 3118220 6354780 3430890 10150100 7844200 8556800 5893380 7884300 2641730 TRUE FALSE 12841537.56 3653750.029 6520390.787 4109509.802 8424789.628 6022503.43 7886095.657 5814388.881 7600545.583 3159326.415 4.064644129 1.156496528 2.063854737 1.300755054 2.666641088 1.906261855 2.496131967 1.840388778 2.405748753 1 21.59118557 -0.71050658 8.164391626 1.000015328 2.142831884 0.17569095 0.774423014 0 0 0.672382588 0.158482096 0.194757154 0.71050658 1.142816555 GGNVGINSFGFGGSNVHIILRPNTQPPPAPAPHATLPR ddPTM_MDA-MB-175_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 ; 286.24 2.67E-77 4383800000 114903 287007 293161 358321 313143 355490 199091 235959 247878 324237 FALSE TRUE 119439.4592 336298.2196 300801.0165 429195.8243 259915.0647 272932.835 183485.7272 232796.3556 238956.9192 387765.0323 0.308020191 0.867273198 0.775730124 1.106845096 0.670290106 0.703861391 0.473187915 0.600354174 0.616241536 1 18.56482318 3.022492351 24.998963 0.63828754 0.78710898 0.015777168 0.224194496 592.0876848 658067.0568 0.063172839 0.075501547 1053.155138 -3.022492351 0.148821439 GGPAS(ph)PGGLQGLETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 239.7 8.59E-18 587027000 417460 460735 458686 454391 486650 540850 437290 438481 400164 464292 TRUE FALSE 433941.6431 539862.6522 470639.734 544268.1836 403929.4068 415245.7842 403014.0672 432603.8794 385762.1758 555261.128 0.781509134 0.972268047 0.847600724 0.980202208 0.727458463 0.747838743 0.725809978 0.779099882 0.694740108 1 19.08280688 3.226027588 24.99526282 0.764052032 0.897472088 0.251990595 0.095989448 248.7835082 496160.8399 0.025148574 0.030252106 1682.780952 -3.226027588 0.133420056 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGK 35 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK;GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK 182.21 2.17E-20 159841000 286361 162827 207343 210696 243219 283150 305382 222560 231532 137425 TRUE FALSE 297666.7534 190791.2706 212746.5289 252371.0399 201876.7213 217392.7037 281445.3609 219576.9472 223199.2085 164350.7976 1.811167075 1.160878276 1.294466057 1.53556322 1.228328211 1.322735921 1.712467265 1.336026052 1.358065868 1 17.32641893 0.673752351 2.020598389 1.000328428 1.41591516 0.293397456 0.196941154 1.977619488 10.54376792 0.177745051 0.048956618 4.717939318 -0.673752351 0.415586732 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGKQK 37 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 GGPEGVAAQAVAS(0.001)AAS(0.012)AGPADAEMEEIFDDAS(0.988)PGKQK 46.898 0.043319 26590000 85228 36984 56202 35134 81650 79121 67536 53052 59708 34589 TRUE FALSE 88592.86725 43335.7143 57666.67029 42083.40034 67771.16216 60746.34684 62242.35185 52340.92472 57559.12074 41366.0523 2.141680492 1.047615421 1.394057859 1.017341467 1.63832801 1.468507229 1.504672271 1.26531109 1.391457911 1 15.33615966 -3.677634147 0.202025114 1.24E-14 1.479977474 0.172536155 0.297509183 149.1494236 2.39189733 62.57590216 0.683210097 0.000210071 3.677634147 1.479977474 GGPEVQQVPAGERPLWFICSGMGTQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 283.81 2.50E-61 18037180000 1989675 2350978 2360361 2701528 2419307 2746046 2138357 2179434 2228541 2476666 FALSE TRUE 2068228.905 2754740.183 2421873.947 3235882.175 2008074.06 2108318.433 1970746.991 2150222.252 2148336.245 2961921.284 0.698272745 0.930051787 0.817669922 1.092494319 0.677963345 0.711807719 0.665361028 0.725955232 0.72531848 1 21.49810187 GGPGAAPGGAS(ph)PASSSSAASSPSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 GGPGAAPGGAS(0.499)PAS(0.396)S(0.083)S(0.018)S(0.004)AASSPSSGR 137.64 1.41E-12 0 23199 29463 28028 27561 28031 34744 28608 24980 23678 29165 TRUE FALSE 24114.91443 34523.04106 28758.43271 33012.48354 23266.30063 26675.23255 26365.63021 24645.18396 22825.83341 34879.32335 0.691381372 0.989785287 0.824512345 0.946477178 0.667051376 0.764786412 0.755910026 0.706584348 0.654423057 1 15.09008443 3.237810359 24.99999977 0.741426274 0.869340438 0.153027985 0.116647786 28.86488768 961843.8795 0.030346817 0.038359685 1729.061173 -3.237810359 0.127914164 GGPGAAPGGASPAS(ph)SSSAASSPSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 GGPGAAPGGAS(0.009)PAS(0.97)S(0.017)S(0.004)SAASSPSSGR 197 7.01E-25 126750000 79426 124300 102910 116490 101940 120020 97013 99267 100390 107020 TRUE FALSE 82561.79981 145647.5581 105591.9191 139531.3743 84612.27521 92147.17392 89408.86756 97936.48823 96776.98351 127988.52 0.645071916 1.13797361 0.825010862 1.090186638 0.661092692 0.719964368 0.698569431 0.765197443 0.756138 1 16.96565489 3.224744895 24.99947679 0.749259001 0.932693858 0.196413967 0.153505432 299.9563065 542768.2994 0.040412062 0.04853763 1677.818175 -3.224744895 0.183434858 GGPGGGFRPFVPHIPFDFYLCEMAFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGPGGGFRPFVPHIPFDFYLCEMAFPR 27 1 Q12905;A0A0A0MRL0 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 167.07 4.97E-12 471630000 266170 337040 300640 395790 400640 416940 375060 326200 329800 408460 FALSE TRUE 276678.5971 394923.9982 308474.9254 474076.0807 332539.3559 320112.0038 345661.8172 321827.8226 317930.5624 488489.9166 0.566395718 0.808458854 0.631486782 0.970493074 0.680749683 0.655309338 0.707613004 0.658821834 0.650843654 1 18.89796926 -1.125967688 4.145221051 1.000062322 0.706819101 0.409566922 0.106779575 154914.8347 56105911.63 7988.633516 0.023783281 0.074822517 1.125967688 -0.29324322 GGPGKLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 73.951 0.025719 12155220000 8814720 7515730 8640140 7000710 10275200 10121560 9474670 8506600 8432200 7897990 TRUE FALSE 9162731.952 8806498.163 8865309.146 8385429.543 8528625.174 7770981.084 8732020.608 8392582.941 8128726.769 9445449.924 0.970068342 0.932353486 0.938579868 0.887774496 0.902934772 0.822722173 0.924468467 0.888531834 0.860597095 1 23.17118809 4.000461054 1.629933617 0.89161882 0.958158677 0.197038998 0.044098014 0.563780153 2.820977438 0.011716913 0.037797756 10010.6218 -4.000461054 0.066539857 GGPNYQEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGPNYQEGLR 10 0 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ; 96.668 0.015316 228890000 153009 204456 194466 170931 214028 219248 183842 188139 171761 197818 FALSE TRUE 159049.9135 239569.7276 199533.9437 204740.6416 177647.597 168330.9747 169431.9837 185617.3044 165579.3552 236576.6496 0.672297599 1.01265162 0.843421969 0.865430472 0.75090926 0.711528272 0.716182193 0.784596894 0.699897287 1 17.85194816 3.240051948 24.9160889 0.760756153 0.859819913 0.074520273 0.111731601 68.33328511 1141646.075 0.029036695 0.037299245 1738.008707 -3.240051948 0.09906376 GGPPFAFVEFEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGPPFAFVEFEDPR 14 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 107.24 0.002082 117930000 139866 150015 135767 186647 149298 169355 182291 158470 139106 132858 FALSE TRUE 145388.0177 175778.9093 139305.1996 223565.2195 123920.3793 130024.8678 168002.5551 156345.9689 134099.6022 158888.9814 0.915028949 1.106300184 0.876745501 1.40705301 0.779918017 0.818337853 1.057358123 0.983995035 0.843983019 1 17.27765955 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;;;;; 202.22 1.93E-24 4033674000 955745 1254877 1112552 1053247 1200692 1373427 981136 1121498 1069237 1403777 FALSE TRUE 993478.5506 1470392.363 1141546.019 1261576.113 996598.8027 1054469.394 904231.9966 1106466.154 1030755.369 1678820.226 0.59177185 0.875848611 0.679969184 0.751465877 0.593630448 0.628101435 0.538611569 0.659073638 0.613976025 1 20.67901632 -1.055279502 4.598135953 1.000011646 0.660610081 0.559505828 0.090719178 1.45E-05 2.97E-06 0.088861991 0.020944024 0.088048203 1.055279502 -0.339401565 GGPRPVS(ph)SSIDPSLLSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.665)S(0.267)S(0.069)IDPSLLSTK;GGPRPVS(0.837)S(0.106)S(0.057)IDPSLLSTK 141.69 7.15E-08 477340000 535400 468420 520040 491770 775880 764130 642160 584300 625310 628020 TRUE FALSE 556538.0054 548867.4912 533592.6696 589040.6382 643996.1947 586672.388 591825.8212 576468.4142 602805.2152 751068.4948 0.740995008 0.730782206 0.710444751 0.784270199 0.857440033 0.781117025 0.787978494 0.767531082 0.80259686 1 19.51858496 -5 0.20475189 2.053564791 0.73826973 0.799256384 0.035069564 67.86336733 0.674285675 29.30677654 0.088262509 1.00E-05 5 -1.315295061 GGQGDPAVPAQQPADPST(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGQGDPAVPAQQPADPSTPER 21 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 GGQGDPAVPAQQPADPS(0.005)T(0.995)PER;GGQGDPAVPAQQPADPS(0.024)T(0.976)PER;GGQGDPAVPAQQPADPS(0.07)T(0.93)PER;GGQGDPAVPAQQPADPS(0.205)T(0.795)PER;GGQGDPAVPAQQPADPS(0.121)T(0.879)PER 294.28 9.06E-54 3155030000 1758160 2060940 1884456 2112491 1898114 2272992 2009397 1943426 1912885 2031150 TRUE FALSE 1827573.514 2414890.413 1933566.471 2530335.415 1575473.26 1745124.056 1851895.213 1917377.553 1844040.643 2429114.954 0.752361889 0.994144147 0.795996282 1.041669687 0.648579129 0.718419708 0.762374465 0.789331748 0.759140954 1 21.21199933 3.23102498 24.99999204 0.766765876 0.895904036 0.191868996 0.11522803 239.0417406 793036.6457 0.030550033 0.037186617 1702.256416 -3.23102498 0.12913816 GGQGDPAVPAQQPADPST(ph)PERQS(ph)SPSGSEQLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.342)T(0.657)PERQS(0.519)S(0.385)PS(0.078)GS(0.02)EQLVR;GGQGDPAVPAQQPADPS(0.095)T(0.902)PERQS(0.584)S(0.329)PS(0.082)GS(0.008)EQLVR 92.819 0.00053621 987950000 209488 296010 235147 195639 254770 327820 192976 234490 272641 328710 TRUE FALSE 217758.748 346847.4149 241275.124 234335.8103 211464.2864 251688.7732 177850.0369 231347.0451 262828.7037 393114.431 0.553932216 0.882306493 0.613752905 0.596100758 0.537920437 0.640243027 0.452412893 0.588497971 0.668580655 1 18.5845898 0.818514971 4.004191169 0.999976778 0.607750988 0.556558536 0.104365074 1.143288786 24.3656231 0.102383156 0.026160787 6.584381272 -0.818514971 -0.392225791 GGQGDPAVPAQQPADPST(ph)PERQSS(ph)PSGSEQLVR ddPTM_MDA-MB-175_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(0.038)T(0.961)PERQS(0.196)S(0.799)PS(0.006)GSEQLVR 170.07 5.19E-14 498530000 94468 127470 118390 96804 121440 127250 94946 118860 123490 169970 TRUE FALSE 98197.66959 149361.9809 121475.3407 115951.5423 100797.6722 97698.11599 87503.88442 117266.8761 119045.619 203272.3672 0.483084203 0.734787433 0.597598888 0.570424519 0.495874936 0.480626646 0.430476044 0.576895314 0.585645854 1 17.63305458 0.545780184 2.111375591 0.9999636 0.547084511 0.741713881 0.079887192 2.036599823 8.83832022 0.080710321 0.022035477 3.513825449 -0.545780184 -0.45287909 GGQLHGARPLGTGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGQLHGARPLGTGER 15 1 Q6N063;F5H145;Q6N063-4;Q6N063-2 Q6N063 OGFOD2 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 0 ; 96.673 0.0021684 98082000 53370 66292 65506 52704 61584 61920 49222 56281 52171 59185 FALSE TRUE 55477.08881 77677.13532 67213.14017 63128.69389 51115.97368 47540.01841 45363.85102 55526.64525 50293.3759 70781.16758 0.783783183 1.097426589 0.949590724 0.891885456 0.722169122 0.671647841 0.640902836 0.784483319 0.710547418 1 16.11107794 3.364312751 3.47593702 0.735339204 0.95512626 0.34862855 0.116750108 0.215197711 5.060029771 0.031479759 0.043942754 2313.730389 -3.364312751 0.219787055 GGQS(ph)DDDEDEGVPASYHTVSLQLLDLMHTLHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;GGQS(1)DDDEDEGVPASYHTVSLQLLDLMHTLHTR 235.46 1.70E-46 7607360000 372701.6 812504.6 848974.8 832403.6 897931.61 1008283.6 633979.1 866156.4 779245.4 1053776 TRUE FALSE 387416.147 952045.9446 871099.7807 997050.5476 745301.5157 774125.0146 584286.1615 854546.9902 751200.5103 1260243.231 0.307413789 0.755446188 0.691215599 0.791157233 0.591394976 0.614266354 0.463629676 0.678081 0.596075814 1 20.26527078 -1.184542056 3.332421812 1.00072769 0.619449145 0.431258117 0.134004837 75522822.4 112885840.1 577279.2706 0.031242103 0.065381961 1.184542056 -0.381278545 KAS(ph)VHSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.791)VHS(0.163)S(0.046)GR;KAS(0.85)VHS(0.075)S(0.075)GR;KAS(0.776)VHS(0.182)S(0.043)GR;KAS(0.966)VHS(0.03)S(0.004)GR 137.62 9.76E-05 674880000 99296 580351 670740 634842 879230 1007380 694870 997460 788710 897580 TRUE FALSE 103216.2828 680021.7697 688220.0354 760411.8528 729778.7987 773431.262 640404.2737 984090.6802 760324.4812 1073443.616 0.096154359 0.633495565 0.641132916 0.708385463 0.679848283 0.720514101 0.596588646 0.916760476 0.708304069 1 20.03381498 4.722188462 2.429221345 0.740313437 8.50E-33 0.73512424 0.116481039 0.262595544 1.958448264 0.028062293 0.400229309 52745.87027 -4.722188462 -0.740313437 down GGQSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGQSWR 6 0 Q9UBG0 Q9UBG0 MRC2 C-type mannose receptor 2 0 111.81 0.064042 64373000 48285 117300 99612 97543 105940 139300 94070 115890 96034 108500 FALSE TRUE 50191.32908 137445.3625 102207.9706 116836.7143 87932.35664 106949.6861 86696.54759 114336.6841 92577.7551 129758.4976 0.38680572 1.05923978 0.787678437 0.900416669 0.677661643 0.824221057 0.668137726 0.881149876 0.713461983 1 16.9854695 -2.13330592 2.288833103 1.4403633 0.781961599 0.14039406 0.169483445 9156381.181 2005843.042 20984317.87 0.037014101 0.007356887 2.13330592 -0.658401701 GGQVSLTVHGTQQVHS(ph)PPEQSPVQANSSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGQVSLTVHGTQQVHSPPEQSPVQANSSSSK 31 0 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 GGQVSLTVHGTQQVHS(1)PPEQSPVQANSSSSK 151.72 1.53E-08 92261000 32768 68240 70220 60296 73354 85542 63342 70388 68139 66846 TRUE FALSE 34061.70594 79959.68917 72049.99089 72222.36883 60885.31328 65676.1669 58377.08853 69444.56399 65686.6907 79943.19386 0.426073869 1.000206338 0.901264853 0.903421109 0.761607216 0.82153544 0.730232127 0.868673875 0.82166708 1 16.28668759 -5 0.270255378 2.268144814 0.80185402 0.145019297 0.145419567 437.2704971 4.245588081 309.5504462 0.167925397 1.00E-05 5 -1.466290795 GGREGFES(ph)DTDSEFTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGREGFESDTDSEFTFK 17 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GGREGFES(0.714)DT(0.278)DS(0.008)EFTFK;GGREGFES(0.953)DT(0.047)DSEFTFK 197.46 9.13E-12 418470000 520700 478590 546190 359510 711620 645180 445320 517790 632540 575990 TRUE FALSE 541257.6381 560784.1096 560424.1601 430620.005 590659.0866 495346.7228 410414.6548 510849.872 609775.009 688844.2125 0.785747529 0.814094246 0.813571704 0.625134097 0.85746396 0.71909833 0.595801848 0.741604361 0.88521468 1 19.39381822 1.052983981 3.332208615 0.997423142 0.740497367 0.530321146 0.078363836 0.16356799 3.836629936 0.076250735 0.019938139 11.29754242 -1.052983981 -0.256925775 GGREGFESDT(ph)DSEFTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGREGFESDTDSEFTFK 17 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GGREGFES(0.059)DT(0.941)DSEFTFK 212.08 3.05E-12 245140000 351440 323930 381870 260650 497860 436150 323270 369410 398980 391470 TRUE FALSE 365315.1226 379562.4577 391821.8459 312205.792 413233.935 334860.7724 297931.2527 364458.6632 384620.7877 468171.0514 0.780302673 0.810734574 0.836920277 0.666862659 0.882655888 0.71525305 0.63637265 0.7784733 0.821539022 1 18.8366762 0.837453678 2.592353396 0.99972429 0.761457404 0.502742469 0.070799634 0.523936528 6.364319215 0.067337664 0.017958826 6.877865492 -0.837453678 -0.238266886 GGRS(ph)PDEVTLTSIVPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR;GGRS(1)PDEVTLTSIVPTR 141.1 3.85E-07 1203100000 400479 453731 385019 399644 426113 525422 412173 390219 384318 455477 TRUE FALSE 416290.2202 531655.7697 395052.9114 478692.3904 353682.4645 403400.7033 379865.8032 384988.7526 370486.4703 544718.9975 0.764229304 0.97601841 0.725241663 0.878787765 0.649293427 0.740566614 0.697361034 0.70676579 0.680142371 1 19.05515266 3.250230725 24.99146985 0.726177737 0.838149398 0.123071426 0.111038307 343.7521219 736139.0105 0.028048399 0.037665859 1779.224397 -3.250230725 0.111971661 GGRSPDEVT(ph)LTSIVPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 GGRS(0.017)PDEVT(0.878)LT(0.095)S(0.011)IVPTR 110.34 0.0057764 0 83244 65361 62119 69042 78045 106560 77750 72737 69982 65678 TRUE FALSE 86530.5374 76586.24331 63737.87217 82698.30153 64778.93878 81813.05493 71655.75184 71762.07949 67463.36149 78546.34662 1.101649423 0.975045264 0.811468323 1.052859937 0.824722493 1.041589564 0.912273517 0.91362721 0.858898783 1 16.26125655 4.663595243 3.811941903 0.925791012 1.107719957 0.300499933 0.079791936 0.245487693 6.073545553 0.017430778 0.105073506 46088.78329 -4.663595243 0.181928945 GGRT(ph)PPQQGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGRTPPQQGGR 11 1 A0A2R8Y4Z8;M0QYB4;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 GGRT(1)PPQQGGR 72.681 0.073768 433420000 88609 117180 87585 98066 86725 107070 88126 91928 82376 107400 TRUE FALSE 92107.35174 137304.7535 89867.53705 117463.1621 71983.51548 82204.61516 81218.45385 90695.85552 79411.30385 128442.9737 0.71710697 1.068993885 0.699668767 0.914516059 0.560431711 0.640008657 0.632330843 0.706117687 0.618261175 1 16.97076845 3.24922488 24.99522251 0.673874965 0.854965706 0.206913005 0.14788806 272.9956269 639851.5378 0.037532839 0.050304948 1775.108406 -3.24922488 0.181090742 GGS(ph)DDSSKDPIDVNYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 1 GGS(0.999)DDSSKDPIDVNYEK 177.93 6.06E-10 138850000 366670 146710 219560 165360 330050 337780 324240 225080 294060 147940 TRUE FALSE 381146.4147 171906.3013 225281.914 198067.7144 273948.2189 259335.7141 298825.2216 222063.1708 283476.838 176926.0105 2.154270102 0.971628201 1.273311444 1.119494606 1.548377302 1.465786254 1.688984116 1.255118849 1.602233822 1 17.43278663 -0.799700897 5.068466721 0.99999965 1.424652367 0.150669309 0.316345726 0.000393626 99309131.06 96.0574036 0.068817111 0.15859851 0.799700897 0.424652717 GGS(ph)DGYGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 GGS(1)DGYGSGR;GGS(1)DGYGSGR 142.19 3.80E-05 257290000 523670 608280 536040 588170 629040 675870 566120 592160 541490 662660 TRUE FALSE 544344.896 712747.3582 550009.6428 704508.2705 522116.0055 518909.4354 521746.0351 584223.0638 522001.8807 792495.5396 0.686874397 0.899370814 0.694022383 0.88897443 0.658825166 0.654778998 0.658358324 0.737194135 0.658681159 1 19.59604329 -1.175835194 3.42645876 1.000401001 0.728825945 0.463204685 0.088342161 77378430.35 122517925 342838.1739 0.020936275 0.066705986 1.175835194 -0.271575056 GGS(ph)GAPILLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGSGAPILLR 10 0 M0QXB5;O95571;M0QX80;M0QY80 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 1 GGS(1)GAPILLR;GGS(1)GAPILLR;GGS(1)GAPILLR;GGS(1)GAPILLR 145.46 3.19E-05 357876000 463908 559360 544220 515960 625880 654110 577570 598960 550120 666230 TRUE FALSE 482223.4461 655425.7288 558402.8203 618015.348 519493.1412 502202.8656 532298.5542 590931.9209 530321.2887 796765.0128 0.605226683 0.822608571 0.700837526 0.775655731 0.652002953 0.630302357 0.668074709 0.741663993 0.665593092 1 19.60379477 -1.36056846 3.289202728 1.00235178 0.700654889 0.670153466 0.063947977 23539967.44 30439582.64 526357.0741 0.01491508 0.043594484 1.36056846 -0.301696891 GGS(ph)LESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGSLESR 7 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 GGS(0.998)LES(0.002)R;GGS(0.999)LES(0.001)R 108.81 0.016885 0 556110 629120 592360 596220 672250 784050 658140 619980 586170 676000 TRUE FALSE 578065.6522 737166.4661 607797.3882 714150.5365 557981.1851 601966.2699 606553.2671 611670.1822 565073.8562 808449.2572 0.715030222 0.911827749 0.751806477 0.883358516 0.690187022 0.744593757 0.750267579 0.756596876 0.698960202 1 19.6247977 5.04434279 16.19063891 0.785458253 0.347183779 0.048384529 0.09644382 14900064.41 144405716.5 0.021246395 198908502.1 110749.7591 -5.04434279 -0.438274474 GGS(ph)PAPLPAKVDEATSGLIR ddPTM_MDA-MB-175_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 186.28 2.02E-17 246930000 331730 295520 341290 249390 414700 409870 315600 331970 374370 326100 TRUE FALSE 344826.9566 346273.2612 350184.2978 298718.5976 344209.4421 314683.9041 290862.4473 327520.4851 360896.4968 389993.0514 0.884187437 0.887895976 0.897924454 0.765958769 0.882604038 0.806896182 0.745814435 0.839811079 0.92539212 1 18.57308889 1.04839461 3.207727793 0.998414917 0.836011863 0.521094679 0.049982163 0.174233401 3.848985556 0.049745278 0.01306201 11.17878517 -1.04839461 -0.162403055 GGS(ph)PDLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GGSPDLWK 8 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK 146.11 0.00058599 10940700000 20839100 14850600 17525370 14660070 21861420 21091370 20278760 17820500 18688050 13983870 TRUE FALSE 21661843.76 17401075.03 17982095.54 17559788.09 18145423.64 16193218.96 18689257.8 17581645.35 18015470.73 16723741.59 1.295274962 1.04050131 1.075243566 1.049991594 1.085009807 0.968277277 1.117528497 1.051298554 1.077239243 1 23.99539432 4.740701955 24.94727642 1.055245024 1.295275048 0.763310203 0.040650725 81.3366793 947531.5892 0.008850122 0.058673198 55042.98214 -4.740701955 0.240030024 GGS(ph)PHHSDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSPHHSDCK 10 0 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 GGS(1)PHHSDCK 77.597 0.020949 37215000 24312 54446 49648 55643 63607 66153 52706 57574 60840 59351 TRUE FALSE 25271.85653 63796.67697 50941.86767 66649.01932 52795.10486 50789.96831 48574.766 56802.3147 58650.38028 70979.69211 0.356043479 0.898801827 0.717696374 0.938987157 0.743805774 0.715556335 0.684347375 0.800261498 0.826298037 1 16.1151187 -5 0.03382724 2.151864771 3.57E-12 0.292155421 0.142576115 1738.69613 4.416490505 231.4445551 83.70835015 1.00E-05 5 -2.151864771 GGS(ph)PLAAPQGGSPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSPLAAPQGGSPTK 15 0 E7EPC8;Q9UQB3-2;Q9UQB3 E7EPC8 CTNND2 Catenin delta-2 1 GGS(1)PLAAPQGGSPTK 130.72 7.78E-05 0 128220 133510 136520 107340 149120 168860 123210 141960 130260 128960 TRUE FALSE 133282.2246 156439.3039 140077.8234 128571.5316 123772.6357 129644.8241 113552.4783 140057.2584 125571.968 154227.2429 0.864193784 1.014342868 0.90825603 0.833649939 0.802534191 0.840609102 0.736267316 0.908122688 0.814200952 1 17.2346981 3.872214003 4.146380675 0.839584204 0.943588254 0.200192363 0.073948398 0.286341747 8.217564808 0.017880646 0.034178346 7450.990388 -3.872214003 0.104004049 GGS(ph)PQMDDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GGSPQMDDIK 10 0 Q13144;A0A3B3IUB1;A0A3B3ITG6 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK;GGS(1)PQMDDIK 141.38 3.95E-05 2281800000 8197210 4923990 5928540 5748480 7505440 8490060 9039970 6415960 6827020 3879996 TRUE FALSE 8520842.18 5769646.979 6083042.623 6885512.186 6229667.99 6518372.233 8331393.53 6329964.551 6581316.884 4640206.929 1.836306508 1.243402949 1.310942101 1.483880416 1.342540987 1.404758954 1.795478878 1.364155661 1.418324007 1 22.14575771 0.592578765 1.897846151 1.00025415 1.464250213 0.363251928 0.186664101 2.531956629 10.48526184 0.171166829 0.047547582 3.913620989 -0.592578765 0.463996063 GGS(ph)PQMDDIKVFQNEVLGTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSPQMDDIKVFQNEVLGTLQR 22 1 Q13144;A0A3B3IUB1;A0A3B3ITG6 Q13144 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 GGS(1)PQMDDIKVFQNEVLGTLQR 201.08 9.51E-23 217300000 106730 99627 110020 93047 143570 136640 99428 97285 129970 123050 TRUE FALSE 110943.7828 116737.1623 112887.2116 111451.4189 119166.0227 104907.4308 91634.57355 95981.0537 125292.4051 147159.2916 0.75390267 0.793270755 0.767108963 0.757352238 0.80977573 0.7128835 0.622689689 0.652225576 0.851406688 1 17.16701911 0.984810694 5.521966922 0.999839913 0.730611786 0.692966085 0.055650899 0.092347446 12.08965788 0.063320863 0.015959439 9.656298754 -0.984810694 -0.269228128 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAK 31 0 Q9UPQ9-1;Q9UPQ9;H0Y720;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 GGS(1)PYNQFDIIPGDTLGGHTGPAGDSWLPAK 333.41 6.00E-106 244410000 229280 261850 297360 270510 355120 367050 327860 295630 313310 278690 TRUE FALSE 238332.1514 306820.7006 305109.4459 324016.0706 294756.8292 281808.2002 302161.4765 291667.5634 302034.0343 333293.9697 0.715080899 0.920570813 0.915436442 0.972163016 0.884374924 0.845524449 0.90659149 0.875106032 0.906209118 1 18.34643569 -3.655283656 0.013980616 1.985491947 1.47E-06 0.280841114 0.062103553 8785.39989 11.72219448 982.7696725 702.802453 0.000221165 3.655283656 -1.985490474 GGS(ph)TEDASQYYCDKNDNGDSYLVLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.84)T(0.16)EDASQYYCDKNDNGDSYLVLIR;GGS(0.996)T(0.004)EDASQYYCDKNDNGDSYLVLIR;GGS(0.982)T(0.018)EDASQYYCDKNDNGDSYLVLIR;GGS(0.986)T(0.014)EDASQYYCDKNDNGDSYLVLIR 256.79 7.34E-53 844577000 427403 385763 437181 391903 578202 569664 487027 466291 486188 394643 TRUE FALSE 444277.2005 452014.7944 448574.296 469420.2437 479919.4306 437368.1693 448852.5511 460041.1318 468690.1889 471965.74 0.941333582 0.957727979 0.950438259 0.994606608 1.016852263 0.926694741 0.951027825 0.974734166 0.993059769 1 18.84832261 3.548640104 0.005134099 1.928179336 1.21E-08 0.196011853 0.025107763 29857.853 37.38579743 6855.612511 7186.054909 3537.041083 -3.548640104 -1.928179324 GGS(ph)TVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGSTVPK 7 0 Q92504;A2AAT0 Q92504 SLC39A7 Zinc transporter SLC39A7 1 GGS(0.977)T(0.023)VPK 73.248 0.051826 202790000 846860 405740 680150 545650 963620 990460 1198300 680720 800030 321830 TRUE FALSE 880294.6867 475422.6888 697875.2677 653577.9414 799824.2166 760440.6756 1104374.115 671596.0618 771237.0766 384886.4267 2.287154406 1.235228514 1.813197919 1.698105976 2.078078522 1.975753424 2.86935064 1.744920099 2.003804299 1 18.55407327 3.241008503 24.83802865 2.029900039 1.724963304 0.014848886 0.491622283 155.893134 1581785.684 0.130670208 0.168923673 1741.840975 -3.241008503 -0.304936735 GGSDDSSKDPIDVNYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 168.09 1.95E-09 2346340000 3678530 1707800 2643130 1803880 3639570 3108070 3245720 2640650 2991260 1575610 FALSE TRUE 3823761.205 2001101.365 2712012.139 2160682.08 3020917.191 2386267.846 2991311.985 2605256.406 2883605.137 1884320.613 2.029251911 1.061974991 1.439251962 1.146663718 1.603186406 1.266381013 1.587475064 1.382597202 1.530315551 1 20.84561303 -1.88668389 2.561962025 0.779542522 1.430457144 0.210865888 0.258577575 13165532.03 7463878.279 17552915.38 0.056257022 0.012981238 1.88668389 0.650914622 GGSDGYGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGSDGYGSGR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 204.42 4.36E-07 8213110000 2524220 3222270 2897690 2836410 2953040 3392080 2668980 3062230 2763760 3270740 FALSE TRUE 2623878.155 3775669.807 2973206.182 3397443.432 2451083.316 2604320.827 2459778.374 3021185.816 2664292.817 3911578.881 0.67079771 0.965254676 0.760103854 0.868560634 0.626622494 0.665797855 0.628845397 0.772369907 0.681129768 1 21.89931963 5.048632228 16.23079682 0.759371857 0.125582663 0.045035295 0.127247311 12956212.57 109440606.6 0.029551759 257323056.6 111849.0314 -5.048632228 -0.633789193 GGSFWSSIPAS(ph)PASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGSFWSSIPASPASR 15 0 O75962-5;O75962;E7EPJ7;O75962-4 O75962-5 TRIO Triple functional domain protein 1 GGSFWSSIPAS(0.894)PAS(0.106)R;GGSFWSSIPAS(0.993)PAS(0.007)R;GGSFWSSIPAS(0.979)PAS(0.021)R;GGSFWSSIPAS(0.98)PAS(0.02)R 133.48 4.30E-05 693480000 396359 474616 437309 514340 549900 586170 451239 502410 447285 602700 TRUE FALSE 412007.5594 556127.606 448705.6318 616074.9168 456428.1944 450040.901 415869.7081 495676.0157 431187.3002 720787.5256 0.571607505 0.771555536 0.622521361 0.854724721 0.633235424 0.624373876 0.57696574 0.687686729 0.598216929 1 19.45921452 -1.989024454 2.451888002 1.315491341 0.664270549 0.586491896 0.085557437 11178514.36 4868549.727 19951619.11 0.019650893 0.010255942 1.989024454 -0.651220791 GGSGS(ph)GPTIEEVD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGSGSGPTIEEVD 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 1 GGS(0.15)GS(0.605)GPT(0.244)IEEVD;GGS(0.033)GS(0.893)GPT(0.074)IEEVD 120.53 0.00027554 187206000 515490 631100 571920 597800 640730 636720 549800 563640 555400 632400 TRUE FALSE 535841.9432 739486.5157 586824.705 716043.0557 531818.9435 488851.4296 506705.2394 556085.3277 535411.2625 756306.672 0.708498236 0.977760138 0.775908407 0.946762844 0.703178966 0.646366676 0.66997325 0.735264342 0.707928784 1 19.52861182 3.2174695 24.92593159 0.721710125 0.855746976 0.154927521 0.11736403 311.1545276 367728.0986 0.031079942 0.037182673 1649.945123 -3.2174695 0.13403685 GGSGSHNWGTVKDELTES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGSGSHNWGTVKDELTESPK 20 1 Q8NC51;Q8NC51-2 Q8NC51 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 GGSGSHNWGTVKDELTES(1)PK;GGSGSHNWGTVKDELT(0.002)ES(0.998)PK;GGSGSHNWGTVKDELTES(1)PK 274.88 1.03E-44 1071360000 1079210 979230 1251230 994490 1623890 1624400 1493040 1406290 1317090 836532 TRUE FALSE 1121818.044 1147405.135 1283838.082 1191197.154 1347861.758 1247157.718 1376011.623 1387440.983 1269688.188 1000434.429 1.121330905 1.146906886 1.283280587 1.190679888 1.347276462 1.246616152 1.375414104 1.3868385 1.269136838 1 19.93219518 4.374153558 0.961251343 1.298866492 1.068661257 0.123591095 0.109514792 1.699704 1.844373214 0.034194004 0.361086943 23667.56388 -4.374153558 -0.230205234 GGSGYHS(ph)RS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGSGYHSRSPAR 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 GGS(0.003)GY(0.001)HS(0.997)RS(1)PAR;GGSGYHS(1)RS(1)PAR 90.498 0.0050225 1386990000 882540 1371410 1227710 1306830 1274450 1560330 1201420 1295950 1186390 1349030 TRUE FALSE 917383.3607 1606938.999 1259705.131 1565317.074 1057819.444 1197967.005 1107249.561 1278579.91 1143692.056 1613346.6 0.568621374 0.99602838 0.780802545 0.970229877 0.655667818 0.742535426 0.686306068 0.792501692 0.708894205 1 20.62162498 4.053773387 24.9980509 0.779581087 0.808846718 0 0.144314704 811.6211536 377292.9758 0.033733975 0.072873704 11318.09637 -4.053773387 0.029265631 GGSISVQVNSIKFDS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 GGSISVQVNS(0.064)IKFDS(0.936)E;GGSISVQVNS(0.014)IKFDS(0.986)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.485)IKFDS(0.515)E;GGSISVQVNS(0.007)IKFDS(0.993)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.001)IKFDS(0.999)E;GGSISVQVNSIKFDS(1)E;GGSISVQVNSIKFDS(1)E 283.31 3.21E-35 6519633000 7814000 4303652 5394940 4068559 7139790 7839560 6216400 5739080 5950840 4236933 TRUE FALSE 8122502.754 5042770.753 5535536.568 4873307.827 5926171.046 6018941 5729142.324 5662157.02 5736670.431 5067078.9 1.602995121 0.99520273 1.092451228 0.961758821 1.169543866 1.187852236 1.130659782 1.117440074 1.132145472 1 22.27272286 4.745567545 24.96312378 1.095951723 1.60299536 0.814821911 0.073630833 336.6423803 1199303.13 0.017757671 0.177421201 55663.11994 -4.745567545 0.507043637 GGSREYDT(ph)GGGSSSSR ddPTM_MDA-MB-175_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(0.002)REYDT(0.98)GGGS(0.013)S(0.002)S(0.002)S(0.002)R;GGS(0.002)REYDT(0.84)GGGS(0.127)S(0.014)S(0.012)S(0.004)R 246.19 2.25E-19 811270000 603730 759540 702230 611840 779790 852090 570380 697810 719460 902200 TRUE FALSE 627565.7266 889985.0866 720530.6907 732860.1258 647241.5743 654205.011 525672.1252 688456.9983 693566.7751 1078968.816 0.581634721 0.82484783 0.667795658 0.679222712 0.59987051 0.606324299 0.487198626 0.638069412 0.642805209 1 20.04122174 -1.515571229 5.827320295 1.000547604 0.635759428 0.643602996 0.08116589 0.000599925 4.99E-05 0.081647926 0.019216755 0.030509056 1.515571229 -0.364788176 GGSSVEAPCPSDVT(ph)PEDDRSFQTVWATVFEHHVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGSSVEAPCPSDVTPEDDRSFQTVWATVFEHHVER 35 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GGSSVEAPCPS(0.116)DVT(0.744)PEDDRS(0.045)FQT(0.045)VWAT(0.051)VFEHHVER;GGSSVEAPCPS(0.021)DVT(0.95)PEDDRS(0.014)FQT(0.014)VWATVFEHHVER;GGSSVEAPCPS(0.037)DVT(0.938)PEDDRS(0.012)FQT(0.012)VWAT(0.001)VFEHHVER 124.9 2.64E-08 355491000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 GGTLGGGTLGPPS(ph)PPGAPS(ph)PPEPGGEIELVFRPHPLLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 2 GGTLGGGTLGPPS(1)PPGAPS(1)PPEPGGEIELVFRPHPLLVEK 91.759 0.00035921 140000000 239820 211860 224920 214190 250580 293520 271170 241530 259140 174710 TRUE FALSE 249288.2788 248245.307 230781.6 256556.1427 207986.5011 225354.4283 249914.9868 238292.6854 249813.602 208941.0795 1.193103239 1.188111536 1.104529567 1.227887514 0.995431351 1.078554916 1.196102688 1.140477909 1.195617457 1 17.67273664 -1.614343677 3.138862293 0.99111014 1.14442534 0.301765839 0.066843484 3372692.137 3934234.301 185733.6837 0.015489877 0.024302801 1.614343677 0.1533152 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 GGTLGGGTLGPPS(1)PPGAPSPPEPGGEIELVFRPHPLLVEK 135.65 2.04E-09 468160000 438950 306830 415290 392220 443490 478670 503700 378380 451410 321650 TRUE FALSE 456280.0849 359525.6657 426112.7986 469799.9453 368105.7282 367506.1468 464218.6778 373308.435 435163.8423 384671.1591 1.186156212 0.934631196 1.10773264 1.221302752 0.956936124 0.955377439 1.206793561 0.970461201 1.131261941 1 18.55326614 -0.814804077 0.008223139 9.24E-08 2.05998312 0.038427416 0.107079503 31144.40449 52.95480179 6933.340005 6338.59135 0.153177833 0.814804077 2.059983027 GGTLKDDDWGNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGTLKDDDWGNIK 13 1 P54578-2;P54578 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14 0 ; 90.707 0.0062629 540840000 617670 362620 453910 350490 601880 569100 564300 452860 494520 292110 FALSE TRUE 642056.0885 424897.1642 465739.2675 419815.8759 499572.6526 436935.1498 520068.6915 446790.1524 476722.3218 349343.3617 1.837894058 1.21627376 1.333184822 1.201728505 1.430033335 1.250732654 1.488703518 1.278942729 1.36462396 1 18.4142862 -4.201808614 0.174550555 1.33E-17 1.448270803 0.322520027 0.172749952 123.304273 1.513712664 44.34469814 0.565363315 6.28E-05 4.201808614 1.448270803 GGTPAFLPSS(ph)LSPQSSLPASR ddPTM_MDA-MB-175_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(0.018)S(0.49)LS(0.49)PQS(0.001)SLPASR 245.48 3.34E-30 110880000 205370 223050 218080 223290 211960 291910 213820 198500 235440 267320 TRUE FALSE 213478.1662 261357.1024 223763.344 267456.0955 175931.1149 224118.3264 197060.2297 195839.4322 226966.5604 319696.2358 0.667753143 0.817516984 0.699924863 0.836594447 0.55030712 0.701035237 0.616398342 0.612579725 0.709944425 1 18.28634223 0.952689135 22.38896704 1.000000001 0.68463822 0.555372033 0.083324103 2582.896822 1222308.946 0.081659168 0.020414792 8.967866518 -0.952689135 -0.315361781 GGTPAFLPSSLS(ph)PQSSLPASR ddPTM_MDA-MB-175_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(0.001)S(0.031)LS(0.872)PQS(0.092)S(0.003)LPASR 250.2 7.62E-31 114190000 141530 150740 152480 145330 150470 183920 148290 152460 153420 175890 TRUE FALSE 147117.7137 176628.4224 156453.7541 174075.8402 124893.1631 141207.3673 136666.6423 150416.5231 147898.4442 210352.2779 0.69938731 0.839679152 0.743770192 0.827544356 0.593733352 0.671289937 0.649703648 0.715069618 0.703098848 1 17.68244792 -1.163640346 9.404817486 1.000000003 0.715779882 0.590844847 0.070920091 6.35E-09 5.05E-10 0.070853573 0.016700347 0.068605614 1.163640346 -0.284220121 GGVDHAAAFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GGVDHAAAFGR 11 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;;;;; 185.61 4.39E-06 4122080000 2094010 2820900 2095400 2305210 2609350 2903040 2168440 2297130 2118090 3428520 FALSE TRUE 2176683.132 3305367.631 2150007.845 2761173.658 2165813.619 2228852.956 1998472.007 2266340.73 2041860.355 4100272.851 0.530862996 0.80613358 0.524357262 0.673412175 0.528212072 0.543586497 0.487399761 0.552729248 0.49798158 1 21.96728849 -1.319866316 5.344833252 1.000098941 0.572851385 0.660689986 0.092091927 0.000106634 1.36E-05 0.087572204 0.020636217 0.047877745 1.319866316 -0.427247556 GGVGAPGS(ph)PSTPPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGVGAPGSPSTPPTR 15 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 GGVGAPGS(0.706)PS(0.147)T(0.147)PPTR 86.699 0.0078211 99597000 53077 69973 71278 63804 66183 79993 59468 64859 58637 67710 TRUE FALSE 55172.52094 81990.31844 73135.56324 76424.24076 54933.2373 61415.83806 54806.74277 63989.67119 56526.66582 80976.47811 0.681340091 1.012520183 0.903170463 0.943783214 0.678385114 0.758440469 0.676822999 0.790225417 0.698062785 1 16.30521528 3.244928456 24.98095508 0.752502219 0.8955809 0.186576093 0.117835826 197.4958674 774768.8059 0.03032172 0.040080898 1757.634044 -3.244928456 0.143078681 GGVGAPGSPST(ph)PPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGVGAPGSPSTPPTR 15 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 GGVGAPGS(0.468)PS(0.034)T(0.498)PPTR;GGVGAPGS(0.436)PS(0.061)T(0.503)PPTR 157.33 2.20E-05 489460000 401410 480470 423490 433150 406650 491930 398470 389810 363360 427600 TRUE FALSE 417257.9768 562986.985 434526.4973 518825.7772 337527.7783 377686.7128 367236.8802 384585.2346 350282.7446 511380.0331 0.815944991 1.100917026 0.84971346 1.014560099 0.660033158 0.738563668 0.718129095 0.752053678 0.684975404 1 18.96403631 3.24168626 24.99906302 0.74350711 0.949574099 0.382855241 0.114839367 70.84760614 566637.4495 0.029172499 0.0378906 1744.561402 -3.24168626 0.206066989 GGVTEISAADKAEEFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GGVTEISAADKAEEFRR 17 2 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ;; 243.86 9.92E-21 776320000 853530 1045380 1008580 952140 1157090 1247550 939100 989880 1016090 1058100 FALSE TRUE 887228.0235 1224915.883 1034864.423 1140470.45 960408.2551 957825.4193 865490.8881 976612.2777 979521.1194 1265414.436 0.701136322 0.967995818 0.817806715 0.901262399 0.758967361 0.756926262 0.683958443 0.77177267 0.774071396 1 20.27117853 3.222240713 24.82157051 0.770426529 0.853600453 0.04612711 0.100196731 414.3200635 630153.9728 0.026710933 0.032014869 1668.171559 -3.222240713 0.083173924 GGVTGS(ph)PEASISGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(1)PEASISGSK;GGVTGS(0.974)PEAS(0.026)ISGSK 351.28 2.37E-82 4677360000 5023380 4196300 4438520 4291610 4975140 6068740 5750800 4616620 4720460 3822600 TRUE FALSE 5221706.921 4916981.882 4554191.477 5140477.649 4129467.48 4659367.108 5300037.269 4554741.76 4550571.567 4571565.282 1.142214231 1.075557622 0.996199594 1.124445859 0.903293998 1.019206075 1.159348482 0.996319965 0.995407762 1 22.12425679 4.581665818 2.944255895 1.028585383 1.145557104 0.223281065 0.068043508 0.470694589 6.728728069 0.016519363 0.10626043 38165.04842 -4.581665818 0.116971721 GGVTGSPEASISGS(ph)KGDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GGVTGSPEAS(0.03)IS(0.202)GS(0.768)KGDLK;GGVTGSPEAS(0.001)IS(0.039)GS(0.96)KGDLK 164.27 1.46E-11 363810000 526050 168784 244220 179741 342310 395090 339230 255520 254730 153190 TRUE FALSE 546818.8602 197771.339 250584.5738 215293.2333 284124.2685 303336.3351 312640.2662 252095.1723 245562.3171 183204.6475 2.984743388 1.079510491 1.367785028 1.175151593 1.550857319 1.655724018 1.70650838 1.376030443 1.340371658 1 17.48309658 4.745609774 24.99627861 1.397210978 2.984744124 0.825580627 0.223308533 336.8328099 1194378.083 0.0538088 0.543498994 55668.53267 -4.745609774 1.587533146 GGVVGIKVDK ddPTM_MDA-MB-175_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 ; 138.71 0.0032931 0 1396950 964260 1284470 746110 1593910 1314350 1071140 1249160 1403870 1020980 FALSE TRUE 1452102.665 1129864.154 1317944.343 893688.3311 1322977.748 1009112.132 987181.2479 1232417.053 1353344.993 1221021.483 1.189252347 0.925343386 1.079378505 0.731918597 1.083500795 0.826449121 0.808488025 1.009332817 1.108371156 1 20.21965715 GGWDHGDTQSIQSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GGWDHGDTQSIQSSR 15 0 Q9P206-2;Q9P206;Q9P206-3;Q9P206-4 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 0 77.222 0.026527 95844000 30687 88644 67438 70677 65293 81041 56036 70776 62661 93632 FALSE TRUE 31898.54646 103867.9174 69195.48968 84656.69965 54194.51918 62220.45594 51643.7519 69827.36349 60405.84285 111977.3977 0.284865938 0.927579311 0.617941577 0.756015958 0.483977305 0.555651919 0.461198 0.623584446 0.539446746 1 16.77284803 -1.586734109 6.224704911 1.001089665 0.592852994 0.3666076 0.163864836 0.002307673 0.000153209 0.14775657 0.034742101 0.02589798 1.586734109 -0.408236671 GGYDKDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGYDKDGR 8 1 Q92804-2;Q92804;A0A075B7D9;A0A075B7E4;A0A075B7F2 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 106.04 0.0038958 1236400000 6720720 6023640 6701860 5382080 8285590 7912180 7159730 6909790 7052320 6439550 FALSE TRUE 6986059.215 7058153.313 6876515.977 6446639.36 6877208.371 6074696.105 6598531.654 6817175.567 6798508.381 7701256.53 0.907132387 0.916493729 0.892908313 0.83708929 0.89299822 0.788792852 0.856812343 0.885203024 0.882779109 1 22.87666242 0.46323787 1.564210377 0.999977741 0.87068341 0.53559651 0.035523928 2.630653055 6.794525225 0.035426777 0.010156416 2.905613668 -0.46323787 -0.12929433 GGYFDEFGIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GGYFDEFGIIR 11 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 226.04 1.17E-11 5034133000 4050109 4683826 4327472 4554645 6081928 5763840 4678307 4386069 4315938 6393630 FALSE TRUE 4210010.431 5488236.68 4440249.475 5455540.187 5048124.051 4425275.512 4311609.073 4327280.919 4160608.234 7646339.385 0.550591625 0.717760016 0.580702641 0.713483919 0.660201411 0.578744323 0.563878852 0.56592844 0.54413073 1 22.86633781 -1.616776538 2.905375899 1.030056444 0.609383265 0.781453963 0.062128575 17409312.87 16908639.31 3951780.384 0.01604314 0.02416704 1.616776538 -0.420673179 GGYIGSTYFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GGYIGSTYFER 11 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 ;;; 256.48 3.95E-20 1074810000 505654 633606 548290 590158 660507 705146 579810 595275 535639 680156 FALSE TRUE 525617.6104 742422.9017 562578.8878 706889.491 548234.2561 541386.5281 534362.9771 587296.3123 516361.457 813419.5458 0.646182666 0.912718296 0.691622043 0.869034307 0.67398707 0.665568624 0.656934026 0.722009098 0.634803355 1 19.63364013 -1.13266723 3.816162498 1.000133456 0.72283146 0.463382914 0.090574969 26602616.47 44632581.92 43723.53414 0.021134444 0.073677142 1.13266723 -0.277301996 GGYLS(ph)DGDSPELTTK ddPTM_MDA-MB-175_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 180.49 6.58E-07 95189000 233150 179330 221220 194890 289280 251420 236450 221830 241830 202770 TRUE FALSE 242354.942 210128.5325 226985.1749 233438.6603 240108.2889 193031.5153 217916.4312 218856.7317 233126.5855 242498.8992 0.999406359 0.866513346 0.936025589 0.96263802 0.990141768 0.796009862 0.898628537 0.902506083 0.961351108 1 17.88761867 GGYVLHIGTIYGDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GGYVLHIGTIYGDLK 15 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 233.24 1.26E-17 901440000 2297700 1636480 2108520 1675260 2473200 2441000 2491500 2119600 2410600 1609300 FALSE TRUE 2388414.97 1917532.71 2163469.763 2006621.428 2052806.347 1874114.744 2296209.72 2091190.229 2323842.977 1924611.523 1.240985488 0.996321952 1.124107248 1.042611147 1.066608156 0.973762612 1.193076988 1.086551859 1.207434825 1 20.87613584 2.216813689 24.99981831 1.126722032 1.071038038 0.065146323 0.087270197 597.5316024 686906.2736 0.030228714 0.022343576 164.7455486 -2.216813689 -0.055683993 GHAVGDIPGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;;;; 119.34 0.00059992 2287740000 449788 452184 431288 506783 418057 510561 510455 483096 406079 422855 FALSE TRUE 467545.9776 529843.0845 442527.7196 607023.1648 346995.8205 391990.9454 470444.2033 476620.8883 391464.2961 505705.3412 0.924542297 1.047730845 0.87507029 1.200349522 0.686162064 0.775137048 0.930273353 0.942487353 0.774095633 1 18.94793749 3.232644816 24.99984286 0.856874207 1.004705709 0.306311687 0.117998826 192.020239 811466.4159 0.033526015 0.041081107 1708.617364 -3.232644816 0.147831501 GHDDIVNFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHDDIVNFER 10 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 0 ; 159.94 7.53E-06 269160000 126588 152470 134909 139060 147223 179123 137660 134544 142083 152471 FALSE TRUE 131585.792 178655.5364 138424.8394 166565.6529 122198.087 137524.3979 126869.8495 132740.6577 136969.4606 182344.7732 0.721631828 0.979767795 0.759137961 0.913465464 0.670148559 0.754199835 0.695769049 0.727965246 0.751156494 1 17.47630932 3.241924223 24.99998287 0.746158369 0.847208199 0.089525453 0.108931483 147.3092965 1094864.32 0.027724847 0.036061361 1745.517564 -3.241924223 0.10104983 GHDDLGDHYLDCGDLSNALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GHDDLGDHYLDCGDLSNALK 20 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6;J3KSA5;J3KRJ4;J3QLT0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ;; 159.75 2.51E-11 717306000 706135 562583 653349 604106 858204 795611 713577 670776 726708 617244 FALSE TRUE 734013.7551 659202.254 670375.8117 723596.3637 712326.7906 610842.4029 657644.9702 661785.3449 700553.921 738181.1439 0.994354517 0.893008795 0.908145402 0.980242275 0.964975598 0.827496622 0.890899172 0.896508059 0.949027115 1 19.49361536 4.750687122 23.42010483 0.91733494 0.994354633 0.149465906 0.048933234 1370.271586 2646305.577 0.011709899 0.183537952 56323.17414 -4.750687122 0.077019693 GHDGGHSHGGDMSNRPVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GHDGGHSHGGDMSNRPVCR 19 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 ;;; 163.18 1.69E-11 226002000 9131.4 20043.2 16434.4 19984.6 18767.8 21201.8 12846.4 21209 16185 26799.5 FALSE TRUE 9491.914723 23485.46369 16862.69397 23937.49423 15577.65606 16278.00327 11839.4656 20924.72805 15602.50501 32050.34892 0.296156362 0.732767801 0.526131369 0.746871564 0.486037019 0.507888488 0.369402081 0.652870523 0.486812329 1 14.96805244 -1.227436517 3.154357662 1.00166115 0.544466339 0.50735079 0.137438789 13119744.62 18504031.15 213525.6877 0.031641748 0.059232966 1.227436517 -0.457194812 GHDGTPESDCFAFTESHYNAELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GHDGTPESDCFAFTESHYNAELFR 24 0 Q9Y3P9;Q9Y3P9-2;Q9Y3P9-3;Q9Y3P9-4 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 0 ;; 124.7 6.02E-05 312039000 697754 419732 524306 430434 612341 711763 634029 487430 506501 320559 FALSE TRUE 725301.8667 491817.7059 537969.8451 515572.5605 508255.4955 546466.8301 584332.1503 480896.7981 488272.1279 383366.3986 1.891928634 1.282892053 1.403278553 1.344855893 1.325769544 1.425442689 1.524213265 1.254405185 1.273643516 1 18.54836437 1.327139878 0.047528795 2.19E-18 2.571650553 0.496405998 0.153851287 42.8453292 1.894092545 51.59285171 49.11029623 21.23928428 -1.327139878 2.571650553 GHDLNEDGLVSWEEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHDLNEDGLVSWEEYK 16 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 168.69 5.89E-09 261990000 625420 499590 619840 633010 691500 790250 839300 623590 650620 404890 FALSE TRUE 650112.0645 585390.6962 635993.5396 758217.4887 573959.077 606726.4139 773513.4729 615231.796 627204.3133 484220.4434 1.342595244 1.208934286 1.313438018 1.565851874 1.185325991 1.252996279 1.59744076 1.270561383 1.295286727 1 18.88530446 0.676229836 1.931227398 1.000354445 1.344965723 0.379786192 0.130735638 1.52469195 7.650789081 0.122441043 0.033973508 4.744930284 -0.676229836 0.344611277 GHEDDSYEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHEDDSYEAR 10 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 147.74 2.63E-05 163548000 28548 66820 47405 63048 50086 80435 38325 64332 49884 96116 FALSE TRUE 29675.09708 78295.81521 48640.41324 75518.70622 41572.39961 61755.19025 35320.98636 63469.73477 48088.68458 114948.0899 0.258160854 0.681140637 0.423151122 0.656980958 0.361662378 0.537244162 0.307277714 0.552159978 0.418351315 1 16.81062297 -1.358430605 3.630886909 1.002444463 0.474718976 0.587894108 0.133898539 57470384.44 96793633.2 1530652.426 0.02826743 0.043809611 1.358430605 -0.527725487 GHEGPVWQVAWAHPMYGNILASCSYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHEGPVWQVAWAHPMYGNILASCSYDR 27 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6;E7ERC8 P55735 SEC13 Protein SEC13 homolog 0 ; 227.09 7.49E-35 1872580000 358330 415730 385960 428350 330780 465250 401430 415880 355300 407270 FALSE TRUE 372477.1451 487128.3936 396018.4347 513076.3515 274554.1338 357202.7384 369964.8677 410305.8088 342512.8224 487066.7588 0.764735302 1.000126543 0.81306808 1.053400468 0.563688917 0.733375317 0.759577329 0.842401583 0.703215352 1 18.89376 3.252059108 24.99997468 0.762978179 0.907656062 0.222561436 0.128774493 337.137806 624394.8025 0.03360384 0.045249712 1786.730733 -3.252059108 0.144677883 GHEYTNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHEYTNIK 8 0 Q06124;Q06124-1 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 111.04 0.0059525 0 95249 75413 84819 69590 125150 115310 96838 87863 94419 87840 FALSE TRUE 99009.50407 88364.59612 87029.45282 83354.69429 103877.0477 88531.00004 89247.58452 86685.3402 91020.87863 105050.5662 0.942493769 0.841162493 0.828452963 0.793472109 0.988829013 0.842746529 0.849567858 0.825177277 0.866448244 1 16.68072441 0.93850851 21.19799696 1 0.859826842 0.348076757 0.055505483 4642.713749 1600489.186 0.052065221 0.013016305 8.679775853 -0.93850851 -0.140173158 GHFEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GHFEEEK 7 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 144.83 0.0023274 1013010000 1812830 1351537 1512430 1423268 1975680 2245840 2131120 1587960 1673100 1114174 FALSE TRUE 1884401.928 1583652.966 1551845.168 1704786.162 1639854.619 1724277.696 1964077.246 1566675.994 1612885.458 1332475.063 1.414211778 1.188504768 1.164633554 1.279413183 1.230683158 1.29404125 1.474006756 1.175763837 1.210443259 1 20.3456771 0.840841734 1.632286561 1.002182027 1.277788027 0.445946359 0.094300615 0.563311189 2.822281382 0.089320079 0.025693393 6.931731539 -0.840841734 0.275606001 GHFFVEDQIYCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHFFVEDQIYCEK 13 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 0 134.61 9.35E-05 95562000 131830 127010 127590 142110 163820 175480 180750 151720 150320 136170 FALSE TRUE 137034.7502 148822.9795 130915.1002 170218.9338 135973.9349 134727.4294 166582.3427 149686.4416 144910.0126 162849.9044 0.84147885 0.913865931 0.803900381 1.045250438 0.834964782 0.827310461 1.0229195 0.919168127 0.889837873 1 17.31318335 -5 0.014790062 2.089172539 2.34E-09 0.173844709 0.074990352 10245.86761 11.49661192 1013.142988 648.4845015 1.00E-05 5 -2.089172537 GHFGPINSVAFHPDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHFGPINSVAFHPDGK 16 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 250.17 5.40E-21 1028400000 1072800 1014900 1107200 971900 1374700 1438300 1412100 1171400 1212300 1104500 FALSE TRUE 1115154.972 1189201.18 1136054.542 1164138.919 1141028.985 1104276.623 1301415.912 1155699.299 1168669.56 1320905.628 0.844235159 0.900292311 0.86005731 0.881318767 0.863823244 0.835999635 0.985245187 0.874929499 0.884748717 1 20.33309597 -5 0.170188454 1.464710147 0.854413911 0.492686762 0.037760452 110.6470793 1.044609899 17.29617184 0.131687289 1.00E-05 5 -0.610296235 GHGDSVDQLCWHPSNPDLFVTASGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHGDSVDQLCWHPSNPDLFVTASGDK 26 0 Q96J01;Q96J01-2 Q96J01 THOC3 THO complex subunit 3 0 86.006 0.0075633 151020000 31788 76764 78888 81654 95317 117150 88131 99118 85647 93826 FALSE TRUE 33043.01479 89947.61986 80943.88609 97804.91749 79115.05039 89943.68793 81223.06193 97789.48533 82564.5812 112209.4083 0.29447633 0.801604974 0.721364521 0.871628493 0.705066104 0.801569933 0.723852511 0.871490963 0.735808008 1 16.77583412 4.738959078 24.70173044 0.795920355 0.294476162 0.754397499 0.087049245 11.90396036 737656.8346 0.018427164 0.108286732 54822.53058 -4.738959078 -0.501444193 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYK 36 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;; 168.26 5.56E-18 261508000 34697.7 96983.4 104613 110871 110343 142673 120065 118778 118279 97211 FALSE TRUE 36067.59199 113639.5445 107339.3007 132800.9529 91586.93627 109539.358 110653.9916 117185.9752 114022.1619 116257.6342 0.310238482 0.977480277 0.92328819 1.142298773 0.787792878 0.942212171 0.951799788 1.007985204 0.980771393 1 16.82696593 4.739109391 24.81651566 0.967180621 0.31023826 0.850158532 0.082864824 13.8295008 625220.541 0.018899096 0.112232294 54841.50829 -4.739109391 -0.656942361 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHIVLLQEAETLIQIEEDSTHIICDNDEMLR 31 0 Q9NV88-3;Q9NV88-2;Q9NV88;H0YBK3 Q9NV88-3 INTS9 Integrator complex subunit 9 0 173.07 3.23E-13 9684500 1984.2 2748 3862.9 3366.1 2894.6 3496.8 3299.3 2429 2644.9 3261 FALSE TRUE 2062.537748 3219.947624 3963.570347 4031.904533 2402.576926 2684.721195 3040.692245 2396.443228 2549.710566 3899.930514 0.528865256 0.825642306 1.016318197 1.033840095 0.616056342 0.688402315 0.77967857 0.614483571 0.653783588 1 11.9292327 3.217363171 24.99867759 0.702333751 0.861139981 0.110075689 0.166695042 422.5259124 498294.1626 0.048461598 0.057975354 1649.541214 -3.217363171 0.15880623 GHLENNPALEK ddPTM_MDA-MB-175_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 ;;;; 228.12 3.51E-12 7364080000 13667630 10913240 12965010 11203640 16674100 16080400 15519300 13204500 13578400 11445030 FALSE TRUE 14207238.59 12787504.08 13302888.81 13419686.55 13839842.44 12345970.8 14302856.71 13027515.28 13089716.04 13687464.5 1.037974461 0.934249296 0.971903073 0.980436264 1.011132664 0.901991074 1.044960278 0.951784406 0.956328766 1 23.70635189 4.763347889 23.65487337 0.972668295 1.037974627 0.207865492 0.038324919 5482.329703 5231695.355 0.008389337 0.521565202 57989.30297 -4.763347889 0.065306332 GHLS(ph)EGLVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHLSEGLVTK 10 0 Q16659 Q16659 MAPK6 Mitogen-activated protein kinase 6 1 GHLS(1)EGLVTK 95.401 0.004797 55542000 122490 119740 116760 123840 150280 164950 128300 137920 132510 124160 TRUE FALSE 127325.9998 140304.4136 119802.8615 148335.1824 124735.4593 126642.8623 118243.5108 136071.408 127740.991 148486.7748 0.857490507 0.944895017 0.806825131 0.998979085 0.840044236 0.852889845 0.796323517 0.91638739 0.860285309 1 17.17997492 -1.034876275 4.49390221 1.000005069 0.876429088 0.286279638 0.059212844 3.13E-06 6.72E-07 0.053205813 0.012540153 0.092283429 1.034876275 -0.123575981 GHLSRPEAQSLS(ph)PYTTSANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GHLSRPEAQSLSPYTTSANR 20 1 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR;GHLSRPEAQSLS(0.999)PYTTSANR;GHLSRPEAQSLS(1)PYTTSANR 177.22 4.00E-17 1185630000 145829 560760 461127 539770 432398 690820 392271 547520 390403 626180 TRUE FALSE 151586.4415 657066.1679 473144.3484 646534.8949 358899.1424 530387.5245 361523.774 540181.39 376352.4723 748867.9821 0.202420781 0.877412553 0.631812762 0.86334963 0.479255558 0.708252372 0.482760357 0.721330599 0.502561842 1 19.51435188 -1.245915702 4.321019999 1.000206908 0.624861646 0.267640709 0.19281455 0.000343397 5.99E-05 0.166807616 0.03929543 0.056765478 1.245915702 -0.375345261 GHMLADVVAIIGTQDIVFGEVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHMLADVVAIIGTQDIVFGEVDR 23 0 O75306 O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 124.31 5.83E-05 20464000 15601 16923 21902 22524 18567 29986 19862 17878 21120 27530 FALSE TRUE 16216.93953 19829.39361 22472.78411 26979.17997 15410.98797 23022.20594 18305.16454 17638.37465 20359.89533 32923.97641 0.492557136 0.602278211 0.682565916 0.819438686 0.468077968 0.699253506 0.555982799 0.535730388 0.618391141 1 15.00685097 0.929251708 21.4402935 1 0.606792936 0.581582663 0.099725782 6436.041501 1950448.165 0.095335087 0.023833772 8.496727856 -0.929251708 -0.393207064 GHNGWVTQIATTPQFPDMILSASR ddPTM_MDA-MB-175_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 ; 269.57 3.89E-45 2529400000 419500 471280 527810 559830 528950 586690 588520 495450 534160 482950 FALSE TRUE 436062.1839 552218.674 541565.1622 670562.7031 439039.2679 450440.1389 542390.2646 488809.3031 514935.6859 577574.8059 0.754988236 0.956098965 0.937653715 1.160997149 0.760142692 0.779881903 0.939082278 0.846313409 0.89154804 1 19.13964829 4.749422031 23.7046546 0.911124613 0.754988048 0.166516746 0.108833434 1518.443996 3313814.259 0.026433982 0.372842817 56159.34467 -4.749422031 -0.156136564 GHPEFSTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GHPEFSTNR 9 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;; 103.55 0.0034048 1518910000 94262 179147 134420 136227 138663 159993 123446 145795 128915 175383 FALSE TRUE 97983.53655 209914.1037 137923.0956 163172.294 115093.1128 122837.0505 113769.98 143840.8565 124275.3743 209745.9409 0.467153434 1.000801745 0.65757218 0.777952094 0.548726294 0.585646854 0.542418029 0.685786127 0.592504312 1 17.67828337 -1.233388768 4.423107647 1.000139219 0.657624298 0.348904462 0.142784595 0.000187474 3.25E-05 0.132220097 0.031151973 0.058426683 1.233388768 -0.34251492 GHPETLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GHPETLEK 8 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 ;;;; 149.65 0.00050176 1478700000 1796121 2228194 2274884 1994540 2850750 2954110 2413040 2150520 2004100 2233060 FALSE TRUE 1867033.244 2610868.987 2334169.346 2389054.059 2366180.533 2268062.722 2223899.619 2121695.797 1931972.832 2670585.352 0.699110119 0.977639222 0.874029113 0.894580679 0.886015694 0.849275504 0.832738642 0.794468447 0.723426731 1 21.34872456 2.340175557 2.610113778 0.816868678 0.874066678 0 0.09211862 0.770786616 10.74629172 0.034747837 0.02675716 218.8646173 -2.340175557 0.057198 GHPFFEGVDWEHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHPFFEGVDWEHIR 14 0 Q9Y2H1;Q9Y2H1-2 Q9Y2H1 STK38L Serine/threonine-protein kinase 38-like 0 143.98 5.19E-06 38161000 23031 30845 28350 30662 31360 34316 29251 25068 24590 35321 FALSE TRUE 23940.28166 36142.38881 29088.82429 36726.85208 26029.4384 26346.62906 26958.23019 24732.00446 23705.0107 42241.47369 0.566748259 0.855613823 0.688631853 0.869450066 0.616205736 0.623714723 0.638193411 0.585491042 0.561178591 1 15.36637255 -1.123911032 4.654931357 1.000027635 0.669175457 0.474698203 0.104994203 3.07E-05 5.78E-06 0.103746341 0.024451207 0.075177688 1.123911032 -0.330852179 GHPHSASSPS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHPHSASSPSER 12 0 C9J470;E9PHA2;Q15003;C9JZP1 C9J470 NCAPH Condensin complex subunit 2 1 GHPHS(0.001)AS(0.065)S(0.217)PS(0.717)ER 78.615 0.016266 170650000 8033.1 12461 11828 9787.8 8228.5 12666 8045.1 14233 10600 14122 TRUE FALSE 8350.252991 14601.07982 12136.2474 11723.79763 6829.822509 9724.513455 7414.50404 14042.22992 10218.50807 16888.93552 0.494421509 0.864535234 0.718591612 0.694170311 0.404396269 0.57579197 0.439015474 0.831445528 0.605041571 1 14.04379078 0.340068866 0.95435796 1.000776393 0.623996173 0.365039527 0.14758808 3.035147322 3.407884426 0.154961074 0.046705656 2.188108565 -0.340068866 -0.37678022 GHQFSCVCLHGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GHQFSCVCLHGDR 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 212.17 9.30E-09 1605940000 149905 422083 265551 428120 269887 413099 222446 314152 259768 502410 FALSE TRUE 155823.3652 494572.4719 272471.4772 512800.8582 224011.7041 317163.0178 205010.1013 309941.3063 250419.0004 600847.6203 0.25933924 0.823124625 0.453478499 0.85346241 0.372826149 0.527859323 0.341201487 0.515840116 0.416776221 1 19.19663963 -1.330238241 5.512258084 1.000098683 0.514552159 0.391680705 0.184069645 0.000206084 2.50E-05 0.164534714 0.038773384 0.046747863 1.330238241 -0.485546524 GHQQLYWSHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ;;;;; 206.97 1.42E-08 5985982000 1592121 2348583 2021832 1869061 2890831 2886601 2479311 2227858 2158680 3697234 FALSE TRUE 1654979.166 2751933.861 2074522.603 2238755.687 2399448.579 2216231.665 2284976.125 2197997.208 2080989.528 4421636.214 0.374291119 0.622379076 0.469175324 0.50631838 0.542660785 0.501224334 0.516771624 0.497100417 0.470637888 1 22.0761489 -1.776886137 2.809146925 1.117026996 0.504481755 0.865536172 0.05909186 12228641.79 9934468.698 9852377.678 0.01242259 0.016715288 1.776886137 -0.612545241 GHS(ph)CYRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHSCYRPR 8 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 GHS(1)CYRPR;GHS(1)CYRPR 87.806 0.0091221 91772000 125520 72835 92004 65030 131902 101210 123549 83705 111131 77523 TRUE FALSE 130475.6265 85343.84467 94401.69982 77892.7399 109481.3452 77705.51135 113864.9065 82583.07139 107131.417 92712.14758 1.407319644 0.920524946 1.018223634 0.840156786 1.180873791 0.838137325 1.228155204 0.890747044 1.155527294 1 16.50047076 4.746105229 24.46915385 1.004809705 1.407319906 0.445039296 0.133718035 566.0884448 1835912.764 0.028198771 0.295237501 55732.07707 -4.746105229 0.4025102 GHS(ph)PAQKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHSPAQKPK 9 1 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4 Q14966 ZNF638 Zinc finger protein 638 1 GHS(1)PAQKPK 107.18 0.0017055 146510000 412510 208940 276680 218600 343080 320500 416040 293950 322910 166140 TRUE FALSE 428796.2133 244823.8197 283890.5081 261838.4275 284763.3841 246068.7322 383429.6977 290010.0811 311288.5322 198691.9521 2.158095529 1.232177837 1.428797217 1.317810937 1.433190329 1.238443378 1.929769644 1.459596516 1.566689184 1 17.60017391 4.74863487 24.80734371 1.434744493 2.15809597 0.481201841 0.233529093 1124.620697 2769260.026 0.053603449 0.734354887 56057.64772 -4.74863487 0.723351477 GHS(ph)PFTLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHSPFTLRPK 10 1 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 GHS(0.99)PFT(0.01)LRPK 66.004 0.074083 0 356500 538860 497800 513710 514290 700380 456870 537770 512170 959860 TRUE FALSE 370574.8953 631405.0133 510773.0769 615320.3047 426871.1695 537727.3594 421059.3356 530562.0728 493737.1017 1147926.189 0.322821187 0.550039732 0.444952891 0.536027761 0.371862907 0.468433741 0.366800008 0.462191801 0.430112237 1 20.13059845 -1.331492097 3.291516514 1.003491862 0.442686759 0.858605222 0.068254219 27469743.41 37826468.55 935879.9421 0.015758775 0.046613091 1.331492097 -0.560805103 GHSAQIAKPIRPGQHPAAS(ph)PTHPSAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHSAQIAKPIRPGQHPAASPTHPSAIR 27 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 GHSAQIAKPIRPGQHPAAS(0.996)PT(0.004)HPSAIR;GHSAQIAKPIRPGQHPAAS(0.995)PT(0.005)HPSAIR 143.83 1.12E-07 3198900000 509770 1780560 1578260 1819880 1737980 2095170 1627020 1948800 1562480 1860770 TRUE FALSE 529896.1132 2086357.329 1619390.752 2179846.832 1442558.78 1608598.52 1499489.921 1922679.524 1506246.65 2225352.255 0.238117858 0.937540259 0.727700861 0.979551362 0.648238398 0.722851188 0.673821377 0.863988845 0.676857629 1 21.08560229 -4.999999485 0.034996683 2.143374058 6.18E-09 0.193963714 0.190033056 2076.541392 5.452132509 279.7350465 97.70772802 1.00E-05 4.999999485 -2.143374052 GHTAS(ph)ESDEQQWPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GHT(0.017)AS(0.828)ES(0.155)DEQQWPEEK 162.76 5.13E-09 652960000 550000 543290 743380 613320 840190 847140 890490 781160 809960 546780 TRUE FALSE 571714.4247 636595.8313 762753.0935 734632.8654 697374.8039 650404.5735 820691.0669 770689.8279 780809.6978 653911.0723 0.874299961 0.973520496 1.166447742 1.123444604 1.066467343 0.994637652 1.255049963 1.178585072 1.194060983 1 19.31873493 4.405407825 3.57541698 1.131537354 0.889161599 0.509384456 0.079918283 0.172784931 4.25344206 0.020618214 0.072260088 25433.59928 -4.405407825 -0.242375755 GHTDSVQDISFDHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GHTDSVQDISFDHSGK 16 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;; 292.8 8.14E-46 1217900000 625931 778048 938910 871250 1063870 1173560 1034510 1015130 964660 800200 FALSE TRUE 650643.2392 911671.6916 963378.7659 1043580.65 883033.7574 901018.4755 953422.403 1001523.843 929942.075 956983.8692 0.679889453 0.952651054 1.006682345 1.090489279 0.922725853 0.941518979 0.996278447 1.046542032 0.971742685 1 19.86813508 4.740743343 3.121392202 0.999357091 0.63034297 0.812579146 0.045403066 0.149905624 2.231668542 0.011638064 0.136323408 55048.22795 -4.740743343 -0.369014121 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 GHTDT(0.002)EGRPPS(0.997)PPPT(0.001)S(0.001)TPEK;GHTDT(0.001)EGRPPS(0.998)PPPTSTPEK;GHT(0.002)DT(0.012)EGRPPS(0.986)PPPTSTPEK;GHT(0.001)DT(0.002)EGRPPS(0.997)PPPTSTPEK;GHTDTEGRPPS(0.998)PPPT(0.001)S(0.001)TPEK;GHT(0.003)DT(0.009)EGRPPS(0.987)PPPTSTPEK;GHTDTEGRPPS(0.999)PPPT(0.001)STPEK;GHT(0.001)DTEGRPPS(0.999)PPPTSTPEK 204.53 5.78E-22 8083680000 2389622 1644539 1818118 1553708 2311451 2441498 2149819 1828960 1958426 1610834 TRUE FALSE 2483966.122 1926975.781 1865499.649 1861026.805 1918551.385 1874497.091 1981310.569 1804445.783 1887942.631 1926446.081 1.289403397 1.000274962 0.968363282 0.966041471 0.995901938 0.973033769 1.028479639 0.936670795 0.980013222 1 20.87751038 4.738866297 4.423572443 0.97901504 1.311125319 0.941222838 0.022995298 0.04057017 1.966043541 0.005376721 0.042254921 54810.81964 -4.738866297 0.332110278 GHTEVIVPHLTESYNSHRDPPEEEIPFCTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHTEVIVPHLTESYNSHRDPPEEEIPFCTLK 31 1 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 35.376 0.074379 114360000 11498 23950 21117 20366 23906 30488 17458 25698 18462 27974 FALSE TRUE 11951.94992 28063.22619 21667.32637 24394.33401 19842.46666 23407.62405 16089.59634 25353.56034 17797.55623 33454.96971 0.357254842 0.838835798 0.647656434 0.729169215 0.593109688 0.699675542 0.480932922 0.757841378 0.531985423 1 15.02993292 -1.244072606 4.236399726 1.000204767 0.639828701 0.402611814 0.135670245 0.000257635 4.60E-05 0.116874312 0.027530403 0.057006896 1.244072606 -0.360376066 GHTGGHHS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GHTGGHHSPVK 11 0 H7C280;A0A0A0MQU4;Q96I15-2;Q96I15 H7C280 SCLY Selenocysteine lyase 1 GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHTGGHHS(1)PVK;GHT(0.001)GGHHS(0.999)PVK;GHTGGHHS(1)PVK 188.92 4.91E-06 1554059000 1215178 874036 1058693 800417 1332370 1399280 1246010 774463 1024907 911085 TRUE FALSE 1263154.166 1024144.884 1086283.409 958737.0936 1105894.223 1074318.426 1148344.48 764082.5903 988020.7973 1089594.662 1.159288137 0.939931995 0.996961023 0.879902524 1.014959289 0.985979891 1.053918967 0.701253977 0.906778302 1 20.05536011 1.758744221 25 0.840297357 0.996560216 0.268537691 0.09812978 9.736881477 12071.20012 0.042859459 0.023768432 57.37784346 -1.758744221 0.156262859 GHTNQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHTNQVSR 8 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 65.305 0.064615 82159000 3476.4 7840.8 5980.4 7996.7 5335.7 7579 4580.5 5797.4 5579.3 9594.1 FALSE TRUE 3613.650956 9187.396407 6136.254137 9578.423392 4428.73962 5818.892111 4221.468441 5719.695336 5378.502083 11473.8802 0.31494585 0.800722706 0.534802005 0.834802458 0.385984474 0.507142484 0.367919864 0.498497041 0.468760523 1 13.48606574 -1.443723688 5.832610205 1.000268871 0.527841909 0.435390801 0.162647063 0.000548717 5.23E-05 0.151958208 0.035796979 0.035997829 1.443723688 -0.472426962 GHVQPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GHVQPIR 7 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 88.734 0.042782 24630000 45167 40470 44280 37424 55820 56247 53427 37907 48731 41113 FALSE TRUE 46950.22804 47420.40769 45433.97318 44826.3555 46331.73634 43184.48668 49239.25213 37398.91867 46977.18083 49168.30519 0.95488807 0.964450727 0.924050015 0.911692102 0.942308997 0.878299272 1.001442941 0.760630624 0.955436244 1 15.58544101 3.93488371 0.726708478 0.899686455 0.970846481 0 0.066896724 3.164911005 2.51829608 0.030290351 0.156659699 8607.63237 -3.93488371 0.071160026 GHWDDVFLDSTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHWDDVFLDSTQR 13 0 Q9H6T3;Q9H6T3-3 Q9H6T3 RPAP3 RNA polymerase II-associated protein 3 0 ; 168.61 2.99E-05 263400000 210126 273140 238720 248700 247910 313700 245900 256360 238730 286740 FALSE TRUE 218421.9367 320049.6703 244941.2393 297892.1177 205770.3468 240847.9292 226625.7155 252923.9135 230138.1539 342921.213 0.636944955 0.933303797 0.71427847 0.868689677 0.600051379 0.702341879 0.660868173 0.73755692 0.671110871 1 18.38751763 -1.132980009 3.873378395 1.000114463 0.728591615 0.416141278 0.097632494 5243082.417 3069802.558 4832.815536 0.021812235 0.073624099 1.132980009 -0.271522848 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.581)GS(0.419)DDETGKLQGSGVSLASK;GHYEVT(0.5)GS(0.5)DDETGKLQGSGVSLASK 267.39 2.09E-45 1596740000 1733170 916790 1111040 929290 1405560 1633610 1792980 1215640 1342770 731380 TRUE FALSE 1801596.89 1074241.551 1139994.615 1113100.788 1166643.413 1254228.835 1652441.543 1199346.334 1294443.97 874679.9079 2.059721361 1.228153912 1.303327772 1.272580722 1.333794686 1.433928942 1.889195725 1.37118313 1.479905916 1 19.73839563 2.462131057 24.96489014 1.494783297 1.408225954 0 0.301278192 1365.412388 2273962.937 0.100485314 0.084102161 289.8218048 -2.462131057 -0.086557343 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GHYEVT(0.005)GS(0.995)DDETGKLQGSGVSLASK;GHY(0.002)EVT(0.296)GS(0.701)DDETGKLQGSGVSLASK 241.77 7.60E-39 980640000 1935630 949160 1251700 1073690 1635470 1793260 1905550 1316530 1453250 725070 TRUE FALSE 2012050.167 1112170.847 1284320.33 1286062.677 1357473.394 1376802.542 1756188.012 1298884.069 1400947.816 867133.5842 2.320346258 1.282583061 1.481110124 1.483119442 1.565472054 1.587762909 2.025279661 1.497905389 1.615607839 1 19.72589474 0.370245595 1.667427419 1.000040394 1.637438331 0.31780827 0.285918787 7.032086379 17.24259178 0.258262193 0.073075093 2.34555486 -0.370245595 0.637397936 GHYNNVSCAVFHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GHYNNVSCAVFHPR 14 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 180.48 1.01E-06 636031000 138488 220863 190632 177975 274754 272207 210002 178801 166607 338688 FALSE TRUE 143955.6132 258794.5022 195600.0265 213177.9238 228051.4132 208991.0496 193541.4945 176404.4651 160610.8466 405047.429 0.355404338 0.638923947 0.482906476 0.526303609 0.563023974 0.515966859 0.477824276 0.435515578 0.396523555 1 18.62773132 -1.572227052 5.996206332 1.001383249 0.491939668 0.798136634 0.077218 0.001387032 9.90E-05 0.072626266 0.017077951 0.02677768 1.572227052 -0.509443581 GHYT(ph)EGAELVDSVLDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 1 GHY(0.463)T(0.537)EGAELVDSVLDVVR;GHY(0.454)T(0.546)EGAELVDSVLDVVR 101.96 0.002128 20409100 26842 21416 29374 19166.3 36156 32036 36649 25894 27094 20142.7 TRUE FALSE 27901.74289 25094.03141 30139.51057 22957.33693 30010.21603 24596.12451 33776.35562 25546.93328 26118.89223 24089.27641 1.158264051 1.041709638 1.251158817 0.953010649 1.24579151 1.021040404 1.402132428 1.060510613 1.084253914 1 14.55610344 1.187318263 2.533778724 1.015447412 1.146454444 0.114244428 0.125240188 0.553321453 6.213161167 0.106822994 0.02993187 15.39282255 -1.187318263 0.131007032 GHYTEGAELVDAVLDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GHYTEGAELVDAVLDVVR 18 0 P04350;M0R278;M0R1I1;K7ES63;K7ESM5;Q9BUF5;K7EL29 P04350;K7ESM5 TUBB4A;TUBB6 Tubulin beta-4A chain;Tubulin beta-6 chain 0 ; 161.32 3.84E-11 40611000 28254 40022 33218 41207 38698 47499 37149 39124 33905 42993 FALSE TRUE 29369.48974 46895.46717 34083.68837 49357.62161 32120.12778 36468.0771 34237.16431 38599.60677 32684.76567 51416.6552 0.571205762 0.912067636 0.66289198 0.959953957 0.624702787 0.709265839 0.665876926 0.750721855 0.635684401 1 15.64994814 -1.180607875 5.031640656 1.000020468 0.728378213 0.330764634 0.118521063 2.47E-05 4.02E-06 0.103996099 0.02451027 0.065976933 1.180607875 -0.271642255 GHYTEGAELVDSVLDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 389.53 1.34E-126 46200688000 5134674.8 8126501 7084185 8156939 7484965 9272011 7722203 7558564 7058424 8352939 FALSE TRUE 5337395.726 9522164.331 7268804.681 9770357.188 6212673.323 7118726.964 7116916.551 7457253.813 6804392.699 9989537.47 0.534298584 0.953213736 0.727641765 0.978059016 0.621918016 0.712618275 0.712437044 0.746506416 0.681151927 1 23.25198645 -0.9954495 4.32825356 1.000010513 0.748108521 0.267706148 0.128070592 12997826.57 6006037.67 1307.44896 0.027699431 0.1010533 0.9954495 -0.251901992 GHYTEGAELVDSVLDVVRK ddPTM_MDA-MB-175_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 ;;;; 310.49 1.07E-61 3497206000 2460177 3307000 3300255 2116882 4649219 4092751 2426684 3161798 3429104 4951394 FALSE TRUE 2557306.688 3874951.525 3386262.356 2535594.941 3858946.415 3142271.606 2236474.167 3119419.269 3305691.217 5921524.854 0.431866242 0.654384068 0.57185648 0.428199662 0.651681199 0.530652439 0.377685516 0.526793241 0.558249994 1 22.4975373 0.665316075 3.209575686 0.999992276 0.522859904 0.731648504 0.086422569 2.364515759 22.11581351 0.081552848 0.02118235 4.6271766 -0.665316075 -0.477132371 GHYTIGK ddPTM_MDA-MB-175_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 ;;;;; 111.73 0.0065139 17882920000 27636200 31677200 36815100 39954900 41774500 46728400 48025400 40649200 39253000 28629800 FALSE TRUE 28727298.52 37117512.69 37774531.75 47857859.97 34673685.41 35876437.28 44261043.66 40104363.96 37840292.2 34239261.16 0.839016309 1.084062898 1.103251953 1.397748034 1.012687898 1.047815755 1.292698562 1.171297587 1.105172568 1 25.02914823 4.765953581 2.070649771 1.15694849 0.736163549 0.366002697 0.117921818 0.776962364 3.45569291 0.029262887 0.62871426 58338.27471 -4.765953581 -0.420784941 GHYTIGKEIIDLVLDR ddPTM_MDA-MB-175_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 ; 298.71 5.11E-46 306980000 348820 480280 490900 405540 651220 633410 395290 486790 493440 579090 FALSE TRUE 362591.6829 562764.3539 503693.2573 485754.6016 540525.857 486310.1269 364306.1369 480265.3763 475681.1908 692551.5982 0.523559088 0.81259556 0.727300693 0.701398427 0.7804846 0.70220057 0.526034649 0.693472338 0.686853069 1 19.40156204 0.371859972 4.091777356 1 0.68629228 0.531754007 0.088996511 269.9760491 1755.20931 0.083913766 0.021404478 2.354290077 -0.371859972 -0.313707721 GHYTIGKEIIDLVLDRIR ddPTM_MDA-MB-175_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 ; 217.91 4.90E-19 231160000 204789 245510 260100 224434 429390 367450 290430 293440 279550 360320 FALSE TRUE 212874.2279 287674.4327 266878.4197 268826.3753 356402.4412 282115.3063 267665.3377 289506.9168 269489.0501 430917.8053 0.494001931 0.667585394 0.61932558 0.623846061 0.827077547 0.654684728 0.621151724 0.671837908 0.625383883 1 18.71705319 -5 0.375113778 5.759376333 0.64161027 0.655854274 0.077108378 346.6557807 2.632687513 1340.056071 0.052130455 1.00E-05 5 -5.117766063 GIAPAS(ph)PMLGNASNPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIAPASPMLGNASNPNK 17 0 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNK;GIAPAS(1)PMLGNASNPNK 302.26 1.89E-46 301310000 226310 172095 217060 208652 223420 244340 250620 207000 194993 130638 TRUE FALSE 235244.8935 201650.9775 222716.7619 249922.7428 185443.1482 187595.738 230975.7495 204225.5036 187975.24 156234.0149 1.505721361 1.290698301 1.425533115 1.599669208 1.18695758 1.200735564 1.478396044 1.307176953 1.203164626 1 17.25334906 -4.145680918 0.140104254 5.14E-12 1.502920948 0.497194988 0.122393356 92.97104183 1.000577432 26.70610258 0.795606289 7.15E-05 4.145680918 1.502920948 GIAPAS(ph)PMLGNASNPNKADIPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIAPASPMLGNASNPNKADIPER 23 1 H0YIY6;P27448-6;P27448-7;H0YKP9;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 GIAPAS(1)PMLGNASNPNKADIPER;GIAPAS(1)PMLGNASNPNKADIPER 245.11 1.04E-37 1734470000 987260 1007450 1043910 862280 1257230 1225040 966770 1009240 1078820 981970 TRUE FALSE 1026237.787 1180471.701 1071115.152 1032836.41 1043526.494 940543.0257 890992.0412 995712.7886 1039993.479 1174368.221 0.873863724 1.005197246 0.912077774 0.879482595 0.888585433 0.800892777 0.75869904 0.847871026 0.885576994 1 20.1634534 3.513552722 1.674999834 0.843888678 0.940211899 0.136869056 0.067621223 0.503790715 2.823868227 0.020336965 0.036907799 3262.51654 -3.513552722 0.096323222 GIAYIEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ; 114.6 0.0061059 185960000 684730 573200 623850 501670 1076900 936440 747620 660280 710170 734890 FALSE TRUE 711763.6691 671642.6411 640108.0435 600898.8287 893848.9227 718966.0019 689019.5909 651430.0266 684611.1204 878877.6252 0.809855262 0.764204961 0.728324428 0.683711602 1.017034564 0.818050183 0.783976712 0.741206748 0.778960689 1 19.74530277 -1.564394874 2.712104996 1.013865135 0.789341196 0.354360185 0.084294275 16506960.47 16218498.34 1655589.164 0.022094755 0.027264976 1.564394874 -0.224523939 GICFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GICFIR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 106.15 0.075311 333870000 379420 547220 509060 483950 840160 725460 489290 490750 470890 983710 FALSE TRUE 394399.7946 641200.7782 522326.5218 579673.8656 697349.9033 556982.9095 450938.1713 484172.299 453942.7609 1176449.14 0.335245937 0.545030598 0.443985638 0.492731769 0.592758224 0.473444104 0.383304434 0.411553957 0.385858381 1 20.16600752 -1.792550313 2.566657766 1.160202217 0.453986969 0.830953871 0.074204916 16443313.13 11321761.67 16436919.29 0.019482259 0.016123142 1.792550313 -0.706215248 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GIDDNLDEIPDGEMPQVDHLVFVVHGIGPVCDLR 34 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;;;; 214.41 2.66E-36 562688000 305259 368902 357711 383668 362764 402667 350586 332648 346012 349998 FALSE TRUE 317310.861 432258.0488 367033.2425 459556.3853 301101.5049 309153.6917 323106.1532 328189.3977 333559.0957 418573.407 0.758076972 1.032693529 0.876867083 1.097911089 0.719351731 0.738588947 0.771922315 0.784066527 0.796895097 1 18.67512113 3.216596489 24.99996593 0.785868751 0.943300574 0.268108483 0.111107253 259.0448244 294848.7586 0.02966814 0.035487294 1646.631764 -3.216596489 0.157431822 GIDLLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIDLLKK 7 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 98.997 0.036191 0 919610 706040 783580 635320 1186810 856860 936640 768670 900130 750820 FALSE TRUE 955916.9129 827296.8778 804000.7385 760984.3998 985076.4601 657867.2508 863223.7093 758367.2359 867734.4971 897928.8037 1.064579852 0.921339058 0.895394752 0.847488572 1.097054083 0.73264968 0.961349837 0.844573905 0.966373385 1 19.77624153 2.747679552 24.99601839 0.892683327 0.952321724 0.084944943 0.099160182 1783.085287 4887633.762 0.028952749 0.03029597 559.3447316 -2.747679552 0.059638398 GIDRLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIDRLER 7 1 Q8TF76 Q8TF76 GSG2 Serine/threonine-protein kinase haspin 0 65.252 0.064833 71026000 20186 72557 44588 60366 34917 56619 31476 38397 33840 98344 FALSE TRUE 20982.95887 85018.10033 45749.99991 72306.21463 28981.82081 43470.09532 29008.82887 37882.35102 32622.10501 117612.6239 0.17840737 0.722865433 0.388988855 0.614782769 0.246417603 0.369603992 0.246647238 0.32209426 0.277369078 1 16.84368339 -1.311886661 5.372112233 1.000125011 0.378316526 0.572745934 0.162132406 0.000235632 3.02E-05 0.152379965 0.035909169 0.048765574 1.311886661 -0.621808484 GIEEEEILPGFILCDPNNLCHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GIEEEEILPGFILCDPNNLCHSGR 24 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;;;;; 282.86 2.32E-52 1409812000 921285 941170 906847 1103642 977976 1152283 1065121 1021527 977857 854303 FALSE TRUE 957658.0432 1102808.626 930480.1778 1321939.094 811739.9888 884682.7363 981634.0328 1007835.101 942664.1176 1021687.316 0.937329874 1.079399351 0.910728912 1.293878345 0.794509216 0.865903611 0.960796926 0.986441826 0.922654224 1 19.9625223 3.173679117 24.99999709 0.925642453 1.046759368 0.255308746 0.111287346 88.84511198 34232.70994 0.031244737 0.037344618 1491.691849 -3.173679117 0.121116915 GIEFEDES(ph)SDRDARPALETQPQQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.5)S(0.5)DRDARPALET(0.001)QPQQEK 60.481 0.038316 166250000 50819 44418 45965 40705 61215 58038 52073 53570 44825 45021 TRUE FALSE 52825.37336 52046.44598 47162.88566 48756.32751 50809.69617 44559.55407 47991.38219 52851.98177 43211.75701 53842.00297 0.98111828 0.966651371 0.875949687 0.90554446 0.943681389 0.827598373 0.891337238 0.981612475 0.802565927 1 15.71644446 4.339079804 6.350331513 0.905201383 0.976933047 0.18969108 0.058276051 0.324692231 17.30657211 0.013585521 0.037997984 21831.31037 -4.339079804 0.071731664 GIEFEDESS(ph)DRDARPALETQPQQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEFEDESSDRDARPALETQPQQEK 25 2 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 GIEFEDES(0.023)S(0.977)DRDARPALETQPQQEK 247.36 2.83E-39 193720000 140120 105090 144180 108970 170660 165330 145890 142360 143520 123910 TRUE FALSE 145652.0458 123138.39 147937.4492 130523.9408 141651.2742 126934.6131 134454.7606 140451.8971 138354.7432 148187.7921 0.982888291 0.83096177 0.998310638 0.880800901 0.955890308 0.856579421 0.907326836 0.947796678 0.933644677 1 17.17706708 0.797405852 1.125493355 0.999108158 0.915659252 0.185127133 0.050659453 1.168125791 2.755482189 0.043286439 0.013577776 6.271997149 -0.797405852 -0.083448906 GIEGHS(ph)PGNLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEGHSPGNLPK 12 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 GIEGHS(1)PGNLPK 123.1 0.00022339 398500000 580700 392120 535950 388590 632360 572390 595690 522990 568600 428030 TRUE FALSE 603626.4844 459463.5597 549917.2973 465451.9422 524871.6731 439461.0972 548998.2613 515980.1745 548136.1971 511894.2834 1.179201456 0.897575094 1.074279036 0.909273569 1.025351699 0.858499717 1.072483673 1.007981904 1.070799606 1 18.96548637 -0.318599598 6.853959411 0.999998337 1.004999907 0 0.093069035 0 0 0.080837548 0.019053593 0.480175947 0.318599598 0.00500157 GIEGMIMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEGMIMKR 9 1 Q13393-3;Q13393-4;Q13393-2;Q13393 Q13393-3 PLD1 Phospholipase D1 0 58.676 0.065073 133550000 19764 223420 148330 242150 95818 175440 94610 155840 98656 199240 FALSE TRUE 20544.29798 261790.647 152195.6017 290046.5473 79530.89059 134696.7188 87194.22098 153751.2197 95105.38983 238277.2633 0.086220136 1.09868077 0.638733212 1.217264892 0.333774568 0.565294048 0.365935968 0.645261816 0.399137494 1 17.86228177 GIEHQDSQHSFLAFLNTPTDALDQFETVDS(ph)TPLSVHTPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFET(0.054)VDS(0.243)T(0.243)PLS(0.207)VHT(0.207)PT(0.046)LR;GIEHQDSQHSFLAFLNT(0.073)PT(0.022)DALDQFET(0.022)VDS(0.228)T(0.228)PLS(0.228)VHT(0.164)PT(0.037)LR;GIEHQDSQHSFLAFLNTPTDALDQFET(0.036)VDS(0.259)T(0.259)PLS(0.205)VHT(0.205)PT(0.036)LR 121.33 6.22E-09 775083000 28930.3 50423.9 46599.1 53435.1 66519.6 78248 48407.5 64778.5 54329.5 50897.6 TRUE FALSE 30072.49058 59083.81258 47813.51083 64004.40329 55212.62215 60076.08786 44613.19366 63910.25016 52374.19191 60870.01023 0.494044448 0.970655539 0.785501935 1.051493224 0.907057875 0.986957085 0.73292568 1.049946434 0.860426862 1 15.89344399 4.742156098 24.95063891 0.92618114 0.494044279 0.618929573 0.101965447 208.0519607 1443702.096 0.022174737 0.16452332 55227.59079 -4.742156098 -0.432136861 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLS(ph)VHTPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPTLR 41 0 Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 GIEHQDSQHSFLAFLNTPTDALDQFETVDS(0.075)T(0.075)PLS(0.442)VHT(0.347)PT(0.059)LR;GIEHQDSQHSFLAFLNTPT(0.009)DALDQFET(0.069)VDS(0.059)T(0.059)PLS(0.41)VHT(0.349)PT(0.044)LR 137.71 5.56E-10 737888000 2746.84 14709.6 12184.1 18843.7 8044.9 20253.5 7446.8 9337.1 8972.8 18114.3 TRUE FALSE 2855.287364 17235.85938 12501.62766 22570.92762 6677.430772 15549.93157 6863.100357 9211.951447 8649.870681 21663.45027 0.13180206 0.795619311 0.577083867 1.041889789 0.30823487 0.717795706 0.316805508 0.425230115 0.399284074 1 14.40297541 -1.98168412 2.987163559 1.413375711 0.531115083 0.238151283 0.255237573 2011579.43 22836784.07 5321412.491 0.057267141 0.010430758 1.98168412 -0.882260628 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHT(ph)PTLR ddPTM_MDA-MB-175_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(0.004)DALDQFET(0.026)VDS(0.094)T(0.094)PLS(0.061)VHT(0.661)PT(0.061)LR;GIEHQDSQHSFLAFLNTPTDALDQFETVDS(0.007)T(0.035)PLS(0.163)VHT(0.772)PT(0.022)LR 250.38 1.34E-55 1766692000 48610.1 250471 191566 233735 187133 276291 128726 215116 153562 276835 TRUE FALSE 50529.26428 293487.4459 196558.3673 279967.0854 155324.1995 212126.6025 118636.1198 212232.7219 148035.3336 331075.5179 0.152621567 0.886466773 0.593696473 0.845629079 0.469150363 0.640719688 0.358335526 0.641040217 0.447134643 1 18.33680081 -1.728057339 4.516987152 1.025153043 0.574448589 0.285541742 0.207853419 0.047479456 0.002858474 0.181489128 0.043160648 0.018704352 1.728057339 -0.450704454 GIEHQDSQHSFLAFLNTPTDALDQFETVDSTPLSVHTPT(ph)LR ddPTM_MDA-MB-175_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(0.017)VDS(0.082)T(0.082)PLS(0.252)VHT(0.252)PT(0.315)LR 87.857 0.00023042 24605000 5368.1 13040 13430 14855 13511 16609 13314 12867 10631 12662 TRUE FALSE 5580.036733 15279.51856 13779.99683 17793.27466 11214.40505 12751.81146 12270.41389 12694.53891 10248.39239 15142.87647 0.368492521 1.009023523 0.909998629 1.175026072 0.740572973 0.842099682 0.810309317 0.838317537 0.676779765 1 13.88635166 GIEHSLIEENCGVVVESIQVTLECGLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEHSLIEENCGVVVESIQVTLECGLGHR 29 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 217.68 1.42E-34 24363000 10729 5873.3 7453.6 6863.9 10629 10406 9114.1 7292.5 7717.8 5856.7 FALSE TRUE 11152.5892 6881.993587 7647.846939 8221.558933 8822.286377 7989.364204 8399.713027 7194.755966 7440.037886 7004.208232 1.592269795 0.982551255 1.091893143 1.173802757 1.259569402 1.140652011 1.199238051 1.02720475 1.062223972 1 12.77400626 4.74836688 24.74828471 1.113064479 1.592270094 0.743953012 0.085768272 621.4715916 1568385 0.021189943 0.280947059 56023.06687 -4.74836688 0.479205614 GIEILTDMSRPVELSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GIEILTDMSRPVELSDR 17 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;;;;; 321.81 1.11E-58 5685243000 3026001 3452966 3363381 3942052 3290912 3950230 3852981 3438590 3398743 3288315 FALSE TRUE 3145469.856 4045986.05 3451033.472 4721778.12 2731523.954 3032848.949 3550974.281 3392501.325 3276422.903 3932597.366 0.799845386 1.028833027 0.877545589 1.200676723 0.694585207 0.771207593 0.902959025 0.86266175 0.833144764 1 21.90705105 3.213675751 24.99970979 0.839817147 0.973363263 0.21895389 0.122494654 334.8216108 336365.9235 0.033926526 0.040566145 1635.594913 -3.213675751 0.133546115 GIEILTDMSRPVELSDRETLLNSATTSLNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIEILTDMSRPVELSDRETLLNSATTSLNSK 31 2 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 212.82 5.85E-27 317230000 102620 101810 112600 70014 147990 130420 81836 110160 128370 133940 FALSE TRUE 106671.5168 119295.0755 115534.4485 83862.56023 122834.7127 100131.9315 75421.48048 108683.4854 123749.9888 160182.9786 0.665935406 0.744742523 0.721265452 0.52354227 0.766839984 0.625109687 0.470845786 0.678495845 0.772553925 1 17.28936133 0.923179132 2.512911901 0.998827843 0.646457158 0.599703456 0.087889735 0.245785639 3.447119318 0.084917311 0.022828703 8.378748055 -0.923179132 -0.352370685 GIENLAFVPS(ph)SPDILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIENLAFVPSSPDILR 16 0 Q6ZQN7 Q6ZQN7 SLCO4C1 Solute carrier organic anion transporter family member 4C1 1 GIENLAFVPS(0.5)S(0.5)PDILR;GIENLAFVPS(0.708)S(0.292)PDILR 107.34 0.0011912 67135000 128272 153742 135777 173252 148169 191555 137272 137763 122622 142213 TRUE FALSE 133336.2776 180145.9926 139315.4602 207520.7285 122983.2863 147069.2543 126512.2619 135916.5123 118208.8582 170076.9145 0.783976344 1.059203085 0.8191321 1.220158121 0.723103936 0.864722027 0.743853228 0.799147331 0.695031766 1 17.3758278 GIEYSRVS(ph)PQPMISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GIEYSRVSPQPMISR 15 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 GIEYSRVS(1)PQPMISR;GIEYSRVS(1)PQPMISR;GIEYSRVS(1)PQPMISR;GIEYSRVS(1)PQPMISR 189.55 1.53E-07 3089730000 2704940 2396970 2444540 2018840 2776080 2732680 2170490 2188640 2386370 2387560 TRUE FALSE 2811733.12 2808630.952 2508246.721 2418160.526 2304202.913 2098056.484 2000361.322 2159304.861 2300485.01 2855356.669 0.984722207 0.983635768 0.87843552 0.846885628 0.806975513 0.734779128 0.700564432 0.75622947 0.805673433 1 21.44523954 3.910370304 1.224802017 0.776182341 1.001547489 0.43334517 0.078063607 0.420721641 1.133089587 0.02342635 0.082860924 8135.23877 -3.910370304 0.225365148 GIFEALRPLETLPVEGLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIFEALRPLETLPVEGLIR 19 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 182.34 2.69E-14 978360000 330250 422690 447660 461950 462590 491190 419460 409450 361890 449240 FALSE TRUE 343288.525 495283.7194 459326.3874 553322.3312 383959.117 377118.5666 386581.6291 403961.9925 348865.6496 537259.9768 0.638961657 0.921869748 0.854942499 1.029896801 0.714661679 0.701929388 0.719542951 0.751892957 0.649342338 1 19.03526084 GIFEPFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIFEPFGR 8 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;A0A0U1RQH7;A0A0U1RQW2;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 0 168.45 0.00071364 332570000 352250 477020 390040 429110 445940 446070 380930 367960 387080 459460 FALSE TRUE 366157.102 558944.4743 400204.7628 513986.6772 370139.2781 342477.0028 351071.7112 363028.0981 373149.0664 549482.3901 0.66636731 1.017219995 0.728330462 0.935401546 0.67361445 0.623272026 0.638913489 0.660672852 0.679091947 1 19.06771372 3.218098003 24.70374603 0.684546254 0.841964887 0.145465684 0.137571516 279.5986317 337548.0019 0.036202703 0.043319744 1652.334622 -3.218098003 0.157418632 GIFFSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIFFSHR 7 0 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423;G3V3P2;G3V227;G3V2Y7 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 151.17 0.0018992 620590000 333270 428500 258360 267990 1191320 617830 428010 305700 292760 1720370 FALSE TRUE 346427.7569 502091.5417 265093.0738 320997.6221 988819.8519 474348.3458 394461.4578 301602.5915 282223.6248 2057443.563 0.168377769 0.244036605 0.128845854 0.156017705 0.480606064 0.2305523 0.191724072 0.146590943 0.137171989 1 20.97242143 -1.348004146 3.2333153 1.006148826 0.209608107 0.854641373 0.097824477 39935169.66 54538092.12 2336563.611 0.024981146 0.044874111 1.348004146 -0.796540719 GIFGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIFGFR 6 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 142.14 0.026902 524810000 396400 847610 582880 800090 632870 847120 547190 590680 497620 1064500 FALSE TRUE 412050.1781 993180.424 598070.3316 958345.414 525294.9835 650389.2182 504299.818 582762.9008 479710.7534 1273068.394 0.323666961 0.780146949 0.469786489 0.752783918 0.41262118 0.510883171 0.396129399 0.457762445 0.376814597 1 20.2798785 -1.69811782 6.519990485 1.005347136 0.502961313 0.51903153 0.144942516 0.010743659 0.000497442 0.13383454 0.031410805 0.020039283 1.69811782 -0.502385823 GIFLGDDEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIFLGDDEWR 10 0 Q8TB72-3;Q8TB72;Q8TB72-2;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 0 ; 163.99 1.46E-05 96271000 191078 226100 213800 218761 215990 250440 208271 218940 199134 237700 FALSE TRUE 198621.907 264930.9162 219371.8036 262031.2729 179276.0969 192279.1055 191946.1748 216005.4674 191967.2062 284272.764 0.698701853 0.93196025 0.771694765 0.921760035 0.630648165 0.676389475 0.675218308 0.759852841 0.675292292 1 18.11691636 5.060358979 15.22210081 0.768668525 0.11847487 0.029969011 0.121950576 4968090.348 30323987.23 0.028282072 98592950.59 114910.3054 -5.060358979 -0.650193655 GIFPVLCKDPVQEAWAEDVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GIFPVLCKDPVQEAWAEDVDLR 22 1 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 238.63 1.34E-30 42163679000 9366829 8315088 9649547 8848196 11685194 10680293 10310556 9751647 10266850 8907845 FALSE TRUE 9736638.642 9743139.682 9901022.122 10598342.76 9698948.898 8199956.812 9502387.679 9620942.122 9897348.074 10653166.68 0.913966611 0.914576856 0.929397091 0.994853745 0.91042872 0.769720127 0.891977753 0.903106317 0.929052213 1 23.344779 3.003473485 24.99931282 0.887872525 0.93797746 0.080760569 0.057367143 208.2085578 1498488.267 0.016590849 0.019736651 1008.030064 -3.003473485 0.050104935 GIGIENIHYLNDGLWHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIGIENIHYLNDGLWHMK 18 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 209.73 2.84E-16 2256620000 2457200 2228880 2616300 2260650 3240500 2789800 2558600 2629800 2697100 2641400 FALSE TRUE 2554212.153 2611672.802 2684482.927 2707799.823 2689680.967 2141911.23 2358050.246 2594551.832 2600031.898 3158931.757 0.808568323 0.826758222 0.849807192 0.857188452 0.851452698 0.678049225 0.746470778 0.821338361 0.823073145 1 21.59100534 0.580839001 2.117655868 0.999969896 0.804304627 0.554987386 0.052106587 2.533925691 11.82332285 0.05416897 0.014788874 3.809245834 -0.580839001 -0.195665269 GIGQVLPTHLMEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIGQVLPTHLMEER 14 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80 E7ESA6 PTK2 Focal adhesion kinase 1 0 123.38 0.00010321 60742000 92946 119500 110230 115920 132040 136730 117870 125340 98893 148030 FALSE TRUE 96615.57985 140023.1954 113102.6844 138848.63 109595.888 104976.5297 108631.0414 123660.0223 95333.86025 177033.6443 0.545746998 0.790941157 0.638876779 0.784306455 0.619068135 0.592975025 0.61361806 0.69851142 0.53850702 1 17.43366404 -1.955587352 2.551189981 1.266159988 0.654459064 0.615928013 0.083447655 6494801.903 3742590.962 10255846.42 0.018895584 0.011076758 1.955587352 -0.611700924 GIGT(ph)PQPDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIGTPQPDVAK 11 0 Q9Y6X8;H0YKA3 Q9Y6X8 ZHX2 Zinc fingers and homeoboxes protein 2 1 GIGT(1)PQPDVAK 111.12 0.019042 127900000 146500 111890 143960 113950 175310 174250 151040 134740 153840 119230 TRUE FALSE 152283.9331 131106.2371 147711.7159 136488.9699 145510.8688 133783.0783 139201.0901 132934.0307 148303.3285 142590.8357 1.067978404 0.919457667 1.035913109 0.957207167 1.020478407 0.938230551 0.976227465 0.932276117 1.040062131 1 17.12152174 2.747413913 24.89221156 0.969745571 0.995315676 0.037374356 0.048027913 1853.30665 5210817.36 0.013654689 0.014275273 559.0027092 -2.747413913 0.025570105 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 33 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;; 278.5 8.30E-74 1438100000 551270 594949 689827 557168 800827 854154 692963 670255 697401 650042 FALSE TRUE 573034.5653 697126.8627 707804.4583 667374.1674 664702.7126 655789.6783 638646.7493 661271.328 672301.6742 777405.2841 0.737111745 0.896735431 0.910470346 0.858463637 0.855027263 0.843562157 0.821510687 0.850613369 0.864802038 1 19.56830739 0.673369354 2.866004846 0.999994718 0.849925764 0.515821529 0.044195569 2.530516345 21.25458216 0.041074856 0.010791576 4.713780485 -0.673369354 -0.150068953 GIHDADAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIHDADAEAR 10 0 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 0 107.83 0.0022318 53130000 70576 53810 68788 45953 71743 82439 62454 74954 61562 61675 FALSE TRUE 73362.39498 63051.44892 70580.67179 55042.36624 59548.15049 63293.79163 57558.69229 73949.36423 59346.39565 73759.03541 0.994622483 0.854830172 0.956908823 0.746245744 0.807333639 0.858115772 0.780361239 1.002580414 0.804598316 1 16.17053217 -1.025325992 7.591241051 1.000000003 0.86992269 0.178660389 0.08519612 7.03E-09 9.49E-10 0.080574985 0.018991705 0.094335251 1.025325992 -0.130077313 GIHNFRAS(ph)GDYDNDCTNPITPLCTQPDQVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GIHNFRASGDYDNDCTNPITPLCTQPDQVIK 31 1 Q8TAF3-4;Q8TAF3-3;Q8TAF3 Q8TAF3-4 WDR48 WD repeat-containing protein 48 1 GIHNFRAS(0.933)GDY(0.002)DNDCT(0.065)NPITPLCTQPDQVIK;GIHNFRAS(0.848)GDY(0.124)DNDCT(0.029)NPITPLCTQPDQVIK;GIHNFRAS(0.985)GDY(0.015)DNDCT(0.001)NPITPLCTQPDQVIK;GIHNFRAS(0.971)GDY(0.023)DNDCT(0.006)NPITPLCTQPDQVIK 210.75 1.59E-26 1259360000 563150 543220 609240 439982 819170 774050 528588 582020 630130 819630 TRUE FALSE 585383.5968 636513.8093 625117.2949 527009.1264 679927.776 594288.6183 487155.8914 574218.9739 607451.7444 980220.8057 0.597195646 0.649357579 0.637731102 0.537643277 0.693647566 0.606280355 0.496985871 0.585805739 0.619709091 1 19.90274724 -1.869182538 3.158616474 1.154391885 0.600214492 0.836491233 0.052685048 6646221.996 16329097.26 7252176.364 0.012942719 0.013515044 1.869182538 -0.554177393 GIHNSIGDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIHNSIGDYR 10 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 129.16 0.0010468 141550000 166489 268520 265750 259090 219612 309970 211730 267180 241330 280770 FALSE TRUE 173062.1143 314636.2212 272675.6633 310337.2287 182282.4307 237984.1651 195134.0493 263598.8891 232644.5804 335781.5058 0.515400971 0.937026655 0.812062781 0.924223709 0.542860245 0.70874709 0.581133999 0.785030993 0.692845128 1 18.35716325 -1.279600859 3.473098683 1.000847909 0.729366491 0.261075619 0.139759421 95106364.5 159669147.9 873308.7131 0.032647017 0.052529001 1.279600859 -0.271481418 GIHPTIISESFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIHPTIISESFQK 13 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ; 255.31 7.82E-24 3145200000 1943250 3265100 3747300 3432900 4468400 4610800 3746300 3985100 3908000 3883700 FALSE TRUE 2019971.011 3825855.526 3844957.716 4111917.374 3708862.964 3540011.577 3452655.217 3931686.253 3767351.843 4644636.657 0.434903989 0.823714708 0.827827449 0.885304423 0.798525964 0.762171907 0.743363899 0.846500285 0.811118742 1 22.14713431 4.738576156 23.57483302 0.82355025 0.434903957 0.753328345 0.068169661 0.263504205 391031.3426 0.015225315 0.087512726 54774.21422 -4.738576156 -0.388646293 GIITDS(ph)FGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;GIITDS(1)FGR;GIITDS(1)FGR 176.65 5.56E-05 1499880000 2002230 2504110 2162700 2426980 2568960 2594720 1993350 2229330 1982830 2494020 TRUE FALSE 2081279.586 2934171.413 2219061.739 2907029.4 2132289.097 1992135.603 1837106.018 2199449.478 1911468.336 2982675.468 0.697789488 0.983738072 0.743983636 0.974638183 0.714891419 0.667902232 0.615925547 0.737408243 0.640856961 1 21.50817558 3.115474989 10.84248385 0.706854231 0.851914902 0.158654758 0.129944395 0.486448004 44.03264895 0.034153854 0.040840139 1304.592835 -3.115474989 0.14506067 GILAADES(ph)TGSIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.97)T(0.03)GSIAK;GILAADES(0.86)T(0.14)GSIAK;GILAADES(0.937)T(0.063)GSIAK;GILAADES(0.928)T(0.072)GSIAK;GILAADES(0.5)T(0.5)GSIAK;GILAADES(0.991)T(0.009)GSIAK;GILAADES(0.986)T(0.014)GSIAK 314.16 8.41E-56 1460950000 2494032 2116094 2093534 2223594 4230190 3443950 3284380 2409139 2387902 2570370 TRUE FALSE 2592498.309 2479516.684 2148093.216 2663414.256 3511143.815 2644144.806 3026941.713 2376848.432 2301961.873 3073984.789 0.843367319 0.806613192 0.698797607 0.866437032 1.142212488 0.860168474 0.984696386 0.773214116 0.748852721 1 21.5516786 3.488608172 24.96152461 0.908597089 0.784848499 0.222259535 0.112346252 923.0855224 2005899.482 0.031964641 0.046507556 3080.407498 -3.488608172 -0.123748589 GILAADES(ph)TGSIAKR ddPTM_MDA-MB-175_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(0.555)T(0.207)GS(0.238)IAKR 74.618 0.020988 118050000 105440 75667 86884 71709 135020 100330 64193 79541 94930 89173 TRUE FALSE 109602.8526 88662.21864 89148.26842 85892.82617 112069.3486 77029.87802 59161.38492 78474.883 91513.48784 106644.742 1.027737988 0.831379184 0.835936838 0.805410792 1.050866142 0.722303571 0.554752009 0.735853278 0.858115329 1 16.70245331 2.690494077 24.99098972 0.738046256 0.895928997 0.181819043 0.131994017 546.2987502 284033.748 0.041849481 0.039456146 490.3363353 -2.690494077 0.157882741 GILAADESTGS(ph)IAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADEST(0.002)GS(0.998)IAK;GILAADEST(0.003)GS(0.997)IAK;GILAADEST(0.001)GS(0.999)IAK;GILAADEST(0.013)GS(0.986)IAK 230.86 7.93E-13 427682000 1138740 880240 1086060 840880 1808170 1411230 1192980 1218980 1161220 1023180 TRUE FALSE 1183698.334 1031414.373 1114363.616 1007203.554 1500817.909 1083493.22 1099471.11 1202641.567 1119427.919 1223652.531 0.967348413 0.842898083 0.910686316 0.823112386 1.226506603 0.885458243 0.898515782 0.982829305 0.914824994 1 20.22276252 GILAADESTGS(ph)IAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GILAADESTGSIAKR 15 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 GILAADES(0.001)T(0.019)GS(0.98)IAKR;GILAADESTGS(1)IAKR;GILAADESTGS(1)IAKR;GILAADEST(0.001)GS(0.999)IAKR 210.09 1.26E-09 1518470000 1213510 902500 1034160 690880 1636200 1146520 961180 1006390 1150160 960820 TRUE FALSE 1261420.312 1057497.355 1061111.059 827534.0019 1358079.308 880258.1057 885840.2 992900.9882 1108765.966 1149074.283 1.097770902 0.920303735 0.923448618 0.720174504 1.181889917 0.766058486 0.770916392 0.864087729 0.964921052 1 20.13204063 GILAADESTGSIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GILAADESTGSIAK 14 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 196.88 5.64E-08 83947000 57241 49544 51637 51531 77858 78297 72234 58164 56931 56710 FALSE TRUE 59500.91888 58052.7966 52982.70264 61723.678 64623.72497 60113.70835 66572.11033 57384.40672 54882.06443 67821.23872 0.877319848 0.855967801 0.781211073 0.91009364 0.952853799 0.886355211 0.981582047 0.846112631 0.809216485 1 16.04944951 3.696022598 24.26900068 0.907134834 0.839946369 0.244266104 0.059255473 506.5893716 289021.7169 0.015784431 0.02445336 4966.181612 -3.696022598 -0.067188465 GILADEDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GILADEDSSR 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 ; 148.52 0.006823 0 250700 257840 260270 348810 275080 333390 311100 277390 260110 245410 FALSE TRUE 260597.8296 302122.0143 267052.85 417803.5769 228321.9999 255965.2251 286715.1691 273672.0408 250748.6919 293493.3908 0.887917199 1.02939972 0.90991095 1.423553613 0.777945967 0.872132842 0.976905028 0.932464067 0.854358905 1 18.16296849 GILADEDSSRPVWLK ddPTM_MDA-MB-175_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 ;;;;;;; 322.23 8.25E-56 81005210000 29417380 26213230 31635170 31349600 36800230 37225310 32284780 31073960 31264870 26083610 FALSE TRUE 30578800.88 30715148.34 32459608.52 37550457.31 30544940.05 28580295.91 29754214.58 30657464.39 30139653.44 31194193.98 0.980272191 0.984643115 1.040565707 1.203764307 0.979186706 0.916205622 0.953838224 0.982793927 0.966194333 1 24.8947742 3.025148852 24.99999105 0.962011463 1.052243489 0.326719026 0.060747115 273.7995518 272176.9124 0.018454561 0.022056676 1059.61684 -3.025148852 0.090232026 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 62 GILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVK 38 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 417.21 5.46E-200 22484112900 1102902.05 8680956.5 7336412.3 8275105.4 6732889.2 9980676.4 5893180.2 8525609.7 6609675.6 10023731.1 FALSE TRUE 1146445.475 10171843.25 7527605.231 9911896.549 5588435.099 7662815.565 5431257.337 8411337.847 6371794.666 11987689.29 0.095635234 0.848524098 0.627944639 0.826839627 0.466181177 0.639223738 0.453069579 0.701664653 0.531528179 1 23.51505026 -2.194608768 2.03302321 2.007583675 0.59484197 0.272528326 0.205553693 7009142.915 1350623.43 32450556.37 0.053949258 0.006388387 2.194608768 -1.412741704 GILHLS(ph)PDVYQEMEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 265.7 9.13E-28 270237000 232292 378907 279207 345286 283370 365246 274602 289058 245724 447077 TRUE FALSE 241463.0675 443981.3298 286483.3638 413582.5402 235202.8686 280423.1519 253077.9777 285183.6503 236880.4412 534673.1783 0.451608716 0.830378908 0.53581024 0.773524009 0.439900257 0.524475817 0.473332099 0.533379384 0.443037824 1 19.02829778 -1.809372957 6.866964434 1.021593211 0.560107711 0.512333098 0.129855561 0.038968569 0.001081768 0.114134425 0.028632818 0.015510544 1.809372957 -0.4614855 GILHTDSQSQS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GILHTDSQSQSLR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 GILHTDSQS(0.376)QS(0.624)LR;GILHTDSQS(0.146)QS(0.854)LR 185.26 5.67E-06 277960000 117248 314020 290840 305650 306480 363490 257110 278720 266060 365250 TRUE FALSE 121877.0416 367950.4923 298419.5293 366106.6577 254384.6391 279074.9562 236957.0464 274984.2143 256484.5526 436813.7444 0.279013752 0.842350995 0.683173396 0.838129895 0.582364091 0.638887764 0.542467011 0.629522807 0.587171434 1 18.73665873 -1.17150282 5.070088774 1.000023033 0.634490475 0.356807604 0.150624474 3.65E-05 5.97E-06 0.135820492 0.032011182 0.067374752 1.17150282 -0.365532557 GILQVLPDEITFPLS(ph)PLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GILQVLPDEITFPLSPLRK 19 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-8;A0A0U1RQP0;A0A0U1RRJ3;Q9HCH5-11 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 GILQVLPDEITFPLS(1)PLRK;GILQVLPDEITFPLS(1)PLRK 233.91 2.46E-24 1655400000 1175270 975700 1122820 981670 1524340 1500540 1491410 1339570 1488080 1251220 TRUE FALSE 1221670.567 1143268.885 1152081.612 1175841.396 1265233.231 1152062.326 1374509.387 1321615.255 1434524.291 1496372.603 0.816421368 0.764026876 0.769916269 0.785794523 0.845533545 0.769903381 0.918560915 0.883212679 0.95866784 1 20.51303803 1.710773755 0.699349336 0.999836702 0.780307685 0.834141418 0.032982307 0.230699588 0.228568326 0.028377031 0.013888557 51.37759315 -1.710773755 -0.219529017 GILRT(ph)PDTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GILRTPDTIR 10 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 GILRT(1)PDTIR;GILRT(0.983)PDT(0.017)IR;GILRT(0.997)PDT(0.003)IR;GILRT(0.987)PDT(0.013)IR 109.6 0.0032288 2312540000 1477880 2119390 1824670 1981110 1967440 2272340 1507900 1824540 1674730 2186410 TRUE FALSE 1536227.844 2483378.746 1872222.399 2372967.645 1633015.252 1744623.473 1389706.858 1800085.026 1614456.794 2614795.178 0.587513644 0.949741214 0.71601111 0.907515688 0.624528936 0.667212288 0.531478285 0.688422956 0.617431456 1 21.31826651 3.217181729 24.99852096 0.662395841 0.796292712 0.086094232 0.148735724 405.1272952 473717.8166 0.039215982 0.046913894 1648.852205 -3.217181729 0.133896871 GILSLPHQAS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GILSLPHQASPVSR 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 GILSLPHQAS(0.999)PVS(0.001)R;GILSLPHQAS(1)PVSR;GILSLPHQAS(1)PVSR;GILSLPHQAS(1)PVSR 250.26 1.64E-18 2028790000 1104030 1489960 1297580 1394630 1308470 1455130 1238020 1304230 1186290 1615340 TRUE FALSE 1147617.957 1745849.04 1331396.001 1670483.651 1086056.737 1117198.11 1140980.757 1286748.93 1143595.655 1931834.945 0.594055905 0.903725778 0.689187243 0.864713445 0.562189197 0.578309298 0.590620208 0.666076019 0.59197379 1 20.88154041 -1.395226999 3.124227613 1.004169271 0.67421661 0.425640111 0.114533937 22947238.77 28115156.33 857826.7468 0.028761167 0.04025066 1.395226999 -0.329952661 GILTLK ddPTM_MDA-MB-175_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 ; 126.68 0.040453 3522900000 5312700 4994200 5600000 4756400 6088200 6472000 5871300 5627800 5613100 5306200 FALSE TRUE 5522449.498 5851915.001 5745940.6 5697201.724 5053329.939 4968976.084 5411092.164 5552368.546 5411085.627 6345848.297 0.870246063 0.922164339 0.905464539 0.897784103 0.796320634 0.783027871 0.852698002 0.874960807 0.852696972 1 22.5973816 3.433477971 24.98497223 0.850945556 0.901586597 0.089901961 0.056407006 243.2366539 139247.8137 0.015082023 0.02042117 2713.176027 -3.433477971 0.05064104 GIMVLAGDTLPIEVYCHLPVMCEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIMVLAGDTLPIEVYCHLPVMCEDR 25 0 D6RC52;D6RCB9;Q9NX24;H0YC83 D6RC52 NHP2 H/ACA ribonucleoprotein complex subunit 2 0 ; 255.2 7.37E-45 464780000 164171 199530 149707 170999 172255 219331 150007 174009 174111 198679 FALSE TRUE 170652.5978 233797.7254 153608.4874 204822.0918 142975.1566 168394.6992 138249.0594 171676.694 167844.7791 237606.3461 0.718215656 0.98397088 0.646483101 0.862022817 0.60173122 0.70871297 0.58184077 0.72252571 0.706398553 1 17.85821384 4.220072187 24.97729555 0.711356264 0.851093405 0.109938375 0.132092911 349.4123932 472046.7163 0.029938291 0.064860886 16598.62783 -4.220072187 0.139737141 GINLPTPPGLS(ph)PGDLDVFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GINLPTPPGLSPGDLDVFVR 20 0 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GINLPT(0.017)PPGLS(0.983)PGDLDVFVR;GINLPT(0.003)PPGLS(0.997)PGDLDVFVR;GINLPTPPGLS(1)PGDLDVFVR;GINLPTPPGLS(1)PGDLDVFVR 156.67 1.65E-08 15537600 86299.1 287857.1 205590.9 309957.8 172761.3 308080.5 155991.6 240627.1 181819.1 352243.9 TRUE FALSE 89706.25511 337294.3177 210948.7677 371266.5277 143395.3959 236533.4729 143764.5708 237401.8873 175275.4661 421259.3481 0.212947809 0.800680909 0.500757476 0.881325315 0.340396947 0.561491333 0.341273307 0.563552805 0.416074959 1 18.68434918 -1.649393045 3.901965124 1.020399909 0.523915181 0.356453907 0.195762069 0.032101683 0.002884463 0.175146103 0.040924747 0.022418521 1.649393045 -0.496484727 GIPAPEEER ddPTM_MDA-MB-175_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 376500000 287100 350830 331760 325520 361880 397290 321040 346440 324540 337510 FALSE TRUE 298434.9297 411082.3234 340405.9381 389906.8844 300367.7669 305025.4185 295876.0459 341796.5385 312859.8688 403638.6225 0.739361679 1.018441498 0.843343325 0.965980119 0.744150213 0.755689375 0.733022138 0.846788487 0.775098941 1 18.6227047 GIPDDRDGLFDTIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 143.14 4.07E-06 484650000 290850 280970 282020 322400 300620 362290 283980 292460 284080 362710 FALSE TRUE 302332.9826 329224.4119 289369.6729 386169.7577 249520.7198 278153.6381 261720.9056 288540.0521 273856.0163 433776.08 0.696979378 0.758973182 0.667094582 0.890251389 0.575229321 0.641237843 0.603354859 0.665182027 0.631330377 1 18.72659097 -0.972212855 4.357380693 1.000009775 0.680268682 0.560302939 0.084755481 9325668.748 4280400.799 886.5476365 0.01982717 0.106607349 0.972212855 -0.319741093 GIPHLVTHDAR ddPTM_MDA-MB-175_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 ;;;;;;;;; 164.33 1.32E-05 8185610000 4583448 5486873 4994655 4884955 6203430 6078881 5130707 5216916 4839468 6150825 FALSE TRUE 4764406.066 6429200.756 5124819.812 5851184.519 5148973.184 4667153.014 4728548.779 5146991.774 4665296.492 7355961.394 0.647693185 0.874012303 0.69668933 0.79543437 0.69997284 0.634472201 0.642818596 0.699703478 0.634219817 1 22.81048248 -1.050896534 4.416909425 1.000017231 0.705253222 0.595306759 0.073492331 9769865.552 2324502.677 1785.59008 0.0172503 0.088941299 1.050896534 -0.294764009 GIPLATGDT(ph)SPEPELLPGAPLPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.096)GDT(0.494)S(0.41)PEPELLPGAPLPPPK 115.55 0.0055532 73461000 153270 121640 155790 131330 168600 182030 170010 149180 149050 118110 TRUE FALSE 159321.218 142530.7238 159850.0154 157306.682 139941.4322 139756.2912 156684.172 147180.4861 143685.7196 141251.3931 1.127926701 1.009057119 1.131670363 1.113664641 0.990726032 0.989415312 1.109257533 1.041975465 1.017234 1 17.10790557 3.250343799 24.99298566 1.032002965 1.091977429 0.356721913 0.045871042 300.8359292 638090.9277 0.012996542 0.017456139 1779.6877 -3.250343799 0.059974463 GIPLATGDTS(ph)PEPELLPGAPLPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GIPLATGDTSPEPELLPGAPLPPPK 25 0 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 GIPLAT(0.014)GDT(0.109)S(0.877)PEPELLPGAPLPPPK;GIPLAT(0.02)GDT(0.101)S(0.879)PEPELLPGAPLPPPK;GIPLAT(0.005)GDT(0.173)S(0.822)PEPELLPGAPLPPPK 191.8 4.03E-18 307835000 607290 490370 549080 534060 665770 746830 688650 598030 591730 451697 TRUE FALSE 631266.2781 574587.233 563389.4759 639695.474 552602.6532 573390.0508 634671.8135 590014.386 570433.7529 540198.3789 1.168582326 1.063659677 1.042930705 1.184186216 1.022962443 1.061443487 1.174886557 1.092217987 1.055970871 1 19.04312978 0.990055979 2.889920966 1.000647507 1.100219951 0.256984354 0.054259613 0.342156097 6.816899027 0.049811627 0.013189066 9.773631922 -0.990055979 0.099572444 GIPVVEHK ddPTM_MDA-MB-175_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 ;; 91.853 0.012192 268665000 385368 343027 384604 348359 405587 454679 428788 399142 356594 328699 FALSE TRUE 400582.6262 401939.2189 394627.0962 417263.3705 336645.4666 349086.693 395178.4761 393792.1544 343760.2516 393101.2757 1.019031611 1.022482611 1.003881495 1.061465318 0.856383552 0.88803246 1.005284135 1.001757508 0.874482666 1 18.58454152 3.264894036 24.99998864 0.944462363 1.024781943 0.403332041 0.052656153 268.946978 255326.6227 0.015587031 0.021098714 1840.322925 -3.264894036 0.080319581 GIQLS(ph)PGVGSSAGPPGDLEDDEGLKHLQQEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIQLSPGVGSSAGPPGDLEDDEGLKHLQQEAEK 33 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 GIQLS(1)PGVGSSAGPPGDLEDDEGLKHLQQEAEK;GIQLS(1)PGVGSSAGPPGDLEDDEGLKHLQQEAEK 183 6.38E-20 286000000 553370 257860 420220 262350 574810 555570 521890 370320 441360 248130 TRUE FALSE 575217.4749 302145.4491 431171.2784 314242.047 477104.0015 426547.2872 480982.8981 365356.4661 425475.5398 296746.3228 1.938414837 1.018194417 1.452996197 1.058958521 1.607784039 1.437413894 1.620855462 1.231208066 1.433802232 1 18.17887063 0.034894476 0.960422229 0.99576404 1.409052244 0.18934946 0.259977441 10.69854193 9.097108743 0.380177644 0.073821546 1.083663575 -0.034894476 0.413288204 GIRPFPSEETTENDDDVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GIRPFPSEETTENDDDVYR 19 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 ;;; 287.37 2.16E-40 1382510000 287448 359609 317002 339025 350212 402320 318629 326470 325141 397466 FALSE TRUE 298796.669 421369.0484 325263.3325 406083.1331 290683.0893 308887.2772 293654.0264 322094.2036 313439.2389 475341.8528 0.628593227 0.886454761 0.684272447 0.85429703 0.611524291 0.649821335 0.617774397 0.677605394 0.65939752 1 18.85860591 -1.134886931 4.384740499 1.000048661 0.69767406 0.499192123 0.091150502 4.28E-05 8.45E-06 0.087142627 0.020536414 0.073301535 1.134886931 -0.302374601 GIS(ph)PIVFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 191.53 3.75E-05 7972930000 4405083 5020440 4499503 5559618 4680380 5262068 5457503 4807275 4424801 4281793 TRUE FALSE 4578999.078 5882661.516 4616763.745 6659293.847 3884810.679 4040032.454 5029729.654 4742841.342 4265553.276 5120728.358 0.89420855 1.148793903 0.901583412 1.300458329 0.758644163 0.788956604 0.982229344 0.92620444 0.832997374 1 22.2879176 3.208994617 24.99999818 0.883859485 1.056108388 0.312100064 0.130620837 250.6576333 211946.8468 0.036058339 0.043103622 1618.059983 -3.208994617 0.172248902 GIS(ph)SLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GISSLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GIS(0.569)S(0.431)LPR 98.299 0.011921 398580000 411680 476220 459550 465480 513120 565300 410160 452640 397530 523070 TRUE FALSE 427933.4443 558007.0805 471526.2505 557550.5547 425900.0457 434017.6422 378010.5874 446573.1012 383222.973 625555.5517 0.684085439 0.892018429 0.753771986 0.891288636 0.680834891 0.69381151 0.604279806 0.713882404 0.612612216 1 19.25477848 3.213667322 24.88777318 0.695509043 0.807806019 0.099327715 0.118639264 348.4661095 348387.8461 0.031221923 0.037332298 1635.563167 -3.213667322 0.112296976 GISCLVDAFLGISRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GISCLVDAFLGISRPR 16 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 0 ; 166.09 6.20E-09 79689000 74122 77824 89130 92000 92642 103522 85512 82161 91667 97488 FALSE TRUE 77048.39379 91189.66661 91452.80102 110197.3254 76894.74593 79480.58439 78809.346 81059.76618 88367.92258 116588.9071 0.660855271 0.782147023 0.784403965 0.945178475 0.659537411 0.681716523 0.675959214 0.695261395 0.757944515 1 16.831071 0.94994209 20.74763367 1.000000001 0.735829349 0.477853281 0.082420774 1387.44354 575059.5465 0.083111381 0.020777845 8.911321042 -0.94994209 -0.264170652 GISDLAQHYLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GISDLAQHYLMR 12 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 172.11 3.66E-05 2505700000 1812980 2241840 2102830 2153820 3501430 2994360 2519510 2118060 2183240 3479710 FALSE TRUE 1884557.85 2626858.581 2157631.477 2579839.167 2906258.179 2298965.27 2322024.223 2089670.87 2104665.619 4161492.551 0.452856235 0.631229913 0.518475391 0.619931223 0.698369189 0.552437675 0.557978705 0.502144566 0.50574778 1 21.98866962 -1.067073671 4.455170399 1.000026161 0.561952358 0.786156299 0.068851243 9385840.143 2248036.266 2794.98401 0.01633271 0.085689248 1.067073671 -0.438073803 GISEETTTGVHNLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GISEETTTGVHNLYK 15 0 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 261.27 6.10E-25 9666620000 4976030 5158030 5794700 5294610 7074310 7371900 6406410 5771180 5912590 5819970 FALSE TRUE 5172487.507 6043881.529 5945714.642 6341868.055 5871821.313 5659887.947 5904258.844 5693826.772 5699797.041 6960281.691 0.743143415 0.868338639 0.854234772 0.911151062 0.843618344 0.81316938 0.84827872 0.81804545 0.818903213 1 22.73071426 -1.485836104 5.91264596 1.000147806 0.837908136 0.587925251 0.041285988 7.87E-05 6.84E-06 0.03909474 0.009206361 0.03267111 1.485836104 -0.16223967 GISHVIVDEIHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;;; 230.06 2.73E-12 6916585000 1055178 1318666 1277165 1385958 1363488 1586973 1361882 1385960 1237908 1278931 FALSE TRUE 1096837.242 1545136.628 1310448.969 1660096.356 1131722.797 1218422.572 1255134.13 1367383.473 1193355.933 1529513.043 0.717115325 1.010214744 0.856775282 1.085375743 0.7399236 0.796608161 0.820610283 0.893999224 0.780219521 1 20.54464098 4.783377638 21.69230124 0.879287508 0.717112099 0.181964901 0.106969486 9439.074606 4568102.577 0.024706436 8.918022863 60726.41426 -4.783377638 -0.162175408 GISLNPEQWSQLKEQISDIDDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GISLNPEQWSQLKEQISDIDDAVR 24 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 87.102 0.010462 254030000 39586 44330 55641 36208 57065 63459 43190 40998 54383 71195 FALSE TRUE 41148.88585 51943.33266 57091.05017 43369.83433 47365.11168 48721.60898 39804.65494 40448.48887 52425.76645 85144.29714 0.48328411 0.610062381 0.670521128 0.509368634 0.556292239 0.572223985 0.46749643 0.47505811 0.615728454 1 16.37762228 0.912117975 8.209234487 0.99999967 0.542766228 0.834839796 0.060667683 1.330488709 124.3577472 0.063034839 0.015782982 8.168042245 -0.912117975 -0.457233443 GISQEQMQEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GISQEQMQEFR 11 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 285.28 2.41E-27 1097220000 233459 299192 228517 295549 247145 314041 275240 293450 210852 349412 FALSE TRUE 242676.1416 350575.8986 234472.3407 354007.7101 205135.3812 241109.7371 253665.9696 289516.7827 203263.4777 417872.5915 0.580741945 0.838954039 0.561109643 0.847166618 0.49090413 0.576993423 0.607041416 0.692835062 0.486424527 1 18.67270361 -1.734593787 6.174939242 1.008291446 0.639008057 0.455203301 0.120728215 0.012901989 0.000554543 0.109440468 0.025566935 0.018424946 1.734593787 -0.369283389 GISS(ph)DNESVASCNSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GISSDNESVASCNSVK 16 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 GIS(0.005)S(0.986)DNES(0.009)VASCNSVK 363.8 1.33E-72 0 189100 170470 182700 166670 218950 262450 248780 204240 223390 176450 TRUE FALSE 196565.814 199746.8964 187461.3121 199636.8285 181732.9572 201499.965 229279.9735 201502.4969 215350.2375 211021.9992 0.931494417 0.946569065 0.888349617 0.946047471 0.861203846 0.95487658 1.086521663 0.954888579 1.02051084 1 17.68703388 2.471145342 24.99895086 1.009852748 0.915901987 0.600124262 0.03866939 106.815763 446836.2837 0.012676074 0.010632701 295.9002565 -2.471145342 -0.093950761 GISS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GISSLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 GIS(0.041)S(0.959)LPR;GIS(0.032)S(0.968)LPR;GIS(0.047)S(0.953)LPR 115.49 0.0059452 812630000 1532400 1781960 1697690 1739810 1926800 2086320 1506290 1731240 1502010 1849410 TRUE FALSE 1592900.335 2087997.768 1741933.196 2083939.225 1599283.224 1601803.798 1388223.054 1708035.56 1447952.954 2211766.48 0.720193723 0.944040787 0.787575547 0.942205809 0.723079601 0.724219221 0.627653537 0.7722495 0.654659055 1 21.07676764 3.208952906 24.99160409 0.731904764 0.850976021 0.140872349 0.113394221 299.0410124 252417.0851 0.029879628 0.035717751 1617.904584 -3.208952906 0.119071256 GISTKPVYIPEVELNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GISTKPVYIPEVELNHK 17 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 69.605 0.020671 928450000 754160 427030 534830 470130 782980 642330 647010 590120 670810 445920 FALSE TRUE 783934.8191 500369.0807 548768.1092 563120.3108 649889.3393 493158.5921 596295.6656 582210.4066 646667.6791 533289.4863 1.469998639 0.938269164 1.029024804 1.055937395 1.2186427 0.924748387 1.118146299 1.091734267 1.21260159 1 19.02455936 4.750703764 24.64292821 1.070653596 1.469998939 0.619007207 0.095134326 1009.341465 2048280.316 0.021824923 0.365157028 56325.33255 -4.750703764 0.399345343 GITGVEDKESWHGKPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GITGVEDKESWHGKPLPK 18 2 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 230.07 9.22E-20 2650000000 1090100 1172700 1707300 959010 2594800 1959200 1767700 1715300 1892000 1461800 FALSE TRUE 1133137.99 1374102.103 1751793.641 1148699.316 2153736.823 1504205.492 1629143.055 1692309.209 1823907.29 1748211.722 0.64816977 0.786004398 1.002048904 0.657071052 1.231965668 0.860425241 0.931891163 0.96802303 1.043298856 1 20.73744849 5.490608338 0.624849085 0.979948352 1.01E-10 0.367009471 0.135982844 8.402057984 1.245752218 0.054410112 7.281747112 309462.7195 -5.490608338 -0.979948352 GIVDQSQQAYQEAFEISKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIVDQSQQAYQEAFEISKK 19 1 B7Z2E6;H0YB80;P63104-2;P63104;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ; 312.76 2.26E-61 2146500000 1187660 654750 1108970 763500 1391700 1194050 1148040 1013980 1286970 762470 FALSE TRUE 1234549.734 767198.2193 1137870.669 914518.0212 1155139.331 916749.9835 1058053.625 1000389.257 1240652.201 911861.3981 1.353878711 0.841353983 1.247854851 1.002913407 1.266792665 1.005361106 1.16032286 1.097084775 1.360571029 1 19.79845503 GIVEESVTGVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIVEESVTGVHR 12 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 204.17 1.17E-07 736150000 265490 348950 331360 335830 359110 401510 354440 342520 364840 432440 FALSE TRUE 275971.7502 408879.448 339995.5138 402256.1716 298068.6105 308265.3874 326658.0666 337929.0796 351709.4797 517168.3384 0.533620738 0.79061191 0.657417496 0.777805101 0.576347368 0.596063921 0.631628123 0.653421825 0.680067695 1 18.98027443 0.622409552 2.921531565 0.999997023 0.655710453 0.64787429 0.076461953 3.164836024 23.7740041 0.070389964 0.018449546 4.191886852 -0.622409552 -0.34428657 GIVEFASKPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ; 161.48 5.95E-05 2922100000 3736000 3931700 4027000 3545900 5322700 5367700 4665700 4868900 4855300 5279200 FALSE TRUE 3883500.165 4606938.891 4131946.928 4247268.437 4417949.355 4121133.023 4299990.242 4803640.359 4680558.701 6313558.164 0.615104837 0.729689784 0.654456144 0.672721836 0.699755865 0.652743337 0.681072405 0.76084519 0.741350373 1 22.59002187 0.289042235 0.574462531 1.01555794 0.668184938 0.899894869 0.032358135 0.683364985 0.332520372 0.05397653 0.013305085 1.945549278 -0.289042235 -0.347373002 GIVEFSGKPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 208.79 5.72E-08 3252600000 3806200 3822400 3998700 3669300 5000100 5058200 4478400 4400100 4722200 4766900 FALSE TRUE 3956471.715 4478867.466 4102909.407 4395076.588 4150184.788 3883509.708 4127371.306 4341123.857 4552248.944 5700882.787 0.69401036 0.785644545 0.719697205 0.770946668 0.727989847 0.68121199 0.723988101 0.761482742 0.798516495 1 22.44275391 0.694701062 1.370147538 0.9997683 0.731398375 0.879172292 0.029895483 0.319710297 0.953609853 0.028041275 0.008314504 4.951092748 -0.694701062 -0.268369925 GIWHNNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GIWHNNEK 8 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 148.99 0.00051244 2347600000 3407500 2999500 3329400 3166800 3680000 4143400 3696400 2780000 3093200 2631700 FALSE TRUE 3542030.731 3514640.792 3416166.899 3793183.588 3054474.914 3181158.144 3406666.509 2742738.647 2981876.336 3147331.228 1.125407679 1.116705087 1.085417025 1.205206352 0.970496809 1.010747809 1.082398471 0.871448999 0.947430099 1 21.58569759 2.726432922 0.927684534 0.944721605 1.128762349 0.519241331 0.065255195 0.425061896 0.777280361 0.038565125 0.035389411 532.6389502 -2.726432922 0.184040744 GIYAYGFEKPSAIQQR ddPTM_MDA-MB-175_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 ; 194.77 1.45E-10 7684800000 1465720 1619100 1667090 1540540 1978680 2083710 1649170 1762890 1667350 1804920 FALSE TRUE 1523587.757 1897167.83 1710535.735 1845254.214 1642344.68 1599799.931 1519903.746 1739261.343 1607342.399 2158559.517 0.705835417 0.878904573 0.792443165 0.854854453 0.760852164 0.741142377 0.704128718 0.805750932 0.744636591 1 21.04163744 -1.12106139 4.39173098 1.000024614 0.779567009 0.594845756 0.0552826 0.602861445 31826549.94 1959.597527 0.012726463 0.075672592 1.12106139 -0.220457605 GIYKGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GIYKGDR 7 1 Q15363;E7EQ72 Q15363 TMED2 Transmembrane emp24 domain-containing protein 2 0 89.296 0.016396 288530000 250290 297480 303530 357680 656750 550320 414330 314100 296500 577540 FALSE TRUE 260171.6425 348569.8759 311440.2412 428428.0364 545115.8696 422516.5202 381853.732 309890.0033 285829.0229 690697.9053 0.376679356 0.504663288 0.450906596 0.620282808 0.789224733 0.61172405 0.55285202 0.448662144 0.413826393 1 19.39769532 3.743309292 22.52997568 0.60236918 0.450141053 0.206506362 0.162305191 196.3788811 931695.7635 0.042322544 0.07304102 5537.443302 -3.743309292 -0.152228127 GKAEEQAVR ddPTM_MDA-MB-175_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 ;;;;; 157.78 6.18E-05 1637790000 2583910 2245030 2415570 2085970 3436440 2837220 2648320 2288660 2497750 2489810 FALSE TRUE 2685924.762 2630596.439 2478521.739 2498568.64 2852315.156 2178318.653 2440737.758 2257984.256 2407856.465 2977640.599 0.902031213 0.88344995 0.832377735 0.839110214 0.957911159 0.731558622 0.819688501 0.758313229 0.808645767 1 21.5057382 2.735101729 24.99942945 0.804440791 0.877754371 0.107678943 0.07518808 497.3023862 3594281.882 0.022296457 0.021810117 543.3775974 -2.735101729 0.07331358 GKAS(ph)PFEEDQNR ddPTM_MDA-MB-175_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 191.93 2.87E-06 6465350000 5971710 4715010 5068620 4393370 5962460 6418390 5868820 5031170 5247170 4524010 TRUE FALSE 6207477.722 5524776.29 5200712.401 5262365.473 4948963.179 4927816.194 5408806.553 4963735.395 5058325.377 5410403.142 1.147322586 1.021139487 0.961243047 0.972638329 0.914712462 0.910803884 0.999704904 0.917442798 0.93492578 1 22.36730467 4.89582779 1.267098562 0.944384629 1.298274637 0.789295737 0.031078081 0.79380911 0.856719866 0.008302174 0.400421049 78673.37649 -4.89582779 0.353890008 GKATRPASTSQPDPS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKATRPASTSQPDPSPDR 18 2 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 GKATRPASTSQPDPS(1)PDR 71.527 0.012196 154260000 39854 46667 45675 37990 54057 56749 43470 42116 54455 51049 TRUE FALSE 41427.46669 54681.69423 46865.32802 45504.30861 44868.41045 43569.90479 40062.70781 41551.50391 52495.17519 61051.07416 0.678570644 0.895671288 0.767641334 0.745348206 0.734932367 0.713663197 0.656216264 0.68060234 0.8598567 1 15.89772906 -1.540703148 7.534944828 1.000089023 0.742794268 0.51253211 0.07355106 0.000111981 6.83E-06 0.072501137 0.01708281 0.028793659 1.540703148 -0.257294755 GKDETDSPTVHLGLDS(ph)DS(ph)ESELVIDLGEDHSGR ddPTM_MDA-MB-175_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(1)DS(0.878)ES(0.123)ELVIDLGEDHSGR 129.51 9.81E-08 87530000 23123 21522 18603 19427 24493 22932 17401 21192 19977 20245 TRUE FALSE 24035.91389 25218.23608 19087.80946 23269.60262 20329.68861 17606.39054 16037.06415 20907.9559 19258.03167 24211.62014 0.992742896 1.041575737 0.788373903 0.961092339 0.839666594 0.727187625 0.66237055 0.863550468 0.795404503 1 14.563412 4.239791219 24.99554 0.819777208 1.017159375 0.378857324 0.095333172 29.74164934 604034.996 0.023582288 0.057764569 17369.65608 -4.239791219 0.197382167 GKDIGKPIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKDIGKPIEK 10 2 O60869 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 67.519 0.035282 1114170000 2305130 1247520 1741010 1228350 2769700 2307990 2476100 2018550 2344060 1386000 FALSE TRUE 2396138.312 1461771.856 1786382.151 1471313.964 2298907.383 1771994.3 2282016.812 1991494.639 2259697.738 1657560.163 1.445581503 0.881881628 1.077717835 0.887638347 1.386922438 1.069037697 1.376732418 1.201461451 1.363267403 1 20.66062981 3.233267919 24.99971315 1.24227517 1.059861247 0.14470682 0.188268828 212.2597704 1002595.356 0.049959168 0.061407775 1711.07056 -3.233267919 -0.182413922 GKDILYIGDHIFGDILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GKDILYIGDHIFGDILK 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 207.53 3.60E-12 2839893000 5806180 4281255 5317630 3819318 7512040 6290890 5662990 5304000 5929700 4461943 FALSE TRUE 6035412.47 5016527.243 5456211.806 4574767.701 6235146.124 4829926.137 5219110.046 5232908.556 5716291.255 5336175.302 1.131037143 0.940097909 1.022494858 0.857312109 1.168467258 0.905128835 0.978061955 0.980647797 1.071233783 1 22.34737463 GKDNFLFITYEELQQDLQGSVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKDNFLFITYEELQQDLQGSVER 23 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 248.45 7.62E-38 382040000 513630 457430 586050 491090 640070 640550 554640 531240 586040 468000 FALSE TRUE 533908.509 535990.0442 601322.9444 588226.1362 531271.13 491791.9701 511165.8675 524119.5967 564948.5349 559695.6396 0.953926512 0.95764556 1.074374896 1.05097502 0.949214345 0.878677509 0.913292567 0.936436805 1.009385271 1 19.09428298 3.109287421 7.308362389 0.937725922 1.009916774 0.256184217 0.049820861 0.284000676 17.357393 0.015177829 0.018191941 1286.137559 -3.109287421 0.072190852 GKDSLYAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKDSLYAQGK 10 1 H0Y5B4;H7BZ11;J3KQN4;P83881;H7BY91;H0Y3V9 H0Y5B4 RPL36A;RPL36A-HNRNPH2 60S ribosomal protein L36a 0 ; 118.9 0.00069593 1198900000 1626130 1202100 1489330 1185050 2418800 2104890 1877830 1860930 1830270 2059670 FALSE TRUE 1690330.868 1408551.324 1528143.163 1419449.353 2007653.24 1616061.197 1730640.778 1835987.277 1764398.94 2463222.902 0.686227327 0.571832668 0.620383629 0.576256965 0.815051386 0.656075906 0.70259203 0.745359779 0.716296905 1 21.23211576 -5 0.141276428 2.157084153 0.558302956 0.733982739 0.062096536 66.16642508 0.570824697 21.38421985 0.358372672 1.00E-05 5 -1.598781197 GKDSLYAQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GKDSLYAQGR 10 1 Q969Q0 Q969Q0 RPL36AL 60S ribosomal protein L36a-like 0 ;;;;; 154.15 1.37E-05 1629060000 1241464 1260724 1230276 1107111 2079839 1780474 1445476 1461856 1520736 1884803 FALSE TRUE 1290477.957 1477243.54 1262338.003 1326094.251 1726308.71 1366985.897 1332175.814 1442262.211 1466005.008 2254094.061 0.57250404 0.655360202 0.56002011 0.588304754 0.765854779 0.606445809 0.591002761 0.639841183 0.650374372 1 21.10411629 -5 0.371741715 5.995951996 0.616467669 0.806999692 0.055161608 223.5757505 1.716238155 897.6989435 0.037938408 1.00E-05 5 -5.379484327 GKDYYQTLGLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKDYYQTLGLAR 12 1 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 154.1 6.49E-05 1595510000 1874510 1120860 1111170 1069500 1681640 1790390 1352370 1244960 1188800 1545080 FALSE TRUE 1948517.102 1313358.986 1140128.003 1281043.908 1395795.433 1374599.056 1246367.706 1228273.348 1146015.32 1847808.844 1.054501449 0.710765613 0.617016206 0.69327729 0.755378695 0.743907608 0.67451117 0.664718838 0.620202314 1 20.81738409 4.737797165 6.892654562 0.703262158 1.059960594 0.473678733 0.104486767 0.0815115 28.4416909 0.022593371 0.136531654 54676.05413 -4.737797165 0.356698436 GKEALESEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 72.34 0.044032 398430000 477120 672700 554490 635630 670140 789260 593540 619290 587640 780040 FALSE TRUE 495957.066 788230.9921 568940.4649 761355.7168 556229.8422 605966.3264 547016.7839 610989.4305 566490.9512 932873.9032 0.531644271 0.844949129 0.609879281 0.81614001 0.596254049 0.649569384 0.586378054 0.654953931 0.607253509 1 19.83132256 -0.870224288 6.281287856 1.000000027 0.659022462 0.543088218 0.094814517 3.39E-08 5.99E-09 0.084167311 0.019838424 0.13482664 0.870224288 -0.340977566 GKEDALVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKEDALVTK 9 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 79.693 0.023913 407260000 1467940 1074870 1292750 1068240 1679580 1531770 1551690 1302550 1428500 1243980 FALSE TRUE 1525895.405 1259470.561 1326440.127 1279534.684 1394085.592 1176039.632 1430064.483 1285091.448 1377088.564 1487714.064 1.025664435 0.846581068 0.891596147 0.860067613 0.937065546 0.790501119 0.961249556 0.863802715 0.925640617 1 20.50466584 0.95578123 8.256537435 0.999999351 0.893570969 0.198231851 0.062261654 1.110081235 206.268577 0.053606104 0.013421657 9.031943867 -0.95578123 -0.106428383 GKEDEGEEAASPMLQIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKEDEGEEAASPMLQIQR 18 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 101.17 0.0006522 270630000 166460 138770 170670 149480 197360 205660 175410 151880 144270 123170 FALSE TRUE 173031.9693 162602.668 175117.8004 179046.6978 163812.8177 157898.5818 161660.9059 149844.297 139077.7509 147302.8033 1.174668543 1.103866759 1.188828702 1.215500954 1.112082147 1.071931954 1.097473383 1.017253533 0.944162282 1 17.16842536 2.074137484 0.915691036 0.972210569 1.163979914 0.790065383 0.037878138 0.264185142 0.410901498 0.031730007 0.01612497 118.6144186 -2.074137484 0.191769344 GKEDKENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKEDKENR 8 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 62.2 0.045639 64392000 143486 92034 122347 93550 166643 139179 154863 121880 139210 89419 FALSE TRUE 149150.9381 107840.1236 125535.4633 112053.9108 138317.0824 106856.7865 142724.4334 120246.398 134199.8593 106938.941 1.394729896 1.008427076 1.173898508 1.04783075 1.293421097 0.999231763 1.334634812 1.124439767 1.254920406 1 16.70642777 -2.402828664 1.891060513 5.11E-05 1.173068439 0.144293975 0.131071718 2354856.798 198246.5382 10072665.13 0.029795922 0.003955226 2.402828664 1.173017341 GKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQSPR 41 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 GKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQS(1)PR 212.8 1.81E-36 262500000 55604 103340 107410 96129 126660 138990 101740 108120 123240 124560 TRUE FALSE 57799.28886 121087.8411 110209.1928 115143.0293 105130.3784 106711.6789 93765.35295 106670.8282 118804.6165 148965.1472 0.388005449 0.812860212 0.739832068 0.772952811 0.70573809 0.716353328 0.629444905 0.716079098 0.797532972 1 17.1846153 -5 0.211356697 2.448734777 0.659820359 0.436549614 0.109875757 142.8485243 1.425094584 87.64177018 0.221490388 1.00E-05 5 -1.788914419 GKEKCSEKSR ddPTM_MDA-MB-175_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 1063400000 50077 1487700 1229900 1427600 981610 1624300 780600 1286400 1046100 1744700 FALSE TRUE 52054.07863 1743200.902 1261952.204 1709975.019 814756.2828 1247080.942 719414.5323 1269157.912 1008451.065 2086540.561 0.024947552 0.835450283 0.604805978 0.819526374 0.390481881 0.597678744 0.344788185 0.608259401 0.483312467 1 20.99268154 -1.60836111 3.785300979 1.015169822 0.539264629 0.285424885 0.225022407 0.026747782 0.002767408 0.202297793 0.046976471 0.024639897 1.60836111 -0.475905193 GKELNEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GKELNEFR 8 1 Q9UHV9 Q9UHV9 PFDN2 Prefoldin subunit 2 0 ;;;;; 130.75 0.00192 2972940000 3271950 3350510 3495840 2833380 4754300 4184350 3451890 3487880 3528560 4264520 FALSE TRUE 3401129.112 3925934.029 3586944.462 3393814.107 3946165.784 3212598.127 3181321.842 3441130.674 3401567.815 5100071.045 0.666878771 0.769780263 0.703312646 0.665444477 0.773747218 0.629912426 0.623779907 0.674722106 0.66696479 1 22.28208591 -1.457898453 6.847772229 1.000060959 0.68578611 0.791868969 0.048284485 4.57E-05 3.62E-06 0.047584049 0.011213503 0.034841877 1.457898453 -0.314274849 GKELSDQAT(ph)ASPIVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 GKELSDQAT(0.5)AS(0.5)PIVAR 148.38 1.52E-06 532000000 302200 276570 314220 232930 422560 377140 273050 306140 327440 293150 TRUE FALSE 314131.0893 324068.7461 322408.8313 279002.8588 350733.4021 289554.9506 251647.6275 302036.694 315655.4984 350587.1298 0.896014322 0.924360076 0.919625405 0.795816033 1.000417221 0.825914376 0.71778912 0.861516777 0.900362482 1 18.41941351 GKELSDQATAS(ph)PIVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 GKELSDQAT(0.191)AS(0.809)PIVAR 159.47 5.52E-09 509890000 544060 464770 577960 393010 685540 647630 562670 583290 612280 577450 TRUE FALSE 565539.9089 544590.6321 593022.1124 470746.205 569012.1557 497227.7474 518566.4551 575471.9516 590244.1624 690590.2716 0.818922496 0.788587176 0.858717733 0.681657742 0.823950436 0.720003985 0.750903215 0.833304458 0.85469516 1 19.39747049 0.891650988 1.355606228 0.998531729 0.77847198 0.638374075 0.050210614 0.333443291 1.205814643 0.045539021 0.013670942 7.792036676 -0.891650988 -0.220059749 GKEVDNFVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKEVDNFVDK 10 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 79.633 0.024096 376090000 703320 437550 601380 411330 782690 691650 790400 573750 627220 367960 FALSE TRUE 731087.6167 512695.8088 617052.4568 492689.8463 649648.6334 531024.7696 728446.3827 566059.8197 604646.4747 440054.717 1.661356164 1.165072863 1.402217572 1.11961042 1.47629058 1.206724412 1.655354106 1.286339625 1.374025664 1 18.7473234 -0.099317892 1.904148322 0.999912858 1.364420599 0.280755761 0.178188971 136.8009645 231.5256998 0.209506208 0.042798585 0.795576796 0.099317892 0.364507741 GKEVDNFVDKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKEVDNFVDKLK 12 2 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 119.32 0.00029853 295690000 1597600 817830 1190900 666050 2094000 1509000 1265800 1157800 1369000 961880 FALSE TRUE 1660674.482 958285.9407 1221935.832 797792.702 1738062.628 1158557.619 1166583.288 1142281.585 1319729.957 1150341.97 1.44363548 0.833044404 1.062237026 0.693526554 1.510909515 1.007141919 1.014118687 0.992993053 1.147250115 1 20.13363137 -0.12096821 0.009222944 7.17E-07 2.056545692 0.012691938 0.234256256 34515.22991 91.09842414 10517.91347 9794.444579 0.756888296 0.12096821 2.056544975 GKFDGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKFDGAK 7 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 60.478 0.08871 1861800000 3035100 1817100 2442000 1818000 3586300 2982600 3165700 2401400 2578000 1843600 FALSE TRUE 3154928.092 2129172.79 2505640.526 2177594.974 2976702.007 2289936.352 2917564.162 2369213.161 2485218.284 2204818.122 1.43092442 0.965690897 1.136438648 0.987652883 1.350089596 1.038605556 1.323267499 1.074561723 1.127176096 1 21.07222822 0.842739635 1.489682006 1.001889279 1.158498946 0.098747561 0.150157368 1.473124084 6.167383215 0.129864912 0.038058084 6.962090028 -0.842739635 0.156609667 GKFEDMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 107.21 0.0036916 5725790000 7712630 5897120 6412500 4948410 13184600 10606720 11412260 8715210 9408810 8008330 FALSE TRUE 8017130.588 6909904.487 6579615.018 5927190.728 10943486.4 8143470.026 10517737.24 8598396.865 9070188.766 9577408.935 0.837087634 0.721479529 0.686993222 0.618872053 1.142635391 0.850279035 1.09818191 0.897779026 0.947039938 1 23.19120397 3.247613788 24.99999928 0.979533887 0.714412134 0.663585005 0.095144062 114.6179871 316511.4838 0.025195887 0.033632704 1768.535525 -3.247613788 -0.265121753 GKFGHEFLEFEFRPDGK ddPTM_MDA-MB-175_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 ; 136.35 6.37E-06 1469990000 1729720 1232650 1649780 1127970 2236660 2014830 1923670 1612000 1979420 1302920 FALSE TRUE 1798010.681 1444348.049 1692774.622 1351079.099 1856473.332 1546916.268 1772887.719 1590393.777 1908181.061 1558202.228 1.153900725 0.926932347 1.086363882 0.867075579 1.191420022 0.992757063 1.137777682 1.020659416 1.224604244 1 20.57145105 3.220428545 24.99998796 1.088760293 1.00829375 0.140831007 0.10343437 479.9521396 661743.0013 0.027346581 0.032747817 1661.225333 -3.220428545 -0.080466544 GKFNTSDVSAIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKFNTSDVSAIEK 13 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 112.5 0.00081701 555380000 1042700 650520 887450 679780 1079800 1029400 860900 841300 789070 633730 FALSE TRUE 1083866.601 762241.7497 910577.676 814238.4551 896255.9817 790337.4507 793420.4085 830023.7496 760671.5248 757897.26 1.430097004 1.005732294 1.201452656 1.074338829 1.182556039 1.042802887 1.046870665 1.095166579 1.003660476 1 19.53164277 4.746225767 24.98130549 1.081385709 1.430097173 0.713349946 0.067793285 480.2342226 1565083.219 0.015180629 0.161864191 55747.54759 -4.746225767 0.348711464 GKFQDNFEFVQWFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKFQDNFEFVQWFK 14 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 101.2 0.0013503 594690000 1189900 928630 1279600 955510 1498100 1586100 1301000 1213900 1352000 1146500 FALSE TRUE 1236878.171 1088114.979 1312947.427 1144507.026 1243453.497 1217752.313 1199024.22 1197629.656 1303341.784 1371134.724 0.902083617 0.793587209 0.95756267 0.834715222 0.906879153 0.88813469 0.874475863 0.873458775 0.950557054 1 20.3869389 1.068257906 3.210011968 0.999200729 0.877759384 0.485183016 0.041198449 0.165024589 3.454368809 0.035334964 0.009300025 11.70194104 -1.068257906 -0.121441345 GKGAYQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GKGAYQDR 8 1 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 90.629 0.011911 1796810000 1925960 2029020 1884870 1485410 2658300 2318470 1768660 1958730 1993290 2397600 FALSE TRUE 2001998.388 2377488.401 1933991.261 1779219.664 2206443.116 1780040.479 1630027.808 1932476.428 1921551.882 2867363.815 0.698201734 0.829154776 0.674484085 0.620507121 0.769502323 0.620793382 0.568476103 0.673955784 0.670145822 1 21.45129354 -1.357796477 8.894702046 1.000000624 0.678547464 0.646134035 0.070901157 9.08E-07 6.55E-08 0.071051988 0.016747082 0.043873625 1.357796477 -0.32145316 GKGDPNKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKGDPNKPR 9 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 54.416 0.076033 1395600000 1336800 1037200 1401400 1014400 1561500 1642100 1503300 1500500 1470100 1152800 FALSE TRUE 1389577.896 1215331.032 1437921.635 1215045.292 1296076.788 1260747.161 1385467.418 1480388.252 1417191.388 1378669.088 1.007912564 0.881524829 1.042978078 0.881317571 0.940092731 0.914466838 1.004931081 1.073780695 1.027941658 1 20.39484479 2.050746215 5.18918195 1.041721864 0.94366312 0.391981996 0.050606121 0.165345819 9.783227357 0.018445498 0.013162266 112.3947991 -2.050746215 -0.098058744 GKGEKEPPS(ph)PGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKGEKEPPSPGMER 14 2 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 GKGEKEPPS(1)PGMER 49.528 0.093772 83756000 226210 142810 202460 114730 259640 219990 236760 181070 253580 125440 TRUE FALSE 235140.9455 167336.5066 207736.2739 137423.2516 215506.4855 168900.6565 218202.1325 178643.0528 244453.7053 150017.5663 1.567422744 1.115446082 1.384746327 0.916047733 1.436541672 1.125872527 1.454510548 1.190814231 1.62950054 1 17.19477192 2.242008109 24.99920053 1.323483327 1.249591528 0.015647723 0.230617426 437.1268042 3169808.944 0.075406165 0.060710778 174.5854749 -2.242008109 -0.073891799 GKGFSVVADT(ph)PELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKGFSVVADTPELQR 15 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 GKGFSVVADT(1)PELQR;GKGFSVVADT(1)PELQR 104.81 0.0022056 453990000 380510 339660 314860 259750 402660 410190 248230 345680 333170 417880 TRUE FALSE 395532.8286 397993.9628 323065.5103 311127.7747 334215.997 314929.589 228773.084 341046.725 321179.2768 499755.5852 0.791452543 0.796377218 0.646447023 0.622559875 0.668758903 0.630167222 0.457769939 0.682427041 0.642672711 1 18.93086316 -0.976707612 9.427637952 1.000000181 0.654803257 0.563887359 0.089643584 0 0 0.09128947 0.021517134 0.1055097 0.976707612 -0.345196924 GKGGHSS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKGGHSSPQR 10 1 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 GKGGHS(0.2)S(0.8)PQR 74.46 0.02539 71595000 56314 47262 52612 47977 68576 71269 68729 61507 63376 64354 TRUE FALSE 58537.3202 55378.88085 53983.11194 57466.7074 56919.47601 54717.85484 63341.84139 60682.59927 61095.11014 76962.93417 0.760591067 0.719552619 0.70141702 0.746680308 0.739569984 0.710963731 0.823017496 0.788465252 0.793825116 1 16.23187618 -0.163161105 0.350496937 1.062894703 0.718242863 0.888348857 0.027595517 1.714433577 0.266975425 0.169811106 0.024027434 0.686813614 0.163161105 -0.34465184 GKGGHSS(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKGGHSSPQRR 11 2 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 GKGGHS(0.01)S(0.99)PQRR 57.434 0.058795 205030000 70251 82007 81982 70029 97232 92150 74254 94658 87544 102860 TRUE FALSE 73024.56373 96091.06432 84118.51827 83880.52718 80704.53937 70749.55905 68433.77745 93389.26434 84393.30854 123013.4476 0.593630738 0.781142763 0.683815631 0.681880955 0.656062739 0.575136787 0.556311353 0.75917931 0.686049454 1 16.90845651 0.429091503 1.141248726 1.000022044 0.658877171 0.687892214 0.06848653 1.395203854 2.23219652 0.067854802 0.020654772 2.685910292 -0.429091503 -0.341144872 GKGGVT(ph)GSPEASISGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.67)GS(0.33)PEASISGSK 197.84 7.29E-17 0 115730 79405 90411 67901 116840 118490 116300 94753 102870 68771 TRUE FALSE 120299.1098 93042.19106 92767.18493 81331.61514 96979.57853 90972.49323 107184.1021 93482.99102 99167.72879 82245.36075 1.46268566 1.131275858 1.12793213 0.988890004 1.179149531 1.106110939 1.303223685 1.13663543 1.205754682 1 16.32764668 4.739436652 24.53533082 1.139277155 1.462685793 0.563565059 0.087293564 41.91598205 1173705.664 0.020332653 0.122994166 54882.8495 -4.739436652 0.323408638 GKGGVTGS(ph)PEASISGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GKGGVT(0.032)GS(0.967)PEASISGSK;GKGGVT(0.001)GS(0.999)PEASISGSK 163.18 7.23E-09 105511000 159113 116036 125781 105200 158490 171899 158810 132885 159733 106689 TRUE FALSE 165394.9041 135964.2804 129058.9562 126008.246 131549.9264 131978.0624 146362.0572 131103.8939 153984.2405 127592.6669 1.296272804 1.065612027 1.011491956 0.987582195 1.031014788 1.034370279 1.14710399 1.027519035 1.206842402 1 16.96118589 4.736919633 5.562492412 1.055004278 1.304536732 0.547169392 0.065394182 0.104309029 12.93272654 0.015220547 0.09921839 54565.68764 -4.736919633 0.249532454 GKGS(ph)PRPQAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 82.543 0.0097314 10070360000 7900110 5070350 6913460 4712140 8204380 8168970 8258470 6788520 7210440 4840760 TRUE FALSE 8212012.443 5941143.171 7093630.447 5644187.228 6809802.418 6271850.519 7611149.542 6697530.993 6950937.673 5789214.24 1.41850208 1.026243446 1.225318351 0.974948757 1.176291313 1.083368184 1.314712019 1.156898107 1.200670313 1 22.46493612 4.754350285 24.25199984 1.141164455 1.418502396 0.410968685 0.103114183 1955.190956 3002981.893 0.023223316 0.561454677 56800.25496 -4.754350285 0.27733794 GKHDELADSLPCAEGEFIFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKHDELADSLPCAEGEFIFLR 21 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 177.73 3.82E-17 117582000 153814 141051 149672 157119 239540 216119 227270 174983 175602 147575 FALSE TRUE 159886.6955 165275.412 153572.5753 188196.6692 198823.0764 165928.6376 209455.9835 172637.6391 169282.1183 176489.4958 0.905927544 0.936460333 0.870151363 1.066333543 1.126543399 0.940161548 1.186790084 0.978175151 0.95916257 1 17.42922279 3.735464903 24.94537053 1.040916419 0.907407803 0.405219701 0.073442004 246.1039544 1983118.348 0.018766144 0.030464194 5438.321809 -3.735464903 -0.133508616 GKHQPWQS(ph)PERPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKHQPWQSPERPLSR 15 2 Q9BQ52;G5E9D5;E7ES68;Q9BQ52-2;V9GYS7;J3QRS2;V9GYU5;J3QL08 Q9BQ52 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 GKHQPWQS(1)PERPLSR;GKHQPWQS(1)PERPLSR 197.38 4.41E-09 344790000 313340 304040 336890 284980 369140 405750 343840 339080 371440 348130 TRUE FALSE 325710.9052 356256.5049 345669.6302 341348.1934 306393.7147 311520.7117 316888.9223 334535.1872 358071.947 416339.4081 0.782320623 0.855687686 0.830259215 0.819879614 0.735922924 0.748237389 0.761131222 0.803515547 0.860048172 1 18.6674006 0.876974841 2.168159077 0.999671418 0.791357419 0.763615256 0.035314455 0.249859106 2.359140107 0.037665874 0.010330252 7.533119231 -0.876974841 -0.208314 GKHS(ph)LDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKHSLDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 44 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GKHS(0.468)LDS(0.462)DEEEDDDDGGS(0.016)S(0.047)KY(0.001)DILAS(0.005)EDVEGQEAATLPSEGGVR 67.683 0.0007803 83914000 124030 69725 111560 59311 142020 138170 126050 102680 116640 64079 TRUE FALSE 128926.8002 81699.72636 114467.3452 71042.53877 117879.4911 106082.1115 116169.8716 101303.7426 112442.1492 76634.05318 1.682369584 1.066102117 1.493687734 0.927036165 1.538212925 1.384268574 1.515904051 1.321915498 1.467260891 1 16.22569799 -1.553885789 5.983974327 0.999216537 1.366061804 0.215062398 0.215329668 0.00203892 0.000152005 0.188875861 0.04442859 0.027932783 1.553885789 0.366845267 GKHSYNS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKHSYNSR 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 GKHSYNS(1)R;GKHSYNS(1)R 80.979 0.014563 216900000 316370 365950 357880 285750 468190 418530 307530 369450 376330 398030 TRUE FALSE 328860.5319 428799.0658 367206.6468 342270.4971 388607.231 321332.7504 283424.995 364498.127 362785.9568 476016.3578 0.690859729 0.900807417 0.771416026 0.719030957 0.816373691 0.675045605 0.595410201 0.765726054 0.762129181 1 18.86065163 0.607208221 2.526902578 0.999978102 0.742068128 0.492066335 0.078267131 3.473517854 21.28000116 0.077263557 0.02059231 4.047699108 -0.607208221 -0.257909974 GKLDDYQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GKLDDYQER 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;;;;; 136.02 0.00018642 2349450000 2658320 2433350 2618550 2170100 3241440 3245570 2797540 2602770 2822510 2443730 FALSE TRUE 2763272.526 2851258.934 2686791.564 2599339.303 2690461.187 2491835.555 2578261.505 2567884.125 2720928.416 2922532.105 0.945506303 0.975612527 0.919336886 0.88941343 0.920592517 0.852628975 0.88220126 0.878650442 0.93101746 1 21.47878744 4.06822794 4.407707342 0.898592881 0.959964481 0.196361521 0.038947896 0.240809087 9.164445617 0.009200344 0.02091675 11701.13365 -4.06822794 0.0613716 GKLDGNQDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GKLDGNQDLIR 11 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;; 124.86 0.00031045 1170990000 1796270 1854400 1725780 1814370 2073680 2736370 1914480 1489570 1664800 2424050 FALSE TRUE 1867188.127 2172878.775 1770755.245 2173246.971 1721196.614 2100889.538 1764418.055 1469604.751 1604884.173 2898996.186 0.644080919 0.749527987 0.610816686 0.749654995 0.593721586 0.724695516 0.608630692 0.506935731 0.55359996 1 21.467122 2.211131557 24.34427501 0.612796645 0.67823702 0 0.137786393 547.6188927 486026.9128 0.047940795 0.035416411 162.6041245 -2.211131557 0.065440375 GKLEAIIT(ph)PPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKLEAIITPPPAK 13 1 O75367-2;O75367-3;O75367;D6RCF2 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 1 GKLEAIIT(1)PPPAK;GKLEAIIT(1)PPPAK 114.96 0.0011342 1217580000 2662400 2064600 1784870 2098600 2165600 2845300 2475900 1841750 1817370 1786520 TRUE FALSE 2767513.608 2419178.99 1831385.178 2513696.816 1797492.086 2184522.196 2281832.488 1817064.354 1751963.209 2136554.389 1.295316245 1.132280555 0.857167591 1.176518992 0.841304155 1.022451011 1.067996443 0.850464825 0.819994669 1 21.02685461 7.999999998 0.676434525 0.940149839 40.01995253 0.467333398 0.113287868 213.783986 1.237941207 0.041798398 12582.07804 99999999.59 -7.999999998 39.07980269 GKLEEQRPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GKLEEQRPER 10 2 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;;;;;;; 163.12 3.69E-06 14940590000 15776210 14344500 15891320 13010940 18173430 18288820 17525630 15907670 16068370 14682230 FALSE TRUE 16399066.95 16808056.29 16305460.85 15584465.1 15084316.86 14041518.72 16151925.33 15694453.7 15490072.5 17558931.86 0.93394445 0.957236831 0.928613482 0.887552 0.859068022 0.79967955 0.919869469 0.893815969 0.882176241 1 24.06570175 3.826904264 3.392407224 0.884394317 0.945043575 0.169819563 0.047788053 0.361930565 7.946648418 0.01232942 0.023855837 6712.808598 -3.826904264 0.060649259 GKLPES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKLPESPK 8 1 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 1 GKLPES(1)PK;GKLPES(1)PK 98.156 0.0046766 517460000 1330350 374670 544380 419840 808580 1330740 1012910 595770 633660 252810 TRUE FALSE 1382873.245 439016.658 558566.99 502883.0989 671137.8604 1021695.803 933515.4675 587784.6776 610854.7004 302343.2792 4.573851448 1.452047021 1.847459588 1.663285191 2.219787595 3.379257529 3.087601186 1.944097052 2.020401122 1 18.20582798 4.74917768 24.72426015 2.160095393 4.573853043 0.547451148 0.67882783 1090.46201 2539332.366 0.168375521 2.418244563 56127.75613 -4.74917768 2.41375765 GKLPIVNEDDELVAIIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 231.21 8.33E-20 162830000 270860 277110 309950 298150 342490 348690 315360 326300 310900 304880 FALSE TRUE 281553.7619 324701.4869 318027.5516 357123.1801 284273.6721 267712.0319 290641.2592 321926.4822 299710.7697 364615.3987 0.772193832 0.89053147 0.872227429 0.979451722 0.779653501 0.734231283 0.797117347 0.882920698 0.821991531 1 18.47601597 -1.291194024 3.043001241 1.001105925 0.840278599 0.339401336 0.068182012 15813145.03 19968602.25 159553.8359 0.018498108 0.051145329 1.291194024 -0.160827326 GKNDGTVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GKNDGTVQGR 10 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q6AWB1;C9J1B7;C9JZA4;C9JTE5;C9JJN7;C9JJD0;C9JKG6;E9PCY0 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;;; 172.56 3.36E-06 736740000 808810 785360 894870 743370 1029610 1020280 914140 919560 877100 888450 FALSE TRUE 840742.4433 920239.4707 918191.0473 890406.3673 854597.26 783335.4325 842487.3181 907234.8023 845533.3423 1062524.767 0.791268561 0.866087548 0.864159666 0.838009988 0.804308084 0.737239692 0.792910758 0.853848146 0.795777537 1 20.01906504 -1.336025163 4.628401251 1.0001534 0.818461706 0.674335252 0.038334175 6.50E-05 9.32E-06 0.039735004 0.009357748 0.046129085 1.336025163 -0.181691694 GKNENESEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GKNENESEKR 10 2 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;;;;; 179.19 1.20E-06 2681810000 1670230 942851 1286590 839223 1688070 1394790 1640260 1332870 1484690 898094 FALSE TRUE 1736171.97 1104778.325 1320119.592 1005218.805 1401132.464 1070871.161 1511692.135 1315005.058 1431256.297 1074058.324 1.616459675 1.028601799 1.229094885 0.935907094 1.304521768 0.997032597 1.407458144 1.224333007 1.332568506 1 20.03464091 2.22562133 24.99978554 1.261259956 1.174226284 0.012012115 0.205191919 874.2552477 1689123.085 0.071249747 0.052957418 168.1207543 -2.22562133 -0.087033671 GKPDAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKPDAAK 7 1 P09429 P09429 HMGB1 High mobility group protein B1 0 69.954 0.053207 450120000 494600 285400 447540 299580 640650 499370 558510 423240 512630 327230 FALSE TRUE 514127.1899 334415.2299 459203.2601 358836.0298 531752.5418 383398.8855 514732.5268 417567.1601 494180.5464 391344.4533 1.313745948 0.854529116 1.173399179 0.916931432 1.358783898 0.979696741 1.315292762 1.067006716 1.262776417 1 18.57807947 3.259246133 24.99958664 1.162310227 1.057410491 0.076973749 0.167609859 595.606001 719818.3569 0.041644501 0.056324492 1816.544883 -3.259246133 -0.104899736 GKPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GKPELR 6 1 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32;B9ZVP7 J3KTJ3 RPL23 60S ribosomal protein L23 0 ;;;; 102.98 0.03199 4262060000 10340400 9841500 11261400 9520000 12774900 12359300 11914800 11901900 11839100 10764400 FALSE TRUE 10748646.98 11531701.07 11554881.34 11403027.59 10603427.06 9489039.882 10980886.84 11742374.5 11413013.1 12873478.08 0.834945064 0.895771989 0.897572611 0.885776751 0.823664513 0.737099937 0.852985244 0.912136908 0.886552417 1 23.61789855 0.906291169 1.146720614 0.9968999 0.850437927 0.476464882 0.046825031 0.578898109 1.52911659 0.048887453 0.015371021 8.059185805 -0.906291169 -0.146461973 GKPIFPVYPLVGSS(ph)SPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKPIFPVYPLVGSSSPTRK 19 2 A6NEL2 A6NEL2 SOWAHB Ankyrin repeat domain-containing protein SOWAHB 1 GKPIFPVYPLVGS(0.099)S(0.439)S(0.439)PT(0.023)RK 104.18 0.00018687 256150000 223300 161010 180750 132080 274410 243730 226820 179430 209530 179110 TRUE FALSE 232116.0564 188662.215 185460.4935 158205.0298 227765.8862 187127.4013 209041.2557 177025.0343 201989.0562 214203.1752 1.083625657 0.880762924 0.8658158 0.738574625 1.06331704 0.8735977 0.97590176 0.826435155 0.942978814 1 17.70862034 GKPLALVEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKPLALVEEIR 11 1 Q5TDF0;Q9BSD7 Q5TDF0 NTPCR Cancer-related nucleoside-triphosphatase 0 127.37 0.00026265 241780000 551410 572360 661870 566290 705580 744390 687340 625880 638970 705190 FALSE TRUE 573180.0926 670658.3777 679118.8759 678300.4718 585645.7636 571516.7038 633464.4948 617491.1023 615973.5945 843358.4788 0.679639924 0.795223377 0.805255289 0.804284879 0.694420912 0.677667585 0.751121274 0.732181057 0.730381694 1 19.68578647 -1.842477004 4.311813229 1.05381297 0.742903182 0.738550581 0.046195934 0.02349673 0.000858403 0.043978943 0.011012668 0.014372192 1.842477004 -0.310909788 GKPLISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKPLISR 7 1 Q9Y6Q5;K7EMG5;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 ; 114.78 0.0053147 1064890000 909870 966920 1022850 1037300 1248590 1339150 1014650 1104660 991440 1334370 FALSE TRUE 945792.3702 1132980.988 1049506.311 1242474.844 1036355.118 1028152.708 935119.0817 1089853.84 955758.2681 1595814.253 0.592670712 0.709970466 0.657661948 0.778583624 0.649420893 0.64428094 0.58598241 0.682945297 0.598915736 1 20.60586131 -1.59787244 3.065463569 1.019927923 0.659098633 0.774045097 0.055793538 25238103.37 27878246.64 4067090.458 0.013096459 0.025242221 1.59787244 -0.36082929 GKPSEQLT(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GKPSEQLTPTR 11 1 Q14687;Q14687-2;Q14687-3;H0Y613 Q14687 GSE1 Genetic suppressor element 1 1 GKPSEQLT(0.971)PT(0.029)R;GKPSEQLT(0.976)PT(0.024)R;GKPSEQLT(0.909)PT(0.091)R;GKPSEQLT(0.898)PT(0.102)R 131.86 0.00031452 1438030000 2111820 1746380 1823080 1596290 2151380 2316000 2119270 1978960 2021860 1754640 TRUE FALSE 2195196.284 2046307.18 1870590.962 1912031.398 1785689.196 1778144.099 1953156.08 1952435.278 1949093.654 2098428.113 1.046114599 0.975161916 0.891424848 0.911173171 0.850965151 0.847369556 0.930771022 0.930427526 0.928835084 1 21.00087761 4.510883097 2.731276867 0.906817561 1.046984398 0.505619529 0.04179061 0.242174901 3.174559937 0.010589413 0.059846922 32425.23236 -4.510883097 0.140166837 GKPVDSQTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKPVDSQTSR 10 1 Q9Y450;Q9Y450-4;E9PN23 Q9Y450 HBS1L HBS1-like protein 0 66.663 0.070155 0 26094 32874 28375 28356 42144 40911 31829 33810 30358 33834 FALSE TRUE 27124.21127 38519.85378 29114.47581 33964.73217 34980.37793 31410.04026 29334.15981 33356.83225 29265.42151 40463.12451 0.670343964 0.951974279 0.719531083 0.83939964 0.864500168 0.776263342 0.724960323 0.824376087 0.723261534 1 15.30432011 -1.049098904 4.577077675 1.000009152 0.79399668 0.385512799 0.079894349 0.08513736 44046897.16 882.6621339 0.016899772 0.089310207 1.049098904 -0.206012472 GKQS(ph)PPGPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKQSPPGPGK 10 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 GKQS(1)PPGPGK 73.466 0.027194 199060000 763900 367730 519970 422670 681060 670550 746170 532610 674410 345870 TRUE FALSE 794059.3619 430884.767 533520.8454 506272.8645 565293.6645 514824.9248 687683.2456 525471.2341 650138.1158 413636.6044 1.919702834 1.04169883 1.289829864 1.223955663 1.366643228 1.244630962 1.662529956 1.270369277 1.571761563 1 18.65800434 -1.47442887 3.032982721 0.990385239 1.378051201 0.192091453 0.242079784 62032882.69 70765355.74 4994315.875 0.053057465 0.033540623 1.47442887 0.387665961 GKS(ph)DSEDGEKENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKSDSEDGEKENEK 14 2 O00203;O00203-3 O00203 AP3B1 AP-3 complex subunit beta-1 1 GKS(0.83)DS(0.17)EDGEKENEK;GKS(0.998)DS(0.002)EDGEKENEK 121.44 5.98E-05 209589000 777240 123924 200854 143978 406560 538150 421780 225610 263760 74767 TRUE FALSE 807926.0354 145206.983 206088.4202 172456.4187 337453.0764 413172.8182 388719.7815 222586.067 254267.3291 89416.16215 9.035570482 1.623945599 2.304822923 1.928694036 3.773960639 4.620784524 4.347310063 2.489327003 2.843639483 1 16.448248 4.746026645 24.95680435 2.916764615 9.035573452 0.736521561 1.121120249 480.9030496 1607482.288 0.277881333 2.930256551 55721.99351 -4.746026645 6.118808836 GKS(ph)EEELEASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKSEEELEASK 11 1 Q7RTP6;J3QR21;A0A5F9ZHV5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 GKS(1)EEELEASK;GKS(1)EEELEASK 129.62 0.00014609 525940000 1727340 600490 927700 534820 1402500 1317270 1274880 864230 1076490 443860 TRUE FALSE 1795536.717 703619.4863 951876.6241 640605.7997 1164103.551 1011354.006 1174951.574 852646.4104 1037747.335 530825.8688 3.382534316 1.325518457 1.79319939 1.206809685 2.19300456 1.905246269 2.213440684 1.606263863 1.954967526 1 19.01787915 -2.106924595 0.297493592 5.24E-23 1.983958093 0.206753164 0.569296828 60.10511004 2.572105538 42.30488859 0.575014542 0.007817635 2.106924595 1.983958093 GKT(ph)PEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIR;GKT(1)PEEIR 90.913 0.02079 485370000 1056420 758400 897820 796750 1040750 1181310 1081520 936280 893070 650520 TRUE FALSE 1098128.277 888649.3005 921217.9268 954344.7719 863843.6867 906968.6554 996747.6364 923730.698 860928.5852 777976.939 1.411517774 1.142256609 1.184119838 1.226700592 1.110371842 1.165804036 1.281204604 1.187349717 1.106624814 1 19.56936787 -5 0.130318137 0.334695184 1.283527731 0.439797186 0.078616627 149.085145 1.225306526 25.93888442 0.588229584 1.00E-05 5 0.948832547 GKT(ph)PEEIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKTPEEIRK 9 2 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 1 GKT(1)PEEIRK 71.548 0.079217 1443400000 2363400 1063000 1620900 1056600 2173700 1921800 1926600 1494100 1508700 831380 TRUE FALSE 2456708.857 1245561.981 1663141.986 1265592.326 1804215.25 1475491.075 1775588.058 1474074.033 1454402.182 994272.9933 2.470859486 1.252736411 1.672721674 1.272882131 1.81460752 1.483989895 1.785815435 1.482564691 1.46277953 1 19.9232825 -2.752462857 0.138206322 1.47E-28 1.8871046 0.315959739 0.316981846 86.36434995 1.358273688 29.3419353 2.178225326 0.001768223 2.752462857 1.8871046 GKTPAT(ph)PTSQFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC 41 1 Q13115-2;Q13115 Q13115-2 DUSP4 Dual specificity protein phosphatase 4 1 GKT(0.446)PAT(0.548)PT(0.003)S(0.003)QFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC;GKT(0.155)PAT(0.573)PT(0.134)S(0.134)QFVFS(0.003)FPVSVGVHSAPSSLPYLHSPITTSPSC 124.08 1.71E-08 219933000 14631.2 17738.5 21294 24715.5 26260 20675.2 27181 23907 25656 19599 TRUE FALSE 15208.85107 20784.94939 21848.93913 29604.15213 21796.33458 15873.69814 25050.4822 23586.56577 24732.64557 23439.0488 0.6488681 0.886765908 0.932159804 1.263027027 0.929915491 0.677233034 1.068749948 1.006293641 1.055189815 1 14.5166264 4.686298595 2.041006169 0.992706671 0.575620635 0.365971948 0.137576072 0.717000869 3.566797397 0.036393051 0.533332776 48562.22709 -4.686298595 -0.417086036 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHS(ph)PITTSPSC ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKTPATPTSQFVFSFPVSVGVHSAPSSLPYLHSPITTSPSC 41 1 Q13115-2;Q13115 Q13115-2 DUSP4 Dual specificity protein phosphatase 4 1 GKTPATPTSQFVFSFPVS(0.002)VGVHS(0.008)APS(0.025)S(0.022)LPY(0.418)LHS(0.472)PIT(0.022)T(0.025)S(0.006)PSC 99.663 3.30E-05 318710000 64943 166840 157060 174080 141790 209940 147190 180000 149930 164180 TRUE FALSE 67506.99979 195493.4722 161153.1126 208512.5044 117688.5864 161184.6167 135652.8632 177587.3944 144534.0486 196347.9276 0.343813152 0.995648259 0.820752807 1.06195419 0.599387974 0.820913257 0.690880036 0.904452604 0.736111913 1 17.58305285 -4.999997247 0.024947805 2.048582179 4.93E-08 0.116725455 0.193282213 5766.941362 10.86615277 646.372383 304.8756594 1.00E-05 4.999997247 -2.04858213 GKTPEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GKTPEEIR 8 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 66.435 0.056263 508100000 1524000 1467940 1654710 1518650 1987320 1919760 1832880 1672740 1687690 1610900 FALSE TRUE 1584168.697 1720047.276 1697833.102 1819034.437 1649516.056 1473924.834 1689214.076 1650319.656 1626950.367 1926525.012 0.822293345 0.892823745 0.881293049 0.944204942 0.856213154 0.76506914 0.876819177 0.856630278 0.844499997 1 20.87756949 -0.876343116 4.155787813 1.000002874 0.861554138 0.473100644 0.044301206 1637775.172 788213.2492 40.37761741 0.010626701 0.13294037 0.876343116 -0.138448736 GKTPEEIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKTPEEIRK 9 2 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 63.283 0.043353 121320000 250570 169820 210650 169070 296500 263660 260020 244290 271600 225120 FALSE TRUE 260462.6971 198985.264 216139.7121 202511.5414 246101.0359 202428.9608 239638.953 241015.6921 261825.1691 269227.9538 0.967442992 0.739095852 0.80281304 0.752193591 0.914099121 0.75188686 0.890096848 0.895210504 0.972503655 1 18.03846869 1.497183701 1.237748958 1.000067507 0.817611651 0.445076315 0.070412383 0.357184083 1.050865082 0.058746958 0.020220849 31.41837371 -1.497183701 -0.182455856 GKVEEVELPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GKVEEVELPVEK 12 1 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;Q99873-5;H0YDE4;E9PNR9;Q9NR22-2;Q9NR22 E9PKG1 PRMT1;PRMT8 Protein arginine N-methyltransferase 1;Protein arginine N-methyltransferase 8 0 117.92 0.00062198 177800000 428470 193450 328170 222520 430930 376170 451060 321590 375100 172880 FALSE TRUE 445386.3265 226673.5327 336722.3798 266533.7918 357680.6725 288810.2184 415704.7386 317279.6121 361600.2243 206752.526 2.154200169 1.096351938 1.628625228 1.289144065 1.729994208 1.396888464 2.010639225 1.534586388 1.748951905 1 17.65754543 GKYS(ph)PTVQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.5)PT(0.5)VQTR;GKYS(0.5)PT(0.5)VQTR;GKYS(0.704)PT(0.296)VQTR;GKY(0.001)S(0.67)PT(0.262)VQT(0.067)R;GKYS(0.749)PT(0.251)VQTR 132.31 0.0001375 12814030000 5615970 4694790 4935020 4267090 6057110 6291940 5599850 5211650 5260150 4437110 TRUE FALSE 5837692.832 5501083.662 5063630.675 5111107.666 5027524.606 4830732.29 5160919.125 5141796.356 5070838.229 5306476.751 1.100107116 1.036673469 0.954235911 0.9631829 0.94743176 0.910346453 0.972569817 0.968966152 0.955594167 1 22.33932287 4.459759643 2.391892111 0.956734023 1.102390055 0.814591229 0.021812244 0.133090723 1.325442335 0.005575135 0.031138702 28824.35801 -4.459759643 0.145656032 GKYSPT(ph)VQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GKYSPTVQTR 10 1 O60437;K7EKI8 O60437 PPL Periplakin 1 GKYS(0.326)PT(0.674)VQTR;GKYS(0.037)PT(0.963)VQTR;GKYS(0.063)PT(0.937)VQTR;GKYS(0.045)PT(0.955)VQTR 153.39 2.64E-05 4993280000 4923030 4340440 4507260 4048550 5706220 5589990 5204750 4599990 4805630 4183410 TRUE FALSE 5117395.026 5085876.806 4624722.898 4849341.106 4736278.763 4291799.54 4796788.095 4538334.658 4632676.315 5003069.093 1.02285116 1.016551383 0.92437718 0.969273263 0.946674666 0.857833354 0.958769109 0.907110131 0.925966887 1 22.25438195 4.242844079 24.13575775 0.931657463 1.019701346 0.453875776 0.03633732 53.2662385 300118.0776 0.00851226 0.021626597 17492.18571 -4.242844079 0.088043883 GLAAEDS(ph)GGDSKDLSEVSETTESTDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLAAEDSGGDSKDLSEVSETTESTDVK 27 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GLAAEDS(1)GGDSKDLSEVSETTESTDVK;GLAAEDS(1)GGDSKDLSEVSETTESTDVK 184.43 7.48E-24 37773000 104686 42854 65104 50062 88599 88198 98420 64788 77271 44319 TRUE FALSE 108819.0841 50213.84114 66800.66372 59964.11418 73538.97363 67715.35115 90705.58323 63919.62283 74490.0318 53002.45951 2.053094991 0.947387001 1.260331395 1.13134588 1.387463418 1.277588847 1.711346682 1.205974655 1.405407079 1 15.69377169 -1.684354841 2.199594625 0.928588216 1.353497066 0.123249341 0.295266542 3946433.797 2625817.609 1564560.315 0.069821055 0.020684506 1.684354841 0.42490885 GLAAGS(ph)AETLPANFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLAAGSAETLPANFR 15 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 GLAAGS(1)AETLPANFR 140.1 5.24E-06 51439000 30992 54553 57793 58586 59552 84356 59316 64550 55498 60582 TRUE FALSE 32215.58809 63922.05339 59299.13306 70174.13594 49429.37231 64765.59743 54666.65693 63684.81283 53500.63782 72451.88299 0.444648045 0.882269042 0.818462276 0.968561934 0.682237235 0.893911859 0.754523619 0.878994585 0.738429915 1 16.14473556 4.742369976 24.76381403 0.839547551 0.44464787 0.613159351 0.095588363 201.1475448 1307555.26 0.020312629 0.15291804 55254.79555 -4.742369976 -0.39489968 GLAEDIENEVVQITWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLAEDIENEVVQITWNR 17 0 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 117.92 0.0004517 37215000 35802 59042 48024 56857 56001 62417 50033 48556.1 52358 70708 FALSE TRUE 37215.49061 69182.00422 49275.54489 68103.1449 46481.97002 47921.59769 46111.28272 47905.2849 50473.64581 84561.87881 0.440097726 0.818122837 0.582715824 0.805364614 0.549679958 0.566704505 0.545296336 0.566511596 0.596884158 1 16.36771981 -1.494682634 3.918917785 1.004077826 0.610303997 0.529535171 0.110846132 0.003771126 0.000486261 0.102485045 0.023938639 0.032012336 1.494682634 -0.393773829 GLAGPPAS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLAGPPASPGK 11 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK 173.72 1.24E-05 4617020000 6361170 3686710 4166850 3563530 5718300 6188020 5642600 4666550 4651370 3016720 TRUE FALSE 6612313.903 4319873.764 4275441.534 4268385.598 4746305.409 4750946.135 5200318.268 4604002.53 4483968.102 3607788.525 1.832788662 1.19737444 1.185058798 1.183103047 1.315571956 1.316858264 1.441414382 1.276128714 1.242857798 1 21.78268335 -4.722679958 0.154231054 7.46E-21 1.413764843 0.274177927 0.177816082 187.2565867 1.831053364 58.60763548 0.836448219 1.89E-05 4.722679958 1.413764843 GLAHPPSYSNPPVYHGNS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLAHPPSYSNPPVYHGNSPK 20 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 GLAHPPSYSNPPVYHGNS(1)PK 146.2 2.28E-07 282640000 219270 168070 143250 164880 217560 266500 213830 185740 180740 137730 TRUE FALSE 227926.9489 196934.7151 146983.2127 197492.7719 180579.2289 204609.4138 197069.4459 183250.4591 174235.2027 164715.5565 1.383760913 1.195604831 0.892345664 1.198992834 1.096309497 1.24219848 1.196422791 1.112526728 1.057794457 1 17.32961729 -4.99989967 0.023489139 9.89E-12 1.894533508 0.19482438 0.116966669 4848.761445 8.608791754 492.3876719 242.6343588 1.00E-05 4.99989967 1.894533508 GLALEAESELERQDEALDGVAAAVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLALEAESELERQDEALDGVAAAVDR 26 1 A0A087X0B7;Q5SQN1-4;Q5SQN1 A0A087X0B7 SNAP47 Synaptosomal-associated protein 47 0 ; 127.83 8.43E-05 35076100 26613.8 33587 33324 30774 36594 35234 30149 34518 29970.9 35669 FALSE TRUE 27664.53337 39355.30598 34192.45082 36861.00535 30373.76495 27051.43748 27785.8426 34055.34267 28892.25316 42657.65763 0.648524437 0.922584787 0.801554814 0.86411227 0.712035462 0.634151967 0.651368222 0.798340663 0.677305196 1 15.38051713 5.029248745 17.33519219 0.770562108 0.256332094 0.101949857 0.114531043 24909961.71 382313188.8 0.026850769 379864078.1 106966.7364 -5.029248745 -0.514230014 GLALHDILTEIHLFVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLALHDILTEIHLFVHR 17 0 P40937-2;P40937 P40937-2 RFC5 Replication factor C subunit 5 0 285.65 8.74E-37 50383000 14525 13847 15806 13505 15836 17464 20625 15409 18316 15231 FALSE TRUE 15098.45822 16225.11454 16217.91734 16176.24869 13144.20238 13408.25067 19008.35861 15202.46756 17656.81074 18215.22283 0.828892315 0.890744773 0.890349654 0.888062081 0.721605357 0.73610138 1.043542469 0.834602338 0.969343658 1 14.15285702 1.395018608 0.98038862 0.993822473 0.841587654 0.283168196 0.084616612 0.693099248 1.356483502 0.079590221 0.028704313 24.83239499 -1.395018608 -0.152234818 GLAPDLPEDLYHLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLAPDLPEDLYHLIK 15 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ;;;; 212.87 6.56E-10 4467804400 4022941.9 3360225.3 4047511 3583721 4665809 4636840 4815941 4086420 4143062 3216361.7 FALSE TRUE 4181770.753 3937317.856 4152992.462 4292570.317 3872716.453 3560004.182 4438454.96 4031648.224 3993954.008 3846546.194 1.087149495 1.023598225 1.079667903 1.115954443 1.006803573 0.925506676 1.153880582 1.048121619 1.038322122 1 21.8751322 1.437016329 0.005532952 2.48E-08 2.085919463 0.068323058 0.059547066 12343.56526 67.89358731 12814.16354 12775.45304 27.35371573 -1.437016329 2.085919438 GLAPNT(ph)PGK ddPTM_MDA-MB-175_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 128.14 0.0047599 1468540000 6877950 4482539 5231980 4005603 6538010 6947370 6148640 5615690 5453630 3914866 TRUE FALSE 7149496.777 5252380.204 5368329.697 4797899.318 5426681.396 5333948.606 5666693.53 5540420.861 5257354.922 4681909.038 1.527047347 1.121845846 1.146611276 1.024774142 1.159074504 1.139267885 1.210338237 1.183367899 1.122908386 1 22.15866547 4.739681837 24.69470468 1.134359388 1.527047497 0.78752843 0.062696688 35.7955009 788271.5338 0.014818248 0.091166633 54913.84285 -4.739681837 0.392688109 GLAVFISDIR ddPTM_MDA-MB-175_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 0 130.34 0.0081063 0 95893 104180 85515 90260 130700 119170 106490 95638 80484 150550 FALSE TRUE 99678.92969 122072.1046 87743.59115 108113.1586 108483.6607 91494.57354 98143.03554 94356.12904 77587.39656 180047.39 0.553626074 0.677999856 0.48733609 0.600470568 0.602528371 0.508169396 0.545095575 0.524062743 0.430927638 1 17.45801716 -1.908465371 2.636080273 1.258240964 0.549859817 0.813257565 0.064999877 8907016.671 5636991.627 14267169.38 0.015261312 0.012346238 1.908465371 -0.708381147 GLDDDRGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 111.61 0.0019128 2899950000 3940250 4831960 4275850 4716580 4610070 5082800 4280650 4323460 4253620 4562710 FALSE TRUE 4095814.113 5661811.543 4387282.164 5649505.446 3826451.948 3902396.731 3945121.468 4265511.09 4100533.047 5456685.666 0.750604738 1.037591661 0.804019588 1.035336428 0.701241043 0.715158792 0.722988588 0.781703648 0.751469536 1 22.37959351 3.221887071 24.99004296 0.762344799 0.90887636 0.221050873 0.115363263 290.0521261 434724.5478 0.030359725 0.036380106 1666.813736 -3.221887071 0.146531561 GLDDDRGPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLDDDRGPWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;;; 118.4 0.0007566 4292640000 1178088 1325200 1235290 1390070 1303037 1502920 1366100 1237100 1228420 1357080 FALSE TRUE 1224599.824 1552792.791 1267482.672 1665021.697 1081547.236 1153889.607 1259021.512 1220518.698 1184209.404 1622973.843 0.754540703 0.956757743 0.780963093 1.025907906 0.666398439 0.710972399 0.775749725 0.752026105 0.729654029 1 20.63020832 3.220732517 24.99999701 0.757230221 0.878016446 0.174898953 0.110993529 342.7673113 480654.9309 0.029376927 0.035181083 1662.388467 -3.220732517 0.120786225 GLDDLDADADDGWAGLHEEVDYSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDDLDADADDGWAGLHEEVDYSEK 25 0 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 0 ; 257.2 6.40E-45 146602000 173413 154813 152713 162911 184225 226292 202055 159875 193668 169782 FALSE TRUE 180259.4791 181400.9285 156692.8262 195134.3096 152910.5003 173739.1125 186217.4011 157732.1371 186697.9265 203047.5322 0.887769859 0.893391446 0.77170515 0.961027733 0.753077364 0.855657346 0.917112358 0.776823709 0.919478924 1 17.63145797 0.997158385 23.94635926 1.000000005 0.850640007 0.346673731 0.064057424 51.01038504 429873.4939 0.056676968 0.014169242 9.934782996 -0.997158385 -0.149359998 GLDFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLDFSDR 7 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;;;; 189.62 0.0012852 4116380000 2923410 3437480 3083220 3206550 3514520 3708360 3177650 3201500 2942410 3575280 FALSE TRUE 3038828.484 4027840.45 3163571.246 3840796.019 2917123.146 2847149.591 2928577.49 3158589.129 2836513.239 4275787.663 0.710706126 0.942011336 0.739880344 0.898266313 0.682242285 0.665877217 0.68492117 0.738715151 0.66338964 1 22.02775878 3.226544916 24.98725436 0.720249235 0.825320297 0.102980157 0.112631146 364.7750908 758566.7062 0.029561716 0.03558701 1684.786662 -3.226544916 0.105071063 GLDGIPFTVDATSQIHCIEDFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLDGIPFTVDATSQIHCIEDFHR 23 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ;; 195.39 1.20E-19 455602000 277330 411664 364088 441171 440135 508148 364796 398131 415344 494297 FALSE TRUE 288279.2025 482364.0897 373576.4324 528433.307 365321.0099 390138.3281 336202.3363 392794.7052 400395.8506 591145.0333 0.487662395 0.815982648 0.631953939 0.893914822 0.6179888 0.659970576 0.568730713 0.664464189 0.677322532 1 19.1731526 -1.941664712 2.148311268 1.245798882 0.67188996 0.452641356 0.109254892 3863295.865 1593826.598 4750653.54 0.025742299 0.01143761 1.941664712 -0.573908921 GLDGPRPNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDGPRPNQK 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 120.27 0.0005305 828780000 722890 605950 670990 617270 809930 795640 755500 652030 649110 591450 FALSE TRUE 751430.2554 710017.1989 688476.5506 739364.1636 672258.3879 610864.668 696281.9359 643290.6044 625748.6579 707333.3035 1.062342536 1.003794386 0.973341065 1.04528397 0.950412464 0.863616438 0.984376011 0.909458951 0.884658837 1 19.43203066 3.090734016 5.544082411 0.924686418 1.01594218 0.492135868 0.044534711 0.169419363 8.22348206 0.012400333 0.014900004 1232.349849 -3.090734016 0.091255762 GLDHDFGPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 148.91 2.43E-05 1124650000 656985 897508 761461 757555 1137578 1057229 776944 739845 803517 1241807 FALSE TRUE 682923.2751 1051648.017 781305.2992 907397.1179 944212.8979 811703.5872 716045.0991 729928.5879 774598.5801 1485115.306 0.459845288 0.708125499 0.526090665 0.610994388 0.635784235 0.546559304 0.482147815 0.491496239 0.521574707 1 20.50214352 -1.953251511 2.774100425 1.331205857 0.553538078 0.770179232 0.073151041 21705003.77 13044863.62 46377622.26 0.017785501 0.011136494 1.953251511 -0.777667779 GLDHLLDENRVPDLAQMYQLFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDHLLDENRVPDLAQMYQLFSR 23 1 Q13619;A0A0A0MR50;Q13619-2 Q13619 CUL4A Cullin-4A 0 ; 265.13 3.15E-44 279040000 174671 202529 199814 223260 218120 240290 176782 198511 175851 220460 FALSE TRUE 181567.146 237311.7803 205021.317 267420.1616 181044.0403 184486.2891 162925.3649 195850.2847 169522.1569 263654.916 0.688654506 0.900084792 0.777612343 1.014280961 0.686670452 0.699726339 0.617949278 0.742828117 0.642969831 1 18.00829137 GLDIESYDS(ph)LERPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDIESYDSLERPLRK 16 2 Q9H792 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 GLDIESYDS(1)LERPLRK;GLDIESYDS(1)LERPLRK 179.69 1.35E-09 296760000 422190 381510 420040 366720 538060 494810 429710 441200 455060 408390 TRUE FALSE 438858.3872 447031.3748 430986.5875 439256.1214 446600.7534 379897.8764 396028.2074 435286.4357 438682.4795 488406.2014 0.898552037 0.915286033 0.882434716 0.899366388 0.914404346 0.777831803 0.81085827 0.891238552 0.89819187 1 18.89772199 0.764802696 2.116139629 0.999822149 0.872193755 0.441022574 0.042591531 0.93543392 6.601633752 0.043963244 0.012049633 5.818388224 -0.764802696 -0.127628394 GLDIPEVDLVIQSSPPKDVESYIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDIPEVDLVIQSSPPKDVESYIHR 25 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 148.17 1.32E-07 290060000 324420 349960 423620 267140 453560 438400 379220 353920 404270 413360 FALSE TRUE 337228.3521 410062.9077 434659.8852 319979.4947 376464.0332 336588.244 349495.7455 349176.2813 389720.4017 494349.9777 0.682165201 0.829499193 0.879255396 0.647273205 0.761533428 0.680870353 0.706980401 0.70633417 0.788349184 1 18.91517324 0.876883873 5.028123371 0.999990635 0.737817459 0.577028748 0.067430859 0.803713604 32.07117708 0.065997069 0.016680085 7.531541494 -0.876883873 -0.262173176 GLDIYVWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLDIYVWR 8 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 113.89 0.0064252 465830000 732030 850370 822330 916860 985720 1072340 891790 899010 844810 998600 FALSE TRUE 760931.1097 996414.4325 843760.5954 1098212.171 818167.6665 823305.2865 821889.1695 886960.2414 814405.4531 1194256.551 0.637158833 0.834338679 0.706515359 0.919578101 0.68508535 0.68938729 0.688201517 0.742688195 0.681935094 1 20.18768136 -0.44627452 8.325398335 1 0.735516466 0.502650793 0.079995065 0 0 0.073567648 0.017340061 0.357870154 0.44627452 -0.264483534 GLDLLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLDLLTSR 8 0 H7BZF5 H7BZF5 C2orf80 0 91.853 0.028365 319750000 96168 168620 136970 150740 160640 178610 143990 149580 134340 182590 FALSE TRUE 99964.7869 197579.1733 140539.5507 180555.9221 133334.4702 137130.5344 132703.6876 147575.1248 129505.1296 218365.0146 0.457787559 0.904811486 0.643599209 0.826853708 0.610603628 0.627987659 0.607714967 0.675818537 0.593067208 1 17.73638221 -1.902547307 4.577758599 1.118740152 0.668325177 0.423231073 0.118468111 0.069706766 0.001483939 0.055694041 0.024768402 0.012515629 1.902547307 -0.450414976 GLDQDHAR ddPTM_MDA-MB-175_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 63730000 160760 216020 169900 185970 197700 231910 183220 184450 180150 223930 FALSE TRUE 167106.9289 253119.7546 174327.7336 222754.3109 164095.0246 178052.4171 168858.7376 181977.7494 173666.4367 267804.7961 0.623987813 0.945165129 0.650950753 0.831778647 0.612741172 0.664858956 0.630529177 0.679516394 0.648481428 1 18.03082227 -1.084410458 3.882229702 1.00007746 0.700391884 0.443727229 0.10120027 28277855.8 52174401.53 30231.85552 0.023474109 0.082335958 1.084410458 -0.299685576 GLDVDSLVIEHIQVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 239.75 7.75E-20 1569637000 1231510 1062886 1219208 1110446 1378751 1478986 1351308 1283779 1468281 1181714 FALSE TRUE 1280130.966 1245428.402 1250981.562 1330088.904 1144391.397 1135513.916 1245388.948 1266572.042 1415437.854 1413248.233 0.905807583 0.881252404 0.885181763 0.941157309 0.809759652 0.803478037 0.881224486 0.896213427 1.001549353 1 20.43058346 1.300842564 3.075537732 1.005978932 0.871769772 0.629246589 0.038718499 0.168467935 2.639416422 0.035659807 0.010716361 19.99137031 -1.300842564 -0.13420916 GLDVEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 82.279 0.048121 84270000 245260 174670 207460 169650 276390 255130 244740 202530 227880 179050 FALSE TRUE 254943.0542 204668.2138 212866.578 203206.2636 229409.3265 195879.924 225556.6393 199815.4166 219678.6433 214131.4194 1.19059153 0.955806553 0.994093154 0.948979203 1.071348274 0.914764982 1.053356112 0.933143848 1.025905698 1 17.70813697 4.743831843 24.78278316 0.986302142 1.190591627 0.606314145 0.048797754 300.2209477 1411445.012 0.01028899 0.087396999 55441.10055 -4.743831843 0.204289485 GLECSDWKPEAGLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLECSDWKPEAGLSPPR 17 1 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 GLECSDWKPEAGLS(1)PPR 65.901 0.039523 0 321510 232330 267180 228170 330300 334140 323550 281480 286470 252040 TRUE FALSE 334203.4631 272230.8702 274142.9303 273301.345 274155.724 256541.0489 298189.3056 277707.221 276160.0007 301422.4124 1.108754523 0.903154042 0.909497499 0.906705453 0.909539944 0.851101439 0.989273834 0.921322402 0.916189339 1 18.20142717 4.741707094 24.91115602 0.920129791 1.108754596 0.650696055 0.040786754 165.2673426 1308381.086 0.009189893 0.065870562 55170.52212 -4.741707094 0.188624805 GLEDVRPSVESLLDELESSVPS(ph)PVPAITVNQGEMSSPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLEDVRPSVESLLDELESSVPSPVPAITVNQGEMSSPQR 39 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 GLEDVRPSVESLLDELES(0.002)S(0.002)VPS(0.996)PVPAITVNQGEMSSPQR 147.15 3.53E-13 55477000 51181 66962 57748 60890 65671 79731 67132 68917 63394 78551 TRUE FALSE 53201.6654 78462.20261 59252.96032 72933.86026 54508.26688 61214.68358 61870.01842 67993.28034 61112.46232 93941.5645 0.566327224 0.835223503 0.630742746 0.776374767 0.580235886 0.651625124 0.658601108 0.723782712 0.650536987 1 16.519476 -1.537601786 2.835441586 1.015611327 0.68033085 0.601893626 0.07922305 16514748.83 17445468.52 1973776.931 0.018355125 0.029000014 1.537601786 -0.335280477 GLEFPMTDLDMLS(ph)PIHTPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLS(1)PIHTPQR;GLEFPMTDLDMLS(1)PIHTPQR 161.46 1.45E-11 51856000 32173 41354 44219 47657 42183 53947 52270 45254 46830 47276 TRUE FALSE 33443.21488 48456.22781 45371.38347 57083.41236 35012.74873 41418.62682 48172.94082 44647.44415 45144.59745 56538.82705 0.59150882 0.857043387 0.802481867 1.009632059 0.619269103 0.732569616 0.852032901 0.789677581 0.798470711 1 15.78695433 -4.999999971 0.327946701 3.104313692 0.781140498 0.251253771 0.112961928 506.5732639 4.402292797 742.2864179 0.093021418 1.00E-05 4.999999971 -2.323173194 GLEFPMTDLDMLSPIHT(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLEFPMTDLDMLSPIHTPQR 20 0 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;B0QY01 O60784 TOM1 Target of Myb protein 1 1 GLEFPMTDLDMLSPIHT(1)PQR;GLEFPMTDLDMLSPIHT(1)PQR 177.22 2.44E-16 31671000 25114 31954 36608 40765 32443 44440 35566 34775 37120 43799 TRUE FALSE 26105.52011 37441.85093 37562.03455 48828.19533 26928.35045 34119.48349 32778.24399 34308.89801 35784.05845 52380.57547 0.498381697 0.714804116 0.717098547 0.932181346 0.51409039 0.651376645 0.625770979 0.654992766 0.683155123 1 15.67674429 -1.777807583 2.212081493 1.106748523 0.668923425 0.437119505 0.113734332 2983215.491 1759060.665 1718251.991 0.029318362 0.016679861 1.777807583 -0.437825097 GLEGERPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLEGERPAR 9 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;;;;; 160.36 5.96E-05 19768280000 5284100 6759420 5941040 6063050 6300930 6548950 5886610 6125620 5476770 6761860 FALSE TRUE 5492720.348 7920297.804 6095868.383 7262303.194 5229900.169 5028055.613 5425202.126 6043516.083 5279662.118 8086717.003 0.679227472 0.979420672 0.753812503 0.898053337 0.64672724 0.621767228 0.670878197 0.74733864 0.652880782 1 22.94712269 3.236836256 24.99958719 0.705236699 0.833198224 0.131771366 0.125923169 71.14915294 1031516.373 0.032951376 0.041376522 1725.187314 -3.236836256 0.127961525 GLEGWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLEGWEK 7 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;; 117.02 0.012389 507790000 699650 735100 747090 698130 932480 968430 885420 782350 768500 714150 FALSE TRUE 727272.7222 861347.7067 766559.7791 836218.0303 773977.3827 743526.8092 816018.4668 771863.8779 740841.8351 854074.0193 0.851533598 1.00851646 0.89753319 0.97909316 0.906218156 0.870564837 0.955442325 0.90374354 0.867421112 1 19.70400158 GLEHVTVDDLVAEITPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLEHVTVDDLVAEITPK 17 0 E5RHX8;Q9NPA8-2;Q9NPA8 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 108.89 0.00063344 36559000 65371 55802 65449 54421 78721 87230 71928 66317 67218 57711 FALSE TRUE 67951.89756 65385.55942 67154.65471 65185.31137 65340.03254 66972.15448 66290.09541 65428.12909 64798.83731 69018.36551 0.984548056 0.947364646 0.972996886 0.944463273 0.946705012 0.970352659 0.960470375 0.947981434 0.93886369 1 16.07469269 -1.309790066 5.463599239 1.000007371 0.956493881 0.45592718 0.014051512 1.20E-06 1.51E-07 0.012887128 0.003037011 0.049001563 1.309790066 -0.04351349 GLESDVAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLESDVAELR 10 0 Q03252 Q03252 LMNB2 Lamin-B2 0 116.3 0.0025776 47251000 93911 132850 106800 118960 116720 139220 115800 113380 103360 136250 FALSE TRUE 97618.6788 155665.9541 109583.2957 142489.9329 96879.97609 106888.2649 106723.2934 111860.3266 99640.09379 162945.5788 0.599087619 0.95532481 0.672514692 0.874463327 0.594554187 0.655975238 0.654962805 0.686488872 0.611493079 1 17.31403068 -1.140149907 3.467637533 1.000303755 0.704613681 0.382932454 0.113936396 30106516.92 49278370.48 104116.9297 0.026924145 0.072418595 1.140149907 -0.295690074 GLESTTLADKDGEIYCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLESTTLADKDGEIYCK 17 1 P21291;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;; 244.97 1.38E-20 5784210000 5544620 3160270 4416610 3216200 5864630 5352840 5357970 4393720 4943440 2948900 FALSE TRUE 5763525.879 3703021.789 4531710.485 3852354.761 4867762.287 4109724.033 4937998.311 4334829.37 4765526.56 3526680.495 1.63426369 1.050002061 1.284979031 1.092345838 1.380267448 1.165323606 1.400183067 1.229152847 1.351278225 1 21.74987945 -1.029151078 5.543333098 0.999998857 1.275262837 0.219474976 0.161182877 2.02E-06 3.53E-07 0.138264249 0.032589061 0.093508033 1.029151078 0.27526398 VGGTNPNGGS(ph)FEEVLSSTAHASAQSLAGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGGTNPNGGSFEEVLSSTAHASAQSLAGGSR 31 0 Q16890-5;E9PPQ1;J3KNE7;Q16890 Q16890-5 TPD52L1 Tumor protein D53 1 VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR;VGGTNPNGGS(1)FEEVLSSTAHASAQSLAGGSR 185.97 1.37E-18 144777000 12821.7 31211 43734 36617 39060 54893 44936 42569 52359 39921 TRUE FALSE 13327.91062 36571.24646 44873.74397 43859.73331 32420.59515 42144.93266 41413.7989 41998.43218 50474.60982 47742.75562 0.2791609 0.766006193 0.939906869 0.918667822 0.679068368 0.882750317 0.867436292 0.879681779 1.057220287 1 15.54299422 4.723728077 2.892479669 0.888064048 0.183840403 0.794988265 0.094687965 0.164141693 1.998050116 0.023069201 0.265906279 52933.19121 -4.723728077 -0.704223645 down GLEYLYLNVHDEDRDDQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ;;;;; 270.77 1.57E-39 2795740000 1533460 1928850 1779530 1924030 1882460 2089030 1773560 1835420 1760550 2012130 FALSE TRUE 1594002.185 2260114.983 1825906.014 2304597.391 1562480.122 1603884.442 1634543.733 1810819.197 1697188.149 2406368.349 0.662409886 0.93922237 0.758780764 0.957707656 0.649310453 0.666516597 0.679257493 0.752511226 0.705290256 1 21.19842607 5.031247562 15.89879881 0.773886578 0.312492158 0.074252925 0.123954075 6418464.338 91692848.7 0.02876787 79912097.49 107460.1795 -5.031247562 -0.461394421 GLEYLYLSVHDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLEYLYLSVHDEDR 14 0 O43237;O43237-2;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 141.54 9.65E-06 30858000 19266 29570 25699 35333 31176 43405 38418 30880 28928 29164 FALSE TRUE 20026.63656 34648.41748 26368.73705 42321.76194 25876.71466 33324.84656 35406.69677 30466.10411 27886.88693 34878.12742 0.574188984 0.993413926 0.756025022 1.213418411 0.741918118 0.955465474 1.015154751 0.873501715 0.799552298 1 15.09003496 4.745723516 24.35112241 0.924078313 0.574188745 0.380218172 0.135299029 593.1908713 2016548.662 0.029565024 0.297884634 55683.1142 -4.745723516 -0.349889567 GLEYLYLSVHDEDRDDHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GLEYLYLSVHDEDRDDHTR 19 1 O43237 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 ;;;;;;; 192.55 4.67E-15 1605980000 603061 1166364 1066793 1166227 1144670 1309802 1014703 1126436 1029797 1305005 FALSE TRUE 626870.3139 1366677.944 1094594.502 1396903.22 950099.4023 1005620.336 935167.9274 1111337.968 992734.8071 1560695.744 0.401660808 0.875685059 0.701350347 0.895051598 0.608766575 0.644341051 0.599199383 0.712078554 0.636084779 1 20.57375788 -1.951048966 2.413811219 1.240653272 0.684079013 0.345401904 0.133724977 12096484.11 5644985.195 16332976.38 0.030483741 0.011193117 1.951048966 -0.55657426 GLFDDEDEESDLFTEAPQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLFDDEDEESDLFTEAPQDR 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 0 178.67 1.42E-16 54136000 66752 75378 60881 64448 72775 82309 75030 66238 57446 71161 FALSE TRUE 69387.4205 88323.58514 62467.60887 77195.62204 60404.73149 63193.98215 69148.95255 65350.18795 55378.52968 85103.63549 0.815328512 1.03783563 0.734018101 0.907077842 0.709778509 0.742553262 0.812526423 0.767889498 0.650718731 1 16.37693314 4.222321225 24.99995896 0.782386997 0.926582133 0.201302746 0.107383123 278.9973935 429508.027 0.024485496 0.053144479 16684.80844 -4.222321225 0.144195137 GLFDEYGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 155.07 0.00017261 271040000 241790 238040 225820 246360 308300 325740 276300 238200 239310 189210 FALSE TRUE 251336.0559 278921.5183 231705.0547 295089.2727 255895.2761 250091.8216 254642.884 235007.3186 230697.2798 226282.0769 1.110720122 1.232627534 1.023965565 1.304077092 1.130868515 1.105221523 1.125333865 1.038559138 1.019511943 1 17.78776279 1.803195936 1.073918281 0.998756446 1.16205752 0.423673329 0.070476597 0.449877365 0.960454526 0.055548638 0.022927084 63.56176325 -1.803195936 0.163301074 GLFIIDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLFIIDDK 8 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;; 151.27 0.001107 2376386000 4525500 2913440 3573399 2982491 4593000 4495540 4563970 3580490 3864310 2696262 FALSE TRUE 4704170.234 3413800.657 3666524.714 3572418.818 3812283.501 3451518.966 4206234.106 3532499.388 3725234.238 3224542.916 1.458864204 1.058692889 1.137068046 1.107883787 1.182270976 1.070390147 1.304443518 1.095503915 1.155275131 1 21.62066324 7.999999976 0.017228329 4.77E-08 2.586813151 0.224430842 0.112058808 7547.923219 10.03058159 581.9784838 969.7995826 99999994.49 -7.999999976 2.586813104 GLFIIDDKGILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLFIIDDKGILR 12 1 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;; 158.04 6.80E-05 5045470000 2790800 2993230 3192560 1929710 5033080 3985690 2128670 2986870 3234420 4762730 FALSE TRUE 2900982.939 3507293.968 3275760.736 2311400.878 4177558.859 3060073.901 1961819.283 2946835.893 3118013.856 5695895.756 0.509311101 0.615758104 0.575108969 0.40580112 0.733433166 0.537241908 0.344426824 0.517361275 0.547414136 1 22.44149131 0.740292953 5.217440039 0.999999785 0.527568362 0.661000362 0.100657081 7.696469801 154.4054979 0.097175577 0.024526178 5.499116913 -0.740292953 -0.472431423 GLFIIDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLFIIDGK 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 119.21 0.0040428 648670000 1752430 1491340 1690140 1546520 2217470 2088310 1973550 1846000 1772510 1548840 FALSE TRUE 1821617.29 1747466.044 1734186.437 1852417.04 1840545.241 1603331.651 1818857.994 1821257.389 1708717.711 1852305.544 0.983432402 0.943400537 0.936231305 1.000060193 0.993650992 0.865587028 0.981942747 0.983238103 0.922481562 1 20.82089066 -1.18622924 3.683453597 1.000034935 0.958333724 0.097590165 0.03923622 5500455.228 1772641.17 1815.566019 0.008984924 0.065128453 1.18622924 -0.041701211 GLFIKPTVFSEVTDNMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLFIKPTVFSEVTDNMR 17 1 H0Y2X5;P47895 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 ; 231.06 5.35E-16 433750000 201692 208937 223039 219119 297365 314151 300436 232604 253517 318430 FALSE TRUE 209654.9559 244820.3044 228851.5796 262460.0842 246819.0035 241194.1913 276887.0413 229486.3238 244392.9727 380820.2618 0.550535192 0.642876257 0.600943811 0.689196743 0.648124662 0.633354407 0.727080644 0.602610593 0.641754122 1 18.53875071 -5 0.385756315 6.282087594 0.631136409 0.852323044 0.045360678 216.9381136 1.591214437 960.6429901 0.02879319 1.00E-05 5 -5.650951185 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLFSDEEDSEDLFSSQSASK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6 Q641Q2 FAM21A WASH complex subunit FAM21A 1 GLFS(0.853)DEEDS(0.147)EDLFSSQSASK;GLFS(0.973)DEEDS(0.027)EDLFSSQSASK 145.91 8.98E-08 88481000 90717 76612 88363 75735 107363 108418 99872 93062 100605 76177 TRUE FALSE 94298.57721 89769.51504 90665.81237 90715.15695 89113.47561 83239.56259 92043.77167 91814.65611 96984.2457 91102.42465 1.035083068 0.985369109 0.995207457 0.995749096 0.97816799 0.913692066 1.010332843 1.00781792 1.064562728 1 16.47520183 1.673677886 2.729668917 1.031430741 0.98431902 0.226275854 0.032591168 0.321944202 5.445498839 0.020999201 0.008934979 47.17130447 -1.673677886 -0.047111721 GLGACTLLGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLGACTLLGSPR 12 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR;GLGACTLLGS(1)PR 177.93 2.38E-05 1023960000 820470 850180 790235 900630 848412 918440 984560 842350 827256 805928 TRUE FALSE 852862.7891 996191.8015 810829.1733 1078771.926 704199.2313 705146.2291 907387.6145 831059.6761 797483.2182 963834.1612 0.884864662 1.033571792 0.841253823 1.119250561 0.730622818 0.73160535 0.941435416 0.862243433 0.82740709 1 19.87842541 3.226506839 24.99998446 0.844514092 0.965117756 0.24039667 0.104939023 316.6464506 656735.4111 0.029225214 0.035182718 1684.638955 -3.226506839 0.120603664 GLGAEERRS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGAEERRSPVR 12 2 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 GLGAEERRS(1)PVR 55.885 0.097824 644570000 159630 326410 304280 225290 379310 376220 253880 320000 302490 416070 TRUE FALSE 165932.3157 382468.3784 312209.7868 269851.6896 314835.0217 288848.6067 233980.2222 315710.9234 291603.444 497590.9504 0.333471329 0.768640141 0.627442655 0.542316313 0.632718544 0.580494092 0.47022604 0.634478829 0.586030441 1 18.92460072 0.021205652 1.331762979 1.000838857 0.580197235 0.579634309 0.108518343 9.860425326 12.49971874 0.122210163 0.028299306 1.050039538 -0.021205652 -0.420641621 GLGAFVIDSDHLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLGAFVIDSDHLGHR 15 0 Q13057;Q13057-2;K7EQ60 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 0 ; 82.102 0.0069557 229450000 178838 292270 283100 312130 301760 383730 307780 310740 311960 358880 FALSE TRUE 185898.6623 342465.099 290477.8186 373868.3824 250466.943 294614.523 283655.3994 306575.0386 300732.6205 429195.6648 0.433132666 0.797923015 0.676795789 0.871090771 0.583572863 0.686434061 0.660899964 0.71430134 0.700688859 1 18.71127598 -4.999999995 0.354033623 4.70769275 0.678118833 0.433313309 0.110259945 415.1163086 3.362261872 1169.998525 0.076547522 1.00E-05 4.999999995 -4.029573916 GLGDHDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGDHDLK 8 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 0 86.011 0.020225 0 134020 104480 121070 102120 168400 170610 153750 127270 134880 114260 FALSE TRUE 139311.2131 122423.6273 124225.1837 122319.0312 139775.4282 130988.4131 141698.6732 125564.1538 130025.6951 136647.0594 1.019496605 0.895911173 0.909095185 0.895145726 1.022893788 0.95858933 1.036968332 0.918893933 0.951544042 1 17.06009489 3.249842397 24.99701714 0.976270229 0.925996608 0.222479176 0.046391791 344.6154587 763559.5236 0.012787338 0.017161721 1777.6342 -3.249842397 -0.05027362 GLGGEVPGSHQGPDPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLGGEVPGSHQGPDPYR 17 0 K7EM09;K7EPR0;K7ELQ9;Q6UW68 K7EM09 TMEM205 Transmembrane protein 205 0 ;;;; 153.72 1.65E-07 2882930000 1794930 2354110 1812890 2728150 2163090 2966860 1974440 1861730 1756370 3061940 FALSE TRUE 1865795.222 2758410.08 1860135.403 3267769.927 1795408.734 2277851.728 1819678.234 1836776.555 1693158.587 3661868.519 0.509519993 0.753279389 0.507974383 0.892377733 0.490298525 0.62204629 0.496926152 0.501595441 0.462375582 1 21.80414856 -1.63304716 6.705333731 1.001445387 0.582625962 0.474300657 0.132073831 0.002770495 0.000151617 0.12414721 0.029175349 0.023278385 1.63304716 -0.418819425 GLGHPPSS(ph)PLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLGHPPSSPLLK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.011)S(0.989)PLLK;GLGHPPS(0.011)S(0.989)PLLK 135.37 8.30E-05 483540000 1271660 1015600 1195680 1011730 1543570 1567340 1546000 1387300 1452880 1230130 TRUE FALSE 1321866.119 1190021.4 1226840.403 1211847.174 1281194.523 1203349.038 1424820.48 1368705.513 1400591.133 1471150.421 0.898525467 0.808905318 0.833932673 0.823741173 0.87087935 0.817964649 0.968507679 0.930364083 0.952038019 1 20.48851334 2.235834159 24.99999854 0.954492401 0.840877468 0.793726105 0.029946755 30.87941831 283141.1644 0.01033052 0.007973521 172.1211183 -2.235834159 -0.113614933 GLGHPPSS(ph)PLLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLGHPPSSPLLKK 13 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 GLGHPPS(0.105)S(0.895)PLLKK;GLGHPPS(0.097)S(0.903)PLLKK 123.29 0.00013789 876960000 793640 446150 637130 484670 905430 783110 807950 691430 831010 559410 TRUE FALSE 824973.52 522772.7919 653734.1312 580536.2794 751525.332 601244.5706 744620.7678 682162.5118 801102.1124 669015.6789 1.233115375 0.78140589 0.977158162 0.867746897 1.123329924 0.898700269 1.113009442 1.019651009 1.197433988 1 19.3516805 2.225071999 24.92011262 1.078279692 0.972455012 0.127650317 0.129846626 444.910953 821963.9432 0.045226354 0.033591042 167.9082361 -2.225071999 -0.10582468 GLGKPGGQGDAIQLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 GLGKPGGQGDAIQLS(1)PK 148.89 2.09E-07 1071700000 1513700 559720 686480 518180 1117900 1118700 1027300 779690 930820 479600 TRUE FALSE 1573462.045 655847.556 704370.2327 620674.4574 927879.7573 858898.8791 946777.5417 769239.5309 897319.97 573568.4375 2.743285617 1.143451266 1.228049151 1.082127985 1.61773155 1.497465381 1.650679291 1.341146898 1.564451444 1 19.12960611 4.744389442 24.99950761 1.371457909 2.74328621 0.782212698 0.220659114 295.0224101 1265298.676 0.05278467 0.475276075 55512.32822 -4.744389442 1.371828301 GLGLDDALEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGLDDALEPR 11 0 Q9Y230;X6R2L4;M0R0Z0;A0A1W2PS48 Q9Y230 RUVBL2 RuvB-like 2 0 117.71 0.0019047 88391000 112590 146060 128900 130000 131440 159780 121130 131240 115330 136730 FALSE TRUE 117035.1401 171144.6688 132259.2399 155713.612 109097.8757 122673.5165 111635.5141 129480.9425 111179.2958 163519.6256 0.715725343 1.046630752 0.808827927 0.952262527 0.66718521 0.750206686 0.682704071 0.791837322 0.67991408 1 17.31910427 3.242761299 24.99999984 0.748609009 0.887557023 0.182878362 0.120820799 145.5886782 866452.15 0.030667278 0.040093004 1748.885184 -3.242761299 0.138948014 GLGLPGCIPGLLPENS(ph)MDCI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGLPGCIPGLLPENSMDCI 20 0 K7ES22;Q9NVP2 K7ES22 ASF1B Histone chaperone ASF1B 1 GLGLPGCIPGLLPENS(1)MDCI 102.66 0.0011598 16955000 25062 30875 22698 27004 26279 39947 19796 24926 23916 45327 TRUE FALSE 26051.46711 36177.54108 23289.52853 32345.3106 21812.10497 30669.91465 18244.33779 24591.90774 23055.26783 54207.95781 0.480583814 0.66738432 0.429633018 0.596689341 0.402378283 0.565782514 0.336561983 0.453658628 0.4253115 1 15.72621704 -1.281164183 5.267567226 1.000084582 0.482633534 0.729498608 0.094218763 9.05E-05 1.23E-05 0.088173542 0.020779328 0.052340253 1.281164183 -0.517451048 GLGMEVFPVDLIYRPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLGMEVFPVDLIYRPWK 17 1 A5YKK6-3;A5YKK6-2;A5YKK6;A5YKK6-4 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 115.5 0.0002843 165360000 162960 147260 166890 139590 189090 188090 174070 169910 176170 153400 FALSE TRUE 169393.7866 172550.7595 171239.2905 167200.4854 156948.5493 144408.948 160425.9386 167632.6344 169829.6761 183455.793 0.923349347 0.940557704 0.933409012 0.911393871 0.855511547 0.787159379 0.874466464 0.913749474 0.925725339 1 17.48507294 0.892990585 1.681377351 0.999210432 0.890086019 0.37186609 0.042844904 0.59932649 3.370436378 0.046053409 0.013209625 7.816108592 -0.892990585 -0.109124413 GLGPPS(ph)PPAPPR ddPTM_MDA-MB-175_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 152.38 6.93E-05 2861040000 613340 746806 669662 732471 641633 802472 647565 668029 611028 690177 TRUE FALSE 637555.1368 875064.1212 687113.9419 877351.5776 532568.4518 616110.0396 596807.1632 659075.1639 589037.2216 825403.9689 0.772415885 1.060164664 0.832457763 1.062935981 0.645221579 0.746434549 0.723048575 0.798488 0.713635073 1 19.65474085 3.235633071 24.99961904 0.759441406 0.934038944 0.297016359 0.120413481 82.01157903 700334.9725 0.031228324 0.038897702 1720.414408 -3.235633071 0.174597538 GLGS(ph)SPDLELLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 GLGS(0.994)S(0.006)PDLELLLR;GLGS(0.99)S(0.01)PDLELLLR;GLGS(0.941)S(0.059)PDLELLLR;GLGS(0.987)S(0.013)PDLELLLR 160.69 4.26E-05 185564000 142651 178930 162603 186172 255930 234378 161873 167661 164292 230829 TRUE FALSE 148282.9716 209659.8356 166840.5678 222996.2659 212427.11 179947.2615 149184.9713 165413.7785 158379.163 276055.5231 0.537149085 0.7594843 0.604373229 0.807794981 0.76950864 0.651851698 0.540416542 0.599204742 0.573722131 1 18.07459894 -1.093208044 4.726876067 1.000016904 0.650893488 0.561560949 0.092959528 13399026.79 3098859.569 2516.5744 0.022675347 0.080684843 1.093208044 -0.349123416 GLGTDEDSLIEIICSR ddPTM_MDA-MB-175_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 ;;; 223.31 2.06E-14 192436000 179197 311515 243756 292483 200729 278396 232742 240555 219529 293876 FALSE TRUE 186271.8359 365015.278 250108.4816 350335.2644 166609.1563 213742.7481 214499.0739 237330.7537 211628.1942 351455.3756 0.530001385 1.038582145 0.711636523 0.996812935 0.474054938 0.608164686 0.610316668 0.675279908 0.602148121 1 18.422982 3.238235576 25 0.641896944 0.827236951 0.144922857 0.183404932 13.53987039 1041445.504 0.047455773 0.060173883 1730.754927 -3.238235576 0.185340007 GLGTDEDTIIDIITHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133;P08133-2 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 ;;;;; 266.35 3.49E-27 796747000 467523 906693 834241 965853 616995 999852 786972 659081 693255 1062479 FALSE TRUE 485981.169 1062410.47 855982.0058 1156895.841 512118.4103 767651.5259 725287.0783 650247.0972 668304.888 1270651.418 0.38246616 0.836114811 0.673656043 0.9104746 0.403036115 0.60414014 0.570799409 0.511743101 0.525954545 1 20.27713687 -1.004010423 4.722767347 1.000006543 0.60605926 0.355682334 0.160603579 1.29E-05 2.71E-06 0.151932965 0.035810235 0.099080816 1.004010423 -0.393947283 GLGTDEDTLIEILASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLGTDEDTLIEILASR 16 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 ;;;; 238.87 1.94E-19 161240000 140460 150641 139355 139314 154398 177032 150044 132934 142064 152570 FALSE TRUE 146005.4693 176512.4199 142986.7058 166869.8934 128153.4831 135919.0009 138283.1592 131152.2372 136951.1444 182463.1704 0.800191452 0.967386567 0.783646944 0.91454014 0.702352605 0.744911977 0.757868884 0.718787451 0.750568699 1 17.47724576 3.241781336 24.99999861 0.759188762 0.867737774 0.154977132 0.093213026 113.237187 878966.1573 0.02385594 0.031000645 1744.943368 -3.241781336 0.108549012 GLGTDEESILTLLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLGTDEESILTLLTSR 16 0 P08758;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ;; 290.66 3.75E-45 78063300 57290.2 56990 59881.9 49192.7 80287.3 71344.4 54200 57019.1 60135.3 62364.8 FALSE TRUE 59552.06133 66777.58918 61442.47151 58922.86923 66640.09342 54775.74433 49951.66237 56254.85223 57971.0423 74583.98851 0.798456378 0.895334113 0.823802437 0.790020357 0.89349061 0.734416936 0.669737076 0.754248376 0.777258544 1 16.18657833 2.725809675 24.74376222 0.760956074 0.83958159 0.044940197 0.087686433 1206.105097 2340496.657 0.026550067 0.025184423 531.875119 -2.725809675 0.078625516 GLHEDLQGVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLHEDLQGVPER 12 0 Q9UEU0;J3KMW2;G3V5I2 Q9UEU0 VTI1B Vesicle transport through interaction with t-SNAREs homolog 1B 0 129.37 0.00023546 132030000 21419 30801 24978 34837 30845 38272 25023 26924 26390 36762 FALSE TRUE 22264.63866 36090.83215 25628.9472 41727.65462 25601.97792 29383.90802 23061.63187 26563.12782 25440.22906 43964.81005 0.506419535 0.82090272 0.582942293 0.949114862 0.582328865 0.668350619 0.524547515 0.604190665 0.578649812 1 15.42406162 -0.97937609 4.366631724 1.000011777 0.648702165 0.396020702 0.130982437 36570782.09 73145377.22 6462.078572 0.03026955 0.104863394 0.97937609 -0.351309611 GLHQSIEEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 223.78 4.27E-09 3702190000 437709 2945370 2165070 2727360 2266940 3190000 1930580 2740320 1955360 3180320 FALSE TRUE 454990.0893 3451214.386 2221493.503 3266823.668 1881606.349 2449170.845 1779256.095 2703590.493 1884986.976 3803442.813 0.119625853 0.907392212 0.58407438 0.858912261 0.494711355 0.643935236 0.467801458 0.71082717 0.495600189 1 21.85887448 -1.124805721 3.980688815 1.000126273 0.606012108 0.251189546 0.211647467 10753288.75 6077029.342 11160.92334 0.044301202 0.075022975 1.124805721 -0.394114165 GLHSENREDEGWQVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLHSENREDEGWQVYR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 224.59 4.60E-15 508180000 314360 313730 252670 271620 283500 347030 249460 281750 289820 345940 FALSE TRUE 326771.1755 367610.687 259254.7878 325345.6253 235310.7713 266437.5418 229906.6734 277973.6021 279389.4348 413720.3196 0.789835935 0.888548784 0.626642627 0.786390249 0.56876774 0.644004003 0.555705539 0.67188772 0.675309917 1 18.65829629 4.237318582 24.99732937 0.669952093 0.839192383 0.170612811 0.123787571 40.37464084 812662.6484 0.02790889 0.066138497 17271.04366 -4.237318582 0.16924029 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 142.35 1.16E-07 217760000 222260 134470 175070 144400 231160 265020 214940 174500 201570 143090 TRUE FALSE 231034.9964 157564.1765 179632.468 172961.889 191867.5058 203473.1214 198092.4412 172161.1129 194315.5351 171125.7459 1.350089054 0.920750853 1.049710358 1.010729789 1.121207711 1.189026937 1.157584092 1.006050329 1.135513152 1 17.3846973 GLIAEAAQLGPVGGVFNLAVVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLIAEAAQLGPVGGVFNLAVVLR 23 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;; 170.56 1.67E-11 374085000 606220 236888 284367 305196 426554 506494 385088 283118 316944 244779 FALSE TRUE 630154.0337 277571.6713 291777.8376 365562.8579 354048.5034 388868.4445 354903.7963 279323.2663 305537.2474 292738.7585 2.152615653 0.948189002 0.99671748 1.248768218 1.209435011 1.328380453 1.212356704 0.954172477 1.04371983 1 18.15925424 4.744086442 24.97527694 1.112131904 2.152616102 0.855143926 0.129363293 227.8013845 1029571.371 0.03370467 0.293829815 55473.61164 -4.744086442 1.040484198 GLIHPDDSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLIHPDDSVK 10 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 138.66 5.88E-05 1024410000 2009540 3036350 2697410 2916300 3077380 3920090 2620740 2876040 2521280 3192520 FALSE TRUE 2088878.191 3557819.493 2767706.721 3493135.436 2554288.047 3009708.507 2415319.551 2837491.388 2430539.625 3818033.17 0.547108445 0.931846146 0.724903791 0.914904423 0.669006248 0.788287679 0.63260832 0.74318144 0.636594686 1 21.86439821 -0.933006543 4.395064872 1.00000501 0.738920498 0.323409805 0.115885766 9673541.296 6603003.055 435.8991025 0.024902894 0.116679204 0.933006543 -0.261084513 GLKEGIPALDNFLDKL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLKEGIPALDNFLDKL 16 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 119.23 0.0039745 0 582300 369500 470090 270150 564720 475110 348200 432200 476650 427640 FALSE TRUE 605289.6536 432958.7507 482340.9316 323584.8637 468729.0961 364772.9029 320907.1741 426407.0659 459495.4596 511427.8703 1.183528878 0.84656855 0.943126019 0.632708701 0.916510662 0.713244084 0.627472988 0.833757976 0.898456041 1 18.96417126 5.99507243 1.08272181 0.793865587 5.838565285 0.433612603 0.122278051 18.98663455 2.045552038 0.033504842 199.9246522 988717.9744 -5.99507243 5.044699698 GLKEGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLKEGMNPSYDEYADSDEDQHDAYLER 27 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER;GLKEGMNPSYDEYADS(1)DEDQHDAYLER 190.97 3.28E-18 562951000 134043 167569 176820 121629 348389 263594 143061 171648 177402 380959 TRUE FALSE 139335.1211 196347.6722 181428.0745 145686.8532 289169.9622 202378.2883 131847.505 169347.3393 171017.3367 455600.6221 0.305827329 0.430964452 0.398217354 0.319768776 0.634700543 0.44420108 0.289392724 0.371701291 0.375366776 1 18.79741019 -0.902688419 5.551061694 1.000000489 0.397267097 0.790437836 0.093193986 5.68E-07 1.12E-07 0.090970108 0.021441843 0.125115634 0.902688419 -0.602733392 GLKPSCTIIPLMK ddPTM_MDA-MB-175_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 ; 148.72 3.96E-05 1953790000 3773100 2796400 3703600 3509500 4746100 4499000 3927300 3637700 3985000 3209500 FALSE TRUE 3922064.901 3276659.947 3800118.859 4203668.625 3939359.617 3454175.433 3619467.964 3588942.582 3841580.628 3838340.075 1.021812769 0.853665877 0.990042254 1.095178786 1.026318549 0.89991386 0.942977405 0.935024649 1.000844259 1 21.87205111 2.75308798 24.58007096 0.949350454 0.994441198 0.093457474 0.06297403 1629.000683 2756239.491 0.02045946 0.021603132 566.3540106 -2.75308798 0.045090744 GLKYELISETGGSHDKR ddPTM_MDA-MB-175_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 ; 145.55 2.82E-07 2091660000 1631700 1452830 1790880 1318850 2526150 2257440 1788430 1965180 2199110 1694860 FALSE TRUE 1696120.776 1702342.251 1837551.804 1579714.594 2096755.925 1733183.772 1648248.183 1938839.976 2119964.461 2026935.367 0.836790755 0.839860155 0.906566551 0.779361108 1.034446366 0.855075993 0.813172541 0.956537642 1.045896428 1 20.95086866 1.518808817 4.366921757 1.018829739 0.869901317 0.483345721 0.065825286 0.146792553 6.116134374 0.039960618 0.016624648 33.02241394 -1.518808817 -0.148928422 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_MDA-MB-175_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 150.57 6.14E-09 372005000 572247 366276 458327 366219 565352 592237 549456 502680 524931 404796 TRUE FALSE 594839.7534 429181.0538 470271.3781 438656.0251 469253.669 454698.9322 506388.203 495942.3968 506038.8358 484108.0259 1.228733509 0.886539844 0.971418264 0.906111863 0.969316028 0.939250968 1.046023152 1.024445723 1.04530148 1 18.88496949 2.225603088 24.82171572 1.030816932 0.974431699 0.052597222 0.089311946 550.35462 1054263.506 0.031823122 0.023650304 168.1136929 -2.225603088 -0.056385234 GLLAQGLRPES(ph)PPPAGPLLNGAPAGESPQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGESPQPK 314.78 6.37E-93 16784320000 6874780 5153280 6688330 5527460 7532780 7378220 7366400 6940300 7103630 5601890 TRUE FALSE 7146201.623 6038315.753 6862633.374 6620775.09 6252360.746 5664740.223 6789002.319 6847276.631 6847971.744 6699473.091 1.066681144 0.901312039 1.024354196 0.988253106 0.933261566 0.845550112 1.013363622 1.022061965 1.022165721 1 22.6756162 2.045884398 24.9997693 1.01732463 0.957680463 0.172525421 0.058270181 204.4514541 111392.8729 0.021739533 0.016055698 111.1435843 -2.045884398 -0.059644167 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR;GLLASDLNTDGDMRVT(1)PEPGAGPTQGLLR 216.71 4.21E-34 3169730000 1178910 1530170 1365190 1462300 1424120 1680480 1346570 1420670 1292310 1593240 TRUE FALSE 1225454.277 1792964.794 1400767.973 1751538.575 1182048.591 1290213.988 1241022.325 1401628.242 1245800.016 1905404.874 0.643146396 0.940988878 0.735155028 0.919247452 0.6203661 0.677133771 0.651316863 0.735606517 0.653824304 1 20.86166615 5.033017821 17.10297071 0.754248658 0.235403511 0.067930303 0.129519721 5728574037 78146165230 0.029572212 89564858087 107899.0997 -5.033017821 -0.518845147 GLLDAAHFCYLMAQAGFGVYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLDAAHFCYLMAQAGFGVYTK 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ; 152.81 3.85E-08 44896000 59555 47797 58855 52386 67382 64120 75509 51481 57567 45563 FALSE TRUE 61906.27739 56005.76294 60388.80965 62747.79444 55928.43171 49229.10175 69590.40727 50790.9814 55495.17492 54490.19749 1.13609934 1.027813543 1.108250886 1.151542797 1.026394366 0.903448767 1.277117912 0.932112265 1.01844327 1 15.7337091 3.208869588 24.27339273 1.028270677 1.10051315 0.134810206 0.098420901 333.2277742 272423.336 0.027774001 0.033201898 1617.594227 -3.208869588 0.072242473 GLLDDLRNDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 ; 73.848 0.034742 95442000 59135 95061 72130 99098 99836 127467 66737 66123 70863 143110 FALSE TRUE 61469.69546 111386.9873 74009.76706 118699.2886 82865.91238 97864.72103 61505.97956 65236.72934 68312.65447 171149.6645 0.359157557 0.650816276 0.432427182 0.693540878 0.484172216 0.571807846 0.35936956 0.381167731 0.399139868 1 17.38489894 -1.529681038 5.445159677 1.001426012 0.481098206 0.649055293 0.1144261 0.002004253 0.000173115 0.112099278 0.026358121 0.029533775 1.529681038 -0.520327807 GLLEFEHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLLEFEHQR 9 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 226.47 2.36E-07 2524520000 2058150 2847220 2217590 2584540 3186330 3030860 2141620 2141240 2024910 3205810 FALSE TRUE 2139407.351 3336207.887 2275382.217 3095754.298 2644718.765 2326988.698 1973754.228 2112540.18 1952033.885 3833927.091 0.558019832 0.870180316 0.593486043 0.807463007 0.689819786 0.606946518 0.514812666 0.55101209 0.509147367 1 21.87039147 -0.981589059 4.874993641 1.000003126 0.633897438 0.474720775 0.115677354 0.032455023 78209655.6 728.1838556 0.028173462 0.104330417 0.981589059 -0.366105688 GLLEPLGLECTFIDDISAYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLEPLGLECTFIDDISAYHK 21 0 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 230.99 7.13E-26 937370000 1011380 1183690 1267290 1182830 1490680 1624720 1406950 1243010 1250870 1129910 FALSE TRUE 1051310.063 1386979.55 1300316.618 1416790.244 1237294.746 1247403.403 1296669.583 1226349.484 1205851.433 1351294.231 0.778002332 1.026408252 0.962274972 1.048469098 0.915636815 0.923117537 0.959576051 0.907536979 0.89236778 1 20.36591041 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 GLLPGGTQVLDGTSGFS(1)PAPK 250.45 6.24E-31 102780000 206530 145370 183950 140350 221810 232050 200640 180650 197610 166040 TRUE FALSE 214683.9639 170336.1667 188743.8881 168110.8111 184106.8154 178159.9043 184913.3125 178228.6822 190498.0547 198572.359 1.081137198 0.857804014 0.950504336 0.84659724 0.92715228 0.897203947 0.931213757 0.897550309 0.959338227 1 17.59930529 1.002871686 4.797484745 0.999874594 0.918635485 0.130623322 0.061209162 0.263515532 19.40557191 0.052871644 0.01339734 10.06634212 -1.002871686 -0.081239108 GLLS(ph)CLS(ph)KS(ph)NNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLLSCLSKSNNR 12 1 Q8N4B4 Q8N4B4 FBXO39 F-box only protein 39 3 GLLS(1)CLS(1)KS(1)NNR 62.088 0.06543 182630000 21233 125020 109950 123420 101990 163920 87442 105540 94941 130200 TRUE FALSE 22071.29524 146491.2125 112815.3873 147832.1076 84653.77623 125852.0642 80588.06755 104125.4089 91524.09196 155710.1972 0.141745985 0.940793957 0.724521511 0.949405436 0.543662379 0.808245488 0.517551638 0.668712845 0.587784831 1 17.2485039 -2.184578687 2.214566065 1.850024707 0.668389178 0.175516925 0.223169017 12012209.55 2483333.213 51173402.73 0.053308184 0.006537645 2.184578687 -1.181635529 GLLS(ph)PPMGQSGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLSPPMGQSGLR 13 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 GLLS(1)PPMGQSGLR;GLLS(1)PPMGQSGLR 134.9 9.46E-05 1578550000 414120 665440 597280 602160 648480 712330 569190 580170 611630 698350 TRUE FALSE 430469.7774 779724.1436 612845.6075 721265.4507 538251.6012 546902.153 524575.4005 572393.7701 589617.5558 835178.3118 0.515422601 0.933602002 0.733790137 0.863606538 0.64447507 0.654832801 0.628099884 0.685355166 0.70597805 1 19.67172472 -1.209028005 5.124498464 1.000025596 0.710592529 0.378080849 0.112569917 3.17E-05 4.89E-06 0.104858027 0.024713091 0.061797655 1.209028005 -0.289433068 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 1 GLLS(0.005)DS(0.959)MT(0.036)DVPVDTGVAAR;GLLS(0.016)DS(0.631)MT(0.353)DVPVDTGVAAR 88.992 0.0068447 70785000 160144 140461 150758 133397 176173 191544 166299 146222 154156 138472 TRUE FALSE 166466.6088 164584.0841 154686.8773 159782.5284 146227.1764 147060.8089 153264.0498 144262.1333 148607.9557 165602.9372 1.005215316 0.993847615 0.934082933 0.964853228 0.882998689 0.888032612 0.925491132 0.871132697 0.89737512 1 17.33736874 4.051144461 1.034997769 0.903541857 1.015931157 0.413778975 0.037500058 0.619217854 1.046106455 0.011740038 0.06038759 11249.79117 -4.051144461 0.112389301 GLLSGQT(ph)SPTNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLLSGQTSPTNAK 13 0 G3V1P3;Q969J3 G3V1P3 LOH12CR1 Loss of heterozygosity 12 chromosomal region 1 protein 1 GLLSGQT(0.498)S(0.498)PT(0.003)NAK;GLLSGQT(0.691)S(0.309)PTNAK 190.86 4.53E-05 96316000 528040 407090 459210 406260 553020 602380 564940 479330 492250 386780 TRUE FALSE 548887.4269 477004.5408 471177.3898 486617.0154 459017.8579 462486.3742 520658.5266 472905.3654 474534.0187 462562.1356 1.186624206 1.031222627 1.018625074 1.052003564 0.992337726 0.999836213 1.125596945 1.022360736 1.025881675 1 18.81928765 4.738886697 24.99999988 1.032667454 1.186624252 0.626927338 0.036239297 17.18389737 1316923.619 0.008556453 0.049783853 54813.39435 -4.738886697 0.153956798 GLLSNHTGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLLSNHTGSPR 11 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 GLLSNHT(0.286)GS(0.714)PR;GLLSNHT(0.137)GS(0.863)PR;GLLS(0.001)NHT(0.177)GS(0.823)PR 75.96 0.023613 627256000 235663 719190 586840 704910 581400 797470 582100 697140 537360 730140 TRUE FALSE 244967.1572 842705.288 602133.5325 844339.0941 482573.8357 612269.6783 536473.481 687795.9786 518020.5186 873196.9536 0.280540554 0.965080426 0.689573561 0.966951488 0.552651763 0.701181647 0.614378553 0.787675651 0.593245907 1 19.73594757 -1.437967277 2.969354917 1.006412149 0.700556513 0.193071014 0.191280259 44316781 51228721.26 2370141.413 0.041484174 0.036478143 1.437967277 -0.305855636 GLLTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLLTPR 6 0 O75525-2;O75525;H0YAQ1;H0YAQ3;E5RJZ9 O75525-2 KHDRBS3 "KH domain-containing, RNA-binding, signal transduction-associated protein 3" 0 97.596 0.095131 154220000 127760 199260 170640 178870 231400 232730 173090 181470 185460 238250 FALSE TRUE 132804.0635 233481.355 175087.0186 214249.9521 192066.7107 178681.9846 159522.7535 179037.6915 178785.3308 284930.5259 0.466092789 0.819432576 0.61449021 0.751937517 0.674082603 0.627107201 0.559865437 0.6283556 0.627469908 1 18.12025067 -1.397102733 3.206604602 1.004136916 0.644562188 0.58043779 0.091525535 86049769.02 107682796.4 3252874.936 0.020592445 0.04007719 1.397102733 -0.359574728 GLLYDS(ph)DEEDEERPAR ddPTM_MDA-MB-175_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;GLLY(0.003)DS(0.997)DEEDEERPAR;GLLYDS(1)DEEDEERPAR 370.34 6.98E-104 36113087000 5772249.7 6718651 6040341 6436615.8 6815483 7668845 6703867 6483563 5917439.4 6383147 TRUE FALSE 6000142.575 7872527.045 6197757.249 7709759.194 5656989.634 5887871.971 6178400.387 6396661.443 5704471.912 7633802.442 0.785996575 1.031272044 0.81188337 1.009950055 0.741044804 0.77128954 0.809347692 0.837939086 0.747264807 1 22.86397042 3.227916929 24.9999533 0.809128037 0.911461552 0.169942145 0.098421655 313.0151923 735210.5957 0.025871305 0.031222587 1690.117619 -3.227916929 0.102333515 GLLYDS(ph)DEEDEERPARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 271.72 6.73E-36 3589860000 1885580 1710010 1907260 1434730 2476460 2193060 1765160 1907320 1962060 1929700 TRUE FALSE 1960024.154 2003690.915 1956964.762 1718515.312 2055512.214 1683755.051 1626802.147 1881755.495 1891445.844 2307787.769 0.849308667 0.868230148 0.847982986 0.744659165 0.890685115 0.729597008 0.704918437 0.815393651 0.819592629 1 21.13807912 3.971489017 22.70198875 0.800832986 0.85860374 0.030447633 0.081187173 511.2951759 407123.589 0.019649894 0.03555595 9364.595366 -3.971489017 0.057770754 GLMAGGRPEGQYS(ph)EDEDT(ph)DTDEYKEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 2 GLMAGGRPEGQY(0.147)S(0.853)EDEDT(0.801)DT(0.199)DEYKEAK 112.91 0.0012059 156080000 232230 79621 115380 78184 190260 193290 149040 122430 138310 76242 TRUE FALSE 241398.6197 93295.28738 118386.8976 93648.56184 157919.6732 148401.3268 137357.8554 120789.0261 133332.2501 91180.16016 2.647490631 1.023197231 1.298384401 1.027071697 1.731952136 1.627561594 1.50644455 1.32472926 1.462294537 1 16.47643232 8 0.038388695 1.13E-09 3.778721082 0.164338745 0.423707112 1928.96024 5.643495983 155.8496428 483.7931217 99999999.99 -8 3.778721081 GLMAGGRPEGQYS(ph)EDEDTDTDEYKEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLMAGGRPEGQYSEDEDTDTDEYKEAK 27 2 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35;H0YC88 Q9NPQ8-4 RIC8A Synembryn-A 1 GLMAGGRPEGQY(0.005)S(0.482)EDEDT(0.482)DT(0.031)DEYKEAK;GLMAGGRPEGQY(0.001)S(0.994)EDEDT(0.005)DTDEYKEAK;GLMAGGRPEGQYS(1)EDEDTDTDEYKEAK;GLMAGGRPEGQY(0.001)S(0.999)EDEDTDTDEYKEAK;GLMAGGRPEGQY(0.004)S(0.996)EDEDTDTDEYKEAK 237.28 2.44E-45 792841000 321020 140771 201125 139546 294497 297197 244610 194025 238341 135500 TRUE FALSE 333694.1175 164947.3242 206366.4827 167147.7823 244438.5051 228177.5008 225436.829 191424.4122 229763.154 162048.6307 2.059222075 1.0178878 1.273484891 1.031466798 1.508426847 1.408080401 1.39116775 1.181277567 1.417865446 1 17.3060673 7.999999716 0.027920385 7.14E-11 3.178679779 0.157020943 0.275731561 3681.067321 7.888154429 295.2722252 674.5068939 99999934.55 -7.999999716 3.178679779 GLMELHMVLPAPDTDEKNGLNLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLMELHMVLPAPDTDEKNGLNLLR 24 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 68.369 0.020478 86753000 137930 125380 140050 124930 178360 212990 177640 150320 168260 145480 FALSE TRUE 143375.5829 146913.0397 143699.8181 149640.7811 148042.4309 163526.3004 163716.1126 148305.2063 162204.3555 173984.0206 0.824073282 0.844405361 0.825936874 0.860083475 0.850896711 0.93989264 0.940983615 0.852407053 0.932294557 1 17.40859528 2.829649199 5.107157836 0.918707442 0.840284186 0.607178993 0.036145724 0.185580516 7.914469693 0.011394063 0.012094558 675.537091 -2.829649199 -0.078423256 GLNNDS(ph)PERR ddPTM_MDA-MB-175_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 120.84 0.0003252 129569000 132356 160891 133702 148782 149385 158377 128493 115381 116972 138847 TRUE FALSE 137581.5171 188522.7777 137186.384 178210.6355 123992.5911 121596.342 118421.3829 113834.5064 112762.2006 166051.4113 0.828547713 1.135327765 0.82616813 1.07322566 0.746712058 0.732281292 0.713160954 0.685537723 0.679080049 1 17.34127046 3.216143064 21.31461263 0.73573501 0.967949987 0.389531853 0.124435097 36.12605622 34348.11352 0.032822891 0.039288779 1644.913497 -3.216143064 0.232214977 GLNPDGTPALSTLGGFS(ph)PASKPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 2 GLNPDGTPALSTLGGFS(1)PASKPS(0.076)S(0.924)PR 206.53 1.69E-25 969390000 621380 474960 532570 476930 796300 721000 699990 695120 669550 421050 TRUE FALSE 645912.5622 556530.6853 546449.2117 571265.3305 660945.2104 553558.6769 645122.9547 685803.0534 645453.0263 503546.686 1.28272627 1.105221623 1.085200691 1.134483349 1.312579804 1.099319472 1.281158178 1.361945322 1.281813671 1 18.94176602 3.259734451 24.98889098 1.247107703 1.143808392 0.06101517 0.112716786 445.6257163 525914.1293 0.030966589 0.041889383 1818.588546 -3.259734451 -0.10329931 GLNPDGTPALSTLGGFSPASKPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 GLNPDGTPALSTLGGFS(0.015)PAS(0.031)KPS(0.477)S(0.477)PR;GLNPDGTPALSTLGGFS(0.001)PAS(0.028)KPS(0.486)S(0.486)PR 131.32 3.91E-05 638360000 259070 179115 241008 179786 271774 268899 255640 245479 251289 219775 TRUE FALSE 269298.2836 209876.6079 247288.8665 215347.1342 225577.9526 206451.2825 235602.2688 242188.7555 242245.158 262835.7034 1.024587909 0.798508746 0.9408496 0.819322228 0.858246995 0.785476554 0.896386091 0.921445422 0.921660014 1 18.00380174 1.1456929 1.187440335 0.99434346 0.869068287 0.237069532 0.067482225 0.580489642 1.682451005 0.059149968 0.018871809 13.9859799 -1.1456929 -0.125275173 GLNSSFET(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLNSSFETSPK 11 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 GLNSSFET(0.5)S(0.5)PK 107.2 0.024923 82068000 512950 223670 253820 217400 337620 418770 353880 291490 272860 190490 TRUE FALSE 533201.6621 262083.5826 260434.7577 260401.0711 280231.473 321517.014 326141.9609 287583.0533 263039.8219 227812.8683 2.340524773 1.150433619 1.143195991 1.143048121 1.230095012 1.411320688 1.431622205 1.262365271 1.154631096 1 17.79748972 4.741247049 24.97800707 1.23562182 2.340525173 0.879101128 0.125091423 82.16770008 763939.1937 0.031292673 0.215141394 55112.11138 -4.741247049 1.104903353 GLNSSFETS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLNSSFETSPK 11 0 M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63;M0QZ79 M0QXD7 VRK3 Inactive serine/threonine-protein kinase VRK3 1 GLNSSFET(0.001)S(0.999)PK;GLNSSFETS(1)PK 236.75 1.54E-15 600590000 1809110 707560 884110 713550 1210260 1444090 1189750 939880 997270 647230 TRUE FALSE 1880535.06 829077.9259 907150.6329 854688.0603 1004540.437 1108721.983 1096494.286 927282.4459 961378.4475 774042.3265 2.429499002 1.071101537 1.171965152 1.104187757 1.297784892 1.432379012 1.416581818 1.197973824 1.242023097 1 19.56205293 4.743296984 24.99932215 1.233179855 2.429499487 0.880473585 0.13410316 161.6156321 853005.1339 0.033066793 0.269744766 55372.86363 -4.743296984 1.196319632 GLNVIGASDQS(ph)PLQS(ph)PSNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-5;Q9HAU0-8;H0YGJ6 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 2 GLNVIGASDQS(1)PLQS(1)PSNLR 266.45 1.41E-36 55123000 72563 76676 66232 73045 75176 97083 74093 79417 71086 74560 TRUE FALSE 75427.84327 89844.50654 67958.06033 87493.08298 62397.61037 74536.94456 68285.39705 78352.54502 68527.62875 89168.60446 0.845901354 1.007580046 0.762129908 0.981209513 0.699771077 0.835910184 0.765800894 0.878701035 0.768517453 1 16.44424822 3.255753663 24.99998334 0.819430232 0.897155124 0.119781308 0.098129606 486.5153943 707425.6971 0.024883833 0.033611582 1801.995338 -3.255753663 0.077724892 GLPEQECEQQQKEPQEQELQQQHWEQHEEYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPEQECEQQQKEPQEQELQQQHWEQHEEYQK 32 1 P07476 P07476 IVL Involucrin 0 ; 345.79 1.12E-131 361780000 265900 162742 214940 139998 262760 256910 225794 203738 259720 158784 FALSE TRUE 276397.9373 190691.6725 220541.513 167689.1865 218096.1491 197246.546 208095.6763 201007.2254 250372.7279 189894.6847 1.455532775 1.004196999 1.161388552 0.883064141 1.148511078 1.038715467 1.09584782 1.058519493 1.318482022 1 17.53484 4.745486898 24.78519842 1.077880187 1.455532971 0.512500851 0.1102411 548.4364754 1962484.498 0.024256082 0.239868959 55652.7844 -4.745486898 0.377652784 GLPPS(ph)MER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER;GLPPS(1)MER 126.31 0.0012844 7160650000 4314120 5928360 5486600 5719040 6276130 7103860 5431620 5785870 5614760 6747540 TRUE FALSE 4484444.789 6946509.714 5629585.303 6850249.042 5209315.664 5454096.175 5005875.432 5708319.876 5412685.884 8069591.274 0.555721428 0.860825472 0.697629547 0.848896655 0.645548887 0.675882581 0.620338164 0.707386494 0.670750934 1 22.94406417 -1.920481282 4.819645869 1.123246334 0.702130475 0.506513564 0.089315728 0.054949742 0.000906609 0.040175455 0.019186097 0.012009328 1.920481282 -0.421115859 GLPRPDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPRPDNR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 88.942 0.013003 116578000 280040 813790 673050 712800 633640 891350 585330 737420 638810 968450 FALSE TRUE 291096.1954 953552.1021 690590.2359 853789.7125 525934.0991 684347.471 539450.3051 727536.0911 615819.3529 1158199.235 0.251335165 0.82330576 0.596262037 0.737169985 0.454096396 0.590871976 0.465766414 0.628161433 0.531704161 1 20.14345202 -1.550267311 2.933194426 1.020362139 0.575188314 0.430392599 0.149901534 24832644.15 27437943.32 3994800.747 0.032441383 0.028166487 1.550267311 -0.445173824 GLPS(ph)TASGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPSTASGR 9 0 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GLPS(0.742)T(0.257)AS(0.001)GR;GLPS(0.773)T(0.227)ASGR 79.489 0.02104 0 246260 253570 275050 326670 304740 342850 287160 272760 252930 269660 TRUE FALSE 255982.535 297118.675 282218.029 391284.351 252940.4037 263228.2834 264651.6488 269104.0983 243827.0987 322494.714 0.793757305 0.921313318 0.875109007 1.213304696 0.784324185 0.81622511 0.820638718 0.83444499 0.756065412 1 18.29891599 GLPSPYNMSS(ph)APGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 2 GLPSPY(0.001)NMS(0.026)S(0.974)APGS(1)R;GLPS(0.001)PY(0.001)NMS(0.068)S(0.931)APGS(0.999)R;GLPS(0.001)PY(0.001)NMS(0.061)S(0.937)APGS(1)R;GLPSPYNMS(0.038)S(0.962)APGS(1)R;GLPSPYNMS(0.004)S(0.996)APGS(1)R;GLPSPYNMSS(1)APGS(1)R;GLPSPYNMS(0.032)S(0.968)APGS(1)R;GLPSPYNMS(0.003)S(0.997)APGS(1)R 245.97 8.66E-18 3056190000 3272170 3847810 3363370 3617480 3676080 3784450 2754800 3201900 2872450 3708840 TRUE FALSE 3401357.798 4508641.436 3451022.185 4333006.747 3051221.235 2905568.841 2538871.578 3158983.768 2769071.086 4435516.188 0.766845989 1.016486299 0.778042969 0.976888949 0.687906684 0.65506893 0.572395967 0.71220206 0.624295114 1 22.08067058 3.220739611 24.62838197 0.684080578 0.886380109 0.295219897 0.12986331 200.4685444 277044.0095 0.034230488 0.040999642 1662.41562 -3.220739611 0.20229953 GLPSPYNMSS(ph)APGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMS(0.273)S(0.672)APGS(0.055)R;GLPSPYNMS(0.21)S(0.789)APGSR;GLPSPYNMS(0.019)S(0.97)APGS(0.012)R;GLPSPYNMS(0.058)S(0.915)APGS(0.027)R;GLPSPYNMS(0.044)S(0.954)APGS(0.002)R 151.38 3.16E-06 3328260000 1590130 1878430 1640290 1526610 1737970 1876180 1514310 1593250 1476010 1800620 TRUE FALSE 1652909.56 2201035.74 1683037.305 1828568.902 1442550.48 1440465.629 1395614.425 1571895.09 1422888.688 2153417.014 0.76757523 1.0221131 0.781565899 0.849147606 0.669889051 0.668920891 0.648092969 0.729953873 0.660758543 1 21.0381963 3.287530246 7.196440994 0.70911426 0.862834597 0.205648398 0.116391773 0.263411831 31.1376877 0.029861006 0.040224637 1938.787656 -3.287530246 0.153720337 GLPSPYNMSSAPGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLPSPYNMSSAPGSR 15 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSSAPGS(1)R;GLPSPYNMSS(0.001)APGS(0.999)R;GLPSPYNMSS(0.001)APGS(0.999)R 178.85 7.29E-07 1981190000 1627750 1886820 1677150 1745520 1832400 2147590 1790530 1748300 1529160 1871050 TRUE FALSE 1692014.827 2210866.658 1720857.907 2090778.646 1520929.303 1648844.77 1650183.58 1724866.898 1474125.83 2237646.424 0.75615826 0.988032172 0.769048179 0.934365065 0.679700459 0.736865642 0.737463954 0.770839789 0.658784075 1 21.09355066 3.238920145 24.99999945 0.75096013 0.864277951 0.157845212 0.108331504 14.41826343 1002530.086 0.027767711 0.035386249 1733.485227 -3.238920145 0.113317821 GLPSTAS(ph)GR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPSTASGR 9 0 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GLPST(0.001)AS(0.999)GR;GLPSTAS(1)GR 150.1 9.03E-05 1894370000 1050200 1347850 1293490 1234210 1342550 1432750 1125260 1251930 1128410 1418080 TRUE FALSE 1091662.707 1579332.753 1327199.412 1478333.054 1114343.831 1100015.526 1037059.181 1235149.926 1087798.745 1695925.625 0.643697277 0.931251188 0.782581142 0.871696867 0.657071167 0.648622504 0.61150039 0.7283043 0.641418897 1 20.69364147 5.045314787 15.62566046 0.746952274 0.116515276 0.060422431 0.127439979 6070171.614 57846616.73 0.030102522 111956138.3 110997.9063 -5.045314787 -0.630436998 GLPTGDS(ph)PLGPMTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLPTGDSPLGPMTHR 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 1 GLPTGDS(1)PLGPMTHR;GLPTGDS(1)PLGPMTHR;GLPTGDS(1)PLGPMTHR;GLPTGDS(1)PLGPMTHR 247.79 1.69E-18 2587190000 1209760 1315810 1205570 1243390 1433080 1421540 1346630 1236930 1267120 1350640 TRUE FALSE 1257522.259 1541790.132 1236988.145 1489328.831 1189485.573 1091408.879 1241077.622 1220350.977 1221516.599 1615272.048 0.778520411 0.954508024 0.76580793 0.922029718 0.736399528 0.675681152 0.768339688 0.755508013 0.756229639 1 20.62334574 3.222874954 24.9964122 0.763337937 0.855922456 0.103934518 0.096310011 384.9396751 613432.1489 0.025544788 0.030628981 1670.609528 -3.222874954 0.092584519 GLPTGDSPLGPMTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLPTGDSPLGPMTHR 15 0 J3QQZ9;Q9NVS9-3;Q9NVS9;Q9NVS9-4 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 92.265 0.0040272 128740000 46674 67225 80561 70340 86338 83883 75834 77732 74905 79564 FALSE TRUE 48516.72556 78770.37081 82660.48584 84253.04206 71662.2976 64402.44451 69889.93292 76690.12968 72209.18368 95153.04246 0.50988097 0.827828189 0.868710907 0.885447694 0.753126708 0.676830113 0.734500244 0.805966133 0.758874144 1 16.53796217 -0.354462749 1.011162192 1.00508125 0.765032366 0.332302527 0.102435616 27.97648553 18.6269355 0.69737437 0.031029512 0.442117038 0.354462749 -0.240048884 GLPVTCEVAPHHLFLSHDDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPVTCEVAPHHLFLSHDDLER 22 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 190.83 5.70E-18 589560000 140131 178193 177464 206953 180613 235370 164076 156900 164084 210608 FALSE TRUE 145663.4801 208796.2616 182088.8576 247887.6857 149912.4668 180708.8846 151215.2944 154797.0121 158178.6489 251872.6053 0.578322045 0.82897567 0.722940303 0.984178829 0.595191631 0.71746145 0.600364197 0.614584551 0.628010532 1 17.94233469 GLPWQSSDQDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLPWQSSDQDIAR 13 0 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5;H0YBR2;H0YBB3 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ; 125.54 0.00024666 58828000 108972 123629 121283 107053 176301 167053 111219 121374 150774 137715 FALSE TRUE 113274.2987 144861.319 124443.7346 128227.7639 146333.419 128257.4725 102501.3642 119747.1801 145347.6732 164697.6175 0.687771325 0.879559287 0.755589161 0.778564777 0.888497485 0.77874516 0.622360941 0.727072934 0.8825123 1 17.32946016 1.006541671 4.247667507 0.999244216 0.765107308 0.498912778 0.075355478 0.146853315 7.366702764 0.075783916 0.019332003 10.15176769 -1.006541671 -0.234136908 GLPWSCS(ph)VEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 GLPWS(0.007)CS(0.993)VEDVQNFLSDCTIHDGAAGVHFIYTR 126.88 1.56E-07 110850000 17272 18026 16802 30749 21200 38110 13214 19622 22070 25156 TRUE FALSE 17953.9119 21121.82528 17239.87392 36831.06042 17596.43157 29259.53006 12178.25215 19358.99919 21275.70501 30084.83656 0.596776115 0.702075454 0.573041967 1.224240004 0.584893707 0.97256736 0.404797019 0.643480284 0.707190314 1 14.8767489 2.251750621 24.99995666 0.648392929 0.774774245 0.020797793 0.23266037 687.4803439 1303029.139 0.077634548 0.064599181 178.5462037 -2.251750621 0.126381316 GLPWSCSADEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 166.29 1.82E-06 457150000 178582 210700 191267 191391 221883 232981 194300 197890 177814 216096 FALSE TRUE 185632.5553 246886.086 196251.5751 229247.5686 184167.4069 178874.6936 179070.2583 195237.6082 171414.5089 258435.8738 0.718292521 0.955308883 0.759382095 0.887057842 0.712623229 0.692143436 0.69290016 0.755458619 0.663276759 1 17.97944682 3.227369107 24.98401475 0.734970301 0.833915361 0.096126146 0.1078834 359.5742085 802714.7773 0.028283531 0.03409362 1687.987036 -3.227369107 0.098945059 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR 33 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 176.78 9.16E-20 54012000 7239.7 7143.3 6709.4 6505.3 6543.2 8659.6 5698.2 6853.1 5914.7 7267.4 FALSE TRUE 7525.528946 8370.106208 6884.252476 7792.028924 5430.989201 6648.539138 5251.560195 6761.245404 5701.831102 8691.307887 0.865868411 0.963043344 0.792084755 0.896531227 0.624875942 0.764964172 0.604231292 0.777931871 0.656038329 1 13.08535758 3.258325079 24.99657032 0.72273934 0.879122294 0.271638554 0.111745288 271.6999898 343623.011 0.02816408 0.038083013 1812.696429 -3.258325079 0.156382954 GLQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLQDLK 6 0 Q15847;Q5TBU2;O15350-6;O15350-5;O15350-13;O15350-11;O15350-8;O15350 Q15847 ADIRF;TP73 Adipogenesis regulatory factor;Tumor protein p73 0 ;;; 118.69 0.050377 2840130000 6794500 5586520 6232850 5268870 7942000 7274500 7366800 6456920 6592840 5528680 FALSE TRUE 7062752.106 6545961.353 6395283.191 6311036.76 6592021.677 5585107.621 6789370.966 6370375.549 6355564.976 6611918.993 1.068184912 0.990024433 0.967235563 0.954493963 0.99699069 0.844702972 1.026838195 0.963468481 0.9612285 1 22.65663762 4.791032245 1.898175844 0.962676563 1.110745708 0.320231334 0.04548266 1.072183456 3.617424405 0.011098224 0.292619906 61806.22871 -4.791032245 0.148069145 GLQEFLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLQEFLDR 8 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ;;; 177.97 0.0005864 381072000 465429 655044 528397 579969 558430 636180 528202 549407 512135 706310 FALSE TRUE 483804.4963 767542.7115 542167.4599 694685.1372 463508.2681 488436.8364 486800.147 542043.0978 493703.3614 844697.9214 0.572754453 0.908659406 0.64184775 0.82240659 0.548726659 0.578238473 0.57630087 0.641700523 0.584473276 1 19.68807598 -1.113845576 3.829823162 1.000136158 0.655386264 0.458919165 0.11307205 39007839.23 57343429.97 64028.31654 0.027056434 0.076940397 1.113845576 -0.344749894 GLQEVGLPLHR ddPTM_MDA-MB-175_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 94.767 0.0082582 189070000 87352 80306 77030 79734 89415 99309 85152 78579 86631 80290 FALSE TRUE 90800.72441 94097.93081 79037.46508 95505.14722 74216.27024 76245.98979 78477.56374 77525.77703 83513.16723 96021.28826 0.945631183 0.979969468 0.823124398 0.994624723 0.772914752 0.794052977 0.817293385 0.807381139 0.869735959 1 16.55106667 4.240933362 24.99487349 0.848112242 0.962800359 0.216208416 0.075764923 75.6784579 797161.3548 0.018069046 0.044919658 17415.39631 -4.240933362 0.114688117 GLQLT(ph)PGIGGMQQHFFDDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GLQLTPGIGGMQQHFFDDEDR 21 0 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR;GLQLT(1)PGIGGMQQHFFDDEDR 274.29 3.59E-44 1651273000 962040 944590 926998 1163738 1465090 1618249 1389867 1512890 1377986 1707775 TRUE FALSE 1000022.082 1106815.985 951156.3294 1393921.903 1216054.525 1242435.195 1280925.593 1492612.184 1328392.553 2042380.814 0.489635466 0.541924394 0.465709589 0.68249853 0.595410276 0.608326903 0.627172751 0.730819725 0.650413745 1 20.96182046 -5 0.104946034 2.322328493 0.34535951 0.866450163 0.052389744 55.70620377 0.393599925 15.82230205 0.728634581 1.00E-05 5 -1.976968983 GLQLT(ph)PGIGGMQQHFFDDEDRTVPSTPTLVVPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLQLTPGIGGMQQHFFDDEDRTVPSTPTLVVPHR 34 1 P12270 P12270 TPR Nucleoprotein TPR 1 GLQLT(1)PGIGGMQQHFFDDEDRTVPSTPTLVVPHR 95.657 0.00036746 58763000 18269 29779 27048 26617 50344 36927 28402 36915 36901 62012 TRUE FALSE 18990.27423 34893.3116 27752.8931 31881.76316 41786.54486 28351.26388 26175.77703 36420.21481 35572.94022 74162.06411 0.256064532 0.470500815 0.374219534 0.429893147 0.563449054 0.382287956 0.352953728 0.491089552 0.479664916 1 16.17839378 -5 0.285023825 5.356545233 0.390456266 0.840826928 0.07644244 85.71656589 0.814421194 221.315113 0.082192431 1.00E-05 5 -4.966088968 GLQPS(ph)TPPPKPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLQPSTPPPKPPR 13 1 A0A1B0GTL5 A0A1B0GTL5 1 GLQPS(0.612)T(0.388)PPPKPPR;GLQPS(0.636)T(0.364)PPPKPPR 64.136 0.038614 721970000 1371050 1176460 1192640 1196280 1422000 1600420 1387720 1232300 1200780 1014530 TRUE FALSE 1425180.113 1378507.853 1223721.178 1432900.613 1180288.948 1228746.71 1278946.88 1215783.034 1157564.162 1213307.729 1.174623781 1.136156822 1.008582694 1.180986966 0.972786144 1.012724703 1.054099343 1.00204013 0.95405653 1 20.21051407 8 0.274711093 0.980900969 2.440765519 0.528086022 0.054611821 38.8256135 0.546393047 0.058831325 27.0329114 100000000 -8 1.45986455 GLQSIFQEQGMAESVHTWQDHGYLATYTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLQSIFQEQGMAESVHTWQDHGYLATYTNK 30 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ; 380.17 1.23E-137 769590000 438290 867990 978040 864760 1025130 1099850 905320 978580 966050 983090 FALSE TRUE 455594.0276 1017060.53 1003528.526 1035806.947 850878.7688 844426.5059 834358.6528 965463.7357 931282.0492 1175707.663 0.387506216 0.865062432 0.853552764 0.881007226 0.723716274 0.718228291 0.709665063 0.821176697 0.79210341 1 20.16509795 -5 0.154339401 1.849985989 0.691266733 0.276737121 0.131432661 197.9881982 1.790172563 51.79279372 0.606761769 1.00E-05 5 -1.158719256 GLQTSQDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLQTSQDAR 9 0 P27797 P27797 CALR Calreticulin 0 ;; 204.07 4.00E-05 878510000 1449760 1889390 1428320 1828340 1655600 2006000 1519640 1437920 1377570 1698960 FALSE TRUE 1506997.644 2213878.035 1465543.193 2189980.195 1374181.703 1540136.901 1400526.646 1418647.034 1327991.525 2031838.683 0.74169158 1.089593408 0.721289148 1.077831726 0.676324215 0.758001565 0.689290276 0.698208498 0.653591024 1 20.95435443 3.210559343 24.99997959 0.725622915 0.907293028 0.222741571 0.145037925 258.6310678 230909.2036 0.037851148 0.045249463 1623.90023 -3.210559343 0.181670113 GLQVDLQS(ph)DGAAAEDIVASEQSLGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLQVDLQSDGAAAEDIVASEQSLGQK 26 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 GLQVDLQS(1)DGAAAEDIVASEQSLGQK;GLQVDLQS(1)DGAAAEDIVASEQSLGQK 118.15 0.00041616 48650000 50310 45427 45690 44511 55195 68817 57157 48907 54014 56474 TRUE FALSE 52296.27765 53228.73388 46880.71893 53315.14295 45812.97362 52835.29468 52676.88499 48251.48166 52070.04669 67538.99904 0.774312299 0.788118489 0.694128127 0.789397884 0.678318812 0.782293126 0.779947671 0.714423997 0.770962665 1 16.04343318 0.954487216 22.31585526 1 0.748882991 0.786516539 0.038824738 1161.29101 569405.9924 0.03484059 0.008710147 9.005072538 -0.954487216 -0.25111701 GLS(ph)GEEEDDEPDCCNDER ddPTM_MDA-MB-175_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 413.31 1.68E-147 796770000 488150 583340 468620 624780 558500 661550 554720 538620 547910 499060 TRUE FALSE 507422.5389 683524.1072 480832.6222 748359.6192 463566.3695 507915.0384 511239.5969 531400.6799 528190.8261 596841.2519 0.850180073 1.145236032 0.805629002 1.253867116 0.776699613 0.851005249 0.856575505 0.890355146 0.884977076 1 19.18698773 GLS(ph)LEHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLSLEHQK 8 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 GLS(1)LEHQK;GLS(1)LEHQK;GLS(1)LEHQK;GLS(1)LEHQK 127.76 0.00080925 1441640000 1656500 1293310 1983630 1192170 2644230 1984280 2194060 1932590 2632810 1570380 TRUE FALSE 1721899.899 1515425.932 2035325.027 1427977.668 2194764.729 1523461.042 2022083.844 1906686.792 2538055.682 1878065.894 0.916847436 0.806907754 1.08373462 0.760344816 1.16863031 0.81118615 1.076684184 1.01523956 1.351419932 1 20.84081625 1.700133941 1.952405758 1.162862467 0.933660629 0.262903574 0.149281006 0.377540115 2.978157652 0.098610684 0.03918482 50.1341829 -1.700133941 -0.229201838 GLS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLSPGR 6 0 Q96FF7;A0A044PY82 Q96FF7 LOC113230 Uncharacterized protein LOC113230 1 GLS(1)PGR;GLS(1)PGR 72.875 0.08858 1032270000 1394550 1427220 1259600 1294750 1718240 1696610 1388610 1400220 1439000 1457790 TRUE FALSE 1449607.911 1672333.933 1292426.211 1550847.686 1426174.179 1302598.04 1279767.12 1381452.341 1387210.671 1743416.039 0.831475608 0.959228259 0.741318298 0.889545381 0.818034334 0.747152722 0.734057213 0.792382489 0.79568539 1 20.73348546 3.007298943 21.87323947 0.792753127 0.854551877 0.023587133 0.086035259 87.24652133 261444.3967 0.023295883 0.027752901 1016.948461 -3.007298943 0.06179875 GLS(ph)PMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLSPMR 6 0 Q3KR16-2;Q3KR16;F5H731 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 GLS(1)PMR;GLS(1)PMR 113.41 0.027443 411740000 255930 317080 266860 284720 344410 371670 296790 290160 249710 372170 TRUE FALSE 266034.314 371536.0235 273814.5908 341036.7662 285867.3112 285355.2752 273526.8243 286270.8798 240722.9859 445089.5859 0.59770959 0.834744364 0.615189839 0.766220503 0.642269153 0.641118742 0.614543303 0.643175866 0.54084165 1 18.76373622 -0.973106836 8.030786277 1.000000002 0.658798229 0.622574649 0.080518437 2.77E-09 4.13E-10 0.074260644 0.017503401 0.106388127 0.973106836 -0.341201773 GLS(ph)SAGGGSPHREDAQPEHSASAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.472)S(0.396)AGGGS(0.132)PHREDAQPEHSASAR 122.47 7.24E-05 101900000 37958 51252 40441 43967 48631 52224 44446 47640 38900 51388 TRUE FALSE 39456.61115 60054.13231 41494.92568 52663.54137 40364.71999 40095.76746 40962.20638 47001.46372 37499.9966 61456.49472 0.642025083 0.977181217 0.675191871 0.856923936 0.656801534 0.652425226 0.666523637 0.764792459 0.610187691 1 15.90727786 -1.040242753 4.143267962 1.000027102 0.728790232 0.367363156 0.108982174 6275976.957 2363547.411 1564.450959 0.024195337 0.09115012 1.040242753 -0.27123687 GLSAS(ph)LPDLDSENWIEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.003)AS(0.997)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLS(0.12)AS(0.88)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK;GLSAS(1)LPDLDSENWIEVK 412.04 2.01E-147 10793736000 7212921 4903938 6254878 4879142 7568327 6846987 7144243 6293042 6439576 4981349 TRUE FALSE 7497692.691 5746151.204 6417885.259 5844221.725 6281865.48 5256878.036 6584258.566 6208694.065 6207816.918 5957348.963 1.258561944 0.964548365 1.077305577 0.981010473 1.05447331 0.88241902 1.105232983 1.042190764 1.042043526 1 22.50623904 4.746938434 24.9858969 1.020770788 1.258562063 0.588810907 0.060573703 726.9471314 2167989.269 0.013674182 0.156802182 55839.10313 -4.746938434 0.237791275 GLSAS(ph)LPDLDSENWIEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLSASLPDLDSENWIEVKK 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 GLS(0.002)AS(0.998)LPDLDSENWIEVKK;GLSAS(1)LPDLDSENWIEVKK 245.41 8.61E-25 401268000 301330 172196 216305 130175 373300 261911 206608 227240 269910 248861 TRUE FALSE 313226.7411 201769.3235 221942.086 155923.2265 309846.5993 201086.1395 190413.5251 224194.2195 260195.9918 297620.5482 1.052436544 0.677941509 0.745721649 0.523899399 1.041079325 0.675646022 0.639786218 0.753288779 0.874254125 1 18.18311461 1.013270739 3.155696144 0.99853411 0.752745204 0.180144306 0.158059493 0.345127251 8.112821018 0.142278566 0.037316341 10.31028662 -1.013270739 -0.245788906 GLSDHVS(ph)LDGQELGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;GLSDHVS(1)LDGQELGTR 338.42 7.53E-72 2126610000 1277490 1726050 1677600 1634280 1885330 2028560 1674680 1769380 1653940 1818410 TRUE FALSE 1327926.292 2022485.661 1721319.634 1957535.706 1564862.28 1557457.683 1543414.206 1745664.355 1594415.022 2174692.624 0.610627119 0.930009896 0.791523186 0.900143627 0.719578603 0.716173709 0.709716025 0.802717743 0.733167991 1 21.05238007 -1.026370505 4.465400853 1.00000748 0.774160309 0.374637685 0.089552239 1.03955E+11 22664929264 11356804.8 0.019945078 0.094108639 1.026370505 -0.225847172 GLSEDTTEETLKESFDGSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 238.8 1.11E-29 2106280000 3062200 2456890 2823340 2098300 3809340 3602260 3173450 3008270 3318630 2671860 FALSE TRUE 3183098.021 2878841.746 2896918.56 2513337.477 3161829.747 2765689.708 2924706.697 2967949.061 3199193.155 3195359.811 0.996162626 0.900944468 0.906601676 0.786558518 0.989506639 0.865533108 0.915298079 0.928830941 1.001199659 1 21.60754696 1.333181564 2.586239368 1.004708114 0.905348504 0.29324126 0.05590415 0.329071328 3.654174661 0.046825056 0.014115188 21.53681927 -1.333181564 -0.09935961 GLSSAGGGS(ph)PHREDAQPEHSASAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLSSAGGGSPHREDAQPEHSASAR 24 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 GLSSAGGGS(1)PHREDAQPEHSASAR;GLSSAGGGS(1)PHREDAQPEHSASAR;GLS(0.009)S(0.008)AGGGS(0.983)PHREDAQPEHSASAR;GLSS(0.001)AGGGS(0.999)PHREDAQPEHSASAR 243.54 6.64E-38 4137900000 1698854 3064345 2672853 3027340 2857480 3186570 2361968 2656684 2479790 3029160 TRUE FALSE 1765926.068 3590622.416 2742509.745 3626138.816 2371766.57 2446537.41 2176830.776 2621075.496 2390542.842 3622665.905 0.487465892 0.991154722 0.757041863 1.000958662 0.654701988 0.675341716 0.600891949 0.723521176 0.659884987 1 21.78862033 GLSTS(ph)LPDLDSEPWIEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLSTSLPDLDSEPWIEVK 18 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 GLS(0.002)T(0.015)S(0.983)LPDLDSEPWIEVK;GLST(0.001)S(0.998)LPDLDSEPWIEVK;GLS(0.011)T(0.117)S(0.871)LPDLDSEPWIEVK;GLS(0.014)T(0.136)S(0.85)LPDLDSEPWIEVK;GLS(0.003)T(0.021)S(0.977)LPDLDSEPWIEVK 254.23 1.66E-30 813380000 1056178 793057 992134 803617 1170785 1196572 1118981 971186 1009324 799358 TRUE FALSE 1097876.723 929258.3706 1017989.827 962570.044 971775.3839 918686.2872 1031272.345 958168.8402 972998.6264 955976.8955 1.148434369 0.972051077 1.064868651 1.006896766 1.016526015 0.960992145 1.078762834 1.002292885 1.017805588 1 19.86661623 4.750477574 24.89199514 1.015698469 1.148434455 0.581119664 0.034353233 1181.982669 2468862.334 0.007543376 0.124522319 56296.00462 -4.750477574 0.132735986 GLTDESEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLTDESEILR 10 0 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 0 153.04 3.95E-05 90917000 81297 92146 95274 89932 96228 99322 87254 88011 85753 94113 FALSE TRUE 84506.66833 107971.3587 97756.91871 107720.2812 79871.19893 76255.97074 80414.80348 86831.3565 82666.76628 112552.6404 0.750819066 0.959296541 0.868543984 0.957065785 0.709634164 0.677513832 0.714463945 0.771473296 0.73447203 1 16.78024038 3.231301482 24.99899984 0.750025665 0.888215479 0.231834416 0.100200208 190.7738061 656986.1219 0.026769496 0.032618671 1703.340536 -3.231301482 0.138189814 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSR 33 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;; 342.84 3.87E-118 14495800000 911337 1831105 1721488 1772904 1858771 2140705 1683402 1932966 1705007 2151930 FALSE TRUE 947317.2885 2145583.04 1766351.391 2123579.12 1542817.769 1643558.706 1551452.552 1907057.752 1643644.131 2573559.482 0.368096131 0.833702525 0.686345664 0.825152531 0.5994879 0.638632492 0.602843091 0.741019497 0.638665686 1 21.2953337 GLTMLDHEQVTPEDPGAQFLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 98.993 0.0010754 120430000 75170 181450 161650 163990 144950 212890 146700 172000 166260 214330 FALSE TRUE 78137.76964 212612.626 165862.7318 196426.7325 120311.4508 163449.5239 135201.2707 169694.6213 160276.3351 256323.8599 0.304840016 0.829468728 0.647082686 0.766322466 0.469372811 0.637668003 0.527462682 0.662032093 0.625288395 1 17.96760825 0.105864432 1.30614649 1.000659625 0.61387463 0.412213122 0.140499978 9.430866692 12.67193666 0.138507233 0.036692203 1.276040421 -0.105864432 -0.386784995 GLVAAYSGDS(ph)DNEEELVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLVAAYSGDSDNEEELVER 19 0 P52756 P52756 RBM5 RNA-binding protein 5 1 GLVAAYSGDS(1)DNEEELVER 235.29 3.89E-24 1474500000 877660 1147300 965760 1055200 1140600 1337600 1187100 1043500 990050 1214300 TRUE FALSE 912310.6945 1344339.85 990928.499 1263915.411 946721.2194 1026962.672 1094052 1029513.589 954418.2939 1452218.836 0.62821847 0.925714374 0.682354804 0.870333988 0.651913607 0.707167987 0.753365797 0.708924553 0.657213824 1 20.46982744 -1.043810477 4.589337893 1.000009527 0.735985196 0.435775018 0.091473713 9.25E-06 1.93E-06 0.081055564 0.019104199 0.090404391 1.043810477 -0.264024331 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 2 GLVAAYS(0.025)GES(0.976)DS(1)EEEQER;GLVAAYSGES(1)DS(1)EEEQER 228.3 1.84E-19 187220000 207804 229030 218459 240730 233809 261820 223914 238330 203538 230450 TRUE FALSE 216008.2624 268364.1209 224152.221 288345.6755 194066.2297 201016.2729 206363.0356 235135.5762 196212.7071 275602.2653 0.783768095 0.973736992 0.813317774 1.046238409 0.704153246 0.729370902 0.748771188 0.853169969 0.711941562 1 18.07222822 3.217583406 24.99998901 0.783076074 0.902731434 0.208133943 0.107285761 335.1860242 399463.4246 0.028867325 0.034536354 1650.377925 -3.217583406 0.11965536 GLVDRPLALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLVDRPLALR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 114.4 0.0024532 0 153760 180990 168850 182490 188510 233910 195080 169540 169800 272520 FALSE TRUE 159830.5635 212073.6246 173250.3697 218585.9773 156467.1375 179587.9474 179789.1199 167267.5936 163688.9312 325915.0763 0.490405554 0.6507021 0.53158133 0.670683847 0.480085608 0.551026818 0.551644072 0.513224474 0.502244121 1 18.31413656 -1.667466102 3.28398496 1.036361402 0.55053891 0.8313069 0.060936657 16906719.01 22783631.07 5248145.573 0.014068409 0.021504725 1.667466102 -0.485822492 GLVFDTLYGNLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GLVFDTLYGNLLK 13 0 P49902-2;P49902;Q5JUV4;Q5JUV3;H0YHR8 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 115.78 0.0014821 27821000 118030 119880 141640 115530 179630 180730 159020 164390 141550 130000 FALSE TRUE 122689.9155 140468.4575 145331.2548 138381.4892 149096.5568 138758.1965 146555.5969 162186.6209 136455.6432 155471.011 0.789149789 0.903502567 0.934780406 0.890079046 0.958999082 0.892502053 0.942655457 1.043195255 0.877691875 1 17.24628608 6.83735269 0.402498161 0.969035774 3.79E-29 0.471664993 0.048520216 25.34806597 0.820866136 0.034688544 16.79267151 6876266.341 -6.83735269 -0.969035774 GLVGEIIKR ddPTM_MDA-MB-175_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 ; 175.51 8.64E-05 9177500000 4774100 4731200 4842100 4299000 7069000 6862400 6762200 6345900 6432100 5263500 FALSE TRUE 4962585.154 5543746.796 4968289.104 5149329.369 5867413.905 5268711.601 6232161.094 6260843.59 6200609.977 6294782.049 0.788364889 0.880689236 0.789271029 0.818031399 0.932107555 0.836996668 0.990051926 0.994608478 0.985039661 1 22.585725 2.412481888 0.983900281 1.007118546 0.823733726 0.748194203 0.042307713 0.257170654 0.493945475 0.027178296 0.018032871 258.5127028 -2.412481888 -0.183384819 GLVGPELHDR ddPTM_MDA-MB-175_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 ;;;; 185.29 1.47E-06 2601390000 2301020 2886090 2441030 2637400 2634710 2859370 2468890 2414270 2290930 2912490 FALSE TRUE 2391866.046 3381753.507 2504645.247 3159069.848 2186862.935 2195324.652 2275371.951 2381910.66 2208479.877 3483136.653 0.686698882 0.970893147 0.719077515 0.906961214 0.627842991 0.630272329 0.653253713 0.683840715 0.634049162 1 21.73195564 3.231552706 24.9991528 0.682160516 0.824347356 0.147825584 0.12967168 228.9628239 816772.5509 0.033805541 0.041235334 1704.326143 -3.231552706 0.14218684 GLVLDHGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ;;; 198.65 2.60E-05 2993290000 3153160 3353060 3241050 3524900 3717260 3851730 3490850 3323000 3147630 3517520 FALSE TRUE 3277649.192 3928921.972 3325514.426 4222114.699 3085401.473 2957224.081 3217228.055 3278460.62 3034347.411 4206710.697 0.779147754 0.933965337 0.790526058 1.003661769 0.733447507 0.702977764 0.764784718 0.779340643 0.721311169 1 22.00426117 3.190226341 24.99992961 0.768367757 0.874743838 0.165602378 0.098921551 163.7896337 84716.24787 0.026196553 0.031310937 1549.624025 -3.190226341 0.10637608 GLVRPGSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLVRPGSSR 9 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GLVRPGS(0.224)S(0.776)R;GLVRPGS(0.164)S(0.836)R 61.344 0.054377 329200000 177688 155321 155669 156215 218950 230510 187765 145046 175828 173315 TRUE FALSE 184703.2594 181996.1735 159725.862 187113.8607 181732.9572 176977.5459 173047.4887 143101.8956 169499.9846 207272.7559 0.891112093 0.878051593 0.770607123 0.902742186 0.87678169 0.853838919 0.834878119 0.690403787 0.817762971 1 17.66117097 1.990126089 23.87778352 0.791902251 0.85984587 0 0.081062301 527.9526418 1276732.216 0.030264828 0.021048471 97.75209849 -1.990126089 0.06794362 GLVSSDELAKDVTGAEALLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLVSSDELAKDVTGAEALLER 21 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 170.11 7.87E-12 95188000 158533 149515 176947 118473 235510 214300 155405 166213 201785 199698 FALSE TRUE 164792.0053 175193.0382 181558.3842 141906.6058 195478.0943 164532.0727 143223.95 163985.1866 194522.7973 238824.9997 0.690011538 0.733562393 0.760215155 0.594186563 0.818499297 0.688923157 0.599702503 0.686633254 0.814499309 1 17.86559434 0.94931648 3.139506386 0.999354912 0.695420587 0.684580063 0.063700005 0.152685314 3.735080342 0.060197205 0.015741223 8.898493355 -0.94931648 -0.303934324 GLVVDMDGFEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GLVVDMDGFEEER 13 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;;; 265.23 6.16E-24 364162000 532265 744345 725925 723357 740080 875138 695090 685189 664644 802796 FALSE TRUE 553279.2332 872180.4635 744843.2019 866434.8556 614281.4659 671900.4623 640607.0295 676005.1622 640723.5923 960088.5057 0.576279405 0.908437564 0.775806811 0.902453108 0.63981754 0.699831795 0.667237474 0.70410713 0.667358882 1 19.87280788 -1.274466341 3.524254921 1.000745472 0.730873888 0.38973425 0.102441099 39983765.08 63944628.85 321591.855 0.024335673 0.053153719 1.274466341 -0.269871583 GLVVDMDGFEEERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GLVVDMDGFEEERK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 208.68 1.24E-08 318475000 568618 398286 493619 411071 629770 630446 599414 538812 554171 481120 FALSE TRUE 591067.4777 466688.5223 506483.1167 492379.6169 522721.9203 484034.471 552430.3644 531590.1065 534226.494 575386.2524 1.027253389 0.81108737 0.880248902 0.855737541 0.908471341 0.841233987 0.960103517 0.92388392 0.928465864 1 19.13417123 1.184928375 0.698667776 0.995703436 0.88473073 0.226279959 0.05774963 0.873230098 1.004606299 0.052055134 0.021586582 15.30834973 -1.184928375 -0.110972706 GLWHEEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GLWHEEMK 8 0 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ;;; 133.6 0.00091248 526119000 745410 613980 751020 641890 935280 944170 840250 759210 783480 650440 FALSE TRUE 774839.3624 719426.2889 770592.1982 768853.9261 776301.4397 724900.8265 774389.0094 749034.0318 755282.7078 777881.2646 0.996089503 0.924853601 0.99062959 0.988394966 0.997969067 0.931891356 0.995510555 0.962915635 0.970948578 1 19.56919043 -1.099025417 3.662698493 1.000010659 0.972552835 0.091831597 0.025157068 26892232383 35478044.01 3118642.983 0.005635444 0.079611276 1.099025417 -0.027457824 S(ph)SFSHYSGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSFSHYSGLK 10 0 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.499)S(0.499)FS(0.002)HYSGLK;S(0.499)S(0.499)FS(0.002)HYSGLK 179.35 1.36E-06 529130000 118356 570680 737600 771200 827300 989660 942790 869090 790370 573060 TRUE FALSE 123028.7863 668689.8507 756822.4619 923741.0582 686675.8415 759826.4634 868891.6563 857441.2701 761924.7381 685340.1351 0.17951493 0.975705079 1.104301971 1.347857817 1.001948969 1.108685198 1.267825437 1.251117841 1.111746852 1 19.38646065 4.729038071 2.530443148 1.167848611 1.81E-12 0.878990242 0.10736595 0.150993163 1.245481975 0.026607337 0.37519274 53584.36286 -4.729038071 -1.167848611 down GLYGIKDDVFLSVPCILGQNGISDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLYGIKDDVFLSVPCILGQNGISDLVK 27 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 204.89 3.01E-25 815830000 578640 367680 514410 365870 653470 527790 520300 454320 557060 351590 FALSE TRUE 601485.154 430826.1798 527815.9472 438237.994 542393.4028 405218.7712 479517.5264 448230.5835 537011.5194 420477.3289 1.430481771 1.02461215 1.255278016 1.042239293 1.289946843 0.963711343 1.140412321 1.066004164 1.277147381 1 18.68166849 4.749804081 24.78969042 1.120731145 1.430481974 0.405026356 0.113673354 1380.984158 3044742.374 0.024270922 0.368755731 56208.76987 -4.749804081 0.309750829 GMAFLHTLEPLIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GMAFLHTLEPLIPR 14 0 A0A0A0MTH3;Q13418;Q13418-3;Q13418-2 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ; 177.1 2.14E-06 155017000 201947 249810 223370 240090 262260 286360 240840 235480 228680 290000 FALSE TRUE 209920.0235 292712.9242 229191.2057 287579.0854 217681.1389 219857.2298 221962.3315 232323.7758 220449.8515 346819.9476 0.605270905 0.843991028 0.660836285 0.829188423 0.627648843 0.633923254 0.639992979 0.669868551 0.635631984 1 18.40382735 -1.261002632 8.910600434 1.000000082 0.685258484 0.587064937 0.079755305 1.25E-07 1.03E-08 0.074342323 0.017522649 0.054827364 1.261002632 -0.314741597 GMAYGHIDSYGADDS(ph)EEEGAGPVERPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMAYGHIDSYGADDSEEEGAGPVERPPVR 29 1 Q8NG27-3;Q8NG27;K7EPI8 Q8NG27-3 PJA1 E3 ubiquitin-protein ligase Praja-1 1 GMAYGHIDSYGADDS(1)EEEGAGPVERPPVR 142.38 4.60E-08 56563000 12530 18735 12790 17238 13177 14781 15085 17450 13068 18169 TRUE FALSE 13024.69408 21952.59051 13123.31791 20647.62495 10937.17825 11348.33676 13902.59828 17216.11129 12597.68523 21728.86768 0.599418905 1.010296111 0.603957744 0.950239343 0.503347823 0.522270048 0.639821572 0.792315161 0.579767221 1 14.40732538 -0.756545969 7.692107148 1.00000287 0.698192586 0.238942795 0.165763882 0 0 0.154220291 0.036350072 0.175167701 0.756545969 -0.301810283 GMDDDRGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GMDDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 118.71 0.00086184 2858686000 2508043 3157450 2716440 3108740 3029345 3294790 2897227 2790150 2712815 3066460 FALSE TRUE 2607062.474 3699717.476 2787232.658 3723639.493 2514418.019 2529624.956 2670134.777 2752752.603 2615181.318 3667274.126 0.710899263 1.008846721 0.760028447 1.015369827 0.685636779 0.689783438 0.728097951 0.750626353 0.713113127 1 21.80627668 3.213190711 24.99922275 0.743648599 0.875307851 0.159061452 0.122872042 320.1680483 315489.2271 0.032239251 0.038546524 1633.769225 -3.213190711 0.131659253 GMDTPAFELKET(ph)LTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMDTPAFELKETLTEK 16 1 A0A2R8Y3N3;A0A2R8Y5P7;P49590-2;P49590;D6RJE6;A0A2R8Y6I1;A0A2R8Y5E8;A0A2R8Y4X6 A0A2R8Y3N3 HARS2 "Probable histidine--tRNA ligase, mitochondrial" 1 GMDT(0.416)PAFELKET(0.584)LTEK 54.44 0.034735 0 212280 116270 177910 121910 239080 222360 192180 155580 186410 118950 TRUE FALSE 220660.9783 136238.468 182546.4808 146023.4341 198441.267 170720.2599 177116.4294 153494.7046 179701.1405 142255.9751 1.551154377 0.957699443 1.283225402 1.026483661 1.3949591 1.200092016 1.245054412 1.079003567 1.26322385 1 17.11812972 -4.999999978 0.172010416 0.184851908 1.255453375 0.147751409 0.164555345 261.3222968 2.477233278 72.66878662 0.526656586 1.00E-05 4.999999978 1.070601467 GMGEAVQEFVDKEEKDAIEELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMGEAVQEFVDKEEKDAIEELVK 23 2 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 72.033 0.011987 4775900 19816 7352.9 12611 6013.5 18671 13347 16663 9151.7 13427 5966.7 FALSE TRUE 20598.35098 8615.703377 12939.65302 7202.952351 15497.31009 10247.36153 15356.91052 9029.036431 12943.76489 7135.760626 2.886637047 1.207398038 1.813353012 1.009416197 2.171781104 1.436057354 2.152105616 1.265322214 1.813929246 1 12.8008515 8 0.045083977 6.43E-13 4.555896112 0.185320738 0.520315993 1190.184501 4.066758336 104.1708737 392.8383092 100000000 -8 4.555896112 GMGPGT(ph)PAGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GMGPGTPAGYGR 12 0 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 GMGPGT(1)PAGYGR;GMGPGT(1)PAGYGR;GMGPGT(1)PAGYGR;GMGPGT(1)PAGYGR 193.15 3.55E-05 1180390000 788265 702640 585674 604037 671090 837860 612034 594534 600530 687650 TRUE FALSE 819386.3109 823312.9542 600937.1456 723513.7157 557018.3615 643279.7129 564061.1758 586565.2442 578917.0426 822381.8516 0.996357482 1.001132202 0.730727635 0.87977831 0.677323266 0.782215356 0.685887188 0.713251688 0.703951627 1 19.6494489 4.241800402 24.97289959 0.755689395 0.998744953 0.466850818 0.095872422 57.80413221 445544.8492 0.021786 0.054774238 17450.19973 -4.241800402 0.243055558 GMGS(ph)LDAMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GMGSLDAMDK 10 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK;GMGS(1)LDAMDK 162.1 7.21E-06 771920000 2032370 1470450 1723140 1440290 2192960 2179990 2111660 1846320 1834560 1291060 TRUE FALSE 2112609.537 1722988.349 1768046.444 1725175.063 1820201.443 1673720.361 1946142.571 1821573.1 1768534.544 1544018.488 1.368254042 1.115911734 1.145094089 1.117327983 1.178872829 1.084002798 1.260439941 1.179761197 1.145410212 1 20.5582586 0.811977847 3.490816521 1.000026209 1.176213712 0.325241542 0.077831947 1.391550754 24.20472223 0.070436633 0.018177468 6.486013482 -0.811977847 0.176187503 GMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.615)GS(0.385)PQLNNR;GMKDDKEEEEDGT(0.584)GS(0.416)PQLNNR;GMKDDKEEEEDGT(0.574)GS(0.426)PQLNNR 156.69 2.04E-08 2053060000 1912810 617465 984597 629898 1470118 1573707 1350759 927874 1132241 471012 TRUE FALSE 1988329.216 723509.8105 1010256.407 754489.9443 1220227.867 1208237.399 1244882.98 915437.3667 1091491.868 563297.7833 3.529801243 1.284417997 1.793467748 1.339415788 2.166221675 2.144935476 2.209990909 1.625139303 1.937681809 1 19.10353827 -1.994625153 0.267286791 1.35E-18 2.069001821 0.217173725 0.591849507 52.23382731 2.105842262 34.00701973 0.763723259 0.010124529 1.994625153 2.069001821 GMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 GMKDDKEEEEDGT(0.059)GS(0.941)PQLNNR;GMKDDKEEEEDGT(0.101)GS(0.899)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.284)GS(0.716)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.047)GS(0.953)PQLNNR;GMKDDKEEEEDGT(0.338)GS(0.662)PQLNNR;GMKDDKEEEEDGT(0.006)GS(0.994)PQLNNR;GMKDDKEEEEDGT(0.344)GS(0.656)PQLNNR;GMKDDKEEEEDGTGS(1)PQLNNR;GMKDDKEEEEDGT(0.319)GS(0.681)PQLNNR;GMKDDKEEEEDGT(0.194)GS(0.806)PQLNNR 263.55 4.83E-37 23796623000 12061816 3309848 5475829 3585179 8145589 8357555 8234872 5334477 6468921 2339207 TRUE FALSE 12538025.81 3878288.647 5618533.602 4294316.706 6761004.691 6416639.511 7589401.215 5262977.061 6236105.797 2797529.825 4.481820247 1.386326113 2.008390957 1.535038757 2.416776626 2.293680466 2.712893763 1.881294353 2.229147207 1 21.41572208 8 0.054269483 1.52E-12 6.436086674 0.227710167 0.796205071 810.3518456 3.303732082 86.44401198 424.6613891 100000000 -8 6.436086674 GMKDDKEEEEDGTGSPQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GMKDDKEEEEDGTGSPQLNNR 21 2 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;;; 266.45 2.97E-37 2225000000 1264018 385662 644502 416062 937090 960488 944565 619024 756551 319695 FALSE TRUE 1313922.407 451896.4485 661298.2516 498357.8218 777803.7765 737429.2183 870527.5271 610726.9958 729322.8773 382333.1143 3.436590652 1.181944309 1.729638964 1.303464971 2.034361522 1.928761048 2.276882369 1.59736882 1.907558749 1 18.54447063 -2.111333878 0.381289159 4.85E-12 1.919776709 0.183672939 0.591624896 83.65930571 4.606339981 73.13958309 0.376859465 0.007738666 2.111333878 1.919776709 GMLPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GMLPHK 6 0 P40429;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 93.595 0.04544 1464680000 2268400 2223500 2288500 2011820 3169100 2875700 2673100 2468700 2384900 2748400 FALSE TRUE 2357958.184 2605368.829 2348140.19 2409751.991 2630417.514 2207862.257 2463575.437 2435611.114 2299067.915 3286896.359 0.717381361 0.792653173 0.714394351 0.733139025 0.800273944 0.671716421 0.749514182 0.741006362 0.699464682 1 21.64829454 -1.678822979 2.731162664 1.034830594 0.737433182 0.819413083 0.037240477 11166196.89 9837789.334 2699588.076 0.008253736 0.020949662 1.678822979 -0.297397412 GMNFSVVVFDTAPTGHTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMNFSVVVFDTAPTGHTLR 19 0 O43681 O43681 ASNA1 ATPase ASNA1 0 149.53 8.47E-08 656970000 224930 222900 268240 234830 229510 294370 253420 185950 259360 222430 FALSE TRUE 233810.4101 261181.3411 275230.5548 281278.6731 190497.9722 226007.0287 233556.2782 183457.6444 250025.6843 266010.8998 0.878950488 0.981844508 1.034658937 1.057395292 0.716128446 0.849615669 0.877995144 0.689662132 0.939907667 1 18.02112584 3.247169865 24.99998031 0.823213218 0.991075085 0.321202918 0.098400948 185.9457549 539955.6873 0.026705623 0.0356037 1766.728704 -3.247169865 0.167861867 GMPETTQPDKQCGQVAAAAAAQPPASHGPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMPETTQPDKQCGQVAAAAAAQPPASHGPER 31 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 149.07 7.79E-09 60774000 23998 22706 24610 24333 29094 29292 20451 26291 30434 29851 FALSE TRUE 24945.45957 26605.57887 25251.35682 29145.99477 24148.61227 22489.37692 18847.99718 25938.61215 29338.68628 35699.73192 0.698757616 0.745259907 0.707326231 0.81642055 0.676436796 0.629959266 0.527959068 0.726577225 0.821818112 1 15.12362562 0.983321351 2.477956172 0.99791891 0.687894733 0.650487246 0.070937704 0.188780943 2.633824057 0.073148514 0.019787214 9.623240762 -0.983321351 -0.310024177 GMPTFPWDEDPEEDGS(ph)PDPEPSPEPEPKPSLEPNTSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMPTFPWDEDPEEDGSPDPEPSPEPEPKPSLEPNTSLER 39 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 1 GMPTFPWDEDPEEDGS(0.99)PDPEPS(0.009)PEPEPKPSLEPNTSLER 65.736 0.0026446 31108000 21741 22708 23113 22210 31429 33218 23438 26437 26577 17310 TRUE FALSE 22599.35147 26607.92236 23715.34377 26603.07171 26086.70981 25503.62292 21600.86832 26082.65526 25620.49896 20701.56308 1.091673676 1.285309822 1.145582277 1.285075509 1.260132373 1.231966051 1.043441417 1.259936516 1.23761181 1 14.33745208 GMPVTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMPVTAR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 89.703 0.041126 104160000 116390 201380 179840 175650 168400 224890 158730 184640 164550 184890 FALSE TRUE 120985.1671 235965.4485 184526.7781 210393.0457 139775.4282 172662.7057 146288.3278 182165.2028 158627.8776 221115.6556 0.547157852 1.067158487 0.834526066 0.951506781 0.632137185 0.78087056 0.661591905 0.823845794 0.717397767 1 17.75444165 4.811672363 22.07876575 0.813474867 0.547139713 0.273143395 0.136013296 68774.11954 20763549.37 0.031515059 231.3495591 64814.52805 -4.811672363 -0.266335155 GMWSEGNGSHTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GMWSEGNGSHTIR 13 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 148.48 4.33E-05 400220000 232145 362060 310852 362810 348900 429990 330256 335950 288421 447350 FALSE TRUE 241310.2639 424240.9886 318953.0585 434572.7351 289594.1026 330131.3391 304369.6718 331447.1398 278040.7845 534999.6675 0.451047503 0.792974303 0.596174312 0.812285991 0.541297725 0.617068307 0.568915628 0.619527749 0.519702724 1 19.02917847 -2.0370656 2.824548958 1.483627978 0.61997156 0.538844482 0.107179841 18762649.65 6260738.217 59036600.12 0.024633752 0.009181939 2.0370656 -0.863656417 GMYGIENEVFLSLPCILNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GMYGIENEVFLSLPCILNAR 20 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 56.599 0.089729 0 36986 23055 28743 28705 37269 43751 35023 26969 33133 18932 FALSE TRUE 38446.23584 27014.51691 29492.06619 34382.76332 30934.02869 33590.4933 32277.80574 26607.52467 31940.5498 22641.36292 1.698053071 1.193148884 1.302574686 1.518581873 1.366261775 1.483589721 1.425612312 1.175173277 1.410716745 1 14.46667319 0.075574975 0.423608721 0.946151997 1.424915644 0.421403089 0.143610415 3.840760345 0.957440781 0.505417607 0.089623323 1.190076761 -0.075574975 0.478763648 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_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 194.19 2.63E-18 4379690000 14428800 3749250 5949750 4830130 8216400 10593600 12097900 6544780 7157950 2335150 TRUE FALSE 14998460.17 4393154.522 6104805.373 5785515.298 6819779.263 8133396.948 11149634.99 6457057.929 6900336.778 2792677.933 5.370637261 1.573097445 2.186004086 2.071672937 2.442021395 2.912400621 3.992452854 2.312138415 2.470867369 1 21.41321777 0.728405326 1.755921214 1.004473585 2.794324029 0.222914957 1.038984799 1.555696447 7.45578245 0.947507102 0.267633508 5.350634997 -0.728405326 1.789850444 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 173.07 2.24E-12 2568356000 3546910 737346 1303319 733156 2111932 2314476 2014799 1297217 1509921 528607 TRUE FALSE 3686944.746 863979.4397 1337284.564 878172.0685 1752946.553 1776974.025 1856873.79 1279829.928 1455579.238 632177.4209 5.832136081 1.366672411 2.115362744 1.389122799 2.772871183 2.810878666 2.937266863 2.024479024 2.302485331 1 19.26996998 4.74635228 24.78046141 2.168022059 5.832138093 0.757896271 0.634462349 412.4457116 1311699.871 0.149735404 1.614375821 55763.78964 -4.74635228 3.664116034 GNAEGS(ph)SDEEGKLVIDEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.835)S(0.165)DEEGKLVIDEPAK;GNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 187.95 1.65E-17 663930000 1017960 306910 496020 418410 655530 756500 970180 561830 574520 194356 TRUE FALSE 1058149.847 359619.4051 508946.6887 501170.2492 544103.2447 580814.3399 894134.7565 554299.5878 553843.1374 232436.337 4.552428679 1.547173775 2.189617575 2.156161363 2.340869985 2.498810415 3.846794214 2.384737236 2.38277347 1 17.8264761 0.722453208 2.268368093 1.001229715 2.641881975 0.268718073 0.831305301 1.810216775 12.79858232 0.759536125 0.205769284 5.277803397 -0.722453208 1.64065226 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK;GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK;GNAEGS(0.5)S(0.5)DEEGKLVIDEPAKEK 245.2 3.77E-31 2071960000 4413900 1019320 1930250 1008620 3014050 2966260 3166290 1840510 2378910 683790 TRUE FALSE 4588164.18 1194380.281 1980553.901 1208122.026 2501722.858 2277391.069 2918107.916 1815840.974 2293293.494 817765.5585 5.610610685 1.460541188 2.421909165 1.477345204 3.059217683 2.784894821 3.568391803 2.220490891 2.804341012 1 19.64132778 4.749265039 24.92164074 2.412899332 5.610612575 0.62353527 0.76551504 978.7479025 2278638.569 0.175871356 2.575341136 56139.04745 -4.749265039 3.197713243 GNAEGSS(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNAEGSSDEEGKLVIDEPAK 20 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.051)S(0.949)DEEGKLVIDEPAK;GNAEGS(0.076)S(0.924)DEEGKLVIDEPAK 260.8 1.44E-36 1577730000 2461250 677140 1147510 995780 1754810 1992580 2457770 1301040 1423090 497560 TRUE FALSE 2558422.05 793433.5276 1177415.053 1192742.312 1456528.023 1529833.493 2265123.565 1283601.687 1371873.269 595047.3556 4.299526796 1.333395603 1.978691346 2.004449395 2.447751442 2.570944108 3.806627395 2.157142074 2.305485867 1 19.18264496 3.011901372 23.21466126 2.532104619 2.288279837 0 0.964289237 632.1964094 1233131.63 0.268391465 0.3204726 1027.782863 -3.011901372 -0.243824782 GNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 GNAEGS(0.107)S(0.893)DEEGKLVIDEPAKEK;GNAEGS(0.134)S(0.866)DEEGKLVIDEPAKEK;GNAEGS(0.092)S(0.908)DEEGKLVIDEPAKEK 228.62 1.82E-26 2981040000 3872830 914469 1721951 984139 2735570 2643140 2788290 1735450 2130110 584480 TRUE FALSE 4025732.319 1071521.937 1766826.458 1178798.757 2270578.789 2029310.792 2569736.544 1712189.131 2053447.757 698997.6655 5.759292939 1.532940652 2.527657165 1.68641301 3.248335296 2.903172489 3.676316347 2.449491917 2.937703312 1 19.41492811 4.750056462 24.99148436 2.555584503 5.759294836 0.611002486 0.789678096 1172.576496 2549084.458 0.180820481 2.877789956 56241.44393 -4.750056462 3.203710333 GNAGQSNYGFANSAMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 420.87 4.74E-160 2295397000 386956 592923 537516 643437 564218 675648 518648 521488 501765 677640 FALSE TRUE 402233.3217 694752.9129 551524.1085 770706.9181 468312.4259 518738.9915 477995.0145 514498.3063 483706.5757 810410.5838 0.49633276 0.857285093 0.680548995 0.951007963 0.57787057 0.640094049 0.589818327 0.634861287 0.596866064 1 19.62829349 -0.996804232 4.723837843 1.000005953 0.673687297 0.370461112 0.129177759 7.87E-06 1.67E-06 0.121554688 0.028650193 0.100738567 0.996804232 -0.326318655 GNAMVEEGHFAAEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GNAMVEEGHFAAEDVK 16 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 216.29 1.53E-14 1192540000 1642390 1203520 1464500 1161784 1958650 1925320 1725520 1496340 1586260 1231260 FALSE TRUE 1707232.825 1410215.198 1502666.073 1391581.408 1625719.373 1478193.609 1590269.234 1476284.01 1529170.812 1472501.823 1.159409651 0.957700137 1.020485034 0.945045626 1.104052536 1.003865384 1.079977769 1.002568545 1.038484835 1 20.48983799 -0.975912769 8.652539512 1.000005446 1.030341814 0.023046028 0.06224434 0 0 0.054477358 0.012840436 0.10570298 0.975912769 0.030336367 GNAS(ph)PGAATHDSLSDYGPQDSRPTPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNASPGAATHDSLSDYGPQDSRPTPMR 27 1 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 GNAS(1)PGAATHDSLSDYGPQDSRPTPMR 227.88 6.76E-35 276430000 10544 53127 43915 61479 43753 64236 34007 46645 35245 71052 TRUE FALSE 10960.28526 62251.14898 45059.46098 73639.3627 36315.88069 49318.16251 31341.44248 46019.80007 33976.53933 84973.27903 0.128985081 0.732596761 0.530278006 0.866617877 0.427380008 0.580396132 0.368838802 0.541579666 0.399849691 1 16.37472162 -1.224717843 4.568708126 1.000137354 0.521501173 0.369336591 0.192002146 0.000249239 4.23E-05 0.172490137 0.040644736 0.059604926 1.224717843 -0.478636181 GNDPLTSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 GNDPLTS(0.001)S(0.999)PGR;GNDPLTSS(1)PGR;GNDPLTS(0.074)S(0.926)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLT(0.043)S(0.077)S(0.88)PGR;GNDPLT(0.001)S(0.024)S(0.975)PGR;GNDPLTS(0.001)S(0.999)PGR;GNDPLTSS(1)PGR 189.61 2.76E-06 16757660000 7342020 8452630 7864710 8465560 7951380 9547070 8176260 8274180 7263260 8484050 TRUE FALSE 7631888.619 9904303.45 8069670.804 10140022.5 6599807.268 7329907.68 7535383.377 8163278.151 7001856.691 10146337.16 0.752181649 0.976145706 0.795328469 0.999377641 0.65046205 0.722419092 0.742670311 0.804554197 0.69008713 1 23.27445567 3.235663935 24.99998841 0.758108577 0.881469603 0.191409034 0.111980815 108.042158 932465.8184 0.029338571 0.036558318 1720.536679 -3.235663935 0.123361026 GNDS(ph)DGEGESDDPEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNDSDGEGESDDPEKKK 17 2 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 GNDS(1)DGEGESDDPEKKK 122.34 2.99E-05 333980000 276440 74827 129250 71597 196920 272090 183370 116970 136940 50366 TRUE FALSE 287354.0647 87677.95518 132618.3612 85758.6729 163447.6087 208901.2211 168996.9803 115402.2085 132011.5561 60234.25338 4.77060889 1.455616203 2.201710052 1.423752567 2.713532576 3.4681466 2.805662406 1.915890079 2.191635967 1 15.87829652 0.875331311 1.157824648 1.023961392 2.575038496 0.218115633 0.933506883 1.023880984 2.703557999 0.862487662 0.26975105 7.504665 -0.875331311 1.551077104 GNDVAFHFNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GNDVAFHFNPR 11 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;;;;;;; 138.45 5.73E-05 11493152000 4815554 7171880 5303799 5784360 5570179 6858350 4932340 5246068 5023104 8473810 FALSE TRUE 5005675.79 8403594.601 5442020.359 6928489.143 4623361.963 5265602.152 4545730.303 5175753.039 4842323.468 10134090.83 0.49394424 0.829240111 0.53700134 0.683681374 0.456218722 0.51959295 0.448558275 0.510726924 0.47782515 1 23.27271333 -1.476308016 6.096623024 1.000287893 0.551271013 0.590588207 0.112212195 0.000442212 3.80E-05 0.109419223 0.025774246 0.03339581 1.476308016 -0.44901688 GNEFFCEVDEDYIQDKFNLTGLNEQVPHYR ddPTM_MDA-MB-175_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 ; 329.42 1.65E-105 665160000 489670 495479 503977 468364 608452 658052 510102 537341 527896 530395 FALSE TRUE 509002.5497 580573.664 517111.0546 561005.0013 505027.5464 505229.3959 470118.8723 530138.8228 508897.1261 634315.7452 0.802443505 0.915275505 0.815226578 0.88442547 0.796176904 0.79649512 0.741143312 0.83576488 0.802277304 1 19.27484163 3.229641266 24.99439365 0.81423613 0.855901092 0.006565424 0.070674783 506.7792979 1420128.818 0.018731658 0.022703587 1696.841456 -3.229641266 0.041664962 GNEPGSDRS(ph)PS(ph)PSKNDSFFTPDSNHNSLSQSTTGHLSLPQK ddPTM_MDA-MB-175_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(0.064)DRS(0.289)PS(0.569)PS(0.473)KNDS(0.284)FFT(0.271)PDS(0.022)NHNS(0.007)LS(0.003)QS(0.006)T(0.006)T(0.005)GHLSLPQK 60.88 0.018458 182880000 140950 102100 127080 92656 178440 217040 133110 160550 129830 94338 TRUE FALSE 146514.8148 119634.8808 130391.8092 110983.0802 148108.8325 166635.7493 122676.4904 158398.0899 125157.4437 112821.7249 1.298640089 1.060388687 1.155733165 0.983703098 1.31276873 1.476982819 1.087348119 1.403967986 1.109338151 1 16.78368537 3.212734273 24.99762544 1.263142849 1.122251086 0.080381412 0.157188587 393.715728 381081.0679 0.042827496 0.051204475 1632.053054 -3.212734273 -0.140891763 GNFGGSFAGSFGGAGGHAPGVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNFGGSFAGSFGGAGGHAPGVAR 23 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 243.04 2.27E-37 1639480000 343440 477850 373280 435400 415850 521940 363500 441990 436880 501470 FALSE TRUE 356999.2764 559917.0203 383007.9835 521520.8205 345163.9655 400727.3451 335007.9202 436065.847 421156.7741 599723.4453 0.59527317 0.933625365 0.638641004 0.869602188 0.575538556 0.668186892 0.558604008 0.727111555 0.702251642 1 19.19393785 -1.92719874 6.570924394 1.100194627 0.698549501 0.379868374 0.116293822 0.064840914 0.000718392 0.042772288 0.024914622 0.011825003 1.92719874 -0.401645125 GNFNYIEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;;;; 232.79 1.12E-10 7088990000 2914490 3699320 3140220 3120950 3805710 3797300 3322330 3094780 2905790 4088110 FALSE TRUE 3029556.316 4334649.433 3222056.713 3738264.595 3158816.774 2915434.624 3061917.093 3053299.536 2801211.186 4889096.883 0.619655611 0.886595119 0.659029017 0.764612501 0.646094125 0.596313531 0.626274579 0.624511972 0.572950639 1 22.22113656 -1.116897599 4.410192548 1.000041234 0.667817983 0.562974812 0.088213018 3.74E-05 7.48E-06 0.086897848 0.020479413 0.076401591 1.116897599 -0.332223251 GNFTLPEVAECFDEITYVELQKEEAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GNFTLPEVAECFDEITYVELQKEEAQK 27 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;; 225.84 1.44E-34 333295000 487336 276111 380654 241611 559550 483993 418278 371019 455736 283721 FALSE TRUE 506576.4016 323530.9164 390574.156 289400.9347 464437.8909 371592.9607 385492.2774 366046.0972 439334.1504 339310.6978 1.492957354 0.953494595 1.151081173 0.852908371 1.368768783 1.095140717 1.136104107 1.07879327 1.294784259 1 18.37224739 -4.220062981 0.012147847 2.40E-06 2.069860284 0.04339487 0.181276045 38387.21182 40.18168257 4018.4141 2909.377675 6.02E-05 4.220062981 2.069857889 GNHECASINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 126.03 0.0003935 437340000 392370 542130 455610 480050 528280 644250 426600 467460 396760 594280 FALSE TRUE 407861.0706 635236.6103 467483.5709 575002.4572 438483.1543 494632.7012 393161.9773 461194.4633 382480.6851 710717.7878 0.573872045 0.893795851 0.657762587 0.809044697 0.616958182 0.69596218 0.553190006 0.648913635 0.538161126 1 19.43891728 -1.089513938 4.578441985 1.000021109 0.669127042 0.469664783 0.106629946 2.36E-05 4.70E-06 0.099926592 0.023551328 0.081374075 1.089513938 -0.330894067 GNICIPYEEDIPSLGLSEVSDT(ph)KEDENGSPLNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNICIPYEEDIPSLGLSEVSDTKEDENGSPLNHR 34 1 O15055 O15055 PER2 Period circadian protein homolog 2 1 GNICIPYEEDIPSLGLS(0.007)EVS(0.03)DT(0.589)KEDENGS(0.375)PLNHR 75.758 0.0040312 84936000 88032 54357 62197 56699 86416 91711 69142 63688 65964 45180 TRUE FALSE 91507.57134 63692.39191 63817.90492 67913.89297 71727.03919 70412.51014 63722.46937 62834.36653 63589.96853 54032.15598 1.693576162 1.178786794 1.181109726 1.256916215 1.32748801 1.303159366 1.179343452 1.162906891 1.176891193 1 15.72153063 4.74059358 24.9869989 1.207198837 1.693576329 0.749000828 0.086154065 89.48066044 1099721.892 0.020360374 0.134002417 55029.2483 -4.74059358 0.486377492 GNICIPYEEDIPSLGLSEVSDTKEDENGS(ph)PLNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNICIPYEEDIPSLGLSEVSDTKEDENGSPLNHR 34 1 O15055 O15055 PER2 Period circadian protein homolog 2 1 GNICIPYEEDIPSLGLSEVS(0.001)DT(0.377)KEDENGS(0.621)PLNHR 82.033 0.00062064 85907000 95707 64949 71789 51093 90382 95780 82629 73685 76152 47716 TRUE FALSE 99485.58626 76103.48552 73659.88032 61199.0429 75018.89992 73536.54656 76152.32307 72697.3731 73411.3044 57065.03662 1.743371987 1.333627209 1.290805801 1.072443768 1.314621077 1.288644517 1.334483032 1.273938955 1.28644979 1 15.80031947 4.786072701 2.331900616 1.248426486 1.901524645 0.678445619 0.104804595 0.391473005 2.280879911 0.024837032 0.544237071 61104.43057 -4.786072701 0.653098159 GNIETTS(ph)EDGQVFSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 GNIETT(0.01)S(0.989)EDGQVFSPK 209.19 1.35E-11 93333000 422410 334910 384140 323870 451170 459750 419610 425200 406910 337120 TRUE FALSE 439087.073 392428.1873 394151.004 387930.5193 374480.2846 352980.0301 386719.8718 419500.8895 392265.3886 403172.2094 1.089080702 0.973351283 0.977624436 0.962195584 0.928834567 0.875506847 0.959192778 1.04050051 0.972947488 1 18.62103667 -0.569892097 6.39835549 1 0.974868215 0.017763291 0.054556182 0 2.18E-18 0.055443665 0.013068197 0.269220361 0.569892097 -0.025131785 GNIETTSEDGQVFS(ph)PK ddPTM_MDA-MB-175_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 282.47 1.47E-35 375050000 664090 320550 383367 291432 527227 534288 473847 434629 411898 278912 TRUE FALSE 690308.786 375601.969 393357.859 349076.3798 437609.1429 410207.7092 436705.634 428803.5092 397073.8714 333559.4663 2.069522396 1.126042001 1.179273559 1.046519182 1.311937412 1.22978884 1.309228723 1.28553842 1.190414039 1 18.34758446 4.741758796 24.99040916 1.205336304 2.069522716 0.870666562 0.10186421 101.0368284 789459.3653 0.024249774 0.174346135 55177.09049 -4.741758796 0.864186412 GNIIISTPEKWDILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNIIISTPEKWDILSR 16 1 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 89.484 0.0052664 388880000 148210 185020 244060 188810 222320 263900 228470 197090 181650 222430 FALSE TRUE 154061.4452 216795.7457 250420.4041 226156.0545 184530.1258 202613.2244 210561.9244 194448.3309 175112.452 266010.8998 0.579154634 0.814988205 0.941391515 0.850175894 0.693693852 0.76167264 0.791553747 0.73097881 0.658290514 1 18.02112584 -1.162072482 4.740844368 1.00002503 0.765066644 0.357903766 0.096829627 2.59E-05 4.59E-06 0.094941284 0.022375493 0.068853737 1.162072482 -0.234958386 GNIYYQSYEHRS(ph)PS(ph)PNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GNIYYQSYEHRSPSPNIR 18 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 2 GNIY(0.002)Y(0.003)QS(0.107)Y(0.013)EHRS(0.88)PS(0.994)PNIR;GNIYYQS(0.001)YEHRS(0.999)PS(1)PNIR;GNIYYQSY(0.002)EHRS(0.998)PS(1)PNIR;GNIYYQSYEHRS(1)PS(1)PNIR 190.24 3.80E-14 914100000 447030 592030 543840 547100 585930 658470 514740 576430 555770 659160 TRUE FALSE 464679.0896 693706.5471 558012.9172 655314.7471 486333.8279 505550.3217 474393.3338 568703.8987 535767.9463 788309.7816 0.589462544 0.879992312 0.707859943 0.831290899 0.616932378 0.641309208 0.601785421 0.721421847 0.679641378 1 19.58840315 -1.894510487 6.602960067 1.060376989 0.699797369 0.499912637 0.090976503 0.051496844 0.000822718 0.056098951 0.020271666 0.012749393 1.894510487 -0.360579621 GNKHDDGTQS(ph)DSENAGAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GNKHDDGTQSDSENAGAHR 19 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGTQS(1)DSENAGAHR;GNKHDDGT(0.001)QS(0.999)DSENAGAHR;GNKHDDGT(0.001)QS(0.999)DSENAGAHR 288.82 1.77E-41 862794000 352348 287466 333855 329978 395916 395475 415205 331827 365900 258916 TRUE FALSE 366258.9711 336836.0493 342555.5356 395246.6635 328618.3397 303631.9247 382660.1472 327379.4018 352731.3305 309645.633 1.182832671 1.087811399 1.10628247 1.27644837 1.061272322 0.98057874 1.235800239 1.057271174 1.139145181 1 18.24025857 GNKHDDGTQS(ph)DSENAGAHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNKHDDGTQSDSENAGAHRR 20 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 GNKHDDGT(0.006)QS(0.958)DS(0.036)ENAGAHRR 45.844 0.083719 71142000 3616.2 23849 10222 21405 10709 19403 10716 15026 8747.3 23518 TRUE FALSE 3758.970368 27944.88023 10488.39372 25638.84511 8888.688005 14896.94731 9876.051919 14824.60105 8432.486382 28125.90182 0.133647994 0.993563883 0.372908708 0.911574152 0.316032107 0.529652254 0.351137254 0.527080025 0.299812125 1 14.77961173 -1.012336704 4.630200731 1.000013159 0.507621182 0.257297429 0.25740317 29872730.73 6531306.923 3995.349835 0.054297924 0.097199336 1.012336704 -0.492391977 GNKPWISLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNKPWISLPR 10 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 158.41 7.29E-06 5013800000 3655000 4556600 3684900 3560100 7621900 6166500 5424200 4691100 4671100 8762300 FALSE TRUE 3799302.222 5339160.605 3780931.521 4264277.154 6326332.16 4734423.829 4999037.03 4628223.478 4502988.023 10479104.92 0.362559804 0.509505406 0.360806724 0.40693143 0.603709211 0.451796586 0.477048094 0.441662099 0.429711131 1 23.32101216 -1.962545177 2.624176467 1.436745077 0.452324116 0.855957174 0.067762296 21294825.56 11208494.19 56618900.63 0.015992851 0.010900711 1.962545177 -0.984420961 GNLELRPGGAHPGT(ph)CSPSRPGS ddPTM_MDA-MB-175_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(0.491)CS(0.491)PS(0.017)RPGS(0.001);GNLELRPGGAHPGT(0.496)CS(0.496)PS(0.006)RPGS(0.001) 97.839 0.0020118 385700000 140710 179200 154241 172661 162483 197677 160854 161803 161086 183865 TRUE FALSE 146265.3395 209976.206 158260.6472 206812.8305 134864.1977 151769.5126 148245.8432 159634.2954 155288.5463 219889.8264 0.665175565 0.954915511 0.719727009 0.940529327 0.613326227 0.690207069 0.674182365 0.725973994 0.706210691 1 17.74642133 5.044546589 16.30816141 0.76348088 0.141625012 0.053228358 0.12900597 39399936 377109223.1 0.029337698 754368095.2 110801.7421 -5.044546589 -0.621855867 GNLELRPGGAHPGTCS(ph)PSRPGS ddPTM_MDA-MB-175_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(0.003)CS(0.793)PS(0.204)RPGS;GNLELRPGGAHPGT(0.189)CS(0.621)PS(0.189)RPGS(0.001) 94.96 0.0008815 442845000 249576 307147 283486 326164 295060 325655 282922 298528 272158 312471 TRUE FALSE 259429.4532 359897.108 290873.878 390678.2657 244905.8066 250026.5616 260745.8344 294526.7205 262363.0867 373693.7098 0.694230185 0.963080455 0.778375098 1.045450473 0.655365076 0.669068157 0.697752805 0.788150062 0.702080554 1 18.51149675 5.049434911 15.07147655 0.797793344 0.118531168 0.054391938 0.136395201 3503303.666 29914798.09 0.032040825 68032609.42 112055.9471 -5.049434911 -0.679262176 GNLLHFPSS(ph)QGEEEKEKLEGDHTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNLLHFPSSQGEEEKEKLEGDHTIR 25 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GNLLHFPS(0.174)S(0.826)QGEEEKEKLEGDHTIR 107.45 0.0017195 141310000 258750 96008 148200 80710 237240 229740 180910 150280 173640 94335 TRUE FALSE 268965.6498 112496.6272 152062.2137 96674.1971 196914.0295 176386.3667 166729.8015 148265.7424 167390.7303 112818.1371 2.384063917 0.997150193 1.34785255 0.856902973 1.745411107 1.563457537 1.477863451 1.3142013 1.483721808 1 16.78363949 -2.878924965 0.406092103 6.15E-15 1.442315729 0.107037784 0.3955217 277.0214474 9.845634751 240.106051 0.228377775 0.001321524 2.878924965 1.442315729 GNLQNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNLQNLER 8 0 P21283;E7EV59 P21283 ATP6V1C1 V-type proton ATPase subunit C 1 0 94.806 0.023493 56454000 67923 101130 91474 96686 100270 125090 93097 84725 91763 123500 FALSE TRUE 70604.65249 118498.2908 93857.88759 115810.2022 83226.14122 96039.74326 85799.81388 83589.39996 88460.46755 147697.4604 0.478035657 0.802304186 0.635473943 0.784104221 0.563490672 0.650246409 0.580915973 0.56595015 0.598930187 1 17.17228549 -1.910465665 2.865244953 1.204639079 0.630561749 0.582404939 0.094278856 24452901.07 13228437.82 33520188.61 0.022607344 0.012289503 1.910465665 -0.57407733 GNPS(ph)PPAAGEGQRPPPPLCVPGGGGGAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GNPSPPAAGEGQRPPPPLCVPGGGGGAPAR 30 1 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 1 GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR;GNPS(1)PPAAGEGQRPPPPLCVPGGGGGAPAR 241.46 7.58E-46 5904830000 231680 177398 212028 158403 195653 243054 187880 167195 179299 185336 TRUE FALSE 240826.9053 207864.7265 217553.6239 189734.6406 162395.9729 186608.392 173153.4747 164954.0245 172846.064 221649.0407 1.086523562 0.937810179 0.981522966 0.856013814 0.732671671 0.841909315 0.781205613 0.74421267 0.779818687 1 17.75791759 3.703877926 2.301984035 0.795205522 1.007140628 0.52681099 0.079130247 0.208650986 2.159844663 0.020875656 0.039992954 5056.825022 -3.703877926 0.211935106 GNPTVEVDLFTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNPTVEVDLFTSK 13 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879;K7ERS8;A0A2R8YEG5;A0A2R8Y798 P06733 ENO1 Alpha-enolase;Enolase 0 114.72 0.0016767 97678000 130010 137410 137900 123550 194940 173310 145950 125960 144530 158030 FALSE TRUE 135142.8952 161009.0986 141493.7873 147987.8212 161804.1684 133061.379 134510.0576 124271.7122 139328.3935 188992.9528 0.715068436 0.851931758 0.748672293 0.783033542 0.856138634 0.704054712 0.711719964 0.657546805 0.737214756 1 17.52797291 2.712720027 24.72038783 0.73016976 0.791565105 0 0.097330712 1656.326774 1584522.837 0.029357267 0.027687978 516.0835633 -2.712720027 0.061395345 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(1)GGGGGGGGQGSTNYGK 173.11 2.87E-12 360209000 247073 223877 251802 191063 268242 301313 226362 240885 250994 266494 TRUE FALSE 256827.6328 262326.1332 258364.167 228854.6911 222646.3207 231337.6222 208619.155 237656.3306 241960.775 318708.397 0.805838928 0.823091377 0.810660056 0.718069224 0.69858944 0.725859828 0.654576901 0.745685815 0.759191717 1 18.2818775 0.665507427 3.603375547 0.99999848 0.74477346 0.689463304 0.050541423 4.347794052 46.19258479 0.054071829 0.013909927 4.6292158 -0.665507427 -0.255225021 GNS(ph)PPSSGEACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GNSPPSSGEACR 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(1)PPSSGEACR;GNS(0.966)PPS(0.017)S(0.017)GEACR;GNS(0.946)PPS(0.027)S(0.027)GEACR;GNS(0.749)PPS(0.125)S(0.125)GEACR;GNS(0.996)PPS(0.002)S(0.002)GEACR 138.01 8.60E-05 2162380000 470437 581144 514188 590314 521537 699678 585941 546116 505198 505987 TRUE FALSE 489010.216 680950.9613 527588.1617 707076.3473 432886.327 537188.3882 540013.4133 538796.2083 487016.0227 605125.4649 0.808113762 1.125305413 0.871865741 1.168478916 0.715366237 0.887730594 0.892399089 0.890387596 0.804818258 1 19.20687477 3.231785943 24.99999646 0.864745647 0.994175904 0.216153405 0.119710171 228.4800115 843139.4571 0.031497816 0.038448709 1705.241696 -3.231785943 0.129430257 GNS(ph)PPSSGEACREEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GNSPPSSGEACREEK 15 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 GNS(0.993)PPS(0.003)S(0.003)GEACREEK;GNS(0.996)PPS(0.003)S(0.001)GEACREEK;GNS(0.999)PPSSGEACREEK 134.32 2.17E-05 1896580000 1659800 1342000 1555450 1069000 2163160 2114260 1331750 1521540 1799920 1608780 TRUE FALSE 1725330.186 1572478.061 1595986.305 1280445.009 1795466.836 1623255.157 1227363.955 1501146.245 1735141.231 1923989.639 0.89674609 0.817300691 0.829519178 0.665515543 0.933199847 0.843692255 0.637926489 0.780225743 0.901845413 1 20.8756696 1.022897942 3.780515729 0.998736612 0.795232089 0.350343218 0.086786771 0.204519707 7.015703539 0.083416425 0.021479216 10.54139147 -1.022897942 -0.203504523 GNS(ph)RPGTPS(ph)AEGGSTSSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.983)RPGT(0.021)PS(0.963)AEGGS(0.024)T(0.005)S(0.003)S(0.001)T(0.001)LR 113.17 0.0017074 467350000 383220 430390 392120 465120 389860 494460 479890 415350 377930 384460 TRUE FALSE 398349.8215 504306.1345 402338.9693 557119.3478 323591.7365 379629.1586 442274.9678 409782.9126 364328.3731 459787.5761 0.866377959 1.096824187 0.875054026 1.211688564 0.703785298 0.825662063 0.961911524 0.891243987 0.792384118 1 18.81060796 3.228087592 24.99969861 0.864618237 1.008693774 0.266734119 0.121734579 283.8641834 677598.7241 0.033325854 0.040238493 1690.781907 -3.228087592 0.144075536 GNSRPGT(ph)PS(ph)AEGGSTSSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 GNS(0.492)RPGT(0.51)PS(0.859)AEGGS(0.111)T(0.014)S(0.01)S(0.002)T(0.002)LR 146.97 3.19E-06 356270000 297540 334580 312410 342610 289600 362010 349500 308520 265660 251730 TRUE FALSE 309287.109 392041.5123 320551.6612 410377.2354 240373.8954 277938.6638 322105.2768 304384.794 256098.9485 301051.6738 1.027355553 1.302239936 1.064772892 1.363145503 0.798447298 0.923225771 1.069933519 1.011071588 0.850681032 1 18.19965161 3.235906502 24.99999997 0.955267405 1.188539596 0.510598988 0.118124766 58.4055608 550143.4795 0.032574097 0.04065116 1721.497921 -3.235906502 0.233272191 GNSRPGT(ph)PSAEGGSTSSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 GNSRPGT(0.996)PS(0.004)AEGGSTSSTLR;GNSRPGT(0.999)PS(0.001)AEGGSTSSTLR;GNSRPGT(0.954)PS(0.046)AEGGSTSSTLR 191.53 2.31E-17 1667960000 382800 497560 479890 547540 518230 629940 645600 611240 577940 599470 TRUE FALSE 397913.2396 583012.0595 492396.3276 655841.7778 430141.4497 483645.9818 594996.185 603047.3276 557140.0523 716924.669 0.555027964 0.81321244 0.686817387 0.914798732 0.599981376 0.674611996 0.829928458 0.841158568 0.777124957 1 19.45146201 -4.999999864 0.10948737 1.843308021 0.599679365 0.427102358 0.100291925 164.1979717 1.197470681 30.70778852 1.244618425 1.00E-05 4.999999864 -1.243628656 GNVAGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNVAGDSK 8 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 87.476 0.035587 30434000 148820 97463 120790 115970 157800 150630 187750 142300 157010 93429 FALSE TRUE 154695.5285 114201.5121 123937.8866 138908.5199 130977.2124 115648.4653 173033.6644 140392.7013 151359.2408 111734.6237 1.384490531 1.022078101 1.109216485 1.243200319 1.172216883 1.035028011 1.548612763 1.256483412 1.354631498 1 16.76971678 2.27002963 24.99999859 1.313907657 1.156609281 0.128785395 0.15917881 312.5377462 248288.9658 0.051439829 0.04303395 186.2214183 -2.27002963 -0.157298377 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 49 1 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 252.24 2.39E-73 1537100000 305750 219020 328880 219140 407150 352680 333820 324590 356550 261590 FALSE TRUE 317821.2461 256634.9813 337450.883 262485.2379 337942.7884 270775.4149 307654.3161 320239.402 343717.8351 312843.5521 1.015911129 0.820330097 1.078656986 0.839030359 1.080229355 0.865529793 0.983412681 1.02364073 1.09868921 1 18.25508184 1.732035957 2.975804758 1.050565303 0.949751151 0.169360637 0.089269848 0.357239121 6.726129066 0.047593364 0.022040846 53.95552926 -1.732035957 -0.100814152 GNVGFVFTKEDLTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNVGFVFTKEDLTEIR 16 1 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;F8VWV4;F8VPE8;F8VZS0;F8VS58 F8VWS0 RPLP0 60S acidic ribosomal protein P0 0 ; 208.43 1.36E-11 506782000 525673 660156 595695 460087 833190 859850 563739 601425 742350 793540 FALSE TRUE 546426.9759 773532.6577 611219.3011 551090.8354 691564.6614 660162.8687 519551.6641 593363.8816 715632.9685 949018.9698 0.575780878 0.815086613 0.644053829 0.580695279 0.728715319 0.695626631 0.547461832 0.625239221 0.754076569 1 19.8560774 0.900120165 3.695862668 0.999821078 0.652690916 0.660913559 0.075600356 0.258965542 7.69074002 0.072151749 0.018552666 7.945480488 -0.900120165 -0.347130162 GNVGFVFTKEDLTEIRDMLLANKVPAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNVGFVFTKEDLTEIRDMLLANKVPAAAR 29 3 F8VWS0;P05388;P05388-2;F8VU65;F8VW21;F8VQY6;F8VRK7;G3V210;F8VWV4;F8VPE8 F8VWS0 RPLP0 60S acidic ribosomal protein P0 0 108.63 0.00017741 93019000 109390 126920 150250 74442 227670 165040 78924 115680 132840 239650 FALSE TRUE 113708.8017 148717.5227 154165.6384 89166.40541 188970.7347 126711.9612 72737.73065 114129.4988 128059.1143 286604.8291 0.396744193 0.518893988 0.537903143 0.311112711 0.659342466 0.442113839 0.253791016 0.398212058 0.446814224 1 18.12870339 0.909533435 19.19190891 1 0.436668754 0.70315534 0.109043155 3443.261783 730469.4666 0.106194437 0.026550759 8.11957757 -0.909533435 -0.563331246 GNVLQPEESLLDPFGAKPFHS(ph)PDLSWHPPHQGLSDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIR 37 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 GNVLQPEESLLDPFGAKPFHS(0.843)PDLS(0.151)WHPPHQGLS(0.005)DIR 135.22 2.77E-09 221610000 84028 158370 160160 154630 184590 205350 164990 192490 172500 144460 TRUE FALSE 87345.49032 185568.8156 164333.9012 185215.3525 153213.4577 157660.5746 152057.6527 189909.9864 166291.7587 172764.1711 0.505576415 1.074116319 0.951203598 1.072070391 0.886835834 0.912576801 0.88014576 1.099244045 0.962536142 1 17.39844453 4.745315711 24.98982904 0.982564768 0.505576197 0.784157999 0.074998445 355.780458 1316142.182 0.018088117 0.178465271 55630.852 -4.745315711 -0.476988571 GNVS(ph)S(ph)YIR ddPTM_MDA-MB-175_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 70.028 0.076593 92949000 124720 144090 137620 162370 146650 163150 188230 150610 157660 127790 TRUE FALSE 129644.0419 168836.3366 141206.4903 194486.3014 121722.4854 125260.8851 173476.0408 148591.3193 151985.8474 152828.0038 0.848300303 1.104747379 0.923956911 1.272582881 0.796467155 0.819619978 1.135106371 0.972278088 0.994489515 1 17.2215494 GNVVPS(ph)PLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GNVVPSPLPTR 11 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 GNVVPS(0.996)PLPT(0.004)R;GNVVPS(0.997)PLPT(0.003)R;GNVVPS(0.946)PLPT(0.054)R;GNVVPS(1)PLPTR;GNVVPS(0.998)PLPT(0.002)R;GNVVPS(0.999)PLPT(0.001)R;GNVVPS(1)PLPTR;GNVVPS(0.995)PLPT(0.005)R 144.2 3.86E-05 31607070000 9581210 9626800 9076790 11814070 8442760 10589150 12479120 9782650 8469570 7242740 TRUE FALSE 9959483.569 11280128.01 9313338.604 14150857.78 7007662.671 8129980.393 11500973.97 9651529.578 8164751.83 8661816.232 1.149814693 1.302282075 1.075217755 1.633705611 0.809029248 0.938599963 1.32777857 1.114261642 0.942614298 1 23.04623813 2.68505606 0.38529629 1.007616246 1.272252615 0.116261711 0.21392062 3.829418944 1.167103205 0.23178899 0.384361955 484.2348698 -2.68505606 0.264636369 GNVVPS(ph)PLPTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.999)PLPT(0.001)RR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR;GNVVPS(1)PLPTRR 110.38 0.00091613 34030570000 3433160 4036930 3576180 3833920 3849720 4153880 3531200 3559280 3278960 3906930 TRUE FALSE 3568703.808 4730241.325 3669378.189 4592257.933 3195345.969 3189204.323 3254415.317 3511573.673 3160950.87 4672418.131 0.763780918 1.012375432 0.785327444 0.982843959 0.683874148 0.682559701 0.696516285 0.751553815 0.676512842 1 22.15573795 3.227603915 24.99643057 0.730875856 0.887906161 0.248118002 0.114878289 239.5735957 546558.2921 0.030066034 0.036260304 1688.899921 -3.227603915 0.157030305 GNWDEQFDKENTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNWDEQFDKENTEER 15 1 A0A2R8YD12;A0A024QZX5;A0A087X1N8;P35237;A0A2R8Y6A7 A0A2R8YD12 SERPINB6 Serpin B6 0 ; 157.91 1.70E-06 713000000 435060 333540 420780 346780 517600 471550 479390 390130 466940 338290 FALSE TRUE 452236.5047 390822.9004 431745.8725 415372.049 429618.5369 362039.6589 441814.1591 384900.9455 450134.9206 404571.4485 1.117816164 0.966017008 1.067168417 1.026696398 1.061910173 0.894871994 1.092054718 0.951379409 1.112621571 1 18.62603498 4.759470312 23.31453273 1.017215787 1.117816416 0.173600433 0.064425149 3347.916163 3732809.006 0.013900551 0.560318846 57473.85293 -4.759470312 0.100600629 GNWEQPQNQNQTQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 222.45 1.40E-12 145130000 138840 105190 128400 111420 126320 128690 128670 137270 130180 104450 FALSE TRUE 144321.5104 123255.5642 131746.2095 133458.5434 104848.1715 98803.69782 118584.5092 135430.1202 125494.8472 124914.9777 1.155357933 0.986715657 1.054687051 1.068395047 0.839356284 0.790967582 0.949321782 1.084178396 1.004642114 1 16.93058695 GNYAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 135.87 0.031211 14937970000 9281900 11458990 9938300 9534760 10955200 10812960 10140940 9890250 8631920 11768870 FALSE TRUE 9648356.579 13426982.39 10197300.26 11420707.07 9093039.017 8301813.912 9346066.624 9757687.376 8321258.885 14074754.75 0.685507972 0.953976295 0.724509979 0.811432048 0.646053106 0.589837199 0.664030514 0.693275837 0.591218748 1 23.74660645 3.243895624 24.90129159 0.676014486 0.800340391 0.106093169 0.127900927 204.5795615 954874.0202 0.032815751 0.043159564 1753.459034 -3.243895624 0.124325905 GNYDEGFGHRPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GNYDEGFGHRPHK 13 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 164.81 2.19E-05 390830000 408250 383660 386510 369020 530710 535750 459630 439510 453280 422760 FALSE TRUE 424368.0252 449550.6205 396582.7681 442011.0546 440500.1038 411330.1819 423602.9996 433619.0873 436966.5413 505591.7278 0.839349226 0.889157389 0.784393309 0.874245029 0.871256549 0.81356193 0.837836096 0.857646721 0.864267585 1 18.94761333 0.410948387 1.31669271 1.000069295 0.845305708 0.717538923 0.028863074 1.529003472 2.922770508 0.026235965 0.007759559 2.576014996 -0.410948387 -0.154763587 GNYSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 138.37 0.053807 0 307670 418250 373810 368540 413320 423660 359990 420310 367920 460760 FALSE TRUE 319817.0492 490081.184 383551.7957 441436.112 343064.014 325271.3856 331773.0431 414676.4319 354678.6311 551037.1002 0.580391137 0.889379651 0.696054395 0.801100528 0.622578795 0.590289448 0.602088395 0.752538135 0.643656536 1 19.07178993 -1.550615107 5.145615247 1.00149951 0.692169773 0.487787348 0.096230054 0.001632116 0.000142538 0.091864633 0.021554577 0.02814394 1.550615107 -0.309329738 GPAAEEALNVFYYCTYEGAVDLDHVTDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPAAEEALNVFYYCTYEGAVDLDHVTDER 29 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 0 ;; 118.75 6.49E-07 94512000 28305.1 40911 34218.7 42449 38137 47601 39501 41747 34683.5 40193 FALSE TRUE 29422.6072 47937.14601 35110.46743 50845.2855 31654.48636 36546.38915 36404.8084 41187.44975 33435.24761 48068.04881 0.612103215 0.997276719 0.730432549 1.057777188 0.658534872 0.760305235 0.757359812 0.856857118 0.695581544 1 15.55279062 -1.433810785 3.030893025 1.003803437 0.801699828 0.172174171 0.135399781 34006456.36 40409996.19 1105410.823 0.030007736 0.03682894 1.433810785 -0.202103609 GPAGEAGAS(ph)PPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPAGEAGASPPVR 13 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR 110.25 0.0011257 826690000 727590 840570 783240 846350 811020 995780 815170 772930 704540 786400 TRUE FALSE 756315.815 984931.3588 803651.8778 1013755.504 673163.1101 764525.1862 751274.8453 762570.1376 679183.743 940480.0235 0.804180627 1.047264518 0.854512438 1.077912852 0.715765453 0.812909543 0.798820631 0.810830766 0.722167113 1 19.84303777 3.227180331 24.99997222 0.80089537 0.946670609 0.285793254 0.104630545 239.311459 525713.6645 0.027357018 0.032969465 1687.253472 -3.227180331 0.14577524 GPAGEAGAS(ph)PPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 161.91 2.77E-06 4646550000 1311509 1720100 1512527 1608408 1583319 1868140 1449268 1547317 1563597 1736580 TRUE FALSE 1363288.388 2015513.794 1551944.696 1926546.302 1314187.002 1434292.797 1335670.587 1526577.747 1507323.449 2076829.602 0.656427656 0.970476245 0.747266263 0.927638117 0.632785184 0.690616503 0.643129598 0.735051997 0.725780992 1 20.98595142 5.039743976 16.57775391 0.767938214 0.148172821 0.069371348 0.12786189 64090986.86 707257931 0.029654758 1210578660 109583.1995 -5.039743976 -0.619765393 GPAGNNDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPAGNNDCR 9 0 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;; 95.741 0.018238 204426000 351564 411620 365480 397680 395650 432420 374707 391890 370297 464130 FALSE TRUE 365444.0182 482312.533 375004.709 476339.917 328397.5543 331997.0084 345336.4862 386637.3556 356970.0833 555067.3872 0.658377751 0.868926087 0.67560213 0.858165924 0.59163547 0.598120185 0.622152362 0.696559309 0.643111254 1 19.0823034 -1.096556793 3.814400028 1.000108178 0.691806334 0.499483291 0.092996635 27458337.14 47717462.28 37501.91148 0.022605634 0.080065092 1.096556793 -0.308301844 GPALTPIRDEEWGGHS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPALTPIRDEEWGGHSPR 18 1 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR;GPALTPIRDEEWGGHS(1)PR 188.73 2.19E-14 658864000 448280 743180 493064 788930 575419 835030 569882 564037 448868 796600 TRUE FALSE 465978.4405 870815.3839 505913.6529 944977.9993 477609.4839 641106.9375 525213.1597 556477.0066 432713.3284 952678.5182 0.489124539 0.914070557 0.531043414 0.991916981 0.501333319 0.672952025 0.551301567 0.584118353 0.45420708 1 19.86162993 -1.063419134 4.620472446 1.000017031 0.638021334 0.288697613 0.172967375 0.661156507 99350084.95 3648.966259 0.037760329 0.086413355 1.063419134 -0.361995697 GPAPAPQQCS(ph)EPETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPAPAPQQCSEPETK 15 0 Q3YEC7;Q3YEC7-2;G3V154 Q3YEC7 RABL6 Rab-like protein 6 1 GPAPAPQQCS(0.905)EPET(0.095)K 198.89 1.56E-11 0 189670 136450 145620 118330 169030 208390 174980 160600 169590 116140 TRUE FALSE 197158.3181 159884.2261 149414.9768 141735.3208 140298.341 159994.5807 161264.6104 158447.4197 163486.489 138895.4094 1.419473249 1.151112386 1.07573733 1.020446403 1.010100633 1.151906902 1.161050686 1.140767866 1.177047462 1 17.08363939 4.730628299 3.209323433 1.0998603 1.462708591 0.708727534 0.062528091 0.192149351 3.160254924 0.016408889 0.17267817 53780.92891 -4.730628299 0.362848291 GPAS(ph)DS(ph)ETEDASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPASDSETEDASR 13 0 Q96ST2;Q96ST2-3 Q96ST2 IWS1 Protein IWS1 homolog 2 GPAS(1)DS(0.915)ET(0.085)EDASR 121.42 0.00036094 104620000 110890 116280 105960 133560 111140 144840 144560 122330 114020 105210 TRUE FALSE 115268.0228 136250.1855 108721.4046 159977.7694 92248.4625 111203.1051 133229.0095 120690.3664 109916.4425 125823.8851 0.916106053 1.082864238 0.864076042 1.271441978 0.733155413 0.883799645 1.058853089 0.959200762 0.873573744 1 16.94104629 3.217776033 24.99978003 0.927083256 1.025029219 0.156925927 0.129572718 517.804556 622815.7006 0.036422943 0.043576937 1651.110097 -3.217776033 0.097945963 GPASQFYITPSTSLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPASQFYITPSTSLSPR 17 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 1 GPASQFYITPSTSLS(1)PR;GPASQFYITPSTSLS(1)PR;GPASQFYITPST(0.002)S(0.013)LS(0.986)PR;GPASQFYITPS(0.002)T(0.005)S(0.082)LS(0.912)PR 260.09 3.29E-27 1184420000 923000 1080190 962980 1050050 1036040 1123690 977860 1005700 960680 1110760 TRUE FALSE 959440.7527 1265704.23 988076.0499 1257746.756 859934.2909 862730.0272 901212.778 992220.2365 926105.3145 1328392.155 0.722257166 0.952809172 0.743813524 0.946818867 0.647349721 0.649454323 0.678423743 0.746933225 0.697162589 1 20.34124968 3.228851703 24.99293652 0.717836089 0.842408501 0.148442716 0.11804043 294.8529539 759016.8308 0.031207848 0.037741613 1693.75934 -3.228851703 0.124572413 GPASTPTYS(ph)PAPTQPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 GPAST(0.019)PT(0.127)YS(0.853)PAPTQPAPR;GPAST(0.003)PT(0.132)YS(0.865)PAPTQPAPR 305.9 4.13E-50 418980000 230570 274480 247520 283390 241730 297200 249260 259990 251370 306080 TRUE FALSE 239673.0816 321619.8048 253970.5745 339443.6962 200640.8209 228179.8041 229722.3499 256505.2593 242323.2428 366050.5157 0.654754115 0.878621368 0.693812913 0.927313804 0.548123312 0.623356051 0.627570076 0.700737325 0.661993994 1 18.48168323 -1.190917343 3.320768233 1.000585315 0.703146521 0.39748349 0.110127737 16595224.99 24891954.84 105757.9099 0.026064746 0.064429188 1.190917343 -0.297438794 GPAVGIDLGTTYSCVGVFQHGK ddPTM_MDA-MB-175_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 ;; 310.55 3.50E-67 2497380000 2699580 2627740 2738080 2564340 3217720 3438340 3055010 3057640 2954430 2569040 FALSE TRUE 2806161.503 3079033.904 2809436.614 3071558.798 2670773.104 2639837.644 2815550.333 3016657.337 2848100.641 3072394.201 0.91334683 1.002161084 0.91441281 0.999728094 0.86928074 0.859211895 0.916402698 0.981858818 0.926997141 1 21.5509319 1.746197678 19.42491097 0.965772438 0.925708735 0.157132027 0.047149369 0.801313593 2051.976923 0.022660844 0.012552105 55.74394206 -1.746197678 -0.040063703 GPAWVGSHGVLQHTQGLPADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPAWVGSHGVLQHTQGLPADR 21 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 247 1.38E-30 1071970000 322710 384890 336790 345350 363160 449080 350840 398230 350100 368880 FALSE TRUE 335450.84 450991.8635 345567.0241 413659.1992 301430.1929 344787.9759 323340.2441 392892.3782 337499.9694 441154.9734 0.760392289 1.022298037 0.783323424 0.937673208 0.683275065 0.781557495 0.732940267 0.890599454 0.765037209 1 18.75092602 5.056163585 17.88111282 0.835681705 8.28E-05 0.045218429 0.109402667 291.8389504 92820.21513 0.02394725 18262.20123 113805.5874 -5.056163585 -0.835598893 GPCAPAASS(ph)PTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPCAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPCAPAAS(0.001)S(0.999)PTQK;GPCAPAAS(0.01)S(0.983)PT(0.007)QK;GPCAPAAS(0.309)S(0.684)PT(0.006)QK 261.63 4.75E-24 594289000 1545670 1021050 1186130 1145090 1407060 1666510 1694990 1287970 1280940 849010 TRUE FALSE 1606694.245 1196407.395 1217041.522 1371585.384 1167888.444 1279488.309 1562132.255 1270706.869 1234839.22 1015357.254 1.582393033 1.178311762 1.198633798 1.350840188 1.150224159 1.260136079 1.538505042 1.251487458 1.216162306 1 19.953556 0.880328577 2.259284453 1.00118615 1.308300881 0.326617136 0.13736958 0.555941114 5.755526112 0.126848639 0.034571547 7.591517136 -0.880328577 0.30711473 GPEDSWLLLSAPGPTPASPRPAS(ph)PCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPEDSWLLLSAPGPTPASPRPASPCGK 27 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 GPEDSWLLLSAPGPT(0.007)PAS(0.407)PRPAS(0.586)PCGK;GPEDSWLLLSAPGPT(0.003)PAS(0.329)PRPAS(0.669)PCGK 242.1 1.88E-45 277790000 236180 187589 235140 166831 281300 279980 243440 231390 242780 179708 TRUE FALSE 245504.5688 219805.9515 241267.9416 199829.6739 233484.7265 214958.8881 224358.5367 228288.5955 234042.3952 214918.3419 1.142315573 1.022741705 1.122602843 0.929793484 1.086388088 1.000188659 1.043924566 1.062210854 1.088982881 1 17.71342909 6.917852515 1.54332152 1.04067851 92.7544631 0.244264833 0.052877032 1806.649486 6.100974374 0.013001086 585802.3551 8276610.457 -6.917852515 91.71378459 GPEEEHPSVTLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 232.6 4.74E-13 932420000 462795 1393956 1230336 1479627 1187600 1677361 1256755 1418625 1171387 1393234 FALSE TRUE 481066.504 1633357.1 1262399.567 1772292.804 985732.1762 1287819.328 1158247.259 1399610.652 1129229.011 1666211.527 0.288718747 0.980281959 0.757646641 1.063666152 0.591600862 0.772902664 0.695138186 0.83999578 0.677722481 1 20.66814013 -2.663458771 2.05249776 6.552682859 0.758661539 0.1236064 0.202065435 5254466.211 166322.0062 137212860.3 0.044874672 0.002170407 2.663458771 -5.79402132 GPELLTMWFGESEANVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPELLTMWFGESEANVR 17 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 121.28 0.00021595 179624000 229470 260474 253346 251100 289870 320719 244995 251134 268854 268366 FALSE TRUE 238529.6528 305208.3833 259948.4049 300766.8305 240598.0009 246236.8728 225791.6517 247767.9595 259177.9971 320947.1795 0.743205325 0.950961413 0.809941391 0.937122523 0.749649837 0.767219307 0.703516548 0.771989833 0.807540971 1 18.29197636 3.218220437 24.9629161 0.779646277 0.863185374 0.066954291 0.093082727 407.2755026 499836.3451 0.024781507 0.029652196 1652.800507 -3.218220437 0.083539098 GPESESEDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GPESESEDHR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;; 192.12 7.18E-07 1546170000 997011 1384298 1632048 1659082 1578703 1587419 1401323 1401445 1426216 1470460 FALSE TRUE 1036373.764 1622040.413 1674580.512 1987243.468 1310355.628 1218764.995 1291483.642 1382660.922 1374886.765 1758568.483 0.589328067 0.922364087 0.952240716 1.130034734 0.7451263 0.693043806 0.734394852 0.786242296 0.781821566 1 20.74597009 GPFGLRPVLPDPS(ph)PPGPSTVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPFGLRPVLPDPSPPGPSTVEER 23 1 A0A2R8Y701;Q18PE1-2;Q18PE1;Q18PE1-3 A0A2R8Y701 DOK7 Protein Dok-7 1 GPFGLRPVLPDPS(0.985)PPGPS(0.007)T(0.007)VEER 75.326 0.010494 57747000 79603 83014 88280 97619 93991 101470 92542 88973 93227 98102 TRUE FALSE 82745.78791 97271.00874 90580.64932 116927.7468 78014.44339 77905.13029 85288.31623 87780.46247 89871.77848 117323.2086 0.705280642 0.829085821 0.772060792 0.996629296 0.664953203 0.664021477 0.726951788 0.748193503 0.766018757 1 16.84012891 -0.84479676 3.422728339 1.000022671 0.764090213 0.376302337 0.091268031 5303456.865 9830062.938 1782.077564 0.022495458 0.14295628 0.84479676 -0.235932458 GPGAPAAS(ph)SPTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPGAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.755)S(0.245)PTQK 113.61 0.00084797 272210000 550480 351230 450320 424960 536260 606440 625770 453070 486950 327660 TRUE FALSE 572213.3755 411551.0203 462055.7091 509015.8196 445106.7167 465603.5007 576720.5123 446997.3377 469424.7646 391858.7036 1.460254347 1.050253616 1.179138564 1.298977961 1.135885748 1.188192316 1.471756291 1.1407105 1.197943954 1 18.57997402 0.748674689 1.672020128 1.00109933 1.236974373 0.238013637 0.129619834 1.286450242 5.877170766 0.116905508 0.033342289 5.606278768 -0.748674689 0.235875043 GPGAPAAS(ph)SPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPGAPAASSPTRK 13 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.65)S(0.324)PT(0.027)RK;GPGAPAAS(0.529)S(0.447)PT(0.024)RK;GPGAPAAS(0.626)S(0.371)PT(0.003)RK 99.161 0.0031648 184102000 508657 385195 476037 407577 527313 568938 588491 475729 505625 359005 TRUE FALSE 528739.1711 451349.2448 488442.9153 488194.5141 437680.5246 436810.7718 542363.5377 469352.6309 487427.655 429345.1562 1.231501424 1.051250348 1.13764627 1.137067711 1.019414143 1.017388378 1.263234323 1.093182546 1.135281598 1 18.71177839 4.754433006 23.37408748 1.103021188 1.231501664 0.221937573 0.075352869 1901.537861 2800137.545 0.017564708 0.399676513 56811.07481 -4.754433006 0.128480476 GPGAPAASS(ph)PTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GPGAPAASSPTQK 13 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.078)S(0.922)PTQK;GPGAPAAS(0.058)S(0.942)PTQK;GPGAPAAS(0.058)S(0.941)PTQK;GPGAPAAS(0.048)S(0.952)PTQK;GPGAPAAS(0.036)S(0.964)PTQK 270.16 8.09E-26 3054050000 3863760 2526540 3191830 3041460 3601930 3999310 4340510 3445040 3419300 2149690 TRUE FALSE 4016304.228 2960453.591 3275011.712 3643051.71 2989675.225 3070530.863 4000289.484 3398864.874 3296240.061 2570880.597 1.562229001 1.151532901 1.273887132 1.417044305 1.162899292 1.194349853 1.555999718 1.322062517 1.282144361 1 21.29383118 0.77319026 3.492070689 1.0000298 1.325392608 0.33256754 0.139335525 2.183491605 32.26645266 0.129044898 0.03329187 5.931851362 -0.77319026 0.325362808 GPGAPAASS(ph)PTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPGAPAASSPTRK 13 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 GPGAPAAS(0.414)S(0.576)PT(0.01)RK 71.316 0.026094 269660000 231180 190570 196700 165330 225030 221570 278540 196950 221440 163200 TRUE FALSE 240307.1649 223298.9151 201826.1636 198031.7805 186779.481 170113.7254 256707.307 194310.2074 213470.4177 195175.9153 1.231233703 1.144090523 1.034073099 1.014632262 0.956980172 0.87159179 1.315261191 0.995564473 1.093733401 1 17.57441551 4.452438753 2.642137898 1.037988316 1.229200316 0.255278312 0.108801232 0.431298611 5.478260281 0.027470796 0.136444612 28342.53903 -4.452438753 0.191212 GPGAPAS(ph)PSASHPQGLDTTPKPH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPGAPASPSASHPQGLDTTPKPH 23 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 GPGAPAS(0.99)PS(0.01)ASHPQGLDTTPKPH;GPGAPAS(0.855)PS(0.145)ASHPQGLDTTPKPH;GPGAPAS(0.994)PS(0.006)ASHPQGLDTTPKPH;GPGAPAS(0.996)PS(0.004)ASHPQGLDTTPKPH 202.29 1.27E-24 2319620000 976512 1092285 1324673 1124809 1488010 1508180 1331120 1340390 1291230 1062828 TRUE FALSE 1015065.448 1279876.452 1359195.067 1347292.863 1235078.592 1157928.052 1226783.336 1322424.264 1244758.885 1271068.798 0.798592059 1.006929329 1.069332415 1.059968481 0.971685084 0.910987709 0.965158879 1.040403373 0.979300953 1 20.27761069 4.739394298 24.63300879 1.002118213 0.79859198 0.641474279 0.045249701 39.41817 1164458.176 0.011920945 0.072085438 54877.49743 -4.739394298 -0.203526233 GPGASVHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 143.03 0.00010291 244360000 158148 550590 441430 502250 464010 620840 395550 499600 411210 587220 FALSE TRUE 164391.8052 645149.5495 452934.0284 601593.5509 385137.7459 476659.3189 364545.7574 492903.6792 396410.6324 702274.516 0.234084822 0.918657213 0.644952961 0.856635884 0.548414811 0.67873646 0.51909296 0.701867529 0.564466777 1 19.42167556 -1.17221391 3.754184457 1.000261394 0.643928718 0.272726543 0.180078514 44474648.8 81246109.97 149550.6455 0.03910683 0.067264527 1.17221391 -0.356332676 GPGGSQGSQGPS(ph)PQGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 GPGGSQGSQGPS(1)PQGAR;GPGGSQGSQGPS(1)PQGAR;GPGGSQGS(0.001)QGPS(0.999)PQGAR;GPGGSQGS(0.002)QGPS(0.998)PQGAR 252.7 5.68E-27 517267000 501669 629422 590820 658608 619600 745109 587467 642120 593367 723671 TRUE FALSE 521475.2795 737520.3323 606217.2546 788878.6967 514280.6133 572068.727 541419.8015 633513.4317 572011.8376 865460.4769 0.602540836 0.852171014 0.700456313 0.911513255 0.594227729 0.660999251 0.625585819 0.731995797 0.660933518 1 19.72310841 -1.579820948 8.791527873 1.000058952 0.708583511 0.444179744 0.099074585 0.000109575 5.24E-06 0.091818788 0.02163755 0.026313526 1.579820948 -0.291475441 GPGLLES(ph)PSIFNFTADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.988)PS(0.012)IFNFTADR;GPGLLES(0.787)PS(0.213)IFNFTADR;GPGLLES(0.911)PS(0.089)IFNFTADR 176.17 1.19E-09 139499000 153830 148407 143884 146793 151921 191514 154181 157095 155843 205520 TRUE FALSE 159903.3272 173894.7478 147633.7352 175828.2173 126097.5227 147037.7759 142095.8903 154989.3985 150234.2409 245787.7091 0.650574953 0.707499771 0.600655484 0.715366191 0.513034289 0.598230792 0.578124475 0.63058238 0.611235775 1 17.90705325 -1.214529959 4.084871169 1.000233445 0.622065042 0.800790525 0.056437354 28.21318019 30336812.71 12828.7837 0.013042038 0.061019696 1.214529959 -0.378168403 GPGLLESPS(ph)IFNFTADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 GPGLLES(0.325)PS(0.675)IFNFTADR 156.11 7.89E-08 30647000 17956 30782 27479 29159 24818 36847 25284 28805 26731 39167 TRUE FALSE 18664.91675 36068.56905 28195.12531 34926.56317 20599.44522 28289.84267 23302.17401 28418.91609 25768.95653 46841.02375 0.398473715 0.770020938 0.601932303 0.745640474 0.439773591 0.603954406 0.497473628 0.606709969 0.550136493 1 15.51548499 -1.382262196 2.872932948 1.006965343 0.585184819 0.557943829 0.11222015 16775925.45 19861236.26 970162.6192 0.026906003 0.04147036 1.382262196 -0.421780524 GPGPTVKPSGHLFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPGPTVKPSGHLFFR 15 1 F5GXQ0;Q5VW32-2;Q5VW32 F5GXQ0 BROX BRO1 domain-containing protein BROX 0 ; 189.37 1.57E-07 1717550000 1058030 1509830 1648810 1598580 1722380 1916880 1628830 1626500 1703930 1638320 FALSE TRUE 1099801.841 1769131.558 1691779.343 1914774.353 1429610.463 1471713.671 1501158.048 1604699.428 1642605.892 1959317.436 0.561318866 0.902932585 0.863453421 0.97726602 0.729647191 0.751135902 0.766163777 0.819009415 0.838356185 1 20.90191972 0.686981392 1.918983937 0.999898789 0.803193437 0.247759271 0.105851225 2.003629602 10.18554336 0.098642489 0.027406191 4.863863653 -0.686981392 -0.196705352 GPGQPSS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPGQPSSPQR 10 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 GPGQPS(0.053)S(0.947)PQR;GPGQPS(0.059)S(0.941)PQR 85.813 0.014669 172871000 385710 401850 350230 458860 365840 454890 470260 395580 333700 352330 TRUE FALSE 400938.1286 470864.6115 359357.2815 549621.1384 303654.6475 349248.6914 433399.7924 390277.8971 321690.2022 421362.3177 0.951528202 1.11748154 0.852846271 1.304390818 0.720649747 0.828856015 1.02856799 0.92622876 0.763452707 1 18.68470177 3.215645734 24.99997349 0.885933967 1.046362327 0.276095045 0.140938454 333.2203576 363540.1212 0.039331719 0.047039358 1643.030909 -3.215645734 0.16042836 GPGQVPTATSALSLELQEVEPLGLPQAS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GPGQVPTATSALSLELQEVEPLGLPQASPSR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 GPGQVPTATSALSLELQEVEPLGLPQAS(0.5)PS(0.5)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.809)PS(0.191)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.731)PS(0.269)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.796)PS(0.204)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.848)PS(0.152)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.832)PS(0.168)R;GPGQVPTATSALSLELQEVEPLGLPQAS(0.986)PS(0.014)R 275.81 7.05E-72 3218078700 1293612.9 1522516.2 1466635 1539378.1 1514730 1852681 1464615.5 1514829 1485004 1818285.7 TRUE FALSE 1344685.736 1783996.514 1504856.713 1843862.494 1257256.736 1422423.915 1349815.11 1494525.195 1431558.996 2174543.97 0.61837597 0.820400295 0.692033242 0.847930655 0.578170298 0.654125157 0.620734797 0.687282123 0.658326075 1 21.05228145 -1.226159693 5.692500388 1.00001227 0.688169527 0.570614877 0.081604151 1.24E-05 1.68E-06 0.077023178 0.018153823 0.059407367 1.226159693 -0.311842742 GPGS(ph)PPRT(ph)PPAPGPPSFEEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPGSPPRTPPAPGPPSFEEQLR 22 1 A0A6E1YH78;Q6ZTN6-2;Q6ZTN6;Q6ZTN6-3 A0A6E1YH78 ANKRD13D Ankyrin repeat domain-containing protein 13D 2 GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR;GPGS(1)PPRT(1)PPAPGPPSFEEQLR 183.64 9.59E-17 5918600000 910720 1076710 977530 994380 1078200 1225110 1041900 1051590 1001000 1026900 TRUE FALSE 946675.9288 1261626.567 1003005.235 1191065.396 894927.9491 940596.7692 960233.1555 1037495.156 964974.2055 1228101.394 0.77084509 1.027298376 0.816712073 0.969842883 0.72870852 0.765895043 0.781884265 0.844796009 0.785744736 1 20.22799825 3.242014809 24.99982737 0.807808966 0.899864681 0.132428961 0.096007682 147.6620282 1068699.862 0.02477131 0.032232575 1745.881685 -3.242014809 0.092055715 GPHHLDNSS(ph)PGPGSEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPHHLDNS(0.086)S(0.914)PGPGSEAR;GPHHLDNS(0.013)S(0.987)PGPGSEAR 165.9 1.55E-09 712050000 299430 382670 334430 400080 314310 414980 342210 343810 306110 361230 TRUE FALSE 311251.7276 448390.5957 343145.5205 479214.6299 260883.6985 318607.1841 315386.686 339201.7893 295093.1609 432006.1023 0.720479933 1.037926532 0.794307114 1.109277455 0.60388892 0.737506212 0.730051461 0.785178236 0.683076372 1 18.72069217 3.227667203 24.99999894 0.746119693 0.915586226 0.234347535 0.139919935 272.2178927 624729.4018 0.036863999 0.044464286 1689.146054 -3.227667203 0.169466533 GPHHLDNSSPGPGSEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 0 ; 87.287 0.0026486 89149000 21937 47618 42767 39205 41654 52616 41904 39790 35518 48336 FALSE TRUE 22803.0897 55796.02108 43881.54315 46959.63198 34573.66796 40396.7314 38619.45498 39256.68013 34239.71412 57806.51375 0.394472668 0.965220309 0.759110701 0.812358832 0.598092943 0.698826634 0.668081371 0.679104786 0.592315846 1 15.81894445 -1.150491659 4.991369255 1.000017516 0.69545127 0.303715108 0.142206408 2.57E-05 4.38E-06 0.12788078 0.030140057 0.070714478 1.150491659 -0.304566247 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;GPIAQWADGAIS(1)PNGHRPQLR 199.85 4.71E-22 1254360000 602880 721190 662660 716720 726390 802740 725660 732370 706700 824630 TRUE FALSE 626682.1679 845048.7724 679929.464 858485.0768 602918.4873 616315.8006 668780.873 722553.7781 681266.005 986200.46 0.635451101 0.856873229 0.689443467 0.870497542 0.611354904 0.624939681 0.678138878 0.732664207 0.690798709 1 19.9115214 -1.501777505 4.905088399 1.00103245 0.713123967 0.51126795 0.085006904 0.000931744 9.46E-05 0.079903322 0.018768427 0.031493614 1.501777505 -0.287908483 GPIKFNVWDTAGQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPIKFNVWDTAGQEK 15 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 197.88 7.48E-09 3128500000 2657100 2010280 2445400 1613430 3395000 2808300 2379300 2409460 2709100 2201370 FALSE TRUE 2762004.36 2355529.952 2509129.133 1932561.638 2817919.113 2156114.885 2192804.249 2377165.13 2611600.02 2632686.304 1.049120192 0.894724886 0.953068024 0.734064532 1.070358861 0.818979034 0.832915128 0.902942795 0.991990583 1 21.3281042 1.233373998 7.264241849 0.997048582 0.901258011 0.11823552 0.096228003 0.252263893 76.93575788 0.073992335 0.022059205 17.11488551 -1.233373998 -0.095790571 GPKPEPPGS(ph)GSPAPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.5)GS(0.5)PAPPR;GPKPEPPGS(0.5)GS(0.5)PAPPR 140.35 1.04E-06 1382470000 866570 714550 861400 740080 925540 937220 903910 755970 856200 714150 TRUE FALSE 900782.8527 837268.4041 883848.7916 886465.6151 768217.0414 719564.8587 833059.1723 745837.4587 825385.5292 854074.0193 1.054689444 0.980322999 1.034862051 1.037925982 0.89947361 0.842508778 0.975394583 0.873270281 0.966409832 1 19.70400158 3.239574794 24.99957904 0.916361248 1.024184762 0.500270137 0.048722346 19.95770671 491950.341 0.013009663 0.016653333 1736.100229 -3.239574794 0.107823514 GPKPEPPGSGS(ph)PAPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.128)GS(0.872)PAPPR;GPKPEPPGS(0.023)GS(0.977)PAPPR;GPKPEPPGS(0.416)GS(0.584)PAPPR 121.82 5.86E-05 1720810000 948776 786542 924373 798964 1077586 1098431 992122 903585 949950 836078 TRUE FALSE 986234.4091 921624.4701 948462.9198 956996.6945 894418.3166 843337.0471 914356.8852 891473.921 915761.4851 999891.4764 0.98634145 0.921724499 0.948565862 0.957100563 0.894515393 0.843428579 0.914456125 0.891570677 0.915860878 1 19.93141199 3.238752209 24.99985406 0.901069743 0.95082054 0.203311844 0.039741292 6.629863921 865021.8707 0.010584595 0.013470897 1732.81504 -3.238752209 0.049750797 GPKPEPPGSGS(ph)PAPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPKPEPPGSGSPAPPRR 17 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GPKPEPPGS(0.015)GS(0.985)PAPPRR 146.13 2.34E-07 188170000 431970 328990 395500 333780 489200 442660 420570 374610 425830 328680 TRUE FALSE 449024.5092 385491.4733 405807.0549 399800.6878 406045.9587 339858.9236 387604.6244 369588.9657 410504.4615 393078.553 1.142327674 0.980698312 1.032381573 1.01710125 1.032989349 0.864608158 0.986074212 0.940242002 1.044331873 1 18.58445812 8 0.773737905 0.97499593 32.77870049 0.416124033 0.052359721 415.33867 1.605843063 0.017671665 23091.40185 99999999.91 -8 31.80370456 GPLINSEFYTGWLDHWGQPHSTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPLINSEFYTGWLDHWGQPHSTIK 24 0 P16278-3;P16278;E7EQ29;P16278-2;C9J4G9 P16278-3 GLB1 Beta-galactosidase 0 174.19 1.86E-12 164170000 102710 132090 140590 117980 178960 195550 159970 150630 158040 156180 FALSE TRUE 106765.0701 154775.43 144253.8909 141316.0919 148540.4431 150136.4761 147431.1334 148611.0512 152352.1713 186780.4808 0.571607213 0.828648847 0.772317805 0.756589186 0.795267485 0.803812451 0.789328375 0.795645512 0.815675014 1 17.51098417 -5 0.110902934 1.712092175 0.647521343 0.630774372 0.0593949 108.8447827 0.801300027 17.6714616 0.688353966 1.00E-05 5 -1.064570833 GPLLVQDVVFTDEMAHFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GPLLVQDVVFTDEMAHFDR 19 0 P04040 P04040 CAT Catalase 0 ;;;;;;;; 212.83 6.35E-17 1270989000 866485 1423868 1011018 1336120 1168254 1515013 1081326 1014863 1044787 1344871 FALSE TRUE 900694.4969 1668406.253 1037365.96 1600400.548 969674.6024 1163174.191 996568.8426 1001260.421 1007185.32 1608372.723 0.560003589 1.037325633 0.644978583 0.995043328 0.602891723 0.723199402 0.619613121 0.622530093 0.626213878 1 20.61717034 GPLS(ph)PFNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;GPLS(1)PFNSR;GPLS(1)PFNSR 144.27 0.00010486 2017590000 1204080 1388850 1327380 1261610 1476680 1604920 1337190 1337540 1287070 1397350 TRUE FALSE 1251618.008 1627374.184 1361972.613 1511152.692 1225674.461 1232201.653 1232377.554 1319612.464 1240748.602 1671133.979 0.748963293 0.973814311 0.814999055 0.904267828 0.733438777 0.737344623 0.737449881 0.789650908 0.742459083 1 20.67239597 3.239375965 24.99986076 0.774485296 0.865353347 0.107655216 0.092686977 35.03083901 1074075.6 0.023881243 0.030531976 1735.305587 -3.239375965 0.090868051 GPMDSDDSHGSVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPMDSDDSHGSVLR 14 0 Q8IW45-2;Q8IW45;Q8IW45-4 Q8IW45-2 CARKD ATP-dependent (S)-NAD(P)H-hydrate dehydratase 0 134.04 4.10E-05 286830000 44401 132600 128780 141230 127640 169190 103210 147700 115000 186060 FALSE TRUE 46153.98577 155373.0185 132136.1126 169164.8725 105943.7984 129898.1866 95120.13051 145720.3231 110861.1725 222514.8947 0.207419759 0.698258958 0.593830417 0.760240669 0.47612003 0.583772995 0.427477588 0.654878961 0.498219109 1 17.76354238 -1.702253109 2.764417658 1.066348071 0.558091452 0.454494872 0.149047143 45373227.07 39306745.95 20966532.86 0.032978193 0.019849377 1.702253109 -0.508256619 GPNGESSVIHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPNGESSVIHDR 12 0 O60437;K7EKI8 O60437 PPL Periplakin 0 75.911 0.032535 264570000 74151 94676 83674 87520 94498 130880 104020 109540 91838 96845 FALSE TRUE 77078.53874 110935.8665 85854.61318 104831.1948 78435.26371 100485.1035 95866.64059 108071.7955 88532.76832 115819.9235 0.665503278 0.957830597 0.741276721 0.905122293 0.677217367 0.867597737 0.827721498 0.933101941 0.764400162 1 16.82152392 -5 0.149916983 1.634861915 0.76955673 0.255874116 0.096580171 180.2205755 1.605795711 33.93699434 0.448678495 1.00E-05 5 -0.865305185 GPNGYGFHLHGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPNGYGFHLHGEK 13 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 151.74 2.60E-05 146950000 210940 223090 258120 207590 342580 323330 285930 273470 285890 272560 FALSE TRUE 219268.0741 261403.9721 264846.8192 248650.6824 284348.374 248241.5076 263518.0595 269804.582 275600.8747 325962.9135 0.67267798 0.801943906 0.812505988 0.762818935 0.872333515 0.761563654 0.808429574 0.82771558 0.845497642 1 18.31434831 -5 0.134201453 1.691576202 0.718028567 0.704778319 0.043682098 76.9965342 0.644446155 14.23589086 0.289956503 1.00E-05 5 -0.973547634 GPPAS(ph)SPAPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.554)S(0.446)PAPAPK 69.01 0.05363 17316000 56851 50499 46701 45307 65663 59877 55476 57100 52034 47733 TRUE FALSE 59095.52138 59171.81042 47918.06643 54268.58937 54501.62671 45971.47419 51127.64616 56334.6679 50161.3065 57085.36745 1.035213121 1.036549523 0.839410668 0.950656741 0.954739001 0.805310997 0.895634879 0.986849528 0.878706904 1 15.80083337 4.264353845 24.53083126 0.915173641 1.035881564 0.406868047 0.058889495 176.6247392 167976.3898 0.014190176 0.038829245 18380.35287 -4.264353845 0.120707922 GPPASS(ph)PAPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPAS(0.001)S(0.999)PAPAPK;GPPASS(1)PAPAPK;GPPASS(1)PAPAPK;GPPASS(1)PAPAPK;GPPAS(0.001)S(0.999)PAPAPK;GPPAS(0.003)S(0.997)PAPAPK;GPPAS(0.045)S(0.955)PAPAPK;GPPASS(1)PAPAPK 207.12 8.62E-08 19441475000 21311540 17085430 18839780 15922150 23142380 23315680 21930290 19343430 19126540 16022350 TRUE FALSE 22152936.06 20019719.7 19330760.14 19071503.75 19208646.51 17900966.67 20211336.57 19084162.96 18438179.56 19161622.72 1.156109604 1.044782062 1.008826884 0.995296903 1.002454061 0.934209328 1.054782096 0.995957558 0.962245204 1 24.19171641 4.90869596 1.402233054 0.993810051 1.277917255 0.743856429 0.029012239 0.896262927 1.177988092 0.007721188 0.40007626 81039.35209 -4.90869596 0.284107204 GPPASSPAPAPKFS(ph)PVTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 GPPASSPAPAPKFS(0.958)PVT(0.042)PK;GPPASSPAPAPKFS(0.995)PVT(0.005)PK 196.78 4.96E-16 3462700000 3257240 1730420 2340130 1348340 3825870 2981770 2701910 2344870 2765260 1752810 TRUE FALSE 3385838.35 2027606.174 2401115.71 1615037.628 3175549.984 2289299.107 2490127.234 2313440.853 2665738.833 2096239.56 1.615196285 0.967258806 1.145439556 0.770445162 1.514879332 1.092098036 1.187902033 1.103614729 1.271676617 1 20.99937217 -1.335065026 3.369897501 0.99903856 1.167681734 0.049452642 0.232447344 59681213.11 47944811.78 513522.7896 0.051418637 0.046231179 1.335065026 0.168643174 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 P42166;P42167;G5E972;P42167-3;P42167-2 P42166;P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 2 GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR;GPPDFS(1)S(1)DEEREPTPVLGSGAAAAGR 155.61 2.48E-08 2870750000 1885830 2325310 2063990 2373740 2305110 2854040 2254840 2338830 2207260 2657120 TRUE FALSE 1960284.025 2724663.904 2117779.275 2843258.687 1913288.226 2191232.463 2078099.749 2307481.809 2127821.144 3177731.79 0.616881522 0.857424126 0.666443682 0.894744703 0.602092421 0.689558656 0.653956937 0.726141148 0.669603756 1 21.59956593 -1.135711591 6.857026028 1.000000341 0.712141465 0.477221564 0.091446925 4.39E-07 5.52E-08 0.081432587 0.019193822 0.073162478 1.135711591 -0.287858876 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_MDA-MB-175_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(0.991)S(0.009)DEEREPTPVLGSGAAAAGR;GPPDFS(0.992)S(0.008)DEEREPTPVLGSGAAAAGR;GPPDFS(0.884)S(0.116)DEEREPTPVLGSGAAAAGR;GPPDFS(0.884)S(0.116)DEEREPTPVLGSGAAAAGR;GPPDFS(0.54)S(0.46)DEEREPTPVLGSGAAAAGR 311.55 5.54E-82 6400570000 711830 795315 757159 715214 852351 1000019 795056 763205 748701 932619 TRUE FALSE 739933.5981 931904.1646 776891.1856 856681.1945 707468.6815 767779.7427 732737.4332 752975.4853 721755.3973 1115347.837 0.663410618 0.835527836 0.6965461 0.768084329 0.634303181 0.68837695 0.656958671 0.67510373 0.647112384 1 20.08906227 -0.932096138 9.236235238 0.999999926 0.697008528 0.709917081 0.058265172 0 0 0.056297844 0.013269529 0.116924053 0.932096138 -0.302991398 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_MDA-MB-175_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 GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR;GPPDFSSDEEREPT(1)PVLGSGAAAAGR 253.6 2.42E-52 3317020000 1785039 2328438 1807693 2628367 2169160 3018305 2015935 2005851 1837843 3139526 TRUE FALSE 1855513.718 2728329.114 1854802.965 3148250.148 1800446.958 2317349.407 1857920.747 1978965.848 1771699.389 3754656.01 0.49419007 0.726652217 0.494000771 0.838492298 0.479523811 0.617193533 0.494831149 0.527069815 0.471867299 1 21.84024931 -1.9331697 2.451929099 1.292334535 0.573534631 0.548996622 0.116491358 9167726.084 4545065.139 15337762.78 0.028042858 0.011663538 1.9331697 -0.718799905 GPPHSDSCPGLTLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPPHSDSCPGLTLHR 15 0 Q9BVJ7 Q9BVJ7 DUSP23 Dual specificity protein phosphatase 23 0 ; 207.97 1.81E-09 386930000 91769 136808 125352 129270 118159 143197 118752 129390 102733 139814 FALSE TRUE 95392.11098 160303.7098 128618.7761 154839.2202 98074.37539 109941.6669 109443.9079 127655.7387 99035.6594 167207.8764 0.570500105 0.958709083 0.769214817 0.926028268 0.5865416 0.657514881 0.654537994 0.763455296 0.592290636 1 17.35128328 5.01931945 14.48611017 0.752330943 0.224150978 0.137491148 0.143584133 1453924.846 27042054.23 0.033028257 16380255.73 104548.8956 -5.01931945 -0.528179965 GPPLREGEELVMDEEAYVLYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPPLREGEELVMDEEAYVLYHR 22 1 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 111.81 0.00018804 6655900 12921 19046 13877 12119 18625 16168 10784 16478 16170 26758 FALSE TRUE 13431.13106 22317.00234 14238.64602 14516.10203 15459.12915 12413.22703 9938.721901 16257.13936 15588.04486 32000.71779 0.419713431 0.69739068 0.444947708 0.453618013 0.48308695 0.387904644 0.310578093 0.50802421 0.487115475 1 14.96581665 0.39529984 1.970822196 0.999991041 0.463237876 0.744444907 0.094012969 4.112634919 12.74338061 0.091930425 0.025326092 2.484848069 -0.39529984 -0.536753165 GPPNS(ph)PDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPPNSPDLK 9 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 GPPNS(1)PDLK;GPPNS(1)PDLK;GPPNS(1)PDLK 99.215 0.0057564 308820000 1080670 711190 854950 746320 1104060 1178690 1157000 870740 917430 681410 TRUE FALSE 1123335.686 833331.3502 877230.6993 893939.8685 916392.2756 904957.1107 1066311.317 859069.1545 884411.8735 814919.2431 1.378462585 1.022593781 1.076463351 1.096967431 1.124519127 1.110486859 1.308487099 1.054177039 1.085275481 1 19.63629757 1.594453911 25 1.052264535 1.148128757 0.193216053 0.103961429 1.686357842 3134.982271 0.053761532 0.025109519 39.30555298 -1.594453911 0.095864222 GPPPEADLPRS(ph)PGNLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPPPEADLPRSPGNLTER 18 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 GPPPEADLPRS(0.979)PGNLT(0.021)ER;GPPPEADLPRS(0.998)PGNLT(0.002)ER 95.223 0.0011011 208264000 147603 202001 175487 132277 204987 227450 109507 171340 181289 247230 TRUE FALSE 153430.4804 236693.1004 180060.3354 158440.9958 170143.383 174628.1845 100923.5552 169043.4676 174764.4443 295669.985 0.518924775 0.800531378 0.608990917 0.535871085 0.575450305 0.590618573 0.34133852 0.571730227 0.591079424 1 18.17362827 0.673971202 3.686517763 0.999996872 0.566574092 0.599624883 0.105433391 4.909457401 54.79997107 0.104719585 0.026894588 4.720317399 -0.673971202 -0.43342278 GPPPEADLPRS(ph)PGNLTEREELAGSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPPPEADLPRSPGNLTEREELAGSLAR 27 2 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 GPPPEADLPRS(0.967)PGNLT(0.033)EREELAGSLAR;GPPPEADLPRS(0.998)PGNLT(0.002)EREELAGSLAR;GPPPEADLPRS(0.937)PGNLT(0.063)EREELAGSLAR 108.9 0.00083986 585260000 119712 194551 170621 101066 216340 195756 87367 151513 174004 316602 TRUE FALSE 124438.3222 227963.6209 175067.5234 121056.5531 179566.6041 150294.6357 80518.94625 149482.2161 167741.63 378634.1002 0.328650595 0.602068384 0.462365971 0.319719098 0.474248368 0.396938986 0.212656351 0.394793327 0.443017758 1 18.53044482 0.700535665 3.628053701 0.99999393 0.398824388 0.768437365 0.098442418 2.290820378 27.28111144 0.096994268 0.024941139 5.018057868 -0.700535665 -0.601169542 GPPPPPTASEPTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPPPPPTASEPTRR 14 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 101.3 0.0023098 62329000 33434 38980 38646 36379 40421 48419 34271 36941 36120 41403 FALSE TRUE 34754.00014 45674.51178 39653.14651 43574.65762 33550.25286 37174.42105 31584.74947 36445.86632 34820.04826 49515.12514 0.701886546 0.922435552 0.800828967 0.880027214 0.677575847 0.750769001 0.637880837 0.73605522 0.703220443 1 15.59558167 3.239911921 24.99998048 0.73019238 0.831342811 0.08794927 0.106597105 59.63205768 1103210.535 0.02742215 0.035187016 1737.448423 -3.239911921 0.101150431 GPPPSWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPPPSWGR 8 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 94.539 0.023934 192303000 143273 99831 94411 103135 139255 136645 125226 101315 104858 113803 FALSE TRUE 148929.5287 116976.1977 96871.42822 123534.7952 115584.4848 104911.2696 115410.4589 99957.03814 101084.1811 136100.519 1.094261284 0.859483847 0.711763842 0.907673212 0.849258223 0.770836661 0.847979565 0.734435393 0.742717088 1 17.05431304 4.712007165 3.789977958 0.809821657 1.116067887 0.481464641 0.08391222 0.175414675 4.848001779 0.019052102 0.143014717 51523.71444 -4.712007165 0.30624623 GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;;;;; 289.73 1.67E-70 7703180000 3382090 2050000 2767600 2096290 3389390 3540600 3310770 2762600 2941710 2002230 FALSE TRUE 3515617.525 2402071.553 2839725.93 2510929.905 2813262.698 2718349.308 3051263.196 2725571.866 2835838.432 2394528.633 1.468187716 1.003150065 1.185922728 1.048611351 1.174871187 1.135233578 1.274264652 1.138249853 1.184299236 1 21.19131026 -2.444290749 1.728151718 0.000218413 1.170644053 0.163062806 0.12039799 1944939.945 157023.7831 7577425.335 0.026791255 0.003595086 2.444290749 1.170425639 GPPQS(ph)PVFEGVYNNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GPPQSPVFEGVYNNSR 16 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR;GPPQS(1)PVFEGVYNNSR 300.25 7.41E-46 16807600000 2805400 2857070 2792440 2801470 2926660 3424870 3099350 2850420 2796910 2655950 TRUE FALSE 2916159.358 3347749.548 2865213.28 3355592.404 2429187.379 2629495.847 2856414.848 2812214.782 2696249.755 3176332.551 0.918090065 1.053966955 0.902050788 1.05643611 0.764777409 0.827840223 0.899280791 0.88536535 0.848856255 1 21.59893053 3.247019823 24.99995079 0.866751581 0.98197495 0.361607326 0.072518508 190.5334843 563090.8211 0.018992425 0.025306496 1766.118434 -3.247019823 0.115223369 GPPS(ph)PPAPVMHS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GPPSPPAPVMHSPSR 15 0 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.999)PS(0.001)R;GPPS(1)PPAPVMHS(0.584)PS(0.416)R;GPPS(1)PPAPVMHS(0.925)PS(0.075)R;GPPS(1)PPAPVMHS(0.795)PS(0.205)R;GPPS(1)PPAPVMHS(0.901)PS(0.099)R;GPPS(1)PPAPVMHS(0.983)PS(0.017)R;GPPS(1)PPAPVMHS(0.998)PS(0.002)R;GPPS(1)PPAPVMHS(0.981)PS(0.019)R;GPPS(1)PPAPVMHS(0.832)PS(0.168)R 167.45 6.92E-07 9359070000 2624100 3016710 2882080 2941030 3108660 3488290 3013630 3092050 2750920 3189130 TRUE FALSE 2727701.494 3534806.476 2957189.372 3522756.956 2580251.084 2678187.513 2777413.806 3050606.127 2651914.927 3813978.964 0.715185249 0.926802824 0.775355449 0.92364352 0.676524729 0.702203011 0.728219487 0.799848703 0.695314513 1 21.86286546 5.034966908 17.39716318 0.791539041 0.405395744 0.048036572 0.106776664 33756510.64 432115762.9 0.02423019 408145829 108384.4325 -5.034966908 -0.386143298 GPPS(ph)PPAPVMHS(ph)PSRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GPPSPPAPVMHSPSRK 16 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 2 GPPS(1)PPAPVMHS(0.923)PS(0.077)RK;GPPS(1)PPAPVMHS(0.856)PS(0.144)RK;GPPS(1)PPAPVMHS(0.972)PS(0.028)RK;GPPS(1)PPAPVMHS(0.996)PS(0.004)RK;GPPS(1)PPAPVMHS(0.628)PS(0.372)RK 130.05 2.53E-05 2407300000 2460770 2235510 2534120 2119366 3120390 3118180 2547190 2589960 2652900 2371970 TRUE FALSE 2557923.1 2619441.453 2600161.249 2538570.269 2589987.222 2394029.951 2347534.592 2555245.823 2557422.647 2836712.107 0.901721078 0.923407577 0.916610904 0.894898803 0.913024348 0.843945336 0.827554755 0.900777282 0.901544658 1 21.43578831 0.657580143 2.409950463 0.999975788 0.889283836 0.553385042 0.029405428 1.962946466 12.7904274 0.030942382 0.008302418 4.545484101 -0.657580143 -0.110691952 GPPS(ph)PRPAGPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPPSPRPAGPTPR 13 1 Q14681 Q14681 KCTD2 BTB/POZ domain-containing protein KCTD2 1 GPPS(0.985)PRPAGPT(0.015)PR 74.147 0.021136 234810000 117660 138820 126760 140120 142170 156890 136690 110860 126160 139080 TRUE FALSE 122305.3077 162661.2551 130063.4697 167835.3178 118003.9942 120454.6752 125975.8806 109374.103 121619.5262 166330.0632 0.735316907 0.977942604 0.781960081 1.009049805 0.709456799 0.724190642 0.757384914 0.657572666 0.731193892 1 17.34368943 3.204855385 24.99983487 0.738345239 0.876622401 0.167440597 0.115398021 238.1275489 176623.2653 0.030594056 0.036568853 1602.711617 -3.204855385 0.138277162 GPPS(ph)RGGHMDDGGYSMNFNMSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPPSRGGHMDDGGYSMNFNMSSSR 24 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 GPPS(1)RGGHMDDGGYSMNFNMSSSR;GPPS(0.972)RGGHMDDGGYS(0.028)MNFNMSSSR 186.56 1.27E-17 224014000 64066 78298 70994 50680 84268 96280 62366 66721 70595 98189 TRUE FALSE 66595.37515 91745.07243 72844.16196 60704.35274 69944.15546 73920.42914 57477.58996 65826.71413 68054.29974 117427.2546 0.56712026 0.781292833 0.62033437 0.51695284 0.595638174 0.629499765 0.489474016 0.560574411 0.579544331 1 16.84140777 -1.32171745 4.493352017 1.000365791 0.591684945 0.726647459 0.07481188 0.000285554 4.31E-05 0.075451818 0.017768506 0.047674105 1.32171745 -0.408680846 GPQAAAPPAS(ph)PEPFAHIQAVFAGSDDPFATALSMSEMDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 203.98 1.34E-31 654449000 170147.1 220771.2 218340.8 221616.3 264550.1 269968 163698.6 216930.2 191097.2 300528.7 TRUE FALSE 176864.6389 258686.9362 224030.9406 265451.3427 219581.9685 207272.0234 150867.476 214022.6055 184219.6491 359411.5448 0.492095041 0.719751327 0.623327057 0.738572109 0.610948568 0.57669829 0.419762465 0.595480609 0.512559075 1 18.45527723 -1.815385 5.079768789 1.047264395 0.59042295 0.642087902 0.092329893 0.043212947 0.001570496 0.078166397 0.021566381 0.015297308 1.815385 -0.456841445 GPQES(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPQESPQK 8 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 GPQES(1)PQK;GPQES(1)PQK;GPQES(1)PQK 95.618 0.0099886 568640000 1766940 1061500 1211060 1095200 1581900 1773020 1651980 1278830 1361680 919070 TRUE FALSE 1836700.156 1243804.368 1242621.218 1311827.291 1313009.203 1361262.975 1522493.491 1261689.376 1312673.403 1099144.17 1.671027519 1.131611668 1.130535241 1.19349884 1.194574141 1.238475364 1.385162686 1.147883426 1.194268631 1 20.0679492 7.999999998 0.024066331 7.11E-09 2.880422258 0.275048646 0.147895149 3474.833216 6.431630095 268.2945978 547.1255814 99999999.49 -7.999999998 2.880422251 GPQGPGGGGINVQEILTSIMGS(ph)PNSHPSEELLKQPDYSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPQGPGGGGINVQEILTSIMGSPNSHPSEELLKQPDYSDK 40 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 GPQGPGGGGINVQEILT(0.144)S(0.144)IMGS(0.556)PNS(0.144)HPS(0.01)EELLKQPDYSDK 58.044 0.011101 85423000 18027 22751 22221 22353 26624 35257 23681 25454 29578 29432 TRUE FALSE 18738.71988 26658.30727 22800.09751 26774.35668 22098.46199 27069.09608 21824.82134 25112.83076 28513.49356 35198.63689 0.532370612 0.757367604 0.647755127 0.76066459 0.627821528 0.769038192 0.620047345 0.713460321 0.8100738 1 15.10323194 0.940104381 1.957032818 0.999181211 0.679949134 0.66862944 0.070683678 0.207073088 1.673461774 0.059851435 0.016757615 8.711729477 -0.940104381 -0.319232077 GPQLFHMDPSGTFVQCDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPQLFHMDPSGTFVQCDAR 19 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 ;;; 227.06 1.36E-19 2454850000 1457540 1674170 1537030 1826610 1512110 1912360 1729640 1500610 1612050 1622310 FALSE TRUE 1515084.805 1961695.674 1577086.264 2187908.006 1255082.082 1468243.372 1594066.297 1480496.777 1554032.635 1940170.583 0.780902884 1.011094432 0.81285959 1.127688475 0.646892646 0.756759939 0.821611414 0.763075572 0.800977321 1 20.88775207 3.223395106 24.999987 0.784764435 0.930113659 0.221246074 0.122399506 311.6497961 513746.3471 0.032611384 0.03911962 1672.611607 -3.223395106 0.145349224 GPQPPTVS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPQPPTVSPIR 11 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GPQPPTVS(1)PIR;GPQPPTVS(1)PIR;GPQPPT(0.034)VS(0.966)PIR 162.31 2.65E-05 1182420000 751430 885419 864293 810430 820540 900660 864640 842063 847116 918760 TRUE FALSE 781097.0366 1037482.826 886817.1856 970730.6351 681064.9039 691495.3646 796867.2575 830776.5228 816628.4606 1098773.431 0.710880892 0.944219068 0.807097405 0.883467517 0.619841074 0.629333896 0.72523346 0.756094477 0.743218244 1 20.0674625 3.262277695 24.99092018 0.728571937 0.842022235 0.123708638 0.112652865 374.7538981 394879.1611 0.029413312 0.039804106 1829.269507 -3.262277695 0.113450298 GPREPGPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GPREPGPAGR 10 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 140.07 3.64E-05 518663000 262047 367332 272285 229940 336320 353765 201288 267414 291869 448917 FALSE TRUE 272392.8179 430418.4136 279380.9708 275421.4457 279152.4465 271608.4401 185510.5206 263829.7527 281364.6917 536873.6911 0.507368535 0.80171262 0.520384916 0.513009764 0.519959259 0.505907525 0.345538483 0.491418665 0.524079865 1 19.03422318 -0.792568015 6.516411421 1.000000006 0.522110205 0.646248226 0.105295393 9.59E-09 1.96E-09 0.107270689 0.025283944 0.161224851 0.792568015 -0.477889802 GPRIS(ph)APNVDFNLEGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPRISAPNVDFNLEGPK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 GPRIS(1)APNVDFNLEGPK 172.61 9.57E-10 80679000 76565 81955 76345 48256 109740 101990 61463 73418 89116 107260 TRUE FALSE 79587.84532 96030.13373 78334.61342 57800.89277 91086.434 78304.36817 56645.36946 72433.9518 85908.73257 128275.5434 0.620444422 0.74862387 0.610674579 0.450599477 0.71008418 0.610438795 0.441591343 0.564674683 0.669720278 1 16.96888661 0.846720634 4.026895914 0.999957024 0.591723569 0.6375491 0.091333665 0.664525474 16.56524691 0.090962963 0.023237739 7.026202035 -0.846720634 -0.408233455 GPS(ph)PAPAS(ph)SPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.567)S(0.433)PKR;GPS(1)PAPAS(0.558)S(0.442)PKR;GPS(1)PAPAS(0.616)S(0.384)PKR 101.42 0.0093799 774762000 2455720 1520620 1772910 1560834 2242220 2430710 2362750 1922570 1991210 1363852 TRUE FALSE 2552673.722 1781774.656 1819113.491 1869562.307 1861088.245 1866214.44 2177551.481 1896801.094 1919546.741 1631072.687 1.565027569 1.092394392 1.115286588 1.146216427 1.141021035 1.144163872 1.335042576 1.162916349 1.176861557 1 20.63738964 4.744289666 24.99581808 1.158772087 1.565027743 0.71109947 0.079754252 346.2824845 1510785.088 0.018810639 0.167895573 55499.57603 -4.744289666 0.406255656 GPS(ph)PAPASS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 GPS(1)PAPAS(0.077)S(0.923)PK;GPS(1)PAPAS(0.296)S(0.704)PK;GPS(1)PAPAS(0.025)S(0.975)PK;GPS(1)PAPAS(0.02)S(0.98)PK 153 0.001492 465960000 2914920 1520800 1704910 1584860 2169770 2881380 2316270 1852610 1926150 1284620 TRUE FALSE 3030003.292 1781985.57 1749341.355 1898340.578 1800953.27 2212223.163 2134714.705 1827778.793 1856828.238 1536316.693 1.972251753 1.159907705 1.138659342 1.235644048 1.172253923 1.439952565 1.389501731 1.189714856 1.208623356 1 20.55104421 4.741900458 24.94929821 1.230818292 1.972252038 0.784287007 0.118891317 141.780815 1059082.631 0.028479125 0.206067978 55195.0916 -4.741900458 0.741433746 GPS(ph)PEPPPS(ph)PLQVPTYPQLTLEVPQAPEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSPEPPPSPLQVPTYPQLTLEVPQAPEVLR 31 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 2 GPS(1)PEPPPS(0.972)PLQVPT(0.009)Y(0.019)PQLT(0.001)LEVPQAPEVLR 63.282 0.0066837 15506000 13619 12941 13309 14252 15888 15290 13432 14742 14342 16489 TRUE FALSE 14156.68864 15163.51608 13655.84347 17071.00306 13187.36344 11739.12922 12379.16474 14544.4076 13825.83422 19719.70385 0.7178956 0.768952526 0.692497391 0.865682527 0.66874044 0.595299469 0.627756118 0.737557101 0.701117741 1 14.26735027 -1.677857174 5.421389902 1.005227484 0.708422112 0.60237812 0.071076497 0.004729865 0.000281052 0.072481898 0.016854828 0.020996303 1.677857174 -0.296805372 GPS(ph)PRPPATAYDAPASAFGSSLLGSGGSAFAPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GPS(0.999)PRPPAT(0.001)AYDAPASAFGSSLLGSGGSAFAPPLR;GPS(0.998)PRPPAT(0.002)AYDAPASAFGSSLLGSGGSAFAPPLR 317.53 3.92E-105 1596140000 265805 312645 250395 282025 274555 336875 292487 261287 255428 273464 TRUE FALSE 276299.1866 366339.3467 256920.4994 337808.7032 227886.2392 258640.8866 269561.1047 257784.8751 246235.1962 327044.035 0.844837872 1.120152969 0.785583811 1.032915042 0.69680598 0.790844226 0.824234891 0.788226806 0.752911443 1 18.31912538 3.242118606 24.99991108 0.798037893 0.94687184 0.257745657 0.113031801 110.2960417 774979.1877 0.028983525 0.037746109 1746.299002 -3.242118606 0.148833947 GPS(ph)PSS(ph)PTPPAAAAPAEQAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPSPSSPTPPAAAAPAEQAPR 21 0 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 GPS(1)PSS(0.997)PT(0.003)PPAAAAPAEQAPR;GPS(1)PSS(0.985)PT(0.015)PPAAAAPAEQAPR 324.9 5.08E-66 257980000 375021 437625 415089 420932 464313 496720 386898 400914 396207 453944 TRUE FALSE 389827.1187 512783.6895 425906.5603 504191.0932 385389.2421 381364.3079 356571.9238 395540.4036 381947.5875 542885.6355 0.718064898 0.944551957 0.78452354 0.928724321 0.709890292 0.702476328 0.656808544 0.728588818 0.703550734 1 19.05028879 3.217719642 24.96265709 0.727868398 0.846904991 0.133341135 0.108344598 327.9325193 392786.1593 0.028567573 0.034179156 1650.895723 -3.217719642 0.119036593 GPS(ph)PTPEDVSMKEENLCQAFSDALLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSPTPEDVSMKEENLCQAFSDALLCK 27 1 H1UBN3;O95067 H1UBN3 CCNB2V;CCNB2 G2/mitotic-specific cyclin-B2 1 GPS(0.819)PT(0.18)PEDVS(0.001)MKEENLCQAFSDALLCK 112.95 0.0016488 29242000 56434 33982 49683 40575 59997 60408 61683 52461 55936 38348 TRUE FALSE 58662.0579 39818.14416 50977.7798 48600.6139 49798.73137 46379.15749 56848.12528 51757.8461 53922.87429 45861.55638 1.279111799 0.868224877 1.111557998 1.059724478 1.085849136 1.011286165 1.239559443 1.128567153 1.175775062 1 15.4849977 2.256346245 24.99932426 1.148064512 1.06239182 0.074537295 0.110316494 482.944124 678820.5589 0.035136766 0.029339493 180.4455783 -2.256346245 -0.085672692 GPS(ph)WDPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 105.86 0.0045169 25097159000 8469470 9532690 10000700 10989040 10315260 11923910 13505120 11055220 11012830 9141610 TRUE FALSE 8803851.215 11169855.35 10261326.46 13162639.31 8561875.79 9154762.611 12446553.41 10907042.86 10616480.4 10932733.45 0.805274477 1.021689169 0.938587454 1.203965995 0.783141364 0.837371793 1.138466739 0.997650122 0.971072829 1 23.38215082 2.241255159 24.99933874 1.027494825 0.941703414 0.125600208 0.121232783 173.0602981 1605629.584 0.043648642 0.035005381 174.2830528 -2.241255159 -0.085791411 GPS(ph)WDPFRDWYPHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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;GPS(1)WDPFRDWYPHSR;GPS(0.997)WDPFRDWYPHS(0.003)R;GPS(1)WDPFRDWYPHSR 203.06 3.39E-09 25628024700 8968730.4 12843273.4 12421877.9 11193528.3 14402231.9 15003945.1 11533348.1 13013037.3 14515569.2 17471050.5 TRUE FALSE 9322822.802 15049005.7 12745602.24 13407574.79 11954145.67 11519506.24 10629334.14 12838618.82 13993156.7 20894168.34 0.446192576 0.720249088 0.610007636 0.641689804 0.572128331 0.551326382 0.508722528 0.614459432 0.669715897 1 24.316597 0.721913365 1.959157416 0.999775835 0.585768334 0.760845873 0.070072462 0.516725586 2.921457856 0.0645053 0.017877278 5.271246983 -0.721913365 -0.414007501 GPSFDVQVGLHELLGHGSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSFDVQVGLHELLGHGSGK 20 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 61.102 0.030731 7462600 5432.9 10632 8808.3 9738.4 8773.7 13718 7400.1 10013 6820.9 11036 FALSE TRUE 5647.395087 12457.96329 9037.851534 11664.62645 7282.349608 10532.2024 6820.060825 9878.792113 6575.417141 13198.2929 0.427888298 0.943907169 0.684774281 0.88379812 0.551764509 0.797997323 0.516738102 0.748490141 0.498202092 1 13.68806372 -1.040603483 8.605322955 1.000000001 0.685257056 0.259983458 0.164461118 5.11E-09 6.18E-10 0.142716493 0.0336386 0.091074442 1.040603483 -0.314742945 GPSFPEPLREEQDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSFPEPLREEQDLER 16 1 A0A1B0GVZ4;A0A494C085;P06132;A0A1B0GVN9;H0Y5R6;Q5T446;A0A494BZY8;A0A494C0Q8;A0A494C1D8;A0A494C0S8 A0A1B0GVZ4 UROD Uroporphyrinogen decarboxylase 0 88.551 0.0055556 193100000 75176 150980 123410 153220 120010 167840 126250 145930 116060 146020 FALSE TRUE 78144.00653 176909.6405 126626.166 183526.4587 99610.74307 128861.7036 116354.1951 143974.047 111883.0233 174629.8233 0.447483741 1.013055143 0.725111917 1.050945682 0.570410834 0.737913497 0.666290516 0.824452802 0.640686803 1 17.41394044 -1.025612338 4.29805374 1.000014832 0.755196046 0.158563961 0.176013749 61978.10951 91772234.85 3279.469904 0.03750271 0.094273072 1.025612338 -0.244818786 GPSHPLDLGTSS(ph)PNTSQIHWTPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPSHPLDLGTSSPNTSQIHWTPYR 24 0 O60504-2;O60504;H0YAZ3 O60504-2 SORBS3 Vinexin 1 GPSHPLDLGTS(0.166)S(0.833)PNTSQIHWTPYR;GPSHPLDLGT(0.001)S(0.082)S(0.917)PNTSQIHWTPYR 209.79 8.17E-25 975370000 238700 709630 645750 723560 666390 979620 682970 820720 680760 949290 TRUE FALSE 248124.0603 831503.4323 662578.7755 866678.0084 553117.2658 752118.1013 629437.0268 809719.5908 656259.5806 1135285.2 0.218556588 0.732418103 0.583623195 0.763401133 0.487205564 0.66249265 0.554430752 0.713230112 0.578057021 1 20.11462334 -5 0.175468243 2.57204014 0.514488684 0.442304134 0.144306404 122.619554 1.170902706 67.27554894 0.444074204 1.00E-05 5 -2.057551455 GPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSLNPVLDYDHGSR 15 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 149.99 3.26E-06 199800000 46105 203520 169890 206120 157020 239190 180020 208720 149830 176750 FALSE TRUE 47925.261 238472.9768 174317.473 246889.9208 130329.7965 183641.7475 165909.562 205922.4498 144437.6476 211380.7784 0.226724782 1.128167748 0.824660947 1.167986619 0.616564086 0.868772217 0.78488481 0.974177744 0.683305496 1 17.68948467 4.751720036 24.91495892 0.889303363 0.226724334 0.583175385 0.169264067 1417.023164 2682825.252 0.037423927 0.713466179 56457.29108 -4.751720036 -0.66257903 GPSPAPAS(ph)SPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 GPS(0.001)PAPAS(0.499)S(0.499)PKR 58.487 0.064789 67216000 47476 32290 37024 27730 37400 35334 39743 31131 33618 29094 TRUE FALSE 49350.38914 37835.55632 37988.87586 33214.91123 31042.76136 27128.21399 36627.83981 30713.73987 32408.09475 34794.41226 1.41834237 1.087403231 1.091809672 0.95460475 0.892176627 0.779671569 1.05269316 0.882720468 0.931416645 1 15.08656802 5.579337489 0.792672921 0.918205727 2.826775353 0.792057285 0.075444 3.452599618 0.625577152 0.02521657 7.939626764 379609.8641 -5.579337489 1.908569626 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPSQEEEDNHS(1)DEEDRASEPK 198.99 4.99E-22 340400000 143680 107160 129450 110970 148280 203150 143610 127760 148600 116600 TRUE FALSE 149352.5973 125563.8964 132823.5733 132919.5348 123075.4186 155971.4913 132353.4729 126047.5862 143251.915 139445.5376 1.071046087 0.900451163 0.952512183 0.953200347 0.882605645 1.118511886 0.949140971 0.903919827 1.027296517 1 17.08934224 GPSSEAMHVGHLIPFIFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPSSEAMHVGHLIPFIFTK 19 0 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ; 133.45 6.75E-06 696400000 447330 488280 672690 623710 674090 792370 739720 720520 724770 501150 FALSE TRUE 464990.9338 572138.2917 690220.854 747077.9764 559508.4226 608354.076 681738.8135 710862.6079 698685.6693 599340.7474 0.775837344 0.954612704 1.151633452 1.246499557 0.933539768 1.015038738 1.137481168 1.186074217 1.165756996 1 19.19301694 4.520246666 2.919211958 1.111996627 0.777742998 0.557778447 0.091571268 0.216290339 3.291157467 0.0240734 0.131492341 33131.92473 -4.520246666 -0.334253629 GPSSVEDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSSVEDIK 9 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 76.465 0.082251 279980000 202360 155210 171270 154390 212330 211690 198500 173730 189780 180180 FALSE TRUE 210349.3291 181866.1101 175733.4369 184927.8812 176238.2224 162528.2057 182941.0513 171401.4335 182949.8549 215482.8212 0.976176791 0.843993545 0.815533396 0.858202432 0.817875975 0.754251335 0.848982069 0.795429689 0.849022924 1 17.71721333 4.73582037 4.089254602 0.830259928 0.988251652 0.283159829 0.061368791 0.235586556 8.576434486 0.013306033 0.109503243 54427.74858 -4.73582037 0.157991724 GPSTPKS(ph)PGASNFSTLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPSTPKSPGASNFSTLPK 18 1 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 GPS(0.006)T(0.037)PKS(0.954)PGAS(0.002)NFSTLPK;GPS(0.035)T(0.043)PKS(0.922)PGASNFSTLPK 125.78 1.76E-05 732060000 540900 378370 489530 301467 598260 577560 419860 460690 545940 419800 TRUE FALSE 562255.1497 443352.1042 502287.554 361096.2728 496567.9789 443430.443 386950.2761 454515.2041 526291.726 502051.7724 1.119914679 0.883080448 1.000469636 0.719241107 0.989077235 0.883236485 0.770737795 0.905315406 1.048281781 1 18.93747662 5.278261367 1.780980505 0.897820569 1.820062495 0.263327103 0.10088477 7.266619283 5.92959088 0.024769438 18.33808111 189784.7741 -5.278261367 0.922241925 GPSWDPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;; 157.58 0.00087158 1.25481E+11 57801420 72712700 58013450 65678440 96435760 86702160 78901660 64253000 59470280 100165780 FALSE TRUE 60083464.69 85200540.6 59525328.17 78669439.4 80043643.96 66566897.32 72717141.72 63391793.63 57329956.24 119791346.8 0.501567653 0.711241195 0.496908414 0.656720552 0.668192203 0.555690366 0.607031673 0.529185082 0.478581782 1 26.83594846 -1.512843872 4.234123313 1.003621696 0.581600547 0.733156907 0.076291661 0.00250029 0.00028767 0.07081074 0.016567889 0.030701255 1.512843872 -0.422021149 GPSWDPFRDWYPHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 GPSWDPFRDWYPHS(1)R 58.123 0.070546 35365000 69498 113950 99242 72547 114510 110720 64892 92149 95667 165050 TRUE FALSE 72241.8347 133520.0261 101828.328 86896.58007 95045.6311 85006.95798 59805.59548 90913.89338 92223.96336 197388.3874 0.365988271 0.676433036 0.515878008 0.440231471 0.481515819 0.430658354 0.302984366 0.460583799 0.467220816 1 17.59067759 0.595590591 4.588055597 0.99999997 0.459970666 0.754901806 0.09228891 24.88115847 281.7987877 0.090964776 0.023070247 3.940856228 -0.595590591 -0.540029304 GPSWDPFRDWYPHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;; 174.24 8.95E-07 1.65281E+11 3411148 5427818 4191065 4331509 5201882 5330077 3515648 4413283 4470735 6740986 FALSE TRUE 3545822.757 6360003.519 4300287.597 5188268.552 4317667.956 4092247.395 3240082.323 4354130.16 4309834.121 8061753.143 0.439832713 0.788910725 0.533418417 0.643565793 0.53557432 0.50761259 0.401907906 0.540097183 0.534602591 1 22.94266218 -1.215955148 5.865897225 1.000011369 0.548298705 0.642887972 0.101221856 1.48E-05 1.98E-06 0.096703508 0.022792662 0.060819781 1.215955148 -0.451712664 GPTEADELMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPTEADELMK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 116.3 0.0025776 226700000 312900 233140 264460 239790 330410 325900 344420 280170 310550 243070 FALSE TRUE 325253.5336 273179.9814 271352.0449 287219.7463 274247.0262 250214.6641 317423.4604 276414.7794 299373.3662 290694.9126 1.118882786 0.939748064 0.933459903 0.988045314 0.943418733 0.860746622 1.091947078 0.950875875 1.029854164 1 18.1491463 2.224056595 24.99888969 1.010085275 0.961707986 0.123260193 0.069213519 572.7978542 987258.5927 0.02526854 0.01874574 167.516116 -2.224056595 -0.048377289 GPTEADELMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GPTEADELMKR 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 191.04 3.21E-06 4846490000 4582520 3987130 4489520 3094590 6475970 5031400 3703590 4127400 4740050 5336510 FALSE TRUE 4763441.428 4671888.562 4606520.579 3706690.666 5375186.933 3862933.602 3413292.938 4072078.954 4569456.526 6382096.961 0.746375597 0.732030333 0.721787934 0.580795104 0.842228967 0.605276546 0.534823109 0.638047178 0.71598043 1 22.6055991 -0.898567415 12.89490469 1 0.673097419 0.550314549 0.086675067 0 0 0.085149451 0.020069918 0.126308502 0.898567415 -0.326902581 GPTEQLVSPEPEVHDIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPTEQLVSPEPEVHDIER 18 0 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 ;; 238.94 6.73E-24 1463270000 650770 812410 772260 797920 782630 897550 762200 705150 743040 854200 FALSE TRUE 676462.9021 951935.0978 792385.73 955746.1944 649598.8321 689107.615 702456.7724 695698.6176 716298.1355 1021564.135 0.662183488 0.931840758 0.775659308 0.935571406 0.63588649 0.674561284 0.687628655 0.681013158 0.701177842 1 19.96234835 -0.80760493 6.109899622 1.000000013 0.742890619 0.361435184 0.102546044 1.90E-08 3.61E-09 0.102033343 0.024049488 0.155738171 0.80760493 -0.257109394 GPTKEELCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPTKEELCK 9 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 65.5 0.060541 189690000 143590 88139 120400 91486 152110 139100 145450 114170 136380 83230 FALSE TRUE 149259.0441 103276.1876 123537.7229 109581.6577 126254.3965 106796.1331 134049.2489 112639.7379 131471.7104 99537.32497 1.499528384 1.037562419 1.24111958 1.100910214 1.268412594 1.072925489 1.346723443 1.131633163 1.320828247 1 16.60295 4.755265047 24.69522958 1.179202397 1.499528681 0.425070164 0.114793751 2526.551369 3735090.438 0.024179847 0.65950607 56920.02034 -4.755265047 0.320326285 GPTS(ph)SPCEEEGDEGEEDRT(ph)SDLRDEASSVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 GPT(0.106)S(0.447)S(0.447)PCEEEGDEGEEDRT(0.537)S(0.463)DLRDEASSVTR 114.87 0.00011787 126490000 60104 75321 67358 77425 75907 94004 72652 77932 70511 83549 TRUE FALSE 62476.95233 88256.79583 69113.40482 92739.43391 63004.35525 72172.99564 66957.3464 76887.44901 67973.32288 99918.82691 0.62527708 0.883284948 0.691695519 0.928147745 0.630555394 0.722316283 0.670117419 0.769499116 0.680285438 1 16.60846892 -1.949656131 5.676943096 1.135381362 0.738568351 0.406817216 0.096377012 0.055469333 0.000491909 0.031344678 0.020047184 0.011229072 1.949656131 -0.396813012 GPTSS(ph)PCEEEGDEGEEDRT(ph)SDLRDEAS(ph)SVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPTSSPCEEEGDEGEEDRTSDLRDEASSVTR 31 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 3 GPT(0.038)S(0.181)S(0.781)PCEEEGDEGEEDRT(0.5)S(0.5)DLRDEAS(0.533)S(0.458)VT(0.009)R;GPT(0.004)S(0.028)S(0.968)PCEEEGDEGEEDRT(0.5)S(0.5)DLRDEAS(0.613)S(0.336)VT(0.052)R 225.96 2.30E-34 329590000 278110 122555 137063 109720 144038 163552 115111 131455 113798 126063 TRUE FALSE 289089.9975 143602.8679 140634.9744 131422.2885 119554.4722 125569.5267 106088.299 129693.0607 109702.4322 150762.6312 1.917517592 0.952509695 0.932823825 0.871716601 0.792998048 0.832895563 0.703677683 0.860246731 0.727650024 1 17.20191935 4.864315857 2.16445809 0.826230259 2.481639999 0.933357621 0.085646745 0.224442716 0.880040137 0.020479249 0.807768883 73167.1025 -4.864315857 1.65540974 GPTSS(ph)PCEEEGDEGEEDRTSDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPTSSPCEEEGDEGEEDRTSDLR 23 1 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 GPT(0.032)S(0.157)S(0.811)PCEEEGDEGEEDRTSDLR;GPT(0.006)S(0.033)S(0.961)PCEEEGDEGEEDRTSDLR 139.67 1.23E-07 465410000 379070 331360 316541 351540 390440 422030 396830 383880 361990 310412 TRUE FALSE 394035.9763 388268.5024 324790.3185 421073.5628 324073.1483 324019.9284 365725.4277 378734.7165 348962.0506 371231.2882 1.061429865 1.045893799 0.874900174 1.134262052 0.872968305 0.872824944 0.985168652 1.020212273 0.940012498 1 18.50195878 4.443782093 24.98527088 0.966568077 1.057546009 0.18316365 0.07689904 262.7123536 196883.5974 0.01834168 0.050231516 27783.18899 -4.443782093 0.090977931 GPTSTSIDNIDGT(ph)PVRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;GPTS(0.001)T(0.001)S(0.008)IDNIDGT(0.989)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER 240.87 3.94E-24 3077250000 2090750 2427160 2099050 2103580 2136210 2416280 2020080 2152590 1995250 2577490 TRUE FALSE 2173294.424 2844005.849 2153752.967 2519661.845 1773097.787 1855135.589 1861740.851 2123738.052 1923441.342 3082499.816 0.70504284 0.92262969 0.698703356 0.817408595 0.575214239 0.601828289 0.603971115 0.688966157 0.623987496 1 21.55566938 3.254759113 24.99857867 0.659641003 0.789477633 0.120338489 0.128617087 380.1013326 586593.55 0.032698221 0.044141123 1797.873427 -3.254759113 0.12983663 GPVDHGVQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPVDHGVQIR 10 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 0 ;; 163.94 6.31E-06 685610000 325064 481189 420264 437773 458552 535130 439767 432825 453105 604270 FALSE TRUE 337897.7777 563829.4676 431216.4251 524363.1928 380607.4948 410854.1675 405296.9134 427023.6888 436797.8396 722665.1371 0.467571715 0.780208479 0.596702958 0.72559636 0.526672002 0.568526343 0.560836399 0.590901189 0.604426334 1 19.46296777 -1.279226627 3.065017703 1.00243903 0.605014971 0.658337933 0.085914322 10083456.04 13451005.74 228097.4829 0.020619109 0.052574285 1.279226627 -0.397424059 GPVEGYEENEEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPVEGYEENEEFLR 14 0 F5GYQ2;Q9UI30;Q9UI30-2;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 160.16 5.35E-07 0 124210 129290 153030 172140 152360 187230 164860 169940 162860 126270 FALSE TRUE 129113.9067 151494.5518 157018.0875 206188.7782 126461.9016 143748.67 151937.8424 167662.2323 156998.7004 151010.1889 0.855001293 1.003207485 1.039784723 1.365396466 0.83743953 0.951913715 1.006142986 1.110270992 1.039656341 1 17.20428637 4.701741349 2.754700363 1.048831454 0.827391432 0.163746645 0.127462746 0.715861201 7.801817578 0.031690633 0.344786689 50320.08299 -4.701741349 -0.221440022 GPVS(ph)GTEPEPVYSMEAADYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVS(0.872)GT(0.128)EPEPVYSMEAADYR;GPVS(0.991)GT(0.009)EPEPVYSMEAADYR;GPVS(0.959)GT(0.041)EPEPVYSMEAADYR;GPVS(0.859)GT(0.141)EPEPVYSMEAADYR;GPVS(1)GTEPEPVYSMEAADYR 337.45 4.48E-80 700416000 238049 353420 350885 405202 386310 488300 369429 389262 385152 500362 TRUE FALSE 247447.3583 414117.1358 360029.3514 485349.7462 320645.1642 374899.7253 340472.1897 384044.5796 371290.4548 598398.3539 0.413516108 0.692042572 0.601654983 0.811081352 0.535838981 0.626505275 0.56897247 0.641787493 0.620473723 1 19.19074668 -0.201685208 1.324957642 1.001583869 0.61724069 0.588159128 0.097231115 22.60211704 23.50361598 0.277333319 0.025597099 0.628513763 0.201685208 -0.384343179 GPVS(ph)PSVSFQPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GPVSPSVSFQPLAR 14 0 Q7Z434;Q7Z434-4 Q7Z434 MAVS Mitochondrial antiviral-signaling protein 1 GPVS(0.959)PS(0.038)VS(0.003)FQPLAR;GPVS(0.893)PS(0.09)VS(0.017)FQPLAR;GPVS(0.976)PS(0.024)VSFQPLAR;GPVS(0.987)PS(0.013)VSFQPLAR;GPVS(1)PSVSFQPLAR;GPVS(1)PSVSFQPLAR;GPVS(1)PSVSFQPLAR;GPVS(0.998)PS(0.002)VSFQPLAR 255.39 2.92E-24 3458601000 894313 1142993 973713 1247978 1094685 1502108 1131205 1076089 1003997 1377205 TRUE FALSE 929621.1678 1339293.156 999088.7607 1494824.324 908610.8347 1153266.182 1042538.196 1061665.787 967863.3441 1647041.952 0.564418634 0.813150603 0.606595818 0.907581208 0.551662229 0.700204497 0.632976103 0.644589402 0.587637336 1 20.65144587 -1.060862347 5.723227597 1.000001386 0.671293875 0.461434968 0.10765247 1.74E-06 2.85E-07 0.09504631 0.022402536 0.08692359 1.060862347 -0.328707511 GPVSGTEPEPVYS(ph)MEAADYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVYS(1)MEAADYR 302.66 5.85E-55 1391520000 483900 732800 737100 892200 1010430 1096630 833950 915130 906110 1274860 TRUE FALSE 503004.7457 858652.6996 756309.4315 1068674.497 838677.4695 841954.3021 768582.8199 902864.1792 873499.2781 1524644.408 0.329916106 0.563182271 0.496056279 0.700933602 0.550080704 0.552229948 0.504106279 0.592180166 0.572920002 1 20.54004137 -5 0.257031101 3.878507984 0.50777593 0.734499815 0.084375115 96.60396973 0.951983151 146.5789436 0.111896506 1.00E-05 5 -3.370732055 GPVSGTEPEPVYSMEAADYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 148.62 2.52E-07 123327000 78686 86584 91566 86217 92771 107658 91651 83765 92000 102806 FALSE TRUE 81792.58404 101454.1285 93952.28518 103270.4653 77001.81856 82656.06107 84467.15513 82642.26719 88688.93797 122948.8674 0.665256914 0.825173348 0.764157387 0.839946455 0.626291402 0.672279972 0.687010437 0.67216778 0.72134815 1 16.90769892 -1.01806604 5.475662512 1.000001183 0.718324422 0.612631339 0.066959499 1.01E-06 1.81E-07 0.067649178 0.015944997 0.095925475 1.01806604 -0.281676761 GPVTDVAYSHDGAFLAVCDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GPVTDVAYSHDGAFLAVCDASK 22 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 120.75 2.83E-05 98849000 858360 217460 390940 244690 633700 654380 658570 419590 508990 170160 FALSE TRUE 892248.7156 254807.0634 401128.2176 293088.9517 525983.9004 502410.1622 606949.5625 413966.0824 490671.5493 203499.5941 4.384523319 1.252125659 1.971149964 1.440243422 2.584692627 2.46885093 2.982559082 2.034235421 2.411167214 1 17.63466639 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GPVTIPYPLFQSHVEDLYVEGLPEGIPFR 29 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 254.85 6.41E-58 739020000 217343 214410 251400 261566 269520 297300 246032 223186 227100 257718 FALSE TRUE 225923.8695 251233.2496 257951.6905 313302.9741 223707.0867 228256.5806 226747.369 220194.5567 218926.7154 308212.9078 0.733012355 0.815128904 0.836926955 1.016514773 0.72581998 0.740580861 0.735684208 0.71442354 0.710310016 1 18.23356776 GPWALEEESLVGREPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GPWALEEESLVGREPEER 18 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63 O00515 LAD1 Ladinin-1 0 ;;; 246.45 2.50E-24 589150000 463327 625710 533250 545260 635820 673160 550980 584220 602320 748260 FALSE TRUE 481619.5077 733170.8252 547146.9331 653110.8006 527743.5435 516828.7918 507792.7479 576389.4865 580642.6209 894867.2207 0.538202201 0.819306829 0.611428065 0.729841015 0.589745083 0.57754802 0.567450384 0.644106157 0.648858967 1 19.77131411 0.494544318 2.837461335 0.99999902 0.637096964 0.654498035 0.07932537 8.537469402 47.02510179 0.073322149 0.01926885 3.122801056 -0.494544318 -0.362902056 GPWWDDWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GPWWDDWER 9 0 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ;; 110.87 0.0051568 104745000 191422 211012 192247 229195 198543 223000 206611 219844 187380 176762 FALSE TRUE 198979.4884 247251.6696 197257.1148 274529.0869 164794.7318 171211.6296 190416.2899 216897.3508 180636.2304 211395.1296 0.941268083 1.169618572 0.933120433 1.298653793 0.779557846 0.809912839 0.900760062 1.026028136 0.854495706 1 17.68958261 3.217836032 24.99996771 0.901744897 1.080765992 0.370670272 0.12137775 267.5748491 322773.4696 0.034396582 0.041153594 1651.338216 -3.217836032 0.179021095 GQAALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQAALDR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 115.69 0.013082 212320000 175470 230780 208580 198640 222250 240160 193680 197880 195490 252230 FALSE TRUE 182397.6911 270414.6698 214015.7662 237930.3991 184472.0244 184386.4797 178498.8555 195227.7423 188454.3531 301649.6393 0.60466736 0.89645282 0.709484575 0.788764076 0.611543991 0.611260402 0.591742314 0.647200317 0.624745826 1 18.20251433 -1.289201402 3.560514055 1.000949469 0.67724181 0.521884155 0.092970728 33246561.13 47151291.86 331766.7617 0.02330506 0.051380532 1.289201402 -0.323707659 GQDHCGIESEVVAGIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQDHCGIESEVVAGIPR 17 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ;; 232.15 9.96E-18 1747580000 476490 789340 614150 721740 653980 795730 557460 633030 599760 895200 FALSE TRUE 495302.1931 924903.0048 630155.2535 864498.0178 542816.7132 610933.7669 513764.8285 624545.2683 578174.7548 1070597.3 0.462640988 0.863913074 0.588601572 0.807491311 0.507022307 0.570647588 0.479886161 0.58336152 0.54004877 1 20.02998449 -1.38309065 9.053259786 1.000001031 0.603520799 0.47366959 0.126329346 2.54E-06 1.73E-07 0.118150775 0.027848333 0.041391327 1.38309065 -0.396480232 GQDS(ph)PLLQRPQHLMDQGQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GQDSPLLQRPQHLMDQGQMR 20 1 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR;GQDS(1)PLLQRPQHLMDQGQMR 246.4 2.98E-30 1477558000 656565 734541 696205 783463 693625 786798 535602 604748 581983 660869 TRUE FALSE 682486.6932 860692.7028 714348.6742 938429.643 575722.8703 604076.0885 493620.1157 596642.3422 561037.5455 790353.6274 0.863520669 1.088996967 0.903834245 1.187354129 0.728437057 0.764311148 0.62455602 0.754905553 0.709856355 1 19.59213878 3.213424513 24.90675892 0.742482053 1.008853525 0.485589812 0.123511449 154.6391627 153227.7725 0.032730217 0.039134875 1634.648998 -3.213424513 0.266371472 GQDSIPHHSDYDEEEWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQDSIPHHSDYDEEEWDR 18 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 128.14 1.39E-05 166300000 15836 51676 59713 78031 52653 67347 53662 52104 55451 43924 FALSE TRUE 16461.21751 60550.95102 61269.16983 93465.2989 43703.06187 51706.6799 49455.83222 51405.6311 53455.32934 52530.06682 0.313367534 1.1526913 1.166363828 1.779272416 0.831962807 0.984325416 0.941476667 0.978594436 1.01761396 1 15.6808558 GQDSIPHHSDYDEEEWDRVWANVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQDSIPHHSDYDEEEWDRVWANVGK 25 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 105.79 0.0026148 277237000 40699 155390 174333 157853 181470 201547 133588 193492 166380 170975 FALSE TRUE 42305.82795 182077.0237 178876.2612 189075.8523 150623.7942 154740.7637 123117.0235 190898.5562 160392.0163 204474.2777 0.206900488 0.890464198 0.874810579 0.924692604 0.736639326 0.756773739 0.602114969 0.933606703 0.784411702 1 17.64155984 4.742307431 24.7605091 0.824724916 0.206900216 0.741602489 0.110886051 161.837289 1069437.425 0.026160882 0.195897167 55246.83855 -4.742307431 -0.617824699 GQDTPKPAGQHGSLS(ph)PAAAHT(ph)ASPEPPTQSGPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDTPKPAGQHGS(0.042)LS(0.958)PAAAHT(0.748)AS(0.252)PEPPTQSGPLTR 101.86 4.45E-05 181540000 43038 111230 105360 106080 117260 142060 110690 116330 111660 96827 TRUE FALSE 44737.17347 130332.8873 108105.7682 127062.3074 97328.18708 109068.7179 102013.8286 114770.7866 107641.3784 115798.3968 0.386336726 1.125515472 0.933568781 1.097271732 0.840496844 0.941884525 0.88096063 0.991125869 0.929558452 1 16.82125575 4.748400061 24.99934972 0.965694836 0.386336413 0.813645959 0.083927351 536.1018939 1362061.587 0.018974318 0.255151212 56027.3474 -4.748400061 -0.579358422 GQDTPKPAGQHGSLS(ph)PAAAHTAS(ph)PEPPTQSGPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQDTPKPAGQHGSLSPAAAHTASPEPPTQSGPLTR 35 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 2 GQDTPKPAGQHGS(0.023)LS(0.977)PAAAHTAS(0.997)PEPPT(0.002)QSGPLTR;GQDTPKPAGQHGS(0.381)LS(0.618)PAAAHT(0.001)AS(0.993)PEPPT(0.004)QS(0.001)GPLTR;GQDTPKPAGQHGS(0.017)LS(0.983)PAAAHT(0.01)AS(0.99)PEPPTQSGPLTR 188.65 2.01E-20 593020000 108691 312989 312839 309307 335459 393910 307318 362383 326438 279193 TRUE FALSE 112982.2046 366742.426 320991.8413 370487.0014 278437.799 302430.3723 283229.6121 357525.8486 314689.5601 333895.5229 0.33837592 1.098374794 0.961354134 1.109589605 0.833906956 0.905763485 0.848258191 1.070771616 0.942479125 1 18.34903722 4.745539983 24.98998565 0.97268895 0.338375626 0.810453361 0.092286749 336.7984712 1205894.068 0.021912787 0.219740188 55659.58745 -4.745539983 -0.634313324 GQEETPSWEHILFTCCHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQEETPSWEHILFTCCHNR 19 0 Q8TCD5;J3KSY6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 150.68 4.23E-08 270450000 104879 170096 165426 159891 153699 190242 138051 168223 153295 193243 FALSE TRUE 109019.7039 199308.6648 169737.1375 191516.9626 127573.2989 146061.1786 127230.2019 165968.2458 147777.9429 231105.266 0.471731803 0.862415073 0.734458113 0.828700124 0.552013812 0.632011469 0.55052922 0.718149996 0.639439964 1 17.81819061 -1.39604593 4.444554598 1.000678118 0.67219767 0.419515505 0.117807296 0.000764953 0.000103947 0.110226468 0.025928262 0.040174832 1.39604593 -0.328480448 GQEIKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQEIKER 7 1 Q9NQW5-1;A0A0U1RQY2;Q9NQV7 Q9NQW5-1 PRDM9 Histone-lysine N-methyltransferase PRDM9 0 65.252 0.064833 81833000 366520 383720 401100 383150 482090 487100 434770 423950 407260 435810 FALSE TRUE 380990.4926 449620.9251 411552.9955 458935.9264 400144.514 373978.4071 400691.5913 418267.6437 392602.7922 521198.6254 0.730989059 0.862667135 0.789627937 0.880539403 0.767739005 0.71753529 0.768788657 0.802511026 0.753269048 1 18.99147375 -1.976357386 6.690756534 1.146691815 0.788849139 0.625974468 0.049589225 0.029911002 0.000105694 0.013235311 0.011190164 0.010559482 1.976357386 -0.357842676 GQELAFPLS(ph)PDWQVDYESYTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQELAFPLSPDWQVDYESYTWR 22 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 GQELAFPLS(0.999)PDWQVDY(0.001)ESYTWR 70.213 0.011422 10543000 11502 15786 14620 14257 13415 15379 15130 12925 15566 14305 TRUE FALSE 11956.10784 18497.1227 15001.00921 17076.99205 11134.72309 11807.46032 13944.07107 12751.76152 15005.7827 17107.79086 0.698869184 1.081210476 0.876852501 0.99819972 0.650856863 0.690180305 0.815071401 0.745377449 0.877131526 1 14.06236586 3.251537099 24.9981067 0.777821969 0.923104177 0.153766464 0.129816945 332.6382962 640796.1352 0.033700274 0.045351495 1784.584426 -3.251537099 0.145282208 GQETSTNPIASIFAWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQETSTNPIASIFAWTR 17 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 205.28 1.87E-11 196242000 103924 107019 102454 100120 124658 129011 110563 108907 106235 107289 FALSE TRUE 108026.9998 125398.6808 105124.0354 119923.4372 103468.6777 99050.15043 101896.7832 107447.2798 102411.6231 128310.2254 0.841920427 0.977308553 0.819295852 0.934636634 0.806394638 0.771958354 0.794143903 0.837402315 0.798156365 1 16.96927662 3.225905726 24.99138534 0.821856662 0.894006346 0.120601588 0.072746147 354.2325777 699551.3487 0.019299602 0.023213872 1682.308835 -3.225905726 0.072149685 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQER 39 1 P51148;P51148-2;K7ERI8;K7ERQ8;F8VVK3;F8VWU4 P51148 RAB5C Ras-related protein Rab-5C 0 90.246 0.0002448 17925000 14265 12863 14781 12288 20305 20174 16752 14184 16742 10521 FALSE TRUE 14828.19321 15072.12019 15166.205 14718.52972 16853.56335 15488.89424 15438.93447 13993.88668 16139.45869 12582.38851 1.178487948 1.197874328 1.205351829 1.169772314 1.339456601 1.230997932 1.227027321 1.112180463 1.2827023 1 13.61911819 -0.944607855 4.497507298 0.999996219 1.210999951 0.543856355 0.059182224 3826770.241 850864.7053 142.0425084 0.014104991 0.113603613 0.944607855 0.211003733 GQFQGRPVSVWDVLFSSYLSEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQFQGRPVSVWDVLFSSYLSEAR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 275.2 9.25E-52 937210000 668170 762240 717030 820290 717890 823630 801580 778030 684490 733760 FALSE TRUE 694549.8675 893148.7906 735716.3908 982540.9137 595863.3142 632354.4147 738750.0651 767601.7805 659855.3386 877526.2233 0.791486168 1.017802963 0.838398183 1.119671285 0.67902622 0.720610277 0.841855258 0.874733723 0.751949425 1 19.74308271 3.224432717 24.99999615 0.807943318 0.939876982 0.224806487 0.118572795 340.3813443 602319.8931 0.032801599 0.03938263 1676.612566 -3.224432717 0.131933664 GQFSTDELVAEVEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 282.52 1.27E-33 5007800000 5502070 4125330 5192450 4361470 6205890 5945030 5832820 5251680 5673840 4242050 FALSE TRUE 5719295.972 4833823.337 5327769.513 5224155.748 5151015.034 4564386.88 5375628.327 5181289.82 5469639.607 5073198.479 1.127355059 0.952815735 1.050179593 1.029755838 1.015338756 0.899705955 1.05961325 1.02130635 1.078144218 1 22.27446417 -1.50507917 5.48407682 0.999957454 1.022031275 0.012674126 0.060254256 2.93E-05 2.65E-06 0.054582712 0.012840474 0.031255095 1.50507917 0.02207382 GQGESDPLDHEPAVS(ph)PLLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GQGESDPLDHEPAVSPLLPR 20 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR 235.73 9.68E-30 3928860000 1446730 1977780 1839810 1976990 2017170 2163720 1768160 1833200 1737390 2076660 TRUE FALSE 1503848.018 2317448.33 1887756.96 2368032.721 1674292.164 1661228.821 1629566.999 1808628.953 1674861.673 2483541.767 0.605525559 0.93312235 0.76010679 0.953490194 0.674155026 0.668895061 0.656146404 0.728245837 0.674384339 1 21.24396758 4.014077041 24.98020726 0.747408251 0.788646538 0 0.136468928 1427.900297 2533820.378 0.032801579 0.070806386 10329.44627 -4.014077041 0.041238287 GQGPRS(ph)PHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQGPRSPHK 9 1 Q86U38;Q86U38-2 Q86U38 NOP9 Nucleolar protein 9 1 GQGPRS(1)PHK;GQGPRS(1)PHK 61.958 0.051793 123842000 113054 93218 101623 85611 124981 124201 117333 102203 95827 110145 TRUE FALSE 117517.4592 109227.4664 104271.3789 102544.6003 103736.7743 95357.20003 108136.1329 100833.136 92378.20499 131725.8039 0.892136967 0.829203263 0.79157899 0.778470104 0.787520525 0.723906761 0.820918375 0.765477476 0.70129164 1 17.00717846 4.642792798 1.740938315 0.783987367 0.916691189 0.112937263 0.076733119 1.270131285 4.482750504 0.018145901 0.262546344 43933.196 -4.642792798 0.132703823 GQGS(ph)SPVAMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQGSSPVAMQK 11 0 P18206;P18206-2 P18206 VCL Vinculin 1 GQGS(0.722)S(0.278)PVAMQK 83.617 0.064791 98717000 270480 254660 256510 259970 296940 333900 329870 272850 262450 276880 TRUE FALSE 281158.7593 298395.874 263194.8613 311391.2901 246466.2449 256356.7853 304013.9274 269192.892 253004.4758 331129.3348 0.84909046 0.901145995 0.794840063 0.940391736 0.744320176 0.774189292 0.918112337 0.812953924 0.764065424 1 18.3370353 -1.72231144 2.918910773 1.02548348 0.835049133 0.375140246 0.064530484 13842239.88 14713811.08 2605408.102 0.014871848 0.018953462 1.72231144 -0.190434347 GQGSS(ph)PVAMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQGSSPVAMQK 11 0 P18206;P18206-2 P18206 VCL Vinculin 1 GQGSS(1)PVAMQK;GQGS(0.023)S(0.977)PVAMQK 219.97 9.95E-12 847780000 1705440 1671320 1577140 1743500 1765650 2124000 2179000 1781920 1647850 1797820 TRUE FALSE 1772772.088 1958356.209 1618241.564 2088359.096 1465525.444 1630733.19 2008204.286 1758036.277 1588544.2 2150068.408 0.824518923 0.910834373 0.752646548 0.971298908 0.681618054 0.758456421 0.934018787 0.817665276 0.73883426 1 21.03595113 -0.865868983 6.680837299 1.000000005 0.824714453 0.268045823 0.088508026 6.03E-09 9.03E-10 0.080953623 0.019080951 0.136185546 0.865868983 -0.175285551 GQGTLQHS(ph)PVGPAGPASIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQGTLQHSPVGPAGPASIER 20 0 E7EWR4 E7EWR4 CSTF2 1 GQGTLQHS(1)PVGPAGPASIER;GQGTLQHS(1)PVGPAGPASIER 192.89 6.02E-18 342500000 373690 351450 279960 316300 340590 407700 296870 302950 315830 337240 TRUE FALSE 388443.5698 411808.8036 287255.9876 378863.1959 282696.6335 313017.8538 273600.5537 298889.4508 304463.34 403315.7212 0.963125287 1.021058149 0.712236029 0.939371257 0.700931351 0.776111213 0.678378103 0.741080586 0.754900749 1 18.62155012 4.243674359 24.99972004 0.773190339 0.992091798 0.393854387 0.100018546 104.7143711 511903.9969 0.02287579 0.058800824 17525.65908 -4.243674359 0.218901459 GQGTYEDYLEGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQGTYEDYLEGFR 13 0 P14649 P14649 MYL6B Myosin light chain 6B 0 148.62 0.00010086 52886000 93948 112350 93417 101380 101390 113790 101620 90853 99800 106390 FALSE TRUE 97657.13958 131645.2385 95851.52376 121432.6614 84155.76402 87363.997 93654.75887 89635.26414 96208.21749 127235.0835 0.767533112 1.03466147 0.753341933 0.954396052 0.66141949 0.686634492 0.736076531 0.704485443 0.756145356 1 16.95713701 3.238504183 25 0.735738493 0.879842935 0.18766403 0.1171772 1.937774136 858399.5991 0.030282087 0.038470093 1731.825711 -3.238504183 0.144104442 GQHHQQQQAAGGSESHPVPPTAPLT(ph)PLLHGEGASQQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQHHQQQQAAGGSESHPVPPTAPLTPLLHGEGASQQPR 38 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 GQHHQQQQAAGGSESHPVPPT(0.003)APLT(0.997)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.009)APLT(0.991)PLLHGEGASQQPR;GQHHQQQQAAGGSESHPVPPT(0.073)APLT(0.927)PLLHGEGASQQPR 243.46 3.17E-50 868700000 95189 190616 204378 233868 233564 265968 161463 222277 192689 241075 TRUE FALSE 98947.13522 223352.8152 209704.2586 280126.3924 193862.8747 204200.9628 148807.1082 219297.7404 185754.1605 288309.0306 0.343198182 0.774699338 0.727359314 0.971618516 0.672413467 0.70827113 0.51613752 0.760634309 0.644288388 1 18.1372565 -2.243585057 2.137070043 2.023823174 0.691278168 0.269906952 0.156954943 9876063.6 1545974.474 48868767.93 0.036892126 0.005707093 2.243585057 -1.332545006 GQHPNPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GQHPNPLR 8 0 M0R1K3;Q15102;M0R389;M0QZT2 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;;; 94.114 0.010589 3673160000 1725232 2074270 1745540 1853710 2245450 2241240 1870650 1831680 1708920 2478510 FALSE TRUE 1793345.492 2430509.737 1791030.206 2220368.305 1863769.211 1720745.976 1724023.565 1807129.326 1647416.303 2964126.581 0.605016501 0.819975015 0.604235399 0.749080124 0.628775176 0.580523783 0.581629535 0.609666719 0.555784734 1 21.49917563 -1.220670548 5.208026396 1.000031581 0.638423932 0.657089024 0.078624325 2.89E-05 4.33E-06 0.076333404 0.017990387 0.060162996 1.220670548 -0.361607649 GQICWYQKPGVGLDAINDANLLEACIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQICWYQKPGVGLDAINDANLLEACIYR 28 1 P14324-2;P14324;A0A087WVN4;A0A087X090 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;; 360.36 1.82E-111 1270497000 964174 794222 916405 925706 1056027 1095441 928479 1000059 1008034 800342 FALSE TRUE 1002240.334 930623.4503 940287.2671 1108807.884 876523.9077 841041.4293 855702.3899 986654.8449 971755.0532 957153.6914 1.047104914 0.972282151 0.982378562 1.158442885 0.915760881 0.878690055 0.894007303 1.030821752 1.015254981 1 19.86839107 GQIQEAIALINSLHPELLDTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQIQEAIALINSLHPELLDTNR 22 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 104.41 0.00055203 80585000 49377 80453 82750 112180 71530 126990 99485 95931 79436 60494 FALSE TRUE 51326.44209 94270.17691 84906.53298 134368.8692 59371.35615 97498.49705 91687.10574 94645.20186 76577.11388 72346.64107 0.709451625 1.303034606 1.173607119 1.857292435 0.820651177 1.34765755 1.267330513 1.308218329 1.058475041 1 16.14263842 1.114641804 5.258677054 1.004071786 1.240991315 0.06398036 0.294022846 0.517794795 20.00672377 0.262980094 0.066587436 13.02092401 -1.114641804 0.236919529 GQKPALDCSQVSPPRPAT(ph)SPENNASLSDTSPMDSSPSGIPK ddPTM_MDA-MB-175_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(0.016)QVS(0.111)PPRPAT(0.344)S(0.344)PENNAS(0.111)LS(0.044)DT(0.02)S(0.008)PMDS(0.001)SPSGIPK 44.6 0.072055 81889000 26180 15926 24047 16803 24300 26118 25488 23413 26958 14941 TRUE FALSE 27213.60662 18661.16661 24673.68457 20126.58325 20169.49468 20052.49032 23490.18396 23099.18703 25987.78685 17868.40289 1.523001624 1.044366793 1.380855622 1.126378411 1.128779937 1.122231822 1.314621352 1.292739322 1.454398975 1 14.12512307 2.197262037 24.99785568 1.291031328 1.211691701 0.005604318 0.169596989 506.877686 306807.8369 0.059263711 0.043769507 157.4932833 -2.197262037 -0.079339626 GQKPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQKPEQR 7 1 Q92522 Q92522 H1FX Histone H1x 0 ; 80.18 0.027919 77886000 165627 152597 177591 143481 199892 180634 182018 180746 182943 161110 FALSE TRUE 172166.0819 178804.3477 182219.1674 171861.1136 165914.4292 138684.491 167750.9535 178323.3955 176358.9172 192676.4199 0.893550347 0.92800327 0.94572635 0.891967547 0.861103966 0.719779261 0.870635616 0.925507105 0.915311367 1 17.5558205 1.013803796 1.43025455 0.996175911 0.875482517 0.289746971 0.058683648 0.60896387 2.54289703 0.061092161 0.018276046 10.32294935 -1.013803796 -0.120693393 GQKS(ph)PAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQKSPAEQK 9 1 Q9H6Z4;Q9H6Z4-2;K7EPW1;K7EMT3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 GQKS(1)PAEQK;GQKS(1)PAEQK 107.09 0.001714 161493000 428890 207240 282910 169628 415320 378210 359160 291860 331780 197142 TRUE FALSE 445822.9084 242831.8579 290282.867 203179.9121 344724.0547 290376.4593 331008.1007 287948.0941 319839.3026 235768.2004 1.890937402 1.029960179 1.231221456 0.861778271 1.462131255 1.231618424 1.403955666 1.221318624 1.356583721 1 17.84700962 -4.999999831 0.028307139 5.00E-10 2.03303583 0.098636797 0.260076825 5520.258437 11.77848727 643.5050514 274.465945 1.00E-05 4.999999831 2.03303583 GQLGDVGALDTVWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQLGDVGALDTVWR 14 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 129.71 0.00028048 0 24812 27760 28789 29788 33147 37841 28011 32289 31875 30046 FALSE TRUE 25791.59692 32527.56406 29539.26499 35679.97749 27512.68478 29053.00124 25815.42463 31856.21877 30727.82498 35932.93843 0.717770326 0.905229727 0.822066502 0.992960193 0.765667546 0.808533966 0.718433442 0.886546443 0.855143674 1 15.1330193 0.696205167 1.546480428 0.999417889 0.828623502 0.29459053 0.080418743 1.385700708 5.080694335 0.074172221 0.021436474 4.968269742 -0.696205167 -0.170794388 GQLGHGDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQLGHGDTK 9 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 119.16 0.00087304 475960000 847080 664720 759710 636410 938210 999730 933260 820320 864900 637730 FALSE TRUE 880523.3725 778880.4892 779508.6667 762289.9985 778733.3993 767557.8586 860108.6426 809324.9522 833772.4179 762680.9834 1.154510722 1.021240212 1.022063856 0.999487355 1.021047353 1.006394384 1.127743659 1.061157902 1.093212544 1 19.5407202 2.261679977 24.97795028 1.075936401 1.033548663 0.085221335 0.050927633 452.2327093 488587.3866 0.017142696 0.014333346 182.6753621 -2.261679977 -0.042387738 GQLGHGDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQLGHGDTKR 10 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 90.685 0.0069214 101542000 116881 111730 115647 108818 144690 141038 120001 118254 121346 135576 FALSE TRUE 121495.5521 130918.7584 118660.8558 130341.8756 120095.6455 108284.062 110595.0081 116668.9986 116978.7812 162139.5214 0.749327191 0.807445077 0.731844123 0.803887137 0.740693228 0.667844958 0.682097783 0.719559288 0.721469881 1 17.30687626 -1.144539424 4.936194053 1.000015891 0.734618484 0.777147731 0.042402355 8.09E-06 1.40E-06 0.044770723 0.010551929 0.071690329 1.144539424 -0.265397407 WISLNTVALVTDNAVYHWSMEGESQPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WISLNTVALVTDNAVYHWSMEGESQPVK 28 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 361.4 1.41E-111 1189330000 316871 794750 1082770 952820 1056690 1298640 1080830 1193540 1043550 847130 FALSE TRUE 329381.3118 931242.1302 1110987.876 1141284.952 877074.2112 997050.5411 996111.7204 1177542.549 1005992.839 1013108.904 0.325119353 0.919192523 1.096612488 1.126517542 0.865725499 0.984149421 0.983222748 1.162305991 0.992976012 1 19.95035783 4.729720399 3.240932373 1.032622393 0.231966474 0.869623676 0.080954981 0.107941959 1.831397816 0.020832182 0.215120741 53668.6164 -4.729720399 -0.800655919 down GQMQKPFEDASFALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQMQKPFEDASFALR 15 1 K7EN45;Q13526 K7EN45 PIN1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 0 ; 198.15 7.36E-09 2180900000 1373020 1612330 1617010 1561310 1886790 2034200 1766810 1543400 1829670 1867120 FALSE TRUE 1427227.89 1889235.135 1659150.609 1870132.458 1566074.11 1561787.879 1628322.816 1522713.247 1763820.534 2232946.416 0.639167998 0.846072759 0.743031986 0.83751784 0.70134872 0.699429179 0.729226104 0.681930044 0.789907237 1 21.0905172 0.96849184 18.93838987 1.000000002 0.736739469 0.628086557 0.061135033 88.5436138 53221.19882 0.057346824 0.014336706 9.300190406 -0.96849184 -0.263260533 GQNHNVQGFHPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQNHNVQGFHPYR 13 0 K7EQ55;K7EK33;Q96EP5 K7EQ55 DAZAP1 DAZ-associated protein 1 0 ; 130.44 8.22E-05 215297000 195261 190289 210821 198921 264870 247810 202026 192297 233750 184643 FALSE TRUE 202970.0551 222969.6555 216315.1685 238266.9801 219847.492 190259.8831 186190.6742 189719.5732 225337.3832 220820.2606 0.919164095 1.009733685 0.979598375 1.07900869 0.995594749 0.861605192 0.843177495 0.859158361 1.020456105 1 17.75251302 2.756741605 20.64118594 0.898103012 1.000980101 0.239555128 0.066756267 95.25181882 108139.6772 0.020394316 0.021553134 571.1387216 -2.756741605 0.102877088 GQNQDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQNQDYR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;; 126.04 0.0092852 2552400000 3670010 4440600 3853760 3982190 4230900 4591810 3889690 4041800 3828780 4676300 FALSE TRUE 3814904.829 5203238.507 3954192.151 4769855.296 3511733.129 3525431.717 3584805.934 3987626.282 3690982.956 5592531.452 0.682142758 0.930390567 0.707048711 0.852897357 0.627932656 0.630382099 0.640998797 0.713027064 0.6599843 1 22.41507003 5.055133505 15.61839131 0.735078877 0.297747858 0.01181729 0.126655047 10549314.4 74589980.94 0.029080079 142195104.6 113535.978 -5.055133505 -0.437331019 GQPEGPLPSS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQPEGPLPSSSPR 13 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 GQPEGPLPS(0.001)S(0.754)S(0.245)PR 158.28 4.99E-05 157930000 161920 184520 182350 201970 200810 220190 171240 168620 179990 200000 TRUE FALSE 168312.7266 216209.8746 187102.1908 241919.0632 166676.3879 169054.2095 157817.7613 166359.9247 173512.1951 239186.1708 0.703689206 0.903939697 0.782245019 1.011425796 0.69684793 0.70678923 0.659811396 0.695524846 0.725427371 1 17.86777445 GQPEGPLPSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQPEGPLPSSSPR 13 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 GQPEGPLPSS(0.112)S(0.888)PR;GQPEGPLPS(0.175)S(0.196)S(0.629)PR;GQPEGPLPS(0.001)S(0.384)S(0.615)PR 139.64 4.09E-05 678880000 742570 856310 758370 932920 879890 984060 780760 787730 781770 863630 TRUE FALSE 771887.237 1003374.581 778133.7452 1117448.792 730326.6121 755526.9786 719561.9911 777171.7678 753634.2504 1032841.763 0.74734317 0.9714698 0.753391055 1.081916738 0.707104068 0.731503126 0.696681734 0.752459666 0.729670582 1 19.97818781 GQPFEVLIIAS(ph)DDGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQPFEVLIIASDDGFK 16 0 P47929 P47929 LGALS7 Galectin-7 1 GQPFEVLIIAS(1)DDGFK 53.777 0.095735 789770000 60668 518330 216540 428010 119120 277130 99797 189190 211900 1506300 TRUE FALSE 63063.21949 607349.1455 222183.2103 512669.1005 98872.02495 212770.7574 91974.65037 186654.2175 204273.7604 1801430.645 0.035007298 0.337148226 0.123337088 0.284589974 0.05488528 0.118112101 0.051056448 0.103614434 0.113395296 1 20.78071168 -1.182866666 4.510607998 1.000177815 0.136586996 0.8835863 0.094117318 45276471.02 23746799.02 75755.47995 0.021427377 0.065634674 1.182866666 -0.863590819 GQPGDIYHQTWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQPGDIYHQTWAR 13 0 P04062-4;P04062-5;P04062-2;P04062;A0A0G2JNZ5;A0A0G2JNZ0;A0A0G2JLB3;P04062-3 P04062-4 GBA Glucosylceramidase 0 ; 109.07 0.0011661 517010000 161362 290480 239790 265220 273570 312560 247370 264170 239922 253920 FALSE TRUE 167732.6964 340367.6804 246039.1244 317679.7244 227068.6691 239972.6769 227980.493 260629.2332 231287.2541 303670.7624 0.552350496 1.120844423 0.810216705 1.046132074 0.747746234 0.79023965 0.750748907 0.858262518 0.761638204 1 18.21214849 GQPIYIQFSNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQPIYIQFSNHK 12 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ; 273.44 9.11E-28 5733300000 781580 2080190 2013760 2008080 2642500 2734600 1970870 2214400 2010340 2501800 FALSE TRUE 812437.3819 2437446.451 2066240.24 2405272.23 2193328.794 2099530.593 1816388.059 2184719.59 1937988.256 2991979.81 0.27153839 0.81466006 0.690592976 0.803906571 0.733069383 0.701719506 0.607085667 0.730191956 0.647727718 1 21.51266901 -5 0.286748211 3.42023138 0.660444097 0.324213409 0.14496876 288.8676504 2.736799121 417.9701166 0.148534451 1.00E-05 5 -2.759787284 GQPSNKEDVDDLVSQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GQPSNKEDVDDLVSQLR 17 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;;; 191.21 2.33E-10 900610000 790486 616778 719706 566537 853684 838067 800732 760693 771050 626258 FALSE TRUE 821694.9977 722704.8236 738462.1296 678596.3277 708575.0986 643438.6403 737968.5335 750497.1546 743300.0611 748961.2647 1.09711281 0.964942859 0.985981738 0.906049965 0.946077096 0.859108035 0.985322697 1.002050693 0.99244126 1 19.51453158 -0.4084051 6.692860044 1.000014171 0.968403665 0.019361278 0.059342385 0 0 0.057899025 0.013646931 0.390476498 0.4084051 -0.031610506 GQPVAPYNTTQFLMDDHDQEEPDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQPVAPYNTTQFLMDDHDQEEPDLK 25 0 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 199.92 6.91E-25 225600000 51552 36215 40064 37387 51275 50486 48067 46003 46712 32246 FALSE TRUE 53587.31277 42434.64454 41108.10075 44782.03701 42559.29381 38761.39162 44299.38294 45386.40503 45030.84424 38563.98631 1.389568815 1.100369764 1.065971252 1.161239833 1.103602036 1.005118903 1.148724164 1.176911657 1.167691635 1 15.23496657 4.739956752 24.8566627 1.11147603 1.389568912 0.662305403 0.061074262 70.22248607 1250095.922 0.014824848 0.093529266 54948.61524 -4.739956752 0.278092883 GQRDS(ph)SYYWEIEASEVMLSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQRDSSYYWEIEASEVMLSTR 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 GQRDS(0.843)S(0.156)YYWEIEASEVMLSTR 187.38 1.76E-17 32805000 24804 35800 32914 37005 45189 49540 34423 35456 40864 44166 TRUE FALSE 25783.28107 41948.37151 33771.76588 44324.47855 37507.78992 38035.08579 31724.83531 34980.77031 39393.31262 52819.48209 0.488139604 0.794183696 0.63938086 0.839169125 0.710112792 0.720095773 0.600627535 0.662270225 0.745810278 1 15.68878254 0.850314276 4.183795886 0.999974883 0.686738786 0.512334044 0.092830638 0.827810272 22.12032262 0.084029358 0.02141769 7.084582722 -0.850314276 -0.313236097 GQRDSS(ph)YYWEIEASEVMLSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQRDSSYYWEIEASEVMLSTR 21 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 GQRDS(0.297)S(0.377)Y(0.141)Y(0.185)WEIEASEVMLSTR 89.039 0.0014345 34336000 12617 13647 16642 19224 17497 22269 17807 16881 15475 20357 TRUE FALSE 13115.1289 15990.76609 17075.70419 23026.44982 14522.86619 17097.36224 16411.24081 16654.73781 14918.05777 24345.56439 0.538707121 0.65682462 0.701388718 0.945817047 0.596530274 0.702278327 0.674095722 0.684097421 0.612762864 1 14.57137133 -1.549289488 3.895608121 1.005526532 0.685048124 0.470378051 0.1019598 0.004876676 0.000564217 0.098373977 0.022843678 0.028229976 1.549289488 -0.320478408 GQS(ph)PLAPLLETLEDPSASHGGQTDAYLTLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQSPLAPLLETLEDPSASHGGQTDAYLTLTSR 32 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(1)PLAPLLETLEDPSASHGGQTDAYLTLTSR;GQS(0.985)PLAPLLET(0.015)LEDPSASHGGQTDAYLTLTSR 145.77 2.98E-10 127194000 19184.9 23962.1 26884.2 24128.8 28698.9 30001.1 21688.6 21794.6 23830.5 26075.6 TRUE FALSE 19942.33467 28077.40428 27584.82434 28901.40462 23820.67123 23033.7992 19988.59086 21502.47904 22972.84496 31184.61457 0.639492742 0.900360792 0.884565184 0.926784089 0.763859729 0.738627028 0.640976043 0.689522039 0.736672403 1 14.92854681 3.041793869 9.103711117 0.730213332 0.845793488 0.06132147 0.116669995 0.535463604 109.2081788 0.032419608 0.038711796 1101.016604 -3.041793869 0.115580156 GQSQLS(ph)NPTDDSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 GQSQLS(1)NPTDDSWK 205.68 1.25E-08 169920000 456310 301020 400070 302380 489450 469720 455920 357600 429320 308090 TRUE FALSE 474325.4711 352717.8434 410496.1529 362189.8615 406253.4638 360634.6487 420183.7991 352806.9569 413868.8571 368454.3368 1.287338549 0.957290519 1.114103192 0.98299796 1.102588363 0.97877705 1.140395857 0.957532377 1.123256848 1 18.49112631 4.750758965 24.68338533 1.03981523 1.287338731 0.531539169 0.069755323 1114.286737 2254713.134 0.01451623 0.244001852 56332.49216 -4.750758965 0.247523501 GQSQT(ph)SPDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQSQT(0.752)S(0.248)PDHR 103.75 0.010202 105160000 44182 49256 49223 47397 44065 59683 49117 46953 42743 53986 TRUE FALSE 45926.33948 57715.33484 50505.79182 56771.98513 36574.84704 45822.52775 45267.0812 46323.67183 41204.68778 64563.52308 0.711335709 0.893931001 0.782265115 0.879319814 0.566493978 0.709727809 0.701124707 0.71748984 0.638203831 1 15.97843168 3.269952289 24.99973144 0.707011614 0.819767916 0.131181716 0.115188727 318.3431067 253520.335 0.029034235 0.039308848 1861.88258 -3.269952289 0.112756302 GQSQTS(ph)PDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQSQTSPDHR 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 GQSQT(0.037)S(0.963)PDHR 96.734 0.0042117 106160000 60411 72612 67331 76755 66354 82513 70680 68462 70356 77054 TRUE FALSE 62796.07293 85082.54616 69085.70117 91936.90991 55075.17078 63350.60625 65139.91691 67544.37887 67823.9013 92151.25601 0.681445654 0.923292311 0.749698964 0.997673975 0.597660555 0.687463297 0.706880402 0.73297296 0.73600626 1 16.49171621 5.036783387 17.05423325 0.775692758 0.281894468 0.048066607 0.130255805 27826885.16 338796478.8 0.029950094 425137159.8 108838.7103 -5.036783387 -0.49379829 GQSS(ph)PPPAPPICLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQSSPPPAPPICLR 14 0 O43379-4;O43379;H7C3R4;O43379-3;O43379-2 O43379-4 WDR62 WD repeat-containing protein 62 1 GQS(0.13)S(0.87)PPPAPPICLR;GQS(0.013)S(0.987)PPPAPPICLR 107.37 0.00093099 307850000 490670 514450 501090 550350 500710 578650 517190 510160 475160 562900 TRUE FALSE 510042.0305 602802.7856 514148.8171 659207.5874 415599.493 444267.307 476651.2964 503322.1397 458059.0844 673189.4776 0.757650034 0.895442971 0.763750525 0.979230379 0.617358867 0.659943926 0.708049238 0.747667865 0.680431141 1 19.3606531 3.22995778 24.99999077 0.719615498 0.846243953 0.184244886 0.113951201 263.4460328 765577.7578 0.030326269 0.036782995 1698.078567 -3.22995778 0.126628456 GQSSLFPMEDGFLDDGRGDQPLHSGLGS(ph)PHCFSHQNGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GQSSLFPMEDGFLDDGRGDQPLHSGLGSPHCFSHQNGER 39 1 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0;Q17RY0-3 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 GQSSLFPMEDGFLDDGRGDQPLHS(0.026)GLGS(0.964)PHCFS(0.011)HQNGER;GQSSLFPMEDGFLDDGRGDQPLHS(0.011)GLGS(0.988)PHCFS(0.001)HQNGER;GQSSLFPMEDGFLDDGRGDQPLHS(0.001)GLGS(0.999)PHCFSHQNGER;GQSSLFPMEDGFLDDGRGDQPLHS(0.075)GLGS(0.924)PHCFSHQNGER;GQSSLFPMEDGFLDDGRGDQPLHS(0.208)GLGS(0.722)PHCFS(0.07)HQNGER 226.33 3.96E-40 952804000 294130 515576 439354 497713 445832 588651 391046 478201 442038 542870 TRUE FALSE 305742.4795 604122.1674 450803.9262 596159.1459 370049.6359 451945.7263 360394.7927 471791.4978 426129.1387 649234.9826 0.470927303 0.930513887 0.694361731 0.918248649 0.569977968 0.696120416 0.55510686 0.726688349 0.656355788 1 19.30838121 -1.137567576 4.823463456 1.000020925 0.697597407 0.30667508 0.139092227 2.90E-05 5.18E-06 0.124758009 0.029403712 0.072850481 1.137567576 -0.302423518 GQSSWGTGESFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQSSWGTGESFR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 0 197.3 4.57E-07 232290000 75733 97806 89028 81642 114170 107980 92485 81458 85397 93178 FALSE TRUE 78722.99732 114603.4197 91348.14282 97790.54392 94763.42418 82903.28145 85235.78404 80366.18875 82323.57865 111434.4451 0.706451199 1.028438016 0.819747814 0.877561187 0.85039616 0.743964592 0.764896204 0.721197011 0.738762405 1 16.76583572 2.840706244 5.058670925 0.770038311 0.866886874 0.056649568 0.105457824 0.401161616 15.90099752 0.030148131 0.032055493 692.9569331 -2.840706244 0.096848563 GQTEHDEGMLEYLEDIIGCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQTEHDEGMLEYLEDIIGCGR 21 0 Q9NTJ3;E9PD53;Q9NTJ3-2;C9JR83;C9J578 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 0 ; 165.1 1.51E-11 110563000 70673 102727 87976 101550 91314 115068 91422 85221 84673 106182 FALSE TRUE 73463.22461 120369.5631 90268.72683 121636.2869 75792.4789 88345.20087 84256.10475 84078.75189 81625.63527 126986.3299 0.578512858 0.947893866 0.710853892 0.957869142 0.596855417 0.695706388 0.663505314 0.662108685 0.642790727 1 16.95431367 3.216907496 24.99271469 0.687688016 0.803152784 0.068827603 0.145937626 456.3913017 526779.9936 0.038330779 0.045850959 1647.811372 -3.216907496 0.115464768 GQTGNS(ph)SRGPGDGGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQTGNSSRGPGDGGNR 16 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 GQT(0.152)GNS(0.819)S(0.029)RGPGDGGNR 89.049 0.0035866 57145000 32726 40389 43840 40908 36334 44939 34270 41544 39587 39809 TRUE FALSE 34018.04775 47325.49657 44982.50641 48999.4803 30157.95966 34502.59831 31583.82785 40987.17063 38162.2716 47608.81136 0.7145326 0.99404911 0.944835738 1.029210327 0.633453321 0.724710349 0.663402991 0.860915647 0.801580012 1 15.53894099 3.246196021 24.9999771 0.769285947 0.92762628 0.2293429 0.124399778 229.9024256 752745.8941 0.033729782 0.044823203 1762.771505 -3.246196021 0.158340333 GQTPEAGADKRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQTPEAGADKRSPR 14 2 Q07617 Q07617 SPAG1 Sperm-associated antigen 1 1 GQTPEAGADKRS(1)PR 159.01 2.60E-06 56676000 99977 223870 201060 198880 201300 263620 150310 207220 191060 314020 TRUE FALSE 103924.1692 262317.931 206299.7888 238217.8704 167083.0979 202398.2502 138528.3094 204442.5548 184183.7879 375546.2067 0.276728049 0.698497086 0.549332639 0.634323729 0.444906898 0.538943668 0.368871545 0.544387218 0.490442413 1 18.5186309 -1.28708306 3.114595851 1.002931946 0.511654973 0.622038619 0.115618478 20186667.99 26909056.41 555377.6843 0.027635014 0.051631761 1.28708306 -0.491276972 GQVCLPVISAENWKPATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQVCLPVISAENWKPATK 18 1 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 139.98 1.19E-07 158260000 265760 193250 226960 180340 293770 276400 252920 238320 259740 192710 FALSE TRUE 276252.41 226439.1842 232874.764 216010.7137 243835.0803 212210.2889 233095.4695 235125.7102 250392.0081 230467.8348 1.198659284 0.982519684 1.010443666 0.937270547 1.058000482 0.920780503 1.011401308 1.020210523 1.086450994 1 17.81420589 4.742068893 24.90775684 1.002216368 1.198659362 0.61104735 0.046825008 205.7051516 1460381.966 0.010665408 0.077457849 55216.5023 -4.742068893 0.196442994 GQVFDVGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQVFDVGPR 9 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 93.178 0.022276 153590000 275720 340170 323390 300670 364980 385860 305070 335200 277920 399400 FALSE TRUE 286605.6385 398591.5513 331817.8091 360141.6286 302940.83 296249.8628 281157.8162 330707.1923 267917.7135 477654.783 0.600026732 0.834476206 0.694681223 0.753978901 0.634225471 0.620217515 0.588621377 0.692356078 0.560902399 1 18.86560879 -1.067306712 4.628782521 1.000014456 0.669162758 0.618827776 0.078939659 10596996.94 2443460.247 1716.268666 0.01836305 0.085643279 1.067306712 -0.330851697 GQVLFDLVCEHLNLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQVLFDLVCEHLNLLEK 17 0 Q9H4G0-2;A0A1B0GTW6;A0A0C4DH22;Q9H4G0;Q9H4G0-4;Q4VXN0;Q4VXN1;Q4VXN5;Q4VXN6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ; 261.15 2.81E-27 563420000 902630 806500 912880 849170 1014730 1072420 1152820 950700 954930 723990 FALSE TRUE 938266.5294 945010.1013 936670.4027 1017133.291 842246.5571 823366.7077 1062458.956 937957.4215 920562.2558 865841.9789 1.083646384 1.09143484 1.081802945 1.174733169 0.972748582 0.950943391 1.227081826 1.083289381 1.063198919 1 19.72374422 -2.971460561 1.109779778 0.000116151 1.083537439 0.089791488 0.076977286 136603.998 3704.051244 340765.9447 0.022649312 0.001067922 2.971460561 1.083421288 GQVLNSDELQELYEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GQVLNSDELQELYEGLR 17 0 O00764;F2Z2Y4;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;; 297.83 7.58E-46 615539000 286843 345284 316462 307962 337864 346419 312202 323765 284990 348062 FALSE TRUE 298167.7831 404583.8411 324709.2597 368875.9644 280433.998 265968.4373 287730.7915 319425.4597 274733.2656 416258.0849 0.716305086 0.971954313 0.780067154 0.886171291 0.673702225 0.638950802 0.691231719 0.767373587 0.660007038 1 18.66711877 3.240352406 24.99997893 0.722183109 0.843965363 0.144747958 0.114834199 71.5069208 997690.7199 0.029875544 0.038449827 1739.211529 -3.240352406 0.121782254 GQVQEVGWHDVAGWLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GQVQEVGWHDVAGWLGR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;; 194.37 7.78E-11 3228222000 2549687 2498392 2436309 2450948 2626885 2887486 2442279 2533776 2150037 2765588 FALSE TRUE 2650350.612 2927471.391 2499801.214 2935738.199 2180368.026 2216911.137 2250846.79 2499814.877 2072657.588 3307452.018 0.801327002 0.88511379 0.755808762 0.887613239 0.659228921 0.670277641 0.680538003 0.755812893 0.626662935 1 21.6572888 3.238618125 25 0.716280821 0.830750781 0.17164745 0.104599356 2.223611055 966071.6922 0.02708148 0.034439727 1732.280136 -3.238618125 0.11446996 NMDPLNDNIATLLHQSSDKFVSELWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NMDPLNDNIATLLHQSSDKFVSELWK 26 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 349.93 3.99E-110 5466530000 744237 2370860 3289680 2512420 3684760 3875920 3084920 3594600 3327460 2345420 FALSE TRUE 773620.0514 2778036.762 3375411.763 3009369.177 3058425.811 2975796.32 2843115.909 3546420.267 3207705.365 2804960.143 0.275804294 0.99040151 1.203372451 1.072874131 1.090363376 1.060905028 1.013602962 1.264338916 1.143583224 1 21.41954884 4.730714246 3.382163195 1.11494761 0.173725504 0.910180074 0.077716802 0.079294831 1.534712642 0.019413895 0.191192058 53791.57317 -4.730714246 -0.941222107 down GQYISPFHDIPIYADKDVFHMVVEVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQYISPFHDIPIYADKDVFHMVVEVPR 27 1 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 267.93 3.82E-61 5095920000 736608 2712320 2606130 2667570 2578000 3247090 2426360 2625530 2326200 3068990 FALSE TRUE 765689.8526 3178139.861 2674047.889 3195207.384 2139792.481 2493002.558 2236175.563 2590339.065 2242480.516 3670299.831 0.208617794 0.865907421 0.728563881 0.870557592 0.583002092 0.679236758 0.609262367 0.7057568 0.610980198 1 21.80746649 -2.268664117 2.129033408 2.245241286 0.666422436 0.257295546 0.176046459 7284402.523 1064647.492 43652457.67 0.040113035 0.005386862 2.268664117 -1.578818849 GQYQDHAIDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQYQDHAIDRR 11 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 124.12 0.00023088 354110000 231080 286100 271730 260170 333540 315170 247310 259160 225870 414960 FALSE TRUE 240203.2168 335235.4495 278811.507 311630.8495 276844.9899 241976.5439 227925.196 255686.3841 217740.9828 496263.4671 0.484023574 0.675519098 0.561821543 0.627954444 0.557858896 0.487596932 0.459282641 0.515223064 0.438760854 1 18.92074673 -1.800110586 6.894701854 1.019405625 0.536440435 0.796419075 0.070638981 0.020933488 0.000606898 0.067948943 0.016831672 0.015844897 1.800110586 -0.48296519 GQYTHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GQYTHK 6 0 F5GWE5;Q00169;I3L4H1;I3L471;I3L4U7;A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7 F5GWE5;A0A0A0MSW4 PITPNA;PITPNB Phosphatidylinositol transfer protein alpha isoform;Phosphatidylinositol transfer protein beta isoform 0 ; 107.22 0.031452 252170000 337790 285420 338730 322250 498780 418580 500880 359110 358000 405330 FALSE TRUE 351126.21 334438.6647 347557.5821 385990.0882 413997.5538 321371.1386 461619.7168 354296.7178 345115.6499 484746.653 0.724349942 0.68992465 0.716988101 0.796271796 0.854049329 0.662967215 0.952290674 0.730890488 0.711950558 1 18.88687141 -5 0.207999479 2.0889024 0.729259283 0.42629107 0.082832733 139.5769719 1.389879323 63.6681686 0.175893006 1.00E-05 5 -1.359643118 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(1)DKESGK;GRAEGEWEDQEALDYFS(0.994)DKES(0.006)GK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(0.999)DKES(0.001)GK;GRAEGEWEDQEALDYFS(0.997)DKES(0.003)GK;GRAEGEWEDQEALDYFS(0.999)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK;GRAEGEWEDQEALDYFS(1)DKESGK 253.26 9.02E-44 6242651000 4665705 1628604 2550089 1561444 3884651 3429122 3348566 2581080 2905523 1462935 TRUE FALSE 4849910.636 1908304.068 2616546.414 1870292.963 3224339.411 2632760.384 3086096.647 2546484.844 2800953.795 1749569.104 2.772060061 1.090728034 1.495537621 1.069002052 1.842933442 1.504805028 1.763918122 1.455492578 1.600939219 1 20.73856822 7.999999936 0.037810267 4.94E-09 4.024736305 0.176639294 0.443176944 1941.385947 5.596745972 168.6121182 514.6519737 99999985.3 -7.999999936 4.0247363 GRAEGSEKEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRAEGSEKEESR 12 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 80.69 0.011058 216630000 97183 87592 103290 69661 135500 119640 99132 104920 109720 95231 FALSE TRUE 101019.8599 102635.2446 105981.8223 83439.73788 112467.7584 91855.42316 91361.77481 103513.719 105771.1986 113889.6911 0.8869974 0.901181166 0.930565543 0.73263644 0.987514825 0.806529742 0.802195299 0.908894545 0.928716178 1 16.79727764 1.074261961 1.929178811 0.996972204 0.866082959 0.271923086 0.068614663 0.403321315 3.001322294 0.061422103 0.017453088 11.86484204 -1.074261961 -0.130889245 GRAS(ph)PGGVSTSSSDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK 168.68 3.57E-09 864270000 1203890 847630 1010730 809770 1098300 1206140 1255970 1075100 1051770 795170 TRUE FALSE 1251420.507 993203.8589 1037070.454 969940.0891 911611.3583 926032.2642 1157523.79 1060690.043 1013917.003 950968.3371 1.3159434 1.044413174 1.090541518 1.01994993 0.958613786 0.97377823 1.217205394 1.115378927 1.066194282 1 19.85903778 4.741026718 24.75372461 1.062216602 1.315943503 0.53947264 0.072246185 173.6094913 1742500.462 0.018901825 0.127548241 55084.15832 -4.741026718 0.253726901 GRAS(ph)PGGVSTSSSDGKAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GRASPGGVSTSSSDGKAEK 19 2 P54259 P54259 ATN1 Atrophin-1 1 GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK;GRAS(1)PGGVSTSSSDGKAEK 138.25 1.19E-06 1146070000 1331920 741470 1077490 567993 1576270 1250210 1007330 998150 1240590 879470 TRUE FALSE 1384505.23 868811.7047 1105570.275 680340.3201 1308336.188 959867.6746 928372.8424 984771.4319 1195941.408 1051785.308 1.316338248 0.826035217 1.05113683 0.646843339 1.243919437 0.912607989 0.882663824 0.936285594 1.137058484 1 20.00440882 4.751873283 24.0206246 0.953790281 1.316338661 0.316229153 0.157153754 1430.60695 2581227.024 0.034562361 0.632792406 56477.21637 -4.751873283 0.36254838 GRAS(ph)SHSSQTQGGGSVTK ddPTM_MDA-MB-175_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(0.404)S(0.284)HS(0.284)S(0.027)QT(0.001)QGGGSVTK 88.09 0.0019024 242850000 6041.1 17110 18552 9178.5 100940 43955 30665 49656 34034 102840 TRUE FALSE 6279.607293 20048.5094 19035.48036 10993.9799 83782.25485 33747.11739 28261.39717 48990.44254 32809.12299 122989.529 0.051058064 0.163009888 0.154773179 0.08938956 0.681214535 0.274390167 0.229787018 0.398330191 0.266763547 1 16.90817597 -5 0.161784791 3.732811886 0.069977295 0.679325204 0.15899701 78.48583369 0.725472758 68.93840307 0.659311619 1.00E-05 5 -3.662834592 GRASPGGVS(ph)TSSSDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 GRASPGGVS(0.304)T(0.304)S(0.304)S(0.045)S(0.045)DGK 167.19 1.69E-08 52587000 197650 118170 135330 121750 194720 209190 207480 160170 181980 110850 TRUE FALSE 205453.3746 138464.7783 138856.811 145831.7866 161621.564 160608.7928 191217.1755 158023.1831 175430.5753 132568.9351 1.549785207 1.044473791 1.04743099 1.100044942 1.219151106 1.211511525 1.442398064 1.192007637 1.323315867 1 17.01638322 2.830387811 2.965417915 1.25941386 1.166360444 0 0.171068491 0.859525107 14.67230728 0.054272731 0.057307133 676.6869648 -2.830387811 -0.093053416 GRASS(ph)HS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.028)S(0.967)HS(0.728)S(0.271)QT(0.005)QGGGSVTK 134.91 5.42E-06 368130000 310200 227050 387090 153660 981840 482710 326950 461590 473060 842270 TRUE FALSE 322446.9355 266044.0713 397177.8834 184053.4894 814947.1875 370607.918 301322.8047 455403.1411 456034.663 1007296.68 0.320111187 0.264116895 0.394300797 0.182720238 0.809043853 0.367923299 0.299140075 0.452104281 0.452731228 1 19.94205723 -5 0.238821025 4.443803508 0.331176051 0.585010366 0.156037488 119.241753 1.190047966 199.2338773 0.244332028 1.00E-05 5 -4.112627457 GRASS(ph)HSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.022)S(0.888)HS(0.164)S(0.926)QTQGGGSVTK;GRAS(0.006)S(0.829)HS(0.243)S(0.921)QTQGGGSVTK;GRAS(0.104)S(0.892)HS(0.027)S(0.972)QT(0.006)QGGGSVTK;GRAS(0.042)S(0.958)HS(0.275)S(0.725)QTQGGGSVTK;GRAS(0.462)S(0.538)HS(0.152)S(0.845)QT(0.003)QGGGSVTK 158.65 2.56E-11 1432680000 1536382 1210464 1707750 779882 3982620 2221640 1446162 1984910 2063420 3255960 TRUE FALSE 1597039.548 1418351.776 1752255.368 934140.3319 3305655.675 1705697.779 1332808.044 1958305.528 1989157.917 3893903.023 0.410138501 0.364249384 0.449999745 0.239898201 0.848931177 0.43804321 0.342280749 0.502915845 0.5108391 1 21.89278552 -4.999999987 0.275152475 4.872033964 0.417982087 0.549303148 0.149529198 164.4894622 1.586556716 362.6813777 0.17346515 1.00E-05 4.999999987 -4.454051876 GRASSHS(ph)SQTQGGGSVTK ddPTM_MDA-MB-175_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(0.01)S(0.26)HS(0.629)S(0.1)QT(0.001)QGGGSVTK 160.25 2.48E-11 162620000 6932.7 21823 28032 18015 74753 39641 27300 41045 30452 71996 TRUE FALSE 7206.408349 25570.93049 28762.53695 21578.31323 62046.51176 30434.97852 25160.15466 40494.85891 29356.03847 86102.23775 0.083695947 0.296983344 0.334050981 0.250612688 0.720614393 0.353474884 0.292212552 0.470311341 0.340943967 1 16.39376311 -5 0.188638313 3.698001322 0.240354024 0.645002907 0.148392011 87.35924853 0.853204748 88.71872545 0.410877704 1.00E-05 5 -3.457647298 GRASSHSS(ph)QTQGGGSVTK ddPTM_MDA-MB-175_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 1 GRAS(0.115)S(0.022)HS(0.349)S(0.514)QTQGGGSVTK;GRAS(0.169)S(0.169)HS(0.283)S(0.369)QT(0.01)QGGGSVTK 123.14 2.10E-05 346920000 16213.7 82772 79338 72525 141293 117559 74299 101894 77427 146511 TRUE FALSE 16853.8294 96987.44712 81405.61346 86870.22853 117276.0663 90257.70387 68475.25024 100528.2776 74640.41739 175217.0253 0.096188309 0.553527529 0.464598764 0.495786459 0.669318898 0.515119485 0.390802493 0.573735785 0.425988384 1 17.41878344 -5 0.236487529 3.874536505 0.424512745 0.563983771 0.142467725 123.7834995 1.236514577 171.1426078 0.22309522 1.00E-05 5 -3.450023759 GRDEVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRDEVSK 7 1 Q9UKY7;H0Y8K3;D6R9V8 Q9UKY7 CDV3 Protein CDV3 homolog 0 ; 90.657 0.015484 132894000 198675 373960 333880 330070 335610 432340 305970 353090 321840 527990 FALSE TRUE 206518.8424 438184.721 342581.1871 395356.8608 278563.1321 331935.5872 281987.2719 348357.4061 310257.0413 631439.5315 0.327060363 0.693945658 0.542539974 0.626119907 0.441155674 0.525680719 0.446578426 0.551687673 0.491348777 1 19.26828506 -1.365954938 3.510993257 1.002813201 0.522691119 0.693404486 0.096417972 24579394.38 41521576.49 733546.0867 0.021370241 0.043057128 1.365954938 -0.480122082 GRDIVVLGVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRDIVVLGVEK 11 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 126.32 0.00028267 413090000 661880 517660 594210 487340 1010300 824460 737210 662950 689030 774760 FALSE TRUE 688011.5335 606564.0782 609695.6007 583734.3974 838569.5669 632991.6598 679425.5539 654064.2396 664231.9449 926559.3883 0.742544452 0.654641338 0.658021071 0.63000214 0.905035961 0.683163613 0.733277934 0.70590644 0.716880055 1 19.82152392 -5 0.333827375 3.970617492 0.702453063 0.58429432 0.07232591 258.5093511 2.213301597 545.911414 0.059049496 1.00E-05 5 -3.268164429 GRDPSSDTYEEDSELLLQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GRDPSSDTYEEDSELLLQIR 20 1 Q9UBE0;M0QZS6 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;; 223.76 5.70E-25 181725000 128397 153180 158955 162366 145598 185820 159564 150646 147745 144098 FALSE TRUE 133466.2127 179487.4734 163097.4979 194481.5102 120849.304 142666.1211 147056.9567 148626.8368 142427.6863 172331.2442 0.77447484 1.041526012 0.946418618 1.128533082 0.701261716 0.827859868 0.853338914 0.86244858 0.826476284 1 17.39482476 3.234939856 24.99999647 0.839915738 0.975771579 0.252490781 0.107194946 119.33499 823964.6862 0.029056362 0.036037433 1717.670497 -3.234939856 0.135855841 GRDQVDQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRDQVDQLR 9 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 143.5 9.28E-05 400420000 316241 348259 329770 291235 316643 409061 347071 319660 302313 385236 FALSE TRUE 328726.4389 408069.7742 338364.0771 348840.4138 262820.136 314062.7821 319866.6681 315375.4806 291432.8142 460715.6184 0.713512687 0.885730281 0.734431531 0.757170801 0.57046066 0.681684687 0.694282233 0.684533947 0.632565519 1 18.81351698 -1.16335336 4.79104463 1.000028756 0.706815367 0.561442159 0.077938733 2.50E-05 4.37E-06 0.078870678 0.018588176 0.068650964 1.16335336 -0.293213389 GRDS(ph)PYQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR;GRDS(1)PYQSR 161.33 3.91E-05 40761454000 622389.5 806490 772059.4 878206.6 718155.4 852584.7 786627.9 734218.6 728859.4 884821 TRUE FALSE 646961.918 944998.3839 792179.9022 1051913.244 596083.6016 654584.8245 724969.9497 724377.6006 702627.8926 1058184.734 0.611388444 0.893037249 0.748621556 0.994073351 0.563307693 0.618592202 0.685107171 0.684547393 0.663993601 1 20.01316008 5.029672096 14.6277656 0.742276079 0.255820708 0.073914311 0.145824929 5376761.582 78506488.71 0.034109042 62485999.3 107071.0585 -5.029672096 -0.486455371 GRDSPYQS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 GRDSPYQS(1)R;GRDSPYQS(1)R;GRDS(0.008)PYQS(0.992)R 161.27 0.00017011 13688660000 5121710 5614750 5145650 6021070 4945740 5911080 6137130 5559550 4887430 5152820 TRUE FALSE 5323919.066 6579039.636 5279749.866 7212019.675 4105064.881 4538321.253 5656085.714 5485033.326 4711532.349 6162416.422 0.863933675 1.067607118 0.856766162 1.170323325 0.666145324 0.736451571 0.917835688 0.890078331 0.764559229 1 22.55506474 3.23393947 24.99999215 0.83016418 0.98573314 0.28838271 0.123431377 152.4920747 824968.9375 0.034312602 0.042311574 1713.718442 -3.23393947 0.15556896 GRDSPYQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 93.258 0.0086833 430300000 59584 65406 61744 62423 64191 71454 70086 71701 52970 80121 FALSE TRUE 61936.42233 76638.97171 63353.09936 74770.08309 53279.83675 54859.8914 64592.47618 70739.96537 51063.62005 95819.17594 0.646388593 0.799829167 0.661173494 0.780324839 0.556045658 0.572535621 0.674108033 0.738265224 0.532916502 1 16.54802679 -1.419439971 4.618053221 1.000688284 0.669763758 0.574587535 0.086939385 0.000608445 7.65E-05 0.083134039 0.019555188 0.038067997 1.419439971 -0.330924526 GRDVIAQSQSGTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRDVIAQSQSGTGK 14 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 196.97 2.20E-08 202960000 92156 88572 107330 76158 131510 135530 110780 103740 108580 105440 FALSE TRUE 95794.39004 103783.552 110127.108 91221.82509 109155.9772 104055.2115 102096.7741 102349.535 104672.227 126098.9492 0.759676354 0.823032647 0.873338824 0.723414633 0.865637484 0.825186983 0.809656026 0.811660491 0.830080089 1 16.94419673 -4.999999999 0.362477466 3.333325896 0.809015515 0.644908625 0.041767574 291.5397136 2.302960883 531.2080048 0.0282055 1.00E-05 4.999999999 -2.52431038 GRDWNVDLIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 136.53 8.87E-05 6440510000 9461660 7256840 8817060 6989470 11015650 10675170 9576890 8384540 9396090 7621620 FALSE TRUE 9835213.643 8503145.82 9046839.827 8371966.305 9143213.748 8196023.551 8826228.337 8272158.956 9057926.556 9114930.514 1.079022339 0.932881036 0.992529763 0.918489317 1.003102957 0.899186619 0.968326453 0.907539442 0.99374609 1 23.11980023 4.744032236 24.68673397 0.952413292 1.079022403 0.47011357 0.038449947 387.399968 1747799.704 0.008269673 0.072609278 55466.6882 -4.744032236 0.126609111 GRECS(ph)PTSSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.905)PT(0.063)S(0.023)S(0.009)LER;GRECS(0.902)PT(0.066)S(0.023)S(0.008)LER 95.761 0.003552 1052330000 768700 837660 701490 755420 764610 869100 679810 711300 707680 877370 TRUE FALSE 799048.8696 981521.5889 719771.4057 904839.8213 634641.8653 667264.6963 626524.7158 701766.187 682210.735 1049273.853 0.76152557 0.935429379 0.685970973 0.862348584 0.604839112 0.635929976 0.597103143 0.668811278 0.650174149 1 20.00095983 3.241228078 24.99998597 0.667008446 0.811230283 0.159060142 0.125334214 96.37309952 903219.5563 0.032294772 0.04182239 1742.721856 -3.241228078 0.144221837 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_MDA-MB-175_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 GREDVSNFDDEFT(0.001)S(0.003)EAPILT(0.996)PPREPR;GREDVSNFDDEFT(0.007)S(0.002)EAPILT(0.992)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR 238.17 8.65E-45 5337048000 667120 819602 805067 838731 871673 934811 777225 781639 782228 920750 TRUE FALSE 693458.4127 960362.2679 826047.7074 1004629.488 723506.3348 717715.3124 716304.0736 771162.4077 754075.7671 1101153.334 0.629756449 0.872142179 0.750165923 0.912342957 0.657044131 0.651785079 0.650503478 0.700322457 0.684805416 1 20.07058394 -1.309324376 3.561277791 1.000949766 0.724906829 0.450120542 0.091762016 1266659444 1712161338 12513422.02 0.022590655 0.049054135 1.309324376 -0.276042938 GREETVAEDVCIDLTCDSGSQAVPS(ph)PATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GREETVAEDVCIDLTCDSGSQAVPSPATR 29 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GREETVAEDVCIDLTCDSGSQAVPS(1)PATR;GREETVAEDVCIDLTCDSGSQAVPS(0.999)PAT(0.001)R;GREETVAEDVCIDLTCDSGSQAVPS(0.998)PAT(0.002)R 247.61 4.55E-46 640340000 418151 521167 419692 500444 480754 575788 415284 464460 460678 554616 TRUE FALSE 434659.9244 610673.3781 430629.5183 599430.3295 399035.6068 442069.9632 382732.9549 458234.6734 444098.2888 663282.3864 0.655316549 0.920683845 0.649240093 0.903733224 0.601607422 0.66648832 0.577028672 0.690859101 0.669546332 1 19.33926369 -1.35199599 2.969024515 1.003499078 0.703832064 0.393672682 0.110266292 17877633.08 22495171.96 549603.4213 0.026977795 0.044463537 1.35199599 -0.299667014 GREEYEGPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GREEYEGPNK 10 1 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 85.963 0.01266 134710000 101450 78754 100620 111020 133750 134080 141950 114190 131210 97154 FALSE TRUE 105455.3243 92279.38688 103242.2399 132979.4246 111015.2228 102941.952 130823.5881 112659.4698 126487.7777 116189.4662 0.907615189 0.794214742 0.888567985 1.144504997 0.95546719 0.885983518 1.125950505 0.96961862 1.08863378 1 16.82611975 3.974580855 20.01677112 1.017784939 0.848533926 0.465502907 0.079441743 47.24462106 37204.89379 0.019561365 0.035611931 9431.501864 -3.974580855 -0.169251013 GREEYEGPNKKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 98.531 0.0014355 985260000 538740 431354 582580 383426 646030 572037 601830 496190 539610 392250 FALSE TRUE 560009.8712 505435.694 597762.5134 459266.5184 536218.0514 439190.0761 554656.992 489539.3847 520189.5415 469103.8774 1.19378649 1.077449406 1.274264704 0.979029466 1.143068896 0.936232031 1.182375629 1.043562861 1.108900537 1 18.8395479 3.732462346 24.94818957 1.063126149 1.17139512 0.31656836 0.08376032 579.9575609 2372622.247 0.020261168 0.032296491 5400.852869 -3.732462346 0.108268971 GREFGVTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GREFGVTTGR 10 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;;;; 147.62 2.42E-05 1993050000 1239301 1351780 1309200 1174760 1564450 1624190 1152614 1310670 1260340 1753140 FALSE TRUE 1288229.56 1583937.7 1343318.828 1407124.022 1298525.348 1246996.487 1062269.103 1293102.612 1214980.61 2096634.217 0.614427424 0.755466875 0.640702521 0.671134722 0.61933805 0.594761107 0.506654472 0.61675165 0.579490976 1 20.99964376 -1.712392656 6.301108179 1.005829714 0.621651319 0.778724195 0.060435547 0.005327618 0.000243173 0.062987323 0.014725695 0.019391319 1.712392656 -0.384178395 GREGS(ph)LTGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GREGSLTGTK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 GREGS(1)LTGTK;GREGS(0.999)LT(0.001)GTK;GREGS(0.799)LT(0.2)GT(0.001)K;GREGS(0.997)LT(0.003)GTK 106.58 0.0014523 1527932000 1289840 991160 1247910 965690 1725100 1579390 1385910 1218400 1511860 1251000 TRUE FALSE 1340763.879 1161384.02 1280431.56 1156700.6 1431868.118 1212600.608 1277278.753 1202069.341 1457448.454 1496109.498 0.896166946 0.776269398 0.855840807 0.773138999 0.957061044 0.81050258 0.85373347 0.803463478 0.974158947 1 20.51278434 1.177044248 6.300429616 0.993361856 0.838740146 0.547755373 0.053213159 0.1461999 10.84994016 0.046298329 0.011810127 15.03295122 -1.177044248 -0.15462171 GRES(ph)PAAGPR ddPTM_MDA-MB-175_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 103.2 0.0032979 1069610000 454570 605590 519970 518600 576920 571910 501130 518610 477430 598890 TRUE FALSE 472516.7746 709595.3717 533520.8454 621177.5321 478855.3445 439092.5699 461850.1211 511658.8812 460247.3876 716231.0291 0.659726758 0.990735311 0.744900491 0.867286542 0.668576653 0.613059965 0.644834002 0.714376871 0.64259627 1 19.4500655 3.232931922 24.96980483 0.691662917 0.823113083 0.113148684 0.130292129 209.1246961 927711.0531 0.03421186 0.041982196 1709.747281 -3.232931922 0.131450166 GRGFGS(ph)EEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRGFGSEEGSR 11 1 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 1 GRGFGS(1)EEGSR 104.81 0.0015447 168840000 52237 62052 72495 68590 92792 81170 70865 83885 82611 93072 TRUE FALSE 54299.3571 72708.9483 74384.27926 82156.89728 77019.24898 62319.49764 65310.41613 82760.65878 79637.84625 111307.6764 0.487831198 0.653224922 0.668276274 0.738106301 0.691949122 0.559884993 0.586755723 0.743530558 0.715474878 1 16.76419357 0.643527969 0.975312659 0.999676183 0.636197379 0.696564274 0.072225705 0.677212724 1.074467266 0.071515253 0.023145919 4.400762884 -0.643527969 -0.363478804 GRKDDDS(ph)DDESQSSHTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GRKDDDSDDESQSSHTGK 18 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.974)DDES(0.026)QSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(0.994)DDES(0.006)QSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(1)DDESQSSHTGK;GRKDDDS(0.928)DDES(0.054)QS(0.018)SHTGK;GRKDDDS(0.997)DDES(0.002)QSSHTGK;GRKDDDS(0.99)DDES(0.01)QSSHTGK 316.45 1.26E-61 2804552000 2182505 1429786 2082143 1319975 2849373 2517849 2344796 1977372 2132815 1151722 TRUE FALSE 2268671.983 1675340.623 2136405.357 1581062.115 2365037.595 1933116.728 2161004.763 1950868.563 2056055.405 1377379.875 1.647092443 1.216324308 1.55106474 1.147876591 1.717055431 1.403473917 1.568924305 1.416362035 1.492729379 1 20.39349507 -1.62655885 2.615255965 0.951895537 1.455911004 0.402910728 0.168679977 21076994.93 18650326.41 6877595.083 0.0393294 0.023628772 1.62655885 0.504015467 GRKDDDS(ph)DDESQSSHTGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRKDDDSDDESQSSHTGKK 19 3 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 GRKDDDS(0.973)DDES(0.013)QS(0.013)S(0.001)HTGKK 81.312 0.0043214 54464000 47059 22711 33272 21325 57735 43502 35925 34414 40214 15706 TRUE FALSE 48916.92566 26611.43758 34139.09565 25543.02135 47921.22532 33399.31978 33109.10463 33952.73662 38766.706 18783.28999 2.604278893 1.416761259 1.817524814 1.359880051 2.551268992 1.778140027 1.762689318 1.807603281 2.06389328 1 14.19716216 -1.638544142 2.674083711 0.905359029 1.877020478 0.323815724 0.391013753 23696639.33 21338139.79 15500669.99 0.087151897 0.022985601 1.638544142 0.971661449 GRLDSSEMDHS(ph)ENEDYTMSSPLPGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLDSSEMDHSENEDYTMSSPLPGKK 26 2 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 GRLDSSEMDHS(1)ENEDYTMSSPLPGKK 100.86 0.0023569 114990000 39918 27625 37257 30313 44033 29391 41904 32775 34929 23437 TRUE FALSE 41493.99346 32369.37886 38227.94803 36308.82092 36548.28639 22565.38567 38619.45498 32335.70473 33671.91211 28029.03142 1.480393412 1.154851852 1.363869748 1.295400486 1.303943966 0.805071903 1.377837657 1.153650451 1.201322715 1 14.77463427 8 0.138687916 1.008727344 2.279524875 0.27157727 0.16087603 112.6482096 1.04214425 0.678293056 28.35622555 100000000 -8 1.27079753 GRLPLLLVANAGTAAVGHTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLPLLLVANAGTAAVGHTDK 21 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;J3KNK7;H3BNL6;Q6P474;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 0 293.44 5.18E-55 679590000 295880 222670 267110 217940 313430 334350 321520 270260 233260 202220 FALSE TRUE 307561.5709 260911.8404 274071.106 261047.8815 260153.2806 256702.2796 296318.4223 266637.6068 224865.0182 241841.1373 1.271750432 1.078856324 1.133269175 1.079418847 1.07571972 1.061450019 1.225260622 1.102532058 0.929804667 1 17.88370014 7.999999993 0.076494857 0.895341642 1.624415184 0.335922626 0.076462012 300.6889284 1.683064397 2.543669773 23.2943823 99999998.27 -7.999999993 0.729073541 GRLPNNSS(ph)RPS(ph)TPTINVLESK ddPTM_MDA-MB-175_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(0.45)S(0.549)RPS(0.545)T(0.447)PT(0.008)INVLESK;GRLPNNS(0.469)S(0.509)RPS(0.51)T(0.47)PT(0.041)INVLESK 130.15 8.22E-06 741480000 284912 297072 255260 237573 290962 303828 238268 240343 235572 271451 TRUE FALSE 296160.5458 348091.8051 261912.2853 284564.2303 241504.3832 233268.5516 219591.9316 237121.5952 227093.8097 324636.6262 0.912283217 1.072250563 0.806786001 0.876562308 0.743922169 0.718552784 0.676423773 0.730421573 0.699532312 1 18.30846625 3.79467495 1.288712358 0.739992904 0.989763367 0.368631014 0.102688156 0.414895459 1.293958883 0.029973101 0.086338892 6232.681731 -3.79467495 0.249770463 GRLPNNSS(ph)RPST(ph)PTINVLESK ddPTM_MDA-MB-175_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(0.446)S(0.516)RPS(0.209)T(0.74)PT(0.09)INVLESK 99.614 0.00089483 267700000 312780 227580 239280 175830 277760 255190 228530 203330 229630 171540 TRUE FALSE 325128.7959 266665.0947 245515.8334 210608.6492 230546.4544 195925.9899 210617.2214 200604.6939 221365.6612 205149.9787 1.584834656 1.299854362 1.196762656 1.026608194 1.123794679 0.955037828 1.02664998 0.977844089 1.079043062 1 17.64631948 5.397872662 0.68553296 1.006656325 2.664471069 0.935523325 0.046459108 1.367756187 0.253644407 0.016749199 2.164465292 249961.2354 -5.397872662 1.657814744 GRLPNNSSRPS(ph)TPTINVLESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.075)S(0.075)RPS(0.425)T(0.425)PTINVLESK 145.63 6.08E-08 242060000 137180 111320 129910 122490 193890 184420 206110 143400 173590 137180 TRUE FALSE 142595.9723 130438.3441 133295.5613 146718.1564 160932.6471 141591.2499 189954.5596 141477.9576 167342.5298 164057.7945 0.869181332 0.795075567 0.812491486 0.894307746 0.980950936 0.863057134 1.157851477 0.86236657 1.020021818 1 17.32384461 3.449201457 2.34904832 0.974681905 0.821772769 0.428485537 0.080489508 0.280443785 3.11439804 0.02254392 0.035136752 2813.205493 -3.449201457 -0.152909136 GRLPNNSSRPST(ph)PTINVLESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLPNNSSRPSTPTINVLESK 21 2 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 GRLPNNS(0.072)S(0.072)RPS(0.271)T(0.585)PT(0.001)INVLESK 135.69 0.00029407 369490000 325540 251800 365580 315880 425430 496130 406690 373640 397350 305000 TRUE FALSE 338392.5706 295044.6913 375107.3151 378360.1212 353115.5606 380911.3264 374812.5751 368631.967 383049.4511 364758.9104 0.927715707 0.808875898 1.028370533 1.037288221 0.968079327 1.044282444 1.027562492 1.010618127 1.050144192 1 18.4765837 4.226299545 24.99741512 1.020552522 0.868295807 0.75360961 0.034878533 79.87761468 162852.4919 0.007920194 0.017306809 16838.3505 -4.226299545 -0.152256716 GRLS(ph)PVPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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;GRLS(1)PVPVPR;GRLS(1)PVPVPR;GRLS(1)PVPVPR 115.37 0.00074584 88335859000 6351404.9 6435277.7 5295281.4 6212660.5 6150420.1 7512168.8 5869065.8 5701959.7 4453685 7191130 TRUE FALSE 6602163.27 7540486.585 5433280.783 7441506.204 5104973.888 5767581.444 5409033.087 5625534.257 4293397.747 8600094.241 0.767684991 0.876791158 0.631769912 0.865281937 0.59359511 0.670641656 0.628950443 0.654124722 0.499226825 1 23.03592104 4.236544802 24.98230491 0.677967596 0.822238085 0.116630933 0.137466243 84.56218472 1048052.18 0.031440972 0.073780678 17240.29935 -4.236544802 0.144270489 GRLSPVPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLSPVPVPR 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM0 Q9UKM9 RALY RNA-binding protein Raly 0 89.827 0.010867 0 41508 45957 36371 45257 46175 46676 37461 36925 29619 47637 FALSE TRUE 43146.76789 53849.75725 37318.85814 54208.69952 38326.18999 35836.20638 34524.70893 36430.08077 28553.01798 56970.55808 0.757352031 0.945220813 0.655055162 0.951521301 0.672736783 0.629030285 0.606009667 0.639454518 0.501189016 1 15.79792892 3.089250986 8.647936188 0.646835411 0.823095843 0.196270456 0.145589864 0.352055132 30.52324241 0.038457652 0.046021834 1228.148794 -3.089250986 0.176260432 GRLT(ph)PS(ph)PDIIVLSDNEASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PS(1)PDIIVLSDNEASSPR 156.27 3.79E-08 200090000 155760 191640 181770 185780 182310 203700 165960 188990 167410 211030 TRUE FALSE 161909.5251 224552.6792 186507.0755 222526.7295 151321.0113 156393.7621 152951.6215 186456.8982 161384.9468 252377.2881 0.641537621 0.889749949 0.739001029 0.881722485 0.599582524 0.619682394 0.606043526 0.73880221 0.639459073 1 17.94522256 -1.348783273 3.034245071 1.003040565 0.7097931 0.426609469 0.102115026 17361781.74 21607086.12 471336.0317 0.024833999 0.044793678 1.348783273 -0.293247465 GRLT(ph)PSPDIIVLS(ph)DNEAS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 GRLT(0.983)PS(0.017)PDIIVLS(0.814)DNEAS(0.619)S(0.567)PR 90.518 0.00036982 0 108060 107410 102850 111890 136230 127700 111640 105110 128200 117290 TRUE FALSE 112326.2922 125856.832 105530.3555 134021.508 113073.6733 98043.61031 102889.3651 103701.1724 123586.107 140270.7298 0.800782119 0.897242298 0.752333403 0.955448854 0.806110251 0.698959864 0.733505594 0.739293026 0.881054139 1 17.09785447 3.010132858 24.96337615 0.780599937 0.851784676 0 0.097016054 466.374408 1148953.767 0.026506857 0.031649082 1023.606083 -3.010132858 0.071184738 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(1)PSPDIIVLS(1)DNEASSPR;GRLT(1)PSPDIIVLS(1)DNEASSPR 200.06 1.76E-21 170880000 193016 225200 207812 220930 240600 261620 213170 233260 207580 265610 TRUE FALSE 200636.4207 263876.3482 213227.7514 264629.2946 199702.8979 200862.7199 196461.1784 230133.5312 200109.2363 317651.1941 0.631624954 0.830711022 0.671263812 0.833081378 0.628686124 0.632337368 0.618480843 0.724485019 0.629965321 1 18.27708392 -1.207567218 5.253035266 1.00002113 0.692692251 0.587136361 0.078191405 1.87E-05 2.82E-06 0.073091578 0.017226667 0.062005867 1.207567218 -0.307328879 GRLT(ph)PSPDIIVLSDNEASS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 GRLT(0.74)PS(0.26)PDIIVLS(0.002)DNEAS(0.26)S(0.739)PR;GRLT(0.994)PS(0.006)PDIIVLSDNEAS(0.138)S(0.861)PR 138.55 3.31E-06 158828000 110447 127143 116088 110001 125954 135336 114295 118953 119383 130020 TRUE FALSE 114807.5328 148978.8212 119113.3486 131758.8695 104544.3841 103906.265 105336.2592 117358.6296 115086.4292 155494.9296 0.738336183 0.958094399 0.76602722 0.847351549 0.672333074 0.668229281 0.677425685 0.754742485 0.740129787 1 17.24650801 3.255369676 24.9918858 0.732263858 0.832396433 0.090319485 0.105936304 410.4698856 610287.2414 0.02720934 0.036744479 1800.402785 -3.255369676 0.100132575 GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 GRLT(0.988)PS(0.012)PDIIVLSDNEASSPR;GRLT(0.998)PS(0.002)PDIIVLSDNEASSPR;GRLT(1)PSPDIIVLSDNEASSPR;GRLT(0.965)PS(0.035)PDIIVLSDNEASSPR;GRLT(0.975)PS(0.025)PDIIVLSDNEASSPR 258.87 2.53E-36 1404930000 782933 955100 857630 882765 934110 1022530 851860 955550 829340 1059760 TRUE FALSE 813843.7994 1119130.995 879980.5424 1057373.282 775330.3159 785062.9041 785088.9873 942742.4152 799492.2154 1267399.682 0.642136661 0.883013474 0.694319681 0.834285583 0.611748864 0.619428043 0.619448623 0.743839871 0.630813016 1 20.27344013 -1.150700851 4.21509311 1.00007127 0.701907492 0.498797576 0.090827922 12838974.32 3504983.714 9235.200666 0.021054208 0.070680424 1.150700851 -0.298163778 GRNDS(ph)GEENVPLDLTR ddPTM_MDA-MB-175_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(0.999)GEENVPLDLT(0.001)R;GRNDS(1)GEENVPLDLTR 149.97 5.02E-08 114840000 351932 376619 358270 386014 388284 428306 412840 375659 377432 370370 TRUE FALSE 365826.5471 441300.3836 367606.8105 462366.4171 322283.6244 328838.4225 380480.522 370623.9056 363848.296 442936.9103 0.825911182 0.996305282 0.829930408 1.043865179 0.72760616 0.742404651 0.858994844 0.836741976 0.821444968 1 18.7567417 3.228982207 24.99995775 0.822015005 0.922448001 0.188810656 0.093053832 294.5422427 768763.6391 0.025212897 0.030498464 1694.268384 -3.228982207 0.100432997 GRNDS(ph)GEENVPLDLTREPSDNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRNDSGEENVPLDLTREPSDNLR 23 2 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 GRNDS(1)GEENVPLDLTREPSDNLR 97.047 0.0017854 112430000 13797 28213 29605 25880 33417 38774 28076 26516 24596 45658 TRUE FALSE 14341.71621 33058.36328 30376.53062 30998.98676 27736.79028 29769.32613 25875.32976 26160.59639 23710.79476 54603.81092 0.262650463 0.605422272 0.556307886 0.567707386 0.507964367 0.545187701 0.473874063 0.479098362 0.434233332 1 15.73671402 -1.736269447 2.885605561 1.086736185 0.499680114 0.736632415 0.090945745 36304160.25 30810031.03 22543815.56 0.020773812 0.018353993 1.736269447 -0.587056071 GRNS(ph)ATSADEQPHIGNYR ddPTM_MDA-MB-175_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(0.754)AT(0.176)S(0.071)ADEQPHIGNYR;GRNS(0.714)AT(0.236)S(0.05)ADEQPHIGNYR 154.84 1.40E-08 407560000 56448 67530 57740 62187 59531 71951 65946 62751 58145 70851 TRUE FALSE 58676.61063 79127.75219 59244.75183 74487.40299 49411.94188 55241.47068 60776.9802 61909.92548 56052.37281 84732.89693 0.692489137 0.933849249 0.699194221 0.879084815 0.583149446 0.65194833 0.717277261 0.730648045 0.661518428 1 16.37063457 -1.044281654 4.423969026 1.000015313 0.730478857 0.403234329 0.09933179 12836881.89 3030157.022 1978.242088 0.02279001 0.090306362 1.044281654 -0.269536456 GRPITMFIPSDVDNYDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GRPITMFIPSDVDNYDDIR 19 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ;; 148.91 8.28E-08 336970000 245331 465923 356472 418649 321441 424637 369299 347078 356056 596190 FALSE TRUE 255016.8573 545941.6509 365761.9532 501456.5227 266802.5736 326021.4922 340352.3794 342425.9871 343241.6141 713002.0158 0.35766639 0.7656944 0.512988666 0.703303093 0.3741961 0.457251852 0.477351216 0.480259494 0.481403427 1 19.44354663 -1.043376734 5.093993826 1.000006489 0.515568155 0.587924733 0.122477949 8.63E-06 1.62E-06 0.113349926 0.026716476 0.090494725 1.043376734 -0.484438334 GRPPAEKLS(ph)PNPPNLTK ddPTM_MDA-MB-175_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 107.45 0.00036712 1318120000 1011110 536050 744380 496760 928450 856660 963300 715270 784200 408550 TRUE FALSE 1051029.404 628112.4176 763779.1543 595017.6453 770632.4006 657713.6978 887794.0289 705682.9756 755976.7952 488597.5503 2.151114763 1.285541479 1.563207089 1.217807263 1.577233451 1.346125656 1.817025133 1.444303139 1.547238202 1 18.8982871 -1.974566364 1.365338569 0.508282534 1.532648851 0.287079001 0.258706106 29684.77748 6947.174513 46088.48843 0.066558503 0.010603119 1.974566364 1.024366317 GRPQAKPIPEAEEAQRPEPVGTSSNADSAS(ph)PDLGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPQAKPIPEAEEAQRPEPVGTSSNADSASPDLGPR 36 3 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 GRPQAKPIPEAEEAQRPEPVGTSSNADS(0.073)AS(0.927)PDLGPR 169.82 5.60E-18 526730000 134180 140150 151380 108020 209560 199010 110080 159420 157460 202550 TRUE FALSE 139477.53 164219.6723 155325.0872 129386.0336 173939.0661 152792.9435 101451.642 157283.2357 151793.0454 242235.7944 0.575792402 0.677933138 0.641214431 0.534132595 0.718056827 0.630761213 0.418813587 0.649298078 0.626633424 1 17.88605254 0.479554191 2.107793074 0.999976304 0.605047767 0.68956182 0.079033725 3.298663644 12.66432753 0.074768468 0.020405401 3.016853294 -0.479554191 -0.394928537 GRPS(ph)KTPS(ph)PSQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.5)KT(0.5)PS(1)PSQPK;GRPS(0.691)KT(0.31)PS(0.75)PS(0.249)QPK 145.55 2.24E-05 276504000 748810 262008 377680 254160 584530 609360 528450 388140 456500 201167 TRUE FALSE 778373.597 307005.8359 387522.6511 304432.0894 485171.7994 467845.3749 487028.7082 382937.6182 440070.6542 240581.8221 3.235379923 1.276097393 1.610772783 1.265399384 2.016660258 1.944641415 2.024378666 1.591714681 1.829193288 1 17.87616811 -2.238784005 0.291015173 9.34E-22 1.895556104 0.203880137 0.524431014 66.96557781 2.627920398 45.10345039 0.557898517 0.005770534 2.238784005 1.895556104 GRPS(ph)LTGENLEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPSLTGENLEAK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 GRPS(1)LTGENLEAK 234.91 6.85E-17 120910000 174390 121010 172590 120240 222920 193870 188870 143360 190630 145440 TRUE FALSE 181275.0519 141792.5262 177087.8372 144023.1131 185028.138 148846.6306 174065.8759 141438.4937 183769.2635 173936.1834 1.04219288 0.81519856 1.018119598 0.828022728 1.063770254 0.855754264 1.000745633 0.813163144 1.056532689 1 17.40819856 1.198773777 24.99991505 1.028266577 0.9253945 0.149539668 0.09366618 293.7781659 184587.9918 0.079177271 0.019795389 15.80424585 -1.198773777 -0.102872077 GRPS(ph)SPRT(ph)PLYLQPDAYGSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPSSPRTPLYLQPDAYGSLDR 22 2 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 GRPS(0.727)S(0.29)PRT(0.606)PLY(0.373)LQPDAY(0.001)GS(0.003)LDR 60.382 0.061395 104550000 54718 58016 66256 50020 82761 94167 64781 69252 61491 79343 TRUE FALSE 56878.30889 67979.7967 67982.68579 59913.80671 68693.31478 72298.14136 59703.29595 68323.79021 59277.95092 94888.74174 0.599421047 0.71641583 0.716446277 0.63141112 0.723935353 0.761925388 0.629192619 0.72004106 0.624710053 1 16.53394931 -1.571054984 2.968521776 1.016760646 0.685125605 0.768764507 0.05252867 16077716.43 17493899.39 2133457.896 0.01215429 0.026850045 1.571054984 -0.331635041 GRPSKT(ph)PS(ph)PSQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.307)KT(0.707)PS(0.96)PS(0.025)QPK 67.415 0.058725 99842000 370140 114200 179740 121620 267330 286600 268920 188320 214770 97386 TRUE FALSE 384753.413 133812.9616 184424.1721 145676.073 221889.3421 220041.4935 247841.3477 185795.8784 207040.4697 116466.9221 3.303542379 1.14893533 1.583489704 1.250793533 1.905170481 1.889304615 2.127997745 1.595267352 1.777676149 1 16.82956075 0.275086936 1.177375287 0.998757057 1.81049987 0.165543869 0.564930478 7.875048445 11.06571147 0.525685572 0.154253083 1.88402619 -0.275086936 0.811742814 GRPSKT(ph)PSPS(ph)QPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPSKTPSPSQPK 13 2 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 GRPS(0.343)KT(0.654)PS(0.121)PS(0.881)QPK 83.418 0.011271 101860000 220520 76190 110330 66522 160430 173370 159150 111980 127580 50732 TRUE FALSE 229226.2999 89275.03982 113205.2904 79679.85305 133160.1659 133107.4449 146675.4071 110479.0913 122988.4207 60671.96408 3.778125587 1.471438105 1.865858344 1.313289495 2.194756144 2.193887193 2.417515394 1.820924919 2.027104654 1 15.88874239 0.229687904 1.037748212 0.995333908 2.090536992 0.217314193 0.638737166 6.407148526 7.250394075 0.646294137 0.182640497 1.697023687 -0.229687904 1.095203084 GRPSS(ph)PRT(ph)PLYLQPDAYGSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GRPSSPRTPLYLQPDAYGSLDR 22 2 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 2 GRPS(0.459)S(0.546)PRT(0.975)PLY(0.02)LQPDAYGSLDR;GRPS(0.547)S(0.611)PRT(0.835)PLY(0.007)LQPDAYGSLDR;GRPS(0.469)S(0.534)PRT(0.989)PLY(0.008)LQPDAYGSLDR 150.62 1.03E-07 520798000 238547 338758 301820 304245 411360 464290 304357 359834 296837 541290 TRUE FALSE 247965.0198 396937.0513 309685.6771 364423.7529 341437.1741 356465.6839 280500.7031 355011.0138 286153.8944 647345.4119 0.383049011 0.613176589 0.478393253 0.562951009 0.527442024 0.55065762 0.43330917 0.548410489 0.442042052 1 19.30417619 -1.903498521 2.692882585 1.26916921 0.510330669 0.832138193 0.06673199 4542090.896 3027971.936 7756500.498 0.014740801 0.012488247 1.903498521 -0.758838541 GRPVS(ph)PQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRPVSPQSR 9 1 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GRPVS(0.999)PQS(0.001)R 64.65 0.041658 104560000 38218 46216 32412 30228 39941 50302 21088 37765 27658 47929 TRUE FALSE 39726.87615 54153.23849 33256.68335 36207.00818 33151.84309 38620.12283 19435.06746 37258.82195 26662.59398 57319.76989 0.693074592 0.944756732 0.580195688 0.631667019 0.578366646 0.673766188 0.339063948 0.650016949 0.465155286 1 15.8067452 2.438491876 24.99993824 0.573132102 0.684647339 0.015202078 0.186363875 437.5318708 283157.1898 0.061585325 0.051526054 274.4680998 -2.438491876 0.111515237 GRPYDYNGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GRPYDYNGPR 10 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 158.79 7.19E-06 3992570000 1062060 1766380 1503130 1573460 1812990 2010990 1403960 1507010 1408670 1669000 FALSE TRUE 1103990.949 2069742.024 1542302.803 1884685.692 1504818.607 1543968.049 1293913.947 1486810.996 1357972.242 1996008.595 0.553099296 1.036940437 0.772693468 0.944227242 0.753913892 0.773527756 0.648250689 0.744892081 0.680343885 1 20.9286865 3.039587734 24.97734989 0.745154452 0.839291121 0.02373908 0.1468877 376.8486657 237765.2563 0.038988135 0.046599669 1095.437828 -3.039587734 0.094136669 GRRPS(ph)GPDGAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 86.497 0.0087245 1041080000 448264 826530 564275 683002 634506 765810 490989 570160 503470 1094350 TRUE FALSE 465961.8089 968480.098 578980.4701 818097.757 526652.8968 587962.2335 452503.9992 562517.9378 485350.213 1308766.93 0.35603116 0.739994323 0.442386232 0.625090487 0.402403885 0.449248999 0.345748344 0.429807573 0.370845413 1 20.31977677 -1.161574912 5.130200758 1.000026738 0.464914851 0.646620324 0.119215529 3.57E-05 5.83E-06 0.112977526 0.02662773 0.068932668 1.161574912 -0.535111888 GRRT(ph)PPVQPPPTREDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRRTPPVQPPPTREDR 16 3 Q9Y6R9 Q9Y6R9 CCDC61 Coiled-coil domain-containing protein 61 1 GRRT(1)PPVQPPPTREDR 85.974 0.0071656 130830000 23624 59404 53774 43170 61166 56161 39430 47704 57517 68912 TRUE FALSE 24556.69376 69606.1749 55175.39462 51708.89715 50769.02517 43118.45888 36339.37357 47064.60591 55446.97441 82413.987 0.29796755 0.844591767 0.669490661 0.627428657 0.616024379 0.523193458 0.440936968 0.571075465 0.672785973 1 16.33060159 0.836292491 3.252381673 0.99987261 0.581131684 0.47020877 0.135641121 0.702430742 12.33095497 0.126292542 0.032808673 6.859500481 -0.836292491 -0.418740927 GRS(ph)FAGNLNTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRSFAGNLNTYK 12 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 GRS(1)FAGNLNTYK;GRS(1)FAGNLNTYK 178.22 1.35E-05 622150000 491060 464170 501780 418400 989700 710680 585390 526990 547570 739450 TRUE FALSE 510447.428 543887.5868 514856.799 501158.2712 821471.1475 545635.3405 539505.6022 519926.561 527863.0627 884331.0699 0.577213043 0.615027115 0.582199152 0.566708881 0.928918112 0.617003472 0.610071975 0.58793203 0.596906612 1 19.75422705 -2.179342897 2.277618488 1.94346745 0.631687106 0.545131461 0.101029449 4557067.659 975910.4833 22174582.58 0.024906453 0.006616939 2.179342897 -1.311780345 GRS(ph)IDQDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;GRS(1)IDQDYER;GRS(1)IDQDYER 218.45 4.10E-09 11619770000 2781567 3058733 3013598 2998126 3907123 4012854 3010832 3312670 3148579 4320377 TRUE FALSE 2891385.413 3584046.599 3092134.84 3591146.374 3242991.628 3080929.474 2774835.12 3268269.077 3035262.257 5166872.155 0.559600727 0.69365885 0.598453909 0.695032946 0.627650836 0.596285215 0.537043503 0.632543051 0.58744675 1 22.30085976 -1.757656021 3.135130689 1.06673981 0.616143111 0.850088754 0.048598555 12906847.1 14433555.68 6708066.822 0.011765175 0.017472055 1.757656021 -0.450596699 GRS(ph)KDRDPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRSKDRDPNR 10 3 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 GRS(1)KDRDPNR;GRS(1)KDRDPNR 91.914 0.05429 2944500000 1537340 955600 1253090 885220 1731380 1573440 1300140 1112520 1324970 1051630 TRUE FALSE 1598035.37 1119716.866 1285746.555 1060313.874 1437080.646 1208032.406 1198231.63 1097608.489 1277284.589 1257676.764 1.270624867 0.89030576 1.022318764 0.843073439 1.142647052 0.960526934 0.952734171 0.872727016 1.015590512 1 20.26232975 4.746685836 24.91494654 0.961154585 1.270625027 0.549298532 0.08246591 705.0352189 2161849.332 0.018859034 0.210182444 55806.63494 -4.746685836 0.309470441 GRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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(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 423.06 7.64E-208 16864450300 667250 691690.2 663910.5 695417.4 904141.8 868393.2 759729.8 657027.7 676653.1 722777.6 TRUE FALSE 693593.5452 810482.6112 681212.553 832968.8861 750456.0998 666722.0399 700180.1931 648221.3184 652300.4871 864392.0323 0.802406222 0.937633135 0.788082869 0.963647113 0.868189516 0.771319049 0.8100262 0.749915888 0.754635007 1 19.72132625 2.79991712 7.15579785 0.797154569 0.876436534 0.071266816 0.084086898 0.453470609 45.95023736 0.02383814 0.025248986 630.8369449 -2.79991712 0.079281966 GRS(ph)PSQYHDFAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRSPSQYHDFAEK 13 1 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 GRS(0.994)PS(0.005)QY(0.001)HDFAEK 86.455 0.0053256 70874000 61578 99820 88810 90069 100850 116580 80010 93572 103300 116850 TRUE FALSE 64009.14699 116963.3085 91124.46156 107884.3794 83707.55302 89506.06179 73738.60713 92317.82039 99582.25318 139744.5203 0.458044057 0.83697957 0.652078961 0.772011519 0.599004189 0.640497829 0.527667253 0.660618536 0.712602204 1 17.09243219 0.765546624 2.608269445 0.999882 0.648014924 0.521649126 0.102109202 0.890507378 8.705877584 0.09233251 0.024561111 5.828363429 -0.765546624 -0.351867077 GRS(ph)YENLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GRSYENLLGR 10 1 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 GRS(1)YENLLGR;GRS(1)YENLLGR 205.26 0.0035522 0 80955 164329 120791 155415 141226 181270 132814 139450 109183 206701 TRUE FALSE 84151.16591 192551.2274 123938.9127 186155.6231 117220.455 139172.7897 122403.6916 137580.9008 105253.5252 247200.1034 0.340417195 0.778928588 0.501370796 0.753056413 0.474192581 0.562996486 0.495160358 0.556556809 0.425782691 1 17.91531982 -1.716026818 3.154421919 1.056958345 0.551946199 0.532036194 0.128296363 36468749.6 35551903.15 16341742.47 0.027990581 0.01922973 1.716026818 -0.505012146 GRVEDVVVSDECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRVEDVVVSDECR 13 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 114.69 0.00065943 353040000 211220 262780 183840 255630 290730 319700 241930 226350 204560 284550 FALSE TRUE 219559.1287 307910.4209 188631.0214 306192.851 241311.8184 245454.5201 222966.8944 223316.1485 197197.9256 340302.1245 0.645188828 0.904814865 0.554304566 0.899767674 0.709110526 0.721284125 0.65520277 0.656229075 0.579478973 1 18.37645663 2.805510883 3.254051471 0.691112112 0.752079701 0 0.144158997 0.995504523 20.82741639 0.043285309 0.045168975 639.0147503 -2.805510883 0.060967589 GRWES(ph)QQDVSQTTVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.957)QQDVS(0.033)QT(0.01)TVSR;GRWES(0.998)QQDVS(0.001)QTTVSR;GRWES(1)QQDVSQTTVSR;GRWES(0.611)QQDVS(0.26)QT(0.114)T(0.001)VS(0.015)R 301.33 1.59E-45 4124910000 2118230 2482780 2219800 2239180 2299380 2562040 1730150 2160850 1808940 2425090 TRUE FALSE 2201859.356 2909178.152 2277649.812 2682083.121 1908532.209 1967045.038 1594536.322 2131887.34 1743836.603 2900239.954 0.759199029 1.003081882 0.785331506 0.92477973 0.658060105 0.678235273 0.549794619 0.735072744 0.601273215 1 21.46774084 3.233236081 24.99551517 0.682178023 0.871827853 0.268738305 0.129875038 139.1966974 653445.0496 0.033934835 0.041698277 1710.945124 -3.233236081 0.189649829 GRWESQQDVSQT(ph)TVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GRWESQQDVSQTTVSR 16 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 GRWES(0.243)QQDVS(0.074)QT(0.68)T(0.003)VSR 223.32 5.62E-14 1858400000 1065800 1354700 1257900 1221500 1277500 1277900 910280 1025500 1012800 1370000 TRUE FALSE 1107878.607 1587359.187 1290681.907 1463109.054 1060351.006 981127.0918 838929.875 1011754.85 976349.5258 1638425.27 0.67618501 0.968832217 0.787757569 0.892997124 0.647176912 0.598823218 0.512034263 0.617516629 0.595907268 1 20.64387844 3.189787992 7.384604008 0.62756118 0.837972046 0.233269362 0.142528925 0.235209489 29.38107272 0.037986862 0.045817602 1548.060724 -3.189787992 0.210410866 GRYPDHSVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GRYPDHSVDRR 11 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;; 193.73 4.63E-07 187010000 106665 124876 102923 98604 159935 144188 112465 108390 112470 193808 FALSE TRUE 110876.2166 146322.4816 105605.2579 118107.5769 132749.3058 110702.5222 103649.6994 106937.2093 108422.2267 231780.9669 0.478366356 0.631296364 0.455625237 0.509565468 0.572736008 0.477616966 0.44718814 0.461371832 0.467778818 1 17.82240258 -1.433553043 3.137700629 1.008350581 0.499324649 0.879226932 0.055573843 26475977.69 32913839.1 1957929.663 0.013680328 0.036850803 1.433553043 -0.509025932 GS(ph)AGEEEESLAILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSAGEEEESLAILR 14 0 O15068-4;O15068-10;O15068;H7BYP9;O15068-5;O15068-3;O15068-6;O15068-8;O15068-2;O15068-9 O15068-4 MCF2L Guanine nucleotide exchange factor DBS 1 GS(1)AGEEEESLAILR;GS(1)AGEEEESLAILR;GS(1)AGEEEESLAILR 153.14 2.98E-07 34458000 137959 79739 95419 79576 114543 126959 105880 90776 93701 74853 TRUE FALSE 143405.7278 93433.55297 97905.69753 95315.89529 95073.02177 97474.69633 97580.84893 89559.2962 90328.71931 89519.0122 1.601958336 1.043728597 1.09368608 1.064755888 1.062042793 1.088871447 1.090057257 1.000450005 1.009045085 1 16.4499065 4.73915029 24.99960997 1.053043478 1.601958504 0.957595448 0.034822356 9.155050332 388045.6105 0.008731503 0.051968507 54846.67318 -4.73915029 0.548915026 GS(ph)FGAMDDPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSFGAMDDPFK 11 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R3I1 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 GS(1)FGAMDDPFK;GS(1)FGAMDDPFK 136.38 0.0001054 145136000 783980 443800 597700 612470 772440 824480 1044270 704270 724250 380560 TRUE FALSE 814932.1358 520019.1977 613276.553 733614.738 641140.9247 633007.0151 962417.3887 694830.4126 698184.384 455123.4457 1.79057384 1.142589341 1.347494968 1.611902759 1.408718735 1.390846859 2.114629333 1.526685604 1.53405497 1 18.79589838 GS(ph)FMLGLETHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSFMLGLETHDR 12 0 Q92905 Q92905 COPS5 COP9 signalosome complex subunit 5 1 GS(1)FMLGLETHDR 111.64 0.00087576 36596000 18568 18611 20688 22567 23051 23283 19207 20579 18473 23755 TRUE FALSE 19301.07898 21807.29448 21227.14628 27030.68524 19132.79925 17875.87611 17701.50515 20303.17217 17808.16034 28409.33743 0.679392084 0.767610105 0.747189065 0.951471864 0.67346869 0.629225379 0.623087574 0.714665459 0.626841804 1 14.79407756 -1.112818481 4.574465421 1.00001975 0.714697672 0.462774173 0.092887203 2.47E-05 4.79E-06 0.093914498 0.022133926 0.077122574 1.112818481 -0.285322078 GS(ph)FSSENYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSFSSENYWR 10 0 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 GS(0.981)FS(0.019)SENYWR 164.81 6.34E-06 104420000 89247 88995 93626 100670 84780 113590 104950 100270 97723 73538 TRUE FALSE 92770.54047 104279.199 96065.97047 120582.2255 70369.12588 87210.44397 96723.74476 98926.04466 94205.96832 87946.36313 1.054853631 1.185713601 1.092324538 1.371088255 0.800136849 0.991632182 1.099803805 1.124845203 1.071175259 1 16.4243363 3.246767817 24.99999995 1.032555937 1.170712648 0.315445769 0.114554734 269.0849911 819656.3064 0.032832161 0.043700256 1765.093913 -3.246767817 0.13815671 GS(ph)GFSLDVIDGPISQR ddPTM_MDA-MB-175_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(0.999)GFS(0.001)LDVIDGPISQR 109.79 0.00099097 60345000 269540 285890 264460 320210 245010 293850 328520 270860 240400 250220 TRUE FALSE 280181.6473 334989.3836 271352.0449 383546.5823 203363.2877 225607.7908 302769.744 267229.5647 231748.051 299245.8182 0.936292607 1.119445496 0.906786422 1.28171075 0.679586064 0.753921282 1.011776023 0.893010189 0.774440399 1 18.19097156 3.229464815 24.99971109 0.856468794 1.054209858 0.359360965 0.136469647 221.974085 610092.5134 0.038509589 0.046638939 1696.152181 -3.229464815 0.197741065 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GS(0.999)GGLFS(0.001)PSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.993)GGLFS(0.003)PS(0.003)TAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.824)GGLFS(0.131)PS(0.038)T(0.008)AHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(1)GGLFSPSTAHVPDGALGQR;GS(0.999)GGLFS(0.001)PSTAHVPDGALGQR 244.26 2.46E-30 8549820000 2448261 4383497 4054208 4708579 4191492 4914384 4589457 4561083 3843734 4422566 TRUE FALSE 2544920.235 5136328.511 4159863.991 5639921.872 3479023.687 3773092.794 4229723.368 4499949.143 3705398.764 5289083.133 0.481164726 0.971118884 0.78650002 1.06633262 0.657774438 0.713373698 0.799708241 0.850799473 0.700574877 1 22.33458622 -2.016554764 2.326045077 1.22443456 0.794547266 0.147214576 0.155124437 18021417.48 6717973.69 21608453 0.036120569 0.009625986 2.016554764 -0.429887294 GS(ph)GSLWEVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSGSLWEVDLR 11 0 Q5FC08 Q5FC08 IL4R 1 GS(0.5)GS(0.5)LWEVDLR 68.735 0.059188 102780000 27329 22279 26470 27781 29524 33819 30051 30311 20018 21706 TRUE FALSE 28407.97002 26105.24494 27159.82995 33275.99888 24505.52103 25965.04978 27695.5241 29904.73062 19297.55609 25958.87511 1.094345186 1.005638527 1.046263747 1.281873684 0.94401321 1.000237863 1.066900009 1.152004102 0.743389535 1 14.66394025 1.247436502 24.99999995 0.871694737 1.074381634 0.371956172 0.105103153 169.4575607 477307.019 0.070355314 0.024850849 17.67813726 -1.247436502 0.202686897 GS(ph)GVFCANCLTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSGVFCANCLTTK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK;GS(1)GVFCANCLTTK 220.49 2.17E-11 735830000 509270 476177 509288 469067 666140 648900 588196 584516 594447 567877 TRUE FALSE 529376.3728 557956.6956 522560.4637 561847.0526 552909.7607 498202.8092 542091.6606 576681.5191 573052.9686 679141.6255 0.779478614 0.821561622 0.769442549 0.827289966 0.814130279 0.733577196 0.7982012 0.849132931 0.843790083 1 19.37335293 0.67272453 0.91214678 0.999822578 0.792958428 0.822905005 0.028514802 0.432490806 0.630878603 0.027793573 0.009216457 4.706786835 -0.67272453 -0.206864149 GS(ph)IDEVDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 1 GS(1)IDEVDKR;GS(1)IDEVDKR 73.781 0.026307 561490000 1352980 824770 1200030 918220 1262680 1505410 1645200 1203910 1152890 555140 TRUE FALSE 1406396.695 966417.8317 1231303.768 1099841.175 1048050.105 1155801.342 1516244.925 1187773.556 1111397.714 663909.0542 2.118357456 1.455647917 1.854627166 1.656614213 1.578604928 1.740903118 2.283814199 1.789060637 1.674021023 1 19.3406261 0.784508924 3.16509778 1.000161985 1.805262253 0.524624985 0.230131507 1.065444774 14.54034634 0.219402372 0.057110547 6.088480569 -0.784508924 0.805100268 GS(ph)KSPSPRPNMPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSKSPSPRPNMPVR 14 2 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 GS(0.455)KS(0.455)PS(0.09)PRPNMPVR 64.52 0.031686 155140000 137210 112530 130190 112700 170000 172350 132210 129110 137450 110230 TRUE FALSE 142627.1567 131856.1521 133582.8584 134991.7236 141103.4607 132324.3245 121847.0347 127379.4916 132503.2013 131827.458 1.081922984 1.000217664 1.013315893 1.024003084 1.070364724 1.003769067 0.924291772 0.966259181 1.005125968 1 17.00829137 2.47436347 24.84141211 0.968305331 1.034057176 0.482592717 0.030963629 64.83739314 584023.5364 0.010571645 0.008896881 298.1010257 -2.47436347 0.065751845 GS(ph)LAS(ph)LDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(0.897)LDS(0.103)LR;GS(1)LAS(0.999)LDS(0.001)LR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR;GS(1)LAS(1)LDSLR 140.01 5.86E-05 3919319000 2310480 2457710 2162150 2454210 2136990 2885250 2556530 2428280 2164250 2259290 TRUE FALSE 2401699.534 2879802.574 2218497.405 2939645.413 1773745.203 2215194.414 2356142.498 2395732.878 2086359.065 2701954.619 0.88887486 1.065821962 0.821071305 1.087969943 0.656467429 0.81984886 0.87201409 0.886666586 0.772166583 1 21.36557201 3.25391185 24.99999947 0.834819368 0.962721902 0.257867814 0.109155944 334.2960031 544409.0058 0.028497751 0.038446989 1794.369383 -3.25391185 0.127902534 GS(ph)LAS(ph)LDSLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(1)LAS(0.951)LDS(0.049)LRK 94.487 0.029631 25475000 116060 92056 95504 89939 111700 119840 112660 104080 102830 77254 TRUE FALSE 120642.1384 107865.9019 97992.9127 107728.6658 92713.2739 92008.97619 103829.4148 102684.9778 99129.16839 92390.44218 1.305785919 1.167500657 1.06063907 1.166015263 1.003494211 0.995871153 1.123811212 1.111424249 1.072937482 1 16.49545599 4.894706058 1.275942281 1.070715077 1.482783714 0.653701794 0.054059945 1.258172208 1.381002627 0.015462301 0.743046405 78470.4347 -4.894706058 0.412068636 GS(ph)LASLDS(ph)LRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 2 GS(0.999)LAS(0.351)LDS(0.65)LRK 81.578 0.0053679 0 161330 161550 143060 164090 171320 202300 172780 171710 153350 151990 TRUE FALSE 167699.433 189294.9558 146788.2611 196546.5122 142199.0876 155318.8909 159237.0521 169408.5083 147830.9635 181769.5305 0.922593751 1.041400918 0.807551523 1.081295153 0.782304313 0.854482544 0.876038199 0.931996181 0.813287921 1 17.47175086 3.225224835 24.999883 0.876039019 0.957676928 0.187858545 0.088173573 394.7150035 739949.8547 0.023844468 0.028653623 1679.673361 -3.225224835 0.081637909 GS(ph)LASLDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSLASLDSLR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.942)LAS(0.058)LDSLR;GS(0.971)LAS(0.029)LDSLR;GS(0.828)LAS(0.172)LDSLR;GS(0.866)LAS(0.134)LDSLR 229 1.92E-09 1927740000 1395280 1588850 1287380 1425110 1292950 1788480 1739490 1497800 1302030 1441960 TRUE FALSE 1450366.732 1861722.628 1320930.18 1706992.504 1073174.821 1373132.625 1603144.228 1477724.441 1255170.195 1724484.454 0.841043669 1.079582146 0.765985554 0.989856708 0.622316321 0.796256888 0.929636811 0.856907952 0.727852427 1 20.71773369 4.223547618 24.99995215 0.833719771 0.960312986 0.139408952 0.123331542 373.4330996 621851.1303 0.029102885 0.063264103 16731.99085 -4.223547618 0.126593214 GS(ph)LDESSLGFGYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.992)LDES(0.008)SLGFGYPK;GS(0.949)LDES(0.05)S(0.001)LGFGYPK;GS(0.999)LDES(0.001)SLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK;GS(1)LDESSLGFGYPK 276.51 4.39E-33 2157010000 1599154 1291923 1627897 1334214 1797620 1860350 1835770 1612376 1766927 1293541 TRUE FALSE 1662289.835 1513800.725 1670321.333 1598117.547 1492061.194 1428311.906 1691877.551 1590764.737 1703335.642 1546985.593 1.074534787 0.97854869 1.079726496 1.033052638 0.964495857 0.923287142 1.093660832 1.028299646 1.101067554 1 20.56102833 -0.769018528 5.734767744 0.999999998 1.02834367 0.024395865 0.056519061 1.61E-09 4.21E-10 0.054029084 0.012734776 0.170208589 0.769018528 0.028343672 GS(ph)LTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSLTQR 6 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 GS(1)LTQR;GS(1)LTQR;GS(1)LTQR;GS(1)LTQR;GS(0.994)LT(0.006)QR;GS(1)LTQR 133.86 0.014981 2777225000 1992060 2064547 2134950 2422940 2177780 2373920 2365680 2395136 1839411 2069790 TRUE FALSE 2070708.067 2419116.887 2190588.551 2902190.3 1807601.733 1822613.057 2180251.82 2363033.12 1773210.957 2475325.722 0.836539631 0.977292348 0.884969817 1.172447842 0.730248031 0.736312414 0.88079391 0.954635222 0.716354596 1 21.23918695 3.198861883 24.99995229 0.840869374 0.962573845 0.221710855 0.120292723 256.0990221 161275.5004 0.034717812 0.04149628 1580.745241 -3.198861883 0.121704471 GS(ph)PDGSLQTGKPSAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(1)PDGSLQTGKPSAPK;GS(0.859)PDGS(0.141)LQTGKPSAPK;GS(0.983)PDGS(0.017)LQTGKPSAPK;GS(0.981)PDGS(0.019)LQTGKPSAPK 230.77 1.18E-15 2457293000 2826760 1735253 2365950 2005910 2830900 2879500 3342200 2500180 2753560 1459948 TRUE FALSE 2938362.668 2033269.204 2427608.601 2402673.011 2349704.629 2210779.764 3080229.631 2466669.177 2654459.913 1745996.858 1.682914064 1.164531995 1.390385435 1.376103857 1.345766814 1.266199165 1.764166766 1.412756939 1.520311964 1 20.73561953 GS(ph)PEEELPLPAFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 GSPEEELPLPAFEK 14 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK 310.9 1.06E-55 2320317000 1626237 1453057 1709946 1411490 1945149 1973769 1910576 1669782 1761049 1432512 TRUE FALSE 1690442.092 1702608.237 1754508.597 1690678.509 1614513.268 1515391.063 1760820.061 1647401.304 1697669.19 1713185.299 0.986724608 0.993826084 1.024120741 0.986862606 0.942404344 0.884545918 1.027804792 0.961601354 0.990943123 1 20.70824977 3.47067798 23.90562138 0.965892578 1.001568646 0.144555333 0.036878515 172.8137727 641163.1362 0.01035685 0.014065037 2955.819979 -3.47067798 0.035676068 GS(ph)PHYFS(ph)PFRPY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 45 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.001)FS(0.999)PFRPY;GS(1)PHYFS(1)PFRPY;GS(0.999)PHY(0.002)FS(0.998)PFRPY;GS(1)PHY(0.003)FS(0.997)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.004)FS(0.997)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.017)FS(0.983)PFRPY;GS(1)PHY(0.001)FS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.006)FS(0.994)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHY(0.01)FS(0.99)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY;GS(1)PHYFS(1)PFRPY 186.85 6.39E-06 25707518900 2984624 3356006.1 3093103.7 3118735.7 3543953.2 3777636.8 3145620.7 3311122.3 3073608.8 3496167.4 TRUE FALSE 3102459.26 3932374.042 3173712.523 3735612.313 2941553.301 2900337.904 2899058.73 3266742.121 2962990.22 4181174.464 0.742006651 0.940495087 0.759048098 0.893436125 0.703523215 0.693665842 0.693359905 0.781297731 0.708650224 1 21.99547681 5.074716747 15.4143662 0.7846079 0.138037684 0.011748475 0.105897764 8796581.668 33228007.1 0.024295664 185119326.4 118772.7322 -5.074716747 -0.646570216 GS(ph)PHYFSPFRPY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 24 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(0.993)PHYFS(0.007)PFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(1)PHYFSPFRPY;GS(0.999)PHY(0.001)FSPFRPY 208.08 1.87E-07 67991456200 10402945.4 13177484.6 11424648.5 11657493.3 16518237.7 15455573.1 11714205.5 11310775.3 11205836.9 19545050 TRUE FALSE 10813661.72 15440615.07 11722384.23 13963310.68 13710473.56 11866250.48 10796015.46 11159172.86 10802541.02 23374528.33 0.462625879 0.660574402 0.501502493 0.597372939 0.586556159 0.507657323 0.461870944 0.477407403 0.462150118 1 24.47843392 -1.663693325 3.050903595 1.044747983 0.524809478 0.827920387 0.065075992 23272180.35 23428594.78 8123628.555 0.01676234 0.021692354 1.663693325 -0.519938506 GS(ph)PLAEGPQAFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GSPLAEGPQAFFPER 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER;GS(1)PLAEGPQAFFPER 230.93 2.75E-13 1733438000 195074 230621 213433 260663 219676 280873 247541 259694 226908 237046 TRUE FALSE 202775.6721 270228.3628 218995.2393 312221.3634 182335.552 215644.5024 228138.0896 256213.2267 218741.6254 283490.6252 0.715281756 0.953217986 0.772495525 1.101346343 0.643180182 0.760675956 0.804746504 0.903780245 0.771600914 1 18.1129415 -1.386471427 4.983128277 1.000146642 0.832679517 0.14855997 0.124409166 0.00018971 2.34E-05 0.112749501 0.026552118 0.041070366 1.386471427 -0.167467125 GS(ph)PNLTLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPNLTLPK 9 0 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 GS(1)PNLTLPK;GS(0.982)PNLT(0.018)LPK;GS(0.867)PNLT(0.133)LPK;GS(0.987)PNLT(0.013)LPK 123.67 0.00057817 1321620000 2323270 1761400 2045130 1820360 2456780 2493610 2211060 1938680 1953210 1612570 TRUE FALSE 2414994.494 2063906.748 2098427.768 2180421.775 2039177.413 1914506.869 2037751.34 1912695.166 1882914.354 1928522.217 1.252251321 1.070201178 1.088101423 1.130617919 1.057378233 0.992732597 1.056638768 0.991793171 0.976350875 1 20.87906434 8 0.300031156 0.987484919 2.908007583 0.74745259 0.039763607 27.35403818 0.39111279 0.040165525 28.19294455 100000000 -8 1.920522664 GS(ph)PPFEMLSPSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPPFEMLSPSFR 13 0 H3BMK1;P13631 H3BMK1 RARG Retinoic acid receptor gamma 1 GS(1)PPFEMLSPSFR 147.26 4.48E-05 26773000 8543.1 9995 12043 9344.1 7910.6 12816 10271 10688 10131 10919 TRUE FALSE 8880.388185 11711.5635 12356.85047 11192.33509 6565.959038 9839.678228 9465.932182 10544.74484 9766.387289 13058.36899 0.680053396 0.896862656 0.946278243 0.857100538 0.502816166 0.753515101 0.724893912 0.807508568 0.747902536 1 13.67268709 -1.431193663 2.759728301 1.006084867 0.772596619 0.257547502 0.117712491 13554655.52 14863010.84 646551.7772 0.03030334 0.037051546 1.431193663 -0.233488248 GS(ph)PQQIDHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 GS(1)PQQIDHAK;GS(1)PQQIDHAK;GS(1)PQQIDHAK 155.43 1.83E-05 818090000 1571820 2057290 2196310 1957240 2420610 2675370 2163760 2102300 2187580 2011440 TRUE FALSE 1633876.667 2410613.554 2253547.643 2344376.23 2009155.577 2054055.863 1994158.837 2074122.107 2108849.423 2405543.157 0.679213201 1.002107797 0.936814472 0.974572509 0.835219094 0.853884437 0.828984852 0.862226105 0.876662477 1 21.19793125 3.196015543 24.99749432 0.864720835 0.908361061 0 0.093383563 480.9989028 282611.0455 0.025718327 0.030739504 1570.419006 -3.196015543 0.043640227 GS(ph)PQSAAAELSSGLLASAAASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPQSAAAELSSGLLASAAASSR 23 0 Q12948 Q12948 FOXC1 Forkhead box protein C1 1 GS(0.999)PQS(0.001)AAAELSSGLLASAAASSR 141.21 1.11E-09 0 10134 10481 11696 16514 10898 15095 10429 9608.5 10419 10106 TRUE FALSE 10534.09815 12281.03022 12000.80737 19780.41991 9045.561853 11589.41502 9611.547729 9479.713774 10044.02223 12086.07721 0.871589513 1.016130379 0.992944788 1.636628624 0.74842827 0.958906254 0.795257846 0.784349927 0.831040713 1 13.56105844 GS(ph)PRPQAPK ddPTM_MDA-MB-175_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 101.45 0.010465 3508550000 4205080 3535230 3878000 3327030 4750540 4977890 4564630 4063270 4152310 3578840 TRUE FALSE 4371099.805 4142378.252 3979063.866 3985106.604 3943044.908 3821850.488 4206842.373 4008808.512 4002869.174 4280045.177 1.021274221 0.96783517 0.929678006 0.931089846 0.92126245 0.892946296 0.982896722 0.936627616 0.935239935 1 22.02919459 4.632858506 2.561540509 0.938425075 1.029375753 0.412896443 0.02886652 0.348469114 3.388262801 0.006883469 0.061281824 42939.65061 -4.632858506 0.090950678 GS(ph)PRY(ph)SPRHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(1)PRY(0.621)S(0.379)PRHS(1)R 70.96 0.089828 129950000 124750 158370 156690 127150 174240 169780 107180 147800 144050 188840 TRUE FALSE 129675.2263 185568.8156 160773.4701 152299.8905 144622.747 130351.168 98778.95154 145818.9828 138865.6686 225839.5824 0.574191756 0.821684195 0.711892346 0.674371998 0.640378208 0.577184773 0.437385468 0.645675046 0.614886315 1 17.78493884 -1.103938917 4.369026032 1.000042571 0.633020213 0.576759386 0.094297053 4.36E-05 8.95E-06 0.097158644 0.022897732 0.078715649 1.103938917 -0.367022359 GS(ph)PRYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSPRYSPR 8 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 GS(1)PRY(0.022)S(0.978)PR;GS(1)PRY(0.036)S(0.964)PR;GS(1)PRY(0.208)S(0.792)PR;GS(1)PRY(0.011)S(0.989)PR;GS(1)PRY(0.005)S(0.995)PR;GS(1)PRY(0.012)S(0.988)PR 105.13 0.0025301 9347520000 6928490 7831410 6940340 7195780 7479210 7818420 7018540 6972090 6436310 7312780 TRUE FALSE 7202032.135 9176393.748 7121210.962 8619083.807 6207896.556 6002710.444 6468408.495 6878640.538 6204668.46 8745579.229 0.823505447 1.049260833 0.814264073 0.985536073 0.709832521 0.686370827 0.739620364 0.786527725 0.70946341 1 23.06012251 3.234680725 24.99999695 0.757162048 0.920087447 0.310025143 0.105433847 100.5946379 648180.1233 0.02767103 0.034270642 1716.645917 -3.234680725 0.162925399 GS(ph)PRYS(ph)PRHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GSPRYSPRHSR 11 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 GS(0.999)PRY(0.473)S(0.529)PRHS(0.999)R;GS(1)PRY(0.035)S(0.966)PRHS(0.999)R;GS(1)PRY(0.025)S(0.975)PRHS(1)R;GS(1)PRY(0.276)S(0.725)PRHS(0.999)R;GS(0.996)PRY(0.14)S(0.883)PRHS(0.981)R 88.427 0.0085758 3401623000 1159282 1488328 1366248 1087902 1556741 1499977 1101360 1402686 1262847 1707470 TRUE FALSE 1205051.349 1743936.756 1401853.545 1303085.769 1292126.721 1151630.074 1015032.525 1383885.289 1217397.383 2042016.055 0.590128244 0.854026956 0.686504664 0.638136887 0.632770109 0.563967199 0.497073724 0.677705391 0.596174247 1 20.96156278 -1.908217894 6.113898798 1.099007247 0.63957617 0.596423797 0.08946851 0.054251895 0.000814432 0.038923685 0.02115531 0.012353275 1.908217894 -0.459431077 GS(ph)PSPASVSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 GS(0.998)PS(0.002)PASVSSGR;GS(0.944)PS(0.056)PASVSSGR;GS(0.831)PS(0.168)PAS(0.001)VSSGR;GS(0.997)PS(0.003)PASVSSGR 240.4 3.47E-16 2204703000 490185 725504 609011 831661 601409 995677 669432 641357 586061 763804 TRUE FALSE 509537.8823 850103.6684 624882.327 996161.0635 499181.713 764446.1064 616960.1706 632760.6585 564968.7791 913456.7699 0.557812804 0.930644664 0.684085276 1.09053991 0.546475465 0.836871685 0.675412555 0.692710021 0.618495366 1 19.80097693 GS(ph)PSSHLLGADHGLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPSSHLLGADHGLRK 16 1 F8VU11;Q6NWY9-2;Q6NWY9-3;Q6NWY9 F8VU11 PRPF40B Pre-mRNA-processing factor 40 homolog B 1 GS(0.862)PS(0.024)S(0.114)HLLGADHGLRK;GS(0.981)PS(0.009)S(0.009)HLLGADHGLRK;GS(0.998)PS(0.002)SHLLGADHGLRK;GS(0.974)PS(0.022)S(0.004)HLLGADHGLRK 155.79 1.06E-07 593258000 370030 764130 778530 603280 959490 961050 603470 735150 806050 994340 TRUE FALSE 384639.0701 895363.3834 798819.1314 722606.9834 796396.2325 737860.7024 556168.4445 725296.5167 777040.418 1189161.885 0.323453917 0.752936496 0.671749693 0.607660733 0.669712209 0.620488019 0.467697839 0.609922438 0.653435354 1 20.1815137 0.714495541 2.659111457 0.99994203 0.59769103 0.538590525 0.1129704 1.379825943 11.87511315 0.102436187 0.027160013 5.181977717 -0.714495541 -0.402251 GS(ph)PSYTQASLGLLTPVSGTQEQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSPSYTQASLGLLTPVSGTQEQTK 24 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.995)PS(0.004)YTQASLGLLTPVSGTQEQTK;GS(0.814)PS(0.103)Y(0.082)T(0.001)QASLGLLTPVSGTQEQTK 268.36 6.55E-45 151671000 415410 279210 339360 359680 391010 458150 417680 375250 405170 274360 TRUE FALSE 431810.7076 327162.1455 348204.0004 430823.6305 324546.2599 351751.6058 384941.1502 370220.3875 390588.0108 328115.5891 1.316032282 0.997094184 1.061223581 1.313023961 0.989121732 1.072035641 1.17318763 1.128323066 1.190397603 1 18.32384461 -2.091994992 2.310018178 0.785514924 1.131511313 0.123281331 0.109100864 6314524.421 1912154.692 7121399.322 0.025651323 0.008091052 2.091994992 0.345996389 GS(ph)PTGGAQLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPTGGAQLLK 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 GS(0.82)PT(0.18)GGAQLLK 70.54 0.054007 127940000 103790 134860 146910 159790 140640 177960 143270 147060 129080 147030 TRUE FALSE 107887.7093 158021.1559 150738.5953 191395.9851 116734.063 136631.487 132040.123 145088.9012 124434.436 175837.7134 0.613564105 0.898676131 0.857259756 1.088480857 0.663873868 0.777031755 0.750920382 0.825129595 0.707666368 1 17.42388501 4.750236168 23.52796732 0.831851967 0.613563801 0.230992545 0.123483706 1203.979072 2426090.374 0.028890641 0.439274911 56264.7208 -4.750236168 -0.218288166 GS(ph)PTRPNPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPTRPNPPVR 11 1 Q14195-2;Q14195;H0YBT4 Q14195-2 DPYSL3 Dihydropyrimidinase-related protein 3 1 GS(0.979)PT(0.021)RPNPPVR;GS(0.873)PT(0.127)RPNPPVR;GS(0.993)PT(0.007)RPNPPVR;GS(0.944)PT(0.056)RPNPPVR 96.464 0.0042349 1259010000 365851 418801 340735 381099 360322 393878 321384 367181 311672 353157 TRUE FALSE 380295.08 490726.8139 349614.834 456479.2447 299074.5951 302405.8038 296193.0823 362259.5393 300454.9856 422351.3526 0.900423493 1.16189237 0.827781969 1.080804505 0.708118 0.716005293 0.701295451 0.857720798 0.711386346 1 18.68808415 3.234866119 24.99936082 0.772537632 0.993027246 0.417535554 0.121349837 83.03890881 561895.7292 0.032257484 0.039993995 1717.378887 -3.234866119 0.220489614 GS(ph)PTSAYPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GSPTSAYPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.996)PT(0.004)SAYPER;GS(0.721)PT(0.279)SAYPER;GS(1)PTSAYPER;GS(0.897)PT(0.103)SAYPER;GS(0.965)PT(0.03)S(0.005)AYPER;GS(0.981)PT(0.013)S(0.006)AYPER;GS(0.978)PT(0.022)SAYPER 225.3 3.74E-09 5577322000 1630063 1906153 1778179 1922340 1926253 2231978 1939711 1818793 1660888 1862830 TRUE FALSE 1694419.146 2233519.95 1824519.806 2302573.114 1598829.203 1713634.935 1787671.383 1794415.055 1601112.965 2227815.872 0.760574142 1.00256039 0.818972442 1.033556293 0.717666672 0.769199536 0.802432286 0.805459319 0.718691785 1 21.08719857 3.220362284 24.99998233 0.792129337 0.90489454 0.181282745 0.104528036 344.6884147 473515.2216 0.027539477 0.032975414 1660.971896 -3.220362284 0.112765203 GS(ph)PTSAYPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSPTSAYPERR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(0.925)PT(0.067)S(0.008)AYPERR;GS(0.959)PT(0.031)S(0.01)AYPERR 126.1 0.00019268 303750000 47345 58955 52301 54751 60097 75289 48772 54249 51429 72811 TRUE FALSE 49214.21716 69080.06264 53664.00703 65580.58438 49881.73341 57804.27077 44949.1232 53521.88089 49578.08034 87076.9214 0.56518095 0.793322289 0.616282778 0.753133934 0.572846773 0.663829977 0.516200188 0.614650587 0.569359591 1 16.41000278 -1.901229847 6.683710967 1.080768572 0.630687881 0.646706462 0.082165339 0.04576397 0.000676288 0.036816956 0.01810865 0.012553654 1.901229847 -0.450080691 GS(ph)PVFLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 113.62 0.0029509 493722000 712700 750490 704530 802500 837760 924720 835250 729120 693530 812190 TRUE FALSE 740837.9463 879380.8195 722890.6306 961232.1048 695357.8544 709967.7943 769780.9225 719347.339 668569.9908 971323.0802 0.762710123 0.905343276 0.744232939 0.989611103 0.715887297 0.730928574 0.792507599 0.740585037 0.68830856 1 19.88959172 GS(ph)PVPPVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 GS(1)PVPPVPER;GS(1)PVPPVPER;GS(1)PVPPVPER 82.171 0.019734 488890000 218729 254334 235609 250010 283899 292233 235436 245035 232022 245636 TRUE FALSE 227364.5898 298013.8861 241749.1641 299461.2318 235641.9494 224366.3146 216981.9111 241750.7066 223671.5735 293763.6712 0.773971093 1.014468143 0.822937578 1.019395048 0.802148027 0.763764674 0.738627449 0.822942829 0.761399708 1 18.16429647 3.064835768 24.9698904 0.799570487 0.909454639 0.167232409 0.098044427 81.60685342 31427.78509 0.025769836 0.030800843 1161.009487 -3.064835768 0.109884152 GS(ph)RGPGNPLDHQITNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSRGPGNPLDHQITNER 17 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 GS(1)RGPGNPLDHQITNER;GS(1)RGPGNPLDHQITNER 103.26 0.00054962 348380000 99506 114532 96444 131894 120359 152691 116010 93452 96020 108715 TRUE FALSE 103434.5737 134201.9801 98957.40987 157982.2395 99900.42017 117230.8293 106916.8331 92199.4288 92564.25896 130015.6228 0.795554961 1.032198879 0.761119377 1.215101971 0.768372431 0.901667252 0.822338353 0.709141154 0.711947203 1 16.98832546 2.476679994 1.609931498 0.777638538 0.932958479 0.088445338 0.149176822 0.657791792 3.456533562 0.064960675 0.050159804 299.6953426 -2.476679994 0.15531994 GS(ph)SFQSGRDDTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSSFQSGRDDTWR 13 1 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.553)S(0.447)FQSGRDDTWR;GS(0.55)S(0.45)FQSGRDDTWR 82.877 0.0095764 123760000 140152 562270 626350 406090 787730 634440 441590 625630 740870 565560 TRUE FALSE 145685.3092 658835.4986 642673.1956 486413.3899 653831.936 487100.925 406977.0219 617244.4532 714206.2334 676370.6537 0.215392712 0.974074637 0.950179006 0.719152121 0.966676973 0.720168627 0.601707096 0.912583137 1.055939121 1 19.36745454 4.744814472 24.82759087 0.860048161 0.215392396 0.662918843 0.141199552 402.8691047 1599328.223 0.033991695 0.31716643 55566.68294 -4.744814472 -0.644655765 GS(ph)SGSPAHAESYSSGGGGQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 GS(0.333)S(0.333)GS(0.333)PAHAESYSSGGGGQQK;GS(0.333)S(0.333)GS(0.333)PAHAESYSSGGGGQQK;GS(0.333)S(0.333)GS(0.333)PAHAESYSSGGGGQQK 111.4 5.34E-05 144480000 151479 124770 140919 128764 186603 218507 180485 153896 162102 120106 TRUE FALSE 157459.5079 146198.2769 144591.4649 154233.1349 154884.2887 167762.0608 166338.1141 151833.2758 156267.9807 143638.4711 1.096220996 1.017821171 1.006634669 1.073759235 1.078292518 1.167946577 1.15803317 1.057051601 1.087925675 1 17.13208268 5.070043845 20.84637347 1.076742994 1.658158174 0.010749281 0.054522233 2920.03279 1332927.471 0.013460309 42040.80199 117501.6176 -5.070043845 0.58141518 GS(ph)SPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.558)S(0.442)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.562)S(0.438)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.5)S(0.5)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 350.93 2.03E-145 1636990000 231654 175171 224556 174558 313945 286303 250442 233740 279107 174033 TRUE FALSE 240799.8788 205255.2566 230408.1138 209085.0514 260580.741 219813.4672 230811.7016 230607.0976 269061.9936 208131.4343 1.156960647 0.986180955 1.107031788 1.004581802 1.25200089 1.056128153 1.108970889 1.107987837 1.292750394 1 17.66713535 3.282010456 24.99999871 1.133776663 1.061248537 0.129627465 0.091955846 280.8099857 161569.5069 0.023826721 0.032261341 1914.302013 -3.282010456 -0.072528126 GS(ph)VHSLDAGLLLPSGDPFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSVHSLDAGLLLPSGDPFSK 20 0 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK;GS(0.5)VHS(0.5)LDAGLLLPSGDPFSK;GS(0.56)VHS(0.44)LDAGLLLPSGDPFSK 133.41 6.97E-06 455732000 388590 638930 689040 587690 760190 798700 634540 706220 700810 576010 TRUE FALSE 403931.8333 748661.2573 706996.9485 703933.3279 630973.1753 613214.0294 584803.0967 696754.276 675587.985 688868.1311 0.58637033 1.086799089 1.026316818 1.021869493 0.915956403 0.890176221 0.848933301 1.011447975 0.980721788 1 19.39386831 4.749470367 24.83200513 0.970676531 0.586370088 0.747114106 0.067911792 785.5127192 1787891.263 0.017492099 0.258212136 56165.59535 -4.749470367 -0.384306443 GS(ph)VSDEEMMELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 GSVSDEEMMELR 12 0 P13796;Q5TBN3;Q5TBN5 P13796 LCP1 Plastin-2 1 GS(0.897)VS(0.103)DEEMMELR;GS(0.986)VS(0.014)DEEMMELR;GS(1)VSDEEMMELR;GS(1)VSDEEMMELR;GS(0.989)VS(0.011)DEEMMELR;GS(0.993)VS(0.007)DEEMMELR;GS(1)VSDEEMMELR;GS(1)VSDEEMMELR;GS(0.998)VS(0.002)DEEMMELR;GS(1)VSDEEMMELR;GS(1)VSDEEMMELR 315.09 2.11E-46 2861524000 2119223 2632930 2603580 2799150 2841300 3355960 3164130 3004290 2890810 2986370 TRUE FALSE 2202891.56 3085115.246 2671431.434 3352813.515 2358336.841 2576589.15 2916117.223 2964022.407 2786770.313 3571492.024 0.616798678 0.863816922 0.747987512 0.938771105 0.660322584 0.721432145 0.816498316 0.829911529 0.780281825 1 21.76809547 -4.99999998 0.232779646 2.206768354 0.757270318 0.374679569 0.08903755 175.4381571 1.754471328 99.69169521 0.143214074 1.00E-05 4.99999998 -1.449498036 GS(ph)YGDLGGPIITTQVTIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSYGDLGGPIITTQVTIPK 19 0 P61978;P61978-2;S4R359;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK;GS(0.997)Y(0.003)GDLGGPIITTQVTIPK 295.37 1.19E-49 882230000 490789 317463 398692 391411 474555 493697 550172 440613 456309 333251 TRUE FALSE 510165.7287 371984.8007 409082.241 468830.9276 393890.3106 379043.3538 507048.081 434707.3034 439886.5282 398545.153 1.280070087 0.93335673 1.026438882 1.176355863 0.988320414 0.951067529 1.272247516 1.090735391 1.103730719 1 18.60438366 2.262758204 24.99997452 1.125936166 1.054150081 0.051927493 0.116314995 602.4744203 622450.4033 0.038771538 0.032423076 183.1294555 -2.262758204 -0.071786084 GS(ph)YGYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSYGYIK 7 0 O15117;O15117-2;O15117-3 O15117 FYB FYN-binding protein 1 GS(1)YGYIK 74.376 0.051851 0 154750 125710 152880 125450 176740 180550 169180 156590 160260 122050 TRUE FALSE 160859.6495 147299.7146 156864.1784 150263.6356 146697.7979 138619.9988 155919.2295 154491.1672 154492.2739 145963.3607 1.102054986 1.009155406 1.074681877 1.029461331 1.005031655 0.949690375 1.068207999 1.058424295 1.058431877 1 17.15524675 4.750342175 23.97687169 1.031367425 1.102055063 0.262668646 0.036801583 1568.11778 3191202.581 0.009202726 0.143985181 56278.45616 -4.750342175 0.070687638 GSAADSEESPAIEAIHLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSAADSEESPAIEAIHLLR 19 0 P13716;P13716-2;B7ZBK6 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;; 203.89 4.84E-16 497060000 403773 472745 433103 478862 517630 531276 469394 440162 425867 538865 FALSE TRUE 419714.2698 553935.2763 444390.02 573579.4743 429643.4375 407895.2006 432601.6717 434262.3483 410540.1299 644445.2796 0.65127992 0.859553625 0.689569827 0.890035962 0.666687229 0.632940008 0.671277586 0.673854495 0.637044204 1 19.29769834 -1.085829018 4.601419445 1.00001402 0.709640773 0.507020924 0.086357274 1.60E-05 3.17E-06 0.083496552 0.019679104 0.082067458 1.085829018 -0.290373247 GSALEEKENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSALEEKENK 10 1 Q9Y275-2;Q9Y275 Q9Y275-2 TNFSF13B "Tumor necrosis factor ligand superfamily member 13B;Tumor necrosis factor ligand superfamily member 13b, membrane form;Tumor necrosis factor ligand superfamily member 13b, soluble form" 0 126.67 0.00034328 204410000 288090 176660 162890 140400 361030 384660 388730 382370 368970 238830 FALSE TRUE 299464.0157 206999.9808 167135.0472 168170.7009 299662.2496 295328.5446 358260.3268 377244.9556 355690.8418 285624.1658 1.048454758 0.724728526 0.585157235 0.588783167 1.049148796 1.033976042 1.254306777 1.320773943 1.245310742 1 18.12375852 2.868981851 1.902983359 1.227406674 0.73081084 0.615586015 0.157877859 0.206172845 1.483419144 0.057407749 0.061834944 739.5743672 -2.868981851 -0.496595834 GSAMQVS(ph)PLMFTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GSAMQVSPLMFTDK 14 0 A0A494C1L5;P50851-2;P50851;E9PEM5;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 GSAMQVS(1)PLMFTDK;GSAMQVS(1)PLMFTDK;GSAMQVS(1)PLMFTDK;GS(0.002)AMQVS(0.997)PLMFT(0.001)DK;GSAMQVS(1)PLMFTDK;GS(0.001)AMQVS(0.998)PLMFTDK;GSAMQVS(1)PLMFTDK;GSAMQVS(0.998)PLMFT(0.002)DK 231.15 6.78E-13 1677990000 2733970 2212170 2760300 2298970 3270440 3217580 3057150 2767260 2985510 2282880 TRUE FALSE 2841909.247 2592092.989 2832235.686 2753699.404 2714531.777 2470345.808 2817522.595 2730169.406 2878062.078 2730166.628 1.040928864 0.949426662 1.037385651 1.008619539 0.994273298 0.904833347 1.03199657 1.000001018 1.054170851 1 21.38055757 GSASYS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSASYSPPR 9 0 A0A087WTY1;P0DPB5 A0A087WTY1 POLR1D 1 GSASYS(1)PPR;GSASYS(1)PPR 129.88 0.0003954 283350000 602690 786250 679280 704950 717880 815520 692070 707220 611910 840520 TRUE FALSE 626484.6666 921282.3213 696982.5948 844387.0059 595855.014 626127.8393 637823.745 697740.8727 589887.4786 1005203.801 0.623241442 0.91651297 0.693374412 0.840015731 0.592770355 0.622886462 0.63452182 0.694128765 0.586833713 1 19.9390566 -1.160887677 3.489487921 1.000356567 0.69348671 0.449604194 0.103017567 27627327.53 45592492.34 112127.7653 0.025290572 0.069041835 1.160887677 -0.306869857 GSAVHQLSEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 159.08 6.98E-05 4854140000 2044490 4366180 3788340 4253660 3867810 4910000 3701850 4063280 3614460 4881620 FALSE TRUE 2125208.044 5116037.451 3887067.253 5095021.252 3210361.038 3769726.912 3411689.324 4008818.378 3484376.291 5838079.975 0.364025168 0.87632192 0.665812608 0.872722072 0.549900147 0.645713476 0.584385507 0.68666726 0.596835998 1 22.47706254 -1.959418658 2.441442363 1.271271349 0.659190806 0.352000654 0.142222757 13796297.13 6359328.69 21200672.9 0.031959374 0.010979469 1.959418658 -0.612080542 GSCFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSCFHR 6 0 P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37 P62937 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ; 116.87 0.053984 502590000 192407 635550 499050 538510 537170 646930 393050 544320 417650 748740 FALSE TRUE 200003.3769 744700.7686 512055.653 645025.6707 445862.0353 496690.3118 362241.714 537024.2807 402618.8581 895441.2675 0.223357337 0.83165786 0.57184728 0.720343918 0.497924377 0.554687761 0.404539892 0.59973144 0.449631788 1 19.77223928 -1.50148103 3.024126761 1.013900564 0.551215683 0.429327624 0.158810519 29268886.42 34323644.58 3390733.887 0.037508464 0.03151512 1.50148103 -0.462684882 GSCLESGGHSNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSCLESGGHSNDR 13 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 0 ; 137.84 5.22E-06 0 86657 162457 125672 158921 161603 161742 118770 146771 129649 177571 FALSE TRUE 90078.28527 190357.726 128947.1156 190355.0995 134133.7798 124179.8717 109460.4971 144803.7748 124982.9578 212362.6376 0.424172003 0.896380494 0.607202458 0.896368126 0.631626077 0.584753858 0.515441408 0.681870297 0.588535531 1 17.69617044 -1.813721708 6.068522062 1.025563611 0.654811656 0.355302015 0.142183242 0.043910043 0.001347855 0.122925778 0.030417422 0.015356007 1.813721708 -0.370751955 GSDALS(ph)ETSS(ph)VSHIEDLEK ddPTM_MDA-MB-175_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(0.76)ET(0.261)S(0.15)S(0.827)VS(0.002)HIEDLEK 142.42 8.21E-08 77001000 143720 111130 141300 150490 191590 212170 201270 161770 147530 112670 TRUE FALSE 149394.1766 130215.713 144982.3941 180256.4728 159023.6002 162896.733 185493.9315 159601.7378 142220.4241 134745.5293 1.10871342 0.966382437 1.075971832 1.337754757 1.180177191 1.208921244 1.376624014 1.184467778 1.055474158 1 17.03987788 3.97525234 20.04761524 1.209256944 1.033455139 0.248789594 0.11116827 64.79625307 52492.06245 0.027404056 0.049947994 9446.095668 -3.97525234 -0.175801805 GSDALS(ph)ETSSVSHIEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GSDALS(0.998)ET(0.002)SSVSHIEDLEK;GSDALS(0.998)ET(0.001)S(0.001)SVSHIEDLEK 227 1.44E-19 120536000 121669 128481 148663 142944 196506 226106 207292 178893 174602 126385 TRUE FALSE 126472.5861 150546.6123 152537.2799 171217.8966 163103.9803 173596.3082 191043.9114 176495.2319 168318.1081 151147.721 0.836748217 0.996023039 1.009193383 1.132785168 1.07910314 1.148520845 1.263954959 1.167700253 1.11360004 1 17.2055997 4.787754302 0.724230491 1.155678372 0.636788459 0.645727086 0.067209737 1.719139107 0.652667903 0.025651526 0.743023179 61341.48737 -4.787754302 -0.518889914 GSDALSET(ph)SS(ph)VSHIEDLEK ddPTM_MDA-MB-175_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(0.264)ET(0.733)S(0.197)S(0.806)VS(0.001)HIEDLEK 145.04 2.29E-07 64115000 109360 84875 117330 107670 156180 160050 145250 127590 126600 85247 TRUE FALSE 113677.6172 99451.62101 120387.7162 128966.8046 129632.5794 122880.8131 133864.9255 125879.8647 122043.6907 101949.5175 1.115038306 0.975498692 1.180856164 1.265006523 1.271536958 1.205310394 1.313051094 1.23472742 1.197099248 1 16.63749542 4.083039584 5.530176044 1.230073477 1.04735457 0.355775931 0.086260747 0.16731457 8.424273895 0.019628498 0.043658628 12107.08478 -4.083039584 -0.182718907 GSDALSETSS(ph)VSHIEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.015)S(0.984)VSHIEDLEK;GSDALSETS(0.016)S(0.984)VSHIEDLEK;GSDALSET(0.006)S(0.031)S(0.964)VSHIEDLEK;GS(0.001)DALS(0.106)ET(0.157)S(0.29)S(0.44)VS(0.006)HIEDLEK 319.98 4.29E-62 740500000 1041210 875436 1192150 1185967 1678890 1656500 1410230 1220470 1217380 932493 TRUE FALSE 1082317.775 1025785.323 1223218.408 1420547.733 1393512.877 1271802.98 1299692.488 1204111.596 1173566.732 1115197.15 0.970516984 0.919824197 1.096862926 1.273808612 1.249566391 1.140428829 1.165437419 1.0797298 1.052340146 1 20.08886735 4.141492946 4.792335064 1.1456026 0.945941039 0.469886044 0.079808802 0.165534492 6.326922926 0.020968462 0.048370389 13851.37689 -4.141492946 -0.199661561 GSDASWKNDQEPPPEALDFS(ph)DDEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSDASWKNDQEPPPEALDFSDDEKEK 26 2 Q96HR8-2;Q96HR8 Q96HR8-2 NAF1 H/ACA ribonucleoprotein complex non-core subunit NAF1 1 GSDASWKNDQEPPPEALDFS(1)DDEKEK 97.639 0.0033265 160930000 174720 33672 67440 24661 135910 122290 54848 57043 77777 33580 TRUE FALSE 181618.0805 39454.90407 69197.5418 29538.87219 112808.0667 93890.00082 50548.87044 56278.43189 74977.82096 40159.35807 4.52243485 0.982458534 1.723073902 0.735541443 2.809010705 2.337935797 1.258707132 1.401377776 1.867007456 1 15.29344859 4.74603437 24.84822321 1.598306028 4.522436365 0.67740805 0.611255704 494.4715521 1643942.388 0.145507188 1.53161187 55722.98459 -4.74603437 2.924130337 GSDEPPVFLEIHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSDEPPVFLEIHYK 14 0 P28838-2;P28838;H0Y9Q1 P28838-2 LAP3 Cytosol aminopeptidase 0 ;;; 242.8 1.68E-17 1372720000 1200740 1163630 1237320 1109080 1489260 1501350 1393120 1286530 1322900 1246780 FALSE TRUE 1248146.142 1363474.401 1269565.576 1328452.714 1236116.117 1152684.216 1283923.614 1269286.17 1275289.087 1491062.67 0.837084965 0.914431317 0.851450178 0.89094358 0.829016876 0.773062219 0.861079578 0.851262791 0.855288723 1 20.50790947 0.248275343 2.088181303 1.000002884 0.851602316 0.614155092 0.035319915 16.59585257 44.76052027 0.034912099 0.009526385 1.771231564 -0.248275343 -0.148400567 GSDFDCELR ddPTM_MDA-MB-175_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 17471600000 6977990 8715560 7858880 8418230 8499080 9642160 8074110 8184280 7569430 9493790 FALSE TRUE 7253486.433 10212389.63 8063688.869 10083330.77 7054409.417 7402914.468 7441240.16 8074583.113 7297007.693 11353916.38 0.638853255 0.899459648 0.710212106 0.888092745 0.62131948 0.652014179 0.655389727 0.711171621 0.642686404 1 23.43668669 -1.218287303 3.664485259 1.000366846 0.716380814 0.447099587 0.095608085 38463182.12 71161573.5 175044.5423 0.022697337 0.060494055 1.218287303 -0.283986032 GSDHSASLEPGELAELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GSDHSASLEPGELAELVR 18 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;;; 253.02 1.70E-30 11972900000 1707427 6976720 5462600 6423460 5509620 7613510 4854670 6321450 5178500 7663800 FALSE TRUE 1774837.536 8174917.389 5604959.844 7694001.216 4573096.76 5845387.686 4474148.28 6236721.303 4992126.797 9165374.878 0.193645929 0.891934863 0.611536344 0.839463886 0.498953597 0.637768533 0.488157696 0.680465489 0.544672407 1 23.12776246 -1.159089618 3.563379016 1.00035092 0.613134827 0.294206347 0.185313727 47653266.23 81617581.09 214041.6553 0.04157056 0.069328273 1.159089618 -0.387216094 GSDIDNPTLTVMDISPPSRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 GSDIDNPTLTVMDISPPS(0.065)RS(0.935)PR;GSDIDNPTLTVMDISPPS(0.051)RS(0.949)PR;GSDIDNPTLTVMDISPPS(0.022)RS(0.978)PR;GSDIDNPTLTVMDISPPS(0.165)RS(0.835)PR 137.42 1.83E-06 241438000 236376 274368 264420 269701 260523 299927 248579 250417 218491 258487 TRUE FALSE 245708.307 321488.5697 271311.0024 323047.0528 216239.3935 230273.4997 229094.7284 247060.5697 210627.5516 309132.5786 0.794831487 1.039969877 0.877652571 1.045011348 0.699503736 0.744902076 0.741088919 0.799205864 0.681350224 1 18.23786618 3.231287283 24.99999689 0.766031931 0.942144169 0.350874373 0.107013535 156.9403979 539436.923 0.02800378 0.034119645 1703.284847 -3.231287283 0.176112238 SAVADKHELLSLASSNHLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAVADKHELLSLASSNHLGK 20 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 266.62 5.94E-37 503390000 309540 658440 889260 681260 1007800 1129100 868650 987390 948940 695160 FALSE TRUE 321760.8782 771521.948 912434.8461 816011.1946 836494.516 866883.6367 800562.9432 974155.6521 914787.8348 831363.2924 0.387028007 0.928020223 1.097516398 0.981533828 1.006172059 1.042725418 0.962951998 1.171756873 1.100346675 1 19.66511952 4.732845218 2.906624371 1.049473082 0.276802238 0.912844967 0.060732717 0.106586818 1.298314034 0.015837701 0.192116099 54056.16334 -4.732845218 -0.772670844 down GSDRT(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSDRTPER 8 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 GSDRT(1)PER;GS(0.001)DRT(0.999)PER 92.866 0.01855 550110000 335970 415730 357810 364680 423520 458380 367820 393000 382340 436950 TRUE FALSE 349234.355 487128.3936 367134.8225 436812.6155 351530.2217 351928.1918 338989.3073 387732.4778 368579.6581 522561.9866 0.668311825 0.932192555 0.702567029 0.835905838 0.672705307 0.673466882 0.648706404 0.741983703 0.705331937 1 18.99524266 -1.090498918 3.602863752 1.000138958 0.733010303 0.479593786 0.083970007 24004554.33 39446606.79 39756.35349 0.019831684 0.081189727 1.090498918 -0.267128655 GSDS(ph)DSEGDNPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GS(0.013)DS(0.987)DSEGDNPEK;GSDS(1)DSEGDNPEK;GSDS(0.98)DS(0.02)EGDNPEK 380.81 4.61E-92 925570000 2671750 1734070 2200060 1831030 2592200 2807430 2952660 2365040 2410730 1538600 TRUE FALSE 2777232.753 2031883.033 2257395.371 2193202.269 2151578.77 2155446.93 2721222.794 2333340.507 2323968.298 1840059.212 1.509317056 1.104248722 1.226805831 1.191919399 1.16929866 1.171400853 1.478877841 1.268079034 1.262985606 1 20.81132076 GSDS(ph)DSEGDNPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSDSDSEGDNPEKK 14 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 GSDS(1)DSEGDNPEKK;GS(0.001)DS(0.999)DSEGDNPEKK;GSDS(1)DSEGDNPEKK;GS(0.001)DS(0.998)DS(0.001)EGDNPEKK 277.44 2.37E-33 2108680000 4343040 1592710 2486190 1728410 3570120 3356070 3756350 2422170 3020340 1138420 TRUE FALSE 4514506.573 1866245.553 2550982.154 2070284.339 2963272.278 2576673.604 3461917.472 2389704.773 2911638.553 1361471.603 3.315902119 1.370756136 1.87369472 1.520622491 2.176521546 1.892565074 2.542776114 1.75523659 2.13859661 1 20.37673546 -0.861267408 5.684261623 0.99999966 2.02212305 0.266250661 0.526134505 2.10E-06 4.19E-07 0.464186701 0.109409817 0.137636174 0.861267408 1.02212339 GSDYSWSYQTPPS(ph)SPSSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSDYSWSYQTPPSSPSSSSSR 21 0 A0A087WXN9;Q765P7;H3BPV0 A0A087WXN9;H3BPV0 MTSS1L MTSS1-like protein 1 GSDYSWS(0.046)Y(0.001)QT(0.42)PPS(0.473)S(0.03)PS(0.006)S(0.006)S(0.006)S(0.006)S(0.006)R 106.31 0.00038817 177390000 121400 159880 140720 151450 152040 185570 152120 151710 169750 199420 TRUE FALSE 126192.9657 187338.1463 144387.2788 181406.358 126196.2951 142474.1798 140196.4369 149676.5756 163640.7307 238492.5309 0.529127538 0.78550949 0.605416355 0.760637481 0.529141498 0.597394725 0.587844141 0.627594395 0.686146145 1 17.86358456 0.735025109 2.764283646 0.999965443 0.630562318 0.654358855 0.080693451 0.964022449 9.282445383 0.072969389 0.01926237 5.432817404 -0.735025109 -0.369403125 GSEEDPLLS(ph)PVETWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSEEDPLLSPVETWK 15 0 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 GSEEDPLLS(0.993)PVET(0.007)WK 108.71 0.0011089 19191000 88559 63179 77797 74456 101040 115090 112380 88642 110760 82053 TRUE FALSE 92055.3777 74029.50179 79824.45373 89183.17457 83865.25689 88362.09171 103571.3619 87453.89898 106773.7692 98129.71435 0.938098906 0.754404538 0.813458536 0.908829453 0.854636717 0.900462131 1.055453617 0.891207108 1.088088047 1 16.58240244 2.556522066 1.003521737 1.00271491 0.835412536 0.50646058 0.069442436 0.450552782 0.928757857 0.041096406 0.031446786 360.1820503 -2.556522066 -0.167302374 GSEEDS(ph)PKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSEEDSPKK 9 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(1)PKK;GSEEDS(1)PKK 110.08 0.0014366 767600000 2633270 538020 823070 634300 1228030 1609150 1970030 1029800 1067370 318200 TRUE FALSE 2737233.533 630420.7498 844519.8804 759762.6468 1019289.899 1235449.299 1815613.901 1015997.215 1028955.562 380545.1977 7.192926227 1.656625162 2.219236731 1.996510931 2.678498915 3.246524478 4.771086094 2.669846372 2.703898429 1 18.53770829 0.797526696 1.945305409 1.00673765 3.200674142 0.16794021 1.539860668 1.368752218 8.971446114 1.410104639 0.392255705 6.273742594 -0.797526696 2.193936493 GSEEDS(ph)PKKESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSEEDSPKKESK 12 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 GSEEDS(0.997)PKKES(0.002)K;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK;GSEEDS(1)PKKESK 150.39 3.55E-05 4336670000 12729490 2001036 3520887 1979755 6285360 7238290 6449240 3860768 4337440 1182459 TRUE FALSE 13232060.09 2344698.367 3612644.208 2371344.63 5216976.752 5557306.845 5943731.717 3809020.72 4181336.382 1414139.202 9.356971422 1.658039297 2.554659544 1.676882041 3.689153618 3.929815989 4.203074005 2.693526009 2.956806782 1 20.43149271 4.745020842 24.9661382 2.852200237 9.35697439 0.797640153 1.002461931 320.2424478 1237573.019 0.24127464 2.302295561 55593.0936 -4.745020842 6.504774152 GSEGDCS(ph)PEDKNSVTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSEGDCSPEDKNSVTAK 17 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 GSEGDCS(1)PEDKNSVTAK 148.85 2.10E-07 109950000 460990 190900 252360 199030 420330 391320 340020 251930 305660 183380 TRUE FALSE 479190.2412 223685.59 258936.7089 238397.54 348882.4567 300441.8605 313368.3439 248553.2904 294659.3563 219309.8 2.184992377 1.019952551 1.180689185 1.087035509 1.590820186 1.369942705 1.428884363 1.133343291 1.343575875 1 17.74261076 4.747603462 24.80570784 1.254938333 2.184992915 0.706854831 0.182443982 598.5329754 1641815.188 0.04346497 0.531896019 55924.67414 -4.747603462 0.930054582 GSEHTVNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSEHTVNFK 9 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ; 114.84 0.0015728 394020000 363670 524040 635300 645660 723830 783750 668550 652940 586890 549060 FALSE TRUE 378027.9724 614039.7935 651856.4399 773369.6209 600793.6351 601735.9403 616147.3041 644188.4073 565767.9435 656637.7946 0.575702428 0.935127095 0.992718429 1.177772019 0.914954394 0.916389439 0.938336643 0.981040709 0.861613432 1 19.32473827 4.737804597 3.911040824 0.973616406 0.538244967 0.688874772 0.07957724 0.138955408 4.31949047 0.019674732 0.17280401 54676.98985 -4.737804597 -0.435371439 GSELETAMETLINVFHAHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSELETAMETLINVFHAHSGK 21 0 P23297;Q5T7Y5;Q5T7Y4 P23297 S100A1 Protein S100-A1 0 185.87 1.99E-17 40211000 40202 50676 52007 46135 68570 63838 63882 50483 51393 57609 FALSE TRUE 41789.206 59379.2088 53362.34514 55260.3653 56914.49589 49012.59197 58874.76192 49806.35796 49543.37597 68896.38056 0.606551544 0.861862529 0.774530457 0.802079367 0.826088329 0.711395745 0.854540709 0.722916902 0.719099836 1 16.07214057 -1.406161869 3.033286304 1.003634225 0.769507111 0.476303978 0.07395326 12238462.14 15285065.76 387318.2786 0.016155239 0.039249862 1.406161869 -0.234127115 GSES(ph)PNSFLDQESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSESPNSFLDQESR 14 0 Q5T4Y8;A0A5H1ZRR2;G9CGD6-3;G9CGD6;G9CGD6-2;Q6P9H4 Q5T4Y8 CNKSR3 Connector enhancer of kinase suppressor of ras 3 1 GSES(0.998)PNS(0.002)FLDQESR 215.11 6.33E-08 0 103290 123620 118100 125630 114350 170620 116300 124250 118510 137870 TRUE FALSE 107367.969 144850.7734 121177.783 150479.239 94912.82784 130996.0908 107184.1021 122584.632 114244.8482 164882.9868 0.651176759 0.878506486 0.734931998 0.912642608 0.575637485 0.794479123 0.650061624 0.743464407 0.692884393 1 17.33108302 -1.026701746 4.412543414 1.000012256 0.739758494 0.390017669 0.098588254 86112592443 18993701034 12113263.95 0.021271776 0.094036889 1.026701746 -0.260253762 GSET(ph)PGATPGSK ddPTM_MDA-MB-175_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(0.999)PGAT(0.001)PGSK 251.91 5.35E-20 3239590000 6406500 4890720 5756960 4815400 6611160 6825680 6552460 5788970 5520650 4278580 TRUE FALSE 6659433.567 5730663.115 5906991.107 5767871.747 5487397.385 5240519.264 6038861.064 5711378.326 5321962.885 5116885.833 1.301462214 1.119951334 1.154411355 1.127223068 1.07240958 1.024161851 1.180182881 1.116182481 1.040078489 1 22.28683461 7.999999467 0.82386819 1.089788315 61.14334698 0.594217138 0.05315506 426.9851902 1.320523941 0.017329462 47964.96437 99999877.32 -7.999999467 60.05355867 GSFAGIEDDADEALEISQAQLLFENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSFAGIEDDADEALEISQAQLLFENRR 27 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 209.76 2.52E-25 28514000 15550 21473 21202 17198 19043 23262 14289 19949 17824 28673 FALSE TRUE 16163.92601 25160.82071 21754.54154 20599.71307 15806.07766 17859.75304 13168.99084 19681.61628 17182.51772 34290.92537 0.471376197 0.733745749 0.634411037 0.600733659 0.46094054 0.520830303 0.384037196 0.573959905 0.501080608 1 15.06553922 -1.186614094 5.205309996 1.000026576 0.54458229 0.680568287 0.094050196 3.00E-05 4.68E-06 0.094113608 0.022181498 0.065070764 1.186614094 -0.455444286 GSFKDDPQLYQEIQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSFKDDPQLYQEIQER 16 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 0 62.813 0.067291 188850000 75557 79591 70452 74014 89418 86085 84403 65573 73959 72184 FALSE TRUE 78540.0487 93260.13512 72288.037 88653.74829 74218.7603 66093.06338 77787.27231 64694.10119 71297.23004 86327.07275 0.909796269 1.080311566 0.837373893 1.026951864 0.859739105 0.765612238 0.901076219 0.749406868 0.825896532 1 16.39752545 3.088458443 6.436035251 0.828917494 0.962260248 0.262533176 0.090192851 0.232407453 13.91432111 0.024243284 0.029075107 1225.90959 -3.088458443 0.133342754 GSFLDKIS(ph)PSVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSFLDKISPSVLR 13 1 Q9BW04;Q9BW04-2 Q9BW04 SARG Specifically androgen-regulated gene protein 1 GSFLDKIS(0.993)PS(0.007)VLR;GSFLDKIS(0.867)PS(0.133)VLR 130.27 8.72E-05 557540000 746380 662820 756160 687930 991610 923210 861330 747310 803520 654900 TRUE FALSE 775847.6587 776654.179 775866.1508 824000.5007 823056.4864 708808.4689 793816.7039 737293.5318 774601.4722 783215.1162 0.990593316 0.991623071 0.990616926 1.052074307 1.050869001 0.904998453 1.013535985 0.941367852 0.989002199 1 19.57904908 2.760888093 24.98320628 0.967802047 1.014535783 0.288831054 0.035525201 1008.413909 1128357.638 0.010675194 0.011313613 576.6178643 -2.760888093 0.046733736 GSFS(ph)DTGLGDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GSFS(0.999)DT(0.001)GLGDGK;GSFS(1)DTGLGDGK;GSFS(0.999)DT(0.001)GLGDGK;GSFS(0.963)DT(0.037)GLGDGK;GSFS(0.884)DT(0.116)GLGDGK;GSFS(0.982)DT(0.018)GLGDGK 239.49 3.75E-16 3375580000 9143000 6456370 8561360 6937670 10939600 10248960 10261120 8523570 9213680 6749720 TRUE FALSE 9503972.7 7565201.324 8784476.075 8309920.419 9080090.7 7868794.364 9456826.602 8409325.486 8882081.457 8072198.403 1.177371049 0.937192193 1.088238375 1.029449476 1.124859703 0.974801903 1.171530496 1.041763974 1.100329924 1 22.9445302 GSFSEQGINEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 305.74 4.30E-41 738360000 419369 568260 475830 502310 522300 622670 424025 442429 408377 565370 FALSE TRUE 435926.0119 665854.2346 488230.5207 601665.4188 433519.6326 478064.3292 390788.8125 436498.9629 393679.5915 676143.4268 0.644724173 0.98478253 0.722081294 0.889848803 0.641165196 0.707045739 0.577967332 0.645571554 0.582242725 1 19.36696978 3.226931874 24.99420962 0.665904675 0.816512448 0.126327513 0.141842015 317.8713475 683214.9778 0.037339249 0.044981734 1686.288482 -3.226931874 0.150607773 GSFSQADVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSFSQADVHR 10 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3 Q04206 RELA Transcription factor p65 0 ; 154.05 1.52E-05 507740000 194222 272340 233920 220330 358240 312430 238130 229500 229830 443620 FALSE TRUE 201890.0345 319112.2765 240016.1474 263910.6164 297346.4928 239872.8674 219464.7484 226423.9279 221558.4632 530538.8454 0.380537705 0.601487109 0.452400704 0.497438818 0.560461303 0.452130639 0.413663863 0.426781055 0.417610256 1 19.01709886 -1.400183041 3.187730952 1.006491231 0.468302815 0.857265779 0.065250663 26088878.81 34922752.59 1560564.995 0.017151723 0.039793942 1.400183041 -0.538188416 GSGDGEMGKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSGDGEMGKPR 11 1 O60547 O60547 GMDS "GDP-mannose 4,6 dehydratase" 0 ;; 111.63 0.0014906 447170000 639570 482670 602120 467690 752530 693300 749650 598900 604480 500100 FALSE TRUE 664820.7175 565564.8178 617811.7418 560197.6861 624615.2194 532291.5821 690890.4742 590872.7251 582724.8829 598085.02 1.111582292 0.945626122 1.03298314 0.936652261 1.044358575 0.889993169 1.155171006 0.987941021 0.974317803 1 19.18999106 2.26642355 24.99950211 1.02855234 0.99287313 0.05225804 0.074677313 708.1281257 635352.2358 0.02428066 0.02031065 184.6815666 -2.26642355 -0.035679211 GSGEKPVSAPGDDT(ph)ESLHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVS(0.002)APGDDT(0.743)ES(0.256)LHS(0.999)QGEEEFDMPQPPHGHVLHR 75.887 0.0016043 125660000 29066 21405 33549 22969 35300 32404 30255 30433 32482 25200 TRUE FALSE 30213.54812 25081.14224 34423.3145 27512.19964 29299.71861 24878.66209 27883.53404 30025.09541 31312.97917 30137.45752 1.002524785 0.832224889 1.142210304 0.912890533 0.972202735 0.825506335 0.92521189 0.996271679 1.039005336 1 14.87927009 1.58577925 4.536322675 1.018884722 0.943439063 0.118805349 0.08496788 0.337362086 15.3645915 0.048093061 0.02152015 38.52824706 -1.58577925 -0.07544566 GSGEKPVSAPGDDTES(ph)LHS(ph)QGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 GSGEKPVSAPGDDT(0.442)ES(0.558)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVS(0.001)APGDDT(0.065)ES(0.934)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.113)ES(0.887)LHS(1)QGEEEFDMPQPPHGHVLHR;GSGEKPVSAPGDDT(0.146)ES(0.853)LHS(1)QGEEEFDMPQPPHGHVLHR 188.07 8.49E-24 1952400000 386685 354409 380869 308814 486602 442699 399940 425457 458843 383981 TRUE FALSE 401951.6224 415275.9888 390794.759 369896.4875 403889.5658 339888.8664 368591.6578 419754.4448 442329.3301 459214.7252 0.87530212 0.904317667 0.851006594 0.80549788 0.879522245 0.740152368 0.802656443 0.914070089 0.963229848 1 18.80880938 1.442973952 2.686185874 0.984213806 0.837258688 0.625514512 0.045226313 0.184301869 2.458347788 0.038987173 0.012837536 27.73153773 -1.442973952 -0.146955118 GSGEKPVSAPGDDTES(ph)LHSQGEEEFDMPQPPHGHVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHR 38 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 GS(0.004)GEKPVS(0.023)APGDDT(0.032)ES(0.785)LHS(0.156)QGEEEFDMPQPPHGHVLHR;GSGEKPVS(0.001)APGDDT(0.019)ES(0.49)LHS(0.49)QGEEEFDMPQPPHGHVLHR 105.6 6.44E-06 588770000 172276 214936 260236 208896 277440 301698 274204 266946 270694 223230 TRUE FALSE 179077.5895 251849.586 267017.9639 250215.0053 230280.8479 231633.2118 252711.174 263368.0255 260951.7758 266967.6445 0.670783869 0.943371196 1.000188485 0.937248429 0.862579615 0.867645262 0.946598508 0.986516647 0.977465926 1 18.02630538 4.738445511 9.27965722 0.944728492 0.669759969 0.759570615 0.046581716 0.040839768 81.69336277 0.012195825 0.070893982 54757.73951 -4.738445511 -0.274968522 GSGEQDWVNRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSGEQDWVNRPK 12 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ; 122.52 0.00032563 915010000 1835990 1402640 1684660 1413220 2044700 2066250 1899450 1748670 1929090 1469870 FALSE TRUE 1908476.303 1643532.509 1728563.624 1692750.698 1697142.624 1586394.752 1750566.146 1725231.939 1859662.428 1757862.884 1.085679845 0.934960584 0.983332454 0.962959462 0.965457909 0.902456481 0.995849086 0.98143715 1.057910969 1 20.74539111 1.391721015 4.801650253 1.02863924 0.972193811 0.163822529 0.046586909 0.331499862 11.75363586 0.031405733 0.011173666 24.64455695 -1.391721015 -0.056445429 GSGPQRPHS(ph)FSEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSGPQRPHSFSEALR 15 1 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 GSGPQRPHS(1)FSEALR;GSGPQRPHS(0.99)FS(0.01)EALR;GSGPQRPHS(0.884)FS(0.116)EALR 202.51 3.56E-09 1950640000 505070 690760 656650 704430 731580 878660 679900 645390 694370 813170 TRUE FALSE 525010.5536 809392.6566 673762.8384 843764.1515 607226.2929 674604.5312 626607.6614 636739.6027 669379.7593 972495.0924 0.539859335 0.832284567 0.692818754 0.867628185 0.624400367 0.693684252 0.644329896 0.654748397 0.688311709 1 19.89133144 -1.985564717 2.882060989 1.276926449 0.695232732 0.508312242 0.09052498 19052672.17 9172352.888 34973726.66 0.020703218 0.01033797 1.985564717 -0.581693717 GSGS(ph)PTHSLSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSGSPTHSLSQK 12 0 I3L2R2;I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L2R2 FAM64A Protein FAM64A 1 GSGS(0.999)PTHSLSQK;GSGS(1)PTHSLSQK;GSGS(0.854)PT(0.145)HSLSQK 310.14 3.03E-46 466940000 593240 653160 724330 589070 844170 917340 796860 729610 743170 699390 TRUE FALSE 616661.5733 765335.1491 743206.6348 705586.2878 700678.2849 704301.6874 734400.031 719830.7714 716423.4569 836422.0799 0.737261232 0.915010696 0.888554538 0.843576831 0.837708977 0.842041003 0.878025639 0.860607089 0.856533411 1 19.67387162 -5 0.297775871 2.193781156 0.846725359 0.515243852 0.04380307 210.145977 1.951948651 156.3842927 0.041961487 1.00E-05 5 -1.347055796 GSGTAEVELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSGTAEVELKK 11 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 138.45 9.19E-05 3437380000 4785110 2746790 3724040 2595380 5358150 4401400 4553970 4001730 4480100 2646580 FALSE TRUE 4974029.838 3218529.815 3821091.542 3108738.418 4447373.577 3379241.554 4197017.932 3948093.355 4318862.076 3165126.679 1.571510509 1.016872354 1.207247586 0.982184517 1.405117086 1.067648122 1.326018942 1.247372935 1.364514762 1 21.59383181 GSGTAS(ph)DDEFENLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR;GSGTAS(1)DDEFENLR 355.75 4.28E-82 13074610000 2361510 2651560 2492950 2589760 2734940 2896460 2486080 2436150 2288260 2732840 TRUE FALSE 2454744.238 3106944.804 2557918.325 3102006.798 2270055.876 2223801.061 2291214.553 2403497.394 2205905.97 3268287.675 0.751079612 0.950633822 0.782647851 0.949122938 0.694570399 0.680417785 0.701044333 0.735399583 0.674942413 1 21.64010354 3.222835083 24.9997647 0.728618477 0.859552468 0.191429342 0.107152855 300.337651 477462.6837 0.028107551 0.033701606 1670.456163 -3.222835083 0.130933991 GSIDEVDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSIDEVDKR 9 1 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;; 133.13 0.00045778 3670120000 3613100 2273200 2996720 2458060 3612330 3153730 3680290 2919560 3186060 2179320 FALSE TRUE 3755747.978 2663604.417 3074816.985 2944256.931 2998307.437 2421324.003 3391819.253 2880428.074 3071394.323 2606316.028 1.441017872 1.021980599 1.179756005 1.129662289 1.150400567 0.929021644 1.301384489 1.105172221 1.178442786 1 21.3135806 4.749651044 24.81827673 1.120332636 1.441018077 0.489260335 0.100827394 1248.384981 2793591.492 0.022232324 0.341134094 56188.96654 -4.749651044 0.320685441 GSKPS(ph)PLSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSKPSPLSVK 10 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 GSKPS(1)PLSVK;GSKPS(1)PLSVK;GS(0.001)KPS(0.998)PLS(0.001)VK;GSKPS(1)PLSVK 146.77 1.70E-05 3755510000 8550520 4947080 6930810 4765450 9511030 8179430 8926460 7225250 7830300 4603450 TRUE FALSE 8888101.132 5796702.507 7111432.602 5708041.787 7894348.518 6279881.343 8226780.74 7128407.342 7548489.033 5505407.889 1.614430994 1.052910633 1.291717661 1.036806337 1.433926183 1.140675036 1.494309033 1.294800946 1.371104409 1 22.39241802 GSKS(ph)PLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSKSPLKR 8 2 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 GS(0.002)KS(0.998)PLKR 72.187 0.03686 1854100000 3013700 1871500 2215500 1712700 3194800 2711500 2942400 2269600 2390900 1469000 TRUE FALSE 3132683.203 2192915.567 2273237.75 2051466.948 2651749.037 2081795.218 2711766.999 2239179.724 2304851.976 1756822.424 1.783153015 1.248228356 1.293948505 1.16771446 1.509400723 1.184977599 1.543563517 1.274562354 1.311943623 1 20.74453694 -3.924808998 0.207109468 2.96E-15 1.416994413 0.301513616 0.177441002 114.7971351 1.70732888 48.75823934 0.380265877 0.000118903 3.924808998 1.416994413 GSLAADKVVEEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSLAADKVVEEIRR 14 2 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 108.66 0.00045724 371860000 252050 333400 302108 278579 375930 396970 274482 294116 317352 351870 FALSE TRUE 262001.1286 390658.8565 309981.1827 333681.0947 312029.5529 304779.7336 252967.3836 290173.8561 305930.5635 420812.1895 0.622608221 0.928344915 0.736625959 0.792945411 0.741493618 0.724265459 0.601140817 0.689556679 0.727000242 1 18.68281697 -0.96498019 4.878191581 1.000002421 0.72892284 0.473576555 0.08561048 2.27E-06 4.82E-07 0.083478041 0.019675787 0.108397636 0.96498019 -0.271079581 GSLAPQDS(ph)DSEVSQNR ddPTM_MDA-MB-175_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(0.999)DS(0.001)EVSQNR;GSLAPQDS(0.997)DS(0.003)EVSQNR;GSLAPQDS(1)DSEVSQNR;GSLAPQDS(1)DSEVSQNR;GSLAPQDS(0.999)DS(0.001)EVSQNR;GSLAPQDS(0.998)DS(0.002)EVSQNR 319.33 5.64E-58 1366058000 711943 970640 718914 773422 742334 921691 682924 756109 703963 870004 TRUE FALSE 740051.0594 1137339.869 737649.4894 926402.5632 616152.3318 707642.2336 629394.6324 745974.5956 678627.5091 1040464.627 0.711269793 1.093107676 0.708961622 0.890373915 0.592189601 0.680121376 0.604916896 0.716962957 0.652235061 1 19.98879649 3.251960446 24.97709106 0.687235531 0.858086341 0.17717808 0.146922395 312.8496807 583143.8167 0.037290341 0.050204734 1786.324877 -3.251960446 0.17085081 GSLAS(ph)LDSLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GS(0.011)LAS(0.949)LDS(0.041)LRK;GSLAS(1)LDSLRK 177.36 4.91E-06 686919000 1051890 852410 849830 794360 1022350 1171080 1115800 921140 1003220 866520 TRUE FALSE 1093419.429 998804.7867 871977.2679 951482.0371 848571.3122 899114.4179 1028340.68 908793.625 967114.3082 1036298.003 1.055120656 0.963820043 0.841434862 0.918154849 0.818848738 0.86762149 0.992321395 0.876961667 0.933239575 1 19.9830075 4.566107724 3.524649595 0.900907799 1.052213279 0.393007475 0.056467509 0.232384608 4.973228247 0.013201294 0.069743323 36822.02967 -4.566107724 0.151305479 GSLASLDS(ph)LRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSLASLDSLRK 11 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 1 GSLASLDS(1)LRK;GSLASLDS(1)LRK 115.12 0.00071416 378070000 499980 377810 403880 366930 583040 577360 519390 461660 488230 463940 TRUE FALSE 519719.5965 442695.9285 414405.4446 439507.6588 483935.0691 443276.89 478678.8546 455472.2028 470658.6977 554840.1603 0.936701475 0.797880111 0.746891581 0.792133826 0.872206274 0.79892719 0.862732889 0.820907056 0.848277993 1 19.08171269 -0.663254313 0.525850082 1.035438022 0.820938128 0.510445094 0.049855486 9.701213546 2.027707003 0.643051689 0.022441326 0.217142926 0.663254313 -0.214499894 GSLDES(ph)SLGFGYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.036)LDES(0.888)S(0.076)LGFGYPK 304.08 4.10E-44 1118000000 414950 332440 379270 337280 464390 482040 464800 414780 402810 325340 TRUE FALSE 431332.5464 389533.984 389154.0878 403992.9773 385453.1537 370093.5154 428367.7615 409220.5525 388312.9468 389084.144 1.108584231 1.001156151 1.000179765 1.038317761 0.990667853 0.951191461 1.100964324 1.051753352 0.998017917 1 18.56972266 1.207034513 24.21812593 0.999008826 1.02934482 0.068566043 0.046088953 508.9535314 390957.2655 0.044609873 0.011157957 16.10773638 -1.207034513 0.030335994 GSLDESS(ph)LGFGYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLDESSLGFGYPK 14 0 Q9BUZ4;Q2KJU6 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 1 GS(0.251)LDES(0.21)S(0.539)LGFGYPK 305.67 2.32E-44 986840000 596480 474320 575960 506940 708510 630730 676170 548020 611860 446850 TRUE FALSE 620029.491 555780.7703 590969.9908 607211.2189 588077.7233 484252.5163 623170.0286 540674.6883 589839.2781 534401.702 1.160231131 1.040005614 1.105853497 1.13624492 1.100441337 0.90615826 1.166107866 1.011738335 1.103737649 1 19.02756508 2.961721275 24.99976408 1.042416683 1.106847045 0.204920272 0.069677344 949.6954252 620244.9251 0.020018563 0.02123691 915.6326598 -2.961721275 0.064430362 GSLDQDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSLDQDRR 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2;A0A2R8Y6Q7;A0A2R8Y7I7 A0A2R8Y430 GSS Glutathione synthetase 0 ;; 115.7 0.0038701 421534000 306373 405740 321570 334684 1052600 609260 478180 363625 330007 1241620 FALSE TRUE 318468.8426 475422.6888 329950.3784 400883.4963 873679.428 467768.5984 440699.0021 358751.2016 318130.1125 1484891.667 0.214472779 0.320173316 0.222205017 0.269974911 0.588379238 0.31501867 0.296788656 0.241600926 0.214244662 1 20.50192625 -1.327707183 3.453471231 1.003327732 0.300375305 0.80287808 0.104332381 34310939.88 49836811.07 1166871.517 0.02592736 0.047021104 1.327707183 -0.702952427 GSLDYRPLTTADPIDEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLDYRPLTTADPIDEHR 18 1 O00139-1;O00139-5;O00139;O00139-4;O00139-2;D6R9M0 O00139-1 KIF2A Kinesin-like protein KIF2A 0 116.6 9.35E-05 228870000 176160 224870 204800 225060 208910 232470 193460 216060 200060 223830 FALSE TRUE 183114.9328 263489.6733 210137.2562 269576.1963 173399.5528 178482.3656 178296.0997 213164.0691 192859.8797 267685.203 0.684068192 0.984326628 0.785016332 1.007064243 0.647774142 0.666762165 0.666066326 0.796323692 0.720472695 1 18.03017787 GSLEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLEEEKR 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 69.954 0.084315 178710000 219520 213860 218530 212530 230810 250380 255310 231670 227940 220060 FALSE TRUE 228186.8191 250588.7914 224225.0713 254567.7997 191576.9986 192233.0395 235298.1351 228564.8426 219736.4839 263176.5437 0.867048468 0.952169931 0.851994894 0.967289091 0.727941009 0.730433787 0.894069554 0.868484856 0.83493947 1 18.00567139 3.268643567 24.99997646 0.836834204 0.908547949 0.140957763 0.080222816 392.457318 326143.053 0.022053099 0.029856159 1856.280348 -3.268643567 0.071713745 GSLEQLSEEEMHAEICYAECLLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSLEQLSEEEMHAEICYAECLLQK 24 0 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0;Q5VTQ0-5;Q5VTQ0-6 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 0 ;; 237.97 1.86E-37 60739000 47602 40109 52748 47294 60355 56312 58649 50855 58231 40576.3 FALSE TRUE 49481.36372 46997.40875 54122.65621 56648.61204 50095.87866 43234.39142 54051.93813 50173.37191 56135.27768 48526.4491 1.01967823 0.968490578 1.115322823 1.167376 1.032341735 0.890944881 1.113865513 1.033938663 1.156797555 1 15.56648368 GSLESPATDVFGSTEEGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLESPATDVFGSTEEGEKR 20 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 245.22 9.69E-30 469020000 561450 378020 490500 418110 591710 540330 550680 457030 506760 365370 FALSE TRUE 583616.4795 442941.9944 503282.833 500810.9101 491131.3456 414846.5463 507516.2627 450904.2604 488521.8066 436957.2561 1.33563746 1.013696393 1.151789622 1.146132495 1.123980295 0.949398461 1.161478052 1.031918464 1.118008226 1 18.73713263 4.748255412 24.65927315 1.081838828 1.335637626 0.545690296 0.070588108 817.8333883 2080154.45 0.015873981 0.207083853 56008.68966 -4.748255412 0.253798798 GSLLPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLLPAK 7 0 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 0 86.113 0.020315 2101700000 110720 7550100 4202400 7773600 2213900 6959300 2632600 5134800 2532400 8078000 FALSE TRUE 115091.3111 8846770.943 4311917.996 9311194.878 1837582.069 5343108.044 2426249.933 5065976.405 2441259.419 9660729.437 0.011913315 0.915745648 0.446334619 0.96381903 0.190211524 0.553075011 0.251145625 0.524388602 0.252699285 1 23.20370069 -1.141553022 4.96426931 1.00002877 0.474579827 0.238878557 0.289396256 8.38E-05 1.45E-05 0.254964119 0.060092335 0.072185003 1.141553022 -0.525448944 GSLLPTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSLLPTSPR 9 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128 BRD8 Bromodomain-containing protein 8 1 GSLLPT(0.004)S(0.996)PR;GSLLPT(0.002)S(0.998)PR;GSLLPTS(1)PR;GSLLPT(0.002)S(0.998)PR;GSLLPT(0.012)S(0.988)PR;GSLLPT(0.013)S(0.987)PR 117.94 0.0011217 1104087000 2014330 2514490 2123550 2350430 2393440 2723000 2223430 2316030 2127470 2731840 TRUE FALSE 2093857.304 2946334.097 2178891.458 2815338.039 1986603.924 2090624.517 2049151.747 2284987.406 2050902.77 3267091.744 0.640893329 0.901821659 0.666920806 0.861726042 0.608064933 0.639903829 0.627209735 0.699394931 0.627745693 1 21.63957554 -1.235750123 4.419656933 1.000125849 0.699688391 0.467385735 0.096975604 0.000116885 2.02E-05 0.091265574 0.021502527 0.058109866 1.235750123 -0.300437458 GSLLTILGSPS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLLTILGSPSPER 14 0 Q96A19 Q96A19 CCDC102A Coiled-coil domain-containing protein 102A 1 GSLLTILGS(0.006)PS(0.994)PER 106.14 0.001006 11629000 27371 28041 26825 22568 27447 36495 25245 32762 23205 25527 TRUE FALSE 28451.62822 32856.82362 27524.08154 27031.88304 22781.56874 28019.58934 23266.23093 32322.87898 22369.85658 30528.52691 0.931968591 1.076266265 0.901585642 0.885463066 0.746238717 0.917816619 0.762114432 1.058776242 0.732752571 1 14.89787036 4.090066096 6.843485694 0.876772481 1.003223166 0.194962224 0.105570665 0.327203622 20.8005101 0.0251436 0.05508708 12304.56021 -4.090066096 0.126450686 GSLPQLVS(ph)PIVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSLPQLVSPIVSR 13 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 GSLPQLVS(1)PIVSR;GSLPQLVS(0.988)PIVS(0.012)R;GSLPQLVS(0.995)PIVS(0.005)R;GSLPQLVS(1)PIVSR 187 7.69E-06 402497000 435126 522141 436092 472016 413596 518108 398109 460846 395923 548753 TRUE FALSE 452305.1105 611814.6551 447456.9158 565379.356 343293.0997 397785.269 366904.1763 454669.1132 381673.8086 656270.6438 0.689205154 0.932259672 0.681817662 0.861503347 0.52309684 0.606129914 0.559074491 0.692807331 0.58157989 1 19.32393137 3.249795355 24.99479759 0.639310235 0.793459631 0.157794507 0.143026042 317.637123 706667.7599 0.036221478 0.048608736 1777.44166 -3.249795355 0.154149395 GSLS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSLSPAR 7 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 GS(0.052)LS(0.948)PAR;GS(0.001)LS(0.999)PAR 93.467 0.015644 1339120000 722470 984220 704190 686640 960000 1096420 815370 755550 732220 1161940 TRUE FALSE 750993.6735 1153252.129 722541.7699 822455.3426 796819.5429 841793.0714 751459.1688 745423.0881 705867.5452 1389599.896 0.540438781 0.829916677 0.519963892 0.591864856 0.573416524 0.605780897 0.540773766 0.536430011 0.507964593 1 20.40623812 -1.068363165 5.973460131 1.000001133 0.583689681 0.670197691 0.087766329 1.30E-06 2.03E-07 0.083473943 0.019674943 0.085435199 1.068363165 -0.416311452 GSLS(ph)PVTKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSLSPVTKPR 10 1 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;F5H4Q7 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 GS(0.257)LS(0.741)PVT(0.002)KPR 68.893 0.035496 398630000 756740 648640 685660 578350 921900 841520 773650 742720 698790 633790 TRUE FALSE 786616.6795 760038.8743 703528.8629 692745.9038 765195.7673 646089.7334 713009.2914 732765.0532 673640.6844 757969.0159 1.037795296 1.002730796 0.928176282 0.913950161 1.009534363 0.852395968 0.940683955 0.96674803 0.888744355 1 19.53177935 4.37404762 3.637719536 0.936804714 1.031653396 0.35960579 0.045119072 0.222268049 5.458785289 0.010589746 0.035146842 23661.79133 -4.37404762 0.094848683 GSMNNELLS(ph)PEFGPVRDPLADGVEGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSMNNELLSPEFGPVRDPLADGVEGLGR 28 1 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 GS(0.003)MNNELLS(0.997)PEFGPVRDPLADGVEGLGR 88.59 0.0020022 29077000 24768 32738 28804 40360 29921 40684 37414 32683 29602 22975 TRUE FALSE 25745.85977 38360.49683 29554.6559 48343.08754 24835.03911 31235.75757 34481.39292 32244.93784 28536.6298 27476.51137 0.937013416 1.396119628 1.075633493 1.759433244 0.903864351 1.136816722 1.254940718 1.173545557 1.038582716 1 14.74591122 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKR 42 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 196.69 1.20E-35 105843000 49210 56570 57127 47156 66409 67975 55698 61572 64958 58404 FALSE TRUE 51152.8488 66285.45745 58615.77655 56483.31605 55120.8219 52188.83642 51332.24522 60746.72805 62620.17427 69847.14559 0.732354177 0.949007392 0.839200744 0.808670356 0.789163558 0.747186388 0.734922591 0.869709528 0.896531615 1 16.09191354 1.077999674 1.790554374 0.995673329 0.806522002 0.502063581 0.061622055 0.288286017 1.839061272 0.059678845 0.017179377 11.96739634 -1.077999674 -0.189151327 GSNEEQVNGS(ph)PLER ddPTM_MDA-MB-175_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 381.32 4.50E-98 1193420000 1226720 1478340 1344690 1432190 1468620 1569620 1404340 1394500 1314610 1547710 TRUE FALSE 1275151.853 1732233.395 1379733.726 1715472.907 1218984.497 1205099.543 1294264.161 1375809.008 1267297.443 1850954.142 0.688915962 0.935859704 0.745417563 0.926804651 0.658570879 0.651069368 0.699241614 0.743297188 0.684672523 1 20.81983772 5.053784632 15.68647799 0.768015261 0.137125761 0.039363183 0.120687459 11271991.56 82727608.56 0.027835933 219007056.6 113183.8943 -5.053784632 -0.6308895 GSNMDFREPTEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSNMDFREPTEEER 14 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;;;; 204.23 1.27E-08 7459270000 8004830 11459520 10466210 8849490 11534580 12116520 7992220 10124970 9975680 14604390 FALSE TRUE 8320866.869 13427603.42 10738968.03 10599892.71 9573936.212 9302641.858 7365768.913 9989261.338 9616657.225 17465840.6 0.476408039 0.76879228 0.614855493 0.606892789 0.548152043 0.532619189 0.421724272 0.571931324 0.550598018 1 24.05803274 -1.02658636 6.358427862 1.00000028 0.566934635 0.691383438 0.087030382 3.54E-07 5.39E-08 0.086120441 0.020298769 0.094061877 1.02658636 -0.433065645 GSNS(ph)LPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSNSLPLLR 9 0 H0Y8N0;D6RAA6;P57088 H0Y8N0 TMEM33 Transmembrane protein 33 1 GS(0.156)NS(0.844)LPLLR 89.266 0.012822 113140000 57357 76665 66376 58433 76705 87013 59501 69993 64368 77563 TRUE FALSE 59621.49865 89831.61738 68105.81309 69990.87299 63666.7115 66805.54944 54837.15614 69054.85832 62051.40825 92759.98482 0.642750198 0.968430704 0.73421544 0.754537349 0.686359658 0.720197934 0.591172543 0.744446632 0.668945865 1 16.50121496 4.029766324 24.99917498 0.719291548 0.817023639 0.029828759 0.124097586 443.290296 372290.5126 0.027879498 0.060225386 10709.4292 -4.029766324 0.09773209 GSNYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSNYWR 6 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 130.05 0.037058 7807100000 5660590 7793240 5932180 7264440 7244920 7447500 5862130 6047860 5625890 7521970 FALSE TRUE 5884074.464 9131668.347 6086777.484 8701324.55 6013431.086 5717930.993 5402640.933 5966798.329 5423415.318 8995756.005 0.654094493 1.015108496 0.676627677 0.96726996 0.668474232 0.635625398 0.600576642 0.66329037 0.602885996 1 23.1008131 3.194195902 23.96280421 0.668512136 0.830788392 0.14395794 0.150831833 122.4195323 66122.03362 0.039468414 0.04717412 1563.852909 -3.194195902 0.162276256 GSPAKGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPAKGSPK 9 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 1 GS(0.004)PAKGS(0.996)PK 77.124 0.020282 102480000 412350 154820 243930 122490 355850 347620 284830 211690 270570 153120 TRUE FALSE 428629.8964 181409.1307 250287.0162 146718.1564 295362.7441 266890.5232 262504.2803 208852.6418 260832.2386 183120.9323 2.340693065 0.99065207 1.366785397 0.801209095 1.612938184 1.457455026 1.433502314 1.140517576 1.424371508 1 17.48243719 4.747539715 24.91777831 1.262418488 2.340693647 0.642411373 0.244456276 697.6418091 1935973.292 0.055930893 0.682662348 55916.4659 -4.747539715 1.078275159 GSPAKGS(ph)PKGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPAKGSPKGSPSR 14 2 Q92817;K7EKI0 Q92817 EVPL Envoplakin 2 GS(0.062)PAKGS(0.938)PKGS(0.544)PS(0.456)R 89.353 0.030411 287300000 827730 352290 496150 243850 839280 710820 470810 470340 550980 364660 TRUE FALSE 860409.4195 412793.0671 509080.0766 292082.8022 696619.4854 545742.8276 433906.682 464035.8616 531150.3374 436108.1452 1.972926736 0.946538311 1.167325312 0.66974856 1.597354906 1.251393338 0.994952025 1.064038511 1.217932624 1 18.73432641 4.745031814 24.76270498 1.104888149 1.972927185 0.56819777 0.22800046 468.5013138 1792714.049 0.052854402 0.501391858 55594.49811 -4.745031814 0.868039036 GSPATS(ph)PHLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSPATSPHLGR 11 0 E9PNR2;Q13671-2;Q13671 E9PNR2 RIN1 Ras and Rab interactor 1 1 GSPAT(0.007)S(0.993)PHLGR;GSPAT(0.006)S(0.994)PHLGR 92.19 0.0065575 546480000 178358 217140 243050 207167 221530 232990 201012 186932 201490 242840 TRUE FALSE 185399.7116 254432.1059 249384.0827 248144.0143 183874.4097 178881.6035 185256.1542 184426.4823 194238.4143 290419.8485 0.638385126 0.876083736 0.858701924 0.854432008 0.633133068 0.615941384 0.637890816 0.635034014 0.66881935 1 18.14778053 3.238001068 24.99997096 0.669673563 0.815542442 0.129684217 0.124086183 20.42587166 912626.2953 0.032785988 0.041507933 1729.820615 -3.238001068 0.145868879 GSPDGS(ph)LQTGKPSAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 GS(0.313)PDGS(0.687)LQTGKPSAPK 188.44 3.10E-09 152120000 137290 88148 107920 85784 127730 137980 140670 113180 118280 66620 TRUE FALSE 142710.3152 103286.7333 110732.4839 102751.8192 106018.5002 105936.2361 129643.9178 111663.0072 114023.1259 79672.91348 1.791202417 1.29638454 1.389838516 1.289670663 1.330671813 1.32963929 1.62720192 1.40151781 1.431140408 1 16.28180171 -2.0766269 2.18558506 0.377283009 1.42340569 0.421136619 0.151619306 5558346.159 1538412.407 17249249.27 0.035013463 0.008382491 2.0766269 1.04612268 GSPHSEGGKRS(ph)PEPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSPHSEGGKRSPEPNK 16 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 GSPHSEGGKRS(1)PEPNK;GSPHSEGGKRS(1)PEPNK 149.53 4.32E-07 747540000 269834 209489 284315 193433 404152 346005 359637 282723 310119 159034 TRUE FALSE 280487.2547 245467.1062 291724.4825 231693.4701 335454.3874 265650.5825 331447.7122 278933.5606 298957.8778 190193.6674 1.474745498 1.290616609 1.533828578 1.218197605 1.763751612 1.396737263 1.74268532 1.466576487 1.571860314 1 17.53710969 3.25960082 24.99985955 1.522820127 1.384043699 0.046994571 0.216354063 583.6410786 693474.6455 0.054032284 0.073086551 1818.029056 -3.25960082 -0.138776427 GSPQQIDHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;; 164.65 6.09E-06 1794350000 2172120 1864570 2029900 1727260 2464430 2237890 2198420 2055230 2088900 1791270 FALSE TRUE 2257876.975 2184795.393 2082800.862 2068906.873 2045527.069 1718173.963 2026102.096 2027683.004 2013720.897 2142235.061 1.053981898 1.019867256 0.972255986 0.965770242 0.954856498 0.802047355 0.945788879 0.94652685 0.940009308 1 21.03068536 4.165628884 1.139777462 0.927412241 1.063032954 0.4206704 0.048113658 0.696696513 1.383717992 0.015298354 0.09023311 14642.96027 -4.165628884 0.135620713 GSPSSYNSSSS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSPSSYNSSSSSPR 14 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 GSPSSYNSSS(0.001)S(0.634)S(0.364)PR 114.56 0.00049327 493850000 445430 592390 574110 661610 609430 733960 567980 638200 615940 648950 TRUE FALSE 463015.9203 694128.3743 589071.7782 792474.4833 505839.3063 563508.9133 523460.2435 629645.9729 593772.4397 776099.3276 0.596593637 0.894380847 0.759015963 1.021099304 0.65177135 0.726078342 0.674475837 0.811295604 0.765072741 1 19.56588178 -1.948655311 4.575213511 1.132751818 0.771990262 0.26441134 0.116460034 0.080127592 0.000899221 0.057294712 0.025136356 0.011254979 1.948655311 -0.360761556 GSPSSYNSSSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSPSSYNSSSSSPR 14 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 GSPSSYNSSSSS(1)PR;GSPSSYNSSSS(0.001)S(0.998)PR;GSPSSYNSSS(0.008)S(0.205)S(0.787)PR;GSPSSYNSS(0.002)S(0.031)S(0.19)S(0.777)PR 248.36 6.48E-18 1022950000 957378 1209653 1056797 1162033 1127483 1262327 1150492 1162934 1037289 1262048 TRUE FALSE 995176.0227 1417401.493 1084337.998 1391879.659 935833.8424 969170.685 1060313.431 1147346.772 999957.1715 1509322.142 0.65935296 0.939098058 0.718427145 0.922188591 0.620035853 0.642123148 0.70250969 0.760173551 0.662520706 1 20.52546933 -1.47496272 3.189407057 1.005477383 0.740982231 0.35848371 0.105670949 39166546.04 41594579.67 1849735.923 0.024811719 0.033499419 1.47496272 -0.264495153 GSPTDAEGS(ph)PGLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSPTDAEGSPGLSR 14 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 GSPTDAEGS(1)PGLSR;GSPTDAEGS(1)PGLSR 267.13 6.23E-25 1017560000 652930 833100 711880 793520 790180 892940 635050 654280 605370 746450 TRUE FALSE 678708.1806 976178.4444 730432.1776 950475.8876 655865.4858 685568.2176 585273.1216 645510.4468 583582.852 892702.5859 0.76028477 1.093509148 0.818225677 1.064717301 0.734696523 0.767969342 0.655619386 0.723096871 0.653725957 1 19.76782008 3.212573768 24.7229159 0.734748299 0.937281796 0.301470996 0.130603591 193.49281 184081.2254 0.034334222 0.041050651 1631.449997 -3.212573768 0.202533497 GSQAQPDS(ph)PSAQLALIAASQSFLQPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSQAQPDSPSAQLALIAASQSFLQPGGK 28 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 GS(0.036)QAQPDS(0.482)PS(0.482)AQLALIAASQSFLQPGGK 112.8 0.00032913 117660000 65245 52601 63275 58735 63704 71985 61509 52707 63242 52160 TRUE FALSE 67820.92298 61634.81257 64923.99848 70352.60769 52875.61683 55267.57469 56687.76386 52000.54888 60965.93277 62379.75334 1.087226533 0.988057972 1.040786393 1.127811572 0.847640685 0.885985784 0.908752613 0.833612608 0.977335265 1 15.92879023 3.2328368 24.99996433 0.895142133 1.054320845 0.606805194 0.059262045 84.98698663 371198.1903 0.016420326 0.020141738 1709.372842 -3.2328368 0.159178713 GSQQYR ddPTM_MDA-MB-175_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 ;;;; 139.92 0.027558 1646569000 1670693 2035794 1702674 1736665 2126902 2041320 1792927 1917273 1685019 2435877 FALSE TRUE 1736653.25 2385425.783 1747047.083 2080172.154 1765371.958 1567254.367 1652392.697 1891575.091 1624375.495 2913140.46 0.596144701 0.818850246 0.599712615 0.714065175 0.606003034 0.537994782 0.5672204 0.649325056 0.557602875 1 21.47414383 -1.443628226 5.661988146 1.000261611 0.63032016 0.663185746 0.079628809 0.000261179 2.57E-05 0.076576794 0.018036771 0.036005743 1.443628226 -0.369941451 GSQS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GSQSPKR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 GS(0.004)QS(0.996)PKR;GS(0.007)QS(0.993)PKR;GS(0.049)QS(0.951)PKR;GS(0.007)QS(0.993)PKR;GS(0.006)QS(0.994)PKR 77.192 0.023713 837996000 1486010 1041198 1201184 928220 1609210 1424800 1437344 1142059 1344726 1059431 TRUE FALSE 1544678.822 1220015.657 1232487.842 1111819.146 1335677.059 1093911.793 1324681.221 1126751.567 1296329.574 1267006.22 1.219156463 0.962912129 0.972755952 0.877516722 1.054199291 0.863383127 1.045520693 0.889302317 1.023143812 1 20.27299218 4.738768791 6.944112637 0.959338469 1.223146357 0.571894473 0.065679409 0.068352748 24.56523881 0.013804083 0.084572507 54798.51514 -4.738768791 0.263807888 GSQSSDSSSSLSSHRYETPSDAIEVIS(ph)PAS(ph)SPAPPQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSQSSDSSSSLSSHRYETPSDAIEVISPASSPAPPQEK 38 1 O75376;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 2 GSQSSDSSSSLSSHRYETPSDAIEVIS(1)PAS(0.586)S(0.414)PAPPQEK 148.37 3.62E-13 41227000 16470 51383 53088 39058 70083 74374 38439 61997 60065 80584 TRUE FALSE 17120.24832 60207.63055 54471.51689 46783.55582 58170.31669 57101.76565 35426.05074 61166.03162 57903.27238 96372.89193 0.177645892 0.624736161 0.56521617 0.485443104 0.603596255 0.592508583 0.367593522 0.634680878 0.600825307 1 16.55633978 -5 0.191546315 3.078496421 0.438414667 0.590087359 0.127490619 95.5613869 0.936967192 75.64733003 0.324078054 1.00E-05 5 -2.640081754 GSRDWIGCVEASLCLAHFGGPQGRLCHVPRGVGLHGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSRDWIGCVEASLCLAHFGGPQGRLCHVPRGVGLHGELER 40 3 A0A5F9ZGY7;Q6NVU6 A0A5F9ZGY7 UFSP1 Inactive Ufm1-specific protease 1 0 38.871 0.055865 43756000 4170 17930 5466.4 13484 5087.4 10340 5094.8 6284.4 2810.7 13517 FALSE TRUE 4334.63482 21009.33802 5608.858875 16151.09495 4222.645565 7938.691704 4695.456263 6200.167897 2709.543456 16165.39735 0.268142794 1.299648723 0.346966966 0.999115246 0.26121508 0.491091653 0.290463399 0.383545654 0.167613786 1 13.98062135 3.22557575 24.99948143 0.393974518 0.74201696 0.142000678 0.348433699 349.5446977 672969.5728 0.090950002 0.109339853 1681.031107 -3.22557575 0.348042442 GSRPAS(ph)PAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSRPASPAAK 10 1 A0A590UJ53;Q9P2N6-8;Q9P2N6-6;Q9P2N6-2;Q9P2N6-5;Q9P2N6-4;Q9P2N6-3;Q9P2N6 A0A590UJ53 KANSL3 KAT8 regulatory NSL complex subunit 3 1 GS(0.01)RPAS(0.99)PAAK;GS(0.045)RPAS(0.955)PAAK 83.087 0.0097304 515780000 573170 468320 611270 484080 675760 757180 700640 594180 630180 442690 TRUE FALSE 595799.1942 548750.317 627200.1984 579829.5792 560894.5566 581336.4202 645722.006 586215.989 607499.9449 529426.6297 1.12536688 1.036499273 1.184678222 1.095202898 1.059437749 1.098049073 1.219662876 1.107265778 1.147467677 1 19.01407124 GSRPIDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 98.048 0.0057254 2207800000 891724 1159543 1032428 1043232 1121772 1263410 995708 1035166 954483 1249299 FALSE TRUE 926929.9521 1358685.49 1059333.922 1249580.176 931093.5961 970002.1747 917661.8052 1021291.293 920131.3433 1494075.22 0.620403806 0.909382253 0.709023152 0.836356938 0.623190576 0.64923249 0.614200539 0.683560827 0.615853426 1 20.51082135 -1.250785331 3.626109262 1.000576328 0.69836112 0.475295452 0.095884092 2046761678 2959547542 12852921.91 0.023212249 0.056132537 1.250785331 -0.302215209 GSRPPLILQSQSLPCS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.593)S(0.407)PR 130.6 2.71E-06 0 48545 56638 51282 53504 48679 64512 52332 50358 52513 53770 TRUE FALSE 50461.59408 66365.13592 52618.45105 64086.93151 40404.56097 49530.06569 48230.0811 49683.03338 50623.06739 64305.20201 0.784720248 1.032033706 0.818261189 0.99660571 0.628324921 0.770234198 0.750018344 0.772612974 0.787231294 1 15.97264783 3.253296388 24.99994781 0.770548125 0.910368368 0.226556211 0.109585747 293.597141 498098.7541 0.027648465 0.037278361 1791.828287 -3.253296388 0.139820243 GSRPPLILQSQSLPCSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSRPPLILQSQSLPCSSPR 19 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 GSRPPLILQSQSLPCS(0.355)S(0.645)PR;GSRPPLILQSQSLPCS(0.153)S(0.847)PR 245.38 8.55E-25 1514110000 399130 487940 479870 473520 565790 559490 459400 478020 467410 484970 TRUE FALSE 414887.9606 571739.8994 492375.8064 567180.8427 469617.2179 429556.9267 423391.0276 471612.9238 450588.0054 579990.5862 0.71533568 0.985774447 0.848937583 0.977913877 0.809698 0.740627412 0.729996379 0.813138928 0.776888481 1 19.14566996 3.027219482 24.63605787 0.793006026 0.887888103 0.090627312 0.099600807 306.8523695 277726.2614 0.026616513 0.031812109 1064.680948 -3.027219482 0.094882078 GSS(ph)FQSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSSFQSGR 8 0 Q96KP1 Q96KP1 EXOC2 Exocyst complex component 2 1 GS(0.006)S(0.994)FQSGR;GS(0.001)S(0.999)FQSGR;GS(0.001)S(0.999)FQSGR 171.33 0.00030421 1112930000 1410890 1683610 1713500 1792240 1724600 1949710 1686470 1690080 1667750 1680010 TRUE FALSE 1466593.027 1972756.921 1758155.218 2146739.723 1431453.108 1496919.401 1554280.075 1667427.242 1607728.003 2009175.794 0.729947589 0.981873725 0.87506291 1.068467841 0.712457871 0.745041527 0.773590882 0.829906097 0.8001928 1 20.93817237 3.216227759 24.99992077 0.798352783 0.915928203 0.176371966 0.107874825 342.9329151 383886.1852 0.029455569 0.035231613 1645.234315 -3.216227759 0.11757542 GSS(ph)PGPRPVEGTPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 GS(0.124)S(0.876)PGPRPVEGTPASR;GS(0.045)S(0.955)PGPRPVEGTPASR;GS(0.028)S(0.972)PGPRPVEGTPASR;GS(0.026)S(0.974)PGPRPVEGTPASR;GS(0.047)S(0.953)PGPRPVEGTPASR;GS(0.122)S(0.878)PGPRPVEGTPASR 125.23 4.73E-05 6101530000 4374690 5241320 4795600 5062830 5189760 5824190 5080210 4992550 4882070 5948530 TRUE FALSE 4547406.139 6141475.938 4920577.276 6064242.663 4307606.449 4471610.139 4682009.866 4925633.033 4706365.254 7114030.562 0.639216559 0.863290632 0.691672215 0.85243416 0.605508567 0.628562121 0.65813744 0.692382889 0.661561011 1 22.76223574 -1.038515848 4.328344136 1.00001995 0.701053552 0.534099254 0.084266997 15861738.87 48184675.72 5026.299427 0.020116522 0.091513286 1.038515848 -0.298966399 GSS(ph)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSSPQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 38 1 Q27J81-2;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 GS(0.105)S(0.895)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK;GS(0.137)S(0.863)PQNTTTPKPSVEGQQPAAAAACEPVDHAQSESILK 446.44 4.05E-244 3543100000 397500 305390 418730 313450 502980 542670 479870 411830 497630 328600 TRUE FALSE 413193.6069 357838.3569 429642.4478 375449.4744 417483.6393 416643.1167 442256.5355 406310.0925 479720.3935 392982.8786 1.05142903 0.91056984 1.093285411 0.955383796 1.062345619 1.060206791 1.125383724 1.033912963 1.220715761 1 18.58410693 2.956600713 2.580103517 1.08927802 1.002565054 0.231099871 0.072358003 0.401666214 5.324212953 0.021795609 0.024694875 904.9002593 -2.956600713 -0.086712966 GSS(ph)PSHSATSVHTSV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GS(0.003)S(0.757)PS(0.201)HS(0.037)AT(0.001)SVHTSV 235.31 1.18E-17 453350000 31002 519850 335620 439300 287580 596640 239040 431500 262170 597540 TRUE FALSE 32225.9829 609130.1936 344366.5329 526192.2288 238697.2543 458079.4022 220303.4202 425716.4483 252734.5529 714616.5224 0.045095491 0.852387504 0.481889968 0.736328104 0.33402146 0.641014289 0.308282013 0.595727128 0.353664581 1 19.44680974 -1.56363966 3.124011425 1.021607856 0.501183716 0.32096542 0.224150157 126897193.1 150734633.5 23000765.86 0.049410692 0.02731243 1.56363966 -0.52042414 GSS(ph)PTPPCS(ph)PVQPSK ddPTM_MDA-MB-175_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 GS(0.052)S(0.872)PT(0.076)PPCS(1)PVQPSK;GS(0.086)S(0.724)PT(0.212)PPCS(0.977)PVQPSK 211.9 1.68E-09 633830000 607570 495640 505690 527790 667250 689060 612370 615640 638170 558510 TRUE FALSE 631557.3327 580762.3145 518868.6968 632185.2867 553831.0833 529036.2578 564370.8393 607388.3528 615202.3864 667939.3412 0.945530969 0.869483617 0.776820087 0.946471106 0.829163742 0.792042369 0.844943252 0.909346576 0.921045293 1 19.34935756 1.109123329 1.421165868 0.99602162 0.856210278 0.398885596 0.053627951 0.387706896 1.563912229 0.049934241 0.01510527 12.85651702 -1.109123329 -0.139811341 GSS(ph)PTPPCSPVQPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.004)S(0.99)PT(0.006)PPCSPVQPSK;GS(0.003)S(0.987)PT(0.01)PPCSPVQPSK;GS(0.043)S(0.921)PT(0.035)PPCSPVQPSK 236.4 1.10E-17 1246560000 1515550 1377010 1404980 1228370 1665070 1714310 1529570 1464300 1434130 1211620 TRUE FALSE 1575385.084 1613500.756 1441594.933 1471337.92 1382041.996 1316187.483 1409678.307 1444673.454 1382515.941 1449013.741 1.08721197 1.113516532 0.994880098 1.015406464 0.953781153 0.908333334 0.97285365 0.997004661 0.954108234 1 20.46663985 4.091953888 1.759897274 0.96791802 1.107785242 0.72568898 0.030604748 0.199527511 1.167434756 0.008769733 0.030695627 12358.16211 -4.091953888 0.139867223 GSSAGFDR ddPTM_MDA-MB-175_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 ;;; 130.28 0.0024537 1850630000 1250940 1497050 1278400 1341990 1435410 1605270 1357340 1406620 1261390 1560570 FALSE TRUE 1300328.077 1754156.692 1311716.154 1607431.617 1191419.521 1232470.371 1250948.144 1387766.56 1215992.82 1866333.813 0.696728564 0.939894396 0.702830408 0.861277659 0.638374289 0.660369738 0.67027031 0.743578962 0.651540904 1 20.83177562 5.062558149 15.97980283 0.749117629 0.173434196 0.014468004 0.122461907 17004748.39 92591614.17 0.027616521 320449710.7 115493.6613 -5.062558149 -0.575683433 GSSANASKWS(ph)PPQNYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSSANASKWSPPQNYK 16 1 H3BRF9;Q96K21-2;Q96K21;H3BRM1;Q96K21-3 H3BRF9;Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 GS(0.002)S(0.001)ANAS(0.014)KWS(0.983)PPQNYK;GS(0.003)S(0.003)ANAS(0.02)KWS(0.974)PPQNYK;GS(0.019)S(0.017)ANAS(0.021)KWS(0.943)PPQNYK 84.975 0.0044246 1949210000 1557620 1105250 1375290 677412 1986420 1517910 1030090 1188210 1521340 1404060 TRUE FALSE 1619116.04 1295068.09 1411131.187 811402.0717 1648769.038 1165398.407 949348.8542 1172283.988 1466587.271 1679158.675 0.96424243 0.771260102 0.840379893 0.483219415 0.981901867 0.694037094 0.565371736 0.698137708 0.873406005 1 20.67930714 4.996305468 1.533241299 0.73810613 1.185671911 0.102044053 0.159488975 4.147784743 5.526896097 0.04019623 3.371551724 99152.91072 -4.996305468 0.44756578 GSSCFECTHYQSFLEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 GSSCFECTHYQSFLEYR 17 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ;;;;;;;;;;;;; 237.52 3.21E-20 16928085300 2418341.4 3809281.5 3488701.8 3604989.1 3798688.8 4473318.7 3383612.3 3931406.9 3401396.8 4509497.7 FALSE TRUE 2513819.386 4463495.966 3579620.235 4318045.184 3152989.035 3434458.226 3118395.927 3878712.821 3278981.194 5393047.435 0.466122247 0.827638922 0.663747219 0.800668868 0.584639589 0.63683071 0.578225199 0.719206139 0.608001549 1 22.36266929 -1.759866089 2.711653777 1.075409881 0.662058882 0.505514046 0.102405954 28167243.65 21508538.11 14164989.45 0.022593924 0.017383367 1.759866089 -0.413350999 GSSDGRGS(ph)DS(ph)ESDLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.993)DS(0.75)ES(0.256)DLPHR;GSSDGRGS(1)DS(0.994)ES(0.006)DLPHR;GSSDGRGS(1)DS(0.965)ES(0.035)DLPHR 152.07 1.29E-07 1116530000 508110 752030 652800 689930 733340 822250 645950 699840 685030 744410 TRUE FALSE 528170.5751 881185.3025 669812.5043 826396.0948 608687.1287 631294.8988 595318.7511 690459.7895 660375.9041 890262.8869 0.593274844 0.989803479 0.752376084 0.92826075 0.683716167 0.709110655 0.668699954 0.77556843 0.741776293 1 19.76387189 -1.455594628 2.722700161 1.007714305 0.7648055 0.289488782 0.112462805 18759583.44 19941230.05 1104690.744 0.026631354 0.035027196 1.455594628 -0.242908805 GSSDGRGS(ph)DSES(ph)DLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3;D6RJ93;D6R8Y0;Q9UPQ0-7;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 GSSDGRGS(0.989)DS(0.386)ES(0.625)DLPHR 119.16 7.61E-05 408180000 179350 293080 254780 286960 321670 351270 272800 275630 248220 338320 TRUE FALSE 186430.8765 343414.2102 261419.7761 343719.8315 266992.6483 269692.866 251417.2232 271935.6307 239286.6107 404607.3265 0.460769898 0.848759248 0.646107371 0.849514601 0.659880904 0.666554579 0.62138574 0.672097644 0.591404542 1 18.62616292 -1.920241918 2.787709162 1.194227945 0.675904528 0.455453954 0.108471751 31272729.06 21122535.61 39730340.24 0.023941965 0.012015949 1.920241918 -0.518323417 GSSDGRGS(ph)DSESDLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.003)S(0.003)DGRGS(0.977)DS(0.016)ESDLPHR;GSSDGRGS(0.999)DS(0.001)ESDLPHR;GSSDGRGS(0.974)DS(0.025)ESDLPHR;GSSDGRGS(0.999)DS(0.001)ESDLPHR;GS(0.002)S(0.002)DGRGS(0.984)DS(0.012)ESDLPHR;GS(0.011)S(0.011)DGRGS(0.977)DS(0.002)ESDLPHR 156.92 2.73E-08 3984160000 916997 1288710 1140463 1161962 1234120 1341820 1137308 1178760 1106669 1320450 TRUE FALSE 953200.7496 1510035.918 1170184.403 1391794.615 1024344.723 1030202.64 1048162.827 1162960.65 1066840.199 1579166.896 0.603609886 0.956223134 0.741013762 0.881347386 0.648661472 0.65237097 0.663744174 0.736439355 0.675571532 1 20.59073222 -1.384609383 2.974213622 1.003936307 0.733146565 0.374328685 0.105058618 18104305.92 22159647.87 612795.8477 0.024485214 0.041246834 1.384609383 -0.270789742 GSSERGS(ph)PIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GSSERGSPIEK 11 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 GS(0.001)S(0.001)ERGS(0.999)PIEK;GS(0.104)S(0.104)ERGS(0.792)PIEK;GSSERGS(1)PIEK;GS(0.085)S(0.085)ERGS(0.831)PIEK;GS(0.003)S(0.003)ERGS(0.994)PIEK 89.358 0.0074444 12863190000 11433640 8074770 9998090 7917400 11847750 11925590 11000680 9808490 10208530 7942350 TRUE FALSE 11885048.94 9461548.935 10258648.44 9483438.089 9833873.687 9156052.457 10138417.96 9677023.235 9841126.999 9498501.417 1.251255163 0.996109651 1.0800281 0.998414136 1.035307914 0.963947054 1.067370263 1.018794735 1.036071541 1 23.17926849 4.742838338 24.98218102 1.02393734 1.251255254 0.812412614 0.033065413 160.7907294 938994.1151 0.007217994 0.05635583 55314.41687 -4.742838338 0.227317914 GSSGCSEAGGAGHEEGRAS(ph)PLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSSGCSEAGGAGHEEGRASPLRR 23 2 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 GSSGCSEAGGAGHEEGRAS(1)PLRR;GSSGCSEAGGAGHEEGRAS(1)PLRR 198.93 1.41E-24 82274000 26462.4 40965 38411 43929 36418 45152 40456 40569 37870 39041 TRUE FALSE 27507.15599 48000.42009 39412.02221 52618.02509 30227.68137 34666.13229 37284.95301 40025.23891 36507.0661 46690.33646 0.589140239 1.028058989 0.84411519 1.126957505 0.647407658 0.742469104 0.798558242 0.857248886 0.781897687 1 15.51083636 4.765806876 23.67419711 0.858295546 0.589139466 0.269731502 0.137322927 6460.027591 5612909.159 0.032191709 2.600259582 58318.57132 -4.765806876 -0.26915608 GSSGENNNPGS(ph)PTVSNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSSGENNNPGSPTVSNFR 18 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(0.997)PT(0.003)VSNFR;GSSGENNNPGS(1)PTVSNFR;GSSGENNNPGS(1)PTVSNFR 493.76 1.05E-240 2520560000 1994850 2396940 2110550 2261110 2230440 2631720 2118780 2289810 2063900 2528560 TRUE FALSE 2073608.218 2808595.799 2165552.667 2708350.809 1851310.605 2020542.914 1952704.487 2259118.842 1989620.642 3023982.92 0.685720877 0.928773698 0.716125958 0.895623713 0.612209346 0.668172727 0.645739258 0.747067329 0.65794705 1 21.52801856 5.061389491 15.37929485 0.748830018 0.130952939 0.021162342 0.127336313 6665471.445 39144116.89 0.028876916 127880103.7 115183.2932 -5.061389491 -0.617877079 GSSGGSGAKPSDAASEAARPATSTLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSSGGSGAKPSDAASEAARPATSTLNR 27 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 254.96 4.27E-53 1509650000 583450 503214 568950 494629 702460 690860 578730 570959 634330 522863 FALSE TRUE 606485.0565 589637.09 583777.3044 592465.1399 583056.1001 530418.2351 533367.6304 563306.2285 611500.5872 625307.994 0.969898134 0.942954665 0.933583626 0.947477316 0.932430267 0.848251166 0.852967874 0.900846037 0.97791903 1 19.25420744 2.985862219 23.87664466 0.902610032 0.946136707 0.06288521 0.046165681 669.6252815 1130902.668 0.013820781 0.015214215 967.9707159 -2.985862219 0.043526674 GSSGPTQINQVVSHPNQPLTITAHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSSGPTQINQVVSHPNQPLTITAHDDR 27 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317 F5GYK2 STRN4 Striatin-4 0 ;; 317.84 1.68E-82 1277820000 131484 187276 142238 155314 170197 198609 155950 159164 153173 200222 FALSE TRUE 136675.0898 219439.1962 145944.8391 186034.6456 141266.9747 152485.0697 143726.2315 157030.6669 147660.3337 239451.6674 0.570783621 0.916423755 0.609496024 0.776919399 0.589960288 0.636809388 0.600230656 0.655792748 0.616660286 1 17.86937496 -1.340863279 9.001041773 1.000000389 0.666351811 0.502346107 0.100393325 7.37E-07 5.40E-08 0.091349644 0.021531292 0.04561805 1.340863279 -0.333648578 GSSPS(ph)HSATSVHTSV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSSPSHSATSVHTSV 15 0 F8WA39;Q13613 F8WA39 MTMR1 Myotubularin-related protein 1 1 GSS(0.039)PS(0.96)HS(0.001)ATSVHTSV;GSS(0.007)PS(0.992)HS(0.001)ATSVHTSV 225.26 1.07E-12 561550000 36313 579860 366950 517030 341148 687410 311869 532910 308881 683190 TRUE FALSE 37746.66528 679446.4443 376513.0185 619296.9908 283159.7848 527769.4453 287423.8929 525767.2131 297764.4331 817048 0.046198834 0.831586938 0.460821174 0.757968921 0.346564443 0.645946683 0.351783363 0.643496114 0.364439339 1 19.64006131 -1.381927885 3.010819898 1.006625285 0.514603358 0.314676687 0.222072464 39352176.63 49628640.85 2296045.076 0.047553559 0.041502295 1.381927885 -0.492021927 GSSPSIRPIQGS(ph)QGSSSPVEKEVVEATDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEKEVVEATDSR 30 2 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GS(0.009)S(0.009)PS(0.009)IRPIQGS(0.255)QGS(0.231)S(0.231)S(0.255)PVEKEVVEATDSR 44.107 0.06586 172640000 50223 49279 53703 35761 74536 64717 47951 46628 50861 62097 TRUE FALSE 52205.84282 57742.28491 55102.5443 42834.41906 61866.39734 49687.45755 44192.47532 46003.02793 49030.52255 74263.71823 0.702979114 0.777530216 0.741984722 0.576787967 0.833063558 0.669067732 0.595074908 0.619454951 0.660221757 1 16.18036993 -1.19511669 5.286768152 1.000017643 0.682449409 0.599389329 0.076896676 1.65E-05 2.52E-06 0.077021142 0.018153049 0.063809202 1.19511669 -0.317568235 GSSPSIRPIQGSQGSS(ph)SPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 GSSPSIRPIQGSQGS(0.086)S(0.493)S(0.421)PVEK 163.16 1.07E-11 229780000 188690 138360 159950 155380 188440 188330 190500 160600 171040 109120 TRUE FALSE 196139.6269 162122.2537 164118.4284 186113.7002 156409.0361 144593.2117 175568.1122 158447.4197 164884.3038 130499.9748 1.502985937 1.242316361 1.257612721 1.426158898 1.198536907 1.107994173 1.345349779 1.214156707 1.2634815 1 16.99369 -5 0.071472319 0.11057875 1.595250267 0.486313522 0.098969481 274.7491928 1.411215433 40.66077124 4.865440329 1.00E-05 5 1.484671517 GSSPT(ph)PPCS(ph)PVQPSK ddPTM_MDA-MB-175_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 GS(0.018)S(0.185)PT(0.798)PPCS(1)PVQPSK;GS(0.003)S(0.026)PT(0.971)PPCS(1)PVQPSK 192.78 6.37E-07 546710000 522180 418640 420030 413420 545010 596600 514210 485150 510540 449640 TRUE FALSE 542796.0696 490538.1634 430976.3269 495193.2421 452369.3949 458048.6916 473904.8766 478647.3578 492165.7651 537738.3491 1.009405542 0.912224624 0.801461022 0.920881397 0.841244437 0.851805887 0.881292691 0.890112001 0.915251378 1 19.03654484 0.785187994 1.858239789 0.999914597 0.884082637 0.286766456 0.052513388 0.955111 5.623549519 0.049318823 0.013820207 6.098008058 -0.785187994 -0.11583196 GSST(ph)PTKGIENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.013)T(0.981)PT(0.006)KGIENK 177.88 3.67E-05 250660000 710440 439680 571280 302490 935080 691590 487390 476590 662040 486030 TRUE FALSE 738488.7198 515191.6198 586168.0261 362321.6192 776135.4356 530978.7036 449187.0982 470202.0906 638213.3097 581258.2729 1.270500145 0.886338559 1.008446767 0.62334015 1.335267766 0.913498746 0.772784009 0.80893832 1.097985766 1 19.14881982 2.496800672 24.98533629 0.883384014 1.006928594 0.048580358 0.204056035 2109.400888 2678132.768 0.064928438 0.060415199 313.9067625 -2.496800672 0.12354458 GSTAPVGGGAFPTIVEREPWDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSTAPVGGGAFPTIVEREPWDGR 23 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 233.89 4.29E-37 1287220000 1070590 1545520 1059700 1186040 1299610 1433960 904720 1089520 977010 1592210 FALSE TRUE 1112857.72 1810951.038 1087316.653 1420635.172 1078702.756 1100944.522 833805.6824 1074916.766 941847.6009 1904173.065 0.584430974 0.951043301 0.571017768 0.746064104 0.566494074 0.578174611 0.437883351 0.564505814 0.494622899 1 20.86073318 3.233558335 24.89508752 0.571422999 0.719980688 0.060054237 0.173827796 216.1438343 1075693.222 0.045850699 0.056439541 1712.215149 -3.233558335 0.148557689 GSTDNLMDDIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSTDNLMDDIER 12 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 255.3 9.08E-21 1514380000 990780 1123100 1053330 1052150 1111160 1256070 1056400 1019800 1043870 1152580 FALSE TRUE 1029896.759 1315983.688 1080780.645 1260262.13 922285.4201 964366.7784 973596.6076 1006131.249 1006301.323 1378405.984 0.747165038 0.954714144 0.784080059 0.914289509 0.66909563 0.699624632 0.706320648 0.729923739 0.730047123 1 20.39456944 3.240136249 24.99931308 0.735861377 0.852824316 0.150576315 0.103213802 58.13959571 922441.6642 0.026485838 0.034047217 1738.346104 -3.240136249 0.116962939 GSTDS(ph)LDSLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSTDSLDSLSSR 12 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 GST(0.001)DS(0.991)LDS(0.008)LSSR 141.37 0.00027659 0 163200 177210 157060 152100 170170 202890 172320 162300 157980 170220 TRUE FALSE 169643.262 207644.439 161153.1126 182184.926 141244.5642 155771.8723 158813.1081 160124.634 152294.3307 203571.3499 0.833335644 1.020008164 0.791629631 0.894943842 0.693833215 0.765195458 0.780134868 0.786577453 0.74811279 1 17.63517501 3.865207525 1.828724461 0.787660714 0.918878993 0.141359437 0.094726572 0.498414527 3.212531351 0.024671853 0.061671269 7331.747921 -3.865207525 0.131218279 GSTFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSTFEER 7 0 P05019-4 P05019-4 0 77.496 0.08815 246030000 218020 250680 206430 237390 193540 293880 182630 213220 219300 186290 FALSE TRUE 226627.5979 293732.34 211809.7354 284345.0335 160642.1399 225630.8238 168314.9834 210362.1347 211407.4358 222789.9588 1.017225369 1.318427193 0.950714909 1.276291961 0.721047487 1.012751315 0.755487295 0.944217306 0.948909174 1 17.76532469 3.243644788 24.99980707 0.893352875 1.139794302 0.439767976 0.134653259 108.4967602 533494.5658 0.034202056 0.044927972 1752.446581 -3.243644788 0.246441427 GSTIETEQKEDKGEDSEPVTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSTIETEQKEDKGEDSEPVTSK 22 2 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 163.4 8.52E-12 484550000 613680 154170 276638 126521 454220 407660 402000 281340 359670 129887 FALSE TRUE 637908.5603 180647.4982 283847.4135 151546.4762 377011.8466 312987.1431 370490.1896 277569.0975 346725.547 155335.8708 4.106640385 1.162947729 1.827314014 0.975605154 2.427075245 2.014905775 2.385091014 1.78689633 2.232102251 1 17.2450315 -0.751335605 6.187295237 0.999999981 2.033568304 0.137416077 0.812186057 2.05E-07 4.00E-08 0.72265128 0.170330538 0.177281899 0.751335605 1.033568323 GSTIYTGYPLS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSTIYTGYPLSPTK 14 0 Q5SQL3;J3KP92;Q86Z02;H3BLW0;Q86Z02-4;Q86Z02-3 Q5SQL3 HIPK1 Homeodomain-interacting protein kinase 1 1 GSTIYT(0.001)GYPLS(0.986)PT(0.013)K 83.729 0.0090437 0 74057 61819 64974 56298 83159 84388 69904 66748 67384 60817 TRUE FALSE 76980.82754 72435.93236 66667.27582 67433.57637 69023.66288 64790.16591 64424.74182 65853.35224 64958.863 72732.92674 1.058404096 0.995916645 0.916603783 0.927139597 0.949001587 0.890795528 0.885771338 0.905413204 0.893114933 1 16.15032101 4.492471377 1.870926037 0.913998308 1.072706134 0.642563967 0.03288074 0.281475093 1.47135067 0.008235603 0.06586041 31079.31064 -4.492471377 0.158707826 GSTSSSPYVAASHT(ph)PPINGSDSILGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSTSSSPYVAASHTPPINGSDSILGTR 27 0 Q99081;Q99081-3;F5GY10;B4DGI9;Q99081-4;Q99081-2 Q99081 TCF12 Transcription factor 12 1 GSTSSSPYVAASHT(1)PPINGSDSILGTR 169.36 1.73E-22 0 45208 46463 33349 36463 37655 39335 35269 32938 30968 41129 TRUE FALSE 46992.84675 54442.65882 34218.10234 43675.27257 31254.41655 30200.04238 32504.52362 32496.51999 29853.46773 49187.44009 0.955383054 1.106840663 0.695667477 0.887935467 0.635414579 0.613978738 0.660829748 0.660667031 0.606932739 1 15.58600235 4.053638781 1.313788227 0.681233681 1.050094123 0.396402955 0.137132077 0.447128245 1.341736134 0.037946586 0.159744577 11314.58895 -4.053638781 0.368860441 GSTTATFAAVVLYVENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSTTATFAAVVLYVENER 18 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 179.41 3.38E-14 0 134269 69977 85930 72241 90135 128525 103690 98857 90822 69570 FALSE TRUE 139570.0438 81995.0054 88169.40639 86530.05418 74813.8849 98677.01657 95562.50686 97531.98361 87553.33396 83200.9095 1.677506227 0.985506119 1.059716858 1.040013321 0.899195518 1.186008869 1.148575267 1.172246604 1.052312222 1 16.34431168 4.743599957 24.99750993 1.072621711 1.677506478 0.823576298 0.085517679 228.4469379 1133168.638 0.021860212 0.182763271 55411.50639 -4.743599957 0.604884767 GSVFLESDS(ph)SPPSSSDAGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSVFLESDSSPPSSSDAGLR 20 0 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 GSVFLES(0.006)DS(0.639)S(0.355)PPSSSDAGLR;GSVFLESDS(0.672)S(0.328)PPSSSDAGLR 188.96 2.48E-17 164558000 224143 239110 236374 289120 232199 293480 291820 252810 237358 232788 TRUE FALSE 232992.3387 280175.2825 242534.1006 346307.0731 192729.8969 225323.7177 268946.3859 249421.4955 228815.5319 278398.3516 0.836902724 1.006382692 0.871176497 1.24392645 0.692281028 0.809357227 0.966048773 0.895915849 0.821899737 1 18.08679114 3.204371314 24.9999083 0.866124174 0.982338783 0.183539023 0.129116294 332.076622 242820.2307 0.036350272 0.043448888 1600.926205 -3.204371314 0.116214609 GSVFLESDS(ph)SPPSSSDAGLRFPDSNGLLQTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSVFLESDSSPPSSSDAGLRFPDSNGLLQTPR 32 1 Q8TBP0 Q8TBP0 TBC1D16 TBC1 domain family member 16 1 GSVFLES(0.015)DS(0.654)S(0.179)PPS(0.051)S(0.051)S(0.051)DAGLRFPDSNGLLQTPR 74.874 0.0013995 84478000 33070 46399 38052 35336 47444 48069 34709 38647 33930 55004 TRUE FALSE 34375.62914 54367.66732 39043.66638 42325.35533 39379.48583 36905.70324 31988.41788 38129.00018 32708.86593 65780.98068 0.522577024 0.826495238 0.593540351 0.643428464 0.598645466 0.561039116 0.486286728 0.57963563 0.497238952 1 16.0053829 -1.262107723 7.296185282 1.000001684 0.592453575 0.643630731 0.091533919 2.51E-06 2.54E-07 0.088879907 0.020949108 0.05468803 1.262107723 -0.407548109 GSVILDSGHLSTAS(ph)SSDDLKGEEGSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLST(0.001)AS(0.333)S(0.333)S(0.333)DDLKGEEGSFR 124.03 4.93E-05 385300000 22112 65141 65010 64894 81944 91532 68692 77978 77603 61560 TRUE FALSE 22984.99883 76328.46002 66704.21401 77729.83951 68015.18815 70275.08018 63307.74155 76932.83246 74810.08319 73621.50336 0.312204964 1.03676856 0.906042541 1.055803481 0.923849487 0.954545574 0.859908297 1.044977743 1.016144466 1 16.16783959 4.741830996 24.99730119 0.974607899 0.312204719 0.911629385 0.062140784 79.74150884 609479.9917 0.014273164 0.102844095 55186.26421 -4.741830996 -0.66240318 GSVILDSGHLSTASS(ph)SDDLKGEEGSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSVILDSGHLSTASSSDDLKGEEGSFR 27 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 GSVILDSGHLS(0.001)T(0.002)AS(0.288)S(0.698)S(0.011)DDLKGEEGSFR 278.6 3.31E-61 199960000 42993 127360 123250 117430 146410 151350 127300 130920 136610 112140 TRUE FALSE 44690.39684 149233.0893 126461.9963 140657.3035 121523.2805 116201.2562 117321.8934 129165.2315 131693.4328 134111.686 0.333232682 1.112752317 0.942960305 1.048807213 0.90613491 0.866451386 0.874807386 0.963116902 0.981968364 1 17.03307543 4.747364139 24.93704806 0.958098633 0.333232352 0.872210614 0.072637843 372.19405 1054261.434 0.017591417 0.210770924 55893.86471 -4.747364139 -0.624866281 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.052)S(0.601)S(0.347)PPATHFPDETEITNPVPK;GS(0.004)VPLS(0.075)S(0.506)S(0.416)PPATHFPDETEITNPVPK 286.37 1.63E-61 1199510000 442780 356170 421290 415820 471960 520940 580870 453930 428160 316460 TRUE FALSE 460261.2963 417339.4269 432269.1635 498067.9549 391736.4078 399959.5799 535339.8916 447845.8108 412750.6052 378464.278 1.216128768 1.102718146 1.142166351 1.316023688 1.035068382 1.056796118 1.414505735 1.183323861 1.090593298 1 18.52979761 GSVPLSSS(ph)PPATHFPDETEITNPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 GSVPLS(0.003)S(0.158)S(0.839)PPATHFPDETEITNPVPK;GSVPLS(0.013)S(0.105)S(0.882)PPATHFPDETEITNPVPK;GS(0.001)VPLS(0.007)S(0.035)S(0.955)PPAT(0.002)HFPDETEITNPVPK 281.19 4.80E-61 7112880000 1941110 1629770 2092550 1826680 2258400 2280360 2521910 2083350 2024750 1392440 TRUE FALSE 2017746.522 1909670.32 2147083.572 2187991.852 1874517.975 1750780.949 2324236.104 2055426.101 1951879.643 1665261.958 1.211669138 1.146768717 1.289336829 1.313902501 1.125659519 1.051354678 1.395718009 1.234295956 1.172115674 1 20.66731771 0.86902243 3.872789853 1.000066432 1.223709743 0.33397552 0.093569571 0.821905072 22.07266658 0.091310769 0.023390219 7.396434741 -0.86902243 0.223643311 GSVPS(ph)PSPRPQALDATQVPS(ph)PLPLAQPS(ph)TPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSVPSPSPRPQALDATQVPSPLPLAQPSTPPVR 33 1 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 3 GS(0.034)VPS(0.753)PS(0.213)PRPQALDAT(0.002)QVPS(0.998)PLPLAQPS(0.527)T(0.473)PPVR 99.929 0.00010308 68460000 22375 24939 22953 20066 23133 26987 21766 31970 27281 31124 TRUE FALSE 23258.38228 29222.07925 23551.17404 24034.99491 19200.86092 20719.67824 20059.92405 31541.49444 26299.16214 37222.1519 0.624853242 0.785072269 0.632719304 0.645717501 0.515844999 0.556649124 0.538924351 0.847385034 0.706545989 1 15.18387384 1.019889421 1.052921272 0.986263248 0.623327145 0.587577666 0.093150318 0.390179344 0.915049814 0.09219538 0.030150326 10.46861965 -1.019889421 -0.362936103 GSWS(ph)SAPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSWSSAPTSR 10 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 GSWS(0.5)S(0.5)APT(0.001)SR 93.477 0.0091879 189880000 397520 504850 410910 402010 444410 493730 375360 408520 393460 560820 TRUE FALSE 413214.3966 591554.0603 421618.6522 481526.3781 368869.3469 379068.6901 345938.3024 403044.4576 379299.4515 670701.9415 0.616092441 0.881992468 0.628622979 0.717943916 0.54997507 0.565182038 0.51578545 0.600929314 0.565526097 1 19.35531225 -1.185385573 3.941571212 1.000218045 0.62627409 0.556118313 0.099999312 6907429.4 3116021.709 13073.00442 0.024631279 0.065255095 1.185385573 -0.373943955 GSWSS(ph)APTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSWSSAPTSR 10 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 GSWS(0.14)S(0.86)APTSR 128.51 0.00034363 220990000 410950 486030 413640 423410 479650 499950 400520 420440 398530 503740 TRUE FALSE 427174.6233 569501.8717 424419.7982 507159.2342 398119.2643 383844.1893 369126.1958 414804.6895 384186.9831 602438.2083 0.709076246 0.945328274 0.704503453 0.841844404 0.660846638 0.637151137 0.612720426 0.68854313 0.637720148 1 19.20045375 3.233507713 24.98929254 0.681296991 0.803720637 0.103692365 0.122841623 194.8031159 963404.8772 0.032165532 0.039575574 1712.01558 -3.233507713 0.122423646 GSYGS(ph)DAEEEEYR ddPTM_MDA-MB-175_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 370.77 3.06E-91 7808750000 3355070 3830180 3659630 4052700 3927520 4075900 4350300 3870360 3610220 3379730 TRUE FALSE 3487530.754 4487983.62 3755002.964 4854311.964 3259921.553 3129333.996 4009312.119 3818484.155 3480288.887 4041923.385 0.862839402 1.110358409 0.929013889 1.200990593 0.8065273 0.774219028 0.991931746 0.944719578 0.861047713 1 21.94661054 3.210643057 24.99999845 0.89814784 1.024927404 0.250383793 0.109652207 303.3909713 271683.9538 0.030931855 0.036977652 1624.21328 -3.210643057 0.126779564 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.015)YGS(0.985)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.009)Y(0.011)GS(0.98)DAEEEEYRQQLSEHSK;GS(0.032)YGS(0.968)DAEEEEYRQQLSEHSK;GS(0.007)YGS(0.993)DAEEEEYRQQLSEHSK;GSYGS(1)DAEEEEYRQQLSEHSK;GS(0.003)YGS(0.997)DAEEEEYRQQLSEHSK;GS(0.006)YGS(0.994)DAEEEEYRQQLSEHSK 370.46 1.33E-112 16449030000 2502563 3555720 3889080 2954700 4483860 4453850 3383780 3702990 3786940 3779450 TRUE FALSE 2601366.12 4166387.25 3990432.62 3539130.841 3721695.079 3419510.836 3118550.482 3653357.476 3650648.769 4519960.866 0.575528461 0.921775072 0.882846719 0.783000328 0.823390996 0.756535496 0.68995077 0.808271926 0.80767265 1 22.10787885 0.607826364 2.17856128 0.999958086 0.785833346 0.337254912 0.09167257 3.205911103 16.39677909 0.084501528 0.022981906 4.053464408 -0.607826364 -0.21412474 GSYSLSHVYTPNDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GSYSLSHVYTPNDVR 15 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ;;; 151.22 3.04E-06 1008290000 570090 1449570 1138690 1362480 1206190 1605760 1107060 1280740 1074420 1479870 FALSE TRUE 592597.5934 1698522.371 1168365.197 1631974.477 1001162.255 1232846.576 1020285.744 1263573.775 1035751.834 1769822.193 0.334834536 0.959713568 0.660159649 0.922112111 0.565685219 0.696593466 0.576490536 0.71395521 0.585229318 1 20.75517299 -2.108628854 2.404481903 1.583104863 0.680505797 0.251508879 0.170496747 9478374.801 3017471.602 30169928.42 0.037166657 0.007787017 2.108628854 -0.902599066 GT(ph)GQSDDSDIWDDTALIK ddPTM_MDA-MB-175_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(0.333)GQS(0.333)DDS(0.333)DIWDDTALIK 90.22 0.010104 32016000 91496 68055 72541 62342 88968 78547 89794 80281 82104 67109 TRUE FALSE 95108.33273 79742.91686 74431.47805 74673.06153 73845.25114 60305.64964 82755.71165 79204.96451 79149.09308 80257.72367 1.18503651 0.993585579 0.927405795 0.930415892 0.92010149 0.751399951 1.03112458 0.986882768 0.986186618 1 16.29235262 4.727315574 2.663135958 0.940709135 1.230461582 0.502560566 0.072485032 0.385974847 3.68677597 0.018725912 0.245356146 53372.25772 -4.727315574 0.289752447 GT(ph)PGPDSSGSLGSGEFTGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTPGPDSSGSLGSGEFTGVK 20 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 GT(0.639)PGPDS(0.067)S(0.067)GS(0.222)LGS(0.005)GEFTGVK 92.264 0.004789 0 20274 15988 18963 18991 19318 26357 24022 16885 19826 15967 TRUE FALSE 21074.43317 18733.81463 19457.19136 22747.36312 16034.33326 20235.98619 22139.09287 16658.68419 19112.46613 19095.42794 1.103637648 0.981062833 1.018945028 1.191246574 0.83969489 1.059729389 1.159392339 0.872391247 1.000892265 1 14.22093963 1.72419156 24.99999873 0.950794388 1.044301655 0.155094467 0.098072188 1.638537268 2839.0485 0.04400562 0.024403326 52.9897121 -1.72419156 0.093507267 GT(ph)PPPVFTPPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 GT(1)PPPVFTPPLPK;GT(1)PPPVFTPPLPK 153.38 0.00051066 87435000 130580 108284 130501 99923 143703 156935 136577 123281 124541 104567 TRUE FALSE 135735.3992 126880.9347 133901.9633 119687.4712 119276.4154 120489.2246 125871.7379 121628.6198 120058.7937 125054.9016 1.085406469 1.014601851 1.070745421 0.957079408 0.953792405 0.96349062 1.006531821 0.97260178 0.960048684 1 16.93220208 3.737647924 24.99999625 0.973046897 1.05268631 0.723538432 0.023624242 42.26663041 1157752.722 0.00601883 0.009945563 5465.726855 -3.737647924 0.079639413 GT(ph)PS(ph)QSPVVGR ddPTM_MDA-MB-175_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(1)PS(0.821)QS(0.18)PVVGR 111.79 0.0085547 1233700000 731530 845570 662630 806570 679440 860000 774330 670550 667260 576590 TRUE FALSE 760411.3693 990790.0699 679898.6822 966107.1386 563949.0315 660278.0334 713635.9913 661562.374 643245.4429 689561.771 1.102745833 1.436840196 0.985986623 1.401045097 0.817836857 0.957532829 1.034912348 0.959395375 0.932832228 1 19.39532027 3.234109268 24.99999961 0.955269035 1.228762862 0.519297435 0.132497247 85.58272994 480656.5881 0.034936198 0.043128016 1714.388593 -3.234109268 0.273493827 GT(ph)PSQS(ph)PVVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 GT(0.999)PS(0.005)QS(0.996)PVVGR;GT(1)PS(0.007)QS(0.993)PVVGR;GT(0.999)PS(0.001)QS(1)PVVGR;GT(0.937)PS(0.076)QS(0.988)PVVGR 196.84 3.14E-07 2712760000 1518710 1632220 1420260 1745770 1406450 1678370 1560210 1353150 1223750 1265360 TRUE FALSE 1578669.843 1912541.088 1457273.142 2091078.095 1167382.131 1288594.003 1437916.663 1335013.238 1179707.477 1513283.065 1.043208557 1.263835651 0.962987808 1.381815566 0.771423508 0.85152212 0.950196759 0.882196641 0.77956828 1 20.52925044 3.222097721 24.99999198 0.872137749 1.15588336 0.567331879 0.124211188 164.2679029 249451.1365 0.033159419 0.039740174 1667.622402 -3.222097721 0.283745611 GT(ph)PSQSPVVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTPSQSPVVGR 11 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 GT(0.658)PS(0.342)QSPVVGR;GT(0.996)PS(0.004)QSPVVGR 120.59 0.0048256 432810000 108020 122029 94975 131537 132219 160065 127211 106544 99819 111987 TRUE FALSE 112284.713 142986.5315 97450.12652 157554.626 109744.4616 122892.3296 117239.8694 105115.952 96226.53369 133928.7085 0.838391666 1.067631676 0.727626867 1.17640667 0.819424475 0.917595121 0.875390129 0.784864971 0.718490716 1 17.03110572 2.112032968 2.196309322 0.81277864 0.931787082 0.072212225 0.136582809 0.634457316 5.979434778 0.06442021 0.038383836 129.4294089 -2.112032968 0.119008441 GT(ph)RESGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTRESGQK 8 1 A0A1W2PQW7;A8K830-4;A8K830-2 A0A1W2PQW7 1 GT(0.5)RES(0.5)GQK;GT(0.669)RES(0.331)GQK;GT(0.5)RES(0.5)GQK;GT(0.5)RES(0.5)GQK 85.064 0.027496 3423410000 670020 3223460 2176880 2716280 1435220 2616250 1560160 1863030 1945770 6231500 TRUE FALSE 696472.907 3777064.18 2233611.281 3253552.077 1191261.817 2008665.587 1437870.582 1838059.13 1875742.118 7452443.116 0.093455649 0.506822276 0.299715308 0.436575231 0.159848495 0.269531153 0.192939491 0.246638465 0.251694926 1 22.82928203 -1.564160835 4.144256024 1.011305072 0.276393357 0.779069256 0.116127321 0.011598315 0.001219761 0.107512546 0.025244555 0.027279673 1.564160835 -0.734911715 GT(ph)TPPPPSWEPNSQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTTPPPPSWEPNSQTK 16 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 GT(0.5)T(0.5)PPPPSWEPNSQTK 107.74 0.01235 66343000 59469 44979 55380 56860 57295 72778 71666 61968 63948 41933 TRUE FALSE 61816.88204 52703.79336 56823.2483 68106.73829 47556.01637 55876.41246 66048.63166 61137.42032 61646.52397 50148.96849 1.232665076 1.050944714 1.133089074 1.358088518 0.948295006 1.11420861 1.317048658 1.219116208 1.229268035 1 15.61393241 GTAGKS(ph)PDLSSQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTAGKSPDLSSQKR 14 2 Q9Y2I7 Q9Y2I7 PIKFYVE 1-phosphatidylinositol 3-phosphate 5-kinase 1 GT(0.37)AGKS(0.63)PDLS(0.001)SQKR 64.275 0.032573 96196000 317400 173290 226590 148270 346190 319590 245010 235330 274970 167650 TRUE FALSE 329931.1971 203051.2095 232495.1215 177597.3635 287344.7475 245370.0659 225805.476 232175.7863 265073.8834 200497.8076 1.645560123 1.012735311 1.159589346 0.885782072 1.433156556 1.223804234 1.126224165 1.157996633 1.322078713 1 17.61322694 5.169772224 0.017129683 5.77E-07 2.502835444 0.087424618 0.202846928 8130.301668 19.10897945 1207.949941 1605.849835 147833.2838 -5.169772224 2.502834867 GTCADRDNLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTCADRDNLTR 11 1 P55212;D6RBM3;D6RHU3 P55212 CASP6 Caspase-6;Caspase-6 subunit p18;Caspase-6 subunit p11 0 ; 135.99 9.90E-05 325580000 342830 343670 326360 320990 378160 425240 300210 326500 323430 346400 FALSE TRUE 356365.1931 402692.6491 334865.2097 384480.8639 313880.4983 326484.4546 276678.7557 322123.8015 311789.8175 414270.4478 0.860223545 0.97205256 0.808325121 0.928091458 0.757670502 0.788094966 0.667869884 0.777568864 0.752623845 1 18.66021338 3.231935004 24.96819228 0.771150265 0.891889699 0.220062102 0.089227092 178.0599132 671006.6218 0.023682402 0.028931935 1705.827079 -3.231935004 0.120739433 GTCSGFEPHSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTCSGFEPHSWR 12 0 Q9NZU5;F8WB09;C9IYS1;H7C3D2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;; 184.03 1.48E-05 1312540000 666620 945190 871560 879240 907410 990270 864620 862130 868100 1109020 FALSE TRUE 692938.6723 1107519.03 894273.5696 1053151.048 753168.7723 760294.8002 796848.8251 850574.5575 836857.2506 1326311.236 0.522455555 0.835037056 0.674256197 0.794045183 0.567867294 0.573240111 0.60080078 0.641308416 0.630965966 1 20.33898793 -1.462871221 5.152424679 1.000594529 0.651912437 0.559156152 0.093493954 0.000628633 6.55E-05 0.08912438 0.020972053 0.034445205 1.462871221 -0.348682092 GTCSRPDTECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTCSRPDTECK 11 1 H7C4T5;C9JP00;A0A0A0MQX8;Q9NR56-7;Q9NR56-6;Q9NR56-2;Q9NR56-5;Q9NR56;Q9NR56-3;Q9NR56-4 H7C4T5 MBNL1 Muscleblind-like protein 1 0 ; 120.03 0.00046167 313560000 390190 292530 320740 295010 434270 467360 394710 334300 351580 297420 FALSE TRUE 405595.0025 342769.7519 329098.7479 353362.0975 360452.9405 358822.7229 363771.5988 329819.2553 338926.7045 355693.7546 1.14029273 0.963665365 0.925230605 0.993444762 1.01338001 1.008796804 1.02271011 0.927256245 0.952860994 1 18.44027612 4.741411726 24.76004043 0.976914488 1.140292798 0.678448582 0.03337802 145.0360579 1259468.391 0.008638542 0.05999523 55133.01289 -4.741411726 0.16337831 GTDDLNPVTSTPAKPSS(ph)PPPEFSFNTPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTDDLNPVTSTPAKPSSPPPEFSFNTPGK 29 1 B5MCR8;Q6NXT4-4;Q6NXT4-3;Q6NXT4;Q6NXT4-2 B5MCR8 SLC30A6 Zinc transporter 6 1 GTDDLNPVTSTPAKPS(0.147)S(0.853)PPPEFSFNTPGK 125.42 1.34E-05 108080000 271680 141930 205710 174650 299550 268400 260850 231680 234590 146310 TRUE FALSE 282406.1362 166305.3734 211070.9716 209195.2487 248632.598 206068.1676 240403.8954 228574.7086 226147.1517 174976.6432 1.613964761 0.950443273 1.206280837 1.19556099 1.420947353 1.17768957 1.373919918 1.306315542 1.292441937 1 17.41680283 4.774973454 24.08730745 1.238174884 1.613966192 0.403202951 0.143327935 13579.47368 8982616.681 0.033153241 7.722574275 59562.5735 -4.774973454 0.375791308 GTDDS(ph)PKDSQEDLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTDDSPKDSQEDLQER 16 1 Q969E4;Q5H9L2;Q6IPX3-2;Q6IPX3 Q969E4 TCEAL3;TCEAL5;TCEAL6 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5;Transcription elongation factor A protein-like 6 1 GTDDS(1)PKDSQEDLQER;GTDDS(0.968)PKDS(0.032)QEDLQER;GTDDS(0.994)PKDS(0.006)QEDLQER;GTDDS(1)PKDSQEDLQER 252.55 9.48E-27 4578900000 7053930 2514440 3231780 2392000 4473650 4468780 4166200 3375340 3608550 2047070 TRUE FALSE 7332424.603 2946275.51 3316002.842 2865130.461 3713220.571 3430973.57 3839642.358 3330099.088 3478678.99 2448154.173 2.99508286 1.203468124 1.35449102 1.170322724 1.516742945 1.401453229 1.56838258 1.360248928 1.42093951 1 21.22326298 4.741858601 24.99969769 1.358363316 2.995083468 0.904224906 0.162098563 83.7073227 634497.3182 0.036504815 0.263931914 55189.77219 -4.741858601 1.636720152 GTDLWLGVDALGLNIYEKDDKLTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTDLWLGVDALGLNIYEKDDKLTPK 25 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 218.87 7.80E-34 1135070000 770433 344063 474580 283788 864050 610880 695650 531402 631722 287647 FALSE TRUE 800850.2897 403153.1438 486947.9447 339920.4194 717179.0896 469012.378 641123.1353 524279.4254 608986.4486 344005.9223 2.328013089 1.171936637 1.415521981 0.988123742 2.084787043 1.363384603 1.863697959 1.524041859 1.770278966 1 18.39207388 3.237838869 24.99999921 1.626709351 1.449874746 0.016683936 0.4268521 75.05836235 2599935.536 0.113469894 0.143509538 1729.174685 -3.237838869 -0.176834606 GTDTQTPAVLS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTDTQTPAVLSPSK 14 0 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(1)PSK;GTDTQTPAVLS(1)PSK 285.04 1.40E-33 371160000 836850 436810 630510 501210 624100 795790 863500 652210 657760 391330 TRUE FALSE 869889.4842 511828.7196 646941.6086 600347.842 518015.7049 610979.8328 795816.6137 643468.1918 634087.3461 468003.621 1.858723833 1.093642648 1.382343169 1.282784609 1.1068626 1.305502362 1.700449693 1.374921396 1.354877009 1 18.83616017 -2.197952131 1.737481729 0.169523479 1.376095729 0.2078513 0.224629146 1230838.282 216942.2767 4007129.674 0.057632694 0.006339396 2.197952131 1.20657225 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087-2;P46087;P46087-4 P46087-2 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 GTDTQTPAVLS(1)PSKTQATLKPK 189.12 1.17E-17 496990000 1607700 589050 1082100 552110 1361400 1061300 1243800 939310 1200800 524500 TRUE FALSE 1671173.237 690214.7553 1110300.415 661315.7101 1129989.714 814829.1592 1146307.706 926720.0859 1157583.443 627265.7328 2.664218927 1.100354633 1.770063877 1.054283178 1.801452965 1.299017492 1.827467445 1.477396321 1.845443457 1 19.25871723 4.750872372 24.93436724 1.496645521 2.664219672 0.553642221 0.322115432 1322.30171 2677939.749 0.068209584 1.1872583 56347.20417 -4.750872372 1.167574151 GTEAPAVVT(ph)EEEDDDEETAPPVIAPRPDHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK 31 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK 182.19 4.34E-18 246240000 184060 160760 179100 167270 237880 237920 201100 187500 196230 175280 TRUE FALSE 191326.8309 188369.2795 183767.4931 200355.5067 197445.2426 182666.6857 185337.2565 184986.8692 189167.7206 209622.7601 0.912719739 0.898610816 0.876658112 0.955790806 0.941907465 0.871406739 0.884146628 0.882475115 0.902419759 1 17.67743584 -0.10331813 5.279406781 0.999999998 0.901532977 0.551002899 0.026268453 1104993.151 5284415.742 0.026978855 0.006850434 0.788282472 0.10331813 -0.098467021 GTEAS(ph)PPQNNS(ph)GSSSPVFTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GT(0.02)EAS(0.979)PPQNNS(0.961)GS(0.032)S(0.006)S(0.001)PVFTFR 72.421 0.023005 36982000 61779 73013 63384 71647 67033 86885 65268 69515 63590 70164 TRUE FALSE 64218.08262 85552.41479 65035.83911 85818.56276 55638.7546 66707.2755 60152.12361 68583.26513 61301.40832 83911.29243 0.765309183 1.019557825 0.775054671 1.022729603 0.663066352 0.794973758 0.716853738 0.817330578 0.730550163 1 16.35657736 3.234632429 24.99999988 0.776450225 0.895897587 0.171212174 0.115558602 149.8700338 953812.2605 0.029795987 0.036880251 1716.455025 -3.234632429 0.119447363 GTEAS(ph)PPQNNSGSSS(ph)PVFTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 GTEAS(1)PPQNNSGSS(0.014)S(0.986)PVFTFR;GTEAS(0.552)PPQNNS(0.448)GSS(0.013)S(0.987)PVFTFR;GTEAS(0.995)PPQNNS(0.003)GS(0.002)S(0.075)S(0.925)PVFTFR 264.46 1.17E-36 318804000 337673 424340 417912 428633 390730 518324 434521 407211 402780 479551 TRUE FALSE 351004.5908 497217.0941 428803.13 513415.3281 324313.8542 397951.1063 400462.1086 401753.0026 388284.0265 573509.8369 0.612028893 0.866972216 0.747682258 0.895216254 0.56548961 0.69388715 0.698265457 0.700516324 0.677031154 1 19.12945871 -1.047709018 4.433199403 1.000015148 0.720533457 0.438197388 0.095919918 12303936.13 2907820.007 1999.845218 0.021775129 0.089596487 1.047709018 -0.279481691 GTEAS(ph)PPQNNSGSSSPVFTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEAS(1)PPQNNSGSSSPVFTFR;GT(0.001)EAS(0.999)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR;GTEAS(1)PPQNNSGSSSPVFTFR 363.79 1.60E-97 1142983000 434325 500115 488077 494037 523204 579201 480775 452618 485404 543009 TRUE FALSE 451472.4864 586005.8609 500796.6876 591756.044 434269.971 444690.3456 443090.5992 446551.396 467934.4049 649401.217 0.69521349 0.902378754 0.771166845 0.911233346 0.668723679 0.684769806 0.682306389 0.687635601 0.72056287 1 19.30875056 5.044805016 15.5542218 0.762843657 0.358691677 0.028084872 0.112554971 8506184.424 82357780.58 0.026567234 99662725.83 110867.6944 -5.044805016 -0.40415198 GTEASPPQNNSGSSS(ph)PVFTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTEASPPQNNSGSSSPVFTFR 21 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 GTEASPPQNNS(0.038)GS(0.03)S(0.144)S(0.784)PVFT(0.004)FR;GTEASPPQNNSGSS(0.003)S(0.997)PVFTFR;GTEASPPQNNSGSS(0.027)S(0.973)PVFTFR 365.47 3.26E-112 489257000 197906 220987 202081 215167 223017 238349 198451 216606 186480 228986 TRUE FALSE 205719.4817 258939.7982 207347.3969 257726.3904 185108.65 182996.057 182895.8921 213702.7509 179768.6212 273851.4225 0.751208374 0.945548487 0.757152893 0.941117589 0.675945549 0.668231172 0.667865408 0.7803602 0.656445819 1 18.06303385 3.226191695 24.99936078 0.725794281 0.8491274 0.16969318 0.113108927 318.9234951 644588.873 0.029919707 0.036001202 1683.416948 -3.226191695 0.123333119 GTEDELDKYSEALKDAQEK ddPTM_MDA-MB-175_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 0 129.12 1.13E-05 80719000 248860 77406 131920 80796 202330 186030 256440 148340 169300 81036 FALSE TRUE 258685.185 90699.87836 135357.9436 96777.20765 167938.0189 142827.3518 236339.5627 146351.7449 163206.9261 96913.45267 2.66923918 0.935885327 1.3966889 0.998594158 1.732865915 1.473761876 2.438666214 1.510128273 1.684048206 1 16.56440932 GTEDITSPHGIPLDLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GTEDITSPHGIPLDLLDR 18 0 Q9Y265;H7C4G5;Q9Y265-2;E7ETR0;J3QLR1 Q9Y265 RUVBL1 RuvB-like 1 0 ;;;;; 185.33 5.36E-14 1276391000 1022372 1521145 1410308 1538903 1549684 1741706 1388829 1537164 1389345 1705678 FALSE TRUE 1062736.036 1782389.821 1447061.785 1843293.42 1286269.267 1337221.177 1279968.954 1516560.831 1339342.745 2039872.947 0.520981484 0.87377492 0.709388194 0.903631485 0.630563423 0.655541405 0.627474841 0.743458475 0.656581454 1 20.96004787 -1.923884072 4.583906052 1.130151071 0.709359581 0.397802267 0.109553134 0.068915744 0.001144348 0.050167133 0.023521411 0.0119156 1.923884072 -0.42079149 GTEKRES(ph)PSPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTEKRESPSPAPKPR 15 3 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 GT(0.007)EKRES(0.977)PS(0.017)PAPKPR 88.574 0.037207 69378000 99014 72528 97965 37690 160100 103580 47380 64731 95465 122660 TRUE FALSE 102923.1492 84984.11981 100518.0484 45144.96951 132886.2592 79525.11477 43666.2318 63863.38682 92029.2333 146692.8785 0.701623352 0.579333644 0.685227868 0.30775161 0.90588078 0.542119805 0.297671109 0.435354378 0.627359925 1 17.16243931 -1.143754879 8.896985599 1.000000011 0.550060381 0.352052942 0.176157966 3.77E-08 3.56E-09 0.170258495 0.040130311 0.071819954 1.143754879 -0.44993963 GTEPS(ph)PGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 2 GT(0.417)EPS(0.568)PGGT(0.042)PQPS(0.26)RPVS(0.714)PAGPPEGVPEEAQPPR 68.481 0.00247 167160000 24657 50454 43596 55392 34370 59193 33788 43353 41215 46962 TRUE FALSE 25630.4774 59119.08202 44732.14757 66348.37227 28527.79968 45446.32283 31139.60827 42771.92395 39731.6802 56163.30476 0.45635629 1.052628265 0.796465731 1.181347368 0.507943751 0.809181778 0.554447578 0.761563518 0.707431309 1 15.77734021 3.214649847 24.9999799 0.707566732 0.879249491 0.098106929 0.216579956 452.7448228 473367.5858 0.058010774 0.069369866 1639.267568 -3.214649847 0.171682759 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 GTEPSPGGT(0.001)PQPS(0.018)RPVS(0.981)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.001)RPVS(0.999)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPS(0.001)RPVS(0.999)PAGPPEGVPEEAQPPR;GTEPSPGGTPQPSRPVS(1)PAGPPEGVPEEAQPPR 274.05 9.13E-74 2353580000 163325 176944 164341 168319 182088 219589 153871 186774 165193 205501 TRUE FALSE 169773.1971 207332.7556 168623.8615 201611.9958 151136.7468 168592.7827 141810.189 184270.6 159247.7362 245764.9864 0.690794892 0.843622025 0.686118328 0.820344667 0.61496452 0.68599187 0.577015429 0.749783778 0.64796755 1 17.90691987 -1.008645968 9.391505591 0.99999999 0.703912032 0.558820808 0.079456691 0 0 0.074497969 0.01755934 0.098028878 1.008645968 -0.296087958 GTEVIIITTDTS(ph)PSGTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTEVIIITTDTSPSGTKK 18 1 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 GTEVIIITTDT(0.026)S(0.973)PS(0.001)GTKK 132.14 9.45E-06 208530000 225680 85227 162690 102970 187450 188760 206020 148970 166370 79880 TRUE FALSE 234590.0207 99864.07428 166929.8351 123337.1587 155587.316 144923.3507 189871.6141 146973.3008 160382.3762 95530.95661 2.455644003 1.045358257 1.747389966 1.291070068 1.62865862 1.517030247 1.987540174 1.538488737 1.678852404 1 16.54368069 -2.022115279 2.512873947 0.282521079 1.631309353 0.226094885 0.360963562 9701344.186 3119450.485 40171556.39 0.077456549 0.009503525 2.022115279 1.348788274 GTEVQVDDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ; 138.24 9.90E-05 1071230000 634640 416250 530960 485510 703890 644710 724130 628920 627630 436920 FALSE TRUE 659696.0772 487737.6995 544797.2538 581542.4289 584243.0292 494985.8732 667370.7984 620490.3561 605041.7189 522526.1087 1.262513138 0.933422639 1.042622071 1.112944252 1.118112606 0.947294049 1.277200866 1.187482014 1.157916722 1 18.9951436 2.23266981 24.99992655 1.176793137 1.066264903 0.119596877 0.108419916 230.092651 976476.7378 0.037791915 0.028643602 170.87157 -2.23266981 -0.110528234 GTFHDDRDDGVDYWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GTFHDDRDDGVDYWAK 16 1 E9PK91;Q9NYF8-3;H0YF63 E9PK91 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;;; 91.207 0.0031181 1523483000 1367230 1288850 1380520 1204902 1556930 1603470 1427730 1365390 1480730 1329150 FALSE TRUE 1421209.296 1510199.962 1416497.485 1443228.019 1292283.595 1231088.393 1315820.792 1347089.18 1427438.817 1589571.494 0.89408328 0.95006734 0.891119079 0.907935267 0.812976075 0.774478152 0.827783334 0.847454289 0.898002274 1 20.60020648 3.311311856 8.35619989 0.846282873 0.912606925 0.124818198 0.059275723 0.404017004 41.41989007 0.015813278 0.021402159 2047.914663 -3.311311856 0.066324052 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTFIADSHQNFALFFQLVDVNTGAELTPHQTFVR 34 0 P04844-2;P04844 P04844-2 RPN2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 0 ;; 258.89 7.89E-60 267166000 147368.7 132091.5 142562.4 142783 213251.1 231793 172122.4 186964 156153.9 161211 FALSE TRUE 153186.9301 154777.1876 146277.6933 171025.0512 177002.7542 177962.5886 158630.9965 184458.0534 150533.9516 192797.2089 0.794549522 0.802797865 0.758712712 0.887072236 0.918077369 0.923055835 0.82278679 0.956746493 0.780789061 1 17.55672464 3.68395409 6.650104721 0.897820404 0.787227231 0.430567429 0.059569641 0.203972418 20.33023737 0.014650673 0.022968609 4830.077403 -3.68395409 -0.110593173 GTFNDGFQIEVQGHTDELWGLATHPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTFNDGFQIEVQGHTDELWGLATHPFK 27 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 121.26 5.57E-05 119840000 188040 209230 214310 167130 298660 274940 210750 193160 221760 198500 FALSE TRUE 195463.9644 245163.6249 219895.0947 200187.8152 247893.8799 211089.3518 194230.8643 190571.0061 213778.9009 237392.2745 0.823379635 1.032736324 0.926294232 0.843278559 1.044237351 0.889200595 0.818185279 0.802768357 0.900530152 1 17.85691346 2.483314787 24.89138911 0.855490663 0.937276268 0.057611396 0.083405486 454.3110806 1825856.721 0.027056276 0.023366633 304.3089933 -2.483314787 0.081785605 GTFPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTFPDAR 7 0 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 81.191 0.064841 474520000 879500 1051410 934890 1045250 1017410 1153650 999280 999640 911610 1075480 FALSE TRUE 914223.3391 1231981.489 959254.0014 1251997.33 844471.0116 885732.2712 920953.8225 986241.4609 878801.3342 1286199.715 0.710794233 0.957846184 0.745804863 0.973408185 0.656562898 0.688642876 0.716027077 0.766787187 0.683254182 1 20.29468324 GTFS(ph)DQELDAQS(ph)LDDEDDNMHHAVYPAVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 2 GT(0.179)FS(0.821)DQELDAQS(1)LDDEDDNMHHAVYPAVNR 102.17 0.00018472 43021000 8711.5 13591 8891.2 16685 13110 17809 14253 14613 15368 15767 TRUE FALSE 9055.436747 15925.14853 9122.911976 19985.2432 10881.56688 13673.12965 13135.81262 14417.13664 14814.90868 18856.24177 0.480235503 0.844555809 0.483813906 1.059874149 0.577080365 0.725124859 0.696629412 0.76458166 0.78567664 1 14.20275454 -5 0.146666808 2.004583827 0.624408642 0.259916287 0.159851522 185.7015901 1.635606023 54.26705916 0.784286213 1.00E-05 5 -1.380175185 GTFS(ph)DQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 GT(0.033)FS(0.967)DQELDAQSLDDEDDNMHHAVYPAVNR;GT(0.027)FS(0.973)DQELDAQSLDDEDDNMHHAVYPAVNR 233.58 3.72E-45 266550000 26478.1 28277.5 26190 31947 29457.6 35620.7 36537 37988.6 34498.2 29031.3 TRUE FALSE 27523.47583 33133.94066 26872.53292 38266.02125 24450.40767 27348.33226 33673.13447 37479.42495 33256.61652 34719.4274 0.792739912 0.954334306 0.773991247 1.102150125 0.704228425 0.787695372 0.969864338 1.079494328 0.957867655 1 15.08345553 2.057256829 6.172927496 1.022271626 0.85882444 0.317079164 0.108092738 0.222974435 17.47342263 0.040077933 0.029204961 114.0924298 -2.057256829 -0.163447186 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTGLVLDGDTSYTYHLVCMGPEASGWGQDEPQTWPTDHR 39 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 98.342 7.92E-05 131780000 12309 22735 20540 23062 23577 29074 18886 24436 22006 23411 FALSE TRUE 12794.96882 26639.5594 21075.28927 27623.59477 19569.38996 22322.00412 17405.66597 24108.47539 21214.00836 27997.93722 0.45699684 0.951482932 0.752744358 0.986629642 0.698958277 0.797273169 0.621676727 0.861080415 0.757698976 1 14.77303292 -0.184520167 1.102709133 1.002221686 0.774275015 0.184838954 0.146660351 29.17541499 24.6811175 0.418401875 0.039739089 0.653852567 0.184520167 -0.227946671 GTGNAS(ph)PDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTGNASPDAR 10 0 O14795;O14795-2;A0A1B0GUS7;B1AM27;I6L9J0;F8W8M9;A0A1B0GVW8;A0A0U1RRB5 O14795 UNC13B Protein unc-13 homolog B 1 GT(0.005)GNAS(0.995)PDAR 87.641 0.013362 50802000 50030 59066 53934 54715 56697 60474 56004 53875 50757 65711 TRUE FALSE 52005.22303 69210.12603 55339.56435 65537.46369 47059.66419 46429.82999 51614.26014 53152.89375 48930.26548 78585.81234 0.66176351 0.880694924 0.704192814 0.833960504 0.598831555 0.59081695 0.65678853 0.676367555 0.62263485 1 16.26198126 -1.17065228 3.500817424 1.000377792 0.693409778 0.510191785 0.090586404 26939946.95 44885454.56 115956.1949 0.023266068 0.067506831 1.17065228 -0.306968014 GTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 GT(0.013)GQS(0.987)DDS(1)DIWDDTALIK;GT(0.002)GQS(0.998)DDS(1)DIWDDTALIK;GT(0.364)GQS(0.636)DDS(1)DIWDDTALIK;GT(0.084)GQS(0.916)DDS(1)DIWDDTALIK;GT(0.07)GQS(0.93)DDS(1)DIWDDTALIK;GT(0.387)GQS(0.614)DDS(0.999)DIWDDTALIK;GT(0.019)GQS(0.981)DDS(1)DIWDDTALIK;GT(0.014)GQS(0.986)DDS(1)DIWDDTALIK 214.42 1.47E-18 325433000 1253323 969527 1086215 940888 1326581 1373623 1192528 1077582 1186985 948422 TRUE FALSE 1302805.16 1136035.72 1114522.655 1126992.838 1101089.235 1054619.876 1099054.539 1063138.776 1144265.642 1134247.132 1.14860785 1.001576895 0.982610071 0.993604309 0.970766603 0.92979726 0.968972729 0.937307881 1.00883274 1 20.11330358 GTGQS(ph)DDSDIWDDTALIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 GT(0.001)GQS(0.999)DDSDIWDDTALIK;GT(0.001)GQS(0.999)DDSDIWDDTALIK;GTGQS(1)DDSDIWDDTALIK;GTGQS(1)DDSDIWDDTALIK;GT(0.131)GQS(0.869)DDSDIWDDTALIK;GT(0.009)GQS(0.991)DDSDIWDDTALIK 432.11 4.67E-169 1326441000 1591656 1159571 1388893 1185068 1560051 1708795 1744604 1427021 1606144 1150967 TRUE FALSE 1654495.808 1358718.299 1425088.693 1419470.913 1294874.088 1311953.258 1607857.38 1407894.118 1548339.191 1376476.947 1.201978581 0.987098478 1.035316062 1.031234788 0.940716146 0.953124032 1.168096119 1.022824335 1.124856609 1 20.39254902 -0.438987402 7.867721693 1.000000003 1.045900832 0.029364206 0.083375471 0 0 0.077571495 0.018283777 0.363925593 0.438987402 0.045900829 GTHDLWDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTHDLWDSR 9 0 Q04446;E9PGM4 Q04446 GBE1 "1,4-alpha-glucan-branching enzyme" 0 99.653 0.0051914 69875000 30336 39443 36836 45098 45447 45375 40432 34216 36513 39958 FALSE TRUE 31533.6887 46217.02843 37795.97642 54018.2498 37721.93517 34837.34391 37262.83419 33757.39049 35198.90426 47787.00506 0.659879996 0.967146369 0.790925825 1.130396218 0.789376424 0.729012916 0.779769189 0.706413604 0.736578997 1 15.54433073 3.025837734 24.99989331 0.765469924 0.89518062 0.092734488 0.136967575 379.0700311 366775.292 0.0371722 0.044428053 1061.298948 -3.025837734 0.129710696 GTHDRDPSEKPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTHDRDPSEKPPR 13 2 Q969S3 Q969S3 ZNF622 Zinc finger protein 622 0 ;;; 114.56 0.00044031 92669000 114590 113780 128548 105060 149443 152863 136296 124819 138465 135778 FALSE TRUE 119114.1017 133320.8299 131898.0665 125840.5544 124040.7322 117362.8849 125612.7634 123146.0055 133481.6717 162381.0995 0.733546589 0.821036625 0.812274747 0.774970454 0.763886515 0.72276198 0.773567637 0.758376473 0.822027146 1 17.30902419 0.833759691 3.205522332 0.999959837 0.77130345 0.852478763 0.028688654 0.29445288 5.001945284 0.028676737 0.007460003 6.819612383 -0.833759691 -0.228656388 GTHTAVSSNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTHTAVSSNDR 11 0 Q9NZ08-2;Q9NZ08 Q9NZ08-2 ERAP1 Endoplasmic reticulum aminopeptidase 1 0 ; 89.403 0.0084389 68866000 11933.9 55845 26134.1 42349 21795.8 42571 20219.8 25725.8 17043.7 70740 FALSE TRUE 12405.05959 65435.94434 26815.17612 50725.5058 18090.9577 32684.53042 18634.91924 25380.98773 16430.30057 84600.1486 0.146631652 0.773473161 0.3169637 0.599591214 0.213840732 0.386341289 0.220270526 0.300011148 0.194211249 1 16.36837258 -1.419031847 5.468854985 1.000428049 0.356240216 0.521903573 0.18651219 0.000923993 9.82E-05 0.171420889 0.040378629 0.038103788 1.419031847 -0.644187833 GTHTGVWVGVSGSETSEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 259.49 1.48E-36 2471930000 1297310 1346712 1480388 1591470 1504850.7 1797883 1409418 1351690 1354730 1257934 FALSE TRUE 1348528.801 1577999.31 1518968.127 1906258.016 1249056.716 1380351.92 1298944.134 1333572.806 1305973.532 1504402.083 0.896388549 1.048921248 1.009682282 1.267120033 0.830267872 0.917541883 0.863428833 0.886447062 0.868101385 1 20.52075878 GTHTGVWVGVSGSETSEALSRDPETLVGYSMVGCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 315.62 6.36E-110 875420000 202520 312040 301160 358000 314480 387200 251130 277770 277050 368230 FALSE TRUE 210515.646 365630.4427 309008.477 428811.3315 261024.8019 297278.6681 231445.7744 274046.9475 267079.0246 440377.6183 0.47803439 0.830265725 0.701689787 0.973735525 0.592729492 0.675053989 0.525562074 0.622299899 0.60647729 1 18.74838162 -1.174764654 5.062774819 1.000021877 0.670419775 0.344957834 0.137472287 3.38E-05 5.50E-06 0.132428166 0.031211548 0.066870619 1.174764654 -0.329602102 GTINFLHADCDKFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTINFLHADCDKFR 14 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 132.44 3.03E-05 621720000 1034960 1428970 1350110 1433300 1956900 1989730 1438610 1279210 1270930 1924590 FALSE TRUE 1075821.02 1674384.482 1385294.976 1716802.462 1624266.837 1527645.362 1325847.989 1262064.282 1225189.478 2301676.562 0.467407557 0.727462976 0.601863441 0.745892142 0.705688568 0.663709831 0.576035752 0.548323906 0.53230306 1 21.13425369 -1.154796594 4.232850253 1.000100018 0.621820613 0.635159647 0.086657767 12690473.31 3462191.497 11697.05468 0.020735006 0.070016985 1.154796594 -0.378279405 GTITDAPGFDPLRDAEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTITDAPGFDPLRDAEVLR 19 1 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 ; 171.85 8.65E-12 225550000 70152 159614 116416 99089 94028 141190 72982 89515 88515 165256 FALSE TRUE 72921.65513 187026.4629 119449.8966 118688.5084 78045.15415 108400.7623 67261.48014 88315.19784 85329.36244 197634.7492 0.36897183 0.94632378 0.604397238 0.600544737 0.39489591 0.548490398 0.340332256 0.446860677 0.431752831 1 17.59247711 -1.933103333 2.702612639 1.315628613 0.521389197 0.425117933 0.167350593 18471357.54 10106355.93 36755791.03 0.041312188 0.01166532 1.933103333 -0.794239416 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_MDA-MB-175_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(0.994)DT(0.006)DDIDHR;GTLDEEDEEADS(1)DTDDIDHR 363.38 1.02E-96 10501600000 1715960 2006580 1933470 1896220 1975900 2155320 1935700 1945440 1862260 1879620 TRUE FALSE 1783707.426 2351194.506 1983857.817 2271286.656 1640037.224 1654779.594 1783974.776 1919364.559 1795237.626 2247895.552 0.793501026 1.045953627 0.882540034 1.010405779 0.729587824 0.736146123 0.793619959 0.853849529 0.798630357 1 21.10014357 3.240317265 24.99999625 0.808940968 0.937549643 0.252265082 0.095547334 56.30032441 801234.6931 0.02531449 0.03258275 1739.070807 -3.240317265 0.128608675 GTLDPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTLDPVEK 8 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 105.57 0.01015 261100000 655360 1196010 1069930 1016950 993880 1253300 1001050 923980 1062520 1489270 FALSE TRUE 681234.1188 1401415.414 1097813.255 1218099.675 824940.6326 962240.0689 922585.0852 911595.5594 1024280.113 1781063.943 0.382487177 0.786841719 0.616380596 0.683916869 0.463172946 0.540261383 0.51799661 0.511826408 0.57509452 1 20.76430788 0.91948265 20.50692412 1 0.565614134 0.597157464 0.107399909 5991.000836 1525848.989 0.10086942 0.025217355 8.307735288 -0.91948265 -0.434385867 GTLS(ph)DSEIETNSATSTIFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.002)LS(0.996)DS(0.002)EIETNSATSTIFGK;GT(0.006)LS(0.994)DSEIETNSATSTIFGK;GTLS(1)DSEIETNSATSTIFGK;GTLS(0.998)DS(0.002)EIETNSATSTIFGK;GT(0.109)LS(0.889)DS(0.002)EIETNSATSTIFGK;GTLS(0.999)DS(0.001)EIETNSATSTIFGK;GT(0.012)LS(0.987)DS(0.001)EIETNSATSTIFGK 436.06 2.71E-174 2637848000 906422 820294 971093 862207 1098381 1137068 1041102 959631 1016863 886464 TRUE FALSE 942208.2405 961173.1135 996400.4813 1032748.971 911678.59 873001.1894 959497.7048 946768.7161 980266.2993 1060149.648 0.888750227 0.906639091 0.939867766 0.974153953 0.859952735 0.823469772 0.90505874 0.893051955 0.924648988 1 20.0158365 0.854164897 3.152136684 0.999973623 0.899283519 0.385019971 0.038469952 0.727696867 13.13877767 0.039659558 0.010338153 7.147676643 -0.854164897 -0.100690103 GTLTLCPYHSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GTLTLCPYHSDR 12 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;;;; 189.33 8.07E-06 3448680000 2718820 3560510 2771900 2998060 3768400 3533420 2691460 3010770 2988330 4028660 FALSE TRUE 2826161.113 4171999.896 2844137.991 3591067.32 3127848.714 2712836.754 2480496.332 2970415.553 2880780.587 4817998.794 0.586584023 0.865919664 0.590315214 0.745344172 0.649200809 0.563062979 0.51483955 0.616524761 0.59792057 1 22.2000026 -0.990854751 4.42063067 1.000011846 0.636570814 0.565380063 0.095576097 12270935.92 2775834.067 1489.117667 0.022651934 0.102128099 0.990854751 -0.363441033 GTMTTGHNVADLVVILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTMTTGHNVADLVVILK 17 0 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 79.013 0.0065099 0 142150 107480 150770 136050 191960 171960 146220 154390 161340 163200 FALSE TRUE 147762.1918 125938.8539 154699.1901 162960.2839 159330.7078 132024.8961 134758.8943 152320.6546 155533.4049 195175.9153 0.757071852 0.64525817 0.792614139 0.834940539 0.816344104 0.676440512 0.690448379 0.780427515 0.796888308 1 17.57441551 0.688984835 1.678030599 0.999744232 0.747295796 0.62448821 0.058327788 0.812681202 3.364678376 0.058969713 0.01677399 4.886352969 -0.688984835 -0.252448436 GTPCERPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTPCERPVR 9 1 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;C9JPY0;C9JVS0;F8WAZ5 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 123.88 0.00049725 192840000 47939 66178 54942 61894 82261 81071 49261 58541 58759 73106 FALSE TRUE 49831.66874 77543.55671 56373.83366 74136.44846 68278.3046 62243.48889 45399.7941 57756.35365 56644.27507 87429.721 0.569962573 0.886924444 0.644790273 0.847954764 0.780950732 0.71192597 0.519271863 0.660603202 0.647883516 1 16.41583617 -1.143589365 4.910066518 1.00001886 0.697604555 0.407591891 0.109692547 2.27E-05 3.96E-06 0.106395894 0.02507619 0.07184733 1.143589365 -0.302414305 GTPGPPPAHGAALQPHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTPGPPPAHGAALQPHPR 18 0 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 205.42 5.58E-16 879950000 465880 543180 487760 528140 517660 616410 484270 502910 489440 621620 FALSE TRUE 484273.3021 636466.9396 500471.4263 632604.5157 429668.3381 473258.1193 446311.652 496169.314 471825.15 743414.5374 0.651417584 0.856140024 0.673206403 0.850944505 0.577966016 0.636600571 0.600353678 0.66741944 0.634673021 1 19.50380737 -1.202297015 4.439766979 1.00008644 0.683613899 0.524559214 0.090482693 8.15E-05 1.46E-05 0.087646006 0.020652446 0.062762898 1.202297015 -0.316472541 GTPKPPGPPAQPPGPPNASS(ph)NPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTPKPPGPPAQPPGPPNASSNPDLR 25 1 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 GTPKPPGPPAQPPGPPNAS(0.179)S(0.821)NPDLR 106.49 0.002344 177130000 30004 44831 31516 41573 37252 51030 35671 44099 38486 62406 TRUE FALSE 31188.58109 52530.37551 32337.33285 49796.01532 30919.91835 39179.05587 32875.01381 43507.92504 37100.89638 74633.26086 0.417891175 0.703846715 0.43328313 0.667209428 0.414291403 0.524954362 0.440487437 0.582956239 0.497109411 1 16.1875311 -1.612762562 4.138852868 1.011851595 0.525216519 0.683900033 0.097800083 0.00958342 0.000896639 0.084849243 0.019762863 0.02439144 1.612762562 -0.486635076 GTPLGTPAT(ph)SPPPAPLCHSDDYVHISLPQATVTPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTPLGTPATSPPPAPLCHSDDYVHISLPQATVTPPR 36 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6W1;Q59IT9 A0A2R8YFV7 TSC1 Hamartin 1 GTPLGT(0.004)PAT(0.497)S(0.497)PPPAPLCHS(0.001)DDYVHISLPQATVTPPR;GTPLGT(0.016)PAT(0.492)S(0.492)PPPAPLCHSDDYVHISLPQATVTPPR 104 5.19E-05 687700000 29767 148587 123700 166917 143953 216124 120747 169643 109013 193241 TRUE FALSE 30942.22415 174105.6614 126923.7236 199932.6844 119483.9205 165932.4764 111282.5346 167369.2131 105089.6434 231102.8741 0.133889396 0.753368655 0.549208763 0.86512418 0.51701616 0.718002651 0.481528129 0.724219522 0.45473101 1 17.81817568 -2.663686794 2.034050425 9.999912854 0.59796739 0.289945482 0.196021455 4396043.384 177559.6792 183079968.9 0.044077779 0.002169268 2.663686794 -9.401945464 GTPLIS(ph)PLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTPLISPLIK 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 1 GT(0.001)PLIS(0.999)PLIK;GTPLIS(1)PLIK;GTPLIS(1)PLIK 155.99 1.23E-05 126761000 331864 262425 323755 295777 433211 453937 421315 330960 357859 327891 TRUE FALSE 344966.247 307494.4524 332192.3213 354280.8078 359573.949 348517.0112 388291.2294 326524.0225 344979.7245 392134.9636 0.879713055 0.784154643 0.847137726 0.903466512 0.916964776 0.88876801 0.99019793 0.832682757 0.879747425 1 18.58099076 3.789793354 3.817281873 0.908376146 0.828922457 0.323275628 0.05172395 0.273796957 8.289619855 0.013292389 0.024645047 6163.016841 -3.789793354 -0.079453689 GTPLT(ph)PPACACSSLQVEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTPLTPPACACSSLQVEVER 20 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 GTPLT(1)PPACACSSLQVEVER;GTPLT(1)PPACACSSLQVEVER 176.76 4.86E-15 112050000 83897 79956 89637 88335 105177 110639 87856 86627 85450 93020 TRUE FALSE 87209.31834 93687.82103 91973.01386 105807.3993 87299.05111 84944.769 80969.61715 85465.90676 82374.67119 111245.488 0.783935779 0.842171873 0.826757251 0.951116321 0.784742399 0.763579454 0.727846303 0.768264028 0.740476514 1 16.7633873 3.039906146 24.97340395 0.778062328 0.85104577 0.063451865 0.082875194 275.5341198 172428.471 0.022366905 0.026733535 1096.241265 -3.039906146 0.072983443 GTPSQS(ph)PVVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.046)QS(0.954)PVVGR;GTPSQS(1)PVVGR;GTPSQS(1)PVVGR;GTPSQS(1)PVVGR;GTPS(0.041)QS(0.958)PVVGR;GTPS(0.001)QS(0.999)PVVGR;GTPS(0.017)QS(0.982)PVVGR 233.7 1.85E-15 21869225000 6841847 6678295 6741270 6728848 8252486 8122997 7335311 6961901 6699207 7300436 TRUE FALSE 7111968.403 7825240.216 6916953.034 8059794.051 6849731.377 6236554.052 6760350.157 6868588.104 6458103.849 8730816.659 0.814582264 0.896278152 0.792245824 0.923143202 0.784546469 0.714315086 0.774309028 0.786706258 0.739690696 1 23.05768518 3.119433653 15.76887138 0.783609426 0.854801374 0.08496284 0.080977314 1.531158015 201.8615659 0.021421795 0.025604815 1316.538772 -3.119433653 0.071191948 GTQEVAPPTPLT(ph)PT(ph)SHTANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 2 GTQEVAPPT(0.003)PLT(0.649)PT(0.298)S(0.293)HT(0.276)ANT(0.245)S(0.231)PRPVS(0.004)GMER;GTQEVAPPTPLT(0.999)PT(0.324)S(0.284)HT(0.171)ANT(0.117)S(0.104)PRPVS(0.001)GMER 109.84 0.00026294 124176000 69003 72520 72746 72085 73046 90555 80995 71027 74761 83433 TRUE FALSE 71727.29172 84974.74587 74641.82052 86343.19785 60629.66701 69524.97362 74646.40026 70074.99924 72070.36621 99780.09893 0.718853684 0.851620181 0.748063204 0.865334859 0.607632861 0.696781967 0.748109103 0.702294345 0.72229199 1 16.60646448 -1.013792677 4.143956539 1.000020197 0.739729977 0.549324935 0.07061952 4204212.076 1542800.828 780.2818426 0.016526713 0.09687402 1.013792677 -0.26029022 GTQEVAPPTPLT(ph)PTSHTANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.996)PT(0.002)S(0.002)HTANTSPRPVSGMER;GTQEVAPPTPLT(1)PTSHTANTSPRPVSGMER;GTQEVAPPTPLT(0.917)PT(0.064)S(0.013)HT(0.001)ANT(0.002)S(0.002)PRPVS(0.002)GMER 167.16 3.79E-12 715080000 52576.9 87559 90705 88867 96980 106488 105811 93627 96954 95191 TRUE FALSE 54652.67661 102596.5771 93068.84681 106444.6274 80495.37424 81757.77584 97517.25733 92372.08321 93464.64448 113841.8539 0.480075427 0.901220189 0.817527505 0.935021907 0.707080669 0.718169751 0.856602857 0.811407053 0.821004238 1 16.79667154 -5 0.118418698 1.650207539 0.690123974 0.27849679 0.117086432 229.0904785 1.767105418 36.08946777 1.139246673 1.00E-05 5 -0.960083565 GTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLT(0.008)PT(0.47)S(0.47)HT(0.033)ANT(0.008)S(0.008)PRPVS(0.002)GMER;GTQEVAPPTPLTPT(0.298)S(0.298)HT(0.298)ANT(0.048)S(0.048)PRPVS(0.009)GMER;GTQEVAPPTPLT(0.015)PT(0.187)S(0.187)HT(0.187)ANT(0.187)S(0.187)PRPVS(0.051)GMER;GTQEVAPPTPLT(0.052)PT(0.187)S(0.187)HT(0.187)ANT(0.187)S(0.187)PRPVS(0.015)GMER 98.795 0.0011494 1835830000 125970.2 109270 93567 128082 132699 132041.4 97682 100160 100532 104928.2 TRUE FALSE 130943.6008 128036.2725 96005.43289 153416.2373 110142.8714 101376.786 90025.4296 98817.51903 96913.87296 125486.8718 1.043484461 1.020316075 0.76506356 1.222568027 0.877724257 0.807867664 0.717409146 0.787472965 0.772302884 1 16.93717691 3.008063457 24.99464007 0.799277281 1.002498034 0.351468239 0.124392949 191.8972917 594826.7761 0.034344599 0.040984761 1018.74023 -3.008063457 0.203220752 GTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.063)S(0.063)HT(0.291)ANT(0.291)S(0.291)PRPVS(0.001)GMER;GTQEVAPPTPLTPT(0.061)S(0.061)HT(0.292)ANT(0.292)S(0.292)PRPVS(0.003)GMER 134.78 6.87E-06 900380000 56947 70851 75034 84601 75403 88129 61496 59153 71252 73129 TRUE FALSE 59195.31153 83019.10811 76989.44768 101334.8253 62586.02499 67662.37536 56675.78283 58360.15079 68687.65444 87457.22741 0.67684871 0.94925383 0.880309724 1.158678685 0.715618673 0.773662479 0.648040013 0.667299348 0.785385685 1 16.41628999 GTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.03)S(0.03)HT(0.072)ANT(0.429)S(0.429)PRPVS(0.011)GMER 136.55 5.76E-06 551610000 117710 38749 45520 49214 60944 99369 61623 42315 38903 37713 TRUE FALSE 122357.2817 45403.83932 46706.2886 58948.38231 50584.76065 76292.0557 56792.82824 41747.83664 37502.88863 45102.14029 2.712893022 1.00668924 1.035567011 1.306997449 1.121560093 1.691539586 1.259204727 0.925628726 0.831510176 1 15.46090828 4.7416087 24.99632129 1.143959809 2.712893596 0.807422403 0.231693331 127.8294916 1048236.128 0.058725396 0.4165125 55158.02407 -4.7416087 1.568933787 GTQEVAPPTPLTPTSHTANTS(ph)PRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTQEVAPPTPLTPTSHTANTSPRPVSGMER 30 1 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 GTQEVAPPTPLTPT(0.003)S(0.003)HT(0.081)ANT(0.387)S(0.524)PRPVS(0.001)GMER;GTQEVAPPTPLTPT(0.034)S(0.102)HT(0.102)ANT(0.31)S(0.449)PRPVS(0.002)GMER 143.22 2.80E-08 3476200000 260628 349050 298800 301900 277245 360830 307270 301850 308080 278700 TRUE FALSE 270917.7947 408996.6223 306586.9735 361614.9189 230118.9939 277032.7009 283185.3745 297804.1945 296992.261 333305.929 0.812820209 1.22709075 0.919836543 1.084933953 0.690413743 0.831166436 0.849625974 0.89348604 0.891050039 1 18.34648746 3.262799882 24.98283235 0.854842968 1.020069417 0.266000476 0.123111243 274.5380133 282957.778 0.03174658 0.042964266 1831.470307 -3.262799882 0.165226448 GTQSIPNDS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTQSIPNDSPAR 12 0 Q9NQ92;H9KV77;J3QRX6 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 1 GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR 239.38 3.79E-16 704370000 1181210 1221020 1121210 1343930 1123320 1373080 1379450 1249440 1099200 992030 TRUE FALSE 1227845.083 1430720.687 1150429.654 1609755.343 932378.4676 1054202.979 1271325.104 1232693.3 1059640.007 1186399.285 1.034934106 1.205935223 0.969681682 1.356841127 0.78588927 0.888573512 1.071582831 1.039020603 0.893156309 1 20.1781582 3.228657154 24.9999938 0.960371261 1.13412812 0.372844016 0.123239804 241.877169 610586.4311 0.035182974 0.042534948 1693.000762 -3.228657154 0.173756859 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.1)S(0.9)PRPPEGGLGYSQLGDDDLK;GT(0.018)S(0.982)PRPPEGGLGYSQLGDDDLK 197.1 1.24E-22 524580000 685280 403810 515900 479200 589090 738240 823390 553600 550170 301140 TRUE FALSE 712335.3836 473161.2263 529344.7778 573984.3297 488956.6922 566794.9481 758850.5403 546179.8975 530369.4892 360142.6173 1.977925825 1.313816259 1.469819878 1.593769529 1.357675178 1.573806933 2.107083427 1.51656558 1.472665171 1 18.4582088 2.481649582 24.99576669 1.613424216 1.522395377 0 0.305808408 1105.146987 6100307.977 0.100182407 0.085802411 303.1444221 -2.481649582 -0.091028839 GTS(ph)PRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF ddPTM_MDA-MB-175_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(0.476)S(0.522)PRPPEGGLGY(0.001)S(0.001)QLGDDDLKETGFHLTTTNQGASAAGPGFSLKF 130.45 8.72E-11 484520000 219260 200210 237310 167060 363860 309290 234930 257280 276780 228670 TRUE FALSE 227916.5541 234594.5101 243494.4936 200103.9694 302011.2072 237462.0848 216515.5727 253831.5824 266818.7419 273473.5083 0.833413648 0.857832671 0.890376896 0.731712445 1.104352699 0.868318421 0.79172412 0.928176129 0.975665773 1 18.06104156 -4.999963127 0.050083102 1.520184131 0.630680317 0.187847837 0.092607492 976.477913 3.617276011 66.60410101 14.87860257 1.00E-05 4.999963127 -0.889503814 GTS(ph)PSSSSRPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GT(0.064)S(0.936)PSSSSRPQR;GT(0.231)S(0.768)PS(0.001)SSSRPQR;GT(0.039)S(0.961)PSSSSRPQR 148.08 4.00E-05 5205650000 1675640 1921770 1767440 1855630 1777400 2098300 1733520 1696840 1638380 1853660 TRUE FALSE 1741795.561 2251819.048 1813500.938 2222668.075 1475278.183 1611001.625 1597642.173 1674096.635 1579415.024 2216849.187 0.785707739 1.015774579 0.818053366 1.002624847 0.665484234 0.726707813 0.720681489 0.755169384 0.712459392 1 21.0800792 3.235556866 24.99999939 0.747143658 0.907164966 0.286769283 0.107977454 81.89511573 681608.5723 0.027886757 0.034721163 1720.112554 -3.235556866 0.160021307 GTS(ph)PTQIWCNNSQLPVDHILAGSFETAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTSPTQIWCNNSQLPVDHILAGSFETAMR 29 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 GT(0.212)S(0.784)PT(0.004)QIWCNNSQLPVDHILAGSFETAMR 161.14 4.21E-12 101420000 14028 19740 18975 15614 19295 20819 18779 19157 18640 26742 TRUE FALSE 14581.83627 23130.19144 19469.50409 18702.4026 16015.24279 15984.10276 17307.05291 18900.23175 17969.15004 31981.58289 0.455944795 0.723234729 0.608772372 0.584786646 0.500764545 0.499790858 0.541156858 0.590972367 0.561859308 1 14.96495372 -0.635807855 1.307609257 1.0071297 0.566529424 0.778131558 0.069973225 72.33718266 54.3119326 2.767493258 0.019871319 0.231308794 0.635807855 -0.440600276 GTS(ph)SPDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.053)S(0.473)S(0.473)PDYR 77.732 0.034041 269910000 103200 172650 180480 181320 172110 213910 187530 174790 164420 198290 TRUE FALSE 107274.4157 202301.2945 185183.4571 217184.5548 142854.8037 164232.6443 172830.9086 172447.2259 158502.5563 237141.129 0.45236529 0.853083964 0.780899787 0.915845158 0.602404164 0.692552342 0.728810347 0.727192397 0.668389144 1 17.85538638 -1.500356053 2.924993084 1.009570928 0.722794713 0.328854837 0.122137634 51389827.66 57246718.12 3946259.699 0.027893796 0.031596862 1.500356053 -0.286776215 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPT(ph)TPLSVGTIVPPPRPASRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTSDLLAWDPLFGPSLDSSSSSSLTSSSSARPTTPLSVGTIVPPPRPASRPK 52 3 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 GTSDLLAWDPLFGPSLDSSSSS(0.001)S(0.001)LT(0.001)S(0.001)S(0.004)S(0.004)S(0.018)ARPT(0.424)T(0.424)PLS(0.098)VGT(0.024)IVPPPRPAS(0.002)RPK 135.53 1.54E-14 373460000 68056 72890 83488 62712 94630 99834 75940 78325 72181 77689 TRUE FALSE 70742.90343 85408.29049 85663.76587 75116.24642 78544.8264 76649.0665 69987.62437 77275.18149 69583.21991 92910.6721 0.761407725 0.91925167 0.922001358 0.80847813 0.845380026 0.824975912 0.753278636 0.831714805 0.74892602 1 16.5035567 3.706641345 24.5023888 0.819916207 0.872723426 0.033143817 0.077355523 1191.487193 914628.5744 0.019162747 0.029690312 5089.104221 -3.706641345 0.052807219 GTSGS(ph)LADVFANTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTSGSLADVFANTR 14 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 GTSGS(1)LADVFANTR;GTS(0.001)GS(0.999)LADVFANTR 226.39 2.54E-12 126278000 184602 213650 206783 233050 238560 233840 195588 200168 180306 239860 TRUE FALSE 191890.2295 250342.7255 212171.9349 279146.5944 198009.6564 179534.2039 180257.3015 197485.0754 173816.8223 286855.9746 0.668942767 0.872712259 0.739646211 0.973124561 0.690275518 0.625868797 0.628389566 0.688446792 0.605937605 1 18.12996704 3.045680062 24.99799237 0.681288344 0.814939933 0.12376715 0.129815268 192.1073306 105127.7076 0.03442489 0.041145602 1110.913032 -3.045680062 0.133651588 GTSKEDAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTSKEDAMK 9 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 71.016 0.053283 49877000 113430 67497 73468 65709 104970 109690 121390 87773 104660 66629 FALSE TRUE 117908.304 79089.0847 75382.63643 78706.04408 87127.23689 84216.15987 111875.1346 86596.5465 100893.307 79683.67686 1.47970461 0.992538093 0.94602357 0.987731078 1.093413862 1.056880947 1.403990617 1.086753899 1.266172835 1 16.2819966 GTSPSSSS(ph)RPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTSPSSSSRPQR 12 1 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 GTS(0.004)PS(0.006)S(0.046)S(0.046)S(0.897)RPQR 147.1 0.00017178 344240000 553360 698150 629330 661560 655460 778240 615820 640490 601750 677740 TRUE FALSE 575207.0801 818051.8316 645730.8568 792414.5934 544045.1433 597505.5543 567550.4193 631905.2792 580093.135 810530.1769 0.709667692 1.009279919 0.796677132 0.977649711 0.67122133 0.737178666 0.700221208 0.779619683 0.715695913 1 19.62850637 3.233220757 24.99999978 0.752198648 0.877555743 0.158911545 0.116220614 188.0291618 880309.2592 0.03022617 0.037139813 1710.884759 -3.233220757 0.125357096 GTSS(ph)PDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTSSPDYR 8 0 Q66K14-2;Q66K14;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 GT(0.006)S(0.052)S(0.942)PDYR;GT(0.002)S(0.034)S(0.964)PDYR;GT(0.005)S(0.043)S(0.952)PDYR;GT(0.002)S(0.036)S(0.962)PDYR 145.63 0.00059395 2245210000 2642330 3097940 2844840 3091440 3059630 3437040 2829990 2899030 2799380 3163990 TRUE FALSE 2746651.229 3629987.096 2918978.867 3702917.605 2539555.185 2638839.549 2608167.989 2860173.245 2698630.861 3783913.262 0.725875843 0.959320905 0.771418018 0.978594737 0.67114519 0.697383731 0.689277953 0.755877063 0.71318518 1 21.85144759 3.222394658 24.99982859 0.736436401 0.859740571 0.158635308 0.113207576 338.8715197 524046.4095 0.029802816 0.035723485 1668.762985 -3.222394658 0.12330417 GTSYQSPHGIPIDLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTSYQSPHGIPIDLLDR 17 0 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 ;;; 117.29 0.00022445 1954960000 852720 973720 1059890 1174360 1206200 1326270 1227000 1087150 1064390 872210 FALSE TRUE 886386.044 1140948.836 1087511.604 1406644.903 1001170.555 1018263.892 1130824.534 1072578.532 1026082.812 1043102.85 0.849759009 1.093802817 1.042573706 1.348519854 0.959800421 0.976187432 1.084096869 1.028257695 0.98368326 1 19.99244998 GTTGTQASFLQLFEGDDHKVEQLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTTGTQASFLQLFEGDDHKVEQLDK 25 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;A0A096LNY6;A0A096LP92;A0A096LPA2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 140.55 2.34E-07 313300000 103990 114670 136480 94730 189660 169360 102530 113300 148110 117210 FALSE TRUE 108095.6055 134363.6805 140036.7809 113467.3113 157421.6609 130028.7067 94493.43069 111781.3988 142779.55 140175.0554 0.771147229 0.958542018 0.999013559 0.809468639 1.123036196 0.927616589 0.674110172 0.797441446 1.018580301 1 17.09687011 1.215171616 24.845708 1.009290389 0.881441621 0.148065579 0.121584395 515.0263154 547087.4836 0.122715345 0.030756101 16.41238198 -1.215171616 -0.127848768 GTTITLVLKEEASDYLELDTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GTTITLVLKEEASDYLELDTIK 22 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;; 190.88 1.48E-17 224384000 329368 222633.3 291728 185460.7 468006 338666 270617 256808 340941 201637 FALSE TRUE 342371.703 260868.8374 299330.6713 222144.2729 388454.5073 260015.954 249405.3324 253365.9088 328670.6 241143.9096 1.419781671 1.08179733 1.24129476 0.921210381 1.610882514 1.078260506 1.034259305 1.050683425 1.362964549 1 17.87953485 GTTTVDGAGFGIDRPAELSKEDDEYEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTTTVDGAGFGIDRPAELSKEDDEYEAFR 29 2 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 0 57.688 0.026831 80116000 39804 21880 33465 29516 48565 44086 37964 35653 38816 28461 FALSE TRUE 41375.49266 25637.7198 34337.12539 35354.1767 40309.93865 33847.69463 34988.28248 35175.12985 37419.01974 34037.38803 1.215589534 0.753222303 1.008806121 1.038686537 1.184284135 0.994426911 1.027936763 1.033426238 1.099350506 1 15.05483271 3.877283927 4.577341568 1.054848946 0.962989244 0.047188359 0.116341944 0.498098781 16.29967 0.028167847 0.053121217 7538.482426 -3.877283927 -0.091859703 GTTVTPDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTTVTPDKR 9 1 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ; 97.431 0.010737 235947000 263860 207870 246680 214332 323410 273970 311010 246280 254150 245120 FALSE TRUE 274277.3965 243570.0555 253108.6834 256726.2299 268436.8837 210344.6196 286632.2235 242979.0194 245003.1911 293146.5709 0.935632287 0.830881476 0.863420243 0.875760645 0.915708763 0.717540781 0.977777849 0.828865297 0.835770278 1 18.16126266 -1.052735006 4.974406458 1.000002649 0.863505966 0.266121568 0.067435171 1.79E-06 3.41E-07 0.05900508 0.013907361 0.088565585 1.052735006 -0.136496683 GTVGEPTYDAEFQHFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 331.14 5.20E-72 1868760000 1227790 1431450 1477260 1564850 1436790 1638600 1486790 1377090 1374410 1466470 FALSE TRUE 1276264.097 1677290.402 1515758.609 1874372.659 1192564.949 1258059.983 1370251.515 1358632.361 1324945.253 1753796.719 0.727714953 0.956376748 0.864272691 1.068751377 0.679990409 0.717335122 0.781305781 0.774680638 0.755472535 1 20.74205011 3.217438282 24.9998001 0.770561334 0.905142751 0.207003394 0.112508711 315.1459981 372997.1095 0.030550869 0.036549366 1649.826526 -3.217438282 0.134581417 GTVLLADNVICPGAPDFLAHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTVLLADNVICPGAPDFLAHVR 22 0 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 184.56 3.86E-17 3701000000 780520 932740 877700 1019690 878040 1078020 972890 1035880 875660 901120 FALSE TRUE 811335.5323 1092930.839 900573.583 1221381.639 728791.0744 827666.1926 896632.3396 1021995.723 844145.1677 1077677.211 0.752855794 1.014154172 0.835661712 1.133346447 0.676261006 0.768009367 0.832004547 0.948331943 0.783300564 1 20.03949369 5.035943651 11.47548234 0.88257472 0.417533115 0.087444551 0.129852404 96634.10309 1138422.544 0.02996377 824620.9889 108628.4671 -5.035943651 -0.465041605 GTVQALHATGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTVQALHATGAR 12 0 Q7Z4W1;J3KS22;J3QS36 Q7Z4W1 DCXR L-xylulose reductase 0 ;; 178.15 2.24E-05 422610000 448968 927950 820380 887020 810800 1069300 762980 915220 769720 959490 FALSE TRUE 466693.6033 1087318.194 841759.7767 1062469.909 672980.5056 820971.2804 703175.6339 902952.9729 742017.9276 1147483.695 0.406710444 0.947567446 0.733570142 0.925912859 0.58648372 0.715453548 0.612797931 0.786898304 0.646647905 1 20.13004222 -1.926165752 2.284050486 1.190604847 0.71893214 0.247213153 0.152143142 15163097.6 6969085.157 15426488.87 0.03357465 0.011853163 1.926165752 -0.471672707 GTVSFHSHSDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTVSFHSHSDHR 12 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;;; 171.05 2.28E-05 255174000 37216.7 158283 134106 159609 150218 207608 122547 175731 127124 238770 FALSE TRUE 38686.04405 185466.874 137600.9125 191179.1838 124683.998 159394.1883 112941.4459 173375.6134 122548.8321 285552.41 0.135477911 0.649502044 0.481876208 0.669506462 0.436641379 0.558195913 0.395519148 0.607158642 0.429164062 1 18.12339603 -1.61210547 2.654131885 1.046684968 0.499889514 0.519492405 0.148012167 15362205.99 14086709.59 4974030.877 0.034472329 0.024428372 1.61210547 -0.546795454 HENEALWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HENEALWR 8 0 E9PMQ6;Q00613-2;Q00613;E9PI02 E9PMQ6 HSF1 Heat shock factor protein 1 0 110.76 0.0033646 47062000 47253 19908 16850 20201 23462 26808 24075 21155 20273 17630 FALSE TRUE 49118.58493 23327.04414 17289.12484 24196.69751 19473.93762 20582.24828 22187.93859 20871.45183 19543.37869 21084.26095 2.329632755 1.106372388 0.820001464 1.147618954 0.923624388 0.97619017 1.052346043 0.989906731 0.926917891 1 14.36387883 4.735098924 4.235811229 0.985454077 2.430502706 0.960708797 0.081392424 0.032323717 1.336281648 0.017867878 0.140940735 54337.40874 -4.735098924 1.445048629 up GTVTDFPGFDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 275.13 1.89E-27 3591440000 3261730 4074920 3584680 3766380 3798900 4214610 2751930 3612300 3359230 4127800 FALSE TRUE 3390505.619 4774755.812 3678099.706 4511358.722 3153164.335 3235830.701 2536226.536 3563883.027 3238331.968 4936563.378 0.686814968 0.967222629 0.745072923 0.913866262 0.638736727 0.655482459 0.513763592 0.721936042 0.655989141 1 22.23507562 3.227769133 24.99779909 0.672213249 0.832230426 0.16271233 0.137955083 284.6688359 659416.5807 0.036617627 0.044177257 1689.542546 -3.227769133 0.160017177 GTVTDFPGFDERADAETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTVTDFPGFDERADAETLR 19 1 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 147.56 9.50E-08 82510000 48330 72841 62543 49522 76951 78173 78852 53863 66083 131050 FALSE TRUE 50238.10572 85350.87513 64172.92196 59317.30379 63870.89651 60018.50547 72671.3742 53141.05459 63704.68574 156726.7384 0.320545851 0.544584007 0.409457395 0.378475967 0.407530311 0.382950006 0.463682043 0.33906821 0.406469798 1 17.25789181 -1.263769484 3.535450893 1.001480244 0.406235612 0.899185606 0.059682069 30839941.73 48800976.96 494450.1192 0.014008912 0.054479174 1.263769484 -0.595244633 GTWERPGGAAPLGYDFWYQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GTWERPGGAAPLGYDFWYQPR 21 1 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ; 213.72 2.30E-23 2341700000 242453 300432 283440 289772 301960 351640 297030 283180 288610 308100 FALSE TRUE 252025.2317 352028.859 290826.6792 347088.0367 250632.9471 269976.9392 273748.0125 279384.4353 278222.9825 368466.2961 0.68398449 0.955389578 0.789289773 0.941980421 0.680205896 0.73270457 0.742939084 0.758236067 0.75508394 1 18.49117314 5.028694215 17.28417642 0.801695811 0.315321695 0.111665115 0.104791873 122150977.3 1909848564 0.024094472 1745836820 106830.2427 -5.028694215 -0.486374116 GTYFPTWEGLFWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTYFPTWEGLFWEK 14 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 166.04 9.00E-06 64534000 46180 43435 46016 39860 59703 55339 51110 48955 51675 41052 FALSE TRUE 48003.22206 50894.62337 47215.21476 47744.18903 49554.70539 42487.35592 47103.86465 48298.8383 49815.22684 49095.35341 0.977754894 1.036648478 0.961704346 0.972478773 1.009356323 0.865404829 0.959436309 0.983776161 1.014662761 1 15.58329887 1.436764206 4.123420043 1.006572216 0.969136861 0.117815665 0.041584993 0.491235832 15.15923391 0.030512215 0.011094212 27.33784055 -1.436764206 -0.037435354 GTYHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GTYHNK 6 0 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;; 98.03 0.040398 698180000 1592960 1483630 1734360 1374170 2001330 1809410 1903250 1676400 1876490 1743580 FALSE TRUE 1655851.291 1738431.911 1779558.846 1645976.725 1661144.641 1389201.949 1754068.292 1653930.6 1808955.491 2085201.118 0.794096683 0.833699875 0.853423121 0.789361137 0.796635215 0.666219645 0.841198615 0.793175577 0.867520872 1 20.99175511 0.865455359 1.944146703 1.000002933 0.795258113 0.621160261 0.048780492 0.34515764 2.550334969 0.047142936 0.01315539 7.335933052 -0.865455359 -0.20474482 GTYVPSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 GTYVPS(0.007)S(0.991)PT(0.002)R;GTYVPS(0.002)S(0.989)PT(0.008)R;GTYVPSS(1)PTR;GTYVPS(0.002)S(0.998)PTR 183.4 1.75E-06 13828500000 12330400 14846800 13794500 14983800 15846200 17390700 13775800 14275500 13138300 17421800 TRUE FALSE 12817213.71 17396622.41 14153996 17947550.92 13152668.58 13351973.48 12696016.8 14084160.27 12665455.15 20835268.15 0.615169127 0.834960332 0.679328718 0.861402445 0.631269465 0.640835212 0.609352215 0.675976914 0.607885392 1 24.31252433 -1.006764546 4.499786935 1.000010633 0.686675173 0.544370748 0.086693373 0.138097202 51548218.14 1253.431232 0.020117568 0.098454473 1.006764546 -0.313335459 GVAGAHGLLCLLSDHVDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVAGAHGLLCLLSDHVDKR 19 1 U3KQ56;Q9UBQ7 U3KQ56 GRHPR Glyoxylate reductase/hydroxypyruvate reductase 0 132.47 5.52E-06 618460000 129580 177750 210410 193960 221720 255980 241500 224650 210250 217170 FALSE TRUE 134695.9185 208277.1798 215893.4575 232324.7091 184032.1136 196532.5244 222570.599 221638.9342 202683.1436 259720.3035 0.518619132 0.801928756 0.831253678 0.894518857 0.708578078 0.756708358 0.856962648 0.853375463 0.780390061 1 17.98659927 6.944694925 0.058887649 1.251191217 6.73E-18 0.438716375 0.090462579 311.3676774 1.667746913 8.39639539 35.48440667 8804301.875 -6.944694925 -1.251191217 GVAINMVTEEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVAINMVTEEDKR 13 1 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 141.59 6.40E-05 98870000 69417 59993 58771 58497 74101 76296 74322 63194 60650 63674 FALSE TRUE 72157.63676 70296.33107 60302.62054 70067.532 61505.33849 58577.41028 68496.44744 62346.98779 58467.21835 76149.70119 0.947576099 0.92313338 0.791895695 0.920128785 0.807689821 0.769240186 0.899497258 0.818742383 0.767793142 1 16.21655076 4.368357283 6.362361279 0.840785263 0.941327149 0.20057525 0.070423668 0.262545666 13.4176827 0.015821264 0.044382835 23353.7853 -4.368357283 0.100541886 GVAPADS(ph)PEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 227.06 1.45E-11 2160170000 975610 943542 873574 931669 908882 1154090 972640 886878 842514 939325 TRUE FALSE 1014127.836 1105587.999 896340.0561 1115950.347 754390.5623 886070.0879 896401.9353 874990.851 812192.0857 1123367.749 0.902756766 0.984172814 0.797904388 0.993397174 0.671543724 0.788762263 0.797959471 0.778899743 0.72299751 1 20.09939886 3.247353163 24.99999663 0.782429039 0.915483604 0.297904369 0.093933048 213.4886249 607012.1397 0.02400086 0.032012974 1767.474525 -3.247353163 0.133054566 GVAPADS(ph)PEAPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR 182.1 7.04E-06 2350860000 1552160 1773550 1630230 1688860 1759540 1792580 1565120 1534280 1453440 1696320 TRUE FALSE 1613440.475 2078143.416 1672715.133 2022911.467 1460454.019 1376280.462 1442441.805 1513715.486 1401130.978 2028681.426 0.795314856 1.024381349 0.824533173 0.997155808 0.719903086 0.678411329 0.711024307 0.746157315 0.690660919 1 20.9521109 3.22464251 24.99930346 0.738582331 0.91236215 0.315453382 0.107969552 222.1854904 399082.4282 0.02832065 0.03401149 1677.422678 -3.22464251 0.173779819 GVCHIPMAEPFCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVCHIPMAEPFCPK 14 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 83.047 0.0090134 357080000 200980 185020 166950 175890 220530 212780 206160 189700 177980 187140 FALSE TRUE 208914.8456 216795.7457 171300.8542 210680.517 183044.3894 163365.0697 190000.6405 187157.3818 171574.5346 223806.5 0.933461922 0.96867493 0.765397136 0.941351199 0.81786896 0.729938897 0.848950502 0.836246408 0.76661998 1 17.77189241 4.253965236 24.99571135 0.832410667 0.951068496 0.249436742 0.077713353 292.1565948 474048.0692 0.017592051 0.047803003 17945.89971 -4.253965236 0.118657829 GVCLIDEFDKMNDQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVCLIDEFDKMNDQDR 16 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 ; 205.95 1.94E-11 227970000 439440 313610 369200 294690 489360 470200 425390 392400 432500 374270 FALSE TRUE 456789.4305 367470.078 378821.6553 352978.8024 406178.762 361003.1759 392046.8203 387140.5198 416934.4095 447601.0407 1.02052808 0.820976818 0.846337745 0.788601389 0.907457144 0.806528902 0.875884515 0.86492319 0.931486685 1 18.77185387 1.014021848 2.185824503 0.999873111 0.860389036 0.319598808 0.061601584 0.32549363 3.343235512 0.054570958 0.015095949 10.32813363 -1.014021848 -0.139484075 GVDDLDFFIGDEAIEKPTYATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVDDLDFFIGDEAIEKPTYATK 22 1 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ; 248.89 2.79E-31 1557690000 1572030 1099690 1389140 1029500 1924920 1586840 1710180 1413060 1523940 1039630 FALSE TRUE 1634094.958 1288553.203 1425342.13 1233132.027 1597722.786 1218320.459 1576131.623 1394120.242 1469093.697 1243325.594 1.314293671 1.03637632 1.146394908 0.99180137 1.285039731 0.979888506 1.267674076 1.121283314 1.181584055 1 20.24577272 4.755782739 24.00843044 1.121705025 1.314293941 0.244153566 0.105480069 2875.6693 4008700.26 0.02262329 0.645451902 56987.91125 -4.755782739 0.192588916 GVDIYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVDIYTR 7 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 92.47 0.036399 158980000 48430 75030 66600 57158 69689 84373 65944 67172 62062 67467 FALSE TRUE 50342.0538 87915.81885 68335.65071 68463.6818 57843.28867 64778.64944 60775.13697 66271.66921 59828.40074 80685.86692 0.62392654 1.089606175 0.846934579 0.848521363 0.716894927 0.802850015 0.753231505 0.82135412 0.741497898 1 16.30002837 5.020700348 17.42746067 0.832629223 0.144989551 0.257743118 0.111141624 11918191.06 235405109.2 0.025737296 223680973.9 104881.8521 -5.020700348 -0.687639672 GVDLDAPGSINGVPLLEVDLDSFEDKPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVDLDAPGSINGVPLLEVDLDSFEDKPWR 29 1 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 226.19 9.84E-35 273860000 161709 129021 156880 131225 187959 181840 168908 180512 172764 145610 FALSE TRUE 168093.3962 151179.3531 160968.4217 157180.9133 156009.7963 139610.4158 155668.5496 178092.5319 166546.2574 174139.4916 0.965280159 0.868150881 0.924364831 0.902614978 0.895889811 0.801715995 0.893930194 1.022700424 0.956395679 1 17.40988389 1.761424683 13.34038922 0.992013193 0.890324321 0.542972434 0.041940314 0.27331102 159.3496095 0.019481902 0.010748812 57.73307416 -1.761424683 -0.101688872 GVDLLLEGVQGES(ph)SPTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVDLLLEGVQGESSPTRR 18 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 GVDLLLEGVQGES(0.472)S(0.472)PT(0.055)RR;GVDLLLEGVQGES(0.499)S(0.499)PT(0.002)RR 117.6 7.78E-05 116380000 41134 48638 44248 49737 48423 53291 46272 45666 45773 50162 TRUE FALSE 42758.00208 56991.19815 45401.13923 59574.83015 40192.07576 40914.97288 42645.07973 45053.92196 44125.63867 59990.28349 0.712748792 0.950007148 0.756808213 0.993074656 0.669976426 0.682026663 0.710866448 0.751020321 0.735546427 1 15.87244123 5.058082337 15.16562978 0.790457757 0.122210362 0.036960771 0.121954194 4556686.903 29896092.5 0.028383077 91607278.38 114309.5032 -5.058082337 -0.668247395 GVDLVLNSLAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 225.13 3.02E-11 439246000 1245220 868196 1081152 979560 1449490 1400780 1271450 997941 1100437 913490 FALSE TRUE 1294382.247 1017301.909 1109327.709 1173314.044 1203106.208 1075470.074 1171790.427 984565.2332 1060832.487 1092470.876 1.184820828 0.93119362 1.015430007 1.074000296 1.101270738 0.984438211 1.072605644 0.9012279 0.971039605 1 20.05916339 1.746987552 25 0.950489923 1.046062061 0.281075886 0.06856965 2.378712175 7074.347203 0.030215549 0.016756035 55.84541883 -1.746987552 0.095572138 GVDNEDDHGRGDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVDNEDDHGRGDLGR 15 1 P10600-2;P10600 P10600-2 TGFB3 Transforming growth factor beta-3;Latency-associated peptide 0 125.28 5.49E-05 209080000 77255 92427 77206 85365 89598 106320 65457 80133 58668 96991 FALSE TRUE 80305.08705 108300.6183 79218.05179 102249.9422 74368.16396 81628.7913 60326.3093 79058.94821 56556.55014 115994.5294 0.692317883 0.933670051 0.682946447 0.881506591 0.641135098 0.703729665 0.520078917 0.6815748 0.487579461 1 16.82369724 3.219455629 24.6332153 0.649548992 0.799138526 0.135847435 0.148202236 309.5516864 399122.6485 0.039034371 0.046728544 1657.507982 -3.219455629 0.149589533 GVEEEEEDGEMRE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 ; 233.54 2.98E-16 1736420000 613630 881990 818740 827810 889350 965720 830160 853470 791070 1065840 FALSE TRUE 637856.5862 1033464.922 840077.037 991548.3472 738178.6047 741446.1656 765089.89 842030.6306 762599.5452 1274670.941 0.500408824 0.810769971 0.659054043 0.777885739 0.579113072 0.581676527 0.600225411 0.660586669 0.598271695 1 20.28169343 -1.455326928 3.59529211 1.003894091 0.64623 0.594079223 0.088954637 14186832.05 5750342.741 429313.7579 0.01992775 0.035048793 1.455326928 -0.357664092 GVESVFDIMEMEDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVESVFDIMEMEDEER 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 134.08 7.04E-05 53791000 35920 43812 47373 54984 37676 54368 55589 50079 44926 36172 FALSE TRUE 37338.14934 51336.37019 48607.5793 65859.67109 31271.84698 41741.85596 51231.78893 49407.77292 43309.12204 43259.21085 0.863125993 1.186715365 1.123635368 1.522442731 0.722894532 0.96492412 1.184297816 1.142133015 1.00115377 1 15.40071973 -0.526832318 0.392116515 0.972864866 1.099843019 0.012394834 0.204491958 51.98200884 7.607379898 1.983702748 0.141195008 0.297281362 0.526832318 0.126978153 GVGDDQLGEESEERDDHLLPM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 GVGDDQLGEESEERDDHLLPM 21 1 P20645;F5GX30;H0YF90 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;;;;;;;; 149.36 8.55E-08 3698990000 3119020 4580450 4194210 4476070 4624530 5017910 3870040 4136350 3976490 4834650 FALSE TRUE 3242161.318 5367106.657 4303514.558 5361423.286 3838454.042 3852576.45 3566696.152 4080908.994 3833376.902 5781907.103 0.560742547 0.928258888 0.744307109 0.92727593 0.663873351 0.666315868 0.616871923 0.705806738 0.662995243 1 22.463114 3.164112733 24.99999995 0.69562382 0.796762834 0.041840096 0.139522274 83.45652067 28022.60003 0.037038625 0.044269639 1459.192984 -3.164112733 0.101139013 GVGDGTVSWGLEDDEDMTLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVGDGTVSWGLEDDEDMTLTR 21 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 ; 116.58 0.00029473 69564000 35358 56846 61552 60733 55142 68450 54491 55241 60262 59401 FALSE TRUE 36753.96114 66608.8583 63156.09569 72745.80613 45768.98254 52553.52487 50219.85303 54500.58475 58093.18239 71039.48865 0.517373673 0.937631444 0.889028016 1.024019282 0.644275225 0.739779042 0.706928695 0.767187177 0.817759017 1 16.11633358 0.847535601 4.89919033 0.99999531 0.785396071 0.185303325 0.138269129 3.058778399 96.85174595 0.131300693 0.033215548 7.039399305 -0.847535601 -0.214599239 GVGISVLEMSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVGISVLEMSHR 12 0 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 94.191 0.0021679 0 354370 514190 533650 466630 538390 627900 500370 494300 445560 512100 FALSE TRUE 368360.8012 602498.1327 547557.3574 558928.0212 446874.6601 482079.7409 461149.6919 487674.717 429524.3826 612436.1903 0.60146805 0.983772909 0.894064339 0.912630622 0.729667298 0.78715097 0.752975901 0.796286576 0.701337363 1 19.22420001 3.238971368 24.99997508 0.782253893 0.860974639 0.035257522 0.119996113 26.99367743 1642878.107 0.03174372 0.040449758 1733.689697 -3.238971368 0.078720747 GVGQADWT(ph)PDLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVGQADWTPDLGLR 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GVGQADWT(1)PDLGLR;GVGQADWT(1)PDLGLR 207.21 1.09E-07 238630000 437130 533800 436100 478180 424900 508410 361140 408000 341430 463260 TRUE FALSE 454388.2299 625475.9976 447465.1243 572762.5768 352675.6498 390339.4825 332832.9031 402531.4274 329142.001 554026.9274 0.820155497 1.128963173 0.807659524 1.033817218 0.636567705 0.704549659 0.600752214 0.72655571 0.594090259 1 19.07959657 3.234734133 24.99998955 0.691346068 0.95060065 0.407034204 0.139116598 81.37675387 531668.2607 0.03595372 0.044541181 1716.857039 -3.234734133 0.259254582 GVGSGPHPPDTQQPS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GVGSGPHPPDTQQPSPSK 18 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 GVGSGPHPPDTQQPS(0.999)PS(0.001)K;GVGSGPHPPDT(0.001)QQPS(0.938)PS(0.061)K;GVGSGPHPPDT(0.002)QQPS(0.997)PS(0.001)K;GVGSGPHPPDTQQPS(1)PSK;GVGSGPHPPDTQQPS(0.999)PS(0.001)K;GVGSGPHPPDTQQPS(1)PSK 174.63 3.45E-12 3224650000 2376700 1719290 2009440 1601300 2417880 2649830 2388680 2020030 2141230 1658460 TRUE FALSE 2470533.951 2014564.683 2061807.657 1918032.361 2006889.621 2034447.141 2201449.02 1992954.802 2064167.551 1983403.484 1.245603313 1.015710973 1.039530118 0.967040936 1.011841331 1.025735387 1.109935037 1.00481562 1.040719938 1 20.91954676 4.740113612 24.89573807 1.025502273 1.24560339 0.781822794 0.035122397 57.79711138 926443.3241 0.008422715 0.05328435 54968.46537 -4.740113612 0.220101117 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 GVHIHQAGGS(0.429)PPAS(0.074)S(0.074)T(0.14)S(0.14)S(0.14)S(0.003)SLTNDVAK;GVHIHQAGGS(0.42)PPAS(0.099)S(0.099)T(0.378)S(0.004)S(0.001)SSLTNDVAK;GVHIHQAGGS(0.988)PPAS(0.003)S(0.003)T(0.003)S(0.003)S(0.001)SSLTNDVAK;GVHIHQAGGS(0.734)PPAS(0.034)S(0.034)T(0.153)S(0.034)S(0.009)S(0.003)S(0.001)LTNDVAK 258.09 3.89E-53 3269350000 679742 704074 777226 667824 889880 921330 890660 849368 885720 633403 TRUE FALSE 706578.739 824993.2326 797481.1481 799917.5939 738618.5155 707365.0704 820847.7419 837983.6112 853843.1102 757506.1906 0.93276959 1.089091076 1.05277179 1.055988194 0.975065979 0.933807643 1.083618526 1.106239951 1.127176412 1 19.53089815 2.039532752 24.91873729 1.090939805 1.012867688 0.264779846 0.057596979 187.2732058 118043.3766 0.021726608 0.016046138 109.5299153 -2.039532752 -0.078072117 GVHPHIVEMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVHPHIVEMDR 11 0 O76041-2;O76041 O76041-2 NEBL Nebulette 0 106.29 0.0013597 137230000 24466 30543 26656 27330 27851 35543 25679 27254 26418 29422 FALSE TRUE 25431.93657 35788.52266 27350.67726 32735.79243 23116.89697 27288.67691 23666.21288 26888.70471 25467.22134 35186.67758 0.722771751 1.017104345 0.777302068 0.930346218 0.656978679 0.775540028 0.672590154 0.764172879 0.723774539 1 15.10274168 3.247088541 24.99974889 0.748819373 0.866927105 0.13252053 0.115889138 286.7645897 840650.2562 0.029115801 0.038803696 1766.397905 -3.247088541 0.118107732 GVIDYDRDRFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVIDYDRDRFDR 12 2 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 ; 133.32 9.30E-05 240140000 143918 193389 154759 142906 200477 194240 134371 165520 154085 250746 FALSE TRUE 149599.9938 226602.0564 158792.1467 171172.3803 166399.9911 149130.7037 123838.6499 163301.4751 148539.5109 299874.8779 0.498874713 0.755655352 0.529528008 0.570812672 0.554898071 0.497309761 0.412967738 0.544565374 0.495338296 1 18.19400114 -1.379731214 5.763589355 1.000122187 0.540803302 0.732740329 0.08334303 0.000132803 1.43E-05 0.081898696 0.019298624 0.041712746 1.379731214 -0.459318885 GVIVDKDFSHPQMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVIVDKDFSHPQMPK 15 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;; 160.78 1.02E-06 5134350000 7382430 5306700 7283410 5131710 9048740 8354670 7879540 7259670 7874060 5857580 FALSE TRUE 7673894.037 6218084.445 7473221.648 6146746.921 7510638.407 6414424.509 7261921.065 7162365.998 7590674.119 7005260.651 1.095447324 0.887630704 1.066801368 0.877447283 1.072142606 0.915658222 1.036638239 1.022426767 1.083567692 1 22.7400073 2.099445652 20.30797222 1.035945335 0.983399519 0.09536246 0.074910924 7.517366762 1515.643336 0.025169973 0.01858927 125.7319503 -2.099445652 -0.052545816 GVKPAHCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVKPAHCEK 9 1 Q14894;I3L3Y1 Q14894 CRYM Ketimine reductase mu-crystallin 0 89.886 0.0070923 359670000 674120 481330 606330 443440 793320 705150 719730 632440 658040 520890 FALSE TRUE 700734.7781 563994.6833 622131.4579 531151.1085 658471.7498 541389.5992 663315.6819 623963.1763 634357.2689 622948.4225 1.124868051 0.90536337 0.998688552 0.852640587 1.057024508 0.869076122 1.064800324 1.001628953 1.018314271 1 19.24875319 GVKPVFSIGDEEEYDT(ph)DEIDSSSMSDDDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVKPVFSIGDEEEYDTDEIDSSSMSDDDRK 30 2 Q9NUY8-2;Q9NUY8;E9PGE5 Q9NUY8-2 TBC1D23 TBC1 domain family member 23 1 GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK;GVKPVFSIGDEEEY(0.004)DT(0.996)DEIDSSSMSDDDRK;GVKPVFSIGDEEEYDT(1)DEIDSSSMSDDDRK;GVKPVFS(0.001)IGDEEEY(0.059)DT(0.917)DEIDS(0.006)S(0.006)S(0.006)MS(0.006)DDDRK 299.07 1.83E-79 781470000 865972 395303 587426 442603 786881 757819 845473 594965 672452 335414 TRUE FALSE 900161.2432 463193.2152 602734.8041 530148.5524 653127.2487 581827.0221 779202.617 586990.4673 648250.5839 401131.9514 2.244052712 1.154715334 1.502584878 1.321631325 1.628210484 1.450462921 1.942509477 1.463335108 1.616053225 1 18.61371736 -1.182950007 5.100039847 0.999961044 1.572232592 0.265439326 0.29362561 0.000118576 1.90E-05 0.259189048 0.061087299 0.06562208 1.182950007 0.572271548 GVLCEAQEAAMPEIQEQIHDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVLCEAQEAAMPEIQEQIHDYR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 164.65 1.37E-11 63610000 38166 40575 34781 39366 40463 47991 35143 34945 35450 43785 FALSE TRUE 39672.82315 47543.44062 35687.42143 47152.4773 33585.11371 36845.81756 32388.39983 34476.61943 34174.16142 52363.83244 0.757637883 0.907944251 0.681528066 0.900477966 0.641379978 0.703650131 0.618526153 0.658405197 0.652629111 1 15.67628307 3.224908636 24.99661012 0.686419272 0.809445502 0.119958601 0.12009588 349.2027589 639384.6414 0.031657128 0.038028842 1678.450879 -3.224908636 0.12302623 GVLRPGTALVLLEAQAATGFVIDPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GVLRPGTALVLLEAQAATGFVIDPVR 26 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;;; 223.69 2.02E-34 897378000 392317.4 495265 469586.2 481125 502827.6 617557 540785.7 495230.1 463497 581667 FALSE TRUE 407806.3939 580322.9111 481824.0021 576290.089 417357.1442 474138.7459 498397.5038 488592.3505 446815.8335 695633.512 0.586237418 0.834236564 0.692640584 0.828439227 0.59996699 0.681592732 0.716465632 0.702370346 0.642314992 1 19.40796791 -1.058990166 5.863842027 1.0000009 0.703341496 0.569905105 0.078528691 8.51E-07 1.37E-07 0.070073181 0.016516357 0.087299114 1.058990166 -0.296659404 GVLTGPEYEALDALPDAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVLTGPEYEALDALPDAERR 20 1 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;O60936-1;H3BQJ5 H3BM67 NOL3 Nucleolar protein 3 0 ;;; 237 2.22E-29 443329000 120171 151509 127170 140330 152353 160716 134337 133750 136324 171936 FALSE TRUE 124915.4439 177529.4922 130484.1547 168086.8552 126456.0915 123392.1447 123807.3149 131957.3 131417.7259 205623.5673 0.607495753 0.863371327 0.634577818 0.817449368 0.614988317 0.60008756 0.602106639 0.641742101 0.639118014 1 17.6496461 -0.988516892 4.388076164 1.000010705 0.669466675 0.556564331 0.088636302 25583093.05 70560180.58 5022.598022 0.021178766 0.102679349 0.988516892 -0.33054403 GVNADKVGIEAAEMLLANLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVNADKVGIEAAEMLLANLR 20 1 O00442;O00442-2 O00442 RTCA RNA 3-terminal phosphate cyclase 0 108.18 0.00019686 53512000 120880 105200 128060 103120 170660 157850 151850 137720 143090 120220 FALSE TRUE 125652.4357 123267.2817 131397.3488 123516.8282 141651.2742 121191.7297 139947.6002 135874.0887 137940.2189 143774.8072 0.873953081 0.857363567 0.913910798 0.859099244 0.985230145 0.842927437 0.973380545 0.945047963 0.959418562 1 17.13345138 2.661258814 0.236094721 1.014669441 0.82513191 0.481502762 0.040352578 3.005446802 0.393642731 0.081630517 0.18569298 458.4149934 -2.661258814 -0.189537531 GVNCIDYYSGGDKPYLISGADDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVNCIDYYSGGDKPYLISGADDR 23 1 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 287.1 1.29E-52 3104000000 1724680 1398800 1641010 1397780 1822510 1878260 1798390 1620000 1760310 1502150 FALSE TRUE 1792771.698 1639033.019 1683776.069 1674256.712 1512720.401 1442062.58 1657427.493 1598286.55 1696956.787 1796467.532 0.997942722 0.912364398 0.937270526 0.931971595 0.842052736 0.802721204 0.922603645 0.889682959 0.944607546 1 20.77673143 6.043421692 0.899544025 0.896750825 1.854223008 0.187613881 0.05278809 28.60735276 2.821136356 0.016502251 45.51216366 1105151.18 -6.043421692 0.957472184 GVNTGAVGSYIYDRDPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVNTGAVGSYIYDRDPEGK 19 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ;;; 295.17 1.05E-49 4206020000 3806870 2732700 3377160 2755720 4406040 4223050 3748000 3378150 3954040 2910710 FALSE TRUE 3957168.167 3202019.968 3465171.564 3300793.191 3657102.895 3242310.638 3454221.966 3332871.425 3811734.873 3481007.896 1.136788047 0.919854267 0.995450648 0.948229159 1.05058736 0.931428694 0.992305123 0.957444374 1.095008971 1 21.73107366 1.249428857 24.99794511 1.047504505 0.986451169 0.104783061 0.064115666 353.1588472 812309.4573 0.03962361 0.014162084 17.75942324 -1.249428857 -0.061053336 GVNWAAFHPTMPLIVSGADDR ddPTM_MDA-MB-175_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 ; 223.23 3.63E-25 8874300000 2631500 4168700 3874300 4175700 4020000 4625700 3804600 4152900 3589200 4349300 FALSE TRUE 2735393.652 4884641.797 3975267.441 5001640.997 3336681.836 3551451.278 3506385.511 4097237.168 3460025.393 5201462.063 0.525889379 0.939090152 0.764259624 0.961583673 0.641489219 0.682779425 0.674115368 0.787708748 0.665202466 1 22.31048577 -1.132701116 4.395157135 1.000031452 0.747111144 0.274783924 0.126912445 16996279.35 4380209.654 6366.164418 0.028100861 0.073671393 1.132701116 -0.252920308 GVPAGNS(ph)DTEGGQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.98)DT(0.02)EGGQPGR;GVPAGNS(0.901)DT(0.099)EGGQPGR;GVPAGNS(0.979)DT(0.021)EGGQPGR;GVPAGNS(0.981)DT(0.019)EGGQPGR;GVPAGNS(0.998)DT(0.002)EGGQPGR 165.7 7.27E-09 1315852000 583506 644308 637937 605503 707607 866668 665209 636844 664835 708005 TRUE FALSE 606543.2674 754962.887 654562.1623 725269.6862 587328.2149 665397.4915 613068.1804 628308.1478 640907.7182 846725.0242 0.716340311 0.891626993 0.773051633 0.8565587 0.693646932 0.785848383 0.72404637 0.742045091 0.756925448 1 19.691534 -1.097923272 3.860891044 1.000069536 0.771171792 0.578809973 0.058573065 2769306.801 1969734.751 1545.326772 0.0133359 0.079813568 1.097923272 -0.228897744 GVPAGNS(ph)DTEGGQPGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;GVPAGNS(0.89)DT(0.11)EGGQPGRK 81.884 0.0051146 419950000 83690 255314 224067 241479 249480 312968 225228 281823 221139 245714 TRUE FALSE 86994.14582 299162.1934 229906.3701 289242.8255 207073.4787 240285.9251 207574.0408 278045.6237 213180.2506 293856.9538 0.296042495 1.018053817 0.782375122 0.984298046 0.704674421 0.817696917 0.706377842 0.946193786 0.725455865 1 18.16475451 4.749814841 24.95010805 0.846160975 0.296042166 0.664236048 0.118873197 927.3685144 2055894.467 0.025982424 0.40336336 56210.16255 -4.749814841 -0.550118809 GVPEKS(ph)PVLEK ddPTM_MDA-MB-175_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 154.69 1.93E-05 8897260000 19309380 8982180 12627370 8790310 18127120 17146320 18564870 13932050 15398970 7901570 TRUE FALSE 20071729.23 10524799.54 12956449.64 10529007.08 15045878.62 13164347.03 17109706.98 13745313.66 14844764.08 9449731.357 2.124052894 1.113767063 1.371091849 1.114212318 1.59220173 1.393092199 1.810602475 1.454571896 1.570919163 1 23.17184189 GVPHPEDDHS(ph)QVEGPESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 GVPHPEDDHS(1)QVEGPESLR 80.702 0.011569 88132000 24886 120960 94228 134210 93534 120070 105520 101710 92431 128670 TRUE FALSE 25868.5185 141733.9391 96683.65909 160756.3374 77635.12409 92185.56218 97249.06667 100346.7438 89104.42637 153880.423 0.168107924 0.921065437 0.62830383 1.044683491 0.504515926 0.599072711 0.631978161 0.652108578 0.579049788 1 17.23145017 -1.758911356 2.721632543 1.07685518 0.651737155 0.192024064 0.221700822 51053569.68 42194300.93 26390767.29 0.04932288 0.017421624 1.758911356 -0.425118024 GVPHPEDDHSQVEGPESLR ddPTM_MDA-MB-175_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 ;;;;; 220.34 1.69E-19 3582080000 1059224 1345463 1237275 1253495 1260178 1426955 1117895 1219763 1119894 1407070 FALSE TRUE 1101042.981 1576535.804 1269519.403 1501432.57 1045973.394 1095566.327 1030271.469 1203414.072 1079589.234 1682758.427 0.654308405 0.936875893 0.754427601 0.892244868 0.621582621 0.651053835 0.612251558 0.715143691 0.64155925 1 20.68239665 3.234874142 24.99930281 0.685548332 0.814633842 0.12096187 0.127530523 145.8233222 988880.5418 0.033215319 0.04117623 1717.410611 -3.234874142 0.12908551 GVPLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GVPLYR 6 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5;P13929-3;P13929-2;P13929;E5RGZ4;E5RI09;E5RG95;K7EPM1;K7EKN2 P06733 ENO1;ENO3 Alpha-enolase;Enolase;Beta-enolase 0 ;;;; 148.49 0.02503 3000210000 1836550 1991440 1765210 1831960 2073300 2375010 1752550 1750570 1681510 2195090 FALSE TRUE 1909058.412 2333454.329 1811212.823 2194316.22 1720881.207 1823449.921 1615180.552 1727106.473 1620992.784 2625175.858 0.727211629 0.888875433 0.689939616 0.83587399 0.655529877 0.694601055 0.615265658 0.657901248 0.617479693 1 21.32398264 3.230379086 24.98856035 0.681117504 0.786036935 0.073592849 0.11713344 311.8029769 952328.0345 0.030805099 0.037411297 1699.726657 -3.230379086 0.104919432 GVPYRPTDLFDELVAHEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVPYRPTDLFDELVAHEVAR 20 1 O95248;O95248-5;O95248-4 O95248 SBF1 Myotubularin-related protein 5 0 ; 166.25 9.29E-12 27350000 28396 33951 36167 36428 39052 41265 30446 32723 36039 39076 FALSE TRUE 29517.09601 39781.82015 37109.54173 43633.34967 32413.95499 31681.82913 28059.56296 32284.40171 34741.96343 46732.19404 0.631622303 0.851272254 0.794089439 0.933689303 0.693610811 0.677944397 0.600433246 0.690838561 0.743426756 1 15.51212915 GVQDIVVGEGTHFLIPWVQKPIIFDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVQDIVVGEGTHFLIPWVQKPIIFDCR 27 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ; 246.76 9.49E-46 2158160000 1328970 1514360 1205820 1498470 1326910 1673820 1161980 1192750 1105570 1498770 FALSE TRUE 1381438.762 1774439.55 1237244.66 1794862.894 1101362.312 1285100.672 1070900.971 1176763.137 1065780.752 1792425.286 0.770709258 0.989965698 0.690262891 1.001359949 0.61445368 0.716961919 0.597459197 0.656520049 0.594602609 1 20.77348155 3.221893402 24.99820311 0.672474677 0.859794461 0.240895218 0.140793064 277.0407935 415516.8117 0.036910027 0.044229395 1666.838037 -3.221893402 0.187319784 GVQKPAGPSTS(ph)PDGNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 GVQKPAGPS(0.029)T(0.109)S(0.863)PDGNSR;GVQKPAGPS(0.049)T(0.049)S(0.899)PDGNS(0.003)R;GVQKPAGPST(0.045)S(0.955)PDGNSR;GVQKPAGPS(0.002)T(0.096)S(0.902)PDGNSR 200.74 7.34E-12 850413000 380646 339953 380909 323629 451198 436365 407031 366763 404491 373476 TRUE FALSE 395674.198 398337.2833 390835.8015 387641.8503 374503.5251 335025.8419 375126.8466 361847.1419 389933.4479 446651.4716 0.885867893 0.891830227 0.875035293 0.867884413 0.838469252 0.750083372 0.839864795 0.810133101 0.87301503 1 18.76878999 3.389420315 3.026929363 0.835047476 0.883941082 0.011066389 0.06055035 0.54565741 10.05519111 0.016487003 0.023676536 2451.434619 -3.389420315 0.048893606 GVQLQTHPNVDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVQLQTHPNVDKK 13 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 171.73 1.60E-05 1356400000 2872000 1782500 2484200 1598500 2971400 2883200 2887900 2278200 2682700 1665300 FALSE TRUE 2985388.778 2088630.509 2548940.293 1914678.529 2466322.489 2213620.495 2661538.852 2247664.455 2586150.151 1991583.651 1.499002453 1.048728487 1.279856004 0.96138494 1.238372532 1.111487581 1.336393202 1.128581496 1.298539557 1 20.92548465 4.751455727 24.62777506 1.165505178 1.499002715 0.408386035 0.12339438 1601.843411 3059219.231 0.026544772 0.475467439 56422.94202 -4.751455727 0.333497537 GVQVETISPGDGR ddPTM_MDA-MB-175_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 0 171.32 5.88E-05 126960000 138610 118090 111610 114920 125220 151570 128650 124960 119830 130330 FALSE TRUE 144082.4298 138371.0389 114518.6483 137650.833 103935.1491 116370.1646 118566.0768 123285.1156 115517.3417 155865.6682 0.924401323 0.887758289 0.734726573 0.883137606 0.66682516 0.746605496 0.760693989 0.790970308 0.741133972 1 17.24994366 4.357624411 5.394526798 0.779810733 0.915215572 0.21278789 0.087910031 0.242322613 10.18322033 0.019555872 0.056032856 22783.70828 -4.357624411 0.135404839 GVQVPAS(ph)PDTVPQPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVQVPASPDTVPQPSLR 17 0 Q92613;F2Z2B6;F2Z3N8 Q92613 JADE3 Protein Jade-3 1 GVQVPAS(1)PDTVPQPSLR 90.714 0.0031984 0 50532 60759 56078 53714 43580 55749 52220 50443 51726 60927 TRUE FALSE 52527.04238 71193.88561 57539.43875 64338.46888 36172.28717 42802.13963 48126.85995 49766.89409 49864.39136 72864.47913 0.720886816 0.977072594 0.789677487 0.882988112 0.496432385 0.587421198 0.660498236 0.683006242 0.684344305 1 16.15292806 3.270582242 24.99998762 0.664581304 0.84847333 0.234742445 0.13599433 232.4116005 181447.3016 0.035127299 0.047558748 1864.58524 -3.270582242 0.183892026 GVQYLNEIKDSVVAGFQWATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVQYLNEIKDSVVAGFQWATK 21 1 P13639 P13639 EEF2 Elongation factor 2 0 222.06 3.71E-25 534770000 1315100 1001400 1340300 819870 1554800 1454900 1156600 1296000 1460000 1007700 FALSE TRUE 1367021.163 1173382.66 1375229.319 982037.8389 1290515.651 1117021.524 1065942.67 1278629.24 1407454.885 1205139.521 1.134326059 0.973648809 1.141137017 0.81487481 1.070843357 0.926881497 0.884497314 1.060980258 1.16787713 1 20.20076875 -1.630928518 2.92438684 0.999000801 1.011993913 0 0.112085407 808517.0179 20651667.91 22976.05434 0.024964395 0.023392222 1.630928518 0.012993112 GVRLS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GVRLSLPR 8 1 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 1 GVRLS(1)LPR;GVRLS(1)LPR;GVRLS(1)LPR 98.943 0.0043389 248235000 74029 83789 82859 82808 113998 116789 89451 95697 98415 150918 TRUE FALSE 76951.72208 98179.10896 85018.37361 99187.17524 94620.66068 89666.5247 82439.59688 94414.33824 94873.06337 180487.4926 0.426354874 0.543966275 0.471048561 0.549551516 0.524250514 0.496801875 0.456760719 0.523107374 0.525648963 1 17.46153934 0.185850813 1.455089028 1.000320002 0.500278141 0.943038818 0.036783156 1.87399675 3.114382377 0.03370017 0.009535827 1.534089909 -0.185850813 -0.500041861 GVS(ph)CFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GVSCFR 6 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 GVS(1)CFR;GVS(1)CFR;GVS(1)CFR 101.6 0.038118 921070000 703420 1169910 1213860 1996800 1029700 1352820 1733310 1236480 1373130 1529690 TRUE FALSE 731191.5648 1370832.942 1245494.189 2391761.08 854671.9618 1038648.057 1597448.633 1219907.008 1323711.32 1829403.468 0.39968852 0.749333302 0.680819847 1.307399446 0.467186149 0.567752317 0.873207393 0.666833222 0.723575386 1 20.80294186 -2.245507169 1.943032624 1.828765276 0.723799186 0.113746028 0.237466855 7421582.168 1150777.165 26977207.38 0.062055537 0.00568189 2.245507169 -1.104966091 GVS(ph)MPNMLEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GVSMPNMLEPK 11 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 GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK;GVS(1)MPNMLEPK 159.75 2.97E-05 1008300000 2299290 1836820 2376370 1965550 3386080 2758150 2664460 2287720 2468380 1888640 TRUE FALSE 2390067.745 2152279.547 2438300.154 2354329.923 2810515.331 2117611.463 2455612.663 2257056.855 2379543.486 2258682.848 1.058168812 0.952891438 1.079523031 1.042346395 1.244316055 0.937542632 1.0871879 0.999280115 1.053509344 1 21.10705028 -0.912850454 7.399798167 1 1.048608302 0.033753214 0.080517599 1.10E-09 2.17E-18 0.073591581 0.017345702 0.122222045 0.912850454 0.048608302 GVS(ph)QEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVSQEK 6 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 GVS(1)QEK;GVS(1)QEK 78.516 0.072985 530350000 641190 459560 518990 485590 644580 701340 739790 602150 629370 437960 TRUE FALSE 666504.6763 538485.8551 532515.3058 581638.2527 535014.5218 538464.4139 681803.3267 594079.1642 606719.0966 523769.8767 1.272514335 1.028096267 1.016697083 1.110484353 1.021468675 1.028055331 1.30172306 1.134236982 1.158369589 1 18.99857356 GVS(ph)QEKEAQISSAIVSSVQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVSQEKEAQISSAIVSSVQSK 21 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 GVS(1)QEKEAQISSAIVSSVQSK;GVS(1)QEKEAQISSAIVSSVQSK;GVS(1)QEKEAQISSAIVSSVQSK;GVS(1)QEKEAQISSAIVSSVQSK 317.15 5.71E-67 603131000 1034180 547900 817484 487036 1180000 1023880 718101 797010 974940 600427 TRUE FALSE 1075010.225 641997.5629 838788.3046 583370.2671 979424.0215 786099.3871 661814.3672 786327.3846 939852.0998 718069.1748 1.497084491 0.894060886 1.168116296 0.812415137 1.363968899 1.094740472 0.921658234 1.095057986 1.308860111 1 19.45376331 4.754879124 24.30223944 1.074588451 1.497084969 0.367336145 0.166875097 2274.805178 3387657.389 0.03748077 0.964289697 56869.46253 -4.754879124 0.422496519 GVSFYEVPPHLFAVADTVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVSFYEVPPHLFAVADTVYR 20 0 O00159-3;F5H6E2;O00159-2;O00159;I3L3F5;I3L501;I3L3Y6 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 142.88 1.74E-07 482420000 386230 432520 383100 457360 439760 455320 446440 391560 398550 424070 FALSE TRUE 401478.6586 506801.9455 393083.9007 547824.4429 365009.7523 349578.8304 411446.8662 386311.7787 384206.2634 507158.3972 0.791623802 0.999297159 0.775071266 1.080184112 0.719715486 0.689289248 0.81127882 0.761718195 0.757566601 1 18.95207688 3.190970625 24.99999981 0.774054876 0.908066095 0.20427811 0.114975327 155.2237851 81541.67816 0.030434172 0.036375884 1552.282011 -3.190970625 0.134011218 GVSMSLPS(ph)SPLLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVSMSLPSSPLLPR 14 0 Q9C0D5;Q9C0D5-2 Q9C0D5 TANC1 Protein TANC1 1 GVS(0.004)MS(0.016)LPS(0.49)S(0.49)PLLPR 99.531 0.0083819 89122000 189890 201900 188250 199660 183480 217290 186890 177220 169900 206150 TRUE FALSE 197387.0038 236574.7544 193155.9496 239152.1521 152292.1351 166827.6906 172241.0735 174844.6558 163785.3322 246541.1455 0.800624997 0.959575141 0.783463341 0.97002937 0.617714884 0.676672813 0.698630134 0.709190571 0.664332649 1 17.91146891 3.238283685 24.99999959 0.708964438 0.877436928 0.293192247 0.112348118 7.729347656 697794.9352 0.028921216 0.03668533 1730.946658 -3.238283685 0.168472491 GVTDHTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVTDHTQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 151.04 0.00047959 188784000 150399 187403 187223 187693 174895 205298 178263 162074 171721 199923 FALSE TRUE 156336.8687 219588.0075 192102.1852 224818.1152 145166.4104 157620.6508 164290.2803 159901.6631 165540.7948 239094.0841 0.653871756 0.918416732 0.803458546 0.940291417 0.607151829 0.659241116 0.687136534 0.668781345 0.692366753 1 17.86721891 3.233959735 24.99959352 0.69572419 0.833570757 0.142351163 0.124240677 163.1385504 886438.262 0.032723277 0.040355755 1713.798408 -3.233959735 0.137846567 GVTECYECHPKPTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVTECYECHPKPTQR 15 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;; 266.07 1.72E-25 1412700000 1147840 1139080 1229010 1153650 1412150 1586410 1260070 1302440 1257000 1190610 FALSE TRUE 1193157.61 1334708.129 1261039.01 1381838.527 1172113.247 1217990.32 1161302.421 1284982.922 1211760.816 1423887.234 0.837957937 0.937369265 0.885631236 0.970469075 0.823178423 0.855398019 0.815585949 0.902447112 0.851023021 1 20.44140346 3.222188585 24.99997847 0.867172392 0.90837739 0.063804154 0.058357307 535.1185459 817120.4612 0.015690769 0.018807618 1667.971343 -3.222188585 0.041204998 GVTIPYRPKPSS(ph)SPVIFAGGQDR ddPTM_MDA-MB-175_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 GVTIPYRPKPS(0.089)S(0.607)S(0.304)PVIFAGGQDR 234.69 3.53E-37 5241500000 1963500 1583700 1780200 1695300 2044800 2224200 1962700 1814300 1830900 1472700 TRUE FALSE 2041020.496 1855688.156 1826593.474 2030625.28 1697225.626 1707663.258 1808858.445 1789982.276 1765006.267 1761247.368 1.158849423 1.053621535 1.037102174 1.152947233 0.963649773 0.969576045 1.027032589 1.016315089 1.002134225 1 20.74816612 8 0.38402642 0.999583658 3.118504738 0.478198609 0.046586675 63.24822283 0.860811714 0.034920445 100.0476172 99999999.97 -8 2.11892108 GVTIPYRPKPSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_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 GVTIPYRPKPS(0.022)S(0.035)S(0.943)PVIFAGGQDR 173.4 2.03E-12 15519000000 1990600 1585200 1874400 1773700 2207000 2075200 1923400 1904000 1834300 1484500 TRUE FALSE 2069190.425 1857445.769 1923248.404 2124532.566 1831854.928 1593266.25 1772638.882 1878479.994 1768283.901 1775359.353 1.165505126 1.046236508 1.083300911 1.196677486 1.031822051 0.897433101 0.998467651 1.058084377 0.996014637 1 20.75967964 3.01556529 23.44543496 0.996108345 1.114574904 0.577517671 0.053461643 94.23371942 141938.7806 0.016190059 0.019342607 1036.490414 -3.01556529 0.118466559 GVTIPYRPKPSSSPVIFAGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVTIPYRPKPSSSPVIFAGGQDR 23 2 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 0 ; 140.07 1.12E-07 6424200000 3059700 2012060 2297500 1787590 2772900 2727900 2305100 2218800 2232700 2071010 FALSE TRUE 3180499.319 2357615.653 2357374.737 2141169.967 2301563.448 2094386.567 2124420.239 2189060.615 2152345.563 2476784.758 1.28412423 0.951885563 0.951788293 0.864495778 0.929254527 0.845607015 0.857733088 0.883831592 0.869007917 1 21.24003707 5.978476182 1.128711689 0.885765067 6.392332232 0.859315038 0.04621989 6.943230149 0.768349636 0.012015951 83.82467651 951647.6552 -5.978476182 5.506567165 GVTQYYAYVTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVTQYYAYVTER 12 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 130.56 0.00049846 160769000 109236 138439 112876 120581 141431 171143 116766 125898 132622 134905 FALSE TRUE 113548.7216 162214.8213 115817.6413 144431.5619 117390.6091 131397.6319 107613.5758 124210.5432 127848.9601 161337.0518 0.703798169 1.005440595 0.717861396 0.89521632 0.727610972 0.81442936 0.667010923 0.769882317 0.792433968 1 17.29971827 5.035784466 17.12529271 0.80442333 0.291214452 0.075718703 0.109824298 34035962.07 427085779 0.024426804 539221195.3 108588.6581 -5.035784466 -0.513208878 GVTSEEFDKFLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVTSEEFDKFLEER 14 1 O60784;O60784-3 O60784 TOM1 Target of Myb protein 1 0 ; 161.66 4.16E-06 238897000 369720 274420 336580 292900 428370 407250 407570 352970 383910 262520 FALSE TRUE 384316.8311 321549.5003 345351.5513 350834.7458 355555.8204 312672.3594 375623.5984 348239.0145 370093.1541 313955.7678 1.224111389 1.024187269 1.100000659 1.117465522 1.132502909 0.995912137 1.196422035 1.109197697 1.178806673 1 18.26020179 GVVDSDDLPLNVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 ;;; 283.43 4.36E-33 2431870000 2762330 3788270 2974220 3638660 3463460 3929170 3183760 3134200 2850500 3490480 FALSE TRUE 2871388.921 4438875.904 3051730.617 4358376.088 2874742.306 3016679.815 2934208.572 3092191.176 2747911.062 4174372.727 0.687861173 1.063363574 0.73106328 1.044079284 0.6886645 0.722666617 0.702910057 0.740755888 0.658281194 1 21.99312799 3.203490696 24.99991622 0.734943427 0.88382387 0.161530531 0.141116287 255.2707135 181971.3853 0.036713458 0.043882613 1597.6833 -3.203490696 0.148880443 GVVDSEDLPLNISR ddPTM_MDA-MB-175_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 ;;;;;; 351.63 1.43E-81 3738010000 3530995 4415732 3952383 4041308 4191393 4887406 3940594 4197561 3857097 4470450 FALSE TRUE 3670401.409 5174099.621 4055385.348 4840666.66 3478941.515 3752380.026 3631719.945 4141299.561 3718280.832 5346349.086 0.686524832 0.967781852 0.758533587 0.905415375 0.650713498 0.701858402 0.679289715 0.774603284 0.695480369 1 22.35012261 5.042278106 15.88063734 0.778536243 0.25518461 0.056123492 0.118465306 10211062.49 106044164.2 0.027098407 156629053.1 110224.4919 -5.042278106 -0.523351633 GVVEVTHDLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVVEVTHDLQK 11 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ;;; 181.68 6.12E-06 6630700000 8592600 8221100 8409100 8416800 12262800 11378700 9605400 8474600 8909600 7813200 FALSE TRUE 8931842.483 9633009.974 8628248.054 10081617.92 10178373.64 8736169.371 8852503.649 8361011.849 8588945.236 9344046.947 0.955885874 1.030924826 0.923395195 1.078934853 1.089289651 0.934944936 0.947395031 0.894795574 0.919189007 1 23.15561609 2.592430823 10.34374058 0.929819424 1.014894183 0.333584012 0.053218022 0.465726922 39.08722492 0.017429583 0.016425803 391.2288053 -2.592430823 0.085074758 GVVHDDMECSHYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVVHDDMECSHYMK 14 0 F8VQZ7;P50579-3;P50579;F8VRR3;P50579-2 F8VQZ7 METAP2 Methionine aminopeptidase 2 0 ; 214.23 4.02E-12 183367000 258710 252820 308990 257290 328270 314340 277700 278860 292950 264220 FALSE TRUE 268924.0706 296239.8683 317042.5332 308181.1941 272470.7827 241339.2989 255933.1484 275122.3378 282406.7867 315988.8502 0.851055569 0.937501017 1.003334558 0.975291356 0.862279737 0.763758907 0.809943605 0.87067103 0.893723897 1 18.26951413 3.177211386 7.263143884 0.852085748 0.945744185 0.206823995 0.068430438 0.281684728 27.67011541 0.019846799 0.023879852 1503.873776 -3.177211386 0.093658437 GVVPLAGTDGETTTQGLDGLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GVVPLAGTDGETTTQGLDGLSER 23 0 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 154.6 8.85E-08 52327000 39320 62271 44372 65902 73140 69874 50144 57327 49397 81344 FALSE TRUE 40872.38396 72965.55985 45528.37077 78937.2189 60707.68892 53646.82245 46213.58225 56558.62533 47619.21162 97281.79938 0.420144202 0.75004328 0.468005023 0.811428442 0.624039536 0.551457958 0.475048596 0.581389589 0.489497644 1 16.56988229 -1.039186366 4.809712721 1.000009303 0.58011622 0.532895018 0.119391634 1.20E-05 2.41E-06 0.108247215 0.025513503 0.091372106 1.039186366 -0.419893083 GVVPLAGTNGETTTQGLDGLSER ddPTM_MDA-MB-175_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 ;;; 437.88 3.23E-180 481765000 81842 108898 101408 106039 108636 122476 96547 80939 85931 132380 FALSE TRUE 85073.18536 127600.3844 104050.7758 127013.1977 90170.09152 94032.80514 88979.39386 79854.14509 82838.3601 158317.3264 0.537358653 0.805978646 0.657229238 0.802269724 0.569552895 0.593951447 0.562031938 0.504392961 0.523242541 1 17.27245963 -1.114294224 4.998021347 1.000014347 0.616695455 0.55591301 0.102604269 1.75E-05 3.11E-06 0.106126433 0.025013304 0.076860955 1.114294224 -0.383318892 GVVTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GVVTEEK 7 0 A0A0A0MTS7;Q8WZ42-5;Q8WZ42-11;Q8WZ42-4;Q8WZ42-7;Q8WZ42-2;Q8WZ42;Q8WZ42-8;Q8WZ42-13;Q8WZ42-12;H7C1P9 A0A0A0MTS7 TTN Titin 0 ;; 90.986 0.016736 719700000 41176.2 1860850 1619470 1695160 1198900 1926790 1121770 1731050 1389920 2353420 FALSE TRUE 42801.86817 2180436.512 1661674.719 2030457.588 995111.4062 1479322.223 1033842.736 1707848.106 1339897.051 2814527.59 0.015207479 0.774707812 0.590392052 0.721420389 0.353562498 0.525602317 0.367323717 0.606797429 0.476064635 1 21.42446136 -1.364035265 0.90571814 1.130473983 0.508388443 0.352626101 0.205256084 248.848242 68.65151189 80.80632124 0.060032114 0.043247871 1.364035265 -0.62208554 GVWDHGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GVWDHGGR 8 0 Q9Y3S2;D6RBR7;D6R8Y9 Q9Y3S2 ZNF330 Zinc finger protein 330 0 ; 111.74 0.0031755 91738000 144442 183021 181200 162706 184841 203289 162125 167363 169636 214646 FALSE TRUE 150144.6817 214453.433 185922.2209 194888.7612 153421.7928 156078.2106 149417.2189 165119.7727 163530.8335 256701.7741 0.584899276 0.835418586 0.724273221 0.759203016 0.597665495 0.608013759 0.582065392 0.643235807 0.637045981 1 17.96973374 -1.129149466 4.47517639 1.00004016 0.664478425 0.615106669 0.079843264 3.55E-05 6.91E-06 0.081063328 0.019104393 0.074276347 1.129149466 -0.335561735 GVYSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GVYSGR 6 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;; 133.99 0.033099 1681160000 742170 1045050 941720 1012520 1048100 1117430 883190 881660 908590 1164760 FALSE TRUE 771471.4447 1224529.208 966261.9968 1212793.434 869944.3364 857923.8173 813963.26 869842.7898 875890.0234 1392972.421 0.553831097 0.879076419 0.693669151 0.870651432 0.624523733 0.615894331 0.584335517 0.624450834 0.628792078 1 20.40973526 -1.14764136 4.375958469 1.000057201 0.676308867 0.454797722 0.106735051 15523478.15 4071198.694 8948.58207 0.025387813 0.071180108 1.14764136 -0.323748334 GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 GWAFGSNS(1)LPIAGSVGMGVAR;GWAFGSNS(1)LPIAGSVGMGVAR 275.69 9.25E-45 319790000 236903 299310 287450 267220 317390 364240 293590 279943 284870 380170 TRUE FALSE 246256.1134 350714.1642 294941.1831 320075.3184 263440.1612 279650.7801 270577.6486 276190.822 274617.5843 454657.0327 0.541630494 0.771381809 0.648711362 0.70399289 0.579426122 0.615080731 0.595124741 0.607470691 0.604010418 1 18.79441914 -1.746672558 3.450726555 1.049248137 0.631401237 0.760677309 0.062313096 10924440.15 6457120.663 4089304.872 0.014269631 0.017919564 1.746672558 -0.4178469 GWDDLFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GWDDLFNK 8 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 163.77 0.00077691 467000000 606680 471670 587200 510710 703860 706290 668730 602010 620590 471260 FALSE TRUE 630632.1949 552675.6534 602502.9144 611726.9137 584218.1286 542264.8514 616313.1952 593941.0406 598255.0871 563594.3742 1.11894693 0.980626633 1.069036424 1.085402803 1.036593258 0.962154479 1.093540361 1.053844871 1.061499395 1 19.10429769 GWDLVDAVT(ph)PGPQPTLEQLEEGGPRPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 GWDLVDAVT(0.999)PGPQPT(0.001)LEQLEEGGPRPLER;GWDLVDAVT(0.999)PGPQPT(0.001)LEQLEEGGPRPLER 88.683 0.0028201 182896000 87429 91919 83558 99594 113764 125155 91852 98005 99381 139257 TRUE FALSE 90880.76443 107705.3732 85735.59012 119293.3959 94426.43592 96089.64799 84652.40023 96691.40328 95804.29722 166541.7429 0.545693607 0.646716981 0.514799405 0.716297271 0.566983594 0.576970352 0.50829539 0.580583592 0.575256963 1 17.3455243 -1.695014779 2.54446027 1.070105411 0.581401693 0.82364648 0.058124275 8411558.553 6724947.264 3786132.954 0.013808481 0.020182977 1.695014779 -0.488703718 GWDLVDAVTPGPQPTLEQLEEGGPRPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GWDLVDAVTPGPQPTLEQLEEGGPRPLER 29 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;;; 199.12 3.43E-25 335443000 117936 132592 136547 147510 133934 164728 121002 128042 130964 163992 FALSE TRUE 122592.2043 155363.6446 140105.527 176687.0377 111167.9465 126472.4185 111517.5471 126325.8064 126250.6312 196123.0926 0.625077867 0.792174152 0.714375473 0.900898693 0.56682742 0.644862453 0.568609976 0.644114901 0.643731595 1 17.58139989 -1.095476634 4.347202524 1.000035778 0.677343278 0.496826981 0.0972583 13767004.53 3469227.692 4925.680078 0.023470831 0.080264474 1.095476634 -0.3226925 GWEEGVAQMSVGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GWEEGVAQMSVGQR 14 0 P62942;Q5W0X3;Q1JUQ5 P62942 FKBP1A;FKBP12-Exip2 Peptidyl-prolyl cis-trans isomerase FKBP1A;Peptidyl-prolyl cis-trans isomerase 0 193.81 5.02E-07 133900000 181990 245480 234760 220500 261420 270560 249670 229820 220300 242860 FALSE TRUE 189175.1057 287639.2804 240878.0385 264114.2419 216983.9218 207726.5404 230100.213 226739.6388 212371.446 290443.7672 0.651331263 0.990344132 0.829344836 0.909347253 0.747077219 0.715203987 0.792236705 0.780666223 0.731196431 1 18.14789934 5.014863497 14.89273029 0.81858297 0.372965612 0.224074481 0.098151164 2713339.733 56772863.38 0.022856227 25362197.39 103481.6863 -5.014863497 -0.445617358 GWEFMWNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 GWEFMWNER 9 0 P12532;P12532-2;P17540 P12532 CKMT1A;CKMT2 "Creatine kinase U-type, mitochondrial;Creatine kinase S-type, mitochondrial" 0 ;;;;;; 139.96 0.00025644 3183117000 1756108 2783885 2300816 2751656 2468452 3206415 2081546 2113152 2028843 2929929 FALSE TRUE 1825440.5 3261995.593 2360777.155 3295925.344 2048865.411 2461773.71 1918388.985 2084828.654 1955825.337 3503992.491 0.520960163 0.93093681 0.673739216 0.940619979 0.584723117 0.702562496 0.547486614 0.594986622 0.558170527 1 21.74056825 3.19255207 24.99991445 0.635229369 0.77167615 0.065117823 0.167855569 235.8442826 128151.1699 0.044457629 0.053137209 1557.944816 -3.19255207 0.13644678 GWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GWEVVESDLYAMNFNPIISR 20 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 316.76 4.16E-66 596136400 166881 177263.7 171086.4 184534 176391 220722 199857 185169.9 178690.9 163420.9 FALSE TRUE 173469.5907 207707.3616 175545.0521 221034.2744 146408.1208 169462.6606 184191.6861 182688.0004 172259.8494 195440.0965 0.887584451 1.062767392 0.898203876 1.130956638 0.749120183 0.867082362 0.942445739 0.934751894 0.881394619 1 17.57636696 3.242253848 24.99999584 0.897364332 0.992821983 0.224845346 0.09006316 148.1475089 1002822.66 0.02416423 0.031495072 1746.842895 -3.242253848 0.09545765 GWEWEGEWIVDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GWEWEGEWIVDPER 14 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 197.31 5.49E-08 95598000 95982 112460 108758 132324 111522 135668 114076 107169 104086 102855 FALSE TRUE 99771.44347 131774.1302 111592.3228 158497.2923 92565.53027 104161.1631 105134.425 105732.5748 100339.9652 123007.468 0.811100701 1.071269349 0.907199576 1.288517639 0.752519597 0.846787311 0.85469953 0.859562241 0.815722548 1 16.90838638 GWGS(ph)PGRPK ddPTM_MDA-MB-175_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 92.943 0.005895 1572620000 1393090 1003200 1113830 995590 1342960 1321470 1195370 1039830 1129080 916630 TRUE FALSE 1448090.269 1175491.796 1142857.325 1192514.73 1114684.139 1014578.62 1101673.776 1025892.78 1088444.631 1096226.099 1.320977735 1.0723078 1.042537964 1.087836471 1.016837804 0.92551949 1.004969483 0.9358405 0.992901586 1 20.06411396 8 0.633420308 0.975996195 27.04078819 0.850901692 0.040832287 72.14764376 0.492976357 0.016862602 2626.728722 100000000 -8 26.06479199 GWLRDPSAS(ph)PGDAGEQAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GWLRDPSASPGDAGEQAIR 19 1 P18206;P18206-2 P18206 VCL Vinculin 1 GWLRDPS(0.001)AS(0.999)PGDAGEQAIR;GWLRDPSAS(1)PGDAGEQAIR;GWLRDPS(0.006)AS(0.994)PGDAGEQAIR;GWLRDPSAS(1)PGDAGEQAIR;GWLRDPSAS(1)PGDAGEQAIR 235.7 2.19E-24 1334000000 804726 1024226 818215 981196 835408 1063170 848797 884176 798751 1179570 TRUE FALSE 836497.2039 1200128.848 839538.3551 1175273.64 693405.6466 816264.88 782266.0732 872325.0669 770004.1075 1410684.157 0.592972707 0.850742416 0.595128506 0.833123158 0.491538551 0.578630501 0.554529566 0.618370216 0.545837354 1 20.42796358 -1.07380973 4.612313421 1.000015197 0.630819498 0.493106407 0.11283575 2.23E-05 4.49E-06 0.106609675 0.025126799 0.084370431 1.07380973 -0.369195698 GWMDPQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GWMDPQSK 8 0 J3KN30;F5H8E7;Q99572-7;Q99572-5;Q99572-2;Q99572-8;Q99572 J3KN30 P2RX7 P2X purinoceptor 7 0 77.674 0.075846 65128000 137140 134700 180400 130550 213410 193150 177490 155930 176090 138960 FALSE TRUE 142554.3931 157833.6772 185101.3722 156372.4003 177134.6444 148293.8397 163577.87 153840.0134 169752.5553 166186.5515 0.857797408 0.949737965 1.113816796 0.940944974 1.065878333 0.892333576 0.984302692 0.925706756 1.021457836 1 17.34244411 4.110480926 0.003044155 1.937928843 4.04E-05 0.023722645 0.073407748 480146.9797 281.4686565 87998.21897 91198.22176 12896.76914 -4.110480926 -1.937888479 GWQDVTATSAYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GWQDVTATSAYKK 13 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 132.08 0.00019717 1372290000 549340 539780 565970 421150 767690 744380 585440 553840 674360 694510 FALSE TRUE 571028.3674 632483.0161 580719.6431 504452.213 637198.328 571509.0262 539551.683 546416.6807 650089.9153 830585.9373 0.687500645 0.761490157 0.699168644 0.607344996 0.767167248 0.688079343 0.649603682 0.657868929 0.782688324 1 19.66376992 0.90676479 3.799467016 0.999860593 0.689348899 0.809664174 0.045605619 0.166866638 5.413521687 0.044406228 0.011395313 8.067979573 -0.90676479 -0.310511694 GWS(ph)QEGPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GWSQEGPVK 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK;GWS(1)QEGPVK 147.58 9.66E-05 1621091000 1996590 1571300 2546380 1540630 2717600 2156350 2529300 2146320 3058450 1647660 TRUE FALSE 2075416.915 1841158.552 2612740.755 1845362.016 2255663.323 1655570.392 2331046.857 2117552.091 2948376.982 1970487.431 1.053250522 0.934367062 1.32593627 0.936500272 1.144723528 0.840183178 1.182979815 1.074633646 1.496267845 1 20.91012112 1.424647221 23.04253952 1.260575341 1.063214609 0.157883261 0.17203519 58.576273 25724.20638 0.097493576 0.038469509 26.58564619 -1.424647221 -0.197360733 GWSQEGPVKS(ph)PAECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GWSQEGPVKSPAECR 15 1 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR;GWSQEGPVKS(1)PAECR 166.57 8.24E-07 3075260000 1895680 1285580 1462530 1485820 1830200 1914550 2102000 1645950 1684180 1099624 TRUE FALSE 1970522.91 1506368.365 1500644.733 1779710.761 1519103.258 1469924.778 1937239.747 1623888.732 1623566.691 1315074.269 1.498411882 1.145462579 1.141110254 1.353315781 1.155146362 1.11775039 1.473102921 1.234826633 1.234581749 1 20.32671285 4.749141256 24.34217478 1.224409817 1.498412107 0.318076494 0.125849873 1315.578304 3026577.767 0.028935366 0.406875326 56123.04892 -4.749141256 0.27400229 GWVTFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GWVTFDR 7 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 114.43 0.013741 126513000 192506 225980 209040 206660 269710 276890 215870 214050 204068 276350 FALSE TRUE 200106.2855 264790.3071 214487.7541 247536.7312 223864.7905 212586.4938 198949.5453 211181.0099 196723.6325 330495.4915 0.605473571 0.801191889 0.648988442 0.748986711 0.677361103 0.643235685 0.601973553 0.638983028 0.595238476 1 18.33427107 -1.746298358 7.135402713 1.005200663 0.664013308 0.721923314 0.062854106 0.005235975 0.000186167 0.061278001 0.014327089 0.017935011 1.746298358 -0.341187354 GYADS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GYADSPSK 8 0 Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R5;Q5T0R7;Q5T0R6;Q5T0S3;Q5T0R8 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 1 GYADS(0.996)PS(0.004)K;GYADS(0.998)PS(0.002)K;GYADS(0.909)PS(0.091)K 128.03 0.0012071 2999360000 7738500 4650800 5219000 4867800 6668700 7672100 7246900 5687300 5510900 4069250 TRUE FALSE 8044021.955 5449538.722 5355011.427 5830636.311 5535156.756 5890371.047 6678869.042 5611071.046 5312563.785 4866541.627 1.652923692 1.119797002 1.100373086 1.198106737 1.1373902 1.210381314 1.372405612 1.152989428 1.091650744 1 22.21446546 4.74208862 24.96287855 1.168723986 1.652923879 0.719198689 0.0931601 182.9787553 1294635.393 0.022191991 0.163327162 55219.01051 -4.74208862 0.484199893 GYADSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 105.57 0.01015 70114000 199770 160360 224140 156580 323580 300650 276390 182410 258000 167850 FALSE TRUE 207657.0739 187900.5826 229981.2725 187551.0567 268577.9872 230828.5939 254725.8296 179965.0923 248714.6304 200736.9938 1.034473367 0.936053584 1.145684551 0.934312371 1.337959596 1.149905603 1.268953095 0.896521806 1.239007448 1 17.61494699 GYAFIEYEHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;;; 161.62 2.61E-05 2508590000 2598360 3208980 2910390 3067040 3829820 3810910 2988150 2832310 2818960 4240730 FALSE TRUE 2700945.259 3760097.353 2986237.154 3673691.358 3178828.564 2925883.907 2753930.995 2794347.517 2717506.18 5071619.85 0.532560669 0.741399684 0.588813287 0.724362525 0.626787626 0.576913096 0.543008166 0.550977321 0.535826079 1 22.27401518 -1.861518389 3.202829538 1.142931936 0.603116031 0.735799079 0.071492646 7742876.511 9584968.37 7724881.062 0.017762427 0.013755666 1.861518389 -0.539815905 GYAFNHSADFETVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYAFNHSADFETVR 14 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 158.81 5.01E-06 1686210000 772290 817840 872220 787970 973430 1014620 976380 828660 850020 834250 FALSE TRUE 802780.6055 958297.6581 894950.7697 943828.1141 807966.7163 778989.8817 899848.7843 817553.1681 819427.9462 997705.3148 0.804626971 0.960501707 0.897009123 0.945998884 0.80982501 0.78078153 0.901918403 0.81943351 0.8213126 1 19.92825423 GYAVLGGER ddPTM_MDA-MB-175_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 ;;;;; 157.86 0.00015712 3537050000 1958540 2154770 1862840 1665780 5141010 3093220 2033400 1716090 1879580 6193940 FALSE TRUE 2035864.672 2524834.986 1911387.141 1995266.312 4267142.957 2374866.533 1874016.795 1693088.621 1811934.283 7407523.953 0.274837406 0.34084736 0.258033204 0.269356714 0.576055236 0.320601938 0.252988287 0.228563368 0.24460728 1 22.82055996 -1.924815438 2.659656735 1.437956113 0.305929379 0.825072084 0.095681505 25094032.65 13023308.94 68290670.1 0.026139257 0.011890074 1.924815438 -1.132026734 GYDDRDYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYDDRDYYSR 10 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;;; 169.58 4.19E-06 13792700000 12262600 15832800 13881700 14032600 14897700 16432900 12704700 13881700 13189600 16938500 FALSE TRUE 12746736.92 18551960.24 14243468.51 16808206.4 12365394.28 12616608.02 11708872.42 13695638.52 12714908.87 20257274.77 0.629242436 0.915817179 0.703128563 0.829736803 0.610417463 0.622818625 0.578008274 0.676084946 0.627671245 1 24.27193676 3.237129789 24.99295994 0.66022932 0.775194336 0.067215841 0.13290664 68.82313906 1202173.788 0.034431906 0.043323857 1726.353737 -3.237129789 0.114965016 GYDKVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYDKVDR 7 1 O60828-2;O60828;A0A5H1ZRR1;O60828-3 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 64.836 0.065862 140970000 607780 536820 581130 495370 785220 759670 628410 651070 681360 699460 FALSE TRUE 631775.6237 629014.6591 596274.7252 593352.7075 651748.5849 583248.1554 579153.5822 642343.4716 656837.9867 836505.795 0.755255525 0.751954933 0.712816012 0.709322889 0.779132181 0.697243413 0.692348559 0.767888848 0.785216302 1 19.67401601 0.634541927 1.361335343 0.999788587 0.729753661 0.894529639 0.027518487 0.375248856 1.018701815 0.026312561 0.00779578 4.310641708 -0.634541927 -0.270034927 GYDRYEDYDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYDRYEDYDYR 11 1 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 111.79 0.0014706 506640000 756410 1097600 937960 785680 1104700 1156200 727340 888880 945910 1468700 FALSE TRUE 786273.6509 1286104.262 962404.0081 941085.159 916923.4886 887690.0724 670329.1903 876966.0175 911866.8839 1756463.645 0.447645844 0.732212287 0.547921394 0.535784024 0.522028162 0.505384825 0.381635676 0.499279345 0.519149307 1 20.74424229 -1.431399466 7.385344598 1.000030304 0.520475143 0.743736493 0.0843101 4.33E-05 3.33E-06 0.083987866 0.019794884 0.037033993 1.431399466 -0.479555161 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYDSEDDTWEPEQHLVNCEEYIHDFNR 27 0 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(1)EDDTWEPEQHLVNCEEYIHDFNR;GYDS(0.999)EDDT(0.001)WEPEQHLVNCEEYIHDFNR 338.22 2.58E-95 735908000 105477.7 109808 96634 134525 94949 133507 132547 116898 105476 89788.7 TRUE FALSE 109642.041 128666.6698 99152.36143 161133.6435 78809.60289 102502.0226 122157.6198 115331.1735 101679.9394 107381.0767 1.02105552 1.198224807 0.923369038 1.500577648 0.733924499 0.954563185 1.137608446 1.074036293 0.94690743 1 16.71238025 3.21371384 24.99985863 0.994872274 1.146520268 0.214892515 0.170954465 421.5947716 424191.1036 0.048445838 0.057926708 1635.738366 -3.21371384 0.151647993 GYDS(ph)EDDTWEPEQHLVNCEEYIHDFNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYDSEDDTWEPEQHLVNCEEYIHDFNRR 28 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 GY(0.002)DS(0.989)EDDT(0.009)WEPEQHLVNCEEYIHDFNRR 115.66 0.00016107 160290000 12358 12859 7954.8 8697.8 10862 16063 13748 8187.1 9443.4 9676.7 TRUE FALSE 12845.90338 15067.43322 8162.108623 10418.19888 9015.68112 12332.61169 12670.39584 8077.365316 9103.533879 11572.66409 1.110021278 1.301984841 0.705292105 0.900242053 0.779049754 1.065667472 1.094855578 0.697969392 0.786641158 1 13.4984334 4.246302511 24.99998369 0.874043951 1.206003129 0.465494659 0.140212834 148.4006851 479201.2224 0.034972143 0.09204967 17632.03791 -4.246302511 0.331959178 GYDSGPEGGAAAS(ph)PPPDAELAACHPAAWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GYDSGPEGGAAASPPPDAELAACHPAAWSR 30 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR;GYDSGPEGGAAAS(1)PPPDAELAACHPAAWSR 268.88 2.54E-59 704740000 303741 392940 325701 446280 327650 401870 392940 388540 316932 374790 TRUE FALSE 315732.9292 460424.3884 334189.0356 534552.852 271956.17 308541.7829 362140.336 383332.2568 305525.6792 448222.9247 0.704410488 1.027221864 0.745586665 1.19260489 0.606743107 0.688366806 0.80794693 0.855226798 0.68163778 1 18.77385691 3.199202727 24.99998878 0.77082376 0.913022335 0.157813808 0.162929906 283.7507671 180236.6331 0.044438348 0.05311473 1581.986332 -3.199202727 0.142198575 GYDVDFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GYDVDFPR 8 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9;O94808 Q06210-2 GFPT1;GFPT2 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1;Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2 0 ;;;;; 113.5 0.0065976 1757020000 2701570 3273830 3041200 3395750 3274750 3739050 3161240 3203660 2918230 3207410 FALSE TRUE 2808230.07 3836084.836 3120456.17 4067419.215 2718109.165 2870712.303 2913453.748 3160720.178 2813203.472 3835840.58 0.732102915 1.000063677 0.813499963 1.06037233 0.70860848 0.748391974 0.759534628 0.823996752 0.733399476 1 21.87111133 3.208639234 24.99984909 0.784976378 0.902263222 0.168160074 0.113856341 305.9034016 255586.9426 0.030211915 0.036114573 1616.736466 -3.208639234 0.117286843 GYDYGPHFQGILEASLEGDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 23 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 ;;;;;;;;;;;;;;;;;;;;;; 296.81 1.43E-55 15113639800 5422973.8 5676510.3 6090004.5 7266604.8 6372043.7 6797139.1 6136670 5827414.6 5584004.7 5822400.5 FALSE TRUE 5637076.993 6651406.787 6248715.02 8703917.541 5288925.988 5218606.556 5655661.77 5749307.639 5383037.462 6963188.401 0.809553996 0.955224303 0.897392783 1.24999024 0.759555204 0.749456464 0.812223 0.825671705 0.773070776 1 22.73131663 GYEEWLLNEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 GYEEWLLNEIR 11 0 O43707;O43707-2;F6THM6;A0A494C060;P12814-3;P12814;P12814-2;P12814-4;H9KV75;P35609-2;P35609;A0A494C1A0 O43707;P12814-3 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-1;Alpha-actinin-2 0 ;;;;; 258.52 3.37E-20 1513830000 989042 1438090 933963 1369050 1268920 1444110 1400280 1112741 927668 2114640 FALSE TRUE 1028090.142 1685070.771 958302.843 1639844.004 1053229.432 1108737.338 1290522.395 1097826.527 894281.4099 2528963.221 0.406526332 0.666308927 0.378931111 0.648425406 0.416466884 0.438415762 0.51029702 0.434101421 0.353615823 1 21.27011463 -1.444735581 3.176641746 1.008983738 0.476625367 0.708185485 0.101540919 46525899.51 60583085.53 3765476.588 0.022418818 0.035914053 1.444735581 -0.532358371 GYEEWLLNEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 243.85 3.67E-16 419221000 422553 570610 422666 579268 530767 619754 607503 479788 430059 744074 FALSE TRUE 439235.7187 668607.8288 433681.0232 693845.4815 440547.4149 475825.526 559885.3274 473357.2266 414581.2606 889861.0541 0.49360034 0.751362053 0.487358134 0.779723394 0.495074386 0.534718902 0.629182865 0.531945099 0.465894376 1 19.76322056 -1.967149414 2.75364524 1.342143265 0.578568127 0.592213893 0.105917356 5730048.501 4756368.102 12532824.92 0.024420923 0.010785756 1.967149414 -0.763575138 GYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYEVIYLTEPVDEYCIQALPEFDGKR 26 1 P14625 P14625 HSP90B1 Endoplasmin 0 115.55 0.0018743 317380000 112220 111430 107580 109080 135060 145250 104300 114700 106400 110610 FALSE TRUE 116650.5323 130567.2357 110383.6232 130655.6984 112102.5494 111517.8888 96124.69346 113162.6341 102570.6848 132281.9117 0.881832827 0.987037713 0.834457423 0.987706457 0.84745184 0.843032031 0.726665439 0.855465669 0.775394636 1 17.01325628 3.063390223 8.309798329 0.82599517 0.921009538 0.194965068 0.07855076 0.355134087 41.69736417 0.020937053 0.025044078 1157.1515 -3.063390223 0.095014368 GYFDEEMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 221.36 9.83E-07 6168490000 3753050 4814580 4349540 4376330 5422570 5576630 4688130 4705110 4431930 5932760 FALSE TRUE 3901223.312 5641446.663 4462892.586 5241955.012 4500843.488 4281542.197 4320662.12 4642045.696 4272425.705 7095170.732 0.549842063 0.79511077 0.629004256 0.738806043 0.634353091 0.603444562 0.608958161 0.654254263 0.602159675 1 22.75840597 -1.917269019 2.77488386 1.20629321 0.649933063 0.71065081 0.067686798 13314599.26 5662944.346 17759826.81 0.015331376 0.012098485 1.917269019 -0.556360147 GYFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYFEDR 6 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;; 134.12 0.032967 5499230000 6620500 8234900 7453900 8107900 8054000 9393300 8206400 8260600 7703500 8813100 FALSE TRUE 6881882.452 9649180.016 7648154.757 9711618.42 6684983.957 7211848.432 7563160.925 8149880.169 7426252.54 10539858.21 0.652938808 0.915494291 0.725641143 0.921418318 0.634257485 0.684245299 0.717577104 0.773243815 0.704587518 1 23.32935212 -1.04532512 9.417272537 0.999999999 0.752187307 0.392744153 0.093964787 0 6.81E-11 0.086132697 0.020301671 0.090089646 1.04532512 -0.247812692 GYFEDRRPS(ph)ANCDPFSVTEALIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GYFEDRRPSANCDPFSVTEALIR 23 2 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 GYFEDRRPS(1)ANCDPFSVTEALIR;GYFEDRRPS(1)ANCDPFSVTEALIR;GYFEDRRPS(1)ANCDPFSVTEALIR 187.98 1.18E-17 166414000 103301 128272 115985 122387 137882 140244 102901 113244 114390 147752 TRUE FALSE 107379.4032 150301.7182 119007.6644 146594.7833 114444.8669 107674.4564 94835.35074 111726.1494 110273.1262 176701.1755 0.607689241 0.850598293 0.673496733 0.82961974 0.647674621 0.609359027 0.536699037 0.63228866 0.624065606 1 17.43095211 -1.177640365 4.393788058 1.000077039 0.667527541 0.531619163 0.093503778 7.77E-05 1.45E-05 0.094775772 0.022333438 0.066429294 1.177640365 -0.332549498 GYFEHREDR ddPTM_MDA-MB-175_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 ;;; 173.32 3.34E-05 778150000 684740 894550 779630 739170 1046010 986510 699280 800740 745830 1251590 FALSE TRUE 711774.0639 1048182.004 799947.7983 885375.6198 868209.5938 757408.0032 644468.6064 790007.39 718987.724 1496815.097 0.475525711 0.700274874 0.534433277 0.59150634 0.580037972 0.50601307 0.430559932 0.527792238 0.480345051 1 20.51346458 -1.643739279 6.434045846 1.002359011 0.537695873 0.79186233 0.071319866 0.002451751 0.000135756 0.070153028 0.016471424 0.022712279 1.643739279 -0.464663138 GYFEYIEENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYFEYIEENK 10 0 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 182.65 4.08E-06 417928000 767430 523164 628620 589440 703500 810140 891030 618970 649100 439362 FALSE TRUE 797728.729 613013.3473 645002.3536 706029.4727 583919.3213 621997.2628 821188.7403 610673.7196 625739.0178 525446.5718 1.5181919 1.166652102 1.227531757 1.343675096 1.111282008 1.183749778 1.562839658 1.162199455 1.190870873 1 19.00318455 0.965436372 1.834229158 1.004797859 1.283025986 0.276404718 0.14316374 0.504569021 3.554317011 0.130397385 0.036988796 9.234988786 -0.965436372 0.278228126 GYFEYIEENKYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYFEYIEENKYSR 13 1 Q00839;Q5RI18;A0A1W2PRI6;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;; 217.46 2.35E-11 8102200000 5791150 5356770 6174020 4670690 7156380 6526920 5700820 5876400 6176990 5567430 FALSE TRUE 6019789.074 6276753.578 6334920.033 5594538.541 5939941.084 5011141.746 5253974.832 5797636.47 5954681.337 6658261.314 0.904108263 0.942701598 0.95143758 0.840240158 0.892115945 0.752620168 0.789091113 0.870743306 0.894329774 1 22.66671406 3.735579675 24.88931792 0.850871246 0.933744394 0.184702826 0.064092678 330.3203287 2758006.012 0.01650989 0.026863669 5439.759199 -3.735579675 0.082873148 GYGFVHFETQEAAER ddPTM_MDA-MB-175_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 ;;;;; 252.43 1.21E-24 7620780000 4407840 5842330 4883160 5305970 5537510 6193180 4912020 5340450 5117610 6120320 FALSE TRUE 4581864.927 6845704.73 5010419.161 6355475.029 4596246.028 4754907.804 4527003.037 5268870.003 4933428.216 7319479.523 0.625982341 0.935272065 0.684532164 0.868296032 0.627947112 0.649623759 0.618487014 0.719842167 0.674013528 1 22.80330963 -1.141267315 3.612293258 1.000222065 0.714027656 0.419152604 0.101828512 191595955.8 325930957.5 506050.524 0.023902193 0.072232506 1.141267315 -0.286194409 GYGGNRFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYGGNRFESR 10 1 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;K7EJV1;Q14011-3 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ; 138.66 5.37E-05 322730000 211369 302267 229729 166998 339978 270325 155534 217541 183400 460070 FALSE TRUE 219714.0113 354179.0059 235715.9265 200029.706 282188.661 207546.1156 143342.8387 214625.2187 176799.4698 550211.9079 0.399326165 0.643713814 0.428409351 0.363550303 0.512872689 0.377211239 0.260522967 0.390077379 0.321329777 1 19.06962784 -1.537528673 6.011645761 1.000977625 0.410632676 0.758495617 0.099743611 0.001360658 0.000104674 0.100546696 0.023664194 0.029004897 1.537528673 -0.590344949 GYHYATCLEGALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYHYATCLEGALK 13 0 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 149.41 1.75E-06 0 227950 157740 195650 188520 270020 252500 238000 212300 232590 226080 FALSE TRUE 236949.642 184830.618 200748.7997 225808.6933 224122.0968 193860.7017 219344.9381 209454.4658 224219.1313 270376.0474 0.876370685 0.68360574 0.742479971 0.835165302 0.828927336 0.717003978 0.811258764 0.774678333 0.829286224 1 18.04460782 0.741563707 2.093989167 1.000001065 0.780511931 0.578777065 0.055185652 0.718864347 4.719729139 0.050455489 0.013842413 5.515231004 -0.741563707 -0.219489133 GYIFLEYAS(ph)PAHAVDAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYIFLEYASPAHAVDAVK 18 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 GYIFLEYAS(1)PAHAVDAVK;GYIFLEYAS(1)PAHAVDAVK 201.61 8.91E-16 92488000 167597 143332 153317 134941 188541 192696 172472 162022 167987 139223 TRUE FALSE 174213.859 167948.156 157312.567 161631.927 156492.8682 147945.2743 158953.194 159850.3601 161941.1807 166501.0813 1.046322688 1.008691083 0.944814086 0.97075602 0.939891002 0.888554436 0.954667638 0.960055988 0.972613388 1 17.34517202 4.418517523 2.715204923 0.950536303 1.044820062 0.5475602 0.027503506 0.205957423 2.830173373 0.007046038 0.031421525 26213.048 -4.418517523 0.094283759 GYIWNYGAIPQTWEDPGHNDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYIWNYGAIPQTWEDPGHNDK 21 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;; 277.07 7.91E-45 8007240000 4198550 3276960 3804220 2975760 4337520 4411520 4365760 3523560 3974480 3050370 FALSE TRUE 4364311.996 3839752.389 3903361.098 3564356.446 3600229.9 3387011.337 4023560.323 3476332.442 3831439.241 3648031.599 1.196347092 1.052554586 1.069991033 0.977062931 0.986896578 0.928449013 1.102940096 0.952933753 1.050275782 1 21.7986868 5.315203999 0.99009605 0.999666525 1.592886469 0.578792739 0.049124266 3.507763603 1.234490224 0.013998325 2.909970389 206635.0546 -5.315203999 0.593219944 GYLDDPTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYLDDPTVPR 10 0 E7EUI8;P11413;P11413-3;P11413-2 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 78.934 0.066337 323630000 929220 1102200 1022900 1133400 1132200 1259500 1112500 1059300 1052200 1161300 FALSE TRUE 965906.3231 1291494.276 1049557.614 1357583.137 939749.0484 967000.2129 1025299.343 1045101.816 1014331.528 1388834.501 0.695479787 0.929912294 0.755711076 0.977498137 0.676645812 0.696267419 0.738244436 0.752502775 0.7303473 1 20.40544326 5.035258284 17.53573615 0.7914314 0.297072261 0.065680162 0.113526236 36180119.33 457619179.3 0.025968335 567218119.5 108457.1739 -5.035258284 -0.49435914 GYNDDYYEESYFTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 169.79 2.74E-06 40773000 25399 26661 26668 36292 22076 36891 29344 28187 24261 29831 FALSE TRUE 26401.77213 31239.81936 27362.98999 43470.44928 18323.52941 28323.62434 27043.9406 27809.19937 23387.85135 35675.8133 0.740046819 0.875658225 0.766989942 1.218485166 0.5136121 0.79391671 0.758046926 0.779497278 0.655566032 1 15.1226587 3.209639563 24.99999968 0.744620526 0.889014408 0.162154637 0.166178255 382.6867282 330801.8625 0.045421935 0.054297961 1620.464655 -3.209639563 0.144393882 GYNFEDLTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GYNFEDLTDR 10 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ;; 222 1.19E-08 582920000 777330 891880 764640 855220 848880 937980 815330 846860 776570 874610 FALSE TRUE 808019.5886 1045053.452 784567.1466 1024379.963 704587.6808 720148.3602 751422.3041 835509.2269 748621.3974 1045973.084 0.772505145 0.999120788 0.750083495 0.97935595 0.673619323 0.688496072 0.71839545 0.798786546 0.71571765 1 19.9964143 3.23121631 24.99998844 0.752186406 0.875171462 0.176712113 0.113441377 242.9701686 827068.5617 0.030030523 0.036578988 1703.006519 -3.23121631 0.122985056 GYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 31 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK;GYNHGQGSYSYSNSYNS(1)PGGGGGSDYNYESK 417.35 4.26E-176 2492650000 419867 561863 641809 623765 752470 838800 681680 723786 707080 573849 TRUE FALSE 436443.6734 658358.5996 658535.0698 747143.8552 624565.4182 644001.4121 628248.1404 714084.8325 681632.3289 686283.7245 0.635952242 0.95930965 0.959566789 1.088680714 0.910068818 0.938389458 0.915434999 1.040509642 0.993222343 1 19.38844562 4.743112972 4.232940416 0.980695348 0.607591486 0.795293329 0.052212692 0.096126381 3.933730506 0.012778147 0.109214324 55349.40702 -4.743112972 -0.373103861 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYNHGQGSYSYSNSYNSPGGGGGSDYNYESK 31 0 Q12906;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 393.75 1.69E-155 411680000 33438 67029 67892 66718 77605 88559 80787 74020 71523 64819 FALSE TRUE 34758.15806 78540.70934 69661.32129 79914.62127 64413.72982 67992.51437 74454.70384 73027.88297 68948.9012 77519.04202 0.448382193 1.013179566 0.898634961 1.030903107 0.830940736 0.877107258 0.960469865 0.942063796 0.889444702 1 16.24226312 4.744279787 24.92353517 0.93416713 0.448381975 0.850668575 0.06153303 205.1273546 893896.2255 0.013953769 0.123925114 55498.3136 -4.744279787 -0.485785155 GYNPGLLVHPDLAYLQAEGGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYNPGLLVHPDLAYLQAEGGGDR 23 0 P19838;P19838-2;A0A494C1E9;A0A494C157;D6RH30 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 0 197.92 2.88E-24 211390000 119210 139360 125690 129060 138980 148820 135400 134580 121340 144230 FALSE TRUE 123916.5029 163293.9959 128965.5847 154587.6828 115356.2292 114258.8104 124786.9942 132776.1752 116972.9971 172489.107 0.718401904 0.946691642 0.747673791 0.896217074 0.668773995 0.662411745 0.723448549 0.769765567 0.678147154 1 17.39614573 5.075049036 14.62224666 0.775809492 0.000164631 0.022397537 0.11462263 784465.4674 3175651.818 0.026199539 18576297.31 118863.6429 -5.075049036 -0.775644862 GYPHWPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 135.35 0.00083753 4437400000 3539540 4401300 3593640 3600780 5443110 5016860 4219010 3673160 3440560 6438880 FALSE TRUE 3679283.772 5157189.038 3687293.211 4313003.537 4517892.106 3851770.296 3888312.972 3623927.298 3316734.918 7700455.256 0.477800812 0.669725213 0.478840937 0.560097214 0.586704546 0.500200335 0.504945856 0.470612084 0.430719329 1 22.87651231 -1.823664727 4.282363488 1.084118196 0.521346006 0.828272401 0.065571243 0.036536613 0.001504471 0.044049307 0.014907023 0.01500843 1.823664727 -0.56277219 GYPPEDIFNLVGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYPPEDIFNLVGKK 14 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 179.41 3.00E-06 710990000 1076070 834760 916160 646710 1369180 1147790 928700 930080 1051720 1001310 FALSE TRUE 1118554.075 978123.5365 940035.8822 774627.3078 1136447.273 881233.1674 855906.0673 917613.7989 1013868.803 1197497.523 0.934076316 0.816806313 0.785000273 0.646871741 0.949018474 0.735895608 0.714745585 0.766276156 0.846656284 1 20.19159124 0.900327757 4.076945487 0.999930471 0.788015208 0.333850886 0.087531001 0.529933213 18.74531002 0.081729579 0.02087065 7.949279314 -0.900327757 -0.211915263 GYS(ph)PDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 GYSPDTR 7 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 GYS(1)PDTR;GYS(0.999)PDT(0.001)R;GY(0.455)S(0.545)PDTR;GY(0.001)S(0.999)PDTR;GYS(1)PDTR 128.93 0.0038912 2533930000 3443850 4023840 3669820 3849880 3948190 4541050 3940830 3925020 3588090 4121730 TRUE FALSE 3579815.857 4714903.219 3765458.524 4611374.773 3277078.074 3486459.958 3631937.447 3872411.527 3458955.342 4929304.078 0.726231492 0.956504842 0.763892522 0.935502193 0.664815565 0.707292531 0.736805316 0.785589906 0.701712714 1 22.23295255 GYSDRDGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 191.4 7.26E-07 4723615000 2669504 3789832 3105236 2703755 3843434 3608527 2308804 2995065 2966341 4906683 FALSE TRUE 2774898.079 4440706.165 3186161.001 3238549.669 3190128.462 2770501.292 2127833.91 2954921.053 2859582.967 5868053.59 0.472882198 0.756759647 0.542967264 0.55189504 0.543643376 0.472132923 0.362613237 0.503560679 0.48731371 1 22.48445062 -1.370981852 5.735072197 1.0001183 0.520875667 0.698905513 0.094213746 0.000149689 1.64E-05 0.09581884 0.022579198 0.04256162 1.370981852 -0.479242632 GYSFTTTAER ddPTM_MDA-MB-175_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 ;;;;;;;;;;; 218.73 1.55E-08 61739220000 4405140 4912050 4457510 4504990 5314320 5518760 5069500 4507880 4323840 5624660 FALSE TRUE 4579058.329 5755656.377 4573676.372 5396063.576 4410993.785 4237111.628 4672139.343 4447459.242 4168225.843 6726704.436 0.680728338 0.855642824 0.67992825 0.802185324 0.65574366 0.629894128 0.694565874 0.661164659 0.619653484 1 22.68146844 -1.06139164 4.467018872 1.000017607 0.698796507 0.620580492 0.070902216 9594239.033 2279651.432 1811.680898 0.016770286 0.086817717 1.06139164 -0.3012211 GYSYDLEVEQAYDLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYSYDLEVEQAYDLAR 16 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 210.14 2.43E-11 299870000 195717 209649 222140 259170 223360 240970 250010 227110 224870 203042 FALSE TRUE 203444.0583 245654.5849 227929.1509 310433.0525 185393.347 185008.3694 230413.5629 224065.9619 216776.9726 242824.1924 0.837824503 1.011656139 0.938659153 1.2784272 0.763487959 0.761902542 0.948890473 0.922749746 0.892732188 1 17.88955264 GYT(ph)SDDDTWEPEIHLEDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.5)S(0.5)DDDTWEPEIHLEDCK 139.44 6.80E-07 47639000 66274 75207 72855 76931 83977 91330 85683 76999 85805 55056 TRUE FALSE 68890.54869 88123.21722 74753.66115 92147.72218 69702.61954 70119.99162 78966.94257 75966.95435 82716.89481 65843.16909 1.046282396 1.338380555 1.135329028 1.399503144 1.058615806 1.064954688 1.199318679 1.153756045 1.25627147 1 16.00674616 3.171716799 25 1.133958114 1.230896666 0.170707254 0.114544537 102.4012477 38297.38117 0.031316433 0.037430311 1484.966989 -3.171716799 0.096938552 GYT(ph)SDSEVYTDHGRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GYTSDSEVYTDHGRPGK 17 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 GYT(0.5)S(0.5)DSEVYTDHGRPGK 206.7 9.89E-12 661020000 560460 484470 616640 537560 635570 705140 613220 550430 595040 509500 TRUE FALSE 582587.3936 567673.9538 632710.145 643887.7635 527536.0384 541381.9215 565154.214 543052.3862 573624.6266 609326.77 0.956116524 0.93164125 1.038375755 1.056719966 0.865768688 0.888491936 0.927505965 0.891233428 0.94140723 1 19.2168566 3.231368874 24.99956969 0.911411648 0.994184109 0.371446274 0.048214953 165.8630416 576564.0734 0.014055267 0.017129552 1703.604873 -3.231368874 0.08277246 GYTS(ph)DDDTWEPEIHLEDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYTSDDDTWEPEIHLEDCK 19 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 GYT(0.154)S(0.846)DDDTWEPEIHLEDCK;GYT(0.126)S(0.874)DDDTWEPEIHLEDCK 297.4 6.11E-50 275958000 349610 349010 337050 375300 423420 504160 452450 386110 374450 282272 TRUE FALSE 363412.8728 408949.7526 345833.7999 449533.2198 351447.2196 387076.4806 416985.7867 380934.827 360973.6176 337577.794 1.076530741 1.211423737 1.024456602 1.331643336 1.041085124 1.146628977 1.235228721 1.128435679 1.069304984 1 18.36486048 1.080657881 2.558829997 1.002338839 1.153858937 0.233952913 0.087963122 0.337572236 4.448035398 0.075777901 0.020637043 12.04087039 -1.080657881 0.151520098 GYTS(ph)DSEVYTDHGRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.432)S(0.568)DSEVYTDHGRPGK;GYT(0.085)S(0.915)DSEVYTDHGRPGK;GYT(0.026)S(0.829)DS(0.145)EVYTDHGRPGK;GYT(0.001)S(0.994)DS(0.005)EVYTDHGRPGK;GYT(0.039)S(0.887)DS(0.075)EVYTDHGRPGK;GYT(0.002)S(0.997)DSEVYTDHGRPGK;GYT(0.02)S(0.979)DS(0.001)EVYTDHGRPGK;GYT(0.13)S(0.869)DS(0.001)EVYTDHGRPGK 279.53 4.28E-36 23375140000 5460976 4561299 5627740 4893735 6592015 6886725 5860009 5225228 5558902 4684555 TRUE FALSE 5676579.549 5344666.621 5774403.528 5861701.177 5471506.645 5287387.488 5400686.182 5155192.365 5358838.203 5602403.861 1.013239975 0.953995241 1.030701047 1.046283224 0.976635527 0.943771213 0.963994442 0.92017507 0.956524795 1 22.41761456 3.010481353 8.133624587 0.950952293 1.008843734 0.426784032 0.029178233 0.129246974 60.13785312 0.008691641 0.010161666 1024.427795 -3.010481353 0.057891441 GYWAGLDASAQTTSHELTIPNDLIGCIIGR ddPTM_MDA-MB-175_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 ;; 234.95 2.06E-45 523052000 225586 252579 249479 259927 237516 291374 243665 246046 221692 258037 FALSE TRUE 234492.3095 295957.4785 255980.6277 311339.7848 197143.1152 223706.8043 224565.9006 242748.1558 213713.3482 308594.4097 0.759872188 0.959050032 0.829505071 1.008896386 0.638842147 0.724921765 0.727705666 0.786625254 0.692537977 1 18.2353524 3.236594125 24.99989833 0.749770094 0.89003757 0.241155652 0.109615478 64.20445309 816232.6791 0.028683432 0.035956372 1724.225745 -3.236594125 0.140267476 GYWASLDASTQTTHELTIPNNLIGCIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 GYWASLDASTQTTHELTIPNNLIGCIIGR 29 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;; 315.43 3.41E-92 610921000 584307 705413 656717 702959 696226 800651 617976 691734 605754 761787 FALSE TRUE 607375.8915 826562.1954 673831.5845 842002.1921 577881.7532 614711.9392 569537.4263 682462.4372 583953.0319 911044.5774 0.66668076 0.907268663 0.739625262 0.924216238 0.634306781 0.674733108 0.625147705 0.749098841 0.640970866 1 19.79716212 5.035504981 15.98047075 0.751205812 0.354570695 0.040372143 0.128016079 10171096.98 128477530 0.029271833 113535451.3 108518.7997 -5.035504981 -0.396635116 GYWGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GYWGNK 6 0 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 135.81 0.031271 2176200000 2133220 2086390 2385000 2105060 2644000 2501000 2386700 2232090 2257600 2119220 FALSE TRUE 2217441.173 2444711.253 2447155.059 2521434.585 2194573.824 1920180.653 2199624.218 2202172.485 2176349.417 2534440.584 0.874923321 0.964596001 0.96556024 0.994868296 0.86590068 0.757634906 0.867893385 0.86889884 0.858709978 1 21.27323591 3.170546393 8.30539961 0.858234457 0.952009624 0.274646048 0.06211824 0.29171021 31.81839225 0.017355023 0.020807087 1480.97045 -3.170546393 0.093775166 GYYS(ph)PYSVSGSGS(ph)TAGSR ddPTM_MDA-MB-175_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 GYYS(0.964)PY(0.009)S(0.041)VS(0.243)GS(0.146)GS(0.408)T(0.061)AGS(0.129)R 131.31 5.40E-06 0 325960 314680 225010 244200 213460 197810 142860 150460 140370 147170 TRUE FALSE 338829.1525 368723.8421 230873.9454 292502.0311 177176.1454 151871.6253 131662.2599 148443.3298 135318.1111 176005.1438 1.925109376 2.094960603 1.311745444 1.661894788 1.006653224 0.862881744 0.748059159 0.843403361 0.768830434 1 17.42525807 3.590553646 0.868482303 0.795308467 2.055892133 0.849495624 0.184262495 0.236316095 0.345332249 0.074081684 0.205725402 3895.414222 -3.590553646 1.260583666 GYYS(ph)PYSVSGSGSTAGS(ph)R ddPTM_MDA-MB-175_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 GYYS(0.948)PY(0.051)S(0.001)VSGSGS(0.003)T(0.012)AGS(0.985)R 209.71 2.98E-18 0 294150 337290 246400 220160 209130 188170 146040 150790 128760 151720 TRUE FALSE 305763.2691 395216.9337 252821.3864 263706.9909 173582.1573 144470.3692 134593.0032 148768.9067 124125.9528 181446.6291 1.685141634 2.17814426 1.393365022 1.453358446 0.956656831 0.796214126 0.741777369 0.819904494 0.684090707 1 17.46918573 3.544455371 1.151506198 0.780356715 1.92352576 0.850085183 0.180285253 0.160682724 0.426218305 0.058817845 0.132130399 3503.122879 -3.544455371 1.143169045 GYYS(ph)PYSVSGSGSTAGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.951)PYS(0.049)VS(0.001)GSGSTAGSR;GYYS(0.983)PYS(0.017)VSGSGSTAGSR;GYYS(0.348)PYS(0.348)VS(0.303)GSGSTAGSR;GYYS(0.852)PYS(0.144)VS(0.004)GSGSTAGSR;GYYS(0.796)PYS(0.204)VSGSGSTAGSR 347.98 2.81E-90 4215310000 1520390 1747330 1417160 1283740 1368950 1426370 1106700 1132690 1125340 1170470 TRUE FALSE 1580416.171 2047420.335 1454092.354 1537659.94 1136256.368 1095117.184 1019953.962 1117508.143 1084839.233 1399801.186 1.129029027 1.462650807 1.038784913 1.098484524 0.811726964 0.78233766 0.728642019 0.798333473 0.774995223 1 20.41679051 3.552005185 1.42008081 0.791991072 1.27666295 0.694491354 0.12053907 0.200100707 0.803716696 0.035766621 0.072597654 3564.553892 -3.552005185 0.484671878 GYYSPYS(ph)VSGSGSTAGSR ddPTM_MDA-MB-175_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 GYYS(0.142)PYS(0.848)VS(0.01)GSGSTAGSR 400.75 6.63E-128 1003100000 289840 309470 221040 229710 224630 239150 205180 189380 205070 221440 TRUE FALSE 301283.107 362619.0652 226800.484 275145.9524 186447.4728 183611.0369 189097.4555 186841.6709 197689.5708 264826.9283 1.137660392 1.369268101 0.856410205 1.038965162 0.704035175 0.693324648 0.714041645 0.705523687 0.746485911 1 18.0146903 3.871459951 1.208934707 0.740581483 1.264274316 0.608123908 0.13784429 0.307250583 0.814664762 0.040721043 0.137234084 7438.064694 -3.871459951 0.523692833 GYYSPYSVS(ph)GSGS(ph)TAGSR ddPTM_MDA-MB-175_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 2 GYYSPYS(0.011)VS(0.989)GS(0.179)GS(0.678)T(0.103)AGS(0.04)R;GYYSPYS(0.035)VS(0.964)GS(0.001)GS(0.973)T(0.023)AGS(0.003)R;GYYS(0.001)PY(0.004)S(0.118)VS(0.875)GS(0.143)GS(0.364)T(0.307)AGS(0.187)R 217.35 1.24E-18 338000000 603370 765150 562476 601480 556246 601710 459924 482016 401299 507549 TRUE FALSE 627191.5135 896558.5605 577134.5866 720450.9488 461695.5036 461971.9715 423873.9551 475555.3639 386856.3274 606993.5089 1.033275487 1.47704802 0.950808498 1.186917056 0.760626756 0.761082227 0.698317114 0.783460378 0.637331902 1 19.21132156 3.236902313 24.86982195 0.75862104 1.169428887 0.602011773 0.154436556 24.88523238 373210.0173 0.040998341 0.05150332 1725.449737 -3.236902313 0.410807847 GYYSPYSVS(ph)GSGSTAGSR ddPTM_MDA-MB-175_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 GYYSPYSVS(0.839)GS(0.161)GSTAGSR;GYYSPYS(0.013)VS(0.975)GS(0.013)GSTAGSR;GYYSPYS(0.002)VS(0.997)GS(0.001)GSTAGSR;GYYSPYSVS(0.997)GS(0.003)GSTAGSR 346.15 3.13E-90 1807460000 1377210 1679580 1223330 1306000 1300250 1432340 1164810 1150840 1122120 1309710 TRUE FALSE 1431583.314 1968034.8 1255210.985 1564322.902 1079233.969 1099700.742 1073509.149 1135414.872 1081735.12 1566322.599 0.913977309 1.256468368 0.801374497 0.998723318 0.689024068 0.702090836 0.685369125 0.724892096 0.690620899 1 20.57894995 3.60030553 1.39665469 0.729025506 1.056641107 0.383096034 0.143134083 0.362846766 1.39562293 0.04209072 0.090843847 3983.873411 -3.60030553 0.327615601 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_MDA-MB-175_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 2 GYYSPYSVSGS(0.004)GS(0.994)T(0.003)AGS(1)R;GYYSPYSVSGSGS(1)TAGS(1)R;GYYSPYSVS(0.006)GS(0.343)GS(0.645)T(0.027)AGS(0.979)R;GYYSPYSVSGSGS(0.975)T(0.032)AGS(0.993)R 324.71 6.15E-62 2603560000 2382370 2802390 2490240 2956430 2967660 2902840 2117630 2429040 2132620 2822570 TRUE FALSE 2476427.807 3283678.683 2555137.7 3541203.03 2463218.213 2228699.403 1951644.627 2396482.692 2055867.423 3375598.55 0.73362628 0.972769313 0.756943595 1.049059293 0.72971302 0.660238287 0.578162539 0.709943039 0.609037891 1 21.68671191 3.021283628 24.53894855 0.685209877 0.877855137 0.241898016 0.138322292 216.9380267 250116.4561 0.036493414 0.04361401 1050.228085 -3.021283628 0.19264526 GYYSPYSVSGSGS(ph)TAGSR ddPTM_MDA-MB-175_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 GYYSPYSVS(0.001)GS(0.05)GS(0.316)T(0.316)AGS(0.316)R 111.43 0.0002619 0 55591 45307 45697 41977 55971 62125 47074 48359 46735 45488 TRUE FALSE 57785.77561 53088.12481 46887.90136 50279.92531 46457.06941 47697.41026 43384.21687 47710.8267 45053.01648 54400.50268 1.062228707 0.97587563 0.861901987 0.924254792 0.853982355 0.876782528 0.797496617 0.877029151 0.828172797 1 15.73133236 4.622747481 1.41446397 0.866804768 1.122167066 0.54629255 0.053307326 0.639235235 1.368781037 0.013464108 0.218055196 41951.49873 -4.622747481 0.255362298 GYYSPYSVSGSGST(ph)AGSR ddPTM_MDA-MB-175_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(0.153)T(0.423)AGS(0.423)R;GYYSPYSVSGSGS(0.015)T(0.492)AGS(0.492)R 322.39 1.09E-60 2327100000 481410 446210 406910 452120 461620 565160 357020 435210 364580 440850 TRUE FALSE 500416.4385 522843.0965 417514.4089 541547.9866 383153.9973 433910.1551 329035.8395 429376.7218 351458.837 527226.1169 0.949149563 0.99168664 0.791907676 1.027164568 0.726735617 0.823005806 0.624088657 0.814407155 0.666618792 1 19.00806231 3.226082889 24.99944546 0.761805652 0.933094268 0.336260763 0.111794051 228.9120474 458630.4065 0.029658717 0.035680697 1682.995243 -3.226082889 0.171288616 GYYSPYSVSGSGSTAGS(ph)R ddPTM_MDA-MB-175_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 GYYSPYSVSGSGS(0.021)T(0.017)AGS(0.962)R;GYYSPYSVSGSGSTAGS(1)R;GYYSPYSVSGS(0.038)GS(0.127)T(0.127)AGS(0.707)R;GYYSPYSVSGSGS(0.135)T(0.135)AGS(0.73)R 416.22 9.55E-148 4436220000 850450 902835 766467 893628 916019 1059390 789425 871875 761043 954455 TRUE FALSE 884026.4227 1057889.888 786441.7597 1070384.951 760314.4176 813362.7277 727547.8057 860188.9417 733653.2111 1141462.183 0.774468428 0.926784876 0.688977499 0.937731418 0.666088136 0.712562133 0.637382312 0.753585142 0.642731071 1 20.12245163 4.231165299 24.99844618 0.74245304 0.850626659 0.083846779 0.121143392 307.9321329 1040918.363 0.028106778 0.062687141 17028.06501 -4.231165299 0.10817362 GYYSPYSVSGSGSTAGS(ph)RTGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 GYYSPYSVSGS(0.001)GS(0.016)T(0.054)AGS(0.927)RT(0.005)GS(0.997)R;GYYSPYSVSGS(0.001)GS(0.012)T(0.055)AGS(0.93)RT(0.383)GS(0.618)R;GYYSPYSVSGSGS(0.012)T(0.052)AGS(0.936)RT(0.367)GS(0.633)R;GYYSPYSVSGS(0.002)GS(0.02)T(0.05)AGS(0.926)RT(0.049)GS(0.954)R 107.32 0.00026068 1232770000 1024030 1810780 1622990 1103200 2036670 1968820 822830 1444360 1545690 3004260 TRUE FALSE 1064459.495 2121767.379 1665286.453 1321409.667 1690477.561 1511591.393 758334.4345 1425000.717 1490060.919 3592887.227 0.296268552 0.590546612 0.46349533 0.367784899 0.470506713 0.42071774 0.211065471 0.396617157 0.414725213 1 21.77671222 0.692339615 5.453014273 0.999999969 0.402512783 0.774609539 0.096545987 15.91433066 281.9934973 0.09404702 0.023704626 4.92424457 -0.692339615 -0.597487186 HAAENPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 130.22 0.0018279 2104327000 3512600 2490130 3222760 2680320 3721890 3735870 4146340 3316470 3529170 2050156 FALSE TRUE 3651280.16 2917790.457 3306747.773 3210479.296 3089244.467 2868270.81 3821339.036 3272018.144 3402155.861 2451844.816 1.489197088 1.190038798 1.348677433 1.309413743 1.259967371 1.169841905 1.558556648 1.334512741 1.387590209 1 21.22543624 -2.058965475 2.494780655 0.528499284 1.335984553 0.44009842 0.114554355 5340008.198 1293219.533 14399421.17 0.026459535 0.008730408 2.058965475 0.807485268 HAAENPGKYNILGTNTIMDK ddPTM_MDA-MB-175_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 ; 154.11 2.72E-08 1452060000 1777510 1324890 1920150 1048720 2630400 2016780 1545220 1770670 2222500 1515390 FALSE TRUE 1847687.467 1552429.551 1970190.686 1256153.686 2183285.548 1548413.41 1424101.619 1746937.065 2142512.659 1812301.657 1.019525343 0.856606595 1.087120723 0.693126159 1.204703168 0.85439055 0.785797228 0.96393283 1.18220532 1 20.78939168 1.409489488 8.367211077 1.087254612 0.926204159 0.161188155 0.145896249 0.443316048 47.10696158 0.088908264 0.033326748 25.67376066 -1.409489488 -0.161050453 HAASNPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAASNPSK 8 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 59.8 0.096332 17606000 22901 29924 25474 19242 33973 40585 29615 28204 24132 30917 FALSE TRUE 23805.14916 35063.21422 26137.87337 23048.01017 28198.28159 31159.74882 27293.69892 27825.97151 23263.49403 36974.59421 0.643824487 0.948305586 0.706914408 0.623347211 0.76263938 0.842734031 0.738174401 0.752570031 0.629175101 1 15.17424669 -1.010690345 4.746240072 1.000005142 0.744880033 0.401333318 0.095492579 2.08922E+11 43555241833 12252487.59 0.021515518 0.097568506 1.010690345 -0.255125109 HAASNPSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAASNPSKK 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 118.18 0.0006697 44084000 138630 127840 152410 104130 227480 189180 158380 149090 156800 141870 FALSE TRUE 144103.2194 149795.5255 156381.9298 124726.6032 188813.0309 145245.8121 145965.7618 147091.6924 151156.7986 169666.7102 0.849331134 0.882881063 0.921700725 0.735127139 1.112846654 0.85606547 0.860308787 0.866944919 0.890904282 1 17.372344 -2.805619857 1.714603267 3.744059382 0.885965957 0.128786299 0.088766162 3464360.62 76151.90537 37149607.01 0.021568071 0.001564516 2.805619857 -2.858093425 HADGEKEDQFNGS(ph)PPRPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 232.59 1.05E-26 2944190000 1568697 1036059 1358055 1014424 1800640 1814500 1640397 1326799 1462725 893547 TRUE FALSE 1630630.369 1213994.074 1393447.029 1215074.039 1494567.856 1393109.874 1511818.397 1309015.43 1410081.813 1068620.427 1.525921018 1.136038619 1.303968176 1.137049236 1.398595627 1.303652671 1.414738441 1.22495827 1.319534774 1 20.02731807 -0.666811856 1.062993839 0.988542141 1.299519165 0.386880374 0.115573394 69.01619183 39.30318399 3.316247799 0.031846285 0.215371456 0.666811856 0.310977024 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.52)S(0.344)DT(0.136)EMEDMIAEETLEEMDSELLK;HADNS(0.483)S(0.483)DT(0.033)EMEDMIAEETLEEMDSELLK;HADNS(0.333)S(0.333)DT(0.333)EMEDMIAEETLEEMDSELLK;HADNS(0.457)S(0.457)DT(0.086)EMEDMIAEETLEEMDSELLK 284.8 3.09E-62 364950000 149250 138403 161687 124336 221157 198907 209796 180742 184567 110359.4 TRUE FALSE 155142.5052 162172.6386 165900.696 148929.2897 183564.8121 152713.8637 193351.6413 178319.4491 177924.4697 131982.2115 1.175480419 1.228746183 1.256992849 1.12840426 1.390829947 1.15707914 1.464982585 1.351086992 1.348094321 1 17.00998397 3.239564806 24.99988514 1.312204062 1.203900734 0.079065715 0.127985138 51.23537582 1275513.599 0.033962907 0.043485121 1736.060302 -3.239564806 -0.108303328 HADNSS(ph)DTEMEDMIAEETLEEMDSELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.227)S(0.769)DT(0.004)EMEDMIAEETLEEMDSELLK;HADNS(0.182)S(0.775)DT(0.043)EMEDMIAEETLEEMDSELLK 259.74 3.78E-53 198856000 100403 83836 102996 88716 148032 150022 140179 116989 137788 85503 TRUE FALSE 104366.988 98234.18085 105680.1604 106263.76 122869.5735 115181.6641 129191.4037 115420.9538 132829.0368 102255.6758 1.020647384 0.960672159 1.033489433 1.039196692 1.201591722 1.126408517 1.26341548 1.128748628 1.298989379 1 16.6418214 3.334466405 4.08616926 1.177456316 1.005302274 0.484479583 0.079123428 0.167401319 5.165122127 0.020643454 0.028200111 2160.062934 -3.334466405 -0.172154043 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.303)S(0.303)DT(0.395)EMEDMIAEETLEEMDSELLK;HADNS(0.298)S(0.298)DT(0.404)EMEDMIAEETLEEMDSELLK;HADNS(0.302)S(0.302)DT(0.343)EMEDMIAEET(0.053)LEEMDSELLK 132.24 5.51E-05 103024000 44866.5 37038.7 47478 35551.6 62703 58412 56811.7 47142 47900.2 31628.1 TRUE FALSE 46637.86406 43399.8086 48715.31568 42583.60037 52044.76646 44846.69824 52358.6505 46510.1386 46176.28116 37825.02064 1.232989785 1.147383607 1.287912468 1.12580508 1.375934912 1.18563579 1.38423323 1.22961304 1.220786675 1 15.20705325 0.671697557 2.593376649 1.000035214 1.248007306 0.44950207 0.081236305 2.148675725 15.91511733 0.072380858 0.019240472 4.69566988 -0.671697557 0.247972092 HADNSSDTEMEDMIAEET(ph)LEEMDSELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 HADNS(0.231)S(0.231)DT(0.231)EMEDMIAEET(0.308)LEEMDSELLK 92.675 0.0074995 42936000 17624 14521 18024 17129 21231 25505 20263 15745 18108 15284 TRUE FALSE 18319.80913 17014.86879 18493.72025 20517.06508 17622.1622 19581.85028 18674.73311 15533.96403 17456.29662 18278.60717 1.002254108 0.930862436 1.01176857 1.122463265 0.964086707 1.071298819 1.021671561 0.849843967 0.955012406 1 14.15786852 1.767359328 25 0.920019122 1.018219136 0.270170305 0.060909966 23.66430327 20554.65811 0.027945019 0.015498843 58.52741293 -1.767359328 0.098200014 HAEATLGSGNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HAEATLGSGNLR 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;;; 164.81 5.63E-05 1148500000 561464 716630 708890 721640 744910 881370 695810 756550 657780 748380 FALSE TRUE 583631.0323 839705.6279 727364.2558 864378.2381 618290.4643 676685.1748 641270.594 746409.6847 634106.6263 895010.7324 0.652093892 0.938207328 0.812687747 0.96577416 0.69081905 0.756063755 0.716494865 0.833967301 0.708490528 1 19.77154546 4.777298436 23.14068159 0.813309388 0.65209276 0.185300024 0.10619158 15710.85246 9384630.286 0.024145639 6.396494175 59882.295 -4.777298436 -0.161216629 HAEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HAEELER 7 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;;; 149.4 0.0020189 1291640000 511385 533782 580142 566297 636889 696804 550940 536474 543274 540556 FALSE TRUE 531574.8747 625454.9063 595260.9771 678308.8564 528630.8353 534981.8312 507755.8832 529283.4435 523721.6749 646467.5986 0.822276129 0.96749614 0.920790119 1.049254221 0.817722089 0.827546241 0.785431295 0.818731588 0.810128266 1 19.30221854 3.191709613 24.99542542 0.828690805 0.940552939 0.264986168 0.076619528 129.9773691 69343.60083 0.020745542 0.024795735 1554.925598 -3.191709613 0.111862133 HAEFESLCAQYSADKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAEFESLCAQYSADKR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 236.81 6.28E-20 753020000 752800 631410 830450 706850 1052950 1051460 996930 868050 861260 572770 FALSE TRUE 782521.1253 739849.7558 852092.2092 846662.8203 873969.9351 807274.35 918788.0216 856415.2096 830263.4208 684993.3152 1.142377755 1.080083177 1.243942372 1.236016179 1.27588097 1.178514202 1.341309472 1.250253383 1.212075217 1 19.38573038 4.232319581 24.98610081 1.234732825 1.111230456 0.17335914 0.086077185 164.4206251 658270.5958 0.019480617 0.043782922 17073.38294 -4.232319581 -0.123502369 HAEFESLCAQYSADKREDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAEFESLCAQYSADKREDEK 20 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 173.27 3.08E-12 59355000 193180 87950 136750 69720 253040 197330 136810 132040 164100 85335 FALSE TRUE 200806.8956 103054.7283 140313.8173 83510.40791 210028.3512 151503.0981 126086.4747 130270.2198 158194.0731 102054.7594 1.967638714 1.009798357 1.374887542 0.818290184 2.057996632 1.484527512 1.235478634 1.276473734 1.550090108 1 16.63898394 -1.072558344 5.52949932 0.99999709 1.392095743 0.102901396 0.363562534 1.23E-05 2.06E-06 0.330666128 0.077938173 0.084613889 1.072558344 0.392098653 HAEMVHTGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 196.27 1.95E-07 1976390000 2458437 2057119 2357050 1996458 3102474 3078841 2851843 2435609 2515485 1926455 FALSE TRUE 2555497.991 2410413.186 2418476.659 2391351.434 2575116.578 2363826.838 2628308.094 2402963.645 2424953.186 2303906.973 1.1092019 1.046228522 1.049728434 1.037954857 1.117717255 1.026007936 1.140804783 1.042995083 1.05253954 1 21.13565103 -1.436483611 2.987793172 0.998581759 1.068496301 0.238000632 0.037147305 843183.752 838841.2659 6686.996451 0.007973593 0.036602975 1.436483611 0.069914542 HAFSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAFSLK 6 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 121.68 0.019546 947590000 2340500 2342400 2769100 2245300 3571000 3411200 3073400 2899400 2822500 2371600 FALSE TRUE 2432904.747 2744688.979 2841265.021 2689413.638 2964002.696 2619000.497 2832498.877 2860538.285 2720918.776 2836269.613 0.857783314 0.967710885 1.00176126 0.948222139 1.045035593 0.92339617 0.99867053 1.008556546 0.959330088 1 21.43556325 4.730730148 3.433692283 0.9863949 0.842624246 0.576249002 0.032674533 0.190523844 3.867937919 0.007333147 0.070864231 53793.54292 -4.730730148 -0.143770654 HAGVYSTGLAMVGAICDFCEAWVCHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAGVYSTGLAMVGAICDFCEAWVCHGR 27 0 Q9Y3S2;D6RBR7;D6R8Y9;D6R9C8 Q9Y3S2 ZNF330 Zinc finger protein 330 0 112.23 0.0006826 162440000 62387 86083 87729 77214 100990 116240 74866 97953 87790 94040 FALSE TRUE 64850.08693 100867.0856 90015.28981 92486.69874 83823.75587 89245.02163 68997.80729 96640.10025 84630.45505 112465.3375 0.576622881 0.896872653 0.800382516 0.822357366 0.745329697 0.793533578 0.61350287 0.85928787 0.752502566 1 16.7791209 -0.100190547 1.064550943 1.002157764 0.767605973 0.356418353 0.09540043 13.017675 11.28421293 0.198651696 0.026504965 0.793979799 0.100190547 -0.234551791 HAHGDQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAHGDQYK 8 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 133.23 0.00092812 72252000 214718 188919 190915 171406 219900 307510 205650 157593 189679 222750 FALSE TRUE 223195.2324 221364.3687 195890.4017 205309.5952 182521.4765 236095.4629 189530.6156 155480.7236 182852.4898 266393.5977 0.837840077 0.8309673 0.735342003 0.770700186 0.685157144 0.886265529 0.711468358 0.583650377 0.686399716 1 18.02319988 4.632370509 0.767264976 0.72670322 0.910450946 0.011696269 0.112561706 5.647690859 2.815244334 0.042523805 0.869313134 42891.42836 -4.632370509 0.183747725 HAHLTDTEIMTLVDETNMYEGVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HAHLTDTEIMTLVDETNMYEGVGR 24 0 O60925;E5RGS4 O60925 PFDN1 Prefoldin subunit 1 0 ;;; 250.83 6.06E-39 492103000 132963 190468 204791 194910 218793 251587 201457 179751 186058 207123 FALSE TRUE 138212.4819 223179.3974 210128.0217 233462.6163 181602.644 193159.7321 185666.2739 177341.7319 179361.8089 247704.7862 0.557972593 0.900989443 0.848300208 0.942503453 0.733141441 0.779798142 0.749546574 0.715939868 0.724095047 1 17.91826222 HAIVICNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAIVICNR 8 0 P53621;A0A3B3IT15;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 132.29 0.00096878 307010000 301480 343850 365220 372630 399700 473640 365830 350520 343630 312370 FALSE TRUE 313382.6632 402903.5627 374737.9332 446335.1018 331759.1368 363644.2881 337155.2887 345821.8527 331262.8234 373572.9208 0.838879495 1.078513833 1.003118568 1.194773703 0.888070624 0.973422504 0.902515332 0.925714455 0.886742066 1 18.51103036 HALYPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HALYPPSPR 9 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 HALYPPS(1)PR;HALY(0.001)PPS(0.999)PR 59.198 0.066891 248816000 225050 272400 258290 291730 404160 405930 338230 312190 277020 367700 TRUE FALSE 233935.1478 319182.581 265021.2496 349433.3233 335461.0276 311658.9094 311718.6488 308005.6037 267050.1043 439743.775 0.531980578 0.725837634 0.602671976 0.79462938 0.76285566 0.708728417 0.708864267 0.700420611 0.607285696 1 18.74630363 -2.448433077 2.226348364 4.088988498 0.689969266 0.609468683 0.076018873 2400368.65 253220.295 37341117.79 0.017636151 0.003560959 2.448433077 -3.399019232 HAPEHHPGHGDRLS(ph)PGERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAPEHHPGHGDRLSPGERR 19 2 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 HAPEHHPGHGDRLS(1)PGERR;HAPEHHPGHGDRLS(1)PGERR 134.81 5.60E-06 129979000 47118 51892 47776 49708 57675 59146 43262 47076 45457 60222 TRUE FALSE 48978.25502 60804.04734 49021.08181 59540.09404 47871.4241 45410.23787 39871.0114 46445.02322 43821.01145 72021.34788 0.680051908 0.844250339 0.680646548 0.826700635 0.664683813 0.630510803 0.553599906 0.644878562 0.608444756 1 16.13613698 4.078204173 24.73165981 0.679699605 0.762227667 0.013690903 0.127482597 84.63486397 26759.9333 0.030368122 0.065602639 11973.03283 -4.078204173 0.082528062 HAPGLIAALAYETANFYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAPGLIAALAYETANFYQK 19 0 F5GXQ0;Q5VW32-2;Q5VW32 F5GXQ0 BROX BRO1 domain-containing protein BROX 0 ; 246.96 5.71E-29 211380000 378730 278340 358070 307840 415580 481860 429800 324310 395450 226030 FALSE TRUE 393682.5528 326142.7298 367401.5984 368729.8332 344939.86 369955.3177 396111.1529 319963.1549 381217.8317 270316.2509 1.456377674 1.206522837 1.359154683 1.364068316 1.276060388 1.368601837 1.465361966 1.183662299 1.410266051 1 18.04428872 -2.975062157 0.484214521 6.01E-08 1.337434639 0.555629699 0.091474383 158.5919853 5.641203428 164.3494743 0.042019199 0.001059102 2.975062157 1.337434579 HAPHCLS(ph)EEEGEQDRPR ddPTM_MDA-MB-175_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 224.89 1.55E-15 4105970000 600456 741345 683004 743230 802446 938719 715210 769744 748696 845618 TRUE FALSE 624162.4665 868665.2369 700803.6453 890238.6757 666046.5155 720715.7387 659149.9713 759426.8407 721750.5772 1011300.657 0.617187839 0.858958442 0.6929726 0.880290811 0.658603859 0.712662188 0.65178438 0.750940717 0.713685463 1 19.94778054 -1.040704835 5.176610887 1.000002924 0.729715977 0.506698661 0.080942955 2.51E-06 4.65E-07 0.071911228 0.016949456 0.09105319 1.040704835 -0.270286947 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK 227.42 3.70E-35 571700000 182590 109730 169920 120620 191750 198160 179120 161090 172010 122650 TRUE FALSE 189798.7942 128575.2739 174348.2548 144478.276 159156.4035 152140.3431 165080.1064 158930.852 165819.3937 146680.9192 1.293956945 0.876564413 1.188622595 0.984983437 1.085051855 1.037219728 1.125436814 1.083514154 1.130476919 1 17.16232169 2.239775849 24.99978936 1.092127669 1.069746333 0 0.11015447 247.6253438 5094303.951 0.035661626 0.02830842 173.6904136 -2.239775849 -0.022381336 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 169.57 4.23E-13 369560000 144930 80475 134820 86695 151020 157490 152970 109490 141470 85365 TRUE FALSE 150651.9483 94295.95524 138333.52 103843.0122 125349.6743 120915.3343 140979.8117 108022.4656 136378.5223 102090.6373 1.475668604 0.923649393 1.355006919 1.017164893 1.227827327 1.184392001 1.380927922 1.058103549 1.335857292 1 16.63949104 -1.116199303 3.958717013 0.999936897 1.20279125 0.126226266 0.167734342 13037001.53 38990531.91 12088.87024 0.036691444 0.076524535 1.116199303 0.202854352 HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 HAPT(0.001)YT(0.004)IPLS(0.995)PVLS(0.961)PT(0.039)LPAEAPTAQVPPSLPR;HAPT(0.001)YT(0.001)IPLS(0.998)PVLS(0.969)PT(0.031)LPAEAPTAQVPPSLPR;HAPTYTIPLS(0.999)PVLS(0.943)PT(0.057)LPAEAPTAQVPPSLPR;HAPTYTIPLS(1)PVLS(0.978)PT(0.022)LPAEAPTAQVPPSLPR 209.42 1.44E-27 1102980000 518004 622530 622367 608185 677849 858406 619295 706887 595415 615041 TRUE FALSE 538455.1979 729444.6849 638586.3953 728482.1777 562628.4691 659054.2158 570753.0397 697412.336 573986.1305 735546.5083 0.732047793 0.991704368 0.868179494 0.990395807 0.764912161 0.896006178 0.775957785 0.948155321 0.78035328 1 19.48845704 -1.054456868 4.338280867 1.000009934 0.869129432 0.168556522 0.091056728 8.20E-06 1.79E-06 0.079302327 0.01869026 0.088215141 1.054456868 -0.130880502 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 HAPT(0.004)YT(0.003)IPLS(0.992)PVLS(0.001)PTLPAEAPTAQVPPSLPR;HAPT(0.179)Y(0.165)T(0.165)IPLS(0.479)PVLS(0.011)PT(0.001)LPAEAPTAQVPPSLPR 144.29 3.34E-10 333231000 238600 237470 268682 243690 258611 320542 265514 260768 241475 215701 TRUE FALSE 248020.1122 278253.6252 275684.0736 291891.1547 214652.3946 246100.9784 244702.3189 257272.8315 232784.3619 257963.4811 0.961454355 1.078655103 1.068694191 1.131521227 0.832103807 0.954014798 0.94859287 0.997322685 0.902392699 1 17.97680732 3.251739303 24.99979222 0.944249593 1.062023123 0.495291983 0.059693385 200.7948452 380902.9002 0.016402265 0.022079459 1785.415508 -3.251739303 0.117773529 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HAQGGTWYGVDINNEDIADNFEAFVWEPAMVR 32 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 309.13 5.73E-104 565133000 179138 182119 194581 198613 226742 264117 251875 199860 222186 166043 FALSE TRUE 186210.5066 213396.5216 199651.9407 237898.0586 188200.4758 202779.8295 232132.3793 197181.2036 214189.5693 198575.9468 0.937729416 1.07463429 1.005418551 1.198020518 0.947750616 1.021170151 1.168985384 0.992976273 1.078627965 1 17.59933136 4.744683542 23.92255541 1.05503029 0.937729322 0.177890167 0.075079247 630.0732253 2461593.98 0.016713976 0.151371417 55549.93331 -4.744683542 -0.117300968 HAQPTCPGAQLCTVYYASLNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 254.72 4.63E-37 3159232000 689713 616963 782040 856698 832228 1058466 757695 801146 756513 609447 FALSE TRUE 716943.4018 722921.5959 802420.6049 1026150.307 690766.1818 812653.3127 698304.886 790407.9483 729286.2449 728856.4711 0.983655123 0.991857279 1.100930892 1.407890783 0.947739657 1.114970292 0.958082851 1.08444938 1.000589655 1 19.47527522 HAS(ph)APSHVQPSDSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 HAS(0.99)APS(0.01)HVQPSDSEK 75.548 0.020291 79044000 35882 23294 29207 20122 46184 49351 35200 31771 33868 21542 TRUE FALSE 37298.64907 27294.5633 29968.15841 24102.07154 38333.66018 37889.97817 32440.93202 31345.16171 32649.0973 25762.74245 1.447774791 1.059458765 1.163236347 0.935539824 1.487949516 1.47072767 1.259218893 1.216685753 1.267298982 1 14.65299856 3.234360778 24.99999693 1.29576873 1.145766038 0.117692931 0.175094946 210.4466454 1252707.522 0.049600603 0.061311714 1715.381723 -3.234360778 -0.150002692 HAS(ph)PILPITEFSDIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 193.06 2.80E-10 343945000 218776 233448 200923.9 274738 252296 324002 237946.7 213254.9 209384 324750.5 TRUE FALSE 227413.4454 273540.878 206160.1419 329080.3564 209410.816 248757.4458 219295.8159 210396.5669 201848.3107 388379.1428 0.585544949 0.704314027 0.530821868 0.847317274 0.539191715 0.640501557 0.564643648 0.54172983 0.519719749 1 18.5671062 -1.922154598 2.543666858 1.248501353 0.607910842 0.598022454 0.096367048 8130258.87 4403219.323 12028618.35 0.023366004 0.011963146 1.922154598 -0.640590512 HAS(ph)SSPESPKPAPAPGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.332)S(0.332)S(0.332)PES(0.004)PKPAPAPGSHR;HAS(0.25)S(0.25)S(0.25)PES(0.25)PKPAPAPGSHR 60.464 0.031304 211058000 32669.4 142809 165809 133157 173350 148062 158981 120757 168815 144307 TRUE FALSE 33959.21314 167335.3349 170130.1188 159495.0572 143884.0289 113676.8444 146519.6538 119138.4499 162739.3811 172581.1937 0.196772385 0.969603531 0.985797555 0.924174029 0.833717891 0.658686164 0.848989688 0.690332749 0.942972856 1 17.39691574 4.744922298 24.80039756 0.851897516 0.196772058 0.756624611 0.114459457 339.5316439 1323591.129 0.029000492 0.272310577 55580.48066 -4.744922298 -0.655125458 HASSSPES(ph)PKPAPAPGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HASSSPESPKPAPAPGSHR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HAS(0.001)S(0.023)S(0.009)PES(0.967)PKPAPAPGSHR;HASSSPES(0.999)PKPAPAPGSHR;HASSSPES(1)PKPAPAPGSHR;HAS(0.001)S(0.003)S(0.003)PES(0.993)PKPAPAPGSHR;HAS(0.211)S(0.211)S(0.211)PES(0.368)PKPAPAPGSHR 171.72 5.88E-12 1175200000 82776.8 565595 593710 538494 675177 806630 589806 737910 630221 542926 TRUE FALSE 86044.89198 662731.5415 609182.5703 645006.506 560410.6547 619302.4071 543575.4645 728019.5234 607539.4693 649301.9548 0.132519071 1.020683115 0.938211515 0.993384513 0.863097132 0.953797232 0.837168994 1.121234147 0.935680949 1 19.30853003 4.740905365 24.99638443 0.964620658 0.132518781 0.914526604 0.076126811 55.13245321 587707.8603 0.018148429 0.122183068 55068.76857 -4.740905365 -0.832101877 KKS(ph)SSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKSSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 43 2 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 KKS(0.66)S(0.148)S(0.193)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR;KKS(0.607)S(0.197)S(0.197)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 174.53 7.63E-21 1959020000 122944 1361030 1482110 1502490 1883910 2389760 1408710 2265120 1615180 1641460 TRUE FALSE 127797.9241 1594776.315 1520735.004 1799678.038 1563683.651 1834774.457 1298291.629 2234759.771 1557049.987 1963072.659 0.065100965 0.812387818 0.774670768 0.916765882 0.796549045 0.934644191 0.66135689 1.138398908 0.79316982 1 20.90468214 4.735744951 3.82221856 0.880427683 4.10E-12 0.786632711 0.126102935 0.105693918 3.041046214 0.029474471 0.260749385 54418.29755 -4.735744951 -0.880427683 down HAT(ph)RHSPQQEEENTIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HATRHSPQQEEENTIFK 17 1 O14896;A0A2R8YHF3;B1AJU4 O14896 IRF6 Interferon regulatory factor 6 1 HAT(0.5)RHS(0.5)PQQEEENTIFK;HAT(0.5)RHS(0.5)PQQEEENTIFK 141.31 9.22E-07 288610000 284990 420520 503890 404340 660600 611030 505660 532440 516020 456730 TRUE FALSE 296241.6253 492741.0388 517021.7874 484317.2452 548311.448 469127.5427 466025.0479 525303.5127 497448.541 546217.4989 0.542351034 0.902096765 0.946549293 0.886674715 1.003833544 0.858865825 0.853185863 0.961711248 0.910715131 1 19.05911601 4.738059123 4.856665783 0.923393528 0.522011845 0.84113144 0.049950858 0.060671367 4.231833894 0.011407293 0.082324208 54709.04362 -4.738059123 -0.401381683 HATAEEVEEEERDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HATAEEVEEEERDR 14 1 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 93.494 0.0027277 80037000 14208 25097 28421 21946 25840 30294 26354 28304 22179 27387 FALSE TRUE 14768.94281 29407.21452 29161.67461 26286.8533 21447.72603 23258.67761 24288.30462 27924.63118 21380.78212 32752.95829 0.450919354 0.897849112 0.890352387 0.802579512 0.654833247 0.710124484 0.741560637 0.85258348 0.652789343 1 14.9993376 -2.168825935 2.332072356 1.608032379 0.754453141 0.26314661 0.128646953 7292231.71 1641415.433 23438420.72 0.029889877 0.006779132 2.168825935 -0.853579238 HATLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HATLQK 6 0 Q13263;Q13263-2;M0R3C0 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 103.41 0.03471 335740000 231410 1887250 1657500 1906830 1587280 2405110 1324220 2065970 1660480 2707870 FALSE TRUE 240546.2455 2211370.507 1700695.812 2283995.283 1317474.713 1846559.652 1220424.176 2038279.051 1600719.649 3238425.281 0.07427877 0.682853645 0.525161356 0.705279599 0.406825725 0.570202951 0.37685729 0.629404378 0.494289511 1 21.62686103 -5 0.282859065 4.642685129 0.480058841 0.438144333 0.172785667 212.8913725 2.029823892 455.8847072 0.178946939 1.00E-05 5 -4.162626288 HAVS(ph)DPSILDSLDLNEDEREVLINNINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 1 HAVS(0.993)DPS(0.007)ILDSLDLNEDEREVLINNINR 213.84 6.55E-27 46145000 2969.7 12262 9222.4 8382.8 7191.1 13511 4658 7740.2 7616.7 11342 TRUE FALSE 3086.946049 14367.90311 9462.74332 10040.89282 5968.759391 10373.27501 4292.893789 7636.455279 7342.576455 13564.24774 0.227579598 1.05924806 0.697623893 0.740246935 0.440036153 0.76475122 0.316485947 0.562984061 0.541318368 1 13.72752142 -0.9530732 8.788141604 1 0.600969946 0.222173698 0.227340191 1.55E-09 0 0.208423309 0.049125845 0.111410674 0.9530732 -0.399030055 HAVSDPS(ph)ILDSLDLNEDEREVLINNINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 1 HAVS(0.476)DPS(0.523)ILDS(0.001)LDLNEDEREVLINNINR 58.877 0.028268 56320000 6456.6 11885 11984 11756 11883 16369 9015.8 11697 9706.1 11888 TRUE FALSE 6711.511554 13926.1563 12296.31288 14081.30171 9863.131905 12567.54782 8309.118038 11540.22085 9356.779357 14217.22599 0.472068993 0.97952697 0.864888333 0.990439466 0.693745173 0.883966242 0.584440174 0.811706929 0.658129748 1 13.79535238 HAVSDPSILDSLDLNEDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HAVSDPSILDSLDLNEDER 19 0 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;; 352.05 8.50E-91 1047670000 494207 562279 586916 662090 615289 757220 737310 654363 559317 485583 FALSE TRUE 513718.674 658846.0443 602211.5131 793049.4259 510702.3956 581367.1308 679517.7156 645592.3343 539187.2904 580723.6918 0.884618074 1.134525857 1.037001799 1.365622648 0.879424075 1.001107995 1.170122255 1.11170311 0.92847476 1 19.14749237 HAVSDPSILDSLDLNEDEREVLINNINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HAVSDPSILDSLDLNEDEREVLINNINR 28 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;;;;; 374.19 6.71E-128 2565280000 662684 853743 922644 869772 1004544 1102915 944634 915714 895254 835560 FALSE TRUE 688847.276 1000366.719 946688.8606 1041810.306 833791.9697 846779.7061 870591.1187 903440.3516 863033.9834 999271.9842 0.689349133 1.001095532 0.947378567 1.042569312 0.834399426 0.847396624 0.871225385 0.90409855 0.863662744 1 19.93051788 HAVSDPSILDSLDLNEDEREVLINNINRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HAVSDPSILDSLDLNEDEREVLINNINRR 29 2 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 215.68 1.66E-34 617090000 108257 136875 147365 104146 179872 179235 107114 125263 131831 160184 FALSE TRUE 112531.07 160382.2165 151205.453 124745.768 149297.4217 137610.3876 98718.12479 123584.0544 127086.4281 191568.9879 0.587417991 0.837203444 0.789300265 0.651179344 0.779340244 0.718333323 0.515313704 0.64511514 0.663397711 1 17.5475045 -0.764305727 8.998242895 1 0.686692177 0.506966789 0.092479877 0 0 0.093364419 0.022006204 0.172065687 0.764305727 -0.313307822 HAVSEGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 175.38 0.00026649 1.28422E+11 56457300 45100380 56374190 42211730 69171310 68548600 66397010 56589490 55077880 40002070 FALSE TRUE 58686277.8 52846019.43 57843347.7 50561084.2 57413595.43 52629226.51 61192638.86 55831000.45 53095637.86 47839709.73 1.226727297 1.104647577 1.209107414 1.056885263 1.200124243 1.100115925 1.279118105 1.167043044 1.109865385 1 25.5117053 0.92408338 3.201385905 1.000312991 1.167434325 0.40093134 0.062863751 0.311295148 7.575716082 0.056146778 0.014637296 8.396211703 -0.92408338 0.167121334 HAVTGEAVELR ddPTM_MDA-MB-175_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 0 134.3 0.00014364 55811000 26186 37964 38326 48259 32133 43460 35109 38021 35706 53159 FALSE TRUE 27219.8435 44484.02168 39324.80705 57804.48616 26671.04414 33367.07364 32357.06484 37511.39068 34420.94803 63574.48826 0.428156706 0.699714978 0.618562699 0.90924029 0.419524323 0.524850055 0.50896304 0.590038421 0.541427056 1 15.95616032 -1.473127066 5.956780169 1.000300253 0.586996269 0.461711627 0.135224687 0.000527905 4.67E-05 0.128186228 0.03019235 0.033641313 1.473127066 -0.413303985 HAYGDQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;; 141.52 0.00063223 4217290000 1984580 2325910 1999230 1918960 3743900 3240120 2515280 2148880 2110480 3337390 FALSE TRUE 2062932.751 2725366.949 2051331.576 2298524.56 3107513.215 2487651.234 2318125.781 2120077.778 2034524.237 3991287.672 0.516858949 0.682828995 0.513952324 0.575885466 0.778574102 0.623270342 0.580796468 0.53117639 0.509741318 1 21.92842283 -1.05404199 4.66269649 1.000013896 0.592024999 0.693863561 0.081625489 1.37E-05 2.77E-06 0.08039124 0.018947662 0.088299452 1.05404199 -0.407988897 HCAPS(ph)PDRS(ph)PELSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.994)PELS(0.006)SSR;HCAPS(1)PDRS(1)PELSSSR;HCAPS(1)PDRS(0.978)PELS(0.007)S(0.008)S(0.007)R 161.68 4.75E-09 3271110000 1465192 1632335 1625348 1549855 1800319 2069179 1654974 1636878 1551051 1549094 TRUE FALSE 1523038.912 1912675.838 1667705.904 1856411.693 1494301.419 1588643.536 1525252.813 1614938.328 1495228.977 1852609.31 0.822104749 1.032422664 0.900192985 1.002052447 0.806592848 0.857516762 0.823299767 0.871710144 0.807093524 1 20.82112724 3.233744072 24.99999631 0.853199134 0.943066727 0.205461096 0.074187207 153.2797564 795590.0238 0.019243524 0.023705141 1712.947575 -3.233744072 0.089867594 HCCGVAQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HCCGVAQMR 9 0 O00170;V9GYQ3 O00170 AIP AH receptor-interacting protein 0 ;;; 93.374 0.0071624 104193000 47535.1 42946.6 48315.1 37734 65427.9 56580 56009.3 43839.5 55465.1 50872.5 FALSE TRUE 49411.82245 50322.34447 49574.2312 45197.67258 54306.48893 43440.15248 51619.14471 43251.90321 53468.92189 60839.99236 0.812160234 0.827126081 0.814829675 0.74289412 0.892611699 0.714006541 0.848441012 0.710912371 0.87884498 1 15.89273235 0.986628571 11.71389142 0.999999893 0.794374682 0.570965413 0.055187292 0.454217628 397.386033 0.048626141 0.012159066 9.696802966 -0.986628571 -0.205625211 HCDLQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HCDLQVR 7 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 154.31 0.0016874 426920000 114785 117936 114925 110155 142977 160608 127568 105384 104688 130256 FALSE TRUE 119316.8004 138190.5906 117920.0399 131943.3302 118673.8206 123309.226 117568.8868 103971.4999 100920.2993 155777.1693 0.765945363 0.887104261 0.756978962 0.847000435 0.761817801 0.791574443 0.754724761 0.667437342 0.647850386 1 17.24912428 2.489172459 1.752441318 0.732980435 0.810599362 0 0.09867316 0.813954042 5.064272345 0.040707699 0.032481466 308.4412533 -2.489172459 0.077618928 HCECAEEGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HCECAEEGTR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;;; 162.38 6.79E-06 1323929000 442966.4 424072 485362 478963 478545 609998 532063 493532 471373 398887 FALSE TRUE 460455.0555 496903.0672 498010.9324 573700.4518 397202.0918 468335.2091 490358.5118 486917.0108 454408.3778 477041.2705 0.965231069 1.041635384 1.043957752 1.202622262 0.832636747 0.981749878 1.027916329 1.020702067 0.952555693 1 18.86375456 3.240016416 24.99999978 0.978275548 1.060423716 0.268326163 0.075184212 62.67809937 1076343.347 0.021628511 0.027749835 1737.866518 -3.240016416 0.082148168 HCFECAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HCFECAQR 8 0 O95081;A0A0C4DG34;O95081-2 O95081 AGFG2 Arf-GAP domain and FG repeat-containing protein 2 0 95.741 0.0094349 64205000 24803 31819 27536 40026 38567 43620 34240 30430 27361 40189 FALSE TRUE 25782.24159 37283.66573 28253.61078 47943.02333 32011.39512 33489.91607 31556.17933 30022.13562 26376.28295 48063.26509 0.536423016 0.775720619 0.587842102 0.997498261 0.666026227 0.696788202 0.656555048 0.624637872 0.548782587 1 15.55264704 4.753914921 22.29039621 0.710474547 0.53642243 0.119016798 0.149694986 1352.420818 1963203.335 0.033827127 0.68622716 56743.34339 -4.753914921 -0.174052118 HCFTSNEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HCFTSNEAAR 10 0 Q9BV44;H7C0R6;H7C3J3 Q9BV44 THUMPD3 THUMP domain-containing protein 3 0 79.659 0.026342 110080000 13461 15977 16593 16801 18967 21706 14761 16255 15170 19344 FALSE TRUE 13992.45067 18720.92547 17025.42721 20124.18765 15742.99611 16665.11046 13603.99425 16037.12831 14624.03466 23134.08644 0.60484129 0.809235563 0.735945517 0.869893337 0.680510819 0.720370372 0.588049772 0.693225054 0.632142302 1 14.49773251 -1.088434445 5.031482944 1.000007605 0.706492638 0.533248218 0.083100377 7.12E-06 1.29E-06 0.080846143 0.019055125 0.081576591 1.088434445 -0.293514967 HCGDFEQQLANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HCGDFEQQLANR 12 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 ; 165.7 5.39E-05 351520000 208823 228093 225475 214105 232438 270730 230620 197419 212615 218123 FALSE TRUE 217067.4933 267266.1984 231351.0637 256454.33 192928.2718 207857.0605 212543.4018 194772.9212 204963.0277 260860.0256 0.832122487 1.024557894 0.886878176 0.983110882 0.739585421 0.796814537 0.814779502 0.746656835 0.785720339 1 17.99291636 3.24095918 24.99843115 0.797104351 0.935103177 0.308396877 0.084083117 60.7355122 632993.6632 0.021634926 0.027970118 1741.643167 -3.24095918 0.137998826 HCKDDVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HCKDDVNR 8 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 ;;;; 164.96 0.00019653 325027000 224519 194569 210270 174314 266823 275586 240908 213205 209699 189272 FALSE TRUE 233383.1835 227984.7122 215749.8089 208792.7889 221468.5218 211585.328 222025.0015 210347.3357 202151.974 226356.2246 1.031043807 1.007194358 0.953142814 0.922407985 0.978407032 0.934744907 0.980865456 0.929275685 0.89307009 1 17.78823545 4.304950165 3.172283628 0.946353114 1.026784717 0.474745421 0.029951681 0.191630696 3.767190934 0.007213514 0.023612741 20181.3477 -4.304950165 0.080431603 HCNGVDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HCNGVDWR 8 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;; 108.98 0.0037068 1802000000 1222610 1399730 1381840 1327700 1538630 1792480 1469040 1389110 1257930 1391470 FALSE TRUE 1270879.587 1640122.739 1417851.886 1590315.097 1277094.222 1376203.685 1353892.806 1370491.253 1212657.345 1664101.905 0.763702982 0.985590326 0.852022272 0.955659682 0.76743751 0.826994838 0.813587679 0.823562096 0.728715796 1 20.66631235 3.233004126 24.99989664 0.817598885 0.893467027 0.105482455 0.086450847 240.2261985 1080830.528 0.022585702 0.027724403 1710.031563 -3.233004126 0.075868142 HCPYLDTINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HCPYLDTINR 10 0 Q53GS9;B9A018;Q53GS9-3;F8WC91;A0A087X1B2;C9JIU2 Q53GS9 USP39 U4/U6.U5 tri-snRNP-associated protein 2 0 ; 168.83 4.82E-06 248340000 160399 199726 189472 180702 221558 241560 183649 185399 194651 178082 FALSE TRUE 166731.6764 234027.3868 194409.796 216444.3163 183897.6503 185461.3509 169254.1115 182914.0297 187645.5485 212973.7583 0.782874274 1.098855505 0.912834508 1.016295707 0.863475631 0.870817853 0.794718151 0.858857124 0.881073565 1 17.70031615 3.214903614 24.00101743 0.864402889 0.960304985 0.130690029 0.089252191 212.153783 215237.9043 0.023806213 0.028472368 1640.225705 -3.214903614 0.095902097 HCQLEPDHEGVPEETDDFGEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HCQLEPDHEGVPEETDDFGEFR 22 0 E9PFH4;C9J7E5;Q9Y5L0-5;Q9Y5L0-3;Q9Y5L0;Q9Y5L0-1 E9PFH4 TNPO3 Transportin-3 0 ; 177.03 3.77E-17 204613000 85140 93434 103038 93047 113881 130810 113841 104952 101206 94602 FALSE TRUE 88501.39294 109480.5627 105723.2549 111451.4189 94523.5483 100431.3599 104917.845 103545.2901 97563.61583 113137.4506 0.782246661 0.967677476 0.934467361 0.985097492 0.835475325 0.887693327 0.927348498 0.915216752 0.862345892 1 16.78771704 -1.844394028 3.679870433 1.02540017 0.90506061 0.206233135 0.058174716 0.013891931 0.00058743 0.064547255 0.012544164 0.014308891 1.844394028 -0.12033956 HCSQVDSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HCSQVDSVR 9 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;;;;; 172.88 5.59E-05 2420060000 156163.5 777729 558507 678370 607755.4 929706 453486.8 725929 527625.7 850189 FALSE TRUE 162328.9556 911297.9059 573062.1512 812549.5613 504449.3542 713795.8713 417941.3196 716199.1091 508636.5541 1016767.257 0.159652029 0.896269918 0.563611925 0.799150008 0.496130605 0.702024841 0.411049153 0.704388447 0.500248755 1 19.95555805 -2.01747365 2.835084352 1.450456695 0.5981197 0.279619791 0.199954153 88754250.85 85671285.75 259445536.8 0.045563404 0.009605641 2.01747365 -0.852336996 HDAATCFVDAGNAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDAATCFVDAGNAFK 15 0 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 219.97 1.73E-12 1248250000 1334460 954810 1285840 972390 1601620 1646990 1524920 1300980 1354120 766980 FALSE TRUE 1387145.511 1118791.19 1319350.047 1164725.84 1329377.204 1264501.533 1405392.786 1283542.491 1305385.486 917255.0463 1.512278964 1.219716582 1.438367717 1.269794965 1.449299418 1.378571356 1.532172313 1.399329986 1.423143422 1 19.80696341 -1.350420489 5.710679999 0.999921813 1.40056549 0.633320908 0.091873037 8.53E-05 9.70E-06 0.082933034 0.01954371 0.044625132 1.350420489 0.400643677 HDADGQATLLNLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 160.27 1.72E-06 77807000 78620 84114 95244 89998 114785 124262 101804 104847 97662 85740 FALSE TRUE 81723.97831 98559.92518 97726.13688 107799.3358 95273.8867 95404.03371 93824.33646 103441.6975 94147.1637 102539.1114 0.797002989 0.961193479 0.953062061 1.051299688 0.929146795 0.930416037 0.915010235 1.008802359 0.918158568 1 16.64581478 4.738849978 6.763404325 0.963691204 0.794145006 0.581040617 0.042290962 0.079021518 24.76115503 0.009907708 0.06122427 54808.76017 -4.738849978 -0.169546197 HDDGTQS(ph)DSENAGAHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDDGTQSDSENAGAHRR 17 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 HDDGTQS(0.995)DS(0.005)ENAGAHRR;HDDGTQS(1)DSENAGAHRR;HDDGTQS(1)DSENAGAHRR 163.85 1.25E-09 467017000 18493 24390.9 20305 22704.7 29098.7 30564 23784 22113.5 19619.6 22396.6 TRUE FALSE 19223.11792 28579.84734 20834.16498 27195.62189 24152.51337 23465.9742 21919.74793 21817.1047 18913.49443 26784.78496 0.717687969 1.067017987 0.777835813 1.015338444 0.901725118 0.876093433 0.818365649 0.814533502 0.706128291 1 14.70912609 2.374613714 3.012972146 0.818144488 0.904752859 0.048033917 0.116336138 0.574619157 10.54485991 0.040652083 0.032725315 236.926541 -2.374613714 0.086608371 HDDSSDNFCEADDIQSPEAEYVDLLLNPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDDSSDNFCEADDIQSPEAEYVDLLLNPER 30 0 Q96HE7;G3V3E6;G3V5B3 Q96HE7 ERO1L ERO1-like protein alpha 0 ;; 309.78 3.30E-92 233870000 78750 112602 95691 115868 120641 143003 89704 89309 103740 95415 FALSE TRUE 81859.11081 131940.5176 98184.78607 138786.3446 100134.4859 109792.7205 82672.76608 88111.95894 100006.4177 114109.7424 0.717371796 1.156259884 0.860441747 1.216253246 0.877527929 0.962167806 0.724502258 0.77216859 0.876405603 1 16.80006245 2.339364004 7.497856533 0.815515378 0.977698873 0.121812608 0.151108374 0.346267114 22.71047745 0.04911119 0.040959505 218.4560132 -2.339364004 0.162183494 HDDYLVMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDDYLVMLK 9 0 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;; 89.543 0.0091297 592460000 911960 758980 920570 759770 1253960 1188370 1116040 960090 1007680 820080 FALSE TRUE 947964.885 889328.911 944560.8105 910050.2383 1040812.327 912389.0774 1028561.869 947221.5639 971413.7936 980758.9746 0.966562539 0.906776215 0.963091682 0.927904064 1.06123151 0.930288788 1.048740715 0.965804635 0.990471481 1 19.90353911 3.303990472 24.99999911 0.995798756 0.940204894 0.353189082 0.038482349 63.2614008 24170.5496 0.009675338 0.013100467 2013.680069 -3.303990472 -0.055593862 HDEES(ph)HSLSPPGENTVMADSFQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.353)HS(0.319)LS(0.319)PPGENT(0.009)VMADSFQIK 70.213 0.0527 96762000 44863 36368 46449 37131 63777 61390 49867 44354 42963 33320 TRUE FALSE 46634.22588 42613.9211 47659.4991 44475.40098 52936.20832 47133.10287 45958.29424 43759.50718 41416.77002 39848.41605 1.170290579 1.069400627 1.196019913 1.116114651 1.328439461 1.182809947 1.153328006 1.098149224 1.039358 1 15.28223476 1.432897603 1.624099317 1.005760655 1.176469712 0.503310784 0.06240154 0.305220439 1.504666077 0.057074436 0.01822127 27.09552705 -1.432897603 0.170709057 HDEESHSLS(ph)PPGENTVMADSFQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDEESHSLSPPGENTVMADSFQIK 24 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 HDEES(0.065)HS(0.056)LS(0.747)PPGENT(0.132)VMADSFQIK 121.25 0.00021493 143500000 50841 43565 60127 52050 71317 88221 69853 53946 63616 50040 TRUE FALSE 52848.24194 51046.94986 61693.95901 62345.33465 59194.56181 67733.00975 64377.73933 53222.94211 61326.47259 59844.37993 0.883094486 0.852994883 1.030906479 1.041790971 0.989141535 1.131819059 1.075752467 0.889355729 1.024765779 1 15.86892815 4.237985257 24.99996652 1.018345531 0.868044643 0.520556475 0.059330672 12.31558716 535237.8098 0.016182699 0.038652197 17297.57638 -4.237985257 -0.150300888 HDELADSLPCAEGEFIFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDELADSLPCAEGEFIFLR 19 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 136.35 6.00E-06 89349000 55902 57399 57763 64511 63713 83624 76662 64807 56076 41213 FALSE TRUE 58109.05413 67256.83175 59268.35123 77271.08325 52883.08702 64203.59333 70653.03212 63938.36817 54057.83571 49287.89828 1.178972043 1.364570901 1.202492971 1.567749609 1.072942626 1.302623881 1.433476261 1.297242739 1.096777051 1 15.58894584 1.135611708 3.487433921 1.006171287 1.309320862 0.387326348 0.130356727 0.208238124 4.495786335 0.11489108 0.030377041 13.66506521 -1.135611708 0.303149575 HDELTYF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HDELTYF 7 0 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 ; 102.81 0.019816 206973000 543940 708030 589120 683210 626890 819160 650960 623990 612880 594180 FALSE TRUE 565415.1712 829628.6448 604472.9512 818346.8988 520331.4617 628922.5045 599936.0542 615626.4347 590822.5685 710598.1947 0.795689006 1.167507392 0.850653654 1.151630985 0.732244278 0.885060656 0.844269038 0.866349562 0.831443948 1 19.4386745 3.229488423 24.9996978 0.854338232 0.99390031 0.212825386 0.123557178 260.6773887 718332.1367 0.032030587 0.03879875 1696.244385 -3.229488423 0.139562078 HDGAFLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDGAFLIR 8 0 P62993;J3KT38;J3QRL5 P62993 GRB2 Growth factor receptor-bound protein 2 0 101.72 0.0086455 0 79714 68842 67999 82128 102950 120380 102530 76179 77924 95239 FALSE TRUE 82861.17027 80665.07798 69771.1098 98372.67327 85450.59577 92423.56938 94493.43069 75157.94511 75119.53046 113899.2586 0.727495256 0.70821425 0.612568604 0.863681419 0.750229605 0.81145014 0.829622878 0.659863339 0.659526071 1 16.79739883 3.744297693 24.9550534 0.77611126 0.685304865 0.199260014 0.098629619 887.5457959 3860620.924 0.025241176 0.044017997 5550.060193 -3.744297693 -0.090806395 HDGITVAVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDGITVAVHK 10 0 R4GMU8;E9PLX3;A0A0C4DGV4;O43504 R4GMU8 LAMTOR5 Ragulator complex protein LAMTOR5 0 133.23 0.00011724 109180000 141350 110920 124320 126400 166280 187490 152600 133920 130990 113200 FALSE TRUE 146930.6071 129969.6472 127559.8813 151401.5427 138015.785 143948.2889 140638.8133 132125.0214 126275.6955 135379.3727 1.085324923 0.960040253 0.942240157 1.118350158 1.019474254 1.063295583 1.038849645 0.975961248 0.932754326 1 17.04664841 1.645238258 4.654441132 0.963086387 1.030150254 0.234057732 0.052040023 0.234616817 11.4579266 0.029234375 0.013715936 44.18127637 -1.645238258 0.067063867 HDGKDEIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDGKDEIIK 9 1 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 91.549 0.0064156 45297000 223810 122280 163870 133050 251430 233560 253430 200740 213890 98286 FALSE TRUE 232646.1916 143280.6388 168140.5868 159366.8929 208692.0184 179319.2296 233565.4944 198049.4086 206192.1407 117543.2599 1.979238893 1.218960908 1.430457067 1.355814813 1.775448619 1.525559439 1.987059867 1.684906551 1.754180894 1 16.84283229 3.235573767 24.99967238 1.67726735 1.47163093 0.01720584 0.304943947 184.6094503 1545166.58 0.081041144 0.100903478 1720.179497 -3.235573767 -0.20563642 HDKPPY(ph)T(ph)YLAMIALVIQAAPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDKPPYTYLAMIALVIQAAPSR 22 1 O75593 O75593 FOXH1 Forkhead box protein H1 3 HDKPPY(0.655)T(0.69)Y(0.655)LAMIALVIQAAPS(1)R 42.172 0.077344 81178000 2291.5 1917.2 2487 2472 2855.5 3713.2 2405.5 2391.9 1398.2 2164.8 TRUE FALSE 2381.970189 2246.464186 2551.813263 2960.954222 2370.12313 2850.865574 2216.950624 2359.840493 1347.879055 2588.951112 0.920052209 0.867712092 0.985655253 1.143688735 0.915476201 1.101166245 0.856312278 0.911504463 0.520627465 1 11.33815201 1.60032777 2.665879877 0.758204727 0.979238707 0.2394734 0.140592029 0.287956773 4.680517938 0.092077427 0.035824155 39.84077426 -1.60032777 0.22103398 HDLDLICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 156.75 0.00038786 4748900000 2692488 2723436 2833013 3097260 3341720 3717620 3473520 2955647 2934760 2399495 FALSE TRUE 2798789.505 3191164.948 2906843.646 3709888.784 2773695.628 2854259.096 3201256.426 2916031.386 2829138.561 2869630.104 0.975313683 1.112047488 1.012968062 1.292810798 0.966569045 0.994643558 1.115564135 1.016169778 0.98588963 1 21.45243335 HDLINQLQHNHALVTLVAENLATYMESMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HDLINQLQHNHALVTLVAENLATYMESMR 29 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 ; 219.93 7.25E-35 464580000 188576 182124 206381 226085 247475 313450 242154 195148 219035 198701 FALSE TRUE 196021.1261 213402.3803 211759.4584 270803.9382 205409.2879 240655.9879 223173.3367 192532.3603 211151.9731 237632.6566 0.824891363 0.898034737 0.891121033 1.139590585 0.864398399 1.01272271 0.93915264 0.810210023 0.888564628 1 17.85837359 -0.114047715 7.35044776 0.999999999 0.91794944 0.066252583 0.091472112 12129426.47 1650160.842 0.089450601 0.021694957 0.769045941 0.114047715 -0.082050558 HDMLAWINESLQLNLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HDMLAWINESLQLNLTK 17 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;; 272.71 1.22E-35 966736800 1501624 1038020 1448210 1350393 1724756 1879152 2013083 1555113 1688911 949782 FALSE TRUE 1560909.275 1216291.86 1485951.542 1617496.705 1431582.591 1442747.427 1855292.294 1534269.254 1628127.423 1135873.598 1.37419276 1.070798601 1.308201498 1.424011182 1.26033618 1.270165474 1.633361579 1.350739428 1.43337025 1 20.11537087 4.009079522 24.50992441 1.364484208 1.214246724 0.055253399 0.167189826 315.8420961 852586.6935 0.038962177 0.083972225 10211.26441 -4.009079522 -0.150237484 HDNLLHGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HDNLLHGTK 9 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 164.64 3.59E-05 100300000 89761 74695 89876 84613 122070 119490 115030 99681 102310 60530 FALSE TRUE 93304.83359 87523.2852 92218.24239 101349.1989 101320.585 91740.25839 106013.648 98344.93924 98627.88309 72389.69458 1.288924261 1.209057252 1.273913959 1.400050096 1.399654821 1.26731103 1.464485361 1.35854889 1.362457511 1 16.14349671 3.929114733 6.462793127 1.346556912 1.247054824 0.03127286 0.122302666 0.468860572 34.85180046 0.028627765 0.052694286 8494.04844 -3.929114733 -0.099502087 HDS(ph)PDLAPNVTYSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR 235.25 1.12E-19 697490000 412314 388534 438014 398916 505890 689728 536351 475694 454348 332971 TRUE FALSE 428592.4751 455261.6921 449429.0047 477820.3942 419898.9985 529549.1249 494310.4071 469318.1 437996.1042 398210.2923 1.076296829 1.143269526 1.128622272 1.199919749 1.054465459 1.329822797 1.241330063 1.178568483 1.099911561 1 18.60317098 5.054586421 0.864693543 1.174136002 0.97708451 0.038499079 0.089777519 9.286196713 3.726748403 0.028807192 1.970019765 113393.0459 -5.054586421 -0.197051492 HDS(ph)PEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HDSPEDVK 8 0 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 1 HDS(1)PEDVK;HDS(1)PEDVK 81.335 0.024258 834010000 1226360 780050 1010130 804120 1397270 1634140 1316660 979890 1029330 716190 TRUE FALSE 1274777.64 914017.5196 1036454.818 963172.5359 1159762.544 1254635.751 1213456.749 966756.1773 992284.6144 856513.7182 1.488333009 1.067137047 1.210085484 1.124526689 1.354050169 1.464816878 1.41673942 1.128710675 1.158515729 1 19.70811683 1.598256777 6.745153588 1.100806231 1.292150724 0.326387038 0.136641397 0.174448745 16.98813393 0.07716876 0.036829248 39.65124032 -1.598256777 0.191344492 HDS(ph)PEDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 138.42 8.39E-05 1077875000 1658480 910049 1183160 871648 1774100 2034040 1746360 1299840 1280780 697210 TRUE FALSE 1723958.071 1066342.837 1213994.122 1044057.373 1472539.116 1561665.036 1609475.74 1282417.771 1234684.978 833814.9506 2.067554761 1.278872291 1.455951492 1.252145182 1.76602628 1.872915609 1.930255315 1.538012445 1.480766178 1 19.66936771 3.200719281 24.99695855 1.653511617 1.492741142 0 0.322960377 535.4142889 353678.567 0.090450312 0.108110963 1587.520278 -3.200719281 -0.160770475 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDSEQDNSDNNTIFVQGLGENVTIESVADYFK 32 0 P35637-2;P35637 P35637-2 FUS RNA-binding protein FUS 0 ;; 124.66 8.23E-08 186975000 10604 106034 83036 93193 51554 91830 58423 67476 82653 137262 FALSE TRUE 11022.65411 124244.5147 85199.98637 111626.2972 42790.86949 70503.8742 53843.6526 66571.59459 79678.33468 164155.8609 0.067147491 0.756869197 0.519018852 0.6800019 0.260672201 0.429493494 0.32800323 0.405538945 0.485382211 1 17.32470673 0.828111274 6.15366651 0.999999551 0.440409436 0.45126029 0.186905046 5.403656732 193.3609301 0.170614247 0.042879113 6.731491072 -0.828111274 -0.559590115 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_MDA-MB-175_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;HDSIPAADTFEDLS(1)DVEGGGSEPTQR 222.95 1.54E-34 668600000 72446 300749 265619 311287 297869 441570 273854 340562 238150 325977 TRUE FALSE 75306.22402 352400.3012 272541.2493 372858.6395 247237.3338 339022.0596 252388.6079 335997.3234 229579.028 389845.9519 0.193169183 0.903947571 0.699099857 0.956425577 0.634192384 0.869630832 0.647405999 0.861872034 0.588896786 1 18.57254463 4.745513644 24.83877559 0.787339733 0.193168882 0.631947334 0.137818779 431.1431157 1540159.489 0.028814779 0.287191764 55656.21194 -4.745513644 -0.594170851 HDSPEDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HDSPEDVKR 9 1 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;; 121.73 0.00039313 394720000 358645 501560 658580 551470 792000 820900 733440 742340 709120 571526 FALSE TRUE 372804.5815 587699.0284 675743.1358 660549.12 657376.1229 630258.4159 675951.0563 732390.1465 683598.9097 683505.5772 0.545430197 0.859830626 0.988643192 0.966413651 0.96177141 0.922096961 0.98894739 1.071520366 1.00013655 1 19.38259358 4.780406196 1.810267705 0.992375178 0.365132674 0.931252353 0.03632874 0.260578823 0.797393483 0.011204059 0.28838386 60312.34243 -4.780406196 -0.627242504 HDVPNRHEIS(ph)PGHDGTWNDNQLQEMAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HDVPNRHEISPGHDGTWNDNQLQEMAQLR 29 1 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;C9J1B2 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 HDVPNRHEIS(0.5)PGHDGT(0.5)WNDNQLQEMAQLR;HDVPNRHEIS(0.954)PGHDGT(0.046)WNDNQLQEMAQLR 127.73 9.27E-06 263040000 77951 121098 110402 104223 104332 141328 98931 108909 102401 150759 TRUE FALSE 81028.56567 141895.6395 113279.1668 124837.9983 86597.68391 108506.7138 91176.52971 107449.253 98715.60801 180297.3396 0.449416313 0.787009059 0.628290839 0.692400668 0.480304835 0.601820937 0.505700916 0.595955843 0.547515611 1 17.46001858 -1.229816855 3.728819629 1.000545596 0.591764233 0.624983203 0.095787315 30181372.24 45569372.87 185932.8621 0.022083471 0.058909203 1.229816855 -0.408781364 HEALLYTWLAEHKPLVLCGPPGSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEALLYTWLAEHKPLVLCGPPGSGK 25 1 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 106.05 0.0025714 455320000 633900 426550 575910 490940 764650 694570 639540 603750 660870 403150 FALSE TRUE 658926.8615 499806.6444 590918.6877 588046.4667 634675.0661 533266.6438 589411.1837 595657.7188 637085.4178 482139.5237 1.366672569 1.03664317 1.225617604 1.219660363 1.316372201 1.106042167 1.222490907 1.235446773 1.321371484 1 18.87909117 -0.549910495 8.509737997 1 1.221601125 0.345675883 0.093678768 0 0 0.083779262 0.019746961 0.281896384 0.549910495 0.221601126 HEAMITDLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEAMITDLEER 11 0 P35579 P35579 MYH9 Myosin-9 0 164.9 2.22E-05 968140000 725370 791230 815360 798730 897670 1058000 939550 832330 820650 694300 FALSE TRUE 754008.1677 927117.5976 836608.9514 956716.41 745084.374 812295.5341 865905.6159 821173.9778 791114.9668 830334.7918 0.90807729 1.116558775 1.007556181 1.152205616 0.897330067 0.978274718 1.042839135 0.988967325 0.952766251 1 19.66333362 3.228084699 24.99978691 0.981612943 1.048379197 0.189083089 0.069905114 353.1813699 842833.064 0.019224706 0.023206208 1690.770645 -3.228084699 0.066766254 HEANNPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEANNPQLK 9 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 94.692 0.0085502 50473000 78692 56769 91659 80109 106510 99519 118570 95046 96207 50759 FALSE TRUE 81798.82092 66518.63415 94047.70884 95954.3211 88405.46824 76407.22048 109276.1736 93772.06383 92744.52886 60704.25421 1.347497338 1.095782083 1.549277066 1.580685281 1.456330687 1.258679832 1.800140287 1.54473628 1.527809378 1 15.88951 4.228710865 24.99052866 1.500357468 1.221639696 0.159722902 0.210671052 246.7248091 625988.7961 0.049272513 0.108515513 16932.10156 -4.228710865 -0.278717771 HEAPSS(ph)PISGQPCGDDQNASPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEAPSSPISGQPCGDDQNASPSK 23 0 O75376;O75376-2;A0A088AWL3;E7EVU5;E7EW50;J3KS51;O75376-3 O75376 NCOR1 Nuclear receptor corepressor 1 1 HEAPS(0.112)S(0.888)PISGQPCGDDQNASPSK;HEAPS(0.147)S(0.853)PISGQPCGDDQNASPSK 223.09 9.78E-33 586930000 367120 309590 410430 308170 507820 499980 456480 446640 408930 277380 TRUE FALSE 381614.1811 362759.6742 421126.143 369125.1062 421500.9378 383867.2223 420699.9048 440653.5214 394212.6892 331727.3002 1.150385213 1.093547845 1.269494982 1.112736594 1.27062481 1.157177061 1.268210076 1.328360738 1.188363722 1 18.33963822 4.223446026 0.896439599 1.225066619 1.106950268 0 0.096015228 2.611182253 2.729782453 0.032724485 0.25999273 16728.07726 -4.223446026 -0.118116351 HECQANGPEDLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 HECQANGPEDLNR 13 0 P60981;P60981-2 P60981 DSTN Destrin 0 ;;;;;;;;;; 319.45 1.45E-50 6560859000 2656702 2918987 2873443 2922173 3435730 3706337 3302282 3018600 2833992 2433118 FALSE TRUE 2761590.646 3420300.311 2948327.285 3500170.098 2851725.842 2845596.402 3043440.508 2978140.604 2731997.182 2909840.887 0.949052114 1.175425201 1.013226289 1.202873364 0.980028102 0.97792165 1.045913033 1.023471977 0.938881983 1 21.47250884 HEDEQALLDQNSQT(ph)PPPS(ph)PFSVQAFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 2 HEDEQALLDQNS(0.065)QT(0.935)PPPS(0.997)PFS(0.003)VQAFNK 182.02 2.88E-17 104020000 65835 63588 68171 69169 85753 94385 61406 80030 74570 88952 TRUE FALSE 68434.21664 74508.74435 69947.59226 82850.42175 71176.73569 72465.51417 56592.83727 78957.32875 71886.24027 106380.4413 0.64329698 0.700398903 0.65752305 0.77881254 0.669077274 0.681192081 0.531985359 0.742216593 0.675746776 1 16.6988734 0.104518212 1.384551062 1.000370661 0.675251994 0.714971244 0.061453473 6.130803323 8.820895674 0.062446613 0.016768253 1.272091094 -0.104518212 -0.325118667 HEDEQALLDQNSQT(ph)PPPSPFSVQAFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 HEDEQALLDQNS(0.21)QT(0.79)PPPSPFSVQAFNK;HEDEQALLDQNS(0.104)QT(0.896)PPPSPFSVQAFNK;HEDEQALLDQNS(0.001)QT(0.999)PPPSPFSVQAFNK 225.23 6.30E-34 555160000 260424 242909 277161 221033 298056 325723 214144 245106 261040 226476 TRUE FALSE 270705.7406 284626.7312 284384.0434 264752.6677 247392.5476 250078.7696 197358.8337 241820.755 251645.2214 270849.6361 0.999468726 1.050866212 1.049970188 0.977489472 0.913394425 0.923312186 0.728665678 0.892822891 0.92909566 1 18.04713263 3.275059755 1.814549971 0.87600238 1.035582675 0.449709354 0.066555494 0.27331111 1.854687329 0.02125551 0.030757383 1883.908279 -3.275059755 0.159580295 HEDGDSNGTFFVYHAIYLEELTAVELTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEDGDSNGTFFVYHAIYLEELTAVELTEK 29 0 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0 F8VX55 TFCP2 Alpha-globin transcription factor CP2 0 ; 138.71 6.17E-07 66863000 15040 10631 17038.5 13251.6 22088.9 19729.4 19935.3 16271 20005.7 13016.9 FALSE TRUE 15633.79081 12456.79155 17482.53731 15872.72693 18334.23667 15147.54585 18372.71909 16052.91386 19285.69876 15567.31233 1.004270389 0.800188966 1.123028621 1.019618968 1.177739373 0.973035392 1.180211375 1.031193665 1.2388586 1 13.92623227 4.224923584 24.96684751 1.091658451 0.902229662 0.392555331 0.094892865 174.5866985 319637.1332 0.021092666 0.04595291 16785.08652 -4.224923584 -0.189428789 HEDLKDMLEFPAQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEDLKDMLEFPAQELR 16 1 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 67.605 0.030834 34470000 77607 59935 72554 64126 90880 83902 89382 76346 77699 57631 FALSE TRUE 80670.98429 70228.37002 74444.81684 76809.9314 75432.25006 64417.03205 82376.00528 75322.70675 74902.62817 68922.69104 1.170456102 1.018944109 1.080120577 1.114436048 1.094447256 0.93462735 1.195194268 1.092857891 1.086762966 1 16.07269141 -0.615998389 6.150186398 0.999999698 1.086973644 0.126948823 0.068854998 0 7.62E-11 0.062859659 0.014816164 0.242103803 0.615998389 0.086973945 HEDLLAQATGIESLEGVLQMMQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEDLLAQATGIESLEGVLQMMQTR 24 0 Q9UP83-3;Q9UP83;Q9UP83-2;U3KQU7 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 0 79.783 0.018287 11454000 14209 14905 18619 15663 17433 21930 12677 17107 16732 13954 FALSE TRUE 14769.98229 17464.81781 19104.22644 18761.09465 14469.74489 16837.08985 11683.34361 16877.70865 16129.81859 16688.01913 0.885065038 1.046548285 1.144786945 1.12422538 0.867073843 1.008932799 0.70010368 1.011366808 0.966550821 1 14.0265251 3.234924205 24.99896854 0.92043587 1.056658014 0.238274616 0.108549256 127.0264619 873259.7775 0.030932081 0.038351526 1717.608598 -3.234924205 0.136222144 HEDLVPPAGS(ph)PELS(ph)PPQPLFRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEDLVPPAGSPELSPPQPLFRPR 23 1 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 2 HEDLVPPAGS(1)PELS(1)PPQPLFRPR 64.779 0.039941 70678000 73727 80139 73482 70324 88702 100870 91275 85803 87126 70895 TRUE FALSE 76637.79889 93902.24986 75397.00129 84233.8773 73624.46572 77444.4712 84120.627 84652.95113 83990.35228 84785.51788 0.903901997 1.107526995 0.88926745 0.993493693 0.868361338 0.913416267 0.992157966 0.998436446 0.990621445 1 16.37153024 2.114032685 9.445832174 0.995935062 0.949425923 0.124684628 0.063678759 0.663602932 52.18413094 0.023591766 0.017418574 130.0267433 -2.114032685 -0.046509139 HEDTNLASSTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEDTNLASSTLLR 13 0 P49407-2;P49407;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ;; 151.74 4.33E-05 834590000 454380 552390 542710 625750 620040 734680 703890 557760 596990 478630 FALSE TRUE 472319.2733 647258.6855 556853.4684 749521.4823 514645.8223 564061.7042 648717.2625 550284.1395 575504.4465 572408.3846 0.825143876 1.130763809 0.972825492 1.309417371 0.899088546 0.985418312 1.13331195 0.961348845 1.005408834 1 19.12668528 1.6215905 25 0.987533666 1.041435059 0.027210355 0.128174229 3.301038839 5998.950175 0.056977571 0.031384006 41.8398867 -1.6215905 0.053901392 HEEAPGHRPTTNPNASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HEEAPGHRPTTNPNASK 17 1 P21291;E9PS42;E9PP21;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;;;;; 221.24 2.25E-15 2236316700 1019650 734439 989448 840902 1086206 1200628 1236697 954105 1036991 566909 FALSE TRUE 1059906.569 860573.1851 1015233.828 1007229.906 901573.0921 921800.3427 1139761.458 941316.7831 999669.8965 677983.9644 1.563321 1.269312005 1.497430442 1.485624968 1.329785274 1.359619683 1.681103857 1.388405674 1.474474249 1 19.37089163 -1.196716945 5.269965024 0.999973894 1.446713161 0.584329827 0.113807633 3.29E-05 5.02E-06 0.103936752 0.024496698 0.063574515 1.196716945 0.446739267 HEEEEWT(ph)DDDLVESL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEEEEWTDDDLVESL 15 0 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 HEEEEWT(1)DDDLVESL;HEEEEWT(1)DDDLVESL 156.08 2.45E-05 219530000 267170 280790 282940 275790 307070 362750 316900 314630 272880 244920 TRUE FALSE 277718.0779 329013.4983 290313.6488 330340.4388 254874.3511 278506.81 292060.5499 310412.8995 263059.1021 292907.3847 0.948142971 1.123268021 0.99114486 1.12779826 0.870153381 0.95083574 0.997108865 1.059764675 0.898096517 1 18.16008504 3.250480824 24.99997746 0.973808543 1.048962482 0.245576474 0.071320183 362.8807397 761056.802 0.019631064 0.02637295 1780.249302 -3.250480824 0.075153938 HEEFEEGCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEEFEEGCK 9 0 Q9HC38-2;F6TLX2;I3L3Q4;Q9HC38-3;I3L1F4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 156.35 7.11E-05 408310000 877430 662160 679570 675450 1085300 1107200 879550 753010 808250 660880 FALSE TRUE 912071.6139 775880.8291 697280.1525 809051.994 900821.0937 850069.5798 810608.5727 742917.1326 779161.2404 790366.7827 1.153985256 0.981671859 0.882223504 1.02364119 1.1397507 1.07553809 1.025610628 0.939965025 0.985822352 1 19.59216279 1.878388447 6.513228956 0.970615519 1.037321374 0.139208667 0.074130164 0.525032581 25.61802737 0.034985596 0.021379993 75.57679085 -1.878388447 0.066705855 HEELMLGDPCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEELMLGDPCLK 12 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 160.15 6.88E-05 469520000 643170 518930 623880 587940 780300 838620 773800 685260 686940 420570 FALSE TRUE 668562.8482 608052.1908 640138.8253 704232.7772 647664.8847 643863.2144 713147.534 676075.2106 662217.1636 502972.6392 1.329223095 1.208917033 1.272711029 1.400141324 1.287674188 1.280115784 1.417865463 1.344159022 1.316606734 1 18.9401204 0.898979305 19.65180161 1 1.319875948 0.728026584 0.058202875 8313.853758 1617320.646 0.058522739 0.014630685 7.924635679 -0.898979305 0.319875948 HEENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEENLK 6 0 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 115.78 0.02414 1181890000 1186540 899430 1122460 923680 1487710 1387820 1576190 1210100 1302110 738220 FALSE TRUE 1233385.515 1053900.106 1151712.23 1106381.147 1234829.586 1065519.838 1452644.109 1193880.589 1255247.315 882860.0749 1.39703397 1.19373402 1.304524083 1.253178367 1.398669643 1.206895484 1.645384303 1.352287438 1.421796444 1 19.75182528 3.238788307 24.99999945 1.369581388 1.281690668 0 0.162902041 18.31135302 2010387.53 0.043290777 0.055106116 1732.959076 -3.238788307 -0.08789072 HEERQDEHGYISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HEERQDEHGYISR 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;; 189.99 3.09E-06 13713800000 1031229 1901387 1779313 629363 2659682 2098859 589487 1409677 1695453 3907220 FALSE TRUE 1071942.717 2227935.427 1825683.359 753849.1229 2207590.204 1611430.806 543281.4686 1390782.586 1634433.978 4672764.951 0.229402234 0.476791675 0.390707296 0.161328278 0.472437674 0.344855952 0.116265525 0.297635897 0.34977877 1 22.15584504 0.719612784 4.342782598 0.999998472 0.310969768 0.76740699 0.113233872 3.470086256 53.40012986 0.108532863 0.027599178 5.243397514 -0.719612784 -0.689028703 HEGALETLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEGALETLLR 10 0 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9;F8WEQ7;F8WBR8 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 193.83 5.30E-07 398040000 160811 159110 161936 194858 200203 208020 204838 154158 165786 134473 FALSE TRUE 167159.9425 186435.9048 166156.1852 233400.3308 166172.5656 159710.5076 188782.2623 152091.7642 159819.3942 160820.4097 1.039419951 1.159280126 1.033178472 1.451310385 1.033280327 0.9930985 1.17387005 0.945724267 0.993775569 1 17.29509098 3.045915094 24.99999559 1.023543442 1.170413503 0.26373528 0.120847426 172.2784284 93801.56883 0.034182013 0.040855304 1111.514403 -3.045915094 0.146870061 HEGVFICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEGVFICR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 113.26 0.0028837 223810000 139612 136315 150969 140555 147781 186392 185039 150441 145409 131625 FALSE TRUE 145123.9896 159726.0409 154903.3762 168356.3595 122661.2384 143105.2828 170535.1597 148424.5845 140175.7585 157414.3986 0.921923222 1.014685075 0.98404833 1.069510546 0.779225023 0.909099066 1.083351721 0.942890776 0.890488797 1 17.26420798 HEHQVMLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEHQVMLMR 9 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;; 89.247 0.0067821 65444000 41504.6 66098 57686 57856 75038 81548 63473 60870 57259 85593 FALSE TRUE 43143.23366 77449.81733 59189.34455 69299.74412 62283.06756 62609.71287 58497.8204 60054.13721 55198.25977 102363.3096 0.421471657 0.756616972 0.578228125 0.676997885 0.608451093 0.611642132 0.571472539 0.586676393 0.539238718 1 16.64333917 -2.162932511 2.404714274 1.985467274 0.600228402 0.685604661 0.082290408 4815394.478 1382065.719 25776628.55 0.018136047 0.006871752 2.162932511 -1.385238872 HEIEGTGLPQAQLLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEIEGTGLPQAQLLWR 16 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;; 251 3.89E-21 943600000 519730 533290 601050 570470 666170 756360 697320 656740 675710 516580 FALSE TRUE 540249.3417 624878.4091 616713.8568 683307.2633 552934.6613 580706.8527 642662.2363 647937.4745 651391.3291 617793.9605 0.874481423 1.011467332 0.998251676 1.106043935 0.895014676 0.939968484 1.040253349 1.04879218 1.054382805 1 19.23676624 2.214051995 23.53145653 1.040885238 0.976657295 0.202250683 0.06227934 200.8651472 192854.0304 0.023713364 0.017524752 163.7012497 -2.214051995 -0.064227943 HEIVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEIVPK 6 0 P25788-2;P25788;G3V4X5;H0YJ03 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 79.027 0.06823 335980000 1192800 904680 1112600 937740 1467200 1517100 1424000 1149500 1213300 758750 FALSE TRUE 1239892.665 1060051.753 1141595.27 1123222.173 1217805.868 1164776.517 1312383.159 1134092.833 1169633.57 907412.5354 1.366404603 1.168213697 1.258077474 1.237829685 1.342064189 1.283624009 1.446291635 1.249809528 1.28897665 1 19.79139906 0.28230504 1.942144951 0.999996014 1.292889295 0.593737286 0.072844228 10.34444187 26.90473873 0.068941425 0.019015925 1.915600934 -0.28230504 0.292893281 HEIVQTLSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEIVQTLSLK 10 0 Q13228;Q13228-4;Q13228-2;Q13228-3;A6PVX1;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 115.18 0.0012577 233380000 286800 229820 265670 287130 369450 369490 329530 284240 328920 221990 FALSE TRUE 298123.0855 269289.7972 272593.5785 343923.457 306651.021 283681.5472 303700.5775 280430.2277 317082.2335 265484.6902 1.122938898 1.01433268 1.026777018 1.295454953 1.155061035 1.06854202 1.143947612 1.056295289 1.194352236 1 18.01826914 -1.51689645 2.760903234 0.994677439 1.115275905 0.164003761 0.080539158 7826309.232 8051082.867 313431.6635 0.019667409 0.030416102 1.51689645 0.120598466 HEKEDGAISTIVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 200.44 1.16E-08 1555026000 2026611 1474226 2010052 1713795 2393713 2477864 2590074 1988362 2200143 1239311 FALSE TRUE 2106623.167 1727412.848 2062435.606 2052778.536 1986830.519 1902417.638 2387057.232 1961711.26 2120960.283 1482130.262 1.421348191 1.165493271 1.391534644 1.385018974 1.340523549 1.283569796 1.610558324 1.323575471 1.431021508 1 20.49924082 -1.050662913 5.432226514 0.999997417 1.370801322 0.515822363 0.108261096 3.24E-06 5.67E-07 0.100419108 0.023668846 0.088989156 1.050662913 0.370803905 HELIEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 172.03 0.0009156 2202421000 1783683 1646357 1866039 2110109 2255467 2436124 2467508 1941400 1920995 1411319 FALSE TRUE 1854104.182 1929106.008 1914669.509 2527482.262 1872083.525 1870371.121 2274098.275 1915378.708 1851858.765 1687839.937 1.098507117 1.142943691 1.134390452 1.497465611 1.109159396 1.108144842 1.347342379 1.134810634 1.097176767 1 20.68674666 1.126864026 2.133474449 1.00622633 1.204789235 0.218986149 0.121390746 0.436469004 3.750472971 0.112888408 0.031825071 13.39257312 -1.126864026 0.198562905 HELLQPFNVLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HELLQPFNVLYEK 13 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 160.65 4.35E-05 1371230000 1573600 1482240 1726920 1326900 2137240 2215280 1933530 1831230 1757120 1514290 FALSE TRUE 1635726.943 1736803.19 1771924.954 1589356.86 1773952.708 1700814.793 1781974.866 1806685.357 1693881.594 1810986.133 0.903224444 0.959037266 0.97843099 0.877619564 0.979550686 0.939165001 0.983980404 0.997625175 0.93533659 1 20.78834407 2.447702924 1.742123808 0.981192775 0.938189316 0.234946093 0.034049502 0.52590661 3.243381523 0.014903913 0.011437407 280.3515258 -2.447702924 -0.043003459 HELQANCYEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HELQANCYEEVK 12 0 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 190.03 7.16E-06 2657030000 4167300 2333100 3029830 3182510 3571810 4526660 5639740 3548740 3533170 1402800 FALSE TRUE 4331828.222 2733791.776 3108789.859 3812000.979 2964675.012 3475411.817 5197682.442 3501174.945 3406011.902 1677651.802 2.582078246 1.62953467 1.853060245 2.272224174 1.767157529 2.071593053 3.09818905 2.086949712 2.030225759 1 20.67801188 3.738850432 24.36124876 2.141631766 1.982355451 0 0.53821783 106.6373774 8963010.753 0.136459129 0.227984153 5480.881745 -3.738850432 -0.159276316 HELQANCYEEVKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 HELQANCYEEVKDR 14 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;; 280.5 1.71E-33 56035102000 35876269 21908157.9 29518691 24312053 37319831 41440763 39932682 31019716 32469794 16586194.1 FALSE TRUE 37292691.8 25670713.6 30287972.34 29120904.52 30976219.46 31816773.83 36802654.04 30603947.45 31301212.46 19835941.27 1.880056575 1.294151523 1.526923876 1.468087857 1.561620849 1.60399617 1.855352037 1.5428533 1.578004897 1 24.24161352 3.017854093 22.24321492 1.577319912 1.522402691 0 0.244025741 480.3710108 598446.2556 0.065997879 0.078852928 1041.967309 -3.017854093 -0.054917221 HELS(ph)PPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HELSPPQKR 9 1 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR;HELS(1)PPQKR 117.98 0.00050051 4522760000 1035910 737130 900225 837440 1060241 1226637 1306111 962379 964716 515140 TRUE FALSE 1076808.527 863726.3434 923685.603 1003083.132 880021.6135 941769.1466 1203734.607 949479.8836 929996.0596 616071.82 1.747862005 1.401989696 1.499314809 1.628191876 1.428439972 1.528667788 1.953886816 1.541183759 1.509557862 1 19.23273902 0.715082656 2.613787156 1.00015366 1.589895744 0.570400764 0.153084039 1.299462584 10.95369573 0.146947893 0.039045462 5.188987872 -0.715082656 0.589742084 HEMLPASLIQAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HEMLPASLIQAQR 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 188.09 6.40E-06 1739600000 1337510 1365730 1459060 1297790 1673880 1951800 1489700 1550810 1490460 1396330 FALSE TRUE 1390315.928 1600283.504 1497084.302 1554488.988 1389354.475 1498524.03 1372933.421 1530023.929 1436818.636 1669914.129 0.832567318 0.958302871 0.896503764 0.930879595 0.831991568 0.897365921 0.822158096 0.916229105 0.860414683 1 20.67134249 -1.016707591 4.475487583 1.000003993 0.885502566 0.394084956 0.043442302 5224008.032 1186750.899 232.7503373 0.009488886 0.096225995 1.016707591 -0.114501426 HEMLPEFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEMLPEFYK 9 0 Q86VP6;Q86VP6-2;A0A0C4DGH5;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 89.247 0.012236 99868000 91244 73288 89856 69980 139950 123630 96799 87436 101350 93006 FALSE TRUE 94846.38358 85874.6439 92197.72118 83821.83513 116161.349 94918.80613 89211.64144 86264.06344 97702.4333 111228.745 0.852714679 0.772054417 0.828901928 0.753598678 1.044346486 0.853365793 0.802055633 0.775555487 0.878391942 1 16.76317015 -2.45885175 1.192825567 1.580209922 0.835470559 0.270422281 0.078460352 37754.9797 3146.796093 58239.95156 0.023064831 0.003476548 2.45885175 -0.744739362 HEMPPHIYAITDTAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HEMPPHIYAITDTAYR 16 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ;;;;; 206.63 1.13E-11 1816860000 1117394 1180374 1263832 1173717 1487171 1625579 1435368 1322924 1285892 1213053 FALSE TRUE 1161509.578 1383094.052 1296768.5 1405874.719 1234382.205 1248062.913 1322860.106 1305192.368 1239612.998 1450727.51 0.800639383 0.953379627 0.893874619 0.969082553 0.850871164 0.860301404 0.911859806 0.899681269 0.854476798 1 20.46834513 -1.37081516 4.329021739 1.000203231 0.892416725 0.328603152 0.047588868 8.71E-05 1.27E-05 0.042983191 0.010112174 0.042577959 1.37081516 -0.107786505 LDFLPEMMVDHCSLNSS(ph)PVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCSLNS(0.007)S(0.993)PVSK;LDFLPEMMVDHCSLNS(0.017)S(0.983)PVSK 207.6 2.30E-22 458530000 202015 511670 655370 572740 689180 786290 650710 705090 662610 494870 TRUE FALSE 209990.7082 599545.3423 672449.4806 686026.2625 572033.4298 603686.0638 599705.6499 695639.4218 638762.7955 591830.3016 0.354815743 1.0130359 1.136220093 1.159160423 0.966549749 1.020032368 1.013306768 1.175403523 1.079300593 1 19.17482404 4.73662903 4.194403726 1.07534084 0.298389086 0.909166961 0.067283705 0.058987591 2.351772925 0.017024392 0.137575197 54529.18786 -4.73662903 -0.776951754 down HENVIGLLDVFTPAR ddPTM_MDA-MB-175_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 70.942 0.034133 0 145120 120340 145900 144950 163250 178610 167960 142470 149240 104020 FALSE TRUE 150849.4497 141007.4589 149702.2739 173620.6774 135500.8233 137130.5344 154794.8563 140560.4227 143868.8816 124400.7274 1.212609064 1.133493845 1.203387448 1.395656448 1.089228545 1.102329039 1.244324366 1.129900328 1.156495501 1 16.9246354 HEPLVLFCESCDTLTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HEPLVLFCESCDTLTCR 17 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;;; 322.99 9.11E-59 1891687000 628564 765766 645135 861742 766574 1002018 778532 805799 740830 678644 FALSE TRUE 653380.1921 897280.3537 661947.7481 1032191.996 636272.0253 769314.5052 717508.6275 794998.5824 714167.673 811611.2984 0.805040779 1.105554291 0.81559701 1.271781206 0.783961518 0.947885406 0.884054509 0.979531192 0.879938062 1 19.63042942 HEQISDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEQISDLER 9 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 131.09 0.00034297 118390000 44768 50765 51843 55869 68899 71170 63517 51932 54215 49780 FALSE TRUE 46535.47521 59483.49385 53194.07117 66919.72145 57187.57259 54641.84609 58538.37157 51235.93648 52263.81274 59533.4379 0.781669543 0.999161076 0.893515863 1.124069494 0.960595837 0.917834548 0.983285589 0.860624521 0.877890049 1 15.86141259 -0.113483438 7.75338095 1 0.936600169 0.048214232 0.087889145 0 0 0.08281236 0.01951906 0.770045811 0.113483438 -0.063399831 HEQMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEQMKK 6 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 74.335 0.05232 76223000 242890 210430 232800 169750 302400 271990 217660 269420 262530 218630 FALSE TRUE 252479.4848 246569.7156 238866.9592 203326.0433 250998.156 208824.4445 200599.2405 265808.8656 253081.5966 261466.3626 0.965628933 0.943026526 0.913566689 0.77763748 0.959963467 0.798666576 0.767208594 1.016608266 0.96793176 1 17.99626583 1.641517601 10.73974079 0.994015514 0.876126717 0.375965667 0.070571936 0.119817713 26.75459883 0.034918698 0.01871706 43.80438634 -1.641517601 -0.117888798 HEQNIDCGGGYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEQNIDCGGGYVK 13 0 P27797 P27797 CALR Calreticulin 0 ;; 164.2 3.74E-05 13203900000 11559300 9483100 11116000 10021600 14155100 14529700 12056800 10781500 11275500 8223600 FALSE TRUE 12015670.09 11111748.66 11405692.09 12003842.57 11749021.16 11155397.37 11111756.51 10636991.63 10869696.96 9834856.97 1.221743247 1.129833275 1.159721196 1.220540635 1.194630608 1.13427144 1.129834073 1.081560379 1.105221661 1 23.22947264 1.383289107 0.583115381 1.004153339 1.186036141 0.774530216 0.030387744 0.347528107 0.287551562 0.03116104 0.015766204 24.17069326 -1.383289107 0.181882803 HEQQQLLGVEEVTDPDVVLHNLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEQQQLLGVEEVTDPDVVLHNLLR 24 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 0 128.36 4.52E-05 76753000 32725 34227 32229 35748 38374 40729 34311 29337 31942 31318 FALSE TRUE 34017.00827 40105.221 33068.91422 42818.8477 31851.20119 31270.307 31621.61416 28943.7855 30792.41366 37454.16248 0.908230381 1.070781412 0.882916932 1.143233352 0.850404844 0.834895374 0.84427503 0.772778874 0.822135956 1 15.19283844 3.072173714 13.70552523 0.835295304 0.997782463 0.38796562 0.088875481 0.919031299 172.7903375 0.023657714 0.028278937 1180.792849 -3.072173714 0.162487158 HERGSPS(ph)HSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HERGSPSHSK 10 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 HERGS(0.247)PS(0.752)HS(0.001)K;HERGS(0.489)PS(0.511)HSK;HERGS(0.218)PS(0.781)HS(0.001)K 69.229 0.034789 110595000 96823 69397 83207 54866 109909 108029 91303 81768 91234 65453 TRUE FALSE 100645.6468 81315.39492 85375.44278 65718.33104 91226.70744 82940.90195 84146.43228 80672.03371 87950.50616 78277.26218 1.285758393 1.038812455 1.09067998 0.839558375 1.165430483 1.059578473 1.074979246 1.03059345 1.123576678 1 16.25630568 4.73984337 24.5931259 1.047465503 1.285758488 0.428833925 0.082654558 80.89321165 1550676.489 0.018594502 0.115800367 54934.27154 -4.73984337 0.238292986 HERPAGPGT(ph)PPPDSGPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HERPAGPGTPPPDSGPLAK 19 1 Q9P2K8-2;Q9P2K8;H0YME5 Q9P2K8-2 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 HERPAGPGT(0.933)PPPDS(0.067)GPLAK 75.239 0.02152 113680000 182980 125930 181680 150120 215220 206280 202530 151300 182810 103670 TRUE FALSE 190204.1917 147557.4979 186414.7301 179813.2879 178636.9813 158374.5962 186655.1694 149272.071 176230.7038 123982.1516 1.534125592 1.19015113 1.503561018 1.450315917 1.440828207 1.277398352 1.505500324 1.203980323 1.42141995 1 16.91977292 -1.584359041 0.301243099 0.684951771 1.422276689 0.507061706 0.117409078 18.43596059 1.037113466 4.442032131 0.116523642 0.026039999 1.584359041 0.737324918 HESGASIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HESGASIK 8 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 162.97 0.00033863 3260520000 693217 4742620 4392920 4772910 4693910 6721680 4207130 6023200 4247590 4390280 FALSE TRUE 720585.7424 5557128.093 4507403.104 5716977.352 3896040.855 5160671.688 3877364.157 5942468.856 4094720.066 5250471.309 0.137242106 1.058405573 0.858475904 1.088850318 0.742036405 0.982896846 0.738479258 1.131797225 0.779876667 1 22.3240155 4.744043487 24.96759108 0.933880181 0.137241763 0.749240963 0.137788396 260.122794 1184496.582 0.029807758 0.260013231 55468.12519 -4.744043487 -0.796638419 HESGASIKIDEPLEGSEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HESGASIKIDEPLEGSEDR 19 1 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 177.61 2.39E-14 228612000 49256 206898 207316 140127 297400 298540 106327 241260 205293 297640 FALSE TRUE 51200.66491 242431.1221 212718.8253 167843.7024 246848.0542 229208.6094 97992.81191 238026.3043 197904.545 355956.8593 0.143839523 0.681068831 0.597597208 0.471528215 0.693477447 0.64392244 0.275294068 0.668694248 0.555979018 1 18.44134288 -4.999999998 0.263045452 4.045393985 0.500746728 0.414566326 0.172233655 196.5979887 1.925412138 323.9876536 0.21168086 1.00E-05 4.999999998 -3.544647257 HESQQDYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HESQQDYSK 9 0 Q14247 Q14247 CTTN Src substrate cortactin 0 ;;;; 148.56 0.0014203 244943000 372106 1622800 1576476 1483122 1913952 2350216 1530360 1957342 1577797 1571250 FALSE TRUE 386797.0322 1901503.276 1617560.26 1776479.105 1588619.123 1804413.952 1410406.384 1931107.032 1521012.394 1879106.354 0.205840947 1.011918922 0.860813576 0.945385077 0.845412033 0.960251104 0.750572942 1.027673089 0.809433905 1 20.84161529 4.74362277 24.9999575 0.910037824 0.205840657 0.851684002 0.088448605 170.1360097 840207.3031 0.018827259 0.157896771 55414.41721 -4.74362277 -0.704197167 HETWSGHVISS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HETWSGHVISS 11 0 Q9Y2V2 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ;;; 227.88 3.68E-12 996020000 179525 647237 624103 616416 609994 827493 549031 652426 573047 649465 FALSE TRUE 186612.7856 758394.9199 640367.6369 738341.245 506307.4378 635320.2915 505996.5156 643681.2966 552423.1504 776715.232 0.240258949 0.97641309 0.824456133 0.950594522 0.651857228 0.817957812 0.651456924 0.828722381 0.711229969 1 19.56702623 -4.999999938 0.02885453 2.046500548 7.98E-09 0.150092283 0.195283368 3864.638942 8.402495576 456.9471237 191.7304168 1.00E-05 4.999999938 -2.04650054 HEVININLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HEVININLK 9 0 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ;; 168.8 5.90E-05 1167330000 2187696 1505198 2071497 1687965 2435594 2640919 2643789 2088068 2243880 1100236 FALSE TRUE 2274067.927 1763704.048 2125481.914 2021839.439 2021592.602 2027605.586 2436561.91 2060080.864 2163123.197 1315806.179 1.728269683 1.340398059 1.615345746 1.536578465 1.536390871 1.540960681 1.851763542 1.565641579 1.643952758 1 20.32751556 2.398930144 22.02877092 1.588542617 1.541860774 0 0.223619969 95.32509878 26842.22636 0.071321403 0.059671767 250.5706178 -2.398930144 -0.046681843 HEWQVNGLDDIKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HEWQVNGLDDIKDR 14 1 Q9Y281;Q9Y281-3 Q9Y281 CFL2 Cofilin-2 0 186.56 6.30E-07 210520000 119780 75759 107730 80766 142350 151060 144700 109760 121870 77427 FALSE TRUE 124509.0069 88770.01893 110537.5323 96741.27374 118153.3978 115978.6043 133358.0359 108288.8467 117483.9225 92597.33822 1.344628358 0.95866707 1.193744166 1.04475221 1.275991299 1.252504732 1.440192974 1.169459607 1.268761336 1 16.4986831 3.220887835 24.96856061 1.252598794 1.126984747 0.099035197 0.139153482 413.2825921 583894.9646 0.037379903 0.04477041 1662.983098 -3.220887835 -0.125614047 HFADLLPGFLQAVNDSCYQNDDSVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFADLLPGFLQAVNDSCYQNDDSVLK 26 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 229.71 7.64E-35 356100000 358210 243670 301970 295480 364550 374430 365280 313280 319560 228750 FALSE TRUE 372352.4074 285518.427 309839.5863 353925.0621 302583.9212 287474.307 336648.3991 309080.994 308059.098 273569.1828 1.361090469 1.043679058 1.132582198 1.293731474 1.106059967 1.050828548 1.230578663 1.129809253 1.126073832 1 18.0615462 -5 0.125715203 0.480130509 1.230623669 0.260902489 0.093585358 222.9128989 1.79020946 29.40560142 0.757637007 1.00E-05 5 0.75049316 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 31 2 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 263.92 5.34E-59 89979000 262570 191420 239320 227350 341420 324950 327870 278890 337390 191790 FALSE TRUE 272936.4663 224294.896 245556.8758 272319.1514 283385.5504 249485.2872 302170.6927 275151.9357 325247.3998 229367.5785 1.189952251 0.977884047 1.070582327 1.187260873 1.235508315 1.08770947 1.317408043 1.199611286 1.418018196 1 17.80730195 3.666804229 3.746459114 1.219192468 1.068354797 0.194035939 0.117583526 0.316159435 8.643324874 0.029993478 0.049574725 4643.059283 -3.666804229 -0.15083767 HFCPNVPIILVGNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFCPNVPIILVGNKK 15 1 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;P61586 Q5JR08;P61586 RHOC;RHOA Rho-related GTP-binding protein RhoC;Transforming protein RhoA 0 ; 194.3 3.73E-08 1673000000 3271200 2284870 3060300 2457590 4111500 4053300 3485700 3126000 3598700 2440430 FALSE TRUE 3400349.502 2677278.649 3140053.932 2943693.967 3412628.699 3111982.503 3212481.726 3084101.083 3469183.49 2918585.534 1.16506762 0.917320605 1.0758821 1.008602946 1.169274863 1.066263938 1.10069816 1.056710878 1.188652328 1 21.47683792 3.274718337 24.99992965 1.095631474 1.035273033 0.108378674 0.076644877 349.9229299 241939.1181 0.019503064 0.026406375 1882.427838 -3.274718337 -0.060358441 HFDADGNGYIEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFDADGNGYIEGK 13 0 P22676;A6NER6;H3BN14 P22676 CALB2 Calretinin 0 ; 82.908 0.011071 612930000 1112620 908170 1043410 895580 1335430 1393060 1276140 1090670 1217990 906520 FALSE TRUE 1156547.097 1064141.133 1070602.122 1072723.051 1108434.086 1069542.927 1176112.812 1076051.353 1174154.778 1084135.238 1.066792275 0.981557555 0.987517133 0.989473466 1.022413115 0.986540138 1.084839577 0.992543472 1.083033497 1 20.0481133 HFDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFDKDK 6 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 105.12 0.019979 127260000 586820 354940 511860 259460 772340 658810 576180 445630 510730 399890 FALSE TRUE 609988.1067 415898.184 525199.4921 310780.4136 641057.9227 505811.3619 531017.506 439657.0588 492348.9271 478240.7891 1.275483231 0.869641807 1.098190502 0.649840876 1.340450119 1.057649982 1.110355951 0.91932154 1.029500072 1 18.86737766 0.955835989 0.006130821 4.46E-08 2.029931551 0.008135516 0.186757423 42031.25181 166.2484526 27748.89005 27281.91852 9.033082759 -0.955835989 2.029931506 HFEALANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HFEALANR 8 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;; 160.54 0.00035277 671860000 190311 281042 239999 293747 369636 366471 241117 246071 233860 423970 FALSE TRUE 197824.6252 329308.7773 246253.5711 351849.2799 306805.4048 281363.6642 222217.6195 242772.8207 225443.4243 507038.8041 0.390156776 0.649474507 0.485670069 0.693929689 0.605092554 0.554915446 0.438265509 0.478805209 0.444627556 1 18.95173664 -1.541054798 2.815252327 1.024006196 0.529619595 0.697856664 0.093397975 15972826.03 16757151.55 2911122.667 0.025289128 0.028770354 1.541054798 -0.494386601 HFEELETIMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 536050000 397393 506490 504250 480160 546000 585260 549220 514310 501800 485810 FALSE TRUE 413082.3825 593475.7176 517391.1692 575134.2149 453191.115 449342.2347 506170.7013 507416.5157 483740.316 580995.1681 0.710991081 1.021481331 0.89052577 0.989912217 0.780025618 0.773400984 0.871213272 0.873357548 0.832606436 1 19.14816664 4.779788796 23.45276294 0.882989637 0.710989903 0.292529647 0.083511555 17473.9664 9939626.221 0.019837612 7.048020462 60226.66228 -4.779788796 -0.171999734 HFELGGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 138.06 0.0007214 4416940000 7733640 5674040 7159640 6174700 9608080 9524000 9554260 7381450 7769440 5366860 FALSE TRUE 8038970.079 6648512.232 7346226.1 7396037.23 7974901.994 7312195.338 8805372.136 7282513.736 7489819.372 6418393.462 1.252489447 1.035853017 1.144558392 1.152319077 1.242507497 1.139256323 1.371896595 1.134631864 1.166930544 1 22.6137808 3.461156755 23.6882671 1.191424012 1.135952733 0.004736051 0.101017122 377.1623807 559632.7757 0.026281597 0.035599136 2891.723437 -3.461156755 -0.055471279 HFESQSDDPHFHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFESQSDDPHFHEK 14 0 A0A5F9ZHZ6;A0A0A0MRL7;P55210-4;P55210;P55210-3 A0A5F9ZHZ6 CASP7 Caspase-7;Caspase-7 subunit p20;Caspase-7 subunit p11 0 ; 119.45 6.50E-05 729710000 196301 216613 254950 212650 310210 339870 262820 252710 270180 239840 FALSE TRUE 204051.1151 253814.5977 261594.2064 254711.5353 257480.615 260940.3433 242219.4816 249322.8358 260456.2746 286832.056 0.711395783 0.884889232 0.912011754 0.88801628 0.89767029 0.909732151 0.844464475 0.86922933 0.908044513 1 18.12984674 -2.689978287 0.017509114 1.969476129 1.95E-06 0.443344744 0.051278396 3098.891095 6.346501597 422.4632434 300.1000088 0.00204184 2.689978287 -1.969474184 HFFHHADEDDEEEDDS(ph)PPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 207.22 1.15E-21 1176510000 457963 446448 423859 425684 557016 626487 482040 397815 428681 369560 TRUE FALSE 476043.7329 523121.9711 434905.1137 509883.0247 462334.6193 480994.8888 444256.4452 392482.9406 413252.8545 441968.2063 1.077099497 1.183619011 0.984019003 1.153664488 1.046081172 1.088302013 1.005177383 0.888034331 0.935028467 1 18.75358307 2.053756378 3.326575913 0.930603801 1.08945055 0.571327363 0.057526842 0.152591996 3.398715233 0.023982192 0.015436966 113.176531 -2.053756378 0.158846749 HFGAGGNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HFGAGGNQR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;;; 118.74 0.00093988 471083000 206193 150030 171374 145848 186469 251939 192723 147385 167306 147247 FALSE TRUE 214333.6589 175796.4854 175840.1472 174696.2991 154773.066 193429.9854 177616.8677 145409.5451 161284.6897 176097.2304 1.21713248 0.998292165 0.998540106 0.992044558 0.878906872 1.098427187 1.008629535 0.825734424 0.915884306 1 17.42601269 7.99999506 0.913914797 0.949475304 146.1502632 0.515340463 0.07256391 853.5356669 1.734384792 0.024141518 258684.9595 99998862.62 -7.99999506 145.2007879 HFGDEDQAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFGDEDQAMR 10 0 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 134.84 0.00015989 270370000 95937 85347 83299 85282 109550 124080 88783 94340 101360 75803 FALSE TRUE 99724.66684 100004.6833 85469.84037 102150.5251 90928.73013 95264.30045 81823.95647 93075.52661 97712.0734 90655.14651 1.100044186 1.103132996 0.942801856 1.126803375 1.00301785 1.050842717 0.902584791 1.026698761 1.077843643 1 16.4681013 HFHPLFEYFDYESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 131.26 5.73E-05 1427750000 805480 725250 722700 738340 806410 853000 759230 732380 674740 617500 FALSE TRUE 837280.9724 849806.0458 741534.1557 884381.4483 669336.7162 654903.6773 699719.5687 722563.644 650456.2392 738487.3022 1.133778428 1.150738873 1.004125803 1.197558097 0.906361848 0.88681779 0.947503859 0.978437465 0.880795428 1 19.49421359 3.227780553 24.99271251 0.934268905 1.115247738 0.719648056 0.057500045 110.5737213 256355.8776 0.01613589 0.019467118 1689.586976 -3.227780553 0.180978832 HFIDVGAGVIDEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HFIDVGAGVIDEDYR 15 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0;H0YMP1 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;;; 214.18 2.51E-12 3629760000 2465700 2715860 2844610 2842910 2872940 3733050 3239460 3052490 2813010 2583480 FALSE TRUE 2563047.74 3182287.829 2918742.873 3405229.113 2384598.685 2866105.712 2985542.66 3011576.364 2711770.32 3089663.442 0.829555642 1.029978795 0.944679875 1.102135937 0.771798848 0.927643339 0.966300284 0.974726348 0.877691169 1 21.55901826 -1.397220897 3.109910297 1.000764148 0.942667606 0.038954582 0.090045446 21496211.21 24889301.64 142925.9017 0.020451449 0.040066287 1.397220897 -0.058096542 HFIEITDDQFDFHTYCMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HFIEITDDQFDFHTYCMR 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ;;; 184.01 3.49E-14 201727000 104541 168174 140117 168856 139250 181178 138098 144952 135869 160114 FALSE TRUE 108668.3594 197056.5763 143768.5641 202255.2128 115580.3347 139102.1553 127273.5179 143009.1555 130979.1012 191485.2727 0.567502439 1.029095207 0.750807423 1.056244221 0.603599081 0.726437878 0.664664786 0.746841538 0.684016579 1 17.54687391 5.008173958 16.86699578 0.788414868 0.264053042 0.167080461 0.155493288 1405539655 37702733810 0.035768304 16349398845 101899.947 -5.008173958 -0.524361826 HFILDECDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 2343130000 6191330 3661390 4462320 4156250 6189110 6917030 6408040 4805550 4818770 2816040 FALSE TRUE 6435768.489 4290205.251 4578611.725 4978343.845 5137087.293 5310654.611 5905761.081 4741139.463 4645343.409 3367789.122 1.910977278 1.273893672 1.35953041 1.47822315 1.525358954 1.576896421 1.753601804 1.407789886 1.379345096 1 21.68337037 0.843007767 1.70179625 1.002425983 1.530321588 0.467538515 0.174668413 0.523265252 2.857552403 0.161954296 0.046224106 6.966389732 -0.843007767 0.527895605 HFIMQVVCEATQCPDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFIMQVVCEATQCPDTR 17 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 214.22 6.01E-15 2938200000 1021960 916130 981470 912370 1191160 1450650 1011800 916560 1003720 927680 FALSE TRUE 1062307.77 1073468.201 1007047.914 1092834.063 988687.0487 1113758.522 932492.4722 904275.0124 967596.3133 1109441.134 0.95751612 0.967575627 0.907707388 0.985031138 0.891157735 1.003891498 0.840506489 0.815072548 0.872147501 1 20.08140169 2.224310391 24.99917101 0.860079571 0.949550477 0.23655073 0.056473755 240.7585231 422359.927 0.019709725 0.014625106 167.6140389 -2.224310391 0.089470905 HFKDEDEDEDVAS(ph)PDGLGR ddPTM_MDA-MB-175_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 281.3 6.69E-40 4795870000 5476750 3916610 4525700 3712920 5800500 6097710 5637860 4494950 4883650 2969142 TRUE FALSE 5692976.319 4589257.301 4643643.46 4447324.494 4814533.082 4681609.264 5195949.801 4434702.548 4707888.39 3550888.527 1.603254024 1.292425055 1.307741267 1.252453987 1.355867143 1.318433183 1.463281588 1.248899399 1.325833902 1 21.75974864 -3.725084718 0.247123172 1.38E-13 1.380967103 0.54649074 0.098724294 68.28341724 1.202823609 34.63308953 0.144074226 0.000188328 3.725084718 1.380967103 HFLLEEDKPEEPTAHAFVSTLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 262.38 5.19E-44 17643404000 8459817 5512229 7194896 6297319 10026010 10861960 9522060 6889884 8108531 4472851 FALSE TRUE 8793817.108 6458911.452 7382400.9 7542909.903 8321792.401 8339434.405 8775696.056 6797536.375 7816706.553 5349220.516 1.643943652 1.207449091 1.380089095 1.41009515 1.555701878 1.558999929 1.640556046 1.270752693 1.461279551 1 22.35089725 -1.532832641 10.6025915 0.999995007 1.448240339 0.491608945 0.139589665 1.64E-05 7.23E-07 0.134702174 0.031749254 0.029320229 1.532832641 0.448245331 HFLPLDFSTQVNSSLTS(ph)PTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFLPLDFSTQVNSSLTSPTGR 21 0 P19793 P19793 RXRA Retinoic acid receptor RXR-alpha 1 HFLPLDFSTQVNSSLT(0.003)S(0.971)PT(0.026)GR;HFLPLDFSTQVNSSLT(0.003)S(0.997)PTGR 178.76 3.86E-17 966010000 697460 707590 790440 783860 908740 1121960 940760 942550 992130 992000 TRUE FALSE 724996.2594 829113.0782 811039.5158 938905.1684 754272.6994 861401.7935 867020.773 929916.659 956423.4351 1186363.407 0.611108076 0.698869396 0.683634973 0.791414471 0.63578554 0.726085943 0.730822249 0.783837948 0.806180829 1 20.17811457 -4.999999352 0.128280829 1.989548499 0.59294829 0.82978928 0.043015149 54.64028075 0.444601143 13.73478676 0.329559511 1.00E-05 4.999999352 -1.396600209 HFLQQATQVNAWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFLQQATQVNAWDR 14 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ; 198.74 2.16E-08 1251390000 659080 761740 739830 734010 850860 988660 743590 754810 725960 786890 FALSE TRUE 685100.9873 892562.9195 759110.5776 879194.9872 706231.1211 759058.6983 685305.4728 744693.0066 699832.8414 941066.0296 0.728005226 0.948459398 0.806649644 0.934254303 0.750458628 0.806594516 0.728222517 0.791329177 0.743659658 1 19.84393643 3.216549451 24.97539785 0.788092948 0.857658256 0.052881009 0.0926046 474.7389796 538670.2749 0.024296657 0.029061749 1646.453429 -3.216549451 0.069565309 HFLVEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HFLVEDK 7 0 P53992;P53992-2 P53992 SEC24C Protein transport protein Sec24C 0 ;; 139.28 0.0027038 720850000 1825740 1208510 1629260 1363280 2174880 2313270 2066400 1651450 1798650 1023530 FALSE TRUE 1897821.625 1416062.192 1671719.854 1632932.715 1805194.674 1776048.1 1904430.168 1629315.014 1733916.938 1224071.107 1.550417794 1.15684635 1.365704855 1.334017857 1.474746577 1.4509354 1.555816617 1.331062391 1.416516515 1 20.22325594 -1.205085824 3.184140274 0.998828342 1.398661808 0.540080575 0.111748433 14518841.86 20861862.32 169716.2321 0.025890257 0.062361159 1.205085824 0.399833466 HFNALGGWGELQNSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFNALGGWGELQNSVK 16 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 190.19 8.97E-10 931780000 1401900 1262330 1552540 1283910 1890910 1833540 1621420 1431290 1504800 1344080 FALSE TRUE 1457248.095 1479125.358 1593000.468 1537863.566 1569493.794 1407728.123 1494328.864 1412105.899 1450642.542 1607426.742 0.906572011 0.920182127 0.991025237 0.95672389 0.976401445 0.875765026 0.929640415 0.878488495 0.902462616 1 20.61632156 2.744543999 24.98701818 0.908319528 0.951146965 0.125457031 0.040060948 757.852484 3164845.273 0.01197747 0.012416327 555.3208749 -2.744543999 0.042827436 HFPNIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HFPNIDR 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 133.12 0.0033029 1288483000 1025684 1348512 1270888 1393906 1493356 1704107 1266291 1322890 1185891 1397331 FALSE TRUE 1066178.796 1580108.446 1304008.385 1669616.446 1239515.881 1308353.975 1167035.803 1305158.823 1143211.015 1671111.256 0.638005873 0.945543536 0.780324099 0.9991055 0.741731513 0.782924518 0.69835913 0.781012526 0.684102277 1 20.67237635 HFRHDT(ph)PDS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFRHDTPDSSPR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.554)S(0.446)PR 83.54 0.029198 105180000 73975 90481 82096 65923 101800 105970 67785 82947 84409 94204 TRUE FALSE 76895.59012 106020.4079 84235.4892 78962.37264 84496.07236 81360.07349 62471.83458 81835.23114 81371.13658 112661.4702 0.682536718 0.941052942 0.747686756 0.700881788 0.749999731 0.722164138 0.554509314 0.726381708 0.722262336 1 16.78163468 4.015465126 24.74343318 0.717751689 0.819938616 0.032621093 0.118869242 433.7444976 693958.0598 0.027250402 0.058837526 10362.51391 -4.015465126 0.102186927 HFRHDT(ph)PDSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFRHDTPDSSPR 12 1 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 HFRHDT(1)PDS(0.452)S(0.548)PR 72.433 0.09603 102620000 76919 90952 89581 64629 112610 115140 64937 75890 79870 96435 TRUE FALSE 79955.82151 106572.2985 91915.55445 77412.4233 93468.59242 88400.47996 59847.06826 74872.81868 76995.4943 115329.5919 0.693281058 0.924067247 0.796981529 0.671227757 0.810447613 0.766503016 0.51892205 0.64920735 0.667612649 1 16.81540321 3.83599752 5.373688539 0.701335648 0.81996478 0.046146083 0.130557399 0.448602348 19.68739003 0.032930741 0.060625713 6854.843123 -3.83599752 0.118629132 HFS(ph)QSEETGNEVFGALNEEQPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.829)QS(0.132)EET(0.039)GNEVFGALNEEQPLPR;HFS(0.997)QS(0.003)EETGNEVFGALNEEQPLPR;HFS(0.895)QS(0.104)EET(0.001)GNEVFGALNEEQPLPR;HFS(0.589)QS(0.398)EET(0.012)GNEVFGALNEEQPLPR;HFS(0.947)QS(0.048)EET(0.005)GNEVFGALNEEQPLPR 307.74 1.43E-73 2786700000 905834 1046650 1057864 1173665 1266750 1457860 1117651 1132393 1070015 953399 TRUE FALSE 941597.0258 1226403.996 1085432.805 1405812.434 1051428.287 1119294.109 1030046.594 1117215.124 1031505.369 1140199.28 0.825817944 1.075604955 0.951967629 1.232953273 0.922144318 0.981665336 0.903391725 0.979841983 0.904671128 1 20.12085457 HFSEHPSTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFSEHPSTSK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 152.54 1.03E-05 132024000 58125 288660 242200 290890 264600 435760 205372 351680 240880 352990 FALSE TRUE 60419.81988 338235.1095 248511.931 348427.1738 219623.3865 334561.344 189274.406 346966.3048 232210.7759 422151.6321 0.143123502 0.801217107 0.588679309 0.825360243 0.520247631 0.792514629 0.448356447 0.821899712 0.550064854 1 18.68740177 -5 0.088829754 2.052613566 0.347308431 0.279227783 0.19985164 299.9849091 1.856975699 62.04285925 4.510468191 1.00E-05 5 -1.705305135 HFSGLEEAVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 261.87 1.04E-20 3682080000 378620 2562316 1871407 2554283 2285699 3479671 1672154 2666369 1798960 3305637 FALSE TRUE 393568.21 3002373.841 1920177.404 3059512.554 1897176.7 2671570.145 1541086.2 2630630.685 1734215.781 3953313.28 0.099554015 0.759457606 0.485713443 0.77391098 0.47989536 0.675780025 0.389821421 0.665424291 0.438674008 1 21.91463086 -2.145693932 2.32110344 1.984869784 0.547992879 0.344790623 0.192991779 13517423.35 2830778.072 70219371.31 0.041234274 0.00715 2.145693932 -1.436876905 HFSQSEET(ph)GNEVFGALNEEQPLPR ddPTM_MDA-MB-175_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(0.313)QS(0.313)EET(0.375)GNEVFGALNEEQPLPR 69.548 0.020902 13253000 4006.1 5732 5496.8 6438.3 5543 10161 5725.4 5882.9 6809.3 6884.1 TRUE FALSE 4164.263921 6716.426411 5640.051124 7711.776524 4600.80284 7801.261741 5276.628187 5804.049348 6564.234623 8232.907591 0.505807198 0.815802478 0.685061877 0.936701456 0.558830861 0.947570668 0.640919156 0.704981719 0.797316689 1 13.00718632 -5 0.322548706 3.556732763 0.723211913 0.261738027 0.137586508 437.8886073 3.855782849 765.0764862 0.109783398 1.00E-05 5 -2.83352085 HFSVEGQLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 HFSVEGQLEFR 11 0 P08238;Q58FF7;P07900;P07900-2;Q14568;Q58FG1 P08238;P07900 HSP90AB1;HSP90AB3P;HSP90AA1;HSP90AA2P;HSP90AA4P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-alpha A4 0 ;;;;;;;; 234.3 1.71E-15 2092029400 402082.2 1888694.8 1771953.6 1930482.8 1900948.6 2474694.7 1585903.9 2044681.3 1637637.9 2032435.1 FALSE TRUE 417956.7157 2213063.44 1818132.166 2312326.536 1577826.036 1899984.36 1461596.608 2017275.692 1578699.632 2430651.845 0.171952522 0.91048146 0.748001887 0.951319516 0.649136996 0.781676884 0.601318783 0.829931977 0.649496404 1 21.21291183 -4.999998932 0.036309076 2.122666194 2.57E-09 0.189027686 0.203056873 2033.735632 5.53423841 276.180907 92.76841045 1.00E-05 4.999998932 -2.122666192 HFTILDAPGHK ddPTM_MDA-MB-175_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 ; 176.95 4.74E-06 1846250000 1056140 3323980 2829680 2817110 2508160 3656600 2276940 2738210 2634110 4567100 FALSE TRUE 1097837.223 3894847.708 2903423.785 3374325.95 2081823.859 2807410.066 2098467.493 2701508.774 2539308.896 5461935.803 0.200997826 0.713089251 0.531574132 0.617789383 0.381151287 0.513995435 0.384198491 0.494606468 0.464910059 1 22.38098093 -1.270061064 3.463155905 1.001521707 0.485481955 0.583277306 0.132222824 55223806.38 85492305.7 891052.7581 0.029351518 0.053695629 1.270061064 -0.516039752 HFVALSTNTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HFVALSTNTTK 11 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90 P06744 GPI Glucose-6-phosphate isomerase 0 ; 180.19 6.77E-06 2712200000 2830900 2303600 2876000 2383200 3847500 3762800 3313700 3072800 3098800 2399800 FALSE TRUE 2942666.118 2699225.38 2950950.923 2854589.847 3193503.324 2888946.726 3053963.535 3031614.142 2987274.793 2869994.863 1.02532104 0.940498332 1.028207737 0.994632389 1.11272092 1.006603448 1.064100697 1.056313438 1.04086416 1 21.45261672 3.372397121 22.79151203 1.049699238 0.995303888 0.300127932 0.036900329 5.878160188 1259.806627 0.009424638 0.012760992 2357.203738 -3.372397121 -0.05439535 HFVCEGCEQLLSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFVCEGCEQLLSGR 14 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 179.46 1.86E-06 174740000 78517 85866 78655 74810 89903 99048 79084 89689 85587 79004 FALSE TRUE 81616.91179 100612.8176 80704.81392 89607.19471 74621.32017 76045.60309 72885.18943 88486.86566 82506.74059 94483.32118 0.863823485 1.064873845 0.854169952 0.94839167 0.789782993 0.80485743 0.771407996 0.936534243 0.873241325 1 16.52777206 4.187074619 24.99997014 0.86588778 0.964350223 0.16160357 0.08284264 139.4533555 67713.77346 0.019900296 0.042989642 15384.18942 -4.187074619 0.098462443 HFVDEK ddPTM_MDA-MB-175_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 ;;; 149.06 0.010686 1828480000 4692460 3706470 4410500 3709240 6617570 6473420 5667850 4581920 4731120 3577910 FALSE TRUE 4877721.944 4343027.39 4525441.253 4442916.601 5492717.815 4970066.311 5223589.107 4520506.857 4560847.915 4278932.961 1.139938856 1.014979068 1.057609758 1.038323489 1.283665312 1.161520023 1.220769092 1.056456574 1.065884405 1 22.02881965 5.095929806 19.35553832 1.107387632 3.480816732 0.011820703 0.088597472 2503.301417 521793.6601 0.021175753 8639.367691 124718.1918 -5.095929806 2.3734291 HFVDSHHQKPVNAIIEHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFVDSHHQKPVNAIIEHVR 19 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 150.23 2.61E-08 859760000 161820 250890 323980 299070 347440 396510 320160 324680 325280 304380 FALSE TRUE 168208.7786 293978.4058 332423.185 358225.1534 288382.2729 304426.5617 295065.0226 320328.1957 313573.2363 364017.4333 0.462089898 0.807594304 0.913206771 0.984087905 0.792221049 0.836296655 0.810579372 0.87998037 0.861423678 1 18.47364802 4.727962595 3.245894448 0.87509053 0.408725341 0.791169252 0.064712376 0.136977559 2.339235333 0.015593883 0.158777001 53451.83205 -4.727962595 -0.466365189 HFVGMLPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HFVGMLPEK 9 0 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;; 79.059 0.02125 2341740000 3276260 2385140 2797930 2309270 5413800 4344210 4236150 2971320 3069380 3025840 FALSE TRUE 3405609.275 2794769.241 2870846.354 2766036.714 4493564.21 3335333.065 3904109.494 2931494.315 2958913.613 3618695.415 0.941115204 0.772314031 0.793337384 0.764374007 1.24176359 0.921694888 1.078872092 0.810097004 0.817674127 1 21.78703825 5.074653448 20.35390882 0.907736983 2.045261928 0.003211185 0.148051598 4672.418968 1508592.387 0.035036173 44541.67035 118755.4222 -5.074653448 1.137524946 HFVGMLPEKDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HFVGMLPEKDCR 12 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 135.6 7.50E-05 14534590000 11985330 12103130 12928660 10119490 19346000 17224600 13065240 13908850 14505120 15731410 FALSE TRUE 12458520.08 14181748.43 13265591.5 12121094.92 16057573.83 13224447.69 12041152.35 13722424.62 13983083.56 18813678.59 0.662205428 0.753799867 0.705103547 0.64427033 0.85350527 0.702916637 0.640021157 0.729385513 0.74324027 1 24.16527863 0.593403408 2.112977483 0.999965918 0.712160292 0.682953347 0.058646614 1.587669578 7.578459753 0.054470158 0.014878532 3.921059279 -0.593403408 -0.287805625 HFVLDECDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFVLDECDK 9 0 O00148;O00148-2;O00148-3;K7EQN7;K7EPJ3;A0A0D9SEM9 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 150.08 8.61E-05 422200000 458570 258340 324500 317570 437000 487770 480960 377920 368080 223320 FALSE TRUE 476674.6977 302707.8854 332956.7366 380384.3981 362718.8961 374492.8097 443261.0984 372854.6006 354832.8727 267075.2783 1.784795286 1.133417841 1.246677486 1.42425911 1.35811483 1.402199455 1.659685993 1.39606557 1.328587487 1 18.02688691 0.811735352 2.814881209 1.000246735 1.416741213 0.345841874 0.175428592 0.973709637 12.44097236 0.162954778 0.042979631 6.48239293 -0.811735352 0.416494478 HFWGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HFWGLR 6 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 120.78 0.046378 257410000 199470 167900 188810 169660 248620 261220 207890 203870 206900 167280 FALSE TRUE 207345.2296 196735.5189 193730.5437 203218.2416 206359.6612 200555.6138 191595.0386 201137.4561 199453.7094 200055.3132 1.036439504 0.983405618 0.968384896 1.015810269 1.031513024 1.002500811 0.957710323 1.005409218 0.996992813 1 17.61003942 4.749695537 24.27120132 0.995690543 1.03643954 0.262438455 0.020465015 1647.504838 3591023.776 0.005126526 0.076502496 56194.72331 -4.749695537 0.040748997 HFYWYLTNEGIQYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HFYWYLTNEGIQYLR 15 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 ;; 245.03 4.52E-18 1839119000 1953810 1914601 2333754 2356648 2079260 2814830 2295150 2138746 2558459 1799610 FALSE TRUE 2030947.927 2243418.828 2394573.546 2822785.941 1725828.128 2161128.392 2115250.146 2110079.608 2466380.56 2152209.124 0.943657336 1.042379573 1.11261193 1.31157605 0.801886819 1.004144238 0.982827422 0.98042499 1.145976259 1 21.03738684 3.229421273 24.99970629 0.985237647 1.098976175 0.197230428 0.115226147 336.3884843 920154.2977 0.033525515 0.040605246 1695.982134 -3.229421273 0.113738528 HGAEVIDTPVFELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGAEVIDTPVFELK 14 0 B3KWE1;P12081-4;P12081;B4DDD8;E7ETE2 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 192.86 3.25E-07 213183000 358758 274994 351482 258406 475392 457399 431373 367301 415830 237823 FALSE TRUE 372922.0429 322222.0803 360641.9097 309517.9355 394585.0376 351175.0142 397560.8571 362377.9309 400864.3595 284419.8635 1.311167365 1.132909905 1.26799129 1.088243035 1.387332913 1.23470636 1.397795682 1.274095017 1.409410562 1 18.1176627 3.229504466 24.99969442 1.301211757 1.200131132 0.086857717 0.125821632 365.8408577 1009910.066 0.032751675 0.03968031 1696.307046 -3.229504466 -0.101080625 HGAPAAPS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGAPAAPSPPPR 12 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 HGAPAAPS(1)PPPR;HGAPAAPS(1)PPPR 64.675 0.040456 566730000 653020 702450 683360 694770 892250 947330 760320 762400 710180 718850 TRUE FALSE 678801.7338 823090.3232 701168.923 832193.4323 740585.6637 727326.9644 700724.1317 752181.275 684620.7605 859694.8943 0.789584466 0.957421439 0.815602056 0.968010207 0.861451741 0.846029178 0.815084673 0.874939796 0.796353177 1 19.71346521 3.026103017 24.99773895 0.855733833 0.887146228 0.001090092 0.072504239 799.3073874 765456.8111 0.019098653 0.022826527 1061.947428 -3.026103017 0.031412395 HGAVCHTGAPDATLHTVHPDSVSSSYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGAVCHTGAPDATLHTVHPDSVSSSYSSR 29 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ;; 158.67 2.33E-12 1125770000 133155 206264 241773 222328 268550 311118 238913 265336 232169 213408 FALSE TRUE 138412.0622 241688.2375 248073.803 266303.8148 222901.9669 238865.5595 220186.3748 261779.6049 223813.283 255221.2117 0.542321938 0.946975512 0.97199524 1.043423519 0.873367717 0.935915781 0.862727566 1.025696897 0.876938408 1 17.96138871 4.73850522 8.266418698 0.94999572 0.539512751 0.80286367 0.06038798 0.035529241 34.09359851 0.013838531 0.081562992 54765.26828 -4.73850522 -0.410482969 HGAVSVS(ph)LFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGAVSVSLFIR 11 0 Q9BT04-2 Q9BT04-2 1 HGAVS(0.28)VS(0.72)LFIR;HGAVS(0.053)VS(0.947)LFIR 76.228 0.023141 203270000 12859 173519 98998 160383 71387 151830 56338 113411 63532 186442 TRUE FALSE 13366.68325 203319.5385 101577.9692 192106.2787 59252.66324 116569.7835 51922.08035 111890.911 61245.49573 222971.7403 0.059947881 0.911862365 0.45556432 0.861572316 0.265740686 0.522800707 0.232863951 0.501816557 0.274678287 1 17.76650135 -1.161875608 5.012036251 1.000033453 0.468942192 0.288511342 0.256229531 8.80E-05 1.47E-05 0.228015977 0.053740504 0.068884957 1.161875608 -0.53109126 HGAWGNSAVSRPLEFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGAWGNSAVSRPLEFWR 17 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 117.4 0.00013174 555200000 281430 393970 414110 359330 509810 478310 300930 385490 311880 459230 FALSE TRUE 292541.0737 461631.2828 424902.0468 430404.4015 423152.6783 367229.7514 277342.3203 380323.1371 300655.4997 549207.326 0.532660545 0.840541014 0.773664201 0.783682921 0.77047894 0.668654138 0.504986564 0.692494654 0.547435341 1 19.06699134 -1.038057253 4.618270017 1.000011361 0.685264796 0.426474831 0.111349081 0.212530709 69904704.83 1759.145606 0.026581599 0.091609971 1.038057253 -0.314746566 HGDGTTLDIMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGDGTTLDIMLK 12 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;; 158.41 7.35E-05 586690000 858610 673161 846280 743718 1147540 1126800 983320 858180 927800 634377 FALSE TRUE 892508.5858 788771.1653 868334.752 890823.2006 952481.5607 865117.7768 906244.809 846677.5008 894408.6592 758671.0273 1.176410531 1.039674822 1.144547137 1.174189034 1.25546057 1.14030686 1.194516169 1.116000836 1.178915007 1 19.53311492 -0.910240115 6.264504002 0.999999977 1.155444935 0.442396326 0.053082869 1.74E-08 2.96E-09 0.051883309 0.012229011 0.122958876 0.910240115 0.155444958 HGDLPDIQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGDLPDIQIK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 137.95 7.75E-05 651260000 1013670 706730 987720 779230 1241120 1185740 1053890 895500 1093630 657140 FALSE TRUE 1053690.474 828105.3799 1013460.795 933359.3682 1030154.866 910369.8551 971283.348 883497.2872 1054270.47 785894.0013 1.340753934 1.053711287 1.289564233 1.187640276 1.310806373 1.158387586 1.235896121 1.124193957 1.341491942 1 19.58397521 -1.46348983 3.391258774 0.996724649 1.216438221 0.348186577 0.092147956 6789310.228 2932358.233 162010.9327 0.01933067 0.034396177 1.46348983 0.219713572 HGEAQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HGEAQVK 7 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;; 111.04 0.0066693 6317910000 8277260 5600770 7353010 4987830 10045150 9040210 8746510 7549980 8396860 4916400 FALSE TRUE 8604052.616 6562658.68 7544635.481 5974407.887 8337678.991 6940758.233 8060935.691 7448784.867 8094658.649 5879674.45 1.463355274 1.116160212 1.283172316 1.016112021 1.418051129 1.180466417 1.370983336 1.266870289 1.37671885 1 22.48730485 HGEEGVEAEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HGEEGVEAEKK 11 1 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ;;;;; 201.46 2.82E-08 1331581000 3999600 1367832 2406190 1458031 3930300 3593560 3469650 2304661 2859150 1029873 FALSE TRUE 4157507.296 1602746.506 2468897.288 1746425.18 3262229.01 2759010.151 3197689.767 2273770.789 2756249.75 1231656.896 3.375540144 1.301293007 2.004533321 1.417947795 2.648650789 2.240080139 2.596250446 1.846107301 2.237838929 1 20.23216899 3.226434755 24.9995431 2.157113752 1.971697641 0 0.679074418 1297.216147 2674429.017 0.183908091 0.221360099 1684.359362 -3.226434755 -0.185416111 HGEIDYEAIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HGEIDYEAIVK 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;;; 143.96 3.69E-05 1186850000 3867980 2818250 3710320 2831790 4917220 4811370 4400740 3945030 4206250 2696180 FALSE TRUE 4020690.837 3302262.515 3807013.987 3391909.61 4081392.701 3694002.235 4055798.5 3892153.326 4054867.884 3224444.85 1.246940489 1.024133663 1.180672694 1.051935998 1.265766013 1.145624257 1.25782846 1.207077034 1.257539847 1 21.62061936 3.235415157 24.99788329 1.202343918 1.122561069 0.087491459 0.093730011 147.9945111 1176156.214 0.024220946 0.030131779 1719.551378 -3.235415157 -0.079782849 HGEKLYTGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGEKLYTGLR 10 1 Q13618;Q13618-2;A0A087X1R9;H7C1L6 Q13618 CUL3 Cullin-3 0 62.303 0.051653 533380000 88641 365500 359550 322560 875990 575480 448370 335750 395420 798190 FALSE TRUE 92140.61513 428271.7818 368920.1684 386361.4053 727089.5327 441833.4915 413225.5878 331249.8204 381188.9114 954580.0482 0.096524765 0.448649417 0.386473789 0.404744899 0.76168524 0.462856407 0.432887308 0.347011045 0.399326292 1 19.86450666 -1.813121176 2.374552176 1.207941551 0.422270705 0.570048295 0.152166828 10268401.88 6233877.295 12232867.86 0.039176034 0.015377255 1.813121176 -0.785670845 HGESAWNLENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;;;; 247.3 4.24E-16 16549010000 3992847 4324468 4830742 4518494 5615350 6242950 5660330 5066944 4910780 3693819 FALSE TRUE 4150487.683 5067161.739 4956635.105 5412238.627 4660854.813 4793119.475 5216658.544 4999029.904 4734041.987 4417552.111 0.939544702 1.147051945 1.122032062 1.2251669 1.055076363 1.085017076 1.180893493 1.131628961 1.071643722 1 22.07481572 4.74345251 24.68977348 1.121859902 0.939544613 0.409914892 0.06170603 390.2086445 1969335.125 0.013864758 0.114288624 55392.69693 -4.74345251 -0.182315288 HGEVCPAGWKPGSDTIKPDVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGEVCPAGWKPGSDTIKPDVQK 22 2 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 196.18 1.21E-22 11043950000 7108840 2798360 4442470 2874690 6593660 5422840 6317800 4252350 5277430 1778220 FALSE TRUE 7389502.492 3278956.562 4558244.418 3443295.102 5472872.028 4163467.594 5822594.328 4195354.204 5087496.325 2126628.163 3.474750603 1.54185702 2.143413925 1.619133595 2.573497391 1.957778829 2.73794659 1.972772804 2.392282964 1 21.02013637 -1.496036549 6.806863982 0.999545147 2.22541205 0.326665297 0.543097289 0.003370301 0.000249528 0.472753317 0.111393371 0.031912693 1.496036549 1.225866904 HGFCGIPITDTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HGFCGIPITDTGR 13 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 122.46 0.00023478 2866140000 2210630 2616280 2581760 2413050 3181980 3414850 2632950 2807590 2670620 2381350 FALSE TRUE 2297907.379 3065605.738 2649042.787 2890344.088 2641108.176 2621802.84 2426572.499 2769958.848 2574504.908 2847929.939 0.80686935 1.07643299 0.93016431 1.014892975 0.927378213 0.920599487 0.852047821 0.972621837 0.903991658 1 21.44148222 3.04985728 24.99957673 0.925269099 0.964621772 0.026798387 0.074003355 322.7867788 161850.5081 0.019840247 0.023713625 1121.649792 -3.04985728 0.039352673 HGFELVELSPEELPEEDDDFPESTGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGFELVELSPEELPEEDDDFPESTGVK 27 0 Q6PD74;Q6PD74-2;H0YL49 Q6PD74 AAGAB Alpha- and gamma-adaptin-binding protein p34 0 114.35 0.00090605 36912000 33450 21671 31853 27187 36369 36980 41225 30492 33796 22265 FALSE TRUE 34770.63183 25392.82567 32683.11535 32564.50745 30187.01037 28391.95544 37993.67678 30083.30461 32579.68856 26627.40046 1.305821493 0.953635174 1.227424186 1.222969832 1.133682216 1.066268391 1.426863912 1.129787516 1.223539963 1 14.70062397 HGFLEEFITPIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGFLEEFITPIVK 13 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 93.959 0.0019766 0 129890 109660 138080 117450 164090 163070 166470 134260 142400 98431 FALSE TRUE 135018.1575 128493.252 141678.4782 140681.2594 136198.0404 125199.4638 153421.6464 132460.4643 137275.0518 117716.6699 1.14697568 1.09154678 1.203554929 1.195083582 1.156998754 1.063566137 1.303312832 1.125248144 1.166147938 1 16.84495911 0.006639908 1.893120173 0.999974754 1.162304325 0.374793106 0.062509529 62.95638755 116.8216769 0.060833974 0.015803928 1.015406426 -0.006639908 0.162329571 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 HGGPGPGGPEPELS(1)PITEGSEAR;HGGPGPGGPEPELS(1)PITEGSEAR;HGGPGPGGPEPELS(0.996)PIT(0.004)EGSEAR;HGGPGPGGPEPELS(1)PITEGSEAR 268.82 9.73E-45 1562990000 644932 724145 731764 693310 885340 966790 790210 792270 777650 726476 TRUE FALSE 670394.4134 848511.2707 750834.371 830444.6487 734850.223 742267.6743 728271.2754 781650.9165 749662.5284 868815.063 0.771619234 0.976630479 0.864205057 0.955835924 0.845807416 0.85434485 0.838235093 0.899674683 0.862856274 1 19.72868959 -1.287270827 3.753068884 1.000256555 0.878083058 0.311163808 0.055834918 24.06659363 25550429.3 10806.2207 0.011955439 0.051609443 1.287270827 -0.122173496 HGGPKDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HGGPKDEER 9 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;; 175.93 3.22E-05 2467230000 3034550 1882810 2519320 1801520 3296200 3191250 2972830 2463830 2662250 1665830 FALSE TRUE 3154356.377 2206167.971 2584975.549 2157855.279 2735913.101 2450130.551 2739811.817 2430806.389 2566436.143 1992217.494 1.583339362 1.107393132 1.297536818 1.083142421 1.37330041 1.229850937 1.375257383 1.220151111 1.288230903 1 20.92594373 -0.848282475 0.992060929 0.980196419 1.275035776 0.279371114 0.136185472 110.9492652 50.95791868 7.6887389 0.037524018 0.141813483 0.848282475 0.294839357 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 HGGS(1)PQPLATTPLSQEPVNPPSEAS(0.993)PT(0.007)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.03)EAS(0.779)PT(0.191)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.031)EAS(0.831)PT(0.139)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.001)EAS(0.992)PT(0.007)R;HGGS(0.979)PQPLAT(0.017)T(0.004)PLSQEPVNPPS(0.317)EAS(0.593)PT(0.089)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.002)EAS(0.961)PT(0.037)R;HGGS(0.993)PQPLAT(0.003)T(0.003)PLSQEPVNPPS(0.356)EAS(0.532)PT(0.111)R 239.07 1.69E-45 7610923000 940201 891741 928122 965480 1032154 1274358 1231006 1018636 987146 731379.5 TRUE FALSE 977320.8615 1044890.58 952309.6218 1156449.062 856708.8318 978407.6676 1134516.533 1004982.851 951618.8083 874679.3099 1.117347639 1.194598487 1.088752885 1.32214064 0.979454781 1.118590158 1.297065702 1.148972931 1.087963094 1 19.73839464 0.999748708 2.992089387 1.001184562 1.161516627 0.220199813 0.093614343 0.344066185 7.346197711 0.085543821 0.022563513 9.994215463 -0.999748708 0.160332065 HGGS(ph)PQPLATTPLSQEPVNPPSEASPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGS(1)PQPLATTPLSQEPVNPPSEASPTR 124.55 2.60E-05 142910000 37807 38118 46585 48560 56316 64149 67574 61689 50030 42947 TRUE FALSE 39299.64955 44664.46998 47799.04337 58165.02306 46743.42644 49251.36694 62277.37331 60862.15986 48229.43007 51361.64238 0.765155625 0.869607511 0.930636973 1.132460341 0.910084341 0.958913396 1.212526906 1.184973008 0.939016508 1 15.64840372 5.092750731 0.560044528 1.087316181 0.396209632 0.449456786 0.101316286 4.89893471 0.878305971 0.054346062 2.396542421 123808.5766 -5.092750731 -0.69110655 HGGSDNASTDCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGGSDNASTDCER 13 0 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 95.428 0.0047007 29843000 17201 16474 15933 19259 21411 28635 17352 17410 22322 19393 FALSE TRUE 17880.10876 19303.28135 16348.22707 23068.37272 17771.56587 21984.95522 15991.9049 17176.64743 21518.63558 23192.68705 0.770937353 0.832300341 0.70488715 0.994639934 0.766257305 0.947926179 0.689523593 0.740606183 0.927819857 1 14.50138236 1.048993087 5.293927401 0.999137781 0.804714367 0.326573404 0.093513738 0.184428368 10.80595438 0.087020978 0.021974596 11.19420064 -1.048993087 -0.194423414 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HGGSPQPLATTPLSQEPVNPPS(0.007)EAS(0.942)PT(0.051)R;HGGSPQPLATTPLSQEPVNPPS(0.001)EAS(0.745)PT(0.254)R;HGGSPQPLATTPLSQEPVNPPS(0.015)EAS(0.976)PT(0.008)R;HGGSPQPLATTPLSQEPVNPPS(0.002)EAS(0.927)PT(0.071)R 248.8 4.60E-46 1544380000 337881 417679 395379 477622 450890 594339 523078 477741 414792 319679 TRUE FALSE 351220.8028 489412.1192 405682.9015 572094.206 374247.8789 456312.7745 482077.7796 471337.6633 399863.7169 382313.9794 0.918671097 1.280131372 1.061124948 1.496398868 0.978901895 1.193555034 1.260947299 1.232854901 1.045903991 1 18.54439843 -3.279755145 9.443282393 1.021358506 1.168134539 0 0.169248776 0 0 0 0.034060543 0.000525103 3.279755145 0.146776033 HGGTIPIVPTAEFQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGGTIPIVPTAEFQDR 16 0 P00367;P00367-2;P00367-3 P00367 GLUD1 "Glutamate dehydrogenase 1, mitochondrial" 0 ;; 144.33 1.33E-06 1285560000 1206760 1073590 1191550 1162160 1205960 1701330 1187960 1120820 1060100 1027350 FALSE TRUE 1254403.817 1257970.731 1222602.772 1392031.779 1000971.35 1306221.891 1094844.591 1105797.241 1021947.208 1228639.563 1.020969741 1.023872883 0.995086606 1.13298629 0.81469894 1.063144905 0.891103155 0.900017609 0.831771367 1 20.22863031 2.860409776 0.999068613 0.902386447 1.031923389 0.233558892 0.086022494 0.692084469 1.484405629 0.0421241 0.044523712 725.1198195 -2.860409776 0.129536942 HGIVEDWDLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 HGIVEDWDLMER 12 0 B4DXW1;P61158;F8WDR7 B4DXW1 ACTR3 Actin-related protein 3 0 ;;;;;;;;;;; 265.72 1.19E-21 4207579000 2281770 2563259 2816028 2626704 3103331 3498930 3020282 2828280 2906917 2484473 FALSE TRUE 2371856.042 3003478.794 2889416.003 3146258.211 2575827.905 2686356.534 2783544.405 2790371.533 2802297.625 2971257.916 0.798266629 1.010844187 0.972455467 1.058897713 0.866914949 0.90411422 0.936823555 0.939121278 0.943135098 1 21.50264241 0.682369248 4.09395571 0.999999939 0.940321478 0.06926173 0.068526778 29.640058 379.2872594 0.063491917 0.016196637 4.812483439 -0.682369248 -0.05967846 HGKNPVMELNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGKNPVMELNEK 12 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 169.23 2.67E-05 604430000 1167360 758620 1005530 670100 1464130 1263240 1132870 1004300 1100440 663160 FALSE TRUE 1213448.274 888907.0838 1031734.938 802643.78 1215257.706 969871.6546 1044072.689 990839.0012 1060835.379 793093.505 1.53001918 1.12080994 1.300899492 1.012041802 1.532300666 1.222896983 1.316455982 1.249334404 1.337591813 1 19.59713144 -1.26982522 5.076989852 0.999944638 1.282056101 0.245672579 0.152384129 8.60E-05 1.24E-05 0.132865485 0.031310562 0.053724797 1.26982522 0.282111463 HGLAHDEMKS(ph)PR ddPTM_MDA-MB-175_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 175.15 3.59E-05 4568290000 5973250 3777270 4662840 3896630 6463860 6638300 6440310 4990870 5182820 2890550 TRUE FALSE 6209078.522 4425986.739 4784357.441 4667371.784 5365135.386 5096655.429 5935501.674 4923975.551 4996291.321 3456897.93 1.7961417 1.280334806 1.384003097 1.350161873 1.55200862 1.474343626 1.717002294 1.424391362 1.445310629 1 21.72104658 0.554796968 1.957468328 1.000108464 1.489935711 0.490897385 0.150990104 2.596109321 10.42579869 0.139469257 0.038526859 3.587541784 -0.554796968 0.489827247 HGLAHDEMKS(ph)PREPGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGLAHDEMKSPREPGYK 17 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 HGLAHDEMKS(1)PREPGYK 77.847 0.011099 138110000 68567 40743 64039 29053 99020 79257 55435 52067 69431 46161 TRUE FALSE 71274.07811 47740.29331 65707.90895 34799.59669 82188.61577 60850.7629 51089.85985 51369.12703 66932.19187 55205.36414 1.291071605 0.86477635 1.190245005 0.630366219 1.488779524 1.102261779 0.925451007 0.930509704 1.212421889 1 15.75252084 0.946678689 0.008719972 1.72E-07 2.064546993 0.004409564 0.231923638 18072.61299 100.8210681 12074.85457 11782.9178 8.844610024 -0.946678689 2.064546821 HGLEAISIMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGLEAISIMDSR 12 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;; 149.41 6.32E-05 137750000 308999 377198 371550 354722 466250 509820 404247 377899 381470 423010 FALSE TRUE 321198.5191 441978.8223 381232.8982 424884.9529 386996.9915 391422.0314 372561.0638 372833.882 367740.9692 505890.7105 0.634916816 0.873664634 0.753587465 0.839874985 0.764981415 0.773728442 0.73644575 0.736985033 0.726917814 1 18.94846622 -0.998362634 5.19427632 1.000001484 0.763229867 0.579821211 0.061209117 9.75E-07 1.88E-07 0.054909457 0.012942202 0.100377729 0.998362634 -0.236771617 HGLEVIYMIEPIDEYCVQQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HGLEVIYMIEPIDEYCVQQLK 21 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 308.95 1.77E-66 5424741000 2582668 1981452 2371001 1959580 3010186 2843929 2716352 2576194 2701639 1845118 FALSE TRUE 2684633.727 2321750.967 2432791.234 2347179.075 2498515.659 2183469.59 2503437.232 2541664.333 2604407.54 2206633.545 1.216619648 1.052168799 1.102489917 1.063692284 1.132274847 0.989502582 1.1345052 1.15182892 1.180262824 1 21.07341563 HGLLLPAS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGLLLPASPVR 11 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 HGLLLPAS(1)PVR;HGLLLPAS(1)PVR 70.942 0.032456 351900000 285010 301490 258880 208422 443120 401410 280010 275890 251850 418330 TRUE FALSE 296262.4149 353268.5622 265626.6255 249647.2495 367798.6207 308188.6109 258062.0845 272192.1458 242785.9677 500293.7541 0.592176921 0.706122272 0.530941319 0.499001332 0.735165326 0.616015308 0.51582112 0.544064649 0.485286825 1 18.93241592 -1.348800339 3.348440633 1.002766351 0.580414557 0.709724504 0.080482685 17669732.93 24649592.36 479120.3155 0.019606249 0.044791918 1.348800339 -0.422351794 HGLQLGAQS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HGLQLGAQSPGR 12 0 Q8N1G0;A6PVV7 Q8N1G0 ZNF687 Zinc finger protein 687 1 HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR;HGLQLGAQS(1)PGR 195.6 1.39E-07 6510340000 2548180 3034050 2961910 2664642 3270400 3858370 3096930 3162770 2946080 2677690 TRUE FALSE 2648784.114 3555124.486 3039099.808 3191700.234 2714498.576 2962322.042 2854184.534 3120378.241 2840051.156 3202332.088 0.827142233 1.110167337 0.94902706 0.996679965 0.847663047 0.925051481 0.89128312 0.974408074 0.886869656 1 21.6106915 HGLTSGS(ph)ASPPPPALPLYPDPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLT(0.068)S(0.068)GS(0.506)AS(0.357)PPPPALPLYPDPVR 125.05 3.57E-05 97876000 54915 91970 97088 90448 104750 130780 98694 99892 92648 84426 TRUE FALSE 57083.0866 107765.1321 99618.19304 108338.3444 86944.63242 100408.327 90958.10639 98553.11113 89313.61658 100967.6583 0.565360112 1.067323279 0.986634678 1.073000467 0.861113686 0.994460293 0.900863781 0.976085935 0.884576488 1 16.62353372 4.74727149 24.85596806 0.968791043 0.565359889 0.763909664 0.067729874 482.637599 1377145.713 0.015497974 0.185334568 55881.94199 -4.74727149 -0.403431154 HGLTSGSAS(ph)PPPPALPLYPDPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGLTSGSASPPPPALPLYPDPVR 23 0 Q92610;H0YM74 Q92610 ZNF592 Zinc finger protein 592 1 HGLT(0.055)S(0.281)GS(0.082)AS(0.582)PPPPALPLYPDPVR;HGLT(0.009)S(0.009)GS(0.112)AS(0.871)PPPPALPLYPDPVR 170.16 4.93E-12 726240000 178617 218443 255593 249562 268118 308700 252170 275630 236488 250940 TRUE FALSE 185668.9371 255958.886 262253.9636 298924.6187 222543.3981 237009.1034 232404.2565 271935.6307 227976.8431 300106.8885 0.618676026 0.852892405 0.873868524 0.996060505 0.741547118 0.789748961 0.774404938 0.906129253 0.75965215 1 18.19511691 -2.483942155 2.128796931 2.900168306 0.822777434 0.241884566 0.098062785 3286550.706 232226.6236 30271556.77 0.02333004 0.00328139 2.483942155 -2.077390872 HGLYEK ddPTM_MDA-MB-175_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 ;; 106.76 0.031846 3318520000 8073100 6418200 7848100 6438100 9911700 10226000 9154700 8155000 8316100 5963400 FALSE TRUE 8391832.222 7520475.923 8052627.933 7711536.964 8226912.774 7851166.477 8437130.693 8045695.564 8016805.185 7131814.054 1.17667569 1.054496916 1.129113557 1.08128688 1.153551216 1.10086528 1.183027296 1.128141522 1.124090607 1 22.76583766 HGLYLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 96.367 0.0089915 7299650000 3426870 3854380 2567730 2571680 10935760 6436130 3751870 2631180 2753120 11232960 FALSE TRUE 3562165.474 4516339.782 2634647.153 3080350.628 9076903.421 4941436.348 3457788.626 2595913.336 2654035.749 13433843.44 0.265163539 0.336191188 0.196120132 0.229297791 0.675674349 0.367834892 0.257393846 0.193236831 0.197563397 1 23.67936879 -1.203460037 4.582049249 1.000156602 0.300825808 0.700177447 0.137014064 22715745676 3948900379 38666171.57 0.033945755 0.062595046 1.203460037 -0.699330794 HGNEVCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGNEVCK 7 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 77.282 0.038468 270300000 260690 217860 234130 218470 312180 317400 302300 258310 288350 237100 FALSE TRUE 270982.2425 255275.7603 240231.6201 261682.7139 259115.7551 243688.6602 278604.9361 254847.777 277972.3398 283555.2054 0.955659559 0.900268291 0.847212873 0.922863375 0.913810609 0.859404643 0.982542132 0.898758944 0.980311186 1 18.11327012 1.173499723 0.861064671 1.001662364 0.90178152 0.397439881 0.038584501 0.54893461 0.905436833 0.034751188 0.012697671 14.91075804 -1.173499723 -0.099880844 HGNQYIQVNEPWKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGNQYIQVNEPWKR 14 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 77.776 0.015403 238260000 233530 186180 218890 160840 311770 274550 224500 217650 218080 192220 FALSE TRUE 242749.9447 218154.9667 224594.4532 192653.6719 258775.4468 210789.9233 206903.1034 214732.7578 210231.3434 229881.8287 1.055977091 0.948987434 0.976999594 0.838055243 1.125689004 0.916949045 0.900041141 0.934100616 0.914519188 1 17.81053291 HGNRNS(ph)NSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGNRNSNSYGIPEPAHAYAQPQTTTPLPAVSGSPGAAITPLPSTQNGPVFAK 52 1 P46109 P46109 CRKL Crk-like protein 1 HGNRNS(0.327)NS(0.327)Y(0.281)GIPEPAHAY(0.058)AQPQT(0.003)T(0.003)T(0.001)PLPAVSGSPGAAITPLPSTQNGPVFAK 187.3 2.80E-32 2302300000 96348 93835 110410 102340 148440 154210 110070 102250 124130 87344 TRUE FALSE 100151.8934 109950.4313 113287.3753 122582.5465 123208.2218 118397.0646 101442.4258 100879.506 119662.5855 104457.3845 0.95878232 1.052586486 1.084531992 1.173517288 1.179507054 1.133448489 0.97113695 0.96574796 1.145563678 1 16.67255496 2.24147449 24.9999613 1.010520293 1.101693808 0.190697138 0.075666795 115.1262951 987749.7412 0.028807311 0.023114421 174.371093 -2.24147449 0.091173514 HGQQCLKMPGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGQQCLKMPGPR 12 1 F5GXT3;Q9NQ90;Q9NQ90-2 F5GXT3 ANO2 Anoctamin;Anoctamin-2 0 60.641 0.058388 170020000 229150 107350 122360 115180 184160 230690 145360 112550 127330 115260 FALSE TRUE 238197.0189 125786.5274 125548.8021 137962.2602 152856.549 177115.7436 133966.3034 111041.4513 122747.4182 137842.9902 1.728031426 0.912534814 0.910810205 1.00086526 1.108917826 1.284909326 0.971876068 0.805564731 0.890487198 1 17.07266638 4.741897497 24.84200995 0.983386017 1.72803173 0.757618778 0.125668746 159.7036552 1188884.09 0.03424229 0.247873082 55194.7152 -4.741897497 0.744645714 HGS(ph)DPAFAPGPR ddPTM_MDA-MB-175_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 176.32 2.65E-05 3616100000 1887560 1678658 1847660 1480517 2462950 3089580 2125340 1810849 1727602 1311656 TRUE FALSE 1962082.326 1966954.453 1895811.537 1773358.844 2044298.639 2372071.868 1958750.297 1786577.531 1665425.941 1568649.88 1.250809598 1.253915535 1.208562574 1.130500098 1.303221748 1.512174194 1.24868546 1.138926891 1.061693857 1 20.58109195 1.513068399 2.32304972 1.028943316 1.274142271 0.532736517 0.092357757 0.243730946 2.680986641 0.080927654 0.027652461 32.58880225 -1.513068399 0.245198955 HGS(ph)FVNKPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;HGS(1)FVNKPTR 97.631 0.0035896 1145990000 1167020 676060 1142890 790400 2108880 1570630 1408480 1250900 1413330 877750 TRUE FALSE 1213094.851 792168.046 1172674.652 946738.7609 1750413.331 1205874.986 1298079.657 1234133.732 1362464.529 1049728.307 1.155627454 0.754641025 1.117122063 0.901889331 1.667491787 1.148749612 1.236586313 1.175669669 1.29792111 1 20.00158454 HGS(ph)GADS(ph)DYENTQSGDPLLGLEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 HGS(1)GADS(0.946)DY(0.049)ENT(0.005)QSGDPLLGLEGKR 87.25 0.056187 127140000 173130 105050 119230 74076 211130 209120 117370 127380 138230 107740 TRUE FALSE 179965.3061 123091.5203 122337.2317 88728.01171 175242.198 160555.0492 108170.2327 125672.6795 133255.1293 128849.5902 1.396708409 0.955311694 0.94945767 0.688616949 1.360052428 1.246065657 0.839507775 0.975344037 1.034191332 1 16.97532842 4.74291141 24.05098233 1.002572262 1.396708681 0.30154834 0.178617346 341.4877946 1887605.545 0.043800213 0.342033133 55323.72451 -4.74291141 0.394136418 HGS(ph)GADSDYENTQSGDPLLGLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.999)GADS(0.001)DYENTQSGDPLLGLEGK;HGS(0.999)GADS(0.001)DYENTQSGDPLLGLEGK 309.5 1.30E-73 588970000 851060 555080 750790 621070 1025700 1136780 1061630 779810 833090 389110 TRUE FALSE 884660.506 650410.6721 770356.2042 743915.7923 851351.8804 872780.0731 978416.6665 769357.9225 803107.2536 465348.6545 1.901070299 1.397684652 1.65543877 1.598620271 1.829492515 1.875540124 2.102545386 1.653293536 1.725818364 1 18.82795251 3.25074064 24.58729227 1.760120994 1.622254639 0 0.292504838 632.1719447 1276129.169 0.075931273 0.102023355 1781.314652 -3.25074064 -0.137866355 HGS(ph)GADSDYENTQSGDPLLGLEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGSGADSDYENTQSGDPLLGLEGKR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.952)GADS(0.048)DYENTQSGDPLLGLEGKR;HGS(0.992)GADS(0.008)DYENTQSGDPLLGLEGKR 176.01 4.67E-13 320710000 355890 242050 297960 182518 459560 397770 258380 293070 315040 234590 TRUE FALSE 369940.812 283620.2046 305725.0824 218619.5156 381444.1554 305393.9458 238127.5004 289141.876 303701.7719 280553.419 1.318610956 1.0109312 1.089721464 0.779243812 1.359613284 1.088541166 0.848777753 1.030612555 1.082509609 1 18.09791597 4.740998024 24.21220333 1.030490298 1.318611106 0.255200716 0.146752399 198.2922371 1969561.517 0.03408125 0.227649074 55080.51902 -4.740998024 0.288120809 HGS(ph)GPPSSGGGLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGSGPPSSGGGLYR 14 0 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 HGS(1)GPPSSGGGLYR 114.54 0.0003038 327450000 58278 61638 87329 67512 96157 114290 79500 76585 60431 71251 TRUE FALSE 60578.86044 72223.84702 89604.86548 80865.6721 79812.26749 87747.87958 73268.58227 75558.50334 58256.10011 85211.26927 0.710925456 0.847585626 1.051561211 0.949002084 0.936639815 1.029768484 0.859846155 0.886719609 0.683666616 1 16.37875662 -0.331498044 6.565671105 0.99999756 0.894118629 0.079674428 0.11368982 14874882.52 2265554.09 0.110202476 0.026728027 0.466124527 0.331498044 -0.105878931 HGS(ph)PEFCGILGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGSPEFCGILGER 13 0 Q15464 Q15464 SHB SH2 domain-containing adapter protein B 1 HGS(1)PEFCGILGER 115.31 0.00043422 44584000 40714 39498 37302 42627 53812 78894 52516 44286 43259 36862 TRUE FALSE 42321.42016 46281.47425 38274.12076 51058.49337 44665.05546 60572.06415 48399.65869 43692.41861 41702.11704 44084.40313 0.960008918 1.049837833 0.868200952 1.158198586 1.013171378 1.374002138 1.097886219 0.991108317 0.945960795 1 15.42798071 3.729850204 24.64394908 1.086644456 0.968398091 0.178069081 0.120990785 963.0620201 2724744.271 0.033363023 0.052580796 5368.465968 -3.729850204 -0.118246365 HGS(ph)PTAPICLGSPEFTDQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HGSPTAPICLGSPEFTDQGR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HGS(0.909)PT(0.091)APICLGSPEFTDQGR;HGS(0.809)PT(0.191)APICLGSPEFTDQGR;HGS(0.995)PT(0.005)APICLGSPEFTDQGR;HGS(0.883)PT(0.117)APICLGSPEFTDQGR 245.63 3.64E-30 1112115000 808312 822720 825680 740570 1065970 1389680 1004470 906380 927320 721266 TRUE FALSE 840224.7819 964015.7601 847197.8991 887052.5356 884776.8002 1066947.881 925737.0167 894231.4586 893945.9343 862584.2632 0.974078496 1.117590247 0.98216248 1.02836624 1.025727964 1.236920178 1.073213431 1.036688816 1.036357806 1 19.71830587 4.768077221 22.5352358 1.061347069 0.974077975 0.12091074 0.069103282 6052.396917 4620569.643 0.016681372 1.44290983 58624.23938 -4.768077221 -0.087269095 HGS(ph)YDSLASDHSGQEDEEWLSQVEIVTHTGPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGSYDSLASDHSGQEDEEWLSQVEIVTHTGPHR 33 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-7;Q9H6U6-3;Q9H6U6-8 K7ESE9;Q9H6U6-7 BCAS3 Breast carcinoma-amplified sequence 3 1 HGS(0.483)Y(0.416)DS(0.101)LASDHSGQEDEEWLSQVEIVTHTGPHR;HGS(0.591)Y(0.401)DS(0.008)LASDHSGQEDEEWLSQVEIVTHTGPHR 201.49 2.41E-27 248740000 22988.8 45597 47635 52970 62995 78134 50123 63362 49529 39509 TRUE FALSE 23896.41558 53427.93005 48876.40723 63447.3079 52287.1324 59988.56263 46194.22829 62512.73603 47746.46096 47250.0321 0.505743901 1.130749074 1.034420614 1.342799255 1.106605225 1.269598347 0.977654961 1.323019969 1.010506424 1 15.52802769 4.743482208 4.815865897 1.152497642 0.46781172 0.674671495 0.130056459 0.095458559 6.373218056 0.028389608 0.219731659 55396.48492 -4.743482208 -0.684685922 HGSGADS(ph)DYENTQSGDPLLGLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HGS(0.387)GADS(0.471)DY(0.069)ENT(0.033)QS(0.039)GDPLLGLEGK 55.158 0.066328 164680000 55854 40035 45771 44010 67251 61746 60246 58356 65234 46486 TRUE FALSE 58059.15905 46910.69982 46963.82986 52715.04664 55819.69904 47406.42727 55523.7611 57573.83327 62886.24108 55594.04167 1.044341395 0.843808049 0.844763727 0.948213964 1.004059021 0.852724966 0.998735825 1.035611579 1.131168722 1 15.76264265 1.890302341 2.599162023 1.063849356 0.920805925 0.412269207 0.070483862 0.259935936 3.168186508 0.038639745 0.019703038 77.67877009 -1.890302341 -0.143043431 KSHHANS(ph)PTAGAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KSHHANSPTAGAAK 14 1 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 KS(0.134)HHANS(0.865)PTAGAAK;KSHHANS(1)PTAGAAK;KS(0.001)HHANS(0.999)PTAGAAK;KS(0.049)HHANS(0.95)PT(0.001)AGAAK;KS(0.028)HHANS(0.965)PT(0.007)AGAAK 176.69 1.03E-06 999840000 585256 1050579 1326828 961077 1659455 1661498 1363911 1420485 1395165 1063998 TRUE FALSE 608362.3588 1231007.771 1361406.228 1151175.162 1377381.432 1275640.27 1257004.092 1401445.722 1344953.284 1272468.037 0.478096377 0.96741744 1.069894244 0.90467904 1.082448747 1.002492977 0.987847282 1.101360256 1.056964297 1 20.27919799 4.73689865 3.733427943 1.027974278 0.420952213 0.900967517 0.054116503 0.070631169 1.874943526 0.012903265 0.118382586 54563.05135 -4.73689865 -0.607022065 down AILELHYSQELSLLYLLQDDVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 AILELHYSQELSLLYLLQDDVDR 23 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;;;;; 214.39 2.87E-32 82356000 23011.6 53154.1 66752.1 71900.7 68285.4 84614.9 60117.1 64245.5 66525.7 53708.6 FALSE TRUE 23920.11574 62282.90319 68491.71456 86122.44386 56678.2721 64964.37183 55404.96462 63384.39416 64131.45305 64231.77186 0.372403174 0.969658806 1.066321426 1.340807538 0.882402438 1.01140557 0.862578799 0.986807499 0.998438175 1 15.97099947 4.737167754 4.532476842 1.01502571 0.331151889 0.711076512 0.122859862 0.105850436 5.632555364 0.030558727 0.230975334 54596.87108 -4.737167754 -0.68387382 down HGSLGFLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HGSLGFLPR 9 0 P39023;H7C422;H7C3M2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ; 88.181 0.013202 0 355530 641960 604270 577130 581600 669130 551830 468380 560360 995500 FALSE TRUE 369566.5989 752211.6362 620017.7726 691284.5914 482739.8397 513734.6983 508576.1227 462102.1322 540192.7531 1190549.165 0.310416915 0.631819045 0.520783006 0.580643464 0.40547661 0.431510696 0.427177758 0.388141998 0.453734099 1 20.18319577 -1.454120523 3.557399454 1.006149835 0.461957367 0.765196417 0.089558568 60699481.3 85772567.67 3710392.911 0.021784678 0.035146289 1.454120523 -0.544192468 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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;HGTDLWIDNMS(0.001)S(0.001)AVPNHS(0.998)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSS(0.003)AVPNHS(0.997)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK;HGTDLWIDNMSSAVPNHS(1)PEKK 258.2 1.54E-37 17311483000 10860220 5530574 8224860 5416512 13046410 12565260 11797710 9189460 9873980 3943894 TRUE FALSE 11288989.87 6480407.063 8439206.608 6487881.907 10828785.89 9647168.793 10872974.66 9066290.32 9518617.389 4716624.519 2.393446802 1.373950171 1.789247072 1.375534957 2.295876181 2.045354417 2.30524491 1.92219887 2.018099459 1 22.16932332 3.233385465 24.99998855 2.003138153 1.711409603 0.031362178 0.434710465 299.0640542 1444710.799 0.114984444 0.14139327 1711.533739 -3.233385465 -0.29172855 HGVESTLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 148.69 8.94E-05 932880000 260290 343740 335030 375350 450060 474540 324060 322700 348400 407120 FALSE TRUE 270566.4502 402774.6711 343761.157 449593.1097 373558.962 364335.2767 298659.3304 318374.7343 335861.1521 486887.3692 0.555706447 0.827244033 0.706038355 0.923402697 0.767238966 0.74829478 0.613405377 0.653898118 0.689812826 1 18.89322855 4.75431459 23.36675353 0.749642162 0.555706084 0.221150183 0.115071073 1971.500931 2924065.092 0.027507792 0.629765592 56795.58667 -4.75431459 -0.193936078 HGVIVAADSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGVIVAADSR 10 0 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ;; 120.68 0.00053504 941110000 705460 701430 748070 770250 1005910 1014960 927090 812860 788040 689600 FALSE TRUE 733312.1055 821895.1461 767565.3187 922603.151 834925.7775 779250.9219 854422.2633 801964.9413 759678.5943 824713.9168 0.889171494 0.996582123 0.930704943 1.118694777 1.012382307 0.944874224 1.036022608 0.972415919 0.921141961 1 19.65353423 5.271006794 1.567560045 0.995812341 0.605299676 0.237820224 0.054858902 7.479143421 5.391935121 0.014312154 6.79266032 186640.8889 -5.271006794 -0.390512665 HGVVSCSGVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGVVSCSGVAR 11 0 P07199 P07199 CENPB Major centromere autoantigen B 0 71.555 0.04871 32568000 11286 35298 27845 30177 36927 40081 33518 31649 29767 38866 FALSE TRUE 11731.57999 41360.15692 28570.66357 36145.92053 30650.16173 30772.79518 30890.77158 31224.79692 28695.69148 46481.04857 0.252394908 0.889828397 0.614673387 0.777648561 0.659412011 0.662050365 0.664588527 0.671774796 0.617363256 1 15.50435499 -2.283905532 2.141985308 2.38506116 0.658587079 0.320511 0.153782542 11453788.97 1491552.307 76895242.94 0.033218651 0.005201091 2.283905532 -1.726474081 HGYIGEFEIIDDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 HGYIGEFEIIDDHR 14 0 P62244;I3L3P7;I3L246;H3BN98 P62244 RPS15A 40S ribosomal protein S15a 0 ;;;;;;; 226.59 1.36E-12 17485830000 5492900 5582790 6309100 6244150 7363260 7865420 7069360 6552490 6255030 4882750 FALSE TRUE 5709763.933 6541590.754 6473520.329 7479224.233 6111655.695 6038795.407 6515245.091 6464664.589 6029912.692 5839431.377 0.977794509 1.120244478 1.108587448 1.28081379 1.046618292 1.034141001 1.115732795 1.107070907 1.03261984 1 22.47739646 HGYIPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGYIPGK 7 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 61.837 0.089078 339130000 535560 524830 581900 513020 710440 731770 626100 571250 583420 459410 FALSE TRUE 556704.3223 614965.4699 597064.792 614493.8248 589679.6626 561827.5076 577024.646 563593.3281 562422.8282 549422.5936 1.013253421 1.119294105 1.086713213 1.118435667 1.073271594 1.022578092 1.050238292 1.025792049 1.023661631 1 19.06755671 2.834600344 4.228681653 1.028122739 1.087898491 0.48218043 0.02979698 0.194582304 6.121598656 0.008900931 0.009447153 683.2825723 -2.834600344 0.059775753 HHAS(ph)SSSHDLSSSWEQTNLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHASSSSHDLSSSWEQTNLQR 21 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 HHAS(0.242)S(0.242)S(0.242)S(0.242)HDLS(0.026)S(0.003)S(0.003)WEQTNLQR;HHAS(0.143)S(0.143)S(0.143)S(0.143)HDLS(0.143)S(0.143)S(0.143)WEQTNLQR 195.27 1.16E-18 232244000 24216.1 103832 97133 86612 95243 141535 68138 81818 82240 104321 TRUE FALSE 25172.17033 121664.3383 99664.36578 103743.5951 79053.62888 108665.6412 62797.16551 80721.36354 79280.19846 124760.7026 0.201763615 0.975181574 0.798844217 0.831540645 0.633642062 0.87099254 0.503340909 0.64700953 0.635458095 1 16.92880406 -2.355011542 2.117551448 2.760708569 0.688223769 0.178213058 0.206594526 11680718.97 1256614.875 98482041.69 0.048103129 0.004415587 2.355011542 -2.0724848 HHCAAITPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHCAAITPGR 10 0 Q92896;Q92896-3;Q92896-2 Q92896 GLG1 Golgi apparatus protein 1 0 ; 95.573 0.0073299 15176900 7141 7481.3 6090.1 6034.8 12011.1 13875.2 8515.4 6615.6 7518.7 11909.9 FALSE TRUE 7422.932194 8766.155079 6248.813009 7228.465428 9969.457512 10652.89508 7847.940697 6526.928703 7248.103456 14243.41688 0.521148279 0.615453101 0.438715869 0.507495181 0.699934405 0.747917103 0.550987222 0.45824178 0.508873925 1 13.79800766 -1.373640807 3.201050582 1.004351185 0.559108375 0.658318197 0.094877924 23559909.59 31376322.58 953827.038 0.025806056 0.042301834 1.373640807 -0.44524281 HHDAEHHRGERPGKPD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HHDAEHHRGERPGKPD 16 3 Q5T3G2 Q5T3G2 TLE1 0 ;; 88.974 0.0035658 46023100 22775.8 13129.5 22476.5 5931.18 32105.6 28021.5 13107.5 7907.4 16614.6 21957.9 FALSE TRUE 23675.00617 15384.38949 23062.25605 7104.349701 26648.30158 21513.93129 12080.0999 7801.414237 16016.64379 26260.1301 0.901557079 0.585845898 0.878223222 0.270537491 1.014781781 0.819262175 0.460016758 0.297082086 0.609922485 1 14.68058644 2.232515297 24.97807911 0.505269799 0.734545973 0.036943796 0.259376284 271.5811138 1122108.808 0.092110362 0.069780077 170.8107881 -2.232515297 0.229276175 HHEDNLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHEDNLLR 8 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 105.78 0.0043212 210973000 58815 127717 95675 103487 99946 147089 95755 82131 80621 167431 FALSE TRUE 61137.06162 149651.4012 98168.3691 123956.4197 82957.21462 112929.8089 88249.47289 81030.16828 77719.46596 200235.8988 0.305325179 0.747375481 0.490263583 0.619051931 0.414297412 0.563983829 0.440727529 0.404673531 0.388139522 1 17.61134112 -1.480293601 3.21137383 1.010904178 0.489701704 0.615821152 0.121765782 78869916.77 98915948.25 7671060.735 0.028983082 0.033090734 1.480293601 -0.521202474 HHFETLTES(ph)PCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHFETLTESPCR 12 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 HHFETLTES(1)PCR 164.53 0.00010363 0 147710 144580 149980 139120 175460 187080 160080 126290 153590 135300 TRUE FALSE 153541.7049 169410.4903 153888.602 166637.5208 145635.3719 143633.5052 147532.5113 124597.2891 148062.3259 161809.4445 0.948904468 1.046975291 0.95104833 1.029838037 0.900042468 0.887670714 0.911766997 0.770024824 0.915041309 1 17.30393629 3.123143216 5.124764784 0.876581946 0.99449611 0.350928024 0.061257396 0.189733403 7.755548678 0.017709389 0.021398095 1327.832261 -3.123143216 0.117914165 HHGDVMDLQFFDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HHGDVMDLQFFDQER 15 0 Q8NFH3;B4E301;F5H0E3;B4DVD1;Q8NFH3-2 Q8NFH3 NUP43 Nucleoporin Nup43 0 ;; 133.47 2.38E-05 131032000 105209 129136 123577 113708 137157 173347 121543 134617 127969 143398 FALSE TRUE 109362.7326 151314.1035 126797.5181 136199.103 113843.1021 133089.7863 112016.1421 132812.6793 123363.4207 171494.0926 0.637705538 0.882328372 0.739369597 0.794191222 0.663831042 0.776060472 0.653177846 0.774444631 0.719345016 1 17.38779936 -1.902308808 3.544392047 1.116479738 0.741472785 0.552591875 0.070702843 0.045117853 0.001243547 0.047461403 0.014647433 0.012522504 1.902308808 -0.375006953 HHGKDS(ph)DKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHGKDSDKEER 11 2 Q92766;Q92766-2;Q92766-5;Q92766-3;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 HHGKDS(1)DKEER 105.46 0.0011695 31804000 21767 6148.3 9157.5 7995.4 17659 15282 17429 10462 11498 4381 TRUE FALSE 22626.37797 7204.222698 9396.151973 9576.866256 14657.32949 11732.9871 16062.86944 10321.774 11084.18923 5239.373071 4.318527744 1.375016171 1.793373338 1.827864923 2.797534989 2.239387603 3.0657999 1.9700399 2.115556399 1 12.35517848 0.713841646 1.430814129 1.004697405 2.381956664 0.228532803 0.788324333 1.481583654 4.888268278 0.709876683 0.208632943 5.174181348 -0.713841646 1.37725926 HHGPQTLYLPVTLSSIPVFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHGPQTLYLPVTLSSIPVFQR 21 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 118.52 4.66E-05 684540000 205685 285300 258240 282530 352010 409780 244520 253420 225809 270160 FALSE TRUE 213805.6026 334298.0557 264969.9465 338413.5907 292175.4659 314614.8053 225353.8835 250023.3194 217682.1782 323092.6795 0.661746973 1.034681616 0.820105076 1.047419556 0.90430853 0.973760241 0.697489909 0.773843963 0.673745312 1 18.30158854 2.240766888 24.99972805 0.765613741 0.91511731 0.156920928 0.132915215 81.82539499 927193.6378 0.043646934 0.034877411 174.087219 -2.240766888 0.149503568 HHGT(ph)PTSTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HHGTPTSTKK 10 1 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 HHGT(1)PTSTKK;HHGT(0.999)PT(0.001)STKK;HHGT(0.969)PT(0.025)S(0.005)T(0.001)KK 160.15 5.69E-06 299267000 779115 392727 544764 351835 854847 783694 608330 447572 545620 316906 TRUE FALSE 809875.0618 460174.8073 558960.9974 421426.9129 709540.4123 601692.9455 560647.505 441573.0294 525983.2428 378997.6632 2.13688669 1.214189036 1.474840221 1.111951217 1.872149834 1.58759012 1.479290137 1.165107525 1.38782714 1 18.53182943 -1.405356533 0.075930655 4.76E-11 2.155301255 0.291238942 0.282669785 148.3703899 1.91770314 43.14521283 15.66618901 0.039322712 1.405356533 2.155301255 HHHHDS(ph)DSNS(ph)PCCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 HHHHDS(0.973)DS(0.116)NS(0.912)PCCK 94.882 0.0018867 54883000 25432 17107 16377 14905 24009 32854 24286 21136 19921 18377 TRUE FALSE 26436.075 20044.99418 16803.79807 17853.16451 19927.95876 25224.15641 22382.39986 20852.70649 19204.0471 21977.6213 1.202863342 0.912063863 0.764586751 0.812333795 0.906738654 1.14772004 1.01841776 0.948815443 0.873800073 1 14.42374763 2.936445873 24.99998067 0.996019227 0.904452439 0.08172307 0.125639027 518.7926569 204074.1302 0.040173538 0.042610509 863.8649895 -2.936445873 -0.091566787 HHHHDS(ph)DSNSPCCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDS(0.497)DS(0.497)NS(0.006)PCCK 98.531 0.0042469 113440000 37945 38828 39964 29968 46861 61195 47557 37596 37942 37633 TRUE FALSE 39443.0979 45496.40696 41005.49467 35895.58095 38895.58396 46983.38867 43829.35807 37092.08711 36576.47483 45006.46582 0.876387363 1.010886017 0.911102303 0.797564979 0.864222134 1.043925307 0.973845808 0.824150185 0.81269378 1 15.45784466 1.733383649 24.99999684 0.863359721 0.925442541 0.052155961 0.083168074 1.366887998 6544.703232 0.039710684 0.022021606 54.12322278 -1.733383649 0.06208282 HHHHDSDSNS(ph)PCCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHHHDSDSNSPCCK 14 0 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 HHHHDSDSNS(1)PCCK 153.95 1.04E-05 35081000 4024.3 21297 21306 20172 25383 34900 18269 24174 18202 22822 TRUE FALSE 4183.182471 24954.59408 21861.25186 24161.96139 21068.40673 26795.00391 16837.02804 23849.98707 17546.91358 27293.53395 0.153266429 0.91430425 0.800968167 0.885263207 0.771919341 0.9817345 0.616887065 0.873832869 0.642896358 1 14.73627159 4.743290255 24.90253191 0.823918101 0.15326614 0.735089855 0.122146033 216.195285 1138272.498 0.02620452 0.213493437 55372.00577 -4.743290255 -0.670651961 HHIEVLHYLLQS(ph)WPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HHIEVLHYLLQSWPDPR 17 0 M0QXZ8;Q6ZW31-2;Q6ZW31 M0QXZ8 SYDE1 Rho GTPase-activating protein SYDE1 1 HHIEVLHY(0.46)LLQS(0.54)WPDPR 55.885 0.074223 34732000 3404.3 43602 26415 41714 23217 41866 18652 32413 22594 56558 TRUE FALSE 3538.704393 51090.30432 27103.3966 49964.9047 19270.58263 32143.25599 17190.0075 31978.55675 21780.84635 67639.45723 0.052317161 0.755332855 0.400703934 0.738694643 0.284901497 0.475214576 0.254141713 0.472779618 0.322013914 1 16.04557746 -1.487983785 4.202632569 1.004017217 0.430175246 0.424513178 0.203025071 0.006943715 0.000845968 0.178619714 0.041870398 0.032509944 1.487983785 -0.573841971 HHISIAEIYETELVDIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHISIAEIYETELVDIEK 18 0 P54920;M0R0Y2;M0R2M1;M0R058;M0R0I4;M0R027 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 107.34 0.00024462 198457000 33661 78710 107035 94801 129268 149662 121398 111912 102532 62154 FALSE TRUE 34989.96227 92227.83022 109824.42 113552.3548 107295.0715 114905.2686 111882.5075 110412.0027 98841.89335 74331.88629 0.470726145 1.240757296 1.477487328 1.527639893 1.443459555 1.545840882 1.505175143 1.485392181 1.329737456 1 16.1816936 4.735817583 2.586991895 1.447159381 0.269321647 0.768371765 0.153920676 0.192070644 1.664709534 0.034412227 0.491627498 54427.39935 -4.735817583 -1.177837734 HHLGDDVVLFTTDGAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHLGDDVVLFTTDGAHK 17 0 P16278-3;P16278;C9J4G9;C9J539 P16278-3 GLB1 Beta-galactosidase 0 ; 122.93 1.92E-05 110099000 190474 142663 163597 133336 238080 249670 189352 144192 170087 129471 FALSE TRUE 197994.0606 167164.2605 167860.4722 159709.4628 197611.2466 191687.9263 174510.0955 142259.3421 163965.6021 154838.3636 1.2787145 1.079604929 1.084101306 1.031459253 1.276242154 1.237987291 1.127046886 0.918760305 1.058946881 1 17.24040344 1.873983692 6.14692552 0.988747809 1.158032887 0.448779972 0.085238536 0.223586945 10.10391374 0.039190777 0.023734683 74.8141406 -1.873983692 0.169285078 HHNHGS(ph)PHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HHNHGSPHLK 10 0 Q9UK58 Q9UK58 CCNL1 Cyclin-L1 1 HHNHGS(1)PHLK;HHNHGS(1)PHLK;HHNHGS(1)PHLK;HHNHGS(1)PHLK 130.2 0.00047293 232397000 428000 261245 329112 231130 509770 546010 388422 242066 313237 262692 TRUE FALSE 444897.7705 306111.7965 337688.9291 276846.8241 423119.4775 419207.4524 357976.4687 238821.5012 301963.6616 314161.4679 1.416143659 0.97437728 1.07488971 0.881224633 1.346821685 1.33436941 1.139466502 0.760187119 0.961173449 1 18.26114672 1.759513162 25 0.887406432 1.158214042 0.329039581 0.168892978 11.32455311 13523.70922 0.079612889 0.044150301 57.47952385 -1.759513162 0.270807611 HHPDLIFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HHPDLIFCR 9 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;;; 113.62 0.0022233 668720000 552286 747352 690453 665630 949310 1012840 725659 685850 635479 1025710 FALSE TRUE 574090.6777 875703.8924 708446.7724 797289.6273 787946.6253 777623.2597 668779.9514 676657.3026 612608.2349 1226678.236 0.468004291 0.71388231 0.577532683 0.64995824 0.642341734 0.633926026 0.545195905 0.551617598 0.499404177 1 20.22632544 -1.246100973 4.168556104 1.000292112 0.590557437 0.752904844 0.070973053 0.000189184 3.42E-05 0.066859627 0.015747757 0.056741267 1.246100973 -0.409734675 HHVLHDQNVDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHVLHDQNVDKR 12 1 Q02218;A0A0D9SFS3;E9PDF2;E9PCR7;Q02218-2;E9PFG7 Q02218 OGDH "2-oxoglutarate dehydrogenase, mitochondrial" 0 ; 138.45 3.02E-05 42918000 28940 27264 33190 29448 35417 44135 32813 29198 31009 29816 FALSE TRUE 30082.57355 31946.37992 34054.95867 35272.72651 29396.83099 33885.31512 30241.03132 28806.64857 29892.99215 35657.87434 0.843644612 0.89591375 0.955047358 0.9891988 0.824413444 0.950289824 0.848088448 0.807862193 0.838327935 1 15.12193308 2.213850999 24.51192483 0.851895347 0.910913489 0.026589458 0.06777294 353.1807367 350352.2853 0.02464831 0.01821307 163.6255048 -2.213850999 0.059018142 HHYDS(ph)DEKSETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HHYDSDEKSETR 12 1 Q9BQ39 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 1 HHYDS(0.997)DEKS(0.003)ETR;HHYDS(1)DEKSETR 229.68 4.60E-12 1911960000 1114400 856940 892880 797540 1189230 1533390 1141660 860990 892520 787910 TRUE FALSE 1158397.373 1004112.779 916149.1863 955291.0316 987085.1094 1177283.411 1052173.706 849449.8373 860398.3795 942285.8791 1.229348119 1.065613739 0.972262459 1.013801706 1.047543141 1.249390909 1.116618353 0.901477838 0.913096968 1 19.8458053 1.740050551 8.375646947 0.932514191 1.093560632 0.424512889 0.085577194 0.114292476 28.80173387 0.044049759 0.023585918 54.96048434 -1.740050551 0.161046441 HIADLAGNSEVILPVPAFNVINGGSHAGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIADLAGNSEVILPVPAFNVINGGSHAGNK 30 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 ; 176.28 7.37E-14 10416800000 9661300 8418400 10565500 9770400 13893700 13570100 12092400 10442000 11475800 9918400 FALSE TRUE 10042735.58 9864194.714 10840845.61 11702955.96 11532053.84 10418649.93 11144566.09 10302042.07 11062788.2 11861720.58 0.846650831 0.831598978 0.913935338 0.98661538 0.972207511 0.878342215 0.939540433 0.868511613 0.932646164 1 23.49980996 7.999999781 0.014635373 1.674596084 4.87E-06 0.307443487 0.046805838 9283.465038 10.48905708 482.2173348 744.2188778 99999949.49 -7.999999781 -1.674591214 HIAEDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 164.57 0.00032934 8751240000 2188880 2482260 2402390 2489860 2943930 3124160 2583900 2695110 2493830 2734820 FALSE TRUE 2275298.673 2908568.846 2464998.257 2982346.877 2443521.83 2398621.187 2381367.166 2658986.459 2404077.545 3270655.618 0.695670513 0.889292297 0.75367099 0.911849863 0.747104592 0.733376261 0.728100859 0.812982707 0.735044537 1 21.64114843 -1.93459182 7.833379164 1.066753131 0.782810553 0.486887787 0.068070385 0.039818717 0.000332484 0.033071258 0.014584272 0.011625407 1.93459182 -0.283942578 HIAEEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 182.53 0.00022805 37371657000 8982306 9747737 9651923 9398782 10569129 11871420 10411174 9650476 9790134 9892112 FALSE TRUE 9336934.377 11421835 9903460.043 11257833.03 8772592.228 9114462.618 9595118.977 9521127.154 9437788.99 11830281.95 0.789240224 0.965474454 0.837127981 0.951611557 0.741537037 0.770434945 0.811064269 0.804809826 0.797765347 1 23.49598112 3.239826111 24.99999844 0.807995012 0.888068926 0.122384622 0.080752056 53.62962055 1059439.753 0.020833393 0.026721791 1737.105162 -3.239826111 0.080073913 HIAEEADRK ddPTM_MDA-MB-175_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 ;;; 166.19 3.96E-05 1474400000 1637180 1270220 1628440 1286170 2132020 2377970 1958980 1623410 1806070 1274540 FALSE TRUE 1701817.131 1488370.404 1670878.484 1540570.587 1769620.002 1825722.506 1805430.029 1601650.844 1741069.893 1524261.71 1.116486177 0.976453318 1.096188714 1.010699525 1.160968612 1.197774958 1.18446197 1.050771553 1.142238161 1 20.5396792 5.093210929 20.92471712 1.095023996 3.033939435 0.007629271 0.075692536 7950.603989 1698278.16 0.017920205 35610.9884 123939.8394 -5.093210929 1.938915439 HIAEEADRKYEEVAR ddPTM_MDA-MB-175_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 ;; 130.98 3.39E-05 1217770000 328802 506970 483900 172730 883780 654650 191874 403240 554640 979780 FALSE TRUE 341783.3569 594038.1538 496510.8315 206895.4785 733555.3913 502617.4588 176834.4145 397835.2274 534678.6147 1171749.132 0.29168646 0.50696701 0.423734755 0.176569773 0.626034508 0.428946304 0.15091491 0.339522528 0.456308095 1 20.1602323 0.804095525 3.970601228 0.999972792 0.367544177 0.659721913 0.135354058 1.069275553 21.03729957 0.129647377 0.033142876 6.369356016 -0.804095525 -0.632428614 HIAELIFYMEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIAELIFYMEELR 13 0 Q9Y2A7;Q9Y2A7-2 Q9Y2A7 NCKAP1 Nck-associated protein 1 0 ; 134.77 9.17E-05 127712000 90620 94585 101416 106499 112650 118433 117226 104113 95159 86348 FALSE TRUE 94197.74757 110829.238 104058.9843 127564.1843 93501.79324 90928.73062 108037.5198 102717.5355 91734.24618 103266.2374 0.912183401 1.073237883 1.007676729 1.235294202 0.905443983 0.880527198 1.046203702 0.994686532 0.888327575 1 16.65600912 HIAFTPESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 188.99 1.06E-06 1794910000 882030 1104550 888630 884160 1426940 1500170 1004490 917630 913850 1367130 FALSE TRUE 916853.2255 1294247.87 911788.4278 1059044.209 1184389.248 1151778.253 925755.4491 905330.6708 880960.717 1634992.948 0.560768917 0.791592326 0.557671168 0.647736255 0.724400218 0.704454569 0.566213726 0.553721453 0.538816218 1 20.64085298 -2.010014187 3.76420704 1.406106783 0.627655647 0.644260949 0.083091235 0.045537974 0.000121148 0.012937319 0.019383611 0.009772053 2.010014187 -0.778451136 HIANYISGIQTIGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIANYISGIQTIGHR 15 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 191.52 9.96E-08 750830000 118560 188460 169390 176740 199330 242310 172210 211420 180620 219180 FALSE TRUE 123240.8403 220826.539 173804.4426 211698.6445 165447.9578 186037.1747 158711.7302 208586.2607 174119.5215 262124.1245 0.470162144 0.842450268 0.663061604 0.807627474 0.631181728 0.709729313 0.60548311 0.795753772 0.664263626 1 17.99989061 -4.999999995 0.343417521 4.347884314 0.68718926 0.444954584 0.104481754 355.0447127 2.963178622 872.6332998 0.074311325 1.00E-05 4.999999995 -3.660695053 HIDALEDKIDEEVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIDALEDKIDEEVRR 15 2 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 144.68 2.52E-06 97430000 40720 28152 33430 29457 50926 64799 38247 37071 41438 25904 FALSE TRUE 42327.65704 32986.88701 34301.21326 35283.50668 42269.61671 49750.41429 35249.1002 36574.12388 39946.65447 30979.39284 1.366316547 1.064800953 1.107226776 1.138934738 1.364443033 1.605919604 1.137824114 1.180595245 1.289458921 1 14.91902125 -1.44504323 2.825624853 0.993484766 1.241836368 0.188749855 0.154910062 19882285.62 21554582.38 1025547.025 0.038789014 0.035888621 1.44504323 0.248351602 HIDCAAIYGNEPEIGEALKEDVGPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HIDCAAIYGNEPEIGEALKEDVGPGK 26 1 P14550;Q5T621;V9GYP9;V9GYG2 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;; 245.09 1.57E-45 322013000 728815 380706 546985 393464 765010 689753 679063 545721 687363 341123 FALSE TRUE 757589.179 446089.294 561239.8785 471290.0048 634973.8735 529568.3191 625836.2677 538406.5026 662624.9399 407959.5207 1.857020466 1.0934646 1.375724429 1.155237177 1.556462936 1.298090355 1.534064622 1.319754719 1.624241883 1 18.63806648 -1.368581717 3.394647468 0.997104002 1.403379077 0.250838261 0.217151832 30394940.75 44280181.49 872523.2533 0.047142253 0.042797488 1.368581717 0.406275076 HIDFSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 168.45 0.0010486 7554950000 1173722 1094059 1193082 1084511 1968878 1580489 1386082 1139092 1257830 1983020 FALSE TRUE 1220061.451 1281955.123 1224174.697 1299024.039 1634208.821 1213444.382 1277437.271 1123824.335 1212560.944 2371554.802 0.51445636 0.540554712 0.516190769 0.547752065 0.689087522 0.511666178 0.538649695 0.473876604 0.511293664 1 21.17740178 -1.272506445 3.42221868 1.001498756 0.536902777 0.866814291 0.054306659 14404016.47 21286139.32 223614.3366 0.013781873 0.053394135 1.272506445 -0.464595978 HIDLVEGDEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;; 149.38 3.44E-05 3958230000 1991640 2156860 2139620 2169300 2058810 2455160 2002900 1940490 1659770 1758180 FALSE TRUE 2070271.485 2527283.927 2195380.255 2598381.065 1708854.212 1884986.298 1845907.464 1914480.906 1600035.202 2102661.709 0.984595609 1.201945095 1.044095798 1.235758018 0.812710007 0.896476257 0.877890845 0.910503529 0.760957027 1 21.00378533 3.230478378 24.99993822 0.875690181 1.117516039 0.638436361 0.088543717 102.3545556 316602.1624 0.023350631 0.028369532 1700.11531 -3.230478378 0.241825859 HIDMVEGDEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIDMVEGDEGR 11 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 122.55 0.0003885 224200000 279380 304830 314280 299360 428760 414970 366890 377950 332030 455840 FALSE TRUE 290410.1381 357182.1813 322470.395 358572.5145 355879.5283 318599.5064 338132.2031 372884.1985 320080.3052 545153.1204 0.53271297 0.655196069 0.591522607 0.657746422 0.652806551 0.584422054 0.620251798 0.683999017 0.587138353 1 19.05630198 -5 0.365590021 5.813968771 0.613848875 0.872502395 0.043677871 156.9890858 1.228392243 595.9976477 0.029306629 1.00E-05 5 -5.200119896 HIDSSPYSPAYLS(ph)PPPESSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HIDSSPYSPAYLSPPPESSWR 21 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR;HIDSSPYSPAYLS(1)PPPESSWR 246 1.88E-30 971380000 376989 555750 529850 556270 581450 681950 546160 583760 524710 584040 TRUE FALSE 391872.8168 651195.7394 543658.3263 666298.5457 482615.3367 523577.4476 503350.5521 575935.652 505825.7896 698471.4559 0.561043423 0.932315464 0.778354393 0.953938117 0.690959283 0.749604645 0.720645844 0.824565767 0.724189636 1 19.41384163 -2.049661687 2.702249773 1.300624273 0.779289022 0.282140988 0.108976909 32245167.44 12506847.39 59914469.77 0.025004834 0.008919455 2.049661687 -0.521335251 HIEIFTDLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;; 197.3 5.75E-08 2788880000 1502019 1602310 1787790 1830190 1916860 2049230 1848120 1743640 1688400 1562120 FALSE TRUE 1561319.87 1877494.278 1834381.276 2192196.119 1591032.822 1573327.389 1703259.525 1720269.358 1627634.814 1868187.505 0.835740452 1.004981712 0.981904263 1.17343474 0.851645147 0.842167815 0.911717652 0.920822644 0.871237394 1 20.83320783 HIEPELAGRDS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIEPELAGRDSPIR 14 1 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 1 HIEPELAGRDS(1)PIR;HIEPELAGRDS(1)PIR 131.25 3.47E-05 260970000 137851 140813 145091 141406 141658 180403 174570 169861 136535 137982 TRUE FALSE 143293.4639 164996.5374 148872.1907 169375.6847 117579.0238 138507.1373 160886.7472 167584.2911 131621.132 165016.9311 0.868356132 0.999876415 0.902163128 1.026413979 0.71252703 0.839351068 0.974971151 1.015558161 0.797621984 1 17.33225453 -0.528827848 7.7646972 1 0.913672247 0.072095647 0.097937154 0 0 0.095352623 0.022474829 0.295918524 0.528827848 -0.086327753 HIEPELAGRDS(ph)PIRAEMPGNLQHYGR ddPTM_MDA-MB-175_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 264.31 2.56E-53 1798960000 348310 393350 414960 373240 462770 440810 328440 376920 360320 479990 TRUE FALSE 362061.5478 460904.8027 425774.1985 447065.758 384108.5207 338438.558 302696.0146 371868.0039 347352.1536 574034.8505 0.630730952 0.80292129 0.741721863 0.77881292 0.669137981 0.589578416 0.527312957 0.647814333 0.605106386 1 19.1307788 -1.102184347 3.775179238 1.000133703 0.665891362 0.597847778 0.082203876 17665702.59 33639148.64 30331.38845 0.022771312 0.079034308 1.102184347 -0.334242341 HIEWESVLTNTAGCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIEWESVLTNTAGCLR 16 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30 O60716-13 CTNND1 Catenin delta-1 0 ; 220.14 1.18E-14 654280000 362170 436610 373170 344080 468480 566850 418990 439570 438680 511990 FALSE TRUE 376468.7513 511594.3711 382895.1168 412137.997 388847.9369 435207.6782 386148.469 433678.2831 422891.9925 612304.6379 0.614838967 0.835522613 0.62533434 0.673093051 0.635056331 0.710769854 0.63064763 0.708272086 0.690656197 1 19.22389009 -0.004949654 1.220384484 1.001164405 0.680225222 0.710173201 0.061305103 6.28804122 7.009661606 0.080090204 0.016366992 0.988667701 0.004949654 -0.320939183 HIGHLLPMDYSANAIAFYSYTFS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIGHLLPMDYSANAIAFYSYTFS 23 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H7C286;H0YF44 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 138.04 5.18E-06 275300000 49615 46991 56532 49266 66309 82469 61622 59439 58528 60366 FALSE TRUE 51573.83851 55061.33871 58005.27036 59010.66776 55037.81986 63316.82458 56791.90662 58642.31743 56421.58871 72193.56192 0.714382794 0.762690429 0.803468742 0.817395155 0.762364654 0.877042535 0.786661651 0.812292895 0.781532137 1 16.13958257 -5 0.215013725 2.00542223 0.765883917 0.728362444 0.038887299 77.70754366 0.77642882 33.82507858 0.077592445 1.00E-05 5 -1.239538313 HIGLVYSGMGPDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIGLVYSGMGPDYR 14 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 148.68 1.99E-06 0 397800 468010 429440 467070 756400 740540 496150 493780 423440 619330 FALSE TRUE 413505.4512 548387.0769 440631.5592 559455.0519 627827.3982 568560.808 457260.4666 487161.6868 408200.4771 740675.8557 0.558281262 0.740387408 0.594904715 0.755330483 0.847641236 0.767624331 0.617355707 0.65772589 0.551118919 1 19.49848278 5.357299725 1.617946389 0.712171396 3.59E-12 0.122864922 0.126403305 16.54694955 9.770930187 0.032134364 30.48624625 227666.8113 -5.357299725 -0.712171396 HIGTSALMDLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIGTSALMDLLLR 13 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 0 ; 219.42 2.25E-11 151248000 99618 102934 118428 122071 141812 165784 160478 139343 131703 99434 FALSE TRUE 103550.9956 120612.1138 121514.331 146216.2795 117706.8469 127283.1785 147899.315 137475.335 126963.0348 118916.1885 0.870789729 1.014261517 1.021848518 1.229574218 0.989830303 1.070360395 1.243727342 1.156069133 1.067668215 1 16.8595856 4.800189334 1.063594266 1.119883432 0.724559909 0.412338235 0.083754117 1.818442215 1.541076714 0.02513287 0.838543251 63123.24745 -4.800189334 -0.395323523 HIGYDDSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIGYDDSSK 9 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 131.5 0.00033127 312570000 309020 244000 265000 214580 381090 417220 369860 293960 290230 224680 FALSE TRUE 321220.3482 285905.1019 271906.1177 257023.2835 316312.4579 320326.978 340869.4068 290019.947 279784.679 268701.7442 1.195453156 1.06402399 1.011925391 0.956537459 1.177187959 1.192128391 1.268579062 1.079337791 1.041246233 1 18.03564616 3.208125473 24.9999818 1.139489992 1.054269064 0.11012047 0.092171639 379.1582949 311446.4586 0.02753604 0.032915646 1614.825032 -3.208125473 -0.085220928 HIISATSLST(ph)SPTELGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.001)T(0.986)S(0.013)PTELGSR;HIISATSLS(0.004)T(0.981)S(0.015)PTELGSR;HIISATS(0.001)LS(0.011)T(0.985)S(0.003)PTELGSR;HIISATSLS(0.002)T(0.649)S(0.349)PT(0.001)ELGSR 387.72 1.73E-125 1849350000 893588 939913 962537 937086 1051460 1345690 1008241 1010983 935723 934633 TRUE FALSE 928867.5442 1101335.746 987621.505 1122438.814 872733.2048 1033173.892 929212.4359 997432.4265 902046.512 1117756.442 0.831010683 0.985309237 0.883574872 1.004189081 0.780790137 0.924328282 0.83131924 0.892352206 0.807015266 1 20.09217443 3.245075698 24.99989627 0.868618321 0.927223953 0.110409177 0.073680241 303.4056782 1164230.777 0.018565452 0.024555787 1758.230048 -3.245075698 0.058605632 HIISATSLSTS(ph)PTELGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 HIISATSLS(0.001)T(0.248)S(0.749)PT(0.003)ELGSR;HIISATSLS(0.001)T(0.218)S(0.781)PTELGSR;HIISATSLST(0.008)S(0.991)PT(0.001)ELGSR 253.31 1.08E-30 4053330000 890070 1222130 1100810 1204760 1266610 1456180 1264320 1278040 1137160 1161060 TRUE FALSE 925210.6509 1432021.321 1129498.013 1443057.932 1051312.085 1118004.264 1165219.295 1260909.964 1096233.834 1388547.477 0.66631546 1.031308864 0.813438526 1.039257178 0.757130816 0.805160992 0.839164173 0.908078395 0.789482428 1 20.40514508 -1.055998997 4.418456476 1.000009512 0.858979142 0.13772038 0.110586429 9.39E-06 2.01E-06 0.097042547 0.022871605 0.087902455 1.055998997 -0.14103037 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCTSTAIAS(1)PEK 135.49 2.00E-05 351400000 537520 206590 279180 198600 439430 442540 394710 326890 336620 138340 TRUE FALSE 558741.7047 242070.2255 286455.6601 237882.4872 364735.8456 339766.7918 363771.5988 322508.5742 324505.112 165445.0743 3.377203625 1.463145557 1.731424531 1.437833603 2.204573615 2.053653112 2.198745416 1.949339233 1.96140691 1 17.33599281 0.363393881 1.853448429 0.999987113 2.01117695 0.26817302 0.514888419 11.03077349 30.37663916 0.464915744 0.129272863 2.308840228 -0.363393881 1.011189836 HIKEEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(1)EEEPCT(0.001)S(0.024)T(0.13)AIAS(0.845)PEKK 123.42 6.07E-05 738490000 640610 145720 260820 139200 411070 361870 390230 256240 284900 121400 TRUE FALSE 665901.7775 170746.2765 267617.1835 166733.3445 341196.4682 277831.1767 359642.7529 252805.5219 274646.5047 145186.0057 4.586542446 1.176051891 1.843271204 1.148411955 2.350064434 1.91362229 2.477117208 1.741252683 1.891687173 1 17.14754287 4.746364313 24.97313584 1.792606285 4.586543815 0.766334794 0.472475591 438.1596389 1402151.273 0.1079741 1.175690083 55765.33463 -4.746364313 2.79393753 HIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(0.999)EEEPCT(0.001)STAIASPEK;HIKEEPLS(0.938)EEEPCT(0.055)S(0.004)T(0.004)AIASPEK;HIKEEPLS(0.999)EEEPCT(0.001)STAIASPEK;HIKEEPLS(1)EEEPCTSTAIASPEK;HIKEEPLS(0.68)EEEPCT(0.105)S(0.105)T(0.105)AIAS(0.005)PEK;HIKEEPLS(0.998)EEEPCT(0.002)STAIASPEK 242.74 1.42E-37 9857800000 5402691 2809999 4047546 3010844 5928433 5237333 5202086 4011201 4686149 2444138 TRUE FALSE 5615993.412 3292594.469 4153028.374 3606379.957 4920720.076 4021041.783 4794332.906 3957437.412 4517495.413 2923020.045 1.921298289 1.126435816 1.420800511 1.233785571 1.683436993 1.375646325 1.640198436 1.353886511 1.545489029 1 21.47902829 -1.426747552 5.259514596 0.999554894 1.460779211 0.295129232 0.220137433 0.001034166 0.000112717 0.191851705 0.045177568 0.037432812 1.426747552 0.461224317 HIKEEPLSEEEPCTST(ph)AIAS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIKEEPLSEEEPCTSTAIASPEK 23 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 HIKEEPLS(0.358)EEEPCT(0.024)S(0.209)T(0.409)AIAS(1)PEK 180.65 1.03E-16 266920000 421200 224140 355360 245880 449900 438270 424750 341020 349640 199800 TRUE FALSE 437829.3012 262634.3014 364620.9735 294514.3301 373426.1587 336488.4345 391456.9851 336449.1847 337056.5247 238946.9846 1.832328213 1.099132102 1.525949257 1.232550939 1.56279921 1.408213772 1.638258737 1.40804951 1.410591246 1 17.86633104 0.5745231 2.090755741 1.000070354 1.453370668 0.337776818 0.193166913 3.397895593 15.40602234 0.166070551 0.045422738 3.754249231 -0.5745231 0.453300313 HILANFK ddPTM_MDA-MB-175_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 ; 144.29 0.0023638 1311140000 2176200 1580010 1796490 1586530 4055700 2956200 2730300 1924980 1999330 2786200 FALSE TRUE 2262118.056 1851364.427 1843308.005 1900340.899 3366313.563 2269667.352 2516291.952 1899178.792 1927374.504 3332102.545 0.678886086 0.555614481 0.553196662 0.57031285 1.010267096 0.681151712 0.755166421 0.569964089 0.578425927 1 21.66800137 HILGFDTGDAVLNEAAQILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HILGFDTGDAVLNEAAQILR 20 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;; 329.97 8.42E-80 1860241000 1294063 1653250 1621892 1557005 1742267 1915749 1640202 1617097 1610659 1552273 FALSE TRUE 1345153.606 1937182.827 1664159.838 1864975.942 1446117.078 1470845.328 1511638.681 1595422.46 1552691.697 1856411.174 0.72459896 1.04350957 0.896439248 1.004613616 0.778985333 0.792305793 0.814280103 0.859412226 0.836394285 1 20.82408486 3.229650021 24.99992964 0.836654086 0.924816649 0.104735188 0.09712926 332.1187069 931804.8208 0.026033575 0.0315526 1696.875665 -3.229650021 0.088162563 HILILQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HILILQNK 8 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 0 120.65 0.0014672 310760000 621300 448980 582740 541870 832730 759490 829220 624220 636960 440980 FALSE TRUE 645829.4037 526088.8224 597926.6831 649050.2687 691182.852 583109.9577 764223.5696 615853.3519 614035.934 527381.5879 1.224596039 0.997548709 1.133764805 1.230703315 1.310593445 1.105669919 1.44909035 1.167756642 1.164310526 1 19.00848768 3.831457607 4.571185268 1.222732788 1.102045582 0.076013496 0.124496853 0.405192249 14.46806322 0.030273401 0.056408748 6783.559011 -3.831457607 -0.120687206 HILLAVANDEELNQLLK ddPTM_MDA-MB-175_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 ; 278.84 7.59E-36 900800000 928530 872390 726020 857670 974980 1191160 913950 672980 757230 714350 FALSE TRUE 965189.0814 1022216.196 744940.6776 1027314.566 809253.2479 914531.1422 842312.2108 663959.8039 729977.4402 854313.2054 1.129783638 1.196535638 0.871976077 1.202503437 0.947255928 1.070486955 0.985952465 0.777185463 0.854461146 1 19.70440556 1.967169226 4.679822927 0.856421228 1.065143624 0.380343859 0.108936705 0.186061986 9.681834318 0.046125408 0.028484202 92.71910398 -1.967169226 0.208722396 HIMGQNVADYMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIMGQNVADYMR 12 0 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ; 95.401 0.0046026 335760000 95405 122164 128658 105131 189208 181451 120022 130581 145535 210158 FALSE TRUE 99171.66307 143144.7167 132010.9332 125925.598 157046.4917 139311.7552 110614.362 128830.7753 140297.2238 251334.4364 0.394580482 0.569538814 0.525240135 0.501028032 0.624850673 0.55428837 0.440108262 0.512587042 0.558209316 1 17.93924883 0.689869862 3.322187187 0.999993705 0.518274153 0.849196367 0.060902563 1.425875193 14.89629943 0.057304696 0.014839839 4.896320775 -0.689869862 -0.481719552 HIPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIPESK 6 0 O95202 O95202 LETM1 "LETM1 and EF-hand domain-containing protein 1, mitochondrial" 0 80.377 0.064673 223570000 449250 456350 536800 478050 614270 672440 619740 548670 557540 474860 FALSE TRUE 466986.7369 534724.5626 550789.449 572606.8632 509856.6048 516276.0009 571163.1594 541315.9761 537474.2443 567899.7253 0.822304918 0.94158271 0.969870955 1.008288678 0.897793364 0.909097113 1.005746497 0.953189361 0.946424554 1 19.11527669 4.733990248 3.55323682 0.959186497 0.806878831 0.571674595 0.035840381 0.204726117 4.626426327 0.00873016 0.082903019 54198.87206 -4.733990248 -0.152307666 HIPGAAFFDIDQCSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HIPGAAFFDIDQCSDR 16 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;;;; 288 2.19E-36 2665628000 1054385 1304051 1226672 1308699 1408761 1627344 1258142 1347581 1279902 1362360 FALSE TRUE 1096012.934 1528011.615 1258640.08 1567555.756 1169300.308 1249418.019 1159525.542 1329518.881 1233838.577 1629288.358 0.672694265 0.93783989 0.772509098 0.962110696 0.717675482 0.766848921 0.711676074 0.816012018 0.757286806 1 20.63581053 -1.49876664 3.082090031 1.005818766 0.794680222 0.331453088 0.08907699 68896389.48 82496630.98 3419683.705 0.020134414 0.03171271 1.49876664 -0.211138544 HISDLYEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HISDLYEDLR 10 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;E9PIA2;Q15149-4;Q15149-5;Q15149-8;E9PKG0 Q15149-3;Q15149-4;Q15149-5;Q15149-8;E9PKG0 PLEC Plectin 0 ;;;;; 219.03 6.50E-09 1831256000 216553 1647820 1251016 1871490 1205207 1939710 1278851 1706560 1099264 1369603 FALSE TRUE 225102.6797 1930820.267 1283618.505 2241665.136 1000346.345 1489241.749 1178611.317 1683686.355 1059701.703 1637950.485 0.137429478 1.178802585 0.78367357 1.368579305 0.610730516 0.909210481 0.71956468 1.02792262 0.646968094 1 20.64346031 4.751116638 24.6453572 0.913461849 0.137428885 0.514356298 0.226991666 1267.035282 2486922.304 0.049759375 0.876620562 56378.90516 -4.751116638 -0.776032965 HISQISVAEDDDESLLGHLMIVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HISQISVAEDDDESLLGHLMIVGK 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 133.84 2.27E-05 34953000 3178.5 21982 20441 27009 19980 30867 18844 28625 16932 22107 FALSE TRUE 3303.989634 25757.2375 20973.70925 32351.29959 16583.80674 23698.60704 17366.95804 28241.3287 16322.62063 26438.44339 0.124969144 0.974234267 0.793303484 1.223646155 0.627261087 0.896369226 0.656882774 1.06819181 0.617382059 1 14.69034962 4.743164818 24.95216216 0.875535189 0.124968833 0.578561899 0.19152517 306.9553554 1663465.349 0.041787033 0.33759839 55356.01493 -4.743164818 -0.750566356 HITDKDDFANNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HITDKDDFANNR 12 1 Q9Y6W3 Q9Y6W3 CAPN7 Calpain-7 0 115.57 0.00056175 93110000 36482 192950 104440 199840 84188 204940 68181 111370 56355 315470 FALSE TRUE 37922.33753 226087.6616 107161.7922 239367.7555 69877.75383 157345.7909 62836.79506 109877.2673 54326.79456 377280.3065 0.10051502 0.599256462 0.284037598 0.634456004 0.185214422 0.417052754 0.166552014 0.291235099 0.14399584 1 18.52527727 -1.196500343 3.885201341 1.000509001 0.321246629 0.577826925 0.17590596 75923923.45 123384506 464527.797 0.040874802 0.06360623 1.196500343 -0.679262372 HITIFSPEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HITIFSPEGR 10 0 G3V5Z7;P60900;G3V3I1;G3V295;G3V3U4;G3V4S5;G3V2S7 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;;;; 205.18 1.73E-07 1824199000 849497 1610381 1417813 1517383 1703291 1921178 1414571 1519543 1355753 1946083 FALSE TRUE 883035.7975 1886951.41 1454762.372 1817516.828 1413766.204 1475013.525 1303693.229 1499176.012 1306959.714 2327380.704 0.379411841 0.810761818 0.625064206 0.78092803 0.607449483 0.63376547 0.560154695 0.644147306 0.561558198 1 21.15027579 -1.68405793 6.090077582 1.004393794 0.631063679 0.497739997 0.113450691 0.006204383 0.000321872 0.100697868 0.023544569 0.020698652 1.68405793 -0.373330115 HITLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HITLDK 6 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;;;;;; 153.61 0.010109 7700680000 11750900 12412900 14163710 11562920 19053720 18769880 17073050 15296370 15187650 12655930 FALSE TRUE 12214834.61 14544719.02 14532827.92 13850031.06 15814975.48 14410859.83 15734819.73 15091347.18 14641049.44 15135617.17 0.807025869 0.960959758 0.960174121 0.915062195 1.044884744 0.952115772 1.039588908 0.997075112 0.967324244 1 23.85144417 5.77583935 0.865056913 0.993729284 1.67E-12 0.670792493 0.037120566 6.603608443 0.986565567 0.011433321 9.482651447 596814.4779 -5.77583935 -0.993729284 HIVDCIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIVDCIR 7 0 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 88.942 0.018237 91790000 33659 40945 31229 39308 45974 50251 35140 40546 38766 42034 FALSE TRUE 34987.88331 47976.98524 32042.85339 47083.00508 38159.3559 38580.96681 32385.63498 40002.54719 37370.81923 50269.75751 0.696002627 0.954390624 0.637418101 0.936606966 0.759091704 0.767478673 0.644236944 0.795757711 0.7434056 1 15.61740311 -1.445230867 5.838725993 1.000131108 0.772608406 0.316778301 0.101075273 0.000157005 1.49E-05 0.089073765 0.020982855 0.035873119 1.445230867 -0.227522702 HIVLSGGSTMYPGLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HIVLSGGSTMYPGLPSR 17 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 121.27 6.08E-05 318190000 276070 300020 315090 350040 392570 485820 434540 359300 344050 362410 FALSE TRUE 286969.4568 351546.1012 323301.5042 419276.8672 325841.0916 372995.6677 400479.6193 354484.1712 331667.7077 433417.3007 0.66210891 0.811103065 0.745935854 0.967374552 0.751795305 0.860592475 0.924004692 0.817881913 0.765238737 1 18.72539722 7.999999997 0.040872419 1.331100341 7.08E-31 0.360670743 0.081388139 879.5260186 2.734300851 24.05960398 80.29046929 99999999.24 -7.999999997 -1.331100341 HIVNHAVVNEDPNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HIVNHAVVNEDPNAR 15 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;;; 134.24 2.10E-05 1210101000 344279 402228 373572 401220 437050 499129 382236 414304 393109 360528 FALSE TRUE 357871.4008 471307.5301 383307.5932 480580.1185 362760.3971 383213.8541 352275.3435 408750.9325 378961.0839 431166.5589 0.830007322 1.093098526 0.889001212 1.114604342 0.841346319 0.888783803 0.817028446 0.948011677 0.878920399 1 18.71788576 3.189200866 24.99999581 0.891210364 0.983018962 0.171893752 0.092136952 169.9276399 86065.18855 0.024368081 0.029125478 1545.969304 -3.189200866 0.091808598 HIYDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HIYDTK 6 0 B4DDF4;B4DUT8;Q99439;A0A087X1X5;Q99439-2 B4DDF4 CNN2 Calponin;Calponin-2 0 ;;;;; 149.06 0.010686 7922560000 14821900 12035800 14528900 11746690 17288700 18282700 17023100 14679600 15396400 11379800 FALSE TRUE 15407080.06 14102855.02 14907535.07 14070150.22 14349972.95 14036820 15688784.94 14482843.97 14842286.57 13609453.93 1.132086573 1.03625429 1.095380839 1.033851196 1.054412104 1.031402147 1.152785778 1.064175245 1.090586488 1 23.69810585 HIYLLPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HIYLLPSGR 9 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 118.18 0.0010317 2186700000 814210 997060 953830 914280 1198360 1162330 971370 966210 927430 1015320 FALSE TRUE 846355.6395 1168297.299 978687.5934 1095121.855 994663.1952 892396.4728 895231.4812 953259.5354 894051.9755 1214252.515 0.697017819 0.962153494 0.806000055 0.901889716 0.819156793 0.734934836 0.737269613 0.785058729 0.736298229 1 20.21163704 2.995528711 24.67867354 0.780166351 0.849398961 0.022370356 0.097331158 367.7846031 2029960.938 0.026007241 0.030346188 989.7572937 -2.995528711 0.06923261 HIYYITGETK ddPTM_MDA-MB-175_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 ;;;;; 190.96 8.44E-07 25474780000 19115960 14773480 18471080 15251330 24305160 22169570 21894680 19069560 20072960 13540740 FALSE TRUE 19870672.86 17310710.27 18952451.52 18267997.55 20173777.58 17021023.35 20178517.77 18813963.74 19350538.09 16193788.75 1.22705521 1.068972217 1.17035314 1.12808669 1.245772555 1.05108345 1.246065271 1.161801233 1.194935811 1 23.94893723 -0.86580735 4.279951894 0.999997787 1.164451271 0.374145197 0.064385796 3174986.162 1483707.868 63.05006593 0.01358622 0.136204874 0.86580735 0.164453485 HKAAAYDIS(ph)EDEED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKAAAYDISEDEED 14 1 P49585 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 HKAAAYDIS(1)EDEED;HKAAAYDIS(1)EDEED 162.59 2.67E-06 477580000 375950 388320 415470 219065 754640 548370 278540 389860 454750 490080 TRUE FALSE 390792.7963 455010.9393 426297.4895 262395.4032 626366.5624 421019.3781 256707.307 384634.5644 438383.6363 586101.7929 0.666766082 0.776334324 0.727343773 0.447695957 1.068699277 0.718338322 0.437990994 0.656258979 0.747965015 1 19.16079172 HKASVEDADTQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKASVEDADTQSK 13 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6 Q13561 DCTN2 Dynactin subunit 2 0 ; 79.466 0.012277 142417000 166092 160695 163520 121829 209779 206379 150548 150382 178999 176942 FALSE TRUE 172649.4404 188293.1162 167781.4655 145926.4126 174120.8405 158450.605 138747.6544 148366.3753 172556.861 211610.3971 0.815883542 0.889810325 0.79287912 0.689599446 0.822836887 0.748784592 0.655675034 0.701129894 0.815446043 1 17.69105099 4.026493435 7.088156977 0.753230432 0.850863184 0.057649234 0.094159256 0.308997837 56.47980606 0.022234469 0.047671755 10629.02517 -4.026493435 0.097632751 HKDSNYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKDSNYQR 8 1 Q6PGP7 Q6PGP7 TTC37 Tetratricopeptide repeat protein 37 0 ; 174.02 0.00016485 15236300 21614 31952 25997 27652 38259 38951 30144 30456 31233 33510 FALSE TRUE 22467.33741 37439.50745 26674.50318 33121.48307 31755.74885 29905.22056 27781.23451 30047.78714 30108.93043 40075.64291 0.560623256 0.934221006 0.665603874 0.826474154 0.792395244 0.746219359 0.693219933 0.749776796 0.751302493 1 15.29043804 -1.473363627 2.484868509 1.012229644 0.751074816 0.395885003 0.093746756 3082819.09 2904880.811 258801.1695 0.021024517 0.033622993 1.473363627 -0.261154828 HKEEDKNSER ddPTM_MDA-MB-175_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 ;;;;;; 227.81 1.43E-09 581125000 726850 343055 534642 330862 761121 687452 732747 529323 611125 275046 FALSE TRUE 755546.5993 401972.0277 548575.2097 396305.5161 631745.9243 527801.6914 675312.3755 522228.291 589130.7306 328935.9976 2.296941061 1.222037206 1.667726286 1.204810416 1.920573999 1.604572608 2.053020589 1.587628884 1.791019332 1 18.32744737 HKELAPYDENWFYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HKELAPYDENWFYTR 15 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ;;; 250.95 2.70E-19 6802830000 6217990 6414690 7239080 4862660 9198500 8420100 6496060 7387370 7455020 6883850 FALSE TRUE 6463481.047 7516363.108 7427736.372 5824479.634 7634942.256 6464659.383 5986881.843 7288354.388 7186715.286 8232608.608 0.785107292 0.912998961 0.902233633 0.707488952 0.927402555 0.785250422 0.727215653 0.885303157 0.87295724 1 22.97291821 0.853052503 1.629469218 0.998670353 0.827816956 0.336918302 0.073172366 0.655404069 3.319568335 0.067447242 0.019420096 7.12939214 -0.853052503 -0.170853397 HKEQNNDSQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKEQNNDSQLK 11 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 93.258 0.0056384 37495000 41650 21694 31368 23271 44064 42282 40025 31043 35057 20212 FALSE TRUE 43294.37416 25419.77574 32185.47585 27873.93434 36574.01702 32462.64629 36887.73591 30626.91936 33795.30542 24172.15442 1.791084626 1.05161399 1.331510435 1.153142325 1.513064015 1.342976953 1.52604254 1.267033084 1.398108949 1 14.56105844 -1.194872684 5.163003594 0.99997489 1.360352361 0.244127091 0.196424937 5.15E-05 8.02E-06 0.172384945 0.040628694 0.063845062 1.194872684 0.360377471 HKGPPVFTQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKGPPVFTQEER 12 1 Q99447-3;Q99447;Q99447-4;I3L1R7;I3L2Q1 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 ; 214.81 2.58E-11 235890000 184728 176866 221450 180071 264680 270417 241679 231554 235284 203186 FALSE TRUE 192021.2041 207241.3597 227221.1689 215688.5063 219689.7881 207616.75 222735.5685 228450.3974 226816.1748 242996.4065 0.790222402 0.852857714 0.935080367 0.887620148 0.904086572 0.854402553 0.916620833 0.940138995 0.9334137 1 17.89057545 8 0.08470934 1.074266745 0.417442686 0.672275099 0.03173804 112.2630264 0.688164733 0.75157763 8.594311773 99999999.96 -8 -0.656824059 HKGYS(ph)PPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKGYSPPESR 10 1 Q14669-3;G5E9G6;C9JLD7 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 HKGY(0.008)S(0.992)PPESR 71.241 0.031147 20515000 54591 64117 70152 67682 82036 90387 77046 65616 77108 74463 TRUE FALSE 56746.29483 75128.59599 71980.21875 81069.29759 68091.55002 69395.98908 71006.9332 64736.52485 74332.89814 89052.59917 0.637222219 0.843642933 0.808288803 0.910352964 0.764621703 0.779269665 0.797359469 0.726947057 0.834707789 1 16.4423701 0.976339165 22.79280666 1.000000002 0.786982494 0.480987152 0.067516076 545.7102763 525691.8076 0.063106865 0.015776716 9.469764206 -0.976339165 -0.213017508 HKHEIESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HKHEIESGR 9 1 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 ;;;; 150.1 5.17E-05 281479000 227258 215472 280594 219010 293129 283582 259812 245969 258334 217285 FALSE TRUE 236230.3213 252477.6399 287906.5102 262329.5243 243303.0373 217724.3782 239447.2565 242672.1879 249036.6098 259857.8356 0.909075229 0.971599103 1.107938537 1.009511696 0.936292865 0.837859585 0.921454826 0.933865193 0.958357131 1 17.98736304 3.194651656 5.600119624 0.922862728 1.005386272 0.231358875 0.059653899 0.246455304 18.14267756 0.017901472 0.02194396 1565.494897 -3.194651656 0.082523544 HKLDVTSVEDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HKLDVTSVEDYK 12 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 149.26 3.94E-05 1827740000 2232370 1105790 1737100 1221990 2373060 2061360 2196040 1673310 2022820 1067710 FALSE TRUE 2320505.691 1295700.831 1782370.253 1463695.975 1969688.109 1582640.38 2023908.647 1650882.016 1950019.103 1276907.332 1.817285901 1.014717982 1.395849337 1.146282066 1.542545852 1.239432448 1.585008243 1.292875352 1.527142224 1 20.2842224 -0.935047462 4.242759851 0.999989081 1.378665184 0.217568428 0.22301756 10795534.24 5088920.943 1067.296933 0.04634189 0.116132169 0.935047462 0.378676103 HKLTVS(ph)DGES(ph)GEEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKLTVSDGESGEEKK 15 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 2 HKLT(0.017)VS(0.984)DGES(0.999)GEEKK 84.499 0.004454 103660000 335170 55773 86982 53054 184460 225240 162580 97596 99247 29242 TRUE FALSE 348402.7704 65351.5789 89248.82238 63547.92285 153105.5551 172931.4235 149836.5548 96287.88525 95675.11986 34971.41003 9.962502802 1.86871444 2.552051013 1.81713928 4.378020645 4.944937119 4.284544279 2.753331512 2.735809616 1 15.09388835 4.744805054 24.94482375 3.088409878 9.962505946 0.753113565 1.205406876 352.6435624 1408675.388 0.297405755 2.778007204 55565.47794 -4.744805054 6.874096068 HKMS(ph)PPPSGFGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HKMSPPPSGFGER 13 1 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER;HKMS(1)PPPSGFGER 145.62 4.98E-05 2499747000 1109024 904315 1064297 848157 1353581 1364311 1175147 1055918 1083575 847150 TRUE FALSE 1152809.124 1059624.067 1092033.454 1015919.923 1123499.785 1047470.447 1083035.907 1041765.146 1044577.347 1013132.823 1.137865735 1.045888597 1.077877875 1.002750972 1.108936321 1.033892519 1.06899696 1.028261175 1.031036922 1 19.95039189 8 0.118902949 0.987369139 1.325727717 0.390199028 0.033173776 104.3606174 0.8535387 0.21685352 5.846835415 100000000 -8 0.338358579 HKPGGGDVK ddPTM_MDA-MB-175_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 ; 105.86 0.0018199 982770000 1196320 720310 1043120 742650 1375250 1252400 1253060 1042150 1163900 722540 FALSE TRUE 1243551.637 844017.6393 1070304.564 889543.9534 1141485.496 961549.0803 1154841.883 1028181.684 1122011.466 864107.8791 1.439116188 0.976750311 1.238623776 1.029436225 1.320998829 1.112765088 1.33645568 1.189876529 1.298462256 1 19.72085191 3.216961142 24.99952994 1.221264263 1.161939382 0.010914173 0.150150031 919.4615133 1064194.226 0.039453201 0.047196565 1648.014931 -3.216961142 -0.059324881 HKSDFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKSDFGK 7 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 129.47 0.0021977 5140100000 2156820 13510800 12560100 13463500 15035900 19611700 11945400 16559200 12687500 11846900 FALSE TRUE 2241972.919 15831174.8 12887426.52 16126540.12 12480103.09 15057179.89 11009088.33 16337251.01 12230879.35 14168073.23 0.158241201 1.11738375 0.909610383 1.138230997 0.880860995 1.062754239 0.777034968 1.15310323 0.863270478 1 23.75614024 4.743800584 24.99128624 0.992544543 0.15824085 0.805425317 0.122507528 207.1780364 988075.6363 0.026055139 0.222307899 55437.11032 -4.743800584 -0.834303692 HKSDSPES(ph)DAEREK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HKSDSPESDAEREK 14 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 HKSDS(0.004)PES(0.996)DAEREK;HKSDS(0.012)PES(0.988)DAEREK 135.18 1.80E-05 367920000 170901 354921 485710 306307 634160 594810 508973 509370 483190 281413 TRUE FALSE 177648.3034 415875.9208 498368.0016 366893.6104 526365.7097 456674.3919 469078.3663 502542.7283 465800.0863 336550.4894 0.527850379 1.23570143 1.480811995 1.090159194 1.564002212 1.35692684 1.393783046 1.493216454 1.38404222 1 18.36046343 4.727782237 3.312173349 1.371010888 0.423362939 0.675455468 0.168109491 0.155880223 2.833668291 0.037529762 0.371801724 53429.63862 -4.727782237 -0.947647949 ISHQSQDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISHQSQDKK 9 1 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 117.02 0.00079131 566400000 307890 950230 1219200 865090 1355200 1463900 1188100 1297300 1469500 972620 FALSE TRUE 320045.7349 1113424.611 1250973.354 1036202.22 1124843.588 1123931.411 1094973.617 1279911.815 1416612.982 1163186.267 0.27514573 0.957219529 1.07547122 0.890830858 0.96703651 0.966252304 0.941357071 1.100349834 1.217872857 1 20.14965071 4.737191418 4.320518251 1.015757699 0.221062975 0.863656651 0.088236746 0.071868859 3.193088617 0.022227955 0.175501294 54599.84604 -4.737191418 -0.794694723 down KTESHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTESHHK 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q7L7L0;P04908;Q99878;Q96KK5;Q6FI13;P0C0S8 A0A0U1RR32;Q7L7L0;Q99878 HIST1H2AD;HIST3H2A;HIST1H2AB;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1 0 ; 73.248 0.032073 45014000 41021 69136 88868 63193 125070 106433 93056 85317 96241 80941 FALSE TRUE 42640.54076 81009.5702 91183.97309 75692.38679 103810.6461 81715.54876 85762.02756 84173.46517 92777.30521 96799.83924 0.440502186 0.836877115 0.941984757 0.781947443 1.072425811 0.844170294 0.88597283 0.869562035 0.958444827 1 16.56271703 4.737445666 3.136217039 0.908683739 0.370289081 0.768864719 0.078212377 0.151605346 2.302148929 0.017674697 0.2009568 54631.81962 -4.737445666 -0.538394658 down HKT(ph)Y(ph)S(ph)LSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKTYSLSPR 9 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 3 HKT(1)Y(1)S(1)LS(0.001)PR 54.486 0.035509 0 131110 158150 137610 140920 154230 188800 118690 147670 136830 143020 TRUE FALSE 136286.324 185311.0323 141196.2296 168793.5554 128014.0397 144954.0613 109386.7677 145690.7252 131905.515 171042.0307 0.796800199 1.083423948 0.825506041 0.986854253 0.748436154 0.847476265 0.639531507 0.851783182 0.771187728 1 17.38399136 3.235465989 24.99809416 0.795976178 0.927620239 0.185654063 0.11404672 109.1613552 881796.5851 0.029776087 0.037055716 1719.752658 -3.235465989 0.131644061 HLAAVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLAAVEER 8 0 Q92922;F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 Q92922;F8VXC8 SMARCC1;SMARCC2 SWI/SNF complex subunit SMARCC1;SWI/SNF complex subunit SMARCC2 0 103.56 0.0047486 312350000 35157 42344 43252 43244 53101 57646 50848 43566 44571 48845 FALSE TRUE 36545.02551 49616.25261 44379.18265 51797.53413 44074.91099 44258.59013 46862.40089 42982.06903 42966.89842 58415.24256 0.625607699 0.849371678 0.759719222 0.886712643 0.754510451 0.757654821 0.802228988 0.735802286 0.735542583 1 15.83405725 -1.123214144 4.27939128 1.000033397 0.77145192 0.520230099 0.066895212 2.39E-05 4.90E-06 0.060039232 0.014148881 0.075298419 1.123214144 -0.228581477 HLAEYTHVEAECPFLTFDDLLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLAEYTHVEAECPFLTFDDLLNR 23 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 118.52 0.00015867 50999000 30307 23777 32679 42383 29926 42139 51691 36517 36019 20421 FALSE TRUE 31503.54376 27860.51479 33530.64159 50766.2309 24839.18921 32352.85587 47639.32435 36027.54934 34722.68323 24422.10397 1.289960267 1.140790934 1.372962855 2.078700139 1.017078186 1.324736637 1.950664219 1.475202521 1.421772804 1 14.57589987 4.001572387 24.70821648 1.507569404 1.225750764 0.07565111 0.327705537 96.8144571 1521181.166 0.079124048 0.168966642 10036.27118 -4.001572387 -0.28181864 HLAGEVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLAGEVAK 8 0 Q13200;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;; 116.73 0.002216 650079000 1100080 905210 1126420 899380 1551340 1428140 1300720 1122790 1198260 866040 FALSE TRUE 1143512.008 1060672.776 1155775.431 1077274.68 1287643.781 1096476.129 1198766.168 1107740.837 1155134.857 1035723.957 1.10407025 1.02408829 1.115910686 1.040117565 1.243230663 1.058656722 1.157418596 1.06953289 1.115292206 1 19.98220811 5.11356661 20.36513589 1.096354928 2.689637565 0 0.067714295 22536.35627 2693383.607 0.01447478 558869.0897 129887.2764 -5.11356661 1.593282637 HLAGLGLTEAIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLAGLGLTEAIDK 13 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ; 213.16 8.14E-09 1732010000 2721800 2157160 2602700 2592400 3610400 3897200 3497500 2651500 2750400 1893940 FALSE TRUE 2829258.766 2527635.45 2670528.5 3105168.982 2996705.498 2992134.363 3223356.811 2615960.979 2651413.641 2265021.281 1.249109132 1.115943356 1.179030203 1.370922652 1.323036354 1.321018212 1.423102219 1.154938808 1.170591051 1 21.11109317 1.053730843 1.631114363 1.007982699 1.275702969 0.470236502 0.08976985 0.346218425 1.859643719 0.0911696 0.026628383 11.31698767 -1.053730843 0.26772027 HLAGLGLTEAIDKNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLAGLGLTEAIDKNK 15 1 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 ; 269.36 3.85E-26 1485590000 3610900 2479100 3107900 2132420 5430700 4399400 3018000 3072900 3621100 2394320 FALSE TRUE 3753461.12 2904866.14 3188894.427 2554206.311 4507591.554 3377706.024 2781441.274 3031712.802 3490777.318 2863441.162 1.310821808 1.014466852 1.113658094 0.892005865 1.574186896 1.179596797 0.971363166 1.058765531 1.219084703 1 21.44931853 0.501154776 0.471624576 0.996688862 1.153500073 0.048742357 0.184456342 7.501713392 3.102898361 0.333359722 0.106395104 3.17069725 -0.501154776 0.156811211 HLAQVGDSMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLAQVGDSMDR 11 0 P55957;P55957-2 P55957 BID BH3-interacting domain death agonist;BH3-interacting domain death agonist p15;BH3-interacting domain death agonist p13;BH3-interacting domain death agonist p11 0 ;;; 190.36 2.31E-06 2232630000 907700 1135130 1051120 1114010 1246440 1442170 1087840 1238050 1019870 1192310 FALSE TRUE 943536.6969 1330079.747 1078513.051 1334357.853 1034570.574 1107247.874 1002572.258 1221455.965 983165.0779 1425920.316 0.661703663 0.932786869 0.756362777 0.935787111 0.725545854 0.776514551 0.703105389 0.856608852 0.689495105 1 20.44346193 -1.160433296 4.787694577 1.000020082 0.789914108 0.330139342 0.092545074 1.80E-05 3.15E-06 0.081129904 0.019120675 0.069114107 1.160433296 -0.210105974 HLCEPGADGAETFADGVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLCEPGADGAETFADGVPR 19 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38;K7EMY3 Q14839-2 CHD4;CHD5 Chromodomain-helicase-DNA-binding protein 4 0 ;;; 314.41 1.24E-61 1131910000 514229 561820 623630 634337 654360 760400 642970 629120 606710 500505 FALSE TRUE 534531.158 658308.2146 639882.3101 759806.9653 543132.1209 583808.624 592572.3313 620687.6754 584874.6256 598569.372 0.893014549 1.099802705 1.069019465 1.269371606 0.907383749 0.975339954 0.989981043 1.036951947 0.97712087 1 19.19115893 HLDGEEDGSS(ph)DQSQASGTTGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 HLDGEEDGS(0.074)S(0.926)DQSQASGTTGGR;HLDGEEDGS(0.184)S(0.816)DQSQASGTTGGR 284.9 3.82E-46 921800000 155129 185801 169365 164659 159876 263280 234060 186771 192859 157298 TRUE FALSE 161253.6127 217710.8764 173778.791 197228.0587 132700.3346 202137.21 215713.7656 184267.6402 185918.0423 188117.5314 0.857196092 1.157313062 0.923777756 1.048429975 0.705411843 1.074526167 1.14669677 0.97953465 0.988307899 1 17.52127478 HLDHVAALFPGDVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLDHVAALFPGDVDR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 150.34 3.20E-06 3017010000 1706780 1903840 1856760 1972230 2168000 2421360 1994210 1918150 1893650 1867350 FALSE TRUE 1774164.992 2230809.71 1905148.691 2362331.207 1799484.134 1859035.836 1837898.609 1892440.337 1825497.906 2233221.48 0.794442024 0.998920049 0.853094379 1.057813221 0.805779521 0.832445798 0.822980894 0.847403786 0.817428062 1 21.09069491 HLDQIIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLDQIIPR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 110.87 0.0033424 445700000 187981 210291 223560 243020 260520 291400 207304 202878 197461 209410 FALSE TRUE 195402.635 246406.8434 229386.1573 291088.6307 216236.9035 223726.7662 191054.9708 200158.7523 190354.4172 250439.8801 0.780237696 0.983896188 0.915933026 1.162309415 0.863428394 0.893335223 0.762877584 0.79922875 0.760080292 1 17.93410479 2.716979908 2.411745242 0.814437996 0.959247398 0.168100805 0.111610129 0.406763448 4.674977339 0.038029018 0.037311549 521.1705988 -2.716979908 0.144809402 HLDRS(ph)PESDRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HLDRSPESDRPR 12 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 HLDRS(1)PESDRPR;HLDRS(1)PESDRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(0.999)PES(0.001)DRPR;HLDRS(0.997)PES(0.003)DRPR 161.08 3.46E-05 6584180000 1095614 1339895 1233293 1128122 1326162 1545466 1085999 1322105 1193550 1194743 TRUE FALSE 1138869.687 1570011.543 1265433.629 1351261.164 1100741.457 1186554.943 1000875.561 1304384.345 1150594.369 1428830.016 0.797064503 1.098809183 0.885643229 0.945711631 0.770379572 0.830438142 0.700486097 0.912903796 0.805270295 1 20.44640286 3.2565881 24.51657177 0.828266388 0.940438489 0.166298088 0.102730649 286.497916 389621.4111 0.026540379 0.035857878 1805.46095 -3.2565881 0.112172101 HLDSSSNERPDISSIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLDSSSNERPDISSIQR 17 1 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;; 278.34 4.78E-36 8628700000 58874 59580 75398 46941 81548 85668 69630 69223 52602 58344 FALSE TRUE 61198.39098 69812.40153 77362.93382 56225.7897 67686.50009 65772.90531 64172.21866 68295.17891 50708.8643 69775.38974 0.877077021 1.000530442 1.108742411 0.805811188 0.970062659 0.942637591 0.919697029 0.978786062 0.726744265 1 16.09043066 3.736709555 24.9941075 0.914247209 0.995957999 0.154101713 0.094477265 324.2167382 4377772.518 0.023944467 0.039320129 5453.929948 -3.736709555 0.08171079 HLDSVLSDHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLDSVLSDHTR 11 0 Q2M389;A0A087X256;F8W1W1 Q2M389 KIAA1033 WASH complex subunit 7 0 132.03 0.00011048 161340000 20874 72436 63752 69923 51585 79085 44410 61756 55006 81051 FALSE TRUE 21698.12164 84876.31953 65413.42949 83753.5607 42816.60013 60718.70729 40929.02816 60928.26183 53026.3448 96931.39163 0.223850306 0.875632941 0.67484257 0.864049915 0.441720679 0.626409115 0.422247401 0.628571001 0.547050279 1 16.56467634 -1.286471321 3.227912933 1.001983464 0.600016011 0.298783696 0.188083676 44505796.8 62419195.73 862227.601 0.042013978 0.05170454 1.286471321 -0.401967453 HLDVDLDRQS(ph)LSSIDKNPSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLDVDLDRQSLSSIDKNPSER 21 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 HLDVDLDRQS(0.977)LS(0.02)S(0.003)IDKNPSER;HLDVDLDRQS(0.964)LS(0.018)S(0.018)IDKNPSER;HLDVDLDRQS(0.994)LS(0.005)S(0.001)IDKNPSER;HLDVDLDRQS(0.996)LS(0.004)SIDKNPSER 216.14 3.29E-25 1481840000 1005700 725230 909632 922353 1125960 1204590 1103310 861784 898647 642900 TRUE FALSE 1045405.813 849782.611 933337.7572 1104791.67 934569.7214 924842.2282 1016829.679 850233.1951 866304.87 768863.9459 1.359675945 1.105244453 1.213917966 1.436914393 1.215520283 1.202868509 1.322509248 1.105830491 1.126733637 1 19.5523688 1.325917784 1.250933592 1.01232717 1.2610336 0.462785876 0.09256501 0.373299114 1.136949609 0.0841239 0.027326869 21.17960146 -1.325917784 0.24870643 HLEAADKGHS(ph)PAQKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 257.75 5.26E-27 1707970000 2480600 917950 1443880 738130 2270890 1856760 2050780 1472500 1834410 677750 TRUE FALSE 2578536.003 1075600.772 1481508.699 884129.9109 1884884.929 1425555.629 1890034.505 1452763.546 1768389.942 810542.1362 3.18124856 1.327014012 1.827799732 1.09078834 2.32546199 1.758768071 2.331815239 1.792335625 2.181737214 1 19.62852766 4.750736829 24.74341889 1.790839438 3.181249546 0.472717671 0.454346436 1446.544352 2939477.35 0.101758857 1.723403755 56329.62095 -4.750736829 1.390410109 HLECTK ddPTM_MDA-MB-175_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 76.847 0.073978 116920000 249500 302270 348110 306290 373350 432820 378070 344550 349880 328170 FALSE TRUE 259350.4527 354182.5212 357182.0326 366873.2478 309888.1004 332304.1145 348435.8855 339931.8708 337287.8871 392468.6283 0.660818302 0.902447981 0.910090659 0.934783627 0.789586933 0.846702362 0.887805701 0.866137689 0.859400887 1 18.58221781 -5 0.165178945 1.529412206 0.821018715 0.300686087 0.072319458 182.6136203 1.703226705 31.86679061 0.277916712 1.00E-05 5 -0.708393491 HLEDANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLEDANR 7 0 Q96ED9-2;Q96ED9 Q96ED9-2 HOOK2 Protein Hook homolog 2 0 ; 133.81 0.0032352 284600000 67233 72853 69224 73401 74799 95981 66924 64868 71495 84119 FALSE TRUE 69887.41076 85364.93603 71028.03431 87919.49872 62084.6927 73690.86736 61678.32201 63998.55056 68921.90892 100600.5075 0.694702368 0.848553732 0.706040517 0.873946871 0.617140949 0.732509897 0.6131015 0.636165285 0.685104982 1 16.61827806 4.120594895 20.59554605 0.710845052 0.773094776 0 0.121293256 8.122596739 1401.057232 0.028766753 0.062143793 13200.63718 -4.120594895 0.062249723 HLEEEEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLEEEEGQLK 10 0 P07476 P07476 IVL Involucrin 0 128.81 0.00031972 252920000 681380 490150 582480 479820 798530 789860 732670 624490 676320 512160 FALSE TRUE 708281.4085 574329.4497 597659.9073 574726.9639 662796.1558 606426.9854 675241.4109 616119.733 651979.3753 612507.9461 1.156362808 0.93766857 0.975758619 0.938317564 1.082102134 0.99007203 1.102420655 1.005896718 1.064442314 1 19.22436903 3.225891568 24.99993873 1.040602097 0.995553548 0.071994693 0.066630715 542.1231146 1069774.211 0.018291606 0.022002171 1682.253993 -3.225891568 -0.045048548 HLEEIVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLEEIVEK 8 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 120.15 0.0015563 158540000 632590 505010 571960 523620 812130 811500 664930 599070 673110 501640 FALSE TRUE 657565.1417 591741.5391 586865.7475 627190.4732 674084.4327 623041.4234 612811.0491 591040.4465 648884.9026 599926.7535 1.096075709 0.98635631 0.978228999 1.045445081 1.123611222 1.038529153 1.021476448 0.98518768 1.081606877 1 19.19442684 -0.520261758 6.154104964 1.00000047 1.034358529 0.049840856 0.047102254 0 0 0.04671954 0.011011901 0.301813209 0.520261758 0.03435806 HLEEQEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLEEQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 ;; 116.55 0.0010759 996680000 1290440 1140550 1211460 1041840 1609550 1509470 1421450 1216460 1444580 1118170 FALSE TRUE 1341387.568 1336430.59 1243031.643 1247912.842 1335959.266 1158918.469 1310033.035 1200155.343 1392589.848 1337254.003 1.003091084 0.999384251 0.929540417 0.933190583 0.999031794 0.866640493 0.97964413 0.897477473 1.041380205 1 20.35084209 4.25394518 23.42370457 0.948424606 1.001237785 0.103435872 0.049715512 196.5703535 299275.4067 0.011107989 0.030118332 17945.07096 -4.25394518 0.052813178 HLEFSHDQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;; 227.94 1.34E-09 21568631700 768921 973212 921817 835989 929491 1293485 1025762 958563 939879 1006365 FALSE TRUE 799278.5948 1140353.59 945840.3083 1001345.129 771496.4518 993092.7117 945360.0941 945715.0309 906052.9384 1203542.954 0.664104752 0.94749721 0.785879977 0.831997833 0.64102112 0.825141063 0.785480976 0.785775886 0.752821439 1 20.1988562 -1.696189395 4.767222185 1.007684189 0.784259976 0.394775505 0.081575734 0.006333696 0.00040364 0.075089284 0.017211524 0.020128463 1.696189395 -0.223424213 HLEGLSEEAIMELNLPTGIPIVYELDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HLEGLSEEAIMELNLPTGIPIVYELDK 27 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;;;;;;; 207.13 2.51E-25 5181118600 2845943 2352716 3070466 2392523 3835879 3779566 3581406 3059774 3233149 2212855 FALSE TRUE 2958303.027 2756776.671 3150484.866 2865756.908 3183857.658 2901819.076 3300686.039 3018762.734 3116788.599 2646421.57 1.117850255 1.041699744 1.190469766 1.082879969 1.203080301 1.096506736 1.247226095 1.140696089 1.177737 1 21.33561147 4.239393638 24.99967879 1.150694474 1.079775003 0.106893575 0.069006792 36.66369896 1100136.366 0.015269795 0.037238611 17353.76205 -4.239393638 -0.070919471 HLEHPEQQDGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLEHPEQQDGQLK 13 0 P07476 P07476 IVL Involucrin 0 ;;; 101.6 0.0010817 1025630000 761010 586163 714040 518155 887600 835760 743270 671740 765180 565626 FALSE TRUE 791055.2624 686831.9355 732648.469 620644.5125 736726.069 641667.4061 685010.5552 662736.424 737641.3213 676449.5851 1.169422348 1.015348299 1.08307919 0.917502983 1.089107134 0.948581269 1.01265574 0.979727741 1.090460158 1 19.36762289 HLEHQEGQLEVPEEQMGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLEHQEGQLEVPEEQMGQLK 20 0 P07476 P07476 IVL Involucrin 0 144.17 9.23E-08 572080000 306030 231170 310050 254070 373950 365400 343330 273970 331340 261390 FALSE TRUE 318112.3007 270871.6492 318130.1577 304324.2877 310386.1126 280541.3877 316418.8975 270297.8803 319415.1381 312604.3659 1.017619507 0.866499892 1.01767663 0.973512596 0.992903959 0.897432724 1.012202426 0.864664444 1.021787195 1 18.2539784 HLEIIYAINQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLEIIYAINQR 11 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 138.22 6.21E-05 1406660000 795810 849480 899660 777310 1023620 1228520 973880 825240 868320 879180 FALSE TRUE 827229.1933 995371.582 923105.8787 931059.598 849625.438 943214.8484 897544.7408 814179.0076 837069.3328 1051438.488 0.786759475 0.946676 0.87794568 0.885510288 0.808060051 0.897070879 0.853635045 0.774347731 0.796118215 1 20.00393302 3.268804137 24.84667717 0.840958553 0.879664024 0 0.07020857 575.5095164 472807.9767 0.018728665 0.025355395 1856.966791 -3.268804137 0.038705472 HLEINPDHPIVETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;; 219.53 1.04E-12 24666578000 4806844.2 4805172.8 5013919.4 4935718 5611026.2 6017139.8 5256309.1 5026530.2 4985966.4 4795130.7 FALSE TRUE 4996622.121 5630423.849 5144586.259 5911988.289 4657265.971 4619750.272 4844305.858 4959157.784 4806522.443 5734644.752 0.87130456 0.981826093 0.897106356 1.030924939 0.812128069 0.80558613 0.844743845 0.864771577 0.838155222 1 22.45127269 3.219143256 24.99983272 0.851399334 0.944458489 0.279842111 0.065259708 263.6543089 339453.9447 0.017483447 0.020925483 1656.316224 -3.219143256 0.093059155 HLEINPDHSIIETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HLEINPDHSIIETLR 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;; 268.2 8.26E-26 43699438000 2198020.8 2559625 2454290 2532686 2799571 3161576 2732159 2437300 2349833 2330871 FALSE TRUE 2284800.358 2999220.683 2518250.814 3033643.731 2323700.921 2427347.888 2518005.238 2404631.98 2265262.969 2787560.545 0.819641519 1.075930239 0.903388742 1.088279046 0.833596574 0.870778535 0.903300645 0.862629507 0.812632742 1 21.41057171 3.206137059 24.99999405 0.874141686 0.974360072 0.209453268 0.086331055 253.6184696 195550.3564 0.022801923 0.027255383 1607.448467 -3.206137059 0.100218386 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 230.54 5.65E-35 127540000 29522 27723 25881 30315 36101 35894 32422 30854 31364 30670 FALSE TRUE 30687.55136 32484.20959 26555.48012 36311.21652 29964.56491 27558.16248 29880.67892 30440.4526 30235.21577 36679.19929 0.836647254 0.885630282 0.723992907 0.989967535 0.816936179 0.751329446 0.814649161 0.829910499 0.824315044 1 15.16267452 -1.364761166 4.494026885 1.000237319 0.830131702 0.357229191 0.068259059 0.00015386 2.17E-05 0.06265304 0.014746951 0.043175645 1.364761166 -0.170105617 HLEQQEGQLEHLEHQEGQLGLPEQQVLQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLEQQEGQLEHLEHQEGQLGLPEQQVLQLK 30 0 P07476 P07476 IVL Involucrin 0 98.326 0.00020967 342840000 137060 95887 147220 108560 153120 177540 148110 120500 163440 117450 FALSE TRUE 142471.2346 112354.8464 151056.6741 130032.844 127092.7171 136309.0256 136500.7512 118884.8946 157557.8263 140462.0788 1.014303902 0.799894515 1.07542673 0.925750531 0.904818711 0.970432923 0.971797886 0.846384274 1.121710768 1 17.09982117 1.230657875 24.99999854 1.060855374 0.935313281 0.274072014 0.079442171 232.1901101 734494.3135 0.065964524 0.017678818 17.00818125 -1.230657875 -0.125542092 HLEQQEGQLEQLEEQEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLEQQEGQLEQLEEQEGQLK 20 0 P07476 P07476 IVL Involucrin 0 ;;; 343.19 1.09E-80 756870000 687670 482819 599490 445149 757400 753850 711330 608910 671550 478327 FALSE TRUE 714819.7426 565739.4074 615113.2019 533198.1436 628657.4185 578779.7622 655574.0959 600748.5574 647381.0467 572046.0175 1.249584335 0.988975345 1.075286224 0.9320896 1.098963019 1.011771334 1.146016362 1.050175229 1.131694002 1 19.12577168 2.265357374 24.99919922 1.08443606 1.05296929 0.01224152 0.087180304 961.1194947 896644.0079 0.028458636 0.023803245 184.2287367 -2.265357374 -0.031466771 HLEQQEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLEQQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 ;;; 179.57 2.09E-06 1617220000 2722920 1632820 1970690 1775870 2512710 4003330 2916490 2059570 2430590 1360300 FALSE TRUE 2830422.984 1913244.133 2022047.8 2127131.786 2085600.452 3073617.279 2687887.893 2031964.833 2343113.541 1626824.74 1.739845058 1.176060387 1.242941388 1.307535921 1.282006844 1.88933522 1.65222954 1.249037332 1.440298689 1 20.63362741 HLEQQEGQLKDLEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLEQQEGQLKDLEQQK 16 1 P07476 P07476 IVL Involucrin 0 ; 325.17 5.82E-59 509200000 637510 339190 542820 309870 723050 613560 574570 479420 629250 331550 FALSE TRUE 662679.3871 397443.244 556966.3351 371161.3611 600146.2193 471069.9886 529533.702 472994.1591 606603.4154 396510.8746 1.671276703 1.002351435 1.404668499 0.936068554 1.513568121 1.188038005 1.335483428 1.192890761 1.529853162 1 18.59700091 -1.218810263 4.485640447 0.999909922 1.287576185 0.141183987 0.222887021 0.000176269 3.07E-05 0.18946107 0.044642459 0.060421254 1.218810263 0.287666263 HLEQQEGQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLEQQEGQPK 10 0 P07476 P07476 IVL Involucrin 0 ;; 141.08 3.81E-05 876470000 1563240 1254110 1571370 1201160 2006490 2109790 1866930 1649420 1863360 1166480 FALSE TRUE 1624957.922 1469493.637 1612321.193 1438745.863 1665427.547 1619823.247 1720595.148 1627312.223 1796298.038 1395029.422 1.164819821 1.053378239 1.155761425 1.031337289 1.193829693 1.161139128 1.233375526 1.166507456 1.287641686 1 20.41186412 3.205615021 24.96361551 1.18431602 1.101787802 0.160811942 0.078862671 272.0632486 206147.5667 0.020753627 0.024807029 1605.517415 -3.205615021 -0.082528218 HLEQQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLEQQEK 7 0 P07476 P07476 IVL Involucrin 0 ;;;;; 130.27 0.0035843 1081950000 2829650 2288590 2697010 2087160 3477420 3386530 3145150 2755280 3128300 2177600 FALSE TRUE 2941366.767 2681637.53 2767296.296 2499994.018 2886329.391 2600059.731 2898624.925 2718349.978 3015713.094 2604259.027 1.129444781 1.029712291 1.062604091 0.959963657 1.108311178 0.998387527 1.113032496 1.043809371 1.157992758 1 21.31244152 2.221953768 24.99364319 1.07932452 1.046630065 0.058670737 0.059934346 709.0469045 1067123.742 0.020853938 0.015440339 166.706974 -2.221953768 -0.032694454 HLFLTSKPMVYLVNLSEKDYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLFLTSKPMVYLVNLSEKDYIR 22 2 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 264.64 1.01E-37 747950000 989160 888950 1189340 872050 1568250 1538170 1298560 1311720 1348240 960340 FALSE TRUE 1028212.801 1041620.247 1220335.177 1044538.887 1301679.425 1180953.329 1196775.474 1294138.539 1299717.106 1148500.236 0.895265641 0.906939515 1.062546736 0.909480777 1.133373232 1.028256932 1.042033285 1.126807377 1.13166464 1 20.13131972 4.385611435 0.564709526 1.089018892 0.801256002 0.473262837 0.064881153 2.183335909 0.699350589 0.034283111 0.39181438 24300.2888 -4.385611435 -0.28776289 HLFNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLFNLK 6 0 Q7LBR1 Q7LBR1 CHMP1B Charged multivesicular body protein 1b 0 103.41 0.03471 167430000 243420 310730 295380 326700 353210 414140 298000 303110 296740 346000 FALSE TRUE 253030.4096 364095.4604 303077.8455 391320.2849 293171.4904 317962.2614 274641.9813 299047.3062 286060.3854 413792.0754 0.611491676 0.879899549 0.732439946 0.945693038 0.708499529 0.768410707 0.66371977 0.722699452 0.691314315 1 18.65854649 HLFS(ph)STENLAAGSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.371)S(0.257)T(0.371)ENLAAGSWK;HLFS(0.373)S(0.254)T(0.373)ENLAAGSWK;HLFS(0.502)S(0.34)T(0.158)ENLAAGSWK 211.29 9.36E-10 3483040000 2639250 2228650 2691570 2938230 3107350 3465790 3638200 2764660 2772170 1813230 TRUE FALSE 2743449.628 2611403.301 2761714.525 3519403.124 2579163.757 2660912.797 3353028.377 2727604.255 2672400.143 2168497.702 1.265138361 1.204245362 1.273561195 1.622968344 1.189378137 1.227076604 1.546244838 1.257831287 1.23237398 1 21.04826448 -1.061974283 7.517792302 0.999999972 1.317711929 0.307351221 0.140907516 6.54E-08 7.92E-09 0.133115267 0.031375567 0.086701321 1.061974283 0.317711957 HLFS(ph)STENLAAGSWKEPAEGGGLSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.359)S(0.293)T(0.348)ENLAAGSWKEPAEGGGLSSDR 169.01 4.00E-12 134260000 81489 91170 105970 78933 131720 129990 89983 91008 109520 98339 TRUE FALSE 84706.24864 106827.7383 108731.6653 94545.71181 109330.2814 99801.79252 82929.89733 89788.18662 105578.3966 117606.6442 0.720250537 0.908347815 0.924536755 0.803914714 0.929626741 0.848606753 0.705146362 0.763461854 0.897724761 1 16.84361004 2.459589653 24.957346 0.807123747 0.863753148 0 0.095870663 671.9867117 956609.4397 0.032060417 0.026828447 288.1307785 -2.459589653 0.056629401 HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 HLFS(0.146)S(0.667)T(0.188)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.129)S(0.742)T(0.129)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.146)S(0.818)T(0.037)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.108)S(0.805)T(0.087)ENLAAGSWKEPAEGGGLSSDR;HLFS(0.005)S(0.67)T(0.325)ENLAAGSWKEPAEGGGLSSDR 339.35 7.82E-96 4209040000 2518570 2627760 2985480 2314980 3901540 3851260 2802150 3063230 3159090 2733750 TRUE FALSE 2618005.088 3079057.339 3063284.061 2772876.134 3238357.624 2956863.231 2582510.161 3022172.412 3045394.968 3269375.972 0.800765991 0.941787474 0.936962921 0.848136207 0.990512456 0.904412113 0.789909201 0.924388152 0.931491206 1 21.64058386 0.956651357 2.199132305 0.998849158 0.893423956 0.237925945 0.059911811 0.503934562 5.339444214 0.055326603 0.015214311 9.050057879 -0.956651357 -0.105425201 HLFTGPVLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLFTGPVLSK 10 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 ; 185.61 1.43E-06 715700000 1347880 1198170 1347710 1146370 1980500 1823850 1672060 1454460 1490030 1342480 FALSE TRUE 1401095.343 1403946.377 1382832.43 1373118.564 1643855.317 1400288.478 1540999.568 1434965.343 1436404.111 1605513.253 0.872677532 0.874453309 0.861302407 0.85525209 1.0238815 0.872174973 0.959817408 0.893773589 0.894669732 1 20.61460314 HLIEQDFPGMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLIEQDFPGMR 11 0 A0A024R571;Q9H4M9;C9JC03;C9JIJ3;C9IZH1 A0A024R571 EHD1 EH domain-containing protein 1 0 122.33 0.001036 0 235520 191460 217660 175200 280540 270440 223990 229910 246470 189920 FALSE TRUE 244818.5115 224341.7656 223332.3984 209854.0371 232853.911 207634.4086 206433.0785 226828.4325 237599.5928 227131.1878 1.077872721 0.987718894 0.983274911 0.923933165 1.025195673 0.914160713 0.908871567 0.998667047 1.046089686 1 17.79316629 4.805120768 2.268838464 0.970820386 1.116928319 0.320613566 0.044320635 0.916489779 4.736762819 0.011196608 0.284648948 63844.09979 -4.805120768 0.146107933 HLILVVNYSCPNHYEDYVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLILVVNYSCPNHYEDYVHR 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 191.64 4.83E-18 216540000 47208 32022 33102 32247 60220 64238 46586 43696 51503 47730 FALSE TRUE 49071.80829 37521.5294 33964.66531 38625.36035 49983.82591 49319.69804 42934.46759 43110.32659 49649.41709 57081.77965 0.859675514 0.657329355 0.595017631 0.676667066 0.8756529 0.864018227 0.752157131 0.755237956 0.869794484 1 15.80074269 3.247770145 24.94267323 0.828678678 0.687029658 0.389475866 0.09219998 217.461815 588960.145 0.02595897 0.034669624 1769.172357 -3.247770145 -0.14164902 HLIPAANTGESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;;; 184.1 1.48E-05 4980460000 7620390 5104220 6405940 6035300 7732830 8369630 8885350 6671880 6962330 3697140 FALSE TRUE 7921248.881 5980830.08 6572884.059 7229064.326 6418406.319 6425910.275 8188893.049 6582454.362 6711757.103 4421523.797 1.791520129 1.352662646 1.486565347 1.634971258 1.451627677 1.45332482 1.852052239 1.488729828 1.51797376 1 22.07611222 0.534249954 2.080016366 1.000071881 1.55934273 0.561876139 0.148585392 2.877276786 11.99631448 0.135540316 0.037083077 3.42176322 -0.534249954 0.55927085 HLIPMNPNDDSLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLIPMNPNDDSLFK 14 0 Q14651;C9JAM8 Q14651 PLS1 Plastin-1 0 137.68 1.98E-05 675050000 777170 578890 738780 530360 942620 907050 862630 761350 831290 520050 FALSE TRUE 807853.2717 678309.8544 758033.2137 635263.625 782393.7891 696401.384 795014.8065 751145.3486 801372.0353 621943.8405 1.298916749 1.090628784 1.218812961 1.021416378 1.257981409 1.119717471 1.278274266 1.207738223 1.288495814 1 19.24642479 2.254401376 24.99071642 1.213000572 1.164148232 5.73E-06 0.106331638 805.2062326 1270308.347 0.033806296 0.028197455 179.6393092 -2.254401376 -0.04885234 HLKEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLKEDLEK 8 1 A0A2R8Y4H4;Q6ZRR7-2;Q6ZRR7 A0A2R8Y4H4 LRRC9 Leucine-rich repeat-containing protein 9 0 76.716 0.021079 103010000 313700 223000 316680 204050 461690 387590 343460 307160 360290 271760 FALSE TRUE 326085.1182 261298.5153 324932.941 244410.481 383212.0987 297578.0965 316538.7077 303043.0226 347323.2333 325006.1688 1.003319781 0.803980171 0.999774688 0.752017975 1.179091769 0.915607533 0.973946768 0.932422371 1.068666587 1 18.31010758 3.253876824 24.99961313 0.99621772 0.891502419 0.252735474 0.100554493 372.2759845 607637.2636 0.026046224 0.035135733 1794.224673 -3.253876824 -0.104715301 HLLGVEDLLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLLGVEDLLQK 11 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 106.29 0.0023512 139010000 282380 413690 316560 235510 523340 528110 285760 325860 277430 435350 FALSE TRUE 293528.5804 484738.0394 324809.8137 282093.1751 434382.8537 405464.4561 263361.3845 321492.3797 267445.3485 520648.4972 0.56377495 0.931027444 0.62385624 0.541811177 0.834311164 0.778768129 0.505833371 0.617484505 0.513677366 1 18.98995018 2.260937161 24.99151259 0.621972296 0.715984223 0.003731875 0.171557375 683.69644 763592.4446 0.056396702 0.047151913 182.3631816 -2.260937161 0.094011927 HLLIGVSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLLIGVSSDR 10 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 107.83 0.0022318 183660000 121660 123880 109450 120570 109400 168400 121490 112860 105760 120490 FALSE TRUE 126463.2307 145155.4263 112302.3569 144418.3861 90804.22708 129291.6521 111967.2963 111347.2963 101953.7183 144097.7086 0.877621386 1.007340282 0.779348666 1.002225417 0.630157328 0.897249883 0.777023434 0.772720798 0.707531849 1 17.13668787 3.260403781 24.9999025 0.788574317 0.91330683 0.212369955 0.111591631 337.0446533 385751.1831 0.02829536 0.03828053 1821.393496 -3.260403781 0.124732513 HLLPVETQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLLPVETQR 9 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 93.598 0.0092909 621590000 613418 690160 699510 734000 837640 924950 716170 681150 707360 673520 FALSE TRUE 637636.2163 808689.6113 717739.8053 879183.0092 695258.252 710144.3803 660034.724 672020.2984 681902.2518 805483.3487 0.791619364 1.003980545 0.891067216 1.091497435 0.863156579 0.881637568 0.819426901 0.834306879 0.846575231 1 19.61949524 3.058784602 24.99998527 0.860274396 0.949012341 0.125843785 0.086002221 118.8792199 50555.99048 0.023353804 0.027913133 1144.944941 -3.058784602 0.088737945 HLLQAPLDDAQEILQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLLQAPLDDAQEILQAR 17 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;;;; 292.28 5.08E-46 1355459000 998807 1058986 1129206 978121 1346475 1344502 988635 1115660 1163483 1087182 FALSE TRUE 1038240.672 1240858.608 1158634.036 1171590.414 1117601.66 1032261.787 911143.2054 1100706.403 1121609.474 1300194.498 0.7985272 0.954363836 0.891123627 0.901088581 0.859564982 0.793928746 0.700774543 0.846570574 0.862647455 1 20.31029602 2.989065901 4.686848624 0.82121899 0.890822191 0.039772308 0.078904963 0.375610022 21.8889409 0.023106536 0.026163013 975.1375962 -2.989065901 0.069603201 HLLQAPVDDAQEILHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLLQAPVDDAQEILHSR 17 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 247.4 5.53E-21 1900260000 749325 852090 836638 965629 986062 1104074 839267 860975 872113 831206 FALSE TRUE 778908.9296 998429.8292 858441.4736 1156627.534 818451.5335 847669.5459 773483.0595 849435.0384 840725.8235 994064.9013 0.783559432 1.004390989 0.863566828 1.163533219 0.823338126 0.852730586 0.778101167 0.85450662 0.845745406 1 19.92298052 HLLQEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLLQEAR 7 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ;; 122.74 0.0043113 435016000 398505 468544 429500 376921 666549 626161 492294 439289 412121 561309 FALSE TRUE 414238.2851 549012.7872 440693.1228 451474.8488 553249.2391 480744.5973 453706.7099 433401.0495 397288.8457 671286.7516 0.617080978 0.817851367 0.656490124 0.672551406 0.824162309 0.716153858 0.675876157 0.645627295 0.591831799 1 19.35656964 -1.273629592 5.284941275 1.000044415 0.693554651 0.615741469 0.073238648 3.80E-05 5.22E-06 0.070313169 0.016570576 0.053256229 1.273629592 -0.306489764 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 HLLTDLPLPPELPGGDLS(0.933)PPDS(0.067)PEPK;HLLTDLPLPPELPGGDLS(1)PPDSPEPK;HLLTDLPLPPELPGGDLS(0.998)PPDS(0.002)PEPK;HLLTDLPLPPELPGGDLS(0.999)PPDS(0.001)PEPK 145.26 1.48E-07 262730000 210570 135305 177459 147929 234744 226173 204470 180854 191228 129268 TRUE FALSE 218883.4662 158542.5812 182083.7273 177188.9147 194842.2987 173647.7484 188443.1071 178429.9479 184345.7416 154595.5896 1.415845476 1.025531075 1.177806739 1.146144694 1.260335429 1.123238696 1.218942323 1.154172305 1.192438556 1 17.23813964 -4.071422211 0.34970893 7.26E-13 1.189592234 0.263965689 0.095656403 278.9027755 4.324334507 204.5512472 0.066147543 8.48E-05 4.071422211 1.189592234 HLLVHAPEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLLVHAPEDK 10 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 177.78 1.32E-06 181950000 246450 153370 191390 171430 253810 264590 282230 201950 213850 99047 FALSE TRUE 256180.0363 179710.1044 196377.7806 205338.3423 210667.4669 203142.9824 260108.0751 199243.1906 206153.5803 118453.3633 2.162707999 1.517138049 1.657848922 1.733495248 1.778484469 1.71496171 2.195869057 1.682039117 1.740377601 1 16.85395964 0.503084783 1.915785846 1.000124617 1.797585207 0.582598912 0.203414582 2.771713173 9.877850819 0.186904792 0.051772656 3.184819199 -0.503084783 0.797460589 HLMEQSS(ph)PGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 HLMEQSSPGFR 11 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 HLMEQS(0.005)S(0.995)PGFR;HLMEQS(0.007)S(0.993)PGFR;HLMEQS(0.013)S(0.987)PGFR;HLMEQS(0.003)S(0.997)PGFR;HLMEQS(0.02)S(0.98)PGFR;HLMEQS(0.038)S(0.962)PGFR;HLMEQS(0.027)S(0.973)PGFR;HLMEQS(0.048)S(0.952)PGFR;HLMEQS(0.005)S(0.995)PGFR;HLMEQS(0.008)S(0.992)PGFR;HLMEQS(0.005)S(0.995)PGFR;HLMEQS(0.012)S(0.988)PGFR;HLMEQS(0.001)S(0.999)PGFR;HLMEQS(0.004)S(0.996)PGFR 186.29 2.64E-06 21132530000 6180780 8352880 8061080 8228800 9120850 10237200 8163130 8334460 7867870 8646430 TRUE FALSE 6424801.967 9787422.164 8271158.367 9856432.079 7570491.175 7859765.446 7523282.54 8222750.196 7584706.896 10340532.41 0.621322163 0.946510467 0.799877418 0.953184197 0.732118122 0.760092917 0.727552726 0.795196018 0.73349288 1 23.30180713 HLMLPDFDLLEDIESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;;;;;;;;;; 262.66 5.11E-27 7630586000 3380133 2134464 2876315 2317699 3775728 3725243 3678774 3032464 3159401 2025587 FALSE TRUE 3513583.261 2501041.588 2951274.132 2776132.945 3133931.103 2860111.77 3390422.081 2991818.78 3045694.775 2422461.99 1.450418324 1.032437907 1.218295331 1.145996493 1.293696708 1.180663218 1.399576998 1.23503229 1.257272472 1 21.2080426 3.232673194 24.96287876 1.248469742 1.199441244 0 0.136221625 610.0995643 2586843.174 0.036244372 0.044377954 1708.729017 -3.232673194 -0.049028497 HLMTLVMDPLQTASVQWFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLMTLVMDPLQTASVQWFER 20 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY6 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 ; 242.59 8.53E-30 486770000 317230 387340 370930 386120 466060 507970 417370 373870 403190 384430 FALSE TRUE 329754.4854 453862.6319 380596.7405 462493.3835 386839.2877 390001.6659 384655.4488 368858.8842 388679.2707 459751.6981 0.717244736 0.987190768 0.827831071 1.005963405 0.841409155 0.848287603 0.836659115 0.80230021 0.845411278 1 18.81049538 HLNEIDLFHCIDPNDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;;;;;;; 248.75 3.76E-21 11215070100 7954209 4915270.8 6135852.8 4995004.4 8206949 7776496.1 7394824 6294680.5 7231197 4571291.6 FALSE TRUE 8268247.313 5759430.324 6295758.165 5983001.362 6811934.74 5970522.735 6815198.372 6210310.604 6970947.633 5466948.666 1.512406247 1.053499983 1.151603673 1.094395014 1.246021347 1.092112456 1.246618322 1.135973828 1.275107571 1 22.3823044 4.748366434 24.95944191 1.15235268 1.512406445 0.624897046 0.085421662 811.391938 2065250.811 0.018447087 0.245772251 56023.00938 -4.748366434 0.360053765 HLNRPTLDDSSEEEHAIEITTQEITQLFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 228.62 1.51E-35 379168000 56981.4 84023.6 81948.4 100080.1 95025.1 115376.4 82692 85186.2 83845.5 77692.4 FALSE TRUE 59231.06967 98453.99969 84084.04263 119875.6451 78872.76744 88581.97965 76210.38496 84044.41833 80827.91683 92914.73827 0.637477657 1.059616607 0.904959151 1.290168248 0.848872514 0.953368446 0.820218475 0.904532692 0.869914917 1 16.50361984 HLPDNECIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLPDNECIEK 10 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;; 155.26 1.30E-05 921490000 2646460 2045250 2385870 2238980 3174970 3411350 3034150 2613270 2754290 1776210 FALSE TRUE 2750944.284 2396505.778 2448047.732 2681843.561 2635289.733 2619115.662 2796325.395 2578243.39 2655163.641 2124224.342 1.295034724 1.128179228 1.152443122 1.262504863 1.24058918 1.232975073 1.316398339 1.213734039 1.249945022 1 21.01850471 -1.200675659 5.486694295 0.999990512 1.230584301 0.619094559 0.054675638 6.39E-06 9.31E-07 0.053311905 0.01256522 0.062997649 1.200675659 0.230593789 HLPDYRDPPDGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLPDYRDPPDGSGR 14 1 Q96HQ2;Q96HQ2-2 Q96HQ2 CDKN2AIPNL CDKN2AIP N-terminal-like protein 0 ; 72.898 0.022437 250290000 75799 92148 77846 100343 122673 137321 116243 91492 76190 118337 FALSE TRUE 78791.60305 107973.7022 79874.73071 120190.5459 101821.0873 105430.2789 107131.5699 90265.69939 73447.93678 141522.8695 0.556741136 0.762941725 0.564394511 0.849265892 0.719467374 0.744969907 0.756991222 0.637817052 0.518982812 1 17.11067568 4.750539247 23.40738087 0.713900547 0.556740898 0.125508555 0.130984157 1620.304251 3166081.585 0.028982253 0.449279111 56303.99969 -4.750539247 -0.157159649 HLPHFKPWLHPEQSPLPSLALS(ph)ELSVQHADSLENIDESAVAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQS(0.001)PLPS(0.008)LALS(0.461)ELS(0.461)VQHADS(0.068)LENIDESAVAESR 97.873 1.31E-05 133950000 47700 61356 68455 69748 79989 79564 77574 75254 70767 70295 TRUE FALSE 49583.23283 71893.41572 70238.99354 83543.94622 66392.49835 61086.4668 71493.54718 74245.34322 68220.10949 84067.95937 0.58979941 0.85518212 0.835502539 0.993766791 0.789747947 0.726631968 0.850425628 0.883158623 0.811487635 1 16.35926843 -4.999999978 0.023520669 2.095418674 8.45E-13 0.28847452 0.096118233 3545.652368 6.303356236 398.4068662 196.1341394 1.00E-05 4.999999978 -2.095418674 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 44 1 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 HLPHFKPWLHPEQSPLPSLALSELSVQHADS(0.999)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELSVQHADS(1)LENIDESAVAESR;HLPHFKPWLHPEQSPLPS(0.002)LALS(0.014)ELS(0.106)VQHADS(0.878)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELS(0.002)VQHADS(0.998)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALSELS(0.001)VQHADS(0.998)LENIDESAVAESR;HLPHFKPWLHPEQSPLPSLALS(0.004)ELS(0.025)VQHADS(0.971)LENIDESAVAESR 346.52 1.45E-154 56302420000 1587342 2093482 2114594 2183056 2909330 2701870 2528324 2308891 2411580 2054814 TRUE FALSE 1650011.488 2453021.248 2169702.057 2614857.961 2414803.126 2074401.64 2330147.358 2277944.093 2324787.707 2457415.462 0.671441811 0.998211856 0.882920325 1.064068328 0.982659694 0.844139574 0.948210587 0.926967429 0.946029576 1 21.22871036 4.744695725 24.87688699 0.949798368 0.67144168 0.671908139 0.059309355 379.0306949 1536862.809 0.013854582 0.127658601 55551.49171 -4.744695725 -0.278356689 HLPNLLDETQIFSYFSQFGTVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLPNLLDETQIFSYFSQFGTVTR 23 0 Q9BYG3 Q9BYG3 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 0 ; 165.13 1.35E-11 177467000 136311 143139 171634 138629 160777 173457 174867 156834 161157 151313 FALSE TRUE 141692.6635 167722.0098 176106.923 166049.4024 133448.183 133174.2405 161160.4676 154731.8968 155356.9911 180959.8853 0.783005931 0.926846353 0.97318211 0.91760338 0.737446218 0.735932388 0.890586703 0.855061864 0.858516189 1 17.46531039 0.01863286 1.473356283 1.0001523 0.854990656 0.252244108 0.075824422 32.65790646 46.44373392 0.093008893 0.022592439 1.043837416 -0.01863286 -0.145161644 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR;HLPS(1)PPLTQEVDLHSIAGPPVPPR 281.98 4.44E-52 682140000 165630 260113 212425 256013 224909 299639 194436 219283 199980 285842 TRUE FALSE 172169.2003 304785.3844 217960.97 306651.6073 186679.0485 230052.3833 179195.5983 216343.8701 192782.7589 341847.2671 0.503643635 0.891583504 0.637597521 0.897042734 0.546089048 0.672968327 0.524197838 0.632867046 0.563944128 1 18.38299237 -1.034976589 4.538983977 1.000014324 0.656209635 0.381950857 0.132633536 16582700.07 3781178.516 2362.288106 0.029599978 0.092262116 1.034976589 -0.34380469 HLPS(ph)PPTLDSIITEYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 HLPS(0.998)PPT(0.002)LDSIITEYLR;HLPS(0.998)PPT(0.002)LDSIITEYLR;HLPS(0.994)PPT(0.006)LDSIITEYLR;HLPS(0.829)PPT(0.171)LDSIITEYLR;HLPS(0.944)PPT(0.056)LDSIITEYLR;HLPS(0.995)PPT(0.005)LDSIITEYLR 249.5 3.08E-21 3641724000 446087 506806 513323 455624 585679 627264 544318 495487 573339 501048 TRUE FALSE 463698.8592 593845.9881 526700.6191 545745.0673 486125.4928 481591.4423 501652.9328 488845.8072 552704.6414 599218.7625 0.773839019 0.991033701 0.878978851 0.91076098 0.811265473 0.80369887 0.83717828 0.815805242 0.922375393 1 19.19272327 5.046856438 14.65419136 0.871616057 0.298648673 0.166449866 0.068892527 1059402.965 9837884.736 0.016275312 16482286.06 111392.6248 -5.046856438 -0.572967384 HLPSTEPDPHVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 105.65 0.00083037 746120000 473981 694692 611536 608123 721220 820153 611899 671268 617128 686280 FALSE TRUE 492694.1359 813999.947 627473.1305 728407.9143 598627.282 629684.8953 563936.7575 662270.7504 594917.6838 820743.4264 0.600302263 0.991783694 0.764518009 0.887497714 0.729372009 0.76721284 0.687104812 0.806915693 0.724852207 1 19.64657176 -1.329617103 3.203687193 1.001537128 0.779639123 0.306150177 0.101989492 32363284.66 42853595.62 477987.7431 0.022410409 0.04681477 1.329617103 -0.221898005 HLQDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLQDIK 6 0 Q99733;Q99733-2;C9JZI7;H0YCI4 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 0 ; 155.73 0.0098399 481390000 1312260 965930 1178860 979600 1552960 1616900 1401160 1208250 1313720 975070 FALSE TRUE 1364069.038 1131820.964 1209582.06 1173361.956 1288988.414 1241399.479 1291333.418 1192055.385 1266439.474 1166116.298 1.169753858 0.970590125 1.037273952 1.006213496 1.105368664 1.064558897 1.107379616 1.022243997 1.086031879 1 20.15328025 7.014112337 6.394666149 1.055498409 1.060195049 0 0.057796085 0 0 0.011764697 0 10330285.8 -7.014112337 0.004696641 HLQDLMEGLTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLQDLMEGLTAK 12 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 70.622 0.044029 0 401030 270210 363610 234600 432640 386090 336120 322980 375660 268290 FALSE TRUE 416862.9741 316616.4656 373085.9753 281003.1798 359100.0073 296426.4488 309774.0361 318650.9814 362140.07 320856.2888 1.299220207 0.986785912 1.162782181 0.875791404 1.119192673 0.923860492 0.965460385 0.993126806 1.128667515 1 18.29156773 7.175114427 1.306302685 1.007916473 199.9999985 0.458482848 0.089747181 876.3866996 2.82200353 0.022754838 521112.7505 14966299.34 -7.175114427 198.992082 HLQDLSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLQDLSGR 8 0 P30533 P30533 LRPAP1 Alpha-2-macroglobulin receptor-associated protein 0 ; 154.49 0.0004242 163850000 90560 118666 111027 120764 144723 145429 111211 102487 100153 134621 FALSE TRUE 94135.37873 139045.9624 113920.4548 144650.7588 120123.0362 111655.3187 102493.9912 101113.3294 96548.51309 160997.4075 0.584701209 0.863653425 0.707591859 0.898466385 0.746117829 0.693522464 0.636618892 0.628043215 0.599689862 1 17.29667793 2.762230476 3.948207681 0.676746059 0.772053221 0 0.133583416 0.517082607 18.38564615 0.040086197 0.040891504 578.4029188 -2.762230476 0.095307163 HLQEAEQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLQEAEQTK 9 0 Q96P70 Q96P70 IPO9 Importin-9 0 ;; 175.93 5.35E-05 650880000 687130 505840 697530 521400 860020 853400 770840 698650 699350 485340 FALSE TRUE 714258.423 592714.0851 715708.2048 624531.3638 713834.1076 655210.7834 710419.5466 689285.7395 674180.5301 580433.0806 1.230561191 1.021158347 1.23305895 1.075974793 1.229830159 1.128830877 1.223947377 1.187536966 1.161512933 1 19.14677022 4.180272689 24.99999468 1.165382312 1.125839703 0.007222446 0.084424691 251.687241 107948.7343 0.018841988 0.040703398 15145.11895 -4.180272689 -0.039542609 HLQELVGQETLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLQELVGQETLPR 13 0 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 130.24 2.75E-05 0 84593 97669 91705 102550 85900 121170 94511 96154 86633 103640 FALSE TRUE 87932.79696 114442.891 94094.90764 122834.0839 71298.74868 93030.10385 87102.98086 94865.21291 83515.09525 123946.2737 0.709442844 0.923326596 0.759158826 0.99102684 0.575239146 0.750567977 0.702747878 0.765373658 0.673800775 1 16.91935537 5.056593689 15.35117969 0.78055695 0.183933404 0.027133113 0.131920538 5722326.652 38936575.76 0.029687165 103632375.7 113918.3507 -5.056593689 -0.596623547 HLQGGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLQGGEK 7 0 Q8N163-2;Q8N163;E5RHH8;E5RGU7;E5RFJ3;H0YC58 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;; 159.2 0.0013924 270282000 858240 638760 843700 600980 990830 979980 958800 882460 918310 663290 FALSE TRUE 892123.9779 748462.0611 865687.5151 719852.0503 822409.0705 752394.4967 883646.7506 870632.0671 885260.2025 793248.976 1.124645609 0.943539902 1.091318793 0.907473028 1.03676033 0.948497281 1.113958892 1.097552084 1.115992871 1 19.59741423 2.223258869 24.99233691 1.091669385 1.00617258 0.203171384 0.06981303 308.8761487 504483.885 0.02388291 0.017704239 167.2086993 -2.223258869 -0.085496805 HLQIEIEGLIDQMIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLQIEIEGLIDQMIDK 16 0 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 173.34 4.26E-09 161063000 236274 183871 231514 194616 299160 304600 282314 216421 270257 188979 FALSE TRUE 245602.28 215449.4139 237547.445 233110.4639 248308.8901 233861.2663 260185.491 213520.2305 260530.5034 226005.8168 1.086707782 0.953291455 1.051067837 1.031435682 1.098683625 1.034757731 1.151233604 0.944755465 1.152760168 1 17.78600038 1.211975641 24.99982948 1.076379744 1.042781756 0.034700577 0.06809084 968.639199 910858.4696 0.060092227 0.015044883 16.29204648 -1.211975641 -0.033597987 HLQLAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 17158370000 2230660 2731210 1990220 1664383 7409690 4120660 2590540 1963190 2023270 7604300 FALSE TRUE 2318728.179 3200274.072 2042086.768 1993592.99 6150193.54 3163699.164 2387486.706 1936876.649 1950452.908 9094216.992 0.254967325 0.351902102 0.224547838 0.219215463 0.676275214 0.347880325 0.262528012 0.212978935 0.21447178 1 23.116518 -1.102326973 4.518097355 1.000052174 0.306676702 0.709762589 0.132907765 38288979.17 9341764.91 23111.51831 0.032314619 0.079008356 1.102326973 -0.693375472 HLQLAIRGDEELDSLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 76.85 0.011435 29894000 119846 103965 127689 74362 182281 141250 104080 124134 135787 125972 FALSE TRUE 124577.6126 121820.18 131016.6802 89070.58165 151296.9407 108446.8282 95921.93764 122470.1868 130900.0524 150653.8015 0.82691317 0.808610064 0.869653994 0.591226911 1.004268988 0.719841299 0.636704396 0.812924636 0.86887985 1 17.20087755 0.969010174 2.474249124 0.998488154 0.780094983 0.270207551 0.11040766 0.385050703 5.371859915 0.100246777 0.027092757 9.311296875 -0.969010174 -0.218393171 HLQQGSES(ph)PMMIGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLQQGSESPMMIGELR 16 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 HLQQGSES(1)PMMIGELR;HLQQGSES(1)PMMIGELR 235.21 6.90E-20 237430000 234737 281875 297107 262633 364750 342440 300546 291920 310620 257727 TRUE FALSE 244004.598 330284.8386 304849.8525 314581.0235 302749.9253 262913.4997 276988.4192 288007.2899 299440.8469 308223.6712 0.791647822 1.071575189 0.989053992 1.020625776 0.982240994 0.852995809 0.898660438 0.93441003 0.97150503 1 18.23361814 HLS(ph)ASTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLSASTPK 8 0 I3L2J0 I3L2J0 CIC 1 HLS(0.999)AS(0.001)TPK;HLS(0.998)AS(0.002)TPK 135.87 0.000855 653880000 744690 531750 729030 548460 1006180 965100 826390 763760 730370 503870 TRUE FALSE 774090.9362 623073.9261 748029.1207 656943.751 835149.883 740970.1512 761615.3924 753523.0465 704084.1264 602593.6793 1.284598499 1.033986826 1.241349099 1.090193564 1.385925395 1.229634788 1.263895422 1.25046623 1.168422688 1 19.20082601 5.073958179 21.40388213 1.202203299 4.440176161 0.047587452 0.111823157 2440.292805 792235.1958 0.024457655 46215.4593 118565.4567 -5.073958179 3.237972862 HLS(ph)ESSGKPLSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLSESSGKPLSTK 13 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 HLS(0.976)ES(0.019)S(0.005)GKPLSTK;HLS(0.877)ES(0.098)S(0.025)GKPLSTK;HLS(0.891)ES(0.083)S(0.026)GKPLSTK 132.64 7.05E-05 1950530000 2276560 1521250 2386800 1726470 4266500 3603570 3421640 3120640 3492150 2250750 TRUE FALSE 2366440.347 1782512.854 2449001.969 2067960.613 3541281.854 2766695.48 3153442.916 3078812.925 3366468.204 2691741.369 0.879148485 0.662215499 0.909820682 0.768261259 1.315609997 1.027845956 1.171525226 1.143799683 1.250665551 1 21.36010837 3.251879655 24.99999938 1.153316921 0.802169473 0.717205447 0.106648256 112.075831 210366.5133 0.027202455 0.036620767 1785.992601 -3.251879655 -0.351147447 HLSDAIVEVEEALIQIHDPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLSDAIVEVEEALIQIHDPELR 22 0 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 0 ;;; 209.67 3.13E-23 141410000 9501 53956 51334.7 63614 45601.3 78042 45855.3 59011 44146.2 59836 FALSE TRUE 9876.106816 63222.52328 52672.52445 76196.65933 37850.00731 59917.92824 42261.04177 58220.05407 42557.38689 71559.71857 0.138012097 0.883493179 0.736063885 1.064798197 0.528928957 0.837313637 0.590570262 0.813586962 0.59471149 1 16.12686009 -4.999915779 0.036071693 2.089290634 1.33E-07 0.145701399 0.236451422 2448.004226 6.619357071 326.1667872 110.3372066 1.00E-05 4.999915779 -2.089290501 HLSNVS(ph)STGSIDMVDSPQLATLADEVSASLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLSNVSSTGSIDMVDSPQLATLADEVSASLAK 32 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 HLS(0.067)NVS(0.264)S(0.223)T(0.223)GS(0.223)IDMVDS(0.002)PQLATLADEVSASLAK 78.172 3.20E-07 0 6053.1 10572 8847.5 11035 11812 15969 9899.9 11534 11579 12612 TRUE FALSE 6292.081062 12387.65876 9078.073118 13217.69006 9804.200459 12260.44176 9123.919969 11379.4056 11162.27405 15083.07993 0.417161554 0.821295042 0.601871313 0.876325666 0.650013161 0.812860624 0.604910934 0.754448405 0.740052702 1 13.88064343 -5 0.174553983 2.159930492 0.638631972 0.377267679 0.123895611 139.7135602 1.331639948 56.28601702 0.380821869 1.00E-05 5 -1.52129852 SSS(ph)PGKPQAVSSLNSSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.147)S(0.147)S(0.706)PGKPQAVSSLNSSHSR;S(0.037)S(0.026)S(0.937)PGKPQAVSSLNSSHSR 197.39 4.78E-16 609460000 114758 215718 271524 217947 294581 330844 295733 314598 266334 206825 TRUE FALSE 119288.7345 252765.8884 278600.1385 261056.2661 244508.2268 254010.495 272552.6747 310381.3284 256748.6914 247348.3988 0.48227009 1.021902263 1.126347047 1.055419268 0.988517524 1.026934058 1.101897874 1.254834597 1.038004259 1 17.91618504 4.737546547 3.727106945 1.08763074 0.41872577 0.850545018 0.073783813 0.101180974 2.668956163 0.020212387 0.186824441 54644.51137 -4.737546547 -0.668904969 down HLSPDGQYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 HLSPDGQYVPR 11 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;;;;;;;;;;; 226.4 4.76E-12 31062270000 1188507 7802495 5847193 8179470 5388997 8594222 5403289 6669286 4624771 6455920 FALSE TRUE 1235430.174 9142512.821 5999575.653 9797344.753 4472977.215 6598344.187 4979765.089 6579895.13 4458326.395 7720833.918 0.160012531 1.184135408 0.777063167 1.268949035 0.579338613 0.85461548 0.644977621 0.852225964 0.577441044 1 22.88032525 HLSPNDNENDTSYVIES(ph)DEDLEMEMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLSPNDNENDTSYVIESDEDLEMEMLK 27 0 Q14191 Q14191 WRN Werner syndrome ATP-dependent helicase 1 HLS(0.001)PNDNENDT(0.003)S(0.003)Y(0.003)VIES(0.99)DEDLEMEMLK 47.331 0.081839 31922000 9397.4 11939 14572 11178 14488 16058 11642 14981 13131 13141 TRUE FALSE 9768.416608 13989.43038 14951.75829 13388.97504 12025.33493 12328.77286 10729.46962 14780.2042 12658.41788 15715.72735 0.621569488 0.890154815 0.951388247 0.851947526 0.765178389 0.784486304 0.682721797 0.94047217 0.80546179 1 13.93992142 0.533967316 0.969442049 0.999112352 0.811391611 0.244342861 0.099852379 2.365672954 3.32134019 0.097158591 0.031042921 3.419537071 -0.533967316 -0.187720742 HLSVGAPGVVT(ph)ITHHKSPAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLSVGAPGVVTITHHKSPAAAR 22 1 Q9BXB5 Q9BXB5 OSBPL10 Oxysterol-binding protein-related protein 10 1 HLSVGAPGVVT(0.365)IT(0.365)HHKS(0.271)PAAAR 66.447 0.012122 437160000 60985 134620 146940 125980 180770 218060 107240 148390 139700 188670 TRUE FALSE 63392.73489 157739.9378 150769.3771 150898.468 150042.78 167418.8697 98834.24858 146401.0748 134672.2243 225636.2742 0.280950991 0.699089445 0.668196537 0.668768657 0.664976323 0.741985615 0.438024644 0.648836608 0.59685538 1 17.78363949 -2.298585516 1.931787813 2.473608823 0.60958876 0.449612006 0.132167996 3805758.762 497301.6051 24441844.4 0.03050855 0.005028222 2.298585516 -1.864020063 HLSVNDLPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLSVNDLPVGR 11 0 P30048-2;P30048 P30048-2 PRDX3 "Thioredoxin-dependent peroxide reductase, mitochondrial" 0 ; 193.22 1.05E-06 609510000 47735 353060 271580 388980 222697 502810 224600 320540 242400 371280 FALSE TRUE 49619.61466 413695.3086 278657.5979 465919.083 184843.0435 386039.9977 206995.2651 316243.6856 233676.0714 444025.2074 0.111749544 0.931693295 0.627571573 1.049307731 0.416289527 0.869410095 0.466179085 0.712220118 0.52626758 1 18.76028206 -2.409346343 2.223213311 3.82171185 0.652948799 0.145939199 0.261848583 14769794.58 914344.6851 211147465.2 0.056769263 0.003896311 2.409346343 -3.168763051 HLT(ph)PEPDIVASTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLTPEPDIVASTK 13 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 HLT(1)PEPDIVASTK;HLT(1)PEPDIVASTK 168.1 0.00011324 272590000 855260 587860 784040 610920 1094480 1102200 969800 824130 844610 469620 TRUE FALSE 889026.3252 688820.3821 804472.7265 731758.1526 908440.6805 846230.754 893784.5419 813083.8854 814212.6511 561633.0476 1.582930935 1.226459848 1.432381392 1.302911493 1.617498622 1.506732479 1.591403045 1.44771375 1.449723542 1 19.0992683 0.477315373 2.947281348 1.000000893 1.461065932 0.579547157 0.118085638 13.96748605 77.56667817 0.112747428 0.029511443 3.001341219 -0.477315373 0.461065039 HLTASEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLTASEAK 8 0 P39748;P39748-2 P39748 FEN1 Flap endonuclease 1 0 67.464 0.059028 157610000 421570 333970 422300 324890 540810 506670 470620 393660 393500 345170 FALSE TRUE 438213.9091 391326.7496 433305.4849 389152.2723 448883.3094 389003.5712 433731.5747 388383.6316 379338.0119 412799.4528 1.061566109 0.947982724 1.049675531 0.942715088 1.087412559 0.942354861 1.050707727 0.940853068 0.9189402 1 18.65508153 1.652031549 8.559223465 0.947428978 1.008208438 0.196088685 0.053433542 0.164518606 21.76670627 0.023461044 0.012278691 44.87779897 -1.652031549 0.06077946 HLTDAYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLTDAYFK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 132.57 0.0017451 3527270000 4361280 5677580 6904730 5726490 8869310 8394840 7816180 7125970 6931830 6430370 FALSE TRUE 4533466.702 6652660.2 7084672.936 6859172.63 7361707.854 6445265.635 7203527.388 7030458.028 6682354.792 7690277.885 0.589506227 0.865074097 0.921250577 0.891927799 0.957274622 0.838105688 0.936705734 0.914200778 0.868935413 1 22.8746043 4.744275336 3.066670462 0.911843183 0.536364877 0.838415049 0.042741725 0.126240023 1.769680151 0.00944133 0.115969876 55497.74483 -4.744275336 -0.375478306 HLTGEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 HLTGEFEK 8 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;;;; 223.83 4.35E-06 9312160000 8343720 8620320 10642590 9332950 12551300 12516790 12748350 10897150 10919400 7129700 FALSE TRUE 8673136.508 10100792.9 10919944.64 11178979.65 10417834.51 9609955.216 11749101.02 10751091.53 10526412.93 8526628.209 1.017182443 1.18461749 1.280687321 1.311066858 1.221800019 1.127052216 1.377930493 1.260884287 1.234534058 1 23.02354392 4.684292189 2.968724421 1.243785987 0.993107792 0.27248208 0.099043126 0.36842032 4.999854817 0.022688025 0.204570711 48338.39089 -4.684292189 -0.250678195 HLTGEFEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 250.12 2.00E-11 1148250000 1560400 1069130 1678430 1028790 2299460 2002450 1855260 1666980 1752370 1102040 FALSE TRUE 1622005.797 1252744.761 1722171.265 1232281.591 1908598.611 1537411.335 1709839.873 1644636.86 1689302.546 1317963.638 1.230690855 0.95051542 1.306691031 0.934989066 1.448142085 1.166505122 1.297334633 1.24786209 1.281752013 1 20.32987914 4.22290355 24.99352668 1.222170707 1.090603022 0.082765983 0.155642967 441.4191944 704644.3692 0.035608373 0.077334994 16707.19533 -4.22290355 -0.131567685 HLTSNSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HLTSNSPR 8 0 P14923 P14923 JUP Junction plakoglobin 0 ;;; 101.64 0.0052489 120058000 16062.1 73825 46482.3 84201 57275.7 74349 54716.8 58581 42949.4 89126 FALSE TRUE 16696.24411 86503.86947 47693.66692 100855.7065 47539.99697 57082.57152 50427.95424 57795.81751 41403.65948 106588.5333 0.156642029 0.81156825 0.447455889 0.946215352 0.446014177 0.535541392 0.473108623 0.542232975 0.388443843 1 16.70169272 -1.200510216 4.184157361 1.000191161 0.54149189 0.316103017 0.207592493 28002032.53 8034338.56 52803.88575 0.044333726 0.063021652 1.200510216 -0.458699272 HLTYENVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HLTYENVER 9 0 H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 H3BMH2 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 ;;;; 202.05 2.05E-05 5445480000 1266270 2891090 2688940 3318000 2719840 3606910 2456690 2864270 2531020 2792730 FALSE TRUE 1316263.317 3387612.218 2759015.985 3974290.497 2257522.568 2769259.816 2264128.218 2825879.146 2439929.085 3339911.973 0.3941012 1.014281887 0.826074462 1.189938695 0.675922775 0.829141558 0.677900566 0.8460939 0.730536943 1 21.67137865 HLVQQEGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLVQQEGQLK 10 0 P07476 P07476 IVL Involucrin 0 155.06 1.34E-05 195260000 352040 284960 317610 255440 457550 466580 379070 340790 381480 296080 FALSE TRUE 365938.811 333899.6633 325887.1775 305965.2696 379775.8144 358223.8661 349357.5029 336222.2675 367750.6093 354091.2072 1.033459187 0.942976432 0.920348122 0.864086042 1.072536699 1.011671171 0.986631398 0.949535771 1.038575943 1 18.43376149 3.236185251 24.99996993 1.001923201 0.938995288 0.316370318 0.049300206 88.59402823 932428.074 0.014734916 0.018427904 1722.603207 -3.236185251 -0.062927913 HLVYESDQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLVYESDQNK 10 0 O43852;O43852-3;O43852-15;O43852-5;H0Y875;O43852-9;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 160.36 7.40E-06 271730000 274100 366530 304040 333380 381200 472520 353790 326220 281560 387410 FALSE TRUE 284921.6797 429478.6763 311963.5322 399321.569 316403.7602 362784.3911 326059.0153 321847.5545 271426.7106 463315.5721 0.614962451 0.926967929 0.673328399 0.861878152 0.682911992 0.78301791 0.703751471 0.694661639 0.585835502 1 18.82163565 -1.329982268 5.963011647 1.000027229 0.730620334 0.402558273 0.100219413 3.35E-05 3.77E-06 0.089627151 0.02112319 0.046775424 1.329982268 -0.269406895 HLWDYTFGPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HLWDYTFGPEK 11 0 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ; 171.62 1.43E-05 1288020000 1219510 1101320 1026250 771560 2594900 1755070 1345340 1065590 1196630 1797220 FALSE TRUE 1267657.196 1290463.143 1052994.918 924172.2651 2153819.825 1347481.591 1239888.735 1051307.509 1153563.52 2149350.849 0.589786073 0.600396693 0.489912998 0.429977389 1.002079221 0.626924911 0.576866609 0.489127919 0.536703219 1 21.03546957 HLYDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 82.263 0.059704 2156140000 7009490 5146670 6342080 5156240 8390100 8600300 7825600 6506060 7146600 4846820 FALSE TRUE 7286230.078 6030570.537 6507359.815 6176128.882 6963953.799 6603010.664 7212209.024 6418856.907 6889395.262 5796461.581 1.257013434 1.040388253 1.122643482 1.065499839 1.201414639 1.139145075 1.244243393 1.107375046 1.188551872 1 22.46674105 3.234989118 24.99725679 1.155278985 1.115690488 0.014718223 0.081256974 297.7730411 2084146.162 0.021456599 0.02663019 1717.865341 -3.234989118 -0.039588497 HLYISSS(ph)NPDLITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HLYISSSNPDLITR 14 0 Q16825 Q16825 PTPN21 Tyrosine-protein phosphatase non-receptor type 21 1 HLYISS(0.493)S(0.506)NPDLITR 145.8 5.46E-06 68050000 34823 45396 51972 42690 44906 54582 40734 35132 41090 47783 TRUE FALSE 36197.83893 53192.40987 53326.43302 51133.95458 37272.89416 41906.1577 37541.16264 34661.113 39611.17893 57145.16399 0.63343661 0.930829595 0.933174906 0.894808082 0.652249317 0.733328155 0.656943826 0.606544991 0.693167648 1 15.80234379 3.23996417 24.99607257 0.693718547 0.860053736 0.155634585 0.129987692 48.11231385 856824.9972 0.035067242 0.045016769 1737.657462 -3.23996417 0.166335189 HLYTLDGGDIINALCFSPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 5591629000 2323023 2469741 2608822 2511573 3007556 3350417 2522579 2595358 2829427 2461920 FALSE TRUE 2414737.742 2893899.805 2676810.044 3008354.643 2496332.705 2572333.428 2324852.666 2560571.471 2727596.475 2944286.088 0.820143719 0.982886757 0.909154194 1.021760302 0.847856707 0.873669661 0.78961507 0.869674819 0.926403343 1 21.48948643 3.160611033 24.99999683 0.870633406 0.935307584 0.082919138 0.071150361 58.93814988 18899.71741 0.019541104 0.023356095 1447.47487 -3.160611033 0.064674178 HMEDYHTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HMEDYHTDR 9 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 84.817 0.010664 52312000 22817 7990.8 10768 6406.5 9422.2 31853 9720.1 9483.2 6087.2 10660 FALSE TRUE 23717.83278 9363.15774 11048.62293 7673.686579 7820.61781 24455.62349 8958.213163 9356.093215 5868.122861 12748.6229 1.860423119 0.734444639 0.866652266 0.601922783 0.613448046 1.918295307 0.702680849 0.733890498 0.460294646 1 13.6380538 4.742573433 24.04006787 0.846586839 1.860423814 0.383683673 0.384956943 249.7398593 1496042.211 0.092149238 0.696892978 55280.68714 -4.742573433 1.013836975 HMGIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HMGIGK 6 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;;; 84.566 0.055705 2327690000 7223670 6313730 7475130 6341850 9383380 9335640 8762100 7841780 8089500 6018050 FALSE TRUE 7508866.069 7398064.013 7669938.029 7596249.001 7788396.419 7167579.093 8075303.707 7736673.766 7798360.475 7197171.675 1.0433079 1.027912678 1.065687797 1.055449188 1.082146817 0.995888304 1.122010711 1.074960292 1.083531257 1 22.77899864 2.230032914 24.99993381 1.0778509 1.047380659 0.088665303 0.03564754 355.3993221 1041883.149 0.012384092 0.009287357 169.8372363 -2.230032914 -0.030470242 HMIMANPQMQQLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HMIMANPQMQQLMER 15 0 Q9NRR5 Q9NRR5 UBQLN4 Ubiquilin-4 0 140.74 1.76E-05 0 85016 136790 138520 114540 116770 188790 106370 122320 105090 173110 FALSE TRUE 88372.49733 160282.6184 142129.945 137195.6701 96921.47711 144946.3836 98032.44145 120680.5005 101307.8314 207027.5901 0.426863382 0.774208975 0.686526588 0.662692688 0.468157298 0.700130758 0.47352356 0.582919892 0.489344591 1 17.65946352 -1.900041513 3.137019398 1.198996359 0.590344571 0.551457435 0.112206709 5201937.031 18175909.72 6644804.853 0.025157829 0.012588051 1.900041513 -0.608651787 HMLPSGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HMLPSGFR 8 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ; 91.318 0.012572 1013570000 1154270 1365330 1269700 1303830 2007320 1927870 1703250 1419570 1322480 1734290 FALSE TRUE 1199841.471 1599814.807 1302789.425 1561723.682 1666116.463 1480151.41 1569744.814 1400542.986 1274884.203 2074090.921 0.578490296 0.771333017 0.628125514 0.752967802 0.803299627 0.713638633 0.756835102 0.675256312 0.61467132 1 20.98404771 -2.280997015 2.428576565 2.420459556 0.704905859 0.618117856 0.070763159 3330345.203 917738.333 25749365.99 0.016538141 0.00523604 2.280997015 -1.715553697 HMLPSGFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HMLPSGFRK 9 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 56.258 0.079921 849720000 969080 912300 997650 823370 1858800 1356600 987450 1012700 1119100 1410800 FALSE TRUE 1007340.027 1068980.428 1023649.579 986230.1285 1542841.84 1041550.209 910051.0888 999126.4129 1078823.81 1687219.249 0.597041569 0.633575292 0.606708096 0.584529918 0.914428781 0.617317643 0.539379271 0.592173432 0.639409378 1 20.68621603 -1.094058082 3.151044747 1.00050859 0.633882006 0.558463624 0.097063462 9151925.627 13693408.44 48586.29851 0.024463171 0.080527074 1.094058082 -0.366626585 HMLPTVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HMLPTVLR 8 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 109.01 0.0037001 743600000 483060 527940 534890 514470 969670 826950 642110 574680 566830 921880 FALSE TRUE 502131.5818 618609.5882 548829.6728 616230.6305 804845.8398 634903.395 591779.7404 566977.3546 546429.899 1102504.736 0.45544619 0.561094722 0.497802554 0.558936947 0.730015767 0.575873622 0.536759364 0.514262965 0.495625897 1 20.07235342 -1.127866521 4.744022843 1.00003281 0.54977706 0.788885235 0.070243674 2.54E-05 4.66E-06 0.070754725 0.016675836 0.07449609 1.127866521 -0.45025575 HMNLILCDCDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HMNLILCDCDEFR 13 0 P14678-2;P14678;P14678-3;J3QLE5;P63162;P63162-2;J3KRY3;S4R3P3 P14678-2;S4R3P3 SNRPB;SNRPN Small nuclear ribonucleoprotein-associated proteins B and B;Small nuclear ribonucleoprotein-associated protein N 0 89.624 0.0073643 161120000 380400 466180 500150 490210 546360 610710 523830 481220 459120 608780 FALSE TRUE 395418.4857 546242.7886 513184.3199 587172.0749 453489.9224 468881.8579 482770.8358 474770.033 442596.3609 728058.7852 0.543113405 0.750272917 0.704866599 0.806489925 0.622875421 0.644016483 0.663093208 0.652103982 0.607912946 1 19.47369542 -1.334965309 3.282012165 1.002160095 0.670490438 0.669086207 0.070387867 15883654.92 22641592.37 334571.2457 0.016651026 0.046241796 1.334965309 -0.331669658 HNAQGQGNGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNAQGQGNGLR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5;E9PP44 P35813 PPM1A Protein phosphatase 1A 0 77.379 0.020619 0 7492.2 8242.9 8263.7 10276 11426 11004 10792 9471.3 8141.8 9552.9 FALSE TRUE 7787.997841 9658.553954 8479.058811 12308.56213 9483.812601 8448.487767 9946.09484 9344.352715 7848.778208 11424.60785 0.681686229 0.845416672 0.742175042 1.077372833 0.830121499 0.739499147 0.870585229 0.817914526 0.687006356 1 13.47985703 5.14896398 1.721532803 0.842893541 0.390015833 0.157757689 0.11257362 6.88541172 7.799948026 0.028262239 7.279350339 140917.1918 -5.14896398 -0.452877707 HNAVFDQLDLVTYEEVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNAVFDQLDLVTYEEVVK 18 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8Y3B3;A0A2R8Y6F8;O14936-3;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 79.311 0.010472 59941000 68467 35512 52463 55316 66617 79175 74199 61566 65450 44175 FALSE TRUE 71170.13003 41610.90975 53830.22888 66257.3397 55293.46613 60787.80616 68383.0885 60740.80847 63094.46728 52830.24547 1.347147442 0.787634231 1.018928237 1.254155439 1.046625198 1.150625094 1.294392784 1.149735496 1.194286847 1 15.68907649 3.764731146 22.85070471 1.164716952 1.02487629 0.081802673 0.150787164 471.5615368 411738.3343 0.036216144 0.065246494 5817.429734 -3.764731146 -0.139840662 HNDDEQYAWESSAGGSFTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 32 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 250.83 7.27E-31 2915036700 1380959.8 1389378.4 1577460.3 1519769.9 1657880.7 1993857.8 1816488.5 1623760.4 1653439.3 1277858.5 FALSE TRUE 1435481.159 1627993.332 1618570.211 1820375.85 1376074.731 1530814.543 1674107.385 1601996.548 1593932.343 1528230.407 0.939309382 1.065280029 1.059113995 1.191165836 0.900436691 1.001690934 1.095454833 1.048268992 1.042992166 1 20.54343064 2.266552527 24.97625059 1.052039249 1.031226713 0.012484513 0.076572911 1332.944542 1189339.721 0.026975989 0.022564723 184.7364217 -2.266552527 -0.020812536 HNDLDDVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HNDLDDVGK 9 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 91.855 0.010471 941610000 1543000 1000600 1307290 1135850 1601300 1872900 1760640 1348700 1393410 722510 FALSE TRUE 1603918.831 1172445.266 1341359.051 1360517.74 1329111.598 1437947.359 1622636.436 1330622.883 1343261.446 864072.0012 1.856232848 1.356883761 1.552369536 1.574542096 1.538195424 1.664152243 1.877894937 1.53994445 1.554571198 1 19.72079201 0.573448781 1.992794912 1.000140686 1.615079197 0.616551156 0.145876986 1.877357246 7.991068016 0.136755004 0.037680787 3.744973775 -0.573448781 0.614938511 HNDLDDVGKDVYHHTFFEMLGSWSFGDYFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNDLDDVGKDVYHHTFFEMLGSWSFGDYFK 30 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ; 103.21 0.00012426 715070000 371660 373940 722750 475460 940510 869010 870950 744910 851640 347495 FALSE TRUE 386333.4238 438161.2862 741585.4587 569504.5689 780642.4461 667195.5975 802682.6632 734925.6999 820989.6428 415579.9921 0.929624696 1.054336817 1.784459004 1.370384955 1.87844088 1.605456495 1.931475717 1.768433789 1.975527356 1 18.66476667 4.281281503 5.690628744 1.704282078 0.971710647 0.474371143 0.280929386 0.133105092 10.23289459 0.063362442 0.174176369 19110.91599 -4.281281503 -0.732571431 HNESVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNESVVK 7 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 ; 93.429 0.014942 442710000 975590 884680 1191260 943740 1458190 1395980 1437680 1179150 1235270 846720 FALSE TRUE 1014107.047 1036616.908 1222305.214 1130408.955 1210327.385 1071784.801 1324990.885 1163345.423 1190812.874 1012618.573 1.001469926 1.023699284 1.207073668 1.116322558 1.195245098 1.058428939 1.308479738 1.148848594 1.175973764 1 19.94965942 4.289548623 7.757508401 1.161133755 1.010619819 0.319035231 0.080064098 0.235279743 30.34076752 0.017852643 0.048916147 19478.19112 -4.289548623 -0.150513936 HNGPNDASDGTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HNGPNDASDGTVR 13 0 P31942;P31942-2 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;; 248.21 5.34E-17 1343356000 841477 975110 1021690 966683 1189470 1260450 1003886 1083723 1011030 925393 FALSE TRUE 874699.1617 1142577.557 1048316.081 1157890.012 987284.3143 967729.5898 925198.7922 1069197.466 974643.2278 1106706.041 0.790362689 1.032412868 0.947239865 1.046248931 0.892092641 0.874423338 0.835993261 0.966107915 0.880670379 1 20.07784064 HNGSLS(ph)PGLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HNGSLS(1)PGLEAR;HNGS(0.028)LS(0.972)PGLEAR;HNGSLS(1)PGLEAR;HNGSLS(1)PGLEAR 170.92 4.03E-05 1751830000 749680 860430 977280 899580 1197780 1472800 1195020 1084210 1034910 900980 TRUE FALSE 779277.9453 1008202.159 1002748.72 1077514.239 994181.7834 1130764.52 1101351.21 1069677.938 997663.7913 1077509.781 0.723221227 0.935677965 0.930616814 1.000004138 0.922666134 1.049423904 1.022126415 0.992731535 0.925897666 1 20.03926953 5.412848659 1.079015892 0.989376563 3.31E-12 0.793828851 0.039388473 2.673281425 0.899388811 0.011280074 4.298240937 258731.1144 -5.412848659 -0.989376563 HNGYDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 81.191 0.027872 924170000 893390 1049190 976260 1085550 1150190 1345510 1031620 960060 901550 869100 FALSE TRUE 928661.727 1229380.221 1001702.138 1300268.55 954681.1146 1033035.694 950758.9288 947191.966 869103.3916 1039383.505 0.893473605 1.182797509 0.963746425 1.250999793 0.918507086 0.993892715 0.914733517 0.911301711 0.836172007 1 19.98729664 HNIAGTTHSGAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNIAGTTHSGAEK 13 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 0 ; 133.48 6.17E-05 83488000 107113 87514 103287 99133 129177 142076 145616 112558 112765 69339 FALSE TRUE 111341.9039 102543.8487 105978.7441 118741.2115 107219.5397 109081.0022 134202.2374 111049.3441 108706.6097 82924.64947 1.342687665 1.236590681 1.278012566 1.431916954 1.292975495 1.315423133 1.618363638 1.339159645 1.310908281 1 16.33951339 0.744152278 2.960327856 1.000069235 1.360202457 0.528357473 0.100527262 1.419938552 15.38377477 0.09944738 0.026053172 5.548202176 -0.744152278 0.360133222 HNIAGTTHSGAEKDVDVSEDS(ph)PPPLPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNIAGTTHSGAEKDVDVSEDSPPPLPER 28 1 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 HNIAGTTHSGAEKDVDVS(0.008)EDS(0.992)PPPLPER;HNIAGTTHSGAEKDVDVS(0.001)EDS(0.999)PPPLPER 116.94 0.00016132 1171130000 321110 308740 368510 246490 495000 459070 370740 332000 348270 251084 TRUE FALSE 333787.6708 361763.6933 378113.6733 295244.9863 410860.0768 352457.9498 341680.4301 327550.083 335735.8307 300279.1025 1.111591409 1.204758141 1.259207418 0.98323521 1.368260639 1.173767827 1.137876153 1.090818776 1.11807924 1 18.19594455 1.25560643 0.875378497 1.009971757 1.185229207 0.248995604 0.094657222 0.724182405 1.21167862 0.084802894 0.031237493 18.01384537 -1.25560643 0.17525745 HNIICLQNDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNIICLQNDHK 11 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 103.91 0.0015446 257640000 304860 191550 237210 190220 385480 377850 292190 305000 277480 220850 FALSE TRUE 316896.1082 224447.2224 243391.8875 227844.9482 319956.2473 290100.0639 269287.3843 300911.9739 267493.549 264121.3291 1.199812637 0.849788327 0.921515458 0.862652589 1.211398748 1.098359095 1.019559402 1.139294486 1.012767693 1 18.01084129 3.248487485 24.99858463 1.087276039 0.948043647 0.229548342 0.108178796 263.7614447 664219.9147 0.028848075 0.038600191 1772.096977 -3.248487485 -0.139232393 HNIMDFAMPYFIQVMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNIMDFAMPYFIQVMK 16 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 165.02 7.17E-09 1420350000 1629960 1245310 1940420 1576390 2280900 2245500 2316600 1866940 2084200 1177900 FALSE TRUE 1694312.079 1459182.305 1990988.939 1888195.237 1893193.433 1724016.656 2135018.839 1841916.723 2009190.049 1408686.953 1.20275983 1.035845688 1.413365074 1.340393785 1.343941909 1.223846542 1.515609153 1.307541551 1.426285695 1 20.42591961 4.237155403 24.99979322 1.338780038 1.11930274 0.251315682 0.136896186 38.32207467 681837.9174 0.030459369 0.072007576 17264.55557 -4.237155403 -0.219477297 HNIQFSSFDIFSDEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HNIQFSSFDIFSDEEVR 17 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ;;;; 290.16 5.78E-46 1068163000 559649 791112 730295 821662 825106 1040092 779447 785291 745982 709911 FALSE TRUE 581744.3747 926979.332 749327.0876 984184.2912 684854.7768 798546.3957 718351.9074 774765.4586 719134.2535 849004.4684 0.685207671 1.091842701 0.882594987 1.159221568 0.806656269 0.940567954 0.846110868 0.912557575 0.847032354 1 19.69541262 HNKPEVEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 133.81 0.00016018 3307910000 7651600 5791700 7166500 6032600 9334400 9425400 8378800 7350300 7598300 4704820 FALSE TRUE 7953691.076 6786379.422 7353264.877 7225830.274 7747742.022 7236493.693 7722047.762 7251781.251 7324838.667 5626639.4 1.413577539 1.206115932 1.306866205 1.284217765 1.376975042 1.286112932 1.372408504 1.288829928 1.301814129 1 22.42384208 0.186337017 1.467891307 0.999816704 1.314605114 0.741977137 0.055838542 4.546220404 7.638344571 0.050251836 0.014216743 1.535808324 -0.186337017 0.31478841 HNKS(ph)PTLSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNKSPTLSCR 10 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 HNKS(0.854)PT(0.11)LS(0.036)CR;HNKS(0.495)PT(0.495)LS(0.011)CR 82.202 0.011337 353850000 235508 197475 224409 179841 316430 294580 249812 230414 236015 176705 TRUE FALSE 244806.0377 231389.7951 230257.2829 215413.013 262643.3416 226168.2594 230231.0827 227325.6772 227520.8663 211326.9615 1.158423118 1.094937406 1.089578354 1.019335212 1.242829309 1.070229079 1.089454374 1.075705985 1.07662962 1 17.68911732 0.774647308 0.640974856 0.999176657 1.111734339 0.268086757 0.055378963 1.481621554 1.278668061 0.057036465 0.021964477 5.951786006 -0.774647308 0.112557682 HNLFEDNMALPSES(ph)VS(ph)SLTDLKPPTGSNQASPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNLFEDNMALPSESVSSLTDLKPPTGSNQASPAR 34 1 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 2 HNLFEDNMALPS(0.178)ES(0.79)VS(0.477)S(0.448)LT(0.105)DLKPPT(0.001)GSNQASPAR 61.261 0.077137 53499000 20843 16614 17099 16881 28826 24394 19298 20698 17011 18302 TRUE FALSE 21665.89773 19467.32526 17544.61399 20220.01142 23926.16682 18728.86319 17785.37233 20420.57717 16398.77743 21887.92649 0.989856108 0.889409295 0.801565831 0.923797484 1.093121673 0.855670966 0.812565427 0.932960789 0.749215667 1 14.41784767 -1.672698031 7.692616508 1.000315385 0.896091808 0.101434543 0.094288046 0.000502601 2.14E-05 0.089968777 0.02114233 0.021247213 1.672698031 -0.104223577 HNLFEDNMALPSESVS(ph)SLTDLKPPTGSNQASPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HNLFEDNMALPSESVSSLTDLKPPTGSNQASPAR 34 1 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 HNLFEDNMALPS(0.026)ES(0.153)VS(0.381)S(0.381)LT(0.058)DLKPPTGSNQASPAR;HNLFEDNMALPS(0.018)ES(0.086)VS(0.439)S(0.439)LT(0.018)DLKPPTGSNQASPAR;HNLFEDNMALPS(0.003)ES(0.074)VS(0.413)S(0.413)LT(0.095)DLKPPTGSNQASPAR 151.38 7.15E-11 1362460000 358226 248686 329135 232849 419022 397951 364863 350907 330753 208809 TRUE FALSE 372369.0391 291395.886 337712.5285 278905.8372 347796.7901 305532.9113 336264.0847 346203.6656 318849.2641 249721.1257 1.491139519 1.166885201 1.352358666 1.116869214 1.392740759 1.223496452 1.346558421 1.386361145 1.276821347 1 17.92995835 0.956201423 21.91523863 0.999999998 1.307180596 0.427674064 0.106736551 1785.335013 893319.6872 0.09454058 0.023635145 9.040686777 -0.956201423 0.307180599 HNLFEDNMALPSESVSS(ph)LTDLKPPTGSNQASPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNLFEDNMALPSESVSSLTDLKPPTGSNQASPAR 34 1 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 HNLFEDNMALPS(0.001)ES(0.025)VS(0.035)S(0.905)LT(0.035)DLKPPTGSNQASPAR 199.99 2.32E-27 278940000 197060 166810 199120 171010 258640 256280 193420 202610 182630 126800 TRUE FALSE 204840.081 195458.3199 204309.2308 204835.2676 214676.4652 196762.854 178259.235 199894.3444 176057.182 151644.0323 1.35079553 1.288928532 1.347294897 1.350763789 1.415660491 1.297531139 1.175511046 1.318181411 1.160989848 1 17.2103292 0.802424791 0.566001484 0.991477043 1.346466098 0.782354616 0.05468261 0.525343408 0.371685057 0.063905635 0.026061619 6.344900133 -0.802424791 0.354989055 HNLITEMVALNPDFKPPADYKPPATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNLITEMVALNPDFKPPADYKPPATR 26 2 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 0 182.53 1.11E-17 437050000 670610 360500 579980 365710 787900 675180 688890 518500 616850 291370 FALSE TRUE 697086.2006 422413.0707 595094.7553 438046.3465 653973.0394 518379.6775 634893.0017 511550.3556 594649.689 348458.3729 2.000486299 1.212233953 1.707792958 1.257098066 1.876760871 1.487637313 1.822005299 1.468038639 1.706515714 1 18.4106268 -1.365208927 6.148711216 0.999925148 1.598898195 0.357735077 0.246482621 0.000221579 2.29E-05 0.209085471 0.049275816 0.043131153 1.365208927 0.598973048 HNMNIGTWDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNMNIGTWDEK 11 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 91.937 0.0058724 0 196200 96327 130250 93688 182370 179160 158900 135100 153060 98341 FALSE TRUE 203946.1275 112870.4129 133644.422 112219.2068 151370.8125 137552.8052 146445.0028 133289.2055 147551.4005 117609.0361 1.734102534 0.959708681 1.136344846 0.954171639 1.287067878 1.169576843 1.245184959 1.133324529 1.25459238 1 16.84363938 4.749307173 24.80123006 1.137298979 1.734102914 0.713692809 0.115243829 747.4557811 1724964.022 0.026552825 0.390814665 56144.4941 -4.749307173 0.596803936 HNNCMASHLTPAVYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNNCMASHLTPAVYAR 16 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J8F6;C9J6W7;C9JT96;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 203.99 1.52E-11 809050000 331533 610680 520740 519710 589460 698330 504730 553220 479410 511890 FALSE TRUE 344622.1788 715559.5396 534310.9122 622507.0868 489263.7997 536153.4408 465167.9437 545804.9908 462156.1277 612185.0448 0.562937925 1.168861516 0.872793148 1.016860984 0.799209004 0.875802905 0.759848591 0.891568645 0.754928811 1 19.22360828 3.210957319 24.98083459 0.84038961 0.921858386 0.027129983 0.156876541 635.9064504 575490.1977 0.041703585 0.049855551 1625.389009 -3.210957319 0.081468776 HNQGDS(ph)DDDVEETHPMDGNDSDYDPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNQGDSDDDVEETHPMDGNDSDYDPKK 27 1 Q9P2K3;Q9P2K3-3;B4DV59;Q9P2K3-2;Q9P2K3-4 Q9P2K3 RCOR3 REST corepressor 3 1 HNQGDS(1)DDDVEETHPMDGNDSDYDPKK 165.48 4.53E-12 586030000 241170 98473 152010 74360 216370 255750 198530 126350 177560 59976 TRUE FALSE 250691.5778 115384.9717 155971.5055 89068.18606 179591.5047 196355.9384 182968.6998 124656.4849 171169.6503 71727.14889 3.495072392 1.608665248 2.174511435 1.241763927 2.503814908 2.73753999 2.550898825 1.737926111 2.386399751 1 16.13023167 4.749814505 24.24248979 2.048628076 3.495073696 0.392016419 0.557203806 1155.330033 2488673.754 0.12876254 1.933799543 56210.11902 -4.749814505 1.446445621 HNQVESIFLSAIDMYGHQFCIENLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNQVESIFLSAIDMYGHQFCIENLQK 26 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 132.1 3.36E-05 182100000 52789 43587 55071 50679 77969 63983 78072 56922 55204 34010 FALSE TRUE 54873.15048 51072.72819 56506.1955 60703.15494 64715.85723 49123.91792 71952.51264 56159.0537 53217.21882 40673.60834 1.349109477 1.255672419 1.389259468 1.492445775 1.591101942 1.207759034 1.769022115 1.380724651 1.308396796 1 15.31180536 0.876605344 2.513797186 1.001105589 1.436033855 0.418372378 0.153274367 0.448290039 5.736539427 0.142663314 0.038264171 7.526712787 -0.876605344 0.434928267 HNS(ph)TTSSTSSGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNSTTSSTSSGGYR 14 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 1 HNS(0.295)T(0.295)T(0.266)S(0.103)S(0.015)T(0.016)S(0.002)S(0.007)GGYR 152.94 6.85E-06 163710000 72969 163540 167450 146050 234390 234190 169000 188460 163340 145310 TRUE FALSE 75849.87246 191626.7228 171813.8846 174938.2541 194548.4715 179802.9217 155753.3384 185934.002 157461.4253 173780.7124 0.436468878 1.102692699 0.988682128 1.006660933 1.119505547 1.034654072 0.896263666 1.069934629 0.906092645 1 17.40690844 4.743801276 24.99877364 1.015946878 0.436468635 0.85961303 0.069992725 182.3272793 869703.2372 0.015901701 0.135423088 55437.19856 -4.743801276 -0.579478243 HNS(ph)TTSSTSSGGYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.836)T(0.081)T(0.081)S(0.002)STSSGGYRR;HNS(0.86)T(0.139)T(0.001)SSTSSGGYRR;HNS(0.885)T(0.066)T(0.027)S(0.02)S(0.001)TSSGGYRR 120.82 7.28E-05 265072000 18504 46504.6 37745.8 43163.9 56760.7 59034.2 40897.7 50434 39467.3 57270.8 TRUE FALSE 19234.55221 54491.40329 38729.48656 51701.59059 47112.53649 45324.40172 37692.03141 49758.01472 38046.87958 68491.91674 0.280829522 0.795588821 0.565460691 0.754856822 0.687855425 0.661748187 0.550313573 0.726480103 0.555494449 1 16.06364611 -5 0.382154447 6.213332743 0.625848684 0.395169476 0.139943348 596.3429222 4.426624773 2579.167152 0.084426012 1.00E-05 5 -5.587484059 HNS(ph)WDTVNTVLPEDPEVADLFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HNSWDTVNTVLPEDPEVADLFSR 23 0 Q8N961 Q8N961 ABTB2 Ankyrin repeat and BTB/POZ domain-containing protein 2 1 HNS(0.498)WDT(0.498)VNT(0.004)VLPEDPEVADLFSR;HNS(0.548)WDT(0.441)VNT(0.01)VLPEDPEVADLFSR;HNS(0.491)WDT(0.491)VNT(0.019)VLPEDPEVADLFSR 106.1 0.00095087 263046000 150711 158957 167319 161509 215031 233944 191326 183478 186974 144652 TRUE FALSE 156661.1867 186256.6282 171679.4706 193454.9981 178480.1074 179614.0515 176329.3682 181018.7775 180244.8423 172993.7899 0.9055885 1.076666558 0.992402506 1.118277126 1.031713957 1.038268782 1.019281492 1.046388877 1.041915102 1 17.40036072 4.747797433 24.64255796 1.041773529 0.905588412 0.5793197 0.034487016 662.4835631 1767369.632 0.00751079 0.093066366 55949.65763 -4.747797433 -0.136185117 HNS(ph)WSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HNSWSSSSR 9 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(0.961)WS(0.037)S(0.002)SSR;HNS(0.994)WS(0.005)SSSR;HNS(0.958)WS(0.039)S(0.003)SSR 136.06 0.00021335 2376000000 1242710 2076300 1940790 2039010 2349520 2693310 2168180 2081420 2090280 2063330 TRUE FALSE 1291773.15 2432888.374 1991368.582 2442320.092 1950149.43 2067829.57 1998232.386 2053521.969 2015051.231 2467600.009 0.523493737 0.985933038 0.807006231 0.989755262 0.790302084 0.837992204 0.809787802 0.832194019 0.816603673 1 21.23467713 HNS(ph)WSSSSRHPNQATPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNSWSSSSRHPNQATPK 17 1 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 1 HNS(0.95)WS(0.047)S(0.002)S(0.001)S(0.001)RHPNQATPK 79.143 0.0085557 31252000 9543.4 47549 49847 29035 84950 73744 26694 59336 57561 93079 TRUE FALSE 9920.180801 55715.17087 51146.05377 34778.03634 70510.22934 56618.0736 24601.65453 58540.69797 55489.39085 111316.0479 0.089117257 0.500513375 0.459467028 0.312426079 0.633423757 0.508624539 0.221007258 0.525896302 0.498485096 1 16.76430207 -4.999999997 0.227772622 4.072255961 0.356068127 0.599140723 0.147906485 109.5732878 1.096685754 154.8779275 0.253757137 1.00E-05 4.999999997 -3.716187834 HNST(ph)TSSTSSGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNSTTSSTSSGGYR 14 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12 A0A0A0MRT6 ABI1 Abl interactor 1 1 HNS(0.141)T(0.736)T(0.089)S(0.029)S(0.004)T(0.001)SSGGYR 184.8 1.40E-05 215900000 68063 149570 168690 152290 219950 201200 160750 194970 171500 131940 TRUE FALSE 70750.1798 175257.484 173086.2 182412.5075 182562.9776 154474.3492 148149.995 192356.7461 165327.7485 157791.1169 0.448378725 1.110692969 1.096932473 1.156037875 1.156991478 0.97898001 0.938899463 1.219059412 1.047763346 1 17.26765646 4.739846875 24.96722465 1.087088557 0.448378515 0.834923471 0.083957827 41.01450177 796034.6515 0.02040986 0.127363804 54934.71484 -4.739846875 -0.638710042 HNT(ph)PSLLEAALTQEASTPDSQVWPTAPDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.648)PS(0.296)LLEAALT(0.055)QEAS(0.001)TPDSQVWPTAPDITR;HNT(0.568)PS(0.432)LLEAALTQEASTPDSQVWPTAPDITR 208.15 1.71E-25 285666000 138243 118044 147127 141904 160764 270945 176212 158823 134463 74619 TRUE FALSE 143700.9404 138317.1387 150961.2505 169972.1877 133437.3927 208022.13 162400.043 156694.2375 129623.7029 89239.16438 1.610290071 1.549960039 1.691647961 1.904681524 1.495278375 2.331063176 1.819829266 1.755890909 1.452542769 1 16.44538938 0.956737831 2.427169653 1.001908397 1.778242484 0.53844058 0.221844476 0.242876885 3.233982756 0.211584051 0.057296879 9.051860061 -0.956737831 0.776334087 HNTPS(ph)LLEAALTQEASTPDSQVWPTAPDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.331)PS(0.669)LLEAALTQEASTPDSQVWPTAPDITR 243.24 3.29E-46 196050000 76342 69127 77534 73990 91597 140260 97328 77248 77330 34477 TRUE FALSE 79356.04111 80999.02452 79554.59973 88625.00116 76027.37466 107686.7407 89699.17704 76212.61691 74546.90841 41232.10805 1.924617607 1.964464791 1.929433238 2.149417174 1.843887646 2.611720471 2.175469101 1.848380316 1.807981981 1 15.3314806 0.752330624 1.342424097 1.003890366 2.076177322 0.69773155 0.210650828 0.471742036 1.462800179 0.204369676 0.061032751 5.6536722 -0.752330624 1.072286957 HNTPSLLEAALTQEAS(ph)TPDSQVWPTAPDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.002)PS(0.002)LLEAALT(0.009)QEAS(0.54)T(0.446)PDS(0.001)QVWPTAPDITR 110.65 6.55E-05 65051000 11928 28425 26205 36377 28888 38886 34931 33774 36484 30484 TRUE FALSE 12398.92665 33306.77263 26887.92383 43572.26203 23977.62808 29855.31582 32193.01694 33321.31477 35170.94797 36456.75615 0.340099558 0.913596714 0.737529245 1.195176605 0.657700537 0.818924089 0.883046665 0.913995602 0.964730593 1 15.15389858 4.740034992 24.86631437 0.890382056 0.340099364 0.590345354 0.139357369 79.38339262 1338714.365 0.031149684 0.196602819 54958.51534 -4.740034992 -0.550282692 HNTPSLLEAALTQEAST(ph)PDSQVWPTAPDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNTPSLLEAALTQEASTPDSQVWPTAPDITR 31 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 HNT(0.001)PS(0.001)LLEAALT(0.02)QEAS(0.213)T(0.751)PDS(0.014)QVWPTAPDITR 61.526 0.079902 96645000 27117 31638 33796 35510 41551 47757 36755 37644 31154 37400 TRUE FALSE 28187.6001 37071.58039 34676.75152 42533.77201 34488.17586 36666.16051 33874.04706 37139.44375 30032.77363 44727.81393 0.630202946 0.828826118 0.775283844 0.950946811 0.771067773 0.819761962 0.757337417 0.83034337 0.671456326 1 15.44888463 4.741058992 24.03721394 0.81599988 0.63020283 0.29061941 0.089700577 164.6395728 1583850.051 0.01946075 0.131550834 55088.25198 -4.741058992 -0.18579705 HNVEVLGILSDDVETDTVAPGENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HNVEVLGILSDDVETDTVAPGENLK 25 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ;; 226.4 6.42E-34 302642000 461509 300218 398061 351002 507270 531530 554700 422999 456230 251464 FALSE TRUE 479729.7317 351778.1061 408434.7967 420429.148 421044.4266 408090.2129 511221.1646 417329.3903 439810.3714 300733.5562 1.595198546 1.16973347 1.358128444 1.398012092 1.400058018 1.356982633 1.69991394 1.387704769 1.462458586 1 18.19812633 -1.456457391 6.553270158 0.999884342 1.421850527 0.470595626 0.135299035 0.00022175 1.84E-05 0.12706148 0.029940561 0.034957681 1.456457391 0.421966186 HNVFQNDEFDVFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNVFQNDEFDVFSR 14 0 Q9H1I8;H7C3Y4;Q9H1I8-3 Q9H1I8 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 ; 232.8 3.23E-14 186707000 121546 146460 160786 146337 167476 194752 146069 162815 147351 135495 FALSE TRUE 126344.7299 171613.3657 164976.2152 175282.0218 139008.4893 149523.7995 134619.7301 160632.7312 142047.8663 162042.651 0.779700462 1.059062936 1.018103655 1.081703 0.857851241 0.922743479 0.830767265 0.991299082 0.876607889 1 17.30601407 3.222521382 24.999164 0.912952237 0.992348374 0.126068381 0.091236172 450.5423142 702225.5378 0.025500546 0.030568099 1669.249989 -3.222521382 0.079396137 HNVGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNVGVK 6 0 O75874;C9J4N6;C9JLU6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 69.39 0.09363 719160000 2129270 1709330 2083620 1671560 2787400 2632600 2460840 2277460 2246350 1598910 FALSE TRUE 2213335.224 2002894.131 2137920.849 2002189.579 2313598.744 2021218.547 2267952.931 2246934.374 2165504.302 1912185.802 1.157489624 1.047436985 1.118050792 1.047068531 1.209923608 1.057019954 1.186052594 1.175060693 1.132475882 1 20.86679128 3.260810785 24.99974861 1.138879537 1.091116141 0.042285037 0.066022838 523.6157575 588318.0136 0.017002343 0.023002667 1823.101233 -3.260810785 -0.047763396 HNYECLVYVQLPFMEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HNYECLVYVQLPFMEDLR 18 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 149.36 6.27E-08 1194780000 686400 708530 893890 889420 934470 1055580 916100 791060 881280 670760 FALSE TRUE 713499.602 830214.5159 917185.5077 1065344.621 775629.1232 810437.5425 844293.6882 780457.1346 849562.9049 802182.5795 0.889447889 1.034944584 1.143362535 1.328057538 0.966898488 1.010290629 1.052495666 0.972917082 1.059064266 1 19.61357111 HNYPDLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HNYPDLVER 9 0 Q9NZT2-2;Q9NZT2;A0A087X028;Q4VXW3 Q9NZT2-2 OGFR Opioid growth factor receptor 0 65.5 0.066382 170660000 62588 64784 62180 67403 68466 82991 73036 66825 64688 62282 FALSE TRUE 65059.02257 75910.14805 63800.46188 80735.11222 56828.17378 63717.59799 67311.24748 65929.32018 62359.89152 74484.96544 0.873451739 1.019133829 0.856554897 1.083911522 0.762948247 0.855442405 0.903689048 0.885135944 0.837214479 1 16.18466163 3.229864665 24.99967318 0.870777582 0.955346058 0.199079001 0.082486941 288.925548 830620.4022 0.022025511 0.026714058 1697.714528 -3.229864665 0.084568476 HPAKPDPSGECNPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HPAKPDPSGECNPDLR 16 1 Q16576;E9PC52;Q16576-2;Q5JP01 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;;; 281.92 9.12E-36 2750360000 1982160 1645870 1910060 1845130 2083970 2395980 2304020 2066740 1999360 1445630 FALSE TRUE 2060417.207 1928535.369 1959837.733 2210091.207 1729737.524 1839549.956 2123424.892 2039038.731 1927403.424 1728873.52 1.191768619 1.115486672 1.133592313 1.278341753 1.000499749 1.064016503 1.228212976 1.179403066 1.114831942 1 20.7214009 -2.705621977 1.17508022 0.006307607 1.147262705 0.247666134 0.075805047 67638.79741 3254.348683 176612.51 0.022048871 0.0019696 2.705621977 1.140955098 HPALFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPALFK 6 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 84.566 0.055705 1456560000 4341800 3545100 4120400 3982300 4893600 5299000 5573000 4523300 4471200 3353100 FALSE TRUE 4513217.617 4153943.348 4227781.009 4769987.054 4061787.62 4068387.557 5136173.698 4462672.562 4310282.385 4010075.746 1.125469418 1.03587653 1.054289564 1.189500487 1.012895486 1.014541324 1.280817127 1.112864904 1.074863084 1 21.93519806 HPDASVNFSEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPDASVNFSEFSK 13 0 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 206.18 6.39E-08 2036370000 1584340 1342360 1630710 1427350 1936310 1898330 1978790 1673630 1787100 1107460 FALSE TRUE 1646890.967 1572899.888 1673207.642 1709675.57 1607176.718 1457471.627 1823687.269 1651197.727 1722782.62 1324445.583 1.243456875 1.187591176 1.263326831 1.290861317 1.213471311 1.10043904 1.376943902 1.246708621 1.300757571 1 20.33695714 -1.013622129 4.230148713 0.999983612 1.247459639 0.533095286 0.069363823 0.117350714 19174369.8 724.320969 0.015920228 0.09691207 1.013622129 0.247476028 HPDGRPTGDAFALFACEELAQAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPDGRPTGDAFALFACEELAQAALR 25 1 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 0 ; 124.14 9.32E-05 75172000 44290 58441 62010 59010 50494 77629 57220 67416 52465 49654 FALSE TRUE 46038.6034 68477.78714 63626.03154 70682.00187 41911.04792 59600.84123 52734.94688 66512.39879 50576.7949 59382.75062 0.775285801 1.15315957 1.071456456 1.190278341 0.705778151 1.003672626 0.888051603 1.120062612 0.851708524 1 15.8577563 HPDSHQLFIGNLPHEVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPDSHQLFIGNLPHEVDK 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 88.176 0.0010864 156810000 124670 117580 142380 116670 174780 180440 183360 152830 155500 102810 FALSE TRUE 129592.0679 137773.4504 146090.5398 139746.9778 145070.958 138535.5446 168987.7641 150781.5638 149903.5854 122953.6511 1.053991213 1.120531592 1.188175694 1.136582578 1.179883287 1.126729815 1.374402164 1.226328478 1.219187751 1 16.90775505 HPDVEVDGFSELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 206.32 6.29E-08 2768860000 1634560 1854060 1822460 1948930 1917600 2237630 2126970 1967740 1785420 1725700 FALSE TRUE 1699093.691 2172480.382 1869954.805 2334422.537 1591647.037 1717974.344 1960252.534 1941365.664 1721163.083 2063817.874 0.823276953 1.05265121 0.906065805 1.13111848 0.771214872 0.832425363 0.949818566 0.940667143 0.833970431 1 20.97688423 HPDYAILAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPDYAILAAR 10 0 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 112.13 0.0016617 259770000 60858 136470 109640 122930 147040 166570 99536 123330 114190 192540 FALSE TRUE 63260.72083 159907.6609 112497.3085 147245.1871 122046.1933 127886.6419 91734.10823 121676.9631 110080.3242 230264.5266 0.27473064 0.694452 0.488556836 0.639461011 0.530026032 0.555390115 0.398385759 0.528422527 0.478060281 1 17.81293265 -1.773334123 2.525388853 1.129415812 0.516360456 0.636598665 0.111026505 12484574.02 8816168.986 9992519.995 0.025835934 0.01685256 1.773334123 -0.613055356 HPECNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPECNLR 7 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2;H0YH35 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 88.029 0.018908 163268000 136918 150613 148568 151880 184328 208275 187894 179722 169906 183036 FALSE TRUE 142323.6284 176479.6111 152439.8041 181921.4107 152995.9924 159906.2877 173166.3773 177313.1206 163791.1162 218898.3998 0.650181219 0.806217 0.696395242 0.831076933 0.698936093 0.730504599 0.791081056 0.810024745 0.748251775 1 17.73990188 -5 0.206350714 2.15572593 0.719422191 0.673461678 0.053132076 79.43592103 0.790164545 37.86195891 0.109282606 1.00E-05 5 -1.436303739 HPELADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 133.6 0.0032559 3543320000 5465390 4046790 5280940 4415720 6358060 6810250 6805980 5277250 5332420 3304510 FALSE TRUE 5681167.817 4741794.703 5418565.635 5289136.236 5277319.232 5228672.648 6272509.503 5206517.096 5140507.246 3951965.466 1.437555026 1.199857323 1.371106524 1.338355884 1.335365726 1.32305626 1.587187327 1.317450049 1.300747006 1 21.91413891 0.738132182 2.28600856 1.000264227 1.363769298 0.575753372 0.093394961 0.851550566 6.34225684 0.087736422 0.023750735 5.471824781 -0.738132182 0.363505071 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 38 2 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSASSDPADRLS(1)PFLAAR;HPELTKPPPLMAAEPTAPLSHSAS(0.002)S(0.006)DPADRLS(0.992)PFLAAR 240.33 2.59E-50 5578200000 2336057 2669143 3068615 2986407 3029546 3901792 3409683 3087154 3096650 2284874 TRUE FALSE 2428286.334 3127547.547 3148585.628 3577109.391 2514584.853 2995659.94 3142423.137 3045775.75 2985202.171 2732551.314 0.888651687 1.144552174 1.152251236 1.30907309 0.920233351 1.096286802 1.149996021 1.114627101 1.092459694 1 21.38181716 0.870061584 6.800407452 1.000000136 1.104532972 0.058134579 0.113368093 11.61630724 607.8542962 0.104860555 0.026308479 7.414153691 -0.870061584 0.104532836 HPENYDLATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPENYDLATLK 11 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 0 122.34 0.00039273 190570000 317390 247570 288740 234740 397430 342210 329990 258980 319060 236480 FALSE TRUE 329920.8023 290088.2217 296264.8016 281170.8714 329874.9906 262736.9137 304124.5215 255508.7967 307577.0929 282813.7283 1.166565726 1.025721854 1.0475616 0.994191028 1.16640374 0.929010467 1.075352754 0.903452595 1.087560688 1 18.10949263 2.722964844 24.84865566 0.992099458 1.070489249 0.222970743 0.073977272 1143.999704 1822726.138 0.022565331 0.02134533 528.4024763 -2.722964844 0.078389791 HPEPVPEEGS(ph)EDELPPQVHKV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPEPVPEEGSEDELPPQVHKV 21 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV 171.72 3.07E-12 277390000 163717 133016 152632 140982 194003 204335 171586 154714 163186 124715 TRUE FALSE 170180.6736 155860.4633 156609.7153 168867.8188 161026.4394 156881.293 158136.641 152640.3119 157312.9677 149150.5164 1.14099956 1.044987755 1.050011217 1.132197346 1.079623747 1.051832047 1.060248699 1.02339781 1.054726269 1 17.18640945 1.74560664 0.498619601 1.002931472 1.092185398 0.450852355 0.03088775 0.830667166 0.490098573 0.031514361 0.021604214 55.66813091 -1.74560664 0.089253926 HPGAHQGNLASGLHSNAIASPGS(ph)PSLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPGAHQGNLASGLHSNAIASPGSPSLGR 28 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 HPGAHQGNLASGLHSNAIAS(0.015)PGS(0.985)PS(0.001)LGR;HPGAHQGNLASGLHSNAIAS(0.014)PGS(0.983)PS(0.003)LGR;HPGAHQGNLASGLHSNAIAS(0.026)PGS(0.972)PS(0.002)LGR 215.1 6.16E-34 614740000 64363 136852 126389 138330 143527 172848 111495 151432 119622 136535 TRUE FALSE 66904.10094 160355.2664 129682.8012 165691.2611 119130.3318 132706.6715 102755.7306 149402.3017 115316.8276 163286.4191 0.409734633 0.982049011 0.794204453 1.014727753 0.729578935 0.812723264 0.629297471 0.914970777 0.706224242 1 17.31704528 -2.643063256 1.997570723 4.98783009 0.792921889 0.12953127 0.16893515 10490237.52 383533.8068 190222375.5 0.039008685 0.002274766 2.643063256 -4.194908201 HPGDFGADAQGAMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPGDFGADAQGAMNK 15 0 B0QYF8;P02144;Q8WVH6 B0QYF8 MB Myoglobin 0 182.57 4.11E-07 129640000 106040 116510 109730 108380 154020 154220 126020 115040 101390 129350 FALSE TRUE 110226.5411 136519.6862 112589.6539 129817.2405 127839.7354 118404.7422 116142.2231 113498.077 97740.99371 154693.6559 0.712547263 0.882516386 0.727823344 0.839189169 0.826405806 0.765414338 0.750788534 0.733695744 0.631835825 1 17.23905451 2.561602511 6.091978384 0.754603906 0.8007127 0 0.0988264 0.806904549 46.87675128 0.029911221 0.028000153 364.420258 -2.561602511 0.046108794 HPGSFDVVHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPGSFDVVHVK 11 0 P62701;C9JEH7;P22090 P62701 RPS4X;RPS4Y1 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1" 0 ;; 196.48 3.49E-08 1430560000 1282940 1558470 1864750 1663830 2155070 2283730 2066100 1960020 1982650 1592760 FALSE TRUE 1333591.462 1826125.099 1913346.917 1992930.608 1788751.971 1753368.318 1904153.683 1933749.138 1911294.814 1904830.827 0.700110185 0.958680988 1.004470786 1.046250712 0.939060806 0.92048506 0.999644513 1.015181564 1.00339347 1 20.86123144 4.73834569 3.663054063 0.990714907 0.668166408 0.864232035 0.034377141 0.09735643 2.421276893 0.009033986 0.085748764 54745.15501 -4.73834569 -0.322548498 HPHDIIDDINSGAVECPAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HPHDIIDDINSGAVECPAS 19 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;; 253.71 6.97E-31 4101611000 1392017 1505421 1437100 1547394 1588584 1930217 1509606 1472403 1390379 1580594 FALSE TRUE 1446974.906 1763965.346 1474552.007 1853463.915 1318557.059 1481953.354 1391279.137 1452667.846 1340339.531 1890281.132 0.765481325 0.933176191 0.780070214 0.980522888 0.69754548 0.783985688 0.736017047 0.768493015 0.709068883 1 20.85016938 3.220130455 24.99999101 0.767935206 0.863642798 0.131751772 0.0993311 382.1008502 518307.7664 0.025952212 0.031073047 1660.085494 -3.220130455 0.095707592 HPHTGDTKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPHTGDTKEEK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 ;; 93.058 0.0061503 82615000 140143 61048.5 98229 54754.5 137230 127991 119195 92353 109627 47709.4 FALSE TRUE 145675.9539 71533.10498 100788.9284 65584.77667 113903.6936 98267.02997 109852.1844 91115.15909 105681.5457 57057.14348 2.553158903 1.253709888 1.766455912 1.149457766 1.99630908 1.72225639 1.925301159 1.596910633 1.852205337 1 15.8001199 -1.335315221 4.802832614 0.999532384 1.728214238 0.268500043 0.37222004 0.001685102 0.000233208 0.325854006 0.07675733 0.046204554 1.335315221 0.728681854 HPHVYS(ph)PVIQGNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPHVYSPVIQGNAR 14 0 F8VZC1 F8VZC1 ATXN2 1 HPHVY(0.437)S(0.563)PVIQGNAR 60.518 0.096821 32621000 1785.9 2082.5 3478.8 4271.3 4741.7 6377.6 4101.5 3856.5 3088 4181.1 TRUE FALSE 1856.408711 2440.153175 3569.460386 5116.150391 3935.707528 4896.499053 3780.013713 3804.809925 2976.863483 5000.306493 0.371258985 0.488000721 0.713848319 1.02316736 0.787093258 0.979239785 0.755956403 0.760915342 0.595336203 1 12.28780081 4.227261018 2.877835049 0.829284135 0.397912505 0.627485708 0.126335057 0.163834395 2.709472722 0.03231149 0.099374186 16875.66975 -4.227261018 -0.43137163 HPKGEEGS(ph)DDDETENGPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPKGEEGSDDDETENGPKPK 20 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 HPKGEEGS(1)DDDETENGPKPK 141.53 9.91E-08 284410000 213800 47795 85009 41278 165040 165770 142160 93024 111410 28805 TRUE FALSE 222240.9891 56003.41946 87224.40438 49442.6652 136986.5598 127272.4298 131017.1277 91777.16544 107400.3759 34448.78824 6.451344167 1.625700708 2.532002106 1.435251215 3.976527673 3.694540106 3.803243435 2.664162373 3.117682256 1 15.07216562 HPLLSSGGPQS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HPLLSSGGPQSPLR 14 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR;HPLLSSGGPQS(1)PLR 217.97 3.58E-12 4616020000 1300625 1711480 1708320 1756140 1927520 2212040 1800790 1831830 1794160 1749950 TRUE FALSE 1351974.679 2005413.377 1752840.223 2103499.25 1599880.839 1698327.234 1659639.374 1807277.315 1729588.532 2092819.198 0.64600644 0.958235369 0.837549763 1.005103189 0.764462043 0.811502129 0.793016127 0.863561132 0.826439539 1 20.99701625 -1.309586892 4.852534701 1.000071391 0.840080742 0.216892758 0.09399552 6.71E-05 9.55E-06 0.084131092 0.019821053 0.049024493 1.309586892 -0.159990649 HPNNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPNNLK 6 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 91.26 0.048095 352653000 454390 352022 455019 350016 437950 465213 503150 435018 438108 289579 FALSE TRUE 472329.6681 412479.0401 466877.1689 419248.1201 363507.4154 357174.3311 463711.7883 429187.2953 422340.5787 346316.4607 1.363867219 1.191046592 1.348122951 1.210592529 1.049639439 1.031352453 1.338982812 1.239292219 1.219522103 1 18.40173144 3.488127728 23.79587332 1.168110683 1.288239394 0.276629204 0.108008671 470.0377328 1016215.151 0.030760994 0.044599816 3077.001643 -3.488127728 0.12012871 HPNQATPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPNQATPK 8 0 Q96F86;H3BPW9;H3BQ37 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 68.735 0.055739 33453000 58088 48776 62733 50750 80790 79467 71247 68627 69454 59963 FALSE TRUE 60381.35909 57152.89858 64367.87352 60788.19853 67057.34466 61011.99358 65662.47397 67707.16732 66954.36411 71711.60179 0.842002655 0.796982596 0.897593582 0.847675927 0.935097571 0.850796692 0.915646455 0.944159182 0.933661534 1 16.12991892 7.999999985 0.086442268 1.09162897 0.333455954 0.706916575 0.03136606 81.21670938 0.506810544 0.610867156 7.315345936 99999996.5 -7.999999985 -0.758173016 HPNYS(ph)PPGS(ph)PIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 2 HPNY(0.006)S(0.994)PPGS(1)PIEK;HPNY(0.005)S(0.995)PPGS(1)PIEK;HPNY(0.005)S(0.995)PPGS(1)PIEK;HPNY(0.002)S(0.999)PPGS(0.999)PIEK 109.65 0.00059191 2302370000 3781260 2484346 3091270 2474014 4111190 4306290 3761630 3211310 3247500 2366150 TRUE FALSE 3930547.065 2911013.1 3171831.036 2963366.585 3412371.392 3306219.41 3466783.611 3168267.642 3130623.109 2829751.79 1.389007714 1.028716763 1.120886661 1.04721785 1.205890709 1.168377885 1.225119328 1.119627401 1.106324279 1 21.43224408 0.898103229 1.740424805 1.001028301 1.15806996 0.216339003 0.095709602 0.748937105 4.55089036 0.085836424 0.02446999 7.908665895 -0.898103229 0.157041659 HPNYS(ph)PPGSPIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 193.8 1.92E-07 1208810000 2797920 2079070 2475610 1866690 2834420 2793430 2328470 2110850 2004580 1333950 TRUE FALSE 2908384.042 2436134.1 2540126.43 2235915.71 2352626.301 2144698.217 2145958.437 2082557.508 1932435.557 1595311.962 1.823081698 1.527058128 1.592244332 1.401553905 1.47471238 1.344375437 1.345165389 1.305423364 1.211321424 1 20.60540714 8 0.108870337 0.817610776 3.585916768 0.913915994 0.062119754 27.61939198 0.210033161 0.541016601 11.48454498 99999999.99 -8 2.768305991 HPPEQTNGVHT(ph)PPHVASALAGAVS(ph)PGALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPPEQTNGVHTPPHVASALAGAVSPGALR 29 0 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 2 HPPEQTNGVHT(1)PPHVASALAGAVS(1)PGALR 172.95 3.38E-12 244800000 52836 68812 75958 88335 96250 90466 79536 84783 76416 78228 TRUE FALSE 54922.00608 80629.92572 77937.52788 105807.3993 79889.45938 69456.64253 73301.76049 83646.62256 73665.80309 93555.27883 0.587054058 0.86184261 0.833063926 1.130961295 0.853927864 0.742412864 0.783512822 0.894087684 0.787404025 1 16.51353144 4.742124099 4.878630445 0.872451706 0.571200916 0.390488323 0.108407636 0.194658428 13.73277943 0.026407408 0.199235804 55223.5217 -4.742124099 -0.30125079 HPPFSPPEPPLS(ph)SPASQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPPFSPPEPPLSSPASQHK 19 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 HPPFSPPEPPLS(0.499)S(0.499)PAS(0.001)QHK;HPPFSPPEPPLS(0.499)S(0.499)PAS(0.001)QHK 166.06 3.45E-11 631630000 214698 327569 393990 358713 493160 499880 389130 410160 397450 287741 TRUE FALSE 223174.4428 383826.4276 404257.7031 429665.3607 409332.8394 383790.4458 358628.9738 404662.4761 383145.8521 344118.3398 0.64853981 1.115390792 1.17476361 1.24859768 1.189511839 1.11528623 1.042167569 1.175939871 1.113413055 1 18.39254526 4.737912282 4.976319532 1.141467908 0.624110985 0.814806999 0.068874676 0.065089473 5.011892987 0.016418287 0.11620617 54690.54887 -4.737912282 -0.517356923 HPPLYSDHSPLCADSLGQEPGAASFQNDS(ph)PPQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPPLYSDHSPLCADSLGQEPGAASFQNDSPPQVR 34 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 HPPLYSDHSPLCADSLGQEPGAASFQNDS(1)PPQVR;HPPLYSDHSPLCADSLGQEPGAAS(0.001)FQNDS(0.999)PPQVR;HPPLYSDHSPLCADSLGQEPGAAS(0.001)FQNDS(0.999)PPQVR 299.07 9.54E-90 1257150000 122511 357634 346865 340038 310749 404394 286369 346357 312892 344045 TRUE FALSE 127347.8289 419054.8575 355904.5869 407296.5015 257927.996 310479.6222 263922.6495 341714.6509 301631.078 411454.0306 0.309506821 1.018473089 0.864992345 0.98989552 0.626869533 0.754591276 0.64143897 0.830505052 0.733085729 1 18.65037173 -1.738372783 2.246571315 1.060214348 0.76670326 0.125345708 0.192998522 6176905.361 3936087.677 2068393.927 0.045415027 0.018265317 1.738372783 -0.293511088 HPQGEQMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HPQGEQMYR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 135.55 0.00021771 849301000 12533.8 26350.6 29502.3 28582.2 21186 34230.7 12063.1 23472 26911.3 34360.1 FALSE TRUE 13028.6441 30876.11057 30271.15417 34235.67385 17584.81129 26281.1387 11117.5627 23157.39623 25942.76757 41092.30373 0.317058011 0.751384268 0.736662378 0.833140777 0.427934423 0.639563527 0.270550972 0.563545826 0.631329111 1 15.32658059 0.799911432 3.874876847 0.999970935 0.571504958 0.350155135 0.175709177 2.052477408 38.48217649 0.170242978 0.04358911 6.308286836 -0.799911432 -0.428465978 HPQHLHQQHHGDAAQHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPQHLHQQHHGDAAQHTR 18 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 0 ;; 116.6 4.79E-05 25637200 3776.4 4544 5154.1 4401.5 4888.3 5738 4469.47 2751.9 4229.3 3622.9 FALSE TRUE 3925.495188 5324.396653 5288.42008 5272.103563 4057.388512 4405.43646 4119.141263 2715.015282 4077.088319 4332.73789 0.906007999 1.22887578 1.220572353 1.216806485 0.936449103 1.016778899 0.950701696 0.626628093 0.940995837 1 12.08106325 2.616118608 1.317898409 0.824470959 1.144246558 0.363149562 0.139671619 0.37744637 1.334899498 0.068018172 0.05723546 413.1603224 -2.616118608 0.319775599 HPS(ph)SPSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPSSPSALR 9 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 HPS(0.504)S(0.491)PS(0.005)ALR 72.59 0.038238 0 217820 234850 227750 201540 291640 381450 296330 245720 243150 242950 TRUE FALSE 226419.7018 275183.6606 233685.3521 241404.0105 242067.137 292864.0184 273102.8803 242426.5253 234399.079 290551.4009 0.779275891 0.947108359 0.804282311 0.830847863 0.833130166 1.007959409 0.939946871 0.834367085 0.806738767 1 18.14843389 HPSAVTACNLDLENLVTDSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HPSAVTACNLDLENLVTDSNR 21 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;; 277.07 7.91E-45 367070000 35849.8 258334 284734 299095 300628 378143 303610 309660 280535 265821 FALSE TRUE 37265.17779 302700.8549 292154.402 358255.0983 249527.3599 290325.0191 279812.2549 305509.5142 270438.6001 317903.5355 0.117221653 0.952178322 0.919003312 1.126930211 0.784915335 0.91324879 0.880179751 0.961013264 0.850693905 1 18.27822954 4.739494473 24.99261737 0.930334986 0.117221396 0.888014484 0.086802456 22.36069384 598346.7133 0.01970045 0.119892192 54890.157 -4.739494473 -0.81311359 HPSGGSS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPSGGSSPPPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 HPSGGS(0.05)S(0.95)PPPR;HPS(0.002)GGS(0.067)S(0.931)PPPR 98.253 0.0036449 135830000 26764 119457 97669 115764 95774 125609 96909 102895 78367 110725 TRUE FALSE 27820.66339 139972.8105 100214.3344 138661.7737 79494.36969 96438.21337 89313.01936 101515.8608 75546.58698 132419.4438 0.210095003 1.057041221 0.756794709 1.047140584 0.600322486 0.728278345 0.674470582 0.766623525 0.570509774 1 17.01475545 -2.224334007 2.266598291 1.864308514 0.731990854 0.118938737 0.229325556 11485690.64 1745570.698 51065785.4 0.053139678 0.005965763 2.224334007 -1.13231766 HPSKPDPSGECNPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HPSKPDPSGECNPDLR 16 1 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;;;;; 188.27 7.25E-10 1895850000 408452 1125380 1261400 1290250 1327990 1648790 1343150 1515710 1231870 1141400 FALSE TRUE 424578.0004 1318655.261 1294273.12 1545457.599 1102258.734 1265883.51 1237870.393 1495394.387 1187535.239 1365035.477 0.31103807 0.966022703 0.948160793 1.132173944 0.807494569 0.927363085 0.906841188 1.095498551 0.869966576 1 20.38050702 4.738566965 10.78799215 0.966963331 0.310046026 0.816915395 0.092348425 0.026039522 149.1091062 0.021530155 0.124413269 54773.05507 -4.738566965 -0.656917305 HPSS(ph)PSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPSSPSALR 9 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 HPSS(1)PSALR 134.38 0.00016133 855750000 0 151570 67531 115410 66538 113340 54333 80659 68628 151530 TRUE FALSE 0 177600.9684 69290.91334 138237.7535 55227.89453 87018.50268 50074.23749 79577.89804 66158.09169 181219.4023 0 0.980032856 0.382359242 0.762819829 0.304757073 0.480183146 0.276318302 0.439124603 0.365071791 1 17.4673779 -1.313241603 6.057951946 1.000037647 0.455401157 0.300414541 0.254218955 0.00011695 1.33E-05 0.22270698 0.052488925 0.048613669 1.313241603 -0.54463649 HPSSPCS(ph)VKHSPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPSSPCSVKHSPTR 14 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 HPSSPCS(0.63)VKHS(0.356)PT(0.013)R;HPSSPCS(0.51)VKHS(0.439)PT(0.051)R 134.85 2.19E-05 57755000 6373.1 44588 46059 46436 43420 65391 40593 56574 40766 41302 TRUE FALSE 6624.714909 52245.64215 47259.33538 55620.9022 36039.48391 50204.93126 37411.21459 55815.71807 39298.83962 49394.33613 0.134118918 1.057725364 0.956776406 1.126058301 0.729627863 1.01641069 0.757398875 1.130002394 0.795614289 1 15.592058 4.74289113 24.99586349 0.955847656 0.134118592 0.75868921 0.138394675 192.3690568 1110320.314 0.030321257 0.238725611 55321.14118 -4.74289113 -0.821729064 HPTGNSITKS(ph)PPLMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 300.41 4.18E-46 3042200000 2032510 2902400 4072300 2832700 5468800 4642700 4111800 4364000 4592400 2800900 TRUE FALSE 2112755.064 3400864.622 4178427.483 3392999.605 4539215.329 3564503.286 3789506.372 4305507.718 4427120.421 3349682.729 0.630732889 1.015279624 1.247409926 1.012931636 1.355117991 1.064131613 1.131303075 1.285347917 1.321653655 1 21.67559302 4.690348226 2.34611887 1.187134681 0.529012918 0.651910753 0.120497912 0.283448046 2.028424096 0.028746223 0.36438917 49017.16916 -4.690348226 -0.658121763 HPTLLQDPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPTLLQDPDLR 11 0 O60749;O60749-2;D6RC15 O60749 SNX2 Sorting nexin-2 0 ; 170.04 1.62E-05 874510000 183430 411510 396010 434500 392610 506830 386110 448490 358030 410960 FALSE TRUE 190671.958 482183.6414 406330.3459 520442.8031 325874.2924 389126.4136 355845.6893 442478.7251 345144.5702 491479.7437 0.387954866 0.981085482 0.826748917 1.058930322 0.66304725 0.79174456 0.724029207 0.900299007 0.702255942 1 18.90677243 -2.336443455 2.070889472 1.999845812 0.799073181 0.113330462 0.177270151 11724201.41 1310826.755 54885323.27 0.03988158 0.004608468 2.336443455 -1.200772631 HPTPGSSDPLIQPSSPAVCPEPPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPTPGSSDPLIQPSSPAVCPEPPSSPK 27 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 HPTPGSSDPLIQPSSPAVCPEPPS(0.353)S(0.647)PK;HPTPGSSDPLIQPSSPAVCPEPPS(0.287)S(0.713)PK 209.83 9.96E-26 1305030000 373040 302193 384600 343180 554240 549840 495130 498470 469640 297887 TRUE FALSE 387767.9072 354092.297 394622.992 411059.9797 460030.4828 422147.9929 456320.4168 491788.825 452737.7481 356252.2543 1.088464431 0.993937 1.107706652 1.153845273 1.291305465 1.184969324 1.28089131 1.380451124 1.27083476 1 18.44253962 3.596085143 1.689025006 1.264782231 1.04238258 0.353299503 0.099180262 0.326199559 1.831821216 0.029365665 0.057440469 3945.34643 -3.596085143 -0.222399651 HPVSLEQYLMEGSYNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPVSLEQYLMEGSYNK 16 0 K7EJR3;R4GMR5;P48556;K7EJC1 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 182.1 1.76E-12 0 151200 152150 155280 146300 200910 204300 176420 137710 162120 130650 FALSE TRUE 157169.4928 178280.5789 159326.7244 175237.7033 166759.39 156854.4212 162591.7394 135864.2227 156285.3329 156248.3661 1.005895273 1.141007637 1.019701699 1.12153303 1.067271256 1.003878793 1.040598014 0.869540118 1.00023659 1 17.25348158 2.263103247 1.715565625 0.948125975 1.073190592 0.385162326 0.056004244 0.299316948 1.765160982 0.027437069 0.017500242 183.2750079 -2.263103247 0.125064617 HPWDDISYVLPEHMSM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HPWDDISYVLPEHMSM 16 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;;;;;; 182.89 1.12E-09 849167000 199657.3 894647 791990 772487 781293 1070603 592174 823421 704200 1306215 FALSE TRUE 207539.9244 1048295.663 812629.91 925282.623 648489.0949 821971.6784 545757.8545 812384.3883 678855.9796 1562142.82 0.132855922 0.671062626 0.520202058 0.592316279 0.415127917 0.526182157 0.34936489 0.520044888 0.434567167 1 20.57509493 -1.707882319 2.508429027 1.097439595 0.473172835 0.568562926 0.140206235 10696443.11 8147228.436 6556018.852 0.032127606 0.019593755 1.707882319 -0.62426676 HPWIVHWDQLPQYQLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HPWIVHWDQLPQYQLNR 17 0 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 83.418 0.0032009 382140000 61943 74444 73818 66600 79639 84356 65930 72969 79854 83689 FALSE TRUE 64388.55747 87229.17791 75741.75772 79773.28122 66101.99123 64765.59743 60762.23432 71990.96991 76980.07014 100086.2572 0.643330656 0.871540013 0.756764813 0.797045303 0.660450226 0.647097806 0.607098677 0.71928926 0.769137265 1 16.61088437 0.793044295 2.852485629 0.999905838 0.71391109 0.562810954 0.075726553 0.807905116 9.852888418 0.076632616 0.020173247 6.209323611 -0.793044295 -0.285994748 HPYITVWYDPAEAEAPPPQIYDAQLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HPYITVWYDPAEAEAPPPQIYDAQLEER 28 0 P45984-3;P45984-2;P45984-4;P45984;J3KNK1 P45984-3 MAPK9 Mitogen-activated protein kinase 9 0 ; 157.95 6.54E-10 159192000 23768 35978 31535 35762 33519 40602 33230 35255 34505 38846 FALSE TRUE 24706.37899 42156.94163 32356.82801 42835.61686 27821.45235 31172.80083 30625.34577 34782.46439 33263.17179 46457.12995 0.531810274 0.907437495 0.696487881 0.92204613 0.598862917 0.671001434 0.659217343 0.748700241 0.715997132 1 15.50361241 -1.452053819 3.728542814 1.002512882 0.722530417 0.3495551 0.115643638 18007544.41 7017145.22 366245.8195 0.025083378 0.03531394 1.452053819 -0.279982465 HQADACHAYQIIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQADACHAYQIIHR 14 0 Q99538-3;Q99538-2;Q99538;G3V2T4;G3V4E4;G3V4P5;G3V3Z4 Q99538-3 LGMN Legumain 0 ; 203.32 5.29E-09 398870000 153000 155048 148020 145824 179340 207751 151120 151362 137141 146247 FALSE TRUE 159040.5581 181676.2879 151877.5228 174667.552 148855.8509 159503.9787 139274.8195 149333.24 132205.3222 174901.2996 0.909316046 1.038736066 0.868361317 0.998663546 0.851084876 0.911965658 0.79630523 0.853814353 0.755885305 1 17.41618148 3.004947441 1.527272863 0.843992606 0.955228471 0.215425955 0.077338442 0.476560979 2.282518348 0.026235362 0.031391489 1011.457038 -3.004947441 0.111235864 HQAFEAELHANADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HQAFEAELHANADR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 184.99 7.11E-07 952830000 219282 228740 244678 256452 241298 297982 249844 203028 232857 208053 FALSE TRUE 227939.4227 268024.3156 251054.5097 307177.4402 200282.2521 228780.1965 230260.5744 200306.7417 224476.5221 248817.0019 0.916092634 1.077194539 1.008992584 1.23455165 0.804937969 0.919471719 0.925421385 0.805036393 0.902175174 1 17.92472554 3.215729179 24.9995615 0.881423757 1.05690594 0.439611743 0.091462189 196.988544 215694.4239 0.025412717 0.030393362 1643.346632 -3.215729179 0.175482183 HQAFEAELSANQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HQAFEAELSANQSR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 222.88 3.73E-12 860540000 568270 695190 660690 647300 687060 852320 717830 685990 639830 657020 FALSE TRUE 590705.7384 814583.4747 677908.1242 775334.008 570273.7866 654381.597 661564.6089 676795.4261 616802.6433 785750.4896 0.751772663 1.036694836 0.862752404 0.986743271 0.725769559 0.832810931 0.841952525 0.861336308 0.784985376 1 19.58371174 3.257038343 24.9943099 0.835892892 0.915238302 0.106376988 0.095751725 464.0180679 627660.5209 0.024320299 0.032869011 1807.333686 -3.257038343 0.07934541 HQALQAEIAGHEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQALQAEIAGHEPR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 169.37 1.93E-06 739370000 92520 112402 104174 101995 121327 150443 110411 132732 101395 103442 FALSE TRUE 96172.76104 131706.1691 106888.86 122169.3066 100703.8799 115504.8932 101756.6973 130952.9446 97745.81376 123709.4794 0.777408179 1.064640881 0.864031282 0.987550083 0.814035273 0.933678598 0.822545676 1.058552225 0.790123879 1 16.91659653 -1.966000288 2.2896431 1.072358217 0.913384262 0.06684188 0.102031829 18012579.05 7685793.703 6917145.828 0.024595842 0.010814332 1.966000288 -0.158973955 HQAS(ph)DS(ph)ENEELPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQASDSENEELPKPR 15 1 Q96ST2;B8ZZB6 Q96ST2 IWS1 Protein IWS1 homolog 2 HQAS(1)DS(1)ENEELPKPR;HQAS(1)DS(1)ENEELPKPR 84.166 0.0047987 578700000 1093170 552390 707790 646530 913940 1111870 1086800 695200 748820 377680 TRUE FALSE 1136329.196 647258.6855 726235.5889 774411.7043 758588.8053 853655.0431 1001613.776 685881.9811 721870.1145 451679.1649 2.515788383 1.433005407 1.607857181 1.714517216 1.679485937 1.889958868 2.217533714 1.518515872 1.598192192 1 18.78493884 0.85941213 1.432048849 1.007453859 1.816879721 0.404430836 0.306765667 0.591292015 2.326129982 0.279574683 0.082712319 7.234560116 -0.85941213 0.809425862 HQAS(ph)INELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 74.475 0.025652 142230000 195840 140630 211600 145210 320470 217060 250460 193930 231880 129740 TRUE FALSE 203571.9144 164782.1086 217114.4698 173932.1046 265996.6239 166651.1046 230828.2907 191330.6856 223534.6841 155160.069 1.312012271 1.062013633 1.39929346 1.120984966 1.71433685 1.074059232 1.487678449 1.233118075 1.440671466 1 17.2433978 4.225893027 24.99854918 1.321137373 1.187012895 0.048017525 0.211180837 549.229229 1083869.062 0.047167115 0.102962127 16822.59644 -4.225893027 -0.134124478 HQDDLQDVIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQDDLQDVIGR 11 0 E5RG17;Q6P1N9;H0YBX2;G5EA19;U3KQS5;E5RID7 E5RG17 TATDN1 Putative deoxyribonuclease TATDN1 0 ; 198.32 5.41E-08 578930000 306730 361920 342190 335610 359590 395960 329250 337030 352280 399500 FALSE TRUE 318839.9372 424076.9447 351107.7525 401992.6563 298467.0202 304004.2908 303442.5247 332512.6641 339601.5116 477774.3761 0.667344155 0.887609227 0.734881923 0.841385969 0.624702862 0.636292581 0.635116783 0.695961694 0.710798922 1 18.86596996 -1.205975522 3.22319801 1.000786352 0.714437063 0.51263789 0.083393901 13043801.35 19096316.85 103750.2648 0.021717607 0.062233536 1.205975522 -0.286349289 HQDGLPYIDDS(ph)PSSSPHLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQDGLPYIDDSPSSSPHLSSK 21 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 HQDGLPYIDDS(0.98)PS(0.015)S(0.004)S(0.001)PHLSSK 177.35 4.18E-17 348200000 13829 99960 84106 104140 97337 157070 89229 117270 80529 98446 TRUE FALSE 14374.9796 117127.3524 86297.87145 124738.5812 80791.69151 120592.8729 82234.99782 115698.1875 77630.77702 117734.6088 0.122096465 0.994842159 0.732986437 1.059489494 0.686218711 1.024277178 0.698477692 0.98270329 0.659370917 1 16.84517895 4.744513314 24.98361157 0.868310128 0.122096138 0.685713669 0.152079623 328.945965 1380554.731 0.031437897 0.2859204 55528.16403 -4.744513314 -0.74621399 HQDVFNQPTLNSFMGLGQAAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQDVFNQPTLNSFMGLGQAAWK 22 0 P16930;H0YLC7 P16930 FAH Fumarylacetoacetase 0 ; 191.79 1.30E-17 284150000 263944 278834 285347 263567 332798 361648 289208 299337 317085 230603 FALSE TRUE 274364.7129 326721.5705 292783.3772 315699.7659 276229.1148 277660.7328 266539.1213 295324.8771 305673.1728 275785.2427 0.994849145 1.184695625 1.061635403 1.144730453 1.001609485 1.006800546 0.966473473 1.070850906 1.108373928 1 18.07318573 3.229337334 24.96110548 1.027089226 1.100290211 0.250898923 0.059751539 258.7700162 700311.3998 0.016811936 0.020361536 1695.654373 -3.229337334 0.073200984 HQDVPSQDDSKPTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQDVPSQDDSKPTQR 15 1 Q9NRN7 Q9NRN7 AASDHPPT L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0 ; 127.88 4.53E-05 368850000 305540 269710 320920 247220 413430 423290 347330 350150 370790 238951 FALSE TRUE 317602.9551 316030.5944 329283.4388 296119.3781 343155.3163 324987.3125 320105.367 345456.812 357445.3403 285768.8735 1.111398002 1.105895791 1.152271886 1.036219846 1.200814183 1.137238316 1.120154771 1.208867879 1.250819713 1 18.12448926 3.217222851 24.99723395 1.163332934 1.105394535 0.106878157 0.068828829 455.3620519 533456.7067 0.019015917 0.022747412 1649.008337 -3.217222851 -0.057938399 HQEGEIFDTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HQEGEIFDTEK 11 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 168.31 1.82E-05 4504760000 7851020 5194680 6935730 6120310 8381740 9308000 9259380 7189350 7515780 4549130 FALSE TRUE 8160984.332 6086825.881 7116480.822 7330889.051 6957014.829 7146358.064 8533605.601 7092988.523 7245288.546 5440444.925 1.500058257 1.118810311 1.308069638 1.347479692 1.278758433 1.313561329 1.568549212 1.303751553 1.331745592 1 22.37529321 0.443977365 2.587664507 1.000003431 1.339541184 0.439636331 0.11559285 13.99020755 63.62189315 0.107738258 0.028606377 2.779568399 -0.443977365 0.339537752 HQEGEIFDTEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 171.08 1.54E-05 359660000 741290 322960 519080 328490 743880 718640 728810 529970 642250 290060 FALSE TRUE 770556.7016 378425.8677 532607.6512 393464.3416 617435.5433 551746.7511 671683.9678 522866.619 619135.548 346891.7035 2.22131776 1.090904925 1.535371547 1.134256996 1.779908649 1.590544673 1.936292973 1.507290644 1.784809327 1 18.40412581 HQEGEIFDTEKEKYEITEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HQEGEIFDTEKEKYEITEQR 20 2 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ;; 202.95 6.66E-22 4522400000 3615180 1852950 2817370 1329700 4638800 3773270 2720010 2684710 3200260 1771500 FALSE TRUE 3757910.098 2171179.749 2890792.977 1592710.691 3850298.433 2896985.227 2506808.509 2648725.854 3085083.268 2118591.508 1.773777571 1.024822266 1.364488136 0.751778097 1.817385947 1.36741095 1.183242971 1.250229619 1.456195428 1 21.01467401 -1.909090545 2.310802818 0.80842079 1.310953249 0.094526633 0.302055338 28107529.69 13496701.87 29203994.34 0.067767072 0.012328478 1.909090545 0.502532459 HQEVQDQDPVFQGSDSS(ph)GYQSDHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQEVQDQDPVFQGSDSSGYQSDHKK 25 1 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 HQEVQDQDPVFQGSDS(0.056)S(0.743)GYQS(0.201)DHKK 164.64 7.71E-12 135070000 266950 99127 142060 93081 220590 225880 198060 157390 175970 76672 TRUE FALSE 277489.3921 116151.2911 145762.2003 111492.144 183094.1906 173422.7932 182535.5397 155280.4445 169636.8741 91694.41043 3.026241085 1.266721609 1.589651971 1.215909928 1.996786824 1.891312594 1.990694294 1.693455945 1.850024154 1 16.48454617 -1.193489653 5.316142751 0.999958819 1.798401651 0.213308634 0.476633029 0.000216578 3.29E-05 0.429635405 0.10126084 0.064048704 1.193489653 0.798442832 HQFGTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQFGTDK 7 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 ; 110.12 0.006875 152827000 303380 234701 277260 257080 342550 359090 376570 297640 314990 209760 FALSE TRUE 315357.6767 275009.071 284485.6234 307929.6567 284323.4734 275696.7896 347053.4594 293650.6226 303653.5714 250858.4559 1.257113999 1.09627188 1.134048371 1.227503596 1.133401991 1.09901334 1.383463269 1.170582915 1.210457787 1 17.93651404 HQGATSFQDCETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQGATSFQDCETR 13 0 A0A3B3ISZ7;Q9NQ36-3;Q9NQ36-2;Q9NQ36 A0A3B3ISZ7 SCUBE2 "Signal peptide, CUB and EGF-like domain-containing protein 2" 0 99.834 0.0026786 31011000 11272 28244 21665 22742 22000 33280 21789 22571 21602 27286 FALSE TRUE 11717.02726 33094.68729 22229.6077 27240.29972 18260.44786 25551.22436 20081.12125 22268.47266 20824.54824 32632.16928 0.359063695 1.014173683 0.68121759 0.834768277 0.559584247 0.783007227 0.615378067 0.682408591 0.638160095 1 14.99400728 -1.814456305 6.61894256 1.018062788 0.694586778 0.246422616 0.16437496 0.038483066 0.001078766 0.139791418 0.033465828 0.015330054 1.814456305 -0.32347601 HQGGWTDGGSGGGGGYQDGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQGGWTDGGSGGGGGYQDGGYR 22 0 Q8NCA5 Q8NCA5 FAM98A Protein FAM98A 0 ; 279.73 1.33E-45 621970000 83720 109707 115578 108957 114274 143179 109739 116309 129404 121591 FALSE TRUE 87025.33025 128548.3238 118590.0576 130508.3694 94849.7463 109927.8471 101137.3704 114750.0681 124746.7753 145414.4284 0.598464205 0.884013541 0.815531573 0.897492572 0.652271905 0.755962447 0.695511247 0.789124362 0.857870685 1 17.1498109 0.946826274 2.218652034 0.999067692 0.764351524 0.40956462 0.089372339 0.34782452 3.747484049 0.082615093 0.022670224 8.847616176 -0.946826274 -0.234716167 HQGVMVGMGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 31 HQGVMVGMGQK 11 0 C9JTX5;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JUM1;C9JZR7;Q562R1;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P68133;P68032;P63267;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 C9JTX5;P60709;P63261;P68133 ACTB;ACTBL2;ACTG1;ACTA1;ACTC1;ACTG2;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Beta-actin-like protein 2;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscle" 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 173.24 9.42E-06 66928480000 75452395 61499201 73071933 59349573 96156935 95261155 84936185 75621108 76694714 61069290 FALSE TRUE 78431313.82 72061210.37 74976247.6 71088741.4 79812213.54 73138195.45 78278664.88 74607530.74 73934486.22 73034648.13 1.073891856 0.986671562 1.026584635 0.973356389 1.092799316 1.001417783 1.071801766 1.021536115 1.012320701 1 26.12207771 4.777106952 21.78606058 1.023975472 1.073892548 0.167068036 0.034943118 6330.393589 3577501.161 0.007781446 1.498483316 59855.89822 -4.777106952 0.049917076 HQHMHDRDDLYAEQMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HQHMHDRDDLYAEQMER 17 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ;;;;;; 102.78 0.00031303 2295220000 670407 709255 785042 686791 876914 947764 787843 716574 775536 816329 FALSE TRUE 696875.186 831064.029 805500.8394 822636.2099 727856.4715 727660.1745 726089.807 706969.4976 747624.6109 976273.038 0.713811771 0.851261887 0.82507742 0.842629242 0.745546013 0.745344946 0.743736413 0.724151411 0.76579459 1 19.89692516 -1.279841635 3.569288362 1.000611036 0.77244177 0.678113402 0.046909105 17631775.93 26308562.21 114818.2456 0.012297283 0.052499887 1.279841635 -0.228169266 HQILEQAVEDYAETVHQLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQILEQAVEDYAETVHQLSK 20 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 222.51 4.11E-25 307920000 486020 436210 491150 457760 593770 654450 582310 533430 557330 448890 FALSE TRUE 505208.4449 511125.6743 503949.7725 548303.5617 492841.1875 502463.9058 536667.0206 526280.2434 537271.8022 536841.401 0.941075789 0.952098093 0.9387312 1.021351112 0.91803871 0.935963405 0.999675173 0.98032723 1.000801729 1 19.03413641 2.230521007 24.97968788 0.99236201 0.952363365 0.402055675 0.026168021 201.4801662 626009.6657 0.009734194 0.00731118 170.0282193 -2.230521007 -0.039998645 HQIVEVAGDDKYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HQIVEVAGDDKYGR 14 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;; 160.47 2.85E-06 4869570000 4576450 3318130 4489530 3492180 5514730 5914230 5313860 4475680 4631930 2795780 FALSE TRUE 4757131.78 3887993.016 4606530.84 4182922.781 4577338.164 4540739.714 4897345.768 4415690.83 4465227.744 3343559.563 1.422774648 1.162830493 1.377732549 1.251038811 1.369001532 1.358055578 1.464710192 1.320655651 1.335471273 1 21.67295339 0.341214889 2.646178326 1.000000224 1.339450441 0.617036258 0.080422347 22.97126661 90.79827754 0.073995115 0.019591376 2.193890206 -0.341214889 0.339450218 HQKEECQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQKEECQDR 9 1 E9PQ42;E9PJD7;Q6ZMK1-4;Q6ZMK1-2;Q6ZMK1 E9PQ42 CYHR1 Cysteine and histidine-rich protein 1 0 94.297 0.0052981 52585000 11365 8909.1 8686.6 8100 11712 14558 10515 11228 8806 9527.5 FALSE TRUE 11813.69898 10439.16862 8912.979932 9702.155824 9721.198423 11177.12513 9690.806824 11077.50703 8489.07378 11394.23121 1.036814047 0.916180164 0.782236183 0.851497187 0.853168436 0.980945965 0.850501157 0.972203111 0.745032607 1 13.47601597 HQLEETKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQLEETKK 8 1 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ; 65.347 0.041875 109797000 131514 150343 169555 147206 184473 223160 189847 164422 176311 179577 FALSE TRUE 136706.2743 176163.2407 173973.7426 176322.9074 153116.3454 171334.472 174966.2961 162218.192 169965.6016 214761.6749 0.636548743 0.820273174 0.810078161 0.821016634 0.712959356 0.797788861 0.814699811 0.755340505 0.791414956 1 17.71237704 -4.999999999 0.355104664 3.67130209 0.769499846 0.606075645 0.055209231 301.9919126 2.43838981 615.4257069 0.039210218 1.00E-05 4.999999999 -2.901802244 HQLLEADISAHEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HQLLEADISAHEDR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 185.12 7.02E-07 256840000 98472 174624 129960 143438 148203 188808 141937 136087 118682 162196 FALSE TRUE 102359.7506 204614.3136 133346.8644 171809.6083 123011.507 144960.2034 130811.6071 134262.9764 114410.658 193975.2008 0.527695036 1.054847799 0.687442848 0.885729761 0.634160998 0.747313073 0.67437284 0.692165678 0.589821057 1 17.56551269 3.233250952 24.97547682 0.704672167 0.800674068 0.028618121 0.163539442 340.667377 1602422.136 0.042599986 0.052359944 1711.003714 -3.233250952 0.096001901 HQLSHRPEAPCS(ph)PPSVPSAASEPTVVLLQAEPQLLDTHREEEVSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQLSHRPEAPCSPPSVPSAASEPTVVLLQAEPQLLDTHREEEVSPAR 47 2 Q9H9D4 Q9H9D4 ZNF408 Zinc finger protein 408 1 HQLS(0.078)HRPEAPCS(0.658)PPS(0.263)VPS(0.001)AASEPTVVLLQAEPQLLDTHREEEVSPAR 58.329 0.0048644 196590000 19459 30598 37850 23759 26342 33214 27657 28583 22720 31682 TRUE FALSE 20227.25635 35852.96848 38836.40209 28458.45929 21864.39625 25500.55186 25489.17207 28199.89164 21902.31164 37889.48131 0.533848858 0.946251235 1.024991653 0.751091287 0.577057154 0.67302457 0.672724228 0.744267028 0.578057838 1 15.20950977 3.486706115 24.69703549 0.691929968 0.853134126 0.102035991 0.162691149 667.0210758 1718692.927 0.042191034 0.060515128 3066.945897 -3.486706115 0.161204158 HQNVQLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 2554500000 483108 574178 566797 514212 763562 774160 603421 622162 533009 723537 FALSE TRUE 502181.4769 672788.605 581568.1954 615921.5988 633772.004 594373.0725 556123.2853 613822.936 513826.1102 865300.2222 0.580355192 0.777520435 0.672099903 0.711801041 0.732430187 0.686898093 0.642694028 0.709375683 0.593812525 1 19.72284125 -1.449211832 3.938323878 1.002137591 0.684421977 0.735778421 0.057691911 8948889.92 3294603.616 164537.0402 0.012313122 0.03554579 1.449211832 -0.317715614 HQPADLLEFALQHFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQPADLLEFALQHFTR 16 0 P31323 P31323 PRKAR2B cAMP-dependent protein kinase type II-beta regulatory subunit 0 ; 199.49 2.20E-11 179548000 39753 54603 49252 52090 59730 64518 46638 57383 53236 54423 FALSE TRUE 41322.47914 63980.6405 50535.54758 62393.24653 49577.11594 49534.67228 42982.39169 56613.87474 51320.04676 65086.14486 0.634889026 0.983014751 0.776440941 0.958625629 0.761715355 0.76106324 0.660392343 0.869829898 0.788494185 1 15.99006284 -1.402804784 2.836463978 1.00393539 0.805261645 0.239131644 0.10689305 21496303.59 24406438.42 685397.61 0.023897831 0.039554438 1.402804784 -0.198673745 HQPST(ph)PDPFLKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HQPSTPDPFLKPR 13 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 HQPS(0.005)T(0.995)PDPFLKPR;HQPS(0.009)T(0.991)PDPFLKPR;HQPS(0.005)T(0.995)PDPFLKPR;HQPS(0.004)T(0.996)PDPFLKPR;HQPS(0.029)T(0.971)PDPFLKPR 118.47 0.00062306 1899740000 1140160 1077536 1184700 1058710 1410550 1405490 1325950 1135880 1279490 989003 TRUE FALSE 1185174.397 1262594.426 1215574.255 1268119.678 1170785.215 1079086.248 1222018.574 1120655.387 1233441.405 1182779.202 1.002025057 1.067481085 1.027727113 1.0721525 0.989859487 0.912331098 1.033175568 0.947476405 1.042833187 1 20.17374935 3.137596887 7.116910301 0.981599554 1.042895822 0.303747706 0.040114217 0.236112927 14.57455673 0.010887865 0.013064687 1372.767178 -3.137596887 0.061296268 HQPTAIIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQPTAIIAK 9 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 140.45 0.00010908 1587220000 1547290 1295940 1572430 1187990 3310300 2181500 1818200 1624430 1644520 1994440 FALSE TRUE 1608378.204 1518507.614 1613408.818 1422970.876 2747616.388 1674879.686 1675684.733 1602657.173 1585334.046 2385212.332 0.67431238 0.636634145 0.676421464 0.596580379 1.15193786 0.702193119 0.702530634 0.671913838 0.664651119 1 21.18568627 HQPVPQLQAHS(ph)TPHPDDFANDDIDSYMIAMETTIGNEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQPVPQLQAHSTPHPDDFANDDIDSYMIAMETTIGNEGSR 40 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 HQPVPQLQAHS(0.482)T(0.482)PHPDDFANDDIDS(0.019)Y(0.016)MIAMETTIGNEGSR;HQPVPQLQAHS(0.255)T(0.255)PHPDDFANDDIDS(0.255)Y(0.235)MIAMET(0.001)TIGNEGSR 165.55 5.84E-19 68046000 9527.2 10237.5 14604.4 15156.1 13967 20265.6 18141.9 16741.1 11872.4 17111 TRUE FALSE 9903.341213 11995.71099 14985.00266 18153.93134 11592.89433 15559.22153 16719.89047 16516.71294 11445.11464 20463.57284 0.483949762 0.58619827 0.732276948 0.887134006 0.566513698 0.760337486 0.817056269 0.807127527 0.559292101 1 14.32077043 0.551482246 0.051864398 1.644922789 2.14E-22 0.385784503 0.123452644 88.06605842 2.078065479 36.31903957 28.65515006 3.560264352 -0.551482246 -1.644922789 HQPWQS(ph)PERPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 119.92 0.00018804 810770000 144079 124720 144395 151079 183263 196501 166680 145945 136552 131984 TRUE FALSE 149767.3502 146139.6898 148158.0523 180961.9753 152112.0207 150866.6208 153615.1861 143988.846 131637.5202 157843.7378 0.948833018 0.925850413 0.938637506 1.146462811 0.963687396 0.955797315 0.973210519 0.912224001 0.833973663 1 17.2681375 1.731797245 3.825712098 0.903476329 0.980948685 0.144133547 0.069530446 0.341537295 11.0103563 0.038663091 0.018918819 53.9258805 -1.731797245 0.077472356 HQQGQGDDSSHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQQGQGDDSSHKK 13 1 A0A2R8Y6L5;A0A2R8Y6I6;Q13627-2;Q13627;Q13627-5;A0A2R8Y443;A0A2R8YDF3;Q13627-4;Q13627-3;E7EMI5 A0A2R8Y6L5 DYRK1A Dual specificity tyrosine-phosphorylation-regulated kinase 1A 0 ; 110.29 0.00043517 24785000 17475.9 30761 31069 28370 27906.4 39768 33050 36866 31984 24062.7 FALSE TRUE 18165.86203 36043.96246 31878.68366 33981.50132 23162.8801 30532.48469 30459.45464 36371.87157 30832.90209 28777.32536 0.631256095 1.252512595 1.107770902 1.180842935 0.804900379 1.060991052 1.058453288 1.263907299 1.07143043 1 14.81264489 1.979017072 19.4313689 1.146122032 1.024178563 0.049336076 0.18118991 113.1943557 104821.031 0.071261682 0.046817938 95.28336188 -1.979017072 -0.121943469 HQRKY(ph)RR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQRKYRR 7 3 H3BVB7;H3BT33;H3BMX3;H3BTJ0;Q9BUV0-3;Q9BUV0-2;Q9BUV0 H3BVB7 RSRP1 Arginine/serine-rich protein 1 1 HQRKY(1)RR 62.714 0.039177 255480000 188680 153930 146470 200670 223610 269340 182470 172800 194000 160190 TRUE FALSE 196129.2321 180366.2801 150287.1285 240361.9271 185600.8521 206789.8669 168167.5246 170483.8986 187017.9779 191576.1635 1.023766363 0.941486022 0.78447718 1.254654664 0.968809734 1.079413342 0.877810274 0.889901413 0.976206927 1 17.54755854 0.970089377 21.53016976 1.000000018 0.970808079 0.000678295 0.120808124 6239.259876 4491146.754 0.11514673 0.028786682 9.334463821 -0.970089377 -0.029191938 HQS(ph)FGAAVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;HQS(1)FGAAVLSR;HQS(1)FGAAVLSR 194.05 4.41E-07 3272980000 1326570 1818890 1806360 1690000 2646230 2511450 1594920 1729360 1677290 2237210 TRUE FALSE 1378944.008 2131270.208 1853435.226 2024276.956 2196424.77 1928203.799 1469906.003 1706180.758 1616924.661 2675548.466 0.515387415 0.796573202 0.692730948 0.756583924 0.820925054 0.720676087 0.549384929 0.637693834 0.604333908 1 21.35140323 4.756052336 23.66893103 0.710174516 0.515387078 0.203365641 0.121904308 2981.905672 4034828.636 0.028577131 0.804437305 57023.2986 -4.756052336 -0.194787438 HQTLQGVAFPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQTLQGVAFPISR 13 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 0 110.97 0.00051341 0 190440 417760 359340 389900 462150 504010 344930 394270 343260 399390 FALSE TRUE 197958.7183 489507.0303 368704.6956 467021.0563 383593.9081 386961.3158 317893.4853 388985.4555 330906.1397 477642.8237 0.414449267 1.024839076 0.771925542 0.977762112 0.803097815 0.810147869 0.665546449 0.814385638 0.692789933 1 18.86557266 2.450373585 24.96822646 0.772662381 0.818199785 0 0.174591077 1323.897292 1235815.322 0.056245943 0.047059993 282.0808378 -2.450373585 0.045537404 HQVIQTVHPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQVIQTVHPVEK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 55.314 0.074174 45877000 45340 74427 75384 66170 80826 94835 67609 78656 69434 100990 FALSE TRUE 47130.05821 87209.25829 77348.56897 79258.2285 67087.22539 72811.00849 62309.62992 77601.74498 66935.0839 120777.0569 0.390223602 0.722068086 0.640424357 0.656235799 0.555463323 0.602854634 0.515906179 0.642520583 0.554203634 1 16.8819869 -1.199675791 3.969234578 1.0002674 0.594358542 0.669619751 0.086950244 9380061.054 5670167.518 20330.33617 0.018748127 0.063142854 1.199675791 -0.405908858 HQYINEDEYEVNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQYINEDEYEVNLK 14 0 Q93009;A0A669KBL1;Q93009-3 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 0 128.96 7.07E-05 127950000 84065 73218 76802 76019 91651 101100 102230 95888 96660 60873 FALSE TRUE 87383.95111 85792.62194 78803.52321 91055.33131 76072.19576 77621.05719 94216.94547 94602.7782 93181.22548 72799.89887 1.200330666 1.178471719 1.082467482 1.250761783 1.044949196 1.066224794 1.294190609 1.299490517 1.279963667 1 16.15164883 2.229708601 24.99634082 1.251196859 1.137557593 0.100447354 0.101605795 282.4472809 797569.015 0.036110174 0.02706487 169.7104561 -2.229708601 -0.113639266 HQYSDYDYHS(ph)S(ph)SEKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQYSDYDYHSSSEKLK 16 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 2 HQYSDYDY(0.083)HS(0.923)S(0.906)S(0.087)EKLK;HQYSDYDY(0.044)HS(0.975)S(0.901)S(0.079)EKLK 147.9 1.31E-06 315740000 460960 196539 270190 180176 490360 467660 409010 274100 301040 118239 TRUE FALSE 479159.0567 230293.0444 277231.3734 215814.275 407008.7824 359053.0525 376950.7275 270426.1378 290205.6292 141405.6682 3.388542077 1.628598395 1.960539325 1.526206677 2.878305993 2.539170155 2.665739869 1.912413705 2.052291346 1 17.10948043 0.695209836 1.269515588 1.005205169 2.299538791 0.345361734 0.546781874 1.186539474 3.108722449 0.510960198 0.154257494 4.956896325 -0.695209836 1.294333621 HQYSDYDYHSSSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HQYSDYDYHSSSEK 14 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 89.866 0.0034578 119590000 20266 58258 56603 50271 64223 77182 52264 64533 53603 59921 FALSE TRUE 21066.11733 68263.35832 58078.12068 60214.45376 53306.3974 59257.6502 48167.41111 63668.04069 51673.8385 71661.37269 0.293967538 0.952582343 0.810452249 0.84026375 0.743865145 0.826912017 0.672153062 0.888456895 0.721083571 1 16.12890806 4.747741205 24.81057713 0.818181532 0.293967233 0.733710506 0.096415262 524.7283997 1418047.529 0.020953225 0.260351871 55942.41421 -4.747741205 -0.524214299 HQYYNQEWTLWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 254.4 8.29E-24 684990000 203491 207231 245020 246260 235480 280840 276230 233480 221818 197410 FALSE TRUE 211524.9818 242821.3122 251405.4225 294969.493 195453.1937 215619.1662 254578.3708 230350.5825 213834.8135 236088.7099 0.895955516 1.028517257 1.064876938 1.249401097 0.827880307 0.913297236 1.078316583 0.975695037 0.905739261 1 17.84896953 3.213595245 24.99977466 0.957854396 1.057832221 0.217917059 0.101001038 398.4458237 398993.7144 0.030234983 0.036151374 1635.291747 -3.213595245 0.099977825 HRADHPPAEVTSHAASGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HRADHPPAEVTSHAASGAK 19 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 171.79 6.20E-12 281304000 248182 251786 290746 250794 386681 405013 359122 335493 332879 290256 FALSE TRUE 257980.417 295028.2869 298323.0796 300400.3047 320953.1017 310954.8688 330973.0792 330996.2651 320898.7498 347126.1059 0.743189327 0.849916736 0.859408366 0.865392431 0.924600876 0.895797992 0.953466402 0.953533196 0.924444299 1 18.40510034 7.291685386 0.247081487 0.983355708 8.07E-15 0.888378047 0.022855043 10.27898203 0.18970575 0.028632763 3.900648743 19574261.49 -7.291685386 -0.983355708 HRAEAPPLEREDS(ph)GTFSLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRAEAPPLEREDSGTFSLGK 20 2 O75569;G5E9Q4 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 HRAEAPPLEREDS(0.915)GT(0.085)FSLGK;HRAEAPPLEREDS(0.988)GT(0.012)FSLGK 211.49 1.39E-22 779410000 593400 493750 829340 408610 1097800 862890 662420 651210 857220 702410 TRUE FALSE 616827.8902 578547.7217 850953.2817 489431.8384 911196.3481 662496.8747 610497.7895 642481.5951 826368.8196 840033.791 0.734289378 0.688719582 1.012998871 0.582633513 1.084713922 0.78865503 0.726753847 0.764828275 0.983732831 1 19.68008784 -4.999999938 0.166928993 1.74431502 0.763829546 0.151887513 0.147744211 261.6789045 2.451414657 64.07636452 0.532906478 1.00E-05 4.999999938 -0.980485473 HRDILQDYTHEFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRDILQDYTHEFHK 14 1 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;O95249-2 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 107.61 0.00029378 137820000 82429 77854 87707 79552 116400 121510 100610 91851 86283 98492 FALSE TRUE 85683.36057 91224.81888 89992.71647 95287.14816 96614.36958 93291.144 92723.9253 90619.88758 83177.69168 117789.6217 0.72742708 0.774472467 0.764012272 0.808960474 0.820228202 0.792014973 0.787199449 0.769336774 0.706154672 1 16.8458529 -1.052760375 4.408236138 1.000014515 0.775368016 0.811706213 0.032883042 0.097939044 19686458.67 643.6771896 0.007842541 0.088560411 1.052760375 -0.224646498 HRDLLHNEDRHDDYFQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRDLLHNEDRHDDYFQER 18 2 Q8N684-2;Q8N684;Q8N684-3 Q8N684-2 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 ; 263.09 4.26E-31 1926310000 238290 279970 282820 151134 464730 403980 212870 271290 298090 396930 FALSE TRUE 247697.8732 328052.6696 290190.5215 181027.8541 385735.3606 310161.7674 196184.6932 267653.8013 287361.7991 474700.8338 0.521797847 0.691072453 0.611312433 0.381351456 0.812586229 0.653383658 0.413280701 0.563836805 0.605353475 1 18.85665906 0.787566514 5.622336779 0.999999696 0.580225887 0.521210814 0.119876084 6.639348485 175.5415798 0.113611056 0.028612319 6.131496911 -0.787566514 -0.419773809 HRDLVDEDLSHFQS(ph)GSPPAPNGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRDLVDEDLSHFQSGSPPAPNGFK 24 1 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 HRDLVDEDLS(0.161)HFQS(0.677)GS(0.161)PPAPNGFK 78.836 0.011836 475220000 73045 74955 91882 61731 104720 111150 97242 98792 108190 92061 TRUE FALSE 75928.873 87827.93818 94276.5204 73941.20755 86919.73181 85337.09699 89619.91795 97467.85483 104296.263 110098.5903 0.68964437 0.797720824 0.856291803 0.671590865 0.789471796 0.77509709 0.813996961 0.885277954 0.947298805 1 16.74843647 1.505726388 1.118673482 0.998669238 0.762893345 0.748105471 0.049331604 0.221474813 0.536379931 0.043582118 0.015479585 32.04249961 -1.505726388 -0.235775894 HRDTHPGS(ph)PGSPGPALRPLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.5)PGS(0.5)PGPALRPLPAR 138.23 8.50E-07 254810000 75005 144360 147140 122430 153230 173520 132440 129910 122200 131710 TRUE FALSE 77966.25532 169152.707 150974.5893 146646.2886 127184.0193 133222.6097 122059.0067 128168.7689 117802.0459 157516.0528 0.494973394 1.07387599 0.958471131 0.930992658 0.807435287 0.845771637 0.774898841 0.813687029 0.747873273 1 17.26513934 3.219218943 24.42635886 0.818697059 0.88623477 0 0.153689971 674.4966734 851810.8619 0.042345029 0.050690367 1656.604906 -3.219218943 0.067537711 HRDTHPGSPGS(ph)PGPALRPLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRDTHPGSPGSPGPALRPLPAR 22 2 Q8N0Y2-2;Q8N0Y2 Q8N0Y2-2 ZNF444 Zinc finger protein 444 1 HRDTHPGS(0.004)PGS(0.996)PGPALRPLPAR 107.47 0.00021525 250560000 65265 95092 77416 80862 94392 107580 83810 85800 74413 85035 TRUE FALSE 67841.7126 111423.3113 79433.52456 96856.26225 78347.28156 82596.17539 77240.7532 84649.99134 71734.89067 101695.9802 0.667103188 1.095651088 0.781088146 0.952409939 0.770406868 0.81218722 0.75952612 0.832382865 0.705385705 1 16.63390313 3.221541452 24.97882725 0.803277267 0.883249759 0.047344814 0.126197286 576.8740498 846669.5189 0.033075604 0.039626436 1665.487787 -3.221541452 0.079972492 HRDYETATLSDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ; 102.66 0.0010045 899810000 575020 1784790 1774630 1618010 1899540 2231710 1667740 1900300 1880120 2236570 FALSE TRUE 597722.2336 2091313.799 1820878.316 1938047.549 1576656.869 1713429.174 1537018.181 1874829.587 1812454.848 2674783.07 0.223465686 0.781862956 0.68075738 0.724562515 0.589452239 0.640586219 0.574632836 0.700927716 0.677608165 1 21.35099046 -5 0.188255286 2.566568292 0.563079731 0.424510293 0.139929126 134.3287907 1.311226791 78.83017825 0.368850865 1.00E-05 5 -2.003488562 HREELEQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HREELEQSK 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 110.76 0.0013431 740050000 718620 513390 604320 497420 827080 916520 728030 610080 629290 474540 FALSE TRUE 746991.6725 601560.7389 620069.0757 595808.1913 686493.237 703672.12 670965.1062 601902.8755 606641.9758 567517.0274 1.316245393 1.059987119 1.09259995 1.049850776 1.209643418 1.23991367 1.182281894 1.060589985 1.068940572 1 19.11430415 1.643933885 4.736321663 1.04407681 1.157671393 0.326477681 0.079557906 0.213736276 10.74847356 0.045540132 0.021414831 44.0487801 -1.643933885 0.113594583 HREQEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HREQEELRR 9 2 Q8WXF1;Q8WXF1-2;A0A0U1RQF9 Q8WXF1 PSPC1 Paraspeckle component 1 0 62.823 0.04505 104980000 30174 30927 31540 28737 39011 41840 35071 31911 24905 35380 FALSE TRUE 31365.29282 36238.47167 32361.95831 34421.09283 32379.92415 32123.29409 32322.04338 31483.28524 24008.67391 42312.03361 0.741285401 0.856457811 0.764840532 0.813505991 0.765265136 0.759199957 0.763897185 0.744074027 0.567419523 1 15.36878041 3.053310514 4.130909057 0.751272551 0.796341756 0.005008469 0.101934478 0.811637603 28.99386508 0.028527812 0.033941203 1130.60399 -3.053310514 0.045069205 HRGS(ph)ADYSMEAK ddPTM_MDA-MB-175_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 113.29 0.00020958 0 165820 172870 184580 160070 233000 254470 194200 190830 178060 177670 TRUE FALSE 172366.7016 202559.0778 189390.3064 191731.3682 193394.7432 195373.199 178978.0966 188272.236 171651.6554 212481.0348 0.811209818 0.95330427 0.89132805 0.902345795 0.910174141 0.919485352 0.842325042 0.886066072 0.807844594 1 17.69697455 2.25879076 24.97275085 0.874645321 0.900940655 0.001756856 0.057156173 798.099858 985197.9684 0.018164791 0.01517833 181.4641173 -2.25879076 0.026295334 HRGS(ph)EEDPLLSPVETWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HRGSEEDPLLSPVETWK 17 1 Q13017-2;Q13017;H0YK04;A0A0A0MSK6 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 1 HRGS(1)EEDPLLSPVETWK;HRGS(1)EEDPLLSPVETWK;HRGS(1)EEDPLLSPVETWK 194.97 2.70E-11 734245000 793320 644850 828750 662150 1033030 1057030 975190 828320 968280 639140 TRUE FALSE 824640.8862 755597.9713 850347.9058 793121.2937 857435.9296 811550.8019 898752.0596 817217.7253 933431.7919 764367.2459 1.078854295 0.988527407 1.11248606 1.037618106 1.121759121 1.061728909 1.175811842 1.069142784 1.221182353 1 19.54390643 3.343598139 1.019016637 1.115159488 1.043787619 0.119357632 0.0653387 0.98812783 2.169516935 0.02453291 0.045440521 2205.96257 -3.343598139 -0.07137187 HRHPLDHDCSGEGHPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HRHPLDHDCSGEGHPTSR 18 1 A0A087X0D9;E9PFU9;Q8WV99;B8ZZ56;E7EV05;B4DEN4;Q8WV99-2 A0A087X0D9 ZFAND2B AN1-type zinc finger protein 2B 0 ;;; 117.26 4.60E-05 793520000 10985.3 27855.6 25514.2 25078 24221.5 30142.2 25217.7 29608.4 25093.8 28371.7 FALSE TRUE 11419.00813 32639.58261 26179.12101 30038.35355 20104.33808 23142.13086 23241.07078 29211.54783 24190.67904 33930.59141 0.336540203 0.96195148 0.771549211 0.88528824 0.592513636 0.682043251 0.684959201 0.86092068 0.712945989 1 15.05029896 -4.999999856 0.212398014 2.291896687 0.699131926 0.214118462 0.164529584 239.6803382 2.392285003 131.8164344 0.324062348 1.00E-05 4.999999856 -1.592764761 HRHS(ph)PTGPPGFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.5)PT(0.5)GPPGFPR;HRHS(0.969)PT(0.031)GPPGFPR;HRHS(0.999)PT(0.001)GPPGFPR;HRHS(0.785)PT(0.215)GPPGFPR;HRHS(0.754)PT(0.246)GPPGFPR 149.22 2.64E-05 2742790000 561442 684692 609211 601211 683951 767214 630467 611528 586525 639628 TRUE FALSE 583608.1637 802282.5248 625087.5391 720128.7414 567693.2533 589040.1757 581049.3491 603331.4674 565416.0798 764950.8602 0.762935496 1.048802696 0.817160385 0.941405231 0.742130355 0.770036621 0.759590425 0.788719248 0.739153466 1 19.54500755 3.238644393 25 0.785459576 0.898348183 0.160589887 0.100192576 3.11721978 929903.3503 0.025725804 0.032716387 1732.384915 -3.238644393 0.112888607 HRHSPT(ph)GPPGFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRHSPTGPPGFPR 13 1 P98175-5;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 HRHS(0.375)PT(0.625)GPPGFPR;HRHS(0.375)PT(0.625)GPPGFPR 112.51 0.0013125 2903000000 499270 640720 622760 633100 618070 770350 602630 579620 562150 650090 TRUE FALSE 518981.5651 750758.6759 638989.6372 758325.2904 513010.6822 591447.8873 555394.2859 571851.142 541918.3313 777462.6888 0.667532439 0.965652354 0.821891065 0.975384802 0.659852479 0.760741185 0.714367768 0.735535158 0.697034519 1 19.56841391 3.230133636 24.99995722 0.744260197 0.862780393 0.128180764 0.117921681 284.8778695 845133.745 0.031027741 0.037654651 1698.766296 -3.230133636 0.118520196 HRMS(ph)PGVAGSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HRMSPGVAGSPR 12 1 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR;HRMS(1)PGVAGSPR 140.78 3.63E-05 877620000 420228 492726 478319 456297 567680 635037 473220 492730 477572 496155 TRUE FALSE 436818.9259 577347.8576 490784.3861 546551.1847 471185.9564 487559.2808 436127.7799 486125.7603 460384.277 593367.0728 0.736169811 0.973002858 0.827117662 0.921101304 0.794088479 0.821682401 0.735005024 0.819266492 0.775884437 1 19.17856535 3.21420167 24.94856678 0.809551656 0.869449704 0.030857252 0.087400562 500.6282533 512744.6385 0.023071411 0.0275876 1637.576773 -3.21420167 0.059898048 HRNT(ph)ETSKSPEKDVPMVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRNTETSKSPEKDVPMVEK 19 3 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 HRNT(0.299)ET(0.234)S(0.234)KS(0.234)PEKDVPMVEK 62.064 0.024329 42455000 87897 17352 35230 16303 82372 67568 63039 52073 54938 18267 TRUE FALSE 91367.24143 20332.07102 36148.12274 19527.68474 68370.43686 51876.356 58097.83846 51375.04661 52960.79211 21846.06891 4.182319566 0.93069701 1.654674024 0.893876368 3.129644842 2.374631162 2.659418438 2.351683812 2.424271036 1 14.41508608 3.225190238 24.99988789 2.411905048 1.826433425 0.031584483 0.991300546 626.1953017 1170855.422 0.271345197 0.326051515 1679.539559 -3.225190238 -0.585471623 HRNWYIQATCATSGDGLYEGLDWLANQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRNWYIQATCATSGDGLYEGLDWLANQLK 29 1 P61204;P61204-2;H0YGG7 P61204 ARF3 ADP-ribosylation factor 3 0 195.09 1.62E-19 206220000 135680 80180 123390 73811 215740 182690 179680 150150 175540 134590 FALSE TRUE 141036.7512 93950.29129 126605.6448 88410.5955 179068.5919 140263.0162 165596.2121 148137.4848 169222.3497 160960.3336 0.876220545 0.583685988 0.786564254 0.54926946 1.112501371 0.871413553 1.028801372 0.920335349 1.051329516 1 17.29634567 3.236128318 24.99999998 0.984936251 0.696962211 0.649818172 0.107097885 37.18216966 382172.0973 0.027778093 0.034712663 1722.377398 -3.236128318 -0.28797404 HRNWYIQATCATSGDGLYEGLDWLSNQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRNWYIQATCATSGDGLYEGLDWLSNQLR 29 1 P84077 P84077 ARF1 ADP-ribosylation factor 1 0 ; 185.06 4.61E-18 806020000 375820 450530 391290 316340 758100 754170 377390 528000 466300 936590 FALSE TRUE 390657.6638 527905.0229 401487.3388 378911.1078 629238.4328 579025.4471 347809.1857 520923.0236 449517.9541 1120096.878 0.348771317 0.471303003 0.358439834 0.338284228 0.561771437 0.516942292 0.310517056 0.465069615 0.401320602 1 20.09519209 -1.769726974 2.379038006 1.163706974 0.422012446 0.830165772 0.078805625 3602231.664 2352909.731 3434710.137 0.019987775 0.016993116 1.769726974 -0.741694528 HRPDLIDFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HRPDLIDFDK 10 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3 Q01082;Q01082-3 SPTBN1;SPTB "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic" 0 ;;; 94.297 0.0049271 294778000 658481 470305 549251 447106 777515 734084 698691 592860 630845 421318 FALSE TRUE 684478.3383 551076.2253 563564.9323 535542.2323 645353.278 563604.1162 643925.7737 584913.6814 608141.0117 503867.1955 1.358449894 1.093693398 1.11847911 1.06286386 1.280800345 1.118556876 1.277967249 1.160848904 1.206947023 1 18.94268401 -1.095641211 3.773377379 0.999935571 1.181369075 0.276542029 0.090156387 13454887.9 29109309.23 12292.43017 0.020352648 0.080234064 1.095641211 0.181433504 HRPELIEYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRPELIEYDK 10 1 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 129.16 0.00018661 233500000 269870 211920 220880 285470 658140 451100 543290 274630 260690 389290 FALSE TRUE 280524.676 248315.6115 226636.3143 341935.114 546269.5979 346338.8615 500705.5102 270949.0341 251307.8178 465563.9221 0.602548141 0.533365237 0.486799564 0.734453633 1.173350365 0.743912587 1.075481768 0.581980306 0.539792295 1 18.82861974 3.571502791 5.239599359 0.83461987 0.54457396 0.342229427 0.191620884 0.278209786 11.96782407 0.053343207 0.083112319 3728.230808 -3.571502791 -0.29004591 HRPELIEYDKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRPELIEYDKLR 12 2 O43707;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 113.24 0.00071298 403840000 213784 161805 200476 193940 458303 347242 319894 209893 232077 344215 FALSE TRUE 222224.3574 189593.7501 205700.5693 232300.7531 380400.8198 266600.308 294819.8724 207079.7277 223724.5941 411657.3389 0.539828485 0.460562055 0.499688818 0.564306114 0.924071513 0.647626759 0.716177861 0.503039077 0.543472867 1 18.65108442 3.465423266 24.98140402 0.686293051 0.502066204 0.312328749 0.146448862 305.3794657 652144.8301 0.041074092 0.055655805 2920.271744 -3.465423266 -0.184226846 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPR 36 2 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ; 238.84 6.94E-50 1859530000 793510 753980 941210 746610 1206070 1209020 898430 968670 920120 875300 FALSE TRUE 824838.3875 883470.1998 965738.7058 894287.2296 1001062.652 928243.4279 828008.709 955686.5631 887005.0609 1046798.276 0.787963074 0.843973686 0.922564287 0.854307128 0.956309038 0.886745277 0.790991663 0.912961537 0.847350517 1 19.99755202 HRPS(ph)AGGPDSAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRPSAGGPDSAGR 13 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 HRPS(1)AGGPDSAGR;HRPS(1)AGGPDSAGR 173.87 1.27E-05 144179000 69093 98765 90521 88697 92810 122125 98515 97964 94261 96774 TRUE FALSE 71820.84499 115727.1205 92880.05162 106241.0019 77034.18935 93763.31957 90793.13688 96650.95282 90868.56502 115735.0124 0.620562814 0.99993181 0.802523365 0.917967689 0.665608339 0.810155178 0.784491529 0.835105564 0.78514326 1 16.82046585 -1.026218992 4.562614297 1.000003315 0.809032117 0.246362119 0.103100474 6.55E-06 1.40E-06 0.090593949 0.021352429 0.094141477 1.026218992 -0.190971198 HRPS(ph)PPAT(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 88.385 0.022951 5178440000 2866550 2243200 2710040 2155140 3250390 3371070 3083430 2720840 2783340 1983210 TRUE FALSE 2979723.607 2628452.15 2780665.869 2581420.26 2697889.869 2588190.082 2841742.7 2684371.59 2683168.137 2371782.029 1.256322702 1.108218259 1.172395201 1.088388489 1.137494861 1.091242808 1.198146653 1.131795232 1.131287827 1 21.17754 -4.999998812 0.272968797 7.73E-10 1.153894221 0.463758432 0.048043988 189.895058 1.837137667 107.272782 0.054268666 1.00E-05 4.999998812 1.15389422 HRPS(ph)PPATPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HRPSPPATPPPK 12 1 A9Z1X7;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HRPS(1)PPATPPPK;HRPS(1)PPATPPPK;HRPS(0.983)PPAT(0.017)PPPK;HRPS(1)PPATPPPK 112.5 0.00076733 791950000 990486 775643 962782 774627 1161219 1237000 1102180 970836 996564 712451 TRUE FALSE 1029591.152 908853.6516 987872.8899 927845.9086 963835.4092 949725.4969 1015788.252 957823.5314 960697.8563 852042.1328 1.208380563 1.066676889 1.159417888 1.088967168 1.131206277 1.114646166 1.192180777 1.124150432 1.127523886 1 19.70056525 0.505986922 2.442950243 1.000003161 1.133915581 0.496837576 0.040743592 6.000102309 28.6393041 0.035495299 0.009494331 3.206172773 -0.505986922 0.133912421 HRPTVVECLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRPTVVECLR 10 1 O75843;H0YJ08 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 94.297 0.0049271 55446000 55312 64264 59602 71714 80132 85744 62298 63144 58910 77452 FALSE TRUE 57495.76047 75300.8421 61155.27708 85898.81516 66511.19126 65831.25546 57414.91997 62297.65796 56789.84061 92627.23649 0.620721967 0.812944928 0.660229965 0.927360228 0.718052203 0.710711643 0.619849217 0.672563064 0.613100884 1 16.49914885 -1.052954804 4.860759052 1.000007265 0.708530076 0.471062926 0.09337684 7.30E-06 1.42E-06 0.0897706 0.021158606 0.088520773 1.052954804 -0.291477189 HRS(ph)EPQHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;HRS(1)EPQHPK 131.69 0.00019688 480199000 719560 529778 698740 520984 954459 859872 744217 692525 717198 502771 TRUE FALSE 747968.7844 620763.2504 716949.7384 624033.0802 792220.4001 660179.7595 685883.3269 683242.8351 691386.1841 601279.3513 1.2439622 1.032404071 1.192373789 1.037842192 1.317557968 1.097958475 1.140706604 1.136315148 1.149858518 1 19.19767589 -1.355347325 3.261737881 0.998843171 1.146581144 0.227846861 0.082576316 7833828.157 11731400.45 86723.90704 0.018382792 0.044121744 1.355347325 0.147737973 HRS(ph)IHEVDISNLEAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRSIHEVDISNLEAALR 17 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 HRS(0.998)IHEVDIS(0.002)NLEAALR 122.53 3.42E-05 61745000 49554 58593 58081 62868 89050 78300 54559 61249 70035 75616 TRUE FALSE 51510.43018 68655.89196 59594.63857 75303.10276 73913.31281 60116.01165 50282.52302 60428.05734 67514.45403 90431.50744 0.569607116 0.759203224 0.659003043 0.832708697 0.817340271 0.664768435 0.556028805 0.668219065 0.746581097 1 16.46453789 0.85153409 4.486223713 0.999982861 0.692683557 0.529082575 0.087138018 1.031736901 30.25958589 0.087864085 0.022312707 7.104509341 -0.85153409 -0.307299304 HRS(ph)LS(ph)PVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRSLSPVPR 9 1 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 2 HRS(1)LS(1)PVPR 68.034 0.033693 289830000 169780 171640 188750 149320 224500 220290 192650 193910 198840 188010 TRUE FALSE 176483.0455 201117.8348 193668.9801 178855.0503 186339.5702 169130.986 177549.5896 191310.9536 191683.7872 224846.9598 0.784902965 0.89446544 0.861336885 0.795452384 0.828739558 0.752204905 0.789646388 0.850849635 0.852507801 1 17.77858385 0.644701802 1.426861942 0.999732708 0.819170943 0.656758793 0.039159531 0.821293272 2.439485063 0.039008433 0.01144318 4.412673574 -0.644701802 -0.180561765 HRS(ph)LTAHSLLPLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRSLTAHSLLPLAEK 15 1 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 HRS(0.333)LT(0.333)AHS(0.333)LLPLAEK;HRS(0.333)LT(0.333)AHS(0.333)LLPLAEK 111.3 0.00051538 685330000 392410 323180 405800 284120 610260 528440 393580 371020 414880 338860 TRUE FALSE 407902.6498 378683.651 416375.4814 340318.088 506528.2232 405717.8186 362730.1712 366047.0838 399948.5498 405253.1291 1.00653794 0.934437328 1.027445444 0.839766713 1.249905767 1.001146665 0.895070624 0.903255416 0.986910454 1 18.6284638 0.995386447 24.7479651 1.000000048 0.976854557 0.000541415 0.105491874 1605.698703 8613341.256 0.101170402 0.0252926 9.894331279 -0.995386447 -0.023145491 HRS(ph)NS(ph)FSDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HRSNSFSDER 10 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 HRS(1)NS(0.974)FS(0.026)DER;HRS(1)NS(0.996)FS(0.004)DER;HRS(1)NS(0.981)FS(0.019)DER;HRS(1)NS(0.998)FS(0.002)DER 135.14 8.66E-05 1793970000 990590 1130120 1036110 1281650 1314950 1663570 1557100 1295630 1173060 1055710 TRUE FALSE 1029699.258 1324209.319 1063111.878 1535156.545 1091435.269 1277231.079 1435050.433 1278264.199 1130841.8 1262556.162 0.815567093 1.048832012 0.842031357 1.215911491 0.864464728 1.01162318 1.136623048 1.012441456 0.895676433 1 20.26791613 5.371927457 1.707646622 1.009969379 1.73E-15 0.191143246 0.111507198 12.42193765 7.346404421 0.027133039 35.16964094 235465.5935 -5.371927457 -1.009969379 HRS(ph)PLEKPHNGLLFPQHGDYQYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRSPLEKPHNGLLFPQHGDYQYGR 24 2 H7C1I0;Q96K37-2;Q96K37 H7C1I0 SLC35E1 Solute carrier family 35 member E1 1 HRS(1)PLEKPHNGLLFPQHGDYQYGR;HRS(1)PLEKPHNGLLFPQHGDYQYGR 149.74 8.68E-08 972760000 577907 330675 560550 417800 640730 620310 583000 527170 636750 345057 TRUE FALSE 600723.2146 387465.859 575158.3935 500439.593 531818.9435 476252.4034 537302.9366 520104.1484 613833.4919 412664.3126 1.45571884 0.938937163 1.393768193 1.212703831 1.288744694 1.154091567 1.30203393 1.260356499 1.487488676 1 18.65460915 HRS(ph)PTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRSPTPK 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HRS(0.997)PT(0.003)PK;HRS(0.991)PT(0.009)PK 63.283 0.048669 117154000 203390 142336 179161 145997 225930 262670 240320 191387 213720 129539 TRUE FALSE 211419.9943 166781.1008 183830.0828 174874.7708 187526.4993 201668.8733 221483.0904 188821.7703 206028.2589 154919.6869 1.364707085 1.076564923 1.186615378 1.12880922 1.21047559 1.301764013 1.429663943 1.218836509 1.329903662 1 17.24116096 2.899870594 4.800081847 1.278952388 1.179726613 0.043707798 0.124441681 0.46774572 17.33563355 0.035944883 0.03858375 794.0915857 -2.899870594 -0.099225775 HRTPS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HRTPSLR 7 1 P49023-3 P49023-3 PXN Paxillin 1 HRT(0.019)PS(0.981)LR;HRT(0.016)PS(0.984)LR 87.308 0.011772 101976000 37385.7 42895 47147 49235 51695 62252 54573 48722 50606 49273 TRUE FALSE 38861.7163 50261.88257 48375.68955 58973.53605 42907.90236 47794.91644 50295.42566 48068.96128 48784.69995 58927.10096 0.659488006 0.8529502 0.820941278 1.000788009 0.728152271 0.811085488 0.853519431 0.815736062 0.827882233 1 15.84664367 -5 0.336620713 2.862446813 0.816904565 0.30266552 0.082981255 481.1030644 4.089211265 643.1254594 0.06487671 1.00E-05 5 -2.045542247 HRVS(ph)SQAEDTSSSFDNLFIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HRVSSQAEDTSSSFDNLFIDR 21 1 H8Y6P7;P0CAP2-3;P0CAP2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 HRVS(0.493)S(0.493)QAEDT(0.009)S(0.002)S(0.002)S(0.001)FDNLFIDR 50.029 0.084165 449160000 25716 16360 23980 20060 28200 27648 25735 23354 25307 17023 TRUE FALSE 26731.28754 19169.70274 24604.9385 24027.80813 23406.57407 21227.17101 23717.82345 23040.97783 24396.20601 20358.33092 1.313039248 0.941614654 1.208593111 1.180244501 1.149729521 1.042677373 1.165018073 1.131771456 1.198340183 1 14.31333167 2.939593957 24.99960791 1.119139209 1.150666897 0.051065416 0.101427661 1248.004223 516496.817 0.029238763 0.031012422 870.1496648 -2.939593957 0.031527687 HS(ph)EKSPPSTENKHEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSEKSPPSTENKHEAK 16 2 H3BQL3;Q6PH81 H3BQL3 C16orf87 UPF0547 protein C16orf87 1 HS(0.5)EKS(0.5)PPSTENKHEAK 121.26 4.74E-05 41654000 169310 57399 92068 53128 153800 137690 147530 87600 121800 36721 TRUE FALSE 175994.4895 67256.83175 94467.36771 63636.55983 127657.1309 105713.5842 135966.2131 86425.86528 117416.4418 43915.77688 4.007545853 1.531495889 2.151103189 1.449059184 2.906862636 2.407189209 3.096067581 1.967991265 2.673673338 1 15.42245171 4.752668823 24.26784327 2.20672415 4.007547705 0.432734188 0.639188046 1564.255068 2690640.433 0.144420462 2.956144217 56580.76606 -4.752668823 1.800823555 HS(ph)FSAGPELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSFSAGPELLR 11 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 HS(0.933)FS(0.067)AGPELLR 62.081 0.053614 83522000 28178 46129 40908 51353 46838 57728 41291 42221 38457 53113 TRUE FALSE 29290.4892 54051.29692 41974.09609 61510.47013 38876.49349 44321.54688 38054.50353 41655.09655 37072.94008 63519.47544 0.461126119 0.850940543 0.660806718 0.968371821 0.612040531 0.697763112 0.599099776 0.655784643 0.583646824 1 15.95491138 -0.921851191 4.267139115 1.000007541 0.68324373 0.339553037 0.135016429 42984578.08 72767591.06 4770.873471 0.030815336 0.119715066 0.921851191 -0.316763812 HS(ph)GGDDEGLQEEELIEQVPSTTSVIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSGGDDEGLQEEELIEQVPSTTSVIER 27 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 HS(1)GGDDEGLQEEELIEQVPSTTSVIER;HS(1)GGDDEGLQEEELIEQVPSTTSVIER;HS(1)GGDDEGLQEEELIEQVPSTTSVIER 163.48 7.30E-12 566180000 214285 218205 190733 201960 230801 297552 275560 212580 207796 137462 TRUE FALSE 222745.1373 255680.0114 195703.6587 241907.0852 191569.5285 228450.0574 253960.8872 209730.7128 200317.4626 164395.047 1.35493825 1.555278069 1.190447414 1.471498622 1.165299879 1.389640756 1.544820794 1.275772699 1.21851276 1 17.32680731 0.999847107 1.836393359 1.004324201 1.375735168 0.465628998 0.124524616 0.300109241 2.111959765 0.111988937 0.031848323 9.996480118 -0.999847107 0.371410966 HS(ph)LSLDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 HS(0.575)LS(0.425)LDDIR 61.65 0.092081 345200000 307730 308370 291870 289870 387060 376320 274120 349220 320930 221390 TRUE FALSE 319879.418 361330.1487 299476.372 347205.4208 321267.6795 288925.3832 252633.7581 344539.2771 309379.792 264767.1317 1.208153806 1.364709231 1.131093463 1.311361492 1.213397136 1.091243393 0.954173414 1.301291723 1.168497728 1 18.01436451 2.908230984 4.817573353 1.124678092 1.254091061 0.307994426 0.105708908 0.329362892 12.74734687 0.033223215 0.035723024 809.5263395 -2.908230984 0.129412968 HS(ph)PAPRPLVQQPEPLPIQVAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSPAPRPLVQQPEPLPIQVAFR 22 1 A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4;H3BMG9;H3BSV5 A0A0A0MTL6 FAM65A Protein FAM65A 1 HS(1)PAPRPLVQQPEPLPIQVAFR;HS(1)PAPRPLVQQPEPLPIQVAFR 142.2 7.06E-08 289469000 182246.3 180736 172027 170468.1 221078.1 272897 204473.7 196717 181808.1 167478 TRUE FALSE 189441.5246 211776.0021 176510.1649 204186.1814 183499.3235 209520.8075 188446.5171 194080.3304 175264.862 200292.1075 0.945826208 1.057335732 0.881263706 1.019441973 0.916158534 1.046076204 0.940858426 0.968986411 0.875046272 1 17.61174605 1.607207683 2.797283802 0.936362463 0.975130691 0.039590045 0.060207207 0.647681286 11.73680929 0.037159775 0.014784935 40.47694097 -1.607207683 0.038768228 HS(ph)PESPSIAVVESELVAEYITTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.412)PES(0.343)PS(0.244)IAVVESELVAEYITTER;HS(0.435)PES(0.377)PS(0.186)IAVVES(0.002)ELVAEYITTER;HS(0.332)PES(0.332)PS(0.332)IAVVES(0.003)ELVAEYITTER;HS(0.315)PES(0.315)PS(0.315)IAVVES(0.055)ELVAEYITTER 133.15 2.84E-05 88129000 25466.9 28817.5 25998.3 26036.3 32764.7 35750.6 29236.3 27584.1 30594.3 24289.8 TRUE FALSE 26472.35288 33766.68146 26675.83706 31186.20243 27195.368 27448.06496 26944.68241 27214.38026 29493.21712 29048.92125 0.911302442 1.162407415 0.918307321 1.073575234 0.936192011 0.944891024 0.927562238 0.936846502 1.015294746 1 14.82619697 3.216850288 24.99996188 0.952759544 1.019820876 0.120637066 0.072573103 396.0243413 456030.518 0.019259579 0.023038362 1647.594327 -3.216850288 0.067061332 HS(ph)PQQPSNGSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSPQQPSNGSLR 12 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 HS(0.999)PQQPS(0.001)NGSLR;HS(1)PQQPSNGSLR 153.7 7.43E-05 256850000 180655 203770 201166 195562 259380 296880 242310 231660 216490 183517 TRUE FALSE 187787.3989 238765.9124 206408.5512 234243.5799 215290.6802 227934.1193 223317.109 228554.9766 208698.5672 219473.6425 0.855626201 1.087902445 0.940470796 1.06729709 0.980940936 1.038548942 1.017512201 1.041377789 0.950904923 1 17.74368817 4.755552945 24.87771141 1.015642231 0.855626065 0.524977879 0.045134047 2384.515855 3491002.353 0.009515979 0.281049084 56957.76578 -4.755552945 -0.160016166 HS(ph)PS(ph)PRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSPSPRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 HS(1)PS(1)PRPR 82.417 0.011567 182780000 59034 55775 57716 50942 72192 85572 77490 66028 52095 42278 TRUE FALSE 61364.7079 65353.92238 59220.12637 61018.17555 59920.82963 65699.19986 71416.13132 65143.00266 50220.11113 50561.56464 1.213663152 1.292561313 1.171247899 1.20680948 1.185106317 1.299390166 1.412458887 1.28838977 0.993246777 1 15.62575349 1.235678774 24.9925814 0.996623213 1.262977171 0.707933019 0.067289925 44.06733721 382135.8725 0.061923135 0.018107745 17.20595466 -1.235678774 0.266353957 HS(ph)PTPQQSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.979)PT(0.021)PQQSNR;HS(0.798)PT(0.146)PQQS(0.057)NR;HS(0.994)PT(0.006)PQQSNR 110.51 0.0012087 496237900 244262.5 312784.3 326025 307796 375608 470798 341184 351155 328028.5 279766 TRUE FALSE 253906.1721 366502.5704 334521.4793 368677.1301 311762.2863 361462.2995 314441.1066 346448.3416 316222.8184 334580.7913 0.758878509 1.095408284 0.999822728 1.10190764 0.931799716 1.080343848 0.939806214 1.035469909 0.94513142 1 18.3519951 4.749942971 24.90537033 1.01474492 0.758878351 0.616094555 0.06051323 992.3380507 2171260.72 0.012981978 0.204972601 56226.74866 -4.749942971 -0.255866569 HS(ph)PVQMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;HS(1)PVQMNR;HS(1)PVQMNR 133.89 0.00094484 1717592000 588022 705097 659355 655263 778512 981669 833199 720300 672824 549801 TRUE FALSE 611237.5626 826191.9249 676538.333 784872.0656 646180.8083 753691.2521 767890.6852 710645.5567 648609.1957 657523.9794 0.929604975 1.256519839 1.028918114 1.193678239 0.982748658 1.146256678 1.167851986 1.080790327 0.986441888 1 19.32668398 1.31140782 4.570872147 0.992616443 1.105951905 0.166881297 0.093954018 0.309633611 10.94598855 0.064128874 0.021340259 20.48367234 -1.31140782 0.113335461 HS(ph)QPSPEPHSPTEPPAWGSSIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HS(0.328)QPS(0.259)PEPHS(0.206)PT(0.206)EPPAWGS(0.001)SIVK 68.88 0.041999 636630000 154900 146420 224060 163750 272790 276410 225760 221960 224270 183130 TRUE FALSE 161015.5716 171566.496 229899.1877 196139.2613 226421.2532 212217.9665 208064.3413 218984.9893 216198.5665 219010.8173 0.735194606 0.783369964 1.049716131 0.895568829 1.033835936 0.968983949 0.95001856 0.99988207 0.987159307 1 17.7406426 4.322173748 5.888644521 0.982360242 0.749787919 0.826714126 0.041553471 0.067285029 3.639432049 0.009243078 0.025964892 20997.79776 -4.322173748 -0.232572323 HS(ph)S(ph)ISPVRLPLNSSLGAELSR ddPTM_MDA-MB-175_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(0.688)S(0.73)IS(0.581)PVRLPLNSSLGAELSR 95.366 0.0019069 9986900 6176.7 6527.3 7579.1 4312.9 8668.2 10327 8568 7576 6313.1 8774.3 TRUE FALSE 6420.560885 7648.313 7776.617572 5165.978747 7194.78246 7928.710757 7896.417772 7474.456112 6085.892764 10493.45609 0.61186332 0.728865012 0.741092115 0.492304795 0.685644691 0.755586214 0.752508773 0.712296887 0.579970289 1 13.3572023 2.994328813 24.95018574 0.737591148 0.648142661 0.171256402 0.116467261 545.1062618 2398192.747 0.032826506 0.038114261 987.0265007 -2.994328813 -0.089448487 HS(ph)SADNLANEMTYITETEDVFYTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSSADNLANEMTYITETEDVFYTYK 25 0 J3KN34;P26045-2;P26045;P26045-3 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 HS(0.41)S(0.41)ADNLANEMT(0.095)Y(0.084)ITETEDVFYTYK;HS(0.498)S(0.498)ADNLANEMT(0.002)Y(0.002)ITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK;HS(0.5)S(0.5)ADNLANEMTYITETEDVFYTYK 213.78 1.24E-26 739320000 233541 216266 225468 222477 276525 305309 256192 213208 225787 164453 TRUE FALSE 242761.379 253408.0032 231343.8813 266482.2866 229521.3793 234405.6118 236111.0016 210350.2955 217660.97 196674.4167 1.234331252 1.288464496 1.176278467 1.354941283 1.167011872 1.191845974 1.200517106 1.069535627 1.106707083 1 17.58544978 1.711792816 0.648025185 1.005125225 1.259366458 0.705502438 0.053179006 0.348381323 0.305381984 0.046667064 0.024321648 51.49829087 -1.711792816 0.254241233 HS(ph)SIS(ph)PSTLTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.5)S(0.5)IS(0.883)PS(0.06)T(0.052)LT(0.005)LK 68.809 0.075537 102380000 314910 237360 284590 246080 384650 381350 354680 304250 302980 226690 TRUE FALSE 327342.89 278124.7336 292006.6492 294753.8895 319267.3304 292787.2419 326879.2548 300172.0264 292075.809 271105.5653 1.207436998 1.025890905 1.077095739 1.08722921 1.177649489 1.079975033 1.205726834 1.10721455 1.077350842 1 18.0484952 0.92604236 2.66652708 1.000434012 1.119347616 0.303231847 0.056421914 0.42564647 6.859674714 0.051909991 0.013840681 8.434170182 -0.92604236 0.118913604 HS(ph)SNPPLESHVGWVMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.5)S(0.5)NPPLES(0.001)HVGWVMDSR 77.445 0.022672 1370000000 145500 134380 164980 147830 182350 200000 181650 177240 192910 155530 TRUE FALSE 151244.4524 157458.7197 169279.5143 177070.3328 151354.2121 153553.031 167411.7983 174864.3877 185967.2068 186003.1257 0.813128552 0.84653803 0.910089622 0.951975039 0.813718649 0.825540057 0.900048307 0.940115318 0.999806891 1 17.50496734 1.589591446 1.916701249 1.000689629 0.864352419 0.634824242 0.041765392 0.218628605 1.66663376 0.035720895 0.012721722 38.86793305 -1.589591446 -0.13633721 HS(ph)SPHQS(ph)EDEEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.501)S(0.501)PHQS(0.999)EDEEDPR;HS(0.5)S(0.5)PHQS(1)EDEEDPR;HS(0.5)S(0.5)PHQS(1)EDEEDPR 109.03 0.00041809 1756860000 1118040 1246200 1496710 1526310 1788170 2035080 1579190 1406520 1478290 1094280 TRUE FALSE 1162181.083 1460225.156 1535715.492 1828209.562 1484217.502 1562463.512 1455408.961 1387667.9 1425086.632 1308683.215 0.888053785 1.115797268 1.173481462 1.396984038 1.134130464 1.193920342 1.112117085 1.06035432 1.088946978 1 20.31968448 1.88736295 2.588444383 1.053349824 1.160357343 0.122622456 0.117707315 0.617724138 7.472956166 0.068804497 0.034963597 77.15480005 -1.88736295 0.107007519 HS(ph)SYPAGTEDDEGMGEEPSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 HS(0.499)S(0.499)YPAGT(0.002)EDDEGMGEEPSPFR 133.95 6.84E-09 0 39560 38699 31744 31019 50483 47885 39273 52931 48403 32633 TRUE FALSE 41121.85935 45345.25221 32571.27472 37154.46562 41901.91769 36764.43445 36194.67964 52221.54652 46660.98549 39026.81155 1.053682269 1.161899997 0.834587132 0.952024112 1.073670024 0.942030184 0.927431122 1.338094106 1.19561357 1 15.25217798 1.749601409 25 1.207203975 0.992314513 0.345057638 0.115144971 2.790773511 6330.881121 0.05231026 0.029008728 56.1825451 -1.749601409 -0.214889462 HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 HS(1)YPPALGSPGALAGAGVGAAGPLER;HS(0.987)Y(0.013)PPALGSPGALAGAGVGAAGPLER 287.17 1.13E-61 325130000 145993 128277 152477 153084 185755 218880 183654 166689 161489 118270 TRUE FALSE 151756.9164 150307.5769 156450.6759 183363.5583 154180.4315 168048.4372 169258.7196 164454.8066 155677.0424 141442.7421 1.072921199 1.06267437 1.106106072 1.296380115 1.090055447 1.188102229 1.196658924 1.162695266 1.100636485 1 17.10985862 0.920827675 3.687203152 1.000119716 1.149931169 0.309714201 0.06658791 0.416537012 13.68676492 0.06493504 0.016705559 8.333504518 -0.920827675 0.149811453 HSAS(ph)PVVFTSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSASPVVFTSAR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 HS(0.006)AS(0.994)PVVFTSAR;HS(0.29)AS(0.71)PVVFTSAR;HSAS(0.995)PVVFT(0.003)S(0.003)AR;HS(0.015)AS(0.985)PVVFTSAR 145.7 4.13E-05 983837000 845296 910541 921940 861405 1120338 1208503 1050975 1031333 1011586 972485 TRUE FALSE 878668.9388 1066919.334 945966.5138 1031788.338 929903.3469 927846.4933 968596.8333 1017509.668 975179.2175 1163024.816 0.755503173 0.917365923 0.813367437 0.887159348 0.799555894 0.797787356 0.832825594 0.874882164 0.838485305 1 20.14945045 -0.121479337 0.701561071 1.007827892 0.834018285 0.547780566 0.045100483 4.49150604 2.149622692 0.139171153 0.015237804 0.755998028 0.121479337 -0.173809607 HSCDALNR ddPTM_MDA-MB-175_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 ;;;;; 199.8 0.00012494 1055890000 301601 1689250 612424 1446560 497665 1051920 420585 563760 396521 2029780 FALSE TRUE 313508.4404 1979365.547 628384.2726 1732685.25 413072.0811 807627.522 387618.4487 556203.7193 382250.2867 2427476.529 0.129149937 0.815400488 0.258863171 0.713780434 0.170165221 0.332702505 0.159679587 0.229128361 0.15746817 1 21.21102592 -3.72071078 7.798396802 0.945134336 0.368480677 0 0.305815865 0 0 0 0.062349983 0.000190234 3.72071078 -0.576653659 HSCSGS(ph)SPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.602)S(0.398)PPR;HSCSGS(0.904)S(0.095)PPR;HSCSGS(0.785)S(0.215)PPR;HSCS(0.001)GS(0.622)S(0.377)PPR 105.13 0.001668 594959600 5438.7 21456.52 17126.9 18376.7 14490.76 21911.6 10545.3 15019.3 12380.9 28258.4 TRUE FALSE 5653.424076 25141.5104 17573.24108 22011.55641 12027.62579 16822.96297 9718.731831 14817.99085 11935.31383 33795.09244 0.167285356 0.743939684 0.519993875 0.651324048 0.355898591 0.497793075 0.287578199 0.438465759 0.353167071 1 15.04452614 -1.047925324 4.760081541 1.000014592 0.453967165 0.515252454 0.160998194 1.205347216 194922943.3 6855.132394 0.035956086 0.089551873 1.047925324 -0.546047427 HSCSGSS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSCSGSSPPR 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSCSGS(0.038)S(0.961)PPR;HSCSGS(0.014)S(0.986)PPR;HSCSGS(0.065)S(0.935)PPR;HSCSGS(0.184)S(0.816)PPR;HSCS(0.001)GS(0.415)S(0.584)PPR;HSCS(0.001)GS(0.351)S(0.647)PPR 133.85 0.00019521 8547623000 351615.1 508007.9 474843.9 479079.2 545654.9 616797.3 494928 499546.2 478163.1 437727.1 TRUE FALSE 365497.1357 595254.3051 487218.7221 573839.6359 452904.675 473555.4747 456134.2501 492850.6003 460954.1034 523491.3445 0.698191364 1.137085286 0.930710178 1.096177887 0.865161726 0.904609942 0.871331026 0.94146848 0.880538157 1 18.99780616 HSCSGSS(ph)PPRVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSCSGSSPPRVK 12 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HS(0.04)CS(0.033)GS(0.149)S(0.778)PPRVK 69.456 0.030236 133490000 59850 78608 81648 26293 136040 107690 44377 80639 88678 139050 TRUE FALSE 62212.92421 92108.31251 83775.81395 31493.67692 112915.9694 82680.62956 40898.61478 79558.1661 85486.4961 166294.1852 0.374113648 0.553887753 0.503780778 0.189385317 0.679013336 0.497194953 0.24594134 0.478418208 0.514067861 1 17.3433782 0.662163775 2.255576798 0.999882295 0.440209013 0.603249942 0.135443743 1.33410847 8.06469253 0.125201211 0.033907462 4.593712122 -0.662163775 -0.559673282 HSDENDGGQPHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSDENDGGQPHKR 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 77.644 0.010326 34558000 32670 26730 36760 29705 39666 40643 35506 33831 36472 26260 FALSE TRUE 33959.83683 31320.66957 37717.9958 35580.56034 32923.58749 31204.2792 32722.94694 33377.55078 35159.37984 31405.14422 1.08134631 0.997310165 1.201013297 1.132953254 1.048350145 0.993604073 1.041961365 1.062805206 1.11954206 1 14.93871327 3.19342924 12.79747961 1.045996931 1.102576838 0.201858687 0.057199807 1.954412572 551.5890877 0.017225288 0.020605041 1561.094665 -3.19342924 0.056579907 HSDGNLCVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSDGNLCVK 9 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ;; 95.608 0.00793 1666070000 2704020 2235430 2550010 2228980 3332870 3157610 2686160 2574070 2635050 1952580 FALSE TRUE 2810776.798 2619347.713 2616465.355 2669865.591 2766349.948 2424302.932 2475611.76 2539568.802 2540215.065 2335150.667 1.203681132 1.121703944 1.120469609 1.143337614 1.184655871 1.038178378 1.060150763 1.087539591 1.087816346 1 21.15508421 2.734715049 24.99973208 1.062785018 1.150391983 0.679986484 0.034022944 224.8457181 1461697.474 0.010754472 0.010506705 542.8940089 -2.734715049 0.087606964 HSDLVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSDLVTK 7 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 67.981 0.06369 127696000 400370 348360 406610 345620 585730 552970 408520 372900 434670 458540 FALSE TRUE 416176.9168 408188.1201 417206.5906 413982.6044 486167.8238 424551.0978 376499.1349 367901.8854 419026.3116 548382.1337 0.758917717 0.744349779 0.760795374 0.754916287 0.886549349 0.77418842 0.68656346 0.67088598 0.764113719 1 19.06482204 3.421729021 24.99975297 0.769567179 0.754348782 0 0.091446826 906.1681385 408969.0068 0.025988573 0.035188695 2640.760538 -3.421729021 -0.015218397 HSDSGTSEASLS(ph)PPS(ph)SPPSRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSDSGTSEASLSPPSSPPSRPR 22 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 2 HSDSGTSEAS(0.003)LS(0.993)PPS(0.547)S(0.456)PPSRPR;HS(0.003)DS(0.017)GT(0.019)S(0.02)EAS(0.052)LS(0.89)PPS(0.523)S(0.467)PPS(0.011)RPR 78.206 0.0050933 324240000 107722 127692 137894 128620 151627 179260 136476 147697 133489 116117 TRUE FALSE 111974.9477 149622.1077 141487.6309 154060.6521 125853.4967 137629.5817 125778.6545 145717.3633 128684.757 138867.903 0.806341461 1.077441975 1.018864892 1.109404325 0.906282114 0.99108274 0.905743169 1.049323567 0.926670269 1 17.08335366 3.183701972 24.99999985 0.968650746 1.009467111 0.044938908 0.085767215 304.0082655 138539.9462 0.023927421 0.028598775 1526.51815 -3.183701972 0.040816365 HSEAATAQREEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSEAATAQREEWK 13 1 Q14103-3;Q14103;H0Y8G5;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 249.33 9.25E-18 1193950000 1226490 1082550 1419000 621130 2094880 1785960 862330 1151610 1424300 1380980 FALSE TRUE 1274912.772 1268469.541 1455980.306 743987.6601 1738793.046 1371197.856 794738.3213 1136174.552 1373039.721 1651556.591 0.771946163 0.768044855 0.881580634 0.450476638 1.052820749 0.83024576 0.481205625 0.687941641 0.831360989 1 20.65539497 HSEEAEFTPPLKCS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSEEAEFTPPLKCSPK 16 1 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 HSEEAEFT(0.121)PPLKCS(0.879)PK 70.281 0.02649 114400000 253940 124510 172990 127870 236260 267780 230180 193460 192480 106210 TRUE FALSE 263965.7473 145893.6239 177498.2615 153162.3043 196100.6096 205592.1532 212137.8901 190866.9851 185552.6824 127019.816 2.078146195 1.148589476 1.397406067 1.205814252 1.543858398 1.618583303 1.670116497 1.502655185 1.46081681 1 16.95469406 0.696247254 3.299093035 1.000011744 1.504599013 0.285310307 0.244622978 4.883778822 51.62072483 0.224483198 0.058170266 4.968751239 -0.696247254 0.504587269 HSEHVWVEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSEHVWVEVVR 11 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 137.89 3.98E-05 1130110000 254088 780460 775010 902080 693610 967380 671920 812440 722700 850790 FALSE TRUE 264119.5904 914497.9339 795207.3973 1080508.732 575710.42 742720.6558 619253.1547 801550.5707 696690.1682 1017486.011 0.259580562 0.898781825 0.781541356 1.061939643 0.565816546 0.729956626 0.608610976 0.787775519 0.684717196 1 19.95657753 -1.991274558 2.30938357 1.263627332 0.723793108 0.154171728 0.201909501 15903446.57 6246147.064 22329758.98 0.046245675 0.010202943 1.991274558 -0.539834224 HSELSELNVK ddPTM_MDA-MB-175_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 0 117.71 0.00092211 172130000 118440 206570 182820 182400 222310 252590 172710 203340 205130 204120 FALSE TRUE 123116.1027 242046.7906 187584.4394 218478.1756 184521.8256 193929.8005 159172.5389 200614.5599 197747.4114 244113.4059 0.504339785 0.9915342 0.768431536 0.894986389 0.755885671 0.794425033 0.652043415 0.82180886 0.810063711 1 17.897192 0.648318782 1.877188203 0.999822132 0.78009756 0.23044757 0.123613334 2.391252846 10.87447802 0.107790266 0.030030119 4.449577571 -0.648318782 -0.219724572 HSETFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSETFTR 7 0 Q9UNS2-2;Q9UNS2 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ;;; 145.34 0.0022931 570760000 120708 224866 203280 206949 188648 257235 175322 200887 168187 224517 FALSE TRUE 125473.645 263484.9863 208577.6438 247882.8945 156581.6803 197496.0697 161579.8035 198194.4383 162133.9827 268506.8075 0.467301541 0.981297229 0.776805794 0.923190353 0.583157209 0.735534684 0.60177172 0.738135618 0.60383565 1 18.03459914 3.234635736 24.99994882 0.694128925 0.800277689 0.03986935 0.168969017 250.4993457 1595583.399 0.04437534 0.05495201 1716.468096 -3.234635736 0.106148764 HSEVQQANLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSEVQQANLK 10 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ;; 169.37 4.65E-06 1507750000 2738690 1999450 2473050 1932270 3688380 3447550 2871880 2509350 2644740 2163390 FALSE TRUE 2846815.596 2342839.984 2537499.715 2314467.239 3061430.485 2646908.761 2646774.541 2475716.268 2549556.324 2587264.85 1.100318584 0.905527698 0.980765349 0.894561389 1.183269075 1.023052882 1.023001005 0.956885519 0.985425332 1 21.30299631 4.79095791 21.97312878 0.9960538 1.100321173 0.149735555 0.075429952 22496.31132 9432674.502 0.018063754 15.10488705 61795.65078 -4.79095791 0.104267374 HSGIDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSGIDFK 7 0 A0A0A0MTH3;Q13418;Q13418-3 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 ;; 125.81 0.0040127 291771000 727510 547080 697600 533920 902030 910920 822010 716130 771450 505410 FALSE TRUE 756232.6566 641036.7343 715780.0291 639527.7824 748703.2628 699372.6351 757578.7083 706531.4487 743685.6652 604435.4128 1.251138898 1.060554562 1.184212596 1.058058097 1.238681995 1.157067604 1.253365855 1.168911407 1.230380698 1 19.20522866 3.218700095 24.9946608 1.186573504 1.136189908 0.030652778 0.08510732 619.4629473 779598.9693 0.022275196 0.026659457 1654.626956 -3.218700095 -0.050383596 HSGNITFDEIVNIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 ;;;;;; 293.8 1.27E-43 4402138000 1424606 1692903 1624713 1530213 1881993 2190293 1658393 1736794 1576681 1612520 FALSE TRUE 1480850.545 1983645.921 1667054.355 1832884.564 1562092.502 1681630.645 1528403.823 1713515.117 1519936.559 1928462.42 0.767891834 1.028615285 0.864447416 0.95043831 0.810019675 0.872005919 0.792550483 0.888539543 0.788159802 1 20.8790196 3.2387223 24.99999999 0.851636674 0.909088655 0.05673241 0.084241719 9.938605658 1536574.861 0.021624035 0.027515782 1732.695708 -3.2387223 0.057451982 HSGPNSADSANDGFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSGPNSADSANDGFVR 16 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;;;;; 257.34 1.14E-26 5245020000 1531156 2311430 2196160 2095660 2121190 2856410 2081620 2178160 2048410 2295730 FALSE TRUE 1591607.221 2708400.122 2253393.734 2510175.293 1760630.881 2193052.067 1918457.185 2148965.328 1974688.124 2745534.339 0.579707636 0.986474685 0.820748698 0.914275687 0.641270756 0.798770584 0.698755487 0.782712967 0.71923636 1 21.38865552 4.782336875 23.56983292 0.801962254 0.579706127 0.273014493 0.113986279 22968.20364 12365833.81 0.026033278 12.25522656 60581.06097 -4.782336875 -0.222256127 HSGS(ph)RSDEDRYQNGAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSGSRSDEDRYQNGAER 17 2 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 HS(0.12)GS(0.551)RS(0.329)DEDRYQNGAER 130.19 1.62E-05 299650000 56115 69606 69363 57443 73530 94814 57156 72452 62955 71302 TRUE FALSE 58330.46353 81560.28904 71170.65676 68805.05395 61031.39686 72794.88542 52675.96337 71480.89945 60689.26185 85272.26174 0.684049682 0.956469166 0.834628463 0.806886701 0.715723913 0.853676025 0.617738551 0.838266723 0.711711647 1 16.3797889 5.030797415 15.80787243 0.802195301 0.321599961 0.106061655 0.108462593 4099999.631 59235479.64 0.02415525 52568259.41 107348.8545 -5.030797415 -0.480595339 HSGSDRS(ph)SFSHYSGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSGSDRSSFSHYSGLK 16 1 Q8NC51;Q8NC51-3 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 HS(0.091)GS(0.091)DRS(0.405)S(0.405)FS(0.008)HYSGLK 137.61 6.69E-06 270780000 26042 181280 206990 162240 262180 286400 171420 217420 210860 246930 TRUE FALSE 27070.15827 212413.4298 212384.3294 194330.5878 217614.7372 219887.9404 157983.6525 214505.8405 203271.1898 295311.2057 0.091666546 0.719286724 0.719188183 0.658053552 0.736899694 0.744597347 0.534973443 0.726372167 0.688328739 1 18.17187658 4.007136182 0.102148605 1.146333819 7.80E-39 0.409351956 0.16828963 51.39557444 1.107838699 3.32673852 10.02259547 10165.67408 -4.007136182 -1.146333819 HSGSRS(ph)DEDRYQNGAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSGSRSDEDRYQNGAER 17 2 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 HSGS(0.001)RS(0.999)DEDRYQNGAER;HS(0.093)GS(0.056)RS(0.851)DEDRYQNGAER 213.48 3.29E-13 375038000 75321.3 96691.3 99334 82955.9 110255 136882 84762.1 89020 102857 114172.8 TRUE FALSE 78295.04308 113297.2786 101922.7256 99364.32942 91513.89448 105093.23 78118.22512 87826.83251 99155.19666 136542.7742 0.573410373 0.829756677 0.746452723 0.727715765 0.670221438 0.769672585 0.572115409 0.643218457 0.726184137 1 17.05899344 -1.94042165 4.841179152 1.15747152 0.694063365 0.575318715 0.078498658 0.04944204 0.000608462 0.028166151 0.017832881 0.011470394 1.94042165 -0.463408155 HSHEGDYLESIVFIYSMPGYTCSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSHEGDYLESIVFIYSMPGYTCSIR 25 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ; 164.58 9.53E-12 1013270000 357410 329560 470010 394320 474710 575330 512970 386090 460460 330490 FALSE TRUE 371520.8228 386159.3664 482258.8467 472315.3191 394018.9638 441718.3267 472762.071 380915.0951 443888.1345 395243.1879 0.939980332 0.977017133 1.220157264 1.194999265 0.996902605 1.117586186 1.196129587 0.963748666 1.12307599 1 18.59238107 0.610113944 0.854676392 1.002019083 1.085389468 0.044891066 0.100693869 4.523861786 5.585748151 0.101715882 0.034012944 4.074871742 -0.610113944 0.083370385 HSHS(ph)HS(ph)PMSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 HS(0.429)HS(0.577)HS(0.969)PMS(0.02)T(0.006)R;HS(0.419)HS(0.583)HS(0.995)PMS(0.003)T(0.001)R 72.417 0.024482 249340000 234600 358710 286760 301690 345320 415080 288610 301410 274500 330490 TRUE FALSE 243862.1892 420315.6521 294233.2012 361363.3815 286622.6297 318683.9606 265987.9941 297370.092 264620.7986 395243.1879 0.61699277 1.063435538 0.744435857 0.914281113 0.725180442 0.806298427 0.672973 0.752372466 0.669513876 1 18.59238107 3.221556924 24.97289828 0.753441073 0.84466482 0.037479788 0.138741262 557.0735395 818158.1215 0.03652985 0.043766963 1665.547121 -3.221556924 0.091223748 HSHSHS(ph)PMSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSHSHSPMSTR 11 0 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 HSHS(0.011)HS(0.989)PMSTR 80.746 0.026837 12409000 2503.9 8111.8 9690 8123 6766.3 8677.9 5167.1 7986 7237.4 9337.7 TRUE FALSE 2602.755905 9504.938549 9942.52936 9729.705155 5616.166743 6662.58924 4762.0892 7878.960732 6976.927388 11167.24353 0.233070578 0.851144557 0.890329769 0.87127187 0.502914325 0.596618961 0.42643372 0.705542125 0.624767192 1 13.4469855 -1.320367399 4.037771996 1.000639555 0.645057352 0.231173305 0.199487823 0.001141313 0.000192104 0.191907067 0.045153196 0.047822536 1.320367399 -0.355582203 HSLDS(ph)DEEEDDDDGGSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HS(0.026)LDS(0.974)DEEEDDDDGGSSK;HSLDS(1)DEEEDDDDGGSSK 350.07 1.50E-90 898670000 1041440 497430 651060 584900 924540 1143740 1136190 670460 742860 292580 TRUE FALSE 1082556.855 582859.733 668027.1585 700591.4742 767387.021 878123.7185 1047132.459 661473.5804 716124.6137 349905.4492 3.093855377 1.665763521 1.909164776 2.002230819 2.193126808 2.509602867 2.992615466 1.890435207 2.04662321 1 18.41660561 3.028948173 22.12531294 2.211778717 2.111457963 0 0.592785983 578.84219 442400.7023 0.166131332 0.198557772 1068.92731 -3.028948173 -0.100320754 HSLDS(ph)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSLDSDEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 42 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 HS(0.028)LDS(0.972)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR;HS(0.082)LDS(0.917)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR;HS(0.012)LDS(0.988)DEEEDDDDGGSSKYDILASEDVEGQEAATLPSEGGVR 261.07 3.92E-67 867360000 550420 376835 501580 353914 686300 666120 547400 488510 561320 339486 TRUE FALSE 572151.0066 441553.4799 514651.5869 423917.1329 569642.9711 511423.7251 504493.3576 481962.3225 541118.2028 406001.7818 1.409232748 1.087565374 1.267609183 1.044126287 1.403055348 1.259658819 1.242589023 1.187094107 1.332797606 1 18.63112653 -1.103877133 5.835569781 0.999998592 1.23874498 0.296563489 0.113839669 1.90E-06 2.92E-07 0.100567207 0.023703778 0.078726849 1.103877133 0.238746388 HSLS(ph)GSSPGMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.534)GS(0.296)S(0.169)PGMK 84.479 0.062278 32628000 137610 112180 139270 108480 179840 194400 179570 153920 148010 80066 TRUE FALSE 143042.9491 131446.0424 142899.4906 129937.0202 149270.861 149253.5462 165494.8342 151856.9542 142683.149 95753.39974 1.493868097 1.372755878 1.49236989 1.356996415 1.558909255 1.558728427 1.728344212 1.585917101 1.490110528 1 16.54703609 0.942668092 20.13945224 0.999999999 1.524436704 0.703890094 0.100363556 998.7366172 350836.0119 0.107835872 0.026958968 8.763308332 -0.942668092 0.524436705 HSLS(ph)LDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 HS(0.147)LS(0.853)LDDIR;HS(0.001)LS(0.999)LDDIR;HSLS(1)LDDIR 152.69 8.38E-05 615360000 1152630 1184340 1113740 1052350 1280740 1370040 1072060 1137170 1051370 864140 TRUE FALSE 1198136.722 1387741.182 1142764.979 1260501.689 1063040.272 1051868.973 988029.1359 1121928.096 1013531.399 1033451.688 1.159354362 1.342821535 1.105774941 1.219700644 1.028630834 1.017821138 0.956047726 1.085612525 0.980724509 1 19.97903952 3.221850116 6.894431906 1.016353143 1.209741715 0.689318042 0.064227554 0.085593605 17.30294912 0.017757427 0.022041512 1666.671911 -3.221850116 0.193388572 HSLS(ph)STK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSLSSTK 7 0 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 HS(0.001)LS(0.785)S(0.212)T(0.002)K;HSLS(0.966)S(0.034)TK 88.136 0.012128 159330000 207895 193719 222563 234178 296090 307860 256390 223683 221148 241000 TRUE FALSE 216102.8551 226988.7313 228363.1746 280497.7094 245760.7276 236364.1807 236293.4818 220684.8953 213188.9267 288219.3358 0.749786112 0.787555529 0.792324269 0.973209201 0.852686468 0.820084399 0.819839103 0.765683866 0.739676004 1 18.1368076 -2.435141014 2.321974788 2.91417732 0.813121196 0.444620437 0.06326859 7874302.286 871844.1404 79122977.11 0.017502278 0.003671631 2.435141014 -2.101056124 HSLSFNDCFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSLSFNDCFVK 11 0 P55317-2;P55317;P55318 P55317-2 FOXA1;FOXA3 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma 0 90.614 0.011356 259890000 569020 281290 341210 268090 461960 536610 374360 333280 362010 253820 FALSE TRUE 591485.349 329599.3694 350102.2129 321117.4018 383436.2042 411990.4599 345016.685 328812.9267 348981.3308 303551.1693 1.948552365 1.085811562 1.153354849 1.057869098 1.263168266 1.357235621 1.136601403 1.083220755 1.149662285 1 18.21158021 4.741366987 24.99882714 1.150157443 1.948552652 0.859326175 0.097740671 93.56514862 833424.3339 0.024080106 0.167548101 55127.33356 -4.741366987 0.798395209 HSLSGRPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSLSGRPLK 9 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 102.06 0.0021904 1871760000 1804100 1618430 1988420 1667370 3011600 2710600 2327300 2214600 2127420 1905310 FALSE TRUE 1875327.261 1896382.763 2040239.859 1997170.809 2499689.308 2081104.23 2144880.145 2184916.909 2050854.57 2278619.015 0.82301045 0.832250916 0.895384373 0.876482991 1.097019419 0.913318205 0.941307051 0.958877678 0.90004277 1 21.1197283 3.786374253 1.944423599 0.960425833 0.832473799 0.467795866 0.056324072 0.300033881 2.196919542 0.015711831 0.034869208 6114.687301 -3.786374253 -0.127952034 HSLSGS(ph)SPGMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLS(0.012)GS(0.9)S(0.088)PGMK 110.66 0.0068976 107480000 183570 136570 175960 133180 230220 232990 230510 190530 186940 107100 TRUE FALSE 190817.4853 160024.8351 180545.6622 159522.6065 191087.2866 178881.6035 212442.0239 187976.257 180212.0659 128084.1944 1.489781672 1.249372226 1.409585804 1.245451144 1.491888109 1.396593891 1.658612328 1.467599166 1.406981296 1 16.96673293 3.217307715 24.99343199 1.446297029 1.345823549 0 0.171748177 635.0229666 746785.8941 0.046263748 0.05534446 1649.330596 -3.217307715 -0.10047348 HSLSGSS(ph)PGMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSLSGSSPGMK 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 HSLSGS(0.018)S(0.982)PGMK;HSLS(0.014)GS(0.041)S(0.945)PGMK;HSLSGS(0.003)S(0.997)PGMK;HS(0.004)LS(0.004)GS(0.28)S(0.712)PGMK;HSLS(0.001)GS(0.007)S(0.993)PGMK;HSLSGS(0.002)S(0.998)PGMK 229.56 2.57E-12 933231000 2065090 1764330 2161820 1882120 2730680 2905410 2922000 2349320 2341460 1309850 TRUE FALSE 2146621.348 2067339.953 2218158.805 2254397.718 2266519.989 2230672.559 2692966.005 2317831.208 2257191.312 1566490.029 1.370338341 1.319727489 1.416005697 1.439139526 1.446878018 1.4239941 1.719108296 1.479633554 1.440922872 1 20.57910416 3.930813528 1.747150479 1.464300302 1.342771567 0 0.168978031 1.068535029 6.250745708 0.045502996 0.126829471 8527.338997 -3.930813528 -0.121528735 HSPAPPPDPGFPAPS(ph)PPPADSPSEGFSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSPAPPPDPGFPAPSPPPADSPSEGFSLK 29 0 M0QZS0;A0A590UK10;A0A3B3IPE9;A0A087WZG4;Q6ZSZ5-2;Q6ZSZ5-1;Q6ZSZ5-6;Q6ZSZ5-5;Q6ZSZ5 M0QZS0 ARHGEF18 Rho guanine nucleotide exchange factor 18 1 HSPAPPPDPGFPAPS(1)PPPADSPSEGFSLK 151.38 2.09E-08 172390000 169150 134630 190390 150730 239880 247790 224680 203030 221200 165710 TRUE FALSE 175828.1726 157751.6552 195351.7198 180543.9441 199105.2833 190244.5278 207068.9945 200308.7149 213239.0552 198177.7018 0.887224804 0.796011124 0.985740162 0.911020475 1.004680554 0.959969391 1.044865253 1.010753042 1.075999233 1 17.59643512 3.810245881 0.600250241 1.034153052 0.811443307 0.642246468 0.046905613 0.831623221 0.466780495 0.025511638 0.113020265 6460.19878 -3.810245881 -0.222709745 HSPEEDFRQS(ph)PQEHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSPEEDFRQSPQEHFR 16 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 HSPEEDFRQS(1)PQEHFR;HSPEEDFRQS(1)PQEHFR 225.69 4.01E-15 384150000 143973 165479 186646 149713 180787 220874 166689 167016 163870 138555 TRUE FALSE 149657.1652 193898.731 191510.1481 179325.7846 150056.8903 169579.3609 153623.4806 164777.4237 157972.3507 165702.1995 0.903169455 1.170163894 1.155748981 1.082217286 0.905581765 1.02339837 0.927105863 0.99441905 0.953350959 1 17.33823323 3.310592248 8.669526979 0.968814441 1.090643201 0.337200268 0.075061442 0.294858806 32.14721361 0.0199695 0.027028222 2044.524163 -3.310592248 0.12182876 HSPESPS(ph)IAVVESELVAEYITTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSPESPSIAVVESELVAEYITTER 24 0 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 HS(0.315)PES(0.315)PS(0.369)IAVVES(0.001)ELVAEYITTER 111.13 0.0011868 33978000 8970.3 10616 10796 9922.4 11347 13938 11795 10525 9230.5 9123.3 TRUE FALSE 9324.454371 12439.21542 11077.35263 11885.0211 9418.240993 10701.11073 10870.47708 10383.92959 8898.296108 10910.83596 0.854604946 1.140079043 1.015261587 1.089286023 0.863200678 0.980778262 0.996301028 0.951707974 0.815546686 1 13.41347402 3.246091942 24.999971 0.939868345 1.032359664 0.199740799 0.087567833 268.9719995 892838.0821 0.023263658 0.030895774 1762.349102 -3.246091942 0.092491319 HSPT(ph)PQQSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSPTPQQSNR 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 HS(0.343)PT(0.656)PQQS(0.001)NR 152.23 0.00020573 78281000 74791 73270 76165 81405 104090 122610 94097 85850 85538 81489 TRUE FALSE 77743.80643 85853.55254 78149.92247 97506.66603 86396.81898 94135.68567 86721.43126 84699.32117 82459.50409 97455.20935 0.797738848 0.880953959 0.801906055 1.000528003 0.886528484 0.965937956 0.889859371 0.869110248 0.846127207 1 16.57245168 3.769468224 24.99315224 0.912857904 0.83227505 0.379977545 0.054928106 821.8336817 664565.5952 0.013831504 0.024931763 5881.230814 -3.769468224 -0.080582854 HSPTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.459)S(0.459)PHT(0.083)HR;HSPTSEPTPPGDALPPVS(0.465)S(0.465)PHT(0.069)HR;HSPTSEPTPPGDALPPVS(0.488)S(0.488)PHT(0.023)HR;HSPTSEPTPPGDALPPVS(0.49)S(0.49)PHT(0.019)HR 196.43 3.31E-24 9787930000 502448 1271420 1190300 1130150 1376320 1700540 1130520 1248550 1115220 1284410 TRUE FALSE 522285.035 1489776.495 1221320.196 1353690.297 1142373.618 1305615.357 1041906.888 1231815.229 1075083.45 1536065.548 0.34001481 0.969865184 0.795096406 0.881271179 0.743701087 0.849973726 0.678295851 0.801928818 0.699894254 1 20.55080835 4.750882193 24.89044036 0.810364344 0.340014502 0.671623273 0.101189372 1046.271368 2113500.084 0.022426747 0.387326809 56348.47844 -4.750882193 -0.470349842 HSPTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSPTSEPTPPGDALPPVSSPHTHR 24 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 HSPTSEPTPPGDALPPVS(0.23)S(0.23)PHT(0.54)HR 137.09 3.02E-05 2108000000 69447 141700 126980 151080 165160 211080 135800 151350 132210 140120 TRUE FALSE 72188.82118 166035.8727 130289.2031 180963.1731 137086.1622 162059.8689 125155.6412 149321.4008 127451.7879 167573.8312 0.430788153 0.990822204 0.777503278 1.07990115 0.81806426 0.967095326 0.74686865 0.891078277 0.760570949 1 17.35443735 4.746893949 24.77080987 0.884890441 0.430787894 0.61490607 0.109453173 579.6019699 1722821.229 0.023751448 0.270412505 55833.38374 -4.746893949 -0.454102546 HSQAVEELAEQLEQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HSQAVEELAEQLEQTK 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;; 204.13 2.60E-11 1615829000 1506070 961223 1237930 1056700 1552350 1616300 1713200 1396700 1392690 778517 FALSE TRUE 1565530.807 1126305.573 1270191.473 1265712.106 1288482.101 1240938.82 1578914.907 1377979.521 1342567.359 931052.5005 1.681463511 1.209712205 1.364253328 1.35944225 1.383898438 1.332834421 1.695838749 1.480023436 1.441988887 1 19.828503 HSQAVEELAEQLEQTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 256.25 2.80E-27 6322771000 4905020 3722147 4769511 3684484 6003544 6020814 5388893 4861622 5219364 3164774 FALSE TRUE 5098673.977 4361396.793 4893808.375 4413263.938 4983063.735 4622571.195 4966497.485 4796459.909 5031520.109 3784850.872 1.347126782 1.152329891 1.292998995 1.166033772 1.316581261 1.221335094 1.312204273 1.26727844 1.329383978 1 21.85180503 -1.129358837 4.588623984 0.999973304 1.263933305 0.610101641 0.064044587 1.57E-05 2.99E-06 0.055810947 0.013153437 0.074240547 1.129358837 0.263960001 HSQDLAFLSMLNDIAAVPATAMPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 216.14 1.26E-33 2392640000 1116640 1179520 1298880 1476280 1567030 1772840 1329190 1310920 1328120 1303730 FALSE TRUE 1160725.809 1382093.385 1332729.88 1768283.778 1300666.8 1361124.778 1225004.615 1293349.262 1280321.221 1559170.932 0.744450647 0.886428394 0.854768295 1.134117973 0.83420411 0.872979832 0.785676919 0.829510886 0.821155137 1 20.57234767 HSQEELLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSQEELLQR 9 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 96.171 0.0075485 145710000 170370 194900 218940 197590 266210 272610 228680 200350 197810 227490 FALSE TRUE 177096.3392 228372.5589 224645.7563 236672.7123 220959.7193 209300.4589 210755.4641 197664.636 190690.8567 272062.3099 0.650940364 0.839412703 0.82571436 0.869920984 0.812165858 0.769310747 0.774658806 0.726541784 0.700908762 1 18.05357758 2.735936198 23.08093788 0.771811274 0.807195047 0 0.094295636 346.07197 3043579.303 0.028437535 0.027985502 544.4226663 -2.735936198 0.035383773 HSQFIGYPITLFVEK ddPTM_MDA-MB-175_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 ; 157.42 1.95E-06 3997600000 3151900 2955100 3634300 2795000 5074900 4661600 4258500 3766200 3730300 3424900 FALSE TRUE 3276339.446 3462615.438 3729012.844 3347842.658 4212270.311 3579014.047 3924707.642 3715720.249 3596047.232 4095943.581 0.799898578 0.845376741 0.910416066 0.817355657 1.028400472 0.873794762 0.958193775 0.907170759 0.877953312 1 21.96576441 5.030118672 0.626915454 0.930187034 0.664610934 0.364683269 0.056925089 5.098196396 1.172439047 0.023512202 1.05450384 107181.214 -5.030118672 -0.2655761 HSQFLGYPITLYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 ; 179.46 6.70E-07 3929300000 1543630 1298970 1511150 1099400 2803600 2195900 1979670 1614310 1725090 1800710 FALSE TRUE 1604573.704 1522057.993 1550531.81 1316858.039 2327045.073 1685935.504 1824498.292 1592672.815 1663004.348 2153524.648 0.745091869 0.706775283 0.719997244 0.611489653 1.080575082 0.78287263 0.847214957 0.739565631 0.772224432 1 21.03826841 HSQPS(ph)PEPHS(ph)PTEPPAWGSSIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 HS(0.104)QPS(0.896)PEPHS(0.842)PT(0.158)EPPAWGSSIVK;HS(0.001)QPS(0.999)PEPHS(0.981)PT(0.019)EPPAWGSSIVK;HS(0.119)QPS(0.834)PEPHS(0.524)PT(0.524)EPPAWGSSIVK;HS(0.055)QPS(0.945)PEPHS(0.939)PT(0.061)EPPAWGSSIVK;HS(0.105)QPS(0.893)PEPHS(0.884)PT(0.118)EPPAWGSSIVK;HSQPS(1)PEPHS(0.608)PT(0.392)EPPAWGSSIVK 211.87 2.15E-25 3618755000 1820131 1512089 1791779 1471591 2189605 2308624 2017354 1827100 1967454 1293580 TRUE FALSE 1891991.177 1771778.523 1838474.233 1762667.308 1817416.724 1772481.064 1859228.522 1802610.713 1896645.715 1547032.234 1.222981096 1.145275764 1.1883878 1.139386284 1.174776249 1.145729885 1.201803351 1.165205659 1.225989784 1 20.56107183 -1.440427819 3.512491476 0.998101721 1.176052299 0.764576142 0.029734936 2249426.263 951837.7283 32338.72589 0.006323029 0.036272057 1.440427819 0.177950578 HSQPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 HS(0.157)QPS(0.116)PEPHS(0.568)PT(0.16)EPPAWGSSIVK;HS(0.086)QPS(0.067)PEPHS(0.424)PT(0.424)EPPAWGSSIVK 111.43 0.0016061 724970000 861460 820920 1108990 953280 1412010 1421480 1222720 1110780 1206940 822070 TRUE FALSE 895471.106 961906.6241 1137891.19 1141835.939 1171997.045 1091362.813 1126880.011 1095891.811 1163502.465 983138.877 0.910828701 0.978403608 1.157406361 1.161418763 1.192097141 1.110080008 1.146206337 1.11468668 1.183456877 1 19.9070357 4.343848939 3.917235312 1.138989528 0.924910149 0.682465966 0.052053708 0.104476631 2.897011415 0.011842378 0.036828282 22072.36856 -4.343848939 -0.214079378 HSS(ph)ETFSSTPSATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSSETFSSTPSATR 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 HSS(1)ETFSSTPSATR;HSS(0.997)ET(0.003)FSSTPSATR;HSS(0.972)ET(0.028)FSSTPSATR;HSS(0.999)ET(0.001)FSSTPSATR;HS(0.043)S(0.956)ETFS(0.001)STPSATR;HS(0.088)S(0.912)ETFSSTPSATR 365.28 6.13E-97 1449950000 973037 1197508 1274716 1269620 1628784 1836473 1403554 1404120 1306524 1239193 TRUE FALSE 1011453.252 1403170.684 1307936.146 1520747.047 1351923.877 1409979.978 1293539.77 1385300.068 1259502.456 1481989.143 0.682497073 0.946815765 0.882554473 1.026152623 0.91223602 0.951410464 0.872840247 0.934757232 0.849872931 1 20.49910345 4.74125142 24.93691308 0.927894894 0.682496982 0.670402486 0.052183521 133.6192468 1238240.2 0.011546339 0.079466514 55112.666 -4.74125142 -0.245397911 HSS(ph)IS(ph)PSTLTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSSISPSTLTLK 12 0 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YCQ1 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 2 HS(0.059)S(0.941)IS(0.497)PS(0.194)T(0.309)LTLK;HS(0.087)S(0.913)IS(0.799)PS(0.086)T(0.113)LT(0.003)LK;HS(0.097)S(0.903)IS(0.898)PS(0.057)T(0.044)LT(0.001)LK 200.21 2.38E-07 331676000 1100760 807390 980720 811720 1296770 1328490 1203960 972550 1042850 722830 TRUE FALSE 1144218.855 946052.9519 1006278.369 972275.7933 1076345.499 1019968.331 1109590.469 959514.558 1005318.032 864454.6991 1.323630788 1.094392746 1.164061425 1.124727293 1.245114984 1.179897954 1.28357272 1.109965113 1.162950509 1 19.72143084 0.667840973 1.138189945 1.000946321 1.190802085 0.404018191 0.070155508 1.077024214 2.26983353 0.063084035 0.019565919 4.654156391 -0.667840973 0.189855764 HSS(ph)IS(ph)PVRLPLNSSLGAELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HSSISPVRLPLNSSLGAELSR 21 1 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 HS(0.455)S(0.562)IS(0.983)PVRLPLNSSLGAELSR;HS(0.054)S(0.948)IS(0.998)PVRLPLNSSLGAELSR;HS(0.397)S(0.603)IS(1)PVRLPLNSSLGAELSR;HS(0.005)S(0.995)IS(1)PVRLPLNSSLGAELSR;HS(0.104)S(0.896)IS(1)PVRLPLNSSLGAELSR 166.22 7.79E-12 1152654000 1122887 1179979 1255738 1082451 1523929 1733593 1320840 1225601 1250216 1134617 TRUE FALSE 1167219.446 1382631.214 1288463.564 1296556.577 1264892.093 1330992.299 1217309.109 1209173.823 1205220.97 1356923.478 0.860195483 1.018945605 0.949547698 0.955511934 0.932176437 0.980889726 0.897109623 0.891114232 0.888201133 1 20.37190793 2.22345045 24.99883812 0.907543946 0.952181017 0.065597154 0.048437931 415.8921065 688063.5365 0.016781406 0.012442011 167.2824766 -2.22345045 0.044637071 HSS(ph)NPPLESHVGWVMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 HS(0.252)S(0.748)NPPLESHVGWVMDSR;HS(0.376)S(0.624)NPPLESHVGWVMDSR;HS(0.094)S(0.906)NPPLESHVGWVMDSR;HS(0.146)S(0.854)NPPLESHVGWVMDSR;HS(0.233)S(0.767)NPPLESHVGWVMDSR 299.94 1.08E-49 2623900000 553194 694138 670802 654641 855539 1025212 807733 834011 774029 685100 TRUE FALSE 575034.5263 813350.8019 688283.6512 784127.0359 710114.7864 787122.0502 744420.7768 822832.4467 746171.8475 819332.228 0.70183316 0.992699633 0.84005441 0.957031848 0.866699444 0.960687281 0.908570115 1.004272038 0.910707308 1 19.64408904 4.747207636 24.87879874 0.935887485 0.701833033 0.637999503 0.053317768 641.048826 1844352.376 0.011926722 0.14192151 55873.72629 -4.747207636 -0.234054452 HSS(ph)PHQS(ph)EDEEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSPHQSEDEEDPR 14 0 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 2 HS(0.131)S(0.869)PHQS(1)EDEEDPR 115.63 0.00021558 978690000 682150 717720 746510 850170 980040 983000 825960 759700 781580 600110 TRUE FALSE 709081.8087 840982.8269 765964.6639 1018331.088 813453.1509 754713.1475 761219.097 749517.4641 753451.0885 717690.0647 0.988005608 1.171791095 1.067263853 1.418900914 1.13343237 1.05158645 1.060651574 1.044346997 1.049827949 1 19.45300142 2.794411378 4.693300709 1.045279275 1.168199238 0.231653122 0.104110997 0.321206468 15.12906536 0.032703434 0.034289606 622.8900274 -2.794411378 0.122919963 HSS(ph)PTEERDEPAYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSPTEERDEPAYPR 15 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 HS(0.027)S(0.965)PT(0.009)EERDEPAYPR 200.58 4.15E-09 424440000 45911 66454 66699 86568 70887 94729 56581 53581 60943 65596 TRUE FALSE 47723.60173 77866.95756 68437.23073 103690.892 58837.65306 72729.62538 52146.03337 52862.83434 58749.67333 78448.28029 0.608344779 0.992589733 0.872386628 1.321773934 0.750018392 0.927102865 0.66471863 0.673855872 0.748896893 1 16.2594542 2.251730576 24.40080976 0.734243808 0.925155405 0.097380628 0.193650579 288.0015613 533597.8188 0.065616305 0.054570968 178.5379631 -2.251730576 0.190911597 HSSGILPTFQTNLTFTVPIS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSGILPTFQTNLTFTVPISPGR 23 0 I3L2J0 I3L2J0 CIC 1 HSSGILPTFQTNLTFTVPIS(1)PGR 127.05 3.07E-05 177470000 33670 144120 106270 144740 107290 193640 111780 156850 127010 175390 TRUE FALSE 34999.3176 168871.4889 109039.4835 173369.14 89052.88412 148670.0446 103018.3915 154747.6823 122438.9349 209754.3125 0.166858632 0.805091857 0.519843822 0.826534329 0.424558061 0.708781826 0.491138372 0.737756857 0.583725471 1 17.67834095 -5 0.174613128 2.579897862 0.510856021 0.330373482 0.185547969 152.5673676 1.454330325 83.63206375 0.564937532 1.00E-05 5 -2.069041841 HSSLAGCQIINYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSSLAGCQIINYR 13 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 161.25 4.25E-05 1557590000 317494 913683 756419 991947 779282 1247029 615500 1031454 745695 943209 FALSE TRUE 330028.9083 1070600.948 776131.9005 1188151.156 646819.924 957425.4137 567255.5017 1017629.046 718857.5826 1128012.745 0.292575514 0.949103592 0.688052422 1.053313592 0.57341544 0.848771805 0.502880401 0.902143217 0.637277891 1 20.10535194 -2.667307228 2.003962601 6.759743034 0.735137136 0.127069528 0.218076388 5689501.923 249686.9732 149183837.4 0.048921512 0.002151259 2.667307228 -6.024605898 HSSSPLS(ph)PGGPTHLTKPTTTSSSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSSSPLSPGGPTHLTKPTTTSSSER 25 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 HS(0.035)S(0.03)S(0.162)PLS(0.773)PGGPTHLTKPTTTSSSER 108.1 0.0020848 557440000 16881 129550 125480 145850 132500 222760 94123 199790 125800 148370 TRUE FALSE 17547.47491 151799.2047 128750.1119 174698.6947 109977.6973 171027.366 86745.39332 197112.1418 121272.4826 177440.2608 0.098892297 0.855494712 0.725596949 0.984549357 0.619801261 0.963858851 0.488870975 1.110864811 0.683455277 1 17.43697387 4.739960733 24.70890505 0.826522114 0.098892022 0.580978276 0.185206526 66.31563624 1170181.251 0.039751981 0.249710609 54949.11892 -4.739960733 -0.727630092 HSSVYPTQEELEAVQNMVSHTER ddPTM_MDA-MB-175_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 ;; 207.17 7.18E-25 569276000 50884 410692 288594 400325 258419 500863 236804 442706 261211 433525 FALSE TRUE 52892.93961 481225.1563 296114.9967 479508.0901 214493.0307 384545.1589 218242.6837 436772.2502 251810.0671 518465.9234 0.10201816 0.928171235 0.571136855 0.924859414 0.413707094 0.741698039 0.420939302 0.842431933 0.485682965 1 18.98388964 -5 0.363655926 5.689629898 0.617452786 0.17783747 0.250328796 849.5376577 6.686785658 3123.754865 0.161105727 1.00E-05 5 -5.072177112 HSTENDS(ph)PTNVQQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSTENDSPTNVQQ 13 0 P49354;P49354-2;B3KVN2 P49354 FNTA Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha 1 HS(0.003)T(0.009)ENDS(0.988)PT(0.001)NVQQ;HSTENDS(1)PTNVQQ;HS(0.06)T(0.06)ENDS(0.876)PT(0.004)NVQQ;HS(0.001)T(0.004)ENDS(0.987)PT(0.009)NVQQ;HSTENDS(1)PTNVQQ;HSTENDS(1)PTNVQQ 236.37 1.08E-16 2040699000 1940838 1950999 1999056 1689221 3167242 4189100 2836026 2089543 1910030 1707560 TRUE FALSE 2017463.783 2286067.902 2051153.042 2023343.872 2628875.336 3216245.011 2613730.872 2061536.094 1841288.393 2042123.689 0.987924382 1.11945614 1.00442155 0.990803781 1.287324245 1.57495113 1.279908208 1.009505989 0.901653707 1 20.96163882 1.585081581 5.398810259 0.952953172 1.180714356 0.241349199 0.170266085 0.22935597 14.18555881 0.107637358 0.049672745 38.46640336 -1.585081581 0.227761183 HSTPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSTPSPTR 8 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 HS(0.001)T(0.005)PS(0.99)PT(0.003)R;HS(0.001)T(0.018)PS(0.98)PT(0.001)R;HS(0.01)T(0.07)PS(0.916)PT(0.004)R 107.58 0.0041707 1740070000 474830 762290 743250 727570 791960 1024100 823400 782150 710390 620430 TRUE FALSE 493576.655 893207.3777 762619.7056 871481.1744 657342.9221 786268.2954 758859.7564 771666.5586 684823.2027 741991.3797 0.665205376 1.203797513 1.027801301 1.174516576 0.885917195 1.059673086 1.022733926 1.039993967 0.922953044 1 19.5010429 4.755226851 24.9025266 1.038063344 0.66520507 0.595441145 0.092057576 2156.537448 3222221.794 0.020651298 0.586582604 56915.01446 -4.755226851 -0.372858275 HSTPSNSSNPSGPPS(ph)PNS(ph)PHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 2 HSTPSNSSNPS(0.011)GPPS(0.991)PNS(0.998)PHR;HSTPSNSSNPSGPPS(1)PNS(1)PHR;HSTPSNSSNPS(0.007)GPPS(0.995)PNS(0.999)PHR;HSTPSNSS(0.002)NPS(0.328)GPPS(0.671)PNS(0.999)PHR 186.24 1.75E-17 629033000 74977 261400 251272 282874 283157 374241 246887 288316 240665 234478 TRUE FALSE 77937.14985 306293.4166 257820.3547 338825.6329 235026.0743 287329.1994 227535.3518 284451.5956 232003.5137 280419.4747 0.277930589 1.092268705 0.919409592 1.208281391 0.838123224 1.024640673 0.811410663 1.01437889 0.827344513 1 18.09722702 4.744869102 24.78888529 0.96914974 0.277930241 0.751174551 0.119604052 288.3348395 1132962.891 0.026287925 0.246996798 55573.67313 -4.744869102 -0.6912195 HSTPSNSSNPSGPPS(ph)PNSPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 HSTPSNSSNPSGPPSPNSPHR 21 0 Q9Y5S2 Q9Y5S2 CDC42BPB Serine/threonine-protein kinase MRCK beta 1 HSTPSNSSNPS(0.051)GPPS(0.882)PNS(0.067)PHR;HSTPSNSSNPSGPPS(0.991)PNS(0.009)PHR;HSTPSNSSNPSGPPS(1)PNSPHR;HSTPSNSSNPSGPPS(0.995)PNS(0.005)PHR;HSTPSNSSNPSGPPS(0.988)PNS(0.012)PHR;HSTPSNSSNPS(0.003)GPPS(0.947)PNS(0.05)PHR;HSTPSNSSNPSGPPS(0.979)PNS(0.021)PHR;HSTPSNSSNPSGPPS(0.998)PNS(0.002)PHR;HSTPSNSSNPSGPPS(1)PNSPHR;HSTPSNSSNPSGPPS(0.994)PNS(0.005)PHR;HSTPSNSSNPSGPPS(0.997)PNS(0.003)PHR;HSTPSNSSNPS(0.003)GPPS(0.948)PNS(0.049)PHR;HSTPSNSSNPS(0.049)GPPS(0.782)PNS(0.169)PHR 238.2 1.17E-29 3528202000 200952.2 878046 802682.3 873644.9 832372.5 1193857.7 702606.6 907550 731245.7 889796 TRUE FALSE 208885.948 1028843.57 823600.8601 1046449.254 690886.1198 916602.3423 647534.4588 895385.7767 704928.3101 1064134.49 0.196296568 0.966836034 0.77396313 0.983380638 0.649246995 0.861359491 0.608508102 0.84142163 0.662442874 1 20.02124907 -5 0.031005701 2.070553544 2.24E-13 0.142105338 0.213143407 3361.268755 7.841698578 414.218709 162.9764234 1.00E-05 5 -2.070553544 HSTSGT(ph)DEGEDGDEPDDGSNDVVDLLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HSTSGTDEGEDGDEPDDGSNDVVDLLPR 28 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 1 HS(0.08)T(0.097)S(0.144)GT(0.678)DEGEDGDEPDDGSNDVVDLLPR 197.83 1.95E-24 55098000 16067 18421 19711 18625 23452 27253 19116 18694 20800 14502 TRUE FALSE 16701.33757 21584.66345 20224.68485 22308.96941 19465.63742 20923.90377 17617.63797 18443.43751 20051.41206 17343.38924 0.962980034 1.244547023 1.166132212 1.286309677 1.122366404 1.206448375 1.015812868 1.063427526 1.156141501 1 14.08209824 2.242421746 24.99966855 1.062330063 1.172077572 0.248050811 0.089755875 132.7306835 859396.6808 0.030482215 0.024616747 174.7518356 -2.242421746 0.109747509 HSVDELQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSVDELQK 8 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ; 127.02 0.0011942 387200000 563510 457690 522900 440410 695100 711220 635870 544550 596340 394760 FALSE TRUE 585757.8099 536294.6972 536527.2036 527521.7835 576947.1503 546049.9336 586028.8479 537251.198 574877.8399 472105.6639 1.240734553 1.135963277 1.136455765 1.117380756 1.222072079 1.156626525 1.241308658 1.137989308 1.217688928 1 18.84875027 -1.484248607 4.868044674 0.999460577 1.17483595 0.578457855 0.045610697 0.000252224 2.67E-05 0.041714405 0.009802297 0.032790753 1.484248607 0.175375373 HSVGVVIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HSVGVVIGR 9 0 A0A087WTP3;Q92945;M0R0I5 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;; 169.44 5.85E-05 1907230000 1387870 1524400 1589710 1507040 1856160 2097190 1656250 1619200 1580200 1487150 FALSE TRUE 1442664.179 1786203.842 1631139.149 1805128.014 1540650.586 1610149.406 1526428.797 1597497.272 1523328.911 1778528.569 0.811156033 1.004315518 0.917128449 1.014955871 0.86625012 0.905326703 0.858253741 0.898212882 0.85651079 1 20.76225272 HSVTAAT(ph)PPPS(ph)PTSGESGDLLSNLLQSPSSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8;Q96QU8-2 Q96QU8 XPO6 Exportin-6 2 HS(0.005)VT(0.065)AAT(0.87)PPPS(0.655)PT(0.086)S(0.075)GES(0.242)GDLLS(0.003)NLLQSPSSAK;HSVT(0.002)AAT(0.995)PPPS(0.952)PT(0.027)S(0.024)GESGDLLSNLLQSPSSAK;HS(0.001)VT(0.008)AAT(0.935)PPPS(0.822)PT(0.119)S(0.105)GES(0.012)GDLLSNLLQSPSSAK 165.97 8.87E-14 261299000 426772 277185 354062 320935 430489 465596 523817 368472 395837 218338 TRUE FALSE 443621.2881 324789.3676 363289.1466 384414.9851 357314.6335 357468.3852 482758.8548 363533.2355 381590.9037 261117.1508 1.698935849 1.243845403 1.391287955 1.47219355 1.36840737 1.368996192 1.848820935 1.392222742 1.461378169 1 17.99433769 HSVVAGGGGGEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSVVAGGGGGEGR 13 0 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 0 ; 127.79 0.0001728 200678000 80043 113609 100485 98661 104635 132593 104913 104146 97399 105821 FALSE TRUE 83203.15945 133120.462 103103.7216 118175.8513 86849.18007 101800.2852 96689.64492 102750.0932 93893.62902 126554.5989 0.657448723 1.051881663 0.81469755 0.933793417 0.686258586 0.80439815 0.764015261 0.811903274 0.741921904 1 16.94940041 3.259856969 24.99979434 0.791166798 0.874288778 0.055850571 0.120014656 542.4184941 636741.3479 0.030197078 0.040848679 1819.101654 -3.259856969 0.08312198 HSYTPTTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HSYTPTTSR 9 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 0 ; 86.898 0.013826 108561000 65236 107782 115031 98234 108007 126039 82011 93642 104042 134785 FALSE TRUE 67811.56765 126292.7201 118028.8024 117664.392 89648.00872 96768.35239 75582.76352 92386.88216 100297.5487 161193.5401 0.420684151 0.783484996 0.732217943 0.729957242 0.556151373 0.60032401 0.468894495 0.573142584 0.622218165 1 17.2984344 -1.507477408 5.192325145 1.00107771 0.611098851 0.533891791 0.109404575 0.001399538 0.000132755 0.108618875 0.025535235 0.031082976 1.507477408 -0.389978858 HT(ph)GEKHFK ddPTM_MDA-MB-175_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 5928180000 7677860 5608150 6260110 3364170 10104250 7520260 5133720 6093590 7390130 7282640 TRUE FALSE 7980987.841 6571306.137 6423253.609 4029592.785 8386733.194 5773793.586 4731325.612 6011915.393 7124160.665 8709533.873 0.916350744 0.754495732 0.737496828 0.462664575 0.962937089 0.662927967 0.543235227 0.690268329 0.817972669 1 23.05416408 -0.968933303 9.188939098 0.999999285 0.715724815 0.23691418 0.145266714 0 0 0.13587464 0.03202596 0.107415436 0.968933303 -0.28427447 HT(ph)PSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.835)PS(0.165)PGLPAEGAPEAPRPS(0.454)S(0.546)PPPEVLEPHSLDQPPATSPR 239.51 1.55E-49 190000000 21117 20104 24039 18923 22595 25295 19254 22510 20072 15255 TRUE FALSE 21950.71547 23556.70561 24665.47609 22665.91292 18754.30997 19420.6196 17744.82117 22208.29027 19349.61264 18243.92518 1.203179428 1.29120819 1.351982967 1.242381379 1.027975602 1.064497876 0.972642729 1.217297816 1.060605788 1 14.15512854 3.334205138 5.171092281 1.07288066 1.284605408 0.687277917 0.070804341 0.12911261 5.563637696 0.020722827 0.028144861 2158.763857 -3.334205138 0.211724749 HT(ph)RISELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTRISELK 8 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 HT(0.5)RIS(0.5)ELK 70.919 0.080973 129200000 8915.2 177980 121770 194900 83472 187450 77318 149020 90327 224490 TRUE FALSE 9267.17898 208546.6805 124943.4262 233450.6383 69283.45926 143917.5783 71257.61313 147022.6306 87076.14891 268474.5174 0.034517909 0.776783892 0.465382813 0.869544866 0.258063447 0.536056754 0.265416673 0.547622292 0.324336737 1 18.03442563 -1.420950302 4.27066553 1.001784484 0.469616352 0.32199254 0.23699807 73664976.6 24520211.12 1234746.363 0.05056169 0.037935839 1.420950302 -0.532168133 HTADRWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTADRWR 7 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 106.04 0.0071055 88187000 21165 70267 44440 42848 120400 74389 39603 41565 52957 204210 FALSE TRUE 22000.61054 82334.81065 45598.14291 51323.20651 99934.45101 57113.28213 36498.81338 41007.88916 51051.08791 244221.0397 0.090084829 0.33713234 0.186708496 0.210150635 0.409196731 0.233858975 0.149449914 0.167913007 0.209036404 1 17.89782797 -1.744652431 2.486237599 1.180281622 0.222266616 0.878289359 0.086940334 5395944.626 3890986.543 5981606.53 0.022316578 0.018003111 1.744652431 -0.958015005 HTDDEMTGYVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTDDEMTGYVATR 13 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 124.07 0.00011703 0 30996 53570 48841 48001 54749 74015 46116 51661 44713 55191 FALSE TRUE 32219.74601 62770.23078 50113.83658 57495.45453 45442.78454 56826.13796 42501.30742 50968.5688 43103.78786 66004.61975 0.488143802 0.950997536 0.75924741 0.871082278 0.688478847 0.860941828 0.643914132 0.772196991 0.653041984 1 16.01027938 -1.8815907 2.57734705 1.122499891 0.752534611 0.266424594 0.127014847 26343737.77 13960331.78 19621995.22 0.027997774 0.013134372 1.8815907 -0.36996528 HTDNVIQWLNAMDEIGLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTDNVIQWLNAMDEIGLPK 19 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 176.73 8.49E-14 2786700000 3489700 2535100 3571000 2776700 4312500 4015900 3755200 3253800 3727900 2315300 FALSE TRUE 3627476.051 2970483.705 3664063.194 3325922.972 3579462.79 3083268.087 3460857.612 3210188.133 3593733.607 2768938.706 1.310060076 1.072787815 1.323273493 1.201154423 1.292720125 1.113519805 1.24988596 1.159356878 1.297874019 1 21.40090169 -1.762574567 2.742240608 0.951380153 1.217738183 0.396945749 0.082640205 12539955.05 9247507.419 4092273.848 0.0185278 0.017275293 1.762574567 0.26635803 HTEGGTSEHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTEGGTSEHEK 11 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 73.632 0.024883 51524000 18440 17139 29594 20567 28761 36163 24704 21318 27807 22635 FALSE TRUE 19168.02544 20082.48993 30365.24395 24635.09121 23872.21549 27764.69131 22767.63593 21032.26708 26806.2315 27069.89488 0.708093826 0.741875431 1.121734831 0.910054927 0.881873225 1.025666758 0.841068502 0.776961535 0.990259904 1 14.72440166 4.442819852 24.8858701 0.922752309 0.716538948 0.447845395 0.095152901 142.9771556 103730.6227 0.024264173 0.066450869 27721.69956 -4.442819852 -0.206213361 HTENTFSRPGGR ddPTM_MDA-MB-175_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 ; 109.24 0.00097318 38697000 13705.6 36283.6 40119.6 30969.3 55648.3 44919.4 39214.6 39812.1 47487.6 42695 FALSE TRUE 14246.70767 42515.02605 41165.14973 37094.93511 46189.22184 34487.55011 36140.85718 39278.48392 45778.53055 51060.2678 0.279017488 0.832644008 0.806207086 0.726493156 0.904602029 0.675428304 0.707807827 0.769257303 0.896558763 1 15.63991348 4.741048932 24.9853302 0.795722977 0.279017305 0.732224558 0.096393867 112.0637202 1125172.316 0.021603321 0.146847238 55086.97601 -4.741048932 -0.516705672 HTGCCGDNDPIDVCEIGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HTGCCGDNDPIDVCEIGSK 19 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 293.22 1.33E-49 7722630000 6408070 4518810 5386930 4941900 7219730 7391080 6389140 5963280 6376510 4264756 FALSE TRUE 6661065.552 5294880.466 5527317.821 5919393.07 5992522.873 5674613.683 5888342.512 5883351.986 6147020.651 5100353.285 1.306000816 1.038139943 1.083712738 1.160584912 1.174923096 1.112592279 1.154496989 1.153518523 1.20521468 1 22.28216575 -0.362023327 9.162365692 1.000000103 1.148695717 0.312341044 0.068245333 0 0 0.061720115 0.014547571 0.434486887 0.362023327 0.148695615 HTGMASIDSSAPETTSDSS(ph)PTLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 HTGMASIDSSAPETTS(0.001)DS(0.009)S(0.988)PT(0.002)LSR;HTGMASIDSSAPETTSDS(0.023)S(0.814)PT(0.155)LS(0.008)R 242.71 7.81E-38 455940000 145826 246960 242540 249810 250440 303750 219530 243260 224650 217130 TRUE FALSE 151583.3231 289373.4589 248860.7916 299221.6724 207870.2983 233208.6659 202322.665 239999.4976 216564.8904 259672.4663 0.583748155 1.114378675 0.958364185 1.152304196 0.800509585 0.898087769 0.779145621 0.924239297 0.833992504 1 17.98633352 HTGPGILSMANAGPNTNGSQFFICTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTGPGILSMANAGPNTNGSQFFICTAK 27 0 P62937;F8WE65;C9J5S7;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ;;; 345.29 4.88E-110 4735040000 3259360 3168070 3410200 2676252 4525760 4596510 3556420 3460030 3715730 2836929 FALSE TRUE 3388042.05 3712161.378 3499072.614 3205606.658 3756472.932 3529040.213 3277658.507 3413653.957 3582001.603 3392770.921 0.998606192 1.094138527 1.031331821 0.944834394 1.107199106 1.040164601 0.966071268 1.006155157 1.055774671 1 21.69403259 HTGPNS(ph)PDTANDGFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 HTGPNS(1)PDTANDGFVR;HTGPNS(0.993)PDT(0.007)ANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HT(0.003)GPNS(0.997)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR 335.18 1.11E-71 27002960000 5045052 5173100 5419510 5351799 6371730 7255360 5890117 5419260 5285420 4909805 TRUE FALSE 5244234.549 6061539.684 5560746.883 6410368.869 5288665.611 5570412.596 5428434.239 5346623.684 5095198.767 5871787.286 0.893124068 1.032315952 0.947027985 1.09172362 0.90069094 0.948674113 0.924494362 0.910561542 0.867742396 1 22.48536827 HTGPNSPDTANDGFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HTGPNSPDTANDGFVR 16 0 P31943;G8JLB6;E9PCY7;D6RBM0;D6RIT2;D6RIU0;D6R9T0;D6RFM3;E5RGV0;D6RDU3;D6RJ04;D6RIH9;D6RAM1;E5RGH4;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 333.77 1.21E-71 7810670000 3600640 5087190 4894170 4840110 5431100 6625520 5132230 5316430 4836900 4873090 FALSE TRUE 3742796.047 5960875.31 5021716.091 5797469.312 4507923.562 5086843.391 4729952.402 5245171.952 4662820.914 5827878.685 0.642222711 1.022820761 0.861671349 0.994782085 0.773510192 0.872846479 0.811607904 0.900013922 0.800088877 1 22.47453942 -1.35781304 3.193591672 1.001220469 0.861993621 0.148039767 0.103711651 43349839.03 60831358.11 501494.1241 0.022553574 0.043871952 1.35781304 -0.139226848 HTGYVIELQHVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTGYVIELQHVVK 13 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 176.25 9.76E-06 259630000 295260 267820 328340 277120 362570 366990 313570 285670 317060 329070 FALSE TRUE 306917.0928 313816.0016 336896.8101 331933.5089 300940.4809 281762.1343 288991.564 281841.0609 305649.0725 393544.9661 0.779878081 0.797408247 0.856056713 0.843444936 0.764691476 0.715959188 0.73432921 0.716159741 0.776656034 1 18.58616896 3.189067636 9.153537149 0.760397293 0.820232921 0 0.081408443 0.709306014 123.3636353 0.022040995 0.026438313 1545.495114 -3.189067636 0.059835628 HTKEDSAS(ph)VK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HTKEDSASVK 10 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 HTKEDS(0.014)AS(0.986)VK;HTKEDS(0.012)AS(0.988)VK;HTKEDSAS(1)VK 96.866 0.0038945 336624000 1172580 437014 626620 469467 948250 1018660 922620 651260 714460 371068 TRUE FALSE 1218874.364 512067.755 642950.232 562326.1714 787066.8037 782091.6529 850302.6336 642530.9249 688746.7242 443771.6701 2.746625001 1.153899155 1.448831179 1.267152027 1.773585059 1.762373999 1.916081379 1.447886308 1.552029502 1 18.75945804 0.670878284 1.242622105 1.002438516 1.667084507 0.197126759 0.41920222 1.85322317 4.543183521 0.378553675 0.114765581 4.6868201 -0.670878284 0.664645991 HTLADNFNPVSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTLADNFNPVSEER 14 0 P20645;H0YGT2 P20645 M6PR Cation-dependent mannose-6-phosphate receptor 0 ;;; 209.53 6.51E-09 1547050000 610100 782410 712620 844840 1045090 1137060 860480 783820 703340 865110 FALSE TRUE 634187.2191 916782.8312 731191.4626 1011946.83 867445.9751 872995.0473 793033.3292 773314.175 678026.9308 1034611.741 0.612971218 0.88611292 0.706730297 0.978093318 0.838426572 0.843790006 0.766503315 0.747443842 0.655344323 1 19.98065804 -2.446536118 2.2068072 3.04743145 0.788271257 0.281643979 0.104111782 7934747.33 668323.9562 81245215.06 0.02499346 0.003576547 2.446536118 -2.259160194 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTLDQYVESDYTLLYLHHGLTSDNKPSLSWLR 32 1 Q07960;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 321.9 5.06E-105 8327600000 525550 747330 878340 806140 1057370 1139960 1034000 895110 913770 754950 FALSE TRUE 546299.1198 875678.1141 901230.262 965592.0859 877638.6251 875221.5663 952952.3781 883112.5146 880883.5962 902867.9981 0.605070864 0.969884984 0.998186074 1.069472047 0.97205641 0.96937932 1.055472539 0.97811919 0.975650481 1 19.78415555 4.742259389 3.931612925 1.002472905 0.566373935 0.929384772 0.032657532 0.056641391 1.783698334 0.007824561 0.071221799 55240.7274 -4.742259389 -0.436098969 HTLGDS(ph)DNES ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HTLGDSDNES 10 0 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 HTLGDS(1)DNES;HTLGDS(1)DNES;HTLGDS(1)DNES 98.105 0.0051908 0 377828 396107 367014 390464 436046 538921 458984 404835 419374 354387 TRUE FALSE 392744.9412 464135.296 376578.6863 467696.6138 361927.0567 413764.7652 423007.6347 399408.849 404280.8117 423822.3475 0.926673507 1.095117562 0.888529566 1.103520417 0.853959351 0.976269344 0.998077702 0.942396859 0.953892153 1 18.69310014 3.237828495 24.99999999 0.954689302 1.001797855 0.100484207 0.072269644 47.39137387 1618312.514 0.018826325 0.023777901 1729.133382 -3.237828495 0.047108554 HTNFVEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTNFVEFR 8 0 M0R0N4;M0QYZ2;P53680;M0QZ21 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 ;;; 144.66 0.00058192 1076350000 520960 494347 489163 486879 810490 740440 541261 541720 547489 667110 FALSE TRUE 541527.9031 579247.2518 501910.9896 583182.213 672723.1993 568484.0315 498835.5485 534459.1295 527784.9778 797817.4319 0.678761683 0.726039854 0.629105068 0.730972011 0.843204438 0.712549023 0.62525025 0.669901544 0.661536032 1 19.60569912 -1.449087214 3.025166926 1.006530007 0.696846092 0.697625508 0.05974853 18199065.23 21139280.42 1003109.238 0.01602332 0.035555991 1.449087214 -0.309683915 HTNPSSSS(ph)PGTRT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTNPSSSSPGTRT 13 1 Q8WUH2 Q8WUH2 TGFBRAP1 Transforming growth factor-beta receptor-associated protein 1 1 HTNPS(0.039)S(0.064)S(0.331)S(0.565)PGTRT;HTNPSS(0.001)S(0.016)S(0.937)PGT(0.036)RT(0.01) 95.264 0.00075145 157820000 82833 154590 146044 137645 148370 174305 118172 145099 145573 164204 TRUE FALSE 86103.3108 181139.63 149850.0266 164870.7702 123150.1204 133825.3054 108909.3699 143154.1852 140333.8562 196376.6299 0.438460069 0.922409301 0.763074642 0.839564108 0.627111894 0.681472665 0.554594352 0.728977706 0.71461587 1 17.58326372 -1.786295392 4.845416969 1.027393128 0.702744729 0.327403333 0.130157059 0.036469431 0.001608465 0.119327475 0.028157133 0.016357036 1.786295392 -0.3246484 HTNYTMEHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 178.53 1.28E-06 1697211000 212954.7 604600 390932.5 495513 534701 630565 467342 395491 419956 895100 FALSE TRUE 221362.316 708435.3469 401120.5221 593523.9924 443812.715 484125.8351 430710.5129 390190.09 404841.8656 1070477.707 0.206788347 0.661793648 0.374711701 0.554447784 0.414593141 0.452252141 0.402353557 0.364500902 0.37818804 1 20.02982332 -1.629491168 4.377369452 1.013667205 0.427818577 0.696511779 0.114169475 0.013896689 0.001176242 0.100879444 0.023666298 0.02346977 1.629491168 -0.585848628 HTPLYER ddPTM_MDA-MB-175_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 75.213 0.044081 236320000 116240 164850 130420 145340 198780 222180 134350 136350 138910 187540 FALSE TRUE 120829.245 193161.7051 133818.8523 174087.8182 164991.4466 170582.0622 123819.2959 134522.4513 133910.6562 224284.8723 0.53873114 0.861233766 0.596646804 0.776190638 0.735633415 0.76055982 0.552062628 0.599783881 0.597056123 1 17.77497279 2.266941232 24.99988953 0.64444262 0.717122324 0 0.145608877 657.0113651 578745.2868 0.046385937 0.038802784 184.9018394 -2.266941232 0.072679704 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.002)PS(0.998)PGLPAEGAPEAPRPS(0.552)S(0.448)PPPEVLEPHSLDQPPATSPR;HT(0.193)PS(0.807)PGLPAEGAPEAPRPS(0.49)S(0.49)PPPEVLEPHS(0.013)LDQPPAT(0.004)S(0.004)PR 247.5 4.59E-51 353830000 39631 36296 31244 36112 37066 41323 41662 33263 32743 27587 TRUE FALSE 41195.66248 42529.55566 32058.24431 43254.84582 30765.53456 31726.35951 38396.42358 32817.16389 31564.58583 32992.14446 1.248650645 1.289081275 0.971693257 1.311064998 0.932510907 0.961633747 1.163805027 0.994696296 0.956730347 1 15.00983493 5.031397138 0.447228586 0.999779033 1.563366106 0.376665653 0.114097717 6.771440244 0.869132004 0.075339209 2.140374399 107497.1965 -5.031397138 0.563587073 HTPS(ph)PGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.219)PS(0.78)PGLPAEGAPEAPRPS(0.511)S(0.489)PPPEVLEPHS(0.001)LDQPPATSPRPLIEVGELLDLTR;HT(0.169)PS(0.831)PGLPAEGAPEAPRPS(0.491)S(0.472)PPPEVLEPHS(0.025)LDQPPAT(0.004)S(0.004)PRPLIEVGELLDLT(0.003)R;HT(0.197)PS(0.793)PGLPAEGAPEAPRPS(0.517)S(0.492)PPPEVLEPHS(0.001)LDQPPATSPRPLIEVGELLDLTR 58.612 0.0013958 122976000 7612.7 9945.5 7235.5 5436.5 10011 9812.4 5871.5 10103.6 10831.6 9637.06 TRUE FALSE 7913.255274 11653.56226 7424.063074 6511.823474 8309.333796 7533.618808 5411.276488 9968.177768 10441.77283 11525.25739 0.686601175 1.011132495 0.644155946 0.565004603 0.720967308 0.653661654 0.469514589 0.864898494 0.905990424 1 13.49251135 1.546835958 6.853403364 0.930809839 0.68494488 0.423528616 0.132906543 0.134375291 12.10235799 0.076460868 0.035345704 35.22377987 -1.546835958 -0.245864959 HTPS(ph)PGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HT(0.164)PS(0.836)PGLPAEGAPEAPRPS(0.236)S(0.764)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 114.47 5.34E-10 345050000 9581.4 11890 15104 13067 14279 14560 12711 11472 9058.6 14339 TRUE FALSE 9959.68107 13932.01501 15497.62265 15651.6136 11851.86068 11178.66066 11714.67861 11318.2366 8732.582756 17148.45251 0.580791827 0.812435699 0.903733012 0.912712887 0.691132956 0.651875768 0.68313328 0.660015042 0.509234448 1 14.06579077 3.100397744 9.226988717 0.676554019 0.810173137 0.098437693 0.143330766 0.506751663 42.36400107 0.039948336 0.047794464 1260.078912 -3.100397744 0.133619119 HTPSPGLPAEGAPEAPRPS(ph)S(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.587)S(0.587)PPPEVLEPHS(0.231)LDQPPAT(0.284)S(0.284)PRPLIEVGELLDLT(0.026)R 53.386 0.0017216 254830000 7952.7 9948.5 9513.9 8570.4 8816.3 12730 7672.8 10814 6664.3 6377.8 TRUE FALSE 8266.678737 11657.07749 9761.84005 10265.59954 7317.708475 9773.650425 7071.385887 10669.05602 6424.453145 7627.4078 1.083812345 1.528314441 1.279837175 1.345883137 0.959396517 1.281385588 0.927102113 1.398778759 0.842285258 1 12.89697712 2.653876585 0.356405548 1.00244468 1.367782999 0.212213514 0.195050219 2.816665221 0.746463982 0.216119409 0.380129151 450.6886128 -2.653876585 0.365338319 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPR 40 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPR;HTPSPGLPAEGAPEAPRPS(0.499)S(0.499)PPPEVLEPHS(0.003)LDQPPATSPR 115.01 2.11E-06 555430000 92581 90901.6 105197 108847 98297.2 119641 104881.5 111160 92925 74368.2 TRUE FALSE 96236.16937 106513.2427 107938.5202 130376.6117 81588.67705 91856.19093 96660.61397 109670.082 89580.6474 88939.22492 1.082044165 1.197595805 1.213621103 1.465906768 0.917353138 1.032797295 1.086816464 1.233090148 1.007211919 1 16.44053221 3.220856107 24.9993014 1.071707064 1.234908734 0.381233798 0.118104484 311.91866 440437.6935 0.036082971 0.043213928 1662.861611 -3.220856107 0.16320167 HTPSPGLPAEGAPEAPRPS(ph)SPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.5)S(0.5)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 126.87 3.73E-14 276970000 40474 61509 50177 45331 52914 64512 42684 45893 45549 52364 TRUE FALSE 42071.94477 72072.69228 51484.65384 54297.3365 43919.69718 49530.06569 39338.31655 45277.8794 43909.70039 62623.72323 0.671821198 1.150884817 0.822127002 0.867041014 0.701326828 0.790915377 0.628169558 0.723014811 0.701167195 1 15.93442166 3.443267998 2.267539716 0.73476859 0.909353954 0.117847268 0.145278692 0.441593788 4.572536114 0.039823792 0.062268634 2775.032016 -3.443267998 0.174585364 HTPSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPAT(ph)SPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 HTPSPGLPAEGAPEAPRPS(0.479)S(0.521)PPPEVLEPHS(0.191)LDQPPAT(0.422)S(0.387)PRPLIEVGELLDLTR 100.11 9.63E-07 598790000 26628 37289 34145 29726 36889 40469 30071 41035 30962 34941 TRUE FALSE 27679.294 43693.09568 35034.84675 35605.71408 30618.62096 31070.68806 27713.95644 40484.99294 29847.68367 41787.01996 0.662389757 1.045614062 0.838414579 0.852075934 0.732730426 0.743548788 0.66321926 0.968841353 0.714281222 1 15.35076726 -1.714145481 2.778486004 1.029906755 0.813685061 0.188032061 0.121175099 30958390.07 27445227.61 6463627.584 0.028306026 0.019313213 1.714145481 -0.216221694 HTPSPGLPAEGAPEAPRPSS(ph)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTPSPGLPAEGAPEAPRPSSPPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 53 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 HTPSPGLPAEGAPEAPRPS(0.432)S(0.568)PPPEVLEPHSLDQPPATSPRPLIEVGELLDLTR 169.45 1.05E-24 242700000 30225 37995 37737 29874 45089 47408 27723 43235 34057 33537 TRUE FALSE 31418.30634 44520.34569 38720.45722 35782.98804 37424.78789 36398.21048 25549.99882 42655.50554 32831.29522 40107.93305 0.783343941 1.110013464 0.965406449 0.892167342 0.933101884 0.907506513 0.637031053 1.06351792 0.818573602 1 15.2916 3.744666582 7.656839312 0.892667574 0.968810835 0.03869759 0.129518083 0.394035882 194.6795088 0.03243072 0.055197256 5554.7764 -3.744666582 0.076143261 HTQENCETWGVNGETGTLVDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTQENCETWGVNGETGTLVDMK 22 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 194.97 1.75E-18 228990000 175880 134397 142356 130627 187591 205536 208765 128425 181864 102324 FALSE TRUE 182823.8782 157478.6393 146065.9143 156464.6307 155704.3488 157803.3789 192401.4538 126703.6729 175318.7502 122372.4287 1.493995667 1.286880067 1.193617842 1.278593817 1.272380964 1.289533767 1.572261463 1.035393955 1.432665446 1 16.90091902 -3.510127601 0.33467248 2.83E-14 1.314528507 0.287630255 0.146213847 160.0058357 3.518864706 111.6605473 0.116241721 0.000308939 3.510127601 1.314528507 HTQLEQMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HTQLEQMFR 9 0 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ;; 154.84 7.47E-05 1134540000 584120 660010 672130 578150 839810 863740 716800 663010 687220 710190 FALSE TRUE 607181.5086 773361.5833 689646.26 692506.3444 697059.3962 663149.4751 660615.343 654123.4354 662487.0864 849338.1331 0.714887846 0.910546169 0.811980804 0.815348231 0.820708937 0.780783824 0.777800168 0.770156678 0.780003936 1 19.6959795 -0.965964495 5.703046525 1.000000254 0.799391936 0.62089757 0.047335783 1.48E-07 2.68E-08 0.044236396 0.010426605 0.108152237 0.965964495 -0.200608318 HTQSMS(ph)SARER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTQSMSSARER 11 1 K7EJR8;B5MDG7;Q9P0W2-2;Q9P0W2-3;Q9P0W2 K7EJR8 HMG20B SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related 1 HT(0.023)QS(0.052)MS(0.463)S(0.463)ARER;HT(0.009)QS(0.013)MS(0.489)S(0.489)ARER 64.224 0.042182 1419400000 89741 798790 681570 764000 585730 848960 529540 696470 555520 867600 TRUE FALSE 93284.04398 935975.9688 699332.2741 915116.9197 486167.8238 651801.9061 488033.2711 687134.9588 535526.9437 1037589.609 0.089904566 0.902067601 0.673996991 0.881964229 0.468555024 0.628188544 0.47035289 0.662241558 0.51612597 1 19.98480451 -1.283200557 4.668739997 1.000139225 0.60544716 0.23668353 0.219918073 0.000373019 5.73E-05 0.19534576 0.046022887 0.052095408 1.283200557 -0.394692065 HTSKLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTSKLSR 7 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 HTS(0.008)KLS(0.992)R;HTSKLS(1)R 78.932 0.020589 563040000 81978 609560 512550 561120 527230 844980 476430 775030 491360 625340 TRUE FALSE 85214.55474 714247.1883 525907.4741 672107.8612 437611.6329 648746.2008 439086.1717 764641.9905 473676.0496 747863.4001 0.11394401 0.955050332 0.703213279 0.898704043 0.58514915 0.867466172 0.587120819 1.022435368 0.633372417 1 19.51241526 4.746493324 24.8853054 0.801436385 0.113943653 0.626919191 0.160090875 552.7606804 1733995.705 0.034462234 0.37861335 55781.90271 -4.746493324 -0.687492732 HTTDLDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 153.05 7.90E-05 2655370000 1737970 2804830 3196090 2788020 4015890 4164940 3264290 2981050 2853430 2491420 FALSE TRUE 1806586.398 3286537.734 3279382.731 3339482.035 3333270.452 3197695.805 3008426.42 2941093.901 2750735.612 2979566.048 0.60632534 1.103025636 1.100624278 1.120794767 1.11871004 1.073208566 1.009686099 0.987088003 0.923200079 1 21.5066708 4.742747966 24.8384856 1.050135275 0.606325148 0.815465117 0.063096248 172.5097858 1023250.159 0.016853537 0.130176425 55302.90774 -4.742747966 -0.443810127 HTTEAAAGALQNITAGDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTTEAAAGALQNITAGDRR 19 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ;;; 197.14 5.21E-16 772010000 589871 552683 631238 508732 703108 717584 634390 611974 561537 555278 FALSE TRUE 613159.5626 647602.006 647688.5808 609357.6712 583593.9533 550935.9911 584664.8541 603771.4895 541327.3931 664074.0927 0.923330046 0.975195408 0.975325778 0.917604945 0.878808494 0.829630304 0.880421117 0.909192959 0.815161138 1 19.34098469 3.475667601 3.408352426 0.880404306 0.959149646 0.302180029 0.048818985 0.256226419 6.274789387 0.012994564 0.019475187 2989.975301 -3.475667601 0.07874534 HTTENKPHS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTTENKPHSPK 11 1 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(1)PK;HTTENKPHS(1)PK 118.33 0.00044343 98460000 122703 79143 114411 84690 163238 157872 177192 119897 127157 48582 TRUE FALSE 127547.4092 92735.1946 117392.6446 101441.4292 135490.8631 121208.6206 163303.228 118289.9768 122580.6444 58100.71274 2.195281317 1.596111136 2.02050266 1.74595843 2.332000016 2.086181302 2.810692336 2.035947086 2.109795881 1 15.82626824 3.243561081 24.98164236 2.159815336 1.877869609 0.006997529 0.451620446 317.0900674 1584127.797 0.117238517 0.153951592 1752.108842 -3.243561081 -0.281945727 HTTENKPHSPKT(ph)PEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTTENKPHSPKTPEPR 16 2 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 1 HTTENKPHS(0.003)PKT(0.997)PEPR 114.88 0.0005513 62372000 29381 26595 38590 24771 49751 45105 44983 39355 42814 21413 TRUE FALSE 30540.98457 31162.48437 39595.6871 29670.62987 41294.34279 34630.04732 41457.11492 38827.5106 41273.1325 25608.46737 1.192612745 1.216882054 1.546195113 1.158625756 1.612526911 1.352288945 1.618883095 1.51619814 1.611698658 1 14.64433329 4.711203581 0.740922646 1.475012049 0.994078215 0.111969615 0.203604588 4.39591248 1.884020542 0.072060524 1.757876343 51428.46725 -4.711203581 -0.480933834 HTTSIFDDFAHYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTTSIFDDFAHYEK 14 0 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 99.069 0.0013458 44901000 29651 67798 75539 62116 87727 98484 70080 72043 82678 82297 FALSE TRUE 30821.64438 79441.7791 77507.6084 74402.3594 72815.19588 75612.58354 64586.94648 71077.38142 79702.43493 98421.52148 0.313159601 0.807158616 0.787506708 0.7559562 0.739830017 0.768252537 0.656227881 0.722173162 0.809806979 1 16.5866862 -5 0.039264705 2.182527217 1.24E-14 0.404282552 0.126744738 1043.284216 3.062522773 151.5680913 46.62772711 1.00E-05 5 -2.182527217 GTVT(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GTVTPPPR 8 0 P00519-2;P00519 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 GT(0.002)VT(0.998)PPPR 74.2 0.096371 0 440280 149960 120480 126270 159730 239050 129890 144880 120780 132040 TRUE FALSE 457662.5944 175714.4635 123619.8078 151245.8291 132579.1517 183534.2603 119708.8824 142938.1206 116433.1514 157910.7099 2.89823657 1.1127457 0.782846254 0.957793358 0.839583026 1.162266071 0.758079566 0.905183193 0.737335368 1 17.2687495 4.7382356 3.688475882 0.894142362 3.115011783 0.960573423 0.121111559 0.042415318 1.079635022 0.027466174 0.258409317 54731.27938 -4.7382356 2.220869422 up HTVDDGLDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTVDDGLDIR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 178.46 2.21E-06 2319370000 2284550 2122190 2543370 2337090 3494970 3260540 2737780 2342510 2586620 2310590 FALSE TRUE 2374745.798 2486659.624 2609652.312 2799359.426 2900896.248 2503328.999 2523185.65 2311112.485 2493528.051 2763305.872 0.859385789 0.899885767 0.944395023 1.013047254 1.049791946 0.90591817 0.913104002 0.836357824 0.902371351 1 21.39796383 -0.47386242 8.54571571 1.000000017 0.923510003 0.118719768 0.061262023 0 0 0.066947609 0.015779703 0.335843989 0.47386242 -0.076490014 HTVDDGLDIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HTVDDGLDIRK 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ;;; 174.4 7.17E-06 1233150000 1209210 905250 1191280 940770 1628700 1468330 1083590 1114440 1283840 937640 FALSE TRUE 1256950.545 1060719.646 1222325.735 1126851.498 1351854.156 1127332.61 998655.3844 1099502.755 1237634.849 1121352.606 1.120923551 0.945928729 1.090045833 1.004903803 1.205556708 1.005332849 0.890581053 0.980514736 1.103698197 1 20.09680857 2.494436013 24.98663712 0.98230457 1.06769219 0.182511425 0.080358297 1176.862804 1698311.266 0.025978691 0.023975074 312.2022388 -2.494436013 0.085387619 HTVIAAQS(ph)LEALSGLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HTVIAAQSLEALSGLQK 17 0 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 HT(0.115)VIAAQS(0.885)LEALSGLQK;HT(0.021)VIAAQS(0.979)LEALSGLQK 183.07 4.59E-10 331000000 334170 296820 319300 297430 385200 440540 362600 354510 364140 271050 TRUE FALSE 347363.2896 347796.5261 327621.2203 356260.7663 319723.8416 338231.2614 334178.4645 349758.3733 351034.6725 324157.0579 1.071589469 1.072925971 1.010686679 1.099037511 0.986323863 1.043417853 1.030915281 1.078978121 1.082915408 1 18.30633346 -0.639931262 7.823109789 0.999999832 1.052405016 0.183174344 0.033541724 0 0 0.031125089 0.007336254 0.229123027 0.639931262 0.052405184 HTWMEDADSCVAHNALECAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTWMEDADSCVAHNALECAR 20 0 O94906;O94906-2 O94906 PRPF6 Pre-mRNA-processing factor 6 0 148.24 6.52E-08 100510000 12675 18235 16694 15445 16068 21333 16283 16704 16498 19802 FALSE TRUE 13175.41879 21366.7194 17129.05935 18499.9749 13336.7671 16378.73405 15006.69591 16480.1102 15904.2402 23681.82277 0.556351549 0.902241336 0.723299871 0.781188808 0.56316472 0.691616275 0.633679935 0.695897033 0.67158007 1 14.53149251 -1.857705862 6.357103689 1.038033189 0.694689786 0.482370005 0.09595923 0.042367228 0.000948326 0.076101332 0.02088926 0.013876954 1.857705862 -0.343343403 HTYLPLEVCNIVAGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTYLPLEVCNIVAGQR 16 0 Q9UKV8-2;Q9UKV8;Q5TA58;A0A6I8PTZ8;Q9UL18;Q9H9G7-2;Q9H9G7;Q9HCK5 Q9UKV8-2 AGO2;AGO1;AGO3;AGO4 Protein argonaute-2;Protein argonaute;Protein argonaute-1;Protein argonaute-3;Protein argonaute-4 0 81.651 0.0067422 0 525020 406600 524160 398740 620120 686880 609300 489560 565790 366560 FALSE TRUE 545748.195 476430.3871 537820.0402 477609.5819 514712.2239 527362.5298 561541.4739 482998.249 545427.3284 438380.4138 1.244919202 1.0867967 1.2268341 1.089486589 1.17412231 1.202979223 1.280945627 1.101778806 1.244187266 1 18.74182382 -1.166143037 4.294974518 0.999953302 1.178117607 0.403525819 0.066656726 2.74E-05 5.33E-06 0.059435254 0.014005355 0.0682114 1.166143037 0.178164305 HVAEDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVAEDLGK 8 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 107.9 0.003915 135550000 102840 157810 139210 182990 135700 216200 138380 137940 140010 178250 FALSE TRUE 106900.2026 184912.6399 142837.927 219184.8758 112633.7625 165990.8265 127533.414 136091.1399 134971.0674 213174.6747 0.501467647 0.867423113 0.670051108 1.028193786 0.528363712 0.778661099 0.59825781 0.638402006 0.633147758 1 17.70167653 -1.109356534 4.999225799 1.000010683 0.697166352 0.268139629 0.151680585 1.69E-05 3.00E-06 0.137050602 0.032301997 0.077739808 1.109356534 -0.30284433 HVAEVLEYTKDEQLESLFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HVAEVLEYTKDEQLESLFQR 20 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ;; 298.34 6.20E-55 1824982000 1417904 1154750 1440590 1423832 1896102 1799716 1878452 1581571 1668756 1166132 FALSE TRUE 1473883.945 1353069.33 1478132.959 1705461.72 1573803.259 1381759.234 1731214.024 1560372.628 1608697.798 1394613.238 1.056840638 0.970211161 1.059887371 1.222892249 1.128487251 0.990783104 1.241357802 1.118856888 1.153508194 1 20.41143365 3.992406104 23.79921938 1.129603053 1.013906695 0.238573631 0.078549813 224.8344781 704646.4025 0.018797175 0.038002795 9826.663939 -3.992406104 -0.115696358 HVAVTNMNEHSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 175.88 1.01E-05 2314947000 157595.4 746127 615266 720524 668360 926953 607823 763462 605835 805916 FALSE TRUE 163817.3881 874268.5082 631300.3374 863041.4967 554752.4059 711682.2139 560180.245 753229.0407 584031.1167 963819.81 0.16996682 0.907087091 0.6549983 0.895438637 0.575576887 0.738397579 0.581208478 0.781504004 0.605954672 1 19.87840393 -5 0.231427349 2.726238041 0.639533916 0.214695509 0.198112607 256.2840785 2.563741471 207.9598093 0.309538118 1.00E-05 5 -2.086704126 HVCQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVCQPGR 7 0 F6WR09;Q9ULJ6-2;Q9ULJ6;E7EWM3;Q8NF64-3;Q8NF64-2;Q8NF64 F6WR09 ZMIZ1;ZMIZ2 Zinc finger MIZ domain-containing protein 1;Zinc finger MIZ domain-containing protein 2 0 84.359 0.021603 11527000 13629 16194 15918 18237 17520 17810 14599 15713 14140 23114 FALSE TRUE 14167.08344 18975.19353 16332.83616 21844.22417 14541.95666 13673.89741 13454.69223 15502.39294 13631.10416 27642.74576 0.512506376 0.686443876 0.590854335 0.790233516 0.526067735 0.494664949 0.486735014 0.56081234 0.493116866 1 14.75461331 -1.063211621 4.992798878 1.000008969 0.573463967 0.656940878 0.092932809 9.55E-06 1.79E-06 0.092595837 0.02182459 0.086454654 1.063211621 -0.426545003 HVDAHATLNDGVVVQVMGLLSNNNQALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVDAHATLNDGVVVQVMGLLSNNNQALR 28 0 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 135.8 5.62E-06 95542000 41522 54038 58018 57490 72901 77033 60235 58007 62613 57267 FALSE TRUE 43161.32062 63318.60614 59529.99674 68861.35041 60509.31406 59143.2532 55513.62331 57229.51105 60359.57036 68487.37221 0.630208449 0.924529648 0.869211284 1.005460542 0.883510523 0.863564352 0.810567284 0.835621359 0.881324081 1 16.06355039 4.74376547 24.78885944 0.886706421 0.630208328 0.626383035 0.061364687 345.6766824 1646275.538 0.015059803 0.128131793 55432.62825 -4.74376547 -0.256498093 HVDNIMFENHTVADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HVDNIMFENHTVADR 15 0 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 191.37 1.03E-07 862460000 703911 867826 868186 864518 841639 1085250 773376 889387 826577 1007822 FALSE TRUE 731701.9498 1016868.365 890811.6404 1035517.08 698577.5034 833217.1346 712756.7683 877466.222 796828.6552 1205285.425 0.607077738 0.843674323 0.739087706 0.85914677 0.579595081 0.691302755 0.591359319 0.728015293 0.661111998 1 20.2009434 -1.028368121 9.22510345 0.999999849 0.703360042 0.487858158 0.092143602 6.29E-10 0 0.086832113 0.020466525 0.093676764 1.028368121 -0.296639806 HVDNPNGDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVDNPNGDGR 10 0 Q9GZT9-2;Q9GZT9;A0A590UK27;G3V3M1;A0A590UJZ0;A0A590UJK7;F8W1G2;A0A590UJT7;A0A590UJ78;Q9H6Z9;Q9GZT9-3 Q9GZT9-2 EGLN1;EGLN3 Egl nine homolog 1;Egl nine homolog 3 0 149.94 2.24E-05 129550000 98525 110870 118280 95116 109960 123260 99527 104680 98520 122950 FALSE TRUE 102414.8431 129911.0601 121362.474 113929.6609 91269.03848 94634.73302 91725.81367 103276.9358 94974.28444 147039.6985 0.696511514 0.883510109 0.825372163 0.77482246 0.620710185 0.643599885 0.623816661 0.702374508 0.645909135 1 17.16584619 3.408325617 6.333119435 0.684146512 0.808489755 0.11306463 0.113736385 0.302493837 21.4353361 0.029054437 0.039588632 2560.504936 -3.408325617 0.124343243 HVDSLSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HVDSLSQR 8 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ;;;; 178.94 0.00024695 2168000000 546581 833160 791240 843200 933350 1091820 854330 923180 797840 942740 FALSE TRUE 568160.4399 976248.7489 811860.3644 1009982.443 774699.5004 838261.3517 787365.3822 910806.2821 769125.8942 1127451.853 0.503933217 0.865889524 0.720084288 0.895809821 0.687124242 0.743500797 0.69835832 0.807844947 0.6821807 1 20.1046344 -1.480603207 3.305937685 1.004905121 0.744270447 0.364647134 0.104581736 211496765.5 229575677.5 9243412.056 0.023506514 0.033067152 1.480603207 -0.260634674 HVDSLSQRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HVDSLSQRSPK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 HVDSLS(0.004)QRS(0.996)PK;HVDSLS(0.001)QRS(0.999)PK;HVDSLS(0.005)QRS(0.995)PK;HVDSLSQRS(1)PK;HVDSLSQRS(1)PK 191.01 1.22E-06 10977970000 3240970 3034630 3606150 1602860 5585090 5406410 2427600 3401100 3627850 3617890 TRUE FALSE 3368925.998 3555804.096 3700129.231 1919900.924 4635738.397 4150853.212 2237318.369 3355513.818 3497284.387 4326746.277 0.778628046 0.821819416 0.855175921 0.443728567 1.07141443 0.959347497 0.517090263 0.775528215 0.808294308 1 22.04485109 0.809669243 3.846254241 0.999973258 0.774358304 0.124937272 0.175149544 3.256262611 63.32381666 0.164814591 0.042222302 6.451626877 -0.809669243 -0.225614954 HVDWVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVDWVK 6 0 P40123;E9PDI2;F8WDB9;Q01518-2;Q01518;Q5T0R1;Q5T0R9;Q5T0R4;Q5T0R3;Q5T0R2 P40123;Q01518-2 CAP2;CAP1 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 1 0 123.34 0.018832 746770000 973440 674910 843370 860100 917580 1080800 1286900 934550 1030100 572680 FALSE TRUE 1011872.163 790820.5424 865348.915 1030225.213 761610.0794 829800.5797 1186029.415 922023.8859 993026.9022 684885.6814 1.477432206 1.154675246 1.26349395 1.504229452 1.112025116 1.211589908 1.731718807 1.346244944 1.449916284 1 19.38550367 HVEAVAYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVEAVAYYK 9 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 ; 78.334 0.030064 234870000 421620 396410 432150 399010 580190 583100 523160 458080 476310 415600 FALSE TRUE 438265.8832 464490.3339 443412.184 477932.9871 481569.511 447683.862 482153.3522 451940.1869 459167.6961 497028.8629 0.881771494 0.934533925 0.892125623 0.961579946 0.968896471 0.90072005 0.970071133 0.909283586 0.923825014 1 18.92297011 HVEAVYIDIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HVEAVYIDIADR 12 0 F5GWE5;Q00169;I3L4H1;I3L2X8;I3L4C0;I3L459;I3NI10 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ;;; 139.89 5.92E-05 684850000 463160 587760 624080 757720 1015040 1072600 867860 649200 645190 1040730 FALSE TRUE 481445.9144 688703.2079 640344.0375 907594.7544 842503.8634 823504.9054 799834.8655 640498.5359 621969.7379 1244641.118 0.386815049 0.553334771 0.514480864 0.72920197 0.676905054 0.661640447 0.642622885 0.514604995 0.499718135 1 20.24729838 -2.317513895 2.379479386 3.385373268 0.581221734 0.629230908 0.097671561 4688664.254 565551.4584 60585190.07 0.02482649 0.004813779 2.317513895 -2.804151534 HVEEFSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 154.49 0.00056166 153310000 273512 367780 366450 363570 354400 459350 334781 368090 310701 427720 FALSE TRUE 284310.465 430943.3541 375999.988 435483.0609 294159.2146 352672.924 308539.9904 363156.3556 299518.9317 511523.5448 0.555811102 0.842470221 0.735059005 0.851345095 0.575064858 0.689455896 0.603178473 0.70995042 0.585542806 1 18.96444112 -1.265248114 5.196906765 1.000047188 0.689352013 0.470561415 0.100646579 5.27E-05 7.45E-06 0.093318106 0.021991955 0.054294006 1.265248114 -0.310695175 HVENDGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVENDGYK 8 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 107.15 0.0040577 640200000 663240 492030 559780 499200 744640 781840 653920 576600 646870 470060 FALSE TRUE 689425.2273 576532.325 574368.3267 597940.27 618066.3588 600269.5089 602664.0417 568871.6201 623589.2751 562159.2572 1.226387751 1.025567609 1.021718169 1.063649246 1.099450647 1.067792625 1.072052153 1.011940323 1.109275116 1 19.10061937 4.744141169 24.92441656 1.053084628 1.226387829 0.689894676 0.034995366 331.3868936 1480027.846 0.008192898 0.072876137 55480.60247 -4.744141169 0.173303201 HVEPGNAAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVEPGNAAIR 10 0 H3BPK3;Q16775-2;Q16775;H3BPQ4 H3BPK3 HAGH "Hydroxyacylglutathione hydrolase, mitochondrial" 0 101.66 0.0031773 193660000 122760 346140 299750 372990 303010 423390 272880 318980 242270 428320 FALSE TRUE 127606.6596 405586.8524 307561.7312 446766.3087 251504.4684 325064.089 251490.9526 314704.5948 233550.75 512241.1033 0.249114448 0.791788964 0.600423764 0.872179733 0.490988456 0.634591966 0.49096207 0.614368103 0.455939105 1 18.9664635 -1.369983829 3.089210874 1.004625812 0.590650168 0.3646064 0.166423723 22690775.3 28496993.84 939057.9374 0.038224924 0.04265954 1.369983829 -0.413975644 HVFAIFNTEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVFAIFNTEQR 11 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 193.3 1.01E-06 508110000 351860 343810 384000 376400 491680 469590 391430 401660 411000 395580 FALSE TRUE 365751.7045 402856.693 394007.3555 450850.7966 408104.4092 360534.8392 360748.6938 396276.4047 396208.1903 473086.3272 0.773118316 0.851550066 0.832844521 0.952999 0.862642579 0.762091015 0.762543056 0.83764079 0.8374966 1 18.85174394 0.550916156 2.920287049 0.99999856 0.830518577 0.471265675 0.053969665 9.472752832 60.32255527 0.055101622 0.014438929 3.555626673 -0.550916156 -0.169479982 HVFEDPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVFEDPQR 8 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ; 95.099 0.0098907 214790000 213764 318030 272520 330880 256360 340180 317590 312520 245470 302230 FALSE TRUE 222203.5678 372649.1786 279622.0951 396327.0764 212784.0188 261178.3505 292696.4659 308331.1806 236635.5826 361446.182 0.614762526 1.030994923 0.773620276 1.096503702 0.588701802 0.722592639 0.809792662 0.853048658 0.654691056 1 18.46342133 4.819943862 20.90334655 0.8270166 0.614726928 0.150519664 0.15664406 65511.31047 16817127.68 0.035451113 370.2495467 66060.80506 -4.819943862 -0.212289672 HVFGESDELIGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HVFGESDELIGQK 13 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3;U3KPS5 P60174 TPI1 Triosephosphate isomerase 0 ;;; 168.02 3.09E-05 4333840000 6260120 6940610 7222320 5757240 9068400 8914100 6953500 7399500 7667550 7479920 FALSE TRUE 6507274.371 8132605.777 7410539.592 6896004.888 7526956.607 6843935.369 6408466.5 7300321.806 7391596.373 8945467.112 0.727438186 0.909131482 0.828412815 0.770893772 0.841426894 0.765073001 0.716392606 0.816091738 0.826295182 1 23.09272539 0.677767366 2.246975949 0.999936306 0.798233634 0.559857717 0.05375834 1.34023118 8.366200997 0.050983002 0.013818747 4.761758509 -0.677767366 -0.201702672 HVGDLGNVTADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVGDLGNVTADK 12 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 89.43 0.0094274 187910000 769000 528330 654340 588290 814530 824250 852790 696660 684480 403010 FALSE TRUE 799360.7138 619066.5677 671392.6379 704652.0061 676076.4815 632830.4291 785946.0914 687322.4122 659845.6985 481972.0934 1.658520742 1.284444838 1.393011436 1.46201827 1.402729516 1.313002221 1.630687963 1.426062674 1.369053743 1 18.87859009 0.756182324 2.753987986 1.000107799 1.441516152 0.580109391 0.113378818 0.931559768 9.543972804 0.102602736 0.027105221 5.704036874 -0.756182324 0.441408354 HVGDLGNVTADKDGVADVS(ph)IEDSVISLSGDHCIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 1 HVGDLGNVT(0.004)ADKDGVADVS(0.831)IEDS(0.12)VIS(0.035)LS(0.011)GDHCIIGR;HVGDLGNVTADKDGVADVS(0.997)IEDS(0.002)VIS(0.001)LSGDHCIIGR;HVGDLGNVT(0.002)ADKDGVADVS(0.713)IEDS(0.28)VIS(0.006)LSGDHCIIGR 119.06 1.31E-06 253324000 158331 130667 157771 107140 180151 185630 162984 164061 172007 117390 TRUE FALSE 164582.0301 153108.0408 161882.6419 128331.9722 149528.9974 142520.2457 150208.8882 161862.0306 165816.5017 140390.3229 1.172317484 1.09058828 1.153089746 0.914108391 1.06509476 1.015171436 1.069937622 1.152942933 1.181110622 1 17.09908397 -0.476968717 7.942620122 1 1.088011117 0.107638656 0.077866989 0 0 0.077206314 0.018197703 0.333450431 0.476968717 0.088011117 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGR 36 1 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;; 387.23 2.45E-179 2938729000 676053.9 753580.6 1014485.8 866759.2 1234507.4 1164150.1 1049807.3 1197015.3 1114492 934381.7 FALSE TRUE 702745.03 883002.206 1040924.133 1038201.583 1024666.273 893793.8821 967520.6607 1180971.268 1074381.651 1117455.904 0.628879428 0.790189754 0.931512491 0.929076108 0.916963496 0.799847116 0.865824465 1.056839257 0.961453286 1 20.09178647 4.572846957 1.934249272 0.934111725 0.587990132 0.678342837 0.066101007 0.350146924 1.799777419 0.019224441 0.192100225 37397.87766 -4.572846957 -0.346121593 HVGMAVAGLLADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVGMAVAGLLADAR 14 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 184.31 1.31E-06 2016370000 1362110 1579570 1582610 1516010 1970250 2169580 1615820 1712920 1647510 1636030 FALSE TRUE 1415887.155 1850848.86 1623854.117 1815872.253 1635347.609 1665727.925 1489167.806 1689961.109 1588216.437 1956578.755 0.723654569 0.945961851 0.829945696 0.928085439 0.835819976 0.851347241 0.761108032 0.86373273 0.811731413 1 20.89990175 -1.739665121 6.668729409 1.002883542 0.842953192 0.364074794 0.063628768 0.002538609 9.91E-05 0.057333803 0.013295991 0.018211045 1.739665121 -0.15993035 HVGNQQYNVTYVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVGNQQYNVTYVVK 14 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 ; 161.63 4.57E-06 1117660000 1399980 1169710 1367990 1205140 1738800 1876750 1475020 1508840 1635270 1235980 FALSE TRUE 1455252.291 1370598.593 1403640.943 1443513.095 1443239.397 1440903.255 1359404.078 1488616.468 1576416.952 1478146.617 0.984511465 0.927241302 0.949595207 0.97656963 0.976384467 0.974804014 0.919667956 1.007083094 1.06648213 1 20.49535795 1.538698848 5.534479307 1.034442128 0.958944383 0.599830956 0.025304785 0.087559935 5.686637883 0.013827403 0.006217193 34.56995771 -1.538698848 -0.075497745 HVGSSETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVGSSETK 8 0 A0A0A0MQS1;Q53H96-2;Q53H96;A0A087WTU2;B5MD87 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 ; 102.51 0.0084165 0 66364 121326 123781 122451 130371 166635 132988 145549 126196 133323 FALSE TRUE 68984.10196 142162.7967 127006.8345 146671.4423 108210.584 127936.5466 122564.0531 143598.1537 121654.2306 159445.0892 0.432651155 0.891609754 0.796555323 0.919886859 0.678669908 0.802386246 0.768691301 0.900611956 0.76298512 1 17.28270014 7.914842724 0.077047615 1.118774443 2.40E-26 0.305089606 0.124961562 288.5378229 1.651699372 3.828333982 34.55917153 82194493.61 -7.914842724 -1.118774443 HVHQYHEDKDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVHQYHEDKDSGK 13 1 Q96DZ1;Q96DZ1-3;Q96DZ1-2 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 0 103.76 0.0010226 20105000 28272 15226 15933 15289 25746 31542 25938 19032 17334 12348 FALSE TRUE 29388.20039 17840.94706 16348.22707 18313.11857 21369.70412 24216.84852 23904.91178 18776.90717 16710.15273 14767.35418 1.990078929 1.208134297 1.10705187 1.240108305 1.447090918 1.639890817 1.618767417 1.271514649 1.131560367 1 13.85012375 1.302844987 2.522759318 1.028922253 1.437516994 0.299690723 0.242630786 0.382151596 4.025277613 0.222618523 0.06581167 20.08375834 -1.302844987 0.408594741 HVIADQEVMETNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVIADQEVMETNR 13 0 Q9H307 Q9H307 PNN Pinin 0 180.84 1.26E-05 141030000 100030 109240 89009 116570 115080 143290 112620 111430 99805 88866 FALSE TRUE 103979.2616 128001.1202 91328.64766 139627.1981 95518.74271 110013.0691 103792.5501 109936.4631 96213.03755 106277.5913 0.978374278 1.204403663 0.859340587 1.313797165 0.898766537 1.035148311 0.97661745 1.034427501 0.905299381 1 16.69747791 HVIDFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVIDFFK 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 ; 91.041 0.016695 392100000 816300 701540 775380 688580 974690 1018350 947210 868950 832640 690310 FALSE TRUE 848528.1543 822024.0378 795587.0398 824779.0688 809012.542 781853.6457 872965.2051 857303.1466 802673.449 825563.0277 1.027817533 0.995713241 0.963690249 0.999050395 0.979952487 0.947055064 1.057417999 1.038446633 0.972273978 1 19.65501884 2.234517481 24.99999043 1.023517236 0.985374696 0.204266191 0.0293503 137.7694815 851865.7941 0.010903833 0.008346289 171.6000779 -2.234517481 -0.038142541 HVINFDLPSDIEEYVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 326.37 1.19E-60 3824050000 1116944 1169000 1175324 1198499 1294290 1501170 1300570 1209894 1192806 1092868 FALSE TRUE 1161041.812 1369766.656 1205953.909 1435558.525 1074287.048 1152546.018 1198627.925 1193677.35 1149877.145 1306994.56 0.88832949 1.048027817 0.92269237 1.098366105 0.821952195 0.881829239 0.917087157 0.913299402 0.879787246 1 20.31782171 3.225431215 24.9999984 0.899207937 0.988783424 0.276944114 0.068776618 275.8091009 525173.3389 0.018392059 0.022104513 1680.471746 -3.225431215 0.089575487 HVLDTLIQLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVLDTLIQLAK 11 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 79.693 0.026447 105580000 137350 113890 136240 130070 165270 170120 140590 129960 141300 122000 FALSE TRUE 142772.6841 133449.7216 139790.5263 155797.4578 137177.4644 130612.2082 129570.1884 128218.0988 136214.6406 145903.5642 0.978541442 0.914643328 0.958102203 1.067811185 0.94019269 0.89519546 0.888053621 0.878786612 0.933593647 1 17.1546556 3.002273349 24.98218051 0.90756615 0.977377741 0.245682521 0.048031445 86.99753307 956005.8976 0.01401905 0.01665658 1005.248304 -3.002273349 0.069811591 HVLEGHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVLEGHDR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 110.87 0.0033424 59055000 40369 54272 51867 52031 62042 70175 58858 51303 43118 56238 FALSE TRUE 41962.79929 63592.79382 53218.69663 62322.5765 51496.123 53877.91976 54244.55616 50615.3672 41566.1916 67256.75936 0.623919435 0.945522717 0.791276552 0.926636625 0.765664648 0.801078141 0.806529436 0.752569224 0.618022515 1 16.03739165 2.593721292 1.620027927 0.772367677 0.825091523 0 0.120957491 1.55714812 8.227198456 0.048997478 0.042110426 392.3930366 -2.593721292 0.052723846 HVLEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HVLEISR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;; 122.13 0.0043709 733814000 659790 851940 775855 720998 1531097 1215947 864973 776081 711423 1546761 FALSE TRUE 685839.0187 998254.0678 796074.4187 863609.2524 1270841.679 933561.7371 797174.1561 765678.9036 685819.0252 1849819.203 0.370760027 0.539649532 0.430352554 0.466861438 0.687008588 0.504677287 0.430947065 0.41392094 0.370749219 1 20.81895284 -1.097754019 4.758741058 1.000026911 0.470959786 0.762702393 0.088957617 2.62E-05 4.96E-06 0.088788376 0.020926558 0.079844679 1.097754019 -0.529067125 HVLTGSADNSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HVLTGSADNSCR 12 0 Q13347;Q5TFK1 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;;;; 238.2 3.96E-16 2141600000 1018069 1323890 1217833 1300890 1316958 1617605 1309102 1333279 1212731 1368441 FALSE TRUE 1058263.15 1551257.809 1249570.728 1558202.159 1093101.95 1241940.754 1206491.165 1315408.576 1169085.048 1636560.814 0.646638451 0.947876667 0.763534553 0.952119925 0.667926264 0.758872352 0.737211324 0.803763945 0.714354785 1 20.64223578 -1.296294791 3.429822875 1.000827523 0.782845872 0.317024169 0.097880851 20181636.9 30270283.22 174031.9326 0.022554098 0.050548143 1.296294791 -0.21798165 HVLVILTDMSSYAEALR ddPTM_MDA-MB-175_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 ;; 203.04 1.00E-11 418954000 154888 164789 175079 154284 184623 201776 219737 178120 183581 129762 FALSE TRUE 161003.0978 193090.2289 179641.7026 184800.9147 153240.8484 154916.5819 202513.4398 175732.5927 176973.9557 155186.3795 1.037482145 1.244247269 1.157586788 1.190832052 0.987463262 0.998261461 1.304969163 1.132397014 1.140396189 1 17.24364241 HVLVTLGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVLVTLGEK 9 0 F8VPF3;H0YI43;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;G3V1Y7;P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ; 118.18 0.0010317 6780900000 35237300 20801400 31852700 19885400 44848000 35305300 36811700 32150500 35302000 21230800 FALSE TRUE 36628495.81 24373878.64 32682807.53 23818672.77 37224752.98 27106179.13 33926302.76 31719575.14 34031487.92 25390568.77 1.442602414 0.959957961 1.287202655 0.938091343 1.466085826 1.067568804 1.336177345 1.249266033 1.340320031 1 24.59778938 3.238097843 24.99999977 1.253329694 1.152194601 0.047548071 0.185406277 35.53733075 1919884.721 0.047631747 0.060301228 1730.206118 -3.238097843 -0.101135094 HVNIDHLHVGWYQSTYYGSFVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVNIDHLHVGWYQSTYYGSFVTR 23 0 A0A087WZK9;B3KS98;O15372;E5RJT0;E5RGU4;E5RFH0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 146.39 4.48E-08 53102000 18377 16659 16126 13335 15229 29895 16299 13902 12165 17174 FALSE TRUE 19102.53815 19520.05366 16546.25681 15972.6232 12640.38002 22952.33931 15021.44179 13715.66643 11727.18403 20538.91648 0.930065525 0.950393546 0.805605146 0.777676038 0.615435582 1.117504876 0.731364861 0.667789191 0.570973841 1 14.32607245 2.02853579 24.99992188 0.706900457 0.85783426 0.110748274 0.159698724 365.4302896 320148.3213 0.058251837 0.043021083 106.7912796 -2.02853579 0.150933803 HVPVVYVDYPGPASLTQIYGTFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVPVVYVDYPGPASLTQIYGTFNR 24 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 258.91 5.94E-44 604650000 284480 333110 310020 325020 389860 416120 319930 317560 329320 314340 FALSE TRUE 295711.4901 390319.0513 318099.3759 389307.9859 323591.7365 319482.4364 294853.0506 313303.6276 317467.8375 375928.9046 0.786615465 1.038278905 0.846168975 1.035589392 0.860779079 0.849848023 0.78433195 0.833411913 0.844489034 1 18.52010032 3.026393439 24.99876058 0.845344839 0.93129844 0.097398609 0.08849057 355.758665 336957.224 0.023382891 0.027947249 1062.657812 -3.026393439 0.085953601 HVQELRPIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HVQELRPIAR 10 1 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 152.27 1.10E-05 875180000 212714 184673 208478 225912 217600 232878 230528 211084 182206 148922 FALSE TRUE 221112.113 216389.1512 213911.1079 270596.7193 180612.4297 178795.6138 212458.613 208254.7642 175648.4417 178100.4146 1.241502517 1.214983983 1.201070241 1.519349182 1.014104488 1.003903411 1.192914758 1.169310946 0.986232638 1 17.44233135 3.195224889 24.99999067 1.082543188 1.281913806 0.52347116 0.107560206 127.8554171 73758.24813 0.03205697 0.038315625 1567.562584 -3.195224889 0.199370618 HVQGWPADHAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVQGWPADHAEK 12 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 0 144.27 3.64E-05 83484000 142600 130810 158740 121770 186320 217280 183030 146120 182890 117950 FALSE TRUE 148229.9581 153275.5999 162876.8948 145855.7426 154649.393 166820.0129 168683.6303 144161.5004 176307.8246 141060.0442 1.050828808 1.08659827 1.154663574 1.033997567 1.096337335 1.182617047 1.195828566 1.02198678 1.249877849 1 17.10594987 2.981405502 23.39055549 1.128929749 1.084366336 0.083301131 0.076586135 942.3163545 1185369.396 0.022423255 0.024217952 958.0882237 -2.981405502 -0.044563413 HVSDDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 HVSDDMK 7 0 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ;;;;;;;;; 186.43 0.00051777 4603520000 1413838 4119420 4459900 3879161 5344310 5686780 4761260 5142040 4573310 3785103 FALSE TRUE 1469657.416 4826898.34 4576128.658 4646447.468 4435886.095 4366111.529 4388060 5073119.364 4408717.466 4526721.463 0.324662657 1.066312204 1.010914565 1.026448724 0.97993352 0.96451959 0.969368236 1.120704997 0.973931686 1 22.11003511 4.741046101 24.99679219 1.016883297 0.324662413 0.951178234 0.046737687 45.78675393 460455.4514 0.011738193 0.079836076 55086.61684 -4.741046101 -0.692220884 HVTLPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.5)S(0.5)PR;HVTLPS(0.527)S(0.473)PR;HVTLPS(0.698)S(0.302)PR;HVTLPS(0.695)S(0.305)PR;HVTLPS(0.666)S(0.334)PR 134.13 0.00016589 3904150000 1819850 2473980 2533790 2860830 2680400 3228190 2639270 2428950 2317440 2281270 TRUE FALSE 1891699.083 2898866.82 2599822.649 3426693.635 2224786.565 2478491.796 2432397.121 2396393.898 2234035.787 2728241.179 0.69337678 1.062540527 0.95292992 1.256008326 0.815465503 0.908457733 0.891562351 0.878365856 0.81885568 1 21.37953975 HVTLPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 HVTLPS(0.028)S(0.972)PR;HVTLPS(0.006)S(0.994)PR 147.19 9.76E-05 1303540000 1242580 1532400 1823890 1703410 1904340 2073040 1728050 1679610 1676730 1527640 TRUE FALSE 1291638.018 1795577.78 1871422.072 2040339.414 1580640.967 1591607.877 1592600.926 1657097.575 1616384.815 1826951.81 0.706990743 0.982827117 1.024341234 1.116799799 0.865179343 0.871182189 0.871725744 0.907028618 0.884744089 1 20.80100715 HVTSEQEWDKYCHYVAGLVGIGLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVTSEQEWDKYCHYVAGLVGIGLSR 25 1 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2 E9PNM1 FDFT1 Squalene synthase 0 102.67 0.0031388 602790000 511060 700890 736420 801830 865670 1057200 845590 697260 723800 553900 FALSE TRUE 531237.0434 821262.4053 755611.7102 960429.5808 718523.7226 811681.322 779310.4463 687914.3702 697750.5794 662426.0999 0.801956691 1.239779661 1.140673217 1.449866756 1.084685103 1.225316035 1.176448884 1.038477153 1.053325917 1 19.33739999 1.711454005 4.831300878 1.032596 1.173206438 0.127007744 0.152312864 0.321162046 17.81799856 0.078351862 0.038840593 51.45813059 -1.711454005 0.140610437 HVTSNAS(ph)DSESSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVTSNASDSESSYR 14 0 Q12959;Q12959-3;Q12959-5;A0A590UK48;C9JUA9;Q12959-8;A0A590UJ64 Q12959 DLG1 Disks large homolog 1 1 HVTSNAS(1)DSESSYR 354.71 4.82E-82 192360000 98555 160420 158410 178100 149430 199880 162620 159770 142480 137150 TRUE FALSE 102446.0275 187970.8871 162538.2947 213327.6484 124029.942 153460.8992 149873.4195 157628.5445 137352.1726 164021.9166 0.624587431 1.146010795 0.990954734 1.300604534 0.75617908 0.935612157 0.913740204 0.961021233 0.837401339 1 17.32352908 HVVFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 39792990000 59855810 58104380 60882930 51395500 80671910 76640210 62384010 63802420 60284540 61156640 FALSE TRUE 62218963.6 68083355.28 62469589.17 61561376.5 66959327.55 58841682.72 57494188.29 62947252.92 58114911.18 73139112.69 0.850693443 0.930874778 0.85412014 0.841702534 0.915506425 0.804517317 0.786093598 0.860651033 0.794580479 1 26.12413979 2.734444434 24.94513771 0.837127517 0.878077189 0.035177586 0.062764957 841.9632643 5102503.232 0.018572487 0.018100068 542.555829 -2.734444434 0.040949672 HVVFIAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HVVFIAQR 8 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 132.29 0.00096878 1111740000 724150 815170 546200 555090 2228700 1352300 844940 640080 615310 2387800 FALSE TRUE 752740.0012 955169.1064 560434.4207 664885.1452 1849866.37 1038248.819 778711.395 631500.7746 593165.1133 2855643.693 0.263597312 0.334484694 0.196255024 0.23283197 0.647793131 0.363577859 0.272692072 0.221141306 0.20771678 1 21.44538455 -1.13893843 4.608674802 1.000068598 0.304364014 0.733624847 0.125735128 19.09391308 162108631.1 24048.17696 0.030885454 0.07262089 1.13893843 -0.695704585 HVVRPPPRS(ph)PEPDTLPLAAGSDHPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HVVRPPPRSPEPDTLPLAAGSDHPLPR 27 2 H3BVB1;H3BME1;H7C112;H3BPZ0;Q6PCT2-2;Q6PCT2-3;Q6PCT2 H3BVB1 FBXL19 F-box/LRR-repeat protein 19 1 HVVRPPPRS(1)PEPDTLPLAAGSDHPLPR 193.4 1.18E-18 482180000 49630 72042 67243 68632 83647 102080 76007 86294 74725 73113 TRUE FALSE 51589.43072 84414.65309 68995.40782 82207.20475 69428.71282 78373.46704 70049.37273 85137.37008 72035.66185 87438.09252 0.590010935 0.965421942 0.78907723 0.940176099 0.794032793 0.896330933 0.801131071 0.973687413 0.823847591 1 16.41597431 4.748813158 24.67517353 0.882548453 0.590010739 0.572679961 0.076893807 807.6166565 1943674.684 0.016437371 0.226600378 56080.66537 -4.748813158 -0.292537713 HWDQDDDFEFTGSHLTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HWDQDDDFEFTGSHLTVR 18 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 306.27 1.82E-50 498400000 69582 115020 117490 125890 121730 148900 121860 127940 118180 131850 FALSE TRUE 72329.15109 134773.7903 120551.8859 150790.6663 101038.3781 114320.2316 112308.2948 126225.1736 113926.7249 157683.4831 0.458698335 0.854710891 0.764518157 0.956287008 0.640767036 0.724998138 0.7122388 0.800497117 0.72250259 1 17.26667202 -4.999999792 0.402270237 5.134742353 0.742675849 0.284261996 0.124495249 995.2134507 6.897048874 3617.066021 0.072497922 1.00E-05 4.999999792 -4.392066505 HWELTAEGEEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HWELTAEGEEIAR 13 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 184.98 9.05E-06 203756000 802820 855510 1037440 1008180 1082660 1284140 1140670 1130390 1039870 985790 FALSE TRUE 834515.9535 1002437.188 1064476.539 1207594.995 898629.8399 985917.9463 1051261.305 1115238.971 1002445.282 1178936.676 0.707854773 0.850289254 0.902912396 1.024308616 0.762237581 0.836277271 0.891702944 0.945970206 0.85029612 1 20.1690548 7.999999999 0.05441269 1.172435147 0.30903235 0.266550641 0.080036437 638.9168812 2.611292667 9.122115502 44.99687248 99999999.88 -7.999999999 -0.863402797 HWGGNVLGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HWGGNVLGPK 10 0 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 71.016 0.052248 2211380000 3533800 2869300 3119800 2126280 9050100 5107900 4045700 3009300 3388600 6557400 FALSE TRUE 3673317.153 3362079.955 3201104.551 2546851.838 7511767.235 3921667.636 3728587.463 2968965.256 3266644.948 7842196.981 0.468404092 0.428716591 0.408189766 0.324762543 0.957865156 0.500072575 0.475451901 0.378588457 0.416547169 1 22.90282645 -1.964735948 2.47124311 1.423670426 0.482084731 0.465323483 0.165827405 40045492.55 18225508.54 97178367.52 0.04225251 0.010845861 1.964735948 -0.941585695 HWILPQDYDHAQAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HWILPQDYDHAQAEAR 16 0 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 102.38 0.0008799 215750000 39490 41598 33101 42125 43910 56181 41392 36639 32105 36373 FALSE TRUE 41049.09569 48742.13291 33963.63925 50457.19927 36446.19388 43133.81418 38147.58688 36147.91413 30949.54732 43499.59295 0.943666203 1.120519288 0.780780622 1.15994647 0.837851378 0.991591214 0.876964227 0.830994308 0.711490504 1 15.40871428 2.085522203 2.775983241 0.830380874 0.973817352 0.171680484 0.125107301 0.408598849 6.210565712 0.053915857 0.033844278 121.7649243 -2.085522203 0.143436478 HWKPYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HWKPYYK 7 1 O94992 O94992 HEXIM1 Protein HEXIM1 0 92.925 0.0092002 358710000 671360 497060 692310 538290 850340 825580 763770 689020 727150 542590 FALSE TRUE 697865.8112 582426.1884 710352.1673 644762.1554 705799.5105 633851.5568 703903.7117 679784.8139 700980.0135 648900.122 1.075459516 0.897559068 1.094701855 0.993623107 1.087685896 0.976809119 1.084764339 1.047595448 1.080258717 1 19.30763691 4.209743997 24.99998147 1.046685606 0.986508852 0.147745389 0.05680385 299.2424137 259609.2113 0.012639724 0.027311768 16208.54374 -4.209743997 -0.060176755 HWMLDK ddPTM_MDA-MB-175_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 ;;;; 118.06 0.022193 6297141000 7196680 5610064 6951410 5715865 9136930 8570850 8458180 7016310 7288300 5339983 FALSE TRUE 7480810.483 6573548.852 7132569.455 6846446.037 7583837.902 6580399.98 7795205.75 6922267.841 7025995.507 6386250.429 1.171393225 1.029328387 1.116863414 1.072060376 1.187525918 1.03040118 1.220623249 1.08393304 1.100175382 1 22.6065377 0.64492005 1.949824609 1.000101429 1.113256809 0.239659778 0.06069738 2.43189885 11.59405101 0.052434013 0.014515866 4.414891649 -0.64492005 0.113155381 HWPFMVVNDAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HWPFMVVNDAGR 12 0 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 158.42 6.88E-05 1279340000 500950 533900 525370 650520 651220 818350 733340 628510 580470 497370 FALSE TRUE 520727.8928 625593.1718 539061.5738 779190.9144 540525.857 628300.6147 675858.8946 620085.8515 559578.9981 594820.1288 0.875437578 1.05173504 0.906259805 1.309960569 0.908721529 1.05628674 1.136240793 1.04247624 0.940753298 1 19.18209394 5.552914975 1.275818028 1.050496465 2.31E-14 0.149924909 0.114133341 17.1272661 5.115337126 0.029503136 38.85514339 357202.8991 -5.552914975 -1.050496465 HWPFMVVNDAGRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;; 167.98 3.25E-06 15027400000 5021400 3976970 4990100 3996290 6257750 6359760 5653090 4980510 5206540 3657540 FALSE TRUE 5219648.749 4659983.661 5120146.105 4786744.234 5194059.89 4882802.123 5209986.034 4913754.41 5019157.642 4374164.935 1.193290337 1.065342467 1.170542534 1.094321843 1.187440338 1.116282124 1.191081295 1.123358283 1.14745505 1 22.06057619 -1.24154649 3.104836521 0.999375716 1.141563606 0.518569857 0.041374934 5791424.937 8145422.125 34772.81262 0.009051571 0.057339448 1.24154649 0.142187889 HWVAPGGPYSAETPGVPS(ph)PIAALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HWVAPGGPYSAETPGVPSPIAALK 24 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 HWVAPGGPYSAETPGVPS(1)PIAALK;HWVAPGGPYSAETPGVPS(1)PIAALK 125 6.57E-05 1266890000 989400 746980 786190 674060 1055760 1112120 928790 874470 908890 711880 TRUE FALSE 1028462.276 875268.0043 806678.7573 807387.0561 876302.2923 853846.9843 855989.0129 862749.16 876179.2264 851359.2562 1.208023838 1.028083031 0.947518631 0.948350594 1.029297897 1.002922066 1.005438076 1.013378493 1.029153345 1 19.69940852 4.722638312 3.846606439 0.997832081 1.225530428 0.842906328 0.027145945 0.088674755 2.604797211 0.007015302 0.055539114 52800.53369 -4.722638312 0.227698347 HY(ph)MAYAASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYMAYAASR 9 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 HY(0.5)MAY(0.5)AASR 70.912 0.040979 0 41843 67788 67592 55189 74502 78364 89316 78911 73554 61366 TRUE FALSE 43494.99395 79430.06168 69353.50305 66105.21948 61838.17665 60165.14862 82315.17854 77853.32712 70906.80591 73389.49278 0.592659689 1.082308362 0.945005891 0.900745011 0.842602589 0.819806029 1.121620758 1.060823889 0.966171086 1 16.16328591 2.241902234 24.99999169 1.04705124 0.878183838 0.323483717 0.121385672 103.4654224 774072.2326 0.041914214 0.033728078 174.5429188 -2.241902234 -0.168867401 HYASEEIKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYASEEIKEK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 199.08 1.71E-07 339100000 497600 331750 461700 332640 709310 707970 721470 530820 640770 332570 FALSE TRUE 517245.6322 388725.4818 473732.2813 398435.1992 588741.7396 543554.6969 664919.2962 523705.2261 617708.8129 397730.7241 1.300492019 0.977358445 1.191087971 1.001771236 1.4802521 1.36663995 1.67178258 1.316733142 1.553082967 1 18.60143249 3.232351476 24.99836548 1.424164523 1.112898235 0.346599656 0.186513275 137.7203439 554469.9449 0.048851378 0.059778318 1707.463688 -3.232351476 -0.311266288 HYCDSEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYCDSEKPR 9 1 Q9UGI8-2;Q9UGI8;H7BYK1 Q9UGI8-2 TES Testin 0 ;;; 193.38 2.02E-05 1095080000 1240320 1135200 1242700 1220280 1537660 1719330 1589160 1326590 1402450 1040170 FALSE TRUE 1289288.791 1330161.769 1275085.783 1461647.742 1276289.102 1320041.664 1464597.487 1308809.231 1351976.098 1243971.396 1.036429612 1.069286459 1.02501214 1.174985009 1.025979461 1.061151139 1.177356241 1.052121644 1.086822497 1 20.24652188 HYCESLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYCESLRPR 9 1 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ; 172.59 3.37E-05 891980000 32727 43217 37450 55102 41392 46539 45629 48485 48240 51260 FALSE TRUE 34019.08723 50639.18357 38425.97777 66001.01114 34356.20262 35731.02256 42052.47975 47835.13788 46503.85182 61303.41557 0.55492972 0.826041797 0.626816262 1.076628611 0.560428849 0.582855331 0.685972867 0.780301349 0.758585005 1 15.90367984 0.595688382 1.213158408 0.999416982 0.712999207 0.253277512 0.14890563 2.00254309 4.297515932 0.137286259 0.041723238 3.941743703 -0.595688382 -0.286417775 HYEDGYPGGSDNYGS(ph)LSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 HYEDGYPGGSDNYGS(0.984)LS(0.016)R;HYEDGYPGGSDNYGS(0.993)LS(0.007)R;HYEDGYPGGSDNYGS(0.992)LS(0.008)R;HYEDGYPGGSDNYGS(0.942)LS(0.058)R 258.82 1.18E-30 4909040000 2228690 2701130 2440010 2642800 3362280 3285890 2201530 2668010 2198740 2977830 TRUE FALSE 2316680.402 3165028.066 2503598.665 3165537.952 2790760.847 2522791.846 2028968.326 2632249.69 2119607.777 3561278.775 0.650519251 0.888733589 0.703005528 0.888876764 0.783640098 0.708394935 0.569730272 0.73913048 0.59518165 1 21.76396394 2.727466471 5.422059613 0.696125774 0.790621984 0.031782791 0.129239468 0.383014734 39.61242234 0.038020225 0.037466384 533.9080521 -2.727466471 0.09449621 HYEDGYPGGSDNYGSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYEDGYPGGSDNYGSLSR 18 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;;; 274.6 4.83E-39 2304340000 1003450 1424550 1188870 1288450 1339790 1666310 1344820 1390430 1221340 1389860 FALSE TRUE 1043066.981 1669205.381 1219852.929 1543301.564 1112052.974 1279334.756 1239409.494 1371793.56 1177384.212 1662176.457 0.627530836 1.004228747 0.733888947 0.928482387 0.669034247 0.769674453 0.745654584 0.825299597 0.708338881 1 20.66464212 -1.162523222 3.843059567 1.000121625 0.786762158 0.267154438 0.109088753 11149261.95 6757484.727 11040.64546 0.022998576 0.068782313 1.162523222 -0.213359467 HYELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 150.82 0.010463 2326520000 299521.2 343434 373209 349219 441859 475876 411904 369540 328894 421276 FALSE TRUE 311346.5283 402416.118 382935.1331 418293.4759 366751.965 365361.011 379617.8882 364586.9207 317057.1692 503816.9664 0.617975473 0.798734749 0.760067959 0.830248888 0.727946833 0.725186001 0.753483732 0.723649549 0.629310226 1 18.94254018 -1.521279082 2.981058492 1.009874606 0.735592892 0.624872407 0.062693728 20091151.88 21949117.72 1602720.497 0.014568991 0.030110705 1.521279082 -0.274281714 HYEMLANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYEMLANR 8 0 A0A2R8YFH5;Q15437 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 125.58 0.0012557 573260000 318051 371350 331061 351711 618630 523970 404803 371465 359013 580950 FALSE TRUE 330607.8991 435126.4738 339688.7216 421278.386 513475.4936 402285.9083 373073.4831 366486.1193 346092.1923 694776.0295 0.475848165 0.626283083 0.488918309 0.606351354 0.739051826 0.579015238 0.536969422 0.527488145 0.498134906 1 19.40618845 -1.279546363 3.6880243 1.000949612 0.566610435 0.751814905 0.075101249 17698124.06 31249724.19 191894.0368 0.018445252 0.052535593 1.279546363 -0.434339177 HYFQNTQGLIFVVDSNDR ddPTM_MDA-MB-175_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 ;;; 299.23 1.83E-49 8422546000 1959943.2 2840865 2790870 3422550 2841428 3616259 3247972 3015310 2810438 2102868 FALSE TRUE 2037323.271 3328761.465 2863602.365 4099520.175 2358443.083 2776437.652 2993387.468 2974894.702 2709290.885 2514884.723 0.810106027 1.323623876 1.138661482 1.63010262 0.937793714 1.104001956 1.190268262 1.182914936 1.077302216 1 21.26206084 HYFQNTQGLIFVVDSNDRER ddPTM_MDA-MB-175_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 ;;;;;;; 252.51 4.05E-36 7914830000 507647 595460 676333 628973 698286 842631 588710 696224 650070 636692 FALSE TRUE 527689.2955 697725.623 693958.7936 753381.9821 579591.5951 646942.7204 542565.3719 686892.2561 626674.1077 761439.6072 0.693015297 0.91632431 0.911377327 0.989417907 0.76117868 0.849631034 0.712552075 0.90209683 0.823012228 1 19.53837009 -1.195855341 4.653017885 1.000028056 0.845217125 0.218153199 0.090445001 2.55E-05 4.40E-06 0.084730217 0.019967486 0.063700767 1.195855341 -0.154810931 HYGFQLYQSDPSGNYGGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYGFQLYQSDPSGNYGGWK 19 0 P25789;H0YN18;P25789-2;H0YMZ1;H0YL69;H0YLC2;H0YMI6;H0YMA1;H0YKT8;H0YMV3;H0YKS0 P25789 PSMA4 Proteasome subunit alpha type-4;Proteasome subunit alpha type;Proteasome subunit beta type 0 256.96 5.61E-31 380880000 534130 289520 501020 454080 503730 606660 688130 508590 559620 243930 FALSE TRUE 555217.8648 339242.8078 514076.9928 543895.6687 418106.1545 465772.409 634192.5725 501773.1829 539479.3855 291723.4132 1.903233816 1.162891947 1.762206836 1.864422409 1.433227967 1.596623336 2.173951571 1.72003055 1.849283812 1 18.15424165 HYGGLTGLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HYGGLTGLNK 10 0 P18669;Q8N0Y7;P15259 P18669 PGAM1;PGAM4;PGAM2 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4;Phosphoglycerate mutase 2 0 ;; 152.86 1.73E-05 6414960000 6171160 5925660 6423020 5583852 9810780 8630430 7801230 6737820 6929630 6252159 FALSE TRUE 6414802.162 6943346.01 6590409.178 6688321.259 8143147.12 6626143.428 7189749.208 6647510.544 6680233.97 7477149.851 0.857920771 0.928608647 0.881406593 0.894501433 1.089071007 0.88618572 0.961562808 0.889043376 0.893419833 1 22.83405702 3.422324958 24.99999962 0.945523206 0.892355789 0.201331207 0.059897043 169.1250479 77159.98229 0.016563174 0.022426648 2644.386661 -3.422324958 -0.053167416 HYGIT(ph)SPISLAAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYGITSPISLAAPK 14 0 G3XAH6;P51003;P51003-2;G3V457;G3V3I9;A0A0C4DGK1 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 HY(0.002)GIT(0.536)S(0.434)PIS(0.028)LAAPK 92.575 0.018044 439730000 592120 431790 572390 496080 788420 843140 688620 607400 684300 457350 TRUE FALSE 615497.3548 505946.5736 587306.9536 594203.1433 654404.65 647333.5129 634644.165 599258.7965 659672.1767 546958.976 1.125308079 0.925017407 1.073767832 1.086376071 1.196441925 1.183513831 1.160314014 1.095619275 1.206072495 1 19.0610731 3.671848885 2.529861961 1.144121073 1.024850264 0.260864956 0.073476558 0.320074131 4.004467685 0.01928158 0.034903831 4697.306354 -3.671848885 -0.119270809 HYGITS(ph)PISLAAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYGITSPISLAAPK 14 0 G3XAH6;P51003;P51003-2;G3V457;G3V3I9;A0A0C4DGK1 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 HYGIT(0.026)S(0.973)PIS(0.001)LAAPK;HYGIT(0.017)S(0.983)PISLAAPK 203.87 1.51E-08 241957000 430050 339379 413450 336535 557770 568070 497050 454690 476360 341486 TRUE FALSE 447028.7061 397664.7032 424224.8467 403100.6185 462960.4546 436144.3517 458089.9222 448595.6243 459215.8967 408393.6436 1.094602507 0.973728924 1.038764568 0.987039404 1.133613272 1.067950882 1.121687199 1.098439291 1.12444428 1 18.63960089 3.239724189 24.99999998 1.097044759 1.021064263 0.326190401 0.046990248 30.44907042 654207.1869 0.012065807 0.01545879 1736.697539 -3.239724189 -0.075980495 HYGYNSYSVSNSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYGYNSYSVSNSEK 14 0 P07858 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 278.82 3.41E-33 536350000 290450 434500 451530 481660 551760 618120 594150 513320 481770 354950 FALSE TRUE 301917.1903 509121.9951 463297.2427 576930.9104 457972.0323 474570.9977 547578.9705 506439.785 464431.1918 424495.6566 0.711237408 1.199357372 1.091406321 1.359097323 1.078861527 1.117964319 1.289951881 1.193038791 1.094077606 1 18.69539027 4.740656721 24.96710539 1.171650585 0.711237247 0.631937462 0.101867198 107.9306717 1285493.33 0.022705385 0.150090258 55037.24938 -4.740656721 -0.460413338 HYLDFINHYANLFHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYLDFINHYANLFHEK 16 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 246.03 1.27E-20 1436410000 1079660 930070 1115370 936940 1888170 1531950 1316380 1071530 1231960 1371740 FALSE TRUE 1122285.81 1089802.288 1144437.458 1122263.936 1567219.538 1176177.829 1213198.696 1057167.893 1187622 1640506.189 0.684109464 0.66430855 0.697612399 0.68409613 0.955326806 0.716960312 0.739527046 0.644415669 0.723936312 1 20.64570961 -1.699827351 2.417458758 1.052392787 0.721375326 0.504495245 0.08222615 6629655.235 4878571.204 2110455 0.021261204 0.019960557 1.699827351 -0.331017461 HYLFYDGESVSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYLFYDGESVSGK 13 0 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 206.58 6.08E-08 1020020000 1628790 1519110 1898000 1537250 2273700 2384200 2215620 1942210 1962230 1444490 FALSE TRUE 1693095.887 1780005.325 1947463.439 1841313.462 1887217.286 1830505.683 2041953.915 1916177.852 1891609.726 1727510.159 0.980078686 1.030387761 1.127323871 1.065877067 1.092449313 1.059620792 1.182021364 1.109213652 1.094991955 1 20.72026276 4.434566049 4.023902503 1.098459509 0.988275348 0.380687539 0.045210856 0.178228591 6.02831836 0.010723107 0.036805287 27199.82118 -4.434566049 -0.110184161 HYLGHNDDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 140.49 2.27E-05 2060880000 1675840 1164570 1450510 1211647 1782388 1869860 1850890 1536890 1571280 878853 FALSE TRUE 1742003.457 1364575.838 1488311.482 1451307.16 1479418.324 1435613.353 1705812.405 1516290.503 1514729.94 1051047.419 1.657397589 1.298300927 1.416026961 1.38081987 1.407565727 1.365888282 1.622964269 1.442647093 1.441162323 1 20.00339633 0.571539239 4.801985777 1.000000008 1.444897784 0.619512417 0.105325771 58.08008806 650.3422522 0.096559492 0.024442485 3.728543715 -0.571539239 0.444897776 HYLGHTDCVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYLGHTDCVK 10 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 78.098 0.017939 99887000 103880 109240 107550 131430 220170 199110 156380 117320 110290 199160 FALSE TRUE 107981.2626 128001.1202 110352.8414 157426.4617 182745.582 152869.72 144122.527 115747.5173 106320.6844 238181.5889 0.453356883 0.537409801 0.463313902 0.66095143 0.767253182 0.641820053 0.605095162 0.485963327 0.446384983 1 17.86170237 3.739887365 24.96072413 0.629001105 0.489965151 0.208812719 0.147180287 220.2160581 4142996.165 0.038341986 0.064618946 5493.983682 -3.739887365 -0.139035954 HYLHSQACSVFNYHLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYLHSQACSVFNYHLSPR 18 0 P41162 P41162 ETV3 ETS translocation variant 3 1 HYLHSQACSVFNYHLS(1)PR;HYLHSQACSVFNYHLS(1)PR 231.29 1.46E-19 935660000 274090 363830 340700 388170 472700 530430 410430 445700 348530 394260 TRUE FALSE 284911.2848 426314.9723 349578.9219 464948.8674 392350.6228 407245.6712 378259.4241 439726.1205 335986.4734 471507.6984 0.604255849 0.904152729 0.741406605 0.986089663 0.83211923 0.863709485 0.802233824 0.932595845 0.712578977 1 18.8469218 7.999999989 0.033287173 1.402034029 1.58E-06 0.208328781 0.106463255 1870.332488 4.762333354 60.80093669 162.5909342 99999997.5 -7.999999989 -1.402032451 HYLPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYLPVK 6 0 P07686 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 84.109 0.056225 248100000 344610 271710 266390 245960 435520 407420 322910 266960 293840 273840 FALSE TRUE 358215.4689 318374.0789 273332.3422 294610.1539 361490.466 312802.8795 297599.4704 263381.8379 283264.7558 327493.705 1.093808716 0.972153278 0.834618614 0.89959028 1.103808899 0.955141655 0.90871814 0.804234811 0.864947177 1 18.32110765 2.136035448 3.697396424 0.866127901 0.972430436 0.155423089 0.088625208 0.361217641 9.468386683 0.037102766 0.026211692 136.7840466 -2.136035448 0.106302535 HYNGEAYEDDEHHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 125.73 3.08E-05 1268220000 265786 295726 296273 300538 355777 445138 301835 299515 287740 270524 FALSE TRUE 276279.4365 346514.6401 303994.1178 359983.5194 295302.1526 341761.4456 278176.384 295500.4913 277384.2936 323527.9983 0.853958353 1.07104993 0.939622287 1.112681194 0.912756096 1.056358174 0.859821671 0.913369145 0.857373381 1 18.30353104 2.230474678 24.99982616 0.90035902 0.994335803 0.197680779 0.081658288 246.7165546 762783.3945 0.02754258 0.020693464 170.0100825 -2.230474678 0.093976783 HYQEEGQGTEVVQGVLLGLVVEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 HYQEEGQGTEVVQGVLLGLVVEDR 24 0 A0A087WZK9;B3KS98;O15372;E5RGU4;E5RFH0;E5RFW7 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ;;;;; 216.8 1.30E-32 700382000 434964 449069 469405 452200 446078 559759 497957 496289 496265 369524 FALSE TRUE 452136.7146 526193.1075 481638.0799 541643.8103 370253.8209 429763.4555 458925.8292 489637.0577 478404.5196 441925.1528 1.023106994 1.190683771 1.089863469 1.225646033 0.837820202 0.972480187 1.038469583 1.107963768 1.082546482 1 18.75344252 3.274643946 24.99995808 1.018996469 1.133460473 0.334938317 0.08575192 235.7458604 163332.5547 0.024851493 0.033648082 1882.105421 -3.274643946 0.114464004 HYQFASGAFLHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYQFASGAFLHIK 13 0 Q8WUM4;Q8WUM4-2;A0A3B3IT07;Q8WUM4-3;C9IZF9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 161.76 2.41E-05 126370000 207820 171830 206600 180920 303810 285490 294990 213680 234060 182620 FALSE TRUE 216024.8941 201340.4658 211984.1657 216705.436 252168.4847 219189.2741 271867.913 210815.9691 225636.2263 218400.8925 0.989120931 0.921884812 0.970619503 0.992236952 1.154612885 1.003609791 1.244811364 0.965270639 1.033128682 1 17.73661923 3.461119046 23.91793591 1.068131426 0.960801397 0.279997847 0.078560933 173.451259 259249.9958 0.021014062 0.028463598 2891.472366 -3.461119046 -0.107330029 HYQGEEKS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYQGEEKSD 9 1 P13984 P13984 GTF2F2 General transcription factor IIF subunit 2 1 HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D;HYQGEEKS(1)D 198.32 1.61E-05 2561710000 5330220 2644590 3561450 2551670 4810560 6429050 4797080 3667530 3944980 2173370 TRUE FALSE 5540661.201 3098777.76 3654264.313 3056382.71 3992862.729 4936000.571 4421072.335 3618372.759 3803000.94 2599200.24 2.131679244 1.192204322 1.405918735 1.175893516 1.536188966 1.899045905 1.700935644 1.392110044 1.463142732 1 21.30963635 0.63554179 1.407582574 1.001406969 1.541118065 0.257657136 0.281902424 1.938173075 5.558074741 0.267263935 0.078607806 4.320577399 -0.63554179 0.539711097 HYS(ph)PEDEPSPEAQPIAAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYSPEDEPSPEAQPIAAYK 19 0 A0A096LP25;Q6ZSR9 A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 HYS(1)PEDEPSPEAQPIAAYK 212.39 5.45E-17 470720000 398720 344780 398190 326910 494320 490110 434510 440060 401830 322360 TRUE FALSE 414461.7735 403993.283 408567.1585 391571.8223 410295.663 376289.3802 400451.9708 434161.7155 387368.2168 385520.27 1.075071289 1.047917099 1.059781263 1.015697105 1.064264826 0.976056019 1.038731299 1.126170916 1.004793384 1 18.55644719 -0.43585992 6.43358079 0.999999999 1.048963615 0.101028317 0.039335365 0 0 0.039051729 0.009204581 0.366555786 0.43585992 0.048963616 HYSNWETVLILEELRGDEGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYSNWETVLILEELRGDEGTR 21 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 111.13 0.00015361 70242000 9846.4 35022 27352 34486 33021 47884 24662 33626 24862 45700 FALSE TRUE 10235.14348 41036.75607 28064.81559 41307.22787 27408.10221 36763.66669 22728.928 33175.29847 23967.22148 54654.04002 0.187271489 0.750845794 0.513499379 0.755794592 0.501483554 0.672661466 0.415869129 0.607005419 0.438526072 1 15.73804052 -1.164309373 4.366297595 1.000096539 0.551790908 0.416103956 0.163423932 21123884.09 5632867.816 20274.68568 0.03412652 0.068500009 1.164309373 -0.448305631 HYTEAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYTEAIK 7 0 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 125.25 0.0040673 193540000 211620 476060 337350 410860 411340 491160 379150 348090 373810 470040 FALSE TRUE 219974.921 557819.6018 346141.6181 492126.8817 341420.5737 377095.5336 349431.2323 343424.4229 360356.6511 562135.3385 0.391320214 0.992322602 0.615762067 0.875459783 0.607363655 0.670826948 0.621614064 0.610928364 0.641049631 1 19.10055799 -0.936911894 4.459083057 1.000005408 0.675039418 0.291976917 0.154131401 40936500.91 83625405.45 3601.434622 0.033888964 0.115634681 0.936911894 -0.32496599 HYTEAIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 HYTEAIKR 8 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 178.83 0.00016069 685310000 774220 1018700 1181450 979180 1614550 1477850 1176040 1180170 1216000 1239140 FALSE TRUE 804786.8034 1193653.801 1212239.558 1172858.881 1340109.368 1134641.735 1083858.912 1164351.752 1172236.398 1481925.758 0.543068233 0.805474764 0.818016389 0.791442402 0.904302635 0.765653561 0.731385433 0.785701811 0.791022351 1 20.49904174 -5 0.235246946 2.222139752 0.752495748 0.405584006 0.085535675 177.52993 1.774153628 103.7947695 0.139770731 1.00E-05 5 -1.469644004 HYVGELYNYGVDHLGEEAILQVHDKEVLASQLLVLTGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HYVGELYNYGVDHLGEEAILQVHDKEVLASQLLVLTGQR 39 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 44.915 0.022045 515380000 132810 109520 146180 117930 163790 148480 131480 133810 136180 94558 FALSE TRUE 138053.4414 128329.2081 149989.5709 141256.202 135949.0343 113997.7702 121174.254 132016.4958 131278.9084 113084.8297 1.220795413 1.134804805 1.326345641 1.249117166 1.202186312 1.008073059 1.071534125 1.167411192 1.160888766 1 16.78704588 2.924215851 7.267883887 1.09740122 1.231696123 0.531855592 0.067712942 0.247831326 20.8086495 0.021536572 0.022941357 839.8773149 -2.924215851 0.134294903 HYYEVSCHDQGLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 HYYEVSCHDQGLCR 14 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;;; 210.14 3.27E-09 1539620000 129271 487559 368316 466018 499916 629270 405246 450067 410480 552550 FALSE TRUE 134374.7189 571293.4656 377914.6175 558194.9695 414940.4569 483131.5792 373481.7596 444034.588 395706.905 660811.5933 0.203348005 0.864533055 0.571894654 0.844711224 0.62792551 0.731118497 0.565186452 0.671953387 0.598819556 1 19.33387947 -2.64928489 2.011355705 8.18943874 0.644619901 0.28357423 0.174735053 5221960.519 198565.8768 171846287.7 0.038704308 0.00224241 2.64928489 -7.544818839 HYYFCMMTEAEQDKWQAVLQDCIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HYYFCMMTEAEQDKWQAVLQDCIR 24 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;; 312.01 1.03E-73 1149800000 810644 744287 882790 756217 1031032 1080088 1013005 921709 979845 711056 FALSE TRUE 842648.8511 872112.5025 905796.2326 905794.4655 855777.5489 829253.9309 933603.0211 909354.9985 944580.5699 850373.8092 0.990915809 1.025563691 1.065174189 1.065172111 1.006354546 0.975164007 1.097873677 1.069359132 1.110782764 1 19.69773764 2.217587273 24.99971066 1.075455813 1.024877145 0.266543519 0.038336896 315.3737779 375915.5834 0.014359455 0.010616817 165.0392619 -2.217587273 -0.050578669 HYYTGTQGLIFVVDCADRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 HYYTGTQGLIFVVDCADRDR 20 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;;; 270.95 1.31E-44 1947487000 88633.6 147791.1 134626 128343.5 154985 145231 111748.3 138341.3 144849 157057 FALSE TRUE 92132.92297 173173.0718 138134.4642 153729.4612 128640.7051 111503.3012 102989.1762 136487.0612 139635.9128 187829.3121 0.490514084 0.921970431 0.735425491 0.818452985 0.684880883 0.593641642 0.548312588 0.726654746 0.743419178 1 17.5190627 -1.687555433 5.034579832 1.008030923 0.699535924 0.363432851 0.120646013 0.010848162 0.000673234 0.116523027 0.026981998 0.020532629 1.687555433 -0.308494999 IAAEEEEENDGHYQEEEEGGAHS(ph)LKDVCDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAAEEEEENDGHYQEEEEGGAHSLKDVCDLR 31 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 IAAEEEEENDGHY(0.001)QEEEEGGAHS(0.999)LKDVCDLR 58.98 0.017479 69233000 16909 16405 20149 18228 24712 28244 23589 26240 24685 23699 TRUE FALSE 17576.58038 19222.43114 20674.09949 21833.44399 20511.46307 21684.75904 21740.03254 25888.29572 23796.59167 28342.36531 0.620152206 0.678222545 0.729441572 0.770346573 0.723703292 0.765100541 0.767050749 0.913413381 0.839612058 1 14.79067254 5.306897331 0.083369784 1.249957879 2.67E-14 0.886035151 0.035705462 31.05489135 0.346958911 1.22922363 4.978324823 202720.3423 -5.306897331 -1.249957879 IAAHLADFTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAAHLADFTPR 11 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 141.95 0.0016298 347330000 105932 109295 127294 115013 133799 139577 111165 109062 109069 133029 FALSE TRUE 110114.2772 128065.5661 130611.3862 137762.2281 111055.8938 107162.3571 102451.5968 107600.2023 105143.628 159093.4856 0.692135676 0.804970522 0.820972561 0.865919982 0.698054313 0.67358105 0.643971037 0.676333175 0.660892101 1 17.27951524 3.209720389 24.28988704 0.69949382 0.798424225 0.065350048 0.106061782 257.047226 216489.952 0.028580057 0.034166369 1620.766265 -3.209720389 0.098930405 IAALQAFADQLIAAGHYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAALQAFADQLIAAGHYAK 19 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 273.13 2.27E-39 663950000 1108230 861990 1045060 909680 1227280 1312100 1165920 1039390 1122420 893030 FALSE TRUE 1151983.776 1010030.077 1072295.122 1089611.989 1018667.384 1007384.66 1074532.144 1025458.677 1082024.323 1068002.13 1.078634343 0.94571916 1.004019647 1.02023391 0.953806509 0.943242182 1.006114233 0.960165385 1.013129368 1 20.02648309 4.752029024 24.90230251 0.981475831 1.07863441 0.509302541 0.028147173 1700.71717 3144468.635 0.00651745 0.125722357 56497.47315 -4.752029024 0.097158579 IAAPELHKGDS(ph)DS(ph)EEDEPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 2 IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(0.956)EEDEPT(0.044)K;IAAPELHKGDS(1)DS(1)EEDEPTK;IAAPELHKGDS(1)DS(1)EEDEPTK 198.09 2.11E-21 1288877000 4581520 1348558 2048090 1321578 3150150 3679440 3207930 2223760 2491160 963550 TRUE FALSE 4762401.947 1580162.346 2101464.908 1582982.184 2614688.628 2824945.822 2956484.064 2193954.135 2401503.638 1152339.174 4.132812677 1.371264973 1.823651365 1.373712028 2.269026938 2.451488143 2.565637037 1.903913521 2.084024992 1 20.13613398 0.429926286 1.273817686 1.000111727 2.185356199 0.19567349 0.744153537 4.581906277 8.571106513 0.679416318 0.202480157 2.691078003 -0.429926286 1.185244472 IAASSS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 IAAS(0.001)S(0.199)S(0.801)FR;IAASS(0.016)S(0.984)FR;IAASS(0.012)S(0.987)FR;IAAS(0.001)S(0.016)S(0.984)FR 147.75 0.00055828 20000500000 25735700 30810500 30271600 29610000 38478000 38974000 30772300 30263800 28587400 37104400 TRUE FALSE 26751765.31 36101963.7 31060502.76 35466769.62 31937523.3 29922879.16 28360286.72 29858163.26 27558545.06 44374296.77 0.602866237 0.813578272 0.699966084 0.799263813 0.719730241 0.67432909 0.639115181 0.67287068 0.621047477 1 25.40322092 -1.088784007 4.915283668 1.000010074 0.696556061 0.659227016 0.066049656 7.26E-06 1.35E-06 0.063714292 0.015017104 0.081510957 1.088784007 -0.303454013 IAAYGHEVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAAYGHEVGK 10 0 A0A087WYM2;A0A087X297;Q16719-2;Q16719;B8ZZA3 A0A087WYM2 KYNU Kynureninase 0 ; 87.913 0.012552 343940000 338540 313750 351580 297630 454090 458440 407070 368990 386530 318160 FALSE TRUE 351905.8206 367634.1219 360742.4636 356500.3257 376903.944 351974.2577 375162.7897 364044.2926 372618.8608 380497.3605 0.924857455 0.966193619 0.948081383 0.936932454 0.990556002 0.925037318 0.985980006 0.956759049 0.979294207 1 18.53752692 -5 0.056368096 1.176674225 0.878935416 0.398763399 0.020134246 437.3966395 1.810154632 10.8123065 2.008155331 1.00E-05 5 -0.297738809 IACDEEFS(ph)DS(ph)EDEGEGGR ddPTM_MDA-MB-175_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 173.28 1.27E-11 117335000 255050 251300 238350 273020 272630 339430 306520 274380 277420 221265 TRUE FALSE 265119.5709 294458.8202 244561.5968 327022.5411 226288.45 260602.5266 282494.1615 270702.3849 267435.7084 264617.6404 1.001896814 1.112770939 0.924207458 1.235830463 0.85515255 0.984826734 1.067556044 1.022994478 1.010649585 1 18.01354971 3.219867566 24.99996979 0.998508494 1.061506965 0.147766514 0.090374854 562.8307616 752724.5607 0.025100231 0.030048541 1659.080909 -3.219867566 0.062998471 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 167.85 6.02E-11 5880930000 1516050 1864400 1740550 1621870 2090030 2280830 1647630 1827670 1819250 1909150 TRUE FALSE 1575904.825 2184596.197 1785910.163 1942671.045 1734767.447 1751141.799 1518484.455 1803173.073 1753775.548 2283211.39 0.690214157 0.956808558 0.78219221 0.850850278 0.759792744 0.766964376 0.665065207 0.789753012 0.768117904 1 21.12263301 5.044462326 16.07191368 0.799929109 0.121616249 0.117688346 0.094630051 610099.6687 5904028.47 0.02150936 12494322.62 110780.2462 -5.044462326 -0.67831286 IACDEEFS(ph)DSEDEGEGGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 IACDEEFS(0.991)DS(0.009)EDEGEGGRR;IACDEEFS(0.918)DS(0.082)EDEGEGGRR 271.05 1.58E-39 572790000 202592 229300 237610 201642 275580 297610 252580 226100 226800 218810 TRUE FALSE 210590.4886 268680.4913 243802.3118 241526.1858 228737.01 228494.5878 232782.1196 223069.4993 218637.5123 261681.6301 0.804758395 1.026745711 0.931675302 0.922977229 0.874104193 0.873177791 0.889562326 0.852446155 0.835509593 1 17.99745313 3.291093368 4.847341989 0.877780077 0.930769374 0.043097768 0.065309278 0.411263077 20.26009455 0.01726658 0.023164185 1954.75966 -3.291093368 0.052989297 IACEEEFS(ph)DS(ph)EEEGEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IACEEEFSDSEEEGEGGR 18 0 Q13547 Q13547 HDAC1 Histone deacetylase 1 2 IACEEEFS(1)DS(1)EEEGEGGR;IACEEEFS(1)DS(1)EEEGEGGR 219.23 1.25E-18 204900000 324280 338180 328950 339980 381210 423020 347220 340240 341650 337220 TRUE FALSE 337082.8248 396259.7843 337522.7072 407227.0293 316412.0604 324780.0159 320003.9891 335679.6393 329354.0832 403291.8025 0.835828605 0.982563449 0.836919335 1.009757765 0.784573498 0.805322632 0.793480024 0.832349275 0.816664463 1 18.62146456 3.214861552 24.99926846 0.826072071 0.915335098 0.184521519 0.077135844 304.7744317 321494.5234 0.020244782 0.024209513 1640.066856 -3.214861552 0.089263027 IACEEEFS(ph)DS(ph)EEEGEGGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 175.86 6.13E-12 1567250000 3718140 2295170 2782930 2155580 3825500 3871410 3349850 2818480 3210930 1972540 TRUE FALSE 3864935.038 2689347.594 2855455.442 2581947.29 3175242.876 2972333.699 3087280.004 2780702.886 3095369.257 2359021.446 1.638363672 1.140026767 1.210440645 1.094499287 1.346000004 1.259985874 1.308712139 1.178752694 1.312141211 1 21.1697571 -4.449338405 0.224415166 6.15E-19 1.295016351 0.256469827 0.142434295 174.7757311 2.193000487 79.66761738 0.250685278 3.55E-05 4.449338405 1.295016351 IADDKYNDTFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IADDKYNDTFWK 12 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;; 203.82 1.10E-07 7636160000 7664990 4711600 6152770 5057040 8497410 7767380 8350500 5841510 6833770 3002510 FALSE TRUE 7967609.724 5520780.649 6313116.241 6057307.418 7053023.283 5963523.711 7695965.99 5763214.113 6587823.953 3590794.348 2.218898926 1.537481714 1.758139183 1.686899007 1.96419583 1.66078119 2.143248887 1.604996988 1.834642509 1 21.7758716 -0.285663665 0.91408554 0.977999885 1.815558274 0.570389311 0.21414466 9.699622881 5.954879882 0.988020499 0.061363765 0.518007843 0.285663665 0.837558388 IADGVNEINTENMVSSIEPEKQDS(ph)PPPKPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IADGVNEINTENMVSSIEPEKQDSPPPKPPR 31 2 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 IADGVNEINTENMVS(0.005)S(0.028)IEPEKQDS(0.966)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR;IADGVNEINTENMVSSIEPEKQDS(1)PPPKPPR 421 3.75E-197 2775870000 2058590 730178 1172701 738289 1829610 1730610 1546286 1175779 1456497 564575 TRUE FALSE 2139864.723 855580.3915 1203262.551 884320.3606 1518613.546 1328702.055 1425084.063 1160019.606 1404077.957 675192.6618 3.169265372 1.267164826 1.782102531 1.309730408 2.24915588 1.967885805 2.110633221 1.718057188 2.079521945 1 19.3649397 -1.041890569 4.844167518 0.999979062 1.916602327 0.238815462 0.50932802 0.000105438 2.09E-05 0.451471694 0.106410472 0.090804931 1.041890569 0.916623265 IADGYEQAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IADGYEQAAR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 174.48 7.20E-06 294140000 684340 932930 785710 789870 947180 1064990 791840 831330 835300 1004220 FALSE TRUE 711358.2716 1093153.47 806186.2481 946103.9285 786178.6819 817662.2126 729773.5117 820187.3811 805237.7162 1200977.682 0.592315979 0.910219637 0.671274962 0.78777811 0.654615563 0.680830481 0.60764952 0.682933075 0.670485162 1 20.19577791 -1.03668324 4.660519734 1.000008458 0.697162033 0.522633258 0.087333374 10996142.87 2445975.251 1104.349093 0.019548887 0.091900264 1.03668324 -0.302846425 IADMGHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IADMGHLK 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 83.005 0.018804 884240000 859140 748180 790740 649170 1529800 1119400 1022000 799030 817730 1125800 FALSE TRUE 893059.5106 876674.095 811347.334 777573.8884 1269765.142 859436.3147 941892.9695 788320.3098 788300.057 1346378.955 0.663304716 0.651134728 0.602614391 0.57752974 0.943096398 0.638331661 0.699574935 0.585511461 0.585496419 1 20.3606531 -1.933676752 2.796186071 1.221721637 0.660156425 0.50030997 0.101715639 43588355.37 26635691.32 63117092.4 0.025159731 0.011649928 1.933676752 -0.561565211 IADPEHDHTGFLT(ph)EYVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 1 IADPEHDHTGFLT(0.974)EY(0.025)VAT(0.001)R 260.03 1.59E-30 3723900000 523580 554780 638720 649310 823820 923610 928110 768100 857490 814680 TRUE FALSE 544251.3427 650059.1494 655365.5679 777741.58 683787.3707 709115.5749 855362.313 757804.8759 826629.1024 974300.948 0.558607013 0.667205703 0.672652089 0.798256003 0.701823571 0.727819855 0.877924131 0.77779343 0.848433027 1 19.89400794 5.404982815 0.097031775 1.173165522 2.81E-14 0.835203802 0.048414338 28.47511925 0.362311953 0.899930756 4.68399112 254087.2163 -5.404982815 -1.173165522 IADPEHDHTGFLTEY(ph)VATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLTEY(1)VATR;IADPEHDHTGFLT(0.001)EY(0.999)VATR;IADPEHDHTGFLT(0.001)EY(0.999)VATR 316.41 7.86E-62 13765170000 4923520 5281690 5928990 6095520 6903150 8230990 7450450 7532530 7042460 7526600 TRUE FALSE 5117904.371 6188779.172 6083504.35 7301195.663 5729755.029 6319467.314 6866464.261 7431568.756 6789003.24 9001293.165 0.568574346 0.687543341 0.675847819 0.811127416 0.636547985 0.702062159 0.762830866 0.825611234 0.754225323 1 23.10170085 -5 0.080607999 1.968993127 0.430902037 0.754625373 0.056271792 119.8558352 0.683717408 20.41149019 1.877272948 1.00E-05 5 -1.53809109 IADPEHDHTGFLTEYVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IADPEHDHTGFLTEYVATR 19 0 P27361;E9PQW4;P27361-3;P27361-2;E9PJF0;B3KR49 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ;;; 219.58 1.79E-19 867780000 660183 755288 740791 707608 834150 866300 728990 754460 691417 702287 FALSE TRUE 686247.5346 885002.8387 760096.622 847570.7504 692361.481 665114.9539 671849.8589 744347.6977 666533.0372 839886.6916 0.817071566 1.053716945 0.904999007 1.009148923 0.824351056 0.791910338 0.799929164 0.886247758 0.79359876 1 19.67983518 3.224628911 24.89509898 0.840706106 0.950966094 0.24451021 0.082439478 258.5061062 461933.5889 0.021977305 0.026393821 1677.370155 -3.224628911 0.110259988 IADREDEYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IADREDEYKK 10 2 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 152.07 1.05E-05 1188110000 1860670 887380 1369190 865160 1945580 1695000 1745900 1211590 1553680 735200 FALSE TRUE 1934130.688 1039780.612 1404872.216 1036286.066 1614871.007 1301361.938 1609051.796 1195350.618 1497763.36 879248.3637 2.199754663 1.182578956 1.597810441 1.178604486 1.836649431 1.480084572 1.830031038 1.359514179 1.703458797 1 19.74591122 -1.447727004 4.033396737 0.996623669 1.570139433 0.256625932 0.301579494 0.008214157 0.001124723 0.261957739 0.061441964 0.035667527 1.447727004 0.573515763 IAEFTTNLTEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IAEFTTNLTEEEEK 14 0 P35579 P35579 MYH9 Myosin-9 0 ;; 221.8 1.70E-08 182902000 239833 158662 179577 147827 241090 265135 249745 185755 198006 109979 FALSE TRUE 249301.792 185910.9643 184256.9241 177066.7394 200109.6079 203561.4144 230169.3343 183265.2581 190879.8027 131527.2794 1.895437914 1.413478369 1.400902725 1.346235855 1.521430451 1.547674485 1.749974115 1.393363103 1.451256375 1 17.00500253 0.600687808 1.393774013 1.000785334 1.527581869 0.494277851 0.161920761 1.295095823 3.476763593 0.152176415 0.044802769 3.987381672 -0.600687808 0.526796535 IAEFTTNLTEEEEKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAEFTTNLTEEEEKSK 16 1 P35579 P35579 MYH9 Myosin-9 0 198.42 3.72E-11 302590000 348050 124050 213160 105380 358610 295960 220180 212240 306470 129110 FALSE TRUE 361791.2828 145354.6225 218715.1247 126223.8495 297653.6003 227227.7753 202921.7163 209395.27 295440.2046 154406.6325 2.343107137 0.94137551 1.416487887 0.817476862 1.927725483 1.471619266 1.314203366 1.356128727 1.913390634 1 17.2363752 -0.684780588 6.299877047 0.999999998 1.456690458 0.097684628 0.438472512 1.16E-08 3.69E-09 0.389747654 0.091864402 0.206642388 0.684780588 0.45669046 IAELLENVTLIHKPVSLQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAELLENVTLIHKPVSLQPR 20 1 Q14694;Q14694-3;Q14694-2;J3KT19 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 0 ; 157.51 3.63E-09 272536000 178653 178773 182025 138244 230795 241238 196781 190102 217107 175767 FALSE TRUE 185706.3584 209475.8721 186768.721 165588.2506 191564.5483 185214.1305 181356.791 187553.9936 209293.3615 210205.1784 0.883452824 0.996530503 0.888506755 0.78774582 0.911321737 0.881111169 0.862760815 0.892242499 0.995662253 1 17.68143868 1.239470234 6.176334953 0.999647009 0.887498473 0.455989253 0.048039299 0.131325175 19.80809538 0.040076419 0.012209455 17.35682295 -1.239470234 -0.112148535 IAESHLQSISNLNENQAS(ph)EEEDELGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 29 IAESHLQSISNLNENQASEEEDELGELR 28 0 Q9UD71;J3KSJ8;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQS(0.001)IS(0.001)NLNENQAS(0.998)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(0.999)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR;IAESHLQSISNLNENQAS(1)EEEDELGELR 398.24 1.20E-146 96074009200 2710017.4 3797961.2 3793497.7 3813618.6 4115930 4353872.7 3494668.1 4217883.2 4183830.2 4009523.9 TRUE FALSE 2817010.98 4450231.492 3892359.366 4567940.977 3416305.689 3342751.749 3220746.883 4161349.375 4033254.968 4795113.341 0.587475369 0.928076393 0.811734591 0.952624193 0.71245567 0.697116316 0.671672733 0.867831285 0.841117755 1 22.19313349 0.907624629 1.515358594 0.996901349 0.780095069 0.281707577 0.109037291 0.681014512 3.115835436 0.102405138 0.03001373 8.083968808 -0.907624629 -0.216806279 IAESHLQSISNLNENQAS(ph)EEEDELGELRELGYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IAESHLQSISNLNENQASEEEDELGELRELGYPR 34 1 Q9UD71;J3KSJ8;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 IAESHLQSISNLNENQAS(1)EEEDELGELRELGYPR;IAESHLQSISNLNENQAS(1)EEEDELGELRELGYPR;IAESHLQSISNLNENQAS(1)EEEDELGELRELGYPR;IAESHLQSISNLNENQAS(1)EEEDELGELRELGYPR 471.64 4.76E-257 1278680000 64572.8 114902 124243 81293.2 134627 116212 47635.1 98354.2 98300.1 181212 TRUE FALSE 67122.18401 134635.5247 127480.8746 97372.75232 111743.1506 89223.52421 43901.33639 97035.92282 94762.2986 216717.0219 0.309722713 0.621250345 0.588236556 0.44930828 0.515617784 0.411705197 0.202574473 0.447754043 0.437262831 1 17.72545295 -1.434607373 7.240160964 1.000044881 0.443323935 0.67474758 0.116097108 8.74E-05 6.83E-06 0.116831975 0.027535356 0.036761449 1.434607373 -0.556720947 IAESNHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IAESNHIK 8 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 96.668 0.0087777 1194150000 654800 1324310 1158940 1274710 1561220 1821200 1580210 1384260 1217280 1774460 FALSE TRUE 680652.0096 1551749.941 1189142.928 1526843.833 1295844.382 1398253.901 1456349.011 1365706.259 1173470.331 2122131.463 0.320739795 0.731222343 0.560353093 0.719485979 0.610633415 0.658891273 0.686267103 0.643554032 0.552967783 1 21.0170826 -5 0.258298813 3.3852543 0.590010063 0.523489447 0.111894186 148.1397953 1.458054174 187.6840296 0.138646493 1.00E-05 5 -2.795244237 IAETDFEKR ddPTM_MDA-MB-175_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 0 123.88 0.00087423 327210000 239030 215880 242820 198820 310630 294810 270090 235110 259060 211010 FALSE TRUE 248467.089 252955.7107 249148.0887 238146.0026 257829.2236 226344.8454 248919.6401 231958.735 249736.4812 252353.3695 0.984599847 1.002386896 0.987298443 0.943700506 1.021699152 0.896936093 0.98639317 0.919182238 0.989630064 1 17.94508582 2.763742963 24.99882448 0.952998317 0.986246681 0.140928904 0.03504874 1282.497485 1273149.083 0.009917618 0.010515498 580.4207942 -2.763742963 0.033248364 IAGDYVSEEVWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IAGDYVSEEVWYR 13 0 O95782-2;O95782;O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O95782-2;O94973-3 AP2A1;AP2A2 AP-2 complex subunit alpha-1;AP-2 complex subunit alpha-2 0 ;;; 269.01 1.58E-24 551480000 232104 211288 264221 270667 265616 302691 351692 275940 244472 172538 FALSE TRUE 241267.6451 247575.0704 271106.8163 324204.1247 220466.6872 232395.6026 324125.4621 272241.4756 235673.5005 206343.5177 1.169252361 1.199819957 1.313861562 1.571186381 1.068444939 1.126255892 1.570805159 1.319360447 1.142141528 1 17.65468859 1.026663373 3.792764352 1.002072914 1.30009426 0.252977988 0.160857399 0.260769864 8.848768395 0.156429423 0.040275549 10.63318507 -1.026663373 0.298021346 IAGEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 179.23 0.0016381 30556000000 6120590 7162510 6406760 6275480 7248630 8218560 6822450 6723730 6146910 6966750 FALSE TRUE 6362235.619 8392615.376 6573725.429 7516751.214 6016510.462 6309923.993 6287688.542 6633609.397 5925683.91 8331751.276 0.763613244 1.007305079 0.78899684 0.902181422 0.722118347 0.757334657 0.754665896 0.796184281 0.711217092 1 22.99018834 3.247511037 24.9844072 0.77747068 0.870185125 0.115430139 0.097991428 317.268973 885626.5658 0.024784748 0.033077234 1768.11715 -3.247511037 0.092714444 IAGHPLAQNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAGHPLAQNER 11 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 ; 106.62 0.0023072 606640000 281040 322720 230160 210833 510110 373590 277810 259940 260580 554240 FALSE TRUE 292135.6762 378144.6496 236158.1587 252535.1381 423401.6844 286829.3843 256034.5263 256455.9295 251201.7767 662832.7164 0.440738167 0.570497865 0.356286213 0.380993774 0.63877608 0.43273269 0.386273218 0.386908979 0.378982163 1 19.33828529 -1.622785081 2.768123447 1.050571863 0.440070452 0.785905957 0.087470821 15126043.82 14377148.43 5507500.58 0.021511294 0.023834987 1.622785081 -0.610501411 IAGYVTHLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAGYVTHLMK 10 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ; 147.95 2.60E-05 1275790000 1661520 1585930 1442520 1075020 5380900 2753100 2125120 1514610 1686360 4610000 FALSE TRUE 1727118.093 1858301.141 1480113.256 1287655.747 4466256.54 2113734.249 1958547.541 1494309.13 1625668.233 5513241.236 0.313267281 0.33706146 0.268465172 0.233556939 0.810096339 0.383392302 0.355244303 0.271040041 0.294866153 1 22.3944693 -1.115226672 3.950248584 1.000190559 0.362333576 0.601132965 0.155663889 715753716.2 1350862089 1888991.803 0.038390951 0.076696108 1.115226672 -0.637856983 IAHFLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IAHFLDR 7 0 P60228;H0YBR5;E5RHS5;E5RIP5;E5RJ25;E5RII3 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 120.49 0.0045458 1732380000 1509070 1691710 1676050 1697260 2275110 2341150 1869760 1734140 1711760 2122260 FALSE TRUE 1568649.249 1982248.033 1719729.24 2032972.962 1888387.615 1797453.393 1723203.325 1710896.69 1650154.092 2538076.214 0.61804655 0.781004141 0.677571946 0.800989722 0.744023211 0.7081952 0.678940733 0.674091929 0.650159394 1 21.27530396 -1.484621591 3.370320736 1.005369558 0.705958156 0.728002515 0.054323088 2975436.059 2626002.763 107613.4633 0.012512281 0.032762604 1.484621591 -0.299411401 IAHIMGPPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IAHIMGPPDR 10 0 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 ;;;;;;;;; 123.75 0.00050079 3229720000 1814627 2366904 2237640 2159400 2573252 2839570 2080089 2252268 2079453 2600483 FALSE TRUE 1886269.875 2773401.35 2295954.737 2586522.875 2135851.544 2180122.902 1917046.189 2222080.031 2004613.893 3109997.855 0.606518063 0.891769538 0.738249621 0.831679955 0.686769459 0.701004632 0.616413991 0.71449568 0.644570828 1 21.56848215 -1.039281352 4.296861516 1.000020331 0.718187464 0.500791631 0.085414897 9431954.309 4562611.523 1746.348252 0.019667042 0.091352124 1.039281352 -0.281832867 IAHIPLYFVNAQFPRFS(ph)PVLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAHIPLYFVNAQFPRFSPVLGR 22 1 F8VZ44;Q9NRG9-2;Q9NRG9 F8VZ44 AAAS Aladin 1 IAHIPLYFVNAQFPRFS(1)PVLGR;IAHIPLYFVNAQFPRFS(1)PVLGR 111.95 0.00018623 535120000 43614 40074 64662 46846 71099 58471 61439 47553 62481 48346 TRUE FALSE 45335.9144 46956.39777 66347.14484 56111.99898 59013.61738 44891.99639 56623.25064 46915.62982 60232.32101 57818.47306 0.784107777 0.812134864 1.147507731 0.97048566 1.020670631 0.776429989 0.979328018 0.811429762 1.041748732 1 15.81924289 7.999794516 0.009044009 1.75788288 3.85E-06 0.046783399 0.119422952 87041.94911 60.86093416 5168.909407 6759.398742 99952696.81 -7.999794516 -1.757879027 IAIPGLAGAGNSVLLVSNLNPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAIPGLAGAGNSVLLVSNLNPER 23 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 102.08 7.09E-05 0 10624 43338 49999 52641 55804 57994 48485 44609 53444 45113 FALSE TRUE 11043.44372 50780.96438 51302.01501 63053.23268 46318.45601 44525.77241 44684.61901 44011.08932 51520.56088 53952.02861 0.204690055 0.941224374 0.95088204 1.168690674 0.858511852 0.82528449 0.828228709 0.815744847 0.954932784 1 15.71938959 4.739839573 24.92132591 0.915163938 0.204689816 0.818668676 0.101852407 46.0336387 896893.7603 0.026404498 0.164389747 54933.79128 -4.739839573 -0.710474122 IAIWTTECENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IAIWTTECENR 11 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 ;; 199.46 1.17E-07 584100000 209855 251027 222292 244129 257195 300677 272727 254028 229957 267344 FALSE TRUE 218140.2374 294138.9345 228085.1121 292416.9875 213477.0858 230849.3236 251349.9451 250623.1702 221680.8925 319724.9382 0.682274704 0.919974952 0.713379173 0.914589238 0.667689818 0.722024766 0.786144323 0.783871197 0.69334877 1 18.28647175 -1.950622233 7.93214215 1.093264912 0.770178979 0.402831295 0.085682345 0.046645839 0.000290371 0.027383465 0.017872475 0.01120412 1.950622233 -0.323085933 IAIYELLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAIYELLFK 9 0 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3 P46783 RPS10 40S ribosomal protein S10 0 ; 152.59 0.00018634 243010000 762500 517440 578820 452390 948050 842400 782320 597630 675660 518820 FALSE TRUE 792604.0888 606306.2949 593904.5247 541871.3918 786900.7996 646765.3667 720999.7142 589619.7474 651343.1286 620472.8456 1.277419462 0.977168137 0.957180526 0.873320075 1.268227619 1.042374975 1.162016548 0.950274861 1.049752835 1 19.24300855 1.699091635 16.38103601 1.000214654 1.068894361 0.073949905 0.125173585 0.554689876 210.6230598 0.05833012 0.032235773 50.01400523 -1.699091635 0.068679708 MPGGPKPGGGPGLSTPGGHPKPPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 144.5 9.70E-08 493550000 261430 475110 571680 441440 665370 777200 569730 645820 597750 461830 FALSE TRUE 271751.4583 556706.4467 586578.4504 528755.5144 552270.6451 596707.0786 525073.0739 637163.8392 576237.0943 552316.7462 0.492021037 1.007947795 1.062032709 0.957341087 0.999916531 1.080371151 0.950673825 1.153620352 1.043309112 1 19.07513634 4.738357822 4.934457211 1.036339631 0.464186844 0.888138969 0.05712765 0.050820815 3.779008257 0.013922215 0.099647699 54746.68437 -4.738357822 -0.572152787 down IALLEEARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IALLEEARR 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 160.82 0.00010423 720370000 258254 357739 258349 193962 557290 421386 206942 255456 299251 695780 FALSE TRUE 268450.0673 419177.8904 265081.7872 232327.1047 462562.0449 323525.4877 190721.3453 252032.0302 288481.015 832104.7695 0.322615706 0.503756144 0.318567802 0.27920415 0.555893995 0.38880379 0.229203524 0.302884972 0.346688332 1 19.66640566 -1.361448999 3.810645909 1.002366578 0.358058301 0.803104428 0.09493297 72238353.38 99464098.68 1837858.931 0.02358323 0.043506185 1.361448999 -0.644308277 IANCIVHSTDKGPNSALVQQLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IANCIVHSTDKGPNSALVQQLIK 23 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 61.136 0.032957 346540000 58447 79541 107150 76021 125890 132310 98528 104400 125780 73184 FALSE TRUE 60754.53269 93201.54801 109942.417 91057.7269 104491.2628 101583.0077 90805.1179 103000.6888 121253.2024 87523.00361 0.694155024 1.064880593 1.256154525 1.04038622 1.193871993 1.160643528 1.037500019 1.176841339 1.385386668 1 16.41737463 4.710494847 3.341965504 1.155317597 0.646477259 0.619507457 0.108187944 0.174385196 3.280794089 0.024931033 0.218536871 51344.60855 -4.710494847 -0.508840339 IANDNSLNHEYLPILGLAEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IANDNSLNHEYLPILGLAEFR 21 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ;;; 217.82 5.66E-25 2198871000 599644 825650 830553 831611 1003771 962823 863424 890666 846952 855376 FALSE TRUE 623318.4081 967448.9648 852197.8935 996101.1737 833150.364 739221.95 795746.5707 878728.0791 816470.363 1022970.55 0.609321948 0.945725138 0.833062001 0.973733969 0.814442179 0.722622904 0.777878279 0.858996458 0.798136723 1 19.96433318 -1.20909805 3.550917688 1.000269689 0.822379265 0.237207344 0.098769013 4205651367 6161186079 12591588.87 0.022747209 0.061787689 1.20909805 -0.177890424 IANFVEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IANFVEHK 8 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 102.61 0.0049323 387090000 941350 765000 800120 729950 1331020 1219290 1014380 879710 936840 846380 FALSE TRUE 978515.2249 896382.7991 820971.7845 874331.9313 1104773.696 936128.376 934870.245 867918.9264 903123.3114 1012211.956 0.966709807 0.885568278 0.811067069 0.863783446 1.091445017 0.92483434 0.923591388 0.857447811 0.892227469 1 19.94907999 4.757610421 22.29630536 0.910883265 0.966710031 0.033179564 0.075449566 3514.83399 4113537.205 0.01864157 0.550620477 57228.24415 -4.757610421 0.055826766 IANPVEGSTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IANPVEGSTDR 11 0 F8VZX2;Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 0 ; 127.93 0.00064306 209080000 150162 169168 157220 147489 192086 216653 157792 172258 159676 163515 FALSE TRUE 156090.5117 198221.2881 161317.2824 176661.884 159435.2903 166338.6242 145423.8507 169949.1633 153929.292 195552.6336 0.798202043 1.013646733 0.824930247 0.903398133 0.815306281 0.850607947 0.743655803 0.869071207 0.787150186 1 17.57719744 3.241458363 24.96589478 0.833461087 0.889936323 0.044753381 0.082439704 172.6952133 1487860.358 0.021229714 0.027536928 1743.64618 -3.241458363 0.056475236 IAQLEEQLDNETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 245.69 9.32E-17 202290000 311120 219235 245890 205051 327720 351980 314220 267422 291850 182530 FALSE TRUE 323403.2578 256886.9058 252298.0954 245609.4758 272014.2715 270237.9793 289590.6153 263837.6455 281346.3755 218293.2588 1.481508223 1.176797247 1.155775936 1.125135413 1.24609561 1.237958427 1.326612727 1.20863854 1.288845918 1 17.73590805 -1.271785892 3.368523098 0.999150477 1.241538395 0.373125775 0.096578164 10509246.46 18626720.78 95619.52055 0.022450849 0.053482797 1.271785892 0.242387918 IAQLEEQLDNETKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IAQLEEQLDNETKER 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 259.98 6.36E-25 1038330000 480266 397973 481034 234309 814308 623830 291211 431598 557069 599731 FALSE TRUE 499227.2725 466321.7669 493570.1412 280654.6209 675892.217 478954.9367 268385.1209 425813.1348 537020.1955 717236.8069 0.696042461 0.650164301 0.688155065 0.391299802 0.942355733 0.667777967 0.374193179 0.593685559 0.748734853 1 19.45209 0.928348849 3.740200701 0.999584834 0.619958203 0.360342385 0.152045127 0.336675602 11.81344577 0.144956608 0.037255028 8.479082269 -0.928348849 -0.37962663 IAQNDHDLGDMSTVADPSVISHLFSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAQNDHDLGDMSTVADPSVISHLFSHR 27 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 66.925 0.0084131 271650000 58034 69679 75839 61986 78774 105290 85122 76711 71769 79325 FALSE TRUE 60325.22713 81645.82622 77815.42664 74246.64579 65384.02362 80837.99319 78449.91522 75682.81452 69186.04771 94867.21498 0.6358912 0.860632688 0.820256257 0.782637561 0.689216223 0.85211728 0.826944432 0.797776287 0.729293547 1 16.53362197 -1.942986119 2.701298068 1.151473843 0.784000383 0.480903134 0.069120142 12065177.54 6455589.061 11488827.15 0.016410952 0.011402862 1.942986119 -0.36747346 IAQVS(ph)PGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAQVSPGPR 9 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 IAQVS(1)PGPR 101.57 0.0040857 166470000 181000 319250 292870 304620 273970 323970 260140 271260 243840 304190 TRUE FALSE 188146.0198 374078.7041 300502.4328 364872.9268 227400.6773 248732.8773 239749.5471 267624.2034 235064.246 363790.2064 0.517182751 1.028281404 0.826032223 1.002976222 0.625087408 0.68372615 0.659032439 0.735655327 0.64615331 1 18.47274718 4.804108219 22.01008466 0.781951218 0.517169935 0.232065512 0.151316507 43229.12176 14512870.28 0.036336195 112.883125 63695.422 -4.804108219 -0.264781282 IAS(ph)DEEIQGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IASDEEIQGTK 11 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;A0A3B3ISX8 Q8WX93-8 PALLD Palladin 1 IAS(1)DEEIQGTK;IAS(1)DEEIQGTK;IAS(1)DEEIQGTK;IAS(1)DEEIQGTK 254.4 2.05E-20 1364220000 2347270 1291770 1834070 1331800 2637650 2785390 2843900 2065810 2231310 1153930 TRUE FALSE 2439942.032 1513621.449 1881867.371 1595226.065 2189303.195 2138525.385 2620987.687 2038121.196 2151005.589 1380020.49 1.768047684 1.096810852 1.36365176 1.155943753 1.586428035 1.549633068 1.89923824 1.476877489 1.558676559 1 20.39625826 3.212265946 24.90592409 1.559238458 1.329558852 0.06705565 0.267153774 388.0107172 367516.9154 0.072345807 0.086494684 1630.29406 -3.212265946 -0.229679606 IAS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IASPVSR 7 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 1 IAS(1)PVSR;IAS(1)PVSR 113.71 0.0074071 101590000 114486 122845 119828 129548 143659 144804 131392 115793 121406 128564 TRUE FALSE 119005.9957 143942.6731 122950.8161 155172.2077 119239.8945 111175.4655 121093.1517 114240.9842 117036.6218 153753.6543 0.77400434 0.936190257 0.799661099 1.009226145 0.775525597 0.723075273 0.787579016 0.743013132 0.761195708 1 17.23026117 IASLEVENQSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 230.61 5.21E-06 235680000 577610 298550 398090 314950 527200 480250 531920 388970 420550 262210 FALSE TRUE 600414.4888 349823.6401 408464.5524 377246.17 437586.7323 368719.2158 490226.7205 383756.4934 405414.4876 313585.0292 1.914678422 1.115562312 1.302563944 1.203010778 1.395432472 1.175818937 1.56329759 1.223771729 1.292837508 1 18.25849716 7.999999988 0.029141807 7.65E-13 3.207345421 0.249538778 0.213515913 2466.116485 5.51187832 195.8024267 463.6363132 99999997.15 -7.999999988 3.207345421 IATS(ph)LDGFDVASVQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IATSLDGFDVASVQQQR 17 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 1 IAT(0.043)S(0.957)LDGFDVASVQQQR 159.79 3.33E-09 52175000 59751 55064 62146 54818 77705 78871 75038 65663 68490 58034 TRUE FALSE 62110.01562 64520.81366 63765.57581 65660.83678 64496.73186 60554.40555 69156.32548 64782.89489 66025.05828 69404.65117 0.894897022 0.929632418 0.918750757 0.946058163 0.929285441 0.872483393 0.99642206 0.933408551 0.95130596 1 16.08274473 -4.999999262 0.0926205 1.239363188 0.873452672 0.424590219 0.028565485 195.3051165 1.251032714 9.029194725 0.589277024 1.00E-05 4.999999262 -0.365910516 IAVDEVHCCSQWGHDFRPDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAVDEVHCCSQWGHDFRPDYK 21 1 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 0 99.021 0.00053963 38154000 30254 35571 37755 32378 42521 52922 40889 37268 43189 30434 FALSE TRUE 31448.45128 41680.04255 38738.92632 38782.27176 35293.29561 40631.66754 37684.01334 36768.48342 41634.63633 36396.95961 0.864040613 1.145151765 1.064345119 1.065536028 0.969677028 1.116347848 1.035361573 1.010207551 1.143904238 1 15.15153032 4.755878628 24.62901398 1.057237078 0.864040421 0.517438546 0.056997222 2453.39949 3489060.757 0.012936163 0.397863972 57000.49515 -4.755878628 -0.193196656 IAVHCTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IAVHCTVR 8 0 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;; 83.265 0.018284 270970000 182610 263497 216570 241024 488702 383685 297183 258200 249395 494118 FALSE TRUE 189819.5838 308750.56 222213.9921 288697.8278 405632.6086 294579.9736 273889.0199 254739.2513 240419.3227 590930.9616 0.321221253 0.52248161 0.37604053 0.488547473 0.686429778 0.498501505 0.463487341 0.431081239 0.406848411 1 19.17263006 -1.130954108 4.157741094 1.000117677 0.470245901 0.746055958 0.093423312 38624351.65 104777062 74252.41888 0.022769018 0.073968343 1.130954108 -0.529871776 IAWALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IAWALSR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 119.56 0.011062 167300000 89852 89026 78156 85268 210790 140560 119030 88480 92715 271550 FALSE TRUE 93399.42634 104315.523 80192.80957 102133.7559 174959.9911 107917.0702 109700.1176 87294.07032 89378.20526 324755.0234 0.287599635 0.321212962 0.246933238 0.314494769 0.538744526 0.332303005 0.337793443 0.268799754 0.275217314 1 18.30899232 -1.249864283 3.339274598 1.002105309 0.325046498 0.873990444 0.07691464 16038058.7 23666613.4 346481.4727 0.019115098 0.056251708 1.249864283 -0.677058811 IAWTHITIPESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IAWTHITIPESLR 13 0 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 ; 138.89 4.38E-05 1297860000 1172770 1497490 1544500 1392710 1883030 1977580 1521190 1484080 1518410 1925330 FALSE TRUE 1219071.865 1754672.259 1584750.939 1668183.881 1562953.233 1518317.016 1401955.153 1464188.335 1463762.721 2302561.551 0.529441597 0.762052271 0.688255625 0.724490462 0.678788905 0.659403444 0.608867612 0.635895416 0.635710572 1 21.13480829 -1.54299558 2.884986284 1.016280264 0.660687454 0.741873153 0.060484896 9291188.237 10223723.42 1180979.125 0.01523379 0.028642071 1.54299558 -0.355592811 ICANHYITPMMELKPNAGSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ICANHYITPMMELKPNAGSDR 21 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JJ34;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ; 166.06 8.35E-12 5303400000 3481900 3443200 3979600 3251900 4609900 4801100 4156800 4132700 4209100 3466800 FALSE TRUE 3619368.101 4034542.816 4083311.645 3895116.114 3826310.845 3686117.286 3830979.154 4077307.916 4057615.313 4146053.084 0.872967139 0.973104476 0.984867189 0.939475698 0.922880331 0.889066592 0.924006296 0.98341913 0.978669407 1 21.98330716 1.684506998 5.284612129 0.986599936 0.931895053 0.404621946 0.032054381 0.17264343 10.97686195 0.017982385 0.00884738 48.36230567 -1.684506998 -0.054704883 ICDECNYGSYQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ICDECNYGSYQGR 13 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ; 207.88 1.17E-07 305670000 57346 70762 59996 64517 75435 84814 49001 62115 65305 74387 FALSE TRUE 59610.06436 82914.82305 61559.54505 77278.27004 62612.58564 65117.23387 45160.17358 61282.45002 62954.68581 88961.70842 0.670064294 0.932028223 0.691978 0.868668907 0.703815009 0.731969237 0.507636087 0.688863232 0.707660486 1 16.44089687 3.100012564 8.579750027 0.691375881 0.793584417 0.026197947 0.134656162 0.554084193 42.7482682 0.036448235 0.04362349 1258.961832 -3.100012564 0.102208536 ICDPGLTAFEPEALGNLVEGMDFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ICDPGLTAFEPEALGNLVEGMDFHR 25 0 E9PF82;E9PBG7;H0Y9C2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 0 ;; 162.65 1.45E-11 132463000 66921 84868 81817 77188 84987 107464 83899 83253 83843 90905 FALSE TRUE 69563.09275 99443.41882 83949.21823 92455.55602 70540.9401 82507.11463 77322.77715 82137.12971 80825.50681 108716.0943 0.639860117 0.914707427 0.772187585 0.850431177 0.648854621 0.758922726 0.71123579 0.755519505 0.743454843 1 16.73020601 -1.902203808 8.029668122 1.039685354 0.757952149 0.466937796 0.078469538 0.03966032 0.000483037 0.054052102 0.016830069 0.012525532 1.902203808 -0.281733206 ICDQISDAVLDAHLQQDPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ICDQISDAVLDAHLQQDPDAK 21 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;; 290.71 1.03E-54 404736000 391819 243918 324241 286086 422689 425328 476489 342535 371272 207850 FALSE TRUE 407288.3167 285809.0191 332690.9868 342672.9569 350840.4748 326552.0179 439140.5471 337943.8786 357909.9932 248574.228 1.638497764 1.14979345 1.338396943 1.378553842 1.411411302 1.31370022 1.766637478 1.359529028 1.439851573 1 17.9233172 -1.355365646 5.859505617 0.999930271 1.417493037 0.376559029 0.162742164 0.00014186 1.56E-05 0.150790279 0.035535706 0.044119883 1.355365646 0.417562766 ICDQWDALGSLTHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ICDQWDALGSLTHSR 15 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ; 266.71 2.43E-25 2967900000 1487270 2792800 1857960 2581800 2661100 3063100 2481400 2294800 1896350 3815500 FALSE TRUE 1545988.568 3272441.675 1906379.964 3092472.334 2208767.173 2351741.447 2286901.384 2264041.96 1828100.734 4563074.173 0.338804172 0.717157239 0.417784128 0.677716867 0.484052437 0.515385321 0.501175589 0.496165934 0.400629195 1 22.12157467 -1.490376355 4.305099573 1.003118689 0.512524635 0.64284707 0.110477774 0.002959021 0.000350279 0.095714326 0.022438369 0.032331336 1.490376355 -0.490594055 ICGDIHGQYTDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ICGDIHGQYTDLLR 14 0 P62140;E7ETD8;C9JP48;C9J9S3 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatase 0 ;; 164.65 4.09E-06 719190000 1309890 1456420 1401540 1358240 1748100 1879790 1556010 1470080 1456250 1555920 FALSE TRUE 1361605.469 1706548.806 1438065.284 1626895.818 1450958.586 1443237.261 1434045.87 1450375.982 1403839.847 1860772.734 0.73174195 0.917118342 0.772832306 0.874311939 0.779761311 0.775611785 0.770672229 0.779448213 0.754439175 1 20.82747043 -1.079613451 5.157167606 1.000003638 0.79700212 0.56712068 0.053680149 2.12E-06 3.79E-07 0.049122957 0.011578185 0.083250442 1.079613451 -0.203001519 ICGDIHGQYYDLLR ddPTM_MDA-MB-175_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 ;;;; 164.09 4.18E-06 2035490000 2658410 2893890 2744660 2645330 4008270 3789200 3094020 2903360 2870360 3626030 FALSE TRUE 2763366.08 3390893.096 2816188.094 3168568.378 3326945.697 2909215.726 2851502.628 2864445.208 2767056.304 4336481.154 0.637236963 0.78194577 0.64941781 0.730677309 0.76719939 0.670870142 0.657561402 0.660545983 0.638087935 1 22.04809341 -1.607517806 3.848559148 1.009587574 0.689401266 0.774586657 0.050461273 0.004201582 0.000428484 0.049452723 0.011389276 0.024687789 1.607517806 -0.320186308 ICHQIEYYFGDFNLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ICHQIEYYFGDFNLPR 16 0 P05455;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 0 ; 260.18 8.93E-27 3730900000 888900 978630 930180 1022780 1064140 991020 934300 1001230 980120 1012100 FALSE TRUE 923994.4584 1146702.09 954421.255 1225082.831 883257.8629 760870.6241 861067.1247 987810.1495 944845.6727 1210401.617 0.763378407 0.94737323 0.788516176 1.012129209 0.72972297 0.628610052 0.711389602 0.816101148 0.780605098 1 20.20705439 ICLTDHFKPLWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ICLTDHFKPLWAR 13 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 240.65 4.46E-17 1399700000 786080 724830 733630 686420 1223200 1015100 869440 812160 850550 995720 FALSE TRUE 817115.0454 849313.9141 752749.0005 822191.8272 1015280.901 779358.409 801291.0209 801274.3236 819938.8716 1190812.27 0.686182924 0.71322234 0.632130706 0.690446217 0.852595263 0.654476301 0.672894495 0.672880473 0.688554269 1 20.18351456 -0.894200616 4.389888497 1.000004184 0.695126742 0.722996196 0.056461501 3386213.002 1157093.004 133.3671903 0.01328159 0.127584931 0.894200616 -0.304877442 ICQGCPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ICQGCPHR 8 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;;; 98.299 0.0076207 184102000 139883 186507 205144 191143 209301 238882 214727 191074 193603 179069 FALSE TRUE 145405.6889 218538.1264 210490.2212 228950.5149 173724.0908 183405.2758 197896.1367 188512.9656 186635.2658 214154.1421 0.678976776 1.020471163 0.982891198 1.069092163 0.81121051 0.85641713 0.924082695 0.88026766 0.871499678 1 17.70829006 ICRDPQT(ph)PVLQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ICRDPQTPVLQTK 13 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK;ICRDPQT(1)PVLQTK 177.66 2.47E-05 1620230000 1831760 1369346 1495473 1174146 1708390 1784110 1432241 1333895 1468320 1426924 TRUE FALSE 1904079.299 1604520.523 1534446.255 1406388.574 1417998.478 1369777.491 1319978.208 1316016.319 1415475.45 1706502.438 1.115778833 0.940239221 0.899176128 0.82413511 0.830938443 0.802681239 0.773499163 0.771177521 0.829459964 1 20.70261104 5.134379581 0.868962313 0.812805359 1.50535144 0.640388707 0.063241409 2.195553666 0.805043294 0.019199951 1.700165533 136263.5128 -5.134379581 0.692546081 ICSWNVDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ICSWNVDGLR 10 0 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;H7C4A8;G3V5M0;G3V359;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 129.85 0.00067969 184165000 179590 204428 174172 160916 337620 266420 182770 164382 168868 360830 FALSE TRUE 186680.3519 239536.9188 178711.0654 192744.7045 280231.473 204547.9926 168444.0098 162178.7282 162790.4737 431527.73 0.432603374 0.555090443 0.414135762 0.44665659 0.649393894 0.474008919 0.39034342 0.375824581 0.377242208 1 18.71909374 -1.143387656 4.205106704 1.000131674 0.455840549 0.798546522 0.081778516 41589397.22 98491482.41 80242.30163 0.021162026 0.071880708 1.143387656 -0.544291125 ICTEQSNS(ph)PPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ICTEQSNSPPPIR 13 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 ICTEQS(0.001)NS(0.999)PPPIR 163.62 4.03E-05 68542000 131230 139750 136600 141740 136130 185690 151830 149130 132970 135700 TRUE FALSE 136411.0617 163750.9754 140159.9082 169775.7489 112990.6712 142566.3117 139929.1679 147131.1563 128184.4357 162287.8169 0.84055023 1.009015825 0.863650217 1.046139829 0.696236313 0.878478215 0.86222842 0.906606294 0.789858648 1 17.30819517 3.264978632 24.99997967 0.856297993 0.939338059 0.166189064 0.09246169 396.8285478 375525.3388 0.023781906 0.032191581 1840.681433 -3.264978632 0.083040066 ICYIFHETFGR ddPTM_MDA-MB-175_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 ; 164.43 2.28E-05 702700000 355390 771080 730540 785550 783620 903630 705790 779870 721330 857180 FALSE TRUE 369421.0716 903506.9918 749578.4725 940929.4454 650420.5523 693775.6271 650468.3356 769417.1183 695369.4742 1025128.009 0.360365797 0.881360165 0.731204753 0.917865317 0.634477398 0.676769751 0.63452401 0.750557112 0.678324529 1 19.96737264 -1.477689566 2.75332922 1.010660022 0.707394516 0.280862972 0.144855388 18632984 19833227.71 1514913.205 0.032794619 0.033289742 1.477689566 -0.303265506 IDADKDGFVTEGELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDADKDGFVTEGELK 15 1 O43852-2;O43852-4;O43852-8;O43852-7 O43852-2 CALU Calumenin 0 ; 124.29 8.90E-05 240410000 358770 150912 245721 190791 336560 358770 402150 233007 239545 119698 FALSE TRUE 372934.5166 176829.9621 252124.6911 228528.8903 279351.6514 275451.1047 370628.4322 229883.9223 230923.8222 143150.5313 2.605191285 1.235272831 1.761255713 1.596423626 1.951453821 1.924205954 2.589081778 1.60588941 1.61315379 1 17.1271735 3.21113663 24.88043009 1.857904768 1.756496692 0 0.492421104 1608.924678 1459694.021 0.136830137 0.163580402 1626.060239 -3.21113663 -0.101408076 IDAHLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDAHLNK 7 0 A0AVT1;A0AVT1-2;H0Y8S8 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 67.757 0.064296 83771000 55695 51042 58433 56347 81565 76474 68535 58953 63746 57146 FALSE TRUE 57893.88161 59808.06645 59955.81198 67492.26842 67700.61043 58714.07247 63163.04762 58162.83146 61451.79391 68342.66457 0.847111859 0.875120495 0.87728233 0.987556877 0.990605369 0.859113013 0.924211077 0.851047173 0.899171759 1 16.06049888 3.977433808 23.86811441 0.920128858 0.864887443 0.23960726 0.050263943 712.5396397 753652.815 0.013711327 0.024998984 9493.662926 -3.977433808 -0.055241415 IDASKNEEDEGHS(ph)NSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 IDASKNEEDEGHS(0.887)NS(0.288)S(0.824)PR;IDASKNEEDEGHS(0.999)NS(0.005)S(0.996)PR 114.57 0.00012192 1142540000 1158420 811890 1014840 636130 1369840 1342120 1019300 951480 1097610 707140 TRUE FALSE 1204155.316 951325.7919 1041287.564 761954.6153 1136995.086 1030432.97 939404.6026 938726.9669 1058107.231 845690.544 1.423872272 1.12491005 1.231286753 0.900985143 1.344457608 1.218451569 1.110813653 1.110012372 1.251175431 1 19.68977032 7.997966308 0.018621644 8.31E-06 2.637825576 0.169483677 0.13454275 7165.168026 10.28988352 551.5903126 957.6525428 99532819.72 -7.997966308 2.637817263 IDASKNEEDEGHSNS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHS(0.025)NS(0.869)S(0.106)PR;IDASKNEEDEGHS(0.005)NS(0.498)S(0.498)PR;IDASKNEEDEGHS(0.084)NS(0.458)S(0.458)PR;IDASKNEEDEGHSNS(0.676)S(0.324)PR;IDASKNEEDEGHS(0.002)NS(0.594)S(0.404)PR;IDASKNEEDEGHS(0.009)NS(0.591)S(0.4)PR;IDASKNEEDEGHSNS(0.733)S(0.267)PR 266.74 2.12E-31 32902721000 3917878 2915347 3681334 2375415 5145635 4925353 3822080 3535781 4055579 2666267 TRUE FALSE 4072558.849 3416035.169 3777272.588 2845264.997 4270981.801 3781514.41 3522495.382 3488389.639 3909619.504 3188670.97 1.277196326 1.07130375 1.184591519 0.892304356 1.339423804 1.185921798 1.104690768 1.093994856 1.226096873 1 21.60452381 -1.7139577 2.72396555 0.976057727 1.14422613 0.127960902 0.117780473 15605904.2 13560901.82 2557754.718 0.028766896 0.019321565 1.7139577 0.168168403 IDASKNEEDEGHSNSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IDASKNEEDEGHSNS(0.038)S(0.962)PR;IDASKNEEDEGHSNS(0.113)S(0.887)PR;IDASKNEEDEGHSNS(0.249)S(0.75)PR;IDASKNEEDEGHS(0.004)NS(0.293)S(0.703)PR;IDASKNEEDEGHSNS(0.109)S(0.891)PR;IDASKNEEDEGHSNS(0.248)S(0.752)PR 232.81 2.37E-21 41537270000 18173740 12612840 17306370 11502230 21513400 19878850 16793480 16214930 17476020 11031590 TRUE FALSE 18891253.29 14778997.16 17757388.22 13777336.76 17856559.95 15262288.35 15477163.16 15997595.39 16847061.45 13193018.85 1.431912855 1.12021345 1.345968533 1.044289933 1.353485518 1.156845793 1.173132801 1.212580348 1.276967891 1 23.65327139 -4.933593527 0.207461927 7.55E-16 1.259777658 0.285121242 0.112358206 178.0440547 1.817620738 74.51272164 0.222368302 1.17E-05 4.933593527 1.259777658 IDASKNEEDEGHSNSSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 238.94 4.04E-24 3411070000 4354070 3688690 4777800 3450810 6418100 5704000 4979900 4852500 4924600 3234460 FALSE TRUE 4525972.046 4322193.813 4902313.393 4133369.918 5327153.654 4379332.445 4589562.425 4787460.175 4747364.608 3868190.51 1.170048899 1.117368393 1.267340215 1.068553865 1.377169413 1.132139804 1.186488208 1.237648498 1.22728304 1 21.88322742 4.275803245 24.99967544 1.198052993 1.143708652 0.019821008 0.100581589 564.1981414 378717.6518 0.022059911 0.06041067 18871.36198 -4.275803245 -0.054344342 IDDDDDERENFEITDWDLQNEFNPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDDDDDERENFEITDWDLQNEFNPNR 26 1 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 ;;; 210.5 1.30E-25 211751000 86265.9 88354 104027 89168 113519 135624 117794 103996 108500 81692 FALSE TRUE 89671.74434 103528.1122 106738.0291 106805.1643 94223.08093 104127.3814 108560.9985 102602.1037 104595.1062 97697.98331 0.917846421 1.059675018 1.092530526 1.093217696 0.964432199 1.065808913 1.111189759 1.050196741 1.070596369 1 16.57604116 IDDIFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IDDIFER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;; 153.73 0.004017 1022896000 1037953 1194872 1133556 1114918 1347630 1554530 1319660 1168584 1184503 1114138 FALSE TRUE 1078932.186 1400081.971 1163097.401 1335445.453 1118560.334 1193513.967 1216221.601 1152921.043 1141872.968 1332432.01 0.809746522 1.050771793 0.872913133 1.002261611 0.839487738 0.895740989 0.912783236 0.865275702 0.856984041 1 20.34563049 3.227209777 24.99353359 0.88813275 0.937911733 0.056655181 0.073870353 494.9114869 1089749.67 0.019391385 0.023366989 1687.367876 -3.227209777 0.049778984 IDDIVSGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDDIVSGHK 9 0 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 186.78 4.13E-05 1097320000 1768130 1327270 1880600 1553580 2222590 2206980 2537720 1905940 2140320 934540 FALSE TRUE 1837937.138 1555218.298 1929609.981 1860873.487 1844794.946 1694442.342 2338806.875 1880393.992 2063290.301 1117645.22 1.644472776 1.391513398 1.726495981 1.664994806 1.65060872 1.516082484 2.092620121 1.68246055 1.846104886 1 20.09203087 IDDLQMVLNQTEDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDDLQMVLNQTEDHR 15 0 B7Z641;B7Z2A9;Q93050-1;Q93050;Q93050-3 B7Z641 ATP6V0A1 V-type proton ATPase subunit a;V-type proton ATPase 116 kDa subunit a isoform 1 0 91.969 0.0054235 53749000 43324 65877 54366 63139 74240 76145 65122 53360 65515 52526 FALSE TRUE 45034.46497 77190.8623 55782.82262 75627.70575 61620.71132 58461.47774 60017.56748 52644.79648 63157.12795 62817.46403 0.71690995 1.228812138 0.888014559 1.20392803 0.980948726 0.930656445 0.955428055 0.838059882 1.005407157 1 15.93887808 2.998324558 24.99315572 0.931427567 1.025918576 0.032129972 0.143814573 159.1053559 2373498.625 0.038685057 0.045613844 996.1495833 -2.998324558 0.09449101 IDDPTDSKPEDWDKPEHIPDPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDDPTDSKPEDWDKPEHIPDPDAK 24 2 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;; 147.41 1.07E-07 10712080000 12020190 2704918 4650110 2769020 8219900 8038340 8349540 4673850 5200280 1225082 FALSE TRUE 12494756.38 3169466.625 4771295.687 3316723.891 6822684.334 6171557.357 7695081.237 4611204.686 5013122.939 1465113.362 8.528184033 2.163291051 3.256605127 2.263800179 4.65676207 4.212341185 5.252208761 3.147336448 3.421662151 1 20.48258087 4.747648497 24.72546801 3.448770107 8.528187118 0.629865221 1.203174496 673.4362355 1832177.867 0.279561198 3.410149877 55930.4736 -4.747648497 5.079417011 IDDRDS(ph)DEEGASDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 IDDRDS(1)DEEGASDR;IDDRDS(1)DEEGASDR 203.06 1.07E-08 1896340000 1164360 1053710 1078470 1015770 1182970 1363040 1188380 1001100 919150 817370 TRUE FALSE 1210329.832 1234676.496 1106575.814 1216686.274 981889.1819 1046494.617 1095231.67 987681.892 886069.971 977518.002 1.238166284 1.263072898 1.132026021 1.244668918 1.004471713 1.070563013 1.120420972 1.01039765 0.90644875 1 19.89876375 3.348461685 0.437641133 0.967624444 1.308195473 0.691118876 0.064221659 0.979383826 0.326441968 0.057027376 0.154091065 2230.805388 -3.348461685 0.340571029 IDDVVNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDDVVNTR 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;; 141.2 0.0014829 654197000 433481 388168 484733 431000 513051 632025 507006 464050 460618 384424 FALSE TRUE 450595.1646 454832.8345 497365.5402 516250.5136 425842.7743 485246.7722 467265.5449 457830.1688 444040.4482 459744.5226 0.980099039 0.989316484 1.081830268 1.122907372 0.926259593 1.055470481 1.016359134 0.995836049 0.965841737 1 18.81047286 1.689895647 2.890671428 0.982682578 1.027140609 0.099592841 0.052392146 0.534491316 10.07289845 0.03311677 0.014571377 48.96611482 -1.689895647 0.044458031 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;IDEDGENTQIEDTEPMS(1)PVLNSK 264.44 3.83E-44 1059490000 696604 474896 631967 480486 808570 848160 754292 631627 751790 405543 TRUE FALSE 724106.4638 556455.6938 648436.5792 575524.6967 671129.5602 651187.694 695168.6221 623161.0732 724733.2248 485001.3863 1.492998751 1.147328048 1.336978816 1.186645467 1.383768334 1.342651201 1.433333268 1.28486452 1.494291038 1 18.88762935 -1.149980588 4.918336645 0.999977887 1.335225317 0.464969588 0.110522278 2.47E-05 4.27E-06 0.098731483 0.023269701 0.070797743 1.149980588 0.33524743 IDEDGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDEDGKK 7 1 O75821;K7ENA8;K7ER90;K7EL20;K7EL60 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 ; 84.568 0.034394 429040000 2394780 1009000 1244930 1056690 2850700 2610140 3394800 2260330 2629090 1054740 FALSE TRUE 2489327.764 1182287.901 1277373.899 1265700.128 2366139.032 2003974.542 3128706.705 2230033.974 2534469.564 1261396.109 1.973470305 0.937285198 1.01266675 1.003412108 1.875809681 1.588695675 2.480352273 1.767909349 2.009257478 1 20.26658996 3.229156466 24.88917683 1.858866974 1.1950325 0.263144623 0.443896562 201.8145231 534124.8456 0.121854222 0.147491708 1694.948339 -3.229156466 -0.663834473 IDEPLEGSEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IDEPLEGSEDR 11 0 P61978;P61978-2;S4R359;P61978-3 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 259.58 3.07E-20 7883550000 2173930 2161010 2288800 2228210 2483380 2845850 2732370 2316320 2255610 1700740 FALSE TRUE 2259758.435 2532146.657 2348448.008 2668943.287 2061255.955 2184944.467 2518199.7 2285273.519 2174431.037 2033967.44 1.111010132 1.244929789 1.154614357 1.312185846 1.013416397 1.074227848 1.238072768 1.123554622 1.069058921 1 20.95586515 3.232828702 24.99999068 1.10432798 1.204840321 0.334825546 0.080008452 188.4480404 821923.8727 0.022894298 0.028096523 1709.340971 -3.232828702 0.100512341 IDESIHLQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDESIHLQLR 10 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 182.28 1.79E-06 294310000 147857 345370 332580 315460 313190 410620 279010 339160 351520 533960 FALSE TRUE 153694.5085 404684.6109 341247.308 377857.0464 259954.0757 315259.728 257140.4671 334614.115 338868.8639 638579.2387 0.240681969 0.633726539 0.534385222 0.591715207 0.407081941 0.493689285 0.402675896 0.523997798 0.530660634 1 19.28450612 0.416422212 1.570693021 1.000024053 0.484421766 0.688078518 0.104712851 2.198828266 5.338516068 0.093797798 0.026844027 2.608688431 -0.416422212 -0.515602288 IDFDSVSSIMAS(ph)SQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.5)S(0.5)Q 67.93 0.053716 15346000 22124 20828 26026 23479 24041 30026 24531 23800 26424 25740 TRUE FALSE 22997.4726 24405.04698 26704.25894 28123.07612 19954.51941 23052.91655 22608.19612 23480.99993 25473.0054 30783.26018 0.747077225 0.792802544 0.867492877 0.91358342 0.648226318 0.748878332 0.734431506 0.762784702 0.827495374 1 14.90985841 -1.666275324 6.558114367 1.001419989 0.780775261 0.461270341 0.070483313 0.001519673 7.73E-05 0.070871321 0.016604658 0.021563769 1.666275324 -0.220644728 IDFDSVSSIMASS(ph)Q ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDFDSVSSIMASSQ 14 0 Q9UBQ5;A0A087WVB9;K7ERF1;K7EK53 Q9UBQ5 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 IDFDSVSSIMAS(0.041)S(0.959)Q;IDFDSVSSIMAS(0.169)S(0.831)Q 135.14 3.64E-05 34053000 39427 46377 44167 45081 59944 65471 47917 51324 48828 46724 TRUE FALSE 40983.6084 54341.88899 45318.0283 53997.88725 49754.74029 50266.35247 44161.14033 50636.08573 47070.68982 55878.67321 0.733439183 0.97249784 0.811007594 0.966341614 0.890406615 0.899562384 0.790304025 0.906179099 0.842373076 1 15.77001015 IDFIPVS(ph)PAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDFIPVSPAPSPTR 14 0 Q96E09 Q96E09 FAM122A Protein FAM122A 2 IDFIPVS(1)PAPS(0.893)PT(0.107)R;IDFIPVS(1)PAPS(0.984)PT(0.016)R 88.507 0.0095296 155401000 70704 68446 72295 61046 71784 79747 67515 60170 55853 58258 TRUE FALSE 73495.44852 80201.06806 74179.06709 73120.7166 59582.18132 61226.96783 62222.99788 59363.51957 53842.86144 69672.53968 1.054869664 1.151114462 1.064681544 1.04949119 0.855174529 0.878781915 0.893077792 0.852036108 0.772798892 1 16.08830253 3.313533914 3.861607828 0.867667999 1.091156714 0.749527724 0.058101644 0.100415476 2.925040183 0.015900223 0.021594052 2058.419627 -3.313533914 0.223488715 IDFSSIAVPGTS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGT(0.085)S(0.457)S(0.457)PR;IDFSSIAVPGT(0.088)S(0.456)S(0.456)PR 139.6 5.33E-06 757880000 1040220 997690 1049320 981870 1182470 1235810 1071060 1091450 1051870 1085580 TRUE FALSE 1081288.689 1169035.497 1076666.141 1176080.955 981474.1718 948811.8564 987107.5185 1076820.898 1014013.404 1298278.616 0.832863359 0.900450398 0.829302838 0.905877167 0.755981158 0.730822987 0.760320247 0.82942204 0.781044524 1 20.30816859 3.239151722 24.9999999 0.79625597 0.866802464 0.110631051 0.074333728 26.9997142 1141886.964 0.019680216 0.025109404 1734.409812 -3.239151722 0.070546494 IDFSSIAVPGTSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDFSSIAVPGTSSPR 15 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 IDFSSIAVPGTS(0.09)S(0.91)PR 192.4 5.62E-07 493240000 440300 460240 445600 449280 466810 552480 461560 450960 499220 475820 TRUE FALSE 457683.384 539282.6398 457212.7021 538146.243 387461.8029 424174.8929 425381.7211 444915.6188 481253.1697 569047.8189 0.804296878 0.947693009 0.803469738 0.945695995 0.680894979 0.745411684 0.747532469 0.781859809 0.84571657 1 19.11819037 6.683615656 6.698615931 0.818600712 0.784283344 0 0.09879911 0 0 0.021243813 0 4826314.912 -6.683615656 -0.034317368 IDFVGELNDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDFVGELNDK 10 0 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11;E9PJY4;E9PPD4;A6NEC2-3 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 129.16 0.00072253 57766000 108720 71805 94983 78973 134750 120890 106600 86290 96846 72925 FALSE TRUE 113012.3496 84136.95018 97458.33501 94593.62369 111845.2431 92815.12961 98244.41345 85133.42369 93360.53138 87213.25752 1.295816173 0.964726609 1.117471561 1.084624361 1.282433959 1.064231887 1.126484852 0.97615232 1.070485544 1 16.41225984 1.752332967 24.99995418 1.016733655 1.127725285 0.244939322 0.09464132 6.283757611 11422.73746 0.041662043 0.023103628 56.537027 -1.752332967 0.11099163 IDFYFDENPYFENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDFYFDENPYFENK 14 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;; 278.41 8.27E-33 2655360000 3383630 2162080 3125830 2419810 3974670 3851390 4084520 3122960 3571530 2116310 FALSE TRUE 3517218.325 2533400.421 3207291.698 2898441.196 3299057.013 2956963.041 3764364.649 3081101.829 3442991.333 2530960.425 1.38967733 1.000964059 1.267223172 1.145194198 1.303480284 1.168316585 1.487326555 1.21736468 1.360349731 1 21.27125352 3.231093957 24.92846812 1.275146893 1.191240249 0.020827728 0.15067043 459.9024011 1535446.284 0.039830204 0.048480283 1702.526799 -3.231093957 -0.083906644 IDGATQS(ph)SPAEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDGATQSSPAEPK 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 IDGATQS(0.968)S(0.032)PAEPK 193.51 1.90E-06 794090000 1341600 693080 1027700 734570 1349500 1369100 1219800 1058500 1113000 589220 TRUE FALSE 1394567.404 812111.0986 1054482.706 879865.7535 1120112.472 1051147.274 1124188.889 1044312.539 1072943.347 704666.3777 1.979046323 1.152476015 1.496428295 1.248627409 1.589564236 1.491694946 1.595349124 1.481995696 1.522625999 1 19.42658085 -1.129851797 5.164872914 0.999984199 1.493061888 0.346280216 0.208017524 3.41E-05 5.74E-06 0.181426106 0.042761174 0.074156326 1.129851797 0.493077689 IDGATQSS(ph)PAEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IDGATQSSPAEPK 13 0 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 IDGATQS(0.184)S(0.815)PAEPK;IDGATQS(0.018)S(0.982)PAEPK;IDGATQS(0.426)S(0.574)PAEPK;IDGATQS(0.449)S(0.551)PAEPK;IDGATQS(0.183)S(0.817)PAEPK 270.75 4.73E-32 2857830000 6893260 3868150 5066330 3613570 6827200 7129280 6622460 5047000 5655590 2943880 TRUE FALSE 7165411.228 4532474.672 5198362.722 4328323.361 5666714.983 5473612.765 6103374.281 4979353.22 5452046.421 3520676.922 2.035236799 1.287387276 1.476523645 1.229400895 1.609552682 1.554704645 1.733579768 1.414316999 1.548579021 1 21.74742141 -0.314056737 1.213047496 0.995248321 1.528352021 0.359036354 0.216826798 39.93693447 34.33014734 1.180603111 0.058920542 0.485225106 0.314056737 0.5331037 IDGDKDGFVTVDELKDWIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDGDKDGFVTVDELKDWIK 19 2 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 144.72 7.45E-08 392560000 905070 355370 526560 285990 968650 706740 747720 572410 628020 246500 FALSE TRUE 940802.8625 416402.0331 540282.5862 342557.9684 803999.219 542610.3457 689111.7526 564737.7802 605417.6829 294796.9555 3.191358815 1.412504523 1.832727836 1.16201325 2.727298244 1.840623981 2.337580968 1.915683896 2.05367685 1 18.1693621 4.751631902 24.28165355 1.873663925 3.191360091 0.405769441 0.496311585 1440.576201 2675990.826 0.111537423 2.027248088 56445.83496 -4.751631902 1.317696167 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDGVEQLNNILVIGMTNRPDLIDEALLRPGR 31 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ;; 261.86 6.62E-59 1472882000 356794 405527 408186 365932 451529 579204 513416 446241 443526 362505 FALSE TRUE 370880.5026 475173.1077 418823.6625 438312.2574 374778.2619 444692.6489 473173.1124 440259.8693 427563.5859 433530.9142 0.855488018 1.096053573 0.966075656 1.01102884 0.864478748 1.02574611 1.091440303 1.015521281 0.986235518 1 18.72577535 2.522369007 24.99104642 1.030081463 0.967137865 0.172415445 0.069538231 781.3426328 431546.9171 0.021710214 0.020467586 332.9423246 -2.522369007 -0.062943597 IDHILDAL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDHILDAL 8 0 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 80.462 0.059057 8329600 26786 37899 24262 41052 52564 59707 34138 30551 25703 73033 FALSE TRUE 27843.53196 44407.85844 24894.28765 49171.96307 43629.19006 45840.95412 31462.17436 30141.51382 24777.95405 87342.41805 0.318785907 0.50843404 0.285019447 0.562979182 0.499518917 0.524841825 0.360216434 0.34509594 0.283687521 1 16.41439485 -1.220237867 4.439559398 1.000201807 0.412488765 0.756375157 0.100470355 90.60712322 119950307.9 43690.93792 0.023723857 0.060222965 1.220237867 -0.587713042 IDHYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IDHYLGK 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 119.89 0.0046808 20212630000 7366080 6037100 7402280 6191720 9234080 8959320 8572130 6831180 7654330 5831250 FALSE TRUE 7656898.526 7073924.963 7595189.498 7416423.736 7664474.38 6878653.71 7900224.052 6739619.206 7378852.158 6973771.791 1.097956566 1.014361406 1.089107835 1.063473821 1.099042901 0.986360597 1.13284809 0.966423824 1.058086267 1 22.73350772 1.722157108 24.99999995 1.008944013 1.06545413 0.273064351 0.045231803 1.189259625 1805.270964 0.019007248 0.01054048 52.74206242 -1.722157108 0.056510117 IDIIPNPQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IDIIPNPQER 10 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 ;;;; 119.68 0.0015359 933754000 427078 462017 443250 448058 509360 571684 473195 479274 442604 444432 FALSE TRUE 443939.3692 541364.8258 454801.4591 536682.5351 422779.1691 438919.055 436104.7394 472850.116 426674.7685 531509.9412 0.835241893 1.018541299 0.85567818 1.009731885 0.795430407 0.825796511 0.820501567 0.889635507 0.802759714 1 19.01973715 3.227522043 24.99940819 0.849227678 0.930842815 0.178493121 0.077133978 313.5560599 710119.0893 0.020316976 0.024497585 1688.581563 -3.227522043 0.081615136 IDILDSALLRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 227.56 8.11E-12 2567700000 970230 976770 1147220 1042870 1305650 1354950 1289270 1174310 1098360 1064960 FALSE TRUE 1008535.43 1144522.649 1177117.496 1249146.573 1083716.079 1040283.397 1188213.649 1158570.295 1058830.238 1273618.522 0.791866177 0.898638509 0.924230824 0.980785496 0.850895351 0.816793552 0.932943128 0.909668221 0.831355873 1 20.28050179 -1.169323625 4.059573171 1.000047667 0.887679455 0.280742911 0.056024598 8077274.435 2326587.169 3387.267638 0.013137099 0.067713673 1.169323625 -0.112368213 IDIS(ph)PSTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.969)PS(0.031)T(0.001)FR;IDIS(0.973)PS(0.027)TFR;IDIS(0.641)PS(0.354)T(0.006)FR;IDIS(0.776)PS(0.202)T(0.021)FR;IDIS(0.999)PS(0.001)TFR;IDIS(0.978)PS(0.021)T(0.001)FR;IDIS(0.936)PS(0.064)TFR;IDIS(0.499)PS(0.499)T(0.003)FR;IDIS(0.984)PS(0.016)TFR;IDIS(0.848)PS(0.15)T(0.002)FR 183.08 4.78E-05 24448837000 4213327 4273175 4592832 4337476 5198280 5429132 5205625 4771692 4404792 4112119 TRUE FALSE 4379672.403 5007059.566 4712524.975 5195415.807 4314678.222 4168298.372 4797594.51 4707735.274 4246264.396 4917809.987 0.890573734 1.018148237 0.958256823 1.056449074 0.877357652 0.847592401 0.975555079 0.957282873 0.86344621 1 22.22958456 3.219234234 24.99815035 0.921265232 0.981906381 0.192810986 0.060756467 403.7776635 522274.0229 0.017448919 0.020884406 1656.663233 -3.219234234 0.060641148 IDIS(ph)PSTFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDISPSTFRK 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.99)PS(0.01)TFRK;IDIS(0.425)PS(0.242)T(0.333)FRK;IDIS(0.5)PS(0.5)T(0.001)FRK;IDIS(0.846)PS(0.153)T(0.001)FRK 138.89 3.22E-05 1480640000 3492600 3191130 3440340 2053150 4995960 4024070 2334540 3208900 3562500 3812350 TRUE FALSE 3630490.545 3739181.754 3529998.087 2459256.942 4146748.504 3089540.728 2151552.655 3165889.944 3434286.321 4559306.991 0.796281223 0.820120637 0.774240053 0.539392707 0.909512896 0.677633845 0.47190344 0.694379639 0.75324744 1 22.12038312 0.828406226 4.026551185 0.99997123 0.704443068 0.33001832 0.122839829 1.574538031 35.53590812 0.120257941 0.030718836 6.736064334 -0.828406226 -0.295528162 IDIS(ph)PSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.731)PS(0.268)T(0.002)LR;IDIS(0.991)PS(0.008)TLR;IDIS(0.995)PS(0.005)TLR;IDIS(0.997)PS(0.003)TLR;IDIS(0.964)PS(0.034)T(0.002)LR;IDIS(0.748)PS(0.249)T(0.003)LR;IDIS(0.871)PS(0.127)T(0.002)LR 185.99 4.43E-05 31417208000 2167517 2217384 2342835 2198429 2574036 2762133 2471531 2313355 2254377 1961116 TRUE FALSE 2253092.245 2598202.453 2403891.205 2633271.695 2136502.28 2120669.471 2277805.942 2282348.26 2173242.412 2345359.132 0.960659804 1.107805801 1.02495655 1.122758412 0.910948882 0.904198185 0.97119708 0.973133807 0.926613917 1 21.16137742 3.228620828 24.99954368 0.947822902 1.055807438 0.52238327 0.04981286 152.6670512 383972.1966 0.013766668 0.016636803 1692.859159 -3.228620828 0.107984536 IDIS(ph)PSTLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.966)PS(0.034)TLRK;IDIS(0.95)PS(0.049)T(0.002)LRK;IDIS(0.998)PS(0.002)TLRK;IDIS(0.979)PS(0.02)T(0.001)LRK;IDIS(0.886)PS(0.097)T(0.017)LRK;IDIS(0.984)PS(0.011)T(0.005)LRK 147.73 1.62E-05 6187790000 8611170 6970010 7984480 5496860 11003420 9522380 7259480 7508940 8642910 7576780 TRUE FALSE 8951145.641 8167054.998 8192562.108 6584122.502 9133062.599 7310951.558 6690462.988 7408294.941 8331853.357 9061304.975 0.987842884 0.901311127 0.904126076 0.726619678 1.007919127 0.806832082 0.738355348 0.817574837 0.919498172 1 23.11128741 IDISPS(ph)TFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 IDIS(0.148)PS(0.848)T(0.004)FR;IDIS(0.456)PS(0.541)T(0.003)FR;IDIS(0.201)PS(0.798)T(0.001)FR 161.51 6.76E-05 16639410000 5768460 6009400 5981550 6475950 7208120 7900210 7319090 6640290 6236600 5956000 TRUE FALSE 5996203.255 7041467.703 6137434.107 7756873.581 5982886.337 6065505.956 6745400.601 6551287.774 6012145.984 7122964.165 0.841812919 0.988558631 0.861640458 1.088995171 0.839943344 0.851542394 0.946993477 0.919741785 0.844051134 1 22.7640463 IDISPS(ph)TLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.437)PS(0.527)T(0.036)LR;IDIS(0.084)PS(0.594)T(0.322)LR 159.94 6.89E-05 9102200000 1172130 1250720 1196280 1207530 1417350 1441370 1293510 1291370 1219710 1070390 TRUE FALSE 1218406.597 1465521.431 1227456.04 1446375.83 1176429.353 1106633.662 1192121.306 1274061.297 1175812.875 1280112.427 0.951796555 1.144838063 0.958865811 1.129881876 0.919004713 0.864481618 0.931262975 0.99527297 0.918523132 1 20.28783909 3.215316261 24.99931136 0.937963371 1.047132226 0.376422542 0.068255812 233.0800395 250677.0237 0.01880564 0.022489503 1641.784915 -3.215316261 0.109168855 IDKDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDKDKR 6 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 83.843 0.031793 2072460000 6223500 3522100 5026300 3412900 6857000 5761800 6359800 5061000 5610400 3535200 FALSE TRUE 6469208.586 4126993.277 5157289.507 4087961.434 5691449.589 4423709.271 5861302.258 4993165.573 5408482.8 4227854.755 1.530139743 0.97614358 1.219836018 0.966911512 1.346179072 1.046324798 1.386353742 1.181016346 1.279249907 1 22.01149438 2.262777682 24.99928163 1.227541549 1.171167105 0.002019829 0.184128818 1162.377874 1199918.982 0.058669286 0.049061778 183.1376688 -2.262777682 -0.056374444 IDKEACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDKEACR 7 1 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 96.711 0.011429 382010000 569810 463740 536380 468360 818350 748440 612580 550150 648660 612830 FALSE TRUE 592306.5388 543383.7376 550358.5034 561000.2101 679247.1593 574626.1527 564564.3789 542776.1391 625314.8533 732902.3052 0.808165747 0.741413601 0.750930239 0.765450192 0.926790862 0.78404195 0.77031328 0.740584571 0.853203556 1 19.48326138 0.937550118 5.236559606 0.999962886 0.784681381 0.616998075 0.05129103 0.239650512 17.84421615 0.051428612 0.012981586 8.660642626 -0.937550118 -0.215281506 IDKELINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IDKELINR 8 1 P23381;P23381-2;G3V277;G3V5U1;G3V3Y5;G3V3H8;G3V456;G3V423;G3V3P2;G3V227;G3V3X0;G3V2Y7 P23381 WARS "Tryptophan--tRNA ligase, cytoplasmic;T1-TrpRS;T2-TrpRS" 0 ;;;;; 123.21 0.001238 2118900000 2729930 2449810 2759340 2450950 3728480 3680280 3249220 3118200 3238500 2630990 FALSE TRUE 2837709.744 2870545.811 2831250.667 2935740.595 3094714.301 2825590.745 2994537.646 3076405.629 3121947.018 3146482.117 0.901867431 0.912303234 0.899814638 0.93302313 0.983547399 0.898015828 0.95170973 0.977728624 0.992202371 1 21.58530831 2.432485043 0.335232899 1.008986899 0.888804077 0.644504921 0.023228132 1.119135801 0.291972452 0.030245615 0.04832628 270.6979975 -2.432485043 -0.120182822 IDKLMIEMDGTENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDKLMIEMDGTENK 14 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 95.236 0.0035096 455850000 430060 279570 332490 274700 493790 426540 437360 334550 426490 234850 FALSE TRUE 447039.1009 327583.9727 341154.9625 329034.8401 409855.7522 327482.5493 403078.5804 330065.9045 411140.7082 280864.361 1.591654773 1.166342257 1.214660918 1.17150798 1.459265785 1.165981145 1.435136088 1.17517902 1.46384079 1 18.09951405 -1.265759239 4.697097283 0.99989327 1.299975445 0.275054734 0.151901087 0.000153419 2.40E-05 0.132907275 0.031315446 0.054230144 1.265759239 0.300082175 IDKTDYMVGSYGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IDKTDYMVGSYGPR 14 1 P52565;J3KTF8;J3QQX2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;; 145.69 7.76E-06 8089280000 3667189 3339467 3596400 3205398 5174370 4706470 4544410 3582348 3935040 3084780 FALSE TRUE 3811972.453 3912994.48 3690125.138 3839416.157 4294832.436 3613463.67 4188207.27 3534332.485 3793418.679 3689183.579 1.033283482 1.060666783 1.000255222 1.040722446 1.164168804 0.979475158 1.1352667 0.958025647 1.028254246 1 21.81487015 1.684570977 13.33061913 0.995221195 1.057153349 0.219401765 0.054939446 0.188481505 40.52438411 0.024260167 0.013325095 48.36943078 -1.684570977 0.061932153 IDKVNEIVETNRPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDKVNEIVETNRPDSK 16 2 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 140.81 9.36E-07 1562400000 1261200 590310 919340 575880 1325400 1211900 1177300 849060 1022600 524080 FALSE TRUE 1310993.15 691691.1505 943298.7556 689787.3452 1100108.981 930454.5915 1085020.15 837679.7395 985796.8258 626763.4419 2.091687329 1.103592048 1.505031552 1.10055453 1.755221999 1.48453871 1.731147794 1.336516592 1.57283715 1 19.25756151 -1.365817508 3.138911425 0.994914269 1.498064866 0.226099778 0.286074916 219161532.9 285242000.8 10180872.81 0.062679972 0.043070756 1.365817508 0.503150597 IDLENTLEQEQEALVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDLENTLEQEQEALVNR 17 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 198.74 3.24E-11 8536900 4946.9 5712.6 4720.3 4266.3 6792.2 6522.4 5010 5048.6 7123 6412.7 FALSE TRUE 5142.207432 6693.694612 4843.314896 5110.161406 5637.66427 5007.671448 4617.303109 4980.931775 6866.644621 7669.145786 0.670505891 0.872808367 0.631532511 0.666327326 0.735109806 0.652963392 0.602062242 0.649476736 0.895359772 1 12.90485018 1.096325821 4.066743207 0.995720169 0.684025795 0.691988501 0.071539779 0.112303102 3.201316218 0.07048508 0.018136124 12.4831969 -1.096325821 -0.311694374 IDLEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDLEVR 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 106.76 0.074087 56436000 72170 80971 84924 85932 93683 108690 87369 91235 86158 84551 FALSE TRUE 75019.32733 94877.13938 87137.18921 102929.0931 77758.79712 83448.39471 80520.78948 90012.14406 83057.19041 101117.1496 0.741905083 0.938289298 0.861744912 1.01791925 0.768997123 0.825264508 0.796311899 0.890176833 0.821395685 1 16.62566818 -1.112991515 4.751565083 1.00000878 0.856059411 0.245584975 0.077773648 6.88E-06 1.28E-06 0.071600834 0.016875449 0.077091853 1.112991515 -0.143949369 IDLGERPVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDLGERPVVQR 11 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 0 ; 127.87 0.00025326 430970000 120918 151798 151092 142485 163238 176915 143983 145191 135047 164710 FALSE TRUE 125691.936 177868.1257 155029.5816 170668.1077 135490.8631 135829.1724 132697.2362 143244.9521 130186.6848 196981.7709 0.638089177 0.902967441 0.787025017 0.866415745 0.687834526 0.689551991 0.673652367 0.727199027 0.660907272 1 17.5877026 3.226186866 24.99756807 0.7197938 0.805248908 0.042721848 0.112990162 460.0148288 929324.2367 0.029864826 0.035931641 1683.39823 -3.226186866 0.085455108 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDLGVHVDGFIANVAHTFVVDVAQGTQVTGR 31 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 107.45 7.61E-05 20588000 3312.3 4046.3 2952 3278.2 3204.6 3895 3976 4097.9 3240.8 3903.4 FALSE TRUE 3443.072162 4741.220549 3028.931545 3926.618176 2659.883237 2990.445279 3664.350731 4042.974353 3124.164241 4668.196495 0.737559391 1.015642884 0.648844055 0.841142437 0.569788191 0.640599701 0.784960688 0.866067733 0.669244374 1 12.18864957 -0.211286811 9.026635868 1.000002281 0.760560444 0.2596244 0.124667769 0 0 0.119793577 0.028235617 0.614770739 0.211286811 -0.239441837 IDLMPHDLITQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDLMPHDLITQLLR 14 0 F2Z2B9;Q9BSJ2-3;Q9BSJ2;Q9BSJ2-4;B3KTU7 F2Z2B9 TUBGCP2 Gamma-tubulin complex component 2 0 108.89 0.00079924 58239000 98148 89473 112130 116810 147500 145730 161950 118690 137900 104350 FALSE TRUE 102022.9588 104839.2917 115052.1999 139914.6694 122428.0027 111886.4161 149255.9358 117099.1547 132937.0059 124795.3846 0.817521891 0.840089496 0.921926723 1.121152596 0.981029892 0.896558927 1.196005255 0.93832921 1.065239763 1 16.92920505 4.030538529 3.722938508 1.023949784 0.831434547 0.488793355 0.082222161 0.177990078 5.313109048 0.020229433 0.045801184 10728.48823 -4.030538529 -0.192515237 IDLNLDIS(ph)PQRPRPTLQLPLANDGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDLNLDISPQRPRPTLQLPLANDGGSR 27 2 O14733;O14733-4;O14733-2 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 IDLNLDIS(1)PQRPRPTLQLPLANDGGSR 108.07 0.00089566 129190000 92146 74592 81882 87754 95893 121380 92043 93472 76010 82486 TRUE FALSE 95783.99523 87402.59575 84015.91219 105111.4793 79593.14211 93191.33453 84828.42915 92219.16073 73274.41495 98647.55241 0.970971838 0.886008762 0.851677615 1.065525466 0.806843557 0.944689779 0.85991418 0.934834757 0.742789995 1 16.58999564 IDLPEVQIEHDPELEKES(ph)PGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDLPEVQIEHDPELEKESPGLK 22 1 Q14966;Q14966-3;Q14966-5 Q14966 ZNF638 Zinc finger protein 638 1 IDLPEVQIEHDPELEKES(1)PGLK;IDLPEVQIEHDPELEKES(1)PGLK 176.71 2.89E-14 191988000 727920 236980 364290 218530 573280 634310 554880 389020 432760 192894 TRUE FALSE 756658.8437 277679.4716 373783.6967 261754.5818 475834.0704 487001.1156 511387.0557 383805.8232 417185.0521 230687.8861 3.280011172 1.203702007 1.620300498 1.134669818 2.062674718 2.11108231 2.216791979 1.663745027 1.808439356 1 17.81558272 4.750178031 24.4638007 1.702279271 3.280012449 0.59055811 0.405605693 964.2829841 2030523.069 0.09734858 1.541098453 56257.18943 -4.750178031 1.577733178 IDNSQVESGSLEDDWDFLPPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;; 239.15 2.25E-30 1602125000 2651639 1808094 2207214 1826486 3132040 2942460 2687299 2162683 2567132 1556930 FALSE TRUE 2756327.755 2118620.079 2264735.81 2187759.479 2599656.96 2259118.258 2476661.482 2133695.772 2474741.421 1861980.624 1.480320321 1.137831432 1.216304714 1.174963612 1.396178309 1.213287737 1.330122049 1.145928021 1.329090855 1 20.82840663 -3.517239786 0.381673109 5.01E-14 1.264786737 0.353108994 0.10806918 187.9934768 4.218443784 150.9245841 0.067181702 0.000303921 3.517239786 1.264786737 IDPWSFVSAGPRPS(ph)PLPS(ph)PQPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 2 IDPWS(0.001)FVS(0.001)AGPRPS(0.999)PLPS(1)PQPAPR;IDPWS(0.001)FVS(0.001)AGPRPS(0.998)PLPS(1)PQPAPR;IDPWS(0.001)FVS(0.001)AGPRPS(0.998)PLPS(1)PQPAPR;IDPWS(0.001)FVS(0.001)AGPRPS(0.999)PLPS(1)PQPAPR 109.77 0.0011879 525058000 768718 759372 780759 772385 840350 991791 772523 778025 775809 712106 TRUE FALSE 799067.5802 889788.2339 801106.2209 925160.4477 697507.6072 761462.571 711970.6286 767596.8475 747887.7856 851629.5366 0.938280726 1.044806686 0.940674538 1.086341429 0.819027027 0.894124192 0.836009788 0.901327179 0.878184414 1 19.69986646 3.231813685 24.99998611 0.881248849 1.001127957 0.454414152 0.061132532 125.0686028 463427.0319 0.015962852 0.019485623 1705.350625 -3.231813685 0.119879108 IDPWSFVSAGPRPSPLPS(ph)PQPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDPWSFVSAGPRPSPLPSPQPAPR 24 1 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 IDPWSFVSAGPRPS(0.003)PLPS(0.997)PQPAPR;IDPWSFVSAGPRPS(0.005)PLPS(0.995)PQPAPR 140.55 1.78E-07 556880000 335380 280460 282760 288660 345870 401360 328080 333610 296200 339120 TRUE FALSE 348621.0614 328626.8233 290128.9579 345756.0864 287079.1409 308150.2227 302364.2323 329138.5036 285539.8199 405564.0712 0.859595527 0.810295701 0.715371451 0.852531353 0.707851512 0.759806513 0.745539987 0.811557352 0.704056005 1 18.62957032 -1.511264873 5.814272005 1.000324284 0.774802114 0.605385516 0.054720233 0.000215044 1.81E-05 0.049532558 0.011658369 0.030813081 1.511264873 -0.22552217 IDQLEGDHQLIQEALIFDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDQLEGDHQLIQEALIFDNK 20 0 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 ; 284.07 5.96E-45 311960000 1100620 824780 853090 876470 1278600 1278250 1527320 995510 992160 933230 FALSE TRUE 1144073.327 966429.5491 875322.2262 1049833.15 1061264.029 981395.8096 1407604.667 982166.8168 956452.3554 1116078.551 1.02508316 0.86591535 0.78428371 0.9406445 0.950886502 0.879325034 1.261205734 0.880015852 0.856975842 1 20.09000714 2.982179078 1.808684241 0.984758365 0.892470318 0.076547267 0.120731446 0.872742218 5.768989635 0.042894287 0.050020933 959.7963153 -2.982179078 -0.092288046 IDRAETLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDRAETLGR 9 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 96.171 0.0068843 100160000 24310 29081 28578 29993 41333 42682 29183 24547 29375 39668 FALSE TRUE 25269.77757 34075.43553 29322.76616 35925.52588 34307.23142 32769.75235 26895.5602 24217.98762 28317.79949 47440.18511 0.532666083 0.718282095 0.618099742 0.757280474 0.723168161 0.690759369 0.566936241 0.510495217 0.596915873 1 15.53382202 -0.964688903 4.282559557 1.000012945 0.632723389 0.647878235 0.080720729 8053511.783 5642623.732 892.3191496 0.021082847 0.108470364 0.964688903 -0.367289556 IDRDS(ph)YSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.849)YS(0.151)PR 85.402 0.039037 640460000 586920 705710 705210 632500 719390 818120 693260 680380 721220 725090 TRUE FALSE 610092.0548 826910.2028 723588.3519 757606.6122 597108.3448 628124.0287 638920.4697 671260.619 695263.4331 867157.5028 0.703553914 0.953587094 0.834437054 0.873666675 0.688581189 0.72434826 0.736798641 0.774093076 0.801772955 1 19.72593453 5.812560196 12.39112922 0.799672829 0.596355228 0 0.101178112 0 0 0.021535836 0 649471.6466 -5.812560196 -0.203317601 IDRDSYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDRDSYSPR 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 IDRDS(0.131)YS(0.869)PR 97.594 0.017324 650070000 593890 680260 686530 625030 795070 844580 708700 728720 729250 714420 TRUE FALSE 617337.2358 797089.3633 704421.5358 748659.0685 659924.2854 648439.0947 653150.2422 718952.7003 703004.435 854396.9206 0.722541504 0.932926306 0.82446638 0.876242705 0.772386077 0.758943623 0.764457627 0.84147389 0.822807782 1 19.70454692 0.333278619 1.538963655 1.000017901 0.813971529 0.478864027 0.058661143 5.060889141 10.71337808 0.055303063 0.015845602 2.154163284 -0.333278619 -0.186046372 IDRLDGAHAPELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDRLDGAHAPELTK 14 1 O76003 O76003 GLRX3 Glutaredoxin-3 0 106.52 0.0005628 320330000 773770 581090 708430 568230 906480 886910 812070 750170 767490 564340 FALSE TRUE 804319.0371 680887.6872 726892.2678 680624.198 752396.8534 680938.5938 748417.8314 740115.1982 739868.1848 674911.6181 1.191739801 1.008854595 1.077018454 1.00846419 1.114807974 1.008930022 1.108912354 1.096610546 1.096244553 1 19.36433906 IDRLTDEGAVHVNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDRLTDEGAVHVNDR 15 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 95.654 0.0024046 48590000 22877 28378 30867 24073 37252 42356 21500 26063 29089 41032 FALSE TRUE 23780.20162 33251.70075 31671.41938 28834.56755 30919.91835 32519.46091 19814.77382 25713.66812 28042.09257 49071.43479 0.484603756 0.67761827 0.645414578 0.587603922 0.630100148 0.662696354 0.403794466 0.524004815 0.571454507 1 15.58259583 -2.016918972 2.484165053 1.468771195 0.574472483 0.708361624 0.081538718 5054192.2 2169854.78 13513257.75 0.021109887 0.009617917 2.016918972 -0.894298712 IDRPEAISEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IDRPEAISEER 11 1 Q9Y6B6;D6RD69;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ;;; 213.99 5.88E-10 4572600000 3398450 3863970 3793190 3800150 4473680 4988140 4366690 3911730 4078380 3505010 FALSE TRUE 3532623.43 4527576.79 3892043.648 4551808.328 3713245.472 3829720.081 4024417.428 3859299.658 3931599.9 4191749.602 0.842756311 1.080116233 0.928500988 1.085897002 0.885846204 0.913632837 0.960080589 0.920689455 0.937937681 1 21.99912111 IDRTDAISEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDRTDAISEEK 11 1 Q9NR31;Q9NR31-2;H0Y5E8 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;; 174.89 9.55E-06 673995000 1166760 815610 1112400 853210 1455410 1535570 1290870 1045870 1233650 769940 FALSE TRUE 1212824.586 955684.6729 1141390.058 1021972.391 1208019.928 1178957.139 1189688.236 1031851.823 1189251.177 920795.0016 1.317149402 1.037890813 1.239570215 1.109880472 1.311931457 1.280368744 1.292022909 1.120609714 1.291548255 1 19.81252048 -1.164049188 3.968933029 0.999896819 1.21450323 0.333278678 0.093751913 4.418373468 23592301.18 4685.622331 0.02087759 0.068541059 1.164049188 0.214606412 IDRVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDRVETR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 135.83 0.0027717 942230000 598110 607350 698140 637670 758190 849750 713810 669040 674280 662960 FALSE TRUE 621723.8446 711657.638 716334.1019 763799.2227 629313.1346 652408.4406 657859.707 660072.6131 650012.7945 792854.3189 0.784158993 0.897589407 0.903487671 0.963353802 0.793731105 0.822860423 0.829735919 0.832526982 0.819838877 1 19.59669628 4.754907285 23.07542693 0.864668436 0.784158811 0.134562462 0.064565639 2373.128658 3349812.472 0.015306274 0.363993844 56873.15029 -4.754907285 -0.080509626 IDS(ph)LSAQLSQLQK ddPTM_MDA-MB-175_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(0.883)LS(0.117)AQLSQLQK;IDS(0.988)LS(0.012)AQLSQLQK 287.42 4.17E-33 126979000 498090 282770 385920 323130 479890 478870 493140 402440 415310 229050 TRUE FALSE 517754.9778 331333.5479 395977.3922 387044.1496 398318.4692 367659.6998 454486.3982 397045.9501 400363.0742 273927.9621 1.890113641 1.209564534 1.445553018 1.412941368 1.454099341 1.342176597 1.659145692 1.449453889 1.461563366 1 18.06343702 0.446501251 2.822691356 1.000001164 1.471751317 0.408055167 0.173382853 19.77632037 99.1978969 0.151649989 0.039871319 2.795768781 -0.446501251 0.471750153 IDS(ph)PGFKPASQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDSPGFKPASQQK 13 1 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK;IDS(1)PGFKPASQQK 207.92 3.03E-08 3129910000 9386560 3448990 5439700 3303550 8983030 8035740 8360740 5682970 7024640 2644290 TRUE FALSE 9757148.637 4041327.203 5581463.051 3956982.33 7456097.769 6169561.168 7705403.352 5606799.083 6771824.579 3162387.998 3.085373662 1.277935284 1.764952009 1.251264024 2.357742875 1.950918474 2.436577472 1.772963687 2.141364242 1 21.59258295 IDS(ph)PGFKPASQQVYR ddPTM_MDA-MB-175_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 178.23 4.36E-07 3196572000 3280877 1779729 2344751 1687334 3380084 3320827 3067294 2400729 2644427 1440472 TRUE FALSE 3410408.557 2085383.611 2405857.137 2021083.629 2805538.529 2549615.257 2826871.481 2368551.155 2549254.589 1722704.909 1.979682382 1.210528629 1.396557893 1.173203616 1.628565934 1.480006961 1.640949339 1.374902424 1.479797599 1 20.71624417 -0.099134385 1.238346771 0.997937516 1.471317885 0.302383286 0.22000359 22.7243478 23.74661574 0.40390231 0.05930496 0.79591303 0.099134385 0.473380369 IDS(ph)TEVIYQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.934)T(0.066)EVIYQPR;IDS(0.994)T(0.006)EVIYQPR;IDS(0.919)T(0.081)EVIYQPR 196.38 6.36E-08 984640000 515350 455310 565480 428890 672210 754750 607580 509080 526140 423530 TRUE FALSE 535696.4159 533505.9507 580216.8733 513723.1619 557947.9843 579470.7508 559956.292 502256.6153 507204.3242 506512.5945 1.057617168 1.053292567 1.14551322 1.014235712 1.101548096 1.144040162 1.105513067 0.991597486 1.001365671 1 18.95023862 1.712646025 6.591874855 0.99784326 1.089343818 0.542791439 0.038257948 0.10194417 10.77818378 0.01948009 0.010052588 51.59956319 -1.712646025 0.091500559 IDSDDALNHDFFWSDPMPSDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDSDDALNHDFFWSDPMPSDLK 22 0 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 0 ; 177.47 4.83E-17 93608000 107320 80917 105619 77286 134197 134342 123096 105478 113347 75298 FALSE TRUE 111557.0765 94813.8653 108371.5179 92572.94012 111386.2419 103143.1065 113447.4139 104064.2399 109267.6636 90051.20143 1.238818302 1.052888399 1.203443332 1.028003388 1.236921219 1.145382903 1.259810109 1.155611899 1.213394845 1 16.4584579 IDSEGGVSANHTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDSEGGVSANHTSR 14 0 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7EPL9;E7ER27 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 148.85 1.78E-06 0 15559 84886 62063 91589 70232 115560 48348 68365 61034 87648 FALSE TRUE 16173.28133 99464.51018 63680.41277 109705.0308 58293.98973 88722.94133 44558.35743 67448.679 58837.39826 104820.9475 0.154294363 0.948899171 0.607516096 1.046594535 0.556129201 0.846423768 0.425090199 0.643465649 0.56131336 1 16.67756753 -2.439955544 2.039526743 3.715335146 0.656140033 0.158267108 0.245178077 7502787.546 595316.037 94058093.04 0.055686368 0.003631152 2.439955544 -3.059195113 IDSIEDRYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDSIEDRYPR 10 1 Q13158 Q13158 FADD FAS-associated death domain protein 0 ; 202.56 2.02E-07 651360000 373660 459720 432500 352900 539190 551470 379490 457180 424120 481090 FALSE TRUE 388412.3853 538673.3339 443771.3053 422702.5667 447538.6764 423399.4501 349744.5822 451052.2499 408856.004 575350.3745 0.675088438 0.936252687 0.77130619 0.734687219 0.77785415 0.735898452 0.607881037 0.783960991 0.710620905 1 19.13408126 -1.191585126 3.611294426 1.000283806 0.750788137 0.467663568 0.0805595 25208588.83 38734032.17 84392.08661 0.019143632 0.064330196 1.191585126 -0.249495669 IDST(ph)EVIYQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDSTEVIYQPR 11 0 K7EMR0;K7EQN8;K7EP59;Q15831-2;Q15831 K7EMR0 STK11 Serine/threonine-protein kinase STK11 1 IDS(0.301)T(0.699)EVIYQPR;IDS(0.311)T(0.689)EVIYQPR;IDS(0.22)T(0.78)EVIYQPR 255.41 2.05E-19 1470860000 582602 507463 567672 440737 708710 827960 640568 597360 563007 428519 TRUE FALSE 605603.5768 594615.8227 582465.9987 527913.4631 588243.7273 635678.8379 590358.6063 589353.3663 542744.488 512479.0936 1.181713721 1.160273327 1.136565386 1.030117072 1.147839463 1.240399552 1.151966224 1.1500047 1.059056837 1 18.96713363 1.078639469 3.026146652 1.001007672 1.149433185 0.508802034 0.048937306 0.19722137 3.612929127 0.049383174 0.013122055 11.98503947 -1.078639469 0.148425513 IDTGWLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDTGWLDR 8 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 122.52 0.0032269 670200000 648330 659680 696770 743740 817290 863480 713670 686890 700140 660640 FALSE TRUE 673926.569 772974.9084 714928.3986 890849.5522 678367.3377 662949.8562 657730.6806 677683.3631 674942.0982 790079.7593 0.852985488 0.978350476 0.904881299 1.127543823 0.858606147 0.839092317 0.832486433 0.857740443 0.854270838 1 19.59163878 IDTHNIIVNQLVFPDPEKPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IDTHNIIVNQLVFPDPEKPCK 21 1 O43681 O43681 ASNA1 ATPase ASNA1 0 ; 219.34 3.06E-25 433580000 995150 607230 771800 611820 1057310 1016170 1048770 850140 903250 540210 FALSE TRUE 1034439.29 711517.0289 791913.742 732836.1699 877588.8239 780179.9177 966564.6669 838745.2638 870742.2089 646053.8066 1.601165847 1.101327818 1.225770569 1.134326835 1.358383489 1.207608267 1.496105521 1.298259147 1.347785897 1 19.3012948 IDTHPS(ph)PSHSSTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDTHPSPSHSSTVK 14 0 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594;B7ZBA0 Q8NI27 THOC2 THO complex subunit 2 1 IDTHPS(0.5)PS(0.5)HSSTVK;IDT(0.004)HPS(0.855)PS(0.139)HS(0.001)S(0.001)TVK;IDT(0.002)HPS(0.739)PS(0.205)HS(0.013)S(0.017)T(0.024)VK 106.28 0.0011268 368290000 98711 327101 398640 359047 414960 487200 401680 409630 396280 284107 TRUE FALSE 102608.1865 383278.0523 409028.8859 430065.425 344425.2474 374055.1836 370195.272 404139.5799 382017.9602 339772.3271 0.301991005 1.128043757 1.203832253 1.265745885 1.01369423 1.100899496 1.089539208 1.189442305 1.12433512 1 18.37420883 4.738480865 8.453806956 1.133796003 0.296873853 0.908889811 0.078018566 0.022544079 24.81213077 0.018391261 0.108025334 54762.19718 -4.738480865 -0.836922151 IDTIEIITDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 238.32 7.80E-12 2735543000 2053960 1950794 2210753 2369602 2343279 2666980 2631596 2321746 2164705 1651071 FALSE TRUE 2135051.927 2285827.694 2268367.039 2838302.203 1944969.273 2047614.313 2425324.629 2290626.792 2086797.69 1974566.751 1.081276146 1.157635058 1.14879228 1.437430364 0.985010647 1.036994223 1.228281915 1.160065514 1.05683826 1 20.91310471 1.097789673 3.566036575 1.002332942 1.15805932 0.166929834 0.115627135 0.375081585 8.74824141 0.109455425 0.028567619 12.52534431 -1.097789673 0.155726378 IDVDAPDIDIHGPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 143.14 1.44E-06 306960000 406910 265290 298650 244110 437290 463770 406060 339440 372890 247730 FALSE TRUE 422975.121 310851.4938 306433.0643 292394.2294 362959.602 356066.446 374231.9562 334890.362 359469.7617 296267.9504 1.427677615 1.049224168 1.034310542 0.986924941 1.225105859 1.201839232 1.263153695 1.130363111 1.213326522 1 18.17654304 IDVPANRYDLLCLEGLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDVPANRYDLLCLEGLVR 18 1 Q9NSD9 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 107.98 0.00053016 0 114380 126540 123950 140670 163070 214850 155090 132960 148660 149640 FALSE TRUE 118895.8107 148272.2607 127180.2388 168494.1061 135351.4196 164954.3436 142933.6405 131177.8887 143309.7556 178959.093 0.664374236 0.828525995 0.710666537 0.941523023 0.756326026 0.921743293 0.798694485 0.733004881 0.800796167 1 17.44927032 -2.436788463 2.004896555 2.532396913 0.796008394 0.35644143 0.082599166 3303099.656 293931.9321 22919710.23 0.019682125 0.003657729 2.436788463 -1.736388519 IDWPVGSPATIHYPALDGHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDWPVGSPATIHYPALDGHLSR 22 0 O15498;O15498-2 O15498 YKT6 Synaptobrevin homolog YKT6 0 83.245 0.0020083 154600000 15453 19662 20953 17623 30443 26705 25551 15272 20046 26939 FALSE TRUE 16063.09637 23038.79555 21499.05239 21108.7768 25268.30973 20503.16847 23548.24585 15067.30382 19324.54838 32217.18127 0.498587888 0.715108977 0.667316368 0.655202472 0.784311623 0.63640479 0.730921978 0.467679146 0.599821201 1 14.97554266 -2.047258723 2.548695062 1.476900002 0.638610788 0.573364117 0.093292494 6753558.973 2269852.35 18794401.43 0.024300528 0.008968943 2.047258723 -0.838289214 IDYANLTGISVSSLSDSLFVLHVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IDYANLTGISVSSLSDSLFVLHVQR 25 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ;; 310.16 1.81E-74 149941000 75620.6 90803.3 102971 106211 101630.6 133593.7 102510.4 97120.2 94861.8 80258.5 FALSE TRUE 78606.15968 106398.0604 105654.5089 127219.2188 84355.46691 102568.5878 94475.36699 95818.46258 91447.74235 95983.61643 0.818953928 1.108502309 1.100755658 1.325426396 0.878852767 1.06860516 0.984286387 0.998279354 0.952743247 1 16.55050055 IDYIAGLDS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 1 IDYIAGLDS(1)R 84.605 0.015532 20356000 36990 38043 40200 35764 54738 45214 47298 42084 41053 34809 TRUE FALSE 38450.39376 44576.58932 41247.64502 42838.01246 45433.65431 34713.73372 43590.65917 41519.93282 39575.51055 41629.15709 0.923640939 1.070802112 0.99083546 1.02903867 1.091390205 0.833880293 1.047118467 0.997376255 0.950668073 1 15.34530673 IDYIAGLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDYIAGLDSR 10 0 H3BQB1;P07741-2;P07741;H3BQF1 H3BQB1 APRT Adenine phosphoribosyltransferase 0 140.83 8.98E-05 319180000 225990 251600 243440 211970 367030 311540 269100 240760 241010 251580 FALSE TRUE 234912.2597 294810.3428 249784.2464 253897.0333 304642.3717 239189.5564 248007.2388 237533.006 232336.0972 300872.2842 0.780770686 0.979852111 0.830200253 0.843869797 1.012530524 0.794987006 0.824294067 0.78948118 0.772208373 1 18.19879169 IDYLLPGPGPAHS(ph)PQPSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IDYLLPGPGPAHSPQPSKR 19 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3;A0A0J9YYG8 Q8TDM6-4 DLG5 Disks large homolog 5 1 IDYLLPGPGPAHS(1)PQPSKR 126.04 1.23E-05 402990000 609070 482350 603820 512450 732290 797480 644740 641730 642620 469510 TRUE FALSE 633116.5539 565189.8603 619556.0452 613811.0805 607815.6074 612277.3559 594203.5941 633128.659 619492.2317 561501.4952 1.127542062 1.006568754 1.103391621 1.093160189 1.082482616 1.090428719 1.058240448 1.127563621 1.103277974 1 19.09893034 IECDDKGDGSCDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IECDDKGDGSCDVR 14 1 Q60FE5;P21333-2;P21333;A0A087WWY3;Q14315-2;Q14315 Q60FE5;Q14315-2 FLNA;FLNC Filamin-A;Filamin-C 0 ;;; 92.457 0.0045154 1149910000 2476720 2251830 1882200 1423540 3622740 3203320 1961780 1959250 2022320 2804590 FALSE TRUE 2574502.818 2638564.286 1931251.678 1705111.963 3006947.949 2459397.477 1808010.557 1932989.458 1949537.098 3354095.713 0.767569872 0.786669347 0.575789078 0.508367116 0.89650034 0.733252026 0.539045606 0.576307185 0.581240747 1 21.67749243 2.277617425 24.98465727 0.628576173 0.707807714 0 0.159434181 522.4744299 334225.0923 0.054332966 0.045457569 189.5035825 -2.277617425 0.079231541 IEDFGLHFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEDFGLHFVR 10 0 Q9BT40;C9JZB0;Q9BT40-2 Q9BT40 INPP5K Inositol polyphosphate 5-phosphatase K 0 98.943 0.0050328 141310000 148280 160470 165680 160770 208570 221270 179520 167010 160710 201750 FALSE TRUE 154134.2089 188029.4742 169997.7569 192569.8261 173117.3459 169883.3959 165448.7533 164771.5041 154926.0785 241279.0498 0.638821352 0.779302946 0.704569075 0.798120791 0.717498457 0.704095097 0.685715372 0.682908459 0.642103318 1 17.88034313 -1.174162995 5.111424135 1.000017528 0.708300978 0.767318277 0.04856905 9.60E-06 1.55E-06 0.046545453 0.01097021 0.066963324 1.174162995 -0.29171655 IEDFLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IEDFLER 7 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;;; 196.98 0.0010068 6400100000 4220570 4060670 4555590 4237200 5178330 5490270 5303690 4907940 4798030 4101720 FALSE TRUE 4387201.363 4758058.485 4674312.418 5075305.513 4298119.316 4215237.998 4887972.919 4842157.092 4625349.838 4905373.502 0.894366425 0.969968644 0.952896332 1.034642013 0.876206331 0.859310305 0.996452751 0.987112824 0.942914915 1 22.22593156 IEDFLERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEDFLERR 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ;;; 174.02 0.00043991 905570000 732452 869103 901044 541769 1229380 1058826 563230 830429 910764 1249423 FALSE TRUE 761369.7705 1018364.68 924525.9469 648929.2912 1020410.427 812929.7082 519082.5609 819298.4576 877985.7815 1494223.515 0.509542088 0.681534368 0.618733367 0.434291981 0.682903472 0.544048263 0.347392847 0.54831051 0.587586645 1 20.51096454 0.713414536 3.353317169 0.999985439 0.544647953 0.65714827 0.097816312 2.01134929 22.86914379 0.09532394 0.024668102 5.169095266 -0.713414536 -0.455337487 IEDTVFHVFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEDTVFHVFDK 11 0 Q9Y2L1;G3V1J5;Q9Y2L1-2 Q9Y2L1 DIS3 Exosome complex exonuclease RRP44 0 141.73 3.80E-05 113630000 516690 366760 512380 424620 646420 616030 627060 502810 505110 325770 FALSE TRUE 537089.3202 429748.177 525733.0437 508608.5686 536541.7593 472966.3685 577909.3987 496070.6544 486931.1898 389598.3943 1.378571699 1.103054282 1.349423025 1.305468852 1.377166249 1.213984389 1.483346459 1.273287215 1.249828534 1 18.57162821 -0.073585261 9.107270264 1.000001087 1.304436851 0.459984167 0.098746121 0 0 0.089199606 0.021024549 0.844140503 0.073585261 0.304435764 IEDVGS(ph)DEEDDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IEDVGSDEEDDSGK 14 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK;IEDVGS(1)DEEDDSGK 401.82 2.34E-132 45546050000 24736490 9750340 13941390 13404720 17979010 21259290 26760360 15147680 16233930 5865357 TRUE FALSE 25713105.73 11424885.05 14304714.08 16056133.61 14922944.3 16322142.09 24662813.06 14944650.13 15649674.03 7014561.405 3.665675477 1.628738333 2.039288453 2.288971851 2.127423718 2.326894177 3.515945137 2.130518113 2.231026735 1 22.74192147 2.466006536 24.99402429 2.40997325 2.283080291 0 0.757941053 2164.526158 4867405.442 0.250426015 0.209712601 292.4196388 -2.466006536 -0.126892959 IEDVGS(ph)DEEDDSGKDK ddPTM_MDA-MB-175_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(0.998)DEEDDS(0.002)GKDK;IEDVGS(0.998)DEEDDS(0.002)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.993)DEEDDS(0.007)GKDK;IEDVGS(0.998)DEEDDS(0.002)GKDK 292.38 3.81E-45 1.36752E+11 43152270 9530620 15770010 10187890 25473610 31926040 30263380 15567320 19141290 5185813 TRUE FALSE 44855954.94 11167429.85 16180989.42 12203024.23 21143614.87 24511701.05 27891257.2 15358665.54 18452398.71 6201873.769 7.232645586 1.800654167 2.609048494 1.967635055 3.409230123 3.952305701 4.497230714 2.476455683 2.975294145 1 22.56427273 4.747435551 24.80209561 2.880551966 7.232648092 0.646550736 0.991154123 675.5042551 1887734.341 0.237320602 2.853412466 55903.05611 -4.747435551 4.352096126 IEDVGS(ph)DEEDDSGKDKK ddPTM_MDA-MB-175_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(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.933)DEEDDS(0.067)GKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(1)DEEDDSGKDKK;IEDVGS(0.994)DEEDDS(0.006)GKDKK 283.73 2.06E-36 2.88178E+11 43495041 6567306.5 13206236 6912970 22781834 27360656 26370654 13636463 16479718 3475444 TRUE FALSE 45212258.8 7695190.305 13550401.36 8280334.833 18909385.99 21006558.3 24303653.23 13453688.52 15886616.17 4156390.71 10.87776919 1.851411679 3.260136571 1.992193566 4.549472682 5.05403841 5.847297554 3.236868104 3.822214338 1 21.98689985 4.747112049 24.9773272 3.604701654 10.87777288 0.706113383 1.441611163 618.3161287 1805959.645 0.34615529 4.057436754 55861.42993 -4.747112049 7.273071229 IEDVGS(ph)DEEDDSGKDKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.999)DEEDDS(0.001)GKDKKK 200.35 8.42E-15 1274150000 3916600 582780 1180340 342880 2867400 2290650 1408950 986620 1524610 392360 TRUE FALSE 4071230.392 682867.9316 1211100.63 410700.6406 2380000.372 1758681.253 1298512.817 973395.9727 1469739.584 469235.4298 8.676306463 1.455277859 2.581008494 0.875254967 5.072081563 3.747972001 2.767294912 2.07442983 3.13220079 1 18.83995242 4.745258629 24.98141146 2.609702776 8.676309247 0.695700736 1.219684303 436.5006405 1627963.606 0.288412649 2.814664434 55623.54049 -4.745258629 6.066606471 IEDVTPIPSDST(ph)RR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 IEDVTPIPS(0.001)DS(0.366)T(0.632)RR;IEDVTPIPS(0.002)DS(0.348)T(0.65)RR 136.66 1.51E-05 300440000 166500 206915 239730 179485 232990 272320 278950 219381 280120 210825 TRUE FALSE 173073.5486 242451.0417 245977.5607 214986.5973 193386.443 209077.807 257085.1701 216440.5565 270038.5359 252132.1223 0.686439899 0.961603145 0.975589935 0.852674365 0.767004384 0.829239072 1.019644652 0.858441021 1.071019962 1 17.94382041 1.581814256 1.149837478 1.020309778 0.859446008 0.300018084 0.097315749 0.634887513 1.603369942 0.086098402 0.031285933 38.17809515 -1.581814256 -0.160863771 IEDVTPIPSDSTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 ;;;;; 253.72 4.96E-24 8101610000 2408930 2846090 2753740 2370710 3337630 3117660 2472310 2696680 2734700 2967010 FALSE TRUE 2504036.416 3334883.818 2825504.727 2839629.362 2770300.845 2393630.714 2278523.882 2660535.415 2636278.681 3548338.803 0.705692595 0.939843686 0.796289442 0.800270076 0.780731773 0.674577837 0.642138197 0.749797458 0.742961377 1 21.75871234 5.044234453 15.95620483 0.77541495 0.351571418 0.037799048 0.104017955 11630635.55 113571860 0.024636762 147226889.4 110722.1353 -5.044234453 -0.423843533 IEEACEIYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IEEACEIYAR 10 0 P54920;M0R0Y2;M0R2M1 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;; 174.41 7.25E-06 644000000 398550 418640 402120 382080 534240 537940 446660 453050 457050 404160 FALSE TRUE 414285.0617 490538.1634 412599.5775 457654.2836 443430.0756 413011.5876 411649.6221 446977.6058 440600.8598 483347.4139 0.857116537 1.014876979 0.85362943 0.946843348 0.917414809 0.85448184 0.851664062 0.924754313 0.91156143 1 18.882701 0.541784618 1.761112297 0.999949519 0.903551797 0.255659238 0.049626432 3.753316846 12.83487703 0.045220318 0.012709319 3.481646053 -0.541784618 -0.096397721 IEEAMDGSET(ph)PQLFTVLPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IEEAMDGSETPQLFTVLPEKR 21 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 IEEAMDGS(0.001)ET(0.999)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR;IEEAMDGS(0.003)ET(0.997)PQLFTVLPEKR;IEEAMDGS(0.003)ET(0.997)PQLFTVLPEKR;IEEAMDGSET(1)PQLFTVLPEKR 198.55 4.98E-22 1332110000 1441860 1322229 1499939 1237022 2021210 1739760 1259656 1386730 1345626 1472830 TRUE FALSE 1498785.746 1549311.545 1539028.643 1481701.259 1677645.446 1335727.106 1160920.871 1368143.153 1297197.183 1761402.839 0.850904582 0.879589558 0.873751653 0.841205218 0.952448474 0.758331414 0.659088793 0.776734953 0.736456848 1 20.74829347 2.712378997 24.12038873 0.762350342 0.877124715 0.20045956 0.087007287 580.2669871 534582.6212 0.026092928 0.024609667 515.6784671 -2.712378997 0.114774373 IEEDFPHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IEEDFPHIR 9 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 0 ;; 146.69 9.42E-05 356429000 371775 430070 449450 411813 493160 516250 443980 434760 428068 393588 FALSE TRUE 386452.9641 503931.177 461163.0362 493268.3823 409332.8394 396358.7613 409179.6875 428932.7533 412661.9163 470704.0329 0.821010523 1.070590311 0.97973037 1.047937446 0.869618297 0.842055163 0.869292929 0.911257868 0.876690845 1 18.84446069 3.222091448 24.99940567 0.887767464 0.986294767 0.237074848 0.073687512 286.0585367 434222.212 0.02005914 0.024040018 1667.598318 -3.222091448 0.098527303 IEEDNLTYQHLLPES(ph)PEPSASHALSDYETSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEEDNLTYQHLLPESPEPSASHALSDYETSEK 32 0 Q5JTU8;B1AMJ5;A0A0A0MRG9;Q96SN8-3;Q96SN8-2;Q96SN8;Q96SN8-4 Q5JTU8 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 IEEDNLTYQHLLPES(0.998)PEPS(0.001)ASHALSDYETSEK;IEEDNLTYQHLLPES(0.937)PEPS(0.032)AS(0.032)HALSDYETSEK 154.54 2.20E-10 230360000 67653 71028 91989 77917 117363 124914 104148 105014 110716 94405 TRUE FALSE 70323.99268 83226.50648 94386.30891 93328.75004 97413.67918 95904.61659 95984.60762 103606.4591 106731.3528 112901.8523 0.622877227 0.737158025 0.836003192 0.826636128 0.86281737 0.849451224 0.850159725 0.917668373 0.94534634 1 16.78470963 6.431678592 0.246925664 0.970605837 3.67E-26 0.889330063 0.033453731 7.936937115 0.209564893 0.048537187 2.721356727 2701957.99 -6.431678592 -0.970605837 IEEEEQEPEPPEPFEYIDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;;;; 210.14 4.43E-16 2422280000 5672460 6412700 6787460 6134220 7831560 8277010 7197500 6827910 7042420 6061300 FALSE TRUE 5896413.101 7514031.341 6964346.784 7347550.407 6500354.229 6354799.867 6633341.143 6736393.035 6788964.68 7248895.684 0.813422259 1.036576007 0.960745897 1.013609621 0.896737174 0.876657652 0.915082991 0.92929921 0.936551576 1 22.7893298 3.210395672 24.98677476 0.919796185 0.962170316 0.044813989 0.062871935 500.9238801 444397.8134 0.017270973 0.020646649 1623.288351 -3.210395672 0.042374131 IEEELGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 127.02 0.0027782 1224010000 1432250 892860 1225980 1015940 1773060 1556810 1422520 1226600 1333380 953600 FALSE TRUE 1488796.336 1046201.76 1257930.046 1216889.9 1471675.895 1195264.471 1311019.165 1210159.433 1285391.914 1140439.662 1.305458224 0.917367042 1.103022008 1.067035758 1.290446083 1.048073397 1.149573457 1.061134116 1.127102079 1 20.12115869 -1.412253003 4.527888442 0.999756963 1.111410452 0.094035003 0.108463152 0.000243349 3.16E-05 0.096038365 0.022587331 0.038703211 1.412253003 0.111653489 IEEGERPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEEGERPDR 9 1 Q5JR04;Q9HCE1;Q9HCE1-2 Q5JR04 MOV10 Putative helicase MOV-10 0 ; 107.24 0.0025582 418220000 314540 366770 397330 348460 449750 488100 396180 403540 364620 373730 FALSE TRUE 326958.2821 429759.8944 407684.7462 417384.348 373301.6556 374746.1722 365126.3764 398131.2064 351497.3974 446955.238 0.731523549 0.961527817 0.912137752 0.933839258 0.835210383 0.838442288 0.816919336 0.89076304 0.786426397 1 18.76977083 3.21470634 24.9775954 0.85427333 0.892196518 0.012818171 0.078698612 746.8956902 782065.6995 0.021372584 0.025558644 1639.480818 -3.21470634 0.037923187 IEEIKDFLLTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEEIKDFLLTAR 12 1 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 ; 186.51 1.06E-05 733200000 792270 1984240 1832740 1950110 2123310 2513600 1768090 2179600 1990500 2035150 FALSE TRUE 823549.4314 2325017.785 1880502.71 2335835.938 1762390.525 1929854.494 1629502.486 2150386.027 1918862.294 2433898.677 0.338366358 0.955264821 0.772629825 0.959709605 0.724101846 0.792906669 0.669503008 0.883515015 0.788390376 1 21.21483768 3.433892489 0.041260559 1.52672539 2.02E-24 0.213791016 0.161581584 398.031251 4.274007333 65.34366917 93.16007055 2715.766888 -3.433892489 -1.52672539 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(ph)DDEEDLNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEEPVSMEMDNHMSDKDESCYDNAEAAFSDDEEDLNSK 38 1 Q68E01-2;Q68E01-3;Q68E01;Q68E01-4 Q68E01-2 INTS3 Integrator complex subunit 3 1 IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK;IEEPVSMEMDNHMSDKDESCYDNAEAAFS(1)DDEEDLNSK 225.8 8.87E-40 325668000 106768 149746 178608 151171 257524 234693 196085 196312 215590 130357 TRUE FALSE 110983.2831 175463.7106 183262.6712 181072.1726 213750.1625 180189.1076 180715.3453 193680.7587 207830.958 155897.9583 0.711896963 1.125503583 1.175529643 1.161478794 1.371090198 1.155814415 1.159189942 1.242355967 1.333121744 1 17.25024251 4.951472765 1.710973634 1.213880968 0.291460267 0.686867561 0.097962142 0.916272855 1.691810362 0.023913646 1.637236878 89427.84501 -4.951472765 -0.922420702 IEEVPELPLVVEDKVEGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEEVPELPLVVEDKVEGYK 19 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 77.221 0.0053291 0 116550 63311 102740 85060 155900 128660 144290 98632 109420 78378 FALSE TRUE 121151.484 74184.17176 105417.4888 101884.6141 129400.1737 98780.66486 132980.1728 97309.99937 105481.9956 93734.66846 1.292493866 0.791427259 1.124637133 1.086946973 1.38049428 1.053832765 1.418687183 1.038143101 1.125325318 1 16.51629512 5.062016799 21.37272513 1.125325068 4.829518468 0.086210203 0.171041508 13803478.62 39286972.64 0.039420361 2382866115 115349.7875 -5.062016799 3.7041934 IEFYELDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEFYELDKK 9 1 O15305;H3BV55;H3BPH4 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 102.52 0.0057253 1276820000 1444520 667780 994490 660260 1588080 1278440 1341970 998550 1242550 654560 FALSE TRUE 1501550.765 782466.0204 1020407.226 790857.4573 1318138.729 981541.6849 1236782.885 985166.0705 1197830.868 782808.4997 1.918158484 0.999562499 1.303520883 1.010282154 1.683858478 1.253872033 1.579930322 1.25850201 1.530171004 1 19.5782999 -1.436540896 3.009840479 0.992544607 1.371689449 0.14995194 0.27658481 32408179.57 36453038.52 2034603.439 0.060054354 0.036598148 1.436540896 0.379144842 IEGDMIVCAAYAHELPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEGDMIVCAAYAHELPK 17 0 P46777;A0A2R8Y6J3;A0A2R8Y4A2;Q5T7N0 P46777 RPL5 60S ribosomal protein L5 0 ; 221.49 3.67E-15 455390000 744470 500890 693970 534810 858360 870170 884190 702480 810940 429190 FALSE TRUE 773862.2505 586913.9611 712055.4283 640593.8218 712456.2738 668086.2051 814884.8774 693064.4046 781754.4278 513281.5632 1.507675915 1.143454204 1.387260871 1.248035908 1.388041817 1.301597901 1.587598184 1.350261639 1.523051837 1 18.96939091 IEGVYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEGVYAR 7 0 C9K025;P18077;F8WBS5;F8WB72 C9K025 RPL35A 60S ribosomal protein L35a 0 ; 124.89 0.0095448 813880000 470120 520110 553020 524160 705180 651280 608330 577380 506800 548590 FALSE TRUE 488680.7006 609434.8466 567432.1555 627837.2835 585313.7555 500030.0902 560647.505 569641.1655 488560.367 656075.7071 0.744854131 0.928909332 0.864888228 0.95695859 0.892143619 0.762153033 0.854546966 0.868255232 0.744670717 1 19.32350278 IEGYEDQVLITEHGDLGNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEGYEDQVLITEHGDLGNGK 20 0 P47755;F8W9N7;C9JUG7;A0A0D9SET8;P47755-2 P47755 CAPZA2 F-actin-capping protein subunit alpha-2 0 240.94 1.01E-29 203430000 491420 368910 404680 352660 505820 570530 572050 437500 423430 268050 FALSE TRUE 510821.6411 432267.4228 415226.2932 422415.0954 419840.8971 438033.054 527211.2262 431636.0281 408190.837 320569.2654 1.593482895 1.348436889 1.295277926 1.31770304 1.309672955 1.36642249 1.644609397 1.346467284 1.273331168 1 18.29027659 0.891723324 2.364216896 1.001290426 1.400042876 0.539667664 0.113612771 0.346288236 4.030805112 0.110624652 0.029958923 7.793334623 -0.891723324 0.39875245 IEHFMPLLVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEHFMPLLVQR 11 0 Q9Y6Q5;K7EPR4;K7EMG5;Q9Y6Q5-2 Q9Y6Q5;Q9Y6Q5-2 AP1M2 AP-1 complex subunit mu-2 0 ; 138.71 5.18E-05 504360000 343100 399090 339800 324320 796360 630150 429040 346790 393020 784520 FALSE TRUE 356645.8529 467630.603 348655.4671 388469.528 660995.0117 483807.2125 395410.7237 342141.8473 378875.287 938231.6735 0.380125573 0.498416986 0.371609142 0.414044355 0.704511509 0.51565858 0.421442523 0.364666699 0.403818479 1 19.83958468 -1.14099173 4.962834483 1.000029901 0.451970907 0.741620755 0.09691283 3.39E-05 5.88E-06 0.099356963 0.023417386 0.072278357 1.14099173 -0.548058994 IEHSFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 128.57 0.0037452 586350000 165406 191847 172830 170726 260280 249580 183851 165148 173171 277790 FALSE TRUE 171936.3566 224795.2299 177334.0918 204495.0932 216037.6986 191618.8274 169440.2782 162934.4612 166938.6095 332217.6319 0.517541335 0.67665051 0.533788923 0.615545575 0.650289683 0.576787049 0.510027951 0.490444954 0.502497741 1 18.34176912 -1.363535384 3.699962806 1.001929813 0.562914922 0.817893098 0.061756623 26470843.54 45147239.81 557415.1149 0.016071225 0.043297679 1.363535384 -0.439014891 IEIEAVAIQGPLTT(ph)ASL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEIEAVAIQGPLTTASL 17 0 H0YBX3;H0YB34;P52758 H0YBX3 HRSP12 Ribonuclease UK114 1 IEIEAVAIQGPLT(0.056)T(0.472)AS(0.472)L 84.718 0.012759 0 12375 17622 14537 19999 22358 24957 20973 15492 18936 21515 TRUE FALSE 12863.57456 20648.44142 14915.84616 23954.74251 18557.59515 19161.11498 19329.08146 15284.35508 18254.49706 25730.45232 0.499935811 0.802490417 0.579696228 0.930988006 0.721230817 0.744686286 0.751214212 0.594018126 0.709451075 1 14.6511892 -2.337629643 2.114225967 2.524774879 0.70533586 0.369672245 0.116037451 3331294.158 354119.1441 24322976.62 0.028091008 0.004595898 2.337629643 -1.819439019 IEIESFYEGEDFSETLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEIESFYEGEDFSETLTR 18 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 305.84 9.47E-50 402599000 220341 268840 258275 282150 295059 338883 237895 238301 248146 258676 FALSE TRUE 229040.2328 315011.1787 265005.8587 337958.4279 244904.9766 260182.5591 219248.1683 235106.9649 239215.2739 309358.6095 0.74037129 1.018271899 0.856629977 1.092448755 0.791653987 0.841038688 0.708718495 0.759981968 0.773262054 1 18.23892066 3.097535997 24.87998661 0.792137379 0.930140066 0.18269566 0.113787264 17.43188496 4430.158544 0.030672716 0.036660911 1251.803026 -3.097535997 0.138002687 IEINFPAEYPFKPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEINFPAEYPFKPPK 15 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 160.47 1.56E-06 1720470000 949410 730930 902590 679670 1159200 1055450 1074520 906760 1038120 613400 FALSE TRUE 986893.4399 856461.5417 926112.2369 814106.6974 962159.5981 810337.733 990296.3147 894606.3654 1000758.264 733583.9857 1.345303958 1.167503051 1.26244882 1.10976618 1.311587517 1.104628439 1.349942657 1.219500947 1.364204077 1 19.48460262 2.224900788 24.99938974 1.251761842 1.21613722 0 0.118642909 1214.804134 2223244.381 0.040149272 0.029824948 167.8420551 -2.224900788 -0.035624622 IEKEEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEKEEQEK 8 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 77.662 0.029761 104370000 176330 95660 122480 80433 171550 186580 183020 125160 132490 90468 FALSE TRUE 183291.6446 112088.8609 125671.9294 96342.40733 142389.9923 143249.6226 168674.4142 123482.4349 127721.7108 108193.4725 1.694110008 1.036003913 1.161548165 0.890464139 1.316068234 1.324013541 1.559007307 1.14131132 1.180493683 1 16.72325394 0.946345741 1.986558899 1.004302047 1.256386387 0.118584653 0.222310348 0.889303536 7.452291226 0.209355616 0.058494262 8.837831987 -0.946345741 0.25208434 IEKEQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEKEQSK 7 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4;A0A0G2JNQ3;O60812;B2RXH8 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2 0 73.233 0.045097 345660000 321860 220620 249310 214390 385190 378430 313650 309880 277790 239350 FALSE TRUE 334567.2813 258509.7688 255807.2234 256795.7021 319715.5414 290545.3677 289065.2934 305726.5655 267792.3922 286246.0499 1.168810125 0.903103358 0.893662021 0.897115269 1.116925601 1.015019658 1.009849022 1.068055142 0.935532184 1 18.12689626 3.253237981 24.99985744 1.028912558 0.956059859 0.093615888 0.086501878 481.3456205 819867.9239 0.023563882 0.031772394 1791.587324 -3.253237981 -0.072852699 IELGDVTPHNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IELGDVTPHNIK 12 0 E7EQ69;Q9GZZ1;A0A087WWJ2;C9J5D1;Q9GZZ1-2;F8WCK0;C9JZU6;C9J5J3;A0A0D9SF32 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ; 153.95 6.54E-05 360540000 478110 412490 512040 408230 625740 619070 553600 518440 539670 443600 FALSE TRUE 496986.152 483331.9488 525384.183 488976.6756 519376.9383 475300.3746 510207.3854 511491.1598 520247.3821 530514.9268 0.936799564 0.911061922 0.990328748 0.921702012 0.979005325 0.895922717 0.961721075 0.964140939 0.980646078 1 19.01703382 1.382364034 1.383476986 0.997303329 0.94130993 0.34360994 0.027461363 0.426416788 1.544308599 0.023415673 0.007532047 24.11926305 -1.382364034 -0.055993399 IENFDVSFGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IENFDVSFGDR 11 0 Q9NUQ8-2;Q9NUQ8 Q9NUQ8-2 ABCF3 ATP-binding cassette sub-family F member 3 0 ;; 220.1 2.19E-11 245118000 240824 301091 298505 302469 336957 386820 308882 310165 291790 308768 FALSE TRUE 250331.9175 352801.0371 306284.2855 362296.4654 279681.1695 296986.9173 284671.0217 306007.7455 281288.5349 369265.1779 0.677919101 0.955413774 0.829442644 0.981128162 0.757399252 0.804264618 0.770912176 0.828693751 0.761752128 1 18.4942977 IENHEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 IENHEGVR 8 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;; 169.21 0.00030235 59600465000 20383290 23434077 22739162 21329177 25826451 28234800 23732083 24458052 23482646 23882535 FALSE TRUE 21188038.03 27458697.43 23331763.24 25548024.55 21436480.08 21677695.6 21871900.32 24130231.82 22637510.16 28561860.47 0.741829757 0.961376359 0.816885275 0.894480406 0.750528142 0.758973514 0.765772956 0.844841037 0.792578277 1 24.76758662 5.046541063 15.02653487 0.83169895 0.292109846 0.107123548 0.081993596 2212997.416 20592850.52 0.01862129 33442566.25 111311.7634 -5.046541063 -0.539589104 IENLSNLHQLQMLELGSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IENLSNLHQLQMLELGSNR 19 0 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C003;C9J177;Q15435-2;Q15435-5;Q15435-4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 0 98.292 0.00097974 385720000 119170 160140 165750 133010 173310 188530 138890 147110 150380 157380 FALSE TRUE 123874.9236 187642.7993 170069.5812 159318.981 143850.8281 144746.7647 128003.4389 145138.2311 144967.8532 188215.5978 0.658154399 0.99695669 0.903589199 0.846470659 0.764287497 0.769047658 0.680089431 0.771127541 0.770222314 1 17.52202667 3.321787521 4.468196728 0.771819893 0.868209639 0.039018328 0.110724247 0.411552155 15.0287524 0.029472608 0.04000573 2097.913226 -3.321787521 0.096389746 IEPDMMGVEHGFETAS(ph)HEGEAGPSAEALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEPDMMGVEHGFETASHEGEAGPSAEALQ 29 0 Q96RE7;K7ELC5 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 1 IEPDMMGVEHGFET(0.151)AS(0.849)HEGEAGPSAEALQ 90.322 0.0010335 73001000 20576 22056 21656 20506 24865 24854 26816 23750 22748 23564 TRUE FALSE 21388.35637 25843.94643 22220.37315 24562.0256 20638.45618 19082.03517 24714.09185 23431.6701 21929.30392 28180.91464 0.758966011 0.917072663 0.788490134 0.871583691 0.732355796 0.677126183 0.876979763 0.831473016 0.77816154 1 14.78243082 -1.699686275 2.496120311 1.034202758 0.807705749 0.419937625 0.069102524 21822122.67 16779251.25 4689248.955 0.016760278 0.019967042 1.699686275 -0.226497009 IEPEPFENCLLRPGS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEPEPFENCLLRPGSPAR 18 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 1 IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR;IEPEPFENCLLRPGS(1)PAR 175.77 1.53E-12 294858000 164967 183484 154988 170860 517701 329014 284910 171609 162819 435178 TRUE FALSE 171480.0245 214995.9497 159027.1146 204655.598 429702.3689 252605.4848 262578.0097 169308.8621 156959.176 520442.7971 0.329488707 0.413101979 0.305561179 0.393233606 0.825647643 0.485366473 0.504528089 0.325316947 0.301587757 1 18.98938008 -1.458820078 2.933250639 1.014604167 0.434569235 0.569383884 0.148287404 27768657.81 32133859.16 3327309.354 0.039941394 0.034768017 1.458820078 -0.580034932 IEPGTS(ph)TPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEPGTSTPR 9 0 Q86X27;Q86X27-3;H7C2H2;A0A0A0MR31 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 IEPGT(0.075)S(0.462)T(0.462)PR 112.3 0.0020996 0 243580 225420 196600 193700 239790 249270 190270 207480 187520 157930 TRUE FALSE 253196.7265 264134.1315 201723.5575 232013.2819 199030.5815 191380.8202 175356.1402 204699.07 180771.1918 188873.3597 1.34056347 1.398472139 1.068036052 1.228406601 1.053777948 1.013275882 0.928432366 1.08379006 0.957102643 1 17.5270597 4.143086981 0.680299355 0.995381236 1.480093408 0.749058684 0.07658418 0.769430411 0.448994059 0.034084643 0.257503718 13902.3104 -4.143086981 0.484712172 IEPIPGES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEPIPGESPK 10 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 IEPIPGES(1)PK 103.44 0.002952 49037000 251680 111450 131900 90321 183790 258910 176460 129850 156850 100880 TRUE FALSE 261616.5207 130590.6705 135337.4224 108186.2242 152549.4414 198782.0763 162628.6041 128109.5731 151204.9991 120645.5045 2.168473013 1.08243296 1.121777582 0.896728184 1.264443645 1.647654234 1.347987268 1.061867772 1.253299903 1 16.88041463 4.742627466 24.85047948 1.195171421 2.168473427 0.684817447 0.199824354 232.4700315 1420448.86 0.050852412 0.391046077 55287.5654 -4.742627466 0.973302006 IEPPDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEPPDRR 7 1 Q15428 Q15428 SF3A2 Splicing factor 3A subunit 2 0 ; 81.297 0.047856 751350000 728760 901560 822050 849070 918820 1029090 822400 791370 800870 880000 FALSE TRUE 757532.0075 1056395.917 843473.2983 1017013.512 762639.3046 790099.4435 757938.1391 780762.9796 772046.8451 1052419.151 0.719800667 1.00377869 0.801461373 0.966357853 0.724653579 0.750745977 0.72018657 0.741874545 0.733592546 1 20.00527798 3.221072646 24.99976125 0.759039618 0.877102581 0.140574476 0.107816371 337.1659636 481991.4388 0.028255294 0.03384384 1663.690919 -3.221072646 0.118062962 IEQLQNHENEDIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IEQLQNHENEDIYK 14 0 O00629;H7C4F6 O00629 KPNA4 Importin subunit alpha-3 0 ;; 294.97 1.37E-43 2039010000 2184360 1470030 1863280 1399500 2432220 2486000 2265450 1947840 2200110 1170840 FALSE TRUE 2270600.219 1722496.217 1911838.608 1676316.923 2018792.113 1908664.176 2087878.109 1921732.391 2120928.471 1400243.681 1.621575052 1.230140325 1.365361354 1.197160855 1.44174342 1.363094297 1.491081972 1.372427112 1.514685265 1 20.41724649 -1.260093513 5.104874432 0.999934772 1.390472221 0.494205065 0.120983383 8.39E-05 1.22E-05 0.109358852 0.025771839 0.054942256 1.260093513 0.390537449 IEQSQHLFQAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEQSQHLFQAHK 12 0 P53367;P53367-2;P53367-3 P53367 ARFIP1 Arfaptin-1 0 ; 199.96 9.57E-08 780780000 323410 464320 499500 375870 674110 622730 539980 523230 483360 533900 FALSE TRUE 336178.4765 544063.3481 512517.3803 450215.9641 559525.023 478110.3951 497654.9566 516216.9577 465963.968 638507.4829 0.526506714 0.852086096 0.802680304 0.705106794 0.876301434 0.748793723 0.779403484 0.808474406 0.729770567 1 19.284344 -5 0.193301714 1.987593228 0.727772663 0.394682834 0.091223045 142.035943 1.395686388 54.32040629 0.222031732 1.00E-05 5 -1.259820565 IERDS(ph)REHEEPT(ph)TSEMAEETYSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IERDSREHEEPTTSEMAEETYSPK 24 2 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 2 IERDS(1)REHEEPT(0.411)T(0.327)S(0.261)EMAEETYSPK;IERDS(0.988)REHEEPT(0.409)T(0.333)S(0.27)EMAEETYSPK 182.56 5.75E-17 1143140000 372300 333420 438050 263530 594650 472750 468570 431350 522500 353670 TRUE FALSE 386998.6915 390682.2914 449465.9429 315655.4474 493571.6054 362960.9771 431842.259 425568.4588 503695.3271 422964.8651 0.914966522 0.923675519 1.062655506 0.74629236 1.166932874 0.858135053 1.02098849 1.006155579 1.19086801 1 18.6901783 1.611731089 2.396774834 1.092680945 0.953041819 0.177570901 0.116510222 0.404429237 5.195311183 0.076686077 0.029320266 40.90073281 -1.611731089 -0.139639125 IERPGEGS(ph)PMVDNPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IERPGEGSPMVDNPMR 16 1 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR;IERPGEGS(1)PMVDNPMR 151.22 4.02E-07 1216560000 798900 918670 960240 883080 1005960 1165970 1047810 1016980 973360 893740 TRUE FALSE 830441.1889 1076444.426 985264.6432 1057750.588 834967.2785 895191.1379 965679.9143 1003349.047 938328.9637 1068851.241 0.776947396 1.007104061 0.921797726 0.989614408 0.781181933 0.837526405 0.903474569 0.938717202 0.87788546 1 20.02762965 -1.076231727 4.533912573 1.000006587 0.898388246 0.154888646 0.07412919 0.042117577 43719391.97 612.5106206 0.016933818 0.083901219 1.076231727 -0.10161834 IES(ph)DEEEDFENVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 380.06 8.94E-98 6555910000 6652490 3173500 4630870 3446120 6787600 6816250 6307470 4546880 4878350 2435040 TRUE FALSE 6915135.442 3718523.939 4751554.277 4127752.25 5633846.176 5233279.239 5813074.02 4485936.511 4702779.136 2912139.466 2.374589377 1.276904483 1.631636922 1.417429453 1.934607268 1.797056528 1.996152343 1.540426399 1.61488802 1 21.47364802 0.635046573 1.341992315 1.001601441 1.735106885 0.365867879 0.295407646 1.384746917 3.676380784 0.266368129 0.079174418 4.315653551 -0.635046573 0.733505444 IES(ph)DVQEPTEPEDDLDIMLGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IES(1)DVQEPTEPEDDLDIMLGNK;IES(1)DVQEPTEPEDDLDIMLGNK 146.64 5.41E-08 50658000 177337 106223 147520 115633 207294 203266 198897 157754 177722 90345 TRUE FALSE 184338.4017 124465.9739 151364.4924 138504.8623 172058.2399 156060.552 183306.9334 155639.5657 171325.8199 108046.373 1.706104486 1.15196809 1.400921551 1.281902006 1.592448087 1.444384922 1.696557953 1.440488573 1.585669331 1 16.72129112 3.241534617 24.99211956 1.494049536 1.369684159 0.01125712 0.218578789 214.131731 1799446.289 0.056179753 0.072891692 1743.95236 -3.241534617 -0.124365377 IES(ph)PKLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 151.79 0.00028314 74225726000 60778780 26066916 36116944 23487318 53309060 58031130 44136763 34673389 37906306 20083546 TRUE FALSE 63178373.17 30543706.05 37058181.23 28133039.4 44247605.02 44554279.53 40677208.19 34208648.93 36542065.45 24018532.32 2.630401073 1.271672459 1.542899489 1.171305516 1.842227678 1.854995923 1.693575929 1.424260587 1.521411257 1 24.51764466 -2.645588004 0.142138924 2.13E-29 1.905295129 0.263010635 0.372807668 95.80829731 1.599062853 33.6432073 2.497245346 0.00226158 2.645588004 1.905295129 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 IESDVQEPT(1)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK;IES(0.002)DVQEPT(0.998)EPEDDLDIMLGNK;IES(0.009)DVQEPT(0.991)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK 170.16 2.75E-11 218154000 429915 294753 363046 312506 481362 467316 479808 393635 427875 270596 TRUE FALSE 446888.3762 345374.5349 372507.277 374318.7541 399540.2592 358788.9412 442199.3952 388358.9667 412475.8623 323614.1053 1.380929845 1.067241907 1.151084798 1.156682443 1.23461942 1.108693766 1.366440424 1.200068107 1.27459173 1 18.30391497 IESGAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IESGAFR 7 0 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 ; 85.265 0.064172 230020000 326050 373420 371250 362670 543170 563720 440410 403460 370010 425710 FALSE TRUE 338922.7058 437551.9802 380925.08 434405.0435 450842.1574 432804.5733 405889.5134 398052.2786 356693.4124 509119.7238 0.66570335 0.85942846 0.748203344 0.853247327 0.885532688 0.850103724 0.797237849 0.781844152 0.70060812 1 18.95764543 -2.352056507 2.484425809 2.504362691 0.799241937 0.447272109 0.06858924 3244322.94 1537839.85 26662252.01 0.016164032 0.004445734 2.352056507 -1.705120753 IESLIDRDYMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IESLIDRDYMER 12 1 Q13619;A0A0A0MR50;Q13619-2;A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 Q13619;A0A669KAX4 CUL4A;CUL4B Cullin-4A;Cullin-4B 0 ; 97.86 0.0042719 252430000 126177 155079 135394 128986 192784 193414 142659 143434 125664 225051 FALSE TRUE 131158.5654 181712.6119 138922.4789 154499.0458 160014.6445 148496.5297 131477.0148 141511.5018 121141.3772 269145.4346 0.487314844 0.675146551 0.51616138 0.574035543 0.594528548 0.551733415 0.488498031 0.5257808 0.450096348 1 18.03802643 -1.007176907 4.636329895 1.00000979 0.543019191 0.837509061 0.060726843 7613068.539 1653831.248 883.2981002 0.013900612 0.098361036 1.007176907 -0.456990599 IESPKLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IESPKLER 8 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 88.37 0.016239 0 218429 110578 137779 99410 210251 232434 172001 135709 154946 100259 FALSE TRUE 227052.7456 129568.9113 141369.6339 119073.0013 174512.6101 178454.7261 158519.1122 133890.0428 149369.5237 119902.8315 1.893639565 1.080615943 1.179034992 0.993079144 1.455450284 1.488327872 1.322063126 1.116654554 1.245754766 1 16.8715062 7.999999993 0.029007604 2.27E-09 3.085246235 0.186496498 0.237087461 3060.285125 6.808934271 234.2229983 552.4272234 99999998.38 -7.999999993 3.085246233 IET(ph)DEEES(ph)CDNAHGDANQPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 IET(1)DEEES(1)CDNAHGDANQPAR 183.44 7.65E-17 622860000 148010 134640 124620 135490 196220 259430 160050 125900 147830 114910 TRUE FALSE 153853.5491 157763.3726 127867.6996 162289.5176 162866.5945 199181.3142 147504.8628 124212.5164 142509.6272 137424.4144 1.119550334 1.148001054 0.930458391 1.180936577 1.185135809 1.449388124 1.073352675 0.90386062 1.037003707 1 17.06827881 1.999032413 24.99998411 0.974356101 1.166986804 0.326677927 0.121812479 42.12011992 1088288.351 0.048842466 0.035623243 99.77745287 -1.999032413 0.192630703 IET(ph)DEEESCDNAHGDANQPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR;IET(0.999)DEEES(0.001)CDNAHGDANQPAR;IET(1)DEEESCDNAHGDANQPAR 324.55 7.08E-67 4745990000 742361 711515 731071 759275 893480 1297058 833469 882787 865480 585578 TRUE FALSE 771669.9855 833712.1664 750123.3108 909457.3288 741606.5887 995835.9366 768139.5219 870954.6842 834331.5439 700310.7975 1.101896455 1.190488808 1.071129152 1.29864816 1.058967806 1.421991407 1.096855174 1.243668793 1.19137324 1 19.41763581 3.763026467 24.91056215 1.198843395 1.128103224 0.055211545 0.117962465 2049.428099 2086673.177 0.027416727 0.049395028 5794.640098 -3.763026467 -0.070740171 IETELR ddPTM_MDA-MB-175_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 ;;;;; 142.11 0.026911 4123740000 4447880 4559660 4756810 4926490 5167220 5751430 5475100 4972910 4749870 3932380 FALSE TRUE 4623485.737 5342746.136 4880776.376 5900935.018 4288897.79 4415747.546 5045947.355 4906256.275 4578923.107 4702854.571 0.983123264 1.136064502 1.037832725 1.254756006 0.91197755 0.938950478 1.072954156 1.04325069 0.973647609 1 22.16510529 3.211039768 24.99999888 0.999038674 1.100659342 0.326381351 0.078749846 280.9394205 255205.2598 0.02275438 0.02720295 1625.697613 -3.211039768 0.101620668 IETIAASST(ph)PTPIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IETIAASSTPTPIRK 15 1 Q96P47;Q96P47-2;Q96P47-4;Q96P47-5;H7C5G0;H7C4U6;Q96P47-3;Q96P47-6;E7ESL9 Q96P47;E7ESL9 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 IET(0.009)IAAS(0.178)S(0.192)T(0.612)PT(0.009)PIRK 60.949 0.054681 296590000 129900 100090 118880 84404 124570 147260 111610 120290 103010 95187 TRUE FALSE 135028.5523 117279.6789 121978.1105 101098.8593 103395.6359 113061.0967 102861.7166 118677.7093 99302.69022 113837.0702 1.18615625 1.030241544 1.071514844 0.888101381 0.90827738 0.993183473 0.903587174 1.04252252 0.872322962 1 16.79661091 4.721849853 1.133938446 0.952632119 1.282085145 0.589633331 0.06008849 1.121489084 1.221561088 0.017172472 0.438438272 52704.76162 -4.721849853 0.329453027 IETIEVMEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 IETIEVMEDR 10 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;;;;; 278.65 1.34E-23 5590090000 3276313 3547075 3742257 3841635 4150386 4580190 4069818 3789273 3802403 3618709 FALSE TRUE 3405664.367 4156257.539 3839783.292 4601498.937 3444904.87 3516510.286 3750815.031 3738483.993 3665555.259 4327725.744 0.786940894 0.960379142 0.887251993 1.063260292 0.796008128 0.812553866 0.866694253 0.863844942 0.846993427 1 22.04517765 IETLDPALIRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IETLDPALIRPGR 13 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 176.05 1.57E-05 3150710000 2724710 3173500 3066180 2914780 3572740 3740140 3005710 3042850 3102740 3113890 FALSE TRUE 2832283.655 3718523.939 3146087.17 3491314.784 2965446.931 2871549.167 2770114.596 3002065.573 2991072.993 3723997.126 0.760549366 0.998530292 0.844814607 0.93751812 0.796307524 0.771093282 0.743855192 0.806140679 0.803188856 1 21.82842053 3.221139544 24.84159509 0.802908359 0.890541575 0.098579512 0.087324673 346.4738653 494053.5778 0.023178319 0.027766112 1663.947212 -3.221139544 0.087633216 IETSIGQSTVIIDLTEDS(ph)NEQPDSLVDHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IETSIGQSTVIIDLTEDSNEQPDSLVDHNK 30 0 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 IETSIGQSTVIIDLTEDS(0.951)NEQPDS(0.049)LVDHNK 243.15 6.72E-46 80145000 28422 17100 23693 20284 28886 28470 39173 29022 29446 15409 TRUE FALSE 29544.12251 20036.79198 24310.45904 24296.11466 23975.96804 21858.27397 36102.5179 28633.00756 28386.24421 18428.09853 1.603210579 1.087295683 1.319206049 1.318427651 1.301054908 1.186138328 1.959101632 1.553768964 1.540378361 1 14.1696196 IETWHKPDLGTLENVHGLDPNTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IETWHKPDLGTLENVHGLDPNTWK 24 1 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 201.63 9.03E-25 336790000 393040 200850 291270 244730 354610 348240 379250 288630 389300 161680 FALSE TRUE 408557.5227 235344.4251 298860.7355 293136.8636 294333.5189 267366.5376 349523.394 284761.387 375289.169 193358.1004 2.112957884 1.217142828 1.545633386 1.516030944 1.522219748 1.382753228 1.807648054 1.472715062 1.940902234 1 17.56091568 4.758467284 24.13877329 1.516912759 2.11295878 0.348231481 0.253408956 3223.35397 3908530.388 0.054917552 2.080407099 57341.26694 -4.758467284 0.596046021 IEVEKPFAIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 152.14 0.0012954 0 1591020 1202730 1182160 1121080 1639160 1560230 1371650 1251190 1254460 929430 FALSE TRUE 1653834.698 1409289.522 1212968.061 1342826.278 1360536.169 1197890.228 1264136.489 1234419.845 1209312.23 1111534.013 1.487884921 1.267878 1.091255909 1.208083839 1.224016676 1.077691023 1.137289974 1.110555169 1.087966913 1 20.08412067 7.999999999 0.727208837 1.112180126 58.42110926 0.777393498 0.061507396 150.7036616 0.710160789 0.021707647 14104.8916 99999999.66 -7.999999999 57.30892913 IEVEKPFAIAKE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEVEKPFAIAKE 12 2 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 137.68 0.00034909 1021540000 2056330 1769080 1816340 1250450 2796200 2335400 1597080 1776290 2005160 1611390 FALSE TRUE 2137515.496 2072905.728 1863675.313 1497785.278 2320902.923 1793038.743 1471896.696 1752481.738 1932994.683 1927111.019 1.109181296 1.075654546 0.967082485 0.777217951 1.204343134 0.930428359 0.76378407 0.909382864 1.003053101 1 20.87800826 2.494713159 24.94767164 0.89863885 1.017758236 0.14976016 0.121008019 1274.588374 1807537.534 0.039922704 0.036901295 312.4015347 -2.494713159 0.119119386 IEVIEIMTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 208.25 2.73E-07 2651841000 2186716 2642473 2480994 2416716 2717310 3053639 2698850 2551025 2445925 2348551 FALSE TRUE 2273049.236 3096297.182 2545650.742 2894735.212 2255422.617 2344477.621 2487307.085 2516832.683 2357896.637 2808704.603 0.809287397 1.102393317 0.906343351 1.030629995 0.803011685 0.834718474 0.885570908 0.896083084 0.839496127 1 21.42147347 3.24085879 24.99962331 0.871814702 0.968192768 0.187112604 0.086803585 86.95617702 945903.9844 0.022523327 0.029088905 1741.240619 -3.24085879 0.096378066 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IEVLPVDTGAGGYSGNSGSPK 21 0 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 IEVLPVDTGAGGYSGNSGS(1)PK;IEVLPVDTGAGGYSGNS(0.001)GS(0.999)PK;IEVLPVDTGAGGYSGNS(0.011)GS(0.989)PK 340.78 1.40E-80 414276000 801730 348845 393850 351207 553747 655010 562729 469461 444399 292876 TRUE FALSE 833382.9195 408756.4151 404114.0546 420674.6964 459621.2827 502893.8543 518620.8306 463168.6432 428405.1668 350259.4448 2.379330328 1.167010401 1.153756339 1.20103741 1.312230947 1.435775285 1.48067622 1.322358755 1.223108108 1 18.41806443 4.742143454 24.98791768 1.279928566 2.379330747 0.860232968 0.135614884 126.120112 879566.9412 0.033631676 0.249002199 55225.98287 -4.742143454 1.099402181 IEVLQQHENEDIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEVLQQHENEDIYK 14 0 O00505;H0Y4S9 O00505 KPNA3 Importin subunit alpha-4 0 ;;; 225.55 2.73E-12 1224700000 891739 560678 749253 615028 930006 1031460 972928 742263 890556 436435 FALSE TRUE 926945.5443 656970.085 768779.1487 736678.7027 771923.9123 791919.0469 896667.3611 732314.1786 858505.0635 521946.0822 1.775941186 1.258693393 1.472909128 1.411407668 1.478934202 1.517243014 1.717931012 1.403045647 1.64481561 1 18.99354126 -1.573415425 6.016462574 0.998623356 1.507401684 0.524521562 0.148113633 0.002534248 0.000179686 0.132883361 0.031247572 0.026704508 1.573415425 0.508778328 IEVPLYSLLEQTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IEVPLYSLLEQTHLK 15 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 285.65 4.10E-34 936220000 766760 650390 817440 724360 1101060 978670 1114430 1017610 930330 577500 FALSE TRUE 797032.2769 762089.4232 838743.1579 867636.246 913902.2145 751388.7244 1027078.065 1003970.602 896847.605 690650.0681 1.154031996 1.103437846 1.21442565 1.256260277 1.323249293 1.087944183 1.487117879 1.453660325 1.298555732 1 19.3975954 3.708355111 0.852751151 1.329013752 1.110342306 0.075876918 0.144104311 1.294050997 1.711619677 0.060343066 0.201547945 5109.225967 -3.708355111 -0.218671446 IEVPLYSLLEQTHLKVEDVSAVEIVGGATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEVPLYSLLEQTHLKVEDVSAVEIVGGATR 30 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 224.56 5.25E-35 14131000 11380 11223 11908 6976.4 16060 14559 10733 11227 15807 16374 FALSE TRUE 11829.29119 13150.46295 12218.33226 8356.311098 13330.12694 11177.89289 9891.719415 11076.52043 15238.10916 19582.1718 0.604084741 0.671552833 0.623951847 0.426730558 0.680727708 0.570819877 0.505139037 0.565643103 0.778162367 1 14.25725316 0.997590286 3.090337698 0.998487246 0.57895754 0.774620504 0.071496275 0.102975536 2.381144386 0.068673477 0.018037454 9.94466793 -0.997590286 -0.419529707 IEWLESHQDADIEDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 281.79 1.55E-35 3100410000 5318310 3364230 3926890 3798880 5137270 5725980 5602920 4134030 4059110 2242160 FALSE TRUE 5528280.985 3942010.332 4029227.979 4550287.125 4264038.68 4396207.923 5163748.49 4078620.09 3913023.424 2681468.323 2.061661865 1.47009394 1.502620018 1.696938609 1.590187974 1.639477851 1.925716759 1.521039818 1.459283852 1 21.35459178 0.871573675 1.648715668 1.003279259 1.673314672 0.584140115 0.175530886 0.367952046 1.947090901 0.159607619 0.045896882 7.440012663 -0.871573675 0.670035413 IEWLESHQDADIEDFKAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEWLESHQDADIEDFKAK 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 214.24 6.11E-19 655830000 943260 639350 813740 534890 1187000 1017100 864490 787980 810050 653440 FALSE TRUE 980500.6332 749153.389 834946.7329 640689.6455 985234.164 780893.9393 796729.0149 777418.417 780896.4587 781469.0571 1.254689004 0.95864754 1.068432237 0.819852865 1.260746225 0.999264056 1.019527271 0.994816634 0.999267279 1 19.57582922 4.747162797 24.4554719 1.015479123 1.25468917 0.331339574 0.102795007 936.0987536 2661190.868 0.022835354 0.267569218 55867.95788 -4.747162797 0.239210047 IEYAKPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEYAKPTR 8 1 A0A3B3ITJ4;M0R1W6;B4DVF8;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 90.629 0.013736 0 450320 414780 400940 347590 598430 523830 454010 449100 457440 409200 FALSE TRUE 468098.9813 486015.2385 411388.8258 416342.2645 496709.0824 402178.4212 418423.5099 443080.5491 440976.8238 489374.9054 0.956524285 0.993134779 0.840641441 0.850763413 1.014986827 0.821820688 0.855016277 0.905401042 0.901102241 1 18.9005806 4.254278859 24.97906712 0.893426454 0.974829568 0.19138603 0.061819455 345.2039376 548580.3097 0.014312448 0.038909021 17958.86387 -4.254278859 0.081403114 IEYDCELVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEYDCELVPR 10 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 143.03 8.07E-05 59657000 40545 47825 46027 38542 47355 51708 37048 43120 33081 50375 FALSE TRUE 42145.74791 56038.57172 47226.50143 46165.49256 39305.61401 39699.60064 34144.08095 42542.04693 31890.42127 60245.01676 0.699572349 0.93017771 0.783907184 0.766295622 0.652429298 0.658969036 0.566753614 0.70615047 0.52934538 1 15.87855429 3.418446884 2.629897458 0.663906442 0.816020018 0.13341594 0.130545703 0.405224718 5.671915283 0.034944398 0.052190234 2620.878473 -3.418446884 0.152113576 IEYEPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IEYEPFR 7 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 116.3 0.012765 135250000 136110 183740 170290 192760 205100 249920 213190 184570 172960 208070 FALSE TRUE 141483.7279 215295.9157 174727.8973 230887.3527 170237.1753 191879.8676 196479.6107 182096.141 166735.2034 248837.3328 0.568579185 0.865207456 0.702177183 0.927864602 0.684130365 0.771105627 0.789590567 0.731787867 0.670057027 1 17.92484342 -1.488831823 3.167711861 1.005942279 0.752662233 0.382109019 0.09667339 83529479.89 106869680.8 4368306.98 0.021076189 0.032446524 1.488831823 -0.253280046 IEYQFFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IEYQFFEDR 9 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 ;;;;; 179.51 0.00011567 757986000 605115 783160 680250 771936 1017290 1036431 737962 704796 679770 836584 FALSE TRUE 629005.4075 917661.6379 697977.8738 924622.6368 844371.4092 795735.6075 680118.6101 695349.3624 655305.2105 1000496.617 0.628693187 0.917206137 0.697631418 0.924163681 0.843952288 0.795340627 0.679781019 0.695004211 0.654979936 1 19.93228486 2.377159943 6.989055852 0.726525823 0.810598061 0.00286846 0.124230173 0.52711899 32.12416273 0.040120021 0.033464018 238.3196998 -2.377159943 0.084072238 IFAPNHVVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFAPNHVVAK 10 0 Q02543;M0R3D6;M0R1A7;M0R117 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 134.25 0.00017572 2471840000 5892200 4951400 5940300 4869700 7238500 7375900 6767800 6140300 6275800 5198200 FALSE TRUE 6124828.606 5801764.433 6095109.098 5832912.125 6008102.356 5662959.008 6237322.152 6057999.322 6049935.184 6216687.764 0.985223778 0.933256527 0.980443176 0.938266863 0.966447501 0.910928652 1.003319193 0.974473796 0.97317662 1 22.56771469 2.206064157 24.99999956 0.985053772 0.952823273 0.364865906 0.02271168 217.3483184 167207.9184 0.007895163 0.005831363 160.7178661 -2.206064157 -0.0322305 IFAQDGEGQR ddPTM_MDA-MB-175_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 459410000 639540 867430 699800 655050 908310 935100 694780 716090 717180 1151580 FALSE TRUE 664789.533 1016404.355 718037.3629 784616.9349 753915.7906 717937.1966 640321.3281 706491.9848 691368.8319 1377210.053 0.482707436 0.738016944 0.521370986 0.569714789 0.547422515 0.521298255 0.464940934 0.512987822 0.502006815 1 20.39331719 -1.590676818 6.388226552 1.00111534 0.540530665 0.785678186 0.072067363 0.001144735 7.33E-05 0.069775259 0.016410792 0.025663931 1.590676818 -0.460584675 IFAQLDSIIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFAQLDSIIDDR 12 0 Q9Y2S2-2;Q9Y2S2;A0A087WW38;A0A2R8YFQ7;A0A2R8YCZ4 Q9Y2S2-2 CRYL1 Lambda-crystallin homolog 0 94.297 0.015562 63894000 38851 42760 47674 44146 52560 47952 50047 41876 41360 46218 FALSE TRUE 40384.86748 50103.69737 48916.4236 52877.94704 43625.86997 36815.87472 46124.18537 41314.72072 39871.46168 55273.5322 0.730636633 0.906468166 0.884988197 0.956659452 0.789272338 0.666066981 0.834471465 0.747459391 0.721348177 1 15.75430119 3.0367235 20.31331121 0.774186701 0.873353823 0.109568205 0.099177605 38.03396568 21036.54587 0.02692536 0.032181358 1088.237031 -3.0367235 0.099167122 IFCCHGGLSPDLQSMEQIR ddPTM_MDA-MB-175_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 ;; 157.42 6.16E-09 627840000 245566 304063 271712 260315 336843 378330 292886 319520 305398 251113 FALSE TRUE 255261.1353 356283.455 278793.0379 311804.53 279586.5472 290468.5911 269928.83 315237.357 294406.7856 300313.7845 0.849981414 1.186370634 0.928339132 1.038262465 0.930981399 0.967216978 0.898822645 1.049693265 0.980330577 1 18.19611117 7.257041952 8.919160342 0.987200889 0.111664919 0 0.089474454 0 0 0.017957237 0 18073487.05 -7.257041952 -0.87553597 IFCCHGGLSPDLQSMEQIRR ddPTM_MDA-MB-175_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 ; 184.01 2.70E-17 818120000 182379 271051 271237 224274 269076 324050 195771 263219 249161 334850 FALSE TRUE 189579.4637 317601.9008 278305.659 268634.7278 223338.5576 248794.2985 180425.9575 259690.9798 240193.7443 400457.4464 0.473407263 0.793097753 0.69496937 0.670819659 0.55770859 0.621275246 0.450549638 0.648485831 0.599798422 1 18.61128942 -0.974651054 5.799741289 1.000000434 0.615701249 0.592401876 0.09645495 5.32E-07 9.40E-08 0.091692838 0.021612185 0.106010515 0.974651054 -0.384299185 IFDEVMGCFSDS(ph)PPQS(ph)PTFPEAGHTSLYDEDKVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFS(0.1)DS(0.9)PPQS(0.899)PT(0.1)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.981)PT(0.019)FPEAGHTSLYDEDKVPR;IFDEVMGCFS(0.001)DS(0.999)PPQS(0.929)PT(0.071)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(0.993)PPQS(0.879)PT(0.127)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.998)PT(0.002)FPEAGHTSLYDEDKVPR;IFDEVMGCFSDS(1)PPQS(0.888)PT(0.108)FPEAGHT(0.001)S(0.001)LY(0.001)DEDKVPR;IFDEVMGCFSDS(1)PPQS(1)PTFPEAGHTSLYDEDKVPR 260.93 6.94E-60 2365315000 216154.5 1005699 1062814 1106975 1107159 1332929 877598 1047281 1048424 1051901 TRUE FALSE 224688.4466 1178419.98 1090511.806 1325931.351 918964.5086 1023376.44 808809.5756 1033243.911 1010691.425 1258000.861 0.178607546 0.936740201 0.866860938 1.053998763 0.73049593 0.813494229 0.64293245 0.821338 0.803410758 1 20.26270148 4.743814057 24.95983043 0.837953161 0.178607263 0.75043384 0.116265671 277.5447479 1318612.163 0.028076861 0.239100983 55438.83011 -4.743814057 -0.659345898 IFDEVMGCFSDS(ph)PPQSPTFPEAGHTSLYDEDKVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 IFDEVMGCFS(0.005)DS(0.994)PPQSPTFPEAGHTSLYDEDKVPR 110.79 1.74E-05 97758000 8662.5 26068 29462 22493 28562 36156 20227 24733 23193 23734 TRUE FALSE 9004.502189 30544.97622 30229.80392 26942.04827 23707.04144 27759.31695 18641.55489 24401.49459 22358.28846 28384.22289 0.317236171 1.076125154 1.065021369 0.949190977 0.835218971 0.977984039 0.656757628 0.859685139 0.787701272 1 14.79280162 -0.357530156 8.417642208 1.000001734 0.850351443 0.047409888 0.211907501 0 0 0.193674679 0.04564956 0.439005382 0.357530156 -0.149650291 IFDEVMGCFSDSPPQS(ph)PT(ph)FPEAGHTSLYDEDKVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFDEVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPR 35 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 2 IFDEVMGCFS(0.128)DS(0.153)PPQS(0.862)PT(0.822)FPEAGHT(0.012)S(0.012)LY(0.011)DEDKVPR 57.076 0.091969 97079000 4984.1 46572 36133 33939 29252 38114 21484 22020 31194 44383 TRUE FALSE 5180.876117 54570.37872 37074.65566 40652.0329 24279.75549 29262.60112 19800.02794 21724.85792 30071.33403 53078.99909 0.097606892 1.028097358 0.698480685 0.76587791 0.457426777 0.551302806 0.373029414 0.409292909 0.566539207 1 15.69585355 -1.929693704 2.244210917 1.310449153 0.553525646 0.244968357 0.237060525 11087294.11 4994713.247 18038173.12 0.059384415 0.011757265 1.929693704 -0.756923506 IFDFDDDGTLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFDFDDDGTLNR 12 0 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 ; 116.23 0.0020095 61692000 102610 136468 122089 139089 122498 159698 158297 129206 113543 119931 FALSE TRUE 106661.122 159905.3174 125270.7396 166600.3891 101675.8337 122610.5597 145889.2675 127474.2049 109456.6096 143429.1832 0.743650069 1.114872956 0.873397846 1.161551543 0.708892231 0.854850854 1.017151909 0.888760586 0.763140437 1 17.12997907 3.232609128 24.99589537 0.877312234 0.976334853 0.111275033 0.13959937 326.7418026 1372295.554 0.038122631 0.046710004 1708.476968 -3.232609128 0.099022618 IFDFDDDGTLNREDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IFDFDDDGTLNREDLSR 17 1 Q99828;Q99828-2 Q99828 CIB1 Calcium and integrin-binding protein 1 0 ;;;;; 223.15 2.86E-15 1159618000 1080742 1306784 1177575 1172410 1457786 1498625 1209446 1141363 1089987 1424098 FALSE TRUE 1123410.529 1531213.987 1208263.572 1404309.199 1209992.056 1150592.056 1114646.462 1126064.896 1050758.581 1703122.737 0.659618068 0.899062618 0.709440104 0.824549616 0.710454995 0.675577884 0.654472187 0.661176597 0.616959986 1 20.69975098 IFDIKDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFDIKDGK 8 1 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 63.159 0.093071 0 384700 227650 272980 186540 420650 343720 283920 275270 314270 224150 FALSE TRUE 399888.2531 266747.1166 280094.0831 223437.0552 349148.0633 263896.2391 261665.6085 271580.4559 302959.4841 268067.9009 1.491742397 0.995072949 1.044862448 0.833509176 1.302461287 0.984438041 0.9761169 1.013103229 1.130159497 1 18.03223895 4.74120274 24.49312374 1.029452198 1.491742619 0.594055454 0.114234259 121.1821765 1123302.091 0.025761664 0.17674284 55106.48878 -4.74120274 0.462290421 IFDLGR ddPTM_MDA-MB-175_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 ;;;;;; 166.66 0.016052 5674884000 6005570 7099670 6537730 6668490 7813210 8444970 7004920 6856500 6196350 7483550 FALSE TRUE 6242674.541 8318983.095 6708108.615 7987497.419 6485123.355 6483753.702 6455856.066 6764599.832 5973344.574 8949808.341 0.697520472 0.929515223 0.749525393 0.892476924 0.724610305 0.724457268 0.721340147 0.755837396 0.667427094 1 23.09342536 5.037102963 15.89101132 0.782924641 0.365579447 0.063223828 0.103156566 1212119.172 14629828.29 0.023093523 14307478.97 108918.8287 -5.037102963 -0.417345194 IFDLQDWTQEDERDKDAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFDLQDWTQEDERDKDAAK 19 2 A0A2R8YDQ9;A0A2R8Y6Y7;Q9P2R7-2;Q9P2R7;Q5T9Q5 A0A2R8YDQ9 SUCLA2 "Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial" 0 146.64 6.38E-08 40632000 44263 18898 26937 22413 34014 47642 36867 25238 28021 15758 FALSE TRUE 46010.53742 22143.58449 27639.00035 26846.2245 28232.31243 36577.86752 33977.26821 24899.72589 27012.52968 18845.47839 2.441462958 1.17500782 1.466611766 1.424544601 1.49809476 1.940936004 1.802940074 1.321257299 1.433369274 1 14.2019308 1.034171994 1.282015839 1.019241323 1.632978973 0.261440624 0.337901299 0.642298713 2.169868323 0.307397847 0.094663178 10.81862317 -1.034171994 0.61373765 IFDSEEILAGYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFDSEEILAGYKR 13 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ; 151.26 7.16E-05 1317870000 783740 686510 754790 576190 1001170 940910 755320 719600 725600 717490 FALSE TRUE 814682.6604 804412.7522 774460.4475 690158.6622 830991.481 722397.9121 696116.0447 709954.939 699485.7977 858068.4283 0.949437869 0.937469234 0.902562572 0.804316578 0.968444303 0.841888465 0.811259361 0.827387322 0.815186499 1 19.71073318 2.678369395 24.40200023 0.842917822 0.907280049 0.114440889 0.066137598 318.2996975 129040.4514 0.020457789 0.019287793 476.8363942 -2.678369395 0.064362227 IFEDHENLVENLLNWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFEDHENLVENLLNWTR 17 0 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 0 232.62 8.59E-17 220360000 136700 157610 173020 137440 170970 180730 166990 191150 170120 133160 FALSE TRUE 142097.0216 184678.2915 177529.0433 164625.2218 141908.5805 138758.1965 153900.8875 188587.9469 163997.4144 159250.1525 0.892288135 1.159674189 1.114780994 1.033752365 0.891104833 0.871322221 0.966409671 1.184224592 1.029810093 1 17.28093523 -0.464576438 6.674199063 1.000012224 1.025303107 0 0.106906656 0 0 0.111160942 0.026200885 0.343102247 0.464576438 0.025290884 IFGGLDMLAEKLPNLTHLNLSGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFGGLDMLAEKLPNLTHLNLSGNK 24 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 117.43 0.00042451 161830000 102200 91420 100690 53170 152250 132800 92912 102900 134170 106850 FALSE TRUE 106234.9349 107120.6739 103314.0641 63686.8673 126370.5994 101959.2126 85629.31466 101520.7938 129341.2479 127785.2117 0.831355471 0.838286938 0.808497812 0.498389966 0.988929765 0.797895243 0.670103477 0.794464339 1.012176966 1 16.96336136 1.254785463 6.389827885 1.008252195 0.774706424 0.36810017 0.119330044 0.145476951 22.6981406 0.088225723 0.028747416 17.97982513 -1.254785463 -0.233545771 IFGPIWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFGPIWNR 8 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 184.24 0.00050959 14369500000 1853000 2158700 1997690 2041290 2383000 2457800 2250900 1973050 2068190 2188000 FALSE TRUE 1926157.871 2529439.933 2049751.443 2445051.069 1977938.511 1887013.198 2074468.576 1946604.492 1993756.246 2616696.708 0.736102837 0.966653844 0.783335507 0.934403694 0.75589139 0.721143261 0.792781437 0.743916743 0.761936314 1 21.31931529 3.209566017 24.99726262 0.77714156 0.857962724 0.063044827 0.096389322 379.7043814 327355.4366 0.025329358 0.030279238 1620.190259 -3.209566017 0.080821164 IFHDLDMLTTVQEENEPVIYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IFHDLDMLTTVQEENEPVIYNR 22 0 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 ;;; 263.09 2.15E-37 265325000 115403 139297 149115 154646 120112 152632 144947 118607 110569 122439 FALSE TRUE 119959.1996 163220.1762 153001.0594 185234.5172 99695.40514 117185.5312 133585.6754 117017.2672 106589.6433 146428.5778 0.819233522 1.114674325 1.044885238 1.26501616 0.68084664 0.800291397 0.912292378 0.799142278 0.727929239 1 17.15983762 3.228918819 24.99996475 0.814913258 1.063641968 0.445627303 0.131524049 173.0608412 448724.1867 0.03659849 0.044269441 1694.021113 -3.228918819 0.24872871 IFHELTQTDK ddPTM_MDA-MB-175_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 ;;; 199.67 2.74E-07 2095570000 5064950 3919450 4880310 3936440 6777410 6390880 6092870 4973380 5341520 4103980 FALSE TRUE 5264918.137 4592585.048 5007494.888 4715056.083 5625388.269 4906694.975 5615294.929 4906719.976 5149279.739 4908076.306 1.072705029 0.935719977 1.02025612 0.960672938 1.14614931 0.99971856 1.144092834 0.999723654 1.04914419 1 22.22672625 3.292773003 24.99999918 1.055985919 0.994574191 0.185192702 0.060648299 144.4478656 66610.73078 0.015445629 0.020913468 1962.334334 -3.292773003 -0.061411727 IFHGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFHGLK 6 0 P13796;Q5TBN3 P13796 LCP1 Plastin-2 0 89.775 0.049783 691890000 1774600 1477400 1826400 1496800 2200900 2171100 2031500 1819500 1871000 1645600 FALSE TRUE 1844662.578 1731131.957 1873997.484 1792862.572 1826791.804 1666894.928 1872265.722 1795112.579 1803663.075 1968023.813 0.937317204 0.879629579 0.952222972 0.910996382 0.928236636 0.846989207 0.951343022 0.912139663 0.916484376 1 20.90831625 -0.542424913 0.801524282 1.005837775 0.913883271 0.411483677 0.03047323 18.66993474 7.925324612 0.357550481 0.009407585 0.286797319 0.542424913 -0.091954504 IFHLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFHLWR 6 0 E9PDF6;O43795;O43795-2 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 123.07 0.018947 447390000 235920 311890 273764 268929 388840 376570 302210 277310 269150 410970 FALSE TRUE 245234.3038 365454.6813 280898.5147 322122.3535 322745.1157 289117.3245 278521.9905 273593.113 259463.3441 491491.703 0.498959194 0.74356226 0.571522394 0.655397337 0.656664423 0.588244568 0.566687065 0.55665866 0.527909917 1 18.90680754 -1.583976542 4.654405435 1.004646294 0.598719047 0.760663138 0.067941232 0.003198105 0.000285855 0.06422529 0.015002122 0.026062943 1.583976542 -0.405927247 IFHTVTTTDDPVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IFHTVTTTDDPVIR 14 0 O15371-2;O15371;O15371-3;B0QYA5;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;;; 143.98 8.98E-06 1090340000 931920 1057370 1028600 1049040 1176610 1316150 933290 976580 989760 1158530 FALSE TRUE 968712.9212 1238965.072 1055406.161 1256536.981 976610.2525 1010494.109 860136.2911 963490.5425 954138.7309 1385521.772 0.699168314 0.894222738 0.761739138 0.906905259 0.704868211 0.729323876 0.620803158 0.695399063 0.688649396 1 20.40199795 5.06180532 15.2288425 0.760324095 0.165185866 0.021002374 0.113893112 939688.1007 5486238.969 0.026957218 17178782.74 115293.6318 -5.06180532 -0.59513823 IFLLGLADNEAAIVQAESEETKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFLLGLADNEAAIVQAESEETKER 24 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 156.23 2.77E-08 88455000 213102 153570 204548 161967 279736 260508 211515 192761 219555 151720 FALSE TRUE 221515.4315 179944.4529 209878.6889 194003.5892 232186.5746 200008.965 194935.9016 190177.3541 211653.2584 181446.6291 1.220829687 0.991721112 1.156696544 1.069204703 1.279641158 1.102301905 1.074342921 1.048117317 1.166476663 1 17.46918573 -1.441636476 3.675418698 0.998975516 1.115538031 0.165584433 0.081363461 0.000656934 9.98E-05 0.075769492 0.017703398 0.036171251 1.441636476 0.116562515 IFPGLS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 99.973 0.0052182 48960900 71091 80454 56796 59503 149888 114676 65903 54262 57397 166407 TRUE FALSE 73897.72757 94271.34865 58276.15042 71272.5158 124410.0913 88044.23693 60737.35065 53534.70664 55331.29318 199011.2656 0.371324344 0.473698554 0.2928284 0.358133071 0.625140948 0.442408306 0.30519554 0.269003398 0.27803096 1 17.60249058 -1.450432566 3.521706553 1.007228907 0.376938934 0.760174708 0.104543125 90312172.36 106853704.8 6265721.201 0.027413987 0.035446016 1.450432566 -0.630289972 IFPHLYLGSEWNAANLEELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IFPHLYLGSEWNAANLEELQR 21 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;; 330.09 4.59E-80 788387000 242873 330647 311896 356768 350531 432957 331523 347621 378148 369927 FALSE TRUE 252461.8136 387433.0502 320024.266 427335.6456 290947.8658 332409.2983 305537.361 342961.7091 364538.5273 442407.113 0.570654961 0.875738746 0.723370526 0.965933035 0.657647351 0.751365176 0.690624884 0.775217439 0.823988848 1 18.75501506 0.832825701 2.150894748 0.999665564 0.755812039 0.344570964 0.103925665 0.671989947 5.718609818 0.091938286 0.025195768 6.80496194 -0.832825701 -0.243853525 IFQIHTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFQIHTSR 8 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 177.36 0.00025528 677350000 93849 758290 569320 698320 532520 940110 409200 730310 464840 909020 FALSE TRUE 97554.23099 888520.4088 584156.9469 836445.6117 442002.4406 721783.7 377125.8348 720521.389 448110.4992 1087125.065 0.089735978 0.817312044 0.537341071 0.769410658 0.406579201 0.663938054 0.346901977 0.662776908 0.412197744 1 20.05208649 -2.012577304 2.872721233 1.498400157 0.541401588 0.317079582 0.208466062 154698555.3 144520140.9 507916453.1 0.044720018 0.00971455 2.012577304 -0.956998569 IFQKGESPVDYDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFQKGESPVDYDGGR 15 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 123.29 9.45E-05 402350000 194130 215980 236670 161170 340290 286610 168790 216460 233880 270250 FALSE TRUE 201794.4023 253072.8849 242837.8146 193048.945 282447.6273 220049.1711 155559.7987 213558.7078 225462.7045 323200.3133 0.624363263 0.783021781 0.751353896 0.597304325 0.873908891 0.680844548 0.481310792 0.660762688 0.697594325 1 18.30206907 0.917706246 14.97142612 1.000000001 0.679897115 0.467273353 0.101533476 204.7444622 37250.25896 0.099875001 0.024969431 8.273823376 -0.917706246 -0.320102886 IFQVAQELSGEDMHQFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFQVAQELSGEDMHQFHR 18 0 C4P0D6;C4P0D8;Q99598;C4P0D4;Q5VVQ1 C4P0D6 DISC1;TSNAX Translin-associated protein X 0 67.43 0.017443 103670000 150660 187860 177540 167340 201440 204040 211220 190380 188350 161480 FALSE TRUE 156608.1731 220123.4937 182166.8383 200439.3525 167199.3008 156654.8023 194664.0245 187828.2675 181571.3203 193118.9143 0.810941661 1.139833944 0.943288434 1.037906376 0.86578418 0.811183114 1.008000823 0.972604202 0.940204749 1 17.55912994 6.813039278 9.35350548 0.956072375 0.377932792 0 0.097973267 0 0 0.020747642 0 6501884.908 -6.813039278 -0.578139583 IFRDGEEAGAYDGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IFRDGEEAGAYDGPR 15 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;; 140.81 4.44E-06 2043670000 1155180 2210910 1812050 1320830 2504500 2347990 1202050 1736190 1790540 3203390 FALSE TRUE 1200787.398 2590616.594 1859273.512 1582086.232 2078785.985 1802704.907 1107830.18 1712919.213 1726098.815 3831032.938 0.313436981 0.676218826 0.485319114 0.41296597 0.542617623 0.470553226 0.289172711 0.447116807 0.450557028 1 21.869302 -1.424484558 3.601725971 1.004602732 0.455641686 0.714386418 0.103525858 64722298.43 97389177.22 3055223.585 0.024430687 0.037628373 1.424484558 -0.548961047 IFSNALPDDLRS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IFSNALPDDLRSPIR 15 1 Q9NSY0;E9PR11 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 IFSNALPDDLRS(1)PIR;IFSNALPDDLRS(1)PIR;IFSNALPDDLRS(1)PIR 117.37 0.00022718 130749000 112783 121304 123741 141487 137730 157736 151175 141516 123190 120293 TRUE FALSE 117235.7599 142137.0184 126965.7921 169472.7063 114318.7038 121104.2045 139325.5085 139619.2095 118756.416 143862.1102 0.814917561 0.988008713 0.882551993 1.17802183 0.79464081 0.841807508 0.968465625 0.97050717 0.825487794 1 17.13432715 -1.014579967 3.691708431 1.000016578 0.926589563 0.043010593 0.109500155 19365354.18 36228183.81 4145.253035 0.024894833 0.096698566 1.014579967 -0.073427016 IFSVPPTEETLSEPNFYDTISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFSVPPTEETLSEPNFYDTISK 22 0 E5RKA7;Q96E16 E5RKA7 SMIM19 Small integral membrane protein 19 0 50.425 0.076648 35361000 1540 66243 48437 61194 44363 72452 31178 55555 42998 78944 FALSE TRUE 1600.800389 77619.71995 49699.30801 73297.99055 36822.19311 55626.12102 28734.18689 54810.37609 41450.51038 94411.56533 0.016955554 0.822142072 0.526411228 0.776366649 0.390017822 0.589187573 0.304350286 0.580547266 0.439040601 1 16.52667598 -1.423913023 2.772752522 1.01238592 0.509640996 0.320234379 0.220139376 12830685.25 14204017.29 1248600.908 0.050846425 0.037677925 1.423913023 -0.502744923 IFTLPGDCLIYPAHDYHGFTVSTVEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFTLPGDCLIYPAHDYHGFTVSTVEEER 28 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 183.49 6.85E-18 401120000 51982 69530 60152 61009 68236 84863 68334 56731 66446 70441 FALSE TRUE 54034.2895 81471.23663 61719.61054 73076.39811 56637.26909 65154.85436 62977.80252 55970.61374 64054.62144 84242.56528 0.641413154 0.967102988 0.732641632 0.867452194 0.672311781 0.773419638 0.74757698 0.664398259 0.760359341 1 16.36226175 IFTPLLHQIELEKPKPIPYIYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFTPLLHQIELEKPKPIPYIYGSR 24 2 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 202.15 8.05E-25 15322000000 6209800 5514600 6047800 4895400 9997900 8362600 6233800 6368300 7669200 6609400 FALSE TRUE 6454967.699 6461689.652 6205410.636 5863695.509 8298460.529 6420512.886 5745178.467 6282943.355 7393186.99 7904385.385 0.816631197 0.817481605 0.785059221 0.74182814 1.049855254 0.812272248 0.726834306 0.794868045 0.935327243 1 22.91422186 1.083093991 4.137212193 0.997688507 0.816704875 0.350268983 0.083537256 0.218617892 6.646356132 0.081341959 0.020866643 12.10860161 -1.083093991 -0.180983631 IFTSIGEDYDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IFTSIGEDYDER 12 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 ;;;;; 259.08 6.80E-21 2087782000 2046164 2881763 1949547 2600617 2139373 2919522 2008482 1949779 1639268 2543325 FALSE TRUE 2126948.135 3376683.378 2000353.796 3115011.281 1775723.142 2241507.261 1851051.933 1923645.402 1580271.065 3041640.839 0.699276557 1.110151907 0.657656148 1.024121994 0.583804346 0.736940152 0.608570187 0.632436735 0.519545584 1 21.53641838 3.225892401 24.99802919 0.657944457 0.874387725 0.219094385 0.175106678 281.5523592 555582.7397 0.045948635 0.05526163 1682.257222 -3.225892401 0.216443268 IFTTPLT(ph)PSQYYSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFTTPLTPSQYYSGSK 16 0 P49454 P49454 CENPF Centromere protein F 1 IFTT(0.007)PLT(0.927)PS(0.009)QY(0.001)Y(0.001)S(0.023)GS(0.033)K 95.073 0.0093466 0 83599 79512 77635 77628 83496 107840 80711 85658 71468 57458 TRUE FALSE 86899.55307 93167.56748 79658.23188 92982.5867 69303.37974 82795.79433 74384.66092 84509.89462 68895.88064 68715.795 1.264622684 1.355839185 1.159241945 1.353147216 1.008550942 1.204901935 1.082497276 1.229846713 1.002620731 1 16.06835413 8 0.109937545 0.916896479 2.142278627 0.454158458 0.097016983 95.97659102 0.735819098 0.819480854 17.85328497 100000000 -8 1.225382148 IFVGGIKEDTEEYNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IFVGGIKEDTEEYNLR 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 268.93 1.11E-27 5897310000 4766080 3907950 4633840 3678510 5637870 5682950 5289710 4556220 5121030 3520450 FALSE TRUE 4954248.519 4579110.013 4754601.677 4406108.299 4679546.871 4363170.988 4875088.708 4495151.323 4936725.131 4210214.774 1.17672109 1.087619102 1.129301457 1.046528155 1.111474621 1.036329789 1.157919244 1.067677438 1.172558977 1 22.0054624 -1.820608524 2.815347668 0.967218908 1.104880978 0.315803963 0.047938085 14786126.16 5946843.75 3208218.277 0.010796057 0.01511442 1.820608524 0.13766207 IFVGGLS(ph)PDTPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFVGGLSPDTPEEK 14 0 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;D6RF44;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 IFVGGLS(0.98)PDT(0.02)PEEK;IFVGGLS(0.5)PDT(0.5)PEEK 128.15 0.00022445 13437000 229103 164194 194030 167654 256093 281460 239148 217988 233755 192161 TRUE FALSE 238148.1633 192393.0422 199086.5812 200815.4608 212562.4033 216095.1806 220402.9549 215066.2274 225342.2032 229811.2688 1.036277136 0.837178452 0.866304695 0.873827736 0.924943343 0.940315859 0.959060694 0.935838475 0.980553323 1 17.81009002 2.74357518 1.932905285 0.960286265 0.896656237 0.22447046 0.052318169 0.50783913 3.752626925 0.01899583 0.018768063 554.0834523 -2.74357518 -0.063630028 IFVGGLSPDT(ph)PEEK ddPTM_MDA-MB-175_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(0.161)PDT(0.839)PEEK 199.84 2.86E-07 0 201900 143560 176370 143930 233810 232550 207540 192440 190810 152560 TRUE FALSE 209871.1679 168215.3133 180966.3471 172398.9244 194067.0597 178543.7868 191272.4725 189860.6566 183942.7854 182451.2111 1.150286516 0.921974221 0.991861583 0.944904248 1.063665506 0.978583731 1.048348604 1.040610558 1.008175195 1 17.4771512 3.222321394 24.99747512 1.025944704 0.995779653 0.022123496 0.061069717 774.5540072 1192290.137 0.01671404 0.020031536 1668.481494 -3.222321394 -0.030165051 IFVNDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 187.63 0.0013526 4694410000 5088610 6122840 5497000 5878150 5811470 6616740 5779940 5715340 5063200 5648930 FALSE TRUE 5289512.252 7174390.141 5640256.336 7040830.525 4823638.405 5080102.413 5326893.2 5638735.216 4880976.421 6755729.678 0.78296683 1.061971169 0.834884847 1.04220134 0.714007018 0.751969462 0.788500052 0.834659687 0.722494335 1 22.68768017 3.231060676 24.99982316 0.793466389 0.933066331 0.249198707 0.108695416 206.4987021 688329.1195 0.028581467 0.034794028 1702.396337 -3.231060676 0.139599942 IFYDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IFYDMK 6 0 P60981;F6RFD5 P60981 DSTN Destrin 0 100.82 0.086601 4097100000 1762800 1543200 1813200 1528200 2261400 2135900 2145300 1747500 1746900 1560400 FALSE TRUE 1832396.705 1808232.596 1860453.482 1830473.399 1877008.036 1639869.595 1977145.78 1724077.621 1684029.41 1866130.504 0.98192313 0.968974352 0.996957864 0.980892491 1.005828923 0.878753973 1.059489556 0.923878377 0.902417814 1 20.83161845 IFYPEIEEVQALDDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IFYPEIEEVQALDDTER 17 0 P33316-2;H0YNW5;P33316;A0A0C4DGL3;H0YKC5 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;;;; 270.79 3.16E-35 333924000 66589.9 78705 78942.8 79009.9 85590.9 111316.8 82441.4 83855.4 81830 85512.3 FALSE TRUE 69218.92067 92221.97151 81000.11422 94637.8224 71042.18939 85465.16022 75979.42765 82731.45552 78884.95428 102266.798 0.676846465 0.901778225 0.792047036 0.925401247 0.694675015 0.835707795 0.742953032 0.808976688 0.771364273 1 16.64197831 -0.910380493 5.660611674 1.000000137 0.79821472 0.396549731 0.075951911 1.18E-07 2.28E-08 0.066182157 0.015599273 0.122919138 0.910380493 -0.201785417 IFYPETTDIYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IFYPETTDIYDR 12 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 246.41 3.57E-16 1733789000 880900 1073914 1003774 1096825 1068989 1205707 1149981 1040411 947277 1057732 FALSE TRUE 915678.6122 1258350.376 1029933.175 1313773.711 887282.6316 925699.8219 1059842.484 1026465.992 913184.6858 1264974.334 0.723871297 0.994763563 0.814192942 1.038577366 0.701423426 0.731793363 0.837837145 0.811452031 0.721899774 1 20.27067668 3.218517978 24.99978564 0.792290777 0.894512398 0.133952393 0.113503805 417.3520351 520574.5963 0.030465034 0.036456139 1653.93325 -3.218517978 0.10222162 IFYPETTDIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;; 289.37 2.72E-40 6867020000 3136310 2216195 3035200 2315866 4150560 3744280 3370260 2995880 3292170 2323380 FALSE TRUE 3260133.941 2596809.252 3114299.805 2773937.383 3445049.294 2874727.715 3106090.215 2955725.129 3173685.445 2778601.827 1.17330015 0.934574082 1.120815431 0.998321298 1.239849935 1.034595057 1.117860855 1.063745478 1.142187921 1 21.40592768 IFYVNYLSELSEHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFYVNYLSELSEHVK 15 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 240.2 7.85E-18 755710000 492720 505360 710650 609880 880980 816570 884510 665780 744610 471480 FALSE TRUE 512172.9661 592151.6488 729170.1228 730512.4437 731231.3343 626933.9927 815179.795 656856.3081 717811.6316 563857.479 0.90833763 1.050179648 1.293181611 1.295562214 1.296837165 1.111866059 1.445719575 1.164933219 1.273037351 1 19.10497103 4.425997339 3.471168795 1.247335881 0.927089447 0.453973083 0.116096336 0.17344949 4.123669565 0.026288193 0.097685123 26668.42325 -4.425997339 -0.320246434 IFYYFSNS(ph)PSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IFYYFSNSPSKR 12 1 Q08999;Q08999-2 Q08999 RBL2 Retinoblastoma-like protein 2 1 IFYYFSNS(0.997)PS(0.003)KR;IFYYFSNS(0.998)PS(0.002)KR 127.36 0.00016611 349670000 398570 310850 352610 273320 567640 451800 390570 343750 356670 416140 TRUE FALSE 414305.8514 364236.0694 361799.3063 327381.8802 471152.7556 346876.2971 359956.1028 339142.5935 343833.5164 497674.6655 0.832483307 0.731875851 0.726979554 0.657823078 0.946708338 0.696994083 0.723275923 0.681454406 0.690880087 1 18.92484342 4.745143269 22.86619348 0.746618497 0.832483435 0.0193717 0.110944301 758.7266112 2635342.063 0.024581055 0.225198793 55608.76738 -4.745143269 0.085864938 IGADEEIDDFKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGADEEIDDFKGR 13 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 0 72.496 0.029124 0 68563 47200 54774 37924 63876 64376 54668 54406 56889 38034 FALSE TRUE 71269.92018 55306.23283 56201.45544 45425.25401 53018.38034 49425.64963 50382.97931 53676.77656 54841.576 45486.0341 1.566852807 1.215894811 1.235576074 0.998663764 1.1655969 1.086611542 1.107658215 1.18007159 1.205679438 1 15.47313603 5.130315962 1.302217185 1.122124528 2.225019347 0.771364674 0.073143657 1.489556707 1.114751502 0.019289348 2.792115113 134994.4651 -5.130315962 1.102894819 IGADFLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGADFLAR 8 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 126.28 0.0028522 255350000 353840 420410 435380 391280 552260 542960 457230 436010 433590 477120 FALSE TRUE 367809.8764 492612.1472 446726.3605 468674.0161 458387.0425 416865.7686 421391.1179 430165.9991 417985.1806 570602.529 0.6445991 0.86331925 0.782902875 0.821366875 0.80333861 0.73057119 0.738502016 0.753880288 0.732532997 1 19.12212662 -1.554116907 3.015537158 1.010539717 0.766860893 0.60890975 0.0568147 13963740.88 16286086 1197589.814 0.013136025 0.027917922 1.554116907 -0.243678824 IGAEVYHNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;; 161.63 7.01E-06 14595960000 9767550 8453510 9503740 8070740 15944320 12221180 11293330 9281490 10207000 10994980 FALSE TRUE 10153180.42 9905334.583 9751415.272 9667108.283 13234110.18 9382996.159 10408129.28 9157086.808 9839652.064 13149235.82 0.772149846 0.753301159 0.741595588 0.735184038 1.006454699 0.713577297 0.79153872 0.696396881 0.748306 1 23.64847562 -2.33658632 2.243083207 2.303170852 0.770942381 0.405938268 0.082281844 5960128.397 738828.5998 39405160.25 0.020141424 0.004606952 2.33658632 -1.532228471 IGDEDVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDEDVGR 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 151.56 0.0010961 1192150000 1757390 1845770 1660830 1543310 2103670 2354400 1564220 1598130 1526600 1576810 FALSE TRUE 1826773.114 2162766.639 1704112.594 1848572.112 1746088.925 1807626.281 1441612.349 1576709.681 1471657.964 1885755.73 0.968722028 1.146896496 0.903676212 0.980281848 0.925935898 0.958568627 0.764474596 0.836115546 0.780407526 1 20.84671138 3.08111576 0.891070064 0.834863241 1.031716674 0.355171089 0.086474512 0.537016118 0.941940378 0.042226463 0.058738236 1205.357183 -3.08111576 0.196853432 IGDEYAEDS(ph)S(ph)DEEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDEYAEDSSDEEDIR 16 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 2 IGDEYAEDS(1)S(1)DEEDIR;IGDEYAEDS(1)S(1)DEEDIR 113.29 0.002337 67701000 127414 113773 121781 121228 130728 150971 151315 121658 125225 85821 TRUE FALSE 132444.4031 133312.6277 124954.7129 145206.5366 108506.9013 115910.2732 139454.5349 120027.3735 120718.1767 102635.9818 1.290428569 1.29888783 1.217455231 1.414772227 1.057201377 1.129333701 1.358729487 1.169447317 1.176177931 1 16.64717707 -5 0.121909524 0.215206058 1.349117379 0.390395657 0.097269535 160.9913267 1.266745756 30.96416373 0.88683862 1.00E-05 5 1.133911321 IGDEYFTFITDCKDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDEYFTFITDCKDPK 16 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 162.7 7.28E-09 701970000 1466030 585240 899850 625320 1404180 1098070 1288690 889450 1083480 416360 FALSE TRUE 1523909.996 685750.4175 923300.8302 749006.4296 1165497.985 843059.8839 1187679.11 877528.3776 1044485.766 497937.7703 3.060442664 1.377180962 1.854249437 1.504216941 2.340649886 1.693102902 2.385195864 1.762325395 2.097623094 1 18.92560593 -1.572245018 4.782896779 0.991258537 1.971610246 0.289533617 0.470703868 0.039390271 0.00352284 0.409164582 0.096473796 0.026776572 1.572245018 0.980351709 IGDKDVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDKDVGR 8 1 P45877 P45877 PPIC Peptidyl-prolyl cis-trans isomerase C 0 ; 92.439 0.010741 329330000 721260 654170 673110 520170 964560 980000 727080 731300 743040 729680 FALSE TRUE 749735.9017 766518.6088 690651.7996 623058.0734 800604.4357 752409.852 670089.5697 721498.1197 716298.1355 872646.8254 0.859151583 0.878383541 0.791444808 0.713986524 0.917443819 0.862215767 0.767881748 0.826792809 0.820833944 1 19.73503836 -1.78593206 2.333696387 1.055418516 0.824907848 0.468844148 0.055391797 5421522.311 3382064.97 1706954.976 0.014663319 0.016370726 1.78593206 -0.230510668 IGDKEGALTAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDKEGALTAFR 12 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 69.201 0.04616 842060000 1036900 818830 1051130 755360 1410710 1263050 978560 984530 1050380 997760 FALSE TRUE 1077837.613 959457.6829 1078523.311 904767.9535 1170918.018 969725.7792 901857.9102 971333.9857 1012577.029 1193251.969 0.903277464 0.804069642 0.903852111 0.758237134 0.981283123 0.812674778 0.755798384 0.814022529 0.848586095 1 20.18646729 IGDPLLEDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGDPLLEDTR 10 0 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 138.08 0.0001726 214270000 331340 378750 369740 356280 419900 466120 404490 368130 368470 320350 FALSE TRUE 344421.5591 443797.3662 379375.7281 426751.1206 348525.548 357870.6941 372785.0169 363195.8195 355208.8367 383116.449 0.898999664 1.158387658 0.990236073 1.113894018 0.909711783 0.934104226 0.97303318 0.948003722 0.927156319 1 18.54742344 3.227125946 24.9937624 0.947258679 1.045226863 0.29774762 0.068818884 235.5388177 514837.2708 0.018119226 0.021831289 1687.042199 -3.227125946 0.097968184 IGDQEFDHLPALLEFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGDQEFDHLPALLEFYK 17 0 P46109 P46109 CRKL Crk-like protein 0 144.66 5.04E-07 184520000 451800 320690 365100 316580 472120 539500 482850 370430 386570 269850 FALSE TRUE 469637.4129 375766.0129 374614.8059 379198.5791 391869.211 414209.3012 445002.9553 365464.9918 372657.4212 322721.9409 1.455238561 1.164364629 1.16079745 1.175000925 1.214262687 1.283486645 1.378905178 1.132445444 1.154732214 1 18.29993214 1.056714172 1.559352206 1.007309747 1.246609745 0.401268772 0.095695327 0.394965561 1.937807634 0.089695785 0.026440876 11.39499586 -1.056714172 0.239299998 IGEEFLTDLSQLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGEEFLTDLSQLKK 14 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ; 202.4 2.65E-08 527560000 887160 504200 710700 495220 1247230 875240 905650 646550 887350 435170 FALSE TRUE 922185.7618 590792.4279 729221.4258 593173.0379 1035226.29 671978.7744 834662.7865 637884.0548 855414.4468 520433.2297 1.771957879 1.135193516 1.401181524 1.139767801 1.98916255 1.291191139 1.603784576 1.225678951 1.643658395 1 18.98935356 -0.51550796 8.712656304 0.999999975 1.445308327 0.208130859 0.270258648 0 0 0.239621929 0.05647943 0.30513501 0.51550796 0.445308352 IGEEQS(ph)AEDAEDGPPELLFIHGGHTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 1 IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK 165.8 1.56E-11 112390000 111922 63133 80530 61487 117860 101794 113006 83495 90864 57356 TRUE FALSE 116340.767 73975.60164 82628.67796 73648.94508 97826.1993 78153.8862 104148.2944 82375.8861 87593.82239 68593.81005 1.69608259 1.078458852 1.204608373 1.073696665 1.426166577 1.139372287 1.518333715 1.200923028 1.276993104 1 16.06579077 0.339282479 1.645368405 1.000014413 1.281194872 0.17060236 0.191284034 11.75896243 27.21059697 0.169066334 0.04791253 2.18415009 -0.339282479 0.281180459 IGEEQSAEDAEDGPPELLFIHGGHTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 Q16576;E9PC52;Q16576-2;Q5JNZ6 Q16576 RBBP7 Histone-binding protein RBBP7 0 ;;; 278.52 3.19E-61 1176902000 1084543 672086 926621 670070 1219036 1096034 1107836 870996 1026723 630069 FALSE TRUE 1127361.595 787511.5424 950769.5045 802607.846 1011824.696 841496.7141 1021000.92 859321.7233 989771.4398 753518.9572 1.496129041 1.045111785 1.261772508 1.06514619 1.342799257 1.116755864 1.354977084 1.140411552 1.313532235 1 19.52328428 -1.191256688 3.975756085 0.999866709 1.225694074 0.206557439 0.137879011 10.29393218 31961792.45 8180.839862 0.028235482 0.064378864 1.191256688 0.225827365 IGEGT(ph)YGVVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGEGTYGVVYK 11 0 P06493;A0A024QZP7;A0A087WZZ9;E5RIU6;P06493-2;G3V317;K7ELV5;G3V5T9;P24941;P24941-2;E7ESI2;Q00526 P06493;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 IGEGT(0.935)Y(0.065)GVVYK;IGEGT(0.845)Y(0.155)GVVYK 195.29 1.57E-06 8429100000 1927260 1132770 1569390 1208290 2134450 1987510 1952020 1496390 1660840 1040350 TRUE FALSE 2003349.713 1327314.436 1610289.593 1447286.156 1771636.951 1525940.924 1799015.572 1476333.34 1601066.693 1244186.664 1.610168129 1.066812942 1.294250806 1.163238763 1.423931797 1.226456582 1.445937032 1.186585086 1.286838012 1 20.24677152 0.268413046 0.974463853 0.998549015 1.297081781 0.26801779 0.149581095 4.33787109 4.673554307 0.14509841 0.041801747 1.855295307 -0.268413046 0.298532766 IGEGTY(ph)GVVYK ddPTM_MDA-MB-175_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 1 IGEGT(0.329)Y(0.671)GVVYK;IGEGT(0.33)Y(0.67)GVVYK;IGEGT(0.007)Y(0.993)GVVYK;IGEGT(0.363)Y(0.637)GVVYK 207.68 2.28E-07 10514510000 2714230 1755530 2251020 1709830 3057360 3044040 2892900 2175550 2506050 1538020 TRUE FALSE 2821389.896 2057028.621 2309683.43 2048029.271 2537671.039 2337107.843 2666146.939 2146390.311 2415857.75 1839365.572 1.533892957 1.118335938 1.255695695 1.113443299 1.379644742 1.270605408 1.449492684 1.166918824 1.313419033 1 20.81077681 -0.67850455 0.973856538 0.985563219 1.2796929 0.301515887 0.13109236 62.88907737 31.68062585 3.426900007 0.037549092 0.209650282 0.67850455 0.294129681 IGEHTPSALAIMENANVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IGEHTPSALAIMENANVLAR 20 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BR04;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;; 263.08 1.80E-36 12387441000 1647316 1623132 1883922 1661170 2375312 2325045 2146118 1885826 1814485 1734404 FALSE TRUE 1712353.308 1901892.295 1933018.555 1989744.468 1971557.315 1785088.535 1977899.663 1860549.587 1749182.039 2074227.257 0.825537945 0.916916065 0.931922261 0.959270235 0.950502077 0.860604126 0.953559769 0.896984446 0.843293344 1 20.98414254 4.737473418 5.35714402 0.921248954 0.82179364 0.301446378 0.044727069 0.187988044 19.74924011 0.010262561 0.068843586 54635.31078 -4.737473418 -0.099455314 IGELGAPEVWGLS(ph)PK ddPTM_MDA-MB-175_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 276.14 1.64E-33 3003759000 6180373 2235006 3005414 2278405 4621639 5415548 4892222 3385465 3691882 1480486 TRUE FALSE 6424378.898 2618850.895 3083737.558 2729066.709 3836054.454 4157869.05 4508756.856 3340088.379 3559011.888 1770558.886 3.628446898 1.479109741 1.741674667 1.541358907 2.166578296 2.348337061 2.546516183 1.886459923 2.010106479 1 20.7557734 0.51529144 1.458344904 1.00071529 2.128212172 0.259630761 0.586674694 3.235563561 8.199627644 0.538799178 0.156757101 3.275604356 -0.51529144 1.127496882 IGELVGVLVNHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGELVGVLVNHFK 13 0 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 122.42 0.00023521 81943000 102390 73622 94473 76306 126930 112520 110490 97334 89387 69917 FALSE TRUE 106432.4363 86266.0058 96935.04399 91399.09905 105354.4839 86388.93526 101829.5051 96029.39694 86169.97933 83615.89751 1.272873215 1.031693833 1.159289643 1.093082796 1.2599815 1.033164001 1.217824697 1.148458604 1.030545409 1 16.35148964 1.18991588 4.57372063 1.00536444 1.149584438 0.32451425 0.07931597 0.220549941 9.161595016 0.065916489 0.017562337 15.48516651 -1.18991588 0.144219998 IGEWELIQESGVPLKPLFGPGYTGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGEWELIQESGVPLKPLFGPGYTGIR 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 184.88 1.38E-17 754140000 504230 399280 568730 477530 687160 647530 586650 528980 637650 449840 FALSE TRUE 524137.3898 467853.234 583551.571 571984.0087 570356.7886 497150.9709 540666.8401 521889.8883 614701.1011 537977.5353 0.974273748 0.86965199 1.084713641 1.063211698 1.060186999 0.924111024 1.004998917 0.970096062 1.142614813 1 19.0371864 4.241304393 24.99998715 1.024334923 0.921962873 0.319634898 0.063133297 84.66321762 771371.4692 0.015545859 0.038863523 17430.28118 -4.241304393 -0.10237205 IGEYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGEYLEK 7 0 Q86VP6;Q86VP6-2;H0YH27;Q86VP6-3 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 101.99 0.020244 62631000 107490 65299 91028 73394 118610 115830 108830 87940 107300 62751 FALSE TRUE 111733.7882 76513.59529 93400.26446 87911.11414 98448.71457 88930.23792 100299.6202 86761.30814 103438.294 75045.85701 1.488873506 1.019557886 1.244575892 1.171431944 1.311847429 1.185011958 1.336511091 1.156110565 1.378334502 1 16.19548481 -1.62533262 2.935223975 0.980794212 1.241784235 0.264116746 0.125891211 23855637.01 27728702.67 3554620.413 0.027851802 0.023695582 1.62533262 0.260990023 IGFPWSEIR ddPTM_MDA-MB-175_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 ; 143.61 0.00023621 2835400000 329880 429450 351610 360760 556330 476550 374400 381110 359530 550390 FALSE TRUE 342903.9171 503204.6968 360773.2455 432117.2512 461765.2253 365878.4847 345053.5497 376001.8438 346590.5855 658228.3826 0.520949759 0.764483438 0.54809737 0.656485291 0.701527369 0.5558534 0.524215544 0.571233107 0.526550654 1 19.32822871 -2.026450497 2.937744497 1.480061183 0.598584465 0.698034047 0.079587661 4823398.816 11595429.53 15506372.16 0.018931987 0.009409131 2.026450497 -0.881476718 IGGAQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IGGAQNR 7 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ;;; 106.84 0.01771 604573000 315318 377478 398256 367151 333865 502052 355940 389740 441726 413887 FALSE TRUE 327766.9981 442306.9101 408634.8785 439772.372 277114.7466 385458.0317 328040.4927 384516.1728 425828.3675 494980.2333 0.662181994 0.893584997 0.825557974 0.888464513 0.559850127 0.778734191 0.662734531 0.77683137 0.860293682 1 18.91701139 0.972688023 2.525024386 0.998859822 0.757181167 0.373244894 0.099047557 0.31525293 4.611003997 0.093542299 0.025211325 9.390484998 -0.972688023 -0.241678655 IGGELEEQAVMLEDFSHELESTQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IGGELEEQAVMLEDFSHELESTQSR 25 0 O43752;O43752-2 O43752 STX6 Syntaxin-6 0 ;;;; 223.41 9.38E-34 137930200 78668.8 105902.8 95924.3 108250.8 120278.7 126809.6 96313.3 95101.2 88595.6 97529.3 FALSE TRUE 81774.70497 124090.7821 98424.16606 129662.4851 99833.76954 97359.99222 88764.01188 93826.52397 85407.06166 116638.299 0.701096515 1.063893962 0.84384089 1.111663032 0.855926144 0.834717182 0.76101943 0.804422945 0.732238573 1 16.83168206 3.011244639 24.99937849 0.81202119 0.939800456 0.12702921 0.124899589 347.3027662 772126.7554 0.033405611 0.039897779 1026.229842 -3.011244639 0.127779266 IGGIFAFK ddPTM_MDA-MB-175_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 0 118.06 0.0091514 0 162470 207990 190600 186390 249740 263540 195080 211470 203070 234430 FALSE TRUE 168884.4411 243710.6646 195567.1926 223257.3857 207289.284 202336.829 179789.1199 208635.5905 195761.5504 280362.0701 0.602379776 0.86927117 0.697552249 0.796318081 0.739362796 0.721698299 0.641274762 0.744164824 0.698245488 1 18.09693166 -1.150887444 6.030006361 1.000002069 0.727148032 0.578424827 0.070784572 1.80E-06 2.53E-07 0.062602755 0.014755499 0.070650063 1.150887444 -0.272854038 IGGILANELSVDEAALHAAVIAINEAIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGGILANELSVDEAALHAAVIAINEAIDR 29 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 113.6 0.00024939 3383600000 58379 78923 70383 52264 92125 98878 83267 96757 83807 57209 FALSE TRUE 60683.848 92477.41131 72217.2388 62601.66321 76465.62541 75915.08301 76740.31496 95460.13068 80790.80244 68418.00822 0.886957244 1.351653077 1.055529687 0.914988098 1.117624254 1.109577507 1.121639126 1.395248607 1.180841193 1 16.06208848 1.97849992 22.61802003 1.24157087 1.082500001 0.083194646 0.150697151 368.8061414 387981.2454 0.05935086 0.038816771 95.16996728 -1.97849992 -0.159070869 IGGILANELSVDEAALHAAVIAINEAIDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGGILANELSVDEAALHAAVIAINEAIDRR 30 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 73.805 0.0032437 286510000 239130 56579 81279 50989 92510 121490 86170 85469 76426 54815 FALSE TRUE 248571.037 66296.00313 83397.19751 61074.47201 76785.18324 93275.7887 79415.77024 84323.42785 73675.44319 65554.94975 3.791796622 1.011304308 1.272172396 0.931653098 1.17131023 1.422864163 1.211438199 1.286301464 1.123873078 1 16.0004171 4.740809412 24.99971038 1.180107664 3.791797525 0.968079725 0.14337654 31.16048331 346386.789 0.033860583 0.225546465 55056.603 -4.740809412 2.611689861 IGGVTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGGVTER 7 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 79.939 0.096047 0 45686 71156 73045 56156 56039 95523 71150 53094 59801 74425 FALSE TRUE 47489.71856 83376.48948 74948.61271 67263.48919 46513.5108 73339.23092 65573.07708 52382.36177 57648.77369 89007.1538 0.533549457 0.936739194 0.84205156 0.755708798 0.522581712 0.823970072 0.73671693 0.588518558 0.647686969 1 16.44163367 3.466312962 24.95436878 0.693210637 0.789293387 0.000767761 0.156584244 563.0669435 1300013.508 0.041204451 0.055844505 2926.260343 -3.466312962 0.096082749 IGHKVESESYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGHKVESESYR 11 1 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 143.97 2.22E-05 102640000 30411 32867 32159 24693 51309 42335 30425 31479 36279 35716 FALSE TRUE 31611.64976 38511.65158 32997.08996 29577.2017 42587.51451 32503.33784 28040.209 31057.07549 34973.32588 42713.86638 0.740079334 0.901619424 0.772514707 0.692449647 0.9970419 0.760955179 0.656466187 0.727095862 0.818781554 1 15.38241687 IGHPAPNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 116.73 0.0012671 12437320000 11604390 10259630 11050490 9332450 13859230 13562010 13003290 11228250 11899530 10097230 FALSE TRUE 12062540.28 12021641.64 11338474.85 11178380.76 11503443.03 10412438.71 11984058.15 11077753.67 11471268.24 12075588.9 0.998919422 0.995532537 0.938958335 0.925700672 0.952619631 0.862271712 0.992420184 0.917367573 0.949955181 1 23.52559021 4.241839112 6.57727828 0.937919516 0.997808546 0.25649844 0.036717004 0.150769253 29.77592937 0.008321162 0.020782213 17451.7552 -4.241839112 0.059889029 IGIARPEEEFHVPLDSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGIARPEEEFHVPLDSYR 18 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 65.784 0.019764 83651000 104470 112610 120880 101350 101810 126980 113380 114160 106880 109440 FALSE TRUE 108594.5563 131949.8915 124030.2321 121396.7275 84504.37257 97490.8194 104492.9793 112629.8719 103033.4097 130882.6726 0.82970919 1.008154012 0.947644402 0.927523293 0.645649809 0.744871857 0.798371375 0.86054074 0.787219634 1 16.99791459 3.431193791 24.99995984 0.799037946 0.936654158 0.287657545 0.09350967 138.7921446 75549.06919 0.025200754 0.034121994 2698.943489 -3.431193791 0.137616212 IGIEIIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGIEIIKR 8 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 102.46 0.007953 335990000 203550 185160 192100 164770 221630 276260 206080 176120 196600 195600 FALSE TRUE 211586.3112 216959.7897 197106.2838 197361.0142 183957.4118 212102.8018 189926.9111 173759.3995 189524.4044 233924.075 0.904508487 0.927479524 0.842607944 0.843696888 0.786397945 0.906716428 0.811916906 0.74280255 0.810196233 1 17.83568082 4.156791693 4.337897594 0.826971768 0.916265103 0.125186021 0.067946643 0.304210348 10.5038261 0.016768214 0.039995313 14348.01075 -4.156791693 0.089293336 IGITNHDEYSLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGITNHDEYSLVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 76.588 0.028261 162150000 83159 76621 80109 73826 95884 118690 85185 100270 92394 83547 FALSE TRUE 86442.18153 89780.06072 82196.70635 88428.56245 79585.67193 91126.04626 78507.97711 98926.04466 89068.75799 99916.43505 0.865144773 0.898551481 0.822654514 0.885025195 0.796522333 0.912022594 0.785736371 0.990087813 0.891432505 1 16.60843438 1.705340729 10.06032327 0.954430662 0.854364176 0.517604855 0.047709671 0.086930294 18.03499347 0.020542651 0.011101459 50.73886276 -1.705340729 -0.100066486 IGKPAPDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGKPAPDFK 9 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 70.808 0.046843 10083700000 15716500 9366800 13243600 9624100 18640500 15936200 15647900 14480800 15555900 9175900 FALSE TRUE 16336999.56 10975475.04 13588739.1 11527718.25 15471994.47 12235259.07 14421376.71 14286708.56 14996046.2 10973741.92 1.488735535 1.000157933 1.238295851 1.05048199 1.409910546 1.114957792 1.314171302 1.301899449 1.36653899 1 23.38755222 3.242859361 24.99936841 1.266518064 1.183676311 0.02092713 0.16599845 349.2817442 2031230.113 0.042912801 0.056119247 1749.28012 -3.242859361 -0.082841753 IGKPHTVPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGKPHTVPCK 10 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 109.59 0.0012008 2427100000 4108800 2832300 3982200 2958000 4900500 4640500 4665900 3964200 4315700 2901300 FALSE TRUE 4271018.597 3318725.493 4085979.403 3543083.571 4067514.76 3562814.202 4300174.566 3911066.383 4160378.8 3469754.186 1.230928293 0.956472797 1.177599099 1.021133885 1.172277499 1.026820348 1.239331185 1.127188317 1.199041366 1 21.72640203 2.250437055 24.99905572 1.152451376 1.094689977 0.04149579 0.097043183 565.7585282 1190881.849 0.030394567 0.025238274 178.0069893 -2.250437055 -0.057761399 IGLDDEEKLDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 161.76 3.64E-05 320950000 782560 442690 629620 483060 875720 814550 881080 623710 698970 348700 FALSE TRUE 813456.0731 518718.5638 646028.4144 578607.8262 726865.4272 625383.1071 812018.6473 615350.1876 673814.2062 417021.0887 1.95063534 1.243866504 1.549150467 1.387478576 1.742994412 1.499643841 1.94718845 1.475585298 1.615779692 1 18.66976082 -1.230430445 3.14405182 0.997782963 1.590829099 0.410850665 0.215707396 13519755.41 18794700.87 294908.4403 0.049503284 0.058826032 1.230430445 0.593046136 IGLIHGHQVIPWGDMASLALLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGLIHGHQVIPWGDMASLALLQR 23 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 216.04 1.51E-32 750890000 344810 312760 376150 365210 380180 465940 407980 339270 402720 300880 FALSE TRUE 358423.3651 366474.0971 385952.778 437447.448 315557.1394 357732.4964 376001.4615 334722.6406 388226.1859 359831.6753 0.996086197 1.018459803 1.072592561 1.215700223 0.876957647 0.99416622 1.044937084 0.930220054 1.078910537 1 18.45696266 3.222926704 24.99998309 0.984668067 1.071397832 0.246368474 0.075302289 351.1895823 561581.6963 0.021803354 0.026146207 1670.808609 -3.222926704 0.086729764 IGNFLNYGSHTGDADGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGNFLNYGSHTGDADGFK 18 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 123.19 3.45E-05 595890000 243630 188190 268410 220580 379140 331660 316480 277440 302940 198690 FALSE TRUE 253248.7005 220510.1686 275404.9851 264210.0656 314693.9182 254636.9914 291673.4706 273721.3706 292037.2486 237619.5014 1.065774059 0.927996933 1.159016762 1.111903965 1.324360654 1.071616555 1.2274812 1.151931424 1.229012126 1 17.85829372 4.214967454 18.15982845 1.168498312 0.996887708 0.33586473 0.090702967 8.69608948 6693.988902 0.020460542 0.044371893 16404.66833 -4.214967454 -0.171610604 IGNSYFKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGNSYFKEEK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 83.081 0.014669 582160000 1692900 1057100 1496000 851520 2582600 1899400 1502200 1483500 1854900 1350000 FALSE TRUE 1759736.999 1238648.702 1534986.989 1019948.114 2143610.574 1458293.136 1384453.639 1463616.109 1788142.511 1614506.653 1.08995339 0.767199503 0.950746772 0.631739803 1.327718638 0.903243807 0.857508785 0.906540773 1.107547317 1 20.62266196 IGQQVDREPGDVAT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGQQVDREPGDVATPPR 17 1 H3BT22;Q9Y5N6 H3BT22 ORC6 Origin recognition complex subunit 6 1 IGQQVDREPGDVAT(1)PPR;IGQQVDREPGDVAT(1)PPR 91.531 0.0057109 265480000 202455 226000 209546 212850 255590 288410 242070 228110 235250 242690 TRUE FALSE 210448.0797 264813.742 215006.9409 254951.0947 212144.9031 221431.1484 223095.9209 225052.5586 226783.3985 290240.4589 0.725081818 0.912394306 0.740789005 0.878413353 0.730928086 0.762923092 0.768658931 0.775400368 0.781363836 1 18.14688912 -1.255111505 4.480225855 1.000097811 0.787355432 0.545350367 0.058550889 5.23E-05 8.69E-06 0.05179387 0.012202332 0.055576155 1.255111505 -0.212742379 IGRPSETGIIGIIDPECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IGRPSETGIIGIIDPECR 18 1 Q16531;F5GY55;F5H2L3;F5GWI0;F5GZY8 Q16531 DDB1 DNA damage-binding protein 1 0 ;; 144.72 8.78E-08 544243000 605875 677424 672174 722639 758943 853780 701362 747447 724422 639170 FALSE TRUE 629795.4128 793766.3024 689691.4066 865574.8373 629938.1399 655502.5342 646387.4138 737428.6955 698350.1937 764403.1239 0.823904813 1.038413211 0.902261366 1.132353872 0.82409153 0.857535133 0.845610639 0.964711776 0.91358888 1 19.54397415 4.80015699 21.49688986 0.93623929 0.823899307 0.129476083 0.090790479 31926.12593 11139581.2 0.021328482 38.10723648 63118.54666 -4.80015699 -0.112339983 IGSIS(ph)R ddPTM_MDA-MB-175_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 IGS(0.001)IS(0.999)R;IGSIS(1)R 98.457 0.041867 363690000 171575 192403 243410 163912 302280 225180 227730 232940 266830 227580 TRUE FALSE 178348.9135 225446.7186 249753.4646 196333.3044 250898.5536 172885.3576 209879.9275 229817.8203 257226.8404 272169.9437 0.655285117 0.828330695 0.917637933 0.721362916 0.92184519 0.635211057 0.77113558 0.844390887 0.945096424 1 18.05414823 1.263638365 2.204300009 0.995790336 0.784546362 0.421585139 0.090580949 0.285202816 2.341714954 0.080203594 0.023344064 18.35009704 -1.263638365 -0.211243975 IGSLEWYYEHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGSLEWYYEHVK 12 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 146.5 6.08E-05 728950000 1083200 840780 1124350 826680 1674760 1390110 1208200 1023590 1172240 1191120 FALSE TRUE 1125965.572 985177.4246 1153651.485 990194.8366 1390084.893 1067278.02 1113498.127 1009870.45 1130051.311 1424497.159 0.790430199 0.691596623 0.809865767 0.695118857 0.975842517 0.749231414 0.781678026 0.708931179 0.793298396 1 20.44202131 -2.033410295 2.082219866 1.265575194 0.773735511 0.423422302 0.077848932 4441874.285 1404848.503 5627116.834 0.018754975 0.009259546 2.033410295 -0.491839683 IGSLGLGTGEDDDYVDDFNSTSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IGSLGLGTGEDDDYVDDFNSTSHR 24 0 O95684;O95684-2;A0A087WV25;O95684-3 O95684 FGFR1OP FGFR1 oncogene partner 0 ;; 242.71 1.21E-37 280393000 84900 106873 113147 98829 121873 144907 118309 117938 120246 115234 FALSE TRUE 88251.91756 125227.6064 116095.7038 118377.0812 101157.071 111254.5453 109035.6314 116357.234 115918.3699 137811.896 0.640379533 0.908685027 0.842421497 0.858975783 0.73402278 0.807292756 0.791191723 0.844319231 0.841134716 1 17.0723409 0.490214717 0.948477073 1.000535159 0.80454341 0.423116712 0.069406007 1.66529706 2.159260599 0.06441742 0.020499631 3.091823662 -0.490214717 -0.195991749 IGTEPSTAPAPS(ph)PPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGTEPSTAPAPSPPAPK 17 0 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 IGTEPSTAPAPS(1)PPAPK 176.29 9.56E-14 0 61308 42743 48706 37719 63538 64451 60186 49628 54901 35592 TRUE FALSE 63728.48718 50083.77776 49975.31837 45179.70562 52737.83346 49483.23201 55468.46405 48962.81784 52925.12373 42565.57095 1.497183892 1.176626476 1.174078422 1.061414298 1.238978646 1.162517756 1.303129802 1.150291579 1.243378687 1 15.37739936 -4.999999997 0.027821254 1.26E-07 1.938657561 0.29086516 0.108709192 2617.462381 5.490628409 288.9996461 125.0688407 1.00E-05 4.999999997 1.938657435 IGTLQDRPPS(ph)PFREPPGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGTLQDRPPSPFREPPGSER 20 2 Q86UU1-3;Q86UU1-2;Q86UU1 Q86UU1-3 PHLDB1 Pleckstrin homology-like domain family B member 1 1 IGT(0.012)LQDRPPS(0.984)PFREPPGS(0.004)ER 48.286 0.081702 113920000 28772 52975 58168 58208 52693 70616 45852 57075 49252 53691 TRUE FALSE 29907.94078 62073.04416 59683.90587 69721.36867 43736.26268 54216.5042 42258.00043 56310.00298 47479.43014 64210.72347 0.465777975 0.966708375 0.929500598 1.08582126 0.681136426 0.844352801 0.658114379 0.87695637 0.739431478 1 15.97052663 IGTYTGPLQHGIVYSGGSSDTICDLLGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IGTYTGPLQHGIVYSGGSSDTICDLLGAK 29 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 215.26 2.84E-34 321330000 295580 233350 321190 263280 378420 362190 328200 310510 342670 226350 FALSE TRUE 307249.7266 273426.0473 329560.4753 315355.9982 314096.3036 278076.8615 302474.8264 306348.1213 330337.3736 270698.9488 1.135023716 1.010074286 1.21744276 1.164969423 1.160315934 1.027255048 1.117384562 1.131693059 1.220312732 1 18.04632976 -1.214559357 4.939738732 0.999983009 1.128855042 0.264691129 0.065662344 1.20E-05 1.91E-06 0.062303835 0.014683219 0.061015566 1.214559357 0.128872033 IGVDHVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGVDHVAR 8 0 Q7L5N1;E7EM64;H7C3T0 Q7L5N1 COPS6 COP9 signalosome complex subunit 6 0 146.54 0.0010808 0 96313 138150 123740 128130 130110 144570 122840 117690 113550 149730 FALSE TRUE 100115.5116 161876.1878 126964.7661 153473.7316 107993.9487 110995.8085 113211.4798 116112.5581 109463.3577 179066.7267 0.559096117 0.903999256 0.709036058 0.857075652 0.603093331 0.619857248 0.632230688 0.648431789 0.611299261 1 17.45013776 -1.191274809 4.408816751 1.000085399 0.685967924 0.441414553 0.107030366 6.292298594 45640399.95 7258.029492 0.025709656 0.064376178 1.191274809 -0.314117475 IGYLAASQSFHEGTDVIMLTTNQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IGYLAASQSFHEGTDVIMLTTNQIR 25 0 O14617-5;O14617-2;O14617;O14617-4;A0A2R8Y4J3;A0A2R8YCY8 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 128.17 0.00011402 22352000 9942.5 22044 23014 19906 27032 29477 18854 21236 16590 22017 FALSE TRUE 10335.03758 25829.88552 23613.76375 23843.34739 22437.1103 22631.41348 17376.17421 20951.36616 15992.92914 26330.80961 0.392507398 0.980975743 0.896811154 0.905530356 0.852123829 0.859503138 0.659917962 0.795697757 0.607384633 1 14.68446426 -0.169569033 9.192359207 1 0.786817263 0.139008573 0.166522007 0 0 0.152503164 0.03594534 0.676754211 0.169569033 -0.213182737 IHCTQTLLEGDGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHCTQTLLEGDGPK 14 0 P29762 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 134.88 3.61E-05 521970000 1162300 322300 366340 296650 572930 690390 490140 444630 426920 271400 FALSE TRUE 1208188.501 377652.5179 375887.1214 355326.4846 475543.5632 530057.3855 451721.5461 438670.4621 411555.2326 324575.6337 3.722363529 1.163527014 1.158087922 1.094741711 1.465124038 1.633078181 1.39172969 1.351520005 1.267979447 1 18.30819517 4.740607491 24.9991639 1.3057291 3.722364355 0.943084255 0.179857611 40.29252584 492071.9244 0.045033795 0.295877532 55031.01096 -4.740607491 2.416635255 IHDENLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IHDENLR 7 0 O95232;J3KPP4;D6RDI2 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 170.87 0.0009588 2148260000 537094 573830 624408 626851 660515 729785 617253 647884 578977 585266 FALSE TRUE 558298.8858 672380.8387 640680.5854 750840.2568 548240.8962 560303.4937 568871.097 639200.1747 558139.7309 699937.6671 0.797640864 0.960629596 0.915339487 1.072724461 0.783271028 0.800504845 0.812745368 0.913224427 0.79741348 1 19.41686692 3.19989477 24.99999945 0.846552831 0.936784555 0.184959993 0.087488844 251.6842751 162729.6335 0.024467657 0.029244953 1584.509217 -3.19989477 0.090231724 IHDPQLLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IHDPQLLTER 10 0 P14868;P14868-2;H7BZ35 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;; 142.89 3.49E-05 2275860000 1373900 1551560 1551160 1443240 1792520 1942890 1556880 1481320 1436460 1652050 FALSE TRUE 1428142.633 1818028.361 1591584.504 1728708.564 1487828.091 1491683.242 1434847.677 1461465.328 1384762.085 1975737.567 0.722840248 0.920177047 0.805564732 0.874968717 0.753049451 0.755000698 0.72623394 0.7397062 0.700883613 1 20.9139599 3.222463449 24.95636797 0.759919931 0.835456715 0.046245988 0.092224296 442.6848685 686318.3702 0.024371364 0.029216219 1669.027334 -3.222463449 0.075536785 IHEDIFDIIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IHEDIFDIIDR 11 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;;;;;;; 188.96 2.92E-06 1240004000 851164 878189 923514 945835 1031228 1169197 1077928 948154 951176 780312 FALSE TRUE 884768.612 1029011.129 947581.5335 1132918.34 855940.2329 897668.7161 993437.1867 935445.5465 916943.3616 933199.1964 0.948102629 1.102670398 1.015411862 1.214015555 0.917210641 0.961926156 1.064549981 1.00240715 0.982580531 1 19.83182554 3.182836016 24.99999929 0.99321803 1.068484585 0.235577227 0.071933937 134.6178106 60393.54215 0.020222183 0.024170142 1523.477401 -3.182836016 0.075266555 IHEGCEEPATHNALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IHEGCEEPATHNALAK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 306.69 5.71E-47 8282630000 6210560 4713390 6351270 5126170 7586880 8017230 6778990 5854620 6762700 4575200 FALSE TRUE 6455757.704 5522878.067 6516789.314 6140111.126 6297264.848 6155349.835 6247635.05 5776148.395 6519311.748 5471622.843 1.179861604 1.009367463 1.19101581 1.122173677 1.15089527 1.124958721 1.141824872 1.055655436 1.191476813 1 22.38353736 -1.647936988 2.927655465 0.988484184 1.123665996 0.322908702 0.055728734 24725385.13 28239216.59 2182661.644 0.012379486 0.022493809 1.647936988 0.135181812 IHEKDPNSATATAPPS(ph)PLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHEKDPNSATATAPPSPLKR 20 2 Q92766;Q92766-2;Q92766-5;Q92766-3;C9JU34;Q92766-6 Q92766 RREB1 Ras-responsive element-binding protein 1 1 IHEKDPNSATAT(0.001)APPS(0.999)PLKR 128.07 1.06E-05 105390000 94852 61384 96843 54538 112500 95643 111870 87052 96097 50692 TRUE FALSE 98596.8302 71926.2245 99366.80814 65325.45362 93377.29018 73431.36273 103101.3371 85885.21033 92638.48774 60624.12684 1.626362891 1.186429038 1.639063741 1.077548775 1.540266146 1.211256418 1.700665106 1.416683667 1.528079538 1 15.88760444 -1.158415921 4.7920677 0.999960021 1.431287136 0.295039571 0.202175282 7.68E-05 1.35E-05 0.174143069 0.041042119 0.069435902 1.158415921 0.431327115 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGR 39 0 Q99436;Q5TBG5;Q99436-2 Q99436 PSMB7 Proteasome subunit beta type-7;Proteasome subunit beta type 0 ; 298.06 7.07E-93 887230000 27671.5 50390 34992 57513 41643 53378 37597 54060 53699 47550 FALSE TRUE 28763.99219 59044.09052 35903.92027 68888.89974 34564.53773 40981.76845 34650.0489 53335.41412 51766.38348 56866.5121 0.505816009 1.038292808 0.631371944 1.211414191 0.607818846 0.720666117 0.609322563 0.937905494 0.910314024 1 15.7952917 1.604655237 14.540629 0.943706123 0.77598408 0.149519763 0.203892297 0.145632468 223.0096981 0.098225379 0.048883081 40.23974654 -1.604655237 -0.167722043 IHFPLATYAPVISAEK ddPTM_MDA-MB-175_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 ; 176.32 3.21E-09 8215500000 2097080 1823120 2082980 1907470 2594320 2760310 2390850 2134320 2271850 1781560 FALSE TRUE 2179874.338 2136226.678 2137264.17 2284761.873 2153338.413 2119269.835 2203448.93 2105712.931 2190086.562 2130622.572 1.023116138 1.002630267 1.00311721 1.072344723 1.010661598 0.994671634 1.034180788 0.98830875 1.027909209 1 21.02284362 1.742845536 24.99999997 1.004820903 1.019445993 0.081036162 0.022579093 2.154345084 12627.51532 0.010474592 0.005808889 55.31533358 -1.742845536 0.01462509 IHGS(ph)GHVEEPASPLAAYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHGSGHVEEPASPLAAYQK 19 0 Q12955;A0A087WY90;H0Y951;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IHGS(0.565)GHVEEPAS(0.435)PLAAYQK 78.987 0.01564 448190000 87897 324020 347070 303240 375440 470980 347790 386390 343760 352110 TRUE FALSE 91367.24143 379667.9145 356114.9293 363219.9669 311622.8429 361602.0328 320529.311 381211.0741 331388.1447 421099.2129 0.216973194 0.901611551 0.845679399 0.862551997 0.740022383 0.858709828 0.761172905 0.90527615 0.786959782 1 18.68380065 4.741762439 24.96988655 0.844054869 0.216972959 0.872423271 0.072726403 89.47515187 697752.1558 0.01576365 0.113057478 55177.55331 -4.741762439 -0.627081909 QHWTMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHWTMTK 7 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 103.56 0.0083479 357960000 414210 845020 1068000 885520 1259600 1296800 1174000 1081600 1212100 823900 FALSE TRUE 430563.3306 990145.6117 1095832.957 1060673.213 1045493.642 995637.8532 1081978.812 1067102.921 1168476.758 985327.4305 0.436974875 1.004889929 1.112151071 1.076467761 1.06106215 1.010463956 1.098090623 1.082993214 1.185876615 1 19.9102437 4.738573972 3.57871839 1.079012066 0.362550956 0.9377255 0.049273591 0.058475373 1.346131439 0.011529702 0.112639953 54773.93876 -4.738573972 -0.71646111 down IHGTEEGQQILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHGTEEGQQILK 12 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5;F5H763;F5H0Z7;F5H3L6;F5H2F3;F5GZW1;F5H4Y4;F5H7R5;F5GWK2;F5H073;F5H1L0;F8W6T3;F5H068;F5GWA2 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 123.67 0.00033662 770090000 1049470 935180 1211380 991550 1336070 1486020 1342450 1151360 1178790 857470 FALSE TRUE 1090903.886 1095789.89 1242949.558 1187675.631 1108965.299 1140914.376 1237225.261 1135927.902 1136365.578 1025474.829 1.063803669 1.068568295 1.212072225 1.158171412 1.0814164 1.112571799 1.206490131 1.1077092 1.108136003 1 19.96786065 0.703231228 2.019395357 1.000118069 1.129271636 0.366129834 0.049590422 1.433047171 8.147334011 0.048205444 0.01328778 5.049300623 -0.703231228 0.129153567 IHGVGFK ddPTM_MDA-MB-175_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 2529600000 5580400 4639900 5559200 4810400 6652800 7083300 6637100 5713400 5837100 4567700 FALSE TRUE 5800718.501 5436766.732 5704077.319 5761882.762 5521959.432 5438310.923 6116866.759 5636821.218 5627023.911 5462653.361 1.061886618 0.995261162 1.044195365 1.0547773 1.010856642 0.995543844 1.119761104 1.031883381 1.030089874 1 22.38117045 IHGVNSGSSEGAQPNTENGVPEITDAATDQGPAES(ph)PPTS(ph)PSSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHGVNSGSSEGAQPNTENGVPEITDAATDQGPAESPPTSPSSASR 45 0 Q8IWE2 Q8IWE2 FAM114A1 Protein NOXP20 2 IHGVNSGSSEGAQPNTENGVPEITDAATDQGPAES(0.976)PPT(0.126)S(0.715)PS(0.136)S(0.023)AS(0.023)R 159.76 1.23E-20 100050000 12035 16262 18116 15843 22857 28708 16812 20973 17654 17371 TRUE FALSE 12510.15109 19054.872 18588.11784 18976.69811 18971.7753 22041.00207 15494.23151 20691.89124 17018.63599 20774.51486 0.6021874 0.917223441 0.894755809 0.91346047 0.913223506 1.060963504 0.745828801 0.996022837 0.819207385 1 14.34252717 4.738604292 22.82732953 0.916860615 0.602187358 0.550411646 0.085583898 0.720963244 372261.8837 0.018385306 0.105808761 54777.76287 -4.738604292 -0.314673257 IHIDLPNEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHIDLPNEQAR 11 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 167.18 1.95E-05 567250000 248570 255640 264120 247450 300490 328740 267510 260470 251120 273210 FALSE TRUE 258383.7355 299544.1814 271003.1842 296394.8714 249412.8171 252395.1171 246541.8672 256978.8257 242082.2403 326740.2686 0.790792444 0.916765426 0.829414707 0.907126853 0.763336635 0.772464068 0.754549992 0.786492668 0.740901149 1 18.31778474 3.228971065 24.99835632 0.787443372 0.862748462 0.098980445 0.077724503 316.1500809 824149.3115 0.020328326 0.024588318 1694.224919 -3.228971065 0.07530509 IHIVMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHIVMK 6 0 B8ZZF8;Q9Y4Y9 B8ZZF8 LSM5 U6 snRNA-associated Sm-like protein LSm5 0 ; 72.054 0.086609 584970000 964870 1164190 1179430 1155380 1476180 1655700 1283280 1208670 1174570 1285130 FALSE TRUE 1002963.813 1364130.576 1210166.915 1383910.716 1225259.451 1271188.767 1182693.16 1192469.756 1132297.455 1536926.618 0.652577554 0.887570402 0.787394076 0.900440333 0.797214022 0.827097893 0.769518301 0.775879435 0.736728378 1 20.55161685 -2.302148467 2.339056264 2.03274084 0.79713761 0.45773454 0.067530532 3248932.079 559332.6813 17774282.34 0.015496587 0.00498714 2.302148467 -1.235603231 IHLDDANESDHFENIQSTNWQTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHLDDANESDHFENIQSTNWQTMR 24 0 E1CEI4;P48506;A0A2R8YEL6;B4E2I4;A0A2R8Y648 E1CEI4 GCLC Glutamate--cysteine ligase catalytic subunit 0 86.557 0.0068037 144340000 33288 38524 45026 41718 46557 57025 44853 40641 38535 48224 FALSE TRUE 34602.23594 45140.19732 46199.41455 49969.69588 38643.25777 43781.80797 41337.30466 40096.27387 37148.13288 57672.5695 0.599977359 0.78269787 0.801063919 0.866437829 0.67004571 0.759144397 0.716758504 0.695239942 0.644121342 1 15.81559768 -1.069054747 4.670248448 1.000012099 0.730530221 0.5432804 0.075226391 9.47E-06 1.89E-06 0.072792836 0.017156666 0.085299258 1.069054747 -0.269481878 IHLDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IHLDEK 6 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;; 153.67 0.010102 18771940000 21811040 17032460 20222730 16078310 26993190 26912890 24386510 20604800 21484910 15829450 FALSE TRUE 22672156.7 19957652.51 20749750.96 19258551.73 22404897.21 20662779.17 22475031.62 20328626.36 20711672.29 18930927.65 1.197625236 1.054235317 1.096076819 1.017306287 1.183507624 1.091482654 1.187212377 1.073831496 1.094065366 1 24.17424177 0.689510047 1.530774022 1.000350978 1.111320431 0.261655796 0.056899378 1.506234496 5.372273534 0.051125597 0.014802697 4.892265827 -0.689510047 0.110969453 IHLFDIDVPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHLFDIDVPGK 11 0 Q9NQR4;H7C579 Q9NQR4 NIT2 Omega-amidase NIT2 0 88.441 0.012976 139950000 176960 136330 166540 150070 230210 222130 191840 175460 171150 161100 FALSE TRUE 183946.5174 159743.617 170880.1692 179753.3981 191078.9864 170543.6739 176803.0795 173108.2457 164990.3449 192664.4606 0.954750642 0.829128613 0.886931449 0.932986798 0.991770801 0.885184914 0.91767355 0.898495992 0.856361077 1 17.55573095 IHLGSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 IHLGS(0.004)S(0.996)PK;IHLGS(0.002)S(0.998)PK 133.75 0.00058354 617730000 1587170 906050 1160160 886230 1643590 1935590 1530010 1221390 1217660 819800 TRUE FALSE 1649832.697 1061657.039 1190394.723 1061523.649 1364213.159 1486078.557 1410083.818 1205019.265 1173836.654 980424.114 1.682774499 1.082854883 1.21416304 1.082718829 1.391452066 1.51575072 1.438238613 1.229079587 1.197274361 1 19.90304644 0.993031153 1.759262933 1.004747822 1.324236224 0.254159213 0.17806218 0.555526979 3.567825213 0.169613914 0.048578578 9.840816932 -0.993031153 0.319488401 IHLPETVEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHLPETVEQLR 11 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8YEJ7;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 ;; 133.89 0.0001522 264069000 165924 200454 177890 184526 195075 227995 188911 177314 160514 200736 FALSE TRUE 172474.8076 234880.4152 182525.9595 221024.692 161916.2212 175046.6165 174103.6622 174937.3959 154737.1325 240066.3759 0.718446334 0.978397805 0.760314554 0.920681587 0.674464388 0.729159242 0.725231351 0.728704281 0.644559789 1 17.87307383 3.234506353 24.99999983 0.73386928 0.848016656 0.131554862 0.11367223 159.0029214 980467.7542 0.029421846 0.036397609 1715.956812 -3.234506353 0.114147376 IHLPLNYPPGS(ph)PDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHLPLNYPPGSPDLGR 16 0 Q08174-2;Q08174 Q08174-2 PCDH1 Protocadherin-1 1 IHLPLNYPPGS(1)PDLGR;IHLPLNYPPGS(1)PDLGR 101.64 0.0010609 236821000 96466 120285 98264 126697 121140 154673 118390 87598 112027 152528 TRUE FALSE 100274.5522 140943.0131 100824.8406 151757.2884 100548.6661 118752.5398 109110.2824 86423.89209 107995.1702 182412.9413 0.549711832 0.772659067 0.55272855 0.831943652 0.551214543 0.651009402 0.598149899 0.473781583 0.592036779 1 17.47684856 -0.892841321 4.97056578 1.000001207 0.615581665 0.55119551 0.10302374 1.37E-06 3.05E-07 0.099272683 0.023398722 0.127984884 0.892841321 -0.384419542 IHMS(ph)GPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHMSGPK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IHMS(1)GPK;IHMS(1)GPK;IHMS(1)GPK 100.02 0.0065075 510287000 1730010 1190980 1222430 1103570 1914030 2263190 1618220 1276950 1461230 1049930 TRUE FALSE 1798312.131 1395521.55 1254287.53 1321852.852 1588683.864 1737598.421 1491379.688 1259834.574 1408640.618 1255643.681 1.432183475 1.111399333 0.998919955 1.052729267 1.265234627 1.383830817 1.187741164 1.003337645 1.121847415 1 20.25999569 1.765432706 11.90214298 1.047053011 1.196491685 0.24266512 0.131191297 0.552669236 241.2455162 0.06540506 0.036127546 58.26834812 -1.765432706 0.149438674 IHNAENIQPGEQKYEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 199.41 8.00E-12 195680000 386320 206680 305160 200040 405340 372910 358870 289300 348580 168410 FALSE TRUE 401572.2119 242175.6823 313112.7203 239607.3149 336440.4516 286307.304 330740.8317 285422.4067 336034.6739 201406.7151 1.993837255 1.202421092 1.554629001 1.189668948 1.670453001 1.421538025 1.642153945 1.417144441 1.668438283 1 17.61975226 -1.142308061 4.500293388 0.99992971 1.509045946 0.323790255 0.22768406 0.000142386 2.71E-05 0.195487105 0.046070416 0.072059615 1.142308061 0.509116236 IHPFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHPFFK 6 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 ; 104.64 0.033659 638310000 1681040 1632310 1772800 1629290 2413800 2401200 2043360 1874360 2046970 1905350 FALSE TRUE 1747408.757 1912646.545 1819000.624 1951558.699 2003503.138 1843557.691 1883196.104 1849237.27 1973299.95 2278666.852 0.766855741 0.839370855 0.798274053 0.856447575 0.879243552 0.809050998 0.826446438 0.811543499 0.86598879 1 21.11975858 -5 0.310157381 2.533740008 0.81961602 0.746678665 0.030551225 146.0826443 1.323099549 146.3294567 0.028690535 1.00E-05 5 -1.714123988 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IHPMAYQLQLQAASNFKSPVK 21 1 P67870;Q5SRQ6 P67870 CSNK2B Casein kinase II subunit beta 1 IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK;IHPMAYQLQLQAASNFKS(1)PVK 356.55 7.77E-96 8575751000 5999640 2675599 3774660 2529860 5326410 5338100 4751130 3924430 4833610 2553912 TRUE FALSE 6236510.42 3135112.315 3873030.741 3030258.757 4421028.731 4098407.175 4378724.016 3871829.435 4659649.32 3054302.159 2.041877357 1.026457813 1.268057494 0.992128021 1.447475888 1.341847323 1.433625027 1.267664178 1.525601947 1 21.54241136 4.750223868 24.73461088 1.272872937 2.041877891 0.620131159 0.184120882 1010.530518 2143016.312 0.042263769 0.680722044 56263.12734 -4.750223868 0.769004954 IHPQTIIAGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHPQTIIAGWR 11 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 138.76 5.08E-05 1311650000 317470 284390 245250 205103 442120 416060 291180 285292 251990 464090 FALSE TRUE 330003.9607 333231.7703 251641.4165 245671.7612 366968.6003 319436.3705 268356.5507 281468.1274 242920.9291 555019.55 0.594580787 0.600396455 0.453391987 0.44263623 0.661181395 0.575540754 0.483508285 0.507131915 0.43767995 1 19.08217906 -1.246885341 4.607305596 1.000160125 0.527621731 0.790292504 0.072871143 0.000122489 2.00E-05 0.072106278 0.016989904 0.05663888 1.246885341 -0.472538395 IHPTSVISGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHPTSVISGYR 11 0 P17987;E7ERF2;F5H136;F5H676 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 208.84 1.82E-08 2765900000 254310 745560 705620 767190 714900 915180 709830 780530 719340 796660 FALSE TRUE 264350.3552 873604.1303 724009.0369 918937.8922 593381.5534 702643.3147 654191.6698 770068.272 693451.0939 952750.274 0.277460277 0.916928763 0.759914803 0.964510761 0.622809113 0.737489491 0.686634985 0.808258253 0.727841401 1 19.86173859 -4.999999718 0.033370718 2.101877027 2.45E-06 0.21423076 0.173706683 2236.239102 5.605547962 288.9559036 105.9415165 1.00E-05 4.999999718 -2.101874577 IHPVSTMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHPVSTMVK 9 0 A0A5F9ZHM4;P07195;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 113.62 0.0017705 1154140000 1152540 1053880 1082420 915510 1995490 1480710 1315530 1104490 1310330 1721700 FALSE TRUE 1198043.169 1234875.692 1110628.754 1096595.145 1656297.323 1136837.543 1212415.321 1089686.118 1263171.479 2059034.151 0.581847158 0.599735411 0.539393071 0.532577444 0.804404979 0.552121752 0.588827204 0.529221974 0.613477673 1 20.97353633 -2.017067205 1.846609425 1.440276818 0.590537248 0.720563534 0.075920372 447505.2964 131282.4423 835485.1225 0.020316886 0.009614635 2.017067205 -0.84973957 IHQDS(ph)ES(ph)GDELSSSSTEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHQDSESGDELSSSSTEQIR 20 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 IHQDS(1)ES(1)GDELSSSSTEQIR 60.104 0.0092775 0 22573 30429 26668 21762 26255 39121 27787 26744 22710 22251 TRUE FALSE 23464.19947 35654.94405 27362.98999 26066.45865 21792.18448 30035.74063 25608.98233 26385.54042 21892.67154 26610.65743 0.88175948 1.339874603 1.028271852 0.979549593 0.818926948 1.128710958 0.962358123 0.991540344 0.822703144 1 14.69971653 4.007801092 24.99884418 0.963900511 1.129131095 0.172664882 0.132678733 263.8053442 845354.9993 0.030550953 0.065809369 10181.24978 -4.007801092 0.165230583 IHQDSES(ph)GDELSSSSTEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHQDSESGDELSSSSTEQIR 20 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 IHQDS(0.073)ES(0.927)GDELSSSSTEQIR 98.766 0.00057195 0 64689 106020 94893 74832 130570 127470 96215 108020 111520 109120 TRUE FALSE 67242.97167 124228.1103 97365.98954 89633.54625 108375.758 97867.02433 88673.41689 106572.1686 107506.417 130499.9748 0.515271913 0.951939726 0.746099681 0.68684723 0.830465739 0.749939029 0.679489916 0.816645128 0.823804121 1 16.99369 0.821720066 1.297002537 0.99890247 0.749155568 0.348329358 0.106694546 0.741941961 2.327328055 0.092790408 0.02804156 6.633153777 -0.821720066 -0.249746902 IHQESELHSYLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHQESELHSYLSR 13 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 198.85 7.09E-08 837010000 152346 269330 245940 275940 322560 338850 244910 261730 266800 306090 FALSE TRUE 158360.7377 315585.3324 252349.3984 330520.1084 267731.3664 260157.2228 225713.3142 258221.9375 257197.9201 366062.4751 0.432605767 0.862107847 0.689361559 0.902906282 0.731381621 0.710690772 0.616597793 0.705404009 0.702606625 1 18.48173037 -1.868219853 2.250640609 1.145243626 0.712384478 0.34472479 0.121328073 9252812.551 4743748.817 7174934.923 0.030344786 0.013545035 1.868219853 -0.432859147 IHQETFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHQETFGK 8 0 Q15393;Q15393-2;J3QL37 Q15393 SF3B3 Splicing factor 3B subunit 3 0 67.563 0.058772 307020000 194490 199230 206450 203030 234450 273630 224110 238910 218740 191760 FALSE TRUE 202168.6154 233446.2027 211830.2566 243188.728 194598.2727 210083.5794 206543.6726 235707.8022 210867.5901 229331.7005 0.881555471 1.017941271 0.923685021 1.060423515 0.848545021 0.916068642 0.900632892 1.027802967 0.919487317 1 17.80707627 1.743377231 25 0.983389377 0.938969661 0.099462372 0.064047091 2.25836953 11771.1782 0.028762994 0.015950579 55.3830962 -1.743377231 -0.044419716 IHQIGPGMVQQIQSVCMECQGHGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHQIGPGMVQQIQSVCMECQGHGER 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 200.95 3.71E-25 630040000 31860 47638 37476 36657 25963 39046 28262 30364 35488 55103 FALSE TRUE 33117.8574 55819.45593 38452.65535 43907.64519 21549.81853 29978.15825 26046.75059 29957.02025 34210.79381 65899.37784 0.502551898 0.847040712 0.58350559 0.666283152 0.327010956 0.454908062 0.395250326 0.4545873 0.519136825 1 16.00797722 -1.854008289 5.564172075 1.073352134 0.523858797 0.508779825 0.139142813 0.08275789 0.002171386 0.088060338 0.03386404 0.013995606 1.854008289 -0.549493338 IHRAS(ph)DPGLPAEEPK ddPTM_MDA-MB-175_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 120.92 7.14E-05 2962180000 5041840 2761530 3847390 3386420 4952150 5438870 4936710 3636010 4131720 2491190 TRUE FALSE 5240895.736 3235801.296 3947656.144 4056243.769 4110385.312 4175774.869 4549757.771 3587275.233 3983020.204 2979290.984 1.75910838 1.086097771 1.325032085 1.361479557 1.379652184 1.40160021 1.527127694 1.204070114 1.336902043 1 21.50653761 0.58926229 0.941649133 1.000852868 1.379904408 0.320990876 0.167913772 1.576925584 2.236482359 0.151940132 0.049323113 3.883848578 -0.58926229 0.37905154 IHRAS(ph)DPGLPAEEPKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 181.82 4.08E-10 4483410000 3681930 1606180 2626970 1430480 4562710 3808980 2519220 2301500 3068320 1773880 TRUE FALSE 3827295.439 1882028.921 2695430.996 1713424.674 3787142.184 2924402.121 2321756.954 2270652.157 2957891.763 2121437.823 1.804104461 0.887147811 1.270567993 0.807671408 1.785177083 1.378500038 1.094426114 1.070336416 1.394286333 1 21.01661096 -4.999999952 0.151149981 0.110773174 1.325591485 0.063655104 0.3176326 446.8830502 3.998605647 119.3664219 1.525772515 1.00E-05 4.999999952 1.214818311 IHREEDFQFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHREEDFQFILK 12 1 Q8IV36-2;Q8IV36;Q8IV36-3;X6R4D2;E9PMS4 Q8IV36-2 HID1 Protein HID1 0 50.675 0.096823 198460000 210660 165080 216010 206280 298610 264850 254110 235750 259650 195960 FALSE TRUE 218977.0195 193431.2059 221639.3981 247081.5683 247852.3789 203342.6013 234192.1942 232590.1569 250305.2472 234354.6101 0.934383238 0.825378284 0.945743708 1.054306413 1.057595491 0.867670584 0.999306965 0.992471011 1.068061973 1 17.83833365 4.009792003 7.51933524 1.000920531 0.880706163 0.424676234 0.058607369 0.127030799 44.52639982 0.014712691 0.030726851 10228.03022 -4.009792003 -0.120214368 IHS(ph)PIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHSPIIR 7 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 IHS(1)PIIR 111.61 0.0042132 329980000 119510 119880 132120 104760 168020 183510 160520 127210 125250 106500 TRUE FALSE 124228.3471 140468.4575 135563.1557 125481.2153 139460.0204 140892.5836 147938.023 125504.958 120742.277 127366.6359 0.975360197 1.102866983 1.064353743 0.985196903 1.094949391 1.106196945 1.161513154 0.985383316 0.947989841 1 16.95862788 1.587239637 9.074776485 0.972500332 1.070601163 0.382641067 0.053801083 0.109381885 20.82122525 0.028868682 0.013739781 38.6580227 -1.587239637 0.098100831 IHSEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IHSEIVK 7 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 132.09 0.0034023 1145420000 1661680 1628070 1763450 1776950 2303110 2352430 2083690 1765740 1888600 1815590 FALSE TRUE 1727284.409 1907678.358 1809406.956 2128425.406 1911628.185 1806113.784 1920364.933 1742073.143 1820629.655 2171320.099 0.795499664 0.878579975 0.833321147 0.980244878 0.880399065 0.831804479 0.884422768 0.802310606 0.838489754 1 21.05014099 4.741750299 23.60264249 0.871967597 0.7954996 0.134943769 0.061209229 302.9331463 2241357.971 0.014241095 0.100736258 55176.01088 -4.741750299 -0.076467997 IHSEVVEDTEAVSAVQQLLDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHSEVVEDTEAVSAVQQLLDDER 23 0 Q96GA7;H0YID3 Q96GA7 SDSL Serine dehydratase-like 0 ;; 305.87 1.80E-62 722330000 448393 505282 558100 553900 623740 675980 531830 571840 565770 581520 FALSE TRUE 466095.9019 592060.253 572644.5445 663459.7668 517716.8976 518993.8896 490143.7749 564175.4201 545408.0482 695457.7101 0.670200208 0.851324594 0.823406709 0.953990095 0.744426138 0.746262328 0.704778691 0.811228939 0.784243298 1 19.40760326 -1.026972706 4.791911716 1.000003456 0.790950924 0.411261154 0.076094898 0.024909956 48767868.21 496.6675954 0.017872236 0.093978237 1.026972706 -0.209052532 IHSQEEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHSQEEALR 9 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 236.32 3.18E-10 493720000 350218 436261 384484 418213 519276 508302 416064 367327 359004 602493 FALSE TRUE 364044.8771 511185.4331 394503.9689 500934.2832 431009.651 390256.5639 383451.8165 362403.5824 346083.5162 720539.9679 0.505238978 0.709447714 0.54751157 0.695220675 0.59817591 0.541616817 0.532172861 0.50296111 0.480311338 1 19.45871893 -1.935144073 2.875822696 1.2804857 0.569044602 0.752002508 0.074410568 37783000.07 39749137.74 71832413.01 0.018432279 0.011610634 1.935144073 -0.711441098 IHTDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IHTDFEK 7 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 ;;;;; 163.67 0.0012263 2568820000 3649320 3133300 3651560 2903880 4549140 4544700 4211370 3634630 3801710 2797170 FALSE TRUE 3793397.971 3671419.901 3746722.653 3478258.797 3775878.808 3489262.301 3881271.815 3585913.73 3664887.2 3345221.906 1.133974988 1.097511616 1.120022156 1.039769227 1.128737917 1.043058547 1.160243453 1.071950929 1.095558771 1 21.67367049 -4.999999998 0.320081961 0.07070317 1.102162357 0.397408211 0.036822607 309.3202089 2.739620963 194.6779953 0.029721863 1.00E-05 4.999999998 1.031459187 IHTEPQLSAALEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHTEPQLSAALEYVR 15 0 P47897;A0A1B0GVU9;A0A0U1RQT0;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 165.02 1.45E-06 90391000 94034 91559 100880 118740 107800 129870 130330 97980 86251 87387 FALSE TRUE 97746.53493 107283.546 103509.0157 142226.4176 89476.19451 99709.6607 120114.394 96666.73836 83146.84336 104508.8095 0.935294693 1.026550264 0.990433401 1.360903624 0.856159351 0.954079002 1.149323149 0.924962583 0.795596503 1 16.67326503 1.56394176 6.868724351 0.886475273 1.038973331 0.161548165 0.138183647 0.209909946 19.34276974 0.074135456 0.034527092 36.63884374 -1.56394176 0.152498057 IHTGERPYACPDCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHTGERPYACPDCDR 15 1 Q9BWE0;Q9BWE0-4 Q9BWE0 REPIN1 Replication initiator 1 0 99.481 0.0015177 98081000 56482 74161 60755 49383 70915 123720 53992 63606 71528 45557 FALSE TRUE 58711.95297 86897.57486 62338.32521 59150.81001 58860.89363 94987.90499 49759.96596 62753.46561 68953.72125 54483.02191 1.077619246 1.59494778 1.144178921 1.085674178 1.080352953 1.743440464 0.913311417 1.15179855 1.26560016 1 15.7335191 -4.999988957 0.119540254 0.22290922 1.342617507 0.072580947 0.240811039 401.1513359 3.114511419 74.49578247 2.279218922 1.00E-05 4.999988957 1.119708286 IHTLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHTLELK 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 104.21 0.021034 0 711300 528700 655360 548600 823140 820470 749410 643190 729710 488320 FALSE TRUE 739382.6732 619500.1123 672439.22 657111.4426 683222.9568 629928.2768 690669.286 634569.0901 703447.8796 583996.9545 1.266072824 1.060793395 1.151443025 1.125196694 1.169908424 1.078649935 1.182659054 1.086596574 1.204540322 1 19.15560132 -1.57860065 3.141097724 0.993338724 1.14039034 0.346876067 0.059969657 4436620.756 2235800.154 199353.3018 0.012371033 0.026387567 1.57860065 0.147051616 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVS(ph)TPPPFQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGR 47 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 IHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPT(0.084)VS(0.481)T(0.434)PPPFQGR 58.768 0.012227 41805000 10860 13007 12815 13705 12386 15750 13122 12043 12566 11049 TRUE FALSE 11288.76119 15240.85107 13148.96943 16415.80809 10280.63214 12092.30119 12093.46335 11881.58328 12113.75211 13213.84 0.854313446 1.153400606 0.99509071 1.242319272 0.778020026 0.91512393 0.91521188 0.899177172 0.916747298 1 13.68976216 3.225900266 24.99998653 0.900396643 1.06313314 0.341770806 0.10681457 234.2073698 462480.9054 0.028693032 0.034511191 1682.287684 -3.225900266 0.162736498 IHVFYIDYGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 147.74 3.52E-05 4047300000 2173800 2482300 2511000 2433400 2981100 3175100 2720700 2626600 2467500 3051900 FALSE TRUE 2259623.303 2908615.715 2576438.723 2914719.257 2474373.687 2437731.144 2507444.425 2591394.723 2378695.157 3649861.373 0.619098391 0.796911285 0.705900433 0.798583551 0.677936347 0.667896913 0.686997167 0.709998123 0.651722056 1 21.79941024 -1.649404731 6.552316761 1.001485525 0.7054959 0.727762491 0.054693774 0.001130093 6.05E-05 0.050422374 0.011830969 0.022417918 1.649404731 -0.295989626 IHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIR 34 2 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 260.62 6.51E-60 180350000 77089 92527 105740 94620 126390 154450 122970 102180 113950 109460 FALSE TRUE 80132.53325 108417.7925 108495.6713 113335.5536 104906.2729 118581.3282 113331.2901 100810.4442 109848.9618 130906.5913 0.612135206 0.828207285 0.828802203 0.865774233 0.801382665 0.905846887 0.865741663 0.770094487 0.839140036 1 16.99817821 -5 0.024285054 2.093360579 4.20E-13 0.466024133 0.068992351 2368.323401 4.34544246 268.7345067 129.2986557 1.00E-05 5 -2.093360579 IHVS(ph)DQELQSANASVDDSRLEELK ddPTM_MDA-MB-175_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 150.24 7.91E-08 92799000 69688 58032 66815 51550 85991 93145 64238 66151 72296 61176 TRUE FALSE 72439.33605 67998.54457 68556.25379 61746.43614 71374.28054 71513.48538 59202.85771 65264.35405 69694.08108 73162.26591 0.990118815 0.929420976 0.937043884 0.843965607 0.975561372 0.977464059 0.809199346 0.892049381 0.952595989 1 16.15881214 IHVSDQELQSANASVDDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHVSDQELQSANASVDDSR 19 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 199.12 7.09E-16 828290000 192359 258966 254946 266267 293311 355014 261462 285617 246373 240601 FALSE TRUE 199953.4819 303441.396 261590.1022 318933.8179 243454.101 272567.3788 240967.9252 281788.7713 237506.0839 287742.1594 0.694905058 1.054560085 0.909112877 1.108401419 0.846084222 0.947262575 0.837443932 0.97930999 0.825412878 1 18.13441709 IHVSDQELQSANASVDDSRLEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHVSDQELQSANASVDDSRLEELK 24 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 195.7 1.24E-24 452370000 73521 284230 334280 269320 400260 437090 291650 304980 285620 338450 FALSE TRUE 76423.66585 333044.2915 342991.6114 322590.6922 332223.9482 335582.4717 268789.7109 300892.2419 275340.592 404762.7975 0.188810993 0.822813494 0.847389171 0.796987011 0.820786768 0.829084278 0.664067233 0.743379193 0.680251727 1 18.62671717 4.740640538 24.92089756 0.787149204 0.188810779 0.804043188 0.090379833 74.14545892 888321.2119 0.020960139 0.138384728 55035.19856 -4.740640538 -0.598338425 IHVYGYSMAYGPAQHAISTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHVYGYSMAYGPAQHAISTEK 21 0 Q9NRX4 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ; 235.56 5.84E-30 1597120000 456460 517640 613060 558850 735770 736990 682100 644800 608880 566560 FALSE TRUE 474481.3933 606540.6433 629036.8472 669388.862 610704.0782 565835.2417 628635.2197 636157.5107 586966.5277 677566.5846 0.700272717 0.895174965 0.928376431 0.987930747 0.901319652 0.835099095 0.927783681 0.938885602 0.86628612 1 19.3700032 4.739049527 3.566295046 0.920433367 0.674458367 0.667918102 0.046833834 0.167714798 3.814791546 0.011243488 0.110724579 54833.94936 -4.739049527 -0.245974999 IHWWENVYGFDMSCIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IHWWENVYGFDMSCIK 16 0 E9PKG1;Q99873-2;Q99873-3;Q99873;E9PQ98;E9PIX6;H0YDE4 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ;;; 154.82 1.84E-08 483302000 451404 366141 456823 364139 762439 665399 530056 433098 493545 513459 FALSE TRUE 469225.7785 429022.8686 468728.1827 436164.6074 632839.8911 510870.1665 488508.8257 427293.0297 475782.4119 614061.4603 0.764134877 0.698664379 0.763324542 0.710294711 1.030580702 0.831952825 0.795537348 0.695847333 0.774812364 1 19.22802353 -2.487510678 2.102777727 3.306948935 0.782310794 0.329047276 0.092023509 4357115.12 243235.6822 48111734.56 0.025166737 0.003254538 2.487510678 -2.524638141 IHYFDPQYFEFEFEA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHYFDPQYFEFEFEA 15 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 128.28 0.00016977 94768000 131979 150346 141074 161150 177193 201005 151958 167009 151950 156616 FALSE TRUE 137189.6328 176166.756 144750.5043 193024.989 147073.7972 154324.635 140047.1349 164770.5175 146481.3492 187301.9066 0.732451876 0.940549721 0.772819172 1.030555388 0.785223172 0.823935206 0.747708005 0.879705501 0.782060107 1 17.51500606 -1.641974462 6.215259476 1.00096598 0.837748135 0.240060733 0.088861885 0.001093823 6.30E-05 0.079123212 0.018542683 0.022804762 1.641974462 -0.163217845 IHYLDTTTLIEPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IHYLDTTTLIEPAPR 15 0 P46109 P46109 CRKL Crk-like protein 0 69.258 0.050194 87710000 21098 28664 25280 31916 32476 33629 26076 21825 23185 32976 FALSE TRUE 21930.96533 33586.81903 25938.81757 38228.88954 26955.74112 25819.1744 24032.09498 21532.47157 22350.57638 39437.01584 0.556101035 0.851657214 0.657727696 0.969365677 0.683513713 0.654693918 0.609379145 0.545996474 0.566741066 1 15.26726277 3.010239203 24.99673668 0.637384941 0.766676191 0.033666459 0.158250589 424.8792987 1037239.964 0.043004965 0.05135012 1023.856763 -3.010239203 0.12929125 IHYLDTTTLIEPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IHYLDTTTLIEPVSR 15 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 ;; 190.86 1.99E-07 1817140000 612950 716060 705620 653810 771630 781840 762740 680500 711480 716350 FALSE TRUE 637149.7393 839037.7348 724009.0369 783131.6666 640468.6082 600269.5089 702954.4457 671379.0106 685873.9738 856705.0672 0.743721222 0.979377579 0.845108853 0.914120503 0.747595214 0.700672299 0.820532611 0.783675779 0.800595211 1 19.7084391 5.067323512 13.86320066 0.830434555 9.91E-05 0.080286643 0.092212015 2483853.3 13364131.41 0.021886738 57420119.77 116767.9114 -5.067323512 -0.830335437 IIAEGANGPTTPEADKIFLER ddPTM_MDA-MB-175_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 ; 168.81 9.41E-12 382180000 207101 226303 218101 208824 214200 287366 214104 206055 232898 208531 FALSE TRUE 215277.5074 265168.7799 223784.8912 250128.7639 177790.3605 220629.6016 197321.969 203293.1698 224516.0465 249388.6569 0.863220926 1.063275223 0.89733388 1.002967685 0.71290476 0.884681783 0.79122271 0.815166064 0.900265671 1 17.92803632 3.266400477 24.99999407 0.837370545 0.960071612 0.252406288 0.087500905 242.7371043 217974.5257 0.022151151 0.029986521 1846.717551 -3.266400477 0.122701067 IIALDGDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIALDGDTK 9 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 80.438 0.056094 131551000 371490 311360 432980 339010 671690 533380 519560 478950 496100 356370 FALSE TRUE 386156.7121 364833.658 444263.8145 406065.1662 557516.3737 409510.5785 478835.5296 472530.4587 478245.4579 426193.8784 0.906058795 0.856027448 1.042398394 0.952770996 1.308128535 0.960855139 1.123515737 1.108721834 1.122131223 1 18.70115035 3.958612083 1.603485905 1.099643088 0.876723084 0.388528487 0.098155672 0.373181632 1.81104918 0.026374531 0.081062936 9091.00891 -3.958612083 -0.222920004 IIALPHDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIALPHDNR 9 0 A0A3B3IT47;Q9Y2I8;Q9Y2I8-2 A0A3B3IT47 WDR37 WD repeat-containing protein 37 0 84.213 0.015645 144040000 74629 76221 65646 70311 83530 93464 76056 68182 62758 84464 FALSE TRUE 77575.41055 89311.36383 67356.78869 84218.30594 69331.60044 71758.40246 70094.53198 67268.13181 60499.35184 101013.1036 0.767973736 0.884156219 0.666812386 0.833736445 0.686362441 0.710387067 0.693915239 0.665934709 0.59892578 1 16.62418293 4.235983237 24.99950509 0.716813926 0.826064978 0.092256836 0.110042651 113.6363008 1102272.362 0.025116497 0.058559033 17218.02114 -4.235983237 0.109251052 IIANALSSEPACLAEIEEDKAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIANALSSEPACLAEIEEDKAR 22 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 92.336 0.0019051 102770000 87571 79467 81435 79699 120350 113430 115020 79764 80200 78350 FALSE TRUE 91028.3707 93114.83908 83557.263 95463.22432 99892.94999 87087.60155 106004.4319 78694.89405 77313.61767 93701.1824 0.971475155 0.993742413 0.891741821 1.018804906 1.06607993 0.929418384 1.131303033 0.839849531 0.82510824 1 16.51577963 1.633338017 14.46784301 0.874510751 0.995957991 0.302373969 0.076867652 0.136362941 67.41587394 0.034360161 0.018783439 42.98708708 -1.633338017 0.12144724 IIAPPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 125.08 0.0095001 8697588000 3000591 3242050 3119783 3554490 3178390 3800490 3730050 3228792 3008920 2775401 FALSE TRUE 3119056.65 3798846.868 3201087.108 4257557.513 2638128.403 2917883.794 3437678.934 3185515.324 2900629.557 3319187.688 0.939704814 1.144511015 0.96441883 1.282710685 0.794811457 0.879095751 1.035698869 0.959727386 0.87389742 1 21.66239878 3.22120572 24.99848386 0.930075279 1.078783386 0.3359239 0.109226796 289.0512121 416356.5803 0.030502917 0.036538503 1664.200774 -3.22120572 0.148708107 IIAPPERK ddPTM_MDA-MB-175_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 ;;;;; 122.52 0.0022241 39885160000 10917980 7771320 10479440 7765950 13127210 11781750 11954110 10171760 11264380 8598510 FALSE TRUE 11349030.28 9105983.758 10752542.82 9302031.731 10895851.53 9045617.117 11017115.62 10035424.19 10858977.16 10283223.41 1.103645212 0.885518421 1.045639328 0.904583258 1.059575495 0.879648021 1.071367915 0.975902574 1.055989619 1 23.29378923 IIAPS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIAPSPVK 8 0 Q9HCS5 Q9HCS5 EPB41L4A Band 4.1-like protein 4A 1 IIAPS(1)PVK 96.89 0.0090425 63208000 198070 179510 179410 153780 271090 299420 209570 158910 181960 206430 TRUE FALSE 205889.9565 210339.4461 184085.572 184197.225 225010.2186 229884.2428 193143.3558 156780.0714 175411.2951 246876.0062 0.833981235 0.852004411 0.745660037 0.746112301 0.911430082 0.931172884 0.782349645 0.635055929 0.710523869 1 17.9134271 -1.058542023 4.765412927 1.000006631 0.7886782 0.335672958 0.086513412 7.23E-06 1.43E-06 0.09558201 0.022528161 0.087389243 1.058542023 -0.211328431 IIAPSRGS(ph)PLPVLSWANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIAPSRGSPLPVLSWANR 18 1 I3L413;C9J2U0;P24864-2;P24864-3;P24864;I3L1Q9 I3L413 CCNE1 G1/S-specific cyclin-E1 1 IIAPS(0.062)RGS(0.938)PLPVLSWANR;IIAPS(0.231)RGS(0.769)PLPVLSWANR 116.35 9.87E-05 243990000 147046 157850 154706 147031 161611 173282 163404 137080 153845 168031 TRUE FALSE 152851.4896 184959.5096 158737.7655 176113.293 134140.4199 133039.8816 150595.9675 135242.6668 148308.1485 200953.4573 0.760631301 0.920409691 0.789923038 0.87638847 0.667519841 0.662043258 0.749407199 0.673004927 0.738022378 1 17.61650187 3.244676901 24.99912253 0.724484507 0.839456452 0.129670805 0.101534043 205.6277363 840457.7006 0.02595117 0.034266698 1756.616272 -3.244676901 0.114971946 IIDDSEITKEDDALWPPPDR ddPTM_MDA-MB-175_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 ;;;;; 226.72 3.85E-25 1267260000 1197285 798570 1025779 823865 1296407 1240401 1289684 1077680 1139873 740442 FALSE TRUE 1244554.736 935718.1855 1052511.643 986823.038 1076044.201 952336.6662 1188595.198 1063235.462 1098849.193 885517.4333 1.40545481 1.056690868 1.188583763 1.114402722 1.215158687 1.07545784 1.342260642 1.200693992 1.240911982 1 19.75616118 IIDKNGIHDLDNISFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIDKNGIHDLDNISFPK 17 1 P49721;A0A087WVV1 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 148.56 2.15E-07 2383400000 3370400 2478460 3096400 2053220 4697400 4009900 3152700 3064100 3879400 2771800 FALSE TRUE 3503465.995 2904116.225 3177094.728 2459340.788 3898937.626 3078661.496 2905583.136 3023030.751 3739781.152 3314881.141 1.056890382 0.876084572 0.958433981 0.741909192 1.176192286 0.928739633 0.876527095 0.91195751 1.128179562 1 21.66052571 1.249849938 24.99823579 1.064089793 0.935759069 0.160040572 0.112460275 315.0813554 697702.4765 0.072784637 0.026060926 17.77665066 -1.249849938 -0.128330724 IIDKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIDKPR 6 1 P49903;P49903-2;P49903-3;Q99611 P49903 SEPHS1;SEPHS2 "Selenide, water dikinase 1;Selenide, water dikinase 2" 0 90.986 0.044147 243340000 802390 728190 792560 671190 947410 923210 798930 792560 786850 758240 FALSE TRUE 834068.9768 853250.968 813214.7647 803949.3787 786369.5866 708808.4689 736307.779 781937.0296 758531.4222 906802.6106 0.919791107 0.940944543 0.896793586 0.886575942 0.867189372 0.781656846 0.811982421 0.862301255 0.836490117 1 19.79042902 3.608727344 1.626819595 0.84708451 0.927530531 0.176561938 0.054965155 0.505267235 2.628375753 0.01594436 0.032128279 4061.882388 -3.608727344 0.080446021 IIDSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIDSAR 6 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 107.65 0.07231 324150000 338050 346750 332150 326740 400770 394040 360900 357060 345750 390120 FALSE TRUE 351396.475 406301.6152 340806.1019 391368.1968 332647.2586 302530.1817 332611.715 352274.1947 333306.525 466556.5447 0.753170176 0.870851818 0.730471163 0.838844083 0.712983801 0.648431975 0.712907618 0.755051448 0.714396848 1 18.83169241 -1.114574299 3.571124391 1.000170427 0.74916388 0.604455853 0.06101623 18885510.66 30038916.42 37392.01107 0.015226795 0.076811404 1.114574299 -0.251006547 IIDSLFNTVTDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIDSLFNTVTDKK 13 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 140.27 6.30E-05 484350000 534870 450800 556240 496640 666300 789640 687940 529300 596490 583760 FALSE TRUE 555987.0806 528221.3933 570736.0714 594873.9097 553042.564 606258.0771 634017.4652 522205.5993 575022.4414 698136.5952 0.796387246 0.756616108 0.817513471 0.852088135 0.792169566 0.86839464 0.908156755 0.747999178 0.823653201 1 19.41314981 -2.597408136 2.036462327 4.015453438 0.816887487 0.578584053 0.046559416 1767306.108 96478.97853 24632560.35 0.012124995 0.002526922 2.597408136 -3.198565951 IIECTHCGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IIECTHCGCR 10 0 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ;;; 156.48 1.09E-05 929100000 494189 611350 580454 550930 707231 764412 600685 612377 615832 777542 FALSE TRUE 513699.9633 716344.6069 595581.1081 659902.3096 587016.1272 586888.8978 553601.7401 604169.088 593668.3266 929886.468 0.552432992 0.770357061 0.640487983 0.709659009 0.631277202 0.631140379 0.595343366 0.649723497 0.638430977 1 19.82669506 -1.865170862 2.314866634 1.171172483 0.648800069 0.781522171 0.056054014 4313535.522 2278954.012 4056701.238 0.012766559 0.013640464 1.865170862 -0.522372414 IIEEDDAYDFSTDYV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIEEDDAYDFSTDYV 15 0 Q9BVP2-2;Q9BVP2 Q9BVP2-2 GNL3 Guanine nucleotide-binding protein-like 3 0 155.06 5.51E-06 10165000 66031 71397 76575 73712 83990 100050 79565 78272 74807 76206 FALSE TRUE 68637.95487 83658.87936 78570.60741 88292.01359 69713.4098 76814.90377 73328.4874 77222.89187 72114.71068 91137.10665 0.753128527 0.917945307 0.862114349 0.968782276 0.764928934 0.842849928 0.804595297 0.847326569 0.791277157 1 16.47575095 4.762962027 23.33674692 0.857745418 0.753128216 0.172003205 0.072385744 5235.293182 5006670.864 0.016309931 0.928006042 57937.80356 -4.762962027 -0.104617202 IIEPNEVTHSGDTGVETDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIEPNEVTHSGDTGVETDGR 20 0 Q9NQW7-4;Q9NQW7-3 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ; 135.98 6.20E-06 277850000 57792 90008 90203 94567 109438 121989 107224 113850 101500 93548 FALSE TRUE 60073.67279 105466.1738 92553.76428 113272.0703 90835.76785 93658.90351 98819.5027 112324.027 97847.03483 111876.9395 0.536962068 0.94269806 0.827281875 1.012470227 0.811925748 0.837160043 0.883287504 1.003996243 0.874595205 1 16.77155317 4.741736531 24.88785946 0.908941312 0.536961921 0.705989378 0.07228796 153.6684526 1204152.748 0.01693006 0.121366953 55174.26173 -4.741736531 -0.371979391 IIESDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIESDQER 8 0 Q7Z6W7 Q7Z6W7 DNAJB7 DnaJ homolog subfamily B member 7 0 77.674 0.075846 261950000 328040 285860 306050 284740 320460 372000 292120 270750 259450 295660 FALSE TRUE 340991.2725 334954.2313 314025.9144 341060.7221 265988.3237 285608.6377 269222.8711 267121.0391 250112.4452 353588.9162 0.964372063 0.947298447 0.888110175 0.964568476 0.752253002 0.807742055 0.761400764 0.755456483 0.707353748 1 18.43171353 3.239080521 24.99999926 0.781413744 0.937746881 0.445001485 0.077373131 10.9756047 527748.584 0.020224415 0.02579872 1734.125485 -3.239080521 0.156333138 IIEVVDAIMTTAQSHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIEVVDAIMTTAQSHQR 17 0 Q01813;Q01813-2;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 216.99 5.12E-15 457150000 274100 344240 330620 345650 338200 455770 348740 319650 352490 353550 FALSE TRUE 284921.6797 403360.5422 339236.2288 414018.5383 280712.8848 349924.3248 321404.8475 315365.6146 339803.9538 422821.3534 0.673858303 0.953973916 0.802315744 0.97918077 0.663904229 0.827593786 0.760143368 0.745860189 0.803658451 1 18.68968871 4.803202188 20.82320014 0.820227948 0.673846753 0.16334543 0.104737508 21221.15251 6833731.635 0.023793343 48.05691271 63562.67816 -4.803202188 -0.146381195 IIFEDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IIFEDDR 7 0 P49773;D6REP8;D6RE99;D6RD60;D6RC06 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;;;;;;;;; 195.85 0.0010662 28008600000 34235110 44245270 38100540 40158400 41153910 46261310 38521290 39711420 36348890 44641120 FALSE TRUE 35586738.58 51844050.94 39093471.37 48101611.66 34158583.08 35517821.85 35501890.63 39179153.37 35040700.55 53387692.76 0.666571952 0.971086186 0.732256244 0.900986897 0.639821302 0.665281079 0.664982673 0.733861146 0.656344164 1 25.67000387 4.095463791 20.11690635 0.733891196 0.82705406 0.032776889 0.130215422 9.309666026 1947.996947 0.030296346 0.065448149 12458.44361 -4.095463791 0.093162864 IIGEDS(ph)PSRLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IIGEDSPSRLDR 12 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 IIGEDS(0.882)PS(0.118)RLDR;IIGEDS(0.982)PS(0.018)RLDR;IIGEDS(0.994)PS(0.006)RLDR 132.81 0.00023597 710130000 1126210 1423530 1275770 1331220 1368000 1690640 1393641 1364560 1223250 1433270 TRUE FALSE 1170673.64 1668010.204 1309017.614 1594531.343 1135467.849 1298014.482 1284403.777 1346270.305 1179225.471 1714091.815 0.682970206 0.97311602 0.763679987 0.930248502 0.662431171 0.757260767 0.749320291 0.785413181 0.687959339 1 20.70901296 5.043584404 15.82461267 0.799597845 0.112156614 0.09853505 0.111547562 740732.6707 7388941.254 0.024829505 14983311.4 110556.5312 -5.043584404 -0.687441231 IIGVDINKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIGVDINKDK 10 1 P11766;H0YAG8 P11766 ADH5 Alcohol dehydrogenase class-3 0 156.58 0.0047485 0 1037600 563570 794640 504080 1273400 1055200 1020700 809870 944170 544280 FALSE TRUE 1078565.249 660358.7635 815348.9712 603785.5195 1056947.923 810145.7917 940694.8669 799015.0173 910189.5061 650921.2451 1.656982711 1.01449871 1.252607711 0.927586131 1.623772355 1.244614149 1.445174626 1.227514117 1.398309723 1 19.31212348 -1.019347143 4.378478507 0.999986725 1.296466861 0.146491204 0.222380838 0.309883615 59914932.96 2039.172848 0.048061324 0.095642927 1.019347143 0.296480136 IIGVHQEDELLECLS(ph)PATSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 1 IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR;IIGVHQEDELLECLS(1)PATSR 249.27 1.42E-30 463109000 375825 408395 385493 430908 427945 504402 404138 414144 408928 412085 TRUE FALSE 390662.8612 478533.6644 395539.2643 516140.3163 355203.0618 387262.2798 372460.6075 408593.0771 394210.7612 492825.1659 0.792700715 0.971000869 0.802595508 1.047309172 0.720748627 0.785800537 0.755766209 0.829083223 0.799899819 1 18.9107164 3.211437914 24.99997158 0.803002455 0.901029916 0.155321001 0.098238954 335.4188022 309166.6801 0.026006351 0.0310909 1627.18868 -3.211437914 0.098027461 IIGVHQEDELLECLSPATSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIGVHQEDELLECLSPATSR 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 222.06 7.41E-25 135972000 100500 113424 100130 114879 114878 126757 104363 119890 110345 103096 FALSE TRUE 104467.8176 132903.6897 102739.4701 137601.7233 95351.07859 97319.60777 96182.75536 118283.0707 106373.705 123295.6873 0.847294986 1.077926508 0.833277078 1.116030303 0.77335291 0.789318831 0.780098294 0.959344753 0.862752845 1 16.91176281 4.198785805 24.99993084 0.886324572 0.962612579 0.059703099 0.115948569 388.4637984 244163.5021 0.028341432 0.061225834 15804.68358 -4.198785805 0.076288006 IIHDFPQFYPLGIVQHD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIHDFPQFYPLGIVQHD 17 0 P35244;B5MC59 P35244 RPA3 Replication protein A 14 kDa subunit 0 109.42 0.00060777 827980000 546390 426270 603700 458900 810900 756040 875980 661370 782080 505930 FALSE TRUE 567961.8991 499478.5566 619432.9179 549669.0503 673063.5076 580461.1679 807318.3987 652505.4169 753933.0936 605057.2969 0.938691099 0.825506211 1.023759107 0.908457849 1.112396315 0.959349091 1.334284212 1.078419218 1.246052394 1 19.20671224 3.046816284 1.067284512 1.157798141 0.905411802 0.423764843 0.111989569 0.425421505 1.045361476 0.046366222 0.059826646 1113.823262 -3.046816284 -0.252386339 IIIEELSLVAAS(ph)PTLSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IIIEELSLVAASPTLSPR 18 0 Q16513-3;Q16513-2;Q16513;Q16513-4;B1AL79;H0Y5V5 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 IIIEELSLVAAS(0.985)PT(0.015)LSPR;IIIEELSLVAAS(0.996)PT(0.004)LSPR;IIIEELSLVAAS(0.984)PT(0.016)LSPR;IIIEELSLVAAS(0.963)PT(0.019)LS(0.019)PR;IIIEELSLVAAS(0.985)PT(0.015)LSPR;IIIEELSLVAAS(0.985)PT(0.015)LSPR 219.23 7.81E-19 559746000 470715 517059 484933 533892 549803 660919 481311 540787 457345 528454 TRUE FALSE 489299.1917 605859.8611 497570.7524 639494.2441 456347.6824 507430.5786 443584.5861 533538.6348 440885.2428 631994.4434 0.774214389 0.958647449 0.787302416 1.011866878 0.722075466 0.802903544 0.701880516 0.844214123 0.697609366 1 19.26955235 3.208618762 24.99997596 0.785104962 0.881574802 0.13933538 0.105770933 340.617037 284397.5276 0.027685657 0.033094819 1616.660257 -3.208618762 0.09646984 IIIEELSLVAASPTLS(ph)PR ddPTM_MDA-MB-175_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(0.04)PT(0.158)LS(0.801)PR 122.01 3.88E-05 115370000 22956 20613 12634 28601 21673 28405 22151 20194 13555 20160 TRUE FALSE 23862.32061 24153.1224 12963.25242 34258.19243 17989.0312 21808.36923 20414.74674 19923.33246 13067.1582 24109.96601 0.989728504 1.001789981 0.537671949 1.420914174 0.746124287 0.904537535 0.846734779 0.826352573 0.54198161 1 14.557342 2.234485422 1.362556869 0.77451354 0.944999681 0.076396503 0.232999016 1.135320911 4.106490454 0.135445469 0.078518259 171.5874114 -2.234485422 0.170486141 IIILYDDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IIILYDDDER 10 0 Q9BYV8-5;Q9BYV8-2;Q9BYV8 Q9BYV8-5 CEP41 Centrosomal protein of 41 kDa 0 ;; 156.92 2.35E-05 87600000 104497 121138 123712 128344 122236 154780 134292 128821 108190 136838 FALSE TRUE 108622.6222 141942.5092 126936.0364 153730.0601 101458.3684 118834.6907 123765.8421 127094.3652 104296.263 163648.7862 0.663754524 0.867360599 0.775661337 0.939390164 0.619976297 0.726156872 0.756289399 0.776628829 0.63731767 1 17.32024338 -1.116410549 4.614206988 1.000016089 0.758115514 0.382750008 0.09436569 1.88E-05 3.59E-06 0.087129775 0.020534966 0.076487321 1.116410549 -0.241900574 IILDLISES(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IILDLISESPIK 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLIS(0.001)ES(0.999)PIK;IILDLISES(1)PIK 189.3 8.50E-06 202907000 925050 494010 661700 583900 802570 903420 1000620 712790 715410 421270 TRUE FALSE 961571.6883 578852.3746 678944.4456 699393.6772 666149.4381 693614.3965 922188.7898 703236.2159 689662.5338 503809.7908 1.908600638 1.148950229 1.347620586 1.388209777 1.322224082 1.376738621 1.830430465 1.39583674 1.368894663 1 18.94251963 0.778970313 2.537005111 1.000389361 1.454475118 0.285773992 0.219838637 1.302857913 12.73987873 0.202052614 0.053958233 6.011326443 -0.778970313 0.454085757 IILDLISES(ph)PIKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IILDLISESPIKGR 14 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IILDLISES(1)PIKGR;IILDLISES(1)PIKGR 246.95 5.37E-18 1475410000 625880 419260 550020 446670 699290 681630 680810 573980 627880 502460 TRUE FALSE 650590.2257 491264.6436 564353.973 535019.9928 580424.9356 523331.7627 627446.3332 566286.7369 605282.7214 600907.4168 1.08267964 0.817537993 0.939169591 0.890353452 0.965914081 0.870902485 1.044164734 0.942386 1.007281163 1 19.1967832 2.23949775 24.99999489 0.989967356 0.923302134 0.194185647 0.06934545 41.47947399 1106589.409 0.022971368 0.018192081 173.579227 -2.23949775 -0.066665222 IILLFDAHKLDISDEFSEVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IILLFDAHKLDISDEFSEVIK 21 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8;Q9NZN3 A0A024R571;Q9NZN3 EHD1;EHD3 EH domain-containing protein 1;EH domain-containing protein 3 0 ;; 132.14 7.23E-06 794315000 515864 266908 458818 309185 581651 528532 511540 409897 525190 291405 FALSE TRUE 536230.7091 312747.3727 470775.174 370340.8702 482782.1708 405788.453 471444.1581 404403.0012 506288.5145 348500.2305 1.538681074 0.897409371 1.350860438 1.062670374 1.385313778 1.164385035 1.352780047 1.160409566 1.452763787 1 18.41080008 IILTECAPNPPS(ph)PPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IILTECAPNPPSPPEAR 17 0 A0A087WTE6 A0A087WTE6 SRCIN1 1 IILTECAPNPPS(1)PPEAR 161.19 3.14E-09 122510000 74937 87767 77696 78097 94969 102610 74765 84343 92350 105780 TRUE FALSE 77895.57062 102840.2995 79720.82159 93544.3535 78826.2033 78780.38257 68904.72394 83212.52004 89026.34154 126505.5657 0.61574817 0.812931027 0.630176397 0.739448521 0.623104627 0.622742423 0.54467741 0.657777542 0.703734583 1 16.94884133 0.746421103 3.029646134 0.99996501 0.6559032 0.684893515 0.069624724 1.033387288 11.61743908 0.067304698 0.017589885 5.577262731 -0.746421103 -0.34406181 IILWDHDLNPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IILWDHDLNPER 12 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ;;;; 277.06 6.99E-28 1011138000 722582 659263 687173 642275 780313 833013 755590 647795 652558 731332 FALSE TRUE 751110.0953 772486.2919 705081.2929 769315.078 647675.675 639558.3552 696364.8814 639112.3676 629072.5651 874622.5032 0.858782037 0.883222521 0.806154987 0.879596712 0.74052025 0.731239309 0.796189075 0.730729389 0.719250377 1 19.73830094 3.239976678 24.99990512 0.768460532 0.855189007 0.135280746 0.080118427 55.32784207 976770.7524 0.020760814 0.026651707 1737.707511 -3.239976678 0.086728476 IINEPTAAAIAYGLDKK ddPTM_MDA-MB-175_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 ; 221.41 5.92E-15 2622100000 3638800 2149020 2903500 1944760 4252300 3587400 3242100 2985300 3306500 1977520 FALSE TRUE 3782462.634 2518097.468 2979167.595 2329427.723 3529495.565 2754280.718 2987975.73 2945286.936 3187499.711 2364977.182 1.599365382 1.064744932 1.259702469 0.984968371 1.49240153 1.164611963 1.263426875 1.245376471 1.347793008 1 21.17339483 -1.152368984 3.770565805 0.999840494 1.256727326 0.175097804 0.173382269 6528651.098 5998125.669 7351.774002 0.036634018 0.07040946 1.152368984 0.256886833 IINEPTAAAIAYGLDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 269.33 4.85E-28 4828300000 1293160 1359270 1378050 1310690 1956410 1656910 1484660 1303880 1255160 1255200 FALSE TRUE 1344214.955 1592714.049 1413963.115 1569940.57 1623860.127 1272117.763 1368288.47 1286403.621 1209987.037 1501132.408 0.895467281 1.06100837 0.941930977 1.045837504 1.081756758 0.847438745 0.911504184 0.856955466 0.806049507 1 20.51761981 2.725740758 24.76973928 0.876416031 1.007043308 0.422767896 0.070258218 595.9496254 1151455.186 0.021491515 0.0203834 531.790724 -2.725740758 0.130627278 IINEPTAAAIAYGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 279.86 4.56E-35 1173523000 461228 528332 442669 489909 579848 620705 491500 535705 499740 582720 FALSE TRUE 479437.6376 619068.9111 454205.3178 586811.538 481285.6441 476555.6706 452974.9457 528524.7507 481754.455 696892.8272 0.687964661 0.888327282 0.651757774 0.842039859 0.690616441 0.683829209 0.649992263 0.758401766 0.691289157 1 19.41057728 -1.949088907 7.395431076 1.113693917 0.729450517 0.53640211 0.076074235 0.039931911 0.000274896 0.02062546 0.01621464 0.011243748 1.949088907 -0.3842434 IINEVSKPLAHHIPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IINEVSKPLAHHIPVEK 17 1 P55145 P55145 MANF Mesencephalic astrocyte-derived neurotrophic factor 0 ; 179.1 6.03E-10 795320000 1870810 1625430 2012880 1549070 2466400 2432500 2226000 1863370 2317700 1665320 FALSE TRUE 1944671.023 1904584.958 2065337.306 1855471.422 2047162.209 1867588.74 2051520.303 1838394.573 2234286.43 1991607.57 0.976432834 0.956305342 1.037020213 0.931645095 1.027894371 0.937729284 1.0300826 0.92307069 1.121850742 1 20.92550197 1.241260992 24.99998363 1.06092536 0.97752705 0.322617439 0.04834075 68.52393244 634444.2234 0.031799832 0.010413231 17.42853937 -1.241260992 -0.08339831 IINLGPVHPGPLS(ph)PEPQPMGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IINLGPVHPGPLSPEPQPMGVR 22 0 Q86T03-2;Q86T03 Q86T03-2 TMEM55B "Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase" 1 IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR;IINLGPVHPGPLS(1)PEPQPMGVR 152.41 2.28E-13 216157000 195421 272652 220049 356148 268046 360211 262773 255952 217095 286230 TRUE FALSE 203136.372 319477.8601 225783.6577 426593.0114 222483.6367 276557.4543 242176.1656 252521.3821 209281.7934 342311.2883 0.593425864 0.933296304 0.659585779 1.246213683 0.649945369 0.807912166 0.707473501 0.737695164 0.611378592 1 18.38494934 IIPELVGS(ph)PTQSTSSR ddPTM_MDA-MB-175_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(0.915)PT(0.078)QS(0.002)T(0.002)S(0.002)S(0.002)R;IIPELVGS(0.982)PT(0.018)QSTSSR;IIPELVGS(0.921)PT(0.079)QSTSSR;IIPELVGS(0.987)PT(0.013)QSTSSR 258.14 1.12E-26 309452000 211084 270007 264164 262986 273050 302038 243779 238835 247324 258328 TRUE FALSE 219417.7593 316378.6019 271048.3309 315003.8459 226637.0585 231894.2519 224670.965 235633.8075 238422.8576 308942.4256 0.710222168 1.02406978 0.877342535 1.019619902 0.73358995 0.750606691 0.727226002 0.762711068 0.771738802 1 18.23697848 3.220674995 24.99586415 0.772083663 0.913941132 0.199669511 0.110510768 291.9115827 407957.0946 0.029413605 0.035224096 1662.168297 -3.220674995 0.14185747 IIPELVGSPT(ph)QSTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIPELVGSPTQSTSSR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6;H7C409 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 IIPELVGS(0.373)PT(0.627)QSTSSR;IIPELVGS(0.491)PT(0.509)QSTSSR 231.21 1.73E-14 333510000 230420 272210 251650 259490 242850 310350 252130 255890 222320 273100 TRUE FALSE 239517.1595 318959.95 258208.2057 310816.3475 201570.4437 238275.9159 232367.3918 252460.2131 214318.7466 326608.7162 0.73334589 0.976581255 0.79057353 0.951647437 0.617161863 0.72954549 0.711454962 0.772974512 0.656194204 1 18.31720377 3.247612006 24.99915243 0.73596169 0.865971347 0.186363611 0.116212531 272.3783012 752280.6107 0.029363193 0.039201418 1768.528269 -3.247612006 0.130009657 IIPGFMCQGGDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 261.22 3.95E-24 14804631000 580901 661479 619048 547135 667436 762724 459797 602298 556947 733727 FALSE TRUE 603835.42 775082.8727 635180.8994 655356.67 553985.4671 585592.9102 423756.9097 594225.1805 536902.5863 877486.7576 0.688141918 0.883298655 0.723863801 0.746856479 0.631331997 0.667352419 0.482921145 0.677189912 0.611864033 1 19.74301783 3.421427513 2.357837606 0.649499603 0.777264062 0.055142863 0.132719205 0.535174071 6.012157424 0.036420286 0.055600345 2638.927826 -3.421427513 0.127764459 IIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.994)PT(0.005)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.991)PT(0.008)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.836)PT(0.16)AT(0.003)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.826)PT(0.172)AT(0.002)SQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.898)PT(0.092)AT(0.01)S(0.001)QLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.956)PT(0.044)ATSQLPLESDAVECLNYQHYK;IIPTLEEGLQLPS(0.982)PT(0.017)AT(0.001)SQLPLESDAVECLNYQHYK 207.16 3.53E-30 9926384000 2841655 2772760 3210803 2939497 3436201 3775420 3391858 3180257 3377025 2755563 TRUE FALSE 2953845.734 3248959.961 3294479.164 3520920.733 2852116.781 2898635.922 3125995.307 3137630.857 3255486.53 3295462.811 0.896337147 0.985888826 0.999701515 1.068414646 0.865467749 0.879583867 0.948575507 0.952106286 0.987869297 1 21.65204966 1.165405331 3.572963226 0.999262006 0.950945394 0.089101759 0.057264584 0.639652186 14.54767977 0.056498122 0.015108517 14.63542474 -1.165405331 -0.048316612 IIPTLEEGLQLPSPT(ph)ATSQLPLESDAVECLNYQHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 36 0 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 IIPTLEEGLQLPS(0.388)PT(0.456)AT(0.066)S(0.066)QLPLES(0.009)DAVECLNY(0.008)QHY(0.008)K 82.555 0.0024618 137330000 25688 23500 26356 22447 28635 30103 28249 27699 28845 29294 TRUE FALSE 26702.18208 27535.9422 27042.85901 26886.9496 23767.63293 23112.03447 26034.76956 27327.74021 27806.87408 35033.59843 0.762187822 0.785986694 0.771912114 0.767461831 0.67842397 0.659710549 0.743137181 0.78004377 0.793720181 1 15.09645156 0.619479539 1.200913613 0.999687812 0.739472249 0.794639035 0.039240353 0.621566523 1.351767166 0.04218219 0.012866977 4.163701041 -0.619479539 -0.260215563 IIPTLEEYQHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIPTLEEYQHYK 12 0 P61978-3;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 154.28 7.14E-05 1808270000 1047490 835840 1071650 881180 1274400 1337880 1229460 1049550 1103370 1018510 FALSE TRUE 1088845.714 979389.0181 1099578.079 1055474.774 1057777.943 1027177.646 1133091.713 1035482.499 1063659.929 1218067.534 0.893912434 0.804051492 0.902723411 0.866515808 0.868406647 0.843284643 0.930237184 0.8501027 0.873235596 1 20.21616269 -5 0.336686709 2.380179522 0.864649929 0.585487464 0.032765823 246.9804725 2.098885701 244.6760662 0.024641629 1.00E-05 5 -1.515529593 IIQFKPGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIQFKPGQDR 10 1 Q8TDQ7-3;Q8TDQ7;Q8TDQ7-5;Q8TDQ7-2 Q8TDQ7-3 GNPDA2 Glucosamine-6-phosphate isomerase 2 0 77.64 0.029542 214640000 287770 264610 266350 284580 409580 436280 413260 376190 392150 352360 FALSE TRUE 299131.3818 310054.7091 273291.2998 340869.0746 339959.7379 334960.5819 380867.6013 371147.7884 378036.5981 421398.1957 0.709854444 0.735776072 0.648534575 0.808900176 0.806742272 0.794879013 0.903818776 0.88075315 0.897100657 1 18.68482461 2.51614104 0.335261168 1.002090758 0.648333572 0.85696632 0.037553851 0.617949877 0.155284555 0.046555751 0.07883214 328.2018617 -2.51614104 -0.353757186 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 38 2 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 179.8 1.15E-23 1643870000 162840 166138 204858 171396 292603 248967 167269 213961 240022 278790 FALSE TRUE 169269.0489 194670.9091 210196.7678 205297.6172 242866.4466 191148.1874 154158.0187 211093.2028 231383.6551 333413.5627 0.507684953 0.583872196 0.630438564 0.615744649 0.728424017 0.573306574 0.462362771 0.633127222 0.693983932 1 18.34695327 0.798188126 2.059163758 0.999483504 0.592175524 0.766637043 0.067912535 0.35847915 2.607697881 0.067372256 0.018567035 6.283304771 -0.798188126 -0.40730798 IIS(ph)NASCTTNCLAPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IISNASCTTNCLAPLAK 17 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 IIS(0.624)NAS(0.373)CT(0.002)T(0.001)NCLAPLAK 151.57 2.57E-07 1386200000 417740 399540 452910 342220 547570 544630 454880 457010 472290 541960 TRUE FALSE 434232.6978 468157.887 464713.2067 409910.0946 454494.247 418147.9364 419225.317 450884.5285 455292.3752 648146.6855 0.669960531 0.72230237 0.716987708 0.632434144 0.701221278 0.645143986 0.646806234 0.695651985 0.702452678 1 19.30596083 0.370942959 1.613956402 1.000029898 0.678382924 0.915844245 0.02906045 1.398111451 3.297627612 0.028157373 0.008011757 2.349324234 -0.370942959 -0.321646974 IIS(ph)PGSSTPS(ph)STRSPPPGRDESYPR ddPTM_MDA-MB-175_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(0.931)PGS(0.021)S(0.023)T(0.025)PS(0.295)S(0.266)T(0.241)RS(0.197)PPPGRDESYPR 60.541 0.03918 82875000 98206 87929 103730 77096 111480 133550 98562 94196 108530 94619 TRUE FALSE 102083.2487 103030.1218 106433.289 92345.35869 92530.66942 102535.0365 90836.4529 92933.45669 104624.0265 113157.7815 0.902131938 0.910499662 0.940574193 0.81607608 0.817713711 0.906124485 0.80274155 0.82127323 0.924585346 1 16.78797627 3.74784121 24.9817555 0.855641415 0.917011705 0.087007572 0.059953072 1119.977202 3014779.595 0.014644113 0.025944377 5595.529764 -3.74784121 0.06137029 IISGHIDLDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IISGHIDLDNR 11 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 125.74 0.000322 252940000 94888 156465 134812 151175 144360 166678 139064 140202 118199 139658 FALSE TRUE 98634.25151 183336.6466 138325.3115 181076.9638 119821.7388 127969.5605 128163.8003 138322.8215 113945.0411 167021.3112 0.590548899 1.097684154 0.828189591 1.084154845 0.717403892 0.766187019 0.767349983 0.828174683 0.682218576 1 17.34967267 3.192903444 24.99997436 0.785075075 0.909116716 0.100191068 0.154308464 241.9638374 132488.541 0.040946005 0.048940008 1559.205807 -3.192903444 0.124041641 IISPGSST(ph)PSSTR ddPTM_MDA-MB-175_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 IISPGS(0.131)S(0.131)T(0.738)PSSTR 116.51 0.00075303 0 131810 157780 149970 148480 182380 176100 202180 141570 164370 127710 TRUE FALSE 137013.9606 184877.4876 153878.3414 177848.9008 151379.1127 135203.4438 186332.6033 139672.4857 158454.3558 152732.3293 0.897085517 1.210467282 1.007503402 1.164448297 0.991139947 0.885231335 1.21999451 0.91449195 1.037464409 1 17.22064595 IISPGSSTPSSTRS(ph)PPPGRDESYPR ddPTM_MDA-MB-175_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 1 IISPGSSTPS(0.019)S(0.011)T(0.011)RS(0.958)PPPGRDESYPR;IISPGSSTPS(0.236)S(0.109)T(0.109)RS(0.547)PPPGRDESYPR 231.07 9.37E-35 1175010000 149562 186557 183775 170891 216923 209154 122432 186515 207405 259000 TRUE FALSE 155466.8232 218596.7135 188564.3275 204692.7297 180050.5059 160581.1533 112835.4599 184015.0715 199940.5346 309746.0911 0.501916982 0.705728724 0.608770644 0.660840397 0.581284191 0.518428345 0.364283725 0.594083595 0.645498169 1 18.24072655 0.763848753 2.566755022 0.999806665 0.566843541 0.681712175 0.088482774 0.699014839 6.641446062 0.08991318 0.02396654 5.805621962 -0.763848753 -0.432963124 IISSDRDLLAVVFYGTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IISSDRDLLAVVFYGTEK 18 1 P12956;B1AHC9 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 273.33 4.79E-39 1698030000 2897490 2146590 2884000 2343700 3535420 3456120 3382380 3193950 3352170 2076090 FALSE TRUE 3011885.143 2515250.134 2959159.409 2807276.865 2934470.571 2653488.508 3117260.217 3151140.324 3231526.057 2482860.086 1.213070829 1.013045458 1.191834943 1.130662529 1.181891234 1.068722528 1.255511833 1.269157429 1.301533693 1 21.24357153 2.223096329 24.99694921 1.23423276 1.132505301 0.096783185 0.095843113 360.0768848 582035.6126 0.033092494 0.024528664 167.1461315 -2.223096329 -0.101727459 IISSIEQKEENKGGEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IISSIEQKEENKGGEDK 17 2 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 101.67 0.00057956 244690000 487690 99795 203330 91899 306800 296450 267970 196320 224870 87792 FALSE TRUE 506944.3778 116934.015 208628.9468 110076.3479 254650.2456 227603.9802 246965.8112 193688.6515 216776.9726 104993.1615 4.828356156 1.113729821 1.987071766 1.048414452 2.425398396 2.16779814 2.35220854 1.844773971 2.064677065 1 16.67993584 4.747306633 24.91551819 1.846504319 4.82835775 0.758541005 0.514968218 510.9815088 1455643.387 0.117688286 1.403520638 55886.46411 -4.747306633 2.981853431 IISVEKCLVRY(ph)IDY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IISVEKCLVRYIDY 14 2 F8W6E7 F8W6E7 STK31 1 IIS(0.001)VEKCLVRY(0.499)IDY(0.499) 53.751 0.044352 0 110130 96315 121400 94042 132220 128650 126910 113450 117770 114310 TRUE FALSE 114478.0174 112856.352 124563.7837 112643.2269 109745.2916 98772.98721 116962.4626 111929.3883 113531.4807 136706.8559 0.837397779 0.825535422 0.911174373 0.823976429 0.802778258 0.722516706 0.855571301 0.818754755 0.830473936 1 17.06072607 0.870831783 11.36212354 1 0.824699743 0.584307367 0.04421611 80.31371569 7066.140659 0.043784705 0.010948933 7.427313975 -0.870831783 -0.175300257 IISVT(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 IIS(0.356)VT(0.644)PVK;IISVT(1)PVK;IIS(0.001)VT(0.999)PVK;IIS(0.003)VT(0.997)PVK 124.67 0.014475 458547000 1777020 1249030 1552800 1443720 1780680 1934480 1902530 1532200 1556870 1132600 TRUE FALSE 1847178.122 1463541.186 1593267.244 1729283.507 1478000.65 1485226.337 1753404.727 1511663.365 1500838.553 1354511.285 1.363722947 1.080493904 1.176267235 1.276684459 1.091168945 1.09650348 1.29449252 1.116021241 1.108029567 1 20.36934098 -5 0.111645601 0.422602393 1.275648709 0.331262154 0.089130948 206.1130315 1.524765772 27.01182652 1.030505635 1.00E-05 5 0.853046316 IITDVIGNPEEERR ddPTM_MDA-MB-175_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 ; 125.5 0.00014571 193301000 332060 354060 353370 328850 397080 407250 341600 336620 371370 387710 FALSE TRUE 345169.9852 414867.0508 362579.1125 393895.5485 329584.4834 312672.3594 314824.4994 332108.1595 358004.4662 463674.3513 0.744423288 0.894737976 0.78196931 0.84950903 0.710810254 0.674336112 0.678977602 0.716253031 0.772103234 1 18.8227524 3.236146987 24.98637801 0.733676168 0.820616153 0.046208967 0.096629394 111.5480495 1154769.211 0.025502578 0.03187533 1722.451441 -3.236146987 0.086939985 IIVDELKQEVISTSSK ddPTM_MDA-MB-175_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 ; 214.54 1.54E-14 600640000 1261890 809120 1155810 768870 1447430 1387470 1258540 1099430 1344320 804590 FALSE TRUE 1311710.392 948080.0659 1185931.358 920950.1912 1201396.366 1065251.12 1159892.346 1084693.939 1295938.186 962234.0057 1.36319272 0.985290543 1.232477081 0.957095868 1.248549062 1.107060355 1.205416083 1.127266271 1.346801483 1 19.87602826 2.234174043 24.76139373 1.175666078 1.141109522 0.002849725 0.138522801 628.5172853 3547811.658 0.046599699 0.035626524 171.4644313 -2.234174043 -0.034556556 IIVEETKS(ph)NGQTVIEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIVEETKSNGQTVIEEK 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 IIVEET(0.034)KS(0.965)NGQT(0.001)VIEEK 136.14 6.84E-06 241140000 82581 47621 66171 50988 92432 103110 109520 57452 85513 42942 TRUE FALSE 85841.36165 55799.53631 67895.47062 61073.27422 76720.44166 79164.26515 100935.5362 56681.94991 82435.40383 51355.66273 1.671507232 1.086531326 1.322063956 1.189221811 1.493904228 1.541490479 1.965421744 1.103713727 1.605186253 1 15.64823574 3.218048868 24.78171554 1.471729893 1.301183428 0.046244811 0.286540078 591.6593324 714823.9931 0.080011064 0.095740852 1652.147691 -3.218048868 -0.170546465 IIVEKPFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIVEKPFGR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 154.81 6.82E-05 27239000000 14253000 14837500 18363100 15869200 14205800 17202700 13971200 14102200 12339200 13191500 FALSE TRUE 14815719.45 17385725.21 18841657.47 19008080.4 11791103.19 13207633.63 12876100.84 13913183.08 11895114.6 15776121.86 0.939123035 1.102027822 1.194314905 1.204863943 0.747401883 0.837191406 0.816176558 0.881914022 0.753994848 1 23.91123926 3.238380017 24.99999999 0.835285328 1.115523719 0.662357233 0.094601667 2.780017757 384855.4991 0.026485235 0.033617961 1731.330647 -3.238380017 0.28023839 IIVWDVAAGVAQCEIQEHAKPIQDVQWLWNQDASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIVWDVAAGVAQCEIQEHAKPIQDVQWLWNQDASR 35 1 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 165.04 7.16E-15 79990000 21122 19500 28012 18186 34621 35166 26420 22918 29757 26454 FALSE TRUE 21955.91287 22848.97331 28742.01573 21783.13652 28736.13479 26999.22945 24349.13136 22610.8217 28686.05138 31637.15481 0.693991385 0.722219601 0.908489272 0.6885302 0.908303384 0.853402577 0.769637204 0.714692008 0.906720328 1 14.94933224 -5 0.231359869 2.131302048 0.768320228 0.374112775 0.08406033 182.5622752 1.826289258 96.72123377 0.144220136 1.00E-05 5 -1.36298182 IIWCPFIPEESEDCCEESSPTVALLHEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIWCPFIPEESEDCCEESSPTVALLHEDR 29 0 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 96.019 0.0011178 29286000 14728 27895 18321 21162 21202 28103 16972 21149 20138 22929 FALSE TRUE 15309.47281 32685.74926 18798.46031 25347.78044 17598.09161 21576.50416 15641.69029 20865.53225 19413.23731 27421.49855 0.55830183 1.191975311 0.685537309 0.924376193 0.641762578 0.786846281 0.570417049 0.760918745 0.707956835 1 14.74301979 3.242054323 24.98131008 0.724930601 0.854148891 0.051184567 0.186248569 203.364983 1454124.728 0.047649619 0.062016071 1746.040541 -3.242054323 0.12921829 IIWELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIWELIK 7 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 123.96 0.009755 310140000 705160 605470 743070 637080 999040 954860 859240 741340 832690 735940 FALSE TRUE 733000.2613 709454.7626 762435.0146 763092.5225 829223.5376 733108.236 791890.5236 731403.5499 802721.6496 880133.3526 0.832828638 0.806076443 0.866272153 0.867019208 0.942156703 0.832951318 0.899739251 0.831014468 0.912045484 1 19.7473626 -5 0.178612901 1.549988312 0.834795144 0.571030566 0.037240636 101.5835317 0.975987096 19.8346241 0.120276156 1.00E-05 5 -0.715193168 IIYIVHDEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IIYIVHDEVK 10 0 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ; 159.83 7.57E-06 1336290000 2241800 1348810 1572290 1539950 2717900 2564000 2509400 1823720 2142310 1447010 FALSE TRUE 2330307.995 1580457.625 1613265.169 1844547.514 2255912.329 1968549.858 2312706.671 1799276.016 2065208.682 1730523.905 1.346591046 0.913282747 0.932240904 1.065889647 1.30360079 1.137545602 1.33641995 1.039729074 1.19340084 1 20.72277744 4.785911414 22.85827105 1.112045849 1.346593799 0.221098096 0.136402671 23806.95806 11491755.6 0.033734675 20.73016171 61081.74193 -4.785911414 0.23454795 IIYIVHDEVKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IIYIVHDEVKDK 12 1 P25788-2;P25788;G3V4X5 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 109.24 0.00097318 384660000 720400 333260 485360 253480 748760 624550 511210 467100 591310 279600 FALSE TRUE 748841.9483 390494.8126 498008.8803 303617.5874 621486.0427 479507.7276 471140.0244 460839.2885 570028.8686 334382.2667 2.239478653 1.167809574 1.489339986 0.907995482 1.858609455 1.434010638 1.408986275 1.378181005 1.704722186 1 18.35113881 -2.162453969 1.977097045 5.79E-05 1.477336061 0.155994114 0.348484646 6234203.606 1257404.318 27910019.99 0.078507328 0.006879328 2.162453969 1.477278198 IKAEYEGDGIPTVFVAVAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKAEYEGDGIPTVFVAVAGR 20 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 88.755 0.0019845 634990000 419550 374140 477520 323260 521260 549310 456110 464920 505110 455680 FALSE TRUE 436114.158 438395.6346 489964.5635 387199.8632 432656.4114 421741.0774 420358.9064 458688.5079 486931.1898 544961.7715 0.800265598 0.804452087 0.899080613 0.710508302 0.793920664 0.773891123 0.771354852 0.841689329 0.893514399 1 19.0557955 1.038470456 1.572727928 0.998301542 0.794304413 0.67964285 0.044399273 0.217142434 1.090662297 0.04139952 0.012161493 10.92623296 -1.038470456 -0.203997129 IKDAFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKDAFDR 7 1 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 79.474 0.029664 352920000 242730 176400 218050 210140 276390 314330 378820 268950 295650 155340 FALSE TRUE 252313.1678 206695.3278 223732.5621 251705.0648 229409.3265 241331.6212 349127.0985 265345.1652 285009.6143 185775.8988 1.358158778 1.112605721 1.204314249 1.354885463 1.234871304 1.299046985 1.879291667 1.428307799 1.534158177 1 17.50320382 2.45149676 24.99735267 1.513376737 1.250011353 0.161241692 0.211898608 287.3236158 280290.0094 0.068175436 0.057041402 282.8113015 -2.45149676 -0.263365385 IKDAFDRNPELQNLLLDDFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 213.45 2.25E-23 948810000 3147900 1273400 2030900 1241900 2701500 2556800 2568300 1926600 2379900 1138200 FALSE TRUE 3272181.523 1492096.544 2083826.922 1487544.113 2242299.995 1963021.949 2366989.935 1900777.078 2294247.864 1361208.498 2.403879735 1.096155767 1.530865349 1.092811363 1.647286216 1.442117025 1.738888597 1.396389371 1.685449266 1 20.37645663 -2.037112926 2.567607395 0.342248828 1.528057502 0.178978249 0.353724533 20244452.73 9075522.469 78226968.81 0.079029539 0.009180938 2.037112926 1.185808674 IKDHIQNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKDHIQNGK 9 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ; 120.12 0.00043063 440600000 1158410 767570 1150500 802540 1332700 1292460 1356840 1096390 1247130 763800 FALSE TRUE 1204144.921 899394.1766 1180482.975 961280.0167 1106168.13 992305.7524 1250487.335 1081694.685 1202246.035 913451.9862 1.318235594 0.984610237 1.292331719 1.052359655 1.210975669 1.086325026 1.368968872 1.184183407 1.316156791 1 19.80096937 2.286411845 24.99996472 1.232350423 1.153399683 0.041602107 0.132280394 295.6499447 154461.4925 0.041212515 0.034480785 193.3801288 -2.286411845 -0.07895074 IKDIAWTEDSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKDIAWTEDSKR 12 2 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 185.87 7.02E-06 3531700000 4454500 2944000 3864200 2722700 5483700 4528400 4351100 3831600 4512700 2879100 FALSE TRUE 4630367.1 3449609.099 3964904.226 3261241.934 4551582.633 3476747.729 4010049.413 3780243.669 4350288.809 3443204.521 1.344784218 1.001860063 1.151515747 0.947153128 1.321903072 1.009741857 1.164627134 1.097885312 1.263441884 1 21.71532045 -2.076193639 2.663339311 0.785802631 1.134237919 0.096733394 0.129154575 65978516.94 20439230.83 87392319.65 0.027735353 0.008390858 2.076193639 0.348435288 IKDMDLWEQQEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IKDMDLWEQQEEER 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 242.93 1.51E-17 1553410000 1240930 1123190 1364980 1192800 1626830 1665250 1560620 1311400 1502050 1108000 FALSE TRUE 1289922.875 1316089.145 1400552.5 1428732.28 1350302.018 1278520.925 1438294.526 1293822.828 1447991.514 1325091.386 0.973459558 0.993206325 1.056947856 1.078214148 1.01902558 0.964854906 1.08543044 0.976402716 1.092748417 1 20.33766043 4.409217613 5.947258563 1.031635985 0.978039934 0.189870457 0.042591331 0.287791162 18.12042371 0.009978347 0.028543581 25657.69352 -4.409217613 -0.053596051 IKDPDASKPEDWDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 ;;;;;;; 147.17 2.11E-06 63461890000 55401100 27904790 38710200 29493800 58733800 52784500 51720600 36267100 43085100 20271860 FALSE TRUE 57588378.21 32697220.61 39719019.61 35327585.61 48750249.66 40526099.83 47666604.23 35780998.85 41534475.67 24243742.84 2.375391399 1.348686992 1.638320447 1.457183647 2.010838425 1.671610696 1.966140482 1.475885926 1.713203937 1 24.53110911 0.111133226 0.771250648 0.983565276 1.739479266 0.372726617 0.289840655 4.189534431 2.789222964 0.454536253 0.092425983 1.291615434 -0.111133226 0.75591399 IKDQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKDQYK 6 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 68.915 0.086532 720480000 1602800 939910 1529700 901860 1571400 1495100 1400100 1132800 1201600 819850 FALSE TRUE 1666079.782 1101332.231 1569565.239 1080245.216 1304293.989 1147885.683 1290356.504 1117616.669 1158354.651 980483.9105 1.699242347 1.123253752 1.600806726 1.101747009 1.330255372 1.17073383 1.316040467 1.139862324 1.181411177 1 19.90313443 8 0.182038542 1.040847794 3.083551582 0.432125988 0.161039223 53.9157933 0.611081471 0.318492899 30.60207729 100000000 -8 2.042703788 IKDRDEEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKDRDEEIQK 10 2 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 112.13 0.0009349 145134000 446240 231750 302750 240820 552160 459400 411400 274650 377390 242150 FALSE TRUE 463857.8998 271551.2597 310639.9137 288453.4772 458304.0404 352711.3123 379153.393 270968.766 363807.8076 289594.6563 1.601748823 0.937694304 1.072671429 0.996059392 1.582570778 1.217948276 1.309255488 0.935682894 1.25626561 1 18.14367546 1.748867489 25 1.063397677 1.229261575 0.120431369 0.221708087 6.276808883 15255.13513 0.101487083 0.056279844 56.08768163 -1.748867489 0.165863898 IKEDILACSAAELNYGLAQFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKEDILACSAAELNYGLAQFVR 22 1 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 0 77.66 0.0087101 51486000 71088 48816 64752 38658 67854 77357 59648 48966 47535 30524 FALSE TRUE 73894.60913 57199.76826 66439.49031 46304.43702 56320.20132 59392.00911 54972.6339 48309.69086 45824.22464 36504.59338 2.024255095 1.566919748 1.820030965 1.268455083 1.542825056 1.626973583 1.505910046 1.323386631 1.255300235 1 15.15579039 7.999999986 0.080307855 0.54963268 4.020734048 0.695742204 0.155426815 109.6266856 0.640940639 4.156463497 42.22417909 99999996.76 -7.999999986 3.471101368 IKEEGY(ph)KK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKEEGYKK 8 2 Q4G0S7 Q4G0S7 CCDC152 Coiled-coil domain-containing protein 152 1 IKEEGY(1)KK;IKEEGY(1)KK 60.91 0.071963 416390000 12543 730470 779110 730830 901660 990330 719480 741820 808960 677640 TRUE FALSE 13038.20733 855922.5402 799414.2466 875385.9927 748396.1553 760340.8661 663085.2776 731877.1163 779845.6876 810410.5838 0.016088397 1.056159134 0.986431153 1.080175914 0.923477766 0.938216851 0.818209055 0.903094223 0.962284678 1 19.62829349 4.742382769 24.99949936 0.953455807 0.016088038 0.939530881 0.072039274 90.04341143 588922.0818 0.018880629 0.142270746 55256.42321 -4.742382769 -0.937367768 IKEELIAQGLLESEDRPAEDS(ph)EDEVLAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKEELIAQGLLESEDRPAEDSEDEVLAELR 30 2 O75528-2;O75528 O75528-2 TADA3 Transcriptional adapter 3 1 IKEELIAQGLLES(0.033)EDRPAEDS(0.967)EDEVLAELR 75.46 0.0022836 17055000 28035 21446 31144 24706 33787 34302 35897 30731 32589 23933 TRUE FALSE 29141.84345 25129.18367 31955.63823 29592.77306 28043.89781 26335.88035 33083.29934 30319.10121 31416.12826 28622.21313 1.018154792 0.877960889 1.11646287 1.033909325 0.979794878 0.920120336 1.155860981 1.059285705 1.097613526 1 14.80484761 2.238463197 25 1.083173233 0.993060789 0.268672929 0.070179147 3.46994279 890031.6643 0.025014683 0.019660083 173.1662279 -2.238463197 -0.090112445 IKEEVLSES(ph)EAENQQAGAAALAPEIVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 IKEEVLS(0.442)ES(0.558)EAENQQAGAAALAPEIVIK 98.114 0.001069 288410000 168280 104310 145170 106010 186130 180020 170330 173440 164490 104830 TRUE FALSE 174923.8243 122224.4311 148953.2495 126978.4616 154491.6891 138213.0832 156979.0895 171115.3205 158570.037 125369.4314 1.395266951 0.974914137 1.188114581 1.01283431 1.232291535 1.102446439 1.252132101 1.364888702 1.264822176 1 16.9358261 2.181891188 7.65043072 1.26391058 1.142170858 0.017663909 0.14160514 0.44968459 51.85281944 0.049431838 0.036582321 152.0166607 -2.181891188 -0.121739723 IKEGSVIDHIHLISVGDMIEAINGQSLLGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKEGSVIDHIHLISVGDMIEAINGQSLLGCR 31 1 O14908;O14908-2;K7ESN1;K7EIT0 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 230.69 7.18E-36 1021110000 817310 788430 963970 809009 1167240 1210200 1003470 1078070 1107330 901880 FALSE TRUE 849578.0299 923836.7194 989091.8501 969028.5655 968832.9617 929149.3908 924815.3993 1063620.235 1067477.41 1078586.118 0.787677512 0.85652569 0.917026312 0.898424844 0.898243492 0.861451279 0.857433063 0.986124535 0.989700675 1 20.04070994 1.691005473 5.149730848 0.992662787 0.871600627 0.740568033 0.033511107 0.083482613 5.128387007 0.018840376 0.009272637 49.09140631 -1.691005473 -0.121062159 IKELEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKELEQK 7 1 O60925 O60925 PFDN1 Prefoldin subunit 1 0 66.435 0.061909 344090000 365000 221610 245860 179490 341730 385600 273100 237610 304420 233110 FALSE TRUE 379410.4818 259669.7936 252267.3136 214992.5863 283642.8567 296050.2438 251693.7084 234425.2266 293463.9837 278783.4413 1.360950564 0.931439085 0.904886289 0.771181334 1.017430789 1.061936256 0.902828759 0.84088648 1.052659305 1 18.08878535 4.73855692 12.71994826 0.931212713 1.361153636 0.663587197 0.089034132 0.033780829 733.146315 0.021723743 0.125001834 54771.78819 -4.73855692 0.429940923 IKELNNTCEPVVTQPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKELNNTCEPVVTQPKPK 18 2 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 137.44 2.33E-06 330930000 135840 70362 106780 72784 157370 132320 126480 110030 122770 64926 FALSE TRUE 141203.0681 82446.12616 109562.7745 87180.45796 130620.3036 101590.6853 116566.1671 108555.2278 118351.5317 77647.00662 1.818525584 1.061806884 1.411036681 1.12277938 1.682232314 1.308365767 1.501231949 1.398060692 1.524225296 1 16.24464269 -1.48061525 5.833394642 0.999615665 1.411611509 0.252846173 0.218210744 0.000980185 8.73E-05 0.189871447 0.04471258 0.033066235 1.48061525 0.411995845 IKELQNAGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKELQNAGDR 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 0 115.65 0.00109 310930000 996380 699190 840190 649740 1043600 939210 908160 791740 861260 719010 FALSE TRUE 1035717.852 819270.4436 862086.0416 778256.6327 866209.2448 721092.7114 836976.0462 781128.0203 830263.4208 859886.2432 1.204482407 0.952766078 1.002558244 0.905069291 1.0073533 0.838590822 0.973356712 0.908408556 0.965550301 1 19.71378629 IKELTSTCSPIISKPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKELTSTCSPIISKPKPK 18 3 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 167.53 1.01E-11 1538100000 1368650 667231 1060550 559805 1533470 1123380 1094790 985950 1214890 560009 FALSE TRUE 1422685.359 781822.7339 1088188.804 670532.7581 1272811.317 862492.02 1008977.499 972734.9529 1171166.346 669732.0415 2.124260556 1.167366477 1.624812219 1.001195578 1.900478457 1.287816569 1.506539088 1.452424093 1.748708847 1 19.35322447 -1.525193435 2.891485058 0.978456225 1.508703996 0.19620425 0.320861346 63345366.83 68744462.46 10710554.37 0.07004969 0.029840532 1.525193435 0.530247771 IKENKGEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKENKGEER 9 2 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 75.509 0.021406 59298000 172650 121240 150520 97045 233580 229190 184210 158190 183610 124210 FALSE TRUE 179466.3553 142062.0269 154442.6749 116240.2113 193876.155 175964.0959 169771.1389 156069.7218 177001.912 148546.5714 1.208148755 0.956346724 1.039691953 0.782516959 1.305154022 1.184571911 1.142881571 1.050645063 1.19155838 1 17.18055578 3.225547615 24.99999463 1.143179032 0.996867931 0.257953943 0.123860656 321.885446 618391.1151 0.035169168 0.042278733 1680.922208 -3.225547615 -0.146311101 IKETVDQVEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKETVDQVEELR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 72.209 0.038768 122360000 143640 129270 158070 149330 201840 211840 196210 175660 182520 132200 FALSE TRUE 149311.0181 151471.1169 162189.4341 178867.0283 167531.3089 162643.3705 180830.5475 173305.565 175951.1409 158102.0589 0.944396418 0.958059104 1.025852764 1.13133902 1.059640273 1.028723924 1.143758334 1.096162607 1.112895949 1 17.27049663 4.080149902 3.045186484 1.086981212 0.949154129 0.59804877 0.042400756 0.153098617 2.838541647 0.010677771 0.026835281 12026.79482 -4.080149902 -0.137827083 IKEWVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKEWVDK 7 1 J3KQ32;Q9NTK5;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 85.731 0.018784 605970000 322840 685370 520640 661170 525350 816420 515540 631090 489630 905300 FALSE TRUE 335585.9725 803076.9661 534208.3061 791947.4526 436051.1947 626818.828 475130.6277 622631.2708 472008.3119 1082676.202 0.309959683 0.741751749 0.493414656 0.731472116 0.402753098 0.578953178 0.438848316 0.575085395 0.435964429 1 20.04617041 -1.496021455 2.768766052 1.018750264 0.532470514 0.540507187 0.131650496 13714045.22 14471680.82 1960256.351 0.031384633 0.031913802 1.496021455 -0.48627975 IKFPLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKFPLPHR 8 1 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 87.616 0.0091315 2207090000 3895300 3988400 4016800 3627500 6825200 5741700 4900800 4408100 4409800 5828600 FALSE TRUE 4049089.452 4673376.675 4121481.108 4345008.673 5665054.942 4408277.191 4516662.49 4349016.63 4251092.159 6970602.575 0.580880836 0.670440844 0.591266116 0.623333295 0.812706632 0.632409773 0.647958687 0.623908275 0.609860068 1 22.73285194 -1.267004648 3.795651988 1.00058018 0.645559971 0.749912927 0.061728651 7163906.537 4782824.986 31918.81836 0.014355158 0.054074854 1.267004648 -0.355020209 IKFSDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKFSDDR 7 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 ; 81.548 0.024536 427290000 438380 513050 495780 384840 708740 694140 489710 543470 549930 735400 FALSE TRUE 455687.5809 601162.3465 508700.4341 460960.2034 588268.628 532936.5048 451325.2506 536185.6736 530138.1267 879487.5499 0.518128518 0.683537074 0.578405498 0.524123626 0.668876584 0.605962534 0.513168436 0.609656923 0.602780707 1 19.74630363 0.303106934 1.947205246 1.000009548 0.589261454 0.830125746 0.055762505 4.869382326 13.05576608 0.050761995 0.013999373 2.009587564 -0.303106934 -0.410748095 IKGEHPGLSIGDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IKGEHPGLSIGDVAK 15 1 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ;; 151.8 1.77E-06 14757620000 20494150 14858660 19665090 13622510 24566480 23109490 22198460 19542150 21136310 13706050 FALSE TRUE 21303274.87 17410519.27 20177578.4 16317001.82 20390678.5 17742661.18 20458486.7 19280219.44 20375618.33 16391488.08 1.299654721 1.062168315 1.230979049 0.995455796 1.243979705 1.082431387 1.248116498 1.176233625 1.243060925 1 23.9664435 2.236806275 24.99996235 1.183348229 1.148935907 0 0.107431796 229.2808842 3267222.751 0.035499978 0.027558671 172.5068221 -2.236806275 -0.034412322 IKGEHPGLSIGDVAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKGEHPGLSIGDVAKK 16 2 P09429;Q5T7C4;B2RPK0 P09429 HMGB1;HMGB1P1 High mobility group protein B1;Putative high mobility group protein B1-like 1 0 90.714 0.0032173 242640000 373450 281620 368900 193800 586900 416830 278790 378480 418830 327790 FALSE TRUE 388194.0944 329986.0443 378513.8371 232133.0616 487138.9476 320027.5496 256937.7113 373407.0947 403756.3901 392014.1746 0.99025525 0.841770695 0.965561609 0.592154765 1.242656463 0.816367291 0.655429645 0.952534676 1.029953548 1 18.5805463 1.491255526 12.49142622 1.007093792 0.870865642 0.104382768 0.170273767 0.20717089 119.0686436 0.088570655 0.0410687 30.99242267 -1.491255526 -0.13622815 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 IKGS(0.5)S(0.5)PGIQDTLEAEDGAFETDEAPEDR;IKGS(0.5)S(0.5)PGIQDTLEAEDGAFETDEAPEDR 171.5 1.91E-12 98106000 71981 54891 80600 66520 92040 97529 101447 82209 91259 61715 TRUE FALSE 74822.86546 64318.10226 82700.50221 79677.45746 76395.07368 74879.36782 93495.31906 81107.12282 87974.60642 73806.87264 1.013765558 0.871437848 1.120498664 1.079539813 1.035067209 1.014531102 1.266756275 1.098910168 1.191956836 1 16.17146754 3.968608695 0.665108467 1.130323524 0.919682647 0.246654164 0.090552325 1.769513877 1.121455902 0.044074597 0.247178664 9302.693134 -3.968608695 -0.210640877 IKGSEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKGSEADR 8 1 P56192 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 85.377 0.015308 294110000 781390 656590 733680 635250 1003110 932120 808050 705550 771840 634890 FALSE TRUE 812239.8806 769354.2249 752800.3035 760900.554 832601.7205 715649.2564 744712.9296 696093.2563 744061.6292 759284.5398 1.069743736 1.013262071 0.991460071 1.002128338 1.096560877 0.942531052 0.980808762 0.916775227 0.97995098 1 19.53428111 2.706129934 24.9983827 0.956852729 1.029239781 0.474342569 0.03656604 555.3387425 428068.3271 0.011704506 0.011035573 508.3114991 -2.706129934 0.072387052 IKIGDPLLEDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKIGDPLLEDTR 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 122.78 0.00032138 723300000 2523700 2244900 2507500 2057160 3624400 3158900 2595200 2607900 2817900 2521400 FALSE TRUE 2623337.625 2630444.112 2572847.51 2464060.108 3008325.783 2425293.349 2391781.443 2572945.366 2716484.329 3015420.055 0.869974192 0.872330907 0.853230218 0.817153187 0.997647335 0.804297015 0.793183503 0.85326267 0.900864317 1 21.52392756 0.900591209 3.229113275 0.999849361 0.856486899 0.394088278 0.05355731 0.410551399 9.396580247 0.050911777 0.013251859 7.954102967 -0.900591209 -0.143362462 IKIIAPPER ddPTM_MDA-MB-175_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 ; 96.342 0.006779 12227500000 3284100 3227600 3389400 2727400 4284800 3816600 3056800 3511000 3524700 3291800 FALSE TRUE 3413758.804 3781915.193 3477730.548 3266871.58 3556471.226 2930252.491 2817200.029 3463940.788 3397846.736 3936765.185 0.86714819 0.960665677 0.883398015 0.829836535 0.90339938 0.744330016 0.71561292 0.8798952 0.863106275 1 21.90857923 3.909884762 3.890138143 0.835900984 0.915809849 0.088527963 0.078456942 0.424844363 11.70998835 0.020229459 0.039882705 8126.148645 -3.909884762 0.079908866 IKISFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKISFR 6 1 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 107.43 0.028522 256150000 315790 312540 391030 286250 576380 441000 357150 389840 418560 455530 FALSE TRUE 328257.633 366216.3138 401220.563 342869.3956 478407.1335 338584.4334 329155.6498 384614.8324 403496.1074 544782.3819 0.602548181 0.672224958 0.736478595 0.629369464 0.878161904 0.621504007 0.604196576 0.705997193 0.740655573 1 19.05532052 0.711287681 2.061122303 0.999847816 0.682614701 0.599453605 0.077951781 0.854701565 5.103404712 0.07256102 0.019940566 5.143842723 -0.711287681 -0.317233114 IKKPEGKPDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKKPEGKPDQK 11 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 61.235 0.038812 1237600000 1229600 374370 818790 413340 1160800 947410 1056800 749990 977290 373720 FALSE TRUE 1278145.557 438665.1353 840128.34 495097.4183 963487.6306 727388.3856 973965.2546 739937.6108 942117.5238 446943.2787 2.859748918 0.981478313 1.879720269 1.107741053 2.15572686 1.627473597 2.179169709 1.65555149 2.107912947 1 18.76973223 IKLDVPEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKLDVPEDLR 10 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ; 131.37 0.00022979 319560000 1351670 1132250 1262700 1109670 1618660 1596120 1486550 1355600 1373480 1048010 FALSE TRUE 1405034.975 1326705.13 1295606.999 1329159.414 1343520.751 1225445.319 1370030.327 1337430.399 1324048.723 1253347.494 1.121025878 1.058529367 1.033717309 1.06048755 1.071945935 0.977737878 1.093096953 1.067086666 1.056409918 1 20.25735503 4.727609931 4.01949447 1.04976825 1.126641705 0.31594504 0.032798619 0.27091123 9.271941116 0.007633698 0.059647638 53408.4447 -4.727609931 0.076873455 IKLNGLENR ddPTM_MDA-MB-175_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 ; 142 9.61E-05 1362520000 1486070 1543580 1432570 1261700 2553300 2208960 1982870 1627370 1774640 2053500 FALSE TRUE 1544741.191 1808677.858 1469903.951 1511260.494 2119290.978 1695962.517 1827447.468 1605557.767 1710771.053 2455844.008 0.629006234 0.73647913 0.59853311 0.615373163 0.862958303 0.690582346 0.744121965 0.653770256 0.696612263 1 21.2277875 -1.677851631 2.276240427 1.056785279 0.692690115 0.612699872 0.073476281 2069508.542 1450459.988 677085.1738 0.019269636 0.020996571 1.677851631 -0.364095165 IKLQLWDTAGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKLQLWDTAGQER 13 1 Q14964 Q14964 RAB39A Ras-related protein Rab-39A 0 73.022 0.026275 0 309940 266850 291230 221300 378750 403260 294920 273210 342140 282430 FALSE TRUE 322176.6705 312679.4117 298819.693 265072.4795 314370.2103 309608.9765 271803.3998 269548.0668 329826.4482 337766.7511 0.95384365 0.925725847 0.884692446 0.78477967 0.930731664 0.916635446 0.804707387 0.798030197 0.976491757 1 18.36566779 4.297635808 3.244824201 0.870273835 0.947183643 0.049723812 0.071343545 0.484182333 10.02563683 0.017837553 0.057156116 19844.3011 -4.297635808 0.076909808 SRTS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.209)RT(0.139)S(0.652)PVSR;S(0.191)RT(0.116)S(0.693)PVSR;S(0.075)RT(0.101)S(0.825)PVSR 83.081 0.011268 2025400000 1604085 578111 604236 436954 845676 1112262 828180 489270 656990 464980 TRUE FALSE 1667415.514 677397.0672 619982.8865 523382.197 701928.2956 853956.007 763265.0876 482712.1359 633345.0582 556083.9284 2.998496143 1.218156168 1.114908838 0.941192813 1.262270423 1.53566029 1.372571744 0.868056261 1.138937894 1 19.08494312 4.738601803 5.620979051 1.156095159 3.061028139 0.894758479 0.18913543 0.044572506 5.773097706 0.049275576 0.32645245 54777.449 -4.738601803 1.904932981 up IKNENTEGS(ph)PQEDGVELEGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 IKNENT(0.004)EGS(0.996)PQEDGVELEGLK;IKNENT(0.01)EGS(0.99)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.006)EGS(0.994)PQEDGVELEGLK 327.74 3.21E-80 2014540000 2604680 1216156 1919530 1215945 2777360 2300050 2497190 1806330 2119410 967191 TRUE FALSE 2707514.778 1425021.333 1969554.529 1456455.292 2305265.339 1765898.245 2301453.723 1782119.101 2043132.848 1156693.558 2.340736453 1.231978273 1.702745307 1.259153975 1.992978453 1.526677686 1.989683184 1.540701154 1.766356208 1 20.14157527 -0.901818352 5.047865005 0.999998045 1.683412318 0.295533731 0.325220167 6.37E-06 1.39E-06 0.28037859 0.066085678 0.125366542 0.901818352 0.683414273 IKNVVHELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKNVVHELR 9 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 113.12 0.0011131 465640000 522550 467580 593640 531540 768320 759480 575670 584680 646940 643640 FALSE TRUE 543180.6775 547883.2277 609110.7461 636677.0255 637721.2408 583102.28 530547.4812 576843.3209 623656.7558 769748.9348 0.705659538 0.711768738 0.791310931 0.827122971 0.828479537 0.757522685 0.689247438 0.749391516 0.810208014 1 19.55402844 0.837968181 3.377675015 0.999942035 0.758431341 0.719551561 0.045361774 0.484032279 9.055471835 0.048435949 0.012538898 6.886018432 -0.837968181 -0.241510694 IKPHLMSQELPEDWDKQPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKPHLMSQELPEDWDKQPVK 20 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 173.56 2.83E-12 1903890000 3464180 1913490 2367180 1961130 3669720 3255250 3396160 2490430 3060570 1289810 FALSE TRUE 3600948.501 2242117.023 2428870.655 2349035.661 3045942.305 2499267.521 3129960.105 2457049.859 2950420.684 1542523.575 2.334452815 1.453538254 1.57460845 1.522852357 1.974648787 1.620245915 2.029116544 1.592876699 1.912723236 1 20.55686111 -1.626437576 5.993433899 0.995638707 1.756026375 0.434457042 0.265582539 0.014259044 0.000888746 0.236910158 0.055721835 0.023635371 1.626437576 0.760387668 IKPMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKPMVR 6 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 92.76 0.042307 1607100000 2718800 2861800 3272600 2993200 3810100 3914300 3537100 3361400 3133300 2679100 FALSE TRUE 2826140.323 3353291.888 3357886.644 3585246.026 3162460.563 3005263.147 3259852.86 3316345.931 3020533.145 3204018.351 0.882061216 1.046589477 1.048023537 1.118984236 0.987029479 0.937966896 1.017426401 1.035058345 0.942732786 1 21.61145098 IKQEILPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKQEILPEER 10 1 O75534-2;O75534;O75534-3;O75534-4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 94.402 0.007413 241610000 463330 579490 611890 600190 711570 762570 602070 664410 652590 602070 FALSE TRUE 481622.6262 679012.8997 627836.3561 718905.7906 590617.5856 585474.6744 554878.1802 655504.6707 629103.4134 720034.0892 0.668888645 0.943028823 0.871953655 0.998432993 0.820263366 0.813120772 0.770627653 0.910380051 0.873713374 1 19.45770569 0.681065157 1.374870332 0.999333131 0.853217208 0.212069319 0.087116168 1.777931657 5.234926347 0.08049493 0.023836496 4.798054281 -0.681065157 -0.146115923 IKS(ph)VPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKSVPK 6 1 Q9Y2C9 Q9Y2C9 TLR6 Toll-like receptor 6 1 IKS(1)VPK 72.547 0.051664 559290000 1608300 801270 1191200 998830 1438800 1647300 1753700 1307000 1264700 650590 TRUE FALSE 1671796.926 938881.8895 1222243.651 1196395.593 1194233.29 1264739.54 1616240.412 1289481.803 1219183.694 778060.6542 2.148671722 1.206694985 1.570884794 1.537663659 1.534884566 1.625502502 2.077267888 1.657302417 1.566951995 1 19.5695231 2.478183434 24.9998186 1.674326646 1.573601463 0 0.331213116 218.3101377 5138457.681 0.107290053 0.090834802 300.7346253 -2.478183434 -0.100725183 IKS(ph)VVMEGGEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKSVVMEGGEER 12 1 A0A5H1ZRP3;O43151;O43151-3;O43151-2 A0A5H1ZRP3 TET3 Methylcytosine dioxygenase TET3 1 IKS(1)VVMEGGEER 64.654 0.026009 0 21100 24600 23839 22414 23528 34473 27876 30251 26285 25828 TRUE FALSE 21933.04429 28824.85864 24460.26392 26847.4223 19528.71896 26467.16819 25691.00628 29845.53483 25339.00798 30888.50209 0.710071477 0.933190562 0.791888964 0.869172038 0.632232632 0.856861499 0.83173364 0.96623445 0.820337869 1 14.91478229 1.997878241 2.605321869 0.923127452 0.799845282 0.290006016 0.090029193 0.37621256 4.818714988 0.044524195 0.025003794 99.51263834 -1.997878241 -0.12328217 IKSDYAQLLEDMQNAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKSDYAQLLEDMQNAFR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 258.9 3.20E-27 1138360000 1650700 1819740 2114700 1514500 2440700 2453700 1784110 2085870 2240700 2178380 FALSE TRUE 1715870.911 2132266.189 2169810.819 1814063.58 2025830.686 1883865.361 1644266.796 2057912.324 2160057.645 2605191.853 0.658635144 0.818468009 0.832879474 0.696326291 0.777612859 0.723119627 0.631149984 0.789927361 0.829135728 1 21.31295819 0.904955893 1.929561245 0.998697296 0.740742302 0.62322566 0.062033526 0.28969741 2.211984558 0.059025161 0.01652862 8.034445198 -0.904955893 -0.257954994 IKSEHPGLSIGDTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKSEHPGLSIGDTAK 15 1 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 186.85 2.19E-07 321430000 470670 505740 773190 469160 1016400 865820 741760 762850 852180 606870 FALSE TRUE 489252.415 592596.9109 793339.9666 561958.4477 843632.691 664746.4266 683618.913 752625.2435 821510.2083 725774.5573 0.674110728 0.816502735 1.09309421 0.774287886 1.162389454 0.915913103 0.941916338 1.036995905 1.131908249 1 19.46916196 4.442475994 4.155882875 1.000563777 0.697661202 0.502790923 0.107993346 0.146997978 5.51816255 0.025036999 0.08578897 27699.75921 -4.442475994 -0.302902575 IKTEPSS(ph)PLSDPSDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 IKTEPS(0.133)S(0.865)PLS(0.002)DPSDIIR;IKTEPS(0.024)S(0.974)PLS(0.002)DPSDIIR 141.5 3.77E-07 841510000 707220 573050 722520 509215 907090 887430 724050 747150 788870 622040 TRUE FALSE 735141.5917 671466.8798 741349.4648 609936.2071 752903.1658 681337.8316 667297.069 737135.6763 760478.7228 743916.8283 0.988204008 0.90261015 0.996548857 0.819898386 1.012079761 0.915879041 0.897004939 0.990884529 1.0222631 1 19.50478181 1.584151517 5.413797868 1.009562067 0.932579922 0.27315183 0.053793932 0.174935039 10.86930281 0.027792187 0.0128226 38.38411367 -1.584151517 -0.076982144 IKTVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKTVELR 7 1 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 0 85.212 0.03636 0 445930 431290 526500 439130 623980 591260 523330 512890 508250 502830 FALSE TRUE 463535.6607 505360.7025 540221.0225 525988.6033 517916.1025 453948.8256 482310.0271 506015.5485 489958.1818 601349.9112 0.770825192 0.840377113 0.898347223 0.874679772 0.861255806 0.754883001 0.802045561 0.841466073 0.814763871 1 19.19784518 -1.140591488 4.3049109 1.000033766 0.830894647 0.593266236 0.042507694 1.45E-05 2.89E-06 0.04322754 0.010186796 0.072344998 1.140591488 -0.169139119 IKVNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IKVNGK 6 1 P35268;K7ERI7;K7EMH1;K7EP65;K7EKS7;K7ELC4;K7EJT5 P35268 RPL22 60S ribosomal protein L22 0 ; 91.26 0.043863 2657900000 2835700 1820810 2622000 1728950 3016400 2639200 2653100 2348800 2598100 1716360 FALSE TRUE 2947655.626 2133519.954 2690331.474 2070931.15 2503673.405 2026285.797 2445143.089 2317318.178 2504594.889 2052647.88 1.436025952 1.039398902 1.310663899 1.008907163 1.219728639 0.987157036 1.191214096 1.128940916 1.220177563 1 20.96905473 4.749570057 24.44805678 1.131005731 1.436026193 0.437075127 0.106247151 1050.196418 2332052.501 0.022487279 0.335738746 56178.48938 -4.749570057 0.305020462 IKVPVDWSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKVPVDWSK 9 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2 P13797 PLS3 Plastin-3 0 96.015 0.0069808 232810000 624580 433000 548500 397600 762180 681590 656470 519180 595450 489350 FALSE TRUE 649238.9007 507364.3817 562794.3606 476244.0933 632624.9158 523301.0521 605014.166 512221.2413 574019.8708 585228.7633 1.109376267 0.866950522 0.961665584 0.813774242 1.080987394 0.894182045 1.033807981 0.875249601 0.98084699 1 19.15864115 3.233110161 24.99933475 0.964919969 0.934565434 0.032118543 0.091214946 642.2644158 2945834.761 0.024687565 0.030293802 1710.449123 -3.233110161 -0.030354535 IKWDEQTSNTKGDDDEES(ph)DEEAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKWDEQTSNTKGDDDEESDEEAVK 24 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQTSNTKGDDDEES(1)DEEAVK 228.62 1.80E-33 97428000 231920 42723 89932 45917 145030 151400 134430 84216 109660 31789 TRUE FALSE 241076.3807 50060.34291 92275.7018 54999.24555 120377.8524 116239.6445 123893.0253 83087.22227 105713.358 38017.44591 6.341204015 1.316772911 2.42719361 1.44668439 3.166384525 3.05753429 3.258846626 2.185502479 2.780653868 1 15.21437399 4.748322057 24.89029565 2.393192385 6.34120627 0.710284462 0.77320721 685.051034 1746745.643 0.178974676 2.370156917 56017.28516 -4.748322057 3.948013885 IKWDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IKWDEQTSNTKGDDDEESDEEAVKK 25 3 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 IKWDEQTSNTKGDDDEES(1)DEEAVKK 275.54 2.63E-52 351300000 396740 64877 167900 37123 240560 189580 201300 123740 137840 32394 TRUE FALSE 412403.6015 76019.12008 172275.6119 44465.8186 199669.6971 145552.9181 185521.58 122081.4677 132879.1653 38740.98408 10.64515038 1.962240296 4.446856889 1.147772047 5.153965545 3.757078494 4.788767875 3.151222681 3.42993779 1 15.24157298 4.745477185 24.92636653 3.384717808 10.64515387 0.721315035 1.383445074 385.2124992 1388216.675 0.302002149 3.00197865 55651.53978 -4.745477185 7.260436067 IKWGDAGAEYVVESTGVFTTMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 27 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;; 273.6 1.03E-51 59065489000 23764486 16442652 23493414 14867135.8 29944948 26257010 24937388 22263850 25998186 16447119 FALSE TRUE 24702726.26 19266549.57 24105671.67 17807810.89 24854916.44 20159217.36 22982730.37 21965439.51 25062516.36 19669617.07 1.255882419 0.979508117 1.225528264 0.905346089 1.263619741 1.024891196 1.168438119 1.116719224 1.274174087 1 24.22946554 IKYPENFFLLR ddPTM_MDA-MB-175_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 ; 197.31 5.24E-08 1188630000 1514770 1158200 1307060 1116310 2797500 2021900 1779120 1387480 1508530 2204300 FALSE TRUE 1574574.289 1357111.84 1341123.057 1337112.786 2321981.949 1552344.367 1639667.926 1368883.1 1454238.3 2636190.381 0.597291569 0.514800392 0.508735282 0.507214045 0.880809658 0.588858976 0.621983881 0.519265646 0.551643884 1 21.33002313 -1.940545069 2.413535394 1.297299144 0.586204671 0.578846887 0.105459518 7949316.123 3790080.815 13289433.02 0.027641868 0.011467135 1.940545069 -0.711094473 ILAGDKNYITMDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILAGDKNYITMDELR 15 1 P12814-3;P12814;P12814-2;H9KV75;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 ; 209.66 2.07E-09 1438750000 767130 762580 820010 708690 1161920 1112660 911440 850400 869820 987950 FALSE TRUE 797416.8848 893547.183 841380.1342 848866.7668 964417.2534 854261.5775 839998.9512 839001.779 838515.3481 1181519.887 0.674907713 0.75626927 0.712116777 0.71845322 0.816251393 0.723019212 0.710947789 0.710103815 0.709692115 1 20.17221248 -1.134182353 4.552573536 1.000030527 0.726752083 0.842170097 0.035614899 1.12E-05 2.12E-06 0.034058757 0.008026809 0.073420552 1.134182353 -0.273278443 ILAGDKNYITMDELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILAGDKNYITMDELRR 16 2 P12814-3;P12814;P12814-2;H9KV75;H0YJW3 P12814-3 ACTN1 Alpha-actinin-1 0 153.98 2.25E-07 429160000 556380 539380 525190 380140 881020 703910 530270 573210 642210 719940 FALSE TRUE 578346.312 632014.3192 538876.8828 455330.5574 731264.5351 540437.5704 488706.0518 565527.0575 619096.9875 860998.4589 0.67171585 0.734048142 0.625874387 0.528840154 0.849321538 0.627687036 0.567603864 0.656827026 0.719045407 1 19.71565113 0.781687524 2.870545156 0.999925837 0.656325327 0.600945202 0.083326739 0.774373427 9.155490574 0.078508051 0.02064802 6.049054865 -0.781687524 -0.343600511 ILAT(ph)PPQEDAPSVDIANIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 1 ILAT(1)PPQEDAPSVDIANIR 212.79 9.91E-25 0 12335 16717 15641 16939 22144 21778 13468 15914 13760 23473 TRUE FALSE 12821.99532 19588.01471 16048.61731 20289.48364 18379.97079 16720.38955 12412.34297 15700.69886 13264.78029 28072.08493 0.456752513 0.697775557 0.571693102 0.722763688 0.65474192 0.59562336 0.44215964 0.55929935 0.472525654 1 14.7768486 -1.282578747 6.004414256 1.000020757 0.578446939 0.653522041 0.092842836 2.61E-05 3.12E-06 0.091033116 0.021455657 0.05217005 1.282578747 -0.421573817 ILAYTEGLHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILAYTEGLHGK 11 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 147.91 3.51E-05 522990000 414440 952320 1094500 939570 1285700 1279100 1111500 930730 1116500 1736600 FALSE TRUE 430802.4112 1115873.552 1123023.569 1125414.142 1067157.173 982048.4099 1024377.726 918255.0867 1076317.383 2076853.521 0.20743033 0.537290445 0.540733161 0.541884216 0.513833625 0.472853959 0.493235423 0.442137627 0.518244244 1 20.98596804 0.838595432 6.606875318 0.999999805 0.476932867 0.741276478 0.093499089 3.310817003 135.5484269 0.085568402 0.021477666 6.895971084 -0.838595432 -0.523066938 ILCLFRPQSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILCLFRPQSGR 11 1 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 0 ; 206.27 2.46E-08 1216660000 307600 489760 337780 362730 779180 617300 392550 370450 365470 1072540 FALSE TRUE 319744.2855 573872.4702 346582.8243 434476.9114 646735.2619 473941.4303 361780.9053 365484.7237 352316.8061 1282683.678 0.249277582 0.447399838 0.270201321 0.338724908 0.504204796 0.369492057 0.28204998 0.284937534 0.274671622 1 20.290734 -1.458156636 3.255196855 1.011397138 0.336897795 0.863150674 0.079356178 31822399.03 39970011.24 3293436.256 0.02077284 0.03482117 1.458156636 -0.674499343 ILDAVVAQEPLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILDAVVAQEPLHR 13 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 138.42 4.93E-05 667620000 696260 879150 767460 824160 863860 978090 817190 799490 760080 875030 FALSE TRUE 723748.8824 1030137.174 787460.6381 987176.3881 717021.3858 750943.4206 753136.5125 788774.1443 732724.8693 1046475.375 0.691606224 0.9843874 0.752488455 0.943334561 0.685177504 0.717593016 0.71968871 0.753743627 0.700183575 1 19.99710693 3.225566913 24.99673115 0.745938393 0.846594719 0.093323274 0.115372873 400.4534039 770373.8035 0.030141 0.036236583 1680.996902 -3.225566913 0.100656326 ILDDDTIITTLENLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILDDDTIITTLENLKR 16 1 Q14204;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 312.42 1.70E-57 4173800000 695080 655290 746310 663780 924510 921630 769640 714390 759220 674860 FALSE TRUE 722522.2951 767830.9601 765759.4517 795073.7028 767362.1204 707595.3999 709313.6057 704814.7706 731895.8205 807085.896 0.895223543 0.951362134 0.948795482 0.985116586 0.950781229 0.876728739 0.87885764 0.873283468 0.90683758 1 19.6223627 2.749744234 24.15893362 0.89492319 0.948839512 0.156263762 0.040547923 570.1700254 1231684.34 0.011881387 0.012485228 562.0102476 -2.749744234 0.053916322 ILDEIEEHNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ILDEIEEHNIK 11 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;C9J2Q4 Q15019-2 2-Sep Septin-2 0 ;;;;; 252.97 2.13E-20 2831340000 3740270 2726800 3369240 2686940 4352480 3940500 4002970 3496480 3689240 2649280 FALSE TRUE 3887938.748 3195106.688 3457045.162 3218408.712 3612647.004 3025378.594 3689206.752 3449615.405 3556464.973 3168355.692 1.227115616 1.00844318 1.091116496 1.015797791 1.140227725 0.954873407 1.164391599 1.088771508 1.122495489 1 21.59530288 ILDEWFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILDEWFGR 8 0 Q8IYB7;Q8IYB7-3;Q8IYB7-2;H7C440 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 0 80.229 0.055476 0 85717 73007 76109 67288 73876 97370 71361 68330 79408 75785 FALSE TRUE 89101.17335 85545.38433 78092.46306 80597.36557 61318.58391 74757.29316 65767.53835 67414.14812 76550.12159 90633.61976 0.983091855 0.943859294 0.861627984 0.889265659 0.676554507 0.824829609 0.725641749 0.743809508 0.844610662 1 16.46775868 3.999709354 1.334120687 0.785804979 0.981822126 0.300619948 0.086983285 0.50392928 1.600658918 0.024612788 0.093362659 9993.309878 -3.999709354 0.196017147 ILDILEYIHEHEYVHGDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILDILEYIHEHEYVHGDIK 19 0 Q99986;H0YJ50 Q99986 VRK1 Serine/threonine-protein kinase VRK1 0 82.248 0.0016429 41027000 66785 39808 65540 48333 74865 71473 79336 68918 69430 44157 FALSE TRUE 69421.72337 46644.71434 67248.02624 57893.12314 62139.47404 54874.47893 73117.43701 67994.26694 66931.22786 52808.71871 1.314588293 0.883276767 1.273426583 1.09627964 1.176689675 1.039117787 1.384571313 1.287557596 1.267427605 1 15.68848852 2.246357997 24.99938921 1.266417804 1.12635496 0.093933109 0.145802594 284.6782099 912715.2232 0.04697366 0.038620591 176.3429076 -2.246357997 -0.140062845 ILDKCNEIINWLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILDKCNEIINWLDK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 182.35 1.40E-06 517100000 997520 778100 923160 633640 1325020 1139640 846330 925090 1093850 957630 FALSE TRUE 1036902.86 911732.6222 947218.308 758972.1008 1099793.574 874975.8814 779992.4431 912690.6817 1054482.552 1145259.264 0.90538701 0.796092772 0.827077622 0.662707672 0.960300963 0.763998083 0.681061894 0.796929316 0.920736977 1 20.1272428 1.088800047 3.430109035 0.996959859 0.793855274 0.380326264 0.084984742 0.21009314 4.689890366 0.078391669 0.020524283 12.26874238 -1.088800047 -0.203104585 ILDKCNEIINWLDKNQTAEKEEFEHQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILDKCNEIINWLDKNQTAEKEEFEHQQK 28 3 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 203.47 2.08E-25 434310000 375550 140900 213110 87260 354680 273160 252670 187050 267320 118810 FALSE TRUE 390377.004 165098.479 218663.8217 104519.7676 294391.6203 209722.7298 232865.0652 184542.9007 257699.2054 142088.5447 2.747420664 1.161940811 1.538926464 0.735596017 2.071888489 1.476000266 1.638872898 1.298788027 1.813652226 1 17.11643072 7.999998758 0.03946429 4.71E-06 4.010028931 0.132634172 0.507432363 1970.009423 5.920123419 166.0378476 531.8352667 99999713.99 -7.999998758 4.010024217 ILDLGITGPEGHVLSRPEEVEAEAVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILDLGITGPEGHVLSRPEEVEAEAVNR 27 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ;; 253.69 4.93E-53 968180000 37757.9 55375.6 46969.3 48850.3 55630.6 57975 44536.1 42773.3 41898.8 52462.2 FALSE TRUE 39248.61105 64885.92854 48193.35854 58512.74354 46174.53048 44511.18487 41045.24411 42199.99388 40390.87037 62741.16364 0.625563964 1.034184334 0.768129817 0.932605329 0.735952727 0.709441494 0.654199599 0.672604578 0.643769864 1 15.93712467 3.085156165 7.03243353 0.707361253 0.848434277 0.101382172 0.138372414 0.347698578 24.10717975 0.03678798 0.044078633 1216.623401 -3.085156165 0.141073024 ILDQMPATPS(ph)SPMYVD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.047)PS(0.678)S(0.274)PMYVD 122.42 9.80E-05 56400000 111380 117620 127580 136730 126450 153310 137120 131120 133690 121710 TRUE FALSE 115777.3684 137820.32 130904.8396 163774.7859 104956.0742 117706.0759 126372.1761 129362.5509 128878.523 145556.7442 0.795410539 0.946849428 0.899338882 1.125161096 0.721066377 0.808661093 0.8681987 0.888743092 0.885417737 1 17.15122216 4.758769692 22.81089746 0.897314479 0.795410224 0.089145661 0.102421559 3844.461315 4339183.341 0.02424703 0.841287701 57381.20868 -4.758769692 -0.101904255 ILDQMPATPSS(ph)PMYVD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILDQMPATPSSPMYVD 16 0 P45985;P45985-2 P45985 MAP2K4 Dual specificity mitogen-activated protein kinase kinase 4 1 ILDQMPAT(0.001)PS(0.114)S(0.88)PMY(0.005)VD;ILDQMPATPS(0.013)S(0.986)PMY(0.001)VD;ILDQMPAT(0.001)PS(0.054)S(0.879)PMY(0.066)VD 117.98 0.00032325 202253000 433750 508730 546890 567830 580560 653940 591260 566040 550500 499910 TRUE FALSE 450874.7849 596100.4201 561142.4027 680145.0792 481876.6186 502072.3456 544915.4962 558453.1597 530687.6125 597857.7931 0.754150552 0.99706055 0.938588422 1.137636888 0.806005415 0.839785567 0.911446673 0.93409029 0.887648566 1 19.18944284 -1.061417034 3.897473861 1.000016159 0.917797539 0.061647599 0.100808063 55999963226 1.02791E+11 13089667.94 0.023647958 0.08681264 1.061417034 -0.08221862 ILDSVGIEADDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILDSVGIEADDDR 13 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;; 261.29 1.09E-23 515870000 395740 402980 365210 467860 443220 476540 548720 453200 383590 366580 FALSE TRUE 411364.1208 472188.6803 374727.6726 560401.3116 367881.6227 365870.807 505709.8926 447125.5953 369784.6708 438404.3324 0.938321295 1.077062076 0.85475358 1.278275031 0.839137745 0.834551075 1.153523939 1.019893195 0.843478596 1 18.74190253 5.119835992 10.20182871 0.99456484 0.000117576 0.009767804 0.14330827 423103.1882 907803.0085 0.032568388 9090110.361 131775.9002 -5.119835992 -0.994447265 ILDSVGIEADDDRLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;;;;;; 315.13 7.79E-58 24047080000 16246570 11155660 13805830 11218760 19848100 18801230 17829720 13347320 14150750 11200810 FALSE TRUE 16887997.13 13071557.83 14165621.27 13437797.24 16474327.05 14434929.27 16432179.96 13168421.01 13641467.27 13395394.27 1.260731621 0.975824792 1.05749939 1.003165489 1.229850105 1.077603912 1.226703718 0.983055873 1.018369971 1 23.67523371 1.614840445 25 1.000531619 1.108858582 0.253065361 0.092033006 0.851634428 3042.503761 0.042483718 0.022915131 41.19461465 -1.614840445 0.108326963 ILDVASLEVLNEVNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILDVASLEVLNEVNRR 16 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 203.04 4.62E-11 593540000 204144 277810 275750 271870 274580 362750 235690 256920 241130 279220 FALSE TRUE 212203.7628 325521.7064 282936.2715 325645.0745 227906.9897 278506.81 217216.0019 253476.4076 232451.7784 333927.813 0.635477952 0.974826576 0.847297711 0.975196021 0.682503765 0.834032983 0.6504879 0.759075458 0.696113859 1 18.34917674 3.226128962 24.99995418 0.753367982 0.865751383 0.091931289 0.12786431 399.4959646 803381.5085 0.034070511 0.040986253 1683.1738 -3.226128962 0.112383401 ILDWHVANTDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILDWHVANTDKK 12 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 136.27 7.33E-05 8339500000 21731900 11950700 16355700 11881200 25236500 19916700 21245100 17185400 19147300 11344500 FALSE TRUE 22589892.19 14003139.76 16781942.98 14231265.9 20946808.74 15291348.27 19579853.55 16955057.82 18458192.41 13567237.57 1.665032552 1.032129031 1.236946201 1.048943517 1.543925846 1.127078979 1.443171718 1.249705972 1.360497472 1 23.69362367 -1.584137208 5.958964803 0.999039222 1.288898332 0.170733999 0.197325126 0.002275174 0.000158779 0.172581659 0.04055012 0.026053303 1.584137208 0.28985911 ILEFDRDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILEFDRDFR 9 1 J3QRN6;O94832;K7EIG7;J3QRR2 J3QRN6 MYO1D Unconventional myosin-Id 0 109.66 0.0022003 124640000 34380 46189 40155 33220 53280 54121 39201 38716 40569 59326 FALSE TRUE 35737.34895 54121.60145 41201.47229 39790.81685 44223.48463 41552.21796 36128.32319 38197.07535 39108.92961 70949.79384 0.503699123 0.762815486 0.580713066 0.56083062 0.623306739 0.585656641 0.509209699 0.538367672 0.551219778 1 16.11451087 -1.792419558 3.011664837 1.099622365 0.579736465 0.764218248 0.070064264 22391315.61 14999454.64 16136782.9 0.016891845 0.016127997 1.792419558 -0.5198859 ILEFFGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILEFFGLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 124.08 0.0030712 159801000 391230 426900 400050 428960 579140 573190 537270 422810 390520 412140 FALSE TRUE 406676.0625 500216.7542 410475.6316 513807.0077 480697.9897 440075.3093 495157.3735 417142.9235 376465.2615 492890.9421 0.825083254 1.014862947 0.832791996 1.042435484 0.975262373 0.892845195 1.004598241 0.846318907 0.76379018 1 18.91090894 -0.771312671 5.228184175 1.000000014 0.915968288 0.078770059 0.089926324 3.18E-08 7.50E-09 0.08356125 0.019695568 0.16931184 0.771312671 -0.084031726 ILEFFGLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILEFFGLKK 9 1 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 127.4 0.0023008 0 492180 439570 485040 388900 699310 655680 528730 496570 462700 392770 FALSE TRUE 511611.6464 515062.7281 497680.5409 465823.2592 580441.536 503408.2569 487286.761 489914.2914 446047.5174 469725.7615 1.089170934 1.096517948 1.059512979 0.991691956 1.235703007 1.071706724 1.037385643 1.042979397 0.949591345 1 18.84145919 1.660092375 1.589951444 0.979203836 1.089398538 0.344781124 0.059693875 0.421152551 2.111530669 0.047986226 0.017751653 45.71854236 -1.660092375 0.110194702 ILEHMPVSNQKPDTDEAEDPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILEHMPVSNQKPDTDEAEDPEK 22 1 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 81.949 0.0029075 58078000 93335 37567 61921 45398 90790 88148 87996 59952 66917 29603 FALSE TRUE 97019.93787 44018.84002 63534.71213 54377.5889 75357.54823 67676.9629 81098.64359 59148.4415 64508.67024 35403.14107 2.740433051 1.243359733 1.794606643 1.535953796 2.128555432 1.911608994 2.290718878 1.670711686 1.822117143 1 15.11158975 0.460214415 1.378433566 1.000391156 1.895048636 0.32669481 0.391852848 3.091030606 6.706641516 0.34929902 0.102614236 2.885455723 -0.460214415 0.894657481 ILELT(ph)PEPDRPR ddPTM_MDA-MB-175_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 216.54 6.27E-11 4722590000 1695650 1792980 1702700 1627780 1771850 2051680 1758370 1689550 1739780 1797090 TRUE FALSE 1762595.571 2100910.368 1747073.761 1949750.026 1470671.57 1575208.414 1620544.365 1666904.346 1677165.658 2149195.378 0.820118817 0.977533448 0.812896668 0.90719999 0.684289379 0.73292937 0.754023753 0.775594608 0.780369098 1 21.03536521 3.260951771 24.97081268 0.772025892 0.881691236 0.188689719 0.08942324 303.0633037 337976.5802 0.022815425 0.030869513 1823.693168 -3.260951771 0.109665344 ILENEKDLEEAEEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILENEKDLEEAEEYK 15 1 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 218.43 1.77E-12 1148247000 2541280 722920 1307620 971060 1741250 1991530 2520080 1400490 1564500 522821 FALSE TRUE 2641611.697 847075.8865 1341697.651 1163132.77 1445272.947 1529027.339 2322549.545 1381718.722 1508193.951 625257.7649 4.224836291 1.354762682 2.14583125 1.860245222 2.311483404 2.445435187 3.714547303 2.209838565 2.412115507 1 19.25409154 2.697048007 5.470874982 2.526801441 2.280250273 0 0.932369881 1.268609036 99.06351188 0.289277516 0.276706599 497.792108 -2.697048007 -0.246551168 ILENEKDLEEAEEYKEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;O75347;E5RIW3;E5RHG6 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;;; 219.91 3.98E-19 1946940000 2721130 1003944 1619911 878851 2568610 2186170 2225710 1586193 1869851 838318 FALSE TRUE 2828562.314 1176363.572 1662127.211 1052685.105 2131998.59 1678465.149 2051253.034 1564932.677 1802555.428 1002570.362 2.821310526 1.173347645 1.657865897 1.04998626 2.126532632 1.674161948 2.04599409 1.560920547 1.797934087 1 19.93527206 -0.775319898 5.471541002 0.999999854 1.732704105 0.18683955 0.47540417 7.77E-07 1.72E-07 0.420296006 0.0990647 0.167756788 0.775319898 0.732704251 ILENLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 170.43 0.013353 1599780000 684840 866380 739720 783630 817450 929190 701270 695100 672960 804730 FALSE TRUE 711878.012 1015174.025 758997.7109 938629.6751 678500.141 713399.7045 646302.625 685783.3215 648740.3011 962401.436 0.739689266 1.05483428 0.788649811 0.975299537 0.705007407 0.741270407 0.671552016 0.712575123 0.674084926 1 19.87627927 3.226075584 24.9992546 0.729250244 0.894207344 0.226758222 0.121689443 254.8522094 510299.3283 0.031859267 0.038328369 1682.966938 -3.226075584 0.1649571 ILEPDDFLDDLDDEDYEEDT(ph)PKRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILEPDDFLDDLDDEDYEEDTPKRR 24 2 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 1 ILEPDDFLDDLDDEDYEEDT(1)PKRR;ILEPDDFLDDLDDEDY(0.086)EEDT(0.914)PKRR 212.77 7.44E-24 65274000 94866 54541 63059 36853 88263 81508 60531 58364 73030 56251 TRUE FALSE 98611.38293 63907.99248 64702.36934 44142.4134 73260.08679 62579.00227 55786.42205 57581.72604 70401.66457 67272.30646 1.465854051 0.949989614 0.961797993 0.656175115 1.089008102 0.930234231 0.829262812 0.855949931 1.046517776 1 16.0377251 4.751678784 3.619325341 0.907243811 1.537141074 0.658494982 0.116792043 0.170072319 3.96977885 0.027184835 0.294683198 56451.92867 -4.751678784 0.629897263 ILEPDDFLDDLDDEDYEEDTPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILEPDDFLDDLDDEDYEEDTPKR 23 1 Q92785;J3KMZ8 Q92785 DPF2 Zinc finger protein ubi-d4 0 152.32 1.01E-07 14762000 10091 8505.1 11613 8387.4 12005 13996 11574 9706.7 11917 9613.6 FALSE TRUE 10489.40047 9965.784765 11915.64432 10046.40269 9964.394388 10745.64111 10666.79964 9576.597563 11488.1095 11497.20086 0.912343848 0.866800962 1.036395247 0.873812923 0.86668003 0.934631068 0.927773618 0.832950357 0.999209255 1 13.48899504 1.201235469 23.95732719 0.999605344 0.905424087 0.333093229 0.052724517 141.1420827 90587.89447 0.050047733 0.012513762 15.89408273 -1.201235469 -0.094181256 ILEQQNSSRT(ph)LEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ILEQQNSSRTLEK 13 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 1 ILEQQNSSRT(1)LEK;ILEQQNSSRT(1)LEK;ILEQQNS(0.001)S(0.022)RT(0.976)LEK;ILEQQNSSRT(1)LEK;ILEQQNS(0.039)S(0.118)RT(0.843)LEK 254.53 1.33E-23 3866760000 1424860 1141475 1474124 999735 2083280 1882630 1251158 1468084 1463500 1458388 TRUE FALSE 1481114.573 1337514.452 1512540.882 1197479.599 1729164.81 1445417.714 1153088.967 1448406.735 1410828.921 1744131.206 0.849199056 0.766865731 0.867217373 0.686576557 0.991418996 0.828732213 0.661125128 0.830445972 0.808900681 1 20.73407714 0.348539001 2.598845264 0.999999474 0.807493678 0.294097833 0.08820796 38.68621565 151.65115 0.081069799 0.02150986 2.231202566 -0.348539001 -0.192505796 ILEVHIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ;; 93.551 0.010989 771800000 1542010 1260090 1571430 1290070 1848730 1909310 1754820 1644530 1699450 1304170 FALSE TRUE 1602889.745 1476500.655 1612382.757 1545241.996 1534483.535 1465901.688 1617272.623 1622487.765 1638287.126 1559697.142 1.027692943 0.946658563 1.033779388 0.990732081 0.983834293 0.939863034 1.036914526 1.040258215 1.050387978 1 20.57283449 2.171455531 24.99891714 1.035842125 0.987394544 0.339802671 0.030388963 56.04872463 20879.1448 0.010864742 0.008024146 148.4073912 -2.171455531 -0.04844758 ILEVHVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 ;; 95.358 0.0097068 1351000000 2620710 2213670 2510490 2069280 3238450 3236290 2924130 2666150 2735720 2071810 FALSE TRUE 2724177.654 2593850.603 2575915.432 2478577.408 2687979.426 2484710.694 2694929.05 2630414.62 2637261.972 2477741.502 1.099459993 1.046860861 1.039622345 1.000337366 1.084850628 1.002812719 1.08765545 1.061617856 1.064381401 1 21.24059425 -0.17107275 8.108213671 0.999995786 1.053411322 0.207333659 0.031748021 0 0 0.029126324 0.006865141 0.674415045 0.17107275 0.053415536 ILFIFIDSDHTDNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ILFIFIDSDHTDNQR 15 0 P07237;H7BZ94;H0Y3Z3;I3L398;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 334.72 5.30E-69 3906619000 1208496.1 2139840 1817360 2216551 2048441 2428815 2060024 2092994.1 1744686.5 2096292 FALSE TRUE 1256208.459 2507340.874 1864721.895 2654978.172 1700247.731 1864759.525 1898553.936 2064940.938 1681895.574 2507020.281 0.501076305 1.000127878 0.743800083 1.059017429 0.678194645 0.743815094 0.757295005 0.823663435 0.670874339 1 21.25754224 -1.133953482 4.150467602 1.000053032 0.787601357 0.159316133 0.152505926 4.277557267 76881418.21 8283.883479 0.032529562 0.073459255 1.133953482 -0.212451675 ILFRPVASQLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILFRPVASQLPR 12 1 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0;D6RBK0;P35232-2 P35232 PHB Prohibitin 0 71.888 0.039558 175090000 137440 223280 164680 164620 193790 225360 136660 178410 161530 365380 FALSE TRUE 142866.2373 261626.6031 168971.6961 197181.3447 160849.645 173023.5554 125948.2321 176018.7058 155716.5669 436969.2154 0.32694806 0.598730057 0.386690161 0.45124768 0.368102922 0.395962803 0.288231362 0.402817177 0.35635592 1 18.73717212 -1.210458664 3.635413233 1.000808221 0.39903839 0.838377432 0.079393198 50713816.11 81376806.99 463698.7499 0.018579066 0.061594415 1.210458664 -0.601769832 ILGDINSDFTRVDEDEEIIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILGDINSDFTRVDEDEEIIVK 21 1 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 0 ; 218.57 4.91E-25 72475000 64064 50540 59826 36900 78371 71567 64759 59855 64509 53928 FALSE TRUE 66593.29619 59219.85185 61385.11471 44198.70986 65049.52541 54946.64886 59683.02036 59052.74163 62187.33369 64494.15909 1.032547709 0.918220389 0.951793396 0.685313376 1.00861111 0.85196318 0.925401947 0.915629298 0.964232026 1 15.97688089 1.107209817 1.750688033 1.000268159 0.905243159 0.095403037 0.089906143 0.774445332 4.622932654 0.080811531 0.023435732 12.79999549 -1.107209817 -0.095025001 ILGGSVLHLVLALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILGGSVLHLVLALR 14 0 Q15843 Q15843 NEDD8 NEDD8 0 62.924 0.085228 0 3723.4 5986.2 6361 4862.4 8482.6 8014.4 5596.4 5034.3 5841.3 8101.6 FALSE TRUE 3870.402707 7014.283284 6526.772886 5824.168207 7040.730682 6153.177059 5157.739545 4966.823443 5631.072754 9688.953405 0.399465509 0.723946436 0.673630331 0.601114276 0.72667608 0.635071385 0.532331959 0.512627446 0.581184832 1 13.24212512 -1.763906688 2.397665829 1.108641708 0.599962487 0.614977354 0.095311179 7385572.232 4932057.563 4721284.101 0.024051054 0.017222386 1.763906688 -0.508679221 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGS(0.004)AS(0.996)PEEEQEKPILDRPTR;ILGS(0.003)AS(0.997)PEEEQEKPILDRPTR;ILGS(0.019)AS(0.981)PEEEQEKPILDRPTR;ILGSAS(1)PEEEQEKPILDRPTR 205.8 3.24E-22 1952070000 955902 657297 887744 675866 1074539 1092216 1043140 890926 1011747 663151 TRUE FALSE 993641.7491 770182.6467 910879.3379 809550.2775 891889.2446 838565.3867 961375.9611 878984.5942 975334.4231 793082.7417 1.252885351 0.971125213 1.148530021 1.020763957 1.124585365 1.05734918 1.212201339 1.108313859 1.229801598 1 19.59711186 2.26428929 24.9991514 1.144845495 1.090487364 0.042590584 0.092293386 579.6926941 563254.2476 0.028934014 0.024200922 183.7762095 -2.26428929 -0.054358131 ILGSASPEEEQEKPILDRPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 ILGSAS(0.17)PEEEQEKPILDRPT(0.83)R 155.39 4.00E-08 867980000 434690 307770 414910 275010 522000 537660 540000 436170 490270 336040 TRUE FALSE 451851.8969 360627.1034 425722.8955 329406.1572 433270.6265 412796.6133 497673.389 430323.8546 472625.2785 401880.6041 1.124343629 0.897348864 1.059326803 0.819661745 1.078107831 1.027162319 1.238361304 1.070775375 1.17603406 1 18.61640743 2.73363504 2.31851427 1.122075499 0.977701718 0.239771992 0.102267323 0.36623113 3.885474785 0.033402535 0.033084866 541.5456102 -2.73363504 -0.144373781 ILHCLGLAEEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILHCLGLAEEIQK 13 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 207.95 4.98E-08 1035860000 1142460 871820 1119500 1017300 1381140 1364340 1323930 1107290 1179910 855340 FALSE TRUE 1187565.203 1021548.303 1148675.09 1218518.904 1146374.316 1047492.712 1220156.907 1092448.589 1137445.27 1022927.497 1.160947581 0.998651719 1.122929136 1.191207498 1.120679931 1.02401462 1.192808788 1.067962874 1.111951017 1 19.96427246 -0.106428234 0.88001064 0.99766699 1.109832318 0.223835435 0.061548519 12.52687903 8.401927985 0.157890769 0.018922149 0.782657526 0.106428234 0.112165328 ILHGFK ddPTM_MDA-MB-175_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 722860000 1847200 1691900 2022500 1817800 2437300 2499800 2349800 2007800 2139700 1832800 FALSE TRUE 1920128.882 1982470.664 2075208.012 2177355.414 2023008.617 1919259.335 2165616.536 1980888.725 2062692.615 2191902.069 0.876010343 0.904452207 0.946761281 0.993363456 0.922946625 0.875613633 0.988007889 0.903730487 0.941051448 1 21.06375191 -5 0.225673977 1.36809956 0.920339803 0.253505291 0.038327357 240.1652045 2.403981737 40.37945445 0.069914276 1.00E-05 5 -0.447759757 ILHLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILHLLGK 7 0 Q9UBF2;Q9UBF2-2;H3BS45;F5H1S1;Q92521 Q9UBF2 COPG2;PIGB Coatomer subunit gamma-2;GPI mannosyltransferase 3 0 91.26 0.029937 0 319230 296950 343340 300910 414720 418120 352620 321840 333790 304410 FALSE TRUE 331833.4469 347948.8525 352287.7225 360429.0999 344226.0425 321017.9667 324980.723 317526.2612 321776.9631 364053.3112 0.911496851 0.955763461 0.967681687 0.990044833 0.945537458 0.881788345 0.892673444 0.872197152 0.883873194 1 18.47379021 2.837110447 5.012724208 0.89519294 0.958053636 0.255202372 0.03894032 0.234405682 9.337693768 0.011466495 0.012185429 687.2431937 -2.837110447 0.062860696 ILHLLGQEGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILHLLGQEGPK 11 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ; 176.48 8.60E-06 892440000 1315570 904670 1134550 995510 1676290 1586700 1307530 1127620 1232230 971080 FALSE TRUE 1367509.719 1060040.035 1164117.305 1192418.907 1391354.825 1218212.972 1205042.382 1112506.098 1187882.283 1161344.534 1.177522845 0.912769643 1.002387553 1.026757239 1.198055172 1.048967758 1.037626946 0.957946644 1.022850884 1 20.14736461 1.933406275 5.932560837 0.990301551 1.05540186 0.126102866 0.078414823 0.506301081 33.88701981 0.035038791 0.021461115 85.78399654 -1.933406275 0.065100309 ILHTLLASGEDALDFTQESEPSYIS(ph)DVGPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILHTLLASGEDALDFTQESEPSYISDVGPPGR 32 0 H3BVG0;Q8N1F7;Q8N1F7-2;H3BM93;H3BMX0;H3BP95 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 ILHTLLASGEDALDFT(0.004)QES(0.111)EPS(0.253)Y(0.223)IS(0.409)DVGPPGR 47.537 0.057763 12388000 5044.3 7921 7135.8 7338.5 7565.9 7709.5 7965.8 6855.8 7344.9 8376.8 TRUE FALSE 5243.452859 9281.370133 7321.76481 8790.033397 6279.85102 5919.085464 7341.419781 6763.909215 7080.558484 10018.07358 0.523399316 0.926462564 0.730855564 0.877417532 0.626852156 0.590840686 0.732817515 0.675170647 0.706778447 1 13.29031749 -1.916400395 7.730270171 1.064536847 0.714204574 0.361853939 0.115390709 0.064870471 0.000701547 0.056471442 0.025165024 0.012122707 1.916400395 -0.350332273 ILHVDNHIGISIAGLTADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILHVDNHIGISIAGLTADAR 20 0 P25786;P25786-2;F5GX11;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;; 154.55 2.32E-08 198251000 81599.4 127594.1 107117.8 137529.1 109173 140601 114723.2 120727.6 108019.4 167395 FALSE TRUE 84821.00732 149507.3941 109909.3779 164731.9455 90615.81246 107948.5486 105730.8958 119109.444 104131.8029 200192.8453 0.423696497 0.74681687 0.549017512 0.822866298 0.452642612 0.53922281 0.528145227 0.594973531 0.520157465 1 17.61103089 -1.476224209 3.332732801 1.007518791 0.58118984 0.542412328 0.116915922 61476254.33 91326000.28 4375263.752 0.026284712 0.033402255 1.476224209 -0.426328951 ILIEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ILIEELR 7 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 0 ;;;;;; 148.07 0.0049062 271401000 446869 574894 519169 525791 609021 661464 523334 546377 509809 642470 FALSE TRUE 464511.7332 673627.5724 532698.9706 629790.8905 505499.828 507849.0106 482313.7136 539053.71 491461.0737 768349.6957 0.604557711 0.876720035 0.693302768 0.819667001 0.657903336 0.660960775 0.627726823 0.701573402 0.639632028 1 19.55140354 -1.080794058 4.580524496 1.000014553 0.701394703 0.55049608 0.081815774 1.48E-05 2.97E-06 0.076403345 0.018007333 0.083024438 1.080794058 -0.29861985 ILIPS(ph)DIESSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 ILIPS(1)DIESSK;ILIPS(0.999)DIES(0.001)SK;ILIPS(1)DIESSK;ILIPS(1)DIESSK 155.86 3.29E-05 144771000 744800 493400 573600 471560 689660 775040 732220 589810 622030 439600 TRUE FALSE 774205.2791 578137.6119 588548.4872 564833.1605 572431.8395 595048.7058 674826.6831 581904.5617 599643.2618 525731.2033 1.472625696 1.099682895 1.119485554 1.074376329 1.088829873 1.131849702 1.283596406 1.106848058 1.140589065 1 19.00396584 4.741079987 24.92653792 1.12478911 1.472625824 0.712378604 0.067754277 121.1710737 1198787.497 0.01600994 0.109062041 55090.91518 -4.741079987 0.347836714 ILIQHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILIQHQK 7 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 88.734 0.01839 344810000 404470 384510 375820 441640 712750 735770 756980 594920 652970 528390 FALSE TRUE 420438.7879 450546.6014 385614.1779 528995.0738 591597.0096 564898.5682 697645.9296 586946.0705 629469.7373 631917.9039 0.665337673 0.712982808 0.610228284 0.837126264 0.936192828 0.893942971 1.104013552 0.928832791 0.996125815 1 19.26937762 3.418480809 1.912928979 0.982355787 0.664617285 0.850879541 0.058699809 0.115579311 0.856574746 0.017393794 0.027824945 2621.083216 -3.418480809 -0.317738502 ILIVTQT(ph)PPYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILIVTQTPPYVK 12 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;H0Y9K3;D6R9W6;D6RJB0;Q659C4-4 A0A3B3ISF0 LARP1B La-related protein 1B 1 ILIVT(0.005)QT(0.916)PPY(0.079)VK;ILIVT(0.012)QT(0.988)PPYVK 139.89 0.0006332 0 427870 379680 407600 378040 482080 509890 471770 421770 420920 345360 TRUE FALSE 444762.638 444887.0865 418222.3908 452815.1837 400136.2138 391475.775 434791.4347 416116.863 405771.1714 413026.6797 1.07683755 1.077138859 1.012579602 1.09633398 0.968790234 0.947822003 1.05269576 1.007481801 0.982433318 1 18.65587545 3.235472577 24.99999966 0.996510885 1.062742032 0.539728135 0.0326759 70.4151145 570063.7502 0.009645667 0.012001706 1719.778744 -3.235472577 0.066231146 ILKEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILKEQER 7 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 84.743 0.019445 595120000 676450 641890 706040 507376 1058990 845030 687310 710370 770780 796450 FALSE TRUE 703156.7683 752129.6143 724439.9824 607733.4584 878983.2581 648784.5891 633436.8462 700848.6521 743039.7784 952499.1285 0.738223004 0.789638113 0.760567607 0.63804096 0.922817913 0.681139299 0.665026169 0.735799783 0.780094969 1 19.86135825 0.780810361 3.327627947 0.999975907 0.740636804 0.515985295 0.074712215 1.20035803 17.22520068 0.069004173 0.017876903 6.036849669 -0.780810361 -0.259339104 ILKLPSFELLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILKLPSFELLHK 12 1 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 133.71 9.51E-05 236290000 398810 388030 361320 249290 595660 456340 316080 384760 409900 506810 FALSE TRUE 414555.3267 454671.134 370736.296 298598.8179 494409.926 350361.9509 291304.8237 379602.9215 395147.7791 606109.716 0.683960867 0.750146586 0.611665324 0.49264813 0.81571028 0.578050379 0.480614014 0.626294071 0.651941008 1 19.20921944 0.694066243 3.647984339 0.999996372 0.62626874 0.559155224 0.098067926 3.950127705 46.36088839 0.094792387 0.024364679 4.943860903 -0.694066243 -0.373727632 ILKS(ph)PEIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILKSPEIQR 9 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 1 ILKS(1)PEIQR;ILKS(1)PEIQR 86.288 0.0086237 494590000 430860 292390 353540 275350 428660 498400 407390 333450 396630 307040 TRUE FALSE 447870.6855 342605.708 362753.5428 329813.4082 355796.5263 382654.1533 375457.7073 328980.6482 382355.3638 367198.6094 1.219696028 0.933025614 0.987894653 0.898188064 0.968948458 1.042090421 1.022492182 0.895920191 1.041276721 1 18.48620107 4.744043018 24.96324909 0.971769683 1.219696136 0.669980872 0.051070969 339.0064954 1543566.308 0.012148222 0.105097244 55468.06524 -4.744043018 0.247926453 ILLDHEKEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILLDHEKEWK 10 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 163.34 3.90E-06 847200000 784390 459980 631230 380320 966110 830610 640850 594970 721350 482960 FALSE TRUE 815358.3229 538977.9869 647680.3724 455546.1609 801890.9673 637713.4155 590618.5025 586995.4003 695388.7544 577586.7652 1.411663792 0.933155016 1.121355979 0.788706024 1.388347198 1.104099772 1.022562389 1.016289562 1.203955486 1 19.13967816 1.867912669 0.012629176 3.87E-06 2.153326603 0.036510433 0.180805359 3293.374929 35.87451369 3026.957831 3082.261602 73.77558617 -1.867912669 2.153322735 ILLENY(ph)VRSIENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILLENYVRSIENER 14 1 H0Y9S3;A0A494C037;E7EUS2;Q8TBZ0-2;Q8TBZ0 H0Y9S3 CCDC110 Coiled-coil domain-containing protein 110 1 ILLENY(0.995)VRS(0.005)IENER;ILLENY(0.967)VRS(0.033)IENER;ILLENY(0.997)VRS(0.003)IENER 88.552 0.0077843 540730000 771900 238596 323109 234497 403770 570270 421550 207357 398520 251347 TRUE FALSE 802375.208 279573.007 331529.486 280879.8067 335137.3196 437833.435 388507.8095 204577.7186 384177.343 300593.6323 2.66930208 0.930069625 1.102915865 0.934417022 1.114918227 1.456562575 1.292468528 0.680579016 1.278062147 1 18.19745492 4.741778791 24.98157831 1.077027721 2.669302675 0.837050437 0.209289662 118.4980786 919816.4365 0.052317623 0.375841667 55179.63092 -4.741778791 1.592274954 ILLVDS(ph)PGMGNADDEQQEEGTSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILLVDSPGMGNADDEQQEEGTSSK 24 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK 235.63 1.40E-37 171129000 186875 167539 212835 165853 251869 264333 226729 213197 231836 176678 TRUE FALSE 194252.9693 196312.52 218381.6549 198658.2284 209056.3973 202945.6668 208957.3885 210339.4429 223492.2676 211294.6714 0.919346276 0.929093567 1.033540759 0.940195165 0.98940686 0.96048644 0.988938278 0.995479164 1.057727893 1 17.68889686 8 0.274819653 1.011286102 0.361382357 0.399013665 0.032827769 54.06633307 0.760955329 0.036424681 16.76744831 100000000 -8 -0.649903745 ILLWDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILLWDTR 7 0 Q9BQA1;Q9BQA1-2;H0Y711 Q9BQA1 WDR77 Methylosome protein 50 0 89.55 0.041389 217140000 355380 438620 413010 405470 572100 558760 423490 407040 418090 594610 FALSE TRUE 369410.6768 513949.573 423773.3799 485670.7558 474854.6463 428996.4581 390295.7472 401584.2946 403043.0226 711112.445 0.51948279 0.722740231 0.595930198 0.682973219 0.667763094 0.603275138 0.548852365 0.564726855 0.566778187 1 19.43971818 -1.587757857 5.077573865 1.003154608 0.609037328 0.786894643 0.061188299 0.002231111 0.000181141 0.06049283 0.014163512 0.025837003 1.587757857 -0.39411728 ILMEHIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILMEHIHK 8 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 117.04 0.001247 6511100000 8748200 8090600 9419900 7871000 12269500 11562500 10397000 9803600 9929900 9972500 FALSE TRUE 9093585.691 9480097.614 9665390.333 9427860.307 10183934.77 8877284.606 9582055.972 9672198.777 9572524.839 11926420.44 0.762474016 0.794882057 0.81041838 0.790502092 0.853897012 0.744337721 0.803431006 0.810989251 0.802631845 1 23.50765777 -4.999999987 0.395092735 4.151248729 0.794235881 0.831128607 0.027494092 254.7363526 1.810189804 691.3336906 0.016499392 1.00E-05 4.999999987 -3.357012849 ILMVGLDAAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILMVGLDAAGK 11 0 P61204;F5H423;P61204-2;F5H0C7;F5H1V1;F5H6T5;F8WDB3;P84077;P84085;C9J1Z8;P18085;C9JPM4 P61204;P84077;P84085;P18085 ARF3;ARF4;ARF1;ARF5 ADP-ribosylation factor 3;ADP-ribosylation factor 1;ADP-ribosylation factor 5;ADP-ribosylation factor 4 0 138.66 0.0030819 0 177100 158020 186590 181910 231510 262840 224530 185990 219260 166120 FALSE TRUE 184092.0448 185158.7058 191452.6887 217891.2551 192158.0129 201799.3934 206930.7519 183497.1083 211368.8754 198668.0334 0.926631434 0.932000496 0.9636814 1.096760517 0.967231666 1.01576177 1.041590579 0.923636808 1.063929973 1 17.60000023 3.992137882 22.82289689 1.008630256 0.933947119 0.366243341 0.045860399 132.4065776 384377.2262 0.0115024 0.023171919 9820.596824 -3.992137882 -0.074683137 ILNDVQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILNDVQDR 8 0 O00148;Q13838-2;Q13838;A0A0G2JJZ9;H0Y400 O00148;Q13838-2 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 ;; 151.97 0.0011409 291027000 657590 800470 640840 818240 726920 829550 814150 714270 618740 564820 FALSE TRUE 683552.161 937944.4957 657540.8169 980085.4298 603358.398 636899.5845 750334.7956 704696.379 596471.6683 675485.6649 1.011941772 1.388548336 0.973434154 1.450934462 0.893221617 0.942876537 1.110807874 1.043244018 0.88302639 1 19.36556563 3.207791758 24.99939314 0.992578535 1.202611823 0.352139905 0.150352347 224.2602706 182208.6442 0.040488311 0.048397894 1613.584667 -3.207791758 0.210033288 ILNDVQDRFEVNISELPDEIDISSYIEQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILNDVQDRFEVNISELPDEIDISSYIEQTR 30 1 Q13838-2;Q13838;A0A0G2JJZ9 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 233.49 2.04E-45 54378000 24835 28483 27438 24436 35415 36858 23347 24876 25341 33881 FALSE TRUE 25815.50498 33374.73368 28153.05682 29269.36787 29395.17095 28298.28809 21517.00113 24542.57791 24428.98236 40519.33326 0.63711574 0.823674306 0.69480553 0.722355614 0.725460381 0.698389776 0.531030484 0.605700438 0.602896948 1 15.30632281 -1.062445472 5.095215477 1.000005523 0.669438058 0.618776012 0.077395666 5.35E-06 9.84E-07 0.082556342 0.019458391 0.086607306 1.062445472 -0.330567466 ILNEDGSPNLDFKPEDQPHFDIKDEF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILNEDGSPNLDFKPEDQPHFDIKDEF 26 2 Q9UMX5 Q9UMX5 NENF Neudesin 0 ; 235.48 3.63E-45 265060000 539040 250250 348770 213407 527330 493600 429030 340610 380440 175911 FALSE TRUE 560321.7154 293228.4908 357859.2327 255618.2676 437694.635 378968.8806 395401.5075 336044.6801 366748.0387 210377.3924 2.663412209 1.393821301 1.701034643 1.215046278 2.080521248 1.801376451 1.879486683 1.597342168 1.74328636 1 17.68262015 -2.304497983 0.335849082 3.24E-12 1.801831959 0.293676105 0.370764652 60.90679867 2.654554187 45.89656931 0.294776412 0.004960232 2.304497983 1.801831959 ILNHVLQHAEPGNAQSVLEAIDTYCEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILNHVLQHAEPGNAQSVLEAIDTYCEQK 28 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 301.03 8.51E-72 8449300000 3342300 2580000 3185500 2691200 4149000 3907100 4143600 3148700 3450900 2236700 FALSE TRUE 3474256.585 3023094.93 3268516.747 3223511.328 3443754.462 2999735.238 3818813.805 3106496.827 3326702.783 2674938.541 1.298817349 1.130154912 1.221903493 1.205078651 1.287414424 1.121422116 1.427626746 1.161333907 1.243655782 1 21.35107431 -0.364028559 1.527948142 0.999270153 1.230834364 0.396104405 0.086266087 117.1166538 126.4651686 0.652737385 0.021683774 0.43248539 0.364028559 0.231564211 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKK 38 2 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 292.44 1.07E-92 3356587000 1113072 829116 1018333 618036 1725091 1227265 841799 990526 1246030 863170 FALSE TRUE 1157016.942 971510.2234 1044871.595 740281.6761 1431860.648 942251.3031 775816.5947 977249.6191 1201185.624 1032291.635 1.120823712 0.941119922 1.012186439 0.717124552 1.387069893 0.912776265 0.751547885 0.946679781 1.163610731 1 19.97741918 ILNPEEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILNPEEIEK 9 0 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 80.688 0.054446 46439000 110540 104190 114700 98451 127050 138760 119850 112800 104340 98058 FALSE TRUE 114904.2046 122083.822 117689.1762 117924.314 105454.0864 106535.0929 110455.8438 111288.1005 100584.8238 117270.5877 0.979821171 1.041043832 1.003569425 1.005574512 0.899237298 0.908455351 0.941888721 0.948985613 0.857715697 1 16.83948169 3.252124859 24.24112111 0.925572755 1.009617197 0.534107837 0.03724686 118.2530736 211332.2789 0.009836819 0.013241277 1787.001261 -3.252124859 0.084044442 ILPEAHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ILPEAHQR 8 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;; 128.61 0.0011263 966700000 761330 880960 820940 792360 1049900 1038580 826420 809820 787250 1010980 FALSE TRUE 791387.8963 1032258.027 842334.3708 949086.443 871438.373 797385.5348 761643.041 798965.6875 758917.0263 1209062.175 0.654546898 0.853767531 0.696684082 0.784977368 0.720755633 0.659507469 0.629945305 0.660814393 0.627690653 1 20.205457 -1.018757222 4.538253014 1.000010587 0.699408723 0.6363509 0.06831882 9227036.131 2071306.086 971.4696336 0.01670694 0.095772931 1.018757222 -0.300601865 ILPGPHFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILPGPHFEER 10 0 A0A2R8YF87;Q96AX1;H3BMM5;A0A2R8Y5U3 A0A2R8YF87 VPS33A Vacuolar protein sorting-associated protein 33A 0 91.549 0.0095512 0 67073 89736 70261 93398 73171 101400 78956 70325 71349 85811 FALSE TRUE 69721.09383 105147.46 72092.05938 111871.8456 60733.41956 77851.38673 72767.22241 69382.4084 68781.16343 102624.0225 0.679383756 1.02458915 0.702487172 1.090113629 0.591805097 0.758607827 0.709066168 0.676083501 0.670224785 1 16.64700895 3.214577578 24.99996484 0.714989954 0.872628649 0.157785006 0.154448725 342.9048395 357443.6957 0.040386378 0.048294709 1638.994809 -3.214577578 0.157638695 ILPGSMIVS(ph)SDDTVDSTIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 ILPGS(0.093)MIVS(0.452)S(0.452)DDT(0.002)VDSTIDR 56.407 0.03436 0 10514 13957 11447 11384 15225 17697 13814 14117 16664 15818 TRUE FALSE 10929.10084 16354.00618 11745.31822 13635.72122 12637.05994 13587.13995 12731.22258 13927.78471 16064.2659 18917.23425 0.57773249 0.864503022 0.620879251 0.720809451 0.668018367 0.718241355 0.672995979 0.736248467 0.849186815 1 14.20741356 1.023472573 1.848945877 0.999102279 0.696510657 0.652464127 0.07122927 0.188467633 1.332810596 0.060090398 0.017104962 10.55534842 -1.023472573 -0.302591621 ILPGSMIVSS(ph)DDTVDSTIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 ILPGS(0.005)MIVS(0.442)S(0.554)DDTVDSTIDR 99.044 0.0010393 0 8298.9 7445.5 9392.8 8548.7 10306 13817 11922 8675.3 7681 9582.3 TRUE FALSE 8626.54698 8724.206707 9637.584084 10239.60734 8554.189801 10608.21115 10987.52249 8559.021793 7404.56231 11459.76822 0.752768015 0.761289979 0.840992933 0.893526566 0.746453998 0.925691597 0.958790987 0.746875646 0.646135434 1 13.48429024 4.251379111 7.250491041 0.83827799 0.756323881 0.102411329 0.102524903 0.356664663 93.2725462 0.025265876 0.064807587 17839.35349 -4.251379111 -0.08195411 ILPKPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILPKPTR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 71.342 0.049773 1784750000 2180200 1984420 2283100 2065440 2403500 2652000 2593400 2385100 2160500 2175000 FALSE TRUE 2266275.979 2325228.698 2342599.462 2473977.867 1994953.929 2036113.191 2390122.531 2353131.636 2082744.027 2601149.607 0.871259374 0.893923476 0.900601586 0.95110941 0.76695086 0.782774349 0.918871612 0.904650632 0.80070136 1 21.31071795 -1.319173218 3.750823963 1.000363622 0.869661713 0.317041419 0.058891842 2497734416 453375056.5 8116621.458 0.014248614 0.047954215 1.319173218 -0.130701909 ILPNKVDPLVSLMMVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILPNKVDPLVSLMMVEK 17 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 77.746 0.0063659 0 114810 100260 126770 110370 146430 170170 141580 131890 172570 126500 FALSE TRUE 119342.7875 117478.8751 130073.7303 132200.8566 121539.8809 130650.5965 130482.5896 130122.2303 166359.2394 151285.253 0.788859357 0.776538841 0.859791207 0.873851575 0.80338221 0.863604309 0.862493779 0.860111793 1.099639496 1 17.20691184 1.309488596 5.580801644 1.048746451 0.836505072 0.823563127 0.039610361 0.072546224 3.829566301 0.028903281 0.010054733 20.39335111 -1.309488596 -0.212241379 ILPPGLLAYLESSDLVPEKDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILPPGLLAYLESSDLVPEKDADR 23 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ; 211.75 3.91E-25 213266000 209524 181897 225930 180953 304600 292240 255270 233950 262730 186457 FALSE TRUE 217796.1693 213136.3948 231817.9214 216744.9633 252824.2008 224371.6889 235261.2704 230814.2829 253274.3986 222989.6792 0.97670964 0.955812823 1.039590362 0.971995494 1.133793284 1.00619764 1.055032104 1.035089533 1.135812202 1 17.76661741 3.873721644 1.252443161 1.055696753 0.964804281 0.296400558 0.050243402 0.623026247 1.785692671 0.014859859 0.048874364 7476.901229 -3.873721644 -0.090892472 ILQEHEQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILQEHEQIK 9 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 161.17 6.47E-05 557610000 921630 763590 896840 728160 1226600 1154750 1060220 892450 958200 872060 FALSE TRUE 958016.6641 894730.6426 920212.3872 872187.8747 1018102.97 886576.8129 977117.186 880488.1675 923714.5692 1042923.46 0.918587701 0.857906334 0.88233933 0.836291356 0.976201043 0.85008809 0.936902106 0.844250035 0.885697373 1 19.99220185 -0.921570086 4.332432696 1.000001948 0.885655407 0.385103796 0.042551768 4914923.728 1134506.038 112.4205111 0.009090855 0.119792579 0.921570086 -0.114346541 ILQEKLDQPVS(ph)APPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 127.3 2.32E-05 1250340000 1883290 2397840 2568860 1044550 4293720 3017590 1099950 2292550 2717770 4816960 TRUE FALSE 1957643.743 2809650.367 2635806.602 1251158.872 3563875.008 2316800.455 1013733.045 2261822.117 2619957.989 5760751.086 0.339824393 0.487722925 0.45754565 0.217186762 0.61864763 0.402169859 0.175972374 0.392626254 0.454794514 1 22.45782549 0.713564961 3.044215253 0.999963492 0.385650779 0.698160002 0.120272122 1.369215169 13.9098644 0.113873912 0.02973731 5.170885969 -0.713564961 -0.614312713 ILQEKLDQPVSAPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILQEKLDQPVSAPPSPR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 ILQEKLDQPVSAPPS(1)PR;ILQEKLDQPVSAPPS(1)PR 192.63 1.01E-17 253100000 396630 500550 451230 177310 821650 646460 223290 450170 547280 1061250 TRUE FALSE 412289.2587 586515.5688 462989.4245 212381.3888 681986.2265 496329.4622 205787.9463 444136.2075 527583.4997 1269181.619 0.324846541 0.462121071 0.364793673 0.167337271 0.53734329 0.391062599 0.162142237 0.349939048 0.415687946 1 20.2754671 0.699333508 2.942000866 0.999965072 0.343640983 0.762657554 0.108944819 1.228397178 11.46866281 0.103674667 0.027167103 5.004186745 -0.699333508 -0.656324089 ILQHSHGIEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILQHSHGIEEER 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ;; 196.5 1.19E-07 532820000 226041 251634 230835 240996 275958 311361 297459 273670 280256 263398 FALSE TRUE 234965.2732 294850.1821 236850.7497 288664.2895 229050.7577 239052.1265 274143.3863 270001.9013 270169.6413 315005.795 0.74590778 0.936015104 0.751893309 0.916377711 0.727131886 0.758881678 0.870280454 0.857133124 0.857665623 1 18.26501884 0.619361605 0.795001726 1.0002999 0.815453373 0.388827224 0.069073383 1.28359 1.417439262 0.065406767 0.022336452 4.162570525 -0.619361605 -0.184846528 ILQINKDDVTALHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILQINKDDVTALHCK 15 1 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 177.88 4.41E-07 1370040000 2320600 1495170 1900120 1514430 2624000 2336500 2365700 1993810 2235400 1311330 FALSE TRUE 2412219.08 1751953.817 1949638.688 1813979.734 2177973.417 1793883.285 2180270.252 1967086.238 2154948.391 1568260.007 1.538149969 1.117132242 1.243185875 1.156683029 1.38878337 1.143868541 1.390247946 1.254311294 1.374101477 1 20.58073334 -1.30595335 4.902233752 0.999889028 1.280283179 0.315975207 0.127167851 0.000138734 1.96E-05 0.110752145 0.026094241 0.049436379 1.30595335 0.28039415 ILQLCMGNHELYMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILQLCMGNHELYMR 14 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 253.15 3.20E-24 2453600000 1088860 1319500 1213860 1238240 1648740 1715330 1483620 1209730 1332920 1562550 FALSE TRUE 1131849.034 1546113.861 1245494.189 1483160.176 1368487.764 1316970.604 1367329.988 1193515.548 1284948.47 1868701.756 0.60568736 0.827373258 0.666502391 0.793684798 0.73232005 0.704751627 0.731700489 0.638687016 0.687615595 1 20.8336049 -1.455701068 3.145167942 1.005610097 0.710663004 0.653716654 0.063357889 53613959.95 69728671.5 2671520.618 0.014246295 0.035018612 1.455701068 -0.294947093 ILRPWQSSETR ddPTM_MDA-MB-175_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 ; 193.73 7.51E-07 2633900000 1662950 2193600 1787450 1711430 2574900 2560100 1981100 1803500 1805670 2826300 FALSE TRUE 1728604.55 2570333.736 1834032.415 2049945.746 2137219.418 1965555.574 1825816.205 1779327.032 1740684.289 3380059.372 0.511412481 0.76044041 0.542603609 0.606482171 0.63230233 0.581515103 0.540172821 0.526418869 0.514986306 1 21.68861716 -1.998226575 3.180230941 1.414068393 0.58051812 0.7579677 0.07126763 3756935.468 24005156.81 11350907.71 0.016557349 0.010040918 1.998226575 -0.833550272 ILS(ph)DVTHSAVFGVPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ILSDVTHSAVFGVPASK 17 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 ILS(0.742)DVT(0.15)HS(0.108)AVFGVPASK;ILS(0.997)DVT(0.003)HSAVFGVPASK;ILS(0.333)DVT(0.333)HS(0.333)AVFGVPASK;ILS(0.996)DVT(0.004)HS(0.001)AVFGVPASK;ILS(0.999)DVT(0.001)HSAVFGVPASK 186.89 3.21E-10 1995824000 3255197 2288246 3145739 2449355 4358600 3974773 4040810 3257970 3531847 2027094 TRUE FALSE 3383714.691 2681234.45 3227719.543 2933830.108 3617726.729 3051692.209 3724080.754 3214302.241 3404736.516 2424264.258 1.395769739 1.10599925 1.33142232 1.21019402 1.492298835 1.258811699 1.536169475 1.325887733 1.404441164 1 21.20911554 4.035829384 24.99908218 1.34268259 1.242840964 0.013787865 0.157496081 471.7389234 329138.8682 0.035697928 0.077116027 10859.98897 -4.035829384 -0.099841626 ILSDDVPIRDYR ddPTM_MDA-MB-175_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 59.57 0.089467 253360000 343880 521500 425550 374310 482810 570550 425860 424720 399620 546470 FALSE TRUE 357456.6479 611063.5683 436640.1826 448347.4008 400742.1287 438048.4093 392479.9804 419027.3231 385237.7543 653540.3337 0.546954227 0.935005136 0.668115126 0.686028662 0.613186529 0.670269893 0.600544389 0.641165207 0.58946286 1 19.31791675 -1.082036305 4.612962865 1.000015387 0.664681418 0.5068574 0.100204519 1.95E-05 3.88E-06 0.093892958 0.022129494 0.082787296 1.082036305 -0.33533397 ILSHGGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILSHGGFR 8 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ; 157.33 0.00037865 2720200000 2271300 2546100 2494000 2683300 2753600 3150900 2828100 2570000 2367900 2564900 FALSE TRUE 2360972.678 2983372.869 2558995.689 3214048.731 2285544.056 2419151.227 2606426.132 2535553.354 2282679.742 3067443.047 0.769687535 0.97259275 0.834243912 1.047794101 0.745097471 0.788654 0.849706447 0.826601608 0.744163692 1 21.54860513 3.201409968 24.99999176 0.817835843 0.905700185 0.138512731 0.097014044 287.0706047 193179.1887 0.025927957 0.030990575 1590.047022 -3.201409968 0.087864342 ILSQS(ph)TDS(ph)LNMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 2 ILS(0.196)QS(0.609)T(0.197)DS(0.999)LNMR;ILSQS(0.877)T(0.123)DS(1)LNMR;ILSQS(0.786)T(0.214)DS(1)LNMR 238.01 5.87E-16 435058000 724070 780630 799530 782960 842520 849500 742790 817230 764870 827760 TRUE FALSE 752656.8427 914697.13 820366.4086 937827.1511 699308.7513 652216.4993 684568.1789 806276.3686 737342.4781 989943.7236 0.760302656 0.923989019 0.828700045 0.947354005 0.706412632 0.658841997 0.691522318 0.814466873 0.744832722 1 19.91698699 7.991679831 6.51981983 0.799158294 0.774632 0 0.11105228 0 0 0.024530489 0 98102444.86 -7.991679831 -0.024526294 ILSQS(ph)TDSLNMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 21 ILSQSTDSLNMR 12 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 ILSQS(0.737)T(0.263)DSLNMR;ILSQS(0.936)T(0.064)DSLNMR;ILSQS(0.88)T(0.12)DSLNMR;ILSQS(0.986)T(0.014)DSLNMR;ILSQS(0.946)T(0.054)DSLNMR;ILSQS(0.964)T(0.036)DSLNMR;ILSQS(0.891)T(0.109)DSLNMR;ILSQS(0.84)T(0.16)DSLNMR;ILSQS(0.755)T(0.244)DSLNMR;ILS(0.024)QS(0.851)T(0.115)DS(0.01)LNMR;ILSQS(0.529)T(0.47)DS(0.001)LNMR;ILS(0.004)QS(0.841)T(0.155)DSLNMR;ILSQS(0.878)T(0.122)DSLNMR;ILSQS(0.933)T(0.063)DS(0.004)LNMR;ILSQS(0.543)T(0.457)DSLNMR;ILSQS(0.9)T(0.1)DSLNMR;ILSQS(0.518)T(0.482)DSLNMR;ILSQS(0.59)T(0.405)DS(0.005)LNMR;ILSQS(0.587)T(0.413)DSLNMR;ILSQS(0.557)T(0.443)DS(0.001)LNMR;ILSQS(0.623)T(0.358)DS(0.019)LNMR 342.48 7.29E-59 23836860000 13981974 17136369 16225168 16075421 15938192 18719465 16049774 15758872 15509852 16763134 TRUE FALSE 14533993.13 20079407.07 16648009.21 19255091.29 13229023.82 14372152.95 14791750.78 15547650.1 14951655.46 20047549.16 0.724976056 1.001589118 0.830426157 0.960471085 0.659882348 0.71690324 0.737833371 0.775538694 0.745809642 1 24.25692254 3.24464541 24.99970267 0.757745541 0.884600171 0.179076939 0.108924569 199.5129346 819704.3614 0.027918456 0.036865356 1756.4889 -3.24464541 0.126854629 ILSQST(ph)DS(ph)LNMR ddPTM_MDA-MB-175_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 2 ILS(0.005)QS(0.249)T(0.77)DS(0.975)LNMR 101.62 0.013614 410580000 511640 518340 606260 540180 614700 648540 517240 583380 551790 581680 TRUE FALSE 531839.9423 607360.8629 622059.6336 647025.9917 510213.5136 497926.4137 476697.3772 575560.7453 531931.1857 695649.0591 0.76452334 0.87308515 0.894214727 0.930104028 0.73343521 0.715772425 0.685255548 0.827372276 0.764654503 1 19.40800015 5.040935103 15.32853702 0.813309465 0.557622583 0.021707701 0.096679555 2595318.839 28212184.55 0.02355485 18402492.24 109884.1625 -5.040935103 -0.255686883 ILSQST(ph)DSLNMR ddPTM_MDA-MB-175_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(0.465)T(0.534)DSLNMR 253.06 5.02E-20 495610000 335820 462880 445310 442720 381800 521180 403200 399040 425660 500330 TRUE FALSE 349078.4329 542376.0393 456915.1444 530288.6946 316901.7724 400143.8436 371596.1304 393691.5215 410340.5797 598360.0841 0.583391911 0.906437534 0.763612341 0.886236747 0.529617167 0.668734186 0.621024263 0.657950843 0.685775323 1 19.19065441 -1.315693978 2.990878001 1.002678732 0.701094232 0.3777129 0.115397033 24148272.54 31044695.84 577720.0843 0.028805228 0.04833993 1.315693978 -0.3015845 ILTEAEIDAHLVALAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILTEAEIDAHLVALAER 17 0 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 110.22 0.00056902 29034000 22040 27825 26734 33790 26060 34760 31459 32167 25941 24584 FALSE TRUE 22910.15622 32603.7273 27430.71 40473.56115 21630.33051 26687.51679 28993.16138 31735.85398 25007.38848 29400.76411 0.779236762 1.108941495 0.932993098 1.376615961 0.735706406 0.907715075 0.986136322 1.079422761 0.850569338 1 14.84356603 ILTEAEIDAHLVALAERD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 ILTEAEIDAHLVALAERD 18 1 G3V5Z7;P60900;P60900-2;P60900-3;H0YJC4 G3V5Z7 PSMA6 Proteasome subunit alpha type;Proteasome subunit alpha type-6 0 ;;;;;;;;;;; 264.88 8.55E-31 1788705000 924380.5 1123386.7 1080511 1105694.2 1203437 1346565 1109757 1154143 1094951 1242473 FALSE TRUE 960875.7559 1316319.627 1108670.004 1324397.213 998877.2086 1033845.686 1022771.347 1138673.601 1055543.927 1485911.796 0.646657331 0.885866598 0.746121006 0.891302711 0.672231832 0.695765179 0.688312287 0.76631305 0.710367823 1 20.50291705 -1.036060898 4.386210684 1.000013943 0.748565329 0.478966576 0.079772133 68284107248 44987572.2 10256734.79 0.018534096 0.092032051 1.036060898 -0.251448614 ILTQDTPEFFIDQGHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILTQDTPEFFIDQGHAK 17 0 Q8TDL5 Q8TDL5 BPIFB1 BPI fold-containing family B member 1 0 ; 278.27 8.02E-36 868540000 948780 747380 785310 738410 1036300 1044680 930460 836820 839260 655780 FALSE TRUE 986238.567 875736.7012 805775.8237 884465.2941 860150.0962 802068.9023 857528.1139 825603.7967 809055.1965 784267.5353 1.257528232 1.116630055 1.027424683 1.127759666 1.096755963 1.02269808 1.093412739 1.052706837 1.031606129 1 19.58098636 4.683520885 2.793071746 1.062529982 1.281463386 0.717746465 0.037964412 0.186964137 2.156633419 0.008979644 0.087719091 48252.61842 -4.683520885 0.218933404 ILTTASSHEFEHTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILTTASSHEFEHTKK 15 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1;F2Z3H1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 184.02 1.96E-07 284870000 227510 334440 463040 338540 569990 578800 423970 418350 483590 372090 FALSE TRUE 236492.2705 391877.4684 475107.2028 405502.2016 473103.3034 444382.4718 390738.1236 412742.7025 466185.6904 444993.9114 0.531450576 0.880635574 1.067671244 0.91125337 1.063168037 0.99862596 0.878075213 0.927524382 1.047622627 1 18.76342607 4.704363956 3.202585205 0.976542973 0.483555518 0.825843523 0.062522969 0.117774711 1.957841098 0.015393085 0.138127703 50624.87412 -4.704363956 -0.492987455 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNRVPR 39 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 73.24 0.0017887 450526000 123549.9 154253.7 147072 135942.1 202246 168997 113886.9 156837 136219.6 252030 FALSE TRUE 128427.7455 180745.573 150904.8171 162831.0416 167868.2972 129750.0079 104960.1472 154734.8565 131317.0832 301410.4531 0.426089222 0.599665908 0.500662189 0.540230241 0.55694252 0.430476138 0.348229951 0.513369244 0.435675279 1 18.20136993 -1.572020488 3.692340455 1.013517851 0.485771308 0.827529652 0.070734168 18614170.23 8051515.166 2032040.94 0.017411411 0.026790419 1.572020488 -0.527746542 ILVDVEKVDWDKAWEITKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILVDVEKVDWDKAWEITKK 19 3 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 86.479 0.0012572 85314000 84579 40759 58599 22495 115320 77383 60816 47993 69017 50759 FALSE TRUE 87918.24423 47759.04119 60126.13808 26944.44386 95717.94759 59411.971 56049.08301 47349.73234 66533.09165 60704.25421 1.448304495 0.786749492 0.990476514 0.443864177 1.576791427 0.978711818 0.923313922 0.780006821 1.096020246 1 15.88951 4.750104556 23.99377335 0.942724565 1.448305028 0.230962215 0.270636278 1434.821214 2982137.75 0.062167145 0.949601972 56247.67252 -4.750104556 0.505580463 ILVEDELS(ph)SPVVVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILVEDELSSPVVVFR 15 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;Q6P474;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 1 ILVEDELS(0.5)S(0.5)PVVVFR 60.628 0.079599 0 18443 15945 12695 13608 15910 16743 12971 13841 11313 12027 TRUE FALSE 19171.14388 18683.42972 13025.84213 16299.62178 13205.62388 12854.69199 11954.29913 13655.48403 10905.84734 14383.46038 1.332860339 1.298952354 0.905612543 1.133219778 0.918111743 0.89371345 0.831114267 0.949387955 0.758221391 1 13.81212318 4.755067114 0.654424725 0.881644297 1.698118644 0.700487369 0.10006703 1.666949766 0.532329548 0.040636121 1.028177679 56894.08456 -4.755067114 0.816474347 ILVEDELSS(ph)PVVVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILVEDELSSPVVVFR 15 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q86XE2;Q6P996-2;Q6P474;Q6XYB5;Q6P996-4 H3BND4;Q6P996-4 PDXDC1;PDXDC2P Pyridoxal-dependent decarboxylase domain-containing protein 1;Putative pyridoxal-dependent decarboxylase domain-containing protein 2 1 ILVEDELS(0.016)S(0.984)PVVVFR;ILVEDELS(0.005)S(0.995)PVVVFR;ILVEDELS(0.219)S(0.781)PVVVFR 208.15 3.18E-09 33346400 119070 121796 123584 125937 128073 142818 125375 124406 105880 116006 TRUE FALSE 123770.9755 142713.5156 126804.7006 150846.9627 106303.1972 109650.6839 115547.7799 122738.5411 102069.3995 138735.1546 0.89213852 1.02867594 0.914005545 1.087301651 0.766231151 0.790359763 0.832865903 0.884696755 0.735714028 1 17.08197388 3.228094249 24.99999786 0.830954696 0.979217615 0.412258637 0.085052791 189.7207861 453166.9596 0.022900502 0.027648704 1690.807826 -3.228094249 0.148262919 ILVLDDTNHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ILVLDDTNHER 11 0 K7EN66;C9K0L8;K7ERZ0;K7ERC4;P09543-2;P09543 K7EN66 CNP "2,3-cyclic-nucleotide 3-phosphodiesterase" 0 ;; 192.68 1.28E-06 364853000 459500 545230 500740 540220 565460 653770 557010 522920 523200 563480 FALSE TRUE 477641.4148 638869.0112 513789.6958 647073.9036 469343.3112 501941.8255 513350.1007 515911.1127 504370.1342 673883.1175 0.708789703 0.948041277 0.76243147 0.960216819 0.696475841 0.744849978 0.761779139 0.765579519 0.748453435 1 19.36213886 5.035784478 18.48240959 0.806691879 0.259911814 0.08226163 0.102930882 2046.902109 62733.1341 0.022454042 41423.05304 108588.6609 -5.035784478 -0.546780064 ILVPKS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILVPKSPVK 9 1 Q9Y232;Q9Y232-2;Q9Y232-4 Q9Y232 CDYL Chromodomain Y-like protein 1 ILVPKS(1)PVK 83.314 0.01779 0 1215600 515470 549710 328600 1722700 1083300 865640 509710 722770 828420 TRUE FALSE 1263592.827 603997.9627 564035.8942 393596.0992 1429876.069 831719.9926 797788.8749 502878.1712 696757.6489 990733.0379 1.275412021 0.609647543 0.569311684 0.397277656 1.443250618 0.839499604 0.805251106 0.507581914 0.70327487 1 19.91813684 1.972221569 22.39322323 0.675783389 0.836143225 0.014427523 0.317933013 702.725943 566489.4089 0.132477605 0.085819682 93.80404547 -1.972221569 0.160359836 ILVTLLHTLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ILVTLLHTLER 11 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 261.52 1.08E-20 3265000000 863040 911510 892360 914570 1178060 1190770 998320 1077150 973750 1137280 FALSE TRUE 897113.4856 1068054.752 915615.6347 1095469.216 977813.782 914231.7138 920069.0698 1062712.566 938704.9277 1360108.241 0.659589773 0.785271877 0.673193211 0.805427967 0.718923503 0.672175703 0.676467535 0.781344112 0.690169281 1 20.37529004 -2.093187806 2.411030585 1.465533173 0.72252063 0.73010234 0.051361547 2924421.157 859356.0106 7475981.116 0.0116439 0.00806886 2.093187806 -0.743012543 ILYSQCGDVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ILYSQCGDVMR 11 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;P60660-2;G8JLA2;P14649;F8W1I5 F8VPF3;P60660;P60660-2;P14649 MYL6;MYL6B Myosin light polypeptide 6;Myosin light chain 6B 0 129.88 0.0024495 0 81663 69760 85179 64307 95719 98885 71767 82113 75572 88260 FALSE TRUE 84887.1183 81740.73734 87398.83472 77026.73266 79448.71857 75920.45737 66141.71501 81012.40954 72852.17848 105552.8572 0.804214311 0.774405729 0.828010128 0.729745596 0.752691312 0.719264825 0.62662174 0.767505605 0.690196177 1 16.68760611 -1.158773834 3.887653764 1.000131127 0.742799458 0.66550625 0.05452384 26946915.4 63535805.86 50147.48077 0.013529399 0.069378701 1.158773834 -0.257331669 IMADIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMADIR 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 97.306 0.095899 1864200000 4112600 5298200 4707500 4596100 5982700 6042400 5110100 4733900 4492900 5909700 FALSE TRUE 4274968.624 6208124.636 4830181.317 5505194.862 4965762.791 4639144.173 4709557.009 4670449.814 4331201.407 7067592.567 0.604869138 0.878393113 0.683426679 0.77893495 0.702610223 0.656396663 0.666359438 0.660826126 0.612825565 1 22.75278744 -1.15508057 5.081226378 1.000015434 0.696813661 0.587013495 0.077001108 1.31E-05 2.18E-06 0.072548352 0.017098941 0.069971217 1.15508057 -0.303201774 IMAT(ph)PEQVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMATPEQVGK 10 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 IMAT(1)PEQVGK 151.78 0.00021456 143610000 515200 431720 497620 402470 598760 654690 608460 516110 527580 424870 TRUE FALSE 535540.4938 505864.5517 510588.386 482077.3647 496982.9891 502648.1694 560767.3153 509192.3896 508592.4989 508115.1419 1.05397468 0.995570708 1.004867488 0.948756148 0.978091279 0.989240682 1.103622524 1.002120086 1.000939466 1 18.95479593 IMDPNIVGSEHYDVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IMDPNIVGSEHYDVAR 16 0 P06576;H0YH81 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;;;;;;; 195.92 4.72E-11 4243650000 1614774 2778200 2284651 2850911 1927031 3402663 2119475 2110569 2017958 3043149 FALSE TRUE 1678526.524 3255334.239 2344190.882 3414812.687 1599474.959 2612446.086 1953345.011 2082280.275 1945332.086 3639395.782 0.461210219 0.89447107 0.644115403 0.938291104 0.43948915 0.717824123 0.536722338 0.572149994 0.534520619 1 21.79526752 -1.034359361 4.785761271 1.000006476 0.64127865 0.313557989 0.160761242 1.39E-05 2.81E-06 0.147512981 0.034768312 0.092393334 1.034359361 -0.358727826 IMDYSLLLGIHDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IMDYSLLLGIHDIIR 15 0 Q8TBX8;Q8TBX8-3;Q8TBX8-2;H0YIJ6 Q8TBX8 PIP4K2C Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 0 ;; 196.18 9.06E-09 587229000 210463 280284 270085 272551 357131 334691 290243 279500 269710 344242 FALSE TRUE 218772.2418 328420.5967 277123.637 326460.7743 296426.0002 256964.0875 267492.9953 275753.7597 260003.1898 411689.629 0.531400906 0.797738329 0.67313728 0.792977892 0.720022996 0.624169446 0.649744313 0.669809828 0.631551469 1 18.65119758 -1.43899006 3.034840679 1.006318682 0.681356787 0.622429885 0.075456597 22059955.71 26758621.11 1192618.682 0.01788973 0.036392337 1.43899006 -0.324961895 IMEVIDAITTTAQSHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMEVIDAITTTAQSHQR 17 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 153.24 1.83E-07 597430000 67870 85524 90776 83434 82615 92641 86936 84996 81735 84404 FALSE TRUE 70549.56001 100212.0817 93141.69713 99936.99617 68572.13181 71126.53174 80121.72916 83856.76765 78793.37332 100941.3478 0.698916366 0.992775348 0.922730865 0.990050147 0.679326493 0.704632277 0.793745387 0.830747454 0.780585707 1 16.62315773 5.036612932 14.13514065 0.84277147 0.225289161 0.138945932 0.112924041 5346155.789 65200205.16 0.027986649 79810016.2 108796.0008 -5.036612932 -0.617482309 IMFVDPSLTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMFVDPSLTVR 11 0 O95994;B5MC07;H7C3Z9;Q8TD06;B5MC62;H7C040 O95994;Q8TD06 AGR2;AGR3 Anterior gradient protein 2 homolog;Anterior gradient protein 3 homolog 0 135.63 0.0028479 0 553390 701350 637950 683020 758800 840220 649300 619250 570520 708970 FALSE TRUE 575238.2645 821801.4068 654575.5011 818119.3174 629819.447 645091.6387 598406.1694 610949.9666 549987.0966 847879.0974 0.678443738 0.969243621 0.772015141 0.964900916 0.742817518 0.760829746 0.705768277 0.7205626 0.648662172 1 19.69349903 3.106568515 24.23597761 0.743466501 0.850182046 0.091927896 0.118315499 13.0907599 2934.721056 0.031273875 0.037379434 1278.110831 -3.106568515 0.106715545 IMGPNYTPGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 0 84.479 0.025544 673280000 301430 243160 347730 248440 444580 437410 382560 327200 390870 268030 FALSE TRUE 313330.6892 284920.8385 356792.1295 297580.6905 369010.4504 335828.1565 352573.9476 322814.4192 376802.6651 320545.3468 0.977492552 0.888862813 1.113078487 0.928357543 1.15119578 1.047677528 1.099919095 1.007078788 1.175505023 1 18.29016894 4.24035595 24.99673408 1.062108108 0.933177668 0.341509357 0.073303386 46.62708017 649145.418 0.016528527 0.04075454 17392.25721 -4.24035595 -0.12893044 IMGPNYTPGKKEDLYLKPIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMGPNYTPGKKEDLYLKPIQR 21 3 P13639 P13639 EEF2 Elongation factor 2 0 ; 159.06 1.01E-11 1463050000 835560 648250 906870 415764 1482530 960610 515150 780020 1074240 827570 FALSE TRUE 868548.554 759581.8948 930503.7772 498000.8783 1230530.08 737522.8857 474771.1969 769565.1078 1035578.312 989716.4967 0.87757308 0.767474218 0.940172039 0.503175283 1.243315721 0.745186008 0.479704237 0.777561161 1.046338336 1 19.9166558 IMKDILEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMKDILEK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 108.67 0.0034351 13357600000 16487900 11898900 15751600 9648600 23650000 18908400 16558900 15832500 18230200 12921400 FALSE TRUE 17138855.02 13942443.51 16162099.64 11557064.28 19629981.45 14517210.66 15260970.15 15620291.23 17574098.66 15453100.93 1.109088402 0.902242441 1.045880675 0.747879945 1.270294003 0.939436733 0.987566846 1.010819207 1.137253858 1 23.88139303 3.245958049 24.99988503 1.044724864 0.954528488 0.144341244 0.124345132 383.982498 1297673.991 0.032892617 0.043662886 1761.805855 -3.245958049 -0.090196376 IMLFTNEDNPHGNDSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMLFTNEDNPHGNDSAK 17 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 278.15 8.10E-36 927260000 600480 498630 674920 533670 780860 863340 765880 675450 762140 473380 FALSE TRUE 624187.4141 584265.8237 692508.9697 639228.3332 648129.6961 662842.369 705848.3243 666396.6976 734710.7303 566129.7476 1.102551874 1.032035194 1.223233671 1.129119846 1.144843031 1.170831195 1.246796035 1.177109488 1.297777998 1 19.11077321 4.240728367 24.99999861 1.180896523 1.067293517 0.230538254 0.076878256 67.49976815 778402.3653 0.017500765 0.043377161 17407.17785 -4.240728367 -0.113603006 IMMEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IMMEFER 7 0 O43633;M0R1L7;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 79.116 0.077928 54748000 98502 121560 104220 112230 147870 157800 123220 125250 111560 154830 FALSE TRUE 102390.935 142436.9844 106936.0588 134428.759 122735.1102 121153.3415 113561.6944 123571.2286 107544.9774 185165.9741 0.552968414 0.769239517 0.577514629 0.725990613 0.662838358 0.654295921 0.613296773 0.667353866 0.58080313 1 17.49845949 -2.223975851 2.414714693 2.21683995 0.649753124 0.732984817 0.064233675 2979057.371 566112.1849 19857524.77 0.013669904 0.005970685 2.223975851 -1.567086826 IMNVIGEPIDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IMNVIGEPIDER 12 0 P06576;H0YH81;F8W079 P06576 ATP5B "ATP synthase subunit beta, mitochondrial;ATP synthase subunit beta" 0 ;; 137.17 0.00022564 111384000 136224 178635 136031 172687 150819 228671 163677 147608 125798 191949 FALSE TRUE 141602.2287 209314.1717 139576.0796 206843.9732 125182.8403 175565.6258 150847.569 145629.5562 121270.5546 229557.7315 0.616848005 0.911814951 0.608021689 0.901054266 0.545321821 0.764799446 0.657122581 0.63439186 0.528279112 1 17.8084975 -1.147957506 4.983658934 1.000017636 0.689045469 0.353760971 0.127514062 2.32E-05 3.96E-06 0.11438976 0.026960397 0.071128311 1.147957506 -0.310972167 IMQIHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMQIHSR 7 0 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 144.38 0.0023584 654880000 695310 796920 789470 752990 944170 997170 806940 794500 756480 1048490 FALSE TRUE 722761.3757 933784.8108 810044.2368 901929.1745 783680.3206 765592.3798 743689.9343 783851.027 729254.4326 1253921.541 0.576400797 0.744691578 0.64600871 0.71928677 0.624983538 0.61055844 0.593091282 0.625119676 0.581578997 1 20.25801565 -1.960373247 2.556520257 1.286783613 0.637864569 0.809277665 0.053039985 3736964.667 2049520.525 6361189.283 0.013586842 0.010955363 1.960373247 -0.648919044 IMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDR ddPTM_MDA-MB-175_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 ; 286.82 1.25E-74 1777190000 880700 652350 887200 676660 1041950 1051480 1058110 797320 1014810 628450 FALSE TRUE 915470.716 764386.0379 910321.1608 810501.3284 864839.7112 807289.7053 975172.5733 786633.2296 978287.1863 751582.7451 1.218057123 1.017035107 1.211205508 1.078392677 1.15069128 1.074119531 1.297491966 1.046635563 1.301636038 1 19.51957242 IMSS(ph)IGEGIDFSQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IMSSIGEGIDFSQER 15 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 IMS(0.006)S(0.994)IGEGIDFSQER;IMS(0.034)S(0.966)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMSS(1)IGEGIDFSQER;IMS(0.014)S(0.986)IGEGIDFSQER;IMS(0.009)S(0.991)IGEGIDFSQER 335.23 5.29E-69 676254000 682013 776573 773222 789933 935031 969874 704292 766586 722548 858832 TRUE FALSE 708939.3999 909943.3719 793372.8005 946179.3897 776094.7646 744635.4621 649087.7527 756311.1686 696543.6386 1027103.687 0.690231579 0.885931365 0.772436912 0.92121117 0.755614817 0.724985677 0.631959325 0.73635328 0.678162923 1 19.9701504 5.035772588 15.21356722 0.773867168 0.397410114 0.053040264 0.109010881 4604620.151 57752244.74 0.025685854 45840180.14 108585.6882 -5.035772588 -0.376457053 IMTYLFDFPHGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMTYLFDFPHGPK 13 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 114.72 0.00072071 171616000 316370 201818 273910 313090 294370 337390 471800 307170 287880 135934 FALSE TRUE 328860.5319 236478.6716 281048.3196 375018.2675 244333.0925 259036.2857 434819.0832 303052.8886 277519.255 162567.6647 2.022914782 1.454647651 1.728808248 2.306844158 1.502962431 1.593405959 2.674696004 1.864164618 1.707099967 1 17.3106808 3.96915156 24.72855115 1.883999831 1.702017534 0 0.448435242 2378.297543 1906482.722 0.111132847 0.200677375 9314.328695 -3.96915156 -0.181982297 IMVGS(ph)TDDPSVFSLPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IMVGSTDDPSVFSLPDSK 18 0 O43741 O43741 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 IMVGS(0.978)T(0.021)DDPS(0.002)VFSLPDSK;IMVGS(0.872)T(0.128)DDPSVFSLPDSK;IMVGS(0.97)T(0.03)DDPSVFSLPDSK 235.35 3.37E-23 154014000 375077 277127 319728 268321 421100 401251 387222 318250 363922 239478 TRUE FALSE 389885.3296 324721.4065 328060.3743 321394.0929 349521.5724 308066.5363 356870.5278 313984.3793 350824.5183 286399.129 1.361335598 1.133807242 1.145465684 1.122189491 1.220400263 1.075654585 1.246060102 1.096317508 1.224949669 1 18.12766758 -5 0.162468516 0.385559141 1.215789898 0.317202699 0.080470159 162.1928149 1.502005161 32.46748787 0.304792234 1.00E-05 5 0.830230756 IMVQSAS(ph)PDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 IMVQSASPDIR 11 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 IMVQS(0.037)AS(0.963)PDIR;IMVQS(0.005)AS(0.995)PDIR;IMVQSAS(1)PDIR;IMVQS(0.004)AS(0.996)PDIR;IMVQSAS(1)PDIR;IMVQS(0.005)AS(0.995)PDIR;IMVQS(0.004)AS(0.996)PDIR;IMVQS(0.036)AS(0.964)PDIR;IMVQS(0.006)AS(0.994)PDIR 231.36 1.18E-12 2609070000 2484260 2714870 2566820 2473850 2650420 2957840 2108000 2256680 1933890 2200810 TRUE FALSE 2582340.503 3181127.804 2633713.438 2963170.146 2199902.555 2270926.486 1942769.452 2226432.896 1864289.677 2632016.582 0.981126229 1.208627569 1.000644698 1.125817431 0.835823972 0.862808579 0.73812964 0.845903825 0.708312284 1 21.32773715 3.230164622 23.34962056 0.820804311 1.082708584 0.621154845 0.094333457 45.72343381 127158.6813 0.024875812 0.030246689 1698.887503 -3.230164622 0.261904273 IMYTVFEHTFHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IMYTVFEHTFHVR 13 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 225.15 7.48E-12 706900000 348590 424340 402590 354760 478080 477930 429520 438360 416230 498420 FALSE TRUE 362352.6024 497217.0941 413081.8261 424930.4691 396816.1324 366938.0006 395853.1001 432484.5012 401249.9636 596075.8562 0.607896795 0.834150702 0.69300211 0.712879854 0.665714151 0.615589437 0.66409853 0.725552791 0.673152518 1 19.18513641 -1.218843403 4.09226002 1.000195899 0.691874353 0.705595331 0.060412977 20.87011957 32087036.61 11306.14282 0.013769569 0.060416644 1.218843403 -0.308321546 INAGMLAQFIDKPVCFVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INAGMLAQFIDKPVCFVGR 19 1 P35244 P35244 RPA3 Replication protein A 14 kDa subunit 0 79.92 0.0047003 0 208910 225720 214630 148240 307310 285020 172620 204640 280890 219550 FALSE TRUE 217157.9281 264485.6541 220223.4341 177561.4295 255073.556 218828.4245 159089.5933 201897.1355 270780.8238 262566.619 0.827058401 1.007308755 0.838733556 0.67625287 0.971462241 0.833420583 0.605901824 0.768936799 1.031284269 1 18.00232399 5.132337657 14.05671017 0.838480448 0.00167143 0 0.13954269 8919597.43 6930030.377 0.033654461 236554702.8 135624.3461 -5.132337657 -0.836809018 INEGLEHLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INEGLEHLAK 10 0 Q99747;J3QS28;J3QKW4 Q99747 NAPG Gamma-soluble NSF attachment protein 0 ; 98.353 0.0054345 265840000 1219420 1334010 1322590 1151740 1550250 1616310 1466160 1277740 1402940 1257080 FALSE TRUE 1267563.643 1563115.84 1357057.782 1379550.734 1286739.059 1240946.498 1351238.548 1260613.985 1352448.463 1503380.758 0.843142123 1.039733835 0.902670714 0.917632295 0.855896986 0.825437263 0.898799949 0.838519436 0.899604745 1 20.51977901 3.587156434 2.346494661 0.874602512 0.941442352 0.053048623 0.064780891 0.518704729 5.584488212 0.017229117 0.029777377 3865.061721 -3.587156434 0.06683984 INEKPQVIADYESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 INEKPQVIADYESGR 15 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 153.74 2.37E-06 4998660000 2924360 2244620 2904880 2128650 3459850 3542730 3228010 2834560 3072870 2237870 FALSE TRUE 3039815.991 2630116.024 2980583.559 2549690.617 2871745.933 2719984.648 2974990.141 2796567.36 2962278.009 2676337.78 1.135811785 0.982729476 1.113679888 0.952678932 1.073013263 1.01630843 1.111589936 1.044923171 1.106840112 1 21.35182878 2.265361746 24.99378667 1.068440268 1.042943966 0.024670205 0.059656309 784.4776232 731574.276 0.018796573 0.015722463 184.2305913 -2.265361746 -0.025496303 INENEKS(ph)PSQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INENEKSPSQNR 12 1 K7EQT1;Q9UM11-3;Q9UM11-2;Q9UM11 K7EQT1 FZR1 Fizzy-related protein homolog 1 INENEKS(0.957)PS(0.043)QNR 84.842 0.0094801 0 100550 70783 90832 63801 105670 134800 99538 77026 95754 58471 TRUE FALSE 104519.7916 82939.42963 93199.15654 76420.64737 87708.25114 103494.7429 91735.95147 75993.59246 92307.83224 69927.27296 1.494692803 1.186081283 1.332801246 1.092858968 1.254278158 1.48003402 1.311876577 1.086751839 1.320054799 1 16.09356762 -4.718157167 0.178885927 1.15E-17 1.330815925 0.30678256 0.130581504 156.1677508 1.645208922 55.53886345 0.420603565 1.91E-05 4.718157167 1.330815925 INETDTFGPGDDDEIQFDDIGDDDEDIDDI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 247.52 5.04E-46 273956000 468496 553014 593998 541275 673666 712400 601786 621470 613621 537445 FALSE TRUE 486992.5838 647989.8526 609478.0759 648337.5795 559156.4939 546955.8965 554616.4408 613140.2112 591536.9001 642747.0577 0.757673766 1.008156856 0.948239387 1.008697857 0.869947964 0.850966006 0.862884449 0.953937017 0.920326111 1 19.29389158 0.701392852 1.324985518 0.999309955 0.910844527 0.125706918 0.072929466 2.287192884 6.499503248 0.068316541 0.020419053 5.027972022 -0.701392852 -0.088465428 INFDKYHPGYFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INFDKYHPGYFGK 13 1 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ; 127.32 0.00010711 4941100000 13119400 11384500 13961700 8629000 20120000 16048300 12010400 14144600 15120100 15154000 FALSE TRUE 13637364.04 13339699.32 14325553.37 10335790.45 16700009.59 12321325.54 11068993.46 13955014.77 14575930.55 18123136.16 0.752483672 0.736059101 0.790456643 0.570309154 0.921474597 0.679867184 0.610765894 0.770011032 0.804271977 1 24.1113293 0.844483285 1.966074567 0.999210015 0.725789042 0.44569245 0.0917417 0.501956174 3.668177319 0.082716028 0.023014752 6.990098322 -0.844483285 -0.273420973 INFS(ph)DLDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INFSDLDQR 9 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 INFS(1)DLDQR 80.555 0.024945 39368000 201290 38639 60533 36711 80803 123220 76255 46937 71659 37864 TRUE FALSE 209237.0846 45274.94768 62110.53971 43972.32623 67068.13492 94604.02242 70277.93384 46307.88629 69080.00659 45282.72585 4.620682185 0.999828231 1.371616627 0.971061821 1.481097563 2.08918568 1.551981082 1.022639106 1.525526684 1 15.46667319 4.742272982 24.99656117 1.348127661 4.620683435 0.895726012 0.336311417 110.1002407 741310.1748 0.083273248 0.623596757 55242.45643 -4.742272982 3.272555774 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPT(ph)ASPHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTASPHSNR 40 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 INGEAQPWLSTSTEGLKIPMTPTSSFVS(0.001)PPPPT(0.691)AS(0.304)PHS(0.004)NR 169.73 1.18E-18 532990000 466710 438730 535170 406520 653380 629390 523170 534930 578240 437070 TRUE FALSE 485136.0712 514078.4647 549116.9698 486928.4427 542318.701 483223.711 482162.5683 527760.1383 557429.2554 522705.4983 0.928125059 0.983495422 1.050528398 0.931554086 1.037522473 0.924466478 0.922436381 1.009670149 1.066430824 1 18.99563881 1.514149996 6.693957371 1.034836288 0.971296839 0.2529407 0.045888617 0.170277294 16.37543465 0.02517178 0.01146124 32.67006481 -1.514149996 -0.06353945 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INGEAQPWLSTSTEGLKIPMTPTSSFVSPPPPTASPHSNR 40 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 INGEAQPWLSTSTEGLKIPMTPTSSFVS(0.001)PPPPT(0.22)AS(0.63)PHS(0.149)NR 133.82 3.06E-09 417380000 604660 564750 640180 503130 761620 780050 615380 627840 711310 600470 TRUE FALSE 628532.4437 661741.4194 656863.6167 602647.6123 632160.1044 598895.2093 567144.9076 619424.8317 685710.092 718120.5998 0.875246364 0.921490651 0.914698195 0.839201121 0.880297968 0.833975811 0.789762761 0.862563798 0.954867598 1 19.45386662 1.117205721 3.716373555 0.997287851 0.863014355 0.613016036 0.036625128 0.151396241 3.662113128 0.038586953 0.010063916 13.09802217 -1.117205721 -0.134273496 INHEGEVNR ddPTM_MDA-MB-175_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 ;;;;; 128.86 0.00040557 4831614000 2136527 2585016 2540466 2311006 2917024 3111510 2339494 2642210 2257619 2729485 FALSE TRUE 2220878.736 3028972.389 2606672.631 2768116.089 2421189.302 2388908.958 2156118.347 2606795.497 2176367.733 3264275.327 0.680358889 0.92791572 0.798545579 0.848003251 0.741723372 0.731834395 0.660519758 0.798583219 0.66672309 1 21.63833132 5.027427255 16.41687253 0.784365971 0.387052351 0.093062303 0.102622195 8083924.496 129250211.8 0.023245144 87235686.47 106519.0428 -5.027427255 -0.39731362 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.981)PEPT(0.019)R;INHTVILDDPFDDPPDLLIPDRS(0.98)PEPT(0.02)R;INHTVILDDPFDDPPDLLIPDRS(0.972)PEPT(0.028)R;INHTVILDDPFDDPPDLLIPDRS(0.999)PEPT(0.001)R;INHTVILDDPFDDPPDLLIPDRS(0.967)PEPT(0.033)R;INHTVILDDPFDDPPDLLIPDRS(0.82)PEPT(0.18)R;INHTVILDDPFDDPPDLLIPDRS(0.981)PEPT(0.019)R;INHTVILDDPFDDPPDLLIPDRS(0.968)PEPT(0.032)R;INHTVILDDPFDDPPDLLIPDRS(0.971)PEPT(0.029)R;INHTVILDDPFDDPPDLLIPDRS(0.958)PEPT(0.042)R 255.04 9.86E-54 3289670000 434945 460017 430774 465842 472620 571841 478076 505307 460582 442646 TRUE FALSE 452116.9645 539021.3413 442000.3243 557984.1572 392284.2212 439039.5941 440603.1539 498534.1862 444005.7438 529374.0087 0.854059619 1.018224039 0.834949047 1.054045246 0.741034155 0.829356158 0.83230976 0.941742847 0.838737332 1 19.01392784 5.10266744 12.89409197 0.89460227 5.60E-05 0.017468973 0.096143278 4559674.793 10007079.91 0.021812426 113593854.4 126668.1535 -5.10266744 -0.894546246 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTREQLDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 INHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGR 35 2 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 INHTVILDDPFDDPPDLLIPDRS(0.818)PEPT(0.159)REQLDS(0.023)GR;INHTVILDDPFDDPPDLLIPDRS(0.74)PEPT(0.134)REQLDS(0.126)GR;INHTVILDDPFDDPPDLLIPDRS(0.949)PEPT(0.051)REQLDS(0.001)GR;INHTVILDDPFDDPPDLLIPDRS(0.774)PEPT(0.208)REQLDS(0.018)GR 207.62 4.31E-28 630994000 57997.4 83182 83688.7 54660.3 89565.8 84893.4 51738.5 67493.8 75049.9 109057.8 TRUE FALSE 60287.18214 97467.86143 85869.69627 65471.9442 74341.43731 65178.19442 47683.10118 66589.15601 72348.86876 130425.5879 0.462234314 0.747306284 0.658380749 0.501986959 0.5699912 0.499734718 0.365596214 0.510552853 0.554713764 1 16.99286741 0.922912123 18.61203225 1 0.538359979 0.658659661 0.099143662 1290.848017 311663.4484 0.102270927 0.025567732 8.373598303 -0.922912123 -0.461640021 INISEGNCPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 170.89 3.53E-05 738960000 401030 348310 346690 333350 381600 436410 410700 320430 328400 332150 FALSE TRUE 416862.9741 408129.533 355725.0262 399285.635 316735.7683 335060.3914 378508.2608 316135.16 316580.9481 397228.4331 1.049428841 1.027442899 0.895517532 1.005178889 0.797364292 0.843495489 0.95287303 0.795852295 0.796974541 1 18.59960937 4.185500168 0.844941891 0.857723481 1.091983138 0.394869397 0.075797687 1.100736779 1.029065631 0.027215363 0.207168321 15328.51801 -4.185500168 0.234259657 INLSNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INLSNNK 7 0 Q5T0V4;A0A0A0MSC8;Q5T0V0;O75093-2;O75094-2;O75094-3;O75094;O75094-4;O75093 Q5T0V4 SLIT1;SLIT3 Slit homolog 1 protein;Slit homolog 3 protein 0 64.803 0.072306 51908000 8493.3 61711 51372 63715 39579 65665 34490 50954 41747 81895 FALSE TRUE 8828.622042 72309.38421 52710.79652 76317.63683 32851.37572 50415.29891 31786.58368 50271.04497 40244.53362 97940.75728 0.090142473 0.738297173 0.538190616 0.77922245 0.335420887 0.514753003 0.32454909 0.513280134 0.410906907 1 16.57962173 -1.193220727 3.716656611 1.000515636 0.483616564 0.406828932 0.190904625 73890070.4 120558617.8 443433.5256 0.042153301 0.064088377 1.193220727 -0.516899072 INLWHLEITDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INLWHLEITDR 11 0 P63151;P63151-2;A0A590UJY3;A0A590UJJ1;Q66LE6 P63151 PPP2R2A;PPP2R2D Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform 0 111.79 0.00095432 0 145860 275940 212380 276100 213280 272440 218740 220900 189110 315320 FALSE TRUE 151618.6654 323330.5485 217914.7973 330711.7559 177026.7418 209169.9389 201594.5872 217939.1968 182303.968 377100.9168 0.4020639 0.857411197 0.577868649 0.876984757 0.469441292 0.554678945 0.534590552 0.577933352 0.483435494 1 18.52459113 -1.735434512 8.395750144 1.002405727 0.599620235 0.403518621 0.148341918 0.006321506 0.000199202 0.135924841 0.031915358 0.018389312 1.735434512 -0.402785492 INMAHLCVIGSHAVNGVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INMAHLCVIGSHAVNGVAR 19 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 143.46 8.39E-08 419700000 137490 180790 170690 182130 192530 194770 189440 149560 156620 178540 FALSE TRUE 142918.2114 211839.2761 175138.3216 218154.7704 159803.8194 149537.6193 174591.1978 147555.3928 150983.2768 213521.4946 0.669338755 0.99212155 0.820237428 1.021699341 0.748420292 0.700339886 0.817675045 0.691056388 0.707110434 1 17.70402178 INPPPYLTCESFPHAVDHILQHLL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INPPPYLTCESFPHAVDHILQHLL 24 0 Q9H0R4;Q9H0R4-2 Q9H0R4 HDHD2 Haloacid dehalogenase-like hydrolase domain-containing protein 2 0 114.63 0.00070073 48701000 39063 24815 24659 26408 35768 40103 34669 28791 20789 29374 FALSE TRUE 40605.2374 29076.78322 25301.6338 31631.42358 29688.16814 30789.68602 31951.55319 28405.10374 20040.80795 35129.2729 1.155880383 0.827708085 0.720243595 0.900429214 0.845111945 0.87646807 0.909542115 0.808587864 0.570487411 1 15.1003861 1.546613921 5.6873307 0.756150414 0.879003282 0.079610374 0.141889876 0.292282184 19.72436286 0.076165163 0.034563109 35.20577594 -1.546613921 0.122852868 INPPSSGGTSS(ph)SPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INPPSSGGTSSSPIK 15 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 INPPS(0.004)S(0.035)GGT(0.126)S(0.08)S(0.459)S(0.296)PIK 118.33 0.00031394 529990000 282890 170220 251730 188800 300450 325570 292730 260430 250870 142700 TRUE FALSE 294058.7156 199453.9609 258290.2906 226144.0765 249379.6163 249961.3016 269785.0577 256939.3618 241841.2377 170659.3328 1.72307433 1.168725774 1.513484708 1.325119891 1.461271483 1.464679941 1.580839754 1.50556877 1.417099397 1 17.38075979 0.896808206 9.362481751 1.000000019 1.462189638 0.503546379 0.138408075 8.729705225 792.5413782 0.123070642 0.030791943 7.885118159 -0.896808206 0.462189619 INPPSSGGTSSS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 INPPSSGGTSSS(1)PIK;INPPSSGGTSS(0.029)S(0.971)PIK;INPPSSGGTSSS(1)PIK;INPPSSGGT(0.001)S(0.005)S(0.201)S(0.793)PIK;INPPSSGGT(0.001)S(0.003)S(0.134)S(0.862)PIK 290.77 6.95E-44 1622970000 1447150 927500 1176809 944600 1447250 1625360 1533770 1237140 1333450 791715 TRUE FALSE 1504284.599 1086790.91 1207477.609 1131439.061 1201246.962 1247894.773 1413549.1 1220558.162 1285459.395 946836.396 1.588748179 1.147812774 1.275275871 1.194967859 1.268695381 1.317962404 1.492918001 1.289090879 1.35763623 1 19.85275564 -1.012295719 4.487158762 0.99998822 1.318503923 0.380858925 0.124336306 7622114.518 1719955.331 881.615892 0.027788674 0.097208509 1.012295719 0.318515702 INPYMS(ph)SPCHIEMILTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 1 INPYMS(0.5)S(0.5)PCHIEMILTEK;INPY(0.001)MS(0.499)S(0.499)PCHIEMILTEK 199.89 1.01E-15 158210000 171323 165146 215130 172578 249510 256980 239810 216710 240340 182851 TRUE FALSE 178086.9643 193508.5408 220736.4645 206713.4133 207098.3793 197300.2896 221013.0656 213805.3569 231690.2103 218677.1526 0.81438304 0.884905161 1.009417134 0.945290401 0.947050832 0.902244644 1.010682017 0.977721515 1.059508081 1 17.73844297 5.93285175 0.720395832 0.983853409 4.42E-26 0.601842172 0.043328802 9.640186573 1.014773334 0.016138273 11.41164362 856745.3382 -5.93285175 -0.983853409 INPYMSSPCHIEMILTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INPYMSSPCHIEMILTEK 18 0 A0A087WXM6;J3QQT2;J3KRX5;A0A0A6YYL6;P18621;P18621-3;J3QLC8;A0A0A0MRF8;P18621-2 A0A087WXM6 RPL17;RPL17-C18orf32 60S ribosomal protein L17 0 ; 221.41 6.25E-19 661040000 244507 574800 616140 562050 685940 840200 637860 686640 669530 616570 FALSE TRUE 254160.3252 673517.4287 632197.1146 673221.8124 569344.1638 645076.2834 587862.8665 677436.7139 645433.7461 737375.0866 0.34468255 0.913398677 0.857361641 0.912997774 0.772122864 0.874827879 0.797237223 0.918713863 0.875312657 1 19.49203915 4.741235763 24.99665831 0.872819664 0.344682361 0.872510782 0.061354553 75.03108262 701054.7178 0.013494572 0.093048925 55110.67911 -4.741235763 -0.528137303 INQEDSVPLISDAVENMDSTLHYIHSDSDLS(ph)NNSSFSPDEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INQEDSVPLISDAVENMDSTLHYIHSDSDLSNNSSFSPDEERR 43 1 Q8TF05-2;Q8TF05 Q8TF05-2 PPP4R1 Serine/threonine-protein phosphatase 4 regulatory subunit 1 1 INQEDSVPLISDAVENMDSTLHYIHS(0.001)DS(0.015)DLS(0.266)NNS(0.266)S(0.266)FS(0.188)PDEERR 106.33 2.18E-06 23297000 6179.7 11377 11181 11271 12180 15096 8958.3 10809 10544 11085 TRUE FALSE 6423.679328 13330.91125 11472.38605 13500.37016 10109.64795 11590.18278 8256.125038 10664.12303 10164.5235 13256.89351 0.48455389 1.005583339 0.865390224 1.018366041 0.762595546 0.874275921 0.622779766 0.804420962 0.766734943 1 13.69445513 INQEDSVPLISDAVENMDSTLHYIHSDSDLSNNSSFS(ph)PDEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INQEDSVPLISDAVENMDSTLHYIHSDSDLSNNSSFSPDEERR 43 1 Q8TF05-2;Q8TF05 Q8TF05-2 PPP4R1 Serine/threonine-protein phosphatase 4 regulatory subunit 1 1 INQEDSVPLISDAVENMDSTLHYIHSDS(0.001)DLS(0.134)NNS(0.134)S(0.134)FS(0.596)PDEERR 151.63 3.34E-14 16907000 4381.5 8620.6 8779 9678.1 8438.7 10403 9082.7 9414.9 8255 11895 TRUE FALSE 4554.485003 10101.12099 9007.787952 11592.39929 7004.292788 7987.060909 8370.774241 9288.708665 7957.904163 14225.59751 0.320161245 0.710066553 0.633209814 0.81489718 0.492372485 0.561456973 0.588430415 0.652957365 0.559407375 1 13.79620163 -1.98088292 2.537266542 1.35456067 0.603497784 0.48749856 0.124876944 24996200.33 11270502.75 51956724.06 0.029377963 0.010450019 1.98088292 -0.751062886 INRLS(ph)TPIAGLDNINVFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INRLSTPIAGLDNINVFLK 19 1 Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 Q8WWI1-3 LMO7 LIM domain only protein 7 1 INRLS(0.952)T(0.048)PIAGLDNINVFLK;INRLS(0.941)T(0.059)PIAGLDNINVFLK 234.21 2.39E-24 812230000 965410 874210 1143960 1045850 1444410 1472260 1318300 1177880 1269030 1099070 TRUE FALSE 1003525.132 1024348.767 1173772.537 1252716.008 1198889.704 1130349.927 1214968.201 1162092.445 1223357.858 1314411.724 0.763478531 0.779321082 0.893002182 0.953062108 0.912111238 0.859966407 0.924343704 0.884116008 0.930726527 1 20.32598582 4.222377444 3.926600157 0.914482565 0.766516985 0.730439906 0.036197397 0.099104341 3.325930985 0.008664118 0.023096159 16686.96842 -4.222377444 -0.14796558 INS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.354)S(0.354)PNVNT(0.09)T(0.09)AS(0.112)GVEDLNIIQVTIPDDDNER 89.024 0.0003795 67523000 40598 40458 40207 42463 46107 53398 44390 41635 44148 45182 TRUE FALSE 42200.84039 47406.34678 41254.82745 50862.05466 38269.74861 40997.12375 40910.59581 41076.95093 42559.1221 54034.54784 0.780997382 0.877334015 0.763489825 0.941287689 0.70824593 0.758720585 0.75711924 0.760197921 0.787627986 1 15.72159449 4.220600511 24.97899446 0.795816522 0.829165767 0 0.089675015 1031.780202 1435008.676 0.021031645 0.045581932 16618.83253 -4.220600511 0.033349245 INSS(ph)PNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 INS(0.238)S(0.383)PNVNT(0.146)T(0.146)AS(0.086)GVEDLNIIQVTIPDDDNER 81.967 0.00073874 79598000 27734 28451 30096 28697 27514 40461 27440 28409 31100 26533 TRUE FALSE 28828.95974 33337.23793 30880.32648 34373.18095 22837.18011 31064.54594 25289.1811 28028.22382 29980.71708 31731.63335 0.908524293 1.050599494 0.973171666 1.083246506 0.719697592 0.978977212 0.79697067 0.883289666 0.944821111 1 14.95363416 3.265668201 24.99999949 0.87972376 1.005028325 0.288635563 0.089189266 246.9166639 227717.4986 0.022678258 0.030698743 1843.606375 -3.265668201 0.125304565 INSTATPDQDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INSTATPDQDRDK 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 115.09 0.00063062 320040000 195690 107190 146640 119220 179760 204950 184650 151400 163960 90736 FALSE TRUE 203415.9923 125599.0487 150461.5589 142801.3602 149204.4594 157353.4685 170176.6505 149370.7306 158059.1116 108513.982 1.874560205 1.157445763 1.386563797 1.315971984 1.37497912 1.450075518 1.568246298 1.376511376 1.456578302 1 16.72752142 -1.046004195 4.82259506 0.999991485 1.426707809 0.355129125 0.177091717 1.86E-05 3.68E-06 0.156423256 0.036868391 0.089948889 1.046004195 0.426716324 INVYYNEAAGNKYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 INVYYNEAAGNKYVPR 16 1 Q13885 Q13885 TUBB2A Tubulin beta-2A chain 0 106.6 0.002375 0 121090 74825 84995 61180 115590 123270 79247 73585 80960 86501 FALSE TRUE 125870.7267 87675.61169 87210.03952 73281.2214 95942.05309 94642.41067 73035.41307 72598.71344 78046.26541 103449.2148 1.216739315 0.847523221 0.843022731 0.708378711 0.927431429 0.914868333 0.706002585 0.701781194 0.754440385 1 16.65856317 4.786266939 2.703022917 0.801455501 1.328166271 0.579475392 0.099980158 0.395370564 3.454943603 0.025303837 0.490321337 61131.76558 -4.786266939 0.52671077 INVYYNEATGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 ; 246.08 3.79E-16 605120000 668320 616460 616130 539460 795810 828140 778180 648310 708400 531540 FALSE TRUE 694705.7897 722332.2096 632186.854 646163.5779 660538.5005 635817.0356 717184.2182 639620.4649 682904.8224 635685.0861 1.092845821 1.136305107 0.99449691 1.016483778 1.039097054 1.000207571 1.128206771 1.006190768 1.074281649 1 19.27795272 4.246734326 24.99914374 1.034682298 1.114575482 0.39597354 0.040531442 171.2561744 523772.3134 0.009372293 0.024743509 17649.578 -4.246734326 0.079893184 INYTEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 117.4 0.01219 2397980000 1105650 1682860 1405550 1541230 1481470 1808220 1399630 1586340 1401800 1828180 FALSE TRUE 1149301.916 1971878.114 1442179.788 1846080.694 1229650.259 1388288.309 1289923.343 1565077.707 1351349.492 2186376.868 0.525665055 0.901893055 0.659620859 0.844356122 0.562414594 0.634972099 0.589982158 0.715831625 0.618077108 1 21.06011067 -1.877258772 5.592843858 1.06611862 0.67878464 0.426295327 0.113758265 0.061249901 0.001344197 0.071933829 0.024240194 0.013266038 1.877258772 -0.387333979 IPDEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPDEELR 7 0 Q99961-3;Q99961-2;Q99961;Q99962 Q99961-3 SH3GL1;SH3GL2 Endophilin-A2;Endophilin-A1 0 ; 117.16 0.012315 747170000 440820 449740 469330 444580 508440 550310 450910 424210 404760 457110 FALSE TRUE 458223.914 526979.3465 481561.1254 532516.5971 422015.5504 422508.8425 415566.496 418524.1588 390192.7667 546671.9526 0.838206372 0.963977288 0.88089598 0.974106307 0.771972201 0.772874556 0.760175264 0.765585571 0.713760354 1 19.06031583 3.225084121 24.99065781 0.780918393 0.915459364 0.319838678 0.081408342 214.7007693 398137.9365 0.021448317 0.025768487 1679.129226 -3.225084121 0.13454097 IPDEINDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPDEINDR 8 0 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 ; 107.57 0.014236 0 114394 167767 159498 172169 171749 194488 166252 180951 142740 206716 FALSE TRUE 118910.3635 196579.6772 163654.6489 206223.5143 142555.1663 149321.1095 153220.7338 178525.6478 137602.8153 247218.0424 0.480993872 0.795167195 0.661985053 0.834176633 0.576637388 0.604005711 0.619779739 0.722138425 0.556605068 1 17.91542451 -1.945824902 2.67738609 1.243377849 0.660040414 0.505440098 0.103400206 17962768.94 10638333.21 27273379.67 0.023131415 0.01132857 1.945824902 -0.583337436 IPDHDPAPNVTVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPDHDPAPNVTVLLR 15 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 148.03 3.61E-06 131760000 48227 58528 50356 63729 60416 67821 62503 59065 52689 55175 FALSE TRUE 50131.0392 68579.72872 51668.31873 76334.40599 50146.5099 52070.60059 57603.85154 58273.33029 50792.73318 65985.48486 0.759728284 1.039315372 0.783025522 1.156836328 0.75996274 0.789122042 0.87297762 0.883123469 0.769756156 1 16.00986108 IPDWFLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPDWFLNR 8 0 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ; 114.43 0.0061828 1351690000 1179460 1285050 1348910 1159300 2398400 1802910 1536930 1317430 1367030 2531500 FALSE TRUE 1226025.992 1505747.341 1384063.703 1388606.08 1990720.825 1384211.476 1416461.411 1299772.006 1317830.857 3027498.957 0.404963308 0.497356849 0.457164056 0.458664429 0.657546329 0.457212866 0.467865202 0.429322033 0.435286973 1 21.52969503 -1.910992934 4.050881209 1.228886818 0.474977599 0.851769811 0.065835829 0.035503076 0.000780083 0.01662953 0.015138469 0.012274592 1.910992934 -0.753909219 IPEINSSDMSAHVT(ph)SPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPEINSSDMSAHVTSPSGR 19 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 IPEINSSDMSAHVT(0.721)S(0.279)PS(0.001)GR 146.1 1.33E-06 122200000 63609 122130 111650 119200 116240 145060 115980 124510 116180 110650 TRUE FALSE 66120.33244 143104.8775 114559.6907 142777.4042 96481.56632 111372.0134 106889.1845 122841.1471 111998.7045 132329.749 0.499663401 1.08142635 0.865713807 1.078951674 0.729099594 0.841624913 0.807748714 0.928295777 0.846360742 1 17.0137779 -4.999998826 0.015135332 2.011438891 0.000551035 0.078626723 0.157980172 20584.35855 23.63295044 1968.953485 1247.218157 1.00E-05 4.999998826 -2.010887856 IPEINSSDMSAHVTS(ph)PSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPEINSSDMSAHVTSPSGR 19 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 IPEINSSDMSAHVT(0.065)S(0.933)PS(0.002)GR;IPEINSSDMSAHVT(0.035)S(0.965)PSGR 212.94 3.78E-17 1053030000 183605 298984 250156 294734 280215 357091 290244 287760 256054 316475 TRUE FALSE 190853.8672 350332.1762 256675.2709 353031.5055 232584.1544 274162.027 267493.9169 283903.0479 246838.6666 378482.217 0.504261121 0.925623875 0.678169962 0.932755859 0.614518051 0.724372282 0.706754254 0.750109345 0.652180355 1 18.52986599 -2.334297993 2.286957901 2.570742605 0.729918892 0.311367867 0.123846001 3441322.009 523755.1072 27996974.44 0.026754956 0.00463129 2.334297993 -1.840823713 IPGEETDTIQHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPGEETDTIQHMR 13 0 P50416;P50416-2 P50416 CPT1A "Carnitine O-palmitoyltransferase 1, liver isoform" 0 179.02 1.41E-05 243990000 49912 77942 70342 97817 73545 103740 76727 72159 70882 120050 FALSE TRUE 51882.5643 91327.9322 72175.17031 117164.9106 61043.84717 79647.95719 70712.93725 71191.82663 68330.97067 143571.499 0.361370917 0.636114639 0.502712382 0.816073604 0.425180816 0.554761619 0.49252768 0.495863226 0.475936876 1 17.13140986 -1.632040913 2.909734563 1.039616978 0.533192164 0.588501088 0.118120031 36674114.75 37941251.46 11020860.75 0.027641875 0.023332382 1.632040913 -0.506424814 IPGGNIYIS(ph)PLKSPYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPGGNIYISPLKSPYK 16 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 IPGGNIYIS(0.999)PLKS(0.001)PYK 97.457 0.0018573 335820000 421160 269700 386970 237810 453610 491880 525340 388570 467000 193780 TRUE FALSE 437787.722 316018.877 397054.7561 284848.1082 376505.5342 377648.3245 484162.4781 383361.8547 450192.7612 231747.4809 1.889072194 1.363634573 1.713307755 1.229131411 1.624637009 1.629568197 2.089181191 1.654222317 1.942600453 1 17.82219413 2.672432775 3.481826988 1.740575565 1.540417559 0 0.317729152 0.64342323 15.46300696 0.098876263 0.09456153 470.3625919 -2.672432775 -0.200158005 IPGLLS(ph)PHPLLQLSYTATDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPGLLSPHPLLQLSYTATDR 20 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 IPGLLS(1)PHPLLQLSYTATDR;IPGLLS(1)PHPLLQLSYTATDR 180.66 3.47E-17 460910000 94907 111299 124040 123052 140611 148579 118281 108413 114961 105872 TRUE FALSE 98654.00164 130413.7375 127272.5843 147391.3183 116709.9924 114073.779 109009.8262 106959.9011 110823.5761 126615.5914 0.77916156 1.02999746 1.005188879 1.164085061 0.921766357 0.900945751 0.860951049 0.844760901 0.875275903 1 16.95009554 3.013231142 24.99659146 0.883592064 1.003521045 0.181738973 0.096313735 321.465359 607315.5202 0.027619574 0.032994959 1030.934662 -3.013231142 0.119928981 IPGLLSPHPLLQLSYTATDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 231.42 1.01E-25 28582480000 1323976 2497947 2459621 2837724 2571138 3229443 2352342 2374717 2264776 2489641 FALSE TRUE 1376247.595 2926949.966 2523720.744 3399017.337 2134096.881 2479453.806 2167959.287 2342887.803 2183267.154 2977438.487 0.462225366 0.983042968 0.847614738 1.14159112 0.716755994 0.832747282 0.728128993 0.786880338 0.73327028 1 21.50564027 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 194.52 2.05E-18 4786950000 2341000 2006990 2387550 1800380 2643640 2682510 2305510 2262350 2281640 1948630 TRUE FALSE 2433424.488 2351674.92 2449771.514 2156489.79 2194275.017 2059537.706 2124798.102 2232026.899 2199524.222 2330426.74 1.044196947 1.009117721 1.051211554 0.925362619 0.941576485 0.883759902 0.911763526 0.957776042 0.94382895 1 21.15216273 3.734849229 24.99328529 0.933831703 1.032269641 0.681111612 0.030355372 171.3361029 1153815.316 0.007887571 0.012774121 5430.61768 -3.734849229 0.098437938 IPIFSAAGLPHNEIAAQICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPIFSAAGLPHNEIAAQICR 20 0 P21281;P15313;C9JL73;C9JNS9 P21281;P15313 ATP6V1B2;ATP6V1B1 "V-type proton ATPase subunit B, brain isoform;V-type proton ATPase subunit B, kidney isoform" 0 ; 191.95 1.27E-17 530100000 198444 233148 229129 223654 217662 267516 209286 203716 199492 238608 FALSE TRUE 206278.7224 273189.3554 235100.29 267892.0937 180663.891 205389.4632 192881.6165 200985.5202 192312.3219 285358.6692 0.722875261 0.957354322 0.823876459 0.938790801 0.633111626 0.719758975 0.675926955 0.704325966 0.673931941 1 18.12241687 3.240277606 24.99998703 0.714346851 0.864994379 0.219114943 0.112827698 53.55307917 779741.9714 0.028873621 0.037152327 1738.912005 -3.240277606 0.150647528 IPIHNEDITYDELVLMMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPIHNEDITYDELVLMMQR 19 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 204.29 4.65E-16 506390000 164551 246300 247580 236720 243740 302380 222222 248860 246151 265510 FALSE TRUE 171047.6005 288600.1091 254032.1382 283542.5095 202309.1619 232156.8276 204803.659 245524.4388 237292.0736 317531.601 0.538678985 0.908886259 0.800021596 0.892958397 0.637130797 0.731129837 0.644986698 0.773228359 0.74730223 1 18.27654065 0.165274106 2.051208606 1.000008263 0.746633986 0.338301376 0.108213734 42.00290265 100.498137 0.099711468 0.027225501 1.463100321 -0.165274106 -0.253374277 IPLNLDGPHPS(ph)PPTPDSVGQLHIMDYNETHHEHS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPLNLDGPHPSPPTPDSVGQLHIMDYNETHHEHS 34 0 A0A2R8YFV7;A0A2R8Y5N2;A0A2R8Y5S3;Q92574-2;Q92574;A0A2R8Y6S1 A0A2R8YFV7 TSC1 Hamartin 1 IPLNLDGPHPS(0.965)PPT(0.035)PDSVGQLHIMDYNETHHEHS;IPLNLDGPHPS(0.973)PPT(0.027)PDSVGQLHIMDYNETHHEHS 195.07 9.61E-22 409420000 100533 162891 166266 168390 175329 209835 144339 161020 168186 187447 TRUE FALSE 104502.1205 190866.2621 170599.0285 201697.0394 145526.6392 161104.0013 133025.332 158861.7903 162133.0187 224173.6508 0.466165939 0.851421483 0.761012849 0.899735713 0.649169243 0.718657169 0.593403068 0.708655053 0.723247439 1 17.77425719 -2.009251809 1.707812078 1.297983419 0.712670227 0.360597308 0.116519349 338449.6988 93569.57903 395991.7144 0.030252762 0.009789222 2.009251809 -0.585313192 IPMPPS(ph)SPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.581)S(0.419)PQPR;IPMPPS(0.673)S(0.327)PQPR;IPMPPS(0.5)S(0.5)PQPR 106.67 0.0024133 541830000 421070 575530 558110 545770 643540 709120 513900 569500 560390 659340 TRUE FALSE 437694.1687 674372.8005 572654.8051 653721.677 534151.3007 544437.6268 473619.1752 561866.784 540221.6734 788525.0492 0.5550796 0.855233199 0.726235401 0.82904364 0.677405621 0.690450642 0.600639353 0.712554135 0.68510401 1 19.58879706 -1.930078196 5.3715933 1.123342706 0.707109713 0.518694418 0.085613717 0.051932935 0.000676009 0.034041646 0.018742953 0.01174686 1.930078196 -0.416232993 IPMPPSS(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IPMPPSSPQPR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 IPMPPS(0.208)S(0.792)PQPR;IPMPPS(0.003)S(0.997)PQPR;IPMPPS(0.102)S(0.898)PQPR 149.23 3.61E-05 2015280000 549400 757690 672200 654710 772870 890270 603330 694020 617880 841140 TRUE FALSE 571090.7362 887817.3635 689718.0842 784209.6839 641497.8335 683518.2847 556039.4181 684717.7971 595642.6195 1005945.278 0.567715509 0.882570238 0.685641753 0.779574894 0.637706491 0.679478595 0.552753147 0.680671018 0.592122288 1 19.9401204 -0.983140177 4.727008656 1.000003598 0.676957807 0.518979456 0.094340182 0.037350029 57661576.61 680.6452932 0.021421704 0.103958457 0.983140177 -0.323045792 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 IPMTPTSSFVSPPPPT(0.327)AS(0.662)PHS(0.01)NR;IPMTPTSSFVSPPPPT(0.351)AS(0.599)PHS(0.05)NR;IPMTPTSSFVSPPPPT(0.025)AS(0.878)PHS(0.097)NR;IPMTPTSSFVSPPPPT(0.184)AS(0.772)PHS(0.044)NR 128.06 2.82E-05 2943380000 319357 310326 290060 344615 321911 416597 343054 342598 284181 257567 TRUE FALSE 331965.461 363622.0765 297619.2019 412778.8184 267192.6832 319848.6603 316164.5311 338006.0342 273953.3813 308032.3222 1.077696842 1.180467276 0.966194715 1.340050341 0.867417683 1.038360708 1.026400505 1.097307035 0.889365698 1 18.23272222 3.216219407 24.99998924 1.003535697 1.131420912 0.318540144 0.108729921 320.7943481 358970.4331 0.02996591 0.035840371 1645.202677 -3.216219407 0.127885215 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR 32 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105 Q01105-2;Q01105 SET Protein SET 0 ;; 379.58 6.83E-149 7895730000 1034997 1272271 1339166 1467843 1601199 1657534 1606716 1324087 1456812 1507049 FALSE TRUE 1075859.481 1490773.647 1374065.766 1758177.964 1329027.766 1272596.849 1480777.402 1306339.78 1404381.621 1802326.397 0.596928216 0.827138552 0.762384532 0.975504751 0.737395717 0.706085674 0.821592251 0.72480755 0.779204934 1 20.78142887 -1.536251101 2.342481596 1.018544954 0.773501174 0.356813276 0.092492599 2131340.712 1783850.899 248777.6157 0.023177029 0.029090347 1.536251101 -0.24504378 IPNSYEVLFPES(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IPNSYEVLFPESPAR 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR;IPNSYEVLFPES(1)PAR 137.61 1.64E-05 200024000 106247 132671 106289 110551 140684 143449 110267 115003 126667 157731 TRUE FALSE 110441.7136 155456.2122 109058.9787 132417.6578 116770.5839 110135.1437 101623.9844 113461.5729 122108.2794 188635.3695 0.58547723 0.824109564 0.57814703 0.701976825 0.619028045 0.583852032 0.538732395 0.601486207 0.647324411 1 17.52524068 0.932834171 18.89565871 1 0.628372916 0.675676589 0.076759889 792.31239 222901.63 0.073788626 0.018447157 8.567106609 -0.932834171 -0.371627085 IPNYQLS(ph)PTKLPSINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPNYQLSPTKLPSINK 16 1 O60934;A0A0C4DG07 O60934 NBN Nibrin 1 IPNYQLS(0.846)PT(0.154)KLPSINK 202.95 1.76E-11 1096500000 3283500 1493600 2287900 1631600 3029300 3008200 3152700 2260100 2777700 1305500 TRUE FALSE 3413135.115 1750114.181 2347524.554 1954325.61 2514380.668 2309591.14 2905583.136 2229807.056 2677731.12 1561287.73 2.186102568 1.120942763 1.503582273 1.251739556 1.610453102 1.479286038 1.861017083 1.428184577 1.715078565 1 20.57430501 -1.182165771 4.671781767 0.999916908 1.549920844 0.259982318 0.287635153 0.000226444 3.96E-05 0.253342494 0.059704426 0.065740686 1.182165771 0.550003935 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IPPNATLVFEVELFEFKGEDLTEEEDGGIIRR 32 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 284.08 3.83E-74 1579425000 428878.7 307024.9 447764.7 297048 606334 578861 499423 430240.8 528821.7 321425.5 FALSE TRUE 445811.1622 359754.0383 459433.8159 355803.2078 503269.5633 444429.3055 460276.9203 424474.1258 509789.5103 384402.6727 1.159750423 0.935878088 1.195188922 0.925600244 1.309224933 1.156155607 1.197382206 1.10424343 1.326186176 1 18.55225884 3.23790144 24.99999896 1.181473374 1.055737165 0.221172242 0.117737345 26.05619837 988231.0145 0.030597641 0.038722532 1729.423835 -3.23790144 -0.12573621 IPPYHYIHVLDQNSNVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPPYHYIHVLDQNSNVSR 18 0 Q14764;H3BQK6;H3BP76;H3BRL2;H3BNF6;H3BUK7;H3BQE7;H3BUP3;H3BNF2;H3BPZ2 Q14764 MVP Major vault protein 0 221.49 3.59E-19 616140000 489740 325110 421470 315050 528250 536410 462390 440180 424060 371850 FALSE TRUE 509075.3134 380945.1135 432453.8544 377365.9497 438458.2537 411836.9069 426146.6636 434280.1071 408798.1634 444706.888 1.144743486 0.856620673 0.972446945 0.848572307 0.98594887 0.926086188 0.95826414 0.976553588 0.919253051 1 18.76249522 2.011037095 24.06250483 0.963850015 0.947966439 0 0.079323544 1112.58514 2425585.259 0.027829137 0.020531187 102.5739535 -2.011037095 -0.015883576 IPRPLS(ph)LIGSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPRPLSLIGSTLR 13 1 H7C0I3;A0A2R8YD85;Q96BY6-3;Q96BY6 H7C0I3 DOCK10 Dedicator of cytokinesis protein 10 1 IPRPLS(1)LIGSTLR;IPRPLS(1)LIGSTLR 137.91 3.35E-05 1083560000 358020 216490 235390 246680 338480 368920 284260 224010 264920 227440 TRUE FALSE 372154.9061 253670.4734 241524.4568 295472.5677 280945.2905 283243.921 261978.9584 221007.5124 255385.5809 272002.5134 1.368203924 0.932603417 0.887949357 1.086286167 1.032877553 1.041328323 0.963149035 0.812520111 0.938908901 1 18.05326046 2.068819002 4.038645769 0.894278606 1.044368447 0.19127014 0.12804681 0.332845578 10.79205668 0.05163552 0.035621514 117.1706939 -2.068819002 0.15008984 IPRPLS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPRPLSPTK 9 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 IPRPLS(0.828)PT(0.172)K;IPRPLS(0.954)PT(0.046)K 75.683 0.022751 936900000 1249960 1231950 1079000 865550 1970630 1785750 1307680 1166770 1197600 1682030 TRUE FALSE 1299309.386 1443527.829 1107119.626 1036753.207 1635663.016 1371036.626 1205180.625 1151131.357 1154498.61 2011591.574 0.64591113 0.71760483 0.550369986 0.515389515 0.813118845 0.681568089 0.599117952 0.572249045 0.57392297 1 20.93990598 -1.529052409 6.001166084 1.000554725 0.628197441 0.634287196 0.084294784 0.00064516 5.06E-05 0.084166292 0.019809801 0.029576555 1.529052409 -0.372357284 IPRPSVSQGCS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPRPSVSQGCSR 12 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4M5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 IPRPSVS(0.008)QGCS(0.992)R 56.959 0.070618 294890000 114490 123670 123050 126590 140920 157910 125160 135910 138570 111520 TRUE FALSE 119010.1536 144909.3605 126256.7841 151629.1242 116966.4687 121237.7956 115349.6322 134088.3488 133582.8928 133370.2088 0.892329364 1.086519709 0.946664065 1.136904002 0.877005965 0.90903206 0.864883044 1.00538456 1.001594689 1 17.02507692 5.052407847 14.62287292 0.976200826 0.402648607 0.092045906 0.082264232 1155305.642 9179103.668 0.019587173 18506307.45 112825.6507 -5.052407847 -0.573552218 IPS(ph)PIGFTPGPQQLLGDPFQGMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPSPIGFTPGPQQLLGDPFQGMR 23 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 IPS(0.999)PIGFT(0.001)PGPQQLLGDPFQGMR;IPS(1)PIGFTPGPQQLLGDPFQGMR 145.77 8.74E-08 911420000 386910 407750 433880 427380 457780 548160 408970 484530 437990 417230 TRUE FALSE 402185.5056 477777.8906 445187.2692 511914.4884 379966.7191 420858.1474 376913.8628 478035.6679 422226.8255 498978.2301 0.806018141 0.957512496 0.89219778 1.025925496 0.761489572 0.843439898 0.755371357 0.958029106 0.846182859 1 18.92861735 -1.665935546 2.735839892 1.015078979 0.876310976 0.171353598 0.084052409 21684229.64 19860835.97 2289337.214 0.02099123 0.021580647 1.665935546 -0.138768002 IPS(ph)PNILK ddPTM_MDA-MB-175_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 100.88 0.0060752 2955410000 4440760 3406251 3957920 3255341 5113480 5232260 4771920 4217030 4377590 3117465 TRUE FALSE 4616084.634 3991248.112 4061066.647 3899237.734 4244292.496 4017146.911 4397884.441 4160507.611 4220041.391 3728272.579 1.238129599 1.07053549 1.089262268 1.045856399 1.13840724 1.077482085 1.179603784 1.115934396 1.131902591 1 21.83007591 IPS(ph)TPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPSTPK 6 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 IPS(0.645)T(0.355)PK;IPS(0.5)T(0.5)PK 88.942 0.053213 485980000 2387800 1378190 1647950 1472470 2206100 2568100 1936960 1726470 1613650 1162430 TRUE FALSE 2482072.188 1614883.412 1690896.931 1763720.171 1831107.91 1971697.695 1785136.014 1703329.494 1555575.052 1390185.902 1.785424657 1.161631267 1.216309939 1.268693754 1.317167659 1.418297863 1.284098775 1.225253033 1.118969088 1 20.40684639 7.999999899 0.033264424 9.49E-10 3.212336911 0.407830681 0.154193473 1261.375745 3.209633579 93.9844246 251.1609777 99999976.74 -7.999999899 3.21233691 IPSIVS(ph)SPLNSPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.554)S(0.446)PLNSPLDR 110.77 0.00093851 29388000 26054 28763 22468 24409 29219 28016 28671 31751 25974 22529 TRUE FALSE 27082.63204 33702.8215 23053.53454 29237.02735 24252.36482 21509.70859 26423.6921 31325.42978 25039.20081 26943.12621 1.005177789 1.250887564 0.855636958 1.085138641 0.900131805 0.798337521 0.98072109 1.162650152 0.929335394 1 14.71762964 4.238120286 24.9999999 0.976572329 1.128032645 0.240964826 0.114730941 17.24250824 979228.6229 0.029632359 0.070949903 17302.95532 -4.238120286 0.151460316 IPSIVSS(ph)PLNSPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 IPSIVS(0.163)S(0.837)PLNSPLDR 122.93 0.00011104 70815000 77154 72790 73979 81578 79345 89951 77770 82659 74432 86907 TRUE FALSE 80200.0995 85291.11627 75906.95351 97713.88491 65857.96524 69061.24347 71674.18419 81551.09131 71753.20686 103934.7627 0.771638838 0.820621648 0.730332677 0.940146322 0.633647141 0.664467226 0.689607426 0.784637297 0.690367736 1 16.66531874 -1.172675522 3.666253992 1.000229318 0.748933842 0.446552709 0.08438771 30679542.4 55522308 84744.52373 0.020268214 0.067193069 1.172675522 -0.251295476 IPSKEEEADMS(ph)SPTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.492)S(0.492)PT(0.016)QR;IPSKEEEADMS(0.499)S(0.499)PT(0.002)QR;IPSKEEEADMS(0.588)S(0.402)PT(0.01)QR 110.38 0.00054459 2388650000 1825670 1419180 1817560 1422440 2326300 2410640 2234810 1951230 2146780 1674960 TRUE FALSE 1897748.861 1662913.125 1864927.107 1703794.386 1930876.357 1850805.394 2059639.753 1925076.953 2069517.807 2003136.343 0.947388763 0.830154738 0.93100358 0.850563364 0.963926576 0.923953779 1.028207471 0.961031415 1.033138765 1 20.93382919 2.680287509 1.220636383 1.001113624 0.889082322 0.556697273 0.042657004 0.316389833 0.969222962 0.01902729 0.016828832 478.9470567 -2.680287509 -0.112031302 IPSKEEEADMSS(ph)PTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 IPSKEEEADMSSPTQR 16 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 IPSKEEEADMS(0.001)S(0.991)PT(0.007)QR;IPSKEEEADMS(0.002)S(0.998)PTQR;IPSKEEEADMS(0.076)S(0.898)PT(0.025)QR;IPSKEEEADMS(0.051)S(0.949)PTQR;IPSKEEEADMS(0.04)S(0.959)PT(0.001)QR;IPSKEEEADMS(0.024)S(0.976)PTQR;IPSKEEEADMS(0.023)S(0.977)PTQR;IPSKEEEADMS(0.219)S(0.781)PTQR;IPSKEEEADMS(0.174)S(0.826)PT(0.001)QR;IPSKEEEADMS(0.008)S(0.982)PT(0.01)QR;IPSKEEEADMS(0.203)S(0.792)PT(0.004)QR;IPSKEEEADMS(0.026)S(0.974)PTQR;IPSKEEEADMS(0.203)S(0.792)PT(0.005)QR;IPSKEEEADMS(0.053)S(0.946)PT(0.001)QR 224.59 4.64E-15 30951350000 15709600 12482080 15263560 12181520 19796740 20010410 19157940 16160620 17893100 13489790 TRUE FALSE 16329827.14 14625780.14 15661340.91 14590988.3 16431697.21 15363295.54 17656290.6 15944013.32 17249130.83 16132856.07 1.012209312 0.906583439 0.970772989 0.904426856 1.018523759 0.952298556 1.094430554 0.988294525 1.069192631 1 23.94349853 2.667665323 1.612508561 1.031657548 0.950652021 0.340428955 0.047792991 0.390503914 2.036566314 0.018174996 0.016615915 465.2274406 -2.667665323 -0.081005527 IPTPVIHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IPTPVIHTK 9 0 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 ; 168.83 5.89E-05 1215000000 999950 865020 851640 879640 992880 1186230 1003060 790400 842400 767530 FALSE TRUE 1039428.798 1013580.456 873834.438 1053630.167 824110.6122 910746.06 924437.5362 779805.9808 812082.1886 917912.8083 1.132382933 1.104223023 0.951979785 1.147854303 0.897809253 0.992192343 1.007108222 0.849542542 0.88470515 1 19.80799759 3.68830184 0.530548522 0.910427354 1.155188837 0.423491647 0.075522976 1.447448056 0.658066599 0.051898052 0.196855874 4878.674464 -3.68830184 0.244761483 IPVEGPLS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.888)PS(0.112)R;IPVEGPLS(0.945)PS(0.055)R;IPVEGPLS(0.84)PS(0.16)R;IPVEGPLS(0.899)PS(0.101)R 132.69 0.00018597 951360000 413583 1332740 1078720 1354240 1052070 1475270 1082210 1143310 1005690 1422580 TRUE FALSE 429911.5762 1561627.728 1106832.329 1622104.63 873239.5172 1132660.9 997383.5524 1127985.8 969495.4134 1701307.314 0.252694838 0.917898674 0.650577541 0.953445986 0.513275591 0.665759144 0.58624538 0.663011197 0.569853198 1 20.69821233 -1.486059769 2.911856842 1.011014395 0.654337156 0.244919655 0.187653817 28035199.46 31999219.14 2488077.413 0.041050785 0.032654289 1.486059769 -0.356677239 IPVEGPLS(ph)PSRGDFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IPVEGPLSPSRGDFPK 16 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 IPVEGPLS(0.987)PS(0.013)RGDFPK;IPVEGPLS(0.996)PS(0.004)RGDFPK;IPVEGPLS(0.982)PS(0.018)RGDFPK;IPVEGPLS(0.966)PS(0.034)RGDFPK 172.5 2.76E-09 1511630000 1332920 1088850 1278460 928050 1672950 1633650 1263070 1300790 1418510 1139060 TRUE FALSE 1385544.711 1275851.517 1311777.718 1111615.52 1388582.557 1254259.546 1164067.273 1283355.038 1367458.102 1362236.998 1.017109881 0.936585571 0.962958516 0.816022118 1.019339923 0.920735193 0.854526249 0.942093805 1.003832743 1 20.37754629 1.274743449 5.617637083 1.002578296 0.929527626 0.172296238 0.059637625 0.272175078 21.22743503 0.042977807 0.014365167 18.82536688 -1.274743449 -0.073050671 IPVHPNDHVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IPVHPNDHVNK 11 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ;;;;; 148.28 2.02E-05 1982420000 2463680 2034040 2379430 2047260 2807980 3047860 2691920 2235060 2501400 2071830 FALSE TRUE 2560947.989 2383370.547 2441439.901 2452201.918 2330680.563 2340040.706 2480920.276 2205102.677 2411375.103 2477765.421 1.033571607 0.961903224 0.985339403 0.98968284 0.940638102 0.944415757 1.001273266 0.889956191 0.973205568 1 21.24060818 8 0.556204001 0.952494733 4.317693967 0.23666055 0.033271135 175.7325289 1.573708076 0.01512723 708.1792321 99999999.95 -8 3.365199234 IQALGLHLPDPPLES(ph)EDEDEEGATALNNHSSIPMDPEHVELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQALGLHLPDPPLESEDEDEEGATALNNHSSIPMDPEHVELVK 43 0 A0A2R8Y7W8;A0A2R8Y6W5;Q16626 A0A2R8Y7W8 MEA1 Male-enhanced antigen 1 1 IQALGLHLPDPPLES(0.957)EDEDEEGAT(0.042)ALNNHS(0.001)SIPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK;IQALGLHLPDPPLES(1)EDEDEEGATALNNHSSIPMDPEHVELVK 329.07 1.45E-133 1095220000 58110 192302 204028 212137 218321 284698 213308 255251 224250 218456 TRUE FALSE 60404.22767 225328.3726 209345.1373 254097.0654 181210.8744 218581.2041 196588.3616 251829.7779 216179.2863 261258.2706 0.231205035 0.862473644 0.801295732 0.972589556 0.693608183 0.836647979 0.752467515 0.963911218 0.827454326 1 17.99511718 4.739144396 24.67764775 0.85217546 0.231204806 0.800945424 0.09352477 16.03377512 677589.8455 0.020990629 0.124939678 54845.92886 -4.739144396 -0.620970654 IQALQQQADEAEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQALQQQADEAEDR 14 0 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;; 321.08 8.15E-56 1515450000 546360 633910 554350 569660 554170 740810 583310 561970 548780 572800 FALSE TRUE 567930.7147 742779.1114 568796.8164 682337.0477 459972.3813 568768.1046 537588.638 554437.7113 529029.515 685029.1931 0.829060601 1.084302857 0.830324929 0.996070028 0.671463911 0.830283016 0.784767486 0.809363626 0.772272949 1 19.38580595 3.259009351 24.99929114 0.801604332 0.938135934 0.252733741 0.103230659 285.6759532 349246.6113 0.025907916 0.035039571 1815.554755 -3.259009351 0.136531602 IQDFNDTFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IQDFNDTFYR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;;; 172.59 8.54E-06 377463000 427469 442555 478306 456742 555160 597000 518863 487748 470585 471736 FALSE TRUE 444345.8062 518560.3786 490771.0473 547084.2044 460794.1015 458355.7976 478193.1623 481210.5359 453648.7378 564163.6373 0.787618657 0.919166611 0.869909039 0.969726101 0.816773842 0.812451862 0.847614293 0.852962694 0.804108432 1 19.10575416 IQDPTEDAEAEDT(ph)PR ddPTM_MDA-MB-175_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 131.54 8.84E-05 0 112096 345270 255657 351934 192530 376180 203847 254315 216660 400900 TRUE FALSE 116521.6366 404567.4367 262319.6314 421545.4948 159803.8194 288817.8961 187868.9395 250906.3234 208862.4489 479448.6793 0.243032553 0.843818023 0.547127655 0.879229651 0.333307456 0.602395853 0.39184369 0.523322587 0.43563046 1 18.87101687 -1.053508519 4.830551711 1.000010672 0.541696512 0.342204705 0.193801334 2.38E-05 4.65E-06 0.173944844 0.040998096 0.088407983 1.053508519 -0.45831416 IQDRQEAIDWLLGLAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQDRQEAIDWLLGLAVR 17 1 Q9Y224;G3V4C6;H0YJB9 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ; 192.16 1.84E-10 156963000 161177 204192 206395 134938 247690 255930 148235 178565 201429 272360 FALSE TRUE 167540.3924 239260.3876 211773.8233 161628.3337 205587.7423 196494.1362 136615.9534 176171.6282 194179.6096 325723.7274 0.514363488 0.734550073 0.650163944 0.496212956 0.631172141 0.603253984 0.419422787 0.540862128 0.596148187 1 18.31328929 0.934310248 18.74098713 1.000000001 0.572435116 0.697393023 0.083853819 650.0916213 185469.6503 0.083899177 0.020974794 8.59627396 -0.934310248 -0.427564885 IQEELEHLNQASEEINQVELQLDEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQEELEHLNQASEEINQVELQLDEAR 26 0 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 0 ; 199.1 5.86E-25 25704000 9874.8 14506.4 15464.7 13689.9 16367.6 19005.4 16064.7 15229 13768.8 14891.3 FALSE TRUE 10264.66473 16997.76136 15867.72279 16397.72136 13585.4412 14591.68388 14805.50684 15024.88016 13273.26358 17808.96512 0.576376261 0.954449696 0.890996342 0.920756554 0.762842821 0.819344851 0.83135133 0.84366947 0.745313581 1 14.12031606 -1.623282927 4.541547967 1.003383768 0.826108157 0.22296934 0.10144864 0.003290414 0.000272937 0.092988745 0.021526188 0.02380768 1.623282927 -0.177275611 IQEHFNK ddPTM_MDA-MB-175_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 ; 92.47 0.015646 814950000 1046100 968280 1101420 1017760 1368090 1380750 1206380 1145270 1117750 1061550 FALSE TRUE 1087400.836 1134574.558 1130123.91 1219069.89 1135542.55 1060091.738 1111820.783 1129919.529 1077522.396 1269540.398 0.856531102 0.893689212 0.890183496 0.960245056 0.894451687 0.835020091 0.875766368 0.890022508 0.848749987 1 20.27587487 -1.542467668 6.162593021 1.000174803 0.884618719 0.538638047 0.032515135 8.03E-05 5.96E-06 0.032378298 0.00762014 0.028676909 1.542467668 -0.115556084 IQEQES(ph)S(ph)GEEDSDLSPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 IQEQES(1)S(1)GEEDSDLSPEER;IQEQES(1)S(1)GEEDSDLSPEER 221.99 3.71E-19 1341790000 482680 551780 534390 514230 578240 671170 547420 543630 546770 516380 TRUE FALSE 501736.5791 646543.9227 548316.6424 615943.1592 479950.9713 515300.9392 504511.79 536343.529 527091.8545 617554.7743 0.812456805 1.046941825 0.887883416 0.997390328 0.777179598 0.834421432 0.816950675 0.868495478 0.853514338 1 19.23620758 3.244422858 24.99781548 0.84921685 0.940631589 0.180201152 0.079567368 195.2922546 832761.4727 0.020337768 0.026824179 1755.589029 -3.244422858 0.091414739 IQEQESS(ph)GEEDSDLSPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQEQESSGEEDSDLSPEER 19 0 P41236;E7EMN6;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 IQEQES(0.188)S(0.812)GEEDSDLSPEER;IQEQES(0.064)S(0.936)GEEDSDLSPEER 272.64 2.46E-39 717190000 480930 546630 541390 542620 574350 676710 604970 571050 598200 498090 TRUE FALSE 499917.4878 640509.4503 555499.0682 649948.6164 476722.1922 519554.3581 557550.8706 563396.0088 576670.8989 595681.199 0.83923664 1.075255441 0.932544235 1.091101444 0.80029753 0.872202042 0.935988699 0.945801227 0.968086453 1 19.1841809 7.208477883 9.550613611 0.945300737 0.184539586 0 0.089177298 0 0 0.018850899 0 16161359.19 -7.208477883 -0.760761151 IQESEVFRVTS(ph)TEFISLRIDSSDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQESEVFRVTSTEFISLRIDSSDEDR 26 2 A0A0D9SGJ6;J3KQV8;O43426;J3KPK1;C9JFZ1;O43426-4;O43426-2;C9J1Z6;C9JW66;O43426-5 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 IQES(0.11)EVFRVT(0.11)S(0.226)T(0.226)EFIS(0.226)LRIDS(0.051)S(0.051)DEDR;IQES(0.044)EVFRVT(0.044)S(0.183)T(0.183)EFIS(0.183)LRIDS(0.183)S(0.183)DEDR 49.152 0.068591 993040000 156105 185538 171416 202565 214660 253710 180861 223934 201535 202145 TRUE FALSE 162268.1459 217402.7082 175883.2418 242631.7524 178172.1699 194789.6975 166684.6422 220932.531 194281.7947 241751.4425 0.671218936 0.899281948 0.727537507 1.003641384 0.737005612 0.805743683 0.689487684 0.91388299 0.803642753 1 17.88316497 0.364993855 0.894369198 1.000790541 0.805276679 0.250838111 0.100952193 3.254524212 3.402679656 0.098031261 0.029848971 2.317361859 -0.364993855 -0.195513862 IQEY(ph)IIAFAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IQEYIIAFAKEK 12 1 V9GZ60;P31513 V9GZ60 FMO3 Dimethylaniline monooxygenase [N-oxide-forming] 3 1 IQEY(1)IIAFAKEK;IQEY(1)IIAFAKEK;IQEY(1)IIAFAKEK;IQEY(1)IIAFAKEK 70.488 0.056454 7290690000 1072961 13933700 9305770 12781000 4275000 13134500 4838880 10056400 7985160 30807600 TRUE FALSE 1115322.329 16326704.59 9548286.011 15309043.65 3548337.027 10084211.43 4459595.942 9921610.407 7697775.651 36843759.37 0.030271676 0.443133515 0.259156128 0.415512529 0.096307681 0.273702022 0.121040741 0.269288764 0.208930244 1 25.13491694 -1.330282038 4.448847881 1.000795142 0.241517355 0.773152856 0.124229122 2712.450887 271566885.6 332987.0207 0.026799275 0.046743149 1.330282038 -0.759277787 IQFKPDDGISPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQFKPDDGISPER 13 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ; 128.76 0.00014731 971130000 1192810 964660 1083930 880730 1398640 1443050 1249090 1157190 1176430 903640 FALSE TRUE 1239903.06 1130332.851 1112178.106 1054935.765 1160899.672 1107923.507 1151183.062 1141679.761 1134090.514 1080690.957 1.14732436 1.045935329 1.029136127 0.976167848 1.074219845 1.025199203 1.065228736 1.056435009 1.049412422 1 20.04352259 4.73703964 4.495459968 1.038014287 1.154488948 0.582691259 0.028346315 0.139929421 7.21683059 0.006794248 0.051655717 54580.76769 -4.73703964 0.116474662 IQFKPDDGTTPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 ;; 106.32 0.0012613 1041100000 752530 610590 726050 584850 860340 888730 829800 733210 750790 577770 FALSE TRUE 782240.4655 715454.0828 744971.4595 700531.5844 714099.7141 682335.9263 764758.1077 723382.5192 723769.2146 690972.9694 1.13208548 1.035429915 1.078148484 1.013833558 1.033469825 0.987500172 1.106784406 1.046904222 1.047463861 1 19.39826975 6.836092503 1.466367991 1.040965161 46.05840429 0.39909215 0.033733211 739.6755286 4.178968431 0.008814254 111440.1817 6856342.479 -6.836092503 45.01743913 IQFTSLYHKEEAPAS(ph)PLRPLYPQIS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 2 IQFT(0.006)S(0.007)LYHKEEAPAS(0.985)PLRPLY(0.002)PQIS(1)PLK 96.126 0.0036757 378500000 71795 66340 86138 53716 122930 116430 97072 97232 111970 78959 TRUE FALSE 74629.52204 77733.37895 88382.82704 64340.86447 102034.4025 89390.89701 89463.24299 95928.76408 107940.2216 94429.50429 0.79031996 0.823189527 0.935966229 0.681363997 1.080535192 0.9466416 0.947407737 1.015877027 1.143077287 1 16.52695008 2.933648957 0.722110574 1.0473065 0.804552138 0.478720136 0.095040056 0.628331945 0.72663234 0.061139395 0.075772348 858.3194561 -2.933648957 -0.242754362 IQFTSLYHKEEAPAS(ph)PLRPLYPQISPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQFTSLYHKEEAPASPLRPLYPQISPLK 28 2 P85037;P85037-2;U3KQ26 P85037 FOXK1 Forkhead box protein K1 1 IQFTSLYHKEEAPAS(1)PLRPLYPQISPLK;IQFT(0.037)S(0.037)LY(0.02)HKEEAPAS(0.887)PLRPLY(0.016)PQIS(0.004)PLK 124.28 2.15E-05 3922800000 1340900 577720 871750 655000 1359680 1368270 1113150 1079970 995970 617830 TRUE FALSE 1393839.767 676938.916 894468.5212 784557.045 1128562.079 1050510.029 1025898.394 1065494.769 960125.2343 738881.9594 1.886417376 0.916166523 1.210570254 1.061816485 1.527391574 1.42175623 1.388446938 1.442036519 1.299429797 1 19.49498438 3.231099469 24.98231615 1.37939547 1.239403474 0.006208891 0.270835053 521.9106863 1747523.7 0.073216251 0.089156228 1702.548407 -3.231099469 -0.139991996 IQGDDWEPRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQGDDWEPRPLR 12 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 ; 115.34 0.00087557 1155350000 1010730 1037030 1024160 964690 1244590 1325610 1108650 1103210 1131910 1130620 FALSE TRUE 1050634.401 1215131.836 1050850.451 1155502.803 1033035.036 1017757.167 1021751.116 1088423.274 1091172.78 1352143.342 0.77701407 0.898670872 0.777173853 0.854571233 0.763998168 0.752699167 0.755652958 0.804961457 0.806994899 1 20.36681667 -1.982699765 7.432269468 1.149404442 0.799116844 0.652727035 0.0439653 0.025149036 5.85E-05 0.009836049 0.009971028 0.010406393 1.982699765 -0.350287598 IQHEELNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQHEELNNR 9 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 175.93 5.35E-05 702120000 460970 682290 582080 599210 619120 749030 521490 576350 559410 741230 FALSE TRUE 479169.4515 799468 597249.483 717731.9495 513882.2035 575079.1342 480614.2511 568624.971 539276.9434 886459.8268 0.540542771 0.901866025 0.673746813 0.809661 0.579701627 0.648736826 0.542172625 0.641455996 0.608348993 1 19.75769573 -1.030345479 4.569826933 1.000009259 0.663036368 0.465598958 0.109028163 1.041E+11 22090132464 14292578.4 0.025099378 0.09325122 1.030345479 -0.336972891 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IQHPSNVLHFFNAPLEVTEENFFEICDELGVK 32 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 215.71 5.23E-36 1473307000 65813.1 226299 247441 249813 276595 290019 231939 271658 271771 284265 FALSE TRUE 68411.45201 265164.0929 253889.5157 299225.2658 229579.4807 222666.4825 213759.0151 268016.8689 261990.0148 339961.2842 0.201233067 0.779983208 0.74681891 0.880174537 0.675310664 0.654976001 0.628774584 0.788374681 0.770646621 1 18.37501093 2.580222129 0.065556852 1.431495476 6.04E-19 0.361168864 0.159601152 64.79656992 1.918689425 17.39750345 23.60025701 380.3839023 -2.580222129 -1.431495476 IQHSITAQDHQPTPDSCIISMVVGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQHSITAQDHQPTPDSCIISMVVGQLK 27 0 P61970;H3BRV9 P61970 NUTF2 Nuclear transport factor 2 0 ; 188.69 4.73E-18 633380000 467710 438630 473150 417210 556970 627590 526840 497030 508920 471400 FALSE TRUE 486175.552 513961.2904 485480.6777 499732.8928 462296.4383 481841.7337 485544.9042 490368.1258 490604.0686 563761.8045 0.8623776 0.911663909 0.861145033 0.886425595 0.820020857 0.854690279 0.861258958 0.869814382 0.870232897 1 19.10472621 0.131545046 1.59166702 1.000053318 0.86593554 0.76960117 0.021942737 7.589604037 13.20366864 0.021876279 0.006065244 1.353770501 -0.131545046 -0.134117778 IQIGCHTDDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQIGCHTDDLTR 12 0 Q9Y4C2-2;Q9Y4C2 Q9Y4C2-2 TCAF1 TRPM8 channel-associated factor 1 0 ; 143.31 6.21E-05 244600000 207780 240830 226210 250530 302210 320230 246790 223890 231170 293680 FALSE TRUE 215983.3148 282190.6791 232105.2184 300084.0862 250840.4521 245861.4356 227445.9549 220889.1208 222850.2369 351220.9732 0.614949936 0.80345623 0.660852387 0.854402525 0.714195539 0.700019231 0.647586483 0.628917797 0.634501507 1 18.42201947 -0.991051519 4.88413225 1.00000359 0.695923473 0.601039662 0.074441336 2.96E-06 6.11E-07 0.073245503 0.017263927 0.102081838 0.991051519 -0.304080117 IQILEGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQILEGWK 8 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 138.1 0.0016748 1280970000 2764200 1608920 1586680 1355060 3233200 2767000 2587900 1703210 2008480 1999790 FALSE TRUE 2873332.75 1885239.494 1628030.184 1623086.824 2683621.819 2124406.184 2385053.636 1680381.256 1936195.197 2391610.562 1.201421668 0.788271939 0.680725453 0.678658494 1.122098163 0.888274294 0.997258364 0.702614917 0.809577959 1 21.18955106 -2.029564314 2.256571077 1.161358513 0.861587692 0.040526325 0.173780996 21573646.65 7355124.182 18008860.67 0.045504534 0.00934191 2.029564314 -0.299770821 IQLLCLMEMTFTRPANHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQLLCLMEMTFTRPANHR 18 1 Q9UNM6;A0A087WUL9;Q9UNM6-2;E9PL38 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ; 138.55 1.07E-06 174693000 42315 44461 43824 36784 46653 55573 46622 43245 42562 44048 FALSE TRUE 43985.62887 52096.83089 44966.08944 44059.76541 38722.93972 42667.01297 42967.64582 42665.37151 41030.20193 52678.36225 0.834984745 0.988960717 0.853596952 0.836392088 0.735082453 0.809953293 0.815660244 0.809922133 0.778881502 1 15.68492287 4.00864895 23.71724517 0.815749834 0.91429932 0.163383872 0.073602597 136.4559693 374176.9435 0.016680084 0.035925127 10201.14569 -4.00864895 0.098549486 IQLVEEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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 ;;;;;;;;;;; 292.82 8.50E-32 13814387000 3971716 4478775 4491291 4793819 4494634 5366437 5104690 4773395 4098792 4073407 FALSE TRUE 4128522.415 5247969.766 4608337.733 5742022.09 3730637.718 4120163.336 4704571.059 4709415.448 3951277.277 4871513.112 0.847482562 1.077277151 0.945976666 1.178693757 0.765806769 0.845766652 0.965730965 0.966725397 0.811098561 1 22.21593852 3.228036926 24.99999595 0.898934656 1.012253184 0.235621137 0.105360896 322.8537411 766967.7186 0.029773783 0.035943815 1690.584667 -3.228036926 0.113318528 IQLVEEELDRAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 256.37 2.37E-24 23085249000 3204293.4 3844586.6 3750761 2989304.4 4275709.7 4303337.5 2943568 3512437.2 3774835 4583046.7 FALSE TRUE 3330801.378 4504864.442 3848508.913 3580579.888 3548926.092 3303952.583 2712843.449 3465358.725 3638979.426 5481006.953 0.607698805 0.82190453 0.702153627 0.653270452 0.647495273 0.60280029 0.494953477 0.632248555 0.663925344 1 22.38600953 -1.829441939 6.112500937 1.032162602 0.645278523 0.647752341 0.077994902 0.033289576 0.000928884 0.073539792 0.019147981 0.014810102 1.829441939 -0.386884079 IQPAGNTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQPAGNTSPR 10 0 P49674;H0Y5S9;H0Y682 P49674 CSNK1E Casein kinase I isoform epsilon 1 IQPAGNT(0.057)S(0.943)PR;IQPAGNT(0.004)S(0.996)PR;IQPAGNT(0.115)S(0.885)PR 147.39 2.83E-05 2109160000 2349610 2573940 2551350 2493330 2799690 3006250 2466650 2587170 2467690 2523330 TRUE FALSE 2442374.417 3015994.173 2617840.277 2986503.232 2323799.694 2308093.998 2273307.528 2552493.218 2378878.319 3017728.201 0.809342079 0.999425386 0.867487097 0.989652823 0.770049368 0.764844891 0.753317521 0.845832708 0.788301053 1 21.52503144 3.227973482 24.9995205 0.808019976 0.91890248 0.229796704 0.084326615 249.8951384 590079.4739 0.022436525 0.027080206 1690.337716 -3.227973482 0.110882505 IQPFDDDEDEDIWEDSDTR ddPTM_MDA-MB-175_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 ;; 215 9.69E-19 302834000 198952 193495 228375 196631 249149 269405 227014 213714 218098 191775 FALSE TRUE 206806.7786 226726.2611 234326.6401 235524.0249 206798.742 206839.7716 209220.0495 210849.5134 210248.6956 229349.6395 0.90170963 0.988561663 1.021700495 1.026921278 0.901674589 0.901853485 0.912231866 0.919336581 0.916716922 1 17.80718911 3.227146509 24.99944533 0.919271952 0.987638671 0.322476227 0.041562211 220.781812 483560.8179 0.011854613 0.014287008 1687.12208 -3.227146509 0.06836672 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IQPQPPDEDGDHSDKEDEQPQVVVLK 26 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK 226.64 9.07E-35 2883067000 1553170 487085 797049 498053 1015310 1335050 1101400 765044 861150 382680 TRUE FALSE 1614490.351 570738.0598 817820.7517 596566.3969 842727.9689 1025004.87 1015069.39 754789.8365 830157.3797 457658.8191 3.527716026 1.247081966 1.786966005 1.303517756 1.841389117 2.239670312 2.217960952 1.649241323 1.813921954 1 18.80391296 -2.067608507 0.277736985 2.19E-19 2.010817493 0.197635928 0.602928793 59.59066033 2.419034385 39.51586953 0.71650886 0.008558379 2.067608507 2.010817493 IQQFDDGGS(ph)DEEDIWEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IQQFDDGGSDEEDIWEEK 18 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK 280.4 1.86E-39 880425000 2020720 1334550 1635740 1364190 2261830 2385100 2134460 1718710 1967350 1226190 TRUE FALSE 2100499.586 1563748.581 1678368.728 1634022.71 1877364.945 1831196.672 1967155.448 1695673.504 1896545.458 1466438.454 1.432381687 1.066358139 1.144520402 1.114279775 1.280220755 1.248737488 1.34145108 1.156320949 1.293300413 1 20.48388509 -1.656673852 6.629461011 0.998824657 1.2219391 0.293237205 0.106710777 0.001776675 9.20E-05 0.099025603 0.023225078 0.022045814 1.656673852 0.223114443 IQQFDDGGS(ph)DEEDIWEEKHIAFTPESQR ddPTM_MDA-MB-175_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 374.1 6.82E-128 1152590000 531495 704016 774076 362637 1200852 920500 296357 665984 753601 1413130 TRUE FALSE 552478.833 824925.2715 794249.0565 434365.5162 996731.606 706727.8253 273127.764 657057.5738 726479.0472 1690005.767 0.326909436 0.488119797 0.469968252 0.257020138 0.589780003 0.418180718 0.16161351 0.388790137 0.429867792 1 20.68859674 0.684395095 3.493519397 0.999992805 0.386703039 0.719025877 0.114244825 2.672177372 29.03259229 0.109613574 0.028266728 4.834984604 -0.684395095 -0.613289766 IQRPNTTQEGEEMETDMDVADVAMESS(ph)PGSSISMEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.092)S(0.908)PGSSISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.048)S(0.952)PGSSISMEHR;IQRPNTTQEGEEMETDMDVADVAMES(0.393)S(0.486)PGS(0.084)S(0.025)IS(0.012)MEHR 263.57 1.19E-62 374064000 111998 197946 201625 210073 199617 264166 181060 203238 198549 204748 TRUE FALSE 116419.7675 231941.6857 206879.5131 251624.8124 165686.1736 202817.45 166868.0441 200513.927 191403.2603 244864.4505 0.475445771 0.947224823 0.844873614 1.027608589 0.676644459 0.828284586 0.681471091 0.818877247 0.781670267 1 17.90162381 -0.87197974 4.245933121 1.000002549 0.795564933 0.160193232 0.145161699 36337396.33 79541266.01 1859.625662 0.032699219 0.13428276 0.87197974 -0.204437616 IQRPNTTQEGEEMETDMDVADVAMESSPGS(ph)SISMEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IQRPNTTQEGEEMETDMDVADVAMESSPGSSISMEHR 37 1 A0A087X1S3 A0A087X1S3 HUWE1 1 IQRPNTTQEGEEMETDMDVADVAMES(0.293)S(0.254)PGS(0.393)S(0.052)IS(0.008)MEHR 78.867 0.0026613 55848000 6107.1 9604.5 9226.2 8418.3 10093 8491.1 7607.9 10043 10634 10047 TRUE FALSE 6348.213024 11253.99816 9466.642351 10083.41461 8377.395465 6519.170709 7011.572918 9908.390012 10251.28442 12015.51729 0.528334559 0.936622027 0.787868065 0.839199376 0.697214715 0.542562634 0.583543159 0.824632829 0.85317046 1 13.55261114 1.130641493 1.919275411 0.989141177 0.715931608 0.349652455 0.126157125 0.374535216 2.613309128 0.122721016 0.035167354 13.50956896 -1.130641493 -0.273209569 IQRPPEDSIQPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IQRPPEDSIQPYEK 14 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0;C9JTZ5;C9JUW1 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;; 208.79 6.88E-09 1106220000 597428 506401 585390 486558 712060 701240 628240 559530 588339 458162 FALSE TRUE 621014.9188 593371.4325 600645.7443 582797.7202 591024.2955 538387.6374 578996.9072 552030.4156 567164.7943 547930.0719 1.133383529 1.082932774 1.096208759 1.063635216 1.07864913 0.982584576 1.05669854 1.007483334 1.035104338 1 19.06363226 4.360840202 0.367000875 1.005529986 1.190934216 0.710393176 0.024165352 2.425537808 0.32151645 0.021278398 0.195191033 22953.03939 -4.360840202 0.18540423 IQSQNDREK ddPTM_MDA-MB-175_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 ; 92.866 0.008925 67730000 51035 50082 57440 46587 94525 72663 46677 50182 65024 69389 FALSE TRUE 53049.90121 58683.19392 58936.93359 55801.76955 78457.67426 55788.11947 43018.33477 49509.39237 62683.79894 82984.44602 0.639275235 0.707158952 0.71021663 0.672436489 0.945450359 0.672272 0.518390335 0.596610507 0.755368047 1 16.34055333 0.975364961 20.72764157 1.000000006 0.679924818 0.458784304 0.103423788 214.1458628 180181.4482 0.107696768 0.026924192 9.44854555 -0.975364961 -0.320075188 IQSSLSSAS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 IQSSLSSAS(0.956)PS(0.044)K;IQSSLSSAS(0.977)PS(0.023)K 171.81 3.93E-05 167745000 411440 267050 326460 255400 398620 459900 427080 327500 357910 240960 TRUE FALSE 427683.9689 312913.7601 334967.8158 305917.3577 330862.7148 353095.1949 393604.3536 323110.3982 345028.889 288171.4985 1.48413001 1.085859503 1.162390512 1.061580896 1.148145172 1.225295342 1.365868435 1.121243426 1.197304004 1 18.13656813 0.386674874 1.439916393 1.000069794 1.199556934 0.199799963 0.123039738 6.643443172 13.85862542 0.113961933 0.033106575 2.43598648 -0.386674874 0.19948714 IQVHPYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IQVHPYK 7 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7;Q5T6H2 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 66.682 0.067212 349990000 513400 457620 533760 457080 637410 626970 613620 606080 606000 487720 FALSE TRUE 533669.4284 536212.6752 547670.2241 547489.0598 529063.2759 481365.7193 565522.861 597956.4889 584190.1784 583279.396 0.914946477 0.919306732 0.93895006 0.938639464 0.907049485 0.825274684 0.969557411 1.025163057 1.001561486 1 19.15382759 2.007662569 24.98258295 1.008118125 0.909636597 0.695189701 0.030569921 101.6996689 331573.932 0.012033131 0.008870961 101.7800287 -2.007662569 -0.098481529 IQVLQQQADDAEER ddPTM_MDA-MB-175_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 ;; 318.64 1.19E-55 719760000 481093 536339 480886 531834 534549 611520 525663 494724 472792 538651 FALSE TRUE 500086.9231 628451.0511 493418.2842 637029.1778 443686.5519 469503.7477 484460.1605 488093.034 455776.3083 644189.3504 0.776304239 0.97556883 0.765952253 0.988884988 0.688751765 0.728828795 0.752046212 0.757685661 0.70751916 1 19.29712528 3.224792094 24.99096135 0.757073056 0.875832313 0.180739931 0.105673113 314.8980735 571563.7965 0.02763024 0.03318508 1678.000531 -3.224792094 0.118759257 IQVLQQQADDAEERAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 263.15 2.01E-27 4323580000 892240 1295680 1164650 684740 1392980 1345880 643567 1046664 1146930 1902370 FALSE TRUE 927466.3242 1518202.961 1195001.736 820179.5283 1156201.757 1033319.767 593122.5369 1032635.181 1105652.213 2275102.978 0.407659052 0.667311755 0.525251713 0.360502156 0.508197549 0.454185932 0.260701402 0.453885029 0.485978975 1 21.11750042 0.676843724 3.672420134 0.999996683 0.453730981 0.722556039 0.100884992 3.566663048 39.98985982 0.100470943 0.025810684 4.751642127 -0.676843724 -0.546265702 IQVTPPGFQLVFLPFADDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IQVTPPGFQLVFLPFADDKR 20 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 183.54 6.95E-17 1372670000 1213600 889160 1125560 1018060 1326900 1493960 1575900 1249030 1213620 795910 FALSE TRUE 1261513.865 1041866.313 1154893.018 1219429.229 1101354.012 1147010.431 1452376.84 1232288.796 1169942.053 951853.3259 1.325323798 1.094566027 1.213309852 1.281110436 1.157062734 1.205028548 1.52584101 1.294620466 1.229120098 1 19.86037976 2.384609661 23.09672567 1.304941558 1.207906818 0 0.135003753 22.36996209 5570.416443 0.04433942 0.037097022 242.4430065 -2.384609661 -0.09703474 IQWIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IQWIDR 6 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 0 128.48 0.038633 190730000 166410 169860 193710 200520 205940 215780 179510 166150 175440 183100 FALSE TRUE 172979.9953 199032.1337 198758.2417 240182.2575 170934.3924 165668.3652 165439.5371 163923.031 169125.9487 218974.9393 0.789953388 0.908926539 0.907675747 1.096848152 0.780611667 0.756563129 0.755518132 0.748592654 0.772352988 1 17.74040624 3.10120583 24.84683642 0.781881111 0.925272721 0.25758298 0.099216922 12.64387685 3083.98321 0.027541093 0.032917901 1262.425707 -3.10120583 0.14339161 IQYQLVDISQDNALRDEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 IQYQLVDISQDNALRDEMR 19 1 Q5T123;Q9H299 Q5T123 SH3BGRL3 SH3 domain-binding glutamic acid-rich-like protein 3 0 ;;;;;;;; 308.02 1.73E-61 7075420000 2472150 2967370 3057197 2703057 3211793 3667776 2719631 3021635 3040328 3280113 FALSE TRUE 2569752.391 3476992.715 3136870.065 3237713.607 2665853.573 2815990.61 2506459.216 2981134.925 2930907.189 3922788.341 0.655083111 0.886357461 0.799653153 0.82536026 0.679581293 0.717854333 0.63894837 0.75995304 0.74714895 1 21.90344806 0.205329344 2.965866548 1.000000055 0.747059575 0.518832531 0.073499245 160.1024859 592.8737745 0.072000142 0.018829731 1.604461659 -0.205329344 -0.25294048 IRANS(ph)ISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRANSISR 8 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 IRANS(0.927)IS(0.073)R 85.958 0.009916 92550000 43055 38327 45227 31841 63547 59430 47000 47936 42330 60695 TRUE FALSE 44754.84465 44909.36411 46405.65277 38139.05476 52745.30364 45628.28317 43316.01719 47293.49633 40806.55157 72587.02317 0.616568123 0.618696871 0.639310592 0.52542525 0.726649218 0.628601108 0.59674602 0.651542029 0.562174198 1 16.14742403 -1.916607729 2.698842921 1.22563443 0.621105482 0.835969781 0.050696006 4534202.607 2813778.504 6474770.612 0.011585769 0.012116921 1.916607729 -0.604528948 IRCEEEDVEMSEDAYTVLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRCEEEDVEMSEDAYTVLTR 20 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 ; 186.06 3.11E-17 78059000 38735 50404 58176 40973 73714 76119 38324 54291 52075 70834 FALSE TRUE 40264.28771 59060.49491 59692.11435 49077.33711 61184.12061 58441.51584 35320.06474 53563.31795 50200.83092 84712.5661 0.475304781 0.697186942 0.704642972 0.579339517 0.722255545 0.689880127 0.416940088 0.632294834 0.592601939 1 16.37028837 -2.160485673 2.271182827 1.891851514 0.614744233 0.593311335 0.096283079 3659380.916 804471.4328 16806703.67 0.023007367 0.006910577 2.160485673 -1.277107282 IRDIDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IRDIDLK 7 1 Q13243;Q13243-3;B4DJK0;B4DUA4;G3V5K8;Q13243-2 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 ;;; 133.58 0.002971 1792120000 2648590 2038410 2424720 1775330 2932540 3072480 2868290 2469990 2427690 1725470 FALSE TRUE 2753158.378 2388491.061 2487910.195 2126484.975 2434067.898 2358943.084 2643465.935 2436883.824 2340317.911 2063542.81 1.334190095 1.157471049 1.205649906 1.030501991 1.179557742 1.143151997 1.281032757 1.18092235 1.134126173 1 20.97669194 0.869465781 2.90999145 1.000193242 1.185490293 0.359276993 0.076361389 0.579615311 9.655487994 0.071671328 0.018855342 7.403989269 -0.869465781 0.185297051 IRDPNQGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 144.77 9.01E-05 1381843000 1722080 1370740 1580550 1370714 1930230 1940060 1959710 1592510 1628390 1170446 FALSE TRUE 1790069.048 1606153.932 1621740.431 1641837.138 1602130.194 1489510.467 1806102.809 1571165.008 1569784.562 1399772.484 1.278828573 1.147439281 1.158574304 1.172931428 1.144564715 1.064108978 1.290283121 1.12244313 1.121456937 1 20.41676092 -5 0.183016702 0.308584904 1.198963109 0.42066052 0.062932781 134.5559273 1.30287017 33.78791218 0.181979569 1.00E-05 5 0.890378206 IRDSAGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRDSAGQK 8 1 P52209-2;P52209;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 131.11 0.0018567 483090000 354170 329060 370330 289740 493730 481460 436440 521770 413700 451750 FALSE TRUE 368152.9051 385573.4953 379981.104 347049.7072 409805.951 369648.2116 402230.6924 514776.5266 398811.0178 540261.7632 0.681434316 0.713679038 0.703327775 0.642373255 0.758532213 0.68420206 0.744510753 0.952827984 0.738181091 1 19.04329905 1.4843414 0.581943494 0.983209903 0.679852135 0.638550334 0.067639303 0.440848228 0.353273211 0.066111169 0.034759208 30.50291893 -1.4843414 -0.303357768 IRDTPEDIVLEAPASGLAFHPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRDTPEDIVLEAPASGLAFHPAR 23 1 Q9H6Y2;D6RGJ8 Q9H6Y2 WDR55 WD repeat-containing protein 55 0 146.39 7.74E-08 56025000 16934 30022 24879 24860 27973 31677 23455 23971 26076 27138 FALSE TRUE 17602.5674 35178.04496 25527.36718 29777.2338 23218.15945 24320.49682 21616.53581 23649.70795 25137.52985 32455.17151 0.542365564 1.083896443 0.786542359 0.917488105 0.715391673 0.749356595 0.666042877 0.728688429 0.774530797 1 14.98616076 5.003566834 21.87205274 0.802267769 0.231332478 0.28693127 0.12923749 5106.706428 32969.44399 0.02956256 80078.7896 100824.6758 -5.003566834 -0.570935292 IRDVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRDVTK 6 1 Q99613-2;Q99613;B5ME19;H3BPE4;H3BPE3;H3BTY8 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 77.741 0.065319 771010000 1073960 812890 1009100 839600 1338130 1286060 1164250 918130 1023550 815290 FALSE TRUE 1116360.77 952497.5341 1035397.975 1005670.374 1110675.141 987392.0554 1072993.043 905823.9691 986712.6354 975030.4658 1.144949629 0.976890023 1.061913459 1.031424565 1.139118396 1.012678157 1.100471298 0.929021196 1.011981338 1 19.89508777 1.742493423 25 0.976671474 1.062475557 0.349031789 0.053805649 0.726491619 4640.929053 0.023047383 0.012781017 55.27050381 -1.742493423 0.085804083 IREDLPNLESSEETEQINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IREDLPNLESSEETEQINK 19 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 303.73 3.35E-50 497060000 522980 351020 455800 363190 539950 554250 567820 466760 518430 277030 FALSE TRUE 543627.6542 411304.9544 467678.5224 435027.898 448169.4919 425533.8372 523312.7847 460503.8457 499771.8056 331308.7244 1.640849196 1.241455247 1.411609438 1.313058987 1.352724691 1.284402751 1.579532159 1.389953876 1.508477648 1 18.33781667 4.75667141 23.48731554 1.366165394 1.640849737 0.247963823 0.150905605 2333.676 3026356.849 0.033105795 0.972516474 57104.64153 -4.75667141 0.274684344 IREDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IREDYR 6 1 O60826 O60826 CCDC22 Coiled-coil domain-containing protein 22 0 98.418 0.036441 105340000 46267 39867 37653 36747 44984 44667 39091 37156 41994 39919 FALSE TRUE 48093.65689 46713.84713 38634.26811 44015.44692 37337.63575 34293.76618 36026.94527 36657.98459 40482.64414 47740.36375 1.007400302 0.97849793 0.809257933 0.921975525 0.782097848 0.718339021 0.754643292 0.767861443 0.847975192 1 15.54292194 4.367293883 1.014643431 0.796558328 1.065973233 0.362484619 0.082838788 0.991967099 1.239099812 0.025418879 0.255413373 23296.67189 -4.367293883 0.269414905 IREEIDKFGIHVYQFPECDS(ph)DEDEDFKQQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IREEIDKFGIHVYQFPECDSDEDEDFKQQDR 31 3 E7EQM7;C9JM82;E7EPG2;B4DJ62;E7EX32;G3XAH0;Q99719-2;Q99719;H7C299 E7EQM7 5-Sep Septin-5 1 IREEIDKFGIHVYQFPECDS(1)DEDEDFKQQDR 86.891 0.00046842 76694000 68163 50900 51890 33014 103870 67523 42321 60085 74964 53269 TRUE FALSE 70854.12787 59641.67905 53242.29603 39544.07066 86214.2145 51841.80657 39003.76943 59279.65885 72266.06028 63706.04065 1.11220423 0.936201315 0.835749569 0.620727175 1.353313024 0.813765948 0.612246014 0.930518649 1.134367472 1 15.95914256 IREESGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IREESGAR 8 1 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;;;;; 134.66 0.00079086 4403210000 955848 1293082 1185295 1134780 1401686 1425897 1136894 1172796 1142972 1465826 FALSE TRUE 993585.6171 1515158.775 1216184.761 1359236.097 1163427.914 1094754.031 1047781.278 1157076.588 1101836.661 1753026.54 0.566782986 0.864310232 0.693762892 0.775365384 0.663668169 0.624493701 0.597698468 0.660045106 0.62853393 1 20.74141641 -1.029366124 4.603470008 1.000009576 0.677562318 0.579071597 0.08311013 90957123378 19181255421 11045055.38 0.019397077 0.093461743 1.029366124 -0.322447258 IREESNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IREESNTK 8 1 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7BZC3 Q00341 HDLBP Vigilin 0 ;; 181.55 0.00021271 500030000 385556 293617 377485 286579 430480 464540 420660 373263 370915 310160 FALSE TRUE 400778.0486 344043.4357 387322.5692 343263.4708 357307.1634 356657.6252 387687.57 368260.02 357565.8416 370929.9136 1.080468395 0.927516016 1.044193404 0.925413288 0.963274059 0.961522951 1.04517742 0.992802162 0.963971436 1 18.50078709 -0.026232557 7.983241904 0.999999999 0.988464129 0.003840098 0.049453102 0 0 0.043895549 0.01034628 0.941385366 0.026232557 -0.01153587 IREEYPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 209.6 4.19E-05 1.49521E+11 19874080 22911750 23179740 22245040 27161180 27639280 23066370 22477390 21097710 25911300 FALSE TRUE 20658724.02 26846664.83 23783823.07 26645042.52 22544332.33 21220476.1 21258367.65 22176117.35 20338407.54 30988123.13 0.666665869 0.866353368 0.767514153 0.859846929 0.727515256 0.684793848 0.686016625 0.715632801 0.656329118 1 24.88521204 3.073675722 15.76985429 0.722936956 0.793920421 0.016888864 0.105145492 4.529477841 965.3162887 0.027807969 0.033237955 1184.883693 -3.073675722 0.070983465 IREHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IREHLEK 7 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 157.68 0.0013313 6283690000 6054630 5283560 6161040 4974170 8112130 7973070 7600470 7951160 7164200 6204280 FALSE TRUE 6293671.468 6190970.33 6321601.764 5958045.98 6733233.04 6121445.326 7004725.301 7844587.706 6906361.841 7419889.878 0.84821629 0.834374961 0.851980537 0.802983074 0.907457274 0.825004876 0.94404707 1.057237753 0.930790343 1 22.82296634 2.076327408 4.275692278 1.002409632 0.846227575 0.763924089 0.038257237 0.089591037 3.148248746 0.014548743 0.010216597 119.2140407 -2.076327408 -0.156182056 IREIADGLCLEVEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IREIADGLCLEVEGK 15 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7 Q5W0H4 TPT1 Translationally-controlled tumor protein 0 ;;; 134.85 2.97E-05 1223193000 2264175 1594611 2102278 1567236 2865624 2654680 2258447 2041485 2420251 1790792 FALSE TRUE 2353566.377 1868473.035 2157065.092 1877230.603 2378526.256 2038170.802 2081424.023 2014122.233 2333146.639 2141663.406 1.098943172 0.8724401 1.00719146 0.876529243 1.110597608 0.951676532 0.971872619 0.940447611 1.08940865 1 21.03030033 3.274109895 24.99999587 0.997846553 0.960353275 0.062778358 0.079597886 613.4373533 431395.1969 0.02083988 0.02821634 1879.792426 -3.274109895 -0.037493278 IRELESQISELQEDLESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IRELESQISELQEDLESER 19 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;; 323.14 3.11E-62 2244977000 782151 893660 1054815 923042 951078 1123826 1036222 954572 1060171 861947 FALSE TRUE 813030.9254 1047139.153 1082304.345 1105616.953 789414.1013 862834.4432 955000.212 941777.5237 1022015.653 1030829.012 0.788715603 1.015822354 1.049935861 1.072551257 0.765805087 0.837029647 0.926439013 0.913611776 0.991450222 1 19.97537362 4.756996685 23.23537705 0.944616039 0.788715243 0.222054297 0.090901437 2600.29037 3277060.869 0.023324715 0.701457099 57147.42747 -4.756996685 -0.155900796 IREPLTAQQLETTTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IREPLTAQQLETTTER 16 1 Q6P1N0-2;Q6P1N0;K7EMP1 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 0 ; 204.13 2.37E-11 789220000 87500 79024 79198 87459 100804 119978 105590 104840 89864 100018 FALSE TRUE 90954.56756 92595.75728 81261.96494 104758.1292 83669.37209 92114.92778 97313.57989 103434.7913 86629.81219 119614.6121 0.760396794 0.77411744 0.679364866 0.875797089 0.699491229 0.770097617 0.813559298 0.864733743 0.724241049 1 16.86803411 -4.999999916 0.192009822 1.970032755 0.738691896 0.549100507 0.061359801 98.91019145 0.970373081 36.63808185 0.155024103 1.00E-05 4.999999916 -1.231340859 IRETTDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRETTDFK 8 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 ; 90.709 0.01186 482450000 636030 694570 572720 626570 997070 836770 758030 635540 617850 793780 FALSE TRUE 661140.9555 813856.9945 587645.5537 750503.6759 827588.3975 642442.8489 698613.6279 627021.6258 595613.6992 949305.9932 0.696446626 0.857317873 0.619026487 0.790581416 0.871782548 0.676750019 0.735920381 0.660505285 0.62742014 1 19.85651367 4.280248162 24.99978825 0.734673185 0.776881743 0 0.117897323 769.4435299 461419.2726 0.027013811 0.073979286 19065.49838 -4.280248162 0.042208558 IREYFGEFGEIEAIELPMDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IREYFGEFGEIEAIELPMDPK 21 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 ;; 135.86 5.37E-06 499854000 703075 521271 686851 437121 897310 843760 727921 671173 765300 559448 FALSE TRUE 730832.9439 610795.2393 704750.9013 523582.2291 744785.5667 647809.5273 670864.65 662177.0238 737757.0025 669061.1243 1.092326123 0.912913958 1.053343074 0.782562624 1.113180156 0.968236688 1.002695607 0.989710805 1.102675041 1 19.35177849 IREYFGGFGEVESIELPMDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IREYFGGFGEVESIELPMDNK 21 1 Q14103-3;Q14103;H0Y8G5;H0YA96;D6RAF8;Q14103-2;Q14103-4 Q14103-3;Q14103-2 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;; 235.5 7.64E-30 1065538000 1705713 1152203 1608405 1172083 2232761 2074371 1955843 1678368 1864422 1288893 FALSE TRUE 1773055.866 1350084.902 1650321.356 1403917.519 1853237.083 1592629.773 1802538.915 1655872.222 1797321.816 1541426.906 1.150269182 0.875866963 1.070645224 0.910790848 1.202286709 1.033217836 1.169396296 1.074246347 1.166011706 1 20.55583505 3.240367537 24.99994185 1.109472942 0.997802073 0.238044575 0.092430204 61.39147761 849378.8134 0.023411138 0.030135624 1739.272128 -3.240367537 -0.111670869 IRFQESEERPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRFQESEERPK 11 2 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 117.98 0.00044012 256150000 152407 102553 118478 104321 184881 156640 158358 138006 155096 127895 FALSE TRUE 158424.146 120165.68 121565.634 124955.3824 153454.9937 120262.7339 145945.4862 136156.2553 149514.1253 152953.5766 1.035766208 0.78563498 0.794787783 0.816949726 1.003278231 0.786269511 0.954181585 0.890180265 0.977513103 1 17.22273432 1.333030976 0.831883111 1.002943851 0.865557599 0.190727168 0.086249426 0.860190199 1.292092851 0.077315728 0.029805646 21.52935287 -1.333030976 -0.137386252 IRGDGSGFS(ph)L ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IRGDGSGFSL 10 1 R4GMM2;Q9NPB6-2;Q9NPB6 R4GMM2 PARD6A Partitioning defective 6 homolog alpha 1 IRGDGSGFS(1)L;IRGDGSGFS(1)L;IRGDGSGFS(1)L 123.01 0.0012455 231359000 356367 376518 400188 349957 476900 534770 468486 419775 426869 366033 TRUE FALSE 370436.6443 441182.0376 410617.228 419177.4501 395836.7083 410577.772 431764.8432 414148.6027 411506.0681 437750.1582 0.846228465 1.007839813 0.938017315 0.957572355 0.904252576 0.937927181 0.986327098 0.946084416 0.940047788 1 18.73974817 IRIDS(ph)LSAQLSQLQK ddPTM_MDA-MB-175_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(0.81)LS(0.19)AQLSQLQK;IRIDS(0.996)LS(0.004)AQLSQLQK 289.24 4.38E-44 1442980000 1244850 981650 1233230 899120 1680030 1483190 1158430 1294310 1349490 1183180 TRUE FALSE 1293997.639 1150240.751 1265368.987 1076963.252 1394459.101 1138741.6 1067629.23 1276961.892 1300922.119 1415001.468 0.914485016 0.812890147 0.894252773 0.761103983 0.985482441 0.804763547 0.754507507 0.90244563 0.919378635 1 20.43237212 1.090723957 1.987059831 0.995700759 0.848228756 0.320782985 0.068342209 0.341676789 2.656096069 0.060901529 0.017258938 12.32321305 -1.090723957 -0.147472002 IRIDSLSAQLSQLQK ddPTM_MDA-MB-175_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 ; 181.74 5.25E-07 1481750000 869710 702340 825240 576030 1314240 1129690 825390 930010 960650 1173610 FALSE TRUE 904046.8224 822961.4316 846746.4323 689967.0147 1090845.954 867336.6181 760693.775 917544.7371 926076.3942 1403556.409 0.644111499 0.586340119 0.603286356 0.491584813 0.777201363 0.617956366 0.541975919 0.653728437 0.659807036 1 20.42065562 0.411718444 1.277984973 1.000235381 0.610760082 0.727315451 0.070500488 1.449411453 2.662684032 0.065624119 0.019520705 2.580586638 -0.411718444 -0.389475299 IRIEDPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IRIEDPPR 8 1 P61160;P61160-2;F5H6T1 P61160 ACTR2 Actin-related protein 2 0 ;;;;; 134.77 0.00078667 1598557000 2182637 2317114 2370947 2143352 2980550 2917990 2532660 2551700 2374832 2699000 FALSE TRUE 2268809.194 2715060.305 2432735.827 2567300.628 2473917.176 2240331.045 2334143.491 2517498.635 2289362.26 3227817.375 0.702892677 0.841144337 0.753678274 0.795367374 0.766436539 0.69406995 0.723133691 0.779938374 0.709260158 1 21.62212752 -1.595739415 6.540773805 1.000555701 0.75508353 0.741040806 0.043982946 0.000345702 2.14E-05 0.041306313 0.009714633 0.025366502 1.595739415 -0.245472171 IRLDETDDPDDYGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;; 136.63 1.98E-05 1510390000 874381 962360 960450 1033600 998190 1207870 1242780 1076990 1037160 771133 FALSE TRUE 908902.237 1127637.844 985480.116 1238042.995 828518.0203 927360.4979 1145367.656 1062554.711 999832.8142 922221.7471 0.98555715 1.222740461 1.068593447 1.342456951 0.898393497 1.005572142 1.241965568 1.152168352 1.084156622 1 19.81475416 -2.749213068 1.233597825 7.02E-05 1.119057009 0.062154178 0.126498044 252492.3291 10539.75669 698994.4436 0.035252334 0.001781505 2.749213068 1.118986782 IRLDETDDPDDYGDRESGCSFVLALMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRLDETDDPDDYGDRESGCSFVLALMQK 28 2 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 91.389 0.0016048 277650000 93423 95781 99437 76085 124110 122160 102860 89635 130100 102010 FALSE TRUE 97111.41218 112230.6417 102028.4099 91134.38591 103013.8265 93790.19135 94797.56443 88433.58944 125417.7264 121996.9064 0.796015367 0.91994662 0.836319649 0.747022106 0.844397039 0.768791555 0.777048921 0.724883868 1.028040219 1 16.89648504 1.228268913 25 1.014020297 0.80039536 0.719929152 0.052939678 126.8600747 308150.5916 0.052488233 0.013702512 16.91487969 -1.228268913 -0.213624937 IRLEETLEQLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRLEETLEQLAK 12 1 P22059 P22059 OSBP Oxysterol-binding protein 1 0 151.16 6.27E-05 161890000 625140 527600 642410 506620 816400 790060 739610 647670 725480 527180 FALSE TRUE 649821.0099 618211.1958 659151.7323 606827.9239 677628.6196 606580.5385 681637.4356 638989.043 699370.1165 630470.8275 1.030691638 0.980554799 1.045491248 0.962499607 1.074797738 0.962107225 1.081156186 1.01351088 1.109282279 1 19.26607009 2.222869796 24.9996967 1.04901451 1.010534995 0.173956747 0.044314353 433.2911614 690345.1199 0.015002562 0.011119169 167.0589688 -2.222869796 -0.038479514 IRNPFRGS(ph)PK ddPTM_MDA-MB-175_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 75.102 0.020872 330230000 247340 197020 259520 204260 379650 408340 255280 254950 284380 238380 TRUE FALSE 257105.1742 230856.6524 266283.3044 244662.0183 315117.2286 313509.2235 235270.4865 251532.8123 274145.2194 285085.9969 0.90185129 0.809778996 0.934045542 0.858204265 1.105340957 1.099700535 0.825261462 0.882305041 0.961622887 1 18.12103765 IRPLS(ph)DGNSPWSTILIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRPLSDGNSPWSTILIK 17 1 Q5TCX8;Q5TCX8-3 Q5TCX8;Q5TCX8-3 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 IRPLS(0.998)DGNS(0.002)PWSTILIK;IRPLS(0.999)DGNS(0.001)PWSTILIK 207.17 3.83E-12 831770000 996630 849910 961600 897800 1210130 1305950 1014480 941410 1068690 967510 TRUE FALSE 1035977.722 995875.4311 986660.086 1075382.16 1004432.535 1002662.904 934962.4067 928791.9388 1030228.056 1157075.06 0.895341847 0.860683516 0.852719171 0.929397061 0.868078977 0.866549577 0.808039546 0.802706731 0.890372709 1 20.14205103 2.688498119 3.336154729 0.850250301 0.881626294 0 0.056643623 0.782495845 17.65083471 0.018506583 0.017875567 488.0879876 -2.688498119 0.031375993 IRPYWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRPYWK 6 1 P36405 P36405 ARL3 ADP-ribosylation factor-like protein 3 0 65.897 0.093785 519940000 259500 336400 307490 284220 556120 463360 382230 334060 296770 727280 FALSE TRUE 269745.2604 394174.0832 315503.442 340437.8677 461590.921 355751.6623 352269.8138 329582.4721 286089.3057 869776.5914 0.310131663 0.453190034 0.362740783 0.391408404 0.530700556 0.409014988 0.405011836 0.378927733 0.328922747 1 19.73028536 -1.707288508 2.90150191 1.084835254 0.400334391 0.90326035 0.059223004 24192803.55 21816998.96 14959322.06 0.013867191 0.019620564 1.707288508 -0.684500863 IRQPS(ph)VDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IRQPSVDLTDDDQTSSVPHSAISDIMSSDQETYSCKPHGR 40 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 IRQPS(0.948)VDLT(0.047)DDDQT(0.003)S(0.001)S(0.001)VPHS(0.001)AIS(0.001)DIMSSDQETYSCKPHGR;IRQPS(0.811)VDLT(0.189)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR;IRQPS(0.956)VDLT(0.044)DDDQTSSVPHSAISDIMSSDQETYSCKPHGR 129.36 4.35E-09 521818000 270325 136943 194759 107727 295174 268212 248612 199035 233705 131948 TRUE FALSE 280997.6397 160461.895 199834.5795 129035.0791 245000.4289 205923.8278 229125.1418 196367.2614 225294.0027 157800.6843 1.780712428 1.01686438 1.266373339 0.817709249 1.552594211 1.304961564 1.4519908 1.244400569 1.427712457 1 17.26774394 IRS(ph)IEALLEAGQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRSIEALLEAGQAR 14 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 IRS(1)IEALLEAGQAR 111.66 0.00038686 23935000 29456 28327 31255 23389 40208 39029 31900 27994 32723 28598 TRUE FALSE 30618.94562 33191.9419 32069.53098 28015.27439 33373.45852 29965.10624 29399.59464 27618.78622 31545.30562 34201.23056 0.895258595 0.970489697 0.937671846 0.819130597 0.97579701 0.876141172 0.859606341 0.807537792 0.92234417 1 15.06176061 2.518583822 24.54276237 0.872053714 0.91871369 0 0.063231503 895.2825738 529939.2169 0.019951994 0.018808934 330.0531044 -2.518583822 0.046659976 IRS(ph)SVEKENQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.605)S(0.395)VEKENQK;IRS(0.5)S(0.5)VEKENQK 147.64 2.77E-05 3512200000 3185200 1505130 2071140 1352410 3368700 2889850 2569480 2157000 2537920 1428320 TRUE FALSE 3310954.156 1763624.369 2125115.61 1619912.661 2796089.577 2218726.134 2368077.444 2128088.943 2446580.755 1708171.957 1.938302606 1.032463015 1.244087635 0.948331141 1.63688999 1.298889216 1.386322632 1.245828287 1.432280131 1 20.70402178 -1.60306365 2.819606861 0.975011867 1.32902499 0.127796802 0.26978987 34091130 34096665.43 6311618.109 0.05976584 0.024942291 1.60306365 0.354013123 IRSS(ph)VEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 IRSSVEK 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.024)S(0.976)VEK;IRS(0.24)S(0.76)VEK;IRS(0.026)S(0.974)VEK;IRS(0.443)S(0.557)VEK;IRS(0.061)S(0.939)VEK;IRS(0.056)S(0.944)VEK;IRS(0.001)S(0.999)VEK;IRS(0.039)S(0.961)VEK 120.45 0.0027579 5681620000 4762700 3122070 3907090 3598760 4697750 5298440 6159050 4111930 4288750 2422610 TRUE FALSE 4950735.074 3658261.236 4008911.975 4310583.987 3899228.133 4067957.609 5676287.567 4056816.304 4134398.725 2897274.046 1.708756229 1.262656269 1.383684081 1.487806786 1.345826481 1.404063801 1.959182141 1.400218357 1.426996087 1 21.46626472 IRSS(ph)VEKENQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IRSSVEKENQK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 IRS(0.045)S(0.955)VEKENQK;IRS(0.013)S(0.987)VEKENQK;IRS(0.012)S(0.988)VEKENQK;IRS(0.28)S(0.72)VEKENQK 172.09 1.08E-05 4281400000 3688341 1753949 2699175 1517179 3646890 3228698 2932158 2523054 3186240 1666590 TRUE FALSE 3833959.551 2055176.097 2769517.718 1817272.478 3026992.94 2478881.821 2702327.794 2489236.588 3071567.845 1993126.402 1.92359077 1.031131841 1.38953441 0.911769809 1.518715992 1.24371531 1.35582359 1.248910549 1.541080306 1 20.92660178 -2.230592235 2.109754822 3.68E-05 1.326213807 0.128286603 0.267691848 5810248.573 1067102.918 27664922.12 0.058458579 0.005880412 2.230592235 1.326176992 IRTPS(ph)GEFLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRTPSGEFLER 11 1 Q9UNN5;B3KT28;B1ANM7;Q9UNN5-2 Q9UNN5 FAF1 FAS-associated factor 1 1 IRT(0.002)PS(0.998)GEFLER;IRT(0.009)PS(0.991)GEFLER 176.29 5.34E-06 418250000 139640 172187 171215 155408 198613 217050 154512 168465 171240 185904 TRUE FALSE 145153.095 201758.7778 175677.0036 186147.2386 164852.8332 166643.4269 142400.9457 166207.0022 165077.1058 222328.3295 0.65287719 0.907481194 0.790169224 0.837262795 0.741483704 0.74953753 0.640498429 0.747574556 0.742492449 1 17.76233227 -1.300486715 3.49071703 1.000872754 0.757881936 0.491223616 0.074303581 32464379.72 53489523.71 303382.9014 0.018005568 0.050062587 1.300486715 -0.242990818 IRTS(ph)PTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IRTSPTFR 8 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 IRT(0.21)S(0.789)PT(0.001)FR;IRT(0.056)S(0.944)PTFR 91.701 0.0074492 2321550000 141024 202280 142197 174145 170474 187868 183038 214346 200686 200467 TRUE FALSE 146591.7364 237020.0165 145902.7706 208590.3612 141496.8904 144238.5042 168691.0033 211473.0425 193463.3501 239744.6705 0.611449406 0.988635184 0.608575658 0.87005213 0.590198273 0.601633829 0.703627751 0.882076094 0.80695579 1 17.87113922 1.219924254 1.226740667 0.977975568 0.718282048 0.308627306 0.129022857 0.516858195 1.557610679 0.116605442 0.037265741 16.59297481 -1.219924254 -0.25969352 IRVDIIENQVMDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IRVDIIENQVMDFR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 184.31 1.19E-06 351890000 282150 333000 379090 333750 402950 453220 350540 367030 407370 370640 FALSE TRUE 293289.4999 390190.1596 388969.3968 399764.7539 334456.7029 347966.5236 323063.7588 362110.5632 392708.8333 443259.8117 0.661664992 0.880274163 0.877520106 0.901874574 0.754538747 0.785017081 0.728836114 0.816926222 0.885956324 1 18.75779304 0.967442099 2.602273886 0.999165703 0.803976375 0.438774516 0.070450701 0.281631841 4.424100153 0.067886926 0.018209052 9.277737897 -0.967442099 -0.195189329 IRVDVADQAQDKDRDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IRVDVADQAQDKDRDDR 17 3 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 263.08 9.73E-28 8441817000 5009002 3455381 4381176 2686675 5627684 5461916 4375120 4211210 4669361 3460344 FALSE TRUE 5206761.267 4048815.808 4495353.046 3218091.296 4671092.284 4193468.785 4032186.662 4154765.618 4501311.61 4138332.155 1.258178675 0.97836898 1.086271686 0.777630015 1.128737885 1.013323394 0.974350659 1.003971035 1.087711532 1 21.98061801 4.742088906 24.66825251 1.003779766 1.258178791 0.411052777 0.09067794 265.7917464 1858200.982 0.020146882 0.147900673 55219.04682 -4.742088906 0.254399025 IRYESLTDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 136.3 9.31E-05 1984120000 3740300 2307660 3011520 2464210 3667500 3569900 3887200 3107500 3179010 1950820 FALSE TRUE 3887969.932 2703982.654 3090002.685 2951623.383 3044099.66 2740844.827 3582511.107 3065849.045 3064598.051 2333045.828 1.666478166 1.158992516 1.324450059 1.265137336 1.30477491 1.174792537 1.535551108 1.314097224 1.313561017 1 21.15378322 0.613656308 2.878490746 1.000010361 1.334785148 0.328285388 0.145976441 6.175200992 44.64730867 0.12935099 0.033955516 4.108244744 -0.613656308 0.334774787 IRYESLTDPSKLDSGK ddPTM_MDA-MB-175_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 4526100000 8110700 4572400 6689700 3943100 9685400 8477100 7675800 6523600 8136600 4634200 FALSE TRUE 8430916.699 5357674.132 6864039.078 4723033.411 8039079.168 6508421.997 7074150.739 6436161.812 7843765.355 5542182.763 1.521226755 0.96670831 1.238508251 0.85219734 1.450525815 1.174342723 1.276419606 1.161304505 1.415284499 1 22.40202286 3.203592997 24.99958064 1.246629976 1.138651017 0.056437112 0.203025502 522.7882852 373758.229 0.054391307 0.065012736 1598.059691 -3.203592997 -0.107978959 IS(ph)APNVDFNLEGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 279.32 3.41E-33 2006193000 2377760 1411679 1693045 1388558 2541300 2772400 2553060 1877941 2092324 1235051 TRUE FALSE 2471635.801 1654123.887 1737167.144 1663210.628 2109330.734 2128552.116 2352944.486 1852770.273 2017021.668 1477035.597 1.67337592 1.119894395 1.176117317 1.126046408 1.428083885 1.441097371 1.593018131 1.254384306 1.365587716 1 20.49427317 -1.161251154 4.158733237 0.999888517 1.34304288 0.257098022 0.179323638 11.4326787 49738660.07 10709.06072 0.042006538 0.068984075 1.161251154 0.343154364 IS(ph)ASS(ph)ATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISASSATR 8 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 2 IS(0.991)AS(0.238)S(0.77)ATR;IS(0.991)AS(0.081)S(0.925)AT(0.003)R;IS(0.999)AS(0.078)S(0.923)ATR 110.74 0.0049226 736030000 1874350 1768890 1904520 1713320 2382080 2674040 2359870 2091390 2119710 1632560 TRUE FALSE 1948350.785 2072683.097 1954153.356 2052209.582 1977174.892 2053034.735 2174897.223 2063358.338 2043422.051 1952428.875 0.997911274 1.061592114 1.000883249 1.051105937 1.012674478 1.051528566 1.113944406 1.056816135 1.046605117 1 20.89683856 2.489363245 24.58611026 1.0635364 1.027514271 0.142005273 0.032300628 694.2324197 1394261.87 0.010098202 0.009046373 308.5767819 -2.489363245 -0.036022129 IS(ph)ASSATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(1)ASSATR;IS(1)ASSATR;IS(0.997)AS(0.003)SATR;IS(0.999)AS(0.001)SATR;IS(0.998)AS(0.002)SATR 188.38 0.00020695 8222790000 2700440 2956030 3171610 2784780 3826400 4031470 3679450 3387120 3254360 3222600 TRUE FALSE 2807055.456 3463705.158 3254264.762 3335601.172 3175989.895 3095222.19 3391045.095 3341721.197 3137236.219 3854006.77 0.728347308 0.898728353 0.844384807 0.865489184 0.82407481 0.803117995 0.87987523 0.867077148 0.814019385 1 21.87792768 -5 0.290708838 2.239564911 0.832189003 0.531620515 0.046027464 190.2332625 1.79008505 143.0656272 0.045953415 1.00E-05 5 -1.407375908 IS(ph)DAELEAELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 268.35 5.35E-22 1877020000 3217376 1564707 2346718 1792937 3332551 3536069 3837184 2417267 2775432 1308340 TRUE FALSE 3344400.489 1833433.256 2407875.399 2147574.587 2766085.171 2714870.564 3536415.491 2384867.49 2675544.744 1564684.173 2.137428464 1.171759315 1.538889087 1.372529117 1.767823321 1.735091727 2.260146521 1.52418458 1.709958335 1 20.57744005 3.21663585 24.98236661 1.723972145 1.526604683 0.004563756 0.371037445 700.2183217 797867.9233 0.101396335 0.121286911 1646.781008 -3.21663585 -0.197367462 IS(ph)DAELEAELEKLSLSEGGLVPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 IS(1)DAELEAELEKLSLSEGGLVPSSK;IS(1)DAELEAELEKLSLSEGGLVPSSK 251.33 2.04E-40 137531000 199800 85778 137696 72560 256464 211787 173088 140797 175633 92529 TRUE FALSE 207688.2583 100509.7042 141284.4709 86912.15143 212870.3409 162602.6789 159520.9103 138909.8465 169312.0026 110658.286 1.876843261 0.908289003 1.276763594 0.785410244 1.923672855 1.469412593 1.441563177 1.25530452 1.530043604 1 16.75575196 3.249896418 24.99955473 1.437727741 1.194783854 0.091561472 0.345276647 510.7786462 1126445.623 0.091260697 0.122480486 1777.85533 -3.249896418 -0.242943888 IS(ph)EDETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISEDETER 8 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 IS(1)EDETER;IS(1)EDETER 175.07 0.00028141 687950000 860960 638040 700220 906890 826530 1079110 1343800 852520 783230 372680 TRUE FALSE 894951.3656 747618.4067 718468.3084 1086270.135 686036.7258 828503.0566 1238469.445 841093.3638 755041.7053 445699.5106 2.007970268 1.677404594 1.612001565 2.437225326 1.539235986 1.858882581 2.778709456 1.887131002 1.694059983 1 18.76571185 2.435169966 24.99998679 1.989028892 1.847308679 0 0.474565359 796.6583541 474747.7236 0.158790022 0.132853141 272.3767074 -2.435169966 -0.141720213 IS(ph)EDETERNGDDGTHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.997)EDET(0.003)ERNGDDGTHDK;IS(0.999)EDET(0.001)ERNGDDGTHDK;IS(0.967)EDET(0.033)ERNGDDGTHDK;IS(0.996)EDET(0.003)ERNGDDGT(0.001)HDK 125.23 2.88E-05 878590000 466081 279340 330353 232209 439336 530810 480286 323682 350293 189128 TRUE FALSE 484482.2378 327314.472 338962.2706 278139.2471 364657.8236 407537.422 442639.9283 319343.5722 337686.0234 226184.0105 2.141982701 1.447115874 1.498612876 1.229703402 1.612217516 1.801795896 1.956990361 1.411875099 1.492970359 1 17.78713742 0.793611044 1.486364488 1.004110715 1.63142849 0.366649978 0.254558773 0.825831057 3.252364891 0.24467034 0.071564241 6.217431994 -0.793611044 0.627317775 IS(ph)LQQELSR ddPTM_MDA-MB-175_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 45312000 4845.5 2939.4 4772 5524.8 5271 6862.9 4420.4 4124.6 3867.1 7626.4 TRUE FALSE 5036.804082 3444.219085 4896.36224 6617.58895 4375.037303 5269.095483 4073.917497 4069.316483 3727.923826 9120.647064 0.552241968 0.377628809 0.536843736 0.725561345 0.479684969 0.577710709 0.446669789 0.446165327 0.408734578 1 13.15492046 -2.013260475 2.938627892 1.542805981 0.503793646 0.709092642 0.094975456 11417614.1 12998725.65 42085972.01 0.025010972 0.009699281 2.013260475 -1.039012335 IS(ph)MSEVDLNVAAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 IS(1)MSEVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(0.981)MS(0.019)EVDLNVAAPK;IS(0.983)MS(0.017)EVDLNVAAPK;IS(1)MSEVDLNVAAPK;IS(1)MSEVDLNVAAPK 314.55 8.14E-56 1153111000 1794386 1241564 1515252 1175900 2112997 1965120 2046068 1595650 1679491 1076660 TRUE FALSE 1865229.745 1454792.959 1554740.712 1408489.51 1753830.525 1508750.662 1885691.844 1574262.922 1619046.447 1287610.913 1.448597341 1.129838948 1.207461583 1.093878202 1.362081128 1.171744233 1.464488864 1.222623159 1.257403483 1 20.29626528 0.315532841 2.46303698 1.000000565 1.258530215 0.29934639 0.120152754 38.6168217 136.2518845 0.108851355 0.029067036 2.067915751 -0.315532841 0.25852965 IS(ph)PPIKEEETKGDSVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISPPIKEEETKGDSVEK 17 2 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 IS(1)PPIKEEETKGDSVEK;IS(1)PPIKEEETKGDSVEK;IS(1)PPIKEEETKGDSVEK 138.93 1.05E-06 1676010000 5825200 1148100 2286790 1107730 4008250 3972360 4087860 2417670 2724110 652640 TRUE FALSE 6055183.394 1345277.244 2346385.626 1326835.688 3326929.097 3049839.592 3767442.852 2385265.088 2626069.813 780512.3125 7.757960121 1.723582348 3.006212187 1.699954846 4.262494061 3.907484281 4.826884588 3.056024934 3.3645463 1 19.57406187 4.749780546 24.91899366 3.155826045 7.75796292 0.600432941 1.160884171 1131.664825 2513330.805 0.272683213 4.19568812 56205.72393 -4.749780546 4.602136875 IS(ph)PTAGNQNGLLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISPTAGNQNGLLNK 14 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 IS(1)PTAGNQNGLLNK;IS(0.998)PT(0.002)AGNQNGLLNK;IS(1)PTAGNQNGLLNK 252.36 3.51E-24 216426000 313426 217175 288262 218034 330070 356760 312386 267378 275254 203643 TRUE FALSE 325800.3005 254473.1169 295774.3445 261160.4744 273964.8193 273907.8968 287900.3691 263794.2353 265347.6623 243542.9469 1.33775297 1.044879846 1.214464834 1.072338484 1.12491379 1.124680063 1.182133881 1.083152843 1.089531295 1 17.89381668 7.999999999 0.034572599 0.58601282 1.957268232 0.369334466 0.072915265 1163.888082 3.075276433 36.25910261 100.681253 99999999.84 -7.999999999 1.371255412 IS(ph)SKSPGHMVILDQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISSKSPGHMVILDQTK 16 1 Q9NWH9;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 IS(0.402)S(0.402)KS(0.196)PGHMVILDQTK;IS(0.333)S(0.333)KS(0.333)PGHMVILDQTK 240.21 4.50E-20 2937400000 4797800 3998800 5724300 2942400 8212700 6252000 5272200 5425700 6132400 4015400 TRUE FALSE 4987220.849 4685562.794 5873479.961 3524397.938 6816708.188 4800067.75 4858951.188 5352977.366 5911696.122 4802140.751 1.038541165 0.975723753 1.22309617 0.733922249 1.41951445 0.999568317 1.011830232 1.11470647 1.231054321 1 22.19524626 3.246686667 24.99925486 1.119731883 1.008047988 0.139976645 0.163116763 436.3133421 1342281.982 0.043173271 0.057472276 1764.764126 -3.246686667 -0.111683895 IS(ph)WYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;IS(1)WYLR;IS(1)WYLR;IS(1)WYLR 153.71 0.010591 246168000 397073 353920 383074 385746 494077 524569 502512 363585 383392 289178 TRUE FALSE 412749.7486 414703.0069 393057.2231 462045.4075 410093.968 402745.7997 463123.7964 358711.7378 369593.7968 345836.8925 1.193480966 1.199128884 1.13653931 1.336021164 1.18580168 1.164554183 1.339139364 1.037228085 1.068693956 1 18.39973225 1.632862699 8.097361992 1.03806325 1.218269459 0.631398664 0.06527825 0.072190198 10.07918527 0.031743908 0.016176694 42.94006513 -1.632862699 0.18020621 ISAEDGLKHEYFR ddPTM_MDA-MB-175_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 0 119.96 0.00018462 63434000 76130 84342 98645 69694 128130 122180 86910 85862 104940 89449 FALSE TRUE 79135.67119 98827.08241 101215.7697 83479.26518 106350.5084 93805.54666 80097.7671 84711.16033 101163.2299 106974.8189 0.739759805 0.923835005 0.946164441 0.780363697 0.994163948 0.876893717 0.748753472 0.791879446 0.945673299 1 16.70691171 ISAHQGAQVDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISAHQGAQVDSR 12 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 0 ; 105.03 0.0010193 50084000 38034 75161 78970 81686 85875 123884 75023 81989 69658 88796 FALSE TRUE 39535.61169 88069.31708 81028.02307 97843.24699 71277.99817 95113.81848 69142.50122 80890.07156 67151.02219 106193.8761 0.372296531 0.829325761 0.763019734 0.921364306 0.671206295 0.895661991 0.651096878 0.76172068 0.63234364 1 16.69634105 4.742861376 24.72941847 0.779688745 0.372296342 0.537475647 0.116248978 275.9833122 1586839.194 0.025325344 0.198213735 55317.35117 -4.742861376 -0.407392403 ISAPELLLHS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISAPELLLHSPAR 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR;ISAPELLLHS(1)PAR 162.41 2.61E-05 201642000 226352 223093 216739 212266 228854 272204 221330 230967 200215 236247 TRUE FALSE 235288.5517 261407.4873 222387.3964 254251.5812 189953.4788 208988.7463 203981.5763 227871.2652 193009.3013 282535.0764 0.832776428 0.925221359 0.787114291 0.899893863 0.672318217 0.739691329 0.721969034 0.806523806 0.683133945 1 18.10807046 3.256454172 24.99982413 0.759539226 0.860525253 0.17881822 0.093367197 356.353058 497872.4982 0.02368726 0.032006091 1804.904267 -3.256454172 0.100986027 ISDDKYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ISDDKYGR 8 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 159.58 0.00032678 3546090000 3472390 2783900 3385430 2607520 4136630 3817370 3848000 3337610 3458610 2554200 FALSE TRUE 3609482.638 3262013.169 3473657.087 3123279.673 3433487.11 2930843.67 3546383.705 3292874.797 3334135.302 3054646.587 1.181636741 1.067885622 1.137171515 1.022468421 1.124021065 0.959470625 1.160980036 1.077988796 1.091496252 1 21.54257404 2.265866941 0.010464499 5.27E-07 2.159209691 0.193053158 0.061296182 2872.720992 17.45677462 1768.929256 1830.423511 184.445023 -2.265866941 2.159209164 ISDEDWDIIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISDEDWDIIHR 11 0 P51659-3;P51659;P51659-2;A0A2R8YD50;E7ER27;A0A2R8YDT8;A0A2R8YF45 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ;;;;; 240.1 1.14E-15 3651300000 2653120 2998510 2928720 3269180 3426540 3780710 3302740 2923930 3047170 2414590 FALSE TRUE 2757867.226 3513480.767 3005044.849 3915814.046 2844097.955 2902697.4 3043862.609 2884739.501 2937502.947 2887682.68 0.955045111 1.2167129 1.040642336 1.356040286 0.984906678 1.005199574 1.054084865 0.998980782 1.01725268 1 21.46148079 ISDSEGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISDSEGFK 8 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 74.301 0.07728 0 165400 103730 129910 97380 166790 171700 150250 140480 131270 101390 FALSE TRUE 171930.1197 121544.8206 133295.5613 116641.4733 138439.0954 131825.2771 138473.0124 138597.0954 126545.6183 121255.4293 1.417916878 1.002386626 1.099295612 0.961948459 1.141714612 1.0871701 1.141994327 1.143017646 1.043628472 1 16.88768982 4.746738502 24.88775892 1.080121527 1.417917056 0.731758122 0.063050775 515.8716816 1569914.081 0.015030141 0.170101126 55813.40287 -4.746738502 0.337795528 ISDYFEYQGGNGSS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ISDYFEYQGGNGSSPVR 17 0 B3KRP1;Q9UKI8;Q9UKI8-4;Q9UKI8-5;Q9UKI8-2;C9JWT6 B3KRP1 TLK1 Serine/threonine-protein kinase tousled-like 1 1 ISDYFEYQGGNGS(0.106)S(0.894)PVR;ISDYFEYQGGNGSS(1)PVR;ISDYFEYQGGNGS(0.17)S(0.83)PVR;ISDYFEYQGGNGS(0.002)S(0.998)PVR 375.76 5.41E-105 1248860000 849420 933810 933790 856470 1025080 1079150 956020 920510 940060 858710 TRUE FALSE 882955.7575 1094184.603 958125.3345 1025877.21 850837.2677 828533.7672 881084.6543 908172.0691 906227.4242 1026957.784 0.859778047 1.065462107 0.932974412 0.998947791 0.828502672 0.806784641 0.857956061 0.884332427 0.882438829 1 19.96994545 3.241747494 24.99962239 0.867481529 0.969280264 0.275753107 0.068412712 90.18100099 707423.1406 0.018021717 0.023416094 1744.807397 -3.241747494 0.101798735 ISEEDELDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISEEDELDTK 10 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 151.83 4.45E-05 340370000 391010 224590 285290 232590 422720 445230 369460 300640 331860 191600 FALSE TRUE 406447.3767 263161.5854 292724.8918 278595.6078 350866.2054 341832.08 340500.7598 296610.4125 319916.4234 229140.3516 1.773792236 1.148473342 1.277491676 1.215829538 1.531228363 1.491802197 1.485992133 1.294448623 1.396159259 1 17.80587201 -0.801592947 5.969209486 0.999999973 1.388210749 0.325362353 0.172546238 5.95E-08 1.20E-08 0.159851615 0.037677384 0.157909062 0.801592947 0.388210777 ISEGLPT(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISEGLPTPTK 10 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.999)PT(0.001)K;ISEGLPT(0.963)PT(0.037)K 173.37 3.84E-05 192620000 840810 517330 652800 559290 772720 906960 1062170 729290 784330 402650 TRUE FALSE 874005.828 606177.4032 669812.5043 669915.8927 641373.3304 696332.2851 978914.3399 719515.0604 756102.1165 481541.5583 1.815016405 1.258826767 1.390975488 1.391190191 1.331916881 1.446048162 2.032876131 1.494190996 1.570170016 1 18.87730079 2.447379613 24.99650912 1.595159349 1.419136251 0 0.273538144 513.3150577 431415.5839 0.088922732 0.074399034 280.1428952 -2.447379613 -0.176023098 ISEGLPT(ph)PTKMT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 IS(0.001)EGLPT(0.999)PTKMT(1)PR;ISEGLPT(0.998)PT(0.168)KMT(0.834)PR;ISEGLPT(0.999)PT(0.001)KMT(1)PR 159.26 2.43E-05 586740000 1213430 767930 977740 774660 1368090 1332630 1242140 1026240 1060000 652130 TRUE FALSE 1261337.153 899816.0038 1003220.708 927885.4359 1135542.55 1023146.879 1144777.821 1012484.931 1021850.807 779902.3877 1.61730131 1.153754647 1.286341372 1.189745602 1.456005993 1.311890943 1.467847565 1.298220069 1.310229105 1 19.57293404 0.514890911 1.822958142 1.000061578 1.340371077 0.387985538 0.130046783 3.391672141 11.58701697 0.11640757 0.032512226 3.272584813 -0.514890911 0.340309499 ISEGLPTPTKMT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISEGLPTPTKMTPR 14 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 ISEGLPT(0.019)PT(0.243)KMT(0.739)PR 73.918 0.095306 294200000 516940 469870 616810 459480 700860 748310 618830 621020 641530 511210 TRUE FALSE 537349.1904 550566.5174 632884.5753 550363.7726 581728.0675 574526.3432 570324.4876 612696.2427 618441.4606 611371.8118 0.878923725 0.900542856 1.035187693 0.900211233 0.95151274 0.939733125 0.932860293 1.002166326 1.011563583 1 19.22169051 1.703229289 4.795773036 1.00621278 0.936199635 0.39335805 0.039995549 0.172755815 9.385332193 0.021254193 0.010451351 50.49278078 -1.703229289 -0.070013146 ISEKEEVTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISEKEEVTTR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 113.61 0.0013365 1064140000 925480 801600 837310 755760 1197070 1234260 1106620 878240 956840 742210 FALSE TRUE 962018.665 939268.5644 859130.9865 905247.0723 993592.469 947621.8204 1019880.233 866468.6293 922403.5153 887631.839 1.083803693 1.058173584 0.967891133 1.019845202 1.119374526 1.067584305 1.148990142 0.976157672 1.039173534 1 19.75960189 1.627997455 25 1.005753309 1.062685831 0.245645239 0.048989999 1.358221396 1682.375795 0.023966314 0.013268601 42.46170761 -1.627997455 0.056932521 ISELGSQLSDEAVEDGLFHEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISELGSQLSDEAVEDGLFHEFKR 23 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 0 78.413 0.0088241 10938000 13310 13399 14464 13177 16938 18899 12431 12906 15140 15033 FALSE TRUE 13835.48908 15700.17402 14840.94372 15783.37127 14058.88481 14509.99367 11456.62574 12733.01618 14595.11436 17978.42853 0.769560535 0.87327844 0.825486149 0.877906055 0.7819863 0.807077974 0.637242889 0.708238552 0.811812575 1 14.1339793 2.86750954 2.411140107 0.755186027 0.837088189 0 0.094875918 0.607306453 6.924641434 0.03067356 0.03304749 737.0713659 -2.86750954 0.081902163 ISEQFTAMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISEQFTAMFR 10 0 Q13509;A0A0B4J269;Q13509-2;Q5JP53;P07437;Q5ST81;P68371;Q13885;Q9BVA1;P04350 Q13509;Q5JP53;P68371;Q13885;Q9BVA1;P04350 TUBB3;TUBB;TUBB4B;TUBB2A;TUBB2B;TUBB4A Tubulin beta-3 chain;Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2A chain;Tubulin beta-2B chain;Tubulin beta-4A chain 0 ; 128.81 0.00074382 2172131000 166343 227356 261091 260845 292773 359898 236615 255193 203724 396640 FALSE TRUE 172910.3501 266402.6244 267895.2459 312439.3625 243007.55 276317.1438 218068.498 251772.5552 196392.013 474354.0139 0.364517523 0.561611405 0.564758046 0.658662841 0.512291544 0.582512503 0.459716776 0.530769316 0.414019925 1 18.85560463 -1.195018221 4.273822396 1.000152346 0.52341429 0.759702004 0.081488398 24.55994059 45045502.02 14435.20246 0.018509248 0.063823671 1.195018221 -0.476738057 ISESVLRDS(ph)PPPHEDYEDEVFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ISESVLRDSPPPHEDYEDEVFVR 23 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 ISES(0.007)VLRDS(0.993)PPPHEDYEDEVFVR;IS(0.001)ES(0.01)VLRDS(0.989)PPPHEDYEDEVFVR;IS(0.001)ES(0.004)VLRDS(0.995)PPPHEDYEDEVFVR;ISES(0.005)VLRDS(0.994)PPPHEDYEDEVFVR 241.46 1.63E-37 392025000 262067 243932 252996 267722 248620 288685 330436 253326 256699 173925 TRUE FALSE 272413.6075 285825.4235 259589.2836 320676.6125 206359.6612 221642.2838 304535.5629 249930.5793 247460.4531 208002.2738 1.309666489 1.374145668 1.248011759 1.54169763 0.992102911 1.065576255 1.464097278 1.201576189 1.189700712 1 17.66623977 -4.999999989 0.101361923 0.147556869 1.446865025 0.250847776 0.154254583 273.406911 1.881078471 49.20008984 2.506670028 1.00E-05 4.999999989 1.299308157 ISESVLRDS(ph)PPPHEDYEDEVFVRDPHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISESVLRDSPPPHEDYEDEVFVRDPHPK 28 2 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 IS(0.01)ES(0.051)VLRDS(0.939)PPPHEDYEDEVFVRDPHPK;IS(0.024)ES(0.205)VLRDS(0.771)PPPHEDYEDEVFVRDPHPK;IS(0.014)ES(0.061)VLRDS(0.925)PPPHEDYEDEVFVRDPHPK 208.5 8.71E-26 1767500000 1250620 1013110 1199090 856350 1429840 1375870 1308020 1037080 1255460 930760 TRUE FALSE 1299995.443 1187103.762 1230339.27 1025733.474 1186796.308 1056345.044 1205493.975 1023179.639 1210276.24 1113124.602 1.167879536 1.066460808 1.105302379 0.921490256 1.0661846 0.948990834 1.08298206 0.919195962 1.087278314 1 20.08618366 4.441913766 1.195783097 1.001553685 1.186102876 0.366708959 0.063906777 0.913301095 1.601376999 0.017230518 0.184913892 27663.92291 -4.441913766 0.184549191 ISEVFDCWFESGSMPYAQVHYPFENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISEVFDCWFESGSMPYAQVHYPFENKR 27 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 214.57 2.66E-34 201820000 269770 235780 330770 230060 365000 410360 332760 308970 340910 212290 FALSE TRUE 280420.7279 276273.3809 339390.1379 275565.1813 302957.4304 315060.1091 306677.4017 304828.7625 328640.7157 253884.161 1.104522341 1.088186754 1.336791301 1.085397294 1.19329 1.240960081 1.207942238 1.200660811 1.294451432 1 17.95381087 ISFCLDIHNMSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISFCLDIHNMSVK 13 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 167.98 8.18E-07 0 371990 338920 390410 355440 564530 527440 448340 417900 474420 348380 FALSE TRUE 386676.4524 397126.8736 400584.4053 425744.9711 468571.3922 404950.0534 413197.9393 412298.734 457345.7169 416638.3909 0.928086468 0.95316918 0.96146782 1.021857276 1.124647662 0.971946086 0.991742356 0.989584117 1.097704213 1 18.66843626 3.815378077 3.658133625 1.025153998 0.944346939 0.393053701 0.046229873 0.267439492 6.904158977 0.012642988 0.023991101 6536.993853 -3.815378077 -0.080807059 ISFPGSSES(ph)PLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISFPGSSESPLSSK 14 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 ISFPGS(0.011)S(0.211)ES(0.778)PLSSK 140.03 1.06E-05 132100000 112560 109870 122910 104850 163200 149230 135570 123520 127900 105100 TRUE FALSE 117003.9557 128739.3178 126113.1356 125589.0171 135459.3223 114573.5941 124943.6692 121864.4164 123296.904 125692.3327 0.930875839 1.024241615 1.00334788 0.999178027 1.077705532 0.911540041 0.994043681 0.969545348 0.980942125 1 16.93953712 2.728067087 24.99964113 0.971285699 1.007378569 0.165747322 0.04021774 1287.063301 3066277.703 0.012372 0.011816446 534.6469416 -2.728067087 0.03609287 ISGETIFVTAPHEATAGIIGVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISGETIFVTAPHEATAGIIGVNR 23 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 329.54 1.69E-86 1342730000 551740 499900 607830 584920 594980 728410 600970 529300 553360 454760 FALSE TRUE 573523.1212 585753.9363 623670.5491 700615.4302 493845.5121 559247.8167 553864.4011 522205.5993 533444.6817 543861.5151 1.054538895 1.077027736 1.14674514 1.288223952 0.908035407 1.028290845 1.01839234 0.960181195 0.980846533 1 19.05287982 3.2199903 24.99999867 0.983798701 1.137384357 0.584427881 0.065644438 179.3323339 241422.8848 0.019547208 0.023402455 1659.549839 -3.2199903 0.153585657 ISGLIYEETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISGLIYEETR 10 0 P62805 P62805 HIST1H4A Histone H4 0 101.38 0.0078415 59798000 45274 46469 62730 47641 69506 74538 64393 48095 61289 70689 FALSE TRUE 47061.45248 54449.68927 64364.79533 57064.24761 57691.39495 57227.67913 59345.7084 47450.36519 59083.22086 84539.15613 0.556682307 0.644076565 0.76136075 0.675003752 0.682422177 0.676936957 0.701990783 0.561282693 0.69888586 1 16.36733209 0.963024897 23.4705479 1.000000001 0.658063143 0.755921108 0.058031676 1460.721613 927218.1183 0.057601179 0.014400295 9.183852442 -0.963024897 -0.341936858 ISHEGS(ph)PVKPVAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISHEGSPVKPVAIR 14 1 Q96II8-3;Q96II8;Q96II8-2 Q96II8-3 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 ISHEGS(1)PVKPVAIR 78.95 0.01235 39868000 39548 32050 44514 37956 51086 54776 50825 42458 47860 36858 TRUE FALSE 41109.38558 37554.33819 45674.07141 45463.58351 42402.41997 42055.10414 46841.20369 41888.91996 46137.52795 44079.61941 0.932616618 0.851966026 1.036172091 1.031396916 0.961950682 0.954071399 1.062649912 0.950301307 1.046686168 1 15.42782415 4.236742053 25 1.001561088 0.892291312 0.536793827 0.041907934 32.09329745 441217.8123 0.009925615 0.023338333 17248.13145 -4.236742053 -0.109269776 ISHQQNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISHQQNER 8 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 66.351 0.061908 20742000 5783.9 18205 15146 16590 13314 19882 10206 15171 14116 22433 FALSE TRUE 6012.252838 21331.56713 15540.7172 19871.45248 11050.89104 15264.70681 9406.027052 14967.65756 13607.96792 26828.31684 0.224101008 0.795113881 0.579265456 0.740689496 0.411911455 0.568977432 0.350600714 0.557905203 0.507224065 1 14.71146893 -1.542927049 3.722479183 1.009266978 0.533999665 0.436571062 0.161257573 26377183.35 11017882.87 1987705.591 0.035219607 0.028646591 1.542927049 -0.475267313 TNS(ph)DSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.176)NS(0.822)DS(0.002)ALHQSTMTPTQPESFSSGSQDVHQK;T(0.102)NS(0.897)DS(0.001)ALHQSTMTPTQPESFSSGSQDVHQK 334.44 3.12E-105 730890000 43545 264440 311610 278568 348800 409430 304780 390450 304110 231673 TRUE FALSE 45264.19022 309855.5129 319730.8126 333667.919 289511.1006 314346.0875 280890.5472 385216.6564 293165.1405 277064.8887 0.163370359 1.118349981 1.153992533 1.204295212 1.04492165 1.134557644 1.013807807 1.390348153 1.05811004 1 18.07986437 4.738670625 5.921372659 1.145508013 0.135517574 0.873493064 0.109484781 0.041430613 6.799893092 0.026097339 0.168781203 54786.13021 -4.738670625 -1.00999044 down ISHSLYSGIEGLDES(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISHSLYSGIEGLDESPSR 18 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 ISHSLYSGIEGLDES(0.999)PS(0.001)R 252.11 1.15E-30 162400000 57403 68353 73515 72915 93878 102430 77174 74641 64728 91898 TRUE FALSE 59669.31476 80092.09604 75430.86129 87337.36937 77920.65109 78642.18484 71124.90022 73640.55948 62398.45192 109903.6536 0.54292385 0.728748257 0.686336248 0.79467212 0.708990543 0.715555691 0.647156831 0.67004651 0.567755938 1 16.74587982 -1.776451576 2.537844222 1.086755766 0.679630897 0.655634387 0.070848992 17885163.68 12471341.91 9624332.177 0.016752835 0.016732022 1.776451576 -0.407124869 ISICS(ph)SDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 IS(0.088)ICS(0.87)S(0.043)DKR;ISICS(0.968)S(0.032)DKR;ISICS(0.954)S(0.045)DKR 107.09 0.0017332 979150000 1719070 1398040 1631850 1356780 2131540 2162090 1992710 1642000 1774720 1423310 TRUE FALSE 1786940.211 1638142.495 1674377.352 1625147.034 1769221.592 1659977.364 1836516.183 1619991.676 1710848.174 1702180.344 1.049794881 0.962378928 0.983666248 0.954744332 1.039385514 0.975206517 1.078919863 0.951715652 1.005092193 1 20.69895247 3.243693358 24.99959088 1.005628847 0.985557035 0.057148797 0.039989917 415.8034863 2025200.4 0.010762591 0.014113221 1752.642576 -3.243693358 -0.020071812 ISICSSDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISICSSDKR 9 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 0 69.276 0.093527 0 75274 215330 218190 198390 275710 251600 210960 217770 211840 240320 FALSE TRUE 78245.87564 252311.2525 223876.2106 237630.9499 228844.9127 193169.713 194424.404 214851.1493 204215.9198 287406.1028 0.272248484 0.877891075 0.778954269 0.82681247 0.796242357 0.672114166 0.676479734 0.747552495 0.710548307 1 18.13273117 -5 0.31899849 3.622216515 0.707426763 0.238797852 0.157774828 479.6976855 4.25942085 849.2114101 0.13323315 1.00E-05 5 -2.914789752 ISIEMNGTLEDQLSHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISIEMNGTLEDQLSHLK 17 0 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 210.98 1.73E-17 0 255720 260480 233650 277790 299290 317220 339010 248480 242640 282690 FALSE TRUE 265816.0231 305215.4137 239739.1109 332736.0329 248416.7927 243550.4625 312437.5104 245149.532 233907.4338 338077.6931 0.786257208 0.902796665 0.70912431 0.984199903 0.734792025 0.720397907 0.924158904 0.725127795 0.691874793 1 18.3669953 ISINQT(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISINQTPGK 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK;ISINQT(1)PGK 175.97 0.00059815 1097860000 3599600 2008930 2534910 1952570 3153340 3681960 3337440 2590100 2573930 1700230 TRUE FALSE 3741714.987 2353948.1 2600971.837 2338782.518 2617336.393 2826880.591 3075842.732 2555383.946 2481294.762 2033357.516 1.840165814 1.157665625 1.279151264 1.150207231 1.287199311 1.390252609 1.51269155 1.256731257 1.220294387 1 20.95543247 -4.149914988 0.193480022 1.04E-16 1.396946782 0.259388169 0.189679667 146.7254196 1.941336067 57.62279332 0.495639228 7.08E-05 4.149914988 1.396946782 ISKEEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISKEEAMR 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;;; 107.79 0.0035894 3085400000 1747830 1596200 1798700 1418670 2630640 2348720 2047720 1854330 1972260 1920670 FALSE TRUE 1816835.678 1870334.933 1845575.6 1699278.692 2183484.752 1803265.375 1887214.356 1829475.739 1901278.748 2296988.513 0.790964198 0.81425524 0.803476199 0.739785455 0.950585839 0.785056331 0.821603741 0.796467082 0.827726711 1 21.13131221 0.938946571 17.62128129 1.000000001 0.813265871 0.545376085 0.050988061 306.6921764 88519.09858 0.046251416 0.011563421 8.688535315 -0.938946571 -0.18673413 ISKPGAVST(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISKPGAVSTPVK 12 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 ISKPGAVS(0.226)T(0.774)PVK;ISKPGAVS(0.104)T(0.896)PVK 136.63 0.00017224 1175970000 1512640 847440 1221000 1008580 1492900 1570350 1690710 1183420 1395380 736100 TRUE FALSE 1572360.195 992981.2278 1252820.263 1208074.114 1239137.391 1205660.011 1558187.732 1167558.191 1345160.546 880324.7015 1.786113911 1.127971561 1.423134283 1.372305141 1.4075913 1.369562855 1.770014779 1.326281301 1.52802772 1 19.74767622 -1.264178816 5.322766821 0.999946132 1.444563864 0.343429455 0.188794881 0.000110517 1.53E-05 0.167399084 0.039451579 0.054427851 1.264178816 0.444617732 ISKSDMSRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISKSDMSRLR 10 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 0 52.725 0.083379 60648000 8156.8 147640 85817 136350 57572 149340 49182 99008 60160 222310 FALSE TRUE 8478.836762 172996.0215 88053.46152 163319.623 47785.932 114658.0483 45326.98633 97680.9597 57994.85335 265867.3881 0.031891225 0.650685376 0.331193164 0.614289794 0.179735967 0.431260295 0.170487199 0.367404819 0.218134513 1 18.0203473 -1.556322758 3.745995272 1.014295436 0.343518181 0.53618153 0.185926563 59630574.66 25234119.56 6984412.46 0.039557746 0.027776482 1.556322758 -0.670777255 ISLEVQLEQLRPFSHL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISLEVQLEQLRPFSHL 16 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 0 ; 139.67 1.62E-06 270680000 223888 278100 280650 254060 317170 328970 275760 283230 273190 304230 FALSE TRUE 232727.2711 325861.5117 287963.9696 304312.3097 263257.5567 252571.7031 254145.2106 279433.7651 263357.9453 363838.0437 0.639645235 0.895622427 0.791461956 0.83639497 0.723556982 0.694187173 0.698511921 0.768016896 0.723832897 1 18.47293688 -1.03814238 4.260580284 1.000018683 0.756186806 0.523472468 0.070798089 9130367.863 2224725.684 1646.592732 0.016361888 0.091592016 1.03814238 -0.243831878 ISLPGQMAGT(ph)PITPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISLPGQMAGTPITPLK 16 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 ISLPGQMAGT(1)PITPLK;ISLPGQMAGT(1)PITPLK 148.44 1.04E-05 248080000 486780 334890 452210 385400 527780 574230 626720 456940 527380 355380 TRUE FALSE 505998.4503 392404.7524 463994.9641 461630.9697 438068.1441 440873.785 577596.0488 450815.4667 508399.6968 425009.9068 1.190556837 0.923283778 1.091727408 1.086165198 1.030724548 1.037325902 1.359017848 1.060717549 1.196206697 1 18.69713694 ISLS(ph)PFSTTDSAYEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISLSPFSTTDSAYEWK 16 0 Q9UPY3-2;Q9UPY3;H0YJZ6;Q9UPY3-3 Q9UPY3-2 DICER1 Endoribonuclease Dicer 1 ISLS(0.941)PFS(0.059)TTDSAYEWK 290.32 1.72E-45 147360000 195890 147340 178710 175390 227000 244870 252500 207400 201330 138130 TRUE FALSE 203623.8885 172644.4989 183367.3294 210081.6185 188414.6211 188002.6535 232708.3902 204620.1422 194084.1726 165193.9288 1.232635424 1.04510196 1.110012521 1.271727236 1.140566257 1.138072415 1.4086982 1.238666237 1.174886837 1 17.33380114 3.75740796 23.96279717 1.215623198 1.120835147 0.051730282 0.109137086 981.4143874 1247779.255 0.027440019 0.049342943 5720.15715 -3.75740796 -0.094788051 ISLSKS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISLSKSPTK 9 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.001)LS(0.009)KS(0.963)PT(0.027)K 84.169 0.0094925 764660000 819130 362570 509080 360650 843150 785100 811510 523960 623230 306670 TRUE FALSE 851469.8849 424838.5771 522347.043 431985.4936 699831.6642 602772.4233 747901.7257 516937.1732 600800.074 366756.1149 2.321624235 1.158368081 1.424235403 1.177854918 1.908166314 1.643523853 2.039234508 1.409484811 1.638146031 1 18.48446149 0.104897749 1.384871398 0.999333574 1.616490547 0.224088337 0.352851124 18.22611516 26.24062421 0.352547477 0.094706595 1.273203282 -0.104897749 0.617156973 ISLSKS(ph)PTKTDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISLSKSPTKTDPK 13 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 IS(0.002)LS(0.046)KS(0.917)PT(0.034)KT(0.002)DPK;IS(0.007)LS(0.036)KS(0.957)PT(0.001)KTDPK 118.55 0.00032993 5588100000 18963400 4844780 9135300 4798060 15129400 13781600 14087800 9562300 11462700 3603990 TRUE FALSE 19712089.67 5676833.278 9373373.423 5747101.947 12557709.99 10581032.26 12983561.42 9434133.009 11050159.67 4310122.838 4.573440344 1.317093153 2.174734636 1.333396324 2.91353877 2.454925917 3.012341391 2.188831586 2.563769081 1 22.03929756 4.752407294 24.44014595 2.198325877 4.573442536 0.554766917 0.658395753 1321.576235 2332599.093 0.15134414 3.022794032 56546.70382 -4.752407294 2.375116659 ISMPDFDLHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISMPDFDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 165.63 2.14E-05 1105810000 1987940 1692400 1949400 1824310 2286980 2541600 2577400 2119950 2149760 1697040 FALSE TRUE 2066425.406 1983056.535 2000202.965 2185153.073 1898239.956 1951351.918 2375376.653 2091535.538 2072390.558 2029542.496 1.018173017 0.97709535 0.985543771 1.076672736 0.935304365 0.961473791 1.170400057 1.030545328 1.021112177 1 20.95272312 ISMPDLDLHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISMPDLDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 113.67 0.0013605 350960000 224340 201330 209810 193090 266720 296170 245030 229330 213540 180890 FALSE TRUE 233197.1164 235906.8614 215277.821 231282.6257 221383.0297 227389.006 225823.9083 226256.2065 205854.7371 216331.9322 1.077959754 1.090485621 0.995127344 1.069109971 1.02334883 1.051111612 1.043876908 1.045875217 0.951568893 1 17.72288711 8 0.116301185 0.974115481 1.292788671 0.355913157 0.032555685 117.6437119 0.944899518 0.238695829 6.05528318 99999999.9 -8 0.318673191 ISMPDLDLHLKS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMPDLDLHLKS(1)PK 123.55 6.17E-05 245710000 722190 321460 412960 299690 670150 644060 582530 508300 600650 362010 TRUE FALSE 750702.6189 376668.2544 423722.0769 358967.7875 556238.1424 494486.8258 536869.7764 501487.0699 579032.7238 432938.9284 1.733968857 0.870026301 0.978710966 0.829141858 1.284795859 1.142163001 1.240058912 1.158332127 1.33744666 1 18.723804 ISMPDVDLHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 158.05 3.03E-05 854900000 1540550 1310240 1424150 1389490 1735870 1866840 1943000 1576020 1428730 1091100 FALSE TRUE 1601372.104 1535263.528 1461264.519 1664326.975 1440807.437 1433294.702 1790702.583 1554896.03 1377310.286 1304880.155 1.227217762 1.176555197 1.119845768 1.275463474 1.104168404 1.09841099 1.372311914 1.191600642 1.055507114 1 20.31548588 1.155865217 4.090200963 1.007051379 1.197652188 0.425205304 0.079224587 0.199704677 5.783720307 0.074564809 0.019512422 14.31743489 -1.155865217 0.190600809 ISMQDVDLSLGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 ISMQDVDLSLGSPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLS(0.002)LGS(0.998)PK;ISMQDVDLSLGS(1)PK;ISMQDVDLSLGS(1)PK 335.61 1.42E-68 2110769000 5139808 2063689 2444425 2022145 3743389 4438930 3478702 2848513 2953625 1849020 TRUE FALSE 5342731.589 2418111.532 2508128.724 2422119.245 3107089.075 3408055.78 3206032.247 2810333.342 2847324.613 2211300.067 2.416104294 1.093524831 1.134232645 1.09533721 1.405096088 1.541200053 1.449840433 1.270896421 1.287624712 1 21.07646338 4.744148865 24.98375214 1.275327196 2.416104785 0.812818607 0.167127315 266.8811958 1193127.959 0.042243117 0.372169703 55481.58571 -4.744148865 1.140777589 ISNDNPEEHVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISNDNPEEHVLK 12 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ; 80.96 0.018935 357960000 292590 368860 395710 361134 431500 441550 387420 398340 382360 462030 FALSE TRUE 304141.6791 432208.8357 406022.5277 432565.2273 358153.7841 339006.7043 357053.0081 393000.9039 368598.9383 552555.9324 0.550426955 0.78219925 0.734808015 0.782844237 0.648176525 0.613524685 0.646184372 0.71124185 0.667079868 1 19.07576098 -1.584644541 2.571968878 1.026757622 0.686621971 0.651106666 0.06979199 8634978.678 7860232.184 1570578.003 0.017485679 0.026022886 1.584644541 -0.340135651 ISNLLSDYGYHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISNLLSDYGYHLR 13 0 P30876;C9J2Y9;C9J4M6 P30876 POLR2B DNA-directed RNA polymerase II subunit RPB2;DNA-directed RNA polymerase 0 134.24 9.78E-05 334770000 127980 176530 149010 159060 210640 231480 174780 173570 153850 187020 FALSE TRUE 133032.7492 206847.6543 152893.323 190521.5933 174835.488 177722.2781 161080.2869 171243.5781 148312.9686 223662.9883 0.594791075 0.924818433 0.683587947 0.851824411 0.78169164 0.794598514 0.720191964 0.765632165 0.663109125 1 17.77096701 -1.099023898 4.397279963 1.000022472 0.76032292 0.400077976 0.09024466 11056133.8 2763289.285 2779.375596 0.01877004 0.079611554 1.099023898 -0.239699551 ISNLS(ph)PEEEQGLWK ddPTM_MDA-MB-175_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 400.75 2.54E-115 1395542000 1924790 1323750 1700290 1209990 2083920 2145250 1937740 1671500 1772600 1151805 TRUE FALSE 2000782.195 1551093.765 1744600.954 1449322.411 1729696.023 1647048.199 1785854.875 1649096.277 1708804.472 1377479.137 1.452495462 1.126037937 1.266517152 1.052155616 1.255696712 1.195697383 1.296466006 1.197184213 1.240530202 1 20.39359904 -1.239059141 4.6695337 0.999950121 1.224502955 0.320816519 0.100563124 5.95E-05 9.69E-06 0.088097167 0.020758904 0.057668793 1.239059141 0.224552834 ISNYGWDQSDKFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISNYGWDQSDKFVK 14 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 199.58 1.87E-08 3390600000 2753400 1712210 2370200 1805460 3233700 2898200 3041400 2507700 3008700 1657110 FALSE TRUE 2862106.358 2006268.748 2431969.359 2162574.599 2684036.829 2225136.973 2803007.121 2474088.383 2900417.475 1981788.977 1.444203389 1.01235236 1.227158586 1.091223447 1.354350468 1.122792082 1.414382234 1.248411618 1.463534972 1 20.91837192 2.791723098 1.487122766 1.289086516 1.192374674 0.006018228 0.167017308 1.222318389 5.465325343 0.062907587 0.063141234 619.0462519 -2.791723098 -0.096711842 ISPFEHQTYCQR ddPTM_MDA-MB-175_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 ;;; 168.19 4.72E-05 1963440000 647180 1225980 1121600 1164600 1441810 1554900 1211700 1260310 1125360 1406150 FALSE TRUE 672731.1661 1436532.528 1150829.817 1394954.404 1196731.651 1193798.04 1116723.788 1243417.606 1084858.513 1681658.17 0.400040376 0.85423575 0.684342298 0.82951127 0.711637878 0.709893402 0.664061108 0.739399735 0.645112385 1 20.68145305 -2.22943458 2.180614322 1.936289582 0.7041365 0.378212176 0.117276462 9469943.234 1731837.291 43665250.95 0.02642037 0.005896108 2.22943458 -1.232153082 ISQEHLADHFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISQEHLADHFDSR 13 0 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 0 ;; 181.75 6.81E-06 612750000 159939 344313 340711 363778 322701 448015 326702 354659 326661 390164 FALSE TRUE 166253.5152 403446.0794 349590.2086 435732.2026 267848.3993 343970.306 301094.2436 349905.3762 314904.5344 466609.1657 0.356301435 0.86463385 0.749214191 0.933826926 0.574031586 0.737170059 0.64528146 0.749889633 0.674878587 1 18.83185512 -1.15367797 4.051991455 1.000107274 0.709922391 0.262341301 0.150623088 16114861.44 9176417.812 14300.17714 0.032483958 0.070197562 1.15367797 -0.290184883 ISQMPVILTPLHFDRDPLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISQMPVILTPLHFDRDPLQK 20 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ; 209.67 2.68E-22 528680000 694070 580530 674270 662960 913710 921690 800180 719130 810210 582450 FALSE TRUE 721472.4195 680231.5116 691842.0301 794091.5093 758397.9006 707641.4658 737459.8007 709491.2386 781050.7004 696569.9258 1.035750171 0.976544474 0.993212604 1.140002575 1.088760615 1.01589437 1.058701752 1.018549915 1.121281111 1 19.40990866 ISQRDPS(ph)PESNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISQRDPSPESNK 12 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.993)PES(0.007)NK;ISQRDPS(1)PESNK 178.68 3.34E-05 798170000 814050 554550 676120 479590 845970 901820 769170 699180 753630 503790 TRUE FALSE 846189.3226 649789.6487 693740.2426 574451.4706 702172.3216 692385.9722 708880.4455 689808.6357 726507.0035 602498.0049 1.404468257 1.078492615 1.1514399 0.953449581 1.165435098 1.149192141 1.176568951 1.14491439 1.205824746 1 19.20059694 4.743876786 24.85852906 1.121253186 1.404468386 0.560871571 0.076879618 393.3297203 1839156.18 0.017820582 0.152695243 55446.83824 -4.743876786 0.2832152 ISQRDPS(ph)PESNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ISQRDPSPESNKK 13 2 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;Q8NDX5-3 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 1 ISQRDPS(0.995)PES(0.005)NKK;ISQRDPS(0.998)PES(0.002)NKK;ISQRDPS(0.962)PES(0.038)NKK 127.2 9.38E-05 426000000 1469900 694800 1015340 638470 1527040 1306350 1280940 995880 1222690 603060 TRUE FALSE 1527932.787 814126.4952 1041800.595 764757.4604 1267474.286 1002970.01 1180536.576 982531.8575 1178685.626 721218.0607 2.118544821 1.128821558 1.444501533 1.060369259 1.757407857 1.390661251 1.636864965 1.362322869 1.634298543 1 19.460076 -1.023209342 4.524157463 0.999982809 1.479006779 0.206575164 0.292583073 17212673.62 3892917.296 3112.112549 0.062105888 0.094796141 1.023209342 0.47902397 ISQSALPPLPGS(ph)PAIQINGEWETHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISQSALPPLPGSPAIQINGEWETHK 25 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 ISQSALPPLPGS(1)PAIQINGEWETHK;ISQSALPPLPGS(1)PAIQINGEWETHK 181.88 1.50E-17 490680000 793660 636300 854490 624970 1000980 1039920 1040910 835230 896330 653010 TRUE FALSE 824994.3096 745579.5753 876758.7114 748587.2007 830833.7771 798414.3401 959320.7543 824035.108 864071.2584 780954.8069 1.056391871 0.954702588 1.12267535 0.958553804 1.063869215 1.02235665 1.228394711 1.055163629 1.106429272 1 19.57487954 ISQTVEILK ddPTM_MDA-MB-175_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 532860000 975130 371290 519670 398630 734150 706010 653730 534730 661360 390000 FALSE TRUE 1013628.885 435056.1693 533213.0271 477477.8242 609359.4452 542049.8772 602488.9344 527562.819 637557.7828 466413.033 2.173243056 0.932770181 1.143220685 1.02372316 1.306480313 1.16216709 1.291749783 1.131106512 1.366938181 1 18.83124858 4.746548127 24.95294765 1.161042643 2.173243564 0.840189268 0.133695281 346.5503568 1082596.44 0.030277692 0.335989656 55788.9422 -4.746548127 1.012200921 ISRPGDSDDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ISRPGDSDDSR 11 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;; 140.91 3.50E-05 17213280000 7261340 7910960 7690280 8096870 8079440 9152360 8665980 7685380 7187030 7056770 FALSE TRUE 7548023.31 9269605.841 7890695.014 9698406.719 6706099.675 7026863.095 7986717.843 7582370.052 6928370.194 8439408.971 0.894378189 1.098371447 0.934981945 1.149180796 0.794617218 0.832625024 0.946359854 0.898447993 0.820954431 1 23.00871054 3.227048559 24.99996424 0.8807863 1.018863629 0.366276538 0.088309169 222.5168423 483224.117 0.023969455 0.028881891 1686.74161 -3.227048559 0.138077329 ISS(ph)LLEEQFQQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISSLLEEQFQQGK 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 1 IS(0.033)S(0.967)LLEEQFQQGK 123.76 0.00023044 43120000 120530 103320 114930 85624 148370 157300 140980 115780 130760 95337 TRUE FALSE 125288.6175 121064.4063 117925.1702 102560.1716 123150.1204 120769.4589 129929.6192 114228.1585 126053.9731 114016.4598 1.098864301 1.061815167 1.034281984 0.899520752 1.080108263 1.059228283 1.139568966 1.001856738 1.105576979 1 16.79888259 ISS(ph)PTETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 IS(0.029)S(0.97)PT(0.001)ETER;IS(0.002)S(0.985)PT(0.012)ETER;ISS(0.993)PT(0.007)ETER;IS(0.011)S(0.983)PT(0.006)ETER;IS(0.003)S(0.849)PT(0.148)ETER 233.14 4.03E-10 9126550000 7533590 7429030 8045110 7086760 9289250 9777170 8598960 8023100 7958600 6793180 TRUE FALSE 7831021.95 8704908.113 8254772.176 8488499.976 7710266.603 7506570.442 7924951.046 7915563.468 7672171.541 8124173.558 0.963916132 1.071482293 1.016075311 1.044844736 0.949052423 0.923979576 0.975477812 0.9743223 0.944363323 1 22.95378963 3.235008056 24.99936784 0.960208556 1.026893791 0.483490761 0.03177637 71.46382617 502891.844 0.008666615 0.010752779 1717.940253 -3.235008056 0.066685235 ISSDLDGHPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ISSDLDGHPVPK 12 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;;; 111.12 0.0014159 3775580000 7311340 8389470 9835590 8423220 16275600 13274600 12005170 10694310 10784730 9634790 FALSE TRUE 7599997.349 9830296.211 10091913.56 10089307.78 13509079.33 10191775.33 11064173.41 10550970.27 10396589.67 11522542.63 0.659576414 0.853136024 0.875840852 0.875614706 1.172404369 0.884507496 0.960219785 0.915680732 0.902282596 1 23.45795577 5.019641605 1.016674808 0.956198402 0.359689643 0.5533135 0.081448989 2.322861138 1.324276996 0.024478049 1.721016343 104626.4778 -5.019641605 -0.59650876 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ISSIQATTAAGSGHPTSCCSAAEIMAVLFFHTMR 34 0 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 373.89 9.32E-149 2062729000 155653.8 307947 376039 325400 409847 453533 353368 350399 355612 420396 FALSE TRUE 161799.1322 360834.5018 385838.8853 389763.1488 340181.3533 348206.8341 325670.0928 345702.4745 342813.5936 502764.5472 0.321818897 0.717700768 0.767434552 0.775239923 0.676621602 0.692584304 0.647758667 0.687603126 0.681857135 1 18.9395234 -5 0.240257751 2.849877477 0.639602736 0.432618462 0.118443872 171.8046578 1.713518703 155.5707554 0.183753408 1.00E-05 5 -2.210274741 ISSIQSIVPALEIANAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 124.84 3.10E-05 150340000 241530 280580 241380 323020 241650 378160 282360 246910 247500 289420 FALSE TRUE 251065.7909 328767.4324 247670.5611 386912.3919 200574.4193 290338.0711 260227.8854 243600.5753 238592.5233 346126.3077 0.72535888 0.949848148 0.715549658 1.11783584 0.579483312 0.83882116 0.751829259 0.703790986 0.689322129 1 18.40093907 3.211945261 24.99992082 0.746172068 0.870798746 0.125120977 0.147779931 401.4521691 377084.7395 0.039201499 0.046867157 1629.090686 -3.211945261 0.124626678 ISSLPVSRPIS(ph)PSPSAILER ddPTM_MDA-MB-175_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(0.984)PS(0.012)PS(0.004)AILER;ISSLPVSRPIS(0.948)PS(0.044)PS(0.008)AILER;ISSLPVSRPIS(0.983)PS(0.013)PS(0.004)AILER;ISSLPVS(0.009)RPIS(0.91)PS(0.061)PS(0.02)AILER;ISSLPVSRPIS(0.966)PS(0.033)PSAILER 269.06 1.88E-37 4738798000 1617030 2006486 1984507 1933846 2219080 2390095 2004603 2068797 1860480 2019123 TRUE FALSE 1680871.593 2351084.362 2036224.883 2316354.967 1841881.574 1835031.658 1847476.979 2041068.16 1793521.688 2414731.493 0.696090475 0.97364215 0.843251056 0.959259849 0.762768688 0.759931969 0.765085884 0.845256777 0.742741664 1 21.20343135 4.80675389 21.69291137 0.839464579 0.696081537 0.192587704 0.092341348 46502.35767 14789054.48 0.021387349 82.03138379 64084.63123 -4.80675389 -0.143383043 ISSLPVSRPISPS(ph)PSAILER ddPTM_MDA-MB-175_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(0.316)PS(0.466)PS(0.218)AILER 93.229 0.00093268 559250000 183070 235920 221540 184410 247890 274400 237230 215950 216890 235300 TRUE FALSE 190297.745 276437.4248 227313.5144 220885.7476 205753.7463 210674.7586 218635.2927 213055.5435 209084.1713 281402.5299 0.676247456 0.982355862 0.807787743 0.784945848 0.73117234 0.748659789 0.776948568 0.757120213 0.743007433 1 18.10227577 6.095005912 14.05787451 0.793102125 0.522744838 0 0.101210892 0 0 0.020742737 0 1244531.552 -6.095005912 -0.270357287 ISSPTETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;; 206.03 3.25E-05 10802550000 2867100 3347890 3197280 3037510 3487920 3878860 3309090 3246210 3134230 3152480 FALSE TRUE 2980295.322 3922864.065 3280603.743 3638320.412 2895044.604 2978053.55 3049714.879 3202699.865 3021429.675 3770148.098 0.79049821 1.040506623 0.870152487 0.965033818 0.767886176 0.789903599 0.808911162 0.84948914 0.80140875 1 21.84618977 3.24424402 24.99979589 0.826354075 0.922088037 0.169611378 0.084995472 194.7781763 856771.7576 0.02178095 0.028698327 1754.866245 -3.24424402 0.095733962 ISSVSSQFSDGPIPS(ph)PSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISSVSSQFSDGPIPSPSAR 19 0 E7EM83;Q92932-2;Q92932-4;Q92932;Q92932-3 E7EM83 PTPRN2 Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase N2 1 ISSVSSQFSDGPIPS(0.945)PS(0.054)AR;ISSVSSQFSDGPIPS(0.996)PS(0.004)AR 180.86 3.43E-14 123335000 101123 120889 100724 114557 119961 143880 92193 108391 92553 129767 TRUE FALSE 105115.4141 141650.7454 103348.9502 137216.0327 99570.07207 110466.0505 84966.67176 106938.1959 89222.03561 155192.3591 0.677323386 0.912743038 0.66594097 0.884167452 0.64159133 0.711800833 0.547492623 0.689068692 0.574912554 1 17.243698 3.214227792 24.99429765 0.670468598 0.78565781 0.080665808 0.136987779 414.314082 425575.8104 0.035962971 0.043003292 1637.675272 -3.214227792 0.115189212 ISTCAPSTLHITQNTEQELHS(ph)PTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISTCAPSTLHITQNTEQELHSPTVK 25 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 ISTCAPSTLHITQNTEQELHS(0.885)PT(0.115)VK 309.28 3.19E-74 1103300000 515040 587540 781010 611490 1044200 1115000 893810 924610 889110 691240 TRUE FALSE 535374.1769 688445.4246 801363.7622 732440.8969 866707.257 856058.148 823750.8367 912217.1153 857111.1048 826675.2434 0.647623334 0.832788244 0.96938159 0.886008022 1.04842532 1.035543467 0.996462448 1.103476997 1.036817192 1 19.65696116 5.389796155 0.606016577 1.047640425 2.11E-13 0.869208801 0.046041657 2.270665167 0.355172717 0.020172575 1.974890388 245355.702 -5.389796155 -1.047640425 ISTKNEEPVRS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ISTKNEEPVRSPERR 15 3 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 ISTKNEEPVRS(1)PERR 83.423 0.048185 188390000 136220 142420 172730 78811 270280 185270 105000 150090 182740 222690 TRUE FALSE 141598.0708 166879.5271 177231.4857 94399.58057 224337.9021 142243.8503 96769.82563 148078.289 176163.2231 266321.8418 0.531680278 0.62660849 0.665478597 0.354456773 0.842356378 0.534105086 0.3633567 0.55601256 0.661467426 1 18.02281123 0.843888999 3.127218915 0.999788321 0.557922777 0.496171688 0.133343904 0.574910639 9.811987537 0.124377516 0.03244222 6.980539661 -0.843888999 -0.441865544 ISTLYYQLGDHELSLSEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ISTLYYQLGDHELSLSEVR 19 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ;;; 195.56 2.25E-21 290400000 207739 243085 228358 208040 271665 310832 225038 243218 215005 211537 FALSE TRUE 215940.6961 284832.9578 234309.1971 249189.6911 225487.4803 238645.9787 207398.9335 239958.0605 207267.012 252983.625 0.853575784 1.125894839 0.926183254 0.985003243 0.891312552 0.943325793 0.819811691 0.948512223 0.819290229 1 17.94868448 3.240518141 24.91784851 0.900503693 0.980289259 0.141526902 0.082119634 81.26000304 1034367.643 0.021256083 0.027393952 1739.875373 -3.240518141 0.079785566 ISVPPS(ph)PTYPPAGPPAFPAGDSKPELPLTVAIRPFLADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISVPPSPTYPPAGPPAFPAGDSKPELPLTVAIRPFLADK 39 2 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 ISVPPS(0.962)PT(0.038)YPPAGPPAFPAGDSKPELPLTVAIRPFLADK;ISVPPS(0.983)PT(0.017)YPPAGPPAFPAGDSKPELPLTVAIRPFLADK 209.83 2.12E-31 810670000 558430 317382 455097 329622 679570 595010 564270 490780 565260 342902 TRUE FALSE 580477.2476 371889.8896 466957.2017 394820.2478 564056.9341 456827.945 520041.043 484201.8969 544916.403 410087.0816 1.415497521 0.9068559 1.138678155 0.962771727 1.375456481 1.113977897 1.268123446 1.180729456 1.328782172 1 18.64557077 3.246444704 24.99996588 1.216781598 1.094067471 0.091359239 0.160254382 367.4979788 1165306.623 0.040852193 0.054343778 1763.781179 -3.246444704 -0.122714127 ISVSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 ISVSSPGR 8 0 O75864;O75864-2 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 ISVS(0.079)S(0.921)PGR;ISVS(0.014)S(0.986)PGR;ISVS(0.059)S(0.941)PGR;ISVS(0.004)S(0.996)PGR;ISVS(0.008)S(0.992)PGR;ISVS(0.05)S(0.95)PGR 154.04 0.00045258 8092150000 10781500 11768100 11809500 10869200 12704000 14427800 11245700 11330600 10464200 10580200 TRUE FALSE 11207161.95 13789179.63 12117265.27 13019095.32 10544578.62 11077162.11 10364232.65 11178731.84 10087595.49 12653187.62 0.885718467 1.089779117 0.95764527 1.028918223 0.833353534 0.875444389 0.819100527 0.883471594 0.797237486 1 23.59299754 3.236964974 24.99999848 0.860845298 0.995257696 0.41505026 0.070791508 34.79960709 545231.3252 0.018240283 0.022922262 1725.698708 -3.236964974 0.134412398 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 IS(0.047)Y(0.062)T(0.892)PPES(0.999)PVPS(0.001)YASSTPLHVPVPR;IS(0.099)Y(0.006)T(0.895)PPES(0.999)PVPS(0.001)YASSTPLHVPVPR;IS(0.116)Y(0.185)T(0.701)PPES(0.987)PVPS(0.006)YAS(0.002)S(0.002)T(0.002)PLHVPVPR;IS(0.116)Y(0.257)T(0.628)PPES(0.999)PVPSYASSTPLHVPVPR 151.41 2.62E-07 1051860000 316527 436371 447997 415994 471220 509411 427648 439675 436184 444329 TRUE FALSE 329023.7304 511314.3248 459672.1699 498276.3716 391122.1927 391108.0154 394127.8323 433781.8758 420485.823 531386.7604 0.61917939 0.962226316 0.865042572 0.937690603 0.73604053 0.73601385 0.741696748 0.816320443 0.791299021 1 19.01940276 4.766283236 23.47458333 0.829033053 0.619178701 0.333465736 0.09305191 5266.450925 4459284.372 0.022355296 1.840287913 58382.57365 -4.766283236 -0.209854352 ISYT(ph)PPESPVPSYASSTPLHVPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 1 IS(0.326)Y(0.248)T(0.399)PPES(0.028)PVPSYASSTPLHVPVPR;IS(0.101)Y(0.413)T(0.472)PPES(0.014)PVPSYASSTPLHVPVPR 92.01 0.045934 348900000 104119 124582 140482 127064 151763 155142 134002 145080 130787 135787 TRUE FALSE 108229.6985 145977.9894 144143.0763 152196.88 125966.3795 119112.6217 123498.5731 143135.4399 126080.0014 162391.8629 0.666472424 0.898924286 0.887624994 0.937219866 0.775693913 0.733488856 0.760497299 0.881420026 0.77639359 1 17.30911982 -1.065523924 4.189828736 1.000018979 0.82029038 0.316773211 0.081738628 0.453765034 45823667.55 2153.532584 0.019206464 0.085995569 1.065523924 -0.179728598 IT(ph)SPLMEPSSIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.689)S(0.311)PLMEPSSIEK 170.79 0.00029285 183250000 593990 459610 584910 462370 791740 721650 687510 572840 647620 489100 TRUE FALSE 617441.1839 538544.4422 600153.2351 553825.406 657160.3176 554057.7242 633621.1697 565162.0168 624312.2827 584929.7806 1.05558172 0.920699305 1.026026123 0.946823746 1.123485826 0.947220919 1.083243136 0.966204894 1.067328598 1 19.15790392 ITADGAHFELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITADGAHFELR 11 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 134.75 0.00013427 302450000 468170 490370 518150 536370 578750 634790 574560 576810 579560 510520 FALSE TRUE 486653.7131 574587.233 531653.4147 642462.3851 480374.2817 487369.6428 529524.4859 569078.8054 558701.7488 610546.6195 0.797078712 0.941102963 0.870782669 1.052274085 0.786793779 0.798251317 0.867295746 0.932080839 0.915084501 1 19.21974193 0.999729329 1.29102265 0.996503042 0.879170961 0.194884955 0.075959007 0.820256643 2.803941264 0.071865065 0.022018981 9.99376951 -0.999729329 -0.117332081 ITADLLSNGIDVYPQKEFDEDSEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ITADLLSNGIDVYPQKEFDEDSEDR 25 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4 Q9UHD8 9-Sep Septin-9 0 ;;; 339.62 2.64E-88 1348090000 713395 503591 668756 569008 784024 859086 938799 686857 770659 405448 FALSE TRUE 741560.3855 590078.8369 686184.3307 681556.0841 650755.8805 659576.2961 865213.4813 677650.8054 742923.1331 484887.7728 1.52934437 1.216938991 1.415140511 1.405595526 1.342075253 1.360265886 1.784358216 1.397541541 1.532154809 1 18.88729135 ITADLLSNGIDVYPQKEFDEDSEDRLVNEK ddPTM_MDA-MB-175_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 ; 338.03 6.98E-106 604532000 255886 136004 197378 132966 288440 270267 267482 194653 255598 139928 FALSE TRUE 265988.5769 159361.629 202521.8328 159266.2779 239411.0718 207501.5852 246516.0619 192043.9949 246399.0779 167344.2125 1.589469829 0.952298419 1.210211156 0.951728629 1.430650443 1.239968697 1.473107783 1.147598665 1.472408721 1 17.35245913 3.215392872 24.99995625 1.300446759 1.162402158 0.064992931 0.216061036 566.6907751 611505.8953 0.057807782 0.069133842 1642.074558 -3.215392872 -0.138044601 ITDFENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITDFENRR 8 1 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 80.438 0.040804 450940000 364790 382040 408220 404070 505060 514590 440050 408410 402340 432900 FALSE TRUE 379192.1909 447652.3981 418858.5486 483993.84 419210.0816 395084.2712 405557.7311 402935.932 387859.862 517718.4666 0.732429332 0.864663764 0.809046954 0.934859139 0.809725958 0.763125708 0.783355737 0.778291597 0.749171388 1 18.98180825 3.013503537 24.99539237 0.795772361 0.840080826 0 0.082185965 697.8023922 1291641.19 0.022131593 0.026441291 1031.58148 -3.013503537 0.044308465 ITDKEAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITDKEAAER 9 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;; 112.89 0.0017225 735480000 1423600 1176600 1281150 1127310 1794290 1750750 1606650 1455340 1525840 1171720 FALSE TRUE 1479804.827 1378671.897 1314537.821 1350288.553 1489297.227 1344164.845 1480716.575 1435833.548 1470925.316 1401296.1 1.056025794 0.983854802 0.938087119 0.963599737 1.062799808 0.959229705 1.05667644 1.024646788 1.049689153 1 20.41833041 2.629124553 1.199843029 1.032015622 0.988018757 0.108220663 0.04176226 0.881114563 2.601194573 0.021288432 0.017847805 425.7204901 -2.629124553 -0.043996866 ITDLYTDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITDLYTDLR 9 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 132.9 0.00067957 199683000 353554 378689 355956 384541 405167 490140 418266 390034 351003 341881 FALSE TRUE 367512.5849 443725.89 365232.5058 460602.0621 336296.8581 376312.4131 385481.218 384806.2322 338370.4706 408866.0362 0.898858189 1.085259842 0.893281597 1.126535396 0.822511112 0.920380711 0.942805672 0.941154799 0.82758273 1 18.6412687 3.222320805 24.9967607 0.911399179 0.999310525 0.225121111 0.083447669 355.2586411 546822.8781 0.022261491 0.026680891 1668.479231 -3.222320805 0.087911346 ITDLYTDLRDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ITDLYTDLRDGR 12 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 154.94 6.22E-05 642200000 758710 1113930 1012840 665280 1113870 1131970 638310 936440 1014050 1254980 FALSE TRUE 788664.4567 1305238.812 1039235.442 796870.3983 924534.7753 869087.1227 588277.5943 923888.5535 977554.5386 1500869.303 0.525471775 0.869655212 0.692422345 0.530939234 0.615999523 0.579055832 0.391957909 0.615568958 0.65132556 1 20.51736692 0.728810465 3.036815544 0.999958956 0.60277534 0.508441946 0.116502097 1.853355918 19.7092362 0.116448179 0.030420944 5.355628756 -0.728810465 -0.397183616 ITDSAGHILYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITDSAGHILYSK 12 0 P49755;G3V2K7 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 117.23 0.00075578 1510990000 1607660 2047090 2164900 3301300 5103800 4877800 3640800 2371800 2521900 4552600 FALSE TRUE 1671131.658 2398661.783 2221319.072 3954287.287 4236257.899 3745004.874 3355424.583 2340009.9 2431137.312 5444594.805 0.306934073 0.440558365 0.407986113 0.726277607 0.778066697 0.687839042 0.616285454 0.429785867 0.446523093 1 22.37639325 3.799368241 7.439910557 0.63520939 0.38893743 0.390024334 0.158871499 0.352531303 38.162466 0.042747692 0.077334257 6300.401719 -3.799368241 -0.24627196 ITEAEKNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 ITEAEKNER 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 211.78 4.19E-06 9430240000 7746900 6377300 6991500 5590890 9944270 9998510 8746630 7711000 8264840 6655520 FALSE TRUE 8052753.594 7472551.666 7173704.234 6696751.355 8253946.537 7676507.581 8061046.286 7607646.658 7967390.023 7959541.716 1.011710709 0.938816823 0.901271014 0.841348861 1.03698766 0.964440901 1.012752565 0.955789533 1.000986025 1 22.92425394 3.218759621 24.99985811 0.990268789 0.922823522 0.379753653 0.044735893 274.3100059 346330.7866 0.013191055 0.015785489 1654.85376 -3.218759621 -0.067445267 ITEDYYVHLIADNLPVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITEDYYVHLIADNLPVATR 19 0 A0A0C4DFM1;Q92544 A0A0C4DFM1 TM9SF4 Transmembrane 9 superfamily member 4 0 128.32 2.17E-05 128810000 103270 107410 103700 170410 167380 208670 157880 106600 104220 190340 FALSE TRUE 107347.1793 125856.832 106402.5072 204116.5894 138928.8074 160209.5549 145504.9531 105171.2014 100469.1426 227633.4787 0.471579049 0.552892451 0.467429078 0.896689672 0.610317991 0.703804888 0.639207176 0.462019919 0.441363648 1 17.79635323 ITEFCHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 186.43 0.00059898 8473480000 5395130 7380500 5565630 7213190 7359860 8281100 6551720 6038290 5363080 6821980 FALSE TRUE 5608133.898 8648043.463 5710674.89 8639937.453 6108833.626 6357940.026 6038179.067 5957356.599 5170063.798 8158616.366 0.687387867 1.059988983 0.699956296 1.058995431 0.748758534 0.779291456 0.740098418 0.730192024 0.633693701 1 22.95989307 ITESEEVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ITESEEVVSR 10 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 148.5 5.82E-05 1816530000 828419 955500 867170 962790 1059370 1092850 969770 942250 909670 880380 FALSE TRUE 861125.6218 1119599.692 889769.1626 1153226.988 879298.6658 839052.1498 893756.8934 929620.68 876931.1544 1052873.605 0.817881289 1.063375211 0.845086398 1.095313799 0.835141713 0.796916311 0.848873872 0.882936637 0.832893094 1 20.00590082 ITEYLCEPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITEYLCEPLRK 11 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;K7ERB2;K7EN71;Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 P63010;Q10567-4 AP2B1;AP1B1 AP-2 complex subunit beta;AP-1 complex subunit beta-1 0 ; 140.39 6.19E-05 1116450000 1361070 1062510 1215910 1148650 1824720 1740090 1468760 1284950 1341090 1205130 FALSE TRUE 1414806.095 1244987.827 1247597.613 1375849.542 1514554.746 1335980.469 1353634.753 1267727.347 1292824.433 1441252.15 0.981650639 0.863823743 0.86563452 0.954620981 1.050860355 0.926958179 0.939207448 0.879601357 0.897014747 1 20.45889133 3.717645606 24.16981917 0.943477783 0.899715038 0.119106834 0.055265907 1215.404919 1404547.491 0.015733104 0.024407472 5219.700758 -3.717645606 -0.043762745 ITFHGEGDQEPGLEPGDIIIVLDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITFHGEGDQEPGLEPGDIIIVLDQK 25 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 198.55 7.58E-25 349590000 218924 155563 194927 170134 241450 249400 267530 204761 220604 149221 FALSE TRUE 227567.2886 182279.7351 200006.9578 203785.9974 200408.4152 191480.6297 246560.2995 202016.5137 212664.5051 178457.9979 1.275186829 1.021415332 1.120750877 1.141926951 1.123000468 1.072973091 1.381615295 1.132011544 1.191678196 1 17.44522503 ITGCDPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITGCDPFR 8 0 A0A087WT90 A0A087WT90 MRPL46 0 80.462 0.059057 421010000 512220 627020 507370 588830 860430 767980 717120 574670 549370 834480 FALSE TRUE 532442.8411 734705.8075 520592.479 705298.8165 714174.4159 589628.2838 660910.2606 566967.4886 529598.281 997980.3789 0.53352035 0.736192638 0.521646006 0.706726136 0.715619697 0.590821519 0.66224775 0.568114865 0.530670033 1 19.92865193 -1.008144352 4.600781095 1.000008913 0.621703938 0.683291852 0.077910863 0.117138078 45281897.94 1069.330936 0.017284108 0.098142168 1.008144352 -0.378304975 ITGMLLEIDNSELLHMLESPESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ITGMLLEIDNSELLHMLESPESLR 24 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YB75;H0YAS6;H0YAS7;B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0Y6X6;H0YER0 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ;;; 183.42 2.15E-17 414807000 142716.5 134158.1 135633.4 152899.5 168787.7 169941.4 172535.9 144503.1 148804.9 129267.3 FALSE TRUE 148351.0576 157198.7101 139168.1178 183142.5647 140097.227 130475.0853 159012.0853 142566.2723 143449.4407 154594.7525 0.959612505 1.016843765 0.90021243 1.184662234 0.906222396 0.843981334 1.028573627 0.922193477 0.927906274 1 17.23813182 ITHEVDELTQIIADVSQDPTLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITHEVDELTQIIADVSQDPTLPR 23 0 P36954;K7EKS1 P36954 POLR2I DNA-directed RNA polymerase II subunit RPB9 0 ;; 159.74 1.97E-11 288470000 140901 181549 175025 172349 187976 209347 175402 177281 165735 187488 FALSE TRUE 146463.8803 212728.6285 179586.2953 206439.1178 156023.9067 160729.3319 161653.5329 174904.8382 159770.2297 224222.6839 0.653207239 0.948738213 0.80092831 0.920687926 0.695843542 0.716829043 0.720950843 0.780049704 0.712551589 1 17.77457271 5.017858814 15.19548216 0.796043529 0.386471663 0.156797982 0.104716086 3566622.172 70590409.36 0.024128654 32515637.11 104197.8635 -5.017858814 -0.409571866 ITHQEVDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITHQEVDSR 9 0 Q8WTS6;D6RJA0 Q8WTS6 SETD7 Histone-lysine N-methyltransferase SETD7 0 ;; 121.9 0.00060094 186370000 532730 616170 661260 644510 685650 831250 690840 653240 629770 659460 FALSE TRUE 553762.5918 721992.4044 678492.9788 771992.1543 569103.4579 638204.7852 636690.1556 644484.3863 607104.7007 788668.5609 0.702148684 0.915457317 0.860301795 0.978854988 0.721600285 0.809217987 0.807297498 0.817180268 0.769784331 1 19.58905961 4.759565556 23.50069294 0.843028096 0.702148363 0.214476219 0.084753037 3651.872175 4085629.445 0.019492796 0.778598583 57486.45868 -4.759565556 -0.140879733 ITITNDKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 182.64 4.20E-05 2387880000 1903590 1681190 1650150 1260220 2922370 2246780 1698080 1704490 1912820 2295850 FALSE TRUE 1978745.203 1969921.305 1693154.265 1509487.755 2425626.591 1724999.395 1564980.052 1681644.1 1843977.982 2745677.851 0.720676391 0.717462649 0.616661661 0.549768704 0.883434519 0.628259938 0.569979487 0.612469558 0.671592984 1 21.38873093 -1.835102239 2.597983807 1.127484031 0.658129117 0.551964989 0.090876443 15020925.71 10164084.49 11946309.02 0.02194727 0.01461833 1.835102239 -0.469354914 ITITNDQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITITNDQNR 9 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 126.24 0.0031918 0 100180 104360 104430 97199 150680 137580 119580 96428 113790 135260 FALSE TRUE 104135.1838 122283.0182 107151.5316 116424.6721 125067.4674 105629.13 110207.0071 95135.54038 109694.7201 161761.6073 0.643757103 0.755945865 0.662403974 0.719729941 0.773159154 0.652992585 0.681292731 0.588121879 0.678125805 1 17.30350971 -1.313533699 3.118930631 1.002296071 0.681196177 0.770534005 0.051722424 38240508.43 52259437.33 823034.8614 0.013745317 0.048580983 1.313533699 -0.321099894 ITKPGS(ph)IDSNNQLFAPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 IT(0.001)KPGS(0.999)IDSNNQLFAPGGR;ITKPGS(1)IDSNNQLFAPGGR;IT(0.015)KPGS(0.984)IDSNNQLFAPGGR 235.25 2.25E-24 1008809000 340165 349106 485262 360546 459717 440049 418414 434990 545682 442631 TRUE FALSE 353594.9769 409062.2398 497908.3264 431860.9227 381574.4685 337854.2888 385617.6174 429159.6706 526043.0114 529356.0698 0.667971895 0.772754415 0.940592457 0.815823124 0.720827606 0.638236356 0.728465468 0.810720222 0.993741342 1 19.01387895 1.295876026 3.360833128 1.005932226 0.760048759 0.594081291 0.078703857 0.18071472 3.435647245 0.073386041 0.022279702 19.76405374 -1.295876026 -0.245883468 ITKPGSIDSNNQLFAPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 197.09 7.33E-16 262170000 240440 283330 301980 248610 361020 400630 333030 329810 343640 281230 FALSE TRUE 249932.7569 331989.7235 309849.8469 297784.316 299653.9494 307589.7541 306926.2384 325389.4364 331272.4635 336331.634 0.743114033 0.987090389 0.921262871 0.885388961 0.890947859 0.914543037 0.912570235 0.967466047 0.984957792 1 18.35952495 1.673350966 1.212421238 1.000641359 0.893525651 0.359486106 0.057034009 0.50212988 1.396748936 0.046092413 0.017331536 47.13580902 -1.673350966 -0.107115707 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;ITKPGSIDSNNQLFAPGGRLS(1)WGK 227.57 2.24E-33 4584880000 3073420 1725060 2174410 1323230 2448090 2379950 1914880 1677910 1965640 1383600 TRUE FALSE 3194760.995 2021325.636 2231076.911 1584960.945 2031964.536 1827242.681 1764786.702 1655420.361 1894897 1654689.929 1.930730911 1.221573662 1.348335341 0.957859788 1.228003205 1.104281019 1.066536195 1.000441431 1.145167422 1 20.65812947 7.663891911 0.890901743 1.074987894 200 0.851908562 0.103664618 141.0625655 0.63307761 0.030131538 56594.54014 46120277.4 -7.663891911 198.9250121 ITLDNAYMEK ddPTM_MDA-MB-175_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 ;;;;; 157.78 1.99E-05 1272968000 1221980 1036480 1206770 972960 1586960 1557610 1435460 1187030 1246930 1120400 FALSE TRUE 1270224.714 1214487.377 1238219.418 1165408.584 1317209.106 1195878.683 1322944.894 1171119.804 1202053.233 1339920.929 0.94798483 0.906387348 0.924098871 0.869759222 0.983049878 0.892499444 0.98733057 0.874021578 0.897107588 1 20.35371644 ITLPVDFVTADKFDENAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITLPVDFVTADKFDENAK 18 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 228.39 2.23E-19 7614600000 5744100 2891870 4757200 2825670 6333700 5777300 5819100 4471200 5085100 2567880 FALSE TRUE 5970881.503 3388526.177 4881176.54 3384579.092 5257099.936 4435609.631 5362983.737 4411270.877 4902088.244 3071006.921 1.944274844 1.103392556 1.589438469 1.102107283 1.711848938 1.444350255 1.746327467 1.436424922 1.596247866 1 21.55028033 -1.706594936 7.221693354 0.996158318 1.505136911 0.273080424 0.253258878 0.01407498 0.000571842 0.220325749 0.0517499 0.019651923 1.706594936 0.508978593 ITLQDVVSHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITLQDVVSHSK 11 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 178.32 7.59E-06 2939200000 5730400 4014400 5098500 4356500 6216500 5867500 6336000 5093800 5858400 3336100 FALSE TRUE 5956640.617 4703841.972 5231371.098 5218202.697 5159821.55 4504862.048 5839367.764 5025525.943 5647557.328 3989744.922 1.492987831 1.178983134 1.311204401 1.307903838 1.293271037 1.129110291 1.463594259 1.259610838 1.415518395 1 21.92786508 -1.498571264 3.068194022 0.991070509 1.30892898 0.42590692 0.110029395 33104056.78 40032783.39 2503516.126 0.024087506 0.03172698 1.498571264 0.317858471 ITNDFYPEEDGKTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITNDFYPEEDGKTK 14 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ; 186.85 9.26E-07 623820000 964240 445390 680650 444980 938500 814360 885300 662050 776780 417810 FALSE TRUE 1002308.94 521882.2678 698388.2982 532995.7159 778974.1052 625237.2317 815907.8727 653176.3026 748823.8395 499671.87 2.005934294 1.044449966 1.397693847 1.066691459 1.558971301 1.251295639 1.632887344 1.307210475 1.498631171 1 18.93062148 -1.000853107 5.542998159 0.999998852 1.397993219 0.174877035 0.269318585 3.43E-06 6.18E-07 0.233074011 0.054935912 0.099803758 1.000853107 0.397994368 ITNFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITNFFR 6 0 P42574;A8MVM1 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ; 170.4 0.0029686 0 452960 458260 448360 423820 622080 588150 490750 466650 429040 506600 FALSE TRUE 470843.2106 536962.5902 460044.6299 507650.331 516339.0638 451561.076 452283.7327 460395.32 413598.9342 605858.5706 0.777150367 0.886283724 0.759326767 0.837902368 0.852243558 0.745324236 0.746517017 0.759905599 0.682665814 1 19.20862153 2.734663 24.88505311 0.767932085 0.8234574 0.018540096 0.085674691 764.7053689 4882387.204 0.02499572 0.024414793 542.8289483 -2.734663 0.055525315 ITNQVHGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITNQVHGLK 9 0 P51665 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 121.73 0.0006056 1145260000 1889390 2063180 2223910 2112640 2659600 2700500 2268520 2266160 2187030 2110620 FALSE TRUE 1963984.576 2417515.116 2281866.922 2530513.886 2207522.142 2073349.801 2090707.475 2235785.832 2108319.218 2524155.579 0.778075881 0.957752024 0.904011995 1.002518984 0.874558668 0.821403331 0.828279957 0.885755954 0.835257238 1 21.2673694 3.022822994 24.98255806 0.86324303 0.916619897 0.045285023 0.071686394 505.5589871 553392.2909 0.019597852 0.023422708 1053.957245 -3.022822994 0.053376867 ITPAHDQNDYEVGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ITPAHDQNDYEVGQR 15 0 P26640;A0A140T936 P26640 VARS Valine--tRNA ligase 0 ;;;; 255.16 1.02E-24 3301610000 606798 725772 788449 728797 838092 961610 736094 746124 752769 765605 FALSE TRUE 630754.8536 850417.6953 808996.6287 872950.8714 695633.4212 738290.6508 678397.0289 736123.4282 725676.9907 915610.6414 0.688889824 0.928798396 0.883559662 0.953408394 0.759748074 0.806336905 0.74092305 0.803969935 0.792560678 1 19.8043747 3.213763258 24.99475126 0.801739204 0.869737734 0.038941953 0.093949745 495.535295 499478.5112 0.025539922 0.030538218 1635.924506 -3.213763258 0.067998529 ITPFNLQEEMEEGHFDADGNYFLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITPFNLQEEMEEGHFDADGNYFLNR 25 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 0 ;; 250.06 1.96E-39 221443000 57928 68482 75001 70917 83947 93597 64839 73764 71102 79202 FALSE TRUE 60215.04217 80243.25078 76955.58767 84944.17093 69677.71893 71860.51523 59756.74975 72775.31423 68543.05291 94720.11549 0.635715464 0.847161665 0.812452427 0.896791252 0.735616913 0.758661609 0.630877079 0.768319526 0.723637768 1 16.53138322 -1.11658223 4.563394254 1.000022364 0.759597206 0.457476359 0.079463238 1.81E-05 3.51E-06 0.077224512 0.0182003 0.076457091 1.11658223 -0.240425159 ITPHTS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 ITPHTSPAPR 10 0 A0A0C4DFZ9;Q58A45-2;Q58A45-4;Q58A45-3;Q58A45 A0A0C4DFZ9 PAN3 PAB-dependent poly(A)-specific ribonuclease subunit PAN3 1 ITPHT(0.141)S(0.859)PAPR;ITPHT(0.139)S(0.861)PAPR;ITPHT(0.047)S(0.953)PAPR;ITPHT(0.021)S(0.979)PAPR 154.28 9.51E-06 2145420000 469476 612727 554320 564765 598070 677370 530151 562990 487667 559480 TRUE FALSE 488011.275 717958.0959 568766.0346 676473.8313 496410.275 520061.0831 488596.3793 555444.0399 470115.9599 669099.3941 0.729355428 1.07302159 0.850047152 1.011021438 0.741908122 0.777255349 0.730229894 0.830136815 0.702610052 1 19.35186101 3.226784786 24.96172936 0.786107399 0.922386122 0.199009936 0.115263069 280.7903639 595202.289 0.030188148 0.036358912 1685.717464 -3.226784786 0.136278723 ITPLEIEVLEETVQTMDTS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 ;; 200.13 3.03E-21 63542500 50761.2 66381 66313 61826.7 70554 78572 74021 66966.1 68830 70063 FALSE TRUE 52765.29137 77781.42038 68041.17126 74055.83673 58561.25628 60324.84377 68219.0406 66068.52896 66352.82175 83790.50341 0.629728779 0.928284438 0.812039175 0.883821361 0.698900877 0.719948459 0.814161961 0.788496623 0.791889523 1 16.35449912 -1.609605244 3.008070514 1.014061663 0.789924788 0.378297544 0.082393656 28312010.54 30601202.9 3141651.361 0.019285686 0.024569412 1.609605244 -0.224136875 ITPPAAKPGS(ph)PQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 169.43 2.02E-06 6012000000 3671100 1640930 2470620 1628220 3354500 3284800 3111100 2461470 2756800 1310440 TRUE FALSE 3816037.863 1922746.963 2535006.387 1950277.056 2784303.288 2521954.982 2867243.853 2428478.021 2657583.307 1567195.628 2.434946725 1.226871061 1.617543044 1.24443753 1.776615017 1.609215172 1.829537935 1.549569165 1.695757223 1 20.57975385 -1.205670887 4.334150816 0.999769029 1.640177507 0.27659236 0.320364322 0.000647562 0.000118681 0.280933638 0.066193174 0.062277205 1.205670887 0.640408478 ITPSYVAFTPEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 207.88 2.05E-08 730230000 243050 330346 288296 306675 350202 360927 284061 292279 270875 329198 FALSE TRUE 252645.8017 387080.3558 295809.2306 367334.3997 290674.7891 277107.1742 261795.5566 288361.4781 261126.2617 393698.0452 0.641724806 0.983190952 0.751360679 0.933035874 0.738319107 0.703857125 0.664965345 0.732443256 0.663265324 1 18.58673002 3.039992846 24.34053217 0.728216243 0.833365404 0.065760977 0.125908591 216.6639839 131864.7641 0.033077961 0.039535664 1096.460135 -3.039992846 0.105149162 ITQAVLGAHDGGVFGLCALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 ITQAVLGAHDGGVFGLCALR 20 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7EKG3;K7EII6 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;; 161.8 2.20E-11 619631000 215721 210244 249951 232943 253680 287520 230592 236250 225240 254154 FALSE TRUE 224237.8317 246351.7715 256464.9284 279018.4301 210559.5642 220747.8374 212517.5965 233083.4552 217133.6564 303950.6102 0.737744305 0.810499348 0.843771717 0.917972923 0.692742693 0.726262195 0.699184635 0.766846479 0.71437151 1 18.21347739 3.222459534 24.99401695 0.749562644 0.827445461 0.075892912 0.093466916 453.9647615 704696.6716 0.025321603 0.030352857 1669.012287 -3.222459534 0.077882817 ITS(ph)PLMEPSSIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 IT(0.005)S(0.995)PLMEPSSIEK;IT(0.005)S(0.995)PLMEPSSIEK;IT(0.015)S(0.985)PLMEPSSIEK;ITS(1)PLMEPSSIEK;IT(0.04)S(0.959)PLMEPSSIEK 162.52 4.15E-05 575065000 2541000 1973520 2421890 1926580 3079770 3030910 2861680 2430780 2766460 1921090 TRUE FALSE 2641320.642 2312456.708 2485006.443 2307651.774 2556271.795 2327027.086 2637374.044 2398199.37 2666895.645 2297490.804 1.1496545 1.006514021 1.08161758 1.004422638 1.112636356 1.012855887 1.147936714 1.043834154 1.160786211 1 21.13162766 2.254704073 24.99942447 1.08865896 1.059467909 0.043016975 0.061679628 777.9845677 1204768.165 0.019436477 0.016209423 179.7645588 -2.254704073 -0.029191051 ITSDEPLTKDDIPVFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITSDEPLTKDDIPVFLR 17 1 A0A1W2PQD2;Q9UBB4-2;Q9UBB4;B1AHE4 A0A1W2PQD2 ATXN10 Ataxin-10 0 179.14 8.51E-10 151910000 300290 251940 271340 225430 370480 383410 337580 271680 341520 252460 FALSE TRUE 312145.6811 295208.7352 278411.3433 270019.3812 307505.9419 294368.8381 311119.5975 268038.574 329228.7619 301924.7034 1.033852737 0.977756149 0.922121775 0.894326891 1.018485531 0.974974339 1.030454262 0.887766291 1.090433337 1 18.20382928 ITSEIPQTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITSEIPQTER 10 0 F8VZQ9;H0YHG0;P82979 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 99.815 0.010325 152780000 57172 76156 60524 77280 68691 99560 61600 74991 72845 96451 FALSE TRUE 59429.19471 89235.20059 62101.30516 92565.75334 57014.92836 76438.69885 56771.63104 73985.86831 70223.32268 115348.7268 0.51521327 0.773612359 0.538378766 0.80248613 0.494283118 0.662674838 0.492173885 0.641410359 0.608791485 1 16.81564255 -1.466689504 2.773720107 1.0127116 0.616674845 0.551436645 0.104331281 10483218.28 11336881.72 1028265.899 0.024105889 0.034143693 1.466689504 -0.396036755 ITSIS(ph)PTPEPPAALEDNPDAWGDGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITSISPTPEPPAALEDNPDAWGDGSPR 27 0 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 IT(0.025)S(0.025)IS(0.904)PT(0.045)PEPPAALEDNPDAWGDGS(1)PR 156.52 1.01E-08 46296000 43701 55410 53953 57746 55815 69811 54875 52418 56570 57012 TRUE FALSE 45426.34922 64926.23647 55359.0595 69167.98645 46327.58624 53598.45325 50573.75411 51715.42245 54534.05675 68182.40984 0.666247341 0.952243205 0.811925827 1.014454998 0.679465369 0.786103826 0.741741957 0.758486281 0.799825892 1 16.05711197 4.786548748 22.17632915 0.821574122 0.666244529 0.169159082 0.108851094 17253.20069 7972191.939 0.025316658 13.76920377 61171.44612 -4.786548748 -0.155329593 ITVGNDHFCVS(ph)TPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITVGNDHFCVSTPERR 16 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.792)T(0.208)PERR;ITVGNDHFCVS(0.683)T(0.317)PERR 134.06 1.43E-05 256420000 108074 109975 99188 117441 118497 148338 113020 116283 133949 130391 TRUE FALSE 112340.845 128862.3508 101772.9208 140670.4793 98354.92227 113888.7476 104161.1971 114724.4166 129128.2017 155938.62 0.720417078 0.826365853 0.652647309 0.902088779 0.630728438 0.730343436 0.667962799 0.735702398 0.828070697 1 17.25061875 0.919187023 2.71496054 0.999528691 0.732658903 0.532868302 0.076622112 0.25671764 4.25911756 0.067844849 0.018039025 8.302082077 -0.919187023 -0.266869788 ITVGNDHFCVST(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITVGNDHFCVSTPER 15 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 ITVGNDHFCVS(0.17)T(0.83)PER;ITVGNDHFCVS(0.189)T(0.811)PER 136.68 7.86E-05 231800000 194361 225380 210555 214990 225120 267780 207902 229090 213110 225650 TRUE FALSE 202034.5224 264087.2618 216042.2363 257514.3803 186854.1828 205592.1532 191606.098 226019.4233 205440.2127 269861.7972 0.748659219 0.978601879 0.80056621 0.954245406 0.692406946 0.761842378 0.710015645 0.837537679 0.761279347 1 18.04186123 ITVNGDS(ph)SAEAEELANEI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 ITVNGDS(0.5)S(0.5)AEAEELANEI;IT(0.012)VNGDS(0.494)S(0.494)AEAEELANEI 155.98 1.62E-09 26233000 94607 89937 101026 107602 107519 127993 111562 100084 98534 80049 TRUE FALSE 98342.15741 105382.9801 103658.8206 128885.3544 89242.95878 98268.5655 102817.4789 98742.53768 94987.78059 95733.06892 1.027253785 1.100800187 1.082790113 1.346299204 0.932206183 1.026485065 1.074001702 1.031436042 0.992214933 1 16.54672974 ITVQAS(ph)PGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ITVQASPGLDR 11 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 ITVQAS(1)PGLDR;ITVQAS(1)PGLDR 138.87 5.09E-05 759780000 666920 697350 672080 644310 677200 872420 602960 656370 547480 620410 TRUE FALSE 693250.5166 817114.4379 689594.9569 771752.5949 562089.7859 669813.6767 555698.4197 647572.4338 527776.3017 741967.461 0.934340861 1.101280691 0.929414015 1.04014345 0.757566626 0.902753438 0.748952547 0.872777403 0.71132001 1 19.50099639 3.244997353 24.9907766 0.826737989 1.003302291 0.451060815 0.091239518 122.8382965 476919.4193 0.023000263 0.030420832 1757.912901 -3.244997353 0.176564301 ITVQAS(ph)PNLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITVQASPNLDK 11 0 Q5TCX8;Q5TCX8-2 Q5TCX8 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 ITVQAS(1)PNLDK 119.87 0.00088362 0 149320 95488 110200 97455 155480 153420 128480 106220 124270 87011 TRUE FALSE 155215.2689 111887.3212 113071.9025 116731.3081 129051.5651 117790.5301 118409.4019 104796.2946 119797.547 104059.1395 1.491606308 1.075228199 1.086611931 1.121778526 1.240175209 1.131957564 1.137904872 1.007084002 1.151244836 1 16.66704416 4.741511086 24.94155173 1.107677818 1.491606452 0.751188599 0.066607836 134.8354103 1139761.315 0.016331738 0.114200346 55145.62787 -4.741511086 0.383928634 ITVYEALNHPWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ITVYEALNHPWLK 13 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;A0A2R8YEJ7;A0A2R8Y6D8;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 186.58 7.68E-06 454710000 472010 402700 447790 362310 516170 584090 483170 418400 473780 400760 FALSE TRUE 490645.3193 471860.5924 459459.7753 433973.8366 428431.6078 448443.9495 445297.8729 412792.0324 456728.7503 479281.249 1.023710651 0.984517115 0.958643336 0.905468006 0.89390438 0.935659282 0.929095127 0.861273069 0.952945168 1 18.87051297 4.220569127 1.717553063 0.915929946 1.020817038 0.422734819 0.036081857 0.344342037 1.822606768 0.009576891 0.043064144 16617.6316 -4.220569127 0.104887093 IVAEEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVAEEFLK 8 0 F8WCF6;P59998;P59998-3;R4GN08;P59998-4;H7C0A3 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 112.94 0.0068495 16854000 27774 33020 28788 24084 47113 42887 36812 37094 34679 35025 FALSE TRUE 28870.53897 38690.92814 29538.23893 28847.74332 39104.74909 32927.14421 33926.57925 36596.8156 33430.90956 41887.47816 0.689240323 0.923687217 0.705180647 0.688696111 0.933566565 0.786085619 0.809945615 0.873693457 0.798112253 1 15.35423141 -5 0.143062267 1.690754243 0.737654961 0.372847813 0.082367242 146.019238 1.268676086 28.57137681 0.455875871 1.00E-05 5 -0.953099282 IVAFENAFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVAFENAFER 10 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 123.6 0.0010652 88558000 27645 49701 42713 47705 47777 54680 38887 42348 38336 67543 FALSE TRUE 28736.44595 58236.76013 43826.13587 57140.90661 39655.88261 41981.39868 35838.93533 41780.39433 36956.29485 80776.75766 0.355751416 0.720959368 0.54255874 0.707392922 0.490931844 0.519721265 0.443678805 0.517232872 0.457511491 1 16.30165262 -1.473853719 3.362467231 1.007931198 0.533538353 0.638537538 0.106380697 30209123.17 45759752.56 2291496.59 0.024591858 0.033585072 1.473853719 -0.474392845 IVAHAVEVPAVQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVAHAVEVPAVQSPR 15 0 Q96FF9;B5MBX0;H0YCL8 Q96FF9 CDCA5 Sororin 1 IVAHAVEVPAVQS(1)PR 68.41 0.033953 340780000 69268 69524 65635 69077 77992 97219 72145 70557 72454 92070 TRUE FALSE 72002.75413 81464.20618 67345.50202 82740.22443 64734.9477 74641.36062 66490.08638 69611.29882 69846.39469 110109.3537 0.653920414 0.739848191 0.611623806 0.751436837 0.587915064 0.677883923 0.603855024 0.632201502 0.634336615 1 16.7485775 -1.951719284 2.465754807 1.2632476 0.653723838 0.799011173 0.05194051 6666589.993 3171434.149 10056724.93 0.012660451 0.011175854 1.951719284 -0.609523762 IVALDRDFHVHCYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVALDRDFHVHCYR 14 1 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 127.71 5.03E-05 301450000 97221 128660 124920 91421 163680 167620 80115 115650 138690 224090 FALSE TRUE 101059.3602 150756.3542 128175.5178 109503.8009 135857.7321 128692.7953 73835.37696 114099.9009 133698.574 267996.145 0.377092589 0.562531801 0.478273737 0.40860215 0.506939128 0.480203905 0.275509101 0.425752023 0.498882452 1 18.03185272 0.755482807 3.735299846 0.999987067 0.43924958 0.83597092 0.074036567 1.064624412 15.88026013 0.073094184 0.01875905 5.694856784 -0.755482807 -0.560737487 IVALNAHTFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 161.19 2.66E-05 473840000 159610 185790 201270 160560 289510 244980 202420 155500 198640 309040 FALSE TRUE 165911.526 217697.9873 206515.2615 192318.2888 240299.1936 188087.1077 186553.7915 153415.7768 191490.9852 369590.4711 0.448906395 0.589024892 0.558767819 0.520355106 0.650176919 0.50890681 0.50475812 0.415096678 0.518116673 1 18.49556804 -1.31523808 5.158598878 1.000140511 0.521234407 0.837599063 0.06289751 0.000109165 1.45E-05 0.06540742 0.015412197 0.048390702 1.31523808 -0.478906104 IVDAVIQEHQPSVLLELGAYCGYSAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IVDAVIQEHQPSVLLELGAYCGYSAVR 27 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 312.64 4.67E-82 6856167000 796277 1076740 1014472 991396 1135965 1234578 1038774 1015031 1085247 1213348 FALSE TRUE 827714.6308 1261661.719 1040909.974 1187491.17 942874.0751 947865.9697 957352.1795 1001426.17 1046189.172 1451080.31 0.570412696 0.869463744 0.717334504 0.818349723 0.649773875 0.653213997 0.659751341 0.690124567 0.72097262 1 20.46869594 -1.776964095 5.051935522 1.021842918 0.707535152 0.540047733 0.081519 0.019395317 0.000856276 0.076333063 0.017822085 0.016712288 1.776964095 -0.314307767 IVDDLKDEAEQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVDDLKDEAEQYR 13 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 137.46 5.52E-05 334250000 247473 145787 204817 170088 249080 249180 260280 196734 204646 131185 FALSE TRUE 257243.4251 170824.7832 210154.6993 203730.8987 206741.4706 191311.7214 239878.5735 194097.1025 197280.8304 156888.1891 1.639660874 1.088831379 1.339518931 1.298573844 1.317763127 1.219414428 1.528977898 1.237168353 1.257461327 1 17.25937722 0.756404691 1.598893954 1.001062414 1.3281536 0.322132079 0.146356889 0.956274166 4.086687467 0.126486882 0.036395373 5.706958194 -0.756404691 0.327091186 IVDDLKDEAEQYRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IVDDLKDEAEQYRK 14 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;; 175.45 1.34E-06 632370000 882150 395374 635420 395640 835740 716530 678800 532300 650130 350333 FALSE TRUE 916977.9632 463276.4089 651979.5672 473896.4111 693681.2133 550126.7666 625593.8823 525165.3892 626731.9483 418974.0438 2.18862714 1.105740119 1.556133552 1.131087756 1.65566632 1.31303305 1.493156656 1.253455666 1.495872972 1 18.67650134 8 0.037823627 7.99E-13 3.659722592 0.255162477 0.282804628 1303.057356 3.757811568 102.8861165 314.1610535 100000000 -8 3.659722592 IVDHLLASLQQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVDHLLASLQQGR 13 0 H0Y5G7;A2RRP1-2;A2RRP1;H7BZR3 H0Y5G7 NBAS Neuroblastoma-amplified sequence 0 69.456 0.048893 0 149700 151220 172290 134490 326060 258230 169660 167680 196500 269410 FALSE TRUE 155610.2716 177190.8587 176780.0189 161091.7206 270636.4377 198259.996 156361.6059 165432.5239 189428.0034 322195.7313 0.482968135 0.549947878 0.548672753 0.499980927 0.839975243 0.615340232 0.485300054 0.513453494 0.587928346 1 18.29757785 -2.039295 2.025775723 1.51931325 0.567672222 0.627763522 0.099492883 1965234.356 596868.6978 4732387.399 0.027857639 0.009134925 2.039295 -0.951641028 IVDNVRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IVDNVRPDR 9 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;;;; 104.42 0.0029754 2691100000 1518950 1934200 1771970 1845320 1923050 2260860 1771290 1817990 1653160 2030390 FALSE TRUE 1578919.319 2266383.804 1818148.994 2210318.788 1596170.648 1735809.529 1632451.661 1793622.818 1593663.095 2428206.046 0.650241079 0.933357285 0.748762238 0.910268217 0.657345636 0.714852651 0.672287125 0.738661705 0.656312959 1 21.21145942 5.028831573 16.2340799 0.765707448 0.311009684 0.086613231 0.118295773 21344221.03 327472397.4 0.026803672 263284302.4 106864.0362 -5.028831573 -0.454697764 IVDQIRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 144.65 9.03E-05 7116170000 3644100 4042160 3818130 3894610 4199170 4681800 4090200 4059220 3731750 3724970 FALSE TRUE 3787971.882 4736369.536 3917633.604 4664952.234 3485396.583 3594522.903 3769599.436 4004812.795 3597445.046 4454806.553 0.850311195 1.063204312 0.879417222 1.047172796 0.782390109 0.806886418 0.84618701 0.898986914 0.807542371 1 22.08693135 3.233549139 24.99983883 0.852255128 0.961638435 0.266339012 0.083530698 150.2218126 749383.9184 0.022186368 0.02730916 1712.178895 -3.233549139 0.109383307 IVDS(ph)PEKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IVDSPEKLK 9 1 E9PQC4;Q9BZD4 E9PQC4 NUF2 Kinetochore protein Nuf2 1 IVDS(1)PEKLK;IVDS(1)PEKLK;IVDS(1)PEKLK 141.13 6.51E-05 481850000 2148600 833550 1131280 832840 1693620 1927880 1551500 1196620 1273100 701350 TRUE FALSE 2233428.387 976705.7284 1160762.086 997573.2662 1405739.077 1480159.087 1429889.376 1180581.266 1227281.38 838766.1043 2.662754701 1.164455411 1.383892458 1.189334263 1.67596076 1.764686341 1.704753409 1.407521429 1.463198588 1 19.67790904 -3.104027475 0.141286508 1.43E-39 1.800915683 0.207179997 0.394207126 137.9102092 1.996919877 45.95478098 2.587040693 0.000786996 3.104027475 1.800915683 IVEDEPNKICEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IVEDEPNKICEADR 14 1 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 ;;;; 192.4 3.44E-07 2002960000 1630040 1095330 1419640 1317070 1900440 1895670 1726500 1458510 1645510 1070980 FALSE TRUE 1694395.238 1283444.407 1456636.985 1577582.515 1577403.888 1455429.372 1591172.419 1438961.059 1586288.417 1280818.026 1.322900837 1.00205055 1.137270834 1.231699182 1.231559719 1.136327989 1.242309514 1.123470337 1.238496324 1 20.28863409 -1.54963116 7.63039086 0.999934834 1.178036229 0.297200526 0.084774111 8.75E-05 5.17E-06 0.076439024 0.018010282 0.028207776 1.54963116 0.178101394 IVEIDAHIGCAMSGLIADAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVEIDAHIGCAMSGLIADAK 20 0 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 166.25 1.55E-11 17458000 29642 22886 28496 23670 34232 42575 32160 26747 36501 27636 FALSE TRUE 30812.28905 26816.49247 29238.62917 28351.85535 28413.25687 32687.60148 29639.21517 26388.50021 35187.33614 33050.74508 0.932272146 0.811373311 0.8846587 0.857828024 0.85968582 0.989012544 0.896779032 0.798423762 1.064645776 1 15.01239517 1.228172765 24.99943714 1.032322973 0.876108204 0.562361455 0.054148946 167.128455 402198.4148 0.05024378 0.013113888 16.91113532 -1.228172765 -0.156214768 IVENLGILTGPQLFSLNKEELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVENLGILTGPQLFSLNKEELKK 23 2 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 117.64 0.00020258 246450000 166400 94047 128170 72463 179190 158640 151180 124620 166160 71514 FALSE TRUE 172969.6005 110198.8407 131510.2155 86795.96512 148731.3478 121798.2642 139330.1166 122949.6727 160179.9341 85525.79908 2.022426009 1.288486537 1.537667194 1.014851262 1.739023188 1.424111385 1.629100436 1.437574089 1.87288439 1 16.38407206 -1.939574789 2.739915932 0.640780298 1.526113859 0.261085415 0.27545338 7831493.965 8727534.137 18108293.49 0.062318856 0.011492783 1.939574789 0.885333561 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 IVEPEVVGES(0.979)DS(0.021)EVEGDAWR;IVEPEVVGES(0.993)DS(0.007)EVEGDAWR;IVEPEVVGES(0.991)DS(0.009)EVEGDAWR;IVEPEVVGES(0.943)DS(0.057)EVEGDAWR;IVEPEVVGES(0.956)DS(0.044)EVEGDAWR 268.65 3.96E-34 806081000 569372 617748 587093 599931 592399 738005 666682 669269 650529 609686 TRUE FALSE 591851.2462 723841.4136 602393.1259 718595.5612 491703.2296 566614.5233 614425.7228 660298.5438 627116.5884 729142.2986 0.811708836 0.992729972 0.826166754 0.98553542 0.674358394 0.777097316 0.842669153 0.905582552 0.86007435 1 19.47584087 -0.81992833 5.221164719 1.000000099 0.855878228 0.194786654 0.089549753 1.99E-05 61651207.11 16.71567379 0.020736144 0.151381105 0.81992833 -0.144121872 IVEYS(ph)PPSAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 IVEYS(0.995)PPS(0.005)APR;IVEYS(0.989)PPS(0.011)APR 138.42 0.001344 240150000 298988 309640 318400 272720 323010 350330 323800 308350 268050 336300 TRUE FALSE 310792.2771 362818.2613 326697.7656 326663.202 268104.8756 268971.1668 298419.7099 304217.0726 258402.9329 402191.5461 0.772746916 0.902103152 0.812293965 0.812208027 0.666609923 0.66876385 0.741984044 0.756398476 0.642487231 1 18.61752323 3.398139481 7.470985661 0.731997182 0.832436828 0.124480504 0.09881425 0.365382926 29.38377396 0.025343205 0.034385261 2501.14852 -3.398139481 0.100439646 IVFLDTQPILSPSILDHLINNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVFLDTQPILSPSILDHLINNDR 23 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 0 135.21 1.61E-05 93597000 76805 159670 234900 173720 219700 218490 225340 197760 256700 130760 FALSE TRUE 79837.32071 187092.0804 241021.687 208081.2975 182355.4725 167749.0087 207677.262 195109.3507 247461.4171 156379.9184 0.510534354 1.196394539 1.541257275 1.330613928 1.166105433 1.072701728 1.328030249 1.24766244 1.582437308 1 17.25469574 4.726352955 4.318977347 1.287235126 0.460786099 0.63781396 0.173498146 0.116848133 5.149422748 0.04060941 0.290720733 53254.08845 -4.726352955 -0.826449026 IVFSGNLFQHQEDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVFSGNLFQHQEDSK 15 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 212.7 7.42E-10 1051950000 571950 432220 553980 460150 731060 688080 634000 526350 591270 463200 FALSE TRUE 594531.0276 506450.4228 568417.1739 551166.2966 606794.6823 528283.848 584305.4233 519295.1392 569990.3082 553955.1715 1.073247545 0.914244417 1.02610681 0.994965522 1.095385897 0.953658121 1.054788281 0.937431702 1.028946632 1 19.07940971 -3.186266098 10.09810642 0.999999556 1.003853874 0 0.056540229 0 0 0 0.011431869 0.000651229 3.186266098 0.003854318 IVFSGNLFQHQEDSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVFSGNLFQHQEDSKK 16 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 212.69 2.51E-12 959730000 1192890 717150 1162240 710380 1505260 1294890 1251550 1045920 1283290 721500 FALSE TRUE 1239986.218 840314.9338 1192528.929 850891.0437 1249396.443 994171.4217 1153450.241 1031901.153 1237104.644 862864.111 1.437058515 0.973867059 1.38205879 0.986124041 1.447964317 1.152176118 1.336769285 1.195902275 1.433718969 1 19.71877385 IVGAPMHDLLLWNNATVTTCHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVGAPMHDLLLWNNATVTTCHSK 23 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 228.15 4.25E-33 1227120000 1135520 1108890 1204170 1083200 1334860 1498760 1289750 1209170 1292780 1181010 FALSE TRUE 1180351.206 1299333.232 1235551.659 1297453.727 1107960.974 1150695.704 1188656.025 1192963.054 1246253.1 1412406.298 0.835702311 0.919942961 0.87478487 0.91861225 0.784449188 0.814705872 0.841582218 0.844631645 0.882361614 1 20.42972373 0.836568672 3.79685322 0.999986681 0.854742101 0.543793829 0.039906938 0.835135296 18.25468757 0.040062963 0.010274237 6.863864028 -0.836568672 -0.14524458 IVGCICEEDNTSVVWFWLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVGCICEEDNTSVVWFWLHK 20 0 P10606 P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" 0 164.01 1.88E-11 12892000 10135 8767.5 7968.6 10969 11172 14388 10825 8667.1 8530.9 11964 FALSE TRUE 10535.13763 10273.24992 8176.268262 13138.63546 9272.987431 11046.60505 9976.508214 8550.931701 8223.874575 14308.11674 0.736304981 0.718001545 0.571442658 0.918264486 0.648092799 0.772051644 0.697262148 0.597628036 0.574769883 1 13.80454617 IVGCSVHK ddPTM_MDA-MB-175_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 ; 119.27 0.0017256 1108280000 403840 1027900 840840 970530 1993710 1780530 1004040 1046540 829020 2168700 FALSE TRUE 419783.915 1204433.829 862752.9812 1162497.937 1654819.886 1367028.892 925340.7212 1032512.843 799183.7321 2593615.243 0.16185281 0.464384157 0.332644938 0.448215263 0.638035997 0.527074668 0.356776405 0.398097924 0.308135038 1 21.30653304 -1.180091261 3.765829423 1.000477372 0.412400445 0.678311493 0.123025004 83463198.12 147778455.6 481419.9791 0.029695179 0.066055463 1.180091261 -0.588076927 IVGCTHITAQTAVLIETLCALGAQCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IVGCTHITAQTAVLIETLCALGAQCR 26 0 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 ;; 186.91 1.23E-17 149129000 55648.6 80575.8 75440.4 88821 85891 112909 88261.1 85459 92263.2 75351.9 FALSE TRUE 57845.6497 94414.06686 77406.4388 106389.5287 71291.2785 86687.5959 81342.96435 84313.56189 88942.66545 90115.66211 0.641904507 1.047698753 0.858967653 1.180588659 0.791108636 0.961959263 0.902650688 0.935614963 0.986983432 1 16.45949025 4.749288234 24.57821371 0.955363346 0.641904281 0.475425357 0.100860503 1028.121849 2355487.984 0.021955278 0.318379265 56142.04581 -4.749288234 -0.313459065 IVGELEQMVSEDVPLDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 IVGELEQMVSEDVPLDHR 18 0 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ;;;;;;;;;;;;; 241.32 5.46E-24 2164150000 785203.9 970817.8 942673.5 921157.7 1103513.7 1209362.8 990687 1052804 979436.8 1057773.2 FALSE TRUE 816204.3563 1137548.205 967240.3458 1103359.944 915938.8354 928506.6178 913034.3643 1038692.884 944187.0609 1265023.606 0.645208795 0.899230812 0.764602606 0.872205023 0.724048809 0.733983629 0.721752827 0.821085772 0.746379005 1 20.27073288 -1.731553543 3.074477582 1.033577457 0.775414066 0.477177959 0.072064357 4396219.492 3927420.869 963485.7922 0.015647116 0.01855438 1.731553543 -0.258163391 IVGWYHTGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVGWYHTGPK 10 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 147.2 2.73E-05 1043570000 1252520 1073820 1202470 991220 1893080 1708710 1413200 1203200 1356140 1515970 FALSE TRUE 1301970.457 1258240.232 1233807.356 1187280.358 1571294.938 1311887.998 1302429.691 1187073.072 1307332.786 1812995.297 0.718132286 0.694011857 0.680535332 0.654872277 0.866684509 0.723602538 0.718385588 0.654757944 0.721090004 1 20.78994375 0.933096391 21.82103848 1 0.711418146 0.695918413 0.056581153 5181.066035 1689840.746 0.055919571 0.013979893 8.572280851 -0.933096391 -0.288581854 IVHKGDECILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVHKGDECILK 11 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 85.845 0.00896 301510000 255690 136320 184860 164460 287630 250230 249490 188220 223170 175390 FALSE TRUE 265784.8386 159731.8996 189677.6035 196989.6971 238738.7553 192117.8748 229934.3219 185697.2188 215138.1553 209754.3125 1.267124549 0.761519025 0.904284643 0.939144921 1.138182822 0.915918593 1.09620784 0.885308228 1.025667376 1 17.67834095 4.767392385 24.12032393 0.963347467 1.267125297 0.438626542 0.103244851 6549.466037 5479056.255 0.024009856 2.459387746 58531.86803 -4.767392385 0.30377783 IVIFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVIFRK 6 1 A0A3B3ITJ4;M0R1W6;B4DVF8;M0QYL7;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 138.39 0.019764 757950000 1868890 1477250 1741080 1481020 3270500 2493300 2291100 1643440 1970780 2426500 FALSE TRUE 1942675.22 1730956.196 1786453.975 1773961.336 2714581.578 1914268.861 2111517.595 1621412.375 1899852.013 2901926.217 0.669443354 0.596485254 0.615609716 0.611304769 0.935441281 0.65965456 0.727626217 0.558736596 0.654686533 1 21.46857941 -2.096844229 2.43516587 1.574080034 0.66649281 0.498880682 0.099203175 9633391.506 2981519.273 30633436.89 0.026408126 0.008001212 2.096844229 -0.907587223 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 175.76 1.49E-13 683516000 976300 326888 576339 327452 859060 709690 848590 579245 692950 220457 FALSE TRUE 1014845.078 383028.4712 591358.8678 392221.0283 713037.288 544875.253 782075.2984 571481.1682 668010.8649 263651.3282 3.849193875 1.452784151 2.242958045 1.487650492 2.704470684 2.066650893 2.966324136 2.167564154 2.533690497 1 18.00827174 IVLANDPDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVLANDPDADR 11 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 98.943 0.011968 41417000 66834 72248 70792 81152 99212 107320 85696 80765 82283 83691 FALSE TRUE 69472.65793 84656.03199 72636.89768 97203.62339 82347.97968 82396.55645 78978.9236 79682.47728 79321.6509 100088.6491 0.694111256 0.845810517 0.725725628 0.971175296 0.822750436 0.823235773 0.789089715 0.796119021 0.792513953 1 16.61091884 -2.573723143 2.148298522 4.253202631 0.809561789 0.406194544 0.070029699 3040197.476 165054.4652 48474067.06 0.016792368 0.002668559 2.573723143 -3.443640842 IVLDKLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVLDKLER 8 1 P30047;H0YNX7;P30047-2 P30047 GCHFR GTP cyclohydrolase 1 feedback regulatory protein 0 80.688 0.022618 360140000 677530 471630 523060 613170 692100 701640 822300 488440 487900 463570 FALSE TRUE 704279.4076 552628.7837 536691.3733 734453.1959 574457.0892 538694.7435 757845.9773 481893.2607 470340.5743 554397.6659 1.2703506 0.996809362 0.968062108 1.324776854 1.036182373 0.971675706 1.366971804 0.869219498 0.848381231 1 19.08056166 1.611885867 25 0.89408513 1.119232542 0.340882692 0.143840209 0.407482488 2518.058046 0.06676719 0.035308772 40.91531197 -1.611885867 0.225147412 IVLDNSVFSEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 220.53 2.93E-11 8953015000 4271447 7131034 7362782 8033484 7789809 8746418 7509160 7600820 7184286 7697561 FALSE TRUE 4440087.026 8355733.618 7554662.148 9622483.158 6465700.049 6715194.973 6920572.418 7498943.44 6925724.95 9205750.699 0.48231667 0.907664556 0.820645963 1.04526871 0.702354459 0.729456531 0.751766221 0.814593365 0.752325929 1 23.13410394 -1.527760304 2.619414341 1.012243996 0.788575002 0.186067053 0.137539634 22715968.74 21992859.26 1971347.192 0.033742491 0.029664682 1.527760304 -0.223668994 IVLEDGTLHVTEGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVLEDGTLHVTEGSGR 16 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 0 ; 238.22 8.75E-20 646270000 311670 527140 471040 499670 510640 628840 479910 519390 471810 592420 FALSE TRUE 323974.9723 617672.1944 483315.6894 598503.2346 423841.5952 482801.4402 442293.4002 512428.4266 454829.6503 708493.3564 0.457273127 0.871810849 0.682173919 0.8447549 0.598229456 0.681448084 0.624273179 0.723264971 0.641967417 1 19.4343948 -2.034583941 2.128309535 1.368604551 0.688849347 0.417475094 0.112815228 4720867.993 1542072.306 8482629.486 0.026296007 0.009234557 2.034583941 -0.679755204 IVLEEQSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVLEEQSSR 9 0 H7C5U4;H0YCV8;A0A0G2JNU3;A6H8Y1-8;A6H8Y1-2;A6H8Y1-7;A6H8Y1-6;A6H8Y1 H7C5U4 BDP1 Transcription factor TFIIIB component B homolog 0 66.435 0.063739 7636900000 41283 93674 57478 78073 59942 76337 60068 62274 38508 96679 FALSE TRUE 42912.88472 109761.7808 58975.9239 93515.60638 49753.08025 58608.88865 55359.7132 61439.31889 37122.1046 115621.399 0.371150021 0.949320643 0.51007793 0.808808812 0.430310312 0.506903472 0.47880162 0.531383632 0.321066039 1 16.81904891 -1.23101417 5.133598364 1.000050213 0.554876392 0.356306157 0.182935752 9.97E-05 1.49E-05 0.167966894 0.039585725 0.058747018 1.23101417 -0.445173821 IVNGWQVEEADDWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IVNGWQVEEADDWLR 15 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;;;; 359.65 1.77E-82 923314000 343227 393722 385568 409232 388680 471472 431854 391241 373951 378887 FALSE TRUE 356777.867 461340.6908 395616.2188 490176.8682 322612.3124 361979.7732 398004.155 385997.0543 360492.5766 453122.6534 0.787375922 1.018136452 0.873088591 1.081775242 0.711975687 0.79885605 0.878358546 0.85185998 0.795573944 1 18.78954209 3.232462161 24.99999671 0.834359863 0.940882402 0.19241031 0.10069798 220.8597396 905391.3401 0.027102873 0.033183708 1707.898909 -3.232462161 0.106522539 IVNHPTMLQDPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IVNHPTMLQDPDVR 14 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 ;; 122.93 0.00010585 424190000 320028 592270 558760 562810 631260 699170 531140 563080 559450 636760 FALSE TRUE 332662.9526 693987.7653 573321.7446 674132.1382 523958.6507 536798.3635 489507.8589 555532.8336 539315.5038 761520.9305 0.436840196 0.911318045 0.752864067 0.885244399 0.68804235 0.704902967 0.642802895 0.729504353 0.708208379 1 19.53852416 -1.518929052 2.671402178 1.014217132 0.725264441 0.31744979 0.123720929 18939661.53 18665806.91 1954352.635 0.027997284 0.03027408 1.518929052 -0.288952691 IVNHWAS(ph)PELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 IVNHWASPELR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR;IVNHWAS(1)PELR 223.58 7.17E-12 1381478000 1091136 1216000 1125636 1095481 1190094 1349357 1135034 1092614 1076224 1342005 TRUE FALSE 1134214.892 1424838.541 1154970.999 1312163.872 987802.247 1035989.286 1046067.069 1077969.296 1037490.908 1604945.186 0.706700081 0.887780189 0.719632676 0.817575506 0.615474133 0.645498236 0.651777443 0.671654899 0.646433858 1 20.61409259 4.025581708 23.68639665 0.700008057 0.798856899 0.043171197 0.11676262 257.1712908 238111.5133 0.026998394 0.058318794 10606.73475 -4.025581708 0.098848842 IVNTQEQLNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVNTQEQLNHR 11 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 78.903 0.019075 0 139700 84136 79533 81117 93236 101310 93527 79026 83258 92307 FALSE TRUE 145215.4639 98585.70351 81605.69532 97161.70049 77387.77802 77782.28787 86196.10935 77966.78573 80261.56084 110392.7893 1.31544338 0.893044773 0.739230305 0.880145353 0.701022037 0.704595729 0.780812858 0.706267014 0.727054379 1 16.75228642 4.750656641 2.303650621 0.763959756 1.46307963 0.754535146 0.091058412 0.262435412 1.601740969 0.021075235 0.374737555 56319.22125 -4.750656641 0.699119874 IVPEGEWGQFMDALREPLPATLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVPEGEWGQFMDALREPLPATLR 23 1 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 ; 144.92 1.32E-07 282600000 44566 43527 50881 27707 59757 50905 43534 42664 43848 48542 FALSE TRUE 46325.50009 51002.42366 52207.00066 33187.3619 49599.52648 39083.08522 40121.69133 42092.15886 42269.91905 58052.87551 0.797988036 0.878551204 0.899300856 0.57167473 0.854385352 0.673232547 0.691123239 0.725065873 0.728127912 1 15.82507991 3.825728498 24.9999876 0.734897409 0.860607604 0.162173607 0.110815339 108.7907079 31198.74065 0.025752033 0.046425134 6694.659571 -3.825728498 0.125710196 IVQIPFCGEIDCEDWIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVQIPFCGEIDCEDWIKK 18 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 116.82 0.00023967 304490000 230970 177410 179030 135730 307560 267140 196630 224050 240760 185700 FALSE TRUE 240088.8739 207878.7874 183695.6689 162576.9889 255281.0611 205100.7835 181217.6268 221046.9762 232095.0946 222084.3596 1.081070609 0.936035243 0.827143655 0.732050601 1.14947789 0.923526465 0.815985543 0.995328877 1.045076272 1 17.76074827 1.544163148 7.929667072 1.021365995 0.920652437 0.114263744 0.116036051 0.260679008 28.61009492 0.064202235 0.029823589 35.00766531 -1.544163148 -0.100713559 IVRPWAEGTEEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVRPWAEGTEEGAR 14 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 88.768 0.0058505 83238000 43561 69798 72226 69873 73350 91932 66248 71953 66167 79588 FALSE TRUE 45280.82192 81785.26355 74108.26889 83693.67085 60881.9932 70582.18624 61055.30865 70988.58773 63785.6626 95181.7448 0.47573011 0.85925367 0.778597504 0.87930381 0.63963939 0.741551717 0.64146028 0.745821459 0.670145969 1 16.53839728 -1.221151995 3.59811256 1.000434222 0.722766719 0.368763722 0.111557582 21852942.64 36650975.81 107432.5994 0.026031039 0.060096337 1.221151995 -0.277667503 IVS(ph)PGLTIHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IVSPGLTIHER 11 0 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 IVS(0.996)PGLT(0.004)IHER 67.102 0.039223 93706000 18181 27868 24596 25443 25140 32604 22253 25349 24153 27325 TRUE FALSE 18898.79992 32654.11222 25236.99197 30475.54946 20866.71178 25032.21512 20508.75171 25009.23812 23283.73825 32678.81058 0.5783197 0.999244209 0.772273884 0.932578295 0.638539513 0.766007534 0.627585623 0.765304418 0.712502623 1 14.99606785 5.008418056 18.03793213 0.782881218 0.288147984 0.199881861 0.129218149 20420868.76 575017677.3 0.029471292 242880202.9 101957.2366 -5.008418056 -0.494733233 IVSGIITPIHEQWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVSGIITPIHEQWEK 15 0 Q5QPM7;Q5QPM9;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 ; 184 4.82E-07 789400000 525470 567030 514320 478390 693700 810870 550730 535870 556010 727490 FALSE TRUE 546215.9614 664412.9916 527723.6017 573014.1141 575785.1218 622557.7314 507562.3435 528687.5392 535999.3087 870027.7369 0.627814423 0.763668747 0.606559515 0.658615915 0.66180088 0.715560786 0.583386393 0.607667453 0.616071518 1 19.73070187 -1.623434419 6.052349897 1.001851726 0.64788586 0.803012598 0.052148746 0.001323655 8.24E-05 0.051293011 0.012034663 0.023799377 1.623434419 -0.353965866 IVSRPEELREDDVGTGAGLLEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IVSRPEELREDDVGTGAGLLEIK 23 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 203.79 1.04E-24 1657420000 2098280 1647950 2022090 1629330 2430160 2552540 2372550 1894380 2278390 1628860 FALSE TRUE 2181121.715 1930972.593 2074787.327 1951606.611 2017082.271 1959751.269 2186583.331 1868988.935 2196391.189 1948003.931 1.119670079 0.991257031 1.065083748 1.001849421 1.035461089 1.006030449 1.122473778 0.959437969 1.127508602 1 20.89356516 4.757781871 23.61185472 1.03288343 1.119670248 0.189644484 0.05283594 3065.973847 3766185.384 0.011276523 0.379695091 57250.841 -4.757781871 0.086786818 IVTDRETGSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IVTDRETGSSK 11 1 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 176.18 8.16E-06 2454060000 2276190 2066590 2381180 1437340 3195140 2687450 1666990 2329920 2596410 2665750 FALSE TRUE 2366055.739 2421510.757 2443235.507 1721641.562 2652031.244 2063330.466 1536326.968 2298691.233 2502965.711 3188052.674 0.742163314 0.759557951 0.766372377 0.540029208 0.831865567 0.647207144 0.481901375 0.721033016 0.785108017 1 21.60424404 0.900913685 2.457725822 0.99895336 0.681777131 0.473151368 0.100882736 0.355806687 4.579767103 0.096463182 0.025985958 7.960011322 -0.900913685 -0.31717623 IVYGHLDDPASQEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IVYGHLDDPASQEIER 16 0 A2A274;Q99798 A2A274 ACO2 "Aconitate hydratase, mitochondrial" 0 ; 199.58 3.78E-11 490980000 276360 378940 333210 465680 300590 512530 332510 313050 328560 416020 FALSE TRUE 287270.9062 444019.9973 341893.7263 557790.1141 249495.8192 393502.675 306446.9973 308854.0768 316735.1898 497531.1538 0.5773928 0.892446621 0.687180539 1.121115954 0.501467732 0.790910623 0.615935294 0.620773341 0.636613783 1 18.92442734 2.254558516 24.73072248 0.677133435 0.768806994 0 0.191696593 706.0381381 1091443.374 0.062866925 0.052436623 179.7043193 -2.254558516 0.091673559 IWDDGDDFCIFSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IWDDGDDFCIFSESR 15 0 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 0 ;;; 143.17 1.04E-05 105010000 60070 71304 74923 72239 87667 89483 81785 74274 72079 77919 FALSE TRUE 62441.60998 83549.90733 76875.55493 86527.65859 72765.39465 68701.92938 75374.47799 73278.47852 69484.89087 93185.7362 0.670076908 0.896595453 0.824971268 0.928550464 0.780864085 0.737257999 0.808862827 0.78637012 0.745660159 1 16.50782152 -1.100367645 4.720836547 1.000011191 0.802363518 0.417939811 0.071433826 8.15E-06 1.55E-06 0.066967822 0.015783574 0.079365609 1.100367645 -0.197647672 IWDILGDRPSLVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWDILGDRPSLVHSR 15 1 Q13610;B4DJV5 Q13610 PWP1 Periodic tryptophan protein 1 homolog 0 90.561 0.003585 131560000 40567 104960 85985 93246 102250 120800 81076 94976 76996 114640 FALSE TRUE 42168.61648 122986.0635 88225.83974 111689.7805 84869.58152 92746.03074 74721.05127 93703.00207 74224.929 137101.5131 0.307572218 0.897043809 0.643507411 0.81465024 0.619027315 0.676477076 0.5450053 0.683457097 0.541386651 1 17.06488497 -1.496584496 3.563015165 1.005641644 0.648923275 0.337455691 0.151916996 14357.34124 47466749.09 309970.8397 0.033085722 0.031872454 1.496584496 -0.35671837 IWDLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 143 0.005702 1955501000 3229574 2546681 3214116 2602044 3923849 3933788 3871832 3287414 3379352 2273320 FALSE TRUE 3357080.075 2984053.651 3297878.503 3116720.537 3256874.549 3020225.354 3568347.691 3243351.592 3257729.782 2718733.529 1.234795555 1.097589602 1.213020132 1.146386913 1.197938126 1.110894217 1.312503654 1.192964135 1.198252696 1 21.37450332 -1.401528057 5.739343906 0.9999303 1.189723053 0.48419976 0.058635046 4.95E-05 5.17E-06 0.053784376 0.012672454 0.03967089 1.401528057 0.189792753 IWDPTPSHTPAGAAT(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWDPTPSHTPAGAATPGR 18 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHT(0.019)PAGAAT(0.981)PGR 96.131 0.0060696 140150000 137740 130030 138910 167220 142920 164360 174710 145210 131460 98556 TRUE FALSE 143178.0816 152361.641 142530.1087 200295.6169 118626.5094 126189.8809 161015.7737 143263.6975 126728.7803 117866.1612 1.214751376 1.292666525 1.209253845 1.699347928 1.006450946 1.070620096 1.366089911 1.215477759 1.075192226 1 16.84679006 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHAT(ph)PGHGGATSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 3 IWDPT(0.001)PS(0.004)HT(0.046)PAGAAT(0.949)PGRGDT(0.995)PGHAT(0.953)PGHGGAT(0.018)S(0.017)S(0.016)AR;IWDPT(0.003)PS(0.032)HT(0.133)PAGAAT(0.832)PGRGDT(0.985)PGHAT(0.948)PGHGGAT(0.024)S(0.023)S(0.021)AR;IWDPTPS(0.002)HT(0.01)PAGAAT(0.988)PGRGDT(0.988)PGHAT(0.914)PGHGGAT(0.034)S(0.033)S(0.031)AR 74.709 0.0013879 558220000 221651 238120 256137 225199 285705 328906 244019 262476 219146 249234 TRUE FALSE 230401.9526 279015.2577 262812.1406 269742.69 237140.9662 252522.5661 224892.1532 258957.9385 211258.9783 298066.6304 0.772988081 0.93608351 0.881722789 0.904974467 0.795597165 0.847201734 0.754502954 0.868792116 0.708764272 1 18.18527534 3.238547986 25 0.821614144 0.878936632 0.06064499 0.082337408 0.772272084 1521654.896 0.021342737 0.027111224 1732.000393 -3.238547986 0.057322488 IWDPTPSHTPAGAAT(ph)PGRGDT(ph)PGHATPGHGGATSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 IWDPT(0.001)PS(0.009)HT(0.142)PAGAAT(0.849)PGRGDT(0.856)PGHAT(0.143)PGHGGATSSAR;IWDPTPSHT(0.006)PAGAAT(0.994)PGRGDT(0.987)PGHAT(0.013)PGHGGATSSAR;IWDPTPSHT(0.015)PAGAAT(0.985)PGRGDT(0.893)PGHAT(0.105)PGHGGAT(0.001)S(0.001)S(0.001)AR;IWDPTPS(0.002)HT(0.03)PAGAAT(0.967)PGRGDT(0.817)PGHAT(0.148)PGHGGAT(0.013)S(0.012)S(0.011)AR;IWDPTPS(0.001)HT(0.04)PAGAAT(0.959)PGRGDT(0.944)PGHAT(0.056)PGHGGATSSAR 124.09 1.44E-08 2056150000 315092 603186 589646 584345 539428 679815 519101 574660 529225 633406 TRUE FALSE 327532.0755 706778.5034 605012.6592 699926.6969 447736.2212 521938.2689 478412.5072 566957.6227 510178.2956 757509.7784 0.432379997 0.933028884 0.79868627 0.923983712 0.591063289 0.689018523 0.631559514 0.748449246 0.673494007 1 19.53090499 -1.15820553 4.800799941 1.00002521 0.722756483 0.263152639 0.143064972 3.66E-05 6.42E-06 0.131449833 0.030980208 0.069469547 1.15820553 -0.277268727 IWDPTPSHTPAGAAT(ph)PGRGDTPGHATPGHGGATSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSAR 37 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 IWDPTPSHTPAGAAT(0.991)PGRGDT(0.007)PGHAT(0.002)PGHGGATSSAR;IWDPTPSHT(0.001)PAGAAT(0.999)PGRGDTPGHATPGHGGATSSAR;IWDPT(0.002)PS(0.009)HT(0.151)PAGAAT(0.838)PGRGDTPGHATPGHGGATSSAR 151.93 1.04E-13 3047680000 275850 819442 741263 848575 714365 1032795 610738 789101 643355 857773 TRUE FALSE 286740.771 960174.7891 760580.9227 1016420.602 592937.4925 792944.0134 562866.7597 778524.3918 620200.7792 1025837.196 0.279518789 0.935991396 0.74142459 0.990820577 0.578003503 0.772972569 0.548690145 0.758916127 0.604580124 1 19.96837036 -2.232780422 2.23951808 1.980727589 0.704785879 0.183671745 0.193785113 10100817.95 1824664.224 50137741.5 0.042942543 0.005850858 2.232780422 -1.27594171 IWDPVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWDPVHR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4;A0A494C159 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 79.116 0.033497 142520000 261710 293390 280120 290930 311140 343150 279010 274390 281020 288720 FALSE TRUE 272042.5129 343777.4502 287420.1573 348475.0857 258252.5339 263458.613 257140.4671 270712.2509 270906.1451 345289.1561 0.787868684 0.995621913 0.832404239 1.009226845 0.747931203 0.76300865 0.74471052 0.784016081 0.784577622 1 18.3974455 3.218456087 24.99673598 0.786947575 0.907385128 0.21078428 0.093460518 285.155353 354543.7914 0.024563998 0.029393865 1653.697566 -3.218456087 0.120437553 IWEDLDDDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWEDLDDDDPK 11 0 O75717;C9JYB3 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 0 147.12 8.25E-05 10795000 66964 32623 36441 32960 47171 51642 52151 38485 36545 29098 FALSE TRUE 69607.79043 38225.74648 37390.6824 39479.38962 39152.89027 39648.92814 48063.26835 37969.17152 35229.75259 34799.19599 2.000270077 1.09846637 1.074469721 1.13449143 1.125109048 1.139363339 1.381160311 1.091093356 1.012372602 1 15.08676635 4.739848133 24.98782275 1.130661338 2.00027036 0.875324421 0.099847495 35.71796798 693130.9614 0.023941899 0.149382698 54934.87403 -4.739848133 0.869609021 IWEQIQPDLHTNDECVATYK ddPTM_MDA-MB-175_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 ; 277.07 1.44E-44 396320000 374701 323145 352604 335269 427891 415564 371368 366748 376859 276009 FALSE TRUE 389494.4848 378642.64 361793.1499 401584.2075 355158.2407 319055.5589 342259.2058 361832.3429 363295.9182 330087.679 1.179972806 1.147097163 1.096051664 1.216598598 1.075951219 0.966578213 1.036873617 1.096170399 1.100604298 1 18.33248976 3.055513287 8.088823793 1.046982284 1.153896642 0.59034211 0.046988644 0.20465723 26.39075125 0.014220456 0.017001572 1136.353064 -3.055513287 0.106914357 IWEVIGDHFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWEVIGDHFNK 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 214.26 1.37E-11 160370000 484890 354050 499450 422300 555760 552400 532970 490350 528980 342690 FALSE TRUE 504033.8316 414855.3334 512466.0773 505829.6796 461292.1137 424113.4717 491194.4187 483777.6603 509942.1131 409833.5443 1.229850115 1.012253241 1.250424921 1.234232011 1.125559682 1.034843237 1.198521755 1.180424753 1.244266411 1 18.64467855 IWGEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IWGEDLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 128.38 0.0087545 1174373000 2531120 3024740 2981210 2933850 3356270 3661450 3158570 3116590 3021350 3202580 FALSE TRUE 2631050.572 3544215.566 3058902.782 3514156.773 2785772.424 2811133.727 2910993.03 3074817.209 2912612.204 3830064.234 0.686946853 0.925367135 0.798655739 0.917519018 0.727343526 0.733965165 0.760037653 0.802810872 0.760460406 1 21.86893716 -1.387657326 2.991454869 1.003011538 0.794145926 0.420183838 0.073762701 10826603.21 13411215.49 283350.9178 0.017066358 0.040958371 1.387657326 -0.208865612 IWGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWGLGR 6 0 P41743 P41743 PRKCI Protein kinase C iota type 0 130.51 0.036597 219650000 76985 87887 81437 85970 92580 87968 73862 87149 80322 93784 FALSE TRUE 80024.42725 102980.9086 83559.31512 102974.6094 76843.28467 67538.76517 68072.50344 85980.9102 77431.22691 112159.1792 0.713489772 0.918167459 0.745006478 0.918111296 0.685127024 0.602168861 0.606927618 0.766597177 0.690369058 1 16.77518817 5.072636127 15.12059197 0.755732637 0.184016466 0.005922832 0.129473492 6850572.645 28758735.06 0.030728533 123743626.7 118205.0762 -5.072636127 -0.571716171 IWHHTFYNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 175.15 8.90E-06 30910985000 2020680 5147027 2842682 2690153 10446607 7575082 3457641 3573975 3196992 14841080 FALSE TRUE 2100458.007 6030988.849 2916764.628 3222257.234 8670896.474 5815884.007 3186622.064 3526071.711 3081932.882 17748905.48 0.11834296 0.339794973 0.164334901 0.181546814 0.488531334 0.327675643 0.179539075 0.198664178 0.173640729 1 24.08122672 -1.919343895 2.815793837 1.448133347 0.244001792 0.820679915 0.106382116 31556382.72 18065258.37 93181045.4 0.025959096 0.012040821 1.919343895 -1.204131554 IWLS(ph)TETLANED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 IWLS(0.499)T(0.499)ET(0.002)LANED;IWLS(0.495)T(0.495)ET(0.01)LANED 188.48 9.60E-06 225850000 272360 311270 311200 341250 336740 388000 289050 295290 308020 359710 TRUE FALSE 283112.9831 364728.2012 319310.1277 408748.2315 279501.0551 297892.8802 266393.5057 291332.1205 296934.4204 430188.2874 0.658114113 0.847833871 0.742256675 0.950161228 0.649717957 0.692470922 0.619248626 0.67722002 0.690242922 1 18.71460872 IWNVHSVLNVLHSLVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWNVHSVLNVLHSLVDK 17 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 248.1 4.61E-21 56023000 83831 66556 86579 68340 124070 109150 101380 87070 97534 80136 FALSE TRUE 87140.71261 77986.47527 88835.31987 81857.44803 102980.6257 83801.56668 93433.57069 85902.96907 94023.77039 95837.1149 0.909258513 0.813739806 0.926940674 0.854130971 1.074538041 0.874416626 0.974920528 0.896343438 0.981078891 1 16.54829686 IWTAHYDPGHCFAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWTAHYDPGHCFAESR 16 0 Q9H553;A0A0A0MTE0 Q9H553 ALG2 "Alpha-1,3/1,6-mannosyltransferase ALG2" 0 103.5 0.0008294 242010000 95585 273270 210870 302530 227140 324080 153480 228120 172900 399000 FALSE TRUE 99358.76961 320201.9968 216365.4454 362369.531 188530.8239 248817.3315 141449.8366 225062.4245 166677.3628 477176.4107 0.2082223 0.671034841 0.453428628 0.759403698 0.395096697 0.521436781 0.296430908 0.471654548 0.349299251 1 18.8641632 -1.256921021 4.399372269 1.000286991 0.466727954 0.517687577 0.156633773 45533492.85 13009296.18 125986.5806 0.034405259 0.055345075 1.256921021 -0.533559037 IWTVDDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IWTVDDYR 8 0 Q676U5-3;Q676U5;E7EVC7;Q676U5-2;Q676U5-4;Q676U5-5 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 0 75.38 0.089662 67710000 103050 121200 101950 107820 118720 130950 99685 109050 112980 108800 FALSE TRUE 107118.4936 142015.1572 104606.9008 129146.4742 98540.01681 100538.8471 91871.42922 107588.3631 108913.8719 130117.2769 0.823245737 1.091439666 0.803943206 0.992539018 0.757316931 0.77267869 0.706066338 0.826856861 0.837043892 1 16.98945301 3.233398045 24.99690482 0.799945835 0.930634699 0.201380901 0.105247211 162.3500009 786090.159 0.027980419 0.034411183 1711.583319 -3.233398045 0.130688864 IWYEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 IWYEHR 6 0 O75874;P48735;P48735-2;H0YL11 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ;;;;;;;;; 133.99 0.014227 9658900000 3696464 4310203 3809899 4259901 4317226 4978132 4208628 3811998 3768197 4302484 FALSE TRUE 3842403.253 5050446.837 3909188.098 5102496.703 3583385.467 3822036.287 3878744.74 3760904.402 3632580.326 5145473.364 0.746754085 0.981532015 0.759733424 0.991647676 0.696415123 0.742795855 0.753816892 0.730915143 0.705975927 1 22.29487237 3.216998647 24.99955111 0.754116635 0.870019157 0.149478009 0.110162641 343.1984505 397912.9824 0.028785409 0.0344349 1648.157258 -3.216998647 0.115902522 IYDALDVSLIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IYDALDVSLIER 12 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 149.96 0.00015753 72353000 112031 130046 125651 133420 146023 164240 142469 134488 133946 121994 FALSE TRUE 116454.0704 152380.3889 128925.5683 159810.0778 121202.0626 126097.7491 131301.9075 132685.4083 129125.3096 145896.3886 0.798197073 1.0444425 0.883678956 1.09536692 0.830740663 0.864296576 0.899966811 0.909449573 0.885048019 1 17.15458465 IYDDDFFQNLDGVANALDNVDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYDDDFFQNLDGVANALDNVDAR 23 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 273.64 1.13E-51 300854000 188791 222209 214294 213721 240839 264183 215030 225030 216395 236601 FALSE TRUE 196244.6145 260371.6672 219878.6777 255994.3759 199901.2728 202830.502 198175.3867 222013.8409 208606.9862 282958.436 0.693545728 0.920176373 0.777070586 0.90470664 0.70646868 0.716820834 0.700369247 0.784616441 0.737235437 1 18.11023062 4.084900427 24.65178085 0.777377883 0.817300749 0 0.103904632 101.539459 29468.39397 0.024359635 0.052622825 12159.07192 -4.084900427 0.039922866 IYDLNKPEAEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYDLNKPEAEPK 12 1 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 72.937 0.036981 124630000 205410 103210 149090 93363 223580 178370 187910 143990 158260 89360 FALSE TRUE 213519.7454 120935.5146 152975.4079 111829.9227 185575.9515 136946.2707 173181.1232 142060.0496 152564.2535 106868.3811 1.997969308 1.131630454 1.431437496 1.046426657 1.736490715 1.281447977 1.62050853 1.329299163 1.4275902 1 16.70547554 0.032727867 1.086254718 0.997403462 1.432409437 0.197222042 0.268383493 13.17341835 13.1403955 0.345196909 0.072349613 1.078270855 -0.032727867 0.435005976 IYEDGDDDMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;;;; 167.6 3.06E-05 5641050000 5240380 3499060 4617120 3487740 6158640 5729530 5666100 4603140 5227050 3356460 FALSE TRUE 5447274.249 4099996.336 4737445.94 4177604.562 5111796.573 4398933.489 5221976.276 4541442.438 5038929.492 4014094.074 1.357037017 1.021400162 1.180203018 1.040734095 1.273462076 1.095872047 1.300910288 1.131374192 1.255309268 1 21.936643 IYEFPETDDEEENKLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYEFPETDDEEENKLVK 17 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 233.52 3.76E-20 403750000 669400 261190 388550 247720 647530 594570 602570 401780 502170 206760 FALSE TRUE 695828.4289 306047.3507 398675.9322 296718.2766 537463.0819 456490.1283 555338.9889 396394.7963 484096.9998 247270.6633 2.814035517 1.237701823 1.61230583 1.199973635 2.173582077 1.846115193 2.245874951 1.603080571 1.957761561 1 17.91573156 IYEKDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYEKDEEK 8 1 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 90.15 0.012221 428430000 871070 366490 501330 329000 801820 819550 649150 507690 512710 371300 FALSE TRUE 905460.5162 429431.8066 514395.0716 394075.218 665526.9228 629221.9329 598267.9268 500885.246 494257.6673 444049.126 2.039099872 0.967081752 1.158419286 0.887458605 1.498768681 1.417009732 1.347301214 1.127995117 1.11306979 1 18.76035977 4.7478073 24.78672959 1.18687966 2.039100376 0.654414159 0.189362915 716.6184043 1920927.142 0.046524244 0.583547338 55950.9288 -4.7478073 0.852220716 IYEKDEEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYEKDEEKQR 10 2 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 77.64 0.018219 280860000 598220 325810 403240 324320 612770 517210 476510 410620 513740 276410 FALSE TRUE 621838.1875 381765.3331 413748.7657 388469.528 508611.5743 397095.8159 439159.9011 405116.3105 495250.5978 330567.2473 1.88112462 1.154879487 1.251632668 1.175160368 1.538602443 1.201255778 1.328503972 1.225518601 1.498184112 1 18.33458426 7.999888641 0.027318621 5.78E-07 3.164845383 0.216125939 0.21184385 3001.565656 6.295712629 242.0028248 543.1109272 99974361.82 -7.999888641 3.164844805 IYGADDIELLPEAQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 227.41 5.06E-15 3157880000 5182190 4081090 4982470 4124340 6025240 6029370 5807780 5184660 5478210 3820760 FALSE TRUE 5386786.863 4781985.461 5112317.261 4940122.142 5001071.857 4629140.193 5352551.028 5115168.113 5281050.292 4569364.769 1.178891845 1.046531783 1.118824502 1.081139806 1.094478578 1.01308178 1.171399373 1.119448407 1.155751523 1 22.12356219 2.203346303 24.99984723 1.123151249 1.088173349 0.020006903 0.059331238 483.9812948 343592.3963 0.020533519 0.015165529 159.7152195 -2.203346303 -0.0349779 IYGFYDECK ddPTM_MDA-MB-175_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 ; 107.29 0.0065065 143620000 204166 172982 184268 157992 386290 299990 255630 200840 223885 237175 FALSE TRUE 212226.6313 202690.3129 189070.1755 189242.346 320628.5638 230321.8689 235593.0526 198148.0683 215827.4226 283644.9003 0.748212399 0.714591775 0.666573505 0.667180499 1.130387197 0.812007791 0.830591533 0.698577934 0.760907114 1 18.1137264 IYHDGALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IYHDGALR 8 0 Q7Z6K5;A0A0A6YYH1;Q7Z6K5-2 Q7Z6K5 ARPIN;C15orf38-AP3S2 Arpin 0 ;; 169.06 0.0003032 732700000 606840 712910 650810 609110 802390 828010 693230 694220 668530 815020 FALSE TRUE 630798.5118 835346.7468 667770.6432 729590.14 666000.0344 635717.2261 638892.8212 684915.1164 644469.7359 974707.5645 0.64716694 0.857022944 0.685098452 0.748522087 0.683281898 0.652213289 0.655471286 0.702687802 0.661192915 1 19.89460992 -0.991853654 5.977399359 1.000000281 0.701223276 0.692690192 0.060095343 2.20E-07 3.70E-08 0.056787832 0.013385008 0.101893469 0.991853654 -0.298777005 IYHLPDAES(ph)DEDEDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IYHLPDAESDEDEDFK 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0 Q15019-2 2-Sep Septin-2 1 IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK 292.31 9.37E-46 1610670000 2519280 1066390 1364880 1284180 1819570 2186170 2442090 1524520 1625390 799480 TRUE FALSE 2618743.12 1249534.187 1400449.894 1538186.971 1510280.141 1678465.149 2250672.605 1504086.303 1566892.531 956122.799 2.738919229 1.306876259 1.464717603 1.608775539 1.579588043 1.755491189 2.353957679 1.573109965 1.638798419 1 19.8668364 4.74959094 24.51275606 1.638712588 2.738920067 0.519559404 0.328975981 1040.912125 2313166.823 0.077885485 1.158382966 56181.19084 -4.74959094 1.100207479 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 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(0.999)DEDEDFKEQT(0.001)R;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 312.01 1.61E-66 1.89261E+11 12951575 6956489 8270515 6320266 11549474 11946271 10850052 8482241 9233128 6072291 TRUE FALSE 13462913.18 8151211.872 8486051.415 7570395.751 9586298.535 9171930.608 9999596.573 8368550.434 8900829.527 7262040.16 1.853874791 1.122441035 1.168549227 1.04246129 1.320055841 1.262996404 1.376967953 1.152369066 1.225665148 1 22.79194348 4.742626712 24.96799295 1.198675149 1.853875051 0.76330013 0.111411558 188.9323059 1160100.151 0.02612625 0.200920702 55287.46945 -4.742626712 0.655199902 IYHPNIDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 IYHPNIDEK 9 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ;; 127.4 0.00044656 1138930000 2897520 2118040 2531200 2099800 3265320 3191510 2872290 2656620 2779000 2144390 FALSE TRUE 3011916.327 2481796.894 2597165.151 2515134.173 2710282.073 2450330.17 2647152.404 2621012.354 2678984.333 2564542.164 1.174446016 0.967734876 1.012720784 0.980734187 1.056828822 0.955464958 1.032212471 1.022019599 1.044624795 1 21.29026986 4.747585118 24.98451273 1.009592292 1.174446102 0.718805969 0.031210704 601.8128422 1666094.799 0.006988237 0.085989647 55922.31195 -4.747585118 0.16485381 IYHPNVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 IYHPNVDK 8 0 P61088;F8VSD4;F8VV71;F8VQQ8;Q5JXB2 P61088 UBE2N;UBE2NL Ubiquitin-conjugating enzyme E2 N;Putative ubiquitin-conjugating enzyme E2 N-like 0 ;;;; 119.27 0.0017256 5069270000 8519700 6763510 7964250 6807540 12038800 10881400 9986700 7994650 8648830 7925970 FALSE TRUE 8856064.335 7925090.23 8171804.898 8154051.094 9992449.076 8354359.759 9203916.359 7887494.793 8337560.298 9478912.07 0.934291221 0.836075931 0.862103672 0.860230692 1.054176788 0.881362724 0.970988684 0.832109712 0.879590425 1 23.17629005 IYIDSNNNPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYIDSNNNPER 11 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 246.86 1.09E-15 2383020000 1212250 1139560 1068060 1045830 1278780 1392570 1171680 1090550 1063730 1151370 FALSE TRUE 1260110.566 1335270.565 1095894.521 1252692.053 1061413.432 1069166.722 1079840.66 1075932.961 1025446.565 1376958.907 0.915140284 0.969724339 0.795880338 0.909752677 0.770838859 0.776469593 0.784221413 0.781383493 0.74471835 1 20.39305407 4.038352098 1.091997571 0.798151552 0.953328101 0.213279242 0.078885707 0.825187892 1.599551315 0.02358986 0.113499588 10923.25565 -4.038352098 0.155176549 IYITLTGVHQVPTENVQVHFTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYITLTGVHQVPTENVQVHFTER 23 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 290.36 9.67E-62 6881621000 1199644 1967885 1833406 1930690 2014717 2383909 1721153 1828493 1891404 1937018 FALSE TRUE 1247006.871 2305853.941 1881186.067 2312574.719 1672256.124 1830282.263 1586244.53 1803985.042 1823332.74 2316539.591 0.538305875 0.995387236 0.812067307 0.998288451 0.721876773 0.790093237 0.68474743 0.778741296 0.787093278 1 21.14353991 IYKDQMEYMLQNHVFPLFSSELGYMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYKDQMEYMLQNHVFPLFSSELGYMR 26 1 O95373 O95373 IPO7 Importin-7 0 77.939 0.012785 146300000 83851 84920 100110 73197 107750 119280 110610 107400 105490 68103 FALSE TRUE 87161.50223 99504.34941 102718.9488 87675.14813 89434.69349 91579.02771 101940.0992 105960.4787 101693.4355 81446.47894 1.070169065 1.221714563 1.26118342 1.07647561 1.098079311 1.12440745 1.251620702 1.300982928 1.248592165 1 16.31356471 2.236804517 24.98990636 1.234418227 1.146070049 0.035553975 0.096036193 85.68212776 1219254.073 0.03434804 0.026685435 172.506124 -2.236804517 -0.088348178 IYKTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYKTDR 6 1 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7;P62837-2;A0A0A0MQU3;P62837 P61077-3;A0A0A0MQU3 UBE2D3;UBE2D2 Ubiquitin-conjugating enzyme E2 D3;Ubiquitin-conjugating enzyme E2 D2 0 ; 74.415 0.073312 886930000 1131630 1286570 1292000 1067980 1788240 1574360 1152610 1311130 1427180 1673090 FALSE TRUE 1176307.626 1507528.389 1325670.581 1279223.256 1484275.604 1208738.75 1062265.416 1293556.447 1375816.071 2000899.952 0.587889277 0.753425171 0.662537165 0.639323948 0.741804008 0.604097545 0.530893819 0.64648732 0.687598632 1 20.9322176 -1.609039206 2.721688955 1.030255395 0.64933104 0.728480623 0.064017505 11946889.45 11077164.04 2566912.576 0.015500253 0.024601455 1.609039206 -0.380924355 IYNDDKNTYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYNDDKNTYIR 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 153.63 2.95E-05 544280000 962770 763310 927630 739440 1152940 1196010 1036040 933570 969270 734990 FALSE TRUE 1000780.903 894402.5548 951804.7999 885699.025 956963.6706 918254.8032 954832.4776 921057.0212 934386.162 878997.2183 1.13854843 1.017526036 1.082830275 1.007624378 1.088699316 1.044661785 1.086274743 1.047849757 1.063013787 1 19.74549907 IYNISGNGS(ph)PLADSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 IYNIS(0.001)GNGS(0.999)PLADSK;IYNIS(0.001)GNGS(0.999)PLADSK;IYNIS(0.034)GNGS(0.966)PLADSK;IYNIS(0.016)GNGS(0.984)PLADSK 206.64 3.98E-09 379799000 683830 482012 589410 487204 700630 696830 700910 567570 598030 425490 TRUE FALSE 710828.1364 564793.8115 604770.5088 583571.497 581537.1629 535001.7931 645970.8427 559962.6525 576507.0171 508856.619 1.396912431 1.109927218 1.188489029 1.14682894 1.142831087 1.051380238 1.269455518 1.100433072 1.132945894 1 18.95689968 4.742008243 24.8719467 1.135637298 1.396912536 0.573495885 0.069485212 211.1095527 1522919.79 0.015071316 0.109606314 55208.79182 -4.742008243 0.261275238 IYNYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYNYYK 6 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 97.64 0.095015 251570000 216920 329800 318320 364800 410250 375160 360000 352960 317680 420050 FALSE TRUE 225484.1691 386440.5845 326615.6807 436956.3512 340515.8515 288034.7756 331782.2593 348229.1485 306246.7589 502350.7552 0.448858028 0.769264464 0.650174559 0.86982322 0.677844809 0.573373828 0.660459362 0.693199214 0.609627348 1 18.93833552 -1.040042564 4.802863943 1.00000399 0.670056735 0.476189508 0.106188806 13365142.46 2894172.661 1143.943018 0.023625356 0.091192146 1.040042564 -0.329947256 IYNYYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYNYYKK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 103.68 0.013344 567560000 581800 478260 527730 352610 1091900 751130 609600 524400 639850 683130 FALSE TRUE 604769.9132 560397.4347 541483.0773 422355.2056 906299.228 576691.441 561817.9591 517371.2757 616821.9235 816976.2442 0.740253976 0.685940918 0.662789256 0.516973668 1.109333637 0.705885202 0.687679676 0.633275789 0.755005948 1 19.6399346 0.964003563 21.57217288 1.000000005 0.714030404 0.255134551 0.143694247 1250.435405 749371.4719 0.136341822 0.034085456 9.204571241 -0.964003563 -0.2859696 IYPTFLHLHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYPTFLHLHGK 11 0 Q08945;E9PMD4 Q08945 SSRP1 FACT complex subunit SSRP1 0 ; 185.08 2.67E-06 762590000 451940 421990 455750 390650 586000 586650 514010 476010 464090 436760 FALSE TRUE 469782.9402 494463.4999 467627.2194 467919.404 486391.9293 450409.4283 473720.5531 469629.8645 447387.4916 522334.7597 0.899390537 0.946641001 0.895263451 0.895822833 0.931188132 0.862300316 0.906929023 0.899097477 0.856514875 1 18.99461519 IYQY(ph)IQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;IYQY(1)IQSR 190.26 0.0019309 17402630000 2949183 3201340 3094590 2888144 3412230 3705860 2920100 3007410 2972057 3255670 TRUE FALSE 3065619.022 3751145.242 3175237.558 3459410.263 2832220.363 2845230.178 2691214.932 2967100.588 2865093.249 3893556.203 0.787357075 0.963423936 0.815510909 0.888496296 0.727412221 0.730753591 0.691197145 0.762054131 0.735855115 1 21.89265702 3.240630424 24.999725 0.755204597 0.867378547 0.165524609 0.091966138 70.90974347 856457.9213 0.023677949 0.030539404 1740.325261 -3.240630424 0.11217395 IYS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYSPVR 6 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 IYS(1)PVR;IYS(1)PVR 85.212 0.057662 382560000 427340 442360 429490 393300 544990 608790 469900 422120 434600 376380 TRUE FALSE 444211.7132 518331.8889 440682.8622 471093.5661 452352.7945 467407.7488 433068.0101 416462.1718 418958.8309 450124.4548 0.986864207 1.151530168 0.979024484 1.046585141 1.004950497 1.038396701 0.96210727 0.92521561 0.930762207 1 18.77996442 2.178163964 4.011832411 0.943679177 1.036960022 0.388426225 0.048838271 0.196567742 6.384504918 0.01820384 0.013295526 150.7175978 -2.178163964 0.093280845 IYSFTDNAPS(ph)PSIGGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYSFTDNAPSPSIGGSSR 18 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 IYSFTDNAPS(0.992)PS(0.007)IGGS(0.001)S(0.001)R;IYSFTDNAPS(1)PSIGGSSR 181.41 7.72E-14 184800000 138837 135166 130626 150697 128285 151258 147543 141155 120825 115978 TRUE FALSE 144318.392 158379.7091 134030.2209 180504.4168 106479.1615 116130.6218 135978.1941 139263.0481 116476.5319 138701.6686 1.040494995 1.141873135 0.966320177 1.301386052 0.767684792 0.837269105 0.980364516 1.004047389 0.839763018 1 17.08162562 3.229012399 24.9999722 0.913878244 1.104172618 0.469506614 0.107738184 190.9546433 499973.412 0.030996658 0.037499421 1694.386173 -3.229012399 0.190294374 IYSHDGTDSPPDADEVVIVLNNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 IYSHDGTDSPPDADEVVIVLNNFK 24 0 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 131.09 1.18E-08 0 29645 35017 37780 37408 47366 47908 42126 37120 39008 32313 FALSE TRUE 30815.40749 41030.89736 38764.57784 44807.19075 39314.74424 36782.09305 38824.05404 36622.46712 37604.1097 38644.11368 0.7974153 1.061763188 1.003117271 1.159482945 1.017354016 0.95181619 1.004656346 0.947685524 0.973087648 1 15.23796106 1.762974008 24.99999302 0.968617666 1.006936535 0.012166242 0.086478359 56.90799352 58316.56875 0.039805209 0.022075177 57.93940196 -1.762974008 0.038318869 IYSPVRS(ph)PSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYSPVRSPSAR 11 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 IYS(0.001)PVRS(0.986)PS(0.013)AR;IYSPVRS(0.996)PS(0.004)AR;IYS(0.007)PVRS(0.979)PS(0.014)AR;IYSPVRS(0.999)PS(0.001)AR 172.85 7.79E-06 1346360000 319645 432021 365809 350619 455520 525115 382467 388329 415170 476445 TRUE FALSE 332264.8314 506217.2461 375342.2831 419970.3917 378090.8731 403164.9994 352488.2371 383124.0849 400228.1128 569795.2757 0.583130197 0.888419521 0.658731827 0.737054886 0.663555648 0.707561148 0.618622604 0.672389016 0.702406864 1 19.12008413 0.920222805 18.68626823 1 0.692795018 0.585229546 0.077720967 1617.508715 378872.7093 0.069860037 0.017465009 8.32190599 -0.920222805 -0.307204982 IYVASVHQDLSDDDIK ddPTM_MDA-MB-175_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 0 207.39 1.76E-11 96599000 135600 157430 155290 148720 215710 243450 214840 194850 169110 147270 FALSE TRUE 140953.5927 184467.3779 159336.985 178136.3721 179043.6912 186912.427 198000.2794 192238.3545 163023.7641 176124.7368 0.800305484 1.047367798 0.904682601 1.011421651 1.016573222 1.061250284 1.124204828 1.091489804 0.925615374 1 17.42623803 5.972558327 0.629415649 1.049198309 2.24E-14 0.443654841 0.06863153 12.65370672 1.149179405 0.028470075 13.59161475 938768.108 -5.972558327 -1.049198309 IYVDDGLISLQVK ddPTM_MDA-MB-175_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 ; 220.25 4.91E-11 515120000 828210 701760 906310 669830 1085210 1015530 1011240 896120 971330 791350 FALSE TRUE 860908.3703 822281.8211 929929.1831 802320.3748 900746.3918 779688.548 931976.3664 884108.9772 936372.023 946399.8812 0.909666609 0.868852414 0.982596471 0.847760435 0.951760889 0.823846836 0.984759598 0.9341812 0.989404206 1 19.85209037 1.641153032 1.29325316 0.994297657 0.902402578 0.33771067 0.049411202 0.4642156 1.483260976 0.038627883 0.014145835 43.76763019 -1.641153032 -0.091895079 IYVEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 IYVEIER 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;; 130.77 0.0082156 641578000 657018 730630 737250 808700 776660 884260 815340 753520 734740 683290 FALSE TRUE 682957.578 856110.019 756463.3407 968658.4463 644643.6106 678904.0161 751431.5203 743420.2969 708296.8509 817167.5931 0.835761946 1.047655372 0.925713828 1.185385292 0.788875643 0.830801444 0.919556192 0.909752544 0.866770607 1 19.64027247 3.197565923 24.99999039 0.883263105 0.996924362 0.239220116 0.098343925 205.6878494 125434.9854 0.027155053 0.032456815 1576.035235 -3.197565923 0.113661256 IYVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IYVLLR 6 0 P84090 P84090 ERH Enhancer of rudimentary homolog 0 ; 138.97 0.02809 438290000 390330 457290 418330 457710 657970 579910 531400 448440 427400 684790 FALSE TRUE 405740.5298 535826.0003 429232.0235 548243.6719 546128.4944 445234.6911 489747.4794 442429.3953 412017.9575 818961.4894 0.495432978 0.654274966 0.52411747 0.669437671 0.666854915 0.543657665 0.59801039 0.540232234 0.503098086 1 19.64343609 -1.571655199 4.092640063 1.007410779 0.580313555 0.798814935 0.06363261 17150.56593 33762611.13 245581.7491 0.014487264 0.026812962 1.571655199 -0.427097224 KAAALEAMKDYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAAALEAMKDYTK 13 2 P31948;P31948-2;P31948-3;H0YGI8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 106.42 0.00077341 772350000 1203710 905840 1302570 740120 1852220 1465340 1236600 1242060 1540440 1193730 FALSE TRUE 1251233.4 1061410.974 1336516.044 886513.527 1537380.306 1125036.992 1139672.061 1225412.217 1484999.865 1427618.538 0.876447991 0.743483602 0.936185689 0.620973673 1.076884521 0.788051543 0.798302929 0.858361099 1.040193739 1 20.44517911 1.288121298 5.331294221 1.020850205 0.834385657 0.293299271 0.113706164 0.205605221 12.07467316 0.077219085 0.026038631 19.4142804 -1.288121298 -0.186464547 KAAALEFLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAAALEFLNR 10 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 137.78 0.00013173 579330000 810050 812410 891790 757630 1228700 1160800 943160 886800 927820 992330 FALSE TRUE 842031.3995 951935.0978 915030.78 907486.9527 1019846.013 891221.7921 869232.6547 874913.8965 894427.9394 1186758.064 0.709522374 0.802130718 0.771033969 0.7646773 0.85935461 0.75097176 0.732443015 0.73723021 0.753673361 1 20.17859442 -0.956088468 4.680998178 1.000002843 0.764806121 0.762362911 0.039434461 0.006064582 25097567.32 184.2375776 0.00941558 0.110639838 0.956088468 -0.235196722 KAADKLIQNLDANHDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAADKLIQNLDANHDGR 17 2 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 202.5 6.33E-12 1229500000 785940 836980 878940 562680 1256200 1029800 617960 832710 982680 1020400 FALSE TRUE 816969.5181 980724.8042 901845.8985 673976.4246 1042671.573 790644.5568 569522.6805 821548.8845 947313.5388 1220327.843 0.669467244 0.803656828 0.739019357 0.552291278 0.854419227 0.647895204 0.466696457 0.673219815 0.776277903 1 20.21883735 -1.845756692 6.328036518 1.03366927 0.681366835 0.420134055 0.110139045 0.046869327 0.00114242 0.095536711 0.025264368 0.014264065 1.845756692 -0.352302435 KAALEEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 137.17 0.0002762 1351640000 1158120 1111150 1148660 1060150 1475420 1441420 1296890 1147270 1215400 1097490 FALSE TRUE 1203843.472 1301981.369 1178595.023 1269844.506 1224628.635 1106672.05 1195236.373 1131892.722 1171657.991 1312522.153 0.917198593 0.991969062 0.897962004 0.967484246 0.933034641 0.843164474 0.910640914 0.862379899 0.892676736 1 20.32391034 2.975575012 22.77818785 0.891234797 0.944643238 0.141986145 0.045875591 328.6449753 306487.1579 0.012740972 0.013596494 945.3116542 -2.975575012 0.053408441 KAALLAQYADVT(ph)DEEDEADEKDDSGATTMNIGSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAALLAQYADVTDEEDEADEKDDSGATTMNIGSDK 35 2 Q96MW1 Q96MW1 CCDC43 Coiled-coil domain-containing protein 43 1 KAALLAQYADVT(1)DEEDEADEKDDSGATTMNIGSDK 320.32 5.98E-105 824340000 398920 94357 159120 94593 276260 234590 236070 166910 216700 59762 TRUE FALSE 414669.6696 110562.0808 163266.7979 113303.2131 229301.4239 180110.0277 217566.2165 164672.8445 208901.0093 71471.21969 5.801911195 1.546945487 2.284371228 1.58529844 3.208304334 2.520035737 3.044109468 2.304044134 2.922868957 1 16.12507479 8 0.059394195 1.17E-12 7.98210058 0.20831447 1.118814429 719.4481479 3.192523336 87.64205194 498.2184131 99999999.91 -8 7.98210058 KAAS(ph)PS(ph)PQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(1)PS(0.998)PQS(0.002)VR;KAAS(1)PS(1)PQSVR;KAAS(1)PS(0.994)PQS(0.006)VR;KAAS(0.999)PS(0.99)PQS(0.011)VR;KAAS(0.968)PS(0.849)PQS(0.182)VR 140.82 0.00052054 4584280000 9922000 6213794 7464132 5911782 9155590 10357280 9137680 7903496 8376213 5515156 TRUE FALSE 10313728.22 7280964.783 7658653.412 7081114.835 7599326.082 7951958.686 8421444.765 7797562.564 8074754.73 6595745.224 1.56369415 1.103888118 1.161150583 1.07358829 1.152155795 1.205619443 1.276799585 1.182211001 1.224236907 1 22.65310424 4.743907304 24.98838947 1.164770296 1.563694319 0.723765876 0.075764079 306.8941646 1434263.292 0.017886461 0.154634747 55450.73462 -4.743907304 0.398924022 KAAS(ph)PSPQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.792)PS(0.207)PQS(0.001)VR;KAAS(0.663)PS(0.336)PQS(0.001)VR;KAAS(0.526)PS(0.291)PQS(0.183)VR;KAAS(0.845)PS(0.155)PQSVR;KAAS(0.519)PS(0.104)PQS(0.377)VR;KAAS(0.898)PS(0.102)PQSVR;KAAS(0.995)PS(0.005)PQSVR 166.52 1.24E-05 7671680000 3393463 2430274 2973690 2244636 3804525 3620668 3245867 2965487 2990765 2280682 TRUE FALSE 3527439.54 2847654.655 3051186.804 2688618.301 3157833.199 2779822.729 2991447.463 2925739.497 2883127.952 2727537.972 1.293268719 1.044038501 1.118659698 0.985730842 1.157759574 1.019169213 1.096757403 1.072666825 1.057044112 1 21.37916785 4.742034511 24.94080618 1.066576498 1.293268807 0.651316649 0.050783583 182.1700934 1307830.632 0.010660156 0.078347877 55212.13116 -4.742034511 0.22669231 LISS(ph)TESELQQSYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LISSTESELQQSYAK 15 0 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 LIS(0.001)S(0.308)T(0.308)ES(0.308)ELQQS(0.04)Y(0.034)AK 68.034 0.034673 802030000 1443100 302530 324790 194370 471150 592820 392710 250140 315530 199790 TRUE FALSE 1500074.702 354487.1741 333254.2942 232815.8059 391064.0913 455146.5393 361928.364 246787.2824 304174.1369 238935.0253 6.278169977 1.48361327 1.394748609 0.974389609 1.636696381 1.904896692 1.514756422 1.032863567 1.273041224 1 17.86625883 4.738773043 5.99784197 1.356901782 6.41168582 0.965015352 0.281190913 0.02232083 3.887589689 0.071489653 0.460437919 54799.05167 -4.738773043 5.054784037 up KAASLTEDRDR ddPTM_MDA-MB-175_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 0 ;; 142.97 2.10E-05 931290000 1386990 1474690 1532000 1409730 2135470 2011450 1603690 1600890 1697530 1840180 FALSE TRUE 1441749.436 1727956.536 1571925.179 1688570.386 1772483.572 1544321.221 1477988.587 1579432.688 1636436.227 2200728.039 0.655123855 0.785174954 0.714275072 0.767278081 0.80540782 0.70173197 0.671590747 0.717686448 0.743588575 1 21.06954944 0.789799603 5.861972364 0.999999903 0.728602024 0.765586717 0.045046377 4.632183118 129.1276441 0.043461318 0.010934208 6.163105518 -0.789799603 -0.271397879 KAASPS(ph)PQS(ph)VR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KAAS(0.492)PS(0.514)PQS(0.994)VR;KAAS(0.304)PS(0.7)PQS(0.996)VR;KAAS(0.315)PS(0.716)PQS(0.969)VR 158.89 1.96E-05 1939930000 3497410 2075630 2530060 2045040 3088430 3561340 3277550 2599660 2822560 1842650 TRUE FALSE 3635490.447 2432103.306 2595995.442 2449542.808 2563459.772 2734272.758 3020647.067 2564815.81 2720976.617 2203681.988 1.649734611 1.103654393 1.178026347 1.111568194 1.163262116 1.240774655 1.370727302 1.163877467 1.234741052 1 21.07148461 4.835494933 0.021765229 1.40E-13 2.583564966 0.2194934 0.150406047 2652.88142 8.720287279 437.5985723 607.5353425 68469.1495 -4.835494933 2.583564966 KAASPS(ph)PQSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAASPSPQSVR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAAS(0.4)PS(0.6)PQSVR 67.136 0.028461 0 218240 166650 177480 133410 231640 231520 207110 169550 190110 141280 TRUE FALSE 226856.2837 195270.8411 182105.2746 159798.0998 192265.9155 177752.9887 190876.177 167277.4596 183267.9782 168961.111 1.342653835 1.155714708 1.077794017 0.945768519 1.137929991 1.052034919 1.129704793 0.990035272 1.084675504 1 17.3663317 4.664442145 1.952139223 1.051311085 1.403125316 0.70921314 0.057199264 0.33026133 1.515927322 0.014136551 0.19796948 46178.74698 -4.664442145 0.351814231 KACQIFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KACQIFVR 8 1 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 119.41 0.0027262 727320000 302160 338020 211930 186420 962940 492530 333290 256620 261330 1156800 FALSE TRUE 314089.5101 396072.3056 217453.0699 223293.3196 799259.8028 378147.3719 307165.8589 253180.4286 251924.7843 1383452.812 0.227033049 0.286292602 0.157181415 0.161402917 0.577728272 0.273335938 0.222028432 0.18300619 0.182098574 1 20.39984201 -1.794132952 2.708002877 1.207279706 0.251578372 0.78712253 0.116661857 23805526.9 18168614.13 32557890.06 0.02964752 0.016064494 1.794132952 -0.955701335 KADGPPGPHDGGDRPSAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KADGPPGPHDGGDRPSAEAR 20 2 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 0 177.32 3.96E-17 140120000 129360 109640 111610 115920 155190 164760 147800 138350 121310 110920 FALSE TRUE 134467.2327 128469.8171 114518.6483 138848.63 128810.8592 126496.987 136215.0498 136495.6445 116944.0768 132652.6503 1.013679202 0.968467775 0.8632971 1.046708299 0.971038716 0.953595625 1.026855095 1.028970354 0.881581156 1 17.01729397 3.702576587 24.99986466 0.990907317 0.950479801 0.086429934 0.056209575 1374.55215 954968.342 0.014837633 0.022986979 5041.695206 -3.702576587 -0.040427516 KADGYNQPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 200.21 7.64E-08 1073660000 1817530 1154970 1654010 1107980 1936610 1956080 1946510 1563450 1817370 1129860 FALSE TRUE 1889287.488 1353327.113 1697114.859 1327135.137 1607425.724 1501810.065 1793937.46 1542494.51 1751963.209 1351234.435 1.398193711 1.001548716 1.255973661 0.982164977 1.189597958 1.111435608 1.327628585 1.141544702 1.296564951 1 20.36584657 KADKVEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KADKVEQR 8 2 Q99832-3;Q99832;Q99832-4 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 85.731 0.0092999 1304990000 3727910 2396650 3218100 2261530 4490280 3961370 3904320 3365190 3853740 2254920 FALSE TRUE 3875090.765 2808255.994 3301966.33 2708853.884 3727023.809 3041401.853 3598289.196 3320085.132 3715044.65 2696728.401 1.436959971 1.041356628 1.224434143 1.004496368 1.382053828 1.127811704 1.334316498 1.231152952 1.37761172 1 21.3627788 3.221782842 24.99603101 1.253000348 1.170537906 0.038077195 0.153979538 695.1989899 1035726.043 0.04082004 0.048913646 1666.413755 -3.221782842 -0.082462441 KADLVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KADLVNR 7 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;; 96.492 0.020351 2146850000 1515510 1611720 1662740 1460810 2223510 2372830 1951040 1863180 1876510 2006740 FALSE TRUE 1575343.505 1888520.373 1706072.37 1749753.858 1845558.564 1821776.193 1798112.387 1838207.12 1808974.772 2399922.282 0.656414384 0.786908971 0.710886508 0.729087717 0.769007638 0.759097995 0.749237757 0.765944436 0.753763897 1 21.19455626 -5 0.257663769 2.627420374 0.723576658 0.854683027 0.032357106 61.80697638 0.608706828 53.15106671 0.039915057 1.00E-05 5 -1.903843717 KADPQEAINCLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KADPQEAINCLMR 13 1 P54920;M0R2M1;M0R058;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 66.533 0.089169 333420000 218030 176340 171240 128530 185820 212040 183110 162650 198830 136740 FALSE TRUE 226637.9928 206625.0233 175702.6551 153952.8504 154234.3828 162796.9235 168757.3597 160469.9428 191674.1471 163531.585 1.385897365 1.263517524 1.074426418 0.941425783 0.943147361 0.995507526 1.031955752 0.981277977 1.172092518 1 17.31920978 4.305622542 2.348854316 1.004801089 1.376211268 0.807944101 0.061864651 0.123063113 1.28482961 0.016033584 0.06441156 20212.6168 -4.305622542 0.371410179 KADRDQS(ph)PFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KADRDQSPFSK 11 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 KADRDQS(1)PFSK;KADRDQS(1)PFSK;KADRDQS(1)PFSK;KADRDQS(0.999)PFS(0.001)K 141.06 2.00E-05 1147620000 2811400 1677440 2350180 1143780 3420500 2705390 1867720 2072200 2619160 1985370 TRUE FALSE 2922396.243 1965527.271 2411427.621 1370016.27 2839084.632 2077104.173 1721323.226 2044425.548 2524896.943 2374365.239 1.230811585 0.827811677 1.015609385 0.57700317 1.195723634 0.874803985 0.724961433 0.861040886 1.063398715 1 21.17911045 4.745498516 23.957008 0.891889504 1.230811872 0.251429532 0.167658282 592.6528709 2046371.374 0.037588983 0.365767621 55654.27319 -4.745498516 0.338922368 KADS(ph)DSEDKGEESKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 KADSDSEDKGEESKPK 16 3 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 1 KADS(0.995)DS(0.005)EDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(0.969)DS(0.031)EDKGEESKPK;KADS(0.998)DS(0.002)EDKGEESKPK;KADS(0.863)DS(0.12)EDKGEES(0.017)KPK;KADS(0.798)DS(0.202)EDKGEESKPK;KADS(0.998)DS(0.002)EDKGEESKPK;KADS(1)DSEDKGEESKPK;KADS(1)DSEDKGEESKPK 193.64 1.89E-09 34528740000 26244220 2315275 5058084 2015869 9880648 15479300 10856580 5391324 6238118 1107137 TRUE FALSE 27280362.07 2712905.471 5189901.824 2414601.871 8201138.982 11884467.17 10005612.89 5319062.12 6013609.352 1324059.298 20.60358031 2.048930494 3.919689876 1.823635751 6.193936326 8.975781664 7.556770991 4.017238601 4.541797608 1 20.3365363 4.744557246 24.92944091 4.750724641 20.60358752 0.798562849 2.429313252 293.2223849 1218960.895 0.605280416 5.543927232 55533.78133 -4.744557246 15.85286288 KADYQAVDDEIEANLEEFDISEDDIDDGFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KADYQAVDDEIEANLEEFDISEDDIDDGFRR 31 2 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;; 305.23 2.84E-82 417227000 75059 68651 85356 62888 105569 95436 85827 73077 82984 71272 FALSE TRUE 78022.38728 80441.27522 87580.44748 75327.0587 87624.41909 73272.43535 79099.65547 72097.52234 79997.42205 85236.38382 0.915364822 0.943743406 1.02750074 0.883743014 1.028016619 0.85963801 0.928003417 0.845853838 0.938536086 1 16.37918177 2.719858435 24.98814166 0.901262991 0.958338507 0.111352183 0.058239888 1325.644408 1771203.056 0.01756014 0.016584982 524.6364192 -2.719858435 0.057075515 KAEAAASALADADADLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KAEAAASALADADADLEER 19 1 O43633;M0R1T5 O43633 CHMP2A Charged multivesicular body protein 2a 0 ;;; 223.89 3.36E-19 1191300000 2135730 2061540 2255750 1945210 2692310 2806310 2637960 2311770 2371840 2000480 FALSE TRUE 2220050.27 2415593.458 2314536.698 2329966.732 2234672.108 2154587.033 2431189.802 2280784.504 2286477.942 2392435.754 0.927945616 1.009679551 0.967439436 0.973888945 0.934057311 0.900583027 1.016198574 0.953331558 0.955711324 1 21.19004875 -1.13683991 4.443470787 1.000005641 0.961382807 0.11323558 0.033449604 1.81E-06 3.51E-07 0.031337858 0.007385325 0.072972645 1.13683991 -0.038622834 KAEAGAGS(ph)ATEFQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 KAEAGAGS(0.888)AT(0.112)EFQFR;KAEAGAGS(0.979)AT(0.021)EFQFR;KAEAGAGS(0.996)AT(0.004)EFQFR 146.72 2.67E-06 0 187561 177855 205722 152209 234992 235374 230638 174498 181289 176729 TRUE FALSE 194966.0531 208400.2127 211083.2843 182315.4859 195048.1438 180711.9556 212559.9909 172159.1397 174764.4443 211355.6639 0.922454831 0.986016693 0.998711274 0.862600427 0.922843231 0.855013546 1.005698106 0.814547084 0.826873721 1 17.68931325 3.739086091 24.99996851 0.891749999 0.97075651 0.198277198 0.064331101 66.67787089 3172252.476 0.016337327 0.027281479 5483.856619 -3.739086091 0.079006511 KAEAGAGSATEFQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 84.375 0.013393 261000000 197870 186120 229680 163600 246610 266320 203000 197210 209530 232140 FALSE TRUE 205682.0604 218084.6622 235665.6495 195959.5917 204691.3203 204471.2161 187088.3296 194566.7225 201989.0562 277623.3884 0.740867193 0.785541389 0.848868141 0.705846841 0.737298545 0.736505729 0.673892537 0.700829723 0.727564984 1 18.08276959 -0.982475138 4.452843782 1.000006697 0.737461639 0.741760386 0.046060804 0.043302636 30150563.15 546.1713294 0.01189082 0.104117771 0.982475138 -0.262545058 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 211.74 4.21E-12 5475740000 6619010 3389590 4355670 3168260 5672780 6497370 5452770 4206370 4518900 2866070 TRUE FALSE 6880333.626 3971725.715 4469182.338 3794932.372 4708522.882 4988454.286 5025367.639 4149990.49 4356265.672 3427621.542 2.007320103 1.15874103 1.303872754 1.107162014 1.373699758 1.455369044 1.466138422 1.210749331 1.270929599 1 21.70877639 7.999998507 0.033417162 1.49E-07 3.343087662 0.277662236 0.225009872 1741.676815 4.451674603 134.72725 361.6552824 99999656.13 -7.999998507 3.343087513 KAEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEEER 6 1 Q14152-2;Q14152;A0A0J9YW31;A0A0J9YW26;A0A0J9YWE1;A0A0J9YY18;Q96T17-5;Q96T17-4;Q96T17;Q96T17-2;Q9Y2J2;A0A1B0GTF8;A8K968;A0A0A0MRA8;A0A0A0MSA4;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2-4 Q14152-2;Q96T17-5;Q9Y2J2;REV__H7BXY5 EIF3A;MAP7D2;EPB41L3 "Eukaryotic translation initiation factor 3 subunit A;MAP7 domain-containing protein 2;Band 4.1-like protein 3;Band 4.1-like protein 3, N-terminally processed" 0 95.352 0.069657 236710000 423270 312840 381590 300860 510060 463840 487800 369930 463670 348990 FALSE TRUE 439981.0264 366567.8364 391534.5489 360369.21 423360.1834 356120.1896 449564.9614 364971.6934 446982.6073 417367.9087 1.054180298 0.878284671 0.938104106 0.863432963 1.014357296 0.853252447 1.077143096 0.874460364 1.070955859 1 18.67096015 1.226308285 24.99992753 1.035477944 0.941702571 0.178254155 0.078292606 387.4699673 790577.9747 0.06499405 0.016734383 16.83868934 -1.226308285 -0.093775373 KAEELLQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEELLQELR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;E9PIK8;E9PJA0 E9PP16 PPFIBP2 Liprin-beta-2 0 92.925 0.014648 169250000 140470 132980 138610 121240 201060 176440 170690 166550 153360 143700 FALSE TRUE 146015.8641 155818.2806 142222.2905 145220.9101 166883.893 135464.484 157310.8718 164317.6697 147840.6036 171855.2637 0.84964441 0.906683201 0.827570174 0.845018692 0.97107234 0.788247512 0.915368365 0.956139871 0.860262295 1 17.39083451 -0.620361749 0.212885077 1.075808335 0.84715178 0.32627768 0.053646016 15.74989573 0.916828697 0.89786331 0.141336809 0.239683563 0.620361749 -0.228656555 KAEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEFER 6 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 92.187 0.075427 437080000 775320 659780 816170 648050 931530 899640 914640 796400 777010 636380 FALSE TRUE 805930.2323 773092.0826 837440.0607 776232.3558 773188.8633 690712.2442 842948.1268 785725.5606 749045.5619 761066.4768 1.058948537 1.015800993 1.10035074 1.019927141 1.015928157 0.907558361 1.107588039 1.032400696 0.984205171 1 19.53766295 3.508530797 23.94817819 1.013701604 1.055114989 0.162632395 0.050099898 866.6862751 660801.4114 0.013507208 0.020896142 3225.008002 -3.508530797 0.041413385 KAEFPSSGSNSVLNTPPTTPES(ph)PSSVTVTEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEFPSSGSNSVLNTPPTTPESPSSVTVTEGSR 33 1 Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3;H7C5R6 Q4LE39-2 ARID4B AT-rich interactive domain-containing protein 4B 1 KAEFPSSGSNSVLNTPPT(0.001)T(0.004)PES(0.994)PS(0.001)SVTVTEGSR 188.69 3.52E-20 147200000 39379 41421 45628 40007 56004 58513 49139 47921 53592 39849 TRUE FALSE 40933.71333 48534.73454 46817.10316 47920.26519 46484.46008 44924.24252 45287.35678 47278.69738 51663.23439 47656.64859 0.858929751 1.018425256 0.982383456 1.005531581 0.975403463 0.942664746 0.950284129 0.992069287 1.084071917 1 15.54038988 1.44050955 5.530493586 1.042270087 0.966854295 0.325240783 0.045333537 0.210681502 12.76296819 0.028058894 0.010904856 27.5746209 -1.44050955 -0.075415792 KAEGAPNQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KAEGAPNQGR 10 1 Q9P2E9;A0A087WVV2;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;; 120.86 0.00085056 471830000 424142 447006 429532 417637 510247 542196 458313 425380 449871 437261 FALSE TRUE 440887.4537 523775.8033 440725.9568 500244.3521 423515.3972 416279.1961 422389.2295 419678.4769 433680.2306 522933.9211 0.843103566 1.001609921 0.842794738 0.956611021 0.8098832 0.796045503 0.807729643 0.802545905 0.829321283 1 18.99626913 3.226677427 24.99687216 0.825026413 0.912625888 0.164748319 0.072159938 280.6905253 590445.2808 0.018989306 0.022864817 1685.300801 -3.226677427 0.087599474 KAEGAQNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KAEGAQNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;;;;; 159.09 1.25E-05 1198401000 1845227 1343638 1662760 1324850 2151370 2008630 1957519 1515909 1774948 1405350 FALSE TRUE 1918077.987 1574397.374 1706092.892 1586901.376 1785680.896 1542156.124 1804083.546 1495590.719 1711067.968 1680701.425 1.141236604 0.936750187 1.01510766 0.944189939 1.062461701 0.917566975 1.073411088 0.889861041 1.018067779 1 20.68063202 4.748440461 24.754837 0.980774842 1.141236704 0.395878985 0.058077974 1123.647776 2815335.028 0.012468726 0.167885919 56032.55954 -4.748440461 0.160461862 KAEGDAKGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEGDAKGDK 10 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ; 115.14 0.0007103 392080000 734060 288537 561440 214181 921870 570550 577800 526630 752050 365407 FALSE TRUE 763041.2556 338090.9852 576071.5876 256545.3625 765170.8667 438048.4093 532510.5262 519571.3862 724983.8674 437001.5055 1.746083814 0.773660916 1.318237078 0.587058304 1.750957049 1.002395653 1.218555358 1.188946445 1.658996269 1 18.73727872 3.230176729 24.99944497 1.284642901 1.097644135 0.062302548 0.369675332 574.6996466 1713663.174 0.099097889 0.120265833 1698.934867 -3.230176729 -0.186998766 KAEGEPQEES(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 202.6 5.67E-08 12987260000 22444690 7137366 11292100 7957660 15721340 17368050 19500790 12361790 13823740 4870184 TRUE FALSE 23330823.69 8363153.089 11586381.4 9531661.397 13049032.24 13334583.6 17972267.12 12196100.42 13326226.3 5824403.309 4.00570195 1.435881522 1.989282127 1.636504358 2.240406708 2.289433422 3.085683832 2.093965644 2.287998545 1 22.47367883 3.011788716 24.76041365 2.283226361 2.156511727 0 0.810165081 2116.550006 4445451.469 0.223908368 0.267406575 1027.51629 -3.011788716 -0.126714634 KAEGEPQEES(ph)PLKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(1)PLKSK;KAEGEPQEES(0.999)PLKS(0.001)K 244.72 3.73E-18 6954510000 14203190 3627370 6481430 3459570 10915940 9407180 9066270 6643940 7967810 2734567 TRUE FALSE 14763942.91 4250342.58 6650341.39 4143862.62 9060452.418 7222505.012 8355632.067 6554888.852 7681050.075 3270353.047 4.514479842 1.299658636 2.033523994 1.267099472 2.770481439 2.20847869 2.554963316 2.004336766 2.348691399 1 21.64101496 -1.78642235 0.489945493 5.15E-15 2.286152244 0.1747107 0.862666354 97.76998134 8.724145859 115.4983803 0.388899629 0.016352255 1.78642235 2.286152244 KAEGS(ph)PNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEGSPNQGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(1)PNQGK;KAEGS(1)PNQGK 119.96 0.00038142 199828000 562260 269671 417440 272183 598110 517470 545380 439360 474930 272773 TRUE FALSE 584458.459 315984.8965 428318.8293 326019.985 496443.4758 397295.4348 502631.6905 433471.0978 457837.3621 326217.6468 1.791621222 0.968632137 1.312984854 0.99939408 1.52181674 1.217884559 1.540786329 1.328778814 1.403472089 1 18.3154753 3.200026381 24.99999521 1.358600999 1.24996318 0.009640012 0.255034703 584.0926583 378942.0566 0.068069724 0.081360354 1584.98947 -3.200026381 -0.108637819 KAEGS(ph)PSEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEGSPSEGK 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.891)PS(0.109)EGK;KAEGS(0.5)PS(0.5)EGK 95.854 0.0043725 242750000 923590 422951 625570 443507 879966 796904 859216 629207 705336 388532 TRUE FALSE 960054.0464 495589.5441 641872.8681 531231.3609 730389.6936 611835.1232 791868.4048 620773.5093 679951.0951 464657.4065 2.066154618 1.066569772 1.381389512 1.143275354 1.571888629 1.316744583 1.704198392 1.335981092 1.463338549 1 18.82580788 -1.371788249 4.737190487 0.999544212 1.431242769 0.195038857 0.271847535 0.001184383 0.000157063 0.238227664 0.056092924 0.042482665 1.371788249 0.431698557 KAEGS(ph)PSEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.984)PS(0.016)EGKK;KAEGS(0.771)PS(0.229)EGKK 95.981 0.0038366 699050000 2629290 748804 1385440 820062 2162560 1829890 2006030 1326730 1687780 582080 TRUE FALSE 2733096.399 877405.2621 1421545.705 982267.816 1794968.824 1404925.78 1848792.127 1308947.354 1627037.127 696127.4314 3.926143801 1.260408975 2.042076839 1.411045983 2.578506093 2.018202008 2.655824269 1.880327215 2.337269089 1 19.4089919 -1.012130403 4.665311861 0.999971056 2.175672421 0.210229565 0.709599786 0.000193086 4.09E-05 0.62095809 0.146357637 0.097245519 1.012130403 1.175701366 KAEGSPS(ph)EGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEGSPSEGKK 11 2 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KAEGS(0.183)PS(0.817)EGKK 111.64 0.00085187 525310000 2458500 699670 1310400 662910 1971000 1633200 1894000 1189700 1513500 513670 TRUE FALSE 2555563.478 819832.8798 1344550.101 794031.6194 1635970.124 1253914.051 1745543.331 1173754.017 1459029.431 614313.8017 4.160029404 1.334550644 2.188702414 1.292550513 2.663085413 2.041162103 2.841452245 1.910674991 2.375055593 1 19.22861627 -1.336069576 2.652515028 0.978407465 2.24946413 0.198778129 0.781164241 5777302.922 6386339.999 975610.7163 0.178218383 0.046124368 1.336069576 1.271056665 KAEGVALTNATGAVESTSQAGDRGS(ph)VS(ph)SYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAEGVALTNATGAVESTSQAGDRGSVSSYDR 31 2 F6U236;Q9BY11 F6U236 PACSIN1 Protein kinase C and casein kinase substrate in neurons protein 1 2 KAEGVALTNAT(0.001)GAVES(0.131)T(0.136)S(0.142)QAGDRGS(0.591)VS(0.507)S(0.429)Y(0.062)DR 49.479 0.044991 291750000 69725 73295 79844 77096 87926 101340 88205 67593 92522 73803 TRUE FALSE 72477.79684 85882.84609 81924.80023 92345.35869 72980.36993 77805.32082 81291.26162 66687.02639 89192.15129 88263.28481 0.821154538 0.97303025 0.928186623 1.046248833 0.82684856 0.881513995 0.921008795 0.755546619 1.010523815 1 16.42952582 3.201512857 24.99927364 0.879009998 0.943363251 0.024402918 0.088487057 375.2845548 253235.2805 0.024757737 0.029591816 1590.423768 -3.201512857 0.064353253 KAEGVALTNATGAVESTSQAGDRGS(ph)VSSYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEGVALTNATGAVESTSQAGDRGSVSSYDR 31 2 F6U236;Q9BY11 F6U236 PACSIN1 Protein kinase C and casein kinase substrate in neurons protein 1 1 KAEGVALTNATGAVES(0.141)T(0.141)S(0.02)QAGDRGS(0.699)VSSYDR;KAEGVALTNATGAVES(0.001)T(0.006)S(0.001)QAGDRGS(0.794)VS(0.172)S(0.025)YDR 233.08 5.90E-46 542990000 165872 144103 164784 138937 191529 199485 163416 170464 178256 174722 TRUE FALSE 172420.7546 168851.5693 169078.4064 166418.3239 158972.969 153157.632 150607.0269 168179.2089 171840.6014 208955.4306 0.825155652 0.808074568 0.809160144 0.796429762 0.760798456 0.732967942 0.720761487 0.804856846 0.822379207 1 17.67283573 0.709524821 1.861060534 0.999808876 0.779725455 0.802030052 0.032385414 0.530419965 2.693986219 0.034336097 0.009594874 5.123005481 -0.709524821 -0.220083421 KAELLDNEKPAAVVAPITTGYTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAELLDNEKPAAVVAPITTGYTVK 24 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 128.98 4.15E-05 601380000 357010 188580 300090 209810 383070 370320 400150 294210 354930 188260 FALSE TRUE 371105.0305 220967.1481 307910.5919 251309.7918 317955.8982 284318.7923 368785.1974 290266.5962 342156.1386 225145.9425 1.648286557 0.981439619 1.367604446 1.116208398 1.412221311 1.262819969 1.637982871 1.289237518 1.519708216 1 17.78050095 KAELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAELVK 6 1 P46940;H0YLE8;F2Z2E2;Q86VI3 P46940;F2Z2E2 IQGAP1;IQGAP3 Ras GTPase-activating-like protein IQGAP1;Ras GTPase-activating-like protein IQGAP3 0 ; 91.041 0.077516 1133190000 1395550 874880 1274690 984050 1527640 1385170 1611920 1260770 1295070 922320 FALSE TRUE 1450647.392 1025133.834 1307909.469 1178692.153 1267972.298 1063485.26 1485573.498 1243871.44 1248460.684 1103030.945 1.315146595 0.929379034 1.18574141 1.068593912 1.149534656 0.964148163 1.346810355 1.12768499 1.131845565 1 20.07304184 KAENVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAENVPR 7 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 0 72.485 0.082541 52363000 75319 74248 75213 71772 83051 97144 79064 80065 79220 84515 FALSE TRUE 78292.65228 86999.51643 77173.11257 85968.28738 68934.02069 74583.77823 72866.75708 78991.85963 76368.88767 101074.0961 0.774606504 0.860749883 0.763530079 0.85054718 0.682014713 0.737911899 0.720924153 0.781524274 0.755573293 1 16.62505378 -1.765554051 9.031889858 1.001756516 0.769780461 0.644686936 0.051289558 0.001834532 4.76E-05 0.050220239 0.011763062 0.017157182 1.765554051 -0.231976055 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 292.65 8.89E-62 3885215000 3145728 1268868 1866789 1232515 2540369 2544974 3112867 1843468 2131751 761471.4 TRUE FALSE 3269923.77 1486786.209 1915439.055 1476302.788 2108557.985 1953942.358 2868872.351 1818759.327 2055029.698 910667.1416 3.590690408 1.632634077 2.103336079 1.621122275 2.315399215 2.145616404 3.150297424 1.997172451 2.256620014 1 19.7965643 KAEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 33 2 Q5STZ8;Q8NE71 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK;KAEQGS(1)EEEGEGEEEEEEGGESKADDPYAHLSK 201.09 2.86E-27 973990000 340880 82775 136368 61200 247763 249230 200861 144911 190919 63687 TRUE FALSE 354338.2056 96990.96235 139921.8621 73305.17734 205648.3338 191350.1096 185116.99 142968.7051 184047.8625 76165.24829 4.652229377 1.273428034 1.837082728 0.962449135 2.700028404 2.512302053 2.43046526 1.877085788 2.416428314 1 16.21684527 -0.884733486 6.925466928 0.999999978 2.211338888 0.137598433 0.952292806 3.08E-07 5.19E-08 0.861638014 0.203090024 0.130396674 0.884733486 1.21133891 KAERS(ph)PNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 134.61 8.66E-05 2388400000 2952730 1675140 2349720 1287590 3471050 2760430 2233200 2173250 2693320 1935770 TRUE FALSE 3069306.06 1962832.264 2410955.634 1542271.459 2881042.161 2119361.967 2058155.949 2144121.138 2596387.939 2315047.069 1.325807195 0.847858469 1.041428343 0.666194428 1.24448535 0.915472517 0.88903417 0.926167406 1.121527063 1 21.1426101 4.749140888 24.44399462 0.955089814 1.325807482 0.348674587 0.149214915 1179.400102 2724737.942 0.032904462 0.468874288 56123.00138 -4.749140888 0.370717668 KAEVEGK ddPTM_MDA-MB-175_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 ;;; 114.28 0.0095247 4999610000 6931100 4091010 5808200 3641540 8009700 6665800 7588600 5685500 6811700 3765360 FALSE TRUE 7204745.18 4793609.144 5959566.463 4361825.743 6648214.055 5117768.971 6993785.703 5609295.172 6566548.248 4503110.2 1.599948671 1.064510734 1.323433405 0.968625139 1.476360506 1.136496498 1.553101166 1.245649101 1.458225084 1 22.10249035 KAFEEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KAFEEAEK 8 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 109.66 0.005732 3852700000 6469720 3565980 5104220 3233960 7674560 6429770 6201400 4914330 5841280 3440020 FALSE TRUE 6725149.541 4178409.326 5237240.166 3873627.636 6370041.032 4936553.362 5715318.064 4848461.445 5631053.474 4114026.056 1.634688125 1.015649699 1.27302066 0.941566141 1.548371582 1.199932449 1.389227483 1.178519868 1.368745214 1 21.9721195 -1.177268589 3.943560745 0.999847214 1.268273475 0.142992188 0.205120522 0.00024815 5.18E-05 0.178865511 0.042135093 0.066486185 1.177268589 0.26842626 KAFSGYLGTDQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAFSGYLGTDQSK 13 1 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 162.87 6.37E-05 466100000 579960 429770 550990 363910 719340 635880 578560 531140 630640 489450 FALSE TRUE 602857.2686 503579.6544 565349.252 435890.3118 597066.8437 488206.5069 533210.9554 524020.9371 607943.3896 585348.3564 1.029911952 0.860307625 0.965833842 0.744668208 1.020019681 0.83404438 0.910929278 0.895229194 1.038601002 1 19.15893594 1.241838978 24.98884879 1.019300531 0.903654489 0.230461979 0.081374545 100.3991316 765328.0628 0.053839404 0.017819908 17.45174979 -1.241838978 -0.115646042 KAGEQQETASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KAGEQQETASR 11 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;;;;; 193.81 1.26E-06 1302651000 1132750 1021864 1152961.5 921575.8 1288054 1370253 1154374 1172329.6 1136536 989781.3 FALSE TRUE 1177471.845 1197361.193 1183008.624 1103860.743 1069111.041 1052032.507 1063891.149 1156616.439 1095632.291 1183709.995 0.994730001 1.011532553 0.99940748 0.93254323 0.90318663 0.888758658 0.898776857 0.977111323 0.925591822 1 20.17488424 3.740567564 5.316166264 0.929032725 1.003510118 0.485874037 0.032724473 0.142227313 14.12317051 0.008925398 0.015243416 5502.595193 -3.740567564 0.074477393 KAGNFYVPAEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAGNFYVPAEPK 12 1 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 116.24 0.0013842 1619970000 3911000 2436200 3620700 2469100 4708100 4016600 4388300 3555600 4064700 2738600 FALSE TRUE 4065409.3 2854598.399 3715058.416 2957480.61 3907818.844 3083805.522 4044333.579 3507942.998 3918412.241 3275176.236 1.241279555 0.871586197 1.134307942 0.902998922 1.193162921 0.941569338 1.234844566 1.071069996 1.196397372 1 21.64314111 2.240277267 24.99994249 1.128716633 1.043489588 0.080706139 0.128523172 106.0996999 1545180.711 0.041403322 0.032979471 173.8910649 -2.240277267 -0.085227045 KAGTQIENIDEDFRDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAGTQIENIDEDFRDGLK 18 2 O43707;F5GXS2;O43707-3;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 ; 224.97 2.43E-19 1112960000 1392570 799600 1124140 915600 1789920 1385180 1603060 1109700 1348530 902700 FALSE TRUE 1447549.739 936925.08 1153436.012 1096702.947 1485670.038 1063492.938 1477407.968 1094826.287 1299996.669 1079566.782 1.340861689 0.86787135 1.068424882 1.015873187 1.376172427 0.985110839 1.368519292 1.014134841 1.204183651 1 20.04202106 5.071270561 17.43367614 1.109535795 5.384227896 0.169056866 0.158924907 12421871.74 44429884.93 0.035409986 1986718732 117833.9837 -5.071270561 4.274692101 KAGTQIENIEEDFRDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAGTQIENIEEDFRDGLK 18 2 P12814-3;P12814;P12814-2;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-3 ACTN1 Alpha-actinin-1 0 ; 218.69 4.35E-19 483610000 961940 576660 815110 526160 1005650 933140 922580 807490 924980 503070 FALSE TRUE 999918.134 675696.8692 836352.4362 630232.8776 834709.9722 716432.3769 850265.7689 796666.9173 891690.1505 601636.9346 1.661995925 1.123097387 1.390128146 1.047530232 1.387398154 1.190805178 1.413253941 1.324165575 1.482106731 1 19.19853361 -2.181122491 2.439247444 0.10631757 1.323074936 0.256105423 0.170392723 6903793.272 2375312.742 33854715.51 0.038813678 0.00658988 2.181122491 1.216757366 KAHEILPNLVCCSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAHEILPNLVCCSAK 15 1 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 118.33 0.00019429 853810000 1037300 699740 854180 572525 1170840 1073930 930910 825300 967020 755080 FALSE TRUE 1078253.405 819914.9018 876440.6325 685768.7362 971821.035 824526.0331 857942.8417 814238.2034 932217.1391 903023.4691 1.194048042 0.907966326 0.970562408 0.759414079 1.076185801 0.913072651 0.950078122 0.901680002 1.032328805 1 19.78440396 4.742933063 24.45914837 0.939188724 1.194048181 0.449091121 0.082235571 274.326831 1534486.797 0.018064489 0.140724495 55326.48287 -4.742933063 0.254859457 KAHHAACKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAHHAACKEEK 11 2 Q9UNF0-2;Q9UNF0;A0A0U1RR22 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 63.408 0.024073 49294000 145360 63562 104990 68980 169880 137670 125120 104090 135310 77016 FALSE TRUE 151098.925 74478.27906 107726.1257 82624.03812 141003.8583 105698.2289 115312.7675 102694.8438 130440.2195 92105.81064 1.640492864 0.808616509 1.169590983 0.897055653 1.530889933 1.14757395 1.251959748 1.114965962 1.41619968 1 16.49100455 4.771988701 24.09243654 1.159441844 1.640494415 0.334087102 0.207852458 11609.64654 8367104.965 0.046807189 7.781650573 59154.62444 -4.771988701 0.481052571 KAHS(ph)NMLTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAHSNMLTVK 10 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 KAHS(1)NMLTVK 64.82 0.030326 101040000 105470 137230 156200 143130 153120 148940 150730 140210 122930 130110 TRUE FALSE 109634.037 160798.185 160270.7003 171440.6868 127092.7171 114350.9422 138915.3887 138330.7143 118505.7733 155602.5634 0.70457732 1.033390334 1.030000386 1.101785749 0.816777785 0.734891121 0.892757714 0.889000228 0.76159268 1 17.2475063 3.205743544 24.99988355 0.844617537 0.976618174 0.18706003 0.119952082 286.8690071 218534.6383 0.034323207 0.041026769 1605.992616 -3.205743544 0.132000637 KAIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KAIVER 6 1 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;; 91.906 0.075939 2779320000 3989550 3817570 4405720 3659840 5006100 5160870 4645940 4425100 4295050 4381660 FALSE TRUE 4147060.515 4473207.951 4520536.683 4383745.428 4155164.91 3962336.156 4281779.083 4365788.773 4140471.989 5240162.385 0.791399237 0.853639186 0.862671106 0.836566714 0.79294583 0.75614759 0.817108091 0.833139978 0.790141924 1 22.32118009 -1.098368872 4.760339826 1.000009341 0.816993374 0.759979898 0.031192574 3.29E-06 6.23E-07 0.032136678 0.007574301 0.079731719 1.098368872 -0.183015967 KAKPAMPQDSVPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAKPAMPQDSVPSPR 15 2 P53396 P53396 ACLY ATP-citrate synthase 1 KAKPAMPQDS(0.002)VPS(0.998)PR 65.022 0.032757 423310000 780440 682250 900760 611560 997890 957470 868050 777080 863550 806480 TRUE FALSE 811252.3738 799421.1303 924234.5456 732524.7427 828269.0142 735112.1031 800009.9728 766664.5136 832471.0042 964494.315 0.841116802 0.828850018 0.958258158 0.759490991 0.858759872 0.762173599 0.829460537 0.79488754 0.863116548 1 19.87941321 0.935112759 9.152688606 0.999999901 0.828249121 0.481079738 0.053110674 2.281158704 321.9906396 0.049029814 0.012268377 8.612173266 -0.935112759 -0.17175078 KALDSNSLENDDLSAPGREPGHFNPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KALDSNSLENDDLSAPGREPGHFNPESR 28 2 Q32MZ4-2;Q32MZ4;Q32MZ4-3 Q32MZ4-2;Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 237.13 2.22E-45 648930000 136856 151737 174899 121855 211105 199182 145741 158436 172949 163351 FALSE TRUE 142259.1806 177796.6494 179457.0116 145957.5553 175221.4475 152924.9991 134317.4396 156312.4246 166724.5993 195356.5009 0.728202952 0.91011381 0.91861295 0.747134365 0.896931746 0.782799643 0.687550396 0.800139355 0.853437682 1 17.57574974 3.738998037 24.9997243 0.808284037 0.85809029 0 0.09429959 127.564948 7290540.65 0.023806465 0.039789302 5482.744869 -3.738998037 0.049806253 KALELDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KALELDQER 9 1 A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P35241-2 A0A2R8Y5S7 RDX Radixin 0 82.171 0.030799 208070000 340360 375580 392550 353240 726670 559600 455130 401920 454070 542770 FALSE TRUE 353797.6756 440082.9434 402780.1755 423109.8177 603150.893 429641.3808 419455.7213 396532.9198 437728.1094 649115.3895 0.545045891 0.677973363 0.62050628 0.651825276 0.92918902 0.661887528 0.646195928 0.610882019 0.674345604 1 19.30811544 -2.255889272 2.038773346 2.099703165 0.66920645 0.523974098 0.094746321 6209817.819 946428.0504 31445203.5 0.023591398 0.005547671 2.255889272 -1.430496715 KALERPYTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KALERPYTSK 10 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 128.28 0.0001877 2438100000 1680800 1567470 1624030 1401060 2423000 2259070 2276780 1993520 2211440 1880980 FALSE TRUE 1747159.282 1836670.779 1666353.556 1678185.486 2011139.325 1734435.229 2098320.034 1966800.125 2131850.706 2249522.017 0.776680232 0.816471573 0.740758945 0.746018698 0.894029625 0.771023896 0.93278484 0.874319126 0.947690527 1 21.10118706 1.818537439 0.534146102 0.999021678 0.768306441 0.71114342 0.047133711 0.43141904 0.274290355 0.043994913 0.02900065 65.84721924 -1.818537439 -0.230715237 KALVVPEPEPDSDS(ph)NQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KALVVPEPEPDSDSNQER 18 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 1 KALVVPEPEPDS(0.011)DS(0.989)NQER;KALVVPEPEPDS(0.023)DS(0.977)NQER;KALVVPEPEPDS(0.001)DS(0.999)NQER;KALVVPEPEPDS(0.286)DS(0.714)NQER 155.17 1.27E-08 2850650000 1701540 1880710 2024230 1702780 2416090 2468490 2019110 2071750 2149820 1980000 TRUE FALSE 1768718.113 2203707.313 2076983.097 2039584.802 2005403.885 1895220.608 1860846.882 2043981.58 2072448.398 2367943.091 0.74694283 0.930642008 0.877125428 0.861331849 0.846896994 0.800365775 0.785849495 0.863188642 0.875210391 1 21.17520298 0.751423011 1.900217137 0.999779586 0.841005491 0.497155 0.048676298 0.789624813 4.520992013 0.045982156 0.012820463 5.641869164 -0.751423011 -0.158774095 KAMAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAMAMK 6 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 90.285 0.078894 376510000 112130 134250 132270 115450 255980 212870 154940 130780 161010 236000 FALSE TRUE 116556.979 157306.3932 135717.0649 138285.6654 212468.611 163434.1686 142795.3979 129027.108 155215.2816 282239.6815 0.412971622 0.557350378 0.48085749 0.489958268 0.752794965 0.579061625 0.505936646 0.457154385 0.549941386 1 18.10656131 0.938366573 21.96058602 1 0.530000332 0.721265222 0.087402621 3841.194667 1368657.224 0.087261407 0.021815352 8.676939581 -0.938366573 -0.469999668 KAMEAVAAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAMEAVAAQGK 11 1 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ; 79.633 0.04267 852070000 1919630 1337960 1700250 1265180 2350200 2251510 2109970 1630370 1993820 1425450 FALSE TRUE 1995418.475 1567744.222 1744559.912 1515428.828 1950713.843 1728630.924 1944585.038 1608517.557 1922062.808 1704739.636 1.170512161 0.919638512 1.023358568 0.88895031 1.144288431 1.014014626 1.140693275 0.943556144 1.127481738 1 20.70111998 3.227711241 24.99998683 1.05427486 0.99645539 0.090202976 0.092861648 545.9318894 1257978.02 0.025249909 0.030462068 1689.317346 -3.227711241 -0.057819469 KAMLS(ph)QMNVT(ph)APTSPPVQQNMMNSASAMNQRISQS(ph)APVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAMLSQMNVTAPTSPPVQQNMMNSASAMNQRISQSAPVK 39 2 P46937-6;P46937-7;P46937-5;P46937-3 P46937-6 YAP1 Transcriptional coactivator YAP1 3 KAMLS(0.837)QMNVT(0.259)APT(0.233)S(0.233)PPVQQNMMNS(0.091)AS(0.091)AMNQRIS(0.256)QS(0.999)APVK 51.607 0.024046 251690000 0 0 0 0 0 2495.7 0 0 0 0 TRUE FALSE 0 0 0 0 0 1916.111498 0 0 0 0 0 KANAPEMLSDGEYIS(ph)DVEEGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KANAPEMLSDGEYISDVEEGNR 22 1 Q12955-4;H0Y8Z4 Q12955-4 ANK3 Ankyrin-3 1 KANAPEMLSDGEYIS(1)DVEEGNR 150.95 3.20E-08 91785000 65805 77522 77626 68199 100170 95953 106030 82807 85686 71493 TRUE FALSE 68403.03221 90835.80046 79648.99733 81688.55865 83143.13918 73669.36993 97719.09154 81697.10761 82602.1776 85500.68453 0.800029059 1.062398517 0.931559762 0.955414089 0.972426591 0.861623159 1.142904201 0.955514076 0.966099605 1 16.38364835 2.272792365 24.99980521 1.01098567 0.939643364 0.207885857 0.080406507 328.2789069 239744.41 0.026400671 0.022087238 187.4098291 -2.272792365 -0.071342306 KANEDELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KANEDELKR 9 2 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 51.927 0.085209 75793000 69686 42617 59258 39685 86994 71668 69044 59197 69114 44501 FALSE TRUE 72437.25709 49936.13824 60802.31216 47534.57455 72206.79095 55024.19314 63632.15087 58403.56104 66626.60064 53220.11893 1.361087847 0.938294375 1.142468551 0.893169266 1.356757414 1.03389835 1.1956409 1.09739629 1.251906271 1 15.69968411 3.247358686 24.99941913 1.153529469 1.077558884 0.05045088 0.152244194 608.4926156 1729003.386 0.038908156 0.051880405 1767.497001 -3.247358686 -0.075970586 KANLQIDQINTDLNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KANLQIDQINTDLNLER 17 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 289.95 9.38E-46 3266020000 3686270 3771080 4159190 3052930 4874110 4811290 3462630 4035420 4401950 4506980 FALSE TRUE 3831806.786 4418733.655 4267581.908 3656790.442 4045610.523 3693940.813 3191220.013 3981331.796 4243524.679 5390036.44 0.710905544 0.81979662 0.791753814 0.678435199 0.750572017 0.685327614 0.592059079 0.738646545 0.787290536 1 22.3618636 -1.49429835 5.005667058 1.00080698 0.725693088 0.625492295 0.063039585 0.000595616 6.02E-05 0.064036316 0.015050543 0.032040675 1.49429835 -0.275113892 KANNSQEPS(ph)PQLASSVASTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KANNSQEPSPQLASSVASTR 20 1 Q96HC4;Q96HC4-4;Q96HC4-7;H0Y8Y3 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 KANNS(0.002)QEPS(0.998)PQLASSVASTR 115.63 6.54E-05 58831000 50463 46136 49948 44726 62872 60787 56649 52655 52692 44139 TRUE FALSE 52455.31821 54059.49911 51249.68591 53572.66931 52185.0399 46670.14049 52208.70336 51949.24585 50795.62521 52787.19196 0.993712987 1.024102573 0.970873502 1.014880074 0.988592838 0.884118642 0.989041118 0.984125958 0.962271781 1 15.6879003 4.225620707 24.52572616 0.973772657 1.008907779 0.142336637 0.034026358 307.6084293 583031.2971 0.008664907 0.018918441 16812.05133 -4.225620707 0.035135123 KAPAGPSLEETSVSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPAGPSLEETSVSSPK 17 1 K7EIX2;Q6AI08;A0A087WXZ7 K7EIX2 HEATR6 HEAT repeat-containing protein 6 1 KAPAGPSLEETSVS(0.203)S(0.797)PK 166.06 1.47E-09 290240000 383200 122690 184450 123140 249570 269470 201990 159030 168160 81064 TRUE FALSE 398329.0319 143761.0531 189256.9185 147496.7245 207148.1805 206889.6764 186157.496 156898.463 162107.9544 96946.93874 4.108732437 1.482883885 1.952170135 1.521417039 2.136717087 2.134050637 1.920199837 1.618395227 1.67213072 1 16.56490772 4.742755631 24.96925873 1.764251053 4.108733376 0.825257022 0.32971081 156.2042449 929712.4578 0.074167974 0.576222287 55303.88375 -4.742755631 2.344482324 KAPAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(1)PPS(0.507)S(0.447)PLS(0.047)AEQLDR 84.641 0.011077 237540000 238910 199610 236230 168640 268130 282470 267130 247170 251200 206960 TRUE FALSE 248342.3513 233891.4647 242386.3479 201996.4887 222553.3584 216870.6234 246191.6526 243857.0904 242159.3611 247509.8495 1.00336351 0.944978413 0.979299807 0.816114951 0.899169705 0.876210073 0.994674164 0.985241965 0.978382725 1 17.91712641 2.219201012 24.90254041 0.988238496 0.918044192 0.321712394 0.049536724 299.0042934 384610.9443 0.019607087 0.014502856 165.6536508 -2.219201012 -0.070194304 KAPAGQEEPGT(ph)PPSS(ph)PLSAEQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 KAPAGQEEPGT(0.999)PPS(0.33)S(0.669)PLS(0.003)AEQLDR 79.917 0.015668 229720000 187580 154390 174400 143650 178920 198770 199760 181440 177950 142000 TRUE FALSE 194985.8032 180905.2815 178945.0073 172063.5412 148507.2423 152608.6799 184102.2892 179008.0936 171545.6143 169822.1812 1.148176297 1.065262972 1.053719873 1.013198276 0.87448672 0.898638086 1.084088591 1.054091358 1.010148456 1 17.37366538 4.421555871 1.428123668 0.995683614 1.157986833 0.393111051 0.061008762 0.865399619 2.449284952 0.019733185 0.171010997 26397.07895 -4.421555871 0.162303219 KAPAGQEEPGT(ph)PPSSPLSAEQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 KAPAGQEEPGT(0.999)PPS(0.001)SPLSAEQLDR 164.55 9.01E-12 593330000 564270 463930 569100 430100 625120 655530 605140 575730 567340 472720 TRUE FALSE 586547.8153 543606.3686 583931.2135 515172.4963 518862.3257 503293.0922 557707.5456 568013.2811 546921.5442 565340.4332 1.037512587 0.961555793 1.032884222 0.91126066 0.917787399 0.890247827 0.986498599 1.004727855 0.967419827 1 19.10876036 -0.304562385 6.837798829 1.000000104 0.967638549 0.039793595 0.047498076 0 0 0.047873956 0.011284 0.495949681 0.304562385 -0.032361556 KAPAPFRPASER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPAPFRPASER 12 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 105.65 0.0011287 305080000 113700 150930 138860 167740 184480 218380 146050 154820 162120 182320 FALSE TRUE 118188.9638 176851.0534 142478.8057 200918.4713 153122.1555 167664.5546 134602.2194 152744.8911 156285.3329 218042.1133 0.542046497 0.811086679 0.65344627 0.921466355 0.702259546 0.768954915 0.617322119 0.70052931 0.716766732 1 17.73424728 -1.144756361 5.498248344 1.000005603 0.717670986 0.42607716 0.099226974 6.34E-06 9.87E-07 0.089444612 0.021081879 0.071654528 1.144756361 -0.282334617 KAPDFVFYAPR ddPTM_MDA-MB-175_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 ; 160.52 4.39E-05 3612800000 3513900 3392300 3473000 3339400 5895100 4855400 4653300 3836300 3822000 4632800 FALSE TRUE 3652631.485 3974901.137 3563509.233 3999923.353 4893053.008 3727806.934 4288562.187 3784880.673 3684446.967 5540508.46 0.659259256 0.717425335 0.643173683 0.721941566 0.88314151 0.672827586 0.774037657 0.68312876 0.665001596 1 22.40158695 -1.548890355 3.129422297 1.011008917 0.715755525 0.619484654 0.067378897 29437269.15 32164813.22 2702032.5 0.016069342 0.028255933 1.548890355 -0.295253392 KAPEPEEEIEEVEES(ph)EDEGEDPALDSLSQAIAFQQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPEPEEEIEEVEESEDEGEDPALDSLSQAIAFQQAK 37 1 G3V1V1;Q8TBF4 G3V1V1 ZCRB1 Zinc finger CCHC-type and RNA-binding motif-containing protein 1 1 KAPEPEEEIEEVEES(1)EDEGEDPALDSLSQAIAFQQAK 190.52 7.59E-24 19112000 55983 34517 51625 36978 59362 59931 56841 46530 60439 35909 TRUE FALSE 58193.25207 40445.02625 52970.38991 44292.13803 49271.66844 46012.93351 52385.65389 45906.34146 58263.8122 42944.68103 1.35507473 0.941793612 1.233456359 1.031376575 1.147328779 1.071446624 1.21984033 1.068964546 1.356717777 1 15.39019184 2.248774256 24.98529766 1.15849283 1.122517534 0.01046351 0.136665235 1196.835742 2927780.276 0.043481719 0.036002291 177.3267504 -2.248774256 -0.035975296 KAPETCSTAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAPETCSTAGR 11 1 Q86VY4 Q86VY4 TSPYL5 Testis-specific Y-encoded-like protein 5 0 ; 170.66 2.48E-05 114157000 96856 91739 99334 88367 129828 120491 100888 93660 109335 87399 FALSE TRUE 100679.9497 107494.4596 101922.7256 105845.7289 107759.8829 92508.79131 92980.13494 92404.6409 105400.0547 104523.1607 0.96323101 1.028427182 0.975120968 1.01265335 1.030966555 0.885055434 0.889564899 0.884059 1.008389471 1 16.67346313 2.740987039 24.99916469 0.919205625 1.002633262 0.332446944 0.046518334 208.1044228 2144085.906 0.014221325 0.014425063 550.7912589 -2.740987039 0.083427637 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPGFGGFGSSAVSGGSTAAMITETIIETDKPK 33 2 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 168.87 1.50E-14 205840000 159540 91541 122710 76004 161020 153630 169810 134700 143650 73700 FALSE TRUE 165838.7624 107262.4547 125907.9234 91037.36435 133649.8779 117951.7608 156499.8485 132894.5668 138480.0646 88140.10393 1.881535816 1.21695403 1.42849756 1.03287108 1.516334472 1.338230335 1.775580485 1.507765034 1.571135708 1 16.42751098 KAPKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPKPER 7 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 0 58.815 0.060342 114660000 155530 156130 150750 129190 189820 211360 179950 158990 189110 205710 FALSE TRUE 161670.4445 182944.113 154678.6688 154743.3964 157554.4642 162274.8432 165845.0488 156858.9991 182303.968 246014.9359 0.657157029 0.743630106 0.628736903 0.629000007 0.640426418 0.659613786 0.674125935 0.637599496 0.741028049 1 17.90838638 0.846965277 3.186809331 0.999928681 0.659071174 0.911792344 0.031887154 0.184806378 3.293339026 0.03120037 0.00812297 7.030161095 -0.846965277 -0.340857507 KAPKS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPKSPAK 8 2 P10412 P10412 HIST1H1E Histone H1.4 1 KAPKS(1)PAK 52.278 0.075096 2950700000 3492900 1365100 2170800 918960 3960600 3272200 2819300 1866600 2668700 1481000 TRUE FALSE 3630802.389 1599545.306 2227372.831 1100727.545 3287378.627 2512281.141 2598315.899 1841581.28 2572654.008 1771173.595 2.049941576 0.903099115 1.257568901 0.621467906 1.856045414 1.418427391 1.467002392 1.039751996 1.452513755 1 20.75627419 -2.128330004 0.524115466 0.637423394 1.310725876 0.054870429 0.402463563 360.1288243 26.90424696 154.9001925 0.172141518 0.007441663 2.128330004 0.673302482 KAPPPPIS(ph)PTQLSDVSSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAPPPPISPTQLSDVSSPR 19 1 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 KAPPPPIS(0.991)PT(0.003)QLS(0.006)DVSSPR;KAPPPPIS(0.995)PT(0.005)QLSDVSSPR 196.2 5.18E-16 307070000 170832 186231 191700 173694 219628 269441 208781 212586 229903 229296 TRUE FALSE 177576.5793 218214.7256 196695.8595 208050.1548 182295.711 206867.4112 192416.1997 209736.6324 221628.8359 274222.1611 0.647564656 0.795758901 0.71728652 0.758691982 0.664773811 0.754378896 0.701679977 0.764842023 0.808209063 1 18.06498564 0.754330047 1.232451986 0.999786135 0.722999963 0.800523352 0.04193968 0.322628793 0.859738249 0.036014224 0.010986156 5.679760813 -0.754330047 -0.276786172 KAPSS(ph)PPPPPPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 KAPS(0.237)S(0.763)PPPPPPPLR;KAPS(0.164)S(0.836)PPPPPPPLR 65.175 0.036076 653650000 774380 612360 733220 614090 927100 852460 781090 762060 807260 639470 TRUE FALSE 804953.1204 717528.0665 752328.3155 735555.1691 769511.8732 654489.0842 719866.1248 751845.8322 778206.8703 764761.9031 1.052553896 0.9382372 0.983741884 0.961809376 1.006211044 0.855807646 0.941294437 0.983110991 1.017580592 1 19.54465113 1.474848166 4.46900086 1.007483981 0.960244245 0.125444261 0.048075833 0.374385036 15.43219312 0.031263404 0.012300023 29.84339078 -1.474848166 -0.047239736 KAPT(ph)PQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 103.91 0.0072532 1760940000 10519470 3464136 5282140 3760149 7323210 7793010 8410590 5615070 6166890 2358757 TRUE FALSE 10934786.8 4059074.411 5419796.908 4503895.249 6078413.38 5983201.532 7751345.979 5539809.171 5944944.834 2820910.273 3.876332722 1.438923616 1.921293619 1.596610602 2.154770195 2.121018023 2.747817275 1.963837427 2.107456196 1 21.42772935 4.748608005 24.73758846 1.970005672 3.876333933 0.630013365 0.452285367 793.249615 1953007.722 0.10440638 1.418402156 56054.18011 -4.748608005 1.906328261 KAPTTDEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAPTTDEDKK 10 2 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 75.045 0.022595 380490000 356120 110010 179510 116780 283770 246780 268360 177310 215800 127980 FALSE TRUE 370179.8926 128903.3617 184188.1781 139878.7354 235534.8768 189469.085 247325.242 174933.4495 208033.4002 153055.2307 2.418603343 0.84220161 1.203409888 0.913910193 1.538888124 1.237913165 1.615921526 1.142943294 1.359204774 1 17.22369282 4.750350907 24.72785126 1.22760411 2.418604179 0.697672828 0.239083402 863.9791644 1811990.151 0.055242137 0.898936557 56279.58762 -4.750350907 1.191000069 KAQCPIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KAQCPIVER 9 1 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;; 192.26 5.60E-05 3816530000 3366000 3349810 3469050 3405280 4394660 4447810 3753160 3756290 3672260 3476710 FALSE TRUE 3498892.279 3925113.81 3559456.293 4078834.22 3647657.263 3414873.535 3458977.512 3705943.077 3540096.08 4157904.759 0.84150371 0.944012438 0.856069703 0.980983081 0.877282544 0.821296719 0.831903979 0.891300617 0.851413461 1 21.98742528 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAQLNIGNVLPVGTMPEGTIVCCLEEKPGDR 31 2 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 142.22 1.29E-08 721180000 1798800 1113400 1529700 1093600 2035300 1875300 1670600 1596300 1803500 1172800 FALSE TRUE 1869818.013 1304617.789 1569565.239 1309910.816 1689340.433 1439789.995 1539654.007 1574904.21 1738592.387 1402587.705 1.333120208 0.930150595 1.11904962 0.933924353 1.204445488 1.026524038 1.097723872 1.122856135 1.23956055 1 20.41965956 1.724355105 3.857809531 1.136847156 1.082194418 0.003027065 0.125286936 0.776960646 25.88516596 0.063387686 0.030818346 53.00967055 -1.724355105 -0.054652738 KAQLVVIAHDVDPIELVVFLPALCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAQLVVIAHDVDPIELVVFLPALCR 25 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ; 130.51 5.86E-05 458910000 442720 354470 456790 330720 617530 548640 449030 451230 621480 490500 FALSE TRUE 460198.9275 415347.4651 468694.3227 396135.4289 512562.4712 421226.6747 413833.8553 445181.9999 599113.0562 586604.0838 0.784513678 0.708054166 0.79899601 0.675302883 0.873779241 0.718076615 0.705473874 0.758913912 1.021324387 1 19.16202759 1.2413435 22.07774121 1.010662662 0.751253691 0.782670746 0.054328027 6.135585805 48694.18916 0.037505616 0.012246646 17.43185079 -1.2413435 -0.259408971 KAQPAQPADEPAEKADEPMEH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KAQPAQPADEPAEKADEPMEH 21 2 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 160.13 1.22E-11 101740000 420230 241840 352960 223370 464040 411270 397930 351160 410690 222800 FALSE TRUE 436821.0049 283374.1387 362158.4276 267551.9193 385162.6466 315758.7754 366739.2068 346453.2746 395909.3471 266453.3942 1.639389906 1.06350358 1.359181138 1.004122766 1.445516007 1.185043171 1.376372809 1.300239674 1.485848391 1 18.02352369 KAQPQDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KAQPQDSR 8 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;;; 120.15 0.0024954 611549000 884893 852420 919710 765066 1032780 1038530 995940 960540 928700 918610 FALSE TRUE 919829.2589 998816.5041 943678.3982 916393.7713 857228.4245 797347.1466 917875.6204 947665.5324 895276.2684 1098594.042 0.83727858 0.909177063 0.858987362 0.834151412 0.780295898 0.725788705 0.835500272 0.862616669 0.814929113 1 20.06722694 -1.466547158 3.090223147 1.003808081 0.830399104 0.546965204 0.046735044 9184313.44 10854406.18 298819.7475 0.012285719 0.034154886 1.466547158 -0.173408978 KAQVS(ph)PQS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.789)PQS(0.211);KAQVS(0.975)PQS(0.025) 76.682 0.037255 8982300000 6018700 5026200 5814900 4965900 6426800 6765700 6390900 5974900 5983100 4725500 TRUE FALSE 6256322.923 5889410.752 5966441.071 5948140.198 5334374.832 5194468.71 5889964.558 5894816.238 5767769.4 5651371.25 1.107045113 1.042120663 1.055751039 1.052512733 0.943908053 0.919151916 1.042218658 1.043077154 1.020596444 1 22.43016954 3.449145948 23.9997185 0.999727049 1.063761254 0.417921335 0.040167721 164.026768 140715.9707 0.012628349 0.017099212 2812.84595 -3.449145948 0.064034205 KAQVSPQS(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KAQVSPQS 8 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KAQVS(0.489)PQS(0.511);KAQVS(0.03)PQS(0.97);KAQVS(0.373)PQS(0.627);KAQVS(0.112)PQS(0.888) 74.944 0.042019 14222910000 14178870 12172620 13139900 10386920 14593250 15576730 14411310 13265330 13721540 11197020 TRUE FALSE 14738662.74 14263172.8 13482336.59 12441421.77 12112694.58 11959270.53 13281713.87 13087529.95 13227704.46 13390861.69 1.100650808 1.065142268 1.006831144 0.929097922 0.904549301 0.893091931 0.991849081 0.977347855 0.987815778 1 23.67474546 4.155157638 2.380043822 0.95339092 1.092669104 0.676719657 0.035349459 0.182493542 2.037599441 0.010284209 0.031948273 14294.12704 -4.155157638 0.139278184 KAS(ph)GS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGR;KAS(0.999)GS(0.999)ENEGDY(0.001)NPGR;KAS(1)GS(1)ENEGDYNPGR 188.09 2.10E-07 1025960000 2380580 1524280 1832890 1461350 2484470 2659080 2364410 1886470 1922950 1102230 TRUE FALSE 2474567.137 1786063.233 1880656.619 1750400.668 2062160.677 2041548.969 2179081.366 1861184.955 1853743.405 1318190.865 1.877244944 1.354935222 1.42669523 1.327881049 1.564387018 1.548750657 1.653084863 1.411923724 1.406278449 1 20.33012785 0.691828454 1.422556325 1.000976884 1.515133433 0.518106741 0.151527466 0.849302349 2.688855325 0.139421919 0.040993517 4.918452191 -0.691828454 0.514156548 KAS(ph)GS(ph)ENEGDYNPGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KAS(1)GS(1)ENEGDYNPGRK;KAS(1)GS(1)ENEGDYNPGRK;KAS(1)GS(1)ENEGDYNPGRK 98.703 0.0024076 509690000 1292750 545262 797620 457664 1221490 1129190 922820 756013 843040 455145 TRUE FALSE 1343788.768 638906.507 818406.6325 548188.5732 1013861.566 866952.7355 850486.9571 745879.8823 812699.1551 544321.9485 2.4687389 1.173765836 1.50353414 1.007103562 1.862613788 1.592720518 1.562470445 1.370291763 1.493048659 1 19.05410068 7.999956608 0.039202955 1.14E-07 3.924809929 0.221031347 0.363750696 1487.031568 4.440063247 123.181333 391.5658968 99990009.12 -7.999956608 3.924809815 KAS(ph)GSENEGDYNPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.779)GS(0.221)ENEGDYNPGR;KAS(0.833)GS(0.167)ENEGDYNPGR 112.74 0.00045309 372570000 129774 115380 124012 106971 185507 161910 161798 133197 139436 91877 TRUE FALSE 134897.5777 135195.6175 127243.8546 128129.5445 153974.5864 124308.8563 149115.85 131411.7121 134417.7256 109878.5391 1.227697227 1.230409674 1.158041012 1.166101639 1.401316287 1.131329715 1.35709713 1.195972509 1.223330113 1 16.74555011 -0.453800619 8.706683865 1.000000001 1.232962812 0.425300618 0.081031177 0 0 0.072327689 0.0170478 0.351721876 0.453800619 0.232962811 KAS(ph)GSENEGDYNPGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.987)GS(0.013)ENEGDYNPGRK;KAS(0.659)GS(0.341)ENEGDYNPGRK;KAS(0.971)GS(0.029)ENEGDYNPGRK;KAS(0.5)GS(0.5)ENEGDYNPGRK 196.76 2.35E-11 1471010000 1719130 1053700 1481500 834398 2083270 1627040 1466840 1245380 1538160 868096 TRUE FALSE 1787002.58 1234664.778 1520109.107 999439.434 1729156.51 1249184.618 1351865.248 1228687.718 1482801.922 1038182.79 1.721279332 1.189255678 1.464201797 0.962681565 1.665560752 1.2032415 1.302145692 1.183498445 1.428266713 1 19.98562905 -1.650426194 0.043754199 3.56E-18 2.160254228 0.21528841 0.215546758 538.1825686 3.652002571 122.3495383 64.43190776 0.022365253 1.650426194 2.160254228 KAS(ph)LLSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASLLSAK 8 1 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 KAS(1)LLSAK 76.655 0.013443 0 137000 102740 123930 101960 176130 155730 142160 120270 141120 116590 TRUE FALSE 142408.8658 120384.7958 127159.7176 122127.3837 146191.4855 119564.0676 131017.1277 118657.9774 136041.1188 139433.5782 1.021338386 0.86338454 0.911973423 0.87588216 1.048466857 0.857498381 0.939638281 0.851000016 0.975669709 1 17.08921851 4.759920586 23.6524318 0.917685837 1.021338606 0.163524434 0.063656639 4111.993348 4553161.303 0.014153754 0.599240404 57533.47229 -4.759920586 0.103652769 KAS(ph)LTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASLTSK 7 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 KAS(0.99)LT(0.007)S(0.003)K 74.841 0.027617 777580000 1075400 570130 796820 573610 1022500 1040300 1028900 844990 1140700 541960 TRUE FALSE 1117857.622 668045.3925 817585.7838 687068.3459 848695.8152 798706.0909 948252.1295 833664.2912 1099646.43 648146.6855 1.724698509 1.030700931 1.261420913 1.060050697 1.309419355 1.232292178 1.463020873 1.286227809 1.696601177 1 19.30596083 2.259584686 24.33827764 1.377473561 1.250788128 0.028791637 0.239431798 521.9280481 604202.1692 0.07741804 0.064701492 181.796152 -2.259584686 -0.126685433 KAS(ph)PEAASTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASPEAASTPR 11 1 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;P29590-4;H3BVD2;P29590-14;P29590-10;H3BT29;P29590-12;P29590-13;P29590-11;H3BT57;H3BUJ5 P29590-2;P29590-12 PML Protein PML 1 KAS(0.99)PEAAS(0.003)T(0.007)PR;KAS(1)PEAASTPR 109.84 0.0011485 212940000 85066 124429 97897 128425 99976 140712 118958 95831 101291 160492 TRUE FALSE 88424.47137 145798.7128 100448.2762 153827.0817 82982.11523 108033.7705 109633.7611 94546.54219 97645.5567 191937.3346 0.460694484 0.759616221 0.523338914 0.801444294 0.432339625 0.562859595 0.571195601 0.49259068 0.50873665 1 17.55027584 -1.558800891 3.811986543 1.008953794 0.569619915 0.559096808 0.115057445 19305684.05 7954076.223 1444906.362 0.025413762 0.027618438 1.558800891 -0.439333878 KAS(ph)PEAASTPRDPIDVDLPEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.999)PEAASTPRDPIDVDLPEEAER;KAS(1)PEAASTPRDPIDVDLPEEAER;KAS(1)PEAASTPRDPIDVDLPEEAER 163.29 8.85E-12 488120000 139723 113043 129479 90707 167412 161442 141156 117944 137321 118726 TRUE FALSE 145239.3719 132457.2559 132853.3291 108648.5739 138955.368 123949.5422 130091.8239 116363.1536 132378.844 141988.0866 1.022898297 0.932875843 0.935665325 0.765195 0.978641035 0.872957339 0.916216473 0.819527584 0.9323236 1 17.11541036 4.669804014 1.731249323 0.889505844 1.054484761 0.213761207 0.067073732 1.023249366 3.409425509 0.01647598 0.266679775 46752.41115 -4.669804014 0.164978917 KAS(ph)PEPEGEAAGK ddPTM_MDA-MB-175_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 193.42 1.15E-06 3708230000 6167890 2670993 4017630 2540403 5512710 5281560 5365010 4007039 4379580 2034540 TRUE FALSE 6411403.06 3129715.27 4122332.738 3042887.131 4575661.523 4054997.733 4944486.497 3953331.196 4221959.771 2433169.159 2.635000955 1.286271141 1.694223652 1.250585936 1.880535723 1.666549864 2.032117857 1.624766277 1.73516903 1 21.21440519 0.042703638 1.618891137 0.999647931 1.732678724 0.270392271 0.370804787 34.30399295 55.54471832 0.356581255 0.09303451 1.103325454 -0.042703638 0.733030794 KAS(ph)PEPPDSAEGALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 KAS(1)PEPPDSAEGALK;KAS(0.999)PEPPDS(0.001)AEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK;KAS(1)PEPPDSAEGALK 189.47 1.57E-07 10931200000 7512750 3319760 5044840 3354230 7071780 6622340 7030100 5026180 5824580 2650790 TRUE FALSE 7809359.171 3889902.956 5176312.675 4017686.683 5869721.362 5084401.898 6479062.392 4958812.278 5614954.504 3170161.548 2.463394705 1.227036193 1.632822995 1.267344462 1.851552759 1.603830537 2.043764109 1.564214379 1.771188761 1 21.59612493 -0.628083263 6.512782913 1.000000387 1.689839327 0.278377255 0.342861239 0 1.39E-09 0.302726316 0.071353277 0.235459782 0.628083263 0.689838939 KAS(ph)SPSPLTIGTPESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.483)S(0.483)PS(0.035)PLTIGTPESQR 85.248 0.0031136 246260000 74173 158050 144450 155930 132750 184330 124200 150450 135100 144230 TRUE FALSE 77101.40731 185193.858 148214.4857 186772.4886 110185.2024 141522.151 114464.8795 148433.4638 130237.7774 172489.107 0.446992907 1.073655382 0.85926867 1.082807441 0.638795135 0.820470078 0.663606424 0.860538189 0.755049288 1 17.39614573 4.761201589 24.56803548 0.84737259 0.446992355 0.413579157 0.147229536 5183.89864 5625006.045 0.034249248 1.847472815 57703.42461 -4.761201589 -0.400380235 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHRSEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VILSNMVSISSEPFGHLVDDDDISDQEDHRSEEK 34 1 A8MUM1;Q53HC9 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(0.983)DQEDHRS(0.017)EEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK;VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHRSEEK 290.19 6.98E-90 660389000 193412 352238 431157 339965 487599 531395 471535 466469 456854 409784 TRUE FALSE 201048.0551 412732.1365 442393.3056 407209.0623 404717.0961 407986.5646 434574.8546 460216.746 440411.9138 490073.329 0.41024076 0.842184449 0.90270839 0.830914555 0.825829671 0.832501057 0.886754755 0.939077315 0.898665338 1 18.90263811 4.739193691 4.007081151 0.883566937 0.367548796 0.887010282 0.050968844 0.072670944 2.455678126 0.012594028 0.109203435 54852.1545 -4.739193691 -0.51601814 down KAS(ph)VVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 2 KAS(0.999)VVDPSTESSPAPQEGSEQPASPAS(0.999)PLS(0.001)S(0.001)R;KAS(0.995)VVDPS(0.002)T(0.002)ESSPAPQEGSEQPASPAS(0.997)PLS(0.002)S(0.001)R 258.18 1.07E-58 394720000 216770 172558 244190 185575 314950 265050 263090 245480 291260 189198 TRUE FALSE 225328.247 202193.4942 250553.792 222281.1811 261414.9115 203496.1544 242468.3183 242189.7421 280777.6095 226267.7257 0.995847933 0.893602893 1.10733332 0.982381294 1.155334508 0.899360056 1.07159922 1.07036804 1.240908789 1 17.78767129 1.720005671 2.660988525 1.123662613 1.011193658 0.168572093 0.094836074 0.384836925 5.843315292 0.05575881 0.024733186 52.48143133 -1.720005671 -0.112468955 KASDSELER ddPTM_MDA-MB-175_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 ; 110.52 0.0036452 1247910000 1987130 1760330 1932060 1818360 2618700 2372500 2130500 2005550 1934260 1997520 FALSE TRUE 2065583.427 2062652.984 1982411.071 2178026.181 2173574.309 1821522.831 1963505.843 1978668.883 1864646.36 2388895.799 0.864660329 0.863433635 0.829844094 0.911729252 0.909865684 0.762495723 0.821930301 0.828277601 0.780547381 1 21.1879125 2.763171623 24.99841766 0.826852343 0.874644772 0.063001386 0.064140898 1654.181444 1680218.462 0.01827415 0.019375798 579.6577186 -2.763171623 0.047792429 KASDVHEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KASDVHEVR 9 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;; 128.81 0.00026413 38560744000 52130970.6 58526706 64151711 58635090 74861041 77000919 73219133 69407657 66347015 58576577 FALSE TRUE 54189141.57 68578212.48 65823557.29 70232935.79 62136187.99 59118622.52 67480026.03 68477360.89 63959198.89 70053535.75 0.773538994 0.97894006 0.939617916 1.002560899 0.886981468 0.843906334 0.963263671 0.977500424 0.913004579 1 26.06195453 KASDVHEVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASDVHEVRK 10 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 57.164 0.071698 461910000 2149200 2037600 2541100 1369800 4032400 3089200 1950600 2515100 3013800 3174200 FALSE TRUE 2234052.076 2387541.95 2607323.154 1640742.352 3346974.088 2371780.117 1797706.875 2481389.198 2905333.927 3796123.716 0.588508764 0.628942081 0.686838298 0.432215195 0.881682036 0.624789995 0.473563827 0.653663943 0.765342266 1 21.85609558 0.939469309 2.39992862 0.998621548 0.619523997 0.510882572 0.114645973 0.267749709 3.440082511 0.105112852 0.028479677 8.698999554 -0.939469309 -0.379097551 KASFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASFLR 6 1 P46777;A0A2R8Y4A2 P46777 RPL5 60S ribosomal protein L5 0 ; 110.61 0.045786 1560170000 1972300 1932980 1897470 1645990 2802300 2542000 2123000 1960320 2043770 2591800 FALSE TRUE 2050167.927 2264954.279 1946919.627 1971561.909 2325966.047 1951659.024 1956593.713 1934045.117 1970215.117 3099613.587 0.661426939 0.730721496 0.628116884 0.636066998 0.750405166 0.629645912 0.631237946 0.623963298 0.635632495 1 21.56365694 -1.379305583 3.295417132 1.003085864 0.657315917 0.850744059 0.042899004 13481639.78 18564285.99 397376.7554 0.010815825 0.041753647 1.379305583 -0.345769947 KASGS(ph)ENEGDYNPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.05)GS(0.95)ENEGDYNPGR;KAS(0.352)GS(0.648)ENEGDYNPGR;KAS(0.403)GS(0.597)ENEGDYNPGR;KAS(0.039)GS(0.961)ENEGDYNPGR 246.48 2.16E-18 3367680000 1708870 1490970 1646950 1421240 2037830 1903710 1832090 1707010 1662610 1303380 TRUE FALSE 1776337.507 1747032.499 1689870.87 1702357.03 1691440.384 1461602.204 1688485.999 1684130.323 1602772.991 1558752.356 1.1395893 1.120789003 1.084117604 1.092127959 1.085124509 0.937674415 1.083229155 1.080434821 1.028240942 1 20.57196031 3.740093673 1.032120088 1.04073743 1.135300713 0.438242168 0.042755157 0.68960468 1.360470092 0.015995897 0.049940036 5496.594165 -3.740093673 0.094563283 KASGS(ph)ENEGDYNPGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASGSENEGDYNPGRK 16 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KAS(0.432)GS(0.567)ENEGDYNPGRK 62.362 0.061049 62758000 43598 21156 26622 20459 52656 33469 31413 34646 37503 20802 TRUE FALSE 45319.2827 24789.37843 27315.79119 24505.72914 43705.55193 25696.33198 28950.76698 34181.62704 36153.27436 24877.75362 1.821679055 0.996447622 1.098000712 0.985045897 1.756812636 1.03290403 1.163721107 1.373983663 1.453237093 1 14.6025686 -1.219323589 4.369372035 0.99989117 1.280423532 0.084608786 0.288890265 0.000287944 5.14E-05 0.262981074 0.061961264 0.06034988 1.219323589 0.280532362 KASS(ph)PNLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASSPNLHR 9 1 A0A087X030;P51956-2;P51956 A0A087X030 NEK3 Serine/threonine-protein kinase Nek3 1 KAS(0.143)S(0.857)PNLHR;KAS(0.161)S(0.839)PNLHR 128.85 0.00019085 93786000 203160 198679 237760 201214 259640 284170 262160 216980 234760 198453 TRUE FALSE 211180.9137 232800.5727 243956.2209 241013.5286 215506.4855 218175.8241 241611.2142 214071.738 226311.0335 237336.0657 0.889796976 0.980889997 1.027893591 1.01549475 0.908022491 0.919269574 1.018013058 0.901977276 0.953546747 1 17.85657182 3.24268303 24.99906787 0.945623628 0.982214959 0.068157565 0.04900011 244.7471603 1484183.883 0.013805417 0.018033126 1748.570027 -3.24268303 0.03659133 KASS(ph)PSPLTIGTPESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KAS(0.29)S(0.71)PS(0.001)PLTIGTPESQR 170.11 1.16E-09 224490000 86587 52241 76602 48798 86911 85203 93191 71703 69712 63775 TRUE FALSE 90005.52162 61212.98537 78598.31105 58450.09875 72137.89926 65415.89451 85886.44591 70741.93857 67203.07874 76270.4902 1.180083167 0.802577579 1.030520596 0.766352735 0.945816646 0.857682891 1.126077015 0.927513884 0.881115076 1 16.21883735 -0.827491286 8.720710062 0.999986499 0.943446392 0.015448174 0.126348346 0 0 0.111358989 0.026247565 0.148767722 0.827491286 -0.056540107 KASSPS(ph)PLTIGT(ph)PESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 KAS(0.006)S(0.007)PS(0.987)PLT(0.37)IGT(0.629)PESQR;KAS(0.004)S(0.005)PS(0.991)PLT(0.01)IGT(0.99)PESQR 112.64 0.00039033 210630000 190201 153263 202518 168551 217809 209540 168909 181864 166791 153233 TRUE FALSE 197710.2823 179584.728 207795.7855 201889.8847 180785.904 160877.5106 155669.4712 179426.4105 160788.2245 183256.0725 1.078874384 0.979966042 1.133909412 1.101681827 0.986520673 0.877883654 0.84946419 0.979102128 0.877396434 1 17.48350148 3.020949382 4.265354857 0.915895779 1.070287258 0.630937845 0.056432262 0.134632825 5.772585475 0.017046686 0.019882376 1049.42011 -3.020949382 0.154391478 KASSPS(ph)PLTIGTPESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 KASS(0.001)PS(0.999)PLTIGTPESQR;KASSPS(0.999)PLTIGTPESQR;KASS(0.001)PS(0.999)PLTIGTPESQR;KAS(0.028)S(0.015)PS(0.956)PLTIGTPESQR;KAS(0.09)S(0.056)PS(0.854)PLTIGTPESQR 199.6 8.05E-12 2409130000 1540760 1367270 1508930 1268260 1763270 1831390 1415910 1557740 1546720 1313400 TRUE FALSE 1601590.395 1602087.987 1548253.955 1519118.043 1463549.995 1406077.427 1304927.274 1536861.043 1491053.849 1570735.583 1.019643542 1.019960332 0.985687198 0.967137982 0.931760896 0.895171308 0.830774631 0.978433964 0.949271071 1 20.58300891 3.675562999 1.577872867 0.924770176 1.018928628 0.390118187 0.04387837 0.395628954 1.916030841 0.013812136 0.030303736 4737.650277 -3.675562999 0.094158453 KASTAPGAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASTAPGAEER 11 1 F5GYV5;F8WCT1;Q66PJ3-2;A0A0C4DH18;Q66PJ3-5 F5GYV5 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 0 ; 107.53 0.0035035 173382000 154826 170496 184660 153609 206164 224589 197833 188733 194209 181971 FALSE TRUE 160938.65 199777.3617 189472.3913 183992.4017 171120.3169 172431.6084 182326.3325 186203.3428 187219.456 217624.7334 0.739523709 0.91799015 0.870638132 0.845457218 0.78630914 0.792334611 0.83780152 0.855616638 0.860285746 1 17.731483 0.490581638 1.076771444 1.000131329 0.831328819 0.545876364 0.046414456 1.443970686 2.274792447 0.044505313 0.013807648 3.094436949 -0.490581638 -0.16880251 KASVHS(ph)SGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASVHSSGR 9 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 KAS(0.256)VHS(0.707)S(0.037)GR;KAS(0.179)VHS(0.411)S(0.411)GR 135.1 0.0001411 508340000 66644 380334 426590 406890 540030 592630 410580 587770 486580 598890 TRUE FALSE 69275.15658 445653.4059 437707.2858 487371.6276 448235.8935 455000.6639 378397.6667 579891.9045 469068.0808 716231.0291 0.096721803 0.622220189 0.611125835 0.680467067 0.625825851 0.635270807 0.528317891 0.80964365 0.6549117 1 19.4500655 3.447196568 0.131919337 1.128676191 4.70E-20 0.561926042 0.143092929 15.94987799 0.596381024 1.339076464 3.864650267 2800.248467 -3.447196568 -1.128676191 KASVVDPSTESSPAPQEGSEQPASPAS(ph)PLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 KASVVDPSTESSPAPQEGSEQPAS(0.002)PAS(0.982)PLS(0.008)S(0.008)R;KASVVDPSTESSPAPQEGSEQPASPAS(0.992)PLS(0.004)S(0.004)R;KASVVDPSTESSPAPQEGSEQPAS(0.004)PAS(0.897)PLS(0.049)S(0.049)R;KASVVDPSTESSPAPQEGSEQPASPAS(1)PLSSR 301.02 5.72E-90 2569590000 899920 898780 1014750 897890 1137910 1231390 991710 999990 1068820 920180 TRUE FALSE 935449.5365 1053138.473 1041195.219 1075489.962 944488.4647 945418.3344 913977.1788 986586.7697 1030353.377 1100471.653 0.850044191 0.956988279 0.946135428 0.977299105 0.858257877 0.859102851 0.830532233 0.896512661 0.936283433 1 20.06969055 4.783797567 21.59794058 0.909153253 0.850042933 0.107373996 0.053596025 13543.3822 6465272.199 0.013390193 4.92279133 60785.16043 -4.783797567 -0.05911032 KASWTWGPEGQGAILLVNCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KASWTWGPEGQGAILLVNCDR 21 1 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 211.06 2.72E-22 1330970000 548240 562560 621470 512730 711840 723670 504140 599080 558890 656260 FALSE TRUE 569884.9385 659175.3039 637666.0187 614146.4637 590841.6911 555608.6098 464624.1895 591050.3125 538775.6581 784841.5821 0.726114609 0.839883257 0.812477363 0.782510098 0.752816498 0.707924532 0.591997417 0.753082311 0.686476953 1 19.58204195 3.13295895 2.768724219 0.722223292 0.796726385 0.006951656 0.101892718 0.624250855 9.691796976 0.029266516 0.036623984 1358.185063 -3.13295895 0.074503093 KATEGSGSMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KATEGSGSMR 10 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 76.143 0.043601 0 34229 27912 33852 25707 42813 38604 28458 34005 34793 35043 FALSE TRUE 35580.38735 32705.66887 34734.21093 30791.76787 35535.66155 29638.80605 26227.3876 33549.2186 33540.80673 41909.00491 0.848991462 0.780397171 0.82880066 0.734729158 0.84792425 0.707218081 0.625817474 0.800525297 0.800324579 1 15.35497265 0.689613324 2.231466022 0.999876976 0.767894768 0.519834129 0.065392203 1.326308495 8.439537836 0.06381754 0.017318809 4.893429368 -0.689613324 -0.231982208 KATGAAT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KATGAATPK 9 1 P10412 P10412 HIST1H1E Histone H1.4 1 KATGAAT(1)PK;KATGAAT(1)PK;KATGAAT(1)PK;KAT(0.001)GAAT(0.999)PK;KAT(0.002)GAAT(0.998)PK 112.15 0.001177 1967163000 5525940 2244880 3916910 2036070 4429730 5060910 4781790 3475850 4060290 2127900 TRUE FALSE 5744108.378 2630420.677 4018987.892 2438798.569 3676766.077 3885590.351 4406980.805 3429261.916 3914160.956 2544821.264 2.257175567 1.033636709 1.579281009 0.958337862 1.444803267 1.52686179 1.731744727 1.347545293 1.53808875 1 21.2791329 -2.109385098 2.28179586 0.172777039 1.465606281 0.152007464 0.343166087 6617567.971 1613533.191 28436981.95 0.080917129 0.00777347 2.109385098 1.292829242 KATLELTHNWGTEDDETQSYHNGNSDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KATLELTHNWGTEDDETQSYHNGNSDPR 28 1 Q04760 Q04760 GLO1 Lactoylglutathione lyase 0 ;; 144.4 4.19E-08 667550000 123000 287358 288780 235815 288366 340738 196663 283786 271908 393926 FALSE TRUE 127856.135 336709.5012 296305.844 282458.5032 239349.6503 261606.7634 181248.0402 279982.3129 262122.0842 471108.2575 0.271394383 0.714717893 0.628954894 0.599561775 0.50805658 0.555300739 0.384726944 0.594305679 0.556394587 1 18.84569909 0.308822728 1.696211915 1.000030293 0.539086905 0.578427084 0.119233276 5.817358968 13.41086413 0.108436669 0.030554773 2.036210759 -0.308822728 -0.460943388 KATQAS(ph)QEY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KATQASQEY 9 1 P16104 P16104 H2AFX Histone H2AX 1 KAT(0.004)QAS(0.996)QEY 62.338 0.040011 0 408930 378870 406240 355580 487500 476160 420430 407450 418230 357510 TRUE FALSE 425074.8722 443937.9753 416826.9481 425912.6627 404634.9241 365579.0563 387475.598 401988.7992 403177.984 427557.2396 0.99419407 1.038312381 0.974903263 0.996153552 0.946387727 0.855041203 0.906254326 0.94019879 0.942980136 1 18.70575805 3.176381822 3.704127954 0.922759714 1.002628795 0.454048421 0.037091859 0.188759187 5.20853011 0.010936419 0.013701852 1501.003903 -3.176381822 0.079869081 KATVS(ph)PGPHAGEAEPPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KATVSPGPHAGEAEPPSR 18 1 O15055 O15055 PER2 Period circadian protein homolog 2 1 KAT(0.278)VS(0.722)PGPHAGEAEPPSR 59.789 0.034282 71365000 120110 97778 112200 97252 140650 138430 97188 104860 106010 95227 TRUE FALSE 124852.0355 114570.6109 115124.0242 116488.1553 116742.3632 106281.7304 89570.15061 103454.5232 102194.7208 113884.9074 1.096300101 1.006021021 1.01088043 1.022858586 1.025090733 0.933238063 0.78649711 0.908412937 0.89735087 1 16.79721704 2.63800171 3.74963454 0.886146832 1.029471512 0.578675854 0.054201267 0.154809821 3.983278339 0.017407609 0.016381529 434.5119345 -2.63800171 0.143324679 KAVAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVAVR 6 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 ; 103.71 0.05524 1208090000 2318510 2064270 2417600 2098300 2805900 2804000 2632200 2476900 2483900 2317100 FALSE TRUE 2410046.565 2418792.315 2480604.642 2513337.477 2328954.12 2152813.495 2425881.286 2443701.207 2394504.924 2771091.381 0.869710245 0.872866312 0.895172443 0.906984697 0.840446524 0.776882895 0.8754245 0.88185515 0.864101754 1 21.40202286 -1.292930269 3.813193284 1.000270545 0.865568363 0.58791562 0.033945401 5617719.038 1904802.064 12507.52231 0.008507483 0.050941266 1.292930269 -0.134702183 KAVDVFFPPEAQNDFPVAMQISEKHDVVFLITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVDVFFPPEAQNDFPVAMQISEKHDVVFLITK 33 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 111.61 3.93E-06 187741000 84001 73282 114481 62232 143489 123379 99865 114552 132572 95214 FALSE TRUE 87317.42434 85867.61345 117464.4689 74541.30386 119098.791 94726.09708 92037.32035 113016.6178 127800.7596 113869.3603 0.766821067 0.754088837 1.031572221 0.654621258 1.045924827 0.831883984 0.808271164 0.992511221 1.12234546 1 16.79702008 1.586840271 4.103203339 1.060686901 0.846487038 0.381049187 0.11639575 0.16975449 6.477857156 0.065412461 0.028591685 38.62249011 -1.586840271 -0.214199863 KAVEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVEEAR 7 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 0 ; 105.57 0.012663 360120000 1232610 1156990 1246770 1069820 1584380 1540780 1369460 1177550 1308290 1242550 FALSE TRUE 1281274.395 1355694.032 1279261.85 1281427.203 1315067.654 1182957.196 1262118.147 1161766.868 1261204.898 1486003.882 0.862228161 0.91230854 0.860873828 0.862330993 0.884969191 0.79606602 0.849337045 0.781806079 0.848722479 1 20.50300645 2.776715488 24.96238489 0.836461959 0.876869201 0 0.058037062 1238.346039 810171.4524 0.016472576 0.017471507 598.0196959 -2.776715488 0.040407242 KAVIFCLSADKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVIFCLSADKK 12 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 147.18 3.68E-05 1928040000 4225900 2118250 3058100 2163450 5518500 4067600 3998800 3373200 4015100 2789300 FALSE TRUE 4392741.795 2482042.96 3137796.598 2591373.953 4580467.341 3122961.545 3685363.607 3327987.771 3870597.335 3335809.931 1.316844151 0.744060067 0.940640103 0.776835014 1.373120003 0.936192892 1.104788247 0.997655094 1.160317109 1 21.66960566 KAVLFCLSEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVLFCLSEDKK 12 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 164.68 3.19E-05 5188600000 1772390 806290 1148420 860620 1899220 1542140 1554690 1261100 1666800 803930 FALSE TRUE 1842365.326 944764.0354 1178348.769 1030848.067 1576391.263 1184001.356 1432829.335 1244197.017 1606812.194 961444.6913 1.916246813 0.982650426 1.225602241 1.072186551 1.639606809 1.231481506 1.490287843 1.294091099 1.671247663 1 19.87484434 3.252120094 24.9997225 1.394649407 1.271308029 0.017278762 0.296504486 905.5208714 1669507.062 0.076728225 0.103323534 1786.981653 -3.252120094 -0.123341378 KAVPMAPAPAS(ph)PGSSNDSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KAVPMAPAPASPGSSNDSSAR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 KAVPMAPAPAS(0.992)PGS(0.007)S(0.002)NDSSAR;KAVPMAPAPAS(0.999)PGS(0.001)SNDSSAR;KAVPMAPAPAS(1)PGSSNDSSAR;KAVPMAPAPAS(0.987)PGS(0.01)S(0.002)NDS(0.001)S(0.001)AR 200.09 4.69E-22 1776430000 1060723 1116493 1258165 942172 1323288 1430192 1077192 1157177 1210771 1331883 TRUE FALSE 1102601.163 1308241.988 1290953.813 1128530.809 1098355.978 1098051.583 992758.8763 1141666.935 1167195.588 1592839.973 0.692223438 0.821326693 0.810473014 0.708502316 0.689558271 0.689367169 0.623263412 0.716749299 0.732776429 1 20.6031699 -1.581231402 8.966833569 1.000049323 0.719408776 0.69565605 0.05546278 5.97E-05 2.79E-06 0.058612855 0.013812769 0.026228207 1.581231402 -0.280640546 KAVVLPGGTATS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVVLPGGTATSPK 14 1 Q8N1G0;F8WCX2;Q8N1G0-2;H0Y5I5 Q8N1G0 ZNF687 Zinc finger protein 687 1 KAVVLPGGTAT(0.07)S(0.93)PK;KAVVLPGGTAT(0.061)S(0.939)PK 132.79 2.96E-05 1743500000 3722800 1472040 2038780 1399780 2948200 3304500 2588100 2054930 2365130 1464200 TRUE FALSE 3869779.019 1724851.419 2091912.282 1676652.306 2447066.017 2537079.955 2385237.959 2027387.025 2280009.433 1751081.956 2.20993598 0.985020383 1.194639848 0.95749505 1.397459444 1.448864199 1.362150955 1.157791054 1.302057522 1 20.73981518 4.746829797 24.89911611 1.21625288 2.209936502 0.761375685 0.169312408 486.98878 1466324.546 0.041058206 0.464975155 55825.13698 -4.746829797 0.993683622 KAVVVCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KAVVVCPK 8 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 116.37 0.0036627 889920000 2652700 1844230 2647500 1958070 3084500 2973800 3135100 2572900 2806600 1931890 FALSE TRUE 2757430.644 2160962.156 2716496.025 2345370.402 2560197.792 2283180.018 2889362.67 2538414.484 2705591.014 2310406.857 1.193482713 0.935316717 1.175765219 1.015133068 1.108115561 0.988215565 1.250586087 1.098687219 1.171045267 1 21.1397155 2.256361379 24.9999937 1.138069127 1.067382626 0.086909203 0.094925015 497.1549052 698220.0118 0.029765806 0.02485541 180.4518668 -2.256361379 -0.070686501 KAYS(ph)FCGTVEYMAPEVVNR ddPTM_MDA-MB-175_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(1)FCGTVEYMAPEVVNR;KAYS(0.997)FCGT(0.003)VEYMAPEVVNR 239.96 1.62E-24 1357430000 1028360 940850 1268750 940230 1559420 1366500 1054730 1084100 1298590 1079570 TRUE FALSE 1068960.447 1102433.669 1301814.667 1126204.688 1294350.345 1049151.085 972057.5066 1069569.413 1251854 1291091.072 0.827951235 0.85387754 1.00830584 0.872289114 1.002524433 0.812608117 0.752896157 0.828422902 0.969609369 1 20.30015934 2.696556407 24.99673175 0.849500624 0.912739983 0.017247086 0.088146589 1147.124891 682653.8205 0.028361831 0.02674001 497.2289507 -2.696556407 0.063239359 KAYWQVHLDQVEVASGLTLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 187.06 1.96E-17 3487955000 3316977 2943899 3172588 2441150 4457811 4129072 3055761 3443055 3660128 3625309 FALSE TRUE 3447933.813 3449490.753 3255268.25 2924002.184 3700073.879 3170157.605 2816242.468 3396906.479 3528400.708 4335618.888 0.795257587 0.795616691 0.750819741 0.674414025 0.853413082 0.731189177 0.649559507 0.783488256 0.813817081 1 22.04780651 0.806971901 2.050898005 0.999572428 0.751183049 0.633458078 0.05633813 0.442992931 3.261104206 0.05358597 0.014782226 6.411680913 -0.806971901 -0.248389379 KCDSWWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCDSWWAK 8 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 96.665 0.014078 258450000 639910 446940 734420 570900 917580 747870 784750 629820 736350 525480 FALSE TRUE 665174.1409 523698.4683 753559.5885 683822.316 761610.0794 574188.5266 723239.2444 621378.2931 709848.9073 628437.7451 1.058456699 0.833333886 1.199099822 1.088130561 1.211910146 0.913676066 1.15085265 0.988766665 1.12954531 1 19.26141031 4.239738434 24.99996088 1.08192853 0.94589533 0.224992974 0.103305957 41.553851 881902.1775 0.023656328 0.057882809 17367.54506 -4.239738434 -0.136033199 KCEAEEAEPPAATQPQTSETQTSHLPESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KCEAEEAEPPAATQPQTSETQTSHLPESER 30 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 146.89 2.26E-08 136410000 99282 106450 116990 91939 132000 151280 128880 126390 116580 80870 FALSE TRUE 103201.73 124731.9594 120038.8555 110124.2598 109562.6871 116147.5127 118778.0488 124695.9488 112384.3086 96714.92815 1.067071361 1.28968673 1.241161606 1.138648003 1.13284153 1.200926423 1.228125286 1.289314392 1.162016151 1 16.56145097 4.768404294 23.31328286 1.200800342 1.067070834 0.14084622 0.082714893 7632.838305 5962367.076 0.019106833 1.915926108 58668.40671 -4.768404294 -0.133729508 KCEEEIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCEEEIAK 8 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 78.655 0.048203 493580000 522270 358680 483760 359280 569520 547850 526000 466690 528570 364890 FALSE TRUE 542889.6229 420280.4999 496367.183 430344.5117 472713.1938 420620.1402 484770.7456 460434.7839 509546.869 436383.2093 1.24406625 0.963099613 1.137457108 0.986161939 1.08325248 0.96387792 1.11088313 1.05511572 1.1676592 1 18.73523607 4.757751403 24.13064971 1.055217202 1.244066525 0.408621914 0.069236823 2508.517815 3154148.01 0.014981153 0.516295747 57246.82475 -4.757751403 0.188849323 KCEPIVMTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCEPIVMTVPR 11 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 139.89 6.23E-05 2013410000 2437200 2350400 2551700 2146260 3067800 3057700 2608100 2456700 2638300 2444200 FALSE TRUE 2533422.538 2754062.916 2618199.398 2570783.822 2546336.452 2347595.515 2403670.307 2423771.955 2543348.098 2923094.193 0.866692064 0.942173852 0.895694502 0.87947348 0.871109955 0.803120036 0.822303405 0.829180244 0.87008763 1 21.47906489 3.380122674 2.076585735 0.84897087 0.905006581 0.032048311 0.05446629 0.552250741 4.843094002 0.01559683 0.023734909 2399.510608 -3.380122674 0.056035711 KCHS(ph)LGYNFIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCHSLGYNFIHK 12 1 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 KCHS(1)LGYNFIHK;KCHS(1)LGYNFIHK 134.44 6.84E-05 1792970000 2209620 1583710 2095820 1530680 3194500 2510890 2305300 2147340 2439160 1902850 TRUE FALSE 2296857.504 1855699.873 2150438.791 1833443.935 2651500.031 1927773.85 2124604.562 2118558.42 2351375.108 2275677.025 1.009307331 0.815449579 0.944966604 0.80566966 1.165147779 0.847121023 0.933614278 0.930957423 1.033263983 1 21.11786439 1.548678336 0.358859841 1.010827582 0.908134431 0.062442877 0.101273166 3.593969438 1.468384806 0.13770979 0.115843586 35.37352471 -1.548678336 -0.102693151 KCLELFSELAEDKENYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KCLELFSELAEDKENYKK 18 3 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 152.04 1.90E-08 1214900000 1568500 518830 961010 566660 1482600 1200700 1290600 1009600 1298800 444420 FALSE TRUE 1630425.591 607935.0166 986054.7101 678743.6567 1230588.182 921855.6218 1189439.4 996067.9634 1252056.442 531495.5901 3.067618286 1.143819493 1.855245328 1.277044757 2.315330935 1.734455824 2.237910195 1.874085095 2.355723105 1 19.0196982 3.186210653 24.99961119 1.969501183 1.787852843 0 0.605238801 509.2790599 243202.9173 0.161832227 0.193426678 1535.361525 -3.186210653 -0.181648339 KCS(ph)LPAEEDSVLEK ddPTM_MDA-MB-175_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 205.21 7.69E-09 1231840000 1379680 803653 1035425 749337 1525710 1327730 1351350 1029673 1261988 660398 TRUE FALSE 1434150.832 941674.1512 1062409.026 897553.6221 1266370.359 1019384.829 1245427.656 1015871.918 1216569.298 789790.344 1.815862707 1.19230902 1.345178545 1.136445424 1.603425984 1.29070308 1.576909195 1.286255176 1.540369932 1 19.5911102 -1.333757244 3.756287906 0.998738245 1.403095583 0.278922131 0.201180468 14418372.05 5120441.718 148059.9686 0.042756248 0.046370604 1.333757244 0.404357338 KCSLPAEEDS(ph)VLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KCSLPAEEDSVLEK 14 1 E7EVA0;P27816-6;P27816 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 KCS(0.315)LPAEEDS(0.685)VLEK 196.78 2.58E-08 160540000 233530 127390 167570 115970 251520 226350 216560 161990 203440 111610 TRUE FALSE 242749.9447 149268.2415 171937.0119 138908.5199 208766.7202 173783.6429 199585.4613 159818.789 196118.2341 133477.8426 1.818653493 1.118299776 1.288131487 1.040685983 1.564055248 1.301966225 1.495270357 1.197343214 1.469294306 1 17.02624075 -1.462857276 3.208031477 0.993470713 1.345291738 0.195190384 0.219349544 41565795.77 60867709.84 2494415.722 0.050205943 0.034446311 1.462857276 0.351821025 KCSTPEEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KCSTPEEIK 9 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 120.77 0.0010144 1943000000 2426920 1490310 2023690 1377850 2769060 2471800 2544790 2018670 2345620 1561070 FALSE TRUE 2522736.676 1746259.149 2076429.024 1650384.618 2298376.17 1897761.91 2345322.71 1991613.031 2261201.594 1866931.778 1.351274163 0.935363129 1.11221473 0.884009066 1.231098103 1.016513797 1.256244464 1.066784043 1.21118598 1 20.83223778 KCSTPEEIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCSTPEEIKK 10 2 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ; 151.1 1.15E-05 2921400000 9110900 4510000 6847600 4467100 10605000 8568600 9338700 7232700 8460700 4359700 FALSE TRUE 9470605.367 5284557.417 7026054.081 5350679.047 8802365.888 6578672.508 8606708.292 7135757.487 8156201.06 5213899.744 1.816414936 1.01355179 1.347562176 1.026233589 1.688249932 1.261756618 1.65072378 1.368602742 1.564318737 1 22.31393141 3.235749536 24.99816796 1.443650161 1.283742997 0.03871156 0.279273901 201.4008734 1791006.303 0.072958729 0.09095609 1720.875836 -3.235749536 -0.159907165 KCTENDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KCTENDIR 8 1 Q92879-4;G5EA30;Q92879-6;Q92879;Q92879-5;Q92879-3;Q92879-2 Q92879-4 CELF1 CUGBP Elav-like family member 1 0 ; 79.906 0.043011 271510000 778620 759780 847510 774470 1036920 1049570 941490 863270 923090 764940 FALSE TRUE 809360.5188 890266.3047 869596.8068 927657.8544 860664.7088 805823.2739 867693.5537 851699.2777 889868.1712 914815.3473 0.884725558 0.97316503 0.950570855 1.01403836 0.940807029 0.880858936 0.948490377 0.931006766 0.972729823 1 19.80312104 1.016926435 4.217083218 0.999832194 0.942311189 0.215882247 0.036662412 0.277872091 12.82278298 0.035267918 0.009003233 10.39744029 -1.016926435 -0.057521005 KDAAEQVR ddPTM_MDA-MB-175_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 77.662 0.052323 103390000 51755 56145 55497 55329 62377 74704 66057 51745 55266 81246 FALSE TRUE 53798.32736 65787.467 56943.29741 66272.91106 51774.17982 57355.12815 60879.27973 51051.44291 53276.98746 97164.59815 0.553682394 0.677072393 0.586049842 0.682068493 0.532850244 0.590288328 0.626558241 0.52541197 0.548316861 1 16.56814314 -2.037692741 2.685933472 1.515970205 0.591349802 0.84347751 0.052808862 7262071.948 1553825.646 23127157.58 0.013328802 0.009168689 2.037692741 -0.924620403 KDAENHEAQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDAENHEAQLK 11 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ;;; 167.18 1.27E-05 707590000 1816900 1146660 1486400 1125160 2035570 1897720 1875040 1554440 1737730 1025970 FALSE TRUE 1888632.615 1343589.935 1525136.805 1347713.29 1689564.538 1457003.29 1728069.465 1533605.274 1675189.437 1226989.178 1.539241461 1.09502998 1.242991244 1.098390527 1.377000359 1.187462217 1.408381994 1.249893073 1.365284606 1 20.22669109 -1.017422872 4.579415081 0.999991272 1.275811288 0.287759797 0.133764579 1.09E-05 2.33E-06 0.118076663 0.027830056 0.096067641 1.017422872 0.275820017 KDCEVVMMIGLPGAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDCEVVMMIGLPGAGK 16 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 137.19 2.14E-05 438940000 855720 639110 866200 596380 990290 928190 897290 850680 1001900 547290 FALSE TRUE 889504.4864 748872.1709 888773.8836 714342.184 821960.8595 712631.9394 826958.0652 839278.026 965841.8147 654520.997 1.359015968 1.144153013 1.357899728 1.091396895 1.25582046 1.088783924 1.263455365 1.282278231 1.4756468 1 19.32007995 2.018423349 24.9770948 1.281221201 1.212196644 0.006204699 0.140010481 763.367161 1034915.77 0.048684451 0.035949447 104.3333973 -2.018423349 -0.069024557 KDDDS(ph)DDESQSSHTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KDDDSDDESQSSHTGK 16 1 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.995)DDES(0.005)QSSHTGK;KDDDS(0.999)DDES(0.001)QSSHTGK;KDDDS(0.999)DDES(0.001)QSSHTGK;KDDDS(0.989)DDES(0.011)QSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK;KDDDS(1)DDESQSSHTGK 328.13 1.11E-71 7135944000 3975360 1979415 2967367 1863684 4388135 4013341 4155429 2971781 3119938 1227136 TRUE FALSE 4132310.282 2319364.129 3044699.022 2232315.133 3642241.38 3081303.376 3829715.617 2931949.137 3007652.041 1467569.804 2.815750413 1.580411454 2.07465363 1.521096391 2.481818152 2.099595785 2.609562834 1.997826017 2.049409869 1 20.4849977 4.760405526 23.60623743 2.009682244 2.815752222 0.24113066 0.451579621 3872.418806 4184503.446 0.100453539 4.497462174 57597.75099 -4.760405526 0.806069977 KDDDS(ph)DDESQSSHTGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KDDDSDDESQSSHTGKK 17 2 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 KDDDS(0.999)DDESQSSHTGKK;KDDDS(1)DDESQSSHTGKK;KDDDS(1)DDESQSSHTGKK 147.9 2.00E-07 251568000 359786 123966 208467 117763 376066 301389 289803 191885 226473 76527 TRUE FALSE 373990.6291 145256.1962 213899.8213 141056.1699 312142.4356 231395.9723 267087.4836 189313.0954 218322.281 91521.00045 4.086391399 1.587135143 2.337166554 1.54124375 3.41060996 2.528337444 2.918319099 2.068520826 2.385488357 1 16.4818152 0.418573793 0.982315774 0.996812837 2.539122908 0.288158445 0.736530202 2.785263506 3.536210998 0.686784546 0.213490799 2.621644459 -0.418573793 1.542310071 KDDEENYLDLFSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDDEENYLDLFSHK 14 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;;; 260.49 1.19E-24 5680550000 10222630 5100643 7941990 5211219 10978770 9634510 10454240 7843300 9458500 4355685 FALSE TRUE 10626227.33 5976638.758 8148964.784 6241982.564 9112602.597 7397041.065 9634809.352 7738173.393 9118090.433 5209098.081 2.03993612 1.147346175 1.564371539 1.198284706 1.749362837 1.42002338 1.849611814 1.485511171 1.750416347 1 22.31260217 3.186939513 24.99996819 1.576044778 1.468670733 0 0.318042728 460.5953989 223063.1921 0.084108887 0.100529475 1537.940427 -3.186939513 -0.107374045 KDDEVQVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDDEVQVVR 9 1 P61254;E5RIT6;J3QRI7;J3QQQ9;J3QQV1;J3QRC4;Q9UNX3 P61254;Q9UNX3 RPL26;RPL26L1 60S ribosomal protein L26;60S ribosomal protein L26-like 1 0 166.66 9.71E-05 457190000 900410 642620 853140 668600 1138100 989880 1062900 958590 995250 677750 FALSE TRUE 935958.8821 752984.9861 875373.5293 800847.0844 944646.1685 759995.3718 979587.1206 945741.669 959431.1469 810542.1362 1.154731926 0.928989318 1.079985222 0.988038806 1.165449798 0.937638326 1.208557923 1.166801363 1.183690649 1 19.62852766 2.221225588 24.98239485 1.157030868 1.042134673 0.203803812 0.091697944 303.6220436 437562.3274 0.031320988 0.023186376 166.4276909 -2.221225588 -0.114896195 KDDPTLLSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KDDPTLLSSGR 11 1 F6S8N6;A0A0A0MRJ6;P22061;P22061-2;A0A3F2YNX8 F6S8N6 PCMT1 Protein-L-isoaspartate O-methyltransferase;Protein-L-isoaspartate(D-aspartate) O-methyltransferase 0 ;; 153.75 5.18E-05 1680570000 2047170 2037650 2005190 1886840 2918720 2843600 2246050 2299340 2277820 2283270 FALSE TRUE 2127993.852 2387600.537 2057446.899 2260051.32 2422597.017 2183216.995 2069998.732 2268521.108 2195841.703 2730633.041 0.77930422 0.874376198 0.753468836 0.827665705 0.88719245 0.799527788 0.758065511 0.830767472 0.804151151 1 21.38080402 -1.214525241 5.156065828 1.000016589 0.813883498 0.639711714 0.042155305 7.69E-06 1.17E-06 0.03905201 0.009203827 0.061020359 1.214525241 -0.186133091 KDDRVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDDRVEER 8 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 96.89 0.0048485 174237000 269910 214071 272890 213965 305380 325490 281200 258970 290900 192733 FALSE TRUE 280566.2552 250836.029 280001.7376 256286.6384 253471.6167 249899.8803 259158.8092 255498.9307 280430.5658 230495.3413 1.217231783 1.088247717 1.214782633 1.111895091 1.099682168 1.084186253 1.124355954 1.108477635 1.216643097 1 17.81437807 -2.107929684 2.46689897 0.751125423 1.134806358 0.391565796 0.052133059 4212947.4 1089442.745 5910953.374 0.011918794 0.007799564 2.107929684 0.383680935 KDDS(ph)DDDGGGWITPSNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDDSDDDGGGWITPSNIK 18 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK;KDDS(1)DDDGGGWITPSNIK 261.39 5.37E-31 2677410000 6450070 2017220 3206850 2105640 4499950 4961970 5286180 3434040 3818450 1271180 TRUE FALSE 6704723.744 2363661.843 3290423.145 2522129.307 3735050.106 3809627.667 4871835.399 3388012.311 3681024.73 1520243.383 4.410296285 1.554791733 2.164405504 1.659029953 2.456876411 2.505932741 3.20464174 2.228598624 2.421339091 1 20.53587088 KDDS(ph)HS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 KDDS(1)HS(1)AEDS(1)EDEKEDHK;KDDS(1)HS(1)AEDS(1)EDEKEDHK 141.36 8.91E-08 1253350000 4726900 413070 677970 486120 1380360 3387900 1826710 800550 862210 183296 TRUE FALSE 4913521.662 484011.5593 695638.4552 582273.0851 1145726.9 2601111.569 1683527.697 789819.9367 831179.2305 219209.3418 22.41474575 2.207987832 3.173397856 2.656242112 5.22663355 11.8658792 7.679999781 3.603039589 3.791714458 1 17.74194976 4.743920853 24.93300578 4.884247959 22.41475341 0.761012219 2.99420348 286.406136 1332168.818 0.759912652 6.537225278 55452.46456 -4.743920853 17.53050545 KDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.11)HS(0.89)AEDS(1)EDEKEDHK;KDDS(0.114)HS(0.886)AEDS(1)EDEKEDHK;KDDS(0.022)HS(0.978)AEDS(1)EDEKEDHK;KDDS(0.006)HS(0.994)AEDS(1)EDEKEDHK;KDDS(0.024)HS(0.976)AEDS(1)EDEKEDHK;KDDS(0.076)HS(0.924)AEDS(1)EDEKEDHK 160.92 2.11E-11 7062970000 6767670 846114 1631712 1007708 2783184 4655970 3629804 1697036 1987242 424160 TRUE FALSE 7034862.837 991427.4976 1674235.755 1207029.635 2310099.378 3574691.529 3345290.478 1674290.008 1915721.549 507266.031 13.86819225 1.954452767 3.300508319 2.379480511 4.554019463 7.046975968 6.594745703 3.300615271 3.776561866 1 18.95238303 4.745950622 24.78672939 4.004315283 13.86819753 0.733483903 1.821555421 430.2759578 1443144.047 0.451854204 4.684090176 55712.24017 -4.745950622 9.863882242 KDDSHS(ph)AEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KDDSHSAEDSEDEKEDHKNVR 21 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 KDDS(0.018)HS(0.982)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.025)HS(0.975)AEDS(1)EDEKEDHKNVR;KDDS(0.398)HS(0.602)AEDS(1)EDEKEDHKNVR;KDDS(0.133)HS(0.867)AEDS(1)EDEKEDHKNVR;KDDS(0.419)HS(0.581)AEDS(1)EDEKEDHKNVR;KDDSHS(1)AEDS(1)EDEKEDHKNVR;KDDS(0.152)HS(0.848)AEDS(1)EDEKEDHKNVR;KDDS(0.001)HS(0.999)AEDS(1)EDEKEDHKNVR;KDDS(0.451)HS(0.549)AEDS(1)EDEKEDHKNVR 229.7 6.73E-26 25499710000 10565927 1731938 3240943 1493087.8 5829691 7330401 4881481 2990399 3697483 1089250.5 TRUE FALSE 10983077.96 2029384.879 3325404.637 1788416.11 4838762.206 5628026.461 4498857.764 2950317.593 3564411.309 1302668.281 8.431216236 1.557867731 2.552763959 1.372886818 3.714500674 4.320383435 3.453571282 2.264826462 2.736238659 1 20.31303832 4.745346199 24.97701974 2.668296302 8.431218897 0.750212444 1.015662175 398.3947467 1466411.603 0.246525179 2.429344194 55634.75742 -4.745346199 5.762922594 KDDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDDSHSAEDSEDEKEDHK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK;KDDSHSAEDS(1)EDEKEDHK 314.97 1.31E-61 3524541000 5056998 702349 1409736 733490 2311159 2905985 3011320 1464645 1647512 357438.8 TRUE FALSE 5256652.186 822971.9772 1446474.878 878572.1328 1918309.019 2231114.024 2775284.87 1445013.829 1588218.365 427472.0893 12.29706528 1.925206342 3.383787888 2.055273677 4.487565544 5.219320934 6.492318304 3.380370007 3.715373248 1 18.7054707 4.74615155 24.71774079 3.744499929 12.29707009 0.739789903 1.556820567 411.76668 1340764.955 0.376481711 3.96643024 55738.02161 -4.74615155 8.552570162 KDDSHSAEDS(ph)EDEKEDHKNVR ddPTM_MDA-MB-175_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;KDDSHS(0.371)AEDS(0.629)EDEKEDHKNVR;KDDSHSAEDS(1)EDEKEDHKNVR 210.56 8.03E-23 4041510000 2251040 431194 775761 402260 1373100 1371680 1163100 754676 947445 250106 TRUE FALSE 2339912.797 505248.2153 795977.969 481825.8274 1139700.952 1053128.108 1071933.183 744560.8026 913346.6395 299109.4821 7.822930857 1.689174852 2.661159263 1.61086778 3.810313683 3.520878377 3.583748583 2.489258439 3.053552943 1 18.19031412 4.745673449 24.99365705 2.71937792 7.822933232 0.753281585 0.89409582 409.5314605 1439010.049 0.20741372 2.113469094 55676.69515 -4.745673449 5.103555312 KDDVS(ph)PVMQFSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(1)PVMQFSSK;KDDVS(1)PVMQFSSK;KDDVS(1)PVMQFSSK 219.72 1.35E-11 6996450000 8965620 4347280 6866970 4482700 9542360 8495940 8755940 6969460 8398550 4127390 TRUE FALSE 9319589.601 5093891.523 7045928.879 5369364.68 7920353.056 6522886.692 8069626.543 6876045.788 8096287.826 4936073.047 1.888057472 1.031972476 1.427436104 1.087780636 1.604585868 1.321472885 1.634827213 1.393019456 1.640228528 1 22.23493231 3.187688995 24.99972692 1.456302565 1.340359695 0.010315919 0.280096107 386.9144949 190138.9505 0.074181616 0.088664121 1540.596813 -3.187688995 -0.11594287 KDDYEYCMSEYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDDYEYCMSEYLR 13 1 P53611;Q5T4U8 P53611 RABGGTB Geranylgeranyl transferase type-2 subunit beta 0 121.31 0.00039784 128060000 43564 29616 37397 38153 56639 36272 42637 31773 34634 23909 FALSE TRUE 45283.94036 34702.31762 38371.59654 45699.54952 47011.52301 27848.37771 39295.00053 31347.13491 33387.52911 28593.51078 1.583713896 1.213643119 1.341968702 1.598248983 1.644132592 0.973940483 1.374262882 1.096302414 1.16766106 1 14.80340015 2.737408197 24.9998605 1.146591717 1.461054592 0.553911349 0.157760509 91.55951485 1986216.614 0.05047329 0.050097056 546.2710648 -2.737408197 0.314462875 KDEDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDEDLFR 7 1 O75531 O75531 BANF1 "Barrier-to-autointegration factor;Barrier-to-autointegration factor, N-terminally processed" 0 ;;;;; 135.83 0.004873 6445444000 4756435 3870594 4681738 3755875 6564390 5923674 5842070 5012985 5164886 4401687 FALSE TRUE 4944222.727 4535338.41 4803747.938 4498775.865 5448577.333 4547990.488 5384153.288 4945794.136 4979002.762 5264113.292 0.939231823 0.861557903 0.912546458 0.85461228 1.035041807 0.863961362 1.02280346 0.939530337 0.945838831 1 22.32775911 3.258108248 24.99999388 0.962205469 0.891282131 0.345391571 0.050812579 274.1929624 350670.6154 0.012856086 0.017382539 1811.791625 -3.258108248 -0.070923338 KDEEGQKEEDKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDEEGQKEEDKPR 13 3 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 0 ; 83.729 0.0044112 442260000 204443 58314 104907 58121 175721 151452 152745 88589 134667 57073 FALSE TRUE 212514.5675 68328.97588 107640.9626 69617.16033 145852.0072 116279.5683 140772.4478 87401.60936 129820.361 68255.36162 3.113521963 1.001078512 1.577033072 1.019951527 2.136857878 1.703596106 2.062437945 1.280509066 1.901980414 1 16.05865476 -2.415094714 0.349032986 2.80E-12 1.733071349 0.123629553 0.591255534 121.7133707 5.168685138 94.37049104 0.432451212 0.003845079 2.415094714 1.733071349 KDEEKEDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDEEKEDPK 9 2 P55209;F8VY35;P55209-2;H0YIV4;F5H4R6;F8W0J6;F8VV59;B7Z9C2;F8W543;F8W118;F8VUX1;H0YHC3;H0YH88;F8W020;P55209-3;F8VXI6 P55209 NAP1L1 Nucleosome assembly protein 1-like 1 0 ; 66.595 0.035593 333840000 2247800 336970 637410 395840 1105110 1196930 1550390 698120 864120 187354 FALSE TRUE 2336544.88 394841.9762 654021.4282 474135.9705 917263.7969 918961.1471 1428866.381 688762.8433 833020.49 224062.4292 10.4280976 1.762196267 2.918925009 2.116088682 4.093786719 4.101362064 6.377090464 3.073977399 3.717805314 1 17.77354123 4.747111368 24.8770409 3.440130503 10.42810136 0.692420672 1.431637015 598.1916869 1740302.002 0.342800603 3.985130133 55861.34236 -4.747111368 6.987970861 KDEESGGGSNPFQHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDEESGGGSNPFQHLEK 17 1 Q9Y678;D6RG17 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 240.13 1.70E-20 801068000 1110524 748745 1085005 835896 1446900 1271860 1382710 1094627 1211820 604608 FALSE TRUE 1154368.345 877336.1293 1113281.122 1001233.734 1200956.455 976489.7902 1274329.577 1079955.316 1168206.835 723069.3617 1.596483555 1.213349888 1.539660205 1.384699431 1.660914593 1.350478726 1.762389122 1.493570842 1.615622092 1 19.46377452 KDEKKEES(ph)EES(ph)DDDMGFGLFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDEKKEESEESDDDMGFGLFD 21 3 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 2 KDEKKEES(1)EES(1)DDDMGFGLFD 72.425 0.006446 261690000 1901700 338470 693150 161990 1548900 1472600 480260 576800 785800 357570 TRUE FALSE 1976780.584 396599.5896 711214.0584 194031.1385 1285618.531 1130610.967 442615.9663 569068.9395 757519.2115 427628.9954 4.622653294 0.92743849 1.663156769 0.453737096 3.006387652 2.643906236 1.035046667 1.330753867 1.771440243 1 18.70600015 4.7460082 24.58384961 1.563007152 4.622655143 0.605081679 0.747613125 499.1279552 1647528.935 0.180868413 1.876074986 55719.62695 -4.7460082 3.059647992 KDEKTDTLEDLFPTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDEKTDTLEDLFPTTK 16 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 68.919 0.026804 632580000 303410 121910 192800 94516 329140 257580 201670 165610 240000 98260 FALSE TRUE 315388.8611 142847.0942 197824.5264 113210.9827 273192.9004 197760.9487 185862.5784 163390.2688 231362.4469 117512.1657 2.683882636 1.21559409 1.683438691 0.963397977 2.324805255 1.68289766 1.581645418 1.390411519 1.968838252 1 16.8424506 -2.608904755 0.264231314 6.94E-13 1.74450227 0.16100054 0.483196114 92.03206182 2.77727598 54.67415299 0.614838455 0.002460907 2.608904755 1.74450227 KDELSDWSLAGEDDRDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 188.32 2.16E-14 3162590000 3731550 3169520 3805910 3362580 4297810 4464860 4919440 3876060 4065430 3050680 FALSE TRUE 3878874.475 3713860.405 3905095.141 4027688.288 3567269.791 3427963.931 4533841.438 3824107.756 3919115.968 3648402.337 1.063170702 1.01794157 1.070357592 1.103959464 0.977762171 0.939579469 1.242692285 1.048159551 1.074200597 1 21.7988334 2.283973501 24.99999996 1.095495652 1.031288065 0.149259511 0.072634916 239.9218356 132077.059 0.024912934 0.020843563 192.2974393 -2.283973501 -0.064207586 KDELYLNLVLEYVPETVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDELYLNLVLEYVPETVYR 19 1 P49840;A8MT37;M0QYV0 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 ; 94.384 0.0025735 144620000 263952 186563 278494 245699 281470 343600 357120 287862 287320 168384 FALSE TRUE 274373.0288 218603.744 285751.7824 294297.5289 233625.8299 263804.1073 329128.0012 284003.6807 276979.4093 201375.6209 1.362493769 1.085552179 1.41899889 1.461435737 1.16014952 1.31001015 1.634398443 1.410318089 1.37543665 1 17.61952951 2.444196734 24.9986184 1.409241388 1.295101526 0 0.181383694 494.7292326 375630.7696 0.060243961 0.050403918 278.0972752 -2.444196734 -0.114139861 KDENEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDENEIEK 8 1 G8JLG1;Q14683 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 98.943 0.011488 211620000 177740 92359 135230 97315 190400 177830 184560 132630 164610 85332 FALSE TRUE 184757.3124 108220.9398 138754.2049 116563.6165 158035.876 136531.6775 170093.7049 130852.3118 158685.7183 102051.1716 1.810437935 1.060457593 1.359653228 1.142207529 1.548594431 1.33787467 1.666749164 1.282222533 1.554962238 1 16.63893322 -1.028215166 4.932070206 0.999993536 1.401220708 0.241382882 0.220551137 1.43E-05 2.81E-06 0.194600797 0.045867109 0.093709762 1.028215166 0.401227172 KDENKVDGMNAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDENKVDGMNAPK 13 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 97.69 0.01759 75442000 178630 82252 123390 76480 179730 165130 164690 127310 154170 60932 FALSE TRUE 185682.4503 96378.14117 126605.6448 91607.51573 149179.5588 126781.0601 151781.1675 125603.6177 148621.4518 72870.45879 2.548116938 1.322595504 1.737406994 1.257128297 2.047188412 1.739814215 2.082890241 1.723656195 2.03952952 1 16.15304645 KDEQEHEFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDEQEHEFYK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 113.44 0.00096542 1033760000 2137140 1308630 1807020 1367920 3004300 2375300 2528700 1695010 2062360 1375620 FALSE TRUE 2221515.937 1533377.023 1854112.426 1638490.493 2493630.159 1823672.573 2330493.886 1672291.163 1988136.066 1645146.401 1.350345438 0.932061136 1.127019713 0.995954215 1.515749697 1.10851689 1.416587536 1.016499907 1.208485801 1 20.64978454 5.067284901 19.44271332 1.157177773 5.278339415 0.101108078 0.179706095 559.3238449 166979.598 0.039639139 3259.887629 116757.5304 -5.067284901 4.121161643 KDETNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 118.06 0.0081639 3075830000 4822860 2750260 3389630 2635710 5218270 4576890 4891240 3602840 3656390 2855650 FALSE TRUE 5013270.237 3222595.761 3477966.542 3157045.571 4331270.329 3513976.661 4507851.828 3554549.823 3524797.238 3415159.943 1.467945959 0.943614886 1.018390529 0.924421001 1.268248165 1.028934726 1.319953356 1.040815037 1.032103122 1 21.70352172 -0.405399889 0.012576079 4.62E-06 2.111765674 0.063016744 0.166813218 11144.84148 34.69021768 3078.829653 2748.347785 0.39318787 0.405399889 2.111761053 KDGADFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 105.98 0.00687 5123400000 7608300 5090700 6736900 5133600 9984700 9184600 9727800 6879700 7585000 4770000 FALSE TRUE 7908681.559 5964988.125 6912469.148 6149010.758 8287504.26 7051615.844 8965309.617 6787488.874 7312017.332 5704590.173 1.386371557 1.045647092 1.211738081 1.077905787 1.452778203 1.236130139 1.571595741 1.18982936 1.281777851 1 22.44369181 3.252188898 24.99572288 1.307474162 1.173026654 0.085113171 0.166521061 464.4350187 851818.5889 0.042985713 0.057893988 1787.264783 -3.252188898 -0.134447508 KDGNASGTTLLEALDCILPPTRPTDKPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDGNASGTTLLEALDCILPPTRPTDKPLR 29 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 ; 153.97 8.68E-09 7900500000 384070 263320 336150 329710 420840 425870 499580 362200 415680 240154 FALSE TRUE 399233.3802 308543.1617 344910.3452 394925.6539 349305.7671 326968.1466 460421.6142 357345.3014 400719.758 287207.5783 1.390051692 1.074286283 1.200909625 1.375053041 1.216213615 1.138438437 1.603097025 1.244205684 1.395226966 1 18.13173429 KDHPYTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDHPYTWR 8 1 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 67.993 0.03743 305680000 368910 434470 432990 406150 583670 587510 478920 471540 440270 495890 FALSE TRUE 383474.8517 509086.8428 444274.0751 486485.2578 484457.9819 451069.7063 441380.999 465219.7776 424424.7687 593050.1511 0.646614542 0.858421234 0.749134073 0.820310486 0.816892098 0.760592853 0.744255774 0.784452675 0.715664211 1 19.17779459 -1.044743042 4.611328253 1.000008995 0.771441109 0.602836449 0.056776682 4.76E-06 9.86E-07 0.049813152 0.011740611 0.090210473 1.044743042 -0.228567886 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJV7;H0YJU4 P25490 YY1 Transcriptional repressor protein YY1 1 KDIDHET(0.001)VVEEQIIGENS(0.985)PPDY(0.01)S(0.003)EY(0.001)MTGK;KDIDHETVVEEQIIGENS(0.806)PPDY(0.139)S(0.047)EY(0.003)MT(0.005)GK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(1)PPDYSEYMTGK;KDIDHETVVEEQIIGENS(0.997)PPDY(0.002)S(0.001)EYMTGK 250.08 1.34E-46 764222000 473075 335672 448406 309890 537483 504757 487570 422782 458483 271437 TRUE FALSE 491752.3663 393321.0548 460091.8287 371185.3171 446121.8316 387534.8364 449352.9894 417115.2988 441982.2864 324619.8832 1.514855965 1.211635748 1.417324855 1.143446031 1.374289915 1.193811151 1.38424358 1.284934536 1.361537938 1 18.30839184 -1.803780153 2.650379182 0.905377291 1.313540239 0.440936795 0.108056671 17178566.33 11568387.05 10417261.18 0.023481932 0.015711579 1.803780153 0.408162948 KDIHFMPCSGLTGANLK ddPTM_MDA-MB-175_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 ; 190.57 1.89E-10 1123650000 1343750 944090 1215620 965670 1473200 1462280 1419930 1230150 1329010 1011900 FALSE TRUE 1396802.288 1106230.113 1247300.056 1156676.644 1222785.99 1122687.631 1308632.176 1213661.851 1281179.19 1210162.431 1.154227112 0.914117052 1.030688132 0.955802803 1.010431293 0.92771648 1.081369032 1.002891695 1.058683658 1 20.20676927 2.218951293 24.99996756 1.034053317 0.994999415 0.066562564 0.066668382 657.8420711 838679.8 0.022959331 0.016979545 165.5584276 -2.218951293 -0.039053903 KDIS(ph)ENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 KDIS(1)ENKR 64.55 0.052426 147220000 472860 186580 288490 196710 462360 422450 372330 285770 340500 164250 TRUE FALSE 491528.8779 218623.6636 296008.2864 235618.6509 383768.2124 324342.3898 343145.8017 281939.7206 328245.4715 196431.6427 2.502289708 1.112975794 1.506927714 1.199494377 1.953698533 1.651171803 1.746896767 1.435307044 1.671041727 1 17.58366782 -2.448130708 0.462491612 2.29E-12 1.621156192 0.207917716 0.373054317 166.6236143 8.757476741 168.7529541 0.179561033 0.003563439 2.448130708 1.621156192 KDISENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDISENKR 8 2 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 120.12 0.00087915 398073000 555513 400749 498875 359039 657141 594166 566516 459283 505217 377164 FALSE TRUE 577445.0822 469574.5234 511876.0923 430055.8426 545440.4075 456179.9512 522110.9956 453127.0626 487034.3389 451062.0646 1.280189862 1.041041932 1.13482408 0.95342942 1.209235825 1.011346302 1.157514756 1.00457808 1.079750166 1 18.78296643 4.743152834 24.75452952 1.068579841 1.28018996 0.414748378 0.076354212 373.9174507 2015535.912 0.016194525 0.129716769 55354.48747 -4.743152834 0.21161012 KDISQNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDISQNKR 8 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 90.906 0.0072356 1540010000 1084040 830650 1015380 734950 1790590 1391330 1207520 1002250 1144790 1059040 FALSE TRUE 1126838.736 973307.6759 1041841.637 880320.9164 1486226.151 1068214.693 1112871.427 988816.4781 1103589.232 1266538.611 0.889699474 0.768478487 0.822589716 0.695060465 1.173455067 0.843412655 0.878671536 0.780723516 0.871342746 1 20.27245963 KDITGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDITGK 6 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 87.323 0.084294 5201600000 4008500 2881500 3640600 2593200 4992900 4118000 4359900 3507600 4179500 2530500 FALSE TRUE 4166758.675 3376375.21 3735477.027 3106127.22 4144208.641 3161656.909 4018159.646 3460586.359 4029080.611 3026303.026 1.376847804 1.115676514 1.234336745 1.026376802 1.369396457 1.04472582 1.327745309 1.143502924 1.331353991 1 21.52912502 -1.034271685 4.354520225 0.999987832 1.209743742 0.212699437 0.125228525 1.39E-05 3.08E-06 0.105902236 0.024959841 0.092411988 1.034271685 0.20975591 KDKS(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 208.69 3.34E-15 33057610000 5404360 2495133 3698260 2268865 5272570 4970000 5024900 3727990 4293170 2036359 TRUE FALSE 5617728.306 2923652.683 3794639.694 2717639.725 4376340.435 3815792.821 4631035.208 3678022.392 4138659.65 2435344.558 2.30674887 1.200508846 1.558153109 1.115915905 1.797010785 1.566838996 1.901593429 1.510267769 1.699414416 1 21.21569447 KDLQHPNEFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDLQHPNEFIR 11 1 P53618;E9PP73;E9PP63;E9PKQ1 P53618 COPB1 Coatomer subunit beta 0 142.83 2.43E-05 46808000 115010 93575 117360 103910 131620 129470 108650 101410 113070 83491 FALSE TRUE 119550.6836 109645.7783 120418.498 124463.0879 109247.2794 99402.55464 100133.7291 100050.7648 109000.6328 99849.46292 1.19730923 1.098110847 1.206000458 1.246507334 1.09411985 0.995524179 1.002846947 1.002016054 1.091649665 1 16.60746705 3.000658569 4.653487514 1.017439214 1.181889935 0.768459966 0.043519479 0.092889039 5.342269812 0.013491471 0.015458338 1001.517561 -3.000658569 0.164450721 KDLTEYLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDLTEYLSR 9 1 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ; 108.53 0.0049113 0 379920 1052630 755220 935930 825690 1130390 592200 856670 675460 1441760 FALSE TRUE 394919.535 1233411.014 774901.6536 1121054.161 685339.5087 867874.0537 545781.8166 845187.7399 651150.3265 1724245.268 0.229039071 0.715333855 0.449414981 0.650170936 0.39747217 0.503335616 0.316533748 0.490178373 0.377643679 1 20.71753358 -1.281237136 3.675188833 1.001211577 0.466759483 0.581337494 0.137636185 94437899.91 148122618.6 1270393.844 0.03041239 0.052331462 1.281237136 -0.534452093 KDLYANTVLSGGTTMYPGIADR ddPTM_MDA-MB-175_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 ;;;; 236.77 2.69E-30 29262200000 16549630 16484850 18522720 15827530 20614210 22114000 21130250 18783280 17718020 16298040 FALSE TRUE 17203022.17 19315994.75 19005437.3 18958168.19 17110213.95 16978358.64 19474005.79 18531520.85 17080351.92 19491328.89 0.882598732 0.991004506 0.975071397 0.972646262 0.877837219 0.8710724 0.999111241 0.950757178 0.876305152 1 24.21632912 -1.395041281 2.992357811 1.000964407 0.937566774 0.137317421 0.049211849 10376943.3 12650246.45 85922.5883 0.011964809 0.040267876 1.395041281 -0.063397633 KDNDFIYHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 143.17 2.24E-05 4893440000 8240630 6864223 8302870 7326720 9841750 10028980 10103250 8568810 8678400 6180071 FALSE TRUE 8565976.436 8043099.904 8519249.613 8775923.348 8168852.85 7699901.386 9311330.865 8453959.118 8366066.079 7390937.588 1.158983733 1.088238104 1.152661555 1.187389725 1.105252582 1.041803059 1.259830807 1.143827697 1.131935696 1 22.81732596 0.747939845 4.164478205 1.000001801 1.143356579 0.370109563 0.055353138 4.714775165 77.01390083 0.052608437 0.013408479 5.596800738 -0.747939845 0.143354778 KDNDFIYHDRVPDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDNDFIYHDRVPDLK 15 2 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 120.29 8.73E-05 262610000 518150 380730 498150 315770 865950 519980 400820 463250 577070 435350 FALSE TRUE 538606.9621 446117.4158 511132.1982 378228.3635 718756.1283 399222.5254 369402.6811 457040.8915 556301.3634 520648.4972 1.034492493 0.856849522 0.981722219 0.726456267 1.380501686 0.766779367 0.709504941 0.877830041 1.068477805 1 18.98995018 KDPDMVKDIINEEEVQFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDPDMVKDIINEEEVQFLK 19 2 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 89.049 0.0013829 113760000 472690 265190 469490 253520 586600 529980 488690 359350 553520 313610 FALSE TRUE 491352.1662 310734.3196 481725.2951 303665.4993 486889.9415 406900.1769 450385.2008 354533.501 533598.9233 375055.8751 1.310077241 0.828501405 1.28440941 0.809654026 1.298179748 1.084905487 1.200848276 0.945281822 1.422718477 1 18.51674602 KDPEDTGAEKS(ph)PTTSADLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDTGAEKS(0.957)PT(0.028)T(0.007)S(0.007)ADLK 113.6 9.07E-05 266260000 373380 96598 152140 101630 293390 288910 329030 166580 216300 53674 TRUE FALSE 388121.3307 113187.9551 156104.8934 121732.1107 243519.6726 221815.031 303239.7688 164347.2676 208515.4053 64190.39265 6.046408422 1.763316135 2.431904323 1.89642259 3.793709036 3.455579906 4.724067829 2.560309429 3.248389621 1 15.97006977 KDPEDTGAEKSPTTS(ph)ADLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 KDPEDTGAEKS(0.126)PT(0.167)T(0.3)S(0.406)ADLK 113.54 9.14E-05 312640000 204810 51648 85449 60586 171090 160990 184190 103840 120540 34348 TRUE FALSE 212896.0569 60518.14223 87675.87114 72569.72997 142008.1829 123602.5123 169752.7065 102448.1946 116201.7889 41077.83297 5.182748007 1.473255473 2.134384041 1.766639687 3.457051472 3.008983274 4.132464988 2.494001929 2.828819842 1 15.32607245 3.215227618 24.98950117 2.963938364 2.519907628 0 1.20867853 1012.055217 1083902.27 0.334167352 0.399630626 1641.449849 -3.215227618 -0.444030736 KDPEDTGAEKSPTTSADLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDPEDTGAEKSPTTSADLK 19 2 O75363;G3XAF7;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 0 74.953 0.0084855 85895000 84753 26005 48505 28013 70183 68821 65718 34444 68946 26387 FALSE TRUE 88099.11388 30471.15646 49769.08015 33553.88779 58253.31873 52838.36574 60566.85144 33982.33452 66464.64693 31557.02744 2.791743109 0.965590201 1.577115596 1.063277834 1.845969771 1.674377152 1.919282529 1.076854738 2.106175781 1 14.94567369 -2.099781302 2.190672463 0.000228607 1.604404199 0.115251185 0.529518774 6651321.544 1746817.582 33146645.14 0.119575345 0.007947283 2.099781302 1.604175592 KDPELWGSVLLESNPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 215.88 8.77E-15 3582300000 259012 266179 309930 319145 353630 371200 353760 302303 309646 257963 FALSE TRUE 269237.9938 311893.1727 318007.0304 382270.9284 293520.0989 284994.4256 326031.3668 298251.1228 298501.9009 308505.9109 0.872715836 1.010979569 1.030797204 1.239104066 0.951424555 0.92378919 1.056807521 0.966759833 0.967572712 1 18.23493861 KDPELWGSVLLESNPYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDPELWGSVLLESNPYRR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 175.21 2.20E-12 2424190000 337130 244540 314440 283970 398850 371700 353150 277430 312690 256630 FALSE TRUE 350440.1527 286537.8427 322634.5647 340138.4184 331053.6195 285378.3082 325469.1802 273711.5046 301436.348 306911.735 1.141827153 0.933616444 1.051229158 1.108261365 1.078660676 0.929838372 1.060465088 0.891824826 0.982159734 1 18.22746428 2.744962845 24.8865119 0.967395764 1.057438411 0.31844245 0.065260776 590.2772279 2294506.279 0.019830242 0.020579643 555.8567003 -2.744962845 0.090042647 KDPSGASNPSADS(ph)PLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.003)ADS(0.997)PLHR;KDPSGASNPS(0.001)ADS(0.999)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPSADS(1)PLHR;KDPSGASNPS(0.003)ADS(0.997)PLHR;KDPSGASNPSADS(1)PLHR 224.49 1.27E-15 15402830000 8310000 7318330 8715890 6990000 9523230 9802980 8885540 8246160 8336310 7523520 TRUE FALSE 8638085.217 8575196.249 8943033.254 8372601.137 7904474.766 7526386.461 8189068.157 8135633.713 8036287.832 8997609.698 0.960042223 0.953052704 0.99393434 0.930536156 0.878508296 0.836487324 0.910138185 0.904199447 0.893158083 1 23.10111036 3.482585748 5.167099936 0.897092891 0.967097887 0.342565298 0.039784759 0.173446408 14.15254658 0.010485193 0.015308009 3037.985857 -3.482585748 0.070004996 KDQGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDQGELER 8 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 130.66 0.0016652 4212800000 4792360 3843880 4678350 3950600 5616830 5437630 5354110 4646080 4853750 3611770 FALSE TRUE 4981566.073 4504036.489 4800271.644 4732016.889 4662083.243 4174822.841 4934440.868 4583806.897 4679064.486 4319427.18 1.153293218 1.042739303 1.11132135 1.095519543 1.079329052 0.966522334 1.142383159 1.061207124 1.083260416 1 22.04240857 2.996314619 24.83766779 1.058628156 1.096095604 0.167218289 0.050891709 325.7008789 2195098.723 0.014325917 0.016809428 991.5500007 -2.996314619 0.037467448 KDREDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDREDSPER 9 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 KDREDS(1)PER 130.07 0.00029263 565290000 377890 254130 317000 233190 360800 408510 412490 321780 341290 177650 TRUE FALSE 392809.389 297774.8506 325261.2804 279314.286 299471.3449 313639.7435 380157.956 317467.0654 329007.0396 212457.1162 1.848887889 1.401576262 1.530950275 1.314685481 1.409561375 1.476249651 1.789339716 1.494264213 1.548580935 1 17.69681214 -2.073005466 2.321255712 0.220519841 1.527638355 0.505860399 0.15845372 3126227.021 917352.73 12908050.32 0.03740596 0.008452682 2.073005466 1.307118514 KDRHDT(ph)PDPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDRHDTPDPSPR 12 2 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 2 KDRHDT(1)PDPS(1)PR 88.73 0.0018677 0 160930 121790 123320 93880 207520 192510 139730 152600 152710 133420 TRUE FALSE 167283.6407 142706.4851 126533.8205 112449.1838 172245.8245 147802.47 128777.5975 150554.6466 147213.9969 159561.0945 1.048398679 0.894368928 0.793011736 0.704740614 1.079497637 0.926306444 0.807073917 0.943554863 0.92261837 1 17.2837494 3.235396962 24.9999995 0.933316251 0.857781488 0.135645463 0.10359126 200.2856712 1582713.122 0.030696546 0.03818505 1719.479341 -3.235396962 -0.075534763 KDS(ph)DDEKSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDSDDEKSDR 10 2 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 KDS(1)DDEKSDR;KDS(1)DDEKSDR;KDS(0.965)DDEKS(0.035)DR;KDS(1)DDEKSDR;KDS(1)DDEKSDR;KDS(0.999)DDEKS(0.001)DR 170.11 2.31E-06 2527150000 6228460 1625936 2431471 1602590 3886450 5448720 4210820 2600918 2927300 1373769 TRUE FALSE 6474364.41 1905177.86 2494837.132 1919577.519 3225832.617 4183337.356 3880764.925 2566056.948 2821947.045 1642932.733 3.940736148 1.159620124 1.518526645 1.168384731 1.963459947 2.546262103 2.362096054 1.561875844 1.717627866 1 20.64784198 4.747701702 24.77345658 1.724647854 3.940737461 0.662001136 0.48592709 702.1673005 1902913.318 0.121769742 1.506596055 55937.32608 -4.747701702 2.216089608 KDS(ph)DTESSDLFTNLNLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KDSDTESSDLFTNLNLGR 18 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 1 KDS(0.979)DT(0.007)ES(0.007)S(0.008)DLFTNLNLGR;KDS(0.996)DT(0.004)ESSDLFTNLNLGR;KDS(1)DTESSDLFTNLNLGR 189.09 2.11E-14 229666000 223513 157630 174778 158675 197047 278684 263996 189148 184022 153300 TRUE FALSE 232337.4658 184701.7263 179332.8583 190060.4414 163553.0213 213963.8645 243303.3037 186612.7804 177399.0842 183336.1999 1.267275453 1.007448209 0.978163933 1.036677107 0.89209344 1.167057377 1.327088179 1.017871978 0.967616239 1 17.48413215 1.491254008 24.99999919 0.986780192 1.088145574 0.12308377 0.124757222 1.938288204 3420.942849 0.070691298 0.032726168 30.99231429 -1.491254008 0.101365382 KDS(ph)EEEVSLLGSQDIEEGNHQVEDGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDSEEEVSLLGSQDIEEGNHQVEDGCR 27 1 Q9Y487 Q9Y487 ATP6V0A2 V-type proton ATPase 116 kDa subunit a isoform 2 1 KDS(1)EEEVSLLGSQDIEEGNHQVEDGCR 132.82 1.64E-05 207990000 119760 59033 96826 80320 124300 137010 104650 86636 102230 49091 TRUE FALSE 124488.2173 69171.45854 99349.3651 96207.05627 103171.5304 105191.5039 96447.25955 85474.78613 98550.76227 58709.44155 2.12041222 1.178199906 1.692221259 1.638698201 1.757324336 1.791730617 1.642789592 1.455895064 1.678618629 1 15.84130491 -0.507155439 0.520241301 0.889199206 1.668137195 0.436655726 0.226272116 8.713430405 1.992855587 1.954604304 0.098572838 0.311060282 0.507155439 0.778937989 KDS(ph)EGYSESPDLEFEYADTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSEGYSESPDLEFEYADTDK 21 1 Q5VSL9;Q5VSL9-4 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 KDS(0.899)EGYS(0.101)ESPDLEFEYADTDK;KDS(0.997)EGYS(0.002)ES(0.001)PDLEFEYADTDK 253.69 1.39E-36 242012000 318960 102651 169941 129915 282950 288690 343170 180487 239340 74604 TRUE FALSE 331552.7871 120280.5107 174369.8021 155611.7992 234854.2601 221646.1226 316271.4387 178067.867 230726.2002 89221.22542 3.716075245 1.348115431 1.954353364 1.74411188 2.632268936 2.484230872 3.544800435 1.995801628 2.586001247 1 16.44509934 3.214949336 24.97454783 2.478192948 2.113602293 0 0.831058328 832.0735364 880113.6138 0.227830583 0.272452566 1640.398396 -3.214949336 -0.364590656 KDS(ph)GSSSVFAESPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDS(0.967)GS(0.032)S(0.001)SVFAESPGGK;KDS(0.964)GS(0.034)S(0.001)SVFAESPGGK;KDS(0.78)GS(0.175)S(0.04)S(0.005)VFAESPGGK 225.83 3.99E-15 1240770000 2114960 977410 1425360 1027140 2267550 2031560 2319430 1687660 2097750 908970 TRUE FALSE 2198460.254 1145272.564 1462506.053 1230305.226 1882112.661 1559760.979 2137627.016 1665039.678 2022252.387 1087065.268 2.022381101 1.053545355 1.345370968 1.131767579 1.73137043 1.43483655 1.966420121 1.531683264 1.860286081 1 20.05200713 3.220812986 24.99028173 1.626702926 1.361293586 0.064508689 0.347016391 492.4036964 693347.8256 0.093172048 0.111584055 1662.696514 -3.220812986 -0.26540934 KDS(ph)IPQVLLPEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSIPQVLLPEEEK 14 1 Q15052-2;Q15052 Q15052-2 ARHGEF6 Rho guanine nucleotide exchange factor 6 1 KDS(1)IPQVLLPEEEK;KDS(1)IPQVLLPEEEK 118.46 0.0001497 116813000 460770 236924 273192 251388 429880 508060 501750 303204 331920 224226 TRUE FALSE 478961.5554 277613.854 280311.6079 301111.7961 356809.1511 390070.7647 462421.5239 299140.0463 319974.264 268158.7916 1.786111701 1.035259192 1.045319477 1.122886161 1.330589048 1.454626053 1.724431711 1.115533242 1.193226827 1 18.03272803 1.593129371 25 1.115714925 1.33308014 0.177311753 0.246628573 1.938694746 3280.016285 0.136881756 0.063788593 39.18585897 -1.593129371 0.217365214 KDS(ph)IPQVLLPEEEKLIIEETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KDSIPQVLLPEEEKLIIEETR 21 2 Q15052-2;Q15052 Q15052-2 ARHGEF6 Rho guanine nucleotide exchange factor 6 1 KDS(1)IPQVLLPEEEKLIIEETR;KDS(1)IPQVLLPEEEKLIIEETR;KDS(1)IPQVLLPEEEKLIIEETR 202.04 3.44E-22 205002000 242666 97701 163764 79361 277274 218447 191775 146028 204133 113469 TRUE FALSE 252246.6411 114480.3867 168031.8244 95058.36893 230143.0645 167715.9948 176743.1744 144070.7335 196786.2932 135701.0781 1.858840362 0.843621793 1.238249738 0.700498259 1.695956051 1.235922347 1.30244488 1.061677148 1.450145393 1 17.05007266 -0.59559381 0.017172369 1.79E-06 2.299154097 0.033561878 0.337196494 8672.022605 33.79252477 2457.079408 2072.977335 0.253750082 0.59559381 2.299152311 KDS(ph)ISEDEMVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSISEDEMVLR 12 1 Q8N5D0-5;Q8N5D0-3;Q8N5D0-6;Q8N5D0-2;Q8N5D0-4;Q8N5D0 Q8N5D0-5 WDTC1 WD and tetratricopeptide repeats protein 1 1 KDS(0.998)IS(0.002)EDEMVLR;KDS(0.993)IS(0.007)EDEMVLR 145.69 3.93E-05 464390000 251481 177163 202997 196263 296260 320810 252146 222172 244517 168090 TRUE FALSE 261409.6641 207589.3671 208287.2686 235083.2356 245901.831 246306.7394 232382.1377 219194.1477 235716.8809 201024.0172 1.30039021 1.03265953 1.036131262 1.169428603 1.22324603 1.225260259 1.15599191 1.090387859 1.172580691 1 17.61700835 -1.297972881 4.674807168 0.999922121 1.14902534 0.24862394 0.080607634 6.60E-05 9.92E-06 0.078759207 0.01855404 0.050353205 1.297972881 0.149103219 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 41 1 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(0.983)LDLEEEAAS(0.017)GASSALEAGGSSGLEDVLPLLQQADELHR;KDS(0.961)LDLEEEAAS(0.012)GAS(0.013)S(0.013)ALEAGGSSGLEDVLPLLQQADELHR;KDS(0.995)LDLEEEAAS(0.004)GASSALEAGGSSGLEDVLPLLQQADELHR;KDS(0.988)LDLEEEAAS(0.01)GAS(0.001)S(0.001)ALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHR 350.15 3.26E-154 2673145300 148594.4 106890.8 104275.9 113901.9 145920.5 196909.7 166223 113914.8 108288.5 86897.6 TRUE FALSE 154461.0217 125248.4634 106993.4156 136431.3559 121116.9855 151180.4064 153194.0069 112387.9584 104391.218 103923.521 1.486295116 1.205198421 1.029539941 1.312805365 1.165443438 1.454727524 1.474103317 1.081448717 1.004500397 1 16.66516269 1.569182943 6.248158686 1.01601991 1.290727402 0.458025911 0.13825438 0.131331118 10.40670912 0.080033805 0.037157344 37.08369008 -1.569182943 0.274707492 KDS(ph)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDSLDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 48 3 Q96TC7;H0YLG5;H0YMB1;Q96TC7-2 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR;KDS(1)LDLEEEAASGASSALEAGGSSGLEDVLPLLQQADELHRGDEQGKR 274.52 1.03E-86 1613340000 590508 296824 364526 252882 531423 571037 336190 319951 333227 241210 TRUE FALSE 613821.7118 347801.213 374025.847 302901.3048 441091.9083 438422.3109 309838.5493 315662.5802 321234.2254 288470.4813 2.127849301 1.205673494 1.29658274 1.050025304 1.529071212 1.519816894 1.074073673 1.094263021 1.113577458 1 18.13806417 4.739026416 24.00650288 1.217397493 2.127849781 0.70551066 0.177978454 12.54551359 646223.7675 0.044380651 0.261550192 54831.03153 -4.739026416 0.910452289 KDS(ph)LESDSSTAIIPHELIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDSLESDSSTAIIPHELIR 19 1 Q9UMX1-2;Q9UMX1-3;Q9UMX1 Q9UMX1-2 SUFU Suppressor of fused homolog 1 KDS(0.688)LES(0.174)DS(0.046)S(0.046)T(0.046)AIIPHELIR 56.468 0.04457 136800000 95394 71873 76865 89635 93009 98411 109270 76803 90024 62914 TRUE FALSE 99160.22878 84216.62866 78868.16505 107364.5355 77199.3634 75556.53668 100705.1319 75773.58141 86784.05383 75240.79374 1.31790514 1.119294793 1.048210168 1.426945811 1.026030688 1.004196433 1.338437925 1.007081101 1.153417575 1 16.19922745 4.265928921 0.021140637 3.32E-07 2.381314277 0.148875181 0.140195324 2357.823705 9.069845827 446.2081294 580.6514741 18447.13478 -4.265928921 2.381313945 KDS(ph)LSVNEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 1 KDS(0.958)LS(0.042)VNEFK 69.716 0.059473 36313000 129080 80994 103100 72035 144040 136320 123690 100480 116480 71462 TRUE FALSE 134176.1781 94904.08945 105786.8707 86283.308 119556.1322 104661.7459 113994.8546 99133.22995 112287.9076 85463.61068 1.569980217 1.11046197 1.237800157 1.009591185 1.398912722 1.2246352 1.333840844 1.159946662 1.313868051 1 16.38302265 -1.607310241 2.476587793 0.973545206 1.24886501 0.213399089 0.149029845 9496284.614 7939178.34 1625587.459 0.032921717 0.024699591 1.607310241 0.275319804 KDS(ph)LTQAQEQGNLLN ddPTM_MDA-MB-175_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(1)LTQAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN;KDS(0.999)LT(0.001)QAQEQGNLLN;KDS(0.991)LT(0.009)QAQEQGNLLN;KDS(0.986)LT(0.014)QAQEQGNLLN 204.07 5.39E-09 3772870000 6835620 4250220 5569170 4245700 7605150 7336000 6778780 5882230 6670170 3774910 TRUE FALSE 7105495.556 4980162.223 5714307.145 5085486.788 6312429.319 5632325.178 6247441.511 5803388.328 6430111.885 4514531.339 1.573916542 1.10314047 1.265758661 1.126470591 1.398246871 1.247599087 1.383851621 1.285490761 1.424314375 1 22.1061448 -0.855584319 5.162844709 0.999999628 1.301585749 0.325193444 0.134104608 5.26E-07 1.17E-07 0.118954966 0.02803792 0.139449089 0.855584319 0.301586121 KDS(ph)PHSR ddPTM_MDA-MB-175_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(0.771)PHS(0.229)R;KDS(0.992)PHS(0.008)R 73.499 0.029845 216822000 178392 107775 149149 96698 196479 178619 202006 157330 175437 111702 TRUE FALSE 185435.0539 126284.5179 153035.9455 115824.5758 163081.5698 137137.4442 186172.2419 155221.2487 169123.0566 133587.8682 1.38811298 0.945329239 1.14558266 0.86702915 1.220781287 1.026571096 1.393631355 1.161941206 1.266006104 1 17.02742947 2.283818002 24.99999425 1.219030654 1.089042798 0.088167194 0.163635905 251.168546 138743.4245 0.052487032 0.043913609 192.2285994 -2.283818002 -0.129987855 KDS(ph)QNSSQHSVSSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.998)QNS(0.001)SQHSVSSHR;KDS(0.688)QNS(0.156)S(0.156)QHSVSSHR;KDS(0.888)QNS(0.112)SQHSVSSHR;KDS(0.995)QNS(0.005)SQHSVSSHR;KDS(0.992)QNS(0.008)SQHSVSSHR;KDS(1)QNSSQHSVSSHR;KDS(0.796)QNS(0.102)S(0.102)QHSVSSHR 250.94 2.12E-19 757251300 73410 339865.9 362676.5 325320.3 434017.3 472778.7 354211.7 423801.4 363938 336036.7 TRUE FALSE 76308.28348 398235.2245 372128.1475 389667.6844 360243.1944 362983.012 326447.6614 418121.0354 350839.9425 401876.6576 0.18987986 0.990938929 0.925976019 0.969620099 0.896402385 0.903219944 0.812308093 1.040421302 0.873004032 1 18.61639326 4.741232904 24.99798869 0.933835486 0.189879595 0.923848812 0.064147747 57.83268842 540967.7831 0.014709812 0.101206988 55110.31632 -4.741232904 -0.743955892 KDS(ph)SSVVEWTQAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;Q8TC07;F8WCB5 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 KDS(0.912)S(0.032)S(0.056)VVEWTQAPK;KDS(0.945)S(0.052)S(0.003)VVEWTQAPK 229.96 6.68E-13 1268140000 1305720 581350 951930 528510 1471430 1064770 1119160 816630 1136510 487260 TRUE FALSE 1357270.834 681192.3402 976738.0778 633047.7006 1221316.854 817493.3042 1031437.315 805684.4106 1095607.227 582729.2678 2.329161943 1.168968812 1.676143849 1.086349589 2.095856381 1.402869822 1.770011173 1.382605019 1.88013077 1 19.15246625 -1.233192458 4.091741934 0.999560682 1.608833607 0.203070937 0.376861535 0.001350823 0.000253149 0.323264538 0.076140091 0.058453099 1.233192458 0.609272924 KDSETGENIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDSETGENIR 10 1 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ;;; 157.68 1.40E-05 1626260000 1525500 1436210 1445800 1422670 1508950 2171680 1613850 1296490 1528790 1434230 FALSE TRUE 1585727.918 1682867.895 1483478.736 1704069.88 1252459.218 1667340.232 1487352.22 1279112.672 1473769.147 1715239.909 0.924493367 0.981126831 0.864881191 0.993487775 0.730194774 0.972074066 0.867139467 0.745733973 0.859220415 1 20.70997895 3.268518233 24.99911662 0.848191036 0.938426796 0.155610263 0.085879212 328.8892186 274450.2264 0.023150782 0.031342289 1855.744717 -3.268518233 0.09023576 KDSGSS(ph)SVFAESPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDSGSSSVFAESPGGK 16 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 KDS(0.162)GS(0.208)S(0.315)S(0.315)VFAESPGGK 155.01 1.84E-07 131870000 251270 122780 171080 103590 290390 266730 295890 214180 266510 112580 TRUE FALSE 261190.3336 143866.5099 175538.4853 124079.7928 241029.6115 204785.9998 272697.3686 211309.2674 256918.3572 134637.8955 1.939946644 1.068543959 1.303782153 0.921581493 1.79020632 1.521013078 2.025413184 1.569463535 1.908217268 1 17.03872501 3.210707309 24.99900902 1.678442427 1.290991701 0.159543951 0.359148218 310.9838006 279114.5699 0.096790998 0.115710297 1624.453592 -3.210707309 -0.387450726 KDSLSVNEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSLSVNEFK 10 1 Q99584 Q99584 S100A13 Protein S100-A13 0 ; 167.2 8.52E-06 5719600000 8552700 5133900 7868600 6143700 11022600 10137200 10556600 7983900 8849000 5233300 FALSE TRUE 8890367.2 6015607.389 8073662.18 7358905.523 9148982.389 7782988.931 9729146.107 7876888.88 8530526.219 6258664.937 1.4204894 0.961164633 1.289997509 1.175794774 1.461810543 1.243554178 1.554508223 1.258557369 1.362994553 1 22.57742351 3.273446478 24.99402398 1.334817598 1.199535695 0.065716515 0.17487736 366.4317372 262528.1748 0.044221231 0.059873005 1876.923092 -3.273446478 -0.135281903 KDSNELS(ph)DS(ph)AGEEDSADLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDSNELSDSAGEEDSADLKR 20 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 2 KDS(0.15)NELS(0.85)DS(0.995)AGEEDS(0.005)ADLKR;KDS(0.218)NELS(0.782)DS(0.901)AGEEDS(0.099)ADLKR 95.519 0.0059736 302540000 1035990 377770 585300 382310 913480 902530 863550 616770 678630 304510 TRUE FALSE 1076891.685 442649.0589 600553.3988 457929.7769 758206.9959 692931.0855 795862.6945 608503.207 654206.2389 364172.9043 2.957088988 1.21549147 1.649088638 1.257451533 2.081997279 1.902752998 2.185397884 1.670918401 1.796416568 1 18.47426406 0.354281371 1.528604814 0.999979177 1.833647187 0.228525186 0.471765093 7.775021026 16.7715388 0.425817691 0.122245035 2.26090009 -0.354281371 0.833668009 KDSNELSDS(ph)AGEEDSADLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDSNELSDSAGEEDSADLKR 20 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KDS(0.002)NELS(0.211)DS(0.787)AGEEDSADLKR 109.39 0.00010341 120330000 101690 65873 92662 51262 126240 108220 97976 79456 101910 43234 TRUE FALSE 105704.7997 77186.17533 95076.84784 61401.4706 104781.7699 83087.54509 90296.38511 78391.02228 98242.27901 51704.87454 2.04438751 1.492822022 1.838837222 1.187537368 2.026535618 1.606957677 1.746380509 1.516124408 1.900058358 1 15.65801268 -1.466426381 4.610054676 0.997625567 1.684485938 0.410616746 0.252725746 0.005517222 0.00063857 0.218895953 0.051448997 0.034164386 1.466426381 0.686860371 KDSPHS(ph)R ddPTM_MDA-MB-175_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(0.137)PHS(0.863)R 66.682 0.041168 72865000 60338 34004 54059 31040 68195 69191 60948 50652 54849 36048 TRUE FALSE 62720.19083 39843.92249 55467.82195 37179.61935 56603.23826 53122.43885 56170.7365 49973.09279 52874.9952 43110.91542 1.454856391 0.924218892 1.286630576 0.862417766 1.312967672 1.232227113 1.302935369 1.15917494 1.226487415 1 15.39576558 KDTDDIES(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KDTDDIESPKR 11 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;Q9UPQ0-8;Q9UPQ0;Q9UPQ0-3;G5EA03;D6RD46;D6RJ93;D6R8Y0;Q9UPQ0-7;D6RGH8 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 KDTDDIES(1)PKR;KDTDDIES(1)PKR;KDT(0.002)DDIES(0.998)PKR;KDTDDIES(1)PKR 156 2.46E-05 2589170000 3562950 1085040 1690310 1055690 2733030 2760430 2653270 1828150 2111800 837480 TRUE FALSE 3703618.017 1271387.18 1734360.867 1264502.331 2268470.537 2119361.967 2445299.764 1803646.64 2035796.731 1001568.171 3.697819203 1.269396548 1.73164535 1.262522479 2.264918756 2.116043648 2.441471119 1.800822641 2.032609251 1 19.93382919 0.050957561 1.321154238 0.998087208 2.024708209 0.189231256 0.657798037 21.74612715 28.08341908 0.715390588 0.175421801 1.124495085 -0.050957561 1.026621001 KDTDFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDTDFEHR 8 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 128.27 0.00074051 110820000 296250 248490 296920 251530 358230 341300 307040 278130 339080 248470 FALSE TRUE 307946.1788 291166.2245 304657.9791 301281.8833 297338.1926 262038.2475 282973.4025 274402.1223 326876.577 297152.9393 1.03632217 0.979853086 1.025256489 1.013895013 1.000623427 0.881829566 0.952282024 0.923437348 1.100028079 1 18.18084613 2.976643525 24.50777657 0.959610022 1.011600535 0.098655692 0.055291366 1062.931909 1115327.636 0.016498252 0.017602507 947.6403081 -2.976643525 0.051990514 KDVFFYQADDEHYIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDVFFYQADDEHYIPR 16 1 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ; 159.88 5.83E-09 100651000 174507 164476 183851 176187 226000 234520 195524 203104 200853 185479 FALSE TRUE 181396.6711 192723.4736 188642.3081 211036.2627 187584.6007 180056.2842 180198.318 200381.7231 193624.3398 221820.0588 0.817764958 0.86882798 0.850429439 0.951384937 0.845661126 0.811722281 0.812362592 0.903352583 0.872889227 1 17.75903031 0.540469026 1.157757623 0.999759141 0.856798806 0.523383 0.040813674 1.379119345 2.571318756 0.0401899 0.01231609 3.471115189 -0.540469026 -0.142960336 KDVGRPQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KDVGRPQPGR 10 2 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 ;;;;; 178.46 1.25E-06 3216696000 1308219 1445783 1418028 1367643 1469941 1761493 1403053 1406448 1339606 1410166 FALSE TRUE 1359868.496 1694084.984 1454982.975 1638158.703 1220080.954 1352412.946 1293078.04 1387596.865 1291393.842 1686461.028 0.806344453 1.004520683 0.862743313 0.971358766 0.723456358 0.801923628 0.76674054 0.822786202 0.765741882 1 20.68556755 3.245448285 24.99936719 0.802315716 0.914440399 0.230470149 0.086041746 193.6324171 702800.3366 0.02173127 0.028786602 1759.739105 -3.245448285 0.112124683 KDVHMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDVHMPK 7 1 P46783;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;A0A2R8Y6L3;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 ; 73.931 0.030871 1373680000 1331450 898290 1359080 1012190 1841150 1600450 1776350 1461090 1647620 968640 FALSE TRUE 1384016.674 1052564.32 1394498.741 1212398.161 1528191.981 1228769.743 1637115.045 1441506.478 1588322.478 1158426.462 1.194738483 0.90861557 1.203787022 1.046590526 1.319196367 1.06072313 1.413223108 1.244365979 1.371103415 1 20.14373503 3.28089303 1.237861643 1.259460364 1.068663205 0.144676699 0.147147322 0.658349398 2.122216342 0.050203375 0.080786813 1909.382905 -3.28089303 -0.190797159 KDVLETFTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDVLETFTVK 10 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ; 169.89 1.08E-05 454230000 1746170 1300770 1599000 1225590 2289700 1886430 1763870 1631830 1782430 1427940 FALSE TRUE 1815110.14 1524167.129 1640671.254 1468008.044 1900497.612 1448335.222 1625613.26 1609957.988 1718280.692 1707717.503 1.062886652 0.892517132 0.960739262 0.859631667 1.112887587 0.848111716 0.951921648 0.942754282 1.00618556 1 20.70363791 1.235564482 24.6202154 1.003092815 0.950320345 0.0578322 0.078293696 181.4190853 1490616.374 0.058936914 0.017229098 17.2014272 -1.235564482 -0.05277247 KDWDDDQND ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KDWDDDQND 9 1 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;; 119.21 0.017722 10825910000 10120400 6941430 8862900 6751360 10997900 10737900 10522900 8492600 9405100 5985440 FALSE TRUE 10519961.21 8133566.606 9093874.455 8086758.857 9128480.886 8244185.459 9698087.602 8378770.588 9066612.288 7158172.37 1.46964346 1.136263027 1.270418479 1.129723963 1.275253014 1.151716532 1.354827336 1.170518137 1.266609942 1 22.77115985 -3.630594043 0.375560245 9.22E-15 1.245784372 0.344634388 0.102040776 195.3778115 4.050305914 154.2621956 0.062934594 0.000234102 3.630594043 1.245784372 KDWYDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KDWYDVK 7 1 P61247;E9PFI5;D6RG13;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 90.629 0.027255 3424500000 6096600 4648000 5962900 4271600 7362900 6781500 6466300 5579800 6340700 4399100 FALSE TRUE 6337298.476 5446257.844 6118298.073 5116509.731 6111356.888 5206599.4 5959454.509 5505011.908 6112499.446 5261019.419 1.204576142 1.035209607 1.162949152 0.972531999 1.161629791 0.989655993 1.132756608 1.046377416 1.161846965 1 22.32691094 -3.665684445 0.010140597 8.65E-07 2.021668555 0.106863957 0.077550909 24849.00871 24.00929236 2701.324221 2116.903878 0.000215931 3.665684445 2.02166769 KDYEEIGPSICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KDYEEIGPSICR 12 1 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 113.37 0.0018811 280340000 209600 169140 182750 183330 236300 228890 212830 169800 184320 166530 FALSE TRUE 217875.1698 198188.4793 187512.6151 219592.1268 196133.8104 175733.7664 196147.8285 167524.1087 177686.3592 199158.3651 1.093979506 0.995130077 0.941525178 1.10260057 0.984813318 0.882382049 0.984883705 0.841160293 0.892186272 1 17.60355655 2.926023725 5.032657191 0.910974083 1.026298417 0.422872954 0.061733234 0.202786237 9.432484596 0.018657798 0.020122438 843.3808295 -2.926023725 0.115324334 KEAEDSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEAEDSLRR 9 2 O43776;K7EIU7;O43776-2;K7EJ19;K7EPK2;K7EMQ6 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 103.34 0.0019336 96893000 230220 207070 262720 187650 291330 281790 253250 230900 257170 210470 FALSE TRUE 239309.2634 242632.6617 269566.699 224766.6099 241809.8307 216348.5431 233399.6033 227805.1632 247914.5019 251707.5668 0.950743223 0.963946634 1.070951908 0.892967235 0.960677638 0.859523398 0.927264946 0.905038995 0.984930668 1 17.94138906 3.708733616 24.99896774 0.925573253 0.992087247 0.237470081 0.0498659 836.0595643 700728.5121 0.012622986 0.019557687 5113.680802 -3.708733616 0.066513993 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEAESCDCLQGFQLTHSLGGGTGSGMGTLLLSK 33 1 Q3ZCM7;A0A075B736;Q5SQY0 Q3ZCM7 TUBB8 Tubulin beta-8 chain 0 ; 321.77 7.36E-105 3616600000 1806280 1497980 1975830 1268240 2352900 2200200 2008560 1871120 1953960 1680210 FALSE TRUE 1877593.329 1755246.412 2027321.753 1519094.087 1952954.898 1689236.894 1851123.819 1846040.697 1883637.361 2009414.98 0.934397995 0.873511161 1.008911436 0.755988236 0.971902229 0.840661044 0.921225251 0.918695598 0.937405852 1 20.93834411 0.891429287 1.101973713 0.999417483 0.898945758 0.172629632 0.066050391 1.031724799 2.508918436 0.056515798 0.017969795 7.788059963 -0.891429287 -0.100471726 KEAESSPFVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KEAESSPFVER 11 1 P14625 P14625 HSP90B1 Endoplasmin 0 ;;;;; 186.13 6.67E-06 5690900000 2843550 3014340 3247710 2941730 4207570 4012460 3207290 3092850 3239130 2741580 FALSE TRUE 2955815.55 3532029.447 3332347.991 3523595.414 3492368.754 3080626.974 2955894.229 3051395.405 3122554.344 3278740.11 0.901509559 1.077252032 1.016350146 1.074679693 1.065155711 0.939576444 0.901533555 0.930660956 0.952364091 1 21.64471012 2.723302793 23.02312753 0.936186522 1.031840179 0.370752476 0.052735304 258.6962231 390355.6947 0.016375526 0.015507678 528.8138162 -2.723302793 0.095653656 KECSEAMEVETSVISIDS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KECSEAMEVETSVISIDSPQK 21 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVISIDS(1)PQK 224.21 2.00E-25 156810000 380780 175080 256490 179470 347550 308030 327760 281340 320720 121670 TRUE FALSE 395813.4884 205148.6281 263174.3401 214968.6303 288473.5751 236494.7007 302069.3148 277569.0975 309177.3498 145508.907 2.720201097 1.409869899 1.808647632 1.477357193 1.982514893 1.625293638 2.075950682 1.907574617 2.124800167 1 17.15074794 4.752572178 24.21513837 1.765079481 2.720202109 0.444886012 0.333071446 1435.683397 2481118.179 0.073799344 1.481792264 56568.17629 -4.752572178 0.955122628 KECSEAMEVETSVISIDS(ph)PQKLAILDQELEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KECSEAMEVETSVISIDSPQKLAILDQELEHK 32 2 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KECSEAMEVETSVIS(0.003)IDS(0.996)PQKLAILDQELEHK 104.24 2.82E-06 37629000 81768 27634 58239 28355 83730 57090 57122 47733 61453 28908 TRUE FALSE 84996.26378 32379.92454 59756.75618 33963.53437 69497.60451 43831.71271 52644.62838 47093.21721 59241.31853 34571.96912 2.458531172 0.936594743 1.728474186 0.982400923 2.010229856 1.267839635 1.522754697 1.362179199 1.713565065 1 15.07731516 -3.429846248 0.18360704 2.00E-36 1.628707693 0.127508642 0.436686786 156.5473843 2.557441612 63.16850984 1.239465488 0.000371667 3.429846248 1.628707693 KEDESQMEDPSTS(ph)PSPGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEDESQMEDPSTSPSPGTR 19 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3;G3V314 H0YJN0 EVL Ena/VASP-like protein 1 KEDESQMEDPS(0.131)T(0.131)S(0.614)PS(0.123)PGTR 90.884 0.0013262 460030000 337570 254820 336320 250460 400710 410830 380780 325510 333310 274400 TRUE FALSE 350897.5243 298583.3528 345084.7755 300000.2405 332597.4573 315420.9587 350933.4686 321147.0709 321314.2382 328163.4263 1.069276757 0.90986176 1.051563788 0.914179389 1.013511655 0.96117036 1.069386289 0.978619325 0.979128728 1 18.32405493 KEDEVEEWQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEDEVEEWQHR 11 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;; 231.83 5.05E-13 1475860000 2310440 1646690 1979360 1813810 2501360 2634540 2821590 2102710 2348340 1613840 FALSE TRUE 2401657.955 1929496.198 2030943.748 2172576.204 2076179.721 2022708.012 2600426.403 2074526.612 2263823.702 1930041.049 1.244355894 0.9997177 1.052280079 1.125663211 1.075717908 1.048012949 1.347342537 1.074861394 1.172940701 1 20.8802001 KEDGTFYEFGEDIPEAPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;;; 220.1 4.77E-19 2805300000 3225900 2697300 3238330 2793090 3925170 4067510 3758760 3289220 3637250 2575530 FALSE TRUE 3353261.023 3160540.293 3322723.54 3345554.865 3257971.005 3122892.446 3464138.57 3245133.386 3506346.083 3080155.792 1.088666045 1.026097544 1.078751779 1.086164172 1.057729292 1.013874835 1.124663427 1.053561445 1.138366472 1 21.55457189 2.234666144 24.99997373 1.081857797 1.059208812 0.052914848 0.042020116 299.7181487 1923960.614 0.014343518 0.010976915 171.6588285 -2.234666144 -0.022648985 KEDIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEDIQK 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 91.065 0.077472 843490000 2411000 1313910 1957340 1359720 2453700 2213700 2464100 1860410 2164000 1184750 FALSE TRUE 2506188.142 1539563.822 2008349.888 1628668.558 2036620.95 1699601.724 2270957.403 1835474.247 2086118.063 1416879.079 1.76880877 1.086588012 1.417446215 1.149476043 1.437399268 1.199539007 1.602788436 1.295434645 1.472333168 1 20.43428521 4.75903751 24.16156521 1.318518954 1.768809462 0.375761426 0.180803213 3261.065401 3847773.173 0.038956456 1.580698464 57416.6051 -4.75903751 0.450290508 KEDIYAVEIVGGATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEDIYAVEIVGGATR 15 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 82.482 0.017474 266552000 348390 356640 392070 384720 417840 440870 421970 376060 397830 319620 FALSE TRUE 362144.7062 417890.1457 402287.6663 460816.4677 346815.706 338484.6239 388894.8888 371019.5308 383512.176 382243.4195 0.947419073 1.093256612 1.052438435 1.205557622 0.907316355 0.885521128 1.017401135 0.970636803 1.003319237 1 18.54413214 3.209965906 24.99999809 0.963218133 1.074408085 0.37345304 0.070198355 223.4046147 195319.2479 0.020273957 0.024236461 1621.682782 -3.209965906 0.111189952 KEDLELIMTEMEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEDLELIMTEMEISR 15 1 Q9NX55 Q9NX55 HYPK Huntingtin-interacting protein K 0 ;;; 169.98 1.87E-06 292112000 425230 408010 495317 418634 582926 578827 542815 491479 540129 387532 FALSE TRUE 442018.4087 478082.5436 508225.3679 501438.5557 483840.4467 444403.2015 500267.7419 484891.5279 520689.8628 463461.4757 0.953732795 1.031547537 1.096586005 1.081942259 1.04397123 0.958878407 1.079416021 1.046239123 1.123480354 1 18.8220899 KEDLRPSAPQQEGEASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KEDLRPSAPQQEGEASK 17 2 O76070 O76070 SNCG Gamma-synuclein 0 ;;;; 224.86 1.45E-15 8901410000 8579160 4556680 6606960 5138860 8241720 8376220 9928520 6967260 8008720 3615640 FALSE TRUE 8917871.861 5339254.344 6779142.805 6155311.17 6840795.378 6430969.848 9150296.659 6873875.276 7720487.732 4324055.432 2.06238611 1.234779347 1.56777426 1.423504223 1.582032304 1.487254257 2.116137687 1.589682506 1.785473811 1 22.04395359 KEDLVFIFWAPESAPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KEDLVFIFWAPESAPLK 17 1 G3V1A4;E9PQB7;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;; 184.15 1.04E-09 9810672000 14563830 9424600 13695730 9934801 16539930 15507860 16564240 13980390 15217000 8853515 FALSE TRUE 15138821.25 11043201.74 14052651.97 11899874.99 13728478.61 11906394.54 15265891.59 13793005.74 14669343.14 10588191.75 1.429783442 1.042973342 1.327200366 1.123881704 1.296583867 1.124497442 1.441784579 1.302678121 1.385443661 1 23.33595289 2.252372684 24.99984719 1.311950517 1.219336381 0.019335251 0.15190688 583.319827 1055808.273 0.047729575 0.039743705 178.8021284 -2.252372684 -0.092614136 KEDLVFIFWAPESAPLKS(ph)K ddPTM_MDA-MB-175_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(0.001)APLKS(0.999)K;KEDLVFIFWAPES(0.009)APLKS(0.991)K 150.94 3.68E-08 234110000 1627370 443880 864970 378020 1250730 1003700 803120 780550 931740 391830 TRUE FALSE 1691619.824 520112.9371 887511.8288 452791.2277 1038131.361 770605.8862 740169.3558 770088.004 898206.8594 468601.5865 3.609931919 1.109925686 1.893958225 0.966260552 2.215381662 1.644479892 1.579528062 1.643374726 1.916781516 1 18.83800231 4.747023369 24.96113862 1.591378827 3.609932953 0.708162902 0.395573474 534.9261849 1577745.236 0.085419126 0.989488517 55850.02464 -4.747023369 2.018554126 KEDLYLKPIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 ; 164.13 1.30E-05 14463300000 16296700 11356500 15248800 11986400 19890100 18911100 19042700 16367200 17316900 11314800 FALSE TRUE 16940106.3 13306890.53 15646196.26 14357274.14 16509187.91 14519283.63 17550083.42 16147824.46 16693668.15 13531718.43 1.251881377 0.983385119 1.156260851 1.061008934 1.220036317 1.072981507 1.296958957 1.193331397 1.233669489 1 23.68984173 2.952939638 1.538915015 1.190086269 1.109631581 0.015031299 0.104003536 0.889609954 4.298103314 0.036176429 0.041482523 897.3040698 -2.952939638 -0.080454688 KEDMEYALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KEDMEYALR 9 1 Q13242;H0YIB4 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;;;; 152.04 0.00013055 5123910000 9095380 5803990 6689960 5449110 8759970 10174520 8077810 6913310 7229880 5986610 FALSE TRUE 9454472.626 6800780.134 6864305.853 6526927.694 7270953.428 7811641.926 7444650.145 6820648.387 6969678.031 7159571.609 1.32053608 0.94988646 0.958759299 0.911636624 1.015557051 1.091076723 1.03981782 0.952661522 0.973476964 1 22.77144184 4.742583369 24.96516827 0.988147868 1.320536212 0.806840304 0.048797526 178.9144639 1110298.918 0.012823609 0.097396225 55281.95194 -4.742583369 0.332388343 KEDMMFHKIY(ph)IQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEDMMFHKIYIQK 13 2 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK;KEDMMFHKIY(1)IQK 72.958 0.013892 1284763000 51648.7 2468412 1559054 2079511 1111809 2790335 817133 1953807 1165911 4114746 TRUE FALSE 53687.83056 2892342.559 1599684.228 2490832.069 922824.1033 2142321.984 753083.9803 1927619.413 1123950.091 4920951.697 0.01091005 0.587760811 0.32507619 0.50616877 0.1875296 0.435347087 0.153036247 0.391716792 0.22840096 1 22.23050592 -1.335317418 3.047843074 1.006347935 0.325793562 0.605521421 0.165864217 18833953.27 24155986.24 1074447.338 0.036914127 0.04620432 1.335317418 -0.680554373 KEDMTYAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEDMTYAVR 9 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 122.69 0.00092792 1718820000 1624280 1603180 1758150 1523150 2460250 2144050 1962210 1752820 1738120 1989530 FALSE TRUE 1688407.829 1878513.694 1803968.833 1824424.524 2042057.584 1646126.881 1808406.853 1729326.315 1675565.401 2379340.312 0.709611744 0.789510305 0.75818025 0.766777461 0.858245277 0.691841715 0.760045482 0.726809152 0.70421427 1 21.1821302 -1.156474553 3.999316007 1.000103882 0.753259808 0.721871138 0.046229285 6427317.774 1862155.337 5801.744479 0.010567443 0.069746986 1.156474553 -0.246844074 KEDQYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KEDQYMK 7 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 124.98 0.0065635 547940000 1160910 764950 991850 834520 1473800 1315620 1415450 1101470 1229770 788750 FALSE TRUE 1206743.623 896324.212 1017698.426 999585.5652 1223284.002 1010087.193 1304503.33 1086706.596 1185510.818 943290.461 1.279291664 0.950210194 1.078881286 1.059679501 1.296826432 1.070812475 1.382928572 1.152038149 1.256782367 1 19.84734255 3.261304619 24.87237037 1.20470296 1.080948483 0.125468698 0.127458269 362.9756815 396940.0504 0.032393603 0.043829387 1825.175453 -3.261304619 -0.123754476 KEDVT(ph)S(ph)KLDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEDVTSKLDEK 11 2 Q9NQW6;Q9NQW6-2;H7C1K5 Q9NQW6 ANLN Actin-binding protein anillin 2 KEDVT(1)S(1)KLDEK 76.143 0.068351 62021000 11365 39289 38772 45829 24335 44441 36281 59341 47423 39223 TRUE FALSE 11813.69898 46036.58012 39782.43017 54893.83941 20198.54539 34120.25126 33437.20042 58545.63096 45716.25549 46907.99588 0.251848299 0.981422874 0.848094859 1.170244825 0.430599198 0.727386677 0.712825176 1.248094911 0.974594089 1 15.51754624 1.751467425 24.99999147 1.089674379 0.750961839 0.275659804 0.252682437 5.038655605 9774.716966 0.114346048 0.063410805 56.42446183 -1.751467425 -0.338712541 KEECPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KEECPAVR 8 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;;;; 158.76 0.00058226 5166890000 5758470 5867030 5328910 5943330 6543040 7269390 6740240 5430790 5318580 4476520 FALSE TRUE 5985818.842 6874646.763 5467785.772 7118902.935 5430856.398 5581184.341 6211922.376 5357999.143 5127165.345 5353608.386 1.118090531 1.284114614 1.021327183 1.329739201 1.014429149 1.042508891 1.160324388 1.000820149 0.957702726 1 22.35208018 2.380420539 0.602143532 0.977981622 1.186626357 0.333615606 0.09898862 0.910241895 0.667437604 0.081844451 0.066730062 240.1156896 -2.380420539 0.208644734 KEEEDDDMKELENWAGSM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEEEDDDMKELENWAGSM 18 2 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 111.33 0.0012235 50857000 235740 86984 125900 81503 192160 200670 191000 125070 168830 66154 FALSE TRUE 245047.1972 101922.8254 129181.0574 97624.05014 159496.7118 154067.4337 176028.9209 123393.6412 162753.8413 79115.60971 3.097330579 1.288277064 1.632813776 1.233941703 2.015995483 1.94737087 2.224958154 1.559662394 2.057164722 1 16.27167475 -1.193973781 6.89417846 0.999997648 1.847987121 0.212123523 0.510351182 1.72E-05 2.01E-06 0.461032666 0.108666139 0.063977346 1.193973781 0.847989473 KEEEESQPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEEEESQPAKK 11 2 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 84.289 0.0090399 104650000 77311 36956 54429 35992 88125 65026 70276 50112 67253 24226 FALSE TRUE 80363.29798 43302.90552 55847.46445 43111.11017 73145.54398 49924.69698 64767.58349 49440.33061 64832.57767 28972.62087 2.773766942 1.494614717 1.927594494 1.487994834 2.524643674 1.723168132 2.235475478 1.70645006 2.237718775 1 14.82240258 -1.177644654 4.827845214 0.999895556 1.975323209 0.35102604 0.410185152 0.000412333 7.02E-05 0.355085679 0.083685649 0.066428638 1.177644654 0.975427653 KEEELQAALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KEEELQAALAR 11 1 P35579;P35749;P35749-2;P35749-4;P35749-3;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 P35579;P35749;Q7Z406 MYH9;MYH11;MYH14 Myosin-9;Myosin-11;Myosin-14 0 ;;;; 215.72 2.02E-11 3593160000 3312450 2709940 3021160 2785980 3659580 3683500 3928800 3069820 3144400 2384460 FALSE TRUE 3443228.084 3175351.115 3099893.912 3337038.529 3037525.899 2828062.949 3620850.39 3028674.084 3031233.658 2851649.284 1.207451457 1.1135139 1.087053001 1.170213514 1.065182144 0.99172888 1.269739028 1.062078041 1.062975617 1 21.44336513 -5 0.103144709 0.637173484 1.18780997 0.227569103 0.074207666 296.6780645 2.068761441 23.04333175 1.116426534 1.00E-05 5 0.550636486 KEEELQGALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEEELQGALAR 11 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ; 119.39 0.00095111 186779000 178565 152295 186464 161364 216700 217960 201112 169836 184024 161884 FALSE TRUE 185614.8841 178450.4816 191323.405 193281.3176 179865.4114 167342.0932 185348.3159 167559.6262 177401.0122 193602.0703 0.958744314 0.921738498 0.98823016 0.998343237 0.929046942 0.864361073 0.957367427 0.865484682 0.916317743 1 17.56273486 3.013521403 20.62866786 0.910188193 0.964908129 0.192156963 0.042416476 37.64991933 57436.01463 0.011706913 0.013974851 1031.62392 -3.013521403 0.054719935 KEEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEEEMR 6 1 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;H0Y961;B1AMS2;Q14141-2;Q14141-4;Q14141;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;B1AMS2;A0A087X142 SEPT11;SEPT6;SEPT8 Septin-11;Septin-6;Septin-8 0 ; 91.041 0.077516 903490000 1215150 1148870 1343390 1151710 1661500 1583920 1520550 1274860 1318570 1436750 FALSE TRUE 1263125.06 1346179.486 1378399.847 1379514.8 1379078.823 1216078.585 1401365.318 1257772.587 1271114.923 1718253.654 0.735121417 0.78345795 0.802209757 0.802858645 0.802604912 0.707741015 0.815575346 0.732006351 0.739771407 1 20.7125116 -1.439590131 3.304050504 1.003237656 0.769896988 0.788356503 0.035898138 16390830.42 22558958.04 497348.2303 0.008518123 0.036342087 1.439590131 -0.233340668 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KEEENADSDDEGELQDLLSQDWR 23 1 Q96NB3;J3QQQ3 Q96NB3 ZNF830 Zinc finger protein 830 1 KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR 269.59 4.47E-45 1876750000 558336 368018 445564 346615 590101 617434 542907 403802 516213 318515 TRUE FALSE 580379.5364 431222.2287 457175.7639 415174.4125 489795.8428 474044.3108 500352.5307 398389.6947 497634.595 380921.9159 1.523618128 1.132048881 1.20018236 1.089919994 1.285816915 1.244465837 1.313530437 1.045856586 1.306395285 1 18.53913577 -5 0.10681126 0.33467823 1.350750454 0.249889969 0.127513191 259.4006766 1.857315802 38.5878882 1.686141735 1.00E-05 5 1.016072225 KEEESAGGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEEESAGGTK 10 1 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 122.45 0.00078295 158970000 259260 159450 204660 150010 264180 253810 241820 225380 216370 117210 FALSE TRUE 269495.785 186834.2972 209993.6077 179681.5303 219274.778 194866.474 222865.5165 222359.1497 208582.886 140175.0554 1.922565925 1.332864087 1.498081147 1.281836699 1.56429243 1.39016513 1.589908532 1.586296143 1.488017147 1 17.09687011 -1.641490986 2.143354653 0.913006558 1.51055356 0.45855038 0.16843929 897367.0982 606988.026 428962.4218 0.041287717 0.022830163 1.641490986 0.597547002 KEEEVER ddPTM_MDA-MB-175_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 ; 98.392 0.018113 1986960000 1538560 1115290 1365780 1094110 1799570 1695550 1699600 1421170 1499960 940440 FALSE TRUE 1599303.537 1306832.382 1401373.349 1310521.692 1493679.734 1301784.209 1566380.911 1402121.541 1445976.733 1124701.212 1.421980807 1.161937382 1.245996122 1.16521764 1.32806804 1.157448925 1.392708476 1.246661358 1.285654107 1 20.10111036 -1.382871322 4.154438396 0.99928097 1.2633723 0.450417478 0.088482117 0.000535359 7.95E-05 0.077834078 0.0182966 0.041412236 1.382871322 0.26409133 KEEGEAFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEEGEAFAR 9 1 P61019;P61019-2;H7C125 P61019 RAB2A Ras-related protein Rab-2A 0 ; 123.51 0.00089088 941910000 641660 589480 631130 574510 808860 820740 746440 648320 609000 507590 FALSE TRUE 666993.2323 690718.6045 647577.7663 688146.3633 671370.2661 630135.5734 687932.0823 639630.3308 587082.209 607042.5421 1.098758631 1.137842172 1.066774932 1.133604839 1.105969054 1.038041866 1.133251847 1.053682875 0.967118724 1 19.2114381 1.43590515 3.748222849 0.985281555 1.10076879 0.703011012 0.030551937 0.11399547 2.889822756 0.021277749 0.00755064 27.28381841 -1.43590515 0.115487235 CGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVKLLSISGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 CGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGK 38 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.001)GPVHIS(0.001)GQHLVAVEEDAES(0.998)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK;CGS(0.021)GPVHIS(0.02)GQHLVAVEEDAES(0.956)EDEEEEDVKLLS(0.002)ISGK;CGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVKLLSISGK 395.08 5.81E-180 5630983000 226330.9 739604.5 958555.6 646815.4 1270178 1303214 739002.7 1201463.6 969173.6 726726.4 TRUE FALSE 235266.6187 866625.8196 983536.3464 774753.5556 1054273.597 1000562.299 681077.7373 1185359.946 934293.2315 869114.5241 0.270696913 0.997136506 1.131653331 0.891428614 1.213043354 1.15124333 0.783645559 1.363870828 1.074994383 1 19.72918677 4.739300095 3.60729921 1.088568317 0.176836584 0.708219115 0.153982171 0.143304094 3.383399663 0.036300534 0.353515598 54865.5952 -4.739300095 -0.911731733 down KEELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEELLK 6 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ; 89.55 0.080234 2581900000 3972700 2368600 3420200 2440000 4844100 4247600 4628300 3561500 4124100 2772700 FALSE TRUE 4129545.264 2775388.625 3509333.222 2922624.717 4020701.612 3261159.273 4265521.752 3513763.918 3975674.447 3315957.478 1.245355313 0.836979558 1.058316714 0.881381844 1.212531113 0.983474394 1.286362018 1.059652888 1.19895218 1 21.66099408 3.230375193 24.99997198 1.126593963 0.997242605 0.152710649 0.135475115 292.7372445 894078.3613 0.035556344 0.043187679 1699.711421 -3.230375193 -0.129351358 KEELMFFLWAPELAPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEELMFFLWAPELAPLK 17 1 P60981;P60981-2;F6RFD5 P60981 DSTN Destrin 0 ;;; 123.41 8.61E-05 1849340000 2059110 1516950 2168200 1552080 2925230 2758560 2664230 2154930 2537190 1847430 FALSE TRUE 2140405.253 1777474.362 2224705.073 1859076.792 2428000.449 2117926.246 2455400.691 2126046.688 2445877.028 2209398.537 0.968772821 0.804505992 1.00692792 0.84144022 1.09894182 0.958598555 1.111343494 0.962273964 1.107032971 1 21.07522225 3.238837466 24.9999995 1.033903233 0.905455341 0.434257675 0.074913601 6.783633842 612520.9685 0.019215133 0.024478988 1733.155245 -3.238837466 -0.128447892 KEELTLEGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEELTLEGIR 10 1 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3KTB5;J3KTN0 P60842;J3KTN0 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;; 116.54 0.0017268 3458750000 3564360 2855400 3828550 3194970 5026560 4694120 4616690 3957320 4378770 2991060 FALSE TRUE 3705083.685 3345792.738 3928325.158 3826925.53 4172147.127 3603981.77 4254821.774 3904278.598 4221178.923 3577100.94 1.035778343 0.935336406 1.098186835 1.069839961 1.166348727 1.007514697 1.18946092 1.091464475 1.180055859 1 21.7703594 4.189608713 9.674159555 1.105636251 0.985711826 0.323599769 0.066043136 0.324708615 61.61752444 0.014941554 0.032491741 15474.21808 -4.189608713 -0.119924425 KEENLADWYSQVITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEENLADWYSQVITK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 186.68 5.96E-07 1132930000 2470790 1557260 2050440 1672680 2822330 2662950 2570100 2195360 2557430 1596960 FALSE TRUE 2568338.697 1824707.291 2103876.151 2003531.112 2342591.355 2044520.22 2368648.846 2165934.79 2465388.594 1909853.736 1.344782927 0.955417295 1.101590196 1.049049502 1.226581549 1.070511412 1.24022526 1.134084118 1.290878221 1 20.86503072 3.243326849 24.9965566 1.166040966 1.100680529 0.031113223 0.12075742 353.6403109 1854653.506 0.031269911 0.040990022 1751.164116 -3.243326849 -0.065360436 KEEPS(ph)PLNLSHHTPDHQGEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEEPSPLNLSHHTPDHQGEGR 21 1 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 KEEPS(1)PLNLSHHTPDHQGEGR;KEEPS(1)PLNLSHHTPDHQGEGR 219.43 1.91E-25 370260000 155402 392900 445980 378020 456220 549810 421530 480940 450950 400200 TRUE FALSE 161537.391 460377.5187 457602.6052 452791.2277 378671.8874 422124.96 388489.3771 474493.786 434720.3976 478611.5277 0.337512537 0.961902278 0.956104437 0.946051655 0.791188397 0.881978255 0.811700836 0.991396484 0.908294875 1 18.86849562 4.741568348 24.99951202 0.91227109 0.337512327 0.869669313 0.067224853 95.08716843 790301.8797 0.016265197 0.114906777 55152.89935 -4.741568348 -0.574758763 KEEPSNNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEEPSNNVK 9 1 Q14974;Q14974-2;J3KTM9;J3QRG4 Q14974 KPNB1 Importin subunit beta-1 0 ; 174.98 8.70E-05 441520000 776190 473310 685220 468930 937290 895560 774980 664930 753760 449810 FALSE TRUE 806834.5805 554597.3107 703077.3961 561682.9544 777969.7806 687579.7623 714235.0426 656017.701 726632.3248 537941.6574 1.499855179 1.030961821 1.306977042 1.044133591 1.446197315 1.278167907 1.327718411 1.219496003 1.350764186 1 19.03709019 -1.001976317 4.755478865 0.999997752 1.268321379 0.250214183 0.143578351 0.024025847 41187064.45 455.7138433 0.030419387 0.09954597 1.001976317 0.268323627 KEEQEVQATLESEEVDLNAGLHGNWTLENAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEEQEVQATLESEEVDLNAGLHGNWTLENAK 31 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 312.3 8.28E-93 105760000 71640 45345 73520 45096 83993 77565 86106 64639 78261 44677 FALSE TRUE 74468.40252 53132.65101 75435.9916 54015.8542 69715.89986 59551.70426 79356.78672 63772.61993 75444.4019 53430.60276 1.393740641 0.994423575 1.411849908 1.010953488 1.304793438 1.114561715 1.485230984 1.193559807 1.412007314 1 15.70537867 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGK 41 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;; 304.09 2.78E-97 1813407500 430504.7 355758.3 571252.6 428824.6 671032.9 611908 626732.6 636330 603251.3 394024.2 FALSE TRUE 447501.358 416857.0206 586139.912 513644.826 556970.9673 469801.6406 577607.6612 627801.0372 581540.4036 471225.6979 0.949653977 0.884622851 1.243862367 1.090018707 1.18196221 0.996977972 1.225755861 1.332272497 1.234101633 1 18.84605869 4.242959792 24.99986847 1.178437595 0.917138321 0.467814622 0.103920908 90.14246247 512247.9686 0.026953783 0.068711949 17496.84691 -4.242959792 -0.261299275 KEES(ph)DEEETASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(0.998)DEEET(0.002)ASK;KEES(0.831)DEEET(0.168)AS(0.001)K;KEES(1)DEEETASK;KEES(0.972)DEEET(0.027)ASK;KEES(1)DEEETASK 241.08 1.90E-16 2692660000 5954192 1571573 2540807 1657935 4086055 4464822 4051154 2537605 2816105 935298 TRUE FALSE 6189268.098 1841478.438 2607022.518 1985869.595 3391508.831 3427934.756 3733613.964 2503592.556 2714753.931 1118551.736 5.533287286 1.646306003 2.330712505 1.775393601 3.032053612 3.064618869 3.337900112 2.238244755 2.427025809 1 20.09320056 4.747457988 24.88031192 2.422411951 5.533288996 0.661704489 0.686206145 671.9949728 1879101.388 0.160496919 1.940791074 55905.94432 -4.747457988 3.110877045 KEES(ph)DEEETASKAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEESDEEETASKAER 15 2 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(1)DEEETASKAER 152.13 1.51E-06 419990000 739460 286370 421840 200850 713280 620180 367750 433620 492510 275680 TRUE FALSE 768654.4518 335551.8199 432833.4969 240577.5305 592036.9204 476152.5939 338924.7941 427808.0332 474784.6613 329694.2178 2.331416235 1.017766772 1.312833145 0.729698968 1.795715207 1.444224885 1.027997386 1.297590343 1.440075791 1 18.33076906 4.745924313 24.78371141 1.243122103 2.331416817 0.573257948 0.284990191 563.1116184 1895190.713 0.065585207 0.680971617 55708.86532 -4.745924313 1.088294714 KEES(ph)EES(ph)DDDMGFGLFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 43 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 2 KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD;KEES(1)EES(1)DDDMGFGLFD 199.15 9.06E-12 41540596000 54707240 25710571 34839233 26762603 49658808 57870481 45930487 37011990 39724883 21659217 TRUE FALSE 56867124.08 30126161.57 35747172.03 32056165.99 41217821.55 44430938.82 42330335.41 36515904.81 38295192.22 25902925.88 2.195393846 1.163040875 1.380043791 1.237550003 1.591241922 1.71528649 1.634191273 1.409721241 1.478411836 1 24.62661173 0.4174483 1.241343846 0.999964506 1.523965833 0.257378633 0.273581488 3.891101588 6.915233297 0.252141729 0.075452791 2.614859149 -0.4174483 0.524001327 KEES(ph)EESDDDMGFGLFD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387;P05386 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 KEES(0.955)EES(0.045)DDDMGFGLFD;KEES(0.794)EES(0.206)DDDMGFGLFD;KEES(0.715)EES(0.285)DDDMGFGLFD;KEES(0.732)EES(0.268)DDDMGFGLFD;KEES(0.642)EES(0.358)DDDMGFGLFD;KEES(0.75)EES(0.25)DDDMGFGLFD 153.21 1.95E-07 1914479000 3380780 1890469 2380120 1859002 3410600 3482880 3306280 2631650 2799110 1663351 TRUE FALSE 3514255.805 2215142.345 2442147.882 2226707.047 2830867.43 2674033.904 3047125.134 2596377.036 2698370.578 1989252.782 1.766621033 1.113554982 1.227670965 1.119368573 1.423080795 1.344240374 1.531793828 1.305202164 1.356474452 1 20.92379519 -0.817274656 6.613740014 0.999999995 1.343128704 0.248005437 0.184134072 1.26E-08 2.67E-09 0.169111887 0.039860054 0.152308922 0.817274656 0.343128709 KEES(ph)PPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KEESPPPPK 9 1 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 KEES(1)PPPPK;KEES(1)PPPPK;KEES(1)PPPPK 72.089 0.02924 1229610000 3816600 1600310 2328760 1564720 3471340 3313540 3072380 2370590 2714870 1422090 TRUE FALSE 3967282.315 1875150.794 2389449.399 1874216.946 2881282.867 2544020.552 2831558.827 2338816.119 2617162.359 1700721.308 2.332705715 1.102562063 1.404962346 1.102012974 1.694153447 1.495847991 1.664916418 1.375190696 1.538854336 1 20.69771532 -1.828215609 0.772500152 0.633678694 1.497336231 0.178954221 0.33199451 515.1731251 75.93066575 346.7267221 0.104034744 0.014851981 1.828215609 0.863657536 KEESDEEET(ph)ASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEESDEEETASK 12 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KEES(0.396)DEEET(0.507)AS(0.098)K 204.35 2.21E-07 151220000 247430 70609 120500 63662 186850 216840 187720 125290 133700 46462 TRUE FALSE 257198.7275 82735.54649 123640.329 76254.15359 155089.3037 166482.1962 173006.0159 123610.6925 128888.1631 55565.33933 4.628761932 1.488977616 2.225134058 1.372333086 2.79111593 2.996151886 3.113559963 2.224600695 2.31957844 1 15.76189762 KEESEES(ph)DDDMGFGLFD ddPTM_MDA-MB-175_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(0.067)EES(0.933)DDDMGFGLFD;KEESEES(1)DDDMGFGLFD;KEES(0.021)EES(0.979)DDDMGFGLFD;KEES(0.286)EES(0.714)DDDMGFGLFD;KEES(0.038)EES(0.962)DDDMGFGLFD;KEES(0.019)EES(0.981)DDDMGFGLFD;KEES(0.317)EES(0.683)DDDMGFGLFD;KEES(0.071)EES(0.929)DDDMGFGLFD;KEES(0.233)EES(0.767)DDDMGFGLFD;KEES(0.004)EES(0.996)DDDMGFGLFD;KEESEES(1)DDDMGFGLFD;KEES(0.008)EES(0.992)DDDMGFGLFD;KEES(0.076)EES(0.924)DDDMGFGLFD;KEES(0.117)EES(0.883)DDDMGFGLFD;KEES(0.247)EES(0.753)DDDMGFGLFD;KEES(0.17)EES(0.83)DDDMGFGLFD;KEES(0.195)EES(0.805)DDDMGFGLFD 263.08 2.35E-27 7939800000 7314474 4392612 5847407 4223936 7719503 8002149 7667887 6140585 6711953 4150942 TRUE FALSE 7603255.082 5147008.941 5999795.23 5059417.934 6407344.637 6143771.168 7066857.981 6058280.502 6470391.123 4964239.61 1.531605176 1.036817186 1.208603069 1.01917279 1.290700115 1.237605686 1.423552958 1.220384385 1.303400245 1 22.24314132 KEESEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEESEKPR 8 2 P83916;J3KS05;K7ELA4 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 99.802 0.0036867 657870000 896160 545310 736590 543820 1043290 911190 998320 838870 934020 536317 FALSE TRUE 931541.0888 638962.7506 755786.1405 651385.9729 865951.9385 699579.9317 920069.0698 827626.3198 900404.8027 641398.0477 1.452360343 0.996203142 1.178341816 1.015572116 1.350100677 1.09071104 1.434474385 1.290347426 1.403815939 1 19.29086044 2.250049626 24.99406673 1.309215663 1.172276609 0.0682035 0.17115068 425.7160897 926134.6587 0.055099043 0.045733986 177.8482621 -2.250049626 -0.136939053 KEESHSNDQSPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEESHSNDQSPQIR 14 1 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 116.58 0.00022913 198402000 91673 137598 119402 127580 136844 171197 122597 133668 131019 159723 FALSE TRUE 95292.32083 161229.3861 122513.7142 152814.9432 113583.3058 131439.0913 112987.5268 131876.3991 126303.6518 191017.6638 0.498866539 0.844054853 0.641373744 0.800004252 0.594622003 0.688099146 0.591503029 0.690388504 0.661214514 1 17.54334653 -1.935365503 2.523840287 1.224861938 0.672548875 0.523768196 0.094934807 11207052.07 5929740.192 14844507.88 0.021388346 0.011604715 1.935365503 -0.552313063 KEETPGT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEETPGTPK 9 1 Q99442 Q99442 SEC62 Translocation protein SEC62 1 KEET(0.002)PGT(0.998)PK;KEET(0.095)PGT(0.905)PK 119.25 0.00050227 918990000 4971000 2064100 2422600 3338000 4034500 5257100 4879600 2871900 3141200 1758080 TRUE FALSE 5167258.918 2418593.119 2485734.946 3998246.437 3348717.131 4036218.197 4497124.202 2833406.878 3028148.826 2102542.116 2.457624454 1.150318512 1.182252155 1.901624899 1.592699193 1.919684827 2.138898512 1.347610046 1.440232185 1 21.00370327 1.109575739 1.655491565 1.032449416 1.711638072 0.255355902 0.390077564 0.508900213 2.726114356 0.362613648 0.10625963 12.86991678 -1.109575739 0.679188656 KEFSPFGTITSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEFSPFGTITSAK 13 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YAP2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ; 196.95 2.21E-07 1936090000 3368700 2527500 3443500 2563300 4136700 3932400 3653300 3306000 3646300 2733700 FALSE TRUE 3501698.877 2961578.464 3533240.439 3070313.089 3433545.212 3019159.696 3366944.8 3261688.478 3515070.375 3269316.175 1.071079911 0.905870924 1.080727666 0.939130058 1.050233452 0.923483547 1.029862093 0.997666883 1.075169909 1 21.64055748 1.300946248 24.32458692 1.037585211 0.997965585 0.058764771 0.060216735 117.275507 45725.35128 0.035314228 0.012895756 19.99614364 -1.300946248 -0.039619626 KEGGLGPLNIPLLADVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEGGLGPLNIPLLADVTR 18 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ; 129.02 3.54E-05 4557100000 12903400 3438600 4824500 3633300 5891500 8456600 5665500 4799500 4885000 3706800 FALSE TRUE 13412836.2 4029152.801 4950230.433 4351955.896 4890064.934 6492682.811 5221423.306 4735170.553 4709189.804 4433076.489 3.025627063 0.908884115 1.116658024 0.981701062 1.103086073 1.464599771 1.177832893 1.068145466 1.062284807 1 22.07987682 4.742229361 24.99992296 1.110374529 3.02562779 0.942595181 0.142671875 78.74211569 536550.1148 0.035261441 0.263448579 55236.9081 -4.742229361 1.915253261 KEGGLGPLNIPLLADVTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEGGLGPLNIPLLADVTRR 19 2 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 167.45 1.01E-11 516330000 317100 337390 373440 245420 564820 454270 245680 323080 428270 570210 FALSE TRUE 329619.3529 395334.108 383172.1532 293963.3435 468812.0981 348772.677 226422.9596 318749.6411 412856.6464 681931.7322 0.483361218 0.57972681 0.561892247 0.431074446 0.687476585 0.511448083 0.332031711 0.467421629 0.605422254 1 19.37926779 0.857218993 4.102836287 0.999942482 0.505105747 0.732511749 0.089182495 0.481609586 13.0718073 0.089461218 0.022829209 7.198118524 -0.857218993 -0.494836735 KEGITGPPADSSKPIGPDDAIDALSSDFT(ph)CGSPTAAGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGKK 39 3 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;A0A0C4DGB5;E7EVY3 P20810-6;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 KEGITGPPADSSKPIGPDDAIDALSSDFT(0.6)CGS(0.343)PT(0.058)AAGKK 175.74 1.91E-19 525240000 482770 162950 302200 209090 415040 383320 330380 270510 408610 147790 TRUE FALSE 501830.1324 190935.3949 310075.5803 250447.3779 344491.649 294299.7393 304483.9523 266884.2559 393904.2059 176746.6209 2.839262951 1.080277484 1.754350825 1.416985381 1.949070637 1.665094007 1.722714419 1.509982225 2.228637832 1 17.43132311 -1.977062929 2.976995928 0.365810828 1.742331467 0.206891386 0.456852306 6884619.793 33311553.62 29769129.27 0.10422574 0.010542341 1.977062929 1.376520639 KEGITGPPADSSKPIGPDDAIDALSSDFTCGS(ph)PTAAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGK 38 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0YA91;A0A0C4DGB5;E7EVY3 P20810-6;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 KEGITGPPADSSKPIGPDDAIDALSSDFT(0.011)CGS(0.96)PT(0.029)AAGK 127.81 7.21E-09 253690000 241710 122980 183580 117480 264740 194830 211290 165120 184960 85818 TRUE FALSE 251252.8974 144100.8583 188364.2456 140717.1934 219739.5894 149583.6852 194728.5377 162906.8365 178303.3257 102632.394 2.448085713 1.404048495 1.835329356 1.371079713 2.141035406 1.457470486 1.897339915 1.587284775 1.737300659 1 16.64712664 -2.378577868 0.270922736 3.87E-15 1.821981265 0.353632763 0.318419626 44.53879893 1.526761655 27.4070147 0.369946813 0.004182367 2.378577868 1.821981265 KEGVFAK ddPTM_MDA-MB-175_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 ; 82.426 0.03932 2554100000 4656800 2941100 3814900 3585400 6245700 5335600 5375300 4294800 4986900 3189600 FALSE TRUE 4840654.06 3446211.046 3914319.428 4294581.419 5184058.145 4096487.762 4953969.94 4237235.231 4807422.443 3814541.051 1.269000384 0.903440545 1.026157374 1.125844855 1.359025391 1.073913665 1.298706679 1.110811281 1.260288559 1 21.86307806 3.478664301 24.99565973 1.191337866 1.054269788 0.137295106 0.130741545 90.28209793 1462484.244 0.033347367 0.045796857 3010.677945 -3.478664301 -0.137068078 KEIHTVPDMGK ddPTM_MDA-MB-175_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 ; 114.82 0.00078326 2188330000 3294400 2433200 2996100 2235600 4515800 3804400 3630200 3045400 3221900 2556400 FALSE TRUE 3424465.456 2851083.172 3074180.827 2677795.007 3748205.929 2920885.756 3345655.438 3004581.394 3105944.448 3057277.635 1.120102871 0.932556187 1.005528838 0.875875641 1.225994619 0.955387801 1.09432503 0.982763672 1.015918349 1 21.54381614 5.799907828 13.8028088 1.018919932 1.123685153 0 0.096236225 0 0 0.019495648 0 630823.4476 -5.799907828 0.104765221 KEKPELSEPSHLNGPSS(ph)DPEAAFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 KEKPELSEPSHLNGPS(0.045)S(0.955)DPEAAFLSR;KEKPELSEPSHLNGPS(0.041)S(0.959)DPEAAFLSR;KEKPELSEPS(0.002)HLNGPS(0.429)S(0.569)DPEAAFLSR;KEKPELSEPSHLNGPS(0.064)S(0.936)DPEAAFLSR 269.74 2.69E-54 2985770000 1764360 1686700 2192490 1520805 2868950 2538280 2234380 2289430 2383430 1580880 TRUE FALSE 1834018.295 1976377.604 2249628.091 1821615.69 2381286.904 1948802.938 2059243.457 2258743.936 2297650.82 1890623.168 0.970060203 1.045357762 1.189887085 0.963500141 1.259524872 1.030772801 1.089187677 1.194708694 1.215287562 1 20.85043041 5.938991396 0.822988681 1.128627546 1.60E-14 0.177552273 0.094693495 22.6257667 2.561382019 0.029639585 36.57099283 868943.215 -5.938991396 -1.128627546 KEKT(ph)PELPEPSVK ddPTM_MDA-MB-175_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 217.11 1.26E-09 1931990000 3387200 801050 1262650 698160 2218910 2167920 2012180 1337110 1510960 563760 TRUE FALSE 3520929.271 938624.1062 1295555.696 836253.9642 1841740.471 1664453.435 1854460.074 1319188.228 1456580.845 674217.9782 5.222241746 1.392167128 1.921568007 1.240331749 2.731669179 2.468717075 2.750534892 1.956619773 2.160400482 1 19.36285557 0.488418134 0.856218958 0.991808036 2.411334536 0.151930014 1.044834916 3.429341402 3.781499131 1.008591808 0.325705979 3.079059875 -0.488418134 1.4195265 KELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 34 2 Q01105-2 Q01105-2 SET Protein SET 1 KELNSNHDGADET(0.5)S(0.5)EKEQQEAIEHIDEVQNEIDR 105.89 1.58E-05 94047000 47812 28519 44177 33322 52748 59769 64307 47071 50645 22451 TRUE FALSE 49699.65468 33416.9164 45328.28891 39912.99214 43781.9138 45888.55556 59266.4493 46440.09024 48822.29634 26849.8436 1.85102213 1.244585142 1.688214263 1.486526057 1.630620813 1.709080926 2.207329405 1.729622374 1.818345651 1 14.71262606 2.783028776 3.331145956 1.781545719 1.555923575 0 0.317394705 0.586023925 13.27202469 0.096583155 0.09952291 606.7765334 -2.783028776 -0.225622145 KELNYFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KELNYFAK 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 120.99 0.002329 1600360000 2347540 2145010 2368410 1697410 3489500 3037100 2628200 2248320 2361970 2467500 FALSE TRUE 2440222.692 2513398.782 2430132.71 2033152.632 2896356.036 2331779.553 2422194.816 2218184.948 2276963.161 2950959.382 0.826925205 0.851722595 0.823505984 0.688980216 0.981496409 0.79017677 0.820816048 0.751682643 0.771600983 1 21.49275263 4.010118841 23.48053968 0.814601768 0.838896532 0 0.092064109 694.0959705 1610570.264 0.021771947 0.046928542 10235.73047 -4.010118841 0.024294764 KELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KELQAEATVSGSPEAPGTNVVSEPR 25 1 Q9BZV1-2;Q9BZV1;K7EJ02 Q9BZV1-2 UBXN6 UBX domain-containing protein 6 1 KELQAEATVS(0.008)GS(0.992)PEAPGTNVVSEPR;KELQAEATVS(0.133)GS(0.867)PEAPGTNVVSEPR 244.44 5.60E-39 796860000 269151 212486 268519 227095 318370 320650 276730 290907 307007 248565 TRUE FALSE 279777.2893 248978.8176 275516.8257 272013.7132 264253.5811 246183.897 255039.1795 287007.8675 295957.878 297266.5527 0.941166394 0.83756082 0.926834261 0.915049846 0.888944884 0.828158751 0.857947782 0.965489945 0.995597639 1 18.18139762 1.600920004 4.291955968 0.992959681 0.884187979 0.646357579 0.034961044 0.104497597 4.341046517 0.02082387 0.009308646 39.89514101 -1.600920004 -0.108771702 KELS(ph)PAGSISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KELSPAGSISK 11 1 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 KELS(1)PAGSISK 147.36 2.16E-05 202640000 891820 488070 710930 439440 946120 820920 874480 685150 800690 394240 TRUE FALSE 927029.7422 571892.2258 729457.4198 526359.9204 785298.8603 630273.7712 805935.9726 675966.6849 771873.3233 471483.7798 1.966196467 1.212962673 1.547152736 1.116390304 1.665590406 1.336787814 1.709360973 1.433700827 1.637115329 1 18.84684861 -1.153668444 4.380444868 0.999904191 1.497304168 0.291776028 0.238942821 0.000203248 3.93E-05 0.206530146 0.048670122 0.070199102 1.153668444 0.497399977 KELSDIAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 6907860000 6667900 7109940 7580710 7088010 9949930 9762680 8767170 8187190 7864160 7755680 FALSE TRUE 6931153.841 8331016.887 7778269.53 8489997.222 8258644.453 7495445.525 8079976.307 8077454.11 7581130.418 9275257.005 0.747273508 0.898197956 0.838604205 0.915338218 0.890395215 0.808111896 0.871132337 0.870860409 0.817349904 1 23.14495583 -2.171341051 2.43733173 1.377416694 0.855730221 0.464740738 0.047771482 3145326.628 866163.5793 6576133.211 0.011018346 0.006739985 2.171341051 -0.521686473 KEMQPTHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 106.16 0.001357 3770260000 3030885 2768014 3216725 2820116 3646365 3677819 3537354 3431625 3303543 2596997 FALSE TRUE 3150546.68 3243398.872 3300555.496 3377926.528 3026557.18 2823701.275 3260086.95 3385629.68 3184649.133 3105828.84 1.014398038 1.044294145 1.062697163 1.08760872 0.974476488 0.909161908 1.049667293 1.090088944 1.025378183 1 21.5665469 -1.090501877 3.279624227 0.999966729 1.031979844 0.023402391 0.051597349 10327285.31 19110946.54 3919.092408 0.013579007 0.081189174 1.090501877 0.032013115 KENALVQMADGNQAQLAMSHLNGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KENALVQMADGNQAQLAMSHLNGHK 25 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20;K7EK45 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 116.38 0.00052652 167650000 139800 146760 158610 158700 236610 191310 204130 194200 173080 146200 FALSE TRUE 145319.4119 171964.8884 162743.5069 190090.3863 196391.1167 146881.1518 188129.7572 191597.0666 166850.8846 174845.0908 0.831132354 0.983527118 0.930786825 1.087193157 1.12322923 0.840064489 1.075979636 1.095810387 0.954278349 1 17.41571776 5.265639108 1.006197216 1.028891329 0.476378421 0.305688314 0.082647755 5.724683671 2.227909508 0.024931742 4.394626953 184348.2877 -5.265639108 -0.552512908 KENPLQFK ddPTM_MDA-MB-175_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 ; 169.44 0.00048265 4940200000 6044900 4451900 5563000 4309600 7726800 6547100 6787400 5340200 5998200 4680300 FALSE TRUE 6283557.32 5216479.194 5707976.35 5162026.017 6413401.296 5026635.247 6255385.852 5268623.354 5782325.954 5597315.175 1.12260202 0.931960955 1.019770403 0.922232509 1.145799566 0.898043989 1.117568987 0.941276878 1.033053486 1 22.41630356 4.762547423 23.54033901 1.001309193 1.122602334 0.17872321 0.078149806 4986.70236 4893708.984 0.016510328 0.920000509 57882.519 -4.762547423 0.121293141 KENQWCEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KENQWCEEK 9 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;;; 158.05 0.0001076 2944190000 2238710 1289860 1772740 1266780 2514590 2232320 2183300 1674160 2087750 1218330 FALSE TRUE 2327095.999 1511383.421 1818939.061 1517345.303 2087160.89 1713897.511 2012167.241 1651720.624 2012612.285 1457038.437 1.597141119 1.03729825 1.248380972 1.041390031 1.432467968 1.176288468 1.38099805 1.133614997 1.381303495 1 20.47460751 -1.480590623 3.194100507 0.994498255 1.253555842 0.176434236 0.171693298 4060175.323 3908599.735 139991.7968 0.035962911 0.03306811 1.480590623 0.259057586 KENSETTLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KENSETTLTR 10 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 0 ;; 171.49 6.42E-06 657530000 466067 475169 512810 389385 587150 605870 599250 514460 532380 458041 FALSE TRUE 484467.685 556775.5794 526174.2499 466404.1908 487346.4527 465165.8745 552279.2192 507564.5052 513219.7478 547785.3642 0.884411517 1.01641193 0.960548208 0.851436021 0.889666801 0.849175434 1.008203678 0.926575514 0.936899343 1 19.06325119 2.227375793 24.99997382 0.959683997 0.912409661 0.22563695 0.052674607 444.3190397 993120.7717 0.020869708 0.015553381 168.8013025 -2.227375793 -0.047274336 KEPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEPAITSQNSPEAR 14 1 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR;KEPAITSQNS(1)PEAR 201.61 1.08E-08 1884670000 1591360 1340580 1512540 1362100 1853270 1923010 1770630 1556490 1628290 1279970 TRUE FALSE 1654188.122 1570814.187 1551958.035 1631519.315 1538251.827 1476420.071 1631843.394 1535627.797 1569688.161 1530755.615 1.080635018 1.026169149 1.01385095 1.065826118 1.004897067 0.964504103 1.06603783 1.003182861 1.025433548 1 20.54581254 7.998805728 1.037695837 1.017436242 81.38313377 0.295113936 0.028763042 2486.922306 2.835390442 0.008176642 475697.5656 99725386.53 -7.998805728 80.36569753 KEPAVLELEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEPAVLELEGK 11 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 145.6 0.0027144 0 297780 196830 256480 197560 369300 317350 339110 251690 273180 179740 FALSE TRUE 309536.5843 230634.0214 263164.0795 236636.7783 306526.5179 243650.272 312529.6721 248316.5072 263348.3052 214956.6117 1.439995643 1.072932903 1.224266039 1.100858338 1.425992509 1.133485823 1.453919792 1.155193624 1.225123075 1 17.71368596 -0.896688727 7.58863216 1 1.242269517 0.228040416 0.136510746 3.55E-09 2.34E-10 0.119143186 0.028082318 0.126856076 0.896688727 0.242269517 KEPAVLELEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEPAVLELEGKK 12 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 122.34 0.00020263 190780000 395000 285180 345780 242990 503990 420230 356840 308810 390330 222430 FALSE TRUE 410594.905 334157.4466 354791.3109 291052.6967 418321.9598 322637.9511 328869.9484 304670.9071 376282.0995 266010.8998 1.54352662 1.256179528 1.333747268 1.094138236 1.572574508 1.212874929 1.23630253 1.145332418 1.414536396 1 18.02112584 -5 0.092658152 0.092668872 1.520525848 0.300535604 0.148220819 256.7224891 1.644985301 46.33234023 3.020578141 1.00E-05 5 1.427856976 KEPEKPIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEPEKPIDR 9 2 O00422;O00422-2;U3KQ12 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 120.09 0.00040573 523320000 834490 462700 651590 451180 852420 752600 842390 664520 751680 393880 FALSE TRUE 867436.3096 542165.1257 668570.9707 540422.0574 707525.9529 577820.0558 776361.2706 655613.1963 724627.1836 471053.2447 1.841482506 1.150963573 1.419310828 1.147263209 1.502008448 1.226655505 1.6481391 1.391802739 1.538312689 1 18.84553062 -1.99970749 2.886174592 0.584262164 1.416548135 0.273958003 0.208821066 55328006.5 50191904.28 152876667.3 0.045809568 0.010006738 1.99970749 0.832285971 KEPQEPEVCPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEPQEPEVCPTK 12 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 0 45.257 0.081003 192370000 17356 131310 148960 71138 169620 146860 106760 113450 133530 148820 FALSE TRUE 18041.22828 153861.471 152842.02 85208.88407 140788.053 112753.9907 98391.87223 111929.3883 128724.2814 177978.4297 0.101367499 0.864495048 0.8587671 0.478759613 0.791039977 0.633526158 0.55283032 0.628892999 0.723257766 1 17.44134288 -4.999999969 0.2855948 3.760567722 0.613880149 0.232434149 0.210277563 363.924623 3.454524181 597.0413839 0.218517622 1.00E-05 4.999999969 -3.146687574 KEPVDEDLYPEHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEPVDEDLYPEHYR 14 1 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 77.562 0.01579 135540000 229060 197120 240010 194270 280890 263950 285400 235590 254290 190420 FALSE TRUE 238103.4657 230973.8266 246264.8578 232696.0262 233144.4181 202651.6127 263029.6022 232432.3014 245138.1526 227729.1532 1.045555487 1.014247949 1.081393639 1.02181044 1.02377941 0.889879973 1.155010672 1.020652376 1.076446073 1 17.79695947 KEQQLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEQQLQER 8 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 125.97 0.001987 173951000 221300 202983 240580 201439 286530 291460 242770 240430 247960 235640 FALSE TRUE 230037.0949 237843.7513 246849.7124 241283.033 237825.7329 223772.8321 223741.053 237207.4291 239035.968 281809.1464 0.81628683 0.843988757 0.875946418 0.856193051 0.843924819 0.794058089 0.79394532 0.841730768 0.84821934 1 18.10435891 0.578883483 2.26871837 0.999988618 0.833419993 0.804568975 0.024511873 1.698440134 8.594850844 0.026008523 0.007030128 3.792132318 -0.578883483 -0.166568624 KEQSEVSVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KEQSEVSVS(1)PR;KEQSEVSVS(1)PR;KEQSEVSVS(1)PR;KEQS(0.002)EVS(0.032)VS(0.966)PR 178.03 4.73E-06 2643885000 3236381 2642147 3100027 2674820 3684220 3826513 3460447 3308375 3341003 2480572 TRUE FALSE 3364155.821 3095915.194 3180816.25 3203891.412 3057977.6 2937863.347 3189208.122 3264031.645 3220760.955 2966592.59 1.134013424 1.043592978 1.072212026 1.079990364 1.030804705 0.990315744 1.075040817 1.100262859 1.085676869 1 21.50037538 -1.578474937 0.005509151 6.09E-07 2.071558502 0.171392556 0.038723378 53789.92867 46.81634546 9155.813674 8457.732614 0.026395206 1.578474937 2.071557893 KEQTADGVAVIPVLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEQTADGVAVIPVLQR 16 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;H0YEY4 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 88.551 0.0097675 251750000 216590 218970 253830 227140 306670 309630 299520 270570 249340 210430 FALSE TRUE 225141.1404 256576.3941 260445.0183 272067.6141 254542.3429 237723.125 276042.8398 266943.4517 240366.3021 251659.7296 0.894625218 1.019536954 1.034909394 1.081093167 1.011454409 0.944621237 1.096889201 1.060731696 0.955124217 1 17.94111485 4.738534697 4.318646204 1.029546728 0.884608368 0.394729329 0.047059283 0.205108969 9.089859098 0.011427091 0.091475471 54768.98562 -4.738534697 -0.14493836 KEQTPEHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KEQTPEHGK 9 1 O76021;J3QSV6;O76021-2 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 ; 97.597 0.0042737 139169000 295420 171193 264640 166163 301790 271350 312640 241742 261001 158688 FALSE TRUE 307083.4097 200594.0661 271536.7358 199029.5455 250491.8436 208333.0748 288134.4599 238501.8439 251607.625 189779.8753 1.618103127 1.056982811 1.430798367 1.048738941 1.319907304 1.09776168 1.518256134 1.256728847 1.325786649 1 17.53396749 4.759292839 24.26467089 1.249449854 1.618103664 0.32270093 0.16689866 3996.855296 4677745.437 0.036175486 1.504654913 57450.37113 -4.759292839 0.36865381 KES(ph)APPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KESAPPSLR 9 1 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI41;F8VWY3;C9JEB6 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 KES(0.998)APPS(0.002)LR 67.519 0.037161 150050000 94877 73554 81975 77378 123270 113950 91128 84269 96723 75557 TRUE FALSE 98622.81722 86186.32733 84111.33584 92683.13745 102316.6094 87486.83943 83985.14924 83139.51189 93241.95812 90360.94752 1.091431862 0.953800615 0.930837249 1.025699044 1.132310055 0.968193028 0.929440777 0.920082338 1.03188336 1 16.46341178 2.503497646 24.96148317 0.956673693 1.020653823 0.152920772 0.062970381 1264.042078 1196233.779 0.021349301 0.020066067 318.7848296 -2.503497646 0.06398013 KES(ph)APQVLLPEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 137.43 1.30E-05 552450000 2704710 996390 1648640 1128670 2545580 2517540 3038380 1830100 2375770 941890 TRUE FALSE 2811494.039 1167512.232 1691604.913 1351917.557 2112883.221 1932879.489 2800223.836 1805570.503 2290266.502 1126435.312 2.495921434 1.036466293 1.501732851 1.200173275 1.875725307 1.715925867 2.485916241 1.602906517 2.033198425 1 20.10333304 3.191731866 24.99791302 1.845140549 1.517219041 0.036465719 0.502620209 291.8340655 155784.4969 0.136289443 0.162897486 1555.005274 -3.191731866 -0.327921508 KES(ph)APQVLLPEEEKIIVEETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KESAPQVLLPEEEKIIVEETK 21 2 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 KES(1)APQVLLPEEEKIIVEETK 180.71 2.76E-17 87897000 213440 92793 144230 73190 263220 191520 189980 139170 193340 82922 TRUE FALSE 221866.776 108729.4759 147988.7523 87666.76355 218477.9584 147042.3825 175088.8712 137304.6538 186381.7312 99168.97826 2.237259876 1.096406132 1.492288767 0.884013984 2.203087722 1.482745765 1.765560907 1.38455247 1.879435832 1 16.59760127 -1.484781306 6.495672266 0.999743141 1.570675535 0.155737888 0.415035729 0.001418878 0.000112541 0.369323907 0.087012608 0.032750557 1.484781306 0.570932395 KESEDQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KESEDQKR 8 2 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 0 ; 69.954 0.029575 20694900 96309 54273 64731 50112 87290 86032 85689 61017 68659 76293 FALSE TRUE 100111.3537 63593.96556 66417.94304 60024.00403 72452.47698 66052.37183 78972.47227 60199.16692 66187.976 91241.15263 1.097217109 0.696987749 0.727938448 0.657861089 0.794076739 0.7239318 0.865535671 0.659780868 0.725418017 1 16.47739705 4.743611588 24.86293267 0.747239848 1.097217266 0.500408746 0.099814934 362.866125 1786112.185 0.021521284 0.181123243 55412.99049 -4.743611588 0.349977418 KESETSREDEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KESETSREDEYK 12 2 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YHI8 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 172.57 1.99E-05 110560000 140880 70661 96955 71377 150740 144720 129420 109950 131390 63846 FALSE TRUE 146442.0512 82796.47708 99481.72695 85495.15756 125117.2686 111110.9733 119275.7222 108476.3001 126661.2996 76355.40129 1.917900354 1.084356518 1.302877403 1.119700193 1.638617131 1.455181577 1.56211244 1.420676183 1.658838765 1 16.22044259 3.225021671 24.99965395 1.479832632 1.332981173 0.023808671 0.273626025 682.184737 1259651.297 0.073840512 0.088709656 1678.88779 -3.225021671 -0.14685146 KESYSIYVYK ddPTM_MDA-MB-175_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 7770300000 16179370 13118010 15663580 12892520 19208410 18668980 17367270 15713060 16874230 12656150 FALSE TRUE 16818144.02 15370926.17 16071785.76 15442621.98 15943371.33 14333392.33 16005978 15502452.13 16266929.76 15135880.28 1.111144097 1.015529054 1.061833568 1.020265865 1.053349461 0.946981085 1.057485769 1.024218734 1.074726376 1 23.85146925 4.744563765 24.33794708 1.029187505 1.11114415 0.331968494 0.035248816 534.7675068 2167959.827 0.007863755 0.072395137 55534.61497 -4.744563765 0.081956644 KESYSVYVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 142.1 5.83E-05 56778730000 37606970 30952830 36900740 28662160 46930460 41807680 42922740 37520550 38010240 29364050 FALSE TRUE 39091722.21 36268737.77 37862403.6 34331449.7 38953237.17 32098479.92 39558343.48 37017648.4 36642258.89 35117373.39 1.113173294 1.032786176 1.078167299 0.977620089 1.109229803 0.914034189 1.12646077 1.054112105 1.043422539 1 25.06568161 5.940699715 1.647553503 1.040767441 3.693905925 0.121122814 0.059632184 119.830984 10.76780763 0.014376269 1115.097001 872367.9776 -5.940699715 2.653138484 KET(ph)ES(ph)EAEDNLDDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 237.32 8.08E-20 1753870000 3978300 1070850 1799830 1058320 2947880 3565950 2760210 1830680 2176410 920220 TRUE FALSE 4135366.356 1254760.157 1846735.048 1267652.537 2446800.411 2737812.155 2543857.528 1806142.729 2098081.429 1100519.49 3.757649358 1.140152599 1.678057558 1.151867412 2.223314019 2.487745269 2.311506112 1.641172869 1.906446408 1 20.06975327 4.750438205 24.88401337 1.786234192 3.757650625 0.600913409 0.494395626 1263.728929 2647509.975 0.120263911 1.995427486 56290.90168 -4.750438205 1.971416434 KET(ph)PPPLVPPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KETPPPLVPPAAR 13 1 Q9BQA1;Q9BQA1-2 Q9BQA1 WDR77 Methylosome protein 50 1 KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR;KET(1)PPPLVPPAAR 66.022 0.033403 2523220000 2579560 1539780 2105420 1587780 2807630 2771380 2636080 2162360 2346670 1327500 TRUE FALSE 2681403.021 1804225.237 2160288.975 1901838.145 2330390.055 2127768.996 2429457.161 2133377.101 2262213.805 1587598.208 1.688968283 1.13644953 1.360727773 1.197934172 1.467871432 1.340244014 1.530272048 1.34377646 1.424928419 1 20.59841441 -1.582688936 6.527638516 0.999285195 1.378655348 0.375737861 0.149572596 0.001420217 9.08E-05 0.132188759 0.031102085 0.02614033 1.582688936 0.379370154 KET(ph)PSAPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KETPSAPAK 9 1 P49454 P49454 CENPF Centromere protein F 1 KET(0.909)PS(0.091)APAK 67.519 0.035553 216850000 1150700 476480 767170 475770 1136100 993130 1088400 765830 897810 426370 TRUE FALSE 1196130.525 558311.7335 787163.0804 569875.886 942986.1278 762490.6085 1003088.364 755565.3015 865497.9935 509909.0382 2.345772354 1.094924176 1.543732355 1.11760303 1.849322246 1.495346329 1.967190791 1.481764874 1.697357624 1 18.95988038 KETES(ph)EAEDNLDDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KET(0.08)ES(0.92)EAEDNLDDLEK;KET(0.25)ES(0.75)EAEDNLDDLEK;KET(0.433)ES(0.567)EAEDNLDDLEK;KETES(1)EAEDNLDDLEK;KET(0.113)ES(0.887)EAEDNLDDLEK;KET(0.013)ES(0.987)EAEDNLDDLEK;KET(0.123)ES(0.877)EAEDNLDDLEK;KET(0.31)ES(0.69)EAEDNLDDLEK 284.45 5.99E-36 18720590000 19509310 5877610 9388040 5446760 15127070 16070450 14315090 9538320 11082540 4251780 TRUE FALSE 20279552.62 6887043.796 9632700.035 6524112.871 12555776.04 12338331.54 13193035.84 9410474.422 10683681.55 5084834.886 3.988242112 1.354428207 1.894397803 1.283053043 2.469259342 2.426496005 2.594584905 1.850694198 2.101087211 1 22.2777695 0.411770761 1.182245213 0.999819576 2.188745813 0.204204288 0.724207296 4.329573708 7.13818115 0.664401859 0.200526881 2.580897527 -0.411770761 1.188926237 KETQS(ph)PEQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.001)QS(0.999)PEQVK;KET(0.003)QS(0.997)PEQVK;KETQS(1)PEQVK;KET(0.001)QS(0.999)PEQVK;KET(0.004)QS(0.996)PEQVK;KET(0.004)QS(0.996)PEQVK;KET(0.005)QS(0.995)PEQVK;KET(0.005)QS(0.995)PEQVK 230.96 5.57E-10 17506620000 13582110 5883370 8731120 6123920 11065150 11204020 12980570 8841070 9735190 3979700 TRUE FALSE 14118342.19 6893793.031 8958660.16 7335213.098 9184299.755 8602056.154 11963119 8722569.918 9384822.414 4759446.019 2.966383511 1.448444421 1.882290528 1.541190523 1.929699322 1.807365 2.513552829 1.832685964 1.971830834 1 22.18236223 0.051775875 2.096245175 0.999952939 1.963084516 0.326426427 0.424445496 90.47095146 195.8600166 0.385298767 0.103541521 1.126615897 -0.051775875 0.963131577 KETQS(ph)PEQVKSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KETQSPEQVKSEK 13 2 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 1 KETQS(1)PEQVKSEK;KET(0.002)QS(0.998)PEQVKSEK;KET(0.198)QS(0.802)PEQVKSEK;KET(0.025)QS(0.975)PEQVKSEK;KET(0.021)QS(0.979)PEQVKSEK 207.53 2.77E-08 3348070000 3694100 1444158 2312700 1024204 3963660 2874530 2294150 2120340 2800430 1248599 TRUE FALSE 3839945.92 1692180.903 2372970.862 1226788.494 3289918.489 2206963.971 2114328.528 2091920.31 2699643.071 1493238.068 2.571556406 1.133229147 1.589144365 0.821562563 2.203210968 1.477971945 1.415935324 1.400928864 1.807912033 1 20.51001276 7.999999589 0.036773083 1.33E-09 3.92905853 0.132588178 0.473973487 2282.903954 6.405741306 196.7812122 582.7168007 99999905.46 -7.999999589 3.929058529 KETS(ph)FGSSENITMTSLSK ddPTM_MDA-MB-175_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(0.137)S(0.722)FGS(0.138)S(0.003)ENITMTSLSK 192.63 1.01E-14 138720000 414980 330910 438860 284050 562250 489700 455280 414020 476000 282950 TRUE FALSE 431363.7308 387741.2184 450297.0521 340234.2422 466678.9458 375974.5965 419593.9639 408470.7391 458868.853 338388.6351 1.274758328 1.145845865 1.330709739 1.005454105 1.379121216 1.111073356 1.239976525 1.207105372 1.35604097 1 18.36832159 -1.477816603 4.739398952 0.999255333 1.22222747 0.274361199 0.110803149 0.000768523 8.47E-05 0.094570485 0.022217511 0.033280006 1.477816603 0.222972137 KETSFGS(ph)SENITMTSLSK ddPTM_MDA-MB-175_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(0.03)S(0.03)FGS(0.886)S(0.053)ENITMTSLSK 246.59 1.63E-24 148040000 407090 306470 422540 269510 483580 465120 405920 342770 408410 266550 TRUE FALSE 423162.2275 359103.8385 433551.7395 322818.2736 401381.2443 357102.929 374102.9297 338175.7288 393711.4039 318775.3691 1.327462121 1.126510619 1.360054074 1.012682613 1.259135063 1.120233756 1.173562847 1.06085903 1.235074733 1 18.28218063 7.999999936 0.056488323 0.763500603 1.967330044 0.294003226 0.100469268 456.3666105 1.932126861 8.786168454 45.98566547 99999985.27 -7.999999936 1.203829441 KETTSGTSTEPVKNSS(ph)PAPPQPAPGK ddPTM_MDA-MB-175_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(0.16)S(0.84)PAPPQPAPGK;KETTSGTSTEPVKNS(0.16)S(0.84)PAPPQPAPGK 138.4 4.04E-06 553900000 264359 127937 185932 116891 267698 238734 230849 182436 228782 99381 TRUE FALSE 274796.0974 149909.1845 190777.5407 140011.6909 222194.7896 183291.6465 212754.4522 179990.7438 220548.1805 118852.8042 2.312070795 1.2613012 1.605158094 1.178025978 1.869495559 1.542173513 1.790066744 1.514400481 1.855641371 1 16.85881642 -1.299541845 4.477519718 0.999539064 1.630896024 0.285349479 0.309930887 0.001290836 0.000201937 0.271628149 0.063978107 0.050171624 1.299541845 0.63135696 KETVESHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KETVESHFR 9 1 O94886 O94886 TMEM63A CSC1-like protein 1 0 132.78 0.0001918 66827000 175990 173300 181730 171750 270840 256610 227890 174800 179300 205110 FALSE TRUE 182938.2211 203062.9269 186466.0331 205721.6374 224802.7135 197016.2165 210027.3863 172457.0919 172847.028 245297.3774 0.745781398 0.827823473 0.760163174 0.838662197 0.916449723 0.803172943 0.856215376 0.703053142 0.704642788 1 17.90417228 5.556434411 1.894634911 0.811967105 2.62E-14 0.050916488 0.0869099 73.41890143 23.81950267 0.022122951 216.9705109 360109.3614 -5.556434411 -0.811967105 KEVEGDDVPESIMLEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEVEGDDVPESIMLEMK 17 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 120.24 0.00012969 45500000 113200 69501 87639 64815 137040 110520 106630 86754 99614 56046 FALSE TRUE 117669.2234 81437.25611 89922.94434 77635.21355 113745.9897 84853.40495 98272.06197 85591.20453 96028.9116 67027.14063 1.755545922 1.214989262 1.341590041 1.158265336 1.697013906 1.265955912 1.466153278 1.276963387 1.432686979 1 16.03245777 -3.185734712 0.334372905 1.67E-10 1.404642992 0.293391982 0.186829191 119.6135753 3.179248777 83.98672863 0.144217253 0.000652027 3.185734712 1.404642992 KEVEVVEIIQATIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KEVEVVEIIQATIIR 15 1 Q14764;H3BQK6;I3L155 Q14764 MVP Major vault protein 0 ;; 188.27 4.91E-07 616301000 1001313 740782 919455 872707 1079213 1122396 1109660 994857 1091335 658040 FALSE TRUE 1040845.61 868005.546 943416.7526 1045325.84 895768.7597 861736.5391 1022681.95 981522.5692 1052058.067 786970.3391 1.322598272 1.102971107 1.19879582 1.328291281 1.138249709 1.095005105 1.299517782 1.247216725 1.336845894 1 19.58594974 KEVLAS(ph)PDRLWGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEVLASPDRLWGSR 14 2 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KEVLAS(0.99)PDRLWGS(0.01)R;KEVLAS(0.999)PDRLWGS(0.001)R;KEVLAS(1)PDRLWGSR;KEVLAS(1)PDRLWGSR 118.96 0.00016924 2170826000 865355 766509 901304 820382 1051782 1037799 904959 811721 901683 876454 TRUE FALSE 899519.8836 898150.9581 924792.7227 982651.111 873000.4713 796785.9102 834025.9489 800841.2077 869231.605 1048178.381 0.858174429 0.856868425 0.88228563 0.93748462 0.832873953 0.760162511 0.795690852 0.764031412 0.829278319 1 19.99945283 3.011703135 24.17810653 0.807207025 0.882122023 0.08474806 0.067928264 223.0224105 460748.2 0.018402764 0.0219771 1027.313831 -3.011703135 0.074914998 KEVQDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KEVQDEEK 8 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;;;;;; 150.35 0.00078659 30590870000 29020740 13892360 20849250 13591220 28718120 27348420 27804200 19935020 23578070 12135170 FALSE TRUE 30166501.22 16278264.76 21392598.58 16279522.75 23836624.22 20997163.92 25624834.15 19667823.66 22729499.87 14512824.22 2.078609977 1.121646932 1.474047936 1.121733613 1.642452486 1.446800678 1.765668333 1.355203051 1.566166552 1 23.79082496 -1.281961089 6.572093541 0.999990684 1.48778279 0.235073998 0.272737402 3.38E-05 3.70E-06 0.239998433 0.056567094 0.0522443 1.281961089 0.487792106 KEVS(ph)PEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KEVSPEVVR 9 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KEVS(1)PEVVR;KEVS(1)PEVVR;KEVS(1)PEVVR;KEVS(1)PEVVR 131.06 0.00021055 3173540000 6221500 4541400 5362380 4332600 7161000 6770900 6397000 5678500 5818800 4221680 TRUE FALSE 6467129.624 5321350.123 5502128.028 5189575.348 5943775.778 5198461.089 5895586.425 5602388.996 5609382.525 5048837.367 1.280914625 1.053975348 1.089781197 1.027875325 1.177256336 1.029635283 1.167711692 1.109639426 1.111024602 1 22.26751978 4.74583782 24.89236051 1.092673878 1.280914719 0.517458265 0.05628193 641.7233225 2195020.464 0.012403562 0.126410878 55697.77156 -4.74583782 0.188240841 KEVVEEAENGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KEVVEEAENGR 11 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;;; 221.56 1.33E-11 10066120000 9168690 7715480 8985450 8292830 10764830 11106020 10853530 9809010 9515730 7264770 FALSE TRUE 9530676.961 9040553.672 9219618.209 9933127.022 8935028.042 8526815.168 10002801.96 9677536.265 9173260.736 8688162.589 1.096972676 1.040559909 1.061170082 1.14329433 1.028414 0.981429051 1.151313854 1.113876054 1.055834377 1 23.05061967 2.211604644 24.99908715 1.094529927 1.060407087 0.009531391 0.054676209 608.5440869 564363.0534 0.020517345 0.015156934 162.7813493 -2.211604644 -0.03412284 KEWDLKPIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEWDLKPIADR 11 2 P30038-2;P30038;P30038-3;Q5TF55 P30038-2 ALDH4A1 "Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial" 0 94.688 0.0046782 700350000 440080 556640 483930 543240 586640 784790 535840 503300 459840 677640 FALSE TRUE 457454.6982 652238.5899 496541.6134 650691.2506 486923.1423 602534.4161 493839.4606 496554.0867 443290.4482 810410.5838 0.564472759 0.804824867 0.612703762 0.802915539 0.600835122 0.743492778 0.609369461 0.612719153 0.54699489 1 19.62829349 -1.091951207 4.390742513 1.000033302 0.658489143 0.56962236 0.089831351 1.291670965 49348420.3 3630.774387 0.01973736 0.080918681 1.091951207 -0.34154416 KEYEEDGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KEYEEDGAR 9 1 P61163 P61163 ACTR1A Alpha-centractin 0 ;;;;; 157.97 0.00010786 3886425000 5059600 4191200 4829880 4229050 6197570 5930000 5845770 4975360 5146690 3890770 FALSE TRUE 5259356.915 4911005.997 4955750.641 5065543.468 5144109.265 4552847.37 5387563.272 4908673.437 4961461.632 4653091.888 1.130292941 1.055428544 1.065044654 1.088640325 1.105524969 0.978456364 1.15784588 1.054927252 1.066272008 1 22.14975825 0.70151713 1.766605206 1.000152186 1.078889073 0.213252338 0.045848988 1.737191717 7.993453256 0.040261744 0.011350518 5.029411028 -0.70151713 0.078736886 KEYEEDGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEYEEDGSR 9 1 P42025 P42025 ACTR1B Beta-centractin 0 93.345 0.015171 447280000 703720 791590 860890 707890 1075800 952640 822800 804420 829220 676760 FALSE TRUE 731503.409 927539.4248 883325.5006 847908.5292 892935.9003 731403.7974 758306.786 793638.0657 799376.5342 809358.1646 0.903806795 1.146018494 1.091390115 1.047630785 1.103264215 0.90368372 0.936923626 0.98057708 0.987667227 1 19.62641875 2.744535241 24.99134403 0.960187949 1.06452059 0.358307969 0.064396372 500.0616628 2091716.449 0.019173315 0.019844807 555.3096757 -2.744535241 0.104332641 KFAADAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFAADAVK 8 1 P37837 P37837 TALDO1 Transaldolase 0 111.65 0.0051186 540460000 434180 355020 269330 214800 1741000 840050 598060 451430 473180 1683300 FALSE TRUE 451321.7617 415991.9233 276348.9611 257286.7989 1445065.442 644961.1186 551182.4945 445379.3192 456150.3442 2013110.406 0.224191262 0.206641385 0.137274618 0.127805608 0.717827218 0.320380401 0.273796456 0.22123939 0.22658983 1 20.94099487 -1.938581243 2.519651277 1.508739626 0.273360022 0.654460683 0.158505672 25525897.52 12660321.09 76258669.22 0.039206626 0.011519106 1.938581243 -1.235379604 KFAEAFEAIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFAEAFEAIPR 11 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 117.03 0.0014584 845150000 1118600 991770 1114300 952970 1488900 1338500 1275900 1187800 1232000 1157300 FALSE TRUE 1162763.192 1162098.783 1143339.573 1141464.622 1235817.31 1027653.66 1175891.624 1171879.484 1187660.561 1384050.777 0.840115992 0.839635945 0.826082101 0.824727416 0.892898823 0.74249708 0.849601506 0.846702667 0.858104761 1 20.40046544 0.440271576 1.118025788 1.000205704 0.830906408 0.670435684 0.035083711 1.253188869 1.971418738 0.032044809 0.009805733 2.755951533 -0.440271576 -0.169299296 KFAETQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFAETQPK 8 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 121.73 0.0022779 2170800000 4342100 2891880 3945900 2728350 5067000 4841600 4749000 3973200 4342700 3013900 FALSE TRUE 4513529.461 3388537.894 4048733.396 3268009.487 4205713.15 3717211.775 4376760.971 3919945.753 4186407.075 3604416 1.252222124 0.940107328 1.123270287 0.906668233 1.166822351 1.031293773 1.214277423 1.087539771 1.161466122 1 21.7813341 KFAMEPEEFDSDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFAMEPEEFDSDTLR 15 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 185.61 6.67E-07 203001000 123382 134691 137137 129632 176155 187745 123987 139159 142653 151637 FALSE TRUE 128253.2166 157823.1315 140710.9029 155272.8227 146212.236 144144.0691 114268.575 137293.8012 137518.9464 181347.3669 0.707224035 0.8702808 0.775919195 0.856217685 0.806255081 0.794850631 0.630108818 0.757076342 0.758317856 1 17.46839627 2.456979765 24.99989901 0.754325879 0.807560736 0 0.096530204 696.9270664 865030.6407 0.030974305 0.025917825 286.4044523 -2.456979765 0.053234857 KFAYLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFAYLGR 7 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 135.35 0.0049478 2050090000 1497110 1517450 1547130 1154750 2697800 2155500 1743820 1531990 1615150 2524600 FALSE TRUE 1556217.059 1778060.233 1587449.479 1383156.103 2239228.92 1654917.792 1607134.832 1511456.18 1557021.067 3019247.034 0.515432173 0.588908497 0.525776613 0.458112929 0.741651443 0.548122685 0.532296567 0.500606993 0.515698467 1 21.52575737 -1.13660231 4.949690151 1.000024129 0.547009823 0.77886694 0.072348363 1.90E-05 3.32E-06 0.069215679 0.016313424 0.073012579 1.13660231 -0.453014306 KFDEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KFDEGR 6 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6;H0Y4J5;Q13087-2;Q13087 P07237 P4HB;PDIA2 Protein disulfide-isomerase;Protein disulfide-isomerase A2 0 ;;; 125.08 0.028984 4725130000 9353830 9074730 8808640 9158510 10230710 11549390 10798060 9159070 8191300 7349300 FALSE TRUE 9723126.431 10633244.29 9038200.395 10970035.94 8491697.569 8867219.205 9951679.842 9036307.648 7896496.713 8789254.624 1.106251536 1.20980046 1.028323877 1.248119028 0.966145359 1.008870443 1.132255267 1.02810853 0.898426209 1 23.06730939 2.793742841 0.469557296 0.975813741 1.164266802 0.32355395 0.085579386 1.457319286 0.657624223 0.077709984 0.114016818 621.9319118 -2.793742841 0.188453061 KFDEVLVNHFCEEFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFDEVLVNHFCEEFGK 16 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 239.86 4.98E-20 1725160000 2602560 1588410 2239840 1601950 2905640 2611580 2881880 2231130 2685820 1395130 FALSE TRUE 2705311.078 1861207.061 2298212.07 1918810.929 2411740.351 2005080.124 2655990.715 2201225.352 2589157.863 1668479.012 1.621423499 1.115511222 1.377429416 1.150036 1.445472393 1.201741292 1.591863425 1.319300594 1.551807271 1 20.67010211 KFDGVEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFDGVEGPR 9 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 0 ; 82.261 0.030391 340200000 388530 489130 461130 426150 599080 651610 457260 433430 449000 726480 FALSE TRUE 403869.4644 573134.2726 473147.4266 510441.1981 497248.5956 500283.4527 421418.7664 427620.5798 432840.5777 868819.8467 0.464848341 0.659669867 0.544586347 0.587510978 0.57232647 0.57581955 0.485047352 0.492185557 0.498193704 1 19.72869753 -1.463692103 5.8806603 1.000320865 0.542736462 0.85653995 0.05620116 0.000242024 2.21E-05 0.055704991 0.013120835 0.03438016 1.463692103 -0.457584403 KFDGVEGPRT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFDGVEGPRTPK 12 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YAN4 Q6PKG0 LARP1 La-related protein 1 1 KFDGVEGPRT(1)PK;KFDGVEGPRT(1)PK 109.35 0.0025841 1155960000 1469160 671760 982090 631700 1408720 1267420 1295940 1033220 1204060 656020 TRUE FALSE 1527163.571 787129.5544 1007684.072 756648.3746 1169266.278 973080.9129 1194360.836 1019371.376 1160726.116 784554.5587 1.946535845 1.003282112 1.2844028 0.964430537 1.490356871 1.240297315 1.522342612 1.299299538 1.479471508 1 19.58151425 -1.783318681 2.530710916 0.904169411 1.339049718 0.136226718 0.266954237 23720963.08 15988750.7 14019649.41 0.058718393 0.016469534 1.783318681 0.434880307 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 AATFPLQVLGFEIDAVNSVQFSNHTGYAHWK 31 0 O00764;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;; 317.75 4.54E-93 1506590000 247675 604189 739933 759457 825669 934392 689997 786421 710695 712219 FALSE TRUE 257453.4002 707953.7608 759216.2618 909675.3278 685322.0783 717393.6188 635913.2322 775880.3128 685117.2258 851764.6768 0.302258837 0.831161212 0.891345089 1.067989026 0.804590865 0.842243918 0.74658324 0.910909238 0.804350362 1 19.70009538 4.739321574 4.154539376 0.876637079 0.254780552 0.785865392 0.090419425 0.097124955 3.733075146 0.021578616 0.180651717 54868.30879 -4.739321574 -0.621856527 down KFDLGQDVIDFTGHALALYR ddPTM_MDA-MB-175_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 ;; 223.23 4.29E-25 8915022000 7732306 8029325 9436546 7684364 10747995 10727522 9193558 8725442 9140492 9754830 FALSE TRUE 8037583.412 9408299.109 9682470.141 9204308.264 8921054.649 8236217.593 8472942.901 8608491.722 8811527.478 11666102.17 0.688969057 0.806464659 0.82996617 0.788978883 0.764698827 0.705995668 0.72628739 0.737906423 0.75531033 1 23.47581928 -1.981466955 5.471782168 1.192571853 0.75677871 0.75486429 0.04170106 0.027284474 9.24E-05 0.011245487 0.010132999 0.010435975 1.981466955 -0.435793142 KFDPFLDLSLDIPSQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFDPFLDLSLDIPSQFR 17 1 H0YLB7;H0YKU8;Q6JHV3;H0YMI4;Q9Y6I4-2;Q9Y6I4 H0YLB7 USP3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 3 0 78.078 0.026337 128940000 89882 57728 72452 61804 88761 89775 93902 89784 85457 64196 FALSE TRUE 93430.61076 67642.33494 74340.15864 74028.64673 73673.43692 68926.1168 86541.71587 88580.59234 82381.41926 76773.97709 1.216956765 0.881058107 0.968298914 0.964241394 0.959614699 0.897779683 1.127227208 1.153784078 1.073038318 1 16.22832976 2.222613883 24.99439661 1.107873079 0.974411896 0.224446146 0.09439687 280.5622684 439741.4577 0.033617665 0.024907458 166.9605564 -2.222613883 -0.133461183 KFDQLLAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 181.66 2.99E-06 10279300000 21300900 12287650 16493390 11586580 27348400 21764900 22283200 16644050 19395800 13823060 FALSE TRUE 22141875.98 14397958.3 16923221.29 13878370.94 22699728.74 16710331.83 20536584.56 16420963.73 18697748.95 16531423.95 1.339381051 0.870944835 1.023700157 0.83951455 1.373126042 1.010822291 1.242275597 0.993318167 1.131042855 1 23.97870766 4.769327912 23.30671779 1.060238404 1.339382223 0.238973765 0.152474442 7168.26851 5429844.675 0.034700751 3.838888385 58793.31005 -4.769327912 0.279143819 KFDSLLELVEYYQCHSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFDSLLELVEYYQCHSLK 18 1 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 0 161.65 2.44E-11 91700000 85695 72862 91811 75798 98328 112070 97453 99946 107030 56572 FALSE TRUE 89078.30477 85375.48171 94203.67008 90790.61817 81614.24168 86043.44094 89814.37921 98606.38735 103178.0112 67656.20026 1.316631801 1.261901812 1.392387833 1.341940839 1.206308385 1.271774658 1.327511431 1.457462686 1.525034081 1 16.04593453 1.987749338 22.78744157 1.381867859 1.298944188 0 0.139147116 507.9275153 944793.2004 0.051842286 0.03542469 97.21859452 -1.987749338 -0.082923671 KFDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 102.71 0.056608 429550000 869990 951590 862880 916840 1024420 1161280 1091460 875820 847580 1057510 FALSE TRUE 904337.877 1115018.18 885367.3617 1098188.216 850289.4543 891590.3194 1005908.513 864081.0655 817075.7614 1264708.837 0.715056186 0.881640222 0.700056278 0.868332839 0.672320323 0.704976745 0.795367664 0.683225293 0.646058395 1 20.27037385 -1.178153845 4.925989541 1.000023035 0.742487305 0.503153863 0.077259816 1.88E-05 3.14E-06 0.071963545 0.016960454 0.066350799 1.178153845 -0.257535731 KFDVNTSAVQVLIEHIGNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 292.31 6.03E-55 6285260000 2501030 2259840 2820950 2665830 3343020 3251160 3170870 2670200 3001350 2240440 FALSE TRUE 2599772.596 2647949.941 2894466.274 3193123.217 2774774.654 2496127.362 2922328.924 2634410.337 2893332 2679411.322 0.970277529 0.988258099 1.080262015 1.191725657 1.035591151 0.931595437 1.09066081 0.983204898 1.079838685 1 21.35348464 1.719100785 25 1.020928256 1.042025179 0.01613944 0.07200274 5.875859239 7518.643196 0.035223795 0.019533534 52.37219605 -1.719100785 0.021096923 KFEDATVQSDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFEDATVQSDMK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ; 151.54 0.00011071 434400000 678860 441600 571270 419670 774760 721770 693080 591130 668330 419690 FALSE TRUE 705661.917 517441.3648 586157.7655 502679.4734 643066.5719 554149.856 638754.5786 583206.8692 644276.9339 501920.22 1.405924465 1.03092353 1.167830548 1.001512697 1.281212723 1.104059637 1.27262173 1.161951334 1.283624186 1 18.93709854 KFEDEYSEYLK ddPTM_MDA-MB-175_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 0 132.47 0.00029148 109520000 378230 236460 321250 234530 454190 355330 385980 287480 330990 198510 FALSE TRUE 393162.8125 277070.1656 329622.0389 280919.334 376986.946 272809.9926 355725.879 283626.8008 319077.7346 237404.2338 1.656090147 1.167081821 1.388442125 1.183295384 1.587953761 1.149137015 1.498397368 1.194699843 1.344027145 1 17.85698614 -4.026514778 0.199002408 1.22E-09 1.403049749 0.295718247 0.170158804 111.1273487 1.558799608 44.89095161 0.380652808 9.41E-05 4.026514778 1.403049748 KFESEILEAISQNSVVIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KFESEILEAISQNSVVIIR 19 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 222.79 3.77E-19 588722000 414287 360407 459493 401894 534418 562678 514628 463782 485435 395818 FALSE TRUE 430643.3707 422304.0987 471467.7651 481387.4337 443577.8192 432004.562 474290.1126 457565.7609 467964.2892 473370.9587 0.909737623 0.892120843 0.995979488 1.016934869 0.937061751 0.91261315 1.00194172 0.966611391 0.988578367 1 18.85261167 4.244411699 24.99972665 0.974840436 0.900929204 0.500534239 0.030491599 117.7654741 503157.6803 0.007735059 0.020016057 17555.43919 -4.244411699 -0.073911232 KFFDANYDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFFDANYDGK 10 1 Q15691;C9JB30;Q9UPY8;Q9UPY8-2 Q15691;C9JB30;Q9UPY8-2 MAPRE1;MAPRE3 Microtubule-associated protein RP/EB family member 1;Microtubule-associated protein RP/EB family member 3 0 ; 115.14 0.0020249 863080000 1642950 1006550 1287040 1044280 1775530 1652330 1736180 1340590 1412550 965280 FALSE TRUE 1707814.935 1179417.133 1320581.32 1250835.467 1473726.045 1268601.399 1600093.675 1322621.584 1361712.601 1154408.135 1.479385742 1.021663914 1.143946651 1.083529672 1.276607467 1.098919317 1.386072765 1.145714019 1.179576409 1 20.13872194 0.601186422 1.957829898 1.000122607 1.197396749 0.169902677 0.134285129 4.143847618 18.19106555 0.11868022 0.03280676 3.991962212 -0.601186422 0.197274142 KFFDANYDGKDYDPVAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFFDANYDGKDYDPVAAR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 169.28 1.05E-11 1436060000 1545600 1204860 1739500 853660 2328770 1831850 1349150 1495240 1846980 1596070 FALSE TRUE 1606621.481 1411785.332 1784832.799 1022511.4 1932926.507 1406430.599 1243400.098 1475198.754 1780507.551 1908789.358 0.841696584 0.73962343 0.935060116 0.535685824 1.012645266 0.736818127 0.651407706 0.772845232 0.932794152 1 20.86422647 1.135652438 3.894824348 0.994535924 0.773935675 0.264993163 0.127344946 0.263167944 6.826886441 0.111845637 0.029170845 13.66634682 -1.135652438 -0.220600249 KFGDPVVQSDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;;;;;; 167.89 7.70E-05 14618990000 13566270 7958680 11140260 7813770 16093180 12886580 13326940 11257700 12464750 8096440 FALSE TRUE 14101876.82 9325521.38 11430584.33 9359310.384 13357667.01 9893867.093 12282339.62 11106808.95 12016146.08 9682782.402 1.456386835 0.963103475 1.180506166 0.966593072 1.379527749 1.021800004 1.26847213 1.147067907 1.2409807 1 23.20699024 -2.348955964 2.175380753 0.018103017 1.170978405 0.103368365 0.157244457 6492134.004 1207152.664 31012736.44 0.034563479 0.004477587 2.348955964 1.152875388 KFGEEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFGEEIAR 8 1 Q8WUM4;Q8WUM4-2;F8WDK9 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ; 131.44 0.0016114 711800000 1734040 1685390 1764920 1643560 2425880 2435020 2312620 1972340 2144300 1767580 FALSE TRUE 1802501.238 1974842.622 1810915.265 1968651.262 2013529.784 1869523.508 2131350.801 1945904.008 2067127.062 2113903.459 0.852688533 0.934216089 0.85666886 0.931287214 0.95251738 0.884393987 1.008253614 0.920526432 0.977872028 1 21.01147806 8 0.118583241 1.028867812 0.526250838 0.503805704 0.036826634 77.09800752 0.629178699 0.239027443 6.39689054 100000000 -8 -0.502616973 KFGGPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFGGPGAR 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ; 111.04 0.0053081 5652900000 5681200 5633500 6393900 5063300 7226500 7484900 6285400 6214000 5897600 6015700 FALSE TRUE 5905498.163 6601009.802 6560530.287 6064805.628 5998142.111 5746645.41 5792733.924 6130711.494 5685346.528 7194361.237 0.820850937 0.917525488 0.911898926 0.842994316 0.833728237 0.798770762 0.805176962 0.852155083 0.790250356 1 22.77843517 5.110474097 12.69261683 0.853373281 2.81E-05 0.022674498 0.062308997 1989658.873 3625116.107 0.014357865 46973988.77 128965.6635 -5.110474097 -0.853345134 KFGNPGER ddPTM_MDA-MB-175_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 ;;; 145.72 0.0009056 2548810000 2573640 2547290 2569290 2193900 3349690 3305130 3022850 2586880 2824740 2797040 FALSE TRUE 2675249.294 2984767.242 2636247.808 2627846.872 2780310.89 2537563.647 2785911.118 2552207.105 2723078.159 3345066.435 0.79975969 0.892289376 0.788100284 0.785588843 0.831167615 0.758598879 0.83284179 0.762976507 0.81405802 1 21.67360343 -1.96141551 6.491632208 1.109090223 0.805794221 0.708552997 0.037072345 0.024286315 0.000144351 0.014893823 0.008195556 0.010929102 1.96141551 -0.303296002 KFGQGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFGQGSR 7 1 A0A2R8Y851;P62273;P62273-2;A0A2R8Y6P7 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 ; 117.04 0.0085324 8029800000 9395400 7064200 8604500 6076400 10292500 10039100 8957600 8701100 8736300 7637800 FALSE TRUE 9766337.647 8277421.398 8828740.339 7278293.784 8542984.526 7707671.169 8255479.906 8584475.987 8421882.27 9134280.675 1.069196141 0.906193021 0.966550148 0.796810832 0.93526626 0.843818079 0.903790917 0.93980865 0.922008264 1 23.12285969 5.064369458 1.901049531 0.906444882 1.286973743 0.407820648 0.055594215 2.432557124 4.102770036 0.013361066 2.211559208 115976.3556 -5.064369458 0.380528861 KFGYVDFESAEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 ;;;;; 285.59 6.69E-34 4983074000 7601604 4185375 5729890 3978816 7876404 6780257 6863663 5796594 6497008 3589496 FALSE TRUE 7901721.196 4904180.599 5879215.641 4765813.929 6537575.661 5205645.068 6325671.159 5718900.139 6263181.951 4292789.016 1.840696378 1.142422928 1.36955616 1.11019058 1.522920329 1.212648711 1.473557432 1.332210858 1.459000647 1 22.03348384 -1.864044277 2.467167534 0.829520052 1.36911706 0.242525526 0.202313399 10378274.18 6517975.894 10398675.3 0.046438185 0.013675894 1.864044277 0.539597008 KFHTVSGSK ddPTM_MDA-MB-175_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 ; 136.33 0.00012718 2715600000 4681800 3914700 5024800 4031500 6529300 6228500 6091200 5205900 5436300 4085600 FALSE TRUE 4866641.079 4587019.273 5155750.416 4828918.667 5419451.918 4782025.269 5613755.828 5136123.426 5240648.625 4886095.096 0.996018494 0.938790421 1.055188308 0.988298134 1.109158093 0.978700818 1.148924799 1.051171401 1.07256378 1 22.22025051 3.855799662 1.069099915 1.064248138 0.965965123 0.238317411 0.053726888 0.763992522 1.547570906 0.016871962 0.061054106 7174.632522 -3.855799662 -0.098283014 KFIEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 2602750000 6013270 5389340 6060530 5496690 7326400 7137900 6878900 6193900 6564300 5576560 FALSE TRUE 6250678.543 6314917.222 6218472.391 6583918.876 6081061.145 5480230.901 6339713.843 6110880.902 6328052.125 6669180.162 0.937248416 0.946880586 0.932419314 0.987215627 0.911815395 0.821724825 0.950598678 0.916286673 0.948850079 1 22.66907799 0.907885811 3.601086896 0.999977116 0.925486928 0.240952355 0.040168995 0.589992544 17.35099804 0.039522365 0.010185172 8.088831919 -0.907885811 -0.074490189 KFIQENIFGICPHMTEDNKDLIQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFIQENIFGICPHMTEDNKDLIQGK 25 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 213.02 3.37E-26 209880000 320140 185560 265320 149160 401760 368680 215730 243440 275090 176050 FALSE TRUE 332779.3744 217428.4865 272234.4572 178663.4028 333468.9787 283059.6574 198820.5189 240177.085 265189.5646 210543.6268 1.580572062 1.032700395 1.293007351 0.848581387 1.583847413 1.344422824 0.944319816 1.140747353 1.259546863 1 17.68375968 2.716182918 0.028028408 2.71E-06 2.397023831 0.113405185 0.227841544 756.7915695 8.466057857 333.8808827 387.653325 520.2150563 -2.716182918 2.397021122 KFLDAGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFLDAGHK 8 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ; 103.7 0.0030655 4652300000 11298400 9122400 10159300 8951000 15266400 13732200 12331200 11028100 11544800 9055300 FALSE TRUE 11744469.56 10689101.24 10424059.7 10721481.08 12671422.78 10543104.66 11364648.32 10880286.36 11129304.9 10829512.66 1.084487356 0.987034373 0.962560369 0.990024336 1.170082457 0.973553011 1.049414565 1.004688456 1.027682893 1 23.36846499 KFLDGIYVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFLDGIYVSEK 11 1 A0A2R8Y5Y7;P32969;D6RAN4;H0Y9R4;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 214 9.74E-10 3350100000 7244900 5497900 7380600 5236200 9966700 8595000 8662000 7552200 8188500 6680400 FALSE TRUE 7530934.246 6442121.557 7572944.499 6271904.732 8272563.894 6598941.508 7983049.806 7450975.112 7893797.485 7989296.476 0.942627961 0.806344035 0.947886278 0.785038426 1.035455865 0.825972791 0.99921812 0.932619679 0.988046633 1 22.92963704 2.072396261 0.569309902 0.999502791 0.876270629 0.218286995 0.074844202 1.160461467 0.771246283 0.06306227 0.044356382 118.139808 -2.072396261 -0.123232162 KFLDGNELTLADCNLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFLDGNELTLADCNLLPK 18 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 175.39 5.58E-12 1049200000 1756600 1161090 1440350 1042440 1949030 1706140 1659380 1521510 1927720 1102360 FALSE TRUE 1825951.924 1360498.175 1477886.704 1248631.521 1617734.577 1309914.842 1529313.46 1501116.647 1858341.734 1318346.336 1.385032047 1.031973267 1.121015521 0.947119498 1.227093771 0.993604492 1.160024053 1.138636037 1.40960056 1 20.33029799 1.43891871 15.60238116 1.227901818 1.116782082 0.038270772 0.149036642 3.769765773 1537.51826 0.07750496 0.034002536 27.4737986 -1.43891871 -0.111119736 KFLETVELQISLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFLETVELQISLK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 88.974 0.012286 210930000 337300 240970 325380 227250 364920 341450 329190 304360 350920 234570 FALSE TRUE 350616.8645 282354.723 333859.6701 272199.3717 302891.0287 262153.4122 303387.2276 300280.552 338290.4577 280529.5004 1.24983955 1.006506348 1.190105389 0.970305695 1.07971186 0.934494988 1.081480654 1.070406327 1.205899762 1 18.09779297 4.749293668 24.31286708 1.061458465 1.249839709 0.318467514 0.083338402 1261.969194 2858573.279 0.01876759 0.270111978 56142.74822 -4.749293668 0.188381244 KFLPLFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFLPLFDR 8 1 P61604;B8ZZL8;S4R3N1 P61604;S4R3N1 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 ; 123.86 0.0021318 1995400000 2034010 2255500 2224900 2126500 2949600 3202900 2480900 2148300 2376700 3218400 FALSE TRUE 2114314.285 2642864.58 2282882.722 2547115.353 2448228.046 2459075.015 2286440.575 2119505.552 2291163.031 3848983.86 0.549317524 0.686639559 0.593113093 0.661763064 0.636071268 0.638889407 0.594037455 0.550666261 0.59526439 1 21.87604619 -2.215346433 2.465489376 2.320452258 0.61115234 0.882841465 0.042429866 2283696.398 430450.5327 16921601.1 0.010604661 0.006090509 2.215346433 -1.709299918 KFLVYVANFDEKDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFLVYVANFDEKDPR 15 2 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 ; 103.4 0.00082979 1118730000 4204900 2605000 3814500 2586800 4858200 4383300 3877000 3634800 4250800 2908400 FALSE TRUE 4370912.699 3052388.486 3913909.004 3098461.319 4032404.899 3365345.005 3573110.609 3586081.451 4097814.538 3478245.295 1.256643028 0.877565619 1.125253877 0.890811618 1.1593216 0.967541021 1.0272739 1.031003034 1.178126955 1 21.72992825 KFMTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFMTNR 6 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 119.89 0.033075 2687900000 2027300 2222200 2168300 1999750 2904600 2625000 2351200 2237000 1884870 2978200 FALSE TRUE 2107339.369 2603845.564 2224807.679 2395294.581 2410877.129 2015383.532 2166906.8 2207016.674 1817033.897 3561721.269 0.59166319 0.731063822 0.62464396 0.672510396 0.676885401 0.565845382 0.608387529 0.619648902 0.510156118 1 21.76414319 -2.148408996 2.596011604 1.908243311 0.625974073 0.788718488 0.058616558 3357261.481 1792893.719 17751464.14 0.01414326 0.00710544 2.148408996 -1.282269239 KFNALFAQGNYSEAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFNALFAQGNYSEAAK 16 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 205.42 3.63E-11 1631550000 2708500 1598520 2102400 1657280 2926000 2763500 2498300 2137700 2510900 1795050 FALSE TRUE 2815433.671 1873053.375 2157190.271 1985085.038 2428639.565 2121719.006 2302476.718 2109047.628 2420533.199 2146755.679 1.311483043 0.872504213 1.004860633 0.924690712 1.131306925 0.988337437 1.072537849 0.982434866 1.127530824 1 21.03372658 3.234587828 24.99979262 1.043621573 1.015570058 0.001629787 0.118606372 693.0112808 4360946.533 0.032003476 0.039532994 1716.278761 -3.234587828 -0.028051514 KFPGYYVTGDGCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFPGYYVTGDGCQR 14 1 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 98.439 0.0053726 0 193780 159980 175220 149320 276570 237550 163980 165190 178070 183840 FALSE TRUE 201430.584 187455.3205 179786.3771 178855.0503 229558.7302 182382.6126 151126.8191 162975.8982 171661.2955 219859.9282 0.916176885 0.852612489 0.817731447 0.813495446 1.04411355 0.829540035 0.687377734 0.741271498 0.780775728 1 17.74622516 2.476135769 24.99652104 0.771378754 0.884494121 0.118441643 0.098648497 49.78623785 1262747.6 0.032904125 0.027744104 299.3200226 -2.476135769 0.113115367 KFQEQECPPS(ph)PEPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFQEQECPPSPEPTRK 16 2 P62070-2;P62070-3;P62070;P62070-4 P62070-2 RRAS2 Ras-related protein R-Ras2 1 KFQEQECPPS(0.999)PEPT(0.001)RK;KFQEQECPPS(0.997)PEPT(0.003)RK 136.58 8.71E-06 311930000 249200 196585 203860 212350 262480 321660 234660 225510 227420 202607 TRUE FALSE 259038.6084 230346.9445 209172.7591 254352.1962 217863.7434 246959.3398 216266.736 222487.4073 219235.1986 242303.9625 1.069064681 0.950652817 0.863265945 1.049723635 0.899134051 1.019212964 0.892543126 0.918216132 0.904794112 1 17.88645847 2.221258653 24.99943214 0.92060515 0.968906319 0.097647144 0.065423137 543.6481877 785506.4698 0.023296709 0.017248097 166.4403625 -2.221258653 0.048301169 KFQGIKHECQANGPEDLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFQGIKHECQANGPEDLNR 19 2 P60981;P60981-2 P60981 DSTN Destrin 0 160.97 1.83E-11 790630000 598040 629810 743930 429560 1169800 950890 533870 651130 889030 1030900 FALSE TRUE 621651.081 737974.9683 763317.4269 514525.6859 970957.8138 730060.2084 492023.8744 642402.6674 857033.984 1232885.117 0.504224662 0.598575616 0.619131025 0.417334656 0.787549302 0.59215591 0.399083311 0.521056389 0.695145048 1 20.23360694 0.912600742 3.635253069 0.999672021 0.554561228 0.627480786 0.104294397 0.237940534 7.297587921 0.10036187 0.025845778 8.177126987 -0.912600742 -0.445110793 KFS(ph)APGQLCISMTSNLGGSAPISAASATSLGHFTK ddPTM_MDA-MB-175_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(1)APGQLCISMTSNLGGSAPISAASATSLGHFTK 164.28 5.97E-15 361230000 64798 80617 105210 95652 165590 154780 130590 135940 143070 99898 TRUE FALSE 67356.27507 94462.34264 107951.859 114571.6801 137443.0709 118834.6907 120354.0146 134117.9467 137920.9386 119471.1004 0.563787182 0.790671068 0.903581357 0.958990749 1.150429438 0.994673107 1.00739019 1.122597399 1.154429298 1 16.86630215 5.065485467 0.678340642 1.081744573 8.11E-10 0.873512551 0.060999687 1.447021379 0.370012217 0.024750132 1.330583765 116274.7641 -5.065485467 -1.081744572 KFS(ph)GSGLAMGLGSASASAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFSGSGLAMGLGSASASAWR 20 1 Q92796-2 Q92796-2 DLG3 Disks large homolog 3 1 KFS(0.972)GS(0.028)GLAMGLGSASASAWR;KFS(0.984)GS(0.016)GLAMGLGSASASAWR 210.96 1.95E-22 362080000 353539 319611 347575 319386 419981 431817 446866 358862 416122 361229 TRUE FALSE 367496.9927 374501.703 356633.09 382559.5975 348592.7796 331534.046 411839.4753 354052.0419 401145.8505 432004.9064 0.850677822 0.866892245 0.825530184 0.885544566 0.806918566 0.767431205 0.953321291 0.819555604 0.928567812 1 18.72068817 1.017571328 3.795857702 0.999744145 0.848216719 0.520010648 0.047454945 0.142392305 5.056385879 0.043250513 0.011130095 10.41289115 -1.017571328 -0.151527426 KFS(ph)NSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFSNSLK 7 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 KFS(0.976)NS(0.024)LK;KFS(0.877)NS(0.123)LK 112.85 0.0066339 1200250000 1401750 715600 1103970 696100 1564530 1309030 1384060 1049800 1338670 609500 TRUE FALSE 1457092.172 838498.7334 1132740.365 833786.5023 1298591.749 1005027.621 1275573.761 1035729.148 1290491.528 728919.8554 1.998974457 1.150330489 1.553998504 1.143865812 1.781528847 1.378790293 1.749950631 1.420909501 1.770416211 1 19.47540067 -0.735454896 6.18858721 0.999999992 1.528666885 0.271729594 0.268041834 2.41E-08 5.56E-09 0.231037583 0.054456079 0.183884492 0.735454896 0.528666893 KFS(ph)PSQVPVQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFSPSQVPVQTR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 KFS(0.858)PS(0.142)QVPVQTR 97.291 0.00078887 0 172890 181000 163270 140120 195540 222970 187510 187940 162400 164980 TRUE FALSE 179715.8307 212085.342 167524.9503 167835.3178 162302.1806 171188.5966 172812.4762 185420.9717 156555.2557 197304.6723 0.910854409 1.074912923 0.849067325 0.850640362 0.822596742 0.867635797 0.875866112 0.939769797 0.793469581 1 17.59006559 4.220255084 24.99996411 0.873374443 0.992883703 0.335912133 0.066340014 214.0513468 292331.8906 0.015500243 0.033583991 16605.61956 -4.220255084 0.11950926 KFSAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFSAPR 6 1 P39023;H7C422;H7C3M2;F8WCR1;Q92901 P39023;Q92901 RPL3;RPL3L 60S ribosomal protein L3;60S ribosomal protein L3-like 0 110.61 0.045786 695240000 657540 735550 663150 557040 1566900 1059000 851160 708240 616560 1542100 FALSE TRUE 683500.1869 861874.9907 680432.2338 667220.8494 1300558.898 813063.2993 784443.8551 698747.2012 594370.126 1844244.97 0.370612472 0.467332163 0.368948944 0.36178537 0.70519856 0.440865131 0.425346886 0.37887982 0.322283718 1 20.81459887 -1.48426936 5.14402232 1.001269152 0.429253034 0.740966717 0.101662742 0.001494379 0.000149824 0.099409648 0.023384425 0.032789186 1.48426936 -0.572016118 KFSGFSAKPNNSGEAPSS(ph)PTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFSGFSAKPNNSGEAPSSPTPK 22 2 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 KFSGFSAKPNNSGEAPS(0.008)S(0.988)PT(0.004)PK;KFSGFSAKPNNSGEAPS(0.16)S(0.837)PT(0.002)PK 132.28 5.65E-06 3810900000 4753900 1689570 2803900 1667070 3900100 3293800 3458300 2735500 3338800 1401320 TRUE FALSE 4941587.643 1979740.504 2876971.937 1996811.47 3237162.395 2528864.868 3187229.409 2698835.097 3218637.24 1675881.824 2.948649226 1.181312713 1.716691413 1.191498972 1.931617342 1.508975652 1.901822291 1.610397021 1.920563368 1 20.67648899 4.749480903 24.82778996 1.591651346 2.948650081 0.630455323 0.319583937 888.2242491 2019377.376 0.069421931 1.032218396 56166.95804 -4.749480903 1.356998735 KFSIEEALQSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFSIEEALQSGR 12 1 O60437;K7EKI8 O60437 PPL Periplakin 0 ; 100.54 0.0050908 348180000 451900 423310 442450 408310 569280 575470 447010 410970 459140 464190 FALSE TRUE 469741.3609 496010.1996 453980.6105 489072.4993 472513.9889 441825.8138 411972.1882 405461.6194 442615.6411 555139.143 0.846168689 0.893488067 0.817778058 0.880990839 0.851163163 0.795883013 0.742106179 0.730378364 0.797305769 1 19.0824899 2.729156196 4.102143141 0.784491057 0.859649552 0.018837326 0.074102971 0.355204967 14.43015271 0.022765464 0.02256845 535.9893945 -2.729156196 0.075158495 KFSNS(ph)LK ddPTM_MDA-MB-175_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(0.003)NS(0.997)LK 58.592 0.066536 457490000 856890 481940 819120 474270 1044400 842020 929020 667050 851780 589050 TRUE FALSE 890720.6789 564709.446 840466.9401 568079.1904 866873.2611 646473.6159 856200.9849 658109.2858 821124.6042 704463.0695 1.264396556 0.801616821 1.193060327 0.806400243 1.23054465 0.917682763 1.215395131 0.934199839 1.165603478 1 19.42616455 3.198665853 24.99999787 1.066661198 1.013647452 0.027849968 0.169093501 740.4112565 463975.6854 0.044047327 0.052647242 1580.031892 -3.198665853 -0.053013746 KFTDFDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFTDFDEVR 9 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;E5RHK8;Q9UQ16-5;Q9UQ16-2;Q9UQ16-3;Q9UQ16;Q9UQ16-4 P50570-2 DNM2;DNM3 Dynamin-2;Dynamin-3 0 ; 128.01 0.00068823 430040000 1045200 855260 1020470 980510 1283280 1244280 1301260 1041680 1049010 847540 FALSE TRUE 1086465.303 1002144.252 1047064.287 1174451.951 1065148.524 955314.8272 1199263.841 1027717.983 1011256.335 1013599.236 1.071888439 0.988698705 1.033016058 1.15869459 1.050857663 0.94249758 1.183173584 1.013929319 0.997688533 1 19.95105591 1.513478633 15.21651427 1.00118038 1.059134528 0.135583196 0.066925491 0.294492308 108.9509296 0.035561063 0.016482132 32.61960011 -1.513478633 0.057954148 KFTNFQSPNIDPTEENDLDDSLS(ph)VK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFTNFQSPNIDPTEENDLDDSLSVK 25 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 KFTNFQSPNIDPTEENDLDDS(0.031)LS(0.969)VK 150.77 9.92E-08 88194000 149140 48759 75528 53592 115810 107640 80830 77701 81058 44221 TRUE FALSE 155028.1624 57132.97896 77496.32173 64192.33764 96124.65757 82642.2413 74494.33339 76659.54519 78140.73841 52885.25829 2.931405979 1.08031956 1.465367179 1.213803992 1.817607792 1.562670657 1.408602998 1.449544687 1.477552364 1 15.69057801 4.746494444 24.87481763 1.418312453 2.93140677 0.805058623 0.227621993 373.20827 1170085.652 0.051477654 0.566426337 55782.04659 -4.746494444 1.513094317 KFVADGIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFVADGIFK 9 1 P23396;P23396-2;E9PPU1;E9PL09;F2Z2S8;H0YCJ7;E9PQ96;E9PJH4;E9PK82;E9PQX2 P23396 RPS3 40S ribosomal protein S3 0 106.62 0.0046603 410930000 385370 378880 377050 327450 750950 549090 421970 452420 447830 641060 FALSE TRUE 400584.7052 443949.6927 386876.2328 392218.6327 623303.7872 421572.169 388894.8888 446356.0499 431712.6858 766663.4332 0.522503993 0.579067259 0.504623301 0.511591679 0.813008369 0.549879061 0.507256342 0.582205999 0.563105878 1 19.54823385 -0.981562949 4.789370242 1.000004715 0.57150819 0.69290037 0.085805376 5.16E-06 1.10E-06 0.082426982 0.019427969 0.104336689 0.981562949 -0.428496525 KFVEEQHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KFVEEQHTK 9 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ;; 99.568 0.0034073 821720000 1967950 1286840 1538330 1197180 2130300 2025410 1984820 1629030 1865860 1402270 FALSE TRUE 2045646.186 1507844.76 1578420.144 1433978.631 1768192.367 1555039.223 1829244.622 1607195.517 1798708.063 1677017.958 1.219811735 0.899122608 0.941206465 0.855076491 1.054366984 0.927264502 1.090772232 0.95836512 1.072563388 1 20.67746671 2.255672097 24.99935821 1.021885833 0.974559967 0.044564703 0.100827298 837.4099839 1223429.35 0.033758105 0.028178666 180.1656931 -2.255672097 -0.047325866 KFVHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFVHEK 6 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 56.51 0.098116 196650000 338230 288170 337120 259680 482260 423020 372090 334050 387340 316640 FALSE TRUE 351583.5816 337660.9558 345905.6241 311043.9289 400285.6175 324780.0159 342924.6135 329572.6061 373399.7091 378679.5456 0.928446191 0.891679944 0.913452095 0.82139089 1.057056348 0.857664534 0.905579975 0.870320592 0.986057244 1 18.53061797 1.159599104 6.843945839 0.996834563 0.904533193 0.261979356 0.058675648 0.292528332 20.24587266 0.052317367 0.013184174 14.44106106 -1.159599104 -0.09230137 KFVHLLDQSDQDFQEELDLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFVHLLDQSDQDFQEELDLMK 21 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 172.84 3.30E-12 861690000 1397590 929320 1441800 950080 1804130 1544860 1331140 1351290 1662050 1080840 FALSE TRUE 1452767.932 1088923.481 1479374.492 1138002.988 1497464.627 1186089.678 1226801.769 1333178.168 1602233.145 1292609.904 1.123902832 0.842422356 1.144486428 0.880391667 1.158481474 0.917592906 0.949088944 1.031384769 1.239533397 1 20.30185552 1.438114026 11.71686015 1.125138178 0.999690471 0.133464078 0.117737753 0.757279053 220.3489946 0.061599447 0.026159148 27.42294079 -1.438114026 -0.125447706 KFYEQFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KFYEQFSK 8 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 155.42 0.00065622 1013480000 2161690 1911190 1982220 1549730 3512600 2945800 2767200 2380120 2633580 2505420 FALSE TRUE 2247035.19 2239422.016 2033878.282 1856261.969 2915529.507 2261682.594 2550299.633 2348218.384 2538797.97 2996309.08 0.749934379 0.747393528 0.678794553 0.619516184 0.973040307 0.754822862 0.85114705 0.783703657 0.847308439 1 21.51475502 -5 0.087164678 1.767892553 0.572602024 0.461094556 0.083584371 198.5533225 1.209965285 28.26459923 2.154765491 1.00E-05 5 -1.19529053 KFYGPEGPYGVFAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFYGPEGPYGVFAGR 15 1 O00264 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 0 99.344 0.0041346 338460000 62887 95292 73935 86940 100410 120510 71855 78780 62045 113140 FALSE TRUE 65369.82732 111657.6597 75861.80684 104136.4725 83342.34407 92523.37885 66222.81734 77724.08296 59812.01257 135307.6168 0.483120085 0.825213409 0.560661762 0.769627571 0.615947173 0.683800225 0.489424165 0.574425038 0.442044683 1 17.04588353 KFYPLEIDYGQDEEAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KFYPLEIDYGQDEEAVK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 161.86 4.67E-09 287710000 368550 205100 287150 205710 396440 317000 355330 320450 342520 224570 FALSE TRUE 383100.6386 240324.3295 294633.3649 246398.824 329053.2704 243381.5542 327478.3061 316154.8919 330192.7721 268570.1918 1.426445116 0.894828752 1.097044176 0.917446655 1.225203989 0.906212087 1.219339733 1.177177891 1.229446834 1 18.03493967 KGAAPT(ph)PPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 64.65 0.041799 624160000 1385060 803250 1095390 813440 1442500 1385860 1429800 1190640 1256960 714830 TRUE FALSE 1439743.238 941201.9391 1123936.763 974336.0041 1197304.365 1064015.018 1317728.54 1174681.418 1211722.255 854887.2523 1.684132305 1.100966164 1.314719292 1.139724568 1.40054067 1.244626136 1.541406234 1.374077594 1.417405923 1 19.70537464 KGADSLEDFLYHEGYACTSIHGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 176.23 2.68E-13 1267720000 356326 798210 937530 848490 1082580 1147450 964920 1019900 934180 751116 FALSE TRUE 370394.0256 935296.3583 961962.802 1016318.79 898563.4383 880972.1273 889287.0491 1006229.909 900559.0443 898282.7992 0.412335654 1.041204796 1.070890818 1.131401815 1.000312417 0.980729151 0.989985615 1.120170518 1.002533996 1 19.77681018 4.738538375 9.307726911 1.043679795 0.410009684 0.929590268 0.051588689 0.018667169 37.85787857 0.012783352 0.074442586 54769.44939 -4.738538375 -0.633670111 KGAGDGS(ph)DEEVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 KGAGDGSDEEVDGK 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK;KGAGDGS(1)DEEVDGK 196.71 2.59E-08 46307385000 28672960 8807498 13473206 9797112 21216331 23433110 26568410 15028409 16949927 5135078 TRUE FALSE 29804990.6 10320117.27 13824328.82 11734951.51 17609986.63 17991125.33 24485908.6 14826977.76 16339902.44 6141198.217 4.853285881 1.680472915 2.251080054 1.910856985 2.867516405 2.929579001 3.987154906 2.414346066 2.660702661 1 22.55008874 KGAGDGS(ph)DEEVDGKADGAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGAGDGSDEEVDGKADGAEAK 21 2 P35579;P35579-2 P35579 MYH9 Myosin-9 1 KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK;KGAGDGS(1)DEEVDGKADGAEAK 267.77 1.81E-37 1909740000 4433780 829750 1545460 962760 2795020 2963400 3315130 1670240 2049510 407573 TRUE FALSE 4608829.058 972253.1079 1585735.957 1153191.054 2319923.499 2275195.261 3055281.448 1647853.165 1975748.535 487429.1259 9.455382974 1.994655338 3.253264676 2.365864068 4.759509384 4.667745811 6.268155278 3.380703116 4.053406804 1 18.89483294 0.550711859 1.439428479 1.004314766 4.391230041 0.209277288 2.035930971 3.118407013 8.168515007 1.850117719 0.540211799 3.553954465 -0.550711859 3.386915276 KGAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 20 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;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE;KGAGDGS(1)DEEVDGKADGAEAKPAE 203.59 6.52E-24 78814372000 29082870 5750577 10847751 5295597 19327880 18802550 16147130 10520945 13404187 3375127 TRUE FALSE 30231084.16 6738193.866 11130452.3 6343050.281 16042533.86 14435942.72 14881475.76 10379928.94 12921772.93 4036418.515 7.489581185 1.669349658 2.757506998 1.571455055 3.974447596 3.57642367 3.686801976 2.571569054 3.201296615 1 21.94464434 7.999999976 0.068931161 6.68E-11 10.35478115 0.217280326 1.526730237 521.4254979 2.655490757 70.68830051 525.3968958 99999994.58 -7.999999976 10.35478115 KGAGSVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGAGSVFR 8 1 P62917;E9PKZ0;G3V1A1;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 91.087 0.020421 1268440000 858100 1127000 1019700 870130 1562890 1380470 948230 1077380 1020800 1979270 FALSE TRUE 891978.4506 1320553.483 1046274.22 1042239.117 1297230.516 1059876.764 873905.2549 1062939.483 984061.6074 2367070.061 0.376828073 0.557885254 0.442012358 0.440307676 0.548032159 0.447758933 0.369192813 0.449052819 0.415729819 1 21.17467098 -1.435499844 3.295099864 1.007565359 0.451467149 0.887647609 0.058736987 26455286.68 34394727.54 1857544.981 0.014728181 0.036685983 1.435499844 -0.55609821 KGASLS(ph)NGQGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGASLSNGQGSR 12 1 O43639 O43639 NCK2 Cytoplasmic protein NCK2 1 KGAS(0.04)LS(0.96)NGQGS(0.001)R 63.918 0.04121 70610000 73419 69660 73493 59858 90947 96528 82639 85564 87871 78077 TRUE FALSE 76317.63881 81623.56312 75408.28796 71697.73374 75487.86143 74110.8349 76161.53924 84417.15453 84708.53987 93374.69328 0.817326795 0.874150803 0.807588066 0.767849738 0.808440261 0.793692941 0.815655041 0.904068882 0.907189485 1 16.51074398 1.289572752 1.163943927 0.991879791 0.810102105 0.814384153 0.02889077 0.185002631 0.501218337 0.028627169 0.009428113 19.47927337 -1.289572752 -0.181777686 KGAVAEDGDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 155.98 9.71E-05 1134190000 1775670 1653890 1789570 1911320 2088930 2263320 2448240 1985580 1946960 1393660 FALSE TRUE 1845774.823 1937932.742 1836207.664 2289373.391 1733854.425 1737698.231 2256340.552 1958966.548 1876889.29 1666720.994 1.107428796 1.162721745 1.101688688 1.373579261 1.040278746 1.042584954 1.353760203 1.175341617 1.126096867 1 20.66858119 4.789866789 1.697241427 1.168434751 1.084242576 0 0.119686744 6.026629123 15.42689008 0.030577695 0.858675579 61640.59032 -4.789866789 -0.084192174 KGAVAEDGDELRTEPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGAVAEDGDELRTEPEAK 18 2 P27695;G3V3M6;G3V5Q1;G3V3C7;A0A0C4DGK8;G3V5D9 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 134.37 6.01E-06 755920000 431950 264910 394220 280820 579120 495480 428220 374410 471340 300880 FALSE TRUE 449003.7195 310406.2318 404493.6971 336365.3578 480681.3893 380412.2791 394654.9975 369391.6464 454376.5655 359831.6753 1.247815994 0.862642877 1.124119206 0.934785292 1.335850683 1.057195086 1.0967767 1.026567897 1.262747547 1 18.45696266 KGAVECCPNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGAVECCPNCR 11 1 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 132.5 0.00029049 179981000 229560 212784 201737 189956 262810 287230 203667 214932 227150 232430 FALSE TRUE 238623.2061 249327.9968 206994.4319 227528.7298 218137.6501 220525.1855 187703.0484 212051.1881 218974.9159 277970.2084 0.858448851 0.89695942 0.744664089 0.818536386 0.784751903 0.793341081 0.675263185 0.762855809 0.787763974 1 18.08457074 4.24459149 24.99984359 0.78060643 0.877704165 0.122595447 0.079528916 213.9258704 886763.599 0.017964963 0.046594358 17562.70836 -4.24459149 0.097097735 KGDECELLGHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGDECELLGHSK 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 145.71 4.16E-05 89913000 274940 205100 245500 219530 264420 373430 278010 220280 279020 218620 FALSE TRUE 285794.8435 240324.3295 251897.9317 262952.3788 219473.9828 286706.5419 256218.8498 217327.5069 268978.1247 261454.4033 1.09309631 0.919182567 0.963448802 1.005729395 0.839435022 1.096583337 0.979975271 0.83122527 1.028776419 1 17.99619984 4.747858355 24.16078694 0.954302673 1.093096428 0.194229662 0.078001194 1204.724697 3130448.271 0.01831592 0.224475215 55957.50671 -4.747858355 0.138793755 KGDEVDGVDEVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGDEVDGVDEVAK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 130.06 0.00023489 742300000 1681490 747890 1222890 756690 1684920 1523960 1559700 1230690 1371800 633410 FALSE TRUE 1747876.524 876334.2897 1254759.518 906361.0235 1398517.9 1170043.386 1437446.638 1214194.614 1322429.186 757514.5621 2.307383397 1.156854711 1.656416366 1.196493201 1.84619276 1.544582038 1.897582846 1.602866366 1.745747543 1 19.5309141 KGDEVQCEIEELGVIINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGDEVQCEIEELGVIINK 18 1 Q96GK7;Q6P2I3 Q96GK7 FAHD2A;FAHD2B Fumarylacetoacetate hydrolase domain-containing protein 2A;Fumarylacetoacetate hydrolase domain-containing protein 2B 0 114.34 0.00035446 33047000 61034 49028 64452 47328 85484 78316 83597 68622 79357 50150 FALSE TRUE 63443.66945 57448.17762 66131.67207 56689.33714 70953.46021 60128.29589 77044.4487 67702.23433 76500.95707 59975.93232 1.057818812 0.957853849 1.102636833 0.945201432 1.183032218 1.002540412 1.28458943 1.128823375 1.275527601 1 15.87209606 2.803854655 1.29609385 1.172599123 1.021232932 0.229231247 0.103013143 0.533790432 1.845754548 0.041345294 0.041459341 636.5824405 -2.803854655 -0.151366191 KGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 51 2 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KGDGGGAGGGGGGGGS(0.076)GGGGS(0.919)GGGGGGGS(0.004)S(0.001)RPPAPQENTTSEAGLPQGEAR 135.19 1.69E-12 91401000 2875.6 2344.9 3276 4618 4973.8 4896.9 3554.4 3585 3834.2 3139.9 TRUE FALSE 2989.130908 2747.618334 3361.375251 5531.426617 4128.355253 3759.669188 3275.79684 3536.948939 3696.207891 3755.103288 0.796018293 0.731702466 0.895148547 1.473042468 1.099398588 1.001215919 0.872358651 0.941904568 0.984315905 1 11.87463688 3.995933812 24.42564942 1.044600462 0.776251515 0.367137631 0.153837598 152.1231067 913837.975 0.04219631 0.087850628 9906.809497 -3.995933812 -0.268348947 KGDIFLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDIFLVR 8 1 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 133.13 0.0014951 4968500000 5548300 5711100 5553800 5130000 6846100 6923200 5577300 5963000 5543500 6124200 FALSE TRUE 5767351.168 6691936.999 5698536.59 6144698.688 5682402.367 5315391.722 5140136.652 5883075.739 5343990.518 7324119.735 0.787446325 0.913684817 0.778050714 0.838967536 0.775847825 0.725737961 0.701809479 0.8032468 0.729642703 1 22.80422395 7.89511368 10.96093463 0.796221646 0.789283299 0 0.087370717 0 0 0.018163381 0 78544120.27 -7.89511368 -0.006938347 KGDIIQLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDIIQLQR 9 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 125.68 0.00079325 1852460000 546230 677770 647850 604120 860800 851570 600750 646280 584220 805720 FALSE TRUE 567795.5822 794171.7252 664733.5032 723613.1329 714481.5235 653805.7732 553661.6452 637617.6737 563194.0363 963585.4076 0.58925299 0.824184052 0.689854265 0.750958999 0.741482299 0.678513568 0.574584921 0.661713709 0.584477548 1 19.87805302 -1.130911 4.751097855 1.000023757 0.68017283 0.61552916 0.07649758 11034945.51 2626665.106 2743.045306 0.018106332 0.073975686 1.130911 -0.319850927 KGDIMTVLEQDTQGLDGWWLCSLHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGDIMTVLEQDTQGLDGWWLCSLHGR 26 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 0 154.14 4.54E-08 77565000 87860 132490 161950 147590 165210 196630 156560 166290 158190 153480 FALSE TRUE 91328.78064 155244.1269 166170.55 176782.8615 137127.6632 150965.6625 144288.4181 164061.1545 152496.7728 183551.4674 0.497564971 0.845779819 0.905307663 0.963124207 0.747080179 0.822470474 0.786092425 0.893815543 0.83081206 1 17.48582512 4.737519625 5.549125858 0.860667269 0.484909183 0.694159269 0.073363872 0.078493414 9.621276837 0.017052929 0.112162977 54641.12413 -4.737519625 -0.375758086 KGDIVDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGDIVDIK 8 1 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 ;;; 85.377 0.026914 4921870000 7075700 4141980 5956730 4182510 7489230 6805970 6880830 5197050 6210260 3599690 FALSE TRUE 7355054.1 4853332.845 6111967.277 5009797.994 6216213.36 5225386.613 6341492.565 5127392.045 5986753.956 4304980.335 1.708498884 1.12737631 1.419743367 1.163721458 1.443958596 1.213800344 1.473059589 1.191037275 1.390657678 1 22.03757522 -4.031464557 0.214990318 3.72E-13 1.381756436 0.283672026 0.168431878 119.2483868 1.736439048 52.38581117 0.310650937 9.30E-05 4.031464557 1.381756436 KGDLLLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDLLLNR 8 1 Q15008;Q15008-4;Q15008-3;Q15008-2 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 110.76 0.0053949 1970240000 1191850 1048490 1210050 924290 1862570 1416270 1264740 1150790 1115740 1596410 FALSE TRUE 1238905.158 1228560.001 1241584.897 1107111.803 1545971.017 1087362.756 1165606.374 1135365.542 1075584.735 1909195.974 0.648914609 0.643496015 0.650318204 0.579883793 0.809749778 0.569539623 0.61052212 0.594682556 0.563370523 1 20.86453377 -1.218232083 3.452132024 1.000738464 0.629636351 0.730258117 0.067451867 39911789.31 65478553.9 322435.1705 0.015805131 0.060501747 1.218232083 -0.371102113 KGDRS(ph)PEPGQTWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 KGDRS(0.987)PEPGQT(0.004)WT(0.009)R;KGDRS(0.997)PEPGQT(0.002)WT(0.001)R;KGDRS(0.964)PEPGQT(0.036)WTR;KGDRS(1)PEPGQTWTR;KGDRS(1)PEPGQTWTR;KGDRS(0.996)PEPGQT(0.004)WTR;KGDRS(1)PEPGQTWTR;KGDRS(0.986)PEPGQT(0.014)WTR 215.64 3.35E-12 17919020000 5345781 4301665 4593098 3944269 5411514 6051430 5240615 4709084 5272783 4033093 TRUE FALSE 5556836.562 5040442.501 4712797.907 4724433.636 4491666.783 4646077.093 4829841.903 4645966.431 5083016.57 4823300.355 1.152081801 1.045019412 0.977089868 0.979502268 0.931243433 0.963256847 1.001356239 0.963233904 1.053846162 1 22.20158922 4.643154259 2.090134906 0.979396091 1.180997138 0.737904896 0.030711681 0.259936881 1.475343584 0.007712252 0.091615504 43969.77657 -4.643154259 0.201601048 KGDSSAEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGDSSAEELK 10 1 P26373;P26373-2 P26373 RPL13 60S ribosomal protein L13 0 ;;; 159.44 1.23E-05 8362100000 5920880 3127130 4340790 3367110 6554800 5932680 6892940 5101090 5680150 2724450 FALSE TRUE 6154640.914 3664190.252 4453914.553 4033114.308 5440617.437 4554904.981 6352653.351 5032718.232 5475722.511 3258253.815 1.888938451 1.124587113 1.366963658 1.237814651 1.669795463 1.397958919 1.949711015 1.544605951 1.680569662 1 21.63566756 KGDSVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGDSVGLR 8 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83;A0A3B3IS03;A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 Q9UDY2-7;A0A087X0K9;G3V1L9 TJP2;TJP1 Tight junction protein ZO-2;Tight junction protein ZO-1 0 73.196 0.070858 159920000 307140 279210 306920 282540 393920 407570 343280 336860 313170 280540 FALSE TRUE 319266.1244 327162.1455 314918.5873 338425.5687 326961.6191 312918.0443 316372.8166 332344.9427 301899.0729 335506.4417 0.951594618 0.975129252 0.938636486 1.008700658 0.974531569 0.932673729 0.942970916 0.990576935 0.899830928 1 18.35598094 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;KGDVEGSQS(1)QDEGEGSGESER 320.56 3.65E-67 3172590000 1817820 1410289 1758490 1361953 2067830 2158290 1990380 1749980 1953120 1267963 TRUE FALSE 1889588.937 1652495.165 1804317.694 1631343.238 1716340.995 1657059.857 1834368.815 1726524.38 1882827.593 1516396.073 1.246105137 1.089751678 1.189872307 1.075802864 1.131855341 1.092761902 1.209689768 1.13857086 1.241646313 1 20.5322152 2.252366737 24.99901722 1.158642366 1.13480592 0 0.076008708 1149.018543 2080542.345 0.024304943 0.020226654 178.79968 -2.252366737 -0.023836445 KGDVEGSQSQDEGEGSGESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ;; 198.48 1.37E-21 420410000 164775 171426 191954 168339 245680 268496 222113 209964 222093 192212 FALSE TRUE 171280.4442 200867.082 196956.4789 201635.9518 203919.4014 206141.8731 204703.2027 207149.776 214099.9163 229872.2613 0.745111408 0.873820447 0.856808376 0.877165216 0.887098775 0.896767065 0.8905085 0.901151687 0.93138648 1 17.81047286 8 0.095725429 1.056247177 0.338879419 0.792058307 0.027493473 63.65651715 0.434071872 0.392684188 5.995173859 100000000 -8 -0.717367759 KGDVVHCWYTGTLQDGTVFDTNIQTS(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 1 KGDVVHCWYTGTLQDGTVFDTNIQT(0.232)S(0.768)AK;KGDVVHCWYTGTLQDGTVFDTNIQT(0.053)S(0.947)AK 180.23 7.09E-18 518120000 753680 276425 391638 278219 555160 467437 530984 399082 459024 255609 TRUE FALSE 783435.8684 323898.8435 401844.408 333249.8878 460794.1015 358881.8408 489364.0866 393732.9586 442503.8159 305690.6896 2.5628385 1.059563979 1.314545787 1.090153868 1.507386771 1.174003177 1.600847207 1.28801096 1.447554116 1 18.22171309 4.745211779 24.99697498 1.29863486 2.562839073 0.803786539 0.190469892 304.1775728 1143156.868 0.042069714 0.408290819 55617.54041 -4.745211779 1.264204213 KGDVVHCWYTGTLQDGTVFDTNIQTSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDVVHCWYTGTLQDGTVFDTNIQTSAK 28 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 322.73 1.77E-83 647218000 610035 415284 603302 423585 728060 729117 641927 592036 652262 389717 FALSE TRUE 634119.6528 486605.7965 619024.5457 507368.8487 604304.6213 559790.6266 591611.0844 584100.7258 628787.218 466074.5846 1.360554027 1.044051344 1.328166277 1.08860012 1.296583511 1.201075204 1.269348521 1.25323445 1.349112865 1 18.83020132 KGDVVIVLTGWRPGSGFTNTMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGDVVIVLTGWRPGSGFTNTMR 22 2 P14618;P14618-3;B4DNK4;P14618-2;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 141.53 6.84E-08 1908200000 1444390 1911800 2000130 1854160 1988960 2390900 2030820 2298050 2127080 2290450 FALSE TRUE 1501415.633 2240136.778 2052255.031 2220907.314 1650877.29 1835649.709 1871639.022 2267248.399 2050526.806 2739219.824 0.548117978 0.817801024 0.749211514 0.810780973 0.602681565 0.670135961 0.683274488 0.827698595 0.748580595 1 21.38533362 0.592906306 0.801769575 1.000296386 0.706870485 0.510727646 0.085653214 1.108508017 1.212376999 0.085135849 0.028786169 3.916573728 -0.592906306 -0.293425901 KGDYIEAESSYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 ;; 151.56 7.18E-05 477576000 283596 278967 290994 219662 343805 380504 339936 324719 318201 306555 FALSE TRUE 294792.5891 326877.4122 298577.5427 263110.488 285365.1489 292137.7126 313290.9281 320366.6729 306749.0082 366618.5829 0.804085234 0.891600774 0.814409189 0.717668171 0.778370662 0.796843712 0.854541866 0.873841883 0.836697927 1 18.48392039 0.621290872 0.62030234 1.002011713 0.802883525 0.616935248 0.044673471 1.00887744 0.734006679 0.056740589 0.020289689 4.181103053 -0.621290872 -0.199128189 KGEDFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGEDFVK 7 1 P40926;G3XAL0;P40926-2 P40926 MDH2 "Malate dehydrogenase, mitochondrial;Malate dehydrogenase" 0 ; 84.476 0.034502 1049930000 1454790 1004820 1169450 1130690 1321530 1687660 1409450 1048960 1234900 867330 FALSE TRUE 1512226.233 1177390.019 1199926.828 1354337.107 1096896.803 1295726.542 1298973.626 1034900.407 1190456.19 1037266.707 1.457895276 1.135088989 1.156816101 1.305678759 1.057487717 1.249173942 1.252304366 0.997718715 1.147685722 1 19.98435546 8 0.117188276 0.940685522 2.101116906 0.39733347 0.106190016 103.9635368 0.840244074 0.75868701 19.65229598 100000000 -8 1.160431384 KGEDVLGSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGEDVLGSVR 10 1 P56192;P56192-2;F5H2V6 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;;; 129.84 0.00046903 586910000 858280 1041930 996340 1080480 1350960 1424670 1075560 1074690 1009280 1216870 FALSE TRUE 892165.5571 1220873.372 1022305.439 1294195.719 1121324.302 1093811.984 991254.7967 1060285.538 972956.21 1455292.378 0.613049014 0.83891965 0.702474262 0.889302891 0.77051479 0.75160978 0.681137902 0.728572179 0.66856408 1 20.4728776 -1.782176284 2.68390791 1.067000289 0.742455341 0.508303568 0.077134738 18685641.8 13999045.31 8208494.674 0.017804749 0.016512914 1.782176284 -0.324544948 KGEFETGFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGEFETGFEK 10 1 P15170-2;P15170-3;P15170;H3BR35;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 149.23 3.80E-05 2249000000 2605200 1532810 2057980 1520530 2971000 2469300 2703100 2048880 2432500 1231740 FALSE TRUE 2708055.308 1796058.194 2111612.649 1821286.296 2465990.481 1895842.498 2491223.959 2021418.115 2344954.8 1473075.87 1.838367842 1.219257087 1.433471753 1.236383226 1.674041732 1.286995827 1.691171521 1.372243043 1.591876459 1 20.49040031 -1.158752723 4.251045005 0.999875813 1.468026111 0.339902339 0.200851446 12903183.17 3517166.901 14839.49146 0.042016096 0.069382074 1.158752723 0.468150297 KGEIFELK ddPTM_MDA-MB-175_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 ; 87.298 0.02473 2852400000 5378200 3001000 4234800 3400400 5594900 5078200 5135900 4132500 4379400 2445900 FALSE TRUE 5590535.489 3516398.405 4345162.367 4072988.971 4643880.896 3898865.011 4733334.738 4077110.597 4221786.249 2925127.275 1.911211022 1.202135181 1.485460959 1.392414274 1.587582508 1.332887305 1.618163687 1.393823315 1.443282925 1 21.48006797 -2.92413433 0.330575807 4.54E-14 1.497846468 0.401721884 0.180336446 73.0264811 2.236670586 51.21396987 0.138839032 0.001190874 2.92413433 1.497846468 KGENSVSVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGENSVSVDGK 11 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 101.6 0.0050768 52533000 201580 122670 184160 145100 229180 218330 226500 170160 198990 129370 FALSE TRUE 209538.5341 143737.6183 188959.3609 173800.3469 190224.0655 167626.1663 208746.3382 167879.2835 191828.3888 154717.5746 1.354329233 0.929032262 1.221318014 1.123339397 1.229492293 1.083433261 1.349208962 1.085069256 1.23986166 1 17.23927756 3.339184161 19.08567106 1.17226578 1.14532074 0 0.134554708 19.37804291 3616.853967 0.03406614 0.04612574 2183.655684 -3.339184161 -0.026945039 KGENYVYINEATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGENYVYINEATR 13 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 74.12 0.056079 202580000 62025 44841 74354 53703 63654 56596 71368 61435 71887 41619 FALSE TRUE 64473.79489 52542.09294 76291.72632 64325.29311 52834.11582 43452.43672 65773.98967 60611.56431 69299.80091 49773.44621 1.295345205 1.055624976 1.532779667 1.292361651 1.061492017 0.873004384 1.321467463 1.217748999 1.392304656 1 15.60308866 -2.063333562 2.384033395 0.686625476 1.22133954 0.125433127 0.179201962 7795799.353 2983562.804 13281326.83 0.044502002 0.008643038 2.063333562 0.534714064 KGEQPTGQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGEQPTGQQR 10 1 Q92733;H0YE12;H0Y679 Q92733 PRCC Proline-rich protein PRCC 0 74.76 0.065783 16188000 21917 17068 20735 16140 24452 25735 24811 21652 21368 14872 FALSE TRUE 22782.30008 19999.29623 21275.37113 19332.44383 20295.65777 19758.43627 22866.24899 21361.79036 20598.96985 17785.88366 1.280920337 1.124447714 1.196194215 1.086954362 1.141110454 1.110905516 1.28564031 1.20105308 1.158163983 1 14.11844503 -2.476933114 1.580381858 1.96E-05 1.176302472 0.408583642 0.063579946 551704.2772 41929.59864 1961615.949 0.017660677 0.003334778 2.476933114 1.176282921 KGESGQSWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGESGQSWPR 10 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ;;;; 145.23 4.94E-05 12101500000 5679820 5249580 5963890 5080590 7234510 7316780 6420220 6099510 6359080 5185140 FALSE TRUE 5904063.679 6151154.529 6119313.873 6085515.538 6004790.574 5617568.732 5916986.38 6017756.045 6130217.953 6201068.907 0.952104188 0.991950682 0.986815977 0.981365572 0.968347661 0.905903291 0.954188136 0.970438506 0.988574397 1 22.56408549 1.181378917 2.715800604 0.999135201 0.963690278 0.230992339 0.022901783 0.42532676 5.514457522 0.023261768 0.006459305 15.18374553 -1.181378917 -0.035444922 KGESQTDIEITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KGESQTDIEITR 12 1 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;;;;; 179.39 3.33E-05 4020980000 2689160 1909992 2359650 2325238 2949600 3109390 3229150 2587330 2801540 1591071 FALSE TRUE 2795330.113 2238018.268 2421144.417 2785163.136 2448228.046 2387281.296 2976040.785 2552651.073 2700713.123 1902810.9 1.469053028 1.17616431 1.272404114 1.463709892 1.286637598 1.254607747 1.564023407 1.341515898 1.419328176 1 20.85970076 -0.470492652 7.863647981 1.000000082 1.358213363 0.481432232 0.112316004 0 0 0.105505542 0.024867895 0.338459998 0.470492652 0.35821328 KGESVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGESVKR 7 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;; 93.429 0.0084039 2944928000 1596200 1080478 1392700 971516 1977820 1520260 1607230 1407740 1566450 1112049 FALSE TRUE 1659219.209 1266041.692 1428994.906 1163678.965 1641630.863 1167202.655 1481251.113 1388871.548 1510073.77 1329933.71 1.247595422 0.951958494 1.074485815 0.874990202 1.234370443 0.877639724 1.113778154 1.044316373 1.135450406 1 20.34292291 KGETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGETLR 6 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 100.74 0.059833 101060000 213720 206520 242340 202560 249950 223580 256370 227710 211510 178250 FALSE TRUE 222157.8306 241988.2035 248655.5795 242625.7634 207463.5883 171656.9334 236275.0495 224657.9199 203897.7964 213174.6747 1.042139883 1.135163939 1.166440525 1.138154726 0.973209358 0.805240743 1.108363598 1.053867774 0.956482268 1 17.70167653 3.239616825 24.99711751 0.990633937 1.124807281 0.41812997 0.079145279 30.84030228 729879.2048 0.024029268 0.030762533 1736.268257 -3.239616825 0.134173345 KGFLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGFLFR 6 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 91.584 0.076526 1030780000 1188480 1139420 1130270 1065200 1469850 1439970 1172090 1136750 1025820 1120610 FALSE TRUE 1235402.108 1335106.522 1159725.765 1275893.381 1220005.422 1105558.79 1080218.523 1121513.726 988900.9386 1340172.074 0.921823497 0.996220222 0.865355865 0.952036985 0.910334908 0.82493794 0.806029721 0.83684308 0.73789102 1 20.35398682 2.820652384 3.844515644 0.828527147 0.933115248 0.285382406 0.068820205 0.256375052 7.17670806 0.020204963 0.021315235 661.6866675 -2.820652384 0.1045881 KGFNGCDS(ph)PEPDGEDSLEQSPLLEDKYR ddPTM_MDA-MB-175_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 204.98 1.55E-25 368010000 176276 98617 133443 90739 196197 177193 162562 132711 161721 81995 TRUE FALSE 183235.5126 115553.7026 136920.6342 108686.9034 162847.504 136042.6111 149819.9657 130932.2261 155900.6928 98060.35036 1.868599408 1.178393736 1.396289466 1.10836748 1.660686541 1.387335561 1.527834289 1.335220868 1.589844338 1 16.5813823 -1.031529249 4.364162045 0.999974415 1.431071984 0.280735022 0.214247363 0.834796425 56911497.95 3246.904228 0.045801853 0.092997388 1.031529249 0.431097569 KGFSEGLWEIENNPTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGFSEGLWEIENNPTVK 17 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 228.9 2.06E-15 2610200000 4211500 2788290 3823000 2921600 4767400 4570600 4069600 3843800 4288100 2905060 FALSE TRUE 4377773.272 3267157.118 3922630.521 3499483.76 3957039.051 3509147.418 3750614.118 3792280.148 4133772.119 3474250.886 1.260062504 0.940391821 1.129057932 1.007262824 1.138961802 1.010044333 1.079546136 1.091538945 1.189831205 1 21.72827051 1.580983686 4.922444971 1.108243008 1.074208151 0 0.093129369 0.715035287 37.52465194 0.047918714 0.021724028 38.10515091 -1.580983686 -0.034034857 KGGDGIKPPPIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGGDGIKPPPIIGR 14 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 132.65 2.77E-05 2237200000 2040080 1606990 1929240 1380710 2667400 2560400 2355300 2176000 2377500 1680430 FALSE TRUE 2120623.934 1882978.032 1979517.579 1653810.317 2213996.301 1965785.903 2170685.432 2146834.279 2291934.239 2009678.085 1.055205781 0.936955051 0.98499237 0.822922999 1.101667136 0.978159596 1.080115989 1.068247843 1.140448441 1 20.93853299 3.199728087 24.99999529 1.062494126 0.951583492 0.384870629 0.068988551 160.1829292 103123.6901 0.019238318 0.022994542 1583.901197 -3.199728087 -0.110910634 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 224.79 1.78E-25 3381167000 1497608 803538 1216976 866495 1574269 1461854 1538580 1138889 1404409 751146 TRUE FALSE 1556734.72 941539.4008 1248691.394 1037885.125 1306675.318 1122360.563 1417982.079 1123624.056 1353864.594 898318.6771 1.732942618 1.048112908 1.390031651 1.155364072 1.454578816 1.249401345 1.578484468 1.250807853 1.50710948 1 19.7768678 -1.351224469 4.903495754 0.999764075 1.358131521 0.244490706 0.195478825 0.000446054 5.90E-05 0.167452452 0.039443222 0.044542597 1.351224469 0.358367446 KGGEFDEFVNDDT(ph)DDDLPISKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGGEFDEFVNDDTDDDLPISKK 22 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 KGGEFDEFVNDDT(1)DDDLPISKK 174.89 1.01E-10 179490000 496630 225540 364220 161670 589400 425520 357920 316230 422280 210820 TRUE FALSE 516237.3359 264274.7405 373711.8724 193647.8435 489213.9985 326699.4288 329865.2952 311991.4541 407082.2253 252126.1426 2.04753593 1.048184602 1.482241661 0.768059359 1.940354116 1.295777683 1.308334359 1.237441905 1.614597443 1 17.94378619 -2.207704727 2.002068543 6.70E-05 1.383841821 0.098510591 0.366042365 8217540.161 1545689.759 37142255.6 0.080834944 0.006198624 2.207704727 1.383774794 KGGHERPPS(ph)PGLR ddPTM_MDA-MB-175_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 97.502 0.0019562 394150000 117070 90769 111496 90712 146155 133111 116643 105695 116613 89025 TRUE FALSE 121692.014 106357.8697 114401.6774 108654.5629 121311.6253 102197.9876 107500.2169 104278.3314 112416.1209 106467.7443 1.142994198 0.998968001 1.074519594 1.020539729 1.139421391 0.959896242 1.009697516 0.979435905 1.055870223 1 16.70005689 2.720714819 24.88250233 0.998768652 1.067964233 0.36951371 0.048015131 852.3624601 1188453.548 0.014507023 0.013708289 525.6719683 -2.720714819 0.069195581 KGGPDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGGPDDR 7 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 70.919 0.089348 283470000 1165000 1045500 1214200 852950 1448800 1469000 1499600 1330100 1395800 1103000 FALSE TRUE 1210995.1 1225056.492 1245843.049 1021660.964 1202533.493 1127847.013 1382057.434 1312272.185 1345565.431 1319111.732 0.918038306 0.928698049 0.944456045 0.774506768 0.911623682 0.855004914 1.047718249 0.994815036 1.020054176 1 20.33113534 2.238453003 25 1.014189945 0.88892126 0.637234914 0.046910338 1.895539651 440160.9519 0.017166321 0.013495558 173.1621633 -2.238453003 -0.125268685 KGHAVGDIPGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGHAVGDIPGVR 12 1 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 ;; 110.98 0.00092926 2162050000 2165880 2331140 2420160 2224290 2698000 2862920 2301030 2530050 2449060 2724050 FALSE TRUE 2251390.615 2731495.161 2483231.358 2664247.923 2239394.924 2198050.218 2120669.256 2496138.818 2360918.809 3257775.442 0.691082198 0.838454095 0.762247553 0.817812022 0.687400026 0.674708941 0.650956241 0.7662096 0.724702746 1 21.63545573 -1.687732733 4.424149621 1.010947009 0.736480591 0.648400134 0.058566144 0.006732652 0.000475207 0.060373326 0.013832708 0.020524249 1.687732733 -0.274466418 KGHYAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGHYAER 7 1 P16104 P16104 H2AFX Histone H2AX 0 75.38 0.082545 0 34660 48867 52229 35750 66293 62134 51832 48657 44239 65134 FALSE TRUE 36028.40356 57259.52712 53590.13065 42821.2433 55024.53954 47704.32015 47769.2724 48004.8325 42646.84703 77895.76023 0.462520726 0.735078866 0.687972368 0.549724955 0.706386835 0.61241228 0.613246116 0.616270158 0.547486114 1 16.24925719 -1.738207802 2.865157765 1.067431078 0.620705975 0.687878214 0.077790279 18699280.94 17375270.73 9022073.339 0.01792457 0.018272257 1.738207802 -0.446725103 KGIGPVYSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGIGPVYSSK 10 1 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 126.19 0.00062381 1142920000 772290 625140 757070 601950 1166470 1002330 887750 819950 942440 792050 FALSE TRUE 802780.6055 732502.9321 776799.8661 721013.9134 968193.8461 769554.048 818165.8353 808959.9114 908521.7685 947237.0328 0.847497065 0.773304787 0.820069148 0.761175808 1.022124149 0.812419723 0.863739283 0.854020571 0.959128219 1 19.85336596 -4.999931692 0.063415943 1.587484134 0.621616357 0.389094145 0.068035351 369.7803893 1.705660268 32.34013102 4.889077792 1.00E-05 4.999931692 -0.965867777 KGLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGLEAR 6 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 88.734 0.081721 439620000 1503960 1404330 1594250 1322730 1878090 1931410 1663240 1629170 1507980 1527660 FALSE TRUE 1563337.502 1645512.753 1635797.465 1584362.046 1558852.933 1482869.298 1532870.903 1607333.641 1453708.094 1826975.728 0.855696919 0.90067576 0.895358072 0.867204759 0.853242278 0.811652435 0.839020945 0.879778322 0.795690973 1 20.80102604 KGLIAAICAGPTALLAHEIGFGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGLIAAICAGPTALLAHEIGFGSK 24 1 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 249.78 1.62E-38 898660000 876660 752770 951530 775740 1272900 1141320 986660 928210 1096040 840840 FALSE TRUE 911271.2137 882052.3918 976327.6535 929179.0566 1056532.913 876265.7269 909323.011 915768.8632 1056593.734 1005586.499 0.90620868 0.877152182 0.970903701 0.924017036 1.050663383 0.871397665 0.9042713 0.910681343 1.050723867 1 19.93960575 0.386088771 0.010428184 1.932867769 1.95E-06 0.160676089 0.058529417 4891.980384 20.11996174 1916.079694 1811.395963 2.432701211 -0.386088771 -1.932865815 KGLVGPELHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGLVGPELHDR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 136.7 6.09E-05 884150000 1518760 1485360 1656140 1505180 1954450 2008080 1731430 1675690 1725940 1664630 FALSE TRUE 1578721.818 1740459.026 1699300.369 1802900.111 1622233.287 1541733.853 1595715.992 1653230.116 1663823.757 1990782.377 0.793015769 0.874258807 0.853584193 0.905623906 0.814872236 0.774436157 0.801552199 0.830442411 0.835763756 1 20.92490409 0.64521901 4.526381536 0.999999973 0.831748657 0.650693539 0.037047062 16.11236201 205.03128 0.037840335 0.009602931 4.417931829 -0.64521901 -0.168251316 KGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAK;KGNAEGS(1)S(1)DEEGKLVIDEPAK 112.8 0.00011592 343530000 1061820 148808 287556 188149 484720 693690 691980 341190 364880 76849 TRUE FALSE 1103741.474 174364.6164 295049.9456 225364.3106 402327.4675 532591.0105 637740.7994 336616.9061 351748.0401 91906.09019 12.00944868 1.897204158 3.210341611 2.45211509 4.377593114 5.794947967 6.939048306 3.662618064 3.827254966 1 16.48787284 4.747653953 24.68247793 3.937749562 12.00945372 0.686129525 1.681332385 614.9235166 1669073.637 0.413790508 5.07147696 55931.17632 -4.747653953 8.071704155 KGNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 KGNAEGS(1)S(1)DEEGKLVIDEPAKEK;KGNAEGS(1)S(1)DEEGKLVIDEPAKEK 138.34 5.77E-06 1435690000 2157770 223231 476770 238410 948880 1137410 940280 529160 610660 113961 TRUE FALSE 2242960.426 261569.1878 489195.0179 285566.7864 787589.7165 873263.7651 866578.3966 522067.4757 588682.4659 136289.476 16.45732665 1.919217796 3.589382189 2.095295945 5.778800678 6.407418904 6.358366191 3.830578053 4.319353798 1 17.05631464 4.745029875 24.91465603 4.172945026 16.45733243 0.813505219 1.796953305 299.4031817 1153041.063 0.436093905 4.172231528 55594.24987 -4.745029875 12.28438741 KGNAEGS(ph)SDEEGKLVIDEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAK 21 2 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 227.24 1.11E-25 486190000 1463400 310590 614730 383500 859750 954540 1306100 633180 708220 168580 TRUE FALSE 1521176.162 363931.4164 630750.3688 459355.1554 713610.0021 732862.5512 1203724.469 624693.2578 682731.3005 201610.0233 7.54514154 1.80512561 3.128566518 2.278434116 3.53955617 3.635050178 5.970558652 3.098522819 3.386395623 1 17.62120784 2.746102433 5.679468254 3.721705964 3.448504206 0 1.842100316 1.885730336 238.7104052 0.560694453 0.566723233 557.3171821 -2.746102433 -0.273201759 KGNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.502)S(0.498)DEEGKLVIDEPAKEK 139.75 1.12E-06 196360000 259060 35143 84126 40869 157750 156520 160570 80133 116170 24736 TRUE FALSE 269287.8888 41178.53688 86318.39267 48952.76622 130935.7113 120170.6021 147984.1038 79058.94821 111989.0644 29582.5456 9.102931589 1.391987608 2.917882519 1.654785456 4.426113733 4.062213026 5.002412768 2.672486312 3.785646641 1 14.85245858 1.608337774 16.55622451 2.66986359 3.850696898 0.097451053 2.122713552 0.175950566 606.7372839 1.017286701 0.518125692 40.58240435 -1.608337774 1.180833308 KGNAEGSS(ph)DEEGKLVIDEPAKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGNAEGSSDEEGKLVIDEPAKEK 23 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 KGNAEGS(0.23)S(0.77)DEEGKLVIDEPAKEK 139.93 1.43E-07 160700000 409700 70659 140560 71796 240070 228330 257140 162040 182710 36126 TRUE FALSE 425875.2724 82794.1336 144223.1091 85997.03451 199262.9872 175303.8179 236984.6949 159868.1188 176134.3028 43204.19803 9.857266002 1.916344647 3.338173503 1.990478667 4.612120957 4.057564447 5.485223791 3.700291318 4.076786767 1 15.39888388 0.318327705 1.590475818 0.999701932 4.205607321 0.18059065 2.119141965 11.75016187 25.39939326 1.901412948 0.541527854 2.081266555 -0.318327705 3.205905389 KGNCSQHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGNCSQHDR 9 1 Q9BRX2 Q9BRX2 PELO Protein pelota homolog 0 90.108 0.0075647 4709700 4688.9 11636 8450.1 9229.6 12051 13972 7899.1 11015 6733.8 12217 FALSE TRUE 4874.021393 13634.39248 8670.316548 11055.18733 10002.57532 10727.21475 7279.947902 10867.36194 6491.451853 14610.68724 0.333592891 0.933179409 0.593422911 0.756650741 0.684606765 0.734203297 0.49826184 0.743795399 0.444294765 1 13.83473642 -1.731464397 2.959149029 1.055825437 0.652082456 0.296294006 0.166696132 54761623.78 44388759.04 22348036.57 0.035686382 0.018558189 1.731464397 -0.40374298 KGNEAVAS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGNEAVASR 9 1 Q8NBJ4-2;Q8NBJ4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 1 KGNEAVAS(1)R;KGNEAVAS(1)R;KGNEAVAS(1)R 93.011 0.0059341 747490000 629190 579240 590530 680440 896260 988310 868730 635240 623230 694620 TRUE FALSE 654030.907 678719.9641 605919.6969 815029.0011 743914.0453 758789.9805 800636.6726 626725.6468 600800.074 830717.4897 0.787308459 0.81702862 0.729393211 0.981114532 0.895507865 0.913415198 0.963789354 0.754438969 0.723230318 1 19.6639984 3.758731651 24.97217633 0.878276672 0.781821954 0.246838078 0.088107767 1406.207587 1740909.92 0.023865749 0.042961008 5737.61827 -3.758731651 -0.096454718 KGNEQHAFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGNEQHAFTR 10 1 Q13045-3;Q13045;Q13045-2;K7EQZ7 Q13045-3 FLII Protein flightless-1 homolog 0 ;;; 101.39 0.0021825 325932000 652900 673848 737192 615948 866292 893020 729279 732343 724150 751970 FALSE TRUE 678676.9961 789576.1522 756403.8291 737780.676 719039.9953 685629.6388 672116.2064 722527.14 698087.983 899304.1242 0.754669058 0.87798569 0.841099033 0.820390629 0.799551538 0.762400194 0.747373651 0.803429141 0.77625351 1 19.77844956 -1.466028753 3.300499738 1.003462836 0.799458826 0.709850892 0.0387106 10956023.8 17907158.08 363055.5139 0.00980421 0.03419568 1.466028753 -0.20400401 KGNFNYIEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGNFNYIEFTR 11 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 91.202 0.017505 406670000 802540 582550 613350 582560 873590 912440 773830 640140 668580 614190 FALSE TRUE 834224.8989 682598.4309 629334.4049 697788.6292 725097.4838 700539.6382 713175.1826 631559.9704 644517.9364 734528.7711 1.135728009 0.929301149 0.856786595 0.949981344 0.987160085 0.953726615 0.97092886 0.859816518 0.877457714 1 19.48645948 1.75666718 25 0.898700803 0.962607512 0.095982918 0.074440067 15.08060544 20843.37605 0.034109436 0.018915707 57.10408542 -1.75666718 0.063906709 KGNS(ph)PNSEPPTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KGNS(0.826)PNS(0.174)EPPTPK;KGNS(0.942)PNS(0.058)EPPTPK;KGNS(0.996)PNS(0.004)EPPTPK;KGNS(0.917)PNS(0.083)EPPTPK 135.23 5.29E-05 1229309000 1762647 852693 1268260 827270 1717873 1620771 1588962 1266368 1413819 708171 TRUE FALSE 1832237.665 999136.3897 1301311.897 990901.5368 1425869.561 1244371.498 1464415.006 1249394.408 1362935.93 846923.5487 2.163403848 1.179724417 1.536516371 1.170001163 1.6835871 1.469284329 1.729099408 1.475215101 1.609278585 1 19.69187222 -1.357688904 4.317357421 0.999092763 1.538031423 0.275503074 0.269511556 0.002128028 0.000316595 0.23595129 0.055525244 0.043884494 1.357688904 0.53893866 KGNYAER ddPTM_MDA-MB-175_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 ;;;;;;;;; 127.02 0.0062459 53613020000 16174260 16270170 16968770 13443110 22681450 20201070 18015660 17144070 16150930 18078130 FALSE TRUE 16812832.27 19064445.13 17410990.09 16102117.03 18826065.23 15509677.64 16603545.49 16914281.78 15569661.18 21620193.45 0.777644859 0.881788832 0.805311485 0.744772107 0.870763034 0.717369975 0.767964706 0.782337208 0.720144398 1 24.3658761 4.008076918 24.71645665 0.78771646 0.833175182 0.002425619 0.083178023 521.0625047 1594484.728 0.018722235 0.040324348 10187.71808 -4.008076918 0.045458721 KGNYSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGNYSER 7 1 A0A0U1RR32;A0A0U1RRH7;P20671;A0A3B3IS11;Q7L7L0;P04908 A0A0U1RR32;Q7L7L0 HIST1H2AD;HIST3H2A;HIST1H2AB Histone H2A type 1-D;Histone H2A type 3;Histone H2A type 1-B/E 0 ;;;; 123.72 0.0067604 13263730000 5103580 4876890 5191370 3863950 6541310 5858190 5687900 5216070 4982930 5432870 FALSE TRUE 5305073.279 5714457.921 5326661.367 4628227.777 5429420.463 4497714.154 5242067.535 5146157.113 4803595.323 6497336.858 0.816499651 0.879507719 0.819822257 0.712326893 0.835637828 0.692239644 0.806802487 0.792040989 0.739317574 1 22.63141707 -1.178801064 3.64031686 1.000210257 0.789234047 0.572631382 0.054874864 12531996.58 19206833.38 30376.47604 0.013483331 0.066251991 1.178801064 -0.210976211 KGPEADSEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGPEADSEWR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 79.82 0.036695 0 235430 199830 217660 196380 299220 268770 243220 235220 231700 201920 FALSE TRUE 244724.9582 234149.248 223332.3984 235223.3779 248358.6913 206352.2407 224155.7809 232067.2606 223361.1623 241482.358 1.013427897 0.969632937 0.924839397 0.974081005 1.02847551 0.854523049 0.928249097 0.961011241 0.924958511 1 17.88155827 2.764599194 24.99778456 0.933395939 0.977773522 0.239632183 0.04270969 1245.077891 1195308.27 0.013076298 0.013865985 581.5662488 -2.764599194 0.044377583 KGPEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPEFTR 7 1 Q9NQG5;E9PIQ9 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ; 81.594 0.042935 556740000 410780 495130 473620 414670 570430 570440 425890 480950 431970 520840 FALSE TRUE 426997.9116 580164.7259 485962.9263 496690.4883 473468.5124 437963.9551 392507.6289 474503.6519 416423.4841 622888.6259 0.685512456 0.93141005 0.780176272 0.797398552 0.760117447 0.703117599 0.630140948 0.761779285 0.668536022 1 19.2486147 3.157812584 2.72583464 0.73014531 0.80875735 0.015444814 0.109330415 0.634881168 9.588252674 0.031032476 0.039415843 1438.177812 -3.157812584 0.07861204 KGPGAGSALDDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPGAGSALDDGR 13 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ; 111.81 0.001524 350240000 852870 757960 821560 736470 978070 995300 912250 857030 841630 649080 FALSE TRUE 886541.9662 888133.7339 842970.5285 882141.5679 811818.0108 764156.6589 840745.4613 845542.9147 811339.9007 776254.7986 1.142075988 1.144126562 1.085945659 1.136407233 1.045813839 0.984414731 1.083079245 1.089259501 1.04519792 1 19.56617076 3.234946099 24.97796464 1.048885357 1.125409902 0.597463886 0.034168708 75.3129902 520447.4503 0.010473539 0.012992031 1717.695189 -3.234946099 0.076524544 KGPGLAVQSGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGPGLAVQSGDK 12 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 99.991 0.0023853 0 683930 452990 563780 449200 743610 770310 784800 589330 597500 410090 FALSE TRUE 710932.0845 530787.5087 578472.57 538050.4193 617211.4378 591417.1767 723285.3253 581430.9953 575996.0917 490439.2839 1.449582258 1.082269562 1.179498847 1.097078552 1.258486949 1.20589275 1.474770372 1.185531042 1.174449337 1 18.90371502 0.860537785 2.337186729 1.000862731 1.237703645 0.260583094 0.123365317 0.737188363 7.845506985 0.115150089 0.031192955 7.25333581 -0.860537785 0.236840915 KGPGQPS(ph)SPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.927)S(0.073)PQR;KGPGQPS(0.887)S(0.113)PQR;KGPGQPS(0.5)S(0.5)PQR 86.43 0.0088668 2116650000 1029900 839620 1011580 938190 1080000 1270110 1290390 1080290 1051170 697490 TRUE FALSE 1070561.247 983818.2037 1037942.606 1123761.182 896421.9858 975146.2012 1189245.86 1065810.48 1013338.597 834149.8112 1.28341604 1.179426274 1.244311983 1.347193474 1.074653466 1.169030057 1.425698171 1.277720699 1.214816072 1 19.66994699 5.137734187 15.40468737 1.234150615 7.806322808 0.006123757 0.118044854 4883379.409 1853151.543 0.027481122 1126037217 137320.1239 -5.137734187 6.572172193 KGPGQPS(ph)SPQRLDR ddPTM_MDA-MB-175_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 119.4 9.89E-05 179900000 229770 198860 253530 180120 295950 303160 231990 275440 268360 224470 TRUE FALSE 238841.497 233012.6581 260137.2001 215747.1984 245644.5247 232755.6844 213806.0176 271748.1773 258701.776 268450.5988 0.889703722 0.86799083 0.969031923 0.803675609 0.915045546 0.867033583 0.796444555 1.012283745 0.963684854 1 18.0342971 1.672144975 8.6551436 0.990316387 0.87520118 0.558673744 0.048433711 0.086515509 10.75987102 0.022660052 0.011986225 47.00509931 -1.672144975 -0.115115206 KGPGQPSS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGPGQPSSPQR 11 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.354)S(0.646)PQR;KGPGQPS(0.319)S(0.681)PQR;KGPGQPS(0.087)S(0.913)PQR;KGPGQPS(0.131)S(0.869)PQR;KGPGQPS(0.043)S(0.957)PQR 116.79 0.0005771 4600400000 3660500 2640920 3286930 3042200 3526800 4017290 4380250 3458520 3438400 2029000 TRUE FALSE 3805019.367 3094477.466 3372590.096 3643938.08 2927315.796 3084335.28 4036914.559 3412164.196 3314652.656 2426543.702 1.568081944 1.275261378 1.389874039 1.501698929 1.206372584 1.271081694 1.663647993 1.406182874 1.36599751 1 21.21047141 0.746030333 3.607302237 1.000016019 1.408453944 0.457893521 0.133080483 2.554036065 35.33602203 0.126446385 0.032533547 5.572246668 -0.746030333 0.408437925 KGPGQPSS(ph)PQRLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 KGPGQPS(0.025)S(0.975)PQRLDR;KGPGQPS(0.002)S(0.998)PQRLDR;KGPGQPS(0.033)S(0.967)PQRLDR 168.69 1.80E-06 2790480000 1690650 1422550 1797960 1317560 2175330 2047330 1694610 1687990 1880600 1502250 TRUE FALSE 1757398.167 1666861.897 1844816.315 1578169.435 1805568.184 1571868.635 1561782.04 1665365.255 1812917.573 1796587.125 0.978186998 0.927793522 1.026844893 0.87842633 1.004998955 0.874919236 0.869304927 0.926960475 1.009089706 1 20.77682747 4.751496996 22.34756196 0.940045946 0.978187105 0.015638702 0.057860685 1860.187355 3213202.512 0.013375965 0.214112787 56428.30381 -4.751496996 0.038141158 KGPGRPTGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPGRPTGSK 10 2 P26583 P26583 HMGB2 High mobility group protein B2 0 ; 80.737 0.012998 5557600000 4034400 2553400 3497700 2572500 4241000 4173700 4392100 3792300 4217900 2602700 FALSE TRUE 4193681.227 2991926.587 3588852.935 3081332.822 3520116.335 3204421.428 4047835.725 3741470.421 4066098.603 3112649.233 1.347302864 0.961215467 1.152989838 0.989938985 1.130906848 1.029483629 1.300447118 1.202021218 1.306314428 1 21.56971158 2.242911846 24.99999121 1.220116064 1.094116549 0.120238423 0.128170885 175.138184 1006262.006 0.041485801 0.033587888 174.9491538 -2.242911846 -0.125999515 KGPQASS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPQASSPR 9 1 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 KGPQAS(0.081)S(0.919)PR;KGPQAS(0.024)S(0.976)PR 79.201 0.016912 224880000 416120 382010 418300 330130 481900 516640 480220 427780 450210 365850 TRUE FALSE 432548.7389 447617.2459 429201.2416 395428.7287 399986.8101 396658.1898 442579.1016 422046.3088 434007.03 437531.3029 0.988612097 1.023051935 0.980961222 0.90377243 0.914190156 0.906582425 1.011537 0.96460826 0.991945096 1 18.73902671 2.210851327 24.99996936 0.987254287 0.953340245 0.200260079 0.03785458 475.276957 428803.1284 0.016186872 0.01195726 162.4992372 -2.210851327 -0.033914042 KGPQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGPQVR 6 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 112.27 0.043518 5859700000 4417230 3532370 4434970 4136570 4489410 5063310 5385730 4579350 4374240 3070040 FALSE TRUE 4591625.651 4139027.069 4550548.962 4954771.2 3726301.692 3887432.988 4963582.41 4517971.304 4216811.957 3671555.559 1.250594081 1.127322467 1.239406265 1.349501899 1.014910882 1.058797266 1.351901757 1.23053328 1.148508279 1 21.80796 -2.703028239 0.989157646 0.006697939 1.200275692 0.235979266 0.106112772 14218.2546 737.387827 30983.51501 0.03303146 0.001981398 2.703028239 1.193577753 KGPSGYGFNLHSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPSGYGFNLHSDK 14 1 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ; 109.84 0.00048324 4037300000 3405000 2314500 3104000 2179500 5056000 3917200 3859500 2947000 3434700 2764800 FALSE TRUE 3539432.029 2711997.371 3184892.79 2610598.595 4196582.926 3007489.666 3556982.305 2907500.285 3311085.818 3306509.625 1.070443589 0.820199449 0.963218968 0.78953304 1.269188178 0.909566282 1.075751384 0.879326122 1.001383995 1 21.65687767 KGPSS(ph)TGASGQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGPSSTGASGQAK 13 1 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 KGPS(0.15)S(0.837)T(0.013)GASGQAK;KGPS(0.003)S(0.921)T(0.071)GAS(0.004)GQAK;KGPS(0.186)S(0.768)T(0.045)GAS(0.001)GQAK;KGPS(0.022)S(0.972)T(0.006)GASGQAK;KGPS(0.034)S(0.927)T(0.039)GASGQAK 195.6 1.82E-07 645193000 849414 511192 733744 553613 999280 861557 910978 686860 791311 445185 TRUE FALSE 882949.5206 598985.2495 752865.9714 663115.999 829422.7425 661473.4438 839573.164 677653.7652 762831.8717 532410.4772 1.658399972 1.125044069 1.414070541 1.245497652 1.557863299 1.242412522 1.576928329 1.272803212 1.432788993 1 19.02217944 -1.323884162 3.999718754 0.999247593 1.380825399 0.340695283 0.162854684 0.000958187 0.000161972 0.138277834 0.032529734 0.04743685 1.323884162 0.381577806 KGPST(ph)PYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGPSTPYTK 9 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 KGPS(0.142)T(0.853)PY(0.004)T(0.001)K;KGPS(0.123)T(0.877)PYTK 105.17 0.0018408 813040000 2306700 1534110 1987080 1409860 2540500 2404000 2330100 2046200 2211900 1390130 TRUE FALSE 2397770.297 1797581.459 2038864.937 1688726.1 2108666.717 1845707.433 2147460.673 2018774.036 2132294.151 1662499.358 1.442268405 1.081252423 1.226385398 1.01577549 1.268371448 1.110200389 1.291706167 1.214300641 1.282583443 1 20.66492235 4.752380918 24.27971036 1.178404996 1.442268671 0.384865278 0.103798884 1655.316302 2908007.581 0.023012841 0.45960854 56543.26966 -4.752380918 0.263863675 KGPTRPPRPST(ph)PDLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGPTRPPRPSTPDLSK 16 3 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 KGPT(0.006)RPPRPS(0.177)T(0.816)PDLSK 62.684 0.076992 515630000 568210 321870 449480 317820 555930 564350 493960 423170 457830 253680 TRUE FALSE 590643.3696 377148.6687 461193.8181 380683.8474 461433.2172 433288.2653 455242.1245 417498.0983 441352.7877 303383.739 1.94685243 1.243140684 1.52016657 1.254793183 1.520955667 1.428185527 1.500548863 1.376138681 1.454767448 1 18.21078424 -3.352888586 0.223399889 4.01E-15 1.523443956 0.395045106 0.181118131 69.26094334 1.341600687 32.63138301 0.320219166 0.000443722 3.352888586 1.523443956 KGQAVDYEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KGQAVDYEGSR 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;;;; 193.15 1.73E-06 5786820000 4671630 4559550 4520970 4412640 5668720 6608860 4722740 4519150 4567100 4305770 FALSE TRUE 4856069.56 5342617.244 4638790.192 5285447.022 4705152.999 5074052.423 4352559.298 4458578.186 4402730.963 5149403.193 0.943035412 1.03752164 0.900840353 1.026419339 0.913727829 0.985367087 0.845255098 0.865843675 0.854998298 1 22.29597381 2.244390895 24.99828982 0.877537708 0.968147469 0.283599599 0.057715879 139.9671865 600134.086 0.018620432 0.015186011 175.5459827 -2.244390895 0.090609761 KGQGGAGAGDDEEED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KGQGGAGAGDDEEED 15 1 P46781 P46781 RPS9 40S ribosomal protein S9 0 ;;;;;; 208.03 6.35E-08 5519009000 6477351 3925264 5783406 3886464 7232210 6962177 6965699 5649789 6429879 3667613 FALSE TRUE 6733081.819 4599397.558 5934126.311 4655194.979 6002881.527 5345316.905 6419709.311 5574062.82 6198468.911 4386211.547 1.535056334 1.048603677 1.352904722 1.061324774 1.368580029 1.218663726 1.46361142 1.270814862 1.413171445 1 22.06454396 KGQSEEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGQSEEIQK 9 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;;; 155.11 0.00011879 1391440000 1578258 1136665 1453053 1139861 2138735 1962984 2009213 1706804 1907115 1249515 FALSE TRUE 1640568.845 1331878.372 1490920.755 1365322.104 1775193.589 1507110.715 1851725.635 1683927.084 1838478.304 1494333.541 1.097859882 0.891285871 0.997716182 0.913666237 1.187950039 1.008550417 1.239164875 1.126874983 1.230299832 1 20.51107077 3.236833549 24.99909261 1.139227536 0.970756176 0.41249706 0.091501881 39.70318244 574702.8726 0.024170589 0.030349912 1725.176561 -3.236833549 -0.16847136 KGRPMVISSGMQSMDTMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGRPMVISSGMQSMDTMK 18 2 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 142.01 6.51E-08 355580000 198080 181240 209670 127380 285940 252080 222260 200620 248400 201050 FALSE TRUE 205900.3514 212366.5601 215134.1724 152575.3838 237336.0209 193538.2403 204838.6804 197931.017 239460.1325 240441.8982 0.856341399 0.883234419 0.894744943 0.634562383 0.987082629 0.804927268 0.8519259 0.823196866 0.995916828 1 17.87532879 1.234012658 24.85665909 0.997958544 0.841415095 0.355312415 0.08402671 114.4085548 625253.107 0.066876224 0.018931186 17.14007265 -1.234012658 -0.156543449 KGRPYDYNGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGRPYDYNGPR 11 2 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 193.28 5.74E-07 1652410000 593550 638260 658760 700170 860140 967120 678340 649980 692540 674290 FALSE TRUE 616983.8123 747876.19 675927.8268 838661.5362 713933.71 742521.0368 625169.9383 641268.0813 667615.6207 806404.2154 0.765104895 0.927420983 0.838199769 1.040001429 0.885329834 0.920780203 0.775256288 0.795219158 0.827892027 1 19.62114365 2.254213372 24.96659822 0.826484166 0.900975614 0.036684833 0.087622908 447.6552093 714021.8974 0.029110101 0.024276137 179.5615608 -2.254213372 0.074491448 KGS(ph)FSALVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGSFSALVGR 10 1 Q13619;A0A087WWN2 Q13619 CUL4A Cullin-4A 1 KGS(0.958)FS(0.042)ALVGR;KGS(0.939)FS(0.061)ALVGR;KGS(0.958)FS(0.042)ALVGR 166.86 3.32E-06 1882000000 2335690 1650860 2201280 1603740 3120620 2800280 2358540 1933890 2499660 1699970 TRUE FALSE 2427904.845 1934382.363 2258647.165 1920954.985 2590178.127 2149957.409 2173671.472 1907969.368 2409697.725 2033046.574 1.194219983 0.951469774 1.11096676 0.944865214 1.274037772 1.057505242 1.069169541 0.938477944 1.185264399 1 20.95521183 -4.999999913 0.149022095 0.753085368 1.090917514 0.030884067 0.109631834 547.7842123 4.865659122 39.97111394 0.541563858 1.00E-05 4.999999913 0.337832147 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER;KGS(1)GS(1)EQEGEDEEGGER 111.11 0.001839 321980000 1034720 509520 684330 426623 951230 1144210 847930 680400 752470 404024 TRUE FALSE 1075571.545 597026.0965 702164.202 511007.7561 789540.2644 878484.5682 781467.0309 671280.3509 725388.7517 483184.7673 2.226004662 1.235606205 1.453200203 1.057582504 1.634033848 1.818113127 1.61732547 1.389282933 1.50126577 1 18.88221545 0.377072843 1.067577249 0.999318364 1.538863112 0.229731466 0.302711419 4.119794174 5.651655585 0.290502103 0.088485875 2.382719083 -0.377072843 0.539544747 KGS(ph)IQIQPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGSIQIQPSR 10 1 Q9BVG3-2;Q9BVG3 Q9BVG3-2 TRIM62 E3 ubiquitin-protein ligase TRIM62 1 KGS(0.999)IQIQPS(0.001)R 43.544 0.09716 192360000 241140 292740 275890 197100 423930 383940 274690 295440 281800 391440 TRUE FALSE 250660.3934 343015.8178 283079.92 236085.7917 351870.53 294775.7537 253159.08 291480.11 271658.073 468135.1734 0.535444478 0.732728146 0.604696968 0.504311159 0.751643008 0.629680849 0.54078201 0.622640909 0.580298359 1 18.83656564 -1.15447923 4.629675839 1.000044545 0.613819808 0.700345305 0.076249644 3.51E-05 6.40E-06 0.069924572 0.016479377 0.070068169 1.15447923 -0.386224738 KGS(ph)ITEYTAAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.903)IT(0.097)EYTAAEEK;KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.999)IT(0.001)EYTAAEEK;KGS(0.986)IT(0.014)EYTAAEEK 264.23 1.94E-24 3112570000 5440580 1868548 2957253 2080226 4378500 4298650 5018010 3067760 3456900 1158913 TRUE FALSE 5655378.299 2189456.584 3034321.443 2491688.494 3634244.134 3300353.684 4624685.264 3026641.695 3332486.844 1385979.814 4.080418953 1.579717513 2.189296996 1.79778123 2.622147955 2.381242246 3.336762353 2.183755972 2.404426682 1 20.40247481 KGS(ph)ITEYTAAEEKEDGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KGSITEYTAAEEKEDGRR 18 3 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 KGS(0.997)IT(0.001)EYT(0.003)AAEEKEDGRR;KGS(0.998)IT(0.002)EYTAAEEKEDGRR;KGS(0.982)IT(0.018)EYTAAEEKEDGRR;KGS(0.979)IT(0.02)EYTAAEEKEDGRR 225.84 2.12E-18 2744160000 2958640 1160920 1834460 1028780 3090360 2408180 2119350 1720640 2130790 1055470 TRUE FALSE 3075449.392 1360298.979 1882267.535 1232269.613 2565061.711 1848916.691 1953229.809 1697577.635 2054103.284 1262269.138 2.436445048 1.0776616 1.491177656 0.976233654 2.03210364 1.464756315 1.547395678 1.344861871 1.627310073 1 20.26758812 -3.07572318 0.238598592 3.12E-15 1.587749799 0.14890363 0.402828192 122.7766901 2.788070557 63.03794282 0.628769393 0.000839995 3.07572318 1.587749799 KGS(ph)PTPGFSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.892)PT(0.108)PGFSTR;KGS(0.906)PT(0.094)PGFSTR;KGS(0.899)PT(0.101)PGFSTR;KGS(0.626)PT(0.36)PGFS(0.013)TR;KGS(0.833)PT(0.167)PGFSTR;KGS(0.947)PT(0.053)PGFSTR 140.27 2.37E-05 11923980000 3640220 2386590 2939320 2275440 4139520 4110060 3710930 2972700 3144730 2038250 TRUE FALSE 3783938.696 2796468.267 3015921.094 2725515.24 3435885.869 3155560.854 3420057.61 2932855.819 3031551.782 2437606.063 1.55231756 1.147219114 1.237247125 1.118111446 1.40953287 1.294532739 1.403039507 1.203170547 1.243659436 1 21.21703356 0.645313875 1.266762081 1.000822849 1.291923287 0.339686141 0.124282407 1.387390395 3.399976419 0.112911997 0.034031588 4.418896961 -0.645313875 0.291100438 KGS(ph)SGNASEVSVACLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.992)S(0.008)GNASEVSVACLTER;KGS(0.969)S(0.031)GNASEVSVACLTER;KGS(0.955)S(0.045)GNASEVSVACLTER;KGS(0.764)S(0.236)GNASEVSVACLTER;KGS(0.988)S(0.012)GNASEVSVACLTER 290.39 2.28E-49 10338380000 4991830 2910660 3884200 2782577 5619630 5628650 4979810 4130600 4817470 3018440 TRUE FALSE 5188911.303 3410543.213 3985425.443 3332962.425 4664407.3 4321481.341 4589479.48 4075236.063 4644090.196 3609845.526 1.43743306 0.94478924 1.10404321 0.923297798 1.292134875 1.19713747 1.271378358 1.128922563 1.286506628 1 21.78350567 3.208160487 24.99933138 1.202488638 1.091251165 0.079178004 0.15360619 440.0572154 361876.8454 0.041684881 0.0498286 1614.955229 -3.208160487 -0.111237473 KGS(ph)SSQAPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGSSSQAPASK 11 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 KGS(0.752)S(0.131)S(0.117)QAPASK 73.887 0.025928 67645000 111620 55355 72533 49825 112310 107310 115840 84325 100410 55045 TRUE FALSE 116026.8438 64861.79065 74423.26957 59680.23629 93219.58632 82388.8788 106760.1581 83194.7613 96796.26371 65830.01385 1.762521941 0.985292071 1.130537049 0.906580947 1.416065118 1.251539746 1.621755061 1.263781616 1.470397134 1 16.00645788 KGS(ph)VSHDTVQPR ddPTM_MDA-MB-175_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(0.818)VS(0.182)HDTVQPR;KGS(0.985)VS(0.015)HDTVQPR 169.92 2.60E-05 330130000 172325 169770 201044 155877 273080 285490 244810 238790 227883 169108 TRUE FALSE 179128.5241 198926.6769 206283.3718 186709.0054 226661.9591 219189.2741 225621.1525 235589.4106 219681.5353 202241.4748 0.885716069 0.983609702 1.0199855 0.923198397 1.120749141 1.083799821 1.115602785 1.164891676 1.086233848 1 17.62571936 3.232770439 24.98198264 1.108330245 0.960080294 0.633988679 0.052215268 82.02269786 353890.6405 0.014734645 0.018065592 1709.111667 -3.232770439 -0.148249951 KGSLESPATDVFGSTEEGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGSLESPATDVFGSTEEGEKR 21 2 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 210.64 1.08E-22 692980000 400000 237870 345010 218150 414810 382700 378300 307160 359580 197265 FALSE TRUE 415792.3089 278722.3221 354001.244 261299.4189 344300.7444 293823.7249 348647.8575 303043.0226 346638.786 235915.2999 1.762464364 1.18145081 1.500543815 1.107598443 1.459425245 1.245462778 1.477851829 1.284541625 1.469335758 1 17.84790946 -2.141904139 2.420049047 0.179755995 1.37190658 0.289007176 0.180890063 2251190.59 798372.8845 10215745.94 0.039510876 0.007212667 2.141904139 1.192150585 KGSPT(ph)PGFSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGSPTPGFSTR 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 KGS(0.182)PT(0.818)PGFSTR 104.86 0.0014907 5858600000 1353500 905570 1064700 828720 1633200 1576100 1379300 1130100 1171300 673540 TRUE FALSE 1406937.225 1061094.603 1092446.957 992638.3425 1355589.247 1210074.661 1271186.862 1114952.858 1129145.142 805507.2673 1.746647463 1.317299851 1.356222347 1.232314571 1.682901325 1.502251699 1.578119669 1.384162382 1.401781446 1 19.61953808 0.553946119 1.351312536 1.000355836 1.470481167 0.465160377 0.152607443 1.609721866 3.859572626 0.143467056 0.042458215 3.58052012 -0.553946119 0.470125331 KGSS(ph)GNASEVSVACLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGSSGNASEVSVACLTER 18 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 KGS(0.472)S(0.527)GNASEVSVACLTER 100.08 0.00056146 376930000 79523 44203 58506 44813 87180 87402 73845 66140 73617 49340 TRUE FALSE 82662.62945 51794.5214 60030.71442 53676.87765 72361.17474 67104.21009 68056.83594 65253.50148 70967.53855 59007.22833 1.400889887 0.877765705 1.017345097 0.90966614 1.226310349 1.137220168 1.153364391 1.105856068 1.20269229 1 15.84860407 3.223838806 24.99737373 1.141283465 1.036579335 0.075349681 0.143805463 518.7615824 880846.3053 0.039368161 0.047242573 1674.321315 -3.223838806 -0.10470413 KGT(ph)QTSPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGTQTSPVPR 10 1 F5H7S1;Q2M1K9-2;Q2M1K9 F5H7S1 ZNF423 Zinc finger protein 423 1 KGT(0.673)QT(0.292)S(0.035)PVPR 56.205 0.073613 71720000 102420 94700 106520 80639 127110 131000 113620 92731 101530 85559 TRUE FALSE 106463.6207 110963.9883 109295.9987 96589.15352 105503.8876 100577.2353 104714.1675 91488.09262 97875.95513 102322.6479 1.040469758 1.084451884 1.068150609 0.943966516 1.031090279 0.98294207 1.023372339 0.89411381 0.956542438 1 16.64276598 3.492563334 0.631408636 0.953480394 1.081481919 0.405520971 0.043201791 0.960574534 0.734614767 0.027020083 0.073630661 3108.589202 -3.492563334 0.128001525 KGTDLWLGVDALGLNIYEKDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGTDLWLGVDALGLNIYEKDDK 22 2 P15311;E7EQR4 P15311 EZR Ezrin 0 137.45 1.68E-06 94582000 244500 117840 184090 150980 238190 230860 283430 195530 221090 104080 FALSE TRUE 254153.0488 138078.1033 188887.5366 180843.3934 197702.5489 177246.2637 261214.016 192909.2402 213133.0141 124472.4833 2.041841234 1.109306248 1.517504365 1.452878489 1.588323328 1.423979494 2.098568367 1.549814345 1.712290207 1 16.92546732 KGTENGVNGTLTSNVADS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGTENGVNGTLTSNVADSPR 20 1 G3XAN4;Q15629-2;Q15629 G3XAN4 TRAM1 Translocating chain-associated membrane protein 1 1 KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR;KGTENGVNGTLTSNVADS(1)PR 219.43 5.64E-25 1888770000 1058615 1091993 1145743 1517830 1405600 1879440 1342100 1185870 1166361 1318540 TRUE FALSE 1100409.938 1279534.303 1175602.004 1818052.244 1166676.614 1442968.543 1236902.695 1169975.352 1124383.895 1576882.668 0.697838818 0.81143279 0.745522814 1.152940723 0.739862666 0.915076671 0.784397419 0.741954602 0.713042206 1 20.58864389 -0.666068756 9.16346018 0.999979671 0.813959012 0.162281498 0.128467961 0 0 0.121365633 0.028606154 0.215740283 0.666068756 -0.186020659 KGTQTS(ph)PVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGTQTSPVPR 10 1 F5H7S1;Q2M1K9-2;Q2M1K9 F5H7S1 ZNF423 Zinc finger protein 423 1 KGT(0.009)QT(0.072)S(0.919)PVPR 74.76 0.013551 0 82194 79959 84121 58536 102010 127650 114840 106670 98124 72488 TRUE FALSE 85439.08259 93691.33626 86313.26237 70114.24609 84670.37664 98005.22205 105838.5407 105240.2631 94592.53641 86690.63573 0.985562995 1.08075498 0.995646896 0.808786849 0.976695763 1.130516823 1.220876278 1.213974984 1.091150568 1 16.40358854 2.709149162 4.56078749 1.159724167 0.967381231 0.448913245 0.087323718 0.170431457 8.891658576 0.029551232 0.028708326 511.8576073 -2.709149162 -0.192342936 KGTVEGFEPADNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGTVEGFEPADNK 13 1 P37108;H0YLA2 P37108 SRP14 Signal recognition particle 14 kDa protein 0 ; 171.08 4.12E-05 1077140000 2022730 1179150 1630460 1086010 2285830 2162560 1790020 1630640 1874880 1115520 FALSE TRUE 2102588.942 1381659.84 1672951.127 1300819.537 1897285.433 1660338.214 1649713.555 1608783.938 1807403.435 1334084.786 1.576053459 1.035661192 1.2540066 0.975065116 1.422162559 1.244552244 1.236588238 1.205908316 1.354789031 1 20.34741893 -0.856753195 5.165876479 0.999999699 1.242096142 0.173875747 0.164942365 5.18E-07 1.14E-07 0.144865567 0.034145099 0.139074275 0.856753195 0.242096443 KGTVLLADNVICPGAPDFLAHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGTVLLADNVICPGAPDFLAHVR 23 1 P21964-2;P21964 P21964-2 COMT Catechol O-methyltransferase 0 ; 156.89 8.22E-09 7870500000 2106300 2251970 2465980 1761780 3033910 2939020 2048960 2575850 2715870 2958540 FALSE TRUE 2189458.35 2638728.33 2530245.465 2110254.826 2518207.062 2256477.146 1888357.161 2541324.944 2618126.369 3538209.268 0.618804085 0.745780741 0.715120354 0.596418885 0.711717954 0.63774553 0.533704204 0.718251734 0.739958033 1 21.75458795 0.771556375 1.729255131 0.999260323 0.657891344 0.737353864 0.061330464 0.402849381 2.032094697 0.058476545 0.016588679 5.909576721 -0.771556375 -0.341368979 KGVAINFVTEEDKR ddPTM_MDA-MB-175_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 ; 198.78 1.21E-08 2790300000 3475600 1807710 2807300 1905270 3790400 3177000 3413500 2825400 3415700 2027350 FALSE TRUE 3612819.372 2118170.13 2880460.544 2282126.719 3146109.162 2439189.898 3145940.95 2787530.134 3292769.624 2424570.417 1.490086387 0.87362698 1.188029238 0.941249924 1.297594469 1.00602972 1.297525091 1.14970063 1.358083726 1 21.20929772 2.226756521 24.97919348 1.209924423 1.122288656 0.02820463 0.188619507 744.520609 1575503.638 0.064213378 0.047797976 168.5607755 -2.226756521 -0.087635767 KGVAINMVTEEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ; 185.12 6.83E-07 6362600000 3478800 1849050 2686100 2003790 3809700 3332900 3531800 2917300 3352600 1901070 FALSE TRUE 3616145.71 2166609.954 2756101.973 2400133.681 3162128.555 2558884.486 3254968.287 2878198.365 3231940.581 2273548.268 1.590529553 0.952964133 1.212246958 1.055677469 1.390834142 1.125502599 1.431668873 1.265949971 1.421540341 1 21.1165142 3.229008242 24.99702218 1.288380367 1.185676089 0.022276196 0.198651043 603.0401099 1578055.549 0.052898537 0.064005664 1694.369955 -3.229008242 -0.102704278 KGVCGDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGVCGDWK 8 1 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 67.334 0.095187 410450000 332430 361390 369810 341260 622690 585700 443390 398720 425700 443960 FALSE TRUE 345554.5931 423455.9213 379447.5524 408760.2094 516845.3762 449680.0514 408635.9332 393375.8106 410379.1402 530945.4619 0.650828791 0.797550693 0.714663896 0.76987231 0.973443439 0.846942075 0.769638245 0.740896832 0.772921457 1 19.01820415 -2.77774717 1.933451885 7.893710459 0.783873453 0.397126861 0.080596503 3069717.707 55370.87861 93660565.71 0.020915119 0.001668218 2.77774717 -7.109837006 KGVEGLIDIENPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGVEGLIDIENPNR 14 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ;;;; 210.9 7.35E-09 2238310000 2189226 2123603 2373152 1893223 2730900 2689580 2364760 2356710 2447570 2206710 FALSE TRUE 2275658.333 2488315.296 2434998.291 2267696.859 2266702.593 2064965.806 2179403.932 2325122.157 2359482.434 2639072.574 0.862294715 0.942874902 0.92267197 0.859277945 0.858901197 0.782458893 0.825821902 0.881037596 0.894057426 1 21.33159959 5.112801548 15.68164052 0.87697527 0.000172685 0 0.058364558 19920067.3 17229897.07 0.014080805 616250162.5 129658.6656 -5.112801548 -0.876802586 KGVNLPGAAVDLPAVSEK ddPTM_MDA-MB-175_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 ; 181.88 1.14E-13 2842500000 5619500 3720800 4762700 3939500 6145700 6227300 6480200 5215100 5839200 3475700 FALSE TRUE 5841362.199 4359818.456 4886819.875 4718721.342 5101056.109 4781103.951 5972264.991 5145200.115 5629048.333 4156696.869 1.405289436 1.048866105 1.175649808 1.135209396 1.227189827 1.150217132 1.436781459 1.237809799 1.354211892 1 21.98700611 KGVNLPGAAVDLPAVSEKDIQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGVNLPGAAVDLPAVSEKDIQDLK 24 2 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 128.98 4.15E-05 1566000000 535320 347680 484840 266340 701970 660050 429560 459000 564380 465070 FALSE TRUE 556454.847 407391.3354 497475.3287 319021.2571 582649.3901 506763.3907 395889.9648 452847.8558 544068.074 556191.5622 1.000473371 0.732465868 0.894431636 0.57358162 1.047569632 0.911131029 0.711787074 0.814194041 0.978202675 1 19.08522233 1.221365507 8.773288968 0.990206918 0.828253078 0.173709179 0.133052159 0.343927249 139.5837273 0.110774739 0.030493933 16.64813187 -1.221365507 -0.16195384 KGVSASAVPFTPS(ph)SPLLSCSQEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGVSASAVPFTPSSPLLSCSQEGSR 25 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 KGVSASAVPFT(0.017)PS(0.51)S(0.457)PLLS(0.005)CS(0.006)QEGS(0.005)R 47.719 0.094574 521220000 107000 197890 187790 154700 197550 216700 170120 210450 199150 235920 TRUE FALSE 111224.4426 231876.0681 192683.9617 185299.1983 163970.5216 166374.7091 156785.5499 207629.262 191982.6304 282144.007 0.394211608 0.821835879 0.682927714 0.656753975 0.581158974 0.58968011 0.555693355 0.735898182 0.680441993 1 18.10607218 0.51148085 0.992321103 1.000183304 0.626949824 0.526885505 0.106606908 1.297303608 1.844918953 0.098692748 0.031255345 3.246989242 -0.51148085 -0.373233481 KGWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KGWEVVESDLYAMNFNPIISR 21 1 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;; 287.14 2.00E-45 16520220000 13510010 14583653 15844490 13702655 18806310 18356460 16900240 15704410 17259830 16229710 FALSE TRUE 14043395.63 17088281.96 16257410.43 16412999.26 15609620.14 14093450.36 15575555.03 15493918.07 16638652.09 19409610.94 0.72352793 0.880403116 0.837595894 0.845611966 0.804221176 0.726106793 0.802466112 0.798260105 0.857237795 1 24.21026786 0.851281378 2.796859551 0.999918845 0.804731588 0.62514848 0.04621731 0.391857009 5.697888643 0.044288374 0.011701407 7.100376493 -0.851281378 -0.195187258 KGWLYYEAGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGWLYYEAGQR 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 0 102.66 0.0045514 506960000 278250 243330 274550 220740 343890 368970 264740 262440 288500 316280 FALSE TRUE 289235.5249 285120.0347 281704.9985 264401.7132 285435.7006 283282.3093 243988.987 258922.4211 278116.9414 378249.0105 0.764669614 0.753789241 0.744760702 0.69901495 0.754623787 0.748930735 0.64504858 0.684529011 0.735274736 1 18.52897678 -1.957516351 4.743777446 1.175138448 0.721442747 0.836538918 0.036343058 0.025996966 0.00023282 0.013589428 0.009126574 0.011027667 1.957516351 -0.453695701 KGWSMS(ph)EQSEESVGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.279)MS(0.721)EQSEESVGGR 272.06 2.22E-35 565040000 165650 126620 164440 114770 231130 195950 199000 166830 213530 132360 TRUE FALSE 172189.9899 148366 168725.4415 137471.1634 191842.6052 150443.5822 183401.86 164593.9167 205845.097 158293.4078 1.087790024 0.937284768 1.065903147 0.868457918 1.211943111 0.950409649 1.158619696 1.039802725 1.300402208 1 17.27224165 2.541902336 0.964823005 1.123563992 1.004756517 0.12578214 0.117948866 1.072137993 2.038715108 0.069047162 0.052089647 348.2589902 -2.541902336 -0.118807475 KGYEVIYLTEPVDEYCIQALPEFDGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KGYEVIYLTEPVDEYCIQALPEFDGKR 27 2 P14625 P14625 HSP90B1 Endoplasmin 0 168.96 3.74E-12 333070000 350900 309350 329500 315440 486180 447180 317030 362750 365390 272800 FALSE TRUE 364753.803 362478.4561 338087.0407 377833.0905 403539.2973 343329.2221 292180.3602 357887.9296 352239.6853 326249.9369 1.118019536 1.111045291 1.036282317 1.158109314 1.2369023 1.052350309 0.895572158 1.096974709 1.079662079 1 18.3156181 2.493278062 24.98221727 1.022173262 1.128788296 0.386061477 0.068524601 817.3533674 1263821.316 0.023473072 0.021559713 311.3709286 -2.493278062 0.106615034 KGYFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KGYFEDR 7 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;; 103.83 0.013288 2016830000 5064220 5086210 5410190 4713150 6858040 7029890 6358540 5826190 5949730 5505720 FALSE TRUE 5264159.316 5959727.002 5551183.996 5645397.003 5692312.81 5397304.587 5860141.02 5748099.453 5735600.38 6584460.421 0.799482263 0.905120028 0.843073485 0.857381872 0.864507104 0.819703399 0.889995633 0.872979574 0.871081306 1 22.65063379 -5 0.246960116 1.842896894 0.846840745 0.703183487 0.028259669 91.55297368 0.909615997 38.82157592 0.038498728 1.00E-05 5 -0.996056148 KGYNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KGYNAR 6 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ; 95.9 0.068659 891220000 1070060 1429910 1490800 1314820 1585490 1714150 1257810 1382100 1450150 1732360 FALSE TRUE 1112306.795 1675485.919 1529651.473 1574887.472 1315988.976 1316064.641 1159219.566 1363575.21 1397959.385 2071782.774 0.53688389 0.808716985 0.738326186 0.76016052 0.635196408 0.635232929 0.559527562 0.658165145 0.674761564 1 20.98244131 -1.87081362 4.913045607 1.076763845 0.668979189 0.606708865 0.080317486 0.0482773 0.00126943 0.055592951 0.018645403 0.013464381 1.87081362 -0.407784656 KHAEPSS(ph)SPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHAEPSSSPSK 11 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 KHAEPS(0.063)S(0.467)S(0.467)PS(0.002)K 58.831 0.063597 214390000 284360 217630 249880 201440 288430 339570 324540 264680 264220 205500 TRUE FALSE 295586.7524 255006.2596 256392.0781 241284.2308 239402.7716 260710.0137 299101.7068 261132.3975 254710.7738 245763.7905 1.202727024 1.037607123 1.043245946 0.981772906 0.974117347 1.0608154 1.21702919 1.062534058 1.036404807 1 17.90691285 2.468783697 24.99823876 1.093162391 1.040798475 0.017257179 0.07896148 517.3409802 1551113.947 0.027611001 0.023137959 294.2955509 -2.468783697 -0.052363915 KHALLEADVAAHQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHALLEADVAAHQDR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 121.79 4.59E-05 59217000 50213 69255 69645 73562 71514 87900 77615 73204 72747 76918 FALSE TRUE 52195.44801 81149.00752 71460.00591 88112.34404 59358.07582 67486.55714 71531.33349 72222.82012 70128.84968 91988.60942 0.567412078 0.882163651 0.776835375 0.957861463 0.645276368 0.733640367 0.777610771 0.785127861 0.762364494 1 16.48916761 -1.905711977 2.343790434 1.137096789 0.771941393 0.316054298 0.103140754 15474249.78 7687719.933 11678273.96 0.023983026 0.01242476 1.905711977 -0.365155396 KHDNEGSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHDNEGSGSK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 136.48 7.57E-05 191749000 144690 99106 146640 96635 189372 158830 171583 132327 160403 97778 FALSE TRUE 150402.4729 116126.6846 150461.5589 115749.1146 157182.6151 121944.1396 158133.8761 130553.373 154630.1274 116935.727 1.286197784 0.993081306 1.286703069 0.989852439 1.344179568 1.042830474 1.352314473 1.11645411 1.322351443 1 16.83535625 KHDNEGSGSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHDNEGSGSKR 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 59.57 0.059547 18757000 26187 18701 28686 18803 31964 32037 37398 28078 28432 18359 FALSE TRUE 27220.88298 21912.75128 29433.58073 22522.17728 26530.7707 24596.89228 34466.64704 27701.66034 27408.73787 21956.09455 1.239787109 0.998025912 1.340565403 1.025782487 1.208355641 1.120276296 1.569798625 1.261684325 1.248343043 1 14.42233384 KHDSGAADLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KHDSGAADLER 11 1 Q9NX55;Q9NX55-3;J3QT56 Q9NX55;J3QT56 HYPK Huntingtin-interacting protein K 0 ;;;; 141.38 2.48E-05 421067000 104197.4 498475 454982 472767 484272 666279 428013 557905 409348 642017 FALSE TRUE 108311.1938 584084.2037 466839.2047 566278.9015 401955.6184 511545.7998 394464.2227 550427.196 394615.6454 767807.939 0.141065478 0.760716546 0.6080156 0.73752676 0.523510631 0.666241874 0.513753769 0.716881355 0.513950984 1 19.55038595 -5 0.224001122 3.076106228 0.544863157 0.364556364 0.16926405 168.6827961 1.688421872 158.6817148 0.287118402 1.00E-05 5 -2.531243071 KHEAFESDLAAHQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 205.68 1.74E-09 2683410000 1713310 2242730 1679670 2271140 2265610 2646310 2952440 1985510 1762350 2890200 FALSE TRUE 1780952.802 2627901.431 1723443.58 2720364.713 1880502.421 2031744.608 2721020.038 1958897.486 1698923.368 3456479.354 0.515250525 0.760282693 0.498612433 0.787033404 0.544051397 0.587807535 0.787222998 0.566732008 0.491518448 1 21.72087188 -1.156217493 4.699624407 1.000040932 0.621971842 0.509879217 0.112959489 4.42E-05 7.94E-06 0.099783794 0.023516724 0.069788282 1.156217493 -0.37806909 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTR 40 2 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 56.475 0.0070406 443160000 63121 72506 61965 63591 68082 90779 72215 63608 63551 90006 FALSE TRUE 65613.06582 84958.34148 63579.8588 76169.11 56509.44596 69696.95302 66554.5996 62755.4388 61263.81192 107640.9524 0.609554861 0.789275267 0.590666074 0.707622037 0.524980917 0.647494763 0.618301846 0.583007093 0.569149664 1 16.71586754 -1.002953352 6.326977793 1.000000184 0.626810198 0.712386689 0.071163538 1.78E-07 2.81E-08 0.066671874 0.015714704 0.099322273 1.002953352 -0.373189985 KHEAIETDIAAYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHEAIETDIAAYEER 15 1 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 136.01 1.65E-05 517780000 604720 938060 744330 548950 1068590 1046390 661330 735610 639840 1020860 FALSE TRUE 628594.8125 1099164.508 763727.8513 657530.6715 886951.4535 803381.7807 609493.2265 725750.3512 616812.2834 1220877.971 0.514871123 0.90030661 0.625556255 0.538571984 0.726486573 0.658036101 0.499225345 0.594449542 0.505220258 1 20.21948758 -1.570149493 6.166001433 1.00084658 0.621446966 0.488129884 0.117283408 0.001344081 9.37E-05 0.111824814 0.026302362 0.026906085 1.570149493 -0.379399614 KHEDFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHEDFDK 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 116.25 0.0035689 1738360000 4122230 2739720 3216600 2605000 4742890 4524630 4293820 3441580 3858010 2564540 FALSE TRUE 4284978.823 3210245.598 3300427.238 3120261.225 3936695.252 3473853.254 3957259.169 3395451.249 3719160.974 3067012.512 1.397118142 1.046701174 1.076104915 1.017361753 1.283560219 1.1326505 1.290265088 1.107087511 1.212633127 1 21.54840262 -0.974907097 4.073408655 0.999989339 1.165276174 0.165262813 0.115735603 5879404.978 2886724.875 533.0677955 0.025627939 0.105948034 0.974907097 0.165286834 KHEEEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KHEEEEAK 8 1 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ; 96.331 0.0058532 270360000 620180 369080 462520 387380 578930 610420 701360 501380 523190 294860 FALSE TRUE 644665.1853 432466.619 474573.6512 464002.6078 480523.6854 468659.206 646385.5705 494659.8212 504360.4941 352632.1716 1.828151931 1.226395814 1.345803615 1.315826079 1.362676818 1.329031336 1.833030627 1.4027643 1.430273624 1 18.42780458 4.753049434 24.08687837 1.392564745 1.828152438 0.324571746 0.19755015 1933.513361 3214270.3 0.046150555 0.967209016 56630.37451 -4.753049434 0.435587693 KHEEEEAKAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHEEEEAKAER 11 2 P25789;H0YN18;P25789-2 P25789 PSMA4 Proteasome subunit alpha type-4 0 ;;; 235.21 9.72E-16 2893880000 1974830 1043610 1502690 867490 2258140 2032200 1734830 1460530 1753530 1011260 FALSE TRUE 2052797.813 1222841.899 1541851.336 1039076.933 1874302.169 1560252.348 1598849.491 1440953.984 1690420.798 1209397.035 1.69737295 1.011116998 1.274892604 0.859169406 1.549782342 1.290107634 1.322022003 1.19146479 1.3977385 1 20.20585652 -1.95120632 2.516235971 0.796336282 1.270215713 0.120918186 0.228533858 26831075.09 14847422.71 31998876.36 0.050667334 0.011189062 1.95120632 0.473879431 KHEPEPLPHWDDWERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KHEPEPLPHWDDWERPR 17 2 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 0 ; 163.41 8.76E-10 324650000 0 15444.6 14727.9 12503.3 11097.2 17518.6 16500.3 9125.1 12232.7 6720.9 FALSE TRUE 0 18097.08991 15111.72117 14976.41542 9210.901908 13450.17065 15206.96337 9002.79296 11792.44752 8037.731676 0 2.25151705 1.880097742 1.863263919 1.145957875 1.673378907 1.891947129 1.120066372 1.467136251 1 12.9725727 1.665548642 10.07529042 1.222450899 1.573662764 0.057942163 0.594028757 0.333864736 50.0428342 0.271168436 0.145799152 46.29655137 -1.665548642 0.351211865 KHFGAGGNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KHFGAGGNQR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 192.32 4.51E-07 1192590000 502320 498890 507320 444050 649730 671670 444620 524780 519160 647700 FALSE TRUE 522151.9815 584570.4767 520541.176 531881.7646 539289.1267 515684.8218 409769.5226 517746.1825 500475.533 774604.414 0.67408857 0.754669695 0.672009049 0.68664954 0.696212308 0.665739586 0.52900489 0.668400764 0.646104675 1 19.5631002 -1.544962701 6.813145776 1.000266431 0.66440074 0.779043534 0.053377696 0.000227642 1.52E-05 0.054463221 0.012827146 0.028512631 1.544962701 -0.335865691 KHGGPKDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KHGGPKDEER 10 2 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;;;; 167.6 3.12E-06 19791780000 13131208 7711203 11381832 7138505 14883873 13261487 12715466 10361299 12857450 7117607 FALSE TRUE 13649638.23 9035542.13 11678451.89 8550479.983 12353917.58 10181707.62 11718794.55 10222422.73 12394712.89 8512165.817 1.603544682 1.061485681 1.371971851 1.004501107 1.451324827 1.196135959 1.376711263 1.200919126 1.456117415 1 23.02109482 -1.354466869 5.168689521 0.999867914 1.286692219 0.201490684 0.178181814 0.00023765 2.97E-05 0.151177572 0.035616575 0.044211284 1.354466869 0.286824304 KHGLAHDEMKS(ph)PR ddPTM_MDA-MB-175_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 157.54 2.27E-05 2460281000 3968634 2096004 3039722 2098036 3973690 3835866 3889162 2406810 3314628 1872585 TRUE FALSE 4125318.735 2455976.382 3118939.652 2513021.259 3298243.593 2945044.255 3584319.32 2374550.649 3195335.186 2239482.178 1.842085986 1.096671546 1.392705726 1.122143897 1.472770637 1.315055902 1.600512545 1.060312367 1.426818761 1 21.09473375 -4.355787711 0.156868208 2.37E-13 1.450340904 0.203591928 0.227262523 175.7432941 1.92857285 56.21334631 0.972779933 4.41E-05 4.355787711 1.450340904 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHHYLRPSLFVYPEESLVIGSSTLFSALLIK 31 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 136.43 4.46E-07 109830000 105440 84206 172460 98740 226400 178840 197600 109080 186580 99674 FALSE TRUE 109602.8526 98667.72547 176954.4493 118270.4773 187916.6089 137307.1203 182111.5957 107617.961 179865.0222 119203.2119 0.919462243 0.827727071 1.484477192 0.992175256 1.57643914 1.151874334 1.527740677 0.902810917 1.508894092 1 16.86306358 4.25651793 24.96155709 1.256745403 0.873594363 0.304058691 0.238217176 272.4726084 378743.7739 0.052973819 0.144425608 18051.69264 -4.25651793 -0.38315104 KHIKEEPLS(ph)EEEPCTSTAIASPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHIKEEPLSEEEPCTSTAIASPEK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 KHIKEEPLS(1)EEEPCTSTAIASPEK 169.13 5.01E-12 132330000 250350 108030 191210 117350 288250 230320 228280 165970 211070 104710 TRUE FALSE 260234.0113 126583.3121 196193.0897 140561.4797 239253.368 176831.6705 210386.8171 163745.4436 203473.6319 125225.9197 2.078116191 1.010839549 1.566713107 1.122463146 1.910573853 1.412101192 1.680058071 1.307600248 1.624852366 1 16.93417368 -1.159868621 5.615104307 0.999990442 1.498659215 0.197119861 0.313431488 3.33E-05 4.99E-06 0.269817605 0.063595402 0.069204029 1.159868621 0.498668773 KHISQISVAEDDDESLLGHLMIVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHISQISVAEDDDESLLGHLMIVGK 25 1 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 135.1 1.77E-05 104500000 12611 81292 85970 82915 103520 130070 82650 106530 90729 99612 FALSE TRUE 13108.89202 95253.26864 88210.44883 99315.33952 85923.70738 99863.21373 76171.67703 105102.1396 87463.68101 119129.0642 0.110039411 0.799580432 0.740461191 0.8336785 0.721265696 0.838277497 0.639404645 0.882254388 0.73419263 1 16.86216591 4.739042426 24.94664531 0.790169739 0.110039198 0.825854646 0.094808497 13.2502746 685860.2368 0.019935008 0.117853775 54833.05286 -4.739042426 -0.680130541 KHLEINPDHPIVETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHLEINPDHPIVETLR 16 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;; 227.67 1.96E-15 5813100000 1687660 1645550 1734850 1411480 2341750 2216820 1738780 1705500 1845450 2082210 FALSE TRUE 1754290.12 1928160.412 1780061.616 1690666.531 1943700.171 1701997.151 1602489.88 1682640.562 1779032.615 2490179.183 0.704483489 0.774305891 0.714832743 0.678933686 0.78054631 0.683483808 0.643523924 0.675710637 0.714419519 1 21.24781813 0.926284122 20.07270999 1 0.704957234 0.824244021 0.040482642 1798.585867 489753.6585 0.041487138 0.010371784 8.438866614 -0.926284122 -0.295042766 KHLEINPDHSIIETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KHLEINPDHSIIETLR 16 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 247.5 1.09E-20 7673070000 2410654 2711342 2903959 2217971 3510909 3537015 2741450 2763010 3072972 2967576 FALSE TRUE 2505828.481 3176993.897 2979638.557 2656679.044 2914125.942 2715596.87 2526567.986 2725976.37 2962376.338 3549015.7 0.706062946 0.895176062 0.83956759 0.748567848 0.821108214 0.765169022 0.71190668 0.768093635 0.834703644 1 21.75898753 -1.975525145 6.774493715 1.145465129 0.786909716 0.555577214 0.056926889 0.034163066 0.000123424 0.015055854 0.012908995 0.010579737 1.975525145 -0.358555413 KHLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHLFSSTENLAAGSWKEPAEGGGLSSDR 28 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 KHLFS(0.029)S(0.942)T(0.029)ENLAAGSWKEPAEGGGLSSDR 198.74 2.61E-25 297020000 68541 56653 68811 66811 113320 100750 65129 84208 83508 75817 TRUE FALSE 71247.05161 66382.71205 70604.27119 80026.01639 94057.90688 77352.33938 60024.0188 83079.3295 80502.56339 90671.88955 0.785767805 0.732120091 0.778678723 0.882589045 1.037343628 0.853101659 0.661991485 0.916263353 0.887844775 1 16.46836773 -3.179606419 0.023834508 2.012211323 3.70E-06 0.252584071 0.095811186 2652.763678 6.632031439 361.1957576 215.0208913 0.000661292 3.179606419 -2.012207623 KHNGVGGS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHNGVGGSPPK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 KHNGVGGS(1)PPK 79.652 0.016269 49415000 64007 23800 35057 26371 50829 46655 53081 32445 36431 24468 TRUE FALSE 66534.04578 27887.46486 35970.61422 31587.10509 42189.10474 35820.08331 48920.37252 32010.12784 35119.85543 29262.03613 2.27373261 0.95302544 1.229258759 1.079456841 1.441769279 1.22411452 1.671803435 1.093913209 1.200184952 1 14.83674254 4.748141372 24.91901957 1.23228432 2.273733191 0.710635219 0.203128457 673.6998359 1752218.671 0.046816584 0.612281168 55993.98438 -4.748141372 1.04144887 KHNMCGETEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 KHNMCGETEEEK 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;;;; 208.42 3.20E-08 1962627000 5620402 2044138 3544804 2544631 4682123 4259095 5578672 3644844 4430705 1602349 FALSE TRUE 5842299.811 2395202.8 3637184.504 3047951.417 3886257.405 3269984.733 5141401.111 3595990.828 4271244.793 1916298.608 3.048741875 1.249911048 1.89802596 1.590540955 2.028001998 1.706406674 2.682985361 1.876529479 2.228903562 1 20.86989096 KHPDASVNFSEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHPDASVNFSEFSK 14 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;; 189.32 1.17E-06 3915300000 2261530 1728100 2168590 1874740 2774580 2625810 2603410 2185100 2367510 1583370 FALSE TRUE 2350816.951 2024887.732 2225105.237 2245557.976 2302957.883 2016005.422 2399347.921 2155812.309 2282303.778 1893601.036 1.241453139 1.069331762 1.175065494 1.18586647 1.216179036 1.064641064 1.26708207 1.13847229 1.20527172 1 20.85270097 -1.173889058 5.529675514 0.999995384 1.170777133 0.401497629 0.06353476 3.25E-06 4.86E-07 0.05534493 0.013044573 0.067005576 1.173889058 0.17078175 KHPEVDVLINFASLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KHPEVDVLINFASLR 15 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 180.74 4.01E-07 2033470000 3118800 2659100 3260600 2840500 4575400 4114000 3919600 3371300 3740900 3565900 FALSE TRUE 3241932.632 3115779.74 3345573.915 3402342.422 3797675.142 3158585.848 3612371.51 3326113.238 3606265.74 4264569.832 0.760201558 0.730619937 0.784504428 0.797816088 0.890517753 0.740657551 0.84706586 0.779941089 0.845634116 1 22.02396879 -5 0.179263011 1.83316277 0.753029231 0.684793602 0.043461538 76.53112593 0.736177605 22.67730499 0.135125608 1.00E-05 5 -1.080133539 KHPS(ph)SPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.918)S(0.082)PAR;KHPS(0.5)S(0.5)PAR;KHPS(0.5)S(0.5)PAR 104.22 0.002831 787310000 110711 488590 388920 355881 528630 594980 409970 448160 392896 649270 TRUE FALSE 115081.9558 572501.5318 399055.5747 426273.1996 438773.6614 456804.912 377835.4801 442153.1482 378755.7497 776482.0255 0.148209427 0.737301719 0.51392764 0.548980125 0.565078968 0.588300691 0.486599133 0.569431273 0.487784311 1 19.566593 -2.364219943 2.037475923 3.601166425 0.528997356 0.512530695 0.141055447 3977204.31 383773.2402 47701430.13 0.030775042 0.004322948 2.364219943 -3.07216907 KHPSS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHPSSPAR 8 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 KHPS(0.169)S(0.831)PAR;KHPS(0.36)S(0.64)PAR;KHPS(0.142)S(0.858)PAR;KHPS(0.178)S(0.822)PAR 108.7 0.0023036 1406260000 257759 1033691 952090 801778 1386540 1370990 1068623 1040259 979855 1483920 TRUE FALSE 267935.5244 1211219.388 976902.2476 960367.2953 1150856.426 1052598.35 984861.5369 1026316.03 944590.21 1774665.713 0.150978025 0.682505657 0.550471134 0.541153913 0.648491949 0.593124859 0.554956085 0.578315128 0.53226374 1 20.75911586 -5 0.217221686 3.21783941 0.489938152 0.530327833 0.133773233 117.5687661 1.175530183 114.2257416 0.247164509 1.00E-05 5 -2.727901258 KHQALQAEIAGHEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHQALQAEIAGHEPR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 190.87 8.08E-08 125520000 54525 63359 65725 60350 76447 89303 69151 68405 65669 64763 FALSE TRUE 56677.6891 74240.41539 67437.84749 72287.04987 63452.56625 68563.73165 63730.76393 67488.14286 63305.58552 77452.06989 0.731777591 0.958533652 0.870704264 0.933313338 0.819249458 0.885240791 0.822841327 0.871353638 0.817351758 1 16.24101617 -1.016724868 4.413457956 1.00000588 0.861410695 0.32850397 0.061128604 3.45E-06 7.68E-07 0.053525459 0.012615495 0.096222167 1.016724868 -0.138595184 KHQLLEADISAHEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHQLLEADISAHEDR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 99.055 0.0010941 140380000 85957 111460 98731 104170 102850 134880 101450 98683 96886 119660 FALSE TRUE 89350.64873 130602.388 101304.011 124774.5151 85367.59374 103556.1641 93498.08391 97360.3158 93399.09179 143105.086 0.624370882 0.912632749 0.707899445 0.87190832 0.596537804 0.723637203 0.653352627 0.680341409 0.652660883 1 17.12671542 -1.229016092 4.43671271 1.000107948 0.715653387 0.437094397 0.097446258 11.72381903 55476080.31 10631.09381 0.021958282 0.059017921 1.229016092 -0.28445456 KHS(ph)PS(ph)PPPPTPTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(0.999)PPPPT(0.001)PTESR;KHS(0.999)PS(0.993)PPPPT(0.007)PTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR 108.18 0.0038464 3344040000 2488940 2331570 2526090 2111610 2935360 3256980 2747560 2526070 2527980 2301570 TRUE FALSE 2587205.273 2731999.01 2591921.981 2529280.155 2436408.556 2500595.755 2532199.068 2492212.163 2436998.494 2752518.575 0.939941077 0.992545168 0.941654674 0.918896671 0.885156081 0.908475524 0.919957122 0.905429735 0.885370408 1 21.39232087 3.890695018 3.164792516 0.911714715 0.966491969 0.245385274 0.032895341 0.270737769 5.121638308 0.007957635 0.016324235 7774.903682 -3.890695018 0.054777254 KHS(ph)QTDLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KHSQTDLVSR 10 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 1 KHS(0.997)QT(0.002)DLVS(0.001)R;KHS(0.996)QT(0.004)DLVSR;KHS(1)QTDLVSR;KHS(0.997)QT(0.003)DLVSR 182.72 1.07E-06 5275560000 2395350 2442070 2482940 3331230 3291190 4062970 2904840 2383920 3053890 2748360 TRUE FALSE 2489920.268 2861476.526 2547647.456 3990137.351 2731754.699 3119406.792 2677151.05 2351967.452 2943981.095 3286848.521 0.757540316 0.870583633 0.775103398 1.213970563 0.831116701 0.949057059 0.814503934 0.715569165 0.895685054 1 21.64827354 0.978818582 23.54557006 1.000000016 0.862603818 0.084359328 0.13214209 2071.432037 2302639.297 0.129199054 0.032299764 9.523982342 -0.978818582 -0.137396197 KHSDEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KHSDEGK 7 1 D6RDX7;Q6PCB8-2;Q6PCB8 D6RDX7 EMB Embigin 0 67.032 0.043015 151680000 126270 115090 131880 116500 179070 169240 138040 114990 134170 123840 FALSE TRUE 131255.2371 134855.8122 135316.9011 139543.3523 148631.7454 129936.5749 127220.0641 113448.7471 129341.2479 148104.0769 0.886236489 0.910547603 0.913660879 0.942197914 1.003562822 0.87733287 0.858990966 0.766006915 0.873313217 1 17.17625183 2.499527189 11.80109452 0.848465379 0.930803533 0.117684837 0.062132533 1.360677197 714.6889555 0.020268966 0.018652557 315.8836802 -2.499527189 0.082338153 KIADDKYNDTFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIADDKYNDTFWK 13 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 163.64 2.16E-05 1269960000 1456450 896020 1242910 711490 1938700 1432780 1177220 1062140 1325300 841290 FALSE TRUE 1513951.771 1049904.465 1275301.256 852220.5984 1609160.466 1100038.559 1084946.42 1047903.751 1277602.712 1006124.668 1.504735764 1.043513292 1.267538006 0.847032804 1.599364887 1.093342201 1.078341934 1.041524757 1.269825453 1 19.94037765 4.748258274 24.17293328 1.139707433 1.504736079 0.244368186 0.193530764 1156.683181 2883118.791 0.043238491 0.548481112 56009.05866 -4.748258274 0.365028647 KIAVAAASKPAVEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIAVAAASKPAVEIK 15 2 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ; 170.91 6.26E-07 1253480000 2058850 1023930 1614780 1088500 2275900 1852560 2233300 1644450 2130700 1021910 FALSE TRUE 2140134.988 1199782.012 1656862.493 1303802.051 1889043.331 1422331.016 2058248.11 1622408.838 2054016.523 1222133.699 1.751146368 0.981710932 1.355712959 1.066824401 1.545692859 1.163809669 1.684143161 1.327521563 1.680680702 1 20.22097069 2.269267606 24.99997702 1.445565793 1.297483387 0.034235258 0.276813107 577.1980999 469921.4704 0.087634797 0.07331268 185.8949561 -2.269267606 -0.148082406 KIAVAAASKPAVEIKQEGDTFYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIAVAAASKPAVEIKQEGDTFYIK 24 3 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 70.533 0.013618 174540000 71969 48237 53977 45536 90554 80563 50096 67566 82940 65810 FALSE TRUE 74810.39169 56521.32952 55383.68496 54542.88489 75161.66343 61853.46419 46169.34462 66660.38829 79955.0056 78704.20949 0.950525927 0.718148748 0.703694063 0.693011025 0.954989116 0.785897789 0.586618491 0.846973608 1.015892366 1 16.26415318 1.353155038 4.274461398 1.006878659 0.76730777 0.431699331 0.107171477 0.197523767 5.550215806 0.080338701 0.027187221 22.55044091 -1.353155038 -0.239570888 KICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7;Q9UER7-2 Q9UER7-3 DAXX Death domain-associated protein 6 1 KICTLPSPPS(1)PLASLAPVADSSTR;KICTLPSPPS(1)PLASLAPVADSSTR 214.44 9.15E-33 719120000 661350 680770 676540 599870 774810 870380 733650 732000 667710 691900 TRUE FALSE 687460.6087 797686.9518 694171.1882 718522.4956 643108.073 668247.4357 676144.596 722188.7373 643679.2475 827464.5578 0.830803691 0.964013436 0.8389135 0.868342322 0.777203165 0.807584361 0.817128165 0.872773016 0.777893435 1 19.65833799 4.071285054 24.9997914 0.83794347 0.898423183 0.08013707 0.06776749 86.8130109 30442.79313 0.015397272 0.033261934 11783.79163 -4.071285054 0.060479713 KIDASQTEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIDASQTEFEK 11 1 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 0 122.66 0.00061911 142600000 351800 213360 271650 204120 347030 308410 311530 280340 296450 184830 FALSE TRUE 365689.3356 250002.9203 278729.4222 244494.3268 288041.9646 236786.4515 287111.4646 276582.5008 285780.8224 221043.8997 1.654374249 1.131010268 1.260968624 1.106089456 1.303098457 1.071219119 1.298888886 1.251255978 1.292869076 1 17.75397339 4.744328225 24.95347571 1.204824954 1.654374449 0.642781726 0.103231064 365.7006044 1582151.687 0.022422107 0.199967155 55504.50387 -4.744328225 0.449549494 KIDFLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIDFLTK 7 1 Q99471;H3BPF6;Q99471-3;H3BMQ1 Q99471 PFDN5 Prefoldin subunit 5 0 83.783 0.035318 556870000 1033100 799750 992120 750520 1354300 1221800 1133200 967040 1118100 856570 FALSE TRUE 1073887.586 937100.8413 1017975.462 898970.6159 1124096.57 938055.4666 1044376.823 954078.4106 1077859.799 1024398.491 1.048310394 0.914781551 0.993729951 0.877559488 1.097323531 0.91571344 1.0195025 0.931354759 1.052187999 1 19.9663456 3.271377929 24.99987409 0.99189128 0.957975547 0.08473928 0.065436064 589.7439613 449256.7104 0.016777692 0.022715761 1868.004548 -3.271377929 -0.033915733 IHGSGHVEEPAS(ph)PLAAYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IHGSGHVEEPASPLAAYQK 19 0 Q12955;A0A087WY90;H0Y951;Q12955-4;Q12955-5;Q12955-6;A0A087WZ65;H0Y3A4;A0A087WTF3;Q12955-7 Q12955;Q12955-4;Q12955-7 ANK3 Ankyrin-3 1 IHGS(0.002)GHVEEPAS(0.998)PLAAYQK;IHGS(0.004)GHVEEPAS(0.996)PLAAYQK 118.54 0.00012909 882350000 98954 458600 584600 521110 592090 804060 546660 631920 567620 596180 TRUE FALSE 102860.7803 537360.9826 599835.1563 624184.0026 491446.7533 617329.2506 503811.3608 623450.146 547191.4671 712990.0564 0.144266781 0.753672478 0.841295262 0.875445593 0.689275746 0.865831501 0.706617654 0.874416327 0.767460166 1 19.44352243 4.739443046 3.866042367 0.817331449 0.078044435 0.848173798 0.086096951 0.080346703 2.395713053 0.01868578 0.168647535 54883.65755 -4.739443046 -0.739287014 down KIDYFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KIDYFER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 111.82 0.010411 2861800000 3357790 3406730 3525070 3025210 4617440 4510280 4135310 3518070 3730980 3848990 FALSE TRUE 3490358.142 3991809.377 3616936.22 3623587.509 3832569.198 3462835.824 3811173.597 3470916.026 3596702.759 4603125.897 0.75825824 0.867195351 0.785756527 0.787201478 0.832601429 0.752279191 0.827953369 0.754034563 0.781360936 1 22.13418247 -0.996512963 7.411587864 1.000000008 0.794221491 0.747532911 0.035902472 4.11E-09 5.87E-10 0.032438283 0.007645776 0.100806152 0.996512963 -0.205778516 KIEDLGAAMEEALILDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEDLGAAMEEALILDNK 18 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 150.29 8.98E-08 240130000 854600 532000 590840 408350 926770 837560 698780 624600 621160 493580 FALSE TRUE 888340.2679 623366.8616 606237.7758 489120.4112 769237.9664 643049.3833 644007.7977 616228.2586 598804.5729 590287.5508 1.504928008 1.056039316 1.02702111 0.828613801 1.303158038 1.089383272 1.091006911 1.043945883 1.014428599 1 19.17105839 4.738533231 9.566613565 1.054484779 1.506347806 0.605895202 0.109930109 0.051227135 124.9457342 0.0257859 0.149832622 54768.80068 -4.738533231 0.451863027 KIEEAMDGSET(ph)PQLFTVLPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEEAMDGSETPQLFTVLPEKR 22 2 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 1 KIEEAMDGS(0.001)ET(0.999)PQLFTVLPEKR;KIEEAMDGS(0.035)ET(0.965)PQLFTVLPEKR 153.12 1.73E-06 948870000 829290 661850 741780 563640 1096810 936200 630410 745950 773640 648440 TRUE FALSE 862031.0096 775517.589 761111.3962 675126.3097 910374.628 718781.7382 580996.8169 735951.7604 745796.8475 775489.4029 1.111596118 1.000036346 0.981459441 0.870580961 1.173935614 0.926874997 0.749200202 0.949015883 0.961711204 1 19.56474754 2.498528321 24.97684186 0.900187299 1.018285645 0.234100512 0.097656918 1062.574316 1239765.311 0.031339611 0.029280301 315.1579894 -2.498528321 0.118098345 KIEEIKDFLLTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIEEIKDFLLTAR 13 2 J3KT73;J3QL01;P63173;J3KSP2 J3KT73 RPL38 60S ribosomal protein L38 0 201.3 5.79E-08 2047700000 3896400 2324800 3604700 2311100 4782200 3718100 3939600 3610400 3821500 2558000 FALSE TRUE 4050232.881 2724066.316 3698641.443 2768228.682 3969323.352 2854627.623 3630803.858 3562008.493 3683964.961 3059191.124 1.323955489 0.890453131 1.209025946 0.904889093 1.297507475 0.933131507 1.186850939 1.164362849 1.204228442 1 21.54471881 KIEFPLPDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEFPLPDEK 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 113.65 0.0023413 975550000 1559940 956970 1318720 943300 1857990 1715370 1712580 1344760 1522190 952130 FALSE TRUE 1621527.636 1121322.153 1353086.927 1129881.925 1542169.523 1317001.314 1578343.505 1326735.692 1467406.679 1138681.644 1.424039497 0.984754746 1.188292561 0.992272011 1.354346521 1.156601866 1.386114822 1.16515068 1.28868915 1 20.11893302 KIEFPLPDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEFPLPDRR 10 2 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 105.17 0.0014537 1822990000 1865790 1844800 1980030 1673850 2621400 2507600 2013340 1928580 2139500 2369400 FALSE TRUE 1939452.83 2161630.049 2031631.208 2004932.534 2175815.364 1925247.903 1855529.15 1902730.54 2062499.813 2833638.565 0.68443903 0.762846072 0.716969071 0.707547024 0.767852115 0.679426066 0.654822098 0.671479617 0.727862699 1 21.43422432 0.948355059 20.71549859 1 0.704693473 0.863678197 0.034883478 591.8463034 237398.565 0.036361921 0.00909048 8.878816057 -0.948355059 -0.295306527 KIEFPMPNEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KIEFPMPNEEAR 12 1 P17980;E9PM69;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 106.58 0.0030576 1449660000 1003080 1589710 1510320 1498860 1573870 1984860 1340250 1488460 1360390 1743570 FALSE TRUE 1042682.373 1862730.326 1549680.18 1795330.034 1306344.14 1523906.346 1235197.703 1468509.628 1311429.83 2085189.159 0.500042103 0.893314795 0.74318446 0.860991449 0.626487115 0.730824031 0.592367219 0.704257272 0.628926073 1 20.99174683 -1.114950031 5.041373897 1.000010218 0.704032761 0.389157442 0.113335837 1.23E-05 2.15E-06 0.103432322 0.024378391 0.076744978 1.114950031 -0.295977457 KIEFSLPDLEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEFSLPDLEGR 12 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 136.33 0.00017946 1437700000 1346950 1204320 1370090 1251420 1687380 1637560 1520700 1369280 1523260 1177890 FALSE TRUE 1400128.626 1411152.592 1405795.671 1498947.141 1400559.75 1257261.507 1401503.56 1350927.041 1468438.17 1408674.993 0.993933045 1.001758815 0.997956007 1.06408302 0.994239095 0.892513542 0.994909093 0.959005482 1.042425099 1 20.42590736 2.99846532 24.99989338 0.972159482 1.01445185 0.149761596 0.040079796 96.61756712 1573942.118 0.011483508 0.013544739 996.4725049 -2.99846532 0.042292369 KIEIDNGDELTADFLYEEVHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIEIDNGDELTADFLYEEVHPK 22 1 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 226.12 3.59E-26 108000000 164000 104370 150990 112120 190660 167410 194140 146060 157670 87368 FALSE TRUE 170474.8466 122294.7356 154924.9234 134297.0014 158251.6813 128531.5646 178922.7995 144102.3046 151995.4875 104486.0868 1.631555471 1.170440384 1.482732564 1.285309895 1.514571807 1.230130906 1.71240789 1.379153043 1.454695951 1 16.67295132 -1.205666858 5.588096955 0.999984545 1.424518715 0.387132073 0.161843452 2.79E-05 3.97E-06 0.140345237 0.033078487 0.062277783 1.205666858 0.42453417 KIEITVEPSQRPGTAINRS(ph)PS(ph)PISNQPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEITVEPSQRPGTAINRSPSPISNQPSPR 30 3 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 2 KIEIT(0.001)VEPS(0.076)QRPGT(0.38)AINRS(0.545)PS(0.982)PIS(0.015)NQPSPR;KIEIT(0.001)VEPS(0.034)QRPGT(0.432)AINRS(0.545)PS(0.887)PIS(0.094)NQPS(0.007)PR 74.328 0.002302 191756000 262852 253791 276769 228417 316197 354400 298940 270958 297387 289113 TRUE FALSE 273229.5999 297377.63 283981.8275 273597.2008 262449.9469 272095.971 275508.3017 267326.2512 286684.1 345759.1569 0.790230987 0.860071596 0.821328436 0.791294158 0.759054219 0.786952321 0.796821418 0.773157401 0.829143912 1 18.39940793 0.875856623 5.872439638 0.999998479 0.797336642 0.844010841 0.025998953 0.733753543 34.51609297 0.027201512 0.006843421 7.513747965 -0.875856623 -0.202661837 KIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVAR 35 2 Q86U44 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 0 79.408 0.00065159 167610000 39300 45616 56893 39135 66957 67718 54682 59119 60019 63607 FALSE TRUE 40851.59435 53450.19316 58375.67832 46875.78619 55575.67306 51991.52078 50395.88196 58326.6065 57858.92791 76069.57382 0.537029357 0.702648779 0.767398519 0.616222543 0.730590041 0.683473275 0.66249723 0.766753428 0.760605391 1 16.2150319 -5 0.167934438 2.212043291 0.618638974 0.738500077 0.059131167 66.07561339 0.620516863 26.50076409 0.214472581 1.00E-05 5 -1.593404317 KIEMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIEMVR 6 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 119.89 0.033075 2832400000 3271200 3568600 3366900 3082700 3999300 3814000 3773100 3353900 3258300 3446500 FALSE TRUE 3400349.502 4181479.29 3454644.18 3692448.859 3319500.415 2928256.302 3477354.563 3308946.456 3141034.419 4121775.688 0.824971993 1.014484923 0.838144635 0.895839351 0.805356882 0.710435629 0.843654489 0.802796345 0.762058554 1 21.97483456 3.242665316 9.669213834 0.807049063 0.898143799 0.136513256 0.085113679 0.176647544 221.8505596 0.022353163 0.028747099 1748.498708 -3.242665316 0.091094737 KIEPELDGSAQVTSHDASTNGLINFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIEPELDGSAQVTSHDASTNGLINFIK 27 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48 P06744 GPI Glucose-6-phosphate isomerase 0 327.05 2.62E-95 1130800000 653640 491620 712610 436720 897060 718010 727790 712250 722720 553750 FALSE TRUE 679446.2119 576051.9107 731181.202 523101.9125 744578.0616 551263.059 670743.9181 702703.4538 696709.4484 662246.7103 1.025971441 0.869844881 1.10409186 0.789889786 1.124321269 0.832413435 1.01283088 1.061090139 1.052039123 1 19.33700925 2.010867175 24.9628067 1.042613315 0.957207924 0.110956077 0.103767837 400.3722361 919684.565 0.035087463 0.025891291 102.5338287 -2.010867175 -0.085405391 KIFDIDEAEEGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIFDIDEAEEGVK 13 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 165.34 5.69E-05 195980000 955260 507560 755790 480160 933830 737420 956960 740930 835560 440340 FALSE TRUE 992974.4024 594729.4817 775486.5083 575134.2149 775097.9102 566165.3807 881950.9747 730999.0453 805488.3588 526616.1922 1.885575144 1.129341427 1.472583866 1.092131658 1.471845951 1.075100593 1.674750962 1.388105904 1.529554865 1 19.00639236 4.753251592 24.25600209 1.341008797 1.885575727 0.375506118 0.218476332 1811.573068 2990977.656 0.048123218 1.032431777 56656.74129 -4.753251592 0.54456693 KIFVGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIFVGTK 7 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 90.657 0.047363 0 6722800 5874200 6865100 5826800 11659500 11385900 10763300 9909800 10177300 8670000 FALSE TRUE 6988221.335 6883048.155 7044010.146 6979323.649 9677622.355 8741697.28 9919644.421 9776975.34 9811020.961 10368720.5 0.673971425 0.663828112 0.679351917 0.673113298 0.933347789 0.84308351 0.956689345 0.94292978 0.946213273 1 23.30573454 3.238844275 24.9528202 0.93191971 0.672426692 0.925031459 0.036868212 1.823149524 160365.2722 0.010475101 0.013340511 1733.182418 -3.238844275 -0.259493017 KIGDEYFTFITDCKDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIGDEYFTFITDCKDPK 17 2 P49368;P49368-2;B4DUR8 P49368 CCT3 T-complex protein 1 subunit gamma 0 211.13 1.55E-12 930760000 1816500 739770 1195400 772550 1937300 1483000 1768000 1221800 1487900 641750 FALSE TRUE 1888216.823 866819.7429 1226553.106 925358.0842 1607998.438 1138595.725 1629419.54 1205423.769 1434350.77 767488.6255 2.46025382 1.129423569 1.598138481 1.205696154 2.095143022 1.483534332 2.123053666 1.570607993 1.868888635 1 19.54978584 -1.229597616 5.3154302 0.999943699 1.700757085 0.22820795 0.39813824 0.000241349 3.50E-05 0.350218963 0.082540809 0.058938949 1.229597616 0.700813386 KIGELVR ddPTM_MDA-MB-175_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 ; 85.212 0.059902 0 568820 533510 560440 483710 739430 696360 580650 605080 620070 624990 FALSE TRUE 591277.4528 625136.1924 575045.5268 579386.3943 613741.9527 534640.9434 535137.1358 596969.8923 597753.8018 747444.8243 0.791065017 0.836364334 0.769348463 0.775156072 0.821120078 0.715291519 0.71595537 0.798680883 0.799729669 1 19.51160756 0.553241842 1.885641085 0.999955774 0.776722671 0.762769942 0.036963614 1.415971054 5.403963956 0.037044274 0.010294589 3.57471845 -0.553241842 -0.223233103 KIGGIFAFK ddPTM_MDA-MB-175_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 0 103.55 0.0066564 0 352360 306560 378610 233910 534990 437430 380710 365150 394930 410330 FALSE TRUE 366271.4449 359209.2953 388476.8876 280176.6998 444052.5909 335843.5118 350868.9554 360255.7615 380716.5464 490726.3073 0.746386406 0.731995188 0.791636564 0.570942898 0.904888498 0.684380492 0.714999278 0.734127672 0.775822573 1 18.90455909 0.713252134 2.479420775 0.999971906 0.734266874 0.501763244 0.0788114 1.243459167 9.719185198 0.068690357 0.018376194 5.167162668 -0.713252134 -0.265705032 KIHIDLPNEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIHIDLPNEQAR 12 1 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 123.02 0.00022603 1653370000 2564400 2413290 2930000 2110900 3492200 3220700 2745500 2852400 2746700 2668300 FALSE TRUE 2665644.492 2827753.785 3006358.207 2528429.72 2898597.091 2472741.235 2530300.536 2814168.244 2647846.804 3191102.297 0.835336584 0.88613699 0.942106497 0.792337407 0.908337252 0.774886232 0.792923667 0.881879671 0.829759298 1 21.60562343 -1.566568375 2.699657442 1.01006755 0.85080555 0.42993196 0.052033148 18558412.05 18504479.16 1349367.307 0.012339811 0.027128865 1.566568375 -0.159262 KIHPQTIIAGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIHPQTIIAGWR 12 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 147.87 4.28E-05 1613750000 1418320 1512460 1567850 1354400 2026800 2013650 1507500 1586930 1612040 2019560 FALSE TRUE 1474316.369 1772213.24 1608709.459 1622296.278 1682285.26 1546010.305 1389338.211 1565659.799 1554022.995 2415254.115 0.610418738 0.733758501 0.666062196 0.671687616 0.69652516 0.640102544 0.575234797 0.648238125 0.64342008 1 21.20374356 -2.010273919 2.63870546 1.368203376 0.654109077 0.86327892 0.041315785 7035301.736 1535426.932 15726617.89 0.010286847 0.00976621 2.010273919 -0.714094299 KIHSQEEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KIHSQEEALR 10 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;;;;; 215.89 5.18E-09 5628090000 1684980 1677530 1706750 1391190 2392680 2227140 1732300 1654020 1658750 2300510 FALSE TRUE 1751504.311 1965632.728 1751229.307 1666363.23 1985973.108 1709920.488 1596517.799 1631850.567 1599051.912 2751250.889 0.63662108 0.714450556 0.636521124 0.605674763 0.721843695 0.621506564 0.580287972 0.59313041 0.581209049 1 21.39165628 -1.992250177 2.944379333 1.349806798 0.631305287 0.843961577 0.047422001 868097.1924 5762816.964 2022837.425 0.011841777 0.010180048 1.992250177 -0.718501511 KIIDSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIIDSVR 7 1 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 94.114 0.023151 511640000 387470 361110 426630 408270 544720 509680 378690 397500 433360 415990 FALSE TRUE 402767.6148 423127.8335 437748.3283 489024.5874 452128.689 391314.5443 349007.2883 392172.1627 417763.4583 497495.2759 0.809590833 0.850516284 0.879904493 0.982973329 0.908810015 0.786569367 0.701528849 0.78829324 0.839733518 1 18.9243233 2.735632122 24.80921103 0.79841118 0.88937661 0.090104342 0.083113174 364.9394741 3091626.57 0.026135626 0.025657561 544.0416158 -2.735632122 0.09096543 KIIPTLEEGLQLPS(ph)PTATSQLPLESDAVECLNYQHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK 37 1 P61978;P61978-2 P61978 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 KIIPTLEEGLQLPS(0.617)PT(0.128)AT(0.128)S(0.128)QLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.977)PT(0.023)ATSQLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.866)PT(0.131)AT(0.002)SQLPLESDAVECLNYQHYK;KIIPTLEEGLQLPS(0.395)PT(0.395)AT(0.099)S(0.099)QLPLES(0.009)DAVECLNY(0.003)QHY(0.001)K 251.09 1.65E-51 9289577000 1357639 1105838 1495737 1009691 1657201 1605053 1334598 1383167 1516207 1262104 TRUE FALSE 1411239.636 1295757.074 1534717.135 1209404.866 1375510.566 1232303.766 1229988.721 1364627.909 1461639.006 1509389.114 0.934974039 0.858464568 1.016780312 0.801254531 0.911302826 0.816425502 0.81489174 0.904092852 0.968364613 1 20.52553334 -1.639816206 4.521586328 1.002635013 0.887956956 0.187901192 0.067021816 0.00174317 0.000138859 0.063540453 0.014643371 0.022918374 1.639816206 -0.114678057 KILDSVGIEADDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KILDSVGIEADDDR 14 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ; 166.3 6.14E-06 437080000 604180 529940 565240 582210 810150 771140 770350 645050 644560 512980 FALSE TRUE 628033.4929 620953.0726 579970.6187 697369.4003 672440.9924 592054.4217 709967.9541 636404.1598 621362.4115 613488.6094 1.023708482 1.01216724 0.945364934 1.136727544 1.096093688 0.9650618 1.157263465 1.037352854 1.012834472 1 19.22667703 3.752196805 24.99207726 1.061785937 0.995588928 0.192987049 0.059718935 1253.950714 2298204.849 0.014884324 0.026665935 5651.930399 -3.752196805 -0.06619701 KILDSVGIEADDDRLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KILDSVGIEADDDRLNK 17 2 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 ;;; 280.25 3.68E-36 4139990000 7168940 3999210 4993530 3903880 7673250 6662300 6661460 5003650 5670370 3845710 FALSE TRUE 7451975.287 4686043.208 5123665.494 4676055.812 6368953.706 5115081.793 6139317.359 4936584.256 5466294.491 4599203.244 1.620275272 1.018881523 1.114033284 1.016709974 1.384795011 1.112166939 1.334865418 1.073356404 1.188530752 1 22.13295252 7.924553686 0.019990475 3.22E-06 2.688412067 0.145713601 0.176530281 7317.38729 11.40566622 570.524176 1024.471526 84053090.43 -7.924553686 2.688408851 KILGVGGEDDDGEVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KILGVGGEDDDGEVHR 16 1 E9PN66;E9PNB3;E9PKN9;E9PS55;E9PMY0;E9PMW4;E9PQ46;E9PIN5;E9PIK4;U3KQ32;E9PKZ4;E9PPM1;O14683 E9PN66 TP53I11 Tumor protein p53-inducible protein 11 0 116.43 0.00027806 66512000 60819 57279 50556 70787 66714 105980 68869 61250 61006 84456 FALSE TRUE 63220.18108 67116.22268 51873.53089 84788.45732 55373.97811 81367.75114 63470.86782 60429.04393 58810.40598 101003.5362 0.625920472 0.664493791 0.513581334 0.839460285 0.548238014 0.805593093 0.628402432 0.598286419 0.582260861 1 16.62404628 -1.122076416 4.554007159 1.000035635 0.645233231 0.537867368 0.098679521 12826914.05 3160465.184 4565.280568 0.021293651 0.075495938 1.122076416 -0.354802403 KILIEDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KILIEDWK 8 1 K7ELL7;P14314-2;P14314;K7EPW7 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 110.14 0.0095417 0 2406200 1523990 1793120 1567060 2588700 2318700 2109040 1809240 1902380 1273280 FALSE TRUE 2501198.634 1785723.428 1839850.18 1877019.791 2148673.699 1780217.065 1943727.934 1784990.097 1833913.715 1522754.838 1.642548474 1.172692664 1.208237948 1.2326474 1.411043752 1.169076611 1.276454939 1.172211083 1.204339445 1 20.53825226 7.998551896 0.029898719 8.53E-07 3.054171989 0.434116937 0.122671038 1398.781857 3.206818984 104.5367003 253.0457557 99667117.12 -7.998551896 3.054171136 KIPEPS(ph)PVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KIPEPSPVTR 10 1 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR;KIPEPS(1)PVTR 173.44 2.09E-06 9900070000 5443230 4611820 5106160 4541040 5775060 5975360 5636590 5150360 5070100 4346080 TRUE FALSE 5658132.923 5403864.21 5239230.724 5439244.158 4793417.364 4587673.197 5194779.347 5081327.848 4887628.091 5197611.165 1.08860258 1.039682277 1.00800744 1.04648924 0.922234698 0.882650328 0.999455169 0.977627546 0.940360473 1 22.30941728 3.250015736 24.95567728 0.954222118 1.042573906 0.585154581 0.03790052 168.8567437 367862.4518 0.011132078 0.014943639 1778.343844 -3.250015736 0.088351788 KIPEPS(ph)PVTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIPEPSPVTRR 11 2 A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;Q7Z4S6-3;H0YHT2;H0YI78 A0A1B0GV47 KIF21A Kinesin-like protein KIF21A 1 KIPEPS(0.978)PVT(0.022)RR 75.764 0.019408 209870000 301430 298760 313200 212850 390220 323690 231100 291860 304650 316740 TRUE FALSE 313330.6892 350069.706 321362.2493 254951.0947 323890.5438 248517.9031 212985.7781 287948.0941 293685.706 378799.1386 0.827168431 0.924156552 0.848371119 0.673050883 0.855045618 0.656067762 0.56226574 0.760160372 0.775307217 1 18.53107352 3.883109507 5.608713537 0.73499651 0.878027522 0.154430752 0.114729215 0.320674819 13.48349296 0.028463612 0.052538412 7640.284078 -3.883109507 0.143031011 S(ph)VSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.943)VS(0.057)HGSNHTQKPDEQR;S(0.963)VS(0.037)HGSNHTQKPDEQR;S(0.971)VS(0.029)HGSNHTQKPDEQR;S(0.797)VS(0.203)HGSNHTQKPDEQR;S(0.573)VS(0.427)HGSNHTQKPDEQR;S(0.5)VS(0.5)HGSNHTQKPDEQR;S(0.89)VS(0.11)HGSNHTQKPDEQR 240.21 4.50E-20 2616316000 189751 849308 899840 981831 1040469 1433530 871120 1179298 971157 990129 TRUE FALSE 197242.516 995170.0423 923290.5696 1176034.241 863610.451 1100614.383 802839.3382 1163491.439 936205.2493 1184125.82 0.166572262 0.840425929 0.779723365 0.993166622 0.729323216 0.929474186 0.678001716 0.982574165 0.790629875 1 20.17539095 4.739649961 5.853977064 0.856369755 0.145876702 0.783818158 0.108985809 0.054390003 8.433786997 0.02334008 0.153830099 54909.81249 -4.739649961 -0.710493052 down KIQALQQQADEAEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KIQALQQQADEAEDR 15 1 P67936;A0A2R8Y5V9;A0A2R8YGX3;A0A590UJB9;A0A590UK79 P67936 TPM4 Tropomyosin alpha-4 chain 0 ;;;;; 283.1 1.15E-33 15711300000 10220200 10123420 11222600 9621270 11921600 13018900 11470100 11061400 11750600 10761500 FALSE TRUE 10623701.39 11862038.64 11515070.18 11524328.49 9895170.69 9995457.778 10571043.59 10913140.03 11327698.2 12870009.88 0.825461789 0.921680616 0.89472116 0.895440531 0.768854941 0.77664725 0.821370278 0.847951177 0.880162354 1 23.61750983 0.796259631 2.407119719 0.999919935 0.844247972 0.49586462 0.047233344 0.776692278 7.355037578 0.049892601 0.013426645 6.255465465 -0.796259631 -0.155671963 KIQEESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIQEESLR 8 1 Q99613-2;Q99613;B5ME19 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ; 154.56 0.00067847 1286220000 782910 626750 676400 631430 1126270 948650 852560 694240 724520 717300 FALSE TRUE 813819.8913 734389.4371 694027.5397 756324.9694 934827.0277 728340.4144 785734.1194 684934.8483 698444.6667 857841.2015 0.948683614 0.85609019 0.809039643 0.881660811 1.08974368 0.849038742 0.915943555 0.798440139 0.814188763 1 19.71035108 -0.617230922 5.973104975 1.000000001 0.881779893 0.149713983 0.082115393 6.06E-10 2.03E-10 0.081359725 0.019176671 0.241417683 0.617230922 -0.118220107 KIQNDAGVR ddPTM_MDA-MB-175_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 ;;; 123.79 0.00087832 1292820000 1673550 1710860 1664240 1501390 2396060 2327980 1966660 1753840 1917430 2157420 FALSE TRUE 1739623.046 2004686.896 1707611.462 1798360.461 1988778.577 1787341.926 1812508.05 1730332.644 1848422.069 2580125.143 0.674239795 0.776972738 0.661832805 0.69700513 0.770807022 0.692734587 0.702488426 0.670639038 0.716407913 1 21.29900961 0.936382146 22.22749407 1 0.705477914 0.849382829 0.037036445 3284.63649 1147623.668 0.034428152 0.008607038 8.637382381 -0.936382146 -0.294522086 KIQSLGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIQSLGDSK 9 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 87.667 0.021335 398230000 564360 411060 500920 345560 695500 627790 592590 503970 591620 468430 FALSE TRUE 586641.3686 481656.3574 513974.3867 413910.7366 577279.1584 481995.2867 546141.2474 497215.1065 570327.7118 560209.8899 1.047181385 0.85977839 0.917467535 0.738849392 1.030469417 0.860383395 0.974886837 0.887551461 1.01806077 1 19.09560793 1.233423351 24.94163436 1.009030446 0.910947155 0.163543288 0.0851347 213.7902578 1037900.632 0.067641456 0.018935631 17.11683053 -1.233423351 -0.098083292 KIQVLQQQADDAEER ddPTM_MDA-MB-175_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 ;;;;;;; 314.06 4.76E-56 15635160000 5976800 5762520 6373080 5841430 6501630 7525510 6479600 6431840 6552160 5867720 FALSE TRUE 6212768.679 6752187.984 6539167.7 6996847.419 5396485.255 5777824.353 5971712.021 6345631.705 6316349.041 7017387.39 0.885339277 0.962208242 0.931852175 0.997072989 0.769016296 0.823358329 0.850987937 0.904272681 0.900099808 1 22.74250258 5.087412554 13.76374361 0.897850228 0.685748394 0 0.070687642 3089347.725 9388953.433 0.01734539 19165096.83 122296.0849 -5.087412554 -0.212101834 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.821)ENS(0.091)YS(0.088)LDDLEIGPGQLSSSTFDSEK;KIS(0.869)ENS(0.065)YS(0.065)LDDLEIGPGQLSSSTFDSEK;KIS(0.9)ENS(0.066)YS(0.034)LDDLEIGPGQLSSSTFDSEK;KIS(0.896)ENS(0.099)YS(0.005)LDDLEIGPGQLSSSTFDSEK;KIS(0.328)ENS(0.328)Y(0.017)S(0.328)LDDLEIGPGQLSSSTFDSEK;KIS(0.998)ENS(0.002)YSLDDLEIGPGQLSSSTFDSEK 364.73 1.45E-127 4906709000 2059733 949144 1643966 1431474 2529151 2450120 3190652 2146039 2430630 1055975 TRUE FALSE 2141052.849 1112152.099 1686809.104 1714615.285 2099246.816 1881116.762 2940560.359 2117274.857 2343152.101 1262873.083 1.69538244 0.88065231 1.335691707 1.357709898 1.662278533 1.489553295 2.328468631 1.676553951 1.855413764 1 20.26827823 3.17627545 1.708311507 1.764335579 1.261956787 0.161054739 0.364236324 0.46747134 2.820360304 0.115014675 0.155822422 1500.636308 -3.17627545 -0.502378791 KIS(ph)ENSYSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KISENSYSLDDLEIGPGQLSSSTFDSEKNESR 32 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KIS(0.655)ENS(0.155)Y(0.005)S(0.185)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.995)ENS(0.005)YSLDDLEIGPGQLSSSTFDSEKNESR;KIS(0.964)ENS(0.036)YSLDDLEIGPGQLSSSTFDSEKNESR;KIS(0.33)ENS(0.33)Y(0.01)S(0.33)LDDLEIGPGQLSSSTFDSEKNESR;KIS(0.983)ENS(0.013)YS(0.004)LDDLEIGPGQLSSSTFDSEKNESR 237.84 6.17E-47 5931439800 667605.7 376136 570828.4 406039.9 997400.2 811450 912397.7 736019.3 888536.1 431035.4 TRUE FALSE 693963.2885 440734.4321 585704.657 486353.3803 827862.4703 623003.0351 840881.5842 726154.1652 856557.8593 515488.534 1.34622449 0.854983968 1.136212774 0.943480501 1.605976497 1.208568172 1.631232372 1.408671808 1.661642894 1 18.97558081 3.242928128 24.99953363 1.442062347 1.059564397 0.363825049 0.224788829 102.4139016 586210.1106 0.057378812 0.075070087 1749.55713 -3.242928128 -0.38249795 KIS(ph)PPSYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KISPPSYAR 9 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 KIS(0.998)PPS(0.002)YAR;KIS(0.984)PPS(0.016)YAR;KIS(0.66)PPS(0.34)YAR;KIS(0.637)PPS(0.363)YAR 106.49 0.0017928 2804950000 566173 456853 510749 397836 610665 654963 581165 510294 559417 463382 TRUE FALSE 588525.9472 535313.9489 524059.5385 476526.7734 506864.3814 502857.7693 535611.7687 503454.3436 539283.6914 554172.8309 1.061989896 0.965969313 0.945660829 0.859888372 0.914632319 0.907402423 0.966506726 0.908478936 0.973132679 1 19.07997646 4.722864362 2.008205682 0.927620927 1.098070044 0.497510767 0.038194174 0.534409851 2.38742753 0.009360461 0.165489953 52828.02351 -4.722864362 0.170449117 KIS(ph)PVKFSNTDSVLPPKR ddPTM_MDA-MB-175_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(0.892)PVKFS(0.1)NT(0.007)DS(0.001)VLPPKR 65.753 0.023509 302820000 415180 142210 268540 121350 386790 333270 331770 273990 312980 171330 TRUE FALSE 431571.627 166633.4613 275538.373 145352.6678 321043.574 255873.0933 305765.0005 270317.6122 301715.9109 204898.8332 2.106266884 0.813247487 1.344753256 0.709387484 1.566839444 1.248777698 1.492273019 1.319273556 1.472511611 1 17.64455224 KIS(ph)TEDINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KISTEDINK 9 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 KIS(0.626)T(0.374)EDINK;KIS(0.965)T(0.035)EDINK 96.464 0.0045022 305380000 616820 298690 401280 290270 681390 614300 621350 430510 556680 315580 TRUE FALSE 641172.5299 349987.684 411737.6865 347684.5396 565567.5712 471638.1348 572646.9634 424739.7176 536645.1955 377411.8589 1.69886694 0.927336213 1.09095058 0.921233744 1.498542131 1.249664322 1.517299867 1.125401091 1.421908673 1 18.52578023 3.233119846 24.99652754 1.308071103 1.138103526 0.068726586 0.251562496 318.5990181 1463739.051 0.06842914 0.08402101 1710.487268 -3.233119846 -0.169967577 KISELDAFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KISELDAFLK 10 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 102.62 0.0072898 0 382350 289340 341820 305050 497420 453360 456500 355710 386960 268120 FALSE TRUE 397445.4732 339031.8942 350728.11 365387.9795 412868.7261 348074.0107 420718.3372 350942.2893 373033.3852 320652.9805 1.239487849 1.057317146 1.093793388 1.139512188 1.287587364 1.085516218 1.312067446 1.094461335 1.163355427 1 18.29065329 0.339804078 1.363753437 1.000009253 1.162886132 0.253970994 0.084147048 6.022174167 11.04008217 0.077063832 0.022536671 2.186774886 -0.339804078 0.16287688 KISELDAFLKEPALNEANLSNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KISELDAFLKEPALNEANLSNLK 23 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 257.2 7.48E-44 429530000 1163900 609120 996890 621700 1357600 1059000 1110900 880280 1125000 571490 FALSE TRUE 1209851.671 713731.6217 1022869.772 744670.4044 1126835.637 813063.2993 1023824.755 868481.2864 1084511.47 683462.5237 1.770179972 1.044287868 1.496599648 1.089555577 1.648716057 1.189623822 1.49799692 1.270707985 1.586789959 1 19.38250271 -1.329893931 4.699226981 0.999730429 1.379886715 0.206035331 0.232382797 0.000568195 8.10E-05 0.194796491 0.045881813 0.046784939 1.329893931 0.380156286 KISENS(ph)YSLDDLEIGPGQLSSSTFDSEKNESR ddPTM_MDA-MB-175_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(0.431)ENS(0.445)YS(0.124)LDDLEIGPGQLSSSTFDSEKNESR 152.98 9.94E-11 37108000 23463 9877.3 15115 10674 27431 25370 22643 17926 24587 13472 TRUE FALSE 24389.33736 11573.64944 15508.90932 12785.28534 22768.28842 19478.20199 20868.18249 17685.73129 23702.11867 16111.58046 1.51377684 0.718343521 0.962593915 0.793546317 1.41316294 1.208956628 1.295228767 1.097703067 1.47112313 1 13.9758104 3.237088919 24.99984759 1.243390038 0.97469424 0.211457155 0.235437561 55.45873481 942090.6414 0.063081341 0.079333054 1726.191283 -3.237088919 -0.268695797 KISENSYS(ph)LDDLEIGPGQLSSSTFDSEKNESR ddPTM_MDA-MB-175_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(0.006)ENS(0.004)YS(0.99)LDDLEIGPGQLSSSTFDSEKNESR 137.19 1.11E-08 55747000 77278 35802 62260 34307 66405 56124 56832 42687 54081 29830 TRUE FALSE 80328.99511 41950.715 63882.54675 41092.8222 55117.50182 43090.05157 52377.35934 42114.85059 52134.63537 35674.61737 2.251712871 1.175926137 1.790700264 1.151878429 1.54500611 1.207863034 1.468196808 1.180527044 1.46139298 1 15.12261034 6.304181345 1.790920947 1.340505916 199.9746514 0.578361541 0.230393694 211.0031267 3.848768518 0.053101912 169830.2975 2014565.283 -6.304181345 198.6341455 KISSDLDGHPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KISSDLDGHPVPK 13 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 ;;; 120.53 0.00017063 4931560000 8604110 7706810 9780900 7486770 14430800 11691700 11458400 9983300 10986800 8484340 FALSE TRUE 8943806.907 9030394.667 10035798.29 8967630.76 11977857.77 8976479.864 10560260.67 9849490.193 10591387.21 10146683.98 0.881451213 0.889984815 0.989071731 0.883799158 1.180470171 0.884671276 1.040759788 0.970710255 1.043827445 1 23.27450498 4.111555203 1.249364433 1.005934573 0.869377702 0.25224209 0.079515227 0.822289955 2.123120276 0.022419849 0.109655884 12928.71027 -4.111555203 -0.136556871 KISSIQSIVPALEIANAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KISSIQSIVPALEIANAHR 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 116.39 7.75E-05 408590000 404960 456460 444210 442090 456910 641890 403450 418750 450990 578400 FALSE TRUE 420948.1335 534853.4542 455786.4775 529534.0825 379244.6014 492820.7754 371826.5348 413137.3412 434758.958 691726.4059 0.608547151 0.77321532 0.658911491 0.765525326 0.548258095 0.71245043 0.537534105 0.597255414 0.628512884 1 19.39984201 -1.408171095 8.574916126 1.000002981 0.64578975 0.648608105 0.077757637 4.40E-06 3.04E-07 0.074787998 0.017627552 0.039068695 1.408171095 -0.354213231 KITIADCGQLE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 126.66 0.0062096 507330000 1118030 1249140 1079850 958320 1720980 1599220 1047370 1161350 1129680 1814560 FALSE TRUE 1162170.688 1463670.078 1107991.778 1147872.836 1428448.434 1227825.391 965274.4026 1145784.003 1089023.037 2170088.29 0.53554074 0.674474898 0.510574516 0.528952136 0.658244386 0.565795132 0.444808816 0.527989579 0.501833516 1 21.04932231 -1.695307668 2.895496632 1.059124418 0.549163038 0.807300931 0.065984661 35994362.94 35723090.85 15670118.98 0.016741546 0.02016937 1.695307668 -0.509961379 KITSLSS(ph)SLDTSLDFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KITSLSSSLDTSLDFSK 17 1 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 KIT(0.015)S(0.015)LS(0.081)S(0.444)S(0.444)LDTSLDFSK 109.85 0.00035941 29071000 23924 16557 21369 16331 32778 32557 25667 25169 29073 20272 TRUE FALSE 24868.53799 19400.53595 21925.89369 19561.22306 27206.40727 24996.13016 23655.15347 24831.65072 28026.66841 24243.91027 1.025764314 0.800223056 0.904387677 0.806850992 1.122195511 1.031027168 0.975715271 1.024242808 1.156029209 1 14.56533479 3.239537673 24.99999996 1.04467441 0.879734915 0.529425148 0.077026538 20.30735532 519595.515 0.021007859 0.026885254 1735.951841 -3.239537673 -0.164939495 KITSLSSS(ph)LDTSLDFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KITSLSSSLDTSLDFSK 17 1 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 KIT(0.059)S(0.047)LS(0.031)S(0.217)S(0.643)LDT(0.001)SLDFSK 76.744 0.011794 448290000 429750 330920 458630 411340 627500 585060 500310 423260 515180 379020 TRUE FALSE 446716.8618 387752.9358 470582.2746 492701.8243 520837.7741 449188.6817 461094.3949 417586.892 496638.7724 453281.7122 0.985517063 0.855434767 1.038167351 1.086966032 1.149037696 0.990970228 1.017235821 0.921252459 1.095651466 1 18.79004843 4.218195414 24.99404755 1.031793423 0.920475917 0.32714489 0.066691835 260.5249604 319740.8826 0.017862183 0.038657447 16527.05277 -4.218195414 -0.111317506 KIVDQIRPDR ddPTM_MDA-MB-175_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 ; 178.67 1.23E-06 5446100000 5013800 5655300 5797100 4948300 6655800 6651200 5710900 6048900 5518700 6069800 FALSE TRUE 5211748.695 6626553.783 5948177.188 5927058.971 5524449.493 5106559.6 5263264.735 5967824.39 5320083.065 7259061.097 0.717964572 0.912866512 0.819414124 0.816504902 0.761041879 0.703473842 0.725061363 0.8221207 0.732888592 1 22.79135153 -1.408056598 3.63573775 1.001519066 0.783061236 0.537053587 0.061443407 1382012.135 30005006.34 80177.07211 0.014633481 0.039078996 1.408056598 -0.218457829 KIVEACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIVEACK 7 1 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 89.355 0.050362 0 351620 335700 413740 378840 450340 496190 370880 345600 427030 395170 FALSE TRUE 365502.2291 393353.8636 424522.4043 453773.4213 373791.3677 380957.3923 341809.4565 340967.7973 411661.2737 472595.9955 0.773392565 0.83232585 0.898277616 0.960171956 0.790932152 0.806095261 0.723259316 0.721478389 0.871063821 1 18.85024788 KIVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_MDA-MB-175_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 137.25 1.26E-05 122236000 247778 247288 267001 189763 315347 302245 218714 262722 280793 276317 TRUE FALSE 257560.4668 289757.7904 273959.2654 227297.555 261744.4296 232053.1793 201570.6252 259200.6413 270687.3148 330456.0257 0.7794092 0.876842205 0.829033953 0.68782996 0.792070379 0.702221056 0.609977151 0.784372567 0.819132634 1 18.33409878 0.841076701 2.395929145 0.999550477 0.755252356 0.509930989 0.071623497 0.522185032 5.553841738 0.073345452 0.019780393 6.935482835 -0.841076701 -0.244298121 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 KIVEPEVVGES(1)DSEVEGDAWR;KIVEPEVVGES(0.996)DS(0.004)EVEGDAWR;KIVEPEVVGES(0.989)DS(0.011)EVEGDAWR 200.52 4.55E-22 358340000 300186 334051 333596 257362 396260 391820 281605 346090 360624 366489 TRUE FALSE 312037.5751 391421.6607 342289.7858 308267.4355 328903.8667 300825.7431 259532.0643 341451.2296 347645.2127 438295.5027 0.711934239 0.893054248 0.780956646 0.703332417 0.750415792 0.686353707 0.592139465 0.779043425 0.793175405 1 18.74154435 0.777974601 2.073835603 0.999560285 0.736066612 0.539783746 0.072939925 0.687158783 4.835215603 0.073539465 0.020229095 5.997560001 -0.777974601 -0.263493673 KIVLATNIAETSITINDIVHVVDSGLHKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIVLATNIAETSITINDIVHVVDSGLHKEER 31 2 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 ; 107.76 4.14E-05 175158000 107218 101099 141024 100947 164484 171290 124223 129643 149998 110410 FALSE TRUE 111451.0494 118461.9668 144699.2013 120914.0153 136525.0684 131510.4934 114486.0767 127905.3476 144599.6013 132042.7256 0.84405293 0.897148755 1.095851367 0.915718869 1.033946155 0.995969243 0.867038121 0.96866637 1.095097065 1 17.0106453 4.462811011 24.62899839 0.98680374 0.857326837 0.359779968 0.067824337 176.6891531 304095.5981 0.016234603 0.044504294 29027.59206 -4.462811011 -0.129476903 KIVSWLEYESSFSNEEAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIVSWLEYESSFSNEEAQK 19 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 271.72 3.97E-39 539280000 319210 196430 279380 190620 365530 302440 344390 288900 314810 221430 FALSE TRUE 331812.6573 230165.3245 286660.8723 228324.0671 303397.3412 232202.8935 317395.8119 285027.768 303480.0496 264814.969 1.252998116 0.869155265 1.082494972 0.862202269 1.145695586 0.876849577 1.198556914 1.076328008 1.146007912 1 18.01462515 2.221457179 24.99840775 1.110912598 1.010351568 0.1051242 0.128264719 485.8263709 710080.0045 0.043461884 0.03217656 166.5164635 -2.221457179 -0.10056103 KIWCFGPDGTGPNILTDITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIWCFGPDGTGPNILTDITK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 198.31 2.51E-21 1319780000 2678720 1979870 2473140 1636570 2936900 2788120 2321250 2503060 2826040 2079560 FALSE TRUE 2784477.934 2319897.271 2537592.06 1960278.661 2437686.787 2140621.384 2139304.36 2469510.575 2724331.372 2487009.966 1.119608675 0.93280578 1.020338517 0.788206999 0.980167679 0.860720871 0.860191309 0.992963683 1.095424389 1 21.24598086 -0.811153227 4.769696336 1.000000102 0.952950548 0.007486953 0.099806576 1.03E-07 2.57E-08 0.093564887 0.022053408 0.154470934 0.811153227 -0.047049554 KIYEDGDDDMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KIYEDGDDDMKR 12 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ;;; 203.82 6.79E-08 2326840000 4644970 2432210 3589100 2034250 5169540 4016350 4014170 3405500 4051820 2559480 FALSE TRUE 4828357.002 2849923.148 3682634.894 2436618.578 4290823.437 3083613.581 3699528.866 3359854.843 3905995.79 3060961.102 1.577399007 0.931055003 1.20309758 0.796030559 1.4017896 1.007400447 1.208616752 1.097647024 1.276068418 1 21.54555328 4.752814893 24.52203166 1.109719916 1.577399427 0.41593699 0.168657101 1752.488803 3014787.812 0.036263297 0.750474083 56599.79955 -4.752814893 0.467679512 KIYPTIWWLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KIYPTIWWLFR 11 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 138.45 9.19E-05 64502000 103694 84420 109761 88691 169097 140849 142672 104824 120887 124795 FALSE TRUE 107787.9192 98918.4783 112621.4618 106233.8151 140353.9523 108138.9543 131488.9958 103419.0057 116536.3005 149246.1909 0.722215546 0.662787289 0.754601917 0.711802522 0.940418992 0.7245676 0.881020782 0.692942347 0.780832662 1 17.18733459 -5 0.196522108 2.026829746 0.722937205 0.450738552 0.08011624 131.2139013 1.294078265 53.11484981 0.199197435 1.00E-05 5 -1.30389254 KKAEPSEVDMNS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKAEPSEVDMNSPK 14 2 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 KKAEPSEVDMNS(1)PK;KKAEPSEVDMNS(1)PK 145.91 7.49E-06 192094000 1024280 209127 410830 221096 575760 573270 529420 387030 468080 186543 TRUE FALSE 1064719.365 245042.9355 421536.5673 264828.1289 477892.5209 440136.7305 487922.677 381842.4959 451233.8922 223092.5293 4.772546032 1.098391489 1.889514493 1.187077531 2.142126957 1.972888702 2.187086581 1.711588 2.02263112 1 17.76728268 4.746123457 24.99090015 1.746621232 4.772547482 0.826406528 0.423106807 343.8783268 1136295.974 0.095188098 1.009530278 55734.41625 -4.746123457 3.02592625 KKANEVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KKANEVDR 8 2 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ;; 119.68 0.00092662 1855650000 2105710 1475150 1969530 1307410 2516520 2113180 2091240 1775570 2359350 1583820 FALSE TRUE 2188845.057 1728495.537 2020857.57 1566011.796 2088762.829 1622425.971 1927323.144 1751771.388 2274437.454 1894139.205 1.155588275 0.91254937 1.066900239 0.826767004 1.102750433 0.856550546 1.017519272 0.924837723 1.200776294 1 20.85311093 1.252870509 24.99548076 1.100388223 0.977170052 0.15214784 0.110237612 322.4109487 563169.6888 0.066088343 0.023882897 17.9007204 -1.252870509 -0.123218171 KKDASDDLDDLNFFNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKDASDDLDDLNFFNQK 17 2 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 180.74 4.74E-10 1532130000 3104120 1337530 2447240 1288140 3233240 2486390 2550430 1928220 2642970 1132220 FALSE TRUE 3226673.055 1567240.373 2511017.085 1542930.247 2683655.02 1908963.604 2350520.632 1902375.365 2547850.026 1354056.831 2.382967228 1.157440616 1.854439952 1.139487067 1.981936768 1.409810549 1.735909881 1.404944993 1.881641868 1 20.36885686 -1.996550232 3.23788185 0.390849666 1.625141084 0.216425897 0.371712401 0.130568904 0.000139113 0.028747246 0.073723384 0.01007975 1.996550232 1.234291417 KKDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KKDELER 7 2 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;; 131.06 0.00197 10560620000 10464840 6323910 8531620 6102180 12138410 10300790 10759090 8670250 9393730 5421860 FALSE TRUE 10877999.96 7409992.349 8753961.026 7309172.991 10075127.4 7908587.632 9915764.412 8554039.48 9055651.492 6484169.659 1.677624204 1.142781997 1.350051199 1.127233459 1.553803792 1.219676234 1.529226552 1.319218949 1.396578432 1 22.62849041 -1.059391261 4.262042173 0.999965745 1.359278287 0.294175949 0.170690386 1.144161807 43451270.06 3312.254931 0.035807054 0.087218525 1.059391261 0.359312542 KKDELS(ph)DYAEK ddPTM_MDA-MB-175_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 172.91 6.68E-06 372280000 1220510 311327 541347 313525 943650 801540 898530 548728 634007 195707 TRUE FALSE 1268696.677 364794.9905 555454.9475 375539.3092 783248.7101 615394.4825 828100.8707 541373.1987 611189.2119 234052.0396 5.420575182 1.55860633 2.37321131 1.604512013 3.346472483 2.629306215 3.538105765 2.313046276 2.611338969 1 17.83646981 0.462875322 1.25775982 1.00051696 2.783860169 0.21420896 1.054372771 3.678893225 7.045251073 0.943762496 0.282557264 2.903189084 -0.462875322 1.783343208 KKDQEDDEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KKDQEDDEQQR 11 2 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;;; 184.31 2.79E-06 218920000 75669.4 47187.5 70161.1 46754.3 76986.3 83206 66834.8 64984.2 73188.9 44387.1 FALSE TRUE 78656.88634 55291.58606 71989.5559 56002.16099 63900.19622 63882.6675 61596.11374 64113.19309 70554.84579 53083.9024 1.481746495 1.041588571 1.35614664 1.054974455 1.203758453 1.203428245 1.16035391 1.20777091 1.329119424 1 15.69598681 4.757212949 24.19545894 1.18381435 1.481746902 0.407240398 0.111056015 2519.735011 3268471.125 0.023690915 0.788245804 57175.89202 -4.757212949 0.297932552 KKDQVTAQEIFQDNHEDGPTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKDQVTAQEIFQDNHEDGPTAK 22 2 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 161.68 1.03E-11 493310000 462460 241000 383330 246990 477600 381160 429820 355640 402120 204070 FALSE TRUE 480718.2779 282389.8753 393319.8947 295843.8848 396417.7226 292641.3665 396129.5853 350873.2275 387647.7797 244053.6093 1.969724108 1.157081332 1.611612693 1.212208603 1.624305921 1.199086411 1.623125289 1.437689155 1.588371427 1 17.89683856 -1.889520091 2.39731708 0.741843037 1.475078354 0.274510212 0.238354833 17431348.21 9206828.131 25445456.21 0.051612055 0.012896739 1.889520091 0.733235318 KKEEEDDDMKELENWAGS(ph)M ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKEEEDDDMKELENWAGSM 19 3 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 1 KKEEEDDDMKELENWAGS(1)M 65.833 0.028624 252990000 454880 101500 161580 113370 393980 401340 392460 195050 310110 81165 TRUE FALSE 472839.0136 118931.8354 165790.9075 135794.2476 327011.4203 308134.8674 361697.9597 192435.6738 298949.2017 97067.72775 4.871227797 1.2252459 1.707992052 1.398963907 3.368899509 3.174431652 3.726243192 1.982488704 3.079800142 1 16.5667041 3.225809677 24.99476733 2.805254745 2.181680299 0.02237057 1.195781363 711.3641181 1394434.211 0.334105659 0.401780524 1681.936816 -3.225809677 -0.623574446 KKEEEDDDMKELENWAGSM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKEEEDDDMKELENWAGSM 19 3 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 73.138 0.021602 81055000 343240 70076 131550 67173 241770 223430 218150 141360 187680 50428 FALSE TRUE 356791.3802 82111.00788 134978.3011 80459.61891 200674.0218 171541.7686 201050.833 139465.3004 180925.4335 60308.4011 5.916114069 1.361518568 2.2381343 1.334136164 3.327463804 2.844409162 3.333711876 2.3125352 3.000003817 1 15.88007137 -1.256600286 8.245376713 0.999998704 2.746990242 0.164618396 1.231317097 2.71E-05 2.45E-06 1.102373077 0.259831637 0.055385963 1.256600286 1.746991538 KKEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KKEEER 6 2 Q13442;F8WFC5;Q8NFW9-5;Q8NFW9-2;Q8NFW9 Q13442;Q8NFW9-5 PDAP1;MYRIP 28 kDa heat- and acid-stable phosphoprotein;Rab effector MyRIP 0 ;;; 76.134 0.042664 307906000 529512 299121 414025 286684 578844 476750 514654 363112 465803 284513 FALSE TRUE 550417.5426 350492.7049 424814.8316 343389.2395 480452.3036 366032.0377 474314.0747 358245.0776 449038.841 340257.875 1.61764821 1.030079627 1.248508448 1.009202916 1.412024053 1.075748909 1.393984121 1.052863442 1.319701538 1 18.37626903 -4.999999996 0.030640567 1.47E-07 1.91618851 0.132484376 0.189400091 3235.399518 7.46102027 367.1334831 146.0350352 1.00E-05 4.999999996 1.916188363 KKEEPSQNDIS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 199.49 6.13E-08 4069270000 11116830 2230050 4130840 2120000 6222290 6882060 6172620 4198410 4606720 1641436 TRUE FALSE 11555731.03 2613043.74 4238493.084 2539329.672 5164627.368 5283805.864 5688793.915 4142137.181 4440925.047 1963043.957 5.886638957 1.331118303 2.159143237 1.293567402 2.630928029 2.691639097 2.897945252 2.110058293 2.262264699 1 20.90466105 4.746157097 24.81464089 2.133156882 5.886640959 0.777095611 0.616009706 381.731778 1246931.05 0.144729455 1.526897879 55738.73361 -4.746157097 3.753484077 KKEIQNGNLHES(ph)DSESVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKEIQNGNLHESDSESVPR 19 2 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 KKEIQNGNLHES(1)DSESVPR 216.65 1.97E-19 203450000 212320 189410 204620 208360 319710 362420 240900 234360 280410 266200 TRUE FALSE 220702.5575 221939.6941 209952.5653 249572.9861 265365.8084 278253.4475 222017.6285 231218.7875 270318.0989 318356.7933 0.693255373 0.69714138 0.659488253 0.783941136 0.83354844 0.874030187 0.697386182 0.726288216 0.849104227 1 18.28028502 -5 0.14697492 1.862951721 0.672912539 0.615333759 0.063098479 105.2944566 0.928447686 26.60048467 0.381204674 1.00E-05 5 -1.190039182 KKEPAITSQNS(ph)PEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KKEPAITSQNSPEAR 15 2 A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193;E5RIS7 A0A1W2PRL9 TCEA1 Transcription elongation factor A protein 1 1 KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.004)QNS(0.996)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.018)QNS(0.982)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITSQNS(1)PEAR;KKEPAITS(0.001)QNS(0.999)PEAR;KKEPAITS(0.004)QNS(0.996)PEAR;KKEPAITSQNS(1)PEAR 296.01 2.39E-44 40091070000 14647450 10214660 13408470 10018432 16543650 15387250 15209930 13345890 15271640 9767382 TRUE FALSE 15225742.64 11968948.4 13757905.74 12000047.95 13731566.28 11813794.38 14017735.94 13167010.17 14722016.66 11681113.5 1.303449593 1.02464105 1.177790606 1.027303429 1.17553573 1.011358582 1.200034222 1.127205055 1.26032648 1 23.47767447 KKEPEPNFQLLDNPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKEPEPNFQLLDNPAR 16 2 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 176.83 1.71E-09 891810000 517120 347700 558590 347340 665070 572900 552390 501920 612490 411910 FALSE TRUE 537536.2969 407414.7703 573147.3143 416042.8153 552021.639 439852.6574 509092.2284 495192.5834 590446.6045 492615.878 1.091187517 0.827043521 1.163477143 0.844558273 1.120592461 0.892891758 1.033446649 1.005230658 1.198594343 1 18.9101036 1.399839251 11.56480766 1.100616343 0.994284451 0.109357426 0.116574753 1.034725689 149.4261986 0.067916302 0.025021054 25.10956861 -1.399839251 -0.106331892 KKEPPR ddPTM_MDA-MB-175_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 ; 71.949 0.048867 945320000 721840 723120 725670 684140 1167460 1159690 1287620 1058980 1126850 914810 FALSE TRUE 750338.8006 847310.2349 744581.5563 819460.85 969015.5662 890369.5728 1186692.98 1044786.105 1086294.889 1094049.504 0.685836242 0.774471568 0.680573917 0.749016244 0.885714552 0.813829328 1.084679418 0.954971508 0.992912006 1 20.06124659 2.811249158 1.097368609 1.003554782 0.714260783 0.806155868 0.059342757 0.195165524 0.495578429 0.027777557 0.02780071 647.5139934 -2.811249158 -0.289293999 KKEPPRAS(ph)PPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 47 3 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 KKEPPRAS(0.996)PPGGLAEPPGS(0.004)AGPQAGPTVVPGSATPMETGIAETPEGR;KKEPPRAS(0.997)PPGGLAEPPGS(0.003)AGPQAGPTVVPGSATPMETGIAETPEGR 94.987 9.43E-06 1383050000 217321 190154 256039 183354 270840 281002 269982 244431 258424 160324 TRUE FALSE 225901.0009 222811.4703 262711.5867 219620.8739 224802.7135 215743.5441 248820.1054 241154.8023 249123.3707 191736.4182 1.178185151 1.162071725 1.370170514 1.145431191 1.172457041 1.125209004 1.297719587 1.25774125 1.299301265 1 17.54876486 2.228093849 24.99966335 1.239821346 1.1959411 0 0.102298368 810.4198905 1935655.401 0.036496959 0.027237535 169.0806266 -2.228093849 -0.043880247 KKEPPRS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKEPPRSK 8 3 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 KKEPPRS(1)K 56.783 0.082368 217990000 430590 171530 193770 144070 304040 318240 302750 193520 247030 127400 TRUE FALSE 447590.0257 200988.9432 198819.8054 172566.616 252359.3894 244333.583 279019.6639 190926.1809 238139.4386 152361.5908 2.937682807 1.319157552 1.304920777 1.132612328 1.656318946 1.603642898 1.83129923 1.253112283 1.56298866 1 17.21713973 4.741090537 24.92116199 1.428511233 2.937683365 0.780416744 0.243323971 100.3291355 988239.1901 0.057342828 0.391624899 55092.25347 -4.741090537 1.509172132 KKEQSEVSVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKEQSEVSVSPR 12 2 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 KKEQSEVS(0.008)VS(0.992)PR;KKEQSEVSVS(1)PR 146.3 3.37E-05 598560000 1517480 1396120 1550930 1286130 1965210 1887480 1709930 1651430 1755270 1326000 TRUE FALSE 1577391.282 1635892.75 1591348.51 1540522.675 1631164.306 1449141.375 1575901.219 1629295.282 1692098.176 1585804.312 0.994694787 1.03158551 1.003496142 0.971445634 1.028603778 0.913821058 0.99375516 1.027425181 1.067028361 1 20.59678332 1.674130996 4.303250279 1.03703214 0.990783635 0.223685112 0.034442303 0.237723568 10.26037527 0.019072254 0.009010668 47.22054503 -1.674130996 -0.046248505 KKFS(ph)FK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKFSFK 6 2 P49006 P49006 MARCKSL1 MARCKS-related protein 1 KKFS(1)FK;KKFS(1)FK 78.905 0.053989 2242130000 6025500 2004820 4023700 2333200 5939700 4671400 6339700 3811600 5104400 1530920 TRUE FALSE 6263391.393 2349132.24 4128560.928 2794699.996 4930071.916 3586538.146 5842777.748 3760511.737 4920693.641 1830874.463 3.420983536 1.283065708 2.25496669 1.526429066 2.692741647 1.958920843 3.191249792 2.053942973 2.687619354 1 20.80410144 3.206994547 24.99894212 2.347003198 2.071024286 0 0.759796378 832.9155676 659630.6296 0.201730394 0.241135472 1610.625413 -3.206994547 -0.275978912 KKGDGGGAGGGGGGGGSGGGGS(ph)GGGGGGGSSRPPAPQENTTSEAGLPQGEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKGDGGGAGGGGGGGGSGGGGSGGGGGGGSSRPPAPQENTTSEAGLPQGEAR 52 3 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 KKGDGGGAGGGGGGGGS(0.211)GGGGS(0.768)GGGGGGGS(0.01)S(0.01)RPPAPQENTTSEAGLPQGEAR 71.279 2.53E-05 159640000 50779 37617 43114 33478 48330 57695 47043 48363 43702 40072 TRUE FALSE 52783.79413 44077.42713 44237.58626 40099.84848 40114.88386 44296.21063 43355.64674 47714.77309 42129.17356 47923.34118 1.101421413 0.919748625 0.92309061 0.836749849 0.837063587 0.924313905 0.904687479 0.995647881 0.879095082 1 15.54844087 -0.711182196 7.99043309 1.000002144 0.923682577 0.086040569 0.073617478 0 0 0.071387404 0.016826173 0.194454413 0.711182196 -0.076319567 GQYISPFHDIPIYADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GQYISPFHDIPIYADK 16 0 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 157.42 6.87E-08 238220000 180520 503800 532420 646400 565240 744270 675780 665070 548130 475110 FALSE TRUE 187647.069 590323.731 546295.3026 774255.9907 469160.7067 571424.572 622810.5978 656155.8245 528402.9084 568198.708 0.330249024 1.038938883 0.961451152 1.362650037 0.825698299 1.005677352 1.096114069 1.154799923 0.929961475 1 19.11603603 4.739711313 5.917672455 1.054538682 0.30931102 0.706588491 0.137347676 0.069154304 11.26595891 0.031546544 0.207115344 54917.5701 -4.739711313 -0.745227661 down KKGEQPTGQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKGEQPTGQQR 11 2 Q92733;H0YE12;H0Y679 Q92733 PRCC Proline-rich protein PRCC 0 ; 151.26 1.88E-05 418960000 343397 263356 356622 282994 420920 403856 415460 335303 371263 310463 FALSE TRUE 356954.5787 308585.3444 365915.8623 338969.3685 349372.1687 310066.5645 382895.1596 330808.8117 357901.3172 371292.2807 0.961384325 0.831111662 0.985519714 0.912944831 0.940962651 0.835101026 1.031249987 0.890966037 0.963934172 1 18.5021958 0.389941086 0.446010727 1.007228623 0.915641067 0.137237154 0.059335417 4.706647275 1.623030294 0.12044629 0.033449901 2.454375943 -0.389941086 -0.091587555 KKGFNGCDS(ph)PEPDGEDSLEQSPLLEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKGFNGCDSPEPDGEDSLEQSPLLEDK 27 2 Q14814-4;Q14814;Q05BX2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 KKGFNGCDS(0.968)PEPDGEDS(0.032)LEQS(0.001)PLLEDK 62.237 0.020643 114410000 76854 27542 47921 27152 74356 59421 59775 49749 49900 21379 TRUE FALSE 79888.25526 32272.12425 49169.86063 32522.58456 61716.99368 45621.37328 55089.67931 49082.19603 48104.10875 25567.80572 3.124564389 1.262217204 1.92311617 1.272013129 2.413855704 1.784328846 2.154650262 1.91968746 1.881432817 1 14.64204073 0.562969956 2.488964153 1.000021833 1.947045032 0.245804631 0.509892634 7.331582403 40.04608198 0.443695601 0.118440012 3.655695012 -0.562969956 0.947023199 KKGWEVVESDLYAMNFNPIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKGWEVVESDLYAMNFNPIISR 22 2 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 232.73 7.13E-28 3444600000 2324100 2345200 2838500 1731190 3760200 3272500 2625700 2613800 3229600 2906800 FALSE TRUE 2415857.263 2747969.857 2912473.642 2073614.215 3121042.547 2512511.47 2419890.773 2578766.286 3113367.327 3476331.806 0.694944383 0.790479738 0.837800821 0.596494906 0.897797656 0.722747888 0.696104661 0.741806718 0.895589806 1 21.72913436 1.065007529 3.286834057 0.997911069 0.747783638 0.529336746 0.078590033 0.156487065 3.451008222 0.070260227 0.018428534 11.6146875 -1.065007529 -0.250127431 KKIYPTIWWLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKIYPTIWWLFR 12 2 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 131.69 0.00010924 72572000 92481 92485 134050 68987 226630 161520 148330 123420 169660 153840 FALSE TRUE 96132.22129 108368.5793 137543.4531 82632.42269 188107.5136 124009.4279 136703.507 121765.7568 163553.9697 183982.0026 0.522508832 0.589017283 0.747591891 0.449133184 1.022423449 0.67403021 0.74302652 0.661835153 0.888967222 1 17.48920512 0.614805154 0.060594012 1.661437318 5.53E-12 0.414708499 0.139765494 56.88365022 1.661399524 25.17701597 19.44775508 4.119126734 -0.614805154 -1.661437318 KKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE 33 3 P09429 P09429 HMGB1 High mobility group protein B1 0 ; 300.51 9.00E-90 1153570000 1531360 189423 419320 149770 860150 1184430 728500 424600 522630 124512 FALSE TRUE 1591819.275 221954.9267 430247.8237 179394.059 713942.0102 909364.0827 671398.2664 418908.9315 503820.6484 148907.7425 10.68996984 1.490553299 2.889358314 1.204732917 4.794525781 6.106895905 4.508820396 2.813211218 3.383441586 1 17.18405924 4.747288287 24.96069608 3.30489381 10.68997367 0.672041073 1.579724572 702.7663903 2009831.98 0.39085503 4.668618949 55884.10329 -4.747288287 7.385079865 KKLEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 127.56 0.0021612 681280000 1928000 1198940 1534390 1162180 2379490 2008180 2109300 1657120 1953910 1244900 FALSE TRUE 2004118.929 1404848.619 1574377.464 1392055.735 1975025.14 1541810.629 1943967.554 1634909.017 1883589.161 1488814.32 1.346117445 0.943602301 1.057470662 0.935009636 1.326575862 1.035596319 1.305715245 1.098128219 1.265160561 1 20.50573241 3.246912019 24.99716074 1.174228112 1.060548125 0.101117895 0.146672572 379.3139891 1135342.903 0.037702879 0.050222011 1765.680087 -3.246912019 -0.113679988 KKNDIYGED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KKNDIYGED 9 2 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;; 144.77 0.00039238 8135600000 7064920 4502090 6432720 4497720 8314180 7305570 7556680 6345550 6882550 4241760 FALSE TRUE 7343848.497 5275288.936 6600361.968 5387355.592 6900938.653 5608962.084 6964367.676 6260498.281 6634848.37 5072851.659 1.447676572 1.039906012 1.30111472 1.061997463 1.360366736 1.10568226 1.372870359 1.234118146 1.307912948 1 22.27436554 -1.22842116 4.53507598 0.999923356 1.241905659 0.241060632 0.131596884 8.97E-05 1.53E-05 0.112081316 0.026409469 0.059098824 1.22842116 0.241982303 KKNEGVNWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKNEGVNWLR 10 2 F8VUA2;F8VVT7;Q9HD42 F8VUA2 CHMP1A Charged multivesicular body protein 1a 0 137.89 4.45E-05 649730000 613520 611660 642800 475470 812830 774160 719820 663320 678810 790270 FALSE TRUE 637742.2433 716707.8469 659551.8961 569516.5469 674665.4469 594373.0725 663398.6275 654429.2804 654379.7607 945108.2759 0.674782202 0.758334114 0.697858555 0.602593969 0.713849899 0.628894157 0.701928704 0.692438419 0.692386023 1 19.85012009 -0.41236118 0.964259871 1.009319946 0.68337761 0.84271771 0.040877272 8.414513017 5.048320455 0.347976541 0.012422085 0.386935717 0.41236118 -0.325942336 KKNLQYYDISAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKNLQYYDISAK 12 2 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 134.98 7.64E-05 579430000 843350 667570 810560 432820 1300200 990540 650140 798270 1003600 886870 FALSE TRUE 876646.1092 782219.9545 831683.8595 518430.5042 1079192.468 760502.0968 599180.328 787570.4964 967480.632 1060635.196 0.82652934 0.737501412 0.784137527 0.488792476 1.017496376 0.717025137 0.564925933 0.74254607 0.912170966 1 20.0164971 1.132657802 3.554027174 0.993596716 0.728823875 0.311116578 0.134520195 0.251602684 5.615312245 0.122644016 0.032313932 13.57243599 -1.132657802 -0.264772842 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(ph)TGSPTEFLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCS(0.001)ET(0.001)S(0.001)QIEDT(0.001)PS(0.002)S(0.002)KPT(0.002)LLANGGHGVEGS(0.049)DT(0.264)T(0.24)GS(0.219)PT(0.219)EFLEEK 47.663 0.018002 135500000 57443 25688 39686 20720 59130 48753 54325 41208 44744 20340 TRUE FALSE 59710.894 30099.71418 40720.24976 24818.35416 49079.10372 37430.85461 50066.86455 40655.67416 43133.67218 24325.23357 2.454689441 1.23738644 1.673992139 1.020271978 2.017621068 1.538766504 2.058227495 1.671337463 1.773206907 1 14.57016604 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDTTGSPTEFLEEK 44 3 P27816-6;P27816;P27816-2;P27816-5;H7C456 P27816-6 MAP4 Microtubule-associated protein 4 1 KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.001)DTT(0.01)GS(0.986)PT(0.003)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGS(0.011)DT(0.047)T(0.039)GS(0.898)PT(0.005)EFLEEK;KKPCSETSQIEDTPSSKPTLLANGGHGVEGSDT(0.009)T(0.008)GS(0.977)PT(0.006)EFLEEK 153.38 2.29E-14 2794640000 1539260 658497 1188760 645469 1615110 1244690 1534740 1147490 1417310 441251 TRUE FALSE 1600031.173 771588.7374 1219740.062 773140.8417 1340574.179 955629.611 1414443.069 1132109.773 1366301.29 527705.6852 3.03205218 1.462157333 2.311402163 1.465098564 2.540382294 1.810913996 2.680363521 2.145343143 2.589135058 1 19.009374 KKPLKQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKPLKQPK 8 3 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 71.379 0.021419 2031100000 3170700 1484600 2509500 1525000 3780000 3352200 3435300 2649600 2833300 1360000 FALSE TRUE 3295881.684 1739568.501 2574899.632 1826640.448 3137476.95 2573702.353 3166032.21 2614086.446 2731330.086 1626465.961 2.0264068 1.06953883 1.583125435 1.123073272 1.929014824 1.582389312 1.946571453 1.607218662 1.679303565 1 20.6333092 3.230942224 24.9991255 1.670626607 1.432792652 0.04585603 0.347475064 391.9106352 1286021.075 0.091315971 0.111115583 1701.932077 -3.230942224 -0.237833955 KKPNATRPVT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 103.61 0.0016426 2407700000 1268100 931970 1300800 1080000 1656600 1588600 1655700 1386200 1491600 934660 TRUE FALSE 1318165.567 1092028.598 1334699.917 1293620.777 1375011.724 1219671.725 1525921.908 1367620.256 1437917.607 1117788.732 1.179261814 0.97695438 1.19405383 1.157303469 1.230117718 1.091146914 1.365125506 1.223505138 1.286394796 1 20.09221611 4.097228984 9.260017203 1.208574361 1.078416432 0.149742942 0.105662117 0.409139863 35.34842321 0.024671821 0.053494364 12509.1841 -4.097228984 -0.130157929 KKPRPPPALGPEETSASAGLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKPRPPPALGPEETSASAGLPK 22 3 Q01105 Q01105 SET Protein SET 0 44.729 0.077335 376850000 213990 101760 184350 123040 251950 196670 233190 178720 220790 110790 FALSE TRUE 222438.4904 119236.4884 189154.3124 147376.9448 209123.629 150996.3731 214911.9585 176324.5507 212843.811 132497.1793 1.678816799 0.899917184 1.427610108 1.112302507 1.578325139 1.139619529 1.622011575 1.330779656 1.606402583 1 17.01560212 3.24666807 24.99966685 1.396863709 1.263104846 0.028767565 0.266475883 564.7053928 1741281.769 0.067163721 0.089383666 1764.688559 -3.24666807 -0.133758863 KKPS(ph)SEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 60.434 0.072707 134468000 217266 113590 155414 118718 196483 186744 258030 161107 178839 82269 TRUE FALSE 225843.8294 133098.1989 159464.2165 142200.0661 163084.8898 143375.5361 237804.9344 158947.6242 172402.6193 98388.03541 2.295439974 1.35278846 1.620768377 1.445298358 1.657568313 1.457245645 2.4170107 1.615517817 1.752272201 1 16.58619527 KKPSVLPAPPEGATPTS(ph)PVGHFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKPSVLPAPPEGATPTSPVGHFAK 24 2 P98177-2;P98177 P98177-2 FOXO4 Forkhead box protein O4 1 KKPSVLPAPPEGATPT(0.171)S(0.829)PVGHFAK 109.41 0.0011235 445400000 447590 169100 240920 150190 357250 343930 302260 190170 248020 184630 TRUE FALSE 465261.1988 198141.6096 247198.5731 179897.1337 296524.7726 264057.4698 278568.0714 187621.0822 239093.8086 220804.7135 2.107116245 0.897361322 1.119534856 0.814734119 1.342927729 1.195886925 1.261603826 0.849715023 1.082829278 1 17.75241144 4.74417312 24.97591771 1.064222234 2.107116696 0.779548732 0.166614028 276.2577996 1229323.918 0.039876315 0.352906341 55484.68442 -4.74417312 1.042894462 KKQDPPVTHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKQDPPVTHDLR 12 2 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 121.28 0.00022766 2068300000 1341500 959570 1262000 924690 1428000 1427300 1367800 1211000 1560900 1032600 FALSE TRUE 1394463.456 1124368.683 1294888.757 1107590.922 1185269.07 1095831.206 1260588.262 1194768.526 1504723.514 1234918.2 1.129194999 0.910480292 1.048562372 0.896894161 0.959795613 0.887371492 1.020786852 0.967487989 1.218480313 1 20.23598405 1.273235968 24.99832058 1.109240264 0.97335111 0.273049087 0.085714683 176.2607461 127070.7588 0.05197617 0.018978562 18.76013539 -1.273235968 -0.135889154 KKQPAS(ph)PDGRT(ph)SPINEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKQPASPDGRTSPINEDIR 19 3 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 KKQPAS(1)PDGRT(0.537)S(0.463)PINEDIR 73.574 0.032283 336890000 392120 265020 372170 200610 510700 440220 323070 349010 408160 306380 TRUE FALSE 407601.2004 310535.1234 381869.0559 240290.0592 423891.3964 337985.5766 297746.9292 344332.0918 393470.4013 366409.295 1.112420471 0.847508859 1.0421926 0.655796844 1.156879485 0.922426317 0.812607467 0.939747153 1.073854858 1 18.48309658 1.291559352 8.474643315 1.036588329 0.928597361 0.074555464 0.140042499 0.58268281 84.54997139 0.088151411 0.03191287 19.56858178 -1.291559352 -0.107990968 KKQPAS(ph)PDGRTS(ph)PINEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKQPASPDGRTSPINEDIR 19 3 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 2 KKQPAS(1)PDGRT(0.328)S(0.672)PINEDIR 82.479 0.0063148 358420000 278730 161260 263490 154630 323410 292400 247560 237470 273050 207540 TRUE FALSE 289734.4756 188955.1506 270356.7659 185215.3525 268436.8837 224494.5314 228155.6003 234287.1031 263222.9838 248203.4894 1.167326359 0.761291274 1.089254492 0.746223806 1.081519379 0.904477741 0.919228013 0.943931544 1.060512825 1 17.92116387 1.25176905 23.85818646 1.030256378 0.944289473 0.05375547 0.1289786 304.5489607 550113.8 0.076885397 0.027656783 17.85537806 -1.25176905 -0.085966905 KKQQEEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 128.85 0.00017929 222850000 389940 322180 347330 279230 574150 509690 461580 444100 522400 376610 FALSE TRUE 405335.1323 377511.9088 356381.7051 334460.8606 476556.1881 391322.2219 425400.1535 438147.5659 503598.926 450399.5189 0.899945749 0.838171208 0.791256851 0.742587073 1.058074372 0.86883357 0.944495133 0.972797589 1.118116039 1 18.78084576 2.346471534 0.718277572 1.041587379 0.82898251 0.470938837 0.081565864 0.629771911 0.639488296 0.066724132 0.046294585 222.0606131 -2.346471534 -0.212604869 KKS(ph)EPDDELLFDFLNSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKSEPDDELLFDFLNSSQK 19 2 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQK;KKS(1)EPDDELLFDFLNSSQK 198.55 5.79E-16 698830000 2367520 619050 917500 879360 1474630 1680410 2014740 1069990 1176400 375300 TRUE FALSE 2460991.518 725367.022 941410.8037 1053294.783 1223972.919 1290160.244 1856819.414 1055648.534 1134061.594 448832.8494 5.483091357 1.61611839 2.097464134 2.346741743 2.727012786 2.874478207 4.136995357 2.351985902 2.526690271 1 18.77581874 0.746344329 1.691963822 1.006008827 2.893982166 0.237282348 1.053193 1.337894253 6.215406031 0.957987601 0.272598727 5.576276868 -0.746344329 1.887973339 KKS(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKSEPDDELLFDFLNSSQKEPTGR 24 3 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 KKS(1)EPDDELLFDFLNSSQKEPTGR;KKS(1)EPDDELLFDFLNSSQKEPTGR 235.34 1.58E-37 2366200000 3296600 890640 1617550 895440 2448900 2365100 2060000 1491600 1686310 757920 TRUE FALSE 3426752.314 1043600.492 1659704.682 1072555.359 2032636.853 1815841.368 1898531.817 1471607.542 1625620.033 906419.9127 3.78053512 1.151343298 1.831054965 1.183287508 2.242489186 2.003311427 2.094538955 1.623538408 1.793451368 1 19.78982003 7.999999987 0.054283611 4.75E-09 5.467140839 0.218914872 0.665497093 788.9509644 3.217273526 71.47449101 351.2645203 99999996.9 -7.999999987 5.467140834 KKS(ph)PIINESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(0.994)PIINES(0.006)R;KKS(1)PIINESR;KKS(1)PIINESR;KKS(0.984)PIINES(0.016)R;KKS(1)PIINESR 151.07 1.61E-05 15037210000 17388450 9260460 12499870 8596680 17604690 15547790 15978040 12567140 14420830 8231380 TRUE FALSE 18074959.43 10850871.97 12825626.88 10297077.65 14612251.08 11937051.4 14725639.47 12398698.04 13901827.15 9844161.312 1.836109635 1.102264746 1.302866387 1.046008626 1.484357135 1.212602173 1.495875475 1.259497651 1.4121901 1 23.23083687 -2.047257206 2.614249874 0.557083547 1.33322145 0.18811538 0.21567771 24777472.91 6301084.077 65803018.37 0.048519168 0.008968975 2.047257206 0.776137903 KKS(ph)PNELVDDLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK;KKS(1)PNELVDDLFK 226.79 5.31E-12 21085814000 8328470 2284754 4195445 2151194 6770390 6232320 6301960 4235192 5213590 1752106 TRUE FALSE 8657284.427 2677142.727 4304781.743 2576693.753 5619561.526 4784958.132 5807995.908 4178426.179 5025953.914 2095397.625 4.131571175 1.277629933 2.054398503 1.229692027 2.681859262 2.28355615 2.771787006 1.994097029 2.398568107 1 20.99879261 4.752183009 24.51261178 2.043152749 4.131572997 0.546296528 0.588337697 1363.891567 2454178.147 0.134786672 2.655298027 56517.50853 -4.752183009 2.088420248 ASS(ph)HSSQTQGGGSVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(0.125)S(0.803)HS(0.043)S(0.029)QTQGGGSVTK;AS(0.131)S(0.864)HS(0.005)SQTQGGGSVTK;AS(0.22)S(0.613)HS(0.145)S(0.023)QTQGGGSVTK;AS(0.015)S(0.328)HS(0.328)S(0.328)QT(0.001)QGGGSVTK;AS(0.094)S(0.599)HS(0.154)S(0.154)QT(0.001)QGGGSVTK;AS(0.134)S(0.85)HS(0.005)S(0.011)QTQGGGSVTK;AS(0.041)S(0.735)HS(0.109)S(0.109)QT(0.006)QGGGSVTK;AS(0.028)S(0.661)HS(0.201)S(0.108)QT(0.001)QGGGSVTK;AS(0.025)S(0.975)HSSQTQGGGSVTK;ASS(0.786)HS(0.186)S(0.028)QTQGGGSVTK;AS(0.478)S(0.492)HS(0.016)S(0.015)QTQGGGSVTK 276.14 2.30E-35 60616517000 1797829.8 6699273 7275014 7308230 7947969 10398167 7655524 9321408 8048744 8340064 TRUE FALSE 1868809.509 7849821.025 7464606.841 8753776.081 6596976.068 7983350.3 7055464.025 9196469.773 7759071.276 9974139.861 0.187365481 0.78701734 0.748396047 0.877647216 0.661408017 0.800404888 0.707375686 0.922031363 0.777918837 1 23.249761 4.739776331 5.589586715 0.804245971 0.165641631 0.792347306 0.095500543 0.05906923 7.436209511 0.021342214 0.144049614 54925.79237 -4.739776331 -0.638604341 down KKSEAPSGESR ddPTM_MDA-MB-175_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 ;; 105.17 0.001407 120734000 250314 187872 265984 188720 333464 309507 267262 235418 285930 215417 FALSE TRUE 260196.59 220137.5546 272915.7615 226048.2527 276781.9084 237628.6899 246313.3061 232262.6068 275639.4352 257623.8367 1.009986472 0.854492183 1.05935757 0.877435316 1.074364515 0.92238627 0.956096723 0.90155713 1.069929858 1 17.97490656 1.230707441 24.99971611 1.034964931 0.954423285 0.160465507 0.071180652 315.8502467 1005434.228 0.057463124 0.015419765 17.0101225 -1.230707441 -0.080541645 KKSPIINES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKSPIINESR 10 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KKS(0.446)PIINES(0.554)R 109.6 0.0015729 7103900000 10589000 5958900 8294400 5967500 11041000 10188000 9858300 7990800 9351700 4879900 TRUE FALSE 11007061.9 6982294.721 8510558.878 7147853.689 9164254.764 7821991.401 9085580.686 7883696.396 9015134.144 5836022.974 1.886055272 1.196413166 1.458280565 1.224781623 1.570291071 1.340294827 1.556810302 1.350867951 1.544739317 1 22.47655413 -1.182823525 4.195313113 0.99983539 1.441334691 0.338983185 0.190786663 12368524.91 3487187.011 18587.75462 0.0396461 0.065641195 1.182823525 0.441499301 KKSPNELVDDLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKSPNELVDDLFK 13 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 117.79 0.00026928 744680000 1349990 631170 1075430 555720 1482110 1180170 1152410 996350 1223000 650810 FALSE TRUE 1403288.648 739568.5377 1103456.589 665639.7573 1230181.472 906093.4031 1062081.093 982995.5579 1178984.469 778323.759 1.802962625 0.950206812 1.417734685 0.8552222 1.580552382 1.16416002 1.364574935 1.262964861 1.51477384 1 19.57001087 -1.78735714 2.697367064 0.919209881 1.303100215 0.109661467 0.271037224 30663900.1 25098463.82 16391013.25 0.058019172 0.016317096 1.78735714 0.383890333 KKSS(ph)SDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKSSSDPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 43 2 Q68CZ2;E9PCX8;C9JHU5 Q68CZ2 TNS3 Tensin-3 1 KKS(0.303)S(0.349)S(0.349)DPGIPGGPQAIPATNSPDHSDHTLSVSSDSGHSTASAR 78.035 0.0005225 1059100000 13962 126630 131570 125230 152790 214320 105030 185910 149990 122730 TRUE FALSE 14513.23054 148377.7175 134998.8223 150000.1202 126818.8104 164547.4281 96797.47416 183418.1805 144591.8892 146776.5937 0.098879734 1.010908577 0.919757155 1.021962129 0.864026117 1.121074034 0.65948849 1.249641894 0.985115444 1 17.1632624 4.739532635 24.72798956 0.986355263 0.098879406 0.76454428 0.146890795 30.75459012 782260.3762 0.032861787 0.20055143 54894.98051 -4.739532635 -0.887475857 KKT(ph)GGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKTGGSK 7 2 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 KKT(1)GGSK;KKT(1)GGSK 91.065 0.026816 484960000 55740 2627200 1483950 2426400 851160 2369800 809270 1778950 890330 3071500 TRUE FALSE 57940.65824 3078401.163 1522622.956 2906334.678 706480.1272 1819449.865 745837.3028 1755106.085 858287.1972 3673301.618 0.015773455 0.83804748 0.414510736 0.791205019 0.192328374 0.495317307 0.203042761 0.4778007 0.233655519 1 21.80864593 -1.362014088 3.161369348 1.005546429 0.422653301 0.336713228 0.248861413 59006793.12 77818412.51 3019764.735 0.057388448 0.043449613 1.362014088 -0.582893128 KKTATAVAHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKTATAVAHCK 11 2 P62249;M0R210;M0R3H0;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 124.86 0.00020444 787420000 1142970 886050 1290510 657110 1874480 1350890 1004250 1214020 1475680 1276200 FALSE TRUE 1188095.338 1038222.195 1324141.751 787084.3967 1555856.559 1037166.27 925534.2609 1197748.048 1422570.565 1526246.956 0.778442397 0.680245219 0.867580273 0.515699241 1.01940027 0.679553375 0.606411864 0.784766871 0.932071025 1 20.54155699 1.209458873 3.188148407 0.991962371 0.735857908 0.329170064 0.131085127 0.258777104 4.643995213 0.111839071 0.031180291 16.19790594 -1.209458873 -0.256104463 KKTDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKTDELR 7 2 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;A0A494C198;D6RDA2;D6R9L5 H0Y993 DEK Protein DEK 0 ; 95.815 0.007418 799810000 2065820 1591650 1847630 1513600 2669600 2377000 2372100 1902320 2236900 1570740 FALSE TRUE 2147380.169 1865003.506 1895780.756 1812985.562 2215822.346 1824977.774 2186168.604 1876822.512 2156394.406 1878496.429 1.143137743 0.992817169 1.009201149 0.965125903 1.179572296 0.971509844 1.163786404 0.999108906 1.147936388 1 20.84114694 KKTEFLDLDNSPLSPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKTEFLDLDNSPLSPPSPR 19 2 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 KKTEFLDLDNSPLS(0.028)PPS(0.972)PR;KKTEFLDLDNSPLS(0.009)PPS(0.991)PR 173.35 1.02E-14 0 760170 614890 742570 601970 917610 889280 818250 786360 904740 672840 TRUE FALSE 790182.0986 720492.5743 761921.9842 721037.8693 761634.98 682758.1972 754113.4269 775820.1304 872178.5841 804670.1157 0.981995085 0.895388757 0.946874961 0.896066419 0.946518288 0.848494537 0.937170913 0.964146817 1.083895831 1 19.61803793 1.4791683 3.226787707 1.040799601 0.919415165 0.58213201 0.039865706 0.142825147 2.943809918 0.027060743 0.009700036 30.14173866 -1.4791683 -0.121384436 KKVEEEDEEEEEEEEEEEEEEDE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKVEEEDEEEEEEEEEEEEEEDE 23 2 O15347 O15347 HMGB3 High mobility group protein B3 0 ; 131.09 0.00012745 632480000 644250 229593 415550 228436 659840 576440 571610 376140 474350 185670 FALSE TRUE 669685.4875 269023.8118 426379.5744 273619.959 547680.6325 442570.546 526805.7146 371098.4585 457278.2362 222048.4816 3.015942656 1.211554386 1.920209367 1.232253231 2.46649123 1.993125748 2.372480598 1.671249701 2.059362139 1 17.76051518 -1.439128866 2.858006939 0.976193604 1.955235737 0.24274895 0.522541211 28515296.04 32332536.73 5466604.353 0.125392073 0.036380707 1.439128866 0.979042133 KKVEEVLEEEEEEYVVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKVEEVLEEEEEEYVVEK 18 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ; 118.45 5.75E-05 87153000 411620 179975 310169 166376 443190 348510 363880 278134 373360 133282 FALSE TRUE 427871.0754 210884.3062 318252.2589 199284.6762 367856.7221 267573.8342 335358.1348 274406.0687 359922.8465 159396.0561 2.684326614 1.323020854 1.996613133 1.250248476 2.307815709 1.678672866 2.103929941 1.721536125 2.258041105 1 17.28225641 -1.147450165 6.36612744 0.999996679 1.888575576 0.296008902 0.42459526 1.77E-05 2.37E-06 0.363097805 0.085582652 0.071211451 1.147450165 0.888578897 KKVENTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKVENTR 7 2 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 82.426 0.013792 2665500000 3228900 2725400 3040300 2627900 4021300 3813700 4036200 3248300 3440400 2812400 FALSE TRUE 3356379.465 3193466.249 3119532.716 3147690.777 3337760.862 2928025.972 3719832.097 3204761.852 3316580.676 3363435.933 0.997902006 0.949465461 0.927483912 0.935855726 0.992366416 0.870546082 1.10596193 0.952823813 0.986069229 1 21.68150435 2.254402909 24.9997633 1.004971864 0.946637771 0.295014414 0.049295705 326.2557257 514843.3131 0.016335806 0.013625657 179.6399431 -2.254402909 -0.058334093 KKVVDPFSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKVVDPFSKK 10 3 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 53.08 0.063932 275700000 561050 273400 427800 243740 734320 543210 436980 419760 589310 351870 FALSE TRUE 583200.6872 320354.3232 438948.8194 291951.0445 609500.5487 417057.7099 402728.3658 414133.8038 568100.8482 420812.1895 1.385893046 0.761276244 1.043099108 0.693779914 1.448390907 0.991078016 0.957026378 0.984129771 1.350010438 1 18.68281697 3.265418617 24.99999471 1.094493651 0.961180353 0.084305628 0.232333804 636.1811016 592166.5197 0.061750859 0.083589849 1842.547178 -3.265418617 -0.133313298 KKYDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KKYDVDTLDMVFLDHWK 17 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;; 290.16 3.47E-46 5592590000 6114440 3838170 6105730 3556490 8136310 6571390 5923060 5412650 6639500 4377760 FALSE TRUE 6355842.813 4497345.841 6264850.34 4259953.107 6753302.932 5045284.263 5458795.08 5340102.28 6400545.692 5235498.255 1.213990055 0.859010093 1.196610148 0.813667181 1.289906443 0.963668407 1.04265054 1.019979765 1.222528474 1 22.31989541 3.241568383 24.99895019 1.076990636 1.021818128 0.043921372 0.150674814 340.5211468 2830205.852 0.038966326 0.050577486 1744.087957 -3.241568383 -0.055172508 KKYDVDTLDMVFLDHWKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKYDVDTLDMVFLDHWKDR 19 3 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 192.62 4.24E-15 1028900000 2272900 1852400 2572700 975390 5058300 3001800 1490600 2365700 3375000 3277600 FALSE TRUE 2362635.847 2170535.29 2639746.675 1168319.231 4198491.973 2304677.443 1373762.877 2333991.661 3253534.409 3919782.967 0.602746598 0.55373864 0.67344205 0.298057122 1.071103173 0.587960472 0.350469117 0.595439003 0.830029223 1 21.90234235 1.073400021 3.342967526 0.994745735 0.587405689 0.321000552 0.195744349 0.245374791 5.449508289 0.18138845 0.047529408 11.84131736 -1.073400021 -0.407340046 KKYELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KKYELR 6 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 119.89 0.011602 6109300000 10238200 10490700 10716200 8686400 15537400 14109900 10699600 10940600 11047900 15510200 FALSE TRUE 10642412.04 12292396.12 10995472.98 10404543.99 12896358.3 10833089.56 9860937.394 10793959.15 10650288.24 18549126.73 0.573741945 0.662694061 0.592775775 0.560918266 0.695254202 0.58402154 0.531611948 0.581911985 0.574166557 1 24.14484793 -1.275330069 3.553813685 1.001073508 0.594976404 0.875357287 0.045821187 15626875.24 21966785.35 176925.9376 0.011145649 0.053048112 1.275330069 -0.406097104 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 33 1 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ; 297.68 6.66E-90 670110000 628070 683140 876700 682880 1092510 1090900 819880 894420 1003220 881020 FALSE TRUE 652866.6886 800463.9809 899547.5222 817951.6258 906805.5404 837555.0077 755615.6632 882431.7629 967114.3082 1053639.001 0.619630336 0.759713697 0.853753061 0.776311075 0.860641586 0.794916482 0.717148532 0.837508636 0.917880135 1 20.00694922 -5 0.062538674 1.759803809 0.48499542 0.593168235 0.064287263 295.3776963 1.345251787 33.73435424 5.231768919 1.00E-05 5 -1.274808389 KLAEPAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLAEPAER 8 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 0 101.65 0.0084132 159670000 105770 81660 91889 88763 123100 121220 118880 95550 102980 88749 FALSE TRUE 109945.8813 95684.46977 94283.70283 106320.0565 102175.506 93068.49211 109561.875 94269.30854 99273.76992 106137.6673 1.035879947 0.901512839 0.888315197 1.00171842 0.962669602 0.876865814 1.032261945 0.888179577 0.93533024 1 16.69557722 KLALDIEIATYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLALDIEIATYR 12 1 K7EPI4 K7EPI4 GFAP 0 ;; 137.8 0.00032107 539206000 791070 711002 768434 693336 905725 962636 869956 772299 821349 708974 FALSE TRUE 822302.0544 833111.0627 788460.0213 830475.7914 751770.188 739078.3779 801766.5755 761947.5951 791788.8099 847883.8812 0.96982862 0.982576838 0.929915097 0.979468781 0.886642858 0.871674051 0.945608937 0.898646161 0.933841093 1 19.69350717 3.248705953 24.99764823 0.915724642 0.964132857 0.236227051 0.036304496 253.2205672 623919.6772 0.009558525 0.012794376 1772.988639 -3.248705953 0.048408214 KLAPEYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLAPEYEK 8 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 84.17 0.028287 548350000 475430 409430 484220 410010 641990 625800 524340 449010 485140 349870 FALSE TRUE 494200.3435 479746.4176 496839.171 491108.7542 532864.7691 480467.4341 483240.8607 442991.7554 467679.9062 418420.3278 1.181109785 1.146565751 1.187416428 1.173721068 1.273515491 1.148288938 1.154917265 1.058724268 1.117727498 1 18.67459342 1.647497205 1.048187634 1.029433585 1.189445696 0.66695551 0.040709774 0.288553285 0.600765336 0.035835952 0.013763882 44.41168033 -1.647497205 0.160012111 KLAS(ph)YMNK ddPTM_MDA-MB-175_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 51.268 0.06451 544560000 42582 943810 960220 779130 991630 1044300 816840 876070 954690 963920 TRUE FALSE 44263.17024 1105902.026 985244.122 933239.5885 823073.0868 801777.1515 752813.9464 864327.7146 920330.8934 1152781.669 0.038396837 0.959333459 0.854666715 0.809554501 0.713988702 0.695515182 0.653041219 0.749775728 0.798356635 1 20.13668787 4.746942689 24.96968607 0.783247727 0.038396459 0.820422966 0.107040506 438.0346103 1304849.189 0.025890976 0.299305891 55839.6502 -4.746942689 -0.744851268 KLAVNMVPFPR ddPTM_MDA-MB-175_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 ; 169.99 2.60E-05 5471500000 2617400 2875800 2858600 2432000 5053600 3967700 3180400 2729300 2801600 4765600 FALSE TRUE 2720736.973 3369696.279 2933097.464 2913042.341 4194590.877 3046261.806 2931111.938 2692718.198 2700770.963 5699328.077 0.47737855 0.591244482 0.514639169 0.511120311 0.735979895 0.534494903 0.51429079 0.472462396 0.473875328 1 22.44236041 -1.256405395 5.172471442 1.000066033 0.536570234 0.775892377 0.074784329 5.85E-05 8.41E-06 0.074385346 0.017530307 0.055410824 1.256405395 -0.463495799 KLCLNICVGESGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLCLNICVGESGDR 14 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 172.09 4.67E-06 1429210000 966830 922210 956410 918190 1134030 1133170 1027900 972340 987380 921860 FALSE TRUE 1005001.195 1080592.394 981334.8303 1099805.241 941267.9857 870008.4409 947330.5121 959307.3727 951844.3867 1102480.817 0.911581571 0.980146209 0.890115107 0.997573132 0.853772665 0.789137033 0.859271651 0.870135206 0.86336594 1 20.07232212 3.216354088 24.98500738 0.861837705 0.943464962 0.265784328 0.057142799 257.8132728 290070.0967 0.015453288 0.018483572 1645.712954 -3.216354088 0.081627257 KLCQPQSTGSLLGDPAASS(ph)PPGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLCQPQSTGSLLGDPAASSPPGER 24 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 KLCQPQSTGSLLGDPAAS(0.228)S(0.772)PPGER;KLCQPQSTGSLLGDPAAS(0.137)S(0.863)PPGER;KLCQPQSTGSLLGDPAAS(0.075)S(0.925)PPGER;KLCQPQSTGSLLGDPAAS(0.023)S(0.977)PPGER 189.38 8.77E-18 1929750000 813280 820410 882570 742970 937850 1052750 820080 895550 932110 955680 TRUE FALSE 845388.9224 961309.0356 905570.4992 889927.2485 778434.592 808264.7671 755799.9867 883546.6171 898563.5432 1142927.198 0.739669966 0.841093848 0.792325618 0.778638613 0.681088518 0.707188322 0.661284453 0.773055903 0.786194908 1 20.12430208 -1.623046847 4.568378733 1.004737622 0.750181161 0.671091784 0.052255746 0.002758364 0.000227602 0.055349465 0.012835082 0.023820625 1.623046847 -0.254556461 KLDDFVETGDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLDDFVETGDIR 12 1 A0A1W2PPX5;A0A1W2PQR6;A0A1W2PQB7;A0A1W2PS43;Q14108;A0A1W2PRS1;A0A1W2PPU6;A0A1W2PRF6;Q14108-2 A0A1W2PPX5 SCARB2 Lysosome membrane protein 2 0 ;; 105 0.0033305 898525000 2438520 1943510 1956110 2096660 2746810 2966570 2407350 2088060 2036760 1889920 FALSE TRUE 2534794.653 2277292.724 2007087.834 2511373.09 2279908.217 2277629.076 2218655.617 2060072.971 1963457.405 2260213.639 1.12148454 1.007556403 0.888008018 1.111121996 1.008713591 1.007705217 0.981613232 0.911450553 0.868704343 1 21.10802771 1.965241268 2.510108652 0.917603944 1.020801094 0.289786381 0.067620209 0.357141584 4.15898071 0.035842383 0.019297406 92.30840959 -1.965241268 0.10319715 KLDDTDPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDDTDPVPR 10 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 90.685 0.017096 278820000 901540 783770 893260 716790 1121100 1126200 1043400 976700 1007000 797140 FALSE TRUE 937133.4953 918376.4006 916539.0894 858568.9226 930535.8224 864657.1177 961615.5816 963608.9341 970758.2667 953324.3208 0.983016456 0.963340996 0.961413728 0.900605286 0.976095755 0.906991565 1.008697209 1.010788158 1.018287529 1 19.86260758 2.172907067 11.87385292 1.010411846 0.94891398 0.57641897 0.025555124 0.472173821 83.84593811 0.009314419 0.006880012 148.9042408 -2.172907067 -0.061497866 KLDDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDDTK 6 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 87.323 0.084294 332580000 775550 351010 543260 346860 780610 645150 725820 583530 600560 352000 FALSE TRUE 806169.3129 411293.237 557417.8019 415467.8727 647922.191 495323.6898 668928.3318 575708.7348 578945.9629 420967.6606 1.915038585 0.977018606 1.324134498 0.986935367 1.539125809 1.176631215 1.589025463 1.367584232 1.375274201 1 18.68334988 KLDEAVAEAHLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLDEAVAEAHLGK 13 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;;; 133.47 6.93E-05 10458490000 19573460 12278790 16845510 11876250 22608350 19780670 19959430 16672120 18556490 11307210 FALSE TRUE 20346235.31 14387576.67 17284517.83 14225336.8 18765390.74 15186909.17 18394957.72 16448657.5 17888645.55 13522641.31 1.504605117 1.063962013 1.278190956 1.051964367 1.387701582 1.123072691 1.360308042 1.216379043 1.322866232 1 23.68887364 -1.173876587 4.167753636 0.999910738 1.247595873 0.232231685 0.13909086 8897090.383 2505929.883 7195.803411 0.028731874 0.0670075 1.173876587 0.247685134 KLDELYGTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 150.06 3.57E-05 8526260000 12605000 12752750 13205470 10703750 21133970 17184080 14417420 11023760 13220020 14466870 FALSE TRUE 13102655.13 14942935.61 13549615.4 12820919.8 17541625.33 13193337.85 13287344.95 10876004.53 12744234.06 17301376.19 0.757318666 0.863684799 0.783152464 0.741034682 1.013886129 0.762560024 0.767993528 0.628620776 0.736602333 1 24.04438346 2.499126104 24.88544442 0.742859473 0.832077411 0.005603589 0.114090902 1539.286286 1740789.868 0.035901714 0.033580751 315.5920862 -2.499126104 0.089217937 KLDEQYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLDEQYQK 8 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 117.01 0.0034643 354985000 1102420 769990 964070 682180 1384480 1276010 1163830 947670 1146000 870680 FALSE TRUE 1145944.393 902229.7928 989194.4562 817113.1679 1149146.584 979676.0156 1072605.963 934968.0337 1104755.684 1041273.076 1.100522446 0.866467994 0.949985627 0.784725147 1.103597712 0.94084447 1.030090942 0.897908585 1.06096634 1 19.98991704 3.224303626 24.99987697 0.99231707 0.922968322 0.14476037 0.092034395 503.0115199 882037.3482 0.025435838 0.030536254 1676.114279 -3.224303626 -0.069348748 KLDGFPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDGFPLLR 9 1 P09661;H0YKK0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 123.79 0.00087832 454850000 578740 668200 642360 605550 788590 811680 701230 608320 659900 707900 FALSE TRUE 601589.1021 782958.1521 659100.4293 725325.9826 654545.7535 623179.6211 646265.7603 600166.4654 636150.3279 846599.4514 0.710594722 0.924827143 0.77852688 0.856752247 0.773146914 0.73609736 0.763366618 0.708914309 0.751418309 1 19.69132003 3.114111303 7.562029952 0.765362308 0.822353621 0 0.092411543 0.594656432 37.15564486 0.024638055 0.029523066 1300.502833 -3.114111303 0.056991312 KLDLEAWFPGSGAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLDLEAWFPGSGAFR 15 1 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ; 97.579 0.0052263 383880000 818340 652580 790570 693970 987270 889590 953870 821110 866950 693300 FALSE TRUE 850648.6951 764655.5386 811172.9037 831235.1947 819454.198 682996.2044 879103.1769 810104.3635 835748.6388 829138.861 1.025942378 0.922228561 0.978331787 1.002528326 0.988319613 0.823741639 1.060260492 0.977043052 1.007971859 1 19.66125421 KLDNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDNTK 6 1 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 91.9 0.07595 718450000 1467700 1003400 1451400 971650 1825000 1547400 1692300 1420000 1574500 1142300 FALSE TRUE 1525645.929 1175726.145 1489224.676 1163839.47 1514787.152 1188039.801 1559653.104 1400967.223 1517834.053 1366111.814 1.116779691 0.860636832 1.090119169 0.851935733 1.108831017 0.869650484 1.141673096 1.025514316 1.111061362 1 20.38164414 2.221342336 24.9964451 1.069240584 0.982062761 0.147515291 0.101936541 437.1916463 634684.3272 0.034042576 0.025202987 166.4724366 -2.221342336 -0.087177824 KLDPAQS(ph)ASRENLLEEQGSIALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.761)AS(0.239)RENLLEEQGSIALR;KLDPAQS(0.568)AS(0.432)RENLLEEQGSIALR 94.006 0.0034548 1060470000 304536 288060 285140 264302 313679 338191 254928 260126 297078 255331 TRUE FALSE 316559.3164 337532.0642 292570.9826 316580.1467 260359.9556 259651.2656 234946.0772 256639.4365 286386.2208 305358.2208 1.036681821 1.105364261 0.958123812 1.036750037 0.85263778 0.850316932 0.769411338 0.840453667 0.937869693 1 18.22014316 3.238885528 24.998054 0.857165272 1.033874875 0.562113538 0.067696009 5.65329667 434925.5859 0.018832159 0.023989919 1733.347059 -3.238885528 0.176709603 KLDPAQSAS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLDPAQSASR 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.012)AS(0.988)R;KLDPAQS(0.016)AS(0.984)R 86.214 0.0083977 838060000 2179600 1698520 1749870 2007830 1924000 2056990 2210700 1898580 1611830 1174540 TRUE FALSE 2265652.291 1990227.597 1795473.05 2404972.781 1596959.167 1579285.246 2037419.557 1873132.641 1553820.553 1404668.625 1.612944328 1.416866271 1.278218234 1.712128212 1.136893883 1.124311612 1.450462779 1.333505004 1.106183 1 20.42179839 7.999999991 0.041083446 0.095493532 3.381341034 0.441134072 0.165105597 736.8033397 2.302028535 49.58649822 166.4965876 99999997.89 -7.999999991 3.285847502 KLDPAQSAS(ph)RENLLEEQGSIALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 KLDPAQS(0.078)AS(0.922)RENLLEEQGSIALR;KLDPAQS(0.22)AS(0.78)RENLLEEQGSIALR;KLDPAQS(0.032)AS(0.968)RENLLEEQGSIALR 181.9 2.14E-17 1886763000 347778.2 378704.8 357224.4 281160.9 409064.7 410458.7 314913.5 313148.8 326966.2 318124.2 TRUE FALSE 361508.7519 443744.4035 366533.9613 336773.6868 339532.0284 315135.8875 290229.757 308951.5525 315198.7503 380454.5461 0.950202214 1.166353269 0.963410649 0.885187706 0.892437827 0.828314159 0.762850017 0.812059037 0.82847939 1 18.53736458 3.759110456 1.85582876 0.835322938 1.059972481 0.497731203 0.078842835 0.240922151 1.606227948 0.021681651 0.047822173 5742.624984 -3.759110456 0.224649543 KLDPDSIPS(ph)PIQVIENDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLDPDSIPSPIQVIENDR 18 1 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 KLDPDS(0.001)IPS(0.999)PIQVIENDR;KLDPDS(0.021)IPS(0.979)PIQVIENDR 114.2 0.00013776 122994000 128122 115020 116336 105874 153466 137830 127916 114109 126209 112751 TRUE FALSE 133180.3555 134773.7903 119367.8117 126815.5612 127379.9041 105821.0713 117889.6097 112579.5555 121666.7627 134842.3997 0.987674172 0.999491188 0.88523945 0.940472444 0.944657648 0.784775943 0.874277007 0.8348973 0.90228862 1 17.04091468 2.951051404 23.03760922 0.865840344 0.950530814 0.257856651 0.059218457 179.0151606 84252.93627 0.017292564 0.018342169 893.4112235 -2.951051404 0.08469047 KLDPDSIPSPIQVIENDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDPDSIPSPIQVIENDR 18 1 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 0 110.41 0.00053592 40519000 36633 36920 43456 30152 46960 46972 42368 38366 36408 33807 FALSE TRUE 38079.29913 43260.7228 44588.49906 36115.97561 38977.75597 36063.46487 39047.08545 37851.76652 35097.68319 40430.83438 0.941838073 1.069993322 1.102834006 0.893278018 0.964060143 0.891979239 0.965774911 0.936210373 0.868091983 1 15.30316836 3.730953081 24.99665682 0.930900448 1.041398954 0.456715534 0.053383731 460.7334223 1513867.117 0.013508957 0.021388608 5382.116331 -3.730953081 0.110498506 KLDPELHLDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLDPELHLDIK 11 1 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 129.34 0.00016032 2185018000 7684896 4230603 6260038 4416721 8383214 7516173 7944941 6598649 6958035 3903880 FALSE TRUE 7988301.628 4957176.156 6423179.733 5290335.231 6958238.279 5770655.729 7322195.764 6510204.903 6707616.68 4668770.542 1.711007546 1.061773354 1.375775416 1.133132413 1.490379152 1.236011853 1.568334896 1.394415263 1.436698724 1 22.15461125 KLDPGSEETQTLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 149 1.22E-05 4183800000 2010040 1661640 1977610 1674080 2315880 2216920 1915160 1851560 2016970 1613500 FALSE TRUE 2089397.931 1947013.744 2029148.141 2005208.027 1922227.545 1702073.928 1765044.755 1826742.867 1944379.644 1929634.433 1.082794697 1.009006531 1.051571275 1.039164721 0.996161507 0.882070665 0.914704218 0.946678208 1.007641453 1 20.87989613 3.025172669 4.176182636 0.943323925 1.042387612 0.570609454 0.038620172 0.146123356 5.859014381 0.011671999 0.013654455 1059.674953 -3.025172669 0.099063686 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLDTNSDGQLDFSEFLNLIGGLAMACHDSFLK 32 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;; 186.98 6.38E-20 2050080000 61635 1286310 1049440 1256710 832223 1318090 777253 1081590 970470 1497540 FALSE TRUE 64068.39739 1507223.736 1076789.269 1505283.487 690762.0317 1011983.573 716329.8789 1067093.055 935542.9743 1790954.291 0.035773329 0.84157577 0.601237717 0.840492409 0.385694953 0.565052709 0.399971056 0.595823724 0.522371218 1 20.77229709 -1.216936674 3.231889223 1.001322842 0.546876335 0.285588349 0.220935947 23538641.83 34177846.07 316040.1527 0.049164225 0.060682481 1.216936674 -0.454446507 KLDVEEPDSANSSFYSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLDVEEPDSANSSFYSTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 343.5 1.26E-75 2263150000 1658900 1394520 1678800 1411130 1904910 1912200 1908100 1682050 1599690 1404470 FALSE TRUE 1724394.653 1634017.962 1722550.907 1690247.302 1581114.079 1468120.53 1758538.136 1659504.871 1542117.469 1679649.006 1.026639879 0.972832988 1.025542182 1.006309828 0.941336001 0.874063881 1.046967628 0.988006938 0.918118883 1 20.67972836 3.261776315 23.60887476 0.964546037 1.006596465 0.192752435 0.046241385 244.8030484 248945.8032 0.013310509 0.018007803 1827.15889 -3.261776315 0.042050428 KLDVLSNDLVMNMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLDVLSNDLVMNMLK 15 1 P09467;A0A3B3IUC7 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 286.44 5.05E-34 1413340000 3579500 2467800 3353700 2536600 5716200 4211300 4034600 3357800 4128800 3423900 FALSE TRUE 3720821.424 2891625.453 3441100.177 3038331.909 4744562.366 3233289.398 3718357.51 3312794.183 3980205.295 4094747.65 0.908681497 0.706179159 0.84036929 0.742007119 1.158694692 0.78961872 0.908079771 0.809035004 0.972027005 1 21.96534311 0.374785552 0.023409473 1.857219598 4.03E-06 0.139931589 0.119509124 888.8804733 8.163602088 343.57437 302.5745709 2.370203046 -0.374785552 -1.857215571 KLDVSIEMPEELDISQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLDVSIEMPEELDISQLR 18 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 73.783 0.031482 613680000 115800 98178 115370 104780 124380 150050 118350 103190 123040 110470 FALSE TRUE 120371.8734 115039.3078 118376.637 125505.1713 103237.932 115203.1615 109073.4177 101806.9068 118611.8144 132114.4814 0.911117934 0.870754716 0.896015605 0.949972856 0.781427826 0.871994957 0.825597744 0.77059612 0.897795708 1 17.01142909 3.245279774 24.99996728 0.839959951 0.90359668 0.083393466 0.064630533 264.091843 982600.2662 0.0171843 0.022753906 1759.05644 -3.245279774 0.063636729 KLEAAEDIAYQLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 ;; 215.23 1.06E-11 2291820000 2645283 2828040 2390853 2617370 2739130 3449960 2441231 2148826 2240532 2425000 FALSE TRUE 2749720.815 3313733.871 2453160.593 3135077.974 2273533.661 2648759.075 2249880.935 2120024.502 2159895.691 2900132.321 0.94813633 1.142614717 0.84587885 1.081012046 0.783941355 0.913323525 0.775785615 0.731009577 0.744757636 1 21.4676873 3.096840864 1.26744232 0.792016096 1.012303995 0.315343055 0.113602197 0.424274323 1.43837891 0.041587033 0.055113961 1249.800989 -3.096840864 0.220287899 KLEAAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 152.28 0.00073707 3684930000 6200250 5572850 6217260 5497900 7893420 7498270 7106730 6412960 6337210 5851520 FALSE TRUE 6445040.658 6529943.637 6379286.903 6585368.21 6551699.288 5756910.43 6549685.933 6327004.761 6109135.05 6998013.31 0.92098148 0.933113921 0.91158542 0.941033965 0.936222753 0.822649254 0.935935049 0.904114422 0.872981342 1 22.73851398 KLEAELLQIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 140.31 9.55E-05 64584000 154980 120210 138310 129580 183240 165430 162010 154230 149910 139960 FALSE TRUE 161098.7301 140855.1324 141914.4722 155210.5372 152092.9303 127011.3896 149311.2329 152162.7991 144514.7684 167382.4823 0.962458722 0.84151657 0.847845427 0.927280652 0.908655005 0.758809332 0.892036196 0.909072425 0.863380483 1 17.35278902 -1.312707431 4.224296133 1.000151721 0.878555744 0.31750822 0.053214 7.41E-05 1.21E-05 0.050204199 0.011818504 0.048673499 1.312707431 -0.121595977 KLEDGPK ddPTM_MDA-MB-175_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 ;;;;;;; 91.069 0.026738 69376000000 63349290 32830420 45946320 30687620 64456180 59521530 62308680 45256010 51134850 25813110 FALSE TRUE 65850368.89 38468789.25 47143718.84 36757539.64 53499941.55 45698556.72 57424762.85 44649427.21 49294516.74 30870694.68 2.133102917 1.246126452 1.527135017 1.190693634 1.733033289 1.480321618 1.860170736 1.446336977 1.596806202 1 24.87973461 -1.086608155 4.336965688 0.999945461 1.561794141 0.298147975 0.265424577 16573670.77 4152464.872 9627.084038 0.056933804 0.081920359 1.086608155 0.56184868 KLEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEDIR 6 1 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 94.407 0.07138 2400100000 4359900 3722100 4349600 3794400 5132100 5078400 4799500 4467300 4362300 3850900 FALSE TRUE 4532032.219 4361341.721 4462954.149 4544920.995 4259747.475 3899018.564 4423302.649 4407423.151 4205301.675 4605410.125 0.98406702 0.947003981 0.96906769 0.986865637 0.92494422 0.846617013 0.960457924 0.957009915 0.913122081 1 22.13489821 3.228459541 24.77652779 0.931194638 0.969791762 0.187959537 0.038459219 315.7042902 774378.1149 0.011306305 0.013664355 1692.230587 -3.228459541 0.038597124 KLEDNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLEDNPK 7 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;; 120.46 0.0073002 6319300000 9058600 5341600 6797180 4861530 9970300 8517000 9638200 7137620 8182920 4606950 FALSE TRUE 9416240.523 6258978.248 6974320.095 5823126.124 8275551.967 6539055.826 8882732.699 7041951.879 7888418.308 5509593.647 1.709062614 1.136014496 1.265850177 1.056906643 1.502025829 1.186849021 1.612230097 1.278125453 1.431760455 1 22.39351449 -0.979543273 4.928949357 0.99999681 1.341604981 0.217678748 0.199790982 0.016456521 60665245.05 454.6595632 0.043228431 0.104823034 0.979543273 0.34160817 KLEDQLQGGQLEEVILQAEHELNLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEDQLQGGQLEEVILQAEHELNLAR 26 1 A0A087X1G1;H7BYD0;Q16718-2;Q16718;A0A087WXR5 A0A087X1G1 NDUFA5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 0 ; 167.78 6.51E-12 57037000 71974 64268 60343 59148 60773 97088 64920 61110 59953 67592 FALSE TRUE 74815.5891 75305.52906 61915.58815 70847.29786 50442.82717 74540.78338 59831.40076 60290.92041 57795.30324 80835.35827 0.925530494 0.931591455 0.765946851 0.876439461 0.624019343 0.922130921 0.740163736 0.745848372 0.714975531 1 16.30269886 4.242603559 24.98255225 0.785534292 0.928561041 0.191598133 0.103932212 130.5575557 806723.1253 0.02331889 0.059197296 17482.5009 -4.242603559 0.143026749 KLEDSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLEDSTR 7 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ;; 138.1 0.0045197 271615000 402621 420080 444650 395630 497960 537900 461413 427558 415655 392387 FALSE TRUE 418516.788 492225.4722 456237.9443 473884.4332 413316.9371 412980.877 425246.2434 421827.2844 400695.6577 469267.7199 0.891850793 1.048922505 0.972233812 1.009838122 0.880770016 0.880053878 0.906191126 0.898905393 0.853874325 1 18.8400517 3.235338559 24.99985141 0.897544915 0.984978006 0.346525445 0.051585008 77.71414457 602983.3464 0.013544227 0.016837193 1719.248122 -3.235338559 0.087433091 KLEEEEDGKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEEEEDGKLK 11 2 P11387 P11387 TOP1 DNA topoisomerase 1 0 ; 79.466 0.015224 100747000 278540 355010 342350 352870 338700 403760 323090 329300 286920 386690 FALSE TRUE 289536.9743 415980.2059 351271.9222 422666.6328 281127.895 309992.859 297765.3616 324886.2721 276593.8052 462454.5019 0.626087481 0.89950515 0.759581582 0.913963711 0.607903899 0.670320773 0.643880339 0.702525915 0.598099498 1 18.81895191 3.228620685 24.98574645 0.68457489 0.804035762 0.104529431 0.130334675 340.7847642 856620.2181 0.034257191 0.041402891 1692.858604 -3.228620685 0.119460872 KLEEEGEQFVK ddPTM_MDA-MB-175_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 2936780000 3718650 2240700 3140380 2194120 3988940 3503570 4080620 2971690 3497890 1858300 FALSE TRUE 3865465.173 2625522.795 3222220.883 2628110.387 3310901.404 2689918.965 3760770.342 2931859.356 3372001.622 2222398.306 1.739321508 1.181391647 1.449884512 1.182555971 1.489787584 1.210367627 1.692212567 1.319232178 1.517280504 1 21.08368597 -2.184031769 2.114230237 2.10E-05 1.40823582 0.304532042 0.189736599 2509793.184 463008.3993 12025489.46 0.041113389 0.006545883 2.184031769 1.408214778 KLEEEQIILEDQNCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLEEEQIILEDQNCK 15 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 302.13 3.52E-44 5280940000 15438750 8196340 11491130 8463890 16443300 14739200 14337310 11914470 13738640 7484540 FALSE TRUE 16048283.77 9603997.636 11790598.29 10138022.18 13648273.74 11316244.17 13213514.18 11754776.02 13244189.03 8950992.313 1.792905547 1.0729534 1.317239237 1.132614332 1.52477773 1.264244653 1.476206628 1.313237193 1.479633606 1 23.0936162 -1.220307458 4.745329816 0.999928318 1.359185257 0.241683373 0.197454662 0.000134973 2.22E-05 0.172322617 0.040608752 0.060213316 1.220307458 0.359256939 KLEEHEESLVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEEHEESLVGR 12 1 Q14789;Q14789-2;Q14789-4;Q14789-3;E7EU81;H0Y867 Q14789 GOLGB1 Golgin subfamily B member 1 0 169.62 2.81E-05 60474000 174270 130870 154280 153700 198020 209520 162460 160330 168180 150010 FALSE TRUE 181150.3142 153345.9045 158300.6635 184101.4013 164360.6311 160862.1553 149725.9607 158181.0386 162127.2347 179401.5874 1.009747555 0.854763365 0.882381621 1.02619717 0.916160406 0.896659598 0.834585484 0.881714821 0.90371126 1 17.45283313 2.83460495 4.272725945 0.889239808 0.936295431 0.054316493 0.062257471 0.531700131 16.99525924 0.019189055 0.020368169 683.2898188 -2.83460495 0.047055624 KLEEIIHQITNVEALIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEEIIHQITNVEALIAR 18 1 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 231.42 5.19E-20 329550000 426350 357140 399820 395150 515150 518140 503520 424330 467310 352370 FALSE TRUE 443182.6272 418476.0168 410239.6377 473309.4906 427584.987 397809.8375 464052.7867 418642.5504 450491.6044 421410.155 1.051665751 0.993037334 0.973492529 1.123156348 1.014652784 0.943996799 1.101190328 0.993432516 1.069009845 1 18.68486555 KLEELELDEQQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEELELDEQQKK 13 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 113.59 0.00045569 183410000 401380 221710 270440 222080 365000 367250 328320 319120 273420 267920 FALSE TRUE 417226.7923 259786.9678 277487.8886 266006.7612 302957.4304 281961.7532 302585.4205 314842.7184 263579.6676 320413.7944 1.302149906 0.810785841 0.866029782 0.830197594 0.945519312 0.879992554 0.944358282 0.982612871 0.822622722 1 18.28957673 4.746534731 24.99622797 0.901210756 1.302150102 0.780579089 0.064260498 460.2539222 1442711.779 0.01548256 0.17210252 55787.22145 -4.746534731 0.400939347 KLEELELDEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KLEELELDEQQR 12 1 Q02750;Q02750-2 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 0 ;;;; 194.86 1.57E-06 1577680000 2106958 1854087 2116450 1904226 2444810 2550400 2347100 2198800 2295760 1869002 FALSE TRUE 2190142.329 2172512.019 2171606.426 2280876.219 2029242.069 1958108.252 2163128.169 2169328.683 2213136.046 2235197.158 0.979843018 0.971955432 0.971550281 1.020436256 0.907858201 0.876033796 0.967757212 0.970531246 0.990130127 1 21.09197066 1.380995535 2.141882163 0.997460357 0.955550893 0.144922262 0.03751149 0.663339685 5.334821046 0.035941117 0.011030766 24.04338083 -1.380995535 -0.041909464 KLEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 2718090000 2419470 1326550 2097420 1213250 2380570 2250390 2337150 1911860 2045260 1192900 FALSE TRUE 2514992.544 1554374.643 2152080.488 1453227.229 1975921.562 1727771.027 2153958.076 1886234.644 1971651.492 1426625.916 1.762895596 1.089546059 1.508510721 1.018646313 1.385031311 1.211089052 1.509826825 1.322164853 1.382038186 1 20.44417566 4.755209345 24.25291247 1.293352645 1.762896153 0.400584449 0.178907271 2151.183347 3133642.782 0.038628808 1.035641481 56912.7204 -4.755209345 0.469543509 KLEEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLEEQAR 7 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 130.28 0.0057382 6208350000 5243490 4796690 4825600 4089500 6834800 5986170 5447790 4802660 4959740 4944000 FALSE TRUE 5450507.034 5620484.194 4951359.1 4898390.894 5673023.137 4595972.739 5020777.985 4738288.198 4781239.926 5912682.141 0.921833257 0.950581151 0.837413374 0.828454968 0.959466956 0.777307596 0.84915405 0.801377122 0.808641461 1 22.49538129 2.733399086 24.99964877 0.832589701 0.894983256 0.103962139 0.069724418 804.5659584 3896866.42 0.021277458 0.020602217 541.2514667 -2.733399086 0.062393555 KLEEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLEEQQR 7 1 Q02818;H7BZI1;C9JKZ2 Q02818 NUCB1 Nucleobindin-1 0 ;; 101.72 0.014192 1167400000 1112350 1000810 1036480 1178980 1761760 1645570 1362820 1100950 1073270 1277440 FALSE TRUE 1156266.437 1172691.332 1063491.52 1412178.725 1462296.664 1263411.306 1255998.607 1086193.566 1034643.222 1527729.91 0.756852654 0.767603831 0.696125351 0.924364127 0.957169625 0.826986039 0.822133938 0.710985338 0.677242237 1 20.54295808 3.760879762 24.96566199 0.828902466 0.742934938 0.183820434 0.09735909 1747.583388 1954798.202 0.02699088 0.048615039 5766.068027 -3.760879762 -0.085967528 KLEEVVQILGDKFPCTLVAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEEVVQILGDKFPCTLVAQK 21 2 Q9BY32 Q9BY32 ITPA Inosine triphosphate pyrophosphatase 0 ; 281.15 2.93E-45 366940000 1067230 571140 899350 576350 1164020 973190 1032820 894880 1008410 553510 FALSE TRUE 1109365.064 669228.8521 922787.7998 690350.3098 966160.2962 747181.3713 951864.8696 882885.5973 972117.5211 661959.6869 1.675880097 1.010981281 1.394024165 1.042888749 1.459545521 1.128741502 1.437949906 1.333745264 1.468544898 1 19.33638383 KLEEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEEYK 6 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 88.942 0.081342 743500000 1454200 971640 984970 829700 2383400 2638200 2745000 2334100 2346500 1639100 FALSE TRUE 1511612.939 1138511.612 1010639.127 993812.1836 1978270.519 2025518.032 2529839.727 2302815.207 2262049.923 1960250.263 0.771132629 0.580799112 0.515566378 0.506982298 1.009192835 1.033295631 1.290569768 1.174755719 1.15395976 1 20.90260642 3.106194176 3.476510367 1.149544254 0.586656795 0.857776133 0.103475409 0.081595721 1.928779394 0.032316918 0.039434401 1277.009641 -3.106194176 -0.562887459 KLEGDSTDLSDQIAELQAQIAELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEGDSTDLSDQIAELQAQIAELK 24 1 P35579 P35579 MYH9 Myosin-9 0 ; 253.66 1.39E-43 445350000 526070 233534 358140 275413 447673 422730 530910 341914 400309 192538 FALSE TRUE 546839.6498 273641.6479 367473.4226 329888.8694 371577.7034 324557.364 489295.8869 337331.2021 385901.9573 230262.1347 2.374857032 1.188391866 1.595891669 1.432666599 1.613716054 1.40951253 2.12495158 1.46498773 1.675924518 1 17.81291766 4.754589962 24.53368549 1.541759159 2.374857849 0.450655078 0.286335048 2181.52593 3338859.029 0.063502998 1.614593731 56831.61029 -4.754589962 0.83309869 KLEGETYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEGETYR 8 1 Q709C8-3;Q709C8 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 87.308 0.028692 0 165680 162700 161950 140430 189630 207440 173890 168460 165850 145780 FALSE TRUE 172221.1743 190642.4594 166170.55 168206.6349 157396.7603 159265.2038 160260.0474 166202.0692 159881.0909 174342.7999 0.987830725 1.093492014 0.953125395 0.964804024 0.902800462 0.913517529 0.919223779 0.953306184 0.917050151 1 17.41156726 4.110178099 6.460891574 0.935982185 1.039863172 0.551937053 0.036200108 0.129334241 6.83194469 0.008445656 0.018597535 12887.77956 -4.110178099 0.103880986 KLEHLITELVHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEHLITELVHQR 13 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 187.57 2.79E-06 829260000 940420 859030 1004000 1019120 1180440 1221070 1142240 1020750 1023700 915330 FALSE TRUE 977548.5078 1006561.72 1030165.065 1220698.894 979789.2304 937494.998 1052708.244 1007068.516 986857.237 1094671.388 0.893006356 0.919510394 0.941072431 1.115128163 0.895053293 0.856416828 0.96166599 0.91997336 0.901510031 1 20.06206642 KLEKEEEEGISQES(ph)S(ph)EEEQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLEKEEEEGISQESSEEEQ 19 2 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 2 KLEKEEEEGIS(0.184)QES(0.861)S(0.955)EEEQ;KLEKEEEEGIS(0.004)QES(0.996)S(1)EEEQ;KLEKEEEEGIS(0.062)QES(0.95)S(0.988)EEEQ 138.11 1.25E-05 2501570000 2480140 1318440 2029650 861780 3208940 2482370 1635150 1819210 2122090 1438210 TRUE FALSE 2578057.842 1544871.814 2082544.346 1032237.512 2663485.525 1905877.188 1506982.67 1794826.466 2045716.395 1719999.713 1.498871088 0.898181437 1.210781799 0.600138188 1.548538354 1.108068317 0.876152861 1.043503933 1.189370196 1 20.71397689 4.75165452 24.11530691 1.053374152 1.498871559 0.243888404 0.235650671 1847.662513 3402777.263 0.052929688 0.959935518 56448.77484 -4.75165452 0.445497407 KLEKEEEEGISQES(ph)SEEEQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEKEEEEGISQESSEEEQ 19 2 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KLEKEEEEGISQES(0.981)S(0.019)EEEQ 124.86 2.24E-05 78803000 158860 91119 128000 55501 207110 149080 109740 118670 130340 101020 TRUE FALSE 165131.9155 106767.9794 131335.7852 66478.93215 171905.5162 114458.4293 101138.292 117079.4228 125649.0889 120812.9349 1.366839699 0.883746261 1.087100361 0.550263366 1.422906549 0.947402109 0.837147878 0.969096752 1.040030101 1 16.8824154 KLELSDNIISGGLEVLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLELSDNIISGGLEVLAEK 19 1 Q9BTT0;Q5TB19;Q9BTT0-3;E9PLC4 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 148.91 1.46E-07 115920000 220370 133130 181210 146520 256120 244500 241260 200960 190200 155830 FALSE TRUE 229070.3778 155994.0419 185932.4815 175501.2187 212584.8139 187718.5804 222349.4108 198266.4599 183354.7392 186361.905 1.229169544 0.837048977 0.997695755 0.941722605 1.140709599 1.00727979 1.193105484 1.063878693 0.983863838 1 17.50774746 3.246628697 24.99971215 1.07377941 0.989403962 0.066874857 0.109457142 380.4593366 1178880.554 0.028697502 0.038189103 1764.52858 -3.246628697 -0.084375448 KLELSDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLELSDNR 8 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;; 106.18 0.0068073 9291010000 17739400 16091100 17465900 14269600 25883700 22666200 19048300 17189900 17522300 20520000 FALSE TRUE 18439765.21 18854621.25 17921075.7 17092084.29 21483997.92 17402318.56 17555244.47 16959497.51 16891675.85 24540501.12 0.751401331 0.768306285 0.730265271 0.69648473 0.875450661 0.709126455 0.715358027 0.691081956 0.688318293 1 24.54866137 -2.063456114 2.657222398 1.390858817 0.734937621 0.692727573 0.052702135 14240422.07 7294904.455 33646993.6 0.013283315 0.0086406 2.063456114 -0.655921196 KLELSENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KLELSENR 8 1 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 ;;;; 107.79 0.0063107 7951240000 4489860 4308110 4161750 3361440 7443070 6177850 4929550 4308550 4577000 6856790 FALSE TRUE 4667123.14 5047994.38 4270208.624 4026322.799 6177899.62 4743137.964 4543158.99 4250800.935 4412274.664 8200246.719 0.569144234 0.615590549 0.520741481 0.491000202 0.753379725 0.578414056 0.55402711 0.518374761 0.538066087 1 22.96723589 -0.841123781 11.44733902 0.999999436 0.569508839 0.773887376 0.069567484 0 0 0.068139069 0.016060533 0.144170438 0.841123781 -0.430490597 KLEMDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLEMDLK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 99.802 0.016452 3264200000 6053900 3337400 4560500 3339500 6470800 5623800 6347700 4480300 5211300 3267000 FALSE TRUE 6292912.647 3910572.489 4679350.376 4000043.133 5370895.727 4317757.68 5850150.687 4420248.907 5023746.331 3907106.1 1.610632649 1.000887201 1.197651217 1.023786667 1.374648036 1.10510377 1.497310423 1.131335775 1.285797264 1 21.897669 -1.085701267 3.644025689 0.999898821 1.234940026 0.129672488 0.189851567 16930192.14 32901441.63 23044.9969 0.040949127 0.082091602 1.085701267 0.235041205 KLEMYGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEMYGIR 8 1 O94887-3;O94887-2;O94887 O94887-3 FARP2 "FERM, RhoGEF and pleckstrin domain-containing protein 2" 0 63.565 0.07609 468160000 617900 411910 598950 473680 481000 595350 587920 559750 679460 206180 FALSE TRUE 642295.1691 482652.3383 614559.129 567372.4902 399239.7918 457088.9851 541837.2942 552247.4668 655006.3673 246577.0234 2.604845983 1.957410028 2.492361699 2.300994968 1.619128118 1.853737135 2.197436268 2.239655014 2.656396602 1 17.91167885 3.434964293 24.99788379 2.015341951 2.326219633 0.155752316 0.441554403 329.61132 195449.1757 0.118631578 0.16062806 2722.477459 -3.434964293 0.310877682 KLENCNYAVELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLENCNYAVELGK 13 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2;P13796 P13797;P13796 PLS3;LCP1 Plastin-3;Plastin-2 0 ; 165.33 1.43E-06 323500000 1081860 722780 918160 678460 1235820 1167810 1130060 920600 1040110 667020 FALSE TRUE 1124572.668 846911.8426 942088.0039 812657.363 1025755.758 896603.8258 1041482.944 908260.8628 1002676.644 797709.7981 1.409751605 1.061679128 1.180990889 1.018738099 1.285875841 1.123972437 1.305591265 1.138585567 1.256944125 1 19.60550447 -2.382435837 1.888816413 4.48E-05 1.189513755 0.212612472 0.113260437 1243909.685 130786.0309 5297415.13 0.025862748 0.004145378 2.382435837 1.189468924 KLENDTISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLENDTISK 9 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 127.51 0.00071077 263690000 583590 570600 623300 493670 718000 831250 675610 599090 613860 636290 FALSE TRUE 606630.5838 668596.1113 639543.71 591316.4525 595954.6165 638204.7852 622653.9228 591060.1785 591767.2985 760958.843 0.79719237 0.878623223 0.840444547 0.777067588 0.783162745 0.838685024 0.818249145 0.77673081 0.777660059 1 19.5374589 -1.119463404 4.476075917 1.000020491 0.809739733 0.75364042 0.032631115 7.53E-06 1.48E-06 0.033542638 0.007905171 0.075951542 1.119463404 -0.190280757 KLENEVEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLENEVEQR 9 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 93.561 0.014937 349860000 523310 536610 583210 438230 624310 665100 589990 553860 593130 466820 FALSE TRUE 543970.6829 628768.5933 598408.9317 524910.586 518190.0092 510640.6047 543745.0421 546436.4126 571783.3672 558284.4412 0.974361173 1.126251328 1.071871053 0.940220696 0.928182788 0.914660282 0.973957005 0.978777792 1.024179298 1 19.09064082 3.743768107 24.78614078 0.962717562 1.064370207 0.447981009 0.046418969 315.8032164 1503126.424 0.012047819 0.020937114 5543.296478 -3.743768107 0.101652644 KLENS(ph)PLGEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLENSPLGEALR 12 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 KLENS(1)PLGEALR 68.576 0.032032 54694000 106640 98637 88337 103570 106670 144450 105940 96779 87676 95391 TRUE FALSE 110850.2295 115577.1375 90639.13479 124055.8369 88538.2715 110903.6767 97636.14598 95481.8358 84520.55789 114081.0401 0.971679689 1.013114339 0.794515326 1.087436061 0.776099792 0.97214819 0.855849017 0.836964983 0.740881726 1 16.79969951 2.931554791 0.869615266 0.847478315 0.95907356 0.104230181 0.106134712 1.154945647 1.923920897 0.056069344 0.065485557 854.190606 -2.931554791 0.111595244 KLEPGGFGEKPVRPGGGDT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEPGGFGEKPVRPGGGDTSPR 22 3 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065 Q5JSZ5 PRRC2B Protein PRRC2B 1 KLEPGGFGEKPVRPGGGDT(0.635)S(0.365)PR 108.44 0.00043382 1027500000 748580 489470 594080 533510 863800 771490 770100 681790 791720 399080 TRUE FALSE 778134.5164 573532.665 609562.2128 639036.6856 716971.5845 592323.1395 709737.5497 672651.7202 763226.1519 477272.0852 1.630379276 1.201689105 1.277179688 1.338935809 1.502228198 1.241059676 1.487071152 1.409367405 1.59914266 1 18.86445243 2.200466863 24.99652378 1.410978249 1.358837931 0 0.187090586 944.9730484 620071.3066 0.065362874 0.048274738 158.6597854 -2.200466863 -0.052140318 KLEPGGFGEKPVRPGGGDTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLEPGGFGEKPVRPGGGDTSPR 22 3 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065 Q5JSZ5 PRRC2B Protein PRRC2B 1 KLEPGGFGEKPVRPGGGDT(0.176)S(0.824)PR 97.691 0.007038 1093800000 1461000 939450 1148100 988590 1499900 1405000 1599900 1257100 1480000 830680 TRUE FALSE 1518681.408 1100793.23 1178020.429 1184130.151 1244947.534 1078710.043 1474495.657 1240250.631 1426735.089 993435.8417 1.528716143 1.108066755 1.185804236 1.191954328 1.253173563 1.085837653 1.484238434 1.248445625 1.436162286 1 19.92206727 2.254258618 24.99830773 1.312126678 1.218166277 0.030726725 0.165987824 661.6183828 1053593.564 0.053363835 0.044502636 179.5802689 -2.254258618 -0.093960401 KLES(ph)TESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.703)T(0.294)ES(0.004)R;KLES(0.823)T(0.176)ES(0.001)R;KLES(0.986)T(0.014)ESR;KLES(0.839)T(0.161)ESR;KLES(0.974)T(0.026)ESR;KLES(0.983)T(0.017)ESR 153.34 0.0002711 3230040000 3341730 2482300 3068900 2618780 4361860 4206510 4056030 3470530 3809150 2836020 TRUE FALSE 3473664.081 2908615.715 3148878.055 3136766.868 3620432.595 3229611.803 3738107.77 3424013.222 3672059.436 3391683.82 1.024170962 0.857572778 0.928411439 0.924840591 1.067444015 0.95221488 1.102139223 1.009531962 1.082665611 1 21.69357025 3.24831192 24.9996721 1.035056395 0.927926509 0.446105221 0.055480872 168.7313035 432578.3495 0.014304188 0.019135411 1771.380745 -3.24831192 -0.107129886 KLESTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 153.05 0.0007173 14241470000 15217000 14081190 15124340 13230840 17700930 17365310 16940680 15642810 14643770 12903520 FALSE TRUE 15817778.91 16499524.85 15518492.73 15847860.66 14692132.24 13332479.93 15612825.24 15433143.72 14116743.58 15431717.69 1.025017385 1.069195612 1.005623161 1.02696673 0.952073679 0.863966034 1.011736059 1.000092409 0.914787573 1 23.87939532 3.263618995 7.258880248 0.959503001 1.032859568 0.407695769 0.043989088 0.195760787 38.73115704 0.012973958 0.017212391 1834.927863 -3.263618995 0.073356567 KLEVEANNAFDQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLEVEANNAFDQYR 14 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;; 251.05 1.69E-18 5683800000 3166520 2583000 3153660 2699830 3630510 3811890 3584730 3259370 3414470 2794610 FALSE TRUE 3291536.655 3026610.157 3235846.97 3233848.316 3013397.207 2926636.317 3303749.496 3215683.476 3291583.892 3342160.323 0.98485301 0.90558497 0.968190229 0.967592217 0.901631554 0.875672031 0.988507186 0.962157157 0.984867144 1 21.67234951 KLFADAEEEQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLFADAEEEQRR 12 2 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 91.914 0.0045162 98601000 158020 147870 154170 115600 190750 193340 137510 143570 167140 175180 FALSE TRUE 164258.7516 173265.5222 158187.7969 138465.335 158326.3831 148439.7151 126731.6069 141645.679 161124.664 209503.167 0.784039468 0.827030563 0.755061602 0.660922395 0.755723102 0.708532082 0.604914993 0.676102806 0.769079849 1 17.67661253 0.897945673 6.350692826 0.999997409 0.717258999 0.651085257 0.060817621 1.031593902 63.88228374 0.065143554 0.016362438 7.905797262 -0.897945673 -0.28273841 KLFAPQQILQCS(ph)PAN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLFAPQQILQCSPAN 15 1 P04183;K7ERV3 P04183 TK1 "Thymidine kinase, cytosolic;Thymidine kinase" 1 KLFAPQQILQCS(1)PAN;KLFAPQQILQCS(1)PAN 170.42 1.21E-06 386580000 687030 567600 524540 526340 548010 716090 513420 567020 528200 715760 TRUE FALSE 714154.4749 665080.8847 538209.9433 630448.481 454859.4559 549788.9499 473176.7988 559420.0244 509190.1852 855999.4679 0.834293129 0.776964133 0.628750325 0.736505693 0.531378199 0.64227721 0.552776978 0.653528472 0.594848717 1 19.70725037 -1.161334459 3.810276816 1.000214872 0.656467521 0.551778991 0.091499552 29135363.4 49283211.15 76621.72201 0.022575216 0.068970844 1.161334459 -0.34374735 KLFIGGLSFETTDDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLFIGGLSFETTDDSLR 17 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 283.76 6.30E-36 3082400000 1720340 1766350 1977790 1720390 2180800 2183700 2007280 1948630 1937860 1991330 FALSE TRUE 1788260.352 2069706.872 2029332.832 2060678.007 1810108.395 1676568.769 1849944.149 1922511.802 1868116.797 2381492.987 0.750898853 0.869079558 0.85212631 0.865288295 0.760072948 0.703999037 0.776800166 0.807271662 0.784430946 1 21.18343487 -1.368355171 2.9928321 1.002578151 0.798440246 0.590977707 0.050729372 15062462 18825284.54 340244.6239 0.013344181 0.042819819 1.368355171 -0.204137905 KLFIGGLSFETTDESLR ddPTM_MDA-MB-175_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 ;; 291 8.83E-46 3989830000 2549830 2831340 2875420 2442580 3406620 3361880 2612000 2780920 2806250 3168530 FALSE TRUE 2650499.257 3317600.62 2950355.807 2925715.034 2827563.949 2581134.32 2407264.615 2743646.316 2705253.611 3789342.788 0.699461465 0.875508183 0.77859301 0.772090359 0.746188484 0.681156196 0.635272328 0.724042788 0.713911029 1 21.85351622 -1.255708974 3.423990208 1.000746054 0.735978422 0.623518877 0.061484133 1068008454 1449160072 8142727.729 0.016552578 0.05549975 1.255708974 -0.264767632 KLFIGGLSFETTEESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLFIGGLSFETTEESLR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 262.59 3.81E-27 3553298000 1090355 1169409 1252938 1075812 1612302 1517256 1126090 1239371 1390412 1352724 FALSE TRUE 1133403.057 1370245.899 1285590.594 1288604.403 1338243.482 1164896.288 1037824.123 1222759.259 1340371.344 1617764.368 0.700598356 0.846999678 0.794671102 0.796534049 0.8272178 0.720065487 0.641517482 0.75583273 0.82853311 1 20.62557006 0.885195703 3.294148904 0.999811746 0.76094081 0.60797347 0.058187783 0.342326518 7.63941455 0.059649875 0.015489974 7.677073575 -0.885195703 -0.238870937 KLFVGGIKEDTEEHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLFVGGIKEDTEEHHLR 17 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ; 176.81 3.42E-10 3479300000 2631700 2223600 2978800 1368730 3852500 3328000 2223600 2624800 3100000 2654700 FALSE TRUE 2735601.548 2605486.003 3056429.975 1639460.709 3197653.426 2555122.436 2049308.422 2589618.849 2988431.606 3174837.638 0.86165085 0.82066748 0.962704341 0.516391985 1.007186443 0.804804128 0.64548448 0.815669696 0.941286436 1 21.59825138 1.159865051 3.740984897 0.993276269 0.799605684 0.204388264 0.133509845 0.326450229 8.075241388 0.118595564 0.031436112 14.44990697 -1.159865051 -0.193670585 KLFVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLFVPR 6 1 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 113.82 0.041389 296330000 159940 238160 198200 225250 210110 221350 204690 202390 200260 260580 FALSE TRUE 166254.5547 279062.1274 203365.2548 269803.7777 174395.5772 169944.8171 188645.8629 199677.2931 193052.6817 311635.6619 0.533490146 0.895475587 0.652573757 0.865766697 0.559613673 0.545331738 0.605341063 0.640739548 0.619481996 1 18.24950081 -1.091511454 4.613620052 1.000017042 0.660612904 0.426008499 0.119208076 2.63E-05 5.17E-06 0.113270669 0.026696436 0.081000658 1.091511454 -0.339404138 KLFVQDLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLFVQDLATR 10 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 153.63 2.55E-05 1177920000 1520150 1574900 1607120 1377230 2152360 1996990 1718270 1662130 1609680 2014380 FALSE TRUE 1580166.696 1845376.824 1649002.867 1649641.983 1786502.616 1533219.337 1583587.508 1639851.866 1551747.931 2409059.193 0.655926886 0.766015559 0.684500768 0.684766065 0.741576886 0.636439047 0.657346865 0.680702189 0.644130263 1 21.20003841 -2.196113573 2.407555225 1.934687486 0.684869101 0.853941292 0.039266118 1762869.534 448379.8064 8968122.569 0.009452544 0.00636629 2.196113573 -1.249818385 KLFYSTFATDDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLFYSTFATDDRK 13 2 P30084 P30084 ECHS1 "Enoyl-CoA hydratase, mitochondrial" 0 142.57 2.27E-05 430090000 631630 441240 472200 459830 506310 637720 524340 408470 520050 500140 FALSE TRUE 656567.2401 517019.5376 484505.9199 550783.0015 420247.607 489619.1947 483240.8607 402995.1278 501333.5021 598132.8572 1.097694655 0.864389126 0.810030604 0.920837227 0.7025991 0.818579332 0.807915591 0.673755208 0.838164124 1 19.19010645 7.999996272 0.917402834 0.793782402 171.9936427 0.430309511 0.091277491 824.2953627 1.666638378 0.027213137 295711.1386 99999141.63 -7.999996272 171.1998603 KLGAGEGGEASVS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.005)VS(0.995)PEK;KLGAGEGGEAS(0.003)VS(0.997)PEK 158.8 5.73E-09 375060000 1293950 484590 703600 584820 902510 1005080 1163920 762430 818580 350210 TRUE FALSE 1345036.145 567814.5629 721936.394 700495.6505 749101.6726 771665.4021 1072688.909 752210.8729 789119.4657 418826.9443 3.211436521 1.355725964 1.723710482 1.672518113 1.788570871 1.842444505 2.561174546 1.795994463 1.884118193 1 18.67599473 4.750088611 24.62264813 1.800934221 3.211437557 0.5700683 0.380650199 1058.262556 2260290.926 0.088329359 1.393521337 56245.60735 -4.750088611 1.410503335 KLGCEVLGVSVDSQFTHLAWINTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KLGCEVLGVSVDSQFTHLAWINTPR 25 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;;; 318.22 5.95E-75 5044607000 1389921.9 1756497 2073230 1852790 2376258 2483605 2045486 2141875 2153098 1981696.6 FALSE TRUE 1444797.09 2058161.696 2127260.077 2219266.332 1972342.514 1906825.378 1885155.462 2113166.669 2075608.424 2369972.107 0.6096262 0.868432877 0.897588655 0.936410317 0.832221826 0.804577139 0.795433607 0.891642 0.875794452 1 21.17643865 -5 0.02172616 2.095607845 7.87E-10 0.345644423 0.080117312 3774.835348 6.204370048 413.5654903 214.8647789 1.00E-05 5 -2.095607845 KLGDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLGDMR 6 1 O43399;O43399-7;O43399-2;O43399-3;O43399-6 O43399 TPD52L2 Tumor protein D54 0 86.866 0.085126 1219400000 4412700 4636100 4852500 4333200 5998900 6175800 5267300 5347600 5482600 4865100 FALSE TRUE 4586916.803 5432314.111 4978960.136 5190294.027 4979209.121 4741564.045 4854435.262 5275924.169 5285282.297 5818323.197 0.788357169 0.9336563 0.855737979 0.892060109 0.855780773 0.814936518 0.834335787 0.906777432 0.908385821 1 22.47217201 0.96202071 1.311838272 0.998022933 0.858270825 0.556512407 0.03930191 0.362817254 1.270137985 0.035942638 0.010932518 9.162641836 -0.96202071 -0.139752108 KLGDTYPSISNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLGDTYPSISNAR 13 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 115.63 0.0010409 747980000 789270 713640 864750 690520 1047260 978980 790020 846250 862460 761540 FALSE TRUE 820430.989 836202.1187 887286.0954 827102.795 869247.1193 751626.7316 728096.1681 834907.4029 831420.2331 910749.1824 0.900830882 0.918147537 0.974237597 0.908156506 0.954430853 0.825284004 0.799447512 0.916725943 0.91289704 1 19.79669427 2.765202577 24.85313301 0.880780519 0.931552876 0.104990898 0.05499825 1268.712464 1183524.853 0.016655773 0.017661162 582.3748037 -2.765202577 0.050772356 KLGEMWNNTAADDKQPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KLGEMWNNTAADDKQPYEK 19 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ;;;; 291.69 8.28E-50 9345530000 5505970 2642160 4299400 2671830 5732690 5089440 5264120 4301340 4842450 2422600 FALSE TRUE 5723349.947 3095930.427 4411445.896 3200309.999 4758249.401 3907494.691 4851504.519 4243687.573 4668171.17 2897262.087 1.97543397 1.068571063 1.522625763 1.104598032 1.642326189 1.348685267 1.674513515 1.4647234 1.611235377 1 21.46625877 KLGEMWSEQSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLGEMWSEQSAK 12 1 P26583 P26583 HMGB2 High mobility group protein B2 0 171.73 6.04E-05 852720000 869850 546410 749540 574440 1059900 929560 854940 846980 913260 623740 FALSE TRUE 904192.3497 640251.667 769073.6282 688062.5175 879738.5766 713683.7776 787927.5688 835627.6185 880391.951 745949.9108 1.212135475 0.858303832 1.030999022 0.922397748 1.179353418 0.956744906 1.056274098 1.120219476 1.180229313 1 19.50871923 1.91379938 4.364395692 1.110799284 1.020354224 0.077996225 0.109274119 0.473467275 15.3817153 0.047872642 0.027816807 81.99726747 -1.91379938 -0.09044506 KLGGSLADSYLDEGFLLDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLGGSLADSYLDEGFLLDKK 20 2 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 233.68 9.55E-30 618100000 236200 142170 206480 110370 293550 239690 251730 193050 280730 131950 FALSE TRUE 245525.3584 166586.5916 211861.0384 132200.8566 243652.4759 184025.63 231998.7448 190462.4805 270626.5821 157803.0762 1.555897162 1.055661243 1.34256596 0.837758425 1.544028683 1.166172641 1.470178849 1.20696304 1.71496392 1 17.2677658 KLGGSQEDQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLGGSQEDQIK 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 133.15 0.00026891 525580000 406300 236440 332540 219070 488770 404200 384850 340370 366900 293040 FALSE TRUE 422341.0377 277046.7308 341206.2656 262401.3921 405689.05 310330.6757 354684.4514 335807.8969 353695.3407 350455.5774 1.205120035 0.790533091 0.973607748 0.748743661 1.157604775 0.885506454 1.01206679 0.958203888 1.009244433 1 18.41887206 3.233485304 24.99672864 0.993954294 0.922725331 0.06818686 0.130575327 365.0805548 1798080.81 0.03475986 0.04276993 1711.927246 -3.233485304 -0.071228963 KLGLVFDDVVGIVEIINSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLGLVFDDVVGIVEIINSK 19 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ; 118.52 0.00012437 937380000 714840 458280 664860 466000 1114850 842300 872200 683540 763960 455230 FALSE TRUE 743062.4352 536986.0251 682186.7978 558173.4091 925348.1952 646688.5902 803834.6849 674378.2643 736465.2288 544423.6026 1.364860803 0.98633862 1.253044127 1.025255714 1.6996842 1.187840841 1.476487575 1.238701374 1.352743021 1 19.05437009 5.07150199 20.57762579 1.263577652 4.363382581 0.021595121 0.212853911 2573.696996 753519.6636 0.046653143 6335.520997 117896.7927 -5.07150199 3.099804929 KLGPIS(ph)PPQPPSVSAWNKPLTSFGSAPSSEGAK ddPTM_MDA-MB-175_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 112.14 3.22E-06 652910000 266190 147290 240140 149710 325110 257430 269870 228680 289650 158690 TRUE FALSE 276699.3867 172585.9117 246398.2457 179322.1912 269847.9183 197645.7839 248716.8842 225614.9186 279225.5531 189782.2672 1.457983356 0.909389029 1.298320698 0.944883807 1.421881624 1.041434412 1.31053806 1.188809271 1.471294222 1 17.53398567 KLGQSESQGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLGQSESQGPPR 12 1 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ; 145.6 0.00010267 202215000 129269 126187 123976 122265 142776 157484 126586 125177 127865 124492 FALSE TRUE 134372.6399 147858.6357 127206.9164 146448.6521 118506.9865 120910.7277 116663.8585 123499.2071 123263.1636 148883.8239 0.902533509 0.993114173 0.854403878 0.983643812 0.795969525 0.812114604 0.783589886 0.829500505 0.827915085 1 17.18382749 3.231851454 24.99999865 0.827659972 0.932043157 0.292721019 0.06795855 159.5496654 594521.0529 0.017873067 0.02182474 1705.498939 -3.231851454 0.104383185 KLGSSLDWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLGSSLDWDR 10 1 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 119.74 0.0010452 598790000 765020 747310 738580 715460 1100880 989080 879500 771260 821690 950030 FALSE TRUE 795223.5803 875654.6792 757828.0016 856975.8526 913752.8108 759381.1597 810562.4919 760922.5212 792117.5374 1136170.189 0.6999159 0.770707318 0.667002188 0.754267152 0.804239382 0.668369199 0.71341644 0.669725829 0.697182117 1 20.11574752 -1.343665618 5.696021429 1.000052024 0.715097251 0.786563121 0.044365012 2.95E-05 3.40E-06 0.043226908 0.010186825 0.045324642 1.343665618 -0.284954772 KLGVNNISGIEEVNMFTNQGTVIHFNNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLGVNNISGIEEVNMFTNQGTVIHFNNPK 29 1 P20290-2;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 259.7 2.86E-58 156870000 200900 152480 204450 151940 268450 233260 211810 192760 225900 166670 FALSE TRUE 208831.6871 178667.2539 209778.135 181993.2785 222818.9649 179088.9001 195207.7787 190176.3675 217769.9031 199325.7954 1.047690223 0.896357912 1.052438469 0.913044286 1.117863167 0.898473274 0.979340272 0.954098124 1.092532468 1 17.6047689 1.249641664 24.99851117 1.046266251 0.979882871 0.110844836 0.072054381 366.3969173 826592.4545 0.044193929 0.015804578 17.76812759 -1.249641664 -0.066383381 KLHELTVMQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLHELTVMQDR 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 195.25 1.02E-07 1230250000 907600 824290 948620 894120 1194720 1315380 1166530 987520 978900 951380 FALSE TRUE 943432.7488 965855.3954 973341.8165 1070974.267 991641.9211 1009902.93 1075094.33 974283.9097 943669.5802 1137784.696 0.829183898 0.848891182 0.855471004 0.941280254 0.871554983 0.8876046 0.944901381 0.856299011 0.829392049 1 20.11779615 KLIEFLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLIEFLLK 8 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8;E9PKG4 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 101.65 0.01331 0 451510 351870 461590 364220 682250 578070 557210 476020 516070 455050 FALSE TRUE 469335.9634 412300.9353 473619.4146 436261.6289 566281.3887 443822.0032 513534.4242 469639.7305 497496.7415 544208.335 0.862419653 0.757615988 0.87029063 0.801644519 1.040559933 0.815536945 0.94363572 0.862977835 0.914165972 1 19.05379953 7.999999923 0.056545095 1.173476909 0.29786435 0.303609824 0.070260895 457.5473541 1.938957667 6.401362856 33.55810266 99999982.16 -7.999999923 -0.875612559 KLIGTAVPQRTS(ph)PTGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLIGTAVPQRTSPTGPK 17 2 C9JB30;Q9UPY8 C9JB30 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 KLIGTAVPQRT(0.199)S(0.796)PT(0.006)GPK 115.39 0.00016543 501740000 607400 418440 476380 244130 656250 574990 403560 500950 603950 427470 TRUE FALSE 631380.621 490303.815 488794.8542 292418.1853 544700.8594 441457.2866 371927.9127 494235.5846 582213.9575 511224.5621 1.235035771 0.959077187 0.956125528 0.571995571 1.065482568 0.863529101 0.727523559 0.966768073 1.138861472 1 18.96359763 4.776160805 2.274726365 0.89683196 1.339385892 0.27612081 0.15525547 0.874651709 4.880105126 0.038208484 0.802386913 59725.639 -4.776160805 0.442553933 KLIHLEIKPAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLIHLEIKPAIR 12 2 P36507;G5E9C7;A0A1B0GUL7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 ; 124.86 0.00018952 963270000 796140 651690 738710 663350 947970 921060 912780 764790 899950 679330 FALSE TRUE 827572.222 763612.6881 757961.3895 794558.6501 786834.398 707157.7738 841233.9185 754539.241 867560.9753 812431.7069 1.018636046 0.939910003 0.932953974 0.978000542 0.968492972 0.870421191 1.035451856 0.928741745 1.067857111 1 19.63188702 1.240728707 24.99998114 1.033928561 0.957934188 0.28955534 0.046871911 62.02895134 715319.0541 0.032360184 0.010506427 17.40719151 -1.240728707 -0.075994373 KLISEVDS(ph)DGDGEISFQEFLTAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLISEVDSDGDGEISFQEFLTAAK 24 1 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 1 KLIS(0.035)EVDS(0.965)DGDGEISFQEFLTAAK;KLIS(0.105)EVDS(0.895)DGDGEISFQEFLTAAK 179.74 2.27E-17 391470000 565910 344340 508500 318921 681380 579260 509650 450180 561120 329050 TRUE FALSE 588252.5638 403477.7164 521751.9277 382002.6219 565559.271 444735.6438 469702.3013 444146.0734 540925.4008 393521.0475 1.494843967 1.02530149 1.325855202 0.970729836 1.437176676 1.130144491 1.193588766 1.128646298 1.374578067 1 18.58608127 -1.720147168 2.676835339 0.961715762 1.215105582 0.142190929 0.166182959 21265465.06 17954972.52 5464625.795 0.03503627 0.019048151 1.720147168 0.25338982 KLITSEEERS(ph)PAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLITSEEERSPAKR 14 3 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 KLITSEEERS(1)PAKR 98.572 0.01395 73615000 106200 98750 142600 78127 164950 155850 116200 132110 148610 117340 TRUE FALSE 110392.858 115709.5443 146316.2731 93580.28741 136911.8579 119656.1994 107091.9404 130339.2815 143261.5551 140330.5264 0.786663179 0.824550063 1.042654631 0.666856242 0.975638455 0.852674058 0.76314073 0.928802057 1.020886608 1 17.09846935 1.470679722 4.469024154 1.004544954 0.849540493 0.3093853 0.099540429 0.227180331 9.269326323 0.061916243 0.024194981 29.55831834 -1.470679722 -0.155004461 KLKDVLLQVDDERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLKDVLLQVDDERR 14 3 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 173.71 1.16E-06 2689200000 2767000 2800500 3283800 1902800 4623600 3787200 2375900 3240800 3660900 4101200 FALSE TRUE 2876243.297 3281464.09 3369378.526 2279168.161 3837682.124 2907680.196 2189670.75 3197362.377 3529144.924 4904751.618 0.586419766 0.669037771 0.686962111 0.464685745 0.782441686 0.592829244 0.446438662 0.651890784 0.719535911 1 22.22574865 0.84771232 2.193574886 0.999221443 0.60819466 0.610574033 0.094371061 0.365719231 3.338701177 0.087541318 0.023931997 7.0422643 -0.84771232 -0.391026782 KLLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 116.54 0.037659 6518300000 10896800 10301000 11145100 9787500 13868400 13447200 12155900 11552400 11645800 10215000 FALSE TRUE 11327014.08 12070116.62 11435550.46 11723438.29 11511054.32 10324291.59 11203088.79 11397558.97 11226669.93 12216433.67 0.927194825 0.988022932 0.936079282 0.959644901 0.942259798 0.845115021 0.917050679 0.932969415 0.918980959 1 23.54231985 2.986051426 24.86361239 0.916886131 0.953677054 0.112409442 0.038142286 1052.521862 1876145.506 0.010972997 0.012095189 968.3925201 -2.986051426 0.036790923 KLLEGEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KLLEGEEER 9 1 P20700;E9PBF6;P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8;Q03252 P20700;P02545;P02545-2;Q03252 LMNB1;LMNA;LMNB2 Lamin-B1;Prelamin-A/C;Lamin-A/C;Lamin-B2 0 ;;;;;;; 175.15 8.68E-05 11417850000 14157160 13197110 14821440 12435030 17327820 17896670 16171260 15016380 15178140 13317620 FALSE TRUE 14716095.61 15463610.98 15207698.9 14894641.82 14382443.35 13740439.62 14903714.39 14815109.99 14631881.71 15926952.66 0.923974342 0.970908329 0.954840466 0.935184661 0.903025435 0.862716171 0.935754297 0.930191124 0.918686834 1 23.92496692 -1.74380641 2.464006312 1.017117888 0.926711924 0.391110449 0.027638011 7341057.36 5282897.862 766693.5911 0.008416992 0.018038216 1.74380641 -0.090405964 KLLEPVDHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLLEPVDHGK 10 1 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 107.06 0.0015155 322860000 772960 677930 714390 542520 919580 879170 878700 680980 728090 662120 FALSE TRUE 803477.0577 794359.2039 733007.5903 649828.8367 763270.1201 674996.0915 809825.1979 671852.577 701886.1831 791849.7369 1.014683746 1.00316912 0.925690262 0.820646654 0.963907778 0.85242952 1.022700596 0.848459683 0.886388099 1 19.59486716 4.215669232 4.354325817 0.907587771 1.011448162 0.260986958 0.062918529 0.219449983 9.527116048 0.014683067 0.037436183 16431.19813 -4.215669232 0.103860391 KLLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLLYEK 6 1 H7C4X7;P05408-2;P05408 REV__J3KTF2 SCG5 Neuroendocrine protein 7B2;N-terminal peptide;C-terminal peptide 0 ; 91.906 0.075939 2140200000 1486530 1215420 1509530 1241990 2049970 1830070 1892580 1545960 1601630 1369840 FALSE TRUE 1545219.352 1424158.93 1548869.592 1487651.915 1701516.832 1405063.977 1744234.634 1525238.935 1543987.649 1638233.921 0.943222657 0.869325749 0.945450813 0.90808272 1.038628739 0.857669933 1.06470426 0.931026342 0.942470809 1 20.64370994 KLNCQVIGASVDSHFCHLAWVNTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLNCQVIGASVDSHFCHLAWVNTPK 25 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 184.45 7.65E-18 3184460000 1652090 1895700 2481670 1943690 2885390 3122000 2703840 2519740 2726580 1985520 FALSE TRUE 1717315.789 2221271.729 2546344.359 2328146.081 2394932.438 2396962.814 2491905.956 2485967.007 2628450.918 2374544.629 0.723218999 0.935451666 1.072350601 0.980460023 1.008585987 1.009441046 1.049424772 1.046923682 1.106928413 1 21.17921944 4.670160793 2.510486739 1.033746135 0.679887449 0.871183123 0.036280176 0.136957693 1.208641032 0.00909575 0.096504074 46790.83478 -4.670160793 -0.353858686 KLNCYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLNCYK 6 1 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 104.04 0.054791 738420000 829120 562890 644830 651770 1033290 931520 939420 760650 772310 543600 FALSE TRUE 861854.2978 659561.9788 661634.7995 780688.1607 857651.7349 715188.5973 865785.8057 750454.7309 744514.714 650108.0121 1.325709392 1.014542148 1.017730573 1.200859159 1.319244985 1.100107342 1.331756861 1.154353918 1.145216949 1 19.31031991 4.790079779 21.5288004 1.158026434 1.32571443 0.181066918 0.112598201 14384.11638 6009829.458 0.026977896 18.35083418 61670.82793 -4.790079779 0.167687996 KLNELESDLTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLNELESDLTFK 12 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 105.03 0.0033259 212550000 722000 189130 355980 190480 447230 567880 406300 270850 393140 185650 FALSE TRUE 750505.1175 221611.6063 365257.1312 228156.3755 371210.0043 435998.4763 374453.1443 267219.6988 378990.9682 222024.563 3.380279674 0.99814004 1.64512037 1.027617721 1.671932147 1.963739824 1.68653927 1.20355917 1.706977656 1 17.76035977 4.747030408 24.9889883 1.4575881 3.380280643 0.752187394 0.334932831 523.8325859 1545464.187 0.077712132 0.908227423 55850.92985 -4.747030408 1.922692543 KLNS(ph)GGGLSEELGSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLNSGGGLSEELGSAR 16 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 KLNS(1)GGGLSEELGSAR 75.057 0.0036899 0 22884 27603 30538 20514 33896 35550 28918 34513 38701 31681 TRUE FALSE 23787.47799 32343.60053 31333.84537 24571.60797 28134.37003 27294.05127 26651.3316 34050.40969 37308.15857 37888.28538 0.627832 0.853657013 0.827006159 0.648527842 0.742561183 0.720382329 0.703418783 0.89870548 0.984688491 1 15.20946423 1.561933269 3.112687804 0.986271713 0.73698981 0.723921996 0.066256064 0.115817186 2.539980496 0.045469609 0.017774956 36.46979052 -1.561933269 -0.249281903 KLNTETFGVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLNTETFGVSGR 12 1 Q9BX40;Q9BX40-2 Q9BX40 LSM14B Protein LSM14 homolog B 0 91.812 0.0061102 0 125450 149040 171160 146220 182970 197740 176990 157260 168960 199980 FALSE TRUE 130402.8629 174636.4606 175620.5702 175141.8796 151868.8248 151817.8818 163117.0613 155152.1869 162879.1626 239162.2522 0.545248515 0.73020077 0.73431559 0.732314059 0.635003323 0.634790317 0.682035145 0.64873192 0.681040428 1 17.86763018 0.924559805 20.0125439 1 0.671190172 0.764613372 0.055064438 2162.114865 573561.3045 0.05224223 0.013060558 8.405427476 -0.924559805 -0.328809828 KLNTLVQISVIHPVEQSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLNTLVQISVIHPVEQSLTR 20 1 O15327;D6RJC3;E7EQN9;E9PG59;D6RE59;O15327-2 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 95.206 0.00081731 263210000 207580 326800 316440 296920 371610 383570 295110 327280 321410 375320 FALSE TRUE 215775.4187 382925.3578 324686.6864 355649.8898 308443.8649 294491.6806 271978.5071 322893.3469 309842.5169 448856.7681 0.480722213 0.853112585 0.723363686 0.792346056 0.687176594 0.656092771 0.605936072 0.719368337 0.690292625 1 18.77589562 -1.908996595 2.14897228 1.193978148 0.695684684 0.485626659 0.095596375 2961119.386 1311436.142 2895506.823 0.023189379 0.012331145 1.908996595 -0.498293463 KLNTTTMSNATANSSIRPIFGGTVYHS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLNTTTMSNATANSSIRPIFGGTVYHSPVSR 31 2 O43663-2;O43663-4;O43663;O43663-3;G3V3N7 O43663-2 PRC1 Protein regulator of cytokinesis 1 1 KLNTTTMSNATANS(0.001)S(0.004)IRPIFGGT(0.023)VYHS(0.914)PVS(0.058)R 230.34 6.76E-36 422380000 85004 75263 87341 74276 78930 104400 75534 91456 90888 97470 TRUE FALSE 88360.02356 88188.83479 89617.17821 88967.57111 65513.50679 80154.6822 69613.44771 90230.18191 87616.95863 116567.3803 0.758016722 0.75654814 0.768801512 0.763228708 0.56202264 0.68762532 0.597194923 0.774060305 0.751642169 1 16.8308046 0.63838111 1.440768192 0.99945318 0.70377671 0.608514018 0.070132634 0.925764443 2.766559187 0.069683408 0.020395494 4.348916904 -0.63838111 -0.295676471 KLNVTEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 ;;;;; 215.06 1.05E-06 6869460000 8874110 5388820 6948230 5944170 10745080 9803840 11077590 8173700 8886480 5519830 FALSE TRUE 9224466.715 6314307.916 7129306.582 7119909.084 8918635.14 7527046.739 10209299.55 8064144.921 8566657.321 6601335.005 1.397363822 0.956519842 1.079979516 1.07855594 1.351035076 1.140230989 1.546550742 1.221593044 1.297715888 1 22.65432638 3.246124428 24.89853528 1.281155318 1.11241117 0.116434517 0.169040219 266.9375261 878698.0711 0.044145168 0.058629446 1762.480937 -3.246124428 -0.168744148 KLNVTEQEKIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLNVTEQEKIDK 12 2 P06733;K7EM90;A0A2R8YEM5;A0A2R8Y879 P06733 ENO1 Alpha-enolase;Enolase 0 ; 207.39 4.44E-08 4933600000 7647300 3108000 5051100 2740700 8706500 5519600 5420400 4485000 5744500 2931400 FALSE TRUE 7949221.309 3641774.823 5182735.816 3282802.28 7226572.24 4237756.55 4995534.884 4424885.911 5537756.567 3505751.705 2.267479838 1.038799986 1.47835222 0.936404673 2.061347422 1.208801109 1.424953991 1.262178923 1.579620302 1 21.74129239 7.999997584 0.034796899 1.73E-07 3.583910917 0.137673341 0.392136552 2383.935957 6.33879845 193.4161922 540.5995244 99999443.69 -7.999997584 3.583910744 KLPDFLTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLPDFLTAK 9 1 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7;Q9BZZ5-3 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 97.915 0.0086303 0 169330 103150 160950 120390 222950 206260 190070 157030 166010 125410 FALSE TRUE 176015.2792 120865.2101 165144.4892 144202.7827 185053.0386 158359.2409 175171.8167 154925.2697 160035.3325 149981.6884 1.173578462 0.805866445 1.101097681 0.961469258 1.233837548 1.055857169 1.167954693 1.032961233 1.067032477 1 17.19442684 KLPEEEAECYFHSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLPEEEAECYFHSRPK 16 2 J3QQZ9;Q9NVS9-3;Q9NVS9;J3QQV6 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 103.5 0.00086138 247080000 332570 208830 306180 223290 388590 309270 319230 296170 321380 226670 FALSE TRUE 345700.1204 244694.928 314159.3023 267456.0955 322537.6106 237446.7295 294207.9184 292200.3256 309813.5966 271081.6466 1.275261991 0.902661361 1.158910263 0.986625612 1.189817218 0.875923296 1.085311094 1.077905233 1.142879278 1 18.04836791 4.768611502 23.67914336 1.052767835 1.275262733 0.316529237 0.100411635 6970.179181 5492086.385 0.021741617 2.442224494 58696.40491 -4.768611502 0.222494898 KLPEEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLPEEHAR 8 1 P41743;E9PBE1;Q05513-2;Q05513-3;Q05513 P41743;Q05513 PRKCI;PRKCZ Protein kinase C iota type;Protein kinase C zeta type 0 ; 126.07 0.00080171 51856000 379090 321300 391040 337370 485650 476090 452230 407450 406970 367620 FALSE TRUE 394056.7659 376480.7756 401230.8236 404100.7791 403099.3865 365525.3127 416783.0309 401988.7992 392323.2292 439648.1005 0.896300395 0.856322989 0.912618122 0.919145968 0.916868254 0.831404281 0.947992339 0.914342172 0.892357385 1 18.74598971 -4.999999985 0.214885868 1.496561538 0.886170459 0.485997755 0.031448566 126.6141816 1.265030971 27.11750093 0.062416631 1.00E-05 4.999999985 -0.610391079 KLPEELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLPEELGR 8 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 140.83 0.0010313 949570000 1611640 1373110 1566320 1314550 1877240 1809000 2042310 1767760 1819460 1384140 FALSE TRUE 1675268.792 1608930.961 1607139.586 1574564.066 1558147.415 1388887.166 1882228.406 1744066.069 1753977.99 1655335.732 1.012041702 0.97196655 0.970884368 0.951205267 0.941287852 0.83903654 1.137067466 1.053602623 1.059590484 1 20.65869242 2.225754704 24.99999942 1.068094416 0.949755026 0.540033823 0.051796063 173.1700153 338064.2027 0.019274846 0.014326362 168.1723929 -2.225754704 -0.11833939 KLPEYNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLPEYNPR 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 104.2 0.0074175 606800000 562390 700840 694540 638920 893750 941310 773190 808680 777140 792120 FALSE TRUE 584593.5915 821203.8182 712640.283 765296.469 741830.6942 722705.0182 712585.3474 797840.9673 749170.8832 947320.7479 0.617102067 0.866869875 0.752269265 0.807853592 0.783082917 0.762893687 0.752211275 0.842207847 0.790831284 1 19.85349346 -5 0.20118255 2.013014469 0.74510051 0.571379343 0.060718735 97.71139227 0.968051999 39.70985805 0.131514318 1.00E-05 5 -1.267913959 KLPIDVTEGEVISLGLPFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLPIDVTEGEVISLGLPFGK 20 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;K7ES59;K7EKJ7;K7ELW5 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 150.98 1.30E-07 515160000 1947200 1508100 1964500 1526700 2253100 2460900 2206400 1870000 2084000 1544900 FALSE TRUE 2024076.96 1767104.444 2015696.484 1828676.703 1870118.867 1889393.27 2033456.603 1844935.709 2008997.247 1847593.576 1.095520674 0.956435694 1.090984787 0.989761345 1.012191691 1.022623858 1.100597355 0.998561444 1.087358861 1 20.817216 KLPIQEFHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLPIQEFHLSR 11 1 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 ; 118.76 0.00043982 483600000 76434 344690 336480 348340 384330 485560 338870 399580 332200 468170 FALSE TRUE 79451.67334 403887.8262 345248.9452 417240.6123 319001.7239 372796.0487 312308.4839 394224.2837 320244.1869 559898.9478 0.141903595 0.72135843 0.616627244 0.745206995 0.569748747 0.665827379 0.557794375 0.70409899 0.571967831 1 19.09480694 -5 0.122696911 2.20787236 0.428184917 0.416298267 0.155811596 156.5284145 1.236978443 47.60319882 1.333841749 1.00E-05 5 -1.779687443 KLPVESIQIVLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLPVESIQIVLEELR 15 1 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 ; 181.72 9.24E-07 260230000 428230 384410 476910 408410 574000 589730 513910 423620 509770 470360 FALSE TRUE 445136.8511 450429.4272 489338.6664 489192.279 476431.685 452774.1449 473628.3913 417942.0668 491423.4773 562518.0364 0.791329028 0.800737751 0.869907514 0.869647278 0.846962505 0.804906004 0.841979031 0.742984295 0.873613725 1 19.10153983 0.984731835 24.57323698 1.000000003 0.820340121 0.685248521 0.036760234 427.5737445 688156.9043 0.038247722 0.009561931 9.654545535 -0.984731835 -0.179659882 KLPVESIQIVLEELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLPVESIQIVLEELRK 16 2 K7ENE3;Q9BRG1;K7EKV4 K7ENE3 VPS25 Vacuolar protein-sorting-associated protein 25 0 ; 202.03 1.77E-11 118738000 205325 156134 214997 141066 254274 236706 237539 191732 227965 162153 FALSE TRUE 213431.3895 182948.7999 220599.9984 168968.4338 211052.5963 181734.6188 218920.0725 189162.1462 219760.5842 193923.7757 1.100594235 0.943405723 1.137560351 0.871313655 1.088327594 0.937144598 1.128897535 0.97544587 1.133231773 1 17.56513017 2.240710041 24.99997543 1.051127771 1.012529368 0.057021116 0.089815017 206.1783867 2398081.573 0.029170633 0.02326713 174.0644333 -2.240710041 -0.038598403 KLQDSVLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLQDSVLER 9 1 Q9H4A5;Q5T5I6;Q9H4A5-2 Q9H4A5 GOLPH3L Golgi phosphoprotein 3-like 0 128.03 0.00068734 233940000 508790 429860 541450 446750 644560 582710 569610 529660 531080 524640 FALSE TRUE 528877.4221 503685.1112 555560.6318 535115.8166 534997.9214 447384.4336 524962.4798 522560.774 511966.5345 627433.1632 0.842922327 0.802770942 0.8854499 0.852865051 0.85267715 0.713039189 0.836682711 0.832854884 0.815969835 1 19.25910226 -1.763056083 2.499387976 1.044395723 0.826379428 0.591145009 0.04337726 9173760.377 6366351.154 2498196.76 0.010703352 0.01725615 1.763056083 -0.218016295 KLQELSSK ddPTM_MDA-MB-175_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 ; 147.4 0.00086235 8274500000 9819300 6377100 8778900 7378900 11663400 10823700 10436200 8054400 8892500 6576100 FALSE TRUE 10206973.55 7472317.318 9007685.346 8838424.396 9680859.434 8310059.71 9618183.374 7946443.942 8572460.662 7864560.888 1.297844049 0.950125179 1.145351339 1.123829356 1.230947229 1.056646369 1.2229778 1.01041165 1.090011354 1 22.90693479 1.669842212 9.743530324 1.038352905 1.137901187 0.228665996 0.0941265 0.183252415 26.10207467 0.041979875 0.022513769 46.75652348 -1.669842212 0.099548282 KLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNK 39 3 P29692;P29692-2;E9PRY8;P29692-4;E9PQZ1;H0YE72;P29692-3 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 86.194 0.00032541 225810000 567710 152760 274110 193590 441740 369300 504510 285270 333800 86814 FALSE TRUE 590123.6292 178995.3417 281253.5318 231881.5242 366653.1926 283535.6718 464965.1879 281446.4223 321786.6032 103823.5411 5.683909667 1.724034258 2.708957224 2.233419527 3.531503439 2.730938173 4.478417734 2.710815092 3.0993607 1 16.66377407 4.75298643 24.75321438 2.83387711 5.683911931 0.488228484 0.908759056 1941.338261 3331071.813 0.205563191 4.473469682 56622.15972 -4.75298643 2.850034821 KLQLERPVS(ph)PETQADLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLQLERPVSPETQADLQR 18 2 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 KLQLERPVS(0.998)PET(0.002)QADLQR 111.11 0.00024742 150450000 177470 187220 200580 128940 233440 241080 167140 205470 208910 246540 TRUE FALSE 184476.6526 219373.5786 205807.2796 154443.9472 193759.9522 185092.8236 154039.1301 202716.0107 201391.3699 294844.7927 0.625673769 0.744030704 0.698019041 0.523814396 0.657159146 0.627763583 0.522441413 0.687534648 0.683041976 1 18.16959619 0.56946059 1.591632588 0.999817181 0.633919932 0.730468149 0.066123272 1.038913801 3.237550967 0.064112437 0.018361165 3.71074055 -0.56946059 -0.365897249 KLS(ph)DASDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.802)DAS(0.198)DER;KLS(1)DASDER;KLS(0.989)DAS(0.011)DER 132.79 0.00018079 1230210000 3960230 2367170 2817070 2767660 3683640 4053380 4533420 3165290 3261440 1666510 TRUE FALSE 4116582.938 2773713.033 2890485.158 3315094.887 3057496.189 3112043.925 4178078.695 3122864.465 3144061.411 1993030.727 2.065488947 1.391706106 1.450296335 1.663343591 1.534093854 1.561463093 2.096344345 1.566892282 1.577527817 1 20.92653252 0.664815709 2.26719412 1.000243202 1.657657609 0.43906461 0.224613881 1.880298791 11.51654155 0.209258724 0.056632903 4.621848533 -0.664815709 0.657414407 KLS(ph)DASDERGEPDLASGSDVNGSTESFEMVIEEATIDSATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSDASDERGEPDLASGSDVNGSTESFEMVIEEATIDSATK 41 2 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.723)DAS(0.276)DERGEPDLASGSDVNGSTESFEMVIEEATIDSATK 151.89 6.35E-14 74209000 57140 22745 35272 24893 56963 44870 47985 38461 48384 22176 TRUE FALSE 59395.93132 26651.27682 36191.2173 29816.7611 47280.44961 34449.62251 44223.81031 37945.4932 46642.66929 26520.96261 2.239584294 1.00491363 1.364626836 1.12427145 1.782757673 1.298958225 1.667503965 1.430773602 1.758709515 1 14.69484552 3.238688038 25 1.508784372 1.397837861 0.00030708 0.375573998 18.58695617 3645981.526 0.099048178 0.126037796 1732.559022 -3.238688038 -0.11094651 KLS(ph)FTESLTSGASLLTLNK ddPTM_MDA-MB-175_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(0.635)FT(0.327)ES(0.038)LTSGASLLTLNK;KLS(0.768)FT(0.212)ES(0.02)LTSGASLLTLNK;KLS(0.477)FT(0.477)ES(0.044)LT(0.002)SGASLLTLNK 240.49 1.55E-24 1411740000 2631200 1529010 2044190 1512040 2759960 2548960 2442500 2123750 2345520 1555470 TRUE FALSE 2735081.808 1791605.573 2097463.271 1811116.999 2290822.985 1957002.67 2251050.468 2095284.605 2261105.193 1860234.565 1.470288672 0.963107345 1.127526232 0.973596036 1.23146996 1.052019303 1.210089582 1.126355054 1.215494667 1 20.82705312 2.22035277 24.96499381 1.148339249 1.12498733 0 0.146914125 2418.470778 3315973.273 0.051347754 0.037995228 166.0935509 -2.22035277 -0.023351919 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK;KLS(1)GDQITLPTTVDYSSVPK 284.9 3.05E-45 19236260000 6064770 2745537 4235530 3140142 5765980 5325570 5289500 4000660 4501130 2368567 TRUE FALSE 6304211.803 3217061.622 4345911.391 3761252.715 4785880.779 4088787.077 4874895.168 3947037.696 4339135.211 2832642.355 2.225558688 1.135710485 1.534225238 1.327824781 1.68954643 1.443453343 1.720970937 1.393411946 1.531833062 1 21.43371703 -2.789814435 0.319154994 6.09E-12 1.566302129 0.27463126 0.274698079 84.98128066 2.733869826 58.13599922 0.228400596 0.001622503 2.789814435 1.566302129 KLS(ph)GDQPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 162.94 4.05E-06 17179820000 11443310 8140800 9666040 7740850 11689120 11694780 11500090 10050640 10169640 7250770 TRUE FALSE 11895100.71 9538919.073 9917944.943 9271967.026 9702207.558 8978844.581 10598682.9 9915927.61 9803636.643 8671419.557 1.371759334 1.100041234 1.143751018 1.069255958 1.118871886 1.035452676 1.222254652 1.143518376 1.130568828 1 23.04783676 4.74077172 24.86395384 1.116195683 1.371759429 0.637326183 0.059542637 115.5276088 1299019.083 0.013669503 0.090591126 55051.82491 -4.74077172 0.255563746 KLS(ph)LGQYDNDAGGQLPFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSLGQYDNDAGGQLPFSK 19 1 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 KLS(1)LGQYDNDAGGQLPFSK 126.68 1.53E-05 249260000 267380 189890 232670 187930 333440 289240 277770 248420 270830 182550 TRUE FALSE 277936.3689 222502.1304 238733.5713 225101.9931 276761.9879 222068.3935 255997.6616 245090.3362 261082.8812 218317.1774 1.273085207 1.019169142 1.093517121 1.031077791 1.267705964 1.017182414 1.172595142 1.12263423 1.195887948 1 17.73606612 5.841415572 12.96131406 1.12033407 1.117444088 0 0.098760828 0 0 0.019657092 0 694089.6554 -5.841415572 -0.002889981 KLS(ph)LPTDLKPDLDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSLPTDLKPDLDVK 15 2 H0Y332;Q5T5C0-2;Q5T5C0;Q5JRH0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 KLS(0.998)LPT(0.002)DLKPDLDVK;KLS(0.995)LPT(0.005)DLKPDLDVK 139 5.59E-06 2037470000 3567300 966620 1622670 996920 2742100 2357150 2729200 1656790 2055130 664960 TRUE FALSE 3708139.759 1132629.466 1664958.113 1194107.8 2275998.821 1809737.635 2515278.173 1634583.44 1981166.273 795246.1806 4.662882827 1.424250117 2.093638616 1.501557417 2.862005348 2.275694847 3.16289249 2.055443308 2.491261601 1 19.60104201 -0.138140864 1.160191048 0.990128806 2.442712046 0.202846366 0.886095568 27.85259362 26.04199339 2.017286445 0.240480822 0.727543787 0.138140864 1.45258324 KLS(ph)LQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;KLS(1)LQER 97.813 0.0071795 1494090000 955120 752140 969280 756830 1260490 1160280 1089970 878640 1082270 867320 TRUE FALSE 992828.8751 881314.1942 994540.2331 906528.7151 1046232.36 890822.5542 1004535.303 866863.268 1043319.314 1037254.748 0.957169757 0.849660313 0.958819649 0.873969212 1.008655166 0.858827164 0.968455729 0.835728416 1.005846747 1 19.98433883 1.199353579 24.99850983 1.002923813 0.912189486 0.29152702 0.055453343 204.5011741 130386.0042 0.047745567 0.011937141 15.82535931 -1.199353579 -0.090734327 KLS(ph)MGSDDAAYTQALLVHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSMGSDDAAYTQALLVHQK 20 1 A0A1B0GV57;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 KLS(0.981)MGS(0.019)DDAAYTQALLVHQK 238.63 7.52E-30 334610000 301870 187090 258710 159880 403070 296790 295400 292120 375110 221640 TRUE FALSE 313788.0607 219221.2521 265452.1951 191503.7868 334556.3054 227865.0204 272245.7761 288204.6092 361609.8644 265066.1144 1.183810542 0.82704367 1.001456545 0.72247555 1.262161729 0.859653528 1.027086305 1.087293296 1.364225167 1 18.01599273 1.608626707 3.176404104 1.190960854 0.973122201 0.172850195 0.172303553 0.298232281 7.072597505 0.10253352 0.042482685 40.60941257 -1.608626707 -0.217838653 KLS(ph)PIIEDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSPIIEDSR 10 1 O60566-3;O60566 O60566-3 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 KLS(1)PIIEDSR 97.767 0.0035738 160610000 296640 210210 277150 239120 337610 353910 329070 263150 298720 232730 TRUE FALSE 308351.5763 246311.9323 284372.7567 286417.2223 280223.1728 271719.7661 303276.6335 259622.9047 287969.1256 278328.9876 1.107867272 0.884966867 1.021714479 1.02905998 1.006805562 0.976253923 1.08963366 0.932791467 1.034635767 1 18.08643165 5.104968974 17.24118189 0.997796542 8.211577518 0.276001236 0.053709359 143.3502815 23563.50734 0.011599557 31.10768463 127341.2105 -5.104968974 7.213780976 KLS(ph)PPPLPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLSPPPLPPR 10 1 F5GWN5;O00750 F5GWN5 PIK3C2B Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta 1 KLS(1)PPPLPPR;KLS(1)PPPLPPR;KLS(1)PPPLPPR 99.531 0.0028371 1527190000 1455649 1114133 1296210 1073545 1619846 1636238 1373860 1242386 1435224 1247572 TRUE FALSE 1513119.147 1305476.676 1329990.297 1285888.997 1344505.156 1256246.522 1266173.263 1225733.848 1383570.569 1492009.847 1.014148231 0.874978592 0.891408525 0.861850208 0.901136918 0.841982728 0.848635996 0.821532009 0.927319998 1 20.50882563 4.738677581 8.62033976 0.874356788 1.014929852 0.362785646 0.049250166 0.079403471 97.75649133 0.010986019 0.064636865 54787.00772 -4.738677581 0.140573064 KLS(ph)PQDPSEDVSSVDPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLSPQDPSEDVSSVDPLK 18 1 Q53T59;H7BZZ1;H7C0Y9;F8WDN8 Q53T59 HS1BP3 HCLS1-binding protein 3 1 KLS(0.999)PQDPS(0.001)EDVSSVDPLK;KLS(0.999)PQDPS(0.001)EDVSSVDPLK;KLS(1)PQDPSEDVSSVDPLK;KLS(0.998)PQDPS(0.002)EDVSSVDPLK 220.52 4.13E-19 2135430000 2939600 1181293 1904417 1360361 2325620 2363340 2932230 2002969 2247370 867882 TRUE FALSE 3055657.678 1384170.884 1954047.672 1629436.346 1930311.943 1814490.102 2702394.151 1976122.477 2166487.593 1037926.861 2.944000962 1.333591928 1.882644861 1.56989515 1.859776459 1.748186861 2.603646029 1.903913031 2.08732202 1 19.98527336 KLS(ph)PTEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLSPTEPK 8 1 O14828;O14828-2 O14828 SCAMP3 Secretory carrier-associated membrane protein 3 1 KLS(0.984)PT(0.016)EPK;KLS(0.728)PT(0.272)EPK;KLS(0.818)PT(0.182)EPK;KLS(0.99)PT(0.01)EPK;KLS(0.68)PT(0.32)EPK;KLS(0.992)PT(0.008)EPK 139.86 0.00040356 10657710000 9841140 4196945 6508403 4501225 9189654 9222080 8822335 6300837 6896635 3307018 TRUE FALSE 10229675.81 4917737.656 6678017.329 5391553.87 7627599.896 7080391.682 8130817.33 6216384.586 6648426.454 3954964.86 2.586540252 1.24343397 1.688514959 1.363236858 1.928613822 1.790254005 2.055850713 1.571792622 1.681033002 1 21.91523345 0.495024315 1.328622687 1.000471119 1.759565221 0.300104608 0.355032996 2.725330229 5.883638306 0.315724908 0.093580703 3.126254391 -0.495024315 0.759094102 KLS(ph)QRPTVAELLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSQRPTVAELLAR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 KLS(0.992)QRPT(0.008)VAELLAR;KLS(1)QRPTVAELLAR 74.519 0.025846 584460000 554610 545390 620120 520480 737810 714490 654630 627200 667230 546030 TRUE FALSE 576506.4311 639056.49 636280.8366 623429.3905 612397.3197 548560.5257 603318.39 618793.4099 643216.5226 653014.1241 0.882839145 0.978625831 0.974375305 0.954695109 0.937801032 0.840043891 0.923897919 0.947595752 0.984996341 1 19.31675467 1.270148957 2.537812858 0.99860699 0.929689721 0.301964401 0.039216911 0.379106154 4.058705035 0.037723034 0.010959634 18.62725914 -1.270148957 -0.068917269 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_MDA-MB-175_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(0.747)S(0.199)S(0.053)DAPAQDTGSSAAAVETDASR;KLS(0.61)S(0.14)S(0.25)DAPAQDTGSSAAAVETDASR;KLS(0.7)S(0.15)S(0.15)DAPAQDTGSSAAAVETDASR;KLS(0.658)S(0.171)S(0.171)DAPAQDTGSSAAAVETDASR 283.71 1.15E-53 3883200000 1503810 727782 975400 797809 1439360 1483800 1348160 1172410 1202420 861786 TRUE FALSE 1563181.58 852772.8971 1000819.725 955613.239 1194698.101 1139209.937 1242487.696 1156695.762 1159145.139 1030636.467 1.516714797 0.827423563 0.971069584 0.927206896 1.159184775 1.10534604 1.205553788 1.122312085 1.124688653 1 19.97510411 3.191012984 24.9999173 1.130487003 1.037551643 0.01712561 0.177359809 361.7264575 190189.6917 0.049095697 0.058680716 1552.433423 -3.191012984 -0.09293536 KLS(ph)VPTS(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.919)VPT(0.313)S(0.767)DEEDEVPAPKPR 86.182 0.0015647 134820000 137830 72889 89257 69411 147940 134540 113460 93698 111120 55659 TRUE FALSE 143271.6348 85407.11875 91583.11075 83140.28863 122793.2116 103295.124 104566.7087 92442.13157 107120.8129 66564.31539 2.152379003 1.283076649 1.375858975 1.249021914 1.844730332 1.551809304 1.570912404 1.3887641 1.609282876 1 16.02246135 -2.710010842 0.365884544 3.99E-11 1.554777634 0.292658317 0.259477867 100.4370605 3.728939185 79.09760113 0.179222116 0.001949796 2.710010842 1.554777634 KLSAS(ph)SPR ddPTM_MDA-MB-175_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(0.048)AS(0.476)S(0.476)PR 75.294 0.023742 215380000 583440 523300 630500 456200 763780 696290 629570 603750 640690 566590 TRUE FALSE 606474.6617 613172.7043 646931.348 546434.9984 633952.9484 534587.1999 580222.6583 595657.7188 617631.6921 677602.4625 0.895030191 0.904915106 0.954735828 0.806424163 0.935582415 0.788939281 0.856287706 0.879066638 0.911495643 1 19.37007959 0.853534675 2.539644078 0.999887118 0.87673564 0.365219464 0.048742161 0.592766558 7.275108922 0.045070836 0.012060478 7.137311885 -0.853534675 -0.123151478 KLSASS(ph)PR ddPTM_MDA-MB-175_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(0.035)AS(0.166)S(0.799)PR 80.706 0.015163 224110000 607920 561590 675940 558840 807970 735850 675700 658330 693210 639290 TRUE FALSE 631921.151 658038.7139 693555.5517 669376.884 670631.548 564959.9894 622736.8684 649506.1632 668261.5075 764546.6356 0.82653055 0.8606914 0.907146169 0.875521326 0.877162382 0.738947715 0.814517832 0.849531125 0.874062453 1 19.54424498 0.755973309 2.389306945 0.999939344 0.843942559 0.540345379 0.043119849 0.928681844 7.754977563 0.044374366 0.011941635 5.701292322 -0.755973309 -0.155996785 KLSCS(ph)LEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KLSCSLEDLR 10 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLS(0.082)CS(0.918)LEDLR;KLS(0.21)CS(0.79)LEDLR;KLS(0.156)CS(0.844)LEDLR;KLS(0.092)CS(0.908)LEDLR;KLS(0.311)CS(0.689)LEDLR 138.02 8.03E-05 5278800000 15807210 13108650 14475230 13403790 18390210 18444660 17386510 16079780 15888450 11742790 TRUE FALSE 16431290.86 15359958.67 14852466.39 16055019.66 15264248.67 14161167.25 16023709.92 15864256.85 15316627.79 14043564.87 1.170022783 1.093736441 1.057599443 1.143229643 1.086921221 1.008374111 1.141000171 1.129645998 1.09065098 1 23.74340587 -2.615065529 1.608587138 1.76E-05 1.102472902 0.322877654 0.044466787 636110.2456 33459.05894 2308932.398 0.012613867 0.002426244 2.615065529 1.102455264 KLSCS(ph)LEDLRSESVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSCSLEDLRSESVDK 16 2 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 KLSCS(1)LEDLRSESVDK;KLSCS(1)LEDLRSESVDK 184.35 9.59E-10 826230000 1652610 981790 1368800 579980 2077110 1644270 1002220 1176630 1544910 1169480 TRUE FALSE 1717856.319 1150404.795 1404472.052 694698.3129 1724043.584 1262413.212 923663.3776 1160859.199 1489308.991 1398617.215 1.228253378 0.822530127 1.004186161 0.496703677 1.232677223 0.902615239 0.660411847 0.830004941 1.064843886 1 20.41556974 4.743952865 23.99632803 0.874815637 1.22825364 0.204473674 0.19774624 493.5873771 2196415.884 0.044891363 0.380639041 55456.55214 -4.743952865 0.353438003 KLSDAS(ph)DER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSDASDER 9 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 KLS(0.148)DAS(0.852)DER 61.213 0.096022 399270000 806880 477880 593780 605840 774270 879710 947230 693470 686580 425190 TRUE FALSE 838736.2454 559952.1726 609254.3946 725673.3437 642659.862 675410.6846 872983.6375 684175.1689 661870.1199 508497.8397 1.649439152 1.101188892 1.198145492 1.427092284 1.263839906 1.32824691 1.716789275 1.345482941 1.301618352 1 18.95588212 2.452084428 24.9998505 1.397425505 1.311881289 0 0.214166119 933.4819412 932097.4956 0.071115058 0.059501415 283.1942477 -2.452084428 -0.085544216 KLSEEEILENPDLFLTSEATDYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSEEEILENPDLFLTSEATDYGR 24 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 103.84 0.0050636 48965000 27383 27581 26434 28283 36118 29331 26574 23294 27631 24430.9 FALSE TRUE 28464.10198 32317.8222 27122.89176 33877.29298 29978.67526 22519.31977 24491.06044 22981.78203 26636.56571 29217.6671 0.97420858 1.106105497 0.928304497 1.159479738 1.026046165 0.770743252 0.838227787 0.786571425 0.911659566 1 14.83455337 2.797864852 7.45497555 0.841567916 1.04391558 0.509502072 0.085888602 0.194928847 21.80233852 0.024602667 0.026058749 627.8629443 -2.797864852 0.202347664 KLSELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSELLR 7 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 182.39 0.0010551 9501500000 7861300 7577600 7720600 6675500 12601700 10781000 9710700 8434400 8346800 11241200 FALSE TRUE 8171670.194 8878993.854 7921805.179 7995893.976 10459667.54 8277276.138 8949549.96 8321350.664 8046400.298 13443697.91 0.607843932 0.660457704 0.589257898 0.594768941 0.778035002 0.615699355 0.66570597 0.618977808 0.598525819 1 23.68042669 -1.492792235 2.989574699 1.011000495 0.638112212 0.806812063 0.053344373 13540194.36 15592137.72 1227749.08 0.012376487 0.032151983 1.492792235 -0.372888283 KLSEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSEQR 6 1 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 124.89 0.02912 241310000 336360 327340 362690 349410 445980 458790 420450 379800 422730 380640 FALSE TRUE 349639.7525 383558.0986 372141.9994 418522.2551 370172.4789 352242.9755 387494.0304 374709.4022 407516.0299 455219.1202 0.768069128 0.842579061 0.81750081 0.919386371 0.813174277 0.773787743 0.851225296 0.823140737 0.895208509 1 18.79620163 0.926955681 2.42422422 0.999901867 0.827690551 0.642945775 0.04011445 0.222585312 2.891226377 0.037629844 0.010172175 8.451925909 -0.926955681 -0.172211316 KLSFLS(ph)WGTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSFLSWGTNK 11 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 KLSFLS(1)WGTNK;KLSFLS(0.972)WGT(0.028)NK 188.39 1.94E-06 515800000 1727580 1198130 1594760 1184040 2321200 1788330 1690130 1497430 1705900 1300350 TRUE FALSE 1795786.192 1403899.507 1636320.756 1418239.578 1926643.253 1373017.46 1557653.194 1477359.4 1644504.992 1555128.686 1.154750863 0.902754557 1.052209229 0.911975704 1.23889635 0.882896362 1.001623344 0.949991736 1.057471968 1 20.56860254 KLSFT(ph)ESLTSGASLLTLNK ddPTM_MDA-MB-175_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(0.337)FT(0.445)ES(0.156)LT(0.031)S(0.031)GASLLTLNK 97.509 0.00064754 52924000 82156 50324 66292 51724 96447 85470 79748 72829 82529 50031 TRUE FALSE 85399.58232 58966.75553 68019.62398 61954.85282 80052.97339 65620.88781 73497.14338 71852.84638 79558.79741 59833.61655 1.427284313 0.985512141 1.136812847 1.035452249 1.33792637 1.096722739 1.228358699 1.200877542 1.3296672 1 15.86866865 3.2563745 24.99285845 1.205550616 1.1341079 0.027473666 0.143296298 781.8687149 1096954.083 0.036863856 0.049806576 1804.573188 -3.2563745 -0.071442715 KLSLS(ph)EGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSLSEGK 8 1 K7EMM8;Q49A26-4;Q49A26-2;Q49A26-3;Q49A26;K7EPU6 K7EMM8 GLYR1 Putative oxidoreductase GLYR1 1 KLS(0.079)LS(0.921)EGK 125.97 0.00075901 183230000 475840 259980 381800 279010 610270 504010 513540 389220 464310 249570 TRUE FALSE 494626.5306 304629.5426 391750.0217 334197.3452 506536.5234 386961.3158 473287.3929 384003.1425 447599.5738 298468.4632 1.65721539 1.020642313 1.312534053 1.119707394 1.697119079 1.296489792 1.585719938 1.286578617 1.4996545 1 18.18721898 5.069976027 10.99024102 1.337585208 3.535253713 0.172912742 0.219979023 88400.37925 519609.5441 0.049233279 4044037.503 117483.2701 -5.069976027 2.197668506 KLSPFVLSAGSGS(ph)PSATSILQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSPFVLSAGSGSPSATSILQK 22 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-4 SYNRG Synergin gamma 1 KLSPFVLSAGS(0.001)GS(0.995)PS(0.004)ATSILQK;KLSPFVLSAGS(0.003)GS(0.991)PS(0.006)ATSILQK 237.67 9.64E-31 564760000 505350 461630 610970 404060 850570 724780 544440 634310 681340 644980 TRUE FALSE 525301.6082 540911.3615 626892.3801 483981.862 705990.4152 556460.8291 501765.3702 625808.112 656818.7065 771351.4821 0.681014583 0.701251471 0.812719486 0.627446596 0.915264223 0.721410203 0.650501596 0.811313813 0.851516749 1 19.55702888 1.019586825 1.623642075 0.996976597 0.735759684 0.517231932 0.080208515 0.296061892 1.595553514 0.072307921 0.021071194 10.46132813 -1.019586825 -0.261216913 KLSS(ph)IGIQVDCIQPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSSIGIQVDCIQPVPK 17 1 Q9Y2H0-3;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 KLS(0.409)S(0.591)IGIQVDCIQPVPK;KLS(0.335)S(0.665)IGIQVDCIQPVPK 105.92 0.00047655 627450000 924580 504980 649340 546470 976630 956330 890440 776570 729460 498600 TRUE FALSE 961083.1323 591706.3868 666262.3338 654560.1349 810622.7814 734236.8508 820644.9861 766161.3494 703206.8771 596291.1237 1.611768303 0.992311244 1.117344041 1.097719065 1.359441302 1.231339562 1.376248871 1.284878005 1.179301266 1 19.18565734 3.242947653 24.99889921 1.263706127 1.183363112 0 0.182131083 412.4214279 2350106.521 0.048533738 0.063507724 1749.635786 -3.242947653 -0.080343016 KLSSWDQAET(ph)PGHT(ph)PSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 KLS(0.029)S(0.033)WDQAET(0.939)PGHT(0.966)PS(0.034)LR 86.856 0.0020907 284760000 237690 285040 311500 254600 363610 377520 229110 300610 296540 356260 TRUE FALSE 247074.1847 333993.4027 319617.9459 304959.1201 301803.7021 289846.7014 211151.7595 296580.8146 285867.5833 426062.326 0.579901507 0.783907382 0.750167115 0.715761759 0.708355758 0.680291788 0.4955889 0.696097253 0.670952501 1 18.70070496 -1.909165435 6.214521686 1.088097525 0.676810616 0.604182463 0.078749144 0.0481378 0.000703606 0.038185552 0.018291199 0.012326352 1.909165435 -0.411286909 KLSSWDQAET(ph)PGHTPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAET(1)PGHTPSLR;KLSSWDQAET(1)PGHTPSLR 162.65 2.67E-11 381950000 316460 311630 328180 254360 365020 356060 258070 304310 282720 339480 TRUE FALSE 328954.0852 365150.0284 336732.6404 304671.6488 302974.0308 273370.4611 237841.7991 300231.2222 272544.9624 405994.6063 0.810242501 0.899396255 0.829401759 0.75043275 0.746251369 0.673335204 0.585825022 0.739495593 0.671301929 1 18.63110104 3.641882898 1.955213821 0.710795254 0.858041803 0.165403708 0.104030413 0.442876762 3.306324134 0.028440158 0.0546438 4384.124694 -3.641882898 0.147246549 KLSSWDQAETPGHT(ph)PSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 KLSSWDQAETPGHT(0.989)PS(0.011)LR;KLSSWDQAET(0.023)PGHT(0.97)PS(0.007)LR 117.62 9.62E-05 407640000 478840 457070 509740 357870 635020 599540 467430 439260 545340 529170 TRUE FALSE 497744.9729 535568.217 523024.2432 428655.6179 527079.5272 460305.9211 430791.6152 433372.4382 525713.3199 632850.7299 0.786512442 0.846278896 0.826457517 0.677340797 0.83286548 0.72735307 0.680715996 0.684794088 0.830706666 1 19.27150573 0.957272325 8.129740015 0.999997886 0.754659465 0.588399928 0.061444718 0.507742377 95.93159021 0.064113993 0.01605444 9.063007199 -0.957272325 -0.245338421 KLSVEEFFMDLHNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSVEEFFMDLHNFR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 165.75 9.13E-07 163490000 346940 412370 421530 365610 544790 529820 422830 422440 448830 521980 FALSE TRUE 360637.4591 483191.3397 432515.4181 437926.5668 452186.7904 406777.3345 389687.4797 416777.8828 432676.696 624251.9871 0.577711351 0.774032522 0.692853891 0.701522103 0.724365801 0.651623612 0.624247079 0.667643662 0.693112245 1 19.25176898 0.791122001 6.391541197 0.999999967 0.678942316 0.782362962 0.050914013 6.583464283 201.5215741 0.047423685 0.01190997 6.181900359 -0.791122001 -0.321057652 KLSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 KLS(0.009)VPT(0.992)S(1)DEEDEVPAPKPR 86.791 0.0053306 71697000 85424 75693 88085 72571 103320 117470 103130 94521 93471 84661 TRUE FALSE 88796.60548 88692.68394 90380.56746 86925.3272 85757.7033 90189.37278 95046.40112 93254.1006 90106.99697 101248.702 0.877014754 0.875988355 0.892659023 0.858532756 0.84700052 0.890770657 0.938741922 0.921039961 0.889957058 1 16.62754389 2.38669019 4.346335441 0.929853059 0.870908139 0.552663468 0.028226007 0.176532431 6.109335366 0.00968375 0.008018645 243.6072395 -2.38669019 -0.05894492 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLSVPTSDEEDEVPAPKPR 19 2 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 KLSVPT(0.025)S(0.975)DEEDEVPAPKPR;KLSVPT(0.112)S(0.888)DEEDEVPAPKPR;KLSVPT(0.176)S(0.824)DEEDEVPAPKPR;KLSVPT(0.024)S(0.976)DEEDEVPAPKPR;KLSVPT(0.168)S(0.832)DEEDEVPAPKPR;KLSVPT(0.029)S(0.971)DEEDEVPAPKPR 183.07 1.46E-14 8348770000 2083150 1346860 2022840 1314420 2482750 2226820 2260050 1916240 2127130 1259770 TRUE FALSE 2165394.371 1578172.728 2075556.872 1574408.353 2060733.042 1709674.803 2082901.375 1890555.937 2050575.007 1506597.812 1.437274337 1.047507646 1.377644953 1.045009053 1.367805678 1.134791774 1.382519847 1.25485111 1.361063312 1 20.52286291 2.250214325 24.99327828 1.273120778 1.23036675 0 0.159671973 1245.391751 2670943.705 0.050035819 0.04154018 177.9157209 -2.250214325 -0.042754028 KLTATEGPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KLTATEGPGSPR 12 1 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 KLTAT(0.001)EGPGS(0.999)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR;KLTATEGPGS(1)PR 165.89 4.42E-05 2403590000 2789718 2590107 2843123 2516613 3267238 3503930 3101361 2929455 2932810 2797616 TRUE FALSE 2899858.221 3034937.729 2917217.121 3014391.54 2711874.052 2690195.36 2858268.221 2890190.447 2827258.741 3345755.292 0.86672753 0.907100928 0.871915866 0.900959956 0.810541661 0.8040622 0.854296854 0.863837966 0.845028549 1 21.6739005 -1.086962332 3.753410818 1.000052129 0.858584315 0.646038368 0.031470778 6565345148 13595975440 4514023.578 0.008155732 0.081853578 1.086962332 -0.141467815 KLTATPTPLGGMTGFHMQTEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLTATPTPLGGMTGFHMQTEDR 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 223.85 4.79E-26 1001050000 527430 531420 565160 535700 646880 716570 574770 546110 668820 537490 FALSE TRUE 548253.3437 622687.2511 579888.5339 641659.8611 536923.5687 550157.4772 529718.0255 538790.2887 644749.2988 642800.8746 0.852913189 0.968709402 0.902127792 0.998224935 0.835287551 0.855875433 0.824077948 0.838191592 1.003031147 1 19.29401237 3.220234741 24.98319313 0.875311936 0.931197406 0.030489004 0.071214604 497.4003127 678091.3571 0.019870355 0.023790846 1660.484175 -3.220234741 0.05588547 KLTDIINNDHENVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLTDIINNDHENVK 14 1 Q8N335;C9K0P5;C9JFA7;C9JM46 Q8N335 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein;Glycerol-3-phosphate dehydrogenase [NAD(+)] 0 ; 181.58 1.05E-06 1506240000 1287800 848440 1089030 842300 1562730 1349010 1314850 1061120 1254720 783990 FALSE TRUE 1338643.338 994152.9701 1117411.016 1008904.426 1297097.713 1035722.872 1211788.621 1046897.422 1209562.872 937597.8301 1.42773724 1.060319188 1.191780719 1.076052433 1.38342653 1.10465579 1.292439661 1.116574067 1.290065776 1 19.83860971 -1.441521095 2.847535569 0.994743948 1.204874544 0.211873855 0.123279115 11670615.61 13327382.77 492733.0673 0.026531479 0.036180862 1.441521095 0.210130596 KLTELGTVDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLTELGTVDPK 11 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 142.57 0.0025387 0 2327500 1324800 1801600 1282500 2537900 2134100 2138100 1828800 2042500 1217500 FALSE TRUE 2419391.497 1552324.094 1848551.176 1536174.672 2106508.665 1638487.618 1970510.135 1804287.927 1968990.824 1456045.815 1.6616177 1.066123112 1.269569376 1.055031824 1.446732406 1.125299493 1.353329762 1.23916975 1.352286312 1 20.47362432 -1.724576984 2.556321154 0.946246334 1.272170958 0.1892299 0.175333364 18303316.06 14123217.7 6276535.089 0.037582672 0.018854847 1.724576984 0.325924624 KLTGIKHELQANCYEEVKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLTGIKHELQANCYEEVKDR 20 3 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 170.91 5.16E-12 4187300000 3461200 2244100 3096200 1633100 4898900 3833300 2811500 3089500 3867200 2627700 FALSE TRUE 3597850.849 2629506.718 3176889.516 1956122.306 4066186.728 2943074.169 2591127.284 3048090.306 3728020.227 3142547.505 1.14488352 0.836743666 1.01092808 0.622463878 1.293914164 0.936524958 0.824530824 0.969942475 1.18630513 1 21.58350312 1.385028231 8.475380077 1.09095562 0.945807303 0.088383034 0.177110821 0.593205974 47.76775448 0.111588552 0.040943465 24.26767838 -1.385028231 -0.145148317 KLTPQGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLTPQGQR 8 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 139.74 0.0010595 1539330000 1052470 1176440 921840 706030 2877900 1695810 1277720 889230 982530 2874500 FALSE TRUE 1094022.328 1378484.419 945863.9077 845680.6267 2388715.586 1301983.828 1177568.968 877311.3263 947168.9372 3437703.239 0.318242225 0.400989941 0.275144142 0.246001638 0.694857997 0.378736539 0.342545265 0.255202752 0.275523764 1 21.71301358 -0.986587111 4.312727324 1.000026508 0.353035773 0.708809013 0.124187773 68023962.68 146813999.2 28029.01934 0.030757507 0.103136619 0.986587111 -0.646990735 KLTS(ph)DEEGEPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.25)S(0.75)DEEGEPSGK;KLT(0.101)S(0.899)DEEGEPSGK;KLT(0.204)S(0.796)DEEGEPSGK 184.8 5.64E-06 1310100000 1999260 879030 1289910 861880 1874260 1776350 1957070 1445700 1582100 732420 TRUE FALSE 2078192.329 1029996.565 1323526.114 1032357.292 1555673.955 1363819.633 1803669.74 1426322.756 1525160.53 875923.676 2.372572389 1.175897619 1.51100621 1.178592747 1.776038252 1.557007386 2.059163131 1.6283642 1.741202541 1 19.74044564 KLTS(ph)DEEGEPSGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLTSDEEGEPSGKR 14 2 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 KLT(0.024)S(0.976)DEEGEPSGKR;KLT(0.158)S(0.842)DEEGEPSGKR;KLT(0.018)S(0.982)DEEGEPSGKR;KLT(0.159)S(0.841)DEEGEPSGKR 182.76 7.75E-07 2062190000 2621930 1220400 1688220 1054820 2570310 2330390 1996390 1840820 2150440 1247620 TRUE FALSE 2725445.821 1429994.207 1732216.4 1263460.248 2133409.624 1789192.24 1839907.735 1816146.819 2073046.084 1492067.252 1.826623979 0.958397957 1.160950619 0.846785053 1.429834762 1.199136458 1.233126545 1.217201716 1.389378449 1 20.50888113 6.737396487 0.014406543 1.08E-06 2.611863665 0.058208907 0.256862458 23603.50125 32.64407362 2488.082078 3507.76677 5462563.357 -6.737396487 2.611862588 KLTS(ph)TPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KLTSTPR 7 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 KLT(0.048)S(0.476)T(0.476)PR;KLT(0.051)S(0.474)T(0.474)PR 63.419 0.047377 246430000 1346890 1326900 1343530 1202150 1380330 1535500 1378080 1350370 1268100 1055960 TRUE FALSE 1400066.257 1554784.753 1378543.496 1439931.682 1145702 1178903.396 1270062.489 1332270.499 1222461.329 1262855.144 1.108651506 1.231166346 1.091608568 1.1402192 0.907231526 0.933522266 1.005707182 1.054966997 0.968013896 1 20.26825773 3.259508871 24.19918343 0.9858103 1.145550976 0.711522538 0.051220146 98.89015994 114235.66 0.01525785 0.020634461 1817.644182 -3.259508871 0.159740676 KLVGYLDR ddPTM_MDA-MB-175_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 76.064 0.058957 1151700000 1021300 1038400 1024400 862150 1872700 1532400 1101500 1015900 967520 1940700 FALSE TRUE 1061621.713 1216737.122 1051096.706 1032680.697 1554379.123 1176523.324 1015161.552 1002283.522 932699.1442 2320943.008 0.457409643 0.524242568 0.452874845 0.444940136 0.669718781 0.506916077 0.437391848 0.431843229 0.401862149 1 21.14627967 -1.337389387 3.533259192 1.002360066 0.480999613 0.825218885 0.071683361 461955481.6 645296731.5 11220813.76 0.018089872 0.045984409 1.337389387 -0.521360453 KLVIIEGDLER ddPTM_MDA-MB-175_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 ;;;;; 148.68 5.57E-05 10154380000 9185193 8958557 9984121 9551746 11606489 12033590 11097410 10783484 10702367 10292131 FALSE TRUE 9547831.512 10497119.48 10244315.4 11441052.85 9633622.146 9238971.093 10227566.01 10638949.04 10317190.9 12308677.01 0.775699249 0.852822725 0.832284037 0.929511176 0.78266918 0.750606347 0.830923258 0.864345455 0.838204698 1 23.55317237 0.229663828 0.918663287 1.001335228 0.826591554 0.540098758 0.047761692 2.831010705 2.70235857 0.056907154 0.015520161 1.69692961 -0.229663828 -0.174743674 KLVIIEGDLERTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 195.62 5.25E-09 281220000 291300 533100 479260 299420 640600 572300 220640 444380 495580 928150 FALSE TRUE 302800.7489 624655.7781 491749.9093 358644.3823 531711.0408 439391.9983 203345.6603 438423.813 477744.1726 1110003.222 0.272792676 0.56275132 0.44301665 0.323102109 0.479017565 0.395847498 0.183193757 0.394975262 0.430398906 1 20.08213243 0.649462709 3.0023086 0.999985663 0.383158964 0.770839636 0.100541791 2.053847868 17.05911322 0.096503955 0.025226371 4.461313157 -0.649462709 -0.616826699 KLVIIESDLER ddPTM_MDA-MB-175_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 ;;; 148.68 5.57E-05 2132410000 2911660 2789560 3026550 2758030 3560290 3729970 3456810 3188850 3168490 3324820 FALSE TRUE 3026614.585 3268645.23 3105424.379 3303560.102 2955113.178 2863740.996 3185856.2 3146108.682 3054456.664 3976254.821 0.761172189 0.822041186 0.780992295 0.83082203 0.74319009 0.720210631 0.80122033 0.79122411 0.768174275 1 21.92297879 -1.581299032 2.88335706 1.013554062 0.781508011 0.807704446 0.032210279 9044194.446 9677121.297 940284.3559 0.008105956 0.026224123 1.581299032 -0.232046051 GLYDGPVCEVSVT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 GLYDGPVCEVSVTPK 15 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 GLYDGPVCEVSVT(1)PK;GLYDGPVCEVSVT(1)PK 275.42 1.85E-32 336600000 760800 376350 445020 338140 525810 552080 517290 424030 420580 306440 TRUE FALSE 790836.9715 440985.1849 456617.5868 405023.0828 436433.004 423867.7869 476743.4581 418346.5714 405443.408 366481.0509 2.157920497 1.203296006 1.245951423 1.105167871 1.19087468 1.156588549 1.300867963 1.141523062 1.106314793 1 18.48337908 4.740067818 5.284555176 1.169725489 2.199862218 0.935728239 0.078387657 0.032812287 3.235535089 0.017582671 0.122855468 54962.66955 -4.740067818 1.030136729 up KLVILEGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KLVILEGELER 11 1 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;; 170.66 2.48E-05 8151830000 4318430 4584680 4888140 4454760 5476900 5835800 5504600 4984280 4933810 4857460 FALSE TRUE 4488924.951 5372063.126 5015528.944 5335898.232 4545938.494 4480523.892 5073135.068 4917473.879 4756243.142 5809186.285 0.772728697 0.924753117 0.863378914 0.918527651 0.782543074 0.771282529 0.873295298 0.846499602 0.818745158 1 22.46990466 -2.02549951 6.332895184 1.22553857 0.844498316 0.445260432 0.053032095 0.034799663 0.000140121 0.010581232 0.011911467 0.009429757 2.02549951 -0.381040254 KIDTHPS(ph)PSHSSTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KIDTHPSPSHSSTVK 15 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477;H0Y594 Q8NI27 THOC2 THO complex subunit 2 1 KIDTHPS(0.977)PS(0.022)HSSTVK;KIDTHPS(0.964)PS(0.036)HSSTVK;KIDTHPS(0.963)PS(0.037)HSSTVK;KIDT(0.003)HPS(0.986)PS(0.012)HSSTVK 182.34 2.59E-07 2126820000 685910 2648610 3418090 2860740 3978740 4152870 3427680 3991460 3528560 2515150 TRUE FALSE 712990.2564 3103488.164 3507168.233 3426585.834 3302435.196 3188428.88 3159009.485 3937961.007 3401567.815 3007945.487 0.237035631 1.031763434 1.165968017 1.139178169 1.097903938 1.060002215 1.050221654 1.309186295 1.130860858 1 21.52034699 4.740158797 3.558733126 1.132696501 0.130405432 0.915894193 0.07960942 0.075654841 1.706373707 0.020426854 0.203525823 54974.18471 -4.740158797 -1.002291069 down KLWGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLWGDR 6 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 110.36 0.046126 18360360000 27091390 27518840 29488440 25560110 34331990 35196780 31605050 30232100 28873370 28356050 FALSE TRUE 28160979 32244986.7 30256932.97 30615823.47 28496250.6 27022861.26 29127763.6 29826888.15 27834223.05 33911875.09 0.830416452 0.95084647 0.892222353 0.902805386 0.840303007 0.796855414 0.858925185 0.879541107 0.820781009 1 25.01528722 KLYANMFER ddPTM_MDA-MB-175_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 77.379 0.052542 427340000 3621800 509270 1173700 275720 2319300 1740400 906730 634730 1325000 869220 FALSE TRUE 3764791.461 596733.1609 1204287.586 330256.5931 1925066.214 1336218.476 835658.1333 626222.4826 1277313.509 1039527.017 3.62163888 0.574042955 1.158495707 0.317698903 1.85186742 1.285410051 0.803883035 0.602410974 1.228744889 1 19.98749582 4.74370501 24.9916989 0.964499568 3.62163999 0.784244268 0.415552566 241.3721095 1172559.64 0.09877353 0.836592795 55424.9117 -4.74370501 2.657140422 KLYESLLVGS(ph)LPDMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KLYESLLVGSLPDMNK 16 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 KLYESLLVGS(1)LPDMNK 143.4 8.67E-07 123150000 390720 225320 317140 230910 408710 377270 374700 267330 374690 225420 TRUE FALSE 406145.9273 264016.9573 325404.9289 276583.3088 339237.6202 289654.7601 345330.0349 263746.8786 361204.9801 269586.7331 1.506550128 0.979339577 1.207050975 1.025952968 1.258361702 1.074439965 1.280960791 0.978337753 1.339847017 1 18.04038997 7.999999827 0.016543074 7.22E-07 2.569100139 0.094768663 0.163478901 11963.14775 15.26944798 925.8233156 1511.818802 99999960.2 -7.999999827 2.569099417 KLYGDADYLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KLYGDADYLEER 12 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ;;; 146.59 0.00010401 682930000 1116950 1039430 1170750 977030 1465670 1402180 1280770 1208130 1268980 1162760 FALSE TRUE 1161048.048 1217944.017 1201260.707 1170283.618 1216535.937 1076544.945 1180379.901 1191936.993 1223309.658 1390580.56 0.834937638 0.875852901 0.86385553 0.841579159 0.874840317 0.77416942 0.848839639 0.857150623 0.879711462 1 20.4072559 0.679269478 1.556888418 0.999902024 0.845834086 0.74219241 0.027192957 0.579221988 2.089499874 0.025811916 0.007445843 4.778256703 -0.679269478 -0.154067938 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR 32 1 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 147.54 1.19E-10 20306000 10848 13068 10364 9029.6 17875 15566 12768 13610 11739 18706 FALSE TRUE 11276.28742 15312.32735 10634.09435 10815.62793 14836.61388 11951.03241 11767.2108 13427.58021 11316.51568 22371.08255 0.504056404 0.684469663 0.475350012 0.483464665 0.663205004 0.534217885 0.526000955 0.600220404 0.50585463 1 14.44934745 -1.578285313 2.881215505 1.026976391 0.557243847 0.787837027 0.069560907 13904078.49 14177083.8 2860252.443 0.015870686 0.026406734 1.578285313 -0.469732544 KMDGAPDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMDGAPDGR 9 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 54.416 0.05769 0 16663 17427 19865 16011 22904 21418 17024 16514 19334 19878 FALSE TRUE 17320.86811 20419.95169 20382.69822 19177.92801 19010.78626 16443.99409 15689.6144 16292.65684 18638.17312 23772.71351 0.728602904 0.85896596 0.857398892 0.806720192 0.799689369 0.691717169 0.659984162 0.685351162 0.784015384 1 14.53701897 5.097185626 12.36628011 0.774389014 0.000127152 0.004669955 0.097248724 2146872.84 5871255.921 0.02395149 43576101.37 125079.353 -5.097185626 -0.774261862 KMDLIDLEDETIDAEVMNSLAVTMDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KMDLIDLEDETIDAEVMNSLAVTMDDFR 28 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;; 244.62 1.08E-45 736474000 361054 366654 479089 418675 591183 568230 542956 482520 488026 405499 FALSE TRUE 375308.6907 429623.9723 491574.4529 501487.6654 490693.9248 436267.1941 500397.69 476052.6086 470462.0396 484948.7653 0.773914107 0.88591621 1.013662655 1.034104428 1.011846941 0.899615022 1.031856818 0.981655471 0.970127307 1 18.88747281 4.507640061 2.801223734 0.992404875 0.77434001 0.775073591 0.03739059 0.133727845 1.869813976 0.009458514 0.051728743 32184.0031 -4.507640061 -0.218064865 KMEDSVGCLETAEEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMEDSVGCLETAEEVKR 17 2 P35579 P35579 MYH9 Myosin-9 0 138.46 2.01E-06 1564300000 350010 215800 301050 214800 450680 369270 302710 259340 352000 215340 FALSE TRUE 363828.6651 252861.9713 308895.6103 257286.7989 374073.5746 283512.6388 278982.7992 255863.9715 339331.5888 257531.7501 1.41275266 0.981867173 1.19944671 0.999048851 1.452533812 1.100884216 1.083294775 0.993523989 1.317630112 1 17.97439078 -4.999812357 0.024338681 1.27E-06 1.889307613 0.086602246 0.164384721 5750.293534 10.57398718 589.3387514 283.1029384 1.00E-05 4.999812357 1.889306342 KMEEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMEEEQR 7 1 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 82.279 0.026153 210226000 345140 332970 352270 301130 438200 457460 405290 367120 373260 344530 FALSE TRUE 358766.3937 390155.0074 361450.4456 360692.6152 363714.9205 351221.8479 373522.3108 362199.3569 359826.4455 412034.0571 0.870720242 0.9468999 0.877234392 0.87539515 0.882730236 0.852409751 0.906532614 0.879051988 0.87329297 1 18.65240406 -1.926447649 5.506064338 1.044987717 0.885691668 0.668921521 0.024283223 0.013676638 0.000182698 0.023978854 0.00536343 0.011845471 1.926447649 -0.159296049 KMEENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMEENEK 7 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 88.819 0.029387 124890000 293180 162360 208400 162120 303560 270950 349340 253620 297190 145650 FALSE TRUE 304754.9728 190244.067 213831.0752 194186.8521 251960.9796 208025.9688 321957.818 250220.6387 286494.19 174187.3289 1.749581756 1.092180862 1.227592596 1.114816177 1.446494307 1.194265795 1.848342357 1.436503105 1.644747593 1 17.41028015 KMEIYRPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMEIYRPHK 9 2 Q92769;Q92769-3;H3BM24;E5RFI6;E5RJ04;E5RGV4;E5RHE7;E5RH52;E5RG37;E5RFP9;E5RK19;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ; 159.4 3.97E-05 889560000 1554980 1016080 1510750 1246160 1910750 1708870 1861440 1584800 1717990 1134890 FALSE TRUE 1616371.811 1190583.836 1550121.386 1492646.729 1585961.398 1312010.841 1715535.469 1563558.348 1656159.875 1357249.967 1.190916818 0.877203069 1.142104567 1.099758162 1.168510913 0.966668538 1.26397901 1.152004706 1.220232025 1 20.37225502 3.345566485 0.849748063 1.152338624 1.046452439 0.035233194 0.114350332 1.549516171 2.379592685 0.051855864 0.10305437 2215.98331 -3.345566485 -0.105886185 KMENCLGESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KMENCLGESR 10 1 Q9UHB6;Q9UHB6-4;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;;; 109.72 0.0031765 1222052000 1667630 1663030 1814650 1514500 2192430 2149290 1935520 1736700 1937420 1672580 FALSE TRUE 1733469.32 1948642.466 1861941.27 1814063.58 1819761.532 1650149.97 1783808.885 1713422.377 1867692.633 2000290.028 0.86660899 0.974179963 0.930835651 0.906900277 0.90974884 0.824955355 0.891775123 0.856586972 0.933710915 1 20.93177776 5.068504941 14.76432653 0.904956805 0.472933855 0.049421236 0.049256409 638175.7514 3138486.416 0.011754544 8346133.194 117085.9924 -5.068504941 -0.43202295 KMIDQVFGVLES(ph)PELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMIDQVFGVLESPELSR 17 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KMIDQVFGVLES(0.995)PELS(0.005)R;KMIDQVFGVLES(1)PELSR 93.093 0.0019276 582030000 741290 682060 782170 612660 900080 898720 679090 744530 761630 762190 TRUE FALSE 770556.7016 799198.4993 802553.9928 733842.3194 747084.7231 690005.9002 625861.1513 734550.7932 734219.0851 911526.5375 0.845347524 0.876769317 0.880450497 0.805069616 0.819597337 0.7569784 0.686607713 0.805846855 0.805482951 1 19.79792513 3.637390691 3.760726669 0.793222223 0.868512868 0.070958725 0.075676831 0.418749715 10.75965372 0.019630614 0.031908142 4339.010396 -3.637390691 0.075290645 KMKDTDSEEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KMKDTDSEEEIR 12 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;; 86.028 0.024519 1209020000 683600 644980 798320 582900 903650 901240 850760 741000 847000 642320 FALSE TRUE 710589.0559 755750.2978 819124.875 698195.8802 750047.8958 691940.6684 784075.2082 731068.107 816516.6355 768170.306 0.925041036 0.9838317 1.066332386 0.908907666 0.976408343 0.900764665 1.020704917 0.951700556 1.062936993 1 19.55106667 1.246751185 24.99870296 1.031468503 0.968622709 0.211611589 0.049888403 244.0515126 744894.8289 0.033121164 0.011631551 17.65026315 -1.246751185 -0.062845794 KMKDTDSEEEIREAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMKDTDSEEEIREAFR 16 3 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ; 136.35 7.86E-06 1070930000 792590 728180 955320 466200 1074720 918500 748320 849440 978700 771450 FALSE TRUE 823882.0652 853239.2505 980216.424 558412.9685 892039.4783 705192.295 689664.723 838054.6462 943476.7782 922600.8572 0.892999458 0.924819486 1.062449071 0.605259538 0.966874756 0.764352525 0.747522309 0.90836101 1.022627251 1 19.81534711 1.379128904 4.354377976 1.008975916 0.852918574 0.21461568 0.120231877 0.332052033 9.726855935 0.086550042 0.029972062 23.94026228 -1.379128904 -0.156057342 KMLGEDS(ph)DEEEEMDTSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMLGEDSDEEEEMDTSER 18 1 A0A087X0M4;A0A087WWF4;Q9BWU0;H7C256 A0A087X0M4 SLC4A1AP Kanadaptin 1 KMLGEDS(1)DEEEEMDTSER 92.792 0.00085845 0 59724 51715 53153 42839 76984 74791 54981 50507 60591 44302 TRUE FALSE 62081.94964 60596.64896 54538.21085 51312.42634 63898.28718 57421.92372 50671.44555 49830.03628 58410.34175 52982.12869 1.171752649 1.143718655 1.029369944 0.968485556 1.206034728 1.083797974 0.956387499 0.940506497 1.102453661 1 15.69321819 2.308944931 6.564590955 0.987904144 1.098899324 0.294123248 0.075670339 0.258811488 19.03986368 0.027540667 0.022850659 203.6783797 -2.308944931 0.110995179 KMMDEFEVNIHVPAPELQSDIIAITGLAANLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMMDEFEVNIHVPAPELQSDIIAITGLAANLDR 33 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 127.8 4.14E-08 132290000 32398 40005 41064 38065 48345 51678 36557 41418 39492 42950 FALSE TRUE 33677.09806 46875.54755 42134.16157 45594.14339 40127.33417 39676.56769 33691.56682 40862.85946 38070.69063 51365.23017 0.655639972 0.912592962 0.820285657 0.887646044 0.781215893 0.772440181 0.655921656 0.79553541 0.741176288 1 15.64850449 3.026468304 24.69721032 0.771079861 0.82688968 0 0.103714249 571.6546704 533398.5479 0.027951936 0.033408174 1062.841011 -3.026468304 0.055809819 KMMDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMMDKR 6 2 Q5T5C7 Q5T5C7 SARS 0 62.52 0.056696 5982600 1013.6 10384 6658.4 6996 6223.3 10563 4064.7 8475.2 5894.4 16230 FALSE TRUE 1053.617711 12167.37122 6831.923374 8379.787919 5165.465689 8109.903334 3746.098193 8361.603807 5682.261695 19409.95776 0.054282329 0.626862324 0.351980332 0.431726232 0.26612452 0.417821792 0.192998781 0.430789387 0.292749823 1 14.24450936 -1.299401843 3.225635596 1.003560276 0.351583148 0.642476947 0.147364922 40595157.76 56554937.07 1399837.35 0.034505199 0.0501878 1.299401843 -0.651977128 KMPFTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMPFTEK 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 117.04 0.0085324 2772100000 2971300 2521100 2780200 2409370 4323800 3908700 3946100 3625300 3907400 2885480 FALSE TRUE 3088609.218 2954079.314 2852654.296 2885936.195 3588842.02 3000963.662 3636794.371 3576708.783 3766773.437 3450834.56 0.895032539 0.856047794 0.826656348 0.836300942 1.039992488 0.869634174 1.053888359 1.036476458 1.091554339 1 21.71851388 2.691734697 0.906322212 1.054356379 0.851942359 0.612406324 0.060793071 0.35761849 0.621175671 0.036008566 0.031911613 491.7390489 -2.691734697 -0.20241402 KMPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMPKPR 6 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ; 103.41 0.019522 5034200000 1492380 1306750 1371070 1148630 2125190 1830780 1901230 1636920 1773550 1416510 FALSE TRUE 1551300.315 1531174.147 1406801.211 1375825.586 1763950.963 1405609.091 1752206.625 1614979.765 1709720.282 1694048.014 0.915735742 0.903855224 0.830437626 0.812152651 1.041263854 0.829733915 1.034331147 0.953325851 1.009251372 1 20.69204333 2.487768229 0.913164662 0.998331466 0.875807032 0.333854684 0.068110446 0.666661386 1.122347676 0.044375101 0.031880818 307.4455627 -2.487768229 -0.122524434 KMPLDLS(ph)PLATPIIR ddPTM_MDA-MB-175_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(0.998)PLAT(0.002)PIIR 120.56 7.60E-05 987450000 1561280 1735500 2480220 1592960 3801750 2295540 3234590 2212900 2955230 1885000 TRUE FALSE 1622920.54 2033558.625 2544856.571 1908042.733 3155529.893 1762435.624 2981054.384 2183239.695 2848871.85 2254329.659 0.719912695 0.90206799 1.128875078 0.84639029 1.399764174 0.781800309 1.322368435 0.968465143 1.263733473 1 21.10426707 5.235143634 0.896278804 1.097980605 0.083670989 0.274787491 0.190236276 5.756168346 1.949924723 0.054392497 7.043509841 171847.6643 -5.235143634 -1.014309616 KMQQNIQELEEQLEEEESAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KMQQNIQELEEQLEEEESAR 20 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 268.25 8.23E-37 2097026000 835704 893914 1025908 872547 1241234 1259166 938160 985451 1105036 1065766 FALSE TRUE 868698.2392 1047436.776 1052644.005 1045134.192 1030249.488 966743.7793 864624.5678 972242.6412 1065265.97 1274582.442 0.681555159 0.821788172 0.825873612 0.819981633 0.80830353 0.758478814 0.678359076 0.76279306 0.835776435 1 20.28159326 0.885757084 3.36228607 0.999848061 0.771373074 0.649085198 0.051240536 0.314330047 7.302480197 0.052006856 0.013478929 7.687003583 -0.885757084 -0.228474987 KMS(ph)DDEDDDEEEYGKEEHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMSDDEDDDEEEYGKEEHEK 20 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 KMS(1)DDEDDDEEEYGKEEHEK;KMS(1)DDEDDDEEEYGKEEHEK 165.46 8.68E-12 429370000 292441 49753 87135 55927 150323 191453 191581 89464 108353 27091 TRUE FALSE 303986.7965 58297.69073 89405.80968 66989.19367 124771.1502 146990.9422 176564.3806 88264.88141 104453.3967 32398.96276 9.382608904 1.799369046 2.759526913 2.067633898 3.851084711 4.536902719 5.449692384 2.72431195 3.223973479 1 14.98366001 4.746791482 24.74449482 3.218763283 9.382612441 0.693777991 1.258271315 532.190536 1599885.482 0.3053621 3.446693674 55820.21206 -4.746791482 6.163849157 KMS(ph)GGSTMSSGGGNTNNSNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.307)GGS(0.307)T(0.307)MS(0.062)S(0.016)GGGNT(0.001)NNSNSK;KMS(0.95)GGS(0.02)T(0.027)MS(0.002)SGGGNTNNSNSK;KMS(0.768)GGS(0.183)T(0.045)MS(0.003)S(0.001)GGGNTNNSNSK;KMS(0.969)GGS(0.026)T(0.004)MSSGGGNTNNSNSK;KMS(0.862)GGS(0.119)T(0.019)MSSGGGNTNNSNSK;KMS(0.607)GGS(0.175)T(0.175)MS(0.036)S(0.008)GGGNTNNSNSK;KMS(0.899)GGS(0.043)T(0.055)MS(0.002)SGGGNTNNSNSK;KMS(0.735)GGS(0.072)T(0.192)MS(0.001)SGGGNTNNSNSK;KMS(0.963)GGS(0.017)T(0.017)MS(0.002)SGGGNTNNSNSK;KMS(0.984)GGS(0.012)T(0.003)MSSGGGNTNNSNSK 177.49 2.77E-17 2818080000 2074300 1297342 1740918 1215927 2221300 2079290 2148720 1737510 1971600 1090539 TRUE FALSE 2156194.966 1520150.397 1786287.753 1456433.731 1843724.219 1596406.409 1980297.712 1714221.52 1900642.501 1304209.237 1.653258468 1.165572481 1.369632803 1.116717847 1.413672106 1.224041637 1.518389577 1.314376153 1.457314092 1 20.31474391 -1.910247946 2.601337011 0.796383996 1.348669087 0.322307132 0.155589877 10948578.29 5897310.721 13597566.34 0.03382974 0.012295666 1.910247946 0.552285091 KMS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMSPLR 6 1 Q86SQ7-3;Q86SQ7-4;Q86SQ7;Q86SQ7-2 Q86SQ7-3 SDCCAG8 Serologically defined colon cancer antigen 8 1 KMS(1)PLR 68.735 0.058407 216190000 173620 166180 174910 140080 228180 234080 207860 168760 197620 189090 TRUE FALSE 180474.6517 194720.1223 179468.2983 167787.4059 189394.0451 179718.4675 191567.3901 166498.0482 190507.6948 226138.5652 0.798071092 0.861065525 0.79362093 0.741967235 0.837513252 0.794727195 0.84712393 0.736265608 0.842437886 1 17.78684752 0.97548924 23.41193633 1.000000002 0.800404296 0.704554155 0.038538205 516.6751048 493513.4385 0.036330127 0.009082532 9.45124975 -0.97548924 -0.199595706 KMS(ph)QPGS(ph)PSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMSQPGSPSPK 11 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 2 KMS(0.83)QPGS(0.585)PS(0.585)PK;KMS(0.992)QPGS(0.504)PS(0.504)PK 87.083 0.0093497 36947000 276747 111251 150677 101862 196932 199266 206090 136055 153308 58266 TRUE FALSE 287673.1853 130357.4938 154603.7664 122009.9996 163457.569 152989.4914 189936.1273 134231.4053 147790.475 69682.10713 4.128365187 1.870745579 2.218701081 1.750951637 2.345760995 2.195534804 2.725751776 1.926339641 2.120924311 1 16.08850063 8 0.061653887 3.54E-14 6.980801878 0.386532909 0.598542289 404.4146053 1.858123377 41.54581769 251.7766149 100000000 -8 6.980801878 KMSGGS(ph)TMSSGGGNTNNSNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KMSGGSTMSSGGGNTNNSNSK 21 1 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 KMS(0.269)GGS(0.336)T(0.336)MS(0.048)S(0.011)GGGNTNNSNSK 76.198 0.00407 26381000 46102 25623 41154 27337 53515 45478 51427 42132 43345 27401 TRUE FALSE 47922.14256 30023.55093 42226.50705 32744.17701 44418.53942 34916.42373 47396.01736 41567.28945 41785.02192 32769.70133 1.462391802 0.916198492 1.288583824 0.9992211 1.35547587 1.065509367 1.446336568 1.268467144 1.275111467 1 15.0000749 3.214638541 24.99871355 1.256312829 1.157426071 0.023568877 0.184924789 665.387483 695332.4281 0.049115026 0.058731383 1639.224893 -3.214638541 -0.098886758 KMTDYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KMTDYAK 7 1 K7EJR3;R4GMR5;P48556;K7EJC1 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ; 80.239 0.048829 467930000 464040 345290 430830 326020 627580 572140 492110 453640 500840 465460 FALSE TRUE 482360.6575 404590.8715 442057.7837 390505.7829 520904.1758 439269.1559 453537.1323 447559.6978 482814.8662 556657.9752 0.866529681 0.726821297 0.794128178 0.701518348 0.935770615 0.789118589 0.814750084 0.80401201 0.867345637 1 19.08643165 -1.913339023 0.263945004 1.207960546 0.780963435 0.473274006 0.062362892 24.462439 1.009725265 3.212955396 0.082618497 0.012208463 1.913339023 -0.426997111 KNDFEQGELYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNDFEQGELYLR 12 1 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 148.68 0.00010684 146420000 113800 94296 117600 105090 119100 137330 112670 105330 106660 84396 FALSE TRUE 118292.9119 110490.6045 120664.7526 125876.4883 98855.42454 105437.1888 103838.631 103918.2236 102821.3274 100931.7803 1.172008573 1.094705791 1.195508017 1.247144239 0.979428127 1.044638155 1.028800152 1.029588731 1.018721032 1 16.62302098 3.230949999 24.99996079 1.021151754 1.172736695 0.804002718 0.038755468 77.33197085 254025.9801 0.011519647 0.014017905 1701.962546 -3.230949999 0.151584941 KNDKEAAGEGPALYEDPPDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 0 195.93 5.58E-22 277070000 389520 167070 271610 122300 450400 310030 277120 235180 318550 138970 FALSE TRUE 404898.5504 195762.9729 278688.3797 146490.575 373841.1689 238030.2311 255398.6103 232027.7968 307085.4477 166198.5108 2.436234528 1.177886444 1.676840415 0.8814193 2.249365335 1.432204356 1.536708176 1.396088303 1.847702764 1 17.34254793 -2.10273905 2.252605912 0.000200307 1.586565218 0.147065751 0.443218684 9389813.069 2490986.119 48103171.25 0.097308411 0.007893343 2.10273905 1.586364911 KNEFQGELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNEFQGELEK 10 1 Q8NBJ4-2;Q8NBJ4;C9J941;F8WAT9;C9JYM4 Q8NBJ4-2 GOLM1 Golgi membrane protein 1 0 156.69 1.68E-05 149180000 272380 169220 210640 201200 407390 333150 323960 213850 223790 197780 FALSE TRUE 283133.7727 198282.2187 216129.4514 240996.7595 338141.9933 255780.9614 298567.1687 210983.6905 215735.8416 236531.2043 1.197025034 0.83829201 0.913746041 1.018879349 1.429587248 1.081383584 1.262273913 0.891990937 0.912081948 1 17.851671 1.635894587 11.93203786 0.926729736 1.095770621 0.187613117 0.161833738 0.195390531 61.38784749 0.081895406 0.044193707 43.24088625 -1.635894587 0.169040884 KNGFVVLK ddPTM_MDA-MB-175_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 ; 116.37 0.0073558 0 1154200 933280 1129620 889650 1466700 1459340 1331790 1161640 1176780 962280 FALSE TRUE 1199768.707 1093563.58 1159058.825 1065620.115 1217390.858 1120430.402 1227400.82 1146070.116 1134427.918 1150820.342 1.042533455 0.950247002 1.007158792 0.925965657 1.057846141 0.973592802 1.066544251 0.995872313 0.985755879 1 20.1342312 3.226386352 24.99792364 1.013723809 0.981080023 0.130985331 0.040101626 428.0196299 878868.1118 0.010746522 0.012932382 1684.171647 -3.226386352 -0.032643786 KNGIPLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNGIPLELR 9 1 Q6ICJ4;A0A087WY67;P0CG30;P0CG29 Q6ICJ4 Em:AP000351.3;GSTT2;GSTT2B Glutathione S-transferase theta-2B;Glutathione S-transferase theta-2 0 72.434 0.0667 0 521530 985510 646910 985170 954230 1100000 593050 804860 742220 1111900 FALSE TRUE 542120.4071 1154763.676 663769.006 1180033.686 792030.3254 844541.6707 546565.1914 794072.1682 715507.6472 1329755.516 0.40768427 0.868402997 0.499166198 0.887406498 0.595621011 0.635110485 0.411026828 0.597156514 0.538074585 1 20.34272959 -0.89320434 4.146982483 1.000009637 0.608724636 0.367043895 0.155754392 4.57542E+11 9.48669E+11 68278652.53 0.035261297 0.127877948 0.89320434 -0.391285001 KNGSTAVAESVAS(ph)PQK ddPTM_MDA-MB-175_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;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK 194.25 1.49E-10 2433520000 4098960 2002760 2774770 2018250 3927280 3639270 3731410 3008540 3332900 1719500 TRUE FALSE 4260790.106 2346718.451 2847082.786 2417453.826 3259722.348 2794104.696 3438932.334 2968215.442 3212949.58 2056403.103 2.071962496 1.141176284 1.384496445 1.175573905 1.585157279 1.358733943 1.672304583 1.443401558 1.562412338 1 20.97169166 -1.873564485 2.667885474 0.783484862 1.470770976 0.248689031 0.25299171 8826535.807 6264682.371 12106477.05 0.057419513 0.013379365 1.873564485 0.687286114 KNHLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNHLEGK 7 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 114.78 0.0037829 2140130000 6117000 4247300 5746400 4224100 7179600 6674100 6828800 5930100 6382200 4117800 FALSE TRUE 6358503.883 4976740.736 5896155.905 5059614.372 5959214.156 5124141.422 6293540.812 5850616.709 6152505.869 4924604.07 1.291170578 1.010586976 1.197285268 1.027415463 1.210090004 1.040518456 1.277979046 1.188037988 1.249340207 1 22.23157631 2.236339075 24.99942328 1.196796854 1.126208095 0.036633845 0.108595027 140.2820233 1578581.568 0.035674588 0.027630133 172.3213446 -2.236339075 -0.070588758 KNIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNIIEATHMYDNAAEACSTTEEVFNSPR 28 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KNIIEATHMYDNAAEACSTTEEVFNS(1)PR;KNIIEATHMYDNAAEACSTTEEVFNS(1)PR 257.56 6.41E-54 806730000 410050 436980 483500 441580 528990 508640 438120 502270 498780 485050 TRUE FALSE 426239.0906 512027.9158 496100.4072 528923.206 439072.4688 390516.0685 403779.0096 495537.8922 480829.0052 580086.2607 0.734785703 0.882675475 0.855218337 0.911800954 0.756908926 0.673203444 0.696067183 0.854248628 0.828892249 1 19.14590792 0.700866285 1.615887775 0.999393349 0.795667859 0.395092767 0.075963767 1.235265448 4.909164332 0.078616437 0.022530266 5.021879468 -0.700866285 -0.20372549 KNLDSTTVAVHGEEIYCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNLDSTTVAVHGEEIYCK 18 1 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 144.66 6.28E-08 275190000 407350 339190 381040 327600 493790 508280 424790 408020 462480 304200 FALSE TRUE 423432.4925 397443.244 390970.2154 392398.3022 409855.7522 390239.6731 391493.8498 402551.1593 445835.4351 363802.1657 1.163908664 1.092470803 1.074678087 1.078603536 1.126589643 1.072670011 1.076117425 1.106511168 1.225488678 1 18.47279461 1.458514175 19.19890863 1.130494665 1.096014838 0 0.057713924 3.519099888 3632.626186 0.028588495 0.013221595 28.74181401 -1.458514175 -0.034479827 KNLQEEIDALESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNLQEEIDALESR 13 1 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 78.191 0.038323 42136000 87484 107180 113050 104240 131950 137780 116800 111430 104380 104620 FALSE TRUE 90937.93587 125587.3313 115996.1759 124858.3609 109521.1861 105782.6831 107644.9108 109936.4631 100623.3842 125118.2859 0.72681571 1.003748815 0.927092111 0.997922565 0.875341165 0.845461415 0.860345153 0.87866024 0.804226045 1 16.93293313 3.034333865 24.97813951 0.868702395 0.923177666 0.032692712 0.085297864 454.9157036 330951.7706 0.02319668 0.02772523 1082.265627 -3.034333865 0.054475271 KNLS(ph)PGAVESDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KNLSPGAVESDVR 13 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 KNLS(1)PGAVESDVR;KNLS(1)PGAVESDVR;KNLS(1)PGAVESDVR 118.72 0.00024828 678230000 796030 707850 805530 632860 1013090 958870 789710 773820 845950 753950 TRUE FALSE 827457.8791 829417.7312 826522.7736 758037.8191 840885.3237 736186.9743 727810.4667 763448.2086 815504.4247 901672.0673 0.917692706 0.919866281 0.916655626 0.840702342 0.932584422 0.816468649 0.807178677 0.846702739 0.904435719 1 19.7822433 3.762154738 21.21347379 0.866184458 0.918251113 0.06942885 0.055467468 216.6960758 194826.9509 0.013725427 0.024703468 5783.02058 -3.762154738 0.052066655 KNLTQDEMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNLTQDEMQR 10 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 100.55 0.0063086 207056000 171417 171493 192268 170815 240400 239840 210149 188010 196566 184447 FALSE TRUE 178184.6755 200945.5887 197278.662 204601.6972 199536.8939 184140.7948 193676.9723 185490.0335 189491.6281 220585.8582 0.807779234 0.910963152 0.894339572 0.927537689 0.904577 0.834780599 0.878011736 0.840897213 0.859037971 1 17.75098078 KNNHHEENISSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNNHHEENISSK 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 134.98 8.82E-05 24416000 61102 70394 68256 53019 81550 88808 70023 65208 62897 62472 FALSE TRUE 63514.35414 82483.62191 70034.80743 63505.99995 67688.16013 68183.6879 64534.41429 64333.99342 60633.34926 74712.1923 0.850120338 1.104018225 0.937394624 0.850008519 0.905985463 0.912617952 0.863773533 0.86109096 0.811558962 1 16.18905608 3.998127413 24.99994346 0.881053581 0.987978567 0.194242349 0.073977467 88.04293568 1175487.948 0.016946448 0.035755505 9956.974922 -3.998127413 0.106924986 KNNIDTHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNNIDTHAR 9 1 O43847;O43847-2;F5H7V1;G3V1R5 O43847 NRD1 Nardilysin 0 78.655 0.018927 75409000 57105 54428 64549 54603 76298 83242 70956 64335 68636 63297 FALSE TRUE 59359.54949 63775.58561 66231.19997 65403.31043 63328.89321 63910.30704 65394.28331 63472.69456 66165.80377 75698.83526 0.784154066 0.842490976 0.874930238 0.863993616 0.836590061 0.844270679 0.863874366 0.838489712 0.874066339 1 16.20798348 -4.999999998 0.273106284 2.072231584 0.836803895 0.805973221 0.023022133 91.65394521 0.886541314 55.47318864 0.0279647 1.00E-05 4.999999998 -1.23542769 KNPDDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KNPDDFK 7 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ;;; 102.95 0.013607 1332170000 3068690 1899540 2606580 1809130 3630050 3495460 3683710 2783010 3195700 1648130 FALSE TRUE 3189844.251 2225771.219 2674509.616 2166970.514 3013015.398 2683692.389 3394971.185 2745708.303 3080687.381 1971049.518 1.618348104 1.129231507 1.356896208 1.099399327 1.52863506 1.361555032 1.722418008 1.393018429 1.562968029 1 20.91053259 2.454087897 24.97057823 1.466433823 1.333662261 0.004936862 0.226730761 630.8198971 683870.9669 0.073163174 0.061215639 284.5036856 -2.454087897 -0.132771561 KNPDSQYGELIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNPDSQYGELIEK 13 1 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 214.58 4.90E-11 1102930000 1639010 1066450 1389410 1053060 1946950 1708920 1699930 1398660 1628930 1042760 FALSE TRUE 1703719.38 1249604.492 1425619.166 1261352.125 1616008.134 1312049.229 1566685.045 1379913.25 1570305.127 1247068.857 1.366179077 1.002033275 1.143175982 1.011453472 1.295845153 1.052106483 1.256293937 1.106525307 1.259196811 1 20.2501097 2.251024937 24.99333087 1.161464917 1.13931314 0 0.12900293 2062.699894 4136090.663 0.041485016 0.034497596 178.2481115 -2.251024937 -0.022151777 KNPEVPVNFAEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNPEVPVNFAEFSK 14 1 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 153.74 1.01E-05 2407100000 2459260 2044520 2556200 1841150 2902600 2801400 2894700 2335520 2618200 1896230 FALSE TRUE 2556353.484 2395650.406 2622816.672 2205323.975 2409217.089 2150817.306 2667805.85 2304216.175 2523971.493 2267759.963 1.127259289 1.056395053 1.156567148 0.972467991 1.062377469 0.948432524 1.176405746 1.016075869 1.112980004 1 21.11283651 3.752774017 24.98871344 1.045454885 1.107705945 0.192060951 0.067131517 1479.262821 2600695.772 0.016205991 0.029061669 5659.44726 -3.752774017 0.06225106 KNPGVGNGDDEAAELMQQVNVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNPGVGNGDDEAAELMQQVNVLK 23 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 210.38 1.08E-24 414030000 539180 367130 478720 349740 627770 570970 548100 497130 583840 345490 FALSE TRUE 560467.2427 430181.7216 491195.8365 418917.5281 521061.8796 438370.8706 505138.4898 490466.7855 562827.7124 413182.1507 1.356465282 1.041143043 1.188811849 1.01388099 1.261094843 1.060962749 1.222556417 1.18704737 1.362178186 1 18.65641841 KNPTRWS(ph)TTAGFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNPTRWSTTAGFLK 14 2 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 KNPT(0.001)RWS(0.871)T(0.126)T(0.001)AGFLK;KNPT(0.001)RWS(0.498)T(0.498)T(0.003)AGFLK 137.13 1.82E-05 746020000 357070 303720 401680 270250 631030 492660 312840 355980 442900 422520 TRUE FALSE 371167.3993 355881.5474 412148.1108 323704.6434 523767.746 378247.1813 288318.7833 351208.6704 426960.1155 505304.7044 0.734541745 0.704290984 0.815642734 0.640612764 1.036538432 0.748552662 0.570584008 0.695043342 0.84495575 1 18.94679409 0.964969325 4.555615718 0.999742296 0.740807698 0.317952104 0.116496839 0.242803834 16.34280177 0.113652328 0.028858499 9.225062662 -0.964969325 -0.258934598 KNPVISQTGS(ph)WR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNPVISQTGSWR 12 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5;E9PLU3 Q8IVL1-9 NAV2 Neuron navigator 2 1 KNPVIS(0.022)QT(0.204)GS(0.773)WR 62.377 0.047897 53133000 78599 71166 75677 83707 85555 120560 89487 89099 85258 89706 TRUE FALSE 81702.14921 83388.20691 77649.20479 100263.9948 71012.39166 92561.7671 82472.77511 87904.77364 82189.58123 107282.1732 0.761563145 0.777279248 0.723784786 0.934582063 0.661921637 0.862787958 0.768746313 0.819379129 0.766106603 1 16.71105084 -4.999999991 0.351804024 3.469245699 0.781828769 0.450904984 0.070627138 372.4752149 3.036362769 694.2433979 0.048001277 1.00E-05 4.999999991 -2.687416931 KNQIVFDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNQIVFDNR 9 1 Q8N8S7 Q8N8S7 ENAH Protein enabled homolog 0 104.52 0.0063141 0 1177900 1070200 1162800 1111700 1522200 1519500 1287400 1262100 1351300 1479200 FALSE TRUE 1224404.402 1253998.525 1193103.523 1331590.942 1263456.988 1166619.153 1186490.224 1245183.614 1302666.977 1769020.919 0.692136757 0.708865854 0.674442857 0.75272764 0.714212576 0.659471655 0.670704462 0.703882922 0.736377373 1 20.75451968 0.621910942 2.092671589 0.999972339 0.696699675 0.929326542 0.02491424 0.557472386 2.788853226 0.024757738 0.006775345 4.187076948 -0.621910942 -0.303272663 KNQTALDALHAQTVSQTAASS(ph)PQDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNQTALDALHAQTVSQTAASSPQDAYR 27 1 Q8TEK3;Q8TEK3-1 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 KNQTALDALHAQTVSQTAAS(0.173)S(0.819)PQDAY(0.007)R 94.08 0.0025234 338840000 54912 49532 56550 50924 48193 79459 58486 45165 54773 41969 TRUE FALSE 57079.96816 58038.73569 58023.73946 60996.61521 40001.17107 61005.85146 53901.7145 44559.63705 52801.73043 50192.022 1.137231892 1.156333883 1.156035106 1.215265151 0.796962734 1.21544917 1.073910003 0.887783263 1.051994487 1 15.61517045 3.321501843 24.99997282 1.005569146 1.164784419 0.360003806 0.105713789 30.66049494 9238.512645 0.02901428 0.039285512 2096.533676 -3.321501843 0.159215273 KNREELDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KNREELDK 8 2 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 164.68 0.00018485 11035660000 12163020 5957600 8425990 6370820 11725790 10842190 13099090 8851650 9874770 4269240 FALSE TRUE 12643225.42 6980771.456 8645578.221 7630949.181 9732644.404 8324255.687 12072349.1 8733008.11 9519378.957 5105715.838 2.476288501 1.367246372 1.69331363 1.49458948 1.906225241 1.630379745 2.36447728 1.710437554 1.8644553 1 22.28368182 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 KNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;; 244.48 8.79E-51 5135727000 1134624.7 807151.8 1103441 788836.3 1405170 1307318 1196211.7 1064162.5 1268647 772276.3 FALSE TRUE 1179420.559 945773.8429 1132197.579 944865.7657 1166319.705 1003713.207 1102449.501 1049899.142 1222988.642 923589.0549 1.276997116 1.024020194 1.225867254 1.023036989 1.262812394 1.086753034 1.19365804 1.136760052 1.324169701 1 19.81689155 KNS(ph)FGYR ddPTM_MDA-MB-175_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 129.16 0.0022588 3825140000 4711680 3626660 4492660 3742900 6010000 5529960 5512390 4617720 5009540 3556110 TRUE FALSE 4897700.765 4249510.644 4609742.41 4483234.449 4988422.347 4245710.597 5080314.468 4555827.016 4829247.634 4252861.669 1.151624752 0.999212054 1.083915436 1.054168886 1.172956643 0.998318527 1.19456377 1.071237997 1.135528971 1 22.0200025 KNS(ph)IHELLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNSIHELLLER 11 1 F5H527;Q76I76;A0A3B3IS79 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 KNS(1)IHELLLER 94.544 0.00516 147830000 125700 98464 117800 91868 185850 144950 129680 122290 121610 99209 TRUE FALSE 130662.7331 115374.4261 120869.9648 110039.2162 154259.2834 111287.5592 119515.3427 120650.9026 117233.2799 118647.1041 1.101271995 0.972416705 1.018735061 0.927449659 1.300152116 0.937971138 1.007317824 1.016888727 0.988083786 1 16.85631736 KNS(ph)LISSLEEEVSILNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.916)LIS(0.081)S(0.003)LEEEVSILNR;KNS(0.999)LISSLEEEVSILNR;KNS(0.999)LISSLEEEVSILNR;KNS(1)LISSLEEEVSILNR;KNS(0.999)LIS(0.001)SLEEEVSILNR;KNS(0.626)LIS(0.373)S(0.001)LEEEVSILNR 329.5 3.56E-72 3930416800 1223737.7 888529 1201673.9 822667.3 1431288 1432613 1338873 1043410.6 1148735 714102.5 TRUE FALSE 1272051.809 1041126.944 1232990.509 985388.4365 1187998.177 1099910.342 1233928.636 1029425.388 1107392.252 854017.2126 1.489492004 1.21909363 1.443753698 1.153827373 1.391070531 1.287925262 1.444852185 1.20539185 1.296686104 1 19.70390562 0.204691979 0.65301225 0.988136331 1.336911092 0.470942489 0.10600731 2.452003206 1.368561262 0.163726741 0.036744048 1.602108702 -0.204691979 0.34877476 KNS(ph)SRDSGRGDS(ph)VSDSGSDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNSSRDSGRGDSVSDSGSDALR 22 3 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 2 KNS(0.986)S(0.016)RDS(0.121)GRGDS(0.581)VS(0.106)DS(0.106)GS(0.084)DALR 88.842 0.0037623 262660000 119570 98315 128370 96651 161820 157750 141310 142660 155290 115020 TRUE FALSE 124290.7159 115199.8365 131715.4277 115768.2793 134313.8942 121114.9532 130233.753 140747.876 149701.1432 137555.9668 0.9035647 0.837476113 0.957540634 0.841608561 0.976430883 0.880477641 0.946769202 1.02320444 1.088292618 1 17.0696592 1.808687809 2.401312621 1.047443043 0.900236126 0.641409991 0.045977165 0.159271708 1.757253915 0.025970102 0.012123854 64.37063735 -1.808687809 -0.147206917 KNS(ph)TGSGHSAQELPTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.859)T(0.116)GS(0.025)GHSAQELPTIR;KNS(0.956)T(0.035)GS(0.009)GHSAQELPTIR;KNS(0.999)T(0.001)GSGHSAQELPTIR 215.99 3.33E-15 1487700000 680910 610500 715550 542730 986610 942640 692490 736220 758730 650460 TRUE FALSE 707792.8526 715348.626 734197.8208 650080.3741 818906.3846 723726.1458 638210.8243 726352.1751 731423.4555 777905.1832 0.909870339 0.919583314 0.943814023 0.835680734 1.052707197 0.930352646 0.820422383 0.933728417 0.940247567 1 19.56923479 2.825154141 0.006201016 1.845446094 2.93E-07 0.071701673 0.062191675 27421.3351 62.55041382 9137.77026 9474.809263 668.5811696 -2.825154141 -1.845445801 KNS(ph)WEPKPITVPQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNSWEPKPITVPQFK 15 2 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 KNS(1)WEPKPITVPQFK;KNS(1)WEPKPITVPQFK 134.06 1.95E-05 2482700000 1812620 708540 1349170 764520 1853980 1588500 1703350 1195090 1571630 594650 TRUE FALSE 1884183.637 830226.2333 1384330.479 915739.7741 1538841.142 1219594.949 1569836.976 1179071.773 1515067.343 711160.2822 2.649450039 1.167424917 1.946580135 1.287670019 2.163845732 1.714936814 2.207430611 1.657955039 2.13041614 1 19.43981523 KNSLIS(ph)SLEEEVSILNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 KNS(0.096)LIS(0.899)S(0.004)LEEEVSILNR;KNS(0.467)LIS(0.531)S(0.002)LEEEVSILNR;KNS(0.138)LIS(0.86)S(0.002)LEEEVSILNR 338.16 1.59E-72 3160740000 1769817 1248021 1595324 1100491 1998898 1927142 1751036 1474273 1717644 1049436 TRUE FALSE 1839690.742 1462358.898 1636899.454 1318164.835 1659126.032 1479592.477 1613785.223 1454512.782 1655826.328 1255052.892 1.46582726 1.165177108 1.304247387 1.050286282 1.321957061 1.178908464 1.285830449 1.158925486 1.319327926 1 20.25931673 -4.216961875 0.272673077 7.43E-21 1.256889665 0.308240391 0.110808071 161.2993125 2.327298431 90.52043236 0.122608492 6.07E-05 4.216961875 1.256889665 KNSLISSLEEEVSILNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNSLISSLEEEVSILNR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 223.29 4.95E-15 342820000 381520 414320 441990 335880 527030 556710 444420 457810 443740 403750 FALSE TRUE 396582.7042 485476.237 453508.6225 402316.0615 437445.6289 427422.5395 409585.1991 451673.8058 427769.8841 482857.0822 0.82132523 1.005424286 0.939219159 0.833199049 0.9059526 0.88519472 0.848253477 0.935419242 0.885914072 1 18.88123671 -1.230765678 4.174597662 1.000055886 0.898878434 0.26036841 0.052546316 2.92E-05 5.37E-06 0.048805161 0.011496423 0.058780642 1.230765678 -0.101177452 KNSTGS(ph)GHSAQELPTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNSTGSGHSAQELPTIR 17 1 O94763-3;O94763;O94763-2;O94763-4;I3L280 O94763-3 URI1 Unconventional prefoldin RPB5 interactor 1 1 KNS(0.347)T(0.013)GS(0.64)GHSAQELPTIR 237.39 1.98E-20 958440000 135420 129600 167740 147570 250430 252430 205560 220140 222270 155200 TRUE FALSE 140766.4862 151857.7919 172111.4422 176758.9055 207861.9981 193806.9581 189447.6701 217189.3834 214270.5461 185608.4685 0.758405515 0.818161979 0.927282271 0.952321341 1.119895012 1.044170881 1.020684409 1.170148028 1.154422251 1 17.50190301 4.042011036 0.77611083 1.104254572 0.696795207 0.807596052 0.056926 0.479215598 0.410037 0.023737109 0.144058698 11015.673 -4.042011036 -0.407459365 KNTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 KNT(0.001)FT(0.001)AWS(0.999)DEES(0.995)DY(0.005)EIDDRDVNK 79.9 0.0063258 63786000 63657 31370 41107 30384 54288 57032 54956 47144 50457 36811 TRUE FALSE 66170.22751 36757.55348 42178.28219 36393.86451 45060.14515 43787.18233 50648.40512 46512.11179 48641.06243 44023.41066 1.503069083 0.834954696 0.958087562 0.826693433 1.023549618 0.994634029 1.150487987 1.056531311 1.104890823 1 15.4259833 2.273885909 24.15654486 1.082307428 1.003011324 0.013767817 0.180137857 456.2003942 311961.8269 0.060333639 0.050476245 187.8823178 -2.273885909 -0.079296104 KNTFTAWS(ph)DEESDYEIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNTFTAWSDEESDYEIDDR 19 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 KNT(0.002)FT(0.002)AWS(0.995)DEES(0.001)DYEIDDR 52.927 0.075617 97121000 37645 47591 62714 53642 53520 63558 66035 59020 58405 41110 TRUE FALSE 39131.25367 55764.38404 64348.37836 64252.22749 44422.68952 48797.61773 60859.00415 58228.93344 56303.01546 49164.7174 0.79592146 1.13423583 1.308832467 1.306876779 0.903548151 0.99253327 1.23785933 1.184364246 1.145191479 1 15.58533573 2.227444773 24.97756203 1.163006071 1.089969857 0.028975639 0.161421152 859.472774 1931242.326 0.063322739 0.047202154 168.8281155 -2.227444773 -0.073036214 KNTLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNTLAR 6 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ; 118.69 0.034721 1908350000 4149800 3699900 4424700 3649400 6326000 6331100 5871500 5566600 5212000 5227300 FALSE TRUE 4313637.308 4335329.044 4540011.317 4371240.428 5250708.78 4860797.974 5411276.488 5491988.832 5024421.138 6251489.352 0.690017541 0.693487391 0.726228753 0.699231844 0.839913256 0.77754239 0.865597969 0.878508868 0.80371586 1 22.57576851 6.240968467 0.081509837 1.204675534 2.21E-14 0.83474333 0.038896146 45.76725335 0.392732728 1.177427777 6.507670239 1741680.412 -6.240968467 -1.204675534 KNVFIIGATNRPDIIDPAILRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KNVFIIGATNRPDIIDPAILRPGR 24 3 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 151.91 4.51E-08 3737600000 3898300 3698200 4104600 3707400 4850300 5089100 4137300 3973600 4343700 3803200 FALSE TRUE 4052207.894 4333337.082 4211569.248 4440712.655 4025847.738 3907233.651 3813007.615 3920340.391 4187371.085 4548364.223 0.890915436 0.952724291 0.925952505 0.976331806 0.885119911 0.859041506 0.838325039 0.861923144 0.920632315 1 22.11691636 3.121875605 8.591341203 0.879856821 0.936779904 0.120149142 0.047561011 0.349210463 24.78977292 0.013099582 0.015681046 1323.962259 -3.121875605 0.056923083 KNWVVTGADDMQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KNWVVTGADDMQIR 14 1 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 108.63 0.0013056 319300000 183570 173750 192060 146620 228980 255690 210460 189150 203490 218020 FALSE TRUE 190817.4853 203590.2109 197065.2414 175620.9984 190058.0614 196309.8725 193963.5953 186614.7536 196166.4346 260736.8448 0.731839359 0.780826396 0.755801281 0.673556507 0.728926752 0.752904227 0.743905586 0.715720687 0.752354102 1 17.99223494 0.937922961 18.71556989 1 0.735293253 0.897454204 0.026692954 264.8324493 79844.84961 0.026626644 0.006656661 8.668080991 -0.937922961 -0.264706747 KPAFNLSAFGTLS(ph)PSLGNSSILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPAFNLSAFGTLSPSLGNSSILK 23 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 KPAFNLSAFGTLS(0.999)PS(0.001)LGNSSILK;KPAFNLSAFGTLS(0.993)PS(0.007)LGNSSILK 283.75 2.37E-52 1974210000 1034960 795150 936830 814520 1196810 1147910 1131270 953130 1039870 763380 TRUE FALSE 1075821.02 931710.8271 961244.5594 975629.6249 993376.6637 881325.2992 1042598.101 940354.8514 1002445.282 912949.6952 1.178401204 1.020550017 1.052899809 1.068656499 1.088095728 0.965360199 1.14201046 1.030018254 1.098029045 1 19.80017584 4.748707035 24.26610722 1.054703929 1.178401308 0.378668296 0.048541872 925.2921423 2212855.121 0.010477259 0.137995758 56066.96336 -4.748707035 0.123697379 KPALPVS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPALPVSPAAR 11 1 A0A087X0M4;A0A087WWF4;Q9BWU0 A0A087X0M4 SLC4A1AP Kanadaptin 1 KPALPVS(1)PAAR;KPALPVS(1)PAAR;KPALPVS(1)PAAR 107.5 0.00071666 770250000 1327370 1069810 1233230 1181690 1263590 1437180 1445280 1262420 1218840 1034960 TRUE FALSE 1379775.593 1253541.546 1265368.987 1415424.755 1048805.423 1103416.726 1331995.177 1245499.325 1174974.186 1237740.596 1.114753444 1.012765962 1.022321632 1.143555248 0.84735479 0.891476557 1.076150512 1.006268461 0.949289528 1 20.23927756 3.255897608 24.99956792 0.969681462 1.065376854 0.377413528 0.069469961 325.2792517 469042.8408 0.020501386 0.027693881 1802.592701 -3.255897608 0.095695392 KPALVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPALVAK 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;H0YE72;H0YE58;P29692-3;E9PL71;P24534 P29692;P29692-3;P24534 EEF1D;EEF1B2 Elongation factor 1-delta;Elongation factor 1-beta 0 ; 79.469 0.073128 0 1866650 1384200 1493130 1267600 2717000 2130850 1973640 1528550 1606110 1999240 FALSE TRUE 1940346.783 1621925.582 1532042.194 1518327.497 2255165.31 1635992.381 1818940.94 1508062.287 1548306.415 2390952.8 0.81153705 0.678359515 0.64076639 0.635030309 0.943207792 0.684242859 0.760759869 0.630736954 0.647568791 1 21.18915422 -1.226098589 4.017431497 1.000222587 0.711006046 0.449827718 0.09458064 41.86263584 50255474.37 20131.33781 0.021967916 0.059415726 1.226098589 -0.289216541 EGHLSPDIVAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 EGHLSPDIVAEQK 13 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;;;;;; 192.15 2.96E-06 27385940000 8534800 23653540 26734400 24129160 31919950 35825000 29551230 32572660 29650480 24475220 FALSE TRUE 8871760.494 27715851.5 27431120.43 28901835.83 26494208.3 27505186.68 27234927.37 32136076.77 28583365.02 29270670.75 0.303093857 0.946881325 0.937153803 0.987399164 0.90514524 0.939684195 0.930451085 1.097893418 0.976518962 1 24.80295247 4.740272895 4.996137332 0.974776456 0.26913189 0.940169126 0.050426345 0.040415185 3.152418069 0.013615153 0.098820441 54988.62943 -4.740272895 -0.705644566 down KPASFMTSICDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPASFMTSICDER 13 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 220.21 3.40E-11 4391600000 2390660 2528730 2701450 2503800 3302300 3323500 2934180 2870120 2792210 3075190 FALSE TRUE 2485045.103 2963019.707 2771852.006 2999044.167 2740976.226 2551667.493 2704191.305 2831650.736 2691718.908 3677714.602 0.675703629 0.805668745 0.753688719 0.815464083 0.745293347 0.693818789 0.735291233 0.769948471 0.731899889 1 21.8103781 -2.041575552 2.492397218 1.316579325 0.750613122 0.770546504 0.04131629 7912268.224 2628195.53 14296710.31 0.009771522 0.009087082 2.041575552 -0.565966204 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 328.49 1.24E-116 9591200000 2621550 759792 1240305 740378 1820450 1987530 1863660 1175466 1477021 582506 TRUE FALSE 2725050.818 890280.3656 1272628.367 886822.5586 1511010.559 1525956.279 1717581.459 1159710.801 1423863.303 696636.8979 3.911723347 1.277969008 1.826817343 1.273005437 2.169007361 2.190461463 2.465533285 1.664727786 2.043910259 1 19.41004736 0.039612711 0.805326313 0.976733755 2.057857164 0.174297272 0.711289364 8.98776306 6.000336271 1.270264597 0.224085493 1.095500829 -0.039612711 1.08112341 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 144.39 2.14E-10 339570000 176580 68790 110960 38231 211780 178530 84234 89374 137460 92562 TRUE FALSE 183551.5147 80604.14739 113851.7088 45792.97769 175781.7112 137069.1131 77631.51898 88176.08772 132512.8415 110697.7517 1.658132274 0.728146201 1.028491609 0.41367577 1.587942922 1.238228519 0.701292644 0.796548136 1.197068951 1 16.7562664 4.750528054 23.90795721 0.952524486 1.658133075 0.304640197 0.313266661 1242.742476 2482603.892 0.074468022 1.182938124 56302.54853 -4.750528054 0.705608588 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR 389.42 1.70E-166 1.89101E+11 5325814 2113847.9 3014711 2344418.3 4274615 4714006 4765562.8 3088264 3482875 1467211.5 TRUE FALSE 5536081.249 2476884.833 3093276.845 2808137.242 3548017.469 3619249.548 4392025.535 3046870.872 3357527.009 1754683.502 3.155031231 1.411584956 1.762868826 1.600366812 2.022027029 2.06262243 2.503030051 1.736421907 1.913465879 1 20.7427794 0.502153441 1.418078795 1.00074568 2.004065274 0.29945301 0.470603682 2.933310567 7.013755336 0.426295095 0.124683729 3.177996696 -0.502153441 1.003319594 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 329.37 7.52E-117 16675380000 1576950 705201 1138135 444034 1850940 1526850 846563 1008551 1257490 822908 TRUE FALSE 1639209.204 826313.786 1167795.733 531862.5999 1536317.88 1172262.227 780207.18 995033.0235 1212233.181 984141.0671 1.665624227 0.839629413 1.186614168 0.540433295 1.561074861 1.191152637 0.792779822 1.011067475 1.231767702 1 19.9085056 4.75016562 24.32891219 1.037049165 1.665624775 0.333286309 0.265697751 1395.764856 2926022.86 0.060748369 0.955978763 56255.58175 -4.75016562 0.62857561 KPDGVKES(ph)TESSNTTIEDEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPDGVKESTESSNTTIEDEDVK 22 2 Q13557;D6R938;Q13557-8;Q13557-12;H0Y9J2 Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 KPDGVKES(0.949)T(0.051)ESSNTTIEDEDVK;KPDGVKES(0.962)T(0.036)ES(0.002)SNTTIEDEDVK 234.37 1.02E-30 488460000 1289430 282570 667310 376450 988220 893630 1056460 541280 829070 190908 TRUE FALSE 1340337.692 331099.1994 684700.6468 450910.6864 820242.7174 686097.9756 973651.9047 534025.027 799231.9326 228312.7674 5.870620846 1.450200105 2.998959079 1.974969212 3.592627458 3.005079318 4.264553032 2.339006412 3.500601134 1 17.80065201 4.755252192 24.54170066 2.799822614 5.87062395 0.492635782 0.964387329 2158.116197 3173020.9 0.213526896 5.841530428 56918.33565 -4.755252192 3.070801336 KPDHVPISSEDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPDHVPISSEDER 13 1 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 137.8 3.67E-05 700350000 728790 813160 859700 795180 933290 963920 902880 826810 852930 668540 FALSE TRUE 757563.1919 952813.9045 882104.4883 952464.2306 774649.6992 740064.1883 832109.9064 815727.9643 822233.2159 799527.613 0.947513481 1.191721073 1.10328208 1.191283722 0.968884234 0.925626803 1.04075193 1.020262404 1.028398773 1 19.60878833 3.223543501 24.99981004 0.999508314 1.114028885 0.374682259 0.070150029 239.3919864 398528.1948 0.01974851 0.023690542 1673.18322 -3.223543501 0.114520571 KPDIYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPDIYER 7 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ;; 92.062 0.025567 672740000 1119010 1158090 1236370 1151920 1420860 1501960 1305400 1263910 1192370 1245330 FALSE TRUE 1163189.379 1356982.949 1268590.818 1379766.338 1179342.725 1153152.552 1203079.337 1246969.354 1149456.837 1489328.57 0.781015957 0.911137392 0.851787069 0.92643515 0.791862016 0.774276795 0.807799811 0.837269477 0.771795331 1 20.50623064 5.053467911 12.12532869 0.843293734 0.503923902 0.071317779 0.070683056 353758.0909 2900436.949 0.016096808 2637859.129 113101.3819 -5.053467911 -0.339369832 KPEDRPNTSEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPEDRPNTSEILR 13 2 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 0 ; 183 6.03E-06 420860000 267150 232088 240614 198972 324160 304140 264670 265500 284760 234986 FALSE TRUE 277697.2883 271947.3086 246884.5985 238328.0677 269059.399 233508.0943 243924.4738 261941.4068 274511.5432 281027.0076 0.988151604 0.967691009 0.878508442 0.84806108 0.957414738 0.830909799 0.867975202 0.93208624 0.976815522 1 18.10034926 1.272045726 2.774267719 0.996221483 0.903771695 0.305066013 0.049603758 0.329066692 4.212607058 0.046121798 0.013438333 18.7087911 -1.272045726 -0.092449788 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;;;;;;;;; 239.19 2.72E-37 7270316000 4803088 2462218 3228023 2557192 4657030 4452793 4453525 3075831 3761173 1778841 FALSE TRUE 4992717.623 2885084.788 3312147.931 3062996.945 3865429.704 3418699.308 4104446.073 3034604.516 3625809.118 2127370.836 2.346895773 1.356173893 1.556920813 1.439803956 1.81699854 1.607006757 1.929351481 1.426457703 1.70436158 1 21.02064011 -2.458093981 0.355850572 9.08E-11 1.69213541 0.357344141 0.277477591 64.13879399 2.702892196 50.13074505 0.196471389 0.003482619 2.458093981 1.69213541 KPEDWDERPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPEDWDERPK 10 2 P27824;P27824-2;P27824-3;D6RGY2 P27824 CANX Calnexin 0 ; 78.653 0.016513 179006000 434880 228790 284700 354410 446560 496780 525250 281740 366650 248783 FALSE TRUE 452049.3982 268082.9028 292119.5159 424511.2402 370653.8907 381410.3738 484079.5325 277963.7361 353454.3381 297527.2656 1.519354528 0.901036422 0.981824356 1.426797774 1.245781256 1.281934188 1.627008979 0.934246263 1.187972932 1 18.18266236 1.623875983 25 1.04583192 1.262511743 0.20383644 0.216953835 1.521320134 2370.003541 0.102253619 0.056473166 42.06065034 -1.623875983 0.216679823 KPEEES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 72.817 0.019737 470240000 737080 486650 581670 563090 645430 735060 902150 673910 663280 409570 TRUE FALSE 766180.4875 570228.3519 596828.798 674467.5213 535720.0391 564353.4549 831437.1257 664877.3387 639408.6824 489817.3998 1.564216559 1.164165161 1.218472023 1.376977465 1.093713779 1.152171105 1.697443019 1.357398367 1.305402141 1 18.9018845 KPEEES(ph)PRKDDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 138.55 3.41E-05 871430000 2677660 519595 1076570 556922 1751050 1788540 1820640 1075190 1347210 439502 TRUE FALSE 2783376.084 608831.3994 1104626.299 667079.5094 1453407.146 1373178.691 1677933.479 1060778.837 1298724.175 525614.0021 5.295475526 1.158324164 2.101592222 1.269143338 2.765160632 2.61252304 3.192330251 2.018170811 2.470870582 1 19.00364418 0.18760505 1.179986414 0.996768125 2.474400447 0.147848209 1.100380684 11.51450877 14.8034669 1.070938941 0.299686014 1.540299058 -0.18760505 1.477632322 KPEENPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPEENPASK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 157.97 0.00010786 398670000 1185150 711440 902880 685120 1331790 1170860 1199990 939070 1125830 647420 FALSE TRUE 1231940.637 833624.2858 926409.7945 820634.6911 1105412.812 898945.5096 1105931.648 926483.3027 1085311.598 774269.5534 1.591100453 1.076659003 1.196495188 1.059882424 1.427684721 1.161023968 1.42835482 1.196590126 1.401723203 1 19.56247639 -1.04340728 4.565112688 0.999988458 1.268730405 0.203038196 0.165797372 1.78E-05 3.72E-06 0.146371603 0.034498637 0.090488361 1.04340728 0.268741947 KPEPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPEPDAR 7 1 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 0 ; 75.38 0.069955 209050000 589880 576770 636030 618080 736860 750930 738030 685830 641920 577740 FALSE TRUE 613168.9179 675825.7609 652605.4643 740334.3792 611608.8004 576537.888 680181.2801 676637.5706 618817.4246 690937.0915 0.887445363 0.978129224 0.944522262 1.071493177 0.88518739 0.834428916 0.984433009 0.979304164 0.895620502 1 19.39819484 -1.268017777 4.893577675 1.000014397 0.945010081 0.067861745 0.06433142 1.01E-05 1.51E-06 0.062245412 0.014667544 0.053948854 1.268017777 -0.055004316 KPESPYGNLCDAPDS(ph)PRPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPESPYGNLCDAPDSPRPVK 20 2 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 KPESPYGNLCDAPDS(1)PRPVK;KPESPYGNLCDAPDS(1)PRPVK;KPESPYGNLCDAPDS(1)PRPVK 161.39 1.18E-11 687340000 588380 401509 494010 432779 662000 643660 643920 574030 629090 424652 TRUE FALSE 611609.6967 470465.0474 506884.3064 518381.3945 549473.4765 494179.7198 593447.8678 566336.0668 606449.1738 507854.4289 1.204301197 0.926377758 0.998089763 1.020728313 1.081950742 0.973073565 1.168539318 1.115154333 1.194139776 1 18.9540555 2.232771282 24.99913942 1.128975414 1.029123208 0.19335016 0.084170786 191.9379093 828805.9442 0.029032599 0.022030362 170.9114987 -2.232771282 -0.099852207 KPFSQHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPFSQHVR 8 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 156.35 0.00025603 470020000 250840 605440 387910 388030 1641400 1000500 606640 491230 495680 2418600 FALSE TRUE 260743.3569 709419.6103 398019.2533 464781.1758 1362395.414 768149.0377 559089.9716 484645.8653 477840.5736 2892478.363 0.090145309 0.245263584 0.13760492 0.160686137 0.471013174 0.265567773 0.193290978 0.167553843 0.165201088 1 21.46387474 -2.000682496 3.225833107 1.790723907 0.21327603 0.850380019 0.09931776 147492356.2 175479279.9 866055155 0.024574744 0.009984297 2.000682496 -1.577447877 KPFSVSS(ph)TPTMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPFSVSSTPTMSR 13 1 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 KPFSVS(0.013)S(0.493)T(0.493)PT(0.002)MSR 110.12 0.00066358 425290000 214910 207590 233550 190540 225310 309560 244670 224200 223330 211440 TRUE FALSE 223394.8127 243241.9677 239636.5049 228228.2433 187011.8867 237669.3814 225492.1261 221194.9657 215292.3969 252867.6197 0.883445706 0.961934027 0.947675725 0.902560176 0.739564389 0.939896463 0.891739821 0.874746106 0.851403581 1 17.94802278 4.304649048 0.001531521 1.784018195 6.66E-08 0.012189998 0.0679802 3921053.727 1086.264694 626638.9159 638747.0589 20167.35985 -4.304649048 -1.784018129 KPFSVSST(ph)PTMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPFSVSSTPTMSR 13 1 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 KPFS(0.001)VS(0.032)S(0.156)T(0.799)PT(0.012)MSR 86.411 0.0051796 534750000 170150 161580 156610 153560 157530 178340 162920 157590 164000 124810 TRUE FALSE 176867.6534 189330.1081 160691.3853 183933.7097 130753.1069 136923.2378 150149.9047 155477.7638 158097.672 149264.1299 1.184930723 1.268423353 1.076557277 1.232270002 0.875984786 0.917321783 1.005934278 1.041628447 1.059180609 1 17.18750798 3.250742354 24.99999926 0.98774745 1.187966082 0.687392157 0.068406739 140.5741865 288492.0379 0.020042248 0.026940437 1781.321683 -3.250742354 0.200218632 KPGADLSDYFNYGFNEDTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPGADLSDYFNYGFNEDTWK 20 1 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 ; 138.04 4.03E-06 560580000 337524 224371 309676 219606 389150 383100 345474 327304 339210 261922 FALSE TRUE 350849.7081 262904.9739 317746.411 263043.4113 323002.422 294130.8309 318394.8452 322917.0252 327001.8984 313240.6011 1.120064599 0.839306823 1.014384501 0.839748776 1.031163971 0.938993317 1.016454585 1.030891347 1.043932036 1 18.2569117 2.151717688 5.632428679 1.027023961 0.958077548 0.112006567 0.080186609 0.390795503 19.75181893 0.027957593 0.020560446 141.8135368 -2.151717688 -0.068946413 KPGDLSDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPGDLSDELR 10 1 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;;; 131.12 0.00041474 2409030000 4900900 4677300 4951300 4288720 6223900 6022700 5448000 5044600 5192900 4423060 FALSE TRUE 5094391.316 5480589.891 5080334.946 5137016.015 5165963.701 4624019.2 5020971.524 4976985.388 5006008.543 5289673.922 0.963082298 1.0360922 0.960424975 0.971140394 0.976612883 0.874159592 0.949202465 0.940886993 0.946373749 1 22.33474736 3.438641381 1.528840051 0.940458527 0.993495833 0.205540218 0.03543353 0.504776216 2.397406398 0.011016551 0.019300008 2745.626016 -3.438641381 0.053037305 KPGGAVT(ph)PQQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPGGAVTPQQQQR 13 1 O95622 O95622 ADCY5 Adenylate cyclase type 5 1 KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR;KPGGAVT(1)PQQQQR 168.29 1.79E-05 583420000 686680 704870 571549 858480 773720 1075470 801830 663990 579070 732350 TRUE FALSE 713790.6566 825925.9394 586444.0365 1028284.782 642203.3508 825708.3914 738980.4694 655090.3001 558229.3838 875839.9608 0.814978408 0.943010112 0.66957899 1.174055567 0.733242806 0.942761724 0.843739156 0.747956624 0.637364597 1 19.74030775 1.910565291 4.796205347 0.770700219 0.880676011 0.050110245 0.153434095 0.533209201 20.08418024 0.06526688 0.038449176 81.38892108 -1.910565291 0.109975792 KPGGEREER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPGGEREER 9 2 E9PKP7;P17480-2;P17480;E9PLT2 E9PKP7 UBTF Nucleolar transcription factor 1 0 77.379 0.01843 38158000 76123 76039 87698 62486 119350 99593 72031 86965 97896 111530 FALSE TRUE 79128.39482 89098.10675 89983.48192 74845.5443 99062.92963 76464.0351 66385.022 85799.37642 94372.74208 133382.1681 0.593245678 0.667991142 0.674629024 0.56113606 0.74269995 0.573270297 0.497705375 0.643259722 0.707536423 1 17.02520628 0.797704707 2.310770956 0.999683503 0.618390583 0.757034186 0.064827494 0.378586288 3.362373903 0.062154793 0.016826449 6.276314638 -0.797704707 -0.381292919 KPGGFDISLFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPGGFDISLFYR 12 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 162.48 0.00010031 1611200000 722550 751920 803220 690970 1188900 1092000 966890 839450 914800 1081400 FALSE TRUE 751076.8319 881056.4109 824152.5731 827641.8037 986811.2027 838399.5494 891102.6353 828198.5458 881876.5267 1293279.625 0.580753626 0.681257474 0.637257834 0.639955805 0.763030039 0.648273995 0.689025496 0.640386294 0.681891611 1 20.30260281 -5 0.412492605 6.908289151 0.657531764 0.840880778 0.044171068 303.5103856 2.027587137 1621.428088 0.025365148 1.00E-05 5 -6.250757387 KPGMFFNPEESELDLTYGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 283.88 9.94E-45 24532140000 4896408 5335426 5530902 5348300 6578600 6937830 5811960 5638150 5848670 5976440 FALSE TRUE 5089721.969 6251743.912 5675041.85 6406177.777 5460371.922 5326624.126 5356403.388 5562579.821 5638177.509 7147408.992 0.712107279 0.874686746 0.793999875 0.896293718 0.763965225 0.745252459 0.749418901 0.778265219 0.788842155 1 22.76898891 -0.778615494 4.484271875 1.000000681 0.790346782 0.579372949 0.053875367 11975492.24 31958438.42 148.4634898 0.01287832 0.166488602 0.778615494 -0.209653899 KPGPPLS(ph)PEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KPGPPLSPEIR 11 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR;KPGPPLS(1)PEIR 127.88 0.00016995 5375990000 4428620 3926770 4401270 4242060 5537180 5572810 5114490 4862560 4784440 4118650 TRUE FALSE 4603465.337 4601162.201 4515970.712 5081126.807 4595972.121 4278609.334 4713602.91 4797385.337 4612248.939 4925620.611 0.934596003 0.93412842 0.916832836 1.031570884 0.93307473 0.868643704 0.956956145 0.973965661 0.936379251 1 22.23187408 0.358670599 0.686953387 1.000859677 0.941350772 0.155036507 0.039470205 4.457765517 3.076725482 0.052862763 0.015158776 2.283865891 -0.358670599 -0.059508906 KPGPSGPSES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPGPSGPSES(1)PK;KPGPSGPS(0.001)ES(0.999)PK 131.72 0.00011867 586220000 1970210 518800 685590 475370 995260 1281260 1027190 701410 792680 377820 TRUE FALSE 2047995.412 607899.8643 703457.0386 569396.7672 826086.0607 983706.7827 946676.1637 692008.7462 764151.6016 451846.5952 4.532501592 1.34536781 1.556849263 1.260155046 1.828244518 2.177081322 2.095127359 1.531512583 1.691174858 1 18.78547353 4.742306807 24.99407816 1.654421766 4.532502694 0.864459147 0.346816305 127.4176729 850078.9181 0.084100516 0.631743886 55246.75913 -4.742306807 2.878080928 KPGQSFQEQVEHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPGQSFQEQVEHYR 14 1 O15042-2;O15042;E7ET15;O15042-3;H7C4V2 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 ; 209.39 4.35E-09 342140000 503100 515210 544100 509370 645770 661780 591030 625220 633820 602300 FALSE TRUE 522962.7765 603693.3097 558279.693 610121.8657 536002.2461 508091.6244 544703.5242 616839.9486 611008.942 720309.1533 0.726025449 0.838103066 0.775055669 0.847027784 0.744128051 0.705379936 0.756207972 0.85635445 0.848259305 1 19.45825671 0.939408838 1.161627238 0.99676588 0.774762102 0.689908476 0.046028681 0.325135465 0.893946739 0.044776954 0.014061956 8.697788402 -0.939408838 -0.222003778 KPGTPLPPPATSPSS(ph)PRPLS(ph)PVPHVNNVVNAPLSINIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPGTPLPPPATSPSSPRPLSPVPHVNNVVNAPLSINIPR 39 2 Q06190;Q06190-2 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 2 KPGT(0.059)PLPPPAT(0.249)S(0.25)PS(0.254)S(0.26)PRPLS(0.928)PVPHVNNVVNAPLSINIPR 56.896 0.044529 275570000 80734 67743 78888 72814 95017 91101 74355 84799 84385 69215 TRUE FALSE 83921.44066 79377.33328 80943.88609 87216.39187 78866.04428 69944.1734 68526.86081 83662.40811 81348.00033 82776.35405 1.013833499 0.958937298 0.977862422 1.053638963 0.952760546 0.844977702 0.82785551 1.010704193 0.982744423 1 16.33693108 3.01041853 24.86102537 0.928256372 0.997251 0.21402315 0.061014627 331.0675457 789996.5688 0.018977287 0.022660511 1024.279617 -3.01041853 0.068994628 KPIDSLRDS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;KPIDS(0.005)LRDS(0.995)R;KPIDS(0.002)LRDS(0.998)R 124.51 0.00034142 3183440000 2928440 2329390 2434580 2850100 3001230 3233750 3761160 2885980 2683710 2018600 TRUE FALSE 3044057.072 2729444.612 2498027.155 3413841.273 2491081.997 2482760.57 3466350.451 2847298.159 2587123.801 2414106.022 1.260945893 1.13062334 1.03476282 1.414122347 1.031885913 1.028438912 1.43587333 1.179442051 1.071669503 1 21.20305761 1.102925843 3.683686872 1.004812907 1.19082421 0.171310332 0.13952285 0.36613378 8.898992955 0.129659348 0.033744749 12.67435429 -1.102925843 0.186011303 KPIDYTVLDDVGHGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPIDYTVLDDVGHGVK 16 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7 A0A0A0MRT6 ABI1 Abl interactor 1 0 122.31 6.10E-05 218930000 219610 164210 195760 158290 268370 247810 201840 199030 217460 172790 FALSE TRUE 228280.3724 192411.7901 200861.6664 189599.2896 222752.5633 190259.8831 186019.2534 196362.3284 209633.6571 206644.8922 1.104698838 0.931122894 0.972013701 0.917512586 1.077948556 0.920709344 0.900188006 0.950240416 1.014463289 1 17.65679418 KPIETGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KPIETGSPK 9 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KPIET(0.274)GS(0.726)PK;KPIETGS(1)PK;KPIET(0.001)GS(0.999)PK;KPIET(0.006)GS(0.994)PK;KPIET(0.006)GS(0.994)PK;KPIETGS(1)PK 111.88 0.0012578 20989400000 31051300 9196490 14377450 9141160 21395900 28771600 19657700 14510490 16580090 7882580 TRUE FALSE 32277229.3 10775915.62 14752138.16 10949254.16 17759032.56 22089831.94 18116878.11 14316000.62 15983375.8 9427020.63 3.423905661 1.143088155 1.564878103 1.161475571 1.883843608 2.343246377 1.921803168 1.518613481 1.695485395 1 23.16837045 7.9999698 0.046356968 1.71E-08 4.851325235 0.182204948 0.611127286 1298.694171 4.557632301 118.5935877 464.0066495 99993046.51 -7.9999698 4.851325218 KPIKS(ph)PSKDASSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPIKSPSKDASSGK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.497)PS(0.497)KDAS(0.003)S(0.004)GK 62.658 0.053725 1540200000 5929400 1532200 2790900 1934300 4788300 3763100 5128600 3018700 3637200 786800 TRUE FALSE 6163497.29 1795343.431 2863633.147 2316898.767 3974386.476 2889177.055 4726606.931 2978239.264 3506297.882 940958.3958 6.550233589 1.907994486 3.043315368 2.46227546 4.223764296 3.070462061 5.023183758 3.165112589 3.726304902 1 19.84377141 -0.377069174 9.254147469 1.000472613 3.602036342 0.285777492 1.267595792 0 4.81E-17 1.125033124 0.26517285 0.41969213 0.377069174 2.601563729 KPIKSPS(ph)KDASSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPIKSPSKDASSGK 14 3 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 KPIKS(0.475)PS(0.514)KDAS(0.006)S(0.006)GK 93.495 0.0032392 990800000 5177400 1316100 2556300 1536500 3669600 3462900 4405700 2611900 3320500 731290 TRUE FALSE 5381807.75 1542129.937 2622919.278 1840415.114 3045842.703 2658693.956 4060369.722 2576891.753 3200995.854 874572.2741 6.153645512 1.763296165 2.999088075 2.104360232 3.482665519 3.039993417 4.642692024 2.946459463 3.660070126 1 19.73821809 KPITDDDVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KPITDDDVDR 10 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 138.94 8.26E-05 4739670000 6892500 5545280 6680790 6009850 7429950 7478160 7454040 6275660 6598090 5006960 FALSE TRUE 7164621.222 6497638.704 6854896.876 7198580.392 6167009.753 5741470.673 6869772.867 6191545.043 6360626.03 5987977.948 1.196500936 1.085114 1.144776573 1.202172161 1.029898541 0.958832969 1.147260883 1.033995966 1.062232708 1 22.51363748 3.225986725 24.9983106 1.043698957 1.151112972 0.53054571 0.054339803 192.040823 381798.212 0.015570632 0.018729902 1682.622629 -3.225986725 0.107414015 KPLAAPGDGEGLGQTAQPS(ph)PPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPLAAPGDGEGLGQTAQPSPPAR 23 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQT(0.001)AQPS(0.999)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR;KPLAAPGDGEGLGQTAQPS(1)PPAR 200.04 1.53E-24 2717210000 1339930 1245690 1351280 1202650 1480670 1628620 1447820 1430270 1434760 1324310 TRUE FALSE 1392831.471 1459627.567 1386495.467 1440530.58 1228986.242 1250397.687 1334336.085 1411099.57 1383123.268 1583783.189 0.87943317 0.921608196 0.87543262 0.909550367 0.775981366 0.789500543 0.84249921 0.89096764 0.873303415 1 20.59494342 0.492554199 1.250789693 0.99987108 0.858736631 0.464961913 0.044752764 2.059544046 4.062307155 0.046962686 0.01410013 3.108523816 -0.492554199 -0.141134449 KPLFFGEGTVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPLFFGEGTVLR 12 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 175.88 4.25E-05 5896300000 2005030 1941110 2143300 2038600 2424700 2441400 2319400 2187100 1868760 2230300 FALSE TRUE 2084190.133 2274480.543 2199156.159 2441828.995 2012550.36 1874421.85 2137599.367 2157785.502 1801503.693 2667284.583 0.781390237 0.852732609 0.824492509 0.915473741 0.754531546 0.702745354 0.80141406 0.808982107 0.67540738 1 21.34694033 5.071210937 14.23500906 0.807313522 0.514123984 0.005772922 0.090742482 3095296.23 14534992.54 0.020574704 26480974.75 117817.8075 -5.071210937 -0.293189538 KPLFHGDSEIDQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPLFHGDSEIDQLFR 15 1 P06493;A0A024QZP7;A0A087WZZ9;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 ; 238.02 6.07E-18 4061900000 4388400 4583700 5076300 4967400 5805200 6576200 5385700 5381200 5072300 5363000 FALSE TRUE 4561657.421 5370914.819 5208592.548 5949936.894 4818434.178 5048977.213 4963554.761 5309073.816 4889748.914 6413777.169 0.711227924 0.837402778 0.812094404 0.927680638 0.751263109 0.78720808 0.773889493 0.827760877 0.762382101 1 22.6127428 -1.905657224 2.64004803 1.110850093 0.803294823 0.536343432 0.055939365 7055246.591 4302544.614 4854156.207 0.012804355 0.012426327 1.905657224 -0.30755527 KPLHYAADCGQLEILEFLLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPLHYAADCGQLEILEFLLLK 21 1 P58546 P58546 MTPN Myotrophin 0 ;;; 211.03 2.75E-22 6323190000 6558030 5135730 6368750 5387190 7544100 7956280 7040680 6680900 7018270 5601050 FALSE TRUE 6816946.088 6017751.677 6534724.857 6452760.103 6261756.577 6108554.549 6488813.104 6591353.463 6765683.834 6698468.509 1.017687264 0.898377244 0.975555061 0.963318719 0.934804212 0.91193301 0.968700994 0.984009025 1.010034432 1 22.67539985 1.688074349 2.401842431 1.003035833 0.948891448 0.313352894 0.031731691 0.290369461 3.660663955 0.020124731 0.008376102 48.76119597 -1.688074349 -0.054144385 KPLIS(ph)PQTSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPLISPQTSHK 11 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 KPLIS(1)PQTSHK 98.943 0.0024188 388380000 602150 410870 549420 429480 672300 654250 660920 503200 592250 406170 TRUE FALSE 625923.347 481433.7264 563738.3366 514429.8621 558022.6861 502310.3528 609115.3634 496455.4271 570935.0382 485751.2349 1.288567691 0.991111688 1.160549467 1.059039741 1.148782846 1.034089708 1.253965651 1.022036366 1.175365078 1 18.88985814 -2.021587303 2.28267793 0.868391279 1.117503822 0.132165583 0.094619702 6974105.412 2419725.48 4808872.229 0.020862169 0.009515086 2.021587303 0.249112543 KPLPDHVSIVEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPLPDHVSIVEPK 13 1 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 0 ; 127.26 0.00011619 2379000000 1363060 3416500 3951800 3483200 4577200 4898100 4366900 4440300 4192200 2853000 FALSE TRUE 1416874.661 4003257.298 4054787.154 4172166.564 3799169.179 3760590.506 4024610.967 4380785.041 4041323.541 3411990.726 0.415263339 1.173290791 1.188393369 1.2227954 1.113475822 1.102169029 1.179549211 1.283938144 1.184447399 1 21.70218229 4.738555499 10.0657827 1.175110137 0.413488862 0.901972674 0.073609449 0.019719298 68.28217381 0.017619702 0.102109601 54771.60894 -4.738555499 -0.761621275 KPLPDHVSIVEPKDEILPT(ph)TPISEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPLPDHVSIVEPKDEILPTTPISEQK 26 2 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 KPLPDHVSIVEPKDEILPT(0.554)T(0.438)PIS(0.007)EQK 75.479 0.024479 3030200000 62389 130930 143560 64046 250970 159450 97637 119930 181470 108950 TRUE FALSE 64852.16589 153416.209 147301.2915 76714.10764 208310.209 122420.154 89983.95681 118322.5345 174938.9301 130296.6665 0.497726977 1.177437713 1.130506984 0.588764929 1.598737823 0.939549393 0.69060828 0.90810101 1.342620151 1 16.99144065 4.749895264 23.76102985 1.020373612 0.497726353 0.249320492 0.281021448 1239.368088 2598009.428 0.065525916 0.968602716 56220.5725 -4.749895264 -0.522647259 KPLPDHVSIVEPKDEILPTT(ph)PISEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPLPDHVSIVEPKDEILPTTPISEQK 26 2 P23396;P23396-2;E9PPU1;E9PL09;H0YEU2;E9PSF4 P23396 RPS3 40S ribosomal protein S3 1 KPLPDHVSIVEPKDEILPT(0.369)T(0.624)PIS(0.008)EQK;KPLPDHVSIVEPKDEILPT(0.139)T(0.861)PISEQK;KPLPDHVSIVEPKDEILPT(0.017)T(0.983)PIS(0.001)EQK 152.01 1.33E-07 1655090000 406090 647960 1006290 349004 1582700 1097630 598780 964870 1118960 788420 TRUE FALSE 422122.7468 759242.0896 1032514.744 418035.9495 1313673.219 842722.0672 551846.059 951937.4959 1078688.848 942895.8038 0.447687587 0.805223744 1.095046494 0.443353282 1.39323265 0.893759484 0.585267276 1.00958928 1.144017021 1 19.84673883 4.681714263 3.291205568 0.92869674 0.409313063 0.252666496 0.256553053 0.384225814 6.852031671 0.059805687 0.462918414 48052.30923 -4.681714263 -0.519383678 KPLRPDS(ph)LIIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPLRPDSLIIYR 12 2 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 KPLRPDS(1)LIIYR;KPLRPDS(1)LIIYR 142.91 4.86E-05 3143500000 1640960 1670360 1677440 1689100 2439100 2387000 1878130 1947380 1831630 2100870 TRUE FALSE 1705746.368 1957231.336 1721155.464 2023198.939 2024502.653 1832655.425 1730917.263 1921278.556 1765709.994 2512495.253 0.67890531 0.778999019 0.685038295 0.80525483 0.805773723 0.729416473 0.688923595 0.764689427 0.702771475 1 21.26068944 -1.868492364 2.805062632 1.110848821 0.740802993 0.740928493 0.046490084 22511985.21 11105954.65 16484708.53 0.010719569 0.013536539 1.868492364 -0.370045828 KPLSLAGDEETECQSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPLSLAGDEETECQSSPK 18 1 Q86TN4;Q86TN4-4;F5H1K3;Q86TN4-2 Q86TN4 TRPT1 tRNA 2-phosphotransferase 1 1 KPLSLAGDEETECQS(0.002)S(0.998)PK 244.01 2.47E-24 541330000 1182600 321880 504800 397030 713940 720040 687360 575130 578900 255310 TRUE FALSE 1229289.961 377160.3861 517955.5027 475561.349 592584.7338 552821.6223 633482.9271 567421.3231 558065.5021 305333.1063 4.026061818 1.235242358 1.696362078 1.557516493 1.940781139 1.810552511 2.074727287 1.85836816 1.827726803 1 18.2200245 4.74613912 24.9911285 1.72844276 4.026062917 0.832281459 0.316638813 346.5812842 1142871.037 0.072271428 0.769463179 55736.42642 -4.74613912 2.297620158 GACHGQTGMFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GACHGQTGMFPR 12 0 P62993;P62993-2 P62993 GRB2 Growth factor receptor-bound protein 2 0 99.5 0.0037613 78305000 211440 67444 81716 47804 92096 100600 83407 78008 46461 74461 FALSE TRUE 219787.8145 79026.98236 83845.58609 57259.48852 76441.55482 77237.17461 76869.3414 76962.43036 44788.87769 89050.20731 2.468133664 0.887442991 0.941554081 0.643002305 0.858409622 0.86734413 0.863213503 0.864258857 0.502962082 1 16.44233135 4.740698211 4.953808627 0.81990848 2.554086724 0.928744522 0.136626547 0.038127119 2.870163304 0.031002447 0.227491681 55042.50754 -4.740698211 1.734178245 up KPLTSSSAAPQRPISTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPLTSSSAAPQRPISTQR 18 2 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ; 200.6 8.41E-16 2583000000 646860 636920 655950 582470 755140 750650 614320 683580 591280 646260 FALSE TRUE 672398.5323 746306.0555 673044.5959 697680.8275 626781.5725 576322.9137 566167.9932 674417.7282 569999.9483 772882.2736 0.869988296 0.965614145 0.870824211 0.902699999 0.810966423 0.745680078 0.732541051 0.872600849 0.737499057 1 19.55988915 3.233031771 5.93755342 0.805248361 0.905050098 0.214075062 0.078716225 0.204696489 25.93482422 0.021205769 0.026915747 1710.140417 -3.233031771 0.099801738 KPLVIIAEDVDGEALSTLVLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ;;; 208.39 1.11E-22 443680000 499195 587860 563283.5 582547 541464 791194 565829 512929.5 512939 600293 FALSE TRUE 518903.6041 688820.3821 577963.1308 697773.0579 449426.1427 607451.1842 521477.8445 506054.519 494478.4256 717908.92 0.722798658 0.959481576 0.805064702 0.971952066 0.626021115 0.846139625 0.726384406 0.704900726 0.688775988 1 19.4534413 3.243937824 24.99982246 0.748846985 0.867316923 0.138012356 0.117421471 208.1151387 967566.2677 0.0301039 0.039607227 1753.629426 -3.243937824 0.118469938 KPLVLCGDLNVAHEEIDLR ddPTM_MDA-MB-175_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 ;; 201.37 3.91E-16 3907060000 2726990 2523140 3075420 2801130 3239560 3419720 3201120 3048100 2973800 2690290 FALSE TRUE 2834653.671 2956469.668 3155567.972 3355185.153 2688900.748 2625541.856 2950207.85 3007245.205 2866773.519 3217400.817 0.881038401 0.918900018 0.98078174 1.042824735 0.835736951 0.816044381 0.916953783 0.934681557 0.891021567 1 21.61746424 4.724184371 5.602026282 0.92359812 0.879898725 0.039259856 0.066217104 0.58582666 70.97412972 0.016627392 0.093996399 52988.835 -4.724184371 -0.043699395 KPMGPAHWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPMGPAHWEK 10 1 Q8NCA5;E9PH82 Q8NCA5 FAM98A Protein FAM98A 0 65.5 0.044649 307930000 215640 223070 255680 232330 405160 355560 296650 274410 266840 371130 FALSE TRUE 224153.6337 261380.5373 262343.2308 278284.1806 336291.0479 272986.5786 273397.7978 270731.9828 257236.4805 443845.8178 0.5050259 0.588899403 0.591068385 0.626983897 0.757675378 0.615048216 0.615974708 0.609968534 0.5795627 1 18.75969908 -1.863977883 2.459906406 1.178691302 0.613866109 0.796018287 0.05919477 8921928.898 5158684.625 9319216.186 0.015002401 0.013677985 1.863977883 -0.564825193 KPMS(ph)PITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPMSPITAQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 48 2 B1AKL4;Q9NRA8;B0QYZ7;H7C0J7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 KPMS(0.46)PIT(0.509)AQMS(0.031)QLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR;KPMS(0.954)PIT(0.046)AQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR;KPMS(0.885)PIT(0.114)AQMSQLELQQAALEGLALPHDLAVQAANFYQPGFGKPQVDR 204.25 5.05E-39 1911630000 191762 124909 188666 138973 220426 213578 204456 171088 211165 146835 TRUE FALSE 199332.9118 146361.1491 193582.791 166461.4446 182958.0673 163977.7463 188430.2045 168794.8452 203565.2129 175604.5069 1.135124123 0.833470346 1.1023794 0.947933783 1.041875692 0.933790079 1.073037405 0.961221601 1.159225446 1 17.42197035 1.258272166 24.99989738 1.07961287 0.999916723 0.097205967 0.092108575 419.2806622 531770.9155 0.054100608 0.019701548 18.12475591 -1.258272166 -0.079696147 KPMVLGHEASGTVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPMVLGHEASGTVEK 15 1 Q00796;A0A6I8PIS1;H0YKB3;Q00796-2 Q00796 SORD Sorbitol dehydrogenase 0 ; 127.88 4.90E-05 463070000 330880 310090 366380 304630 444660 466700 405650 375370 427520 323330 FALSE TRUE 343943.3979 363345.5453 375928.1638 364884.9048 369076.852 358315.9979 373854.093 370338.7791 412133.6387 386680.323 0.889477373 0.939653568 0.972193674 0.94363453 0.95447539 0.926646578 0.966829887 0.957738879 1.065825216 1 18.56078183 1.360522902 5.044228996 1.03194783 0.944631529 0.644929615 0.026495128 0.122415984 4.424123332 0.018336872 0.006439665 22.93627578 -1.360522902 -0.0873163 KPNAGGS(ph)PAPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPNAGGSPAPVR 12 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 KPNAGGS(1)PAPVR 59.862 0.058817 96255000 45471 112830 117330 127740 115150 149710 108510 119060 122010 117260 TRUE FALSE 47266.23019 132207.6748 120387.7162 153006.5907 95576.84413 114942.1214 100004.7027 117464.1954 117618.8839 140234.8519 0.337050523 0.942759043 0.85847216 1.091073928 0.681548437 0.819640195 0.713123031 0.83762484 0.838727908 1 17.09748541 8 0.04455208 1.285620813 7.85E-08 0.147686383 0.181448489 1610.720007 5.441309358 40.12297374 148.9942608 100000000 -8 -1.285620734 KPNEGADGQWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPNEGADGQWK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 150.14 5.46E-05 944630000 1670890 981510 1313630 1032360 1631150 1631810 1760960 1313280 1506020 879790 FALSE TRUE 1736858.027 1150076.707 1347864.277 1236557.727 1353887.706 1252846.858 1622931.354 1295677.63 1451818.634 1052168.006 1.650742104 1.093054247 1.281035224 1.175247413 1.286760002 1.190728905 1.542464079 1.231436066 1.379835374 1 20.00493366 -2.267724341 1.936136009 4.00E-05 1.30313955 0.250467849 0.162176684 3944981.057 553733.5496 17245860.33 0.037012858 0.005398532 2.267724341 1.303099554 KPNEGADGQWKK ddPTM_MDA-MB-175_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 ; 157.52 4.17E-05 1068530000 2550400 1585330 2086230 1246220 3211100 2465000 2087900 2052570 2729100 1705070 FALSE TRUE 2651091.761 1857598.095 2140598.868 1492718.596 2665278.369 1892541.107 1924244.942 2025058.656 2630880.224 2039145.821 1.300099156 0.910968738 1.049752718 0.732031315 1.307056289 0.928104841 0.943652446 0.993091635 1.29018739 1 20.95953352 1.301565315 24.9998526 1.145106793 1.010227914 0.070733392 0.177345724 133.0129881 52777.55176 0.109315039 0.039918641 20.02466757 -1.301565315 -0.134878879 KPNIFYSGPAS(ph)PARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 174.5 2.36E-09 7967200000 2509740 2508880 2889200 2427370 3077290 3432310 3141930 3085660 2829080 3151370 TRUE FALSE 2608826.473 2939760.624 2964494.926 2907496.541 2554213.345 2635208.02 2895657.317 3044301.775 2727261.963 3768820.615 0.69221296 0.780021371 0.786584247 0.771460581 0.677722186 0.699212907 0.76831922 0.807759797 0.72363804 1 21.8456817 -1.890698469 0.425659734 1.231321206 0.742292125 0.760712183 0.042764721 23.29653642 1.651575444 5.400450414 0.026320816 0.012861793 1.890698469 -0.489029081 KPNVS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPNVSPEK 8 1 A0A0U1RR07;Q9HCH5-13;Q9HCH5;Q9HCH5-14;Q9HCH5-15;Q9HCH5-6 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 KPNVS(1)PEK;KPNVS(1)PEK 89.301 0.008577 830460000 1060830 437120 586980 496130 889880 916950 921310 641020 735610 394950 TRUE FALSE 1102712.388 512191.9597 602277.181 594263.0332 738618.5155 704002.259 849095.3148 632428.1754 709135.5398 472332.8907 2.334608513 1.084387663 1.27511167 1.25814451 1.563766847 1.490479009 1.797662901 1.338945874 1.501346939 1 18.84944447 0.161295285 1.304085522 0.999365955 1.494664378 0.176352297 0.331527154 14.29786298 20.28184388 0.318489 0.088697829 1.449757237 -0.161295285 0.495298423 KPNVS(ph)PEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPNVSPEKQR 10 2 A0A0U1RR07;Q9HCH5-13 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 KPNVS(1)PEKQR 62.042 0.045741 346250000 275880 180530 231820 135130 321750 264670 280550 155520 261340 163380 TRUE FALSE 286771.9554 211534.6232 237861.4196 161858.3107 267059.0499 203204.4036 258559.7579 153435.5088 251934.4244 195391.1829 1.467681147 1.08262113 1.217360047 0.828380832 1.366791715 1.039987581 1.323292863 0.785273452 1.289384816 1 17.57600584 4.739691939 23.5956262 1.094115298 1.46768137 0.248513778 0.189238461 57.7778565 1204696.489 0.041889141 0.256984358 54915.12026 -4.739691939 0.373566072 KPPAPPS(ph)PVQSQS(ph)PSTNWS(ph)PAVPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 3 KPPAPPS(1)PVQS(0.159)QS(0.837)PS(0.004)T(0.001)NWS(1)PAVPVKK 144.69 1.77E-07 1677100000 2003000 1013500 1507400 901030 1837700 1750800 1815200 1449600 1883000 906370 TRUE FALSE 2082079.987 1187560.741 1546684.082 1079251.045 1525328.41 1344203.234 1672919.881 1430170.483 1815231.198 1083955.848 1.920816231 1.095580363 1.426888452 0.995659599 1.407186846 1.240090393 1.543346884 1.319399204 1.674635735 1 20.04787456 2.265075881 24.99941681 1.405880038 1.326544638 0 0.283439392 1234.66825 1164078.85 0.091536146 0.076564358 184.1093653 -2.265075881 -0.0793354 KPPAPPS(ph)PVQSQS(ph)PSTNWSPAVPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQS(0.018)QS(0.932)PS(0.042)T(0.008)NWSPAVPVK 160.86 7.53E-11 682610000 749710 479670 618220 521110 710790 725430 759780 656050 684940 412550 TRUE FALSE 779309.1297 562049.5912 634331.3211 624184.0026 589970.1697 556959.8765 700226.4583 647256.7228 660289.1432 493381.2738 1.579527175 1.13917901 1.285681794 1.265114904 1.195769278 1.128863024 1.419240039 1.311879387 1.338293888 1 18.91234343 4.751108311 24.5596822 1.25106034 1.579527439 0.439653 0.115985887 1545.735159 3025407.564 0.026748462 0.473119314 56377.82419 -4.751108311 0.328467099 KPPAPPS(ph)PVQSQSPSTNWS(ph)PAVPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVKK 26 2 A9Z1X7;Q8IYB3-2;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KPPAPPS(1)PVQSQSPS(0.067)T(0.076)NWS(0.857)PAVPVKK 176.86 1.43E-17 860590000 1446900 820660 1214800 746610 1521200 1378700 1396200 1169900 1395100 740570 TRUE FALSE 1504024.729 961601.9712 1246458.686 894287.2296 1262626.967 1058517.819 1286762.196 1154219.404 1344890.624 885670.5124 1.698176363 1.085733303 1.407361619 1.009729032 1.425617032 1.19515983 1.45286783 1.303215347 1.518499944 1 19.75641056 2.248012062 24.87203116 1.343444416 1.290626059 0 0.221390013 1215.972647 3199898.515 0.070977211 0.058648829 177.0158123 -2.248012062 -0.052818357 KPPAPPS(ph)PVQSQSPSTNWSPAVPVKK ddPTM_MDA-MB-175_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 198.81 3.12E-25 2195800000 1043780 705030 921140 622516 1120230 1002430 979480 951790 1088040 699810 TRUE FALSE 1084989.24 826113.4181 945145.6651 745647.8068 929813.7047 769630.8245 902705.7982 939032.8119 1048881.653 836924.3708 1.296400581 0.987082521 1.129308332 0.890938098 1.110988922 0.919594233 1.07859901 1.122004382 1.25325739 1 19.67473773 -0.307325435 6.531610733 1 1.078481722 0.038853492 0.123426545 7617535.286 1166256.789 0.112897734 0.027381722 0.492804387 0.307325435 0.078481722 KPPCGSTPYSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPPCGSTPYSER 12 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 65.472 0.097265 130680000 115360 128560 143670 130810 145060 182140 199830 157040 133530 133820 FALSE TRUE 119914.5019 150639.1799 147414.1582 156683.8276 120402.753 139840.7454 184166.8024 154935.1357 128724.2814 160039.4669 0.749280813 0.941262695 0.92111128 0.979032426 0.75233163 0.873789123 1.15075866 0.968105797 0.804328357 1 17.2880682 2.383939631 21.89451174 0.986865625 0.874645523 0.21281667 0.104345225 10.92168689 2556.290436 0.036419619 0.030470804 242.0692538 -2.383939631 -0.112220102 KPPLS(ph)PAQTNPVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KPPLSPAQTNPVVQR 15 1 Q8IY33;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR;KPPLS(1)PAQTNPVVQR 225.54 6.03E-13 3594440000 2440030 2152980 2470160 2132570 2703310 2887540 2560330 2453950 2597030 2371450 TRUE FALSE 2536364.269 2522737.567 2534534.399 2554385.981 2243802.332 2216952.596 2359644.644 2421058.814 2503563.398 2836090.223 0.8943172 0.889512451 0.893671992 0.900671622 0.79116042 0.781693254 0.832006198 0.853660717 0.882751676 1 21.435472 0.782980547 2.627991615 0.999957317 0.853055911 0.536529064 0.040403563 0.870697448 9.093273985 0.043267739 0.011502513 6.067091527 -0.782980547 -0.146901406 KPPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPPSPK 6 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 1 KPPS(1)PK;KPPS(1)PK;KPPS(1)PK 67.993 0.059605 5233890000 7608430 1752560 3086780 1771960 4712670 5588440 4793160 3008100 3699900 1457980 TRUE FALSE 7908816.691 2053548.547 3167224.023 2122448.399 3911612.037 4290609.504 4417459.595 2967781.34 3566741.322 1743643.266 4.53579975 1.177734337 1.816440372 1.217249216 2.243355687 2.460715209 2.533465233 1.702057638 2.04556826 1 20.73367348 8 0.055081492 6.09E-11 6.081268158 0.181662002 0.874542266 914.5442904 3.781112552 90.98304406 457.4547494 100000000 -8 6.081268158 KPQSSSTEPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPQSSSTEPAR 11 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ; 137.16 0.00013501 277870000 322900 321040 334960 309260 381230 407810 381060 356620 351690 321260 FALSE TRUE 335648.3413 376176.1227 343689.3328 370430.705 316428.6608 313102.3079 351191.5215 351840.0922 339032.7456 384204.7461 0.873618415 0.979103268 0.894547338 0.964149217 0.823593836 0.814936075 0.914073876 0.915761962 0.882427271 1 18.55151582 -1.475213443 3.177728973 1.002188232 0.897874423 0.281786147 0.0498069 16005207.29 21585883.16 311879.3353 0.012278564 0.033480085 1.475213443 -0.104313809 KPRPLS(ph)MDLTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPRPLSMDLTAR 12 2 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KPRPLS(0.927)MDLT(0.073)AR;KPRPLS(0.996)MDLT(0.004)AR 95.767 0.0046166 1114570000 614600 636050 693840 638830 849360 904000 765020 788050 821190 863800 TRUE FALSE 638864.8826 745286.6397 711922.0404 765188.6673 704986.0906 694059.7003 705055.7334 777487.4787 791635.5323 1033045.072 0.618428857 0.721446392 0.68914906 0.740711793 0.682434978 0.671858101 0.682502393 0.75261719 0.766312675 1 19.97847177 0.566131699 0.878809825 1.001285288 0.688476612 0.892844361 0.032218113 0.403820331 0.500505746 0.030794214 0.010126235 3.682406253 -0.566131699 -0.312808676 KPS(ph)ASERLPDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPSASERLPDEK 12 2 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 KPS(0.993)AS(0.007)ERLPDEK 78.234 0.013711 60851000 52454 45734 56019 50196 68260 69085 57635 54635 58583 52963 TRUE FALSE 54524.92442 53588.45874 57478.90116 60124.61898 56657.18958 53041.05574 53117.4181 53902.70719 56474.60927 63340.08581 0.860828079 0.846043356 0.907464845 0.949234884 0.894491835 0.837401072 0.838606665 0.851004644 0.891609295 1 15.9508312 KPS(ph)ASERLPDEKVELFSK ddPTM_MDA-MB-175_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(0.873)AS(0.127)ERLPDEKVELFSK 143.91 5.64E-07 316390000 485810 205790 326420 182030 543290 368000 355130 340910 407910 211880 TRUE FALSE 504990.1539 241132.8317 334926.7734 218034.9907 450941.7599 282537.5771 327293.9826 336340.6591 393229.3988 253393.8293 1.992906281 0.95161288 1.321763731 0.860458959 1.779608292 1.115013644 1.291641488 1.327343527 1.551850729 1 17.95102187 -1.085187058 4.445377429 0.999972656 1.32946881 0.088845411 0.332033086 8.38E-05 1.72E-05 0.289779243 0.068295771 0.082188857 1.085187058 0.329496154 KPS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPSFSK 6 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 KPS(0.982)FS(0.018)K;KPS(0.71)FS(0.29)K;KPS(0.998)FS(0.002)K 87.308 0.032211 5377310000 8095980 4883570 6961820 5001760 9437840 7929380 8170730 6643690 7870460 4431090 TRUE FALSE 8415615.542 5722285.159 7143250.748 5991093.199 7833599.328 6087901.666 7530286.832 6554642.202 7587203.682 5299277.247 1.588068551 1.079823699 1.34796698 1.130549114 1.478239194 1.148817354 1.421002616 1.236893617 1.431743109 1 22.33736418 -1.447207432 4.371664083 0.998829415 1.305512417 0.262745559 0.158605331 0.001579451 0.000199721 0.134041257 0.031477662 0.035710223 1.447207432 0.306683002 KPS(ph)GSPDLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.894)GS(0.106)PDLWK;KPS(0.637)GS(0.363)PDLWK 94.547 0.0085058 394500000 1649280 824880 1208050 848950 1582720 1481390 1492230 1223380 1327370 706390 TRUE FALSE 1714394.848 966546.7233 1239532.775 1016869.776 1313689.82 1137359.623 1375265.113 1206982.592 1279598.213 844793.5958 2.029365346 1.144121745 1.467261094 1.203690204 1.555042351 1.346316578 1.627930325 1.428730755 1.514687397 1 19.68823937 -1.963739248 2.347890549 0.619129229 1.463377555 0.273863291 0.23296684 10781081.21 4320299.798 22336610.94 0.050451504 0.010870781 1.963739248 0.844248326 KPS(ph)LIGLDPEQGHLNPMSYTQHCITTMAAPSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 150.69 9.52E-11 668860000 73092 70328 92473 70615 123110 107980 92431 93239 102890 76393 TRUE FALSE 75977.7286 82406.28692 94882.92235 84582.43624 102183.8062 82903.28145 85186.0167 91989.28371 99187.009 91360.74572 0.831623341 0.901987897 1.038552407 0.925807201 1.118465106 0.907427811 0.932413763 1.006879738 1.085663303 1 16.47928681 4.435652422 4.040458078 0.996898663 0.843079003 0.42478397 0.06488715 0.184425527 6.319993198 0.01554775 0.053355769 27267.94579 -4.435652422 -0.15381966 KPS(ph)LVASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPSLVASK 8 1 P56211;H3BMD8;P56211-2;H3BQ52 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 KPS(0.992)LVAS(0.008)K;KPS(0.999)LVAS(0.001)K;KPS(0.995)LVAS(0.005)K 85.672 0.0088465 0 1896500 1005320 1515710 1017900 2077020 1552850 1814820 1404640 1763120 717110 TRUE FALSE 1971375.284 1177975.89 1555210.648 1219237.582 1723968.882 1192224.121 1672569.666 1385813.098 1699665.656 857613.9746 2.298674395 1.373550251 1.813415702 1.421662447 2.010192153 1.390164056 1.950259343 1.615893793 1.981853965 1 19.70996889 -1.194212658 3.361991626 0.998566043 1.737252957 0.373269558 0.294578982 26882847.81 41039085.01 409445.5302 0.06610363 0.063942166 1.194212658 0.738686915 KPS(ph)PAAS(ph)PATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 2 KPS(1)PAAS(0.888)PAT(0.112)K 96.096 0.025432 318840000 505190 306360 396180 295990 519800 487520 472120 415080 464150 309260 TRUE FALSE 525135.2913 358974.9469 406504.7763 354535.9386 431444.5817 374300.8684 435114.0007 409516.5315 447445.3322 369853.5759 1.419846462 0.97058666 1.099096515 0.95858459 1.16652808 1.012024468 1.176449355 1.107239617 1.209790472 1 18.4965947 KPS(ph)PAASPATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPSPAASPATK 11 1 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 KPS(1)PAASPATK 186.85 2.36E-06 1021700000 916470 549410 815070 517050 1058500 942840 1052300 770800 964950 546470 TRUE FALSE 952652.9433 643766.8937 836311.3938 619320.9468 878576.5481 723879.6989 969817.9763 760468.6868 930221.638 653540.3337 1.457680413 0.985045391 1.279663015 0.947639977 1.344334087 1.107628193 1.483945101 1.163614008 1.423357657 1 19.31791675 KPS(ph)PAQAAETPALELPLPSVPAPAPL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSPAQAAETPALELPLPSVPAPAPL 26 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 1 KPS(0.875)PAQAAET(0.125)PALELPLPSVPAPAPL;KPS(0.86)PAQAAET(0.14)PALELPLPSVPAPAPL 93.006 0.0055403 24710000 76206 63380 76075 60950 92011 94503 84363 76236 76731 62791 TRUE FALSE 79214.67172 74265.02197 78057.577 73005.72808 76371.00309 72556.11046 77750.40762 75214.18112 73969.4663 75093.69424 1.05487781 0.988964822 1.03946913 0.972195187 1.017009535 0.966207765 1.035378648 1.001604487 0.985028997 1 16.19640415 6.540691927 1.873844315 1.00172057 41.97016366 0.313825364 0.023436742 1317.535414 7.452270287 0.005649817 231546.8187 3472897.19 -6.540691927 40.96844309 KPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KPSPEPEGEVGPPK 14 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK 156.73 3.36E-06 11226510000 7004990 2946460 4764620 3029720 6380560 5920570 6358500 4627870 5259130 2263614 TRUE FALSE 7281552.414 3452491.585 4888789.911 3628989.573 5295994.69 4545607.345 5860104.155 4565840.972 5069854.939 2707125.824 2.689772433 1.275334731 1.805896818 1.340532288 1.956316416 1.679126735 2.164695894 1.686600945 1.872781418 1 21.36833051 -1.338598061 2.831959815 0.989274776 1.803720184 0.29510271 0.382939491 11398048.35 13544426.6 1022121.334 0.086191644 0.045856609 1.338598061 0.814445408 KPS(ph)PQPS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(1)PQPS(0.581)S(0.419)PR;KPS(1)PQPS(0.736)S(0.264)PR;KPS(0.947)PQPS(0.571)S(0.481)PR 117.7 0.0032278 2243290000 2586080 2028930 2295320 1883490 2761530 2873280 2604530 2352220 2460980 1831150 TRUE FALSE 2688180.435 2377382.945 2355137.925 2256038.7 2292126.117 2206004.265 2400380.133 2320692.338 2372409.811 2189928.783 1.227519569 1.085598291 1.075440418 1.030188159 1.046666967 1.007340641 1.096099632 1.059711328 1.08332738 1 21.06245252 4.951193174 1.632449099 1.051478248 1.375443882 0.767656094 0.029316784 0.838925391 1.403234503 0.00752222 0.504537504 89370.29141 -4.951193174 0.323965634 KPS(ph)PQPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 2 KPS(0.972)PQPS(0.037)S(0.991)PR;KPS(1)PQPS(0.004)S(0.997)PR;KPS(0.725)PQPS(0.6)S(0.675)PR;KPS(0.999)PQPS(0.454)S(0.547)PR 141.73 2.47E-05 1906490000 2333560 1733910 2087760 1561870 2522060 2566520 2361380 2120100 2295570 1587940 TRUE FALSE 2425690.751 2031695.555 2142168.741 1870803.224 2093361.142 1970484.626 2176288.865 2091683.527 2212952.884 1899066.44 1.277306944 1.069839112 1.128011477 0.985117311 1.10231064 1.037606997 1.145978266 1.10142725 1.165284604 1 20.85685895 4.74159525 24.63430135 1.086244378 1.27730703 0.514218252 0.056875421 185.4234474 1505126.019 0.01287926 0.089921682 55156.31584 -4.74159525 0.191062652 KPS(ph)VSEEVQATPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 KPS(0.994)VS(0.006)EEVQATPNK;KPS(0.998)VS(0.002)EEVQATPNK;KPS(0.956)VS(0.044)EEVQATPNK 206.81 5.12E-08 2646680000 2607910 1618821 2147740 1461247 3176530 2702880 2731550 2440700 2685300 1591680 TRUE FALSE 2710872.301 1896840.914 2203711.869 1750277.295 2636584.565 2075177.083 2517443.973 2407986.409 2588656.578 1903539.221 1.424122114 0.99648113 1.157691864 0.919485806 1.385096002 1.090167757 1.322507015 1.265004882 1.359917646 1 20.86025287 3.220496637 24.99995066 1.250205423 1.117679573 0.09667253 0.16533952 474.3837908 656530.049 0.044585013 0.053386989 1661.485811 -3.220496637 -0.13252585 KPSDEEFASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSDEEFASR 10 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 87.719 0.020338 488880000 641920 571490 639690 604550 665720 612970 558900 500320 531030 476830 FALSE TRUE 667263.4973 669638.9619 656360.8469 724128.1856 552561.1522 470617.0072 515091.9576 493614.0288 511918.334 570255.709 1.170112787 1.174278401 1.150993908 1.269830664 0.968970838 0.825273644 0.903264885 0.865601205 0.897699621 1 19.12124946 3.097784601 4.961890016 0.889255327 1.185834817 0.87878363 0.051545352 0.060234207 2.454565789 0.01415 0.017049193 1252.519803 -3.097784601 0.29657949 KPSDGS(ph)PDTKPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 KPS(0.001)DGS(0.977)PDT(0.023)KPSR;KPS(0.017)DGS(0.948)PDT(0.028)KPS(0.007)R;KPSDGS(0.997)PDT(0.003)KPSR;KPSDGS(1)PDTKPSR 144.33 2.15E-05 1024420000 934860 452629 635334 417467 892160 834023 835840 635119 762315 424022 TRUE FALSE 971768.9947 530364.5098 651891.326 500040.7266 740510.9619 640333.798 770324.6767 626606.2687 734879.4321 507100.9925 1.916322407 1.045875511 1.285525636 0.9860772 1.460283006 1.262734263 1.519075466 1.235663661 1.449177665 1 18.95191357 -2.225205435 2.135310412 0.000171488 1.330290909 0.146256923 0.250000384 4800365.542 754068.1882 23216997.87 0.056445044 0.005953804 2.225205435 1.33011942 KPSDGSPDTKPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPSDGSPDTKPSR 13 2 Q92733 Q92733 PRCC Proline-rich protein PRCC 0 ;; 88.092 0.0045373 205909000 371500 227071 318228 231870 429720 372840 361730 320648 375910 263197 FALSE TRUE 386167.1069 266068.6779 326521.2831 277733.1939 356676.3479 286253.5604 333376.6574 316350.238 362381.0725 314765.4129 1.226840977 0.845291976 1.037348037 0.882349783 1.133149747 0.909418725 1.059127349 1.00503494 1.151273481 1 18.2639175 KPSETQELVQQVLSLATQDSDNPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSETQELVQQVLSLATQDSDNPDLR 26 1 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ; 208.37 3.62E-25 473410000 252667 179252 222977 241283 220329 288820 295850 227129 240695 149820 FALSE TRUE 262642.4883 210037.1366 228787.9638 289008.0572 182877.5553 221745.9321 272660.5039 224084.7073 232032.434 179174.3605 1.465848615 1.172249958 1.276901244 1.61299896 1.020668106 1.237598569 1.52176072 1.250651637 1.295009137 1 17.45100468 0.484095176 1.722016614 1.000084766 1.317216029 0.250880297 0.165072321 4.966495101 14.99885743 0.151169532 0.042612718 3.048563013 -0.484095176 0.317131263 KPSGS(ph)PDLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSGSPDLWK 10 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPS(0.009)GS(0.991)PDLWK;KPS(0.203)GS(0.797)PDLWK 117.08 0.00061558 822720000 2502300 1244990 1813500 1236750 2469200 2302600 2386300 1813800 2061750 961700 TRUE FALSE 2601092.736 1458807.348 1860761.3 1481375.459 2049486.266 1767856.046 2199255.571 1789488.978 1987548.02 1150126.702 2.2615706 1.268388383 1.617875054 1.288010665 1.781965641 1.537096776 1.912185472 1.555905949 1.72811223 1 20.13336137 -0.688251258 5.527902402 0.999999964 1.641797553 0.336896717 0.277098728 4.65E-06 92734120.81 9.752112958 0.058920042 0.204997584 0.688251258 0.641797589 KPSKYPLCSADAAVSTT(ph)PPGS(ph)PPPPPPLPEPPVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 KPS(0.002)KYPLCS(0.002)ADAAVS(0.355)T(0.069)T(0.571)PPGS(1)PPPPPPLPEPPVLK 150.94 1.11E-10 419760000 1001200 575500 815330 556120 1085900 949580 945270 821180 987390 536050 TRUE FALSE 1040728.149 674337.6482 836578.1696 666118.8761 901319.1059 729054.436 871177.2674 810173.4253 951854.0268 641078.7342 1.623401454 1.051879609 1.304953861 1.039059386 1.405941358 1.137230729 1.358923984 1.263765872 1.484769305 1 19.29014203 KPSKYPLCSADAAVSTTPPGS(ph)PPPPPPLPEPPVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPSKYPLCSADAAVSTTPPGSPPPPPPLPEPPVLK 35 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 KPS(0.009)KYPLCS(0.009)ADAAVS(0.043)T(0.043)T(0.043)PPGS(0.851)PPPPPPLPEPPVLK 76.358 0.0015107 79140000 63893 40436 55664 60718 94222 74470 106840 90850 94163 62761 TRUE FALSE 66415.54498 47380.56845 57114.64957 72727.83917 78206.1781 57175.4711 98465.60163 89632.30435 90774.09202 75057.81632 0.884858476 0.631254289 0.760942063 0.968957568 1.041945822 0.761752392 1.311863394 1.194176819 1.209388928 1 16.1957147 2.939088371 0.811137027 1.189055894 0.745923614 0.506744295 0.147178851 0.467817459 0.682183807 0.087569892 0.10494598 869.137264 -2.939088371 -0.443132279 KPSPQPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPSPQPSSPR 10 1 O75909;G3V5E1;O75909-1;O75909-4 O75909 CCNK Cyclin-K 1 KPS(0.002)PQPS(0.029)S(0.969)PR;KPS(0.025)PQPS(0.18)S(0.796)PR;KPS(0.013)PQPS(0.081)S(0.905)PR;KPSPQPS(0.003)S(0.997)PR 107.09 0.0024684 841337000 722170 787918 818527 755622 909860 998950 829120 842813 822331 841495 TRUE FALSE 750681.8292 923236.7873 839858.486 905081.7763 755202.3222 766959.0017 764131.4079 831516.4703 792735.4679 1006369.834 0.745930377 0.917393145 0.834542588 0.899353047 0.750422257 0.762104523 0.759294826 0.826253374 0.787717836 1 19.94072915 5.044184335 13.20111931 0.825711975 0.440324208 0.095208288 0.077364253 1585273.182 16002510.51 0.017661457 14228867.82 110709.3588 -5.044184335 -0.385387767 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KPSPSES(0.999)PEPWKPFPAVSPEPR;KPSPSES(1)PEPWKPFPAVSPEPR 245.11 3.83E-31 2864500000 1330830 868200 1152250 794770 1437910 1285360 1295910 1069050 1225340 795290 TRUE FALSE 1383372.196 1017306.596 1182278.582 951973.1338 1193494.572 986854.6198 1194333.188 1054721.133 1181240.253 951111.8488 1.454478985 1.069597227 1.243048946 1.000905556 1.25484145 1.037579987 1.255723172 1.108934911 1.241957246 1 19.85925548 4.746880899 24.66243444 1.14206069 1.454479174 0.470068973 0.101581061 705.8795498 2092264.611 0.021093278 0.241107792 55831.70609 -4.746880899 0.312418484 KPSQTAS(ph)YER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 KPSQT(0.137)AS(0.863)YER;KPSQT(0.149)AS(0.851)YER;KPSQT(0.018)AS(0.982)YER;KPSQT(0.146)AS(0.853)YER 84.468 0.0091268 1891150000 1473920 1826420 1767150 1400060 2342110 2129750 1576730 1706360 1556670 1768860 TRUE FALSE 1532111.5 2140093.427 1813203.381 1676987.689 1943998.979 1635147.839 1453141.783 1683489.035 1500645.751 2115434.25 0.724253897 1.011656792 0.857130578 0.792739216 0.918959773 0.772960842 0.686923634 0.795812508 0.709379528 1 21.01252242 2.711398159 21.19691447 0.77306357 0.865319276 0.077171268 0.106310749 204.2910166 159421.9646 0.031983593 0.03017206 514.5151398 -2.711398159 0.092255705 KPSQTASYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSQTASYER 10 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ; 101.56 0.0052139 109630000 91299 90072 92946 77607 143387 120752 96620 91837 95177 139305 FALSE TRUE 94903.55502 105541.1653 95368.24912 92957.43297 119014.129 92709.17801 89046.67193 90606.07523 91751.59836 166599.1476 0.569652104 0.633503633 0.572441399 0.55797064 0.714374177 0.556480506 0.534496564 0.543856776 0.5507327 1 17.34602149 -1.410463243 5.771281636 1.000166107 0.580463407 0.85679337 0.051327003 0.000112885 1.15E-05 0.05114027 0.012049166 0.038863039 1.410463243 -0.4197027 KPSSET(ph)DIENWASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSSETDIENWASK 14 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 KPS(0.233)S(0.233)ET(0.534)DIENWASK;KPS(0.219)S(0.219)ET(0.562)DIENWASK 134.21 2.35E-05 398220000 271870 224491 277060 201439 298810 333180 303980 288840 279030 209848 TRUE FALSE 282603.6375 263045.583 284280.4112 241283.033 248018.3829 255803.9944 280153.2533 284968.5722 268987.7648 250963.6978 1.126073771 1.048141963 1.13275511 0.961426035 0.98826398 1.01928684 1.116309872 1.135497184 1.071819419 1 17.93711917 -0.742789457 8.200249454 1.000000013 1.068383449 0.101882195 0.059130447 0 0 0.061975914 0.014607863 0.180805044 0.742789457 0.068383436 KPSVGVPPPAS(ph)PSYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPSVGVPPPASPSYPR 16 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 KPSVGVPPPAS(0.953)PS(0.047)YPR;KPSVGVPPPAS(0.987)PS(0.013)YPR 96.79 0.0020172 1687880000 1321510 1398560 1380600 1300510 1553010 1665620 1492660 1583240 1363080 1522740 TRUE FALSE 1373684.235 1638751.801 1416579.57 1557746.996 1289029.915 1278804.998 1375661.409 1562019.257 1314023.017 1821091.748 0.754319071 0.899873278 0.777873806 0.855391826 0.707833593 0.702218874 0.755404779 0.857737815 0.721557834 1 20.79637218 -1.702565517 6.148834343 1.003164735 0.786590992 0.502991071 0.065014646 0.002871217 0.000138888 0.064079642 0.014912871 0.019835104 1.702565517 -0.216573743 KPTETQELVQQVLSLATQDSDNPDLR ddPTM_MDA-MB-175_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 ; 228.46 1.71E-34 771360000 633620 433200 620090 663490 603700 776200 909750 634720 666270 451570 FALSE TRUE 658635.8069 507598.7302 636250.0548 794726.3417 501083.2896 595939.3134 838441.4178 626212.6166 642291.0728 540046.4957 1.219590928 0.939916719 1.178139401 1.471588739 0.927852127 1.103496307 1.552535614 1.159553153 1.189325508 1 19.0427241 KPTGSLPS(ph)PSGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPTGSLPSPSGVR 13 1 G3V497;G3V4H6;G3V538;G3V500;G3V3N9;F8W717;A0A3B3IU69;O00423;O00423-3 G3V497 EML1 Echinoderm microtubule-associated protein-like 1 1 KPT(0.001)GS(0.014)LPS(0.9)PS(0.085)GVR 73.688 0.022142 114550000 208250 160820 177930 182410 206350 209020 229440 220550 188680 172870 TRUE FALSE 216471.8708 188439.584 182567.002 218490.1536 171274.7007 160478.2727 211455.8933 217593.888 181889.4437 206740.5667 1.047070124 0.911478511 0.883072949 1.056832517 0.828452313 0.776230206 1.022807941 1.052497299 0.879795613 1 17.65746198 -0.669773021 5.355173688 1.000000004 0.944339835 0.03243747 0.095788108 4.99E-09 1.33E-09 0.09569077 0.022554529 0.213907976 0.669773021 -0.055660168 KPTTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KPTTEEK 7 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 78.516 0.056318 1507790000 1724290 914480 1413970 931690 1740350 1608760 1742100 1401800 1457760 927640 FALSE TRUE 1792366.301 1071534.826 1450819.22 1115975.501 1444525.929 1235149.871 1605549.65 1383011.164 1405295.502 1109393.297 1.615627483 0.965874617 1.307759136 1.005933156 1.302086404 1.113356169 1.447232153 1.246637389 1.266724349 1 20.08133948 KPVTDCVISVPSFFTDAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTDCVISVPSFFTDAERR 20 2 Q92598-2;Q92598;Q92598-4 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 113.26 7.95E-05 266410000 328260 302270 378860 275450 383030 388330 301530 405020 376510 364500 FALSE TRUE 341219.9583 354182.5212 388733.4028 329933.1879 317922.6974 298146.2427 277895.2907 399591.3694 362959.4786 435916.7962 0.782763961 0.812500285 0.891760552 0.756871932 0.729319678 0.683952179 0.637496176 0.916668898 0.832634764 1 18.73369327 1.146625396 1.462552871 0.983378204 0.76537357 0.447717948 0.077973762 0.368590767 1.543029101 0.077782194 0.023486386 14.01604219 -1.146625396 -0.218004634 KPVTVS(ph)PTTPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVT(0.006)VS(0.9)PT(0.09)T(0.09)PT(0.152)S(0.757)PT(0.004)EGEAS(0.001) 69.522 0.015238 60623000 51321 50738 55762 50161 66457 68915 66798 60775 64338 59260 TRUE FALSE 53347.19271 59451.85681 57215.20353 60082.69608 55160.66288 52910.53567 61562.19822 59960.41053 62022.48795 70870.8624 0.752738021 0.838875877 0.807316316 0.847777127 0.778326396 0.746576715 0.868653155 0.846051657 0.875147922 1 16.11290498 0.820004814 0.762469299 1.000171819 0.801497894 0.73586118 0.03591021 0.454180984 0.546654287 0.035132176 0.012782831 6.607007713 -0.820004814 -0.198673925 KPVTVS(ph)PTTPTSPTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVS(0.853)PT(0.077)T(0.011)PT(0.054)S(0.002)PT(0.003)EGEAS 197.15 8.49E-16 123000000 92612 89434 92864 83557 106900 121620 100060 99194 97006 100100 TRUE FALSE 96268.39327 104793.5938 95284.11213 100084.3252 88729.17618 93375.59817 92217.03574 97864.46668 93514.77301 119712.6785 0.804162053 0.875375901 0.795940024 0.836037807 0.741184454 0.779997569 0.77031971 0.817494587 0.781160143 1 16.86921643 -1.168252297 3.569960206 1.000203397 0.800910237 0.743118418 0.035241673 2720011119 4147657696 6474363.304 0.00863105 0.067880917 1.168252297 -0.19929316 KPVTVSPT(ph)TPT(ph)SPTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.034)PT(0.386)T(0.589)PT(0.687)S(0.297)PT(0.006)EGEAS 142.4 1.24E-07 630230000 401810 357220 420960 372650 458310 521470 467560 427120 451580 420110 TRUE FALSE 417673.7691 418569.7562 431930.5634 446359.0578 380406.6299 400366.4955 430911.4255 421395.155 435327.724 502422.511 0.831319776 0.83310311 0.859695881 0.888413731 0.757144876 0.796872128 0.857667433 0.838726661 0.866457443 1 18.93854158 0.531456588 1.187726492 1.000102273 0.831276015 0.687738378 0.033769046 1.022941442 1.961476468 0.03354902 0.01021331 3.399825193 -0.531456588 -0.168826258 KPVTVSPT(ph)TPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.05)PT(0.722)T(0.228)PT(0.427)S(0.572)PT(0.001)EGEAS;KPVTVS(0.01)PT(0.614)T(0.376)PT(0.007)S(0.988)PT(0.004)EGEAS(0.001) 174.46 9.87E-12 462932000 338994 324255 383733 329679 450779 492538 398523 408639 416399 369867 TRUE FALSE 352377.7449 379943.2739 393733.3972 394888.5222 374155.7466 378153.514 367285.7259 403161.8626 401412.8813 442335.3571 0.796630292 0.85894846 0.89012418 0.892735604 0.845864434 0.8549023 0.830333185 0.911439378 0.907485406 1 18.75478104 0.954989087 1.09307011 0.998466113 0.856214455 0.704028973 0.028813614 0.31942219 0.788610519 0.027699026 0.008880684 9.015484833 -0.954989087 -0.142251658 KPVTVSPTT(ph)PT(ph)SPTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 2 KPVTVS(0.001)PT(0.521)T(0.479)PT(0.785)S(0.212)PT(0.001)EGEAS(0.002) 199.65 5.47E-16 291530000 258570 232870 278250 242990 307100 338140 303400 298580 280490 262120 TRUE FALSE 268778.5433 272863.611 285501.4236 291052.6967 254899.2517 259612.1096 279618.7152 294578.0235 270395.2197 313477.3954 0.857409648 0.870441107 0.910756015 0.928464703 0.813134393 0.828168517 0.891990042 0.939710575 0.862566882 1 18.25800189 0.099545691 0.548448654 1.008031944 0.87333594 0.464201376 0.039017807 3.454645787 1.338548089 0.10750012 0.018986069 1.257609158 -0.099545691 -0.134696004 KPVTVSPTT(ph)PTSPTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.115)T(0.619)PT(0.034)S(0.228)PTEGEAS(0.003) 186.96 3.75E-14 1508000000 552110 547310 645270 563780 712250 804620 711410 674240 717400 633800 TRUE FALSE 573907.7291 641306.235 662086.2663 675294.0013 591181.9994 617759.1991 655647.8253 665202.9156 691580.9141 757980.9752 0.757153211 0.846071677 0.873486655 0.890911544 0.779943058 0.815006206 0.864992456 0.877598432 0.912398776 1 19.53180211 1.034289749 0.952701185 0.999050708 0.83144105 0.659717853 0.038248344 0.36261076 0.712142531 0.037170423 0.01266327 10.82155694 -1.034289749 -0.167609659 KPVTVSPTTPT(ph)SPTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPT(0.257)T(0.251)PT(0.367)S(0.113)PT(0.006)EGEAS(0.006) 138.81 2.30E-06 1228100000 301620 297760 332610 298960 381960 422030 354460 365490 353000 293080 TRUE FALSE 313528.1905 348897.9637 341278.0898 358093.3957 317034.5756 324019.9284 326676.499 360591.2044 340295.599 350503.4146 0.894508234 0.995419586 0.973679786 1.021654514 0.904512089 0.924441574 0.932020874 1.02878086 0.970876701 1 18.41906897 1.74415124 25 1.000818236 0.952246745 0.252786974 0.03951497 1.628081177 7307.368959 0.018673375 0.010355222 55.48188914 -1.74415124 -0.048571491 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 KPVTVSPTTPTS(0.997)PT(0.002)EGEAS;KPVTVSPTTPT(0.02)S(0.979)PT(0.001)EGEAS;KPVTVSPTTPT(0.002)S(0.993)PT(0.002)EGEAS(0.002);KPVTVSPTTPT(0.009)S(0.954)PT(0.037)EGEAS(0.001) 225.37 1.85E-19 2406990000 2012410 2075960 2345660 2104850 2790500 2861710 2597510 2548680 2633830 2328940 TRUE FALSE 2091861.501 2432489.981 2406789.827 2521183.048 2316171.807 2197121.222 2393910.379 2514519.113 2539038.973 2785251.203 0.751049492 0.873346712 0.864119482 0.905190543 0.831584528 0.788841315 0.859495322 0.902797963 0.911601428 1 21.40937602 1.115846856 1.068060281 0.99656515 0.841124686 0.589503852 0.042158946 0.354932646 0.857200405 0.040161663 0.013226352 13.05710378 -1.115846856 -0.155440464 KPVVDCVVSVPCFYTDAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPVVDCVVSVPCFYTDAER 19 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 153.82 6.73E-08 4238600000 2590600 2192060 2486160 2646550 2816900 3134530 3050450 2648420 2659240 2231500 FALSE TRUE 2692878.888 2568529.253 2550951.372 3170029.691 2338084.344 2406582.912 2811347.758 2612922.262 2563534.472 2668719.7 1.009052726 0.962457486 0.955870851 1.187846626 0.876107125 0.901774327 1.053444376 0.979092057 0.960585884 1 21.34771635 5.126706181 15.37415006 0.987570508 2.915799351 0.006694941 0.081746583 13564452.89 8598975.064 0.019124474 910802306.7 133877.0645 -5.126706181 1.928228843 KPVVDCVVSVPCFYTDAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPVVDCVVSVPCFYTDAERR 20 2 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 131.11 8.40E-06 710490000 156070 151560 184890 126570 193980 196440 166140 155480 178670 164010 FALSE TRUE 162231.7641 177589.251 189708.3853 151605.1682 161007.3489 150819.7871 153117.5127 153396.0449 172239.7016 196144.6193 0.827102801 0.905399555 0.967186283 0.77292545 0.820860391 0.768921358 0.780635804 0.782055839 0.878126059 1 17.58155823 5.099214751 18.43333375 0.839356129 0.000930218 0 0.080286629 2958.043717 702914.6366 0.018812565 28939.87725 125665.1201 -5.099214751 -0.838425911 KPWTSLS(ph)SESVSCPQGS(ph)LSPATSLMQVSERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.139)S(0.147)LS(0.651)S(0.042)ES(0.014)VS(0.011)CPQGS(0.497)LS(0.437)PAT(0.027)S(0.028)LMQVS(0.006)ERPR 56.638 0.023669 188720000 34438 33497 37885 35446 49246 50279 48122 39574 36156 34533 TRUE FALSE 35797.63883 39249.84918 38872.31422 42457.113 40875.18251 38602.46424 44350.0719 39043.57526 34854.75262 41299.08018 0.866790221 0.950380711 0.941239225 1.02804016 0.989735905 0.934705182 1.073875537 0.945386074 0.843959538 1 15.33382203 4.892454478 1.559860253 0.973798153 0.79502575 0.218658419 0.058276515 2.431802013 4.169065502 0.015352904 0.740807396 78064.66097 -4.892454478 -0.178772403 KPWTSLS(ph)SESVSCPQGSLS(ph)PATSLMQVSERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPWTSLSSESVSCPQGSLSPATSLMQVSERPR 32 2 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 2 KPWT(0.144)S(0.169)LS(0.678)S(0.009)ESVSCPQGS(0.097)LS(0.871)PAT(0.026)S(0.006)LMQVSERPR 151.6 1.30E-10 277580000 47000 33898 61789 50085 49123 74006 59444 48222 52428 46681 TRUE FALSE 48855.59629 39719.71781 63399.2721 59991.66351 40773.09001 56819.22807 54784.62395 47575.66297 50541.12652 55827.24819 0.875120983 0.711475473 1.135633121 1.074594673 0.730343897 1.01776874 0.981324098 0.852194305 0.905312874 1 15.76868182 4.265894414 24.99997965 0.9505566 0.793298266 0.253513318 0.114522211 320.2411569 292892.8467 0.027992322 0.076619807 18445.66913 -4.265894414 -0.157258334 KPYCNAHYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KPYCNAHYPK 10 1 Q14847;Q14847-2;C9J9W2;F6S2S5;O76041-2 Q14847;O76041-2 LASP1;NEBL LIM and SH3 domain protein 1;Nebulette 0 ; 81.338 0.013834 3594700000 3072900 2314400 2806400 2339860 4197900 3582200 3376600 2864800 3191500 3306400 FALSE TRUE 3194220.465 2711880.196 2879537.089 2802677.324 3484342.457 2750288.339 3111933.269 2826402.042 3076638.538 3954225.775 0.807799212 0.685818249 0.728217672 0.708780298 0.881169325 0.695531438 0.786989273 0.714780137 0.778063447 1 21.91496382 0.95609451 20.17127244 1.000000001 0.74918443 0.629134859 0.056951367 414.5944614 190476.1181 0.051075937 0.012768984 9.038461444 -0.95609451 -0.250815571 KPYPDDENLVEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPYPDDENLVEVK 13 1 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 117.2 0.00043865 0 232150 145590 200730 138070 281500 234930 243320 189750 218550 133990 FALSE TRUE 241315.4613 170593.95 205961.1887 165379.8339 233650.7305 180371.0679 224247.9426 187206.7116 210684.4282 160242.7751 1.505936608 1.064596827 1.285307176 1.032057974 1.458104619 1.125611234 1.39942623 1.168269281 1.314782698 1 17.28989979 -1.319525827 3.799316178 0.999349304 1.251326898 0.201447395 0.15503155 10749515.08 3776524.031 57541.82103 0.031901503 0.047915296 1.319525827 0.251977593 KQAEEIGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQAEEIGEK 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 115 0.0024794 325870000 310040 186160 295290 229730 374160 301890 317890 252170 316960 165380 FALSE TRUE 322280.6186 218131.5319 302985.5 275169.9083 310560.4168 231780.6227 292972.9511 248790.0736 305552.6715 197783.0446 1.629465353 1.10288287 1.531908362 1.391271476 1.570207484 1.171893289 1.481284464 1.257893841 1.544888098 1 17.59355923 -1.90822792 2.741481026 0.779313763 1.393886403 0.339834486 0.169865057 24058881.55 10945517.1 34002454.8 0.037628761 0.01235299 1.90822792 0.61457264 KQAEILQESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KQAEILQESR 10 1 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 138.75 9.03E-05 1057820000 1443730 1403040 1480070 1329380 1932570 1903890 1577230 1595370 1709490 1686930 FALSE TRUE 1500729.575 1644001.206 1518641.84 1592327.396 1604072.442 1461740.401 1453602.591 1573986.675 1647965.789 2017451.635 0.74387388 0.814890021 0.752752539 0.789276614 0.795098338 0.724547928 0.72051422 0.78018558 0.816855165 1 20.94410266 0.755898208 2.045392561 0.999845237 0.764862884 0.856368239 0.028874403 0.336155849 2.197121538 0.028238586 0.007779452 5.700306504 -0.755898208 -0.234982352 KQALYLMFDTSQESPVKS(ph)SPVR ddPTM_MDA-MB-175_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(0.021)PVKS(0.489)S(0.489)PVR 198.06 1.01E-22 601380000 720470 487610 790230 432020 851720 841790 666670 649800 858340 494180 TRUE FALSE 748914.7119 571353.2244 810824.043 517472.2665 706944.9386 646297.03 614414.6634 641090.4939 827448.5111 591005.1094 1.267188219 0.966748367 1.371940835 0.875580022 1.196173988 1.09355574 1.039609732 1.084746111 1.400069979 1 19.17281108 5.210870236 8.723943244 1.114613969 11.81378685 0.076661476 0.159202557 169858.8716 79536.79367 0.033620365 35578323.01 162506.3127 -5.210870236 10.69917288 KQASVDS(ph)GIVQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQASVDSGIVQ 11 1 A0A096LNH6;Q14185 A0A096LNH6 DOCK1 Dedicator of cytokinesis protein 1 1 KQAS(0.407)VDS(0.593)GIVQ;KQAS(0.245)VDS(0.755)GIVQ 95.659 0.0080435 430830000 1370780 1003090 1546000 963360 2603600 1630040 1602200 1500740 1969170 1302410 TRUE FALSE 1424899.453 1175362.905 1586290.03 1153909.733 2161041.002 1251487.913 1476615.377 1480625.035 1898299.956 1557592.303 0.914808997 0.754602409 1.018424415 0.740829118 1.387424037 0.803475923 0.948011475 0.950585742 1.218739944 1 20.57088623 KQDADSLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KQDADSLQR 9 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;;; 187.99 6.40E-05 11689870000 10765740 9099380 10535060 9329880 12815390 12804810 12093700 11326280 11503590 9056200 FALSE TRUE 11190779.73 10662127.73 10809612.32 11175302.42 10637034.59 9831086.936 11145764.19 11174469.74 11089578.04 10830589 1.0332568 0.984445789 0.9980632 1.031827763 0.982128912 0.907714893 1.029100467 1.031750881 1.023912739 1 23.36860837 KQDAETPPPPDPPAPETLLAPPPLPS(ph)TPDPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQDAETPPPPDPPAPETLLAPPPLPSTPDPPRR 33 2 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 KQDAETPPPPDPPAPETLLAPPPLPS(0.5)T(0.5)PDPPRR 120.8 7.25E-08 335010000 218870 181620 197230 161170 264610 259440 217070 213070 231930 203420 TRUE FALSE 227511.1566 212811.8222 202369.9758 193048.945 219631.6867 199188.9919 200055.4862 210214.1452 223582.8846 243276.2543 0.935196726 0.874774329 0.831852564 0.79353797 0.902807746 0.81877696 0.822338731 0.86409644 0.919049355 1 17.89223598 0.989840527 2.312770285 0.999339119 0.851667245 0.564124434 0.039885433 0.214096963 2.538777658 0.037893979 0.01036574 9.768784457 -0.989840527 -0.147671874 KQDDS(ph)PPRPIIGPALPPGFIK ddPTM_MDA-MB-175_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 136.96 2.12E-06 2912300000 2819100 1442710 2103150 1415260 2701200 2799200 2769400 2137290 2524600 1314620 TRUE FALSE 2930400.245 1690484.22 2157959.817 1695194.204 2242050.989 2149128.222 2552327.192 2108643.123 2433740.139 1572194.619 1.863891537 1.075238523 1.372578045 1.078234325 1.426064535 1.366960678 1.623416822 1.341209986 1.547989104 1 20.58434839 KQDFDEDDILKELEELSLEAQGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQDFDEDDILKELEELSLEAQGIK 24 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 77.681 0.011922 24304000 67376 20794.8 27045 17352.4 52353 48343 43621 28256 37032 13066.2 FALSE TRUE 70036.05651 24366.14514 27749.81492 20784.65293 43454.05576 37116.0709 40201.87204 27877.27454 35699.22555 15626.27172 4.48194283 1.559306377 1.775843618 1.330109529 2.780833236 2.375235216 2.572710417 1.78400037 2.284564494 1 13.93168599 -1.535944653 0.200254605 1.39E-45 2.566501985 0.204361423 0.831092206 49.27510553 1.750952329 30.15774242 2.33066259 0.029110881 1.535944653 2.566501985 KQDIFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQDIFWK 7 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 0 72.23 0.083648 386190000 633390 538440 665920 565180 854890 831310 744780 679130 791530 729510 FALSE TRUE 658396.7263 630912.8815 683274.4223 676970.9171 709576.1032 638250.8511 686402.1975 670027.3732 763042.9899 872443.5172 0.754658283 0.723156135 0.783173247 0.775948132 0.813320392 0.731566959 0.786758322 0.7679894 0.874604458 1 19.73470221 0.979394102 2.301837607 0.99979076 0.766327266 0.894562107 0.025243379 0.087721467 1.032867552 0.023764338 0.006499611 9.536611742 -0.979394102 -0.233463494 KQDPPVTHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQDPPVTHDLR 11 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0;M0R128;A0A1B0GX60;M0R1D6 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 ; 128.31 0.00017425 550650000 357510 385750 391880 339700 420410 483290 415520 373340 401710 343920 FALSE TRUE 371624.7709 451999.5618 402092.7147 406891.6461 348948.8584 371053.2218 382950.4566 368335.988 387252.5356 411304.5393 0.903527035 1.098941341 0.977603397 0.989270984 0.84839535 0.902137434 0.931063045 0.895531055 0.94152264 1 18.64984747 3.382425754 8.762105691 0.913415379 1.000516291 0.27128847 0.05735629 0.285468069 23.62815526 0.014832273 0.020093438 2412.269101 -3.382425754 0.087100912 KQEAEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KQEAEWK 7 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496;P09496-5;C9J8P9 P09496-2 CLTA Clathrin light chain A 0 ;;;; 122.52 0.006948 5981820000 8380650 5103600 6568050 4677657 9024190 8015510 8451350 6553210 7286760 4880070 FALSE TRUE 8711524.533 5980103.6 6739218.779 5602883.593 7490261.407 6154029.279 7788911.104 6465374.939 7024510.931 5836226.282 1.492663943 1.024652457 1.154721982 0.960018225 1.283408327 1.054453508 1.33458004 1.107800593 1.203604965 1 22.47660439 -2.541386082 1.424577041 9.87E-05 1.169343753 0.109647356 0.150989394 481543.8263 31846.02751 1539800.962 0.038669307 0.002874842 2.541386082 1.169245058 KQEEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KQEEEAR 7 1 Q9NQS7-2;Q9NQS7;Q7Z3H0 Q9NQS7-2 INCENP;ANKRD33 Inner centromere protein;Ankyrin repeat domain-containing protein 33 0 ;; 123.92 0.0067298 405448000 838480 651180 731870 627830 898800 907670 918630 785940 839630 592185 FALSE TRUE 871583.8378 763015.0995 750943.1334 752012.9001 746022.297 696877.3984 846625.3802 775405.7598 809411.8803 708212.3127 1.230681566 1.077381861 1.060336173 1.06184669 1.053387923 0.983995034 1.195440075 1.094877547 1.142894392 1 19.4338224 4.739045469 24.14450645 1.079423494 1.230681624 0.386604258 0.058734318 26.80839082 1334363.471 0.013955446 0.082120339 54833.43708 -4.739045469 0.15125813 KQEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQEEEER 7 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 80.219 0.048916 119580000 389080 315590 378490 310750 459550 440540 460420 392040 411650 330970 FALSE TRUE 404441.1788 369790.1276 388353.7603 372215.4225 381435.8551 338231.2614 424331.0773 386785.345 396834.7969 395817.2347 1.021787692 0.934244634 0.98114414 0.940371944 0.963666616 0.85451373 1.072037901 0.977181667 1.002570788 1 18.59447491 2.216456606 24.99999614 1.009595968 0.950300553 0.316817005 0.04567606 303.0461666 342747.928 0.016385769 0.012111068 164.6101482 -2.216456606 -0.059295415 KQEELQQLEQQR ddPTM_MDA-MB-175_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 ;;; 208.82 1.00E-07 1897210000 1373220 1070000 1327280 1143270 1390150 1491170 1403830 1264470 1455280 1014130 FALSE TRUE 1427435.786 1253764.177 1361870.007 1369405.394 1153852.8 1144868.366 1293794.136 1247521.848 1402904.757 1212829.357 1.176946928 1.033751508 1.122886744 1.129099808 0.951372749 0.94396492 1.066756942 1.028604594 1.156720646 1 20.20994515 8 0.625487581 1.036065684 10.47174488 0.234302716 0.069086776 307.9343003 2.167058788 0.029012351 3999.601092 99999999.99 -8 9.435679195 KQEFLEK ddPTM_MDA-MB-175_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 ; 88.819 0.029387 3208800000 683990 460010 535140 438060 750660 768790 729720 574030 653670 453990 FALSE TRUE 710994.4534 539013.1391 549086.188 524706.9605 623063.0813 590250.1736 672522.6396 566336.0668 630144.5444 542940.6483 1.309525186 0.992766227 1.01131899 0.966416794 1.147571255 1.087135722 1.238666955 1.043090195 1.160614049 1 19.05043497 KQEFLEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQEFLEQK 8 1 Q9BY43;Q9BY43-2;H0YI89;E9PQI5;E9PQ80;E9PSI1 Q9BY43 CHMP4A Charged multivesicular body protein 4a 0 114.4 0.0079303 0 195980 136340 172640 131030 236720 192070 200440 165700 192420 127620 FALSE TRUE 203717.4417 159755.3344 177139.1402 156947.3429 196482.419 147464.6533 184728.989 163479.0625 185494.8418 152624.6956 1.334760675 1.046720086 1.160619122 1.02832207 1.287356664 0.966191302 1.210347961 1.071118025 1.215365843 1 17.21962889 -5 0.221057369 0.328945761 1.154174295 0.126041531 0.112881767 325.1453181 3.253636062 97.90655854 0.191446895 1.00E-05 5 0.825228534 KQEGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQEGLLK 7 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 78.516 0.056318 537380000 517930 351950 504390 346800 705530 648010 557250 513050 545970 389880 FALSE TRUE 538378.2763 412394.6747 517534.8178 415396.0049 585604.2626 497519.4982 513571.2889 506173.4039 526320.6463 466269.5213 1.154650372 0.884455569 1.109947775 0.890892469 1.25593511 1.067021273 1.101447265 1.085581152 1.128790586 1 18.8308046 3.25020459 24.99996122 1.106794165 1.008160189 0.186983764 0.098522599 346.3690959 743660.2718 0.024867448 0.033395378 1779.117329 -3.25020459 -0.098633976 KQELEEICHDLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 KQELEEICHDLEAR 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;; 229.68 7.77E-13 24420997000 11412067 10182426 11585765 10249554.7 14038183 14218549 13036164 12272537 12743570 10309778.5 FALSE TRUE 11862624.22 11931178.46 11887699.55 12276886.03 11651977.67 10916506.48 12014355.4 12108043.72 12284931.41 12329782.2 0.962111416 0.967671469 0.964145137 0.995709886 0.945027047 0.885377073 0.974417488 0.982016025 0.996362401 1 23.55564398 1.733511819 2.949549026 0.994262739 0.954859497 0.295711411 0.026845455 0.330225328 6.08812808 0.017095796 0.00791036 54.13919814 -1.733511819 -0.039403242 KQELEEILHDLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;; 240.24 1.41E-17 144725000 450223 428994 512109 448468 612901 606148 560542 546216 563018 439656 FALSE TRUE 467998.1517 502670.3824 525454.9812 537173.6319 508720.3069 465379.3133 516605.2533 538894.8679 542755.0922 525798.1755 0.890071844 0.956013934 0.999347289 1.021634644 0.967520107 0.885091153 0.982516253 1.024908212 1.032249858 1 19.00414961 1.899805747 4.626081081 1.019867246 0.957523277 0.340342173 0.040545865 0.290738641 9.811258618 0.020200055 0.011767806 79.39730235 -1.899805747 -0.06234397 KQELELVVSELEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQELELVVSELEAR 14 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;M0QY43 Q7Z406 MYH14 Myosin-14 0 ; 224.59 4.96E-12 151740000 290810 290900 313460 275760 371730 403730 343190 331280 342260 281380 FALSE TRUE 302291.4034 340859.8121 321629.0251 330304.5049 308543.4674 309969.8261 316289.871 326839.7335 329942.1295 336511.0237 0.898310552 1.012923168 0.955775599 0.981556269 0.916889628 0.921128297 0.93990939 0.971260109 0.980479409 1 18.36029424 1.32452509 1.998399841 0.995912376 0.949099064 0.242483262 0.031333879 0.484286072 3.335582649 0.028277078 0.008468927 21.11179157 -1.32452509 -0.046813312 KQELLEALTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQELLEALTK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 163.45 0.0054552 0 3376300 2262060 3148800 2190490 4177200 3612100 3724500 3015300 3126200 2363650 FALSE TRUE 3509598.931 2650551.209 3230860.315 2623762.384 3467161.036 2773244.517 3432563.958 2974884.836 3013688.673 2826761.963 1.241561538 0.937663391 1.142954503 0.928186532 1.226548638 0.98106758 1.214309519 1.052400193 1.066127503 1 21.43071897 0.864839813 2.082632767 1.000638808 1.087263498 0.057801531 0.110682404 1.597851898 13.59057226 0.093240351 0.025722402 7.325542855 -0.864839813 0.086624691 KQEQANNPFYIKS(ph)SPSPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQEQANNPFYIKSSPSPQK 19 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 KQEQANNPFYIKS(0.517)S(0.378)PS(0.105)PQK 98.7 0.00047715 706530000 398120 162120 297950 171300 372900 319170 253580 240390 293560 129630 TRUE FALSE 413838.085 189962.8489 305714.8218 205182.6287 309514.5912 245047.6046 233703.737 237167.9652 282994.8329 155028.5166 2.669432012 1.225341331 1.971990886 1.323515397 1.996501018 1.580661481 1.5074887 1.529834449 1.825437276 1 17.24217409 8 0.047353486 2.21E-15 4.619523129 0.305703668 0.37644302 729.1967155 2.611653843 62.40024421 251.2797245 100000000 -8 4.619523129 KQEQANNPFYIKSS(ph)PSPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQEQANNPFYIKSSPSPQK 19 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 KQEQANNPFYIKS(0.151)S(0.76)PS(0.088)PQK 92.95 0.00095719 438540000 339860 185760 245350 151500 344980 287920 256360 251560 273440 113820 TRUE FALSE 353277.9352 217662.835 251744.0226 181466.2478 286340.4228 221054.9435 236265.8333 248188.2497 263598.9478 136120.8498 2.595325667 1.599041112 1.849415596 1.333126028 2.103575046 1.623960942 1.735706423 1.82329342 1.936506775 1 17.05452854 -2.020659475 2.715084163 0.068460509 1.81863236 0.382123889 0.320627342 14230929.33 4154419.528 82952679.38 0.074930398 0.009535435 2.020659475 1.75017185 KQESGISHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQESGISHR 9 1 Q9BZI7-2;Q9BZI7 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 0 113.93 0.0011173 18275000 49109 51647 57381 42338 71554 66851 61480 60348 57746 51575 FALSE TRUE 51047.86124 60516.97049 58876.396 50712.33003 59391.27664 51325.86839 56661.03695 59539.13377 55667.73274 61680.13379 0.827622414 0.981142011 0.954543909 0.822182556 0.962891502 0.832129654 0.918627011 0.965288661 0.902522892 1 15.91251827 0.69790471 0.673301625 0.999329401 0.903620205 0.191706482 0.057738109 1.971442488 1.752674548 0.058759259 0.021561073 4.987750371 -0.69790471 -0.095709197 KQEVQAWDGEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQEVQAWDGEVR 12 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 138.77 0.00010997 2140000000 2443600 2302300 2578000 2255900 3114500 3130700 2782800 2650300 3007100 2487600 FALSE TRUE 2540075.215 2697702.116 2645184.798 2702110.287 2585098.402 2403642.371 2564676.865 2614777.064 2898875.058 2974997.592 0.853807486 0.906791361 0.889138467 0.9082731 0.868941343 0.807947669 0.862076955 0.878917371 0.974412573 1 21.50445707 1.194748721 3.639891535 0.99829617 0.87160516 0.745123426 0.027176609 0.116193977 2.82635418 0.027025267 0.007381921 15.65844823 -1.194748721 -0.12669101 KQFS(ph)LENVQEGEILHDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQFSLENVQEGEILHDAK 18 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 KQFS(1)LENVQEGEILHDAK;KQFS(1)LENVQEGEILHDAK 193.19 6.40E-15 200800000 226451 156332 200934 150185 280475 261790 237829 204073 251987 168026 TRUE FALSE 235391.4603 183180.8049 206170.5051 179891.1447 232799.9597 200993.24 219187.3415 201337.7352 242918.0371 200947.4776 1.171407888 0.91158549 1.025992003 0.895214744 1.15851148 1.000227733 1.09076931 1.001942087 1.208863331 1 17.61645894 3.232823645 24.99999962 1.069189924 0.99644128 0.127716078 0.095368694 290.0544563 1263972.513 0.025527336 0.031301403 1709.321066 -3.232823645 -0.072748645 KQFY(ph)S(ph)T(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;KQFY(1)S(1)T(1)AK 49.358 0.082104 1255180000 1295200 1504200 1275100 1066760 1587990 1834250 1174020 1296440 1390440 1567560 TRUE FALSE 1346335.496 1762534.649 1308330.154 1277761.944 1318064.027 1408273.236 1081997.245 1279063.342 1340398.336 1874693.369 0.718163044 0.940172232 0.697890212 0.681584501 0.703082461 0.751201908 0.577159584 0.682278693 0.71499604 1 20.83822321 -1.17690127 3.30322783 1.000543223 0.715137595 0.491639077 0.085811796 18662268.3 27942324.33 106051.6445 0.021807389 0.066542441 1.17690127 -0.285405628 KQGGLGPMNIPLVSDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQGGLGPMNIPLVSDPK 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 141.93 9.71E-07 921120000 1654640 958230 1371740 1096060 1710610 1682260 1882770 1484410 1716940 962670 FALSE TRUE 1719966.465 1122798.549 1407488.671 1312857.397 1419841.123 1291580.61 1735193.568 1464513.912 1655147.665 1151286.755 1.493951405 0.975255334 1.222535276 1.140339182 1.233264534 1.121858307 1.507177565 1.27206702 1.437650227 1 20.13481578 2.278172537 24.99958667 1.327461006 1.187863929 0.074375502 0.174215306 297.132056 187522.6157 0.055066223 0.046071052 189.7459595 -2.278172537 -0.139597078 KQGGLGPMNIPLVSDPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQGGLGPMNIPLVSDPKR 18 2 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 194.19 4.81E-15 5823700000 3660200 2656720 3639600 2517570 4437600 4007700 3579600 3383400 3944100 2880790 FALSE TRUE 3804707.522 3112990.994 3734450.966 3015537.832 3683298.337 3076972.412 3299021.598 3338051.057 3802152.611 3445225.644 1.104342042 0.90356665 1.083949602 0.875280212 1.069102206 0.893112014 0.957563289 0.968891853 1.103600462 1 21.71616704 1.261809815 24.80251348 1.05180027 0.97756614 0.105702962 0.080424592 351.2787379 374749.866 0.047929488 0.017480914 18.27299837 -1.261809815 -0.07423413 KQGGS(ph)PDEPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQGGSPDEPDSK 12 1 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 KQGGS(1)PDEPDSK;KQGGS(1)PDEPDSK;KQGGS(0.826)PDEPDS(0.174)K;KQGGS(0.945)PDEPDS(0.055)K 130.61 0.00022602 892019000 2267160 797610 1266210 805352 1964230 1834750 1787510 1278440 1645650 645660 TRUE FALSE 2356669.227 934593.313 1299208.473 964648.2219 1630350.886 1408657.118 1647400.295 1261304.603 1586423.378 772164.7151 3.052029161 1.210354857 1.682553537 1.249277781 2.111402987 1.824296152 2.133483003 1.633465734 2.054514208 1 19.5585491 -0.912770483 5.116878659 0.999997706 1.839330734 0.215840107 0.498843557 1.20E-05 2.54E-06 0.442509461 0.104300194 0.122244553 0.912770483 0.839333028 KQGIFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQGIFGK 7 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 102.72 0.013689 298550000 248370 284430 243390 294790 474630 495650 477280 439210 507010 342210 FALSE TRUE 258175.8394 333278.6399 249732.9433 353098.5821 393952.5621 380542.7991 439869.5465 433323.1084 488762.8091 409259.4975 0.630836525 0.814345524 0.610206837 0.862774314 0.96259846 0.929832543 1.074793741 1.058797929 1.194261372 1 18.64265637 3.163256897 0.847593252 1.091503324 0.670701812 0.803158234 0.079415758 0.252173029 0.399637566 0.039177045 0.061248275 1456.320279 -3.163256897 -0.420801512 KQIS(ph)VR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 113.71 0.01587 15101940000 15298100 15660100 18730600 13651400 22017500 19374100 17541300 16133300 18900100 16523500 TRUE FALSE 15902080.8 18349600.36 19218734.82 16351606.17 18274973.21 14874758.89 16166367.07 15917059.5 18219889.09 19760963.46 0.804721937 0.928578224 0.972560617 0.827470088 0.924801731 0.752734497 0.818096096 0.805479932 0.922014209 1 24.23614995 4.80186908 20.39955192 0.869812245 0.804716235 0.061928904 0.076825565 26034.38215 8385618.634 0.018453611 29.84678576 63367.86574 -4.80186908 -0.06509601 KQIT(ph)MEELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 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 200.19 1.55E-07 14356576000 14920477 12034263 14368477 9459743 20703761 17025884 15488400 15538260 15936077 12164323 TRUE FALSE 15509548.95 14101054.06 14742931.31 11330851.93 17184543.1 13071880.47 14274378.74 15329995.04 15362540.7 14547689.19 1.066117701 0.969298551 1.013420834 0.77887641 1.18125586 0.898553736 0.981212793 1.053775265 1.056012436 1 23.79428667 1.760054874 8.78246527 1.040670958 0.981029715 0.054513556 0.099122126 0.434455872 119.8832251 0.044314761 0.024184099 57.55126496 -1.760054874 -0.059641244 KQITTS(ph)PITVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQITTSPITVR 11 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 KQIT(0.018)T(0.065)S(0.916)PIT(0.001)VR;KQIT(0.001)T(0.01)S(0.989)PITVR 158.81 1.80E-05 531720000 237780 247790 281790 251640 310830 322390 275570 263090 262490 254370 TRUE FALSE 247167.738 290346.005 289133.6789 301413.6409 257995.2276 247519.8084 253970.1033 259563.7089 253043.0362 304208.9313 0.812493364 0.954429588 0.950444412 0.990811281 0.848085645 0.813650695 0.834854198 0.853241579 0.831806729 1 18.21470298 3.207351029 24.95529932 0.851997797 0.93067215 0.171057512 0.065293102 257.2850264 205725.3448 0.01794585 0.021451499 1611.948006 -3.207351029 0.078674353 KQLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQLELR 6 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ; 114.02 0.041111 1932070000 3815200 3890600 3988100 3584200 4970800 4907100 4234800 4295800 4030200 4280500 FALSE TRUE 3965827.042 4558780.285 4092033.162 4293144.062 4125865.192 3767500.393 3902865.31 4238221.828 3885153.889 5119182.02 0.774699361 0.890529047 0.799352933 0.838638682 0.805961807 0.735957498 0.762400183 0.827909969 0.758940369 1 22.28748187 -1.246763769 3.529641862 1.000434221 0.801860686 0.662854581 0.042891287 10801042.68 20271527.3 53307.46346 0.010378185 0.056654737 1.246763769 -0.198573535 KQLQDEMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 175.93 8.58E-05 4748720000 5838230 5517250 5852890 4997850 7409450 7452920 6402240 5949450 5904060 6037080 FALSE TRUE 6068727.828 6464794.769 6005421.122 5986409.813 6149994.336 5722092.28 5900415.7 5869707.354 5691574.034 7219930.239 0.840552142 0.895409589 0.831783815 0.829150645 0.851808 0.792541214 0.817239988 0.812986713 0.78831427 1 22.78355347 4.144657445 9.887312551 0.830017193 0.867896704 0.009671753 0.058713329 0.796777297 76.22641049 0.01320965 0.028619555 13952.67392 -4.144657445 0.037879512 KQMVIDVLHPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQMVIDVLHPGK 12 1 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 136.24 7.36E-05 4190700000 12185700 9358800 12108300 9222500 14694900 14057800 13913500 12827600 13674900 10637300 FALSE TRUE 12666800.85 10966101.1 12423852.25 11046682.97 12197066.15 10793089 12822923.51 12655667 13182743.02 12721475.27 0.995702195 0.862014889 0.976604677 0.868349208 0.958777649 0.848414886 1.007974566 0.994826994 1.036258982 1 23.60076265 2.202280024 24.55618509 1.007731309 0.917969868 0.46999653 0.047557208 117.9563649 79836.87 0.016047231 0.011852076 159.323568 -2.202280024 -0.08976144 KQNGAIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQNGAIGR 8 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ; 121.85 0.0022699 389250000 187863 221430 186161 181086 256983 261537 219815 171744 238098 221049 FALSE TRUE 195279.9763 259458.88 191012.5086 216904.2703 213301.1215 200798.9954 202585.3259 169442.0526 229528.8995 264359.3193 0.738691478 0.98146296 0.722548799 0.82049035 0.806860609 0.759568439 0.766325645 0.640953582 0.868245917 1 18.01214066 KQNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQNLER 6 1 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2;CON__Q3MHN2;P02748 F1T0B3 DDX1;C9 ATP-dependent RNA helicase DDX1;Complement component C9;Complement component C9a;Complement component C9b 0 ;;; 128.75 0.02644 1397750000 1703190 1652630 1798820 1577510 2174740 2209860 1985230 1805940 1812190 1691260 FALSE TRUE 1770433.256 1936456.347 1845698.727 1889536.77 1805078.472 1696653.506 1829622.485 1781734.328 1746969.636 2022630.016 0.875312461 0.957395239 0.912524146 0.934197928 0.892441256 0.838835325 0.904575958 0.880899776 0.863711911 1 20.94780101 KQNS(ph)PVAPTAQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQNSPVAPTAQPK 13 1 Q6P1N0-2;Q6P1N0 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK;KQNS(1)PVAPTAQPK 182.31 6.93E-06 3931640000 5255210 2775436 4030487 3067478 5158060 5157190 5321305 4141665 4792580 2411099 TRUE FALSE 5462689.749 3252095.543 4135524.802 3674215.993 4281294.804 3959510.78 4904207.209 4086152.755 4620095.982 2883507.686 1.894459923 1.127826209 1.434199334 1.274217513 1.484752347 1.3731577 1.700778269 1.417077116 1.602248541 1 21.45939344 KQPPKEPSEVPT(ph)PK ddPTM_MDA-MB-175_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;KQPPKEPSEVPT(1)PK 127.22 0.0038533 2234230000 6657320 1602276 2937830 1436773 4287920 4049860 3992010 2829990 3578580 1420829 TRUE FALSE 6920156.134 1877454.439 3014392.263 1720962.411 3559060.89 3109341.391 3679105.825 2792058.613 3449787.605 1699213.239 4.072564864 1.104896311 1.773992924 1.012799554 2.094534581 1.829871213 2.165181944 1.643147869 2.030226416 1 20.69643548 4.74704695 24.94585191 1.677376271 4.072566102 0.748598891 0.424084232 506.9951747 1490295.029 0.096192944 1.120681552 55853.05724 -4.74704695 2.395189831 KQPPVS(ph)PGTALVGSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.999)PGT(0.001)ALVGSQK;KQPPVS(1)PGTALVGSQK 189.47 6.21E-10 1365380000 2587130 1404170 1954180 1564080 2062930 2306780 2619230 1990650 2168190 1316080 TRUE FALSE 2689271.89 1645325.275 2005107.536 1873450.356 1712273.895 1771065.305 2413927.909 1963968.593 2090157.265 1573940.678 1.708623411 1.045354058 1.273940984 1.190292863 1.087889728 1.125242729 1.533684174 1.24780344 1.327977156 1 20.58594974 -2.307496316 1.842673737 5.48E-05 1.271255093 0.157975307 0.194026647 1677432.761 215429.8636 6965328.044 0.051023137 0.004926105 2.307496316 1.271200294 KQPPVS(ph)PGTALVGSQKEPSEVPTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVS(0.935)PGT(0.065)ALVGSQKEPSEVPTPK;KQPPVS(0.924)PGT(0.076)ALVGSQKEPSEVPTPK 183.59 1.06E-17 1175030000 1167520 546140 986780 492970 1179470 932200 1001920 891220 1156480 545640 TRUE FALSE 1213614.591 639935.2966 1012496.297 590477.9946 978984.1107 715710.6776 923386.8924 879274.6536 1114858.511 652547.7111 1.859809743 0.980672042 1.551605009 0.904880953 1.500249091 1.096794404 1.415048856 1.347448836 1.708470495 1 19.31572386 KQPPVSPGTALVGSQKEPSEVPT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 KQPPVSPGTALVGSQKEPS(0.008)EVPT(0.992)PK 191.12 3.54E-16 1387300000 1573200 443080 677250 365100 1070000 748920 757050 715330 725450 345660 TRUE FALSE 1635311.151 519175.5433 694899.6914 437315.6903 888121.7822 574994.68 697710.4428 705742.1714 699341.1962 413385.4589 3.955899066 1.255911479 1.68099694 1.057888421 2.148410794 1.390940749 1.687796287 1.707225438 1.691741161 1 18.65712812 4.74294984 24.9769459 1.557080238 3.955900031 0.829427615 0.331757012 158.1737093 900057.4316 0.072238912 0.572982439 55328.62018 -4.74294984 2.398819793 KQQEEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQQEEEAER 9 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75 Q9UM54-1 MYO6 Unconventional myosin-VI 0 69.721 0.087291 41451000 49210 52056 58559 51152 67255 70488 54242 55581 56831 62837 FALSE TRUE 51152.8488 60996.21306 60085.09565 61269.71293 55823.01912 54118.23026 49990.3703 54836.02761 54785.66341 75148.70706 0.680688342 0.811673486 0.799549294 0.815312935 0.742834059 0.720148521 0.6652193 0.729700214 0.72903002 1 16.19746066 -0.922823994 4.568811373 1.000002761 0.744279619 0.7113921 0.048955384 0.007895741 32221015.6 244.9122081 0.012384826 0.119447209 0.922823994 -0.255723142 KQQLAEEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQQLAEEEAR 10 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 137.01 0.00016457 172940000 195190 165990 216360 183420 242930 242180 221560 193550 199940 188760 FALSE TRUE 202896.2519 194497.4913 221998.5193 219699.9285 201636.8454 185937.3653 204193.5483 190955.7788 192744.1985 225743.908 0.89878949 0.861584674 0.983408683 0.97322639 0.893210573 0.823665041 0.904536251 0.845895602 0.85381794 1 17.78432753 3.010640357 24.45820503 0.873608173 0.928903641 0.105339894 0.055641179 283.6210588 651932.5517 0.01568988 0.018734573 1024.802928 -3.010640357 0.055295468 KQQLEVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQQLEVELR 9 1 P15924 P15924 DSP Desmoplakin 0 ; 125.74 0.00079063 538320000 483650 461100 516630 454960 604080 631290 534520 487800 492060 517660 FALSE TRUE 502744.8755 540290.3381 530093.8022 544949.7301 501398.6974 484682.4648 492622.9257 481261.8389 474350.8567 619085.5658 0.812076558 0.872723203 0.856252886 0.880249452 0.809902096 0.782900606 0.795726718 0.777375318 0.766212109 1 19.2397793 3.158849 7.593952947 0.804985036 0.856526923 0.020772788 0.066093788 0.479197057 39.1234012 0.017621625 0.021141788 1441.614029 -3.158849 0.051541886 KQQMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KQQMAR 6 1 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 114.67 0.040228 4590965000 3940617 3594900 4009862 3083333 5821090 4917170 4521340 4073670 3998376 5504350 FALSE TRUE 4096195.602 4212296.111 4114362.298 3693207.065 4831623.201 3775231.788 4166945.556 4019069.117 3854475.229 6582821.995 0.622255258 0.639892149 0.625014971 0.561037055 0.733974457 0.573497474 0.633002922 0.610538933 0.585535388 1 22.65027476 -1.063309113 4.582587352 1.000019317 0.621208712 0.863401067 0.04528056 0.215666985 25398073.37 1058.113475 0.009732938 0.086435249 1.063309113 -0.378810604 KQQMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQQMGK 6 1 P31946-2;P31946;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ; 110.54 0.04589 1271810000 1041280 804750 1121480 773860 1366200 1149990 1322570 1009980 1224010 934060 FALSE TRUE 1082390.538 942959.5524 1150706.69 926927.1983 1133973.812 882922.2508 1218903.508 996442.8701 1179958.119 1117071.173 0.968953961 0.844135607 1.030110451 0.829783473 1.01513121 0.790390328 1.091160113 0.892013771 1.056296275 1 20.09128968 2.225712087 24.99999946 0.992430304 0.916121606 0.213783848 0.08831732 418.5386048 814365.0863 0.030045183 0.022327776 168.1558911 -2.225712087 -0.076308698 KQQNQELQEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQQNQELQEQLR 12 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 229.75 1.20E-11 1440170000 1078630 1086030 1127480 864140 1557330 1491160 1173310 1147350 1228340 1152550 FALSE TRUE 1121215.145 1272547.204 1156863.055 1035064.313 1292615.603 1144860.689 1081342.896 1131971.65 1184132.283 1378370.106 0.813435478 0.923226062 0.839297842 0.750933518 0.937785576 0.830590191 0.784508378 0.821239263 0.859081518 1 20.39453189 0.863262043 5.937060123 0.999999188 0.837403775 0.450435011 0.053482689 2.306703171 99.82222322 0.050490353 0.012699195 7.298977813 -0.863262043 -0.162595412 KQQNVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQQNVDR 7 1 Q13268;C9JZP6;Q13268-2 Q13268 DHRS2 "Dehydrogenase/reductase SDR family member 2, mitochondrial" 0 ;;; 129.47 0.0058649 656000000 695100 815150 754940 868410 845340 1083560 850700 724500 802340 992070 FALSE TRUE 722543.0847 955145.6715 774614.3566 1040178.906 701649.4087 831919.6115 784019.9111 714789.2625 773463.9401 1186447.122 0.608997292 0.805046979 0.652885697 0.876717459 0.591387004 0.701185578 0.660813193 0.602461963 0.651916066 1 20.17821637 -1.104815061 5.053400308 1.000009499 0.682745309 0.544312443 0.086877223 8.98E-06 1.59E-06 0.081207773 0.019140283 0.078557009 1.104815061 -0.31726419 KQQPQLPRPPTTGGSEGAGAAPCPPNPANSWVPGLS(ph)PGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQQPQLPRPPTTGGSEGAGAAPCPPNPANSWVPGLSPGGSR 41 2 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 KQQPQLPRPPTTGGSEGAGAAPCPPNPANSWVPGLS(0.938)PGGS(0.062)R 89.677 0.00013066 320800000 89622 103450 90815 81986 103060 118760 90739 97605 77959 88121 TRUE FALSE 93160.34576 121216.7328 93181.71351 98202.5861 85541.89801 91179.78983 83626.64008 96296.76462 75153.27082 105386.6228 0.883986443 1.150209861 0.884189198 0.931831607 0.81169598 0.865193204 0.793522345 0.913747515 0.713119643 1 16.68533222 4.057840034 12.50557018 0.859097814 1.017337108 0.292686482 0.095635709 0.923357354 197.2312748 0.021609879 0.046706863 11424.57451 -4.057840034 0.158239295 KQQSIAGSADSKPIDVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQQSIAGSADSKPIDVSR 18 2 Q12904;Q12904-2;A0A5F9ZHC5 Q12904 AIMP1 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2 0 86.727 0.0019091 452070000 817200 644370 837810 607230 978630 954400 830400 769150 877870 606520 FALSE TRUE 849463.687 755035.535 859644.0169 727338.2816 812282.8222 732755.0641 765311.0782 758840.8023 846275.6302 725355.9815 1.171099031 1.040917224 1.185133974 1.002732865 1.119840248 1.010200623 1.055083432 1.046163293 1.166703869 1 19.46832967 8 0.548259173 1.060098126 5.145391332 0.17506182 0.063573036 236.8251787 2.17585093 0.027571236 1138.541126 100000000 -8 4.085293206 KQS(ph)AGPNS(ph)PTGGGGGGGSGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.819)PT(0.177)GGGGGGGS(0.003)GGT(0.001)R 60.541 0.027058 0 145900 106970 113270 103540 154050 157480 136410 119290 133830 94745 TRUE FALSE 151660.2447 125341.2654 116221.9093 124019.903 127864.636 120907.6566 125717.8278 117691.1127 129013.4844 113308.4687 1.338472281 1.106195034 1.025712469 1.094533395 1.128464954 1.067066372 1.109518372 1.038678873 1.138604077 1 16.78989617 4.730591601 4.151856179 1.077954105 1.358014681 0.773184012 0.042455602 0.088463355 3.399207892 0.009450387 0.073070467 53776.38453 -4.730591601 0.280060575 KQS(ph)FDDNDS(ph)EELEDKDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 KQS(1)FDDNDS(1)EELEDKDSK 135.58 4.35E-06 132010000 179670 42970 65808 33787 113770 126250 99161 75838 84413 34514 TRUE FALSE 186763.5103 50349.76324 67523.01054 40469.96776 94431.41604 96930.35084 91388.50171 74821.51566 81374.99262 41276.35749 4.5247091 1.219820893 1.635876193 0.980463641 2.287784625 2.348326178 2.21406411 1.812696667 1.971467386 1 15.33302804 4.745783135 24.88910326 1.779905507 4.524710468 0.746936504 0.488785015 418.9505825 1443683.49 0.118718044 1.219773308 55690.75875 -4.745783135 2.74480496 KQS(ph)LGELIGTLNAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK;KQS(1)LGELIGTLNAAK 273.33 2.02E-33 73920373000 8690649 4833570 6951322 4885566 9255771 8147134 8642355 6741568 7627764 4612180 TRUE FALSE 9033762.533 5663698.048 7132479.162 5851916.373 7682478.351 6255085.6 7964944.633 6651208.308 7353242.264 5515848.365 1.637782973 1.026804523 1.293088332 1.06092771 1.392800861 1.134020587 1.444010804 1.20583596 1.333111749 1 22.39515137 -0.973514569 4.069675809 0.999982815 1.268705517 0.183112769 0.176315845 32371684.05 42415798 7135.86528 0.037667211 0.106288293 0.973514569 0.268722702 KQS(ph)LPATSIPTPASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQSLPATSIPTPASFK 16 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 KQS(1)LPATSIPTPASFK 144.92 7.78E-07 424440000 840150 570660 712260 486080 964440 869540 947100 784080 983160 552590 TRUE FALSE 873319.7707 668666.4159 730822.0807 582225.1732 800504.8333 667602.513 872863.8272 773570.6901 947776.2636 660859.4305 1.321490971 1.011813383 1.10586616 0.881012128 1.211308784 1.010203505 1.320801046 1.170552548 1.434157129 1 19.33398391 2.240191247 24.9999851 1.240236719 1.083412965 0.169205987 0.152203877 67.55992872 1035815.384 0.050807952 0.040433488 173.8566258 -2.240191247 -0.156823754 KQS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KQSPPR 6 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KQS(1)PPR;KQS(1)PPR;KQS(1)PPR;KQS(1)PPR;KQS(1)PPR 61.962 0.073889 1064200000 414633 319241 376121 308674 463138 456177 412735 389298 399199 334801 TRUE FALSE 431003.031 374068.1584 385923.0222 369728.7959 384413.9682 350236.8052 380383.7522 384080.0971 384831.906 400398.8458 1.076434249 0.934238853 0.96384649 0.923401253 0.960077613 0.874719817 0.95001211 0.959243767 0.961121417 1 18.61107829 4.741386264 24.86119502 0.944857549 1.076434301 0.607979165 0.031021602 154.8342807 1362219.703 0.007052792 0.04864175 55129.78063 -4.741386264 0.131576752 KQS(ph)SEGIPVAQPSVMDDIEVWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.787)S(0.213)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR;KQS(0.644)S(0.356)EGIPVAQPSVMDDIEVWLR;KQS(0.5)S(0.5)EGIPVAQPSVMDDIEVWLR 124.09 3.76E-07 264055000 158980 136532 171555 136670 229744 191120 184521 170514 185520 132153 TRUE FALSE 165256.6532 159980.3089 176025.8642 163702.9181 190692.1969 146735.2765 170057.7619 168228.5387 178843.1714 158045.8501 1.045624754 1.012239858 1.113764544 1.035793841 1.206562506 0.928434858 1.076002703 1.0644287 1.13159043 1 17.26998363 -1.312695093 5.206711569 0.999982297 1.067088833 0.077832973 0.070393135 1.33E-05 1.76E-06 0.062830355 0.014805351 0.048674882 1.312695093 0.067106536 KQS(ph)SSEISLAVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQSSSEISLAVER 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 KQS(0.953)S(0.046)S(0.001)EISLAVER;KQS(0.982)S(0.018)SEISLAVER 228.46 4.53E-12 475390000 440470 366560 413620 325130 556360 501690 465560 394120 460660 389230 TRUE FALSE 457860.0957 429513.8286 424399.277 389439.7436 461790.1259 385180.1007 429068.1907 388837.4661 444080.9366 465492.1662 0.983604299 0.922709037 0.911721631 0.836619329 0.992047041 0.827468492 0.92175169 0.835325478 0.954003029 1 18.82839736 4.729148685 1.987228746 0.898788772 1.00744222 0.098936945 0.05968459 1.307532162 5.616368325 0.013980844 0.257545069 53598.01239 -4.729148685 0.108653449 KQSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.97)PT(0.03)GGGGGGGSGGTR;KQSAGPNS(0.989)PT(0.011)GGGGGGGSGGTR;KQSAGPNS(0.996)PT(0.004)GGGGGGGSGGTR 150.4 3.45E-08 1513610000 629740 548260 668170 543570 759310 829240 614370 640780 675310 601130 TRUE FALSE 654602.6215 642419.3901 685583.0591 651086.5236 630242.7574 636661.5773 566214.074 632191.3922 651005.725 718909.9142 0.910548886 0.893602074 0.953642516 0.905658012 0.87666444 0.885592986 0.78760087 0.879374981 0.905545621 1 19.45545147 3.322765698 4.042564989 0.875773106 0.918446481 0.028059148 0.051135477 0.459943625 14.24206669 0.014086505 0.019172821 2102.643757 -3.322765698 0.042673376 KQSDS(ph)VKGK ddPTM_MDA-MB-175_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;KQSDS(1)VKGK 146.36 4.96E-05 1827040000 1783660 510010 1374920 527160 3217030 1314160 1704770 1127960 1662890 777610 TRUE FALSE 1854080.274 597600.2502 1410751.545 631430.6746 2670200.39 1008966.256 1571145.673 1112841.541 1603042.914 929967.7913 1.993703751 0.642603169 1.516989683 0.67898123 2.871282656 1.084947528 1.689462461 1.196645251 1.723761757 1 19.82682122 5.050961462 19.54880535 1.403564657 7.844361609 0.08177899 0.613400813 463.5534451 184717.9484 0.132077219 4736.213766 112450.5185 -5.050961462 6.440796952 KQSEPFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQSEPFFK 8 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 160.59 0.00056519 4833400000 9295600 6998000 9291800 7575700 12347100 11921500 11716700 9970400 11456500 8994500 FALSE TRUE 9662597.466 8199852.063 9533951.941 9074150.849 10248344.35 9152912.297 10798314.44 9836763.096 11044182.8 10756800.06 0.898278057 0.762294736 0.886318597 0.843573441 0.952731694 0.850895456 1.003859361 0.914469269 1.026716378 1 23.35874563 2.525175379 0.511203859 1.006068559 0.825604732 0.536529205 0.05388375 0.713329949 0.388017412 0.045302013 0.048571496 335.100734 -2.525175379 -0.180463827 KQSFDDNDS(ph)EELEDKDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQS(0.001)FDDNDS(0.999)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK;KQS(0.005)FDDNDS(0.995)EELEDKDSK;KQS(0.023)FDDNDS(0.977)EELEDKDSK;KQS(0.002)FDDNDS(0.997)EELEDKDS(0.001)K;KQSFDDNDS(1)EELEDKDSK;KQS(0.01)FDDNDS(0.99)EELEDKDSK;KQSFDDNDS(1)EELEDKDSK 217.94 6.41E-19 7425900000 7428110 1253669 2533763 1250849 4387460 4481350 4121000 2448883 3027831 875808 TRUE FALSE 7721377.519 1468976.899 2599794.945 1498263.199 3641681.116 3440624.378 3797985.252 2416059.729 2918859.954 1047405.809 7.371906333 1.402490692 2.482127674 1.430451488 3.476857856 3.284900988 3.626087633 2.306708353 2.786751733 1 19.99838908 7.999999945 0.07287792 1.57E-08 9.864670945 0.204775581 1.533058361 479.218913 2.567533895 58.10425549 481.786627 99999987.28 -7.999999945 9.86467093 KQSFDDNDSEELEDKDS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQSFDDNDSEELEDKDSK 18 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KQSFDDNDS(0.027)EELEDKDS(0.973)K 166.59 1.99E-11 667390000 491830 94654 168420 81641 290920 311940 288190 162670 179370 59394 TRUE FALSE 511247.8282 110910.0882 172809.1636 97789.34613 241469.5223 239496.6625 265600.9148 160489.6747 172914.5087 71031.11713 7.197519183 1.561429591 2.43286563 1.376711364 3.399489295 3.37171471 3.739219169 2.259427716 2.434348715 1 16.11616355 7.999999998 0.075493283 4.64E-09 9.983117881 0.223430259 1.480033089 424.7118757 2.349218288 49.98604789 445.380485 99999999.54 -7.999999998 9.983117876 KQSS(ph)EGIPVAQPSVMDDIEVWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQSSEGIPVAQPSVMDDIEVWLR 23 1 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 KQS(0.434)S(0.566)EGIPVAQPSVMDDIEVWLR 92.238 0.0030306 20990000 13546 12518 15051 12726 17029 18101 19556 14297 18540 11695 TRUE FALSE 14080.80654 14667.86912 15443.24142 15243.16482 14134.41666 13897.31707 18023.14962 14105.3721 17872.74902 13986.41134 1.006749065 1.048722848 1.104160392 1.089855321 1.01058208 0.993629941 1.288618588 1.008505453 1.27786525 1 13.77173822 KQTDFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQTDFEHR 8 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ; 189.13 0.00012549 198939000 382460 368300 390900 352380 507040 492570 463620 408060 412750 438670 FALSE TRUE 397559.8161 431552.66 401087.1751 422079.7123 420853.5219 378178.0825 427280.253 402590.6232 397895.2081 524618.9877 0.757806762 0.82260206 0.76453042 0.804545246 0.802207949 0.720862362 0.814458232 0.767396211 0.758446068 1 19.0009105 -1.49129073 5.953505854 1.000205626 0.780374773 0.830421011 0.029928452 7.54E-05 6.44E-06 0.026743357 0.006297624 0.032263336 1.49129073 -0.219830853 KQTIDNSQGAYQEAFDISKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQTIDNSQGAYQEAFDISKK 20 2 P27348 P27348 YWHAQ 14-3-3 protein theta 0 ; 232.39 1.90E-26 2089100000 1041700 531930 760080 488960 1071680 871310 911450 698330 971990 500450 FALSE TRUE 1082827.12 623284.8397 779888.3092 585674.8286 889516.2164 668961.4573 840008.1674 688970.0286 937008.2698 598503.5958 1.809224085 1.041405338 1.303063699 0.978565263 1.486233705 1.117723372 1.403513986 1.151154368 1.56558503 1 19.19100039 4.750920645 24.76788642 1.235602273 1.809224488 0.441366913 0.196154517 1498.07322 3001881.746 0.041836865 0.721114183 56353.46766 -4.750920645 0.573622215 KQTIGNSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KQTIGNSCK 9 1 P55010;H0YLZ1;H0YN40 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 127.83 0.00069652 1371060000 1306500 1036550 1192930 971620 1831780 1738770 1643770 1424770 1534780 1343390 FALSE TRUE 1358081.629 1214569.399 1224018.736 1163803.536 1520414.69 1334967.019 1514927.012 1405673.289 1479543.568 1606601.55 0.845313282 0.755986697 0.761868265 0.724388406 0.946354552 0.830926012 0.942938847 0.874935848 0.920915063 1 20.61558074 3.236668881 24.99999542 0.908222046 0.770037487 0.661292478 0.051323257 29.98592378 396277.3741 0.013741142 0.017234363 1724.522563 -3.236668881 -0.138184559 KQVEELFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQVEELFER 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 179.57 7.96E-05 292320000 204900 192130 212200 185960 278910 270800 224620 204920 216700 210380 FALSE TRUE 212989.6102 225126.8329 217730.1063 222742.333 231500.9778 207910.804 207013.6975 202173.3826 208901.0093 251599.933 0.846540806 0.894780973 0.865382211 0.885303626 0.920115419 0.826354767 0.82278916 0.803551019 0.830290401 1 17.94077201 2.715063823 24.80697448 0.838445405 0.882324223 0.000652159 0.055619259 1440.438991 1520755.949 0.01676393 0.015813442 518.8762866 -2.715063823 0.043878818 KQVENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQVENER 7 1 Q9H307 Q9H307 PNN Pinin 0 ;;; 127.02 0.0062459 1164490000 809310 724910 786360 720790 909130 969550 974580 833640 825220 674450 FALSE TRUE 841262.1837 849407.6535 806853.1876 863360.1107 754596.4073 744386.7062 898189.873 822466.4194 795520.4934 806595.5644 1.042978936 1.053077516 1.000319396 1.070375475 0.935532553 0.922874783 1.113556673 1.019676348 0.986269363 1 19.62148595 4.059009957 1.475313757 1.007476629 1.04882398 0.080164911 0.053485132 1.496108396 5.890960667 0.016360165 0.062798734 11455.39205 -4.059009957 0.041347351 KQVENERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KQVENERR 8 2 Q9H307 Q9H307 PNN Pinin 0 ;;;; 120.31 0.00085893 362160000 443762 465193 462288 344666 663611 606513 436580 488167 479633 635891 FALSE TRUE 461282.0664 545086.2791 474335.6051 412839.9061 550810.6393 465659.5475 402359.7188 481623.9198 462371.102 760481.6666 0.606565663 0.716764523 0.623730493 0.542866349 0.724291805 0.612321859 0.529085363 0.633314307 0.607997697 1 19.53655394 -1.893411319 2.3621183 1.211755169 0.621880633 0.786172241 0.059159131 4036649.39 2116793.754 4759175.64 0.014245142 0.012781702 1.893411319 -0.589874536 KQVEVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQVEVFR 7 1 A0A087X1Z3;Q9UL46;H0YLG1;H0YLD2 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;; 143.89 0.0038344 5621920000 4243450 4326830 4513570 4071880 5058160 5600380 4829680 4457090 4442610 4525620 FALSE TRUE 4410984.683 5069929.394 4631197.342 4877285.711 4198375.77 4299776.62 4451117.062 4397349.999 4282721.334 5412328.591 0.814988338 0.936737175 0.855675568 0.901143681 0.775706001 0.794441163 0.822403331 0.812469148 0.791289971 1 22.367818 3.252992143 24.9997182 0.820370352 0.879860506 0.078776247 0.066578912 417.4202603 723092.7715 0.016796756 0.022641648 1790.573458 -3.252992143 0.059490154 KQVVES(ph)FVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KQVVESFVPR 10 1 A2A341;Q9BX26 A2A341 SYCP2 Synaptonemal complex protein 2 1 KQVVES(1)FVPR;KQVVES(1)FVPR;KQVVES(1)FVPR;KQVVES(1)FVPR 53.327 0.067868 8689640000 12194960 5608910 6911190 6016860 9019900 8976480 9612320 4878210 7464450 3720460 TRUE FALSE 12676426.44 6572196.661 7091301.289 7206976.949 7486700.62 6891828.56 8858881.241 4812825.574 7195805.903 4449412.904 2.849011029 1.477093001 1.593761119 1.619759079 1.682626625 1.548929872 1.991022508 1.081676544 1.6172484 1 22.08518356 4.739935649 24.64809614 1.528592721 2.849011554 0.684430879 0.272065434 53.58399072 960396.0322 0.061495731 0.386158155 54945.94521 -4.739935649 1.320418833 KQYQDS(ph)PNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KQYQDSPNQK 10 1 H0Y9T5;Q8IU60 H0Y9T5 DCP2 m7GpppN-mRNA hydrolase 1 KQYQDS(1)PNQK 91.62 0.0061403 79053000 184470 88762 124360 84505 155280 155790 134910 115470 125730 62534 TRUE FALSE 191753.018 104006.183 127600.9238 101219.8368 128885.5611 119610.1335 124335.4017 113922.3135 121205.0019 74786.34001 2.564011262 1.390710964 1.70620629 1.353453542 1.723383723 1.599358031 1.662541604 1.523303768 1.620683695 1 16.19048716 7.999999011 0.045885216 9.00E-10 4.454036235 0.400636159 0.292614266 667.9720602 2.321303525 56.4273966 217.7858411 99999772.3 -7.999999011 4.454036234 KRAPS(ph)PLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRAPSPLPK 9 2 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 KRAPS(1)PLPK;KRAPS(1)PLPK 118.48 0.00077339 704750000 2411700 1296250 1916170 1268180 3070100 2520000 2585000 2132540 2271600 1638900 TRUE FALSE 2506915.778 1518870.854 1966106.964 1519022.219 2548245.499 1934768.191 2382380.945 2103956.789 2189845.56 1960011.076 1.279031434 0.77492973 1.003110129 0.775006956 1.300117907 0.98712105 1.215493613 1.073441275 1.117261829 1 20.90243038 3.240610321 24.99999816 1.117012335 0.948162508 0.192530422 0.157535521 80.46354305 981391.2528 0.040756356 0.052565368 1740.244704 -3.240610321 -0.168849828 KRAQEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRAQEEAER 9 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 146.11 5.38E-05 69768000 111371 42049 67398 35014 225572 114086 136322 103489 98336 132109 FALSE TRUE 115768.0131 49270.58865 69154.44725 41939.66469 187229.352 87591.25549 125636.7254 102101.8992 94796.90657 157993.2292 0.732740344 0.311852533 0.437705132 0.265452291 1.185046682 0.554398793 0.795203225 0.646242246 0.600006134 1 17.26950321 3.276166545 24.99999987 0.759342102 0.428057771 0.399816949 0.212950163 174.9695815 116316.6699 0.055932241 0.075730909 1888.715503 -3.276166545 -0.331284331 KRDAEDDGEEEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KRDAEDDGEEEDD 13 2 Q9BTT0;Q5TB19;Q9BTT0-3;Q9BTT0-2;Q5TB25;H0YCE2 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;;;;;; 196.57 5.59E-07 3945526000 4904279 3013265 3992715 2584321 5172077 5292962 4980264 3991330 4498842 2782119 FALSE TRUE 5097903.722 3530769.824 4096768.433 3095491.98 4292929.199 4063751.791 4589897.894 3937832.75 4336929.555 3327221.951 1.532180238 1.061176524 1.231287991 0.930353318 1.290244313 1.221364805 1.379498561 1.183519707 1.303468665 1 21.66588668 KRDEDRHDINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRDEDRHDINK 11 3 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 75.739 0.016324 92864000 169260 70152 113610 63865 182540 137010 141090 99767 129170 79732 FALSE TRUE 175942.5155 82200.06029 116570.7699 76497.30638 151511.916 105191.5039 130030.9971 98429.78655 124521.1969 95353.95884 1.845151661 0.862051889 1.222505823 0.802245731 1.588942062 1.103168711 1.363666477 1.032256948 1.305883872 1 16.54100522 7.941265062 0.020585194 2.31E-06 2.740114729 0.064816099 0.298745895 10868.34998 17.39439508 852.9214943 1560.845352 87350432.88 -7.941265062 2.740112418 KRDFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRDFTNEAPPAPLPDASASPLSPHRR 26 3 A0A494BZV2;Q6WCQ1-2;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 KRDFTNEAPPAPLPDAS(0.087)AS(0.207)PLS(0.706)PHRR 79.616 0.013684 251200000 281720 279500 322840 208710 470400 433230 306890 357860 434470 491070 TRUE FALSE 292842.5231 327501.9508 331253.4756 249992.2151 390441.576 332618.8982 282835.1599 353063.472 418833.5096 587285.7644 0.49863719 0.557653481 0.564041384 0.425673889 0.664823838 0.566366356 0.481597166 0.601178325 0.713168163 1 19.16370314 0.893118125 1.616427543 0.999117723 0.54002124 0.844928113 0.060415437 0.174400024 0.903132364 0.055232223 0.015963235 7.81840431 -0.893118125 -0.459096484 KRDS(ph)DAGSSTPTTSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(1)DAGSSTPTTSTR 79.143 0.0151 36929000 23620 19030 20986 18724 33509 34318 26940 17327 25413 19350 TRUE FALSE 24552.53584 22298.25447 21532.9124 22427.55131 27813.15215 26348.16459 24828.37241 17094.75991 24498.39109 23141.26202 1.060985171 0.963571237 0.930498621 0.969158523 1.201885711 1.138579416 1.072904856 0.738713381 1.058645422 1 14.49817992 1.811345083 24.99999985 0.903662091 1.046786446 0.17566363 0.109703362 189.8126655 65208.83719 0.047524411 0.030484081 64.76570282 -1.811345083 0.143124355 KRDS(ph)QGTYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KRDSQGTYSSR 11 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 KRDS(0.959)QGT(0.004)YS(0.036)S(0.001)R;KRDS(1)QGTYSSR;KRDS(0.999)QGT(0.001)YSSR;KRDS(0.998)QGT(0.002)YSSR;KRDS(0.977)QGT(0.022)YS(0.001)SR;KRDS(1)QGTYSSR;KRDS(0.996)QGT(0.004)YSSR 160.46 2.16E-05 8715660000 1572567 1321537 1530364 1251868 1927980 1904470 1755369 1617443 1669670 1415171 TRUE FALSE 1634653.159 1548500.7 1570246.543 1499483.754 1600262.648 1462185.705 1617778.591 1595763.822 1609578.903 1692446.662 0.965852098 0.914948006 0.927796768 0.885985826 0.945532101 0.863947879 0.955881581 0.942873922 0.951036708 1 20.69067894 1.042078132 0.933895844 0.998199849 0.919297983 0.402002058 0.028878781 0.537684458 1.020414968 0.02576096 0.008861111 11.017375 -1.042078132 -0.078901866 KRDS(ph)SLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.63)S(0.37)LR;KRDS(0.5)S(0.5)LR;KRDS(0.5)S(0.5)LR;KRDS(0.5)S(0.5)LR 86.624 0.015703 389084000 630435 480110 575045 446876 777644 690406 678068 606208 650674 539206 TRUE FALSE 655325.0606 562565.1578 590031.1451 535266.739 645460.3506 530069.6697 624919.2584 598082.7733 627256.3698 644853.092 1.016239309 0.872392743 0.91498537 0.830059971 1.000941701 0.822000664 0.969087791 0.927471359 0.972712045 1 19.298611 1.267718377 1.156138623 0.999065827 0.910504322 0.168393171 0.061753793 0.70412541 1.895312185 0.052505048 0.017251549 18.5233007 -1.267718377 -0.088561504 KREAEEVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KREAEEVYR 9 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 164.97 3.48E-05 31703000 47037 35239 44658 38096 74283 63276 56757 56812 51832 67037 FALSE TRUE 48894.05708 41291.02413 45821.82417 45631.27509 61656.40219 48581.10796 52308.23803 56050.52807 49966.57644 80171.61665 0.609867421 0.515032949 0.571546715 0.569169951 0.769055244 0.605963931 0.652453327 0.699131818 0.623245215 1 16.29080395 -4.999999999 0.169182537 2.456499636 0.535697625 0.777382146 0.062046374 58.81514916 0.553975369 28.71229499 0.224643024 1.00E-05 4.999999999 -1.92080201 KREDS(ph)APPSSVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KREDSAPPSSVAR 13 2 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 1 KREDS(1)APPSSVAR 84.653 0.0075961 111750000 48900 28770 41827 29496 53150 49217 46898 36641 41484 35011 TRUE FALSE 50830.60976 33711.0237 42917.04598 35330.22076 44115.58198 37787.09764 43222.01221 36149.88733 39990.99894 41870.73512 1.21398895 0.805121372 1.024989073 0.843792703 1.053613744 0.902470366 1.032272591 0.863368824 0.955106205 1 15.35365463 4.757604777 24.7207029 0.940408869 1.213989235 0.497050833 0.081967744 2887.162783 3747676.924 0.017358569 0.632427477 57227.50044 -4.757604777 0.273580365 KREEGS(ph)DIEDEDMEELLNDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KREEGSDIEDEDMEELLNDTR 21 2 F5H5U2;Q8NHQ9;Q8NHQ9-2 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 KREEGS(1)DIEDEDMEELLNDTR;KREEGS(1)DIEDEDMEELLNDTR 216.51 3.21E-25 198324000 281960 215577 285660 226740 323970 336100 329760 283700 280940 174101 TRUE FALSE 293091.9985 252600.6728 293104.5343 271588.4952 268901.6951 258045.8686 303912.5495 279897.4655 270829.0243 208212.7576 1.407656293 1.213185377 1.4077165 1.304379705 1.291475596 1.239337453 1.459625016 1.344285858 1.300732133 1 17.66769894 0.774439541 4.272162591 1.000003875 1.332902 0.650968151 0.072799831 1.96919776 36.81988211 0.066854255 0.017016392 5.948939349 -0.774439541 0.332898126 KREEILEEIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KREEILEEIAK 11 2 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6 B7Z8Z7 RBM47 RNA-binding protein 47 0 75.695 0.021026 125230000 318130 146270 213920 153910 344690 282100 331100 227990 257790 145510 FALSE TRUE 330690.018 171390.7347 219494.9309 184352.9386 286099.7169 216586.5503 305147.5168 224934.167 248512.1883 174019.8985 1.900300028 0.984891591 1.261320876 1.059378497 1.644063233 1.244607956 1.753520829 1.292577279 1.428067654 1 17.40889276 3.240889726 24.9999721 1.417947399 1.275991876 0.015611483 0.300985274 209.5146475 2248846.726 0.079021416 0.1020713 1741.36466 -3.240889726 -0.141955523 KREELSNVLAAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KREELSNVLAAMR 13 2 Q9Y3U8 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ; 168.76 1.67E-05 2208300000 2853900 2536400 2864800 2215500 5153000 3949700 3395700 2742300 2979700 4505900 FALSE TRUE 2966574.176 2972006.97 2939459.041 2653719.287 4277094.901 3032442.033 3129536.161 2705543.954 2872461.179 5388744.834 0.550513017 0.551521191 0.545481208 0.492455919 0.793708931 0.562736245 0.580754194 0.502073124 0.533048283 1 22.36151784 -1.117981574 4.935822416 1.00001919 0.566919276 0.725596472 0.079690254 1.69E-05 3.01E-06 0.077349809 0.018230718 0.076211134 1.117981574 -0.433099915 KREENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KREENLK 7 2 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 110.31 0.0038428 290130000 337750 218505 319200 233270 409320 377160 315920 304390 339330 251080 FALSE TRUE 351084.6308 256031.534 327518.6142 279410.1098 339743.9326 289570.3059 291157.3649 300310.1499 327117.5796 300274.3188 1.169212979 0.852658779 1.090731354 0.930516172 1.131445186 0.964352553 0.969637917 1.000119328 1.089395793 1 18.19592157 5.208321175 7.254089416 1.004884349 6.502163222 0.284889563 0.078849727 5248.038617 4203.089544 0.017094829 456726.6643 161555.2868 -5.208321175 5.497278873 KREGELTVAQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KREGELTVAQGR 12 2 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 130.01 0.00012607 198255000 82024 119093 90870 112110 127057 152640 111345 110567 111879 194334 FALSE TRUE 85262.37086 139546.2963 93238.14685 134285.0234 105459.8965 117191.6733 102617.488 109085.0302 107852.4966 232410.0266 0.366861844 0.600431481 0.401179537 0.577793589 0.453766553 0.504245342 0.441536406 0.469364562 0.46406129 1 17.82631278 -1.622026262 2.554160424 1.056512736 0.478079278 0.843072563 0.067881883 3832240.422 3316469.747 1436918.25 0.015481762 0.023876669 1.622026262 -0.578433458 KREHS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KREHSPSK 8 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.991)PS(0.009)K;KREHS(1)PSK;KREHS(0.997)PS(0.003)K;KREHS(0.999)PS(0.001)K;KREHS(0.991)PS(0.009)K 91.549 0.0064743 498362000 615237 293020 446515 311519 615953 580479 718778 456408 542693 252586 TRUE FALSE 639527.0318 343343.9056 458151.5477 373136.5284 511253.5291 445671.5495 662438.3022 450290.5973 523161.5849 302075.3906 2.117110667 1.136616607 1.516679484 1.235243055 1.692469976 1.4753653 2.192956867 1.490656344 1.731890783 1 18.20454913 3.134598076 17.58854238 1.647370684 1.474605255 0.002919853 0.369629161 5.209995827 856.7853391 0.099987826 0.119509887 1363.320847 -3.134598076 -0.172765429 KREHS(ph)PSKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KREHSPSKEK 10 3 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 1 KREHS(0.925)PS(0.075)KEK;KREHS(0.998)PS(0.002)KEK;KREHS(0.999)PS(0.001)KEK 73.927 0.031059 1052791000 1575930 547963 1086670 468887 1708700 1420710 1242180 982290 1385530 613951 TRUE FALSE 1638148.933 642071.3827 1114989.513 561631.4491 1418255.784 1090771.634 1144814.686 969124.0093 1335665.046 734242.9436 2.231072082 0.874467216 1.518556661 0.764912287 1.93158926 1.485573192 1.559176967 1.319895571 1.819105049 1 19.48589797 -1.056545461 5.260888111 0.999994948 1.464629107 0.106077 0.424531321 2.28E-05 4.09E-06 0.372510334 0.087800573 0.087791918 1.056545461 0.464634159 KREPEDEGEDDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KREPEDEGEDDD 12 2 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;;;;;;; 224.24 8.16E-11 21876295000 10596646 6960467 8957035 6923746 11862842 11193831 10887166 9115423 9813379 6158816 FALSE TRUE 11015009.77 8155873.062 9190462.69 8293242.293 9846400.354 8594233.394 10033801.48 8993245.665 9460197.407 7365518.078 1.495483366 1.107304738 1.247768669 1.125955052 1.336823866 1.166819944 1.3622669 1.220992953 1.284389952 1 22.81235557 -0.915575455 4.233698382 0.999993836 1.253443648 0.327876218 0.111595028 5436733.599 2568314.098 302.7333461 0.023356399 0.121457558 0.915575455 0.253449812 KREQSNDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KREQSNDIAR 10 2 P45973 P45973 CBX5 Chromobox protein homolog 5 0 104.43 0.0015086 51477000 51491 38246 52958 28035 88250 63142 49145 49350 58765 74099 FALSE TRUE 53523.90444 44814.45299 54338.12899 33580.23932 73249.29652 48478.22743 45292.88648 48688.54397 56650.05913 88617.28034 0.603989473 0.505707835 0.613177574 0.378935566 0.826580281 0.547051627 0.511106709 0.54942494 0.639266505 1 16.43530043 0.794135762 3.276008238 0.999957668 0.565236754 0.594490708 0.10675085 0.832725745 12.35196856 0.09610074 0.024935449 6.224948485 -0.794135762 -0.434720914 KRES(ph)ES(ph)ESDETPPAAPQLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.753)ES(0.655)ES(0.561)DET(0.031)PPAAPQLIK 113.65 0.00066758 360330000 587580 203220 296590 220540 443200 435840 400730 321650 318740 162160 TRUE FALSE 610778.1121 238121.4542 304319.3791 264162.1538 367865.0223 334622.7652 369319.7355 317338.8079 307268.6097 193932.1473 3.149442322 1.227859628 1.569205433 1.362137002 1.896874899 1.725463106 1.904376044 1.636339371 1.584412971 1 17.56519245 8 0.046881421 5.75E-10 4.735850898 0.255745652 0.475921696 982.2076338 3.484270776 86.82347683 344.8942156 99999999.96 -8 4.735850898 KRESES(ph)ES(ph)DETPPAAPQLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 KRES(0.129)ES(0.929)ES(0.816)DET(0.125)PPAAPQLIK 204.61 4.65E-21 515630000 854980 310940 493270 286870 648280 640880 657630 523140 532770 250860 TRUE FALSE 888735.2706 364341.5262 506125.0214 343612.0298 538085.5972 492045.3326 606083.2422 516128.164 513595.7118 300011.214 2.96234017 1.214426359 1.687020344 1.14533062 1.793551614 1.640089802 2.020201959 1.720362906 1.711921714 1 18.1946569 4.748676315 24.97341538 1.599879958 2.962340926 0.6478112 0.310725729 881.9564486 2177310.913 0.071590384 0.988370471 56062.99761 -4.748676315 1.362460968 KRET(ph)DDEGEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 236.05 2.47E-15 26567120000 11087670 6149450 8790410 6331490 11115770 11662250 11123050 8991380 9701830 6354150 TRUE FALSE 11525419.77 7205570.201 9019495.306 7583839.824 9226315.386 8953869.181 10251196.28 8870865.258 9352663.033 7599124.035 1.516677412 0.948210632 1.1869125 0.997988688 1.214128805 1.178276488 1.348997099 1.16735366 1.230755412 1 22.8574017 KRFDTEEEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRFDTEEEFK 10 2 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;; 179.57 1.18E-06 622612000 959230 444870 636540 440479 949570 826950 859600 670800 738470 422167 FALSE TRUE 997101.1411 521272.9619 653128.7553 527604.4315 788162.4306 634903.395 792222.3059 661809.0232 711892.609 504882.5408 1.974917056 1.03246383 1.293625156 1.045004311 1.56108078 1.257526937 1.569122007 1.310817804 1.410016294 1 18.94558826 -1.428286022 2.937338191 0.99237351 1.366226419 0.159058745 0.261972219 24191082.55 29010046.95 1546061.413 0.057661102 0.037300442 1.428286022 0.37385291 KRGDYDANIVAVVNDTVGTMMTCGYDDQHCEVGLIIGTGTNACYMEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRGDYDANIVAVVNDTVGTMMTCGYDDQHCEVGLIIGTGTNACYMEELR 49 2 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 40.845 0.038655 22070000 4504.7 5210.5 5897.2 3882.3 6800.6 7729.9 5117.3 5706.8 5768.5 3563.4 FALSE TRUE 4682.549034 6105.362843 6050.885877 4650.207352 5644.636441 5934.747873 4716.192654 5630.30968 5560.892812 4261.580005 1.098782383 1.432652405 1.419869126 1.091193254 1.324540765 1.392616792 1.106677019 1.321178923 1.304889925 1 12.0571727 -1.938830869 2.49299483 0.802506711 1.280584361 0.303116924 0.125861734 16457742.12 7801423.371 18874149.82 0.029042693 0.011512486 1.938830869 0.478077651 KRGHTAS(ph)ESDEQQWPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRGHTASESDEQQWPEEK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 KRGHT(0.313)AS(0.66)ES(0.027)DEQQWPEEK 149.84 3.09E-08 222320000 208490 47805 109210 63412 408660 187370 288070 191410 170050 126100 TRUE FALSE 216721.3462 56015.13688 112056.1023 75954.70433 339196.1192 143856.1571 265490.3207 188844.462 163929.9337 150806.8807 1.437078635 0.371436215 0.743043698 0.50365543 2.249208509 0.953909772 1.760465567 1.252227095 1.087018928 1 17.20234273 3.302216179 25 1.392473955 0.734293261 0.313925019 0.448064061 68.5249238 26911.48326 0.115152717 0.155917486 2005.470043 -3.302216179 -0.658180694 KRKPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRKPSPEPEGEVGPPK 16 3 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 KRKPS(1)PEPEGEVGPPK;KRKPS(1)PEPEGEVGPPK 170.91 2.82E-08 2483200000 3465700 1248380 2113150 954460 4214600 2726600 2501400 2198900 2768400 1474360 TRUE FALSE 3602528.512 1462779.554 2168220.425 1143249.339 3498203.797 2093388.472 2305333.732 2169427.342 2668765.825 1763232.614 2.043138542 0.829601008 1.229684846 0.648382596 1.983971809 1.187244641 1.307447307 1.230369337 1.513564237 1 20.74979138 -1.41629008 2.936861486 0.994214813 1.301005338 0.049598261 0.41636327 65150519.64 77953402.09 3168772.282 0.094034296 0.038345104 1.41629008 0.306790525 KRKS(ph)ELEFETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRKSELEFETLK 12 3 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 KRKS(1)ELEFETLK 101.39 0.014921 1214900000 523260 229690 317470 220040 515280 468180 538890 365130 419990 206960 TRUE FALSE 543918.7088 269137.4708 325743.529 263563.2552 427692.8897 359452.2903 496650.3937 360236.0296 404874.6419 247509.8495 2.197563895 1.087380851 1.316083096 1.064859664 1.727983313 1.452274691 2.006588403 1.455441189 1.635792041 1 17.91712641 3.188431343 24.99941134 1.58795435 1.385787739 0.01801993 0.378773273 319.1763527 159171.5835 0.103759646 0.124016694 1543.232436 -3.188431343 -0.202166611 KRLS(ph)QSDEDVIR ddPTM_MDA-MB-175_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(0.898)QS(0.102)DEDVIR;KRLS(0.654)QS(0.346)DEDVIR;KRLS(1)QSDEDVIR 198.89 9.29E-08 1927690000 1409310 1199910 1490940 1219390 1907630 1749230 1586390 1496240 1727480 1356800 TRUE FALSE 1464950.647 1405985.208 1529795.121 1460581.702 1583371.734 1342997.842 1462044.607 1476185.35 1665308.332 1622638.982 0.902819828 0.866480606 0.942782182 0.900127335 0.975800379 0.82766275 0.901028893 0.909743551 1.026296268 1 20.62991062 1.24731401 17.82162009 1.013148605 0.903385218 0.574554762 0.037808175 3.392902842 6914.865823 0.025636373 0.008846378 17.67315187 -1.24731401 -0.109763387 KRLSQS(ph)DEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRLSQSDEDVIR 12 2 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 KRLS(0.126)QS(0.874)DEDVIR 179.55 1.62E-05 1083600000 1031700 931640 951220 706940 1404400 1252900 1049500 889550 1001100 935650 TRUE FALSE 1072432.313 1091641.923 976009.5746 846770.622 1165680.59 961932.9629 967237.4476 877627.0373 965070.6066 1118972.703 0.95840793 0.975575114 0.872237162 0.756739302 1.041741757 0.859657219 0.864397715 0.784314965 0.862461259 1 20.09374341 2.514651301 24.99490039 0.853160088 0.916002714 0.040743897 0.086574849 1304.88716 869049.3102 0.027929467 0.026326485 327.0779757 -2.514651301 0.062842626 KRNDS(ph)EEEERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;KRNDS(1)EEEERER 178.14 0.00012368 937131000 670524 480022 620281 524232 733932 791961 892816 633299 723485 369599 TRUE FALSE 696996.8053 562462.0444 636446.0324 627923.5249 609178.5008 608040.06 822834.749 624810.6628 697446.9162 442014.8476 1.576862879 1.272495816 1.439874782 1.420593739 1.378185606 1.375610035 1.861554546 1.413551301 1.577881195 1 18.75373531 KRNEDEDSPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KRNEDEDSPNK 11 2 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 ;;;;; 199.7 2.78E-08 5630312000 8207364 3837771 5739616 4057827 7955810 6826504 8418019 6067844 6814616 3095879 FALSE TRUE 8531397.068 4496878.316 5889195.108 4860453.069 6603484.258 5241151.903 7758192.674 5986514.476 6569359.301 3702457.216 2.304252709 1.214565909 1.590618004 1.312764142 1.783541003 1.415587432 2.095417238 1.61690308 1.774324163 1 21.82005163 KRNEDEDSPNKLYTLVTYVPVTTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 0 153.83 4.11E-08 517870000 732380 426500 607240 310320 931430 722110 579520 559900 726080 451730 FALSE TRUE 761294.9279 499748.0573 623065.1733 371700.3698 773105.8613 554410.8962 534095.7081 552395.4563 699948.5226 540237.8446 1.409184742 0.925051923 1.153316413 0.688030973 1.431047212 1.026234837 0.988630681 1.022504184 1.295630304 1 19.04323518 2.543300906 0.00865291 1.85E-05 2.159798332 0.011738552 0.21782479 23029.55794 90.51143431 11069.44035 11513.23426 349.3823053 -2.543300906 2.159779816 KRPAS(ph)PSHNGSSGGGYGASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRPASPSHNGSSGGGYGASK 20 2 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 KRPAS(0.948)PS(0.04)HNGS(0.01)S(0.002)GGGYGASK;KRPAS(0.9)PS(0.071)HNGS(0.014)S(0.014)GGGYGASK;KRPAS(0.829)PS(0.057)HNGS(0.057)S(0.057)GGGYGASK 113.6 7.12E-05 314211000 260665 347305 420164 336563.8 528480 547959 491493 479115 487789 346056 TRUE FALSE 270956.2555 406951.9321 431113.819 403135.1151 438649.1584 420703.8266 452968.4944 472693.2471 470233.5692 413859.0476 0.654706613 0.983310464 1.041692387 0.974087959 1.059899889 1.016538914 1.094499437 1.142159994 1.136216719 1 18.65877997 5.165819866 1.252131058 1.071690811 2.71E-20 0.839651944 0.052578888 1.467950502 0.960679286 0.016090279 2.624800579 146494.0096 -5.165819866 -1.071690811 KRPQS(ph)PS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 KRPQS(1)PS(1)PR 84.718 0.075271 249220000 590000 461070 506140 405540 641520 618570 625630 548360 549880 408520 TRUE FALSE 613293.6556 540255.1859 519330.4242 485754.6016 532474.6595 474916.492 576591.4858 541010.1311 530089.9262 488561.6724 1.255304479 1.10580755 1.062978235 0.994254419 1.089882178 0.97207071 1.180181579 1.10735279 1.085001047 1 18.89818116 4.728331197 2.823693684 1.06929454 1.286708156 0.492323692 0.05863282 0.363433194 4.097822941 0.014716637 0.180044226 53497.21782 -4.728331197 0.217413616 KRPQS(ph)PSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KRPQSPSPR 9 2 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 KRPQS(0.973)PS(0.027)PR;KRPQS(0.993)PS(0.007)PR;KRPQS(0.993)PS(0.007)PR;KRPQS(0.584)PS(0.416)PR;KRPQS(0.982)PS(0.018)PR;KRPQS(0.999)PS(0.001)PR;KRPQS(0.998)PS(0.002)PR 109.24 0.001295 2519477000 2047417 1858161 2215744 1798346 2571195 2558262 2401056 2060116 2147802 1790927 TRUE FALSE 2128250.604 2177285.697 2273488.109 2154053.471 2134144.192 1964144.421 2212854.957 2032503.515 2070503.026 2141824.856 0.993662296 1.016556368 1.061472465 1.005709437 0.996413963 0.9170425 1.033163356 0.948958786 0.966700437 1 21.03040908 3.188996767 3.058065676 0.972418563 1.023467627 0.298866856 0.032934674 0.28323607 5.403335909 0.009495156 0.012160024 1545.242936 -3.188996767 0.051049065 KRPYEENR ddPTM_MDA-MB-175_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 ;;;;; 196.99 8.30E-05 2023049000 784244 924783 971081 846604 1085928 1189930 929225 946927 924893 989653 FALSE TRUE 815206.5587 1083607.286 996388.1686 1014059.744 901342.3464 913586.7911 856389.9164 934234.9924 891606.2816 1183556.557 0.68877702 0.915551758 0.841859362 0.856790272 0.761554098 0.771899564 0.723573294 0.789345458 0.753327989 1 20.17469722 4.792556217 21.71943372 0.809780345 0.688773275 0.182886803 0.080874559 18645.76693 7498940.954 0.018608448 17.05425826 62023.49248 -4.792556217 -0.12100707 KRQEAVAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRQEAVAGR 9 2 Q12933-4;Q12933-3;Q12933;Q12933-2 Q12933-4 TRAF2 TNF receptor-associated factor 2 0 71.451 0.027866 25516000 35296 52017 42935 45216 48447 56527 39136 46220 41102 54417 FALSE TRUE 36689.51333 60950.51511 44053.92137 54159.58984 40211.99624 43399.46092 36068.41806 45600.4965 39622.74705 65078.96927 0.563769121 0.936562392 0.676930226 0.832213393 0.617895408 0.666873821 0.554225404 0.700694818 0.608841036 1 15.98990378 -1.203044259 4.409819156 1.000090443 0.688543535 0.411963752 0.113075259 0.000101493 1.83E-05 0.104914892 0.024721139 0.062655001 1.203044259 -0.311546909 KRQEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRQEEIER 8 2 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;H0YFJ7 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;; 183.43 0.00012561 422617000 330710 293871 338208 313022 412790 417550 368504 363880 350110 300180 FALSE TRUE 343766.6862 344341.0583 347021.9783 374936.8173 342624.1032 320580.3405 339619.6936 359002.7838 337509.6095 358994.5237 0.957581978 0.959181925 0.966649783 1.044408181 0.954399247 0.892995072 0.946030291 1.000023009 0.940152529 1 18.45360231 1.750001357 25 0.979357089 0.960821984 0.054639317 0.037794903 12.27476212 26869.99266 0.018715288 0.010378547 56.23430829 -1.750001357 -0.018535105 KRQS(ph)APSPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRQSAPSPTR 10 2 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 2 KRQS(1)APS(0.013)PT(0.987)R;KRQS(0.999)APS(0.246)PT(0.755)R 114.56 0.0014776 376560000 602560 461540 557260 449870 737340 773410 705050 581970 659480 522130 TRUE FALSE 626349.5341 540805.9047 571782.6534 538852.9433 612007.2102 593797.2486 649786.3387 574169.6441 635745.4436 624431.3767 1.003071847 0.866077402 0.915685333 0.862949819 0.980103232 0.950940761 1.040604881 0.919507996 1.018118992 1 19.25218351 3.212173358 24.99720696 0.979020288 0.908936857 0.353032179 0.047907771 239.4387897 226824.8107 0.01309904 0.015660661 1629.94653 -3.212173358 -0.070083431 KRQS(ph)LYENQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRQSLYENQV 10 2 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 KRQS(1)LYENQV;KRQS(1)LYENQV 145.83 2.34E-05 1577630000 2367700 2270300 2104790 2052520 2678800 2830800 2070640 2165900 2092720 2199170 TRUE FALSE 2461178.624 2660206.365 2159642.557 2458502.33 2223458.533 2173389.601 1908337.826 2136869.653 2017403.416 2630055.256 0.935789702 1.011464059 0.821139614 0.934772121 0.845403734 0.826366517 0.725588492 0.812480897 0.767057426 1 21.32666168 3.661894151 0.906475375 0.807727974 0.969065179 0.245393154 0.080113189 0.788122794 1.219178404 0.030200269 0.091050671 4590.861082 -3.661894151 0.161337205 KRQS(ph)PEPSPVTLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KRQSPEPSPVTLGR 14 2 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 KRQS(0.999)PEPS(0.001)PVTLGR;KRQS(0.996)PEPS(0.002)PVT(0.001)LGR;KRQS(0.968)PEPS(0.032)PVTLGR;KRQS(0.975)PEPS(0.025)PVTLGR;KRQS(0.99)PEPS(0.006)PVT(0.005)LGR;KRQS(0.997)PEPS(0.003)PVTLGR 157.54 4.15E-06 1762396000 1300945 1134535 1362064 1038612 1594240 1495000 1392469 1321920 1386404 1135318 TRUE FALSE 1352307.313 1329382.561 1397560.507 1244046.354 1323251.654 1147808.907 1283323.641 1304201.825 1336507.591 1357761.825 0.995982718 0.979098496 1.029311976 0.91624785 0.974583045 0.845368374 0.945175816 0.960552728 0.984346125 1 20.372799 3.736496794 24.99067575 0.942996876 0.999227806 0.258313082 0.042234313 240.4580148 2911694.466 0.011032559 0.018084462 5451.258709 -3.736496794 0.05623093 KRQS(ph)VSGLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRQSVSGLHR 10 2 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KRQS(0.993)VS(0.007)GLHR;KRQS(1)VSGLHR 101.39 0.0017562 310840000 107700 122053 137822 105794 154710 159236 132186 137951 147034 147311 TRUE FALSE 111952.0792 143014.6533 141413.7545 126719.7374 128412.4495 122255.8522 121824.9159 136101.9925 141742.2751 176173.77 0.635463947 0.811781761 0.802694717 0.719288333 0.728896529 0.693950366 0.69150428 0.77254402 0.80455947 1 17.42663962 0.771058455 1.517231915 0.999470683 0.732105845 0.72768036 0.04979897 0.410157992 1.628612024 0.04749186 0.01381788 5.902805247 -0.771058455 -0.267364837 KRS(ph)EGFSMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 KRSEGFSMDR 10 2 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 1 KRS(0.991)EGFS(0.009)MDR;KRS(0.978)EGFS(0.022)MDR;KRS(0.958)EGFS(0.042)MDR;KRS(0.927)EGFS(0.073)MDR;KRS(0.997)EGFS(0.003)MDR;KRS(0.991)EGFS(0.009)MDR;KRS(0.628)EGFS(0.372)MDR;KRS(0.952)EGFS(0.048)MDR;KRS(0.933)EGFS(0.067)MDR;KRS(0.995)EGFS(0.005)MDR 125.29 0.00032518 26883870000 19522650 17434110 22536790 18804590 33915400 30228400 30347000 27150100 29610200 24504630 TRUE FALSE 20293419.3 20428282.77 23124117.26 22524081.78 28150472.42 23208312.22 27968322.84 26786197.32 28544534.69 29305843.08 0.692470073 0.697072004 0.789061663 0.768586719 0.960575417 0.791934638 0.954359947 0.91402241 0.974021959 1 24.80468501 4.715663286 0.271931811 1.008114165 0.395707618 0.786844673 0.051996094 3.543412367 0.221222487 0.062107632 0.73268156 51959.29935 -4.715663286 -0.612406547 KRS(ph)FVPEEEKHEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRSFVPEEEKHEER 14 3 A0A0U1RRH6;O94880;O94880-2;B4DG57 A0A0U1RRH6 PHF14 PHD finger protein 14 1 KRS(1)FVPEEEKHEER;KRS(1)FVPEEEKHEER;KRS(1)FVPEEEKHEER 161.22 3.30E-06 425293000 254559 219056 270807 248786 368317 396000 325594 276739 311214 357539 TRUE FALSE 264609.1859 256677.164 277864.4529 297995.1282 305710.6079 304035.0014 300073.0915 273029.7664 300013.4689 427591.9216 0.618835793 0.600285345 0.6498356 0.696914776 0.714958802 0.711040097 0.701774464 0.638528823 0.701635026 1 18.70587507 -5 0.278617005 3.390695937 0.647740475 0.885471607 0.035986125 78.88325646 0.757044351 108.9941394 0.047694853 1.00E-05 5 -2.742955462 KRS(ph)GNSDSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.704)GNS(0.279)DS(0.016)IER;KRS(0.975)GNS(0.024)DS(0.001)IER;KRS(0.701)GNS(0.285)DS(0.013)IER;KRS(0.887)GNS(0.11)DS(0.003)IER 138.01 5.23E-05 2595400000 1373010 1103610 1329830 923550 1657630 1645100 1332350 1314550 1441380 1256380 TRUE FALSE 1427217.495 1293146.433 1364486.462 1106225.433 1375866.645 1263050.457 1227916.926 1296930.607 1389505.015 1502543.606 0.949867604 0.860638205 0.908117712 0.736235161 0.915691657 0.840608187 0.817225484 0.863156718 0.924768512 1 20.51897543 1.001545001 2.737248768 0.999303159 0.857729772 0.379141636 0.055795712 0.248337823 4.301597526 0.050422969 0.013463292 10.03563831 -1.001545001 -0.141573387 KRS(ph)PGGSGGASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRSPGGSGGASR 12 2 E7ER77;Q7Z2K6 E7ER77 ERMP1 Endoplasmic reticulum metallopeptidase 1 1 KRS(1)PGGSGGASR;KRS(1)PGGSGGASR 144.97 3.31E-05 69472000 17466.7 20031.4 17351.7 16042.2 27499 28695 24027 17384.8 25637 27375 TRUE FALSE 18156.2988 23471.63713 17803.89956 19215.29928 22824.7298 22031.02113 22143.70096 17151.78519 24714.32938 32738.60712 0.554583728 0.716940615 0.543819702 0.586930874 0.697180846 0.672937033 0.676378835 0.523900883 0.754898621 1 14.99870532 0.955378116 6.024596503 0.999957938 0.62350645 0.763130137 0.064660778 0.134181864 16.20037287 0.061396452 0.015438539 9.023564269 -0.955378116 -0.376451487 KRS(ph)PPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRSPPLGGAPSPSSLSLPPSTGFPLQASGVPSPYLSSLASSR 42 2 I3NI13;I3L270;Q8NBZ0 I3NI13 INO80E INO80 complex subunit E 1 KRS(0.273)PPLGGAPS(0.181)PS(0.181)S(0.181)LS(0.181)LPPS(0.002)T(0.002)GFPLQASGVPSPYLSSLASSR 91.295 9.12E-05 67632000 30044 27543 36243 35076 36122 48601 39531 37338 34537 33750 TRUE FALSE 31230.16032 32273.296 37187.52235 42013.92811 29981.99534 37314.15431 36432.45692 36837.54518 33294.02012 40362.66632 0.773738783 0.799582856 0.921334633 1.040910622 0.742815034 0.924471986 0.902627607 0.912663819 0.824871674 1 15.30073386 7.999992265 0.021588188 1.562103662 2.97E-06 0.187019541 0.08312335 5007.603426 8.324031896 217.9371878 413.101105 99998218.98 -7.999992265 -1.562100695 KRS(ph)PS(ph)PSPTPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.925)PS(0.672)PS(0.403)PTPEAK;KRS(0.954)PS(0.908)PS(0.138)PTPEAK;KRS(0.998)PS(0.951)PS(0.052)PTPEAK;KRS(0.832)PS(0.957)PS(0.211)PTPEAK;KRS(0.967)PS(0.9)PS(0.132)PTPEAK;KRS(0.666)PS(0.666)PS(0.666)PT(0.001)PEAK 168.05 1.66E-05 3074060000 3375260 1581771 2414200 1546190 3377430 3198540 3159750 2398110 2829590 1577189 TRUE FALSE 3508517.871 1853427.865 2477116.035 1852021.767 2803335.655 2455727.559 2912080.539 2365967.258 2727753.609 1886208.987 1.86008968 0.982620631 1.313277612 0.981875168 1.486227493 1.301938213 1.54388011 1.254350538 1.446156617 1 20.8470581 -0.965883709 5.124519866 0.999998323 1.334135662 0.150898788 0.247343618 4.32E-06 8.72E-07 0.218311869 0.051456343 0.108172357 0.965883709 0.334137339 KRS(ph)PSPS(ph)PTPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRSPSPSPTPEAK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 KRS(0.651)PS(0.39)PS(0.921)PT(0.039)PEAK 163.11 0.00019328 1237600000 4725600 2021400 3097900 1991900 4295200 4021100 4065700 2970800 3617900 1753000 TRUE FALSE 4912170.337 2368559.726 3178633.819 2385891.875 3565103.438 3087260.465 3747019.81 2930981.285 3487692.486 2096466.787 2.343070908 1.12978643 1.516186108 1.138053743 1.700529415 1.472601658 1.787302252 1.398057581 1.663604932 1 20.99952854 -1.093688268 4.456386931 0.999950266 1.543912049 0.207155239 0.331677174 0.000148072 3.01E-05 0.290155786 0.06838414 0.080595674 1.093688268 0.543961783 KRS(ph)PTESVNTPVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.968)PT(0.031)ESVNTPVGK 123.63 8.01E-05 175230000 110190 66603 95295 73248 115970 119240 111580 89604 104420 63570 TRUE FALSE 114540.3863 78041.54715 97778.46599 87736.23578 96257.46082 91548.3171 102834.068 88403.00494 100661.9446 76025.32438 1.506608321 1.02652041 1.286130204 1.154039611 1.266123645 1.204181868 1.352629126 1.162809967 1.324058074 1 16.21419245 -1.163735264 4.327439919 0.999941731 1.242285223 0.270132231 0.123826432 2.044595891 31384988.52 3521.381528 0.025472685 0.068590621 1.163735264 0.242343492 KRS(ph)SITEPEGPGGPNIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRSSITEPEGPGGPNIQK 18 2 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 KRS(0.333)S(0.333)IT(0.333)EPEGPGGPNIQK 74.786 0.0093776 67661000 62557 80133 85748 46474 130470 113810 65773 82523 93684 87419 TRUE FALSE 65026.79866 93895.2194 87982.66332 55666.41849 108292.756 87379.35231 60617.54039 81416.91417 90312.33114 104547.0793 0.621985799 0.898114228 0.841560222 0.532453119 1.035827655 0.835789511 0.579810941 0.77875838 0.863843655 1 16.67379323 0.970022048 3.069524473 0.998932426 0.76777716 0.202284944 0.14526128 0.40591391 9.485727904 0.134241527 0.035229959 9.333016818 -0.970022048 -0.231155266 KRS(ph)SSEDAESLAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRSSSEDAESLAPR 14 2 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 KRS(0.976)S(0.023)S(0.001)EDAESLAPR;KRS(0.8)S(0.178)S(0.022)EDAESLAPR 167.14 2.91E-06 1047270000 485300 416710 498700 387260 707020 649720 488710 514800 536360 531130 TRUE FALSE 504460.0187 488276.7009 511696.5317 463858.8721 586840.9929 498832.3766 450403.6332 507899.948 517056.5084 635194.7544 0.794181651 0.768703925 0.80557424 0.730262441 0.923875691 0.78532194 0.709079586 0.799597202 0.81401256 1 19.27683947 0.675719906 2.522941563 0.99997111 0.788610769 0.577069628 0.053716507 1.605518 11.60939526 0.050569313 0.01349016 4.739362266 -0.675719906 -0.211360341 KRS(ph)VSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KRSVSHGSNHTQKPDEQR 18 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 KRS(0.891)VS(0.109)HGSNHTQKPDEQR;KRS(0.924)VS(0.074)HGS(0.002)NHTQKPDEQR;KRS(0.749)VS(0.251)HGSNHTQKPDEQR 167.59 9.29E-12 429939000 26538.5 122481 144936 101496 194952 204934 113859 178932 161157 167878 TRUE FALSE 27586.26047 143516.159 148713.1512 121571.6059 161814.1287 157341.1843 104934.4341 176533.7092 155356.9911 200770.4799 0.137401975 0.714826996 0.740712237 0.605525304 0.805965741 0.783686847 0.52265868 0.879281204 0.773803953 1 17.61518763 4.740284244 4.581102664 0.749421251 0.097752854 0.689111615 0.125232048 0.103731398 5.734570253 0.028178485 0.218220143 54990.06637 -4.740284244 -0.651668397 KRS(ph)WGHES(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRSWGHESPEER 12 2 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 2 KRS(1)WGHES(1)PEER;KRS(1)WGHES(1)PEER 118.23 0.00034737 428510000 316560 254935 291260 229389 391500 341490 334540 306072 309550 242677 TRUE FALSE 329058.0332 298718.1031 298850.4749 274761.4595 324952.9698 262184.1228 308317.8806 301969.6055 298409.356 290224.9118 1.133803543 1.029264171 1.029720271 0.946719073 1.119659122 0.903382557 1.062341198 1.040467559 1.02820035 1 18.14681183 4.755602175 3.348233405 1.018854965 1.151458535 0.278628475 0.056234028 0.44211163 7.947861597 0.012623504 0.153806008 56964.22266 -4.755602175 0.13260357 KRSS(ph)ISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.075)S(0.924)IS(0.001)K;KRS(0.011)S(0.989)ISK 88.392 0.0097267 1255760000 1031490 616230 840380 547040 1391570 1014000 1063130 840460 1066560 815210 TRUE FALSE 1072214.022 722062.7089 862280.9932 655242.8792 1155031.428 778513.8673 979799.0926 829195.0084 1028174.714 974934.7914 1.099780243 0.740626671 0.884449915 0.672088928 1.184726854 0.798529168 1.004989361 0.850513302 1.054608701 1 19.8949462 3.255823438 24.99999777 0.959654572 0.843993965 0.158511315 0.144405543 490.8103899 710786.487 0.037377104 0.050488603 1802.284874 -3.255823438 -0.115660608 KRT(ph)EEPDRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 1 KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER;KRT(1)EEPDRDER 157.23 3.16E-05 22611523000 22438067.6 14583726 17033757 13122818 23568365.1 23597239 20901457 18665066 20720978 14444403 TRUE FALSE 23323939.83 17088367.49 17477670.7 15718472.23 19562222.82 18117137.86 19263146.18 18414891.32 19975234.05 17274507.21 1.350194222 0.9892246 1.011760885 0.909923047 1.132433046 1.048778853 1.115119867 1.066015435 1.156341759 1 24.04214122 2.25899363 24.29930448 1.088216433 1.062285711 0 0.115212561 1269.677634 1509917.441 0.039252023 0.032799144 181.5489035 -2.25899363 -0.025930722 KRTEEPDRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KRTEEPDRDER 11 3 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;;;;;; 174.9 4.58E-06 787175000 517742 456709 554025 360437 709119 687247 525877 516543 582371 616963 FALSE TRUE 538182.8539 535145.218 568463.3466 431730.3628 588583.2057 527644.2996 484657.3866 509619.586 561411.5815 737845.0874 0.729398167 0.725281265 0.770437259 0.585123314 0.797705664 0.715115285 0.656855206 0.690686426 0.760880015 1 19.49295842 0.827184403 3.710427413 0.999972014 0.707534048 0.710570283 0.055512616 0.567396719 11.47815368 0.050817816 0.01305326 6.717140049 -0.827184403 -0.292437966 KRTS(ph)ESR ddPTM_MDA-MB-175_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(0.17)S(0.822)ES(0.008)R 70.056 0.045727 170500000 346350 281970 328900 229670 404310 406590 402410 337740 382340 308780 TRUE FALSE 360024.1654 330396.1541 337471.4042 275098.0405 335585.5306 312165.6344 370868.0527 333213.1477 368579.6581 369279.529 0.9749367 0.894704765 0.91386437 0.744958815 0.90875747 0.84533696 1.004301683 0.902333115 0.998104766 1 18.49435376 2.242526892 24.9990833 0.962300167 0.877725574 0.353563845 0.062246893 128.1783867 807901.4203 0.022097649 0.017858138 174.7941495 -2.242526892 -0.084574594 KRVPDHHPC ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRVPDHHPC 9 2 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 92.439 0.0056666 243450000 622790 535710 510960 500470 1112410 894260 718330 682550 589300 953740 FALSE TRUE 647378.2301 627714.0253 524276.0374 599461.4722 923322.9455 686581.6676 662025.4176 673401.5337 568091.2081 1140607.093 0.567573386 0.550333265 0.459646482 0.525563515 0.809501319 0.601944063 0.580414958 0.590388696 0.498060385 1 20.12137048 -1.996934439 3.244144071 1.411460741 0.57899614 0.673574214 0.088539861 0.051751024 4.89E-05 0.016837142 0.020826546 0.010070837 1.996934439 -0.832464601 KRVS(ph)LEPHQGPGT(ph)PESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRVSLEPHQGPGTPESK 17 2 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 2 KRVS(1)LEPHQGPGT(0.709)PES(0.291)K 130.15 5.91E-05 199830000 156120 95837 131520 81239 163310 181040 141670 123050 143280 100240 TRUE FALSE 162283.7382 112296.2592 134947.5192 97307.83173 135550.6245 138996.2037 130565.5352 121400.716 138123.3808 119880.1088 1.353716974 0.936738049 1.125687327 0.811709571 1.130718231 1.159460106 1.089134274 1.0126844 1.152179308 1 16.87123277 3.081241268 0.007838948 3.07E-07 2.147530598 0.032087011 0.137223314 28993.34886 71.02177478 9459.911248 9994.785364 1205.705572 -3.081241268 2.147530291 KRVS(ph)VELTNSLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRVSVELTNSLFK 13 2 P14923 P14923 JUP Junction plakoglobin 1 KRVS(1)VELTNSLFK;KRVS(1)VELTNSLFK 223.93 1.18E-11 6175800000 3233250 2541800 2746370 2405980 3791900 4097200 3378800 3025730 2981900 3087090 TRUE FALSE 3360901.207 2978334.378 2817942.658 2881875.663 3147354.192 3145687.394 3113960.827 2985175.038 2874582.001 3691946.18 0.910333207 0.806711212 0.763267535 0.780584419 0.852491894 0.852040425 0.843446972 0.808564073 0.778608859 1 21.81595009 3.211731697 24.98760517 0.842912629 0.81090482 0.062472697 0.06577145 729.9655443 679864.7561 0.018474074 0.022086882 1628.289782 -3.211731697 -0.032007809 KRYDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KRYDGLK 7 2 E9PGT1;Q15631 E9PGT1 TSN Translin 0 77.282 0.021636 196370000 307880 233350 274480 215280 424620 353770 331080 288990 306710 236510 FALSE TRUE 320035.3401 273426.0473 281633.1743 257861.7415 352443.2441 271612.2789 305129.0845 285116.5617 295671.567 282849.6062 1.131468219 0.9666835 0.995699368 0.91165671 1.246044669 0.960271017 1.078767931 1.008014703 1.045331372 1 18.10967564 4.763103428 22.63976779 1.026154953 1.131468679 0.122744358 0.086264384 4130.453755 3809956.688 0.019444144 1.049018926 57956.67046 -4.763103428 0.105313726 KRYEDLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KRYEDLLTR 9 2 Q99988;A0A0A0MTT8 Q99988 GDF15 Growth/differentiation factor 15 0 ; 139.43 6.27E-05 792410000 359553 300741 360470 297878 564690 538910 491530 452970 494070 533640 FALSE TRUE 373748.4301 352390.9273 369864.1443 356797.3793 468704.1955 413756.3198 453002.5942 446898.6781 476288.5172 638196.5408 0.585632178 0.552166777 0.579545831 0.559071315 0.734419831 0.648321157 0.70981675 0.700252429 0.746303821 1 19.28364126 -5 0.10171764 2.204553643 0.397185166 0.905852134 0.039053479 48.05912958 0.331549931 12.07419428 0.60901513 1.00E-05 5 -1.807368476 KS(ph)HSSPSLHQDEAPTTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSHSSPSLHQDEAPTTAK 18 1 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 KS(0.378)HS(0.378)S(0.122)PS(0.122)LHQDEAPTTAK;KS(0.416)HS(0.416)S(0.084)PS(0.084)LHQDEAPTTAK 91.729 0.0011597 115013000 24830 111447 117554 100897 155530 163795 107891 149120 136410 112378 TRUE FALSE 25810.30757 130587.1553 120617.5538 120854.1255 129093.0662 125756.0936 99434.2215 147121.2903 131500.6307 134396.3175 0.192046241 0.971657243 0.897476628 0.899236882 0.960540203 0.935710858 0.739858229 1.094682452 0.978454121 1 17.03613408 4.740016241 24.97004412 0.940362007 0.192045992 0.87249317 0.086001682 40.05115585 686977.5293 0.020468181 0.129059793 54956.14246 -4.740016241 -0.748316015 KS(ph)KS(ph)PTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSKSPTLR 8 2 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 KS(0.989)KS(0.995)PT(0.016)LR 94.191 0.051816 859170000 5893400 1670600 2613300 1511900 4153400 4660800 4320100 2538700 2923500 1166600 TRUE FALSE 6126075.983 1957512.555 2681404.745 1810949.307 3447406.552 3578399.835 3981479.274 2504672.879 2818283.806 1395172.934 4.390907989 1.403060873 1.921915685 1.298010636 2.47095286 2.564843216 2.853753235 1.795241878 2.020024713 1 20.41201253 4.74746615 24.88974376 2.000231358 4.390909295 0.631173986 0.562814403 738.1019183 2062846.694 0.134403194 1.625861075 55906.99509 -4.74746615 2.390677937 KS(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSKSPPKVPIVIQDDSLPAGPPPQIR 26 3 Q7Z422-5;Q7Z422;Q7Z422-4 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 KS(0.709)KS(0.291)PPKVPIVIQDDSLPAGPPPQIR;KS(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR 249.04 5.68E-45 2302200000 2458390 803640 1400230 728820 2036150 1797030 1625600 1315670 1691570 727760 TRUE FALSE 2555449.135 941658.9185 1436721.144 872978.4207 1690045.95 1379697.017 1498181.224 1298035.596 1630690.726 870350.6382 2.936114508 1.08193052 1.650738313 1.003019223 1.941798944 1.585219745 1.721353623 1.491393857 1.873602034 1 19.73123721 8 0.037906016 2.54E-09 4.188176244 0.153099847 0.502610896 2074.778737 5.996004558 187.2291188 573.0758795 99999999.94 -8 4.188176242 KS(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_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(1)LVGTPYWMAPELISR;KS(1)LVGTPYWMAPELISR 194.97 2.73E-11 605930000 419360 344120 390440 385620 464610 488740 519850 467070 491120 306240 TRUE FALSE 435916.6566 403219.9331 400615.1872 461894.485 385635.7582 375237.5419 479102.7986 460809.6906 473444.6871 366241.8647 1.190242566 1.100966252 1.09385416 1.261173365 1.052953786 1.024562122 1.308159566 1.258211404 1.292710454 1 18.48243719 2.229541592 24.99828601 1.241203745 1.121827464 0.149428532 0.102530145 274.0394963 759557.2715 0.036408827 0.027275968 169.6452063 -2.229541592 -0.11937628 KS(ph)MSEDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.744)MS(0.256)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 207.73 8.31E-31 137540000 25164 19040 23518 22236 28978 34490 26604 22889 27987 21840 TRUE FALSE 26157.49415 22309.97189 24130.8984 26634.21443 24052.32991 26480.2202 24518.70896 22582.21039 26979.75334 26119.12985 1.00146882 0.854162142 0.923878343 1.019720587 0.920870261 1.013824747 0.938726103 0.864585096 1.03294993 1 14.67281921 KS(ph)PEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSPEIHR 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHR;KS(1)PEIHR;KS(1)PEIHR 98.943 0.010118 275770000 653310 847330 789130 817250 832870 1064960 931580 789960 849920 1054890 TRUE FALSE 679103.1833 992852.3362 809695.3761 978899.6108 691299.0549 817639.1796 858560.3254 779371.8783 819331.5452 1261575.498 0.538297695 0.786993991 0.641812858 0.775934228 0.547964871 0.64810959 0.680546132 0.617776645 0.64945106 1 20.26679512 -1.943284262 2.552953361 1.246252784 0.656298264 0.644202468 0.077103849 18383153.26 9598314.066 26919341.81 0.017367634 0.011395037 1.943284262 -0.58995452 KS(ph)PEIHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPEIHRR 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(1)PEIHRR 70.977 0.026055 17864000 88371 24537 37787 25525 54979 68063 43221 34098 43629 24405 TRUE FALSE 91859.95532 28751.03888 38771.76026 30573.76882 45633.68922 52256.39975 39833.22508 33640.97208 42058.80081 29186.69249 3.147323231 0.985073553 1.328405412 1.047524273 1.563510125 1.790418691 1.364773521 1.152613373 1.44102662 1 14.83302311 4.744864648 24.99800483 1.314076136 3.147324045 0.834168505 0.247390058 280.6894496 1113016.103 0.06017342 0.56755166 55573.10311 -4.744864648 1.833247909 KS(ph)PESEILSLHLLVEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPESEILSLHLLVEELR 18 1 A0A0A6YYJ5;O94854-2;O94854 A0A0A6YYJ5 MACF1;KIAA0754 Uncharacterized protein KIAA0754 1 KS(0.972)PES(0.024)EILS(0.004)LHLLVEELR 92.336 0.0011068 9689000 6614.9 6434.5 7932.2 7084.3 13058 9651.2 9433.3 8463.9 6612.9 5570.1 TRUE FALSE 6876.06136 7539.575322 8138.919648 8485.553395 10838.40582 7409.855065 8693.893297 8350.455265 6374.903021 6661.454449 1.032216224 1.131821193 1.221793185 1.27382893 1.627032941 1.11234793 1.305104368 1.253548355 0.956983654 1 12.70162149 1.241155472 24.96562342 0.978491729 1.252433855 0.331134385 0.151026157 71.20906759 685174.7428 0.114183525 0.037364439 17.42430529 -1.241155472 0.273942126 KS(ph)PGADVTCSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSPGADVTCSLPR 13 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 KS(0.999)PGADVT(0.001)CSLPR;KS(1)PGADVTCSLPR;KS(1)PGADVTCSLPR 112.91 0.00052907 914240000 369974 192965 252237 209970 350436 332049 312073 255738 255416 212748 TRUE FALSE 384580.8592 226105.2377 258810.5034 251501.4393 290869.0139 254935.652 287611.9028 252310.2504 246223.6281 254431.8973 1.511527695 0.888667027 1.017209344 0.988482348 1.143209704 1.00197992 1.130408199 0.991661239 0.967738836 1 17.95692002 4.748174233 24.99085308 1.020991664 1.511527958 0.816246425 0.070702514 527.8729096 1372191.714 0.016457545 0.216646267 55998.22135 -4.748174233 0.490536294 KS(ph)PGVEIK ddPTM_MDA-MB-175_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 84.605 0.010617 360930000 1232710 573700 917360 667420 1304160 1389080 1287810 928820 1039390 581330 TRUE FALSE 1281378.343 672228.5122 941267.1552 799433.684 1082479.349 1066487.222 1186868.087 916370.6871 1001982.557 695230.4833 1.843098618 0.966914611 1.353892238 1.149882957 1.557007892 1.534005265 1.707157721 1.318081858 1.441223567 1 19.40713181 3.225494493 24.98923496 1.457380681 1.30444083 0.019717934 0.271561708 641.8012519 1227456.515 0.073624807 0.088495114 1680.716613 -3.225494493 -0.152939851 KS(ph)PHS(ph)KSPAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPHSKSPAEQR 12 2 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 KS(0.997)PHS(0.581)KS(0.422)PAEQR 65.225 0.032889 25112000 49101 26652 36203 25135 54199 53599 36857 34499 33480 20592 TRUE FALSE 51039.54539 31229.27368 37146.47992 30106.62798 44986.27334 41151.44455 33968.05203 34036.59733 32275.06134 24626.60814 2.072536547 1.268111041 1.508387989 1.222524345 1.826734444 1.671015526 1.379323203 1.382106587 1.310576802 1 14.58793032 1.073858586 0.849537809 1.007155756 1.563981014 0.362599893 0.238994238 0.67711556 1.091460707 0.219176681 0.07920156 11.85382703 -1.073858586 0.556825258 KS(ph)PPKADEK ddPTM_MDA-MB-175_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 72.705 0.023999 1519280000 3830500 741270 1280590 749040 2296880 2987900 2536100 1380260 1697780 409830 TRUE FALSE 3981731.098 868577.3562 1313963.227 897197.8763 1906457.158 2294005.507 2337313.855 1361759.872 1636677.229 490128.3418 8.123854015 1.772142686 2.680855432 1.830536616 3.889710093 4.680417987 4.768779227 2.778374063 3.339282979 1 18.90280005 0.636211043 1.265049536 1.009497584 3.718262013 0.188540462 1.750759591 2.198341628 5.312692185 1.612499806 0.485977103 4.327240599 -0.636211043 2.708764428 KS(ph)PPPAKDEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSPPPAKDEAR 11 2 Q8IXJ6-5;Q8IXJ6-2;Q8IXJ6-3;Q8IXJ6 Q8IXJ6-5 SIRT2 NAD-dependent protein deacetylase sirtuin-2 1 KS(1)PPPAKDEAR;KS(1)PPPAKDEAR;KS(1)PPPAKDEAR;KS(1)PPPAKDEAR 130.24 0.00011916 990450000 911630 477501 654616 455648 938830 856860 905020 712724 751750 347065 TRUE FALSE 947621.8563 559508.0823 671675.8307 545773.8144 779248.0119 657867.2508 834082.1676 703171.1006 724694.6643 415065.7418 2.283064491 1.347998705 1.618239626 1.314909325 1.877408645 1.58497121 2.009518213 1.694119822 1.745975616 1 18.66298034 KS(ph)PRPAGPQLFLPDPDPQR ddPTM_MDA-MB-175_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 121.62 1.81E-05 9733600000 8876800 6985120 8308600 6220790 10674900 11039600 9064000 8902400 9463200 6737080 TRUE FALSE 9227262.918 8184760.023 8525128.942 7451243.695 8860384.311 8475820.207 8353539.996 8783077.889 9122621.281 8057081.837 1.145236341 1.015846703 1.058091393 0.924806753 1.099701417 1.051971468 1.036794731 1.090106575 1.132248805 1 22.94182598 1.733693507 8.244210416 1.082878197 1.044149029 0.02990749 0.061664009 0.306152536 68.41610935 0.028596359 0.015251083 54.16185212 -1.733693507 -0.038729168 KS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSPTMEQAVQTASAHLPAPAAVGR 24 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 KS(0.987)PT(0.013)MEQAVQTASAHLPAPAAVGR;KS(0.993)PT(0.007)MEQAVQTASAHLPAPAAVGR 191.74 4.13E-18 1201660000 298700 274380 350470 351860 425100 445420 451210 407350 429480 228000 TRUE FALSE 310492.9066 321502.6306 359603.5361 421456.8578 352841.6538 341977.9554 415842.9812 401890.1395 414023.0987 272672.2347 1.138703789 1.179080925 1.318812444 1.545653734 1.294013871 1.25417227 1.525065365 1.473894619 1.518391116 1 18.05680828 4.16421141 3.366732469 1.400000793 1.151368501 0.208277465 0.158152665 0.292075814 6.520751885 0.038504635 0.101133418 14595.2457 -4.16421141 -0.248632292 KS(ph)PVGMLDLSSWSSPEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPVGMLDLSSWSSPEVLR 19 1 O95613-2;O95613 O95613-2 PCNT Pericentrin 1 KS(1)PVGMLDLSSWSSPEVLR 129.27 1.22E-05 195420000 100560 85177 115200 108760 134360 169470 144070 103060 111860 94220 TRUE FALSE 104530.1864 99805.48716 118202.2066 130272.4034 111521.5352 130113.1608 132777.4169 101678.6493 107834.1805 112680.605 0.927667955 0.885737942 1.049002236 1.156120908 0.98971367 1.154707687 1.178352006 0.902361584 0.956989718 1 16.78187969 4.233283032 24.94984651 1.049523937 0.906702929 0.296645247 0.087264984 145.8872516 689697.1093 0.023192009 0.052533412 17111.30105 -4.233283032 -0.142821009 KS(ph)QGAGSSPRRPQGGSDAPSGHAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSQGAGSSPRRPQGGSDAPSGHAAPSR 27 3 Q96IQ9-2;M0R0Q5;M0R398 Q96IQ9-2 ZNF414 Zinc finger protein 414 1 KS(0.327)QGAGS(0.327)S(0.327)PRRPQGGS(0.018)DAPSGHAAPSR 75.534 0.011658 8779100 3880.9 8278.3 10456 5716.3 14462 12228 4900.8 11504 8440.7 13517 TRUE FALSE 4034.120929 9700.033629 10728.49195 6846.967079 12003.75441 9388.232317 4516.66249 11349.8077 8136.920856 16165.39735 0.249552847 0.600049193 0.663670166 0.423556992 0.742558574 0.580760999 0.279403122 0.702105086 0.503354213 1 13.98062135 -5 0.343416288 6.096609068 0.523313893 0.442682646 0.159196017 374.5437263 3.12592659 1401.514661 0.119353199 1.00E-05 5 -5.573295174 KS(ph)RDSESHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSRDSESHSR 10 2 Q15424;Q15424-3;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 KS(0.854)RDS(0.146)ESHSR 99.834 0.0023089 114930000 46989 49052 61625 29580 81760 66951 57855 57248 54518 46638 TRUE FALSE 48844.162 57476.29943 63230.99813 35430.83571 67862.4644 51402.6449 53320.17392 56480.6842 52555.90783 55775.82316 0.875722835 1.030487695 1.133663199 0.635236447 1.216700365 0.921593658 0.955972873 1.012637394 0.942270411 1 15.76735228 KS(ph)REDLSAQPVQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSREDLSAQPVQTK 14 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 KS(1)REDLSAQPVQTK;KS(0.966)REDLS(0.034)AQPVQTK 156.08 4.47E-06 111980000 187098 90594 127564 87862 181193 175121 153816 120894 147746 62752 TRUE FALSE 194484.7735 106152.8148 130888.4226 105240.8414 150393.8786 134451.8017 141759.5 119273.6137 142428.6503 75047.05294 2.591504475 1.414483456 1.744084778 1.402331434 2.003994463 1.79156671 1.888941597 1.589317755 1.897858007 1 16.1955078 -2.223263641 0.454627079 4.00E-14 1.797706451 0.359944253 0.323420097 83.14698408 5.058532334 84.90437184 0.158173393 0.005980484 2.223263641 1.797706451 KS(ph)SGTGTEPVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.613)S(0.382)GT(0.005)GTEPVAK;KS(0.789)S(0.211)GTGTEPVAK 166.92 3.10E-05 794100000 683550 383380 551800 391380 744180 681340 678720 537640 699580 361580 TRUE FALSE 710537.0818 449222.5327 566180.3613 468793.7958 617684.5494 523109.1108 625520.1529 530433.8152 674402.2525 432424.6781 1.643146466 1.038845735 1.309315564 1.084105093 1.428421135 1.209711511 1.446541293 1.226650194 1.559583175 1 18.72208933 KS(ph)SMCSAPSSSSSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSMCSAPSSSSSAK 15 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 KS(0.48)S(0.48)MCS(0.039)APSSSSSAK;KS(0.499)S(0.499)MCS(0.003)APSSSSSAK 117.37 0.00022977 73670000 194657 127857 166243 115890 262270 211600 187246 159456 213520 122141 TRUE FALSE 202342.2087 149815.4452 170575.4292 138812.6961 217689.4391 162459.1068 172569.1692 157318.7531 205835.4569 146072.1904 1.38522061 1.02562606 1.167747459 0.95030201 1.490286676 1.112183684 1.181396464 1.076993182 1.409135143 1 17.15632201 -1.426902515 4.09870844 0.999178196 1.183538817 0.106433884 0.167838264 0.001163741 0.000162719 0.150046194 0.035210719 0.037419457 1.426902515 0.184360621 KS(ph)SMCSLAQPATTTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSMCSLAQPATTTAR 16 1 H3BPV0 H3BPV0 MTSS1L 1 KS(0.409)S(0.409)MCS(0.181)LAQPATTTAR;KS(0.552)S(0.429)MCS(0.019)LAQPATTTAR;KS(0.499)S(0.499)MCS(0.002)LAQPATTTAR;KS(0.497)S(0.497)MCS(0.006)LAQPATTTAR 92.31 0.0020663 1055830000 671491 609975 649143 540179 952300 886000 650319 692611 808274 707139 TRUE FALSE 698001.9832 714733.4613 666060.1999 647024.7939 790428.3862 680239.9275 599345.2975 683327.6824 779184.3766 845689.3481 0.82536452 0.845148946 0.787594406 0.765085661 0.93465572 0.80436147 0.708706216 0.80801264 0.921360046 1 19.68976828 1.071961621 3.398364276 0.997712385 0.807745461 0.567114241 0.054775169 0.154323066 3.541784265 0.05384424 0.01407768 11.80216333 -1.071961621 -0.189966924 KS(ph)SMDGAQNQDDGYLALSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSMDGAQNQDDGYLALSSR 20 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 KS(0.662)S(0.338)MDGAQNQDDGYLALSSR;KS(0.652)S(0.348)MDGAQNQDDGYLALSSR;KS(0.69)S(0.31)MDGAQNQDDGYLALSSR;KS(0.58)S(0.42)MDGAQNQDDGYLALSSR 299.67 5.42E-55 861910000 330396 298034 377870 266662 490652 457909 441387 378647 441537 356067 TRUE FALSE 343440.2892 349219.0211 387717.6026 319406.9477 407251.1483 351566.5744 406789.9336 373571.8563 425646.1696 425831.5113 0.80651685 0.820087316 0.91049533 0.750078233 0.956366867 0.825600185 0.955283775 0.877276215 0.999564753 1 18.69992319 1.868701624 0.378552255 1.011848686 0.811525899 0.4874107 0.059443719 0.987344826 0.389523965 0.066913005 0.065835711 73.90973135 -1.868701624 -0.200322787 KS(ph)SPEMEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSPEMEDAR 10 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 KS(0.5)S(0.5)PEMEDAR 48.568 0.083843 0 140260 84223 103980 82465 150190 153810 143830 110240 128650 83941 TRUE FALSE 145797.5731 98687.64509 106689.8042 98776.33087 124660.7574 118089.9585 132556.2288 108762.4131 124019.9116 100387.6318 1.452345976 0.983065775 1.062778375 0.983949209 1.241793986 1.176339718 1.320443827 1.083424434 1.235410273 1 16.61522201 3.196545982 24.99998669 1.183536462 1.106589034 0.028002492 0.148443313 444.7369979 264630.5666 0.041156118 0.049191354 1572.338259 -3.196545982 -0.076947428 KS(ph)SPQKEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 65.179 0.052995 1405500000 1221500 437460 728450 299250 1235900 1020300 825070 683240 884800 312200 TRUE FALSE 1269725.763 512590.352 747434.0054 358440.7568 1025822.159 783350.7878 760398.8575 674082.2854 852956.2208 373369.6126 3.400720681 1.37287646 2.001860838 0.960015879 2.747470937 2.098057157 2.036584746 1.805402107 2.284482165 1 18.51024499 -1.215498956 5.104707861 0.999898687 2.024196571 0.199424263 0.640028922 0.000678232 0.000104231 0.569453136 0.134208308 0.060883701 1.215498956 1.024297884 KS(ph)SPSSPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.474)S(0.474)PS(0.047)S(0.005)PAVR;KS(0.458)S(0.265)PS(0.265)S(0.011)PAVR 70.488 0.057021 111135000 199740 152317 198292 165077 234690 224000 214010 177059 193359 150257 TRUE FALSE 207625.8894 178476.2599 203459.6524 197728.7379 194797.4776 171979.3948 197235.337 174685.8137 186400.0474 179696.9823 1.155422238 0.993206773 1.132237447 1.100345344 1.084033105 0.957052214 1.097599606 0.972113229 1.037302046 1 17.45520666 2.878076666 8.463019346 1.015020836 1.090814463 0.36280229 0.053155018 0.342572526 22.27449084 0.015114961 0.016049373 755.2255366 -2.878076666 0.075793627 KS(ph)SPSTGSLDSGNESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSSPSTGSLDSGNESK 16 1 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 KS(0.474)S(0.474)PS(0.039)T(0.012)GSLDSGNESK;KS(0.498)S(0.498)PS(0.003)TGSLDSGNESK;KS(0.496)S(0.496)PS(0.006)T(0.001)GSLDSGNESK 153.06 2.99E-07 1072590000 957050 456681 695980 438760 940790 939910 826020 661600 692920 393460 TRUE FALSE 994835.073 535112.4093 714117.8106 525545.4184 780874.8518 721630.147 761274.394 652732.3342 667981.9446 470550.9538 2.114192023 1.137203963 1.517620578 1.116872496 1.65949053 1.533585558 1.617836258 1.387166106 1.419574095 1 18.84399143 0.562390717 1.238641934 1.000467034 1.497173661 0.248979388 0.265833655 2.240994827 4.762621167 0.233968127 0.070641836 3.650822491 -0.562390717 0.496706628 KS(ph)SPSVKPAVDPAAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSPSVKPAVDPAAAK 16 2 Q6FI81-3;Q6FI81;H3BV90;H3BT65;H3BPG7 Q6FI81-3 CIAPIN1 Anamorsin 1 KS(0.5)S(0.5)PSVKPAVDPAAAK 164.98 3.75E-09 782250000 1323500 448100 784500 480130 1214800 1099400 1125700 790090 1000300 420940 TRUE FALSE 1375752.802 525057.6893 804944.7145 575098.281 1008308.73 844081.0116 1037464.693 779500.1359 964299.3984 503415.1336 2.732839579 1.042991468 1.59896805 1.142393708 2.002936866 1.676709648 2.060853207 1.548424121 1.915515315 1 18.94138906 KS(ph)SSKDSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSSKDSRPSQAAGDNQGDEAK 22 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.226)S(0.226)S(0.226)KDS(0.116)RPS(0.205)QAAGDNQGDEAK 190.79 9.15E-17 151400000 375960 74359 152870 79166 230750 254350 250900 158270 186240 50522 TRUE FALSE 390803.1911 87129.57982 156853.9178 94824.79851 191527.1974 195281.0672 231233.8024 156148.6495 179537.2588 60420.8186 6.468022118 1.44204567 2.596024374 1.569406054 3.169887497 3.232016244 3.827055107 2.584351771 2.971446977 1 15.88275811 4.749563486 24.84934786 2.616044047 6.468024527 0.65700144 0.858239577 932.2981419 2105498.14 0.200993719 3.029424131 56177.63934 -4.749563486 3.85198048 KS(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_MDA-MB-175_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(0.317)S(0.317)S(0.317)LES(0.049)LQTAVAEVTLNGDIPFHRPRPR 129.84 1.08E-05 261100000 96279 75644 92918 77110 111760 107570 82369 106130 102270 94021 TRUE FALSE 100080.1693 88635.26857 95339.51941 92362.12785 92763.07512 82588.49774 75912.70255 104707.5009 98589.32268 112442.6148 0.890055514 0.788271144 0.847894898 0.821415688 0.824981483 0.734494639 0.675123953 0.931208342 0.876796781 1 16.77882938 1.611130424 15.91977215 0.928207523 0.798838745 0.505121923 0.062681868 0.058377241 140.3959004 0.03148495 0.016294576 40.84420276 -1.611130424 -0.129368778 KS(ph)STSDWPTDNQDGWDGKQENEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSTSDWPTDNQDGWDGKQENEER 24 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ISZ3;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 1 KS(0.496)S(0.496)T(0.004)S(0.004)DWPTDNQDGWDGKQENEER 138.34 3.81E-06 189590000 115160 53076 80752 56735 122080 120400 99183 88397 103780 58711 TRUE FALSE 119706.6057 62191.39013 82856.46346 67957.01366 101328.8852 92438.92468 91408.77729 87212.1828 100044.9781 70214.29636 1.704875103 0.885736856 1.180051183 0.967851523 1.443137516 1.316525686 1.30185421 1.242085833 1.424851964 1 16.09947719 3.225032396 24.99626512 1.298176645 1.162952228 0.041299478 0.232024037 628.1211423 1160585.768 0.06265974 0.075285042 1678.929252 -3.225032396 -0.135224417 KS(ph)STTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.69)S(0.31)TTLR 99.815 0.006279 181910000 226630 186350 210050 169060 272320 248200 229580 222790 238410 161670 TRUE FALSE 235577.5274 218354.1629 215524.0756 202499.5634 226031.1437 190559.3115 211584.9197 219803.8645 229829.6707 193346.1411 1.218423735 1.129343268 1.114705855 1.047342151 1.169049159 0.985586319 1.094332261 1.136841228 1.188695411 1 17.56082645 4.801527449 1.727005812 1.096048482 1.273636818 0.270184747 0.062938729 1.531474543 3.99884984 0.015961699 0.470478746 63318.03801 -4.801527449 0.177588336 KS(ph)STVATLQGTPDHGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.574)S(0.333)T(0.092)VATLQGTPDHGDPR;KS(0.619)S(0.33)T(0.051)VATLQGTPDHGDPR;KS(0.415)S(0.415)T(0.17)VATLQGTPDHGDPR;KS(0.296)S(0.296)T(0.296)VAT(0.111)LQGTPDHGDPR 213.05 7.63E-17 7802880000 3353900 2847780 3242990 2756100 4825930 4290730 3473520 3311770 3773110 3460840 TRUE FALSE 3486314.562 3336864.062 3327504.984 3301248.354 4005620.142 3294272.984 3201256.426 3267381.14 3637316.508 4138925.336 0.842323618 0.80621509 0.803953856 0.797610028 0.967792317 0.795924719 0.773451117 0.789427418 0.878806988 1 21.98082479 0.934344402 4.743424522 0.999943789 0.820568398 0.520702313 0.051946938 0.265717124 15.99344929 0.051227127 0.012979928 8.59695003 -0.934344402 -0.179375391 KS(ph)SVNGSSATSSG ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.785)S(0.215)VNGSSATSSG 115.1 0.00073171 415630000 482960 383600 514630 424030 650650 605660 629830 588770 602010 460490 TRUE FALSE 502027.6337 449480.316 528041.6806 507901.8684 540052.7454 465004.6439 580462.2788 580878.5012 580343.7777 550714.1989 0.911593772 0.816177097 0.9588307 0.922260347 0.980640678 0.844366542 1.054017274 1.054773061 1.053802097 1 19.07094428 2.223550318 24.99984123 1.046551374 0.90815983 0.655407289 0.047859154 141.7410112 236069.9184 0.017728929 0.01314521 167.3209485 -2.223550318 -0.138391543 KS(ph)TAALEEDAQILK ddPTM_MDA-MB-175_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(0.5)T(0.5)AALEEDAQILK;KS(0.921)T(0.079)AALEEDAQILK;KS(0.944)T(0.056)AALEEDAQILK;KS(0.855)T(0.145)AALEEDAQILK 224.03 2.02E-12 711080000 1837677 1046117 1571765 1066634 2477341 2043697 2038624 1741501 1896356 1047432 TRUE FALSE 1910229.907 1225779.457 1612726.487 1277611.022 2056243.462 1569079.344 1878831.324 1718159.028 1828106.518 1252656.246 1.524943426 0.978544162 1.287445372 1.019921487 1.641506573 1.252601701 1.499877823 1.37161255 1.459384028 1 20.25655913 3.25288451 24.99904686 1.391199953 1.192753851 0.126905196 0.21138054 393.3981487 686581.3941 0.052983042 0.071415241 1790.12975 -3.25288451 -0.198446102 KS(ph)VYRGSLTQR ddPTM_MDA-MB-175_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(0.684)VYRGS(0.316)LTQR 68.83 0.044232 172240000 137190 141980 163240 111700 217380 203220 120540 147710 167180 226040 TRUE FALSE 142606.3671 166363.9605 167494.1685 133793.9266 180429.8252 156025.2348 111091.7598 145730.1891 161163.2245 270328.2102 0.527530468 0.615414723 0.619595596 0.494931426 0.667447268 0.577169637 0.410951413 0.539086131 0.596176124 1 18.04435255 0.77294714 4.355150082 0.999996155 0.555321349 0.790561218 0.068066782 1.623946121 30.80623309 0.067444453 0.017149381 5.928531618 -0.77294714 -0.444674806 KSADTLWDIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSADTLWDIQK 11 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 155.02 5.09E-05 1359360000 2882300 1925130 2338930 1743380 4765900 3160900 2770400 2165880 2631700 2710500 FALSE TRUE 2996095.43 2255756.102 2399884.437 2088215.361 3955794.02 2426828.879 2553248.809 2136849.921 2536985.631 3241570.579 0.924272773 0.695883692 0.740346193 0.644198641 1.220332528 0.748658349 0.787657941 0.659202035 0.782640874 1 21.62826155 4.779103567 21.46973577 0.794699681 0.924275047 0.035311465 0.167139293 12019.63133 6364216.951 0.039400404 8.980617939 60131.71179 -4.779103567 0.129575365 KSADTLWGIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSADTLWGIQK 11 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 80.522 0.03877 790840000 1163300 875550 1011800 772820 2087000 1528200 1215800 1037200 1203900 1400000 FALSE TRUE 1209227.982 1025918.902 1038168.339 925681.4894 1732252.485 1173298.71 1120502.419 1023298.031 1160571.874 1674303.195 0.722227602 0.6127438 0.62005994 0.552875663 1.034610989 0.700768363 0.669235072 0.611178449 0.69316709 1 20.67512937 KSAEFLLHMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 111.91 0.0010368 282340000 184250 148260 179450 127330 579050 320740 259180 189990 223990 485920 FALSE TRUE 191524.3323 173722.5017 184126.6144 152515.494 480623.2878 246252.9959 238864.7944 187443.4948 215928.6437 581126.7205 0.329574128 0.298940826 0.316844172 0.262447911 0.827054188 0.423750943 0.411037362 0.322551843 0.371568947 1 19.14849327 -1.189678014 3.948418828 1.000379102 0.395646796 0.587311235 0.151898355 115212757 221383089.5 556952.1678 0.037504237 0.064613309 1.189678014 -0.604732306 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_MDA-MB-175_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 KSAEPSANTTLVS(0.995)ET(0.005)EEEGSVPAFGAAAK;KSAEPSANTT(0.001)LVS(0.987)ET(0.012)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.978)ET(0.022)EEEGSVPAFGAAAK;KSAEPSANTTLVS(0.999)ETEEEGSVPAFGAAAK 319.72 1.28E-92 1192070000 1620560 882470 1246950 1009630 1614740 1604080 1924620 1381360 1600250 720480 TRUE FALSE 1684540.96 1034027.358 1279446.541 1209331.801 1340267.072 1231556.73 1773763.255 1362845.129 1542657.315 861644.2616 1.955030672 1.200062954 1.484889529 1.40351634 1.555476119 1.429309966 2.058579549 1.581679574 1.79036452 1 19.71673284 KSATQFTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSATQFTGR 9 1 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ; 125.72 0.00079153 1491250000 1177000 1228480 1131070 1119480 1495680 1697780 1249970 1159680 1176760 1263550 FALSE TRUE 1223468.869 1439461.884 1160546.613 1340909.803 1241444.848 1303496.325 1151994.085 1144136.386 1134408.637 1511118.43 0.809644595 0.952580456 0.768005068 0.887362483 0.821540405 0.862603684 0.762345334 0.757145412 0.750707962 1 20.5271853 2.249665381 24.84652914 0.79175945 0.851577211 0 0.082680929 432.0403426 966675.4833 0.026618595 0.022072645 177.6909793 -2.249665381 0.059817761 KSDGIYIINLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSDGIYIINLK 11 1 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 ; 164.11 0.0016627 0 5511800 3731900 5111500 4142700 6596500 6153400 6908300 5453200 5591500 3529300 FALSE TRUE 5729410.12 4372824.795 5244709.889 4962113.695 5475229.286 4724366.106 6366809.395 5380108.774 5390263.007 4220798.762 1.35742319 1.036018309 1.242587051 1.175633802 1.297202163 1.119306172 1.508437088 1.274666023 1.277071784 1 22.00908462 3.241360805 24.99999998 1.272667118 1.193828023 0 0.144379897 219.1562871 1956608.574 0.038430779 0.049815828 1743.254538 -3.241360805 -0.078839095 KSDGIYIINLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSDGIYIINLKR 12 2 C9J9K3;A0A0C4DG17;P08865;F8WD59 C9J9K3 RPSA 40S ribosomal protein SA 0 65.395 0.034233 365060000 308620 293210 330910 218210 467100 456580 310880 283830 344930 376710 FALSE TRUE 320804.5559 343566.5366 339533.7864 261371.2867 387702.5088 350546.2145 286512.4133 280025.7231 332516.0367 450519.112 0.712077573 0.762601469 0.753650128 0.580155824 0.860568394 0.778093993 0.635960619 0.621562361 0.738073098 1 18.78122878 0.957741441 22.47715413 1.000000002 0.708676496 0.540045835 0.078883502 1965.055754 1045207.153 0.07908458 0.019771145 9.072802167 -0.957741441 -0.291323506 KSDIDEIVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;; 216.72 3.48E-12 4941120000 3981310 3889050 3968940 3850860 5154390 5480100 4553730 4009750 4155210 3559380 FALSE TRUE 4138495.193 4556964.085 4072373.837 4612548.614 4278248.629 4207429.827 4196796.744 3956005.86 4005664.804 4256772.363 0.972214354 1.070520971 0.95668114 1.083578877 1.0050452 0.988408463 0.985910541 0.929344001 0.941009869 1 22.02132851 2.310132553 1.73219111 0.951392159 1.020254804 0.278136878 0.04073321 0.384129111 2.330507608 0.018897523 0.012677155 204.2361207 -2.310132553 0.068862645 KSDIYVCMISFAHNVAAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSDIYVCMISFAHNVAAQGK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 300.74 4.98E-55 1347480000 679640 605130 868370 533240 1032360 884470 804260 736280 975060 669880 FALSE TRUE 706472.712 709056.3702 891000.4356 638713.2804 856879.8159 679065.2468 741219.9997 726411.3709 939967.7811 801130.1604 0.881845107 0.885070124 1.112179368 0.797265303 1.069588761 0.847634105 0.925217944 0.906733271 1.173302202 1 19.61167713 1.253589208 24.99785678 1.086651119 0.929258309 0.292872656 0.098477703 233.6896367 388712.0607 0.060427639 0.021871879 17.93036822 -1.253589208 -0.15739281 KSDLFQDDLYPDTAGPEAALEAEEWVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSDLFQDDLYPDTAGPEAALEAEEWVSGR 29 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;; 244.02 2.28E-45 1954460000 517900 479725 591838 465810 712639 670894 578014 566945 593871 528797 FALSE TRUE 538347.0919 562114.037 607261.7845 557945.8277 591504.8773 515089.036 532707.7523 559346.0296 572497.6987 632404.6477 0.85126998 0.888851844 0.960242444 0.882260796 0.935326582 0.814492806 0.842352684 0.884474887 0.905271175 1 19.27048844 0.79332867 2.900202499 0.999965137 0.882979081 0.434601987 0.040119851 1.046388832 13.08458705 0.039736532 0.010440676 6.213390796 -0.79332867 -0.116986056 KSDPVVSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSDPVVSYR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;; 141.1 0.00017242 370510000 206348 258731 187172 243461 373161 414270 333695 321674 326404 313385 FALSE TRUE 214494.7784 303166.0366 192049.8561 291616.8591 309731.2265 318062.0708 307539.114 317362.4862 314656.7838 374786.7906 0.572311468 0.808902673 0.512424293 0.778087346 0.826419805 0.848648028 0.820570846 0.846781408 0.839562097 1 18.51571058 6.186176644 0.1347296 1.058272239 2.63E-12 0.622164675 0.082514791 31.8049552 0.460027977 0.444906875 6.064777459 1535241.295 -6.186176644 -1.058272239 KSDTPQS(ph)PSLNSSQPTNSADSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSDTPQSPSLNSSQPTNSADSK 22 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 KS(0.001)DT(0.044)PQS(0.954)PSLNSSQPTNSADSK 166.35 7.22E-12 113710000 206020 117390 161540 130730 216190 223460 230090 176110 188060 112080 TRUE FALSE 214153.8287 137550.8193 165749.8651 156588.0038 179442.101 171564.8016 212054.9446 173749.5335 181291.7573 134039.9301 1.597686813 1.026192861 1.236570811 1.16821908 1.338721237 1.279952932 1.582028164 1.296252045 1.35252053 1 17.03230331 3.20454518 22.75087973 1.338275198 1.239198065 0 0.189247591 211.0451822 141153.6991 0.051449319 0.061499827 1601.567251 -3.20454518 -0.099077133 KSDVEAIFSK ddPTM_MDA-MB-175_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 ; 108.59 0.0034161 4109100000 9837700 6921500 7702100 6659100 11714500 10737600 9577500 8392700 7847200 6885400 FALSE TRUE 10226099.99 8110213.783 7902823.053 7976250.105 9723273.474 8243955.13 8826790.524 8280209.584 7564780.805 8234462.301 1.24186615 0.984911156 0.959725452 0.968642495 1.180802476 1.001152817 1.071932836 1.005555588 0.918673318 1 22.97324302 4.743251256 24.6016105 1.014891171 1.241866266 0.507928834 0.06827652 332.5750729 1744225.231 0.016361193 0.132410357 55367.03365 -4.743251256 0.226975095 KSDVETIFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSDVETIFSK 10 1 Q9UKM9;Q9UKM9-2;Q5QPM1;Q5QPL9;Q5QPM2 Q9UKM9 RALY RNA-binding protein Raly 0 113.77 0.0023161 706490000 1260200 807550 860440 810400 1414100 1328200 1174300 952650 946200 902800 FALSE TRUE 1309953.669 946240.4306 882863.7733 970694.7012 1173731.787 1019745.679 1082255.298 939881.285 912146.4468 1079686.375 1.213272391 0.876403049 0.817703913 0.899052469 1.08710438 0.944483234 1.002379323 0.870513241 0.844825375 1 20.04218087 1.722161406 10.05989667 0.894166316 0.967125064 0.072242405 0.112314275 0.28180315 86.91018193 0.053458009 0.02892598 52.74258432 -1.722161406 0.072958748 KSDYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSDYIK 6 1 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 98.418 0.064069 1547400000 2029000 1429200 1723300 1522200 2587700 2423900 2410500 1779300 2018800 1211900 FALSE TRUE 2109106.487 1674653.982 1768210.614 1823286.617 2147843.678 1860985.96 2221558.711 1755451.394 1946143.782 1449348.602 1.455209936 1.155452857 1.22000367 1.258004192 1.481937248 1.284015424 1.532798051 1.211200253 1.342771353 1 20.46697321 -0.14083961 1.241860449 0.998438183 1.322316212 0.398668932 0.120150543 22.08198212 22.35998289 0.275247797 0.033584448 0.723036781 0.14083961 0.323878029 KSEAPAEVTHFS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSEAPAEVTHFSPK 14 1 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 KSEAPAEVTHFS(1)PK 132.59 2.33E-05 297660000 593650 283060 367440 255570 558860 507210 479460 396510 423260 256670 TRUE FALSE 617087.7604 331673.3531 377015.7883 306120.9832 463865.1768 389418.1643 441878.6724 391195.432 408026.9553 306959.5723 2.010322584 1.080511517 1.228226198 0.99726808 1.511160487 1.268630137 1.439533777 1.274420045 1.329253075 1 18.22768913 7.999975273 0.025773505 3.87E-07 3.112042386 0.162406701 0.259527392 4517.020959 8.945901914 366.8848131 786.7728766 99994306.47 -7.999975273 3.112041999 KSEAPSGESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 159.44 1.23E-05 849550000 1445430 1298930 1483090 1259870 1720590 1783390 1657310 1475980 1489590 1291260 FALSE TRUE 1502496.693 1522011.123 1521740.544 1509068.526 1428124.726 1369224.7 1527405.712 1456196.902 1435979.947 1544257.674 0.972957245 0.985594016 0.9854188 0.977212903 0.924796911 0.88665559 0.989087338 0.942975338 0.92988364 1 20.55848207 3.33287518 7.129298393 0.943155384 0.981546337 0.23829597 0.030263361 0.305995742 19.85337585 0.008316458 0.011266583 2152.163096 -3.33287518 0.038390953 KSEDSLLRNS(ph)DEEESASESELWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSEDSLLRNSDEEESASESELWK 23 2 Q70Z53 Q70Z53 FRA10AC1 Protein FRA10AC1 1 KS(0.008)EDS(0.348)LLRNS(0.644)DEEESASESELWK 78.836 0.010303 90235000 72446 36935 53956 34909 80077 68596 70216 59078 67135 38564 TRUE FALSE 75306.22402 43278.29894 55362.13769 41813.89601 66465.54014 52665.61858 64712.28644 58286.15604 64718.82446 46119.87745 1.632836603 0.938387119 1.200396461 0.90663502 1.441147371 1.141928849 1.403132229 1.263796854 1.40327399 1 15.49310106 3.206887078 24.99994509 1.289361573 1.155252655 0.048152505 0.222271203 505.3050215 398836.2679 0.059609781 0.071253464 1610.226901 -3.206887078 -0.134108917 KSEEEIDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KSEEEIDFLR 10 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ;;;;; 184.03 2.57E-06 1968560000 4546410 3647500 4688610 3835810 5763830 5494560 5188700 4591620 4968600 3744870 FALSE TRUE 4725905.777 4273929.751 4810799.028 4594521.769 4784096.235 4218531.711 4781996.136 4530076.844 4789781.057 4478605.577 1.055218125 0.954299207 1.074173411 1.025882206 1.06821111 0.941929723 1.067742192 1.011492699 1.069480439 1 22.09461819 KSEEWPDWS(ph)EPEEPENQTVNIQIWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSEEWPDWSEPEEPENQTVNIQIWPR 26 1 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 KSEEWPDWS(1)EPEEPENQTVNIQIWPR;KSEEWPDWS(1)EPEEPENQTVNIQIWPR;KSEEWPDWS(1)EPEEPENQTVNIQIWPR;KSEEWPDWS(1)EPEEPENQTVNIQIWPR 267.19 1.71E-53 389306000 333997 254928 344248 252772 388105 394937 333066 307461 364994 259068 TRUE FALSE 347183.4595 298709.9009 353219.3857 302769.5472 322135.0507 303218.8671 306959.4166 303339.9882 351857.9372 309827.4144 1.120570496 0.964117076 1.140052072 0.977220004 1.039724168 0.97867023 0.990743241 0.979061161 1.135657856 1 18.24110528 4.761855281 23.48879338 1.02015211 1.120570755 0.184414536 0.06145237 4626.721389 4665105.355 0.013823496 0.723169158 57790.34417 -4.761855281 0.100418645 KSEGDGDKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSEGDGDKEEK 11 2 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 81.494 0.012104 173976000 661380 123921 274311 146518 431090 401920 500850 281339 351562 87434 FALSE TRUE 687491.7931 145203.4678 281459.77 175498.8231 357813.4758 308580.1712 461592.0683 277568.1109 338909.3523 104565.0183 6.574778109 1.388642877 2.691720182 1.678370319 3.421923332 2.951084179 4.414402406 2.654502581 3.241135113 1 16.67404076 KSEIEYYAMLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSEIEYYAMLAK 12 1 E5RI99;P62888 E5RI99 RPL30 60S ribosomal protein L30 0 ; 157.52 0.0001188 4383400000 7850200 4925800 7465700 5704200 9816200 8415500 9596700 7441100 8108700 4558900 FALSE TRUE 8160131.958 5771767.833 7660262.275 6832473.735 8147645.83 6461127.663 8844485.578 7341364.226 7816869.471 5452129.17 1.496687203 1.058626392 1.405003814 1.253175323 1.494397065 1.185065038 1.622207637 1.346513261 1.433727857 1 22.37838831 KSES(ph)DKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSESDKDVK 9 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 KS(0.018)ES(0.982)DKDVK;KS(0.028)ES(0.972)DKDVK 68.034 0.030896 385250000 938060 224598 298090 173766 579270 638960 546230 340910 387490 147382 TRUE FALSE 975095.3331 263170.9594 305858.4703 208136.3962 480805.8923 490571.2235 503415.0653 336340.6591 373544.3106 176258.6811 5.532183306 1.493095022 1.735281737 1.18085756 2.727842336 2.783245741 2.856115013 1.908221808 2.119295959 1 17.42733479 4.744241725 24.96218492 2.055700567 5.53218483 0.741378979 0.628219884 322.2760277 1416004.513 0.154093661 1.366976607 55493.44995 -4.744241725 3.476484263 KSES(ph)PFRETEPLVSPHQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSESPFRETEPLVSPHQDK 19 2 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 KS(0.005)ES(0.993)PFRET(0.002)EPLVSPHQDK 186.82 1.03E-14 255430000 211840 144350 189900 107880 257380 228590 235500 185180 210400 115130 TRUE FALSE 220203.6068 169140.9896 194848.95 129218.342 213630.6395 175503.4368 217040.8946 182697.965 202827.7451 137687.5192 1.59929969 1.22844097 1.415153321 0.93848987 1.551561396 1.274650294 1.576329473 1.326902874 1.473101892 1 17.07103827 -1.040443002 4.570267735 0.999984857 1.367828794 0.261163012 0.189274683 0.284228104 53306479.52 1783.644726 0.040965875 0.091108102 1.040443002 0.367843937 KSFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSFSKEELMSSDLEETAGSTSIPK 24 2 O00567 O00567 NOP56 Nucleolar protein 56 1 KS(0.007)FS(0.109)KEELMS(0.412)S(0.412)DLEET(0.053)AGS(0.005)T(0.001)SIPK 60.093 0.036172 546740000 540110 276260 473970 247670 682050 458020 425170 427620 497120 264170 TRUE FALSE 561433.9599 323705.506 486322.0476 296658.3868 566115.3846 351651.7964 391844.0644 421888.4533 479228.7483 315929.0537 1.777088727 1.024614553 1.539339424 0.939003182 1.791906689 1.11307204 1.240291325 1.335389856 1.516887234 1 18.26924109 -1.417608183 3.39518592 0.996405627 1.345545183 0.128850074 0.280335668 69173930.78 113946166 2519333.576 0.059708344 0.038228901 1.417608183 0.349139556 KSGIS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSGISPK 7 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 1 KS(0.001)GIS(0.999)PK;KS(0.001)GIS(0.999)PK;KS(0.001)GIS(0.999)PK 74.094 0.028859 1086460000 4039220 1571380 2129040 1543300 3326690 3222110 3400700 2441360 2708110 1298830 TRUE FALSE 4198691.525 1841252.291 2184524.531 1848560.134 2761220.422 2473823.784 3134144.248 2408637.562 2610645.65 1553310.871 2.703059383 1.185372694 1.406366602 1.190077381 1.77763542 1.592613449 2.017718608 1.550647464 1.68069747 1 20.56691516 SDSDMWINQSSSLDSSTS(ph)SQEHLNHSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSDMWINQSSSLDSSTSSQEHLNHSSK 28 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 SDSDMWINQSSSLDSST(0.003)S(0.485)S(0.485)QEHLNHS(0.022)S(0.005)K;SDSDMWINQSSSLDSS(0.001)T(0.003)S(0.395)S(0.39)QEHLNHS(0.18)S(0.031)K 216.94 5.52E-34 267240000 46214 209091 231996 239109 261670 318990 206883 315350 254480 254280 TRUE FALSE 48038.5644 245000.7527 238042.0063 286404.0465 217191.4269 244909.4068 190666.9699 311123.2491 245321.3145 304101.2975 0.157968956 0.805655072 0.782772084 0.94180475 0.714207498 0.805354692 0.626985059 1.023090831 0.8067092 1 18.21419245 4.740719766 4.950637113 0.833331702 0.122673122 0.751352507 0.116785982 0.081346529 6.107497915 0.027072885 0.198795895 55045.23955 -4.740719766 -0.71065858 down KSHFGGPDYEEGPNSLINEEEFFDAVEAALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSHFGGPDYEEGPNSLINEEEFFDAVEAALDR 32 1 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2R8YFA1 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 ; 80.342 0.00060563 22238000 18736.7 17004.9 22084.8 18450.6 22745.5 26929 24034.5 22577.7 25468.7 17079 FALSE TRUE 19476.43938 19925.3593 22660.34803 22100.07361 18879.22803 20675.14786 22150.61309 22275.08286 24552.08646 20425.30305 0.953544696 0.975523313 1.109425303 1.081994894 0.924305896 1.012232123 1.08446925 1.090563151 1.202042702 1 14.31806986 2.162070068 3.749677063 1.103314877 1.011679067 0.266233385 0.068873703 0.317242792 8.777767423 0.028123406 0.020204512 145.2345916 -2.162070068 -0.091635809 DKQSPS(ph)QANGCSDHRPIDILEMLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(0.126)PS(0.874)QANGCSDHRPIDILEMLSR 145.86 1.42E-07 183920000 90142 163650 190010 166960 247220 249710 193520 223030 196200 161830 TRUE FALSE 93700.87576 191755.6145 194961.8167 199984.1897 205197.6327 191718.6369 178351.3967 220040.6477 189138.8003 193537.4901 0.48414845 0.990793124 1.007359435 1.033309823 1.060247462 0.990602063 0.9215341 1.136940691 0.977272157 1 17.56225353 4.740835745 4.4942087 1.021968656 0.447212315 0.898151858 0.053465773 0.055853119 2.867262015 0.012901156 0.102121829 55059.94143 -4.740835745 -0.574756341 down KSHS(ph)LSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSHSLSIR 8 1 A0A3B3IT47;Q9Y2I8;Q9Y2I8-2;E7EQ49;A0A087WTQ2;Q9Y2I8-3 A0A3B3IT47 WDR37 WD repeat-containing protein 37 1 KS(0.003)HS(0.609)LS(0.389)IR 57.348 0.068505 55886000 61660 54293 72939 46193 82286 70277 76098 56989 72273 67123 TRUE FALSE 64094.38441 63617.40041 74839.85026 55329.83753 68299.05511 53956.23181 70133.23991 56225.15567 69671.90885 80274.4667 0.798440489 0.792498574 0.932299563 0.689258239 0.85081917 0.672146873 0.873668089 0.700411451 0.867921167 1 16.29265356 0.990488161 22.98882943 1.000000005 0.788091203 0.402448762 0.079422646 128.4907415 310547.1106 0.069483643 0.017370911 9.78336284 -0.990488161 -0.211908802 KSHS(ph)PVKRPR ddPTM_MDA-MB-175_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 KS(0.058)HS(0.942)PVKRPR 55.724 0.091877 132750000 190250 99745 179540 98850 230370 210040 216850 153380 208020 147560 TRUE FALSE 197761.2169 116875.4278 184218.9599 118402.235 191211.7897 161261.3932 199852.7304 151324.192 200533.4008 176471.5568 1.120640745 0.662290456 1.04390171 0.670942316 1.083527528 0.913809546 1.13249259 0.857499048 1.136349701 1 17.42907615 KSLDFYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSLDFYTR 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ; 84.738 0.027642 1581200000 430520 534650 510870 417400 958770 774660 571560 589450 604080 1254210 FALSE TRUE 447517.262 626471.9785 524183.6919 499960.4742 795798.6179 594756.9551 526759.6337 581549.3869 582339.2788 1499948.436 0.298355098 0.417662343 0.349467808 0.333318441 0.53055065 0.396518267 0.351185161 0.387712919 0.388239532 1 20.51648148 KSLDQDPVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSLDQDPVVR 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 85.845 0.022387 682280000 1320940 1349790 1359700 1163680 1687930 1794390 1416320 1431470 1445570 1475180 FALSE TRUE 1373091.731 1581605.933 1395134.899 1393852.431 1401016.262 1377670.117 1305305.138 1412283.486 1393544.218 1764213.277 0.778302572 0.896493612 0.790797188 0.790070253 0.794130891 0.780897715 0.739879443 0.800517434 0.789895551 1 20.75059355 -1.509845205 9.164325951 1.00000658 0.7957349 0.729806194 0.037299049 5.08E-06 2.72E-07 0.036572342 0.008619906 0.030913971 1.509845205 -0.20427168 KSLDS(ph)DES(ph)EDEEDDYQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KS(0.004)LDS(0.996)DES(1)EDEEDDYQQK;KS(0.002)LDS(0.998)DES(1)EDEEDDYQQK;KS(0.002)LDS(0.998)DES(1)EDEEDDYQQK;KS(0.132)LDS(0.869)DES(0.999)EDEEDDYQQK;KS(0.021)LDS(0.979)DES(1)EDEEDDYQQK 289.6 1.36E-48 8399100000 10837880 2969594 5101060 3224952 8084220 9016110 7794250 5403400 5981510 2020531 TRUE FALSE 11265767.87 3479598.669 5233997.814 3862837.88 6710067.172 6922255.093 7183316.319 5330976.261 5766236.624 2416415.364 4.662181858 1.439983672 2.166017437 1.598581907 2.776868278 2.864679308 2.972715877 2.206150623 2.38627709 1 21.20443703 4.750948975 24.64194453 2.253365301 4.662183687 0.590839578 0.620806419 1168.267585 2323774.221 0.145760777 2.523001256 56357.14385 -4.750948975 2.408818387 KSLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KSLDSDESEDEEDDYQQKR 19 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 KSLDS(1)DES(1)EDEEDDYQQKR;KS(0.03)LDS(0.97)DES(1)EDEEDDYQQKR;KS(0.184)LDS(0.816)DES(1)EDEEDDYQQKR;KS(0.002)LDS(0.998)DES(1)EDEEDDYQQKR;KSLDS(1)DES(1)EDEEDDYQQKR;KS(0.011)LDS(0.989)DES(1)EDEEDDYQQKR 183.99 1.27E-13 6708800000 14204900 4393218 7640220 4014129 12311380 12364440 9020900 7381330 8576400 3761584 TRUE FALSE 14765720.42 5147719.017 7839330.41 4808111.735 10218696.03 9492986.195 8313818.286 7282395.345 8267737.039 4498594.365 3.282296474 1.144294995 1.742617754 1.068803129 2.271530882 2.110211641 1.848092451 1.618815735 1.837848974 1 22.10104286 -2.193738212 0.292621325 6.17E-13 1.90908015 0.175436975 0.585654302 70.53295445 2.844618249 47.73179669 0.613802515 0.006401206 2.193738212 1.90908015 KSLESINSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSLESINSR 9 1 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ;;; 158.05 0.0001076 1974070000 1096330 1131110 1299640 1046820 1581600 1616490 1370350 1350190 1332580 1314170 FALSE TRUE 1139613.955 1325369.344 1333509.686 1253877.872 1312760.197 1241084.696 1262938.386 1332092.912 1284620.706 1571656.45 0.72510373 0.843294566 0.848474033 0.797806589 0.835271727 0.789666657 0.803571535 0.847572579 0.817367374 1 20.58385446 -5 0.288781244 2.4351464 0.804300523 0.732036178 0.034443321 121.5019613 1.147171323 104.9123303 0.035396817 1.00E-05 5 -1.630845877 KSLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSLPAPVAQRPDSPGGGLQAPGQK 24 2 Q5JVS0;Q5JVS0-2 Q5JVS0 HABP4 Intracellular hyaluronan-binding protein 4 1 KSLPAPVAQRPDS(1)PGGGLQAPGQK;KSLPAPVAQRPDS(1)PGGGLQAPGQK 232.53 1.50E-34 2039700000 1763730 1188360 1509160 1029720 1982660 1841280 1826810 1540480 1823950 1328290 TRUE FALSE 1833363.422 1392451.586 1548489.949 1233395.543 1645648.161 1413670.625 1683619.859 1519832.385 1758306.396 1588542.994 1.154116338 0.876558954 0.974786301 0.776431955 1.035948141 0.889916502 1.059851616 0.956746145 1.106867364 1 20.59927271 2.231151553 24.99755849 1.020870464 0.944863632 0.124302729 0.101239771 371.4257419 1253148.035 0.035518026 0.026748822 170.2752602 -2.231151553 -0.076006832 KSLS(ph)DS(ph)ESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 KS(0.02)LS(0.955)DS(0.491)ES(0.299)DDS(0.235)K 95.57 0.00066314 0 635330 161600 242610 164170 432310 517570 408570 253780 305940 103760 TRUE FALSE 660413.319 189353.5429 248932.6159 196642.336 358826.1006 397372.2113 376545.2158 250378.4942 294929.2792 124089.7854 5.322060288 1.525939805 2.00606855 1.584677863 2.891665091 3.202295903 3.034457789 2.017720422 2.376740988 1 16.92102484 4.747236688 24.93289788 2.27057042 5.322061892 0.655716576 0.679840776 696.2958403 2000938.405 0.16451371 1.949895793 55877.46402 -4.747236688 3.051491473 KSLS(ph)DSESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KS(0.002)LS(0.605)DS(0.393)ESDDSK;KS(0.003)LS(0.952)DS(0.045)ESDDSK;KS(0.005)LS(0.702)DS(0.293)ESDDSK;KS(0.07)LS(0.911)DS(0.018)ESDDSK 216.72 2.35E-11 7855610000 8699930 2793517 4542090 2912112 6845190 6934770 6752830 4617370 5466710 2112388 TRUE FALSE 9043409.954 3273281.814 4660460.597 3488119.062 5681647.049 5324274.765 6223525.539 4555481.708 5269964.175 2526269.984 3.579748012 1.295697544 1.844799101 1.38073883 2.249026068 2.10756364 2.463523526 1.803244204 2.086065309 1 21.2685774 -0.25454132 1.179435418 0.990893265 2.046313686 0.222156606 0.606575633 41.23771972 35.85694061 2.400385679 0.164391286 0.556491686 0.25454132 1.055420422 KSLS(ph)PGVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSLSPGVSR 9 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KS(0.005)LS(0.994)PGVS(0.001)R;KS(0.002)LS(0.998)PGVSR;KS(0.017)LS(0.971)PGVS(0.012)R 107.2 0.0017228 1325640000 2000860 1828490 1950150 1495880 2430000 2488550 2012700 1989040 2077710 1806620 TRUE FALSE 2079855.498 2142518.934 2000972.511 1791760.599 2016949.468 1910621.977 1854939.315 1962380.172 2002933.623 2160592.599 0.962631964 0.991634857 0.92612208 0.829291279 0.93351679 0.884304601 0.858532662 0.908260156 0.927029753 1 21.04299563 4.073872581 5.243822195 0.89851745 0.975501725 0.277366008 0.044164403 0.206882383 10.25972982 0.010295369 0.022966346 11854.20902 -4.073872581 0.076984274 KSLSDS(ph)ESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KSLSDSESDDSK 12 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 KSLS(0.25)DS(0.75)ESDDSK;KSLS(0.247)DS(0.742)ES(0.011)DDSK;KS(0.009)LS(0.49)DS(0.501)ESDDSK;KS(0.008)LS(0.095)DS(0.895)ES(0.003)DDSK;KS(0.001)LS(0.048)DS(0.949)ES(0.001)DDSK;KS(0.002)LS(0.156)DS(0.836)ES(0.006)DDSK 233.09 3.35E-16 12583050000 10463240 3644500 5806810 3625080 8524290 8539420 8217580 5638550 6353760 2697590 TRUE FALSE 10876336.79 4270414.525 5958140.239 4342110.004 7075334.231 6556269.121 7573464.607 5562974.46 6125089.419 3226131.112 3.3713251 1.32369528 1.8468376 1.345918642 2.193132884 2.032238893 2.347537761 1.724348536 1.898586637 1 21.62137364 0.434608045 1.178503419 0.999848614 1.991074759 0.235749232 0.549478145 3.560813188 6.003967607 0.494639624 0.149740601 2.720245153 -0.434608045 0.991226145 KSLTPAVPVESKPDKPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSLTPAVPVESKPDKPSGK 19 3 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 106.03 0.0001411 300180000 750720 345830 535720 343270 670310 575150 514160 402630 476000 274240 FALSE TRUE 780359.0053 405223.6123 549681.3033 411167.7814 556370.9456 441580.129 473858.7957 397233.4034 458868.853 327972.0774 2.379345863 1.235543024 1.67600031 1.253667034 1.696397297 1.3463955 1.444814447 1.211180557 1.399109512 1 18.32321347 4.743677875 24.92506601 1.381086942 2.379346294 0.696815161 0.200872693 272.9679152 1329524.191 0.044056327 0.370507074 55421.44881 -4.743677875 0.998259352 KSMS(ph)EDGGLQESNPCADDFVSASTADVSHTNLGTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSMSEDGGLQESNPCADDFVSASTADVSHTNLGTIR 36 1 H7C0I1;B8ZZW5;Q8NBF6-2;Q8NBF6;A0A1W2PRP5 H7C0I1 AVL9 Late secretory pathway protein AVL9 homolog 1 KS(0.431)MS(0.569)EDGGLQESNPCADDFVSASTADVSHTNLGTIR 127.45 8.34E-09 407940000 17980 10758 17177 15168 23852 17970 15210 11573 9053 14721 TRUE FALSE 18689.86428 12605.60281 17624.64673 18168.18513 19797.64556 13796.73984 14017.80046 11417.88286 8727.184298 17605.2981 1.061604534 0.716011893 1.001099023 1.031972593 1.12452771 0.783669766 0.796226248 0.648548113 0.49571352 1 14.10372204 KSNFAEALAAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSNFAEALAAHK 12 1 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 89.46 0.006109 2401700000 3653500 3235200 3561100 2891300 6594600 5282000 4971600 3968000 4655800 4450400 FALSE TRUE 3797743.001 3790820.434 3653905.191 3463190.51 5473652.248 4055335.549 4581913.001 3914815.45 4488238.667 5322370.672 0.713543501 0.712242846 0.686518361 0.650685705 1.02842372 0.761941586 0.860878222 0.735539798 0.843278107 1 22.34363756 -4.999999966 0.035521884 2.115007443 0.076855166 0.399870946 0.096042874 1129.130043 3.007872598 145.6726101 50.09144998 1.00E-05 4.999999966 -2.038152277 KSNLDEEVNVIPPHT(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR;KSNLDEEVNVIPPHT(1)PVR 131.33 1.01E-05 2399000000 2672660 2287900 2685510 2085740 3401210 3332570 2901640 2695260 2805510 2342280 TRUE FALSE 2778178.681 2680829.028 2755496.597 2498293.147 2823073.539 2558631.123 2674201.875 2659134.448 2704540.243 2801204.92 0.99177988 0.957027102 0.983682621 0.891863758 1.007806861 0.913403766 0.95466128 0.949282371 0.965491751 1 21.4176161 0.887989376 4.577182244 0.999995784 0.955011936 0.137712503 0.032738646 1.300447323 50.15913613 0.02846679 0.007223035 7.726616839 -0.887989376 -0.044983848 KSPLSWIEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPLSWIEEK 10 1 P53004 P53004 BLVRA Biliverdin reductase A 0 110.31 0.0030522 713640000 1073800 1442700 1805300 1438500 1997100 2218600 1721700 1948900 1962500 1632700 FALSE TRUE 1116194.453 1690472.502 1852347.601 1723031.007 1657633.655 1703363.773 1586748.655 1922778.183 1891870.008 1952596.305 0.5716463 0.865756274 0.948658766 0.882430742 0.848938232 0.872358392 0.812635285 0.984728988 0.968899717 1 20.89696228 4.732093778 3.686583827 0.908147733 0.537338266 0.752734912 0.05855073 0.129235225 3.30043299 0.014550847 0.130244791 53962.71326 -4.732093778 -0.370809467 KSPS(ph)LESLSRPPSLGFGDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPSLESLSRPPSLGFGDTR 20 2 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 KS(0.006)PS(0.994)LESLSRPPSLGFGDTR 96.052 0.00059416 62665000 139180 110460 134940 94930 156190 171070 160020 127330 146070 116720 TRUE FALSE 144674.9339 129430.6457 138456.6473 113706.8707 129640.8796 131341.5851 147477.2143 125623.3496 140812.9692 139589.0493 1.036434696 0.927226358 0.991887601 0.81458303 0.928732449 0.940916109 1.056509913 0.899951323 1.008768023 1 17.09082624 2.444580689 24.99973552 0.979452944 0.934996808 0.119445831 0.064548545 475.2743406 365133.6946 0.022278193 0.018639358 278.343247 -2.444580689 -0.044456136 KSPSDLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 78.556 0.048613 475360000 483240 434250 477630 397590 714220 642740 587710 472890 509790 385170 FALSE TRUE 502318.6883 508829.0595 490077.4302 476232.1153 592817.1395 493473.3758 541643.7545 466551.683 491442.7575 460636.687 1.090487802 1.104621221 1.063913153 1.033856245 1.286951639 1.07128544 1.175858914 1.012840914 1.066877154 1 18.81326979 1.675097744 8.703325385 1.030461642 1.116828593 0.268268976 0.069041038 0.168447322 21.14965914 0.03306099 0.017515891 47.32577603 -1.675097744 0.086366951 KSPSGPVKS(ph)PPLSPVGTTPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPSGPVKSPPLSPVGTTPVK 21 2 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 KS(0.026)PS(0.205)GPVKS(0.767)PPLS(0.002)PVGTTPVK 169.36 5.01E-12 842490000 1343400 567010 873890 580650 1284500 1115500 1065800 861000 968840 488960 TRUE FALSE 1396438.469 664389.5568 896664.2913 695500.8369 1066161.149 856442.0306 982259.811 849459.7033 933971.6377 584762.3503 2.388044423 1.1361702 1.533382392 1.189373489 1.82323836 1.464598448 1.679758983 1.452657995 1.597181551 1 19.1574909 -2.593397741 0.413611232 2.37E-14 1.572630017 0.216863364 0.332456594 138.141982 6.029604582 123.9826264 0.181464831 0.002550365 2.593397741 1.572630017 KSPSSDSWTCADTSTER ddPTM_MDA-MB-175_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 0 ;;; 237.39 5.19E-20 832930000 564500 502710 600330 498390 660960 661840 599790 605340 605020 543930 FALSE TRUE 586786.8959 589046.532 615975.093 596970.0545 548610.2553 508137.6903 552776.8925 597226.4074 583245.4484 650502.6693 0.90205148 0.905525157 0.946921699 0.917705772 0.843363573 0.781146203 0.84976883 0.918099857 0.89660731 1 19.31119545 0.639864072 1.387344548 0.999591401 0.881209436 0.377096745 0.045059751 1.556435188 4.388514248 0.048335506 0.014263431 4.363792301 -0.639864072 -0.118381965 KSPSSDSWTCADTSTERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSPSSDSWTCADTSTERR 18 2 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7;H0YIQ0 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 0 ; 153.14 1.99E-08 212180000 115895 106763 113509 83068 125815 149563 88619 109560 118568 122698 FALSE TRUE 120470.6241 125098.7147 116467.1378 99498.60247 104429.0112 114829.2599 81672.81122 108091.5274 114300.7608 146738.3239 0.820989506 0.85252926 0.793706339 0.678068277 0.711668284 0.782544443 0.556588143 0.736627791 0.7789428 1 17.16288619 3.963065685 5.262846129 0.727222895 0.834532128 0.074486963 0.106089959 0.324150657 23.43420547 0.025484778 0.049479558 9184.714998 -3.963065685 0.107309233 KSPVGKS(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSPVGKSPPSTGSTYGSSQK 20 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 KS(0.182)PVGKS(0.451)PPS(0.182)T(0.182)GS(0.001)TYGSSQK 107.47 0.00011806 636680000 397010 207770 303150 209030 427230 406230 407650 340060 339700 182170 TRUE FALSE 412684.2614 243452.8813 311050.338 250375.5101 354609.5972 311889.239 375697.3278 335502.0519 327474.2634 217862.7236 1.894239889 1.11746001 1.42773547 1.149235197 1.627674488 1.431586064 1.724468149 1.53996997 1.503122048 1 17.73305985 3.192745247 24.99990368 1.515848748 1.379368579 0 0.268134434 384.3460022 209723.22 0.071980611 0.086033607 1558.637952 -3.192745247 -0.136480169 KSS(ph)GTGTEPVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSGTGTEPVAK 12 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 KS(0.008)S(0.956)GT(0.029)GT(0.007)EPVAK;KS(0.348)S(0.651)GT(0.001)GTEPVAK 175.6 2.01E-05 446610000 688260 378552 533020 328428 763210 657630 740970 521080 684810 339340 TRUE FALSE 715433.0363 443565.3613 546910.9391 393390.0781 633479.8368 504905.399 682890.8352 514095.7749 660163.8219 405827.1759 1.762900758 1.092990779 1.347644937 0.969353709 1.560959626 1.244138956 1.68271342 1.26678499 1.626711716 1 18.63050595 KSS(ph)LKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSLKK 6 2 P98171-2;P98171;E7EQN5;A0A0B4J1X7;S4R352;S4R314;H7C3G3 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 KS(0.08)S(0.92)LKK 82.279 0.031131 358650000 444700 138550 268080 143270 464110 360350 438310 289170 387350 148270 TRUE FALSE 462257.0994 162344.8847 275066.385 171608.3784 385220.748 276664.1737 403954.1169 285294.1491 373409.3492 177320.6677 2.606899158 0.915544064 1.551237025 0.967785541 2.172452614 1.560247755 2.278099458 1.608916506 2.105842224 1 17.43600117 3.222108123 24.99988845 1.826198244 1.47079822 0.052387883 0.553297173 582.9606094 885818.3083 0.147602356 0.176895874 1667.662345 -3.222108123 -0.355400024 KSS(ph)LVTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSLVTSK 8 1 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-6;O43768-5;O43768-7 A6NMQ3 ENSA Alpha-endosulfine 1 KSS(0.999)LVT(0.001)SK;KS(0.14)S(0.7)LVT(0.148)S(0.012)K;KS(0.007)S(0.985)LVT(0.008)SK;KS(0.006)S(0.993)LVTSK 154.15 0.00045511 26926230000 39096950 22175730 33661500 21609180 43220630 34239240 38138180 31194980 38521810 17939090 TRUE FALSE 40640527.78 25984239.12 34538746.34 25883411.31 35874002.75 26287695.41 35148809.8 30776862.32 37135417.58 21453911.22 1.894317887 1.211165594 1.609904413 1.206465853 1.67214278 1.225310161 1.638340414 1.434557177 1.730939277 1 24.35473735 -2.099479336 2.391052084 0.143113808 1.495508974 0.310695034 0.228096962 5403004.969 2274213.315 25055480.64 0.050056788 0.007952811 2.099479336 1.352395166 KSS(ph)MDGAQNQDDGYLALSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSMDGAQNQDDGYLALSSR 20 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 KS(0.197)S(0.803)MDGAQNQDDGYLALSSR 275.17 1.02E-44 334190000 97940 79944 93518 82517 142290 128490 131370 104620 135320 94266 TRUE FALSE 101806.7468 93673.76012 95955.15591 98838.61631 118103.5966 98650.14478 121072.8761 103217.74 130449.8596 112735.6179 0.903057514 0.830915392 0.851152082 0.876729273 1.047615641 0.875057472 1.073954074 0.915573463 1.157130835 1 16.78258387 3.067271756 0.71984401 1.025925637 0.844266449 0.434345516 0.078350336 0.701078092 0.807596838 0.046710747 0.068218706 1167.539967 -3.067271756 -0.181659188 KSS(ph)PSKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.061)S(0.656)PS(0.283)KDR 59.496 0.07738 371200000 740530 280390 476770 289000 716330 613540 685730 463090 567970 259320 TRUE FALSE 769766.6962 328544.8014 489195.0179 346163.3374 594568.4825 471054.6333 631980.6908 456883.036 547528.8706 310128.789 2.482087196 1.059381821 1.577393119 1.116192207 1.917166363 1.51890005 2.037800788 1.473204205 1.765488694 1 18.24250793 KSS(ph)PSSPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.189)S(0.811)PS(0.001)SPAVR;KS(0.027)S(0.962)PS(0.009)S(0.002)PAVR;KS(0.041)S(0.954)PS(0.004)S(0.001)PAVR 139.48 2.51E-05 1530510000 676670 599760 648020 592470 869180 849870 752860 679900 704650 702940 TRUE FALSE 703385.4541 702764.1145 664907.9336 709658.7977 721437.0941 652500.5724 693848.866 670787.0526 679289.7841 840667.6344 0.836698625 0.835959523 0.790928432 0.84416096 0.858171606 0.776169494 0.825354561 0.797921824 0.808036085 1 19.68117601 -0.560111399 6.2021365 1 0.818289715 0.830372323 0.024502346 3.48E-10 0 0.023386064 0.005512148 0.275352232 0.560111399 -0.181710285 KSS(ph)SSSEDRNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSSSSEDRNR 11 2 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 KS(0.024)S(0.635)S(0.037)S(0.152)S(0.152)EDRNR 70.438 0.040768 100930000 43584 37460 48409 29841 83592 64900 47488 42088 57030 64061 TRUE FALSE 45304.72997 43893.4636 49670.57831 35743.46073 69383.0617 49827.95857 43765.76647 41523.8792 54977.50144 76612.52643 0.591348858 0.572928027 0.648334948 0.466548519 0.905635996 0.650389184 0.571261235 0.541998563 0.717604601 1 16.22529268 0.925082005 6.014868085 0.999984688 0.617881222 0.527575479 0.108799251 0.515173564 40.31353166 0.10398955 0.026148762 8.415540324 -0.925082005 -0.382103466 KSS(ph)TPEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.095)S(0.452)T(0.452)PEEVK;KS(0.129)S(0.552)T(0.319)PEEVK 82.85 0.010587 616820000 2171880 815243 1209470 792518 1743520 1685990 1798870 1228020 1362510 624326 TRUE FALSE 2257627.499 955254.6435 1240989.782 949275.695 1447157.093 1294444.374 1657869.869 1211560.401 1313473.531 746650.7263 3.02367281 1.279386211 1.66207537 1.27137852 1.938198199 1.73366787 2.220408835 1.622660178 1.759153892 1 19.510074 0.415782001 1.4528125 1.000124958 1.811394171 0.215063694 0.478445334 5.491817102 12.04528144 0.427607724 0.124150346 2.604845691 -0.415782001 0.811269213 KSS(ph)TTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KSSTTLR 7 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 KS(0.012)S(0.986)T(0.002)TLR;KS(0.004)S(0.988)T(0.006)T(0.001)LR;KS(0.014)S(0.819)T(0.084)T(0.084)LR;KS(0.001)S(0.976)T(0.006)T(0.017)LR;KS(0.001)S(0.99)T(0.003)T(0.006)LR 109.15 0.004345 2898660000 3029940 2179680 2890260 2224150 3474390 3159000 3291080 2780790 2996140 2136650 TRUE FALSE 3149564.371 2554023.084 2965582.55 2664080.232 2883814.429 2425370.125 3033116.55 2743518.059 2888309.507 2555285.659 1.232568406 0.999505897 1.160567915 1.042576286 1.128568314 0.949158117 1.186997054 1.073663936 1.130327444 1 21.28505315 -1.057975624 0.009219696 5.99E-07 2.099289121 0.105758138 0.082692614 17561.15719 30.45032497 3661.991273 3277.393442 0.087503289 1.057975624 2.099288522 KSS(ph)TVATLQGTPDHGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.131)S(0.61)T(0.259)VATLQGTPDHGDPR;KS(0.236)S(0.681)T(0.082)VATLQGTPDHGDPR 238.7 4.20E-24 7867300000 2349390 2042860 2176400 1811770 3207100 2927060 2373030 2311670 2606160 2223650 TRUE FALSE 2442145.731 2393705.314 2233118.772 2170132.698 2661958.288 2247294.675 2187025.708 2280685.845 2512364.811 2659331.643 0.918330641 0.90011538 0.839729327 0.816044401 1.000987708 0.845059954 0.822396753 0.85761618 0.944735425 1 21.34263228 1.041204784 3.932906444 0.999171827 0.872880482 0.378444696 0.052147923 0.191781384 6.520689795 0.050108324 0.012870797 10.99524179 -1.041204784 -0.126291345 KSS(ph)VNGSSATSSG ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSSVNGSSATSSG 13 1 R4GMX3;P35226 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 1 KS(0.308)S(0.688)VNGS(0.004)SATSSG;KS(0.373)S(0.626)VNGS(0.001)SATSSG;KS(0.219)S(0.556)VNGS(0.207)S(0.013)AT(0.005)SSG 117.06 0.00056826 1935300000 1298890 1141180 1460680 1215500 1886270 1872130 1795550 1653950 1717410 1310370 TRUE FALSE 1350171.18 1337168.788 1498746.521 1455922.272 1565642.499 1437356.18 1654810.099 1631781.506 1655600.75 1567111.913 0.861566535 0.853269493 0.956374914 0.929048053 0.999062343 0.917200723 1.055961661 1.041266735 1.056466188 1 20.57967678 3.785298558 0.481959726 1.045107766 0.806716374 0.7132855 0.038476608 1.025757979 0.34982149 0.028873389 0.12779865 6099.560708 -3.785298558 -0.238391392 KSSEAS(ph)PTAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSSEASPTAQR 11 1 J3KNN7;Q7Z569 J3KNN7 BRAP BRCA1-associated protein 1 KS(0.023)S(0.015)EAS(0.901)PT(0.061)AQR;KS(0.025)S(0.025)EAS(0.931)PT(0.019)AQR;KS(0.002)S(0.002)EAS(0.981)PT(0.014)AQR 142.38 3.99E-05 343113000 406494 358311 402284 323794 497120 506280 395576 374329 432665 395075 TRUE FALSE 422542.697 419848.127 412767.8515 387839.4868 412619.72 388704.1427 364569.7195 369311.732 417093.4712 472482.3821 0.894303604 0.888600597 0.873615329 0.820854918 0.873301811 0.822684945 0.771604896 0.781641276 0.882770421 1 18.84990101 3.909890309 3.265422983 0.833265456 0.890677077 0.017420469 0.062177059 0.508339743 10.30773711 0.015943986 0.032893902 8126.252425 -3.909890309 0.057411622 KSSGEIVYCGQVFEKS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSGEIVYCGQVFEKSPLR 19 2 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 1 KSSGEIVYCGQVFEKS(1)PLR 85.849 0.0015502 525700000 895760 128510 194880 110690 271430 459170 257670 199090 264490 157760 TRUE FALSE 931125.2965 150580.5928 199958.7329 132584.1516 225292.4256 352534.7263 237473.1521 196421.5242 254971.0566 188670.0515 4.935204549 0.798116032 1.059832927 0.702730246 1.194108041 1.868525097 1.258669037 1.041084807 1.35141245 1 17.52550591 4.741811638 24.99954328 1.151157251 4.935205949 0.932523443 0.306129457 75.0131274 576805.7487 0.076925714 0.554208736 55183.80439 -4.741811638 3.784048698 KSSLVT(ph)SK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.043)S(0.218)LVT(0.69)S(0.049)K 130.98 0.0019819 2270600000 5562300 3179700 4893900 3104200 6338700 4863500 5360300 4340700 5345300 2547000 TRUE FALSE 5781903.899 3725788.74 5021439.054 3718201.495 5261250.038 3734025.832 4940145.679 4282520.016 5152923.697 3046035.885 1.898173271 1.223159832 1.648516053 1.220668973 1.72724493 1.225864032 1.621827801 1.405932227 1.691681875 1 21.53850151 -1.738420709 2.557737011 0.893017664 1.499506476 0.313326944 0.22861582 40007900.35 29733191.12 27132282.1 0.047855376 0.018263302 1.738420709 0.606488812 KSSPS(ph)KDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSPSKDR 8 2 Q9BUQ8;F8VVA2;F8W1J5;Q9BUQ8-2 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 KS(0.135)S(0.135)PS(0.73)KDR 59.908 0.049908 211250000 305240 115270 190260 108390 284650 258860 243480 188430 254290 110740 TRUE FALSE 317291.1109 135066.7258 195218.3319 129829.2185 236265.2947 198743.6881 224395.4014 185904.4041 245138.1526 132437.3828 2.395782099 1.019853481 1.474042509 0.980306435 1.783977377 1.50066155 1.694350921 1.403715478 1.850974004 1 17.01495088 KSSPS(ph)SPAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSPSSPAVR 10 1 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 KS(0.092)S(0.05)PS(0.429)S(0.429)PAVR 86.911 0.01402 75139000 203960 175800 196620 163000 253140 257770 232810 209170 212860 151220 TRUE FALSE 212012.4983 205992.2825 201744.0787 195240.9135 210111.3532 197906.824 214561.7439 206366.4183 205199.2102 180848.6637 1.17231996 1.139031266 1.115540887 1.079581731 1.161807607 1.094322844 1.186415976 1.141100045 1.134645985 1 17.46442341 0.881672649 16.5919769 1 1.136107799 0.627382173 0.031464836 2415.177976 338663.1491 0.029666317 0.007416579 7.615048069 -0.881672649 0.136107799 KSSS(ph)LESLQTAVAEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSSLESLQTAVAEVR 16 1 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 KS(0.114)S(0.114)S(0.771)LESLQTAVAEVR 187.06 8.58E-10 186110000 71973 73346 68316 62150 85432 95232 70408 69043 74508 66721 TRUE FALSE 74814.54962 85942.60495 70096.37108 74443.0845 70910.29916 73115.81125 64889.23698 68117.59152 71826.47163 79793.7025 0.937599676 1.077059997 0.878469966 0.932944357 0.88867037 0.916310548 0.813212509 0.853671272 0.900152135 1 16.28398727 4.219262638 24.97529444 0.888073834 1.007329841 0.364092324 0.056647133 185.0632027 239507.9588 0.013581766 0.029409244 16567.71586 -4.219262638 0.119256006 KSSS(ph)LESLQTAVAEVTLNGDIPFHRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSSLESLQTAVAEVTLNGDIPFHRPR 27 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 KS(0.231)S(0.231)S(0.531)LES(0.006)LQTAVAEVTLNGDIPFHRPR 73.239 0.009618 49326000 82149 53026 73568 48767 79426 70196 77879 73251 50813 46881 TRUE FALSE 85392.30595 62132.80301 75485.24252 58412.96705 65925.19689 53894.04283 71774.64048 72269.19016 48984.25006 56066.43436 1.523055763 1.108199651 1.346353543 1.041852718 1.175840726 0.96125326 1.280171306 1.288992086 0.873682277 1 15.7748497 7.398763849 1.135174509 1.132528507 200 0.389009507 0.148636134 911.1296277 2.940229168 0.041394666 469655.9915 25047469.05 -7.398763849 198.8674715 KSSSISEEKGDS(ph)DDEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSSISEEKGDSDDEKPR 18 3 S4R3H4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR;KSSSISEEKGDS(1)DDEKPR 192.58 1.19E-14 1217710000 3705480 603408 1135400 535663 1988640 2355040 1759690 1196160 1351040 366072 TRUE FALSE 3851775.212 707038.6301 1164989.457 641615.5426 1650611.683 1808117.651 1621760.9 1180127.432 1302416.334 437796.7995 8.798089013 1.614992688 2.661027806 1.46555558 3.770268958 4.130038531 3.704369017 2.695605434 2.97493343 1 18.73990188 4.745553507 24.9979123 2.805083282 8.798091778 0.770421094 1.001317612 394.1335707 1408897.988 0.239634005 2.414400279 55661.32078 -4.745553507 5.993008496 KSST(ph)PEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 1 KS(0.055)S(0.055)T(0.89)PEEVK;KSS(0.077)T(0.923)PEEVK;KS(0.012)S(0.156)T(0.833)PEEVK 149.96 5.06E-05 2024740000 6437400 2558140 3857000 2402860 5479900 5385100 5373300 3851690 4460350 2031430 TRUE FALSE 6691553.523 2997480.645 3957516.589 2878138.536 4548428.555 4134492.137 4952126.705 3800064.396 4299822.875 2429449.814 2.754349352 1.233810482 1.628976472 1.18468738 1.872205192 1.70182241 2.03837374 1.564166657 1.769875158 1 21.2121982 -1.065617452 3.318256451 0.999439736 1.717618886 0.220668691 0.418815299 25743695 41091035.41 162312.5549 0.092636534 0.085977052 1.065617452 0.71817915 KSST(ph)VATLQGTPDHGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSSTVATLQGTPDHGDPR 18 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 KS(0.29)S(0.29)T(0.415)VAT(0.004)LQGTPDHGDPR 112.45 0.00016142 2904400000 595260 484310 534390 458570 806430 652400 573840 538860 610360 525990 TRUE FALSE 618761.3244 567486.4751 548316.6424 549273.7773 669353.3166 500889.9872 528860.9213 531637.4631 588393.2628 629047.6698 0.983647749 0.902135883 0.871661511 0.873183073 1.064074074 0.796267137 0.840732661 0.845146542 0.935371501 1 19.26280982 KSSTPEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KSSTPEEVK 9 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 160.18 0.00010501 9072600000 7504840 4178950 5907020 4143720 8467940 7551270 7500720 5870810 6606220 3976790 FALSE TRUE 7801136.878 4896652.155 6060961.794 4963335.448 7028562.583 5797601.983 6912793.967 5792121.395 6368463.433 4755965.86 1.640284457 1.029581014 1.274391359 1.043601993 1.477841261 1.219016737 1.453499493 1.217864376 1.33904734 1 22.18130693 -1.183764518 4.946146608 0.9999736 1.287631295 0.195667903 0.180718255 4.74E-05 7.83E-06 0.157721103 0.037171812 0.065499123 1.183764518 0.287657696 KSSTPEEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSSTPEEVKK 10 2 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 115.14 0.0007103 3130430000 4657580 1973900 3214270 1946210 5351850 3847030 4369400 2936300 4301200 1552750 FALSE TRUE 4841464.855 2312901.97 3298036.517 2331164.529 4442144.449 2953615.585 4026915.011 2896943.701 4146400.652 1856981.633 2.60716895 1.24551688 1.776019998 1.255351419 2.392131602 1.590546472 2.168527108 1.560028193 2.232871116 1 20.82452812 -0.687905822 6.532169698 0.999999998 1.830469798 0.249942045 0.447384938 8.68E-09 3.10E-09 0.388145114 0.09148668 0.205160703 0.687905822 0.8304698 KST(ph)AALEEDAQILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.362)T(0.638)AALEEDAQILK 131.25 0.00011092 71684000 161340 86266 130360 87483 176970 174490 171180 140290 147320 85690 TRUE FALSE 167709.8278 101081.5144 133757.2887 104786.8763 146888.7026 133967.3419 157762.4643 138409.642 142017.982 102479.3149 1.636523702 0.98636017 1.305212558 1.022517339 1.433349772 1.307262271 1.539456665 1.350610532 1.385820955 1 16.64497321 3.174970233 24.99999557 1.365567023 1.224513711 0.037411217 0.2112557 144.9786043 56995.78056 0.056240392 0.067220148 1496.133105 -3.174970233 -0.141053312 KSTDEPSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSTDEPSEK 9 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 73.499 0.070145 56769000 213280 99636 152950 120570 223250 212240 251180 148520 191610 94515 FALSE TRUE 221700.4591 116747.7079 156936.0026 144418.3861 185302.0447 162950.4765 231491.8553 146529.3323 184713.9935 113033.4047 1.961371152 1.032860227 1.388403748 1.277661118 1.639356483 1.441613451 2.047995068 1.296336537 1.634154028 1 16.78638967 -0.835558348 5.591438943 0.999999844 1.506999567 0.219000479 0.295455537 5.40E-07 1.12E-07 0.26841521 0.063266053 0.146029854 0.835558348 0.506999723 KSTDEPSEKDALQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSTDEPSEKDALQPGR 16 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ; 171.26 2.80E-09 593960000 318770 186037 242938 143415 319230 286900 226213 258100 290400 168170 FALSE TRUE 331355.2857 217987.4076 249269.1639 171782.0589 264967.3986 220271.823 208481.834 254640.5917 279948.5607 201119.6917 1.647552674 1.083869042 1.23940705 0.854128492 1.317461241 1.095227529 1.036605775 1.266114668 1.391950029 1 17.61769482 4.74319386 24.81661713 1.149432677 1.647552897 0.490025973 0.154356646 362.6132093 1942157.764 0.03529573 0.284446721 55359.71678 -4.74319386 0.49812022 KSTGSVDYLALDFQPS(ph)SPSPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSTGSVDYLALDFQPSSPSPHR 22 1 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 KSTGSVDYLALDFQPS(0.555)S(0.401)PS(0.043)PHR 71.86 0.0074874 105110000 175800 164010 167870 151490 228090 236570 203280 187100 198680 154880 TRUE FALSE 182740.7197 192177.4417 172244.8301 181454.2698 189319.3433 181630.2028 187346.3824 184592.2305 191529.5456 185225.7706 0.986583666 1.037530798 0.92991828 0.979638358 1.022100449 0.980588188 1.011448794 0.996579633 1.034032926 1 17.49892531 2.220437275 0.977293938 1.012285252 0.987781755 0.108801341 0.028374911 1.384874853 2.511862753 0.020985137 0.011734351 166.1258725 -2.220437275 -0.024503497 KSVAAEGALLPQTPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSVAAEGALLPQTPPSPR 18 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 KSVAAEGALLPQT(0.039)PPS(0.961)PR;KSVAAEGALLPQT(0.145)PPS(0.855)PR 143.32 6.51E-08 663040000 816890 753580 849990 694400 934810 1037180 878180 882800 944540 848300 TRUE FALSE 849141.448 883001.503 872141.4377 831750.2474 775911.3301 796310.6636 809345.9569 870967.51 910546.1899 1014508.143 0.836998159 0.870373992 0.859669233 0.819855664 0.76481528 0.78492289 0.79777177 0.858512093 0.897524772 1 19.95234901 0.986649235 1.603428004 0.99860115 0.820102089 0.761044412 0.031157935 0.216639439 1.142984807 0.033763815 0.009836441 9.697264359 -0.986649235 -0.178499061 KSVQPTSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KSVQPTSEER 10 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 Q9UHD8 9-Sep Septin-9 0 ; 153.34 2.63E-05 965950000 444190 410480 492170 446420 512800 558080 546450 513550 502020 412760 FALSE TRUE 461726.9642 480976.7469 504996.3545 534720.5436 425634.4392 428474.3778 503617.8211 506666.7022 483952.3983 493632.4192 0.935365965 0.974362153 1.023021047 1.083236276 0.862249768 0.868002913 1.020228416 1.026404836 0.980390224 1 18.91307762 KSVS(ph)NGALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSVSNGALR 9 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 KS(0.005)VS(0.995)NGALR 92.781 0.0060294 318230000 294530 389130 379300 336840 524940 484860 433210 408560 440530 367690 TRUE FALSE 306158.2718 455960.0505 389184.8696 403465.9466 435710.8863 372258.6131 399253.8682 403083.9215 424675.4114 439731.8156 0.696238618 1.036904846 0.885050514 0.917527302 0.990855951 0.846558288 0.907948559 0.916658534 0.96576003 1 18.74626439 KSYESSEDCSEAAGS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSYESSEDCSEAAGSPAR 18 1 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 KSYESSEDCSEAAGS(1)PAR 178.79 5.33E-14 438460000 245590 200250 236210 199890 298320 310050 275610 236740 266180 221940 TRUE FALSE 255286.0828 234641.3798 242365.8266 239427.6454 247611.673 238045.5864 254006.968 233566.8875 256600.2338 265424.8937 0.961801583 0.884021753 0.913123947 0.90205422 0.932887905 0.896847251 0.956982461 0.879973556 0.966752704 1 18.01794416 1.034970193 5.858861558 0.999853299 0.91478967 0.527708409 0.026417831 0.101897944 9.082391978 0.022778289 0.005733085 10.83852523 -1.034970193 -0.085063628 KSYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KSYSPR 6 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 KS(0.085)Y(0.002)S(0.913)PR 63.486 0.068667 196660000 633240 598910 740370 590840 765830 749000 801330 803120 711670 648840 TRUE FALSE 658240.8042 701768.1336 759664.6504 707706.3885 635654.4901 575056.1012 738519.6607 792355.49 686057.1357 775967.7752 0.848283685 0.904377934 0.978989946 0.912030642 0.819176402 0.741082452 0.951740116 1.021119066 0.884130962 1 19.56563722 2.021722525 24.99996452 0.974679883 0.871634181 0.330809189 0.067503273 281.2431528 323674.9612 0.027177745 0.020070728 105.1289981 -2.021722525 -0.103045703 KT(ph)ASFGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KTASFGNILDVPEIVISGNGQPR 23 1 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 KT(0.773)AS(0.227)FGNILDVPEIVISGNGQPR;KT(0.612)AS(0.388)FGNILDVPEIVISGNGQPR;KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR;KT(0.5)AS(0.5)FGNILDVPEIVISGNGQPR 277.45 4.98E-52 2921556000 2193232 1964341 2189072 1956704 2755433 2798887 2473469 2262440 2316455 1931412 TRUE FALSE 2279822.493 2301701.286 2246121.015 2343734.211 2287065.483 2148887.912 2279592.037 2232115.692 2233086.237 2309835.202 0.987006558 0.996478573 0.972416133 1.014675943 0.990142275 0.930320877 0.986906786 0.96635279 0.966772969 1 21.13935849 2.963741533 24.99995218 0.968388277 0.992840302 0.244289664 0.01933734 733.7519103 505916.7075 0.005541019 0.005879032 919.9019366 -2.963741533 0.024452025 KT(ph)GSYGALAEITASK ddPTM_MDA-MB-175_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(0.5)GS(0.5)YGALAEITASK 154.84 1.41E-06 145030000 95806 68839 85854 63393 117680 104610 88594 81669 94584 62415 TRUE FALSE 99588.49486 80661.56276 88091.42577 75931.94619 97676.79563 80315.91288 81649.77078 80574.36064 91179.94032 74644.02424 1.33417907 1.08061648 1.180153759 1.017254187 1.308568189 1.075985837 1.093855424 1.079448241 1.22153034 1 16.18773915 6.990926331 0.016947255 9.83E-07 2.481709051 0.206823554 0.098555678 6006.561034 9.314087652 550.5151198 840.9529164 9793238.502 -6.990926331 2.481708067 KT(ph)MELLQSDMNQHFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTMELLQSDMNQHFLK 16 1 A0A6I8PIP2;A0A6I8PU78;A0A6I8PIF8;A0A5F9ZHQ6;O75071 A0A6I8PIP2 EFCAB14 EF-hand calcium-binding domain-containing protein 14 1 KT(0.872)MELLQS(0.128)DMNQHFLK 53.278 0.052691 563210000 12541 444750 661640 432900 861520 673820 748640 645050 813260 349900 TRUE FALSE 13036.12836 521132.3528 678882.8819 518526.3279 715079.1381 517335.5168 689959.6406 636404.1598 783990.9315 418456.2058 0.03115291 1.24536892 1.622351091 1.239141207 1.7088506 1.236295483 1.648821624 1.520838145 1.873531616 1 18.67471712 4.690051877 3.634020486 1.497321702 6.84E-15 0.751841905 0.248057859 0.103574937 2.429498754 0.054379511 0.383176348 48983.73278 -4.690051877 -1.497321702 KT(ph)MEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTMEVK 6 1 Q68D51-2;Q68D51 Q68D51-2 DENND2C DENN domain-containing protein 2C 1 KT(1)MEVK 53.466 0.062247 0 343900 286190 365000 253490 566200 484090 408780 414120 438060 322660 TRUE FALSE 357477.4375 335340.9063 374512.1999 303629.5654 469957.5262 371667.434 376738.7555 408569.3988 422294.3062 385879.0493 0.926397632 0.86903113 0.970542973 0.786851647 1.217888162 0.963170803 0.97631306 1.058801714 1.094369614 1 18.55778919 3.254673225 24.99999733 1.045739803 0.892717482 0.496266989 0.080535868 211.2131527 327712.1655 0.021403201 0.028892991 1797.517904 -3.254673225 -0.153022322 KT(ph)PESFLGPNAALVDLDSLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KTPESFLGPNAALVDLDSLVSR 22 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.969)PES(0.031)FLGPNAALVDLDSLVSR;KT(0.978)PES(0.022)FLGPNAALVDLDSLVSR;KT(0.5)PES(0.5)FLGPNAALVDLDSLVSR 191.22 8.80E-18 339400000 194721 132174.2 173769.9 158706.4 169489.4 186915.3 270725.9 149955.5 169653.4 111292.2 TRUE FALSE 202408.7354 154874.0907 178298.4863 190098.0522 140679.6523 143507.0543 249505.6965 147945.5918 163547.6073 133097.7758 1.520752201 1.163611411 1.339605304 1.42825867 1.056964713 1.078207757 1.874604554 1.111555704 1.228777914 1 17.02212694 1.038906827 1.962592131 1.013906853 1.325342314 0.153588902 0.234638951 0.606661649 4.825871094 0.214640674 0.060577433 10.93721696 -1.038906827 0.311435461 KT(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 KT(0.66)PES(0.34)FLGPNAALVDLDSLVSRPGPTPPGAK 244.53 2.06E-44 978390000 425920 186520 297820 194220 386000 344780 420020 292130 315740 126650 TRUE FALSE 442735.6505 218553.3591 305581.4339 232636.1363 320387.8579 264710.0702 387097.7349 288214.4752 304376.5791 151464.6426 2.92302971 1.442933184 2.017510018 1.535910509 2.115265004 1.747669064 2.555697014 1.902849868 2.009555324 1 17.20862153 4.754568455 24.41117944 1.882035149 2.923030802 0.392027168 0.406437912 2287.471097 3488202.233 0.089543733 2.256140441 56828.79603 -4.754568455 1.040995653 KT(ph)S(ph)LS(ph)LT(ph)PDVP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSLSLTPDVP 11 1 C9JHQ1 C9JHQ1 SMARCAL1 4 KT(1)S(1)LS(1)LT(1)PDVP 45.257 0.063434 243560000 0 6066.3 11986 0 7214.4 12374 5744.1 0 0 7514.7 TRUE FALSE 0 7108.139836 12298.36501 0 5988.098865 9500.32603 5293.862433 0 0 8987.061587 0 0.790930358 1.36845229 0 0.666302195 1.057111486 0.589053761 0 0 1 13.13363377 1.90134371 7.283261861 0.234840071 0.671019817 0.068819547 0.473974208 0.515862344 33.33166346 0.199038529 0.123572837 79.67896981 -1.90134371 0.436179746 KT(ph)SDANETEDHLESLICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KTSDANETEDHLESLICK 18 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.552)S(0.441)DANET(0.007)EDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.5)S(0.5)DANETEDHLESLICK;KT(0.499)S(0.499)DANET(0.002)EDHLESLICK 260.99 6.98E-31 2587990000 2771460 1443250 2207980 1696920 3254870 2951420 3486600 2607040 2905300 1363120 TRUE FALSE 2880879.381 1691116.961 2265521.773 2032565.711 2701608.36 2265997.434 3213311.181 2572096.893 2800738.821 1630197.265 1.767196794 1.037369524 1.389722471 1.246821936 1.657227881 1.390014253 1.971118005 1.577782608 1.718036755 1 20.63661512 3.23365145 24.99389418 1.601531214 1.339316003 0.078742629 0.290820043 214.2169318 1090636.017 0.077311634 0.095189484 1712.582294 -3.23365145 -0.26221521 KT(ph)SDDGGDSPEHDTDIPEVDLFQLQVNTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSDDGGDSPEHDTDIPEVDLFQLQVNTLR 30 1 Q9HAJ7 Q9HAJ7 SAP30L Histone deacetylase complex subunit SAP30L 1 KT(0.457)S(0.457)DDGGDS(0.085)PEHDTDIPEVDLFQLQVNTLR 180.33 5.49E-18 47736000 78410 66643 88017 67818 109710 103470 102660 98702 92234 72476 TRUE FALSE 81505.68735 78088.41684 90310.79533 81232.19798 91061.53339 79440.6606 94613.24095 97379.06113 88914.51636 86676.28456 0.940345883 0.900920214 1.041932009 0.937190587 1.05059341 0.916521295 1.091570104 1.123479873 1.025822886 1 16.40334969 2.22638998 24.99914538 1.076935976 0.967870291 0.39313121 0.056620067 195.7515495 402081.5211 0.020492598 0.015246405 168.4185716 -2.22638998 -0.109065686 KT(ph)SFDQDSDVDIFPSDFPTEPPSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.375)S(0.375)FDQDS(0.249)DVDIFPSDFPTEPPSLPR 58.861 0.0096643 0 51859 30686 39115 39223 53441 42973 43282 43404 36830 23584 TRUE FALSE 53906.43336 35956.0818 40134.36903 46981.19233 44357.11791 32993.17201 39889.44374 42822.24037 35504.49549 28204.83326 1.911248078 1.274819868 1.422960691 1.665714238 1.572677899 1.169770149 1.414276886 1.518258945 1.258808913 1 14.78365479 -3.297212882 0.116047389 1.17E-13 1.749328419 0.45358104 0.184174644 98.19726211 1.126004567 26.5625186 2.191541004 0.000504414 3.297212882 1.749328419 KT(ph)SLDVSNSAEPGFLAPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.646)S(0.354)LDVSNSAEPGFLAPGAR;KT(0.647)S(0.353)LDVSNSAEPGFLAPGAR 227.03 2.35E-25 663980000 487210 370130 467990 362820 623980 566220 536140 448880 524770 408970 TRUE FALSE 506445.427 433696.9483 480186.2039 434584.7131 517916.1025 434723.9861 494115.9459 442863.4978 505883.6302 489099.8413 1.035464305 0.886724778 0.981775424 0.888539878 1.05891693 0.888824631 1.010255789 0.905466452 1.03431567 1 18.89976947 1.218988862 24.99954688 1.017157876 0.954570917 0.13264916 0.061285016 490.596854 626636.7942 0.051189535 0.012868358 16.557275 -1.218988862 -0.062586959 KT(ph)SPASLDFPESQK ddPTM_MDA-MB-175_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)PAS(0.001)LDFPESQK;KT(0.5)S(0.5)PASLDFPESQK;KT(0.5)S(0.5)PASLDFPESQK 203.89 8.44E-09 4038660000 3722280 1995090 2736490 1879790 3739820 3454410 3558680 2847050 3044180 1690780 TRUE FALSE 3869238.489 2337731.188 2807805.177 2251606.851 3104126.732 2652175.63 3279741.363 2808889.952 2934620.556 2022055.969 1.913517008 1.156115965 1.388589248 1.113523506 1.535133933 1.311623254 1.621983473 1.389125719 1.451305306 1 20.9473915 -1.354323912 4.774855845 0.999654597 1.418153546 0.258255564 0.218230055 0.000733512 9.92E-05 0.193154936 0.045490147 0.04422584 1.354323912 0.418498948 KT(ph)SQSEEEEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSQSEEEEAPR 12 1 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 KT(0.67)S(0.32)QS(0.01)EEEEAPR 138.01 0.00025854 0 141020 91403 137020 112710 181840 165720 158180 131400 151690 102120 TRUE FALSE 146587.5785 107100.7542 140590.8538 135003.7016 150930.9018 127234.0415 145781.4383 129638.7979 146230.7065 122128.4588 1.200273711 0.876951656 1.151171931 1.105423772 1.235837275 1.04180502 1.193672955 1.061495406 1.197351608 1 16.8980399 KTAPTLS(ph)PEHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KTAPTLSPEHWK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 KT(0.078)APT(0.232)LS(0.689)PEHWK;KTAPT(0.006)LS(0.994)PEHWK;KT(0.003)APT(0.039)LS(0.958)PEHWK 153.23 3.31E-05 1099230000 1625420 1111240 1437080 1056560 1841380 1750460 1646790 1464050 1550050 1110890 TRUE FALSE 1689592.837 1302086.826 1474531.485 1265544.414 1528382.885 1343942.193 1517710.297 1444426.804 1494264.003 1328547.626 1.271759328 0.980082912 1.109882293 0.952577378 1.150416331 1.011587516 1.142383056 1.087222449 1.124734992 1 20.34141852 KTATNDEESPLS(ph)VSSPEGTGTWLHYTSGVGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 33 1 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 KTATNDEESPLS(0.464)VS(0.464)S(0.07)PEGTGT(0.001)WLHYTSGVGTGR 190.89 1.82E-20 386910000 116160 172650 203670 156320 255840 273230 185130 226370 216410 226280 TRUE FALSE 120746.0865 202301.2945 208977.8075 187239.6294 212352.4082 209776.4733 170619.0269 223335.8804 208621.4464 270615.2336 0.446191018 0.74756063 0.772232238 0.691903508 0.784702344 0.775183535 0.63048567 0.825289388 0.770915383 1 18.04588353 -4.999999995 0.040074841 2.227466167 0.003084476 0.551590855 0.089989133 676.6414517 2.025795802 101.2751257 30.41524372 1.00E-05 4.999999995 -2.224381692 T(ph)YSDTDSCSDIPLEDPDRPVHCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TYSDTDSCSDIPLEDPDRPVHCSK 24 1 Q9HB20 Q9HB20 PLEKHA3 Pleckstrin homology domain-containing family A member 3 1 T(0.494)Y(0.1)S(0.405)DT(0.002)DSCSDIPLEDPDRPVHCSK;T(0.461)Y(0.014)S(0.372)DT(0.153)DSCSDIPLEDPDRPVHCSK 161.5 2.82E-11 298460000 99763 359410 401790 391830 487570 625280 386560 500970 441610 352920 TRUE FALSE 103701.7203 421135.8717 412260.9775 469332.8045 404693.0256 480068.1962 356260.4171 494255.3166 425716.5424 422067.9169 0.245699131 0.997791717 0.976764546 1.11198408 0.958833897 1.137419304 0.844083151 1.171032663 1.008644641 1 18.68711564 4.740871701 4.859978742 1.031945129 0.202243585 0.868827691 0.090636097 0.052781472 3.677129593 0.019903954 0.148322971 55064.50011 -4.740871701 -0.829701544 down KTEAAATTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTEAAATTR 9 1 E7EVA0;P27816-4;B5MEG9;P27816-6;P27816;P27816-2 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 ; 122.51 0.00093603 338860000 318880 313910 359710 277360 435830 425520 376650 362960 368840 354150 FALSE TRUE 331469.6286 367821.6006 369084.3381 332220.9802 361747.7723 326699.4288 347127.1888 358095.1149 355565.5204 423538.9119 0.782619068 0.868448188 0.871429585 0.784393053 0.854107526 0.771356349 0.819587478 0.84548339 0.83951087 1 18.692135 0.239959994 1.118678644 1.000491683 0.824891673 0.703865307 0.033985651 2.353909413 2.978200781 0.033778131 0.009730591 1.737640754 -0.239959994 -0.175600009 KTEEIAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KTEEIAQER 9 1 Q9NQT8;E7ERX9;A0A1B0GUA8;Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;Q9H1H9 Q9NQT8;A0A1B0GUA8 KIF13B;KIF13A Kinesin-like protein KIF13B;Kinesin-like protein;Kinesin-like protein KIF13A 0 ;;;; 150.46 0.00013661 2019986000 1287130 1063240 1195750 1089490 1465530 1473580 1332310 1253480 1275840 1060550 FALSE TRUE 1337946.886 1245843.199 1226912.227 1304987.87 1216419.734 1131363.377 1227880.061 1236679.151 1229922.768 1268344.467 1.05487659 0.98225934 0.967333606 1.028890734 0.959061017 0.892000089 0.968096675 0.975034135 0.969707205 1 20.27451519 7.9999996 0.81958034 0.964681779 25.90152625 0.371543074 0.032701714 621.576797 1.958136644 0.011177235 28833.11844 99999908.01 -7.9999996 24.93684447 KTEELEEESFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTEELEEESFPER 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 148.57 6.95E-05 764040000 565770 419810 502990 365930 622940 614620 565870 502170 567580 406530 FALSE TRUE 588107.0365 491909.1018 516098.3326 438309.8618 517052.8813 471883.8197 521515.6308 495439.2325 547152.9067 486181.77 1.209644361 1.011780227 1.061533699 0.901534958 1.063497056 0.970591348 1.072676235 1.019041155 1.12540811 1 18.89113627 4.740962347 24.82159092 1.024469488 1.209644433 0.472452377 0.058493073 165.0593334 1705749.787 0.013043416 0.087531297 55075.9944 -4.740962347 0.185174945 KTEKEESTEVLK ddPTM_MDA-MB-175_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 ; 156.74 3.75E-05 1074640000 2002410 791420 1395660 813640 2125470 1696590 1731760 1398860 1800020 709480 FALSE TRUE 2081466.693 927340.2286 1432032.046 974575.5635 1764183.369 1302582.685 1596020.126 1380110.57 1735237.632 848489.0222 2.453145107 1.092931322 1.687743752 1.148601264 2.079205885 1.535179184 1.881014467 1.626550885 2.045091435 1 19.69453647 3.224030574 24.99893592 1.723827282 1.5662812 0.007300593 0.449776264 1043.355105 1795089.558 0.119277187 0.143162401 1675.060797 -3.224030574 -0.157546083 KTEPATGFIDGDLIESFLDISRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTEPATGFIDGDLIESFLDISRPK 24 2 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 248.47 2.40E-38 1103750000 862350 508870 721190 521960 1035790 875200 908750 744940 785010 568660 FALSE TRUE 896396.2439 596264.464 739984.8039 625202.1301 859726.7858 671948.0638 837519.8004 734955.2978 756757.6434 680078.0393 1.318078503 0.876758886 1.088088074 0.919309394 1.264159017 0.988045526 1.231505433 1.08069259 1.112751184 1 19.37534078 3.250903476 24.99904662 1.116749861 1.040825177 0.045119455 0.136819892 641.7269685 1299736.626 0.034681496 0.046617003 1781.982669 -3.250903476 -0.075924684 KTES(ph)PIKLSPATPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTESPIKLSPATPSR 15 2 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 KTES(1)PIKLSPATPSR 137.89 7.28E-06 98791000 189970 94760 134580 86060 204180 181930 160960 136340 167980 92694 TRUE FALSE 197470.1623 111034.2929 138087.2654 103082.4111 169473.5565 139679.5147 148343.5346 134512.5853 161934.4326 110855.6146 1.781327568 1.001611811 1.245649721 0.92987993 1.528777385 1.260012993 1.338168889 1.213403451 1.460768886 1 16.75832232 -1.267415935 4.1821213 0.999753301 1.285708214 0.12733096 0.235146118 0.000494634 8.66E-05 0.20821243 0.049034085 0.054023668 1.267415935 0.285954913 KTESASVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTESASVQGR 10 1 Q9P2E9;A0A087WVV2;V9GY78 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 161.93 1.11E-05 379120000 206601 183210 198047 180439 249010 251020 212266 190139 186218 166667 FALSE TRUE 214757.767 214674.8923 203208.2675 216129.2956 206683.3691 192724.4092 195628.0363 187590.4977 179516.0506 199322.2076 1.077440239 1.077024456 1.019496372 1.084321201 1.036930965 0.96689883 0.981466333 0.941141983 0.900632462 1 17.60474293 2.72391163 1.78826382 0.949275107 1.06389464 0.746728177 0.029702079 0.170031075 1.080463774 0.011251272 0.010890259 529.5556793 -2.72391163 0.114619533 RS(ph)SLPLDHGSPAQENPESEK ddPTM_MDA-MB-175_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(0.499)S(0.499)LPLDHGS(0.003)PAQENPESEK;RS(0.468)S(0.468)LPLDHGS(0.063)PAQENPESEK;RS(0.335)S(0.335)LPLDHGS(0.33)PAQENPESEK;RS(0.463)S(0.463)LPLDHGS(0.074)PAQENPESEK 206.59 3.53E-22 1615760000 325580 832950 960850 845870 1146050 1270330 1026090 1154840 1032680 936920 TRUE FALSE 338434.1498 976002.683 985890.5403 1013180.561 951244.8304 975315.1095 945662.3846 1139361.259 995514.0485 1120491.536 0.302040791 0.871048689 0.87987326 0.904228661 0.84895316 0.870435053 0.84397102 1.016840576 0.888461909 1 20.09570032 4.74132846 4.490069945 0.904956014 0.260288333 0.914343355 0.055241001 0.053333771 2.726329517 0.013728363 0.109339741 55122.44334 -4.74132846 -0.644667681 down KTET(ph)QEKNPLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 KT(0.153)ET(0.847)QEKNPLPSK 110.22 0.051277 343330000 689290 200710 483450 306790 616730 483860 667910 351160 506180 163540 TRUE FALSE 716503.7014 235180.3812 496049.1042 367472.1463 511898.4549 371490.848 615557.4689 346453.2746 487962.6807 195582.5318 3.663434023 1.202461074 2.536264867 1.878859747 2.617301505 1.899407092 3.147302896 1.771391705 2.494919542 1 17.577418 -1.824601479 0.666530423 2.17E-06 2.309221795 0.262201697 0.677485105 198.5649692 24.6795804 314.818032 0.221399572 0.014976093 1.824601479 2.309219624 KTETQEKNPLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;; 119.45 0.00019575 3562818000 3053350 1586420 2355470 1646210 2838600 2510830 3041310 2315880 2612420 1148149 FALSE TRUE 3173898.616 1858875.294 2416855.483 1971825.425 2356095.786 1927727.784 2802924.175 2284839.417 2518399.515 1373106.814 2.311472482 1.353773265 1.760136545 1.436032073 1.715886748 1.403916844 2.0413009 1.663992483 1.834088571 1 20.38901243 -1.985557759 2.604762971 0.351711718 1.707041049 0.373422657 0.280728858 24037363.91 12396712.12 93734337.71 0.06142952 0.010338136 1.985557759 1.355329331 KTETQEKNPLPSKETIEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTETQEKNPLPSKETIEQEK 20 3 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ; 184.38 1.76E-17 3337300000 2353400 896610 1555830 656170 2514400 1682750 1576210 1396080 1902560 794460 FALSE TRUE 2446314.049 1050595.793 1596376.208 785958.4675 2087003.186 1291956.815 1452662.542 1377367.831 1834087.237 950119.2261 2.574744287 1.105751535 1.680185143 0.827220885 2.196569787 1.359783887 1.528926583 1.449678938 1.93037588 1 19.85774904 -2.105019726 2.219662953 4.83E-05 1.584633594 0.125377567 0.485626246 6911531.799 1792483.082 34895978.1 0.116404212 0.007852 2.105019726 1.584585259 KTEVLMENFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTEVLMENFR 10 1 Q9Y265;Q9Y265-2;E7ETR0 Q9Y265 RUVBL1 RuvB-like 1 0 ; 112.51 0.0025842 354480000 627570 599040 682340 537070 1280990 1014530 821230 740830 770190 987770 FALSE TRUE 652346.9482 701920.4601 700122.3409 643300.843 1063247.777 778920.7829 756859.8467 730900.3856 742471.0123 1181304.62 0.55222585 0.594190904 0.592668757 0.544568126 0.900062321 0.659373349 0.640698287 0.61872304 0.628517827 1 20.17194961 -5 0.356034368 5.324816361 0.627627267 0.570605592 0.094593539 349.6725277 2.815704821 1157.527119 0.07207051 1.00E-05 5 -4.697189094 KTFEINPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTFEINPR 8 1 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ; 156.92 0.00061773 1842270000 1925640 2011480 2035830 2027140 2442600 2622600 1911190 2027940 1969830 2040800 FALSE TRUE 2001665.754 2356936.043 2088885.402 2428102.242 2027407.724 2013540.896 1761385.934 2000758.781 1898936.203 2440655.687 0.820134427 0.965697888 0.855870582 0.994856528 0.830681581 0.824999981 0.721685547 0.819762817 0.778043463 1 21.21883735 3.025214294 24.01028304 0.811054605 0.90979914 0.171624767 0.081458402 188.2623139 179270.5174 0.021698387 0.025933345 1059.776521 -3.025214294 0.098744534 KTFLDKDAQRLS(ph)PIPEEVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTFLDKDAQRLSPIPEEVPK 20 3 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 KTFLDKDAQRLS(1)PIPEEVPK 122.41 0.00016873 209740000 767140 386930 579590 264060 920710 728660 519930 510610 647710 364240 TRUE FALSE 797427.2796 453382.2176 594694.5915 316290.2799 764208.0431 559439.7579 479176.528 503766.1081 624399.0436 435605.8542 1.830616535 1.040808367 1.365212579 0.726092813 1.754356687 1.284279705 1.100023159 1.156472309 1.433403701 1 18.73266382 4.748671346 24.66543681 1.213326626 1.830616947 0.333916094 0.264194786 1343.071425 3276385.587 0.059158955 0.805589834 56062.3561 -4.748671346 0.617290321 KTGQIWPNDGEGAFHGDADGS(ph)FGTPPGYGCAADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 34 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 KTGQIWPNDGEGAFHGDADGS(0.519)FGT(0.385)PPGY(0.096)GCAADR 45.408 0.045586 249500000 95246 93901 108360 79264 155680 118100 82850 109400 96555 91924 TRUE FALSE 99006.38563 110027.7663 111183.9506 94942.18262 129217.5692 90673.06482 76356.00051 107933.6719 93080.00441 109934.7478 0.900592284 1.000846125 1.01136313 0.863623054 1.175402425 0.824789856 0.694557472 0.981797604 0.846684113 1 16.74628794 KTGQPMINLYTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTGQPMINLYTDR 13 1 P35637-2;P35637;H3BPE7 P35637-2 FUS RNA-binding protein FUS 0 ; 122.63 0.00037329 1653540000 953870 863190 946850 812020 1157350 1154660 1071310 992870 969370 937910 FALSE TRUE 991529.5241 1011436.168 971525.6888 972635.1324 960624.0604 886507.714 987337.9229 979562.2017 934482.5631 1121675.507 0.883971806 0.901719046 0.866137918 0.867127013 0.856418861 0.790342402 0.880234896 0.873302658 0.833113104 1 20.09722394 -1.434206855 5.505781267 1.000105641 0.862290482 0.668611924 0.029271962 3.90E-05 4.01E-06 0.029104942 0.006854854 0.036795368 1.434206855 -0.137815159 KTGSPGS(ph)PGAGGVQSTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTGSPGSPGAGGVQSTAK 18 1 O43237;O43237-2;J3KRI4;J3KRZ2 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 KT(0.014)GS(0.014)PGS(0.972)PGAGGVQSTAK 156.88 5.14E-09 119920000 41329 23964 30886 22040 37988 44750 41890 32574 38621 28669 TRUE FALSE 42960.70083 28079.63059 31690.91453 26399.44622 31530.81333 34357.49069 38606.55234 32137.39881 37231.03775 34286.14165 1.253004823 0.818979017 0.924306819 0.76997425 0.919637259 1.002080988 1.126010408 0.937329115 1.085891732 1 15.06533794 2.66591325 4.621461165 1.028885911 0.920607588 0.111374512 0.128707191 0.452292562 18.41177696 0.041302633 0.039136308 463.354356 -2.66591325 -0.108278323 KTKFENLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTKFENLCK 9 2 P07900;P07900-2;Q58FG0 P07900 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 ; 141.1 6.05E-05 3234200000 2700700 2039820 2533000 1300060 5154200 3268300 2300600 2325500 2834700 3205400 FALSE TRUE 2807325.721 2390143.217 2599012.061 1557207.988 4278090.925 2509286.857 2120272.961 2294330.476 2732679.701 3833436.759 0.732326082 0.6234988 0.677984854 0.406217211 1.115993609 0.65457891 0.553099762 0.598504846 0.712853732 1 21.87020695 0.960244 19.52758923 1.000000007 0.664813214 0.24707851 0.171422122 496.7889987 244018.0441 0.160191362 0.040047841 9.125233793 -0.960244 -0.335186792 KTKPPRPDS(ph)PATTPNISVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTKPPRPDSPATTPNISVK 19 3 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 KTKPPRPDS(1)PATTPNISVK;KT(0.001)KPPRPDS(0.999)PATTPNISVK 169.19 8.07E-11 1640310000 1362680 683190 1080250 658070 1509490 1191530 1213900 1124430 1248820 652780 TRUE FALSE 1416479.659 800522.568 1108402.202 788234.2819 1252907.429 914815.2153 1118751.346 1109358.855 1203875.212 780679.7428 1.81441836 1.025417369 1.419791166 1.009676873 1.604892967 1.17181882 1.433047746 1.421016576 1.542085885 1 19.57437131 KTKPYIQVDIGGGQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTKPYIQVDIGGGQTK 16 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 123.36 4.97E-05 484170000 493680 284990 391470 301500 577380 459630 412180 386570 492940 304800 FALSE TRUE 513170.8676 333934.8156 401672.0298 361135.8001 479237.1538 352887.8983 379872.2546 381388.6615 475199.1857 364519.7243 1.407799999 0.916095326 1.101921249 0.99071676 1.314708429 0.968089996 1.042117146 1.046277159 1.303630926 1 18.47563736 KTLDSVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTLDSVAK 8 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 98.943 0.011488 1533190000 3127600 2278600 2585700 2008160 3644600 3317500 3206800 2798100 2944700 2146200 FALSE TRUE 3251080.063 2669931.825 2653085.466 2405368.054 3025092.194 2547060.902 2955442.637 2760596.046 2838720.822 2566706.799 1.266634765 1.040216914 1.0336535 0.937141732 1.17858892 0.992345874 1.151453153 1.075540084 1.105977833 1 21.29148707 2.201055228 24.99985946 1.090249138 1.069788016 0 0.094187773 1277.58635 851588.2836 0.034132604 0.02520932 158.8748772 -2.201055228 -0.020461122 KTLEEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KTLEEEAK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;; 152.97 0.00071916 1192620000 1688370 805610 1154730 805980 1648480 1531170 1533320 1113160 1296200 693610 FALSE TRUE 1755028.151 943967.2507 1184823.212 965400.4384 1368271.958 1175578.973 1413134.372 1098239.911 1249550.015 829509.5995 2.115741822 1.137982311 1.428341773 1.163820695 1.649495026 1.417197551 1.703578081 1.323962871 1.506371977 1 19.66189915 -0.441741768 0.899299341 0.981155399 1.476040677 0.227631677 0.270790896 30.8854158 16.52836396 2.337847343 0.078743727 0.361624821 0.441741768 0.494885278 KTLPLTTAPEAGEVTPSDSGGQEDS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTLPLTTAPEAGEVTPSDSGGQEDSPAK 28 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 KTLPLTTAPEAGEVTPSDS(0.008)GGQEDS(0.992)PAK 150.17 1.58E-17 0 126920 52102 78058 47963 101910 99057 98976 77848 83825 41056 TRUE FALSE 131930.8996 61050.1132 80092.25561 57449.93824 84587.3746 76052.51297 91218.00249 76804.57489 80808.15462 49100.13714 2.686976194 1.243379688 1.631202279 1.170056574 1.722752309 1.548926692 1.857795269 1.564243592 1.645782667 1 15.58343943 -2.393593195 0.471593204 3.45E-35 1.655845389 0.209702333 0.391711877 164.0080839 9.114150286 170.4738308 0.183052469 0.004040237 2.393593195 1.655845389 KTNSNKDGDQHS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTNSNKDGDQHSPGR 15 2 A0A2R8YFA9;Q6ZW33 A0A2R8YFA9 MICALCL MICAL C-terminal-like protein 1 KTNSNKDGDQHS(1)PGR;KTNSNKDGDQHS(1)PGR 140.28 2.59E-06 55820000 104668 76690 97258 55800 131817 118247 90451 87811 109962 73907 TRUE FALSE 108800.3735 89860.91093 99792.62338 66837.07345 109410.7934 90785.9263 83361.21427 86634.03717 106004.4891 88387.66162 1.230945264 1.016668043 1.129033414 0.756181035 1.237851431 1.027133478 0.943131799 0.98015985 1.199313198 1 16.43155737 5.115300467 1.866226539 1.0233974 1.574053328 0.167326235 0.130105538 5.502311151 7.761051517 0.031557217 7.484258273 130406.8688 -5.115300467 0.550655928 KTPCGEGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTPCGEGSK 9 1 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ; 105.13 0.0050465 1669790000 1758950 1106800 1583520 1103450 2065300 1816290 1958760 1463090 1706730 1210990 FALSE TRUE 1828394.704 1296884.29 1624787.832 1321709.117 1714241.044 1394484.174 1805227.273 1443479.672 1645305.121 1448260.305 1.262476572 0.895477343 1.121889364 0.912618479 1.18365534 0.962868463 1.24647984 0.996699051 1.136056215 1 20.4658895 KTPEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTPEELLR 8 1 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 90.15 0.021486 115900000 130500 109230 125710 112820 138940 165530 131640 115080 131380 116300 FALSE TRUE 135652.2408 127989.4028 128986.1059 135135.4593 115323.0284 127088.1661 121321.7128 113537.5408 126651.6595 139086.7583 0.975306653 0.92021271 0.927378763 0.97159112 0.829144556 0.913733037 0.872273639 0.816307334 0.910594661 1 17.08562555 3.249665474 24.99969526 0.876775974 0.94507566 0.21085588 0.051173732 268.561611 604593.2581 0.013614918 0.01826292 1776.910175 -3.249665474 0.068299686 KTPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_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 2 KTPEKLDNT(0.005)PAS(0.995)PPRS(1)PAEPNDIPIAK 158.57 2.23E-11 378880000 133210 58829 83498 62123 133030 106830 108660 79514 108080 51406 TRUE FALSE 138469.2337 68932.42312 85674.02647 74410.74398 110417.6081 82020.35152 100142.9453 78448.24489 104190.2219 61478.02147 2.252337182 1.121253116 1.393571628 1.210363349 1.796050124 1.33414104 1.628922709 1.276037241 1.694755612 1 15.90778312 -2.157264099 1.974520275 4.82E-05 1.489198728 0.186344649 0.320947536 4426201.405 943885.9594 19781799.25 0.070978227 0.00696203 2.157264099 1.489150499 KTPSKPPAQLS(ph)PSVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.795)PS(0.205)VPK 122.53 4.84E-05 1422200000 2707000 1218900 2055700 1274500 2623900 2436200 2474000 1963200 2320500 1135900 TRUE FALSE 2813874.45 1428236.593 2109273.231 1526592.296 2177890.415 1870429.471 2280081.415 1936886.515 2236985.658 1358457.857 2.071374122 1.05136614 1.552696847 1.123768609 1.603207935 1.376877068 1.678433677 1.425798015 1.646709647 1 20.37353838 -1.905304656 2.522345236 0.721551697 1.482798843 0.227717702 0.275762597 27498489.9 15460307.47 45418561.18 0.058945769 0.012436419 1.905304656 0.761247146 KTPSKPPAQLSPS(ph)VPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTPSKPPAQLSPSVPK 16 2 F5H8D7;P18887;M0QYS5 F5H8D7 XRCC1 DNA repair protein XRCC1 1 KTPSKPPAQLS(0.451)PS(0.549)VPK 72.876 0.019114 1362800000 1868000 861630 1209700 863780 1644000 1424700 1643700 1197800 1570700 632380 TRUE FALSE 1941750.082 1009608.25 1241225.776 1034633.106 1364553.467 1093835.017 1514862.499 1181745.45 1514170.814 756282.7534 2.567492216 1.334961356 1.6412192 1.368050641 1.804290077 1.446330769 2.003037214 1.562570937 2.002122628 1 19.52856619 4.748899112 24.5377898 1.607606541 2.567492911 0.499385756 0.296777511 898.9342716 2133510.693 0.064083283 0.887677742 56091.76583 -4.748899112 0.95988637 KTQMAEVLPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTQMAEVLPSPR 12 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 KTQMAEVLPS(1)PR;KTQMAEVLPS(1)PR 78.285 0.011218 444910000 739480 720530 825010 683900 855190 893460 829230 780650 789460 759370 TRUE FALSE 768675.2414 844275.4226 846510.4384 819173.3788 709825.1093 685967.4555 764232.7858 770186.6636 761047.4888 908154.0125 0.846415069 0.929661061 0.932122114 0.902020326 0.78161314 0.755342647 0.841523327 0.848079349 0.838015885 1 19.79257746 5.124428905 14.05305017 0.86152183 9.91E-05 0 0.070168564 3203062.863 3057348.505 0.017285766 86976593.96 133176.9012 -5.124428905 -0.861422763 KTQPSMVSNPGSCSDPQPS(ph)PEMKPHSYLDAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTQPSMVSNPGSCSDPQPSPEMKPHSYLDAIR 32 2 C9J494;Q9H000-2;Q9H000 C9J494 MKRN2 Probable E3 ubiquitin-protein ligase makorin-2 1 KTQPSMVSNPGSCSDPQPS(1)PEMKPHSYLDAIR 132.81 3.02E-08 217330000 168970 124780 170600 99256 204200 201720 178130 165360 182890 125910 TRUE FALSE 175641.0661 146209.9943 175045.9761 118888.5406 169490.1569 154873.5871 164167.7051 163143.6197 176307.8246 150579.6538 1.166432925 0.970981076 1.162480931 0.789539208 1.125584716 1.028516026 1.090238296 1.083437341 1.170860871 1 17.20016732 2.291470726 1.842488448 1.094512756 1.032494319 0.032251099 0.110221237 1.116892089 7.682544714 0.050809726 0.034128647 195.6458888 -2.291470726 -0.062018437 KTQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 KT(0.001)QQLHPVLQKPS(0.021)VFGNDS(0.723)DDDDET(0.206)S(0.046)VS(0.003)ESLQR 63.23 0.0054076 891830000 165310 154830 154470 144080 246820 268560 179820 185900 228040 158940 TRUE FALSE 171836.5664 181420.8481 158495.6151 172578.594 204865.6246 206191.0101 165725.2385 183408.3146 219832.8849 190081.2499 0.904016396 0.954438421 0.833830876 0.907920134 1.077779237 1.084751969 0.871865261 0.9648943 1.15652062 1 17.5362567 3.330875534 8.143198856 1.012226104 0.898160738 0.381800138 0.077361028 0.311758851 24.26428786 0.022571453 0.030567333 2142.276548 -3.330875534 -0.114065366 KTQSNNAENKRPEEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTQSNNAENKRPEEDR 16 3 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 0 ; 115.73 0.00021159 61344000 75443 56161 62419 62211 76354 87145 81412 71602 75198 47544 FALSE TRUE 78421.54789 65806.21488 64045.69042 74516.15012 63375.37435 66906.89445 75030.71471 70642.29231 72491.63867 56859.33652 1.379220242 1.157351086 1.126388283 1.310534992 1.114599259 1.176709025 1.319584774 1.242404443 1.27492938 1 15.79510964 -1.902331722 2.591124498 0.87163615 1.22989265 0.407709337 0.084337384 7642393.607 4257832.071 5971710.056 0.019736267 0.012521844 1.902331722 0.3582565 KTQTVCNFTDGALVQHQEWDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTQTVCNFTDGALVQHQEWDGK 22 1 Q01469;I6L8B7 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 ; 314.26 1.74E-67 1004540000 1464640 883040 1191420 960130 1408470 1404860 1473680 1210940 1330080 696760 FALSE TRUE 1522465.118 1034695.251 1222469.384 1150040.848 1169058.772 1078602.556 1358169.111 1194709.33 1282210.681 833276.7817 1.827082131 1.241718567 1.467062818 1.380142677 1.402965735 1.294410908 1.629913542 1.433748493 1.53875724 1 19.66843626 -2.163282234 2.081000428 2.53E-05 1.457304153 0.434342247 0.159916363 1847256.862 386460.0096 8707359.54 0.036997488 0.006866221 2.163282234 1.457278848 KTS(ph)LDVSNSAEPGFLAPGAR ddPTM_MDA-MB-175_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(0.201)S(0.799)LDVSNSAEPGFLAPGAR 243.19 4.88E-30 354780000 375510 255880 272680 257130 427060 407680 365280 344520 373680 295590 TRUE FALSE 390335.4248 299825.3995 279786.2648 307989.5465 354468.4937 313002.4985 336648.3991 339902.2729 360231.3298 353505.2011 1.104185804 0.848149896 0.791462937 0.871244739 1.002724974 0.885425441 0.952315265 0.961519864 1.019026958 1 18.43137192 1.70935332 1.116835814 1.011207799 0.907290089 0.148032914 0.08226118 0.856317111 2.002688645 0.071192023 0.027698979 51.20982829 -1.70935332 -0.10391771 KTS(ph)SVSSISQVSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTSSVSSISQVSPER 15 1 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 KT(0.009)S(0.944)S(0.037)VS(0.004)S(0.004)IS(0.001)QVS(0.001)PER;KT(0.003)S(0.852)S(0.097)VS(0.024)S(0.024)IS(0.001)QVSPER 174.59 1.10E-11 59280000 116382 92994 116598 108206 134012 149757 126971 100582 117285 97886 TRUE FALSE 120976.8512 108964.9961 119636.6397 129608.8238 111232.6881 114978.2063 117018.6812 99233.86281 113063.9358 117064.8876 1.033417054 0.930808532 1.021968604 1.107153704 0.950179771 0.982175003 0.999605293 0.847682553 0.965822785 1 16.83694889 1.889967584 12.69066337 0.921428177 1.002866219 0.195240738 0.058440863 0.96164156 106.6228683 0.024038892 0.015412375 77.618918 -1.889967584 0.081438042 KTSAVSS(ph)PLLDQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 KTSAVS(0.042)S(0.958)PLLDQQR;KTSAVS(0.053)S(0.947)PLLDQQR 135.79 1.89E-05 1391110000 1240270 1056800 1161210 895730 1543820 1463370 1135500 1224170 1303800 1301840 TRUE FALSE 1289236.817 1238297.179 1191472.087 1072902.721 1281402.028 1123524.495 1046496.543 1207762.003 1256876.493 1556910.623 0.82807375 0.795355341 0.765279695 0.689122872 0.823041483 0.721637118 0.672162247 0.77574267 0.80728879 1 20.5702547 0.767472263 2.204555078 0.999808796 0.755420033 0.682031846 0.049309945 0.538319767 4.08822216 0.047647579 0.012978298 5.854263463 -0.767472263 -0.244388763 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 KT(0.014)S(0.099)FDQDS(0.887)DVDIFPSDFPTEPPSLPR;KT(0.016)S(0.016)FDQDS(0.968)DVDIFPSDFPTEPPSLPR;KT(0.044)S(0.035)FDQDS(0.921)DVDIFPSDFPTEPPSLPR;KT(0.004)S(0.004)FDQDS(0.992)DVDIFPSDFPTEPPSLPR;KT(0.035)S(0.035)FDQDS(0.93)DVDIFPSDFPTEPPSLPR;KT(0.006)S(0.018)FDQDS(0.976)DVDIFPSDFPTEPPSLPR;KT(0.007)S(0.007)FDQDS(0.986)DVDIFPSDFPTEPPSLPR 189.2 5.49E-18 7772253000 2929473 2179681 2645596 2013907 3269765 3107138 3050056 2451704 2746209 1784103 TRUE FALSE 3045130.856 2554024.256 2714542.405 2412251.794 2713971.513 2385552.289 2810984.641 2418842.918 2647373.475 2133663.824 1.427183993 1.197013432 1.272244659 1.130567883 1.271977095 1.118054429 1.317444955 1.133656994 1.2407641 1 21.02490146 -5 0.087707498 0.320887331 1.410800573 0.442955232 0.085823514 205.9610095 1.261598631 26.89367836 2.018737241 1.00E-05 5 1.089913242 KTSFDQDSDVDIFPSDFPTEPPSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 0 74.456 0.041116 30260000 40035 52731 52720 49056 62388 59209 53781 51000 49866 38416 FALSE TRUE 41615.61271 61787.13906 54093.92651 58759.13038 51783.31004 45458.60707 49565.50469 50316.42842 48071.3324 45942.87968 0.905812021 1.344868661 1.177416977 1.278960544 1.127123733 0.989459246 1.07885063 1.095195355 1.046328239 1 15.48755367 2.997753469 24.38470374 1.055117377 1.190596547 0.243028101 0.11067054 87.24667689 947035.8924 0.030373643 0.035715242 994.8405278 -2.997753469 0.13547917 KTST(ph)SPPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.158)S(0.22)T(0.37)S(0.252)PPPEK 62.891 0.048136 500470000 909060 513460 697710 603360 871660 885710 1040300 773210 933040 368300 TRUE FALSE 944950.3907 601642.7608 715892.8958 722702.8072 723495.5445 680017.2756 958758.5677 762846.3847 899460.0727 440461.3335 2.145365141 1.365937746 1.625325179 1.64078604 1.642585829 1.543875078 2.176714492 1.731925885 2.042086341 1 18.74865585 KTSTS(ph)PPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTSTSPPPEK 10 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KT(0.016)S(0.016)T(0.244)S(0.724)PPPEK 85.909 0.0085252 385840000 1124500 669330 831620 728340 1004400 957420 1199000 822270 886280 397490 TRUE FALSE 1168896.128 784282.2208 853292.7004 872403.4781 833672.4468 735073.7148 1105019.247 811248.8156 854382.9559 475370.5551 2.458915715 1.649833404 1.795005373 1.835207227 1.753731774 1.546317303 2.324542896 1.706560928 1.797298858 1 18.85869302 -2.128199652 0.438713812 4.07E-11 1.880932467 0.482034534 0.273731936 53.43880652 3.351901879 53.20207378 0.142714742 0.007443897 2.128199652 1.880932467 KTSYLTELIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTSYLTELIDR 11 1 B4DR80;Q9Y6E0-2;H0Y630;Q9Y6E0;Q5JV98;Q9P289-2;Q5JV99;Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 B4DR80;Q8NBY1 STK24;STK26 Serine/threonine-protein kinase 24;Serine/threonine-protein kinase 24 36 kDa subunit;Serine/threonine-protein kinase 24 12 kDa subunit;Serine/threonine-protein kinase 26 0 ; 178.58 1.20E-05 2105160000 2045260 2010100 2124340 1941800 2691500 2598000 2265770 2165080 2204960 2163120 FALSE TRUE 2126008.444 2355319.039 2179702.046 2325882.244 2233999.791 1994653.873 2088173.027 2136060.644 2125603.92 2586941.949 0.82182302 0.910464589 0.842578646 0.899085596 0.863567809 0.771047017 0.807197482 0.825708766 0.821666648 1 21.30281625 2.973366852 24.69491832 0.829327134 0.871097024 0 0.062178523 1465.190182 1358562.098 0.017372593 0.018482832 940.5174376 -2.973366852 0.04176989 KTTHFVEGGDAGNREDQINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTTHFVEGGDAGNREDQINR 20 2 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 195.09 8.15E-19 863830000 464940 454400 560740 437250 666200 624060 487510 525960 572090 555910 FALSE TRUE 483296.1902 532439.6653 575353.3451 523736.7449 552959.562 479131.5227 449297.6923 518910.3665 551500.5927 664829.921 0.726947111 0.800865979 0.865414337 0.787775532 0.83173086 0.720682851 0.675808471 0.780515964 0.82953636 1 19.34262579 0.839450064 2.812816484 0.999832454 0.774116743 0.628959034 0.052293987 0.460468752 6.487057078 0.053900129 0.01422656 6.909554776 -0.839450064 -0.225715711 KTTPS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KTTPSPGR 8 1 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 KT(0.006)T(0.024)PS(0.971)PGR;KTT(0.013)PS(0.987)PGR;KTT(0.002)PS(0.997)PGR;KT(0.01)T(0.01)PS(0.98)PGR;KT(0.003)T(0.059)PS(0.938)PGR 98.898 0.0044076 586235000 923050 673875 803104 634062 986880 945900 860510 780692 788700 630476 TRUE FALSE 959492.7267 789607.7892 824033.55 759477.5711 819130.4901 726229.0603 793060.9777 770228.1007 760314.8411 754005.701 1.272527151 1.047217267 1.092874429 1.007257067 1.086371746 0.963161232 1.051797058 1.021514956 1.008367496 1 19.52421591 7.777662541 1.047866385 1.024266371 199.9820234 0.792125522 0.037275661 510.3588317 0.926347727 0.009796624 243578.7201 59932520.33 -7.777662541 198.957757 KTTTTPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KTTTTPGR 8 1 P17096;P17096-2 P17096;P17096-2 HMGA1 High mobility group protein HMG-I/HMG-Y 0 ;;; 117.31 0.0033725 2522230000 1507182 1461339 1641960 1454074 1728130 1667800 1807640 1681540 1585640 1453104 FALSE TRUE 1566686.709 1712312.606 1684750.826 1741685.497 1434383.08 1280478.726 1665952.453 1659001.707 1528573.126 1737811.907 0.901528354 0.985326777 0.96946673 1.002229004 0.825396048 0.7368339 0.958649464 0.954649752 0.879596416 1 20.72884051 3.253994877 24.95848729 0.89212768 0.966460433 0.186015935 0.07386302 432.7406342 699773.4354 0.021872369 0.029507716 1794.712457 -3.253994877 0.074332753 KTTYHT(ph)MVDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTTYHTMVDLK 11 1 S4R407;Q5T2K3;Q9H8W5-2;Q9H8W5 S4R407 TRIM45 Tripartite motif-containing protein 45 1 KT(0.193)T(0.193)Y(0.158)HT(0.455)MVDLK 69.979 0.025742 300160000 9739 599550 472210 602500 303130 622130 309260 466740 392730 709530 TRUE FALSE 10123.50324 702518.0486 484516.1805 721672.7017 251604.0709 477649.736 285019.3931 460484.1137 378595.724 848548.8187 0.011930372 0.827905282 0.570993878 0.850478706 0.296511014 0.562901893 0.335890389 0.542672506 0.446168465 1 19.69463814 -1.219260772 3.818096859 1.000495083 0.508490698 0.292760575 0.234989269 12520068.38 8025558.173 49116.54076 0.050744751 0.06035861 1.219260772 -0.492004385 KTVEDEDQDS(ph)EEEKDNDSYIK ddPTM_MDA-MB-175_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 246.31 1.44E-30 338190000 1684040 307550 577130 300770 894660 988680 936980 602160 657090 199931 TRUE FALSE 1750527.2 360369.3201 592170.4819 360261.4083 742586.0128 759074.0536 863537.0593 594089.0301 633441.4593 239103.6515 7.321206465 1.507167782 2.476626677 1.506716464 3.105707537 3.17466525 3.611559479 2.484650595 2.649233733 1 17.86727664 0.615654337 1.086736236 1.001833213 3.055697729 0.149397055 1.545319952 2.557810676 4.708818032 1.395389478 0.436815418 4.12718881 -0.615654337 2.053864515 KTVGVEPAADGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTVGVEPAADGK 12 1 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ; 98.582 0.0068591 274910000 696290 427370 607740 470730 854730 787380 770180 652440 732460 470600 FALSE TRUE 723780.0669 500767.473 623578.2037 563838.989 709443.2999 604522.9279 709811.2791 643695.109 706098.9077 562805.0598 1.286022672 0.889770737 1.107982583 1.0018371 1.260548901 1.074124899 1.261202732 1.143726585 1.254606538 1 19.10227577 3.247516556 24.99960683 1.173085205 1.061042335 0.121862456 0.121791904 329.2776925 919140.8358 0.030784796 0.041093027 1768.13962 -3.247516556 -0.11204287 KTVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 KTVSLT(0.004)PS(0.86)PT(0.065)T(0.071)QVET(0.017)PDLVDHDNT(0.626)S(0.356)PLFR;KT(0.001)VS(0.001)LT(0.005)PS(0.988)PT(0.002)T(0.002)QVETPDLVDHDNT(0.618)S(0.382)PLFR 94.832 0.0013178 335710000 168059 170903 183001 157894 234520 222185 169243 174141 199066 188919 TRUE FALSE 174694.0991 200254.2608 187770.1564 189124.9619 194656.3742 170585.901 155977.2914 171806.9247 191901.6535 225934.061 0.773208335 0.886339403 0.831083882 0.837080346 0.861562764 0.755025162 0.690366431 0.760429499 0.849370178 1 17.78554226 2.742890476 24.8878471 0.7834554 0.840129323 0 0.082707103 833.1078355 4788669.197 0.024455873 0.025138756 553.2105787 -2.742890476 0.056673923 KTVSLTPS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KT(0.001)VS(0.001)LT(0.003)PS(0.974)PT(0.011)T(0.011)QVETPDLVDHDNTSPLFR 86.195 0.0009202 42506000 29249 34967 40898 30247 53879 48649 25115 27694 34892 39344 TRUE FALSE 30403.77311 40972.31024 41963.83548 36229.76632 44720.66683 37351.00703 23146.42067 27322.80723 33636.24374 47052.70351 0.646164212 0.870774837 0.891847489 0.769982671 0.950437775 0.793812135 0.491925414 0.580685172 0.714863148 1 15.52199 2.453047727 23.77080592 0.646614473 0.833223804 0.111997854 0.146762139 169.4571307 167324.381 0.048351028 0.040455861 283.8230921 -2.453047727 0.186609331 KTVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 KTVSLTPSPTTQVETPDLVDHDNT(0.32)S(0.68)PLFR;KTVSLTPSPTTQVETPDLVDHDNT(0.096)S(0.904)PLFR 181.08 4.99E-18 1938300000 270946 291900 304510 253881 341420 402550 256595 293420 301856 295230 TRUE FALSE 281643.1573 342031.5543 312445.7808 304097.904 283385.5504 309063.8632 236482.4134 289487.1848 290992.2615 353074.666 0.797687244 0.968723013 0.884928348 0.861284973 0.802622158 0.875349871 0.66978018 0.819903586 0.824166358 1 18.42961378 3.43990948 2.76403989 0.813590116 0.891724817 0.040914712 0.086279259 0.524939779 8.130178139 0.023725817 0.035664302 2753.654698 -3.43990948 0.078134701 KTVT(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTVTPAK 7 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KT(0.001)VT(0.999)PAK;KTVT(1)PAK 104.79 0.0047297 512800000 3160000 1340760 1991980 1180310 2282000 2325400 2428500 1938960 2053200 1131110 TRUE FALSE 3284759.24 1571025.1 2043892.635 1413771.795 1894106.455 1785361.092 2238147.824 1912971.413 1979305.733 1352729.348 2.428245713 1.1613743 1.510939818 1.045125396 1.400210957 1.319821363 1.654542224 1.414156805 1.463194198 1 20.36744179 4.745094844 24.83399541 1.358864644 2.428246243 0.732387815 0.198480866 343.3827515 1305023.118 0.04502274 0.431339974 55602.56725 -4.745094844 1.069381599 KTYVTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KTYVTPR 7 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ; 114.89 0.0093038 3711000000 1762340 1575830 1856890 1483410 2017950 2062810 1872230 1938540 1824900 1678570 FALSE TRUE 1831918.544 1846466.544 1905282.079 1776824.07 1674939.58 1583753.64 1725479.72 1912557.042 1759222.205 2007453.653 0.912558325 0.919805317 0.949103894 0.885113371 0.834360274 0.78893659 0.859536517 0.952727869 0.876345116 1 20.93693525 0.475135871 0.974176534 0.999509032 0.884079414 0.325201909 0.048429437 2.46671382 3.2811969 0.053194276 0.016792165 2.986316752 -0.475135871 -0.115429617 KVACIGAWHPAR ddPTM_MDA-MB-175_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 ; 121.02 0.00024906 2799000000 1987180 2339400 1962020 1563480 3680800 3217800 2038860 2210200 2144530 4432900 FALSE TRUE 2065635.401 2741173.752 2013151.853 1872731.677 3055138.931 2470514.716 1879048.826 2180575.884 2067348.784 5301441.882 0.389636527 0.517061926 0.379736664 0.353249497 0.576284528 0.466008073 0.354441087 0.411317512 0.389959719 1 22.33795337 -1.385691595 3.362868138 1.004904179 0.426816186 0.86083525 0.069187219 41341220.76 55240158.98 1961289.237 0.016540206 0.041144179 1.385691595 -0.578087994 KVAECQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVAECQR 7 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 101.54 0.014404 276730000 157321 175037 143911 115352 309120 232099 161897 138477 153382 294100 FALSE TRUE 163532.1546 205098.2432 147661.4389 138168.2813 256575.8928 178197.5247 149207.0901 136620.9423 147861.8118 351723.2641 0.464945516 0.583123905 0.419822781 0.392832364 0.729482292 0.50664128 0.42421729 0.388433056 0.42039247 1 18.42408124 -1.368460086 3.109266888 1.005661705 0.478582889 0.707574636 0.100063593 44287793.97 57717337.74 2273487.812 0.0251116 0.042809476 1.368460086 -0.527078816 KVAETAVQLFISGDKVNVAGLVLAGSADFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVAETAVQLFISGDKVNVAGLVLAGSADFK 30 2 B7Z7P8;P62495-2;P62495;I3L492 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 204.92 8.43E-26 368360000 526000 176512 390593 229233 454140 437551 563790 370110 480886 170724 FALSE TRUE 546766.8862 206826.5629 400772.1745 274574.6032 376945.445 335936.4114 519598.6666 365149.2808 463579.0068 204174.0991 2.677944404 1.012991187 1.962894296 1.344806243 1.846196196 1.645342935 2.544880418 1.788421168 2.270508399 1 17.63944034 KVAFCGAPEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVAFCGAPEEGR 12 1 Q8IZ83;F5H4B6 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 73.36 0.06319 111460000 203310 165250 186520 165800 258010 254160 220340 204790 212800 158160 FALSE TRUE 211336.8358 193630.402 191380.8644 198594.7451 214153.5524 195135.1918 203069.175 202045.125 205141.3696 189148.4238 1.117306883 1.023695562 1.011802586 1.049941316 1.13219845 1.031651165 1.073596972 1.068182969 1.084552361 1 17.52915923 -0.996361773 6.506098276 0.999999981 1.064136854 0.221749851 0.036896202 9.89E-09 1.52E-09 0.03493889 0.008235173 0.100841252 0.996361773 0.064136873 KVAGAAT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVAGAATPK 9 1 P16402 P16402 HIST1H1D Histone H1.3 1 KVAGAAT(1)PK;KVAGAAT(1)PK 76.465 0.020718 455020000 1509370 651450 1106900 558210 1260840 1527630 1303120 975100 1105220 603180 TRUE FALSE 1568961.093 763331.4699 1135746.723 668622.2719 1046522.867 1172861.084 1200978.049 962030.3794 1065443.348 721361.5724 2.174999547 1.058181499 1.574448608 0.926889229 1.450760488 1.625899034 1.664876666 1.333631311 1.476989334 1 19.46036305 -0.184594845 1.308818612 0.998098716 1.455009436 0.158878051 0.325238998 57.08039554 59.32618351 0.854229402 0.08599761 0.653740145 0.184594845 0.45691072 KVAVAAASKPHVEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVAVAAASKPHVEIR 15 2 P29762;B5MCB5 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 188.44 1.80E-07 609540000 604750 618210 721040 532060 825260 851010 711980 689550 748020 601430 FALSE TRUE 628625.997 724382.7585 739830.8947 637299.88 684982.6 653375.8247 656173.1472 680307.7101 721098.9063 719268.6934 0.873979366 1.00711009 1.02858765 0.886038675 0.952332009 0.908389077 0.912278198 0.945832505 1.002544547 1 19.45617129 1.253126282 6.462498933 1.001845478 0.940871788 0.221304603 0.046457359 0.220402447 36.77318778 0.035620799 0.011558728 17.91126591 -1.253126282 -0.06097369 KVCGDSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVCGDSDK 8 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 ; 91.584 0.019856 376610000 1089800 463080 652260 390450 926240 943190 870430 662820 792120 403650 FALSE TRUE 1132826.146 542610.3877 669258.4314 467679.8446 768798.0556 724148.4167 802203.4222 653935.9821 763611.7559 482737.4892 2.346671164 1.124027862 1.386381722 0.9688078 1.592579969 1.500087383 1.661779829 1.354640973 1.58183645 1 18.88087934 -1.335119884 3.577000912 0.998047933 1.472266566 0.151679361 0.34981516 18618829.47 13902962.76 261024.131 0.076282168 0.04622534 1.335119884 0.474218633 KVCGEEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVCGEEGVR 9 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 137.98 0.0002398 72387000 95803 103720 109660 93090 136290 143090 104880 114780 104870 132930 FALSE TRUE 99585.37642 121533.1032 112517.8297 111502.9242 113123.4745 109859.516 96659.23155 113241.5618 101095.7492 158975.0884 0.626421268 0.764478915 0.707770197 0.701386143 0.711579881 0.691048624 0.608014957 0.712322685 0.635921956 1 17.27844119 -2.091713536 2.599007574 1.541260455 0.687386855 0.814245966 0.045211161 4254734.042 1572168.864 13626222.25 0.010426842 0.008096298 2.091713536 -0.8538736 KVDAETVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVDAETVGR 9 1 P11172-2;P11172-3;P11172;P11172-4;E9PFD2 P11172-2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 ; 84.507 0.024765 281670000 248614 381350 308620 342260 325890 421730 319040 278640 272515 504660 FALSE TRUE 258429.4727 446843.896 316662.8907 409958.0065 270495.3342 323789.5989 294032.8111 274905.2866 262707.2384 603538.4647 0.428190559 0.740373517 0.524677231 0.679257463 0.448182428 0.53648544 0.487181561 0.455489257 0.435278369 1 19.20308619 -1.018466616 4.808811335 1.000008996 0.527883862 0.669145302 0.09995729 0.128304554 63354829.5 1288.170968 0.023136408 0.095837038 1.018466616 -0.472125134 KVDAVFVGTGDLFAAMLLAWTHKHPNNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVDAVFVGTGDLFAAMLLAWTHKHPNNLK 29 2 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 194.7 1.80E-19 332480000 1108870 470870 777110 527500 1062700 1048060 1090970 839280 1191710 593030 FALSE TRUE 1152649.044 551738.2596 797362.125 631837.9256 882062.6336 804663.9485 1005456.921 828030.8244 1148820.59 709222.8743 1.62522824 0.777947638 1.124275815 0.890887686 1.243703024 1.134571342 1.417688229 1.167518497 1.619830143 1 19.43587954 2.365539277 6.978520382 1.302586201 1.107710253 0.088843279 0.258102231 0.474407619 27.40400062 0.084059952 0.070088851 232.0274019 -2.365539277 -0.194875948 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 33 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 KVDEGAGDSAAVASGGAQTLALAGS(1)PAPSGHPK;KVDEGAGDSAAVASGGAQTLALAGS(1)PAPSGHPK;KVDEGAGDSAAVASGGAQTLALAGS(1)PAPSGHPK 288.22 3.80E-75 2726150000 1099640 760140 1087630 769880 1371780 1259020 1310030 1072250 1181770 742180 TRUE FALSE 1143054.636 890688.1319 1115974.531 922159.9661 1138605.326 966631.6856 1207346.425 1057878.243 1139238.329 887595.9611 1.287809641 1.003483759 1.257300146 1.038941147 1.282796875 1.08904471 1.360243262 1.191846616 1.283510041 1 19.75954358 KVDQPPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVDQPPEAK 9 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 107.06 0.0045467 282760000 907860 518800 731700 524670 1055770 900720 902350 755500 862660 526600 FALSE TRUE 943703.0138 607899.8643 750768.7031 628448.16 876310.5925 691541.4305 831621.4491 745373.7582 831613.0351 629777.1876 1.498471257 0.965261804 1.192117971 0.997889686 1.391461313 1.098073166 1.320501068 1.183551537 1.320487708 1 19.26448197 2.254170422 24.98142903 1.220910794 1.180752605 0 0.173843204 1612.814196 2581088.753 0.056085704 0.046764741 179.5438038 -2.254170422 -0.04015819 KVDT(ph)TPNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.765)T(0.235)PNQGK 96.745 0.0043642 178950000 637680 330010 412180 335450 538940 555190 521050 401230 429820 281350 TRUE FALSE 662856.0988 386686.6504 422921.7494 401801.0088 447331.1713 426255.5365 480208.7395 395852.1681 414350.8622 336475.1457 1.970000183 1.149227975 1.256918244 1.194147663 1.329462746 1.266826219 1.427174475 1.176467781 1.231445673 1 18.36014042 4.743006551 24.99920337 1.241891123 1.970000474 0.809703248 0.107987428 177.5378644 998248.9388 0.023982146 0.190552489 55335.84564 -4.743006551 0.728109351 KVDTT(ph)PNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVDTTPNQGK 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 KVDT(0.476)T(0.524)PNQGK;KVDT(0.144)T(0.856)PNQGK 137.84 4.73E-05 307030000 1423570 778610 914790 738010 1291890 1324810 1187050 843160 998750 640930 TRUE FALSE 1479773.643 912330.2108 938630.1789 883986.1753 1072294.999 1017142.955 1094005.919 831858.8193 962805.1826 766507.9622 1.930539167 1.190242314 1.224553723 1.153264178 1.398935239 1.326982896 1.427259694 1.085257897 1.256092865 1 19.54794125 4.741048568 24.9679882 1.239574602 1.930539415 0.73428622 0.126432991 113.2284013 1136242.479 0.029488232 0.200597948 55086.9298 -4.741048568 0.690964813 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLR 35 2 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 ;; 283.68 9.13E-75 708230000 265657 163589 208436 160625 297771 259778 248185 214012 259237 138642 FALSE TRUE 276145.3435 191684.1382 213868.0134 192396.1456 247155.9918 199448.4965 228731.6112 211143.5192 249907.111 165806.2454 1.665470096 1.156073088 1.289867054 1.160367301 1.490631376 1.202900988 1.379511433 1.27343526 1.50722375 1 17.33913882 -1.973394724 2.869948681 0.722081569 1.331364893 0.296782327 0.158677285 20626218.92 27484744.72 38299805.59 0.034610929 0.010631763 1.973394724 0.609283324 KVDWLTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 0 114.4 0.0042704 1622600000 5924600 4351900 5419400 4489800 6371800 6056100 6422600 5463000 5659900 4745800 FALSE TRUE 6158507.783 5099304.972 5560634.016 5377869.039 5288723.712 4649662.556 5919179.83 5389777.421 5456201.305 5675648.646 1.085075586 0.89845325 0.979735421 0.947533819 0.931827187 0.819230161 1.04290808 0.949631973 0.961335284 1 22.43635385 -0.436334512 11.37424216 1 0.954511505 0.031957419 0.068974191 0 0 0.062383553 0.014703944 0.366155438 0.436334512 -0.045488495 KVEAPETNIDKT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVEAPETNIDKTPK 14 2 O75152;E9PBY7;E9PQ61 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 KVEAPETNIDKT(1)PK;KVEAPETNIDKT(1)PK 152.04 0.00032285 539500000 3231200 659860 1110550 617810 1857390 2017650 1851050 1201680 1409960 485620 TRUE FALSE 3358770.271 773185.822 1139491.845 740010.974 1541671.511 1549081.365 1705959.864 1185573.445 1359215.815 580767.9412 5.783325891 1.331316292 1.962043295 1.27419391 2.654539622 2.667298339 2.937420858 2.041389273 2.340376799 1 19.14760229 4.746024433 24.9940579 2.108629837 5.783327639 0.764189765 0.625003918 437.8261212 1466111.746 0.149216364 1.575039192 55721.70964 -4.746024433 3.674697801 KVEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEDAK 6 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 97.071 0.066524 134400000 103110 53968 81073 48486 115180 84332 102760 71183 100110 65195 FALSE TRUE 107180.8624 63236.58419 83185.82898 58076.38608 95601.74474 64747.17106 94705.40269 70228.90832 96507.06066 77968.71202 1.374665037 0.811050773 1.066912956 0.74486784 1.226155239 0.830425043 1.214659063 0.900731928 1.237766511 1 16.25060768 2.226915286 24.99985246 1.065616474 1.00050986 0.029882521 0.202196824 1095.353443 2351456.5 0.069472459 0.051735001 168.6224076 -2.226915286 -0.065106614 KVEDLQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEDLQFR 8 1 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;F5H6A0;Q9UDT6;Q9UDT6-2 J3KP58;Q9UDT6 CLIP1;CLIP2 CAP-Gly domain-containing linker protein 1;CAP-Gly domain-containing linker protein 2 0 118.18 0.0031054 149770000 160630 124430 128970 124750 172480 188900 146980 144090 152130 143680 FALSE TRUE 166971.7964 145799.8846 132331.0642 149425.1777 143161.9112 145030.8378 135459.3235 142158.7092 146654.871 171831.3451 0.971719079 0.848505751 0.770121796 0.869603724 0.833153643 0.844030161 0.788327202 0.827315349 0.853481482 1 17.39063371 0.84583079 6.521861948 0.999999873 0.839031261 0.450730255 0.051134139 4.849752337 205.1439548 0.048000454 0.012050691 7.0118205 -0.84583079 -0.160968612 KVEDMMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVEDMMK 7 1 P13639 P13639 EEF2 Elongation factor 2 0 ; 87.476 0.030968 2115400000 4391100 2732800 3284700 2382500 7117700 5085000 4804800 3462200 3873100 4079700 FALSE TRUE 4564464.019 3202137.142 3370301.98 2853751.389 5907835.896 3904085.814 4428187.221 3415794.872 3733707.888 4879039.104 0.935525197 0.656304873 0.690771668 0.58490029 1.210860534 0.800175143 0.907594124 0.700095818 0.765254758 1 22.21816562 5.08604903 16.75837139 0.803834152 4.579909587 0.039693601 0.1759719 42455397.1 91739989.23 0.041534934 5904151728 121912.7227 -5.08604903 3.776075435 KVEEAEPEEFVVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KVEEAEPEEFVVEK 14 1 Q13185;S4R2Y4;C9JMM0;B8ZZ43 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;; 185.02 1.96E-06 3234590000 6225140 3498460 4987730 3513950 6534800 5715850 6346780 4943530 5603080 2996010 FALSE TRUE 6470913.334 4099293.291 5117714.341 4208998.822 5424017.03 4388430.462 5849302.799 4877270.066 5401426.245 3583020.797 1.805993797 1.144088612 1.428323928 1.17470678 1.513811205 1.224785093 1.632505958 1.361217348 1.50750625 1 21.77274499 -2.194249578 1.999989755 3.91E-05 1.408787115 0.288872554 0.197473826 2658705.125 472331.4737 12032932.59 0.043880182 0.006393673 2.194249578 1.408747976 KVEEDLKADEPS(ph)SEES(ph)DLEIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 2 KVEEDLKADEPS(0.53)S(0.477)EES(0.993)DLEIDK 83.088 0.0019243 86195000 298240 66289 106590 81650 157460 203760 203880 112260 132430 46190 TRUE FALSE 310014.7455 77673.62009 109367.823 97800.1263 130695.0054 156439.828 187899.3529 110755.3383 127663.8702 55240.04614 5.6121377 1.406110703 1.979864801 1.770456999 2.36594671 2.832000314 3.401506081 2.004982727 2.311074648 1 15.7534269 4.746991227 24.97557611 2.214082752 5.612139423 0.719639041 0.651649277 587.0963367 1739226.612 0.156513334 1.818197842 55845.89128 -4.746991227 3.398056671 KVEEDLKADEPSS(ph)EES(ph)DLEIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEEDLKADEPSSEESDLEIDK 22 2 P50502;Q3KNR6;F6VDH7 P50502 ST13 Hsc70-interacting protein 2 KVEEDLKADEPS(0.107)S(0.894)EES(1)DLEIDK 131.2 6.69E-06 56186000 559850 103540 176790 132030 271690 378740 389650 176200 249840 78405 TRUE FALSE 581953.3103 121322.1896 181397.2926 158145.1399 225508.2308 290783.3749 359108.2148 173838.3272 240848.3072 93766.9586 6.206379294 1.293869305 1.93455451 1.686576405 2.404986087 3.101128364 3.829794847 1.853940128 2.568583975 1 16.51679202 1.607012199 24.99999945 1.908338834 2.767051002 0.115319103 1.359994769 0.256240067 6851.202855 0.665638209 0.335958638 40.45872558 -1.607012199 0.858712168 KVEEEEDESALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEEEEDESALKR 13 2 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 81.703 0.0080699 115700000 311860 159550 225100 174360 303560 304710 331190 213190 272350 114200 FALSE TRUE 324172.4736 186951.4714 230966.2909 208847.8876 251960.9796 233945.7204 305230.4624 210332.5368 262548.1767 136575.3035 2.373580474 1.368852688 1.691127788 1.529177547 1.844850227 1.712943075 2.234887674 1.540048101 1.922369345 1 17.0593371 -1.588433171 6.155017721 0.997721235 1.777858718 0.392844844 0.297749811 0.008559974 0.000572378 0.265049926 0.062355631 0.025796859 1.588433171 0.780137483 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 200.98 6.13E-22 5371160000 5418970 4227930 5230540 4029020 6225450 6308170 5811570 4938540 5400560 3857070 TRUE FALSE 5632915.12 4954044.089 5366852.169 4825948.131 5167250.233 4843193.119 5356043.958 4872346.949 5206194.901 4612789.018 1.221151693 1.073980204 1.163472283 1.046210462 1.120200862 1.049948979 1.161129186 1.056269196 1.128643621 1 22.13720788 -4.999901042 0.015696915 3.53E-06 1.938935941 0.333535032 0.052664274 6138.738859 7.308108257 570.8015619 355.5095916 1.00E-05 4.999901042 1.938932413 KVEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEEELR 7 1 Q5T7U0;Q5T7U4;Q9Y5Q8-2;Q9Y5Q8;Q9Y5Q8-3;H7BY84 Q5T7U0 GTF3C5 General transcription factor 3C polypeptide 5 0 75.38 0.069955 120960000 246170 246240 265750 230410 298950 320370 291290 259790 258570 232490 FALSE TRUE 255888.9817 288529.8045 272675.6633 275984.4103 248134.5858 245968.9228 268457.9287 256307.94 249264.1162 278041.9642 0.920325039 1.03772035 0.980699673 0.992599844 0.892435739 0.88464676 0.965530255 0.921831856 0.896498185 1 18.08494312 3.253359041 24.91028173 0.92365228 0.986603929 0.292889882 0.042303541 252.266673 424639.4308 0.011136454 0.015015869 1792.0868 -3.253359041 0.062951649 KVEEEQEADEEDVS(ph)EEEAESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVEEEQEADEEDVSEEEAESK 21 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 KVEEEQEADEEDVS(1)EEEAESK;KVEEEQEADEEDVS(1)EEEAESK 200.52 4.55E-22 379170000 364698 494060 417090 517890 430350 689790 439570 431240 428230 490860 TRUE FALSE 379096.5586 578910.9617 427959.708 620327.0963 357199.2607 529596.7264 405115.3548 425459.9332 412818.086 587034.6189 0.645782287 0.986161536 0.72901954 1.056712971 0.608480742 0.902155868 0.690104709 0.724761231 0.703226135 1 19.16308606 3.217143229 24.99999663 0.756154719 0.854872374 0.06209941 0.151085487 558.1787359 651546.8038 0.039869768 0.047695213 1648.706041 -3.217143229 0.098717655 KVEELEGEITTLNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVEELEGEITTLNHK 15 1 Q10589-2;Q10589 Q10589-2 BST2 Bone marrow stromal antigen 2 0 ;; 236.81 6.61E-18 324986000 560182 378806 464214 404342 680870 613110 622460 502351 564071 373755 FALSE TRUE 582298.4179 443862.9838 476311.7982 484319.6408 565135.9606 470724.4943 573669.9587 495617.8065 543770.1949 446985.1363 1.302724343 0.993015087 1.065609926 1.083525159 1.264328307 1.053109949 1.28342066 1.108801538 1.216528584 1 18.76986733 KVEELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVEELQR 7 1 Q9P2M7;Q9P2M7-2;H0Y4A8;Q13614;Q13614-2;C9JEX3 Q9P2M7;Q13614 CGN;MTMR2 Cingulin;Myotubularin-related protein 2 0 ; 128.69 0.0059864 217840000 548930 482240 492740 461780 707520 682670 585050 515520 581030 540620 FALSE TRUE 570602.1803 565060.9687 505581.2092 553118.7057 587256.0031 524130.2385 539192.2523 508610.2976 560118.8438 646544.1382 0.882541727 0.873971219 0.781974778 0.855500302 0.908299942 0.81066428 0.833960468 0.786659823 0.86632731 1 19.30238934 KVEEVLEEEEEEYVVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVEEVLEEEEEEYVVEK 17 1 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;; 189.9 5.28E-10 348660000 525233 306331 449219 294412 590186 517251 560624 434795 508521 283633 FALSE TRUE 545969.6044 358940.9663 460926.0162 352645.8149 489866.3945 397127.2943 516680.826 428967.2842 490219.4285 339205.4559 1.609554313 1.058181583 1.35884022 1.039623063 1.444158359 1.17075739 1.523209067 1.264623775 1.445199127 1 18.37179985 KVEEVVYDLSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KVEEVVYDLSIR 12 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 ;;; 201.6 2.35E-07 828280000 1749250 1853270 2178620 1919090 2776260 2655960 2485110 2204670 2217510 2076140 FALSE TRUE 1818311.741 2171554.706 2235396.627 2298680.274 2304352.317 2039153.541 2290320.585 2175120.005 2137702.248 2482919.883 0.732327995 0.874597171 0.900309608 0.925797199 0.928081624 0.821272388 0.922430321 0.876033101 0.860963039 1 21.24360628 -0.663357879 0.01665808 1.885438334 2.30E-06 0.363658712 0.054402711 2062.137718 7.567261477 465.2339925 392.4617999 0.217091151 0.663357879 -1.885436034 KVEGAPTQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVEGAPTQGR 10 1 Q9P2E9;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 129.34 0.00049005 186032000 263030 186225 203560 182816 279800 307930 264630 200347 222650 203295 FALSE TRUE 273414.6275 218207.6951 208864.9408 218976.4591 232239.6959 236417.9242 243887.6091 197661.6762 214636.87 243126.7629 1.124576432 0.897505863 0.85907836 0.900667851 0.955220615 0.972406005 1.003129422 0.812998428 0.882818771 1 17.89134919 1.746461092 25 0.880851579 0.950870812 0.086435757 0.081231503 3.645635784 11566.67755 0.037307975 0.020689167 55.77776288 -1.746461092 0.070019233 KVEGAQNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEGAQNQGK 10 1 Q9P2E9 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 118.9 0.0012235 147090000 205890 156330 185350 150950 245210 244120 223310 195340 238520 162950 FALSE TRUE 214018.6962 183178.4614 190180.3733 180807.4595 203529.2918 187426.8297 205806.3787 192721.7868 229935.7118 194876.9326 1.098224881 0.939969954 0.97589987 0.927803291 1.044399093 0.961770216 1.056083837 0.988940991 1.17990215 1 17.5722038 1.286554823 24.99879385 1.089952098 0.996770419 0.238596508 0.064781671 125.9553497 65606.28047 0.039596314 0.0144595 19.34438038 -1.286554823 -0.093181679 KVELS(ph)ES(ph)EEDKGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK;KVELS(1)ES(1)EEDKGGK 101.49 0.0035477 2812720000 6059570 978096 1720630 936131 3049440 3976510 2958100 1712420 2018360 702892 TRUE FALSE 6298806.503 1146076.379 1765471.031 1121294.918 2531097.278 3053025.817 2726236.392 1689467.811 1945719.618 840610.2297 7.493135677 1.363386191 2.10022549 1.333905868 3.011023645 3.631916088 3.243163473 2.009811148 2.314651368 1 19.68107749 1.038257932 1.058660049 1.043526827 2.983120922 0.134181923 1.657652376 1.161865026 2.759052394 1.507249209 0.493002912 10.92088748 -1.038257932 1.939594095 KVELS(ph)ESEEDKGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 KVELS(0.997)ES(0.003)EEDKGGK;KVELS(0.996)ES(0.004)EEDKGGK;KVELS(0.5)ES(0.5)EEDKGGK 185.33 6.21E-07 2175070000 3635900 750000 1307890 691340 2331980 2277220 2079480 1326300 1701700 524430 TRUE FALSE 3779448.14 878806.6658 1341974.688 828084.9886 1935590.873 1748370.167 1916484.924 1308523.118 1640456.149 627182.0177 6.026078607 1.401198761 2.139689357 1.320326421 3.086170869 2.787659909 3.055707705 2.086353054 2.615598189 1 19.25852467 8 0.064635468 1.82E-12 8.070256495 0.196608965 1.212677924 626.1255786 3.005511806 70.87834455 467.1750351 100000000 -8 8.070256495 KVELSSSSQHGPSYDVYNPFYMYQHIS(ph)PDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVELSSSSQHGPSYDVYNPFYMYQHISPDLSR 32 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR;KVELSSSSQHGPSYDVYNPFYMYQHIS(1)PDLSR 349.31 6.57E-132 1155360000 82836 441260 387280 486110 418250 606720 375480 470820 370830 434450 TRUE FALSE 86106.42924 517042.9725 397372.835 582261.1071 347156.0144 465818.4749 346048.8965 464509.428 357483.9007 519572.1595 0.165725641 0.995132174 0.76480779 1.12065494 0.66815746 0.896542408 0.666026634 0.894022937 0.688035135 1 18.9869646 4.746331748 24.90479166 0.846011717 0.165725294 0.657948521 0.148934252 512.6171131 1642786.286 0.032298386 0.348614492 55761.1533 -4.746331748 -0.680286423 KVENEDMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVENEDMNK 9 1 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 93.477 0.015028 52066000 79422 68001 77178 63462 104040 104650 104500 86007 85016 65143 FALSE TRUE 82557.64189 79679.64278 79189.32208 76014.59418 86355.31796 80346.62349 96309.01694 84854.21684 81956.29077 77906.52361 1.059701268 1.022759572 1.016465867 0.975715391 1.108447842 1.031320867 1.236212482 1.089179865 1.051982388 1 16.24945652 3.223270559 24.97619346 1.098182722 1.018796551 0.205266582 0.062477029 309.6887313 505873.0439 0.01783114 0.021389436 1672.132003 -3.223270559 -0.079386171 KVENEDMNKDQILLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVENEDMNKDQILLEK 16 2 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 183.77 1.09E-09 843830000 392760 131380 261510 161970 406170 271140 323120 226380 330310 150240 FALSE TRUE 408266.4681 153943.493 268325.1654 194007.1826 337129.3685 208171.8442 297793.0101 223345.7464 318422.2076 179676.6515 2.272228833 0.856780732 1.493378039 1.079757336 1.876311506 1.158591517 1.657382902 1.24304268 1.772195803 1 17.45504342 -1.509607521 3.312445875 0.989266175 1.452430784 0.111445403 0.402684095 12138206.02 8358634.726 893233.8876 0.083069619 0.030930894 1.509607521 0.463164609 KVEQNSRPVS(ph)CSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 KVEQNSRPVS(1)CSGR;KVEQNSRPVS(0.997)CS(0.003)GR;KVEQNSRPVS(0.998)CS(0.002)GR;KVEQNSRPVS(0.994)CS(0.006)GR;KVEQNSRPVS(0.998)CS(0.001)GR;KVEQNSRPVS(0.982)CS(0.018)GR 235.75 1.58E-17 7631790000 3007090 2796350 3151890 2871030 4098290 4027830 3469160 3490560 3383780 3603930 TRUE FALSE 3125812.235 3276601.36 3234030.843 3438911.165 3401664.13 3092427.525 3197238.174 3443774.753 3261998.419 4310051.082 0.725237863 0.760223324 0.750346291 0.797881765 0.789239864 0.717492082 0.74180981 0.799010194 0.756835211 1 22.03927354 -5 0.380111288 4.364441068 0.756357112 0.878597543 0.026807095 193.303764 1.444527748 536.0772991 0.018448474 1.00E-05 5 -3.608083956 KVEQNSRPVSCSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVEQNSRPVSCSGR 14 2 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 154.88 3.37E-06 38664000 49346 59062 60738 55151 72490 74195 61935 62394 55627 59738 FALSE TRUE 51294.21818 69205.43906 62320.88218 66059.70319 60168.17569 56964.33569 57080.37286 61557.71049 53624.99514 71442.51735 0.717978874 0.968687018 0.872322036 0.924655312 0.842190028 0.797345024 0.798969227 0.861639718 0.750603382 1 16.1244953 3.02141779 23.7613945 0.830888001 0.878674038 0.016022582 0.086147544 385.9511977 428177.8314 0.023046565 0.027543181 1050.552571 -3.02141779 0.047786037 KVESLWPIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVESLWPIFR 10 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 128.28 0.00053509 414960000 596930 324340 446520 284110 536860 599810 536130 408390 486740 341550 FALSE TRUE 620497.2573 380042.872 458156.678 340306.11 445604.729 460513.2177 494106.7297 402916.2 469222.3225 408470.1831 1.519076013 0.930405419 1.121640445 0.833123503 1.090911277 1.127409629 1.209651892 0.986402966 1.148730903 1 18.63987125 4.747943027 24.9085512 1.052894065 1.519076272 0.630690683 0.107704733 771.819398 2048992.245 0.024965802 0.31865898 55968.41746 -4.747943027 0.466182207 KVEWTSDTVDNEHMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVEWTSDTVDNEHMGR 16 1 O60927 O60927 PPP1R11 Protein phosphatase 1 regulatory subunit 11 0 ;; 183.7 1.26E-09 392562000 334751 386036 410315 373061 430695 481932 408241 442807 423226 473849 FALSE TRUE 347967.228 452334.6801 421008.146 446851.3523 357485.6177 370010.5968 376242.0037 436871.8965 407994.1789 566690.6392 0.614033838 0.798203903 0.742924123 0.788527852 0.630830286 0.652932255 0.66392839 0.770917792 0.71995927 1 19.11220185 0.157807006 1.016658178 1.001703663 0.708107556 0.661319153 0.062633499 3.031413533 3.111648285 0.074302866 0.019220002 1.438159341 -0.157807006 -0.293596107 KVFAENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVFAENK 7 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 95.099 0.021992 6938400000 5687000 4182000 4733800 3744400 8689100 6324100 5522900 4276000 4529300 5016200 FALSE TRUE 5911527.151 4900225.969 4857166.717 4485031.144 7212129.886 4855423.618 5090000.667 4218687.214 4366291.378 5999028.349 0.985414105 0.816836608 0.809658904 0.747626263 1.202216337 0.80936834 0.848470847 0.703228418 0.727833096 1 22.51629742 2.50691437 24.99984961 0.792421297 0.903548137 0.089007675 0.139609424 1472.388824 1235501.903 0.045179239 0.042535227 321.3026964 -2.50691437 0.11112684 KVFASLPQVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVFASLPQVER 11 1 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 129.37 0.00039515 1660270000 1788500 1392970 1513210 1363390 1834750 2003240 1740740 1472140 1539850 1475420 FALSE TRUE 1859111.361 1632201.762 1552645.496 1633064.473 1522879.85 1538017.869 1604296.25 1452408.371 1484431.099 1764500.3 1.053619181 0.925022093 0.879934957 0.92551102 0.863065793 0.871645003 0.909207128 0.823127302 0.841275629 1 20.75082825 KVFS(ph)PVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVFSPVIR 8 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 KVFS(1)PVIR;KVFS(1)PVIR;KVFS(1)PVIR 116.54 0.0013794 2806890000 2361240 1985450 2112080 1771790 2584890 2654910 2435390 2231670 2287690 1977330 TRUE FALSE 2454463.578 2326435.593 2167122.54 2122244.774 2145511.321 2038347.388 2244497.768 2201758.114 2205356.484 2364749.955 1.03793789 0.983797711 0.916427775 0.897449969 0.907288873 0.861971636 0.949148033 0.931074387 0.932596057 1 21.17325621 4.458592559 2.702517268 0.920063368 1.036385571 0.528261201 0.034218829 0.212667001 2.839664721 0.008395612 0.041479547 28747.00202 -4.458592559 0.116322203 KVFSDVMEDLYNYINPHNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVFSDVMEDLYNYINPHNGK 20 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 145.71 9.21E-08 283900000 379140 270260 368870 284460 496140 413280 403400 365850 356320 300860 FALSE TRUE 394108.74 316675.0527 378483.0552 340725.339 411806.3 317301.9833 371780.4539 360946.3792 343496.1128 359807.7567 1.095331417 0.880122918 1.051903546 0.946964963 1.144517572 0.881865322 1.033275262 1.00316453 0.954665669 1 18.45686676 5.091481852 18.8662844 0.992999083 6.539920625 0.150655571 0.075420448 437.9994186 90872.81607 0.015753349 624.1818067 123447.3729 -5.091481852 5.546921542 KVFVGR ddPTM_MDA-MB-175_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 ; 154.38 0.016054 5341200000 4739800 4581800 4957200 4327600 5525600 6350300 5251000 5069900 4855000 5210300 FALSE TRUE 4926930.964 5368688.509 5086388.704 5183586.363 4586360.486 4875539.065 4839412.899 5001946.283 4680269.498 6231158.528 0.790692604 0.861587534 0.816282988 0.831881638 0.73603656 0.782445037 0.776647373 0.802731348 0.751107435 1 22.57106899 -1.278996466 3.670031841 1.000460911 0.795785298 0.756573021 0.034982088 13445020.54 17566180.01 64671.32622 0.008649143 0.052602155 1.278996466 -0.204675613 KVGDDIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KVGDDIAK 8 1 P30050 P30050 RPL12 60S ribosomal protein L12 0 ;;; 96.89 0.013822 3841070000 7446400 4351220 6157900 4246750 8691100 7921200 8068200 6727800 7150400 4350350 FALSE TRUE 7740389.622 5098508.187 6318379.933 5086744.475 7213789.926 6081621.347 7435793.402 6637624.845 6893058.501 5202717.79 1.487758886 0.97997016 1.214438335 0.97770909 1.386542614 1.168931622 1.429213288 1.275799517 1.324895714 1 22.31083402 KVGIVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVGIVGK 7 1 Q6P4E4;E9PEL3;P61513;G5E9R3 Q6P4E4 RPL37A 60S ribosomal protein L37a 0 91.626 0.04513 0 704650 535700 630170 550100 870370 801720 769530 947250 730700 703660 FALSE TRUE 732470.1261 627702.3078 646592.7479 658908.1381 722424.8183 615532.6802 709212.2278 934553.6631 704402.2497 841528.7046 0.870404209 0.745907186 0.768354953 0.782989498 0.858467233 0.731445852 0.842766532 1.110542823 0.837050769 1 19.68265296 1.942137215 8.133394751 0.99109972 0.791744074 0.565934132 0.074220116 0.212229791 27.57440358 0.029287108 0.018463809 87.52602694 -1.942137215 -0.199355646 KVGLIAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVGLIAAR 8 1 P62917;E9PKU4;E9PP36 P62917 RPL8 60S ribosomal protein L8 0 ; 141.39 0.0010171 1407480000 1123940 1332290 1001940 862550 3602800 1982720 1255370 1051560 1065390 4490100 FALSE TRUE 1168314.019 1561100.444 1028051.38 1033159.816 2990397.343 1522263.328 1156970.819 1037465.558 1027046.822 5369849.127 0.217569245 0.290715885 0.191448839 0.192400157 0.55688666 0.283483445 0.215456858 0.193201994 0.191261765 1 22.35645012 -1.99292016 5.012802674 1.682998153 0.258844439 0.815342463 0.105769332 0.02549014 3.60E-05 0.003233377 0.024887453 0.010164355 1.99292016 -1.424153715 KVGTLWR ddPTM_MDA-MB-175_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 ; 129.47 0.0058649 2200610000 1699310 1895600 1655730 1567410 2922700 2835200 2322430 2163680 2150040 3135000 FALSE TRUE 1766400.071 2221154.554 1698879.684 1877439.02 2425900.498 2176767.768 2140391.868 2134679.409 2072660.48 3749243.227 0.471135097 0.592427437 0.453126026 0.50075146 0.647037376 0.580588571 0.570886373 0.569362743 0.552821024 1 21.83816799 -5 0.289951621 4.498980606 0.524855804 0.866170076 0.053554036 82.48300616 0.777192452 174.5314083 0.057153506 1.00E-05 5 -3.974124802 KVGWIFTDLVSEDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVGWIFTDLVSEDTR 15 1 Q8TAT6;Q8TAT6-2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 75.961 0.048544 140210000 110170 158810 197320 163940 163470 214930 167020 184180 164160 192690 FALSE TRUE 114519.5967 186084.3821 202462.3213 196366.8427 135683.4278 165015.7648 153928.536 181711.3684 158251.9137 230443.9162 0.496952137 0.807503991 0.87857525 0.852124221 0.588791538 0.716077766 0.667965284 0.788527514 0.686726368 1 17.81405616 -1.784919056 2.559640015 1.076066453 0.729613101 0.354908416 0.112481717 45002272.6 30868162.76 21348083.01 0.027156438 0.016408956 1.784919056 -0.346453352 KVGYTPDWIFLLR ddPTM_MDA-MB-175_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 ; 204.13 1.29E-07 4127100000 2076930 2345180 2818400 2058540 3447900 3293000 2438840 2729480 2824530 3037510 FALSE TRUE 2158928.8 2747946.422 2891849.819 2465713.068 2861827.19 2528250.656 2247677.348 2692895.785 2722875.717 3632651.928 0.594312046 0.756457397 0.796071266 0.678763921 0.787806607 0.69597933 0.618742834 0.741303004 0.749555909 1 21.79259171 0.616879352 1.903302656 0.999902265 0.711127591 0.657813784 0.062723397 1.210694418 5.275451248 0.0584823 0.016245118 4.13884681 -0.616879352 -0.288774674 KVIEINPYLLGTMAGGAADCSFWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVIEINPYLLGTMAGGAADCSFWER 25 1 P28074;H0YJM8;P28074-2 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 241.59 2.05E-38 463230000 659290 641270 800870 660980 911590 944350 722440 815570 833040 726300 FALSE TRUE 685319.2783 751403.1341 821741.3301 791719.8712 756638.2574 725039.0243 665813.2651 804638.6182 803059.0531 868604.5791 0.788988793 0.865069276 0.946047661 0.9114848 0.871096326 0.834717018 0.766532069 0.92635779 0.924539281 1 19.72834003 1.14814338 1.911368559 0.992975647 0.86185841 0.417254719 0.052487858 0.3289209 2.240943516 0.051863958 0.014912937 14.06511798 -1.14814338 -0.131117237 KVIIWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVIIWR 6 1 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 121.87 0.03121 1198100000 1033170 1141260 1078530 1215180 1474130 1728780 1559240 1468660 1458430 1356520 FALSE TRUE 1073960.349 1337262.527 1106637.378 1455538.977 1223557.909 1327297.045 1437022.694 1448975.015 1405941.389 1622304.122 0.661996931 0.824298298 0.682139288 0.897204758 0.754209949 0.818155503 0.885791187 0.893158684 0.866632446 1 20.62961287 7.617368892 0.086157262 1.141912362 1.65E-15 0.654965525 0.058101163 88.84431419 0.59628482 1.173104175 12.0362386 41435147.8 -7.617368892 -1.141912362 KVIQYLAYVASSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVIQYLAYVASSHK 14 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 98.592 0.0016336 370540000 931380 668300 854040 643730 1198100 1050900 916450 945590 1011100 822760 FALSE TRUE 968151.6016 783075.3263 876296.984 771057.8727 994447.39 806844.4015 844616.2543 932915.9127 974710.7085 983964.0693 0.983929832 0.795837318 0.890578235 0.783624013 1.01065417 0.819993765 0.858381196 0.948119898 0.990595835 1 19.90824611 1.548793677 3.153420549 0.992092863 0.874356068 0.321518445 0.069776231 0.239994289 5.320184561 0.044706371 0.017287457 35.38292054 -1.548793677 -0.117736795 KVKS(ph)QS(ph)KMASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVKSQSKMASK 11 3 P49796-1;P49796-4;P49796-6;P49796;P49796-2;H7BXY1;A0A087WUY2;P49796-7;P49796-8;P49796-9 P49796-1 RGS3 Regulator of G-protein signaling 3 2 KVKS(1)QS(1)KMASK 53.569 0.055749 88633000 219050 162000 197900 144320 259170 230980 226590 220760 232230 139660 TRUE FALSE 227698.2631 189822.2398 203057.4366 172866.0652 215116.376 177338.3955 208829.2837 217801.0733 223872.0877 167023.703 1.363269159 1.13649881 1.215740238 1.03497924 1.287939209 1.06175586 1.250297293 1.304012959 1.34036118 1 17.34969333 2.044828976 24.99991009 1.255717445 1.178656556 0 0.125846875 331.5390378 184888.9503 0.043869846 0.032400014 110.8738111 -2.044828976 -0.077060889 KVLGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVLGEK 6 1 P14618;P14618-3;B4DNK4;F2Z349;A0A087WZC3;Q5VXJ5;Q5T6T6;A6XNE0;H0Y4U4;H0Y6A4;P09466-2;P09466;Q15431;P14618-2;H3BTN5;H3BR70;H3BQ34 P14618;P14618-2 PKM;PAEP;SYCP1 Pyruvate kinase PKM;Pyruvate kinase;Glycodelin;Synaptonemal complex protein 1 0 91.906 0.075939 5231200000 5153500 3854700 4938400 3463700 5988700 5429700 6005400 5079800 5333700 3646000 FALSE TRUE 5356964.159 4516714.74 5067098.761 4148809.522 4970742.913 4168734.463 5534681.056 5011713.59 5141741.179 4360363.893 1.228558967 1.035857293 1.162081626 0.951482405 1.139983505 0.956051964 1.269316321 1.149379665 1.179200017 1 22.05601711 2.231719667 24.99965045 1.164413916 1.077793277 0.0951942 0.102331621 304.6435033 1113281.24 0.034929719 0.026373551 170.4981485 -2.231719667 -0.086620638 KVLQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVLQLLR 7 1 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 73.616 0.094272 0 123090 121220 96915 72637 802400 266680 113660 118470 107080 997520 FALSE TRUE 127949.6882 142038.592 99440.68452 87004.3818 666008.3346 204747.6116 104751.0322 116882.1034 103226.2117 1192964.945 0.107253519 0.119063509 0.083355915 0.072931214 0.558279887 0.171629194 0.087807301 0.097976142 0.086529124 1 20.18612022 -1.172440664 4.945485577 1.000064384 0.153788568 0.771541764 0.13812817 38.06321953 375389053.6 48897.61915 0.033324746 0.067229416 1.172440664 -0.846275816 KVLVTVEEDDTIMEELVDNHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVLVTVEEDDTIMEELVDNHGK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 338.76 2.75E-81 312531000 230852 167994 223963 181524 268839 255874 278887 227965 251359 165916 FALSE TRUE 239966.2152 196845.6627 229799.6598 217428.9054 223141.8428 196451.1413 257027.1082 224909.5021 242312.6387 198424.0635 1.209360452 0.992045315 1.158123948 1.095778917 1.124570472 0.990057041 1.295342428 1.133478964 1.221185749 1 17.59822747 2.246222101 24.99997209 1.173670722 1.094560347 0.105625586 0.094016159 320.2900455 1045130.734 0.030135378 0.024760768 176.2877365 -2.246222101 -0.079110374 KVMDDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVMDDLDR 8 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 123.63 0.0021479 760290000 952180 950630 1055430 912800 1259610 1261590 1120890 1037010 1056670 997100 FALSE TRUE 989772.8016 1113893.308 1082935.373 1093349.116 1045501.942 968604.8421 1033031.713 1023110.577 1018640.653 1192462.654 0.83002415 0.934111692 0.908150347 0.916883318 0.876758646 0.812272685 0.866301103 0.857981232 0.854232751 1 20.18551265 4.812154576 21.22282643 0.883486604 0.83001964 0.101863571 0.049779768 67704.40629 19517064.61 0.011626888 64.78364017 64886.53399 -4.812154576 -0.053466964 KVMDS(ph)DEDDDY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(1)DEDDDY;KVMDS(0.981)DEDDDY(0.019);KVMDS(0.997)DEDDDY(0.003) 113.35 0.0014872 16836120000 10596380 6907100 8763120 6683880 11247980 11008080 10857630 9088590 9581450 6334730 TRUE FALSE 11014733.26 8093340.695 8991494.106 8005931.515 9336052.377 8451620.249 10006580.59 8966772.317 9236615.486 7575899.058 1.453917638 1.068301021 1.186855057 1.056763224 1.232335899 1.115593038 1.32084397 1.183591842 1.219210475 1 22.85298568 4.751237909 24.6167831 1.167125776 1.453917863 0.486835571 0.091535632 1400.48483 2719403.369 0.020571648 0.362396419 56394.65047 -4.751237909 0.286792086 KVMDSDEDDDY(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVMDSDEDDDY 11 1 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 KVMDSDEDDDY(1);KVMDS(0.003)DEDDDY(0.997) 144.77 3.84E-05 13618300000 7700500 5059700 6524600 5028200 8601100 8085000 8050400 6864400 7321100 4873200 TRUE FALSE 8004521.686 5928664.116 6694636.436 6022762.952 7139088.094 6207381.279 7419388.612 6772393.946 7057615.041 5828010.237 1.373457039 1.017270711 1.148700185 1.033416674 1.224961488 1.065094437 1.273056894 1.162042219 1.210981923 1 22.47457198 KVNAEGSVDSVFSQVCTHLDALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVNAEGSVDSVFSQVCTHLDALK 23 1 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 ; 215.48 1.75E-32 1340690000 1049610 711800 864800 644590 1173050 1097690 976950 882340 992870 732920 FALSE TRUE 1091049.413 834046.113 887337.3984 772087.9781 973655.38 842768.1332 900374.1062 870513.6755 957136.8026 876521.6414 1.244748973 0.95154081 1.012339407 0.880854438 1.110817274 0.961491529 1.027212637 0.993145673 1.091971672 1 19.74143019 4.746029751 24.69605233 1.002273708 1.244749111 0.569798213 0.062943504 516.6839125 1708321.845 0.013854911 0.144716721 55722.39197 -4.746029751 0.242475402 KVNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KVNELR 6 1 P50502;Q3KNR6;Q8IZP2;F8WAQ7 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;;;; 100.82 0.059688 4750630000 11465890 10701000 11353130 9918100 13940660 13876670 12787580 12068280 12110080 10667340 FALSE TRUE 11918572.19 12538813.51 11649001.89 11879870.58 11571031.59 10654023.7 11785256.07 11906524.45 11674240.59 12757401.03 0.93424767 0.982865826 0.913117167 0.93121401 0.907005397 0.835124934 0.923797569 0.933303297 0.915095524 1 23.60483111 -0.504175406 1.201981655 1.001277504 0.919722197 0.328054373 0.034527946 87.20000109 64.68633356 0.593552212 0.010587456 0.313202048 0.504175406 -0.081555308 KVNIDFEPFKPINTSLYLCDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVNIDFEPFKPINTSLYLCDNK 22 2 B7Z7P8;P62495-2;P62495;I3L492;D6RJE8 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ; 192.45 6.00E-18 901460000 1140140 455870 933790 653990 1195650 1035720 1465270 982350 1155450 388410 FALSE TRUE 1185153.608 534162.1263 958125.3345 783347.27 992413.8401 795189.7265 1350418.309 969183.2051 1113865.58 464511.5029 2.551397759 1.149943808 2.06265147 1.68638939 2.136467738 1.711883821 2.907179478 2.086456845 2.397928949 1 18.8253548 KVNLGVGAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVNLGVGAYR 10 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 134.68 0.00026352 1675820000 948310 972530 1150150 919470 1335120 1270260 1045650 1077180 1066630 1106180 FALSE TRUE 985750.0111 1139554.462 1180123.854 1101338.422 1108176.779 975261.366 963689.2207 1062742.164 1028242.195 1322914.792 0.745134923 0.86139672 0.89206339 0.832508963 0.837678123 0.737206487 0.728459026 0.803333798 0.777255044 1 20.33528871 4.765996758 21.78221451 0.817946601 0.745134338 0.082539503 0.075843509 4085.469815 3243246.404 0.017794852 1.138812578 58344.07491 -4.765996758 -0.072812262 KVNNADDFPNLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVNNADDFPNLFR 13 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 165.51 5.65E-05 789950000 975200 864920 985450 877120 1261470 1252340 798900 872900 1000540 1052110 FALSE TRUE 1013701.649 1013463.282 1011131.637 1050611.718 1047045.78 961503.0144 736280.1305 861200.2033 964530.7608 1258250.811 0.805643549 0.805454106 0.803601021 0.834977978 0.832143934 0.76415847 0.585161658 0.684442399 0.766564784 1 20.2629881 2.47794366 24.99908038 0.716344597 0.814289873 0.006134236 0.101105398 52.37236483 1592088.953 0.032858024 0.027804461 300.5686358 -2.47794366 0.097945275 KVNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 KVNVTVDYIRPAS(0.965)PAT(0.033)ET(0.002)VPAFSER;KVNVTVDYIRPAS(0.984)PAT(0.016)ETVPAFSER;KVNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER;KVNVTVDYIRPAS(0.999)PAT(0.001)ETVPAFSER 212.96 3.07E-26 3989720000 1947890 1725450 2110620 1832550 2316810 2412830 2117560 2118750 2121410 2039680 TRUE FALSE 2024794.201 2021782.615 2165624.491 2195022.92 1922999.464 1852486.799 1951580.114 2090351.622 2045060.868 2439316.244 0.830066297 0.828831694 0.887799807 0.899851721 0.788335448 0.759428714 0.800052112 0.856941623 0.838374636 1 21.21804538 0.28568732 1.403931483 1.000069031 0.830921881 0.606516468 0.040619942 4.314379904 7.689787223 0.043247821 0.012523863 1.930577854 -0.28568732 -0.16914715 KVNVTVDYIRPASPATETVPAFSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVNVTVDYIRPASPATETVPAFSER 25 2 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 214.05 3.24E-27 1906020000 425740 359320 357690 340540 417610 465370 402500 395120 421330 392300 FALSE TRUE 442548.5439 421030.4149 367011.6952 407897.7956 346624.8014 357294.8703 370950.9983 389824.0627 406166.4156 469163.674 0.943271119 0.897406253 0.782267928 0.869414702 0.738814236 0.761556979 0.790664365 0.830891402 0.865724348 1 18.83973179 KVPGVTAIELDEDTGTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVPGVTAIELDEDTGTFR 18 1 B4DXZ6;P51114;P51114-3;P51114-2;E7EU85;E9PFF5 B4DXZ6;P51114-2 FXR1 Fragile X mental retardation syndrome-related protein 1 0 ; 308.19 7.06E-61 749000000 773850 723520 821920 742350 970260 999370 885310 833210 849180 749250 FALSE TRUE 804402.1955 847778.9318 843339.9104 889184.6143 805335.5518 767281.4631 815917.0889 822042.1828 818618.1777 896051.1922 0.897719017 0.946127787 0.941173805 0.992336846 0.89876065 0.856291995 0.910569726 0.917405378 0.913584162 1 19.77322163 KVPLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KVPLDER 7 1 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ;;; 105.57 0.012663 3552640000 6848800 6663700 7398800 6626410 8803400 8624000 7993600 7329000 7542500 6996500 FALSE TRUE 7119195.912 7808138.639 7591618.806 7937094.12 7307001.212 6621206.698 7367040.745 7230766.743 7271046.898 8367330.219 0.850832431 0.933169653 0.907292841 0.948581437 0.8732775 0.791316528 0.88045297 0.864166533 0.868980512 1 22.99633594 5.071462958 12.27084686 0.888536883 0.567115758 0.043225855 0.053944053 21673910.56 115476448.3 0.012790463 168372850.6 117886.197 -5.071462958 -0.321421125 KVPS(ph)DKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVPSDKER 8 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 KVPS(1)DKER;KVPS(1)DKER 69.261 0.042824 149337000 412270 132487 209619 151937 330270 313810 317410 221165 253140 118097 TRUE FALSE 428546.7379 155240.6116 215081.8433 181989.6851 274130.8234 240932.3833 292530.5748 218200.6449 244029.5408 141235.846 3.034263255 1.099158719 1.522855913 1.288551669 1.940943684 1.705886927 2.071220466 1.544938137 1.727815903 1 17.10774677 0.187340587 1.194110584 0.998438155 1.740747013 0.172841861 0.502462057 10.65192522 13.90086089 0.483337481 0.135487315 1.53936138 -0.187340587 0.742308858 KVQEAVLDKWVNDPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVQEAVLDKWVNDPHR 16 2 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 155.2 1.69E-07 289140000 453610 391080 493060 325100 599430 536650 446910 476730 556580 441310 FALSE TRUE 471518.8731 458244.9478 505909.5487 389403.8097 497539.1027 412021.1705 411880.0264 470340.2141 536548.7945 527776.2451 0.893406775 0.868256107 0.958568244 0.737819887 0.942708406 0.780673959 0.780406527 0.89117352 1.016621721 1 19.00956689 1.325615024 4.199783524 1.00921174 0.851979599 0.456040715 0.067244562 0.18182177 5.186080874 0.049915173 0.016459612 21.16484169 -1.325615024 -0.157232141 KVQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_MDA-MB-175_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(0.652)Y(0.348)DEEIHDPR 73.765 0.0026879 267220000 140880 157650 174510 145510 192090 188870 160590 179480 185060 163120 TRUE FALSE 146442.0512 184725.1612 179057.874 174291.4437 159438.6104 145007.8049 148002.5362 177074.3642 178399.7267 195080.2409 0.750675981 0.946918869 0.917867813 0.893434634 0.817297588 0.743323897 0.758675176 0.907700151 0.914494087 1 17.57370813 1.140157382 1.889841664 0.99274474 0.840263686 0.358059141 0.069047441 0.383334616 2.57495631 0.06948727 0.019989701 13.80884585 -1.140157382 -0.152481054 KVQSGNINAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVQSGNINAAK 11 1 P49368;P49368-2;Q5SZX6;E9PRC8;Q5SZW8;E9PM09;Q5SZX9 P49368 CCT3 T-complex protein 1 subunit gamma 0 124.38 0.0016579 0 521820 421080 520450 377780 627610 649910 557040 537700 572580 450260 FALSE TRUE 542421.8565 493397.2145 534013.3546 452503.7564 520929.0764 498978.252 513377.7492 530493.011 551972.9576 538479.8263 1.007320665 0.916277993 0.991705406 0.840335579 0.967406857 0.926642425 0.95338344 0.985167847 1.025057822 1 19.03853277 1.639464344 2.336706388 1.012061039 0.939422604 0.296318494 0.043697371 0.304836731 3.700541328 0.029167822 0.011422385 43.59777679 -1.639464344 -0.072638434 KVQVAALQAS(ph)PPLDQDDR ddPTM_MDA-MB-175_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 247.34 1.39E-24 16021650000 7111740 6471100 7223030 6576870 8202290 8893730 7636950 7799770 7778980 7385100 TRUE FALSE 7392516.987 7582461.087 7411268.096 7877755.256 6808067.676 6828295.993 7038345.904 7695226.841 7499016.029 8832068.949 0.837008523 0.858514707 0.839131594 0.891949021 0.770834978 0.773125304 0.796907944 0.871282469 0.849066744 1 23.07432 0.528974336 1.184670559 0.999793253 0.82741024 0.650412863 0.037419587 1.152774025 2.195117694 0.038348545 0.011679716 3.380448592 -0.528974336 -0.172383013 KVQYAPERPGPQPTAETTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KVQYAPERPGPQPTAETTR 19 2 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;; 212.34 4.88E-17 2336720000 981517 1022697 1110876 999450 1229510 1319435 1112442 1111315 1163270 1151208 FALSE TRUE 1020268.049 1198337.254 1139826.341 1197138.227 1020518.329 1013016.217 1025245.889 1096419.64 1121404.14 1376765.166 0.741061783 0.87040062 0.827901787 0.869529718 0.741243572 0.735794486 0.744677389 0.796373751 0.814521 1 20.39285107 -1.916581949 7.770333796 1.04635231 0.793814804 0.610128807 0.049520512 0.030153984 0.000323717 0.036359499 0.011798997 0.01211764 1.916581949 -0.252537505 KVS(ph)IVSKPVLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVSIVSKPVLYR 12 2 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 KVS(0.999)IVS(0.001)KPVLYR;KVS(0.998)IVS(0.002)KPVLYR 163.7 3.09E-05 1739240000 2411120 1664150 2150610 1644820 3589800 2598400 2267010 2246500 2375170 2310000 TRUE FALSE 2506312.879 1949954.817 2206656.663 1970160.487 2979607.078 1994960.979 2089315.832 2216389.342 2289688.096 2762600.272 0.90722965 0.705840377 0.798760749 0.713154381 1.078551649 0.722131609 0.756285972 0.802283763 0.828816285 1 21.3975954 0.756420777 3.605365664 0.999994086 0.806783892 0.220050851 0.106164679 3.652447903 52.50675161 0.096803126 0.024908752 5.707169574 -0.756420777 -0.193210194 KVS(ph)LVLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVSLVLEK 8 1 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 KVS(1)LVLEK;KVS(1)LVLEK 126.12 0.0013059 805330000 961170 527660 754020 535420 1076300 885450 1014710 803610 956420 489050 TRUE FALSE 999117.7338 618281.5004 773670.3806 641324.4779 893350.9104 679817.6566 935174.3787 792838.9224 921998.631 584869.9841 1.708273225 1.057126399 1.322807464 1.096524861 1.527435045 1.162339794 1.598944046 1.355581486 1.576416394 1 19.15775643 2.254181833 24.99831186 1.412946623 1.30124615 0.012859001 0.23942238 795.9884975 1273801.807 0.076352745 0.063679018 179.5485215 -2.254181833 -0.111700474 KVS(ph)PIKINLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSPIKINLK 10 2 H0Y6F5;Q9H4I2;Q9H4I2-2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 KVS(1)PIKINLK 106.32 0.0012689 582110000 731680 311290 460520 241010 764660 629420 618670 429090 582170 297660 TRUE FALSE 760567.2914 364751.636 472521.5295 288681.0587 634683.3663 483246.744 570177.0288 423338.7504 561217.8154 355980.778 2.136540337 1.024638572 1.327379338 0.810945637 1.782914712 1.357507972 1.601707351 1.189218004 1.576539662 1 18.44143982 -2.040701199 2.515091703 0.504238429 1.391699083 0.104505028 0.361167595 27450286.22 14143884.11 78167676.36 0.082911131 0.009105395 2.040701199 0.887460654 KVS(ph)TSGQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVSTSGQIR 9 1 Q86XP1-2;Q86XP1;Q16760;A0A087WZ02;C9JY42;A0A096LNI6 Q86XP1-2 DGKH;DGKD Diacylglycerol kinase eta;Diacylglycerol kinase delta 1 KVS(0.847)T(0.122)S(0.031)GQIR;KVS(0.914)T(0.058)S(0.028)GQIR;KVS(0.846)T(0.147)S(0.007)GQIR 108.59 0.0015839 406900000 523720 458626 483160 428237 645090 616210 522760 508690 480860 486070 TRUE FALSE 544396.87 537391.4479 495751.5465 512941.0004 535437.8322 473104.5663 481784.7052 501871.8426 463553.9425 581306.1101 0.936506361 0.924455186 0.85282356 0.88239396 0.921094451 0.813864775 0.828796905 0.863352086 0.79743518 1 19.14893855 2.750394456 24.91402428 0.850662355 0.900638514 0.111783525 0.056585661 1302.217706 2741582.843 0.016273591 0.017124654 562.8523142 -2.750394456 0.049976159 KVSAQEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVSAQEVR 8 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 98.048 0.012505 420799000 681230 862960 640580 623410 1519880 1225830 832750 736350 737950 1647080 FALSE TRUE 708125.4864 1011166.667 657274.041 746718.6373 1261531.34 941149.5601 767476.879 726480.4327 711391.3237 1969793.791 0.359492191 0.513336305 0.333676573 0.379084674 0.640438277 0.477790906 0.389622956 0.368810398 0.36115015 1 20.90961318 -1.078679827 5.13990976 1.000010561 0.425583179 0.787727086 0.089573337 1.11E-05 1.99E-06 0.088924468 0.020959313 0.083429602 1.078679827 -0.574427382 KVSHVADTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSHVADTK 9 1 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 111.06 0.0014194 259090000 668820 444690 600480 440520 786610 702600 721980 606070 678820 485050 FALSE TRUE 695225.53 521062.0483 616129.0021 527653.5412 652902.3132 539431.798 665389.3211 597946.623 654389.4008 580086.2607 1.198486462 0.89824925 1.062133417 0.909612202 1.125526249 0.929916522 1.147052372 1.030789149 1.128089812 1 19.14590792 2.228980831 24.99971901 1.076306618 1.01669515 0.071745568 0.097757183 515.0284668 1344023.776 0.032998236 0.024667647 169.4263016 -2.228980831 -0.059611468 KVSMDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSMDNR 7 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 83.843 0.023068 30088000 62958 53658 57956 46596 95515 79763 68413 59150 61457 80910 FALSE TRUE 65443.63045 62873.3441 59466.38097 55812.54972 79279.39442 61239.25207 63050.6103 58357.191 59245.17457 96762.76538 0.676330717 0.649767954 0.614558511 0.576797795 0.819317163 0.632880342 0.651599921 0.603095527 0.612272441 1 16.56216438 -1.741494997 5.223392256 1.015762582 0.646897822 0.735880457 0.063165627 0.011558404 0.000572024 0.060968023 0.014251121 0.018134476 1.741494997 -0.368864761 KVSNDAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSNDAKR 8 2 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 75.509 0.021488 213530000 744360 778500 764380 640940 1200300 930950 699960 752550 793750 975890 FALSE TRUE 773747.9076 912201.3191 784300.3707 767716.019 996273.4347 714750.9712 645095.3062 742463.2982 765183.0926 1167096.961 0.662967974 0.781598573 0.672009608 0.65779969 0.853633818 0.612417815 0.552734972 0.636162481 0.655629411 1 20.15449299 -0.96012433 5.043251469 1.000001859 0.673661977 0.593935275 0.080320888 1.75E-06 3.61E-07 0.081152192 0.019127646 0.109616434 0.96012433 -0.326339882 KVSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSPNELILGWYATGHDITEHSVLIHEYYSR 31 1 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 195.01 3.00E-20 122110000 118810 128980 154040 136990 169940 176510 147970 140790 158890 154960 FALSE TRUE 123500.7105 151131.3117 158054.4089 164086.2131 141053.6595 135518.2275 136371.7248 138902.9403 153171.5799 185321.4451 0.666413487 0.815509029 0.852866266 0.88541406 0.761129719 0.731260365 0.735865861 0.749524375 0.826518376 1 17.49967031 0.886640852 4.801540254 0.999983903 0.777464408 0.55884716 0.060041205 0.64752583 26.32320406 0.061233246 0.015504211 7.7026622 -0.886640852 -0.222519495 KVSQPIEGHAASFAQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVSQPIEGHAASFAQFK 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 216.72 3.38E-15 1356830000 2534400 2451700 3358700 2271000 4051900 3971000 3202200 3177700 3557400 2871400 FALSE TRUE 2634460.069 2872760.403 3446230.481 2720197.022 3363159.485 3048795.431 2951203.197 3135108.129 3429369.869 3433995.854 0.767170428 0.836564902 1.003562796 0.792137538 0.979372029 0.887827348 0.859407909 0.912962118 0.998652886 1 21.71145687 8 0.116238081 1.027427337 0.392933057 0.354666003 0.068108509 124.2643977 0.997631004 0.502444047 12.72715686 100000000 -8 -0.63449428 KVST(ph)SGQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVSTSGQIR 9 1 Q86XP1-2;Q86XP1;Q16760;A0A087WZ02;C9JY42;A0A096LNI6 Q86XP1-2 DGKH;DGKD Diacylglycerol kinase eta;Diacylglycerol kinase delta 1 KVS(0.077)T(0.909)S(0.013)GQIR 123.95 0.00031843 563000000 373160 349110 344780 312390 545950 478000 402220 346370 375230 370300 TRUE FALSE 387892.6449 409066.9268 353765.25 374179.8096 453149.614 366991.7442 370692.9454 341727.4767 361725.5456 442853.1952 0.875894425 0.923707746 0.798831879 0.844929683 1.023250185 0.828698422 0.837056048 0.771649568 0.8168069 1 18.756469 2.579460812 21.80248249 0.830371165 0.890962669 0.037153151 0.078651986 28.26406866 6006.178081 0.024910781 0.023486077 379.717674 -2.579460812 0.060591504 KVT(ph)SPLQS(ph)PTK ddPTM_MDA-MB-175_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(0.567)S(0.433)PLQS(1)PTK 100.11 0.0036981 567210000 1421200 603680 976170 621730 1303900 1386600 1248900 1037900 1236200 612490 TRUE FALSE 1477310.073 707357.344 1001609.792 744706.3383 1082263.544 1064583.164 1151007.955 1023988.648 1191709.403 732495.6887 2.016817431 0.965681239 1.36739343 1.016669927 1.477501589 1.45336441 1.571351166 1.397944949 1.626916611 1 19.48246074 KVTAAMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVTAAMGK 8 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 103.7 0.0075718 1142160000 1444110 1043590 1248670 920820 2729000 1796940 1693730 1302860 1447390 1962320 FALSE TRUE 1501124.578 1222818.464 1281211.366 1102955.448 2265125.555 1379627.918 1560971.017 1285397.293 1395298.717 2346799.033 0.639647689 0.521058023 0.545939958 0.469982914 0.965197924 0.587876464 0.665148994 0.547723633 0.594553985 1 21.16226287 -1.961254571 2.405242066 1.312239148 0.613013236 0.445013793 0.128883351 7087158.92 3239938.02 12345593.14 0.033748565 0.010933153 1.961254571 -0.699225913 KVTAEADSSS(ph)PTGILATSESK ddPTM_MDA-MB-175_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 KVT(0.001)AEADS(0.01)S(0.059)S(0.92)PT(0.01)GILATSESK;KVTAEADS(0.001)S(0.006)S(0.981)PT(0.012)GILATSESK;KVTAEADS(0.041)S(0.19)S(0.729)PT(0.041)GILATSESK 233.42 5.79E-30 1920990000 2507470 1534830 2129960 1459340 2613030 2613330 2516540 2053680 2299330 1408300 TRUE FALSE 2606466.852 1798425.113 2185468.507 1747993.096 2168868.094 2006423.713 2319287.019 2026153.779 2216577.562 1684229.421 1.547572331 1.067802931 1.297607368 1.037859257 1.287750984 1.191300714 1.377061218 1.20301531 1.316078163 1 20.68365724 -2.310913326 1.94675182 3.12E-05 1.248155479 0.231034082 0.140326628 2178913.037 282915.814 9566218.698 0.030866268 0.004887499 2.310913326 1.24812425 KVTEELLTDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVTEELLTDNR 11 1 Q9UHB9;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ;; 142.57 6.03E-05 628350000 1193690 992850 1177100 1134870 1437580 1398760 1291900 1152410 1254440 984360 FALSE TRUE 1240817.803 1163364.264 1207776.193 1359343.899 1193220.665 1073919.188 1190637.502 1136963.829 1209292.949 1177226.495 1.054017904 0.988224669 1.025950569 1.154700395 1.013586315 0.912245173 1.011392036 0.965798709 1.027238984 1 20.16696049 3.003059105 24.99992252 0.980372046 1.053196408 0.32852832 0.048646743 110.591107 903764.8624 0.014208289 0.016899866 1007.068715 -3.003059105 0.072824362 KVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVTGTEGSSSTLVDYTSTSSTGGSPVR 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 KVTGTEGSSSTLVDYTSTSST(0.001)GGS(0.999)PVR;KVTGTEGSSSTLVDYTSTSSTGGS(1)PVR 248.2 6.81E-46 525540000 398870 366020 421970 393960 457940 485500 443710 414350 430910 373340 TRUE FALSE 414617.6956 428881.0878 432966.8849 471884.1121 380099.5224 372749.9828 408930.8508 408796.316 415401.6333 446488.825 0.928618304 0.960563991 0.969714942 1.056877767 0.851308031 0.834847284 0.915881491 0.915580174 0.930374088 1 18.76826454 3.224230846 24.99999111 0.901890607 0.976971733 0.305489247 0.051882794 277.2053271 483616.5732 0.015123624 0.018155063 1675.833416 -3.224230846 0.075081126 KVTHAVVTVPAYFNDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVTHAVVTVPAYFNDAQR 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 193.22 8.76E-15 1378450000 2209910 2357260 2425230 2541760 2836790 3125620 2436920 2291240 2250950 2455890 FALSE TRUE 2297158.953 2762101.068 2488433.486 3044512.542 2354593.449 2399742.124 2245907.843 2260529.676 2169938.749 2937074.625 0.782124817 0.940425907 0.847248982 1.036579907 0.801679818 0.817051805 0.764675104 0.76965347 0.738809539 1 21.48594849 3.057592185 24.9999959 0.798021041 0.902817358 0.161420336 0.091401148 111.4668459 48385.28843 0.024639988 0.029450416 1141.805642 -3.057592185 0.104796317 KVTLGDTLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVTLGDTLTR 10 1 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 ; 156.14 1.84E-05 512500000 961910 873960 914040 843840 1097620 1124220 904220 855300 898210 908500 FALSE TRUE 999886.9496 1024055.832 937860.6333 1010749.033 911046.9445 863136.9427 833344.8737 843836.1025 865883.5976 1086503.181 0.920279818 0.942524467 0.863191797 0.930277105 0.838512911 0.794417318 0.766997178 0.776653136 0.796945295 1 20.05126097 3.094318188 3.959475144 0.806046208 0.912332249 0.25612152 0.066382752 0.233436832 6.925247269 0.018480117 0.022356157 1242.562343 -3.094318188 0.106286041 KVTQLDLDGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVTQLDLDGPK 11 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 ; 111.39 0.0026728 2046760000 5037300 2827500 3564800 2512410 5348400 4741200 4597700 3585400 4160500 2782700 FALSE TRUE 5236176.494 3313101.13 3657701.617 3009357.199 4439280.878 3640128.154 4237320.26 3537343.578 4010764.418 3327916.787 1.573409682 0.995548069 1.099096477 0.904276577 1.333951887 1.093815857 1.273265088 1.062930297 1.205187712 1 21.66618793 3.076354345 0.016678404 5.94E-06 2.314429404 0.089989505 0.178784179 3626.576579 18.97333127 1239.12348 1392.404965 1192.214351 -3.076354345 2.314423462 KVTS(ph)PLQS(ph)PTK ddPTM_MDA-MB-175_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(0.181)S(0.819)PLQS(0.999)PT(0.001)K 113.67 0.0047591 401060000 1160100 490670 716350 457420 1074200 999110 1003800 807070 906480 482430 TRUE FALSE 1205901.644 574938.7556 735018.6695 547896.3107 891607.8677 767081.8442 925119.5331 796252.5468 873855.9619 576952.9218 2.090121392 0.996508959 1.273966457 0.949637813 1.545373693 1.329539751 1.603457575 1.380099687 1.514605315 1 19.13809408 KVTSPLQS(ph)PTK ddPTM_MDA-MB-175_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 1 KVTSPLQS(0.999)PT(0.001)K 125.73 0.0001974 353320000 255220 181450 203610 135870 359790 319930 296270 257120 265850 207690 TRUE FALSE 265296.2827 212612.626 208916.2439 162744.6805 298633.0243 245631.1061 273047.5832 253673.727 256282.1104 248382.879 1.06809408 0.855987445 0.841105654 0.655216982 1.202309215 0.988921245 1.099301145 1.021301178 1.03180264 1 17.92220621 3.229347492 24.9999956 1.055546894 0.854164667 0.453399659 0.108735736 175.9578616 477464.4567 0.030836088 0.037338985 1695.694033 -3.229347492 -0.201382227 KVTSVVFHPSQDLVFSASPDATIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVTSVVFHPSQDLVFSASPDATIR 24 1 Q9UMS4 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 161.66 1.23E-11 217360000 197030 401890 445300 366640 453940 578620 396890 440400 377470 437720 FALSE TRUE 204808.8965 470911.4812 456904.8838 439160.2977 376779.4409 444244.2741 365780.7247 434497.1583 363884.9284 523482.8533 0.391242799 0.899573841 0.872817287 0.838920119 0.719755076 0.848631949 0.698744424 0.830012207 0.695122918 1 18.99778276 -2.692224333 2.108219255 7.651078984 0.769091868 0.208487585 0.140827067 2908079.815 222717.6679 92237359.77 0.034652412 0.002031307 2.692224333 -6.881987116 KVVAEVYDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 116.19 0.0016395 842320000 755220 980060 837430 814620 912660 1018910 931140 802330 750510 1082340 FALSE TRUE 785036.6688 1148377.681 859254.1138 975749.4046 757526.3792 782283.5942 858154.8137 791576.0787 723499.2917 1294403.8 0.606485139 0.88718658 0.663822305 0.753821492 0.585231887 0.604358234 0.662973033 0.611537202 0.558944042 1 20.30385632 -1.077767943 4.378833222 1.000029953 0.661688967 0.552336485 0.091975788 12562147.99 3091938.516 3719.975571 0.021708819 0.083604963 1.077767943 -0.338340986 KVVDNTTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVVDNTTAK 9 1 Q9H0U4;E9PLD0;Q92928 Q9H0U4 RAB1B;RAB1C Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C 0 ; 111.86 0.0032984 760060000 1112500 770020 1040690 854800 1391130 1287320 1157650 908470 1072020 891120 FALSE TRUE 1156422.359 902264.9451 1067811.236 1023876.889 1154666.219 988359.4395 1066910.368 896293.4456 1033438.21 1065717.902 1.085111132 0.846626432 1.001964248 0.960739128 1.083463285 0.927411876 1.001118932 0.841023167 0.969710847 1 20.02339417 KVVDYSQFQES(ph)DDADEDYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 72 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.001)S(0.001)QFQES(0.997)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.003)QFQES(0.997)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(0.999)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(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 341.46 1.26E-80 3.95953E+11 32855394.4 26536262.7 33202666.1 28616904.4 38494968.8 39490243.6 38155595.3 34784361.3 34611437.6 27326710 TRUE FALSE 34152550.74 31093659.4 34067954.85 34277242.68 31951607.75 30319233 35164860.04 34318133.83 33365778.72 32680855.62 1.045032331 0.951433456 1.042443786 1.048847774 0.977685778 0.927736818 1.076007937 1.050099001 1.02095793 1 24.96194242 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 KVVDYSQFQESDDADEDYGRDSGPPTK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYS(0.002)QFQES(0.998)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYS(0.003)QFQES(0.997)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDY(0.029)S(0.027)QFQES(0.943)DDADEDYGRDS(0.001)GPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK;KVVDYSQFQES(1)DDADEDYGRDSGPPTK 271.28 4.95E-61 75528547000 6438959 4657039 6177118 3616659 7898508 6800555 5116597 5430869 6434639 5287009 TRUE FALSE 6693174.073 5456849.222 6338098.77 4332023.356 6555922.431 5221229.165 4715544.757 5358077.084 6203057.599 6322897.188 1.058561269 0.863029883 1.002404211 0.685132658 1.036854188 0.825765311 0.745788618 0.847408542 0.981046728 1 22.59215433 7.566833761 1.135099248 0.869250722 152.5365347 0.152658622 0.112854476 1888.55479 3.974429221 0.02992273 744373.9496 36883638.83 -7.566833761 151.667284 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 162.19 6.23E-12 4266426000 1165830 757515 1157428 459740 1707509 1270041 685472 933491 1170612 967598 TRUE FALSE 1211857.869 887612.3086 1187591.525 550675.1998 1417267.23 975093.2254 631742.9135 920979.08 1128481.903 1157180.302 1.047250689 0.767047544 1.026280453 0.475876749 1.224759208 0.84264589 0.545933 0.795882092 0.975199717 1 20.14218224 2.47723611 25 0.787643458 0.89801269 0.014897393 0.218998397 13.88363233 3023154.631 0.072443144 0.061209076 300.0793495 -2.47723611 0.110369231 KVVDYSQFQESDDADEDYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;;;; 304.91 4.97E-55 3318630000 1545384 1368505 1573310 1313114 1576463 1748481 1473324 1530162 1450342 1171146 FALSE TRUE 1606396.954 1603535.088 1614311.751 1572844.03 1308496.382 1342422.786 1357841.015 1509652.681 1398144.475 1400609.636 1.146926961 1.144883662 1.152577927 1.122971019 0.934233457 0.958456055 0.969464282 1.077853988 0.998239937 1 20.41762349 3.346082594 6.280324098 0.996796812 1.145831132 0.811606016 0.035914266 0.104482187 5.44045948 0.011621148 0.015765711 2218.618317 -3.346082594 0.14903432 KVVDYTTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KVVDYTTAK 9 1 P62820;E7END7;P62820-2 P62820 RAB1A Ras-related protein Rab-1A 0 94.616 0.0097865 0 216620 195910 183910 189290 288110 276780 205060 167180 204080 235400 FALSE TRUE 225172.3249 229556.0185 188702.8457 226730.997 239137.1651 212502.0396 188986.8614 164939.2256 196735.2007 281522.123 0.799838828 0.815410228 0.670294909 0.805375416 0.849443598 0.754832471 0.671303766 0.585883709 0.698826787 1 18.10288877 2.390726213 5.082799588 0.691322851 0.785631079 0 0.112156354 0.419209714 18.50200328 0.038087322 0.031669301 245.8817036 -2.390726213 0.094308228 KVVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 KVVEAVNS(1)DS(0.855)DS(0.145)EFGIPK;KVVEAVNS(1)DS(0.991)DS(0.009)EFGIPK 113.42 0.00086573 645010000 681690 382660 531930 371140 705710 616590 583260 500780 568040 330907 TRUE FALSE 708603.6476 448378.8783 545792.5328 444550.3843 585753.6663 473396.317 537542.5571 494067.8632 547596.3514 395741.8911 1.790570227 1.133008379 1.379162897 1.123334159 1.480140666 1.196224933 1.358316037 1.248459853 1.383720965 1 18.59420026 -5 0.112842309 0.054966065 1.492924972 0.26536594 0.182111836 235.0978572 1.752652265 52.55123706 1.938733669 1.00E-05 5 1.437958908 KVVGDVAYDEAK ddPTM_MDA-MB-175_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 ;;; 157.75 0.00010225 1358720000 3238170 1854460 2543300 1797370 3487360 3054660 3085110 2380380 2763800 1651970 FALSE TRUE 3366015.452 2172949.079 2609580.487 2152884.421 2894579.793 2345261.509 2843291.017 2348474.9 2664331.378 1975641.893 1.703757885 1.099869914 1.320877279 1.089713895 1.46513384 1.187088367 1.439173277 1.188714872 1.348590242 1 20.91389004 -3.693934417 0.296916891 1.01E-13 1.319822048 0.219627442 0.178739985 167.6547709 3.216249097 103.0917917 0.166832598 0.000202332 3.693934417 1.319822048 KVVNPLFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVVNPLFEK 9 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 152.54 0.002279 0 3968100 2880300 3846500 2604200 7435600 4980500 4636800 3800600 4247400 4720300 FALSE TRUE 4124763.652 3374969.119 3946742.95 3119302.987 6171699.368 3823854.355 4273355.5 3749659.174 4094536.904 5645152.409 0.730673568 0.597852613 0.699138422 0.552563113 1.093274179 0.677369551 0.756995594 0.664226384 0.725319107 1 22.4285811 KVVVS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.875)PT(0.125)K;KVVVS(0.999)PT(0.001)K;KVVVS(0.5)PT(0.5)K 99.506 0.0041436 7329380000 11290520 5282970 8298010 5652040 10182350 10119850 11029830 8204260 8830630 5360390 TRUE FALSE 11736278.45 6190279.002 8514262.957 6769996.642 8451557.784 7769668.205 10165283.1 8094295.314 8512817.351 6410655.79 1.830745377 0.965623363 1.328142274 1.056053681 1.318360876 1.211992729 1.585685371 1.262631403 1.327916773 1 22.61204052 -2.239547331 2.129909176 0.003616332 1.307687092 0.143555896 0.233094187 3052353.33 585259.5457 14608487.76 0.052972884 0.0057604 2.239547331 1.30407076 KVVVSPT(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVVVSPTK 8 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 KVVVS(0.382)PT(0.618)K;KVVVS(0.233)PT(0.767)K;KVVVS(0.214)PT(0.786)K 92.112 0.0070374 7576700000 13495300 6953400 9544900 6753600 12053400 12220800 13326700 10354800 10271800 6391600 TRUE FALSE 14028104.86 8147592.36 9793647.935 8089441.923 10004567.37 9382704.408 12282118.43 10216010.84 9902119.924 7643911.645 1.835199766 1.065893058 1.281235104 1.058285639 1.308828233 1.22747421 1.606784458 1.336489917 1.295425743 1 22.86587967 -2.155707583 1.575455814 0.426290555 1.326111152 0.169805642 0.221468594 378913.3428 70043.76426 774189.486 0.057429321 0.006987027 2.155707583 0.899820597 KVVVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVVVVR 6 1 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 136.58 0.021019 2165530000 3747800 3583000 4176400 3570400 4442900 4573200 4243000 4348500 4032200 3867400 FALSE TRUE 3895766.038 4198352.378 4285240.415 4276614.463 3687697.445 3511143.608 3910422.573 4290215.47 3887081.91 4625142.984 0.842301752 0.907723803 0.926509825 0.924644812 0.797315339 0.759142716 0.845470634 0.927585479 0.84042416 1 22.14106654 -1.445151257 3.229455673 1.002143582 0.867107269 0.353489924 0.055198961 16088626.33 26012788.92 326363.9975 0.014555372 0.035879695 1.445151257 -0.135036313 KVYEDSGIPLPAES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KVYEDSGIPLPAESPK 16 1 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 KVYEDSGIPLPAES(1)PK;KVYEDSGIPLPAES(1)PK 131.65 2.66E-05 501260000 1243370 348264 492530 345720 683930 694430 707120 522430 550260 294226 TRUE FALSE 1292459.208 408075.6329 505365.7364 414102.3841 567675.8229 533159.1567 651694.0867 515427.6804 530456.2501 351873.9514 3.673074414 1.159721063 1.436212412 1.176848648 1.613293114 1.515199277 1.852066867 1.46480772 1.507517814 1 18.42469919 4.74315641 24.98907698 1.451725683 3.673075312 0.891265031 0.236391841 139.3175414 757496.3564 0.055120288 0.445511278 55354.94326 -4.74315641 2.221349629 KVYENYPTYDLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KVYENYPTYDLTER 14 1 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;A0A494C198 H0Y993 DEK Protein DEK 0 ;; 231.71 7.02E-13 710220000 630605 671590 731902 606521 787630 833250 718399 704154 711544 709470 FALSE TRUE 655501.7723 786930.3583 750975.9674 726489.0435 653748.9339 639740.3155 662089.0092 694715.9674 685935.6704 848477.0629 0.772562749 0.927462147 0.88508694 0.856227087 0.770496885 0.753986576 0.78032635 0.818779903 0.808431601 1 19.69451613 KWDEFEDILEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KWDEFEDILEER 12 1 Q5TBH8;O15228;A0A2R8YH69 Q5TBH8 GNPAT Dihydroxyacetone phosphate acyltransferase 0 69.108 0.081558 21182000 25805 26303 29696 26611 39743 43254 30364 22812 30839 23664 FALSE TRUE 26823.80133 30820.33564 30469.90216 31874.57637 32987.49906 33208.91402 27983.99034 22506.24245 29729.11041 28300.50773 0.947820498 1.089038258 1.076655672 1.126289913 1.165615097 1.173438807 0.988815841 0.795259317 1.050479755 1 14.78854032 2.026349287 7.815334494 0.917380342 1.098581148 0.373248048 0.085810638 0.160769252 38.22417541 0.0327937 0.0238597 106.2549783 -2.026349287 0.181200806 KWDGS(ph)EEDEDNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK;KWDGS(1)EEDEDNSK 233.63 7.46E-17 3905480000 4671190 1490427 2539739 1457746 3960850 4000950 3721740 2543140 2991500 1307170 TRUE FALSE 4855612.188 1746396.243 2605926.685 1746083.808 3287586.132 3071789.997 3430020.294 2509053.368 2883836.499 1563284.934 3.106031461 1.117132395 1.66695567 1.116932537 2.102998666 1.964958486 2.194110759 1.604987877 1.844728646 1 20.57614933 KWDGS(ph)EEDEDNSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KWDGSEEDEDNSKK 14 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK;KWDGS(1)EEDEDNSKK 201.48 1.40E-08 1692530000 1963310 402046 789543 386108 1334210 1437690 1276660 763616 935570 300136 TRUE FALSE 2040822.995 471094.273 810119.1392 462479.01 1107421.461 1103808.286 1176592.053 753380.9765 901899.0185 358941.9027 5.685663834 1.31245271 2.25696452 1.288450879 3.085238732 3.075172549 3.277945663 2.098893918 2.512660159 1 18.45339083 0.531678842 1.107661045 1.002524635 2.695014905 0.165391023 1.182004705 3.122505994 5.382935207 1.076167108 0.333083593 3.401565528 -0.531678842 1.692490269 KWDSNVIETFDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KWDSNVIETFDIAR 14 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ;; 210.02 9.33E-09 1657338000 1662333 1370523 1736699 1577424 1958758 1945792 2059157 1763543 1857194 1397724 FALSE TRUE 1727963.19 1605899.664 1781958.803 1889433.759 1625809.015 1493911.297 1897754.894 1739905.591 1790353.951 1671581.257 1.0337297 0.96070691 1.066031816 1.130327199 0.972617399 0.893711443 1.1353052 1.040874073 1.071054095 1 20.67278206 KWDTCAPEVILHAVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWDTCAPEVILHAVGGK 17 1 O95861-3;O95861-4;O95861;A6NF51;O95861-2 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ; 168.32 1.37E-09 1261180000 2006170 1439390 1869010 1455110 2427500 2149370 2039270 1848500 2044000 1473630 FALSE TRUE 2085375.141 1686594.036 1917717.936 1742926.415 2014874.417 1650211.392 1879426.689 1823723.881 1970436.839 1762359.584 1.18328584 0.95700903 1.088153606 0.98897321 1.143282242 0.93636475 1.066426344 1.034819396 1.118067423 1 20.74907688 4.762475122 23.71345288 1.039492645 1.183286178 0.315741042 0.064507538 3824.234892 3791959.624 0.013777952 0.765372066 57872.88363 -4.762475122 0.143793532 KWENPGLGAESHTDS(ph)LRNSSTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHT(0.022)DS(0.602)LRNS(0.374)S(0.001)TEIR;KWENPGLGAES(0.001)HT(0.005)DS(0.542)LRNS(0.392)S(0.058)T(0.003)EIR 205.89 4.82E-25 868770000 144558 168162 175205 167109 216521 212084 185746 178051 211570 193423 TRUE FALSE 150265.2615 197042.5154 179770.9862 200162.6614 179716.8378 162830.7052 171186.7432 175664.5176 203955.637 231320.5335 0.649597592 0.85181593 0.77715101 0.865304339 0.776916926 0.703918077 0.740041278 0.759398722 0.881701395 1 17.81953381 1.006209974 3.129020323 0.999123471 0.768633105 0.608867326 0.059912553 0.149068628 3.49161452 0.056405801 0.014801583 10.14401712 -1.006209974 -0.230490366 KWENPGLGAESHTDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KWENPGLGAESHTDSLR 17 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 247.91 5.46E-21 1628560000 1640500 1937640 2116700 1767870 2407180 2450240 2043640 2051100 2185880 2096510 FALSE TRUE 1705268.207 2270414.597 2171862.941 2117549.409 1998008.403 1881208.894 1883454.157 2023608.359 2107210.606 2507280.994 0.680126484 0.905528579 0.866222392 0.844560069 0.796882522 0.75029839 0.751193887 0.807092769 0.840436557 1 21.25769226 0.774734716 2.687624662 0.999942954 0.803540883 0.491668687 0.060729039 0.974042339 10.23953835 0.058475886 0.01549892 5.952984016 -0.774734716 -0.196402071 KWENPGLGAESHTDSLRNS(ph)STEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWENPGLGAESHTDSLRNSSTEIR 24 2 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 KWENPGLGAESHTDS(0.044)LRNS(0.901)S(0.044)T(0.01)EIR;KWENPGLGAESHTDS(0.025)LRNS(0.836)S(0.114)T(0.025)EIR 189.24 7.64E-18 1508450000 214930 299350 320410 312330 337340 389040 307590 305310 330990 340590 TRUE FALSE 223415.6024 350761.0339 328760.1478 374107.9418 279999.0673 298691.356 283480.2921 301217.8188 319077.7346 407322.0895 0.548498616 0.861139238 0.807125752 0.918457288 0.687414394 0.733305076 0.695961008 0.739507693 0.783354851 1 18.63581053 0.811764087 4.625790801 0.999997036 0.754457559 0.377463362 0.095949883 2.712153434 65.84530598 0.08964073 0.022729455 6.482821839 -0.811764087 -0.245539477 KWESPAQNTAHLDQFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWESPAQNTAHLDQFER 17 1 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 ; 134.21 1.15E-05 1210310000 457130 471220 495760 466820 594270 626260 443980 494320 521410 516280 FALSE TRUE 475177.8454 552148.3694 508679.9129 559155.6027 493256.1977 480820.6061 409179.6875 487694.4489 502644.556 617435.1812 0.769599563 0.89426127 0.823859619 0.905610208 0.79887932 0.778738596 0.662708734 0.789871494 0.814084735 1 19.23592816 3.024462839 22.11889078 0.784128502 0.850162787 0.01305162 0.086315732 132.2957321 119616.2753 0.023597235 0.028201361 1057.944388 -3.024462839 0.066034286 KWQDEDGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWQDEDGKK 9 2 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ; 131.82 0.00018135 3533700000 13264400 4707900 7676400 4556400 12101000 9959300 11692800 8204600 10154000 4199400 FALSE TRUE 13788088.75 5516445.203 7876453.29 5457642.321 10044076.34 7646403.51 10776287.78 8094630.757 9788559.523 5022192.028 2.745432408 1.098413834 1.568329775 1.086705226 1.999938729 1.522523127 2.145733919 1.611772452 1.949061181 1 22.25988576 KWQIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWQIFK 6 1 B4DZG7;F8VYN9;P40616-2;P40616;F8W1Z8 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 103.71 0.05524 1764750000 1189980 972000 1232950 982820 1541220 1514980 1381720 1249680 1393490 1135480 FALSE TRUE 1236961.329 1138933.439 1265081.69 1177218.863 1279243.975 1163148.855 1273417.176 1232930.084 1343338.567 1357955.566 0.910899709 0.83871186 0.931607574 0.866905289 0.942036696 0.85654412 0.937745835 0.907931095 0.989236026 1 20.37300484 1.268622185 1.583154519 1.004727225 0.894206798 0.56104288 0.033637797 0.237409234 1.091414459 0.02805041 0.00851217 18.5618896 -1.268622185 -0.110520427 KWQTMIEAHVDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWQTMIEAHVDVK 13 1 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 127.76 0.00011245 1248630000 3671800 2358390 3394800 2603120 4093100 3908500 4213000 3372300 3997100 2454400 FALSE TRUE 3816765.499 2763425.137 3483271.277 3118009.366 3397356.324 3000810.109 3882774.051 3327099.834 3853245.152 2935292.688 1.300301505 0.9414479 1.186686183 1.062248197 1.157416546 1.022320575 1.322789399 1.133481458 1.312729449 1 21.48507294 2.253529969 24.99980755 1.200149992 1.107230095 0.08920935 0.124516897 484.5714193 809265.0889 0.039055858 0.032553368 179.2792263 -2.253529969 -0.092919897 KWQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWQVSR 6 1 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ; 163.84 0.012448 1943410000 1338680 1343410 1449790 1348560 1728190 1782330 1556520 1504950 1499360 1549360 FALSE TRUE 1391532.12 1574130.217 1487572.718 1615301.143 1434432.881 1368410.869 1434515.895 1484778.607 1445398.326 1852927.428 0.750991161 0.849536897 0.80282298 0.871756292 0.774144124 0.738512933 0.774188926 0.801315035 0.780062028 1 20.82137495 -1.079990283 5.253449398 1.000003005 0.79531487 0.715858455 0.038979353 1.39E-06 2.43E-07 0.038135385 0.008988464 0.083178238 1.079990283 -0.204688135 KWS(ph)LNTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWSLNTYK 8 1 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 1 KWS(0.976)LNT(0.024)YK;KWS(1)LNTYK 168.85 0.00018648 1602320000 2139620 1038250 2527860 1142750 3365460 2026310 2581990 2025750 3513540 1676000 TRUE FALSE 2224093.85 1216561.361 2593738.108 1368782.539 2793400.311 1555730.212 2379606.877 1998598.135 3387088.382 2004380.111 1.109616802 0.606951423 1.294035046 0.68289569 1.393647989 0.776165261 1.187203397 0.997115329 1.68984334 1 20.9347247 1.328633943 25 1.345070192 1.005404409 0.181095871 0.288321145 24.87257962 6893.007308 0.170613475 0.062302601 21.31247774 -1.328633943 -0.339665783 KWS(ph)NSQPADLAHMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KWSNSQPADLAHMGR 15 1 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 KWS(0.979)NS(0.021)QPADLAHMGR;KWS(0.917)NS(0.083)QPADLAHMGR 130.73 3.55E-05 297620000 152335 135204 157546 101694 204211 202590 121628 149453 182159 178981 TRUE FALSE 158349.3034 158424.2353 161651.7782 121808.7697 169499.2872 155541.5428 112094.4795 147449.827 175603.1332 214048.9002 0.739780972 0.740131041 0.755209572 0.569069823 0.791871797 0.726663593 0.523686314 0.688860475 0.820387926 1 17.7075809 0.972317041 3.126856959 0.998861654 0.688198957 0.59182131 0.079692121 0.16884384 4.127788147 0.077033987 0.020174764 9.382466904 -0.972317041 -0.310662697 KWSNS(ph)QPADLAHMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 KWSNSQPADLAHMGR 15 1 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 KWS(0.189)NS(0.811)QPADLAHMGR;KWS(0.219)NS(0.781)QPADLAHMGR;KWS(0.348)NS(0.652)QPADLAHMGR;KWS(0.456)NS(0.544)QPADLAHMGR;KWS(0.025)NS(0.975)QPADLAHMGR;KWS(0.079)NS(0.921)QPADLAHMGR;KWS(0.386)NS(0.614)QPADLAHMGR;KWS(0.199)NS(0.801)QPADLAHMGR 188.19 1.89E-07 1606460000 1014835 987827 1086535 807939 1452173 1307677 915718 1042590 1176757 1262260 TRUE FALSE 1054901.469 1157478.603 1114850.995 967746.9227 1205333.152 1003988.835 843941.6304 1028615.786 1134405.745 1509575.68 0.698806614 0.766757585 0.738519446 0.641072148 0.798458248 0.66508016 0.559058841 0.681393984 0.751473252 1 20.52571165 0.830845797 3.569309272 0.999944919 0.691825978 0.675523026 0.06346966 0.599837372 11.73071309 0.064020355 0.016494352 6.774009428 -0.830845797 -0.308118941 KWTWAVEWLGDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KWTWAVEWLGDELER 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 68.481 0.072389 0 49659 44055 58407 45816 71263 71349 62817 58850 60009 58491 FALSE TRUE 51619.57567 51621.10355 59929.1344 54878.26805 59149.74071 54779.27605 57893.2394 58061.21201 57849.28781 69951.19157 0.737937046 0.737958888 0.856727856 0.784522276 0.845585892 0.783107118 0.827623348 0.830024632 0.826995031 1 16.09406101 -5 0.155046618 1.713411007 0.747875671 0.770367556 0.034088262 61.87904854 0.56075033 13.5671122 0.155901566 1.00E-05 5 -0.965535336 KYAEAVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KYAEAVTR 8 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 136.63 0.0012547 3500970000 3703500 3521340 3577130 3190560 4855730 4697570 4120550 3637220 4060750 3755430 FALSE TRUE 3849717.04 4126102.753 3670352.946 3821643.245 4030354.749 3606630.56 3797570.524 3588469.015 3914604.401 4491234.606 0.857162312 0.918701229 0.817225834 0.850911515 0.897382369 0.803037667 0.845551581 0.798993891 0.871609868 1 22.09868065 2.761995082 24.84173131 0.845743936 0.867277123 0 0.059075756 3210.400199 3403178.808 0.016964622 0.017983412 578.0895005 -2.761995082 0.021533187 KYAELLEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYAELLEEHR 10 1 P40222 P40222 TXLNA Alpha-taxilin 0 119.03 0.00048472 49137000 119160 112880 127710 109540 160420 160250 139140 129010 124390 128680 FALSE TRUE 123864.5288 132266.2619 131038.2275 131206.6851 133151.8657 123034.3661 128233.8432 127280.832 119913.2282 153892.3823 0.804877584 0.859472444 0.851492618 0.852587263 0.865227139 0.799483147 0.833269596 0.827076884 0.779201845 1 17.23156229 -1.246474343 5.185921317 1.000020736 0.832331244 0.780464199 0.026981794 6.41E-06 9.31E-07 0.025869533 0.006096754 0.056692506 1.246474343 -0.167689492 KYAVLYQPLFDKR ddPTM_MDA-MB-175_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 ; 177.38 8.72E-06 1439350000 1778050 1559510 1705220 1330100 2801130 2340580 2064200 1909690 1919450 2409680 FALSE TRUE 1848248.787 1827343.711 1749659.434 1593189.81 2324994.923 1797015.767 1902402.61 1884093.729 1850369.369 2881810.66 0.641349834 0.634095687 0.607138928 0.552843333 0.806782679 0.623571768 0.66014143 0.653788174 0.642085684 1 21.45854412 -5 0.389244176 6.289990569 0.639718677 0.75237488 0.060784576 309.864209 2.246348906 1388.202232 0.038209546 1.00E-05 5 -5.650271891 KYCEDESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYCEDESR 8 1 Q92797;A0A087WUE9 Q92797 SYMPK Symplekin 0 74.92 0.063705 71761000 98400 89207 106260 102080 133250 134030 114040 110770 115780 103430 FALSE TRUE 102284.908 104527.6083 109029.2229 122271.1193 110600.2126 102903.5637 105101.2468 109285.3093 111613.1004 123695.1282 0.82691137 0.845042241 0.881435061 0.988487753 0.894135559 0.831912827 0.84967976 0.883505364 0.902324142 1 16.91642915 0.759560124 2.19233341 0.999926544 0.876267706 0.423887927 0.043658129 1.050824956 7.753160518 0.044818136 0.012215139 5.74857397 -0.759560124 -0.123658837 KYDAFLASESLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 ; 186.56 1.23E-05 2927000000 3993600 2622050 3877900 2616160 5408100 4395400 4336500 4033300 4550900 3437460 FALSE TRUE 4151270.412 3072366.691 3978961.26 3133628.64 4488833.094 3374634.963 3996593.799 3979240.211 4387113.998 4110964.473 1.009804497 0.747359096 0.967889965 0.762261182 1.091917267 0.820886433 0.972179114 0.96795782 1.067173902 1 21.97104547 1.744119662 1.61756351 1.029588721 0.898084871 0.189494014 0.103905009 0.551023021 2.819959763 0.072301885 0.028664425 55.47785514 -1.744119662 -0.13150385 KYDTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYDTDR 6 1 P22676;A6NER6;H3BN14;H3BMN5 P22676 CALB2 Calretinin 0 ; 94.662 0.070915 631340000 1227850 1138390 1244230 952480 1406010 1455850 1422430 1304040 1304220 1120720 FALSE TRUE 1276326.466 1333899.627 1276655.656 1140877.701 1167016.922 1117750.901 1310936.22 1286561.477 1257281.377 1340303.627 0.952266666 0.995221979 0.952512275 0.851208397 0.870710859 0.833953501 0.97808899 0.959903004 0.938057133 1 20.35412843 -1.143275203 7.435951063 1.000000031 0.926840734 0.15333637 0.052273949 2.97E-08 3.45E-09 0.055598607 0.013104712 0.071899322 1.143275203 -0.073159298 KYDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 KYDVDTLDMVFLDHWK 16 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;; 311.93 7.12E-58 16434650000 16546800 11529910 15888470 12315180 20327220 18134140 19625560 16526280 18237470 11181580 FALSE TRUE 17200080.44 13510082.35 16302536.58 14751085.85 16872006.41 13922760.81 18087257.33 16304772.25 17581107.02 13372396.52 1.286237693 1.010296272 1.219118545 1.103099645 1.261704017 1.041156744 1.352581589 1.21928573 1.314731207 1 23.6727547 2.238294609 24.99999996 1.241735743 1.152684432 0.061112434 0.120773364 15.14853798 1423479.323 0.039462243 0.03100098 173.09902 -2.238294609 -0.089051311 KYDVDTLDMVFLDHWKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYDVDTLDMVFLDHWKDR 18 2 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 102.37 0.00034025 1770000000 1034900 637350 920420 508090 1427800 1208500 848100 723520 1075100 831230 FALSE TRUE 1075758.651 746809.9046 944406.9013 608588.6855 1185103.066 927844.19 781623.7059 713822.3978 1036407.361 994093.6036 1.082150259 0.751247068 0.950018085 0.612204609 1.192144343 0.933356966 0.786267715 0.718063566 1.042565164 1 19.92302218 1.196395602 24.99696297 1.021283248 0.867869379 0.105328491 0.164644895 351.6757059 208478.4226 0.153079365 0.038271084 15.7179391 -1.196395602 -0.153413869 KYEDICPSTHNMDVPNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 229.96 1.04E-19 5841360000 1498938 2032700 2519190 2117190 2959010 3094610 2951040 2579320 2845770 2020250 FALSE TRUE 1558117.23 2381800.413 2584842.161 2535963.863 2456038.537 2375933.727 2719729.774 2544748.434 2743351.294 2416079.307 0.644894903 0.985812182 1.069849882 1.049619462 1.016538873 0.983383997 1.125679014 1.053255341 1.135455813 1 21.20423638 4.742835468 2.856909506 1.055481301 0.569173626 0.874180742 0.046351176 0.131542196 1.496646467 0.011269817 0.149287852 55314.05126 -4.742835468 -0.486307675 KYEDICPSTHNMDVPNIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYEDICPSTHNMDVPNIKR 19 2 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ; 155.49 1.52E-08 2189700000 1143350 1724810 2243110 1666180 2820800 2517700 1839750 2090810 2293100 1925840 FALSE TRUE 1188490.341 2021032.7 2301567.289 1995745.431 2341321.424 1933002.331 1695545.588 2062786.112 2210571.779 2303171.476 0.516023385 0.877499883 0.999303488 0.866520557 1.016564094 0.839278513 0.736178615 0.895628543 0.959794702 1 21.1351904 4.734811444 5.089709904 0.902301822 0.498917331 0.671883456 0.082619542 0.09592614 8.111132727 0.020189262 0.135773317 54301.45216 -4.734811444 -0.403384491 KYEEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 143.01 0.0039293 53146983000 33244644 30998842 33916559 29290356 40547728 41249129 39269180 34575693 34312788 29522362 FALSE TRUE 34557168.22 36322651.98 34800452.39 35083900.99 33655439.68 31669643.93 36191159.06 34112262.39 33077877.46 35306703.59 0.978770735 1.028774943 0.985661329 0.99368951 0.953230867 0.896986711 1.025050638 0.966169563 0.936872438 1 25.07343879 3.324833889 5.661478185 0.963016559 0.99892208 0.186593998 0.034422827 0.351469302 17.93599056 0.009644553 0.013069644 2112.680819 -3.324833889 0.035905521 KYEFGESDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KYEFGESDLR 10 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 121.08 0.00084119 3590210000 8683900 7873000 9215100 8721500 11162900 11096000 9726800 9236500 9763500 8408400 FALSE TRUE 9026747.077 9225126.507 9455253.076 10446586.67 9265434.245 8519122.162 8964388 9112699.825 9412113.542 10055864.99 0.897659931 0.917387665 0.940272476 1.038855104 0.921396046 0.847179449 0.891458667 0.906207455 0.935982489 1 23.26153385 3.010430347 24.99585466 0.905688305 0.950027293 0.068225788 0.05023116 424.9394258 1018340.72 0.014619733 0.017457253 1024.307486 -3.010430347 0.044338988 KYEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KYEGGR 6 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 107.43 0.050146 6338490000 3316420 3279390 3553160 2769620 4142290 4061040 3928970 3409020 3473300 3275910 FALSE TRUE 3447354.822 3842599.722 3645758.269 3317442.57 3438185.025 3117925.006 3621007.065 3363327.663 3348296.611 3917761.843 0.879929654 0.980815036 0.930571692 0.84676984 0.877589083 0.795843425 0.924254003 0.858481908 0.854645266 1 21.90159827 3.802962772 7.672390141 0.872298066 0.93590978 0.136989463 0.05586332 0.445396978 47.70013354 0.013193667 0.023871889 6352.764738 -3.802962772 0.063611714 KYEHLLQLLDLAQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYEHLLQLLDLAQEK 15 1 O60437;K7EKI8 O60437 PPL Periplakin 0 109.79 0.00063101 57461000 212980 132290 171790 131210 251440 228060 231740 173300 210740 130750 FALSE TRUE 221388.6149 155009.7784 176266.9885 157162.9464 208700.3186 175096.5213 213575.6133 170977.197 203155.5086 156367.9591 1.415818279 0.991314201 1.127257716 1.00508408 1.334674442 1.119772377 1.36585279 1.093428589 1.299214428 1 17.2545854 3.242493555 24.99846012 1.206406851 1.124071091 0.04278232 0.151746881 298.080199 1894640.094 0.039397811 0.051398062 1747.807324 -3.242493555 -0.082335761 KYELGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KYELGR 6 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;; 128.38 0.026698 1706580000 2159450 1858380 2199990 2067440 2256680 2489980 2885400 2272660 2109670 1643870 FALSE TRUE 2244706.753 2177542.309 2257323.547 2476373.461 1873090.34 1911719.881 2659234.808 2242198.71 2033743.389 1965954.853 1.141789574 1.107625796 1.148207215 1.259628856 0.952763659 0.972412911 1.352642867 1.140513836 1.034481227 1 20.90679876 1.171366754 4.964702292 1.007488789 1.137685686 0.15244628 0.111284659 0.391707149 17.37934668 0.106790681 0.027663063 14.83770573 -1.171366754 0.130196897 KYELGRPAANTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYELGRPAANTK 12 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 112.42 0.00071734 6784800000 7961200 5739800 7153400 5171100 9618300 8544900 8405300 7465600 8432000 5935900 FALSE TRUE 8275514.323 6725566.001 7339823.481 6193928.146 7983384.802 6560476.474 7746470.623 7365535.843 8128533.967 7098925.955 1.165741744 0.947406135 1.033934362 0.872516235 1.124590516 0.924150571 1.091217273 1.03755637 1.145037153 1 22.75916934 KYEMFAQTLQQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYEMFAQTLQQSR 13 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 267.11 2.67E-24 4058800000 2627300 2676100 2482500 1857030 4889500 3880900 2702100 2635900 2528800 4915100 FALSE TRUE 2731027.833 3135699.358 2547195.989 2224344.991 4058384.536 2979619.791 2490302.341 2600570.072 2437788.982 5878119.74 0.464609085 0.533452787 0.433335165 0.37841097 0.69042223 0.506900152 0.42365628 0.442415294 0.41472258 1 22.48692332 -1.174380276 4.939011521 1.000041127 0.476328266 0.780633723 0.083263022 4.592610028 110811266.2 9223.355057 0.019700077 0.06692983 1.174380276 -0.523712861 KYEPPVPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYEPPVPTR 9 1 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 92.445 0.016149 397290000 415960 513050 502410 444740 547370 593440 492020 481030 522020 571250 FALSE TRUE 432382.422 601162.3465 515503.2173 532708.2446 454328.2429 455622.5537 453454.1867 474582.5797 503232.6022 683175.5003 0.632900948 0.879953023 0.754569239 0.779753145 0.665024204 0.666918754 0.663744801 0.694671544 0.736608093 1 19.38189671 -1.509527942 8.99710996 1.000010843 0.719470713 0.596987591 0.069177287 1.53E-05 8.34E-07 0.06809756 0.016050129 0.030936563 1.509527942 -0.28054013 KYESVLQLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYESVLQLGR 10 1 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8 A0A087X1E4 ARFIP2 Arfaptin-2 0 ; 143.97 5.30E-05 1277360000 1172670 1029530 1136360 1101740 1588010 1489820 1448750 1216370 1384030 1205880 FALSE TRUE 1218967.917 1206343.769 1165974.475 1319660.884 1318080.627 1143831.883 1335193.189 1200066.55 1334219.031 1442149.098 0.845244031 0.836490326 0.808497871 0.915065499 0.913969734 0.793143986 0.925835748 0.832137642 0.925160257 1 20.4597889 -4.999999982 0.176543216 1.558877398 0.833500306 0.482992394 0.044886463 113.6172521 1.087272004 22.15475832 0.142057494 1.00E-05 4.999999982 -0.725377091 KYHNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYHNPK 6 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 69.439 0.060696 2205500000 3073480 2226560 3241910 2301860 4263900 3711970 3989080 3261310 3578390 2538590 FALSE TRUE 3194823.364 2608954.36 3326396.838 2757161.038 3539123.801 2849921.223 3676405.486 3217597.474 3449604.443 3035978.106 1.05232095 0.859345578 1.095659034 0.908162359 1.165727709 0.938716 1.210945981 1.059822357 1.136241541 1 21.53372996 3.240809445 24.99900546 1.088138708 0.97867632 0.226365702 0.09624631 82.26725032 914507.9154 0.024790396 0.03199419 1741.042789 -3.240809445 -0.109462388 KYHNVGLSK ddPTM_MDA-MB-175_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 ; 119.68 0.00051144 3509200000 4666480 3956270 5042750 3662000 6308200 5972200 5573400 5136220 5218890 4368990 FALSE TRUE 4850716.234 4635728.597 5174168.208 4386332.67 5235934.417 4585247.06 5136542.345 5067377.372 5031063.168 5225009.941 0.928364977 0.887219096 0.990269543 0.839487909 1.002090805 0.877557576 0.983068435 0.969831145 0.962881071 1 22.31700235 2.207908585 24.93003483 0.975961038 0.922456211 0.268393415 0.046854631 269.0854217 218851.9432 0.01594888 0.011780425 161.4018786 -2.207908585 -0.053504827 KYIEIDS(ph)DEEPRGELLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR;KYIEIDS(1)DEEPRGELLSLR 203.4 2.65E-16 556600000 290648 323139 328237 239979 424952 373005 272978 340457 327124 376396 TRUE FALSE 302123.0075 378635.6096 336791.1259 287446.1299 352718.8108 286380.2417 251581.2711 335893.7308 315350.8711 450143.5897 0.671170299 0.841144067 0.748185987 0.638565419 0.783569552 0.636197534 0.558891156 0.746192412 0.700556174 1 18.78002575 -1.889043965 5.739856847 1.068422316 0.703469392 0.57045364 0.077387205 0.046237895 0.000893815 0.051130906 0.017785551 0.012910886 1.889043965 -0.364952924 KYKPLDLRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYKPLDLRPK 10 3 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 74.944 0.017731 1254350000 3839600 2277400 3274200 2280600 4927400 3784000 4155200 3366500 4067000 2421100 FALSE TRUE 3991190.373 2668525.734 3359528.342 2731695.873 4089842.308 2905223.347 3829504.566 3321377.574 3920629.464 2895468.19 1.3784266 0.921621499 1.160271197 0.943438399 1.412497751 1.003369112 1.322585611 1.147095169 1.35405717 1 21.46536522 3.256812399 24.99994771 1.207900085 1.092369085 0.080421744 0.174040881 576.0997535 789093.9326 0.043753359 0.059127241 1806.393653 -3.256812399 -0.115531001 KYNPTWHCIVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYNPTWHCIVGR 12 1 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 142.1 3.96E-05 1446580000 1056550 1375740 1442920 1129570 1647070 1816700 1133760 1428150 1371460 1766940 FALSE TRUE 1098263.41 1612012.643 1480523.681 1352995.575 1367101.63 1394798.957 1044892.929 1409007.985 1322101.423 2113138.063 0.519731024 0.762852495 0.700627993 0.640277887 0.646953294 0.660060496 0.49447452 0.666784632 0.625657853 1 21.0109556 -1.734377853 2.666984342 1.070819325 0.638102946 0.682529008 0.074602668 10395709.93 8227741.363 4877045.704 0.017994646 0.018434109 1.734377853 -0.43271638 KYNWSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYNWSAK 7 1 P61927;D6RG19 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 ; 127.56 0.0061612 1835260000 1628730 1519840 1359600 940970 3711900 2410600 1883290 1450390 1480720 3094200 FALSE TRUE 1693033.518 1780860.697 1395032.293 1127091.057 3080952.564 1850774.683 1735672.809 1430949.894 1427429.176 3700449.248 0.457521075 0.481255269 0.376989981 0.304582223 0.832588791 0.500148647 0.469043809 0.386696263 0.385744833 1 21.819269 -1.374407126 5.264032625 1.00027226 0.465266221 0.584243816 0.135122719 0.000436283 5.18E-05 0.132202014 0.0311448 0.042227257 1.374407126 -0.535006039 KYPDYESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYPDYESK 8 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 79.489 0.044743 190640000 827420 625070 722910 613790 1090600 1012200 892020 722620 770570 563930 FALSE TRUE 860087.1805 732420.9101 741749.6285 735195.83 905220.2016 777131.89 822101.1415 712934.4609 742837.3362 674421.2864 1.27529661 1.0859991 1.099831283 1.09011362 1.34221772 1.152294427 1.218972708 1.057105514 1.101444084 1 19.36329055 1.671021358 6.523120678 1.058787114 1.175354657 0.337089361 0.081625533 0.170980513 14.75932184 0.042082519 0.021275675 46.88364384 -1.671021358 0.116567543 KYPNVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYPNVFK 7 1 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 91.906 0.025751 374910000 249110 246520 212210 241930 493480 424170 417800 352570 402030 344110 FALSE TRUE 258945.0552 288857.8923 217740.3669 289783.0319 409598.4459 325662.9459 385051.7443 347844.3758 387561.0188 411531.7661 0.629222521 0.701909102 0.52909735 0.704157141 0.995302136 0.791343397 0.935654975 0.845243076 0.941752377 1 18.65064427 3.39278391 5.38929938 0.900652087 0.626310499 0.781264285 0.072390907 0.088939569 4.299178191 0.018815606 0.025728249 2470.494607 -3.39278391 -0.274341588 KYPS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 KYPSPQK 7 1 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK;KYPS(1)PQK 88.681 0.011288 5113610000 12243700 5378310 8032300 5313710 11250100 10668500 10741600 8257700 9395300 4484760 TRUE FALSE 12727090.73 6301992.905 8241628.337 6364745.978 9337812.02 8190902.558 9899645.324 8147019.038 9057164.988 5363462.856 2.372924186 1.174985839 1.536624483 1.186685943 1.741004323 1.527166828 1.845756294 1.51898489 1.688678608 1 22.35473333 -1.18783274 6.566711914 0.999997229 1.59752773 0.245223449 0.324640195 1.20E-05 1.49E-06 0.286761333 0.067589981 0.064888429 1.18783274 0.597530501 KYSAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYSAAK 6 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 83.843 0.090636 523320000 456130 472300 402980 395820 1261300 813500 796900 641990 684210 996190 FALSE TRUE 474138.3646 553413.851 413481.9899 474112.0146 1046904.677 624576.9537 734436.8957 633385.1741 659585.4158 1191374.357 0.397975969 0.464517175 0.347063026 0.397953852 0.878736956 0.524249116 0.616461896 0.531642443 0.553634054 1 20.18419538 -5 0.125111858 2.514264087 0.316167482 0.568354864 0.132416156 115.716481 0.926384305 44.45844174 1.164830065 1.00E-05 5 -2.198096605 KYSCDR ddPTM_MDA-MB-175_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 0 ; 94.887 0.070505 656550000 912820 893470 956200 819290 1177570 1113150 1039160 995490 917570 1007040 FALSE TRUE 948858.8385 1046916.522 981119.3575 981343.1167 977407.072 854637.7825 957707.9239 982147.0848 884546.8349 1204350.207 0.787859572 0.869279148 0.814646231 0.814832024 0.811563834 0.709625637 0.795207173 0.815499577 0.734459819 1 20.19982354 -1.323228931 3.415420536 1.000977308 0.797511823 0.676874582 0.042500776 12560445.13 19123770.32 126616.9412 0.010343855 0.047508473 1.323228931 -0.203465485 KYSSCSTIFLDDSTVSQPNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYSSCSTIFLDDSTVSQPNLK 21 1 Q8ND76-3;Q8ND76-2;Q8ND76;R4GNF3 Q8ND76-3 CCNY Cyclin-Y 0 61.102 0.020974 1151800000 3838600 608560 1084400 515730 1773800 1770000 1706300 733660 1503200 504740 FALSE TRUE 3990150.892 713075.4461 1112660.355 617739.8547 1472290.11 1358944.325 1572555.747 723826.4877 1449100.126 603634.1392 6.61021409 1.181304038 1.843269429 1.023367988 2.439043808 2.251271485 2.605147134 1.199114564 2.400626525 1 19.20331488 4.743078028 24.9927328 1.80270275 6.610216024 0.853641162 0.600946763 157.6742684 872307.9084 0.138386865 1.105437102 55344.95359 -4.743078028 4.807513274 KYTGEDFDEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 KYTGEDFDEDLR 12 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 161.76 0.00010344 1879880000 4784890 4085330 5143230 4512500 6156810 6175420 5419490 5003920 5420480 4627770 FALSE TRUE 4973801.152 4786953.648 5277266.799 5405059.032 5110277.635 4741272.294 4994696.213 4936850.637 5225397.984 5534492.927 0.898691392 0.864930846 0.95352309 0.976613233 0.923350649 0.856676909 0.902466816 0.892014987 0.944151172 1 22.40001971 0.957963869 4.442454776 0.999933458 0.9087034 0.402312901 0.034483302 0.237972487 14.53097696 0.035634121 0.009059346 9.077450081 -0.957963869 -0.091230057 KYTLENKEEGS(ph)LSDTEADAVSGQLPDPTTNPSAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 KYT(0.043)LENKEEGS(0.429)LS(0.429)DT(0.1)EADAVSGQLPDPTTNPSAGK 197.26 1.11E-27 874870000 371710 140410 231450 124770 336750 313430 293430 257090 301410 142210 TRUE FALSE 386385.3978 164524.3253 237481.7771 149449.1336 279509.3553 240640.6326 270430.1899 253644.1291 290562.313 170073.3267 2.271875345 0.967372888 1.396349338 0.878733523 1.643463797 1.414922829 1.590079968 1.491381006 1.708453163 1 17.37579737 KYVATLGVEVHPLVFHTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 KYVATLGVEVHPLVFHTNR 19 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 215.98 1.60E-19 1276743000 1162164 1128330 1221280 1063970 1568230 1534280 1226570 1210300 1218870 1136330 FALSE TRUE 1208047.132 1322111.9 1253107.56 1274420.09 1301662.825 1177966.722 1130428.238 1194077.908 1175003.107 1358972.107 0.888941815 0.972876407 0.922099544 0.937782375 0.957828949 0.866807138 0.831825931 0.878662558 0.86462636 1 20.37408441 2.732087259 24.88638156 0.876120068 0.937296978 0.183095981 0.046680174 593.0204462 2279820.734 0.013807856 0.013304641 539.6190325 -2.732087259 0.06117691 KYVIS(ph)DEEEEDDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 147.7 4.53E-05 4739200000 6140930 4911710 5728700 4523910 6937380 6829030 6433700 5894430 6046390 4583000 TRUE FALSE 6383378.658 5755257.985 5877994.628 5418725.895 5758166.626 5243091.277 5929409.783 5815424.807 5828781.605 5480951.103 1.164647985 1.050047314 1.072440625 0.988647006 1.050577996 0.956602454 1.081821325 1.061024756 1.063461705 1 22.38599483 5.181991966 1.472589611 1.035639861 1.405111141 0.505837997 0.038464041 3.215588275 2.640476278 0.010234951 2.395412142 152051.94 -5.181991966 0.369471281 KYYLHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KYYLHDDR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 123.35 0.00087711 106220000 165240 170350 190270 166780 259200 246340 221810 187000 185570 215480 FALSE TRUE 171763.8028 199606.2874 195228.5925 199768.5862 215141.2766 189131.2683 204423.9526 184493.5709 178891.3719 257699.1804 0.666528324 0.774570905 0.757583288 0.775200705 0.83485433 0.733922661 0.793265824 0.715926107 0.69418681 1 17.97532842 -1.958829303 2.538535106 1.194463958 0.752610076 0.7196956 0.046853639 9288929.918 4395304.263 10639484.92 0.011810879 0.010994379 1.958829303 -0.441853883 LAAAEETAVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR;LAAAEETAVS(1)PR 218.11 3.68E-11 9602620000 1807310 1885780 1717070 1982190 1834650 2133840 1993630 1869240 1879000 1728680 TRUE FALSE 1878663.994 2209648.046 1761818.255 2374261.266 1522796.848 1638287.999 1837364.071 1844185.895 1811375.157 2067381.748 0.908716542 1.068814721 0.852197837 1.148438728 0.736582322 0.792445807 0.888739621 0.892039362 0.876168689 1 20.97937338 3.228785621 24.99998849 0.859708257 0.989679735 0.291322606 0.099221083 247.6464383 633366.0797 0.027136515 0.032811226 1693.50164 -3.228785621 0.129971478 LAAAILGGVDQIHIKPGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAAAILGGVDQIHIKPGAK 19 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ; 188.04 1.02E-14 1304800000 761900 507860 686100 535760 833300 786760 845680 646250 747800 551490 FALSE TRUE 791980.4003 595081.0044 703980.3296 641731.7289 691655.9636 604046.9135 779393.3918 637588.0758 720886.8241 659543.9066 1.200800117 0.902261394 1.067374473 0.972993189 1.048688278 0.915855499 1.181715704 0.966710585 1.093008088 1 19.33110918 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVK 36 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 265.05 1.21E-62 113820000 61843 27525 38474 29591 66846 56255 67143 44790 51012 22096 FALSE TRUE 64284.60939 32252.20464 39476.66405 35444.01148 55483.5408 43190.6288 61880.15621 44189.66331 49176.08808 26425.28815 2.432692845 1.220505315 1.493897203 1.34129139 2.099638062 1.634443059 2.341702231 1.672249062 1.860948036 1 14.68963158 3.243123958 24.99992647 1.825207282 1.584254547 0.012788261 0.447601142 345.1910337 1891088.749 0.117191172 0.153527507 1750.346207 -3.243123958 -0.240952735 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 37 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;; 331.23 2.57E-129 8429400000 3006901 929907 1732210 814993 2436736 2104353 2388092 1513627 1874933 665649 FALSE TRUE 3125615.773 1089611.294 1777352.816 976196.1829 2022540.485 1615648.908 2200907.109 1493339.306 1807454.528 796070.1769 3.926306831 1.368737738 2.23265846 1.226269004 2.540656017 2.029530755 2.764714937 1.875889022 2.270471348 1 19.60253609 -0.649124006 0.973745035 0.942120545 2.197260411 0.209402863 0.721032445 72.94048133 37.49379502 16.21458972 0.202441564 0.224324131 0.649124006 1.255139867 LAADFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAADFQR 7 0 O94874;O94874-3 O94874 UFL1 E3 UFM1-protein ligase 1 0 ; 82.913 0.053976 633800000 298610 346760 294300 318870 388910 411100 356950 330180 294870 392890 FALSE TRUE 310399.3534 406313.3326 301969.6998 381941.5343 322803.2171 315628.2553 328971.3263 325754.4772 284257.6863 469869.2732 0.660607899 0.864736972 0.642667476 0.812867655 0.687006441 0.671736318 0.700133729 0.693287465 0.604971856 1 18.8418999 -1.012691512 4.698407464 1.000006716 0.707680043 0.589705198 0.073963604 4.86E-06 1.02E-06 0.066845146 0.01575519 0.097119959 1.012691512 -0.292326673 LAAELEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAAELEDRR 9 1 Q9NQG5;A2A2M0;A0A087X2D2 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 ;;; 160.82 0.00010423 1019990000 755810 919850 860080 834250 994930 1060160 842390 892070 833020 1008510 FALSE TRUE 785649.9624 1077827.082 882494.3914 999262.16 825812.154 813953.9069 776361.2706 880113.2608 803039.7729 1206108.225 0.651392591 0.893640437 0.731687566 0.82850124 0.684691586 0.674859759 0.643691216 0.729713339 0.665810709 1 20.20192794 -1.182265892 4.382750482 1.000071572 0.72542128 0.539999371 0.076752653 5.33E-05 9.95E-06 0.073829441 0.017397241 0.065725532 1.182265892 -0.274650291 LAAFGQLHK ddPTM_MDA-MB-175_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 ; 116.37 0.0013246 1200840000 1056220 935600 891550 821680 1999140 1405980 1225240 980360 1006350 1666760 FALSE TRUE 1097920.381 1096282.022 914784.5254 984205.8515 1659326.897 1079462.453 1129202.487 967219.8777 970131.6601 1993329.71 0.550797179 0.549975258 0.458922837 0.493749652 0.832439756 0.541537332 0.566490572 0.485228245 0.486689008 1 20.92674893 -1.853752758 2.612354303 1.186234243 0.551025577 0.644463584 0.099878036 9722319.408 5914066.146 11261831.59 0.024745256 0.014003843 1.853752758 -0.635208666 LAAGRPFNT(ph)YPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 173.33 5.39E-05 3137690000 763100 1269620 1110800 1068820 1547330 1359610 956070 1176560 984500 1546060 TRUE FALSE 793227.7772 1487667.359 1139748.361 1280229.406 1284315.399 1043861.183 881130.7352 1160790.138 949068.0373 1848980.856 0.429008107 0.804587757 0.616419774 0.692397329 0.694607191 0.564560298 0.47654941 0.627799976 0.513292517 1 20.81829886 -1.966786279 2.670842046 1.31892496 0.608737874 0.554837793 0.106766124 14164687 7358321.843 27958812.98 0.025046173 0.010794778 1.966786279 -0.710187086 LAAPSVSHVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 226.93 9.11E-12 1103310000 576150 1011090 964400 988280 1023650 1223290 969970 1067430 859810 1098780 TRUE FALSE 598896.8469 1184736.842 989533.0563 1183758.834 849650.3386 939199.4366 893941.2169 1053122.847 828865.6061 1314064.904 0.455758955 0.901581679 0.753032102 0.900837418 0.646581715 0.714728347 0.680286959 0.801423768 0.630764587 1 20.3256051 -1.133611561 3.770527543 1.00014149 0.733214936 0.301321074 0.126339288 8938923250 14847086338 15478064.54 0.027965831 0.073517112 1.133611561 -0.266926554 LAAQLGAPTS(ph)PIPDSAIVNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAAQLGAPTSPIPDSAIVNTR 21 0 Q9H8Y5;B8ZZS4 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 LAAQLGAPT(0.171)S(0.829)PIPDSAIVNTR 115.57 0.0001579 64299000 86910 94343 96267 105090 102500 127730 95394 104770 113890 108640 TRUE FALSE 90341.27391 110545.6764 98775.7971 125876.4883 85077.08661 98066.64327 87916.76901 103365.7295 109791.1211 129925.928 0.695329064 0.85083615 0.760247001 0.968832706 0.65481223 0.754788862 0.676668394 0.795574303 0.84502857 1 16.98732984 0.889547394 2.262745313 0.999360365 0.770383801 0.400093842 0.086250787 0.444726564 4.696216018 0.079708001 0.021728815 7.754385618 -0.889547394 -0.228976564 LAASTEPQGPRPVLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAASTEPQGPRPVLGR 16 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;F5GWK5;F5H3G8;F5H5A8;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;; 156.17 1.72E-07 1450890000 1675260 833660 866880 786307 1095110 1248210 917230 908180 920640 889760 FALSE TRUE 1741400.558 976834.62 889471.6049 941836.1777 908963.5934 958332.1443 845335.1159 896007.3326 887506.3462 1064091.437 1.636514024 0.917998761 0.835897719 0.885108314 0.854215683 0.90061071 0.794419621 0.842039793 0.83405083 1 20.0211907 4.739246717 4.248584428 0.85977837 1.697159769 0.949631882 0.052775268 0.03743259 1.560886424 0.011644592 0.095336301 54858.85223 -4.739246717 0.837381399 LADALQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 209.58 1.90E-05 2332788000 1453588 1781173 1589954 1531304 2174102 2116541 1710223 1658853 1614358 2155190 FALSE TRUE 1510976.777 2087075.607 1631389.507 1834191.361 1804548.919 1625006.429 1576171.252 1636618.789 1556257.571 2577458.217 0.586227457 0.809741781 0.632945084 0.711627971 0.700127322 0.630468583 0.611521553 0.634973936 0.60379546 1 21.29751761 -2.113516838 3.0997952 1.764848276 0.659830982 0.725287432 0.063145946 0.034579112 0.001266313 0.006334179 0.013990089 0.007699866 2.113516838 -1.105017294 LADAMAES(ph)PSRDVVGSGTELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LADAMAESPSRDVVGSGTELQR 22 1 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6 K7ESE9 BCAS3 Breast carcinoma-amplified sequence 3 1 LADAMAES(0.959)PS(0.041)RDVVGSGTELQR;LADAMAES(0.998)PS(0.002)RDVVGSGTELQR;LADAMAES(0.808)PS(0.192)RDVVGSGTELQR;LADAMAES(0.986)PS(0.014)RDVVGSGTELQR;LADAMAES(0.994)PS(0.006)RDVVGSGTELQR 271.97 1.48E-45 987280000 471477 549832 548287 560466 649773 739170 558551 597009 617160 582825 TRUE FALSE 490091.276 644261.3689 562575.8096 671324.502 539324.8176 567508.9697 514770.3131 589007.0709 594948.5322 697018.3999 0.703125306 0.924310418 0.807117588 0.963137418 0.7737598 0.814195106 0.738531886 0.845038052 0.853562162 1 19.41083722 0.716284599 2.165090982 0.999884263 0.823990083 0.34358059 0.073898628 1.455336621 9.463310431 0.066677425 0.018186987 5.203368689 -0.716284599 -0.17589418 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;; 324.13 9.72E-106 8524603000 3725550 4489674 4546106 4222730 4956966 5621819 4503286 4779452 4806073 4598630 FALSE TRUE 3872637.591 5260740.585 4664581.257 5057973.39 4114382.69 4316236.737 4150306.676 4715391.264 4633103.372 5499643.502 0.704161568 0.95656029 0.848160659 0.919691138 0.748118071 0.784821186 0.754650129 0.857399441 0.842437036 1 22.39090667 -2.000089135 6.199495554 1.172974852 0.827245103 0.334298259 0.074381913 0.048649377 6.99E-07 0.019702543 0.016354986 0.009997948 2.000089135 -0.34572975 LADELHMPSLPEMMFGDNVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LADELHMPSLPEMMFGDNVLR 21 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 ; 190.83 1.66E-17 525480000 264808 343640 319530 347670 368580 377150 305590 342010 345040 342230 FALSE TRUE 275262.8243 402657.4969 327857.2143 416438.0883 305928.9033 289562.6283 281637.0573 337425.9154 332622.0778 409283.4161 0.672548199 0.983810927 0.801051793 1.017480973 0.747474467 0.707486834 0.688122328 0.82443095 0.812693759 1 18.64274069 5.017354021 13.37970792 0.826970115 0.409072069 0.153298816 0.114712388 406151.2315 7492802.652 0.027288644 3218339.833 104076.8215 -5.017354021 -0.417898046 LADFGVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 146.81 9.39E-05 953650000 1161150 1406590 1263730 1281490 1859940 1670310 1320200 1289290 1236980 2002520 FALSE TRUE 1206993.099 1648160.891 1296663.842 1534964.897 1543788.063 1282405.816 1216719.274 1272009.176 1192461.331 2394875.453 0.503989924 0.688203175 0.541432683 0.640937254 0.64462144 0.535479127 0.508051169 0.531137924 0.497922065 1 21.1915192 -1.997986403 3.076748995 1.42675639 0.567108876 0.80412965 0.064292226 2418722.942 15880455.24 7281241.4 0.015825084 0.010046472 1.997986403 -0.859647514 LADHFGGK ddPTM_MDA-MB-175_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 ;;; 98.997 0.0071262 1926750000 6324770 5412680 6314890 5046580 7681020 7631720 7212110 6667240 6536940 5176680 FALSE TRUE 6574476.803 6342265.685 6479461.221 6044778.461 6375402.964 5859368.69 6646805.973 6577876.553 6301676.806 6190951.332 1.06194936 1.024441212 1.046601867 0.976389272 1.029793746 0.946440761 1.073632406 1.062498508 1.01788505 1 22.56172969 LADILS(ph)PR ddPTM_MDA-MB-175_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 119.53 0.0017588 266564000 596739 638840 583823 608591 613371 706812 554807 586144 496705 535101 TRUE FALSE 620298.7165 748555.8005 599037.907 728968.4833 509110.4165 542665.6248 511319.7776 578287.6984 478828.6841 639943.7958 0.969301868 1.169721162 0.936078935 1.139113291 0.795554891 0.847989508 0.799007321 0.903653887 0.748235528 1 19.28758568 3.232457458 24.99999915 0.844952649 1.053460425 0.546719506 0.091166968 98.8359952 404855.6871 0.023749614 0.029079129 1707.880415 -3.232457458 0.208507776 LADMHSTEISLQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LADMHSTEISLQQR 14 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 126.63 8.43E-05 59529000 53710 71516 69079 74539 79517 84167 80296 73528 67532 72444 FALSE TRUE 55830.51227 83798.31668 70879.25549 89282.59172 66000.72874 64620.48981 74002.18971 72542.47743 65101.53651 86638.01478 0.64441126 0.967223417 0.818108029 1.030524441 0.76179872 0.745867619 0.854153802 0.837305398 0.751419994 1 16.40271256 -1.055800526 5.138964588 1.000002369 0.831401513 0.196573369 0.105995171 2.69E-06 4.95E-07 0.096010501 0.022629574 0.087942635 1.055800526 -0.168600856 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 LADQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68363;F8VQQ4;Q9BQE3;F5H5D3 P68363;Q9BQE3 TUBA1B;TUBA1A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-1C chain 0 ;;;;;;;;;; 378.46 1.62E-148 5613760000 687164.9 726418.8 827278.5 1016630.3 906321.2 1100844.4 1215880 908285.9 903286.1 658002.6 FALSE TRUE 714294.7009 851175.5781 848838.0573 1217716.739 752265.0462 845189.9716 1120576.148 896111.8132 870777.0097 786925.6112 0.907702953 1.081646811 1.078676364 1.547435643 0.955954458 1.074040493 1.423992475 1.138750347 1.106555686 1 19.58586774 4.552571495 1.977479483 1.185276796 0.88655319 0.166730446 0.1746358 0.846024596 4.730258351 0.043939918 0.399742655 35692.05022 -4.552571495 -0.298723606 LADS(ph)PPPQVWQLISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LADSPPPQVWQLISK 15 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 1 LADS(1)PPPQVWQLISK;LADS(1)PPPQVWQLISK 163.56 1.61E-06 368530000 307270 252620 297860 275630 351960 363930 300000 280380 298300 226048 TRUE FALSE 319401.2569 296005.5199 305622.4763 330148.7913 292133.9649 279412.7729 276485.2161 276621.9647 287564.2413 270337.7776 1.181489541 1.094946931 1.130520784 1.221245489 1.080625754 1.033569098 1.022739842 1.023245686 1.063721999 1 18.04440361 3.016750003 5.703344479 1.031260128 1.151342585 0.757913387 0.034115204 0.084464469 9.105415118 0.010161936 0.01186125 1039.321719 -3.016750003 0.120082457 LADVAAPPGGPPPPHS(ph)PYSGPPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LADVAAPPGGPPPPHSPYSGPPSR 24 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LADVAAPPGGPPPPHS(0.996)PYS(0.004)GPPSR;LADVAAPPGGPPPPHS(0.995)PY(0.003)S(0.002)GPPSR 160.01 1.36E-11 478180000 251283 390520 407700 441820 455150 556190 528070 467970 452140 419750 TRUE FALSE 261203.8469 457588.7722 418324.9969 529210.6773 377783.7656 427023.3016 486678.4935 461697.6276 435867.5697 501991.9759 0.520334705 0.911545989 0.833330047 1.054221387 0.752569331 0.850657624 0.969494567 0.919731091 0.86827597 1 18.93730478 4.739283013 24.79179005 0.903641947 0.520334575 0.662306528 0.08272952 30.75445218 1055228 0.018715288 0.112481761 54863.43726 -4.739283013 -0.383307372 LAEAHQQECCQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAEAHQQECCQK 12 0 Q9Y5X3;A0A087WUY5 Q9Y5X3 SNX5 Sorting nexin-5 0 ; 205.8 9.75E-08 273060000 660980 552800 620870 525970 738200 760580 689250 623710 661810 453730 FALSE TRUE 687076.0008 647739.0998 637050.3823 630005.2961 612721.0277 583946.8217 635224.784 615350.1876 637991.5874 542629.7063 1.266196806 1.193703721 1.174005726 1.161022496 1.129169709 1.076142376 1.170641372 1.134014929 1.175740252 1 19.0496085 7.999999999 0.017719496 8.57E-10 2.583885139 0.647065741 0.040207152 2719.566028 3.716389716 207.8676464 351.4586574 99999999.87 -7.999999999 2.583885138 LAEDEAFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAEDEAFQR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 107.69 0.0063561 249710000 176291 177772 178179 192198 231095 243308 187379 197672 199724 163831 FALSE TRUE 183251.1048 208302.9581 182822.4911 230214.1907 191813.5544 186803.4044 172691.7444 195022.5302 192535.9723 195930.5477 0.935286033 1.063146919 0.933098454 1.174978549 0.978987487 0.953416435 0.881392648 0.995365615 0.982674598 1 17.57998282 3.016124869 24.99160702 0.959072706 1.029358814 0.154607308 0.070765769 401.3207685 621994.4225 0.019668169 0.02350228 1037.826771 -3.016124869 0.070286108 LAEDEGDS(ph)EPEAVGQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 489.72 6.74E-232 1928470000 1140470 1461600 1310710 1230460 1308900 1452080 1297630 1178190 1039630 943290 TRUE FALSE 1185496.636 1712618.43 1344868.179 1473841.315 1086413.646 1114856.426 1195918.37 1162398.29 1002213.919 1128109.615 1.050870075 1.518131224 1.192143176 1.306469953 0.96303908 0.988251861 1.060108303 1.030394808 0.888401185 1 20.10547583 3.23948475 24.99875182 0.997499392 1.279508444 0.576839905 0.116515952 16.4458731 444867.3609 0.030730836 0.039322707 1735.740314 -3.23948475 0.282009052 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAEEEDLFDSAHPEEGDLDLASESTAHAQSSK 32 0 Q15424;Q15424-3;Q15424-4;Q15424-2;Q14151 Q15424;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 ;; 302.86 3.92E-90 511420000 242708 370963 434400 336627 488680 509110 449600 451150 437860 340387 FALSE TRUE 252290.2993 434673.0096 445720.8209 403210.8159 405614.3482 390876.9181 414359.1772 445103.0722 422101.5041 407079.3155 0.619757108 1.067784564 1.094923775 0.990496939 0.996401273 0.960198426 1.017883153 1.093406261 1.036902363 1 18.63495039 4.741615828 24.99978755 1.031657388 0.619756958 0.891084728 0.04287625 93.81256405 767599.8835 0.011297833 0.080153135 55158.92944 -4.741615828 -0.41190043 LAEEENKAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAEEENKAK 9 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 152.28 7.37E-05 402520000 860160 441040 603130 292370 1109540 823110 548710 612750 819700 519580 FALSE TRUE 894119.781 516785.1892 618848.0633 350199.9134 920940.7871 631955.1769 505700.6764 604537.0885 790199.1571 621381.753 1.438921849 0.831671008 0.995922491 0.563582551 1.482085341 1.017015987 0.813832518 0.972891601 1.271680659 1 19.24512035 4.751464257 24.11488629 0.986989139 1.438922327 0.240323712 0.236833076 1842.488015 3443220.001 0.054563441 0.975912163 56424.05022 -4.751464257 0.451933188 LAEIGAPIQGNREELVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAEIGAPIQGNREELVER 18 1 Q13435;E9PPJ0;H0YCG1;E9PJ04;E9PJT3 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;; 145.43 8.31E-08 716350000 524040 606880 568950 557680 682050 758650 583440 621020 634390 683510 FALSE TRUE 544729.5038 711106.9191 583777.3044 667987.4395 566115.3846 582465.035 537708.4483 612696.2427 611558.4278 817430.6979 0.666392277 0.869929305 0.71416122 0.817179293 0.692554593 0.712555861 0.657803101 0.749539067 0.748147127 1 19.6407369 -1.740788642 4.935680525 1.013793227 0.737547726 0.617309092 0.062241799 0.009213576 0.000483877 0.058775937 0.01348528 0.018163994 1.740788642 -0.276245501 LAELEEFINGPNNAHIQQVGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LAELEEFINGPNNAHIQQVGDR 22 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;; 327.3 1.18E-80 5976692000 3226233 3141404 3310753 3440035 3628895 4225172 3561411 3532774 3558513 3050740 FALSE TRUE 3353607.17 3680915.7 3397033.943 4120463.656 3012056.724 3243939.836 3282258.3 3485422.943 3430442.812 3648474.093 0.919180755 1.008891829 0.931083477 1.129366291 0.825566154 0.889122344 0.899624943 0.955309769 0.94024042 1 21.79886178 5.116444844 12.73636733 0.949404207 0.000252134 0.014870896 0.077709269 5512218.121 8430595.177 0.018302606 146473112.4 130750.9472 -5.116444844 -0.949152073 LAELSDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAELSDYR 8 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ; 126.67 0.0058034 170850000 457130 581870 551660 588660 754000 747600 640340 583450 553440 693640 FALSE TRUE 475177.8454 681801.6462 566036.7128 705095.191 625835.3493 573981.23 590148.4776 575629.8071 533521.8025 829545.4775 0.572817113 0.821897852 0.682345608 0.849977741 0.754431633 0.69192256 0.711411844 0.693909885 0.643149552 1 19.66196155 -1.42105733 3.072433278 1.004669412 0.7185572 0.555798762 0.076709414 31147384.88 38503470.57 1272421.368 0.017672054 0.037926492 1.42105733 -0.286112212 LAENFCVCHLATGDMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 200.99 1.19E-11 838600000 370370 483700 500630 472370 496080 575800 409540 385260 434750 493440 FALSE TRUE 384992.4936 566771.7123 513676.8291 565803.3761 411756.4988 442079.1763 377439.1847 380096.2199 419103.4324 590120.1205 0.652396826 0.960434482 0.870461473 0.958793568 0.697750313 0.74913422 0.639597213 0.644099746 0.710200208 1 19.17064912 3.219886654 24.96717623 0.710960167 0.868368217 0.157003189 0.125714095 302.8585788 404922.4273 0.034351457 0.041124954 1659.153832 -3.219886654 0.15740805 LAEQAER ddPTM_MDA-MB-175_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 ;;;;;;;;;; 211.87 0.00022076 32749268000 7271572 8474899 7962693 8195473 8654560 9757430 8074274 8227056 7644209 8310210 FALSE TRUE 7558659.277 9930396.978 8170207.321 9816513.098 7183460.983 7491414.758 7441391.306 8116785.771 7369095.411 9938436.541 0.760548125 0.999191064 0.822081752 0.98773213 0.72279588 0.753782019 0.748748686 0.816706505 0.741474313 1 23.24458748 3.228647386 24.99925047 0.784963348 0.894995154 0.174807782 0.099064423 282.6794536 712862.2151 0.026007496 0.031439679 1692.962688 -3.228647386 0.110031806 LAEQAERYDDMAAAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 0 178.12 2.59E-09 309990000 239690 245170 342370 174850 417810 358270 255030 270270 332410 397930 FALSE TRUE 249153.1463 287276.0403 351292.4435 209434.8081 346790.8054 275067.2221 235040.0822 266647.4727 320446.629 475896.7647 0.523544526 0.603652014 0.73816943 0.440084539 0.728710156 0.577997672 0.4938888 0.560305286 0.673353241 1 18.86028912 0.846565202 3.589135448 0.999922587 0.584135479 0.665724937 0.0884893 0.466937153 9.943413497 0.081102705 0.02088934 7.023687844 -0.846565202 -0.415787108 LAEQAERYDEMVESMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LAEQAERYDEMVESMK 16 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ;;;; 262.19 6.52E-27 2286660000 1048173 817919 1166210 864148 1483887 1405103 1198590 1159722 1354607 910867 FALSE TRUE 1089555.679 958390.2257 1196602.391 1035073.895 1231656.418 1078789.123 1104641.384 1144177.824 1305854.959 1089333.949 1.000203547 0.879794692 1.098471586 0.950189697 1.130650907 0.990319932 1.014052105 1.050346246 1.198764584 1 20.05501487 4.234684547 24.99999996 1.05054965 0.939999117 0.271874589 0.074509517 112.4298488 725173.85 0.017411991 0.039991923 17166.61026 -4.234684547 -0.110550533 LAEQAERYDEMVESMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAEQAERYDEMVESMKK 17 2 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 197.09 8.67E-12 2109160000 2197250 1191460 2088740 1237570 3131800 2415200 2221540 2031370 2789700 1213920 FALSE TRUE 2283999.127 1396083.987 2143174.28 1482357.652 2599457.755 1854306.403 2047409.89 2004142.808 2689299.242 1451764.382 1.573257448 0.961646397 1.476254898 1.021073165 1.790550717 1.277277791 1.410290757 1.380487655 1.852435061 1 20.4693759 3.258847652 24.99999038 1.453502871 1.252471377 0.100229927 0.284213691 542.0991319 668031.8152 0.072309188 0.097789967 1814.878901 -3.258847652 -0.201031494 LAEQFVLLNLVYETTDKHLSPDGQYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAEQFVLLNLVYETTDKHLSPDGQYVPR 28 1 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;; 229.82 3.81E-35 20911950000 2784035 8048611 8278482 6495712 10589700 11557380 5866057 8390393 7898553 9389470 FALSE TRUE 2893950.852 9430897.33 8494226.042 7780544.446 8789666.577 8873353.649 5406260.124 8277933.506 7614285.62 11229156.87 0.257717555 0.839858009 0.756443795 0.692887679 0.782753921 0.79020658 0.481448446 0.737182105 0.678081686 1 23.42074627 -3.179680702 0.984602842 5.643798479 0.679861901 0.262038188 0.165908687 35701.20981 717.6494643 366834.6869 0.047468653 0.000661179 3.179680702 -4.963936578 LAERLS(ph)PFLAESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAERLSPFLAESK 13 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LAERLS(1)PFLAESK;LAERLS(1)PFLAESK;LAERLS(1)PFLAESK 220.1 1.29E-11 683929000 1331170 1018869 1211920 994674 1528010 1436240 1404240 1188970 1387690 967436 TRUE FALSE 1383725.619 1193851.825 1243503.631 1191417.548 1268279.406 1102695.026 1294172 1173033.802 1337747.308 1156986.562 1.195973804 1.031863173 1.074777938 1.029759193 1.096191994 0.953075051 1.118571332 1.013869859 1.156234093 1 20.14194068 4.743747587 24.429727 1.052628344 1.195973888 0.361645651 0.057103448 402.7929308 1896999.572 0.012106508 0.101957581 55430.34564 -4.743747587 0.143345544 LAETYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LAETYLHR 8 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;;; 170.66 0.00029388 1483670000 986190 1100714 1058749 1021494 1481226 1352672 1153068 1072623 1061955 1335954 FALSE TRUE 1025125.543 1289753.067 1086340.869 1223542.464 1229447.734 1038534.428 1062687.517 1058246.243 1023735.447 1597708.608 0.641622344 0.807251748 0.679936794 0.765810773 0.76950686 0.650014917 0.665132247 0.66235247 0.640752289 1 20.60757288 -1.002456868 4.936868327 1.000003576 0.699256721 0.712564768 0.057529434 2.29E-06 4.63E-07 0.056350025 0.01328167 0.099435882 1.002456868 -0.300746855 LAFVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAFVIR 6 0 P18124;A8MUD9;C9JZ88;C9JIJ5 P18124 RPL7 60S ribosomal protein L7 0 ; 120.78 0.046378 414980000 858010 440310 543280 437520 652430 642960 548820 477960 469680 499490 FALSE TRUE 891884.8973 515929.8174 557438.3231 524060.1501 541530.1816 493642.2842 505802.0543 471553.728 452776.3085 597355.5022 1.493055465 0.863689738 0.933176845 0.877300281 0.9065459 0.826379404 0.846735407 0.789402167 0.757967922 1 19.18823025 4.738824491 7.506382779 0.858136284 1.50001651 0.888163069 0.066607226 0.029829039 16.27729234 0.016049378 0.096687976 54805.54377 -4.738824491 0.641880226 LAGDKANYWWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAGDKANYWWLR 12 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 130.56 0.00019537 1269940000 695400 794040 731100 541570 1476670 1186160 753780 816590 936740 1550380 FALSE TRUE 722854.929 930410.1932 750153.0666 648690.9296 1225666.161 910692.3164 694696.754 805644.9467 903026.9104 1854147.277 0.389858421 0.501799509 0.404581166 0.349859441 0.661040348 0.491165037 0.37467183 0.434509684 0.487030842 1 20.82232441 0.741729582 4.483642282 0.999998851 0.451717398 0.791939701 0.083991571 2.735427947 47.18932253 0.080887059 0.020537346 5.517337895 -0.741729582 -0.548281453 LAGESESNLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAGESESNLRK 11 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;; 155.33 5.06E-05 1116006000 811900 700374 820034 700412 1100949 1028966 787152 822617 856962 734784 FALSE TRUE 843954.4389 820657.7863 841404.7597 838951.4031 913810.0822 790004.2406 725452.9694 811591.1646 826120.105 878750.8565 0.960402408 0.933891307 0.957500927 0.954709059 1.039896662 0.899008217 0.825550227 0.923573683 0.940107311 1 19.74509466 LAGFLDLTEQEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAGFLDLTEQEFR 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 138.99 9.92E-05 34673000 4066.3 25614 17130 34532 16295 32565 19006 24385 18429 22560 FALSE TRUE 4226.840664 30013.00525 17576.42187 41362.32653 13525.18172 25002.27228 17516.26006 24058.15896 17765.74389 26980.20006 0.156664541 1.112408551 0.651456321 1.533062262 0.501300275 0.926689655 0.64922647 0.891696833 0.658473393 1 14.71961343 4.751169531 24.34196225 0.870250925 0.156663888 0.37149361 0.282158915 1441.346095 2782497.568 0.061876427 1.076898322 56385.77198 -4.751169531 -0.713587037 LAGGDWFTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAGGDWFTSR 10 0 P30153;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;;; 192.6 1.55E-06 2470698000 664940 491847 539450 519877 641802 748674 617576 477690 507813 561384 FALSE TRUE 691192.3446 576317.8962 553508.5102 622707.1189 532708.7253 574805.8098 569168.7794 471287.3469 489536.9093 671376.4465 1.029515331 0.858412444 0.82443838 0.92750814 0.793457572 0.856160225 0.847763996 0.701971821 0.729154131 1 19.3567624 8 0.654550673 0.808280402 19.60899623 0.293022053 0.084394974 258.9349361 1.633027062 0.032770424 7061.856173 99999999.98 -8 18.80071582 LAGIINFQRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAGIINFQRPK 11 1 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 101.38 0.0030333 678610000 489950 1014220 818610 1032300 909110 1124040 760860 806540 733870 1327540 FALSE TRUE 509293.6043 1188404.395 839943.6491 1236485.859 754579.8069 862998.745 701221.8051 795729.6505 707458.1621 1587646.046 0.320785357 0.748532331 0.52904969 0.778817081 0.475282138 0.54357125 0.44167389 0.501200915 0.445601943 1 20.59845788 -1.549604599 3.026257581 1.020020908 0.537341927 0.533140567 0.131393356 42583978.91 46582821.26 6918780.64 0.030091668 0.028209501 1.549604599 -0.482678981 LAGLDINKTEGEEDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAGLDINKTEGEEDAQR 17 1 P61925 P61925 PKIA cAMP-dependent protein kinase inhibitor alpha 0 113.88 0.00035616 226960000 144230 106270 130120 86528 167950 169540 149080 127850 154770 119500 FALSE TRUE 149924.3118 124521.0458 133511.0341 103642.9801 139401.919 130166.9044 137394.7201 126136.3799 149199.8579 142913.737 1.04905459 0.871302146 0.934207144 0.725213561 0.975427009 0.910807506 0.96138218 0.882605007 1.043985421 1 17.12478507 1.236955119 24.99917217 1.021992751 0.909779233 0.224776754 0.08013656 59.06147848 919499.4349 0.061457333 0.018451671 17.25659548 -1.236955119 -0.112213518 LAGLVEELEADEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAGLVEELEADEWR 14 0 A0A087WUN5;Q96DE5 A0A087WUN5 ANAPC16 Anaphase-promoting complex subunit 16 0 ;;; 178.81 2.51E-07 43775000 33845.8 39879.5 37930.3 35544.4 42609.4 44539.4 37844.7 39365.2 36831.4 41745.6 FALSE TRUE 35182.05832 46728.49391 38918.79478 42574.97623 35366.66941 34195.79935 34878.33353 38837.57388 35505.84511 49924.85105 0.704700316 0.935976631 0.779547539 0.852781237 0.708398096 0.684945446 0.698616677 0.777920676 0.711185799 1 15.6074705 5.045955624 15.53397513 0.780755513 0.311178326 0.051116001 0.101666533 5027978.827 47028344.71 0.023338799 68814358.05 111161.8138 -5.045955624 -0.469577187 LAGS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LAGSPIR 7 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 LAGS(1)PIR;LAGS(1)PIR;LAGS(1)PIR 86.136 0.021292 415330000 434630 480810 466190 485400 544080 617720 465930 460000 471520 540970 TRUE FALSE 451789.528 563385.3773 478339.2944 581410.6712 451597.4759 474263.8916 429409.1891 453834.4524 454550.0873 646962.714 0.698323904 0.870815837 0.739361456 0.898677248 0.698027052 0.733062171 0.663730969 0.701484711 0.702590856 1 19.30332304 LAGS(ph)PPGSGQWKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAGSPPGSGQWKPK 14 1 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 LAGS(0.991)PPGS(0.009)GQWKPK;LAGS(1)PPGSGQWKPK 138.66 8.55E-06 5819800000 4584970 2888860 3936500 2726230 5088140 4606450 4734760 3778880 4464590 2460080 TRUE FALSE 4765988.156 3384999.233 4039088.424 3265470.157 4223259.78 3536671.799 4363637.139 3728230.295 4303910.278 2942085.575 1.619935258 1.150544111 1.372865718 1.109916783 1.43546463 1.202096849 1.483178184 1.267206612 1.462877326 1 21.48840778 -1.470007487 3.298046999 0.994065547 1.332664675 0.307171728 0.154413481 4627569.92 3100881.181 186380.0564 0.032019782 0.033883832 1.470007487 0.338599129 LAHALLHTQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAHALLHTQTK 11 0 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 84.658 0.0091353 125840000 59258 135740 69650 128390 79403 114890 61270 82508 61505 153180 FALSE TRUE 61597.5516 159052.2891 71465.13622 153785.1588 65906.10642 88208.53867 56467.4973 81402.11522 59291.44706 183192.6882 0.336244597 0.868224003 0.390109108 0.839472144 0.359763848 0.481506874 0.308240999 0.444352425 0.323656188 1 17.4830024 -1.300610844 7.531557491 1.000002766 0.487973031 0.387990602 0.194532024 8.60E-06 7.99E-07 0.179347525 0.042272389 0.05004828 1.300610844 -0.512029735 LAHEVGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LAHEVGWK 8 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 145.34 0.00057091 9720500000 12108920 10122140 11624340 9828790 13955680 14808770 13961020 12257570 12785650 10882080 FALSE TRUE 12586989.51 11860538.81 11927279.85 11772895.33 11583498.5 11369657.6 12866718.77 12093277.32 12325496.95 13014215.23 0.96717238 0.911352594 0.916480913 0.904618152 0.890065079 0.873633746 0.988666512 0.929236002 0.947079539 1 23.63358498 1.060432037 0.736132475 0.997387719 0.913988359 0.379698513 0.031387704 0.713192523 0.892748532 0.030525972 0.011897386 11.49296376 -1.060432037 -0.08339936 LAHGGQVNLDMEDHRDEDFVKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAHGGQVNLDMEDHRDEDFVKPK 23 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 232.29 3.30E-34 1045400000 953090 594280 781660 614040 1169380 1031490 1032740 864310 1030760 643670 FALSE TRUE 990718.7291 696342.9671 802030.7017 735495.2793 970609.2053 791942.0799 951791.1402 852725.3382 993663.1489 769784.8127 1.287007372 0.904594317 1.041889485 0.95545569 1.260883807 1.028783716 1.23643793 1.107745079 1.290832363 1 19.55409568 3.24563077 24.99979563 1.155766001 1.036666044 0.140237901 0.128541966 282.5425255 999053.3684 0.033059047 0.043827804 1760.478681 -3.24563077 -0.119099957 LAHHLVALYYQSEEQAEEELLDMAVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAHHLVALYYQSEEQAEEELLDMAVLK 27 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 157.83 1.53E-09 548350000 168985 150083 223304 155064 218630 253230 288630 244675 189618 139953 FALSE TRUE 175656.6583 175858.5878 229123.4857 185735.1964 181467.3507 194421.1702 266006.4264 241395.5318 182793.6852 167374.1108 1.049485237 1.050691693 1.368930264 1.10970087 1.08420203 1.161596434 1.589292544 1.442251318 1.092126401 1 17.35271687 2.441334699 24.99998197 1.345136048 1.138207376 0.093422828 0.18018585 259.0731465 180983.5183 0.062010228 0.051881634 276.2706181 -2.441334699 -0.206928672 LAHPNKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 67.757 0.03501 324240000 1104800 645720 903990 653830 1164800 1127900 1004500 862390 1011700 732570 FALSE TRUE 1148418.357 756617.387 927548.722 783155.6225 966807.7121 865962.3185 925764.6652 850831.0726 975289.1146 876103.0656 1.310825635 0.86361687 1.058721009 0.893908095 1.103531936 0.988425167 1.056684655 0.971154087 1.113212763 1 19.74074107 4.756298644 24.80604845 1.006037125 1.310825915 0.580049716 0.077943911 2246.194211 3141172.064 0.016723456 0.522587057 57055.64828 -4.756298644 0.30478879 LAHYIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LAHYIDR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;;; 113.7 0.0060716 1672440000 1697420 2234180 1834430 2116420 2355720 2630910 2064590 2022570 1804710 2482840 FALSE TRUE 1764435.452 2617883.035 1882236.753 2535041.559 1955295.556 2019921.024 1902762.041 1995460.757 1739758.84 2969304.961 0.594225071 0.881648423 0.633898093 0.853749141 0.658502775 0.680267285 0.640810582 0.672029577 0.585914503 1 21.50169384 -1.099215655 4.92393646 1.00001126 0.693124774 0.489364921 0.095220862 1.10E-05 2.01E-06 0.086150559 0.020305137 0.079576411 1.099215655 -0.306886486 LAHYNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LAHYNK 6 0 Q16778;P33778;P23527;P06899;Q6DRA6;Q6DN03;P58876;U3KQK0;Q99879;Q99877;Q93079;Q5QNW6;P62807;O60814;Q5QNW6-2;Q99880 Q16778;P58876;Q99880 HIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BD;HIST1H2BN;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BK;HIST1H2BL Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-D;Histone H2B;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-K;Histone H2B type 1-L 0 ;;;;;;; 112.88 0.026618 28945210000 22020300 19336880 20722600 19686640 29025830 26730520 28672040 22138120 20161420 20524480 FALSE TRUE 22889678.45 22657838.72 21262647.98 23580598.63 24092029.78 20522761.83 26424650.58 21841394.71 19435814.43 24545858.89 0.932527093 0.923081927 0.866241759 0.96067523 0.981510971 0.836098746 1.076542104 0.889819941 0.791816433 1 24.54897631 4.753122092 19.28992254 0.925330914 0.932527223 0.00077678 0.079618985 2747.592178 3638131.302 0.018075629 0.281773371 56639.84964 -4.753122092 0.007196309 LAHYNKR ddPTM_MDA-MB-175_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 ; 135.5 0.0049243 2449500000 897400 783410 815410 531560 1993220 1175080 1002810 734780 810800 1693810 FALSE TRUE 932830.0449 917954.5734 836660.2545 636700.9815 1654413.176 902185.4785 924207.1318 724931.476 781619.4664 2025679.64 0.460502256 0.453158809 0.413026936 0.314314746 0.81672005 0.445374215 0.456245456 0.357870742 0.385855419 1 20.9499746 -1.013615619 4.612632923 1.000014095 0.453634603 0.614988736 0.129142256 29259676.74 12859496.47 4337.550063 0.030242482 0.096913523 1.013615619 -0.546379492 LAILDQELEHKEQEAWEEATSEDSSVVIVDVKEPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAILDQELEHKEQEAWEEATSEDSSVVIVDVKEPSPR 37 2 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LAILDQELEHKEQEAWEEATSEDSS(0.002)VVIVDVKEPS(0.998)PR 130.79 5.45E-09 64648000 28297 8021 16633 9421.4 24258 21215 16933 13487 18198 8126.5 TRUE FALSE 29414.18741 9398.544355 17066.46964 11284.9248 20134.63382 16288.13777 15605.74721 13306.22883 17543.05753 9718.732084 3.026545763 0.967054578 1.756038699 1.161151959 2.071734631 1.675952956 1.605739008 1.369132178 1.805076772 1 13.2465524 8 0.047228616 1.17E-12 4.520050105 0.19093821 0.518044902 1054.970834 3.768903085 88.5114103 355.1435116 100000000 -8 4.520050105 LAILQVGNRDDSNLYINVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAILQVGNRDDSNLYINVK 19 1 V9GYY3;A0A384N5Y3;F5H2F4;P11586 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 125.18 2.54E-05 19327000 26507 25065 28911 23641 32849 33554 26432 26565 28568 28164 FALSE TRUE 27553.51683 29369.71877 29664.44441 28317.11924 27265.33871 25761.59202 24360.19077 26208.93963 27539.84326 33682.19657 0.818043941 0.87196566 0.880715851 0.840714743 0.809488142 0.764842992 0.723236405 0.778124419 0.817637983 1 15.03969861 3.251286213 3.049848033 0.793165411 0.858413554 0.012708145 0.071924511 0.476579817 9.135606245 0.020132034 0.026749207 1783.553796 -3.251286213 0.065248143 LAIQGPEDS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 LAIQGPEDS(0.985)PS(0.015)R;LAIQGPEDS(0.873)PS(0.127)R;LAIQGPEDS(0.684)PS(0.316)R;LAIQGPEDS(1)PSR;LAIQGPEDS(0.922)PS(0.078)R;LAIQGPEDS(0.998)PS(0.002)R;LAIQGPEDS(0.988)PS(0.012)R 286.78 1.38E-28 14536680000 3504880 3806780 3609350 3536740 3932690 4213100 3451370 3516000 3290710 3635950 TRUE FALSE 3643255.369 4460564.852 3703412.626 4236296.616 3264212.759 3234671.375 3180842.601 3468873.771 3172277.99 4348344.788 0.837848778 1.025807536 0.851683297 0.974231995 0.750679377 0.74388567 0.731506529 0.797745795 0.729536903 1 22.05203491 3.233077559 24.99980676 0.777071477 0.92472898 0.32430274 0.090448539 127.4215418 580973.9801 0.02357462 0.02894257 1710.320726 -3.233077559 0.147657504 LAIRES(ph)IESEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAIRESIESEIRR 13 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 LAIRES(1)IESEIRR;LAIRES(1)IESEIRR;LAIRES(1)IESEIRR;LAIRES(0.996)IES(0.004)EIRR 157.11 2.24E-05 685121000 321948 374232 376429 346252 425307 437217 351554 375392 363390 417203 TRUE FALSE 334658.7556 438503.4349 386239.049 414739.6121 353013.4681 335679.9778 323998.2789 370360.4843 350311.6649 498945.94 0.670731494 0.878859611 0.774110015 0.83123156 0.70751847 0.672778253 0.649365498 0.742285796 0.702103448 1 18.92852398 -1.293938964 3.529010151 1.000839243 0.73836703 0.561692362 0.06979922 31248512.47 52129197.79 285152.3841 0.017518013 0.050823086 1.293938964 -0.262472213 LALDMEIHAYR ddPTM_MDA-MB-175_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 ;;;;;;;;; 189.58 2.65E-06 4680970000 2704194 3029495 3117528 2933994 3757838 3823959 3144768 3146748 3032545 3538633 FALSE TRUE 2810957.667 3549787.2 3198773.341 3514329.256 3119082.039 2935902.475 2898272.867 3104570.99 2923404.298 4231960.385 0.664221167 0.838804449 0.755860889 0.83042584 0.737030065 0.693745264 0.684853497 0.733601146 0.690791981 1 22.01289469 -1.161974559 5.167519565 1.000012192 0.739032015 0.66426553 0.056155185 7.94E-06 1.29E-06 0.054753987 0.012905036 0.068869264 1.161974559 -0.260980177 LALGEPPPYGAAPIGIPRPPPPRPGMHS(ph)PPPRPAPS(ph)PGTWESQPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LALGEPPPYGAAPIGIPRPPPPRPGMHSPPPRPAPSPGTWESQPAR 46 3 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;G3V5H0;G3V4K1;G3V4U6 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 2 LALGEPPPYGAAPIGIPRPPPPRPGMHS(1)PPPRPAPS(0.857)PGT(0.137)WES(0.006)QPAR 114.54 3.55E-08 352670000 50628 64337 50154 59404 69115 83193 63324 60818 69439 64712 TRUE FALSE 52626.83253 75386.37928 51461.05444 71153.9339 57366.85699 63872.68655 58360.49941 60002.83419 66939.90395 77391.07741 0.680011628 0.974096521 0.664948159 0.91940746 0.741259314 0.825323651 0.754098552 0.775319794 0.864956351 1 16.23987962 0.927148918 3.677271572 0.999831693 0.794900775 0.326898498 0.091452549 0.334177836 11.23124856 0.076771684 0.019757279 8.45568738 -0.927148918 -0.204930918 LALLEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LALLEEAR 8 0 Q5TZA2-2;Q5TZA2;B1AKD8 Q5TZA2-2 CROCC Rootletin 0 ;;; 156.4 0.00091553 380420000 486800 620860 456210 456723 1059160 866210 647140 495700 492900 1121730 FALSE TRUE 506019.2399 727487.8754 468099.2074 547061.4462 879124.3615 665045.855 596415.4758 489055.9523 475160.6253 1341511.517 0.377200817 0.542289698 0.34893417 0.407794819 0.655323753 0.495743679 0.444584686 0.36455591 0.354197947 1 20.35542801 -1.218874041 3.690778914 1.000711845 0.444450815 0.763864896 0.092838165 47280063.55 78983065.31 395414.0176 0.023151517 0.060412382 1.218874041 -0.556261029 LALLHEGTGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALLHEGTGPR 11 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 133.81 0.001322 94917000 141635 167039 168795 146251 192401 178818 165409 167590 190509 174415 FALSE TRUE 147226.8592 195726.6489 173193.9364 175179.0113 159696.7467 137290.2295 152443.8104 165343.7302 183652.6183 208588.2799 0.705825175 0.938339628 0.830314802 0.839831516 0.765607477 0.658187649 0.730835934 0.792679868 0.880455117 1 17.67029857 0.984530811 2.666409164 0.999088798 0.784009623 0.463121651 0.073672988 0.258432482 4.277209794 0.074331285 0.019893308 9.650077725 -0.984530811 -0.215079176 LALLIHNDS(ph)LTSLIYGEQSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LALLIHNDSLTSLIYGEQSEK 21 0 G3V4J5;Q9P1W3 G3V4J5 TMEM63C Calcium permeable stress-gated cation channel 1 1 LALLIHNDS(0.79)LT(0.21)SLIYGEQSEK;LALLIHNDS(0.852)LT(0.148)SLIYGEQSEK;LALLIHNDS(0.901)LT(0.076)S(0.023)LIYGEQSEK 249.48 7.09E-31 444084000 602287 473423 573077 548017 693305 753845 630522 591192 602966 377977 TRUE FALSE 626065.7558 554729.7175 588011.8574 656413.1269 575457.2637 578775.9234 581100.0381 583268.0382 581265.3714 452034.3563 1.384995957 1.227184858 1.300812315 1.452131055 1.273038776 1.280380385 1.285521841 1.290317937 1.285887595 1 18.7860729 -3.661767018 0.292228369 1.30E-15 1.327543958 0.721700898 0.05837783 55.11672213 1.069949038 33.20963646 0.061434359 0.000217888 3.661767018 1.327543958 LALLNVATQGVHLWDLQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALLNVATQGVHLWDLQDR 19 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 214.66 4.25E-19 437100000 751130 254380 227098 260353 291820 587490 357590 288800 289940 246118 FALSE TRUE 780785.1924 298067.7862 233016.3604 311850.0463 242216.5406 451054.351 329561.1614 284929.1084 279505.116 294340.1099 2.65266325 1.01266452 0.791656837 1.059488788 0.822913808 1.532425707 1.119661067 0.968026779 0.949599143 1 18.16712463 4.738967592 24.964105 1.031628022 2.652663735 0.864341846 0.193030042 11.08692969 679848.5668 0.046677637 0.275370085 54823.60531 -4.738967592 1.621035713 LALPGHAESYNPPPEYLLSEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137;Q14137-2 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 ; 244.81 1.80E-37 167383000 57204 64703 72191 70525 74186 96602 69312 82122 89044 70405 FALSE TRUE 59462.45809 75815.23693 74072.35677 84474.6345 61575.89022 74167.64952 63879.14433 81021.28891 85839.32383 84199.51176 0.70620906 0.900423712 0.879724303 1.00326751 0.73130935 0.880856052 0.75866407 0.962253667 1.019475316 1 16.36152425 1.569554982 5.575968954 1.00372702 0.845356202 0.425713669 0.084076186 0.137986738 8.979640554 0.045851892 0.021039511 37.11547153 -1.569554982 -0.158370819 LALQLHPDRNPDDPQAQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALQLHPDRNPDDPQAQEK 19 1 Q9UBS4 Q9UBS4 DNAJB11 DnaJ homolog subfamily B member 11 0 ; 120.11 2.79E-05 566090000 396060 341590 361020 343030 484100 526020 422210 361490 430750 307010 FALSE TRUE 411696.7546 400255.4253 370428.4778 410880.3102 401812.8549 403859.8269 389116.077 356644.8178 415247.3916 367162.7314 1.12129233 1.090130863 1.008894547 1.119068672 1.09437266 1.099947768 1.059791868 0.971353537 1.130962802 1 18.4860601 1.995574023 20.27886282 1.027085052 1.086388713 0.20383228 0.048149114 22.44536943 102839.7599 0.017984574 0.012864185 98.98605651 -1.995574023 0.05930366 LALS(ph)PEDKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALSPEDKPIR 11 1 H9KVB4;O15417;O15417-2;O15417-3 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 LALS(1)PEDKPIR;LALS(1)PEDKPIR 132.86 0.00010524 214810000 180377 151017 176161 138940 227176 233137 193792 181173 186124 126048 TRUE FALSE 187498.4232 176952.995 180751.9004 166421.9173 188560.7047 178994.465 178602.0767 178744.6723 179425.4336 150744.6923 1.243814428 1.173858876 1.199059799 1.103998521 1.250861319 1.187401442 1.184798443 1.185744384 1.190260373 1 17.20174768 -3.195863817 0.602973305 7.52E-10 1.190091007 0.695445575 0.037931867 404.218268 11.65064105 529.3368442 0.014059973 0.000636995 3.195863817 1.190091006 LALS(ph)PLSLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 LALS(1)PLSLGK;LALS(0.997)PLS(0.003)LGK;LALS(0.848)PLS(0.152)LGK;LALS(0.997)PLS(0.003)LGK 178.71 2.29E-06 1354288000 2189148 1588502 1871520 1484350 2040019 2158717 2201016 1947124 1942843 1477260 TRUE FALSE 2275577.253 1861314.862 1920293.349 1777950 1693257.299 1657387.692 2028494.615 1921025.988 1872920.46 1766700.813 1.288037701 1.053554087 1.086937491 1.006367341 0.958429003 0.938125845 1.148182307 1.087352184 1.060123166 1 20.75262631 4.757602652 3.728144237 1.041101207 1.319340919 0.607217319 0.060395362 0.229808418 5.825066747 0.01613632 0.180317795 57227.22036 -4.757602652 0.278239712 LALVEENGIFELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALVEENGIFELLR 14 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 ; 107.09 0.002103 59557000 84686 72199 74002 60326 108359 111238 83932 74322 84093 68982 FALSE TRUE 88029.46867 84598.61662 75930.55291 72258.30274 89940.17588 85404.66033 77353.19052 73325.83516 81066.50936 82497.70216 1.067053583 1.025466339 0.920395974 0.875882611 1.090214315 1.035236838 0.937640546 0.888822758 0.982651725 1 16.33206632 2.211276891 23.20499616 0.937015763 0.997941267 0.100073035 0.066875719 197.6954301 168138.5165 0.026645366 0.019686184 162.658548 -2.211276891 0.060925504 LALVTGGEIASTFDHPELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LALVTGGEIASTFDHPELVK 20 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 244.46 6.77E-30 450380000 311000 283780 309680 293640 383450 406750 369590 348830 342880 335880 FALSE TRUE 323278.5201 332517.0075 317750.5152 351721.1156 318271.306 312288.4769 340620.5701 344154.5044 330539.8158 401689.2552 0.804797529 0.827796619 0.791035635 0.875604988 0.792332137 0.777437964 0.847970329 0.856768012 0.822874427 1 18.61572035 -1.71045317 0.349446501 1.148477197 0.812290898 0.773896574 0.02910936 13.21786061 0.830479553 1.680247955 0.023204462 0.019478111 1.71045317 -0.336186298 LAMDLPGHADEVYAVDWSPDGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAMDLPGHADEVYAVDWSPDGQR 23 0 A0A0A0MRH0;Q9NVX2;K7EN33;Q9NVX2-2 A0A0A0MRH0 NLE1 Notchless protein homolog 1 0 113.26 0.00078348 71210000 49279 57902 57672 58455 65576 66812 53027 53141 52203 58103 FALSE TRUE 51224.57297 67846.21808 59174.9797 70017.22453 54429.41494 51295.92555 48870.60518 52428.73182 50324.22423 69487.1704 0.737180298 0.976384816 0.85159576 1.007628086 0.783301646 0.738207143 0.703304004 0.754509523 0.724223248 1 16.08445901 3.053872457 13.13418805 0.761172738 0.896143029 0.193425669 0.104137259 1.397759764 338.7429253 0.027687526 0.033095072 1132.06785 -3.053872457 0.134970291 LAMQEFMILPVGAANFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAMQEFMILPVGAANFR 17 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 126.83 9.84E-05 328820000 248530 205940 243840 227700 318540 313590 249640 246140 282670 252870 FALSE TRUE 258342.1563 241308.593 250194.6707 272738.3804 264394.6846 240763.475 230072.5645 242840.8959 272496.7619 302415.035 0.854263599 0.797938479 0.827322195 0.901867794 0.874277579 0.79613593 0.760784147 0.803005366 0.90106883 1 18.20617034 0.976671332 3.941514342 0.999655579 0.825166251 0.653960275 0.039317068 0.131602062 5.899898321 0.042071082 0.010780017 9.477009843 -0.976671332 -0.174489328 LAPEFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAPEFAK 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 91.906 0.059307 0 151010 196620 170570 141990 213380 209630 170410 171210 175140 165390 FALSE TRUE 156971.9914 230387.9555 175015.1943 170075.1982 177109.7438 160946.6095 157052.8189 168915.21 168836.7456 197795.0039 0.793609486 1.16478147 0.884831218 0.859855885 0.895420715 0.813704119 0.794018129 0.853991287 0.853594592 1 17.59364646 4.023093982 24.99956494 0.856841801 0.990598252 0.160478766 0.098469487 293.2137781 317403.6118 0.022163663 0.047874747 10546.15093 -4.023093982 0.133756451 LAPEYEAAATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAPEYEAAATR 11 0 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 123.86 0.00084005 885550000 269261 318979 270585 303502 332621 341437 269489 280969 266290 288139 FALSE TRUE 279891.6322 373761.1619 277636.6674 363533.7897 276082.2012 262143.4313 248365.748 277203.0701 256706.2749 344594.3203 0.812235187 1.084641098 0.805691362 1.054961641 0.801180359 0.760730563 0.720748235 0.804433079 0.744952136 1 18.3945394 3.112788777 9.130344337 0.787392625 0.939981772 0.254800507 0.109983059 0.306727553 23.42159811 0.028798364 0.034458513 1296.54853 -3.112788777 0.152589146 LAPGGHVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;;;;;;; 162.5 6.37E-05 7619730000 7634490 8578540 8547540 8308820 8859530 9915950 8643460 8716500 8315290 8983070 FALSE TRUE 7935905.56 10051837.51 8770295.914 9952279.797 7353590.255 7613120.89 7965963.02 8599669.575 8016024.337 10743130.58 0.738695812 0.93565255 0.81636315 0.926385445 0.684492309 0.708650131 0.741493642 0.800480783 0.746153487 1 23.35691112 5.07967679 13.08890162 0.805631151 5.72E-05 0.040813316 0.100568021 1419761.797 5759070.532 0.023490708 30825937.24 120137.0019 -5.07967679 -0.805573997 LAPPS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LAPPSPAR 8 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 LAPPS(1)PAR;LAPPS(1)PAR;LAPPS(1)PAR;LAPPS(1)PAR;LAPPS(1)PAR 104.2 0.0048525 10460300000 2855510 3708330 3355080 3532310 3264770 4106310 3202130 3420380 3114940 3392220 TRUE FALSE 2968247.74 4345206.831 3442516.141 4230990.375 2709825.562 3152681.734 2951138.683 3374535.401 3002833.918 4056860.561 0.731661267 1.071076209 0.848566543 1.042922307 0.667961228 0.777123514 0.727443953 0.831809561 0.740186623 1 21.95193229 3.238284566 25 0.780972189 0.928737255 0.221422877 0.121011408 9.514952507 861740.9396 0.031284246 0.039672388 1730.950171 -3.238284566 0.147765066 LAPPS(ph)PAREGTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAPPSPAREGTDK 13 1 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 LAPPS(1)PAREGTDK 74.89 0.016301 0 135020 138950 138290 87617 192690 192080 116840 139020 172090 168600 TRUE FALSE 140350.6939 162813.5816 141893.951 104947.3811 159936.6226 147472.331 107681.7755 137156.6643 165896.5145 201633.942 0.696066805 0.807471104 0.703720562 0.520484697 0.793202876 0.73138644 0.534045878 0.680226072 0.822760855 1 17.62137899 0.984227491 3.115427599 0.998703383 0.68088676 0.553890972 0.089137302 0.177184797 4.256213257 0.086525782 0.022685207 9.64334026 -0.984227491 -0.317816623 LAPS(ph)EDELTCFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;LAPS(1)EDELTCFSK;LAPS(1)EDELTCFSK 244.44 5.09E-17 295037000 341729 268258 339159 288900 392897 391905 343708 317360 343465 263473 TRUE FALSE 355220.7248 314329.2247 347997.7622 346043.5577 326112.5083 300891.0031 316767.2688 313106.3083 331103.7617 315095.4899 1.127343095 0.99756815 1.104420004 1.09821806 1.034964063 0.954920057 1.005305627 0.993687052 1.05080451 1 18.26542958 3.018701189 5.949639583 0.999727099 1.076686199 0.494494639 0.038413452 0.140087056 17.11247523 0.010940779 0.012807508 1044.001659 -3.018701189 0.076959099 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 LAPVPS(1)PEPQKPAPVS(1)PESVK;LAPVPS(1)PEPQKPAPVS(0.995)PES(0.005)VK;LAPVPS(1)PEPQKPAPVS(0.999)PES(0.001)VK;LAPVPS(1)PEPQKPAPVS(1)PESVK 216.81 3.44E-25 3601570000 4777780 2250750 3181140 2051600 4291630 4163200 4212460 3219970 3626200 1802840 TRUE FALSE 4966410.444 2637298.804 3264043.122 2457400.357 3562140.266 3196359.894 3882276.378 3176811.569 3495693.77 2156071.981 2.303452987 1.223196084 1.513884115 1.139758032 1.65214348 1.4824922 1.800624661 1.473425562 1.62132517 1 21.03997391 -2.03741787 2.403472673 0.315696397 1.556302273 0.242087612 0.30494684 13999951.88 5621808.83 52689245.07 0.067985872 0.009174494 2.03741787 1.240605876 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(1)PEPQKPAPVSPESVK 181.37 3.06E-17 1216100000 1649290 927440 1349000 883950 1810930 1647720 1610270 1323840 1511660 875230 TRUE FALSE 1714405.243 1086720.606 1384156.048 1058792.672 1503108.765 1265062.001 1484052.83 1306096.09 1457255.652 1046714.561 1.637891844 1.038220586 1.322381573 1.011539068 1.436025466 1.208602659 1.417819991 1.247805408 1.392218763 1 19.99743664 -1.152557859 4.065021907 0.999913765 1.288903581 0.200816613 0.178818969 11385217.55 3234336.54 10398.27583 0.037452637 0.070378846 1.152557859 0.288989817 LAPVPSPEPQKPAPVS(ph)PESVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 LAPVPSPEPQKPAPVS(1)PESVK 191.18 9.30E-18 438850000 702300 367070 535730 380990 710670 670170 680600 555640 644280 346920 TRUE FALSE 730027.3463 430111.4171 549691.5639 456348.6849 589870.5672 514533.174 627252.7936 548192.5546 621092.4887 414892.3318 1.759558542 1.036682011 1.32490172 1.09992075 1.42174372 1.240160723 1.51184475 1.321288712 1.496996789 1 18.66237747 LAQANGWGVMVSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 186.05 8.40E-07 11130250000 3872640 4630350 4062700 4296180 6423770 5656440 4280750 3754350 4092490 6812690 FALSE TRUE 4025534.818 5425576.593 4168577.3 5145951.581 5331859.87 4342817.534 3945213.629 3704029.079 3945202.084 8147506.169 0.494081837 0.665918685 0.511638434 0.631598366 0.654416181 0.533024148 0.48422346 0.454621206 0.484222043 1 22.95792711 -1.37829093 3.218300862 1.00451218 0.544464363 0.776126142 0.073150261 23976109.77 31101746.61 1009981.562 0.019139307 0.041851311 1.37829093 -0.460047816 LAQFVEHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAQFVEHWK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 156.83 7.00E-05 952480000 2134000 2479400 2079500 1808830 2879300 2984600 2338100 2244900 1973900 2588000 FALSE TRUE 2218251.968 2905217.663 2133693.478 2166611.175 2389877.614 2291471.882 2154833.613 2214810.787 1902859.725 3095069.05 0.716705163 0.938660048 0.689384774 0.700020303 0.772156477 0.74036212 0.696215037 0.715593336 0.614803642 1 21.56154017 4.206540421 24.99969615 0.727715055 0.827683122 0.082889763 0.108180639 319.4247767 249390.2284 0.02427641 0.052449766 16089.42118 -4.206540421 0.099968067 LAQGHTTVDELAR ddPTM_MDA-MB-175_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 ;;;;; 180.48 1.29E-05 5170534000 673349 1307597 1216707 1286580 1305478 1570664 1198598 1277578 1159672 1320003 FALSE TRUE 699933.3385 1532166.613 1248415.384 1541061.684 1083573.316 1205901.09 1104648.757 1260454.157 1117935.631 1578632.315 0.443379584 0.970565849 0.790820872 0.976200518 0.68640006 0.763889779 0.699750503 0.79844695 0.708167203 1 20.59024376 -1.357889122 2.944105604 1.002924425 0.77073567 0.19756595 0.143733891 20479591.82 24891290.07 518091.4507 0.033872235 0.043864267 1.357889122 -0.232188755 LAQGLTHLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAQGLTHLGK 10 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 129.16 0.00031058 1315910000 3132200 2868300 3412100 2784300 4075000 4024800 3582900 3437400 3667300 2989100 FALSE TRUE 3255861.675 3360908.213 3501022.129 3335026.23 3382332.956 3090101.196 3302062.936 3391327.275 3535314.589 3574756.915 0.910792468 0.940178113 0.979373482 0.932937906 0.946171456 0.864422748 0.923716777 0.948687521 0.988966431 1 21.76941371 1.300329713 2.59109488 0.999270751 0.929373131 0.477657832 0.027442291 0.255665365 2.835702904 0.025858579 0.00764208 19.96777679 -1.300329713 -0.069897619 LAQMCGLHIVVHADELEELINYYQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAQMCGLHIVVHADELEELINYYQDR 26 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 169.65 4.59E-12 382290000 194508 139744 206231 255438 208338 258191 309347 218747 241171 130908 FALSE TRUE 202187.326 163743.9449 211605.5493 305962.874 172924.7812 198230.0532 285099.5738 215815.0543 232491.3028 156556.9162 1.291462114 1.045906811 1.351620576 1.954323587 1.104548974 1.266185219 1.82106023 1.378508593 1.485027353 1 17.25632772 4.009686213 21.53541475 1.460124976 1.176203188 0.11270195 0.280679812 69.77736849 155119.2217 0.066746381 0.143670389 10225.53908 -4.009686213 -0.283921788 LAQMISDHNDADFEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 234.77 1.10E-19 859670000 595670 593350 765960 656190 880750 1016370 1017660 845920 842160 494150 FALSE TRUE 619187.5116 695253.2469 785921.5468 785982.4235 731040.4296 780333.4707 937893.15 834581.826 811850.8261 590969.2314 1.047749153 1.176462682 1.329885728 1.32998874 1.237019443 1.320429947 1.587042269 1.412225513 1.373761582 1 19.17272349 5.215409285 0.746151785 1.369011719 0.567183693 0.247622888 0.143070083 5.867555864 1.510519903 0.050781297 4.629827783 164213.6617 -5.215409285 -0.801828025 LAQQVCHAIANISDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAQQVCHAIANISDR 15 0 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 0 107.07 0.0011862 109750000 143650 156300 143110 147240 186290 202400 152080 178690 147570 167560 FALSE TRUE 149321.4129 183143.3092 146839.5642 176363.6325 154624.4923 155395.6674 140159.5722 176294.9528 142258.9845 200390.1739 0.745153368 0.913933581 0.732768286 0.8801012 0.771617137 0.775465505 0.699433358 0.87975847 0.709909981 1 17.61245224 -1.50622317 5.720617959 1.000305817 0.795745961 0.429942417 0.072322507 0.000256583 2.21E-05 0.063695362 0.01499094 0.031172873 1.50622317 -0.204559857 LAQTLSTQLFQMVHTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAQTLSTQLFQMVHTQR 17 0 P53367;P53367-2 P53367 ARFIP1 Arfaptin-1 0 149.95 3.05E-07 247710000 88320 121580 124670 117540 164190 129020 126240 125320 123760 126760 FALSE TRUE 91806.9418 142460.4192 127919.0026 140789.0612 136281.0424 99057.06032 116344.9789 123640.2904 119305.9018 151596.195 0.605601887 0.939736114 0.843814072 0.928711048 0.89897403 0.653427088 0.767466353 0.815589668 0.786997997 1 17.20987402 LAS(ph)LNAEALNNLLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LASLNAEALNNLLLER 16 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER;LAS(1)LNAEALNNLLLER 180.05 2.65E-09 132397000 30716.3 34752.6 40006.8 43112.6 50059.1 50716 43475.1 42603.6 49037.1 41602.5 TRUE FALSE 31929.00324 40721.08871 41049.41007 51640.1436 41550.07206 38937.97761 40067.40806 42032.56843 47272.26435 49753.71335 0.64174111 0.818453257 0.825052188 1.037915366 0.835114995 0.782614502 0.805314928 0.84481269 0.950125351 1 15.60251658 7.999999999 0.037956444 1.381590266 2.14E-19 0.336622961 0.0890146 1244.404651 3.600913165 37.014259 113.4610062 99999999.7 -7.999999999 -1.381590266 LAS(ph)LSSHVTELEEDLDTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.681)LS(0.141)S(0.178)HVTELEEDLDTAR;LAS(0.978)LS(0.019)S(0.002)HVTELEEDLDTAR 263.31 1.89E-31 79861000 36913 48220 52395 49854 68082 78865 59672 59068 55166 51419 TRUE FALSE 38370.35374 56501.4099 53760.45674 59714.9724 56509.44596 60549.79896 54994.75272 58276.29008 53180.58644 61493.56857 0.623973444 0.918818199 0.874245193 0.971076712 0.91894888 0.984652548 0.894317146 0.947681057 0.864815422 1 15.90814791 4.744745827 4.621619469 0.930032438 0.60354497 0.819311707 0.043209111 0.072377843 4.101528941 0.009506386 0.076949544 55557.90067 -4.744745827 -0.326487468 LAS(ph)LSSHVTELEEDLDTARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASLSSHVTELEEDLDTARK 20 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.964)LS(0.03)S(0.006)HVT(0.001)ELEEDLDTARK 55.127 0.02727 0 3348.9 4759.8 6442.4 4385.4 9262.7 3908.2 6034.2 7845.8 6525.3 5913.6 TRUE FALSE 3481.117158 5577.258624 6610.294236 5252.819031 7688.229563 3000.579779 5561.223637 7740.639884 6290.455728 7072.256697 0.492221551 0.788610887 0.934679625 0.742735912 1.087097074 0.424274727 0.786343578 1.094507767 0.889455233 1 12.78795492 6.6629317 0.173815481 1.020755022 4.92E-16 0.203118059 0.193330446 66.35479905 1.093621599 0.516391761 16.23890136 4601841.961 -6.6629317 -1.020755022 LAS(ph)PELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LASPELER 8 0 P05412;P17535 P05412;P17535 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 LAS(1)PELER;LAS(1)PELER 145.23 0.0006007 406404000 827200 646510 780820 652040 1003510 1048470 975080 833960 938900 710490 TRUE FALSE 859858.4947 757543.0634 801168.8107 781011.5659 832933.7286 804978.7322 898650.6817 822782.1303 905109.1724 849696.9123 1.011959067 0.891545035 0.942887751 0.919164886 0.980271573 0.94737161 1.057613213 0.968324256 1.065214148 1 19.6965888 2.264927429 23.62946373 1.015933697 0.946066709 0.447426798 0.039882569 108.8723335 97568.77565 0.013087305 0.010945126 184.0464433 -2.264927429 -0.069866988 LAS(ph)PSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.657)PS(0.132)GS(0.132)T(0.023)S(0.027)S(0.027)GLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.242)PS(0.242)GS(0.242)T(0.242)S(0.016)S(0.016)GLEVVAPEGTSAPGGGPGTLDDSATICR;LAS(0.798)PS(0.132)GS(0.03)T(0.035)S(0.004)S(0.001)GLEVVAPEGTSAPGGGPGTLDDSATICR 196.35 1.85E-30 2748270000 761523 988303 903956 873454 963407 1200860 889792 925830 929673 963995 TRUE FALSE 791588.5161 1158036.352 927513.836 1046220.594 799647.4223 921978.4642 820047.778 913420.7632 896214.2503 1152871.363 0.686623453 1.004480109 0.804525002 0.90749118 0.693613744 0.799723624 0.711309001 0.792300678 0.777375758 1 20.13680012 5.039133908 16.311589 0.817128959 0.119136993 0.138609577 0.102868868 10917075.62 123790958.7 0.023465527 226358477.3 109429.3723 -5.039133908 -0.697991967 LAS(ph)YLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LAS(1)YLDR;LAS(1)YLDR;LAS(1)YLDR;LAS(1)YLDR 123.21 0.0044748 209658000 302803 368273 339288 303184 366666 465505 360882 361746 349623 347241 TRUE FALSE 314757.8963 431521.023 348130.124 363152.8903 304340.2443 357398.5185 332595.1259 356897.3866 337040.1365 415276.2256 0.757948269 1.039118053 0.838309786 0.874485145 0.73286219 0.860628412 0.800900955 0.859421668 0.8116047 1 18.66371175 4.084932651 24.7250973 0.838381102 0.908578712 0.03975992 0.090193257 48.95515009 14244.5475 0.020212631 0.04366427 12159.97414 -4.084932651 0.070197609 LASDDRPS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LASDDRPSPPR 11 1 P98175-5;P98175-2;P98175;P98175-4;P98175-3 P98175-5 RBM10 RNA-binding protein 10 1 LASDDRPS(1)PPR;LASDDRPS(1)PPR;LAS(0.001)DDRPS(0.999)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR;LASDDRPS(1)PPR 93.494 0.0055765 10202050000 5123760 5096280 5120120 4773820 6131560 6503450 5866730 5065390 5359780 4992850 TRUE FALSE 5326050.001 5971526.446 5253554.533 5718067.348 5089319.621 4993122.298 5406880.373 4997496.732 5166882.565 5971103.364 0.891970826 1.000070855 0.879829776 0.95762324 0.852324824 0.836214347 0.90550775 0.836946947 0.865314541 1 22.50956611 3.235820006 24.99447373 0.871625842 0.933456053 0.146634084 0.054877374 100.4449486 916066.4806 0.014383739 0.017940912 1721.155094 -3.235820006 0.061830212 LASDLLEWIR ddPTM_MDA-MB-175_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 ; 128.86 0.00074093 1649420000 994250 753280 686960 646590 917230 1071090 879500 666020 734310 887710 FALSE TRUE 1033503.758 882649.9803 704862.7419 774483.5721 761319.5722 822345.58 810562.4919 657093.0913 707882.3265 1061639.778 0.973497583 0.831402514 0.663937765 0.729516346 0.71711666 0.774599442 0.763500491 0.618941664 0.66678203 1 20.0178629 4.555108928 3.122270827 0.724125891 0.973312669 0.325848714 0.099599159 0.273415225 4.621291572 0.022977864 0.130304524 35901.19695 -4.555108928 0.249186778 LASDLLEWIRR ddPTM_MDA-MB-175_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 ; 207.29 3.77E-08 483580000 763410 881410 721270 796030 956830 1045310 883840 866620 792290 1047170 FALSE TRUE 793550.0163 1032785.311 740066.8887 953482.3581 794188.3784 802552.5943 814562.3113 855004.3764 763775.6377 1252342.912 0.63365234 0.824682522 0.590945884 0.761358849 0.634162074 0.640840928 0.650430727 0.682723851 0.609877399 1 20.25619822 -1.484128817 6.403270527 1.000162766 0.672790825 0.679582553 0.067981992 0.000144036 1.16E-05 0.060019371 0.01413975 0.032799799 1.484128817 -0.327371941 LASDS(ph)DAESDSR ddPTM_MDA-MB-175_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 LASDS(1)DAESDSR;LASDS(1)DAESDSR;LASDS(1)DAESDSR 367 2.14E-86 2171390000 742120 799460 805050 756110 855530 1035950 834680 782350 743770 781910 TRUE FALSE 771419.4706 936761.0361 826030.2644 905666.3012 710107.3162 795366.3125 769255.6006 771863.8779 717001.863 935110.2939 0.82495025 1.001765291 0.883350627 0.968512813 0.759383487 0.850558825 0.822636223 0.825425496 0.766756465 1 19.83477701 3.247298946 24.99983733 0.828289015 0.922918059 0.21258814 0.076166956 239.5030303 685199.6001 0.019216472 0.025627658 1767.253889 -3.247298946 0.094629045 LASEAKPAAVAAENEEIGSHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASEAKPAAVAAENEEIGSHIK 22 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 169.56 4.90E-12 85503000 108430 85619 103320 80931 139290 132160 97063 105350 124260 92454 FALSE TRUE 112710.9001 100323.3972 106012.6041 96938.91025 115613.5356 101467.8429 89454.94843 103937.9556 119787.9069 110568.5912 1.019375384 0.90734083 0.958794925 0.876730989 1.045627283 0.917691379 0.809044843 0.940031473 1.083380964 1 16.7545821 1.290481105 8.982629812 1.041386381 0.929627846 0.294020145 0.066259949 0.318661933 51.48643794 0.044116609 0.016012295 19.52005805 -1.290481105 -0.111758535 LASFYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASFYER 7 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 79.469 0.075704 183160000 122900 130970 129760 98362 238980 171790 132470 131160 148380 175660 FALSE TRUE 127752.1869 153463.0787 133141.6522 117817.71 198358.265 131894.376 122086.6553 129402.0147 143039.8328 210077.2138 0.608120151 0.730507969 0.633774838 0.560830506 0.944215993 0.627837611 0.581151345 0.615973586 0.680891707 1 17.68056016 0.939840158 20.28163444 1.000000001 0.661675162 0.483999238 0.103971721 1865.269717 628839.2435 0.098936775 0.024734194 8.706430917 -0.939840158 -0.338324839 LASHLNLAMCHLK ddPTM_MDA-MB-175_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 ; 180.09 7.63E-06 1107410000 652770 576170 613280 429550 1827890 1096790 896010 622690 735850 1660630 FALSE TRUE 678541.8636 675122.7155 629262.5806 514513.7079 1517185.911 842077.1445 825778.3949 614343.8591 709366.9022 1985998.654 0.341662801 0.339941175 0.31684945 0.259070522 0.763941057 0.424006906 0.415800078 0.3093375 0.357183979 1 20.92143321 -2.024595723 2.557541173 1.703727798 0.391228704 0.653334547 0.132869532 13075139.23 4829516.082 53993800.24 0.03348859 0.009449401 2.024595723 -1.312499093 LASLSS(ph)HVTELEEDLDTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 LAS(0.202)LS(0.345)S(0.453)HVTELEEDLDTAR 167.45 1.16E-11 39826000 12149 12249 15198 14117 19734 20384 15200 16898 14545 13920 TRUE FALSE 12628.6519 14352.67047 15594.07237 16909.30046 16379.62173 15650.12492 14008.58428 16671.50995 14021.52829 16647.35749 0.758597988 0.862159083 0.936729591 1.015734808 0.983917222 0.940096645 0.841489966 1.001450829 0.842267507 1 14.02300557 4.544607218 2.262430445 0.946617737 0.747135674 0.501672291 0.05844264 0.3310232 2.631783668 0.014586626 0.111066683 35043.47924 -4.544607218 -0.199482063 LASLSSHVTELEEDLDTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LASLSSHVTELEEDLDTAR 19 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 0 ;;;; 352.97 7.84E-91 286303000 76562.5 235215 219437 240444 222041 292935 215365 260172 207234 243358 FALSE TRUE 79585.24662 275611.3465 225155.7085 288003.1055 184298.5501 224905.2857 198484.1285 256684.8199 199775.6888 291039.3407 0.273451852 0.946990004 0.773626369 0.989567612 0.633242742 0.772765926 0.681983845 0.881959185 0.686421596 1 18.15085465 -4.999999996 0.031919646 2.119323263 5.92E-13 0.173699557 0.187314876 2676.180172 6.423345192 341.8232832 130.8703569 1.00E-05 4.999999996 -2.119323263 LASPS(ph)GSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.409)PS(0.487)GS(0.092)T(0.01)S(0.001)SGLEVVAPEGTSAPGGGPGTLDDSATICR 225.97 9.23E-40 1296200000 488610 663080 541980 648140 627040 673080 550640 638170 570470 600360 TRUE FALSE 507900.7001 776958.832 556104.444 776340.1575 520455.9648 516767.3706 507479.398 629616.375 549938.8961 717989.0474 0.707393381 1.082131872 0.774530539 1.081270195 0.724880089 0.719742693 0.706806601 0.876916406 0.765943294 1 19.45360231 3.19742205 24.99999485 0.788868685 0.913761131 0.136806985 0.136690352 250.9586532 152507.3433 0.036596905 0.043742075 1575.513213 -3.19742205 0.124892446 LASPSGST(ph)SSGLEVVAPEGTSAPGGGPGTLDDSATICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICR 38 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LAS(0.205)PS(0.205)GS(0.205)T(0.243)S(0.071)S(0.071)GLEVVAPEGTSAPGGGPGTLDDSATICR 137.35 8.71E-09 641540000 334650 356730 281960 404460 402940 430920 340090 371570 324800 344740 TRUE FALSE 347862.2404 417995.6025 289308.1092 484460.9808 334448.4027 330845.3607 313432.8571 366589.7119 313110.5114 412285.2026 0.843741755 1.013850606 0.701718392 1.175062743 0.811206419 0.802467221 0.760233099 0.889165339 0.759451248 1 18.65328316 LASQEAELQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASQEAELQLR 11 0 A0A087WYC6;A0A0C4DFR0;Q96DT5 A0A087WYC6 DNAH11 "Dynein heavy chain 11, axonemal" 0 62.466 0.080795 356690000 15608 192410 123040 209190 65555 176090 72964 135130 79124 198490 FALSE TRUE 16224.21589 225454.9208 126246.5235 250567.1576 54411.98452 135195.7662 67244.89102 133318.8034 76276.3427 237380.3152 0.06834693 0.949762496 0.531832319 1.055551542 0.229218604 0.569532339 0.283279138 0.561625353 0.321325476 1 17.85684078 -1.229842042 7.417193232 1.000000922 0.524341722 0.200224034 0.293429847 4.14E-06 4.30E-07 0.263069714 0.062006005 0.058905786 1.229842042 -0.4756592 LASS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LASSPK 6 0 Q9P2E9;Q9P2E9-3;A2A2S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 LAS(0.017)S(0.983)PK;LAS(0.015)S(0.985)PK;LAS(0.031)S(0.969)PK;LAS(0.017)S(0.983)PK 107.29 0.032926 2128630000 11845600 6087840 7536800 6320700 10508200 13547200 10742600 7461400 7655700 5119630 TRUE FALSE 12313273.43 7133379.163 7733215.2 7570915.595 8722019.917 10401068.11 9900566.941 7361392.137 7380172.852 6122723.477 2.011077828 1.165066361 1.263035188 1.236527441 1.424532718 1.698764961 1.617020102 1.202306811 1.20537419 1 22.5457421 1.592117308 5.241347659 1.134152477 1.462481321 0.307400376 0.241905334 0.206429176 12.13969662 0.137364198 0.063417994 39.09464808 -1.592117308 0.328328844 LASTLVHLGEYQAAVDGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 245.78 1.32E-24 6947805000 1209574 1598990 1627391 1698200 1723693 2012534 1537115 1666305 1735415 1762661 FALSE TRUE 1257328.916 1873604.094 1669802.146 2034098.891 1430700.28 1545153.479 1416631.91 1643970.907 1672957.753 2108020.675 0.596449992 0.888797779 0.792118486 0.964933084 0.678693666 0.73298782 0.672019932 0.779864698 0.793615439 1 21.00745759 -1.986238211 5.235893468 1.194986579 0.769824032 0.322758284 0.101327209 0.063262663 0.000166277 0.026911397 0.022281361 0.010321951 1.986238211 -0.425162546 LASVLLYSDYGIGEVPVEPLDVPLPS(ph)T(ph)IRPASPVAGSPKQPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LASVLLYSDYGIGEVPVEPLDVPLPSTIRPASPVAGSPKQPVR 43 2 Q13057;Q13057-2;K7EN91 Q13057 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 2 LASVLLYSDYGIGEVPVEPLDVPLPS(0.518)T(0.518)IRPAS(0.518)PVAGS(0.447)PKQPVR 105.24 9.42E-06 586990000 31395 25336 24426 19629 42836 44539 27336 26161 27720 26439 TRUE FALSE 32634.49884 29687.26091 25062.56163 23511.55761 35554.75202 34195.49225 25193.33289 25810.35459 26722.36261 31619.21584 1.032109683 0.938899341 0.792637039 0.743584462 1.124466596 1.081478188 0.796772855 0.816286992 0.845130466 1 14.94851397 2.181672841 24.99996781 0.843833907 0.942690219 0.097452612 0.122408086 189.3220613 83198.09561 0.049040356 0.036218723 151.9402514 -2.181672841 0.098856312 LASYLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 LASYLDR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;; 206.65 0.0004959 37499517000 11379597 13352940 11547781 11197816 21033184 17078442 14225858 12239729 12156675 21813516 FALSE TRUE 11828872.28 15646203.57 11848725.66 13412710.58 17457970.9 13112232.67 13110798.08 12075675.45 11719158.64 26087456.82 0.453431408 0.599759635 0.45419244 0.514144045 0.669209384 0.502625946 0.502570955 0.462892015 0.449225799 1 24.63685297 -1.19665062 4.235332746 1.000192446 0.513199244 0.824127996 0.067627604 10022978.22 2831907.414 17826.93937 0.015883213 0.063584225 1.19665062 -0.486993202 LAT(ph)QSNEITIPVTFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.971)QS(0.029)NEITIPVTFESR;LAT(0.5)QS(0.5)NEITIPVTFESR 208.52 5.71E-11 594910000 407277 496750 533646 465313 520689 593230 499653 506582 548599 581886 TRUE FALSE 423356.6104 582062.9483 547553.2532 557350.5226 432182.4698 455461.323 460488.8923 499792.0969 528855.0292 695895.4208 0.608362403 0.836423018 0.786832672 0.800911324 0.621045141 0.654496796 0.6617214 0.718200008 0.75996337 1 19.40851099 0.730935816 2.551405724 0.999950158 0.713725264 0.579855696 0.073437356 1.115241625 9.527012229 0.072916022 0.019439167 5.381902375 -0.730935816 -0.286224893 LATKSS(ph)PVKVGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LATKSSPVKVGEK 13 2 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 LAT(0.008)KS(0.142)S(0.849)PVKVGEK;LAT(0.003)KS(0.134)S(0.863)PVKVGEK 122.16 0.00012434 1197000000 4794100 1747750 3070770 1328350 5373900 3836600 3065430 2821690 3609500 1720950 TRUE FALSE 4983374.77 2047912.467 3150796.789 1591093.665 4460446.398 2945607.794 2825153.587 2783869.861 3479594.8 2058137.203 2.421303479 0.995032044 1.53089735 0.773074634 2.167224999 1.431200889 1.372675049 1.352616267 1.690652496 1 20.97290773 -2.144562488 2.158760534 0.000298831 1.4872782 0.098125003 0.465274123 10847766.33 2500790.38 53076285.47 0.11047291 0.007168652 2.144562488 1.486979369 LATLGALETEGTDGHTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LATLGALETEGTDGHTFR 18 0 G3V4I0;O75356 G3V4I0 ENTPD5 Ectonucleoside triphosphate diphosphohydrolase 5 0 ; 312.66 3.33E-61 392970000 162511 249290 223505 267900 287930 298590 243180 231600 236000 252060 FALSE TRUE 168927.0598 292103.6183 229329.7239 320889.8204 238987.7614 229246.9977 224118.9162 228495.7808 227506.4061 301446.331 0.560388508 0.969007044 0.760764688 1.064500667 0.792803683 0.760490257 0.743478666 0.757998215 0.754716123 1 18.20154164 3.027915569 24.97148973 0.78067765 0.853191107 0 0.142626439 666.4330399 596144.1408 0.038612786 0.046150247 1066.388785 -3.027915569 0.072513457 LATNTS(ph)APDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LATNTSAPDLK 11 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;B5MEG9;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 LATNT(0.001)S(0.999)APDLK;LATNT(0.032)S(0.968)APDLK 280.09 2.59E-27 1065720000 4072700 2765200 3186000 2353400 4291100 4188500 3517400 3017200 3404300 2303700 TRUE FALSE 4233493.341 3240101.59 3269029.777 2818895.496 3561700.355 3215784.352 3241696.997 2976759.369 3281779.908 2755065.908 1.536621439 1.176052297 1.186552295 1.02316808 1.292782269 1.167225925 1.176631378 1.080467571 1.191180181 1 21.3936554 4.75785579 3.399314227 1.144536559 1.59630263 0.675073117 0.082025096 0.191109461 3.584369066 0.018728612 0.229281042 57260.58622 -4.75785579 0.451766071 LATQS(ph)NEITIPVTFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LAT(0.005)QS(0.995)NEITIPVTFESR;LAT(0.003)QS(0.997)NEITIPVTFESR;LAT(0.02)QS(0.98)NEITIPVTFESR;LAT(0.011)QS(0.989)NEITIPVTFESR;LAT(0.004)QS(0.989)NEIT(0.007)IPVTFESR;LAT(0.021)QS(0.977)NEIT(0.002)IPVTFESR 290.42 5.98E-46 1873163000 1280595 1549008 1569198 1255569 1648979 1741679 1415103 1510302 1679704 1582309 TRUE FALSE 1331153.879 1815038.074 1610092.589 1503916.801 1368686.139 1337200.448 1304183.529 1490058.872 1619251.781 1892332.153 0.703446209 0.959154063 0.850850939 0.794742508 0.723280073 0.706641509 0.689193769 0.787419307 0.8556911 1 20.85173391 0.917976888 2.702998032 0.999485965 0.77798776 0.438583811 0.07747314 0.364434643 5.972993711 0.079181845 0.02106467 8.278981042 -0.917976888 -0.221498205 LATQSNEITIPVTFES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 LATQSNEITIPVT(0.005)FES(0.995)R;LATQSNEITIPVT(0.002)FES(0.998)R;LATQSNEITIPVTFES(1)R;LATQSNEITIPVTFES(1)R;LATQSNEITIPVT(0.003)FES(0.997)R 385.27 1.03E-121 1348962000 866739 1216019 1156270 898200 1123311 1220641 837358 1071603 1107446 1320150 TRUE FALSE 900958.525 1424860.804 1186403.346 1075861.279 932370.9975 937165.6267 771723.6919 1057239.915 1067589.235 1578808.117 0.570657394 0.902491436 0.751455059 0.681438908 0.590553714 0.593590581 0.488801447 0.669644337 0.676199485 1 20.59040441 -1.163079597 9.467859127 1.000000004 0.65837055 0.47857979 0.106995185 9.79E-09 7.73E-10 0.109132657 0.025722814 0.068694253 1.163079597 -0.341629454 LATQSNEITIPVTFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;; 453.65 1.16E-182 6451112000 2850775 3257620 3058735 2977470 3369530 3857460 3087074 3333725 3113920 3517410 FALSE TRUE 2963325.798 3817090.894 3138448.147 3566404.679 2796778.494 2961623.375 2845101.073 3289041.869 3001850.627 4206579.145 0.704450266 0.907409742 0.746080851 0.847815899 0.664858166 0.704045561 0.676345547 0.78188042 0.713608499 1 22.00421606 -1.109418346 3.576476403 1.000159706 0.752192068 0.512475426 0.073226465 13851913.59 23517415.75 26238.88285 0.017171477 0.077728745 1.109418346 -0.247967639 LATTILQHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LATTILQHWK 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 64.73 0.071091 108170000 135250 105060 129480 98566 266710 194080 135910 114360 135060 202710 FALSE TRUE 140589.7744 123103.2377 132854.3552 118062.0606 221374.7295 149007.8613 125257.0191 112827.1913 130199.217 242427.1434 0.57992588 0.507794779 0.548017657 0.487000172 0.913159832 0.614650073 0.516679021 0.465406595 0.537065343 1 17.88719171 -2.167487575 2.336062647 2.058812389 0.569951541 0.527316204 0.120815554 10710634.42 2388702.789 60031307.97 0.031113847 0.006800055 2.167487575 -1.488860848 LAVYIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LAVYIDR 7 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 133.47 0.0076042 6278803000 3620570 4255710 3946210 4039820 4363600 4835320 3971020 4006620 3747260 4424050 FALSE TRUE 3763512.899 4986595.088 4049051.474 4838884.338 3621876.831 3712390.21 3659761.076 3952917.812 3612396.845 5290857.894 0.711323754 0.942492728 0.765292048 0.914574618 0.684553791 0.701661297 0.691714113 0.74712228 0.682762024 1 22.33507024 3.228309265 24.99977643 0.733203578 0.836345309 0.108071865 0.108197776 332.7697537 811517.8539 0.028288584 0.03417074 1691.64514 -3.228309265 0.103141731 LAWVGDVFTATPAEPRPLT(ph)SPLR ddPTM_MDA-MB-175_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 83.312 0.012579 31230000 16012 19632 17812 13184 21865 23587 16842 16806 17900 18764 TRUE FALSE 16644.16612 23003.64328 18276.19535 15791.75585 18148.39511 18109.27671 15521.88003 16580.74306 17255.7825 22440.44654 0.741703874 1.025097395 0.814431002 0.703718432 0.808735917 0.806992708 0.69169212 0.73887759 0.768958963 1 14.45381376 4.010010058 24.9947999 0.770554899 0.89249155 0.097841154 0.103655314 311.3268196 777359.4327 0.023479009 0.05063273 10233.16692 -4.010010058 0.121936651 LAWVGDVFTATPAEPRPLTS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAWVGDVFTATPAEPRPLTSPLR 23 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 LAWVGDVFTATPAEPRPLT(0.002)S(0.998)PLR;LAWVGDVFTATPAEPRPLT(0.191)S(0.809)PLR 241.84 1.57E-37 3796200000 1282930 1570860 1475330 1347600 1665350 1774360 1265680 1355560 1508000 1773130 TRUE FALSE 1333581.067 1840642.985 1513778.312 1614151.258 1382274.402 1362291.781 1166472.694 1337390.935 1453727.375 2120540.875 0.628887225 0.868006369 0.713864246 0.761197899 0.651849921 0.642426561 0.550082627 0.630683875 0.685545557 1 21.01600086 0.920297061 20.62235353 1 0.678403551 0.575899373 0.082009954 7067.54603 1828663.122 0.085480648 0.021370162 8.323328997 -0.920297061 -0.321596449 LAYIAHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAYIAHPK 8 0 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ; 108.09 0.0038783 2525100000 3121600 3005700 2701300 2157400 6682000 4525600 3384000 2682600 3091700 5884200 FALSE TRUE 3244843.178 3521905.594 2771698.097 2584127.281 5546196.027 3474597.986 3118753.238 2646644.135 2980430.321 7037096.33 0.461105409 0.500477104 0.393869569 0.367214993 0.788137005 0.493754501 0.443187515 0.376098892 0.423531266 1 22.74654883 -1.345025014 5.484736449 1.000135698 0.469183623 0.65719822 0.114400191 0.00019535 2.33E-05 0.113989171 0.026860719 0.045182992 1.345025014 -0.530952074 LAYQELQIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LAYQELQIDR 10 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6;Q8N6H7-3;H0YDN9 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 ; 153.97 3.56E-05 95225000 72481 89761 86897 74891 113959 116537 93248 92327 88963 114583 FALSE TRUE 75342.60585 105176.7535 89161.60721 89704.21627 94588.28989 89473.04789 85938.9781 91089.50758 85761.23901 137033.345 0.549812207 0.767526718 0.650656285 0.654615971 0.690257469 0.652929022 0.627139169 0.664725126 0.625842119 1 17.06416747 -1.05210426 4.86525768 1.000006418 0.657472758 0.800722984 0.05179382 4.23E-06 8.25E-07 0.045115099 0.010633471 0.088694306 1.05210426 -0.34253366 LAYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LAYTDDLGAVGGACLEDEASALRLDEDSEHPPMILR 36 1 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 0 46.804 0.049354 43592000 3498.8 4632.7 4208.6 3040.6 4391.5 5059.9 2807.9 4884.9 3476.6 3352.2 FALSE TRUE 3636.935326 5428.330188 4318.279573 3642.021605 3645.034399 3884.814909 2587.809461 4819.425906 3351.477845 4008.999408 0.907192782 1.354036166 1.077146473 0.908461497 0.909213005 0.969023567 0.645500086 1.202151813 0.835988611 1 11.96902649 3.877147464 4.609271747 0.933872676 1.148393313 0.213840295 0.165228554 0.310226059 10.23911119 0.041017174 0.077276284 7536.114075 -3.877147464 0.214520637 LCAAAASILGKPADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LCAAAASILGKPADR 15 1 P30046;J3KQ18;B5MC82;P30046-2;A6NHG4 P30046 DDT;DDTL D-dopachrome decarboxylase;D-dopachrome decarboxylase-like protein 0 ; 188.59 2.67E-07 2758200000 2515700 2584200 2800200 2553800 3355700 3525600 3077000 2839500 2969900 2320480 FALSE TRUE 2615021.779 3028016.248 2873175.512 3058934.018 2785299.313 2706832.831 2835816.7 2801441.147 2863013.879 2775133.628 0.942304815 1.091124484 1.035328708 1.102265486 1.003663133 0.975388285 1.021866721 1.009479731 1.031667034 1 21.40412581 LCAGIMITAS(ph)HNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 1 LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMIT(0.032)AS(0.968)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK;LCAGIMITAS(1)HNPK 248.81 3.43E-18 9859590000 9315270 5990390 8569220 6652340 10996200 10081940 10117930 8884400 9417420 5547910 TRUE FALSE 9683044.053 7019192.884 8792540.913 7968152.997 9127069.852 7740562.228 9324860.208 8765319.15 9078488.894 6634916.743 1.459407017 1.057917251 1.32519235 1.200942424 1.375611813 1.166640446 1.405422339 1.321089546 1.368289798 1 22.66164693 3.268484675 24.99934638 1.294939222 1.250963395 0 0.147294288 1088.816932 909618.2839 0.037395249 0.050626539 1855.601329 -3.268484675 -0.043975826 LCCTLSSLSSAAETGRDPLDS(ph)EEEATSGAQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LCCTLSSLSSAAETGRDPLDSEEEATSGAQDER 33 1 O43822-2;O43822 O43822-2 C21orf2 Protein C21orf2 1 LCCTLSSLSSAAETGRDPLDS(0.882)EEEAT(0.093)S(0.025)GAQDER 57.829 0.022678 37413000 17010 18880 20018 17748 20816 20140 17072 19968 21539 21882 TRUE FALSE 17681.56793 22122.49313 20539.68552 21258.50143 17277.70376 15462.79022 15733.85203 19700.36162 20763.8156 26169.35894 0.675659193 0.845358619 0.784875379 0.812343224 0.660226481 0.590873864 0.601231848 0.752802606 0.793439978 1 14.67559096 -1.834381065 4.734327232 1.045539372 0.72299904 0.490702264 0.08432015 0.041003663 0.001434413 0.082596493 0.020833433 0.014642625 1.834381065 -0.322540333 LCDDGPQLPTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LCDDGPQLPTSPR 13 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 LCDDGPQLPTS(1)PR;LCDDGPQLPTS(1)PR;LCDDGPQLPT(0.003)S(0.997)PR;LCDDGPQLPTS(1)PR;LCDDGPQLPT(0.099)S(0.901)PR;LCDDGPQLPT(0.054)S(0.946)PR 270.91 4.69E-32 4705810000 6985870 7626070 7413180 7474080 7890510 9118790 7934710 7707060 7338920 7312100 TRUE FALSE 7261677.542 8935788.2 7606373.561 8952430.716 6549283.929 7001089.219 7312766.697 7603759.467 7074793.703 8744765.996 0.830402728 1.021844176 0.869820137 1.023747316 0.748937585 0.800603381 0.836244984 0.869521205 0.809031792 1 23.05998835 3.239412634 24.99996583 0.83735413 0.937793372 0.228964557 0.082501912 29.80846851 874618.8948 0.021583185 0.027596449 1735.452113 -3.239412634 0.100439242 LCDEQLSSQSHYDFGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LCDEQLSSQSHYDFGLR 17 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 246.69 1.12E-20 1268320000 714710 962910 1029590 1100270 1029100 1307360 983960 1053490 948990 996640 FALSE TRUE 742927.3027 1128282.302 1056421.961 1317900.122 854173.9496 1003745.453 906834.6441 1039369.69 914836.0353 1191912.526 0.623306901 0.946615022 0.886325077 1.105702049 0.716641474 0.842130132 0.760823151 0.87201843 0.76753622 1 20.18484693 LCDFGSASHVADNDITPY(ph)LVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LCDFGSASHVADNDITPYLVSR 22 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 LCDFGSASHVADNDIT(0.025)PY(0.967)LVS(0.008)R;LCDFGSASHVADNDIT(0.026)PY(0.896)LVS(0.078)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDIT(0.003)PY(0.997)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.999)LVSR;LCDFGSASHVADNDIT(0.001)PY(0.986)LVS(0.014)R;LCDFGSASHVADNDIT(0.005)PY(0.995)LVSR;LCDFGSASHVADNDITPY(0.999)LVS(0.001)R;LCDFGSASHVADNDITPY(1)LVSR;LCDFGSASHVADNDITPY(0.999)LVS(0.001)R 348.13 3.48E-95 37950735000 4052047 6641780 6447728 6468973 6574623 7865621 6145228 6930413 6409069 6863589 TRUE FALSE 4212024.944 7782454.049 6615761.089 7748516.551 5457070.931 6038949.727 5663548.972 6837522.15 6178407.859 8208377.853 0.513137312 0.948111087 0.805976675 0.943976592 0.664817218 0.735705621 0.689971767 0.832993104 0.752695352 1 22.96866571 -1.579322842 2.622883488 1.01776606 0.774393936 0.242306747 0.123581575 15602054.88 14684069.94 1928172.986 0.02772566 0.026343723 1.579322842 -0.243372124 LCDSYEIRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LCDSYEIRPGK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 183.99 4.66E-06 2351010000 1879210 1692950 1886470 1654000 2342230 2256120 2117990 1952680 2005960 1611270 FALSE TRUE 1953402.662 1983700.993 1935632.958 1981156.263 1944098.581 1732170.322 1951976.409 1926507.519 1933765.891 1926967.507 1.013718527 1.029441849 1.004496937 1.028121261 1.008890173 0.898909979 1.012978373 0.999761289 1.003528022 1 20.87790081 2.983452322 24.99708842 0.983610199 1.018642881 0.239087051 0.030649036 1130.115627 1707165.382 0.009447179 0.010251606 962.6143282 -2.983452322 0.035032682 LCFEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 104.11 0.043161 0 182180 224110 200020 199520 274310 274790 238990 205140 189900 264950 FALSE TRUE 189372.6071 262599.1492 205232.6855 238984.4605 227682.8842 210974.187 220257.3393 202390.4338 183065.5361 316861.8797 0.59765033 0.828749578 0.647703932 0.75422282 0.718555619 0.665823819 0.695120977 0.63873393 0.577745535 1 18.27349458 -1.100438148 4.92195648 1.000011802 0.684096991 0.648906568 0.070463293 8.71E-06 1.59E-06 0.065093162 0.015342033 0.079352726 1.100438148 -0.315914811 LCLTLHNNEGSYLAHTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LCLTLHNNEGSYLAHTQGK 19 0 Q15428;K7EMT0 Q15428 SF3A2 Splicing factor 3A subunit 2 0 185.33 1.33E-14 412720000 129980 160590 148050 150180 194100 207470 187410 182430 171900 165430 FALSE TRUE 135111.7108 188170.0833 151908.3046 179885.1558 161106.9513 159288.2367 172720.3145 179984.8242 165713.3526 197842.8412 0.682924436 0.951108881 0.767823105 0.909232574 0.814317821 0.805125097 0.873017762 0.90973635 0.837600954 1 17.59399534 -4.999999996 0.114571744 1.50648652 0.761988188 0.358896978 0.07079595 173.1538165 1.305000477 20.38096365 0.716370259 1.00E-05 4.999999996 -0.744498332 LCMVRPCEADLEENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LCMVRPCEADLEENIK 16 1 P29279-2;P29279 P29279-2 CTGF Connective tissue growth factor 0 63.128 0.042766 71822000 4791 62142 85448 47283 39654 67685 36867 54242 79912 130820 FALSE TRUE 4980.152379 72814.4051 87674.84508 56635.43627 32913.62724 51966.18453 33977.26821 53514.97471 77035.98273 156451.6743 0.031831889 0.465411479 0.560395697 0.361999554 0.210375679 0.332154864 0.217174206 0.342054343 0.492394748 1 17.25535757 0.807622016 2.29690724 0.999592931 0.322140773 0.694671652 0.136792915 0.417699686 3.769532562 0.131185312 0.035557394 6.421286031 -0.807622016 -0.677452159 LCPSCPASS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LCPSCPASSPK 11 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 LCPS(0.001)CPAS(0.194)S(0.805)PK;LCPSCPAS(0.139)S(0.861)PK;LCPSCPASS(1)PK 237.53 1.46E-15 243020000 964320 452830 548340 454870 909250 981660 810150 652980 750160 480520 TRUE FALSE 1002392.098 530600.03 562630.1909 544841.9283 754696.0098 753684.3422 746648.3261 644227.8712 723161.8881 574668.6939 1.744295642 0.92331466 0.979051403 0.948097459 1.313271486 1.31151105 1.299267446 1.121042225 1.258397918 1 19.13237093 3.199762992 24.99969178 1.22606757 1.12047338 0.013412356 0.236893447 588.9149795 379472.3225 0.067277491 0.080413259 1584.028502 -3.199762992 -0.10559419 LCQFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LCQFHR 6 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 89.457 0.050145 540300000 1286050 1644120 1572000 1624760 1897560 2264300 1613510 1672000 1691610 1929300 FALSE TRUE 1336824.247 1926484.821 1612967.611 1946132.679 1575013.429 1738450.641 1487038.87 1649589.575 1630729.287 2307309.396 0.579386644 0.83494863 0.699068627 0.843464115 0.682619085 0.75345363 0.64449045 0.714940778 0.70676663 1 21.13778004 -1.283522202 3.196070533 1.001421166 0.72069604 0.556426833 0.075577181 14151201.97 19724441.89 195782.1481 0.017792051 0.05205684 1.283522202 -0.280725125 LCS(ph)SSSSDTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.991)S(0.008)SSSDTSSR;LCS(0.455)S(0.455)S(0.079)S(0.004)S(0.008)DTSSR 195.09 0.0001169 0 230770 244020 266140 263470 345090 377250 295440 281480 297620 273190 TRUE FALSE 239880.9778 285928.5368 273075.827 315583.5796 286431.7251 289639.4048 272282.6408 277707.221 286908.7143 326716.35 0.734217855 0.875158335 0.835819288 0.965925273 0.876698473 0.886516407 0.833391536 0.849994869 0.878158422 1 18.31767913 -5 0.394389618 3.144783341 0.858807816 0.377001995 0.054530013 761.5543776 5.424831049 1404.142665 0.034090354 1.00E-05 5 -2.285975525 LCSDLMNCLHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LCSDLMNCLHER 12 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ;;; 191.53 5.25E-06 1087860000 864330 1072360 1022670 980900 1295220 1310560 991050 1030480 1030770 1408810 FALSE TRUE 898454.4158 1256529.488 1049321.62 1174919.092 1075058.967 1006202.302 913368.9114 1016668.101 993672.789 1684839.346 0.533258211 0.745785936 0.622802182 0.697347848 0.638078028 0.597209641 0.542110388 0.603421391 0.58977302 1 20.6841796 -1.865214854 2.721278494 1.163153479 0.620341739 0.777322609 0.061193416 22877510 16981328.49 24246689.02 0.01529967 0.013639082 1.865214854 -0.54281174 LCSS(ph)SSSDTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LCSSSSSDTSSR 12 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LCS(0.058)S(0.789)S(0.136)S(0.012)S(0.005)DTSSR;LCS(0.034)S(0.607)S(0.334)S(0.011)S(0.013)DTSSR 281.54 4.58E-28 1022620000 701060 783310 811290 786870 1041330 1051840 860690 884950 879460 825630 TRUE FALSE 728738.3901 917837.3992 832432.8839 942510.5374 864325.0986 807566.1008 793226.8688 873088.6927 847808.4064 987396.3909 0.738040362 0.929553123 0.843058463 0.954541202 0.875357766 0.817874268 0.803352003 0.884233223 0.858630246 1 19.91326985 0.099028105 1.55959836 1.000070405 0.859169357 0.34841141 0.05890448 19.8440894 32.60250607 0.056658123 0.015434698 1.256111249 -0.099028105 -0.140901049 LCTSYSHSSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LCTSYSHSSTR 11 0 B4DQA8;E9PCW1;K7EJC8;G5E9T8;O95249;F6RU00 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 0 68.548 0.056935 35003000 20107 48861 49983 61339 48413 78450 44688 48420 43343 60793 FALSE TRUE 20900.83989 57252.49666 51285.59804 73471.67112 40183.77555 60231.17642 41185.23779 47771.0091 41783.0939 72704.2244 0.287477654 0.78747139 0.705400525 1.010555738 0.552702073 0.828441221 0.566476544 0.657059607 0.574699672 1 16.14975157 4.743649085 24.69958339 0.724643641 0.28747744 0.419134979 0.159464716 445.0291141 2160102.567 0.035963065 0.301363257 55417.77501 -4.743649085 -0.437166201 LCVQNSHQEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LCVQNSHQEAR 11 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 0 145.09 3.64E-05 108630000 66225 77337 59711 65816 84376 80892 74024 66167 80382 83938 FALSE TRUE 68839.61414 90619.02815 61267.11771 78834.20836 70033.79766 62106.05893 68221.80545 65280.13959 77489.06752 100384.044 0.685762512 0.902723426 0.610327252 0.785326086 0.69765866 0.618684568 0.67960806 0.650303943 0.771926139 1 16.61517045 -1.941650407 5.671775762 1.13655569 0.707412608 0.515714809 0.083830431 0.049027512 0.000504381 0.0274913 0.018418441 0.011437987 1.941650407 -0.429143083 LCWFLDEAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LCWFLDEAAAR 11 0 M0R1L2;O95336 M0R1L2 PGLS 6-phosphogluconolactonase 0 ; 147.51 8.20E-05 829870000 604220 848850 726650 727430 987010 1029820 625420 715060 722800 1163710 FALSE TRUE 628075.0722 994633.3844 745587.0959 871313.4828 819238.3928 790659.9121 576397.9462 705475.7903 696786.5692 1391716.694 0.451295206 0.714680932 0.535731948 0.626071015 0.588653133 0.568118436 0.414163277 0.506910489 0.500666962 1 20.40843413 -1.512591095 2.760689282 1.020494964 0.54557363 0.734790879 0.081979652 12503318.57 13056603.15 1930200.996 0.021805829 0.03071913 1.512591095 -0.474921335 LCYSSDHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LCYSSDHEK 9 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;; 229.48 1.25E-07 5870640000 1736845 2395740 2613310 2082020 4432680 3696950 3367930 2812440 2923580 2768490 FALSE TRUE 1805416.982 2807189.709 2681415.005 2493837.342 3679214.637 2838389.39 3103942.846 2774743.842 2818360.927 3310922.61 0.545291206 0.847857241 0.80986943 0.753215232 1.111235468 0.8572805 0.937485774 0.838057596 0.851231291 1 21.65880186 5.227223558 1.04275503 0.900885541 4.17E-12 0.54576652 0.095826654 3.492404134 1.526183515 0.027741815 4.458398934 168742.1421 -5.227223558 -0.900885541 LCYVALDFEQEMATAAS(ph)SSSLEK ddPTM_MDA-MB-175_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(0.487)S(0.413)S(0.083)S(0.017)LEK 114.21 0.00044548 26954000 30467 24806 29291 22684 38090 40451 35442 34643 37724 29796 TRUE FALSE 31669.86069 29066.23754 30054.34752 27170.8275 31615.47541 31056.86829 32663.96343 34178.66725 36366.32061 35633.95572 0.888755123 0.815689332 0.843418782 0.762498211 0.887228902 0.871552643 0.916652748 0.959160064 1.020552444 1 15.12096503 1.956053085 1.02660607 1.012467115 0.832058529 0.800423174 0.03417093 0.213963167 0.414477172 0.026920898 0.012293976 90.37599364 -1.956053085 -0.180408586 LCYVALDFEQEMATAASS(ph)SSLEK ddPTM_MDA-MB-175_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(0.001)S(0.792)S(0.171)S(0.037)LEK;LCYVALDFEQEMATAAS(0.001)S(0.9)S(0.1)SLEK;LCYVALDFEQEMATAAS(0.108)S(0.768)S(0.108)S(0.015)LEK;LCYVALDFEQEMATAAS(0.009)S(0.537)S(0.396)S(0.058)LEK 243.48 1.39E-37 160498000 248184 199769 246430 198192 281850 316934 287388 248954 282311 202770 TRUE FALSE 257982.496 234077.7718 252852.1682 237393.7861 233941.2377 243330.8817 264861.7776 245617.1788 272150.6823 242498.8992 1.063850173 0.965273544 1.042694087 0.978947891 0.964710514 1.003430871 1.092218474 1.012858943 1.122275949 1 17.88761867 2.337138956 9.325503795 1.05423818 1.000140299 0.259590467 0.044180325 0.380373063 32.67252681 0.014357508 0.011998629 217.3396462 -2.337138956 -0.05409788 LCYVALDFEQEMATAASSSSLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LCYVALDFEQEMATAASSSSLEK 23 0 P60709;A0A2R8Y793;A0A2R8YEA7;P63261;I3L4N8;Q6S8J3 P60709;P63261;Q6S8J3 ACTB;ACTG1;POTEE "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;POTE ankyrin domain family member E" 0 ;; 207.67 1.15E-24 372150000 432880 344573 424710 378130 524210 541650 483420 401953 470030 337976 FALSE TRUE 449970.4367 403750.7323 435778.2915 452922.9854 435104.9714 415859.9963 445528.2772 396565.4775 453113.7121 404195.9263 1.113248322 0.998898569 1.078136278 1.120553068 1.076470452 1.028857466 1.102258208 0.981121906 1.121024935 1 18.62469526 1.759861446 25 1.032927697 1.071468648 0.12220531 0.048768455 22.31667394 26214.18326 0.021528018 0.011939276 57.5256383 -1.759861446 0.038540951 LDADYPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDADYPLR 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 ;; 106.36 0.0097971 397850000 1663760 1941310 1863610 1751210 2144770 2247570 1959770 1908670 1867290 1935020 FALSE TRUE 1729446.53 2274714.891 1912177.208 2097594.111 1780202.761 1725605.93 1806158.106 1883087.401 1800086.598 2314150.121 0.747335496 0.982959088 0.826297823 0.906420933 0.769268487 0.745675881 0.780484416 0.813727417 0.777860771 1 21.14205103 LDAENAIVHMGGQWLGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDAENAIVHMGGQWLGGR 18 0 E7ETJ9;Q01085;Q01085-2 E7ETJ9 TIAL1 Nucleolysin TIAR 0 ; 145.61 8.98E-08 550840000 680670 547950 548790 587470 602920 774620 651440 622740 583520 499660 FALSE TRUE 707543.3772 642056.15 563091.9182 703669.8126 500435.8738 594726.2445 600378.4306 614393.1889 562519.2292 597558.8104 1.184056473 1.074465205 0.942320502 1.177574157 0.83746715 0.99525977 1.004718565 1.028171919 0.941362121 1 19.18872118 6.320114766 0.837004815 0.989605545 3.724091791 0.349143944 0.081293645 30.77407441 1.912378975 0.025099831 136.7283204 2089848.316 -6.320114766 2.734486245 LDAGDADPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDAGDADPRR 10 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 86.898 0.021236 192030000 128010 194470 163950 168160 197630 221340 143790 167270 145050 222080 FALSE TRUE 133063.9336 227868.7097 168222.6717 201421.5461 164036.9232 169937.1394 132519.3641 165028.0192 139829.6788 265592.324 0.501008205 0.857964215 0.633386798 0.758386173 0.617626747 0.639842059 0.498957809 0.621358391 0.52648238 1 18.01885393 -1.173305241 4.884232119 1.000033679 0.63261325 0.522522951 0.106514521 3.79E-05 6.41E-06 0.099996785 0.023567311 0.067095711 1.173305241 -0.367420428 LDALLADEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDALLADEER 10 0 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 121.83 0.001174 17920000 18339 21966 20683 19819 26555 33094 22693 26344 24953 26144 FALSE TRUE 19063.03788 25738.48963 21222.01597 23739.13905 22041.19059 25408.42004 20914.26336 25990.90177 24054.9464 31266.41624 0.609696926 0.823199225 0.678747951 0.759253599 0.704947776 0.812642544 0.668905039 0.831272173 0.769354128 1 14.93232625 -5 0.177125016 2.057236766 0.687311746 0.620088321 0.064562631 80.04431369 0.766864987 29.60605647 0.186879014 1.00E-05 5 -1.369925021 LDALQMFVFDLHWPEQEFAHHLEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDALQMFVFDLHWPEQEFAHHLEQR 25 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7;H0Y8B5;H7BYR4;F8W8P5 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 0 109.11 0.0011079 51734000 3417.2 5852.9 7463.7 4779.9 4837 7628.9 6821.8 6286 6456.2 3629.3 FALSE TRUE 3552.113695 6858.090046 7658.210153 5725.349953 4014.808468 5857.203592 6287.089491 6201.746452 6223.842623 4340.391848 0.818385487 1.58006242 1.764405248 1.319085961 0.924987561 1.349464241 1.448507349 1.42884483 1.433935654 1 12.08360958 3.50408856 24.93807008 1.295651195 1.429342728 0.023863407 0.282166123 2693.182734 2490518.162 0.076269838 0.117766142 3192.188733 -3.50408856 0.133691533 LDALVAEEHLTVDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDALVAEEHLTVDAR 15 0 A6NFX8;Q9UKK9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ;;; 212.87 6.56E-10 719937000 666027 890603 907083 915542 1221303 1150193 875148 952757 877015 1041159 FALSE TRUE 692322.2602 1043557.137 930722.3282 1096633.475 1013706.352 883078.1071 806551.613 939986.8508 845451.4015 1245154.172 0.556013284 0.83809472 0.747475573 0.880721038 0.814121155 0.709211861 0.647752408 0.754916035 0.678993349 1 20.24789295 -2.267562183 2.194128511 1.99501739 0.742512256 0.430055588 0.090801361 4672069.74 693146.9948 23070963.39 0.02306235 0.005400548 2.267562183 -1.252505134 LDAMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDAMFR 6 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;K7EIV0;Q96L46;K7EMQ1 A0A0C4DGQ5 CAPNS1;CAPNS2 Calpain small subunit 1;Calpain small subunit 2 0 110.23 0.067187 223900000 228660 249480 209620 266630 378920 357120 299990 229620 221850 305220 FALSE TRUE 237687.6734 292326.2493 215082.8694 319368.6182 314511.3137 274184.2922 276475.9999 226542.3195 213865.6618 365022.0152 0.65115983 0.80084553 0.589232595 0.874929744 0.861622863 0.751144536 0.757422808 0.620626456 0.585897981 1 18.47762395 -2.343154529 2.4330852 2.891402381 0.723447854 0.40469217 0.101332329 10726528 1073531.379 112853352.3 0.025236572 0.004537801 2.343154529 -2.167954527 LDAQSLNLSQEDFDRYMS(ph)GQTSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMS(0.333)GQT(0.333)S(0.333)PR 66.012 0.056644 92419000 56883 59331 59589 53601 63865 70884 54749 63331 63498 63951 TRUE FALSE 59128.78476 69520.63772 61141.93829 64203.11782 53009.25011 54422.26526 50457.63032 62482.15153 61212.71938 76480.97403 0.77311757 0.908992578 0.799439848 0.839465222 0.693103753 0.711579134 0.659740948 0.816963334 0.800365322 1 16.22281328 0.608727273 1.832905025 0.999847681 0.774093367 0.482636027 0.069500722 1.864620849 7.591916689 0.071253931 0.019914378 4.061881719 -0.608727273 -0.225754314 LDAQSLNLSQEDFDRYMSGQTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;Q3HKR1;A0A0A0MSJ3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 LDAQSLNLSQEDFDRYMSGQT(0.098)S(0.902)PR 144.68 3.40E-07 183830000 159140 179530 199160 162360 224020 230940 165740 198870 202020 209520 TRUE FALSE 165422.9701 210362.881 204350.2732 194474.3234 185941.1604 177307.6849 152748.8657 196204.4729 194749.3397 250571.4325 0.660182881 0.839532579 0.815536995 0.776123285 0.742068474 0.707613327 0.609602077 0.783028101 0.777220842 1 17.93486242 -1.759269543 4.834081445 1.017366656 0.746821492 0.567810518 0.066562819 0.013144444 0.000654575 0.067998024 0.015558537 0.017407262 1.759269543 -0.270545164 LDDFLDLNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDDFLDLNHK 10 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ;;; 182.28 1.79E-06 557772000 1339839 889416 1221889 1004817 1399021 1470582 1621805 1248420 1266380 780328 FALSE TRUE 1392736.878 1042166.279 1253732.431 1203566.804 1161215.91 1129061.617 1494683.686 1231686.972 1220803.231 933218.3313 1.492401972 1.116744329 1.343450283 1.289694773 1.244313224 1.20985795 1.601644156 1.319827237 1.308164649 1 19.83185512 LDDIEEFENIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDDIEEFENIRK 12 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 0 ;; 182.08 2.78E-05 278814000 238983 302561 318725 300951 355196 403550 328083 325675 333182 270877 FALSE TRUE 248418.2334 354523.4982 327031.2353 360478.2096 294819.9108 309831.6284 302366.9972 321309.8593 321190.8449 323950.1619 0.766840899 1.094376666 1.009510949 1.112758232 0.910077986 0.956417575 0.933375046 0.991849664 0.991482279 1 18.30541235 LDDIHPFYADLMNILYDKDHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDDIHPFYADLMNILYDKDHYK 22 1 Q9BZE4-2;Q9BZE4;Q5T3R7 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 208.92 4.07E-23 165520000 315650 167210 263300 193830 360050 280660 355540 247030 290370 139790 FALSE TRUE 328112.1057 195927.0168 270161.8143 232168.9955 298848.8296 215480.9684 327671.8458 243718.9669 279919.6404 167179.1741 1.962637437 1.171958277 1.616001609 1.388743525 1.787596041 1.288922317 1.960003975 1.457830907 1.674369083 1 17.35103561 -1.431393593 6.035779368 0.999786718 1.57672207 0.324830653 0.254463123 0.000644281 6.07E-05 0.217341478 0.051209393 0.037034493 1.431393593 0.576935352 LDDLFLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDDLFLKR 8 1 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 0 83.005 0.030151 86282000 90379 139830 110390 141150 104810 178710 100540 107420 110520 163250 FALSE TRUE 93947.23271 163844.7148 113266.8541 169069.0487 86994.43364 137207.3109 92659.41209 105980.2106 106542.4068 195235.7119 0.481199017 0.839214881 0.580154384 0.865973992 0.445586685 0.702777732 0.474602782 0.542832096 0.545711672 1 17.57485744 -1.075119121 5.060703702 1.000008151 0.609356995 0.410217088 0.140764813 1.22E-05 2.24E-06 0.128817255 0.030361885 0.084116439 1.075119121 -0.390651157 LDDLVRPYVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDDLVRPYVHK 11 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 147.26 2.13E-05 738880000 996360 676950 979220 839850 1120580 1065440 1400150 1016760 1002540 532170 FALSE TRUE 1035697.062 793210.8966 1004739.278 1005969.823 930104.2119 818007.7069 1290402.584 1003131.995 966458.7812 636438.5225 1.627332453 1.2463276 1.57869023 1.580623717 1.461420356 1.285289432 2.027536893 1.576164798 1.518542243 1 19.27966164 LDDPLHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDDPLHLR 8 0 O75146 O75146 HIP1R Huntingtin-interacting protein 1-related protein 0 ;; 141.93 0.00062562 447443000 766510 811410 828600 909780 950030 1066200 898450 845750 842200 781400 FALSE TRUE 796772.4067 950763.3556 850193.9967 1089731.769 788544.2399 818591.2084 828027.1413 834414.1046 811889.3865 934500.3692 0.852618611 1.017402868 0.909784549 1.166111651 0.843813728 0.875966704 0.886064007 0.892898636 0.868795148 1 19.83383571 LDDPSCPRPECYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDDPSCPRPECYR 13 1 P41091;H7BZU1 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ;;; 167.73 2.87E-05 3060040000 3167700 3449610 3504090 3547810 3660540 4251720 4211640 3763920 3663340 3148740 FALSE TRUE 3292763.242 4042053.683 3595409.464 4249556.229 3038322.718 3264322.465 3881520.652 3713470.809 3531497.109 3765675.317 0.874415069 1.073394104 0.954784776 1.128497778 0.806846704 0.866862433 1.030763495 0.986136747 0.937812427 1 21.84447718 6.184806075 10.98787321 0.96895825 0.626309543 0 0.093942195 0 0 0.020162985 0 1530403.94 -6.184806075 -0.342648707 LDDSFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDDSFVR 7 0 Q99615;A0A6I8PUD4;A0A6I8PU73;A0A6I8PS32;A0A6I8PIK4;A0A6I8PR89;A0A6I8PLE7;A0A6I8PU89;A0A6I8PRZ0;K7EIH8;K7EK03;Q99615-2;K7ESP1;K7ER44;K7EPP7;A0A6I8PUC2;K7ELJ8;K7EJV7;K7EN19;K7EJL5;K7EJE9 Q99615 DNAJC7 DnaJ homolog subfamily C member 7 0 81.297 0.064172 61851000 42485 53269 41520 50391 58786 60099 52101 45865 47943 56200 FALSE TRUE 44162.34061 62417.53637 42602.04531 60358.1894 48793.57672 46141.91806 48017.18748 45250.2547 46217.5408 67211.31399 0.657067062 0.928676032 0.63385229 0.898036146 0.725972665 0.686520101 0.714421198 0.673253534 0.68764525 1 16.03641649 -1.011162491 4.720932881 1.000004977 0.734559881 0.416366522 0.094498309 5.33E-06 1.12E-06 0.086031277 0.020277331 0.097462491 1.011162491 -0.265445096 LDDTVHVVIATPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDDTVHVVIATPGR 14 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ;;; 199.13 2.11E-08 1618430000 1643660 1882860 1791990 1846580 1993790 2235400 1868410 1876780 1814550 1839020 FALSE TRUE 1708552.966 2206226.558 1838690.732 2211828.013 1654886.288 1716262.228 1721959.142 1851624.834 1749244.7 2199340.759 0.776847771 1.003130847 0.836019032 1.005677726 0.752446514 0.780353031 0.782943314 0.841899931 0.795349558 1 21.06863972 3.224274621 24.99805431 0.814477052 0.907441171 0.150211879 0.090832804 354.0843592 619586.0231 0.024005606 0.028818242 1676.002342 -3.224274621 0.092964119 LDDYQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDDYQER 7 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 176.41 0.0017515 795020000 819550 819830 885840 817890 928120 1076870 920710 885110 878450 801270 FALSE TRUE 851906.4668 960629.4251 908925.7181 979666.2008 770358.4939 826783.2626 848542.3444 873246.5482 846834.7561 958263.5153 0.889010646 1.002468955 0.94851333 1.022334864 0.803910909 0.862793219 0.885500002 0.91128018 0.883718041 1 19.87006292 3.251040436 24.99884509 0.88685684 0.966997533 0.293882119 0.056225209 261.6276807 524074.2522 0.01482775 0.019937188 1782.54473 -3.251040436 0.080140693 LDEEEEDNEGGEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 368.23 4.03E-97 220340000 191694 189090 226264 202447 254820 275440 243670 221026 219244 195277 FALSE TRUE 199262.2271 221564.7366 232160.6257 242490.4124 211505.7874 211473.2343 224570.5087 218063.508 211353.4513 233537.7893 0.853233336 0.94873184 0.994103037 1.038334794 0.905659799 0.905520408 0.961602443 0.933739711 0.905007502 1 17.83329649 LDEGT(ph)PPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDEGTPPEPK 10 0 Q9Y4G6;H0YMT1;A0A1B0GVU7;H0YN01 Q9Y4G6 TLN2 Talin-2 1 LDEGT(1)PPEPK;LDEGT(1)PPEPK;LDEGT(1)PPEPK;LDEGT(1)PPEPK 146.36 0.000322 3170550000 6448500 3050500 4262510 3403110 5624360 5249010 5949700 4275950 4696740 2211130 TRUE FALSE 6703091.759 3574399.645 4373594.512 4076235.001 4668333.296 4030006.977 5483346.967 4218637.884 4527705.245 2644358.589 2.534864896 1.351707617 1.653933975 1.54148345 1.765393436 1.524001697 2.07360189 1.595335028 1.712213035 1 21.3344864 0.213664209 1.390935309 0.999475128 1.733811364 0.333567527 0.317787594 8.524776584 13.83616738 0.284813853 0.081415733 1.635551446 -0.213664209 0.734336236 LDEIYVAGLVAHSDLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 288.21 2.74E-40 625882000 625439 640962 679587 751609 721294 866091 892847 738224 716328 590278 FALSE TRUE 650131.8147 751042.2375 697297.5955 900275.0169 598688.7035 664954.491 822863.3191 728329.3148 690547.4952 705931.6725 0.920955724 1.063902169 0.987769245 1.275300503 0.848083075 0.941953048 1.165641593 1.031727776 0.978207271 1 19.42916903 LDELYGTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDELYGTWR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ;; 128.69 0.00095471 442340000 347360 330920 337570 344210 438690 467920 473740 346280 348520 350480 FALSE TRUE 361074.041 387752.9358 346367.3515 412293.7106 364121.6305 359252.6714 436607.0209 341638.683 335976.8333 419149.8457 0.861443812 0.925093829 0.826356863 0.983642759 0.868714695 0.857098422 1.041649008 0.815075292 0.801567355 1 18.67710657 LDETDDPDDYGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDETDDPDDYGDR 13 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 206.97 1.34E-07 283560000 458730 396520 439340 516300 469440 590820 698460 467670 468150 305100 FALSE TRUE 476841.0146 464619.2255 450789.5613 618422.599 389644.7565 453611.009 643712.8801 461401.6486 451301.3729 364878.5035 1.306848746 1.273353242 1.235451135 1.694872658 1.067875341 1.243183703 1.764184171 1.264535028 1.236853826 1 18.47705663 0.945452588 2.328549413 1.00332184 1.363384141 0.227183453 0.201984621 0.499959203 6.015821116 0.187416722 0.051035175 8.819675123 -0.945452588 0.360062301 LDETDDPDDYGDRESGCSFVLALMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDETDDPDDYGDRESGCSFVLALMQK 26 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ; 162.82 1.42E-11 170595000 261010 184863 258080 201090 322510 331050 301630 252500 291260 174742 FALSE TRUE 271314.8763 216611.7822 264805.7768 240865.0018 267689.8654 254168.6546 277987.4524 249115.6505 280777.6095 208979.3493 1.298285583 1.036522427 1.267138489 1.152578007 1.280939319 1.216238138 1.33021494 1.192058696 1.343566292 1 17.67300086 3.24482736 24.99552785 1.24003452 1.183373891 0.019499251 0.111240285 461.6923596 1841497.418 0.028165315 0.037196039 1757.224944 -3.24482736 -0.056660629 LDEYWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDEYWDR 7 0 Q6PKC6;E9PBK6;E9PDU5;A0A087X295;Q9NNW5 Q6PKC6 WDR6 WD repeat-containing protein 6 0 ; 100.15 0.023278 129082000 175911 198530 202780 194535 220510 241280 218290 194844 190434 180967 FALSE TRUE 182856.1021 232625.9832 208064.6134 233013.4424 183027.789 185246.3766 201179.8594 192232.4349 183580.3175 216424.0188 0.844897452 1.074862136 0.961374872 1.076652414 0.845690742 0.855941857 0.929563458 0.888221353 0.848243733 1 17.72350109 3.224806477 24.99991376 0.889719265 0.993542704 0.279131005 0.074297761 262.0420513 476294.1219 0.019968535 0.023983245 1678.056106 -3.224806477 0.103823438 LDFIESDS(ph)PCSSEALSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDFIESDSPCSSEALSK 17 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 LDFIESDS(0.998)PCS(0.002)SEALSK;LDFIES(0.003)DS(0.996)PCSSEALSK 276.38 9.88E-36 284670000 429520 287982 361273 316828 458600 448840 501440 372960 438350 268606 TRUE FALSE 446477.7813 337440.6683 370688.0712 379495.6328 380647.3358 344603.7122 462135.8225 367961.0812 422573.8691 321234.2029 1.389882451 1.050450622 1.153949573 1.181367455 1.184952699 1.072749132 1.438625832 1.145460471 1.315469727 1 18.29326598 LDFLPEMMVDHCS(ph)LNSSPVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDFLPEMMVDHCSLNSSPVSK 21 0 Q92879-4;G5EA30;F5H0D8;E9PKU1;F5H3J7 Q92879-4 CELF1 CUGBP Elav-like family member 1 1 LDFLPEMMVDHCS(0.769)LNS(0.059)S(0.17)PVS(0.002)K 95.835 0.00088084 37495000 9356.2 20447 20355 20342 27937 27623 17883 25025 23279 17663 TRUE FALSE 9725.590001 23958.61319 20885.46802 24365.58689 23188.27872 21207.97688 16481.28373 24689.58081 22441.19334 21123.72667 0.46041071 1.134203901 0.988720804 1.153470089 1.097736166 1.003988416 0.78022614 1.168808004 1.062369045 1 14.36657676 4.743960341 24.97969922 1.044260074 0.46041046 0.726516032 0.107282732 302.0373288 1397214.043 0.02554615 0.222320255 55457.50675 -4.743960341 -0.583849614 YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPSQAPS(ph)PNQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPSQAPSPNQPTK 48 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVT(0.029)HNLPT(0.124)VAHPS(0.124)QAPS(0.555)PNQPT(0.169)K 79.415 7.39E-05 267730000 74767 148900 173740 173840 206200 238070 158120 212470 165790 154600 TRUE FALSE 77718.85889 174472.4167 178267.8071 208225.0331 171150.1977 182781.8505 145726.1412 209622.1872 159823.2503 184890.91 0.42034981 0.943650592 0.964178321 1.126204815 0.925682056 0.988592952 0.788173638 1.133761455 0.864419188 1 17.49631477 4.741422401 4.298791401 0.979869223 0.376901931 0.734119147 0.09942267 0.101200692 4.394618562 0.022666461 0.187689029 55134.36806 -4.741422401 -0.602967292 down LDFLRPYTVPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDFLRPYTVPNK 12 1 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 113.76 0.0010317 266580000 505560 339620 380370 325570 523080 584310 460040 435390 464150 343200 FALSE TRUE 525519.8992 397947.0931 390282.7547 389966.7743 434167.0484 448612.8578 423980.8627 429554.3092 447445.3322 410443.469 1.280370962 0.969553966 0.950880655 0.950110804 1.057799871 1.092995483 1.032982359 1.046561443 1.090150937 1 18.64682401 LDGAHAPELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDGAHAPELTK 11 0 O76003 O76003 GLRX3 Glutaredoxin-3 0 ; 119.76 0.0005424 405960000 417930 374790 403350 343320 528690 519520 494610 427940 436120 342250 FALSE TRUE 434430.1991 439157.267 413861.6324 411227.6713 438823.4626 398869.3534 455841.1758 422204.1643 420424.1264 409307.3347 1.061378974 1.072927919 1.011126841 1.004691674 1.072112385 0.974498426 1.113689243 1.031508914 1.027160011 1 18.64282499 4.257453269 24.83777872 1.033499035 1.067153471 0.133350732 0.03737102 477.6787576 627983.3086 0.008634675 0.023550804 18090.6124 -4.257453269 0.033654436 LDGAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDGAIR 6 0 Q99714;Q99714-2 Q99714 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 ;; 105.42 0.076756 2906950000 3223290 2819160 3294820 2592130 3787190 3645370 3167630 3339030 3289240 2813880 FALSE TRUE 3350547.978 3303328.8 3380685.716 3104845.577 3143444.797 2798788.064 2919342.884 3294275.764 3170860.895 3365205.911 0.995644269 0.981612682 1.004599958 0.922631678 0.93410177 0.831684045 0.867507951 0.978922494 0.9422487 1 21.68226335 3.731464222 23.34536494 0.920986297 0.992718341 0.313946839 0.046189259 262.0619817 862121.0785 0.012922613 0.020540248 5388.454521 -3.731464222 0.071732044 LDGEEQRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDGEEQRPR 9 1 P51687 P51687 SUOX "Sulfite oxidase, mitochondrial" 0 101.65 0.0044446 0 107080 105020 110840 106580 142920 147920 124570 116000 126990 115230 FALSE TRUE 111307.6011 123056.3681 113728.5815 127661.2059 118626.5094 113567.8217 114805.8779 114445.2097 122419.6547 137807.1123 0.80770578 0.892960937 0.825273671 0.926376032 0.860815581 0.824107115 0.833091094 0.830473898 0.888340614 1 17.07229082 0.899583613 4.699250882 0.999982626 0.851098414 0.638112515 0.033990702 0.380080904 16.64772707 0.032055531 0.008124263 7.935670237 -0.899583613 -0.148884213 LDGERPGPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDGERPGPNR 10 1 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 0 74.944 0.028527 0 50226 60362 48860 45269 65424 76902 49479 52323 54240 69198 FALSE TRUE 52208.96126 70728.70395 50133.33174 54223.07309 54303.25185 59042.67596 45600.70669 51621.69577 52287.913 82756.02322 0.630878083 0.854665331 0.605796772 0.655216031 0.656184888 0.713454727 0.551025834 0.623781735 0.631832113 1 16.3365767 -1.853905277 6.938955199 1.033264243 0.656661594 0.642457587 0.076512599 0.033547999 0.000706329 0.063121765 0.01739314 0.013998926 1.853905277 -0.376602649 LDGLVET(ph)PTGYIESLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.982)PT(0.018)GYIESLPR;LDGLVET(0.903)PT(0.097)GYIESLPR;LDGLVET(0.981)PT(0.019)GYIESLPR;LDGLVET(0.922)PT(0.078)GYIESLPR;LDGLVET(0.989)PT(0.01)GYIESLPR;LDGLVET(0.921)PT(0.079)GYIESLPR;LDGLVET(0.542)PT(0.458)GYIESLPR 274.08 1.24E-34 1614611000 553401 555775 622049 526499 766132 725988 608554 608847 611754 587960 TRUE FALSE 575249.6988 651225.0329 638260.108 630638.9308 635905.1563 557388.2895 560853.9473 600686.4018 589737.093 703159.5048 0.818092758 0.926141264 0.907703165 0.896864689 0.904354065 0.792691112 0.797619805 0.854267627 0.838696041 1 19.42349246 2.776920271 24.7843507 0.843440111 0.893898728 0.051053369 0.060349403 945.8143412 611093.3739 0.017256109 0.018302387 598.3017477 -2.776920271 0.050458617 LDGLVETPTGYIES(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 LDGLVETPTGYIES(1)LPR 172.97 1.61E-09 26560000 21155 27641 22625 22079 31765 32751 22717 26416 30517 30661 TRUE FALSE 21990.21574 32388.12673 23214.62609 26446.1603 26365.59665 25145.0766 20936.38218 26061.93673 29418.69913 36668.43591 0.599704219 0.883269928 0.633095618 0.721224117 0.719027032 0.685741728 0.570964691 0.710745798 0.802289446 1 15.16225111 0.92191568 2.550618646 0.99917032 0.691508218 0.582100081 0.080673487 0.243568765 3.526616689 0.073478315 0.019709746 8.354407985 -0.92191568 -0.307662102 LDGLVETPTGYIESLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 94.191 0.0066907 36808000 16059 21126 19078 17841 18515 28783 22643 28162 18567 22948 FALSE TRUE 16693.02172 24754.22616 19575.18835 21369.89655 15367.82691 22098.58446 20868.18249 27784.53445 17898.7773 27444.22123 0.608252702 0.901983188 0.713271774 0.778666531 0.559965859 0.805218129 0.760385304 1.012400178 0.652187473 1 14.74421478 1.934009264 10.36720762 0.889022958 0.734196674 0.237538105 0.128631143 0.931830327 143.3822335 0.050703027 0.032305879 85.90318454 -1.934009264 -0.154826284 LDGMGCLEFDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDGMGCLEFDEER 13 0 Q13951-2;A0A494C0A9;Q13951;J3KS23;H3BSC0 Q13951-2 CBFB Core-binding factor subunit beta 0 ; 108.37 0.0028415 68515000 34033 45208 48809 50532 53040 69986 49992 50450 52095 44597 FALSE TRUE 35376.64912 52972.12233 50081.00264 60527.07878 44024.27975 53732.81215 46073.49641 49773.80027 50220.11113 53334.92829 0.663292335 0.993197592 0.938990719 1.134848789 0.82543056 1.007460099 0.863852224 0.933230846 0.941598925 1 15.70279302 4.743231968 24.88924441 0.954453381 0.663292209 0.549641685 0.08039777 336.0631713 1790500.245 0.018135581 0.146867147 55364.57468 -4.743231968 -0.291161172 LDGQTPHDER ddPTM_MDA-MB-175_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 ; 120.77 0.00053271 1625260000 798860 1163570 1042280 1149900 1034850 1336100 985350 979150 950310 1123660 FALSE TRUE 830399.6097 1363404.096 1069442.673 1377346.788 858946.5666 1025811.024 908115.6923 966026.0958 916108.5287 1343819.663 0.617939767 1.014573706 0.795823057 1.024949125 0.639182913 0.763354676 0.675771993 0.718865873 0.681719842 1 20.35790811 3.220668678 24.99891881 0.727766528 0.869303913 0.131228256 0.142140703 372.8008144 520882.3564 0.037450291 0.044848903 1662.144121 -3.220668678 0.141537385 LDHFNFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDHFNFER 8 0 Q9UHL4;R4GNE8;R4GMV4 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ;;; 163.32 0.0003366 1898700000 1392840 1600640 1447150 1428530 1741060 1874100 1404260 1426340 1333620 1467500 FALSE TRUE 1447830.399 1875537.469 1484863.918 1711088.97 1445115.243 1438868.677 1294190.432 1407222.245 1285623.277 1755028.528 0.824961176 1.068664947 0.846062553 0.974963622 0.823414104 0.819854865 0.737418459 0.801823003 0.732536968 1 20.74306305 3.134799332 5.522643135 0.801448201 0.932365355 0.235612847 0.093879315 0.240233345 10.93408849 0.025100401 0.030297917 1363.952771 -3.134799332 0.130917154 LDHGSGEPYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDHGSGEPYRR 11 1 O75157-2;O75157 O75157-2 TSC22D2 TSC22 domain family protein 2 0 ; 82.171 0.012768 90762000 13145.8 63347 52823 60383 53991 72916 39486 65214 50961 80852 FALSE TRUE 13664.80633 74226.35448 54199.61077 72326.57717 44813.62911 55982.36405 36390.98414 64339.913 49126.92356 96693.40139 0.141320981 0.767646534 0.560530605 0.7479991 0.463461089 0.578967781 0.37635437 0.665401279 0.508069039 1 16.56112982 -2.267216015 0.727204494 1.706343151 0.548432338 0.386129819 0.175224556 495.0659223 43.49118224 566.7687939 0.056026215 0.005404854 2.267216015 -1.157910813 LDHKFDLMYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDHKFDLMYAK 11 1 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 ;; 167.44 1.91E-05 15498400000 25704800 17155700 22747000 16956400 44389700 30177800 28701200 22308300 25869800 23151500 FALSE TRUE 26719645.35 20102058.02 23339805.51 20310325.31 36844354.65 23169463.3 26451524.95 22009293.73 24938750.95 27687593.16 0.965040377 0.726031255 0.842969823 0.733553299 1.330717135 0.836817529 0.955356603 0.794915383 0.900719351 1 24.72273631 5.072077255 20.52676698 0.894963716 3.0790762 0.010950986 0.165915522 2890.685392 850711.996 0.037654902 9641.085351 118053.0616 -5.072077255 2.184112484 LDHKFDLMYAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDHKFDLMYAKR 12 2 P68363;P68363-2;P68366-2;P68366;Q9BQE3;F5H5D3;A6NHL2-2;A6NHL2 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA4A;TUBA1C;TUBAL3 Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain;Tubulin alpha chain-like 3 0 163.99 3.51E-05 385000000 470240 393560 460720 297690 640290 539670 500720 486230 567480 524180 FALSE TRUE 488805.4383 461150.8685 472726.7417 356572.1935 531453.7345 414339.8213 461472.258 479712.8822 547056.5057 626883.035 0.779739459 0.735625057 0.75409082 0.568801792 0.847771761 0.66095236 0.736137736 0.765235068 0.872661207 1 19.25783676 1.053947109 1.634883068 0.999520351 0.72337414 0.616759918 0.069078948 0.222543542 1.200763486 0.060584397 0.017687697 11.32262462 -1.053947109 -0.276146211 LDHLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 126.28 0.0039676 3672340000 6409790 5833170 5045180 5356940 7103960 7570300 8325420 5704500 5339300 6689610 FALSE TRUE 6662853.459 6834971.572 5176661.535 6416526.743 5896431.417 5812212.554 7672851.826 5628040.508 5147139.636 8000310.999 0.832824306 0.854338234 0.647057538 0.802034664 0.737025275 0.726498327 0.959069195 0.703477716 0.643367444 1 22.93162465 1.617786878 25 0.755061421 0.78949722 0 0.11710554 4.152931915 10437.93603 0.052433869 0.028636084 41.4750462 -1.617786878 0.034435799 LDHVNIVHYNGCWDGFDYDPETS(ph)DDSLESSDYDPENSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDHVNIVHYNGCWDGFDYDPETSDDSLESSDYDPENSK 38 0 P19525-2;P19525 P19525-2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 LDHVNIVHYNGCWDGFDYDPET(0.174)S(0.786)DDS(0.039)LESSDYDPENSK 148.77 4.37E-13 118220000 51097 36152 46195 37569 52186 57177 52635 49047 56414 29080 TRUE FALSE 53114.34902 42360.82478 47398.87965 45000.03607 43315.44236 43898.50828 48509.33116 48389.60519 54383.67116 34777.66923 1.527254419 1.218046687 1.362911336 1.293934788 1.24549584 1.262261366 1.394841352 1.391398741 1.563752614 1 15.08587363 2.22158312 24.47005505 1.373278265 1.311368259 0 0.155382592 763.0157508 1099742.368 0.053930479 0.039937198 166.5647586 -2.22158312 -0.061910006 LDIDPETITWQR ddPTM_MDA-MB-175_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 ;;;; 259.08 6.80E-21 711722000 948382 1028063 1052545 999307 1229112 1272820 1093076 1061157 1039745 1040023 FALSE TRUE 985824.8537 1204624.823 1079975.187 1196966.942 1020187.981 977226.8448 1007397.847 1046933.926 1002324.781 1243795.594 0.792593942 0.968507067 0.868289928 0.962350202 0.820221575 0.785681224 0.809938427 0.841725064 0.805859729 1 20.24631798 3.206752779 24.98788696 0.831599044 0.90085866 0.102715119 0.07278084 314.2619886 246879.9488 0.019314587 0.023087149 1609.72904 -3.206752779 0.069259616 LDIDS(ph)PPITAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LDIDSPPITAR 11 0 P14618;B4DNK4;H3BUW1;H3BTJ2;H3BT25;H3BN34;H3BQZ3;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 1 LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(1)PPITAR 230.81 1.60E-12 7469070000 3619320 3708040 3924560 3597710 4470250 4738230 4093340 3897350 3812110 3679290 TRUE FALSE 3762213.548 4344867.025 4026837.258 4309326.3 3710398.502 3637847.891 3772493.315 3845112.398 3674912.906 4400176.431 0.855014249 0.987430185 0.91515359 0.979353071 0.843238575 0.826750461 0.857350466 0.873854142 0.83517399 1 22.06912994 3.227720773 24.99835347 0.863932468 0.936674079 0.207468159 0.057291424 261.1170613 602175.2574 0.015188353 0.01832064 1689.354422 -3.227720773 0.072741611 LDIDSPPITAR ddPTM_MDA-MB-175_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 ;;;;; 271.37 1.14E-26 2342680000 963215 1016282 981490 997221 1118648 1275362 1014476 1013627 984089 1038690 FALSE TRUE 1001243.472 1190820.528 1007068.436 1194468.337 928500.6125 979178.5038 934958.7203 1000040.988 948671.8291 1242201.419 0.806023449 0.958637231 0.810712676 0.961573799 0.747463816 0.788260655 0.752662738 0.805055423 0.763702098 1 20.24446769 3.226682561 24.99910978 0.795514891 0.884299396 0.148337938 0.083758387 318.7614217 670879.0808 0.021845754 0.026307828 1685.320724 -3.226682561 0.088784505 LDINLLDNVVNCLYHGEGAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDINLLDNVVNCLYHGEGAQQR 22 0 O14980;C9JKM9;C9J673;C9IYM2;F8WF71;C9IZS4;C9JQ02;C9JV99;C9JF49 O14980 XPO1 Exportin-1 0 ; 313.16 2.93E-67 2750100000 1466370 1492880 1673170 1575270 1635420 1950910 1636990 1681960 1595070 1568170 FALSE TRUE 1524263.42 1749270.527 1716774.185 1886853.704 1357431.893 1497840.719 1508678.446 1659416.077 1537663.742 1875422.887 0.812757182 0.932733912 0.915406438 1.006095061 0.72380043 0.798668252 0.80444707 0.884822345 0.819902409 1 20.83878451 5.065669273 12.47948042 0.868496659 0.44499308 0.039498798 0.086658345 1309610.11 7957826.458 0.020772258 13397515.51 116323.9854 -5.065669273 -0.42350358 LDKAQIHDLVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDKAQIHDLVLVGGSTR 17 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 128.38 2.23E-05 1266781000 394223 418445 486758 330355 714073 580808 420325 473122 562238 589929 FALSE TRUE 409787.2284 490309.6737 499443.3134 395698.233 592695.1265 445924.1442 387378.8282 466780.5735 542003.1642 705514.2927 0.580834765 0.69496774 0.707913813 0.560864942 0.840089468 0.632055437 0.54907297 0.661617459 0.76823839 1 19.42831578 0.900003054 2.703160869 0.999462473 0.654282447 0.633103146 0.080539178 0.250573148 3.950139077 0.075003655 0.019936912 7.943338214 -0.900003054 -0.345180027 LDKDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDKDEIR 7 1 Q15293;Q15293-2 Q15293 RCN1 Reticulocalbin-1 0 123.92 0.0038278 471980000 1346800 992280 1223600 1116700 1714400 1650300 1713800 1208800 1270500 779090 FALSE TRUE 1399972.704 1162696.371 1255488.021 1337579.927 1422986.9 1267042.836 1579467.878 1192598.013 1224774.953 931737.7689 1.502539395 1.247879403 1.347469281 1.435575514 1.527239689 1.359870639 1.695184987 1.27997174 1.31450607 1 19.82956445 -0.161131677 8.804288444 1.000000051 1.410873653 0.484078336 0.127670415 0 0 0.120177634 0.02832614 0.690030557 0.161131677 0.410873602 LDKDIVALMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDKDIVALMTR 11 1 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 86.291 0.013297 483400000 644320 540950 682710 515790 901010 763310 818170 636940 638540 531730 FALSE TRUE 669758.2511 633853.9545 700501.9835 617811.7225 747856.642 586042.8206 754039.6975 628402.8611 615559.0701 635912.3129 1.053224222 0.996763141 1.10157009 0.971536028 1.176037367 0.921578036 1.185760493 0.988191058 0.967993633 1 19.27846832 1.575401344 15.70953571 0.983007585 1.05570696 0.150097169 0.079105486 0.290229242 127.3335649 0.038055699 0.017674015 37.61848868 -1.575401344 0.072699375 LDKDNLSYIEHIFEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 184.83 3.69E-10 2448200000 2193790 1796200 2274960 2086980 2553800 2905500 3157100 2370280 2321470 1512530 FALSE TRUE 2280402.523 2104683.378 2334247.327 2499778.415 2119705.988 2230741.658 2909638.252 2338510.274 2237920.748 1808881.294 1.260670078 1.163527637 1.290436987 1.381947186 1.171832555 1.233216168 1.608529129 1.292793663 1.237184969 1 20.78666631 4.121175059 7.264572994 1.303396864 1.212858423 0.005791507 0.149266629 0.662046605 39.02119107 0.036358482 0.079518584 13218.2834 -4.121175059 -0.090538441 LDKENALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 122.69 0.00052778 3685160000 4386080 3404930 4081150 3446860 5330780 5327440 5357400 4300070 4443780 3605870 FALSE TRUE 4559245.825 3989700.241 4187508.122 4128638.62 4424655.92 4090222.798 4937472.989 4242434.595 4283849.226 4312371.188 1.057248003 0.925175516 0.971045381 0.957394074 1.026037817 0.948485791 1.144955472 0.983782335 0.993386014 1 22.04004993 LDKGQIQEIVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDKGQIQEIVLVGGSTR 17 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 157.14 3.35E-08 581800000 713640 670100 804340 653080 945650 931600 709350 784640 810250 748410 FALSE TRUE 741815.0583 785184.4623 825301.7612 782257.2748 784908.7508 715250.0185 653749.2935 774123.1842 781089.2608 895046.6103 0.828800478 0.877255389 0.922076852 0.873984959 0.876947347 0.799120415 0.730408099 0.864897063 0.872679983 1 19.77160329 2.872803697 11.10563879 0.836630421 0.878535858 0 0.067727601 1.286536074 109.022377 0.020209164 0.021440901 746.1114374 -2.872803697 0.041905437 LDKPFPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDKPFPELR 9 1 Q13564-2;Q13564;Q13564-4;Q13564-3;H3BMR3;J3QRA5 Q13564-2 NAE1 NEDD8-activating enzyme E1 regulatory subunit 0 63.624 0.085906 0 313190 1099900 676210 899100 430300 975930 526100 628750 584000 2686500 FALSE TRUE 325554.983 1288799.269 693832.5881 1076939.296 357157.7597 749285.0479 484862.9073 620322.6347 562981.9541 3212868.239 0.101328458 0.401136671 0.215954262 0.3351956 0.11116477 0.233213749 0.150912789 0.193074408 0.175227215 1 21.61543039 -1.409316061 3.727615203 1.004927373 0.215481778 0.875415373 0.089060922 190307044.5 337062860.6 10308169.42 0.020341741 0.038965831 1.409316061 -0.789445594 LDKSQIHDIVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDKSQIHDIVLVGGSTR 17 1 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 156.13 4.48E-08 3132300000 4050700 5144900 5467500 3736600 7662800 6962900 4115300 5363600 6148900 6880400 FALSE TRUE 4210624.764 6028496.553 5609987.542 4475688.327 6360279.993 5345871.999 3792732.033 5291709.715 5927602.29 8228482.647 0.511713392 0.732637694 0.681776675 0.543926325 0.772959033 0.649678954 0.460927269 0.643096661 0.720376106 1 22.97219499 0.838093681 2.66419902 0.999663107 0.626289449 0.603811977 0.091618675 0.432996468 5.530013229 0.086191587 0.022904696 6.888008612 -0.838093681 -0.373373658 LDLAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 172.15 0.012125 36082690000 13774280 15070190 13902710 14281800 16179360 17065260 15513500 13850490 13300470 13806600 FALSE TRUE 14318099.21 17658377.9 14265026.04 17106697.41 13429198.17 13102111.99 14297511.33 13664846.84 12821788.68 16511738.93 0.867146657 1.069443865 0.863932388 1.036032455 0.813312167 0.793502856 0.865899794 0.827583751 0.776525643 1 23.97698873 3.22267801 24.99933813 0.835990189 0.960217319 0.30218772 0.08326542 246.5894368 388132.75 0.021872137 0.026221777 1669.852111 -3.22267801 0.12422713 LDLAGRDLTDYLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 189.1 6.91E-07 625220000 770080 1117470 950850 560740 1489130 1408960 650190 1048420 1002540 1840980 FALSE TRUE 800483.353 1309386.78 975629.9321 671652.6984 1236008.215 1081750.393 599226.4088 1034367.645 966458.7812 2201684.783 0.363577638 0.594720366 0.443128798 0.305063061 0.561391996 0.49132846 0.272167212 0.469807328 0.438963283 1 21.0701765 0.101203733 2.368130815 1.000005811 0.438532316 0.750861343 0.097152365 51.83347535 134.5032448 0.090629594 0.024269712 1.262419612 -0.101203733 -0.561473495 LDLFEISQPTEDLEFHGVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDLFEISQPTEDLEFHGVMR 20 0 P55196-5;P55196;J3KN01;P55196-3;Q5TIG5;P55196-6;P55196-2;E9PFY5;F8W9I4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 0 ; 151.57 7.44E-08 56700000 21397.6 30857.2 26949.7 33444 32370 45351 37257 29758.2 35168 32129 FALSE TRUE 22242.39377 36156.68406 27652.03132 40059.12338 26867.75896 34818.91755 34336.69899 29359.34 33902.31055 38424.0624 0.578866272 0.940990666 0.719654029 1.042553048 0.69924306 0.906174813 0.893624902 0.76408735 0.882319787 1 15.22972244 -4.99999382 0.022521638 2.083353718 4.13E-10 0.201760661 0.124456904 4792.394984 8.162053681 527.8931526 267.7895656 1.00E-05 4.99999382 -2.083353718 LDLITVEAFKPILSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDLITVEAFKPILSTR 16 1 O95456;O95456-2 O95456 PSMG1 Proteasome assembly chaperone 1 0 106.82 0.0010725 59076000 38601 29537 44868 38603 40907 48019 55574 37304 47158 37529 FALSE TRUE 40124.99729 34609.74998 46037.29694 46238.55818 33953.64275 36867.31498 51217.96466 36804.0009 45460.79279 44882.08901 0.894009129 0.771126094 1.025738729 1.030222951 0.756507629 0.821426003 1.141167129 0.820015327 1.012893869 1 15.45385221 7.999787328 0.036236777 1.269653163 0.376732296 0.078258803 0.119921592 2774.608548 7.675175917 54.82093157 159.8089213 99951042.49 -7.999787328 -0.892920867 LDLLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LDLLEDR 7 0 Q14697;F5H6X6;Q14697-2;E9PKU7;E9PNH1 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;;;; 166.86 0.0025772 964353000 1682250 1947770 1849300 2002880 2330660 2475550 1922000 1762390 1706490 1728990 FALSE TRUE 1748666.529 2282284.346 1897494.277 2399043.686 1934495.246 1900641.03 1771348.618 1738768.045 1645073.758 2067752.487 0.845684646 1.103751228 0.917660256 1.160218015 0.935554549 0.919182079 0.856654086 0.840897571 0.795585433 1 20.97963207 2.703306786 2.29674189 0.860591357 1.00820658 0.251894319 0.097211426 0.345965636 3.600325981 0.03247706 0.031524885 505.017917 -2.703306786 0.147615223 LDLRDDKDTIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDLRDDKDTIEK 12 2 P63000;P63000-2;B1AH77;B1AH80;P15153;B1AH78 P63000 RAC1;RAC2 Ras-related C3 botulinum toxin substrate 1;Ras-related C3 botulinum toxin substrate 2 0 ;;; 109.22 0.0009119 1340590000 10334300 4715060 6694800 4929330 10871500 10220400 8556900 6649500 7676000 4461100 FALSE TRUE 10742306.14 5524834.877 6869271.988 5904336.761 9023566.313 7846866.992 7886187.819 6560374.329 7399742.259 5335167.132 2.013490089 1.035550479 1.287545791 1.106682624 1.691337139 1.470781851 1.478151972 1.229647388 1.38697478 1 22.34710204 0.424638603 0.828878898 0.998058907 1.407457046 0.175996039 0.269903027 3.584213038 3.533449939 0.272575421 0.085595195 2.658511864 -0.424638603 0.409398139 LDLRDPAALFETHGAEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDLRDPAALFETHGAEEIR 19 1 A0A087WVI0;E9PBL8;Q8WTW3;J3KRP4 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 ; 131.18 9.67E-06 113621000 144443 156760 157638 152556 184618 199172 143037 144783 143758 183720 FALSE TRUE 150145.7212 183682.3106 161746.1758 182731.1215 153236.6983 152917.3215 131825.3862 142842.4207 138584.1777 219716.4165 0.683361415 0.835997207 0.73615881 0.83166804 0.697429445 0.695975858 0.599979684 0.650121748 0.630741116 1 17.74528314 3.095469761 7.445139707 0.682438639 0.773609408 0.025015529 0.113300689 0.458662827 31.10097261 0.030340924 0.036348585 1245.861488 -3.095469761 0.091170769 LDLS(ph)HNRLS(ph)FIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDLSHNRLSFIK 12 1 C9K080;Q6UXM1 C9K080 LRIG3 Leucine-rich repeats and immunoglobulin-like domains protein 3 2 LDLS(1)HNRLS(1)FIK 57.836 0.062812 282340000 9642.6 248150 108660 196160 86791 175470 69235 107980 83396 401150 TRUE FALSE 10023.29729 290767.8322 111491.7689 234959.8625 72038.29682 134719.7518 63808.17979 106532.7047 80394.59425 479747.662 0.020892853 0.606084938 0.23239669 0.489757181 0.150158724 0.280813774 0.133003628 0.222059873 0.167576834 1 18.87191625 -1.840516554 3.140443806 1.233005283 0.261724998 0.649089764 0.164091597 72924262.69 38481598.55 125664037.3 0.038329344 0.014437216 1.840516554 -0.971280286 LDMEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDMEIER 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 94.874 0.05235 0 113270 113580 128330 121480 143910 142440 139380 108580 119830 107650 FALSE TRUE 117741.9871 133086.4815 131674.3852 145508.3814 119448.2296 109360.4687 128455.0314 107124.6627 115517.3417 128741.9564 0.914558007 1.033745992 1.022777569 1.130232796 0.927811204 0.849454768 0.997771317 0.832088199 0.897278128 1 16.97412277 3.025423287 24.36983187 0.904196026 1.026157008 0.356694004 0.070380294 161.8745196 155165.5093 0.01966815 0.023507053 1060.286636 -3.025423287 0.121960982 LDNARQS(ph)AER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 131.35 0.00015285 4291020000 2132810 2357640 2338060 1813490 2850990 2674180 2081530 2173040 2168750 2497950 TRUE FALSE 2217014.986 2762546.33 2398991.764 2172192.909 2366379.738 2053142.223 1918374.24 2143913.953 2090697.111 2987375.476 0.742127999 0.924740245 0.803043268 0.727124169 0.792126653 0.687272905 0.642160403 0.717658015 0.699844103 1 21.51044715 3.861942537 4.049128712 0.732166128 0.839465021 0.071753944 0.101852825 0.386893595 10.78195725 0.024727873 0.04726729 7276.83516 -3.861942537 0.107298892 LDNLHSCFCALQALIDSCAGPGSLATEPHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDNLHSCFCALQALIDSCAGPGSLATEPHVR 31 0 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 174.46 1.66E-13 238550000 64714 77507 88108 76791 90770 124620 90180 76617 88933 73681 FALSE TRUE 67268.95869 90818.22433 90404.16686 91980.0306 75340.94782 95678.89363 83111.45596 75590.07444 85732.3187 88117.38124 0.763401701 1.030650515 1.025951584 1.043835272 0.85500666 1.085811815 0.943190263 0.857833873 0.972933121 1 16.427139 0.994910357 24.67280698 1.000000036 0.952664833 0.025249225 0.095881809 751.5038866 3643049.421 0.08987815 0.022469537 9.883490688 -0.994910357 -0.047335203 LDNLVAILDINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDNLVAILDINR 12 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 126.1 0.00068274 486870000 188736 269980 318100 266660 375300 397000 274682 243000 413780 335190 FALSE TRUE 196187.443 316346.9648 326389.9473 319404.5521 311506.6401 304802.7666 253151.7071 239742.9825 398888.1386 400864.0629 0.489411402 0.789162697 0.814216034 0.796790188 0.777087968 0.76036441 0.631515096 0.598065541 0.995070837 1 18.61275356 1.223713396 24.97362627 0.997535809 0.710994765 0.576397681 0.099555398 200.9968435 338075.1417 0.098841279 0.025125798 16.73837895 -1.223713396 -0.286541044 LDNNWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDNNWGR 7 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ;; 221.53 6.01E-05 3365710000 1292300 1811680 1396770 1496480 1618660 1858330 1383090 1441020 1308390 2018040 FALSE TRUE 1343321.002 2122821.947 1433170.974 1792479.277 1343520.751 1426761.021 1274679.792 1421705.484 1261301.299 2413436.3 0.556600977 0.879584826 0.59383004 0.742708344 0.556683742 0.591174095 0.5281597 0.589079349 0.522616362 1 21.20265732 -1.052401241 4.430300894 1.000021806 0.619728646 0.542449353 0.105285398 13899184.99 3301699.14 3242.906819 0.024502017 0.088633676 1.052401241 -0.38029316 LDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 LDNTPAS(1)PPRS(1)PAEPNDIPIAK;LDNT(0.004)PAS(0.996)PPRS(1)PAEPNDIPIAK;LDNT(0.332)PAS(0.669)PPRS(0.999)PAEPNDIPIAK;LDNT(0.008)PAS(0.992)PPRS(1)PAEPNDIPIAK;LDNT(0.015)PAS(0.985)PPRS(1)PAEPNDIPIAK;LDNTPAS(1)PPRS(1)PAEPNDIPIAK 211.11 2.09E-23 5762770000 3572470 2572320 3149180 2893380 3586060 4052510 4525690 3531490 3706470 2172150 TRUE FALSE 3713513.874 3014095.95 3231250.218 3465681.928 2976502.802 3111375.969 4170954.592 3484156.153 3573074.869 2597741.204 1.429516485 1.160275683 1.243869179 1.334113622 1.145804208 1.197723608 1.605608205 1.341225272 1.375454515 1 21.30882628 LDNVPHT(ph)PSSYIETLPK ddPTM_MDA-MB-175_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(0.992)PS(0.007)S(0.001)YIETLPK;LDNVPHT(0.985)PS(0.015)SYIETLPK;LDNVPHT(0.333)PS(0.333)S(0.333)YIET(0.001)LPK;LDNVPHT(0.63)PS(0.37)SYIETLPK 190.63 1.06E-09 731128000 696008 581932 823490 552010 940190 831746 794549 708205 816485 567869 TRUE FALSE 723486.9333 681874.2942 844950.8259 661195.9304 780376.8396 638585.5967 732270.1732 698712.6704 787099.8643 679132.058 1.06531112 1.004037854 1.244162775 0.973589632 1.149079668 0.940296647 1.078244157 1.028831819 1.158979104 1 19.37333261 LDNVPHTPSS(ph)YIETLPK ddPTM_MDA-MB-175_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(0.007)S(0.993)YIETLPK;LDNVPHTPS(0.006)S(0.993)Y(0.001)IETLPK 216.38 3.42E-15 229320000 236243 186889 248319 175080 345400 268883 270727 235876 258253 200011 TRUE FALSE 245570.0561 218985.732 254790.3971 209710.3014 286689.0314 206438.9982 249506.7103 232714.468 248958.525 239199.326 1.026633562 0.91549477 1.065180247 0.876717777 1.198536117 0.863041722 1.043091193 0.972889313 1.040799442 1 17.8678538 LDPAQSAS(ph)RENLLEEQGSIALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDPAQSASRENLLEEQGSIALR 22 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 LDPAQS(0.168)AS(0.832)RENLLEEQGSIALR;LDPAQS(0.089)AS(0.911)RENLLEEQGSIALR;LDPAQS(0.002)AS(0.998)RENLLEEQGSIALR;LDPAQS(0.239)AS(0.761)RENLLEEQGSIALR 293.8 1.10E-55 962869000 109288.6 89620 95228 104930 85016 112942 96749 80760.2 81701 83125.4 TRUE FALSE 113603.3983 105011.5379 97709.71991 125684.8408 70565.01069 86712.93215 89165.56057 79677.74162 78760.59697 99412.2306 1.142750722 1.056324129 0.982874233 1.264279456 0.709822225 0.872256176 0.896927471 0.801488319 0.792262647 1 16.60113574 3.233517235 24.9999847 0.838165398 1.098420286 0.639262202 0.097635771 76.25255017 377983.0404 0.02661936 0.032757772 1712.053118 -3.233517235 0.260254887 LDPDSIPS(ph)PIQVIENDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LDPDSIPSPIQVIENDR 17 0 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 LDPDSIPS(1)PIQVIENDR;LDPDSIPS(1)PIQVIENDR;LDPDSIPS(1)PIQVIENDR;LDPDSIPS(1)PIQVIENDR;LDPDS(0.001)IPS(0.999)PIQVIENDR 179.1 9.81E-10 180388000 121684 129266 140484 139237 147881 161413 123506 132498 124014 125270 TRUE FALSE 126488.1783 151466.43 144145.1284 166777.663 122744.2404 123927.277 113825.277 130722.081 119550.7604 149814.2581 0.844300001 1.011028135 0.962158945 1.113229576 0.81930947 0.827206159 0.759775995 0.872561015 0.797993208 1 17.19281541 3.203073108 24.99889364 0.835400378 0.983238487 0.375250285 0.08563679 161.3962129 113693.8193 0.023345793 0.02790452 1596.147817 -3.203073108 0.147838109 LDPELHLDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDPELHLDIK 10 0 Q12905;B4DY09 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;; 128.17 0.00033681 289778000 1891700 1248170 1593290 1423040 2130320 2114890 2167500 1667030 1874930 1100070 FALSE TRUE 1966385.777 1462533.488 1634812.446 1704513.065 1768208.967 1623738.849 1997605.686 1644686.19 1807451.636 1315607.654 1.494659726 1.111679066 1.242629169 1.29560896 1.344024536 1.234212072 1.518390137 1.250134251 1.373853086 1 20.32729788 -1.022259963 5.007986102 0.999996042 1.311851323 0.400587809 0.116583803 4.80E-06 9.37E-07 0.105189594 0.02479311 0.095003594 1.022259963 0.311855281 LDPHLVLDQLR ddPTM_MDA-MB-175_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 ;;;;; 117.23 0.00088222 3692715000 4489020 4999770 3758597 3760090 8539150 6671930 4940310 4106730 4177720 8622410 FALSE TRUE 4666249.976 5858441.605 3856549.126 4503824.579 7087668.333 5122475.372 4553075.593 4051686.002 4027364.673 10311806.15 0.452515292 0.568129532 0.373993563 0.436763891 0.687335296 0.496758307 0.441540068 0.3929172 0.39055861 1 23.29779371 -1.038666472 4.867278221 1.000008812 0.470253305 0.755926338 0.090147404 0.372415357 122023319.8 2995.75351 0.022013065 0.091481553 1.038666472 -0.529755507 LDPHNHVLYSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LDPHNHVLYSNR 12 0 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;;; 64.827 0.036083 2919290000 2879240 3749130 3314800 3132540 4988630 4600170 3538720 3459990 3276570 4982290 FALSE TRUE 2992914.618 4393013.913 3401186.411 3752147.062 4140664.454 3531850.234 3261345.88 3413614.493 3158646.886 5958474.334 0.502295462 0.737271601 0.570814981 0.629716074 0.694920247 0.592744054 0.547345796 0.572900763 0.53011001 1 22.50651155 -1.224403477 5.672763954 1.000015918 0.600363737 0.753749579 0.068989517 1.34E-05 1.84E-06 0.064631576 0.015233202 0.059648087 1.224403477 -0.399652181 LDPITGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 652050000 121476 856510 465147 813620 337850 764400 350277 531286 342965 865200 FALSE TRUE 126271.9663 1003608.93 477269.1129 974551.6076 280422.3777 586879.6846 322821.3735 524164.9802 330621.7566 1034719.375 0.122034988 0.969933447 0.46125464 0.941851125 0.271012977 0.567187296 0.3119893 0.506576945 0.319527946 1 19.98080812 -1.261588336 6.721342976 1.000005334 0.509993661 0.24784249 0.262070672 1.92E-05 2.11E-06 0.232645591 0.054834495 0.054753472 1.261588336 -0.490011673 LDPPPS(ph)PHANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDPPPSPHANR 11 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211;H7C0A7 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 LDPPPS(1)PHANR;LDPPPS(1)PHANR;LDPPPS(1)PHANR 76.326 0.031908 1063920000 1190920 1451070 1267760 1563370 1337270 1802340 1463090 1359150 1189100 1450250 TRUE FALSE 1237938.441 1700279.985 1300798.867 1872599.92 1109961.323 1383773.85 1348409.183 1340932.817 1146304.523 1734398.721 0.713756546 0.980328205 0.7499999 1.079682484 0.639968947 0.797840677 0.777450517 0.773139879 0.660923298 1 20.72600417 3.210636366 24.99971685 0.765674449 0.878688269 0.129810795 0.133193431 386.4007087 345931.615 0.035125695 0.041991584 1624.188256 -3.210636366 0.11301382 LDPPPS(ph)PHANRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDPPPSPHANRK 12 1 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211;H7C0A7 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 LDPPPS(1)PHANRK 62.378 0.036767 109670000 93644 75779 81928 74873 112400 118320 84854 84333 83080 64610 TRUE FALSE 97341.13743 88793.45377 84063.11098 89682.65593 93294.28815 90841.97316 78202.92176 83202.65408 80089.96703 77269.09247 1.259768095 1.149145809 1.087926729 1.160653672 1.207394641 1.175657307 1.012085418 1.07679088 1.036507153 1 16.23760383 2.244761002 24.99546844 1.041012156 1.169398181 0.699675008 0.045379538 92.17514283 371584.6886 0.016518988 0.013494812 175.6956471 -2.244761002 0.128386025 LDPPPS(ph)PHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDPPPSPHSNR 11 0 Q96P47;Q96P47-2;Q96P47-4;H0Y873 Q96P47 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 LDPPPS(0.988)PHS(0.012)NR 66.285 0.040662 245930000 606020 708090 614620 638000 761840 819230 720130 712820 653990 678570 TRUE FALSE 629946.1375 829698.9493 630637.5021 764194.4958 632342.7089 628976.2481 663684.3289 703265.8138 630453.0276 811522.7995 0.776251928 1.022397584 0.777103863 0.941679638 0.779205106 0.77505678 0.817825857 0.866600192 0.776876544 1 19.6302721 5.024483506 19.01116509 0.853754766 0.54993855 0.067805894 0.090857795 55938132.05 1013774180 0.020117911 541256213 105799.4733 -5.024483506 -0.303816216 LDPPPS(ph)PHSNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDPPPSPHSNRK 12 1 Q96P47;Q96P47-2;Q96P47-4;H0Y873 Q96P47 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 LDPPPS(0.958)PHS(0.042)NRK 62.377 0.03677 35706000 79003 57841 64697 52323 91129 96310 82867 71924 61849 61768 TRUE FALSE 82122.09944 67774.74181 66383.05697 62672.33323 75638.92513 73943.46209 76371.66801 70959.97642 59623.06657 73870.25698 1.111707239 0.917483499 0.898643915 0.848410927 1.0239429 1.000990996 1.033862222 0.96060281 0.807132248 1 16.17270598 -2.702302596 2.230330255 2.586853412 0.956947309 0.022563372 0.086884715 5523600.683 2077701.901 40817972.64 0.020894999 0.001984712 2.702302596 -1.629906103 LDQEVAEVDKNIELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDQEVAEVDKNIELLK 16 1 F5H442;Q99816;Q99816-2 F5H442 TSG101 Tumor susceptibility gene 101 protein 0 165.45 6.40E-09 50834000 72366 42221 59100 44651 81604 71554 72830 68945 65982 35243 FALSE TRUE 75223.06556 49472.12832 60640.19455 53482.83453 67732.98123 54936.66791 67121.39429 68020.90505 63607.32071 42148.19108 1.784728208 1.173766348 1.438737772 1.268923604 1.607019886 1.303416979 1.59250949 1.613851112 1.509135246 1 15.36318309 3.235616663 24.99920519 1.482027574 1.400783726 0 0.229776377 348.5717851 2959979.236 0.06146768 0.0765966 1720.349412 -3.235616663 -0.081243848 LDQLKQEFEFWYPVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDQLKQEFEFWYPVDLR 17 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 72.819 0.025157 118980000 106170 142710 194810 180000 190840 212990 158010 170630 181510 170110 FALSE TRUE 110361.6736 167219.3324 199886.9086 215603.4628 158401.085 163526.3004 145624.7633 168342.9839 174977.4906 203439.7975 0.54247829 0.821959786 0.98253592 1.059789999 0.778614051 0.803806838 0.715812565 0.827483049 0.860094695 1 17.63424241 -3.184877521 0.957710455 3.362209126 0.826819677 0.139399233 0.132540417 45538.52613 940.732009 231168.7512 0.042372943 0.000653315 3.184877521 -2.53538945 LDQPVS(ph)APPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;LDQPVS(1)APPS(1)PR 145.33 8.60E-05 27890710000 5236020 5617200 5799760 5421520 6508820 6929860 5878850 6037620 5596220 5732320 TRUE FALSE 5442742.113 6581910.404 5950906.51 6493880.474 5402453.101 5320505.038 5418050.375 5956695.579 5394813.135 6855458.352 0.793928259 0.960097789 0.868053776 0.947256936 0.788051334 0.776097639 0.790326496 0.868898223 0.786936899 1 22.7088217 LDQPVSAPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 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 184.01 1.56E-05 27067920000 3858360 3701130 3700300 3807430 4194410 4903200 4230540 3988810 3901950 3555890 TRUE FALSE 4010691.032 4336770.287 3796732.858 4560528.29 3481445.686 3764506.109 3898939.22 3935346.526 3761519.582 4252598.564 0.943115362 1.019793009 0.892803024 1.07240978 0.818663138 0.885224893 0.916836885 0.925398075 0.88452261 1 22.01991324 3.234053075 24.9999991 0.902996024 0.978354248 0.276233351 0.060824948 146.4214416 812092.5693 0.016315608 0.020136737 1714.166783 -3.234053075 0.075358223 LDRAS(ph)PDLWPEQLPGVAEFAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDRASPDLWPEQLPGVAEFAASFK 24 1 Q52LA3 Q52LA3 LIN52 Protein lin-52 homolog 1 LDRAS(1)PDLWPEQLPGVAEFAASFK;LDRAS(1)PDLWPEQLPGVAEFAASFK 258.02 3.88E-44 1392380000 254119 191866 235158 209677 286430 293470 277460 245454 272290 205415 TRUE FALSE 264151.8143 224817.493 241286.4107 251150.4848 237742.7309 225316.0401 255711.9602 242164.0906 262490.3361 245662.1363 1.075264663 0.915149141 0.982188034 1.022341043 0.96776302 0.917178542 1.040909128 0.985760745 1.068501398 1 17.90631599 LDRDPASGTALQEISFWLNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDRDPASGTALQEISFWLNLER 22 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 175.61 1.17E-12 257200000 125330 148410 148320 143080 191600 189850 200130 134590 169290 144850 FALSE TRUE 130278.1252 173898.263 152185.341 171380.7969 159031.9004 145760.2147 184443.2877 132786.0412 163197.286 173230.5842 0.752050371 1.003854278 0.87851312 0.989321821 0.91803593 0.841423097 1.064727043 0.7665277 0.942081254 1 17.40233414 4.757698173 23.7388523 0.92218107 0.752050065 0.287652141 0.08403776 2834.001766 3515274.947 0.018940581 0.642500058 57239.80861 -4.757698173 -0.170131005 LDRETEELHHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDRETEELHHDR 12 1 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 145.52 3.84E-05 1270030000 761620 861790 834920 741230 1003240 971670 732360 845540 857740 911880 FALSE TRUE 791689.3457 1009795.729 856678.7011 887843.0816 832709.6231 746014.3683 674955.7095 834206.9193 826870.105 1090545.427 0.725957238 0.92595476 0.785550679 0.814127555 0.763571698 0.684074546 0.618915721 0.764944677 0.758217021 1 20.05661844 5.056485556 15.58077125 0.774612232 0.356889631 0.013311255 0.104071106 12267876.55 82951708.35 0.024600396 158457798.9 113889.9902 -5.056485556 -0.417722601 LDRLDLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDRLDLAR 8 1 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ;;; 155.58 0.00069541 1144020000 1160360 1215810 1288540 1184870 1857590 1720590 1503350 1271710 1356850 1454030 FALSE TRUE 1206171.909 1424615.91 1322120.411 1419233.75 1541837.515 1321009.048 1385513.499 1254664.808 1308017.234 1738919.339 0.693633041 0.819253589 0.760311523 0.816158471 0.886664194 0.759672412 0.796766973 0.721519842 0.752201211 1 20.72975958 -2.336055276 2.378118929 2.38923056 0.779432056 0.62104796 0.051910181 7925951.712 613230.9932 59786081.94 0.013427999 0.004612589 2.336055276 -1.609798504 LDRPAGGPS(ph)AESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.482)AES(0.482)PRPS(0.018)S(0.018)AYNGDLNGLLVPDPLCSGDSTSANK 95.872 5.38E-05 136850000 17437 12812 16614 12050 20379 24107 17559 16712 17928 11132 TRUE FALSE 18125.42622 15012.36134 17046.97449 14433.45403 16914.98486 18508.5146 16182.6797 16488.00298 17282.77478 13313.10226 1.36147277 1.127638099 1.280465976 1.084154072 1.270551711 1.39024806 1.215545361 1.238479405 1.298177873 1 13.70055917 -1.374661162 5.597813985 0.999922156 1.246465957 0.415946926 0.08932815 8.27E-05 9.24E-06 0.082392739 0.019414043 0.042202564 1.374661162 0.246543801 LDRPAGGPSAES(ph)PRPSSAY(ph)NGDLNGLLVPDPLCSGDSTSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 LDRPAGGPS(0.385)AES(0.512)PRPS(0.339)S(0.319)AY(0.446)NGDLNGLLVPDPLCSGDSTSANK 102.21 1.96E-05 75161000 13611 13413 11680 8763.7 18165 18618 13630 11091 12083 9087.8 TRUE FALSE 14148.37279 15716.57841 11984.3904 10497.1337 15077.31979 14294.25166 12561.64498 10942.34329 11648.13519 10868.38041 1.301792195 1.44608284 1.102684111 0.965841579 1.387264635 1.315214514 1.155797323 1.006805326 1.07174526 1 13.40784935 8 0.111686314 0.885912996 2.273508418 0.313934187 0.136906006 134.1662936 1.042186935 1.265112006 28.75210376 100000000 -8 1.387595422 LDRPAGGPSAES(ph)PRPSSAYNGDLNGLLVPDPLCSGDSTSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDRPAGGPSAESPRPSSAYNGDLNGLLVPDPLCSGDSTSANK 42 2 Q6P2E9 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 LDRPAGGPS(0.375)AES(0.608)PRPS(0.007)S(0.007)AY(0.004)NGDLNGLLVPDPLCSGDSTSANK;LDRPAGGPS(0.034)AES(0.946)PRPS(0.009)S(0.009)AY(0.002)NGDLNGLLVPDPLCSGDSTSANK;LDRPAGGPS(0.001)AES(0.972)PRPS(0.013)S(0.013)AYNGDLNGLLVPDPLCSGDSTSANK 383.25 2.41E-194 2773890000 723371 520939 641440 524769 800020 804548 694378 636261 657904 463040 TRUE FALSE 751930.2456 610406.2209 658156.4533 628566.7419 664032.8862 617703.92 639950.8379 627732.962 634226.1636 553763.8226 1.357853682 1.102286202 1.188514718 1.135080907 1.199126521 1.115464562 1.155638581 1.133575247 1.145300826 1 19.07891128 -4.389523736 0.026476002 1.30E-14 1.908237194 0.505840283 0.060269817 1423.771506 3.142116875 161.6358707 78.43923323 4.08E-05 4.389523736 1.908237194 LDS(ph)ELTARKELEQK ddPTM_MDA-MB-175_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 69.331 0.02468 123463000 16034.6 404940 339780 309630 293940 439880 189240 329520 311560 529530 TRUE FALSE 16667.65839 474485.295 348634.9459 370873.8898 243976.1838 337724.5364 174406.8743 325103.3234 300347.0165 633281.265 0.026319519 0.749248906 0.55052149 0.5856385 0.385257227 0.533293112 0.275401917 0.513363242 0.474271123 1 19.27248687 0.265081236 1.990264988 1.00001109 0.464564272 0.436620434 0.185544077 16.27832083 42.54861243 0.164403501 0.045175567 1.841116356 -0.265081236 -0.535446818 LDS(ph)PDPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDSPDPFK 8 0 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LDS(1)PDPFK 64.297 0.071197 42308000 221020 85418 139470 127860 175400 240140 271700 147470 151950 53100 TRUE FALSE 229746.0403 100087.877 143104.7028 153150.3264 145585.5707 184371.1244 250403.444 145493.4059 146481.3492 63503.92834 3.617824067 1.576089537 2.253477958 2.411666969 2.292544327 2.903302665 3.943117388 2.291093003 2.306650203 1 15.95455822 2.760763579 23.6724868 2.665272178 2.372002368 0 0.832993521 1899.21983 2024916.129 0.245288867 0.259934259 576.4525695 -2.760763579 -0.29326981 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 LDS(0.994)PPPS(0.896)PIT(0.107)EAS(0.002)EAAEAAEAGNLAVSSR;LDS(0.998)PPPS(0.884)PIT(0.116)EAS(0.003)EAAEAAEAGNLAVSSR;LDS(0.999)PPPS(0.986)PIT(0.014)EASEAAEAAEAGNLAVSSR 217.1 1.34E-34 342158000 97296 81657 89364 73834 124632 147645 113846 100542 108069 81844 TRUE FALSE 101137.3212 95680.95455 91692.89925 88438.14483 103447.0972 113356.6863 104922.453 99194.39894 104179.6178 97879.7648 1.033281204 0.977535599 0.936791169 0.903538592 1.056879298 1.158121769 1.071952443 1.013431113 1.064363181 1 16.57872301 3.158513446 8.823236527 1.063736351 0.962124236 0.479645826 0.049971438 0.255540517 25.46869566 0.015402546 0.018443155 1440.500609 -3.158513446 -0.101612115 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 LDS(0.971)PPPS(0.025)PIT(0.004)EASEAAEAAEAGNLAVSSR;LDS(0.837)PPPS(0.139)PIT(0.024)EASEAAEAAEAGNLAVSSR 201.88 1.98E-25 48018000 43856 69809 76686 71310 79075 106644 74668 69647 78546 79328 TRUE FALSE 45587.46874 81798.15271 78684.50016 85414.90516 65633.85974 81877.54721 68815.32705 68713.49588 75719.1448 94870.80277 0.480521587 0.862205761 0.829385837 0.900328686 0.691823594 0.863042631 0.72535833 0.724284963 0.798129062 1 16.53367653 -2.773868806 1.344771294 3.540885584 0.768630039 0.274120256 0.1150304 325017.7051 11709.29031 2504205.211 0.030875138 0.001683182 2.773868806 -2.772255544 LDSDAGFHS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDSDAGFHSLPR 12 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 LDSDAGFHS(1)LPR;LDSDAGFHS(1)LPR 186.08 7.87E-06 123500000 227580 261870 260230 260260 337340 340790 249140 256720 249580 261000 TRUE FALSE 236565.0341 306844.1354 267011.8076 311738.6512 279999.0673 261646.6872 229611.7558 253279.0883 240597.6646 312137.9529 0.757886159 0.983040135 0.855428842 0.998720753 0.897036278 0.838240543 0.73560986 0.811433169 0.770805544 1 18.25182426 2.665574249 3.921005296 0.80881727 0.90663173 0.099371034 0.09094244 0.357744847 10.68042809 0.028144084 0.026760838 462.9928129 -2.665574249 0.09781446 LDSEDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LDSEDKDK 8 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 129.1 0.001008 12760350000 34895900 8616290 15265100 9795880 22419800 24427600 29485200 15916100 18662000 5164490 FALSE TRUE 36273617.08 10096070.78 15662921.05 11733475.83 18608890.4 18754660.1 27174072.98 15702770.71 17990358.27 6176372.935 5.872964191 1.63462778 2.535941597 1.899735646 3.012915606 3.036516787 4.399681377 2.54239355 2.912770724 1 22.55832844 LDSEDKDKEGKPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDSEDKDKEGKPLLK 15 3 P13639 P13639 EEF2 Elongation factor 2 0 96.993 0.0015269 2963100000 10988000 2250800 4400900 1702500 8251300 6018800 6163900 4397600 5320700 1396600 FALSE TRUE 11421814.72 2637357.391 4515591.069 2039249.419 6848746.973 4621024.916 5680757.412 4338657.365 5129209.046 1670237.03 6.838439405 1.579031804 2.703563019 1.220934144 4.100464095 2.7666881 3.401168402 2.597629729 3.070946789 1 20.67162143 8 0.06505053 4.21E-12 9.339454021 0.197330713 1.431985528 619.8962965 2.993250589 80.66924932 537.9417007 100000000 -8 9.339454021 LDSHPCLEVTAAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDSHPCLEVTAAALR 15 0 Q9H4A4;A6NKB8;A0A087WU27;A0A087WUS4 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 209.39 2.41E-09 2258070000 1804320 1996060 2061180 2175000 2402860 2508340 2231160 2085890 2052950 2005270 FALSE TRUE 1875555.947 2338867.778 2114896.044 2605208.508 1994422.715 1925816.049 2056275.849 2057932.056 1979064.731 2398164.263 0.78207985 0.975274219 0.881881227 1.086334472 0.831645582 0.80303759 0.857437449 0.858128064 0.825241524 1 21.19349905 LDSLHPDLIYNVSWNHNGSLFCSACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDSLHPDLIYNVSWNHNGSLFCSACK 26 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 264.14 3.20E-53 1822030000 242426 478260 514460 483190 585320 673730 542680 578310 524930 424200 FALSE TRUE 251997.1657 560397.4347 527867.2502 578763.5398 485827.5155 517266.418 500143.3236 570558.7004 506037.8718 507313.8682 0.49672832 1.104636537 1.040514134 1.140839185 0.957646826 1.019618131 0.985865664 1.124666082 0.997484799 1 18.95251907 4.74228794 24.98772973 1.045967536 0.496728109 0.883281 0.059360392 108.131625 724877.4093 0.013747804 0.103054348 55244.35909 -4.74228794 -0.549239427 LDSQNAQGYEWIFIAWSPDHSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDSQNAQGYEWIFIAWSPDHSHVR 24 0 Q12792;Q12792-3;F8VS81;F8W1Q9 Q12792 TWF1 Twinfilin-1 0 ; 176.1 4.74E-13 740590000 96783 123339 123020 168852 134244 185228 161347 151259 168702 149844 FALSE TRUE 100604.0676 144521.5138 126226.0023 202250.4216 111425.2528 142211.6042 148700.2005 149231.6205 162630.448 179203.0629 0.561397032 0.806467878 0.704374134 1.128610295 0.621782078 0.793577977 0.829786044 0.832751506 0.907520471 1 17.45123577 8 0.083970596 1.110646731 3.30E-10 0.270195052 0.136674069 269.8124106 1.641187506 3.089947648 34.64239931 100000000 -8 -1.11064673 LDSQPQETS(ph)PELPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 LDSQPQET(0.004)S(0.996)PELPR;LDSQPQET(0.002)S(0.998)PELPR;LDSQPQET(0.077)S(0.923)PELPR;LDSQPQET(0.003)S(0.997)PELPR;LDSQPQET(0.006)S(0.994)PELPR;LDSQPQET(0.004)S(0.996)PELPR;LDSQPQET(0.034)S(0.966)PELPR;LDSQPQET(0.002)S(0.998)PELPR;LDSQPQET(0.003)S(0.997)PELPR 309.33 1.17E-55 19371899000 4403351 4855549 4661836 4370192 5072536 5625190 4725885 4787063 4702094 4595495 TRUE FALSE 4577198.698 5689451.77 4783327.276 5234602.934 4210308.143 4318824.873 4355457.785 4722900.251 4532866.555 5495894.259 0.832839658 1.035218565 0.87034558 0.952456996 0.766082451 0.785827505 0.79249301 0.85935064 0.824773247 1 22.38992282 3.25182477 24.95670292 0.827660186 0.927010482 0.210002784 0.07869418 289.1513481 544039.4419 0.020270597 0.027287381 1785.766905 -3.25182477 0.099350296 LDSS(ph)PSVSSTLAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.136)S(0.78)PS(0.084)VSSTLAAK;LDS(0.004)S(0.996)PSVSSTLAAK;LDS(0.027)S(0.973)PSVSSTLAAK;LDS(0.006)S(0.994)PSVSSTLAAK;LDS(0.005)S(0.959)PS(0.035)VSSTLAAK;LDS(0.073)S(0.927)PSVSSTLAAK 388.18 6.02E-114 2585231000 3254190 2185640 2904510 2526560 3335950 3511320 3904530 2990210 3142730 1759190 TRUE FALSE 3382667.934 2561006.668 2980203.917 3026306.027 2768906.411 2695869.145 3598482.736 2950131.126 3029623.761 2103869.599 1.607831558 1.217283937 1.416534522 1.43844753 1.316101726 1.281386045 1.71041149 1.402240485 1.440024497 1 21.00461386 LDSSDIYNELKETYPNYLPLYVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDSSDIYNELKETYPNYLPLYVAR 24 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C0A3;A0A494C1S6 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 227.2 4.20E-33 119270000 58273 52616 54705 54879 67831 70571 73793 59108 75342 59610 FALSE TRUE 60573.66304 61652.3887 56130.65724 65733.9024 56301.11085 54181.95476 68008.91184 58315.75394 72630.45614 71289.4382 0.849686357 0.864817991 0.787362878 0.922070703 0.789753886 0.760027798 0.953982996 0.818013936 1.018810892 1 16.12140073 1.234984339 25 1.009405548 0.844349316 0.574543859 0.057198191 64.13376647 448293.5523 0.04557474 0.013141206 17.17846439 -1.234984339 -0.165056232 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LDSSEMDHS(1)ENEDYTMSSPLPGK;LDS(0.006)S(0.006)EMDHS(0.988)ENEDYTMSSPLPGK 205.26 1.02E-24 293280000 200336 181544 233691 194593 283329 273954 290360 236794 272346 158433 TRUE FALSE 208245.42 212722.7698 239781.1794 233082.9146 235168.8378 210332.3353 267600.8245 233620.1637 262544.3207 189474.913 1.099065922 1.122696226 1.265503573 1.230151849 1.241160817 1.110080126 1.412328526 1.232987313 1.385641595 1 17.53164732 4.280418787 6.12134864 1.24723382 1.107666399 0.154840216 0.112888274 0.28245489 26.1751014 0.025539252 0.069850299 19072.99027 -4.280418787 -0.139567421 LDSTQVGEFLGDNDKFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDSTQVGEFLGDNDKFNK 18 1 Q9Y6D6;E5RIF2 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 135.38 7.78E-06 206350000 270930 157320 205110 176440 286060 241980 267110 208150 241910 139640 FALSE TRUE 281626.5256 184338.4862 210455.3351 211339.3054 237435.6234 185783.8122 246173.2202 205360.0897 233203.7064 166999.7844 1.686388558 1.103824696 1.260213214 1.265506456 1.421772035 1.112479354 1.474093042 1.229702723 1.396431182 1 17.34948671 -1.93059305 2.430855596 0.787166363 1.313900722 0.253373362 0.167293883 41142195.05 20846202.28 49723145.26 0.036791222 0.011732943 1.93059305 0.526734359 LDSYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDSYLR 6 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;;; 118.42 0.050903 420131000 303602 398085 360068 369572 510265 506630 400876 397156 364586 546660 FALSE TRUE 315588.4414 466453.0021 369451.6679 442672.2385 423530.3376 388972.8606 369454.2916 391832.7734 351464.6211 653767.5606 0.482722699 0.713484471 0.565111655 0.677109519 0.647830151 0.594971186 0.565115668 0.599345696 0.537598747 1 19.31841827 -2.222521595 2.490993042 2.424019088 0.602622613 0.778213534 0.064319198 1815495.825 496158.6292 14847951.22 0.014966571 0.005990711 2.222521595 -1.821396476 LDT(ph)PDINIVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDTPDINIVLK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 LDT(1)PDINIVLK;LDT(1)PDINIVLK 168.89 0.00019606 65272000 446960 196895 213390 171789 348660 437960 308830 244680 260870 134590 TRUE FALSE 464606.3259 230710.1846 218951.1187 205768.3515 289394.8977 336250.4273 284623.0976 241400.4648 251481.3397 160960.3336 2.88646473 1.433335651 1.360279976 1.278379256 1.797926801 2.089026655 1.768280987 1.49975127 1.56238083 1 17.29634567 -2.32434781 0.12856079 4.37E-43 2.077011302 0.254613358 0.42961099 105.1613247 1.752065717 37.08601617 4.171120856 0.004738623 2.32434781 2.077011302 LDTDDLDEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 231.38 2.58E-12 115900000 489480 291090 393270 283100 540230 538810 496800 372960 452160 263950 FALSE TRUE 508805.0484 341082.4431 403518.9393 339096.335 448401.8976 413679.5432 457859.5179 367961.0812 435886.8499 315665.9489 1.611846479 1.08051706 1.278310001 1.074225257 1.420494986 1.310497837 1.450455836 1.165666055 1.380848493 1 18.26803912 -0.64091699 9.227836798 1 1.293680001 0.243222843 0.161243427 0 0 0.143360196 0.033790322 0.228603571 0.64091699 0.293680001 LDTGS(ph)PEPETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDTGSPEPETR 11 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LDT(0.016)GS(0.984)PEPETR 91.858 0.0053469 0 156710 181610 183010 160620 198840 195710 185410 188340 170990 204220 TRUE FALSE 162897.0318 212800.1048 187779.3909 192390.1566 165041.2478 150259.3185 170877.0797 185815.6104 164836.1033 244232.999 0.666973884 0.871299561 0.768853479 0.787732032 0.675753271 0.615229388 0.699647797 0.760812876 0.674913316 1 17.89789861 -1.943216981 6.536287723 1.115415265 0.728722734 0.57820234 0.070491654 0.04355562 0.000378383 0.025074603 0.016616273 0.011396802 1.943216981 -0.386692531 LDVFARPAS(ph)PSLQLLPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDVFARPASPSLQLLPWR 18 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 LDVFARPAS(0.999)PS(0.001)LQLLPWR;LDVFARPAS(0.85)PS(0.15)LQLLPWR 224.83 2.66E-19 4336300000 1410270 1754750 1621740 1350720 1671010 1957240 1317230 1473100 1573640 1899900 TRUE FALSE 1465948.549 2056114.662 1664003.877 1617888.385 1386972.317 1502700.672 1213982.071 1453355.504 1517005.004 2272149.029 0.645181513 0.904920688 0.732348035 0.712052055 0.610423128 0.661356563 0.534288048 0.639639163 0.66765207 1 21.11562603 -1.341788085 3.268202462 1.002284181 0.676255951 0.525695243 0.091545901 70896698.93 101002832.9 1569313.169 0.023840086 0.045521013 1.341788085 -0.32602823 LDVGNAEVKLEEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDVGNAEVKLEEENR 15 1 P51572;P51572-2;C9JSP1;C9JQ75;C9J0M4 P51572 BCAP31 B-cell receptor-associated protein 31 0 75.911 0.027748 43452000 34129 37557 42609 39469 64176 75913 38332 41793 52607 42591 FALSE TRUE 35476.43927 44007.1226 43719.42554 47275.8504 53267.38644 58283.35622 35327.43768 41232.83319 50713.68435 50935.891 0.696491974 0.863970802 0.858322583 0.928144172 1.045773136 1.144249273 0.693566697 0.809504504 0.995637523 1 15.63639496 4.942151494 1.311534217 0.923323623 0.510568317 0.26829145 0.119747929 3.470461068 3.725413087 0.036456964 2.166244702 87528.9048 -4.942151494 -0.412755305 LDVGNFSWGSECCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LDVGNFSWGSECCTR 15 0 P62241 P62241 RPS8 40S ribosomal protein S8 0 ;; 346.46 7.28E-82 749510000 122275 132289 117240 142947 146628 148107 125011 138750 135987 152245 FALSE TRUE 127102.5114 155008.6067 120295.3707 171221.4899 121704.2249 113711.3938 115212.3112 136890.2832 131092.8544 182074.4928 0.698079722 0.851347184 0.660693153 0.940392513 0.668430943 0.624532256 0.632775681 0.751836685 0.719995714 1 17.4741693 -1.268159549 5.049780935 1.000054761 0.728288968 0.426794877 0.094714059 5.74E-05 8.31E-06 0.090076706 0.021227014 0.053931246 1.268159549 -0.271765793 LDVSNVATDTERLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDVSNVATDTERLELK 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 176.49 2.87E-09 125930000 59681 45468 61759 34451 84095 72399 43035 55395 65038 51027 FALSE TRUE 62037.25196 53276.77531 63368.49028 41265.30497 69800.56194 55585.42947 39661.80425 54652.52063 62697.29508 61024.76368 1.016591433 0.87303534 1.038406156 0.676205896 1.143807165 0.910866771 0.649929666 0.89557939 1.027407421 1 15.89710718 2.471720212 24.98667096 0.865216229 0.944322979 0.017453216 0.149191114 468.2662593 2166299.17 0.050095107 0.042036779 296.2921953 -2.471720212 0.07910675 LDVTILS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 LDVTILS(0.978)PS(0.022)R;LDVTILS(0.996)PS(0.004)R;LDVT(0.001)ILS(0.992)PS(0.008)R;LDVTILS(0.847)PS(0.153)R 139.29 4.43E-05 499654000 278239 367224 339686 351387 388317 451600 375042 358791 343798 397574 TRUE FALSE 289224.0906 430291.8654 348538.4962 420890.2998 322311.015 346722.7441 345645.2281 353981.9935 331424.7771 475471.0133 0.608289638 0.904980227 0.733038369 0.885207064 0.677877318 0.72921952 0.726953312 0.744487011 0.697045178 1 18.85899787 -1.717753967 8.222765136 1.001193822 0.750090636 0.448131776 0.084661952 0.001706358 5.86E-05 0.075491264 0.017717913 0.019153407 1.717753967 -0.251103186 LDVTILSPSRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 93.839 0.014352 319530000 360340 282120 318650 187080 430070 427270 378740 305500 311700 350910 FALSE TRUE 374566.5014 330571.9154 326954.2808 224083.8656 356966.855 328043.0178 349053.3691 301405.2722 300481.9779 419664.0959 0.892538831 0.787705974 0.779085664 0.533960059 0.85060137 0.78167997 0.831744656 0.718206001 0.716005922 1 18.67887551 LDYFLLSHSLLPALCDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LDYFLLSHSLLPALCDSK 18 0 P27695 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 256.45 1.36E-30 2799400000 3905700 2879800 3909800 3170000 5095500 4791400 4760900 4261300 4393000 2717300 FALSE TRUE 4059900.052 3374383.248 4011692.6 3797016.538 4229368.73 3678669.964 4387728.218 4204184.244 4234896.788 3249702.909 1.249314219 1.038366688 1.234479801 1.168419589 1.301463195 1.13200193 1.350193646 1.293713414 1.303164291 1 21.6318764 3.59121982 1.555872732 1.251821458 1.151581 0.022440585 0.111483757 0.845589216 4.038465377 0.032548302 0.06581794 3901.394073 -3.59121982 -0.100240458 LDYVPSSAS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 198.33 3.13E-07 6854640000 4354840 4728770 4665640 4685260 4976310 5529570 4844970 4615240 4365110 3987190 TRUE FALSE 4526772.446 5540899.463 4787230.411 5611990.444 4130438.604 4245411.169 4465208.591 4553380.257 4208010.544 4768403.541 0.949326626 1.162003051 1.003948254 1.17691181 0.866209952 0.890321285 0.936415837 0.954906651 0.882477858 1 22.1850749 3.227490525 24.9974821 0.921509378 1.074465763 0.514547372 0.072002143 158.2598327 357367.7031 0.019240456 0.023201239 1688.459024 -3.227490525 0.152956385 LDYVPSSAS(ph)REVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LDYVPSSASREVR 13 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LDYVPS(0.141)S(0.071)AS(0.788)REVR 147.09 2.58E-05 150190000 166700 254440 257440 118250 333770 306260 114710 206630 232860 389440 TRUE FALSE 173281.4447 298138.0907 264149.0979 141639.4971 277035.8946 235135.7564 105718.7305 203860.4628 224479.4141 465743.3117 0.372053533 0.640133918 0.567155966 0.304114935 0.594825277 0.504861263 0.226989262 0.43770991 0.481980972 1 18.82917553 0.77382875 5.663104771 0.999999765 0.454955364 0.636523104 0.122811953 7.060946288 176.6884818 0.119113862 0.029992438 5.940578648 -0.77382875 -0.545044401 LDYWEDDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 154.12 0.00017788 1948867000 1120189 1228560 1311790 1263396 1458510 1606780 1358020 1263946 1255133 1155547 FALSE TRUE 1164414.927 1439555.623 1345976.325 1513291.958 1210592.991 1233629.696 1251574.844 1247004.871 1209961.009 1381954.31 0.84258569 1.041681054 0.973965865 1.095037619 0.876000735 0.892670392 0.905655733 0.902348842 0.875543424 1 20.39827849 3.191783304 24.9998466 0.902894656 0.991105012 0.242751784 0.0683557 148.3365908 79277.04292 0.018590347 0.022219785 1555.189461 -3.191783304 0.088210356 LDYWEDDLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LDYWEDDLRR 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 A0A494C1L5;Q5T321 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 ;;;;; 159.09 1.25E-05 2606050000 1950890 2182068 2225140 2078489 2523020 2773770 2284556 2297070 2131102 2207316 FALSE TRUE 2027912.644 2556821.205 2283128.976 2489607.921 2094157.962 2129603.954 2105486.531 2266281.534 2054404.055 2639797.309 0.768207709 0.968567244 0.864887986 0.943105712 0.79330256 0.806730103 0.797594014 0.858505889 0.778243105 1 21.33199573 3.229092994 24.99820861 0.82965968 0.890554375 0.073168397 0.077357959 390.5429441 1031183.835 0.020427157 0.024722436 1694.700642 -3.229092994 0.060894695 LEAAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 80.462 0.069435 70628000 77047 135500 109650 124570 136670 173460 110150 127720 120820 201230 FALSE TRUE 80088.87505 158771.071 112507.5691 149209.5742 113438.8822 133176.5438 101516.1552 126008.1223 116471.7118 240657.1657 0.332792397 0.659739636 0.46750143 0.620008857 0.471371305 0.553386987 0.421828932 0.523600126 0.483973587 1 17.87661986 -1.837037749 2.701325727 1.178257411 0.508787824 0.73546796 0.08923094 20742577.36 15248035.1 24017568.9 0.019652592 0.014553326 1.837037749 -0.669469587 LEAAHTLEDCASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEAAHTLEDCASR 13 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 0 ;;; 225.33 1.26E-11 1363070000 719610 771840 803010 823000 888780 996720 869150 852340 797720 839710 FALSE TRUE 748020.7585 904397.5159 823937.1003 985786.9436 737705.4931 765246.8854 801023.7519 840915.7764 769010.213 1004235.097 0.744866178 0.900583457 0.820462362 0.981629647 0.734594414 0.762019658 0.797645645 0.837369435 0.765767115 1 19.93766562 -1.605810514 2.783871837 1.014350133 0.820110981 0.365128713 0.072573749 32659565.07 31300479.28 3417358.243 0.017048322 0.024785032 1.605810514 -0.194239152 LEAALGEAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEAALGEAKK 10 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 0 129.82 0.00046984 230570000 493160 317690 409500 287120 688190 544240 539920 443020 522750 333210 FALSE TRUE 512630.3376 372250.7862 420171.9064 343911.479 571211.7096 417848.508 497599.6596 437082.0415 503936.3296 398496.1198 1.286412369 0.934139049 1.054393972 0.863023407 1.433418498 1.048563555 1.248693864 1.096828852 1.264595324 1 18.60420615 3.262068571 24.99941903 1.179090065 1.028745805 0.180580685 0.15368168 381.0725359 405247.0358 0.039374523 0.053282447 1828.388877 -3.262068571 -0.15034426 LEADYDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEADYDKK 8 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 ; 97.431 0.013207 218620000 605570 348520 363510 259490 820010 595960 588410 420830 445560 372930 FALSE TRUE 629478.3712 408375.5989 372983.3692 310816.3475 680624.9931 457557.3219 542288.8867 415189.4622 429524.3826 445998.4933 1.41139125 0.915643449 0.836288406 0.696899994 1.526070162 1.025916743 1.215898472 0.930921221 0.963062407 1 18.76667931 1.616873277 24.99999999 0.960243179 1.072577656 0.051390408 0.238162404 2.613908787 7235.076023 0.113785797 0.061945035 41.38788911 -1.616873277 0.112334477 LEAEEAIEVDHSHDLDIF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEAEEAIEVDHSHDLDIF 18 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 0 60.474 0.067367 14825000 25562 26777 35860 31361 28738 40745 33351 32054 32245 31474 FALSE TRUE 26571.2075 31375.74145 36794.54106 37564.1122 23853.12502 31282.59125 30736.86147 31624.36856 31084.50875 37640.72769 0.705916414 0.833558312 0.977519387 0.997964559 0.633705204 0.831083594 0.816585209 0.840163581 0.825821143 1 15.2000069 -2.065814614 4.91743683 1.351961431 0.83294639 0.200348264 0.10214715 0.073783198 0.000987509 0.018514328 0.023418599 0.008593803 2.065814614 -0.519015041 LEAEIATYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEAEIATYR 9 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 205.36 3.51E-05 2208590000 2085930 2133040 2026040 2011790 2384560 2601650 2508980 2074940 2055890 2107540 FALSE TRUE 2168284.127 2499373.027 2078840.267 2409716.057 1979233.343 1997456.216 2312319.592 2047128.823 1981898.92 2520472.112 0.860269041 0.991628916 0.824782094 0.956057417 0.785262941 0.792492885 0.917415266 0.812200545 0.786320512 1 21.26526256 3.242076551 24.99897262 0.840008801 0.908187379 0.118625491 0.076815495 164.999515 1173168.258 0.02012386 0.026204253 1746.12991 -3.242076551 0.068178578 LEAEIATYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEAEIATYRR 10 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 206.73 2.33E-07 1342780000 738510 1057650 938265 656127 1397730 1191610 682319 922389 952080 1584810 FALSE TRUE 767666.9451 1239293.16 962716.9567 785906.9623 1160144.354 914876.6365 628837.0539 910025.8842 917814.8268 1895323.176 0.405032215 0.653869048 0.507943431 0.414655913 0.612108989 0.482702184 0.331783551 0.480142857 0.484252416 1 20.85401244 -1.114861419 3.417041474 1.000482363 0.485743995 0.74827573 0.089465935 21107405.6 34168769.35 114549.085 0.022217057 0.076760639 1.114861419 -0.514738369 LEAFHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEAFHER 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 81.548 0.026903 66441000 36014 44334 47046 44359 57262 62263 41437 42712 40542 63756 FALSE TRUE 37435.86053 51948.01963 48272.05741 53133.0778 47528.62569 47803.36185 38189.05966 42139.5155 39082.90134 76247.76752 0.49097648 0.681305451 0.633094699 0.696847652 0.623344489 0.626947692 0.500854791 0.552665565 0.512577648 1 16.21840748 -0.974493439 7.157349881 1.000000019 0.593064708 0.753460533 0.070185171 2.17E-08 3.18E-09 0.071115127 0.016761995 0.106048996 0.974493439 -0.406935311 LEAHSDWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEAHSDWVR 9 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ; 172.23 5.63E-05 1029880000 485220 565560 487920 552570 676080 748600 599230 536090 505750 687890 FALSE TRUE 504376.8603 662690.5306 500635.596 661866.6967 561160.1631 574748.9951 552260.7868 528904.5904 487548.1563 822668.8751 0.613098265 0.80553738 0.60855055 0.804535964 0.682121544 0.698639529 0.671303855 0.642913092 0.592642035 1 19.64995234 -1.723616683 2.66285873 1.058295834 0.682545836 0.64666185 0.070954774 13006973.67 10639442.46 5044247.108 0.01609826 0.018896585 1.723616683 -0.375749998 LEALQKQMDS(ph)R ddPTM_MDA-MB-175_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 76.143 0.018132 294550000 644290 474900 611800 393060 854200 707490 745650 431000 649050 492380 TRUE FALSE 669727.0667 556460.3808 627744.0106 470806.0948 709003.3891 543186.1696 687204.0046 425223.15 625690.8173 588852.4338 1.137342784 0.944991222 1.066046389 0.799531543 1.204042555 0.922448713 1.167022441 0.72212175 1.062559618 1 19.16754661 1.749793107 25 0.902082021 1.025436826 0.094546688 0.142111411 5.76916097 12863.56065 0.060344144 0.033464116 56.2073496 -1.749793107 0.123354805 LEAMCFDGVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEAMCFDGVKR 11 1 P47813;X6RAC9 P47813 EIF1AX "Eukaryotic translation initiation factor 1A, X-chromosomal" 0 ; 117.86 0.0012797 1488490000 1164330 1010420 1145180 969780 1564140 1322800 1082410 1237040 1380000 1064210 FALSE TRUE 1210298.647 1183951.775 1175024.332 1161599.589 1298268.041 1015599.747 997567.8758 1220459.502 1330334.07 1272721.574 0.950953195 0.930251989 0.923237537 0.912689478 1.020072314 0.797974803 0.783806841 0.95893676 1.045267164 1 20.27948541 1.474171369 8.065163417 1.016428324 0.903182748 0.346123525 0.066026045 0.134730722 27.35143068 0.038997013 0.017606945 29.79691962 -1.474171369 -0.113245576 LEAPLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEAPLEELR 9 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 176.44 0.00012365 212958000 274117 301871 315749 310907 372491 364338 306203 286396 287955 327297 FALSE TRUE 284939.3508 353714.996 323977.6783 372403.4766 309175.1129 279726.0211 282202.0087 282557.3301 277591.5558 391424.5807 0.727954668 0.903660663 0.827688639 0.951405443 0.78987148 0.714635807 0.720961387 0.721869152 0.709182738 1 18.57837483 3.008795119 24.80732037 0.749528468 0.85654717 0.106513014 0.097851418 265.6157436 749182.8203 0.02616048 0.031223179 1020.457964 -3.008795119 0.107018703 LEAQHQALVTLWHQLHVDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 196.4 6.11E-22 25589000 33775 26144 37821 29874 38798 45568 42823 31778 39290 18895 FALSE TRUE 35108.46308 30634.02863 38806.64633 35782.98804 32203.12982 34985.52259 39466.42136 31352.06789 37875.96057 22597.11348 1.553670256 1.35566114 1.717327585 1.583520305 1.425099265 1.548229716 1.7465249 1.387436847 1.676141539 1 14.46385088 -1.31281705 3.46738648 0.997752647 1.547195893 0.628041306 0.127977489 16085686.17 27983949.81 390448.5319 0.029167716 0.048661215 1.31281705 0.549443246 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 LEAS(0.004)YS(0.141)DS(0.855)PPGEEDLLVHVAEGSK;LEASYS(0.003)DS(0.997)PPGEEDLLVHVAEGSK;LEASYS(0.021)DS(0.978)PPGEEDLLVHVAEGSK 280.92 1.97E-52 484130000 405446 347747 411152 359847 536300 515190 477898 409611 439952 298869 TRUE FALSE 421453.3212 407469.8422 421866.9589 431023.6626 445139.9176 395544.9303 440439.106 404120.8345 424118.2135 357426.6584 1.17913231 1.140009657 1.180289576 1.205907988 1.245402119 1.106646416 1.232250297 1.130639881 1.186588083 1 18.44728771 -0.933593671 0.548189321 0.952850471 1.181461808 0.625842304 0.041400378 12.35426331 2.289229452 1.004400527 0.017019382 0.11652157 0.933593671 0.228611338 LEAVSHTSDMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 256.96 2.01E-21 5172146000 632477.4 4668357 3420728 4153105 3629506 5842740 2735532 4557489 3029303 5427226 FALSE TRUE 657448.0961 5470111 3509874.982 4974576.773 3012563.867 4485852.183 2521113.854 4496403.315 2920278.977 6490587.024 0.101292548 0.842776005 0.540763874 0.766429408 0.464143514 0.691131968 0.388426169 0.692757573 0.449925248 1 22.62991753 -2.039941149 3.735362505 1.609684273 0.567575469 0.299661013 0.20517988 0.078316715 0.000837418 0.014934856 0.041241974 0.009121344 2.039941149 -1.042108805 LECVEPNCR ddPTM_MDA-MB-175_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 854160000 955640 1155571 1096680 1091280 1195611 1407190 1052266 1088246 1074930 1174617 FALSE TRUE 993369.4051 1354031.33 1125260.382 1307131.927 992381.4693 1080391.449 969786.6413 1073659.842 1036243.479 1404760.712 0.707144923 0.963887528 0.801033494 0.930501484 0.706441646 0.769092871 0.690357178 0.764300876 0.737665476 1 20.42189297 LEDAGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEDAGVR 7 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ; 102.72 0.019862 220740000 242220 259070 266210 273560 307350 329430 299190 263870 265460 231608 FALSE TRUE 251783.0326 303563.2572 273147.6513 327669.3515 255106.7568 252924.8751 275738.706 260333.2543 255906.1465 276987.1532 0.909006175 1.095947064 0.986138339 1.182976711 0.921005736 0.913128541 0.995492761 0.939874833 0.923891753 1 18.07945954 LEDDAKDNQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDDAKDNQQK 11 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 68.536 0.051957 207810000 264850 133270 192390 133450 310230 242360 202020 176250 225460 137200 FALSE TRUE 275306.4825 156158.0858 197403.8415 159846.0117 257497.2154 186075.563 186185.1445 173887.657 217345.7386 164081.7131 1.677862068 0.95170926 1.203082523 0.974185414 1.569323055 1.134042054 1.134709901 1.059762564 1.324618902 1 17.32405493 LEDEHLVFFCQMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEDEHLVFFCQMGK 14 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;; 184.21 1.32E-06 5306280000 5694090 4974100 6018030 5026930 7523000 7531480 6364720 6039730 6659370 5086130 FALSE TRUE 5918897.07 5828362.982 6174864.806 6021241.75 6244243.147 5782407.911 5865836.615 5958777.298 6419700.575 6082659.794 0.973077119 0.958193156 1.015158667 0.989902765 1.026564588 0.950638061 0.964353887 0.979633499 1.055410099 1 22.53627089 7.999999983 0.108009729 1.011570827 0.906562855 0.077622081 0.030285981 397.390945 3.002005541 0.298972111 6.214459751 99999996.16 -7.999999983 -0.105007972 LEDFFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LEDFFAR 7 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 216.54 8.65E-05 2363502000 3721104 4192840 4016130 4348064 4437300 5106070 4590850 4224900 4133650 4271780 FALSE TRUE 3868016.059 4912927.654 4120793.647 5208098.082 3683049.331 3920262.626 4231007.181 4168272.126 3984880.744 5108753.503 0.757134995 0.961668566 0.806614303 1.019445953 0.720929152 0.767361867 0.828187772 0.815907858 0.780010377 1 22.2845399 5.047022848 14.39918031 0.844878141 0.339995158 0.07393681 0.098152246 695914.0855 6464690.407 0.022280054 9332872.435 111435.3157 -5.047022848 -0.504882983 LEDFRDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 113.22 0.0026363 4701335000 5755700 7193810 5737460 6585640 6425690 7778360 7094280 6395900 5856920 8324290 FALSE TRUE 5982939.48 8429290.907 5886982.921 7888259.936 5333453.509 5971953.772 6538211.796 6310173.422 5646130.593 9955275.247 0.600981824 0.846716007 0.591343059 0.792369848 0.535741441 0.599878318 0.656758516 0.633852231 0.567149622 1 23.24702977 -1.836173632 6.879267472 1.02610425 0.650283045 0.5610869 0.093574882 0.032427219 0.000772238 0.078422462 0.020140297 0.014582311 1.836173632 -0.375821205 LEDHEYKPLDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEDHEYKPLDPK 12 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;; 160.69 4.05E-05 462230000 1640510 701960 1085710 687230 1621200 1465700 1515840 1062710 1283080 538450 FALSE TRUE 1705278.602 822516.1695 1114004.495 823162.0428 1345629.003 1125313.388 1397024.5 1048466.111 1236902.201 643948.9683 2.648157984 1.277300237 1.729957729 1.278303225 2.089651617 1.747519514 2.169464614 1.628181987 1.920807801 1 19.29658684 -1.17662782 5.476559957 0.999975135 1.803206065 0.286251593 0.39181245 0.000108711 1.63E-05 0.346708955 0.081717562 0.066584352 1.17662782 0.803230929 LEDIDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDIDRK 7 1 Q92783;Q92783-2 Q92783 STAM Signal transducing adapter molecule 1 0 108.46 0.011621 165280000 131400 128170 131400 147610 162750 177450 165150 148390 151570 152370 FALSE TRUE 136587.7735 150182.2005 134824.3919 176806.8174 135085.8131 136239.9268 152205.1115 146401.0748 146115.0253 182223.9842 0.749559802 0.824162643 0.739882802 0.970271933 0.741317416 0.747650905 0.835263877 0.803412764 0.801842995 1 17.47535333 LEDLASLVYLNESSVLHTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDLASLVYLNESSVLHTLR 20 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;H0YEV9 Q92614 MYO18A Unconventional myosin-XVIIIa 0 120.31 3.81E-05 55389000 82583 100840 96962 141500 125070 170450 138830 110390 121410 101110 FALSE TRUE 85843.44061 118158.4856 99488.90938 169488.2777 103810.6461 130865.5707 127948.1418 108910.4026 117040.4778 120920.5686 0.709915952 0.977157872 0.8227625 1.401649691 0.858502794 1.082244089 1.058117269 0.900677228 0.967912069 1 16.88370014 5.001667695 1.441795293 1.016401854 0.410339016 0.264652665 0.151851286 3.112868158 3.627733675 0.039127127 3.244848042 100384.7392 -5.001667695 -0.606062837 LEDLDTCMMT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 267.77 7.38E-21 1277551000 1977280 1054740 1183050 1154317 1830320 1769190 1537710 1293790 1195960 717543 TRUE FALSE 2055344.541 1235883.39 1213881.255 1382637.457 1519202.86 1358322.435 1417180.272 1276448.861 1152917.633 858131.8127 2.395138498 1.440202277 1.414562701 1.61121804 1.770360728 1.582883206 1.651471547 1.487474118 1.343520443 1 19.71083974 -1.024921539 0.088858152 4.65E-17 2.339859423 0.486804438 0.243305738 65.97442443 1.15684796 23.88785811 8.573170578 0.094423145 1.024921539 2.339859423 LEDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 159.75 0.020987 345551000 668230 699460 694150 821750 810910 907790 973850 748430 677680 628200 FALSE TRUE 694612.2364 819586.814 712240.1193 984289.6973 673071.8078 696969.5302 897517.0923 738398.52 653290.4292 751283.7624 0.924567083 1.090915118 0.948030764 1.310143712 0.895895588 0.92770477 1.194644603 0.982849034 0.869565485 1 19.5189984 LEDLVCDVVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEDLVCDVVDR 11 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;; 157.24 7.14E-05 73657500 129579 109057 125839 175383 131583 165699 209142 145169 147543 89990 FALSE TRUE 134694.879 127786.6914 129118.4677 210073.2339 109216.5687 127217.9184 192748.9035 143223.247 142232.9563 107621.8175 1.251557371 1.187367899 1.199742493 1.951957686 1.014818102 1.182082977 1.790983538 1.330801229 1.321599649 1 16.71561105 LEDS(ph)EVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDSEVR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 LEDS(1)EVR 80.755 0.030475 106130000 170010 167970 178780 194750 204990 222770 213080 173780 159580 129020 TRUE FALSE 176722.1261 196817.5409 183439.1537 233270.9687 170145.873 171035.0436 196378.2328 171450.7633 153836.747 154298.9988 1.145322572 1.275559417 1.188855113 1.511811292 1.102702379 1.108465026 1.272712295 1.111159273 0.997004182 1 17.23536917 1.472799612 2.610444249 0.995735883 1.231377601 0.409334996 0.111394007 0.263513086 3.484317061 0.088609632 0.029822175 29.70295191 -1.472799612 0.235641718 LEDSEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDSEVR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087X2B6 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 94.407 0.033089 93252000 253300 179140 213900 162960 262820 282730 251160 207370 207820 153430 FALSE TRUE 263300.4796 209905.9015 219474.4097 195193.0016 218145.9503 217070.2423 231473.4229 204590.5443 200340.5988 183491.6709 1.43494513 1.143953295 1.196100121 1.063770364 1.188860231 1.182997796 1.261492807 1.114985456 1.091823938 1 17.48535505 8 0.037538437 0.514850697 2.209682567 0.427015069 0.086216645 954.7359261 2.733146389 35.06945238 106.1960275 99999999.99 -8 1.69483187 LEDTENWLYEDGEDQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEDTENWLYEDGEDQPK 17 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 296.22 8.81E-46 225597000 221330 128085 177111 125492 232595 217075 218105 169621 187807 119687 FALSE TRUE 230068.2793 150082.6024 181726.6582 150313.943 193058.585 166662.6211 201009.3602 167347.5079 181047.8628 143137.3761 1.607324974 1.048521403 1.269596126 1.050137617 1.348764315 1.164354312 1.404310779 1.169139134 1.264853861 1 17.12704091 -0.485791017 1.046653389 0.9935585 1.247951675 0.187000769 0.160225446 61.71954729 39.06149128 1.840024972 0.043271974 0.326745024 0.485791017 0.254393175 LEDTYFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEDTYFDR 8 0 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 169.97 0.00069305 590970000 610180 687250 649320 810860 567970 833940 876000 754310 650230 498380 FALSE TRUE 634270.3776 805279.8414 666241.8126 971245.6878 471426.6623 640270.0735 807336.831 744199.7083 626828.3493 596028.0189 1.064162015 1.351077157 1.117802841 1.629530252 0.790947149 1.074228146 1.35452832 1.24859853 1.051675977 1 19.18502063 1.132119962 5.001262646 1.005550609 1.210929515 0.103721797 0.210383844 0.44746205 16.57435396 0.192691108 0.049047639 13.55563797 -1.132119962 0.205378906 LEDVEDELIREEVILS(ph)PVPSVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEDVEDELIREEVILSPVPSVLK 23 1 Q4G0A6 Q4G0A6 FAM188B Protein FAM188B 1 LEDVEDELIREEVILS(0.998)PVPS(0.002)VLK;LEDVEDELIREEVILS(1)PVPSVLK;LEDVEDELIREEVILS(1)PVPSVLK;LEDVEDELIREEVILS(1)PVPSVLK 183.86 2.13E-17 77360000 103015 81823 113602 83045 141011 139531 135738 126193 142857 105202 TRUE FALSE 107082.1117 95875.46376 116562.5614 99471.05314 117042.0006 107127.0399 125098.5009 124501.5892 137715.6045 125814.3177 0.851112288 0.762039373 0.926464997 0.790617912 0.930275685 0.851469386 0.99431053 0.989566144 1.094594057 1 16.94093658 2.174138488 1.077377108 1.045054229 0.838493551 0.683024763 0.055881271 0.272712114 0.597950604 0.037131702 0.019822058 149.3270507 -2.174138488 -0.206560679 LEDVSKPPAYAYPATPSSHPT(ph)SPPPAS(ph)PPPTPGITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEDVSKPPAYAYPATPSSHPTSPPPASPPPTPGITR 36 1 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 2 LEDVSKPPAYAY(0.001)PAT(0.012)PS(0.075)S(0.079)HPT(0.456)S(0.385)PPPAS(0.988)PPPT(0.002)PGIT(0.002)R;LEDVSKPPAYAYPATPS(0.001)S(0.003)HPT(0.526)S(0.47)PPPAS(0.999)PPPT(0.001)PGITR 146.36 5.93E-12 509600000 97506 168745 199870 165261 208488 220595 217860 217292 197913 152881 TRUE FALSE 101355.6122 197725.6411 205078.7764 197949.1325 173049.2842 169365.1544 200783.5639 214379.5562 190790.1498 182835.1049 0.554355315 1.081442435 1.121659741 1.082664802 0.946477343 0.926327329 1.098167467 1.172529511 1.043509396 1 17.48018357 4.739965401 24.95975216 1.061001133 0.554355146 0.80582512 0.073257341 54.30533222 964780.6818 0.019731337 0.123486619 54949.70957 -4.739965401 -0.506645986 LEDYQANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEDYQANR 8 0 P52948-6;P52948-5;P52948;P52948-2;A0A3B3ITD8;P52948-4;P52948-3 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 99.755 0.015327 68511000 33956 56869 53156 58081 41242 82400 48618 50629 46521 74221 FALSE TRUE 35296.6091 66635.80837 54541.28903 69569.24845 34231.69957 63263.84878 44807.19412 49950.40107 44846.7183 88763.1839 0.3976492 0.75071449 0.614458457 0.783762427 0.385652002 0.712726223 0.504794805 0.562737825 0.505240082 1 16.4376738 -2.005138034 2.462939038 1.427121319 0.585126579 0.479452304 0.131259959 11702833.11 5060280.532 28322464.53 0.030233158 0.009882389 2.005138034 -0.84199474 LEEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LEEAEK 6 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;D6R904;A0A494C0G0;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753;H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;H0YL80;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6;H0YKX5;H0YKP3;P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;P67936-2;A0A2R8YHD2;Q8ND24;E9PN76;Q8ND24-2 P06753-2;P06753-3;J3KN67;H7BYY1;P09493-3;P67936;P67936-2;Q8ND24 TPM3;TPM1;TPM4;RNF214 Tropomyosin alpha-3 chain;Tropomyosin alpha-1 chain;Tropomyosin alpha-4 chain;RING finger protein 214 0 ;;;;; 138.62 0.028444 2566930000 4170940 2712640 3469090 2531660 4282150 4378250 4626750 3664180 3863310 2457430 FALSE TRUE 4335611.932 3178514.819 3559497.335 3032414.792 3554271.673 3361467.791 4264093.245 3615067.66 3724270.228 2938916.358 1.475241689 1.081526124 1.211159795 1.031813914 1.209381704 1.143777971 1.450906636 1.230068236 1.267225662 1 21.48685287 LEEAEKAADESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 200.55 9.94E-08 5407840000 4695550 3956100 4820650 2028080 8213800 6416300 3410570 4410260 5930160 5660750 FALSE TRUE 4880933.94 4635529.401 4946280.099 2429228.171 6817621.21 4926211.565 3143240.612 4351147.678 5716734.7 6769865.581 0.720979447 0.684729903 0.730631951 0.358829602 1.007054147 0.727667559 0.464298822 0.642722906 0.844438436 1 22.69069576 1.034112047 3.638639358 0.997603384 0.662571695 0.304491583 0.16245668 0.232849619 6.979985545 0.151778901 0.03924582 10.81712995 -1.034112047 -0.335031689 LEECVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LEECVR 6 0 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ;;;; 171.47 0.012612 1711417000 2138075 2155726 2043740 2110020 2304473 2698400 2240200 2180600 2037697 1885950 FALSE TRUE 2222487.852 2525955.171 2097001.543 2527375.658 1912759.503 2071737.495 2064607.27 2151372.624 1964360.683 2255465.794 0.985378656 1.119926171 0.929742118 1.120555969 0.848055203 0.918540862 0.915379553 0.953848482 0.870933485 1 21.10499398 3.234539368 24.99999821 0.91802292 1.036891215 0.449140286 0.065690922 89.03546173 553531.4495 0.017272606 0.021372996 1716.087264 -3.234539368 0.118868294 LEEDAFAREQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEEDAFAREQR 11 1 D6REZ4;A0A1B0GWD8;Q9C093-2;Q9C093;Q9C093-3 D6REZ4 SPEF2 Sperm flagellar protein 2 0 ; 59.542 0.059679 45694000 8649.2 140183 69861 135946 35469 122415 41455 90768 36601 154018 FALSE TRUE 8990.677095 164258.3398 71681.63505 162835.713 29439.99205 93985.97147 38205.64878 89551.40343 35283.73716 184194.8782 0.048810679 0.891763883 0.389161934 0.884040396 0.159830677 0.510252904 0.207419713 0.486177489 0.19155656 1 17.49087342 -1.133131612 5.042149398 1.000020736 0.435240716 0.284998765 0.275071342 6.77E-05 1.16E-05 0.242413254 0.057134924 0.073598403 1.133131612 -0.56478002 LEEEPSAS(ph)SPQYACDFNLFLEDSADNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPS(0.027)AS(0.522)S(0.428)PQY(0.022)ACDFNLFLEDSADNR 128.4 3.76E-05 27990000 20359 22826 22817 25812 25375 30634 28647 21829 24282 19550 TRUE FALSE 21162.78904 26746.18794 23411.62976 30917.53656 21061.76656 23519.71776 26401.57328 21536.41796 23408.09556 23380.44819 0.905148989 1.143955313 1.00133366 1.322367146 0.900828179 1.005956668 1.129215876 0.921129389 1.0011825 1 14.51301497 LEEEPSASS(ph)PQYACDFNLFLEDSADNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEEEPSASSPQYACDFNLFLEDSADNR 27 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 LEEEPS(0.006)AS(0.22)S(0.765)PQY(0.008)ACDFNLFLEDSADNR 172.2 2.50E-12 44284000 32293 31927 31310 35422 31418 45379 39969 35936 28150 25856 TRUE FALSE 33567.95258 37410.21389 32125.96432 42428.36588 26077.57958 34840.41498 36836.12534 35454.3367 27136.887 30921.98816 1.085569026 1.209825633 1.038935923 1.372109893 0.843334505 1.126719757 1.191259927 1.146573646 0.877591921 1 14.91634546 1.246763565 24.90804693 0.938795948 1.129395675 0.250603497 0.129975086 197.1363185 598613.1176 0.08457794 0.029717916 17.6507663 -1.246763565 0.190599726 LEEERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEEERER 7 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1;Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;Q9ULE0;Q9ULE0-2 P55196-5;P55196-1;Q6Y7W6;Q6Y7W6-4;Q9ULE0 MLLT4;GIGYF2;WWC3 Afadin;PERQ amino acid-rich with GYF domain-containing protein 2;Protein WWC3 0 ; 109.86 0.0063228 110001000 182225 180171 192405 163826 231744 231240 171876 182608 187520 202339 FALSE TRUE 189419.3837 211113.9677 197419.2324 196230.2938 192352.2377 177538.0145 158403.91 180160.4384 180771.1918 241983.453 0.782778249 0.872431421 0.815837736 0.81092443 0.794898309 0.733678325 0.654606371 0.744515529 0.747039475 1 17.88454887 3.003041165 2.902852482 0.749486424 0.824022996 0.009825076 0.087415494 0.525040007 9.017493667 0.025810244 0.029937117 1007.027116 -3.003041165 0.074536573 LEEHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEEHFK 6 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 137.44 0.012735 502350000 659310 502650 625030 558210 848180 807370 765520 583010 665770 477380 FALSE TRUE 685340.0679 588976.2274 641318.7953 668622.2719 704006.6666 619870.5533 705516.5421 575195.7046 641809.0678 570913.471 1.200427215 1.031638343 1.123320482 1.171144676 1.233123236 1.085752193 1.235767902 1.00750067 1.124179233 1 19.12291258 1.698132274 10.92143788 1.050354131 1.149495061 0.355109011 0.067824377 0.137345346 28.31048339 0.031071236 0.016888771 49.9036457 -1.698132274 0.09914093 LEEHQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEEHQAR 7 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 147.34 0.0021584 186080000 173940 183120 188610 175740 214820 243630 198470 186610 185730 187920 FALSE TRUE 180807.2855 214569.4355 193525.3315 210500.8475 178304.9731 187050.6247 182913.4028 184108.7982 179045.6136 224739.3261 0.804520013 0.95474806 0.861110225 0.936644472 0.793385725 0.832300372 0.813891391 0.819210422 0.796681278 1 17.77789307 3.234157171 24.99827715 0.830344143 0.891923327 0.085167611 0.067982665 189.0622525 1073304.382 0.017657946 0.021801886 1714.577698 -3.234157171 0.061579184 LEELHVIDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LEELHVIDVK 10 0 Q16531;F5GY55;F5H2L3;F5GWI0 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;; 148.56 2.49E-05 891137000 4538830 3020520 3924160 3151480 5306390 5199680 5164170 4075430 4422760 2570470 FALSE TRUE 4718026.513 3539270.814 4026426.833 3774833.338 4404411.723 3992133.122 4759388.861 4020805.527 4263585.732 3074104.382 1.534764578 1.151317709 1.309788587 1.227945726 1.432746314 1.298632911 1.548219667 1.307959987 1.386935901 1 21.55173472 -1.751487802 7.388666037 0.994893115 1.350210968 0.444023312 0.119170052 0.009460406 0.000318193 0.108885953 0.025486816 0.017721978 1.751487802 0.355317853 LEELTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEELTNR 7 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;; 160.03 0.0031676 589280000 1531330 1161370 1468860 1116940 1850780 1696370 1577150 1540180 1733620 1288700 FALSE TRUE 1591788.091 1360826.263 1507139.698 1337867.398 1536185.077 1302413.776 1453528.862 1519536.406 1671227.355 1541196.091 1.032826452 0.882967632 0.977902622 0.868070848 0.99674862 0.845066882 0.943117407 0.985946185 1.084370356 1 20.555619 1.544137285 3.238690087 1.041570109 0.931374809 0.343010696 0.058767014 0.206677566 4.811469619 0.036457017 0.014147445 35.00558054 -1.544137285 -0.110195301 LEEPPELNRQS(ph)PNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR 212.34 5.61E-10 40850070000 6377230 6986490 6805670 6286024 7456890 8119600 6751418 6946610 6508629 6892930 TRUE FALSE 6629007.965 8186365.31 6983031.351 7529380.785 6189370.501 6233945.954 6222224.216 6853502.055 6274384.714 8243467.66 0.804152844 0.993073018 0.847098774 0.913375426 0.750821227 0.756228593 0.754806651 0.831385812 0.761134146 1 22.97481991 3.248277137 24.99046469 0.796819652 0.893805156 0.172366041 0.083507634 275.1929799 707780.0251 0.021351283 0.028555576 1771.23888 -3.248277137 0.096985504 LEEPTPAPSTSYS(ph)PQADSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 LEEPTPAPSTS(0.002)YS(0.998)PQADSLR;LEEPTPAPS(0.001)T(0.001)S(0.001)YS(0.996)PQADS(0.002)LR;LEEPTPAPSTS(0.081)YS(0.918)PQADSLR;LEEPTPAPSTSYS(1)PQADSLR 332.91 7.13E-80 1857780000 440696 584166 554826 524526 596038 662831 576234 573611 590126 593328 TRUE FALSE 458095.0184 684491.9663 569285.2214 628275.6772 494723.6737 508898.5456 531067.2734 565922.6828 568887.4805 709579.2616 0.645586819 0.96464483 0.802285597 0.88542001 0.697207064 0.71718351 0.748425584 0.797546819 0.801725066 1 19.43660432 -2.007917453 7.181972004 1.241804784 0.787870065 0.35352492 0.087335832 0.041188244 4.54E-05 0.010300279 0.019125765 0.009819346 2.007917453 -0.453934719 LEEQLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LEEQLGR 7 0 Q9BR76;A9Z1Z3-3;A9Z1Z3 Q9BR76 CORO1B;FER1L4 Coronin-1B;Fer-1-like protein 4 0 ;;;; 244.84 5.93E-08 1737050000 1407910 1837870 1772080 1674100 1949330 2056100 1697710 1749700 1680010 1809530 FALSE TRUE 1463495.374 2153509.876 1818261.861 2005231.983 1617983.583 1578601.935 1564639.054 1726248.133 1619546.768 2164072.758 0.676269025 0.99511898 0.840203664 0.926601001 0.74765674 0.729458808 0.723006677 0.797684887 0.748379075 1 21.04531757 5.030522654 16.21870569 0.819954969 0.227078224 0.166393037 0.101644801 7527762.02 109936845.8 0.024175771 122808979.8 107280.9606 -5.030522654 -0.592876745 LEEQRPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 179.37 0.00022316 14254722000 4963849 5710512 5452147 5378528 5944201 6642090 5884854 5558218 5443756 5474687 FALSE TRUE 5159825.591 6691248.014 5594234.43 6442384.785 4933807.837 5099565.259 5423583.766 5483719.179 5247836.285 6547347.098 0.788078822 1.021978507 0.854427655 0.983968726 0.753558313 0.778875044 0.828363562 0.837548261 0.801521014 1 22.64247903 3.239206257 24.99998473 0.823404078 0.915840514 0.160194015 0.086459385 25.5643347 989854.5389 0.022437901 0.028652387 1734.627621 -3.239206257 0.092436435 LEESHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEESHNR 7 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;; 138.83 0.002748 119280000 224734 229736 262604 221614 302361 314779 264292 258180 264590 263854 FALSE TRUE 233606.6719 269191.3709 269447.676 265448.5877 250965.7852 241676.3478 243576.1024 254719.5194 255067.4576 315551.1395 0.740313194 0.853083184 0.85389543 0.841222086 0.795325238 0.765886468 0.771906902 0.807221041 0.808323678 1 18.26751431 0.472251441 3.338539962 0.999999945 0.805247141 0.72756309 0.035956309 19.63939103 123.1895829 0.036069543 0.009332691 2.96654842 -0.472251441 -0.194752805 LEETDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEETDRR 7 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RR66;A0A0U1RQL2;A0A0U1RQJ6;A0A0U1RRJ7 P47897 QARS Glutamine--tRNA ligase 0 ;; 166.05 0.0018244 3491210000 2764970 2957686 3007929 2722777 3127660 3498120 3034549 2959322 2853962 2967051 FALSE TRUE 2874133.151 3465645.563 3086318.101 3261334.164 2596021.47 2685734.645 2796693.12 2919657.129 2751248.465 3548387.836 0.80998281 0.976681728 0.869780375 0.919103073 0.731605898 0.756888697 0.788158806 0.822812292 0.775351679 1 21.75873227 3.257519498 24.99996194 0.800936797 0.898079028 0.193096543 0.079279096 316.8180876 417766.6229 0.020275587 0.027408241 1809.337139 -3.257519498 0.097142231 LEEVKDKDGKPLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEEVKDKDGKPLLPK 15 3 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 0 114.69 0.00025682 1550600000 4782500 1269500 2438300 1082400 4391800 2929500 3310900 2394900 3084200 908810 FALSE TRUE 4971316.793 1487526.75 2501844.101 1296495.489 3645283.405 2249168.022 3051383.007 2362800.283 2973200.244 1086873.919 4.573959044 1.368628618 2.301871502 1.192866501 3.353915611 2.069391842 2.807485719 2.173941467 2.735552111 1 20.05175316 -0.650064257 6.602840393 0.999999998 2.435155377 0.189591726 0.924554531 2.41E-08 5.47E-09 0.80767426 0.190370649 0.223838993 0.650064257 1.435155379 LEEVMQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LEEVMQELR 9 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;;;;; 158.87 0.00015466 308005000 334961 386183 392588 438587 436373 489259 478939 414172 380809 359373 FALSE TRUE 348185.5189 452506.9262 402819.1658 525338.1995 362198.4733 375636.012 441398.5097 408620.7018 367103.7585 429785.2587 0.810138347 1.052867489 0.937256822 1.222327171 0.842742895 0.874008599 1.027021055 0.950755508 0.854156235 1 18.71325647 LEEWLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEEWLGR 7 0 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ; 132.09 0.0079152 236463000 191179 204870 204858 213630 240810 248930 228900 215250 219180 200033 FALSE TRUE 198726.8945 240054.8288 210196.7678 255885.3764 199877.2022 191119.7801 210958.2199 212364.9258 211291.7546 239225.6365 0.830709022 1.003466152 0.878654858 1.069640278 0.835517485 0.798910112 0.881837846 0.887718093 0.883232072 1 17.86801248 5.042911249 15.32774843 0.907663788 0.480797002 0.085270469 0.079671915 1137802.737 11673845.22 0.018852694 13647843.71 110385.3017 -5.042911249 -0.426866787 LEFLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEFLHK 6 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 121.68 0.019546 790440000 1917470 1595110 1780240 1701310 2161500 2291300 2269200 1849020 1944700 1418580 FALSE TRUE 1993173.196 1869057.734 1826634.517 2037824.04 1794089.002 1759180.3 2091334.175 1824236.911 1874710.627 1696523.591 1.174857342 1.101698641 1.076692671 1.201176365 1.057509021 1.036932413 1.232717415 1.075279425 1.105030686 1 20.69415006 0.628417529 1.521533103 1.000239009 1.119439933 0.257533785 0.060951222 1.989345634 6.376251219 0.055399417 0.016029367 4.250279874 -0.628417529 0.119200924 LEFQQQLGEAPSDAS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEFQQQLGEAPSDASP 16 0 Q9BUW7 Q9BUW7 C9orf16 UPF0184 protein C9orf16 1 LEFQQQLGEAPSDAS(1)P;LEFQQQLGEAPS(0.001)DAS(0.999)P 229.16 3.61E-15 151924000 226590 253470 246940 247870 274560 333100 265170 278270 271080 280570 TRUE FALSE 235535.9482 297001.5008 253375.4593 296897.9462 227890.3893 255742.5732 244385.2825 274540.2458 261323.8838 335542.3197 0.701956011 0.885138724 0.755122214 0.884830106 0.679170334 0.762176805 0.72832924 0.818198569 0.778810506 1 18.35613521 -0.024377083 1.150553546 1.001156916 0.778341004 0.508042153 0.065802389 8.997262011 9.170877325 0.097546106 0.018006254 0.945415934 0.024377083 -0.222815912 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEGDSDDLLEDSDSEEHSR 19 0 Q9NR09;A0A3B3IUB9 Q9NR09 BIRC6 Baculoviral IAP repeat-containing protein 6 1 LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR;LEGDSDDLLEDS(1)DSEEHSR 329.43 2.05E-75 3278260000 1507310 1564130 1798760 1671200 1891250 2094260 2050070 1771620 1799910 1373460 TRUE FALSE 1566819.763 1832757.16 1845637.163 2001758.372 1569776.001 1607899.854 1889380.157 1747874.332 1735131.591 1642563.191 0.953887054 1.115790961 1.123632366 1.218679673 0.955686825 0.978896802 1.1502633 1.064113905 1.056356066 1 20.64751744 3.223784407 24.99974405 1.044569453 1.105385296 0.146790072 0.07881634 536.5014051 907700.6495 0.023612709 0.028327815 1674.111604 -3.223784407 0.060815844 LEGELHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEGELHK 7 0 Q6P9F0-2;Q6P9F0 Q6P9F0-2 CCDC62 Coiled-coil domain-containing protein 62 0 84.244 0.021688 158360000 199050 156570 202830 151280 261710 266480 218560 200610 235470 194260 FALSE TRUE 206908.6477 183459.6796 208115.9164 181202.7325 217224.6277 204594.0585 201428.6961 197921.1511 226995.4807 232321.5277 0.890613323 0.789680067 0.895809865 0.779965311 0.935017215 0.880650453 0.867025532 0.851927727 0.977074673 1 17.82576332 1.192964411 5.07774257 0.995773638 0.860148886 0.566493012 0.044595101 0.131107183 7.189010166 0.038406868 0.010177809 15.59424708 -1.192964411 -0.135624753 LEGELQAPDLELS(ph)LPAIHVEGLDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEGELQAPDLELSLPAIHVEGLDIK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LEGELQAPDLELS(1)LPAIHVEGLDIK 60.029 0.049149 16631000 19835 15999 17119 14743 25572 23124 18556 17101 19762 15635 TRUE FALSE 20618.10112 18746.7038 17565.1352 17659.1214 21225.28057 17753.80145 17101.53223 16871.78907 19050.76948 18698.3789 1.102667842 1.002584443 0.939393479 0.944419914 1.135140147 0.949483458 0.914599727 0.902312931 1.01884605 1 14.19062558 2.517285231 24.9988605 0.9427775 1.017181952 0.187592892 0.06653768 795.6297665 495214.7765 0.021887641 0.02063323 329.0676812 -2.517285231 0.074404452 LEGFHTQISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEGFHTQISK 10 0 Q06323;Q06323-3;Q06323-2;H0YKK6;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;; 150.04 2.23E-05 8934360000 8619320 7325010 8769000 7686040 10744400 10843030 9956950 8598540 8976910 6756790 FALSE TRUE 8959617.409 8583023.487 8997527.344 9206315.771 8918070.726 8324900.61 9176498.241 8483290.636 8653832.763 8080653.634 1.108773846 1.062169458 1.11346529 1.139303352 1.103632346 1.030226141 1.135613362 1.049827281 1.070932273 1 22.94604056 0.662889574 0.520746191 0.996219908 1.102073982 0.456626163 0.032370911 1.339834415 0.744185433 0.042915197 0.016139299 4.601395608 -0.662889574 0.105854074 LEGGRQDS(ph)EDEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEGGRQDSEDEEER 14 1 A0A3B3ISZ4;Q9BYE7-3;Q9BYE7 A0A3B3ISZ4 PCGF6 Polycomb group RING finger protein 6 1 LEGGRQDS(1)EDEEER;LEGGRQDS(1)EDEEER 157.88 3.13E-06 643450000 332600 363680 407290 330490 404950 476580 383290 415490 365470 357670 TRUE FALSE 345731.3048 426139.211 417904.312 395859.9356 336116.7436 365901.5176 353246.7283 409921.0362 352316.8061 427748.5885 0.808258201 0.996237562 0.976985835 0.92545001 0.78578107 0.855412566 0.825827923 0.958322358 0.82365393 1 18.70640357 5.057206625 16.45771367 0.900713801 0.00021116 0.129822234 0.074524117 10110139.58 63866215.03 0.018062687 302785228 114079.2416 -5.057206625 -0.900502642 LEGLTQDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEGLTQDLR 9 0 Q01094 Q01094 E2F1 Transcription factor E2F1 0 ;; 75.213 0.079569 84086000 140013 157079 154532 143992 194490 188441 165247 153801 148716 175588 FALSE TRUE 145540.8214 184056.0963 158559.2309 172473.1878 161430.6593 144678.4336 152294.5083 151739.5492 143363.7402 209991.1068 0.693080881 0.87649472 0.755075933 0.821335677 0.768749981 0.688974099 0.725242658 0.722599883 0.682713389 1 17.6799687 -1.224506217 5.059742034 1.000029769 0.750216549 0.624133727 0.058591282 1.99E-05 3.05E-06 0.057319265 0.013508672 0.059633978 1.224506217 -0.24981322 LEGPVS(ph)PDVEPGKEETEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEGPVSPDVEPGKEETEESK 20 1 O14686;O14686-3;A0A3B3ISC8 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LEGPVS(1)PDVEPGKEETEESK;LEGPVS(1)PDVEPGKEETEESK;LEGPVS(1)PDVEPGKEETEESK 208.17 3.60E-22 756270000 1966710 623140 974740 626780 1491590 1655850 1455850 997620 1179200 412627 TRUE FALSE 2044357.229 730159.4476 1000142.525 750755.2132 1238050.065 1271303.932 1341736.673 984248.5357 1136760.822 493473.3604 4.142791472 1.479632957 2.026740662 1.521369284 2.508848833 2.576236194 2.718964752 1.994532258 2.303591062 1 18.91261268 0.119071623 1.085066469 0.993847569 2.32390893 0.245358424 0.715068315 9.029692475 9.739827799 0.801836743 0.201377461 1.315441756 -0.119071623 1.330061361 LEGRPDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEGRPDGR 8 1 O95248;O95248-5;O95248-4;H0Y5W8 O95248 SBF1 Myotubularin-related protein 5 0 76.827 0.029027 0 27064 36792 31621 34023 38218 39178 33657 31564 29404 29132 FALSE TRUE 28132.50762 43110.7398 32445.06924 40752.64785 31721.71801 30079.50325 31018.87639 31140.93621 28345.75578 34839.85763 0.807480556 1.237397129 0.931262968 1.169713386 0.910500793 0.8633647 0.8903273 0.893830754 0.813601367 1 15.08845111 3.069175035 10.71252756 0.886363621 1.04320052 0.253560779 0.118583909 0.549202176 82.00666353 0.031000026 0.03706569 1172.667895 -3.069175035 0.156836899 LEGVDGGQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 162.52 2.63E-05 1502510000 1652500 1356890 1595150 1279980 1909810 1914310 1654290 1496140 1578730 1243880 TRUE FALSE 1717741.976 1589925.302 1636720.919 1533156.224 1585181.178 1469740.514 1524622.427 1476086.69 1521911.816 1487594.47 1.154711186 1.068789468 1.100246708 1.030627805 1.065600343 0.987998103 1.024891163 0.992264169 1.023069019 1 20.50454986 7.999990988 0.313165155 0.995090016 2.424840629 0.794747073 0.022754541 21.37275349 0.306204166 0.019854543 17.36869888 99997925.02 -7.999990988 1.429750613 LEGVEGVAHIIDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEGVEGVAHIIDPK 14 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 114.74 0.00045984 497230000 1580680 1187370 1617350 1245010 2085460 2036340 1873130 1644860 1842420 1115820 FALSE TRUE 1643086.467 1391291.561 1659499.47 1491269.262 1730974.254 1563430.896 1726309.176 1622813.342 1776111.664 1334443.565 1.231289587 1.042600524 1.243589098 1.117521415 1.297150587 1.171597613 1.293654689 1.216097394 1.330975479 1 20.34780686 4.194855133 24.99995434 1.219291827 1.136943742 0.066826996 0.101581651 254.5560501 145608.1602 0.022856469 0.049376097 15662.28538 -4.194855133 -0.082348085 LEGVLAEVAQHYQDTLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 197.45 1.84E-15 6013300000 39650485 3414370 4511888 2637144 4576943 19150070 7169726 6742115 3224475 3620820 FALSE TRUE 41215916.76 4000761.487 4629471.508 3158763.212 3798955.864 14702756.46 6607744.142 6651747.976 3108426.775 4330250.354 9.51813715 0.923909973 1.069100197 0.729464339 0.877306288 3.395359451 1.52594968 1.536111641 0.717839968 1 22.04601901 4.740458714 24.98331142 1.368398675 9.518139929 0.914656396 0.752131948 44.85626399 590366.5304 0.185173364 1.205086102 55012.16211 -4.740458714 8.149741254 LEGYWGEAQSLCQAVDEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEGYWGEAQSLCQAVDEHLR 20 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 197.84 5.34E-22 0 28460 36317 33807 36305 36415 44222 40047 32047 35981 30541 FALSE TRUE 29583.62278 42554.16224 34688.03819 43486.02064 30225.19131 33952.11069 36908.0115 31617.46238 34686.05084 36524.92421 0.80995713 1.165071884 0.949708697 1.190584829 0.827522355 0.929560059 1.01048838 0.865640739 0.949654287 1 15.15659366 3.216759656 24.99943168 0.925363309 1.03291074 0.154814653 0.112036996 383.6205205 439901.0987 0.029967876 0.035846063 1647.25053 -3.216759656 0.107547431 LEHALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEHALEK 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;; 124.08 0.0041813 1588540000 3619380 2974930 3481460 2766790 4979400 4610520 3929760 3319750 3601120 2970980 FALSE TRUE 3762275.917 3485851.086 3572189.708 3314052.804 4133003.367 3539796.603 3621735.143 3275254.181 3471516.395 3553086.648 1.058875364 0.981076858 1.005376469 0.932725017 1.16321491 0.996259578 1.019320805 0.921805322 0.977042425 1 21.76064144 1.764047052 25 0.958891624 1.021123105 0.154287555 0.0594116 26.28476901 25800.36417 0.026892505 0.014914397 58.0827342 -1.764047052 0.062231481 LEHDVNIQFPDKDDGNQPQDQITITGYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEHDVNIQFPDKDDGNQPQDQITITGYEK 29 1 Q00341;A0A024R4E5;Q00341-2 Q00341 HDLBP Vigilin 0 ; 143.54 4.24E-08 798820000 661470 372330 536200 357780 670030 651160 649790 538070 599420 307632 FALSE TRUE 687585.3464 436274.7812 550173.8125 428547.8161 556138.5399 499937.9584 598857.7619 530858.0518 577846.9913 367906.6004 1.868912777 1.185830264 1.495417076 1.164827746 1.511629689 1.358871947 1.627744001 1.44291527 1.570635022 1 18.48898003 -1.884899524 2.557597333 0.768072523 1.456828676 0.338543452 0.196204803 17811211.64 9462761.747 24907168.78 0.043527315 0.013034683 1.884899524 0.688756152 LEHEVDLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEHEVDLCR 9 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;A0A087X1S3 Q7Z6Z7-2;A0A087X1S3 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 105.4 0.0031047 72831000 116828 158112 161739 158237 183813 199974 163987 162522 167667 153938 FALSE TRUE 121440.4597 185266.5061 165954.0512 189535.8063 152568.5319 153533.0691 151133.2704 160343.6584 161632.6974 184099.2038 0.659646849 1.006340616 0.90143818 1.029530831 0.828729993 0.833969219 0.820933862 0.870963345 0.877965217 1 17.49012386 0.871271974 12.2582601 1 0.87474809 0.136629826 0.097440275 446.1186132 42487.53625 0.089203399 0.022304197 7.434845937 -0.871271974 -0.125251911 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LEHEVFDAGEVFGIMQVEEVEEEEDEAAR 29 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ;;;;;;;;; 325.39 3.29E-93 681376000 199057.5 247410.5 266096.5 272226.2 275208.5 299886.3 276032.9 263284.1 247422.6 239100.6 FALSE TRUE 206916.4438 289901.3288 273031.1934 326071.7298 228428.6575 230242.2516 254396.72 259755.2073 238517.909 285947.7847 0.723616181 1.013826105 0.954828846 1.140319133 0.798847446 0.805189842 0.889661447 0.908400838 0.834130991 1 18.1253922 LEHEYIHNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEHEYIHNFK 10 0 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2;M0QX52;K7ENB3;C9JB30;Q9UPY8;Q9UPY8-2 Q15555-4;C9JB30;Q9UPY8-2 MAPRE2;MAPRE3 Microtubule-associated protein RP/EB family member 2;Microtubule-associated protein RP/EB family member 3 0 ; 171.85 2.25E-06 385520000 259810 203389 246380 215840 320510 303700 318230 278220 281420 182555 FALSE TRUE 270067.4994 238319.4786 252800.8652 258532.5078 266029.8247 233170.2776 293286.3011 274490.916 271291.7492 218323.157 1.237008035 1.091590475 1.157920528 1.184173549 1.218514006 1.068005249 1.343358648 1.257268902 1.242615547 1 17.73610564 2.244029652 24.99951489 1.238898629 1.160174295 0.033326354 0.095615182 257.807164 1178466.119 0.031440986 0.025607284 175.4000253 -2.244029652 -0.078724335 LEHEYIQNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEHEYIQNFK 10 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;; 137.98 7.69E-05 5798900000 8265100 6889500 7974500 6721700 9954700 10094000 9045900 8299300 8766000 6975400 FALSE TRUE 8591412.53 8072718.032 8182322.021 8051232.198 8262603.65 7749821.476 8336858.721 8188061.458 8450513.372 8342096.078 1.029886548 0.96770859 0.980847253 0.965132998 0.990470929 0.929001705 0.999372177 0.981535262 1.012996409 1 22.9919785 1.449223651 2.151588771 1.005786172 0.977580046 0.133978492 0.024821128 0.547724134 4.748772165 0.020019411 0.006416076 28.13349263 -1.449223651 -0.028206126 LEHGDGGILDLDDILCDVADDKDR ddPTM_MDA-MB-175_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 ;; 158.02 1.86E-10 67060000 144759 102403 99240 85260 146010 158929 122199 108454 120857 80976 FALSE TRUE 150474.1971 119989.9187 101826.2759 102124.1735 121191.2724 122020.1483 112620.7231 107000.3515 116507.3802 96841.69682 1.553816197 1.23903156 1.051471414 1.054547544 1.251436895 1.259995976 1.162936284 1.104899594 1.203070413 1 16.56334074 4.694708447 3.243004375 1.144497249 1.59259109 0.695109027 0.082859963 0.163145795 2.809896306 0.020542667 0.17230889 49511.76935 -4.694708447 0.448093841 LEHLSS(ph)LPTQMDYKGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEHLSSLPTQMDYKGQK 17 1 A0A5F9YFS9 A0A5F9YFS9 1 LEHLS(0.004)S(0.97)LPT(0.024)QMDY(0.001)KGQK 66.874 0.050661 198900000 261540 70996 142070 75887 194970 166440 213770 87954 165420 81563 TRUE FALSE 271865.8012 83189.01073 145772.4609 90897.2221 161829.069 127786.8324 197014.1488 86775.12049 159466.5665 97543.70823 2.787117756 0.852838304 1.494432225 0.931861457 1.659041592 1.310046898 2.019752503 0.889602436 1.634821655 1 16.5737612 4.750208326 24.92257106 1.324300246 2.787118662 0.584928415 0.373054261 1150.150583 2460926.421 0.081987655 1.328641104 56261.11384 -4.750208326 1.462818417 LEHQGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEHQGIR 7 0 O75436;S4R3Q6;O75436-2 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 114.78 0.0058274 197838000 187781 202154 195715 210949 246680 262950 235630 199884 197634 208898 FALSE TRUE 195194.7389 236872.377 200815.4937 252674.0826 204749.4217 201883.8475 217160.7049 197204.8819 190521.1909 249827.5635 0.781317866 0.948143486 0.803816404 1.011393935 0.819562977 0.808092769 0.869242376 0.789363988 0.762610771 1 17.93057313 LEHSSSVQEDSES(ph)PSPEDIPDYLLQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEHSSSVQEDSESPSPEDIPDYLLQYR 27 0 Q9HB65-2;Q9HB65 Q9HB65-2 ELL3 RNA polymerase II elongation factor ELL3 1 LEHS(0.002)S(0.002)S(0.002)VQEDS(0.005)ES(0.941)PS(0.049)PEDIPDYLLQYR 186.85 6.70E-18 71805000 4496.9 22288 20847 23779 16227 30649 14159 24777 17475 27137 TRUE FALSE 4674.441084 26115.79062 21390.28995 28482.41523 13468.74034 23531.23424 13049.18058 24444.90484 16846.07816 32453.97558 0.144032927 0.804702356 0.659096137 0.877624843 0.415010491 0.725064767 0.402082652 0.753217577 0.519075949 1 14.9861076 -2.257620564 2.182158333 2.432831216 0.607427485 0.248188057 0.212466057 6121478.058 1048795.806 43191914.75 0.048465374 0.0055256 2.257620564 -1.825403731 LEHSSSVQEDSESPS(ph)PEDIPDYLLQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEHSSSVQEDSESPSPEDIPDYLLQYR 27 0 Q9HB65-2;Q9HB65 Q9HB65-2 ELL3 RNA polymerase II elongation factor ELL3 1 LEHSSSVQEDS(0.01)ES(0.009)PS(0.98)PEDIPDYLLQYR 74.45 0.011161 36126000 5341.8 9459 13158 13771 11022 16850 12181 12881 9012.1 10134 TRUE FALSE 5552.698389 11083.50967 13500.90829 16494.8627 9148.484377 12936.84286 11226.22139 12708.35126 8687.756281 12119.56327 0.458159941 0.914513949 1.113976468 1.361011311 0.754852644 1.067434739 0.926289268 1.048581618 0.716837405 1 13.56505009 4.717910086 3.580411466 1.005811497 0.406480048 0.465799581 0.172355205 0.218551482 5.080753533 0.04067412 0.340802395 52228.80457 -4.717910086 -0.599331449 LEIEPEWAYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEIEPEWAYGK 11 0 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 199.67 1.15E-07 91130000 288380 242610 278300 265830 311470 340500 355260 309950 312090 210150 FALSE TRUE 299765.4651 284276.3803 285552.7266 318410.3806 258526.4407 261424.0353 327413.7929 305795.6272 300857.9419 251324.8689 1.192740959 1.131111225 1.136189697 1.266927471 1.028654433 1.040183713 1.302751273 1.216734454 1.19708783 1 17.93919391 2.241471218 24.99842513 1.20306659 1.134104804 0.030309664 0.096140512 177.9408731 1528308.986 0.033577892 0.026962599 174.3697795 -2.241471218 -0.068961786 LEIFHPFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEIFHPFFK 9 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 76.827 0.034331 113600000 69202 78364 80280 68479 107220 101500 78295 78942 84901 79147 FALSE TRUE 71934.1484 91822.40741 82372.16275 82023.94181 88994.7827 77928.16325 72158.03331 77883.91161 81845.42959 94654.33929 0.759966727 0.970081331 0.870241802 0.866562932 0.940208165 0.823292031 0.762332016 0.822824523 0.864676994 1 16.53038103 2.691193464 24.85848465 0.834440877 0.884892812 0 0.07762539 932.4778146 489367.289 0.023593186 0.0222439 491.1266088 -2.691193464 0.050451935 LEILSGDHEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEILSGDHEQR 11 0 Q4G0J3;Q4G0J3-3;H0YA82;Q4G0J3-2 Q4G0J3 LARP7 La-related protein 7 0 196.16 6.14E-08 218470000 78837 117580 116240 110660 117920 144540 109170 121060 102980 110090 FALSE TRUE 81949.54564 137773.4504 119269.3099 132548.2177 97876.00052 110972.7755 100612.9701 119437.3887 99273.76992 131660.0277 0.622432997 1.046433399 0.905888537 1.006746087 0.743399513 0.842873706 0.764187673 0.90716515 0.754016019 1 17.00645788 4.767357862 24.13778122 0.877212714 0.622432377 0.360962865 0.104521739 7968.742291 6679199.412 0.024301156 2.485530731 58527.21541 -4.767357862 -0.254780338 LEIS(ph)PDSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 LEIS(1)PDS(0.042)S(0.958)PER 130.65 0.00032114 179320000 433930 491690 454640 401870 514520 509990 460780 423300 470630 438200 TRUE FALSE 451061.8915 576133.9327 466488.2919 481358.6865 427062.0742 391552.5515 424662.8596 417626.3559 453692.1182 524056.9002 0.860711673 1.099372859 0.890148172 0.918523707 0.814915468 0.747156561 0.810337312 0.796910327 0.865730645 1 18.99936394 3.563047521 1.907661459 0.821730068 0.972040222 0.237329005 0.086596937 0.36122418 2.59475648 0.024107267 0.043565494 3656.347977 -3.563047521 0.150310154 LEKEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEKEEAK 7 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6;K7EQK3 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 59.8 0.092434 271470000 643740 307710 463570 300290 738930 612020 618530 494370 558470 333160 FALSE TRUE 669155.3523 360556.7988 475651.015 359686.4657 613326.9425 469887.6303 570048.0024 487743.7788 538370.7738 398436.3233 1.679453687 0.90492954 1.193794309 0.902745168 1.539334912 1.1793293 1.430712937 1.224144864 1.35120907 1 18.60398965 3.236389456 24.99988079 1.29817969 1.152963751 0.050064595 0.242907383 152.3049303 1753727.077 0.064040326 0.080192358 1723.413363 -3.236389456 -0.145215939 LEKHELIEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 142.08 2.19E-05 3445660000 3160860 2543240 3259520 2723550 3962720 3786360 3635700 3152020 3264890 2407510 FALSE TRUE 3285653.194 2980021.686 3344465.769 3262260.061 3289138.27 2907035.273 3350724.334 3109772.328 3147387.247 2879215.49 1.141162655 1.035011689 1.161589253 1.133037827 1.142373081 1.009662279 1.163762958 1.08007627 1.093140565 1 21.45724434 -0.798779146 0.399011301 0.962371352 1.113585202 0.308843149 0.0492591 14.52893839 1.842315359 0.706128242 0.030819477 0.158935479 0.798779146 0.15121385 LEKHELIEFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEKHELIEFRR 11 2 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 133.32 9.86E-05 150340000 186350 152000 187320 144090 289100 231190 172430 173590 215880 238460 FALSE TRUE 193707.2419 178104.8176 192201.7131 172590.5719 239958.8853 177499.6262 158914.486 171263.31 208110.521 285181.6714 0.679241555 0.624531081 0.673962363 0.605195176 0.84142464 0.622408955 0.557239479 0.600541084 0.729747182 1 18.12152174 0.89491947 4.901037757 0.999971013 0.647983252 0.676144968 0.072552892 0.431620709 19.25564073 0.071700435 0.018139909 7.850900446 -0.89491947 -0.351987761 LEKPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LEKPAK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 76.847 0.067469 90861700000 38545800 25256540 32575640 27008470 42388260 40281250 46829040 33964830 36340160 19272950 FALSE TRUE 40067617.95 29594154.28 33424587.94 32350664.75 35183118.71 30926540.16 43158457.48 33509587.01 35032284.74 23049115.55 1.738358154 1.283960515 1.450146227 1.403553411 1.526441161 1.341766893 1.87245612 1.453833963 1.519897137 1 24.45820806 LEKPAKYDDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEKPAKYDDIK 11 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 142.57 0.00014935 28980300000 32775900 14474800 22328000 12301700 34402400 27156900 29815500 22002400 26607600 10799700 FALSE TRUE 34069917.84 16960734.3 22909886.02 14734939.54 28554692.34 20850121.54 27478483.2 21707493.82 25649997.67 12915694.44 2.637869608 1.31318795 1.773802108 1.140855384 2.210852267 1.614324467 2.127526578 1.680706672 1.985955752 1 23.62262188 -1.460318175 6.426663986 0.999726938 1.802814474 0.262043239 0.41617245 0.0014732 0.000123712 0.364584919 0.085905683 0.034648292 1.460318175 0.803087536 LEKPAKYDDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LEKPAKYDDIKK 12 3 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 178.84 0.00026008 74493110000 70500100 22759800 43087000 18478420 61529000 41708250 45334810 35969290 44418850 16709880 FALSE TRUE 73283498.39 26668618.6 44209882.62 22133396.32 51070322.56 32022141.03 41781349.13 35487180.5 42820224.27 19983861.06 3.667134103 1.334507808 2.212279323 1.107563561 2.555578345 1.602400104 2.090754585 1.775791995 2.142740292 1 24.25233202 8 0.05364912 2.88E-13 5.680831241 0.227588242 0.656699511 747.7380539 3.015536046 71.11119685 343.1915653 100000000 -8 5.680831241 LEKPETQSS(ph)PITVQSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEKPETQSSPITVQSSK 17 1 Q96CB8;A0A087WXN4;E9PGI3 Q96CB8 INTS12 Integrator complex subunit 12 1 LEKPET(0.001)QS(0.079)S(0.91)PIT(0.011)VQSSK;LEKPETQS(0.02)S(0.979)PITVQSSK 140.48 3.99E-07 477620000 806990 517070 671250 547620 889250 841870 846120 651030 765580 484460 TRUE FALSE 838850.5883 605872.7503 688743.3264 655937.6015 738095.6026 646358.4512 779798.9035 642304.0077 738026.9253 579380.6615 1.447840158 1.045724841 1.188757879 1.132135822 1.273938969 1.115602391 1.345918073 1.108604499 1.273820434 1 19.14415201 -1.318598116 3.439123238 0.999075868 1.203988263 0.228320013 0.116931443 3435571.231 1988873.92 22280.82278 0.02431729 0.048017759 1.318598116 0.204912394 LEKVPDS(ph)PENELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEKVPDSPENELK 13 1 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 LEKVPDS(1)PENELK;LEKVPDS(1)PENELK 158.45 2.86E-05 593950000 1308290 446740 649230 425690 1047530 1027240 988060 650260 774030 365210 TRUE FALSE 1359942.299 523464.1198 666149.4671 509890.2114 869471.2248 788679.078 910613.2754 641544.3283 746172.8115 436765.9071 3.113664041 1.198500412 1.525186504 1.167422189 1.990703053 1.805724909 2.084900082 1.468851661 1.708404432 1 18.73650072 -2.382408362 0.272892203 2.26E-17 1.820610767 0.176464989 0.525331455 78.73860695 2.712938148 48.81255448 0.638497151 0.00414564 2.382408362 1.820610767 LELKAS(ph)PNVEAPQPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LELKASPNVEAPQPHR 16 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR;LELKAS(1)PNVEAPQPHR 183.54 1.19E-09 1320380000 1257950 827050 1094140 950400 1350890 1463320 1414470 1147960 1227450 751210 TRUE FALSE 1307614.837 969089.4039 1122654.187 1138386.283 1121266.2 1123486.107 1303600.145 1132573.474 1183274.314 898395.2167 1.455500667 1.078689407 1.249621733 1.267133064 1.24807677 1.250547739 1.45103193 1.26066285 1.317097745 1 19.77699072 -0.824695514 6.137453463 0.999999984 1.282148873 0.412195671 0.102515456 2.24E-08 4.56E-09 0.093935749 0.022140867 0.149728504 0.824695514 0.282148889 LELQGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LELQGPR 7 0 P19338;H7BY16 P19338 NCL Nucleolin 0 ;;; 148.33 0.0048655 571020000 547368 673340 599740 574850 821570 803840 635290 622160 587680 857710 FALSE TRUE 568978.5113 788980.9071 615369.7171 688553.6142 681919.8249 617160.3423 585494.3098 613820.9628 566529.5116 1025761.853 0.554688703 0.769165772 0.5999148 0.671260695 0.664793512 0.601660454 0.570789709 0.598404943 0.552301209 1 19.96826439 -2.140684579 2.444382343 1.833441449 0.622442542 0.766992229 0.062769524 2765801.68 788624.9004 12782313.03 0.015178878 0.007232949 2.140684579 -1.210998907 LELQGPRGS(ph)PNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LELQGPRGSPNAR 13 1 P19338;H7BY16 P19338 NCL Nucleolin 1 LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR 159.81 6.67E-06 1020340000 453348 991568 743329 270578 1178260 949375 208402 668786 679944 2306900 TRUE FALSE 471246.5291 1161862.091 762700.7644 324097.5208 977979.7861 728897.0442 192066.9067 659822.0176 655472.9483 2758892.887 0.170810013 0.421133454 0.276451749 0.11747376 0.354482695 0.26419911 0.069617384 0.239161883 0.237585501 1 21.39565801 -1.302097836 5.301041153 1.000152061 0.238578283 0.843563272 0.098315312 0.000174687 2.30E-05 0.094116986 0.022179235 0.049877211 1.302097836 -0.761573777 LELTELEAIREDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LELTELEAIREDFLR 15 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 0 ; 173.36 8.89E-07 38196000 48731 52102 56843 57450 57144 66406 59727 58089 59855 53322 FALSE TRUE 50654.93751 61050.1132 58324.37528 68813.43853 47430.68329 50984.21289 55045.44167 57310.41197 57700.83024 63769.42499 0.794345214 0.957357122 0.914613473 1.07909768 0.743784083 0.799508744 0.863194888 0.898713011 0.904835354 1 15.96057725 0.693633664 1.791727668 0.999868575 0.883619813 0.136656698 0.089327958 2.661326301 12.33573103 0.086248293 0.024248918 4.938939018 -0.693633664 -0.116248761 LENEGS(ph)DEDIETDVLYSPQMALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LENEGSDEDIETDVLYSPQMALK 23 0 O60502;O60502-3 O60502 MGEA5 Protein O-GlcNAcase 1 LENEGS(0.997)DEDIET(0.003)DVLYSPQMALK;LENEGS(1)DEDIETDVLYSPQMALK;LENEGS(1)DEDIETDVLYSPQMALK;LENEGS(0.997)DEDIET(0.003)DVLYSPQMALK 180.13 2.99E-17 132473000 312285 224238 315763 233400 345682 355227 355525 284902 313221 193782 TRUE FALSE 324614.2529 262749.1322 323992.0432 279565.8234 286923.0971 272730.9128 327658.0215 281083.3547 301948.2374 231749.8727 1.40070952 1.133761711 1.398024687 1.206325682 1.238072296 1.176833064 1.413843372 1.212873826 1.302905731 1 17.82220902 -1.124944178 3.330355085 0.999673476 1.271000466 0.429494707 0.095251986 8976595.904 13839564.03 31923.37907 0.021554155 0.07499906 1.124944178 0.27132699 LENGELEHIRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LENGELEHIRPK 12 1 M0R1K3;Q15102;M0R389;M0QZT2;M0QXS6;M0R323 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 ;;;;; 234.63 3.01E-16 7398720000 7512740 5929280 7546490 5820720 9295610 8906660 8369680 7450920 7661270 5393890 FALSE TRUE 7809348.776 6947587.717 7743157.729 6972041.043 7715545.533 6838223.197 7713642.612 7351052.605 7385542.389 6450719.473 1.210616709 1.077025244 1.200355675 1.080816035 1.196075192 1.060071396 1.195780198 1.139570963 1.14491762 1 22.62102865 -1.768814512 2.222794901 0.956017513 1.14368413 0.398429556 0.05343762 2969893.688 1788042.033 710713.7739 0.01197301 0.017028857 1.768814512 0.187666617 LENNDNKPVTNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LENNDNKPVTNSR 13 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 ; 186.69 6.92E-06 679840000 759890 550860 711920 567230 943910 916420 829230 757670 775450 639220 FALSE TRUE 789891.044 645465.9199 730473.22 679426.401 783464.5154 703595.3435 764232.7858 747514.6729 747541.706 764462.9204 1.03326273 0.844339081 0.955537804 0.888763056 1.024856137 0.920378641 0.999698959 0.977829863 0.977865225 1 19.544087 3.243215534 24.99998899 0.980290373 0.926113213 0.197629492 0.051750845 176.5342095 948100.4969 0.013247301 0.017358273 1750.715328 -3.243215534 -0.05417716 LENVSLSQQLTETQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LENVSLSQQLTETQHR 16 0 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 168.05 8.43E-10 0 46499 57195 51965 58665 66727 73431 57811 57021 58494 58001 FALSE TRUE 48334.81643 67017.79633 53319.25059 70268.7619 55384.76837 56377.76311 53279.62276 56256.72676 56388.81237 69365.18545 0.696816654 0.966158973 0.768674519 1.013026368 0.798451961 0.812767424 0.768103227 0.811022509 0.812926715 1 16.08192413 LENVSQLSLDKS(ph)PTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 LENVSQLSLDKS(1)PTEK;LENVSQLSLDKS(0.989)PT(0.011)EK 232.29 3.34E-16 1155200000 1239530 383750 608360 398580 1028690 1058580 943390 736180 816830 283950 TRUE FALSE 1288467.602 449656.0773 624214.3614 477417.9344 853833.6412 812740.8379 869444.6267 726312.7112 787432.4479 339584.5659 3.794246649 1.32413579 1.838170588 1.405888201 2.514347608 2.393338566 2.560318442 2.138827214 2.318811062 1 18.37341136 LEPKEES(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEPKEESPTR 10 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 LEPKEES(0.961)PT(0.039)R 85.457 0.0086156 198840000 305450 176460 237620 153580 332370 336840 258270 225640 277220 185670 TRUE FALSE 317509.4019 206765.6323 243812.5724 183957.6656 275873.8661 258614.0149 238026.1225 222615.6649 267242.9064 222048.4816 1.429910259 0.931173367 1.09801504 0.82845721 1.242403749 1.164673647 1.071955641 1.002554322 1.203534041 1 17.76051518 -0.055574077 0.011361569 1.05E-06 2.099188721 0.039563041 0.159977666 12022.87206 40.57965368 3906.13689 3590.381084 0.879885018 0.055574077 2.099187667 LEPKPQPPVAEATPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEPKPQPPVAEATPR 15 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51;K7ER14;K7EJL9 Q9UHD8 9-Sep Septin-9 0 156.22 1.97E-06 120770000 154200 132970 163510 112920 205780 194800 179840 169960 168650 128950 FALSE TRUE 160287.9351 155806.5631 167771.2049 135255.239 170801.5891 149560.6522 165743.6709 167681.9642 162580.3194 154215.2836 1.039377754 1.010318559 1.08790258 0.877054698 1.107552929 0.969817315 1.074755154 1.087323904 1.054242586 1 17.23458623 2.204439165 24.92383542 1.064618049 1.0163136 0.072262831 0.063619107 377.4715554 275719.7422 0.022244093 0.016429167 160.1176344 -2.204439165 -0.048304449 LEPNS(ph)PMHGGTLLEDVVGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LEPNSPMHGGTLLEDVVGGR 20 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 LEPNS(1)PMHGGTLLEDVVGGR;LEPNS(1)PMHGGTLLEDVVGGR 168.79 7.56E-12 124862000 54806 59380 66029 66188 71899 89620 70283 66466 64516 65714 TRUE FALSE 56969.7832 69578.05309 67749.76998 79279.78885 59677.63366 68807.1132 64774.03481 65575.13199 62194.08176 78589.40013 0.724904161 0.885336355 0.862072619 1.008784756 0.759359832 0.875526637 0.824208286 0.834401737 0.791380029 1 16.26204712 -2.296692773 2.297291768 1.745891976 0.844758895 0.292757278 0.074050317 3433780.499 657109.6254 13286108.59 0.017679907 0.005050184 2.296692773 -0.901133081 LEPQELS(ph)PLSATVFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEPQELSPLSATVFPK 16 0 Q3T8J9-3;Q3T8J9;A0A087WUE6;Q3T8J9-2;Q9H869-7;Q9H869-5;Q9H869-6;Q9H869-4;Q9H869-3;Q9H869-2;Q9H869;Q9H869-8;Q9H869-9 Q3T8J9-3 GON4L;YY1AP1 GON-4-like protein;YY1-associated protein 1 1 LEPQELS(1)PLSATVFPK 237.3 9.81E-20 121480000 122180 95125 114590 84370 144530 136770 125600 116140 131360 93680 TRUE FALSE 127003.7607 111461.9788 117576.3095 101058.1342 119962.8422 105007.2403 115755.1438 114583.3333 126632.3793 112034.8024 1.133609897 0.994887092 1.049462373 0.902024478 1.070764081 0.937273401 1.033207015 1.022747671 1.13029502 1 16.77358743 -0.32421252 5.984575145 0.999979602 1.024552895 0.010417138 0.070299302 0 3.30E-18 0.062992063 0.014847372 0.474009974 0.32421252 0.024573293 LEPQIASASEYAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LEPQIASASEYAHR 14 0 O60664-4;O60664;O60664-3;K7ER39;K7EL96 O60664-4 PLIN3 Perilipin-3 0 ;;;;; 268.59 3.22E-25 3924540000 2265880 3728460 3794030 3533410 3938630 4464590 3486170 3744270 3579080 3884070 FALSE TRUE 2355338.692 4368794.002 3892905.539 4232307.952 3269143.079 3427756.634 3212914.886 3694084.185 3450269.61 4645079.151 0.507061046 0.940520895 0.838070873 0.911137962 0.703786302 0.73793288 0.691681408 0.795268297 0.742779509 1 22.14727175 -1.044786138 4.74858008 1.000006662 0.771162758 0.268695662 0.116554463 7.77E-06 1.56E-06 0.106632536 0.025132798 0.090201521 1.044786138 -0.228843905 LEPVS(ph)PPS(ph)PPHTDPELELVPPR ddPTM_MDA-MB-175_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(1)PPHTDPELELVPPR;LEPVS(1)PPS(0.998)PPHT(0.002)DPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR;LEPVS(1)PPS(1)PPHTDPELELVPPR 128.17 9.01E-06 1652190000 692297 786981 757239 740365 842103 915930 764768 789342 756986 769107 TRUE FALSE 719629.4201 922138.8649 776973.2704 886806.9872 698962.6329 703219.1386 704823.4858 778762.1616 729742.2217 919798.7912 0.782377001 1.002544115 0.844720908 0.964131499 0.759908188 0.764535837 0.766280074 0.846665781 0.793371582 1 19.81095878 3.234050015 24.99997 0.810132038 0.902041828 0.148708991 0.087035126 169.5584062 939775.7019 0.022972558 0.02834289 1714.154705 -3.234050015 0.091909789 LEPVS(ph)PPSPPHTDPELELVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEPVSPPSPPHTDPELELVPPR 22 0 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LEPVS(0.799)PPS(0.192)PPHT(0.009)DPELELVPPR 56.688 0.054211 65081000 80994 94710 86855 93172 118230 126370 91851 91806 92606 116100 TRUE FALSE 84191.70566 110975.7058 89118.51265 111601.1435 98133.30683 97022.48266 84651.47861 90575.49073 89273.12815 138847.5721 0.606360661 0.799262847 0.641844227 0.803767339 0.70677006 0.698769746 0.609672012 0.652337591 0.64295779 1 17.08314243 -0.484734621 9.764603249 0.999999681 0.685581951 0.668472194 0.066623804 0 0 0.063126232 0.014878996 0.32754078 0.484734621 -0.31441773 LEPVSPPS(ph)PPHTDPELELVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEPVSPPSPPHTDPELELVPPR 22 0 C9J0Q5;C9JE98;C9J330;H7C1Y3;H0YGK8;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LEPVS(0.006)PPS(0.994)PPHTDPELELVPPR 110.68 0.00022509 43170000 46839 60110 54174 47579 61854 71108 53594 62851 50455 52841 TRUE FALSE 48688.23989 70433.42491 55585.81894 56989.98419 51340.07917 54594.24465 49393.16224 62008.58515 48639.13441 63194.18225 0.770454465 1.114555524 0.879603422 0.901823272 0.81241781 0.863912511 0.781609327 0.981238825 0.769677408 1 15.94750413 4.040045497 24.99998936 0.871974877 0.956148609 0.06101738 0.105374468 329.2426568 205538.7674 0.023970317 0.0517817 10965.93071 -4.040045497 0.084173732 LEQEHTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEQEHTNR 8 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ;;; 171.46 0.00028923 926493000 520245 621614 591238 564198 643640 704963 596066 581646 596222 652224 FALSE TRUE 540784.6743 728371.369 606646.148 675794.6804 534234.3027 541246.0271 549344.7894 573849.9868 574764.0867 780014.8052 0.693300525 0.933791723 0.77773671 0.866386992 0.684902773 0.693891992 0.704274824 0.735691147 0.736863048 1 19.57314198 LEQENDDLAHELVTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 185.25 1.69E-09 428000000 455340 347550 478730 379108 575890 569660 492000 434154 481160 384692 FALSE TRUE 473317.1748 407239.0089 491206.0971 454094.4309 478000.4235 437365.0983 453435.7544 428334.8758 463843.1456 460065.032 1.028804934 0.885177052 1.067688398 0.987022267 1.03898447 0.950659293 0.985590564 0.93103115 1.008212129 1 18.81147828 2.701461662 24.98239462 0.968469066 0.997939993 0.055442446 0.049922396 1575.012332 1060610.411 0.01549836 0.014612582 502.8768721 -2.701461662 0.029470927 LEQMPSKEDAIEHFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEQMPSKEDAIEHFMK 16 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 104.93 0.00079475 382800000 468340 256490 415220 312510 506590 446860 626950 376780 427200 211390 FALSE TRUE 486830.4248 300540.1623 426040.9743 374323.5453 420480.0127 343083.5372 577808.0208 371729.8804 411825.1554 252807.8232 1.92569367 1.18880879 1.685236513 1.480664406 1.663239719 1.357092249 2.285562264 1.470404973 1.629004792 1 17.94768158 LEQQLVHVERPILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEQQLVHVERPILR 14 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;C9JBE1;E7EMB6;E7EPX3;B9ZVU2;F8WAN0;C9JRG3;C9J1E2 E5RIA4 DNPEP Aspartyl aminopeptidase 0 190.86 3.34E-07 422860000 108970 103650 97541 103650 113700 143090 114910 119050 93229 107900 FALSE TRUE 113272.2197 121451.0812 100082.9986 124151.6606 94373.31461 109859.516 105903.0539 117454.3295 89873.7065 129040.9391 0.877800646 0.941182558 0.775591059 0.962110641 0.731343985 0.851353972 0.820693453 0.910209816 0.696474368 1 16.97746932 4.259590899 24.99929275 0.84315682 0.909491596 0.076304695 0.091874551 602.9853649 716773.5196 0.020217319 0.055245755 18179.87527 -4.259590899 0.066334775 LEQTSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEQTSVR 7 0 O15234 O15234 CASC3 Protein CASC3 0 ;; 99.919 0.02367 3150910000 1833280 1954440 1837120 1888280 2574210 2419170 2342890 2013170 1806390 2294820 FALSE TRUE 1905659.31 2290099.867 1884996.856 2261776.148 2136646.704 1857354.43 2159248.16 1986186.749 1741378.377 2744446.042 0.694369385 0.834448858 0.68684056 0.824128481 0.778534783 0.676768427 0.786770127 0.72371135 0.63450997 1 21.38808354 -1.218180186 3.627311468 1.000362954 0.741955569 0.606285472 0.063310869 24152920.15 44172175.07 105712.3697 0.014292158 0.060508978 1.218180186 -0.258407385 LERENAEVDGDDDAEEMEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LERENAEVDGDDDAEEMEAK 20 1 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 144.92 1.38E-07 167480000 143040 110100 138450 87714 196230 172290 124400 127220 157020 124990 FALSE TRUE 148687.3297 129008.8185 142058.1207 105063.5674 162874.8947 132278.2586 114649.2029 125514.824 151368.8809 149479.3974 0.994701158 0.863054178 0.950352511 0.702863199 1.089614338 0.884926357 0.766989999 0.839679756 1.012640427 1 17.18958713 2.495637689 24.62794185 0.874533814 0.914628322 0 0.11550239 3033.483014 4034714.219 0.036861521 0.034185278 313.0672865 -2.495637689 0.040094508 LERT(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LERTPQK 7 1 P35251-2;P35251 P35251-2 RFC1 Replication factor C subunit 1 1 LERT(1)PQK 88.681 0.029794 514640000 635750 455230 645110 512270 659410 685910 740370 595120 623870 412320 TRUE FALSE 660849.9009 533412.2113 661922.0966 613595.477 547323.7237 526617.7976 682337.8648 587143.3898 601417.0406 493106.2097 1.340177609 1.081738986 1.342351979 1.244347496 1.109950986 1.067960182 1.383754354 1.190703703 1.219650105 1 18.9115389 -1.432420138 1.972610332 0.983467683 1.217796063 0.279810575 0.105862584 163419.6245 120234.2531 14870.94055 0.026802979 0.036947058 1.432420138 0.23432838 LES(ph)IDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LESIDNHSSTGGQSDQGYGSKDELIKDDAEIHVPEEQAAR 40 2 Q5VZ89-7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 LES(0.986)IDNHS(0.01)S(0.003)T(0.001)GGQSDQGYGSKDELIKDDAEIHVPEEQAAR 71.796 0.0012568 105940000 14889 18598 39037 17572 63282 38893 41906 43170 57036 19778 TRUE FALSE 15476.82922 21792.06183 40054.33629 21047.68915 52525.34824 29860.69018 38621.29822 42591.37676 54983.2855 23653.12043 0.65432505 0.921318686 1.69340601 0.889848306 2.22065196 1.262441895 1.632820428 1.800666297 2.324567943 1 14.5297429 4.715117332 0.704762154 1.715439197 5.72E-15 0.347600861 0.445155855 2.971681069 1.143561414 0.168579081 4.065668867 51894.02206 -4.715117332 -1.715439197 LES(ph)LNIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LESLNIQR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LES(1)LNIQR;LES(1)LNIQR;LES(1)LNIQR;LES(1)LNIQR 130.94 0.0010766 447487000 505560 520321 745780 622830 915730 809120 622250 640570 671150 737250 TRUE FALSE 525519.8992 609682.0842 765215.6395 746023.915 760074.5417 621214.1423 573476.4191 631984.2069 646995.4426 881700.022 0.596030267 0.69148471 0.867886606 0.846119878 0.862055714 0.704564054 0.650421237 0.716779167 0.733804499 1 19.74992837 4.474879399 5.800615227 0.777945957 0.616310636 0.286166536 0.098460553 0.197341241 25.15121858 0.024696319 0.080720283 29845.53712 -4.474879399 -0.161635321 LES(ph)PADVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LESPADVK 8 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7;H7C408 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 LES(1)PADVK 104.05 0.0048833 100300000 94842 60714 80426 61283 110750 117740 99077 76148 86095 54269 TRUE FALSE 98586.43539 71141.15721 82521.96763 73404.59449 91924.75456 90396.66937 91311.08585 75127.36061 82996.45777 64901.97151 1.519005249 1.096132453 1.2714863 1.13100716 1.416363054 1.392818543 1.406907737 1.157551286 1.278797174 1 15.98597468 0.575272622 1.046833515 1.001317942 1.298844052 0.321119904 0.130884275 1.735032425 2.875623312 0.12309363 0.038790063 3.76073405 -0.575272622 0.29752611 LES(ph)VEEYNELMVR ddPTM_MDA-MB-175_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 192.32 2.96E-06 102305000 45856 57725 70535 51757 79448 72827 67917 68538 71331 56449 TRUE FALSE 47666.43029 67638.81971 72373.20005 61994.38012 65943.45734 55914.03295 62593.48807 67619.36022 68763.81124 67509.10077 0.70607414 1.001921503 1.072051016 0.918311449 0.976808409 0.828244375 0.927185925 1.001633253 1.018585797 1 16.04279438 4.74310402 24.59097327 0.968367722 0.706074006 0.610624415 0.063570832 266.1033528 1440207.842 0.015916276 0.126821044 55348.26604 -4.74310402 -0.262293715 LESDYEILER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LESDYEILER 10 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;;; 220.39 1.36E-08 412999000 535831 566228 598505 611745 615777 716429 653699 584392 581361 523303 FALSE TRUE 556986.0216 663473.2544 614102.532 732746.3351 511107.4455 550049.2223 602460.3643 576559.1811 560437.9312 625834.2036 0.889989742 1.060142208 0.981254346 1.170831397 0.816681866 0.878905658 0.962651707 0.921265054 0.895505436 1 19.25542098 3.22164864 24.9996447 0.911412528 1.024860759 0.325660012 0.079685563 275.4799075 407219.406 0.022206988 0.026606964 1665.898896 -3.22164864 0.11344823 LESESTS(ph)PSLEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.287)S(0.713)PSLEMK;LESEST(0.187)S(0.813)PSLEMK;LESEST(0.236)S(0.764)PSLEMK;LESEST(0.033)S(0.967)PSLEMK;LESEST(0.003)S(0.499)PS(0.499)LEMK;LESEST(0.002)S(0.906)PS(0.092)LEMK 364.3 4.73E-91 900680000 3653550 2391420 3084050 2404660 3969640 4117760 3852240 3159090 3481650 2224680 TRUE FALSE 3797794.975 2802127.782 3164422.877 2880294.571 3294882.011 3161472.645 3550291.363 3116747.566 3356346.097 2660563.452 1.427440106 1.053208402 1.189380721 1.08258819 1.238415122 1.188271846 1.33441334 1.171461468 1.261517027 1 21.34330038 -1.111758807 4.849055637 0.999989698 1.20895074 0.275325263 0.104665682 1.07E-05 1.97E-06 0.093333679 0.021997875 0.077310983 1.111758807 0.208961041 LESLSETPGPS(ph)SPRQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LESLSETPGPSSPRQPR 17 1 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSET(0.002)PGPS(0.981)S(0.017)PRQPR;LESLSET(0.013)PGPS(0.508)S(0.479)PRQPR 140.32 4.03E-07 813340000 524000 1632290 1283690 1371890 1212730 1775750 786080 1268450 1188750 2606600 TRUE FALSE 544687.9246 1912623.11 1317144.016 1643245.747 1006590.588 1363358.974 724464.9956 1251448.503 1145967.12 3117313.364 0.174729923 0.613548555 0.422525381 0.527135246 0.322903241 0.437350633 0.232400439 0.401450979 0.367613706 1 21.57187176 -1.223341902 3.43643827 1.001297764 0.393740707 0.693321077 0.121900122 275945629.1 428030088.6 3831628.716 0.028474248 0.059794068 1.223341902 -0.607557058 LESLSETPGPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LESLSETPGPSSPR 14 0 A0A2R8YF49;H0Y895;Q12774-2;C9J591;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 LESLSETPGPSS(1)PR;LESLSETPGPS(0.001)S(0.999)PR;LESLSETPGPS(0.013)S(0.987)PR;LESLSETPGPSS(1)PR;LESLSETPGPS(0.019)S(0.981)PR;LESLSETPGPSS(1)PR;LESLSETPGPS(0.095)S(0.905)PR 403.17 2.16E-132 9900020000 4987030 5263050 5178920 5271010 5433560 6233900 5638790 5279700 5049300 4566640 TRUE FALSE 5183921.795 6166937.897 5313886.91 6313600.046 4509965.412 4786171.201 5196806.906 5208934.257 4867576.679 5461385.674 0.949195333 1.129189232 0.972992428 1.156043616 0.825791416 0.876365722 0.951554645 0.953775208 0.891271368 1 22.38083561 3.235286603 24.99978942 0.917473225 1.051745958 0.45045961 0.07325724 75.32016105 575132.5791 0.019873428 0.024703765 1719.042456 -3.235286603 0.134272733 LESLYS(ph)DEEDESAVGADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LESLYSDEEDESAVGADK 18 0 I3L4N6;Q9UP95-3;Q9UP95-5;Q9UP95-2;Q9UP95-6;Q9UP95;Q9UP95-7 I3L4N6 SLC12A4 Solute carrier family 12 member 4 1 LES(0.001)LY(0.001)S(0.999)DEEDESAVGADK 119.46 7.68E-05 15625000 21156 17735 16522 18019 21886 27227 24100 18646 20750 13557 TRUE FALSE 21991.25522 20780.84829 16952.57689 21583.10442 18165.82554 20903.94188 22210.97903 18396.08087 20003.21155 16213.23459 1.356376798 1.281721311 1.04560116 1.33120287 1.120431919 1.289313478 1.369928925 1.134633609 1.233758227 1 13.98488432 0.384045126 1.009994566 0.999619846 1.241856621 0.332087156 0.102768731 2.864739844 3.654668038 0.098471637 0.030210916 2.421280618 -0.384045126 0.242236776 LESPTTPLLDDMDGSQDS(ph)PIFMYAPEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LESPTTPLLDDMDGSQDSPIFMYAPEFK 28 0 Q9H3M7-2;Q9H3M7 Q9H3M7-2 TXNIP Thioredoxin-interacting protein 1 LESPTTPLLDDMDGS(0.036)QDS(0.963)PIFMY(0.001)APEFK 98.019 0.0011469 8540800 19801 16445 18831 14004 18532 21936 20507 18478 21094 14508 TRUE FALSE 20582.75877 19269.30083 19321.75133 16773.9494 15381.93726 16841.69644 18899.60775 18230.33263 20334.83106 17350.56483 1.186287534 1.110586371 1.113609356 0.966766763 0.886538128 0.970671365 1.089279107 1.050705427 1.171998218 1 14.08269501 3.905827539 4.866915445 1.020450527 1.140970936 0.347604613 0.074442189 0.277149111 10.68743825 0.021184781 0.039951133 8050.586847 -3.905827539 0.120520409 LESTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LESTESR 7 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 88.029 0.043988 80263000 146470 114730 125590 107510 142080 159610 141700 112120 138860 127250 FALSE TRUE 152252.7487 134433.985 128862.9786 128775.1571 117929.2923 122542.9964 130593.1837 110617.2148 133862.4557 152182.2012 1.000463573 0.883375217 0.84676774 0.846190659 0.774921715 0.805238691 0.858137041 0.726873537 0.879619658 1 17.21544011 5.002558817 1.174267497 0.821570827 1.18067387 0.291772864 0.069673928 2.662279796 2.061901671 0.018524498 1.352148319 100590.9285 -5.002558817 0.359103043 LESTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LESTSPK 7 0 Q03111 Q03111 MLLT1 Protein ENL 1 LES(0.001)T(0.013)S(0.986)PK;LEST(0.004)S(0.995)PK;LEST(0.003)S(0.997)PK;LES(0.019)T(0.101)S(0.88)PK 147.24 0.0022708 2340820000 14059400 5614800 7575200 5506300 10687500 13494800 10737300 8271300 8393600 4447930 TRUE FALSE 14614475.97 6579098.223 7772615.935 6595429.705 8870842.567 10360837.22 9895682.369 8160436.753 8091515.976 5319416.723 2.747383168 1.2368082 1.461178234 1.239878364 1.667634448 1.94773934 1.860294631 1.534084878 1.521128424 1 22.34283663 0.766065383 1.49757727 1.002384499 1.686926983 0.215141154 0.411405912 1.297885006 4.997043618 0.377438148 0.110090457 5.83532949 -0.766065383 0.684542484 LETEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LETEEER 7 0 P25098;E9PRV7 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 143 0.005702 89930000 134890 155110 161350 166820 189860 205690 178360 176850 164490 167790 FALSE TRUE 140215.5614 181748.9359 165554.9136 199816.4981 157587.665 157921.6148 164379.6771 174479.615 158570.037 200665.238 0.69875362 0.905732043 0.82503036 0.995770369 0.785326181 0.786990394 0.819173659 0.869505933 0.790221758 1 17.61443119 -1.301264766 3.4196358 1.000656173 0.8369691 0.305175333 0.076103704 31248346.94 50315020.77 217118.4909 0.017371767 0.049972978 1.301264766 -0.163687073 LETELDEEKNTVELLTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LETELDEEKNTVELLTDR 18 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 ;;; 228.46 2.20E-19 373517000 725020 467408 627182 441547 812778 776338 720243 609698 715914 447146 FALSE TRUE 753644.3494 547681.6881 643526.8782 528883.6787 674622.2859 596045.265 663788.4717 601525.9956 690148.395 534755.6976 1.409324581 1.024171768 1.2034035 0.98901925 1.261552311 1.114612276 1.241292939 1.124861312 1.290586333 1 19.02852042 -1.970701466 2.48161062 0.85333438 1.173425683 0.169336591 0.12031036 11083793.63 4594000.825 9333995.251 0.028620415 0.0106979 1.970701466 0.320091303 LETHMTPEMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LETHMTPEMFR 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 196.48 6.03E-08 1537030000 820790 1433260 1405790 1383660 1803820 1838430 1375280 1383200 1357820 1782340 FALSE TRUE 853195.423 1679411.256 1442426.042 1657343.818 1497207.321 1411482.494 1267481.96 1364660.466 1308952.323 2131555.398 0.400268942 0.787880652 0.676701175 0.777527912 0.702401318 0.662184288 0.594627736 0.640218156 0.614083183 1 21.02347512 -1.545019611 2.793775515 1.018348981 0.657412843 0.507702961 0.103007924 15206062.04 15661207.72 2095968.941 0.026398754 0.028508895 1.545019611 -0.360936138 LETLLR ddPTM_MDA-MB-175_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 0 122.17 0.044989 106580000 145150 167850 159620 147540 185380 198900 182710 164220 172090 161590 FALSE TRUE 150880.6341 196676.9318 163779.8283 176722.9716 153869.1738 152708.4894 168388.7128 162018.8995 165896.5145 193250.4667 0.780751719 1.017730695 0.847500299 0.914476299 0.796216312 0.790210197 0.871349579 0.838388141 0.858453371 1 17.56011237 5.046357305 20.22300295 0.870912655 2.12E-05 0.130852757 0.073464759 800.7183303 211419.3024 0.016320943 46728.87892 111264.6752 -5.046357305 -0.870891501 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(ph)PPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPSPPGSGR 40 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.827)PPGS(0.173)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.933)PPGS(0.067)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.955)PPGS(0.045)GR;LEVSVDGLTLSPDPEERPGAEGAPLLPPPLPPPS(0.838)PPGS(0.162)GR 174.03 1.89E-19 1019230000 385546 434070 437212 424191 468499 523325 457510 454666 437931 415419 TRUE FALSE 400767.6538 508618.1459 448606.1039 508094.7137 388863.7073 401790.6998 421649.1707 448571.946 422169.9489 496812.3994 0.806678042 1.023762987 0.902968816 1.022709406 0.782717396 0.808737262 0.848709032 0.902900062 0.849757271 1 18.92234166 LEVTEIVKPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LEVTEIVKPSPK 12 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK;LEVTEIVKPS(1)PK 137.52 5.50E-05 1820900000 4461480 1326530 1989100 1481810 3231450 3598600 3164520 2159270 2388050 901826 TRUE FALSE 4637622.675 1554351.209 2040937.58 1774907.595 2682169.283 2762879.687 2916476.653 2130328.518 2302104.547 1078521.538 4.299981513 1.441186989 1.89234754 1.645685814 2.486894502 2.561728801 2.704143172 1.975230389 2.1345003 1 20.04062356 0.572590857 1.197998232 1.001972436 2.333006008 0.231593404 0.751402866 2.304358381 4.710851094 0.682568885 0.207839621 3.737583096 -0.572590857 1.331033572 LEYDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LEYDAYR 7 0 A0A087X1E4;P53365;P53365-2;P53365-3 A0A087X1E4 ARFIP2 Arfaptin-2 0 143 0.005702 288210000 376090 403640 392900 340580 709080 548030 445860 376060 376760 660590 FALSE TRUE 390938.3236 472962.0301 403139.2968 407945.7075 588550.8349 420758.338 410912.3282 371019.5308 363200.4812 790019.9627 0.494846133 0.598670986 0.510290013 0.516373923 0.744982232 0.532592033 0.520129044 0.469633108 0.459735827 1 19.59152958 -1.035403174 5.036792725 1.000006388 0.538859595 0.759228129 0.077952516 5.77E-06 1.10E-06 0.077862618 0.018352141 0.092171536 1.035403174 -0.461146793 LFAYPDTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFAYPDTHR 9 0 P04040 P04040 CAT Catalase 0 ; 104.17 0.0033041 330980000 285450 398780 226627 314810 502290 479390 299980 270300 274820 560780 FALSE TRUE 296719.7864 467267.3629 232533.0858 377078.4784 416910.9252 368058.9377 276466.7837 266677.0706 264929.2819 670654.1042 0.442433416 0.696733771 0.346725807 0.562254784 0.621648213 0.548805913 0.412234536 0.397637275 0.39503118 1 19.35520935 -1.212023731 4.726751115 1.000096061 0.490531338 0.669020997 0.107296167 0.000110391 1.84E-05 0.105586221 0.024882247 0.061372847 1.212023731 -0.509564723 LFDANKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 112.11 0.0028315 2671810000 5747800 4467350 5281550 3848000 8939200 6906200 6211600 5406340 6038000 5528170 FALSE TRUE 5974727.582 5234582.611 5419191.532 4609122.915 7419717.977 5302339.714 5724718.561 5333876.855 5820693.559 6611309.068 0.903713247 0.791761897 0.8196851 0.697157381 1.122276678 0.802010564 0.865897888 0.806780745 0.88041468 1 22.65650453 LFDDEAS(ph)VDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFDDEASVDEPR 12 0 A0A2R8Y549;Q8NI35-3;Q8NI35;A0A0X1KG69;A0A087WUZ6;Q8NI35-4;Q8NI35-2;Q8NI35-5;A0A0U1RR46 A0A2R8Y549 INADL InaD-like protein 1 LFDDEAS(1)VDEPR;LFDDEAS(1)VDEPR;LFDDEAS(1)VDEPR;LFDDEAS(1)VDEPR 180.28 2.06E-05 946670000 821980 889740 894620 850560 1054340 1074160 871520 841870 851450 836630 TRUE FALSE 854432.4051 1042545.924 917934.5321 1018798.229 875123.6634 824702.6191 803207.9851 830586.1097 820806.4808 1000551.63 0.853961334 1.041971141 0.917428451 1.018236539 0.874641185 0.824247939 0.802765156 0.830128186 0.820353949 1 19.93236418 3.066773205 6.037101608 0.840407232 0.960540324 0.308633667 0.071330585 0.1937348 13.00660083 0.019032009 0.022784927 1166.200451 -3.066773205 0.120133091 LFDEEEDS(ph)SEKLFDDSDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFDEEEDSSEKLFDDSDER 19 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFDEEEDS(0.948)S(0.052)EKLFDDSDER 184.2 1.54E-14 18076000 44181 21761 23198 25070 34716 41433 45430 28715 34872 15219 TRUE FALSE 45925.3 25498.28247 23802.55894 30028.77117 28814.98672 31810.81367 41869.07789 28330.12239 33616.96353 18200.87166 2.523247284 1.400937435 1.307770275 1.649853465 1.583165205 1.747763198 2.300388611 1.556525584 1.846997449 1 14.15171992 -1.552677582 6.371815579 0.998949808 1.743925888 0.287269285 0.361291622 0.005211064 0.000365834 0.338200064 0.079621133 0.0280106 1.552677582 0.74497608 LFDFPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFDFPGR 7 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ;; 135.87 0.0070624 183786000 662716 715034 747955 761383 813205 918826 826418 781492 706126 671914 FALSE TRUE 688880.5394 837835.5273 767447.3218 911982.2849 674976.7046 705442.5864 761641.1977 771017.378 680712.6632 803562.6837 0.85728289 1.042651114 0.955055949 1.134923639 0.839980151 0.877893661 0.947830472 0.959498734 0.847118311 1 19.61605104 3.204393739 24.99999333 0.914334153 0.99767541 0.213867461 0.080163174 285.6377118 209001.0813 0.022405278 0.026780611 1601.008874 -3.204393739 0.083341257 LFDHPES(ph)PTPNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.497)PT(0.497)PNPT(0.005)EPLFLAQAEVYK;LFDHPES(0.496)PT(0.496)PNPT(0.008)EPLFLAQAEVYK;LFDHPES(0.5)PT(0.5)PNPTEPLFLAQAEVYK;LFDHPES(0.621)PT(0.379)PNPTEPLFLAQAEVYK 374.81 3.82E-120 4457574000 1585727 1167411 1600531 1282492 1809330 1714779 1572949 1343751 1552338 995291 TRUE FALSE 1648332.726 1367904.758 1642242.153 1536165.09 1501780.733 1316547.565 1449657.147 1325740.216 1496469.659 1190299.215 1.384805354 1.149210837 1.379688511 1.29057053 1.261683376 1.106064381 1.217893054 1.113787356 1.257221411 1 20.18289285 2.879924915 4.494927982 1.150161909 1.293950408 0.431437844 0.088671457 0.23189348 7.489008936 0.025443401 0.027259052 758.4464364 -2.879924915 0.143788499 LFDHPESPT(ph)PNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_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 1 LFDHPES(0.184)PT(0.816)PNPTEPLFLAQAEVYK;LFDHPES(0.408)PT(0.592)PNPTEPLFLAQAEVYK;LFDHPES(0.168)PT(0.832)PNPTEPLFLAQAEVYK;LFDHPES(0.132)PT(0.868)PNPTEPLFLAQAEVYK 416.96 1.12E-158 43191200000 1237529 879281 1155766 1061248 1397849 1342490 1238665 1064320 1130572 742019 TRUE FALSE 1286387.601 1030290.672 1185886.211 1271159.687 1160243.126 1030717.043 1141575.201 1050054.531 1089882.935 887403.4162 1.449608574 1.161017248 1.336355247 1.432448494 1.307458485 1.161497718 1.286421913 1.183288809 1.228170767 1 19.75923058 0.151140519 0.242335638 0.891197899 1.370156824 0.563938683 0.085636831 4.765472389 0.521466801 0.65116644 0.183979647 1.416251943 -0.151140519 0.478958925 LFDHPESPTPNPTEPLFLAQAEVYK ddPTM_MDA-MB-175_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 0 ;;;; 335.2 5.20E-88 5569898000 2661576 2037750 2865186 2470347 3342571 3215025 3111616 2569251 2947980 2009132 FALSE TRUE 2766657.076 2387717.711 2939855.101 2958974.263 2774401.975 2468384.168 2867719.407 2534814.393 2841882.776 2402782.948 1.151438617 0.993730088 1.223520877 1.231477968 1.154661921 1.027302183 1.19349915 1.054949385 1.182746356 1 21.1962749 LFDHPESPTPNPTEPLFLAQAEVYKELR ddPTM_MDA-MB-175_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 0 125.11 2.33E-05 167960000 62150 78172 100340 70631 127150 124610 106870 88926 121760 112170 FALSE TRUE 64603.72999 91597.43291 102954.9428 84601.60099 105537.0884 95671.21598 98493.25015 87734.09242 117377.8814 134147.5639 0.481587053 0.682811005 0.767475307 0.630660733 0.786723854 0.713178929 0.73421572 0.65401182 0.874990779 1 17.03346133 -4.999999999 0.106796561 1.970515489 0.516111208 0.632348514 0.080977406 119.9447951 0.858719222 25.53627899 1.116297786 1.00E-05 4.999999999 -1.454404281 LFDQAFGLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LFDQAFGLPR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;; 226.47 1.37E-07 46656240000 12837878.9 16833517 15401314 13719305 19988980 18957809 17520351.2 16729985 14808201 19135218 FALSE TRUE 13344728.27 19724542.6 15802684.9 16432942.58 16591260.32 14555145.17 16147060.29 16505746.92 14275256.74 22884397.6 0.583136533 0.861920988 0.690544063 0.718084997 0.725003149 0.636029203 0.705592543 0.721266393 0.623798668 1 24.44786098 -1.228212429 4.579773044 1.000084899 0.702479634 0.616209445 0.071782032 5.82E-05 9.80E-06 0.063504953 0.014963904 0.059127235 1.228212429 -0.297605265 LFDSTTLEHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFDSTTLEHQK 11 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ;;; 209.85 1.48E-08 1775970000 1921280 1568300 1793930 1476460 2540360 2371670 1966530 1772230 1911510 1816670 FALSE TRUE 1997133.618 1837643.325 1840681.29 1768499.381 2108550.515 1820885.586 1812388.24 1748476.156 1842715.128 2172611.704 0.919231731 0.845822252 0.847220553 0.813996987 0.970514202 0.838109075 0.834197955 0.804780786 0.848156679 1 21.05099892 LFDTPHT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFDTPHTPK 9 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 LFDTPHT(1)PK 167.18 0.00022143 261420000 587450 428790 512100 397830 681450 688200 583910 547470 566200 375390 TRUE FALSE 610642.9796 502431.347 525445.7467 476519.5866 565617.3724 528375.9798 538141.6084 540132.0601 545822.5726 448940.4832 1.360186934 1.119149121 1.170412931 1.061431536 1.259893891 1.176939927 1.198692541 1.203126206 1.215801633 1 18.77616467 -0.94828567 4.531345225 0.999997304 1.191405164 0.377718954 0.07531777 2.32E-06 5.40E-07 0.06789576 0.01600291 0.112645625 0.94828567 0.19140786 LFDVSEITSAAMVHSLPTAVPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFDVSEITSAAMVHSLPTAVPESPR 25 0 A0A3B3ISF0;Q659C4;Q659C4-9;Q659C4-2;D6RJB0 A0A3B3ISF0 LARP1B La-related protein 1B 1 LFDVSEITSAAMVHSLPT(0.004)AVPES(0.996)PR;LFDVSEITSAAMVHSLPT(0.004)AVPES(0.996)PR 110.17 0.0018759 63561000 40359 51022 46623 47417 51236 58932 44798 46779 45031 58478 TRUE FALSE 41952.40448 59784.6316 47838.03368 56795.94107 42526.92302 45245.93612 41286.6157 46152.00402 43410.34311 69935.64447 0.599871565 0.854852087 0.684029354 0.812117219 0.608086525 0.646965313 0.590351544 0.659921051 0.620718425 1 16.09374033 -0.982630269 4.393562368 1.00001033 0.677003325 0.566913655 0.085149723 10764388.87 2450036.522 1129.397092 0.019882831 0.104080587 0.982630269 -0.323007005 LFEAEAQDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LFEAEAQDLFR 11 0 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 0 ;;;;; 189.72 6.01E-06 267087000 292302 372819 360275 358823 409217 428568 369620 368073 356243 416231 FALSE TRUE 303842.3087 436847.7631 369664.0625 429797.1184 339658.4405 329039.577 340648.2186 363139.5835 343421.884 497783.4952 0.610390484 0.877585873 0.742620167 0.863421794 0.682341708 0.661009415 0.684330079 0.729513106 0.689902111 1 18.92515887 -1.182130954 4.860158847 1.000028541 0.730572251 0.508497098 0.080504354 2.42E-05 4.08E-06 0.075868603 0.017880509 0.065745956 1.182130954 -0.26945629 LFEAEEQDLFKDIQSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFEAEEQDLFKDIQSLPR 18 1 A0A024R571;Q9H4M9;C9JC03;C9J2Z4;C9JDQ8 A0A024R571 EHD1 EH domain-containing protein 1 0 81.144 0.0067795 7543400 8977.7 11112 11167 10627 17121 14078 7743.3 12852 12776 15517 FALSE TRUE 9332.146528 13020.39956 11458.02119 12728.98888 14210.77854 10808.59785 7136.359913 12679.73996 12316.19426 18557.25906 0.502883885 0.701633766 0.617441464 0.685930441 0.765780037 0.582445814 0.384558942 0.683276551 0.663686066 1 14.17969602 0.639201919 2.001625492 0.999782807 0.616737959 0.553859512 0.10306914 1.483131411 7.247290028 0.100361236 0.027664342 4.357144053 -0.639201919 -0.383044848 LFEDDDS(ph)NEKLFDEEEDSSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFEDDDSNEKLFDEEEDSSEK 21 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEK;LFEDDDS(1)NEKLFDEEEDSSEK 167.51 7.27E-12 121315000 393690 77095 124065 100761 206421 253010 312640 144632 176405 37990 TRUE FALSE 409233.1852 90335.46653 127298.2358 120691.2251 171333.6322 194252.2619 288134.4599 142693.4446 170056.2185 45433.41314 9.007317675 1.988304648 2.801863805 2.65644196 3.77109313 4.275537506 6.341906539 3.140715935 3.742976958 1 15.47146607 4.748483581 24.67585242 3.500767872 9.007321276 0.607767948 1.366618335 811.8570989 2018830.15 0.328219578 4.35907206 56038.12312 -4.748483581 5.506553403 LFEDDDS(ph)NEKLFDEEEDSSEKLFDDSDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFEDDDSNEKLFDEEEDSSEKLFDDSDER 29 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEDDDS(1)NEKLFDEEEDSSEKLFDDSDER;LFEDDDS(1)NEKLFDEEEDSSEKLFDDSDER 275.47 1.99E-71 88930000 143164 42657 70573 42959 107020 131118 116871 68405 81883 26382 TRUE FALSE 148816.2253 49983.00792 72412.19036 51456.16198 88828.77863 100667.8316 107710.3456 67488.14286 78936.04682 31551.04779 4.716680925 1.584194866 2.295080368 1.630885996 2.815398691 3.19063355 3.413843698 2.139014315 2.501851836 1 14.9454003 4.751106163 24.81633771 2.38567677 4.716682542 0.506018526 0.714455972 1580.488465 3126301.049 0.169457955 2.996120987 56377.54541 -4.751106163 2.331005771 LFEELAMDVYDEVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFEELAMDVYDEVDRR 16 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 0 ;;; 105.14 0.0013713 316189000 39605 42205.8 49732.8 48231.4 58682.6 60657.7 46880.5 48134.6 47107.2 52211.8 FALSE TRUE 41168.63598 49454.31783 51028.87762 57771.42696 48707.75261 46570.86845 43205.88391 47489.43442 45411.82107 62441.70255 0.659313156 0.792007838 0.817224315 0.925205826 0.780051642 0.745829575 0.691939556 0.760540352 0.727267503 1 15.93022225 -0.926137416 4.177262501 1.000007211 0.769381075 0.506436825 0.069075814 16322880.55 40576571.93 1929.859291 0.017552917 0.118539362 0.926137416 -0.230626136 LFEELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFEELGK 7 0 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 132.29 0.007872 109814000 300960 248160 301990 246460 402200 378990 345770 329710 328070 220610 FALSE TRUE 312842.1332 290779.5496 309860.1075 295209.0524 333834.1877 290975.3161 318667.6439 325290.7767 316262.8248 263834.3057 1.185752294 1.102129417 1.174449648 1.118918374 1.265317589 1.102871423 1.207832481 1.232935861 1.198717597 1 18.00927264 LFEES(ph)DDKEDEDADGKEVEDADEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFEESDDKEDEDADGKEVEDADEK 24 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 LFEES(1)DDKEDEDADGKEVEDADEK 115.66 0.00053522 121290000 499170 38989 51040 56035 128530 370670 224590 77162 84546 20496 TRUE FALSE 518877.617 45685.05746 52370.14433 67118.55575 106682.5165 284587.5101 206986.0489 76127.7696 81503.20598 24511.79878 21.16848387 1.863798649 2.136527996 2.738214211 4.352292439 11.61022545 8.44434351 3.105760221 3.325060176 1 14.58118874 4.744394014 24.68957383 4.588142365 21.16849247 0.723415354 3.126625673 311.1721352 1316975.543 0.802551743 7.183130516 55512.91259 -4.744394014 16.5803501 LFEGNALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFEGNALLR 9 0 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ; 96.668 0.016779 561540000 402030 382170 368310 359560 564410 572510 409830 384650 424930 486640 FALSE TRUE 417902.4548 447804.7246 377908.4612 430679.8948 468471.7898 439553.229 377706.4537 379494.3959 409636.8523 581987.7907 0.718060519 0.769440067 0.649340875 0.740015343 0.804951233 0.755261942 0.648993776 0.652065906 0.703858154 1 19.15062936 -1.912684412 2.358385219 1.1789342 0.712461894 0.735150959 0.051144245 5297626.65 2639790.333 5243042.374 0.01462713 0.012226878 1.912684412 -0.466472307 LFEHYYQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFEHYYQELK 10 0 Q08J23;Q08J23-2;A0A140T9Y7 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 94.616 0.0079824 275790000 381750 315090 422740 296200 527210 463850 430410 387890 440380 319300 FALSE TRUE 396821.7848 369204.2564 433756.9517 354787.4759 437595.0325 356127.8672 396673.3395 382690.969 424530.8098 381860.7216 1.039179372 0.966855808 1.135903556 0.929101779 1.145954553 0.932611937 1.03879063 1.002174215 1.111742543 1 18.54268701 -1.11374659 5.370570275 0.999999478 1.030027564 0.015858447 0.074785677 4.09E-07 6.77E-08 0.063453626 0.014955903 0.076957936 1.11374659 0.030028086 LFENLR ddPTM_MDA-MB-175_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 ;;;;;;; 143.97 0.026361 1930591000 1608231 1831842 1739863 1721725 2193250 2239128 1868399 1806455 1659541 1847731 FALSE TRUE 1671725.202 2146446.614 1785205.259 2062277.066 1820442.148 1719124.456 1721949.004 1782242.425 1599814.444 2209758.513 0.756519408 0.971348951 0.807873462 0.933259021 0.823819498 0.777969378 0.779247594 0.806532667 0.723977048 1 21.07545729 3.014250407 24.51396661 0.802508593 0.871456486 0.055119811 0.087966409 376.4850473 647634.4855 0.023081408 0.027575575 1033.357052 -3.014250407 0.068947893 LFFAGEHTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFFAGEHTIR 10 0 R4GMQ1;O60341;O60341-2;R4GMP9 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 152.54 1.78E-05 285120000 204390 239240 200640 213630 265470 257460 194110 238980 235880 282040 FALSE TRUE 212459.475 280327.609 205868.8432 255885.3764 220345.5042 197668.8168 178895.151 235776.864 227390.7249 337300.338 0.629882188 0.831091989 0.610342831 0.75862769 0.653262032 0.586032075 0.530373471 0.699011645 0.674149117 1 18.36367424 0.38876376 2.029966143 0.999992897 0.662318224 0.606727731 0.081311989 6.342274904 20.13197738 0.078294536 0.021472571 2.447731405 -0.38876376 -0.337674674 LFFDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFFDKR 6 1 O15371-2;O15371;O15371-3;B0QYA4 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 106.29 0.051713 368300000 523520 486930 510340 429300 950240 709380 613640 485420 569770 811120 FALSE TRUE 544188.9738 570556.4397 523639.8796 514214.2587 788718.5442 544637.2458 565541.2934 478913.7389 549264.089 970043.4342 0.560994441 0.588176178 0.539810756 0.530094056 0.813075494 0.561456556 0.583006156 0.493703397 0.566226284 1 19.88768982 -1.384679431 5.852042945 1.000105487 0.579194742 0.701681605 0.081780328 0.000114589 1.20E-05 0.080615789 0.018996601 0.041240182 1.384679431 -0.420910745 LFGPYVWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFGPYVWGR 9 0 Q9H4A4;C9JMZ3;H7C2T3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 190.64 8.57E-05 437320000 342440 295770 337600 352640 368730 431070 432290 337460 313670 276030 FALSE TRUE 355959.7956 346566.1967 346398.1333 422391.1395 306053.4063 330960.5254 398405.9802 332936.9007 302381.078 330112.7936 1.078297487 1.049841762 1.049332653 1.279535806 0.927117677 1.002568007 1.20687834 1.008554976 0.915993212 1 18.33259953 1.502948107 7.740624389 0.959231329 1.081995372 0.229799591 0.095167658 0.164198608 22.61470555 0.051558391 0.023678497 31.8381707 -1.502948107 0.122764043 LFGT(ph)SPATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFGTSPATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 41 1 Q3YEC7;Q3YEC7-2;G3V154;F2Z2T0 Q3YEC7 RABL6 Rab-like protein 6 1 LFGT(0.502)S(0.475)PAT(0.023)EAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 45.556 0.062111 231870000 31806 40122 46024 46029 47376 59513 45834 54842 47554 49363 TRUE FALSE 33061.72544 47012.64139 47223.42325 55133.39882 39323.04444 45692.00768 42241.41132 54106.93269 45842.54083 59034.73474 0.560038519 0.796355596 0.799926068 0.933914568 0.666100129 0.773985144 0.715534871 0.916527074 0.776535052 1 15.84927643 -5 0.091392386 1.701241861 0.605079933 0.375237453 0.098414103 236.5163198 1.498660001 32.3274248 2.184779683 1.00E-05 5 -1.096161929 LFGTS(ph)PATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFGTSPATEAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 41 1 Q3YEC7;Q3YEC7-2;G3V154;F2Z2T0 Q3YEC7 RABL6 Rab-like protein 6 1 LFGT(0.267)S(0.73)PAT(0.003)EAAPPPPEPVPAAEGPATVQSVEDFVPDDRLDR 69.059 0.0016393 174780000 108730 128200 144040 139520 170050 191170 151210 157330 169110 174590 TRUE FALSE 113022.7444 150217.3527 147793.8007 167116.6396 141144.9617 146773.6647 139357.7651 155221.2487 163023.7641 208797.5678 0.541302974 0.719440146 0.707832961 0.800376371 0.675989492 0.702947196 0.667430021 0.743405445 0.780774249 1 17.67174538 -5 0.197115515 2.331431859 0.656542839 0.710543658 0.059965474 76.91323728 0.759022 40.15706836 0.148233957 1.00E-05 5 -1.67488902 LFHTAPNVPHYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFHTAPNVPHYAK 13 0 P53582;H0Y955 P53582 METAP1 Methionine aminopeptidase 1 0 ; 165.7 2.02E-05 848840000 618530 560030 593860 494400 757490 845510 699220 659680 613160 672360 FALSE TRUE 642950.042 656210.7961 609336.4795 592190.8444 628732.1204 649153.1163 644413.3093 650838.0686 591092.4914 804096.0689 0.799593565 0.816085069 0.757790646 0.736467777 0.781911695 0.807307909 0.801413331 0.809403371 0.73510183 1 19.61700835 -1.710445928 3.007193386 1.028936726 0.785011586 0.839043916 0.02852608 14457935.32 13928100.56 3163541.306 0.007162071 0.019478436 1.710445928 -0.24392514 LFIGGLS(ph)FETTDDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 LFIGGLS(0.999)FETTDDSLR;LFIGGLS(0.998)FET(0.001)T(0.002)DDSLR;LFIGGLS(0.998)FET(0.001)T(0.001)DDSLR;LFIGGLS(0.987)FET(0.006)T(0.006)DDS(0.001)LR 159.02 9.73E-09 39273600 31396.6 31321.7 30346.9 30245.8 28577.4 39701.5 36384.2 34322.2 33785.3 28666.7 TRUE FALSE 32636.16201 36700.95833 31137.76514 36228.32897 23719.82376 30481.42831 33532.31133 33862.16705 32569.37365 34283.39101 0.951952565 1.070517159 0.908246362 1.056731201 0.691875076 0.889101907 0.978092025 0.987713469 0.950004439 1 15.06522219 -0.110403476 10.42566595 0.999997928 0.94459989 0.028464992 0.099881831 0 0 0.09666809 0.022784887 0.775526289 0.110403476 -0.055398039 LFIGGLS(ph)FETTDESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 LFIGGLS(0.97)FET(0.015)T(0.015)DESLR 66.285 0.057689 9330200 10267 11716 12628 8683.3 11496 15991 14244 12727 13995 15036 TRUE FALSE 10672.34909 13728.13186 12957.09605 10400.83082 9541.914026 12277.3326 13127.51806 12556.41538 13491.32268 17982.01632 0.593501246 0.763436737 0.720558575 0.578401812 0.53063649 0.68275617 0.730035933 0.698276276 0.750267514 1 14.13426718 0.514881609 0.71731719 1.004572254 0.650030951 0.703683979 0.067279249 0.949913536 0.806824326 0.079234054 0.026221523 3.27251472 -0.514881609 -0.354541303 LFIGGLS(ph)FETTEESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 LFIGGLS(0.999)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR;LFIGGLS(1)FETTEESLR 159.13 9.69E-09 97842000 47363.2 57877 54864.1 46532.9 53597.9 62086 57496.3 60840 56866.4 56373 TRUE FALSE 49233.13571 67816.92453 56293.90352 55736.96873 44487.3481 47667.46742 52989.58977 60024.53931 54819.78937 67418.21002 0.730264652 1.005914048 0.834995523 0.826734627 0.659871392 0.707041427 0.785983338 0.890331252 0.8131303 1 16.0408507 -0.540602109 11.42117362 1 0.811171106 0.281270446 0.092692868 0 0 0.093729438 0.02209224 0.288003583 0.540602109 -0.188828894 LFIGGLSFETTDDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 287.13 9.43E-36 297190000 138439.3 157146 145024.9 152135 157780 179614 158150 146904 161755 153322.2 FALSE TRUE 143904.9905 184134.6031 148804.368 182226.8489 130960.612 137901.3706 145753.7898 144934.9922 155933.4691 183362.7496 0.784810387 1.004209435 0.811529978 0.993805172 0.714216013 0.752068623 0.794893129 0.790427677 0.850409745 1 17.48434106 3.236127688 24.99981765 0.801205604 0.899914586 0.134860096 0.096349164 98.72213473 1014434.094 0.025263351 0.031564342 1722.374899 -3.236127688 0.098708982 LFIGGLSFETTDDSLREHFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFIGGLSFETTDDSLREHFEK 21 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;; 323.3 1.92E-67 1875796000 2602921 2731315 3171064 2144835 4221990 3752410 2739004 3060677 3252967 3257047 FALSE TRUE 2705686.331 3200397.105 3253704.533 2569076.961 3504337.648 2880969.646 2524313.709 3019653.631 3135893.353 3895203 0.694620109 0.821625241 0.835310646 0.659548928 0.89965469 0.739619898 0.648057036 0.775223687 0.805065449 1 21.89326709 0.769653219 2.55741053 0.999883842 0.760077003 0.478905702 0.075150016 0.926461895 8.911837561 0.069593156 0.018561324 5.88373656 -0.769653219 -0.239806839 LFIGGLSFETTDESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8VTQ5;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ;; 240.59 1.67E-19 484710000 175855 211801 194318.3 170092 237801 247088 235120 223191 201464 202772 FALSE TRUE 182797.8912 248176.1742 199382.3945 203735.6899 197379.671 189705.5567 216690.68 220199.4897 194213.35 242501.2911 0.753801724 1.023401455 0.822191064 0.840142702 0.813932454 0.78228679 0.893565057 0.908034298 0.80087553 1 17.8876329 -1.593115994 6.076346519 1.000486117 0.855752251 0.271107646 0.073614483 0.00046361 3.10E-05 0.068163784 0.016013135 0.025520196 1.593115994 -0.144733866 LFIGGLSFETTEESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 416.46 4.55E-140 705788000 187083 201423.4 222923.6 205084.8 245142.1 266839 200610.8 191802.7 218920.1 242800.1 FALSE TRUE 194469.1813 236016.3021 228733.1721 245649.9613 203472.9334 204869.6862 184886.4013 189231.8985 211041.2084 290372.1309 0.669723987 0.812806316 0.787724261 0.845983258 0.700731619 0.705541836 0.636722266 0.651687536 0.726795673 1 18.14754347 0.9097742 21.16226007 1 0.723430856 0.607245221 0.065974154 19042.22008 4466319.098 0.07176749 0.017941873 8.124080153 -0.9097742 -0.276569144 LFIHESIHDEVVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFIHESIHDEVVNR 14 0 P49419;P49419-2;A0A1B0GW77;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GV49;A0A1B0GTJ4;A0A1B0GUY0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 ; 231.06 3.93E-13 84933000 25137 57621 47849 62962 56385 74983 47070 58614 47685 65508 FALSE TRUE 26129.42817 67516.95852 49095.98425 75415.69568 46800.69784 57569.33463 43380.53041 57828.3752 45968.82616 78343.03837 0.333525846 0.861811846 0.626679604 0.962634297 0.597381705 0.734836634 0.553725402 0.738143125 0.586763382 1 16.25751746 -0.988082241 4.111935961 1.000021303 0.679049876 0.265426677 0.165362767 5691793.841 2307280.48 1074.860591 0.034911456 0.102782164 0.988082241 -0.320971427 LFIS(ph)VFRT(ph)KKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFISVFRTKKER 12 3 A6NDF3 A6NDF3 PBDC1 2 LFIS(1)VFRT(1)KKER 59.542 0.078309 70895000 73591 55209 75764 55258 79333 88960 81313 73127 75141 50767 TRUE FALSE 76496.4295 64690.71628 77738.47208 66187.86747 65848.005 68300.3882 74939.47459 72146.85218 72436.69009 60713.82166 1.259950822 1.065502295 1.28040815 1.090161444 1.084563666 1.124956169 1.234306663 1.188310177 1.193084015 1 15.88973737 3.693727904 24.99727826 1.145303933 1.188309183 0.110858424 0.083070808 1418.226724 790757.4148 0.021790037 0.033757105 4940.010861 -3.693727904 0.04300525 LFKDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFKDDIR 7 1 Q9UBT2;Q9UBT2-2;K7EPL2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ; 74.127 0.042886 1263660000 2692300 2722000 2832200 2493100 3820200 3692300 3002300 2918700 3139600 2901600 FALSE TRUE 2798594.083 3189482.326 2906009.459 2986227.739 3170843.769 2834819.282 2766971.881 2879579.601 3026606.409 3470112.966 0.806485008 0.91912925 0.83743944 0.860556347 0.913758082 0.816924207 0.797372278 0.829823014 0.872192473 1 21.7265512 0.879347134 5.985126744 0.999998735 0.848021807 0.57566758 0.039034644 1.366200497 67.43199737 0.038084134 0.009577176 7.574380768 -0.879347134 -0.151976929 LFLEFER ddPTM_MDA-MB-175_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 132575000 179237 209913 205397 199253 257668 265042 227626 210097 190245 232040 FALSE TRUE 186313.4152 245963.9249 210749.8146 238664.6487 213869.6854 203490.0123 209784.0793 207280.9934 183398.1196 277503.7953 0.671390512 0.886344364 0.759448404 0.860041025 0.770691028 0.733287312 0.755968325 0.746948319 0.660885086 1 18.08214798 3.017716444 24.74961399 0.759828421 0.800512357 0 0.098806323 827.0696238 1155394.791 0.026143608 0.031241328 1041.63711 -3.017716444 0.040683937 LFNAIIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFNAIIHR 8 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 ; 147.34 0.00053893 739060000 394990 453640 385850 392490 943650 656800 474470 413470 388690 1032640 FALSE TRUE 410584.5102 531549.1412 395905.568 470123.3505 783248.7101 504268.1539 437279.8016 407928.111 374701.1228 1234966.037 0.332466236 0.430416 0.320580126 0.380677149 0.634226923 0.408325524 0.354082451 0.330315247 0.303410063 1 20.23603994 -1.190640553 4.420202566 1.000152741 0.389295463 0.803873735 0.090644923 28062225.5 7558967.622 43863.53579 0.022196559 0.064470264 1.190640553 -0.610857278 LFNHANQEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFNHANQEVQR 11 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 112.89 0.0014648 247880000 211670 102700 116230 73221 216600 192940 142030 115190 131480 160220 FALSE TRUE 220026.895 120337.9261 119259.0493 87703.89526 179782.4094 148132.609 130897.3175 113646.0665 126748.0605 191612.0414 1.148293674 0.628029038 0.622398511 0.45771599 0.938262585 0.773086117 0.683137221 0.593105035 0.661482752 1 17.5478287 4.7431205 24.65754724 0.687370096 1.148293899 0.420173145 0.154301458 354.7274984 1918104.96 0.03564504 0.284822515 55350.36633 -4.7431205 0.460923804 LFNVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LFNVDR 6 0 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 ;;;;; 168.82 0.014504 2414890000 2314750 2648770 2522040 2587790 2938820 3066050 2753780 2736770 2535260 2581430 FALSE TRUE 2406138.117 3103675.643 2587766.434 3099647.138 2439280.426 2354006.354 2537931.528 2700088.075 2444016.488 3087211.784 0.779388745 1.005332922 0.838221222 1.004028021 0.790124098 0.762502387 0.822078855 0.874604097 0.791658188 1 21.55787303 LFPADT(ph)SPSTATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.494)S(0.494)PS(0.011)T(0.001)ATK;LFPADT(0.723)S(0.272)PS(0.004)T(0.001)ATK 145.71 0.00046875 131453000 441840 341300 400180 305670 506400 514110 462060 414380 454870 351410 TRUE FALSE 459284.1844 399915.6201 410609.0196 366130.6137 420322.3089 394715.7439 425842.5298 408825.9139 438499.3176 420262.0613 1.092851881 0.9515863 0.977030899 0.871195969 1.000143357 0.939213363 1.013278544 0.972788057 1.043394962 1 18.6809297 1.610497877 1.549195115 1.016345906 0.969738231 0.071121942 0.055078922 0.920064453 4.351120807 0.044409786 0.015813791 40.78475683 -1.610497877 -0.046607675 LFPADTS(ph)PSTATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 LFPADT(0.071)S(0.925)PS(0.003)TATK;LFPADT(0.013)S(0.986)PS(0.001)TATK;LFPADT(0.056)S(0.934)PS(0.01)TATK 222.56 1.81E-11 387409000 1287820 921560 1125250 930040 1373430 1392410 1315600 1118360 1188900 943620 TRUE FALSE 1338664.128 1079830.761 1154574.939 1113999.136 1139974.859 1069043.88 1212479.834 1103370.213 1146111.721 1128504.272 1.186228675 0.956869006 1.023101966 0.987146583 1.010164416 0.947310441 1.074413154 0.97772799 1.015602465 1 20.10598045 4.746766142 24.98380581 1.00001974 1.186228768 0.728851532 0.034228358 494.6955078 1506192.379 0.007390401 0.085057017 55816.95514 -4.746766142 0.186209028 LFPDIPIGYSGHETGIAISVAAVALGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFPDIPIGYSGHETGIAISVAAVALGAK 28 0 Q9NR45;Q5TBR0;Q5TBR1 Q9NR45 NANS Sialic acid synthase 0 ;; 250.99 1.57E-46 528135000 181211 286099 324498 266857 451851 432683 353814 355608 370681 371284 FALSE TRUE 188365.3502 335234.2777 332954.6845 319640.5181 375045.5284 332198.9306 326081.1342 350841.6564 357340.2632 444029.9911 0.424217629 0.75498116 0.749847288 0.719862452 0.844640083 0.748145254 0.734367364 0.790130539 0.804766053 1 18.7602976 6.094192823 0.091452513 1.125464578 2.53E-24 0.597070858 0.085841084 78.36142121 0.781566651 1.807350354 11.40533362 1242203.712 -6.094192823 -1.125464578 LFPDT(ph)PLALDANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFPDTPLALDANK 13 0 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK;LFPDT(1)PLALDANK 259.61 6.23E-23 529114000 1887552 1318897 1670075 1329286 2031138 2150661 2141419 1656976 1742424 1165377 TRUE FALSE 1962074.01 1545407.3 1713598.526 1592214.803 1685885.888 1651202.576 1973568.983 1634766.947 1679714.501 1393710.311 1.407806196 1.108843989 1.229522745 1.142428804 1.209638671 1.184753075 1.416053945 1.172960359 1.205210644 1 20.41049929 0.621339474 1.879243945 1.000190675 1.230290424 0.341690149 0.096972495 2.168967174 9.367200678 0.087410402 0.024333955 4.181570985 -0.621339474 0.230099749 LFPDT(ph)PLALDANKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 84.375 0.0047807 395550000 334800 169990 245480 170380 325130 304720 343010 256960 256090 145490 TRUE FALSE 348018.1625 199184.4602 251877.4105 204080.6555 269864.5187 233953.3981 316123.9799 253515.8715 246873.3709 173995.9799 2.000150594 1.144764725 1.44760477 1.172904429 1.550981344 1.344590824 1.816846458 1.45702143 1.418845257 1 17.40869445 0.739120391 3.08032306 1.00006325 1.47930215 0.258022835 0.24814447 2.736679181 30.64365335 0.22242104 0.058026703 5.484289747 -0.739120391 0.4792389 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFPEFDDSDYDEVPEEGPGAPAR 23 0 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 LFPEFDDS(0.968)DY(0.032)DEVPEEGPGAPAR;LFPEFDDS(0.908)DY(0.092)DEVPEEGPGAPAR 150.94 5.05E-08 131978000 43552 53459 48655 40221 44064 58939 51093 46559 43618 49198 TRUE FALSE 45271.46659 62640.1674 49922.98927 48176.59375 36574.01702 45251.31048 47088.19715 45934.95276 42048.1967 58837.40615 0.769433419 1.064631694 0.848490655 0.818808933 0.621611648 0.769090846 0.800310555 0.780710024 0.714650755 1 15.84444603 3.823990125 3.156990701 0.770380308 0.921710827 0.16280581 0.112278265 0.338974661 6.525631546 0.027849968 0.054533245 6667.916069 -3.823990125 0.151330519 LFQCLLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFQCLLHR 8 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 187.34 0.00020276 1394910000 579660 692840 433620 411430 1954670 1020470 604610 543000 489360 2440700 FALSE TRUE 602545.4244 811829.8805 444920.4934 492809.626 1622415.892 783481.3079 557219.0883 535721.9732 471748.0292 2918908.435 0.206428341 0.278127902 0.152427013 0.168833534 0.555829663 0.268415857 0.190899818 0.183535039 0.161617961 1 21.47699752 -2.036908782 2.779787357 1.961603488 0.240754629 0.802621581 0.112964191 15607361.52 6487031.009 95577184.54 0.029657379 0.009185255 2.036908782 -1.720848859 LFQECCPHSTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LFQECCPHSTDR 12 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;;;; 232.37 1.22E-12 35256690000 3220453 5579810 4951552 5004549 5375247 6251947 4577897 5320328 4769726 5558465 FALSE TRUE 3347598.971 6538098.963 5080593.513 5994433.855 4461564.435 4800027.058 4219069.471 5249017.705 4598064.493 6647539.794 0.503584646 0.983536641 0.764281775 0.901752233 0.671160245 0.722075716 0.634681341 0.789618095 0.691694166 1 22.66438908 -1.030013832 4.215716304 1.000019681 0.748778568 0.268598774 0.127888633 35621583.9 91621106.13 11108.94154 0.028638888 0.093322458 1.030013832 -0.251241113 LFQEDPEAFLLYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFQEDPEAFLLYHR 14 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 0 ; 193.16 2.91E-07 92426000 73577 97381 83883 89955 101807 113011 81403 88609 85221 106565 FALSE TRUE 76481.87677 114105.4292 86069.05989 107747.8305 84501.8825 86765.90795 75022.42015 87421.34129 82153.91286 127444.3714 0.600119691 0.89533518 0.675346105 0.845449895 0.663049153 0.680813966 0.588667976 0.685956863 0.644625666 1 16.95950813 -0.998858389 4.39043107 1.000011259 0.699888386 0.485005335 0.093425219 99295864917 72997589.97 12118691.37 0.021898606 0.100263211 0.998858389 -0.300122872 LFQLGPPS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 LFQLGPPS(1)PVK;LFQLGPPS(1)PVK 142.85 3.93E-05 622600000 2334200 1338670 1645630 1538590 2024800 2253200 2483700 1805430 1817730 974010 TRUE FALSE 2426356.018 1568576.159 1688516.47 1842918.51 1680625.219 1729928.448 2289021.104 1781231.164 1752310.252 1164848.611 2.082979707 1.34659229 1.449558727 1.582109892 1.442784241 1.485110109 1.96508034 1.529152499 1.504324455 1 20.15171104 0.721200429 2.333714914 1.000317979 1.599026274 0.400989192 0.222749158 1.400982858 10.28492559 0.204193106 0.055091647 5.26260082 -0.721200429 0.598708295 LFQQILSGVDYCHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFQQILSGVDYCHR 14 0 Q13131-2;Q13131;Q96E92 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 ; 141.82 9.57E-06 416410000 275020 327970 319160 361150 350430 432290 338890 349120 316920 369570 FALSE TRUE 285878.002 384296.2962 327477.5718 432584.3921 290864.0338 331897.1989 312326.9163 344440.6174 305514.1111 441980.1657 0.646811835 0.869487652 0.740932732 0.97874164 0.658092956 0.750932337 0.706653693 0.779312386 0.691239415 1 18.7536221 -1.146499179 4.556660952 1.000030576 0.763140632 0.364098774 0.095721055 2.77E-05 5.18E-06 0.086277937 0.020333282 0.071367555 1.146499179 -0.236889943 LFQQIYSDGSDEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFQQIYSDGSDEVKR 15 1 Q9Y2Z0;Q9Y2Z0-2 Q9Y2Z0 SUGT1 Suppressor of G2 allele of SKP1 homolog 0 70.451 0.056401 0 183630 139320 127910 114310 190560 174350 135850 128550 184280 128810 FALSE TRUE 190879.8542 163247.1262 131243.4397 136920.1768 158168.6793 133859.8548 125201.722 126826.9975 177647.7988 154047.8533 1.239094542 1.059716982 0.851965392 0.888815871 1.026750298 0.868949823 0.812745646 0.823296105 1.153198795 1 17.23301905 4.538460048 2.979415123 0.911654352 1.239209252 0.464701158 0.102186037 0.234825256 3.658872206 0.025330019 0.143030268 34550.95437 -4.538460048 0.327554899 LFRPPS(ph)PAPAAPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LFRPPSPAPAAPGAR 15 1 Q86U90 Q86U90 YRDC "YrdC domain-containing protein, mitochondrial" 1 LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR;LFRPPS(1)PAPAAPGAR 133.95 2.31E-05 5275250000 2548060 2838870 2787700 2889850 3102730 3341590 2623570 2853410 2736810 3155190 TRUE FALSE 2648659.376 3326423.839 2860349.752 3461453.705 2575329.063 2565556.365 2417927.728 2815164.706 2638312.743 3773389.071 0.701931162 0.881548066 0.758032023 0.917332838 0.682497621 0.679907721 0.640784102 0.746057365 0.699189162 1 21.84742943 4.025482352 24.96326277 0.748621256 0.798752221 0 0.114480209 919.2359933 900497.4636 0.027517187 0.059440617 10604.30846 -4.025482352 0.050130965 LFS(ph)QGQDVSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFSQGQDVSNK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 LFS(1)QGQDVSNK;LFS(1)QGQDVSNK;LFS(0.982)QGQDVS(0.018)NK;LFS(0.998)QGQDVS(0.002)NK 146.79 3.73E-05 1331210000 2463720 1419310 2079850 1747600 3348830 3053050 2889290 2362000 2492270 1413330 TRUE FALSE 2560989.568 1663065.452 2134052.6 2093270.064 2779597.073 2344025.407 2662819.9 2330341.253 2402573.69 1690244.954 1.515158831 0.983919785 1.262570017 1.238441836 1.644493638 1.386796276 1.575404733 1.378700317 1.421435209 1 20.68880091 5.060716586 22.0464139 1.347681208 5.167260185 0.061541892 0.205004683 2971.392786 1101135.525 0.047297008 11341.75417 115004.9639 -5.060716586 3.819578977 LFSASEFEDPLVGEDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFSASEFEDPLVGEDTER 18 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;P37268-5 E9PNM1 FDFT1 Squalene synthase 0 ; 182.02 1.64E-13 89157000 126849 184479 151589 193095 159323 192011 148980 141213 129473 164451 FALSE TRUE 131857.0965 216161.8332 155539.5339 231288.6147 132241.3334 147419.3552 137302.5583 139320.2707 124813.292 196672.0248 0.670441546 1.099098021 0.790857439 1.176011763 0.67239524 0.74956952 0.698129581 0.708388856 0.634626567 1 17.58543223 3.189006717 24.99999952 0.725320977 0.935658269 0.243199681 0.162443592 128.8808915 65020.05599 0.042646502 0.050972392 1545.278338 -3.189006717 0.210337291 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LFSLS(1)NPSLSTTNLSGPSR;LFSLS(0.975)NPS(0.025)LSTTNLSGPSR;LFSLS(1)NPSLSTTNLSGPSR 414.94 5.46E-148 1544300000 608992 652029 644721 674567 695463 772706 619256 625887 559200 626574 TRUE FALSE 633035.4744 764009.9087 661522.9589 807994.3392 577248.4477 593256.742 570717.0966 617498.0085 539074.5012 749339.1788 0.844791641 1.019578223 0.88280845 1.078275849 0.770343342 0.791706558 0.761627195 0.82405675 0.719399861 1 19.51525936 3.214576643 24.9925236 0.799804071 0.95562499 0.366071176 0.092866569 208.7286742 217505.3407 0.024385877 0.029160933 1638.991278 -3.214576643 0.15582092 LFSSSS(ph)SPPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFS(0.001)S(0.006)S(0.082)S(0.586)S(0.326)PPPAK;LFS(0.004)S(0.045)S(0.036)S(0.511)S(0.404)PPPAK;LFS(0.001)S(0.016)S(0.047)S(0.556)S(0.38)PPPAK 105.17 0.0021597 1129370000 2799750 2394720 2881820 2457140 3297050 3453560 3139030 2913750 2832860 2333430 TRUE FALSE 2910286.292 2805994.532 2956922.597 2943154.958 2736618.619 2651523.029 2892984.626 2874695.947 2730905.922 2790620.932 1.042881266 1.005509025 1.059593068 1.054659529 0.980648639 0.950155214 1.036681332 1.030127709 0.978601533 1 21.41215474 3.242677274 24.99841619 1.000415444 1.039502198 0.386625577 0.027186788 139.319418 846007.3626 0.008409229 0.010998104 1748.546852 -3.242677274 0.039086755 LFSSSSS(ph)PPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFSSSSSPPPAK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 LFSS(0.001)S(0.005)S(0.152)S(0.842)PPPAK 193.34 3.08E-06 724780000 2274600 2230900 2579400 2236400 2839300 3059000 2781600 2633800 2464200 2123700 TRUE FALSE 2364402.964 2614039.721 2646621.283 2678753.245 2356676.8 2348593.61 2563570.924 2598498.219 2375513.923 2539798.354 0.930941214 1.029231205 1.04205961 1.054710993 0.927899176 0.924716565 1.009360022 1.023112018 0.935315955 1 21.27628253 4.760153362 22.81091994 0.995894793 0.930940992 0.144708549 0.045826123 3258.389845 3442029.636 0.011599079 0.458143768 57564.31777 -4.760153362 -0.064953801 LFTEEELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFTEEELAR 9 0 Q9UMX5 Q9UMX5 NENF Neudesin 0 ;;; 214.69 1.55E-06 653750000 524694 709340 591711 652450 712750 757230 572214 618910 572948 680900 FALSE TRUE 545409.3243 831163.6271 607131.4748 781502.6626 591597.0096 581374.8084 527362.3715 610614.5238 552327.7134 814309.3184 0.669781509 1.020697674 0.745578444 0.959712292 0.726501584 0.713948367 0.647619227 0.749855749 0.67827753 1 19.63521739 3.197883296 24.94418433 0.732210064 0.853827644 0.105054752 0.129267659 236.8859964 145262.7162 0.033895408 0.040513193 1577.187391 -3.197883296 0.121617579 LFTLPLLHYLEVSGCGSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFTLPLLHYLEVSGCGSLR 19 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 115.15 0.00014355 159252000 90975 135423 138153 148983 170327 172764 146621 146839 170577 157640 FALSE TRUE 94566.76325 158680.8468 141753.3807 178451.3927 141374.8774 132642.1793 135128.4629 144870.8634 164437.9671 188526.5398 0.501609818 0.8416897 0.751901461 0.946558468 0.749893768 0.703572979 0.716760956 0.768437502 0.872227153 1 17.52440811 -5 0.197404122 2.06899785 0.724192488 0.342943924 0.107947617 171.0584053 1.688604851 71.85270949 0.263198057 1.00E-05 5 -1.344805362 LFTNFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFTNFHR 7 0 F5GWE5;Q00169;I3L4H1 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 170.73 0.00096411 374670000 225240 256210 239000 237910 333380 321360 273430 265210 236500 334800 FALSE TRUE 234132.6491 300212.0745 245228.5363 284967.8879 276712.1867 246729.0103 251997.8421 261655.2937 227988.4112 400397.6499 0.584750308 0.749784807 0.612462477 0.711712189 0.691093434 0.616209936 0.629368934 0.653488585 0.569404968 1 18.61107398 -1.833874047 2.826046381 1.118584242 0.650385128 0.793583209 0.05405698 17599820.87 14293557.38 14227064.29 0.012085416 0.014659729 1.833874047 -0.468199114 LFVFDKTSQSWVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFVFDKTSQSWVER 14 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EIJ4 Q9H6Z4 RANBP3 Ran-binding protein 3 0 86.497 0.0066725 276960000 243300 233950 240450 218710 262620 357890 263320 249430 276160 256300 FALSE TRUE 252905.6719 274129.0926 246716.3245 261970.1852 217979.9462 274775.4714 242680.2903 246086.7988 266221.0555 306517.0778 0.825094881 0.894335463 0.804902377 0.854667502 0.711151065 0.896444248 0.791734973 0.802848574 0.8685358 1 18.22560793 0.892204735 4.111420885 0.999959862 0.822121614 0.525835106 0.05073528 0.405493339 13.77739086 0.045818495 0.011693421 7.801978249 -0.892204735 -0.177838248 LFVGGIKEDTEEHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 194.23 1.59E-10 6489610000 5808590 4829811 5970760 4102281 7306280 7169400 5309040 5728530 6290920 5205300 FALSE TRUE 6037917.618 5659293.469 6126362.911 4913699.938 6064361.135 5504415.503 4892903.572 5651748.425 6064511.018 6225178.874 0.969918735 0.909097326 0.984126406 0.789326707 0.974166568 0.884218047 0.785986021 0.907885306 0.974190644 1 22.56968386 LFVGNLPADITEDEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 278.85 1.22E-35 2827100000 685713 536379 626278 470391 821960 818800 716900 629520 715020 530641 FALSE TRUE 712785.4787 628497.9208 642599.3192 563432.9358 682243.5328 628646.109 660707.5047 621082.3141 689286.5699 634609.9442 1.123186747 0.99036885 1.012589426 0.887841328 1.075059632 0.990602361 1.041123781 0.978683552 1.086157846 1 19.2755106 2.24509205 24.89812974 1.020369021 1.009309292 0.004390009 0.062989366 1431.756878 5457898.335 0.021631307 0.017699849 175.829625 -2.24509205 -0.011059729 LFVGNLPTDITEEDFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFVGNLPTDITEEDFKR 17 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 197.14 2.46E-11 928100000 1156450 979820 1108590 875100 1305780 1445510 1276010 1129620 1184600 951680 FALSE TRUE 1202107.539 1148096.463 1137480.766 1048192.168 1083823.982 1109812.209 1175993.002 1114479.292 1141966.477 1138143.475 1.056200352 1.008744933 0.999417728 0.920966637 0.952273598 0.975107474 1.033255497 0.979208084 1.003358981 1 20.11825101 1.210078769 23.68948368 1.001679535 0.989085266 0.013060694 0.03639029 852.6973142 709184.9714 0.036584755 0.009156672 16.22104275 -1.210078769 -0.012594269 LFVLLPEQS(ph)PVSYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFVLLPEQSPVSYSK 15 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 LFVLLPEQS(1)PVSYSK;LFVLLPEQS(1)PVSYSK 251.87 1.31E-24 947020000 1264490 1038440 1265860 1072440 1371590 1422200 1520000 1296650 1276630 1038530 TRUE FALSE 1314413.042 1216783.992 1298849.352 1284565.431 1138447.622 1091915.604 1400858.428 1279270.528 1230684.336 1242010.07 1.058294996 0.979689313 1.045763946 1.034263298 0.916617063 0.879151973 1.127896192 1.030000126 0.990881125 1 20.24424544 LFVT(ph)PPEGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFVTPPEGSSR 11 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LFVT(0.996)PPEGS(0.002)S(0.002)R 117.79 0.009022 131350000 227130 238100 225020 217020 213970 278600 224180 208740 222450 235630 TRUE FALSE 236097.2678 278991.8228 230884.2061 259945.9083 177599.4558 213899.3722 206608.1858 205942.1817 214444.068 281797.1871 0.837826915 0.99004474 0.819327575 0.922457427 0.630238569 0.75905432 0.733180441 0.730817024 0.760987255 1 18.10429769 3.265461031 24.99980414 0.751304514 0.894167365 0.264720591 0.098069634 237.8358658 221030.2612 0.024774859 0.033536702 1842.727134 -3.265461031 0.142862851 LFYADHPFIFLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LFYADHPFIFLVR 13 0 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 ; 193.23 2.04E-06 4188200000 1805990 2538230 2078370 2453570 3130920 3167550 2352790 2173080 2132540 3022090 FALSE TRUE 1877291.88 2974151.258 2132534.03 2938878.823 2598727.337 2431934.517 2168372.172 2143953.417 2055790.302 3614210.674 0.519419605 0.822904785 0.590041429 0.813145411 0.719030397 0.672881228 0.599957326 0.593201009 0.568807545 1 21.78524917 -1.244707269 5.235131926 1.000037982 0.658308555 0.530244459 0.097247471 4.20E-05 6.06E-06 0.091752768 0.021623936 0.056923649 1.244707269 -0.341729427 LFYAVDVDDDIWEDEVED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LFYAVDVDDDIWEDEVED 18 0 Q9UBS8;Q9UBS8-2 Q9UBS8 RNF14 E3 ubiquitin-protein ligase RNF14 0 90.05 0.0064622 2774500 5782.7 8947.1 9447.6 7112.3 9855.8 11082 8941.5 8928.5 9736.8 12420 FALSE TRUE 6011.005461 10483.69483 9693.812217 8519.091712 8180.514636 8508.373449 8240.641866 8808.828062 9386.37447 14853.4612 0.404687189 0.705808207 0.652629854 0.57354253 0.550748039 0.572820929 0.554796068 0.593048848 0.6319318 1 13.85851153 0.544242958 1.805410722 0.999979584 0.580572631 0.748940492 0.073183267 1.308520787 4.643436568 0.066422072 0.018589892 3.501409919 -0.544242958 -0.419406952 LGADES(ph)EEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGADESEEEGR 11 0 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 LGADES(1)EEEGR;LGADES(1)EEEGR 200.21 5.00E-08 188382000 205400 223140 220040 226900 250630 292390 280030 206065 221290 194351 TRUE FALSE 213509.3506 261462.5592 225774.4232 271780.1428 208028.0021 224486.8537 258080.5169 203303.0357 213325.8161 232430.3574 0.918594942 1.1249071 0.971363748 1.1692971 0.895012185 0.965824156 1.110356323 0.87468366 0.91780531 1 17.82643898 1.706420378 11.81013253 0.923069541 1.022752788 0.176272467 0.089969656 0.177741755 49.90575343 0.040071769 0.021895655 50.86515566 -1.706420378 0.099683247 LGAESANVCGSQQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGAESANVCGSQQGR 15 0 P40126;P40126-2 P40126 DCT L-dopachrome tautomerase 0 61.409 0.051776 194640000 4389.3 0 0 5363.5 0 3484.5 0 0 0 4382.4 FALSE TRUE 4562.592953 0 0 6424.384292 0 2675.277683 0 0 0 5241.047374 0.87054984 0 0 1.225782527 0 0.510447148 0 0 0 1 12.35563943 -1.490774206 5.124724283 1.001804569 0.265460228 0.202193838 0.420854576 0.008397592 0.000834438 0.39436193 0.092766643 0.032301731 1.490774206 -0.736344341 LGAGEGGEASVS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 248.06 2.55E-18 339230000 289830 136110 172840 170950 212070 269220 294250 182230 182700 102240 TRUE FALSE 301272.7122 159485.8337 177344.3524 204763.3998 176022.4171 206697.7351 271185.9161 179787.5049 176124.6627 122271.9705 2.463955647 1.304353181 1.450408885 1.67465527 1.439597452 1.690475211 2.217891108 1.470390182 1.440433666 1 16.89973419 0.981917947 1.922909521 1.010126481 1.702508894 0.298455531 0.343043605 0.450043223 3.51930108 0.313199322 0.08823195 9.592193857 -0.981917947 0.692382413 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LGAGEGGEASVSPEKTSTTSK 21 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK;LGAGEGGEASVS(1)PEKTSTTSK 269.94 3.07E-38 3480880000 3767390 1407251 2152935 1271924 3272680 3195820 2872870 2201370 2574000 1222444 TRUE FALSE 3916129.466 1648935.412 2209042.255 1523506.771 2716391.023 2453639.238 2647686.943 2171864.236 2481362.243 1461958.497 2.678687169 1.127894818 1.511015709 1.042099878 1.858049342 1.678323457 1.811054793 1.485585426 1.697286379 1 20.47947092 -1.075460617 4.667717 0.999970019 1.619942219 0.170015546 0.427724154 0.0001231 2.44E-05 0.382012345 0.090036829 0.084050322 1.075460617 0.6199722 LGAGGGS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGAGGGSPEK 10 0 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(1)PEK;LGAGGGS(1)PEK;LGAGGGS(1)PEK 128.36 0.00034783 804740000 2928040 1487680 1923080 1713160 2494570 2959970 3181390 2132630 2190160 1096780 TRUE FALSE 3043641.28 1743177.467 1973197.045 2052017.935 2070543.882 2272561.826 2932024.339 2104045.583 2111336.569 1311673.042 2.320426801 1.32897255 1.504336051 1.564427925 1.578551831 1.732567304 2.235331706 1.604093029 1.609651569 1 20.32297672 2.723311128 21.94876768 1.717120064 1.627104556 0 0.373939029 1105.513003 1591167.008 0.11589216 0.109839703 528.8239654 -2.723311128 -0.090015508 LGAGGGS(ph)PEKS(ph)PSAQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 LGAGGGS(1)PEKS(0.733)PS(0.267)AQELK;LGAGGGS(1)PEKS(0.976)PS(0.024)AQELK;LGAGGGS(1)PEKS(0.941)PS(0.059)AQELK;LGAGGGS(1)PEKS(0.896)PS(0.104)AQELK;LGAGGGS(1)PEKS(0.895)PS(0.105)AQELK 185.45 3.02E-14 1598630000 7107720 1878450 2936380 1772930 4584790 5140970 4527020 3235540 3541760 1278540 TRUE FALSE 7388338.274 2201059.175 3012904.475 2123610.262 3805469.033 3947057.63 4172180.343 3192172.879 3414292.749 1529045.434 4.831993942 1.439498871 1.970447973 1.388847065 2.488787415 2.581386754 2.72861764 2.087690011 2.232957029 1 20.54419984 7.999999994 0.054014318 6.74E-10 6.668827808 0.208121706 0.895292689 905.3999742 3.674847024 100.4878912 490.0622948 99999998.73 -7.999999994 6.668827807 LGAGGGS(ph)PEKSPSAQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGS(0.915)PEKS(0.084)PS(0.001)AQELK;LGAGGGS(0.998)PEKS(0.002)PSAQELK 249.59 6.45E-25 2164800000 3666800 1319590 2033780 1227400 3034700 2972600 2909800 2223300 2527700 1066000 TRUE FALSE 3811568.095 1546219.318 2086781.978 1470176.057 2518862.778 2282258.7 2681722.273 2193500.3 2436728.571 1274862.29 2.989788093 1.212852031 1.636868542 1.153203815 1.97579205 1.790200179 2.103538785 1.720578228 1.911366106 1 20.28190999 LGAGGGSPEKS(ph)PSAQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 LGAGGGSPEKS(0.996)PS(0.004)AQELK;LGAGGGSPEKS(0.999)PS(0.001)AQELK;LGAGGGSPEKS(0.835)PS(0.165)AQELK;LGAGGGSPEKS(0.984)PS(0.016)AQELK 214.35 6.12E-19 2143660000 3444300 1423630 2047200 1335440 3009050 2801100 2830500 2139340 2354800 1120090 TRUE FALSE 3580283.624 1668127.378 2100551.714 1599586.046 2497572.756 2150586.976 2608638.014 2110665.647 2270051.208 1339550.19 2.672750637 1.245289195 1.568102285 1.194121772 1.864486134 1.605454571 1.947398487 1.57565253 1.69463692 1 20.35331721 -1.827815658 1.092277214 0.55962258 1.67904837 0.222839523 0.393168146 3540.862872 790.8979985 4059.619926 0.108122873 0.014865665 1.827815658 1.11942579 LGAPENSGIST(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGAPENSGISTLER 14 0 A0A1B0GV68;M0QYB0;Q9Y4F1-3;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 LGAPENSGIS(0.003)T(0.997)LER;LGAPENSGIS(0.012)T(0.988)LER;LGAPENSGIS(0.016)T(0.984)LER;LGAPENSGIST(1)LER 307.06 8.13E-44 1902280000 2184710 3448710 2544990 4082660 3126590 4525830 2983610 2904920 2585210 4516150 TRUE FALSE 2270964.038 4040999.115 2611314.53 4890197.962 2595133.349 3474774.572 2749746.852 2865984.299 2492168.797 5401003.126 0.420470788 0.748194182 0.48348695 0.90542402 0.480490992 0.64335726 0.509117804 0.530639259 0.461427024 1 22.36479595 -2.159052053 2.413430857 2.015326202 0.580529252 0.441671702 0.142980078 10425067.86 1938554.935 58128323.45 0.032780735 0.006933427 2.159052053 -1.43479695 LGASNS(ph)PGQPNSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;LGASNS(1)PGQPNSVK 303.49 4.76E-44 16448280000 7795970 5709120 7125050 5599570 8448830 8488830 8448400 7137220 7459110 4769190 TRUE FALSE 8103760.915 6689616.949 7310734.656 6707148.233 7012700.894 6517427.882 7786192.332 7041557.24 7190658.088 5703621.469 1.420809736 1.17287183 1.28177066 1.175945541 1.229517234 1.142682402 1.365131325 1.234576537 1.260717971 1 22.44344681 -1.235873367 3.942318993 0.999757478 1.249694325 0.462516937 0.081966084 5654819.464 1772736.383 11698.74227 0.017649814 0.058093378 1.235873367 0.249936847 LGASNS(ph)PGQPNSVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGASNSPGQPNSVKR 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 LGAS(0.32)NS(0.68)PGQPNSVKR 63.302 0.045331 239570000 156870 149210 164590 123120 242360 221490 138810 187170 202810 184170 TRUE FALSE 163063.3487 174835.6568 168879.3506 147472.7685 201163.7338 170052.3042 127929.7095 184661.2923 195510.9077 220254.5854 0.740340313 0.793788953 0.766746129 0.669555952 0.913323704 0.772071573 0.580826543 0.83839931 0.88765874 1 17.74881253 1.146125771 2.251174549 0.990882805 0.754018499 0.479562548 0.083008995 0.238333423 2.221985252 0.07686198 0.021588944 13.99992698 -1.146125771 -0.236864306 LGCEVLGVSVDSQFTHLAWINTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGCEVLGVSVDSQFTHLAWINTPR 24 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;; 345.48 9.12E-102 2249535000 816465 1246394 1234725 1380726 1267317 1536830 1327442 1303434 1228540 1284176 FALSE TRUE 848699.6686 1460452.474 1266902.948 1653829.482 1051898.909 1179924.523 1223393.627 1285963.599 1184325.085 1535785.7 0.552615947 0.950948087 0.824921698 1.076862144 0.684925578 0.768287218 0.796591365 0.837332708 0.771152567 1 20.55054549 -1.316026033 2.858546586 1.002032083 0.816252095 0.155322355 0.133436119 14066476.78 17200353.03 243785.7236 0.031834631 0.048302985 1.316026033 -0.185779989 LGDAS(ph)DTEAADGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 LGDAS(0.992)DT(0.008)EAADGER;LGDAS(0.979)DT(0.021)EAADGER 375.6 2.47E-97 733970000 605920 583470 610930 560570 719340 817260 707460 650310 620130 491750 TRUE FALSE 629842.1895 683676.4337 626851.3377 671449.0729 597066.8437 627463.7507 652007.4366 641593.6581 597811.6424 588098.9974 1.070979873 1.162519298 1.065894247 1.141727967 1.015248872 1.06693559 1.108669526 1.090962 1.016515323 1 19.16569951 -5 0.095909731 0.701903155 1.153516165 0.341002632 0.04160698 220.5618767 1.453006687 13.03293546 0.774755079 1.00E-05 5 0.45161301 LGDDEDREPSLRPDDDRVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGDDEDREPSLRPDDDRVPR 20 3 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 83.948 0.0012526 147580000 93842 114480 108860 123740 131390 145070 137120 114410 117060 110840 FALSE TRUE 97546.95462 134141.0495 111696.981 148215.4027 109056.3747 111379.6911 126372.1761 112876.5211 112847.0335 132556.9758 0.735886995 1.011950134 0.842633745 1.118126011 0.822713207 0.840240133 0.953342329 0.851532108 0.851309656 1 17.01625307 LGDDIDLIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGDDIDLIVR 10 0 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;; 120.12 0.0014006 129381000 206814 213153 230088 221101 249433 284067 271073 229473 220306 181680 FALSE TRUE 214979.1764 249760.3696 236084.2823 264834.1179 207034.4678 218096.7443 249825.5899 226397.2898 212377.2301 217276.7175 0.989425737 1.149503603 1.086560424 1.218879413 0.952860804 1.003774113 1.149803775 1.041976758 0.977450472 1 17.72917406 3.226151517 24.9999977 1.032319087 1.112083707 0.258852539 0.073199364 350.110902 705350.6649 0.021222241 0.02553174 1683.261217 -3.226151517 0.079764621 LGDLWTLDIDTLTWNKPSLSGVAPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGDLWTLDIDTLTWNKPSLSGVAPLPR 27 1 P51610-2;P51610;A6NEM2;P51610-4;P51610-3 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 0 154.71 3.84E-08 127980000 81177 98205 105100 94137 122550 140980 128990 102600 109860 99626 FALSE TRUE 84381.93064 115070.9448 107838.9923 112757.0176 101718.9948 108239.5316 118879.4267 101224.8148 105906.1601 119145.8072 0.708224088 0.965799364 0.905101026 0.946378393 0.853735411 0.908462782 0.997764248 0.849587721 0.888878614 1 16.86236866 7.999907517 0.016974379 1.633889015 6.26E-07 0.211463636 0.073043906 8288.228673 10.85312297 405.2321407 670.2160921 99978707.27 -7.999907517 -1.633888389 LGDS(ph)SLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.692)S(0.308)LSR 82.645 0.020703 75972000 191060 238720 233220 288620 316840 366970 276920 254160 250060 268980 TRUE FALSE 198603.1963 279718.303 239297.9048 345708.1746 262983.65 281746.779 255214.2868 250753.4009 241060.3894 321681.4811 0.617390829 0.869550532 0.74389705 1.074690944 0.8175281 0.875856385 0.793375752 0.779508351 0.749376025 1 18.29527336 4.742240308 24.4613196 0.845945779 0.617390711 0.323511942 0.102583454 326.6330681 2171216.805 0.023725472 0.176011293 55238.30046 -4.742240308 -0.228555068 LGDSHDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LGDSHDLQR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;;; 142.36 0.00010451 2555740000 6283830 6110880 6377070 5763960 7905140 9333150 7380690 6749900 6646210 6590150 FALSE TRUE 6531920.461 7160376.104 6543261.683 6904054.084 6561427.126 7165667.358 6802172.232 6659428.631 6407014.2 7881363.716 0.828780487 0.908519942 0.83021948 0.875997395 0.83252434 0.909191304 0.863070463 0.844958927 0.812932182 1 22.91001385 -1.11716547 4.910968387 1.000006565 0.857834418 0.650217368 0.031611971 2.11E-06 3.80E-07 0.02848225 0.006713021 0.076354481 1.11716547 -0.142172147 LGDSS(ph)LSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGDSSLSR 8 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 LGDS(0.042)S(0.958)LSR;LGDS(0.042)S(0.958)LSR 149.27 0.00053277 668790000 1184740 1183170 1283060 1430520 1818760 1791220 1512490 1382840 1331020 1310030 TRUE FALSE 1231514.45 1386370.244 1316497.598 1713472.586 1509607.825 1375236.301 1393937.082 1364305.292 1283116.85 1566705.296 0.786053671 0.884895358 0.840296896 1.093678939 0.963555704 0.877788761 0.889725135 0.870811693 0.818990561 1 20.5793024 4.732006768 0.007740139 1.769824891 4.37E-06 0.067856131 0.08431988 49725.77576 59.90762057 6469.217012 7244.331788 53951.903 -4.732006768 -1.769820522 LGDTALHAAAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGDTALHAAAWK 12 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 0 ; 88.187 0.0087973 413690000 739430 659300 748170 608200 1074890 984960 845540 789550 727250 909590 FALSE TRUE 768623.2674 772529.6464 767667.9248 728500.1447 892180.5817 756217.9672 779264.3654 778967.3737 701076.4146 1087806.745 0.706580714 0.710171774 0.705702486 0.669696293 0.820164598 0.695176759 0.716362873 0.716089854 0.644486181 1 20.05299085 -1.4960922 5.678885776 1.000396554 0.711638207 0.804825011 0.042921529 0.000204671 1.82E-05 0.039470645 0.009290795 0.031908604 1.4960922 -0.288758348 LGDVGMAELCPGLLHPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGDVGMAELCPGLLHPSSR 19 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;; 228.49 1.02E-19 1853023000 217196 947740 792679 839227 815276 1083834 767301 1007584 833367 802864 FALSE TRUE 225771.0658 1110506.973 813336.8659 1005223.596 676695.6767 832129.9792 707157.9427 994078.9846 803374.2845 960169.829 0.235136597 1.156573493 0.84707605 1.046922706 0.704766653 0.866648747 0.736492568 1.035315789 0.836700196 1 19.87293008 4.752110232 24.95531165 0.907350911 0.235136142 0.689253067 0.136771815 1248.65538 2299698.445 0.030866615 0.618541916 56508.03839 -4.752110232 -0.672214769 LGDVYVNDAFGTAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;;;;;;;;; 245.19 4.41E-18 33710028000 14247953 16099122 16210678 15707351 17722010 19072291 15905187 16706347 15599932 16166138 FALSE TRUE 14810473.19 18864020.97 16633141.59 18814218.15 14709629.07 14643040.46 14658496.88 16482425.74 15038493.49 19333583.22 0.766049057 0.975712611 0.86032379 0.973136636 0.760833049 0.757388855 0.758188315 0.852528243 0.777843058 1 24.20460571 3.226584285 24.99922511 0.806651662 0.897264489 0.144034944 0.088139584 340.0566615 709828.245 0.023660583 0.028487664 1684.939398 -3.226584285 0.090612827 LGEDLNKWQALLVQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGEDLNKWQALLVQIR 16 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 140.81 1.52E-06 81274000 263340 202870 280560 189520 400760 336130 279220 268550 249910 253780 FALSE TRUE 273736.8665 237711.3444 287871.6241 227006.4903 332638.9583 258068.9016 257334.0068 264950.5265 240915.7879 303503.3321 0.90192376 0.783224826 0.948495761 0.747953865 1.095997715 0.85030006 0.847878687 0.872974029 0.793783008 1 18.21135283 LGEKEETIPPDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGEKEETIPPDYR 13 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 68.83 0.048963 0 191090 100430 174270 103400 212940 214200 177530 151010 183190 106270 FALSE TRUE 198634.3808 117678.0713 178811.6194 123852.2114 176744.5349 164455.2962 163614.7347 148985.958 176597.0277 127091.5718 1.562923315 0.925931355 1.406951042 0.974511603 1.390686513 1.293990576 1.28737675 1.172272526 1.389525876 1 16.95550883 -1.001491015 4.101111399 0.999980727 1.251842394 0.150160757 0.187500763 8900435.722 4348218.142 1498.472104 0.038656365 0.09965727 1.001491015 0.251861667 LGEMWNNTAADDKQPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGEMWNNTAADDKQPYEK 18 1 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 280.65 2.56E-39 2416700000 2910600 1068640 1936970 1283230 2661200 2390100 3093000 1946380 2420600 939940 FALSE TRUE 3025512.735 1252170.607 1987449.029 1537049.064 2208850.175 1835035.497 2850562.578 1920291.96 2333483.079 1124103.247 2.691490078 1.113928468 1.768030681 1.367355773 1.964988697 1.632443908 2.535854768 1.708287887 2.07586188 1 20.10034312 LGETYKDHENIVIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGETYKDHENIVIAK 15 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;; 149.8 1.98E-06 2193223000 4542370 2853010 3904370 2744080 5651210 4771770 4482260 3679220 4203600 2086730 FALSE TRUE 4721706.275 3342992.274 4006121.09 3286850.834 4690619.343 3663598.734 4130928.749 3629906.074 4052313.257 2495584.791 1.892023983 1.33956269 1.605283501 1.317066383 1.87956721 1.468032161 1.655294889 1.454531254 1.623793057 1 21.25094649 -2.471977567 0.511742636 1.39E-11 1.574009263 0.462347664 0.18766622 123.5692265 6.87682448 138.3241636 0.077952468 0.003373047 2.471977567 1.574009263 LGEVVNTHGPVEPDKDNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGEVVNTHGPVEPDKDNIR 19 1 P30419;P30419-2;K7EN82 P30419 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 157.22 4.91E-09 1054900000 169220 108280 141220 111870 198430 182620 155850 137630 164920 101920 FALSE TRUE 175900.9363 126876.2477 144900.3092 133997.5521 164700.9395 140209.2726 143634.0698 135785.295 158984.5614 121889.2726 1.443120731 1.040913978 1.188786397 1.099338352 1.351234083 1.150300347 1.178397956 1.114005294 1.30433596 1 16.89521164 -1.575037294 3.090201267 0.990589331 1.194291184 0.2102023 0.118263094 3586607.281 2936542.7 213878.2615 0.025257421 0.026604966 1.575037294 0.203701853 LGFHLPLEVAYQR ddPTM_MDA-MB-175_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 ; 113.24 0.00083752 1698550000 914160 954990 848670 861280 1128360 1078970 894140 887060 918290 1103970 FALSE TRUE 950251.7427 1119002.104 870787.0374 1031638.613 936561.7702 828395.5694 824054.9704 875170.4116 885240.9223 1320271.785 0.719739491 0.847554357 0.65955135 0.781383519 0.709370435 0.627443212 0.624155556 0.662871404 0.670499008 1 20.33240352 -1.094449081 4.379065918 1.000030986 0.697956103 0.648347817 0.066198879 0.92263521 41029932.35 2797.885501 0.016454067 0.080454607 1.094449081 -0.302074883 LGFSLT(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGFSLTPSK 9 0 P38432 P38432 COIL Coilin 1 LGFSLT(1)PSK;LGFS(0.006)LT(0.993)PS(0.001)K 163.83 0.00070114 966090000 2848300 1882410 2079880 1713060 2672300 2681200 2661900 2282070 2167700 1606290 TRUE FALSE 2960753.083 2205699.274 2134083.381 2051898.155 2218063.401 2058531.934 2453253.322 2251482.584 2089684.9 1921011.771 1.541246716 1.148196647 1.110916348 1.068134087 1.154632904 1.071587361 1.277063139 1.172029562 1.087804318 1 20.87343493 4.738282017 5.429074266 1.132028777 1.556761664 0.757037168 0.071215774 0.072029524 8.009010009 0.016955428 0.114001357 54737.12935 -4.738282017 0.424732886 LGFTQSQIDEIDHDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGFTQSQIDEIDHDYER 17 0 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 0 124.63 4.96E-05 71568000 12316 37012 32958 41249 24894 44652 28171 34143 34217 39107 FALSE TRUE 12802.24519 43368.52309 33816.91256 49407.92908 20662.52677 34282.24971 25962.88341 33685.36893 32985.53685 46769.2679 0.273731999 0.927286764 0.723058411 1.056418698 0.441797097 0.733008047 0.555127001 0.720245803 0.7052823 1 15.51327323 0.466626519 2.20050786 0.999988905 0.690689951 0.168478127 0.211560757 13.09443588 51.68165585 0.188497229 0.051121363 2.928373843 -0.466626519 -0.309298954 LGGAGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGGAGMER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 77.674 0.075846 562080000 1393200 1330000 1568500 1012300 1825400 1399100 1283400 1479500 1357600 1646300 FALSE TRUE 1448204.612 1558417.154 1609376.399 1212529.919 1515119.16 1074180.229 1182803.754 1459669.722 1308740.241 1968860.965 0.735554535 0.791532354 0.817414956 0.615853501 0.769540962 0.545584603 0.600755348 0.741377755 0.664719482 1 20.90892981 -1.515740019 9.23607828 1.000010158 0.698375119 0.532788585 0.084830388 1.82E-05 9.52E-07 0.084067302 0.019814187 0.030497201 1.515740019 -0.301635039 LGGAVPFAPPEVS(ph)PEQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGGAVPFAPPEVSPEQAK 18 0 A0A096LNZ0;A0A096LP25;Q6ZSR9 A0A096LNZ0;A0A096LP25 AAK1 Uncharacterized protein FLJ45252 1 LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK 243.83 4.33E-24 632361000 1608780 971208 1205020 1001478 1655720 1658860 1577960 1326800 1462460 1018029 TRUE FALSE 1672295.877 1138005.419 1236423.811 1199567.359 1374281.306 1273614.905 1454275.372 1309016.416 1409826.35 1217492.291 1.373557672 0.934712628 1.015549601 0.98527717 1.128780294 1.046096895 1.194484255 1.075174295 1.157975587 1 20.21548121 LGGEAAHLPHLRPLPES(ph)QPSSSPLLQTAPGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGGEAAHLPHLRPLPESQPSSSPLLQTAPGVK 32 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LGGEAAHLPHLRPLPES(0.435)QPS(0.186)S(0.186)S(0.186)PLLQT(0.006)APGVK 44.6 0.056204 136770000 155260 109070 154050 101260 173070 195780 153500 147010 141730 126840 TRUE FALSE 161389.7847 127801.9241 158064.6696 121288.9258 143651.6232 150313.0621 141468.2689 145039.5714 136629.165 151691.8695 1.063931674 0.842510047 1.042011481 0.799574336 0.946996195 0.990910472 0.932602844 0.956145981 0.900701965 1 17.21078424 3.017225689 24.99684071 0.953413029 0.929698458 0.008942047 0.078716117 1286.317089 1866610.296 0.021130898 0.025250297 1040.46072 -3.017225689 -0.023714571 LGGLRPES(ph)PESLTSVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LGGLRPES(0.801)PES(0.012)LT(0.005)S(0.005)VS(0.177)R;LGGLRPES(0.986)PES(0.011)LT(0.001)S(0.001)VS(0.001)R;LGGLRPES(1)PESLTSVSR;LGGLRPES(0.989)PES(0.004)LT(0.006)SVSR;LGGLRPES(0.999)PESLTSVSR;LGGLRPES(0.867)PES(0.049)LT(0.049)S(0.028)VS(0.005)R 222.39 2.05E-15 8126960000 1902530 2029560 2013300 1950620 2212570 2501450 2224960 2033840 1993260 1956480 TRUE FALSE 1977643.353 2378121.142 2065768.252 2336446.814 1836478.142 1920526.147 2050561.821 2006579.701 1921522.962 2339814.797 0.845213628 1.016371529 0.882876822 0.998560577 0.784881839 0.820802634 0.876377833 0.857580568 0.821228656 1 21.15796291 3.24147621 24.99942134 0.852815248 0.937736849 0.210039428 0.070944947 101.1107674 866955.6179 0.018320945 0.023769039 1743.717837 -3.24147621 0.084921602 LGGPEGPGS(ph)PLLAT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGGPEGPGSPLLAT 14 0 Q9C086 Q9C086 INO80B INO80 complex subunit B 1 LGGPEGPGS(1)PLLAT 148.18 8.21E-06 55326000 164030 178880 170250 166500 205830 222190 203570 197250 182580 181540 TRUE FALSE 170506.0311 209601.2485 174686.8549 199433.203 170843.0901 170589.7398 187613.6515 194606.1864 176008.9815 217109.2872 0.785346556 0.96541816 0.804603327 0.918584394 0.786899042 0.785732117 0.864143832 0.896351275 0.81069301 1 17.72806192 -1.184504126 4.027211497 1.000075142 0.851434614 0.365985871 0.060318082 3.174550539 30573661.74 4433.283756 0.013332049 0.065387672 1.184504126 -0.148640528 LGGS(ph)AVISLEGKPL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGGSAVISLEGKPL 14 1 G3V1A4;P23528;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 1 LGGS(0.98)AVIS(0.02)LEGKPL;LGGS(1)AVISLEGKPL;LGGS(0.999)AVIS(0.001)LEGKPL;LGGS(0.994)AVIS(0.006)LEGKPL 144.4 2.33E-05 357921000 1411770 1094700 1491520 1121350 1855660 1652500 1425610 1337170 1461950 1103480 TRUE FALSE 1467507.77 1282706.209 1530390.236 1343149.683 1540235.576 1268731.919 1313866.963 1319247.423 1409334.705 1319685.779 1.112013021 0.971978504 1.159662596 1.017779918 1.167122963 0.9613894 0.995590757 0.999667834 1.067932024 1 20.33176303 2.714751065 24.89529318 1.003683101 1.079727354 0.306350133 0.060439361 944.2136971 987269.5418 0.018250851 0.017216903 518.5027514 -2.714751065 0.076044253 LGGSLADSYLDEGFLLDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGGSLADSYLDEGFLLDKK 19 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 199.01 1.14E-15 1054850000 706630 483890 717440 583530 967570 824410 917830 728620 925860 444400 FALSE TRUE 734528.298 566994.3434 736137.0758 698950.4923 803102.797 632953.2716 845888.0863 718854.0407 892538.4795 531471.6714 1.382064816 1.066838317 1.385091841 1.315122762 1.511092388 1.190944514 1.591595812 1.352572638 1.679371691 1 19.01963327 4.08549642 13.56670818 1.396186402 1.224472978 0.083392063 0.197187129 1.593853583 247.4424352 0.044385149 0.095915783 12175.76957 -4.08549642 -0.171713423 LGGSPTSLGTWGSWIGPDHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDK 21 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 286.7 1.54E-45 2130200000 1405600 1237450 1399150 1533360 1643520 1945720 1910560 1508680 1506960 858100 FALSE TRUE 1461094.173 1449972.411 1435612.998 1836654.031 1364155.057 1493856.018 1760805.315 1488458.612 1452724.804 1026228.266 1.423751637 1.412914124 1.398921708 1.789712964 1.329290084 1.455676157 1.715802784 1.450416698 1.415596171 1 19.96892024 0.714492715 2.142981984 1.000286971 1.502029895 0.540808994 0.13685094 0.973187835 6.205815689 0.127298515 0.034774865 5.181943994 -0.714492715 0.501742924 LGGSPTSLGTWGSWIGPDHDKFSAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGGSPTSLGTWGSWIGPDHDKFSAMK 26 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 356.87 2.00E-110 3462000000 1830580 1837400 2204940 1711160 3063900 2603100 2161700 1976930 2294010 1683630 FALSE TRUE 1902852.712 2152959.157 2262402.548 2049622.341 2543099.372 1998569.475 1992260.305 1950432.487 2211449.028 2013505.063 0.94504491 1.069259371 1.123614034 1.017937515 1.263021096 0.992582294 0.989448868 0.968675233 1.098308153 1 20.94127767 LGGSVLGQIPFLQNCEDEDS(ph)DEDDELDSVQHKK ddPTM_MDA-MB-175_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 253.17 1.49E-59 1067880000 672610 382418 532900 385090 737707 603086 551600 518171 627023 398893 TRUE FALSE 699165.1622 448095.3167 546787.8118 461259.6526 612311.8276 463028.4164 508364.1507 511225.7653 604456.5647 477048.4461 1.465606204 0.93930778 1.146189273 0.966903166 1.283542233 0.970610889 1.065644705 1.071643288 1.267075849 1 18.86377626 4.752330137 24.56621754 1.081693308 1.465606531 0.504440205 0.114931066 1454.865131 2595569.103 0.025018713 0.503659381 56536.65856 -4.752330137 0.383913224 LGHDPYR ddPTM_MDA-MB-175_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 ;;; 100.19 0.0099773 1595120000 767820 984510 864940 900400 964530 1051310 861530 878600 849270 977490 FALSE TRUE 798134.1265 1153591.934 887481.047 1078496.433 800579.5351 807159.1853 794001.0274 866823.8041 818704.9386 1169010.45 0.682743363 0.986810626 0.759172894 0.922572106 0.684835225 0.690463618 0.67920781 0.741502186 0.700340137 1 20.1568564 3.227483071 24.99885135 0.729639895 0.842848615 0.104512885 0.118277494 345.177381 778965.4528 0.031006131 0.037385155 1688.430041 -3.227483071 0.11320872 LGHEEQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGHEEQQKR 9 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ;;;; 176.38 3.45E-05 792261000 1070320 1035250 1092530 899530 1502150 1413160 1051620 1008960 1114160 992550 FALSE TRUE 1112577.06 1213046.134 1121002.229 1077454.349 1246815.08 1084975.007 969191.2765 995436.5415 1074061.599 1187021.169 0.937284936 1.021924601 0.944382677 0.907695985 1.050373079 0.914031725 0.816490305 0.838600496 0.90483778 1 20.17891423 2.481605104 24.55642821 0.869690873 0.971169598 0.273539394 0.060627185 154.4933171 846113.4121 0.019820459 0.016989282 303.113378 -2.481605104 0.101478725 LGHGEEELETEKDFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGHGEEELETEKDFSR 16 1 O60306 O60306 AQR Intron-binding protein aquarius 0 144.29 7.99E-07 88515000 42983 45326 50051 38940 68574 67966 58032 50372 47719 48686 FALSE TRUE 44680.00203 53110.38791 51355.37018 46642.21578 56917.81597 52181.92653 53483.3002 49696.84573 46001.60251 58225.08955 0.767366824 0.912156397 0.882014447 0.801067309 0.977547934 0.896210327 0.918561064 0.853529743 0.790064951 1 15.82935333 4.746162125 24.25036824 0.887116544 0.767366735 0.253860499 0.063715421 857.6868046 2736095.182 0.014467357 0.149335112 55739.37889 -4.746162125 -0.119749809 LGHGLLSGEYSKPVPESGDGERVPEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGHGLLSGEYSKPVPESGDGERVPEQK 27 2 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;; 189.08 4.63E-18 487290000 380498 263924 370576 250626 478690 465940 464460 372341 442250 286318 FALSE TRUE 395520.3548 309250.894 380233.515 300199.0748 397322.4448 357732.4964 428054.4116 367350.3779 426333.5089 342416.5302 1.155085459 0.903142421 1.11044147 0.876707309 1.160348318 1.04472905 1.250098561 1.072817301 1.245072802 1 18.38539282 3.192024197 24.99990786 1.132778195 1.010692961 0.221049102 0.107903016 164.5226599 88382.88775 0.028279376 0.033800421 1556.052325 -3.192024197 -0.122085235 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 LGHPEALSAGT(0.012)GS(0.988)PQPPSFTYAQQR;LGHPEALSAGT(0.001)GS(0.999)PQPPSFTYAQQR;LGHPEALSAGT(0.052)GS(0.948)PQPPSFTYAQQR;LGHPEALSAGT(0.011)GS(0.989)PQPPSFTYAQQR;LGHPEALSAGT(0.008)GS(0.992)PQPPSFTYAQQR 351.17 3.80E-103 11009600000 667654 804671 783469 806418 786973 911701 769753 795732 838661 887256 TRUE FALSE 694013.4955 942866.9848 803886.8458 965925.0735 653203.6106 699972.2597 709417.7485 785066.5141 808477.7544 1061096.826 0.654052937 0.888577708 0.757599897 0.910308136 0.615592842 0.659668602 0.66857023 0.73986322 0.761926466 1 20.01712488 0.685367417 3.143033067 0.999993246 0.738669585 0.417915247 0.092605385 3.653096795 35.35724291 0.089787158 0.023369213 4.84582155 -0.685367417 -0.261323661 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 O60256;O60256-2;O60256-3;O60256-4;E7EPA1;I3L0S1;C9K0K7 O60256 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.039)DLVDGRHS(0.961)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.055)DLVDGRHS(0.945)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.109)DLVDGRHS(0.891)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAES(0.011)DLVDGRHS(0.989)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR;LGIAVIHGEAQDAESDLVDGRHS(1)PPMVR 267.36 1.58E-54 7363482000 1513337 1849964 1867265 1819693 1929594 2209762 1893110 1864985 1874001 2100893 TRUE FALSE 1573084.713 2167680.926 1915927.46 2179622.844 1601602.301 1696578.265 1744723.091 1839987.927 1806556.07 2512522.759 0.626097697 0.862750762 0.762551285 0.867503722 0.637447878 0.675248914 0.694410861 0.732326869 0.719020778 1 21.26070523 -1.940882691 6.177351395 1.114901886 0.733611453 0.514766312 0.078361767 0.04771442 0.000456627 0.02919473 0.017605988 0.011458224 1.940882691 -0.381290432 LGIDDLVHFDFMDPPAPETLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGIDDLVHFDFMDPPAPETLMR 22 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 132.45 1.06E-05 280510000 166130 185930 204190 212520 197720 235000 227110 183550 190300 146940 FALSE TRUE 172688.9407 217862.0312 209511.3591 254555.8217 164111.625 180424.8115 209308.5248 181089.8125 183451.1402 175730.0797 0.98269426 1.239753784 1.192233905 1.448561465 0.933884656 1.026715585 1.191079667 1.030499803 1.043937046 1 17.42300163 3.208038139 24.99999269 1.04854254 1.215837549 0.340238385 0.12094974 243.1077403 199121.1477 0.034731573 0.041516778 1614.500334 -3.208038139 0.16729501 LGIHEDSQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 LGIHEDSQNR 10 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 231.38 7.12E-10 75460280000 10020092 13015610 12346554 12191940 14193170 15629530 13001080 13083374 12015817 13043740 FALSE TRUE 10415692.97 15250939.77 12668315.34 14603469.34 11780620.03 11999808.53 11982021.38 12908012.77 11583370.09 15599411.12 0.667697831 0.97766125 0.812102152 0.936155169 0.755196459 0.769247534 0.768107289 0.827467952 0.742551755 1 23.89498823 4.793815895 22.84907239 0.831147072 0.667694654 0.241819319 0.090996624 36291.70053 15005809.55 0.020530672 28.71527527 62203.65365 -4.793815895 -0.163452418 LGIHEDSQNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LGIHEDSQNRK 11 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 171.92 9.06E-06 16253980000 15005760 13297370 16517370 13028960 20187540 18871480 17489950 16280880 16711370 12912690 FALSE TRUE 15598198.99 15581089.86 16947826.23 15606049.4 16756069.16 14488864.77 16119042.02 16062661.43 16109931.06 15442684.38 1.010070439 1.008962527 1.097466335 1.010578797 1.085048995 0.938234857 1.043797932 1.040146975 1.043207947 1 23.88042022 LGIHEDSTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;; 208.63 1.10E-07 49555010000 8528540 10430740 10543960 10159300 11391360 12351010 11053940 10717330 10130850 10324500 FALSE TRUE 8865253.345 12222138.46 10818744.26 12168779.22 9455060.696 9482675.109 10187503.3 10573681.72 9766242.687 12347388.1 0.717986126 0.989856183 0.876196988 0.985534683 0.765753908 0.767990366 0.825073547 0.85634967 0.790956161 1 23.55770256 4.791020525 22.26530746 0.863149837 0.717982946 0.216394419 0.086706408 22339.18834 9480184.382 0.020492771 18.42284127 61804.56081 -4.791020525 -0.145166891 LGIHEDSTNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;; 204.69 2.10E-08 9830900000 4269900 5431120 5457110 5435190 5914670 6568010 5314610 5553450 5523680 5632590 FALSE TRUE 4438478.949 6363872.612 5599326.77 6510254.36 4909296.506 5042689.217 4898036.981 5479015.086 5324883.836 6736188.168 0.658900678 0.944729045 0.831230754 0.966459695 0.728794443 0.748596846 0.727122945 0.813370255 0.790489176 1 22.68350101 4.772317052 23.37338963 0.825046207 0.658899884 0.23167176 0.095392467 10767.92233 7455523.262 0.022417818 3.556812775 59199.36544 -4.772317052 -0.166146324 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWK 51 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 119.28 3.51E-10 396429000 14041.65 84727.6 82439.9 102183.9 82853 128406.3 83533.2 134177.3 80902.3 81226 FALSE TRUE 14596.02518 99278.90621 84588.35152 122395.5704 68769.67665 98585.88284 76985.64951 132378.8728 77990.64203 97140.67953 0.150256569 1.02201165 0.870781962 1.259982646 0.707939012 1.014877426 0.792517099 1.362754238 0.802862842 1 16.56778796 4.739534387 24.67793981 0.998541865 0.150256256 0.61767525 0.195788368 42.63896081 1080397.663 0.044768764 0.272969232 54895.20195 -4.739534387 -0.848285609 LGIYDADGDGDFDVDDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 262.48 1.79E-30 658663000 427512 367313 364080 490075 523736 631416 567491 401410 407949 372844 FALSE TRUE 444390.5039 430396.1505 373568.2239 587010.3723 434711.5418 484779.2032 523009.5726 396029.7555 393266.9952 445895.6433 0.996624458 0.965239641 0.837792944 1.316474788 0.97491767 1.087203274 1.172941652 0.88816691 0.88197093 1 18.76634658 1.639000454 11.15242457 0.913983856 1.047077639 0.174609692 0.125491105 0.180593637 45.77214943 0.059823667 0.032141478 43.55123286 -1.639000454 0.133093782 LGLALNFSVFHYEIANSPEEAISLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGLALNFSVFHYEIANSPEEAISLAK 26 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 238.72 5.16E-45 591070000 189790 224820 243260 225560 318590 325810 291470 288980 300950 253040 FALSE TRUE 197283.0557 263431.0861 249599.5554 270175.0948 264436.1856 250145.5652 268623.8198 285106.6958 290118.8683 302618.3433 0.651920348 0.870506009 0.824799821 0.892791534 0.873827352 0.826604106 0.887665357 0.942132895 0.958695581 1 18.20713991 7.574779842 0.185142489 0.997976545 2.13E-18 0.70413632 0.049320618 28.05512095 0.369051828 0.105862771 7.699052607 37564692.83 -7.574779842 -0.997976545 LGLALNYSVFYYEIQNAPEQACHLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGLALNYSVFYYEIQNAPEQACHLAK 26 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 277.39 1.11E-60 919460000 492391 421376 457893 419830 591371 622280 624834 501541 555611 356249 FALSE TRUE 511830.9769 493744.0501 469826.0677 502871.1209 490849.9687 477764.9007 575857.8784 494818.6633 535614.6686 426049.1708 1.201342502 1.158889828 1.102750809 1.180312404 1.152096993 1.121384417 1.351623047 1.161412103 1.257166321 1 18.70066042 LGLAVIHGEAQCTELDMDDGRHS(ph)PPMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 25 LGLAVIHGEAQCTELDMDDGRHSPPMVK 28 1 C9J168;B4DP31;Q14558;Q14558-2;C9JUN4 C9J168 PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 1 1 LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCT(0.057)ELDMDDGRHS(0.943)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK;LGLAVIHGEAQCTELDMDDGRHS(1)PPMVK 276.36 7.20E-62 12556589200 4189987.7 3759387.1 4538288.4 4136358.1 5431516.9 5505784.7 4814507.6 4541942.1 4818556.3 3808940.8 TRUE FALSE 4355411.65 4405032.59 4656559.924 4954517.386 4508269.597 4227149.644 4437133.914 4481064.795 4645137.4 4555229.823 0.956134338 0.967027518 1.022244783 1.087654757 0.989690921 0.92797725 0.974074654 0.983718708 1.019737221 1 22.11909241 3.009505218 24.99658221 0.977730012 1.010362626 0.091135181 0.039647219 470.029092 1236060.645 0.012335069 0.014724423 1022.12784 -3.009505218 0.032632613 LGLDYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGLDYEER 8 0 Q99623-2;Q99623;F5GY37;J3KPX7;F5H3X6;F5GWA7 Q99623-2 PHB2 Prohibitin-2 0 ; 98.458 0.017467 261390000 498413 730650 532610 763720 491859 885840 529900 527360 496000 776890 FALSE TRUE 518090.7301 856133.4538 546490.2541 914781.5365 408252.9829 680117.085 488365.0534 520291.6018 478149.0569 929106.721 0.557622411 0.921458681 0.588188893 0.984581766 0.439403756 0.732011802 0.525628587 0.559991215 0.514633084 1 19.82548479 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;;;; 319.15 8.64E-105 7970786000 2638101 3022682 3023145 3118483 3416155 3835812 3457094 3425531 3228968 2900815 FALSE TRUE 2742255.265 3541804.12 3101930.642 3735309.63 2835478.193 2945002.795 3186117.939 3379617.36 3112758.072 3469174.16 0.790463418 1.020935807 0.894140939 1.076714358 0.817335211 0.84890601 0.918408184 0.97418498 0.897261979 1 21.72616084 -0.09249737 0.701846838 1.003404718 0.919358454 0.077616278 0.084547962 16.76350092 8.211765858 0.247523315 0.029313911 0.808169823 0.09249737 -0.084046265 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;; 150.98 1.26E-10 1026130000 296217 302605 336582 311864 370491 422443 343395 373284 353054 344153 FALSE TRUE 307911.8759 354575.0548 345353.6034 373549.7684 307515.0722 324337.0154 316478.8026 368280.7385 340347.6555 411583.1911 0.74811577 0.861490611 0.839085781 0.907592381 0.747151679 0.788022986 0.768930339 0.894790522 0.826923117 1 18.65082454 0.428814736 0.890805678 1.000491121 0.816893683 0.505843665 0.053806912 1.687560833 1.867209286 0.054989653 0.017290767 2.684199162 -0.428814736 -0.183597438 LGLGTLSSS(ph)LSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGLGTLSSSLSR 12 0 O95248;O95248-5;O95248-4 O95248 SBF1 Myotubularin-related protein 5 1 LGLGT(0.002)LS(0.023)S(0.169)S(0.792)LS(0.015)R;LGLGT(0.016)LS(0.035)S(0.396)S(0.549)LS(0.004)R;LGLGTLSS(0.111)S(0.889)LSR;LGLGTLSS(0.041)S(0.959)LSR 154.86 7.54E-05 356060000 480209 713600 700080 797140 789780 858770 626830 727370 647280 740050 TRUE FALSE 499168.0221 836155.249 718324.6599 954811.9128 655533.4777 659333.6823 577697.4267 717620.7949 623984.5192 885048.6284 0.564000673 0.944756279 0.811621686 1.078824239 0.740675096 0.744968876 0.652729588 0.810826402 0.705028514 1 19.7553972 LGLPLLTDCAQPS(ph)RPHGSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.499)RPHGS(0.499)PS(0.003)R 98.7 0.00057101 456750000 53875 188910 129930 183530 118610 188240 117510 159670 122180 193560 TRUE FALSE 56002.0266 221353.823 133316.0825 219831.6862 98448.71457 144524.1128 108299.2591 157529.8848 117782.7657 231484.3761 0.24192573 0.956236558 0.575918275 0.949661009 0.425293129 0.62433636 0.467846949 0.680520593 0.508815185 1 17.8205553 -1.474363815 3.515587418 1.00542891 0.61739385 0.239878729 0.210476092 21971151.24 18465168.42 844458.8491 0.04461745 0.033545648 1.474363815 -0.38803506 LGLPLLTDCAQPSRPHGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LGLPLLTDCAQPSRPHGSPSR 21 1 U3KQ90;P55199 U3KQ90 ELL RNA polymerase II elongation factor ELL 1 LGLPLLTDCAQPS(0.009)RPHGS(0.496)PS(0.496)R;LGLPLLTDCAQPS(0.148)RPHGS(0.851)PS(0.001)R;LGLPLLTDCAQPS(0.442)RPHGS(0.55)PS(0.008)R;LGLPLLTDCAQPS(0.012)RPHGS(0.972)PS(0.017)R;LGLPLLTDCAQPS(0.007)RPHGS(0.969)PS(0.024)R;LGLPLLTDCAQPSRPHGS(0.86)PS(0.14)R 223.44 2.15E-25 3647100000 1407502 1518788 1474344 1558552 1770868 2003057 1524814 1598471 1567162 1764973 TRUE FALSE 1463071.266 1779628.024 1512766.616 1866828.934 1469856.49 1537877.368 1405295.094 1577046.111 1510760.146 2110785.667 0.69314061 0.843111668 0.716684143 0.88442373 0.69635516 0.728580543 0.665768731 0.747137019 0.715733563 1 21.00934866 -0.962806351 4.554463681 1.000004522 0.744679344 0.583236999 0.065055799 5792606.523 1271852.513 278.2299006 0.015079629 0.108941575 0.962806351 -0.255325177 LGLVLDQAEAEGVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LGLVLDQAEAEGVCR 15 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;; 253.88 2.58E-24 287907000 308493 360527 303793 356411 403098 438934 339605 359701 358560 396779 FALSE TRUE 320672.5418 422444.7077 311710.0951 426908.032 334579.5459 336998.2306 312985.8727 354879.7964 345655.4956 474520.2483 0.675782631 0.890256442 0.656895246 0.899662414 0.705090135 0.710187251 0.659583809 0.747870713 0.728431499 1 18.85611012 -1.169642682 8.998613776 1.000000009 0.742845122 0.469709047 0.082379579 1.32E-08 1.22E-09 0.073785021 0.017391296 0.067663946 1.169642682 -0.257154886 LGMIVDKIDADKDGFVTEGELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGMIVDKIDADKDGFVTEGELK 22 2 O43852-2;O43852-4;O43852-8;O43852-7 O43852-2 CALU Calumenin 0 146.99 4.58E-08 301380000 350530 125540 171610 115460 365550 254710 264940 174390 197630 95676 FALSE TRUE 364369.1951 147100.5184 176082.2976 138297.6434 303413.9416 195557.4627 244173.3105 172052.5873 190517.3349 114421.8804 3.18443635 1.285597807 1.538886592 1.208664313 2.651712597 1.709091496 2.133973937 1.503668588 1.66504286 1 16.80400343 -2.026019463 0.21330704 3.41E-12 2.019475655 0.198559913 0.579413567 59.17070133 1.849416415 30.78546727 1.30154273 0.009418474 2.026019463 2.019475655 LGMLS(ph)PEGTCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 21 LGMLSPEGTCK 11 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.986)PEGT(0.014)CK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(0.997)PEGT(0.003)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK;LGMLS(0.999)PEGT(0.001)CK;LGMLS(1)PEGTCK;LGMLS(1)PEGTCK 234.79 1.74E-15 36157986000 44856570 30701470 38951100 34953230 51011220 51334970 44927220 37577070 41246690 28438870 TRUE FALSE 46627542.02 35974208.65 39966197.66 41866874.57 42340351.05 39413201.21 41405707.1 37073410.84 39762229.68 34010922.08 1.370957891 1.057725179 1.175098916 1.230983226 1.244904532 1.158839537 1.217423832 1.090044273 1.169101784 1 25.01949478 0.635474774 0.485677205 0.990657668 1.209976918 0.385619467 0.078378477 1.701856195 0.820793048 0.112444944 0.041494939 4.319910745 -0.635474774 0.219319251 LGNDFHTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGNDFHTNK 9 0 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 98.943 0.0056723 1132760000 2142370 1683630 2131230 1803210 2680570 2630770 2860700 2113300 2322830 1735750 FALSE TRUE 2226952.422 1972780.356 2186771.605 2159879.556 2224927.669 2019813.537 2636470.859 2084974.67 2239231.802 2075836.98 1.072797355 0.950354182 1.053440914 1.040486116 1.071821964 0.973011637 1.270076063 1.004401931 1.078712743 1 20.98526172 3.322598616 1.170318997 1.076773169 1.016434998 0.045848741 0.082173211 1.302329112 3.748947719 0.029770204 0.051100232 2101.83498 -3.322598616 -0.060338171 LGNDFHTNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGNDFHTNKR 10 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73;A0A0J9YYC4 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 189.72 6.36E-07 7917900000 8339700 7008400 8478100 6455060 12191300 10152600 8988100 8491000 8637000 8369700 FALSE TRUE 8668957.796 8212038.182 8699046.251 7731851.602 10119027.18 7794812.514 8283589.236 8377192.033 8326156.057 10009582.47 0.866065875 0.820417656 0.86907184 0.772444967 1.010933994 0.778735031 0.827565911 0.83691723 0.831818518 1 23.25487846 -1.356862658 6.362870001 1.000012519 0.845198847 0.35157949 0.062734921 1.02E-05 1.04E-06 0.055831145 0.013158463 0.043968064 1.356862658 -0.154813672 LGNSCEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 125.5 0.0029299 450650000 287460 370960 360060 328060 424120 437950 371090 378680 312480 406860 FALSE TRUE 298809.1428 434669.4943 369443.4594 392949.2888 352028.2339 336242.7497 342002.9961 373604.414 301233.9058 486576.4272 0.614105259 0.893322138 0.759271183 0.80757979 0.723479836 0.691037894 0.702876212 0.767822675 0.619088573 1 18.8923069 -1.252301347 5.126890194 1.000038387 0.738453126 0.504424012 0.079691453 3.29E-05 4.80E-06 0.072634881 0.017117697 0.055936933 1.252301347 -0.261585261 LGPGGLDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGPGGLDDR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71;E9PKC4;E9PRW6;E9PJR7 Q9Y446 PKP3 Plakophilin-3 0 ;; 120.46 0.0015399 240090000 308441 360994 346588 330113 400603 454761 358120 342477 346144 330667 FALSE TRUE 320618.4888 422991.9114 355620.368 395408.3661 332508.6452 349149.6497 330049.6186 337886.656 333686.3451 395454.8676 0.810758737 1.069633847 0.899269163 0.99988241 0.840825774 0.882906441 0.834607551 0.854425331 0.843803863 1 18.59315353 3.228177492 24.99980053 0.865481266 0.950538252 0.151001196 0.077030904 290.3558334 699098.7859 0.020194064 0.024385439 1691.131938 -3.228177492 0.085056986 LGPGRPLPTFPTSECTS(ph)DVEPDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 LGPGRPLPT(0.001)FPT(0.004)S(0.004)ECT(0.135)S(0.856)DVEPDTR;LGPGRPLPTFPT(0.017)S(0.017)ECT(0.25)S(0.717)DVEPDTR;LGPGRPLPTFPT(0.002)S(0.009)ECT(0.163)S(0.826)DVEPDTR;LGPGRPLPTFPTS(0.001)ECT(0.251)S(0.748)DVEPDTR 151.31 6.84E-08 865570000 402967 462266 411715 456550 475500 558100 423161 414203 402101 437384 TRUE FALSE 418876.4483 541656.5896 422444.6311 546854.2273 394674.6798 428489.7331 389992.5351 408651.2863 387629.4636 523081.0206 0.800786937 1.035511839 0.80760841 1.045448422 0.754519213 0.819165132 0.745568124 0.781238986 0.741050522 1 18.9966749 3.211051862 24.99992938 0.791601827 0.922227762 0.223383056 0.10307702 258.2878867 234731.0998 0.026891162 0.032148051 1625.742886 -3.211051862 0.130625935 LGPLFSLLNENHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGPLFSLLNENHR 13 0 Q16401-2;Q16401;F2Z3J2 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 217.09 2.64E-11 715940000 525800 637970 608430 621570 788340 755260 628470 601970 610240 683370 FALSE TRUE 546558.99 747536.3848 624286.1856 744514.6908 654338.2484 579862.3111 579208.8792 593901.5768 588277.5816 817263.2676 0.66876735 0.914682471 0.76387403 0.910985138 0.800645611 0.709517158 0.708717622 0.726695546 0.719814049 1 19.64044137 2.984607977 23.73467449 0.749210545 0.822819623 0.007497401 0.105309211 815.0642192 1256842.001 0.029120018 0.031854548 965.1792512 -2.984607977 0.073609078 LGPNYLHIPVNCPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGPNYLHIPVNCPYR 15 0 P04040 P04040 CAT Catalase 0 ; 74.769 0.033818 1264730000 583250 891510 608430 743140 1012310 1046180 684850 594880 623900 1048990 FALSE TRUE 606277.1604 1044619.908 624286.1856 890130.8739 840237.9078 803220.55 631169.6675 586906.6066 601445.9609 1254519.506 0.483274399 0.832685265 0.497629716 0.709539285 0.669768707 0.640261507 0.503116663 0.467833783 0.479423363 1 20.25870347 2.318403784 8.756004073 0.555288498 0.646213138 0 0.173746433 0.852897014 84.38162036 0.055704029 0.046516699 208.1631179 -2.318403784 0.090924641 LGPRPVPPPRPES(ph)TGTVGPGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGPRPVPPPRPESTGTVGPGQAQQR 25 2 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 LGPRPVPPPRPES(0.968)T(0.032)GTVGPGQAQQR;LGPRPVPPPRPES(0.5)T(0.5)GTVGPGQAQQR 190.31 4.60E-18 296920000 34779 28388 24271 22074.7 32996 49064 28949 33171.1 43760 28130 TRUE FALSE 36152.10178 33263.41817 24903.5222 26441.00977 27387.35171 37669.62957 26679.90174 32726.49566 42185.08615 33641.53492 1.074627001 0.988760419 0.740261176 0.78596324 0.814093405 1.119735757 0.793064341 0.972800312 1.253958425 1 15.03795591 1.43360278 6.686143758 1.125957159 0.899371166 0.308579672 0.132799709 0.221127221 20.23114155 0.084699989 0.033306808 27.13955859 -1.43360278 -0.226585994 LGPSDYFGEIALLMNRPR ddPTM_MDA-MB-175_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 ; 198.07 1.62E-15 443720000 582960 284730 312090 274840 342390 504590 333620 326460 278730 303490 FALSE TRUE 605975.7109 333630.1626 320223.3218 329202.5317 284190.6701 387406.6196 307469.9926 322084.3377 268698.5617 362953.0548 1.669570494 0.919210234 0.882272012 0.907011326 0.782995669 1.067373905 0.847134329 0.88739944 0.740312165 1 18.46942343 4.738948537 5.225000518 0.887025231 1.703445042 0.872284448 0.089248084 0.047020831 4.429705786 0.019927344 0.138233881 54821.19992 -4.738948537 0.816419812 LGQELCGMLHRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGQELCGMLHRPR 13 1 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 93.011 0.0034909 314440000 107330 135240 130960 125970 135780 164680 126990 128050 117380 137910 FALSE TRUE 111567.4713 158466.418 134372.9252 150886.49 112700.1641 126435.5657 117036.192 126333.6992 113155.5167 164930.8241 0.676450093 0.960805349 0.814722936 0.914847124 0.683317777 0.766597551 0.709607756 0.765979919 0.686078648 1 17.33150152 3.239952856 24.9999925 0.753668364 0.848286049 0.086052594 0.109636673 67.46838899 1211487.156 0.028116721 0.036089839 1737.612196 -3.239952856 0.094617685 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQAR 34 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ;; 224.57 7.19E-37 337437000 59745.2 86970.2 109758.1 104403.4 104139.7 122692 95440 114056 116333 106405 FALSE TRUE 62103.98663 101906.6553 112618.4863 125054.0809 86438.07099 94198.64242 87959.16341 112527.2659 112146.1981 127253.0225 0.488035454 0.800819134 0.884996553 0.982719926 0.679261438 0.740246798 0.691214729 0.88427971 0.881285142 1 16.9573404 -4.999999999 0.030510517 2.169908045 6.21E-07 0.294371683 0.125023857 2184.133303 5.015804879 280.1563922 111.8720269 1.00E-05 4.999999999 -2.169907424 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGQHVPTLHPTSEELTIAGMTFTTFDLGGHVQAR 34 0 Q9Y6B6;D6RD69;D6RDB2;D6RAA2 Q9Y6B6 SAR1B GTP-binding protein SAR1b 0 ;; 180.35 2.87E-20 133994000 38617.5 61231 60578 63997 64618 79644 67743 65392 59307 65310 FALSE TRUE 40142.14872 71746.94794 62156.71245 76655.41559 53634.25544 61147.88802 62433.12665 64515.5272 57172.55265 78106.24406 0.513942889 0.918581463 0.795796971 0.981424936 0.686683326 0.782880918 0.799335922 0.82599705 0.731984406 1 16.25315027 -2.418501762 2.229385834 2.776559419 0.792756883 0.223168148 0.120567231 2980379.96 413376.5514 26740731.6 0.026767902 0.003815032 2.418501762 -1.983802536 LGQSDPAPLQHQMDIYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGQSDPAPLQHQMDIYQK 18 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 127.17 1.97E-05 740050000 520180 488240 580430 499390 1111220 801420 689700 595110 586560 613080 FALSE TRUE 540717.1081 572091.422 595556.4826 598167.8515 922335.2213 615302.3506 635639.5118 587133.5239 565449.8202 733201.2879 0.737474302 0.780265162 0.812268735 0.815830334 1.257956357 0.839199768 0.866937255 0.800780814 0.771206802 1 19.48384979 3.458838381 24.9999774 0.909316095 0.783198874 0.207129815 0.130493047 448.0491605 612660.064 0.038152339 0.051667229 2876.327815 -3.458838381 -0.12611722 LGS(ph)FGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSFGK 6 0 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 LGS(1)FGK;LGS(1)FGK 95.741 0.045106 582320000 1488880 571000 935930 608530 1432480 1445810 1212070 903320 1045440 485545 TRUE FALSE 1547662.132 669064.8082 960321.1047 728895.4177 1188987.561 1110042.539 1117064.786 891212.4729 1007814.819 580678.2464 2.66526625 1.152212628 1.653792114 1.255248362 2.047584129 1.911631004 1.923724185 1.534778474 1.735582183 1 19.14737946 0.154990253 0.999630286 0.995333233 1.746987743 0.242327677 0.404969121 7.009332269 7.013726907 0.455097517 0.116337975 1.42886189 -0.154990253 0.75165451 LGS(ph)LSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGSLSAR 7 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4;Q00G26 Q5SW79;Q00G26 CEP170;PLIN5 Centrosomal protein of 170 kDa;Perilipin-5 1 LGS(0.998)LS(0.002)AR;LGS(0.994)LS(0.006)AR;LGS(0.995)LS(0.005)AR 154.12 0.0017834 430060000 633530 222068 282783 263442 397511 562340 357919 283089 315193 208742 TRUE FALSE 658542.2536 260206.4516 290152.5573 315550.0413 329942.2222 431745.0573 329864.3735 279294.655 303849.2655 249640.9983 2.637957139 1.042322589 1.16227927 1.2640153 1.321666811 1.729463751 1.321354969 1.118785203 1.21714489 1 17.92949536 4.744073378 24.89085589 1.258456431 2.637957763 0.82412599 0.193341412 233.9825567 1056428.853 0.048374757 0.420593134 55471.94306 -4.744073378 1.379501332 LGS(ph)PDYGNSALLSLPGYRPTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSPDYGNSALLSLPGYRPTTR 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 LGS(0.748)PDYGNS(0.252)ALLSLPGYRPTTR;LGS(1)PDYGNSALLSLPGYRPTTR 298.55 7.28E-56 997870000 574700 336270 311240 278160 474720 649050 440690 358880 369310 322020 TRUE FALSE 597389.5998 394021.7567 319351.1701 333179.2178 394027.264 498317.9739 406147.5663 354069.8006 356018.6052 385113.6536 1.551203377 1.023131102 0.829238764 0.865145171 1.023145402 1.29395042 1.054617416 0.919390412 0.924450748 1 18.55492475 4.734874256 5.267187323 0.989346538 1.57353597 0.654783676 0.121891674 0.099826918 9.755488656 0.032106452 0.211064467 54309.30642 -4.734874256 0.584189432 LGS(ph)PHRRPLSVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSPHRRPLSVDK 13 2 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 LGS(1)PHRRPLSVDK;LGS(1)PHRRPLSVDK 64.298 0.032628 424620000 259462 168458 208421 123374 346780 289900 220208 221483 230137 136912 TRUE FALSE 269705.7601 197389.3511 213852.6225 147777.009 287834.4595 222575.1185 202947.5216 218514.3827 221854.4143 163737.2851 1.647185978 1.205524759 1.306071628 0.902525096 1.75790419 1.359342916 1.23947042 1.334542603 1.354941327 1 17.32102335 -1.701765336 2.297175847 0.930909826 1.33470717 0.177919418 0.22161105 7636494.064 5219825.522 3039208.952 0.054079267 0.019871684 1.701765336 0.403797344 LGS(ph)PKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 101.93 0.0030663 5804100000 8325900 2559590 3956300 2215830 6420400 8129100 5761700 3949600 4283500 1647530 TRUE FALSE 8654612.961 2999179.672 4059404.428 2654114.56 5329062.701 6241239.723 5310082.899 3896662.072 4129337.672 1970331.96 4.392464386 1.522169732 2.060264215 1.347039288 2.704652216 3.167608226 2.695019422 1.9776678 2.095757343 1 20.91000728 0.811994351 1.248071459 1.012336932 2.454952108 0.233285209 0.824064341 1.104722215 3.194234056 0.765024475 0.233346936 6.486259972 -0.811994351 1.442615177 LGS(ph)PLAVDEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGSPLAVDEALR 12 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR;LGS(1)PLAVDEALR 232.37 1.28E-12 275413000 323036 252312 298214 253515 415698 590919 454935 339073 370507 247350 TRUE FALSE 335789.7107 295644.6233 305985.7018 303659.5103 345037.8024 453687.0177 419276.0059 334528.281 357172.5254 295813.4967 1.135139926 0.999429122 1.034387225 1.026523515 1.166403177 1.533692758 1.417366045 1.130875652 1.20742471 1 18.17432835 3.005636104 8.674848459 1.276018626 1.050364568 0.324109716 0.141050207 0.140464162 106.5521575 0.042672933 0.049608892 1013.062185 -3.005636104 -0.225654058 LGS(ph)PLAVDEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGSPLAVDEALRR 13 1 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LGS(1)PLAVDEALRR 81.428 0.0092473 37274000 18394 17133 16463 16239 24484 34552 21657 18334 20622 18298 TRUE FALSE 19120.20932 20075.45947 16892.0393 19451.02573 20322.21843 26527.82164 19959.46775 18088.26272 19879.81825 21883.14276 0.87374147 0.917393799 0.771920171 0.888858878 0.928670011 1.212249169 0.912093293 0.826584322 0.908453528 1 14.41753233 3.270476529 4.001158621 0.95574908 0.857689224 0.200159529 0.100266182 0.437903581 15.12079068 0.032048515 0.042517516 1864.131431 -3.270476529 -0.098059856 LGS(ph)PSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGSPSGK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LGS(0.997)PS(0.003)GK;LGS(0.998)PS(0.002)GK;LGS(0.998)PS(0.002)GK;LGS(0.998)PS(0.002)GK;LGS(0.849)PS(0.151)GK 144.66 0.002454 3165890000 12757630 5886160 7973870 5775640 12019950 12946180 11798840 8635350 9585410 5260610 TRUE FALSE 13261311.08 6897062.192 8181675.603 6918044.353 9976803.192 9939625.896 10874016.09 8519607.258 9240432.967 6291325.809 2.107872249 1.096281198 1.300469226 1.099616291 1.585802976 1.579893682 1.728414077 1.354183127 1.468757659 1 22.58493265 0.151098495 1.622107232 0.99987209 1.463096933 0.199803622 0.286350953 26.61163476 48.31363443 0.269882378 0.075266401 1.416114908 -0.151098495 0.463224843 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LGSPVDNLEDMDRDDLTDDSVFTR 24 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR;LGS(1)PVDNLEDMDRDDLTDDSVFTR 202.14 8.13E-25 673182000 128882 111999 137920 107589 152264 230469 150347 151066 144788 94213 TRUE FALSE 133970.3609 131233.957 141514.3085 128869.7831 126382.2197 176946.0675 138562.4093 149041.2074 139577.1082 112672.2335 1.189027293 1.164740885 1.2559821 1.14375813 1.121680255 1.570449631 1.229783106 1.322785594 1.238788864 1 16.7817725 LGS(ph)SSNLQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 LGS(0.78)S(0.21)S(0.01)NLQFK;LGS(0.871)S(0.108)S(0.021)NLQFK 161.48 7.41E-06 548700000 737600 382890 520840 373830 788850 788560 608060 508650 523410 315510 TRUE FALSE 766721.0176 448648.379 534413.5183 447772.4582 654761.5588 605428.8907 560398.6683 501832.3787 504572.5763 377328.1437 2.031974106 1.189013824 1.416309722 1.186692447 1.735257679 1.604515594 1.485175908 1.329962758 1.337224866 1 18.52546018 0.913934714 1.024675834 1.005829166 1.50106695 0.305274463 0.237219426 0.804881419 1.732981469 0.216242189 0.070615337 8.202282322 -0.913934714 0.495237784 LGS(ph)VDSFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 LGS(0.999)VDS(0.001)FER;LGS(0.999)VDS(0.001)FER;LGS(0.999)VDS(0.001)FER;LGS(1)VDSFER 140.48 0.00011433 1133340000 4918210 1579220 2426000 1431070 4184740 4306700 2943540 2274480 2917190 1312700 TRUE FALSE 5112384.728 1850438.75 2489223.553 1714131.375 3473419.39 3306534.194 2712817.643 2243994.316 2812200.902 1569898.432 3.256506679 1.178699662 1.585595286 1.09187406 2.212512172 2.106208992 1.728021118 1.429388214 1.791326652 1 20.58223979 7.999999994 0.048534445 1.34E-10 4.839858269 0.19657838 0.571337441 1063.001471 3.897839794 93.51336278 389.6230629 99999998.68 -7.999999994 4.839858269 LGS(ph)VSLDLCDGDTGEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGSVSLDLCDGDTGEPR 17 0 Q8N6R0-3;Q8N6R0-4;Q8N6R0;Q8N6R0-2 Q8N6R0-3 METTL13 Methyltransferase-like protein 13 1 LGS(1)VSLDLCDGDTGEPR 213.55 5.93E-13 27417000 39663 33937 37554 36287 57845 66088 36712 39460 41723 32509 TRUE FALSE 41228.92587 39765.41576 38532.68809 43464.46029 48012.52756 50740.06357 33834.41751 38931.10324 40221.39738 38878.51613 1.060455233 1.022812075 0.991104906 1.117955741 1.234937244 1.305092597 0.870260002 1.001352601 1.034540445 1 15.24668554 2.214980172 24.99980044 0.975497961 1.116540286 0.352368471 0.096470906 305.399552 323780.1222 0.040139787 0.029661002 164.0514874 -2.214980172 0.141042325 LGS(ph)YSGPTSVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGSYSGPTSVSR 12 0 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 LGS(0.999)YS(0.001)GPTSVSR 149.83 7.09E-05 545200000 115590 159990 155880 181440 184980 287630 164890 162800 167940 192330 TRUE FALSE 120153.5825 187467.038 159942.3609 217328.2905 153537.1657 220832.2916 151965.4909 160617.9323 161895.8722 230013.3811 0.522376489 0.815026661 0.695361114 0.94485064 0.667514059 0.960084542 0.660681088 0.69829821 0.703854147 1 17.81135827 -2.464663863 2.223825697 3.752807503 0.745104029 0.273438197 0.126540981 5654644.693 430822.6137 78732166.55 0.028838015 0.003430332 2.464663863 -3.007703475 LGSDEKELILLFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSDEKELILLFWK 14 1 Q6NXG1;Q6NXG1-2;Q6NXG1-4;Q6NXG1-3;A0A2U3TZN9;Q6NXG1-5 Q6NXG1 ESRP1 Epithelial splicing regulatory protein 1 0 ; 161.63 4.16E-06 107035000 648240 498920 702200 477320 967460 799130 706780 641820 777280 603090 FALSE TRUE 673833.0158 584605.6289 720499.9089 571732.4713 803011.4948 613544.1684 651380.7368 633217.4527 749305.8446 721253.9386 0.934252112 0.81054064 0.998954557 0.792692339 1.113354745 0.850663179 0.903122606 0.877939681 1.038893245 1 19.46014777 -5 0.111545932 1.290261238 0.868161123 0.085947874 0.094625276 427.6676223 3.161710979 27.70580989 1.059938035 1.00E-05 5 -0.422100115 LGSLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGSLSER 7 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ;;; 124.34 0.0096679 486960000 474500 739220 624600 679300 684540 823770 634390 641480 617820 822710 FALSE TRUE 493233.6264 866175.2847 640877.5891 813663.5125 568182.1353 632461.9019 584664.8541 632882.0098 595584.7789 983904.2728 0.501302454 0.880345079 0.65136173 0.826974265 0.577477048 0.64280837 0.594229409 0.643235351 0.605327973 1 19.90815843 -1.383410033 8.7171151 1.000001424 0.662432889 0.474043644 0.107948609 2.81E-06 1.98E-07 0.098156618 0.023135639 0.041360899 1.383410033 -0.337568535 LGSPDYGNSALLSLPGYRPTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSPDYGNSALLSLPGYRPTTR 22 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 231.06 1.36E-26 1250220000 331170 362740 371160 356150 326200 423730 399970 382450 341150 359960 FALSE TRUE 344244.8473 425037.7733 380832.7345 426595.407 270752.6405 325325.1292 368619.3063 377323.8833 328872.0781 430487.2701 0.799663245 0.987341096 0.884655043 0.9909594 0.628944592 0.755713703 0.856283871 0.87650416 0.763953085 1 18.71561105 LGSQHS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 LGS(0.002)QHS(0.998)PGR;LGS(0.004)QHS(0.996)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR;LGSQHS(1)PGR 135.73 0.00018542 8661560000 2039158 4240903 3988506 3867126 4245891 5015721 3678354 4208335 3703565 3913628 TRUE FALSE 2119665.532 4969245.101 4092449.743 4632031.981 3524175.964 3850895.812 3390035.002 4151929.153 3570274.419 4680428.476 0.452878522 1.061707304 0.87437502 0.989659815 0.752960115 0.822765657 0.72430014 0.887083132 0.762809311 1 22.15820918 -2.339231043 2.092012099 1.884070491 0.827534528 0.106312346 0.157372005 12150723.14 1404063.843 50781611.04 0.035081952 0.004578982 2.339231043 -1.056535963 LGSQHSPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGSQHSPGR 9 0 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 0 63.184 0.077729 23112000 70015 84552 79814 77068 102410 118810 99641 115120 119190 98425 FALSE TRUE 72779.24626 99073.14828 81894.01841 92311.82037 85002.38478 91218.17808 91830.87806 113577.0047 114900.3752 117709.4943 0.618295463 0.841675082 0.695729932 0.784234279 0.722137031 0.77494325 0.780148438 0.96489247 0.976135153 1 16.84487117 1.76332646 2.453574499 0.99080194 0.74340333 0.79074759 0.055775828 0.108002927 1.308690538 0.031489228 0.014218085 57.98644176 -1.76332646 -0.24739861 LGSQPIRAS(ph)NPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGSQPIRASNPDLR 14 1 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 LGSQPIRAS(1)NPDLR;LGS(0.013)QPIRAS(0.987)NPDLR;LGS(0.011)QPIRAS(0.989)NPDLR;LGSQPIRAS(1)NPDLR 109.07 0.0018383 814737000 737355 806530 762475 714851 887510 1014840 686689 775385 711603 818553 TRUE FALSE 766466.3448 945045.2536 782345.7249 856246.3942 736651.3672 779158.79 632864.5219 764992.2323 685992.547 978932.7882 0.782961153 0.965383186 0.799182267 0.874673322 0.75250454 0.795926747 0.64648414 0.781455317 0.700755512 1 19.90085028 3.236282552 24.99999956 0.761394082 0.859368954 0.109389855 0.09819467 94.86935015 1041121.694 0.02568956 0.032123978 1722.989186 -3.236282552 0.097974872 LGSS(ph)SNLQFK ddPTM_MDA-MB-175_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(0.308)S(0.638)S(0.054)NLQFK 190.68 9.18E-07 262100000 424400 206280 259490 183950 395280 383230 335740 253880 282120 154950 TRUE FALSE 441155.6397 241706.9854 266252.5226 220334.761 328090.4468 294230.6404 309423.8215 250477.1539 271966.5563 185309.4858 2.380642512 1.304342216 1.436799209 1.189009618 1.770500012 1.587779703 1.669767849 1.351669359 1.467634294 1 17.49957721 -2.733064161 0.097351158 1.05E-31 1.985926886 0.297818065 0.301523221 155.1358023 1.74169191 41.84018533 6.486020906 0.001848995 2.733064161 1.985926886 LGSSGLGS(ph)ASSIQAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LGSSGLGSASSIQAAVR 17 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LGSSGLGS(0.978)AS(0.007)S(0.015)IQAAVR;LGSS(0.005)GLGS(0.988)AS(0.002)S(0.005)IQAAVR;LGSS(0.002)GLGS(0.708)AS(0.097)S(0.193)IQAAVR;LGSSGLGS(0.977)AS(0.004)S(0.019)IQAAVR 235.37 3.88E-20 276297000 281242 275589 301552 272417 358591 385780 286710 282153 291435 300379 TRUE FALSE 292345.6513 322919.267 309410.6928 326300.2695 297637.8299 296188.4416 264236.921 278371.2005 280946.3113 359232.5139 0.813806212 0.898914364 0.861310379 0.908326103 0.828538115 0.824503435 0.735559591 0.77490536 0.782073728 1 18.45455841 2.909248607 2.767973752 0.79908904 0.871615009 0.036398395 0.071916622 0.464011811 6.941070572 0.021844341 0.024041905 811.4254156 -2.909248607 0.072525969 LGSSLDWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGSSLDWDR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ; 170.3 0.0001345 581510000 584880 688250 644230 610640 847140 816710 746700 656320 623260 795130 FALSE TRUE 607971.514 806451.5837 661019.163 731422.7694 703143.4454 627041.4799 688171.7029 647523.1039 600828.9943 950920.4998 0.639350518 0.848074664 0.695136095 0.769173416 0.739434522 0.659404735 0.723690049 0.680943469 0.631839354 1 19.85896521 -1.479983998 5.956502974 1.000229472 0.712784935 0.663487493 0.061993307 0.000180601 1.58E-05 0.057382887 0.013514613 0.033114332 1.479983998 -0.287444538 LGTLS(ph)PAFSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LGTLSPAFSTR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 LGT(0.011)LS(0.989)PAFSTR;LGT(0.003)LS(0.997)PAFSTR;LGT(0.013)LS(0.987)PAFSTR 177.64 8.28E-06 316452000 315936 288122 337290 283908 383030 379170 383163 324658 336399 284138 TRUE FALSE 328409.3972 337604.7122 346080.0545 340064.155 317922.6974 291113.5139 353129.6828 320306.4905 324292.0657 339809.4009 0.966451771 0.993511984 1.018453443 1.000749697 0.935591236 0.856696469 1.039199274 0.942606325 0.95433518 1 18.37436624 3.248948195 24.87171193 0.952604393 0.996390447 0.155249792 0.045547933 354.2564335 848216.2308 0.012651818 0.016943906 1773.97786 -3.248948195 0.043786054 LGTQEYLQQLESHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGTQEYLQQLESHMK 15 0 Q6P2E9;Q6P2E9-2;I3L2F4 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 85.176 0.0079406 0 82291 45130 58248 48509 80176 74370 75466 54722 61032 53996 FALSE TRUE 85539.91222 52880.72644 59765.99073 58103.93542 66547.71216 57098.69459 69550.77773 53988.5411 58835.47024 64575.48238 1.324649992 0.818897893 0.925521398 0.899783219 1.030541464 0.884216307 1.077046197 0.836053237 0.911111587 1 15.97869889 4.748547383 24.94207413 0.929272903 1.324650214 0.694409992 0.078237331 711.1282941 1776015.431 0.017605812 0.236861965 56046.35619 -4.748547383 0.395377311 LGVADIIDCVVLTS(ph)SPEATETSQQLQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.066)S(0.436)S(0.436)PEAT(0.054)ET(0.007)S(0.001)QQLQLR;LGVADIIDCVVLT(0.062)S(0.419)S(0.419)PEAT(0.09)ET(0.01)S(0.001)QQLQLR 91.175 0.0018601 43301000 40222 42710 37035 44590 52435 58445 46857 43748 45521 50537 TRUE FALSE 41809.99562 50045.11026 38000.16252 53409.76891 43522.11743 44872.03449 43184.2259 43161.62962 43882.7081 60438.75756 0.691774572 0.828030097 0.628738314 0.883700643 0.720102781 0.74243807 0.714512138 0.714138268 0.726068997 1 15.88318638 -2.099619032 2.358259011 1.448092961 0.739128759 0.576975281 0.067087217 4914039.038 1554444.836 11798835.89 0.014846176 0.007950253 2.099619032 -0.708964202 LGVADIIDCVVLTSS(ph)PEATETSQQLQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVADIIDCVVLTSSPEATETSQQLQLR 28 0 Q8NCF5;H3BSZ7;Q8NCF5-3;Q8NCF5-2 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LGVADIIDCVVLT(0.002)S(0.132)S(0.863)PEAT(0.003)ETSQQLQLR;LGVADIIDCVVLTS(0.02)S(0.98)PEATETSQQLQLR 197.33 3.51E-25 293830000 144196 175129 156910 163068 166104 206635 148444 154762 143420 177449 TRUE FALSE 149888.9694 205206.0434 160999.2035 195322.3637 137869.7014 158647.1528 136808.5714 152687.6685 138258.3422 212216.7341 0.706301367 0.966964478 0.758654609 0.92039096 0.649664608 0.747571362 0.64466439 0.719489296 0.651495947 1 17.6951789 3.235106607 24.99999495 0.715997638 0.841610951 0.138697566 0.11934223 130.8496192 947086.2965 0.030759669 0.038201255 1718.330135 -3.235106607 0.125613313 LGVDLDAQTWR ddPTM_MDA-MB-175_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 ; 143.5 8.64E-05 176253000 153763 230810 210945 226563 225784 273330 201008 214993 202691 268030 FALSE TRUE 159833.682 270449.822 216442.4 271376.4852 187405.3163 209853.2499 185252.4677 212111.3705 195396.1905 320545.3468 0.498630486 0.843717823 0.675231764 0.846608718 0.584645256 0.654675702 0.57792905 0.661720323 0.609574254 1 18.29016894 -1.838588753 5.905550914 1.037172793 0.666229827 0.483430004 0.104893214 0.043008458 0.001175512 0.085084904 0.022652736 0.014501444 1.838588753 -0.370942966 LGVEPSDDDCVSVQHVCTIVSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVEPSDDDCVSVQHVCTIVSFR 23 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 261.54 8.90E-44 243830000 63166 83419 74151 81192 84549 96582 64257 73898 64605 64596 FALSE TRUE 65659.84245 97745.56434 76083.43598 97251.53527 70177.39118 74152.29421 59220.36844 72907.51818 62279.87867 77252.34943 0.849939749 1.265276267 0.984868894 1.258881264 0.908417565 0.959871056 0.766583397 0.94375794 0.806187503 1 16.23729119 3.104280509 9.753815634 0.890343055 1.094601861 0.342515368 0.130439409 0.304510467 26.22680555 0.034411545 0.041161193 1271.395029 -3.104280509 0.204258806 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLK 35 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 240.86 7.06E-48 5852100000 152375 589541 759315 697200 738014 944260 584435 687335 699134 668733 FALSE TRUE 158390.8827 690790.0808 779103.3727 835104.0791 612566.6439 724969.9254 538625.4576 678122.3986 673972.3039 799758.4277 0.198048407 0.863748423 0.974173383 1.04419541 0.765939592 0.906486134 0.673485191 0.847909037 0.842719852 1 19.60920476 4.738358593 8.056359205 0.870220195 0.192809807 0.79139909 0.104912531 0.040843572 33.75442203 0.025657379 0.151365102 54746.78156 -4.738358593 -0.677410388 LGVIEDHSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;;;;;; 210.08 8.38E-08 26385880000 5077370 6448380 5696220 6327680 6380500 7191630 5653220 5524730 5208890 5596180 FALSE TRUE 5277828.488 7555839.104 5844668.173 7579276.218 5295944.889 5521482.923 5210105.844 5450680.031 5021423.066 6692644.326 0.788601371 1.12897664 0.873297293 1.132478561 0.791308283 0.825007673 0.778482404 0.814428463 0.750289844 1 22.67414491 3.205334368 24.99995561 0.813970484 0.983738387 0.295090107 0.115780291 194.0160037 145980.2032 0.03021028 0.03611027 1604.48022 -3.205334368 0.169767903 LGVQVVITDPEKLDQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVQVVITDPEKLDQIR 17 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 116.13 0.00025622 907170000 2730100 962880 1237330 1065740 1666420 1967860 1639700 1327680 1547190 904290 FALSE TRUE 2837886.456 1128247.15 1269575.836 1276540.191 1383162.524 1510854.338 1511176.029 1309884.621 1491506.934 1081468.312 2.624105048 1.043254932 1.173937158 1.180376879 1.278967223 1.397039859 1.397337317 1.211209433 1.379149919 1 20.04455996 4.743687905 24.99556776 1.245240251 2.624105621 0.908282835 0.132904628 147.4222019 718661.572 0.031491679 0.265950056 55422.72887 -4.743687905 1.37886537 LGVS(ph)VS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 2 LGVS(1)VS(0.989)PS(0.011)R;LGVS(1)VS(0.997)PS(0.003)R 117.21 0.0017381 212681000 735420 807390 823500 797170 1005500 1103730 891450 909650 888640 916790 TRUE FALSE 764454.9495 946052.9519 844961.0865 954847.8467 834585.4692 847405.4347 821575.8196 897457.6296 856658.02 1096417.447 0.697229829 0.862858352 0.770656367 0.870879836 0.761193167 0.772885762 0.749327568 0.818536436 0.781324688 1 20.06436576 -2.042132482 1.122343516 1.233420069 0.79063004 0.623590417 0.049531591 3172.083762 545.2320231 1901.29691 0.013399276 0.009075436 2.042132482 -0.442790029 LGVSVS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 LGVSVS(0.904)PS(0.095)R;LGVS(0.003)VS(0.978)PS(0.019)R;LGVSVS(1)PSR;LGVSVS(0.999)PS(0.001)R;LGVSVS(1)PSR;LGVSVS(0.986)PS(0.014)R;LGVSVS(0.998)PS(0.002)R;LGVSVS(0.998)PS(0.002)R;LGVSVS(0.986)PS(0.014)R;LGVS(0.002)VS(0.998)PSR 194.52 3.39E-05 22683180000 6629580 7497500 7104720 6936300 8018050 8805380 7433520 7446960 7100980 7193190 TRUE FALSE 6891320.938 8785137.303 7289874.84 8308279.437 6655144.725 6760463.942 6850861.279 7347145.682 6845417.117 8602557.859 0.801078127 1.021223855 0.847407824 0.965791753 0.773623942 0.785866722 0.796374914 0.854065245 0.795742061 1 23.03633426 3.237499365 24.99997543 0.824209586 0.912509738 0.15591708 0.082898068 41.94567668 988126.3926 0.021562762 0.027199735 1727.823453 -3.237499365 0.088300152 LGWDPKPGEGHLDALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGWDPKPGEGHLDALLR 17 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 118.24 0.00010721 2827300000 6262300 4599400 5751000 4764900 7174300 6604300 6782300 5608300 6191400 4970400 FALSE TRUE 6509540.44 5389311.172 5900875.784 5707382.998 5954815.049 5070551.414 6250685.604 5533129.912 5968572.723 5944254.716 1.09509783 0.906642032 0.992702377 0.960151149 1.001776561 0.853017183 1.051550767 0.930836611 1.00409101 1 22.50306451 LGYFSVDPDSHQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LGYFSVDPDSHQGK 14 0 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A0U1RR79 P47897 QARS Glutamine--tRNA ligase 0 176.87 2.16E-06 206970000 345450 431800 520220 447570 629160 614880 494030 555170 551380 428110 FALSE TRUE 359088.6327 505958.2911 533777.3606 536098.0101 522215.6079 472083.4386 455306.6377 547728.8542 531535.9415 511989.9578 0.701358742 0.98821917 1.042554356 1.047086963 1.019972365 0.922056051 0.889288219 1.069803901 1.038176498 1 18.96575599 4.737075297 5.208444845 1.003536431 0.688497987 0.737607307 0.05384435 0.083798024 7.806723439 0.01394698 0.094765363 54585.24914 -4.737075297 -0.315038443 LGYLVS(ph)PPQQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LGYLVSPPQQIR 12 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 LGYLVS(1)PPQQIR;LGYLVS(1)PPQQIR 122.78 0.00036965 120317000 206727 180131 178753 183080 218290 264780 191018 205216 206740 171975 TRUE FALSE 214888.7416 211067.098 183411.45 219292.6776 181185.1438 203288.8578 176045.51 202465.4152 199299.4678 205670.2086 1.044821917 1.026240502 0.891774513 1.066234527 0.880949871 0.988421508 0.855960186 0.984417804 0.969024484 1 17.64997331 4.389604267 8.302662957 0.95311029 1.040176267 0.228025151 0.059925978 0.293982809 24.04912964 0.013346481 0.03681469 24524.73183 -4.389604267 0.087065976 LHAEFAAERDWEQFHQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHAEFAAERDWEQFHQPR 18 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 193.9 6.46E-15 184770000 15425 14770 15385 13091 15276 19052 12681 10055 11426 16889 FALSE TRUE 16033.99091 17306.63261 15785.94574 15680.36073 12679.39098 14627.46174 11687.03008 9920.229172 11014.78049 20198.07619 0.79383753 0.856845595 0.781556896 0.776329418 0.627752409 0.724200741 0.578620953 0.49114723 0.5453381 1 14.30193027 3.262284764 1.259022144 0.610693061 0.825233953 0.154822529 0.136631056 0.554584963 1.850091056 0.048455294 0.076064531 1829.299282 -3.262284764 0.214540891 LHCESESFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHCESESFK 9 0 C9JLU1;P52434;P52434-2;P52434-4 C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" 0 188.66 3.91E-05 273960000 303130 226700 289740 243110 437990 399050 413910 288010 329330 216550 FALSE TRUE 315097.8065 265633.9615 297290.8624 291196.4324 363540.6162 306376.6852 381466.6526 284149.697 317477.4776 258978.8264 1.216693314 1.025697603 1.147935013 1.124402471 1.403746481 1.183018278 1.472964636 1.097192774 1.225881984 1 17.98247463 3.406986664 24.99999985 1.242167412 1.122405 0.11620265 0.13479469 84.49772356 30118.39128 0.035210995 0.047675919 2552.622915 -3.406986664 -0.119762412 LHDAFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHDAFFK 7 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 119.57 0.004753 981350000 2792000 2600400 2982600 2355800 3487900 3680600 3175000 2860700 2923200 2498600 FALSE TRUE 2902230.316 3046998.472 3060329.006 2821770.209 2895028.004 2825836.43 2926135.204 2822356.996 2817994.603 2988152.831 0.971245609 1.019692982 1.024154111 0.944319239 0.96883532 0.94568002 0.979245497 0.94451561 0.943055714 1 21.51082251 3.73605606 24.9989481 0.958524108 1.006497109 0.459173489 0.021878699 166.3749926 1660657.353 0.005424437 0.008823591 5445.72944 -3.73605606 0.047973002 LHDEKEETAGSYDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LHDEKEETAGSYDSR 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;A0A2R8YEF8 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ;; 177.76 4.45E-07 970640000 991920 954755 1050710 908198 1169144 1415356 1121747 990380 1018233 969149 FALSE TRUE 1031081.768 1118726.744 1078092.366 1087836.854 970413.3205 1086661.019 1033821.539 977105.576 981586.9932 1159035.191 0.889603504 0.965222413 0.930163617 0.938571031 0.837259583 0.937556536 0.891967342 0.843033571 0.846900078 1 20.14449294 3.282209635 24.99923343 0.884238234 0.933290625 0.109568011 0.049566314 227.2739685 130165.7569 0.013122946 0.01776846 1915.180165 -3.282209635 0.049052391 LHDETLTYLNQGQSYEIR ddPTM_MDA-MB-175_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 0 273.88 5.07E-39 176220000 89520 100450 110420 93597 111230 126360 105800 105060 90164 113360 FALSE TRUE 93054.31872 117701.5061 113297.6359 112110.2072 92323.16433 97014.805 97507.11954 103651.8425 86919.01525 135570.7216 0.686389492 0.868192665 0.835708733 0.826949993 0.680996333 0.715602926 0.719234348 0.764559201 0.64113412 1 17.04868612 5.024664705 15.48741795 0.771145667 0.482146589 0.06641645 0.099963996 8386697.993 141746498 0.022771211 59441196.17 105843.6249 -5.024664705 -0.288999078 LHDFGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LHDFGYR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 179.16 0.0007052 1835710000 755199 910386 909995 874957 1104979 1125363 992537 874682 894135 1094716 FALSE TRUE 785014.8397 1066737.714 933710.2173 1048020.883 917155.0643 864014.4983 914739.3564 862958.3185 861955.256 1309204.641 0.59961202 0.814798299 0.7131889 0.800501962 0.700543701 0.659953739 0.698698529 0.659147006 0.658380844 1 20.32025919 -0.807335025 5.565934988 1.000000068 0.70276047 0.676469207 0.062112595 5.14E-08 1.11E-08 0.059021318 0.013911455 0.155834989 0.807335025 -0.297239599 LHDINAQLVEDQGFLDTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHDINAQLVEDQGFLDTLK 19 0 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 150.29 7.71E-08 26335000 27983 20477 25604 27440 28812 31387 43118 26984 31146 18628 FALSE TRUE 29087.79045 23993.76546 26271.26127 32867.5501 23914.54653 24097.84492 39738.29849 26622.32362 30025.06154 22277.79995 1.305685055 1.077025807 1.179257437 1.475349908 1.073469848 1.081697698 1.783762247 1.195015831 1.347757032 1 14.44331915 LHDINAQMVEDQGFLDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LHDINAQMVEDQGFLDSLR 19 0 P63010;P63010-2;P63010-3;A0A087WU93;A0A087WZQ6;A0A087X253;A0A087WYD1 P63010 AP2B1 AP-2 complex subunit beta 0 ;;;;;; 302.74 3.48E-50 1376551000 471945 558501 517793 624909 594415 663216 602057 533934 528240 520308 FALSE TRUE 490577.753 654419.2022 531287.111 748514.135 493376.5506 509194.1351 554866.1992 526777.4881 509228.7456 622252.3907 0.788390306 1.051694155 0.853812888 1.202910822 0.792888156 0.818308041 0.891706014 0.846565631 0.818363663 1 19.24714034 LHDPEGMGIIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LHDPEGMGIIPR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;;;; 221.32 2.75E-11 1421960000 2065085 2307997 2393814 2427560 2584375 3020983 2508080 2448208 2433868 2394248 FALSE TRUE 2146616.15 2704377.531 2456198.759 2907724.122 2145083.861 2319405.482 2311490.136 2415393.776 2346273.566 2863355.055 0.749685634 0.944478585 0.857804468 1.015495482 0.749150496 0.810030694 0.807266333 0.843553709 0.819414121 1 21.44927514 4.776823428 21.61579379 0.861583709 0.749683963 0.151204833 0.083717636 6268.293989 3540727.517 0.019385385 3.576555663 59816.83474 -4.776823428 -0.111899746 LHDTFGFVDEDVFFQLSAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LHDTFGFVDEDVFFQLSAVK 20 0 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 ;; 96.544 0.0010688 45416000 43307.5 51370 60448 47179.3 62773 74330 61451 64967 67003 50856 FALSE TRUE 45017.31354 60192.3979 62023.32454 56511.22472 52102.86788 57067.98398 56634.31005 64096.22363 64591.57512 60820.2595 0.740169705 0.989676769 1.019780663 0.929151325 0.856669608 0.9383055 0.931175081 1.053863041 1.062007555 1 15.89226435 1.772016288 4.993132693 1.043422815 0.920348975 0.370679103 0.073524029 0.210512132 11.15886327 0.036486558 0.019545986 59.15838205 -1.772016288 -0.123073839 LHDVEHVLIDVGTGYYVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHDVEHVLIDVGTGYYVEK 19 0 Q99471;H3BPF6;Q99471-3 Q99471 PFDN5 Prefoldin subunit 5 0 124.43 1.69E-05 27305000 41832 32813 41264 33570 53478 57918 49682 36239 46608 37894 FALSE TRUE 43483.55966 38448.3775 42339.37374 40210.0458 44387.82866 44467.42226 45787.79502 35753.27548 44930.58718 45318.60378 0.959507929 0.848401634 0.93426033 0.887274595 0.979461523 0.981217834 1.010353171 0.788931531 0.991438029 1 15.46781579 3.259262505 24.98587212 0.941967409 0.905071104 0.094604936 0.066484321 788.497532 951660.9256 0.019518544 0.026400988 1816.613365 -3.259262505 -0.036896305 LHDVNSDGFLDEQELEALFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LHDVNSDGFLDEQELEALFTK 21 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ;;; 201.61 6.83E-22 1176890000 637508 573650 680100 738650 1171570 1013810 927790 703910 797690 759950 FALSE TRUE 662677.3081 672169.9251 697823.9647 884752.7653 972426.9499 778367.9919 855067.3955 694475.2378 768981.2927 908847.6524 0.729140144 0.739584818 0.767811814 0.97348853 1.069955946 0.856433958 0.940825883 0.764127229 0.846105825 1 19.79367895 3.862822064 5.455242442 0.907349727 0.739251237 0.486806092 0.082258171 0.227993741 9.175201291 0.023655706 0.043654467 7291.58704 -3.862822064 -0.16809849 LHEADLELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHEADLELQR 10 0 Q96ED9-2;Q96ED9 Q96ED9-2 HOOK2 Protein Hook homolog 2 0 138.25 0.0049483 0 14467 24104 18026 20627 25907 25848 15650 20898 22978 25959 FALSE TRUE 15038.16833 28243.6745 18495.77237 24706.95903 21503.33739 19845.19373 14423.31211 20617.89649 22151.02627 31045.16903 0.484396407 0.909760693 0.595769743 0.795839089 0.692646813 0.639236131 0.464591193 0.66412576 0.713509604 1 14.92208117 -1.638346471 5.075493887 1.004920227 0.663057777 0.393425866 0.125824983 0.006720037 0.000478835 0.116867149 0.027239466 0.022996065 1.638346471 -0.341862451 LHEAVFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHEAVFLR 8 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 157.58 0.00069741 359070000 170603 202699 191932 171408 305730 267070 221510 204230 203647 336120 FALSE TRUE 177338.5382 237510.9765 196933.9056 205311.9908 253762.1238 205047.04 204147.4674 201492.6309 196317.7843 401976.2786 0.441166675 0.59085819 0.489914246 0.510756484 0.631286315 0.510097364 0.507859489 0.501255028 0.488381516 1 18.61675084 -1.972563583 2.88053187 1.399146554 0.52118237 0.888040348 0.051224873 14628047.7 3479493.791 38771185.72 0.011807399 0.010652129 1.972563583 -0.877964184 LHEEGIIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LHEEGIIYR 9 0 P26640;A0A140T936;P26640-2 P26640 VARS Valine--tRNA ligase 0 ;;;; 215.38 6.41E-07 813720000 578834 574500 619924 586505 675568 748831 664904 599451 622641 524364 FALSE TRUE 601686.8133 673165.906 636079.7287 702513.9385 560735.1927 574926.3489 612787.0871 591416.3398 600232.272 627103.0862 0.959470343 1.073453346 1.014314461 1.120252721 0.89416749 0.916797193 0.977171219 0.943092695 0.957150882 1 19.25834309 3.228741096 24.99997932 0.945701104 1.042160037 0.486482544 0.047178933 159.7875964 406809.9431 0.012968959 0.015679092 1693.328024 -3.228741096 0.096458934 LHELNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHELNQK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 124.59 0.0041312 283830000 440890 442710 437880 415690 575080 600400 519290 497510 486200 496780 FALSE TRUE 458296.6776 518741.9987 449291.5125 497912.2413 477328.107 460966.1992 478586.6929 490841.6922 468701.757 594114.5296 0.771394495 0.873134678 0.756237207 0.838074507 0.803427762 0.775887773 0.805546185 0.82617352 0.788908087 1 19.18038155 -2.137572535 2.381612263 1.411306491 0.806579656 0.760438094 0.032928791 3503104.854 704065.2331 7813561.458 0.007300156 0.007284965 2.137572535 -0.604726835 LHEVGHERDS(ph)LQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHEVGHERDSLQR 13 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;E9PPF6;E9PID5;A0A3B3ITS2 Q13136-2 PPFIA1 Liprin-alpha-1 1 LHEVGHERDS(1)LQR;LHEVGHERDS(1)LQR 128.99 9.60E-05 276151000 64249 49819 84147 74876 85342 96152 88233 63603 72331 77947 TRUE FALSE 66785.60013 58375.02571 86339.93995 89686.24932 70835.59732 73822.1552 81317.06691 62750.50582 69727.82144 93219.22226 0.716435929 0.626212323 0.926203178 0.962100382 0.759881874 0.791919879 0.872320804 0.673149854 0.747998318 1 16.50833986 4.252386038 24.99841671 0.823532702 0.671324087 0.303120958 0.100351709 320.6224234 579722.4148 0.025388228 0.068751634 17880.76263 -4.252386038 -0.152208615 LHEWVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHEWVK 6 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 114.67 0.025089 273950000 511320 436750 507210 461900 664490 639130 572180 489540 509300 458720 FALSE TRUE 531507.3084 511758.4151 520428.3093 553262.4414 551540.2271 490701.7436 527331.0365 482978.517 490970.3925 548597.4013 0.96884766 0.932848777 0.948652524 1.008503577 1.005364272 0.894466037 0.961235025 0.880387905 0.894955739 1 19.06538826 2.73193487 24.9926993 0.918664246 0.971258628 0.248024001 0.039475371 682.5816622 2574733.025 0.012659159 0.012197387 539.4297192 -2.73193487 0.052594383 LHFFMPGFAPLT(ph)SR ddPTM_MDA-MB-175_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 105.06 0.003759 210720000 179990 232090 187820 182100 182480 262150 191080 193060 170170 204280 TRUE FALSE 187096.1442 271949.6521 192714.7435 218118.8365 151462.1148 201269.6354 176102.6503 190472.3465 164045.6149 244304.7548 0.765830957 1.113157426 0.788829279 0.892814537 0.61997203 0.823846575 0.720831858 0.779650591 0.671479419 1 17.89832242 3.758877861 2.072186801 0.762767946 0.929999607 0.136421468 0.131762679 0.46897552 3.912903512 0.033907328 0.071145768 5739.550228 -3.758877861 0.167231661 LHFFMPGFAPLTS(ph)R ddPTM_MDA-MB-175_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(0.38)S(0.62)R 132.51 3.22E-05 230240000 137780 176810 144760 163050 140260 185460 148610 158330 141940 169600 TRUE FALSE 143219.6608 207175.7421 148532.5645 195300.8033 116418.6553 142389.7257 136961.5599 156207.8453 136831.6071 202829.8728 0.706107334 1.02142618 0.732301226 0.962879879 0.573971939 0.702015555 0.675253393 0.770142204 0.674612695 1 17.62991062 3.249189989 24.9999891 0.719465375 0.858705061 0.161230854 0.135388976 324.7539718 763807.8072 0.034265552 0.045923207 1774.965798 -3.249189989 0.139239686 LHFFMPGFAPLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 154.24 1.44E-05 9718550000 3733950 5121190 4073960 3903930 7467470 6279900 4490620 4210020 4206530 8287820 FALSE TRUE 3881369.229 6000714.545 4180130.744 4676115.702 6198152.117 4821488.398 4138633.47 4153591.568 4055137.807 9911659.649 0.391596298 0.605419754 0.421738729 0.471779285 0.625339483 0.486446122 0.417552016 0.419061158 0.409128032 1 23.24069522 -1.078581044 4.261547004 1.00006019 0.473024637 0.806375754 0.077616255 45824210.08 97168073.48 40689.26603 0.018892374 0.083448581 1.078581044 -0.527035553 LHGDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHGDEER 7 0 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 ; 150.17 0.0019672 72674000 96194 102644 111748 90715 143321 141123 112633 112572 115744 121016 FALSE TRUE 99991.8134 120272.3085 114660.2447 108658.1562 118959.3476 108349.322 103804.5311 111063.1565 111578.396 144726.7682 0.690900617 0.831030154 0.792253196 0.750781335 0.821958157 0.748647423 0.717244864 0.767398857 0.770958942 1 17.14297226 -2.30523684 1.659212182 1.747805614 0.767015112 0.748011582 0.040793025 364789.0246 46284.58762 1017877.035 0.010642019 0.004951801 2.30523684 -0.980790502 LHGELQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;; 129.42 0.0010914 1049850000 256481 340195 340380 321977 339795 391280 314729 326744 318021 343900 FALSE TRUE 266607.0679 398620.8449 349250.5824 385663.0896 282036.7673 300411.1499 290059.7186 322364.5311 306575.4863 411280.6206 0.648236398 0.969218643 0.84917831 0.937712769 0.68575263 0.730428653 0.705259874 0.783806761 0.745416805 1 18.64976357 5.011832304 14.03837997 0.807176953 0.415284775 0.176637379 0.108454458 748390.58 15999333.56 0.025890936 5534270.454 102761.9423 -5.011832304 -0.391892178 LHGGFDS(ph)DCS(ph)EDGEALNGEPELDLTSK ddPTM_MDA-MB-175_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 153.86 2.79E-08 275056000 182789 122898 143084 127488 200865 200839 175920 158651 160793 122156 TRUE FALSE 190005.6509 144004.7755 146812.8866 152704.7459 166722.039 154197.186 162130.9307 156524.5428 155006.0913 146090.1294 1.300605672 0.985725566 1.004947338 1.045277641 1.141227267 1.055493528 1.10980072 1.071424493 1.061030557 1 17.15649918 3.336833621 0.009430937 7.11E-07 2.168836839 0.125576873 0.081737042 11564.83299 29.55061488 3266.747911 3529.274542 2171.868974 -3.336833621 2.168836128 LHGGFDSDCS(ph)EDGEALNGEPELDLTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHGGFDSDCSEDGEALNGEPELDLTSK 27 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 LHGGFDS(0.386)DCS(0.614)EDGEALNGEPELDLTSK 157.16 7.12E-09 70245000 26012 22373 27775 21737 29161 30980 25728 26065 28293 21829 TRUE FALSE 27038.97385 26215.38871 28498.83932 26036.51372 24204.22364 23785.36451 23711.37213 25715.64131 27274.74046 26105.97461 1.035738916 1.004191152 1.091659658 0.997339272 0.927152654 0.911108084 0.908273776 0.985048124 1.044770052 1 14.6720924 3.481150013 9.36812221 0.957860251 1.040705803 0.399493305 0.044283601 0.118834997 147.7834774 0.012702285 0.018111902 3027.95916 -3.481150013 0.082845552 LHHSQS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LHHSQSPAR 9 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 LHHS(0.13)QS(0.87)PAR;LHHS(0.066)QS(0.934)PAR;LHHS(0.156)QS(0.844)PAR;LHHS(0.183)QS(0.817)PAR;LHHS(0.101)QS(0.899)PAR 138.75 8.22E-05 691792000 96799 317182 233859 227647 377367 423104 214984 254717 233239 591318 TRUE FALSE 100620.6993 371655.5412 239953.5577 272674.8971 313222.2921 324844.5082 198132.9923 251302.9352 224844.774 707175.4406 0.142285342 0.525549276 0.339312629 0.385583098 0.442920206 0.459354906 0.28017516 0.355361514 0.317947656 1 19.43170865 -1.984219993 2.878672843 1.570256985 0.366857111 0.784123311 0.100550746 12510580.39 7844996.545 47423305.53 0.022563214 0.01037003 1.984219993 -1.203399874 LHHYDERS(ph)DGESDSPEKEAEFAPYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHHYDERSDGESDSPEKEAEFAPYPR 26 2 Q02410-2;Q02410 Q02410-2 APBA1 Amyloid beta A4 precursor protein-binding family A member 1 1 LHHYDERS(1)DGESDSPEKEAEFAPYPR;LHHYDERS(1)DGESDSPEKEAEFAPYPR 242.07 1.81E-45 842070000 315850 202023 251510 169059 366340 354250 272670 214916 230198 200461 TRUE FALSE 328320.0019 236718.8787 258064.5572 202498.3656 304069.6577 271980.8062 251297.4129 212035.4026 221913.2189 239737.4949 1.369497925 0.987408661 1.076446375 0.844667063 1.268344185 1.134494236 1.048219066 0.884448228 0.925650863 1 17.87109604 1.911277651 4.58792206 0.92871884 1.100420905 0.245571702 0.13702931 0.326314883 11.43976927 0.062581302 0.036615526 81.52253032 -1.911277651 0.171702065 LHIACFPVQLDTLSDGASVDES(ph)HGISPPLQGEISQTQENSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHIACFPVQLDTLSDGASVDESHGISPPLQGEISQTQENSK 41 0 E9PG22;Q8IW35;Q8IW35-2 E9PG22 CEP97 Centrosomal protein of 97 kDa 1 LHIACFPVQLDTLSDGAS(0.003)VDES(0.499)HGIS(0.499)PPLQGEISQTQENSK 170.18 1.06E-19 183050000 39223 31936 38427 29644 37691 39517 32436 34866 51537 44045 TRUE FALSE 40771.55433 37420.75957 39428.43919 35507.49472 31284.29728 30339.77564 29893.58156 34398.6783 49682.19344 52674.77446 0.774024279 0.710411387 0.748526018 0.674089165 0.593914214 0.575983019 0.567512284 0.653038929 0.943187587 1 15.68482461 1.202896279 5.014758313 0.988215811 0.656330872 0.775600704 0.066716199 0.093562407 5.352848297 0.067976993 0.018359091 15.95498054 -1.202896279 -0.331884939 LHIACFPVQLDTLSDGASVDESHGIS(ph)PPLQGEISQTQENSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHIACFPVQLDTLSDGASVDESHGISPPLQGEISQTQENSK 41 0 E9PG22;Q8IW35;Q8IW35-2 E9PG22 CEP97 Centrosomal protein of 97 kDa 1 LHIACFPVQLDTLSDGAS(0.002)VDES(0.407)HGIS(0.591)PPLQGEISQTQENSK 212.41 6.45E-36 171400000 30811 39897 44112 30080 39008 49362 36363 31685 42868 32928 TRUE FALSE 32027.44207 46748.99939 45261.59496 36029.73422 32377.43409 37898.42359 33512.77304 31260.3144 41325.18905 39379.61116 0.81330011 1.187137151 1.149366224 0.914933722 0.822187755 0.962386943 0.851018384 0.793819783 1.049405716 1 15.26516125 3.620590348 6.498485796 0.891846371 1.0628325 0.20028663 0.119567282 0.291134099 14.42121784 0.031032408 0.048300037 4174.364301 -3.620590348 0.170986129 LHIIEVGTPPTGNQPFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHIIEVGTPPTGNQPFPK 18 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 127.3 2.58E-05 1067950000 649660 617030 744240 711020 789820 906450 770800 687500 758620 629070 FALSE TRUE 675309.0784 723000.1027 763635.5058 851657.6338 655566.6785 695940.7249 710382.6819 678285.187 731317.4144 752324.2222 0.897630381 0.961021965 1.015035118 1.132035376 0.871388504 0.925054258 0.944250711 0.901586267 0.972077454 1 19.52099502 LHIVDTVCAHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHIVDTVCAHFR 12 0 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ; 181.68 1.03E-05 502910000 133299 152660 141959 140052 222827 205637 168881 153912 153223 260449 FALSE TRUE 138561.7474 178878.1675 145658.5682 167753.8676 184950.9461 157880.9232 155643.6659 151849.0614 147708.5342 311478.995 0.444851016 0.574286454 0.467635284 0.538572007 0.593783045 0.506875025 0.499692334 0.487509796 0.474216678 1 18.24877535 -1.760441451 2.766707447 1.106197587 0.511436936 0.915615038 0.044649892 16068238.63 13358506.91 11653264.71 0.010385208 0.017360353 1.760441451 -0.594760651 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LHKTEDGGWEWSDDEFDEESEEGK 24 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKT(0.005)EDGGWEWS(0.995)DDEFDEESEEGK;LHKT(0.001)EDGGWEWS(0.999)DDEFDEESEEGK;LHKT(0.032)EDGGWEWS(0.968)DDEFDEESEEGK 162.07 1.12E-11 728568000 1144552 166341 252487 157520 465488 753187 438453 241264 309162 91225.3 TRUE FALSE 1189739.797 194908.7728 259067.0186 188676.9858 386364.516 578270.7339 404085.9082 238030.2507 298035.32 109099.1509 10.90512425 1.786528778 2.374601603 1.72940838 3.541407177 5.300414614 3.703840999 2.181779131 2.731784047 1 16.73528035 4.743045813 24.99156805 2.823686272 10.90512749 0.815679911 1.168123364 195.8263992 1091108.553 0.291645616 2.325932058 55340.84843 -4.743045813 8.081441222 LHLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHLELK 6 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 80.377 0.064673 260350000 140340 361370 249530 334160 219860 370390 213140 232420 251540 700710 FALSE TRUE 145880.7316 423432.4864 256032.9568 400255.8506 182488.2757 284372.5358 196433.5299 229304.7901 242487.1245 838000.7086 0.174081871 0.505288936 0.30552833 0.477631876 0.217766255 0.339346415 0.234407355 0.27363317 0.289363866 1 19.67659194 -1.698565844 2.963061804 1.087616443 0.314788888 0.807105418 0.100752275 75381411.8 70382273.95 49347416.11 0.022702168 0.020018621 1.698565844 -0.772827555 LHLGFIEIR ddPTM_MDA-MB-175_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 ; 154.84 7.47E-05 1550780000 1032070 1328920 1292070 1215280 1752820 1784140 1505840 1206970 1109980 1838340 FALSE TRUE 1072816.921 1557151.672 1325742.406 1455658.757 1454876.282 1369800.524 1387808.326 1190792.541 1070032.037 2198527.526 0.487970657 0.708270265 0.603013785 0.662106223 0.661750315 0.623053616 0.631244462 0.541631855 0.486703953 1 21.06810616 -1.505338276 5.645779931 1.000636732 0.604899331 0.741965183 0.070613489 0.000560822 4.91E-05 0.067753064 0.015944955 0.031236454 1.505338276 -0.395737401 LHLGIPEAVFVEDVDSFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHLGIPEAVFVEDVDSFMK 19 0 P61758 P61758 VBP1 Prefoldin subunit 3 0 ; 200.69 6.35E-16 412560000 244570 214060 274880 255560 306950 320270 350430 261210 287550 217150 FALSE TRUE 254225.8124 250823.1398 282043.5986 306109.0052 254774.7486 245892.1462 322962.3809 257708.9072 277201.1317 259696.3849 0.978934738 0.965832235 1.086051308 1.178718777 0.981048499 0.946844702 1.243615236 0.992346918 1.067404661 1 17.98646641 4.244190369 24.94818406 1.064699749 0.972383445 0.144287691 0.08710251 239.2118019 1060031.995 0.02085247 0.053821194 17546.49469 -4.244190369 -0.092316304 LHLGTTQNSLTEADFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHLGTTQNSLTEADFR 16 0 O75351 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 151.38 6.49E-07 421510000 34133 54178 44755 43786 55685 66226 51827 49300 46839 62984 FALSE TRUE 35480.5972 63482.65005 45921.35207 52446.74011 46219.68359 50846.01516 47764.66432 48639.21414 45153.27354 75324.5089 0.471036555 0.842788768 0.609646883 0.696277226 0.6136075 0.675026176 0.634118496 0.645728925 0.599449956 1 16.20083174 -1.107018925 3.905857324 1.000112846 0.649052446 0.595595542 0.08810894 15512406.2 23548630.27 21203.24798 0.018688848 0.078159375 1.107018925 -0.351060399 LHLIYLINDVLHHCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHLIYLINDVLHHCQR 16 0 Q8IWX8 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 160.27 3.07E-09 174397000 44549 45951 49290 47796 60745 70954 57443 47635 55965 60451 FALSE TRUE 46307.82892 53842.7268 50574.53789 57249.90614 50419.5866 54476.00882 52940.46756 46996.53074 53950.83058 72295.21605 0.640537942 0.74476196 0.699555803 0.791890657 0.697412489 0.753521627 0.732281753 0.650064186 0.74625727 1 16.14161256 0.961903875 23.6288479 1.000000001 0.714325355 0.794137283 0.043450901 1494.070704 926687.8015 0.040796126 0.010199032 9.160177206 -0.961903875 -0.285674645 LHLPPALSPEEAESALEAAHYFTEDSSSEEALPQEEQEGS(ph)GSEERGEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHLPPALSPEEAESALEAAHYFTEDSSSEEALPQEEQEGSGSEERGEEK 49 1 Q66K14-2;G3V133 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 LHLPPALSPEEAESALEAAHYFTEDSSSEEALPQEEQEGS(0.518)GS(0.482)EERGEEK;LHLPPALSPEEAESALEAAHYFTEDSSSEEALPQEEQEGS(0.549)GS(0.451)EERGEEK 101.87 6.26E-08 141029000 24982 21961 26773 19913.3 35128 35777 33167 28331 32109 20061.4 TRUE FALSE 25968.30865 25732.63092 27470.72637 23852.0913 29156.95511 27468.33396 30567.28387 27951.26929 30953.40336 23992.04723 1.082371521 1.07254836 1.14499301 0.99416657 1.21527583 1.144893293 1.274059007 1.165022268 1.290152652 1 14.55026865 3.21751741 24.99825811 1.192579413 1.078555672 0.284493742 0.082692742 266.6180404 316727.7224 0.021866509 0.026160336 1650.127149 -3.21751741 -0.114023741 LHLSGIDANPNALFPPVEFPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 168.78 9.26E-12 6680210000 321166 2696980 1933630 3363880 2013921 3786600 1722225 2897340 1894764 3572150 FALSE TRUE 333845.8817 3160165.335 1984021.986 4029245.424 1671595.428 2907219.536 1587232.504 2858505.896 1826571.814 4272044.4 0.078146632 0.739731388 0.464419795 0.943165624 0.391286998 0.680521845 0.371539328 0.669118958 0.427563865 1 22.02649521 -2.169947704 2.213488004 2.073868512 0.548492087 0.272487547 0.228749811 12163027.9 2760628.969 65409038.35 0.049732905 0.006761644 2.169947704 -1.525376424 LHLVDLAGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHLVDLAGSER 11 0 O95239;O95239-2;Q2VIQ3;Q5JRK0;H0Y718;J3KPF9;A0A087X011;E9PES4;Q9Y496 O95239;J3KPF9 KIF4A;KIF4B;KIF6;KIF3A Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B;Kinesin-like protein;Kinesin-like protein KIF3A 0 ; 99.522 0.004712 236625000 51123 62188 55883 61793 73960 72621 59070 56817 56804 58943 FALSE TRUE 53141.37552 72868.30524 57339.35689 74015.47097 61388.30562 55755.87333 54439.93905 56055.46105 54759.63514 70491.75232 0.75386657 1.033713915 0.813419372 1.049987673 0.870857988 0.790955984 0.772288066 0.795205953 0.776823293 1 16.10516685 2.996502158 24.95532637 0.810704032 0.920058841 0.120619704 0.103864168 217.1843161 1549518.353 0.027748392 0.032515422 991.9782687 -2.996502158 0.109354808 LHNAIEGGTQLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHNAIEGGTQLSR 13 0 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 117.48 0.00050319 226690000 105970 104940 120530 110870 153450 140880 120870 111560 141300 116480 FALSE TRUE 110153.7774 122962.6287 123671.1108 132799.7551 127366.6238 108162.7551 111395.8936 110064.7207 136214.6406 139302.0259 0.790755029 0.882705244 0.887791187 0.953322497 0.914319968 0.776462183 0.799671741 0.790115722 0.977836753 1 17.08785671 1.150640929 6.853419334 0.995658238 0.849713189 0.490187663 0.05700372 0.213961576 13.51902951 0.061085913 0.015368242 14.14623699 -1.150640929 -0.14594505 LHNFLVEEEDLFLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHNFLVEEEDLFLQR 15 0 H7C0Q6;Q9C037-3;Q9C037-2;Q9C037 H7C0Q6 TRIM4 E3 ubiquitin-protein ligase TRIM4 0 198.59 7.85E-09 23621000 17588 19362 22859 20453 24583 27659 22267 22915 24149 24188 FALSE TRUE 18282.38782 22687.27288 23454.72432 24498.54235 20404.39044 21235.61643 20521.65436 22607.86191 23279.88221 28927.17549 0.632014274 0.784289254 0.810819719 0.846904059 0.705370991 0.734106115 0.709424754 0.781544051 0.804775503 1 14.82013784 0.690172024 1.605874215 0.999776424 0.752574787 0.631877538 0.057241598 0.747407405 2.887558422 0.055096232 0.015803163 4.899728588 -0.690172024 -0.247201637 LHNGNAS(ph)PPRVPS(ph)PPPAPEPPWHCGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHNGNASPPRVPSPPPAPEPPWHCGDR 27 1 O15037 O15037 KHNYN Protein KHNYN 2 LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR;LHNGNAS(1)PPRVPS(1)PPPAPEPPWHCGDR 126.52 9.07E-05 783770000 263010 280310 290490 251590 286960 373780 285540 237140 300100 269150 TRUE FALSE 273393.8379 328451.062 298060.408 301353.7511 238182.6417 286975.2597 263158.6287 233961.5262 289299.4596 321884.7893 0.849353082 1.02039945 0.925984756 0.93621619 0.739962401 0.891546507 0.817555341 0.726848655 0.898767103 1 18.29618488 3.316405745 11.75205612 0.825436619 0.938944045 0.178072009 0.084936806 0.702011493 102.8191477 0.022448106 0.030393357 2072.076306 -3.316405745 0.113507425 LHNQVNGTEWSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHNQVNGTEWSWK 13 0 O14980 O14980 XPO1 Exportin-1 0 ; 194.3 1.14E-06 1248570000 1113440 1011890 1242700 1036660 1433700 1591520 1356240 1255210 1386490 1070600 FALSE TRUE 1157399.471 1185674.236 1275085.783 1241708.254 1190000.186 1221913.6 1249934.365 1238385.963 1336590.496 1280363.572 0.903961575 0.926044962 0.995877898 0.969809108 0.929423651 0.954348926 0.976233932 0.967214305 1.04391481 1 20.28812211 1.429133102 2.852817831 1.021264967 0.951811549 0.49858835 0.02756537 0.221017124 3.242403835 0.022619661 0.007449493 26.86167571 -1.429133102 -0.069453418 LHPCTSSGPDS(ph)PYPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHPCTSSGPDSPYPAK 16 0 Q96H55;Q96H55-4 Q96H55 MYO19 Unconventional myosin-XIX 1 LHPCT(0.004)S(0.004)S(0.004)GPDS(0.981)PY(0.007)PAK;LHPCT(0.001)S(0.001)S(0.001)GPDS(0.971)PY(0.026)PAK 61.102 0.056654 1186160000 622998 484016 575871 495381 779773 718535 731378 592034 677356 475787 TRUE FALSE 647594.4421 567141.9829 590878.6713 593365.8832 647227.464 551666.1358 674050.6813 584098.7526 652978.0899 569008.3532 1.138110607 0.99671996 1.038435847 1.042806982 1.137465664 0.969522034 1.184605951 1.026520524 1.147572063 1 19.11809031 LHPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHPESK 6 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 77.72 0.071677 220760000 497760 531590 555100 481950 615570 695320 646470 584870 590340 501370 FALSE TRUE 517411.9492 622886.4473 569566.362 577278.2715 510935.6313 533842.4677 595797.9922 577030.7743 569093.7787 599603.8522 0.86292299 1.038829963 0.949904441 0.962766115 0.852121996 0.89032528 0.993652709 0.962353347 0.949116282 1 19.19365013 2.221242824 24.99582896 0.972719765 0.93064703 0.176556336 0.052279626 536.5747802 774466.2278 0.020206922 0.01495986 166.4342961 -2.221242824 -0.042072735 LHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHPPSPVPQGVCPAHREPLAAFCGDELR 28 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 LHPPS(1)PVPQGVCPAHREPLAAFCGDELR 106.66 0.00052687 224920000 23163 21762 23313 22139 25503 25275 30148 23169 27194 24561 TRUE FALSE 24077.49313 25499.45422 23920.55593 26518.02812 21168.00917 19405.2643 27784.92098 22858.45745 26215.29325 29373.2577 0.819707959 0.868118017 0.8143651 0.90279493 0.720655822 0.660643926 0.945925756 0.778206411 0.892488451 1 14.84221566 0.966933702 4.11441563 0.999886597 0.815386315 0.352653414 0.078670863 0.229651057 11.61408428 0.07447139 0.019021559 9.266883471 -0.966933702 -0.184500283 LHPTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LHPTDK 6 0 G8JLM4 G8JLM4 USHBP1 0 ;;; 110.24 0.028873 3495750000 5518340 4281130 5264910 4480080 6295900 6070200 6642600 5405490 5798960 3711110 FALSE TRUE 5736208.324 5016380.775 5402117.88 5366226.452 5225725.167 4660488.045 6121935.655 5333038.248 5590256.562 4438230.951 1.29245377 1.130265827 1.217178182 1.209091305 1.177434258 1.050077857 1.379363923 1.201613505 1.259568649 1 22.08155331 4.768577766 22.4160221 1.194136529 1.292454411 0.085924959 0.101094682 7234.610108 5402246.268 0.022654316 2.079038403 58691.8456 -4.768577766 0.098317882 LHPVILASIVDSYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHPVILASIVDSYER 15 0 O00303;E9PQV8;A0A1W2PP79 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 249.32 1.57E-18 881820000 661300 784340 843990 824990 936480 994740 875730 865130 790820 913950 FALSE TRUE 687408.6346 919044.2937 865985.0727 988170.5597 777297.4641 763726.7104 807087.9943 853534.3474 762358.5427 1093021.004 0.628907068 0.84082949 0.792285848 0.9040728 0.711145954 0.698730132 0.738401176 0.780894735 0.697478402 1 20.05988969 -1.99781967 4.233919846 1.23426877 0.760698323 0.487645708 0.075193924 0.051976266 2.68E-05 0.022757909 0.016735653 0.01005033 1.99781967 -0.473570447 LHQDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHQDYK 6 0 Q9HC84 Q9HC84 MUC5B Mucin-5B 0 72.823 0.084581 52736000 54856 62254 61264 62526 74162 91832 73429 64766 60037 71154 FALSE TRUE 57021.75724 72945.64023 62860.59017 74893.45618 61555.96973 70505.40973 67673.44311 63897.91771 57876.2801 85095.26397 0.670093194 0.857223267 0.738708445 0.880113095 0.723377152 0.828546813 0.795266857 0.750898637 0.68013515 1 16.37679122 -1.532226443 3.361957083 1.006039241 0.774200097 0.511155029 0.067512838 188482745.7 394822742.7 11380168.82 0.014898712 0.029361183 1.532226443 -0.231839144 LHQEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LHQEGK 6 0 O43488;H7C5H7;H7C4Q7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ;;; 94.163 0.044794 772009000 1439430 1108260 1415350 1053020 1698640 1555370 1719400 1408090 1607740 1101100 FALSE TRUE 1496259.808 1298595.034 1452235.184 1261304.213 1409905.78 1194158.889 1584628.935 1389216.857 1549877.751 1316839.463 1.136250735 0.98614529 1.102818699 0.957826864 1.070674003 0.906837107 1.203357721 1.054962959 1.17696788 1 20.32864805 2.226667643 24.9991823 1.110353668 1.027232845 0.190086028 0.082957267 351.3117845 738456.8379 0.028281483 0.021050104 168.5262832 -2.226667643 -0.083120823 LHQLAMQQSHFPMTHGNTGFSGIESS(ph)SPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.02)S(0.695)S(0.285)PEVK 225.51 4.26E-35 1127700000 202430 276580 353200 279570 500750 515590 400380 412620 425370 313940 TRUE FALSE 210422.0927 324080.4635 362404.6822 334868.1116 415632.6939 395852.0363 368997.1694 407089.5038 410061.0168 375450.5323 0.560452242 0.863177531 0.965252812 0.891910073 1.10702385 1.054338727 0.982811683 1.084269348 1.092183874 1 18.51826331 5.122309442 0.854089196 1.047062223 2.52E-16 0.865882143 0.05664343 1.353491379 0.488782244 0.018574155 1.549097139 132528.5488 -5.122309442 -1.047062223 LHQLAMQQSHFPMTHGNTGFSGIESSS(ph)PEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LHQLAMQQSHFPMTHGNTGFSGIESSSPEVK 31 0 F8VZX2;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;F8VRH0 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2 Poly(rC)-binding protein 2 1 LHQLAMQQSHFPMTHGNTGFSGIES(0.161)S(0.234)S(0.605)PEVK;LHQLAMQQSHFPMTHGNTGFSGIESS(0.217)S(0.783)PEVK;LHQLAMQQSHFPMTHGNTGFSGIES(0.007)S(0.064)S(0.929)PEVK 318.98 1.13E-92 8734900000 1566340 1599530 2378280 1929580 3204480 3371730 2691980 2467240 2798860 2154810 TRUE FALSE 1628180.313 1874236.835 2440259.931 2311245.165 2659783.634 2588696.807 2480975.573 2434170.683 2698129.575 2577003.763 0.631811383 0.727293014 0.946936891 0.896873027 1.032122526 1.004537457 0.962736496 0.944573973 1.047002575 1 21.29726321 4.37939772 1.479933859 0.98461652 0.584698257 0.897019522 0.041361169 0.174531119 0.565614763 0.011355396 0.08498162 23955.08522 -4.37939772 -0.399918262 LHQLS(ph)GSDQLESTAHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHQLSGSDQLESTAHSR 17 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 LHQLS(0.944)GS(0.056)DQLESTAHSR 256.58 2.72E-27 193760000 61024 71051 76944 78877 94731 105080 79467 89558 83793 88066 TRUE FALSE 63433.27464 83253.45655 78949.22385 94478.63518 78628.65846 80676.7625 73238.16889 88357.6215 80777.3063 105320.8466 0.602286031 0.790474624 0.74960681 0.89705541 0.746563107 0.766009438 0.695381506 0.838937631 0.766964081 1 16.6844315 -5 0.223078708 2.201464033 0.738731333 0.502374395 0.07281671 130.894087 1.310106643 70.74934789 0.131163013 1.00E-05 5 -1.462732701 LHQLSGSDQLESTAHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHQLSGSDQLESTAHSR 17 0 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 0 ; 175.8 6.85E-10 360920000 38576 58428 58580 64878 64055 71185 61427 70054 55442 69660 FALSE TRUE 40099.01027 68462.55449 60106.64292 77710.67476 53166.95398 54653.36257 56612.19123 69115.04072 53446.65325 83308.54328 0.48133131 0.821795122 0.721494346 0.932805589 0.638193298 0.656035509 0.679548447 0.829627287 0.641550688 1 16.34617683 -1.538405145 2.921903871 1.012315518 0.724190542 0.337894978 0.120006073 24927704.19 27865397.45 2437257.886 0.027749099 0.02894642 1.538405145 -0.288124975 LHQMWLSWNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHQMWLSWNQK 11 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ; 210.35 1.30E-08 1531610000 1307660 1330810 1282280 1183490 2214000 1921880 1498590 1288690 1445320 1998800 FALSE TRUE 1359287.427 1559366.265 1315697.27 1417580.79 1837665.071 1475552.496 1381126.6 1271417.218 1393303.216 2390426.591 0.568638013 0.652338069 0.550402709 0.593024189 0.768760303 0.617275804 0.577774112 0.531878797 0.582868021 1 21.18883667 -0.944065883 4.216805608 1.000013451 0.602973313 0.777332383 0.063452333 43322804234 91335973210 8998738.284 0.016267809 0.113745472 0.944065883 -0.397040138 LHQNICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHQNICR 7 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 97.071 0.012267 78657000 69780 75837 64806 73193 105080 96088 78430 71756 69021 93671 FALSE TRUE 72534.96828 88861.41482 66494.8976 87670.35694 87218.53913 73773.01823 72282.45166 70794.22819 66536.94769 112024.039 0.647494671 0.793235234 0.593577041 0.782603071 0.778569849 0.658546316 0.645240542 0.631955684 0.593952408 1 16.77344882 -1.189456539 5.047061769 1.000025847 0.6813835 0.634146155 0.072783913 2.13E-05 3.42E-06 0.070912207 0.016712813 0.064646268 1.189456539 -0.318642347 LHS(ph)PGATSTAELGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSPGATSTAELGSR 15 0 H7C0P0;Q9BV73-2;Q9BV73 H7C0P0 CEP250 Centrosome-associated protein CEP250 1 LHS(1)PGATSTAELGSR;LHS(1)PGATSTAELGSR 130.56 4.93E-05 324300000 83217 139524 110866 130837 120656 150296 104932 125168 107401 152883 TRUE FALSE 86502.47142 163486.1617 113755.259 156716.1681 100146.9362 115392.0318 96707.15565 123490.3277 103535.659 182837.4967 0.473111222 0.894161015 0.622165918 0.857133634 0.547737406 0.631117981 0.528924085 0.675410295 0.566271475 1 17.48020245 -1.564885397 8.642511946 1.000060648 0.650620192 0.403859518 0.129531238 0.000140479 7.07E-06 0.116396824 0.027430273 0.027234199 1.564885397 -0.349440456 LHS(ph)SNPNLSTLDFGEEK ddPTM_MDA-MB-175_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(0.598)S(0.402)NPNLSTLDFGEEK 309.91 2.81E-58 1470900000 1056200 721140 935600 823660 1282400 1303700 1117400 864520 976430 655360 TRUE FALSE 1097899.592 844990.1853 959982.5046 986577.4896 1064418.106 1000935.433 1029815.268 852932.5235 941288.475 783765.2444 1.400801579 1.078116428 1.224834236 1.258766572 1.358082811 1.27708576 1.313933318 1.088249995 1.200982669 1 19.58006207 1.157377663 1.031880729 1.015474238 1.264018195 0.421339305 0.093666281 0.47892103 1.084023687 0.086807483 0.029144757 14.36738279 -1.157377663 0.248543957 LHSEGDQLLAAEHPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSEGDQLLAAEHPGR 16 0 O60437;K7EKI8 O60437 PPL Periplakin 0 ; 170.09 3.12E-09 995230000 176354 252970 210740 216770 238860 264920 211513 230927 217783 246030 FALSE TRUE 183316.5921 296415.6297 216232.0575 259646.459 198258.6625 203396.3449 194934.0584 227831.8013 209945.0324 294234.868 0.623028105 1.007411636 0.734896102 0.882446261 0.673810904 0.691272065 0.662511754 0.774319518 0.713528732 1 18.1666087 5.025285639 16.47720003 0.776751018 0.22182808 0.13536762 0.122851392 21393847.07 363908450.4 0.027882886 317150600 105995.0634 -5.025285639 -0.554922938 LHSELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSELK 6 0 D6RBP0;A0A494C0G8;Q96NL6-2;Q96NL6 D6RBP0 SCLT1 Sodium channel and clathrin linker 1 0 ; 132.94 0.01468 465090000 393240 344280 399710 338540 529790 554730 479860 398230 451610 397570 FALSE TRUE 408765.4188 403407.4119 410126.771 405502.2016 439736.485 425902.3645 442247.3193 392892.3782 435356.6443 475466.2296 0.859714935 0.848445982 0.86257813 0.852851741 0.924853244 0.895757339 0.930134028 0.826330776 0.915641569 1 18.85898335 -5 0.207266245 1.57414279 0.859150768 0.584297685 0.031860803 109.2244368 1.087133574 26.07347574 0.073448443 1.00E-05 5 -0.714992023 LHSFESHKDEIFQVQWSPHNETILASSGTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHSFESHKDEIFQVQWSPHNETILASSGTDR 31 1 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 42.032 0.048916 738270000 148510 190960 241440 192110 275060 270990 268620 211670 197410 214300 FALSE TRUE 154373.2895 223755.8945 247732.1247 230108.7846 228305.3994 208056.6794 247564.8625 208832.9099 190305.2527 256287.982 0.602343068 0.873064327 0.966616237 0.897852419 0.890815861 0.811808177 0.965963603 0.81483692 0.742544583 1 17.9674063 4.737254328 6.519252821 0.881038816 0.59696919 0.555428248 0.075781492 0.085078986 22.36062253 0.017629012 0.107531019 54607.75575 -4.737254328 -0.284069626 LHSFLGDDVFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSFLGDDVFLR 12 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 228.83 9.63E-12 923740000 503540 652150 538820 583600 749070 725860 666580 571760 618910 666810 FALSE TRUE 523420.148 764151.6895 552862.0918 699034.3381 621743.349 557290.0155 614331.7178 564096.4924 596635.55 797458.6527 0.656360234 0.958233617 0.693279946 0.876577533 0.779655907 0.69883249 0.770361844 0.707367699 0.748171141 1 19.60505019 -1.096154051 4.98584634 1.000007273 0.766585076 0.397728753 0.086586348 6.47E-06 1.17E-06 0.077543241 0.018276548 0.080139375 1.096154051 -0.233422197 LHSLLGDYYQAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSLLGDYYQAIK 13 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 104.17 0.0015525 448230000 495600 311010 448530 403310 517460 550890 574320 474590 478930 322090 FALSE TRUE 515166.6707 364423.5482 460219.0603 483083.5142 429502.334 422954.1463 529303.2977 468228.8973 461693.4029 385197.3687 1.337409631 0.946069672 1.194761693 1.254119455 1.115018868 1.098019303 1.374109329 1.215555804 1.198589192 1 18.55523832 LHSQEEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHSQEEDFR 9 0 Q4V328-4;Q4V328;Q4V328-2;A0A087WV84;A0A087WW92;A0A087WZF5 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 0 ; 151.83 0.0017072 0 204896 234552 241699 225797 244469 288900 214428 246821 211446 265600 FALSE TRUE 212985.4523 274834.4814 247997.8745 270458.9727 202914.2467 221807.3533 197620.5731 243512.7682 203836.0998 317639.2348 0.670526273 0.865240976 0.78075328 0.851465887 0.638819845 0.698299609 0.622154166 0.766633153 0.641722046 1 18.2770296 -1.242782109 3.538565241 1.000562088 0.730312206 0.492906889 0.083224933 18526774.6 33188760.77 117543.896 0.0199121 0.057176543 1.242782109 -0.270249882 LHSS(ph)NPNLSTLDFGEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.11)S(0.89)NPNLSTLDFGEEK;LHS(0.021)S(0.978)NPNLSTLDFGEEK;LHS(0.005)S(0.995)NPNLSTLDFGEEK;LHS(0.309)S(0.691)NPNLSTLDFGEEK;LHS(0.169)S(0.831)NPNLSTLDFGEEK;LHS(0.118)S(0.881)NPNLSTLDFGEEK 284.07 2.38E-36 5268810000 3885740 2760275 3426186 3052647 4528634 4800261 4032848 3280785 3742429 2331278 TRUE FALSE 4039152.016 3234330.759 3515475.222 3656451.465 3758858.41 3685473.131 3716742.836 3236811.443 3607739.711 2788047.289 1.448738704 1.160070266 1.260909467 1.311473977 1.348204683 1.321883293 1.333098922 1.160960022 1.294002338 1 21.4108236 0.216393439 0.595106589 0.986900149 1.303742244 0.554132097 0.080022774 2.168783829 1.053333927 0.147450622 0.032658359 1.645862077 -0.216393439 0.316842095 LHSYS(ph)SPSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 LHSYS(0.941)S(0.059)PSTK;LHSYS(0.718)S(0.27)PS(0.011)TK;LHSYS(0.548)S(0.452)PSTK 240.33 2.98E-12 722459000 1071780 916530 1081500 898450 1425420 1448920 1300610 1135930 1222950 807240 TRUE FALSE 1114094.702 1073936.898 1109684.778 1076160.728 1183127.618 1112430.289 1198664.79 1120704.716 1178936.268 965403.2225 1.154020078 1.112423154 1.149452118 1.114726679 1.225526899 1.152296018 1.241620871 1.160866973 1.221185346 1 19.88077212 3.265245638 24.99720299 1.178244718 1.132410093 0.046141572 0.065047791 488.6377918 457728.3976 0.016234878 0.021976019 1841.81344 -3.265245638 -0.045834625 LHSYSS(ph)PSTK ddPTM_MDA-MB-175_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(0.259)S(0.741)PS(0.001)TK 98.407 0.0034769 459160000 540870 456860 553960 470880 697720 706480 617060 554790 564850 414830 TRUE FALSE 562223.9652 535322.1511 568396.6527 564018.6586 579121.8036 542410.7268 568693.2248 547353.9475 544521.1588 496107.9961 1.133269308 1.079043586 1.145711533 1.136886853 1.167330114 1.093331958 1.14630933 1.103295959 1.097585935 1 18.92029468 0.588437401 0.994619278 0.99982051 1.128334774 0.702238008 0.024814269 0.716890381 1.110035767 0.023117487 0.007394493 3.87647869 -0.588437401 0.128514264 LHTDDDLNWLDHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHTDDDLNWLDHSR 14 0 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 0 ; 150.05 4.23E-06 208360000 50010 178855 140029 144499 120230 168689 95930 128004 113180 219427 FALSE TRUE 51984.43342 209571.955 143678.2708 173080.4709 99793.34755 129513.5363 88410.75593 126288.3158 109106.6739 262419.5195 0.198096672 0.798614201 0.547513657 0.65955639 0.380281725 0.493536215 0.336906173 0.481245892 0.415771945 1 18.00151551 -1.112338 4.972760711 1.000016574 0.486737355 0.490615182 0.159070878 3.31E-05 5.90E-06 0.145939267 0.034396891 0.077207946 1.112338 -0.513279219 LHTDDELNWLDHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ;;;;; 280.97 1.56E-33 2360191000 620525 749218 746272 820296 747265 880023 779428 755190 751962 705473 FALSE TRUE 645023.8061 877890.3634 765720.4614 982548.1005 620245.1622 675650.9951 718334.3967 745067.9133 724899.0345 843696.9273 0.764520748 1.040528103 0.907577634 1.164574705 0.735151619 0.800821922 0.85141284 0.883099001 0.859193641 1 19.68636532 3.21053205 24.99992033 0.848851234 0.969979644 0.195383501 0.113277825 319.1596542 284671.7975 0.031178981 0.037273134 1623.798179 -3.21053205 0.12112841 LHTLEEEKEELAQYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHTLEEEKEELAQYQK 16 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 159.22 5.53E-09 65193000 109610 53932 87476 55435 122590 123530 110390 90481 102520 50015 FALSE TRUE 113937.4874 63194.40147 89755.69642 66399.87754 101752.1956 94842.02962 101737.3433 89268.25019 98830.32523 59814.48165 1.904847861 1.056506714 1.500567989 1.110097015 1.701129773 1.585603135 1.700881468 1.492418687 1.652280894 1 15.8682072 3.209775686 24.99847588 1.557496015 1.376651813 0.036244037 0.288771889 515.2744057 447492.2855 0.076418723 0.091352779 1620.972647 -3.209775686 -0.180844202 LHTVQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHTVQPK 7 0 A2A3N6;Q5VWC4;P55036-2;P55036;A6PVX3 A2A3N6;Q5VWC4 PIPSL;PSMD4 Putative PIP5K1A and PSMD4-like protein;26S proteasome non-ATPase regulatory subunit 4 0 83.614 0.041402 0 474550 359360 455880 366860 584120 552550 524200 448200 475690 391420 FALSE TRUE 493285.6004 421077.2846 467760.6073 439423.813 484831.491 424228.6365 483111.8343 442192.6121 458570.0098 468111.2548 1.053778552 0.899523949 0.999250931 0.938716616 1.035718509 0.906256007 1.032044902 0.944631447 0.97961757 1 18.83649193 -1.664923298 2.174682291 1.004871249 0.97382576 0.015700221 0.051443177 5183105.35 3500798.431 139995.6538 0.011729949 0.021631005 1.664923298 -0.031045489 LHVAILER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 1519690000 849103 1259100 1105033 1107511 1506850 1551090 1146070 1111090 1054630 1889130 FALSE TRUE 882626.2421 1475340.631 1133831.068 1326573.37 1250716.175 1190872.854 1056238.039 1096197.656 1016674.072 2259268.854 0.390668973 0.65301685 0.501857522 0.587169326 0.553593333 0.527105418 0.467513212 0.485200181 0.450001367 1 21.10742453 -1.773898235 2.80754128 1.112126865 0.516260868 0.813431039 0.069966942 13656837.82 11714189.55 10582597.29 0.017073185 0.016830684 1.773898235 -0.595865997 LHVENEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LHVENEDKK 9 1 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 190.05 2.43E-05 1855520000 5823490 2514140 3577230 2666530 5406510 5323750 5317670 3879500 4356820 2164810 FALSE TRUE 6053405.882 2945923.988 3670455.553 3193961.675 4487513.361 4087389.745 4900857.13 3827501.648 4200018.899 2588963.072 2.33815845 1.137877948 1.417731907 1.233683752 1.733324593 1.578774834 1.892980701 1.478391751 1.622278411 1 21.30394296 LHVGNIS(ph)PTCTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LHVGNISPTCTNK 13 0 Q9BWF3;E9PB51;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 Q9BWF3 RBM4 RNA-binding protein 4 1 LHVGNIS(1)PTCTNK;LHVGNIS(1)PTCTNK;LHVGNIS(1)PTCTNK;LHVGNIS(1)PTCTNK 177.64 9.84E-06 2839060000 4188470 3298820 3998700 3345180 5071890 4854080 4507760 3890460 4289930 3282830 TRUE FALSE 4353834.03 3865366.674 4102909.407 4006846.62 4209771.949 3726793.484 4154429.992 3838314.747 4135536.257 3926037.685 1.108963892 0.984546503 1.045050949 1.020582822 1.072269878 0.949250563 1.058173743 0.977656114 1.053361325 1 21.90464259 2.781318848 24.99999202 1.008151317 1.041356788 0.165109976 0.04267417 960.4468435 561555.2756 0.011963125 0.012688723 604.3921953 -2.781318848 0.033205472 LHYCVSCAIHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LHYCVSCAIHSK 12 0 P62854;Q5JNZ5 P62854 RPS26;RPS26P11 40S ribosomal protein S26;Putative 40S ribosomal protein S26-like 1 0 184.03 8.58E-06 829630000 673730 632020 717860 678950 914170 853360 869740 690590 776940 760300 FALSE TRUE 700329.3806 740564.5186 736568.0213 813244.2835 758779.7099 655180.0728 801567.5062 681333.7706 748978.0812 909266.2282 0.770213782 0.8144639 0.810068601 0.894396227 0.834496747 0.72055912 0.881554248 0.74932264 0.823717035 1 19.79434324 0.952036072 22.71304055 1.000000001 0.809369573 0.553155171 0.051111722 3172.275928 1502215.425 0.047373378 0.011843345 8.954391374 -0.952036072 -0.190630427 LHYTPPLQS(ph)PIIDNDPLLGQSPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LHYTPPLQSPIIDNDPLLGQSPWR 24 0 C9J5J4;H7C4T7;H0Y322;Q5TKA1-3;Q5TKA1;Q5TKA1-2 C9J5J4 LIN9 Protein lin-9 homolog 1 LHYTPPLQS(1)PIIDNDPLLGQSPWR;LHYT(0.002)PPLQS(0.998)PIIDNDPLLGQSPWR 246.31 4.65E-38 170876000 46628 61267 64611 64583 62636 88444 71131 67044 70225 75995 TRUE FALSE 48468.90944 71789.13066 66294.81574 77357.32464 51989.15509 67904.22138 65555.56635 66145.38484 67697.61597 90884.76524 0.533300706 0.789891798 0.729438158 0.851158326 0.572033772 0.747146358 0.721304238 0.727793978 0.744873091 1 16.47175086 -4.999999999 0.301163477 3.376849992 0.702586128 0.495734304 0.088134265 221.8808236 2.047403061 332.9664878 0.081978718 1.00E-05 4.999999999 -2.674263864 LIALSIDSVEDHLAWSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LIALSIDSVEDHLAWSK 17 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;; 304.71 9.97E-47 16355135000 8325710 9669002 10679451 10149317 13426216 14018356 12173082 12255725 12137717 10541675 FALSE TRUE 8654415.46 11329577.88 10957766.27 12156821.61 11144032.6 10762805.27 11218924.02 12091457.05 11700882.94 12607114.38 0.686470765 0.898665431 0.869173225 0.964282645 0.883947925 0.853708862 0.889888335 0.95909791 0.928117457 1 23.58773476 5.320480931 1.462635118 0.917883587 4.05E-08 0.711515384 0.043970983 3.070988038 1.80033664 0.011679979 6.257367552 209161.1066 -5.320480931 -0.917883547 LIAPVAEEEATVPNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIAPVAEEEATVPNNK 16 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 83 0.019606 21644000 21718 27233 27650 26557 27949 36503 27423 26900 25722 33299 FALSE TRUE 22575.44341 31910.05591 28370.58171 31809.89534 23198.23896 28025.73146 25273.5136 26539.4495 24796.27024 39823.3015 0.566890302 0.801291071 0.712411594 0.798775946 0.582529275 0.703752085 0.634641344 0.666430168 0.622657321 1 15.28132521 -1.452094917 6.287793322 1.000114776 0.680137076 0.61738217 0.076332538 0.000116815 1.02E-05 0.070296878 0.016563236 0.035310599 1.452094917 -0.3199777 LIAQACVSIFPDSGHFNVDNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIAQACVSIFPDSGHFNVDNIR 22 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 219.04 1.13E-25 1821010000 413100 555160 576850 648480 603130 687210 595110 656450 613120 574710 FALSE TRUE 429409.507 650504.4115 591883.1849 776747.4085 500610.178 527615.8923 548463.7232 647651.3615 591053.931 687313.421 0.6247652 0.946445088 0.861154703 1.130121113 0.728357926 0.767649628 0.797981978 0.942294071 0.859948188 1 19.39060861 0.717434685 1.05464251 0.997972552 0.852361441 0.106596058 0.130802535 2.380978771 4.642389737 0.122772321 0.039056227 5.217166361 -0.717434685 -0.145611111 LICCDILDVLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LICCDILDVLDK 12 0 P62258;P62258-2;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 165.11 0.00012907 319290000 612330 411170 496430 541560 626900 605700 658510 536710 528920 364700 FALSE TRUE 636505.2612 481785.249 509367.3736 648678.9516 520339.7619 465035.3545 606894.2655 529516.2803 509884.2725 436155.9824 1.459352358 1.104616854 1.167855983 1.48726368 1.193013011 1.066213404 1.391461518 1.214052545 1.169041107 1 18.73448465 -4.565478378 0.213176194 5.83E-13 1.284574745 0.25924095 0.135888891 175.4105994 2.073745097 74.9086602 0.275314011 2.72E-05 4.565478378 1.284574745 LICCDILDVLDKHLIPAANTGESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LICCDILDVLDKHLIPAANTGESK 24 1 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 207.44 4.51E-25 1030400000 744490 446770 746350 455820 1028500 905780 690360 721240 896130 530640 FALSE TRUE 773883.0401 523499.2721 765800.4941 545979.8355 853675.9374 695426.3222 636247.7793 711572.9575 863878.4563 634608.7483 1.219464815 0.82491657 1.206728549 0.860340859 1.345200393 1.095834755 1.002582743 1.121278204 1.361277257 1 19.27550788 3.249072079 24.99979709 1.144610222 1.026142757 0.123209389 0.164059554 477.7778646 1136309.853 0.043053205 0.05767663 1774.483964 -3.249072079 -0.118467465 LIDDYGVEEEPAELPEGTSLTVDNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIDDYGVEEEPAELPEGTSLTVDNKR 26 1 Q00577 Q00577 PURA Transcriptional activator protein Pur-alpha 0 135.01 5.59E-05 28321000 41888 25366 34787 28419 34817 42408 41553 33667 30383 21117 FALSE TRUE 43541.77058 29722.41318 35693.5778 34040.19338 28898.81878 32559.3847 38295.96728 33215.74893 29289.52176 25254.47184 1.724121211 1.176916839 1.413356732 1.347887756 1.144305015 1.289252252 1.516403413 1.315242272 1.159775661 1 14.62425125 -4.618796761 0.12791347 6.54E-14 1.49095297 0.368698141 0.157008995 157.8165342 1.407437163 41.48782111 1.254844745 2.41E-05 4.618796761 1.49095297 LIDEVIEDTRYTLPLTEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIDEVIEDTRYTLPLTEGK 19 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ; 132.13 1.30E-05 56001000 76228 64203 89862 68717 113241 96894 75030 77521 83186 75067 FALSE TRUE 79237.5403 75229.36582 92203.87754 82309.0175 93992.33527 74391.83694 69148.95255 76481.95779 80192.15211 89774.94141 0.88262425 0.837977331 1.027055837 0.916837329 1.046977406 0.828648126 0.770247816 0.85192991 0.893257638 1 16.45402519 2.673012957 24.99992822 0.850969215 0.939795087 0.155918295 0.080173899 297.0954061 113311.7648 0.025584697 0.024121487 470.9913775 -2.673012957 0.088825872 LIDLES(ph)PTPESQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.992)PT(0.008)PESQK;LIDLES(0.902)PT(0.098)PESQK;LIDLES(0.994)PT(0.006)PESQK;LIDLES(0.671)PT(0.329)PESQK 293.95 1.34E-40 1892490000 2860290 1907840 2476840 1922270 3122020 3058600 3000810 2533260 2679800 1920940 TRUE FALSE 2973216.458 2235496.679 2541388.485 2302489.269 2591340.156 2348286.504 2765598.671 2499305.793 2583354.521 2297311.414 1.294215682 0.973092575 1.10624466 1.002253876 1.127988195 1.02218902 1.203841436 1.087926425 1.124512117 1 21.13151501 LIDLESPT(ph)PESQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 LIDLES(0.474)PT(0.526)PESQK;LIDLES(0.492)PT(0.508)PESQK;LIDLES(0.444)PT(0.556)PESQK 334.72 1.63E-61 1077824000 1176340 757380 1016370 788250 1205560 1284080 1216400 995400 1142940 774080 TRUE FALSE 1222782.812 887454.1234 1042857.437 944163.4973 1000639.342 985871.8804 1121055.39 982058.2911 1101805.813 925746.1553 1.320861885 0.958636575 1.126504746 1.019894592 1.080900348 1.064948393 1.210974934 1.060828917 1.190181354 1 19.82025713 LIDLHSPSEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 0 ;;; 161.99 6.39E-05 3406660000 3586160 3280900 3734410 2979700 4898140 4649850 4347240 3679780 3926320 3706910 FALSE TRUE 3727744.366 3844369.053 3831731.792 3569075.766 4065555.912 3569992.807 4006491.969 3630458.568 3785012.51 4433208.041 0.840868358 0.867175422 0.864324831 0.805077437 0.917068605 0.805284294 0.903745534 0.818923573 0.853786349 1 22.07991964 -0.367962322 6.816303935 1.000000025 0.852516844 0.601598707 0.035906586 0 0 0.030585637 0.007209104 0.428585702 0.367962322 -0.147483181 LIDLHTNVATAVLEHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIDLHTNVATAVLEHIK 17 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 254.59 2.79E-27 106290000 145340 116460 155000 122550 176530 183780 164960 141920 142550 123070 FALSE TRUE 151078.1354 136461.0991 159039.4273 146790.0242 146523.4937 141099.8802 152030.0042 140017.7945 137419.6533 147183.2102 1.026463108 0.927151262 1.080554142 0.997328595 0.995517719 0.958668316 1.032930346 0.951316352 0.933663923 1 17.16725358 1.650751261 8.923158555 0.956906323 1.000467261 0.161246227 0.042125727 0.18908671 26.95635835 0.019540823 0.010283623 44.74569531 -1.650751261 0.043560938 LIDVLENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIDVLENR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 101.64 0.012211 22526000 28656 32401 27467 27575 33605 36977 28290 30158 27097 31703 FALSE TRUE 29787.36101 37965.61971 28182.81258 33029.2527 27892.8341 28389.65214 26072.55588 29753.78134 26121.78426 37914.59586 0.785643638 1.001345757 0.743323566 0.871148748 0.735675364 0.748778973 0.687665404 0.784757972 0.688963806 1 15.21046572 3.717570218 1.406905639 0.76081241 0.879135021 0.078353529 0.105488485 0.769473299 2.932408236 0.030111771 0.07409927 5218.79476 -3.717570218 0.118322611 LIDVNHYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIDVNHYAK 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 114.97 0.0015521 1183800000 2609600 2278700 2445100 2593400 3147800 3301500 3320400 2939500 2869500 2228500 FALSE TRUE 2712629.023 2670048.999 2508821.315 3106366.779 2612738.08 2534776.66 3060138.372 2900100.811 2766227.256 2665131.908 1.017821675 1.001844971 0.941349772 1.165558361 0.980341 0.951088632 1.148212726 1.08816408 1.037932587 1 21.34577551 2.242429011 24.99975527 1.079817477 1.011959433 0.144070357 0.068038792 170.0380776 1098890.132 0.024003634 0.019379902 174.7547586 -2.242429011 -0.067858044 LIDWGLAEFYHPAQEYNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIDWGLAEFYHPAQEYNVR 19 0 P19784;H3BSA1 P19784 CSNK2A2 Casein kinase II subunit alpha 0 141.86 1.61E-07 150660000 123210 89975 100630 89678 120550 161960 106400 86728 111780 81146 FALSE TRUE 128074.4259 105427.5063 103252.5005 107416.0407 100058.9541 124347.2445 98060.08998 85565.55302 107757.0596 97045.00507 1.319742586 1.086377462 1.06396512 1.10686831 1.031057229 1.281335855 1.01045994 0.881710017 1.110382338 1 16.56636634 7.677411818 1.070634241 1.047680427 199.8601631 0.382003077 0.096939793 1277.559507 2.662719305 0.030394085 622218.9072 47578617.42 -7.677411818 198.8124827 LIDWGLAEFYHPGQEYNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIDWGLAEFYHPGQEYNVR 19 0 P68400;E7EU96;A0A2R8YD58;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2;A0A2R8Y4H0;A0A2R8Y4D6 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ; 152.04 5.97E-08 2210700000 611710 703610 691150 699980 876840 896140 745510 730790 635040 662970 FALSE TRUE 635860.7831 824449.5442 709161.9368 838433.9548 727795.05 688025.0661 687074.9782 720994.9554 612185.0344 792866.2782 0.801977333 1.039834291 0.894428173 1.057472083 0.917929126 0.867769364 0.866571069 0.909352529 0.772116372 1 19.59671804 3.000062061 24.99999989 0.880318214 0.955674954 0.113738063 0.084876613 4.057617868 1633042.911 0.022773715 0.026962994 1000.142912 -3.000062061 0.07535674 LIEDFLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617;O43617-2 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 ;;;; 165.11 0.00075883 112220900 300791 346317 319325 331108 363017 407625 337482 340991 321704 370866 FALSE TRUE 312666.4609 405794.2508 327646.8718 396600.1741 301311.5 312960.2714 311029.279 336420.5734 310125.9359 443530.092 0.704949825 0.914919321 0.738725236 0.894190003 0.679348494 0.705612262 0.701258572 0.758506761 0.69922186 1 18.75867246 5.043657468 15.34791424 0.773923713 0.38232612 0.038218581 0.105547317 1641699.188 16472133.99 0.023622686 18183859.21 110575.1324 -5.043657468 -0.391597594 LIEDKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIEDKPR 7 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 135.77 0.0027774 3156040000 4250830 3427410 3777560 3235390 5201540 4998840 5019870 4321450 4483120 3611330 FALSE TRUE 4418656.051 4016041.006 3876006.317 3875340.485 4317384.089 3837935.168 4626399.472 4263528.031 4321773.387 4318900.97 1.02309733 0.929875687 0.897452001 0.897297834 0.999648781 0.888636992 1.071198322 0.987178928 1.00066508 1 22.04223281 2.242791968 24.99999964 1.012905246 0.93783183 0.390987538 0.046070402 110.6323736 653650.7696 0.015997406 0.012941943 174.9008693 -2.242791968 -0.075073416 LIEDTEDWRPR ddPTM_MDA-MB-175_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 ;;;;; 204.69 2.95E-08 2469282000 1958399 2292410 2132700 2080300 2448890 2729610 2357467 2220460 2309092 2425530 FALSE TRUE 2035718.105 2686113.585 2188279.914 2491777.131 2032628.553 2095699.445 2172682.576 2190698.366 2225988.23 2900766.164 0.701786352 0.926001419 0.754379978 0.859006549 0.700721271 0.72246411 0.749003006 0.755213706 0.767379411 1 21.46800257 -1.187971304 3.63428923 1.000251971 0.771721653 0.51322402 0.066998092 15456087.67 31365764.43 47879.24468 0.015595595 0.064867729 1.187971304 -0.228530318 LIEEVMIGEDKLIHFSGVALGEACTIVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIEEVMIGEDKLIHFSGVALGEACTIVLR 29 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 117.03 9.15E-05 142160000 13141 175260 137690 143650 100870 140200 93943 99609 94882 217230 FALSE TRUE 13659.81683 205359.5417 141278.3145 172063.5412 83724.15343 107640.6748 86579.50219 98273.90428 91467.21535 259792.0594 0.052579809 0.790476592 0.543813059 0.66231255 0.32227372 0.414333968 0.333264621 0.378279092 0.352078565 1 17.98699781 -1.13535641 5.132619821 1.000020546 0.436862235 0.442795907 0.192346872 4.34E-05 7.31E-06 0.178743211 0.042128645 0.073222338 1.13535641 -0.563158311 LIEGLSHEVIVSAACGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIEGLSHEVIVSAACGR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 92.211 0.0031837 0 88259 86404 76088 67719 76620 97555 70229 85877 90356 79905 FALSE TRUE 91743.53347 101243.2149 78070.91579 81113.61608 63596.15977 74899.32971 64724.26747 84725.95928 87104.10521 95560.85488 0.960053503 1.05946326 0.816975904 0.84881635 0.665504299 0.783786727 0.677309423 0.886617846 0.911504039 1 16.54413214 4.228060855 24.11167165 0.810071948 1.009758367 0.354624594 0.098958056 114.1238557 262077.5297 0.024263203 0.05337399 16906.77818 -4.228060855 0.199686419 LIELYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIELYK 6 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 135.36 0.059249 0 367110 324880 384260 293220 470930 461700 445610 350280 399800 332270 FALSE TRUE 381603.7863 380675.6128 394274.1313 351218.0408 390881.4868 354477.1721 410681.9238 345585.0695 385411.2761 397371.9448 0.960318893 0.957983113 0.992204247 0.883852133 0.983666542 0.892053847 1.033495014 0.869676569 0.969900571 1 18.60013049 5.064736323 0.000916991 1.893257596 1.05E-05 0.000471202 0.051902356 11370522.48 1523.55643 1561673.236 1583967.4 116074.3668 -5.064736323 -1.893247051 LIESAEELIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LIESAEELIR 10 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ;; 120.12 0.0014006 51507000 50106 68806 67130 67576 74516 78236 68185 61683 61736 70473 FALSE TRUE 52084.22357 80622.89526 68879.46295 80942.33111 61849.79694 60066.87468 62840.48153 60856.24028 59514.13342 84280.83506 0.61798419 0.956598202 0.817261278 0.960388338 0.733853632 0.712699093 0.745608198 0.722064989 0.706140766 1 16.36291699 LIETGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIETGER 7 0 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 130 0.0083885 49819000 35397 61567 60740 67053 84127 80884 78846 72319 73700 60652 FALSE TRUE 36794.50089 72140.65333 62322.9343 80315.88327 69827.12259 62099.91681 72665.84449 71349.6821 71047.5514 72535.59815 0.507261287 0.994555159 0.859204803 1.107261611 0.962660051 0.856130209 1.00179562 0.983650565 0.97948529 1 16.14640158 4.740403234 24.99669386 0.970038431 0.507261131 0.805274771 0.068502293 65.47520667 888159.3447 0.015747885 0.102018438 55005.13491 -4.740403234 -0.462777299 LIEVDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LIEVDDER 8 0 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;;;; 150.35 0.0011413 7104520000 6979170 8280720 7990860 7714310 9074260 9614940 8088220 8733130 8390050 9623410 FALSE TRUE 7254713.021 9702869.245 8199108.376 9240177.493 7531820.526 7382015.901 7454244.182 8616076.677 8088093.739 11508932.94 0.630354965 0.843072881 0.71241256 0.802870044 0.654432567 0.641416189 0.647692034 0.74864253 0.702766606 1 23.45625074 -1.181952791 4.101102941 1.000125394 0.712453604 0.622919444 0.067813722 7145081908 1425220423 8910052.289 0.015645138 0.065772933 1.181952791 -0.28767179 LIEVDDERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LIEVDDERK 9 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ;; 163.94 0.00010044 905630000 1180680 587010 792230 627850 1068010 855740 984400 830940 888520 602430 FALSE TRUE 1227294.158 687824.4012 812876.1646 752036.8561 886470.0417 657007.3539 907240.1557 819802.6084 856542.3388 720464.6243 1.703475947 0.954695592 1.12826659 1.043822043 1.230414391 0.91192174 1.259243168 1.137880447 1.188874942 1 19.45856807 4.747635162 24.83749892 1.106274922 1.703476287 0.729612353 0.110932144 542.9254553 1485980.438 0.024655445 0.304561568 55928.75634 -4.747635162 0.597201364 LIFPYVELDLHSYDLGIENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIFPYVELDLHSYDLGIENR 20 0 O75874;C9J4N6;C9JLU6;C9JJE5 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 336.47 4.82E-80 4600000000 1275450 1519680 1435520 1508730 1809620 1837830 1466060 1535930 1531030 1638370 FALSE TRUE 1325805.751 1780673.219 1472930.83 1807152.291 1502021.439 1411021.835 1351146.386 1515343.371 1475928.529 1959377.233 0.676646502 0.908795503 0.751734176 0.922309528 0.766581041 0.720137915 0.689579507 0.773380105 0.753264101 1 20.90196375 -1.305524734 3.852487908 1.000473418 0.775685078 0.431640486 0.077903757 90.75199597 28525511.2 21602.222 0.018389124 0.049485193 1.305524734 -0.22478834 LIFYDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIFYDLR 7 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 95.62 0.031016 608110000 1207080 1366840 1348980 1385850 1820900 1737680 1576100 1389050 1397610 1623110 FALSE TRUE 1254736.45 1601584.137 1384135.527 1659966.994 1511384.068 1334130.155 1452561.164 1370432.057 1347310.289 1941127.328 0.646395748 0.825079383 0.713057566 0.855156161 0.778611504 0.68729657 0.748308028 0.705998023 0.694086508 1 20.88846332 -1.040422324 4.786654531 1.000006586 0.741906299 0.618743312 0.06135505 4.15E-06 8.33E-07 0.05721208 0.013484673 0.09111244 1.040422324 -0.258100287 LIGDAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIGDAAK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P11142;E9PKE3;E9PNE6;P11142-2;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25;E9PI65;P11021;P54652 A0A0G2JIW1;Q53FA3;P11142;P11021;P54652 HSPA1B;HSPA1A;HSPA1L;HSPA8;HSPA5;HSPA2 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like;Heat shock cognate 71 kDa protein;78 kDa glucose-regulated protein;Heat shock-related 70 kDa protein 2 0 94.262 0.033338 383950000 264830 227960 239560 205610 350380 339300 274430 260240 268030 269000 FALSE TRUE 275285.6929 267110.3567 245803.1304 246279.0443 290822.5328 260502.7171 252919.4595 256751.9085 258383.6527 321705.3997 0.855707405 0.830294913 0.764062806 0.765542153 0.904002647 0.809755501 0.786183445 0.79809636 0.803168529 1 18.29538063 -0.932523786 4.366861802 1.000003839 0.811072649 0.660927655 0.040165606 4474292.595 2049332.932 164.5372964 0.009505364 0.116808975 0.932523786 -0.18893119 LIGEYGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIGEYGLR 8 0 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 ;;; 198.64 0.00031252 937080000 779140 835290 816820 765660 1282920 1081430 936000 800640 817300 1421640 FALSE TRUE 809901.0488 978744.5598 838107.0002 917105.2627 1064849.717 830284.2717 862633.8742 789908.7304 787885.5327 1700183.139 0.476361064 0.575670078 0.492951013 0.539415573 0.626314714 0.488349903 0.507377032 0.464602143 0.463412155 1 20.69725873 -1.093738043 4.407869042 1.000046294 0.515239811 0.895853047 0.049615961 1.538339576 30161437.1 3088.675256 0.012016479 0.080586437 1.093738043 -0.484806482 LIHEDGIIRPYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LIHEDGIIRPYDR 13 1 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 ;; 171.73 1.48E-05 486520000 14961.1 22541.9 23145.5 23932.8 25645.2 26881.9 22574.7 18476.2 20067.3 18514 FALSE TRUE 15551.77578 26413.29597 23748.69074 28666.63641 21286.03806 20638.98612 20805.23603 18228.55676 19345.08179 22141.46383 0.702382458 1.192933592 1.072589009 1.294703757 0.961365438 0.932141898 0.939650431 0.823276948 0.873703832 1 14.43446299 3.012802907 24.80092693 0.903374703 1.081838659 0.184970136 0.148493144 294.9730035 571397.1654 0.04185464 0.049997579 1029.918613 -3.012802907 0.178463955 LIHEQEQQSS(ph)S ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.009)S(0.495)S(0.495);LIHEQEQQS(0.093)S(0.453)S(0.453);LIHEQEQQS(0.007)S(0.496)S(0.496) 149.93 3.58E-05 1397490000 516281 724095 572411 702490 571527 804740 588053 629821 533368 665511 TRUE FALSE 536664.1725 848452.6836 587328.5009 841440.4253 474379.0447 617851.331 541959.8693 621379.2797 514172.1899 795905.1385 0.674281578 1.066022372 0.737937818 1.057211952 0.596024604 0.776287652 0.680935256 0.780720276 0.64602195 1 19.60223696 3.231327806 24.99999717 0.735884591 0.886451529 0.160485579 0.152490151 257.9938409 891746.9409 0.03944459 0.048062343 1703.443784 -3.231327806 0.150566937 LIHEQEQQSSS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ; 110.38 0.0024358 527580000 152346 221970 183107 214890 196444 241240 166584 199317 199545 229580 FALSE TRUE 158360.7377 260091.6208 187878.9188 257394.6006 163052.519 185215.666 153526.7108 196645.4816 192363.4144 274561.8054 0.576776283 0.947297168 0.684286434 0.93747417 0.593864536 0.674586422 0.559169949 0.716215722 0.700619717 1 18.06677142 -1.250835992 3.055216047 1.001444013 0.712157615 0.315457143 0.128110395 13005022.15 17640380.14 180411.983 0.030659792 0.056125989 1.250835992 -0.289286398 LIHEQEQQSSS(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIHEQEQQSSS 11 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 1 LIHEQEQQS(0.014)S(0.239)S(0.747);LIHEQEQQS(0.001)S(0.296)S(0.703) 122.57 0.00040702 651850000 254360 352590 285350 330660 270990 366870 279730 299890 260810 352210 TRUE FALSE 264402.3292 413144.5897 292786.4554 396063.5611 224927.2166 281670.0025 257804.0317 295870.4651 251423.499 421218.806 0.627707798 0.980831301 0.695093503 0.940279863 0.533991392 0.668702343 0.612043024 0.702415136 0.596895237 1 18.68421032 3.24046298 24.99984823 0.667497559 0.814832993 0.134012513 0.151759077 81.23245768 1067498.42 0.038632831 0.049768319 1739.654401 -3.24046298 0.147335434 LIHGEDS(ph)DS(ph)EGEEEGR ddPTM_MDA-MB-175_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 209.12 1.91E-11 299240000 387560 384940 406390 456880 437480 483790 501610 398720 432220 332120 TRUE FALSE 402861.1681 451050.4506 416980.8573 547249.5003 363117.3059 371437.1044 462292.4975 393375.8106 416664.4866 397192.5552 1.0142717 1.135596437 1.049820425 1.377793952 0.914209748 0.93515626 1.163900208 0.990390695 1.049023908 1 18.59947906 LIHLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIHLNK 6 0 O43813;E9PHS0 O43813 LANCL1 LanC-like protein 1 0 93.595 0.04544 290470000 438190 388280 414850 396900 517620 515160 489470 474470 473180 424640 FALSE TRUE 455490.0796 454964.0696 425661.3318 475405.6354 429635.1373 395521.8973 451104.0624 468110.5057 456150.3442 507840.0778 0.896916371 0.895880592 0.838179873 0.936132566 0.846004788 0.778831594 0.88827976 0.921767553 0.898216514 1 18.95401473 0.87136276 0.99557783 0.997578129 0.869030133 0.45291081 0.042082127 0.65436575 1.305356361 0.041407798 0.013606517 7.436400302 -0.87136276 -0.128547996 LIHPDEDISLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LIHPDEDISLEER 13 0 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;;; 214.81 3.02E-11 3099860000 2052170 2349780 2254710 2231310 2622920 2791730 2494580 2304460 2208630 2532910 FALSE TRUE 2133191.256 2753336.436 2313469.595 2672656.458 2177076.995 2143393.017 2299048.301 2273572.483 2129141.838 3029185.219 0.704212883 0.90893631 0.763726688 0.882302093 0.718700521 0.707580706 0.758965905 0.750555783 0.702876082 1 21.53049836 5.04026414 15.44050698 0.785590072 0.363662177 0.066592518 0.095055068 6476071.897 71705879.46 0.021260307 76146493.47 109714.5283 -5.04026414 -0.421927895 LIHPDEDISLEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIHPDEDISLEERR 14 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;O43670-3;J3KS31 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 ;;; 228.8 9.88E-13 391431000 175295 258502 216854 174540 266533 239530 150637 200734 203649 348590 FALSE TRUE 182215.782 302897.7076 222505.3934 209063.4911 221227.8159 183902.7876 138829.6783 198043.4891 196319.7123 416889.5363 0.437084086 0.726565868 0.53372746 0.501484141 0.530662913 0.441130735 0.333013104 0.475050275 0.470915423 1 18.66930564 -0.934190144 5.192312353 1.00000024 0.493600513 0.718997209 0.09482248 0.008925176 138656950.3 504.1721323 0.023447946 0.116361646 0.934190144 -0.506399726 LIHTLDDR ddPTM_MDA-MB-175_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 ;;;;; 157.54 0.0003753 2110770000 923328 1090600 996570 996570 1091150 1205280 999420 986550 962250 1134870 FALSE TRUE 959781.7024 1277902.066 1022541.433 1193688.572 905676.7127 925371.9862 921082.8489 973326.9109 927618.8105 1357226.048 0.707164222 0.941554333 0.753405399 0.879506088 0.667299831 0.681811248 0.678651025 0.71714429 0.683466702 1 20.37222959 4.030172284 24.97756075 0.739874858 0.830139503 0.034715826 0.114360652 451.315394 373607.2041 0.026753404 0.057792888 10719.44459 -4.030172284 0.090264645 LIILDEIHLLHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIILDEIHLLHDDR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 170.79 1.80E-06 43214000 32955 33262 37273 43339 37135 43064 53336 36136 34331 26649 FALSE TRUE 34256.08885 38974.48976 38244.365 51911.32485 30822.80596 33063.03864 49155.38495 35651.65603 33095.43402 31870.36132 1.074857247 1.222907057 1.199997848 1.628827622 0.967130735 1.037422774 1.542354178 1.11864612 1.038439247 1 14.95992776 1.493815819 11.00139588 1.038851233 1.240310714 0.168910217 0.197174857 0.170424899 63.340645 0.105867838 0.04908247 31.17567164 -1.493815819 0.201459481 LIILDEIHLLHDDRGPVLEALVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIILDEIHLLHDDRGPVLEALVAR 24 1 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 258.34 4.03E-44 345870000 353830 434490 446540 465420 465240 515830 422290 424050 429210 435430 FALSE TRUE 367799.4816 509110.2776 458177.1992 557478.6869 386158.671 396036.3 389189.8064 418366.3034 413762.8159 520744.1717 0.706295916 0.977659099 0.879850845 1.070542345 0.741551595 0.76051989 0.747372371 0.803400837 0.794560628 1 18.99021526 3.185797177 24.99999965 0.792377083 0.911471585 0.15814979 0.11028989 141.3636927 66979.27571 0.029928224 0.035771104 1533.900459 -3.185797177 0.119094503 LIIMDNLGPEQERDTGQS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIIMDNLGPEQERDTGQSPQK 21 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 LIIMDNLGPEQERDT(0.009)GQS(0.991)PQK 92.426 0.0013611 0 57251 49009 56634 41946 52997 72871 58661 57656 50662 44981 TRUE FALSE 59511.31369 57425.91451 58109.92857 50242.7936 43988.58887 55947.81462 54062.99754 56883.21563 48838.68452 53794.16574 1.106278216 1.067511945 1.08022734 0.933982206 0.81772044 1.04003499 1.004997416 1.057423511 0.907880694 1 15.71516209 3.753512596 23.11575391 0.972881854 1.082956493 0.399023308 0.066352787 352.9867564 545712.761 0.018507606 0.033149442 5669.080138 -3.753512596 0.11007464 LIKDDFLQQNGYTPYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIKDDFLQQNGYTPYDR 17 1 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ; 211.29 2.38E-12 2757900000 1402510 1262660 1180860 1106430 1631400 1465060 1317580 1388400 1339250 1050710 FALSE TRUE 1457882.178 1479512.033 1211634.182 1325278.552 1354095.211 1124822.018 1214304.637 1369790.769 1291050.654 1256576.507 1.160201682 1.177415003 0.96423431 1.054673984 1.077606658 0.895148056 0.966359493 1.090097388 1.027434976 1 20.26106708 4.248116065 24.99992895 1.014295866 1.168808432 0.566824529 0.055596715 150.5845946 393966.1864 0.014297772 0.038101914 17705.82083 -4.248116065 0.154512565 LIKDDIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 125.71 0.0011402 2981000000 4785100 3909700 4541610 3888790 5665700 5351400 5053800 4446080 4670350 3634420 FALSE TRUE 4974019.443 4581160.562 4659968.088 4657981.055 4702646.338 4108618.451 4657669.95 4386487.57 4502265.016 4346515.014 1.144369553 1.053984755 1.072115953 1.071658798 1.081934912 0.945267286 1.071587222 1.009196461 1.035833306 1 22.0514277 8 0.302915767 1.011052106 2.018177432 0.471697537 0.037543719 48.2805334 0.690868942 0.03587933 26.43169359 100000000 -8 1.007125326 LIKPYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIKPYTR 7 1 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 91.065 0.028178 0 221940 243120 249400 228980 309340 294930 237670 245740 283860 326230 FALSE TRUE 230702.3626 284873.9688 255899.5689 274271.5606 256758.4973 226436.9772 219040.8044 242446.2572 273643.934 390148.5224 0.591319329 0.730168006 0.655902955 0.702992693 0.658104497 0.580386607 0.561429281 0.621420416 0.701384007 1 18.57366391 0.815847342 3.601823891 0.999965155 0.638281112 0.823258064 0.0501395 0.508454419 9.375658387 0.051924793 0.013366721 6.544061042 -0.815847342 -0.361684042 LILADALCYAHTFNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LILADALCYAHTFNPK 16 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 142.97 1.46E-06 272610000 136980 111720 168780 140290 180660 172800 183970 145770 174530 125070 FALSE TRUE 142388.0762 130907.0409 173178.5455 168038.9433 149951.4777 132669.8188 169549.9507 143816.1916 168248.6994 149575.0719 0.951950578 0.8751929 1.157803525 1.12344217 1.002516501 0.886978138 1.13354417 0.961498395 1.124844516 1 17.19051023 4.262154512 24.99998028 1.042962742 0.913571676 0.28718301 0.084835262 304.0020091 322113.3816 0.020457322 0.055958163 18287.50728 -4.262154512 -0.129391065 LILDVFCGSQMHFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LILDVFCGSQMHFVR 15 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 262.66 5.16E-25 6309170000 1302929.6 1669150 1454443 1481721 2438343 2444323 1680632 1533121 1561854 2951702 FALSE TRUE 1354370.267 1955813.528 1492346.979 1774800.991 2023874.328 1876666.027 1548899.672 1512572.021 1505643.18 3530031.493 0.383670874 0.554049881 0.422757412 0.502771999 0.573330389 0.531628693 0.438777862 0.428486835 0.426524008 1 21.75124962 -1.411778453 3.273210033 1.006214729 0.474997669 0.871449293 0.060656013 22550383.29 30302822.9 1315122.915 0.014691236 0.038745525 1.411778453 -0.53121706 LILEVHQFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LILEVHQFSR 10 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 201.56 2.40E-07 1174980000 704530 1001020 824810 915950 1052790 1078500 895490 922230 882050 1249560 FALSE TRUE 732345.3884 1172937.398 846305.2262 1097122.176 873837.1318 828034.7198 825299.1539 909869.0153 850305.1928 1494387.358 0.490063961 0.784895156 0.566322528 0.734161843 0.584746068 0.554096443 0.552265883 0.608857543 0.568999188 1 20.51112272 -1.498959384 2.875015109 1.014173721 0.608555292 0.664184199 0.084239229 14751784.84 16472292.19 1655930.815 0.018748593 0.031698639 1.498959384 -0.40561843 LILIESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LILIESR 7 0 P62277 P62277 RPS13 40S ribosomal protein S13 0 ; 149.4 0.004697 397238000 399156 481155 472794 468984 591320 567410 523936 493201 455195 510894 FALSE TRUE 414914.9871 563789.6284 485115.4 561747.6354 490807.6376 435637.6267 482868.5273 486590.4473 438812.6209 610993.8976 0.679082048 0.922741832 0.793977488 0.919399748 0.803293845 0.712998327 0.790300082 0.796391665 0.718194768 1 19.22079845 3.012749002 24.98988825 0.787318788 0.836563513 0 0.098249015 728.5437548 1428039.899 0.02613561 0.031222397 1029.790787 -3.012749002 0.049244725 LILPHVDIQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LILPHVDIQLK 11 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 160.18 0.0013188 0 489230 475560 476540 527800 522240 760580 544230 424520 503820 532370 FALSE TRUE 508545.1782 557233.7307 488959.0239 632197.2647 433469.8313 583946.8217 501571.8305 418830.0038 485687.6166 636677.7087 0.798748207 0.875221047 0.767985147 0.992962775 0.680830859 0.917178054 0.787795495 0.657836764 0.7628469 1 19.28020373 2.008895902 24.78902562 0.757361339 0.838364659 0 0.114725286 403.8817027 1125438.003 0.039949035 0.02945923 102.06948 -2.008895902 0.08100332 LIMGIGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 110.9 0.0033365 2687500000 1798370 2309300 1952250 2085570 2677900 2682600 2115850 2120950 2036930 2801000 FALSE TRUE 1869371.036 2705904.311 2003127.239 2498089.521 2222711.515 2059606.805 1950004.148 2092522.134 1963621.287 3349802.322 0.558054135 0.807780296 0.597983716 0.74574237 0.663535129 0.614844283 0.582125141 0.624670334 0.586190198 1 21.67564453 -1.920084918 3.018664721 1.203897948 0.644653504 0.674740445 0.074484237 24055195.36 25877527.98 35004144.54 0.017383255 0.012020294 1.920084918 -0.559244445 LIMVQHWPETVCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIMVQHWPETVCEK 14 0 D6RHI9;O00584;H0YAE9;A0A087WZM2;A0A087WWI1;O00584-2;J3QQ64 D6RHI9 RNASET2 Ribonuclease T2 0 96.464 0.003361 448800000 198140 197600 214990 192600 259780 283680 190800 208830 214760 198720 FALSE TRUE 205962.7202 231536.2629 220592.816 230695.7051 215622.6884 217799.6192 175844.5974 206030.9754 207030.8296 237655.3793 0.86664447 0.974252144 0.928204599 0.970715268 0.907291428 0.91645146 0.739914232 0.866931672 0.871138832 1 17.85851153 2.452245752 24.99767944 0.851725372 0.931911978 0.136730348 0.065782489 299.8893096 301360.4635 0.021380226 0.017888554 283.2994632 -2.452245752 0.080186606 LINGVRS(ph)PQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LINGVRSPQTR 11 1 Q92615;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 LINGVRS(1)PQTR 74.678 0.023802 0 134410 116660 100930 107140 143240 125790 131220 98412 100360 128680 TRUE FALSE 139716.6106 136695.4475 103560.3187 128331.9722 118892.116 96577.17887 120934.6335 97092.94811 96748.0632 153892.3823 0.907885163 0.888253502 0.672939863 0.833907243 0.772566609 0.627563089 0.785838985 0.630914582 0.628673504 1 17.23156229 4.254740945 21.69249472 0.728243159 0.898070337 0.226096503 0.110938331 62.31065616 83529.94097 0.025355176 0.068701126 17977.98217 -4.254740945 0.169827178 LINQVLELQHTLEDLSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LINQVLELQHTLEDLSAR 18 0 A0A0C4DGB0;Q9UIL1-3;Q9UIL1-2;Q9UIL1 A0A0C4DGB0 SCOC Short coiled-coil protein 0 ; 254.58 1.55E-30 1191730000 724930 517720 504690 488269 614460 749960 530680 531980 483220 515561 FALSE TRUE 753550.7962 606634.3827 517842.636 584847.1509 510014.3087 575793.1558 489083.9149 524849.6782 465829.0066 616575.3069 1.222155327 0.983877194 0.839869243 0.948541312 0.827172777 0.933856983 0.793226568 0.851233697 0.755510319 1 19.23391759 4.718500863 1.929514572 0.861062748 1.325662964 0.69474024 0.071073736 0.374280536 1.518200905 0.017006389 0.306333411 52299.90056 -4.718500863 0.464600216 LINYHQEQAVNCLLGNVFYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LINYHQEQAVNCLLGNVFYER 21 0 P35573-2;P35573-3;P35573 P35573-2 AGL "Glycogen debranching enzyme;4-alpha-glucanotransferase;Amylo-alpha-1,6-glucosidase" 0 75.184 0.0039355 0 107340 78565 119660 95711 115220 138550 133840 96481 127150 92569 FALSE TRUE 111577.8661 92057.9276 122778.4379 114642.3501 95634.94556 106373.8622 123349.2711 95187.83001 122573.8963 110706.1232 1.007874387 0.831552266 1.109048301 1.035555639 0.863863197 0.960867016 1.114204594 0.859824437 1.107200693 1 16.75637549 1.206887149 24.99966584 1.053600229 0.972196727 0.09968259 0.097057098 527.4459225 416297.6377 0.08864062 0.022168261 16.10227166 -1.206887149 -0.081403502 LIPDSIGKDIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIPDSIGKDIEK 12 1 P61247;D6RG13;D6RAT0;H0Y9Y4;D6RB09;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ; 171.29 3.54E-05 1306200000 2516700 1499600 1967720 1111840 3060900 2394300 1945130 1950670 2428300 1588330 FALSE TRUE 2616061.259 1757144.635 2019000.4 1331758.633 2540609.311 1838260.111 1792665.628 1924524.459 2340905.957 1899532.853 1.377212958 0.925040402 1.062893119 0.701097973 1.33749164 0.967743257 0.94374026 1.013156712 1.232358763 1 20.85721323 4.747959475 24.02671645 1.016714546 1.377213292 0.299627196 0.163574537 880.747114 2251409.54 0.036604511 0.454388532 55970.53712 -4.747959475 0.360498746 LIPGPLS(ph)PVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 LIPGPLSPVAR 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR;LIPGPLS(1)PVAR 196.16 6.44E-08 10670887000 3880530 4456106 4326159 4261042 4472508 4846557 4226553 4208166 3855962 4505155 TRUE FALSE 4033736.321 5221407.542 4438902.258 5103863.39 3712272.688 3721017.587 3895264.732 4151762.418 3717186.681 5387853.866 0.748672184 0.96910712 0.823872059 0.947290613 0.689007679 0.690630756 0.722971489 0.770578141 0.689919729 1 22.36127929 3.234403723 24.99999581 0.745038941 0.875700366 0.208676703 0.103901203 131.4214513 790382.7142 0.027193509 0.033629902 1715.551356 -3.234403723 0.130661425 LIPITGGNARS(ph)PEDQLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIPITGGNARSPEDQLGK 18 1 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 LIPITGGNARS(1)PEDQLGK;LIPIT(0.003)GGNARS(0.997)PEDQLGK 162.65 2.12E-11 357770000 509000 421060 524520 296160 694050 665860 388600 489320 561280 576820 TRUE FALSE 529095.713 493373.7796 538189.4221 354739.5641 576075.6289 511224.1062 358140.5166 482761.4658 541079.6424 689836.8351 0.766986751 0.715203588 0.780169157 0.514236912 0.83508969 0.741079746 0.519166995 0.699819785 0.784358873 1 19.39589564 0.888404981 2.957383032 0.999583059 0.692157269 0.461633181 0.099183379 0.382098644 7.014194226 0.092511493 0.024305255 7.734014476 -0.888404981 -0.30742579 LIQEQHPEEELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIQEQHPEEELIK 13 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 138.87 4.41E-05 102040000 111030 80309 82519 93514 92978 115670 129670 91936 92774 64481 FALSE TRUE 115413.5501 94101.44603 84669.51293 112010.7901 77173.63277 88807.3955 119506.1266 90703.7483 89435.08186 77114.81739 1.496645574 1.220277104 1.097966847 1.452519683 1.000762699 1.15162557 1.549716781 1.176216859 1.159765203 1 16.23472048 1.007878006 2.206402945 1.004661702 1.265843315 0.198067964 0.169857512 0.498603455 5.254072647 0.15599088 0.043061249 10.18305305 -1.007878006 0.261181613 LIQLMEEIMAEKENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIQLMEEIMAEKENK 15 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ; 143.67 3.99E-06 375670000 1681990 344115 725550 321263 1244200 957840 880460 645300 788740 433171 FALSE TRUE 1748396.264 403214.0744 744458.429 384807.8625 1032711.328 735396.1762 811447.2445 636650.809 760353.4015 518042.5639 3.37500504 0.778341593 1.437060352 0.742811285 1.993487409 1.419567092 1.566371764 1.228954633 1.467743105 1 18.98271111 4.747967915 24.99315555 1.321114178 3.375006123 0.750123294 0.360210768 601.8504852 1598953.266 0.081226506 1.044665108 55971.62489 -4.747967915 2.053891945 LIQNLDANHDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 ;;;;;;;; 271.01 1.05E-27 37865060000 11672880 13675220 11304290 13718630 11213430 14709320 13109800 11727760 10683500 12660250 FALSE TRUE 12133734.32 16023832.66 11598889.08 16432134.07 9307375.174 11293303.35 12082219.62 11570568.56 10299002.92 15140783.59 0.801394079 1.058322547 0.766069273 1.085289541 0.614722159 0.74588632 0.797991699 0.764198794 0.680215978 1 23.85193654 3.23501853 24.99959193 0.75738255 0.925544142 0.263913843 0.130763872 110.8523889 782382.5673 0.034114629 0.04233428 1717.981686 -3.23501853 0.168161592 LIQNNHYAMEDVATRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LIQNNHYAMEDVATRR 16 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 198.95 2.56E-11 830091000 216744 252996 217085 243532 231135 301250 227865 234197 215205 272882 FALSE TRUE 225301.2205 296446.095 222742.4134 291701.9027 191846.7553 231289.253 210004.3459 231057.9723 207459.8141 326348.0033 0.690371071 0.908374165 0.682530339 0.893836947 0.587859443 0.708719682 0.643498179 0.708010988 0.63570119 1 18.31605169 4.186578126 24.99956258 0.716872021 0.799377565 0.03047431 0.128523086 241.2995807 116045.8268 0.029402681 0.063517179 15366.61201 -4.186578126 0.082505544 LIQSHPESAEDLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIQSHPESAEDLQEK 15 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 239.58 8.27E-18 787300000 395170 296635 355163 293879 451976 496010 439320 365410 408530 318454 FALSE TRUE 410771.6167 347579.7538 364418.8395 352007.3891 375149.281 380819.1946 404884.9505 360512.2766 393827.0851 380848.9641 1.078568292 0.912644608 0.956859212 0.924270307 0.985034269 0.999921834 1.063111597 0.946601699 1.034076818 1 18.53885945 3.003367251 24.64912088 1.003863184 0.962239725 0.120320997 0.050194832 173.9898637 1273618.652 0.014044205 0.016710695 1007.783517 -3.003367251 -0.041623458 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PK 133.57 3.66E-05 405090000 169490 78455 111240 83855 119240 124280 120000 95843 94209 70360 TRUE FALSE 176181.5961 91929.03595 114139.0058 100441.2687 98971.62739 95417.85348 110594.0864 94558.38135 90818.43649 84145.69488 2.09376839 1.092498387 1.356444985 1.193659032 1.176193595 1.133960016 1.314316634 1.123745921 1.079299858 1 16.36060184 4.74181336 24.99963967 1.177983893 2.093768729 0.881688995 0.102121676 92.03145213 707294.3367 0.022926471 0.165237753 55184.02319 -4.74181336 0.915784836 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPKR 27 3 Q12769;G3V198 Q12769 NUP160 Nuclear pore complex protein Nup160 1 LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR;LIRPEYAWIVQPVSGAVYDRPGAS(1)PKR 129.84 0.0002801 2829400000 1757890 1060040 1322580 951220 1683390 1758960 1380460 1295880 1465950 1052270 TRUE FALSE 1827292.855 1242093.624 1357047.521 1139368.477 1397247.969 1350468.197 1272255.938 1278510.848 1413190.746 1258442.16 1.452027684 0.98700891 1.0783551 0.905380091 1.110299713 1.073126951 1.010976888 1.015947248 1.122968374 1 20.26320748 4.742430072 24.97954433 1.0334025 1.452027847 0.805562387 0.061643676 148.7787548 960413.3065 0.013829426 0.104769731 55262.44194 -4.742430072 0.418625347 LIS(ph)SVEDFTEFV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LISSVEDFTEFV 12 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 LIS(0.599)S(0.401)VEDFTEFV;LIS(0.634)S(0.366)VEDFTEFV;LIS(0.649)S(0.351)VEDFTEFV;LIS(0.5)S(0.5)VEDFTEFV 131.06 0.00021605 91072000 292105 208791 220552 222783 248482 301566 207112 204404 197051 218398 TRUE FALSE 303637.531 244649.2301 226299.7663 266848.8125 206245.1184 231531.8668 190878.0203 201664.2987 189959.173 261188.9066 1.162520778 0.936675425 0.866421814 1.021669779 0.789639656 0.886453677 0.730804469 0.772101317 0.727286528 1 17.9947341 7.99999988 0.47250619 0.799998607 9.860224386 0.499866079 0.09546923 71.58966492 0.817525644 0.051629758 634.2886715 99999972.43 -7.99999988 9.06022578 LIS(ph)WYDNEFGYSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;LIS(1)WYDNEFGYSNR 147.12 8.52E-06 319218000 72876 137065 117769 95975 114834 164061 103688 111573 107582 162689 TRUE FALSE 75753.20075 160604.8475 120838.1569 114958.5685 95314.5577 125960.3191 95560.66362 110077.5464 103710.1448 194564.7947 0.389346906 0.825456876 0.621068971 0.590849792 0.489885942 0.647395225 0.491150847 0.56576292 0.533036539 1 17.56989116 -1.517670388 2.833537016 1.018155317 0.577434788 0.575487169 0.110039781 14680898.01 15543069.67 2053116.155 0.026727074 0.030361947 1.517670388 -0.44072053 LISGGHDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LISGGHDNR 9 0 Q15061;C9JEE7 Q15061 WDR43 WD repeat-containing protein 43 0 127.76 0.0014789 0 31453 69051 67310 58990 60054 63067 54227 61080 50868 62439 FALSE TRUE 32694.78873 80909.97211 69064.1539 70658.04593 49846.04253 48420.64504 49976.54604 60261.32251 49037.27062 74672.72658 0.4378411 1.083527759 0.924891283 0.946236319 0.667526751 0.648438155 0.669274424 0.807005787 0.656695863 1 16.18829379 4.77438063 23.68644585 0.806450212 0.437839429 0.359399222 0.152745985 11693.82297 7732392.937 0.037875798 7.77036919 59481.32448 -4.77438063 -0.368610783 LISKPVASDSTYFAWCPDGEHILTATCAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LISKPVASDSTYFAWCPDGEHILTATCAPR 30 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2;H7C5R5 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 0 173.98 4.49E-13 175450000 75140 67015 74791 73926 81817 102120 81918 84503 82656 80550 FALSE TRUE 78106.58522 78524.30495 76740.1149 88548.34215 67909.77556 78404.17764 75497.05311 83370.3755 79681.22671 96332.23028 0.810804286 0.815140527 0.796619311 0.919197468 0.704953839 0.813893516 0.783715408 0.865446334 0.827150233 1 16.55573095 0.309739183 0.829198626 1.001908792 0.809236268 0.544234021 0.051292926 1.915583111 1.695922658 0.056149712 0.016153531 2.040512138 -0.309739183 -0.192672524 LISQIVSSITASLR ddPTM_MDA-MB-175_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 ; 305.3 6.07E-44 629360000 307820 289670 330550 286250 374220 433700 334040 314540 334280 355517 FALSE TRUE 319972.9713 339418.5692 339164.4045 342869.3956 310610.2181 332979.7478 307857.0719 310324.1058 322249.3281 425173.7494 0.752569912 0.798305563 0.797707773 0.806421836 0.730548907 0.783161586 0.724073564 0.729875977 0.757923857 1 18.697693 -1.557065794 8.352807236 1.000047312 0.763019802 0.853804066 0.029227758 2.83E-05 1.50E-06 0.031058046 0.007318996 0.027729 1.557065794 -0.237027509 KIPNPDFFEDLEPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KIPNPDFFEDLEPFR 15 1 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 0 84.842 0.013104 335850000 147040 279430 367010 336120 444210 470430 347120 349220 488240 341250 FALSE TRUE 152845.2527 327419.9288 376574.5821 402603.5328 368703.3429 361179.7619 319911.8274 344539.2771 470668.3378 408111.4039 0.374518456 0.802280764 0.922724968 0.986504001 0.903437981 0.885002866 0.783883578 0.844228497 1.153283964 1 18.6386035 4.741898876 2.515456704 0.916317635 0.253305129 0.752501618 0.096058415 0.261291066 2.068786221 0.02427959 0.371981685 55194.89045 -4.741898876 -0.663012506 down LISSDGHEFIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LISSDGHEFIVK 12 0 E5RHG8;Q15369-2;Q15369;R4GMY8 E5RHG8 TCEB1 Transcription elongation factor B polypeptide 1 0 ;; 130.56 0.00021426 1268730000 2085830 2909280 3311510 3110110 3658570 4132420 3794990 3544160 3603300 3147510 FALSE TRUE 2168180.179 3408926.209 3397810.671 3725280.475 3036687.578 3172728.082 3497528.767 3496656.332 3473617.937 3764204.322 0.575999599 0.905616677 0.902663719 0.989659476 0.806727616 0.84286819 0.929154867 0.928923096 0.922802707 1 21.84391351 4.738676018 6.959272701 0.910398333 0.570920204 0.771156468 0.055251635 0.050077874 18.2231794 0.013081864 0.079978946 54786.81044 -4.738676018 -0.339478129 LISWYDNEFGYS(ph)NR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR;LISWYDNEFGYS(1)NR 254.89 3.02E-24 340529000 176573.4 243464 229661.7 215603.7 233260.7 261222.6 216040 233952.4 217477.7 299243.7 TRUE FALSE 183544.6542 285277.0481 235646.8726 258249.4683 193611.1295 200557.61 199106.2203 230816.6507 209650.7201 357874.7736 0.512873965 0.797142099 0.658461814 0.721619648 0.541002451 0.560412817 0.556357237 0.644964853 0.585821453 1 18.44909533 -1.335090279 4.781977965 1.000248704 0.623932106 0.648406356 0.083930899 0.000220242 3.06E-05 0.080425573 0.018944106 0.046228491 1.335090279 -0.376316598 LISWYDNEFGYSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 38 LISWYDNEFGYSNR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 422.87 2.33E-152 2.71261E+11 18916138.3 20908109.7 20834236.2 20288406.2 22338786.2 25109305.6 21204678.8 21545345.9 20558726.9 23630969.8 FALSE TRUE 19662962.05 24498914.9 21377193.51 24301392.39 18541647.3 19278049.91 19542600.67 21256565.78 19818822.33 28261005.89 0.695762993 0.866880499 0.756420122 0.859891275 0.656085894 0.682143091 0.691504073 0.752151776 0.701278023 1 24.75230948 -1.142811716 4.276503673 1.000053368 0.742372491 0.56289015 0.068649569 3.67E-05 7.35E-06 0.066929304 0.015771988 0.071976096 1.142811716 -0.257680877 LITSEEERS(ph)PAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 154.69 2.03E-05 660790000 726370 430061 517280 400379 664480 624040 633680 534060 578730 411200 TRUE FALSE 755047.6485 503920.6313 530760.7418 479572.7712 551531.9269 479116.1674 584010.5058 526901.7992 557901.6203 491766.7671 1.535377539 1.024714692 1.079293635 0.975203701 1.121531514 0.974275204 1.187576194 1.071446536 1.134484186 1 18.90761472 4.741798291 24.9892065 1.068113574 1.535377713 0.814592507 0.067547591 116.861727 901927.5626 0.015076276 0.107765292 55182.10847 -4.741798291 0.467264139 LIVAYVDDLDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LIVAYVDDLDRR 12 1 O14776;O14776-2 O14776 TCERG1 Transcription elongation regulator 1 0 ;;;; 199.43 2.75E-07 1033191000 1287923 1331633 1414389 1088555 2746553 2044987 1318319 1467650 1559354 2144254 FALSE TRUE 1338771.195 1560330.609 1451249.139 1303867.93 2279694.902 1570069.761 1214985.712 1447978.552 1503233.154 2564379.517 0.522064377 0.608463216 0.565926038 0.508453574 0.888984991 0.612261076 0.473793252 0.564650647 0.586197614 1 21.29017836 -1.661947882 2.643785542 1.052151495 0.591633045 0.562826023 0.107791575 16509625.13 14177137.86 5817233.316 0.028772278 0.021779711 1.661947882 -0.46051845 LIVENLSS(ph)R ddPTM_MDA-MB-175_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(0.092)S(0.908)R;LIVENLS(0.05)S(0.95)R;LIVENLS(0.033)S(0.967)R;LIVENLS(0.252)S(0.748)R 123.67 0.00057817 417763000 762460 897220 1061250 973430 1095200 1104620 1016980 1033940 1016090 906700 TRUE FALSE 792562.5095 1051310.556 1088907.047 1165971.549 909038.2952 848088.7457 937266.4502 1020081.725 979521.1194 1084350.505 0.730909891 0.969530194 1.004202093 1.075271827 0.838325146 0.782116799 0.864357462 0.940730622 0.903325184 1 20.04839974 0.287145851 1.419073493 1.000005145 0.905841365 0.082143091 0.097918834 17.96169628 32.49983043 0.098355978 0.028445923 1.93707239 -0.287145851 -0.09416378 LIVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIVLDR 6 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 118.06 0.05163 100592000 128975 143414 135010 142190 150798 170832 133968 132389 120926 156579 FALSE TRUE 134067.0326 168044.2389 138528.4715 170314.7576 125165.4098 131158.857 123467.2381 130614.542 116573.8969 187257.6572 0.715949535 0.89739582 0.73977467 0.909520925 0.668412773 0.700419192 0.659344136 0.697512422 0.62253207 1 17.51466519 3.21861219 24.98606992 0.703539909 0.816078133 0.11755003 0.113523662 367.8043373 460686.1106 0.029734645 0.035583066 1654.292078 -3.21861219 0.112538224 LIWDSLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LIWDSLEER 9 0 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073 F6QMI7 DST Dystonin 0 ; 81.594 0.048482 35073000 36305 47337 42527 49068 52815 59675 45781 43120 44271 57291 FALSE TRUE 37738.34943 55466.76152 43635.28856 58773.50395 43837.52517 45816.38563 42192.56559 42542.04693 42677.69536 68516.07455 0.550795557 0.809543773 0.636862063 0.85780606 0.639813729 0.668695426 0.615805355 0.620906075 0.62288588 1 16.06415488 -1.264965794 5.181380337 1.000051124 0.671056556 0.556158807 0.088631782 5.03E-05 7.14E-06 0.082544769 0.019452973 0.054329312 1.264965794 -0.328994568 LKAEATEAAR ddPTM_MDA-MB-175_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 2163360000 2671040 2403530 2798570 2325400 3576610 3581560 3095880 2788970 2986350 2736760 FALSE TRUE 2776494.722 2816317.581 2871503.033 2785357.179 2968659.11 2749796.969 2853216.836 2751588.419 2878871.847 3272975.724 0.848308987 0.860476159 0.877337101 0.851016755 0.907021427 0.84015196 0.871750076 0.840699306 0.879588512 1 21.64217147 0.962025439 22.13938253 1 0.862213248 0.824517149 0.018970273 528.6193155 308188.8336 0.01710513 0.004276283 9.162741604 -0.962025439 -0.137786752 LKAEGSEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKAEGSEIR 9 1 P07237;H7BZ94;I3L3U6;I3L0S0;I3NI03;I3L514 P07237 P4HB Protein disulfide-isomerase 0 ;;; 120.06 0.00066213 4943420000 4850820 4729400 4759880 4397860 6960080 6440680 5092860 4708430 5081500 4623650 FALSE TRUE 5042334.119 5541637.66 4883926.383 5267743.582 5777008.088 4944929.679 4693668.325 4645321.197 4898617.808 5529565.692 0.911886105 1.002183167 0.883238694 0.952650511 1.044748975 0.894270898 0.84883128 0.840087894 0.88589558 1 22.39873474 2.498122532 24.23472795 0.874511352 0.958060738 0.207084469 0.059112424 606.8071603 700234.0449 0.018520411 0.017277993 314.863655 -2.498122532 0.083549386 LKAEKS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKAEKSPK 8 2 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 LKAEKS(1)PK 53.237 0.071929 560020000 709750 188980 326280 190590 643600 491460 500200 300160 427690 193240 TRUE FALSE 737771.478 221435.8449 334783.1248 228288.1331 534201.1019 377325.8631 460993.017 296136.8462 412297.5204 231101.6782 3.192410734 0.958174976 1.448639956 0.98782551 2.311541422 1.632726625 1.994762741 1.281413655 1.784052473 1 17.81816821 -2.619558097 0.220080794 2.21E-19 1.792591337 0.114374237 0.629112437 113.7053152 2.899791847 57.14083307 1.235473125 0.002401275 2.619558097 1.792591337 LKAEMDEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKAEMDEHR 9 1 Q7L7X3-3;Q7L7X3;Q7L7X3-2;F5H5C7;Q9H2K8;G3V1Q8 Q7L7X3-3;Q9H2K8 TAOK1;TAOK3 Serine/threonine-protein kinase TAO1;Serine/threonine-protein kinase TAO3 0 85.958 0.00869 74460000 139790 123940 119390 120060 183990 163310 143850 124830 124140 147630 FALSE TRUE 145309.0171 145225.7309 122501.4015 143807.5097 152715.4455 125383.7275 132574.6611 123156.858 119672.2256 176555.272 0.823022816 0.822551087 0.693841652 0.814518355 0.864972446 0.710166998 0.750896077 0.697554124 0.677817345 1 17.42976038 2.715310129 24.78070381 0.743307397 0.799312803 0.003916724 0.094972641 1926.263126 2053037.125 0.028972061 0.027331769 519.1706451 -2.715310129 0.056005407 LKAEQEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKAEQEAR 8 1 Q8N5G2;Q8N5G2-2;Q8N5G2-3 Q8N5G2 TMEM57 Macoilin 0 ; 84.213 0.016062 255734000 213650 208264 206380 213649 231885 274320 266670 207818 199939 198271 FALSE TRUE 222085.067 244031.7219 211758.4323 255908.1345 192469.2705 210613.3374 245767.7086 205032.5396 192743.2344 237118.4063 0.936599863 1.029155542 0.893049323 1.079241964 0.811701097 0.888220112 1.036476722 0.864684201 0.812856486 1 17.85524813 3.235182077 24.99998055 0.902111903 0.981167486 0.194290275 0.081879799 150.905842 1116651.28 0.022806514 0.028323567 1718.628769 -3.235182077 0.079055583 LKATVT(ph)PS(ph)PVKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 LKAT(0.02)VT(0.981)PS(0.998)PVKGK;LKAT(0.005)VT(0.995)PS(1)PVKGK 122.31 0.00026107 6062500000 11796000 3357800 5475900 2859200 8435100 7629200 7475800 5484500 6199400 2579900 TRUE FALSE 12261715.19 3934476.03 5618606.453 3424741.226 7001304.715 5857433.922 6889827.262 5410989.248 5976284.805 3085382.01 3.974131939 1.275198992 1.821040777 1.109989368 2.269185693 1.898446903 2.23305485 1.753750178 1.936967541 1 21.55701769 7.999999997 0.053291041 1.27E-08 5.59318975 0.206295162 0.712461772 873.8706176 3.501972013 82.2975411 393.1262426 99999999.36 -7.999999997 5.593189737 LKATVT(ph)PSPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKATVT(0.991)PS(0.009)PVK 132.65 0.00028802 8331900000 2148400 1217800 1699200 1173800 2543100 2152300 2074500 1687100 1772100 1145900 TRUE FALSE 2233220.491 1426947.677 1743482.548 1405974.137 2110824.77 1652460.943 1911895.269 1664487.184 1708322.467 1370417.165 1.629591738 1.041250586 1.272227605 1.025946093 1.540278992 1.205808702 1.395119178 1.214584308 1.246571125 1 20.3861837 0.537339119 1.317796687 1.000240113 1.282740743 0.184603942 0.182594732 3.10586909 7.012943988 0.159538533 0.047446744 3.446189212 -0.537339119 0.28250063 LKATVTPS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.001)VT(0.183)PS(0.816)PVK 120.77 0.00025774 9703400000 7845900 3960000 5330500 3970700 9221600 8047100 7915300 5776400 6238400 4494400 TRUE FALSE 8155662.19 4640099.195 5469417.209 4756092.609 7654115.726 6178282.98 7294878.103 5698976.806 6013881.203 5374991.63 1.517334863 0.863275613 1.017567577 0.884855817 1.424023748 1.149449786 1.357188737 1.060276406 1.118863361 1 22.35783108 4.764341524 23.959031 1.111437485 1.517335788 0.346289795 0.17215541 5823.376005 5411696.352 0.041557173 2.988412455 58122.13039 -4.764341524 0.405898302 LKATVTPS(ph)PVKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 LKAT(0.015)VT(0.285)PS(0.7)PVKGK;LKAT(0.005)VT(0.056)PS(0.938)PVKGK 169.67 2.21E-05 19690700000 11916400 5325300 8847200 4416200 12045100 9754500 9953300 8130400 9570100 5261900 TRUE FALSE 12386868.67 6239878.85 9077765.3 5289711.179 9997678.204 7489165.206 9173134.338 8021425.287 9225673.97 6292868.56 1.968397807 0.991579403 1.442548055 0.84058822 1.588731452 1.190103549 1.457703152 1.27468502 1.466052228 1 22.58528638 -2.224100777 2.113634551 0.000219862 1.335777359 0.11009612 0.299344206 4106214.168 791766.599 19579995.25 0.064784994 0.005968968 2.224100777 1.335557497 LKAWNDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKAWNDIKK 9 2 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 83.883 0.0089247 617540000 1211900 701710 971740 591960 1830700 1197900 1203500 1042600 1199400 878880 FALSE TRUE 1259746.748 822223.234 997064.3427 709047.9212 1519518.268 919705.8794 1109166.525 1028625.652 1156233.828 1051079.709 1.19852637 0.782265348 0.948609639 0.674590057 1.445673677 0.875010593 1.05526395 0.978637152 1.100043906 1 20.00344065 LKCGSGPVHISGQHLVAVEEDAES(ph)EDEEEEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKCGSGPVHISGQHLVAVEEDAESEDEEEEDVK 33 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 1 LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK;LKCGSGPVHISGQHLVAVEEDAES(1)EDEEEEDVK 297 6.61E-90 1189120000 74920 276461 352713 202655 517870 427720 265760 421970 409700 319134 TRUE FALSE 77877.89945 323941.0262 361904.9905 242739.5541 429842.6424 328388.5122 244929.0368 416314.1824 394954.977 381662.1971 0.204049288 0.84876372 0.948233787 0.63600628 1.126238453 0.860416658 0.641742983 1.090792291 1.034828652 1 18.54193677 4.738738882 4.032917719 0.910659936 0.141589647 0.640102201 0.159394586 0.144060595 4.982075127 0.037770329 0.323963874 54794.74144 -4.738738882 -0.769070289 LKDALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDALVR 7 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 71.501 0.066711 0 244810 242740 273720 238490 354050 346580 333030 258700 286310 287730 FALSE TRUE 254475.2878 284428.7067 280853.3681 285662.6102 293868.7075 266092.0475 306926.2384 255232.5496 276005.759 344105.1846 0.739527619 0.826574895 0.816184645 0.830160727 0.854008369 0.773286947 0.891954705 0.741728289 0.802097066 1 18.3924901 -1.944674268 2.398085843 1.140820744 0.808862169 0.618392375 0.045154333 5719788.976 2785905.621 4497475.047 0.010662955 0.011358624 1.944674268 -0.331958576 LKDDEVAQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LKDDEVAQLK 10 1 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;;;;; 183.99 1.47E-06 5950060000 11852470 6071150 8679610 6196500 11725320 10669120 12801790 8731630 9629350 5159920 FALSE TRUE 12320414.67 7113822.786 8905807.767 7422149.205 9732254.295 8191378.572 11798352.25 8614596.782 9282791.574 6170907.531 1.996532051 1.152800095 1.443192549 1.202764612 1.577118802 1.327418784 1.91193146 1.396001599 1.504283045 1 22.55705125 LKDDEVAQLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ; 176.51 4.82E-06 14609000000 9106800 3570400 5854300 3447500 8987100 6708300 7652200 6022200 6931900 2601900 FALSE TRUE 9466343.496 4183588.426 6006867.867 4129405.21 7459475.952 5150398.99 7052400.569 5941482.259 6682422.273 3111692.489 3.042184769 1.344473608 1.930418218 1.327060828 2.397240723 1.655176085 2.266419511 1.909405342 2.147520135 1 21.56926806 -0.414586789 12.74389696 1.000000014 1.969089159 0.274676107 0.485904814 0 0 0.421934381 0.099450887 0.384957878 0.414586789 0.969089145 LKDEIAEVANEIENLGSTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDEIAEVANEIENLGSTEER 21 1 K7ENQ8;Q15438-2;Q15438;K7ERV8 K7ENQ8 CYTH1 Cytohesin-1 0 89.483 0.0021006 10106000 19505 17688 22189 18904 26201 29904 28107 21925 23848 16493 FALSE TRUE 20275.07246 20725.77641 22767.26357 22643.15478 21747.36338 22959.2492 25903.8999 21631.13124 22989.71514 19724.48757 1.027913774 1.050763744 1.154263881 1.147971763 1.102556571 1.163997245 1.31328633 1.096663787 1.16554182 1 14.2677002 4.279824561 4.51158595 1.15227593 1.034081984 0.232214511 0.074245245 0.247393793 10.91639515 0.017698206 0.049926153 19046.91135 -4.279824561 -0.118193947 LKDEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDEVLK 7 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 88.948 0.031137 0 436060 246470 346820 270960 470260 423450 445330 352840 418600 220830 FALSE TRUE 453275.9855 288799.3052 355858.4141 324555.0793 390325.3732 325110.1549 410423.8709 348110.7569 403534.6678 264097.4105 1.716321204 1.093533271 1.347451357 1.228921854 1.477959865 1.231023638 1.554062458 1.318114995 1.527976617 1 18.01071063 -1.010586568 4.554417772 0.999988317 1.374760193 0.303359305 0.175473851 1.86E-05 4.05E-06 0.15218754 0.03586983 0.097591823 1.010586568 0.374771876 LKDIALGMQTEIEEQDDILDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKDIALGMQTEIEEQDDILDR 21 1 O95721;C9JAF7 O95721 SNAP29 Synaptosomal-associated protein 29;Synaptosomal-associated protein 0 ; 227.87 1.72E-25 215231000 149988 145632 190028 149613 197371 209597 198791 192188 190674 156367 FALSE TRUE 155909.6421 170643.1631 194980.2858 179206.0048 163821.9479 160921.2732 183209.242 189612.0342 183811.68 187004.1198 0.833723034 0.912510181 1.042652354 0.958299769 0.876033897 0.86052261 0.979706983 1.013945759 0.982928505 1 17.51271053 2.035986125 13.26306063 0.99958921 0.920026074 0.340737522 0.054741784 1.729222132 635.5338393 0.022292582 0.016455533 108.6390914 -2.035986125 -0.079563137 LKDISTLEPLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDISTLEPLKK 12 2 Q92688;Q92688-2 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 87.18 0.0060147 582040000 6511400 4426200 6041500 4348700 8330400 7121800 6311800 5698600 6928900 4477300 FALSE TRUE 6768475.1 5186365.419 6198946.453 5208859.88 6914401.584 5467869.882 5817064.623 5622219.588 6679530.242 5354541.212 1.264062565 0.968591932 1.157698897 0.972792939 1.291315411 1.021164964 1.086379653 1.049990908 1.247451458 1 22.35233154 -2.061669976 4.907485612 0.78562357 1.106790474 0.081067691 0.113661708 0.105315456 0.001323448 0.043475079 0.023120469 0.008676209 2.061669976 0.321166904 LKDLDLDAFAEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKDLDLDAFAEELER 15 1 Q7KZ85 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 ; 178 6.66E-07 158478000 326570 289460 352460 298300 423280 422630 424250 357170 387410 296960 FALSE TRUE 339463.2358 339172.5033 361645.3971 357302.8497 351331.0168 324480.5875 390996.1764 352382.7204 373467.1898 355143.6264 0.955847749 0.955029115 1.01830744 1.006079859 0.989264598 0.913660174 1.100952255 0.992225945 1.051594797 1 18.43804307 2.241545076 24.99999914 1.033239992 0.976511274 0.381757396 0.03915547 90.98449697 762162.668 0.013703942 0.011010025 174.3994359 -2.241545076 -0.056728718 LKDLFDYS(ph)PPLHK ddPTM_MDA-MB-175_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;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK;LKDLFDYS(1)PPLHK 135.28 5.18E-05 42911925000 6151594 3751358 5152834 3744727 6958038 6264670 6666436 5402517 6099556 3412611 TRUE FALSE 6394463.681 4395624.555 5287121.087 4485422.824 5775313.186 4809795.334 6143903.327 5330105.096 5880034.171 4081246.787 1.566791722 1.077029835 1.295467136 1.099032491 1.415085509 1.17851127 1.505398631 1.305999214 1.440744576 1 21.96057852 3.200321919 24.99978045 1.329037402 1.249103253 0.006908529 0.183751665 576.2031482 376709.6843 0.04894558 0.058502177 1586.068422 -3.200321919 -0.079934148 LKDLFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKDLFGK 7 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;Q9H361;H0YBN4;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 117.04 0.0048531 1510570000 3547600 2516400 3204200 2542200 4350900 4120000 4083500 3503500 3623600 2327400 FALSE TRUE 3687661.987 2948572.125 3287704.084 3045039.572 3611335.572 3163192.439 3763424.6 3456541.313 3493187.344 2783409.469 1.324872258 1.059338253 1.181178738 1.093996268 1.297450344 1.136445239 1.352091613 1.241837161 1.255003039 1 21.40842173 3.238724221 25 1.232620801 1.15847669 0.027061008 0.111630314 10.54396829 1610999.281 0.029195345 0.037109819 1732.703372 -3.238724221 -0.074144111 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDLGHPVEEEDELESGDQEDEDDESEDPGK 31 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGK 160.4 1.24E-12 53662000 29751 18050 23207 19882 29331 27923 31132 21559 25879 14820 TRUE FALSE 30925.59245 21149.94709 23811.79348 23814.60026 24345.3271 21438.30643 28691.79249 21270.03687 24947.61985 17723.69525 1.744872726 1.193314757 1.343500503 1.343658866 1.373603346 1.209584464 1.618838063 1.200090419 1.407585692 1 14.11339181 -3.519148829 0.268722043 1.26E-12 1.399261154 0.317431552 0.169511684 101.7512737 2.047380852 56.66944316 0.196957516 0.000302588 3.519148829 1.399261154 LKDLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LKDLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 36 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI;LKDLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI 314.45 6.12E-110 7345690000 2434320 1089138 1718257 1195909 2523053 2201126 2142146 1631249 1978258 907122.3 TRUE FALSE 2530428.833 1276188.979 1763036.189 1432456.231 2094185.352 1689947.845 1974238.999 1609384.775 1907060.881 1084855.547 2.332503015 1.176367658 1.625134511 1.320411953 1.930381753 1.557763013 1.819817399 1.483501449 1.757893838 1 20.04907152 -1.257376164 3.689658819 0.998845927 1.640551733 0.291417837 0.30958297 93040977.12 207420600.6 1333737.241 0.066962529 0.055287103 1.257376164 0.641705805 LKDLPFIVSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKDLPFIVSHR 11 1 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 146.5 2.15E-05 454590000 1508680 1288870 1614270 1436360 2020530 1931680 1821640 1597740 1763510 1453620 FALSE TRUE 1568243.851 1510223.396 1656339.202 1720467.721 1677081.032 1483076.595 1678855.097 1576324.909 1700041.62 1738429.008 0.902104052 0.868728829 0.952779317 0.989668093 0.964710681 0.85311312 0.96573118 0.906752534 0.977918346 1 20.72935272 -5 0.134214973 1.236759055 0.902238217 0.229375309 0.043074691 237.6168991 1.988928959 15.09765081 0.307393753 1.00E-05 5 -0.334520838 LKDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 144.83 0.010235 24352150000 17391400 16023420 17789740 16870250 26114540 22786620 18739270 17577000 16976250 20582590 FALSE TRUE 18078025.9 18775317.74 18253355.24 20207135.1 21675599.82 17494772.84 17270437.05 17341409.07 16365278.08 24615354.43 0.734420703 0.762748218 0.741543466 0.82091587 0.880572322 0.710726018 0.701612366 0.704495607 0.664840237 1 24.55305518 LKDNEK ddPTM_MDA-MB-175_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 ; 66.073 0.093363 441280000 1569230 750380 1120540 702510 1610650 1251880 1642580 1100040 1302150 653990 FALSE TRUE 1631184.412 879251.9279 1149742.193 841464.3812 1336872.288 961149.8424 1513830.288 1085295.763 1255285.876 782126.8191 2.085575347 1.124180768 1.470020161 1.075866932 1.709278158 1.228892577 1.935530467 1.38762121 1.604964624 1 19.57704303 LKDPANFQYPAESVLAYK ddPTM_MDA-MB-175_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 ; 205.88 8.33E-16 14373200000 8407400 6452800 8467400 6382300 9731900 9680100 9350300 8240200 9507500 6720900 FALSE TRUE 8739330.644 7561018.204 8688067.4 7644699.891 8077675.114 7432043.478 8617399.054 8129753.597 9165326.932 8037731.676 1.08728818 0.940690547 1.080910355 0.951101654 1.004969491 0.924644387 1.072118279 1.011448743 1.140287746 1 22.93835699 2.167388086 25 1.052589097 0.997560593 0.17174808 0.061881538 82.25365506 28890.41029 0.021567977 0.01592901 147.0239498 -2.167388086 -0.055028504 LKDSEAELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LKDSEAELQR 10 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 166.69 4.99E-06 5408030000 6728810 6014940 7113620 5662900 9061130 8862110 7931220 7343710 7679550 5836320 FALSE TRUE 6994468.615 7047959.155 7299006.781 6783004.718 7520922.359 6804019.259 7309550.252 7245279.579 7403164.496 6979835.161 1.002096533 1.009760115 1.045727673 0.97180013 1.077521487 0.974810881 1.047238235 1.038030184 1.060650334 1 22.73476153 LKDSEAELQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKDSEAELQRR 11 2 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 86.313 0.0081912 77697000 69201 79643 78398 42253 108370 85528 49071 53044 73337 90002 FALSE TRUE 71933.10891 93321.06571 80441.11628 50610.51729 89949.30611 65665.41819 45224.6868 52333.03194 70697.6157 107636.1687 0.668298675 0.867004714 0.747342805 0.470199914 0.835679188 0.610068335 0.420162547 0.486203035 0.656820254 1 16.71580342 3.938624901 11.02724615 0.605151378 0.777512159 0.069822279 0.172702283 1.426607856 253.9349687 0.043330128 0.078273464 8682.102347 -3.938624901 0.172360781 LKDVLLQVDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKDVLLQVDDER 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 160.27 5.42E-05 4319010000 4822950 4628870 5447210 5030160 6107870 6357330 6696530 5704490 5693060 4375640 FALSE TRUE 5013363.79 5423842.415 5589168.768 6025110.634 5069656.439 4880936.454 6171638.48 5628030.642 5488167.883 5232962.881 0.95803542 1.036476378 1.068069637 1.151376528 0.968792738 0.932729042 1.179377462 1.075495999 1.048768739 1 22.31919659 2.239262122 24.99999941 1.084953934 1.025961583 0.120832346 0.07191587 40.83852085 1455465.716 0.0267044 0.021107303 173.4850765 -2.239262122 -0.058992351 LKDVLLQVDDERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LKDVLLQVDDERR 13 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 223.58 8.75E-12 8472607000 5047570 4656805 5800200 4385223 6330920 6846610 5867150 5863680 5786990 5280350 FALSE TRUE 5246851.961 5456575.034 5951357.977 5252607.021 5254792.48 5256588.589 5407267.452 5785086.961 5578717.36 6314933.484 0.830864169 0.864074823 0.942426075 0.83177551 0.832121588 0.832406011 0.856266731 0.916096262 0.883416646 1 22.59033611 0.707448405 0.83300239 0.99926854 0.857811546 0.593006698 0.034776053 0.764439661 0.98563994 0.035594966 0.012233866 5.098570215 -0.707448405 -0.141456995 LKDYAFIHFDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKDYAFIHFDER 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;; 150.12 3.53E-05 2902755000 6406890 6571570 7289680 6367663 8545520 8673770 7840570 7568700 7578910 7267300 FALSE TRUE 6659838.964 7700186.028 7479655.049 7627167.736 7092955.563 6659418.37 7226005.636 7467253.956 7306146.51 8691188.294 0.766274845 0.885976206 0.860602117 0.877574789 0.816108836 0.766226452 0.831417453 0.859175259 0.840638387 1 23.05112201 0.093848968 1.04560291 1.00101916 0.834054332 0.618798175 0.03922368 4.304740736 4.320708136 0.051139062 0.012032835 1.241220581 -0.093848968 -0.166964828 LKDYAFVHFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKDYAFVHFEDR 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 154.07 3.55E-05 1498129000 3727469 3748548 4330415 3579108 4952174 4915666 4517350 4397605 4433482 4239272 FALSE TRUE 3874632.354 4392331.959 4443269.172 4287044.88 4110405.232 3774077.069 4163268.303 4338662.298 4273921.849 5069876.183 0.764245953 0.866358822 0.876405855 0.845591633 0.810750615 0.744412079 0.821177511 0.855772832 0.843003201 1 22.27351908 0.406998865 1.088833244 1.000199593 0.823005697 0.639737855 0.039776846 1.65118054 2.407868468 0.040915442 0.012512329 2.552694631 -0.406998865 -0.177193896 LKEAETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 128.69 0.003405 947970000 3678990 3331590 3787070 3020400 4549280 4690350 4101510 3852190 4046280 3319080 FALSE TRUE 3824239.366 3903764.666 3885764.155 3617826.105 3775995.011 3601087.295 3780022.929 3800557.694 3900655.173 3969390.178 0.963432465 0.983467105 0.978932274 0.911431213 0.951278368 0.90721424 0.952293113 0.957466392 0.982683737 1 21.92048595 1.157581579 2.127295737 0.999614308 0.949314488 0.341985001 0.023382134 0.353370402 2.918811942 0.023235613 0.006591413 14.37413035 -1.157581579 -0.050299819 LKEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEDFR 6 1 Q96HE7;G3V2H0 Q96HE7 ERO1L ERO1-like protein alpha 0 70.268 0.083281 165980000 355220 349600 389240 350330 532810 472370 462180 368290 379270 313010 FALSE TRUE 369244.3599 409641.0805 399383.9142 419624.2284 442243.1465 362669.2263 425953.1239 363353.675 365620.1468 374338.3166 0.986392105 1.094307108 1.066906316 1.120975892 1.181399624 0.968827422 1.137882779 0.970655845 0.976710453 1 18.5139832 1.665564017 7.788725828 0.980370986 1.08065101 0.344501339 0.061166323 0.130422405 14.3079242 0.029331128 0.015235384 46.29819039 -1.665564017 0.100280024 LKEDILENEDEQNS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 131.59 1.60E-05 599520000 1467550 383390 644050 417110 880570 875090 956910 596260 704740 263419 TRUE FALSE 1525490.007 449234.2501 660834.4721 499613.1131 730891.0259 671863.6096 881904.8938 588268.11 679376.5451 315030.9096 4.842350261 1.426000549 2.097681377 1.585917756 2.320061314 2.132691076 2.79942338 1.867334576 2.156539325 1 18.26513386 4.745781936 24.88004244 2.004728552 4.842351684 0.765751044 0.481427211 365.0173322 1257582.917 0.107724541 1.103845195 55690.60498 -4.745781936 2.837623131 LKEDILENEDEQNS(ph)PPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEDILENEDEQNSPPKK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 LKEDILENEDEQNS(1)PPKK 146.19 4.47E-08 335430000 400420 84798 187890 94383 269490 245390 286170 183670 208510 57041 TRUE FALSE 416228.8908 99361.39686 192786.5678 113051.6757 223682.1861 188401.8914 263739.2476 181208.2041 201005.7658 68217.09183 6.101533789 1.456546947 2.826074266 1.657233879 3.278975694 2.761798933 3.866175478 2.656346074 2.946560172 1 16.05784563 0.230884525 1.59268599 0.999574675 2.985717407 0.202711496 1.218778898 16.26816167 31.64598049 1.079435575 0.305670912 1.701705982 -0.230884525 1.986142731 LKEDLLSHTTAELNYGLAHFVNEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEDLLSHTTAELNYGLAHFVNEIR 25 1 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 0 127.14 8.03E-05 81063000 66245 57223 83343 74396 98852 106160 77093 78951 89852 83050 FALSE TRUE 68860.40375 67050.60512 85514.98705 89111.30675 82049.17235 81505.94887 71050.24921 77892.79098 86618.24407 99322.05741 0.693304242 0.675082724 0.860986867 0.897195538 0.826092154 0.82062284 0.715352169 0.784244638 0.872094742 1 16.59982653 -5 0.208334148 1.982668199 0.761965785 0.466796124 0.069951543 149.580554 1.489796823 61.39424005 0.168110634 1.00E-05 5 -1.220702414 LKEEEEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKEEEEDK 8 1 P27797 P27797 CALR Calreticulin 0 ;; 135.55 0.00075608 700620000 1628790 491000 621470 540340 1066300 1104800 1168740 631270 768370 292392 FALSE TRUE 1693095.887 575325.4306 637666.0187 647217.6392 885050.7069 848226.9434 1077131.105 622808.8582 740716.5138 349680.6142 4.841835143 1.645288321 1.823566972 1.850882242 2.531025945 2.425719096 3.080328337 1.78107917 2.118265879 1 18.41567829 8 0.063325919 6.42E-16 7.284182472 0.26966331 0.854071857 522.4753443 2.4609296 54.52022035 346.3596641 100000000 -8 7.284182472 LKEEEEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKEEEEDKK 9 2 P27797 P27797 CALR Calreticulin 0 ;; 101.95 0.0020602 1812480000 3820830 762200 1122810 625890 2219180 2272740 2085210 1199230 1362500 410469 FALSE TRUE 3971679.319 893101.9209 1152071.351 749689.1739 1841964.576 1744930.579 1921765.792 1183156.283 1313463.891 490892.5416 8.090730622 1.819343023 2.346891128 1.527196098 3.752276558 3.554608047 3.914840069 2.410214422 2.675664794 1 18.90504772 4.744132778 24.96896475 2.678878511 8.090732973 0.763198196 0.922653868 290.3369897 1300966.704 0.221248528 1.945509177 55479.53056 -4.744132778 5.411854463 LKEEEEDKKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LKEEEEDKKR 10 3 P27797 P27797 CALR Calreticulin 0 ;;;;;;; 190.53 3.90E-07 8827820000 18431730 4501994 7381570 4435877 13820800 11320860 13021880 7545160 9544730 2643198 FALSE TRUE 19159428.93 5275176.449 7573939.778 5313280.231 11471545.35 8691761.834 12001191.02 7444029.472 9201217.032 3161082.041 6.061035014 1.668788213 2.395995953 1.680842244 3.628993238 2.749616024 3.796545254 2.354899169 2.910780838 1 21.59198705 0.150547054 0.956050595 0.983981277 2.97067941 0.200185835 1.214991947 7.551163987 7.079726837 1.4232729 0.353452847 1.414317953 -0.150547054 1.986698134 LKEELEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKEELEEAR 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;; 154.24 6.95E-05 1238820000 2114030 1698450 2103510 1624050 2600710 2534780 2441930 2131080 2257150 1633130 FALSE TRUE 2197493.537 1990145.575 2158329.199 1945282.243 2158642.243 1946115.76 2250525.146 2102516.358 2175915.612 1953110.555 1.125125012 1.018962071 1.105072722 0.995991874 1.105233002 0.996418638 1.152277397 1.076496337 1.114077033 1 20.89734218 2.237170701 24.99999236 1.092566545 1.057530445 0.051499009 0.055649716 92.20156259 1658337.305 0.018229166 0.014180971 172.6516371 -2.237170701 -0.0350361 LKEELIDAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKEELIDAIR 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 0 ; 108.72 0.0019283 680940000 1681180 1428600 1684500 1385170 1893830 1899890 1841430 1662360 1758620 1405150 FALSE TRUE 1747554.285 1673950.937 1728399.454 1659152.492 1571917.453 1458669.341 1697093.905 1640078.783 1695327.61 1680462.239 1.039924756 0.996125291 1.028526208 0.987319115 0.93540778 0.868016732 1.009897078 0.975968841 1.008846001 1 20.68042669 3.521155166 4.908314092 0.964106465 1.018094453 0.264819333 0.040833631 0.296114962 16.50914698 0.011694265 0.017846318 3320.130591 -3.521155166 0.053987988 LKEENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 80.239 0.027773 171490000 346090 247600 314450 220710 390640 326610 317810 237990 280830 194900 FALSE TRUE 359753.9004 290123.3739 322644.8253 264365.7792 324239.1523 250759.7773 292899.2218 234800.1333 270722.9832 233086.9234 1.543432361 1.244700345 1.384225338 1.134193954 1.391065391 1.075820873 1.256609412 1.00735009 1.161467916 1 17.83050854 8 0.174635975 0.974062979 3.021216196 0.59543401 0.107939931 36.63092828 0.403158688 0.23486283 19.76085447 100000000 -8 2.047153216 LKEEPDREAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEEPDREAR 10 2 P26358;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 83.182 0.0088763 38751000 50651 58392 66349 44966 77157 70518 48044 53952 61859 74174 FALSE TRUE 52650.74059 68420.37177 68078.10945 53860.14059 64041.8807 54141.26321 44278.18574 53228.86169 59632.70667 88706.97515 0.59353552 0.771307686 0.767449339 0.607169171 0.721948647 0.610338286 0.499151117 0.60005272 0.672243717 1 16.43675993 0.946202721 19.92614126 1.000000001 0.64447565 0.629668773 0.080904639 806.5949689 298758.7876 0.084528768 0.021132192 8.834922025 -0.946202721 -0.355524352 LKEEYQSLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEEYQSLIR 10 1 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 105.65 0.0022993 633700000 1951900 886480 1234500 840990 1795900 1643300 1402700 1214300 1451600 865520 FALSE TRUE 2028962.519 1038726.044 1266672.084 1007335.312 1490633.559 1261668.479 1292752.709 1198024.295 1399357.2 1035102.073 1.960156948 1.003501076 1.223717078 0.973174857 1.440083639 1.218883154 1.248913265 1.157397252 1.351902616 1 19.98134161 4.747184026 24.96397812 1.190454134 1.960157344 0.719555478 0.146027368 552.4641516 1599297.305 0.032498382 0.384003504 55870.68887 -4.747184026 0.769703211 LKEFLEDYDDDRDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEFLEDYDDDRDDPK 16 2 P49756 P49756 RBM25 RNA-binding protein 25 0 169.98 3.06E-09 109620000 613810 191800 298950 221380 442280 451660 478010 304220 346980 150470 FALSE TRUE 638043.6928 224740.158 306740.8826 265168.3032 367101.4036 346768.81 440542.3272 300142.4285 334492.2576 179951.7156 3.545638288 1.248891444 1.704573261 1.473552516 2.039999465 1.927010303 2.448114072 1.667905346 1.858788934 1 17.45725033 0.541231792 1.266006757 1.001246237 1.969878678 0.198973282 0.602895263 2.908146769 6.217010618 0.538920398 0.161743336 3.47721698 -0.541231792 0.968632442 LKEINFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEINFR 7 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 131.06 0.0031944 475760000 349980 356310 325410 284860 413970 436700 340340 368970 399130 332620 FALSE TRUE 363797.4806 417503.4708 333890.4519 341204.4578 343603.5273 335283.0433 313663.2615 364024.5607 384765.3893 397790.5206 0.914545375 1.049556108 0.839362515 0.857749092 0.863780079 0.842863331 0.788513665 0.915116228 0.967256305 1 18.60164937 4.227961749 24.98231062 0.875295904 0.982050756 0.245203578 0.067098584 218.0354875 513929.6323 0.016143747 0.035448313 16902.92049 -4.227961749 0.106754852 LKEIYENMAPGENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEIYENMAPGENKR 15 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 67.136 0.031777 415970000 180140 180400 147360 108880 170900 223720 178950 197490 134890 169970 FALSE TRUE 187252.0663 211382.2967 151200.3227 130416.139 141850.479 171764.4205 164923.4314 194842.9696 130035.3352 203272.3672 0.921188004 1.039896861 0.74383117 0.641583216 0.697834541 0.84499641 0.81134211 0.958531512 0.639709849 1 17.63305458 4.236796674 24.99978985 0.793708078 0.980542456 0.290927015 0.117578648 54.74497273 775934.9259 0.029774281 0.070061725 17250.30087 -4.236796674 0.186834378 LKELDEEHSQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELDEEHSQELK 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 57.159 0.070111 32832000 66881 50556 59178 50618 73183 79187 66257 49700 60882 53389 FALSE TRUE 69521.51352 59238.59973 60720.2273 60630.08932 60743.3798 60797.01934 61063.60321 49033.85279 58690.86871 63849.55236 1.088833217 0.927784104 0.950989084 0.949577359 0.951351694 0.952191787 0.956366974 0.767959226 0.919205641 1 15.96238888 1.957757617 24.39774549 0.867995198 0.964601809 0.154441794 0.068981573 436.5613884 252141.8496 0.026890557 0.017359478 90.73140102 -1.957757617 0.09660661 LKELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELEK 6 1 Q3V6T2;A0A2U3TZV9;A0A2R8Y4X4;A0A2R8YG73;A0A2R8Y7B1;A0A2R8Y4W8;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H7C2C6;A0A2R8Y820;A0A2R8Y885;A0A2R8YCU9;A0A2R8YGU1;A0A2R8YDS8;A0A2R8Y7D4;E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1;Q9P219 Q3V6T2;E7EX90;Q9P219 CCDC88A;DCTN1;DKFZp686E0752;CCDC88C Girdin;Dynactin subunit 1;Protein Daple 0 91.9 0.043199 3126300000 785450 435410 601400 398200 717610 709260 700030 491120 605600 351330 FALSE TRUE 816460.1725 510188.2805 617072.9781 476962.7715 595630.9085 544545.1139 645159.8194 484537.3397 583804.5743 420166.3869 1.943182982 1.214252964 1.468639561 1.135175936 1.417607232 1.296022554 1.535486511 1.15320348 1.389460444 1 18.68060123 4.743479848 24.93086567 1.303918519 1.943183255 0.602059816 0.158951922 313.4530773 1588538.83 0.03390364 0.280724243 55396.18385 -4.743479848 0.639264736 LKELIFEETAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKELIFEETAR 11 1 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ; 155.08 2.89E-05 1301850000 2486700 2326900 2699000 2188080 3352600 3312100 2730400 2663400 2831300 2531000 FALSE TRUE 2584876.836 2726526.974 2769338.157 2620875.693 2782726.25 2542914.97 2516384.113 2627701.479 2729402.066 3026900.991 0.853968083 0.900765166 0.914908735 0.865861058 0.919331771 0.840105103 0.83134008 0.868116099 0.901715013 1 21.52941006 0.85015707 3.615727817 0.999972147 0.874420266 0.641754389 0.028152077 0.522736112 11.45782306 0.028349444 0.007297832 7.082018713 -0.85015707 -0.125551881 LKELIFQETAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELIFQETAR 11 1 P27361;E9PBK7;P27361-2;B3KR49;E9PRH7;H0YEX6 P27361 MAPK3 Mitogen-activated protein kinase 3 0 95.631 0.006944 331720000 777000 770460 824020 716300 1133900 1076000 867080 886140 931470 866890 FALSE TRUE 807676.56 902780.5117 845494.6381 857982.0021 941160.083 826115.3069 799116.0039 874262.7427 897946.5767 1036740.498 0.779053738 0.870787351 0.815531601 0.827576432 0.907806809 0.796839044 0.770796555 0.843280208 0.866124723 1 19.98362339 0.77615994 2.116589783 0.999829808 0.827101797 0.642616023 0.038905439 0.5365206 3.891698199 0.036710519 0.010065058 5.97255201 -0.77615994 -0.172728012 LKELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELLR 6 1 E5RHX8;Q9NPA8-2;Q9NPA8;J3KNT2;E5RI00;E5RHT9;E5RJ84 E5RHX8 ENY2 Transcription and mRNA export factor ENY2 0 94.887 0.040102 401300000 590320 596380 648770 533080 770230 747870 706080 675670 665310 643420 FALSE TRUE 613626.2894 698803.6258 665677.4792 638521.6329 639306.5797 574188.5266 650735.6046 666613.7488 641365.6231 769485.83 0.797449759 0.908143592 0.865093876 0.829802978 0.83082307 0.746197661 0.845675878 0.866310623 0.833498939 1 19.55353523 -1.142470366 3.369636073 1.000206606 0.83842613 0.590873825 0.040918691 12776765.14 18805928.7 28385.95723 0.01025139 0.07203269 1.142470366 -0.161780477 LKELQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELQER 7 1 B4DH95;Q6P9H5-2;Q6P9H5 B4DH95 GIMAP6 GTPase IMAP family member 6 0 81.548 0.024536 352960000 592670 537020 563170 408950 889710 737630 588120 549510 659600 713530 FALSE TRUE 616069.0692 629249.0076 577846.6728 489839.0894 738477.412 566326.6114 542021.6176 542144.7173 635861.1248 853332.5421 0.72195661 0.737401864 0.677164698 0.574030715 0.86540402 0.663664613 0.635182172 0.63532643 0.745150447 1 19.70274854 0.909785739 7.04428812 0.999998615 0.686209744 0.613933678 0.073742415 1.128854261 87.97949618 0.070329561 0.017636503 8.124296027 -0.909785739 -0.313788872 LKELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKELSR 6 1 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YK13;H0YK71;H0YMW6;H0YN22;P36959 A0A087WWM4 GMPR2;GMPR GMP reductase;GMP reductase 2;GMP reductase 1 0 89.298 0.045897 219860000 370190 358460 314800 301040 406390 398560 361400 357600 356620 300590 FALSE TRUE 384805.387 420022.7166 323003.9466 360584.8135 337311.973 306000.4802 333072.5237 352806.9569 343785.3159 359484.8554 1.070435601 1.168401701 0.898518927 1.003059818 0.938320399 0.851219393 0.926527276 0.9814237 0.956327675 1 18.45557147 4.237751723 24.99999999 0.943404705 1.119418678 0.671212433 0.048986206 11.04067915 341279.027 0.012091459 0.028811514 17288.27741 -4.237751723 0.176013973 LKERPS(ph)SREDTPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.5)S(0.5)REDTPSR;LKERPS(0.497)S(0.497)REDT(0.007)PSR 118.46 0.0013506 764840000 350070 317602 375650 275542 499170 429410 340298 368300 432570 415450 TRUE FALSE 363891.0339 372147.6729 385439.7476 330043.3852 414321.2617 329686.0353 313624.5536 363363.5409 417001.8902 496849.4732 0.73239694 0.749014929 0.775767649 0.664272386 0.833896953 0.663553154 0.631226499 0.731335264 0.839292206 1 18.92244931 0.969861029 2.712684166 0.998958995 0.720781655 0.704817709 0.056017594 0.149292536 2.58764319 0.053561121 0.014284308 9.329557136 -0.969861029 -0.278177339 LKERPSS(ph)REDTPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.408)S(0.572)REDT(0.02)PSR;LKERPS(0.215)S(0.785)REDTPSR 178.57 1.09E-05 459490000 166882 171743 185525 123247 236010 211701 162093 179833 207617 193352 TRUE FALSE 173470.6302 201238.5243 190359.9339 147624.8887 195893.1045 162536.6511 149387.7271 177422.6328 200144.9047 231235.6225 0.750189908 0.870274753 0.823229275 0.63841759 0.847157987 0.702904896 0.646041149 0.767280711 0.865545294 1 17.81900414 0.992945585 2.790831594 0.998668219 0.754090754 0.519391502 0.074019225 0.205496494 3.759723267 0.071774738 0.019098773 9.838878227 -0.992945585 -0.244577465 LKETAENSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKETAENSLK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 164.9 5.49E-06 985530000 1437170 792260 1204630 887500 1629810 1462250 1616940 1256350 1505640 736360 FALSE TRUE 1493910.581 928324.4921 1236023.647 1063044.851 1352775.478 1122664.598 1490200.018 1239510.683 1451452.311 880635.6435 1.696400313 1.054152758 1.403558505 1.207133573 1.536135277 1.274834384 1.692186807 1.407518186 1.648187103 1 19.74818571 3.22870935 24.99824324 1.454931595 1.324389039 0.020412646 0.239439826 575.3547014 1459998.743 0.063170422 0.076386303 1693.20425 -3.22870935 -0.130542556 LKETAESVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKETAESVLK 10 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 106.01 0.0037032 0 915560 537400 792800 516570 1092900 1025200 970030 734020 867600 597510 FALSE TRUE 951707.0158 629694.2696 813461.0193 618746.0042 907129.2484 787112.8371 893996.5139 724181.6625 836375.2455 714580.6445 1.331839902 0.881208125 1.138375389 0.865886879 1.269456786 1.101503159 1.251078546 1.013435878 1.170442065 1 19.44673731 3.217701518 24.99906576 1.133157196 1.047965119 0.065503767 0.147193267 643.0862982 770719.8479 0.039447631 0.047195764 1650.826827 -3.217701518 -0.085192078 LKETYEALLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKETYEALLAR 11 1 O95347-2;O95347 O95347-2 SMC2 Structural maintenance of chromosomes protein 2 0 88.552 0.00867 0 166610 182490 183430 187640 219780 246410 199050 193800 171370 183820 FALSE TRUE 173187.8915 213831.2379 188210.3365 224754.632 182421.8741 189185.0119 183447.9409 191202.428 165202.4272 219836.0096 0.787804927 0.972685223 0.856139706 1.022374052 0.829808886 0.860573353 0.834476305 0.869750267 0.751480285 1 17.7460682 LKEVDR ddPTM_MDA-MB-175_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 66.429 0.092506 206110000 448550 384160 393980 378420 566850 557420 436140 433610 479930 405210 FALSE TRUE 466259.1004 450136.4917 404247.4425 453270.3465 470497.0395 427967.6528 401954.2072 427798.1672 462657.413 484603.1413 0.962146261 0.928876545 0.834182464 0.935343393 0.970891435 0.883130166 0.829450272 0.882780425 0.95471402 1 18.88644423 LKEVFSMAGVVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEVFSMAGVVVR 13 1 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 121.99 0.00021914 313550000 307960 309900 372860 306160 457810 466480 373790 388810 330650 391150 FALSE TRUE 320118.4986 363122.9143 382577.0379 366717.5342 379991.6197 358147.0896 344491.3631 383598.6379 318749.9711 467788.3535 0.684323362 0.776254714 0.817842161 0.783939 0.812315264 0.765617799 0.736425694 0.820026055 0.681397835 1 18.83549642 -1.539141846 3.041731883 1.009079222 0.770697174 0.681261603 0.048196918 18272294.89 18645228.05 1342587.846 0.01101808 0.028897359 1.539141846 -0.238382048 LKEVLEYNAIGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKEVLEYNAIGGK 13 1 P14324-2;P14324;A0A087WVN4;A0A087X1D8 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 165.33 3.24E-05 3256700000 6669000 4180500 6374100 4199600 8491200 7214000 7515400 6343800 7319300 4083700 FALSE TRUE 6932297.27 4898468.355 6540214.282 5030268.345 7047868.857 5538657.829 6926323.31 6258771.737 7055879.823 4883822.828 1.419440777 1.002998784 1.339158793 1.029985837 1.443104942 1.134082465 1.418217563 1.281531284 1.444745248 1 22.21957943 2.245931716 24.99980535 1.310458522 1.223707434 0.01710897 0.179141028 540.2508233 1832314.766 0.057111394 0.046871109 176.1699032 -2.245931716 -0.086751088 LKEYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKEYLK 6 1 O75351;K7EKZ3;K7EL71;Q8WWQ8 O75351 VPS4B;STAB2 Vacuolar protein sorting-associated protein 4B;Stabilin-2;190 kDa form stabilin-2 0 67.032 0.091058 228670000 290350 349360 238110 308480 819800 727560 654160 581410 676360 595840 FALSE TRUE 301813.2422 409359.8624 244315.3422 369496.4233 680450.6888 558595.2163 602885.2299 573617.1499 652017.9357 712583.44 0.423547932 0.574472882 0.342858574 0.518530747 0.954906683 0.783901484 0.846055628 0.804982431 0.915005737 1 19.44269943 3.314178492 5.721254782 0.862274814 0.457014264 0.858206401 0.083401904 0.070414096 3.949233546 0.022046301 0.029824217 2061.476993 -3.314178492 -0.40526055 LKFNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKFNFK 6 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 104.04 0.031164 453780000 405700 248600 382550 284660 462840 423610 479410 362030 395420 264520 FALSE TRUE 421717.3493 291295.1162 392519.5673 340964.8984 384166.6221 325232.9974 441832.5915 357177.58 381188.9114 316347.6295 1.333082059 0.920807014 1.24078555 1.077817144 1.214381226 1.028087354 1.396667939 1.129066719 1.204968446 1 18.27115126 LKFS(ph)DDEEEEEVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LKFSDDEEEEEVVK 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK;LKFS(1)DDEEEEEVVK 279.53 1.92E-33 1425240000 4634440 1410230 2189260 1532020 3207660 3690310 3539310 2320620 2557910 950750 TRUE FALSE 4817411.27 1652426.032 2246313.914 1835048.983 2662423.099 2833291.43 3261889.634 2289515.885 2465851.319 1137031.259 4.236832744 1.453281094 1.975595566 1.613894929 2.341556643 2.491832486 2.868777448 2.013590977 2.168675046 1 20.11684049 4.74897738 24.66293997 2.074753998 4.236834206 0.627862928 0.514948751 820.1515129 1941760.929 0.120948003 1.697952636 56101.87551 -4.74897738 2.162080208 LKFS(ph)DDEEEEEVVKDGRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKFSDDEEEEEVVKDGRPK 19 3 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LKFS(1)DDEEEEEVVKDGRPK;LKFS(1)DDEEEEEVVKDGRPK 175.71 1.13E-11 916340000 1157550 296670 457160 271430 857390 793340 682100 465620 550100 216442 TRUE FALSE 1203250.968 347620.7647 469073.9652 325118.0439 711651.1541 609098.8082 628635.2197 459379.1255 530302.0085 258849.6659 4.648454785 1.342944614 1.812148235 1.256011063 2.74928365 2.353098684 2.428572653 1.774694682 2.048687244 1 17.98175493 8 0.061133488 4.47E-10 6.59937564 0.218136891 0.87345856 639.5160652 2.915243397 62.63078167 374.0140243 99999999.96 -8 6.59937564 LKFS(ph)DEEDGRDS(ph)DEEGAEGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 173.95 1.95E-12 1763910000 2096870 1005690 1429530 1155040 1821990 2004050 2023710 1432590 1538860 822508 TRUE FALSE 2179656.047 1178409.434 1466784.726 1383503.465 1512288.791 1538639.759 1865086.322 1413388.474 1483476.729 983662.6947 2.215857182 1.197981219 1.491146034 1.406481584 1.537405859 1.564194482 1.89606288 1.436862943 1.508115269 1 19.90780416 0.590615611 1.584181562 1.00061237 1.577935067 0.306679841 0.266251839 2.189062128 7.013063967 0.237410025 0.068086131 3.895970065 -0.590615611 0.577322697 LKGDDLQAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKGDDLQAIK 10 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;G3V576;P07910-2;G3V4C1;B2R5W2;G3V2D6;A0A0G2JNQ3;O60812;B2RXH8;A0A0G2JPF8;P0DMR1;B7ZW38 B4DY08;P07910;P07910-2 HNRNPC;HNRNPCL1;HNRNPCL2;HNRNPCL4;HNRNPCL3 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 1;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3 0 83.314 0.018291 0 907830 589530 618860 592410 961170 985500 1025600 761820 680360 477880 FALSE TRUE 943671.8294 690777.1916 634988 709586.9298 797790.6667 756632.5604 945210.7921 751609.049 655873.9765 571511.4364 1.651186257 1.208684809 1.11106788 1.241597079 1.395931238 1.323914995 1.653879051 1.315125124 1.147613039 1 19.12442284 1.094872104 3.102011406 1.007280414 1.358391745 0.345577323 0.165589224 0.267400481 4.957168235 0.16100547 0.042764141 12.44148168 -1.094872104 0.351111331 LKGDDLQAIKK ddPTM_MDA-MB-175_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 ; 155.02 1.78E-05 4433700000 7914100 3705900 5053600 3555500 8409400 6780100 6514200 5067900 5408700 3400100 FALSE TRUE 8226554.779 4342359.497 5185300.968 4258767.288 6979973.192 5205524.528 6003599.982 4999973.09 5214041.944 4066284.496 2.023113431 1.067893676 1.275193846 1.047336283 1.716548165 1.280167321 1.476433827 1.229617134 1.282261964 1 21.95527973 -4.514562374 0.119147663 4.35E-13 1.540635777 0.182184346 0.275136588 263.9492638 2.291210318 66.03311017 2.655568529 3.06E-05 4.514562374 1.540635777 LKGDNEKHS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKGDNEKHSPR 11 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 LKGDNEKHS(1)PR;LKGDNEKHS(1)PR;LKGDNEKHS(1)PR 55.213 0.066139 171925000 425392 214957 314250 207401 465737 409331 410443 301627 360710 212677 TRUE FALSE 442186.8046 251874.1926 322439.6132 248424.2988 386571.1911 314270.0787 378271.4052 297584.1834 347728.1176 254346.9862 1.738517964 0.990277873 1.267715486 0.976714143 1.519857565 1.235595843 1.48722582 1.169992961 1.367140703 1 17.95643847 -1.106819986 4.440106229 0.99996873 1.289030475 0.139192047 0.224716906 6.30E-05 1.27E-05 0.197070382 0.046444915 0.078195185 1.106819986 0.289061745 LKGELESSDQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGELESSDQVR 12 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 180.84 1.73E-05 991860000 557100 538700 579280 510990 758750 745640 626860 601910 587650 564750 FALSE TRUE 579094.7382 631217.5345 594376.5127 612062.2968 629777.946 572476.4103 577725.0752 593842.381 566500.5913 675401.9497 0.857407561 0.934580563 0.880033753 0.906219322 0.932449109 0.847608466 0.855379638 0.879242918 0.838760669 1 19.36538682 2.735546141 24.96956629 0.874675103 0.902939142 0.015159388 0.047542107 698.4858933 5785699.3 0.013853051 0.013560556 543.9339184 -2.735546141 0.028264039 HGSGPNIILTGDSS(ph)PGFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 HGSGPNIILTGDSSPGFSK 19 0 Q53ET0;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HGSGPNIILTGDS(0.073)S(0.921)PGFS(0.006)K;HGSGPNIILTGDS(0.015)S(0.985)PGFSK;HGSGPNIILTGDS(0.012)S(0.988)PGFSK 142.41 1.00E-07 1084670000 100007 410320 434140 438820 535810 718750 417270 619470 474840 435790 TRUE FALSE 103955.3536 480789.2682 445454.045 525617.2863 444733.2076 551831.2053 384563.2871 611167.0179 457750.6012 521174.7068 0.199463543 0.922510747 0.854711557 1.008524166 0.853328455 1.058821923 0.737877879 1.172672062 0.87830548 1 18.99140754 4.74236672 4.807245017 0.95173877 0.155736054 0.78518734 0.116677753 0.0749574 4.983622697 0.026203563 0.200334823 55254.3813 -4.74236672 -0.796002716 down LKGEMMDLQHGSLFLR ddPTM_MDA-MB-175_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 ;; 186.85 8.62E-10 2770903000 690494 3953450 4126520 4372170 4284830 5663090 3558230 5051140 3781360 4132030 FALSE TRUE 717755.2363 4632424.284 4234060.501 5236972.176 3556496.127 4347923.172 3279326.635 4983437.73 3645269.592 4941622.166 0.145246887 0.937429882 0.856815912 1.059767825 0.719702156 0.879857469 0.663613389 1.00846191 0.737666594 1 22.23655328 4.741740444 24.96746776 0.87125482 0.145246614 0.749584474 0.12630475 135.0900967 1060653.939 0.027911453 0.199430311 55174.75888 -4.741740444 -0.726008206 LKGIEEEEILPGFILCDPNNLCHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKGIEEEEILPGFILCDPNNLCHSGR 26 1 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 115.45 0.00071456 304490000 342470 274840 383510 302140 469750 438270 364190 373830 381200 345140 FALSE TRUE 355990.98 322041.632 393504.5857 361902.3902 389902.0628 336488.4345 335643.8362 368819.4203 367480.6865 412763.5749 0.862457353 0.780208457 0.953341355 0.876778893 0.944613543 0.815208645 0.813162441 0.893536743 0.8902934 1 18.65495614 0.69043671 1.675188062 0.999780786 0.866532176 0.367031676 0.052229392 1.28506026 5.319664907 0.049638721 0.014124831 4.902715705 -0.69043671 -0.133248609 LKGIVPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKGIVPLAK 9 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 89.247 0.011137 0 468700 406330 430080 353220 768030 655130 447570 436740 522760 575970 FALSE TRUE 487204.6379 476114.0167 441288.2381 423085.8617 637480.5349 502985.9861 412488.2939 430886.2147 503945.9697 688820.2939 0.707302967 0.691202075 0.640643492 0.614218056 0.925467122 0.730213657 0.598832958 0.625542276 0.731607321 1 19.39376812 0.963178841 21.46205655 1.000000002 0.688109533 0.519505547 0.088367006 749.5455651 436891.3858 0.089366956 0.022341739 9.187108412 -0.963178841 -0.31189047 LKGMKDDKEEEEDGT(ph)GSPQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.673)GS(0.327)PQLNNR;LKGMKDDKEEEEDGT(0.546)GS(0.454)PQLNNR 147.25 1.23E-07 556780000 1522360 373500 663370 290260 1214910 1016730 705110 566890 782010 322200 TRUE FALSE 1582463.948 437645.7196 680657.9672 347672.5617 1008400.032 780609.8662 649841.6357 559291.7668 753865.6129 385328.9211 4.106787375 1.135771793 1.766433636 0.902274765 2.616985066 2.025827348 1.686459542 1.451465842 1.956421051 1 18.55573095 4.745981164 24.85834238 1.649846812 4.106788635 0.692914004 0.497034407 459.4733831 1539165.305 0.114455877 1.192936829 55716.15836 -4.745981164 2.456941823 LKGMKDDKEEEEDGTGS(ph)PQLNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKGMKDDKEEEEDGTGSPQLNNR 23 3 P49407-2;P49407 P49407-2 ARRB1 Beta-arrestin-1 1 LKGMKDDKEEEEDGT(0.005)GS(0.995)PQLNNR;LKGMKDDKEEEEDGT(0.012)GS(0.988)PQLNNR;LKGMKDDKEEEEDGT(0.014)GS(0.986)PQLNNR 210.8 3.30E-24 2706260000 2677320 630830 1106178 481687 2131650 1836030 1309107 1055034 1439822 533056 TRUE FALSE 2783022.661 739170.1453 1135005.907 576963.2509 1769312.894 1409639.858 1206495.773 1040892.995 1388003.087 637498.1172 4.365538636 1.159486005 1.780406682 0.905043067 2.775400972 2.211206307 1.892547978 1.632778148 2.177266175 1 19.28206156 4.746950028 24.8410478 1.770447948 4.365540056 0.66715412 0.558520449 583.0826931 1726465.894 0.129466057 1.488271186 55840.59377 -4.746950028 2.595092108 LKGNKHDDGT(ph)QSDSENAGAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGNKHDDGTQSDSENAGAHR 21 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 LKGNKHDDGT(0.859)QS(0.141)DSENAGAHR;LKGNKHDDGT(0.792)QS(0.208)DSENAGAHR 167.57 1.20E-11 115745000 80077 54994 78375 49151 101202 84467 79110 67185 82974 45168 TRUE FALSE 83238.50179 64438.79171 80417.51689 58872.9211 83999.72019 64850.81936 72909.15148 66284.49497 79987.78195 54017.80481 1.540945658 1.19291763 1.488722416 1.089879926 1.555037649 1.200545257 1.349724443 1.227086054 1.480766985 1 15.72114739 -1.514406087 3.1085842 0.989724475 1.333230076 0.302371907 0.156952263 29107392.09 28477484.79 2472039.116 0.03310813 0.030591017 1.514406087 0.343505601 LKGNKHDDGTQS(ph)DSENAGAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKGNKHDDGTQSDSENAGAHR 21 2 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 LKGNKHDDGT(0.178)QS(0.813)DS(0.01)ENAGAHR 77.693 0.0045637 49214000 26490 17326 23548 15530 37080 28971 23397 23804 32809 19480 TRUE FALSE 27535.84565 20301.60572 24161.68022 18601.78765 30777.15484 22242.92431 21563.082 23484.94632 31628.2105 23296.73303 1.181961677 0.871435737 1.037127403 0.798471941 1.321093168 0.954765815 0.925583942 1.008078956 1.357624284 1 14.50784004 1.40465901 24.99999138 1.180162608 1.005425963 0.142107499 0.162939063 74.44108455 25681.51336 0.100372175 0.036696254 25.38978424 -1.40465901 -0.174736645 LKGPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGPQK 6 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 66.994 0.09115 1047860000 600470 917360 777300 825770 1079270 1091550 847000 824580 789540 946420 FALSE TRUE 624177.0193 1074909.444 797557.0766 989104.8413 895816.0709 838054.0551 780609.9268 813527.8538 761124.6096 1131852.879 0.551464798 0.949690074 0.704647301 0.873881102 0.791459816 0.740426668 0.689674375 0.718757596 0.67245896 1 20.11025501 -1.117165004 4.940191682 1.000010916 0.749135905 0.350673367 0.104422926 1.16E-05 2.08E-06 0.093622351 0.02206604 0.076354563 1.117165004 -0.250875011 LKGSGNLEAIHIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGSGNLEAIHIIK 14 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 104.18 0.00064448 1339020000 3399600 2554200 3364100 2508100 4370900 3862200 3666700 3392200 3741000 2651600 FALSE TRUE 3533818.833 2992863.981 3451771.21 3004194.694 3627935.979 2965262.582 3379294.473 3346733.108 3606362.141 3171130.252 1.114372023 0.943784627 1.088498717 0.94735771 1.144051392 0.935080664 1.065643542 1.055375479 1.13724819 1 21.59656571 2.049351812 24.99999792 1.067899325 1.026827189 0.050433732 0.07510946 307.3130824 155673.0627 0.025558837 0.018876446 112.0345081 -2.049351812 -0.041072135 LKGTS(ph)PSSSSRPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKGTSPSSSSRPQR 14 2 H3BVG0;Q8N1F7;Q8N1F7-2 H3BVG0 NUP93 Nuclear pore complex protein Nup93 1 LKGT(0.031)S(0.953)PS(0.014)S(0.001)SSRPQR 93.753 0.002315 271120000 555220 279960 408420 286920 448670 413730 450400 366100 408130 281080 TRUE FALSE 577140.5143 328040.9522 419063.7607 343671.9196 372405.2337 317647.4776 415096.4711 361193.0283 393441.481 336152.2444 1.716902159 0.975870183 1.246648707 1.02236985 1.107846935 0.944951232 1.234846645 1.074492389 1.170426459 1 18.35875526 4.74522882 24.98022586 1.093902199 1.716902445 0.781873321 0.099838103 314.3410938 1177544.406 0.021599021 0.20964281 55619.72274 -4.74522882 0.623000246 LKGYTSWAIGLSVADLAESIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGYTSWAIGLSVADLAESIMK 22 1 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 109.66 0.00024706 0 73849 106943 152079 85909 183269 169680 132465 136663 207036 89488 FALSE TRUE 76764.61554 125309.6283 156042.3037 102901.5438 152117.0008 130274.3915 122082.0472 134831.256 199584.8148 107021.4602 0.717282453 1.170883186 1.458046856 0.961503829 1.421369139 1.217273538 1.140724925 1.259852517 1.864904612 1 16.70754059 4.705975383 3.541712162 1.282650503 0.668901945 0.328501096 0.244649735 0.285103333 6.359902403 0.055915343 0.441890311 50813.06399 -4.705975383 -0.613748559 LKHEDTNLASSTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKHEDTNLASSTLLR 15 1 P49407-2;P49407;H0YET9 P49407-2 ARRB1 Beta-arrestin-1 0 ; 185.67 2.48E-07 2075210000 1803000 1775980 1947690 1653450 2706900 2379400 2105300 2040700 2051100 1941900 FALSE TRUE 1874183.832 2080990.75 1998448.401 1980497.475 2246782.105 1826820.41 1940281.085 2013347.754 1977281.312 2322378.125 0.807010629 0.896060261 0.860518096 0.85278855 0.967448875 0.786616267 0.83547165 0.866933654 0.851403693 1 21.14717146 -1.741901898 2.584665003 1.030148159 0.859909129 0.452937765 0.046703048 8341107.673 6146688.736 1606550.782 0.010663265 0.018117493 1.741901898 -0.17023903 LKHFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKHFEK 6 1 Q9Y2X3;F8WED0 Q9Y2X3 NOP58 Nucleolar protein 58 0 86.866 0.031899 292170000 503580 442550 540040 400470 727230 611510 575530 543880 568600 452850 FALSE TRUE 523461.7272 518554.5199 554113.886 479681.7707 603615.7044 469496.07 530418.4547 536590.1782 548136.1971 541577.2872 0.96655037 0.957489415 1.02314831 0.885712496 1.114551364 0.866905022 0.979395679 0.99079151 1.012110755 1 19.04680771 1.611420508 3.292013672 1.004570618 0.970409712 0.047544839 0.064648718 0.692134722 17.66249568 0.037936514 0.015934795 40.87149357 -1.611420508 -0.034160906 LKKEDIYAVEIVGGATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKKEDIYAVEIVGGATR 17 2 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 166.91 1.29E-09 1505960000 2240000 1573520 1949730 1359540 2934400 2296900 1964110 1983940 2299800 1547720 FALSE TRUE 2328436.93 1843759.82 2000541.566 1628452.954 2435611.736 1763479.785 1810157.926 1957348.529 2217030.647 1850966.101 1.25795763 0.996106746 1.080809402 0.879785401 1.31585972 0.952734782 0.97795304 1.057474001 1.197769449 1 20.81984704 LKLDKDR ddPTM_MDA-MB-175_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 93.162 0.0085139 480420000 1158800 801090 972170 548360 2081100 1300500 880800 963370 1165500 1395400 FALSE TRUE 1204550.319 938670.9759 997505.5488 656823.9713 1727355.365 998478.5843 811760.5945 950457.6009 1123553.883 1668801.913 0.721805452 0.562481963 0.597737539 0.393590136 1.035087119 0.598320613 0.486433164 0.569544889 0.673269771 1 20.67038129 0.878778974 6.158106016 0.999997714 0.614821939 0.330449892 0.160890141 2.421906458 122.607444 0.151181551 0.037995319 7.56447818 -0.878778974 -0.385175776 LKLEDFFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKLEDFFAR 9 1 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 156.48 6.46E-05 19772480000 9303540 7959350 9070000 8030860 12934370 11508480 10989410 9148850 10149640 8099830 FALSE TRUE 9670850.943 9326306.447 9306371.651 9619340.138 10735790.41 8835809.933 10128031.33 9026224.63 9784356.439 9686836.608 0.998349754 0.962781435 0.960723508 0.993032145 1.108286517 0.912146069 1.0455458 0.931803126 1.010067253 1 23.20759418 3.623570325 7.510114835 0.997112102 0.972984979 0.048255252 0.052221037 0.996467908 58.63065881 0.01356774 0.02106677 4203.105828 -3.623570325 -0.024127122 LKLGEIVTTIPTIGFNVETVEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 216.65 2.29E-32 1148277000 1539497 776302 1290752 791634 1648795 1496891 1478206 1233742 1421745 746344 FALSE TRUE 1600277.53 909625.8297 1324390.057 948216.8424 1368533.415 1149260.751 1362340.351 1217205.706 1370576.675 892575.8172 1.792875742 1.019102033 1.483784382 1.06233759 1.533240525 1.287577737 1.526302108 1.363700072 1.535529698 1 19.76761519 -1.327316514 4.938787495 0.999816172 1.386058202 0.225853348 0.220991807 0.000395478 5.39E-05 0.189179892 0.044569104 0.04706342 1.327316514 0.38624203 LKLMAS(ph)DMIES(ph)CVKRTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKLMASDMIESCVKRTR 17 3 H7C4K9;H7C538;F1T0E5;Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4 H7C4K9 CADPS Calcium-dependent secretion activator 1 2 LKLMAS(1)DMIES(0.997)CVKRT(0.003)R 41.136 0.092054 366620000 392210 248760 339370 180830 458760 414130 293440 311780 380160 242570 TRUE FALSE 407694.7537 291482.5949 348214.261 216597.6343 380780.1391 317954.5837 270439.406 307601.0991 366478.1159 290096.9472 1.40537416 1.004776499 1.200337557 0.746638792 1.31259616 1.096028713 0.932238028 1.060338973 1.26329532 1 18.14617559 4.745040741 24.58313894 1.066281052 1.405374355 0.292743799 0.157064266 715.9569561 2715978.115 0.035071486 0.330106912 55595.64085 -4.745040741 0.339093303 LKLS(ph)PSPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.781)PS(0.219)PSSR;LKLS(0.761)PS(0.228)PS(0.011)SR;LKLS(0.5)PS(0.5)PSSR;LKLS(0.805)PS(0.195)PS(0.001)SR;LKLS(0.807)PS(0.188)PS(0.005)SR 143.31 2.07E-05 9830520000 7954400 6191040 6951440 5836600 8702800 8918100 8622400 7200620 7384950 5450880 TRUE FALSE 8268445.854 7254302.96 7132600.237 6991062.059 7223501.165 6847006.43 7946553.758 7104107.467 7119167.092 6518875.573 1.268385285 1.112815068 1.094145786 1.072433732 1.108090051 1.050335499 1.219006816 1.089774975 1.092085132 1 22.63619171 -4.999999859 0.016393577 3.21E-10 1.947758382 0.322488846 0.061058714 6922.044445 8.604015847 653.0902872 398.3145882 1.00E-05 4.999999859 1.947758382 LKLSILYPATTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKLSILYPATTGR 13 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 132.65 6.31E-06 0 508010 625850 684770 503240 836450 864840 531790 682730 680090 778340 FALSE TRUE 528066.6271 733334.8691 702615.6687 602779.37 694270.5278 663994.0168 490106.9102 673579.1211 655613.6937 930840.8208 0.567300676 0.787819843 0.754818282 0.647564392 0.745853117 0.713327136 0.526520646 0.72362439 0.704324176 1 19.82817495 0.497605864 2.105379447 0.999974786 0.685662393 0.59133421 0.07858044 3.598202867 14.23962108 0.073075161 0.019949716 3.144892932 -0.497605864 -0.314312393 LKLSPS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LKLS(0.081)PS(0.918)PSSR 141.58 9.80E-05 515980000 256230 187680 237410 197240 302930 263370 280590 244150 223220 175100 TRUE FALSE 266346.1583 219912.5801 243597.0996 236253.4833 251438.0668 202206.3089 258596.6226 240877.5686 215186.3558 209407.4925 1.27190367 1.050165767 1.163268309 1.128199762 1.200711893 0.965611624 1.234896706 1.150281519 1.027596259 1 17.67595354 -4.999999998 0.153562318 0.494637909 1.175901873 0.228682642 0.086627528 213.5999222 1.92652777 32.64273907 0.390618898 1.00E-05 4.999999998 0.681263964 LKNDSDLFGLGLEEAGPKES(ph)S(ph)EEGKEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKNDSDLFGLGLEEAGPKESSEEGKEGK 28 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 LKNDSDLFGLGLEEAGPKES(1)S(1)EEGKEGK;LKNDSDLFGLGLEEAGPKES(1)S(1)EEGKEGK 126.66 1.66E-05 1059980000 1460390 157323 215039 172323 451720 638480 480230 272351 279480 93984 TRUE FALSE 1518047.325 184342.0014 220643.093 206407.9751 374936.7958 490202.6963 442588.3178 268700.5803 269421.5694 112398.3654 13.50595554 1.640077245 1.96304539 1.836396592 3.335785129 4.361297379 3.937675751 2.390609325 2.397023911 1 16.77826153 4.741892229 24.99998709 2.675449704 13.50595955 0.914361492 1.006014815 88.69375753 665516.5091 0.253077178 1.834620863 55194.04569 -4.741892229 10.83050985 LKNDSDLFGLGLEEAGPKES(ph)SEEGKEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKNDSDLFGLGLEEAGPKESSEEGKEGK 28 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 1 LKNDSDLFGLGLEEAGPKES(0.961)S(0.039)EEGKEGK 186.31 6.47E-18 692420000 513140 72390 139040 69071 300380 322820 267960 149710 185470 49328 TRUE FALSE 533399.1634 84822.41938 142663.4966 82733.03764 249321.5149 247849.9474 246956.595 147703.3823 178794.9709 58992.87716 9.041755363 1.43784171 2.418317321 1.402424185 4.226298613 4.201353779 4.186210385 2.503749426 3.030789132 1 15.84825315 8 0.077310032 1.90E-11 11.70784102 0.187694977 2.000063963 463.5079899 2.619251765 62.15617479 582.0282285 100000000 -8 11.70784102 LKNEITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKNEITR 7 1 Q86VP6 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 103.56 0.0076133 1563820000 2092100 1834630 2191100 2016600 2656700 2538700 2364000 2171500 2227000 1709350 FALSE TRUE 2174697.723 2149713.431 2248201.866 2415477.461 2205115.083 1949125.399 2178703.503 2142394.594 2146850.705 2044264.405 1.063804525 1.05158287 1.099760804 1.181587595 1.078683891 0.953460518 1.065764046 1.048002689 1.050182501 1 20.96315038 2.985790525 24.98398619 1.03015132 1.100113908 0.403756525 0.043692661 753.6183302 1325060.76 0.013724623 0.015099601 967.8109347 -2.985790525 0.069962588 LKNGFPHPEPDCNPSEAASEES(ph)NS(ph)EIEQEIPVEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 2 LKNGFPHPEPDCNPS(0.096)EAAS(0.607)EES(0.675)NS(0.622)EIEQEIPVEQK 123.05 7.14E-08 59203000 38732 24679 32085 26149 43794 35740 38537 35703 35560 21571 TRUE FALSE 40261.16927 28917.42627 32921.16146 31321.19415 36349.91152 27439.92664 35516.36924 35224.45968 34280.20255 25797.42445 1.560666234 1.120942377 1.276141404 1.214120976 1.409051962 1.063669232 1.376740896 1.365425442 1.328822674 1 14.65493942 4.756994934 24.15823015 1.261953046 1.560666647 0.328757188 0.134276407 3061.370629 4011832.192 0.030271705 0.979267667 57147.19702 -4.756994934 0.298713601 LKNGFPHPEPDCNPSEAASEESNS(ph)EIEQEIPVEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKNGFPHPEPDCNPSEAASEESNSEIEQEIPVEQK 35 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 LKNGFPHPEPDCNPS(0.073)EAAS(0.073)EES(0.168)NS(0.686)EIEQEIPVEQK 47.59 0.04948 130760000 74990 37788 57429 41085 65953 65337 61768 61192 69792 35607 TRUE FALSE 77950.6631 44277.79505 58925.64692 49211.49037 54742.33262 50163.47194 56926.46276 60371.82133 67280.19955 42583.50991 1.830536357 1.039787353 1.383766792 1.155646645 1.285528899 1.178002284 1.336819414 1.417727694 1.579958996 1 15.37800725 2.001384938 24.87782619 1.378550717 1.291639855 0 0.240659981 192.2984257 3454215.802 0.084223649 0.061707163 100.3194028 -2.001384938 -0.086910862 LKPDEGGEVPVLNVSYKPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKPDEGGEVPVLNVSYKPQK 20 2 P61221;D6R9I9 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 120.75 1.88E-05 342710000 220580 120650 177670 102870 223040 186140 215490 166590 194400 102780 FALSE TRUE 229288.6687 141370.699 182300.2262 123217.379 185127.7405 142911.806 198599.3307 164357.1335 187403.582 122917.7732 1.865382547 1.150124147 1.483107133 1.002437449 1.506110432 1.162661854 1.615708824 1.337130745 1.524625586 1 16.90733401 -2.196345624 2.087016192 3.08E-05 1.389241606 0.200650004 0.24075799 3119984.902 619347.547 14716565.93 0.053420826 0.006362889 2.196345624 1.389210766 LKPEYDIMCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPEYDIMCK 10 1 J3KQ32;Q9NTK5;Q9NTK5-3;Q9NTK5-2;C9JCJ9 J3KQ32 OLA1 Obg-like ATPase 1 0 ; 130.01 0.00026272 725190000 1749860 1259640 1635020 1276670 2381360 2087350 2044360 1717450 1996960 1394320 FALSE TRUE 1818945.824 1475973.371 1677629.964 1529191.516 1976577.278 1602594.597 1884117.721 1694430.392 1925089.8 1667510.308 1.09081534 0.88513598 1.006068722 0.917050712 1.185346362 0.961070279 1.129898695 1.016143878 1.154469505 1 20.66926425 3.263968239 24.99950572 1.069866639 0.970601225 0.253813556 0.083416178 297.026396 292253.2741 0.020904619 0.028294951 1836.40404 -3.263968239 -0.099265413 LKPGGVGAPSSS(ph)SPSPSPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPS(0.001)S(0.051)S(0.456)S(0.456)PS(0.033)PS(0.003)PSAR 111.27 0.00015289 192310000 184680 122430 141280 125350 190500 184410 200430 133460 162630 88807 TRUE FALSE 191971.309 143456.4001 144961.8729 150143.8559 158118.878 141583.5723 184719.7729 131671.187 156776.9781 106207.0313 1.807519771 1.350724131 1.364899019 1.413690355 1.488779755 1.333090385 1.739242407 1.239759603 1.476144998 1 16.69651976 -3.145276194 0.271171822 1.00E-12 1.495399357 0.419374175 0.167683432 65.91060437 1.58783599 37.53773032 0.197445637 0.000715688 3.145276194 1.495399357 LKPGGVGAPSSSS(ph)PSPSPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPS(0.001)S(0.016)S(0.29)S(0.591)PS(0.098)PS(0.004)PSAR;LKPGGVGAPS(0.001)S(0.009)S(0.244)S(0.729)PS(0.018)PSPSAR;LKPGGVGAPSS(0.002)S(0.041)S(0.83)PS(0.122)PS(0.004)PSAR;LKPGGVGAPSS(0.001)S(0.08)S(0.891)PS(0.025)PS(0.004)PSAR 186.27 2.00E-17 1858080000 1106220 834200 1079300 1092830 1245110 1358200 1302090 1142390 1171600 728260 TRUE FALSE 1149894.42 977467.3608 1107427.445 1308988.512 1033466.647 1042778.634 1200028.783 1127078.131 1129434.345 870948.6036 1.32027816 1.122302001 1.27151871 1.502945761 1.186598891 1.197290666 1.377841102 1.294081104 1.296786447 1 19.73222806 -1.716223122 2.427615395 0.941488864 1.285876366 0.419286191 0.100803089 7221117.999 5292598.991 2564212.187 0.026276272 0.01922104 1.716223122 0.344387502 LKPGGVGAPSSSSPS(ph)PSPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 LKPGGVGAPSSS(0.001)S(0.014)PS(0.973)PS(0.009)PS(0.002)AR 94.006 0.00099134 403340000 56313 59916 58322 61205 59865 67655 73535 59945 71036 43320 TRUE FALSE 58536.28072 70206.10692 59841.91923 73311.16632 49689.16868 51943.15157 67771.13455 59141.53533 68479.42824 51807.72459 1.129875539 1.355128168 1.155077157 1.415062462 0.959107335 1.002614031 1.308127988 1.141558248 1.321799573 1 15.6608796 -1.911324037 2.583188822 0.884155107 1.196336896 0.148036063 0.142905657 21631898.2 11417216.95 15172183.85 0.033198546 0.012265238 1.911324037 0.31218179 LKPGYLEATVDWFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPGYLEATVDWFR 14 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 208.47 7.30E-09 5761900000 5168500 5232400 5602600 5015900 7180200 6900800 6091800 6018700 5483900 6221500 FALSE TRUE 5372556.371 6131023.998 5748608.359 6008030.049 5959712.169 5298193.783 5614308.798 5938029.171 5286535.51 7440483.807 0.722070837 0.824008782 0.772612172 0.807478412 0.800984496 0.712076515 0.75456233 0.798070304 0.710509645 1 22.826965 -1.028861369 5.133095505 1.000002372 0.770869448 0.758034035 0.039447416 1.02E-06 1.94E-07 0.036502495 0.008603632 0.093570431 1.028861369 -0.229132925 LKPKPIDVQVITHHMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKPKPIDVQVITHHMQR 17 2 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 119.46 3.83E-05 1195100000 2973300 2044500 3113600 2398500 3400700 3311200 3672300 3070100 3484900 1998100 FALSE TRUE 3090688.18 2395626.971 3194742.974 2872916.141 2822650.229 2542223.982 3384455.53 3028950.331 3359479.13 2389589.439 1.293397154 1.002526598 1.336942205 1.202263491 1.181228115 1.063874798 1.416333482 1.26756098 1.405881309 1 21.18833134 2.239720355 24.999758 1.296171162 1.180166264 0.084362088 0.140705423 59.58140192 1284392.21 0.046745819 0.037074921 173.668221 -2.239720355 -0.116004898 LKPLEVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPLEVELR 9 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 112.85 0.0017296 1459090000 2053600 2216500 2344400 3107700 5397200 4860200 4123700 2569900 2578900 4700900 FALSE TRUE 2134677.714 2597166.633 2405496.99 3722393.784 4479785.872 3731492.207 3800473.619 2535454.694 2486085.893 5621951.351 0.379704053 0.461968891 0.42787581 0.662117751 0.796838249 0.663736125 0.676006138 0.450991931 0.442210496 1 22.42263954 3.742272712 23.52095464 0.641452524 0.427061476 0.34310212 0.153053299 185.1027446 1172851.775 0.040633284 0.069748322 5524.242209 -3.742272712 -0.214391048 LKPNLGNGADLPNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPNLGNGADLPNYR 15 1 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 ; 225.85 8.61E-13 1527270000 1635800 1697090 1646190 1658560 2116710 2235340 2006140 1873580 1985350 1844930 FALSE TRUE 1700382.647 1988552.006 1689091.064 1986618.218 1756912.39 1716216.162 1848893.505 1848467.725 1913897.641 2206408.71 0.770656243 0.901261855 0.765538613 0.900385413 0.796276946 0.777832391 0.837965104 0.83777213 0.867426616 1 21.07326863 0.655592233 1.269312078 0.999943041 0.823093019 0.573740299 0.045974714 0.779420341 1.94189049 0.039941167 0.012037658 4.524725452 -0.655592233 -0.176850022 LKPPVHYNGPSK ddPTM_MDA-MB-175_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 ; 102.97 0.0013799 895870000 858930 507350 701770 540810 939320 929350 868070 657400 755840 603100 FALSE TRUE 892841.2196 594483.4159 720058.7027 647780.6038 779654.7219 713522.5469 800028.4051 648588.6283 728637.466 721265.898 1.237880818 0.82422227 0.998326283 0.898116223 1.080953258 0.989264221 1.109200376 0.899236509 1.01022032 1 19.46017169 0.10307884 0.002922941 8.57E-07 1.974890743 0.001330455 0.11239492 443695.5549 418.3443657 142711.5571 139937.7058 1.26788201 -0.10307884 1.974889886 LKPQYLEELPGQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPQYLEELPGQLK 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 154.07 5.67E-06 1169880000 1989300 1017080 1651710 1208740 1996720 1771210 2242260 1647400 1897730 892150 FALSE TRUE 2067839.1 1191755.578 1694754.919 1447825.164 1657318.248 1359873.32 2066505.802 1625319.298 1829431.068 1066949.711 1.938084877 1.116974461 1.588411245 1.356976012 1.553323676 1.274543032 1.936835242 1.523332619 1.71463664 1 20.02506075 LKPVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKPVELR 7 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 96.253 0.011735 1282520000 2987300 2920800 3688700 3491200 4087400 3697700 3662100 3316000 3508500 2981000 FALSE TRUE 3105240.911 3422424.679 3784830.552 4181748.94 3392625.208 2838965.214 3375055.033 3271554.444 3382229.77 3565069.875 0.871018246 0.959988107 1.06164274 1.172978114 0.951629372 0.79632807 0.946700949 0.917669094 0.948713458 1 21.76549892 3.010979165 24.99937187 0.914520801 1.021444998 0.208499081 0.086298394 319.8770321 728348.913 0.02595025 0.030990441 1025.602722 -3.010979165 0.106924198 LKPWGLFEVLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKPWGLFEVLVEK 13 1 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 H3BLV9 SRPK1 SRSF protein kinase 1 0 66.533 0.050718 110000000 129260 89376 128770 102310 153480 133720 158460 139100 143700 92238 FALSE TRUE 134363.2846 104725.6328 132125.852 122546.6126 127391.5244 102665.5565 146039.4911 137235.592 138528.2651 110310.2701 1.218048732 0.949373369 1.197765647 1.110926594 1.154847362 0.93069808 1.323897503 1.244087172 1.255805692 1 16.75120759 2.21798594 24.99581886 1.231681233 1.095358666 0.164129348 0.118601079 335.8283607 407989.4418 0.041210242 0.030469173 165.1908318 -2.21798594 -0.136322567 LKQDGDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKQDGDSFR 9 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 182.28 4.24E-05 1330880000 2079780 1817440 2113170 1761330 2748880 2659070 2072580 2033080 2116280 1885490 FALSE TRUE 2161891.32 2129571.182 2168240.946 2109715.817 2281626.359 2041541.291 1910125.764 2005829.888 2040115.496 2254915.666 0.958745976 0.944412784 0.96156188 0.935607415 1.01184554 0.905373679 0.847094103 0.889536544 0.904741373 1 21.10464205 2.509620852 22.46575496 0.89524828 0.959766153 0.265209598 0.04117085 192.1033486 132793.466 0.012506402 0.011776376 323.3112763 -2.509620852 0.064517872 LKQEFHYIEEDLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKQEFHYIEEDLYR 14 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 ; 171.91 1.77E-06 181307000 329920 304250 332590 325980 445040 456510 350570 344400 329300 388020 FALSE TRUE 342945.4964 356502.5708 341257.5686 390457.871 369392.2598 350492.471 323091.4074 339783.8813 317448.5573 464045.0899 0.739034856 0.76824985 0.735397435 0.841422266 0.796026653 0.755298307 0.696250029 0.732221693 0.684089896 1 18.82390547 -0.976448599 4.742881961 1.000002475 0.75042491 0.750584998 0.043270872 1.70E-06 3.67E-07 0.044665469 0.010527605 0.105572645 0.976448599 -0.249577565 LKQEYFVVAATLQDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKQEYFVVAATLQDIIR 17 1 P11216;P11217;P11217-2;E9PK47;P06737-2;P06737 P11216;E9PK47 PYGB;PYGM;PYGL "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form;Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 173.98 1.29E-09 547560000 1274020 1080410 1413480 1155050 1672040 1706690 1571800 1314010 1402620 1336750 FALSE TRUE 1324319.293 1265962.013 1450316.45 1383515.443 1387827.238 1310337.113 1448598.209 1296397.845 1352139.98 1598660.569 0.828393043 0.791889184 0.907207245 0.865421634 0.868118765 0.819646858 0.906132444 0.810927517 0.845795541 1 20.60843222 -1.825069803 2.3640349 1.058209034 0.849149937 0.605958222 0.036461653 4925141.148 2965842.456 1630076.105 0.009308069 0.014959952 1.825069803 -0.209059097 LKQFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKQFEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 144.38 0.0021508 580650000 1305560 1114380 1248090 1076060 1558520 1505280 1287170 1154790 1340760 1142930 FALSE TRUE 1357104.517 1305766.096 1280616.251 1288901.456 1293603.327 1155701.533 1186278.252 1139311.929 1292506.31 1366865.251 0.992859037 0.955299797 0.936900144 0.942961609 0.946401503 0.84551241 0.867882369 0.83352176 0.945598923 1 20.38243959 2.842756155 6.523107305 0.881435933 0.953998799 0.214412404 0.048880952 0.276285271 14.89174006 0.014435208 0.015338809 696.2354868 -2.842756155 0.072562867 LKQNLEEQLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKQNLEEQLDR 11 1 Q8WZA0-2;Q8WZA0 Q8WZA0-2 LZIC Protein LZIC 0 98.592 0.0049299 184170000 216240 194350 198830 194980 245830 240930 224120 190660 204390 195520 FALSE TRUE 224777.3222 227728.1007 204011.6731 233546.462 204043.9044 184977.6588 206552.8888 188104.5146 197034.0438 233828.4005 0.961291792 0.973911211 0.872484577 0.99879425 0.872622419 0.791082941 0.883352443 0.804455379 0.842643765 1 17.83509064 3.076347706 6.852098542 0.848282625 0.947048279 0.2977383 0.062173959 0.221303331 16.2694785 0.016696324 0.019999584 1192.196126 -3.076347706 0.098765654 LKQQSELQSQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKQQSELQSQVR 12 1 Q14847;Q14847-2;C9J9W2 Q14847 LASP1 LIM and SH3 domain protein 1 0 63.128 0.066463 452100000 120930 109360 138270 158020 218650 233680 158000 141610 160000 200850 FALSE TRUE 125704.4098 128141.7293 141873.4298 189275.8844 181483.9511 179411.3615 145615.5471 139711.9496 154241.6313 240202.712 0.523326355 0.533473283 0.590640416 0.787983961 0.755544971 0.746916469 0.606219413 0.581641849 0.642131098 1 17.87389291 -2.306297273 2.091561738 2.568862746 0.641156269 0.596174386 0.088669744 11046517.12 1384211.845 81931873.22 0.028497776 0.004939724 2.306297273 -1.927706477 LKQSAEEQAQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKQSAEEQAQAR 12 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 157.56 5.66E-05 575340000 572590 532000 559810 491250 739080 716230 509040 594170 622100 585530 FALSE TRUE 595196.2953 623366.8616 574399.1085 588417.7838 613451.4456 549896.4371 469140.1147 586206.123 599710.7425 700253.3929 0.84997274 0.890201844 0.820273224 0.840292657 0.87604209 0.785282075 0.669957646 0.837134285 0.856419617 1 19.41751754 2.739450874 24.98760589 0.808008503 0.85450641 0 0.079220994 229.5338649 6442561.479 0.024163687 0.024328437 548.8464677 -2.739450874 0.046497908 LKQVEDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LKQVEDEK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 144.77 0.00052903 3714880000 7863390 3840710 5188610 3965890 8426060 8047580 9343870 6651990 7671230 3485990 FALSE TRUE 8173842.709 4500322.066 5323829.439 4750331.205 6993801.331 6178651.507 8611473.054 6562830.955 7395143.931 4169002.997 1.960622891 1.079472015 1.277003025 1.139440583 1.677571673 1.48204535 2.065595314 1.574196747 1.773839917 1 21.99127098 2.461877052 24.98386865 1.672301635 1.402893079 0.038318866 0.346838807 504.7288266 827199.8213 0.114169918 0.095551006 289.6523469 -2.461877052 -0.269408555 LKQVEDEKNSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKQVEDEKNSFR 12 2 P35579 P35579 MYH9 Myosin-9 0 ;;; 166.38 2.93E-05 5494800000 4983980 3698570 4304050 2609740 7386690 5525720 4106710 4585320 5647990 4115860 FALSE TRUE 5180751.379 4333770.627 4416217.079 3125938.783 6131103.072 4242455.273 3784815.339 4523861.285 5444719.943 4922283.964 1.052509651 0.880438971 0.897188604 0.635058604 1.245580937 0.861887551 0.768914465 0.919057356 1.106136904 1 22.23089646 1.306717146 7.463244281 1.052129193 0.900461012 0.123853394 0.154177375 0.410232636 37.3236316 0.101851911 0.036759811 20.26362528 -1.306717146 -0.151668181 LKS(ph)DERPVHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKSDERPVHIK 11 2 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 LKS(1)DERPVHIK;LKS(1)DERPVHIK;LKS(1)DERPVHIK 168.5 9.39E-06 1490070000 2531900 1052820 1842530 1110580 3045010 2245290 2482460 1993520 2308100 1112550 TRUE FALSE 2631861.367 1233633.645 1890547.845 1330249.409 2527420.288 1723855.425 2287878.298 1966800.125 2225031.932 1330532.871 1.978050617 0.927172618 1.420895256 0.999786956 1.899554939 1.295612805 1.719520312 1.478204836 1.672286329 1 20.34357272 3.247283974 24.99993844 1.53481561 1.308984716 0.054957719 0.351291409 464.8210149 1332105.518 0.089075905 0.118790737 1767.192964 -3.247283974 -0.225830894 LKS(ph)EDELRPEVDEHTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKSEDELRPEVDEHTQK 17 2 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCR2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 LKS(1)EDELRPEVDEHTQK;LKS(1)EDELRPEVDEHTQK;LKS(1)EDELRPEVDEHTQK 209.56 1.98E-12 3392980000 2089840 664998 1142950 739801 1797810 1710710 1694570 1155230 1356460 531768 TRUE FALSE 2172348.497 779206.2335 1172736.216 886131.4297 1492218.898 1313423.529 1561745.175 1139746.031 1307641.27 635957.7583 3.415869165 1.225248412 1.844047345 1.393380957 2.346411973 2.065268505 2.45573728 1.792172541 2.056176299 1 19.27857142 4.754065189 24.46184694 1.863190484 3.415870707 0.53180658 0.451762437 1714.24037 2704527.13 0.103372928 2.469370006 56762.98025 -4.754065189 1.552680224 LKS(ph)EDGVEGDLGETQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR;LKS(0.999)EDGVEGDLGETQSR 223.89 1.75E-15 1698711000 1434580 772710 952757 771874 1550260 1647330 1417610 1146370 1175710 750571 TRUE FALSE 1491218.326 905416.9317 977586.6301 924548.3734 1286747.359 1264762.573 1306494.024 1131004.785 1133396.427 897631.0169 1.661282084 1.008673848 1.089074031 1.029987106 1.433492532 1.409000524 1.455491176 1.25998853 1.262652922 1 19.775763 3.229149633 24.99944367 1.327458423 1.176057064 0.046940206 0.210387433 451.7501174 1200032.625 0.058791801 0.071143753 1694.921671 -3.229149633 -0.151401358 LKS(ph)IEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKSIEER 7 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 LKS(1)IEER;LKS(1)IEER;LKS(1)IEER;LKS(1)IEER 140.07 0.0016042 1068760000 3220350 2238400 3145230 2501220 4556240 4396490 4087790 3712930 3972370 2601680 TRUE FALSE 3347491.905 2622827.788 3227197.278 2995953.851 3781771.952 3375471.827 3767378.338 3663164.246 3829405.18 3111429.384 1.075869477 0.842965552 1.037207302 0.962886661 1.215445214 1.084862104 1.210819168 1.177325208 1.230754328 1 21.56914607 3.246110689 24.97284191 1.163728273 0.974068517 0.490276112 0.086173875 123.2977559 407820.7387 0.022158048 0.029437997 1762.425182 -3.246110689 -0.189659756 LKS(ph)PSMAVPSPGWVASPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKSPSMAVPSPGWVASPK 18 1 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 LKS(0.966)PS(0.034)MAVPSPGWVASPK;LKS(0.982)PS(0.018)MAVPSPGWVASPK 161.66 2.27E-11 1500670000 971490 645020 937090 685030 1235870 1124210 1115290 903950 1025490 583700 TRUE FALSE 1009845.175 755797.1674 961511.3352 820526.8894 1025797.259 863129.2651 1027870.656 891834.0288 988582.8152 698064.8394 1.44663521 1.082703389 1.377395452 1.175430767 1.469487075 1.23646002 1.472457281 1.277580503 1.416176205 1 19.41300152 -1.129416015 4.778464482 0.999977697 1.322419211 0.376852797 0.126432403 2.68E-05 4.89E-06 0.109300873 0.025760682 0.074230773 1.129416015 0.322441514 LKSDEDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKSDEDEER 9 1 Q96AY3;H0Y827;Q96AY3-2 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 103.31 0.0040903 0 274140 190310 222750 219860 307730 296890 281890 216730 231490 147690 FALSE TRUE 284963.2589 222994.2621 228555.048 263347.6518 255422.1645 227941.7969 259794.7252 213825.0888 223158.7201 176627.0278 1.61336157 1.262514944 1.293998154 1.490981618 1.446110302 1.290526143 1.4708662 1.210602316 1.263446047 1 17.4303466 0.949634451 0.75223561 1.000844972 1.4076475 0.571418723 0.108434444 0.535744427 0.674848917 0.10104243 0.038014069 8.905010811 -0.949634451 0.406802528 LKSDEDEERVHEEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKSDEDEERVHEEL 14 2 Q96AY3;H0Y827;Q96AY3-2 Q96AY3 FKBP10 Peptidyl-prolyl cis-trans isomerase FKBP10 0 ; 79.646 0.010409 110837000 123277 130185 160163 102160 223733 197342 141172 135725 162471 143093 FALSE TRUE 128144.0712 152543.2611 164336.9794 122366.9431 185702.9446 151512.3112 130106.5698 133905.8284 156623.7004 171129.3337 0.748814177 0.891391661 0.96030865 0.715055335 1.085161384 0.885367272 0.760282103 0.782483199 0.915235846 1 17.38472755 -2.908672517 1.292386897 3.130647845 0.85739243 0.131852971 0.107165433 478486.6758 12467.04617 2978318.994 0.029996935 0.001234035 2.908672517 -2.273255415 LKSDTAAAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LKSDTAAAAVR 11 1 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 183.37 4.90E-06 1006600000 1890380 1806490 1796540 1615480 3454680 2678250 2317070 1956400 2139210 2635990 FALSE TRUE 1965013.662 2116740.605 1843359.308 1935017.122 2867454.728 2056267.027 2135451.999 1930177.658 2062220.25 3152461.771 0.623326722 0.671456391 0.584736451 0.613811447 0.909592228 0.652273422 0.677391878 0.612276309 0.654161858 1 21.58804745 -2.092687553 2.385267044 1.555800465 0.665992461 0.575326852 0.085941849 6247937.731 1860484.455 18854004.77 0.02110758 0.00807816 2.092687553 -0.889808004 LKSEDEPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKSEDEPTR 9 1 O14787-2;O14787;A0A075B780;K7ENW1;K7ESC1;E7EW37;Q92973-2;Q92973 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 ; 119.53 0.000741 633650000 1276280 986650 1136980 916140 1466360 1431760 1380500 1136850 1247840 986130 FALSE TRUE 1326668.52 1156099.462 1166610.633 1097349.758 1217108.651 1099255.439 1272292.803 1121612.385 1202930.482 1179343.293 1.12492141 0.98029087 0.989203602 0.93047526 1.032022362 0.932091144 1.078814634 0.951048259 1.020000274 1 20.1695523 4.740774882 24.75928098 0.988866886 1.124921464 0.458683635 0.043798635 143.2232642 1601360.447 0.009386904 0.062961148 55052.22568 -4.740774882 0.136054578 LKSEDGVEGDLGETQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 98.816 0.002173 0 39032 35414 34927 35889 50213 43951 39445 34201 37032 31097 FALSE TRUE 40573.0135 41496.07902 35837.22631 42987.73708 41677.8122 33744.04633 36353.19783 33742.59154 35699.22555 37189.86176 1.090969731 1.115790085 0.96362892 1.155899351 1.120676717 0.907345302 0.977502903 0.907306183 0.959918211 1 15.18262176 2.739401392 24.99999183 0.943929865 1.087567379 0.622536187 0.053982119 48.67090493 1447216.34 0.01667173 0.016759322 548.7839378 -2.739401392 0.143637514 LKSIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKSIFR 6 1 E9PGK7;O94759-3;O94759-2;O94759 E9PGK7 TRPM2 Transient receptor potential cation channel subfamily M member 2 0 103.29 0.031752 397820000 288550 324260 377940 274590 562590 458420 332310 399560 423610 439980 FALSE TRUE 299942.1768 379949.1326 387789.4269 328903.0824 466961.1528 351958.9024 306262.6739 394204.5517 408364.3588 526185.6571 0.570031077 0.722081888 0.736982131 0.625070406 0.887445613 0.668887298 0.582042991 0.749173883 0.77608417 1 19.0052124 0.808659125 1.732610596 0.999175259 0.693526269 0.536158568 0.086814752 0.518892072 2.793267296 0.080278303 0.022800131 6.436638598 -0.808659125 -0.30564899 LKSSLEEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKSSLEEESR 10 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 96.059 0.0063829 232430000 255330 280830 293870 264244 409160 376310 311170 340340 328970 341050 FALSE TRUE 265410.6256 329060.3679 301528.4936 316510.6745 339611.1293 288917.7055 286779.6823 335778.299 317130.434 407872.2177 0.650720039 0.806773185 0.73927196 0.776004495 0.832640995 0.708353482 0.703111587 0.82324386 0.77752399 1 18.63775772 0.191289944 0.779893622 1.004607652 0.752831209 0.653666987 0.053668551 2.007491089 1.456491626 0.073861916 0.017641387 1.553423763 -0.191289944 -0.251776444 LKSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKSTPR 6 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 67.035 0.091051 147920000 171410 152190 180670 160960 261230 236680 208130 205370 209370 197900 FALSE TRUE 178177.3992 178327.4486 185378.4086 192797.4076 216826.2179 181714.6569 191816.2268 202617.3511 201834.8146 236674.716 0.752836645 0.753470635 0.783262411 0.814609228 0.916135959 0.767782296 0.810463534 0.856100535 0.852794156 1 17.85254607 -4.999999998 0.102919153 1.60447452 0.689896035 0.705292979 0.040624461 103.291818 0.719055453 13.29472278 0.648225949 1.00E-05 4.999999998 -0.914578485 LKTDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKTDLK 6 1 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 0 89.55 0.045636 566510000 648480 382380 514760 443520 778000 728700 698370 596980 674740 463910 FALSE TRUE 674082.4911 448050.7905 528175.0685 531246.9322 645755.8379 559470.4686 643629.9345 588978.4596 650456.2392 554804.2824 1.214991507 0.807583511 0.952002508 0.95753935 1.163934487 1.008410509 1.160102679 1.061596816 1.172406666 1 19.0816194 3.255662466 24.80971359 1.095541365 0.968281142 0.194460036 0.10940583 306.9797406 445333.5703 0.028158829 0.038029344 1801.616977 -3.255662466 -0.127260224 LKTEAEIALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 110.31 0.0027872 0 1438400 888400 1231370 812590 1711390 1457490 1472530 1235740 1359560 851380 FALSE TRUE 1495189.143 1040975.789 1263460.514 973317.8767 1420488.539 1119010.036 1357109.251 1219176.927 1310629.701 1018191.61 1.468475214 1.022377103 1.240886785 0.955928007 1.395109255 1.099017144 1.332862339 1.197394394 1.28721322 1 19.95757765 -0.91804944 4.596155832 0.999998467 1.213996894 0.157379779 0.153162422 8714206.154 1896072.371 199.3385418 0.032054579 0.120767635 0.91804944 0.213998427 LKTEEGEIDYS(ph)AEEGENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;LKTEEGEIDYS(1)AEEGENRR 139.47 9.64E-08 179292000 149561 122817 147759 106105 191632 185152 147831 166626 169837 121362 TRUE FALSE 155465.7838 143909.8644 151609.7209 127092.2523 159058.4611 142153.254 136243.6199 164392.651 163724.5995 145140.5603 1.071139477 0.991520662 1.044571694 0.875649454 1.095892566 0.97941784 0.938701213 1.132644456 1.128041667 1 17.14709122 1.714755248 10.44538791 1.096624602 0.999185621 0.24795123 0.069003504 0.128846771 35.58122339 0.030978335 0.016800451 51.8507745 -1.714755248 -0.097438982 LKTEGSDLCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKTEGSDLCDR 11 1 P04843;B7Z4L4 P04843 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 60.55 0.08476 151850000 112830 126070 118550 148470 179320 192660 132730 130780 131800 170930 FALSE TRUE 117284.6155 147721.5418 121639.5104 177836.9229 148839.2505 147917.6348 122326.2758 129027.108 127056.5437 204420.4608 0.573742056 0.722635793 0.595045671 0.86995657 0.728103487 0.723595056 0.598405244 0.631184899 0.621545139 1 17.64118008 -1.329297514 3.101722585 1.00269138 0.675209678 0.568230136 0.085295616 11071833.5 14504955.37 273845.5509 0.022611131 0.046849233 1.329297514 -0.327481702 LKTEKEPDATPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LKTEKEPDATPPSPR 15 2 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 LKTEKEPDAT(0.023)PPS(0.977)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDATPPS(1)PR;LKTEKEPDAT(0.034)PPS(0.966)PR 134.9 1.69E-05 2696070000 4448170 2574950 3546490 2347590 5272800 4382370 4356900 3625240 4159390 2383210 TRUE FALSE 4623787.186 3017177.632 3638914.443 2811936.295 4376531.339 3364630.983 4015394.793 3576649.587 4009694.366 2850154.37 1.622293597 1.058601479 1.27674293 0.986590875 1.535541859 1.180508333 1.408834144 1.254896796 1.406834103 1 21.44260863 -1.057197442 4.616104002 0.999987058 1.291139195 0.185773301 0.189001781 2.27E-05 4.64E-06 0.165124661 0.038918527 0.08766022 1.057197442 0.291152137 LKTNILQYASTRPPTLS(ph)PIPHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKTNILQYASTRPPTLSPIPHIPR 24 2 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 LKTNILQYAST(0.002)RPPT(0.198)LS(0.801)PIPHIPR;LKTNILQYASTRPPT(0.027)LS(0.973)PIPHIPR 183.49 1.34E-17 582500000 348140 300330 374710 301200 413880 435400 357820 413810 427850 369620 TRUE FALSE 361884.836 351909.3413 384475.2504 360776.461 343528.8254 334284.9486 329773.1334 408263.5538 412451.7621 442039.9622 0.818669955 0.796103003 0.869774869 0.816162546 0.777144274 0.756232416 0.746025612 0.923589695 0.933064423 1 18.75381728 1.60882601 4.773049212 0.954921062 0.798574605 0.79101392 0.03678531 0.075226711 3.770070657 0.022621216 0.010397731 40.62805297 -1.60882601 -0.156346457 LKVDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKVDSFR 7 1 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;K7ENH2;B7Z8D3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 117.4 0.0047788 1322800000 2038280 2098540 2186100 1912180 3512100 3311000 3054800 2927100 2569700 3836600 FALSE TRUE 2118752.868 2458947.921 2243071.562 2290403.497 2915114.496 2542070.429 2815356.794 2887867.012 2477216.999 4588308.314 0.461772122 0.535916018 0.488866791 0.499182561 0.635335356 0.554032174 0.613593639 0.629396896 0.539897677 1 22.12953091 -5 0.190640675 2.921967606 0.474747001 0.888414364 0.048817915 40.14137293 0.393117836 29.26695774 0.128459892 1.00E-05 5 -2.447220605 LKVPEWVDTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKVPEWVDTVK 11 1 P39019;M0R2L9;M0QYF7;M0R140 P39019 RPS19 40S ribosomal protein S19 0 ; 166.45 1.86E-05 5934400000 6068200 4248400 5703300 3948700 7018900 6180800 6716500 5589200 5853000 4049300 FALSE TRUE 6307777.222 4978029.652 5851932.683 4729741.074 5825829.885 4745402.871 6190043.18 5514285.916 5642351.673 4842682.806 1.302537761 1.027948732 1.208407182 0.976677859 1.20301703 0.979911975 1.278226022 1.138684101 1.165129309 1 22.20737508 2.226208946 24.99989574 1.159424322 1.114161449 0.008897173 0.116881646 926.6485438 1875531.109 0.039764744 0.029571318 168.3483817 -2.226208946 -0.045262873 LKVPPAINQFTQALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKVPPAINQFTQALDR 16 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ; 245.96 3.36E-20 3009300000 856580 847080 1031010 854940 1125870 1145420 988280 1073610 1007220 1042020 FALSE TRUE 890398.4398 992559.4006 1057878.968 1024044.58 934495.0196 879413.564 910816.0312 1059220.014 970970.3489 1246183.868 0.714500053 0.796479096 0.848894769 0.821744372 0.749885345 0.705685241 0.730884145 0.849970892 0.779154966 1 20.24908552 0.19059709 0.911567192 1.001938501 0.77580279 0.645478095 0.049566749 2.610540999 2.376242554 0.065060718 0.016799097 1.550947476 -0.19059709 -0.226135711 LKVTEGGEPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKVTEGGEPYR 11 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 63.76 0.078982 0 73589 82091 75432 75677 116130 115060 83373 80976 89850 81165 FALSE TRUE 76494.35054 96189.49067 77397.81989 90645.68473 96390.26408 88339.05875 76838.00641 79890.64917 86616.31605 97067.72775 0.788051315 0.990952327 0.797358934 0.933839566 0.993020712 0.910076508 0.791591687 0.823040273 0.892328666 1 16.5667041 0.961418741 22.55730714 1.000000002 0.87783409 0.191995061 0.074308272 3400.545559 1988201.439 0.072371039 0.01809276 9.14995042 -0.961418741 -0.122165912 LKWGMEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKWGMEYK 8 1 P62306;A0A0B4J254;F8W0W6 P62306 SNRPF Small nuclear ribonucleoprotein F 0 103.7 0.0043067 511820000 463000 449900 468640 317900 1032600 670030 554200 552760 510310 729800 FALSE TRUE 481279.5975 527166.8253 480853.1434 380779.6712 857079.0208 514425.6869 510760.3559 545351.1563 491944.0428 872790.3371 0.551426359 0.604001675 0.550937749 0.436278514 0.981998751 0.589403509 0.585203953 0.624836382 0.563645153 1 19.7352756 -2.124741001 2.381159867 1.767097505 0.612936476 0.433477933 0.133796975 5433194.784 1634703.856 22503174.2 0.032889109 0.007503416 2.124741001 -1.154161029 LKYALTGDEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LKYALTGDEVKK 12 2 P62701;C9JEH7;P22090;Q8TD47 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 1;40S ribosomal protein S4, Y isoform 2" 0 79.466 0.012913 640380000 245000 175170 203510 136020 313760 267810 206000 204790 245100 167900 FALSE TRUE 254672.7892 205254.0849 208813.6378 162924.35 260427.1873 205615.1862 189853.1817 202045.125 236278.8989 200796.7904 1.268311056 1.022198037 1.039925177 0.811389215 1.296968875 1.023996379 0.945499086 1.006216905 1.176706552 1 17.61537668 4.739998919 23.99950464 1.031610914 1.268311176 0.245114108 0.122163928 99.16361141 1654343.604 0.02799679 0.176431317 54953.95057 -4.739998919 0.236700262 LLAAGQLADALSQFHAAVDGDPDNYIAYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLAAGQLADALSQFHAAVDGDPDNYIAYYR 30 0 Q13217;X6R9L0 Q13217 DNAJC3 DnaJ homolog subfamily C member 3 0 ; 263.4 1.90E-58 469320000 219337 296360 289040 357790 340250 352720 324930 294280 302920 252720 FALSE TRUE 227996.5941 347257.5246 296572.6198 428559.7941 282414.4265 270806.1255 299461.1376 290335.6579 292017.9684 302235.6454 0.75436699 1.148962837 0.98126288 1.417965752 0.934417998 0.896009884 0.990820051 0.96062679 0.966193011 1 18.2053143 LLAAVEAFYS(ph)PPSHDRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFY(0.001)S(0.996)PPS(0.003)HDRPR;LLAAVEAFY(0.03)S(0.917)PPS(0.053)HDRPR 122.53 2.17E-05 229450000 162283 177403 169828 176184 176370 212660 170297 176072 168386 199196 TRUE FALSE 168690.0581 207870.5852 174253.8572 211032.6693 146390.6904 163272.9379 156948.6762 173712.0428 162325.8208 238224.6424 0.708113386 0.872582211 0.731468649 0.88585575 0.614506916 0.68537384 0.658826369 0.729194264 0.681398109 1 17.86196313 -1.328672269 3.29739502 1.001645843 0.730638085 0.492064296 0.08238179 25275779.31 35585800.49 406490.378 0.020353811 0.04691673 1.328672269 -0.271007758 LLAAVEAFYSPPS(ph)HDRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 LLAAVEAFY(0.277)S(0.319)PPS(0.404)HDRPR 74.816 0.010824 16575000 14171 16374 16099 13989 17413 19032 16229 15557 15273 19896 TRUE FALSE 14730.48202 19186.10713 16518.55317 16755.98245 14453.14448 14612.10643 14956.92857 15348.48386 14723.32771 23794.24027 0.619077636 0.806334092 0.694224862 0.704203297 0.607421978 0.614102668 0.6285945 0.645050386 0.618776962 1 14.53832477 -1.822253877 6.555722283 1.023172625 0.660976771 0.753902788 0.058315211 0.019617741 0.000531898 0.056083803 0.013886826 0.015057266 1.822253877 -0.362195854 LLAAVEAFYSPPSHDRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLAAVEAFYSPPSHDRPR 18 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 143.14 6.47E-08 253210000 174160 198560 198170 196710 219110 242280 199930 201640 196880 237620 FALSE TRUE 181035.9713 232661.1354 203334.473 235618.6509 181865.7605 186014.1418 184258.9642 198937.3456 189794.3273 284177.0895 0.637053366 0.818718834 0.715520288 0.829126132 0.639973338 0.654571212 0.64839486 0.700047094 0.667873429 1 18.11643072 -1.885076573 7.442278303 1.041419231 0.703179319 0.644166983 0.066597536 0.034613288 0.000534497 0.048766226 0.015163259 0.01302937 1.885076573 -0.338239912 LLACIASRPGQCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLACIASRPGQCGR 14 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 228.62 1.45E-12 6001100000 872600 880060 792180 765740 1060110 1114020 786250 875730 878250 1128860 FALSE TRUE 907050.9218 1031203.459 812824.8616 917201.0865 879912.8809 855305.7381 724621.6705 863992.2718 846641.9541 1350038.504 0.671870409 0.763832629 0.602075318 0.679388835 0.65176873 0.633541737 0.536741484 0.639976022 0.627124302 1 20.36456912 -1.626759837 5.208259098 1.004059879 0.643183831 0.789843386 0.054904104 0.002694238 0.000193078 0.055336882 0.012926976 0.023617839 1.626759837 -0.360876047 LLALLSLGEVGHHIDLSGQLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLALLSLGEVGHHIDLSGQLELK 23 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 193.63 3.21E-18 333528000 228387 232278 283277 238169 339645 331899 303334 246758 284386 207318 FALSE TRUE 237403.8951 272169.9396 290659.4313 285278.1173 281912.2642 254820.4872 279557.8885 243450.6126 274151.0034 247937.9928 0.957513177 1.0977339 1.172306947 1.150602674 1.137027291 1.027758934 1.127531466 0.9819012 1.105724058 1 17.91961983 2.056993714 1.466349427 1.03151798 1.104498311 0.118508689 0.068719717 0.788533472 3.185506489 0.045349537 0.022692988 114.0233284 -2.056993714 0.072980331 LLANQQVFHISCFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLANQQVFHISCFR 14 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 233.24 3.50E-17 800980000 104280 481760 331410 438830 385720 589980 285350 434130 302110 610240 FALSE TRUE 108397.0549 564498.5324 340046.8169 525629.2642 320155.4522 452966.0862 262983.5214 428311.1974 291237.1201 729804.8442 0.148528824 0.773492444 0.465942121 0.720232633 0.43868639 0.620667415 0.360347733 0.586884563 0.399061643 1 19.4771512 -1.827745871 2.854702702 1.156059379 0.515785703 0.4207364 0.174745044 21619905.85 12126492.4 22880381.93 0.037736903 0.014868054 1.827745871 -0.640273676 LLASIAEDYRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLASIAEDYRK 11 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 70.942 0.070114 0 92364 91516 101500 80173 121970 129550 106460 87296 108210 86809 FALSE TRUE 96010.60204 107233.1611 104145.1734 96030.98011 101237.583 99463.97585 98115.38702 86125.93991 104315.5432 103817.5615 0.924801167 1.032900018 1.00315565 0.924997454 0.97514892 0.958065037 0.945075049 0.829589317 1.0047967 1 16.66369098 2.16937672 3.796542561 0.918189226 0.972891011 0 0.056217635 0.417341528 11.96329491 0.022184557 0.01603029 147.6987161 -2.16937672 0.054701785 LLCEHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLCEHFR 7 0 Q13155;A8MU58;Q13155-2 Q13155 AIMP2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 0 ; 107.32 0.019524 0 88031 140280 90445 98756 286610 199710 137161 125838 119276 330780 FALSE TRUE 91506.53185 164371.9988 92802.071 118289.642 237892.1346 153330.3791 126409.9624 124151.3474 114983.2801 395590.0078 0.231316591 0.415510998 0.234591545 0.299020804 0.601360322 0.387599222 0.319547916 0.313838431 0.290662751 1 18.59364646 -1.19583429 4.491856462 1.00015871 0.346731849 0.78782802 0.102163366 0.000164081 2.94E-05 0.099431043 0.023430465 0.063703854 1.19583429 -0.653426861 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLCEQNEEEVSPQLFTFHEAVSQMVEMEEQVVEDHR 36 0 O00139-1;O00139-5;O00139;O00139-4;O00139-2 O00139-1 KIF2A Kinesin-like protein KIF2A 0 ;; 292.44 3.59E-92 178596000 25034 39919.8 38420.6 33070.7 37531.4 49482 39515.1 43459 38791.4 39454.9 FALSE TRUE 26022.36165 46775.71512 39421.8724 39611.98575 31151.82603 37990.55541 36417.80321 42876.50319 37395.30509 47185.33225 0.551492602 0.991318973 0.835468789 0.839497867 0.660201477 0.80513485 0.771803471 0.908682871 0.792519694 1 15.52605084 0.404374773 0.593771223 1.005935922 0.789609432 0.230693806 0.114686648 3.140969866 1.775916515 0.159479855 0.046453692 2.537317255 -0.404374773 -0.21632649 LLCGLLAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLCGLLAER 9 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ; 143.89 0.00023467 229880000 229730 281950 209046 227870 475050 384380 270680 225460 219030 647820 FALSE TRUE 238799.9178 330372.7192 214493.9105 272942.0059 394301.1707 295113.5703 249463.3943 222438.0775 211147.1531 774747.9257 0.30822918 0.426426078 0.276856386 0.352297821 0.508941241 0.380915599 0.321992981 0.287110259 0.272536584 1 19.56336746 -1.484309917 3.314006108 1.01270435 0.348670017 0.884556316 0.070622968 44975380.09 58455649.23 5250850.206 0.018451917 0.032786124 1.484309917 -0.664034332 LLDCLLESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLDCLLESHR 10 0 Q9Y6D6;E5RIF2;E5RHL7;E5RHZ1 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 ;; 132.78 0.0002146 372481000 170774 300061 245512 288837 359587 369257 231509 238818 224743 451383 FALSE TRUE 177516.2894 351594.1426 251910.2444 345968.0965 298464.5302 283502.6579 213362.7196 235617.0353 216654.5433 539822.8566 0.328841744 0.651313923 0.466653535 0.640891901 0.552893466 0.525177203 0.395245805 0.436471025 0.401343775 1 19.04212654 -1.433752495 3.467972705 1.005495613 0.49215204 0.700990595 0.10014689 48020708.05 64235565.2 2574440.074 0.023636558 0.036833883 1.433752495 -0.513343573 LLDDAMAADKSDEWFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDDAMAADKSDEWFAK 17 1 Q9HC38-2;F6TLX2;Q9HC38;I3L1I0 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 211.99 1.80E-12 1899100000 2473800 1596890 2089280 1528160 2868800 2669800 2417380 2084970 2387400 1635010 FALSE TRUE 2571467.534 1871143.435 2143728.353 1830425.487 2381162.401 2049779.411 2227899.439 2057024.387 2301477.94 1955358.905 1.315087234 0.95693094 1.096334973 0.936107168 1.217762322 1.048288069 1.139381334 1.051993259 1.177010488 1 20.89900201 -1.346506988 0.006433934 1.12E-05 2.11682612 0.042016789 0.111407684 77030.98088 84.18766858 14452.93186 13261.95512 0.045029074 1.346506988 2.116814901 LLDDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 180.15 0.0016069 396612400 885737 1109170 1018239 988634 1310484 1325084 1051527 1091019 1004855 1353945 FALSE TRUE 920706.5807 1299661.319 1044775.145 1184182.854 1087728.398 1017353.323 969105.5661 1076395.675 968690.4648 1619224.6 0.568609556 0.802644253 0.645231764 0.731327115 0.671758815 0.628296607 0.59849978 0.664759957 0.598243422 1 20.62687168 -1.944664196 2.507522005 1.246862902 0.660195052 0.712494806 0.065406217 8693552.536 4651964.204 12537389.53 0.015097283 0.011358888 1.944664196 -0.58666785 LLDDVSFHPCIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDDVSFHPCIR 12 0 Q9Y2T2 Q9Y2T2 AP3M1 AP-3 complex subunit mu-1 0 129.84 0.00022713 159050000 52136 110840 103490 124320 133820 148460 110680 109750 120960 143560 FALSE TRUE 54194.36954 129875.9078 106187.0344 148910.1249 111073.3242 113982.4149 102004.6124 108278.9808 116606.6732 171687.8334 0.315656436 0.756465413 0.618488989 0.867330678 0.646949303 0.663893374 0.594128369 0.630673581 0.679178431 1 17.38942828 0.774211733 4.358429312 0.999997569 0.646259842 0.400699735 0.132048983 3.544296051 67.65523661 0.118889562 0.03022945 5.945819671 -0.774211733 -0.353737727 LLDEDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDEDEIR 8 0 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 85.161 0.043476 0 198990 167900 174730 178310 213640 229790 198690 156920 175890 202000 FALSE TRUE 206846.2789 196735.5189 179283.6073 213579.1858 177325.5491 176424.755 183116.1586 154816.7441 169559.7533 241578.0325 0.856229669 0.814376692 0.74213539 0.884100196 0.734030107 0.730301316 0.758000041 0.640856052 0.70188399 1 17.88212975 3.199366925 23.91590813 0.734756968 0.817645559 0.0550083 0.096140486 184.1592375 112372.6535 0.026312015 0.031449543 1582.584563 -3.199366925 0.082888591 LLDEEEATDNDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;;;;; 279.3 5.59E-32 3078310000 1253150 1446840 1433450 1345930 1605990 1727870 1440950 1424510 1443960 1427580 FALSE TRUE 1302625.33 1695323.515 1470806.885 1612150.937 1333004.393 1326598.379 1328004.574 1405416.773 1391992.162 1707286.968 0.762979718 0.992992711 0.861487794 0.944276485 0.780773483 0.777021323 0.777844966 0.823187197 0.815324071 1 20.70327414 3.23221557 24.99722409 0.814736813 0.895692189 0.100643857 0.083031053 241.6332533 951948.587 0.02191326 0.026792531 1706.929446 -3.23221557 0.080955377 LLDEVFFSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 173.37 7.98E-06 169736000 240078 184415 220929 215161 303837 316934 290795 241066 280658 200551 FALSE TRUE 249556.4648 216086.8417 226686.5912 257719.2036 252190.8953 243330.8817 268001.728 237834.9046 270557.1734 239845.1287 1.040490029 0.900943217 0.945137358 1.074523402 1.05147391 1.014533349 1.117394919 0.991618658 1.128049483 1 17.87174361 3.742752693 24.9842774 1.052074133 0.956065497 0.380131048 0.053483336 331.2189523 1974015.048 0.012872883 0.022183311 5530.350957 -3.742752693 -0.096008636 LLDGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDGKR 6 1 Q68DA7-5;A0A5F9ZHS8;H0YM30;Q68DA7;H0YLM7 Q68DA7-5 FMN1 Formin-1 0 ; 102.98 0.056243 1787120000 3379600 2841100 3294200 2692400 4429000 3821100 3543700 3309600 3591800 3030000 FALSE TRUE 3513029.218 3329036.824 3380049.558 3224948.684 3676160.162 2933707.434 3265935.534 3265240.225 3462531.82 3623670.487 0.969467072 0.918691927 0.932769569 0.889967423 1.014485223 0.809595532 0.901278288 0.901086409 0.955531644 1 21.78902034 2.764951396 24.99981059 0.905950458 0.939865123 0.064479135 0.054832695 1990.51376 1885598.843 0.015952952 0.016915566 582.0380758 -2.764951396 0.033914665 LLDGNLLDGQAEVFGS(ph)DDDHIQFVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLDGNLLDGQAEVFGSDDDHIQFVQK 26 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK;LLDGNLLDGQAEVFGS(1)DDDHIQFVQK 299.96 9.22E-71 661683000 436009 361751 449573 392952 515539 552020 549610 462803 493573 376641 TRUE FALSE 453222.972 423878.9202 461289.2417 470676.7328 427907.8649 423821.7209 506530.1321 456599.8828 475809.4041 450436.5927 1.006185952 0.941040153 1.024093622 1.044934493 0.949984686 0.940913167 1.124531488 1.013682925 1.056329374 1 18.78096451 2.257508781 24.99987062 1.048578932 0.985523156 0.329260426 0.044813655 288.2082084 380255.8761 0.015457795 0.012912965 180.9292491 -2.257508781 -0.063055776 LLDGNLLDGQAEVFGSDDDHIQFVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDGNLLDGQAEVFGSDDDHIQFVQK 26 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 0 114.57 0.0013671 42960000 23867 20167 25192 21855 24776 32568 28450 22875 26532 20237 FALSE TRUE 24809.28759 23630.52537 25848.52422 26177.85377 20564.58437 25004.57557 26220.01466 22568.39804 25577.1185 24202.05269 1.025090223 0.976385172 1.068030243 1.081637748 0.84970414 1.03315929 1.083379786 0.932499335 1.056816082 1 14.56284179 LLDHMAPPPVADQAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 LLDHMAPPPVADQASPR 17 0 A0A0C4DFS6;Q9C004 A0A0C4DFS6 SPRY4 Protein sprouty homolog 4 1 LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR;LLDHMAPPPVADQAS(1)PR 157.28 2.04E-08 5138855000 2882534 2831835 2711422 3315925 2801401 3412912 2837685 2684082 2492507 2419287 TRUE FALSE 2996338.668 3318180.633 2782083.885 3971805.068 2325219.859 2620314.911 2615259.835 2648106.271 2402802.16 2893299.968 1.035612865 1.14684985 0.961560818 1.372759518 0.803656684 0.905649238 0.903902072 0.915254658 0.830471153 1 21.46428447 3.20610859 24.99998403 0.892110904 1.118483374 0.5239356 0.11003415 145.3844352 111999.0176 0.029548136 0.035319261 1607.343101 -3.20610859 0.22637247 LLDIACWIHHK ddPTM_MDA-MB-175_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 29457000000 8035600 7906800 7934500 7330600 12230000 11405000 9910500 8807300 8548700 11457400 FALSE TRUE 8352851.693 9264731.394 8141279.588 8780570.8 10151148.97 8756361.594 9133689.114 8689252.549 8241033.957 13702258.16 0.609596724 0.676146317 0.59415605 0.640811952 0.740837667 0.639045148 0.666582764 0.634147485 0.601436191 1 23.70791034 -1.822270891 2.868457069 1.109179551 0.646792246 0.872685179 0.040699861 9538646.603 8361823.702 7246055.524 0.009886636 0.015056676 1.822270891 -0.462387305 LLDLS(ph)SGDLLSEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDLSSGDLLSEVER 15 0 A0A0A0MSE4;A0A0A0MS79;O14513-2;O14513 A0A0A0MSE4 NCKAP5 Nck-associated protein 5 1 LLDLS(0.972)S(0.027)GDLLS(0.001)EVER 72.175 0.043559 4336100 5397 5190.4 7444.2 5512.4 7074.9 8665.2 4010.7 6304.7 5680 5679.4 TRUE FALSE 5610.077727 6081.810824 7638.201967 6602.736267 5872.311025 6652.838622 3696.330854 6220.195809 5475.57791 6792.169691 0.82596254 0.895415029 1.124559944 0.972110028 0.864570718 0.979486515 0.544204727 0.915789224 0.806160352 1 12.72965679 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 LLDLSDSTSVAS(1)FPSADETDGNLPESR 202.91 2.58E-25 70279000 35412 40535 39898 41220 50980 62426 49264 45354 49235 48710 TRUE FALSE 36810.0931 47496.57093 40937.77466 49373.19297 42314.43781 47928.50758 45402.55895 44746.10381 47463.04197 58253.79189 0.631891795 0.8153387 0.702748668 0.84755329 0.726380832 0.822753438 0.779392336 0.768123454 0.814763133 1 15.83006434 -5 0.180724351 1.947534795 0.721477247 0.63147513 0.05661714 81.65101263 0.787501703 27.761641 0.159036342 1.00E-05 5 -1.226057548 LLDPEDISVDHPDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLDPEDISVDHPDEK 15 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;;; 261.35 6.05E-25 1392666000 1797080 1416551 1699770 1361370 1834090 1968070 1935260 1813060 1981090 1133659 FALSE TRUE 1868030.106 1659832.615 1744067.403 1630644.923 1522332.037 1511015.569 1783569.264 1788758.896 1909790.958 1355777.776 1.377829125 1.224265986 1.286396217 1.202737611 1.122847759 1.114500913 1.315532159 1.319359948 1.408631261 1 20.3706893 4.741277814 23.42582839 1.234735178 1.377829253 0.135896394 0.113933025 233.7208799 2014696.685 0.027379472 0.185910419 55116.01552 -4.741277814 0.143094076 LLDPS(ph)SPLALALSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDPSSPLALALSAR 15 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LLDPS(0.5)S(0.5)PLALALSAR;LLDPS(0.551)S(0.449)PLALALSAR 97.45 0.0034713 75930000 241340 209697 235784 217175 286563 284844 228280 242702 250159 246197 TRUE FALSE 250868.2896 245710.8285 241928.7247 260131.5668 237853.1236 218693.2979 210386.8171 239448.9767 241155.8265 294434.5884 0.852034032 0.83451754 0.82167223 0.883495272 0.807830102 0.742756817 0.714545184 0.813250162 0.819047204 1 18.16758764 3.022161573 22.85614261 0.796216412 0.845167082 0.002022796 0.073517949 216.8826461 223675.678 0.020150963 0.024082091 1052.353313 -3.022161573 0.04895067 LLDRDACDTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDRDACDTVR 11 1 Q9NZL4;Q9NZL4-3;Q9NZL4-2;K7EN20;K7EL16 Q9NZL4 HSPBP1 Hsp70-binding protein 1 0 130.1 0.00021088 266930000 163840 230110 182160 188740 208430 266120 170250 184710 181170 256650 FALSE TRUE 170308.5297 269629.6025 186907.2392 226072.2087 173001.143 204317.6631 156905.3601 182234.2646 174649.7271 306935.6536 0.55486721 0.878456443 0.608946002 0.736545937 0.563639776 0.66566937 0.511199524 0.593721395 0.569010882 1 18.22757671 -1.051814436 4.682152442 1.00001207 0.631959165 0.540504909 0.101972299 1.39E-05 2.82E-06 0.096673306 0.022785289 0.088753515 1.051814436 -0.368052905 LLDRS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDRSPSR 8 1 A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1;A0A1B0GTX4 A0A096LNR9 CDKL5 Cyclin-dependent kinase-like 5 1 LLDRS(1)PSR;LLDRS(0.997)PS(0.003)R 117.52 0.0012495 175834000 109525 136107 126267 124263 135403 154300 123845 126194 121261 147909 TRUE FALSE 113849.1316 159482.3185 129557.6217 148841.8505 112387.2464 118466.1634 114137.7053 124502.5758 116896.8403 176888.9367 0.643619289 0.901595778 0.732423543 0.841442395 0.635354865 0.669720592 0.645250672 0.70384603 0.660848793 1 17.43248429 -1.167816931 3.645518024 1.000257767 0.716953726 0.50191568 0.085180759 29981942.78 52368216.41 92115.33837 0.020663503 0.067949 1.167816931 -0.283304041 LLDSDQELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLDSDQELYR 10 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 0 143.03 0.011409 0 124040 162070 171950 158020 190030 205620 159550 159320 161690 183460 FALSE TRUE 128937.195 189904.2618 176431.1583 189275.8844 157728.7685 157867.8712 147044.0541 157184.576 155870.8085 219405.4744 0.587666262 0.865540216 0.80413289 0.862676216 0.718891672 0.719525671 0.670193187 0.716411368 0.710423516 1 17.74324 -1.538334283 5.765590075 1.000560841 0.742596329 0.482623248 0.080858874 0.000585122 4.69E-05 0.078586373 0.018483743 0.028951143 1.538334283 -0.257964511 LLDSSTVTHLFK ddPTM_MDA-MB-175_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 ; 210.91 3.80E-08 3062600000 4087000 3891100 4704000 3988900 6336400 5958200 5899500 4733100 5082000 4723500 FALSE TRUE 4248357.916 4559366.156 4826590.104 4777892.514 5259340.991 4574498.347 5437081.775 4669660.536 4899099.813 5648979.388 0.752057606 0.807113258 0.854418077 0.845797477 0.931024992 0.809792005 0.962489222 0.826637914 0.867253972 1 22.42955881 7.99999992 0.031737889 1.444853481 4.30E-10 0.516434302 0.050718758 1043.90842 2.536933536 35.83955301 91.58504368 99999981.56 -7.99999992 -1.44485348 LLDSVEQDFHLEIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDSVEQDFHLEIAK 15 0 Q6IBS0;H0Y858;H7C5I2;Q9NR96-4 Q6IBS0 TWF2 Twinfilin-2 0 ; 155.22 2.34E-06 90135000 157092 143971 171131 139683 213710 216580 198201 169448 193856 159824 FALSE TRUE 163294.1135 168696.8993 175590.8144 167311.8805 177383.6505 166282.5773 182665.4877 167176.8267 186879.1604 191138.4528 0.854323717 0.882590064 0.918657716 0.875343909 0.928037493 0.869958791 0.95567106 0.874637334 0.977716193 1 17.54425852 -5 0.098174167 1.338443709 0.828120386 0.558663031 0.031819505 137.291111 0.921314715 9.387761757 0.523392979 1.00E-05 5 -0.510323323 LLDTVDDMLANDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDTVDDMLANDIAR 15 0 A0A024R571;Q9H4M9;C9J2Z4 A0A024R571 EHD1 EH domain-containing protein 1 0 ; 179.02 1.60E-06 23807000 20707.6 26750 23505 26590 24826.9 30793 22659 23924 23822 24148 FALSE TRUE 21525.15204 31344.10441 24117.55961 31849.42264 20606.83241 23641.79242 20882.92837 23603.33791 22964.65087 28879.33826 0.745347828 1.085347044 0.83511469 1.102844613 0.713549328 0.818640379 0.723109657 0.817308821 0.795193112 1 14.81775006 3.219345903 24.99998518 0.797726413 0.944744676 0.209360828 0.122856778 307.5240592 400114.1688 0.032149599 0.038481181 1657.08926 -3.219345903 0.147018263 LLDVVHPAAK ddPTM_MDA-MB-175_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 1475620000 4438700 3696900 4434200 3811800 5461800 5499300 4924600 4524800 4747300 4012100 FALSE TRUE 4613943.303 4331813.817 4549758.895 4565762.663 4533405.187 4222170.918 4538596.984 4464152.457 4576445.6 4798194.179 0.961599954 0.902800857 0.94822317 0.951558543 0.944814865 0.87994999 0.945896897 0.930381783 0.953784993 1 22.19406011 0.853510578 2.196793931 0.999987799 0.932164138 0.42952864 0.023355503 0.4976178 4.612392009 0.021390232 0.005847807 7.136915879 -0.853510578 -0.067823661 LLDWLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDWLVDR 8 0 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 ; 117.04 0.0050165 77660000 173428 189145 189363 214836 200051 243270 235120 203348 168424 173992 FALSE TRUE 180275.0714 221629.1824 194297.9553 257329.9196 166046.4025 186774.2293 216690.68 200622.4527 162362.4531 208082.4011 0.866363856 1.065102965 0.93375487 1.236673155 0.797983883 0.897597434 1.041369567 0.964149066 0.780279602 1 17.66679543 LLDWLVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLDWLVDRR 9 1 J3QQY1;Q96JB5;J3KRI2;J3KRK4;J3KS63;J3QS62;Q96JB5-4;J3QL95 J3QQY1 CDK5RAP3 CDK5 regulatory subunit-associated protein 3 0 ; 157.66 0.00010904 176246000 208840 245210 221770 212640 345620 290800 236400 237640 208020 315370 FALSE TRUE 217085.1645 287322.91 227549.5084 254699.5573 286871.6359 223266.1071 217870.3503 234454.8245 200533.4008 377160.7134 0.575577351 0.761804981 0.603322404 0.675307762 0.760608477 0.591965439 0.577659185 0.621631088 0.531692177 1 18.52481988 -1.244598527 5.192697796 1.00004345 0.636452282 0.691043849 0.073533128 3.64E-05 5.30E-06 0.070121489 0.016525823 0.056937904 1.244598527 -0.363591167 LLEAFTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEAFTER 8 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 0 96.492 0.020712 18845000 24020 24157 23997 26395 32363 35394 28365 26606 24027 23250 FALSE TRUE 24968.32815 28305.77683 24622.38153 31615.85222 26861.94882 27174.2799 26141.67718 26249.39009 23162.27296 27805.39235 0.897967122 1.017995951 0.885525413 1.13704032 0.966069764 0.977302516 0.940165737 0.94403955 0.833013707 1 14.76307707 2.049685962 1.829042231 0.918205802 0.985200497 0.098762417 0.07523813 0.744655694 4.703578895 0.042227321 0.022307171 112.1207416 -2.049685962 0.066994696 LLEAHEEQNVDSYTESVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEAHEEQNVDSYTESVK 18 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 258.8 1.13E-30 210436000 329140 250990 303060 293290 352140 396700 437160 307710 327530 221752 FALSE TRUE 342134.7014 294095.5801 310957.9926 351301.8866 292283.3686 304572.437 402894.2569 303585.6508 315742.2593 265200.0587 1.290100398 1.108957447 1.172541191 1.324667454 1.102124072 1.148462932 1.519208777 1.144742019 1.190581408 1 18.01672157 0.75594546 2.014850566 1.00067861 1.227365485 0.242722969 0.119943121 1.364171241 8.69850408 0.111861248 0.03089162 5.700926739 -0.75594546 0.226686875 LLEAHEEQNVDSYTESVKEYDSISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEAHEEQNVDSYTESVKEYDSISR 25 1 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 208.65 1.61E-25 308090000 268770 223320 289140 194350 419550 399150 231760 254020 328970 216830 FALSE TRUE 279381.2471 261673.4728 296675.2259 232791.8499 348235.0409 306453.4617 213594.0456 250615.2774 317130.434 259313.687 1.0773872 1.00910012 1.144078546 0.897722957 1.342910376 1.181786682 0.823689825 0.966456033 1.222960645 1 17.98433883 -1.21927674 5.594594242 0.99999735 1.061820851 0.015932903 0.148958458 4.97E-06 6.93E-07 0.14545038 0.034281514 0.060356391 1.21927674 0.061823502 LLEAQIATGGIIDPEESHRLPVEVAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEAQIATGGIIDPEESHRLPVEVAYK 27 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 238.42 2.59E-45 478130000 299100 259530 355790 297720 397810 439240 410730 352010 364360 266890 FALSE TRUE 310908.699 304102.2586 365062.1797 356608.1274 330190.3983 337233.1667 378535.9094 347291.8817 351246.7548 319181.9856 0.974079719 0.952755081 1.143743056 1.117256435 1.034489455 1.056554511 1.185956371 1.088068555 1.100459207 1 18.2840197 4.248459289 24.99967276 1.096232971 0.963417328 0.50024344 0.050703857 150.7618843 380749.9884 0.012058536 0.032187149 17719.81933 -4.248459289 -0.132815644 LLEAQIATGGIIDPVHSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 128.14 1.27E-05 181791000 99928.1 130196 127251 147743 120733 146156 122802 134440 126548 122597.8 FALSE TRUE 103873.3385 152556.1502 130567.2656 176966.1244 100210.8478 112213.484 113176.4584 132638.0517 121993.5622 146618.4916 0.708460013 1.040497338 0.890523863 1.206983665 0.68348028 0.765343326 0.771911217 0.904647499 0.832047587 1 17.16170754 3.203930267 24.99999855 0.820778229 0.962173663 0.180289466 0.141125618 291.2965995 210289.1415 0.039285249 0.046956815 1599.301214 -3.203930267 0.141395434 LLEAQIATGGVIDPVHSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 216.17 2.25E-19 620279000 500976 550386 553842 575444 560802 659030 639071 586219 548192 559244 FALSE TRUE 520754.9193 644910.5141 568275.5775 689265.1057 465477.0764 505980.2702 588978.9451 578361.6932 528462.677 668817.1544 0.778620757 0.964255342 0.849672551 1.030573306 0.6959706 0.756530042 0.880627749 0.864753078 0.790145219 1 19.35125233 6.79210519 11.40436772 0.858245301 0.35626805 0 0.104548096 0 0 0.022071871 0 6195911.276 -6.79210519 -0.501977251 LLEAQSHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEAQSHFR 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A1B0GUH3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 200.56 2.29E-05 456980000 215540 368670 225100 214610 366690 354810 215220 233750 184244 497750 FALSE TRUE 224049.6856 431986.2046 230966.2909 257059.2175 304360.1648 272410.7547 198350.494 230616.9636 177613.0944 595274.5825 0.3763804 0.72569234 0.387999585 0.431833015 0.511293735 0.457622016 0.333208405 0.387412751 0.298371709 1 19.18319577 -1.079305085 4.911024952 1.000016958 0.436450751 0.692502469 0.113056272 2.10E-05 3.94E-06 0.109497757 0.025808093 0.083309574 1.079305085 -0.563566207 LLEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEASR 6 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 129.2 0.037913 3260400000 1741820 2143900 1897320 2112300 2480600 2567400 1980210 1947270 1874980 2584000 FALSE TRUE 1810588.399 2512098.148 1946765.718 2530106.635 2058948.498 1971160.259 1824995.966 1921170.031 1807499.836 3090285.326 0.585896837 0.812901685 0.629963098 0.818729136 0.666264853 0.637857043 0.59055905 0.621680469 0.584897395 1 21.55930862 -1.045109153 4.888090346 1.000007255 0.662555674 0.605292117 0.082122964 6.46E-06 1.26E-06 0.07915849 0.018657434 0.090134457 1.045109153 -0.337451581 LLEDFGDGGAFPEIHVAQYPLDMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLEDFGDGGAFPEIHVAQYPLDMGR 25 0 Q13573;G3V3A4;G3V5R3 Q13573 SNW1 SNW domain-containing protein 1 0 ;; 182.39 2.23E-17 300996000 145997 177911 190172 182932 192537 199936 188949 195039 189838 213957 FALSE TRUE 151761.0743 208465.8303 195128.0385 219115.4036 159809.6295 153503.8941 174138.6837 192424.8212 183005.7675 255877.7777 0.593099861 0.814708617 0.762582981 0.856328383 0.624554547 0.599911002 0.680554151 0.752018495 0.715207741 1 17.96509533 0.00570378 1.29139089 1.000718504 0.71374894 0.51425316 0.084227485 12.09391228 14.57088771 0.112566436 0.024616039 1.013220062 -0.00570378 -0.286969564 LLEDFLQEGEEPDEDDAYQVLSTLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEDFLQEGEEPDEDDAYQVLSTLKR 26 1 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 0 ; 162.82 2.50E-11 20345000 19853.5 27012 25626 18495.4 28102 33601 31067 27316 29653 29236 FALSE TRUE 20637.33151 31651.10088 26293.83461 22153.73492 23325.23208 25797.67698 28631.88736 26949.8737 28585.79432 34964.23444 0.590241195 0.905242211 0.752020887 0.633611325 0.667116911 0.737830454 0.818890727 0.770784035 0.817572436 1 15.0935923 0.650831326 0.624255939 1.004592268 0.720953077 0.507250963 0.082670067 1.131911226 0.852123747 0.093839329 0.03416723 4.475394527 -0.650831326 -0.283639191 LLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 LLEDGEDFNLGDALDS(0.444)S(0.278)NS(0.278)MQTIQK 183.42 1.33E-17 15753000 14931 12666 19947 16180 18721 19430 19780 17038 21593 16017 TRUE FALSE 15520.48741 14841.28697 20466.83521 19380.35571 15538.81111 14917.67696 18229.59191 16809.63348 20815.87215 19155.22449 0.810248265 0.774790553 1.068472741 1.011752993 0.811204855 0.778778499 0.951677279 0.877548237 1.086694242 1 14.22545031 1.245905691 24.90792615 1.043347136 0.888820553 0.300492488 0.09619417 187.3514752 635345.4008 0.070405135 0.024551732 17.61593466 -1.245905691 -0.154526582 LLEDGEDFNLGDALDSSNSMQTIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 282.37 2.35E-53 172495000 120924 97207 111349 96724 123097 132510 125576 109305 127393 90840 FALSE TRUE 125698.1729 113901.5461 114250.8464 115855.7185 102173.0159 101736.5607 115733.025 107839.9453 122808.1508 108638.3588 1.157033062 1.04844686 1.051662117 1.066434727 0.940487477 0.936469971 1.065305352 0.992650722 1.130430837 1 16.72917406 5.821383487 0.913121677 1.015010055 1.946414001 0.344025745 0.056038126 14.56715449 2.09837096 0.017522684 21.37157921 662801.506 -5.821383487 0.931403947 LLEDS(ph)EES(ph)SEETVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEDSEESSEETVSR 15 0 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 LLEDS(1)EES(0.984)S(0.016)EETVSR;LLEDS(1)EES(0.991)S(0.009)EETVSR;LLEDS(1)EES(0.99)S(0.01)EETVSR;LLEDS(1)EES(0.989)S(0.011)EETVSR 193.32 1.43E-07 2512600000 1323960 1444220 1402430 1290700 1560620 1735050 1473120 1374430 1407680 1342320 TRUE FALSE 1376230.963 1692253.551 1438978.478 1545996.608 1295346.37 1332110.932 1357653.005 1356008.014 1357017.872 1605321.904 0.857292833 1.054152159 0.896380019 0.963044611 0.806907553 0.82980923 0.845720103 0.844695392 0.84532446 1 20.61443119 3.249246911 24.9998502 0.851249911 0.947367235 0.239608029 0.068573386 239.6964821 560749.9591 0.01740228 0.023328753 1775.198455 -3.249246911 0.096117324 LLEEALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLEEALLR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ;; 107.66 0.0092114 64840000 89957 121893 141620 136273 156137 149934 135307 131636 129614 146916 FALSE TRUE 93508.57182 142827.1746 145310.7335 163227.3927 129596.8885 115114.1008 124701.2838 129871.6347 124949.2175 175701.3773 0.532201701 0.812897296 0.82703241 0.929004628 0.737597454 0.655169029 0.709734242 0.739161165 0.71114535 1 17.42276598 -1.033782273 4.803414221 1.000004369 0.745445414 0.375667856 0.100536437 6.32E-06 1.27E-06 0.098203064 0.023146155 0.092516187 1.033782273 -0.254558955 LLEEDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEEDVKR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 99.139 0.011265 205651000 240390 171211 198595 151705 260550 216996 222676 191020 212182 160074 FALSE TRUE 249880.7828 200615.1574 203770.5488 181711.7962 216261.8041 166601.9676 205222.0733 188459.6893 204545.6113 191437.4355 1.305286932 1.047941104 1.064423728 0.949196774 1.129673533 0.870268488 1.072005968 0.98444533 1.068472374 1 17.54651345 5.138809721 1.54252846 1.01243911 1.789884526 0.603415094 0.069504624 2.029642551 1.98355423 0.016524385 3.235117973 137660.6198 -5.138809721 0.777445415 LLEEGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEEGVLR 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 100.45 0.014179 47096000 58043 71071 66955 70890 74564 84142 73088 63295 64196 81704 FALSE TRUE 60334.58246 83276.89139 68699.9023 84911.83041 61889.63791 64601.29568 67359.17158 62446.63405 61885.5985 97712.33448 0.617471507 0.852265907 0.703083215 0.868998073 0.633386135 0.661137573 0.689362013 0.639086502 0.633344795 1 16.57625307 -1.00272031 4.527619653 1.00000912 0.701251037 0.526947766 0.085322152 7.81E-06 1.72E-06 0.082101631 0.01935095 0.099375583 1.00272031 -0.298758083 LLEEHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEEHAK 7 0 P51572;P51572-2;A0A2R8Y5M6 P51572 BCAP31 B-cell receptor-associated protein 31 0 ; 117.17 0.0052914 263730000 519700 506700 462500 640310 684560 866210 609140 515510 569650 579330 FALSE TRUE 540218.1573 593721.7834 474553.1299 766961.4069 568198.7357 665045.855 561394.0151 508600.4317 549148.4078 692838.6216 0.779717153 0.856940945 0.684940353 1.106984199 0.820102572 0.959885656 0.810281063 0.734082102 0.792606519 1 19.40215983 -0.470980895 7.495829521 0.999999999 0.836558398 0.154598321 0.113299861 0 0 0.107807022 0.025410358 0.338079709 0.470980895 -0.163441601 LLEELEEGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEELEEGQK 10 0 I3L0A0;Q13404;Q13404-7;Q13404-2;Q13404-1;Q13404-8;Q15819;E5RIF1;D6RG00;H0YBX6 I3L0A0 TMEM189-UBE2V1;UBE2V1;UBE2V2 Ubiquitin-conjugating enzyme E2 variant 1;Ubiquitin-conjugating enzyme E2 variant 2 0 141.88 8.55E-05 16018000 41718 28756 38495 33460 44065 47623 49303 35173 34315 21739 FALSE TRUE 43365.05885 33694.61931 39498.21132 40078.28813 36574.84704 36563.27998 45438.50203 34701.56347 33080.00985 25998.34083 1.667993321 1.296029602 1.519258924 1.541570995 1.406814661 1.406369746 1.747746224 1.334760695 1.272389268 1 14.66613194 1.053170318 1.796596838 1.008811753 1.496018698 0.59877399 0.128996006 0.220038358 1.438735504 0.114697747 0.03290917 11.30239075 -1.053170318 0.487206945 LLEELEEGQKGVGDGTVSWGLEDDEDMTLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 231.41 6.86E-36 315925000 206983 183551 229033 139869 281880 264796 176225 208466 251363 210171 FALSE TRUE 215154.8487 215074.4564 235001.7881 167534.6707 233966.1383 203301.142 162412.024 205671.8543 242316.4947 251349.9835 0.855997067 0.855677225 0.934958439 0.666539414 0.930838089 0.808836902 0.646158881 0.818268819 0.964060118 1 17.93933807 -1.126987384 8.047207934 1.000000019 0.823771258 0.197485748 0.101036961 2.90E-08 3.17E-09 0.095240542 0.022448409 0.074647044 1.126987384 -0.176228761 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 LLEENETEAVTVPTPS(0.997)PT(0.003)PVR;LLEENETEAVTVPT(0.001)PS(0.996)PT(0.003)PVR;LLEENETEAVTVPT(0.018)PS(0.977)PT(0.005)PVR;LLEENETEAVTVPTPS(0.998)PT(0.001)PVR;LLEENETEAVTVPTPS(0.998)PT(0.002)PVR;LLEENETEAVTVPT(0.21)PS(0.673)PT(0.117)PVR;LLEENETEAVTVPT(0.027)PS(0.97)PT(0.003)PVR;LLEENETEAVTVPT(0.008)PS(0.992)PTPVR 346.99 3.11E-95 5650820000 3133324 3618720 3534390 3562060 3826580 4251020 3526840 3619720 3474780 3844240 TRUE FALSE 3257030.051 4240207.01 3626499.107 4266624.836 3176139.298 3263785.03 3250397.065 3571203.574 3349723.347 4597445.226 0.70844347 0.922296363 0.788807463 0.92804256 0.690848752 0.70991276 0.707000716 0.776780016 0.728605385 1 22.13240096 5.042750248 16.27190814 0.791880337 0.294524183 0.059514705 0.10355389 39101144 397112578.5 0.023892326 590235444.6 110344.3874 -5.042750248 -0.497356153 LLEGEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 198.92 0.00030729 6640630000 3047790 3605630 3484690 3363300 3878760 4126560 3822110 3570820 3313120 3454440 FALSE TRUE 3168119.103 4224868.905 3575503.884 4028550.702 3219449.761 3168228.979 3522523.031 3522958.999 3193881.458 4131271.379 0.766862985 1.022655865 0.865473012 0.97513582 0.779287891 0.766889581 0.852648666 0.852754195 0.773098924 1 21.9781544 3.233490028 24.99999837 0.829626633 0.912750851 0.124921365 0.089020656 212.749853 1048940.825 0.023632956 0.029078296 1711.945867 -3.233490028 0.083124218 LLEIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEIVER 7 0 Q12792;Q12792-3;Q12792-4 Q12792 TWF1 Twinfilin-1 0 ;;; 130 0.0083885 242328000 335752 374498 371285 386706 413371 453845 397000 383028 367414 368063 FALSE TRUE 349007.7482 438815.1183 380960.9921 463195.2926 343106.3451 348446.3768 365882.1026 377894.1362 354190.8419 440177.8979 0.792878856 0.996904025 0.865470515 1.052291119 0.779471997 0.791603528 0.831214162 0.858503205 0.804653854 1 18.74772718 3.204968144 24.99995229 0.835501066 0.927500972 0.173334241 0.08716967 273.4408611 203497.5431 0.02330747 0.027859199 1603.127795 -3.204968144 0.091999906 LLEKIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEKIR 6 1 Q53EZ4;Q53EZ4-2 Q53EZ4 CEP55 Centrosomal protein of 55 kDa 0 ; 86.113 0.0492 569590000 695150 613240 736440 610500 1088620 1050230 872230 881540 953840 831510 FALSE TRUE 722595.0588 718559.1997 755632.2314 731255.0778 903576.7612 806329.9989 803862.3335 869724.3982 919511.4847 994428.4643 0.726643579 0.722585108 0.759865851 0.735352118 0.908639277 0.810847666 0.808366174 0.874597248 0.924663279 1 19.92350807 4.417723177 0.098906582 1.159129693 0.320457836 0.802109403 0.040499746 22.24771915 0.395464398 0.83784587 2.923418625 26165.14685 -4.417723177 -0.838671857 LLEKPYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEKPYVR 8 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 96.331 0.0082232 327570000 457900 409820 412190 426770 537050 532510 431310 445260 384820 377090 FALSE TRUE 475978.2456 480203.397 422932.01 511183.8322 445762.4328 408842.6228 397502.7952 439292.018 370970.4034 450973.5657 1.055445999 1.064814955 0.937819957 1.133511742 0.988444704 0.906577799 0.881432584 0.974097046 0.822598998 1 18.78268335 2.944248347 4.710366544 0.918605195 1.043539165 0.483741974 0.063657792 0.182097416 8.471752476 0.018576513 0.020268908 879.5253211 -2.944248347 0.12493397 LLELDPEHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLELDPEHQR 10 0 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 143.89 3.32E-05 209070000 304630 400340 327190 407890 378040 436380 328680 308770 309110 349870 FALSE TRUE 316657.0276 469095.2808 335716.8402 488569.4246 313780.8958 335037.3584 302917.2028 304631.4432 297985.1915 418420.3278 0.756791691 1.12111016 0.802343524 1.16765222 0.749917905 0.800719602 0.723954317 0.728051251 0.7121671 1 18.67459342 3.167511048 24.99994315 0.765963114 0.961947879 0.267460993 0.140550601 49.75267384 17505.29985 0.03687104 0.044069335 1470.655826 -3.167511048 0.195984765 LLELLGHYQESGSVIIFVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLELLGHYQESGSVIIFVDK 20 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;;;; 198.24 1.57E-21 54490400 133470 123716 141010 140973 154801 176613 182008 141079 162429 99554 FALSE TRUE 138739.4987 144963.2606 144684.8364 168857.0386 128487.9813 135597.3073 167741.7374 139188.0668 156583.212 119059.7002 1.165293533 1.217567828 1.215229302 1.418255197 1.079189525 1.138901804 1.408887617 1.169061122 1.315165515 1 16.86132564 -1.339672035 3.017474808 0.99760794 1.235771729 0.306770161 0.106604562 15200991.08 19114512.72 322983.3445 0.025945528 0.04574335 1.339672035 0.23816379 LLELLGHYQESGSVIIFVDKQEHADGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLELLGHYQESGSVIIFVDKQEHADGLLK 29 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 77.322 0.0031108 40304000 17298 13588 20782 13199 33176 23590 15377 25914 28418 16617 FALSE TRUE 17980.9384 15921.6333 21323.59599 15809.7228 27536.75537 18111.58001 14171.71056 25566.66522 27395.24173 19872.783 0.904802231 0.801177837 1.073005024 0.795546492 1.385651691 0.911376127 0.713121587 1.2865166 1.378530714 1 14.2785063 3.72805152 0.402150965 1.154080931 0.77687046 0.137424723 0.218551372 5.210666849 1.186706425 0.204982443 0.884390068 5346.277782 -3.72805152 -0.377210471 LLEMILNKPGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEMILNKPGLK 12 1 S4R3P0;P52895;B4DK69 S4R3P0 AKR1C2 Aldo-keto reductase family 1 member C2 0 117.79 0.00063414 117750000 213540 153330 203490 173630 263940 251240 206920 201350 257950 162250 FALSE TRUE 221970.7241 179663.2348 208793.1166 207973.4958 219075.5731 192893.3176 190701.0697 198651.2326 248666.4299 194039.781 1.143944416 0.925909284 1.07603253 1.071808547 1.129024017 0.994091606 0.982793676 1.023765496 1.281522936 1 17.56599293 LLEMNLMHAPQVADAILGNQMFTHYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEMNLMHAPQVADAILGNQMFTHYDR 27 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 252.8 5.00E-53 6861730000 865050 1000640 1091140 1054390 1211410 1176570 1032010 1006390 981250 1078840 FALSE TRUE 899202.842 1172492.136 1119576.005 1262945.195 1005494.961 903329.4486 951118.3595 992900.9882 945935.0042 1290218.042 0.696938667 0.90875503 0.867741706 0.978861831 0.779321733 0.700137046 0.737176453 0.769560613 0.733159027 1 20.29918347 3.033588181 24.9975151 0.766461164 0.868223324 0.100900316 0.102047966 299.6638376 223018.6083 0.02773559 0.033150243 1080.40897 -3.033588181 0.101762159 LLEPVDHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLEPVDHGK 9 0 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ;; 110.14 0.002336 244380000 408408 300151 356296 330175 414308 427125 466572 374206 393837 261343 FALSE TRUE 424532.2632 351699.5994 365581.3665 395482.6295 343884.0741 327931.6919 430000.8675 369190.3806 379662.8833 312548.1571 1.358293925 1.125265312 1.169680122 1.265349421 1.100259484 1.049219726 1.375790763 1.181227188 1.214734033 1 18.25371897 4.749456692 23.90445655 1.177818854 1.35829412 0.234253738 0.102581519 1319.501334 2894694.457 0.02352603 0.337200369 56163.82694 -4.749456692 0.180475266 LLEQALVIEEQLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 190.41 9.73E-07 337480000 200660 227090 248040 218590 272090 294420 217480 241570 244410 253930 FALSE TRUE 208582.2117 266090.941 254504.1262 261826.4496 225840.239 226045.417 200433.3493 238332.1493 235613.7318 303682.7217 0.686842539 0.876213633 0.83805929 0.862171045 0.743671677 0.74434731 0.660009065 0.784806419 0.775854914 1 18.2122053 -1.108626738 2.896549467 1.00058686 0.775900551 0.504639986 0.066966269 2299194.916 3137201.352 12777.15352 0.017620353 0.077870554 1.108626738 -0.224686309 LLEQGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 199.65 0.00086569 9784895000 3101050 3729277 3478120 3908052 4409214 4514451 3419244 3437372 3175960 4557178 FALSE TRUE 3223481.849 4369751.315 3568762.665 4681053.021 3659737.379 3466038.172 3151234.721 3391299.651 3061657.82 5450069.777 0.591456987 0.801778967 0.654810454 0.858897815 0.671502848 0.635962165 0.578200803 0.62224885 0.561764885 1 22.37784327 -1.038685291 4.996554995 1.000005254 0.665992969 0.550965448 0.090965648 5.45E-06 1.05E-06 0.090217179 0.021264059 0.091477589 1.038685291 -0.334012285 LLEQWEKDDDIEEGDLPEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEQWEKDDDIEEGDLPEHK 20 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 ;;; 224.97 3.26E-25 583660000 1310210 534257 786690 644360 1171420 1155950 1153280 766080 912110 403461 FALSE TRUE 1361938.103 626011.4838 807191.7877 771812.4848 972302.4468 887498.1311 1062882.9 755811.9507 879283.3393 482511.4582 2.822602612 1.297402317 1.67289662 1.599573381 2.015086751 1.839330685 2.202813803 1.56641244 1.822305614 1 18.88020368 0.272387915 0.974455066 0.995826716 1.85983695 0.305179734 0.396020689 4.040599362 4.370295794 0.394526604 0.114019386 1.872353793 -0.272387915 0.864010234 LLEQYKEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEQYKEESK 10 1 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 116.01 0.001046 764370000 1626570 988890 1394670 1137490 1886090 1720740 1768270 1427930 1485710 808720 FALSE TRUE 1690788.24 1158724.165 1431016.246 1362482.127 1565493.095 1321124.213 1629668.377 1408790.934 1432239.587 967173.2001 1.748175238 1.198052391 1.47958633 1.408726097 1.618627455 1.365964455 1.684980908 1.45660667 1.480851193 1 19.88341474 0.354436988 2.485624826 1.000000877 1.488814307 0.488111863 0.151575687 19.65955816 74.13006374 0.132701808 0.035398935 2.261710361 -0.354436988 0.48881343 LLEQYKEESKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLEQYKEESKK 11 2 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 138.94 2.65E-05 3314900000 1406800 504920 943340 458450 1397100 1118100 1290800 875490 1047600 375290 FALSE TRUE 1462341.55 591636.0823 967924.2154 549130.0417 1159621.441 858438.22 1189623.723 863755.4886 1009897.081 448820.8901 3.25818513 1.318200858 2.156593502 1.223494837 2.583706477 1.912652104 2.650553371 1.924499299 2.250111576 1 18.7757803 4.758195646 24.13437763 1.962440058 3.258187058 0.363006882 0.535837291 3054.183329 3753949.774 0.117702295 4.296353637 57305.41285 -4.758195646 1.295747 LLESDYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLESDYFR 8 0 Q96HE7;G3V3E6;G3V503 Q96HE7 ERO1L ERO1-like protein alpha 0 ; 83.753 0.041731 235270000 276300 422180 340010 360290 499730 499110 345670 350640 323960 521300 FALSE TRUE 287208.5374 494686.1309 348870.9399 431554.2866 414786.0731 383199.2666 318575.4822 345940.2443 312300.7429 623438.7541 0.460684446 0.793479917 0.559591359 0.69221601 0.665319681 0.614654229 0.510997239 0.554890504 0.500932515 1 19.24988831 -1.111793049 9.562849014 1.000000001 0.598257806 0.618511267 0.095443606 2.40E-09 2.79E-10 0.089615256 0.021122518 0.077304887 1.111793049 -0.401742195 LLESIFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLESIFHR 8 0 Q7Z7E8 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 117.04 0.0021563 123140000 37112 64654 61207 67009 76559 81239 67534 69412 62706 81673 FALSE TRUE 38577.21042 75757.82156 62802.1047 80263.1802 63545.52853 62372.47344 62240.50861 68481.64568 60449.22331 97675.26063 0.394953749 0.775609106 0.642968386 0.821734999 0.650579565 0.638569818 0.637218762 0.701115566 0.61887957 1 16.57570558 -1.689276227 2.762322027 1.046635418 0.663415763 0.482332618 0.107245231 18954705.49 17182317.18 6195449.111 0.025297421 0.020451434 1.689276227 -0.383219656 LLESIQQHS(ph)LDAVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLESIQQHSLDAVLAR 16 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 1 LLESIQQHS(1)LDAVLAR;LLESIQQHS(1)LDAVLAR;LLESIQQHS(1)LDAVLAR;LLESIQQHS(1)LDAVLAR 226.45 3.83E-15 358144000 270631 397768 362021 305697 357574 392576 386506 389648 384047 327480 TRUE FALSE 281315.7209 466081.5598 371455.5647 366162.9542 296793.6992 301406.1735 356210.6498 384425.4059 370225.2235 391643.436 0.718295508 1.190066057 0.948453441 0.934939592 0.757816095 0.769593323 0.909527946 0.981569894 0.945311958 1 18.57918125 -0.437737546 6.781018447 0.99999563 0.913494628 0.042683057 0.129182881 0 0 0.124373674 0.029315156 0.364974442 0.437737546 -0.086501002 LLESLQENHFQEDEQFLGAVMPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLESLQENHFQEDEQFLGAVMPR 23 0 P49903;P49903-2;P49903-4;Q5T5U6 P49903 SEPHS1 "Selenide, water dikinase 1" 0 118.51 0.00020906 48421000 16029 19962 15105 15394 22869 21423 17488 18335 16837 12812 FALSE TRUE 16661.8373 23390.31822 15498.64871 18438.88725 18981.73555 16447.83292 16117.24486 18089.24932 16231.03966 15322.2661 1.087426441 1.526557369 1.011511522 1.203404714 1.238833435 1.073459553 1.05188389 1.18058577 1.05931065 1 13.90334206 3.71065345 0.18192118 0.971615648 1.424885449 0.204441643 0.132994743 16.5629553 0.827782445 0.417271364 1.838751853 5136.336286 -3.71065345 0.453269801 LLETIDQLYLEYAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLETIDQLYLEYAKR 15 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H7C5W8;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 159.31 2.84E-06 47341000 47010 53132 53928 60293 56769 79974 77354 59910 57823 69426 FALSE TRUE 48865.9911 62257.00769 55333.40798 72218.77544 47119.42566 61401.25052 71290.79135 59107.00444 55741.96153 83028.69546 0.588543405 0.749825194 0.66643716 0.869805012 0.56750772 0.73951843 0.858628345 0.711886464 0.67135779 1 16.34132241 -5 0.26104766 2.801763375 0.697634212 0.453858308 0.094110415 177.5590132 1.742715518 171.857934 0.118236803 1.00E-05 5 -2.104129163 LLETTDRPDGHQNNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLETTDRPDGHQNNLR 16 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;;; 231.13 9.75E-16 5374020000 2521063 3036070 2884800 3242920 2869640 3377160 3020130 2831760 2852540 3088840 FALSE TRUE 2620596.514 3557491.405 2959980.258 3884359.897 2381859.618 2592865.771 2783404.319 2793804.889 2749877.643 3694039.059 0.709412237 0.963035677 0.801285588 1.051521068 0.644784633 0.701905348 0.753485352 0.756300852 0.744409466 1 21.81676769 5.051538898 14.88349799 0.809531381 0.123910601 0.055988072 0.129386719 2984143.406 24080212.91 0.030495091 58206277.53 112600.1316 -5.051538898 -0.68562078 LLEVEHPAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEVEHPAAK 10 0 P17987;E7ERF2;F5H136;F5GZI8;F5H676;F5H726 P17987 TCP1 T-complex protein 1 subunit alpha 0 ;;; 138.22 7.05E-05 3106910000 5859500 5031800 5735100 4883400 7215200 7185700 6641200 5978600 6282500 5196000 FALSE TRUE 6090837.585 5895972.508 5884561.417 5849321.945 5988762.881 5516930.075 6120645.39 5898466.646 6056394.052 6214056.717 0.980170903 0.948812149 0.946975814 0.941304885 0.963744484 0.887814567 0.984967738 0.949213519 0.974628062 1 22.56710398 0.989352827 1.199734461 0.999819833 0.947919734 0.283136392 0.025087416 0.621851017 1.845546452 0.022345935 0.006981187 9.757820555 -0.989352827 -0.051900099 LLEVQGSRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLEVQGSRPGK 11 1 P62136;E9PMD7 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit;Serine/threonine-protein phosphatase 0 ; 93.623 0.0083099 6009200000 761080 707810 740530 549780 964080 896230 739960 778480 752070 662790 FALSE TRUE 791128.0261 829370.8615 759828.8202 658524.8431 800206.026 688094.165 681960.0017 768045.7489 725003.1476 792651.0106 0.998078619 1.046325369 0.958591877 0.830787868 1.009531326 0.868092207 0.860353412 0.968958266 0.914656183 1 19.59632629 4.045196252 5.957774652 0.919259147 1.019406766 0.328244417 0.056827981 0.194887285 16.58869776 0.013494137 0.02947656 11096.76151 -4.045196252 0.100147619 LLEVSDDPQVLAVAAHDVGEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLEVSDDPQVLAVAAHDVGEYVR 23 0 G3V126;Q9UI12-2;Q9UI12 G3V126 ATP6V1H V-type proton ATPase subunit H 0 ;;; 266.09 4.28E-44 337286000 295826 355712 349494 367794 382111 439553 355879 337518 338226 373630 FALSE TRUE 307505.4389 416802.7689 358602.1008 440542.5554 317159.9087 337473.4772 327984.2741 332994.1233 326053.3123 446835.6449 0.688184666 0.932787645 0.802536917 0.985916322 0.709790976 0.755251917 0.734015466 0.745227305 0.729694052 1 18.76938475 3.194051048 24.99999745 0.760967404 0.854544256 0.086568258 0.107471632 232.2414347 130443.9096 0.028474201 0.034033355 1563.331389 -3.194051048 0.093576853 LLFEDWTYDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLFEDWTYDDFR 12 0 Q9BWS9-3;Q9BWS9;Q9BWS9-2 Q9BWS9-3 CHID1 Chitinase domain-containing protein 1 0 ;;;; 225.67 3.99E-11 259547000 347662 425727 394825 453659 474969 514637 394720 391418 392844 435407 FALSE TRUE 361387.9642 498842.3006 405114.4639 543391.3962 394233.939 395120.3561 363780.815 386171.6819 378705.6212 520716.6653 0.694020354 0.95799181 0.777994043 1.043545238 0.757098755 0.758801057 0.698615657 0.741615753 0.727277705 1 18.99013905 LLFEVFDENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 157.96 1.92E-05 49890000 60189.6 65068.3 68326 64108.9 79759 83526 71015.1 66092.1 66756.6 76215 FALSE TRUE 62565.93188 76243.27436 70106.63169 76789.44907 66201.59367 64128.35235 65448.7509 65206.2435 64354.04301 91147.87003 0.686422314 0.836478947 0.769152715 0.84247113 0.726309827 0.703563916 0.71805025 0.715389657 0.706040009 1 16.47592132 -0.965258354 4.733826635 1.000002251 0.745976732 0.6838114 0.052040089 1.83E-06 3.99E-07 0.052156041 0.012293141 0.10832823 0.965258354 -0.254025519 LLFGHSTEGDILELVDGHFDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLFGHSTEGDILELVDGHFDTK 22 0 Q9UHY7;A0A0C4DGY8;D6RA00;Q9UHY7-2 Q9UHY7 ENOPH1 Enolase-phosphatase E1 0 ;;; 284.88 3.44E-46 1270602000 498458 515070.9 623021 554549 824689 783792 664878 652938 740595 494181 FALSE TRUE 518137.5067 603530.3204 639257.4391 664237.137 684508.6584 601768.1865 612763.125 644186.4341 713941.1306 591006.3053 0.876703856 1.021191001 1.081642333 1.123908715 1.158208723 1.018209419 1.036813177 1.089982337 1.20800933 1 19.172814 4.696607422 2.005450895 1.091420073 0.825554205 0.539712883 0.05990691 0.506347641 2.362801295 0.015292474 0.239295723 49728.73622 -4.696607422 -0.265865869 LLGELLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLGELLLDR 9 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 ; 98.233 0.014314 54218400 121163 117524 125968 108432 160777 154616 145275 111462 125035 136625 FALSE TRUE 125946.6088 137707.8328 129250.8296 129879.526 133448.183 118708.7772 133887.9659 109968.0342 120535.0148 163394.0529 0.770815134 0.842795869 0.791037539 0.794885271 0.816726072 0.726518347 0.81941762 0.673023481 0.737695238 1 17.31799595 2.768504662 24.64414851 0.765647163 0.804305465 0 0.084691322 2031.662439 1672067.731 0.024227221 0.02569302 586.8196696 -2.768504662 0.038658302 LLGGQLGLEDFIFAHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLGGQLGLEDFIFAHVK 17 0 Q8TF65 Q8TF65 GIPC2 PDZ domain-containing protein GIPC2 0 ;;; 219.58 4.28E-15 599035700 614429 522605 708850 629220 807563 824359 882188 676223 777733 552088 FALSE TRUE 638687.1314 612358.3434 727323.2133 753677.838 670293.7297 632914.1155 813039.7994 667159.3368 749742.5413 660259.0732 0.967328064 0.927451614 1.101572463 1.141488044 1.015198059 0.958584503 1.231395118 1.010450842 1.135527813 1 19.3326727 4.240167314 24.99999347 1.075704702 0.947389804 0.296860874 0.078088053 46.75114756 727380.9681 0.018388276 0.045256849 17384.70453 -4.240167314 -0.128314898 LLGHEVEDVIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLGHEVEDVIIK 12 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 113.22 0.0011888 109010000 67932 58526 74912 54285 102370 105810 82378 69330 80270 82150 FALSE TRUE 70614.00781 68577.38523 76864.26826 65022.41098 84969.18397 81237.23107 75920.99711 68400.74475 77381.09838 98245.71964 0.71874895 0.698019064 0.782367604 0.661834543 0.864863979 0.82687807 0.772766461 0.696221118 0.78762819 1 16.58410693 -5 0.378719292 4.427757389 0.748434984 0.602741544 0.05958152 414.7581045 3.113497147 1167.289517 0.041565163 1.00E-05 5 -3.679322405 LLGHWEEAAHDLALACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLGHWEEAAHDLALACK 17 0 P50502;Q8IZP2;H7C3I1 P50502 ST13;ST13P4 Hsc70-interacting protein;Putative protein FAM10A4 0 ;;; 201.3 6.71E-12 5230516000 3909986 3336878 3776059 3597992 4679734 4926376 4546376 4206733 4424812 3751448 FALSE TRUE 4064355.266 3909960.839 3874466.2 4309664.079 3884274.486 3782299.834 4190019.169 4150348.625 4265563.88 4486472.41 0.905913354 0.87150003 0.863588549 0.96059079 0.86577474 0.843045379 0.933922866 0.925080608 0.950761197 1 22.09715011 1.251340418 1.001131339 0.997261925 0.8874256 0.546685704 0.032409961 0.370162314 0.781054517 0.030307815 0.010475795 17.83776416 -1.251340418 -0.109836326 LLGIFENQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LLGIFENQDR 10 0 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4 Q9NZJ9 NUDT4 Diphosphoinositol polyphosphate phosphohydrolase 2 0 ;;;;; 183.43 6.27E-05 607640000 504950 559165 541572 552627 611002 693090 549776 590511 546988 581465 FALSE TRUE 524885.8159 655197.2391 555685.8112 661934.9712 507144.0983 532130.3514 506683.1205 582596.1659 527302.0087 695391.9339 0.754805729 0.942198503 0.799097292 0.951887617 0.729292466 0.765223646 0.728629562 0.837795404 0.758280306 1 19.40746681 5.04020531 16.45581923 0.82408771 0.437006036 0.051050982 0.093773408 22459127.64 246779641.2 0.021213613 263194422.3 109699.6671 -5.04020531 -0.387081675 LLGLELALSS(ph)DAESAAGGPAGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLGLELALSSDAESAAGGPAGVR 23 0 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 LLGLELALS(0.376)S(0.622)DAES(0.002)AAGGPAGVR;LLGLELALS(0.03)S(0.97)DAESAAGGPAGVR 206.21 1.48E-24 41041000 94022 106180 94550 102058 109519 126649 96752 91365 89337 111432 TRUE FALSE 97734.06116 124415.589 97014.05067 122244.7678 90902.9995 97236.68913 89168.32543 90140.40162 86121.77882 133264.9669 0.733381499 0.933595617 0.72797865 0.917306105 0.682122253 0.729649295 0.669105523 0.676399835 0.646244702 1 17.02393804 4.177437373 24.99984548 0.739004978 0.833493074 0.048928849 0.1186622 141.0929673 57707.1494 0.028345677 0.061233715 15046.56524 -4.177437373 0.094488096 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 33 0 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 LLGPAPEDDGGHNDHSQPQASQDQDSHTLS(1)PQV;LLGPAPEDDGGHNDHSQPQASQDQDS(0.035)HT(0.019)LS(0.946)PQV;LLGPAPEDDGGHNDHSQPQASQDQDS(0.001)HT(0.005)LS(0.994)PQV 271.84 2.89E-73 750170000 228911 291836 258845 300247 270403 344558 266272 291833 264560 320013 TRUE FALSE 237948.583 341956.5628 265590.7133 359634.9605 224439.9946 264539.6263 245400.9049 287921.456 255038.5373 382713.4203 0.621740891 0.893505544 0.693967599 0.939697803 0.586444015 0.691221191 0.641213221 0.752316069 0.666395595 1 18.54590497 -1.078553446 4.310274148 1.000028432 0.725193109 0.373051078 0.108475601 44644470236 9543793201 13590739.24 0.0238664 0.083453884 1.078553446 -0.274835322 LLGQIVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLGQIVDR 8 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 75.692 0.087781 26890000 38470 44231 48610 43515 48046 54580 41321 49480 41461 55371 FALSE TRUE 39988.82531 51827.33018 49876.81653 52122.13712 39879.15808 41904.62217 38082.15205 48816.80153 39968.82671 66219.88731 0.603879392 0.782655065 0.753199961 0.787107004 0.602223285 0.632810231 0.575086331 0.737192459 0.603577389 1 16.01497694 -1.876151597 5.492430533 1.066724824 0.680466654 0.605754209 0.078484601 0.045774726 0.001032171 0.054244786 0.018097527 0.013299901 1.876151597 -0.38625817 LLGS(ph)LDEVVLLSPVPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLGSLDEVVLLSPVPELR 18 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 LLGS(0.994)LDEVVLLS(0.006)PVPELR;LLGS(1)LDEVVLLSPVPELR;LLGS(0.771)LDEVVLLS(0.229)PVPELR 244.05 4.20E-24 890323000 74138.1 96425 118411 99394 101640 128967 97555 97717 107397 94089 TRUE FALSE 77065.12944 112985.2437 121496.8879 119053.8365 84363.2691 99016.36876 89908.38419 96407.26345 103531.8029 112523.9381 0.684877642 1.004099622 1.079742586 1.058031194 0.749736194 0.87995826 0.79901562 0.856771146 0.920086914 1 16.77987242 3.243948792 24.99998452 0.856232454 0.968863934 0.110694002 0.119188764 241.6940189 1121400.576 0.033125731 0.043583157 1753.673712 -3.243948792 0.11263148 LLGS(ph)SEDLSSDSESHLPEEPAPLSPQQAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLGSSEDLSSDSESHLPEEPAPLSPQQAFR 30 0 C9JIE2;Q86TI0-2;Q86TI0;H0Y8P0;H0YA01;H7C380;H7C0Z7 C9JIE2 TBC1D1 TBC1 domain family member 1 1 LLGS(0.869)S(0.125)EDLS(0.003)S(0.003)DSESHLPEEPAPLSPQQAFR 128.33 7.25E-06 67473000 6166.4 14078 12505 17431 14426 18428 13232 14568 14640 11053 TRUE FALSE 6409.854233 16495.78699 12830.89057 20878.79977 11973.87367 14148.37628 12194.84126 14372.73979 14113.10926 13218.62373 0.484910863 1.247920156 0.970667661 1.579498759 0.905833612 1.070336562 0.922549996 1.08730985 1.067668583 1 13.69028436 4.747727647 24.54922918 1.093640934 0.484910452 0.489062324 0.186963215 782.3052517 2094949.044 0.042617752 0.520890728 55940.66787 -4.747727647 -0.608730483 LLGSENDTGS(ph)PDFYTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLGSENDTGSPDFYTPR 17 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 LLGSENDT(0.271)GS(0.729)PDFYTPR 190.25 3.24E-10 60821000 66935 84888 81226 70430 94613 108900 83487 86126 84189 93306 TRUE FALSE 69577.64549 99466.85366 83342.81629 84360.84379 78530.71605 83609.6254 76943.07079 84971.62184 81159.05434 111587.5242 0.623525309 0.891379698 0.746882923 0.756006053 0.703758925 0.749273953 0.689531122 0.761479587 0.727312976 1 16.76781621 -0.821075375 5.269101181 1.000000158 0.742576357 0.596384896 0.064397392 1.09E-07 2.45E-08 0.057086225 0.013455344 0.150981809 0.821075375 -0.257423802 LLGWDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLGWDDR 7 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 ; 154.46 0.0039011 143962000 371970 427170 403920 617610 445060 655840 493660 420930 397860 472380 FALSE TRUE 386655.6628 500533.1246 414446.487 739771.4146 369408.8602 503531.0994 454965.6393 415288.1219 383541.0963 564933.8167 0.684426479 0.886003121 0.73361954 1.309483328 0.653897588 0.891309892 0.805343256 0.735109334 0.678913326 1 19.10772234 2.0711474 5.0832424 0.773948775 0.865961536 0.011495202 0.188386495 0.710073263 34.32860809 0.070645737 0.050835823 117.8005723 -2.0711474 0.09201276 LLHDLQIGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHDLQIGEK 10 0 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 90.913 0.010507 285920000 421170 349370 395980 323450 474920 503720 444930 379520 414370 313680 FALSE TRUE 437798.1168 409371.5798 406299.5641 387427.4446 394193.268 386738.664 410055.224 374433.1552 399456.9046 375139.5902 1.16702723 1.091251338 1.083062344 1.032755419 1.050790901 1.030919354 1.093073711 0.998116874 1.064822042 1 18.517068 8 0.572105794 1.03514991 7.938200115 0.680776712 0.027195613 79.62486258 0.676557061 0.011329576 680.9558388 99999999.98 -8 6.903050204 LLHDQIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHDQIEK 8 0 P12270 P12270 TPR Nucleoprotein TPR 0 95.608 0.0095297 107730000 296230 272560 313270 250800 371570 378120 333120 287120 334780 272100 FALSE TRUE 307925.3891 319370.0598 321434.0736 300407.4914 308410.6641 290307.3605 307009.184 283271.626 322731.3332 325412.7853 0.946260882 0.981430583 0.987773339 0.923158232 0.947752141 0.892120327 0.943445365 0.870499374 0.991759844 1 18.31191141 3.730644925 24.57253506 0.928365183 0.9727825 0.096020186 0.039301223 691.7877984 2147503.459 0.009931989 0.015711856 5378.298779 -3.730644925 0.044417317 LLHDQVGVIQFGPYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHDQVGVIQFGPYK 15 0 P53621;P53621-2;A0A3B3IS84;A0A3B3ISC6 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 97.836 0.0031603 502700000 625790 481320 501240 466320 1091200 866970 709100 550940 624310 700390 FALSE TRUE 650496.6724 563982.9659 514302.7262 558556.7042 905718.2138 665629.3566 653518.8891 543555.5505 601841.2051 837618.0107 0.776603015 0.67331762 0.614006289 0.666839415 1.081302219 0.794669346 0.780211123 0.648930113 0.718515119 1 19.67593294 LLHEDLDES(ph)DDDMDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLHEDLDESDDDMDEK 16 0 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK 203.56 9.20E-11 306740000 269621 279912 281886 318433 280746 451971 311287 275624 297883 394834 TRUE FALSE 280265.8453 327984.7086 289232.1807 381418.097 233024.8952 347007.5849 286887.5115 271929.7111 287162.249 472194.1627 0.593539411 0.694597126 0.612528073 0.807756908 0.493493807 0.734883258 0.607562596 0.575885372 0.608144428 1 18.84902068 -1.38523483 3.033011784 1.0049542 0.635541372 0.627550226 0.084010782 14402333.32 18033910.07 627676.1449 0.019679633 0.041187475 1.38523483 -0.369412828 LLHEVQELTTEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLHEVQELTTEVEK 14 0 Q13561;Q13561-3;Q13561-2;F8W1I6;F8VW18;F8VX93;F8VRV7;H0YHL1 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 242.79 1.68E-17 718550000 1237330 980410 1158450 914820 1502270 1496050 1353390 1251520 1298490 948810 FALSE TRUE 1286180.744 1148787.791 1188640.159 1095768.666 1246914.682 1148615.06 1247307.755 1234745.421 1251757.599 1134711.153 1.133487355 1.012405481 1.047526637 0.965680704 1.098882899 1.012253257 1.099229307 1.088158354 1.103150872 1 20.11389367 2.226956665 24.99561708 1.081544724 1.042509303 0.052279865 0.051650092 471.628005 1015909.144 0.018096524 0.013475166 168.6384746 -2.226956665 -0.039035421 LLHHDDPEVLADTCWAISYLTDGPNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLHHDDPEVLADTCWAISYLTDGPNER 27 0 P52292 P52292 KPNA2 Importin subunit alpha-1 0 ; 233.26 3.46E-45 223830000 67106 87505 82817 83885 79895 99184 81050 65737 77778 102747 FALSE TRUE 69755.3967 102533.3031 84975.27905 100477.2026 66314.47644 76150.01915 74697.08922 64855.90304 74978.78497 122878.3074 0.567678691 0.83442965 0.691540117 0.817696831 0.539676024 0.619718978 0.607894841 0.52780596 0.610187319 1 16.90687072 -1.06644088 4.376076381 1.000027703 0.644008444 0.524737056 0.100965188 14291850.75 3482895.498 3993.07349 0.024932216 0.085814193 1.06644088 -0.356019258 LLHIEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 ;;;;; 210.1 4.19E-05 2263468000 1736963 2195053 1930470 2034307 2156817 2407680 1957927 2005899 1965509 2247389 FALSE TRUE 1805539.64 2572036.278 1980779.634 2436686.853 1790202.017 1848532.809 1804459.566 1979013.205 1894770.715 2687721.846 0.67177325 0.95695776 0.736973447 0.906599341 0.666066699 0.687769388 0.671371395 0.736316226 0.70497277 1 21.35795241 5.035927065 17.21773254 0.768751998 0.268827199 0.061045359 0.118580824 25242946.03 314341142.5 0.027173623 392777532.6 108624.3186 -5.035927065 -0.499924799 LLHMDS(ph)DDEIPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLHMDSDDEIPIR 13 0 Q1MSJ5-1;Q1MSJ5;Q1MSJ5-2 Q1MSJ5-1 CSPP1 Centrosome and spindle pole-associated protein 1 1 LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR 240.2 4.98E-17 240855000 189685 245199 225670 227503 256656 292738 238872 237900 239263 263409 TRUE FALSE 197173.9103 287310.0209 231551.1456 272502.4144 213029.7048 224754.036 220148.5885 234711.3396 230651.9714 315018.9503 0.625911267 0.912040436 0.735038782 0.86503499 0.676244095 0.713461955 0.698842366 0.745070541 0.732184433 1 18.26507909 -1.762597014 8.567540426 1.00233142 0.747895743 0.474870505 0.080430904 0.003374625 9.35E-05 0.073372457 0.017171822 0.017274401 1.762597014 -0.254435677 LLHQLADLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLHQLADLVER 11 0 H0Y2X5;P47895;H0YNQ3;H0YKF9 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 ; 161.99 2.57E-05 598370000 576020 676750 617990 585730 777890 848930 733680 657170 688320 787350 FALSE TRUE 598761.7144 792976.5481 634095.3271 701585.6458 645664.5357 651778.8732 676172.2445 648361.7111 663547.4977 941616.1578 0.635887256 0.84214416 0.673411689 0.745086668 0.685698233 0.692191683 0.718097538 0.688562644 0.704690008 1 19.84477955 -2.082920146 2.418209857 1.458675507 0.710955414 0.737639756 0.051963347 4753185.162 1408279.352 12017873.72 0.011598027 0.008261898 2.082920146 -0.747720092 LLHTLEGHAMPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHTLEGHAMPIR 13 0 H3BQA8;H0YL19;H0YN81;Q9GZS3;H0YLA1 H3BQA8 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 178.1 8.61E-06 135520000 40451 41340 39315 41134 56187 48474 43346 44412 42511 52245 FALSE TRUE 42048.03671 48439.82342 40339.5812 49270.18243 46636.35381 37216.64813 39948.42726 43816.72978 40981.03741 62481.40746 0.672968783 0.775267802 0.64562536 0.788557499 0.746403702 0.595643563 0.639365035 0.701276293 0.655891714 1 15.93113933 -1.41495864 6.242016532 1.00006857 0.692409318 0.709191153 0.059314023 5.67E-05 5.31E-06 0.057486287 0.013546641 0.038462841 1.41495864 -0.307659252 LLHVAVSDVNDDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHVAVSDVNDDVR 14 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 198.23 2.23E-08 419100000 203280 235420 225680 241830 241520 262390 273810 223180 192290 232930 FALSE TRUE 211305.6514 275851.5537 231561.4062 289663.2522 200466.5167 201453.8991 252348.0567 220188.6371 185369.5205 278568.1738 0.75854197 0.990247916 0.831255786 1.039828952 0.719631801 0.723176292 0.905875403 0.790429984 0.665436823 1 18.08767091 3.217912158 24.99946359 0.794168895 0.905794924 0.161086199 0.115915251 394.5313464 477665.0385 0.031600706 0.037809307 1651.627699 -3.217912158 0.11162603 LLHVAVSDVNDDVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLHVAVSDVNDDVRR 15 1 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 127.32 5.12E-05 395880000 84961 75594 86499 67565 109070 107990 92246 83663 86976 84949 FALSE TRUE 88315.32588 88576.68146 88753.235 80929.15534 90530.32036 82910.9591 85015.51748 82541.63433 83845.75075 101593.1301 0.869304113 0.871876685 0.873614534 0.796600668 0.891106714 0.81610793 0.836823488 0.812472598 0.825309257 1 16.63244332 LLHYAGEVTYSVTGFLDKNNDLLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLHYAGEVTYSVTGFLDKNNDLLFR 25 1 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 ; 248.89 2.08E-39 286260000 175645 206567 225871 191933 248588 266280 210336 212034 220038 231624 FALSE TRUE 182579.6002 242043.2754 231757.3838 229896.7745 206333.1006 204440.5055 193849.3147 209192.031 212118.8754 277006.2881 0.659117168 0.873782603 0.836650263 0.829933415 0.744867931 0.738035613 0.699801135 0.755188745 0.76575473 1 18.0795592 -1.268521258 5.176719211 1.000037815 0.768620505 0.563264072 0.061531877 2.75E-05 3.88E-06 0.060898167 0.014351493 0.053886347 1.268521258 -0.23141731 LLIDGDGAGDDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLIDGDGAGDDRR 13 1 Q6I9Y2;H7C5E3 Q6I9Y2 THOC7 THO complex subunit 7 homolog 0 72.496 0.063161 67081000 49293 84118 72169 76764 72743 92047 63094 73320 67267 113710 FALSE TRUE 51239.1257 98564.61215 74049.78343 91947.69008 60378.17084 70670.47924 58148.52741 72337.26533 64846.07381 135989.2974 0.376787929 0.724796834 0.544526554 0.676139166 0.443992079 0.519676773 0.427596352 0.531933518 0.476846892 1 17.05313359 -1.302178307 5.561880002 1.000061907 0.529090223 0.661986072 0.101846699 7.43E-05 9.33E-06 0.093747741 0.022093664 0.04986797 1.302178307 -0.470971684 LLIDPNCSGHS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLIDPNCSGHSPR 13 0 Q8WYQ5-3;Q8WYQ5;Q8WYQ5-2;C9JSD5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 LLIDPNCS(0.002)GHS(0.998)PR;LLIDPNCS(0.125)GHS(0.875)PR 129.88 9.57E-05 185866000 236520 325730 301570 310410 330040 399850 311910 321880 319720 411690 TRUE FALSE 245857.9922 381671.5937 309429.1619 371808.1715 273939.9187 306990.8973 287461.6792 317565.7251 308213.3397 492352.7732 0.499353321 0.775199439 0.628470436 0.755166197 0.556389511 0.623518164 0.583853072 0.644996316 0.626001023 1 18.90933286 -1.664170618 2.513805884 1.052040617 0.636273788 0.662948914 0.078560548 6572341.891 5336201.749 2195405.716 0.019318151 0.021668527 1.664170618 -0.415766828 LLIPERDPLEEIAESS(ph)PQTAANSAAELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLIPERDPLEEIAESSPQTAANSAAELLK 29 1 Q68CZ2;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 LLIPERDPLEEIAES(0.149)S(0.848)PQT(0.002)AANSAAELLK;LLIPERDPLEEIAES(0.275)S(0.724)PQT(0.001)AANSAAELLK 117.54 7.63E-05 59744000 42739 36790 41978 34211 50292 51431 47704 36269 44452 35683 TRUE FALSE 44426.36872 43108.39631 43071.98117 40977.83369 41743.3838 39486.92969 43964.83583 35782.87338 42852.1812 42674.40066 1.04105431 1.01016993 1.009316604 0.960243918 0.978183247 0.925307189 1.030239093 0.838509102 1.004165976 1 15.38108327 3.994559675 0.772827388 0.944965909 1.050634344 0.188339949 0.051288543 1.536580332 1.348869951 0.021156243 0.118338036 9875.513235 -3.994559675 0.105668435 LLIQESVWDEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLIQESVWDEAMR 13 0 Q8IZ83;F5H4B6;Q8IZ83-3 Q8IZ83 ALDH16A1 Aldehyde dehydrogenase family 16 member A1 0 ; 124.1 0.00050176 14595000 26009.3 32734 33538 33433 40045 40886 34010 30915 30443 35388 FALSE TRUE 27036.16725 38355.80986 34412.02783 40045.94761 33238.1652 31390.84613 31344.20733 30500.63499 29347.36238 42321.60106 0.638826665 0.906293923 0.813107892 0.946229505 0.785371167 0.741721611 0.740619602 0.720687172 0.69343696 1 15.36910659 3.009488767 24.97703059 0.756456796 0.835273527 0.017184845 0.110213434 462.5470901 1217540.385 0.029821149 0.035598989 1022.089125 -3.009488767 0.078816732 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264;O00264-2 O00264 PGRMC1 Membrane-associated progesterone receptor component 1 1 LLKEGEEPTVY(0.002)S(0.998)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPT(0.001)VY(0.039)S(0.96)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR;LLKEGEEPTVYS(1)DEEEPKDESAR 241.57 1.39E-37 7479850000 4807129 2094385 2681443 2319234 4663390 5150735 3500283 2642312 2943884 2218682 TRUE FALSE 4996918.165 2454079.332 2751323.607 2777971.563 3870708.634 3954554.856 3225921.672 2606896.13 2837934.19 2653390.259 1.883220212 0.924884428 1.036908762 1.046951746 1.458778489 1.490378147 1.215773542 0.982477463 1.069550241 1 21.33940545 1.838023489 4.779624099 1.020708176 1.277683015 0.190537167 0.261870691 0.420714521 14.46556954 0.125260742 0.071293003 68.8689544 -1.838023489 0.256974839 LLKGEGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLKGEGPK 8 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 76.465 0.029428 0 208520 133040 165540 132400 235870 245630 190780 172620 205110 153750 FALSE TRUE 216752.5306 155888.5851 169854.1084 158588.3248 195776.9017 188586.1551 175826.1651 170306.3112 197728.1312 183874.3688 1.178807748 0.84779943 0.923750871 0.862481954 1.064731876 1.02562503 0.956229877 0.926210175 1.07534363 1 17.48836086 3.230018575 24.99970721 0.996359848 0.943576445 0.062865066 0.094757931 558.7741623 1635344.119 0.026928927 0.032669586 1698.316289 -3.230018575 -0.052783403 LLKPGEEPSEYT(ph)DEEDTKDHNKQD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLKPGEEPSEYTDEEDTKDHNKQD 24 3 U3KQM0;O15173;O15173-2;U3KPU8 U3KQM0 PGRMC2 Membrane-associated progesterone receptor component 2 1 LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD;LLKPGEEPSEYT(1)DEEDTKDHNKQD 213.37 4.74E-26 1126910000 1090770 285110 433970 371350 772370 753740 693310 450490 518440 248778 TRUE FALSE 1133834.442 334075.4247 445279.6147 444801.9216 641082.8233 578695.308 638966.5506 444451.9184 499781.4457 297521.286 3.810935538 1.122862264 1.496631118 1.495025541 2.154746075 1.945055145 2.147633063 1.493849144 1.679817443 1 18.18263336 7.999999996 0.056661395 2.43E-07 5.451500283 0.223543496 0.664760056 715.0979657 3.036238851 62.17162871 327.0068338 99999999.16 -7.999999996 5.451500041 LLLAEDS(ph)EEEVDFLSER ddPTM_MDA-MB-175_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(0.999)EEEVDFLS(0.001)ER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(0.996)EEEVDFLS(0.004)ER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER 353.38 9.36E-64 536737000 320332.6 342068.5 372316.9 337537.3 379708.2 399578 364865.9 357349.8 363022.1 350568.8 TRUE FALSE 332979.5784 400816.104 382019.7843 404301.1705 315165.5358 306782.0652 336266.7574 352560.1104 349957.0055 419256.0443 0.794215332 0.956017473 0.911184918 0.964329974 0.751725682 0.731729618 0.802055837 0.840918372 0.834709506 1 18.67747206 5.053437993 15.12103377 0.855350193 0.401350978 0.045799065 0.086917356 4036811.4 30556165.77 0.021566829 53741947.07 113093.5907 -5.053437993 -0.453999215 LLLDTS(ph)PPGGVVLSSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLLDTSPPGGVVLSSFR 17 0 O15211;A2AB89 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LLLDT(0.011)S(0.988)PPGGVVLSSFR;LLLDT(0.056)S(0.943)PPGGVVLSSFR 134.85 1.63E-05 530240000 1214660 1368830 1270570 1294850 1498900 1686940 1410820 1380790 1301220 1723960 TRUE FALSE 1262615.715 1603915.904 1303682.098 1550967.465 1244117.513 1295173.751 1300236.242 1362282.769 1254389.346 2061736.955 0.612403882 0.777944005 0.632322225 0.752262534 0.603431738 0.628195439 0.630650888 0.660745186 0.608413864 1 20.97542885 -1.838435581 2.891916255 1.116406813 0.658641792 0.76245537 0.057545127 25652202.31 21085016.94 20788908.92 0.013423993 0.014506559 1.838435581 -0.457765021 LLLEAQAATGFLLDPVKGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 94.057 0.0012971 28128000 31554 33070 33567 26261 44434 41756 35724 32250 41193 32044 FALSE TRUE 32799.77628 38749.51525 34441.7836 31455.34742 36881.12455 32058.80182 32923.85953 31817.7415 39710.47198 38322.40828 0.855890268 1.011145097 0.898737453 0.820808212 0.962390575 0.836554988 0.859128145 0.830264666 1.03622068 1 15.22590061 1.229095373 24.98970134 1.018110431 0.884015116 0.4590579 0.058072829 196.7790955 519508.5811 0.053518292 0.014092329 16.94709926 -1.229095373 -0.134095315 LLLEFTDTSYEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LLLEFTDTSYEEKR 14 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;; 297.5 1.76E-43 2563716000 1779828 1248752 1622727 1237178 2109982 1969094 1908577 1577680 1782090 1387857 FALSE TRUE 1850096.984 1463215.442 1665016.599 1481888.116 1751328.013 1511801.76 1758977.748 1556533.78 1717952.929 1659781.007 1.114663306 0.881571386 1.003154387 0.892821468 1.055156075 0.910844114 1.059764957 0.937794669 1.03504795 1 20.66256147 2.237912689 24.99999992 0.998013689 0.973060715 0.034086503 0.074290745 80.95610075 3123496.128 0.02460283 0.019279483 172.9468631 -2.237912689 -0.024952975 LLLEGISSTHVNHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLLEGISSTHVNHLR 15 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 132.86 2.59E-05 742200000 101807 314540 263820 304740 301710 362580 241780 306220 256660 385670 FALSE TRUE 105826.419 368559.7982 270695.3659 365016.6624 250425.442 278376.29 222828.6518 302115.6218 247422.8567 461234.6524 0.229441605 0.799072221 0.58689295 0.79139037 0.542945853 0.603545914 0.483113423 0.655015013 0.536435967 1 18.81514138 -2.004046852 2.844637434 1.417319031 0.593600415 0.399038784 0.153592923 115644351.8 107434736.6 315690230.7 0.033572589 0.009907251 2.004046852 -0.823718617 LLLEHLECLVSR ddPTM_MDA-MB-175_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 ; 199.4 1.72E-07 545830000 519290 673090 619980 640520 742390 815670 684690 686470 639380 795510 FALSE TRUE 539791.9702 788687.9716 636137.1881 767212.9442 616198.813 626243.0041 631022.2087 677268.9925 616368.8387 951374.9535 0.567380892 0.82899804 0.668650342 0.806425418 0.647692911 0.658250463 0.663273935 0.711884405 0.647871627 1 19.85965452 -2.026117883 2.661391759 1.359064879 0.694053421 0.615046989 0.073727871 6602894.778 4023471.848 14448866.88 0.016163522 0.00941634 2.026117883 -0.665011458 LLLERPS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 145 1.89E-05 1628982000 1179909 1249406 1117356 1190236 1183561 1333045 1195522 1165252 1055959 1146572 TRUE FALSE 1226492.718 1463981.761 1146475.215 1425661.128 982379.724 1023465.501 1101813.862 1149633.703 1017955.242 1371220.831 0.894453097 1.067648426 0.836098161 1.039702064 0.716427071 0.746389989 0.803527657 0.838401574 0.742371483 1 20.3870295 3.238945941 24.99999561 0.799501761 0.958389415 0.372308975 0.09607675 9.979086601 647412.5005 0.025214556 0.032135172 1733.588194 -3.238945941 0.158887654 LLLERPS(ph)PIRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 163.02 3.19E-05 4926540000 2757137 3415632 3528315 3111251 3818234 4136867 3275995 3462681 3373239 3748710 TRUE FALSE 2865990.898 4002240.226 3620265.787 3726647.162 3169211.949 3176142.334 3019213.952 3416269.425 3251836.787 4483197.951 0.639273779 0.892719944 0.807518612 0.831247516 0.70690877 0.708454627 0.673450957 0.762016191 0.725338658 1 22.09609677 -1.141237702 4.333607243 1.000046925 0.752857043 0.515973342 0.072680836 3.30E-05 6.54E-06 0.070490728 0.016611674 0.072237432 1.141237702 -0.247189882 LLLEVTYEAIVDGGINPDSLR ddPTM_MDA-MB-175_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 65.805 0.035102 0 36560 39003 49041 43378 50250 72267 40024 41989 63845 45850 FALSE TRUE 38003.41703 45701.46185 50319.04875 51958.03893 41708.52295 55484.08447 36886.8143 41426.20614 61547.23092 54833.42965 0.693070218 0.833459846 0.91767101 0.947561356 0.76064042 1.011866024 0.672706678 0.755491794 1.12243993 1 15.74276809 1.237384348 24.99945501 1.06122003 0.824715569 0.437577767 0.107547268 29.09916378 618320.1565 0.086465309 0.026237705 17.27365925 -1.237384348 -0.236504461 LLLFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLLFDR 6 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 104.25 0.079083 95279000 63304 83910 74965 92616 85958 98852 91975 84235 81350 102480 FALSE TRUE 65803.2908 98320.88977 76918.64948 110935.1684 71346.88986 75895.12112 84765.75917 83105.96761 78422.22939 122558.9939 0.536911154 0.802233167 0.627605099 0.905157303 0.582143241 0.619253787 0.691632303 0.678089506 0.639873312 1 16.90311683 -1.993847133 3.029766432 1.305544602 0.681048928 0.475663774 0.101960432 54757171.18 38118881.8 116866529.7 0.022735096 0.010142683 1.993847133 -0.624495674 LLLIQAFRPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLLIQAFRPDR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 205.52 2.69E-08 1688470000 866760 924380 954240 1061340 1163690 1250920 1030170 983460 991460 1158480 FALSE TRUE 900980.3541 1083135.074 979108.2783 1271269.884 965886.3895 960412.7879 949422.5836 970278.3273 955777.5483 1385461.976 0.650310416 0.781786215 0.70670166 0.917578329 0.697158353 0.693207612 0.685275093 0.70032837 0.689861985 1 20.40193569 -0.969715244 5.14834326 1.000001359 0.726160829 0.569981892 0.071728942 1.11E-06 2.22E-07 0.068868931 0.016232482 0.10722221 0.969715244 -0.27384053 LLLPGELAK ddPTM_MDA-MB-175_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 ;; 111.74 0.0048295 2033308100 3627185 3834031 3875759 3607258 4840069 5008194 4524344 4100868 3945037 4141360 FALSE TRUE 3770389.065 4492496 3976764.464 4320762.866 4017355.8 3845116.843 4169714.095 4045902.572 3803055.889 4952780.201 0.76126719 0.90706549 0.802935786 0.872391403 0.811131453 0.776355236 0.841893629 0.81689524 0.767862844 1 22.23980717 -1.468122245 5.581394739 1.000192641 0.820787576 0.607512787 0.043928707 9.73E-05 9.27E-06 0.03930657 0.009254756 0.034031239 1.468122245 -0.179405065 LLLPHAFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLLPHAFSR 9 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 0 107.15 0.0035111 0 20377 45123 30839 34017 58956 46969 26596 33450 31491 63209 FALSE TRUE 21181.49969 52872.52424 31642.68967 40745.46107 48934.68018 36061.16157 24511.33602 33001.65746 30357.64506 75593.59334 0.280202313 0.699431287 0.418589569 0.539006803 0.647338988 0.477039918 0.3242515 0.436566857 0.401590184 1 16.20597635 -1.76539415 2.84377505 1.113383383 0.473090366 0.62080597 0.124390016 33910911.72 28612864.08 26925721.92 0.030338828 0.0171635 1.76539415 -0.640293016 LLLPWLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLLPWLEAR 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 112.94 0.0043759 1797300000 615600 807240 638670 686910 982560 933850 673250 635770 604390 1013430 FALSE TRUE 639904.3633 945877.1905 655314.2649 822778.7478 815544.8022 716977.4901 620478.9058 627248.5431 582638.122 1211992.205 0.527977293 0.780431744 0.540691815 0.678864719 0.672896079 0.591569391 0.511949584 0.51753513 0.480727615 1 20.20894899 -1.228860171 5.052252551 1.000052115 0.58983739 0.653332879 0.089774633 5.43E-05 8.28E-06 0.089486315 0.021089455 0.059039114 1.228860171 -0.410214724 LLLQQLEATLETGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLLQQLEATLETGKR 15 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 85.469 0.012716 45571000 47638 42613 59807 48018 63826 63696 55731 55717 63303 45820 FALSE TRUE 49518.78502 49931.45127 61365.61955 57515.81708 52976.87932 48903.56932 51362.65859 54970.20475 61024.7374 54797.55172 0.903667837 0.911198579 1.119860607 1.049605599 0.966774567 0.892440771 0.937316668 1.003150743 1.113639852 1 15.74182382 1.448163572 6.690089343 1.058209162 0.972557094 0.194528124 0.070935897 0.293425106 30.68834903 0.046603102 0.01912846 28.06490473 -1.448163572 -0.085652068 LLLSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLLSDR 6 0 Q7Z6L1-3;Q7Z6L1;Q7Z6L1-2;Q7Z6L1-4;C9JUV4 Q7Z6L1-3 TECPR1 Tectonin beta-propeller repeat-containing protein 1 0 ; 127.1 0.040029 217640000 272250 290700 320610 318100 347600 357180 355760 318330 316460 301930 FALSE TRUE 282998.6402 340625.4637 328965.36 381019.2306 288515.0762 274230.3581 327874.6016 314063.307 305070.6664 361087.4027 0.783739998 0.943332448 0.91104081 1.055199455 0.799017285 0.759457007 0.90802005 0.869770877 0.844866545 1 18.46198856 4.757836646 23.10205217 0.892155446 0.783739716 0.140643906 0.083941724 3223.994829 3863734.728 0.020283132 0.646792651 57258.0622 -4.757836646 -0.108415729 LLMHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 84.566 0.055705 4719500000 14233800 13235800 14469100 12878100 19710100 18665100 16705500 14906400 15098300 15684800 FALSE TRUE 14795761.41 15508945.69 14846176.63 15425349.74 16359784.24 14330413.4 15396079.26 14706604.09 14554915.13 18757936.26 0.788773414 0.826793816 0.791461088 0.822337251 0.872152673 0.763965353 0.820776819 0.784020368 0.775933713 1 24.16099778 -1.585416539 2.943632693 1.011689609 0.80573805 0.792402967 0.029920713 5650924.73 6056403.374 514721.5986 0.007018677 0.025976669 1.585416539 -0.205951559 LLNFPTIVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLNFPTIVER 10 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ; 81.338 0.049578 97916000 104569 99517 116626 105065 114571 143863 117289 119780 115783 117453 FALSE TRUE 108697.4649 116608.2706 119665.3694 125846.5434 95096.26234 110452.9985 108095.5817 118174.545 111615.9924 140465.6666 0.773836536 0.830154966 0.851918994 0.895923869 0.677007162 0.786334492 0.769551623 0.841305551 0.794614052 1 17.09985802 -1.462197022 3.161960552 1.003895963 0.804468681 0.527583447 0.056091224 13019986.83 17522847.42 452952.667 0.013544659 0.03449872 1.462197022 -0.199427282 LLNGNHENGDLDPTS(ph)PLENMDYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73;F8WE35;F5H8I0;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;F5H6X8;F5H221;F5H592 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 LLNGNHENGDLDPT(0.16)S(0.84)PLENMDYIK;LLNGNHENGDLDPT(0.164)S(0.836)PLENMDYIK;LLNGNHENGDLDPT(0.115)S(0.885)PLENMDYIK 148.04 1.08E-07 197130000 122511 83034 110733 112457 117785 130408 151359 111298 119190 72834 TRUE FALSE 127347.8289 97294.44359 113618.7929 134700.6589 97763.94777 100122.7184 139495.0861 109806.2324 114900.3752 87104.42781 1.462013265 1.116986197 1.304397443 1.546427229 1.122376327 1.149456128 1.601469519 1.260627446 1.319110613 1 16.41045844 0.258154639 2.240602158 0.999999489 1.318383125 0.259176707 0.162428009 42.03736064 123.9513792 0.15029408 0.040620143 1.811985171 -0.258154639 0.318383636 LLNIWQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLNIWQER 8 0 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 0 104.06 0.010826 177820000 185710 228970 173120 204440 225090 265380 204270 195770 190700 257380 FALSE TRUE 193041.9742 268293.8164 177631.6494 244877.6218 186829.2822 203749.5169 188258.7836 193146.0234 183836.7443 307808.6832 0.627149216 0.871625237 0.577084596 0.795551377 0.6069656 0.661935572 0.611609724 0.627487248 0.597243529 1 18.2316744 -1.169012385 5.172128068 1.000016883 0.664701428 0.555938436 0.090067374 1.66E-05 2.66E-06 0.082395205 0.019419759 0.067762218 1.169012385 -0.335315455 LLNQADPCVQILIQETGEHVLVTAGEVHLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLNQADPCVQILIQETGEHVLVTAGEVHLQR 31 0 Q7Z2Z2-2;Q7Z2Z2 Q7Z2Z2-2 EFTUD1 Elongation factor Tu GTP-binding domain-containing protein 1 0 ; 108.75 6.91E-05 40153200 8986.5 6217.4 7241 11828.6 12118.3 10769.5 11754 9533.3 6629.42 10636.6 FALSE TRUE 9341.293959 7285.190085 7429.706409 14168.26178 10058.43569 8268.446838 10832.69077 9405.521707 6390.828469 12720.63812 0.734341616 0.572706339 0.584067115 1.113801182 0.790717855 0.65000252 0.851583911 0.739390714 0.502398418 1 13.63488342 LLNTWTNRYPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLNTWTNRYPDAK 13 1 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 145.86 3.83E-05 669620000 586760 456930 693410 492500 904230 683160 551300 555780 689710 694430 FALSE TRUE 609925.7379 535404.1731 711480.8342 589915.03 750529.3076 524506.4434 508087.6654 548330.6782 664887.4718 830490.2628 0.734416483 0.644684468 0.856699791 0.710321429 0.903718371 0.631562424 0.611792441 0.660249376 0.800596348 1 19.66360373 0.93207998 5.479533175 0.999966545 0.716562739 0.469723623 0.090330566 0.391573126 29.42972953 0.089073312 0.022451582 8.552241969 -0.93207998 -0.283403806 LLPDGAADGSFYLHS(ph)PEGPSKPSLASPYLPEGTSKPLSDRPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLPDGAADGSFYLHSPEGPSKPSLASPYLPEGTSKPLSDRPTK 43 3 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 LLPDGAADGS(0.001)FYLHS(0.94)PEGPS(0.059)KPSLASPYLPEGTSKPLSDRPTK 156.57 1.16E-14 647780000 165030 96760 158940 109040 193900 170620 198400 169940 223160 92476 TRUE FALSE 171545.5118 113377.7773 163082.107 130607.7865 160940.9473 130996.0908 182848.8896 167662.2323 215128.5152 110594.9016 1.551115913 1.025162784 1.474589737 1.180956668 1.455229354 1.184467718 1.653321147 1.516003268 1.945193784 1 16.75492535 2.233529487 24.99951961 1.568587398 1.306841136 0.132507746 0.263640415 198.6514616 987081.2761 0.088197806 0.067173446 171.2101418 -2.233529487 -0.261746262 LLPEEYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLPEEYHR 8 0 Q5JTH9-2;Q5JTH9-3;Q5JTH9 Q5JTH9-2 RRP12 RRP12-like protein 0 107.9 0.003915 73802000 23301 27913 24297 31073 28294 32192 24708 25095 26388 30361 FALSE TRUE 24220.94147 32706.84062 24930.19978 37219.14666 23484.59599 24715.89587 22771.3224 24758.64257 25438.30103 36309.65665 0.667066111 0.900775266 0.686599711 1.025048158 0.646786507 0.680697593 0.627142322 0.681874874 0.700593269 1 15.14806567 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 LLPEGEETLES(1)DDEKDEHTSK 229.67 7.30E-26 432720000 187340 120910 194510 146450 277920 268650 269910 228230 216590 113970 TRUE FALSE 194736.3279 141675.352 199579.0904 175417.3729 230679.2577 206260.1089 248753.7489 225170.9502 208794.9682 136300.2394 1.428730637 1.039435826 1.464260747 1.286992405 1.692434721 1.513277672 1.825042641 1.652021678 1.531875286 1 17.05642857 3.249629096 24.7805209 1.592038715 1.297282437 0.167623463 0.232390215 246.149969 551085.981 0.060053665 0.080540927 1776.761342 -3.249629096 -0.294756278 LLPEKHEIENLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLPEKHEIENLR 12 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;; 222.79 1.44E-11 524101000 485646 407969 489672 417860 633285 603111 501618 503260 520111 443074 FALSE TRUE 504819.6791 478034.5022 502433.2546 500511.4608 525639.4419 463047.6105 462299.8704 496514.6229 501392.3067 529885.8671 0.952695119 0.902146164 0.948191461 0.944564654 0.991986151 0.873862919 0.872451785 0.937021826 0.946226985 1 19.01532212 0.856744525 2.459828801 0.99982191 0.926441862 0.280024543 0.034855124 0.735568587 8.570190708 0.034425211 0.009254415 7.19025884 -0.856744525 -0.073380047 LLPETVS(ph)PSAPSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPETVSPSAPSWR 14 0 B0QXZ6;O95503 B0QXZ6 CBX6 Chromobox protein homolog 6 1 LLPET(0.249)VS(0.737)PS(0.014)APSWR;LLPET(0.424)VS(0.555)PS(0.021)APSWR 135.5 3.41E-05 52858000 82189 76377 78511 85785 77643 102851 92142 91995 83707 82942 TRUE FALSE 85433.88518 89494.15562 80557.06116 102753.017 64445.27059 78965.41397 84919.66927 90761.9575 80694.40142 99192.89688 0.861290353 0.90222343 0.8121253 1.035890877 0.649696426 0.796079321 0.856106354 0.915004606 0.813509878 1 16.59794919 -1.129244873 4.587835927 1.000014915 0.852596279 0.188813275 0.093579183 1.38E-05 2.61E-06 0.08743897 0.020607478 0.074260031 1.129244873 -0.147418636 LLPGPENHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLPGPENHR 9 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 0 123.86 0.00054588 109400000 94919 100170 94660 95986 104500 117920 86304 94551 84107 108130 FALSE TRUE 98666.47541 117373.4183 97126.91736 114971.7443 86737.12733 90534.86709 79539.26697 93283.6985 81080.0055 129316.0032 0.762987356 0.907648051 0.751081962 0.889075918 0.670737768 0.70010567 0.61507675 0.721362369 0.626991273 1 16.9805413 3.23000585 24.99927834 0.701315818 0.827936423 0.162227285 0.111233492 252.0526586 736563.4871 0.029045097 0.035233803 1698.26653 -3.23000585 0.126620605 LLPLEEHYR ddPTM_MDA-MB-175_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 ; 154.56 7.54E-05 354630000 92643 120369 87285 89093 156246 135870 95861 89637 96187 186018 FALSE TRUE 96300.61718 141041.4394 89559.71881 106715.3295 129687.3607 104316.2516 88347.16433 88435.56263 92725.24866 222464.6656 0.432880507 0.633994792 0.402579522 0.479695637 0.58295712 0.468911552 0.397128974 0.397526333 0.416808883 1 17.76321668 -1.332599656 3.230912999 1.003703407 0.466530496 0.811760142 0.076844567 24834865.08 34266215.01 883618.1064 0.01992995 0.046494368 1.332599656 -0.537172912 LLPPAS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLPPASP 7 0 Q9Y4R8 Q9Y4R8 TELO2 Telomere length regulation protein TEL2 homolog 1 LLPPAS(1)P 47.082 0.079365 45975000 162600 114800 159920 139980 190540 200620 197100 181850 167150 137200 TRUE FALSE 169019.5736 134516.007 164087.6466 167667.6262 158152.0789 154029.0454 181650.787 179412.5982 161134.3042 164081.7131 1.030093911 0.819811083 1.000036161 1.021854435 0.963861699 0.938733772 1.107075149 1.093434453 0.982036944 1 17.32405493 2.24780256 24.9958199 1.059625956 0.960397108 0.267064679 0.065894916 219.0332876 592398.9478 0.022960433 0.018961216 176.9304411 -2.24780256 -0.099228848 LLPPVGTGRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPPVGTGRSPR 12 1 Q9NWZ5;Q9NWZ5-4;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 LLPPVGT(0.067)GRS(0.933)PR;LLPPVGT(0.105)GRS(0.895)PR 94.45 0.0039986 411210000 257770 333860 294250 287320 342100 370080 260690 287050 294510 388020 TRUE FALSE 267946.9586 391197.8579 301918.3967 344151.0384 283949.9642 284134.5286 240256.4366 283202.5643 283910.6426 464045.0899 0.577415782 0.84301691 0.650622975 0.741632755 0.611901667 0.612299397 0.517743732 0.610291048 0.611816931 1 18.82390547 -0.965364023 4.394501048 1.000009278 0.64144557 0.610251564 0.085863533 9814281.491 4467317.572 902.8693601 0.020803892 0.108301875 0.965364023 -0.358563708 LLPPYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPPYLR 7 0 P43490;A0A0C4DFS8 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ; 77.906 0.08556 252200000 277410 390750 379200 383830 427890 475140 366000 406690 376620 430120 FALSE TRUE 288362.361 457858.2729 389082.2635 459750.4284 355157.4106 364795.9358 337311.9636 401238.9858 363065.5198 514393.7789 0.560586797 0.890092944 0.756389909 0.893771362 0.690438775 0.709176415 0.655746585 0.780023014 0.705812424 1 18.97251367 -1.978154266 4.26768106 1.206191463 0.744435041 0.399648091 0.096043364 0.062898912 0.000321972 0.03104308 0.020561962 0.010515883 1.978154266 -0.461756422 LLPQGTVIFEDISIEHFEGTVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPQGTVIFEDISIEHFEGTVTK 23 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ; 122.73 6.44E-05 24688000 31336 28363 37146 27502 45717 46043 38353 32794 38368 29257 FALSE TRUE 32573.16948 33234.12462 38114.05528 32941.81351 37946.04067 35350.21104 35346.79164 32354.45007 36987.14317 34989.34899 0.930945285 0.949835466 1.089304499 0.941481178 1.08450262 1.010313483 1.010215756 0.924694257 1.057097209 1 15.0946282 4.452588299 24.99442158 1.007978873 0.93566772 0.246802736 0.051319627 270.6553682 275746.2559 0.012274549 0.033617931 28352.30025 -4.452588299 -0.072311153 LLPQLTYLDGYDRDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLPQLTYLDGYDRDDK 16 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ;; 137.81 9.10E-06 853696000 354196 597856 516279 621731 508506 822620 522115 583252 513383 687642 FALSE TRUE 368179.9316 700533.1173 529733.6549 744707.5361 422070.3318 631578.9719 481190.262 575434.4609 494906.4461 822372.2842 0.447704694 0.851844269 0.644153098 0.90556011 0.513235112 0.767996422 0.58512461 0.699725017 0.601803411 1 19.64943212 -1.717209 2.805766192 1.051973238 0.676700797 0.345521218 0.136430291 35921624.33 31281032.17 13127822.41 0.029089163 0.019177456 1.717209 -0.375272441 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;LLPSAPQT(0.001)LPDGPLAS(0.999)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR 316.6 1.06E-61 17189479000 4793583 5042104 4655676 5934822 4786013 5614623 5783137 5273231 4793655 4756737 TRUE FALSE 4982837.358 5908046.14 4777006.741 7108712.078 3972488.22 4310711.899 5329839.611 5202551.964 4621132.293 5688728.542 0.875914068 1.038553008 0.839731885 1.249613517 0.698308627 0.757763684 0.936912277 0.914536864 0.812331307 1 22.43967481 3.20591576 24.99999509 0.854956153 0.992124018 0.231803369 0.13125967 298.3824813 228505.6479 0.036928944 0.044141366 1606.629587 -3.20591576 0.137167864 LLPYPTLAS(ph)PASD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLAS(0.995)PAS(0.005)D;LLPYPTLAS(0.745)PAS(0.255)D 110.08 0.0011402 19709000 46535 59985 49946 54147 65165 75700 51077 57342 61793 69253 TRUE FALSE 48372.23773 70286.95713 51247.63379 64857.11499 54088.27658 58119.82224 47073.45128 56573.42428 59569.082 82821.79942 0.584052002 0.848652862 0.618769867 0.783092319 0.653068117 0.701745466 0.568370304 0.683074078 0.719243996 1 16.33772293 -1.789469608 3.209290748 1.066558179 0.684604898 0.571983719 0.081888767 12895060.28 9044716.624 6050516.189 0.017603985 0.01623792 1.789469608 -0.381953282 LLPYPTLASPAS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 LLPYPTLASPAS(1)D;LLPYPTLASPAS(1)D 188.96 5.94E-06 83141000 113934 126048 119927 131988 120631 151048 121552 126844 114770 132815 TRUE FALSE 118432.2023 147695.7635 123052.3961 158094.8325 100126.1857 115969.3912 112024.4366 125143.8637 110639.4501 158837.5564 0.745618385 0.929854166 0.774705926 0.995324003 0.630368459 0.730113166 0.705276757 0.787873262 0.696557242 1 17.27719255 3.232482525 24.9998218 0.745830845 0.86007625 0.161206321 0.112947034 224.1125671 921797.6446 0.02966537 0.036326021 1707.978993 -3.232482525 0.114245405 LLQAMEPVHVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLQAMEPVHVAR 12 0 Q16401-2;Q16401 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ; 139.89 5.92E-05 1142040000 732720 1095890 927330 973570 1260150 1132490 905610 986030 888740 1333180 FALSE TRUE 761648.3514 1284100.583 951496.9816 1166139.24 1045950.153 869486.3606 834625.9218 972813.8807 856754.421 1594391.096 0.477704845 0.805386198 0.596777656 0.731400999 0.656018562 0.545340703 0.523476281 0.610147588 0.537355247 1 20.60457413 -1.847833545 4.237640612 1.087498407 0.613786993 0.604336394 0.094778932 0.053757215 0.00193033 0.062964646 0.02091093 0.014196015 1.847833545 -0.473711414 LLQDFFNGK ddPTM_MDA-MB-175_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 2689900000 2994000 2729090 3084900 2677790 3930500 3896900 3443000 3280100 3372000 2877930 FALSE TRUE 3112205.432 3197789.978 3165295.028 3207448.87 3262395.014 2991904.033 3173128.663 3236135.625 3250642.379 3441805.282 0.904236346 0.929102525 0.919661273 0.93190887 0.947873208 0.869283352 0.921937298 0.940243668 0.944458536 1 21.71473405 0.858182985 1.181626554 0.999380146 0.918882482 0.602284286 0.019995071 0.445417126 1.207589133 0.018933749 0.005879469 7.214113737 -0.858182985 -0.080497664 LLQDFFNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLQDFFNGR 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 217.66 1.30E-06 10244800000 1271390 1680690 1399760 1503680 1789200 1967260 1538470 1665100 1415370 1902030 FALSE TRUE 1321585.459 1969335.434 1436238.896 1801103.416 1485072.423 1510393.679 1417880.701 1642782.058 1364431.11 2274696.362 0.580994229 0.865757499 0.631398071 0.791799489 0.652866223 0.663997931 0.623327458 0.722198393 0.599829996 1 21.11724255 -1.63691491 6.105965147 1.001897328 0.687300396 0.558856672 0.084783998 0.001988904 0.000118268 0.074559198 0.01748024 0.023071992 1.63691491 -0.314596932 LLQDFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQDFNR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 85.064 0.049054 41633000 46126 50558 48867 53821 86549 72843 56015 50315 53853 73765 FALSE TRUE 47947.0901 59240.94321 50140.51416 64466.63316 71837.43189 55926.3172 51624.39793 49640.60972 51914.84105 88217.83943 0.543507871 0.671530198 0.568371596 0.730766403 0.81431865 0.633957004 0.585192272 0.562704891 0.588484612 1 16.42878281 -2.360285153 2.272010293 3.414754334 0.633333191 0.649600932 0.080817245 4789130.113 416587.4315 59755539.4 0.021159612 0.004362293 2.360285153 -2.781421143 LLQDHPWLLSQNLVVKPDQLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLQDHPWLLSQNLVVKPDQLIK 22 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ; 264.72 9.98E-38 2108130000 3157600 2285740 3103400 2262980 3915000 3517400 3438200 3076300 3328600 2175130 FALSE TRUE 3282264.486 2678298.064 3184277.153 2710590.69 3249529.698 2700537.157 3168704.9 3035067.23 3208804.336 2601305.078 1.261776065 1.02959783 1.224107538 1.04201184 1.249192079 1.038147036 1.218121214 1.166747897 1.233536337 1 21.31080418 -0.526678805 8.394250347 0.999999999 1.158800594 0.234828593 0.087805091 0 0 0.074640816 0.017593009 0.297386462 0.526678805 0.158800595 LLQDMDINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQDMDINR 9 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 103.7 0.0078629 49266000 73040 78460 83015 73870 127840 112080 83422 78752 78867 131070 FALSE TRUE 75923.6756 91934.89467 85178.4391 88481.26552 106109.8025 86051.11859 76883.16566 77696.45825 76028.59208 156750.657 0.484359537 0.586504047 0.543400843 0.564471417 0.676933701 0.548968153 0.49048066 0.495669107 0.485028857 1 17.25811196 -1.781888796 2.755628339 1.114691489 0.542295024 0.854752133 0.05666939 13465905.74 10549896.11 10406189.18 0.01473874 0.016523848 1.781888796 -0.572396465 LLQDSS(ph)SPVDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.013)S(0.733)S(0.254)PVDLAK 161.66 4.38E-05 40479000 147030 113100 122670 112100 162010 163310 148200 130160 143110 105550 TRUE FALSE 152834.8579 132524.0452 125866.881 134273.0454 134471.5981 125383.7275 136583.6968 128415.4181 137959.4991 126230.5016 1.210760125 1.04985755 0.997119392 1.063713157 1.065286094 0.993291842 1.082018173 1.017308942 1.0929173 1 16.94570103 4.735307781 5.232509099 1.039817588 1.217746077 0.688196788 0.034508152 0.077943152 7.406848559 0.007522668 0.049917232 54363.54645 -4.735307781 0.177928489 LLQDSSS(ph)PVDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLQDSSSPVDLAK 13 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 LLQDS(0.004)S(0.382)S(0.614)PVDLAK;LLQDSS(0.008)S(0.992)PVDLAK;LLQDS(0.002)S(0.01)S(0.988)PVDLAK 210.86 2.78E-08 385705000 1600950 1049650 1297450 1035340 1648420 1685760 1508780 1297760 1428060 958370 TRUE FALSE 1664156.742 1229919.222 1331262.613 1240127.162 1368222.157 1294267.788 1390517.881 1280365.65 1376664.4 1146144.252 1.451960989 1.073092867 1.161514015 1.081999198 1.193760868 1.129236381 1.213213676 1.117106898 1.201126644 1 20.1283572 7.99999017 0.017274077 1.64E-09 2.596933368 0.266396827 0.098731316 6541.755574 8.716246762 506.0030701 844.3447642 99997736.51 -7.99999017 2.596933366 LLQEALEAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 131.83 0.00045424 29315000 22271 25260 24811 19441.5 31083 30991 22863 24252 24007 27195 FALSE TRUE 23150.27628 29598.2085 25457.59504 23286.97067 25799.52276 23793.80992 21070.93832 23926.94161 23142.99276 32523.33957 0.711805017 0.910060556 0.782748493 0.71600798 0.793261796 0.731591843 0.647871301 0.735685262 0.71158107 1 14.98918778 3.99939309 24.99036166 0.744379566 0.819800715 0.01358887 0.099486099 51.21070067 2109084.599 0.022703126 0.048169412 9986.035136 -3.99939309 0.075421149 LLQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQELR 6 0 Q8N163-2;Q8N163;H0YB24;G3V119;A0A087WXM7;E9PNP6;I3L400;I3L0W2;J3KRA9;Q96Q15-2;Q96Q15;P11532-2;A0A087WTU7;A0A5H1ZRP8;A0A087WV90;P11532-3;P11532-4;A0A075B6G3;P11532-11;P11532;H0Y304 Q8N163-2;J3KRA9;P11532-2 CCAR2;SMG1;DMD Cell cycle and apoptosis regulator protein 2;Serine/threonine-protein kinase SMG1;Dystrophin 0 98.133 0.093712 38471000 123990 150170 136470 149500 176160 178530 144580 144120 147270 155350 FALSE TRUE 128885.2209 175960.5293 140026.5203 179070.6538 146216.3861 137069.1131 133247.4418 142188.3071 141969.7815 185787.8581 0.693722519 0.947104569 0.753690374 0.963844761 0.787007222 0.73777218 0.717202099 0.765326155 0.764149944 1 17.50329669 3.025260465 24.99996055 0.773362394 0.845420853 0.016702336 0.105700219 517.9848156 512639.1616 0.027951126 0.033406914 1059.889195 -3.025260465 0.072058459 LLQELSHPNIIGLLDAFGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQELSHPNIIGLLDAFGHK 20 0 D6RAD4;P50613 D6RAD4 CDK7 Cyclin-dependent kinase 7 0 114.88 6.80E-05 19988000 94946 56913 85452 60712 107220 99944 110780 87537 90120 49650 FALSE TRUE 98694.54139 66687.36503 87678.94932 72720.65239 88994.7827 76733.52067 102096.7741 86363.7097 86876.5988 59377.96689 1.6621408 1.123099502 1.476624309 1.224707685 1.498784606 1.292289458 1.719438699 1.454474011 1.463111712 1 15.85764008 LLQHGINADDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLQHGINADDKR 12 1 Q96P70 Q96P70 IPO9 Importin-9 0 ;;; 141.38 3.93E-05 1601470000 9921970 2403880 4091080 2317940 5549360 5452900 5920780 3128090 4852600 2078240 FALSE TRUE 10313697.04 2816727.69 4197696.906 2776421.614 4606081.769 4186546.614 5456693.793 3086163.07 4677955.874 2485431.338 4.149660818 1.133295315 1.68892089 1.117078381 1.853232354 1.68443463 2.19547155 1.241701198 1.882150516 1 21.24506482 4.744381353 24.99703653 1.562646488 4.149661937 0.812508954 0.376857916 247.6467891 1063483.721 0.083931335 0.755570111 55511.29427 -4.744381353 2.587015448 LLQLVEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLQLVEDR 8 0 P17844;P17844-2;J3KTA4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 120.87 0.0033911 311702000 279651 375486 331365 372299 358455 419227 344994 382516 326894 405252 FALSE TRUE 290691.8374 439972.7996 340000.6441 445938.631 297524.9471 321867.8827 317952.4688 377388.9987 315129.1488 484653.3704 0.599793286 0.907809223 0.701533642 0.920118704 0.613892248 0.664119766 0.656040973 0.778678168 0.650215531 1 18.88659376 -1.281515853 9.182435206 1.000000069 0.728189864 0.371915557 0.108304884 1.43E-07 1.11E-08 0.098465682 0.023208578 0.052297888 1.281515853 -0.271810205 LLQQQQAVPVPPAPS(ph)SPPPLWAGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLQQQQAVPVPPAPSSPPPLWAGLAK 26 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 LLQQQQAVPVPPAPS(0.5)S(0.5)PPPLWAGLAK 62.57 0.032032 164420000 179970 152360 153660 137950 182810 212240 170790 170640 171630 152460 TRUE FALSE 187075.3546 178526.6448 157664.5058 165236.0983 151736.0215 162950.4765 157403.0335 168352.8499 165453.0698 182331.618 1.026017082 0.979131578 0.86471292 0.906239412 0.832198075 0.893703891 0.863278872 0.923333275 0.907429395 1 17.47620523 4.393929669 4.319659299 0.893805536 1.016716584 0.494022682 0.042778539 0.140591415 4.742128108 0.009815641 0.030578196 24770.20888 -4.393929669 0.122911047 LLQTCFS(ph)SPADDSMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQT(0.002)CFS(0.499)S(0.499)PADDSMDR;LLQTCFS(0.5)S(0.5)PADDSMDR;LLQT(0.007)CFS(0.497)S(0.497)PADDSMDR;LLQT(0.011)CFS(0.494)S(0.494)PADDSMDR 155.2 1.10E-06 657660000 1041000 1116920 1089810 1141360 1243390 1374290 1172650 1183310 1235070 1278520 TRUE FALSE 1082099.484 1308742.322 1118211.344 1367117.601 1032039.012 1055131.975 1080734.629 1167449.665 1190620.072 1529021.515 0.707707166 0.855934536 0.731324793 0.89411273 0.674966965 0.690070064 0.706814533 0.763527297 0.778681045 1 20.54417728 -1.743521748 4.72502817 1.01496526 0.756246292 0.538761277 0.067755059 0.010774561 0.000584852 0.066175188 0.015084737 0.018050043 1.743521748 -0.258718968 LLQTCFSS(ph)PADDSMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LLQTCFSSPADDSMDR 16 0 Q9NZL4;Q9NZL4-3;Q9NZL4-2 Q9NZL4 HSPBP1 Hsp70-binding protein 1 1 LLQTCFS(0.173)S(0.827)PADDSMDR;LLQTCFS(0.464)S(0.536)PADDSMDR;LLQTCFS(0.364)S(0.636)PADDSMDR;LLQTCFS(0.065)S(0.935)PADDSMDR;LLQTCFS(0.004)S(0.996)PADDSMDR;LLQTCFS(0.183)S(0.817)PADDSMDR;LLQTCFS(0.355)S(0.645)PADDSMDR;LLQTCFS(0.004)S(0.996)PADDSMDR 331.4 1.54E-71 1832950000 1640290 2067570 1847830 1909630 2004930 2300540 1771750 1847540 1836080 2198280 TRUE FALSE 1705049.916 2422659.064 1895985.968 2287349.114 1664132.715 1766274.45 1632875.605 1822776.748 1769999.839 2628990.877 0.648556802 0.921516725 0.721183928 0.870048327 0.632992959 0.671845028 0.621103565 0.693337038 0.67326207 1 21.32607771 4.046004616 24.99986612 0.716029401 0.794115237 0.00472172 0.127272047 358.9033334 195031.0126 0.029718864 0.064200049 11117.43543 -4.046004616 0.078085836 LLREELQLLQEQGSYVGEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLREELQLLQEQGSYVGEVVR 21 1 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 194.24 4.00E-18 173395000 122882 153617 150726 122377 165219 180250 150107 157216 147706 186824 FALSE TRUE 127733.4762 179999.5248 154654.0434 146582.8053 137135.1334 138389.6692 138341.2211 155108.7767 142390.0899 223428.5858 0.571697107 0.80562442 0.692185572 0.656061107 0.613776133 0.619391063 0.619174223 0.694220823 0.637295758 1 17.76945425 -1.211596971 3.757334555 1.000369142 0.660545286 0.740047648 0.06101667 19733343.83 32784122.29 84821.19449 0.01451565 0.061433185 1.211596971 -0.339823856 LLRPNS(ph)LR ddPTM_MDA-MB-175_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 102.52 0.0029969 1162300000 196510 272580 300900 254710 283910 342210 268230 266240 298520 390140 TRUE FALSE 204268.3665 319393.4946 308741.7012 305090.8778 235651.0796 262736.9137 247205.4317 262671.4883 287776.3235 466580.4633 0.437798799 0.684541081 0.661711592 0.653886954 0.505059895 0.563111691 0.529823795 0.562971468 0.616777482 1 18.83176637 0.754115469 4.049123773 0.999996662 0.578603206 0.755671076 0.072050089 1.766943461 28.67643688 0.069331219 0.017699671 5.676955232 -0.754115469 -0.421393457 LLS(ph)AACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;LLS(1)AACR 84.615 0.022464 157012000 116143 267940 223760 256690 223740 291310 161762 239510 192824 337460 TRUE FALSE 120728.4153 313956.6107 229591.3694 307462.5159 185708.7547 223657.6673 149082.6718 236299.7602 185884.3019 403578.8259 0.299144572 0.777931325 0.568888541 0.761840057 0.460154851 0.554185832 0.369401619 0.585510797 0.460589828 1 18.62249096 -1.355866197 3.633560546 1.002072296 0.545939508 0.478254717 0.144675754 38798972.24 65942913.97 867456.7244 0.032794521 0.044069062 1.355866197 -0.456132788 LLS(ph)DSLPPSTGTFQEAQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LLSDSLPPSTGTFQEAQSR 19 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 LLS(0.98)DS(0.02)LPPSTGTFQEAQSR;LLS(1)DSLPPSTGTFQEAQSR;LLS(0.978)DS(0.022)LPPSTGTFQEAQSR;LLS(0.615)DS(0.385)LPPSTGTFQEAQSR;LLS(0.997)DS(0.003)LPPSTGTFQEAQSR;LLS(0.982)DS(0.018)LPPSTGTFQEAQSR;LLS(0.837)DS(0.163)LPPSTGTFQEAQSR 273.94 2.26E-39 893440000 481596 474510 478932 443674 572171 639971 554254 516395 516322 452729 TRUE FALSE 500609.782 556003.4013 491413.3614 531431.393 474913.5778 491347.4341 510810.1232 509473.5697 497739.6721 541432.5795 0.924602251 1.026911609 0.907616904 0.981528288 0.877142595 0.907495139 0.943441792 0.940973242 0.919301296 1 19.04642218 LLS(ph)FQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LLSFQR 6 0 Q13946-3;Q13946-2;Q13946;A1E5M1;Q9NP56 Q13946-3;A1E5M1 PDE7A;PDE7B "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A;cAMP-specific 3,5-cyclic phosphodiesterase 7B" 1 LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR;LLS(1)FQR 118.32 0.023039 2756717000 1453862 1494509 1572819 1602171 1731160 1953097 1753961 1543017 1545819 1235942 TRUE FALSE 1511261.594 1751179.295 1613807.955 1919075.642 1436898.042 1499519.821 1616480.954 1522335.381 1490185.276 1478101.171 1.022434474 1.184749278 1.091811566 1.298338489 0.972124283 1.014490652 1.093619967 1.029926375 1.008175425 1 20.49531359 3.20103658 24.99996202 1.026579388 1.147755057 0.437116487 0.071792271 157.8328128 105153.8684 0.019891093 0.023774908 1588.680556 -3.20103658 0.121175669 LLS(ph)PGAR ddPTM_MDA-MB-175_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 124.74 0.0043183 688170000 1121980 1322160 1317060 1179870 1496150 1508070 1270230 1315610 1270250 1399620 TRUE FALSE 1166276.637 1549230.695 1351383.666 1413244.764 1241834.957 1157843.598 1170666.053 1297976.4 1224533.951 1673848.742 0.696763458 0.925549995 0.807351126 0.844308526 0.741903929 0.691725345 0.699385807 0.775444261 0.731567865 1 20.67473773 5.032725148 17.05557228 0.787416886 0.369202119 0.082066159 0.094945563 15340213.99 211198422.2 0.022032009 192145581 107826.4105 -5.032725148 -0.418214767 LLS(ph)PLSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LLSPLSSAR 9 0 A0A087WZ13;Q8IY67-2;E9PAU2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 LLS(0.996)PLS(0.004)SAR;LLS(1)PLSSAR;LLS(0.999)PLS(0.001)SAR;LLS(0.999)PLS(0.001)SAR;LLS(0.997)PLS(0.003)SAR;LLS(0.957)PLS(0.04)S(0.003)AR;LLS(1)PLSSAR 228.98 1.50E-07 4178770000 2673560 2956880 2881370 2738630 3504030 3733080 3117320 3014650 2981140 3409840 TRUE FALSE 2779114.213 3464701.139 2956460.869 3280322.84 2908416.232 2866128.745 2872976.313 2974243.548 2873849.354 4077932.863 0.681500728 0.849621918 0.724990079 0.804408251 0.713208464 0.70283863 0.704517806 0.729350788 0.704731895 1 21.95940659 -1.975452531 6.664348776 1.180667339 0.736686853 0.721941783 0.049325005 0.024920147 9.18E-05 0.008988713 0.010864546 0.010581506 1.975452531 -0.443980487 LLS(ph)PQQPALQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;LLS(1)PQQPALQR;LLS(1)PQQPALQR 217.91 1.15E-11 4750425000 1616959 1704920 1691202 1534978 1842971 2018233 1756323 1756575 1683727 1625038 TRUE FALSE 1680797.79 1997726.748 1735276.113 1838592.067 1529703.448 1549528.972 1618657.814 1733030.985 1623129.994 1943433.083 0.864860131 1.027936987 0.892892134 0.946053704 0.787114031 0.797315321 0.832885798 0.891736896 0.835186973 1 20.890176 3.264232232 24.83695575 0.850395594 0.936861334 0.221396665 0.068518098 271.8041947 262965.0108 0.01801748 0.024386962 1837.520664 -3.264232232 0.086465739 LLS(ph)PRPS(ph)LLTPTGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 LLS(1)PRPS(0.593)LLT(0.366)PT(0.04)GDPR;LLS(1)PRPS(0.76)LLT(0.237)PT(0.003)GDPR 86.727 0.0038187 97338000 100983 113432 112210 109891 125784 127999 102342 123663 113168 112193 TRUE FALSE 104969.8868 132913.0636 115134.2848 131627.1118 104403.2806 98273.17209 94320.16662 122005.4998 109095.1058 134175.0703 0.782335247 0.990594328 0.85808999 0.981010195 0.77811236 0.732424972 0.702963422 0.909300808 0.813080295 1 17.03375712 5.051904549 14.91652606 0.854083432 0.355748817 0.047036601 0.102075062 2801367.612 22327903.51 0.02465116 39907158.97 112694.9745 -5.051904549 -0.498334614 LLS(ph)PRPSLLTPTGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLSPRPSLLTPTGDPR 16 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 LLS(1)PRPSLLTPTGDPR;LLS(0.997)PRPS(0.003)LLT(0.001)PTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(1)PRPSLLTPTGDPR;LLS(0.999)PRPS(0.001)LLTPTGDPR 107.72 0.00066962 3030403000 2309547 2559219 2578486 2357588 2771340 3070950 2532931 2570370 2596880 2536780 TRUE FALSE 2400729.699 2998744.955 2645683.463 2823911.87 2300268.617 2357768.403 2334393.25 2535918.394 2503418.796 3033813.471 0.791324095 0.98844078 0.872065303 0.930812621 0.758210298 0.777163272 0.769458397 0.835884743 0.825172286 1 21.53270096 3.249417984 24.9991994 0.814487711 0.900602468 0.136646672 0.079346754 315.7981197 727124.2939 0.020419732 0.027383823 1775.897861 -3.249417984 0.086114757 LLS(ph)TKGDTLDVVLLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSTKGDTLDVVLLEAR 17 1 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 LLS(0.975)T(0.025)KGDTLDVVLLEAR;LLS(0.989)T(0.011)KGDTLDVVLLEAR 203.71 5.71E-12 74006000 70706 50278 72373 55721 126950 93814 85828 85973 90490 70765 TRUE FALSE 73497.52748 58912.85539 74259.09984 66742.44749 105371.0843 72027.12026 79100.57709 84820.67256 87233.28258 84630.04687 0.868456656 0.696122212 0.877455497 0.788637723 1.245078884 0.851082127 0.934663042 1.002252459 1.030760183 1 16.36888235 LLS(ph)VHDFDFEGDSDDSTQPQGHSLHLSSVPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLS(1)VHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 83.59 0.00076578 89525000 1867.3 8131.6 7404.7 4370.8 6755.3 9733 6109.5 9121.6 5863.7 11595 TRUE FALSE 1941.022446 9528.139045 7597.672565 5235.331194 5607.036519 7472.658255 5630.621426 8999.339872 5652.666582 13866.81825 0.13997605 0.687117901 0.54790309 0.377543796 0.404349175 0.538887733 0.406049991 0.648983762 0.407639769 1 13.75934918 -4.999999962 0.259746372 4.37369995 0.435827832 0.547923871 0.147250382 143.704213 1.412344568 258.4970657 0.183933396 1.00E-05 4.999999962 -3.937872119 LLS(ph)WSDNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 1 LLS(0.962)WS(0.038)DNWR;LLS(0.963)WS(0.037)DNWR;LLS(0.999)WS(0.001)DNWR;LLS(0.999)WS(0.001)DNWR 189.17 4.04E-05 778778000 650674 734860 743834 692952 717895 914280 766430 738930 670711 660200 TRUE FALSE 676363.1119 861066.4886 763218.9251 830015.8373 595867.4643 701952.326 706355.2139 729025.852 646572.2421 789553.5497 0.856639948 1.090573893 0.966646183 1.051247047 0.754689108 0.889049674 0.894626101 0.923339338 0.818908663 1 19.59067759 3.263716726 24.99998988 0.880962456 0.996610089 0.3019051 0.082654342 262.4557081 260825.006 0.02143039 0.029005595 1835.340831 -3.263716726 0.115647633 LLSAEFLEQHYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LLSAEFLEQHYDR 13 0 Q9Y376 Q9Y376 CAB39 Calcium-binding protein 39 0 ;;;; 223.58 1.56E-11 1454858000 1255491 1277296 1282768 1666020 1359696 1611416 1713783 1404446 1317645 1090376 FALSE TRUE 1305058.754 1496661.652 1316197.988 1995553.783 1128575.36 1237189.055 1579452.21 1385621.699 1270223.214 1304014.301 1.000800952 1.147734079 1.009343216 1.530315873 0.86546241 0.948754208 1.211223074 1.062581674 0.974086874 1 20.31452826 LLSDATVEKDESHAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLSDATVEKDESHAGK 16 1 Q14320 Q14320 FAM50A Protein FAM50A 0 ;; 200.58 2.11E-11 680080000 1179460 661440 892800 639950 1316220 1090970 1108310 872140 1049880 588480 FALSE TRUE 1226025.992 775037.1747 916067.1014 766530.1999 1092489.395 837608.7513 1021437.766 860450.3898 1012095.024 703781.3889 1.742055148 1.101247045 1.301635871 1.08915952 1.552313562 1.190154733 1.451356604 1.222610321 1.438081541 1 19.42476784 -1.358495196 3.743142949 0.998732899 1.325942069 0.209882406 0.197220305 0.001906319 0.000326707 0.170955337 0.040140355 0.043803096 1.358495196 0.327209169 LLSDFLDSEVSELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSDFLDSEVSELR 14 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 0 ; 128.28 0.00017365 10450400 18234.7 17171.9 19198.3 20676.1 20725 22842.8 18753.6 21028.2 21359.3 20225.8 FALSE TRUE 18954.62004 20121.04025 19698.62347 24765.77087 17202.1719 17537.90589 17283.64383 20746.35137 20590.58297 24188.65826 0.783616017 0.831837799 0.814374376 1.02385881 0.71116685 0.72504666 0.714535037 0.857689217 0.851249488 1 14.56204313 0.796218549 1.70173617 0.999142908 0.806424805 0.31147447 0.08645169 0.91948995 4.691018646 0.084830816 0.024160244 6.254873766 -0.796218549 -0.192718103 LLSEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSEVKK 7 1 P61163;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 75.109 0.083237 0 256260 188750 198770 153290 316680 313890 200680 189070 247110 210470 FALSE TRUE 266377.3427 221166.3442 203950.1095 183610.3045 262850.8467 240993.8045 184950.1772 186535.8259 238216.5594 251707.5668 1.058281028 0.878663868 0.810266104 0.729458819 1.044270739 0.957435677 0.734781952 0.741081519 0.946402059 1 17.94138906 2.252857185 24.99938006 0.820492216 0.904444911 0.017063039 0.121617411 592.1337777 1035420.476 0.043465524 0.036204755 179.001712 -2.252857185 0.083952694 LLSFS(ph)PEEFPTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSFSPEEFPTLK 13 0 Q5JSZ5;A0A1W2PQP5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LLSFS(1)PEEFPTLK 209.39 4.40E-07 0 238930 201660 232320 199580 311480 288110 269140 265740 269800 208320 TRUE FALSE 248363.1409 236293.5363 238374.4501 239056.3283 258534.7409 221200.8188 248044.1035 262178.19 260089.9507 249136.3155 0.99689658 0.948450794 0.956803305 0.959540274 1.037724028 0.887870636 0.995616007 1.052348348 1.043966433 1 17.92657581 1.996158173 24.98784589 1.034436611 0.964494247 0.392202555 0.037712468 146.0595471 949996.092 0.013737279 0.00992457 99.11928789 -1.996158173 -0.069942364 LLSHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSHGK 6 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 117.56 0.022615 1571740000 4194500 3818500 4273400 3755200 5076500 5263600 5105600 4498200 4528200 4099700 FALSE TRUE 4360102.099 4474297.671 4384768.315 4497967.352 4213598.343 4041208.671 4705409.731 4437908.987 4365230.967 4902957.722 0.889279971 0.912571131 0.894310856 0.917398764 0.859399282 0.824238939 0.959708404 0.905149348 0.890326047 1 22.22522089 -0.611563025 0.507768051 1.021106586 0.891849931 0.465232799 0.033834534 10.12487433 2.078170329 0.39757645 0.016466452 0.24458903 0.611563025 -0.129256655 LLSLGAQANFFHPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSLGAQANFFHPEK 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;F8W822;Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4;R4GNG3;Q14161-9;Q14161-5;F8WAK2;Q14161-11;Q14161-7;Q14161-10;Q14161-8;Q14161-2 J3QRU8;Q14161-3 GIT1;GIT2 ARF GTPase-activating protein GIT1;ARF GTPase-activating protein GIT2 0 70.783 0.045661 103320000 153050 200330 211540 181900 242910 234570 182130 220030 231090 213230 FALSE TRUE 159092.5322 234735.1191 217052.9062 217879.2771 201620.245 180094.6724 167854.1747 217080.8577 222773.116 255008.336 0.623871889 0.920499788 0.851160043 0.854400607 0.790641781 0.706230531 0.658230148 0.851269653 0.873591505 1 17.96018488 1.023614051 1.944963598 0.9961033 0.78307666 0.378475548 0.08865342 0.362797929 2.86132762 0.085166156 0.024035223 10.55878752 -1.023614051 -0.21302664 LLSLLEKDEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSLLEKDEFK 11 1 P35270 P35270 SPR Sepiapterin reductase 0 ; 186.91 3.49E-06 657780000 1555630 801120 996750 769300 1797680 1594240 1756140 1267410 1513530 843930 FALSE TRUE 1617047.474 938706.1282 1022726.124 921465.2439 1492110.996 1224001.921 1618489.158 1250422.442 1459058.351 1009281.925 1.602176194 0.930073257 1.013320558 0.91299093 1.478388702 1.212745309 1.603604619 1.238922852 1.445640028 1 19.94489779 3.231518694 24.99975756 1.347880171 1.094219754 0.159360896 0.238220645 246.1624385 873908.8181 0.064778584 0.079006316 1704.192675 -3.231518694 -0.253660417 LLSLVEKVT(ph)YLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSLVEKVTYLKK 13 2 H7BY35;Q92736;Q92736-2 H7BY35 RYR2 Ryanodine receptor 2 1 LLSLVEKVT(0.58)Y(0.42)LKK 99.653 0.0032267 0 377470 211840 320010 233480 380490 361170 356740 312040 289500 200360 TRUE FALSE 392372.8071 248221.8721 328349.7235 279661.6471 315814.4457 277293.7411 328777.7866 307857.6142 279080.9516 239616.7059 1.637501883 1.035912213 1.370312317 1.167120824 1.317998445 1.157238766 1.372098767 1.284791947 1.164697388 1 17.87036897 -4.456106777 0.206999997 2.99E-12 1.317342797 0.260627592 0.152962936 157.1057467 1.918285237 65.42677701 0.310170268 3.50E-05 4.456106777 1.317342797 LLSPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLSPGAR 7 0 P21964-2;P21964;E7EMS6;E7EUU8;F8WBW9 P21964-2 COMT Catechol O-methyltransferase 0 ; 101.21 0.021463 130337000 160937 172586 157024 168130 199345 207765 163092 162040 156956 203707 FALSE TRUE 167290.917 202226.303 161116.1744 201385.6122 165460.4081 159514.7275 150308.4229 159868.1188 151307.1842 243619.4864 0.686689392 0.830090835 0.661343544 0.82664 0.679175589 0.654769985 0.616980296 0.656220572 0.621079974 1 17.89427001 -1.067583269 4.603610463 1.000015699 0.692139233 0.622207958 0.071869414 1.19E-05 2.42E-06 0.071711 0.016901583 0.085588759 1.067583269 -0.307876466 LLSSNEDDANILSS(ph)PTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLSSNEDDANILSSPTDR 18 0 F5GY88;A0A0B4J1W0;O75448-2;O75448;H0YEG1 F5GY88 MED24 Mediator of RNA polymerase II transcription subunit 24 1 LLSSNEDDANILS(0.004)S(0.996)PTDR;LLSSNEDDANILS(0.019)S(0.98)PT(0.002)DR;LLSSNEDDANILSS(0.994)PT(0.006)DR;LLSSNEDDANILS(0.007)S(0.993)PTDR 334.08 5.50E-75 788380000 1016090 1087170 1208160 1153290 1335860 1433300 1109580 1169720 1163240 1200300 TRUE FALSE 1056206.018 1273882.99 1239645.642 1381407.32 1108790.994 1100437.797 1022608.22 1154041.817 1121375.22 1435475.804 0.735788102 0.887429093 0.863578222 0.962334103 0.772420539 0.766601425 0.712382764 0.803943761 0.781187127 1 20.45309758 3.135546745 22.00322001 0.788843301 0.864618617 0.068746329 0.088404767 8.94794661 1884.980172 0.024118349 0.028826989 1366.30213 -3.135546745 0.075775317 LLSSS(ph)LTADCSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLSSSLTADCSLR 13 0 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLS(0.008)S(0.053)S(0.887)LT(0.053)ADCSLR;LLSS(0.017)S(0.983)LTADCSLR;LLSS(0.072)S(0.928)LTADCSLR;LLSS(0.001)S(0.921)LT(0.078)ADCSLR 344.55 9.02E-64 491931000 603058 738880 768878 868310 973074 1064390 854369 904725 894013 1067919 TRUE FALSE 626867.1955 865776.8923 788915.5923 1040059.126 807671.2291 817201.5535 787401.3253 892598.6412 861837.6468 1277157.282 0.490830068 0.677893714 0.617712167 0.814354772 0.632397623 0.639859761 0.616526513 0.698894846 0.674809328 1 20.28450477 -5 0.284721149 3.597343503 0.634824539 0.666964916 0.07480196 139.5178726 1.326260854 214.5762212 0.080308925 1.00E-05 5 -2.962518963 LLSSSLT(ph)ADCSLRSPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSSSLTADCSLRSPSGR 18 1 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSSS(0.001)LT(0.768)ADCS(0.06)LRS(0.167)PS(0.003)GR 93.258 0.013902 89139000 104750 127610 121920 108850 129500 158910 114430 110070 118820 154100 TRUE FALSE 108885.6109 149526.0248 125097.3354 130380.2051 107487.6363 122005.5608 105460.6776 108594.6917 114543.6914 184292.9446 0.590828971 0.811349697 0.678796118 0.707461728 0.58324336 0.662019705 0.572244791 0.589250402 0.621530529 1 17.49164131 -0.986283218 12.88113515 1 0.645126103 0.698024821 0.069787721 0 0 0.070596163 0.016639675 0.103208813 0.986283218 -0.354873897 LLSSSLTADCSLRS(ph)PSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLSSSLTADCSLRSPSGR 18 1 Q147X3;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 LLSSSLT(0.041)ADCS(0.029)LRS(0.901)PS(0.029)GR;LLSSSLTADCSLRS(0.995)PS(0.005)GR;LLSSSLTADCS(0.001)LRS(0.954)PS(0.045)GR 184.56 3.49E-14 1051730000 420597 451635 458534 418542 523014 571526 404114 456641 480456 576471 TRUE FALSE 437202.4943 529199.798 470483.7727 501328.3584 434112.2671 438797.7481 372438.4887 450520.4743 463164.4824 689419.4552 0.634160366 0.767602066 0.68243472 0.727174661 0.629678005 0.636474275 0.540220451 0.65347804 0.67181812 1 19.39502249 -1.486838227 5.329445716 1.000628277 0.658791989 0.757218976 0.057692591 0.000457158 4.40E-05 0.059294881 0.013951086 0.03259581 1.486838227 -0.341836288 LLSVHDFDFEGDS(ph)DDSTQPQGHSLHLSSVPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LLSVHDFDFEGDSDDSTQPQGHSLHLSSVPEAR 33 0 Q9BV36-2;Q9BV36-5;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.993)DDS(0.006)T(0.002)QPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(0.996)DDS(0.002)T(0.002)QPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR;LLSVHDFDFEGDS(1)DDSTQPQGHSLHLSSVPEAR 359.42 5.24E-132 2679906000 49373.1 733300 486403 675455 433871 837552 361913 716806 411099.7 856435 TRUE FALSE 51322.38811 859238.5707 499079.0618 809057.983 360121.7624 643043.2412 333545.3134 707198.388 396304.3021 1024237.041 0.05010792 0.838905972 0.487269101 0.789912833 0.351600018 0.627826583 0.325652461 0.690463594 0.386926352 1 19.96611821 -1.547380319 3.094610133 1.01874938 0.52655963 0.292391811 0.228704317 44755019.87 50380164.5 6983399.154 0.048842789 0.028354349 1.547380319 -0.492189749 LLSWSDNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLSWSDNWR 9 0 Q8TCD5;J3KSY6;J3KSX6 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 131.22 0.00078905 176120000 134100 182900 183010 170330 216590 230670 194800 163680 175410 198410 FALSE TRUE 139394.3715 214311.6522 187779.3909 204020.7656 179774.1092 177100.3883 179531.067 161486.1373 169097.0284 237284.6407 0.587456361 0.903183837 0.79136766 0.859814462 0.757630619 0.746362629 0.756606354 0.680558745 0.712633687 1 17.85625919 3.032099889 24.70863908 0.751439129 0.796091487 0 0.112891624 692.3925402 532959.1751 0.0305997 0.036573428 1076.712832 -3.032099889 0.044652358 LLT(ph)PTHSFLAR ddPTM_MDA-MB-175_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(0.982)PT(0.018)HSFLAR;LLT(0.992)PT(0.008)HSFLAR 168.31 6.70E-05 329150000 234940 208970 196217 169907 230170 274200 207880 192999 203021 223580 TRUE FALSE 244215.6126 244858.9719 201330.5762 203514.0975 191045.7856 210521.2055 191585.8224 190412.1641 195714.3139 267386.2203 0.913344047 0.915750152 0.752957935 0.761124104 0.714493759 0.787330048 0.716513447 0.712124072 0.731953627 1 18.02856559 4.238725302 24.99083822 0.754917297 0.914547157 0.311403887 0.081626519 3.758618712 569909.1859 0.018178447 0.043866636 17327.07685 -4.238725302 0.15962986 LLTDDGNKWLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLTDDGNKWLYK 12 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 176.05 2.37E-05 1392210000 1648810 1316860 1530540 1040990 2251440 1960070 1653550 1626720 1812130 1526460 FALSE TRUE 1713906.292 1543020.461 1570427.13 1246894.715 1868741.033 1504873.448 1523940.43 1604916.479 1746911.795 1825540.611 0.938848625 0.845240282 0.860253188 0.683027651 1.023664454 0.824343999 0.834788567 0.879145865 0.956928476 1 20.79989233 1.175855385 2.532620844 0.998461497 0.856283282 0.25848675 0.081576627 0.344485535 3.907135735 0.072305795 0.020181549 14.99185542 -1.175855385 -0.142178215 LLTQHENIKNEIDNYEEDYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLTQHENIKNEIDNYEEDYQK 21 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 274.8 5.65E-45 132880000 227100 138730 167330 98549 214930 200890 206900 172180 190560 118150 FALSE TRUE 236066.0834 162555.7983 171690.7573 118041.6981 178396.2754 154236.342 190682.6374 169872.2087 183701.7828 141299.2304 1.670682018 1.150436544 1.215086287 0.835402272 1.262542442 1.09155826 1.34949523 1.202216093 1.30009047 1 17.10839408 4.739691682 24.19000867 1.166319257 1.670682277 0.533549777 0.14400816 47.82943472 1022714.796 0.0334703 0.20627025 54915.08774 -4.739691682 0.50436302 LLVDADNCLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLVDADNCLHR 11 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ;;; 221.32 8.50E-12 712880000 1101830 1268810 1228000 1356080 1367080 1477930 1213420 1223880 1169860 1258430 FALSE TRUE 1145331.099 1486718.248 1260002.689 1624308.577 1134704.23 1134703.156 1118308.97 1207475.89 1127756.967 1504995.264 0.761019736 0.987855765 0.837213723 1.079278198 0.753958671 0.753957958 0.743064776 0.802312086 0.749342535 1 20.52132752 LLVDSQGLSGCS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLVDSQGLSGCSPR 14 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 LLVDS(0.012)QGLS(0.024)GCS(0.965)PR;LLVDSQGLS(0.002)GCS(0.998)PR 98.328 0.0027495 554377000 648256 957410 777417 976970 838424 1094210 749825 872080 835198 1031260 TRUE FALSE 673849.6474 1121837.72 797677.1257 1170211.75 695908.988 840096.3104 691051.7572 860391.194 805139.3871 1233315.652 0.546372412 0.909611191 0.646774509 0.94883394 0.56425862 0.681168936 0.560320268 0.697624483 0.652825078 1 20.23411066 -1.047844337 4.408659678 1.00001773 0.693293253 0.334686544 0.131140918 0.608094784 72201216.76 3079.348877 0.028760199 0.089568575 1.047844337 -0.306724476 LLVDVDESTLSPEEQKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 304.9 5.56E-50 766680000 1062290 839229 1103830 833143 1374230 1268780 1077420 1037870 1201980 898215 FALSE TRUE 1104230.029 983360.0525 1132596.717 997936.1987 1140638.875 974125.0735 992969.0051 1023959.05 1158720.975 1074203.032 1.027952814 0.915432207 1.054360007 0.929001473 1.061846636 0.906835156 0.924377399 0.953226736 1.078679672 1 20.03483527 2.722958208 24.96976769 0.964388334 0.992476292 0.027220553 0.062636886 2980.357597 4769700.846 0.019491539 0.01845075 528.3944016 -2.722958208 0.028087958 LLVGNDDVHIIARS(ph)DDELLDDFFHDQSTATSQAGTLSSIPTALTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLVGNDDVHIIARSDDELLDDFFHDQSTATSQAGTLSSIPTALTR 45 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 LLVGNDDVHIIARS(0.999)DDELLDDFFHDQSTATSQAGTLSSIPTALTR;LLVGNDDVHIIARS(0.754)DDELLDDFFHDQS(0.185)T(0.056)AT(0.005)S(0.001)QAGTLSSIPTALTR 199.82 2.20E-36 227230000 17245.3 24814.4 22743 22755.6 23893.4 25220.6 18390.4 21579.5 21601 30138.6 TRUE FALSE 17926.15776 29076.08017 23335.70126 27256.58976 19832.0084 19363.49787 16948.91239 21290.2621 20823.58423 36043.68163 0.497345358 0.806690073 0.647428348 0.756209924 0.550221495 0.537223086 0.470232552 0.590679452 0.577731888 1 15.13745876 -1.831341558 6.585395741 1.030611224 0.605030748 0.576873071 0.101803242 0.041751942 0.001069308 0.089949414 0.023915016 0.014745464 1.831341558 -0.425580477 LLVHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLVHLK 6 0 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ; 84.566 0.055705 644440000 869220 903750 938110 867170 1344820 1266580 1098300 1005590 1070920 1136620 FALSE TRUE 903537.4768 1058962.032 962557.9173 1038693.638 1116227.977 972435.9902 1012212.376 992111.7109 1032377.798 1359318.927 0.664698665 0.779038687 0.708117792 0.764127989 0.821167097 0.71538472 0.744646717 0.729859411 0.759481662 1 20.37445255 0.816026451 6.354568669 0.999999937 0.743203833 0.787183515 0.040185582 3.762930068 129.9895905 0.036543044 0.009178399 6.54676047 -0.816026451 -0.256796104 LLVLDVDYTLFDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLVLDVDYTLFDHR 14 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 ;; 226.04 2.55E-12 263704300 250533 283791 276746 294252 309561 350674 302973 278869 284568 279934 FALSE TRUE 260424.2363 332529.8967 283958.2281 352454.1673 256941.9318 269235.278 279225.1846 275131.2172 274326.4533 334781.7076 0.77789267 0.993273793 0.848189198 1.052788009 0.767490953 0.804211437 0.834051497 0.821822731 0.819418884 1 18.35286118 3.199060289 24.9998263 0.829583314 0.918421892 0.14015205 0.090588532 244.0369692 154450.6902 0.023986233 0.028669418 1581.467564 -3.199060289 0.088838577 LLVQTSVQAKPGHVS(ph)PLQLTNIQVPQQALPTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLVQTSVQAKPGHVSPLQLTNIQVPQQALPTQR 33 1 P22670 P22670 RFX1 MHC class II regulatory factor RFX1 1 LLVQT(0.028)S(0.028)VQAKPGHVS(0.944)PLQLTNIQVPQQALPTQR 137.71 7.57E-09 191070000 89016 95883 101350 76403 105600 118530 94370 104060 119240 103560 TRUE FALSE 92530.42042 112350.1594 103991.2643 91515.28536 87650.14972 91003.20384 86973.03281 102665.2459 114948.5757 123850.5992 0.747113223 0.907142639 0.839650877 0.738916775 0.707708725 0.734782104 0.702241518 0.828944281 0.928122887 1 16.91824132 1.207281294 2.414617557 0.994317073 0.771468386 0.632416632 0.059819498 0.192228457 1.931198534 0.060958866 0.01727726 16.11689194 -1.207281294 -0.222848688 LLVSMCQGNRDENQSINHQMAQEDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LLVSMCQGNRDENQSINHQMAQEDAQR 27 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 242.44 1.80E-45 623001000 67522.8 169093 142654 151743 120684 169520 114868 137278 133589 186315 FALSE TRUE 70188.65228 198133.4074 146371.6804 181757.3125 100170.1768 130151.5491 105864.346 135438.013 128781.158 222819.857 0.315001783 0.889208933 0.656905908 0.81571416 0.449556777 0.584111088 0.475111812 0.607836369 0.577960868 1 17.76551828 -1.675939138 6.604067458 1.002868382 0.60394385 0.364716901 0.159383813 0.006394458 0.000313775 0.146601875 0.034371313 0.021089237 1.675939138 -0.398924532 LLVVDRETDEFFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLVVDRETDEFFKK 14 2 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 103.76 0.00061701 186440000 144830 642210 529990 602180 404020 666920 350120 542330 456870 886640 FALSE TRUE 150548.0002 752504.5718 543801.9748 721289.4067 335344.8247 512037.9373 322676.6795 535060.9534 440427.3379 1060360.132 0.141978179 0.709668865 0.512846493 0.680230598 0.316255595 0.482890597 0.304308574 0.504603047 0.415356372 1 20.0161229 -1.333955519 4.504030836 1.000538357 0.461785488 0.504625376 0.162622488 0.000815569 0.000120605 0.146074134 0.034396693 0.046349439 1.333955519 -0.538752869 LLWAGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLWAGDDR 8 0 A0A087X091 A0A087X091 WDR13 0 84.244 0.040921 27707000 106840 138450 116020 119620 126390 165830 118410 133780 117860 149190 FALSE TRUE 111058.1257 162227.7105 119043.5765 143280.479 104906.2729 127318.4957 109128.7148 131986.8979 113618.2416 178420.9241 0.622450121 0.90924151 0.667206367 0.803047511 0.587970685 0.713585003 0.611636305 0.739750108 0.636798863 1 17.44492529 -1.864995776 8.234156231 1.022935241 0.703415006 0.480959453 0.093685465 0.033025416 0.000541473 0.075946911 0.019755911 0.013645964 1.864995776 -0.319520234 LLWEQELYNNFVYNSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLWEQELYNNFVYNSPR 17 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 0 163.27 8.58E-09 0 10638 11430 12149 8686.8 17129 17418 13888 10152 13368 13530 FALSE TRUE 11057.99645 13393.01359 12465.61292 10405.02311 14217.4187 13372.93347 12799.42227 10015.92905 12886.88829 16180.94445 0.683396231 0.827702834 0.770388463 0.643041767 0.878651969 0.826461861 0.791018244 0.61899533 0.79642374 1 13.9820082 -2.434810585 1.934984711 2.698736856 0.755236182 0.443502622 0.080667493 3955409.051 307044.2996 29416587.21 0.020433249 0.003674425 2.434810585 -1.943500675 LLWHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LLWHGSR 7 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 86.953 0.019698 630870000 32675 323550 226510 314800 269510 382670 226750 278140 209370 394790 FALSE TRUE 33965.03423 379117.1956 232413.0367 377066.5004 223698.7865 293800.6919 208976.7425 274411.9882 201834.8146 472141.5418 0.071938246 0.802973604 0.492252886 0.798630214 0.473796027 0.622272488 0.442614606 0.581207041 0.427487939 1 18.8488599 -1.654744558 2.88662205 1.046259846 0.54017733 0.339520181 0.198103834 43266685.01 42168366.87 14875379.92 0.042312867 0.022143968 1.654744558 -0.506082517 LLYDLADQLHAAVGASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLYDLADQLHAAVGASR 17 0 H0YL12;P13804-2;P13804;H0YK49;H0YNX6 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 ; 216.96 5.13E-15 457990000 340160 597000 457310 578440 414220 668140 421230 459010 418890 639920 FALSE TRUE 353589.7795 699530.106 469227.8743 692853.7055 343811.0324 512974.6108 388212.8919 452857.7217 403814.2307 765300.072 0.462027631 0.914059898 0.61312927 0.905335999 0.449249967 0.670292124 0.507268856 0.591738768 0.527654766 1 19.54566601 -1.147997655 4.665701132 1.000039074 0.630960814 0.337001135 0.156958342 6.02E-05 1.10E-05 0.143312401 0.033775487 0.071121735 1.147997655 -0.36907826 LLYNNVSNFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LLYNNVSNFGR 11 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 243.65 1.82E-15 1026390000 344500 345600 305970 299110 365810 376380 324680 305730 314800 340200 FALSE TRUE 358101.126 404954.1116 313943.8296 358273.0652 303629.7469 288971.4491 299230.7332 301632.1894 303470.4095 406855.6765 0.880167457 0.995326193 0.771634385 0.880590062 0.746283669 0.710255419 0.735471447 0.741373924 0.745892037 1 18.63415759 3.917056355 1.28976204 0.763338164 0.936896608 0.213692027 0.092604704 0.586663065 1.771507299 0.026493711 0.09079947 8261.451451 -3.917056355 0.173558444 LMDLLGEGLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMDLLGEGLKR 11 1 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 72.096 0.075732 651240000 254450 255450 260760 249700 438760 356130 367130 320140 362670 336030 FALSE TRUE 264495.8825 299321.5504 267555.6198 299089.9147 364179.7319 273424.2047 338353.3913 315849.0469 349617.5775 401868.6448 0.658165015 0.744824346 0.665778789 0.744247949 0.906215841 0.680382031 0.841950213 0.785950959 0.869979736 1 18.61636449 -4.99999991 0.054775121 1.962535512 0.326377916 0.648308071 0.063783526 284.606744 1.146798736 37.89757962 7.375170512 1.00E-05 4.99999991 -1.636157596 LMEDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 26 LMEDLDR 7 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;;;;;;;;;;; 249.47 1.87E-08 2.71574E+11 63582161 81736403 75622892 84440291 81144444 90953623 86681085 80265995 71792873 77654190 FALSE TRUE 66092433.81 95773994.39 77593686.69 101142328.5 67351540.39 69831022.47 79886795.06 79190160.63 69209061.52 92869041.75 0.711673477 1.031280097 0.835517253 1.089085519 0.725231349 0.751930042 0.860209103 0.852707847 0.745232859 1 26.46869441 3.203720674 24.99997482 0.817270383 0.919248358 0.1266979 0.120794771 333.5404735 239336.5898 0.032642038 0.039016322 1598.529568 -3.203720674 0.101977974 LMEDLDRNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 LMEDLDRNK 9 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;;;;;;;;; 196.88 2.64E-05 27857037000 11799089 10316133 12391762 7290814 18712750 14846054 10340799 11494428 13445003 13793971 FALSE TRUE 12264926.14 12087848.59 12714701.5 8732915.248 15531963.44 11398282.95 9530260.154 11340363.99 12961119.97 16496635.52 0.743480459 0.732746297 0.770745131 0.529375535 0.941523102 0.690945917 0.577709324 0.687434961 0.785682629 1 23.97566848 0.887802335 3.707775474 0.999869474 0.706485376 0.410819999 0.104915393 0.48737116 13.60404046 0.097422433 0.025040237 7.723289871 -0.887802335 -0.293384098 LMEEDELPSWIIKDDAEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 116.39 8.72E-05 23435000 13588 26340 24091 28113 21948 36262 23625 22807 25613 28655 FALSE TRUE 14124.46473 30863.6901 24718.83125 33673.66749 18217.2868 27840.70006 21773.21077 22501.30947 24691.19313 34269.39862 0.412159691 0.900619542 0.721309164 0.982616236 0.531590502 0.812407021 0.635354329 0.656600652 0.720502668 1 15.06463325 0.921510017 19.57563813 1.000000001 0.712398553 0.234176844 0.158243475 5902.930985 1472214.926 0.140289618 0.035072405 8.346607988 -0.921510017 -0.287601448 LMELHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMELHFK 7 0 A0A087WUB9;Q8WYA6;Q8WYA6-4;Q8WYA6-3;Q8WYA6-2 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 0 86.866 0.036526 0 136800 131300 147030 127290 223930 194230 171770 150290 164520 177610 FALSE TRUE 142200.9696 153849.7536 150861.7226 152467.5821 185866.4586 149123.0261 158306.2186 148275.6084 158598.9573 212409.279 0.669466844 0.724308064 0.710240736 0.717800949 0.875039261 0.70205514 0.745288621 0.698065589 0.746666803 1 17.69648727 0.942572217 21.21937003 1 0.73135304 0.703534297 0.052264016 1798.503696 664542.8015 0.04980061 0.012449949 8.761373953 -0.942572217 -0.26864696 LMELHGEGSSSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LMELHGEGSSSGK 13 0 P61247;D6RG13;D6RAT0;H0Y9Y4;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;;; 182.1 1.15E-05 4175250000 4424180 6005940 6836790 5894050 7814510 8376530 7202540 7349380 7144100 6099320 FALSE TRUE 4598850.043 7037413.475 7014962.364 7059875.498 6486202.381 6431207.855 6637986.094 7250873.582 6886985.237 7294364.975 0.630466128 0.964773973 0.961696102 0.967853339 0.889207272 0.881667956 0.910015624 0.994037672 0.944151446 1 22.79835096 4.740884524 24.99832386 0.943845664 0.630466019 0.856485967 0.038731818 77.98849307 838872.1216 0.009857787 0.065837006 55066.12592 -4.740884524 -0.313379645 LMELYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LMELYER 7 0 Q9UG63;Q9UG63-2;C9JHK9;C9JZV3 Q9UG63 ABCF2 ATP-binding cassette sub-family F member 2 0 ;; 117.18 0.030951 37133000 159852 217649 200830 211511 243235 277417 215124 200181 193460 278194 FALSE TRUE 166163.0804 255028.5227 206063.7948 253347.2445 201890.0016 212991.106 198262.0188 197497.9011 186497.4124 332700.788 0.499436991 0.766540182 0.619366717 0.761486758 0.606821531 0.640188162 0.59591689 0.593620178 0.560555968 1 18.34386576 -1.353335938 5.419178674 1.000115617 0.630670257 0.671812667 0.078153314 0.000103462 1.23E-05 0.071714394 0.016897991 0.044326563 1.353335938 -0.36944536 LMFEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LMFEELR 7 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;;;; 140.12 0.0061558 490820000 1167109 1558281 1367790 1350741 1737517 1799620 1455332 1452922 1366964 1881880 FALSE TRUE 1213187.365 1825903.64 1403435.731 1617913.538 1442174.481 1381685.529 1341259.275 1433447.957 1317767.233 2250598.355 0.539051031 0.811296976 0.623583381 0.718881507 0.640796025 0.613919194 0.595956747 0.636918602 0.585518615 1 21.10187718 -1.953904096 2.667607946 1.268029116 0.644235415 0.691749492 0.071926905 10291093.72 4141008.991 17055933.74 0.016538756 0.011119773 1.953904096 -0.623793702 LMHNAS(ph)DS(ph)EVDQDDVVEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 2 LMHNAS(1)DS(1)EVDQDDVVEWK;LMHNAS(1)DS(1)EVDQDDVVEWK 112.88 0.00017689 180627000 195837 138032 171667 154669 212640 204034 209500 188867 189773 110782 TRUE FALSE 203568.796 161737.9223 176140.783 185262.0666 176495.5288 156650.1957 193078.8426 186335.5468 182943.1068 132487.6119 1.536511928 1.220777701 1.329488702 1.398335014 1.332166278 1.182376174 1.457335066 1.406437509 1.380831794 1 17.01549794 -2.210081799 2.121678262 0.000108931 1.358278369 0.545579265 0.098676562 2237859.552 452083.7937 10714944.32 0.023244373 0.006164789 2.210081799 1.358169438 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LMHNASDSEVDQDDVVEWK 19 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LMHNAS(0.988)DS(0.012)EVDQDDVVEWK;LMHNAS(0.956)DS(0.044)EVDQDDVVEWK;LMHNAS(0.999)DS(0.001)EVDQDDVVEWK;LMHNAS(0.989)DS(0.011)EVDQDDVVEWK;LMHNAS(0.96)DS(0.04)EVDQDDVVEWK;LMHNAS(0.713)DS(0.287)EVDQDDVVEWK;LMHNAS(0.86)DS(0.14)EVDQDDVVEWK 260.01 2.78E-31 1940090000 1675754 1334224 1578727 1353492 1744609 2004610 1955826 1558872 1719375 1120012 TRUE FALSE 1741914.062 1563366.593 1619869.923 1621208.678 1448060.985 1539069.708 1802523.248 1537977.871 1657495.03 1339456.907 1.300462936 1.167164531 1.209348291 1.210347768 1.081080681 1.149025175 1.34571201 1.148210041 1.237438114 1 20.35321674 -1.192466035 3.474791702 0.999694244 1.201456339 0.415170383 0.073005792 11299990.21 16353250.36 37944.61348 0.017008693 0.064199843 1.192466035 0.201762095 LMIWDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 118.69 0.011517 2001432000 2903927 3782055 3356224 3246562 4944851 4396104 3645141 3290526 3297983 5571164 FALSE TRUE 3018576.28 4431593.526 3443689.955 3888722.274 4104326.993 3375175.47 3359425.324 3246421.881 3179289.236 6662726.919 0.45305418 0.665132097 0.516858937 0.583653258 0.616013089 0.506575687 0.504211769 0.487251229 0.477175378 1 22.66768133 -1.675764488 6.544402756 1.003504954 0.535901546 0.828752707 0.063486055 0.003248663 0.000160952 0.061508691 0.014429284 0.021097719 1.675764488 -0.467603408 LMKPPS(ph)PEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LMKPPSPEHQSLDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR 43 1 Q9Y6X9;Q9Y6X9-2;H7C1V1 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 LMKPPS(0.502)PEHQS(0.469)LDT(0.03)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.999)PEHQS(0.001)LDTQQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.333)PEHQS(0.333)LDT(0.333)QQEGGEEEVGPVAQQAIAVAEPSTSECLR;LMKPPS(0.942)PEHQS(0.054)LDT(0.003)QQEGGEEEVGPVAQQAIAVAEPSTSECLR 316.85 1.97E-114 521035000 144285 233999 287299 250289 331535 402614 303973 317690 279550 233304 TRUE FALSE 149981.4832 274186.508 294786.248 299795.4172 275180.7991 309113.0002 280146.802 313431.8852 269489.0501 279015.4519 0.53753827 0.982692916 1.05652302 1.074476037 0.986256486 1.107870543 1.004054794 1.12334956 0.965857082 1 18.0899855 4.743850968 3.267798853 1.047364383 0.463093419 0.900142787 0.049817155 0.084991429 1.450218086 0.011151233 0.126542714 55443.5421 -4.743850968 -0.584270964 LMLDWAEDNLIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMLDWAEDNLIHK 13 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 136.24 7.46E-05 316450000 155930 152950 200860 185830 216650 235160 197000 185870 207210 166820 FALSE TRUE 162086.2368 179217.9727 206094.5766 222586.6194 179823.9104 180547.6539 181558.6252 183378.7167 199752.5526 199505.185 0.812441224 0.898312356 1.033028673 1.115693406 0.901349558 0.904977251 0.910044645 0.919167673 1.001239905 1 17.60606672 8 0.007068761 1.816046056 1.39E-05 0.063930483 0.079786881 125301.5659 68.49822475 7919.871847 9767.762369 99999999.99 -8 -1.816032175 LMLLLEVISGERLPKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMLLLEVISGERLPKPER 18 2 O43707 O43707 ACTN4 Alpha-actinin-4 0 ; 186.75 2.61E-14 129996000 164676 132318 149432 130807 216131 192577 176129 164650 178381 169127 FALSE TRUE 171177.5356 155042.5872 153326.3207 156680.2342 179393.1298 147853.9103 162323.5488 162443.1361 171961.1027 202264.1975 0.846306651 0.766535003 0.758049732 0.774631576 0.886924785 0.730993978 0.802532286 0.803123529 0.850180629 1 17.62588145 0.751737647 1.604801584 0.999929742 0.793030407 0.679215013 0.042274524 0.469441098 2.004647244 0.038438792 0.011050455 5.645958045 -0.751737647 -0.206899336 LMLPDS(ph)PLVEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LMLPDSPLVEEGR 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR 242.4 6.54E-17 2019267000 1244436 1553326 1417548 1536365 1549976 1814130 1564875 1600363 1495723 1765901 TRUE FALSE 1293567.294 1820097.657 1454490.465 1840253.411 1286511.633 1392825.801 1442216.008 1578912.752 1441892.221 2111895.491 0.612514824 0.86183131 0.688713278 0.871375226 0.60917391 0.659514548 0.682901221 0.74762826 0.682747905 1 21.01010701 -1.369602773 4.022116083 1.000822905 0.717589783 0.497293743 0.086473393 0.000599164 9.39E-05 0.078618797 0.018477885 0.042696987 1.369602773 -0.283233121 LMLPDS(ph)PLVEEGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LMLPDSPLVEEGRR 14 1 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR;LMLPDS(1)PLVEEGRR 272.24 3.44E-33 1043116000 677575 829882 762905 792644 902291 992271 779316 841077 851140 1082968 TRUE FALSE 704326.1842 972407.7779 782786.931 949426.6174 748919.8981 761831.0983 718231.1756 829803.7385 820507.6377 1295154.845 0.543816198 0.750804262 0.604396404 0.733060314 0.578247382 0.588216229 0.55455236 0.640698478 0.63352088 1 20.30469316 0.316350964 2.317697302 1.000000725 0.626196491 0.744982443 0.065790358 11.36482853 37.60181668 0.060472334 0.016274182 2.071814959 -0.316350964 -0.373804234 LMLSTSEYSQS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMLSTSEYSQSPK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LMLSTSEYSQS(1)PK;LMLSTSEYSQS(1)PK 271.43 4.56E-32 196985000 433560 182045 222890 185091 270650 327800 262860 229170 249060 175506 TRUE FALSE 450677.2836 213309.8126 228698.6965 221701.4474 224645.0097 251673.4179 242256.3463 226098.351 240096.3793 209893.0404 2.147175927 1.016278635 1.089596377 1.056259164 1.07028327 1.199055563 1.154189514 1.07720747 1.143898715 1 17.67929481 4.741196844 24.9944297 1.09587656 2.147176301 0.96685535 0.05873087 38.15208743 361704.9086 0.013928405 0.09584126 55105.74063 -4.741196844 1.051299741 LMNESLMLVTALNPHIGYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMNESLMLVTALNPHIGYDK 20 0 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 ; 229.1 2.59E-25 1052420000 903020 891040 1022840 890470 1151950 1339880 1147570 1015130 1101750 959050 FALSE TRUE 938671.9269 1044069.189 1049496.051 1066602.308 956141.9505 1028713.176 1057620.465 1001523.843 1062098.233 1146957.485 0.818401675 0.910294585 0.915026114 0.929940579 0.833633297 0.89690611 0.922109562 0.873200494 0.926013602 1 20.12938048 0.925424438 4.102679806 0.999962661 0.890095341 0.489109503 0.035103087 0.279507459 11.78086193 0.032354279 0.008260819 8.422178437 -0.925424438 -0.109867321 LMQLVDHR ddPTM_MDA-MB-175_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 3505378000 2660495 3419695 2925788 3030705 4049283 3973170 3049631 2982593 2811296 4090577 FALSE TRUE 2765533.397 4007001.015 3002036.439 3630169.403 3360987.322 3050461.481 2810592.953 2942616.219 2710118.006 4892047.244 0.565312079 0.819084693 0.613656469 0.742055263 0.687030839 0.623555197 0.574522856 0.60151018 0.55398443 1 22.22200691 -1.108074537 4.998807394 1.000012376 0.644252173 0.641281281 0.080246614 1.10E-05 1.97E-06 0.077533647 0.018274221 0.077969628 1.108074537 -0.355760203 LMS(ph)DVEDVSLENVHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LMSDVEDVSLENVHTR 16 0 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 1 LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR;LMS(1)DVEDVSLENVHTR 210.12 6.77E-12 110194000 73551 56204 69704 65894 72681 87319 87084 66411 77485 41265.1 TRUE FALSE 76454.85027 65856.59979 71520.5435 78927.63653 60326.70958 67040.48558 80258.12853 65520.86917 74696.32999 49350.20628 1.549230612 1.334474661 1.449245077 1.59933752 1.222420616 1.358464141 1.626297732 1.327671637 1.513597118 1 15.59076849 -1.324095623 3.718512146 0.998667545 1.435132918 0.530065724 0.124774132 6903443.227 5011883.594 68462.10384 0.027539037 0.047413758 1.324095623 0.436465373 LMSELYHPDDHVL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LMSELYHPDDHVL 13 0 P49770 P49770 EIF2B2 Translation initiation factor eIF-2B subunit beta 0 ;; 133.07 0.00011148 136834000 247029 346140 323791 329080 372329 414658 312089 320787 323872 378240 FALSE TRUE 256781.8957 405586.8524 332229.2595 394171.0418 309040.6496 318359.9637 287626.6487 316487.375 312215.91 452348.8862 0.567663376 0.896623966 0.734453581 0.871387228 0.683190915 0.703792965 0.635851347 0.699653265 0.69021041 1 18.78707639 -1.020826797 4.599407713 1.000007488 0.723356667 0.445249851 0.093601217 8.03E-06 1.71E-06 0.087431118 0.020607066 0.095317623 1.020826797 -0.276650822 LMSLLTSPHQPPPPPPASASPSAVPNGPQS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMSLLTSPHQPPPPPPASASPSAVPNGPQSPK 32 0 Q96RU3-5;Q96RU3-2;Q96RU3 Q96RU3-5 FNBP1 Formin-binding protein 1 1 LMSLLTSPHQPPPPPPASASPSAVPNGPQS(1)PK 179.5 1.19E-19 396020000 210600 142800 191160 135470 239890 257540 226630 207870 212050 156460 TRUE FALSE 218914.6506 167324.7892 196141.7866 162265.5617 199113.5835 197730.2381 208866.1484 205083.8427 204418.3619 187115.3414 1.16994496 0.894233407 1.048240006 0.867195391 1.064122172 1.056729163 1.116242778 1.096029011 1.092472485 1 17.51356832 3.026125614 24.99041815 1.080985469 0.988289491 0.162671467 0.082976776 314.2068627 300551.7829 0.022237327 0.026577939 1062.002684 -3.026125614 -0.092695978 LMSNLDSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMSNLDSNR 9 0 P26447 P26447 S100A4 Protein S100-A4 0 ; 121.5 0.0014239 755760000 861390 1053970 934660 999780 1294220 1315420 950840 982790 869640 1236330 FALSE TRUE 895398.3423 1234981.149 959018.0074 1197533.5 1074228.947 1009933.64 876310.6762 969617.3076 838341.8263 1478565.193 0.605585974 0.835256474 0.648613948 0.809929455 0.726534719 0.683049787 0.592676387 0.655782587 0.566996863 1 20.49576643 -1.158262435 5.023654394 1.000018699 0.683475945 0.564764619 0.084108931 1.75E-05 2.93E-06 0.080808042 0.019045514 0.069460446 1.158262435 -0.316542754 LMSSLPNFCGIFNHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMSSLPNFCGIFNHLER 17 0 Q96PU8-5;Q96PU8-9;Q96PU8-8;Q96PU8-6;Q96PU8-3;Q96PU8;H0YFB7 Q96PU8-5 QKI Protein quaking 0 ; 227.22 1.82E-15 286960000 124045 142836 157314 146157 198225 200329 150943 140124 180214 190496 FALSE TRUE 128942.3924 167366.9719 161413.7321 175066.4184 164530.7853 153805.6258 139111.6932 138245.867 173728.1333 227820.0439 0.565983529 0.734645508 0.708514182 0.768441685 0.722196267 0.675118936 0.610620957 0.606820474 0.762567377 1 17.79753516 0.93107215 6.319068771 0.999989306 0.675694592 0.727150576 0.060289059 0.362120463 32.49033119 0.062514941 0.015703981 8.532418518 -0.93107215 -0.324294714 LMSTGTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMSTGTSR 8 0 Q92828 Q92828 CORO2A Coronin-2A 0 76.847 0.080829 80114000 34085 39404 46474 43427 68082 54095 48169 51794 57265 46963 FALSE TRUE 35430.70212 46171.33048 47685.15062 52016.73098 56509.44596 41532.25607 44393.38791 51099.78615 55204.04384 56164.50069 0.630838015 0.822073194 0.849026521 0.92614962 1.006141696 0.739475212 0.79041721 0.909823563 0.982899219 1 15.77737093 4.874324905 1.521053548 0.893418872 0.462322359 0.493616601 0.082998641 1.418212939 2.380702131 0.022833042 1.006447609 74872.94312 -4.874324905 -0.431096513 LMVESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LMVESHR 7 0 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 126.67 0.0039297 331470000 273750 373020 330220 349160 436870 440630 371470 347720 338640 519410 FALSE TRUE 284557.8614 437083.2833 338825.8045 418222.8059 362610.9934 338300.3603 342353.2107 343059.3822 326452.4125 621178.4448 0.458093586 0.703635625 0.545456474 0.673273211 0.583746903 0.544610592 0.551135046 0.552271871 0.525537251 1 19.24464824 -0.971120432 4.65789882 1.000006155 0.574205187 0.78553327 0.067248686 5828359.111 1251284.867 408.9020668 0.015142054 0.106875847 0.971120432 -0.425800968 LMWSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LMWSQR 6 0 P0CB38 P0CB38 PABPC4L Polyadenylate-binding protein 4-like 0 122.15 0.045 959350000 181460 391090 284010 345890 363490 455940 262870 286470 262100 484130 FALSE TRUE 188624.1809 458256.6652 291411.5339 414306.0096 301704.0996 350054.8448 242265.5625 282630.3382 252667.0722 578986.0043 0.325783662 0.791481421 0.503313606 0.715571718 0.521090488 0.604599839 0.418430775 0.488147099 0.43639582 1 19.14316895 -1.934729241 2.509974327 1.316227401 0.538847617 0.528988385 0.13187872 10238261.29 4954549.599 18946136.6 0.031766742 0.011621729 1.934729241 -0.777379785 LMYEHELEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LMYEHELEQLR 11 0 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 0 ;;; 191.53 1.79E-06 511188000 316070 387944 363774 335766 398909 430943 352934 342850 310611 429319 FALSE TRUE 328548.6877 454570.3642 373254.2493 402179.5126 331102.5907 330863.0193 325270.1109 338254.6565 299432.1708 513435.8382 0.639902132 0.885349893 0.726973502 0.783310168 0.644876275 0.64440967 0.633516569 0.658806089 0.583192969 1 18.96982448 3.241204225 24.992659 0.669822927 0.765637902 0.040211389 0.122954072 139.5534466 1319324.563 0.031480975 0.040763346 1742.626142 -3.241204225 0.095814975 LMYEHNLQRTACNMTYGSFGGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 72.644 0.012362 33689341000 5600288 5820772 7107432 6131760 8125560 8636270 7472455 7572764 7631194 6169534 FALSE TRUE 5821391.695 6820444.312 7292657.517 7344603.827 6744380.214 6630627.176 6886744.451 7471263.485 7356548.819 7378336.064 0.788984351 0.924387864 0.988387823 0.995428205 0.914078751 0.898661584 0.933373648 1.012594631 0.997047133 1 22.81486407 4.703327433 2.947894456 0.96512803 0.766456953 0.670186655 0.037541363 0.227153776 2.986102539 0.010225735 0.102275269 50504.19269 -4.703327433 -0.198671077 LNAS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNASPAAR 8 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 LNAS(1)PAAR;LNAS(1)PAAR 160.91 0.0003678 1007830000 1114110 1257280 1145050 1255830 1199810 1397000 1314990 1209190 1077430 1020300 TRUE FALSE 1158095.923 1473208.06 1174890.944 1504229.426 995866.7248 1072567.922 1211917.648 1192982.786 1038653.505 1220208.25 0.949096945 1.207341501 0.962861006 1.23276451 0.816144887 0.879003991 0.993205584 0.977687854 0.851210033 1 20.21869596 3.230787107 24.99991605 0.925672244 1.087599606 0.398071118 0.101323022 176.4740949 567547.4801 0.027623322 0.033597985 1701.324309 -3.230787107 0.161927362 LNATNIELATVQPGQNFHMFTKEELEEVIKDI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNATNIELATVQPGQNFHMFTKEELEEVIKDI 32 2 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 186.98 5.53E-20 149110000 110650 72669 120740 58143 177550 125590 70430 93047 137370 106480 FALSE TRUE 115018.5474 85149.33546 123886.5836 69643.51186 147370.1144 96423.62583 64909.51257 91799.85716 132426.0805 127342.7173 0.903220458 0.668662781 0.972859589 0.54689827 1.157271633 0.757197803 0.509723005 0.72088816 1.039918759 1 16.95835693 LNCQVIGASVDSHFCHLAWVNTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNCQVIGASVDSHFCHLAWVNTPK 24 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ;; 210.32 2.49E-25 4507500000 1285950 1636930 1965230 1899950 2313820 2656720 2207950 2162110 2328720 1789880 FALSE TRUE 1336720.299 1918059.994 2016445.508 2275754.439 1920517.703 2039737.043 2034885.11 2133130.452 2244909.822 2140572.717 0.624468531 0.896049912 0.942012151 1.063152128 0.897198067 0.952893133 0.950626481 0.996523237 1.048742612 1 21.02956542 4.837257707 1.780733724 0.980737085 0.440668739 0.841880664 0.046595953 0.430385023 1.124646802 0.012056039 0.423361365 68747.6262 -4.837257707 -0.540068346 LNDDWAYGNDLDARPWDFQAEECALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNDDWAYGNDLDARPWDFQAEECALR 26 1 Q5VSL9;Q5VSL9-2 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 ; 131.5 5.74E-05 124719000 33845 34829 32441 35860 36070 41191 40196 32521 31204 28200 FALSE TRUE 35181.22673 40810.60982 33286.43911 42953.00097 29938.83428 31625.01451 37045.33249 32085.10919 30080.97414 33725.25008 1.043171708 1.210090651 0.986988652 1.273615492 0.88772757 0.93772513 1.098445005 0.951367569 0.891942211 1 15.04154152 3.221823093 24.9999754 0.966610643 1.124191396 0.436234625 0.092981128 228.3826646 341122.6503 0.025614272 0.030693482 1666.56821 -3.221823093 0.157580754 LNDGHFMPVLGFGTYAPPEVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNDGHFMPVLGFGTYAPPEVPR 22 0 A0A0A0MSS8;P42330 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 ; 157.9 9.93E-10 473990000 425150 465340 506740 411250 632910 616270 494140 546750 555320 498300 FALSE TRUE 441935.2503 545258.5252 519946.0607 492594.0225 525328.1843 473150.6322 455408.0156 539421.7106 535334.1417 595932.3445 0.74158628 0.914967161 0.872491761 0.826593869 0.881523195 0.793967028 0.764194157 0.905172736 0.89831362 1 19.18478903 1.043953441 1.535532124 0.995858988 0.835682175 0.483250465 0.053517594 0.334234269 1.597809334 0.049356259 0.014577745 11.06505153 -1.043953441 -0.160176813 LNDPFQPFPGNDS(ph)PKEKDPEIFCDPFTSATTTTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNK 35 2 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 LNDPFQPFPGNDS(1)PKEKDPEIFCDPFTSATTTTNK 240.41 1.10E-47 476870000 892260 150890 293560 189610 466600 556660 458080 306920 340480 90935 TRUE FALSE 927487.1138 176804.1837 301210.4148 227114.2921 387287.4987 427384.1513 422174.4926 302806.2394 328226.1913 108751.9722 8.528462473 1.625756114 2.769700711 2.088369411 3.561199773 3.929897938 3.8819939 2.784374695 3.01811714 1 16.73068204 4.746508714 24.8174949 2.885627178 8.528465524 0.781880066 0.914296387 405.3416999 1265624.776 0.214629624 2.36226578 55783.87946 -4.746508714 5.642838346 LNDRYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNDRYPK 7 1 P23258;K7EIS0;Q9NRH3 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 103.92 0.019738 0 215350 328010 357360 254810 289290 325250 242520 317190 314720 240220 FALSE TRUE 223852.1843 384343.1659 366673.0952 305210.6575 240116.5891 249715.6167 223510.6487 312938.5869 303393.2887 287286.5097 0.779194904 1.33783924 1.276332451 1.062391192 0.835808787 0.86922152 0.778006071 1.089290921 1.056065212 1 18.13213072 3.462635052 8.931826907 0.939086943 1.154800103 0.219336449 0.164562215 0.250933883 129.0519556 0.045737523 0.06303032 2901.58336 -3.462635052 0.21571316 LNDS(ph)PTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LNDSPTLK 8 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 LNDS(0.993)PT(0.007)LK;LNDS(0.966)PT(0.034)LK;LNDS(1)PTLK;LNDS(0.996)PT(0.004)LK;LNDS(0.937)PT(0.063)LK 187.85 0.00020987 3050550000 4993390 2975350 3798890 2770560 5298700 4988400 4703590 3920430 4269560 2433490 TRUE FALSE 5190532.893 3486343.217 3897892.194 3318568.499 4398028.867 3829919.7 4334910.325 3867883.048 4115899.37 2910285.774 1.783513131 1.197938446 1.339350324 1.140289565 1.51120172 1.315994372 1.489513629 1.329038916 1.414259523 1 21.47272939 -1.1705639 4.282070365 0.99989375 1.378470585 0.317858906 0.1710227 0.000158244 3.07E-05 0.151052256 0.035593406 0.06752057 1.1705639 0.378576834 LNDSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNDSHK 6 0 P11387 P11387 TOP1 DNA topoisomerase 1 0 72.138 0.086386 45360000 162200 131000 181820 133240 170880 148810 182230 142360 166460 122780 FALSE TRUE 168603.7812 153498.231 186558.3786 159594.4743 141833.8786 114251.1327 167946.3364 140451.8971 160469.1371 146836.3902 1.148242483 1.04536914 1.270518693 1.086886391 0.965931391 0.778084592 1.143765085 0.95651968 1.092843108 1 17.16385003 3.403703735 4.798761317 0.987115759 1.14903323 0.34310681 0.10332378 0.230491857 9.942976156 0.028557156 0.039405744 2533.399819 -3.403703735 0.161917471 LNDSQYCKPWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNDSQYCKPWLR 12 1 Q01968-2;Q01968 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 69.352 0.045788 436130000 241150 202020 237850 194590 283230 302970 277120 218380 251230 204310 FALSE TRUE 250670.7882 236715.3635 244048.5664 233079.3212 235086.6658 232609.8091 255398.6103 215452.9733 242188.2814 244340.6327 1.025907093 0.968792463 0.998804675 0.953911425 0.962126778 0.951989878 1.0452564 0.881773002 0.991191185 1 17.89853427 7.999999173 0.791074174 0.964047238 14.74064349 0.110023302 0.040863424 914.5389283 3.271536665 0.013296419 22561.03478 99999809.48 -7.999999173 13.77659625 LNECIS(ph)PVANEMNHLPAHSHDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNECISPVANEMNHLPAHSHDLQR 24 0 P23497;P23497-2;P23497-3;P23497-4;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 LNECIS(1)PVANEMNHLPAHSHDLQR;LNECIS(1)PVANEMNHLPAHSHDLQR;LNECIS(1)PVANEMNHLPAHSHDLQR 232.68 2.82E-34 1101200000 206201 222502 234001 226927 257336 304821 273073 214030 230706 207336 TRUE FALSE 214341.9747 260714.9877 240099.2583 271812.4833 213594.1186 234030.9424 251668.8247 211161.2779 222402.9361 247959.5195 0.864423254 1.051441736 0.968300224 1.096197008 0.861407213 0.943827213 1.014959318 0.85159577 0.896932437 1 17.91974509 3.219223614 24.99975848 0.922791905 0.997202112 0.159785785 0.074573182 395.2257499 510964.6944 0.020892482 0.025006481 1656.622723 -3.219223614 0.074410207 LNEDKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNEDKPK 7 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 ; 96.492 0.011575 1249360000 3882900 1735820 2792200 1615820 4025900 3306600 3666100 2643600 3197100 1429570 FALSE TRUE 4036199.89 2033933.582 2864967.026 1935424.373 3341578.956 2538692.262 3378741.502 2608166.866 3082036.996 1709666.871 2.360810728 1.189666605 1.675745769 1.132047656 1.954520505 1.484904636 1.976257223 1.525540976 1.802712007 1 20.70528381 -1.67270074 7.315369943 0.997364568 1.653381716 0.246245396 0.353516244 0.013627935 0.000609732 0.30699143 0.072210158 0.02124708 1.67270074 0.656017147 LNEELKVDEETQEVLENLKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNEELKVDEETQEVLENLKDR 21 2 A0A5F9UP49;Q9BRK5;A0A5F9UJX7;Q9BRK5-6;Q9BRK5-2 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 ; 182.77 2.56E-17 139821000 227953 94516 155281 88410 259307 226140 221427 141663 177665 75653 FALSE TRUE 236952.7605 110748.3878 159327.7504 105897.2341 215230.0888 173622.4122 204070.9731 139764.2392 171270.8714 90475.75689 2.618964114 1.224066994 1.760999365 1.170448723 2.378870276 1.918993752 2.255532091 1.544770047 1.893002913 1 16.46524365 -0.094448619 1.115588491 0.993865632 1.83963293 0.248602016 0.447516865 19.04692979 17.59507396 0.891102746 0.124882474 0.804546928 0.094448619 0.845767298 LNEHFLNTTDFLDTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNEHFLNTTDFLDTIK 16 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 204.05 2.62E-11 641330000 499350 405270 468980 416420 509210 716510 479210 431190 506070 441340 FALSE TRUE 519064.7236 474871.9699 481202.0041 498786.6331 422654.6661 550111.4113 441648.268 425410.6033 487856.6396 527812.123 0.983427058 0.899698869 0.911691837 0.945007914 0.800767257 1.042248534 0.836752793 0.805988693 0.9242998 1 19.00966496 7.999999561 0.814170227 0.891271515 24.66802063 0.049849788 0.075747229 1339.586368 4.331551666 0.024717416 58828.29271 99999898.95 -7.999999561 23.77674912 LNEQYEHASIHLWDLLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNEQYEHASIHLWDLLEGK 19 0 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 ; 154.26 2.17E-08 331810000 127224 406130 392840 368240 444180 611410 418110 538810 443130 437370 FALSE TRUE 132246.9018 475879.6682 403077.7331 441076.7729 368678.4423 469419.2935 385337.4457 531588.1333 427181.8379 523064.2775 0.252831072 0.909791948 0.770608414 0.843255393 0.704843474 0.897440933 0.736692338 1.016296 0.816690904 1 18.99662872 4.741959001 24.99662252 0.851434857 0.252830848 0.770422127 0.098607689 146.6514597 1078638.807 0.022630967 0.164998201 55202.53231 -4.741959001 -0.598604009 LNFDMTAS(ph)PK ddPTM_MDA-MB-175_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(0.002)AS(0.998)PK;LNFDMT(0.001)AS(0.999)PK;LNFDMTAS(1)PK 114.56 0.0052341 348711000 895200 459121 538942 495306 792842 907926 719591 558077 613400 440564 TRUE FALSE 930543.1872 537971.4603 552987.2713 593276.0485 658075 697073.9463 663187.5771 550596.8906 591323.8538 526884.0807 1.766125076 1.0210433 1.049542568 1.12600868 1.248993895 1.323011971 1.258697314 1.045005744 1.122303511 1 19.00712607 4.745392096 24.98602343 1.142115833 1.766125364 0.764070419 0.10547285 410.2749582 1500535.848 0.02707373 0.26817918 55640.63728 -4.745392096 0.624009531 LNFGDDIPSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNFGDDIPSALR 12 0 Q9UNE7;Q9UNE7-2;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 171.92 8.64E-05 107956000 180365 208744 195430 191396 239546 270004 212569 200636 210683 224584 FALSE TRUE 187485.9495 244594.1582 200523.0663 229253.5575 198828.0565 207299.663 195907.2863 197946.8026 203100.56 268586.9349 0.69804568 0.910670351 0.746585333 0.853554391 0.740274491 0.771815885 0.729399911 0.736993416 0.75618183 1 18.0350296 -0.976401048 4.757117349 1.000002632 0.77194577 0.564216835 0.060243055 1.87E-06 4.03E-07 0.055486908 0.013078213 0.105584204 0.976401048 -0.228056862 LNFSHGTHEYHAETIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LNFSHGTHEYHAETIK 16 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;; 179.85 8.90E-10 11002015800 2525193.5 3726330.5 4226043.6 3664669.5 5451123.6 4876476.4 4439710.8 4379606.4 4669157.3 3886115.2 FALSE TRUE 2624890.089 4366298.777 4336177.768 4389530.189 4524543.558 3743988.66 4091714.666 4320904.94 4501115.241 4647525.069 0.5647931 0.939489021 0.933007935 0.944487684 0.973538279 0.80558762 0.880407229 0.929721707 0.968497248 1 22.14803122 4.740034161 24.94133976 0.924286675 0.564792978 0.817078071 0.051838663 50.59940494 856365.9797 0.012462855 0.07855936 54958.41011 -4.740034161 -0.359493697 LNGPGENVS(ph)EDEAQSSNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 399.64 8.53E-128 269070000 110519 117972 129277 115152 133529 159078 126287 124518 126725 127315 TRUE FALSE 114882.3755 138232.7733 132646.0648 137928.7219 110831.7883 122134.5454 116388.295 122849.0399 122164.192 152259.9367 0.754514799 0.907873577 0.871181663 0.905876654 0.727911693 0.80214499 0.76440525 0.806837587 0.802339701 1 17.21617686 5.002638608 13.62392421 0.830527708 0.671951931 0.087051311 0.0768746 426269.5583 10593576.48 0.017855593 1098793.149 100609.4115 -5.002638608 -0.158575777 LNGTDPEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 145.91 8.38E-05 469140000 495590 567550 588280 570240 650480 712730 580950 596610 598460 596440 FALSE TRUE 515156.2759 665022.2976 603611.0601 683031.77 539911.6419 547209.259 535413.621 588613.4188 576921.5415 713300.9985 0.722214433 0.93231651 0.846222088 0.957564579 0.75691979 0.767150558 0.750613867 0.825196404 0.808805179 1 19.44415147 4.78559135 22.15887794 0.836798099 0.722212409 0.157920936 0.083671521 17281.07253 8141221.671 0.019661251 9.961014226 61036.74284 -4.78559135 -0.11458569 LNHQEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LNHQEFK 7 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 140.98 0.0025874 777600000 1572210 1540730 1498400 1209490 2066320 2016310 1661900 1497010 1464800 1502190 FALSE TRUE 1634282.065 1805338.392 1537449.535 1448723.512 1715087.664 1548052.56 1531635.935 1476945.03 1412082.134 1796515.369 0.909695565 1.004911187 0.85579537 0.806407525 0.954674641 0.861697365 0.852559328 0.822116557 0.786011719 1 20.77676985 4.221404246 24.59125275 0.859156559 0.957303364 0.223380429 0.065619707 216.0891631 309734.8998 0.015589834 0.033818257 16649.61694 -4.221404246 0.098146806 LNHS(ph)PPQSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LNHSPPQSSSR 11 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR;LNHS(1)PPQSSSR 106.6 0.0014875 2312360000 607738 1212705 1246906 1294623 1289800 1908040 1270371 1357316 1194749 1206957 TRUE FALSE 631731.9655 1420977.65 1279401.395 1550695.565 1070560.257 1464926.627 1170796.002 1339123.399 1151750.217 1443437.116 0.437658114 0.984440288 0.886357556 1.074307671 0.741674331 1.014887736 0.811116736 0.927732414 0.797921991 1 20.46107683 4.744015348 24.97102792 0.910839697 0.43765791 0.665574946 0.101543652 319.5584638 1462850.917 0.02177414 0.189881358 55464.53142 -4.744015348 -0.473181787 LNHVAAGLVS(ph)PSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNHVAAGLVSPSLK 14 0 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 LNHVAAGLVS(0.98)PS(0.02)LK;LNHVAAGLVS(1)PSLK 193.8 2.28E-07 1057590000 3047010 1513620 1958210 1663830 2474750 2692760 2350770 1985070 2043680 1398400 TRUE FALSE 3167308.308 1773572.461 2009242.561 1992930.608 2054092.879 2067407.299 2166510.505 1958463.384 1970128.356 1672389.706 1.893881729 1.0605019 1.201420072 1.191666393 1.228238174 1.236199489 1.295457929 1.171056828 1.17803186 1 20.67347964 4.744948328 24.99993311 1.188707968 1.893882043 0.872618734 0.082375395 225.9876849 884436.7951 0.018474242 0.174236786 55583.81202 -4.744948328 0.705174075 LNIHQKT(ph)HTGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNIHQKTHTGEK 12 1 Q9GZX5 Q9GZX5 ZNF350 Zinc finger protein 350 1 LNIHQKT(0.973)HT(0.027)GEK;LNIHQKT(0.998)HT(0.002)GEK 111.52 0.0020119 1008650000 1488140 333112 632827 352956 932850 1132210 1055980 475976 741389 258536 TRUE FALSE 1546892.916 390321.3947 649318.9915 422769.6433 774284.4902 869271.3863 973209.5283 469596.3203 714706.5547 309191.1792 5.003030553 1.262394987 2.100056648 1.36734057 2.504225677 2.811436563 3.147597971 1.518789512 2.311536042 1 18.23813964 4.7484822 24.73367095 2.069751888 5.003032408 0.639066717 0.67476886 768.7342099 1916344.789 0.159719008 2.128808961 56037.94485 -4.7484822 2.93328052 LNKSELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNKSELK 7 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 93.551 0.013545 2938400000 2280400 1515010 2099330 1148130 2852800 2231600 1769740 1919960 2254800 1624320 FALSE TRUE 2370431.953 1775201.182 2154040.264 1375226.687 2367882.075 1713344.72 1631023.154 1894226.077 2173650.188 1942574.405 1.22025285 0.913839479 1.108858564 0.70794029 1.218940222 0.88199696 0.839619399 0.975111209 1.118953376 1 20.88953843 4.746383034 24.19645698 0.967962401 1.220253045 0.212571452 0.141816841 895.1263132 2768717.754 0.031324797 0.330541745 55767.73854 -4.746383034 0.252290644 LNLEAINYMAADGDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNLEAINYMAADGDFK 16 0 P09382 P09382 LGALS1 Galectin-1 0 191.49 2.53E-12 0 49976 60446 79140 56496 104740 91245 145260 120650 164700 53246 FALSE TRUE 51949.09107 70827.1303 81202.45341 67670.74018 86936.33221 70054.73158 133874.1416 119032.8841 158772.4792 63678.53424 0.815802243 1.112260688 1.275193507 1.062693119 1.365237646 1.100131032 2.102343328 1.869278015 2.49334381 1 15.95851951 2.244196585 24.98035597 1.93709019 1.136788062 0.482851314 0.374336222 100.3433551 444754.1571 0.122058028 0.099481545 175.4674582 -2.244196585 -0.800302129 LNLGTDS(ph)DSSPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 LNLGTDS(0.903)DS(0.073)S(0.024)PQK 226.88 1.05E-11 421880000 559990 342390 404250 335560 526760 572210 525670 423660 426730 288710 TRUE FALSE 582098.8376 401192.8191 414785.0871 401932.7665 437221.5234 439322.8994 484466.6118 417981.5307 411372.0707 345277.1968 1.685888448 1.16194415 1.201310399 1.164087203 1.266291337 1.272377393 1.403123682 1.210568015 1.19142554 1 18.39739553 -5 0.131332389 0.104258738 1.386104024 0.30973284 0.143633456 199.7507293 1.649727384 47.38633531 1.044850967 1.00E-05 5 1.281845286 LNLGTDSDSS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 LNLGTDS(0.074)DS(0.074)S(0.851)PQK;LNLGTDSDS(0.075)S(0.925)PQK;LNLGTDSDS(0.017)S(0.983)PQK 254.94 8.40E-24 713270000 2480380 1529880 1920490 1514640 2444660 2703020 2347270 1916130 2076990 1396470 TRUE FALSE 2578307.318 1792624.989 1970539.547 1814231.271 2029117.566 2075284.57 2163284.844 1890447.412 2002239.536 1670081.559 1.5438212 1.073375716 1.179906176 1.086312977 1.214981122 1.242624684 1.295316885 1.131949156 1.198887278 1 20.67148713 -5 0.189925578 0.114832953 1.246258078 0.233544381 0.124805407 216.4793815 2.118028293 72.60242482 0.32483366 1.00E-05 5 1.131425124 LNLGTVGFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNLGTVGFYR 10 0 E9PLK3;P55786;P55786-2;H0YCQ5 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 101.65 0.0074206 63292000 96381 77513 116770 94948 130150 137320 121980 85493 91492 102950 FALSE TRUE 100186.1963 90825.25478 119813.1221 113728.431 108027.1495 105429.5111 112418.8889 84347.10617 88199.22079 123121.0814 0.813720893 0.737690522 0.973132471 0.923712087 0.877405788 0.856307546 0.913075873 0.685074442 0.716361648 1 16.90971828 1.753711137 25 0.768846466 0.871284193 0.068854343 0.099747305 8.752662413 14461.23824 0.044965515 0.024935715 56.71672388 -1.753711137 0.102437726 LNLKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNLKPR 6 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 94.669 0.040328 918280000 1975980 1690650 1819210 1450220 3609100 2689500 2353300 1932560 1925900 2589300 FALSE TRUE 2053993.216 1981005.986 1866620.107 1737069.188 2995626.471 2064904.385 2168842.197 1906657.194 1856587.235 3096623.76 0.663300864 0.639730926 0.602792025 0.560955842 0.967384708 0.666824434 0.700389316 0.615721296 0.599552086 1 21.56226468 LNLTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.088)S(0.912)PK;LNLT(0.009)S(0.991)PK;LNLT(0.005)S(0.995)PK;LNLT(0.016)S(0.984)PK;LNLT(0.189)S(0.811)PK 139.32 0.002832 2888810000 14852100 6910910 8348960 6478060 11854200 13942300 11604100 9340610 9813000 5707010 TRUE FALSE 15438472.38 8097805.033 8566540.756 7759400.933 9839227.318 10704412.12 10694540.32 9215414.401 9459832.047 6825189.342 2.261984482 1.186458665 1.255135986 1.136877022 1.441605035 1.568368522 1.566922144 1.35020641 1.386017526 1 22.70243764 -3.454109247 0.2234417 4.73E-33 1.501816099 0.192392666 0.297661175 134.7176437 2.508049795 63.31693994 0.56041468 0.000351472 3.454109247 1.501816099 LNLVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 101.47 0.084885 111220000 270330 304810 293000 321900 416970 447910 347700 337110 312600 335830 FALSE TRUE 281002.8371 357158.7464 300635.8207 385570.8592 346093.5883 343889.6906 320446.3655 332591.5919 301349.5871 401629.4586 0.699656938 0.889274277 0.748540263 0.960016381 0.861723613 0.856236223 0.797865691 0.82810557 0.75031744 1 18.61550557 4.749593185 23.86647398 0.846171097 0.699656775 0.258393604 0.077591645 1174.337981 2540321.03 0.017167266 0.246547792 56181.48116 -4.749593185 -0.146514322 LNNMNKYDYVLTGYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNNMNKYDYVLTGYTR 16 1 O00764;F2Z2Y4 O00764 PDXK Pyridoxal kinase 0 ; 268.21 1.69E-27 2829500000 935080 943810 1103120 881440 1279660 1254360 1084770 1035180 1069790 1125320 FALSE TRUE 971997.6804 1105902.026 1131868.213 1055786.201 1062143.85 963053.9 999742.8929 1021305.105 1031288.467 1345804.908 0.722242633 0.821740223 0.841034392 0.784501672 0.789225722 0.715596959 0.742858706 0.758880503 0.766298637 1 20.36003786 -1.907162837 7.717491002 1.043805863 0.771964628 0.765579187 0.037951823 0.022570227 0.000271507 0.028994243 0.009200458 0.012383322 1.907162837 -0.271841235 LNPEDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 98.033 0.012522 1721160000 2464000 1234280 1851500 1250970 2564500 2186000 2179700 1659610 2082200 1171220 FALSE TRUE 2561280.623 1446257.989 1899751.611 1498408.132 2128587.206 1678334.629 2008849.418 1637365.643 2007262.029 1400698.135 1.828574308 1.032526533 1.356289099 1.069758069 1.519661627 1.198212939 1.434177264 1.168963963 1.433043979 1 20.41771464 -3.607457568 0.302967956 4.24E-19 1.334864735 0.162576944 0.225723899 197.47339 3.991341934 124.4871037 0.201997452 0.000246912 3.607457568 1.334864735 LNPNFLVDFGKEPLGPALAHELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNPNFLVDFGKEPLGPALAHELR 23 1 Q13228;Q13228-4;Q13228-2;Q13228-3 Q13228 SELENBP1 Selenium-binding protein 1 0 227.38 5.13E-33 589920000 423470 455310 528140 389940 636040 621440 565840 506120 566560 417800 FALSE TRUE 440188.9226 533505.9507 541903.7623 467068.9681 527926.148 477119.978 521487.9823 499336.2892 546169.6163 499659.9107 0.880977067 1.067738154 1.084545209 0.934773749 1.056570953 0.954889451 1.043685857 0.999352316 1.093082724 1 18.93058695 1.316911534 25 1.046575609 1.007208386 0.065083177 0.064594487 85.71760711 27344.77944 0.039989466 0.014603074 20.74490899 -1.316911534 -0.039367223 LNPTWNHPDQDTEAGFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNPTWNHPDQDTEAGFKR 18 1 F8VR84;Q9HB07 F8VR84 C12orf10 "UPF0160 protein MYG1, mitochondrial" 0 100.77 0.00051188 171610000 80819 68824 82945 68657 101100 113240 82187 82014 91036 86003 FALSE TRUE 84009.79653 80643.98662 85106.61484 82237.14968 83915.05811 86941.72617 75744.96818 80914.73648 87759.63214 102853.6412 0.816789717 0.784065451 0.827453592 0.799555064 0.815868618 0.845295559 0.736434484 0.786697831 0.853247694 1 16.65023334 0.883085573 3.650567548 0.999921308 0.80022651 0.82001209 0.028013952 0.212193069 5.621507739 0.027609377 0.007104588 7.639863035 -0.883085573 -0.199694799 LNQIRPGLQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNQIRPGLQYK 11 1 Q96SI9;Q96SI9-2 Q96SI9 STRBP Spermatid perinuclear RNA-binding protein 0 82.261 0.014611 0 524250 560380 561980 445990 835270 848950 635670 681530 713340 741000 FALSE TRUE 544947.7948 656620.9058 576625.6605 534205.4909 693291.1038 651794.2285 585844.5244 672395.2051 687667.0327 886184.7627 0.614936995 0.740952602 0.650683339 0.602815026 0.782332458 0.735506021 0.661086208 0.75875284 0.775986072 1 19.757248 -5 0.170318572 2.199054714 0.630400756 0.770279223 0.052313795 60.70734575 0.573303738 24.41591768 0.185241006 1.00E-05 5 -1.568653958 LNQLKPGLQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNQLKPGLQYK 11 1 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 94.616 0.0035601 0 552540 485970 563740 482220 803220 742640 674480 587690 621460 576550 FALSE TRUE 574354.7059 569431.5672 578431.5275 577601.6767 666688.9513 570173.1148 621612.4952 579812.9768 599093.776 689513.9338 0.832984915 0.825844902 0.838897518 0.837693988 0.966896996 0.826920366 0.901522746 0.84090103 0.868863915 1 19.39522018 -5 0.223617924 1.715587337 0.843091504 0.518820655 0.041127842 126.796575 1.269139275 41.0168218 0.074968696 1.00E-05 5 -0.872495833 LNQPGT(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 LNQPGT(0.957)PT(0.043)R;LNQPGT(0.984)PT(0.016)R;LNQPGT(0.764)PT(0.236)R;LNQPGT(1)PTR;LNQPGT(0.719)PT(0.281)R;LNQPGT(0.996)PT(0.004)R 150.44 0.00095269 59640510000 11812580 12796390 12645720 12605870 13740860 14783290 12730870 12613980 11835240 12854260 TRUE FALSE 12278949.78 14994070.44 12975277.85 15099273.46 11405193.53 11350094.94 11732991.14 12444910.23 11409292.02 15372806.14 0.798744853 0.975363269 0.844040947 0.982206718 0.741907068 0.738322909 0.763230281 0.809540569 0.742173675 1 23.8738772 3.227143082 24.99999998 0.786024691 0.901462265 0.228757221 0.08878732 258.8837299 566854.4716 0.023431753 0.028237789 1687.108765 -3.227143082 0.115437574 LNQS(ph)PSLAPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNQSPSLAPVKR 12 1 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 1 LNQS(0.873)PS(0.127)LAPVKR;LNQS(0.97)PS(0.03)LAPVKR 134.81 8.51E-05 392590000 528650 436980 505400 341910 580200 563050 481250 456970 505110 468220 TRUE FALSE 549521.5102 512027.9158 518571.1392 409538.7775 481577.8112 432290.1706 443528.3675 450845.0646 486931.1898 559958.7444 0.981360709 0.914402929 0.926088117 0.731373126 0.860023736 0.772003607 0.792073295 0.805139788 0.869584045 1 19.09496101 3.891895377 7.76855971 0.820221789 0.941105663 0.3197012 0.070658457 0.265129831 16.93564478 0.016600531 0.030122624 7796.422688 -3.891895377 0.120883874 LNS(ph)CETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNSCETK 7 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 LNS(0.997)CET(0.003)K;LNS(0.991)CET(0.009)K;LNS(0.998)CET(0.002)K 112.95 0.0065456 485266000 1371140 824857 1085130 711395 1487250 1467890 1419790 1115880 1323160 726806 TRUE FALSE 1425273.666 966519.7733 1113409.379 852106.8077 1234447.776 1126994.794 1308503.15 1100923.454 1275539.73 869209.7202 1.639735075 1.11195233 1.280944464 0.980323607 1.42019555 1.29657408 1.50539406 1.266579777 1.467470624 1 19.72934478 -0.957871898 5.873480742 0.99999976 1.317278868 0.224960806 0.182354558 5.40E-07 9.58E-08 0.166346018 0.039208103 0.110186427 0.957871898 0.317279108 LNS(ph)KWNILCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSKWNILCEK 11 1 Q9Y234 Q9Y234 LIPT1 "Lipoyltransferase 1, mitochondrial" 1 LNS(1)KWNILCEK 92.838 0.02551 85570000 182080 163760 187830 158310 242630 282800 222850 197780 212360 164740 TRUE FALSE 189268.659 191884.5061 192725.0041 189623.2455 201387.8393 217123.9859 205382.4347 195129.0826 204717.2051 197017.6489 0.96066855 0.973945772 0.978211877 0.96246832 1.02218172 1.102053482 1.042457038 0.990414228 1.039080541 1 17.58796535 3.175209616 5.436416995 1.033896369 0.969865697 0.550208799 0.028396053 0.16875241 9.639015801 0.009011332 0.010971879 1496.958002 -3.175209616 -0.064030672 LNS(ph)PTLSVNSDGFIPMLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSPTLSVNSDGFIPMLAK 19 0 Q96JB2;Q96JB2-2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 LNS(0.995)PT(0.005)LSVNSDGFIPMLAK 275.99 1.96E-39 96593000 120840 64966 98043 72768 130150 131540 126020 89727 107450 54015 TRUE FALSE 125610.8565 76123.40513 100598.0811 87161.29321 108027.1495 100991.8285 116142.2231 88524.35633 103582.8955 64598.20507 1.944494532 1.178413627 1.557289108 1.349283515 1.672293361 1.563384438 1.797917186 1.37038415 1.603494948 1 15.97920646 -1.229839797 3.459876159 0.998830599 1.5431768 0.384486125 0.21151112 42688440.32 65052528.74 535306.8816 0.046602532 0.058906091 1.229839797 0.544346201 LNS(ph)SENGEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 249.04 6.78E-13 550560000 240530 238440 248690 230080 292170 335780 266610 240340 253420 216580 TRUE FALSE 250026.3101 279390.2152 255171.0657 275589.1373 242507.0478 257800.1838 245712.4115 237118.6354 244299.4637 259014.7043 0.965297745 1.07866546 0.985160539 1.063990317 0.936267493 0.995310998 0.948642712 0.915463993 0.943187625 1 17.98267448 3.226403552 24.9749198 0.951070606 1.024512016 0.405223117 0.03930942 190.9029184 392181.4051 0.010851781 0.013056891 1684.238349 -3.226403552 0.07344141 LNS(ph)SSGSGSGSSGSSVSSPSWAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSSSGSGSGSSGSSVSSPSWAGR 24 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 LNS(0.791)S(0.065)S(0.065)GS(0.07)GS(0.007)GS(0.001)SGSSVSSPSWAGR 58.366 0.085068 54549000 27569 21587 28539 26968 35932 38750 37351 32124 29619 22701 TRUE FALSE 28657.44541 25294.39933 29282.74979 32302.18991 29824.29147 29750.89976 34423.33102 31693.43032 28553.01798 27148.82631 1.055568483 0.931694027 1.078600948 1.18981902 1.098548097 1.095844786 1.267949142 1.167395966 1.051722003 1 14.72860221 4.022597591 6.28573382 1.13935002 0.994887786 0.302860521 0.076310208 0.162137977 22.55150068 0.018714901 0.039976546 10534.10374 -4.022597591 -0.144462234 LNS(ph)VQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.968)VQS(0.016)S(0.016)ERPLFLVHPIEGSTTVFHSLASR;LNS(0.697)VQS(0.251)S(0.052)ERPLFLVHPIEGSTTVFHSLASR;LNS(0.93)VQS(0.035)S(0.035)ERPLFLVHPIEGSTTVFHSLASR;LNS(0.481)VQS(0.259)S(0.259)ERPLFLVHPIEGSTTVFHSLASR 224.34 5.42E-35 9769478000 1150239.7 1314951 1435337 1075062.9 1818238 1852897 1630245 1525420 1456501 1095430 TRUE FALSE 1195652.052 1540783.605 1472743.061 1287707.133 1509174.554 1422589.753 1502462.137 1504974.24 1404081.814 1310058.535 0.912670709 1.176118138 1.124181112 0.982938623 1.15199017 1.085897855 1.146866416 1.148783966 1.071770288 1 20.32119984 3.196349394 24.99997007 1.113367396 1.063429596 0.067572204 0.08049959 370.7897657 219602.3254 0.022396321 0.026768912 1571.626683 -3.196349394 -0.0499378 LNSDRLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSDRLESR 9 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 74.944 0.036169 102420000 73866 93775 90959 89794 126650 138450 90409 87012 94337 124690 FALSE TRUE 76782.28672 109880.1268 93329.46626 107554.9852 105122.0782 106297.0857 83322.50634 85845.74646 90941.8298 149120.6182 0.514900539 0.736854019 0.625865607 0.721261664 0.704946637 0.712826214 0.558759126 0.575679926 0.609854163 1 17.18612022 -1.076005443 4.534255708 1.000023165 0.640609343 0.687428958 0.072803604 10168585.2 2413065.191 2346.416262 0.017530447 0.083944947 1.076005443 -0.359413822 LNSEQSQALQHQQETGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSEQSQALQHQQETGR 17 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 244.32 1.66E-20 308260000 52803 62743 63138 64403 65226 78148 65287 60096 74646 64998 FALSE TRUE 54887.70321 73518.62218 64783.42815 77141.72118 54138.90782 59999.31134 60169.63434 59290.51142 71959.50504 77733.11364 0.706104524 0.945782547 0.833408378 0.992392014 0.696471623 0.771862962 0.774054087 0.762744584 0.925725237 1 16.24624168 1.043941493 4.820270891 0.999150136 0.81283022 0.328929705 0.090068513 0.195077308 9.893152035 0.085775033 0.021744412 11.06474712 -1.043941493 -0.186319915 LNSHMNALHLGSQANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 LNSHMNALHLGSQANR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;;;;; 300.18 4.12E-46 22958380000 2665131 5614295 5114139 5466784 5573384 6808586 4828916 5253567 5040158 6703064 FALSE TRUE 2770352.43 6578506.493 5247417.664 6548097.558 4626022.178 5227395.087 4450412.946 5183151.527 4858763.698 8016401.053 0.345585558 0.82063091 0.654585222 0.81683757 0.577069703 0.652087521 0.55516346 0.646568391 0.606102872 1 22.93452326 -1.199435515 5.289701044 1.000021042 0.638729742 0.428464027 0.127704743 2.90E-05 4.39E-06 0.1132554 0.026693001 0.063177798 1.199435515 -0.3612913 LNSNDEDIHTANER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNSNDEDIHTANER 14 0 A0A5F9ZHC6;A0A5F9ZHM8;P04424-3;P04424-2;P04424;F8W943 A0A5F9ZHC6 ASL Argininosuccinate lyase 0 ;; 182.1 1.05E-07 0 238955 286071 301957 289281 341303 346700 299451 310800 314873 284833 FALSE TRUE 248389.1279 335201.4689 309826.2475 346499.9184 283288.438 266184.1793 275979.2482 306634.2344 303540.7822 340640.5729 0.729182451 0.984032718 0.909540061 1.017200962 0.831634457 0.781422416 0.810177266 0.900169442 0.891088163 1 18.37789076 0.655510346 1.874600304 0.999868381 0.874262923 0.175816082 0.083615864 2.99227584 13.77693406 0.080528782 0.022443983 4.52387239 -0.655510346 -0.125605458 LNSS(ph)ENGEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSSENGEDR 10 0 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 LNS(0.074)S(0.926)ENGEDR 232.92 4.94E-12 746530000 346410 303940 361910 301130 451550 523510 461430 348520 365000 250150 TRUE FALSE 360086.5343 356139.3307 371341.6719 360692.6152 374795.6923 401932.7364 425261.9109 343848.6595 351863.7213 299162.1031 1.20365023 1.190456034 1.241272434 1.205676158 1.252818082 1.343528248 1.421509966 1.149372383 1.176164085 1 18.19056791 0.968273896 1.650546922 1.004950294 1.258387245 0.529481446 0.073247091 0.338277289 1.895782419 0.073740583 0.021331756 9.295524414 -0.968273896 0.253436952 LNSSS(ph)GSGSGSSGSSVSSPSWAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNSSSGSGSGSSGSSVSSPSWAGR 24 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 LNS(0.03)S(0.286)S(0.684)GSGSGSSGSSVSSPSWAGR 319.19 9.06E-74 82055000 32206 26000 29493 30046 47975 50656 45975 38331 40852 25098 TRUE FALSE 33477.51775 30465.29775 30261.61181 35989.00912 39820.22664 38891.9117 42371.35937 37817.23564 39381.7445 30015.47257 1.115342018 1.014986443 1.008200412 1.199015242 1.326656662 1.295728782 1.411650583 1.259924712 1.312048125 1 14.87341876 3.552039916 3.642793123 1.289275623 1.044363001 0.464087928 0.104562704 0.174121731 4.424095185 0.026740146 0.042018034 3564.838967 -3.552039916 -0.244912622 LNSVQSSERPLFLVHPIEGS(ph)TTVFHSLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 LNSVQSSERPLFLVHPIEGS(0.817)T(0.174)T(0.008)VFHS(0.001)LAS(0.001)R 75.515 0.0026305 94954000 29208 41091 39737 34576 44775 43624 33149 34020 45943 43967 TRUE FALSE 30361.15439 48148.05961 40772.57886 41415.0296 37164.16149 33492.98713 30550.69476 33564.01755 44289.5204 52581.49185 0.57741143 0.915684548 0.775416928 0.787635119 0.70679169 0.636972934 0.581016127 0.638323797 0.842302469 1 15.68226745 0.990798436 4.714512155 0.999562559 0.704259519 0.477607343 0.098530384 0.146151637 10.91948514 0.100840907 0.025569588 9.790354911 -0.990798436 -0.295303039 LNSVQSSERPLFLVHPIEGSTTVFHSLASR ddPTM_MDA-MB-175_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 ; 286.44 3.00E-72 42348000000 4329300 7426500 7221700 9321100 8234100 9831000 6643800 8167600 7393700 8137700 FALSE TRUE 4500224.107 8701943.605 7409903.435 11164785.76 6834470.623 7547899.24 6123041.596 8058126.681 7127602.181 9732126.509 0.462409125 0.894146166 0.761385852 1.147209271 0.702258712 0.775565261 0.629157624 0.827992389 0.732378702 1 23.21432364 -2.535465924 2.057340788 3.776821636 0.780327552 0.141549449 0.168085872 6676130.515 373151.3154 86632821.5 0.040414113 0.002914299 2.535465924 -2.996494084 LNT(ph)SDFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LNTSDFQK 8 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 LNT(0.873)S(0.127)DFQK;LNT(0.949)S(0.051)DFQK;LNT(0.978)S(0.022)DFQK;LNT(0.727)S(0.273)DFQK;LNT(0.973)S(0.027)DFQK;LNT(0.995)S(0.005)DFQK;LNT(0.982)S(0.018)DFQK;LNT(0.982)S(0.018)DFQK;LNT(0.908)S(0.092)DFQK;LNT(0.981)S(0.019)DFQK 200.06 0.0013736 21683060000 22139590 10483940 15383350 11067530 25872970 23798290 21065180 17005160 18009720 9927080 TRUE FALSE 23013678.11 12284475.14 15784252.74 13256654.4 21475091.8 18271497.81 19414036.15 16777233.65 17361553.7 11872101.26 1.938467134 1.0347347 1.329524773 1.116622417 1.808870336 1.539028131 1.635265377 1.413164635 1.462382548 1 23.50107197 0.149627787 1.987521943 0.999977205 1.463273194 0.222803491 0.26547671 54.13239037 122.9556148 0.246713624 0.067562453 1.411327446 -0.149627787 0.463295989 LNTLLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNTLLQR 7 0 Q00839;A0A1X7SBS1;Q5RI18;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQ74;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PPE9;Q00839-2;A0A1W2PPS1;A0A1W2PP35;A0A1W2PQL0;A0A1W2PP34 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 87.251 0.045317 186250000 166600 209540 182510 181020 272960 265110 166580 175470 166460 294660 FALSE TRUE 173177.4966 245526.865 187266.3605 216825.2157 226562.3567 203542.2203 153523.0243 173118.1117 160469.1371 352392.9854 0.491432871 0.696741636 0.531413417 0.61529379 0.642925274 0.577600091 0.435658571 0.491264352 0.455369839 1 18.42682568 -2.018885966 2.551415177 1.504067604 0.548853401 0.739976131 0.080269025 5122307.493 2170676.248 15123559.16 0.02067116 0.009574454 2.018885966 -0.955214203 LNTQEIFDDWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LNTQEIFDDWAR 12 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 247.3 2.95E-16 982942000 824971 853627 904539 971023 953257 1050948 911670 901788 868569 865591 FALSE TRUE 857541.4921 1000230.797 928112.0294 1163088.451 791222.7156 806881.2543 840210.9232 889701.0069 837309.3714 1035186.984 0.828392847 0.966232007 0.896564625 1.123553976 0.764328308 0.779454598 0.81165136 0.859459229 0.808848435 1 19.98145995 3.188749069 24.99999978 0.828036628 0.950504959 0.271797086 0.092535906 130.7496909 65621.64709 0.025436274 0.030402212 1544.361864 -3.188749069 0.122468331 LNTVAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNTVASPK 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 LNTVAS(1)PK;LNT(0.001)VAS(0.999)PK 79.036 0.030502 473230000 992360 448130 585820 507050 789780 1001610 844190 666220 687190 374040 TRUE FALSE 1031539.139 525092.8415 601086.9505 607342.9766 655533.4777 769001.257 778020.1819 657290.4106 662458.1661 447325.9766 2.306012155 1.17384831 1.343733612 1.357718998 1.465449162 1.719107088 1.739268951 1.469376797 1.480929346 1 18.77096701 0.595699971 1.754247707 1.000296393 1.550823148 0.249395437 0.294839683 2.9083681 10.87450475 0.269405227 0.075844868 3.94184888 -0.595699971 0.550526756 LNVDFALIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNVDFALIHK 10 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2 B1ALA9 PRPS1 Ribose-phosphate pyrophosphokinase 1 0 ; 84.658 0.014771 588380000 357930 332450 307620 330650 486420 479470 401210 356110 378900 388660 FALSE TRUE 372061.3528 389545.7014 315636.8299 396051.5831 403738.5021 368120.3589 369762.1118 351336.9279 365263.463 464810.4857 0.800458174 0.838074255 0.67906564 0.852071103 0.868608852 0.791979463 0.795511554 0.755871347 0.785833096 1 18.82628309 -1.264065477 5.551037526 1.000016859 0.794865707 0.592676852 0.050625403 1.05E-05 1.39E-06 0.048812425 0.011504254 0.054442057 1.264065477 -0.205151152 LNVEAVNTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LNVEAVNTHR 10 0 O60825;O60825-2 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 0 139.32 4.13E-05 193530000 84734 106940 100070 92795 130710 119230 95615 104490 101730 100610 FALSE TRUE 88079.36375 125306.1131 102677.9064 111149.574 108491.9609 91540.63945 88120.44646 103089.4825 98068.75717 120322.6032 0.732026746 1.041417903 0.853355094 0.923763043 0.901675645 0.760793376 0.732368184 0.856775699 0.815048499 1 16.87654816 2.769668684 23.40986717 0.818636042 0.898625107 0.066937672 0.097971272 602.8630123 453672.9981 0.027880444 0.029567415 588.3946077 -2.769668684 0.079989064 LNWLSVDFNNWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LNWLSVDFNNWK 12 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 256.96 8.08E-21 726760000 998850 869340 944370 1011260 1182380 1230190 1499150 1053180 1065410 768880 FALSE TRUE 1038285.369 1018642.382 968981.058 1211284.21 981399.4699 944497.0162 1381642.706 1039063.845 1027066.102 919527.3149 1.129151198 1.10778915 1.053781701 1.317290079 1.067286914 1.027154932 1.502557546 1.129997802 1.116950074 1 19.81053291 LNYSDHDVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LNYSDHDVIK 10 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ;; 113.69 0.0014551 1266790000 1756010 2478760 2706960 2253250 3154290 3207180 2874390 2826500 2804020 2021120 FALSE TRUE 1825338.631 2904467.748 2777505.601 2698936.125 2618124.912 2462361.05 2649087.801 2788615.391 2703103.868 2417119.767 0.75517095 1.201623431 1.149097218 1.116591805 1.083158951 1.018717022 1.095968779 1.153693511 1.118316065 1 21.20485753 4.747899634 24.91386704 1.109036832 0.755170754 0.767136406 0.057620884 562.6206939 1500880.956 0.013872824 0.176515591 55962.82555 -4.747899634 -0.353866078 LPADVSPINYSLCLKPDLLDFTFEGKLEAAAQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPADVSPINYSLCLKPDLLDFTFEGKLEAAAQVR 34 2 E9PLK3;P55786;P55786-2;E9PP11;E9PJY4;E9PPD4;E9PJF9;E9PPZ2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 103.5 1.03E-05 16326000 9229.7 7361.4 10786 5757.7 12490 12227 6556.6 8714.8 11655 9923.7 FALSE TRUE 9594.095683 8625.663186 11067.09202 6896.555875 10366.95426 9387.464552 6042.67656 8597.992361 11235.53883 11868.05901 0.808396358 0.726796452 0.9325107 0.581102257 0.873517249 0.790985665 0.509154576 0.724464915 0.94670399 1 13.53479639 1.188547539 5.359110443 0.986610938 0.737255306 0.374447839 0.119184333 0.202155424 12.15325225 0.109076634 0.028566553 15.43645385 -1.188547539 -0.249355632 LPCPAEGEAELELRVS(ph)EDEEKLPASPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPCPAEGEAELELRVSEDEEKLPASPK 27 2 Q7RTP6;J3QR21;J3QLA3 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 LPCPAEGEAELELRVS(1)EDEEKLPASPK 174.02 1.22E-12 164090000 375120 139830 224210 141750 311780 309910 290920 207560 244510 112000 TRUE FALSE 389930.0273 163844.7148 230053.0968 169787.7269 258783.747 237938.0992 268116.9302 204777.9977 235710.1329 133944.2556 2.911136617 1.223230619 1.717528652 1.267599914 1.93202572 1.776396443 2.001705329 1.52883001 1.759762908 1 17.03127319 -2.343846584 0.301431429 3.44E-19 1.814236255 0.228741965 0.443789595 66.74242563 2.573630741 45.48629888 0.427844785 0.004530576 2.343846584 1.814236255 LPDAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LPDAYER 7 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;; 182.95 0.0015117 14364900000 3753890 4673410 4386790 4698170 4744820 5351660 4776770 4409020 4471570 4434360 FALSE TRUE 3902096.476 5476031.813 4501113.351 5627454.003 3938297.191 4108818.07 4402354.286 4349924.299 4310639.069 5303187.941 0.735802034 1.032592447 0.848756145 1.061145497 0.742628252 0.774782662 0.83013356 0.820247056 0.812839205 1 22.33842845 3.214410767 24.99980017 0.818749701 0.922588518 0.140696017 0.106011981 361.9990641 374738.6144 0.028181257 0.033698696 1638.365399 -3.214410767 0.103838816 LPDGYEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPDGYEFK 8 0 P09382 P09382 LGALS1 Galectin-1 0 ; 104.44 0.010656 487200000 1413100 1200920 1351580 1113230 1804090 1783730 1738270 1388790 1483610 1224100 FALSE TRUE 1468890.279 1407168.668 1386803.285 1333423.571 1497431.426 1369485.74 1602019.855 1370175.542 1430215.166 1463938.958 1.003382191 0.961220863 0.947309502 0.910846428 1.022878323 0.935480084 1.094321485 0.93595128 0.976963662 1 20.48142397 3.22511674 24.99946185 0.991528402 0.955486224 0.135752662 0.047381275 497.9120609 925887.014 0.013294544 0.015972725 1679.255347 -3.22511674 -0.036042177 LPDLS(ph)PVENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LPDLSPVENK 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8;A0A2R8YET2;A0A2R8Y7F4 E7EPN9 PRRC2C Protein PRRC2C 1 LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK;LPDLS(1)PVENK 215.72 8.45E-09 1282330000 3368570 1829000 2489980 2236020 2943400 3458850 4186140 2773970 2879700 1344800 TRUE FALSE 3501563.745 2143116.522 2554870.924 2678298.082 2443081.919 2655584.507 3858019.408 2736789.469 2776060.16 1608287.812 2.177199701 1.332545398 1.588565744 1.66531019 1.519057659 1.65118736 2.398836439 1.701678921 1.726096622 1 20.61709418 2.441791042 24.99860409 1.811466912 1.630233745 0 0.377616182 594.7662943 420835.8775 0.123058598 0.102958541 276.5610671 -2.441791042 -0.181233167 LPDS(ph)DDDEDEETAIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR 445.8 4.60E-182 22110868000 337973.3 362143.5 384377 325363.1 420224.9 490722.1 413951.6 437623.3 381118.8 309444.7 TRUE FALSE 351316.7469 424338.829 394394.1804 389718.9501 348795.2216 376759.3292 381504.9919 431757.6755 367402.4088 370074.4643 0.949313667 1.146630935 1.065715737 1.053082522 0.942500105 1.018063567 1.030887102 1.166677837 0.992779682 1 18.49745607 LPEADDIQYPSMLLLTADHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LPEADDIQYPSMLLLTADHDDR 22 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 ;;; 264.49 1.73E-37 869007000 253675 309375 321041 337745 318084 387795 328778 303092 313873 279544 FALSE TRUE 263690.2849 362507.7496 329407.5922 404549.9529 264016.1953 297735.4883 303007.5213 299029.5475 302576.772 334315.2946 0.788747297 1.084328942 0.985320138 1.210085089 0.789722156 0.890582911 0.906352554 0.894453686 0.905064102 1 18.35084983 3.209215841 24.99996074 0.892944243 1.01964997 0.224928132 0.108348471 283.5410128 241558.8537 0.02983853 0.035668777 1618.88441 -3.209215841 0.126705727 LPEASQS(ph)PLVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LPEASQSPLVLK 12 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 LPEAS(0.107)QS(0.893)PLVLK;LPEAS(0.001)QS(0.999)PLVLK;LPEAS(0.001)QS(0.999)PLVLK;LPEAS(0.002)QS(0.998)PLVLK 168.5 4.86E-05 348766000 794293 750477 781496 803407 967300 1003630 873546 826653 835889 887011 TRUE FALSE 825652.301 879365.5868 801862.4278 962318.5067 802878.6915 770552.1427 805075.1819 815573.0687 805805.5182 1060803.823 0.778327042 0.828961555 0.755900771 0.907159728 0.756858784 0.726385149 0.758929375 0.768825537 0.759617849 1 20.01672645 -1.454733633 5.852713838 1.000140217 0.782183924 0.644742977 0.048472768 8.88E-05 8.27E-06 0.047001928 0.011071373 0.035096707 1.454733633 -0.217956293 LPEDPLLSGLLDSPALK ddPTM_MDA-MB-175_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 ; 195.88 3.84E-11 173513000 281320 218333 290140 256110 334850 336740 301140 249990 272410 196478 FALSE TRUE 292426.7308 255829.9944 297701.2868 306767.7936 277932.3166 258537.2383 277535.8599 246639.293 262606.0173 234974.1023 1.244506216 1.088758258 1.266953608 1.305538741 1.182821059 1.100279715 1.181133824 1.04964458 1.117595576 1 17.84214223 1.844356154 0.69725335 1.020424991 1.218991806 0.525074699 0.064850902 0.556575007 0.531175025 0.060280837 0.031341558 69.88052417 -1.844356154 0.198566815 LPEEWSQWLGGSSWPGYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 252.43 1.75E-30 1959090000 131341 104777 129271 111151 103703 152836 124670 112399 104456 95462 FALSE TRUE 136526.4441 122771.6347 132639.9085 133136.336 86075.6011 117342.1553 114898.0396 110892.4753 100696.649 114165.9512 1.19585956 1.075378722 1.161816698 1.166164997 0.753951596 1.02782094 1.006412494 0.971327039 0.882019971 1 16.80077292 3.288418033 24.99998307 0.949560898 1.145347229 0.623220014 0.0795935 74.16460514 37187.76663 0.021393455 0.02896683 1942.754988 -3.288418033 0.195786332 LPEEWSQWLGGSSWPGYVRPLPPAAIES(ph)PAVAAPAYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 LPEEWSQWLGGSSWPGYVRPLPPAAIES(1)PAVAAPAYSR 273.85 1.36E-76 711500000 167390 241840 215610 224240 282530 310680 249680 249020 281080 344060 TRUE FALSE 173998.6865 283374.1387 221228.9737 268594.0027 234505.6515 238529.2784 230109.4292 245682.2942 270963.9857 411471.9696 0.422868869 0.688683944 0.537652599 0.652763791 0.569918898 0.579697515 0.559234763 0.597081484 0.658523559 1 18.65043463 0.634138417 1.654109322 0.999940884 0.578969087 0.784893585 0.066441968 0.603609193 2.218464968 0.056254419 0.016019803 4.306638485 -0.634138417 -0.420971797 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPEEWSQWLGGSSWPGYVRPLPPAAIESPAVAAPAYSR 38 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 310.84 4.90E-110 797350000 235360 305726 323760 326100 343860 378960 300467 329090 332720 359860 FALSE TRUE 244652.1945 358232.0623 332197.4516 390601.6067 285410.8 290952.2832 276915.6114 324679.0868 320745.4722 430367.6771 0.568472512 0.832386077 0.771892197 0.907599775 0.663178987 0.676055147 0.643439613 0.754422565 0.745282439 1 18.7152102 -1.587294052 3.436608883 1.010187846 0.733069887 0.434582643 0.092573183 26556869.63 41908206.09 2437250.896 0.022036097 0.025864611 1.587294052 -0.277117959 LPEHCIEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPEHCIEYVR 10 0 Q8TBC4;F8W8D4;Q8TBC4-2 Q8TBC4 UBA3 NEDD8-activating enzyme E1 catalytic subunit 0 ;; 116.77 0.0010468 1042970000 812500 1230730 1009540 1125870 1139640 1382950 944820 1094420 1005860 1327930 FALSE TRUE 844578.1274 1442098.304 1035849.442 1348563.726 945924.3999 1061780.821 870762.5396 1079751.09 969659.2951 1588112.459 0.531812544 0.908058051 0.652251946 0.849161354 0.595628096 0.668580374 0.548300301 0.679895863 0.610573445 1 20.59888165 -1.015286463 4.517044415 1.000011555 0.675795996 0.42281883 0.115018114 1.15011E+11 25069605005 14482058.81 0.02543358 0.096541388 1.015286463 -0.324215559 LPEHEINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPEHEINR 8 0 O43815-2;O43815 O43815-2 STRN Striatin 0 97.431 0.0082369 133010000 37976 79557 55872 80705 56648 78726 59910 55956 55801 95241 FALSE TRUE 39475.3218 93220.29588 57328.07022 96668.20812 47018.99319 60443.0796 55214.09765 55206.00135 53792.73291 113901.6505 0.346573747 0.818427964 0.503312024 0.848698923 0.412803441 0.530660261 0.484752393 0.484681312 0.472273516 1 16.79742913 -1.071904851 4.902782578 1.000012707 0.548869034 0.438717677 0.154435129 2.01E-05 3.81E-06 0.140450514 0.033103572 0.084741305 1.071904851 -0.451143673 LPELDPRGS(ph)DEENLDSETSASTESLLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPELDPRGSDEENLDSETSASTESLLEER 29 1 M0R300;Q13459-2;Q13459;M0R0P8;M0R240;M0QXP0 M0R300 MYO9B Unconventional myosin-IXb 1 LPELDPRGS(0.987)DEENLDS(0.002)ET(0.002)S(0.002)AS(0.003)T(0.003)ES(0.001)LLEER 55.3 0.036813 127580000 59124 79890 74636 79839 79128 91344 73379 74503 79371 85025 TRUE FALSE 61458.26117 93610.48604 76581.07547 95630.9159 65677.85082 70130.74033 67627.36224 73504.40915 76514.45321 101684.0208 0.604404317 0.920601735 0.753127923 0.940471424 0.645901394 0.689692832 0.665073644 0.722870797 0.752472734 1 16.63373346 0.918045272 18.60064676 1 0.745102588 0.352306705 0.1042302 2915.113647 661625.7201 0.098181419 0.024545355 8.280284748 -0.918045272 -0.254897412 LPESENLQEFWDNLIGGVDMVTDDDRR ddPTM_MDA-MB-175_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 ; 225.2 2.75E-34 1153130000 283251 279370.7 298033.3 325345.7 385141.2 401063.2 348532.5 286425.4 327368.2 342377 FALSE TRUE 294433.9682 327350.4445 305800.2926 389698.1084 319675.0364 307922.35 321213.6119 282586.336 315586.2824 409459.2179 0.719080082 0.799470204 0.746839439 0.951738516 0.780724972 0.752022024 0.784482551 0.690145254 0.77073923 1 18.64336024 -1.505237194 3.094852711 1.006606342 0.775516915 0.50579789 0.066034831 92252449.47 108690050.7 5160896.627 0.016456023 0.031243725 1.505237194 -0.231089427 LPFPIIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LPFPIIDDR 9 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;; 157.34 0.00015999 3374632000 868278 938537 939692 938905 979673 1068381 1048387 920374 816751 808939 FALSE TRUE 902558.2859 1099723.429 964181.1455 1124617.607 813148.5334 820265.7042 966211.6875 908037.892 787356.2911 967435.109 0.932939354 1.136741285 0.996636505 1.162473427 0.840519975 0.847876717 0.998735397 0.93860341 0.813859538 1 19.88380537 3.230281672 24.99998524 0.90960334 1.058553542 0.432876118 0.08439906 169.1915064 510907.9681 0.023434359 0.028455385 1699.345447 -3.230281672 0.148950202 LPGAWDPAAHQGGNGVLLEGELIDVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPGAWDPAAHQGGNGVLLEGELIDVSR 27 0 Q7Z6K5;A0A0A6YYH1;Q7Z6K5-2 Q7Z6K5 ARPIN;C15orf38-AP3S2 Arpin 0 201.98 4.34E-25 131500000 38425 45927 41009 41029 49808 51812 40620 42890 44526 46204 FALSE TRUE 39942.04867 53814.60499 42077.72823 49144.41374 41341.65395 39779.44822 37436.09826 42315.1297 42923.51796 55256.78917 0.722844184 0.973900326 0.761494268 0.889382363 0.748173294 0.719901551 0.677493188 0.765790599 0.776800799 1 15.75386411 5.056449361 15.99832283 0.796811777 0.131201535 0.045021027 0.103122748 11554318.9 76631506.22 0.023980601 245933685.1 113880.4988 -5.056449361 -0.665610242 LPGEYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPGEYFR 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ;; 139.27 0.0062933 135370000 168766 202124 179880 179971 204567 221266 192949 186861 173228 206949 FALSE TRUE 175429.012 236837.2247 184567.8206 215568.7266 169794.7744 169880.3248 177825.1532 184356.4339 166993.5581 247496.6943 0.708813556 0.956930861 0.745738528 0.870996388 0.686048656 0.686394319 0.718495064 0.74488443 0.674730459 1 17.91704973 4.111164311 19.11342444 0.752139758 0.837539947 0.043818971 0.110590731 4.185452981 700.6312157 0.025410801 0.054894507 12917.07887 -4.111164311 0.085400189 LPGGELNPGEDEVEGLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPGGELNPGEDEVEGLKR 18 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;; 141.18 1.95E-07 397700000 330615 257738 322152 275521 376417 406095 397499 335977 346896 249833 FALSE TRUE 343667.9355 302002.4966 330547.5458 330018.2315 312433.7728 311785.5907 366341.9897 331473.7779 334411.2807 298782.993 1.150225895 1.010775391 1.106313122 1.104541554 1.045687941 1.043518533 1.22611393 1.109413138 1.119244698 1 18.18873851 LPGMEYVDGDFQCHTFDS(ph)SNVE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPGMEYVDGDFQCHTFDSSNVE 22 0 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 1 LPGMEYVDGDFQCHTFDS(0.84)S(0.159)NVE;LPGMEYVDGDFQCHTFDS(0.5)S(0.5)NVE;LPGMEYVDGDFQCHTFDS(0.844)S(0.155)NVE 85.423 0.0020234 123609000 62989 79603 76601 77748 92476 100340 80309 88384 86499 108901 TRUE FALSE 65475.85436 93274.19602 78597.28499 93126.32235 76756.96255 77037.55567 74014.17073 87199.35705 83385.91789 130238.0659 0.502739763 0.716182288 0.603489344 0.715046877 0.589358895 0.591513358 0.568299062 0.669538176 0.640257649 1 16.99079165 0.097135051 1.115073198 1.001682703 0.621231711 0.768970187 0.062351973 3.074562557 3.364856998 0.069986401 0.017161079 1.250647878 -0.097135051 -0.380450992 LPGPPPAS(ph)PIPTEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPGPPPASPIPTEGPR 16 0 Q9H6A9;Q9H6A9-3 Q9H6A9 PCNXL3 Pecanex-like protein 3 1 LPGPPPAS(1)PIPTEGPR 80.387 0.016477 29486000 45297 36926 27411 34230 51772 42367 30764 34236 40810 36531 TRUE FALSE 47085.36054 43267.75326 28125.35318 41000.59183 42971.81393 32527.90633 28352.63729 33777.12242 39341.25607 43688.55002 1.077750589 0.99036826 0.643769435 0.938474539 0.983594418 0.744540762 0.648971808 0.773134435 0.900493517 1 15.4149676 2.730651891 24.73270163 0.783761963 0.915249109 0.124006173 0.138262837 953.2385954 2981024.973 0.045269041 0.043396585 537.8385051 -2.730651891 0.131487146 LPGS(ph)PGLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPGSPGLSK 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LPGS(1)PGLSK;LPGS(1)PGLSK 189.58 3.99E-05 583320000 1391540 1041070 1227600 1391850 1563390 1829580 1829300 1291030 1182500 795160 TRUE FALSE 1446479.074 1219865.674 1259592.264 1667153.776 1297645.526 1404687.773 1685914.686 1273725.855 1139942.056 950956.3777 1.521078261 1.282777741 1.324553149 1.753133808 1.364568929 1.47713166 1.772862274 1.33941565 1.198732226 1 19.85901964 -0.518871176 7.855449665 0.999999996 1.453132192 0.354792436 0.18123697 0 0 0.172636355 0.040690779 0.302781143 0.518871176 0.453132196 LPHLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPHLLK 6 0 Q5XPI4;Q5XPI4-2;C9JI97 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 0 ; 84.566 0.055705 929760000 1528790 1313600 1585450 1446260 1899530 2050050 1976420 1728400 1820880 1501410 FALSE TRUE 1589147.81 1539200.582 1626768.129 1732325.911 1576648.569 1573956.956 1821503.036 1705233.625 1755346.884 1795582.543 0.885031889 0.857215162 0.905983485 0.96477097 0.878070783 0.876571763 1.014435701 0.949682671 0.977591863 1 20.77602054 2.274925492 0.484965232 1.003282189 0.877032464 0.524506047 0.037344552 0.82210556 0.412715644 0.037413455 0.035562457 188.3325955 -2.274925492 -0.126249725 LPHSS(ph)SSENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHS(0.223)S(0.553)S(0.223)S(0.002)ENIK 62.162 0.053284 94660000 23590 45306 43260 36928 42568 50970 39859 43279 35406 40952 TRUE FALSE 24521.35142 53086.95307 44387.39114 44232.24818 35332.30656 39132.98996 36734.74743 42698.9158 34131.74498 48975.76033 0.500683425 1.083943418 0.906313467 0.903145717 0.72142436 0.799027717 0.750059768 0.871837732 0.696910977 1 15.57978027 4.768391179 24.10108641 0.84801719 0.500682511 0.456063245 0.116884328 6915.313931 5586952.202 0.027486986 3.059119099 58666.63499 -4.768391179 -0.347334678 LPHSSS(ph)SENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPHSSSSENIK 11 0 F5H527;Q76I76;A0A3B3IS79;K7EKN7 F5H527 SSH2 Protein phosphatase Slingshot homolog 2 1 LPHSS(0.001)S(0.999)SENIK 194.06 0.00046757 0 36496 172010 147270 153140 176700 212090 153140 183930 166290 164040 TRUE FALSE 37936.89026 201551.3794 151107.9772 183430.6349 146664.5971 162835.3118 141136.4866 181464.7192 160305.2554 196180.4973 0.19337748 1.027377248 0.770249741 0.935009532 0.747600292 0.83002803 0.719421597 0.924988578 0.817131456 1 17.5818221 4.748018404 24.936335 0.852644437 0.19337712 0.798693645 0.100800346 494.1966436 1302967.493 0.021958078 0.283177374 55978.13222 -4.748018404 -0.659267318 LPIGDVATQYFADRDMFCAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPIGDVATQYFADRDMFCAGR 21 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 202.39 5.84E-22 2093510000 262782 377010 387220 255070 455450 454250 247281 355880 370080 521900 FALSE TRUE 273156.8363 441758.5348 397311.2713 305522.0847 378032.7717 348757.3217 227898.4691 351110.0107 356760.8931 624156.3126 0.43764171 0.707769073 0.636557323 0.489496106 0.605670029 0.558765993 0.36513044 0.562535384 0.571589017 1 19.25154785 0.597002529 2.973032255 0.999993906 0.546921423 0.681677767 0.092743366 4.057927086 29.22738246 0.08922132 0.023340413 3.953689225 -0.597002529 -0.453072483 LPISSS(ph)TSNLHVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LPISSSTSNLHVDR 14 0 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 LPIS(0.004)S(0.019)S(0.882)T(0.09)S(0.005)NLHVDR;LPISS(0.003)S(0.98)T(0.017)SNLHVDR;LPISSS(0.97)T(0.03)SNLHVDR;LPIS(0.002)S(0.227)S(0.738)T(0.033)S(0.002)NLHVDR 191.64 3.00E-07 1053170000 473879 919388 811702 1007047 842327 1040721 802637 852534 736007 1035150 TRUE FALSE 492588.1088 1077285.737 832855.6209 1206237.891 699148.5574 799029.32 739724.2146 841107.1762 709518.2518 1237967.823 0.397900575 0.870204958 0.672760313 0.97436934 0.564755032 0.645436258 0.597531051 0.679425717 0.573131416 1 20.23954239 -0.962795935 4.140230387 1.000015908 0.67358141 0.301372212 0.152865346 38468112.55 82105480.45 9302.405897 0.034618214 0.108944188 0.962795935 -0.326434498 LPKS(ph)PPYTAFLGNLPYDVTEESIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPKSPPYTAFLGNLPYDVTEESIK 24 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 LPKS(0.999)PPYT(0.001)AFLGNLPYDVTEESIK;LPKS(0.96)PPYT(0.04)AFLGNLPYDVTEESIK 160.53 1.24E-11 484230000 547010 250007 405260 271600 557710 511620 586730 444260 503820 200105 TRUE FALSE 568606.3772 292943.7575 415821.4085 325321.6694 462910.6534 392804.0087 540740.5695 438305.4214 485687.6166 239311.7435 2.376006998 1.224109411 1.737572099 1.359405371 1.934341569 1.641390443 2.259565542 1.831524918 2.029518525 1 17.86853167 LPLDINPVVHPHGHIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPLDINPVVHPHGHIFK 17 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 78.326 0.0055273 583690000 342120 308394 312089 300110 390090 414520 363650 346650 345310 330660 FALSE TRUE 355627.1618 361358.2705 320222.2957 359470.8623 323782.6411 318254.0121 335146.1628 342003.7238 332882.3606 395446.4961 0.899305381 0.913798135 0.809774012 0.909025281 0.818777368 0.804796642 0.847513295 0.864854606 0.841788621 1 18.59312299 -1.83232981 8.005379615 1.006544724 0.856068831 0.560177261 0.03810967 0.004546406 9.52E-05 0.037685924 0.008619575 0.014711948 1.83232981 -0.150475893 LPLLPHEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPLLPHEVR 9 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;; 114.84 0.0015728 1501310000 1234910 1379210 1311200 1249710 1675520 1620990 1357930 1303300 1247730 1701610 FALSE TRUE 1283665.2 1616078.589 1345370.949 1496898.908 1390715.709 1244539.639 1251491.898 1285831.395 1202824.441 2035007.9 0.630791261 0.79413873 0.661113379 0.735574003 0.68339573 0.611565016 0.614981346 0.631855727 0.591066227 1 20.95660296 -1.075823412 5.051082268 1.000007247 0.66253729 0.746428231 0.059167072 5.02E-06 9.19E-07 0.05957402 0.01404143 0.083980139 1.075823412 -0.337469956 LPLLPPES(ph)PGPLR ddPTM_MDA-MB-175_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 162.72 4.19E-05 997470000 485078 543725 533914 590784 530609 705362 595870 588139 549831 603952 TRUE FALSE 504229.254 637105.5392 547828.2375 707639.3119 440416.2717 541552.3654 549164.1524 580255.9587 530042.6897 722284.831 0.698103065 0.882069665 0.758465655 0.979723347 0.609754286 0.749776739 0.760315223 0.803361685 0.733841647 1 19.46220835 -1.580827638 5.9508108 1.000706938 0.779302796 0.33426684 0.095069221 0.000836885 5.89E-05 0.086395816 0.020300577 0.026252602 1.580827638 -0.221404142 LPLPDDEHDLS(ph)DRELELEDSAALSDLHWHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPLPDDEHDLSDRELELEDSAALSDLHWHDR 31 1 Q8NF91;Q8NF91-4;A0A0C4DG40;E7ENN3;H0Y325;Q8NF91-2;Q8NF91-8;Q8NF91-11;Q8NF91-3;Q8NF91-9;A0A5F9ZH87;A0A5F9ZHE1;Q5JV20;F8WAI0;H0Y326;A0A5F9ZHB2 Q8NF91 SYNE1 Nesprin-1 1 LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR;LPLPDDEHDLS(1)DRELELEDSAALSDLHWHDR 338.2 2.76E-106 73998000 18797.5 25677 23599.4 23891.2 25829.9 31307 26099.4 25679.9 23483.1 27150.9 TRUE FALSE 19539.63981 30086.82501 24214.41975 28616.80805 21439.34282 24036.42371 24053.66083 25335.70294 22637.94782 32470.59902 0.60176407 0.926586694 0.745733694 0.881314448 0.660269397 0.740251934 0.740782787 0.780265955 0.697182944 1 14.98684638 -1.052558602 5.020434259 1.000004214 0.759401417 0.397865296 0.090937905 3.90E-06 7.36E-07 0.08003249 0.018863509 0.088601566 1.052558602 -0.240602797 LPLPS(ph)PALEYTLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR 190.86 2.09E-07 242960000 101958 102705 99635 108694 102945 109800 95718 95501 82865 80379 TRUE FALSE 105983.3806 120343.7848 102231.57 130193.3488 85446.44567 84300.61404 88215.37305 94220.9653 79882.70484 96127.7261 1.102526658 1.251915443 1.063497225 1.354378742 0.888884499 0.876964612 0.917689169 0.980164299 0.831005872 1 16.55266499 3.219061228 24.9998655 0.917637867 1.188026218 0.710202494 0.086747896 121.0852115 155241.146 0.023322424 0.027912953 1656.003413 -3.219061228 0.270388352 LPLQLDDAVRPEAEGEEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LPLQLDDAVRPEAEGEEEGR 20 1 P14868;P14868-2;C9J7S3;C9JLC1 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ;;;;;; 256.9 3.05E-36 4467020000 1537000 1714760 1724878 1813430 1771960 1880740 1765970 1720470 1704010 1542030 FALSE TRUE 1597681.947 2009256.691 1769829.738 2172121.041 1470762.872 1443966.638 1627548.657 1697409.914 1642683.013 1844161.255 0.86634612 1.089523319 0.959693591 1.177836827 0.797524006 0.782993697 0.882541401 0.920423802 0.890748035 1 20.81453338 3.218527143 24.99517153 0.874116286 1.023529837 0.357782134 0.094581217 247.7270098 309080.9972 0.026498911 0.031711241 1653.968152 -3.218527143 0.149413551 LPLS(ph)PPLVEDSAFEPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPLSPPLVEDSAFEPSR 17 0 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR 107.34 0.00074385 174734000 48178 48142 50907 62599 52329 65038 78244 62797 51384 43712 TRUE FALSE 50080.10464 56410.01401 52233.67824 74980.89536 43434.13527 49933.91016 72111.03083 61955.30893 49534.69988 52276.52948 0.957984494 1.079069605 0.999180297 1.4343128 0.830853458 0.955187933 1.379415037 1.185145792 0.947551423 1 15.67387575 LPLS(ph)PPLVEDSAFEPSRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPLSPPLVEDSAFEPSRK 18 1 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 LPLS(1)PPLVEDSAFEPSRK;LPLS(1)PPLVEDSAFEPSRK 128.95 1.36E-05 367230000 658380 515730 699220 575060 782690 861360 903040 725110 790940 515170 TRUE FALSE 684373.3508 604302.6157 717442.2476 688805.1516 649648.6334 661322.194 832257.3651 715391.0865 762474.2239 616107.698 1.110801493 0.980839255 1.164475383 1.117994717 1.054440052 1.073387325 1.35083098 1.161146158 1.237566462 1 19.23282304 LPLVPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LPLVPESPR 9 0 C9J0I9;Q86WB0;Q86WB0-2;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR 134.57 0.00025732 428246000 195937 253174 221542 223028 250338 293329 242945 250066 218052 261065 TRUE FALSE 203672.7441 296654.6651 227315.5665 267142.2727 207785.6362 225207.7852 223902.3361 246714.2743 210204.3511 312215.6884 0.652346284 0.950159381 0.728072211 0.855633726 0.665519524 0.721321169 0.717139927 0.790204604 0.67326646 1 18.25218351 -1.133767956 4.153088131 1.000054356 0.756469924 0.416412298 0.088381181 11562629.33 3156529.734 6414.909416 0.019244344 0.073490642 1.133767956 -0.243584432 LPLVPES(ph)PRR ddPTM_MDA-MB-175_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 102.97 0.0017618 2606430000 1211452 1360700 1248398 1278010 1366850 1586090 1283487 1332710 1215054 1459910 TRUE FALSE 1259281.06 1594389.64 1280932.277 1530796.564 1134513.325 1217744.635 1182883.935 1314847.202 1171324.444 1745951.413 0.721257792 0.913192445 0.733658605 0.87676928 0.649796619 0.697467653 0.677501061 0.753083501 0.670880321 1 20.73558198 5.072333834 15.57705011 0.761337435 0.184863467 0.007587478 0.112209737 10637017.15 43495115.26 0.025270014 200766775.9 118122.8276 -5.072333834 -0.576473969 LPLVTPHTQCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPLVTPHTQCR 11 0 P62191 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 159.94 3.28E-05 356270000 457870 389150 411720 419700 472170 467210 461080 411340 369340 438420 FALSE TRUE 475947.0612 455983.4853 422449.7614 502715.4073 391910.7121 358707.5581 424939.3448 405826.6601 356047.5255 524320.0049 0.907741564 0.869666389 0.805709791 0.958795016 0.747464732 0.684138608 0.810458004 0.774005676 0.679065308 1 19.00008807 3.217855662 24.99474221 0.769101653 0.878651055 0.224476725 0.091385092 312.6772337 377458.901 0.024644018 0.029484932 1651.412858 -3.217855662 0.109549402 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(1)PNSSSAAASVASR;LPNGLGGPNGFPKPTPEEGPPELNRQS(0.994)PNS(0.005)S(0.001)SAAASVASR 280.76 1.12E-77 3447890000 542280 472733 625285 491853 745063 734190 529860 607457 694653 573297 TRUE FALSE 563689.6331 553921.2154 641580.4408 589140.0554 618417.4574 563685.4993 488328.1887 599315.0325 669652.5742 685623.5707 0.822156147 0.807908653 0.935761937 0.859276257 0.901978117 0.822150118 0.712239499 0.874116728 0.976705882 1 19.38705718 1.264036931 4.109904763 0.994665296 0.839315414 0.526953937 0.056327981 0.166434114 5.522864154 0.049158145 0.014935416 18.36694521 -1.264036931 -0.155349882 LPNNSS(ph)RPS(ph)TPTINVLESK ddPTM_MDA-MB-175_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(0.224)S(0.769)RPS(0.56)T(0.407)PT(0.04)INVLESK 49.266 0.087118 138870000 166250 117650 121200 90121 166750 156870 126420 103530 141430 73754 TRUE FALSE 172813.6784 137855.4723 124358.5716 107946.6648 138405.8946 120439.3199 116510.8701 102142.3497 136339.9619 88204.68419 1.959234704 1.56290421 1.409886252 1.223820093 1.569144494 1.365452651 1.320914769 1.158015026 1.545722466 1 16.42856765 7.999999997 0.704576722 1.301311806 87.41476707 0.60996185 0.158604061 189.2357849 0.97835889 0.05564551 25693.71737 99999999.41 -7.999999997 86.11345527 LPNNSSRPST(ph)PTINVLESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPNNSSRPSTPTINVLESK 19 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 LPNNS(0.001)S(0.001)RPS(0.035)T(0.957)PT(0.006)INVLESK 110.26 0.00038692 181620000 236700 186500 238100 210710 280230 326730 341500 280890 281170 196900 TRUE FALSE 246045.0988 218529.9242 244305.0816 252387.8091 232596.6047 250851.9091 314732.3377 277125.129 271050.7466 235478.7851 1.044871616 0.928023831 1.037482343 1.071806995 0.987760339 1.065284539 1.336563451 1.176858157 1.151062277 1 17.84523756 2.46153276 24.82863782 1.187857974 1.015009658 0.409386548 0.084741142 179.4014104 285740.3938 0.027925497 0.023370998 289.4228129 -2.46153276 -0.172848315 LPNTYPNSSS(ph)PGPGGLGGSVHYATMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.074)S(0.39)S(0.536)PGPGGLGGSVHYATMAR 120.69 6.40E-05 144620000 26244 36675 35539 41406 35333 52782 34888 40846 41446 46885 TRUE FALSE 27280.13338 42973.64596 36465.17554 49595.98322 29327.10928 40524.18042 32153.3874 40298.52618 39954.36656 56071.21808 0.486526498 0.76641185 0.650336782 0.884517671 0.523033212 0.72272695 0.573438361 0.718702528 0.712564626 1 15.77497279 0.527612163 1.464191412 0.999886169 0.669170619 0.444433733 0.111731797 1.904411734 4.941711645 0.097692662 0.028408807 3.369862359 -0.527612163 -0.33071555 LPPEEASPYVVDHGESGPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPPEEASPYVVDHGESGPLR 20 0 P53992;G5EA31 P53992 SEC24C Protein transport protein Sec24C 0 117.84 7.44E-05 118970000 23689 31547 24571 34071 34949 37220 33889 30618 27960 24650 FALSE TRUE 24624.26001 36964.95185 25211.34045 40810.14211 29008.38146 28576.21907 31232.69163 30207.61579 26953.72506 29479.69555 0.835295601 1.253912266 0.85521034 1.384347475 0.984012247 0.969352585 1.059464525 1.024692258 0.914314906 1 14.847434 LPPQSSGVDTSPCPNS(ph)PVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPPQSSGVDTSPCPNSPVFR 20 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 LPPQSSGVDT(0.004)S(0.015)PCPNS(0.981)PVFR 103.24 0.00030231 93206000 10972 14715 12936 12106 16839 16836 13293 13093 13948 16207 TRUE FALSE 11405.18303 17242.18678 13273.12279 14500.53067 13976.71279 12926.09415 12251.05993 12917.50975 13446.0142 19382.45135 0.588428307 0.889577199 0.684801037 0.748126767 0.7211014 0.666896768 0.632069685 0.666453872 0.693721035 1 14.24246342 -1.263813256 8.732145143 1.000000112 0.699951961 0.583232453 0.076324644 1.60E-07 1.35E-08 0.071265936 0.016797536 0.054473684 1.263813256 -0.300048151 LPPVLSHPIFDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPPVLSHPIFDNR 13 0 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4;E9PQS6;E9PI38 Q04206 RELA Transcription factor p65 0 ; 147.26 4.27E-05 564820000 823220 678890 715650 717790 792170 956270 768670 787480 723670 682550 FALSE TRUE 855721.3613 795484.0765 734300.4269 859766.7196 657517.2264 734190.7849 708419.6369 776925.1187 697625.2581 816282.6043 1.048315077 0.974520432 0.899566428 1.053270908 0.805501946 0.89943211 0.867860755 0.951784486 0.854636929 1 19.63870919 5.734298387 0.689507925 0.906044979 1.500179975 0.273188618 0.067748577 12.91990821 1.664124694 0.024489673 8.221328357 542373.4059 -5.734298387 0.594134995 LPQTLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPQTLSR 7 0 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 117.4 0.01219 136060000 74443 98943 81048 85393 117970 90410 85027 86296 75277 85810 FALSE TRUE 77382.06712 115935.6906 83160.17746 102283.4805 97917.50154 69413.64768 78362.36156 85139.34327 72567.79547 102622.8266 0.75404342 1.129726148 0.810347758 0.996693269 0.954149333 0.676395788 0.763595822 0.829633583 0.707131132 1 16.64699214 2.763812146 24.61122565 0.786097029 0.937313739 0.218456392 0.125286262 816.4300135 795726.1615 0.035091865 0.037206239 580.5132629 -2.763812146 0.15121671 LPS(ph)AESLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSAESLSR 9 0 O43281-3;O43281-2;O43281 O43281-3 EFS Embryonal Fyn-associated substrate 1 LPS(0.999)AES(0.001)LSR;LPS(0.996)AES(0.004)LSR 99.174 0.0057856 238410000 183193 1395450 749570 1151320 489690 1161080 429760 835940 578630 2838000 TRUE FALSE 190425.6011 1635107.682 769104.41 1379047.66 406452.6687 891436.7663 396074.2882 824735.5916 557805.2193 3394051.763 0.056105686 0.481756849 0.226603618 0.40631309 0.119754411 0.26264678 0.116696596 0.242994406 0.164347882 1 21.69457714 -1.250225952 4.006627994 1.000751722 0.236423989 0.773850582 0.124713214 101318876.6 180650876.8 940943.225 0.028805903 0.056204883 1.250225952 -0.764327732 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 LPS(0.999)GS(0.001)GAAS(0.982)PT(0.018)GSAVDIR;LPS(1)GSGAAS(0.918)PT(0.08)GS(0.002)AVDIR 296.85 3.41E-49 417410000 260950 286070 273940 295200 333510 366460 335300 315340 325270 347020 TRUE FALSE 271252.5075 335200.2972 281079.1014 353589.6789 276820.0893 281355.2188 309018.3099 311113.3831 313563.5962 415011.9249 0.653601719 0.807688351 0.677279578 0.851998841 0.667017193 0.677944902 0.744601038 0.749649262 0.75555322 1 18.66279327 0.145280878 0.996088877 1.001917586 0.729053958 0.642505595 0.06045164 2.911133219 2.872724887 0.068203488 0.017143696 1.397271747 -0.145280878 -0.272863628 LPS(ph)LGLHSVAPSIDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSLGLHSVAPSIDEK 16 0 Q5TBK7 Q5TBK7 UCHL3 1 LPS(0.759)LGLHS(0.241)VAPSIDEK 72.421 0.01014 0 27318 21482 33403 22015 43987 33180 32895 29528 38527 20307 TRUE FALSE 28396.53573 25171.36639 34273.50962 26369.50129 36510.10545 25474.44785 30316.60394 29132.22546 37140.4208 24285.76785 1.16926654 1.036465742 1.411259048 1.0858006 1.503353968 1.048945539 1.248327997 1.199559579 1.529308072 1 14.56782348 4.263309899 24.99894426 1.252971918 1.102866137 0.104798583 0.17588861 487.1946633 492100.4184 0.038736744 0.105984253 18336.22373 -4.263309899 -0.150105781 LPS(ph)PTSPFSSLSQDQAATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.992)PT(0.004)S(0.004)PFSSLSQDQAATSK;LPS(0.97)PT(0.025)S(0.005)PFSSLSQDQAATSK;LPS(0.986)PT(0.009)S(0.005)PFSSLSQDQAATSK 222.44 7.51E-25 218176000 159534 118418 156912 147261 173563 196794 204784 160517 153186 102498 TRUE FALSE 165832.5255 138755.3703 161001.2556 176388.7863 144060.8233 151091.5759 188732.495 158365.5322 147672.8658 122580.5207 1.352845661 1.131952855 1.31343263 1.438962613 1.175234225 1.232590424 1.539661391 1.291930654 1.204700918 1 16.90337021 0.920034358 2.889556001 1.000827163 1.310951163 0.413212217 0.112858143 0.342681135 6.551354124 0.10816341 0.028529348 8.318295757 -0.920034358 0.310123999 LPS(ph)QENELLENPSVVLSTNSPAALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSQENELLENPSVVLSTNSPAALK 25 0 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 LPS(0.999)QENELLENPS(0.001)VVLSTNSPAALK 90.545 0.0087494 25399000 17158 16167 17614 15357 20262 21621 23329 18783 22207 16799 TRUE FALSE 17835.41109 18943.55649 18073.03531 18394.56876 16817.87248 16599.85042 21500.41202 18531.24461 21407.77441 20090.44241 0.887756015 0.942913854 0.899583739 0.915588039 0.83710812 0.826256091 1.070181113 0.922391067 1.065570084 1 14.29422171 2.240987564 24.99999994 1.001106785 0.887400517 0.609030633 0.050415267 49.07641158 505542.0113 0.018179653 0.014550095 174.1756996 -2.240987564 -0.113706269 LPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPS(0.642)S(0.357)PVY(0.001)EDAASFK 68.83 0.046044 0 40593 34094 40757 38760 45372 53319 50906 40461 46841 35916 TRUE FALSE 42195.64298 39949.37929 41819.1609 46426.61231 37659.68365 40936.47031 46915.8547 39918.68648 45155.20156 42953.05255 0.982366572 0.930070785 0.973601605 1.080868752 0.876763848 0.95305148 1.092258918 0.929356218 1.051268743 1 15.39047304 LPS(ph)VEEAEVPKPLPPASKDEDEDIQSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSVEEAEVPKPLPPASKDEDEDIQSILR 29 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR;LPS(1)VEEAEVPKPLPPASKDEDEDIQSILR 114.18 0.00012067 375925000 81969 38503 66714 47250 91534 91659 106948 76816 81674 33626 TRUE FALSE 85205.19941 45115.59074 68452.62165 56595.90897 75975.08338 70372.58636 98565.1363 75786.40717 78734.56869 40214.37089 2.118774894 1.121877322 1.702193025 1.407355324 1.889252068 1.749936274 2.450992869 1.884560307 1.957871451 1 15.29542353 3.209002906 16.18179095 1.906181373 1.562483587 0.048932964 0.411460837 8.54280799 4675.410925 0.110919603 0.132774077 1618.090866 -3.209002906 -0.343697786 LPSANQGS(ph)PFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSANQGSPFK 11 0 E5RFP7;E5RIE3;E5RFE4;Q56NI9 E5RFP7 ESCO2 N-acetyltransferase ESCO2 1 LPSANQGS(1)PFK;LPSANQGS(1)PFK 143.98 3.87E-05 288680000 923860 557380 680980 584150 816340 1079750 978050 729400 779280 470410 TRUE FALSE 960334.7062 653105.6792 698726.8982 699693.1265 677578.8184 828994.4263 901387.8853 719623.5861 751233.865 562577.833 1.707025499 1.160916127 1.242009296 1.243726797 1.204417911 1.473563972 1.602245649 1.279153824 1.3353421 1 19.10169318 0.499892446 1.930894932 1.000081405 1.355121088 0.288340102 0.170329755 5.59051783 20.0077098 0.16172944 0.044741449 3.161494613 -0.499892446 0.355039682 LPSEGPRPAHVVVGDVLQAADVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSEGPRPAHVVVGDVLQAADVDK 24 1 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 114.88 0.00070146 553180000 1247900 740210 929170 882160 1107300 1194600 1312500 968320 1019800 660380 FALSE TRUE 1297168.056 867335.3095 953384.9335 1056648.615 919081.5415 917172.2543 1209622.82 955341.2543 983097.5972 789768.8173 1.642465526 1.098214174 1.207169633 1.337921417 1.163734908 1.161317381 1.531616334 1.209646714 1.24479161 1 19.59107088 0.680808728 1.862894991 1.000404521 1.285580082 0.223730217 0.163522723 2.056603368 9.870608167 0.14641572 0.040875526 4.795222109 -0.680808728 0.285175561 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTR 39 2 P30043;M0R192;A0A2R8YEP4;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 ; 327.34 1.43E-129 1875150000 1071500 926790 1033900 848650 1275850 1237700 1126990 973440 1169330 995050 FALSE TRUE 1113803.647 1085958.973 1060844.283 1016510.437 1058981.473 950262.9325 1038653.579 960392.629 1127246.042 1190010.996 0.935960803 0.912562133 0.891457547 0.854202558 0.889892174 0.798532901 0.872810068 0.807045172 0.947256828 1 20.18254347 4.238621657 1.74833673 0.866180843 0.935311752 0.039625246 0.057825188 0.805970805 4.409549447 0.014764186 0.067690436 17322.94224 -4.238621657 0.069130909 LPSFELLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSFELLHK 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ; 128.36 0.0004195 428310000 391270 351200 334690 282910 447360 445450 383050 376290 368200 339150 FALSE TRUE 406717.6417 411515.868 343412.2964 338868.7536 371317.907 342000.9884 353025.5401 371246.448 354948.5539 405599.9491 1.002755653 1.014585601 0.846677366 0.835475336 0.915478189 0.843197809 0.87037866 0.915302008 0.875119819 1 18.62969795 4.24717738 24.98507825 0.883095396 1.008670698 0.522587762 0.046080002 125.5938992 364162.4355 0.010483099 0.02776862 17667.59276 -4.24717738 0.125575302 LPSGSGAAS(ph)PTGSAVDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 LPSGSGAAS(0.958)PT(0.037)GS(0.005)AVDIR;LPSGSGAAS(0.965)PT(0.035)GSAVDIR;LPSGSGAAS(0.977)PT(0.023)GSAVDIR;LPSGSGAAS(1)PTGSAVDIR;LPSGSGAAS(0.984)PT(0.016)GSAVDIR;LPSGSGAAS(0.869)PT(0.131)GSAVDIR;LPSGSGAAS(0.991)PT(0.009)GSAVDIR;LPSGSGAAS(0.97)PT(0.029)GS(0.001)AVDIR 423.29 1.09E-168 9523200000 1015106 1215942 1086424 1174510 1063567 1318126 1169956 1071209 1087524 1187672 TRUE FALSE 1055183.169 1424770.58 1114737.102 1406824.572 882782.2612 1012011.213 1078251.792 1056851.195 1048384.224 1420373.589 0.742891291 1.003095658 0.784819649 0.990460949 0.621514134 0.712496501 0.759132527 0.744065648 0.73810456 1 20.43783901 3.243070332 24.99987341 0.747149982 0.882265545 0.189303465 0.116782016 155.2747446 860767.9656 0.029864607 0.039106407 1750.130093 -3.243070332 0.135115563 LPSLS(ph)GSDGIPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSLSGSDGIPYR 13 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 1 LPS(0.009)LS(0.548)GS(0.443)DGIPYR;LPS(0.062)LS(0.469)GS(0.469)DGIPYR 89.013 0.008019 129927000 61584 89741 80677 93960 95377 112896 77925 80501 76968 92596 TRUE FALSE 64015.38387 105153.3187 82779.5089 112545.0076 79164.85161 86677.61496 71817.03488 79422.01577 74197.93671 110738.4133 0.578077489 0.949564975 0.747522981 1.01631407 0.714881577 0.78272401 0.648528661 0.717203844 0.670028895 1 16.75679623 LPSLSGS(ph)DGIPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSLSGSDGIPYR 13 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 1 LPS(0.002)LS(0.094)GS(0.904)DGIPYR;LPSLS(0.032)GS(0.968)DGIPYR 158.11 5.02E-05 162990000 149222 164915 162004 225050 191360 233570 195437 167393 155325 170801 TRUE FALSE 155113.3998 193237.8684 166225.9573 269564.2183 158832.6956 179326.9073 180118.1373 165149.3706 149734.8836 204266.1858 0.759368954 0.946010068 0.813771289 1.319671277 0.777577037 0.877907945 0.881781469 0.808500781 0.733038036 1 17.64009087 LPSPEPS(ph)MSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSPEPSMSPK 11 0 O43303-2;O43303 O43303-2 CCP110 Centriolar coiled-coil protein of 110 kDa 1 LPSPEPS(0.607)MS(0.392)PK 63.537 0.077197 0 109880 83262 84665 78154 119490 147520 104800 97191 100570 88354 TRUE FALSE 114218.1472 97561.60081 86871.43945 93612.62793 99179.13248 113260.7157 96585.50216 95888.31362 96950.50535 105665.2747 1.080943078 0.92330807 0.822138018 0.885935595 0.938616142 1.071882092 0.914070422 0.907472336 0.917524756 1 16.68914181 4.739332642 23.26370572 0.926505896 1.080943186 0.334027055 0.063109974 29.10602991 876601.2048 0.015750706 0.094470808 54869.70709 -4.739332642 0.154437291 LPSPT(ph)SPFSSLSQDQAATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSPTSPFSSLSQDQAATSK 20 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 LPS(0.051)PT(0.473)S(0.473)PFS(0.002)SLS(0.001)QDQAATSK 150.7 9.43E-07 26944000 34252 30952 31107 33812 39718 41631 45040 31816 40274 30173 TRUE FALSE 35604.29541 36267.76523 31917.67397 40499.91268 32966.74855 31962.83117 41509.64711 31389.55856 38824.54661 36084.82165 0.986683425 1.005069821 0.884517992 1.122353134 0.913590453 0.88576941 1.150335382 0.869882602 1.075924581 1 15.1391045 LPSQDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPSQDCK 7 0 P21709 P21709 EPHA1 Ephrin type-A receptor 1 0 ;; 67.757 0.064296 238965000 31622 536920 404980 450860 300144 546470 234948 455740 348373 789630 FALSE TRUE 32870.46098 629131.8333 415534.1115 540038.7623 249125.6301 419560.6243 216532.1618 449631.5507 335835.1238 944342.8801 0.034807761 0.666211232 0.440024614 0.571867246 0.263808449 0.444288439 0.229294006 0.476131668 0.355628375 1 19.84895126 -1.23998053 3.533102209 1.001222827 0.399073764 0.535258498 0.171049224 64589317.73 101916890.4 872911.2587 0.037202945 0.057546574 1.23998053 -0.602149063 LPSS(ph)PASPSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSPASPSPK 11 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 LPS(0.24)S(0.755)PAS(0.004)PS(0.001)PK 67.385 0.058389 0 135180 107040 119620 129370 162290 166810 149970 136980 133560 99973 TRUE FALSE 140517.0108 125423.2873 122737.3955 154958.9999 134704.0038 128070.9055 138214.9595 135144.0072 128753.2017 119560.7953 1.175276649 1.049033566 1.026568912 1.296068661 1.126656974 1.0711781 1.156022417 1.130337138 1.076884788 1 16.86738487 0.950691348 2.950457103 1.000267268 1.127840522 0.238523763 0.071463051 0.423146983 8.91648056 0.067813054 0.017865055 8.9267084 -0.950691348 0.127573254 LPSS(ph)PLGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSPLGCR 9 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 LPS(0.123)S(0.877)PLGCR 72.275 0.049524 282060000 142290 174560 164420 144770 180450 181150 159030 151140 147930 172510 TRUE FALSE 147907.7191 204539.3221 168704.9203 173405.0739 149777.1735 139080.6579 146564.8131 149114.2155 142606.0282 206310.0316 0.716919667 0.99141724 0.817725241 0.840507234 0.72598105 0.674134247 0.710410502 0.722767644 0.691221978 1 17.65445445 3.267641465 5.762677494 0.732556986 0.851800676 0.116077408 0.107794857 0.260132039 24.31385325 0.027941611 0.037016307 1852.002058 -3.267641465 0.11924369 LPSS(ph)PVYEDAAS(ph)FK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 LPS(0.244)S(0.756)PVYEDAAS(1)FK 136.36 4.02E-05 93117000 224330 113930 171380 216850 261210 319700 347920 246840 223580 135610 TRUE FALSE 233186.7216 133496.5912 175846.3036 259742.2828 216809.6175 245454.5201 320649.1213 243531.5135 215533.3995 162180.1831 1.437824999 0.823137505 1.084265045 1.601566097 1.336844079 1.513468017 1.977116533 1.501610794 1.328974942 1 17.30723802 3.745959621 24.09146017 1.513413666 1.085881947 0.243424315 0.272877218 389.0607252 1266790.596 0.068441963 0.120198174 5571.339459 -3.745959621 -0.427531718 LPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSS(1)PVYEDAASFK;LPS(0.02)S(0.98)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.012)S(0.988)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.002)S(0.998)PVYEDAASFK;LPS(0.001)S(0.999)PVYEDAASFK;LPS(0.119)S(0.881)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.151)S(0.849)PVYEDAASFK;LPS(0.201)S(0.799)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPSS(1)PVYEDAASFK;LPS(0.158)S(0.842)PVYEDAASFK 371.71 3.85E-97 1.07287E+11 9230813 6877869 8982315 8537793 10084562 10959633 13160704 9902106 9824241 6229455 TRUE FALSE 9595252.625 8059089.498 9216401.508 10226542.97 8370391.753 8414424.331 12129133.63 9769384.466 9470668.485 7449997.437 1.287953816 1.081757352 1.237101299 1.372690804 1.123542904 1.129453319 1.628072188 1.311327225 1.271231107 1 22.8288085 LPSSPASPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSPASPSPK 11 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 LPSS(0.003)PAS(0.172)PS(0.825)PK 121.68 0.00042648 131230000 93973 45787 52842 41372 71999 98035 77906 56266 57071 40446 TRUE FALSE 97683.1266 53650.56108 54219.10593 49555.25812 59760.6357 75267.85698 71799.52415 55511.8463 55017.02586 48370.61931 2.019472316 1.109155968 1.120909897 1.024490875 1.235473859 1.556065605 1.484362309 1.147635633 1.13740586 1 15.56184339 4.74343152 24.87691988 1.219972723 2.019472667 0.663400484 0.174311645 316.8380225 1618114.176 0.04477047 0.368435645 55390.01974 -4.74343152 0.799499944 LPSSPVYEDAAS(ph)FK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 LPSSPVYEDAAS(1)FK;LPSSPVYEDAAS(1)FK 171.08 3.22E-06 203552000 335390 162538 210140 269410 352500 430470 454980 323460 277700 169078 TRUE FALSE 348631.4562 190452.6371 215616.421 322698.4939 292582.1759 330499.8663 419317.4787 319124.5478 267705.6312 202205.5969 1.724143454 0.94187619 1.066322715 1.595892986 1.446953894 1.634474374 2.073718459 1.578218173 1.3239279 1 17.6254634 3.724760039 23.77739103 1.580658062 1.213890336 0.116628936 0.319893726 598.4150746 1031025.925 0.083306767 0.129913285 5305.911953 -3.724760039 -0.366767727 LPSSSGLPAADVSPATAEEPLS(ph)PSTPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LPSSSGLPAADVSPATAEEPLSPSTPTR 28 0 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 LPSSSGLPAADVSPAT(0.008)AEEPLS(0.842)PS(0.128)T(0.018)PT(0.003)R 61.732 0.019749 53473000 32358 29308 39427 33333 42259 44246 42569 33046 40447 34798 TRUE FALSE 33635.51883 34341.42102 40454.50001 39926.16791 35075.83027 33970.53705 39232.33055 32603.07242 38991.32037 41616.00185 0.80823523 0.825197508 0.972090018 0.959394611 0.842844788 0.816285456 0.942722241 0.78342635 0.936930955 1 15.34485075 1.001064084 24.97412719 1.000000014 0.869881793 0.305540711 0.063749425 32.68667626 767135.4921 0.062445581 0.015611395 10.02453147 -1.001064084 -0.130118221 LPSTSDDCPAIGT(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LPSTSDDCPAIGTPLR 16 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR;LPSTSDDCPAIGT(1)PLR 250.26 9.75E-20 337635000 170777 171420 141672 193222 169439 209287 188293 169616 140723 147605 TRUE FALSE 177519.4078 200860.0515 145364.0887 231440.7349 140637.8193 160683.266 173534.1026 167342.575 135658.4067 176525.3737 1.005631112 1.137853711 0.823474188 1.311090469 0.796700306 0.910255918 0.983054725 0.94798029 0.768492392 1 17.42951605 LPYDVTPEQALAHEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LPYDVTPEQALAHEEVK 17 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 234.48 3.90E-20 1386190000 1865490 1234030 1679680 1456760 2052240 2258490 2315210 1687620 1813180 1011610 FALSE TRUE 1939140.986 1445965.053 1723453.841 1744902.78 1703400.978 1733989.925 2133737.791 1665000.214 1747924.006 1209815.611 1.602840109 1.195194573 1.424559102 1.4422882 1.407983962 1.433267937 1.763688426 1.376242957 1.444785462 1 20.20635575 0.366916047 2.071647115 1.000010949 1.453526048 0.488850461 0.139490828 9.634029523 30.2916296 0.130889663 0.035784713 2.327641262 -0.366916047 0.453515099 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 LQAALDDEEAGGRPAMEPGNGS(0.99)LDLGGDS(0.01)AGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR;LQAALDDEEAGGRPAMEPGNGS(1)LDLGGDSAGR 328.1 4.06E-117 4836350000 1523571 1856007 2261316 1941371 1994887 2299213 1962107 1977787 2159317 2045874 TRUE FALSE 1583722.76 2174761.765 2320247.753 2325368.389 1655796.82 1765255.626 1808311.926 1951278 2081603.603 2446723.84 0.647283005 0.888846436 0.948307984 0.950400839 0.67674038 0.721477266 0.739074797 0.797506432 0.850771783 1 21.22241984 0.854099118 3.056821373 0.999892192 0.800320239 0.271711006 0.100479639 0.915248044 15.69279669 0.101666763 0.026587827 7.146594125 -0.854099118 -0.199571953 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ;;;;;;;;; 323.51 8.86E-105 4664030000 1427780 1633174 1564458 1539270 1688535 1917600 1562823 1617728 1488360 1682657 FALSE TRUE 1484149.857 1913658.93 1605229.061 1843733.012 1401518.424 1472266.462 1440324.85 1596045.002 1434794.214 2012341.423 0.737523881 0.950961357 0.797692202 0.916212821 0.696461549 0.731618623 0.715745764 0.793128335 0.712997406 1 20.94044367 3.239354012 24.99999987 0.760814237 0.853987447 0.113292886 0.098779643 35.32694645 1113127.407 0.025430088 0.032507021 1735.217872 -3.239354012 0.093173211 LQAEAPHIVVGTPGR ddPTM_MDA-MB-175_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 ;;; 182.57 5.41E-07 1457990000 1562500 1949790 1835540 1903270 2014000 2245920 1781150 1861780 1933490 1992910 FALSE TRUE 1624188.707 2284651.265 1883375.68 2279731.125 1671660.999 1724339.117 1641538.809 1836825.884 1863904.073 2383382.558 0.681463704 0.958575138 0.790211237 0.956510787 0.701381737 0.723483988 0.688743317 0.770680258 0.782041501 1 21.18457911 5.02424507 16.26283549 0.802398376 0.381661967 0.109617791 0.108676815 1368358.913 23833965.48 0.025445366 14963130.29 105741.4033 -5.02424507 -0.420736409 LQAEEAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 164.33 1.00E-04 775850000 1343090 1166610 1380430 1036310 1802260 1526430 1346520 1275210 1367150 1283020 FALSE TRUE 1396116.23 1366966.193 1416405.14 1241289.025 1495912.489 1171939.766 1240976.244 1258117.896 1317946.539 1534403.204 0.909875727 0.890878088 0.923098398 0.808971867 0.974914863 0.763775625 0.808768022 0.819939565 0.858931039 1 20.54924621 2.734446701 24.99321637 0.834291321 0.897009175 0.096462615 0.069713709 634.0236557 3851856.617 0.020641539 0.020094157 542.5586611 -2.734446701 0.062717854 LQAFGFCEYKEPESTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQAFGFCEYKEPESTLR 17 1 P49756;P49756-2;P49756-3;E9PQU5 P49756 RBM25 RNA-binding protein 25 0 ; 105.89 0.00071126 607900000 322480 219990 269030 214120 315850 357530 301860 287990 294590 192928 FALSE TRUE 335211.7594 257771.5712 276041.1428 256472.2969 262161.9298 274499.0759 278199.4244 284129.9651 283987.7634 230728.5478 1.452840416 1.117207098 1.196389201 1.111575916 1.13623534 1.189705732 1.205743403 1.231446944 1.230830628 1 17.81583699 -2.118074662 2.484477754 0.604004351 1.201507495 0.313169888 0.091957912 4492600.322 1648798.625 10055454.36 0.021320013 0.00761948 2.118074662 0.597503144 LQAKES(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 104.94 0.0019254 2130936000 2931060 2112420 2573170 1588186 3540110 3282970 2408370 2440380 2749890 2340470 TRUE FALSE 3046780.512 2475211.703 2640228.924 1902324.451 2938363.367 2520549.971 2219595.666 2407670.698 2650921.996 2799040.285 1.088508989 0.88430728 0.943262209 0.679634538 1.049775304 0.900505071 0.792984538 0.860177222 0.947082473 1 21.41650082 4.738679926 20.81073107 0.884890647 1.088509449 0.24756317 0.099571022 1.219848853 209523.0243 0.022440149 0.129727806 54787.30346 -4.738679926 0.203618802 LQAKES(ph)PQRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQAKESPQRK 10 2 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 LQAKES(1)PQRK;LQAKES(1)PQRK 97.86 0.0030112 450540000 682220 317980 490310 285970 662490 587290 438490 498410 551870 333080 TRUE FALSE 709154.5724 372590.5915 503087.8814 342534.0125 549880.1864 450900.798 404120.008 491729.6292 532008.3065 398340.6488 1.780271671 0.935356692 1.262958935 0.859902231 1.380426999 1.131947742 1.014508585 1.234445018 1.335561179 1 18.60364318 4.750001657 24.88273708 1.138483339 1.780272073 0.580689249 0.165993141 1115.322894 2425630.461 0.036788375 0.5824839 56234.34708 -4.750001657 0.641788735 LQALDTGWNELHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQALDTGWNELHK 13 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 162.94 3.96E-05 816820000 691850 636920 666040 567910 752370 827120 752400 707060 647800 657190 FALSE TRUE 719164.7722 746306.0555 683397.5496 680240.903 624482.4161 635033.9151 693424.922 697583.0172 624485.8045 785953.7978 0.91502169 0.949554614 0.869513642 0.865497317 0.794553596 0.807978684 0.882271864 0.887562372 0.794557907 1 19.58408498 4.210489402 0.001920621 1.737624041 2.55E-05 0.01684857 0.063119416 2018675.942 713.4856395 318946.5438 326574.6338 16236.3873 -4.210489402 -1.737598584 LQALKDTANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQALKDTANR 10 1 P29401;P29401-2;E9PFF2;F8W888;F8WAX4 P29401 TKT Transketolase 0 ; 67.214 0.058043 3503600000 784410 928800 932320 722370 1404370 1220620 744330 906690 1027430 1387040 FALSE TRUE 815379.1125 1088314.175 956617.0251 865252.6299 1165655.689 937149.5037 685987.4697 894537.3036 990452.995 1658803.932 0.491546407 0.656083672 0.576690835 0.521612358 0.70270854 0.564954957 0.413543431 0.539266448 0.597088647 1 20.66171194 0.784352971 4.689042858 0.999997603 0.558205564 0.749703824 0.076109593 2.016210902 43.51981605 0.074968905 0.018997302 6.086294607 -0.784352971 -0.441792039 LQASLS(ph)SSDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQASLSSSDVR 11 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LQAS(0.04)LS(0.889)S(0.066)S(0.005)DVR;LQASLS(0.48)S(0.48)S(0.039)DVR;LQAS(0.018)LS(0.958)S(0.023)S(0.001)DVR;LQAS(0.006)LS(0.631)S(0.309)S(0.054)DVR 159.6 2.99E-05 1054970000 1400710 1402450 1351920 1600190 1585570 1689540 1435220 1407480 1359110 1334390 TRUE FALSE 1456011.112 1643309.878 1387152.146 1916702.806 1316055.378 1297169.94 1322723.706 1388615.033 1310195.897 1595838.172 0.912380176 1.029747193 0.869231085 1.201063391 0.824679721 0.81284554 0.828858295 0.870147774 0.821007994 1 20.60588293 LQASLS(ph)SSDVRFPQSPHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQASLSSSDVRFPQSPHSGR 20 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LQASLS(0.973)S(0.027)SDVRFPQSPHSGR;LQASLS(0.98)S(0.019)S(0.001)DVRFPQSPHSGR 166.79 8.87E-12 302700000 69796 114415 112210 100285 123410 142226 80483 112412 98562 151054 TRUE FALSE 72551.59997 134064.8862 115134.2848 120121.0737 102432.8123 109196.167 74174.53216 110905.301 95014.77287 180650.1392 0.401613861 0.742124456 0.637332943 0.66493762 0.567023157 0.604462125 0.410597703 0.613923142 0.525960142 1 17.46283884 -1.53014191 2.877942728 1.018648235 0.579736392 0.614660685 0.101052282 11300868.41 12383852.74 1648421.812 0.023991882 0.02950245 1.53014191 -0.438911843 LQASVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 101.69 0.084302 537400000 247460 297580 265330 285700 325110 354200 272020 247300 263340 340040 FALSE TRUE 257229.9119 348687.0501 272244.7178 342210.6073 269847.9183 271942.418 250698.3616 243985.348 253862.4448 406664.3275 0.632536209 0.857432104 0.669458075 0.841506334 0.663564272 0.66871471 0.616474927 0.599967421 0.624255504 1 18.63347892 -1.099392056 4.748427409 1.000016684 0.684639864 0.546693347 0.085772646 1.58E-05 3.00E-06 0.086702303 0.020434848 0.079544095 1.099392056 -0.31537682 LQAVTDDHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LQAVTDDHIR 10 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ;;;;;;;; 196.44 3.33E-07 24408590000 8712390 10558600 9159840 9207330 10334390 11283390 9658440 10009410 9010730 10853610 FALSE TRUE 9056361.885 12371957.42 9398552.955 11028512.39 8577754.079 8662993.674 8901386.235 9875250.231 8686435.587 12980167.07 0.697707651 0.953143156 0.724070261 0.849643331 0.660835414 0.667402324 0.685768233 0.76079531 0.669208304 1 23.62980562 LQAYHTQTTPLIEYYR ddPTM_MDA-MB-175_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 ; 211.78 6.21E-12 1266740000 505180 619820 546590 640820 621540 713290 456580 470110 491670 621110 FALSE TRUE 525124.8965 726269.2635 560834.5844 767572.2833 515890.8528 547639.2075 420792.0666 463808.9444 473974.8927 742804.6126 0.70694889 0.977739302 0.755023023 1.033343453 0.694517568 0.73725876 0.566490918 0.624402348 0.638088246 1 19.50262325 3.087569581 11.37576589 0.677056497 0.8679365 0.209767303 0.142308631 0.550315417 68.07721021 0.038242908 0.045723407 1223.403112 -3.087569581 0.190880003 LQCPQVDLFYLHAPDHGTPVEETLHACQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQCPQVDLFYLHAPDHGTPVEETLHACQR 29 0 O43488;H3BLU7;H7C5H7 O43488 AKR7A2 Aflatoxin B1 aldehyde reductase member 2 0 ; 250.05 1.01E-46 620670000 144734 213376 202310 211013 237478 252920 177166 216510 185938 232280 FALSE TRUE 150448.2101 250021.6682 207582.3648 252750.7416 197111.5744 194183.163 163279.266 213608.0376 179246.1277 277790.8187 0.54158813 0.900035751 0.747261431 0.909859954 0.709568355 0.699026569 0.587777763 0.768952835 0.645255767 1 18.08363939 -1.205288203 4.545404501 1.000061074 0.730493902 0.349480073 0.112882132 7.20E-05 1.26E-05 0.104482988 0.024620876 0.062332106 1.205288203 -0.269567172 LQDAEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LQDAEIAR 8 0 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 ;;;;;;;;; 219.25 1.52E-05 58938561000 13908325 15445070 15103971 15998576 16286930 17918560 16502060 15511300 14285098 15194850 FALSE TRUE 14457436.41 18097640.63 15497592.89 19163046.58 13518483.46 13757246 15208585.42 15303396.39 13770980.11 18171989.93 0.795589061 0.995908576 0.852828609 1.054537596 0.743918718 0.75705776 0.836924601 0.842142025 0.757813545 1 24.11521308 3.217775752 24.99999987 0.815062274 0.92466643 0.212112923 0.095331134 325.7103391 391762.9135 0.025622358 0.030655352 1651.109028 -3.217775752 0.109604156 LQDFKLDFGNSQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQDFKLDFGNSQGK 14 1 O75223;B8ZZK2;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 164.65 3.73E-06 1038050000 2779900 1680440 2365000 1401070 2727600 2697300 2323000 2349300 2853900 1517490 FALSE TRUE 2889652.599 1969042.498 2426633.843 1678197.464 2263963.526 2070892.953 2140917.19 2317811.476 2751188.696 1814813.111 1.592259049 1.084983619 1.337126026 0.92472192 1.247491277 1.141105351 1.179690171 1.277162624 1.515962541 1 20.79138956 4.749059669 24.44619992 1.198165206 1.592259352 0.358759417 0.161067326 1215.19035 2829396.775 0.036593171 0.51363183 56112.50648 -4.749059669 0.394094145 LQDLIEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQDLIEEIR 9 0 O75843;G3V2V9;G3V3Z2;G3V532 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ;;; 121.83 0.0014025 110352000 191129 236065 223362 241597 244664 269206 222422 216053 220959 230921 FALSE TRUE 198674.9205 276607.3274 229182.9972 289384.1655 203076.1007 206686.9864 204987.9824 213157.1629 213006.7288 276165.5487 0.719405159 1.001599688 0.829875407 1.047864829 0.735341905 0.748416982 0.74226486 0.771845597 0.771300873 1 18.07517383 3.196880816 24.99999249 0.777224456 0.901980075 0.165743579 0.11101279 198.0123901 118769.3161 0.029368452 0.035102325 1573.550975 -3.196880816 0.124755619 LQDLQGEKDALHSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQDLQGEKDALHSEK 15 1 H9KV28;A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610 H9KV28 DIAPH1 Protein diaphanous homolog 1 0 ; 144.97 2.49E-06 274820000 610140 399810 516300 323460 729270 608970 522560 450270 543540 350520 FALSE TRUE 634228.7983 468474.2574 529755.2021 387439.4226 605308.9459 467545.9465 481600.3817 444234.8671 523978.1016 419197.6829 1.512958741 1.11754973 1.263735998 0.924240372 1.443970162 1.115335236 1.148862223 1.059726438 1.24995467 1 18.67727122 4.741693753 24.60576919 1.149706339 1.512958909 0.384007027 0.138997518 236.6914404 1858718.686 0.030484568 0.217411657 55168.82737 -4.741693753 0.36325257 LQDSSDPDTGSEEEGSSRLS(ph)PPHS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQDSSDPDTGSEEEGSSRLSPPHSPR 26 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 2 LQDSSDPDT(0.002)GS(0.001)EEEGS(0.2)S(0.237)RLS(0.56)PPHS(1)PR 132.6 3.09E-05 594200000 355870 383710 366430 389550 437770 496730 432670 410740 388730 431330 TRUE FALSE 369920.0224 449609.2077 375979.4668 466601.8273 363358.0118 381371.9855 398756.1948 405234.7021 374739.6832 515840.8552 0.717120443 0.871604494 0.728867175 0.904546087 0.704399444 0.739321017 0.773021739 0.785580859 0.726463752 1 18.97656652 -1.019180001 5.147372673 1.000002005 0.775694389 0.535613925 0.063529313 1.34E-06 2.55E-07 0.056300591 0.013270058 0.095679743 1.019180001 -0.224307616 LQEALRR ddPTM_MDA-MB-175_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 87.323 0.031149 354280000 153600 205280 181610 189730 230540 268390 185830 198930 176170 291680 FALSE TRUE 159664.2466 240535.2431 186342.9058 227258.0277 191352.8931 206060.49 171264.159 196263.6687 169829.6761 348829.1114 0.457714799 0.689550371 0.534195397 0.651488136 0.548557694 0.590720451 0.490968653 0.562635578 0.486856373 1 18.41216092 -1.604636834 3.083477509 1.026480952 0.560989342 0.787806887 0.068950204 204579810 209364418.6 43553060.32 0.015282904 0.024852104 1.604636834 -0.46549161 LQEDGLLSNVSHVIVDEVHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQEDGLLSNVSHVIVDEVHER 21 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;;; 206.85 2.31E-22 155099000 76003 95941 99640 104096 103173 118135 114463 104561 100769 82233 FALSE TRUE 79003.65713 112418.1204 102236.7003 124685.8781 85635.69031 90699.9366 105491.091 103159.5308 97142.34337 98344.9819 0.803331859 1.143099711 1.039572109 1.267841792 0.870768276 0.922262985 1.072663688 1.048955715 0.987771226 1 16.58556382 LQEDKEQMAQQLAEETQGFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQEDKEQMAQQLAEETQGFQR 21 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 259.93 1.30E-36 582780000 371566 327175 388148 351217 472200 488220 434525 404860 440200 329602 FALSE TRUE 386235.7126 383364.7612 398263.4557 420686.6743 391935.6127 374838.304 400465.7951 399433.5139 424357.288 394181.2013 0.979843055 0.972559726 1.010356289 1.06724185 0.994303156 0.95092892 1.015943413 1.013324615 1.076553845 1 18.58849945 1.551141015 3.281074306 1.039516562 0.998877898 0.167481265 0.033973155 0.358770313 8.657464729 0.023518347 0.009241987 35.57468101 -1.551141015 -0.040638664 LQEDPNYS(ph)PQRFPNAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LQEDPNYSPQRFPNAQR 17 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;H0Y710;H0Y4L1 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR 248.46 4.33E-21 2115080000 1707870 2088020 1963270 1857150 2002020 2370880 1866920 1910890 1897370 2120800 TRUE FALSE 1775298.026 2446621.192 2014434.429 2224488.727 1661717.356 1820279.051 1720585.932 1885277.645 1829084.024 2536330.155 0.69994753 0.964630408 0.794231944 0.877050144 0.655166029 0.717682218 0.678376168 0.743309242 0.721153759 1 21.27431112 3.252974988 24.9845316 0.733662801 0.840460182 0.1020591 0.109223038 378.976472 656878.6431 0.027572318 0.037164496 1790.502734 -3.252974988 0.106797381 LQEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQEEER 6 0 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;; 180 0.007406 1362560000 2149860 2669910 2634430 2590080 2659770 3324390 2674720 2753920 2489320 2436410 FALSE TRUE 2234738.133 3128446.273 2703085.41 3102390.093 2207663.245 2552350.804 2465068.457 2717008.207 2399729.859 2913777.892 0.766955553 1.073673557 0.92769096 1.064731153 0.757663531 0.875959287 0.846004242 0.932469223 0.823580228 1 21.47445948 3.243825522 24.9999611 0.871962196 0.964322699 0.150565243 0.099239487 225.4129156 1070347.043 0.025859309 0.034010566 1753.176021 -3.243825522 0.092360503 LQEEERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQEEERER 8 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;;;; 111.61 0.0029193 2103990000 977800 1221670 1267960 922283 1494590 1451950 981117 1101951 1223700 1572770 FALSE TRUE 1016404.299 1431482.319 1301004.079 1104707.825 1240540.126 1114756.617 904214.4859 1087181.149 1179659.276 1880924.169 0.540374947 0.761052648 0.691683429 0.58732183 0.659537554 0.592664306 0.480728836 0.578003711 0.627170035 1 20.84301026 0.932945887 20.15025419 1 0.610577468 0.709123607 0.074384047 1756.847896 527947.6982 0.076133795 0.019033449 8.569310659 -0.932945887 -0.389422532 LQEGYDHSYYFIATFITDHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQEGYDHSYYFIATFITDHIR 21 0 P10768;X6RA14 P10768 ESD S-formylglutathione hydrolase 0 ;; 263.02 5.77E-37 4596630000 971044 979158 1087762 1064352 1224620 1377967 1330950 1130291 1267327 1055387 FALSE TRUE 1009381.567 1147320.77 1116109.971 1274877.649 1016459.53 1057955.048 1226626.661 1115141.298 1221716.149 1262169.876 0.799719266 0.909006617 0.884278727 1.010068195 0.80532704 0.838203373 0.971839595 0.88351126 0.967949063 1 20.26747467 1.129306153 0.993502852 1.00129682 0.884382876 0.27751446 0.062946757 0.715504867 1.52006469 0.057948618 0.019667465 13.46809443 -1.129306153 -0.116913945 LQEIEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQEIEELER 9 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 0 111.06 0.0050869 23395000 38629 94210 70570 98979 60957 98072 65574 71940 59713 92651 FALSE TRUE 40154.10275 110389.8346 72409.11217 118556.7508 50595.55091 75296.2643 60434.13853 70975.76197 57563.94079 110804.1895 0.362387947 0.996260476 0.653487133 1.069966319 0.456621281 0.679543478 0.54541384 0.640551249 0.519510508 1 16.75765291 3.199289545 24.99989982 0.61927124 0.778291798 0.068796639 0.22628284 342.2664629 217885.2737 0.059769734 0.071439567 1582.302613 -3.199289545 0.159020558 LQEKEDLQELNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LQEKEDLQELNDR 13 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;; 258.09 5.80E-24 33636080000 11457010 8865270 10767870 8232560 13088020 12863340 11977050 10647810 11548170 8306230 FALSE TRUE 11909341.6 10387811.16 11048489.54 9860935.796 10863323.04 9876024.231 11038257.52 10505093.52 11132553.62 9933676.736 1.19888556 1.04571665 1.112225597 0.99267734 1.093585318 0.994196257 1.111195564 1.057523191 1.120688131 1 23.24389637 4.742582961 24.69262969 1.061373822 1.198885624 0.435222907 0.047835792 297.9391182 1828925.201 0.010282384 0.077888825 55281.89999 -4.742582961 0.137511803 LQEKEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQEKEELR 8 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;;;;; 129.85 0.00097858 4726160000 9103950 7896150 8870830 6965530 10913860 10968710 9517330 8533170 8923010 7547910 FALSE TRUE 9463380.976 9252252.339 9102011.117 8343291.044 9058725.976 8421393.335 8771336.806 8418796.814 8601872.613 9026778.451 1.04836748 1.024978334 1.008334387 0.924282244 1.003539194 0.932934533 0.971701793 0.932646886 0.952928297 1 23.10577977 3.960811609 3.773037569 0.956932927 1.034516661 0.591423822 0.026213239 0.135536355 4.048503069 0.00635434 0.013191731 9137.167974 -3.960811609 0.077583734 LQEKLS(ph)PPYSSPQEFAQDVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQEKLSPPYSSPQEFAQDVGR 21 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LQEKLS(1)PPYSSPQEFAQDVGR;LQEKLS(1)PPYSSPQEFAQDVGR 155.09 1.68E-08 284640000 250162 177261 209362 144634 273791 265550 243815 221796 228909 183273 TRUE FALSE 260038.5889 207704.1979 214818.1457 173242.1735 227252.1036 203880.0369 224704.1432 218823.1874 220670.6098 219181.8354 1.186405746 0.947634175 0.980091007 0.790403882 1.036819968 0.93018674 1.025195098 0.998363697 1.006792417 1 17.74176871 2.211844756 24.92881225 1.007111452 0.971344215 0.019393571 0.092771102 944.7859575 881583.1193 0.034347743 0.025374713 162.8713726 -2.211844756 -0.035767237 LQELESCSGLGS(ph)TSDDTDVR ddPTM_MDA-MB-175_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(0.946)T(0.054)SDDTDVR;LQELESCSGLGS(0.975)T(0.024)S(0.001)DDTDVR;LQELESCSGLGS(0.97)T(0.028)S(0.002)DDTDVR 273.51 1.96E-44 1127840000 532770 505650 576980 583120 650350 726340 584720 608080 558880 581230 TRUE FALSE 553804.171 592491.4541 592016.5728 698459.3956 539803.7393 557658.5428 538888.1185 599929.6822 538766.018 695110.8902 0.796713415 0.85236969 0.851686517 1.004817225 0.776572122 0.802258389 0.775254893 0.863070469 0.775079236 1 19.40688362 LQELPDAVPHGEMPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQELPDAVPHGEMPR 15 0 P33992;B1AHB1;B1AHB2 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 138.55 9.91E-06 736720000 350870 506610 420540 421200 467060 509410 432640 430380 421180 460850 FALSE TRUE 364722.6185 593616.3266 431499.6179 504512.1028 387669.308 391107.2477 398728.5463 424611.4601 406021.8141 551144.734 0.661754701 1.077060688 0.782915251 0.915389501 0.703389299 0.709627115 0.723455241 0.77041734 0.736688186 1 19.0720717 3.24087818 24.9999791 0.75689022 0.869381172 0.08659191 0.127177119 109.3854483 1179946.815 0.032720332 0.042261821 1741.318365 -3.24087818 0.112490951 LQELSAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQELSAEER 9 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 96.618 0.016857 151190000 133670 158090 173020 162950 190930 205000 174760 155270 161370 175530 FALSE TRUE 138947.3948 185240.7277 177529.0433 195181.0236 158475.7868 157391.8568 161061.8545 153188.8596 155562.3252 209921.7428 0.661900921 0.882427543 0.845691547 0.929779932 0.75492793 0.749764435 0.767247129 0.729742701 0.741049132 1 17.67949208 LQELSSKADEASELACPT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;LQELSSKADEASELACPT(1)PK 136.53 8.44E-06 249682000 892490 334090 432030 324970 825330 628220 400990 421540 557270 394770 TRUE FALSE 927726.1944 391467.3586 443289.0567 389248.0961 685040.7014 482325.4258 369559.356 415889.9458 537213.9616 472117.6232 1.965031909 0.829173366 0.938937746 0.82447271 1.450995828 1.021621312 0.78276967 0.880903244 1.137881611 1 18.84878681 4.743799227 24.96439451 0.976844307 1.965032331 0.71354995 0.186178484 301.8668768 1438489.31 0.045628297 0.389712469 55436.93702 -4.743799227 0.988188023 LQEPTPSSGDPGEHDPASTHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQEPTPSSGDPGEHDPASTHK 21 0 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 ; 94.446 0.00090913 233302000 130398 206920 217492 197182 258330 288920 232960 234480 225816 184847 FALSE TRUE 135546.2137 242456.9004 223160.0202 236184.0111 214419.1589 221822.7086 214699.9865 231337.1791 217688.9263 221064.2305 0.61315308 1.096771286 1.009480456 1.068395418 0.969940539 1.00343103 0.971210883 1.046470424 0.984731568 1 17.75410608 4.745529091 24.9769952 1.016927491 0.613152891 0.902943194 0.039692933 215.1217742 771038.1605 0.00902045 0.090018778 55658.1915 -4.745529091 -0.4037746 LQEQLRAAGALS(ph)KR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQEQLRAAGALSKR 14 2 F2Z3J4;Q5W0C9;Q9H497-2;Q9H497 F2Z3J4 TOR3A Torsin-3A 1 LQEQLRAAGALS(1)KR 70.622 0.02075 385080000 328790 240170 264130 187510 341690 284810 319140 210170 262190 206730 TRUE FALSE 341770.8831 281417.3292 271013.4448 224598.9183 283609.6558 218667.1938 294124.9729 207353.0149 252753.8331 247234.7854 1.382373773 1.138259443 1.096178454 0.908443842 1.147126831 0.884451569 1.189658536 0.838688676 1.022323103 1 17.91552222 LQEVFGHAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQEVFGHAIK 10 0 P54136;P54136-2;E5RH09;E5RJM9 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 112.13 0.0016622 588240000 1109610 1476050 1197270 1445090 1605760 1423000 1253160 1117730 1188960 1457080 FALSE TRUE 1153418.26 1729550.105 1228471.84 1730924.489 1332813.489 1092529.816 1154934.045 1102748.658 1146169.562 1742566.929 0.661907581 0.992530087 0.704978282 0.993318799 0.764856412 0.62696577 0.662777438 0.632830016 0.657747799 1 20.73278264 3.000077744 24.99999967 0.685451313 0.844617996 0.122262691 0.142577799 3.973662836 1276836.68 0.037728319 0.044670678 1000.179029 -3.000077744 0.159166683 LQEVPHEGPMCDLLWSDPDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 191.41 1.45E-17 2806626000 1309663 1422844 1496666 1327977 1812854 1749217 1512647 1562093 1637546 1375117 FALSE TRUE 1361369.507 1667206.389 1535670.345 1590646.887 1504705.725 1342987.861 1394081.776 1541155.698 1578611.039 1644544.848 0.827809292 1.013779825 0.933796574 0.967226214 0.914967887 0.816631947 0.847700674 0.937132058 0.959907564 1 20.64925692 1.156234191 2.427623218 0.99616347 0.907933944 0.218208204 0.058585249 0.449862135 4.797688425 0.057060186 0.015911539 14.32960409 -1.156234191 -0.088229526 LQFHDVAGDIFHQQCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQFHDVAGDIFHQQCK 16 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;; 252.3 9.17E-27 27986970000 11898020 10547740 12045170 10959450 16003460 15077800 13859940 11797650 13197720 11279250 FALSE TRUE 12367763.02 12359232.29 12359077.03 13127196.5 13283197.59 11576209.46 12773561.69 11639521.8 12722736.64 13489203.08 0.916863876 0.916231464 0.916219954 0.973163234 0.984728119 0.858183347 0.946947096 0.862876904 0.943179264 1 23.68530178 2.750149257 24.99650339 0.911731816 0.940401917 0.01787963 0.044761263 1897.007542 4091810.379 0.013293976 0.013997274 562.534622 -2.750149257 0.028670101 LQFIADHCPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQFIADHCPTLR 12 0 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3KSA5;J3KRJ4;J3QLT0;J3QS84;J3KRE8;J3QLE8;J3KTB0;J3QS88;J3QL53 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ; 109.22 0.0016213 937750000 278990 444290 341070 440130 398770 491820 371520 388130 323210 507840 FALSE TRUE 290004.7406 520593.3514 349958.5644 527186.4003 330987.2178 377602.2586 342399.2916 382927.7522 311577.7352 607341.5248 0.477498621 0.857167393 0.576213794 0.86802298 0.544977092 0.621729691 0.5637673 0.630498223 0.513018989 1 19.21214849 -1.620220532 8.147295639 1.000294096 0.634685825 0.436585937 0.126545005 0.000622939 2.90E-05 0.112908226 0.026592127 0.023976151 1.620220532 -0.365608271 LQGAEHGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQGAEHGKK 9 1 O43237;O43237-2;H3BUM4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 88.056 0.0084664 166010000 306070 195920 237170 169770 365870 305200 328970 294280 317660 199050 FALSE TRUE 318153.8799 229567.736 243350.845 203349.9993 303679.5481 234321.9254 303184.4718 290335.6579 306227.4787 238050.0365 1.336500026 0.964367573 1.022267623 0.85423217 1.275696289 0.98433896 1.273616574 1.219641308 1.286399629 1 17.86090532 2.233218679 24.99749745 1.216063154 1.064944161 0.124525648 0.153606145 221.1055112 1034647.528 0.053959976 0.041025839 171.0876572 -2.233218679 -0.151118993 LQGAVVPPVNGVEIHVDSVLPVPPIEFGVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQGAVVPPVNGVEIHVDSVLPVPPIEFGVSPK 32 0 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 LQGAVVPPVNGVEIHVDSVLPVPPIEFGVS(1)PK 142.83 3.69E-10 45273000 15816 7801 13805 8454.2 15828 14166 12522 11585 16128 6393.5 TRUE FALSE 16440.42789 9140.761067 14164.76964 10126.41553 13137.56221 10876.16119 11540.49292 11429.72202 15547.55643 7646.183914 2.15014811 1.195467068 1.85252798 1.324375092 1.718185485 1.422429974 1.509314064 1.494826982 2.033374636 1 12.90052419 -1.946518693 2.718517766 0.57046334 1.600443675 0.290409174 0.292981588 22387719.5 8619483.448 60610022.2 0.064044431 0.011310487 1.946518693 1.029980335 LQGDANNLHGFEVDSR ddPTM_MDA-MB-175_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 ;;; 142.35 1.52E-06 2159470000 1562210 1586330 1706130 1744900 1879820 1979730 2028000 1747130 1768250 1507520 FALSE TRUE 1623887.257 1858769.838 1750593.149 2090036.012 1560288.868 1519967.711 1869040.061 1723712.58 1704611.028 1802889.681 0.900713601 1.030994773 0.970992939 1.159270051 0.865437794 0.843073055 1.036691308 0.956083225 0.94548826 1 20.78187969 4.773894389 22.02076246 0.9767092 0.900712816 0.070106469 0.084904949 10279.72761 6405964.583 0.020328339 3.076245797 59414.76577 -4.773894389 -0.075996384 LQGERDEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQGERDEWR 9 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 78.513 0.026959 166890000 144325 485060 337590 413440 282910 451740 236520 360440 285930 631060 FALSE TRUE 150023.0624 568365.2818 346387.8727 495217.198 234821.0593 346830.2312 217980.9444 355608.8914 275639.4352 754704.1246 0.198783944 0.753096827 0.45897175 0.656173965 0.311143204 0.459557885 0.288829671 0.471189808 0.365228473 1 19.52555163 -1.444655245 5.754278782 1.000351632 0.448308034 0.529207033 0.158202505 0.000664384 6.41E-05 0.14260151 0.033590824 0.035920697 1.444655245 -0.552043597 LQGPPT(ph)PAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQGPPTPAGK 10 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 LQGPPT(1)PAGK;LQGPPT(1)PAGK;LQGPPT(1)PAGK;LQGPPT(1)PAGK 129.54 0.0033588 1526710000 2910720 2106960 2433900 2104260 2960460 2937310 2980080 2579820 2506110 1741590 TRUE FALSE 3025637.473 2468813.99 2497329.433 2520476.347 2457242.067 2255164.268 2746493.543 2545241.733 2415915.591 2082821.216 1.452663076 1.185322087 1.199012865 1.210126116 1.179766198 1.082745005 1.318641044 1.222016423 1.159924612 1 20.99010758 -5 0.134712123 0.296019957 1.303161828 0.409506067 0.089109342 159.4529837 1.337674666 30.63822873 0.615298548 1.00E-05 5 1.007141872 LQGQLQGGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQGQLQGGSR 10 0 Q9UP83-3;Q9UP83;Q9UP83-2;U3KQU7 Q9UP83-3 COG5 Conserved oligomeric Golgi complex subunit 5 1 LQGQLQGGS(1)R 74.698 0.028679 0 110140 107110 114140 118530 140370 142540 127060 130980 124600 112130 TRUE FALSE 114488.4122 125505.3093 117114.5822 141974.8802 116509.9575 109437.2452 117100.7052 129224.4273 120115.6703 134099.7266 0.853755747 0.935910255 0.873339455 1.058726097 0.868830686 0.816088503 0.873235972 0.963644226 0.89571898 1 17.03294677 0.347747977 0.948831448 1.00009955 0.90507755 0.160191034 0.064924124 5.131100683 5.756693244 0.067725361 0.02049139 2.227142355 -0.347747977 -0.095022 LQGS(ph)PTPTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQGSPTPTSK 10 0 Q8WXD9 Q8WXD9 CASKIN1 Caskin-1 1 LQGS(0.775)PT(0.225)PTSK 153.49 0.0051565 0 195070 151320 166580 153830 203410 225930 194850 181420 192050 145930 TRUE FALSE 202771.5142 177308.0329 170921.2116 184257.1149 168834.4409 173461.1815 179577.1479 178988.3616 185138.158 174522.1895 1.161866665 1.015962689 0.979366648 1.055780445 0.967409596 0.993920498 1.02896456 1.025590856 1.060828761 1 17.41305095 4.738216475 7.910752377 1.014258536 1.163118556 0.703627651 0.028752315 0.049573144 36.92471811 0.006735487 0.039747824 54728.86926 -4.738216475 0.14886002 LQGSPT(ph)PTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQGSPTPTSK 10 0 Q8WXD9 Q8WXD9 CASKIN1 Caskin-1 1 LQGS(0.32)PT(0.659)PT(0.02)S(0.001)K 98.407 0.014364 0 235010 192090 217130 175100 247780 270940 225270 213210 206020 172400 TRUE FALSE 244288.3763 225079.9632 222788.5862 209734.2574 205662.4441 208018.2911 207612.7488 210352.2687 198605.3804 206178.4792 1.184839355 1.091675349 1.080561788 1.017246117 0.997497144 1.008923395 1.006956447 1.020243575 0.963269208 1 17.65353423 5.149705534 0.664232667 0.998319177 1.410378966 0.924814156 0.016784772 1.262606168 0.286783145 0.006902334 0.44408653 141158.0123 -5.149705534 0.412059788 LQHSSALTASVEEGGVPGEDPS(ph)S(ph)RPATPELAEPESAPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 2 LQHSSALTASVEEGGVPGEDPS(0.686)S(0.686)RPAT(0.627)PELAEPESAPTLR 86.227 0.00054504 118090000 5203.5 33349 27718 34057 22114 39674 19533 32655 25072 36046 TRUE FALSE 5408.938198 39076.43133 28440.35385 40793.37295 18355.07018 30460.31477 18001.95242 32217.31314 24169.66362 43108.52356 0.125472592 0.906466474 0.659738527 0.94629483 0.425787493 0.706596103 0.417596126 0.747353666 0.560670179 1 15.39568553 -2.016672122 2.603952889 1.410510768 0.628544159 0.197487089 0.232955879 32507869.23 11857692.09 79831295.99 0.050695387 0.009623385 2.016672122 -0.781966609 LQHSSALTASVEEGGVPGEDPSS(ph)RPAT(ph)PELAEPESAPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQHSSALTASVEEGGVPGEDPSSRPATPELAEPESAPTLR 40 1 Q6NV74 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 2 LQHSSALTASVEEGGVPGEDPS(0.468)S(0.539)RPAT(0.994)PELAEPESAPTLR 178.22 1.04E-22 142180000 7435.1 45687 33339 46436 31899 63295 26783 48142 32015 51844 TRUE FALSE 7728.643489 53533.38685 34207.84173 55620.9022 26476.81937 48595.6955 24683.67848 47496.73523 30862.7864 62001.83919 0.124651842 0.863416111 0.551723016 0.897084714 0.427032806 0.78377829 0.398112037 0.76605365 0.497772111 1 15.92002339 -2.290302851 2.204693475 2.702466371 0.610116968 0.217528776 0.230468867 13160840.88 1875563.595 111621339.5 0.051524655 0.005125039 2.290302851 -2.092349404 LQHYAK ddPTM_MDA-MB-175_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 1798640000 4259900 3979400 4430900 3889600 5530100 5479000 4697100 4728100 4616200 4448700 FALSE TRUE 4428084.141 4662830.995 4546372.894 4658951.271 4590095.577 4206585.285 4328929.028 4664727.553 4450063.864 5320337.589 0.832293829 0.876416377 0.854527146 0.875687152 0.862745174 0.790661347 0.813656832 0.87677285 0.836425093 1 22.34308636 -1.355481614 3.23078163 1.001245474 0.848055888 0.738069254 0.02740669 11915463.17 15758107.04 140735.9643 0.00689313 0.044108104 1.355481614 -0.153189587 LQIDVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQIDVDGR 8 0 Q08J23;Q08J23-2;Q08J23-3 Q08J23 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 138.4 0.0016451 65388000 79533 85400 90147 96209 90038 109430 105940 96569 87934 92999 FALSE TRUE 82673.02425 100066.7857 92496.30488 115238.853 74733.37292 84016.54093 97636.14598 95274.65051 84769.27252 111220.3735 0.74332626 0.899716325 0.831648933 1.036130786 0.671939597 0.755406031 0.877862058 0.856629478 0.76217396 1 16.76306156 -1.415290591 5.411547977 1.000115005 0.832158576 0.22389152 0.09654362 0.000129425 1.40E-05 0.090315825 0.021273112 0.038433453 1.415290591 -0.167956429 LQINS(ph)PPFDQPMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQINSPPFDQPMSR 14 0 Q00537;Q00537-2;F5H6Z0;F8VQZ9 Q00537 CDK17 Cyclin-dependent kinase 17 1 LQINS(1)PPFDQPMSR 85.909 0.0079191 50314000 73119 96079 106250 89456 127030 129750 92786 110120 110860 130850 TRUE FALSE 76005.79458 112579.8209 109018.9623 107150.1298 105437.486 99617.52888 85513.19087 108644.0215 106870.1703 156487.5522 0.485698661 0.719417099 0.696662199 0.684719828 0.673775546 0.636584364 0.546453629 0.694266221 0.682930807 1 17.25568838 0.483164586 1.522030177 0.999932979 0.645345381 0.704877052 0.069130837 1.50267969 3.853578983 0.063877851 0.018415355 3.042037662 -0.483164586 -0.354587598 LQIS(ph)TPDIKDNIVAQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQISTPDIKDNIVAQLK 17 1 O14896;O14896-2 O14896 IRF6 Interferon regulatory factor 6 1 LQIS(0.84)T(0.16)PDIKDNIVAQLK 90.968 0.0022236 189180000 264070 147180 190570 130930 291050 257720 247630 206980 281770 175560 TRUE FALSE 274495.6875 172457.0201 195536.4108 156827.5632 241577.425 197868.4358 228220.1135 204205.7717 271629.1527 209957.6207 1.30738616 0.821389667 0.93131371 0.746948659 1.150600889 0.942420833 1.086981805 0.972604714 1.293733239 1 17.67973863 1.898136325 1.16555227 1.110328171 0.966019836 0.076267261 0.169033049 1.156672797 2.897985614 0.128218542 0.055492884 79.09268607 -1.898136325 -0.144308335 LQIVEMPLAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQIVEMPLAHK 11 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ; 129.84 0.00023666 1386240000 2250610 2186360 2309100 2344300 3133600 3197400 2497600 2228480 2406950 2181110 FALSE TRUE 2339465.821 2561850.322 2369277.043 2807995.543 2600951.791 2454852.307 2301831.586 2198610.871 2320324.34 2608456.745 0.896877368 0.982132569 0.90830605 1.076496878 0.997122838 0.941112906 0.88244959 0.842878026 0.889539129 1 21.31476508 2.391259814 3.729367976 0.885404211 0.974679928 0.197619208 0.060353884 0.276038843 7.520665423 0.021779301 0.017967656 246.1839946 -2.391259814 0.089275717 LQKEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQKEEEKR 8 2 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 101.11 0.003167 331060000 913020 348190 517240 318650 860870 820170 645430 540710 623230 364350 FALSE TRUE 949066.7346 407988.924 530719.6993 381678.0189 714539.6249 629697.9473 594839.5101 533462.6669 600800.074 435737.4066 2.17807037 0.936318337 1.21798058 0.875935858 1.639839991 1.445131719 1.365132993 1.224275582 1.37881225 1 18.73309944 -3.512152563 0.303615231 3.86E-17 1.354012256 0.087951768 0.34772591 283.5673225 6.035755936 179.0907836 0.327577702 0.000307502 3.512152563 1.354012256 LQLATLEAGPGAAGAGS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LQLATLEAGPGAAGAGSE 18 0 C9JI98 C9JI98 TMEM238 Transmembrane protein 238 1 LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E;LQLATLEAGPGAAGAGS(1)E 296.47 2.54E-49 143696000 292996 347522 296697 433030 336109 490157 364762 318015 325914 444690 TRUE FALSE 304563.7083 407206.2002 304429.1676 518682.0415 278977.3122 376325.4652 336171.0013 313752.5291 314184.4188 531818.4914 0.572683563 0.765686426 0.57243058 0.975298998 0.524572419 0.707620121 0.632116045 0.589961677 0.590773777 1 19.02057442 -0.97953336 4.592980532 1.000005753 0.660058823 0.39998441 0.125283747 14878782.24 3239461.451 1046.507661 0.02736751 0.104825427 0.97953336 -0.33994693 LQLEEEQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQLEEEQHR 9 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 132.78 0.00029547 362990000 253497 278951 221166 220959 312943 288706 246361 236324 251648 277353 FALSE TRUE 263505.2573 326858.6643 226929.7676 264664.0307 259749.0606 221658.4069 227050.5811 233156.4633 242591.2376 331695.0101 0.794420324 0.985419299 0.684151889 0.797913814 0.783096075 0.668259697 0.684516119 0.702924241 0.731368366 1 18.33949778 4.229087168 24.99999218 0.739668163 0.889919828 0.201299607 0.101947798 213.4344349 563248.4851 0.023348154 0.051492651 16946.77908 -4.229087168 0.150251665 LQLEETDHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 176.78 2.40E-06 2268440000 2322780 1778820 2130480 1732820 2730590 2596260 2458510 2100530 2298820 1809950 FALSE TRUE 2414485.148 2084318.498 2186002.059 2075566.624 2266445.287 1993317.962 2265805.562 2072375.831 2216085.917 2164575.049 1.115454578 0.962922722 1.009898945 0.958879492 1.047062465 0.92088189 1.046766922 0.957405396 1.02379722 1 21.04565239 4.74647358 24.83745055 0.990683289 1.115454645 0.467180471 0.039545349 699.0014866 2193992.873 0.008213035 0.089088669 55779.36675 -4.74647358 0.124771356 LQLERPVS(ph)PETQADLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQLERPVSPETQADLQR 17 1 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 LQLERPVS(1)PETQADLQR;LQLERPVS(0.995)PET(0.005)QADLQR;LQLERPVS(0.906)PET(0.094)QADLQR;LQLERPVS(0.908)PET(0.092)QADLQR 233.89 2.45E-20 1432100000 1091810 1234620 1198730 1374360 1156250 1564590 1514740 1414840 1178840 1216210 TRUE FALSE 1134915.502 1446656.381 1229969.889 1646204.306 959711.038 1201237.684 1396010.721 1395876.384 1136413.779 1454503.064 0.780277148 0.994605248 0.845628943 1.131798445 0.659820568 0.825874977 0.959785342 0.959692983 0.781307243 1 20.4720949 -2.013497626 8.931155946 1.142514867 0.892028093 0.066801946 0.127427747 0.083515096 0.000126216 0.02849584 0.027516733 0.009693986 2.013497626 -0.250486774 LQLGT(ph)PPPLLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQLGTPPPLLAAR 13 0 Q9P2N5 Q9P2N5 RBM27 RNA-binding protein 27 1 LQLGT(1)PPPLLAAR 104.55 0.017024 58267000 202890 223330 194350 187060 206610 245440 193410 208210 190730 246070 TRUE FALSE 210900.2539 261685.1902 199414.9207 224059.9097 171490.506 188440.2797 178250.0188 205419.2855 183865.6646 294282.7052 0.716658676 0.889230613 0.677630446 0.76137641 0.582740688 0.640337595 0.605710141 0.698033836 0.624792627 1 18.16684323 -1.180687623 4.777944373 1.000037888 0.688736073 0.551481057 0.084275523 3.52E-05 6.03E-06 0.084402982 0.019891556 0.065964819 1.180687623 -0.311301814 LQLHESQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQLHESQK 8 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;; 154.49 0.0004242 5274010000 2869430 6662080 6984640 6267570 8697400 9706500 7091830 8075130 6908760 7345970 FALSE TRUE 2982717.312 7806240.416 7166665.456 7507276.639 7219019.055 7452312.478 6535953.834 7966896.091 6660115.077 8785272.174 0.339513364 0.888559883 0.81575907 0.854529773 0.821718316 0.848273375 0.743967142 0.906846815 0.758100028 1 23.06665555 4.741776668 24.94749567 0.842253284 0.339513173 0.825451336 0.070180611 104.1428633 807816.2847 0.014797131 0.106302701 55179.36115 -4.741776668 -0.502740112 LQLKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQLKPR 6 1 Q15056;K7EJP0;Q15056-2 Q15056;Q15056-2 EIF4H;TNNI3 Eukaryotic translation initiation factor 4H 0 ; 95.378 0.039593 3135200000 2161810 2340900 2297960 2094560 3483400 3033800 2713100 2427580 2398190 2919300 FALSE TRUE 2247159.928 2742931.365 2357846.725 2508857.716 2891292.912 2329245.928 2500440.133 2395042.261 2311879.61 3491280.942 0.643649126 0.78565186 0.675352905 0.718606654 0.828146735 0.667160841 0.716195624 0.686006741 0.662186644 1 21.73532502 -1.880735088 2.766706385 1.134935429 0.711475018 0.716214553 0.054894918 23170720.53 18801500.48 20615076.85 0.013008565 0.013160273 1.880735088 -0.42346041 LQLLEDDKENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;;;; 206.69 2.33E-08 3963040000 5335440 3104960 4326760 3527950 5507860 5366050 5722580 4248920 4812430 2733900 FALSE TRUE 5546087.291 3638212.727 4439518.92 4225767.98 4571635.925 4119866.211 5274029.226 4191970.177 4639231.584 3269555.361 1.696281811 1.112754587 1.357835678 1.292459528 1.398243926 1.260069262 1.613072312 1.282122403 1.418918193 1 21.64066302 -1.158745199 3.946135665 0.999866153 1.370598626 0.332383815 0.161480343 10336795.17 3035314.333 15626.00499 0.034033112 0.069383276 1.158745199 0.370732473 LQLLSNLFHGMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQLLSNLFHGMDK 13 0 Q7L2H7;J3KNJ2;E9PN86 Q7L2H7 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 ;;; 197.14 1.36E-07 963960000 1103685 1004667 1250790 1131830 1559080 1608680 1603000 1308950 1373370 935308 FALSE TRUE 1147259.336 1177210.742 1283386.615 1355702.596 1294068.138 1235088.45 1477352.671 1291405.666 1323942.682 1118563.695 1.025654007 1.052430673 1.147352288 1.212003037 1.156901609 1.104173553 1.320758646 1.154521349 1.183609559 1 20.09321598 4.228929351 3.197280236 1.174446298 1.030891876 0.277416655 0.076860604 0.255475709 5.307204516 0.018286761 0.053447369 16940.62196 -4.228929351 -0.143554422 LQLNGNLQLELAQVLAQERPK ddPTM_MDA-MB-175_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 ;; 382.44 2.51E-114 1928470000 1576670 1125220 1386850 1397700 1578420 1655180 1663580 1295700 1551340 1056910 FALSE TRUE 1638918.149 1318467.782 1422992.45 1674160.888 1310120.732 1270789.529 1533184.253 1278333.261 1495507.576 1263991.279 1.296621406 1.043098797 1.125792934 1.324503512 1.036495073 1.0053784 1.212970594 1.011346583 1.183162892 1 20.26955508 3.16183846 24.99999902 1.077329914 1.181400389 0.254118341 0.101366614 56.05660025 18263.78022 0.028313272 0.033840845 1451.571592 -3.16183846 0.104070475 LQLQGLDLS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 LQLQGLDLS(0.965)S(0.035)R;LQLQGLDLS(0.976)S(0.024)R;LQLQGLDLS(0.977)S(0.023)R;LQLQGLDLS(0.701)S(0.299)R 159.75 2.97E-05 195322000 401319 405361 375424 389273 401572 458428 374096 378387 362327 479911 TRUE FALSE 417163.384 474978.5985 385207.8579 466270.0375 333312.9349 351965.0445 344773.378 373315.3412 349286.922 573940.372 0.726840983 0.827574817 0.671163551 0.812401532 0.580744884 0.613243225 0.600712887 0.650442728 0.608577021 1 19.13054133 -1.221492362 3.598477424 1.000510609 0.675205807 0.579825308 0.082513963 28034566.73 41207107.73 156843.8377 0.020974774 0.060049257 1.221492362 -0.325304802 LQLQVTVSS(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQLQVTVSSAK 11 0 Q9H0M0-3;Q9H0M0;Q9H0M0-2 Q9H0M0-3 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 1 LQLQVTVS(0.15)S(0.85)AK 151.3 3.51E-05 161100000 455040 265810 331100 279920 448370 454430 388090 347920 376510 251400 TRUE FALSE 473005.3306 311460.7998 339728.738 335287.3405 372156.2276 348895.5195 357670.4917 343256.7015 362959.4786 300657.0167 1.573238955 1.035933913 1.129954464 1.115182158 1.237809886 1.160443629 1.189629617 1.141688643 1.207221048 1 18.1977591 8 0.019661095 1.94E-07 2.673685276 0.222804703 0.130913656 5786.020891 8.76667553 444.0913079 795.2075658 100000000 -8 2.673685083 LQLS(ph)PWESSVVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQLSPWESSVVNR 13 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 LQLS(1)PWESSVVNR;LQLS(0.999)PWES(0.001)S(0.001)VVNR;LQLS(1)PWESSVVNR;LQLS(1)PWESSVVNR 242.93 6.17E-17 440160000 533175 566220 561394 529310 492446 604060 586460 524080 522530 606180 TRUE FALSE 554225.1607 663463.8804 576024.3888 634005.9382 408740.2048 463776.2196 540491.7328 517055.5648 503724.2474 724949.365 0.764501891 0.915186512 0.794571892 0.874552029 0.563818971 0.639736017 0.745557909 0.713229902 0.694840594 1 19.46752071 3.282654502 24.99797463 0.709667545 0.839728354 0.180650172 0.112508081 186.753627 105874.2156 0.029058354 0.03934498 1917.142974 -3.282654502 0.13006081 LQLSADPERPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQLSADPERPGR 12 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 0 62.732 0.069021 71638000 47629 53610 47970 49193 59563 64993 52415 44244 55480 61552 FALSE TRUE 49509.4297 62817.10047 49220.13761 58923.22857 49438.50254 49899.36073 48306.57534 43650.98155 53483.28564 73611.93592 0.672573396 0.853354822 0.668643434 0.800457532 0.671609868 0.677870513 0.656232916 0.592987822 0.726557249 1 16.16765209 0.958203536 22.59688573 1.000000002 0.695485393 0.615849639 0.070791377 1765.69632 954609.737 0.071731863 0.017932966 9.082460891 -0.958203536 -0.304514609 LQLWDTAGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 236.95 3.36E-15 2426647000 2108965 2378780 2234240 2439688 2526544 2665952 2206762 2158560 1955159 2314149 FALSE TRUE 2192228.567 2787316.961 2292466.13 2922251.005 2097082.953 2046825.051 2033790.228 2129628.034 1884793.21 2767562.189 0.792115377 1.007137968 0.828334098 1.055893528 0.757736524 0.739576895 0.734867038 0.769496 0.68103012 1 21.40018431 3.197746437 24.99556309 0.764260633 0.920422587 0.284847182 0.107172105 155.5052503 95234.59379 0.028097563 0.03358336 1576.690448 -3.197746437 0.156161954 LQMEAPHIIVGTPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQMEAPHIIVGTPGR 15 0 P60842;J3KT12;P60842-2;J3KSZ0;J3QS69;J3QL43;J3KTB5;J3QR64;J3QLN6;J3KS25;J3QKZ9 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 ;;;;; 179.14 6.83E-07 5236210000 2319040 2672280 2575135 2619769 2799530 3336950 2699061 2645407 2515874 2848680 FALSE TRUE 2410597.49 3131223.303 2642245.134 3137951.489 2323666.891 2561993.934 2487501.546 2609949.646 2425328.186 3406824.305 0.707579046 0.919103253 0.775574229 0.921078168 0.682062438 0.752018216 0.730152577 0.766094583 0.711902925 1 21.69999612 5.035325235 16.01571187 0.792829161 0.393933042 0.066087977 0.100368018 20920404.23 266110688.7 0.022535111 235188181.9 108473.8951 -5.035325235 -0.398896119 LQMES(ph)PDLPKPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQMESPDLPKPLSR 14 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44 Q07002 CDK18 Cyclin-dependent kinase 18 1 LQMES(1)PDLPKPLSR;LQMES(1)PDLPKPLSR 75.97 0.017421 484469000 340960 286645 342040 277830 434540 458460 391540 359380 391050 327170 TRUE FALSE 354421.3641 335874.049 350953.8434 332783.9448 360677.046 351989.613 360850.0717 354563.0989 376976.1869 391272.6975 0.905816752 0.858414224 0.896954594 0.850516652 0.921804788 0.899601775 0.922247001 0.906178993 0.963461518 1 18.57781492 1.06801469 0.489141955 1.004845376 0.878946345 0.744317299 0.021270271 0.468094239 0.292301871 0.023441976 0.011867057 11.69538949 -1.06801469 -0.125899032 LQNDPQLEAEYQQLQEDHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQNDPQLEAEYQQLQEDHQR 20 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 289.14 2.04E-54 603320000 504995 659750 588180 619840 657900 778040 631200 646230 679020 716940 FALSE TRUE 524932.5925 773056.9304 603508.454 742442.502 546070.393 597352.0013 581724.8947 637568.3439 654582.2028 857410.6664 0.61223007 0.901618047 0.703873275 0.86591237 0.636883135 0.696692991 0.678467061 0.743597402 0.763440704 1 19.70962684 -1.159281519 3.634785878 1.000227257 0.735828307 0.455954359 0.087258573 28177090.01 49440313.13 76952.95605 0.019558463 0.069297646 1.159281519 -0.26439895 LQPERGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LQPERGSPK 9 1 S4R3H4;Q9UKV3;E7EQT4;A0A087WYN3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK;LQPERGS(1)PK 87.216 0.030317 14251840000 5253240 2502830 3231610 2260620 4471160 4825070 3707960 3171200 3199230 2160790 TRUE FALSE 5460641.972 2932671.583 3315828.411 2707763.889 3711153.82 3704520.617 3417320.406 3128695.251 3084090.337 2584155.43 2.113124431 1.13486656 1.283138148 1.047833214 1.436118655 1.43355178 1.322412873 1.21072255 1.193461625 1 21.30126142 4.743084168 24.99519982 1.246981867 2.113124778 0.782241523 0.139637903 208.7579046 1153465.818 0.032788131 0.263131059 55345.73617 -4.743084168 0.866142912 LQPFATEADVEEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQPFATEADVEEALR 15 0 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ; 130.24 0.00014185 37095000 19462.7 25857 23638.8 27156 25858 31364 25929 25179 21807 28182 FALSE TRUE 20231.10242 30297.73861 24254.84655 32527.37575 21462.6664 24080.18633 23896.61723 24841.51669 21022.17033 33703.72332 0.600263129 0.89894337 0.719648874 0.9650974 0.636804017 0.714466651 0.709020098 0.737055561 0.623734361 1 15.04062036 -0.999364136 4.844463005 1.000002022 0.740450826 0.342300357 0.110322831 4.11E-06 8.49E-07 0.09987682 0.023540858 0.10014652 0.999364136 -0.259551195 LQPFHS(ph)TELEDDAIYSVHVPAGLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.777)T(0.223)ELEDDAIYSVHVPAGLYR;LQPFHS(0.959)T(0.041)ELEDDAIYSVHVPAGLYR;LQPFHS(0.938)T(0.062)ELEDDAIYSVHVPAGLYR;LQPFHS(0.994)T(0.006)ELEDDAIYSVHVPAGLYR;LQPFHS(0.916)T(0.084)ELEDDAIYSVHVPAGLYR 310.28 3.01E-74 1575102000 104943.4 307781 299149 338404 335583 377446 285702 350783 323565 406117 TRUE FALSE 109086.6465 360639.9925 306945.0687 405339.3012 278540.7215 289789.8867 263307.9307 346081.3277 311919.9589 485687.8506 0.224602379 0.742534515 0.631980125 0.834567512 0.573497404 0.596658711 0.542134069 0.712559162 0.642223104 1 18.88966987 -5 0.211839837 2.819451322 0.570284656 0.393853083 0.149904115 155.6793264 1.553458353 120.4658294 0.300570243 1.00E-05 5 -2.249166665 LQPFHST(ph)ELEDDAIYSVHVPAGLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQPFHSTELEDDAIYSVHVPAGLYR 25 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 LQPFHS(0.375)T(0.625)ELEDDAIYSVHVPAGLYR 108.32 0.0063365 29043000 4354.6 9103 8738.2 10163 9062.6 14283 9409.9 9116.3 8875.8 13067 TRUE FALSE 4526.52297 10666.36944 8965.924671 12173.21107 7522.142489 10965.98971 8672.32745 8994.11091 8556.361692 15627.22847 0.289656159 0.682550297 0.573737351 0.778974409 0.481348468 0.70172326 0.554949809 0.575541013 0.547529059 1 13.93177431 -1.569904685 2.816877896 1.025484024 0.58465668 0.499657982 0.126967833 36385079.3 37440823.06 6968179.449 0.028020049 0.026921256 1.569904685 -0.440827345 LQPQEIS(ph)PPPTANLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(1)PPPTANLDR;LQPQEIS(0.997)PPPT(0.003)ANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(1)PPPTANLDR;LQPQEIS(0.998)PPPT(0.002)ANLDR;LQPQEIS(0.999)PPPT(0.001)ANLDR 284.9 9.25E-36 12575700000 1063314 1211286 1195023 1107220 1284701 1422840 1174311 1164519 1152079 1160204 TRUE FALSE 1105294.458 1419314.948 1226166.281 1326224.811 1066327.983 1092406.973 1082265.435 1148910.528 1110615.902 1387523.76 0.796594977 1.022912175 0.883708313 0.955821334 0.768511512 0.787306859 0.779997767 0.828029444 0.800430186 1 20.40408105 3.242019171 24.99975073 0.814554745 0.920266497 0.20380392 0.082011628 109.6084288 792283.9501 0.021057091 0.027407249 1745.899221 -3.242019171 0.105711753 LQPS(ph)SSPENSLDPFPPR ddPTM_MDA-MB-175_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(0.595)S(0.065)S(0.34)PENSLDPFPPR 124.25 5.34E-05 71114000 82377 73727 88089 82401 91234 114040 94983 90018 86511 98607 TRUE FALSE 85629.30757 86389.03873 90384.67171 98699.67186 75726.07727 87555.93829 87537.98427 88811.45595 83397.48601 117927.1537 0.726120362 0.732562739 0.766444952 0.836954584 0.642142839 0.742457827 0.74230558 0.75310438 0.707194937 1 16.84753642 -2.125240856 2.440097771 1.524147743 0.740684634 0.743222901 0.046045248 14077337.19 5129203.217 40682502.02 0.010996347 0.007494784 2.125240856 -0.783463109 LQPSSS(ph)PENSLDPFPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.001)S(0.004)S(0.996)PENSLDPFPPR;LQPS(0.054)S(0.353)S(0.593)PENSLDPFPPR;LQPS(0.016)S(0.111)S(0.873)PENSLDPFPPR;LQPS(0.042)S(0.251)S(0.707)PENSLDPFPPR;LQPS(0.002)S(0.013)S(0.985)PENSLDPFPPR;LQPS(0.043)S(0.243)S(0.714)PENSLDPFPPR;LQPS(0.002)S(0.009)S(0.989)PENSLDPFPPR 251.04 1.35E-21 1511721000 1112084 1223335 1215028 1194840 1341471 1468470 1223067 1273243 1250013 1314017 TRUE FALSE 1155989.935 1433433.27 1246692.628 1431175.786 1113448.239 1127440.097 1127199.813 1256177.26 1205025.276 1571473.473 0.73560894 0.912158745 0.793327186 0.910722205 0.708537725 0.71744138 0.717288476 0.799362689 0.766812356 1 20.58368649 5.047989642 15.97065445 0.800808165 0.354848422 0.043236028 0.093707309 7510227.579 64992875.95 0.021507519 102424213 111683.661 -5.047989642 -0.445959743 LQQELDDLLVDLDHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 20 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;;;;;;;;;; 331.56 1.45E-71 52254477600 1887572.6 2139524.8 2074858.7 2031477.7 2279833 2554378.7 2170961.9 2212765.5 2148618.8 2366539.2 FALSE TRUE 1962095.424 2506971.541 2128931.222 2433297.926 1892307.801 1961162.959 2000796.234 2183106.998 2071290.429 2830217.246 0.693266719 0.88578767 0.752214773 0.859756589 0.668608674 0.692937251 0.706940867 0.771356687 0.731848565 1 21.43248137 -1.949687141 8.087210362 1.096476995 0.753785038 0.545684786 0.068015742 0.038438392 0.000239136 0.021395723 0.015284508 0.01122827 1.949687141 -0.342691957 LQQELDDLLVDLDHQRQS(ph)ACNLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQQELDDLLVDLDHQRQSACNLEK 24 1 P35579 P35579 MYH9 Myosin-9 1 LQQELDDLLVDLDHQRQS(1)ACNLEK 137.44 8.25E-06 10415000 12902 9616.1 10858 9900 9589.8 14128 12824 9822.7 10803 10693 TRUE FALSE 13411.38092 11267.59037 11140.9684 11858.19045 7959.729221 10846.98611 11818.82137 9691.042773 10414.20214 12788.08862 1.048740067 0.881100429 0.871198873 0.927284038 0.622433067 0.848210114 0.924205464 0.757817924 0.814367373 1 13.64251303 5.742889013 0.953234032 0.826782962 2.176454314 0.268307268 0.098512679 14.00172696 2.362677884 0.029009249 30.55390512 553208.7143 -5.742889013 1.349671352 LQQELDDLTVDLDHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQQELDDLTVDLDHQR 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 ;;;;; 272.16 3.61E-35 585593000 290705 347854 345010 349435 369578 418934 359102 346627 353271 381789 FALSE TRUE 302182.2579 407595.2186 354001.244 418552.2 306757.2636 321642.9275 330954.6469 341981.032 340556.8457 456593.2448 0.661819379 0.892687799 0.775309859 0.916685047 0.671839251 0.704440837 0.724834742 0.748983994 0.745864836 1 18.80054999 -1.070528627 3.83848829 1.000061708 0.762446448 0.444866328 0.080304902 12928502437 23165148664 10530050.75 0.019029237 0.085010266 1.070528627 -0.237615259 LQQELEFLEVQEEYIKDEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQQELEFLEVQEEYIKDEQK 20 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 245.88 4.94E-30 454700000 225084 104813 141811 89710 206823 175378 197191 157706 169943 92296 FALSE TRUE 233970.4901 122813.8174 145506.7112 107454.3702 171667.3003 134649.1174 181734.6542 155592.209 163826.7846 110379.6341 2.119688945 1.112649253 1.318238753 0.973498156 1.555244332 1.219872837 1.646450957 1.409609756 1.484212065 1 16.75211448 4.748454632 24.8018265 1.329996566 2.119689424 0.555094698 0.218287624 939.2783836 2354483.767 0.050577572 0.675068296 56034.38792 -4.748454632 0.789692858 LQQGAGLESPQGQPEPGAAS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 LQQGAGLESPQGQPEPGAAS(1)PQR 169.18 5.66E-12 275440000 156270 177340 168430 163860 169400 204210 152230 168050 137470 149900 TRUE FALSE 162439.6603 207796.7655 172819.4242 196271.0189 140605.4485 156785.3223 140297.8148 165797.5646 132522.4816 179270.035 0.906117189 1.159127154 0.964017351 1.094834499 0.78432209 0.874576291 0.782606055 0.924848175 0.739233869 1 17.45177484 3.239530522 24.99997465 0.848971142 1.035388088 0.462084728 0.095130851 20.75480787 534957.8915 0.024407107 0.031228358 1735.92326 -3.239530522 0.186416946 LQQLFNHTMFILEQEEYQR ddPTM_MDA-MB-175_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 ; 257.81 5.25E-31 2567100000 1045900 901190 1055110 1176230 1130160 1210230 1377840 1196620 1165970 825660 FALSE TRUE 1087192.94 1055962.372 1082607.033 1408884.783 938055.8069 929172.4237 1269841.3 1180581.266 1124006.967 987432.2688 1.101030394 1.069402333 1.096386119 1.426816631 0.94999509 0.940998642 1.286003446 1.195607338 1.138312979 1 19.91332227 2.204589896 24.99936071 1.17798492 1.104385286 0.026821557 0.141782834 627.3307581 461654.5955 0.054216061 0.040043324 160.173216 -2.204589896 -0.073599633 LQQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQQLFR 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 148.12 0.025139 270250000 187690 219450 190060 214620 264360 280090 218290 205200 215210 266290 FALSE TRUE 195100.1461 257138.8304 195013.1197 257071.1954 219424.1816 215043.3423 201179.8594 202449.6296 207464.6341 318464.4271 0.612627752 0.807433448 0.612354483 0.80722107 0.689006881 0.675250747 0.631718466 0.635705631 0.651453087 1 18.2807727 -1.619416197 2.903235353 1.025071435 0.680456197 0.663018338 0.068374314 19433071.54 18866850.25 3674075.575 0.015711568 0.024020597 1.619416197 -0.344615238 LQQLGEAHQAETEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQQLGEAHQAETEVLR 16 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 256.45 1.22E-26 893140000 339660 390060 397830 446320 420230 467620 432500 429520 395370 379020 FALSE TRUE 353070.0391 457049.7708 408197.7766 534600.7639 348799.4547 359022.3418 398599.5199 423762.987 381140.7109 453281.7122 0.778919664 1.00831284 0.900538816 1.179400689 0.769498185 0.792051239 0.87936378 0.934877749 0.840847316 1 18.79004843 4.767984042 22.84657894 0.918011782 0.778918966 0.124807756 0.113648868 7525.779557 5843270.376 0.02701775 2.450236138 58611.66278 -4.767984042 -0.139092816 LQQLGEAHQAETEVLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQQLGEAHQAETEVLRR 17 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 296.34 2.43E-46 1816280000 545160 914230 845910 922406 820089 1055950 797020 809308 771794 938930 FALSE TRUE 566683.3378 1071241.891 867955.1095 1104855.154 680690.5647 810721.6156 734547.4898 798460.55 744017.2847 1122895.357 0.504662642 0.953999751 0.772961705 0.983934208 0.606192341 0.721992135 0.654154891 0.711072982 0.662588264 1 20.09879206 3.210289449 24.99999837 0.706768638 0.812402969 0.046555616 0.157099675 489.9742222 433279.4412 0.041943664 0.050141571 1622.891365 -3.210289449 0.105634332 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LQQQAALS(0.935)PT(0.042)T(0.023)APAVSSVSK;LQQQAALS(0.997)PT(0.001)T(0.002)APAVSSVSK;LQQQAALS(0.991)PT(0.006)T(0.003)APAVSSVSK 277.25 1.49E-44 143670000 376884 307246 345675 321773 408536 443650 362849 338892 370351 328933 TRUE FALSE 391763.6713 360013.1105 354683.5745 385418.739 339093.1966 340619.0111 334407.9473 334349.7071 357022.1399 393381.1235 0.995888333 0.915176375 0.901628353 0.979759109 0.861996614 0.865875332 0.85008641 0.84993836 0.907573136 1 18.58556821 3.225831521 24.99957322 0.876011829 0.942440091 0.224339296 0.04967761 272.0393938 534276.8456 0.013594209 0.016350535 1682.021417 -3.225831521 0.066428262 LQQQHSEQPPLQPS(ph)PVMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LQQQHSEQPPLQPSPVMTR 19 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;Q5JTV8-2;H0YDU3 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 LQQQHSEQPPLQPS(0.99)PVMT(0.01)R;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(1)PVMTR;LQQQHSEQPPLQPS(0.999)PVMT(0.001)R;LQQQHSEQPPLQPS(0.999)PVMT(0.001)R;LQQQHSEQPPLQPS(0.69)PVMT(0.31)R 213.2 2.98E-17 2910080000 862756 1030567 840660 1255364 912545 1370414 889203 843246 849489 1229553 TRUE FALSE 896818.2731 1207558.866 862568.2902 1503671.252 757430.9269 1052156.117 819504.9454 831943.6666 818916.0568 1470460.369 0.609889455 0.821211432 0.586597441 1.022585364 0.515097817 0.715528374 0.557311821 0.565770887 0.556911342 1 20.48783647 -1.452645829 5.673133922 1.000266759 0.660114644 0.320003948 0.148150327 0.000483652 4.67E-05 0.138795461 0.032689148 0.035265835 1.452645829 -0.340152115 LQQTVPADAS(ph)PDSKCPICLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQQTVPADASPDSKCPICLDR 21 1 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 LQQTVPADAS(1)PDSKCPICLDR 128.17 5.61E-06 0 104560 75177 93727 65698 118640 134660 101610 87684 109750 72680 TRUE FALSE 108688.1095 88088.06495 96169.60262 78692.86831 98473.61518 103387.2558 93645.54269 86508.7394 105800.1189 86920.25446 1.250434783 1.013435424 1.106411885 0.905345581 1.132919085 1.18944953 1.077373085 0.995265602 1.217209034 1 16.40740478 -1.023267458 5.899169858 0.99999985 1.086536588 0.066948147 0.101815356 1.92E-07 3.17E-08 0.094221924 0.022208282 0.094783457 1.023267458 0.086536738 LQQTVPADAS(ph)PDSKCPICLDRFDNVSYLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQQTVPADASPDSKCPICLDRFDNVSYLDR 30 2 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 LQQTVPADAS(0.998)PDS(0.002)KCPICLDRFDNVSYLDR;LQQTVPADAS(1)PDSKCPICLDRFDNVSYLDR 182.15 3.31E-18 264660000 162767 158233 172647 119372 235040 221280 133356 165824 200235 205101 TRUE FALSE 169193.1668 185408.2869 177146.3227 142983.4253 195087.9848 169891.0735 122903.2083 163601.4005 193028.5815 245286.6141 0.689777416 0.755884244 0.722201345 0.582923882 0.795347049 0.692622686 0.501059582 0.666980549 0.786951144 1 17.90410898 0.926151665 3.2524905 0.999461368 0.673299416 0.610146601 0.07923681 0.218141282 5.535790819 0.078437779 0.020415803 8.436293194 -0.926151665 -0.326161952 LQQVLQMESHIQSTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQQVLQMESHIQSTSDR 17 0 Q14974;Q14974-2;J3KTM9;J3QKQ5 Q14974 KPNB1 Importin subunit beta-1 0 ;; 153.98 1.55E-07 2358641000 425144 527434 563520 513109 578569 612668 593448 545899 526813 512037 FALSE TRUE 441929.0134 618016.6866 578205.7941 614600.4287 480224.048 470385.1421 546931.9951 538582.1168 507853.103 612360.8466 0.721680715 1.009236123 0.944223977 1.003657291 0.784217428 0.768150258 0.893153111 0.879517559 0.82933634 1 19.22402252 4.768700053 23.6407045 0.893330841 0.721680128 0.284902542 0.084520078 8243.057942 6465440.999 0.020837963 2.274824818 58708.37416 -4.768700053 -0.171650713 LQQWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LQQWYR 6 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;A0A0J9YX90;K7ERC6;K7EPY4;K7EP41;A0A2R8YF08;K7ELR7;K7ENA0;K7ERK8;A0A0J9YXM3;A0A0J9YXH9;K7EIL4;A0A0J9YYI8 P06744 GPI Glucose-6-phosphate isomerase 0 ;; 174.6 0.010375 5848790000 2163660 2587360 2284760 2261160 3901380 3159230 2687840 2503290 2331140 3556080 FALSE TRUE 2249082.968 3031718.953 2344302.723 2708410.699 3238224.821 2425546.711 2477160.077 2469737.492 2247242.727 4252825.791 0.528844368 0.712871653 0.551234129 0.636849669 0.761428984 0.57033766 0.582473912 0.580728582 0.528411658 1 22.01999033 -1.417736704 3.126698322 1.005895875 0.608827674 0.721054331 0.073514751 13201437.75 16439522.72 692032.2527 0.017063266 0.03821759 1.417736704 -0.397068201 LQS(ph)IGTENTEENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 169.67 2.02E-06 328300000 113080 176510 140090 171480 117350 189380 137810 155120 123900 183230 TRUE FALSE 117544.4857 206824.2194 143740.8605 205398.2322 97402.88892 145399.3651 127008.0921 153040.8701 119440.8632 219130.4103 0.536413387 0.943840789 0.655960349 0.937333307 0.44449736 0.663528923 0.579600485 0.698400874 0.545067492 1 17.74143019 -1.159880725 3.846602137 1.000184108 0.67429146 0.292215936 0.155036088 8448929133 13992304556 19471169.2 0.035178618 0.0692021 1.159880725 -0.325892648 LQS(ph)PLEPHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQSPLEPHSK 10 0 O15211;O15211-2 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 LQS(1)PLEPHSK;LQS(1)PLEPHSK 122.64 0.00031126 452360000 372090 327960 431090 321210 558290 515740 459650 440470 483790 360120 TRUE FALSE 386780.4005 384284.5788 442324.5595 384744.3793 463392.0652 395967.2011 423621.4319 434566.2201 466378.4924 430678.6191 0.898071981 0.89227689 1.027040907 0.893344508 1.075957906 0.919402969 0.983613797 1.009026687 1.082892142 1 18.71625218 7.860809918 0.290618492 1.02307262 3.93E-08 0.324725175 0.057415726 54.86057468 0.842001456 0.05672649 28.44257749 72578822.47 -7.860809918 -1.02307258 LQSECHPDTCTQMTATEQWIFLCAAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQSECHPDTCTQMTATEQWIFLCAAHK 27 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 118.52 0.00021337 140850000 101770 126230 136170 123920 152750 153350 156320 150830 143100 138550 FALSE TRUE 105787.9582 147909.0206 139718.7021 148431.0061 126785.6096 117736.7865 144067.2299 148808.3706 137949.859 165696.2198 0.638445212 0.89265175 0.843222025 0.895802006 0.765168992 0.710558072 0.869466003 0.898079454 0.832546808 1 17.33818116 -4.999999993 0.13776036 1.628165716 0.75542054 0.36653181 0.07898369 162.6217843 1.382627845 27.82024443 0.513635513 1.00E-05 4.999999993 -0.872745175 LQSEPESIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LQSEPESIRK 10 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;;;; 164.48 9.85E-06 3282440000 3660410 3040420 3536440 2760530 4539100 4202230 3661110 3429290 3652250 3196850 FALSE TRUE 3804925.813 3562588.484 3628602.532 3306554.595 3767545.403 3226325.768 3374142.632 3383325.977 3520806.236 3823211.55 0.995217179 0.931831377 0.949098025 0.8648631 0.985439951 0.843878432 0.882541441 0.884943439 0.920902804 1 21.8663536 5.599383571 0.771442689 0.903571655 1.252067681 0.179284255 0.048320691 11.95660752 2.046705597 0.015719087 4.893705392 397542.5059 -5.599383571 0.348496026 LQSFDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQSFDSPER 9 0 P78332;E9PGM9;P78332-2 P78332 RBM6 RNA-binding protein 6 1 LQSFDS(1)PER;LQSFDS(1)PER 166.24 6.39E-05 705560000 407450 478420 481690 435660 500310 596420 470400 454050 438910 473710 TRUE FALSE 423536.4406 560584.9134 494243.2371 521832.2477 415267.4849 457910.4938 433528.8188 447964.2024 423113.7148 566524.4048 0.747604935 0.989515913 0.872412967 0.921111683 0.733008996 0.808280261 0.765242971 0.790723575 0.746858761 1 19.11177858 3.249559412 24.99999388 0.793877148 0.88956182 0.132307421 0.08992868 319.0434264 725173.5181 0.022736375 0.030497332 1776.476277 -3.249559412 0.095684671 LQSIGTENTEENR ddPTM_MDA-MB-175_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 0 ; 274 8.93E-17 0 35782 60728 53411 56712 67887 71126 56004 54076 51421 65492 FALSE TRUE 37194.70099 71157.5616 54802.93454 67929.46433 56347.59199 54608.06442 51614.26014 53351.19967 49570.36825 78323.90348 0.474883137 0.90850377 0.69969616 0.867289056 0.719417566 0.697208157 0.658984778 0.681161144 0.6328894 1 16.25716505 -1.110633357 4.695508178 1.000019255 0.711210951 0.3768864 0.113708625 2.13E-05 4.04E-06 0.102404134 0.024135277 0.07751159 1.110633357 -0.288808304 LQSIGTENTEENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 LQSIGTENTEENRR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;;;;;;;; 282.15 3.69E-33 1.23032E+11 9060316 10693390 9789775 10192401 11248447 12329049 10146673 10145757 9243568 11275005 FALSE TRUE 9418024.272 12529896.55 10044904.58 12208427.5 9336439.997 9465814.218 9351350.257 10009769.72 8910893.793 13484126.36 0.698452686 0.929233101 0.744942929 0.905392546 0.692402292 0.701996849 0.693508056 0.742337283 0.660843243 1 23.68475872 LQSLHEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQSLHEGR 8 0 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298;P85298-2;P85298-5 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 0 ; 67.897 0.057906 228130000 230813 281930 308170 317050 422950 433450 398600 397790 389140 395510 FALSE TRUE 239925.6755 330349.2844 316201.1634 379761.5437 351057.1101 332787.8065 367356.6905 392458.2757 375134.9274 473002.612 0.507239642 0.698409007 0.668497711 0.802874094 0.742188523 0.703564416 0.776648334 0.829716931 0.793092719 1 18.85148862 4.829803134 0.081139187 1.251356704 2.11E-14 0.787898894 0.055384606 41.50787178 0.519814696 2.106030049 6.927553697 67577.6576 -4.829803134 -1.251356704 LQTLS(ph)PSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LQTLSPSHK 9 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 LQT(0.016)LS(0.967)PS(0.018)HK 93.766 0.0059577 0 124370 80853 101410 77313 117630 111150 103870 104050 97793 79947 TRUE FALSE 129280.2236 94738.8738 104052.8279 92605.28064 97635.29462 85337.09699 95728.39799 102655.3799 94273.44903 95611.08397 1.352146825 0.99087752 1.088292524 0.968562188 1.021171297 0.892543976 1.001226992 1.073676562 0.986009625 1 16.54489026 4.740140993 24.98987579 1.006578934 1.35214694 0.805209516 0.05155865 59.06188877 933838.9303 0.012618818 0.08052563 54971.93098 -4.740140993 0.345568006 LQTMKEELDFQK ddPTM_MDA-MB-175_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 ; 220.19 2.75E-11 5177900000 4883400 2976200 4116900 2809600 5482500 4725600 4476300 4038500 4447700 2500900 FALSE TRUE 5076200.403 3487339.198 4224189.796 3365330.494 4550586.608 3628151.017 4125435.909 3984370.513 4287628.146 2990903.472 1.697213049 1.165981862 1.412345746 1.125188601 1.521475584 1.213061889 1.379327667 1.332162856 1.433556176 1 21.51214992 -1.266578045 3.523235987 0.99910961 1.352177573 0.308744554 0.162676892 24489577.1 36386855.63 237589.1869 0.034586176 0.054127997 1.266578045 0.353067963 LQVEEVHQLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQVEEVHQLSR 11 0 Q9NR28-2;Q9NR28;Q9NR28-3 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ;;; 177.64 7.89E-06 1751680000 1165584 1465350 1362400 1526640 1429840 1708930 1357380 1225160 1137470 1195990 FALSE TRUE 1211602.156 1717012.464 1397905.263 1828604.835 1186796.308 1312056.907 1250985.009 1208738.734 1096532.677 1430321.342 0.847083883 1.200438261 0.977336506 1.278457352 0.829741033 0.917316178 0.874618152 0.84508194 0.766633794 1 20.44790787 3.202452758 24.99541727 0.865550872 1.077694807 0.396569171 0.122861396 154.9019839 107229.3846 0.032787817 0.039190059 1593.869491 -3.202452758 0.212143935 LQVVDQPLPVR ddPTM_MDA-MB-175_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 ;;; 172.27 3.15E-05 450952000 818243 899085 856917 1005150 947018 1107420 861940 828316 838664 963620 FALSE TRUE 850547.8655 1053495.855 879248.961 1203965.67 786044.2186 850238.4881 794378.8905 817213.7789 808480.6465 1152422.889 0.738051867 0.91415735 0.76295687 1.044725579 0.682079665 0.737783409 0.689311969 0.709126646 0.701548584 1 20.13623879 LQWDGSSDLS(ph)PSDSGSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LQWDGSSDLSPSDSGSSK 18 0 K7EKG9;Q14CW9;K7EJK2;K7ENU1;Q14CW9-2 K7EKG9 ATXN7L3 Ataxin-7-like protein 3 1 LQWDGSSDLS(1)PSDSGSSK;LQWDGSSDLS(0.969)PS(0.031)DSGSSK;LQWDGSSDLS(0.998)PS(0.002)DSGSSK;LQWDGSSDLS(0.992)PS(0.008)DSGSSK 371.36 1.26E-107 605790000 1427270 982940 1217950 933540 1545450 1562510 1422650 1237580 1341760 907170 TRUE FALSE 1483619.722 1151752.299 1249690.778 1118191.426 1282754.961 1199640.733 1311138.976 1220992.264 1293470.32 1084912.593 1.367501614 1.061608379 1.15188153 1.030674207 1.182357887 1.10574874 1.208520377 1.125429157 1.19223459 1 20.04914738 4.74805242 24.82720466 1.125658248 1.367501755 0.555465201 0.0667172 844.106261 2207834.086 0.014574052 0.186758678 55982.51698 -4.74805242 0.241843508 LQYKT(ph)PPPSYNSALAQPVTTVPSMGETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LQYKTPPPSYNSALAQPVTTVPSMGETER 29 1 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 LQY(0.083)KT(0.753)PPPS(0.126)Y(0.012)NS(0.026)ALAQPVTTVPSMGETER;LQY(0.13)KT(0.835)PPPS(0.027)Y(0.004)NS(0.005)ALAQPVTTVPSMGETER 104.98 0.0014347 230832000 200279 150186 189207 172829 254490 262250 246490 220530 237240 159148 TRUE FALSE 208186.1696 175979.2772 194137.8899 207014.0604 211231.8807 201346.4119 227169.4697 217574.1561 228701.7787 190330.0035 1.093816874 0.924600819 1.020006758 1.087658575 1.109819139 1.057880566 1.193555748 1.143141659 1.201606549 1 17.53814348 3.429062941 1.27960161 1.136007052 1.000918057 0.30040596 0.068638777 0.453346565 1.522685886 0.022771674 0.042477237 2685.73365 -3.429062941 -0.135088995 LRAELDEVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRAELDEVNK 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 158.08 7.39E-06 509980000 831490 622750 738640 632930 1025410 1025250 960170 784880 811210 685930 FALSE TRUE 864317.8673 729702.4682 757889.5652 758121.6649 851111.1745 787151.2253 884909.3665 774359.9674 782014.7106 820324.8506 1.053628775 0.889528664 0.92388956 0.924172496 1.03752943 0.95956038 1.078730415 0.943967462 0.953298818 1 19.64583581 3.258126068 24.95871725 0.993492474 0.941934045 0.148762991 0.055072563 425.7819236 543146.2861 0.01478686 0.01999324 1811.865971 -3.258126068 -0.051558429 LRAETEQGEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 247.88 1.00E-16 2332770000 537946 730870 709610 586300 744290 837320 573278 700070 654890 827560 FALSE TRUE 559184.5235 856391.2371 728103.0196 702268.3901 617775.8517 642865.1197 528342.9724 690686.7067 631320.6368 989704.5374 0.565001475 0.8652999 0.735677156 0.70957378 0.624202303 0.649552564 0.533839093 0.697871618 0.637887989 1 19.91663837 -1.76544516 8.165011022 1.003989649 0.671846139 0.558528765 0.088307009 0.006465912 0.000185745 0.086203033 0.020187144 0.017161484 1.76544516 -0.332143509 LRAPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRAPSSR 7 1 Q6EEV4-2;Q6EEV4 Q6EEV4-2 POLR2M "DNA-directed RNA polymerase II subunit GRINL1A, isoforms 4/5" 1 LRAPS(0.327)S(0.673)R 59.153 0.06374 20537000 27022 36134 35575 35011 45152 42763 34627 35295 39066 40614 TRUE FALSE 28088.84943 42339.73342 36502.11373 41936.0713 37477.07917 32831.94133 31912.84526 34821.92826 37660.02229 48571.5357 0.578298566 0.871698471 0.751512449 0.863387799 0.771585222 0.675950242 0.657027718 0.716920471 0.77535169 1 15.56782348 0.847149133 5.192919872 0.999996894 0.739440491 0.465099019 0.08446138 1.891743999 63.69255418 0.08050567 0.020323303 7.033137899 -0.847149133 -0.260556403 LRDDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRDDFEK 7 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 131.22 0.0031802 673970000 822820 662910 767630 642520 980260 992190 987630 812850 808960 550790 FALSE TRUE 855305.569 776759.6358 787635.0684 769608.5383 813635.7553 761768.9093 910216.9799 801955.0753 779845.6876 658706.755 1.298461815 1.179219174 1.195729454 1.168362906 1.235201779 1.156461359 1.381824269 1.217469032 1.183904191 1 19.32927682 0.803318988 2.923588564 1.000106165 1.228559523 0.535000918 0.063924006 0.747222385 9.804755222 0.060330426 0.015839991 6.357977515 -0.803318988 0.228453358 LRDDFEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRDDFEKK 8 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 78.113 0.017698 263890000 452000 260530 351870 253630 503770 481180 460790 345630 433590 235570 FALSE TRUE 469845.309 305274.0009 361040.0213 303797.257 418139.3553 369433.2374 424672.0757 340997.3952 417985.1806 281725.4312 1.667741911 1.08358695 1.281531524 1.078345166 1.484208768 1.311323709 1.507397021 1.210389114 1.483661517 1 18.10393028 -1.048245823 4.34919463 0.999976445 1.32918393 0.239042875 0.182816123 0.611415276 48845023.12 2556.491149 0.039445311 0.089485811 1.048245823 0.329207485 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRDDQYTLEHMHAFGMYNYLHCDSWYQDSVYYIDTLGR 38 1 Q96RS6-2;Q96RS6;E5RHQ3;E5RGX7 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 77.911 0.00069417 325930000 34330 47502 48138 65648 70653 63022 67430 81964 91385 70620 FALSE TRUE 35685.37491 55660.09899 49392.51583 78632.97846 58643.4283 48386.09561 62144.6604 80865.40665 88096.0717 84456.6369 0.422528959 0.659037596 0.584826932 0.93104558 0.694361396 0.572910518 0.73581737 0.957478413 1.043092348 1 16.36592318 4.729610324 0.176737654 1.108893877 1.58E-16 0.596303382 0.127178547 13.78380439 0.437027495 0.410829645 3.494051771 53655.01546 -4.729610324 -1.108893877 LRDDTELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRDDTELRK 9 2 P16930;H0YLC7;P16930-2 P16930 FAH Fumarylacetoacetase 0 ; 64.73 0.038563 304430000 455420 363110 428400 354600 547840 521770 476340 446920 475470 357330 FALSE TRUE 473400.3333 425471.3179 439564.4559 424738.8216 454718.3525 400596.825 439003.2261 440929.7684 458357.9276 427341.972 1.107778698 0.995622583 1.028601178 0.993908508 1.064061998 0.937415118 1.027287875 1.031796073 1.072578772 1 18.70503149 -1.703041791 2.776275297 0.996184234 1.025477327 0.031082742 0.044918427 1000725.711 7501583.345 43994.72189 0.009799217 0.019813364 1.703041791 0.029293093 LRDEELAELEDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LRDEELAELEDALR 14 1 Q15628-2;Q15628 Q15628-2 TRADD Tumor necrosis factor receptor type 1-associated DEATH domain protein 0 ;;; 178.22 1.83E-06 456084000 289565 351844 337667 337554 418144 448583 354278 364060 348450 369420 FALSE TRUE 300997.2498 412270.47 346466.8794 404321.1737 347068.0322 344406.3966 326508.7646 359180.3712 335909.3526 441800.776 0.681296336 0.933159226 0.78421519 0.915166282 0.785575877 0.779551362 0.739040722 0.812991716 0.760318611 1 18.75303643 -1.747172731 7.018417342 1.003309282 0.803129286 0.41245922 0.071807027 0.003499875 0.000126077 0.065443091 0.015213412 0.017898938 1.747172731 -0.200179997 LRDEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRDEYR 6 1 P18074;E7EVE9;A8MX75;K7EIT8;P18074-2 P18074 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 84.244 0.051138 82423000 33009 46668 43682 45199 48115 50189 39165 47254 35337 51707 FALSE TRUE 34312.22081 54682.86597 44820.38881 54139.22729 39936.42949 38533.36537 36095.14496 46620.63742 34065.22827 61837.99666 0.554872775 0.884292327 0.724803377 0.87550099 0.645823468 0.623134116 0.583704953 0.753915714 0.550878588 1 15.91620596 -1.060115909 4.535141701 1.000012576 0.69735222 0.393522891 0.115529538 1.87E-05 3.87E-06 0.108277219 0.025519792 0.087073117 1.060115909 -0.302660356 LRDLEDSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 243.77 1.80E-12 18082920000 4496699 5669800 5446030 4294539 6215750 6217970 4603747 5257300 5278540 6570230 FALSE TRUE 4674232.149 6643544.045 5587958.016 5143985.996 5159199.035 4773940.702 4242893.28 5186834.493 5088566.377 7857540.774 0.594872147 0.84549915 0.711158641 0.654655972 0.656592079 0.607561684 0.539977253 0.660109141 0.647602923 1 22.90564642 -0.857145403 6.087688402 1.000000038 0.658049812 0.643113218 0.076528701 4.14E-08 7.56E-09 0.077227279 0.018202642 0.138948735 0.857145403 -0.341950226 LRDTEEMLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRDTEEMLSK 10 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 ; 115.04 0.0013391 721020000 627410 572180 684500 552130 872630 851970 746350 698680 739400 595040 FALSE TRUE 652180.6313 670447.4641 702338.6323 661339.6661 724300.6643 654112.8792 687849.1368 689315.3374 712789.1384 711626.6953 0.916464539 0.942133662 0.986948125 0.9293351 1.017809856 0.919179794 0.966587034 0.968647385 1.001633501 1 19.44076111 8 0.11997217 1.010972251 0.767416261 0.296711633 0.029175538 127.8939679 1.053679539 0.188502237 5.210159313 100000000 -8 -0.24355599 LRDYQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRDYQVR 7 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 136.16 0.0027429 60815000 56843 84902 92801 103290 94438 119840 84387 103120 77879 98882 FALSE TRUE 59087.20553 99483.25805 95219.4703 123720.4537 78385.46249 92008.97619 77772.52644 101737.8451 75076.15 118256.0347 0.499654886 0.841253119 0.805197558 1.046208374 0.662845348 0.778048887 0.657662221 0.860318421 0.634861047 1 16.85155428 -2.259104671 2.289010776 1.911160692 0.767472007 0.204418462 0.143390994 9061877.554 1371718.199 42818807.41 0.032731616 0.00550675 2.259104671 -1.143688685 LREAAEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LREAAEGLR 9 1 Q9Y490;Q9Y4G6 Q9Y490;Q9Y4G6 TLN1;TLN2 Talin-1;Talin-2 0 88.681 0.011509 75056000 42318 87007 59195 76501 84743 96214 51900 66447 52550 141560 FALSE TRUE 43988.74732 101949.7754 60737.67033 91632.66947 70338.41513 73869.75664 47831.94238 65556.38665 50658.73577 169295.9717 0.259833396 0.602198472 0.358766188 0.541257235 0.415476012 0.436334993 0.282534439 0.387229454 0.299231785 1 17.36918812 -1.297929604 4.289040315 1.000579971 0.402624836 0.751059859 0.103928786 31171089.08 9433307.829 170333.4581 0.023018683 0.050358223 1.297929604 -0.597955135 LREAIAELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 202.65 2.00E-07 411017000 311015 330315 343271 280444 461679 425287 315187 346452 348377 441233 FALSE TRUE 323294.1124 387044.0318 352216.9243 335914.9862 383202.9685 326520.5395 290481.8194 341808.3776 335838.9798 527684.1584 0.612665943 0.733476694 0.667476783 0.63658342 0.726197598 0.618780258 0.550484252 0.647751827 0.636439382 1 19.00931515 -1.94736361 2.296451848 1.266676002 0.647699691 0.813050662 0.050671155 5819587.264 2561457.184 8289658.034 0.013017787 0.011288504 1.94736361 -0.618976311 LREANQQQQFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LREANQQQQFNR 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 210.93 3.45E-08 105875000 72238 74980 64382 51968 94946 96991 66436 78302 78613 103552 FALSE TRUE 75090.01202 87857.23174 66059.84781 62247.11529 78807.11283 74466.31016 61228.57272 77252.48977 75783.73349 123841.0318 0.606341945 0.70943556 0.533424559 0.502637247 0.636357043 0.601305634 0.49441265 0.623803667 0.611943654 1 16.91812987 0.343882538 1.601807545 1.000043305 0.58661896 0.800201365 0.061433068 2.56683606 5.785238343 0.059410089 0.016914407 2.207407624 -0.343882538 -0.413424345 LREAQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LREAQDR 7 1 Q9Y3Q3 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 ; 156.51 0.0014034 218409000 160318 173749 161813 196859 310800 286840 199956 175178 162214 301800 FALSE TRUE 166647.4784 203589.0392 166029.9797 235797.1226 257970.327 220225.7571 184282.9262 172830.0254 156375.9498 360931.9317 0.461714423 0.564064914 0.460003577 0.653300808 0.71473401 0.610158697 0.510575291 0.478843821 0.433256069 1 18.46136726 -1.831517481 2.968281091 1.143800161 0.545144148 0.708413018 0.087956006 114452699.3 75059531.77 116664888.7 0.022985245 0.014739492 1.831517481 -0.598656013 LRECLPLIIFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRECLPLIIFLR 12 1 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ; 184.1 1.35E-05 1258810000 596020 734630 748570 672720 930070 852950 751860 764700 762630 851910 FALSE TRUE 619551.3298 860796.9879 768078.3492 805782.0081 771977.0336 654865.2891 692927.2486 754450.4473 735183.0953 1018825.454 0.608103505 0.844891522 0.753886101 0.790893087 0.757712747 0.642764947 0.680123613 0.74051001 0.721598673 1 19.95847548 -1.917736004 3.156148215 1.148453139 0.730085041 0.607341324 0.065870375 9140850.467 27143872.51 9877059.892 0.015541039 0.012085483 1.917736004 -0.418368099 LREDGIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LREDGIQK 8 1 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 59.368 0.090344 226400000 224040 125570 151220 130930 230400 223160 194650 161590 166430 131120 FALSE TRUE 232885.2722 147135.6707 155160.9174 156827.5632 191236.6903 171334.472 179392.8244 159424.1504 160440.2168 156810.4536 1.485138694 0.938302692 0.9894807 1.00010911 1.219540445 1.092621494 1.144010621 1.016667873 1.023147457 1 17.25866221 4.748166572 24.83260506 1.053855251 1.485138946 0.733189092 0.079179414 656.8132474 1697906.544 0.01977959 0.257845171 55997.23356 -4.748166572 0.431283694 LREDGIQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LREDGIQKR 9 2 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 117.01 0.00068637 304600000 82050 73277 89646 55250 111290 105560 75869 81427 88416 91832 FALSE TRUE 85289.39736 85861.75473 91982.24841 66178.2851 92372.96555 81045.28978 69922.18953 80335.60425 85233.92543 109824.7222 0.776595612 0.781807165 0.837536819 0.602580947 0.841094461 0.737951239 0.636670762 0.731489255 0.776090517 1 16.74484332 -1.849906862 7.65289291 1.018246748 0.743059729 0.518336125 0.073120896 0.021367206 0.000419066 0.066453957 0.016135342 0.014128405 1.849906862 -0.275187019 LREDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LREDLER 7 1 P62269;J3JS69 P62269 RPS18 40S ribosomal protein S18 0 ;;;;;; 187.78 0.00052833 13578820000 3735100 4636810 4259360 4275010 4783910 5228250 4289950 4497250 4207790 4778250 FALSE TRUE 3882564.632 5433146.048 4370362.421 5120594.218 3970742.687 4014068.172 3953692.509 4436971.72 4056352.46 5714456.602 0.679428492 0.950772125 0.764790552 0.896077191 0.69485919 0.702440923 0.691875498 0.776446831 0.709840452 1 22.44618489 5.034934508 16.2062297 0.784128249 0.293872904 0.085877111 0.107706704 11393224.69 146626228.9 0.024540977 159373380.9 108376.347 -5.034934508 -0.490255345 LREDTHHLVNYIPQGSIDSLFEGTWYLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LREDTHHLVNYIPQGSIDSLFEGTWYLVR 29 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ; 226.4 6.74E-35 787000000 194804 258164 263218 188215 367490 359270 203918 295105 300310 493010 FALSE TRUE 202495.0123 302501.6588 270077.6773 225443.3652 305024.1811 275834.9873 187934.3743 291149.6002 289501.9018 589605.8703 0.34344131 0.513057407 0.45806477 0.382362823 0.517335726 0.467829445 0.318745765 0.493803768 0.491009192 1 19.16939136 0.41576723 1.486781068 1.000050738 0.437285388 0.870949513 0.06471887 1.13694735 2.569981584 0.058833768 0.017007868 2.6047571 -0.41576723 -0.56276535 LREEIEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LREEIEELKR 10 2 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;; 191.53 4.40E-07 1843480000 1379499 1009007 1283023 995012 1653368 1509838 1504121 1236653 1379355 890206 FALSE TRUE 1433962.686 1182296.103 1316459.633 1191822.404 1372329.098 1159201.006 1386224.066 1220077.689 1329712.283 1064624.822 1.346918329 1.110528403 1.236547943 1.119476439 1.289026021 1.088835224 1.302077537 1.146016573 1.248996131 1 20.02191368 -1.239556623 4.715322411 0.999947163 1.203551099 0.350049339 0.085389315 4.09E-05 6.59E-06 0.071282942 0.016797196 0.057602771 1.239556623 0.203603936 LREEIVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LREEIVDK 8 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 115.82 0.0021791 341680000 292970 205220 289090 220680 353210 314250 328800 270080 297590 205520 FALSE TRUE 304536.6818 240464.9386 296623.9229 264329.8453 293171.4904 241270.2 303027.7968 266460.0194 286879.794 245787.7091 1.239023233 0.978344033 1.206829764 1.07543964 1.192783364 0.981620281 1.232884256 1.084106363 1.167185272 1 17.90705325 LREETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LREETER 7 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4;K7EMQ3 P50570-2 DNM2 Dynamin-2 0 ;;; 170.3 0.0008938 1394030000 826448 896700 893210 907490 989000 1050800 955980 878900 877593 877920 FALSE TRUE 859076.8052 1050701.25 916487.7864 1086988.813 820890.1333 806767.625 881047.7896 867119.7831 846008.5994 1049931.615 0.818221675 1.000733033 0.872902362 1.035294868 0.781851048 0.768400164 0.839147785 0.825882153 0.805774954 1 20.00186393 3.216884744 24.99816962 0.825227067 0.932506577 0.234270045 0.082500291 281.714696 324892.7894 0.021933699 0.026237744 1647.725048 -3.216884744 0.10727951 LREEWQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LREEWQR 7 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;; 151.04 0.0017405 1392420000 662910 728290 661284 684780 795670 864640 778100 738140 691320 799410 FALSE TRUE 689082.1987 853368.1422 678517.6043 820227.4401 660422.2976 663840.4637 717110.4888 728246.4407 666439.5282 956039.0839 0.720767812 0.892608008 0.709717433 0.857943419 0.690790062 0.694365403 0.750084909 0.761732918 0.697083979 1 19.86671007 -1.104437957 9.350952244 1.000000001 0.755560161 0.555232683 0.066335523 1.23E-09 1.46E-10 0.060895116 0.014353116 0.078625251 1.104437957 -0.24443984 LREFASHLQQLQDALNELTEEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LREFASHLQQLQDALNELTEEHSK 24 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 135.68 1.69E-05 207421000 157283 122096 178717 122808 219650 203712 177620 165691 171980 133583 FALSE TRUE 163492.6543 143065.0382 183374.5118 147099.0559 182313.9715 156402.9753 163697.6803 163470.1832 165790.4734 159756.0312 1.023389559 0.895521985 1.147840932 0.920773098 1.141202432 0.979011397 1.024672928 1.023248899 1.03777286 1 17.28551087 4.269785623 24.99994869 1.031989699 0.959455916 0.15172678 0.070630451 344.0454666 275450.5759 0.015163248 0.041518252 18611.68198 -4.269785623 -0.072533783 LRENELTYYCCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRENELTYYCCK 12 1 E9PNW4;A0A2U3TZL5;P13987;P13987-2;H0YET2 E9PNW4 CD59 CD59 glycoprotein 0 105.65 0.0018306 104110000 64674 66693 58528 59152 92967 86760 77149 70438 69914 78220 FALSE TRUE 67227.37946 78147.00395 60053.28776 70852.08905 77164.50255 66611.30486 71101.85979 69493.89382 67397.8088 93545.71139 0.71865806 0.835388419 0.6419673 0.757406064 0.824885517 0.712072247 0.760076103 0.74288701 0.720479943 1 16.51338389 -1.029747546 4.217590494 1.000019767 0.747514256 0.67504749 0.052863097 5460969.745 2666650.755 961.4021023 0.011533748 0.093379696 1.029747546 -0.252505511 LRENVFQEHQTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LRENVFQEHQTLK 13 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 131.08 8.09E-05 3612540000 2226900 2604520 2885730 2487610 3790370 3814640 3033410 3069480 3150390 3106120 FALSE TRUE 2314819.732 3051826.05 2960934.494 2979651.833 3146084.261 2928747.671 2795643.398 3028338.641 3037008.079 3714704.744 0.623150396 0.821552791 0.797084748 0.802123463 0.846927139 0.788420042 0.752588319 0.815229971 0.817563787 1 21.82481611 -5 0.194480113 1.927154333 0.751942308 0.59946074 0.055340079 97.18697358 0.956317161 34.9589637 0.138460002 1.00E-05 5 -1.175212025 LREQGTES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.001)ES(0.999)R;LREQGT(0.003)ES(0.997)R 98.105 0.0037787 92006000 39061 52762 47481 42328 46113 62575 42045 40291 37933 62748 TRUE FALSE 40603.15844 61823.46307 48718.39387 50700.35206 38274.72873 48042.90458 38749.40304 39750.96505 36567.79874 75042.26922 0.541070504 0.823848528 0.649212695 0.67562392 0.510042262 0.640211245 0.516367688 0.529714326 0.487296015 1 16.19541583 -1.004718884 4.786775491 1.000005049 0.597720487 0.603540447 0.097976079 13119584.86 2753731.509 957.431542 0.023941596 0.098919319 1.004718884 -0.402284561 LREQLQLLEEQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 178.58 8.70E-06 1815691000 1207996 1483095 1390480 1427950 1652617 1778225 1365269 1473571 1469429 1610640 FALSE TRUE 1255688.615 1737805.029 1426717.051 1710394.248 1371705.753 1365259.193 1258255.648 1453820.191 1416544.537 1926214.07 0.651894633 0.902186863 0.740684576 0.887956471 0.71212529 0.708778538 0.653227317 0.754755255 0.735403483 1 20.87733662 -1.146185476 4.34785885 1.000045854 0.751652726 0.465675699 0.080419558 2.076076847 45455837.92 4304.870207 0.018359804 0.071419125 1.146185476 -0.248393129 LREVVETPLLHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LREVVETPLLHPER 14 1 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ;; 154.88 3.60E-06 896770000 258858 286336 269255 227004 363701 345318 242149 281932 262148 356749 FALSE TRUE 269077.9137 335511.9806 276272.0065 271904.7137 301879.2339 265123.1278 223168.7286 278153.1627 252713.3447 426647.1362 0.630680229 0.786392201 0.647542156 0.637305845 0.707561843 0.621410776 0.523075651 0.651951318 0.592324015 1 18.70268384 -1.241600674 7.238727326 1.00000115 0.644706575 0.728642669 0.065129368 1.24E-06 1.30E-07 0.064567727 0.01521871 0.057332295 1.241600674 -0.355294575 LREYEAALNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LREYEAALNSK 11 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 ;;; 191.48 1.65E-06 1435760000 1297550 1129130 1338420 1018890 1726650 1669250 1392540 1290440 1337450 1183180 FALSE TRUE 1348778.276 1323049.294 1373300.325 1220423.401 1433154.65 1281591.985 1283389.076 1273143.763 1289315.436 1415001.468 0.953199206 0.935016199 0.970529258 0.862489141 1.012829091 0.905717778 0.906987806 0.899747309 0.911176041 1 20.43237212 LRGTQEVAPPTPLTPT(ph)SHTANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLT(0.002)PT(0.236)S(0.236)HT(0.236)ANT(0.236)S(0.053)PRPVSGMER 114.61 3.08E-06 255510000 34068 47391 53570 39363 67440 67485 40261 55860 50700 65687 TRUE FALSE 35413.03095 55530.0356 54966.07821 47148.88391 55976.57289 51812.6315 37105.23762 55111.28807 48875.3169 78557.11 0.450793454 0.706874726 0.699695778 0.60018608 0.712558964 0.659553686 0.472334555 0.701544241 0.622162869 1 16.26145424 -0.17893112 1.2829155 1.001699696 0.629745541 0.607528812 0.090306036 18.04606603 18.40704909 0.23720545 0.024386381 0.662321541 0.17893112 -0.371954154 LRGTQEVAPPTPLTPTS(ph)HTANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLTPT(0.15)S(0.615)HT(0.107)ANT(0.107)S(0.019)PRPVSGMER 150.48 1.49E-10 325780000 58511 65839 64694 56133 92990 102590 66685 73650 73654 96884 TRUE FALSE 60821.05946 77146.33609 66379.97879 67235.93986 77183.59302 78765.02727 61458.05545 72662.84222 71003.20693 115866.5648 0.524923299 0.665820517 0.572900205 0.580287678 0.666142067 0.679790821 0.530420968 0.627125196 0.612801519 1 16.82210479 0.120135765 1.901842074 1.000035619 0.607853621 0.836864835 0.052100672 12.06012735 25.27206959 0.047959837 0.013149824 1.318668904 -0.120135765 -0.392181998 LRGTQEVAPPTPLTPTSHT(ph)ANTSPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLT(0.001)PT(0.1)S(0.1)HT(0.361)ANT(0.361)S(0.076)PRPVSGMER;LRGTQEVAPPTPLT(0.001)PT(0.096)S(0.079)HT(0.275)ANT(0.275)S(0.275)PRPVSGMER 108.33 0.00015709 601780000 115300 123921 137073 101417 172509 161441 114945 136146 142989 178835 TRUE FALSE 119852.133 145203.4678 140645.235 121476.9799 143185.9818 123948.7744 105935.3105 134321.1856 137842.8538 213874.2942 0.560385873 0.678919682 0.657607009 0.567983078 0.669486636 0.579540308 0.495315769 0.628038007 0.644504073 1 17.70640357 0.597945026 2.2276754 0.999960448 0.604952593 0.828045443 0.053732304 1.203559671 6.199002219 0.05210038 0.014122295 3.962278755 -0.597945026 -0.395007856 LRGTQEVAPPTPLTPTSHTANT(ph)SPRPVSGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRGTQEVAPPTPLTPTSHTANTSPRPVSGMER 32 2 P48730-2;H7BYT1;P48730 P48730-2 CSNK1D Casein kinase I isoform delta 1 LRGTQEVAPPTPLTPT(0.007)S(0.006)HT(0.102)ANT(0.442)S(0.442)PRPVS(0.001)GMER 112.34 3.11E-06 284990000 67411 111290 90765 68170 105270 108480 81651 103570 92812 133110 TRUE FALSE 70072.43833 130403.1918 93130.41046 81653.82253 87376.243 83287.16403 75250.98126 102181.8136 89471.71425 159190.356 0.440180172 0.81916515 0.585025455 0.512931968 0.548878998 0.523192272 0.472710679 0.641884447 0.562042303 1 17.28039341 -0.274639699 1.144426941 1.004537477 0.570908835 0.627335359 0.099968254 16.77868223 13.85028728 0.460563586 0.028575656 0.531325061 0.274639699 -0.433628642 LRGYDYGPHFQGILEASLEGDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 229.99 1.41E-33 3243338000 858085.6 760774.4 901576.7 728564 1355904.8 1281788.4 880457.3 919614.8 922123.3 1293059.5 FALSE TRUE 891963.4821 891431.4852 925072.5295 872671.7847 1125428.586 984112.4698 811444.7562 907288.8678 888936.2626 1546409.752 0.576796338 0.576452317 0.598206606 0.564321186 0.727768682 0.636385323 0.524728168 0.586706639 0.574838759 1 20.56049121 -1.364833992 3.283949515 1.003311742 0.595989028 0.847661718 0.05134896 12311029.12 17166251.05 391663.1971 0.012854327 0.043168406 1.364833992 -0.407322714 LRIEEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 1049824000 1257094 1408950 1378600 1355315 1708490 1730580 1452690 1433660 1372350 1582400 FALSE TRUE 1306725.042 1650926.202 1414527.449 1623392.262 1418081.48 1328679.022 1338824.362 1414444.133 1322959.392 1892440.983 0.690497116 0.872379227 0.747461855 0.857829796 0.74933987 0.702097996 0.707458977 0.74741783 0.69907564 1 20.85181688 -1.070132192 4.742232613 1.00000954 0.754986575 0.598959047 0.060699714 74189184521 14548272346 8025240.903 0.014093725 0.0850879 1.070132192 -0.245022965 LRLEGPGDEDADGAGS(ph)PSDWASPLEDPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRLEGPGDEDADGAGSPSDWASPLEDPLR 29 1 O60347 O60347 TBC1D12 TBC1 domain family member 12 1 LRLEGPGDEDADGAGS(0.982)PS(0.018)DWASPLEDPLR 162.24 3.68E-12 71384000 30083 40836 37399 36721 46732 55028 39065 45713 42879 44159 TRUE FALSE 31270.70007 47849.26534 38373.64866 43984.3042 38788.51133 42248.58096 36002.98322 45100.29201 41335.79317 52811.11057 0.592123508 0.906045429 0.726620748 0.832860808 0.734476342 0.799994177 0.681731227 0.853992494 0.782710167 1 15.68855386 -4.999989263 0.250167071 2.386562535 0.7534785 0.416826627 0.084216459 168.8658396 1.673909213 119.5331824 0.109049438 1.00E-05 4.999989263 -1.633084034 LRLPLDKEPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRLPLDKEPAR 11 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 122.42 0.00021997 1304300000 753530 790000 711230 796860 1212060 1041580 1056710 857630 844500 968640 FALSE TRUE 783279.9463 925676.3547 729765.2381 954476.5296 1006034.474 799688.8303 973882.309 846134.8726 814106.61 1158426.462 0.676158541 0.799080809 0.629962507 0.823942271 0.868449148 0.690323345 0.840694115 0.730417424 0.702769348 1 20.14373503 -2.234662912 2.306082365 1.851449807 0.755117647 0.496633688 0.075022697 3308225.14 508055.2976 14756818.75 0.017118369 0.005825552 2.234662912 -1.09633216 LRLS(ph)PS(ph)PTSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.994)PS(0.901)PT(0.059)S(0.047)QR;LRLS(0.994)PS(0.715)PT(0.158)S(0.132)QR;LRLS(0.999)PS(0.884)PT(0.062)S(0.055)QR 76.156 0.020555 14152680000 1351090 1509860 1494240 1374950 1469410 1710420 1373590 1404280 1286170 1428950 TRUE FALSE 1404432.076 1769166.71 1533181.122 1646911.006 1219640.213 1313200.877 1265924.427 1385457.924 1239880.993 1708925.394 0.821821761 1.035250993 0.897160946 0.963711472 0.71368839 0.768436634 0.740772202 0.810718788 0.725532547 1 20.70465798 3.247435977 24.99839367 0.781083524 0.934731985 0.343489706 0.091279706 179.0351772 504268.4764 0.023103168 0.030823165 1767.81159 -3.247435977 0.15364846 LRLS(ph)PSPTS(ph)QR ddPTM_MDA-MB-175_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(0.754)PS(0.245)PT(0.002)S(0.999)QR;LRLS(0.765)PS(0.266)PT(0.067)S(0.902)QR 179.33 8.55E-05 19460600000 2301950 2409850 2322080 2206260 2324770 2607140 2266610 2167870 1970960 2455500 TRUE FALSE 2392832.763 2823722.991 2382595.312 2642651.643 1929606.426 2001671.247 2088947.186 2138813.249 1900025.535 2936608.212 0.814828738 0.961559319 0.81134259 0.899899289 0.657086777 0.681626932 0.711346913 0.728327749 0.647013629 1 21.48571937 3.247157535 24.9836033 0.720257847 0.873985148 0.283246666 0.102475472 195.9943194 569577.9475 0.02597756 0.034629466 1766.678544 -3.247157535 0.153727302 LRLS(ph)PSPTSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(0.988)PS(0.012)PTSQR;LRLS(0.975)PS(0.025)PTSQR;LRLS(0.996)PS(0.003)PTSQR;LRLS(0.956)PS(0.044)PTSQR;LRLS(0.883)PS(0.117)PTSQR;LRLS(0.94)PS(0.059)PT(0.001)SQR;LRLS(0.892)PS(0.108)PTSQR;LRLS(0.994)PS(0.006)PTSQR;LRLS(0.998)PS(0.002)PTSQR;LRLS(0.991)PS(0.008)PTSQR;LRLS(0.954)PS(0.046)PTSQR 131.66 0.00012029 83503059000 2250682.4 3397765.5 3114623 2848462.9 3273294.1 3726495 2678504.5 2819116.1 2784494.4 3698894.5 TRUE FALSE 2339541.079 3981305.294 3195792.634 3411880.36 2716900.738 2861073.012 2468556.318 2781330.46 2684280.99 4423622.058 0.52887454 0.900010273 0.722437991 0.771286587 0.614180123 0.646771576 0.558039608 0.628745047 0.606806132 1 22.0767967 -1.096538994 4.354126528 1.000036813 0.666529561 0.485688569 0.103661663 36005020712 61045134.5 14020580.72 0.02533478 0.080068373 1.096538994 -0.333507252 LRLSPS(ph)PT(ph)SQR ddPTM_MDA-MB-175_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(0.35)PS(0.672)PT(0.964)S(0.015)QR;LRLS(0.351)PS(0.685)PT(0.888)S(0.076)QR 135.02 0.0032258 3716090000 833110 901890 823570 824920 876500 950560 804110 821640 774340 890990 TRUE FALSE 866001.8261 1056782.592 845032.9108 988086.7139 727512.8431 729806.8459 741081.757 810627.2597 746471.6547 1065562.431 0.812718054 0.99176037 0.793039324 0.927291245 0.682750087 0.684902944 0.695484127 0.760750601 0.700542392 1 20.02318369 3.240766171 24.99993464 0.736513455 0.882801915 0.259528222 0.102647169 64.72064385 733598.6745 0.026487463 0.034198164 1740.869317 -3.240766171 0.14628846 LRLSPS(ph)PTS(ph)QR ddPTM_MDA-MB-175_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(0.045)PS(0.955)PT(0.409)S(0.591)QR 160.44 0.00032859 5628100000 1485500 1592400 1544500 1529600 1504300 1689900 1489800 1480400 1419400 1539500 TRUE FALSE 1544148.687 1865882.313 1584750.939 1832150.315 1248599.623 1297446.336 1373025.583 1460557.659 1368316.071 1841135.549 0.838693646 1.013441033 0.860746477 0.995119732 0.678168223 0.704698976 0.745749319 0.793291759 0.743191381 1 20.81216442 3.242559271 24.9999812 0.763720513 0.928442159 0.361829847 0.096206997 95.42277705 596588.2809 0.024946691 0.032568909 1748.071819 -3.242559271 0.164721646 LRLSPS(ph)PTSQR ddPTM_MDA-MB-175_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 1 LRLS(0.073)PS(0.925)PT(0.001)S(0.001)QR;LRLS(0.286)PS(0.684)PT(0.003)S(0.026)QR 172.92 3.37E-05 7732800000 1891720 2251910 2155200 2047240 2264520 2415150 2127610 2077830 1889610 2229960 TRUE FALSE 1966406.566 2638658.025 2211366.283 2452177.962 1879597.699 1854268.014 1960842.369 2049980.087 1821603.305 2666877.967 0.737344037 0.98941836 0.829196652 0.919493877 0.704793291 0.695295412 0.735257628 0.768681624 0.683047116 1 21.34672038 3.238420887 24.99999995 0.749141411 0.874640991 0.184245423 0.104326653 4.908039824 878202.8384 0.027011499 0.034294475 1731.493584 -3.238420887 0.125499579 LRLSPSPT(ph)SQR ddPTM_MDA-MB-175_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 1 LRLS(0.009)PS(0.156)PT(0.732)S(0.103)QR 97.957 0.037445 1076200000 584310 657250 640060 609410 723590 734040 622770 651620 640530 703470 TRUE FALSE 607379.01 770127.5748 656740.4894 729949.4791 600594.4303 563570.3345 573955.6601 642886.0997 617477.4504 841301.4778 0.721951674 0.91540024 0.780624433 0.867643168 0.713887288 0.669879169 0.682223525 0.764156627 0.733955029 1 19.68226335 5.063475678 15.5910161 0.777400646 0.180707634 0.023604851 0.101717693 7824356.341 42244065.48 0.023715517 148693712 115737.9213 -5.063475678 -0.596693012 LRLT(ph)PQHDQIQTQPLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRLTPQHDQIQTQPLGK 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 LRLT(1)PQHDQIQTQPLGK 112.58 0.0011891 0 64829 69561 69270 62135 82766 81399 65233 71163 63244 66542 TRUE FALSE 67388.49898 81507.56064 71075.23311 74425.11755 68697.46488 62495.31586 60119.86701 70209.17638 60967.86079 79579.63088 0.846805875 1.024226423 0.893133486 0.935228233 0.86325438 0.785317991 0.75546803 0.882250591 0.766123946 1 16.28011159 3.105537705 3.844150489 0.827724027 0.929727414 0.21095147 0.077956553 0.289452624 8.083804318 0.021665357 0.026332325 1275.080796 -3.105537705 0.102003387 LRNELQTDKPFIPLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRNELQTDKPFIPLVEK 17 2 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 87.486 0.0025484 865290000 1125300 998030 1165300 999990 1441800 1464400 1295800 1177200 1308700 1198400 FALSE TRUE 1169727.713 1169433.889 1195668.675 1197785.037 1196723.351 1124315.293 1194231.81 1161421.56 1261600.143 1433203.535 0.816163011 0.815957999 0.834262996 0.835739661 0.834998883 0.784477058 0.833260441 0.810367496 0.88026586 1 20.45081208 0.902312664 2.944181828 0.999886482 0.820869675 0.927978102 0.015238766 0.090975408 1.729834015 0.014473407 0.003806282 7.985693984 -0.902312664 -0.179016807 LRPENVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LRPENVR 7 1 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ;; 147.04 0.0019868 552980000 1099330 1134180 1059510 961600 1297890 1391610 1246900 1060360 1130240 1156080 FALSE TRUE 1142732.397 1328966.592 1087121.701 1151801.61 1077275.121 1068429.668 1149164.72 1046147.609 1089562.883 1382591.742 0.826514699 0.961214039 0.786292633 0.833074273 0.779170806 0.772773072 0.831167065 0.75665692 0.78805829 1 20.39894378 4.217332796 24.99936117 0.805499663 0.893864421 0.127710742 0.072900269 299.8333768 353105.3997 0.016355119 0.035383148 16494.25849 -4.217332796 0.088364758 LRPKS(ph)PPPK ddPTM_MDA-MB-175_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 72.652 0.024077 4706700000 7117700 3807490 5636740 3712300 7657400 6877000 6588900 5568200 6142700 3597840 TRUE FALSE 7398712.292 4461396.789 5783638.075 4446581.86 6355797.883 5279920.972 6072444.801 5493567.387 5921625.427 4302767.863 1.719523927 1.036866717 1.344166885 1.033423601 1.477141711 1.227098728 1.411288035 1.27675198 1.376236324 1 22.03683358 -1.209282239 4.012329609 0.999792142 1.309305649 0.198902136 0.192534413 0.000317863 6.26E-05 0.165524227 0.038988383 0.061761489 1.209282239 0.309513507 LRPLFEACGEVVQIRPIFSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRPLFEACGEVVQIRPIFSNR 21 2 A0A499FI31;Q15020-4;Q15020 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 226.23 1.41E-25 572520000 117710 136760 148490 113170 157380 169170 140720 122820 125320 138350 FALSE TRUE 122357.2817 160247.4662 152359.7714 135554.6882 130628.6038 129882.8313 129689.9987 121173.7988 120809.7577 165457.0336 0.739510911 0.968514077 0.920841913 0.819274257 0.789501667 0.784994318 0.783828864 0.7323581 0.730157885 1 17.3360971 3.527816891 4.12820136 0.785132433 0.88498305 0.092718242 0.090285657 0.345653686 12.22564067 0.023397964 0.036007186 3371.4513 -3.527816891 0.099850617 LRPLWK ddPTM_MDA-MB-175_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 0.028984 5899300000 3521200 3311800 3505900 3297100 4838400 4407800 4209000 3726400 3738300 3329600 FALSE TRUE 3660219.695 3880575.888 3597266.634 3949256.539 4015970.496 3384155.251 3879087.582 3676453.703 3603759.313 3981971.371 0.919197893 0.974536361 0.903388372 0.991784262 1.008538265 0.849869307 0.974162599 0.92327477 0.905018891 1 21.92505142 LRPLYDIPYMFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRPLYDIPYMFEAR 14 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 217.39 5.27E-12 2140600000 780660 1050740 932710 1001050 1143270 1225520 1035420 1003380 905780 1117470 FALSE TRUE 811481.0596 1231196.421 957017.1888 1199054.702 948937.3738 940911.5529 954261.0748 989931.3323 873181.1547 1336416.851 0.607206546 0.921266759 0.716106796 0.89721609 0.710060916 0.704055439 0.714044479 0.740735446 0.653374846 1 20.34993865 -1.217524988 5.034658333 1.000029172 0.746217036 0.411040215 0.092974901 2.83E-05 4.39E-06 0.083597687 0.019701901 0.060600333 1.217524988 -0.253812136 LRPQTYDLQESNVQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRPQTYDLQESNVQLK 16 1 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3;C9J4G8;C9JV02;A0A0A0MRP8 A0A087X142 8-Sep Septin-8 0 185.67 1.15E-12 0 83134 62736 73584 61810 84883 95984 81940 80116 82202 59417 FALSE TRUE 86416.19451 73510.41998 75501.65949 74035.83352 70454.61798 73693.17065 75517.32869 79042.17606 79243.56608 71058.62354 1.216125365 1.034503855 1.062526344 1.04189794 0.991499898 1.037075685 1.062746855 1.112351635 1.115185774 1 16.11672212 4.743131291 24.75794855 1.05533421 1.21612544 0.618906909 0.038761292 303.7217204 1645101.176 0.010151054 0.08052349 55351.74172 -4.743131291 0.160791229 LRPSGDDVELIGEEEDVSVYDIADHPDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRPSGDDVELIGEEEDVSVYDIADHPDFR 29 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 0 ; 245.69 6.68E-46 141494000 59004.3 68550 69298 67393 74851 86385 63237 67607 64025 78158 FALSE TRUE 61333.83533 80322.92926 71103.96281 80723.13425 62127.85376 66323.39293 58280.3187 66700.83875 61720.75276 93471.56367 0.656176413 0.859330112 0.760701544 0.863611681 0.664671172 0.7095569 0.623508545 0.713594981 0.660315826 1 16.51223991 -1.21529409 3.83720736 1.000265778 0.725320089 0.526838585 0.078594744 9275826.031 5897995.693 19091.15101 0.018768693 0.060912428 1.21529409 -0.274945689 LRPT(ph)RTSSESIYSRPGSSIPGSPGHTIYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRPTRTSSESIYSRPGSSIPGSPGHTIYAK 30 3 O14639-3;F8W8M4;O14639-2;O14639;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 LRPT(0.307)RT(0.307)S(0.307)S(0.07)ES(0.004)IYS(0.004)RPGS(0.001)S(0.001)IPGSPGHTIYAK 178.33 4.32E-18 966510000 44244 302980 263450 195520 304280 385450 209410 299930 276320 391550 TRUE FALSE 45990.78728 355014.4581 270315.7234 234193.2724 252558.5943 295935.0791 192995.897 295909.9289 266375.2972 468266.7258 0.098214938 0.758145814 0.577268699 0.500127939 0.539347727 0.63197973 0.4121495 0.631926021 0.56885378 1 18.836971 -5 0.224167963 3.41731793 0.479826247 0.453152233 0.162236503 139.5575598 1.396903301 152.5108507 0.274742688 1.00E-05 5 -2.937491683 LRPTVTNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRPTVTNDR 9 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 0 ; 96.171 0.0068843 275210000 362020 373470 365380 338335 441270 459960 407770 407680 346565 384090 FALSE TRUE 376312.8291 437610.5673 374902.103 405256.6532 366263.083 353141.2608 375807.9219 402215.7164 334092.1933 459345.0817 0.819237746 0.95268369 0.816166577 0.882248813 0.797359322 0.768792951 0.818138556 0.875628656 0.727322892 1 18.80921886 5.120318182 12.69942803 0.843549182 0.000249996 0.008734518 0.078447441 3470053.926 4801124.332 0.017478179 82015684.52 131922.2901 -5.120318182 -0.843299186 LRQDLQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 ;; 119.75 0.0014909 965820000 480599 597150 583320 614831 650379 835910 609884 584645 560897 775910 FALSE TRUE 499573.4196 699705.8673 598521.7984 736442.7367 539827.8099 641782.5708 562079.6984 576808.7901 540710.4265 927934.7088 0.538371304 0.754046444 0.645004215 0.793636373 0.581751932 0.691624707 0.605731948 0.62160493 0.582703095 1 19.82366377 -1.224519005 4.206601108 1.000191505 0.649224966 0.661777624 0.075880539 0.000128027 2.36E-05 0.068907461 0.016232825 0.059632222 1.224519005 -0.350966539 LRQEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRQEVK 6 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 79.939 0.060035 109190000 114580 112320 126670 118160 136710 150490 133150 127400 117690 84565 FALSE TRUE 119103.7069 131610.0863 129971.1243 141531.6953 113472.083 115540.9782 122713.3551 125692.4114 113454.3599 101133.8927 1.177683403 1.301345007 1.285139144 1.399448707 1.121998571 1.142455562 1.213375179 1.242831736 1.121823327 1 16.62590704 3.218430797 24.9999467 1.163502298 1.291238111 0.44360956 0.080099765 253.3989088 314704.5079 0.023133505 0.027681305 1653.601271 -3.218430797 0.127735813 LRQPFFQK ddPTM_MDA-MB-175_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 ; 166.61 0.00028951 3330400000 1955220 1806260 1533870 1232270 3852100 2560460 1940820 1749200 1722830 3603500 FALSE TRUE 2032413.595 2116471.104 1573843.912 1476009.328 3197321.418 1965831.969 1788693.457 1725754.835 1660825.685 4309536.832 0.471608359 0.491113358 0.365200246 0.342498367 0.741917645 0.456158526 0.415054686 0.400450188 0.385383801 1 22.03910139 -0.964054186 4.46079485 1.000012045 0.450798644 0.703233726 0.106763784 48430885.5 93540483.63 9391.30667 0.026042933 0.108629008 0.964054186 -0.549213401 LRRES(ph)PESEGPIYEGLIL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LRRESPESEGPIYEGLIL 18 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 LRRES(0.879)PES(0.121)EGPIYEGLIL;LRRES(0.999)PES(0.001)EGPIYEGLIL;LRRES(0.999)PES(0.001)EGPIYEGLIL 143.93 8.03E-08 106880000 119828 114898 118988 125080 147400 150716 131242 131139 131161 143185 TRUE FALSE 124558.902 134630.8377 122088.925 149820.4507 122345.0006 115714.4931 120954.9091 129381.2962 126440.5412 171239.3593 0.727396449 0.786214327 0.71297233 0.874918309 0.714467755 0.675747057 0.706349928 0.755558166 0.738384807 1 17.38565482 -1.20878955 5.337136764 1.000015318 0.744132431 0.684536005 0.052225022 9.46E-06 1.40E-06 0.050273283 0.011848817 0.061831595 1.20878955 -0.255882888 LRRPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.906)PPEPWDEEDGAS(0.069)CS(0.015)T(0.009)FFGSEER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER;LRRPS(1)PPEPWDEEDGASCSTFFGSEER 277.5 3.16E-61 1945560000 322279 357478 342179 307372 476162 455363 356514 416104 393118 543663 TRUE FALSE 335002.8238 418872.0657 351096.4658 368169.2642 395224.1533 349611.8443 328569.5011 410526.8065 378969.76 650183.3558 0.515243617 0.644236833 0.539996084 0.56625452 0.607865689 0.537712695 0.505348988 0.631401593 0.582865982 1 19.3104871 -0.130585872 0.909016148 1.008594375 0.566871326 0.896129542 0.043995234 2.544366326 1.749375277 0.118523809 0.013207385 0.740310873 0.130585872 -0.441723048 LRRY(ph)CVFS(ph)HEELICK ddPTM_MDA-MB-175_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 92.264 0.012554 594900000 27061 707270 640920 825280 547050 933990 561820 698630 638190 922650 TRUE FALSE 28129.38918 828738.1207 657622.9017 988517.9208 454062.6364 717084.9773 517783.0804 689266.0076 615221.6666 1103425.602 0.025492783 0.751059355 0.595983001 0.895862774 0.41150272 0.649871614 0.469250559 0.624660155 0.557556092 1 20.07355793 -5 0.337530831 5.562081555 0.553979243 0.274673177 0.218450125 509.7644889 4.322439848 1674.480192 0.165124366 1.00E-05 5 -5.008102312 LRS(ph)DGAAIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRSDGAAIPR 10 1 O43295-2;O43295 O43295-2 SRGAP3 SLIT-ROBO Rho GTPase-activating protein 3 1 LRS(1)DGAAIPR 124.07 0.00026972 214080000 41916 41478 46365 35687 690710 56267 443950 58342 41813 35849 TRUE FALSE 43570.87605 48601.52385 47573.30999 42745.78208 573303.3609 43199.84198 409152.039 57560.02092 40308.1583 42872.92518 1.016279525 1.133618097 1.109635272 0.99703442 13.37215407 1.007625251 9.543366524 1.342572747 0.940177469 1 15.38777923 LRS(ph)PFLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;LRS(1)PFLQK 116.74 0.0013408 7885660000 5763440 4200550 5030440 4181990 6129060 6381640 5739290 5589390 5575230 4563640 TRUE FALSE 5990985.062 4921961.787 5161537.399 5009175.14 5087244.57 4899600.825 5289429.453 5514473.369 5374578.561 5457797.882 1.097692731 0.901821924 0.945717945 0.917801511 0.93210571 0.897724857 0.969150849 1.010384314 0.984752217 1 22.37988754 1.998542325 24.94606358 0.997091394 0.943454867 0.141819797 0.05361277 89.97537171 1539816.335 0.019554055 0.014245578 99.66492053 -1.998542325 -0.053636527 LRS(ph)PPEALVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 162.26 3.83E-05 18940550000 1595175 1749540 1809740 1696790 2026170 2271180 1943210 1905280 1836500 1916250 TRUE FALSE 1658153.741 2050009.885 1856903.311 2032409.998 1681762.347 1743732.865 1790896.123 1879742.838 1770404.724 2291702.499 0.723546683 0.894535781 0.810272412 0.88685595 0.733848459 0.760889717 0.781469725 0.820238595 0.772528164 1 21.12798834 -1.478062014 5.623145845 1.000230333 0.801715552 0.549668235 0.054704356 0.000151874 1.41E-05 0.050925242 0.011989375 0.033261206 1.478062014 -0.198514781 LRS(ph)PRGS(ph)PDGSLQTGKPSAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRSPRGSPDGSLQTGKPSAPK 21 3 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 2 LRS(0.999)PRGS(0.862)PDGS(0.118)LQT(0.02)GKPS(0.001)APK;LRS(1)PRGS(0.672)PDGS(0.326)LQT(0.001)GKPSAPK 138.11 3.12E-06 412710000 356700 225271 309605 171492 426890 369900 299399 284104 358890 239798 TRUE FALSE 370782.7914 263959.5419 317673.5606 205412.6057 354327.3903 283996.3309 275931.324 280296.0506 345973.619 286781.8269 1.292908953 0.920419347 1.107718589 0.716267861 1.235529441 0.990287055 0.962164608 0.977384284 1.20640008 1 18.12959408 4.750045665 24.17119663 1.008383071 1.292909224 0.262976939 0.140441266 1404.856064 2956541.65 0.030906536 0.475813796 56240.04572 -4.750045665 0.284526153 LRS(ph)PRGSPDGS(ph)LQTGKPSAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRSPRGSPDGSLQTGKPSAPK 21 3 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 2 LRS(0.995)PRGS(0.176)PDGS(0.823)LQT(0.006)GKPSAPK;LRS(0.996)PRGS(0.026)PDGS(0.88)LQT(0.098)GKPSAPK 136.53 6.88E-06 516430000 376073 257118 344872 192096 474070 408858 307400 317766 377068 257121 TRUE FALSE 390920.6524 301276.0164 353859.6476 230092.0155 393487.7507 313906.9258 283305.1848 313506.8665 363497.3963 307498.9371 1.271291069 0.97976279 1.15076706 0.748269303 1.279639385 1.02083906 0.921320859 1.01953805 1.18210944 1 18.2302219 4.746447316 23.55917159 1.030502324 1.27129134 0.20673081 0.139575129 651.135881 1944968.469 0.030993026 0.324021254 55775.9936 -4.746447316 0.240789016 LRS(ph)PS(ph)NDSAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 LRS(1)PS(0.999)NDS(0.001)AHR;LRS(1)PS(1)NDSAHR 93.424 0.005269 496020000 310450 479330 402910 381100 417440 576420 409910 446550 398620 519920 TRUE FALSE 322706.8057 561651.1988 413410.1656 456480.4425 346483.6979 442555.1907 377780.1831 440564.7277 384273.7441 621788.3695 0.518997816 0.903283539 0.664872786 0.734141172 0.557237341 0.711745688 0.607570359 0.708544497 0.618013721 1 19.24606411 -1.658601652 3.910716117 1.014988557 0.675756057 0.48453598 0.102112515 0.012465439 0.00108821 0.092358249 0.021187984 0.021948172 1.658601652 -0.3392325 LRS(ph)PSNDSAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LRSPSNDSAHR 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 LRS(0.984)PS(0.016)NDSAHR;LRS(0.996)PS(0.004)NDSAHR;LRS(0.888)PS(0.112)NDSAHR;LRS(1)PSNDSAHR;LRS(0.997)PS(0.003)NDSAHR;LRS(0.999)PS(0.001)NDSAHR 151.07 2.03E-05 2371320000 779727.1 1565026 1314292 1309073 1264621 1631038 1138459 1296452 1163697 1764890 TRUE FALSE 810511.328 1833807.041 1348543.529 1568003.732 1049661.174 1252254.143 1049223.609 1279075.182 1121815.772 2110686.405 0.384003671 0.868820227 0.638912311 0.742888062 0.497307971 0.593292372 0.497100662 0.605999631 0.531493343 1 21.00928082 -1.440369025 4.923157918 1.000698954 0.602259049 0.467879018 0.129222849 0.000937916 0.000106616 0.118373886 0.027853816 0.036276967 1.440369025 -0.398439905 LRS(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 LRSYEDMIGEEVPSDQYYWAPLAQHER 27 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 LRS(0.987)Y(0.013)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.545)Y(0.455)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.998)Y(0.002)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.815)Y(0.179)EDMIGEEVPS(0.005)DQYYWAPLAQHER;LRS(0.909)Y(0.091)EDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.983)Y(0.015)EDMIGEEVPS(0.001)DQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(0.903)Y(0.097)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.556)Y(0.444)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.641)Y(0.359)EDMIGEEVPSDQYYWAPLAQHER;LRS(0.948)Y(0.043)EDMIGEEVPS(0.009)DQYYWAPLAQHER;LRS(0.997)YEDMIGEEVPS(0.003)DQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER;LRS(1)YEDMIGEEVPSDQYYWAPLAQHER 295.35 7.59E-71 7051188000 1260345.1 1383173.1 1338599.9 1227013.2 1481969.9 1638594.9 1377828.9 1327182.9 1381421.3 1206068.9 TRUE FALSE 1310104.498 1620722.32 1373484.913 1469712.749 1230065.186 1258056.068 1269831.071 1309394.184 1331704.217 1442375.009 0.908296725 1.123648365 0.952238429 1.018953281 0.852805392 0.872211498 0.880375119 0.907804264 0.923271832 1 20.46001488 3.249612637 24.99740268 0.898713143 1.006092681 0.342182505 0.063671046 205.2877035 464316.0392 0.016429615 0.022036358 1776.694004 -3.249612637 0.107379538 LRTACER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 103.8 0.007564 198496000 144827 110811 71964 84850 330760 136792 160076 131966 70768 300060 FALSE TRUE 150544.8818 129841.9273 73839.44096 101633.0767 274537.5333 105024.1311 147528.8248 130197.2116 68221.0735 358851.012 0.419519179 0.361826839 0.205766289 0.28321803 0.765046006 0.292667786 0.411114418 0.3628169 0.190109743 1 18.45302546 -1.074185354 4.555287696 1.000034536 0.3696804 0.608168914 0.152690396 5.954933169 182383313.6 14857.04525 0.035155516 0.084297491 1.074185354 -0.630354136 LRVEFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LRVEFPR 7 1 J3KTL2;Q07955;Q07955-3;Q07955-2;Q13242;S4R3G0 J3KTL2;Q13242 SRSF1;SRSF9 Serine/arginine-rich splicing factor 1;Serine/arginine-rich splicing factor 9 0 ; 155.75 0.0014498 2701300000 397180 536170 359880 372140 991250 689970 521450 390080 388031 1356640 FALSE TRUE 412860.9731 628253.0267 369258.7684 445748.1813 822757.6791 529734.9241 480577.3864 384851.6156 374065.8401 1622447.634 0.254467981 0.387225457 0.227593644 0.274738101 0.507108927 0.326503557 0.296205176 0.237204337 0.230556495 1 20.62974048 -1.914991842 2.758143552 1.404971444 0.305147203 0.865294245 0.082309836 44087034.13 22446464.1 115165507.2 0.020410321 0.012162088 1.914991842 -1.099824242 LRVQS(ph)PEPPAPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRVQSPEPPAPER 13 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LRVQS(1)PEPPAPER 97.073 0.0023895 308820000 94862 128220 111020 124320 139280 164720 138150 137250 126540 144980 TRUE FALSE 98607.22501 150240.7876 113913.2724 148910.1249 115605.2353 126466.2764 127321.442 135410.3882 121985.8501 173386.0552 0.568714854 0.866510213 0.656992122 0.858835647 0.666750479 0.729391278 0.734323426 0.780976233 0.703550525 1 17.40362835 -4.999999869 0.404159302 5.366021943 0.73183135 0.467919617 0.086220867 631.8749375 4.349812446 2437.824238 0.046670419 1.00E-05 4.999999869 -4.634190593 LRYDSYS(ph)SYCNAVAEAEIEAEEGGVEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LRYDSYSSYCNAVAEAEIEAEEGGVEMK 28 1 Q08357 Q08357 SLC20A2 Sodium-dependent phosphate transporter 2 1 LRY(0.133)DS(0.184)Y(0.117)S(0.225)S(0.225)Y(0.117)CNAVAEAEIEAEEGGVEMK 83.198 0.0025305 27689000 13713 13668 14817 17371 25185 22356 21522 17890 17994 21568 TRUE FALSE 14254.39983 16015.37268 15203.14319 20806.93195 20904.0627 17164.15781 19835.0494 17650.21381 17346.39945 25793.83666 0.552628134 0.620899205 0.58940992 0.806662934 0.810428591 0.6654364 0.768984067 0.684280282 0.672501718 1 14.65473876 -5 0.1426513 2.010705233 0.587354158 0.600478782 0.079400966 105.0956029 0.911645281 30.60119725 0.493809729 1.00E-05 5 -1.423351075 LS(ph)ASSSISSADLFEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LS(1)ASSSISSADLFEEPR;LS(1)ASSSISSADLFEEPR 144.97 6.34E-07 23782000 31193 33590 36166 36687 45743 48951 41467 42680 36962 34695 TRUE FALSE 32424.52373 39358.82121 37108.51567 43943.5791 37967.6212 37582.87211 38216.70819 42107.94441 35631.74484 41492.82097 0.781449006 0.948569422 0.89433581 1.05906463 0.91504073 0.905768064 0.921043865 1.014824816 0.858744814 1 15.34057412 4.980793942 2.060324061 0.950425167 0.62538302 0.41039925 0.058682097 1.76327786 4.418938553 0.014213489 1.353201108 95674.00224 -4.980793942 -0.325042147 LS(ph)DETLLEISKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSDETLLEISKR 12 1 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 1 LS(0.986)DET(0.014)LLEISKR;LS(0.986)DET(0.014)LLEISKR 58.487 0.064789 273950000 112679 274210 389650 339220 444490 416980 580470 415930 425160 210580 TRUE FALSE 117127.6539 321303.4344 399804.5991 406316.7035 368935.7486 320142.7144 534971.2446 410355.1387 409858.5747 251839.1192 0.465089198 1.275828138 1.587539697 1.61339789 1.464966006 1.271219163 2.124257924 1.629433664 1.627461913 1 17.94214287 4.743767065 2.06543988 1.587528445 0.133960706 0.576191845 0.274626313 0.470455807 2.174466136 0.0674355 1.288469247 55432.83177 -4.743767065 -1.45356774 LS(ph)EEISAPVSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSEEISAPVSER 12 0 A0A2R8YCV2;Q8NCS4 A0A2R8YCV2 ZMYM6NB Uncharacterized protein ZMYM6NB 1 LS(0.499)EEIS(0.499)APVS(0.002)ER 53.567 0.090593 1947200000 272730 188000 271170 177460 5272200 345630 3730700 379040 261700 180770 TRUE FALSE 283497.591 220287.5376 278236.913 212561.0583 4376033.327 265362.6706 3438277.986 373959.5888 252281.4681 216188.4204 1.311344939 1.018960854 1.287011175 0.983221293 20.24175633 1.227460148 15.90408024 1.729785471 1.166951808 1 17.72192973 LS(ph)FSDTYQDYEEYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 1 LS(0.966)FS(0.034)DTYQDYEEYWR 93.909 0.0049039 24390000 32446 22141 28546 35244 35791 39566 45043 33634 38302 21199 TRUE FALSE 33726.99313 25943.54452 29289.93221 42215.15801 29707.2586 30377.39613 41512.41196 33183.19124 36923.5185 25352.53817 1.33032018 1.023311526 1.155305714 1.665125508 1.171766645 1.198199404 1.637406546 1.308870576 1.456403231 1 14.62984257 3.907740676 24.98554975 1.365429058 1.154805852 0.132060561 0.205516542 91.21202807 24696.68418 0.049604483 0.089425791 8086.129201 -3.907740676 -0.210623206 LS(ph)GPAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGPAELR 8 0 Q96PC5;Q96PC5-11;Q96PC5-10;Q96PC5-9;Q96PC5-13;Q96PC5-6;G3V599;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5-8;Q96PC5-5;Q96RT6 Q96PC5 MIA2;CTAGE1 Melanoma inhibitory activity protein 2;cTAGE family member 2 1 LS(1)GPAELR 64.692 0.069444 117170000 458210 382310 434500 425250 517220 609870 530640 498290 513070 410680 TRUE FALSE 476300.4846 447968.7685 445823.4269 509363.1808 429303.1291 468236.9352 489047.0502 491611.2376 494604.7109 491144.8831 0.969775928 0.91209088 0.907722838 1.03709353 0.874086535 0.953358065 0.995728688 1.000949525 1.007044414 1 18.90578914 2.270192163 4.170483133 1.001511318 0.939788404 0.335595856 0.040693759 0.239332947 9.165150087 0.014675818 0.01155424 186.291124 -2.270192163 -0.061722914 LS(ph)GSRQDLIPSYSLGSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.5)GS(0.5)RQDLIPSYSLGSNK 73.389 0.012286 2169600000 50426 62186 49597 54845 50076 71157 41553 45978 45857 46079 TRUE FALSE 52416.85742 72865.96176 50889.53856 65693.1773 41564.09941 54631.86514 38295.96728 45361.74011 44206.61553 55107.29781 0.951178147 1.322256119 0.923462782 1.192095782 0.754239476 0.991372601 0.694934588 0.823153047 0.802191675 1 15.74995577 3.236742355 24.99999993 0.831333227 1.10090697 0.444253904 0.138109147 39.09552563 537542.423 0.036177754 0.045400185 1724.814342 -3.236742355 0.269573743 LS(ph)LQGHPTDLQTSNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLQGHPTDLQTSNVK 16 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 LS(1)LQGHPTDLQTSNVK;LS(1)LQGHPTDLQTSNVK 200.14 2.34E-11 971070000 714740 606980 845280 710390 892220 975240 895440 751530 815410 486050 TRUE FALSE 742958.4871 711224.0934 867308.6912 850903.0217 740560.7631 748755.2899 825253.073 741456.9696 786063.5534 581282.1915 1.278137362 1.22354358 1.49206135 1.463838105 1.274012474 1.288109804 1.419711605 1.27555425 1.352292509 1 19.14887918 -1.371423578 0.531343678 0.839222037 1.347058273 0.58604054 0.085859452 26.89174283 3.541509129 6.125545985 0.039375002 0.042518352 1.371423578 0.507836236 LS(ph)LQGHPTDLQTSNVKNEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLQGHPTDLQTSNVKNEEK 20 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 LS(1)LQGHPTDLQTSNVKNEEK;LS(1)LQGHPTDLQTSNVKNEEK 228.63 1.76E-25 581580000 724670 433780 604800 349540 937950 779830 624460 542040 721610 393940 TRUE FALSE 753280.5312 508278.3407 620561.5848 418677.9687 778517.594 598726.3009 575513.1935 534774.8404 695639.3971 471125.0006 1.598897384 1.078860897 1.317190945 0.888677035 1.652465042 1.270843832 1.221572179 1.135101809 1.476549528 1 18.84575037 -1.720362232 2.506853888 0.945889428 1.272184069 0.127821823 0.22381968 24726854.54 18750796.39 8385283.336 0.050128428 0.019038721 1.720362232 0.326294642 LS(ph)LTSDPEEGDPLALGPESPGEPQPPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLTSDPEEGDPLALGPESPGEPQPPQLK 29 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 LS(0.333)LT(0.333)S(0.333)DPEEGDPLALGPESPGEPQPPQLK;LS(0.333)LT(0.333)S(0.333)DPEEGDPLALGPESPGEPQPPQLK 67.33 0.0059691 60931000 40359 33097 36177 30560 44603 48374 41213 36378 39729 27379 TRUE FALSE 41952.40448 38781.15229 37119.80234 36604.67679 37021.39799 37139.87162 37982.61737 35890.41241 38299.16105 32743.39085 1.281248014 1.18439634 1.133657858 1.117925659 1.130652539 1.134270784 1.160008673 1.096111657 1.16967608 1 14.99891611 8 0.01746225 1.53E-11 2.558042415 0.614243025 0.041835432 2913.843239 3.924461359 221.3680803 371.4473239 100000000 -8 2.558042415 LS(ph)PANQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPANQR 7 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 LS(1)PANQR;LS(1)PANQR 109.66 0.0073191 983340000 1054450 932820 1009360 963960 1066680 1393360 1267870 1137030 1031280 764550 TRUE FALSE 1096080.5 1093024.579 1035664.751 1154628.411 885366.1146 1069773.257 1168491.036 1121789.973 994164.4342 914348.9343 1.198755157 1.195412974 1.13268 1.262787507 0.968302233 1.169983599 1.277948705 1.226872948 1.087292167 1 19.80238531 4.331045844 9.17734456 1.158782531 1.197670705 0.024879911 0.098523896 1.451603008 130.1789629 0.023880048 0.065613577 21431.16815 -4.331045844 0.038888173 LS(ph)PDFAEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPDFAEELR 10 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 LS(1)PDFAEELR 180.2 2.12E-06 12265000 29281 25897 25630 30671 31355 36971 38863 29528 29993 19505 TRUE FALSE 30437.03649 30344.6083 26297.93886 36737.63226 26025.2883 28385.04555 35816.81651 29132.22546 28913.55779 23326.6313 1.304819204 1.300856858 1.127378339 1.574922318 1.115689958 1.216851468 1.535447448 1.248882665 1.2395085 1 14.50969036 0.789905341 2.155364483 1.000563971 1.305807529 0.289194905 0.142761843 0.988003996 7.639068299 0.129003914 0.035285264 6.164606236 -0.789905341 0.305243559 LS(ph)PENNQVLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSPENNQVLTK 11 0 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(1)PENNQVLTK;LS(0.999)PENNQVLT(0.001)K;LS(1)PENNQVLTK 270.16 1.91E-22 1110740000 1682550 1004820 1328610 1188680 1536820 1746800 2078940 1439230 1431750 678593 TRUE FALSE 1748978.373 1177390.019 1363234.668 1423797.356 1275591.885 1341132.173 1915987.251 1419939.476 1380221.597 811550.3059 2.155107774 1.450791171 1.679790714 1.754416634 1.571796444 1.65255581 2.3608977 1.749662918 1.70072217 1 19.630321 0.722940266 3.053842477 1.000089072 1.791748891 0.462669931 0.256031883 2.091050501 21.96800709 0.243861773 0.063667027 5.283725733 -0.722940266 0.791659819 LS(ph)PEVAPPAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 LS(1)PEVAPPAHR 113.99 0.0008489 154180000 73067 71733 78526 70086 94587 101190 100050 77176 72985 53866 TRUE FALSE 75951.74158 84052.58474 80572.45207 83948.80161 78509.13553 77690.15605 92207.81957 76141.58195 70358.28411 64420.01137 1.179008509 1.304758924 1.250736384 1.303147886 1.21870726 1.205994137 1.431353668 1.181955426 1.09218056 1 15.97522129 1.225508254 2.55472017 1.012743824 1.269172083 0.632058019 0.068539139 0.158716111 1.758886145 0.059749678 0.016988112 16.80769869 -1.225508254 0.25642826 LS(ph)PGSYPTVIQQQNATSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(1)PGSYPTVIQQQNATSQR;LS(1)PGSYPTVIQQQNATSQR;LS(1)PGSYPTVIQQQNATSQR 290.88 1.62E-49 624786000 136192 121416 142155 129134 153140 181124 150842 150724 145507 134789 TRUE FALSE 141568.9653 142268.2535 145859.6761 154676.3198 127109.3175 139060.696 139018.6099 148703.7913 140270.2315 161198.3239 0.87822852 0.882566581 0.904846109 0.959540497 0.788527538 0.862668374 0.862407292 0.922489687 0.870171774 1 17.29847722 -1.547461107 6.248128416 1.000173868 0.883120094 0.414882762 0.042248077 0.000102365 7.41E-06 0.040922948 0.009631364 0.028349075 1.547461107 -0.117053774 LS(ph)PHKVQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 LSPHKVQGR 9 1 Q9GZP8-2;Q9GZP8 Q9GZP8-2 IMUP Immortalization up-regulated protein 1 LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR;LS(1)PHKVQGR 108.35 0.0015858 37099850000 10623280 6446510 8403540 6828390 10299410 10790270 11530730 8604830 8996910 4598900 TRUE FALSE 11042695.3 7553647.946 8622543.156 8179025.161 8548719.967 8284393.321 10626921.25 8489496.329 8673112.967 5499966.404 2.007775046 1.373398925 1.567744696 1.487104568 1.554322216 1.506262532 1.932179303 1.543554216 1.576939263 1 22.39099138 0.506847778 2.203059185 1.00003914 1.612009153 0.493462646 0.187767697 4.569006843 19.39573123 0.16949233 0.045973209 3.212534332 -0.506847778 0.611970013 LS(ph)PIPEEVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSPIPEEVPK 10 0 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK;LS(1)PIPEEVPK 194.96 4.26E-07 2920439000 7783530 3837530 5539450 4895350 7449100 7800870 8630090 5702140 6080140 2612300 TRUE FALSE 8090829.775 4496595.926 5683812.618 5863635.619 6182904.643 5989236.166 7953640.995 5625712.14 5861316.949 3124130.169 2.589786384 1.439311322 1.819326439 1.876885821 1.979080354 1.917089187 2.545873752 1.80072911 1.87614364 1 21.57502314 4.763966338 23.94854966 1.872833371 2.589787992 0.264706904 0.377372401 6348.464499 5984168.428 0.084799874 5.758917356 58071.94043 -4.763966338 0.71695462 LS(ph)PISHGNTIALFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPISHGNTIALFFR 15 0 Q9BQ70 Q9BQ70 TCF25 Transcription factor 25 1 LS(0.999)PIS(0.001)HGNTIALFFR;LS(0.986)PIS(0.014)HGNTIALFFR 202.35 1.18E-11 328480000 292673 257962 306127 351748 362120 383930 413730 323630 327330 246951 TRUE FALSE 304227.956 302264.9668 314104.9211 421322.7045 300566.9717 294768.076 381300.7615 319292.2692 315549.4572 295336.3203 1.030106814 1.023460191 1.063549924 1.426586151 1.01771083 0.998075942 1.291073042 1.081114131 1.068441081 1 18.17199926 1.039020764 2.491780622 1.002749503 1.121822044 0.07213304 0.130574689 0.739172658 9.857494925 0.123530585 0.03357585 10.94008671 -1.039020764 0.119072541 LS(ph)PLPVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSPLPVVSR 9 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR;LS(1)PLPVVSR 152.54 8.42E-05 237794000 341502 276597 298610 389650 314650 407626 496323 337562 295475 200931 TRUE FALSE 354984.7627 324100.3831 306392.0219 466721.607 261165.9054 312961.0391 457419.9064 333037.5335 284840.9125 240299.5824 1.477259174 1.348734691 1.275041841 1.942248931 1.08683462 1.302378623 1.903540164 1.385926393 1.185357501 1 17.87447462 1.126416177 3.022798455 1.013932007 1.472966862 0.272826114 0.253655606 0.303217027 5.111609879 0.233064932 0.062616352 13.37876967 -1.126416177 0.459034855 LS(ph)PSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSPSFR 6 0 B4DF95;Q15735 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 LS(0.848)PS(0.152)FR;LS(0.993)PS(0.007)FR;LS(0.979)PS(0.021)FR 155.88 0.010303 617030000 781870 813360 865180 794440 1062850 1194770 990130 943450 958380 847700 TRUE FALSE 812738.8313 953048.2529 887727.3016 951577.8608 882187.1366 917302.7744 912521.0234 930804.5959 923888.091 1013790.585 0.801683152 0.940083946 0.875651555 0.938633555 0.870186752 0.904824712 0.900108008 0.918142869 0.911320449 1 19.95132824 -5 0.140041899 1.351669375 0.861329892 0.481757765 0.035530877 116.7900793 1.002510137 11.45241466 0.19856095 1.00E-05 5 -0.490339483 LS(ph)PSTSGPHSHDYLPQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPSTSGPHSHDYLPQER 18 0 Q5JR04;Q9HCE1 Q5JR04 MOV10 Putative helicase MOV-10 1 LS(0.996)PS(0.004)TSGPHSHDYLPQER 91.166 0.004297 303170000 27985 52612 51433 55708 60310 70342 59914 62749 55861 44554 TRUE FALSE 29089.86941 61647.70174 52773.38623 66726.87613 50058.52774 54006.13654 55217.78412 61907.95229 53850.57352 53283.50326 0.545945136 1.156975386 0.990426361 1.252298968 0.93947516 1.013562045 1.036301683 1.161859647 1.010642511 1 15.70140132 4.744480292 24.98054497 1.068808516 0.545944905 0.737750449 0.092302934 308.8561383 1303310.384 0.02083495 0.189175575 55523.94205 -4.744480292 -0.522863611 LS(ph)PSWNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPSWNPK 8 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 LS(0.965)PS(0.035)WNPK;LS(0.997)PS(0.003)WNPK 121.6 0.001496 471400000 499610 339146 439090 379070 484320 534200 536710 474700 473000 275322 TRUE FALSE 519334.9886 397391.6873 450533.0461 454048.9146 401995.4594 410140.1459 494641.2678 468337.423 455976.8224 329266.0745 1.57725022 1.206901403 1.368294765 1.37897266 1.220883323 1.245619205 1.50225397 1.422367681 1.384827827 1 18.32889435 4.758066562 24.26494658 1.329806845 1.577250561 0.245584357 0.137135564 4579.226613 5696315.994 0.031595959 1.148722873 57288.38274 -4.758066562 0.247443716 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58;Q9UK58-6;Q9UK58-5;Q9UK58-4 Q9UK58 CCNL1 Cyclin-L1 1 LS(0.996)PT(0.004)PSMQDGLDLPSETDLR;LS(0.859)PT(0.141)PSMQDGLDLPSETDLR 244.52 7.03E-30 170997000 154322 123319 152612 165762 180686 211775 233008 156334 171135 91157 TRUE FALSE 160414.7517 144498.079 156589.1941 198549.2288 149973.0583 162593.4657 214744.2241 154238.5984 164975.8848 109017.4688 1.471459147 1.325458025 1.436367912 1.821260675 1.375679144 1.491444146 1.969814805 1.41480627 1.513297699 1 16.7341998 0.499540275 1.867621421 1.000153894 1.544175189 0.411782408 0.192346622 3.828696524 13.13995489 0.182845895 0.050854463 3.15893198 -0.499540275 0.544021295 LS(ph)PTSLVHPVMSTLPELSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPTSLVHPVMSTLPELSCK 20 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 LS(0.333)PT(0.333)S(0.333)LVHPVMSTLPELSCK;LS(0.508)PT(0.246)S(0.246)LVHPVMSTLPELSCK 159.46 1.64E-11 922320000 1248890 1197210 1596060 1614070 1887150 1952100 2371350 1803360 1863330 1046570 TRUE FALSE 1298197.142 1402821.504 1637654.635 1933328.228 1566372.917 1498754.359 2185477.391 1779188.909 1796269.117 1251625.354 1.037209048 1.120799847 1.308422388 1.544654095 1.251471067 1.197446468 1.746111473 1.421502771 1.435149194 1 20.25537136 4.215824504 2.877419018 1.40191949 1.055692918 0.256862095 0.191915153 0.300227171 4.965059837 0.047854517 0.144775036 16437.07375 -4.215824504 -0.346226572 LS(ph)S(ph)Y(ph)T(ph)LRILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSYTLRILR 10 1 Q96DU3-2;Q96DU3 Q96DU3-2 SLAMF6 SLAM family member 6 4 LS(1)S(1)Y(1)T(1)LRILR 47.189 0.074578 204660000 7142.2 18459 9823.9 19610 16652 24391 16963 16105 15452 17899 TRUE FALSE 7424.179571 21629.18966 10079.9189 23488.79947 13821.49899 18726.5599 15633.39574 15889.13882 14895.88554 21405.96635 0.346827583 1.010428088 0.470892962 1.097301523 0.645684421 0.874828989 0.730328894 0.742276175 0.695875407 1 14.38572535 -4.999999996 0.030055879 2.049801275 2.08E-07 0.13125996 0.212526591 3548.755946 8.030645576 427.313156 172.9693111 1.00E-05 4.999999996 -2.049801067 LS(ph)SGFDDIDLPSAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.985)S(0.015)GFDDIDLPSAVK;LS(0.5)S(0.5)GFDDIDLPSAVK;LS(0.903)S(0.097)GFDDIDLPSAVK;LS(0.839)S(0.161)GFDDIDLPSAVK 363.68 3.71E-84 296395000 351668 219519 303843 269746 446517 412807 507124 352772 398640 218002 TRUE FALSE 365552.1242 257219.6806 311761.3982 323100.9537 370618.1998 316938.8304 467374.2958 348043.6684 384293.0243 260715.318 1.402112185 0.986592129 1.195792409 1.239286422 1.421543631 1.215650975 1.792661434 1.33495673 1.473994805 1 17.99211582 3.339517807 2.129833868 1.412150054 1.173261383 0.111557521 0.212633954 0.494991745 4.585147575 0.061371532 0.090202517 2185.33392 -3.339517807 -0.23888867 LS(ph)SLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSLAR 6 0 A6NI03;A6NGJ6 A6NI03 TRIM64B;TRIM64 Putative tripartite motif-containing protein 64B;Tripartite motif-containing protein 64 1 LS(0.5)S(0.5)LAR 84.244 0.058817 44949000 72421 88162 84259 83085 63818 86789 64559 82515 67414 29747 TRUE FALSE 75280.237 103303.1377 86454.85876 99518.96502 52970.23916 66633.57005 59498.69689 81409.02139 64987.78331 35575.35511 2.116078301 2.90378374 2.430189621 2.797413117 1.488958831 1.87302614 1.672469514 2.288354428 1.826764149 1 15.11859054 3.242515302 24.99997455 1.797787969 2.576883469 0.558258008 0.372029586 80.62177502 509655.3743 0.100756545 0.13152689 1747.894847 -3.242515302 0.7790955 LS(ph)SLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSLPR 6 0 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ES05 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 LS(0.518)S(0.482)LPR;LS(0.529)S(0.471)LPR;LS(0.745)S(0.255)LPR 105.12 0.034879 230324000 419457 466960 513600 525070 676360 763050 587750 604970 583780 629010 TRUE FALSE 436017.4863 547156.7476 526984.8379 628927.2788 561392.5688 585843.2016 541680.6192 596861.3667 562769.8718 752252.4664 0.579615895 0.727357865 0.700542519 0.836058779 0.746282125 0.778785352 0.720078223 0.79343225 0.74811303 1 19.52085741 -5 0.133456423 1.84463274 0.641212043 0.680925399 0.057557218 85.03626051 0.70931947 19.30525686 0.401388209 1.00E-05 5 -1.203420697 LS(ph)SLRAS(ph)TSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.5)S(0.5)LRAS(0.966)T(0.028)S(0.005)K;LS(0.5)S(0.5)LRAS(0.983)T(0.015)S(0.002)K;LS(0.74)S(0.26)LRAS(0.967)T(0.027)S(0.006)K;LS(0.5)S(0.5)LRAS(0.982)T(0.017)S(0.001)K 131.24 0.00014535 5970950000 7041700 4185250 6384500 5013800 8722400 7959400 8294100 6295500 6093600 2698290 TRUE FALSE 7319711.753 4904034.131 6550885.315 6005514.675 7239769.564 6110949.976 7643986.769 6211119.12 5874292.526 3226968.264 2.268293691 1.519703242 2.030043304 1.861039274 2.243520534 1.89371245 2.368782754 1.924753705 1.820375054 1 21.62174796 0.733421068 2.162198123 1.000585029 2.010276405 0.633904012 0.230634858 0.704049851 4.764031845 0.208300742 0.056851802 5.412788633 -0.733421068 1.009691376 LS(ph)SPVKRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSPVKRPR 9 2 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.5)S(0.5)PVKRPR 51.762 0.079612 296190000 310740 391170 522450 405970 690080 638050 602920 575000 522400 418830 TRUE FALSE 323008.2551 458350.4046 536065.4762 486269.6543 572780.4481 489872.5572 555661.555 567293.0655 503598.926 500891.7195 0.64486643 0.91506884 1.070222276 0.970807932 1.143521495 0.978000909 1.109344661 1.132566268 1.005404774 1 18.93413924 4.797171705 1.570553546 1.064158935 0.440463808 0.802599191 0.061188573 0.476198471 0.995896294 0.01572743 0.475700668 62686.16555 -4.797171705 -0.623695128 LS(ph)SPVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.668)S(0.332)PVLHR 148.94 0.00033052 1941700000 121500 139590 129300 126370 153770 169770 142180 139500 122810 128850 TRUE FALSE 126296.9138 163563.4966 132669.6642 151365.6088 127632.2303 130343.4904 131035.5601 137630.2307 118390.0921 154095.6905 0.819600557 1.061441083 0.860956356 0.982283205 0.828266059 0.845860711 0.85035188 0.893147824 0.768289442 1 17.23346699 3.231329884 24.99909302 0.859636628 0.935374362 0.134543897 0.082136572 279.5351089 966446.5559 0.021528824 0.026235078 1703.451935 -3.231329884 0.075737734 LS(ph)STSSEETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.579)S(0.4)T(0.017)S(0.003)S(0.001)EETQLFHIPR;LS(0.585)S(0.388)T(0.02)S(0.004)S(0.004)EETQLFHIPR;LS(0.304)S(0.304)T(0.125)S(0.125)S(0.125)EET(0.016)QLFHIPR 191.61 4.30E-10 290522000 55034 71899 72807 71451 87293 101028 80907 84003 78699 86263 TRUE FALSE 57206.78482 84247.09395 74704.41023 85583.79454 72454.96704 77565.77809 74565.29793 82877.07719 75866.63836 103164.5832 0.554519613 0.816628065 0.724128455 0.829585036 0.702324041 0.751864406 0.722780004 0.803348151 0.735394221 1 16.65458825 -5 0.224519353 2.328891126 0.713896808 0.55401937 0.07200541 112.6955162 1.128040018 67.85656771 0.121115088 1.00E-05 5 -1.614994318 LS(ph)TGSFPEDLLESDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LS(0.35)T(0.35)GS(0.3)FPEDLLESDSSR;LS(0.981)T(0.017)GS(0.002)FPEDLLESDSSR;LS(0.473)T(0.473)GS(0.054)FPEDLLESDSSR;LS(1)TGSFPEDLLESDSSR;LS(0.987)T(0.009)GS(0.004)FPEDLLESDSSR 251.05 1.32E-21 183109000 241781 255234 252628 272557 279441 339624 298680 266361 266522 245941 TRUE FALSE 251326.7006 299068.4541 259211.6932 326467.9611 231941.7186 260751.4731 275268.6811 262790.8665 256929.9253 294128.4301 0.854479455 1.016795466 0.881287447 1.109950374 0.788572932 0.886522506 0.935879204 0.89345619 0.87352972 1 18.16608671 3.214565128 24.99998396 0.893539312 0.96325888 0.145050646 0.08217726 424.9653859 442754.0508 0.022154416 0.026492644 1638.947824 -3.214565128 0.069719567 LS(ph)TPQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSTPQKK 7 1 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 1 LS(0.658)T(0.342)PQKK;LS(0.5)T(0.5)PQKK;LS(0.5)T(0.5)PQKK 83.948 0.013417 908340000 1108550 555330 771100 494123 1027210 1006540 1002400 798360 803020 504528 TRUE FALSE 1152316.41 650703.6076 791195.4995 591859.0546 852605.2111 772786.3393 923829.2687 787659.2901 774119.4671 603380.6018 1.90976708 1.078429777 1.311271024 0.980905009 1.413047102 1.280760994 1.531088779 1.305410362 1.282970425 1 19.20270879 0.731232524 2.500642747 1.000132435 1.335363462 0.159941352 0.238804408 2.69138514 22.38161067 0.213501958 0.057069677 5.385580528 -0.731232524 0.335231026 LS(ph)YSDKNLIDSMDQSAFAGFSFVNPK ddPTM_MDA-MB-175_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(0.999)YS(0.001)DKNLIDSMDQSAFAGFSFVNPK;LS(0.847)YS(0.153)DKNLIDSMDQSAFAGFSFVNPK;LS(0.499)YS(0.499)DKNLIDS(0.002)MDQSAFAGFSFVNPK 337.64 1.84E-95 2560636000 1392244 804778 1155706 891112 1561323 1333171 1516544 1053439 1293357 558611 TRUE FALSE 1447210.868 942992.3612 1185824.648 1067371.294 1295929.874 1023562.24 1397673.319 1039319.373 1246809.334 668060.1302 2.166288337 1.411538151 1.775026819 1.597717399 1.939840166 1.532140886 2.092137003 1.555727286 1.866313043 1 19.34961844 -1.24898155 5.053201982 0.999879354 1.7526104 0.48588135 0.23718883 0.000282791 4.20E-05 0.201446121 0.047473792 0.05636616 1.24898155 0.752731046 LSAEERDQLLPNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSAEERDQLLPNLR 14 1 P61457 P61457 PCBD1 Pterin-4-alpha-carbinolamine dehydratase 0 218.11 5.02E-12 88756000 40248 61203 71027 58340 43262 66521 44309 57479 74569 50228 FALSE TRUE 41837.02212 71714.13916 72878.02197 69879.47787 35908.34069 51072.50589 40835.9448 56708.58802 71885.27626 60069.21493 0.696480255 1.193858439 1.213234134 1.163315984 0.597782753 0.850227624 0.679814858 0.94405409 1.196707437 1 15.87433819 3.283700447 24.99966857 0.865264341 1.086268625 0.162872814 0.206384991 209.6666806 116117.6445 0.057477252 0.077824247 1921.765742 -3.283700447 0.221004284 LSAEKVEIATLTR ddPTM_MDA-MB-175_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 ; 187.16 6.56E-06 1849780000 1883540 1726440 1929580 1555880 2937700 2738200 2403900 2269700 2736400 2077200 FALSE TRUE 1957903.614 2022942.64 1979866.44 1863628.42 2438350.803 2102294.548 2215476.037 2239278.384 2637917.499 2484187.57 0.78814645 0.814327656 0.7969875 0.750196339 0.981548589 0.846270456 0.891831222 0.901412764 1.061883382 1 21.24434268 2.19036126 0.462808583 1.02146747 0.778644962 0.622680776 0.060158143 0.701411408 0.331198285 0.060176068 0.05725171 155.0105511 -2.19036126 -0.242822509 LSAIYGGTYMLNKPIEEIIVQNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSAIYGGTYMLNKPIEEIIVQNGK 24 1 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ; 270.54 6.36E-52 431210000 342020 242690 333520 234560 439060 354880 378230 360920 381070 237370 FALSE TRUE 355523.2137 284370.1196 342211.8052 280955.2679 364428.738 272464.4983 348583.3443 356082.4577 367355.3651 283878.1068 1.252379825 1.001733184 1.205488543 0.989703895 1.28375077 0.959793981 1.227933173 1.25434984 1.294060219 1 18.11491206 LSAKPAPPKPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSAKPAPPKPEPK 13 2 Q15651;A0A087WZE9;Q15651-2;P05204 Q15651;P05204 HMGN3;HMGN2 High mobility group nucleosome-binding domain-containing protein 3;Non-histone chromosomal protein HMG-17 0 83.966 0.0056022 1137500000 3692400 1511600 2649900 1635100 3799100 3182500 3635400 2769700 3478500 1300600 FALSE TRUE 3838178.803 1771205.541 2718958.571 1958517.9 3153330.339 2443412.606 3350447.849 2732576.702 3353309.464 1555427.669 2.467603529 1.138725752 1.748045651 1.25915074 2.027307603 1.570894395 2.154036421 1.756800883 2.155876183 1 20.56887988 3.199944211 24.99996767 1.826758785 1.623379436 0.008848935 0.458840722 556.1272307 360030.8324 0.121672639 0.145429184 1584.689614 -3.199944211 -0.203379349 LSAKPAPPKPEPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSAKPAPPKPEPKPK 15 3 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 96.208 0.0016596 3082900000 3932700 1601000 2731500 1218100 4314900 2947500 2846700 2407400 3480000 1547100 FALSE TRUE 4087966.033 1875959.296 2802685.134 1459036.544 3581454.839 2262987.795 2623568.216 2375132.741 3354755.48 1850224.624 2.209443102 1.013908945 1.514781015 0.788572655 1.935686507 1.22308814 1.417972813 1.283699671 1.813161189 1 20.819269 -2.130121295 2.543777719 0.082478235 1.428144103 0.098725097 0.408341712 18020468.87 3800443.693 96456684.49 0.090277053 0.007411032 2.130121295 1.345665869 LSAKPPAKVEAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSAKPPAKVEAKPK 14 3 P05114;A6NEL0;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 P05114 HMGN1 Non-histone chromosomal protein HMG-14 0 139.6 4.46E-06 786730000 852610 428260 650280 305150 1200000 743640 658570 588800 782670 410220 FALSE TRUE 886271.7012 501810.3236 667226.831 365507.7592 996024.4286 570940.88 606949.5625 580908.0991 754501.8596 490594.7549 1.806525024 1.022861167 1.360036618 0.745029896 2.030238641 1.163772899 1.237170917 1.184089502 1.537932993 1 18.90417228 -1.881516426 2.509212078 0.8404504 1.316691453 0.073283165 0.355012283 29595511.26 16486035.1 28014599.29 0.078362937 0.013136618 1.881516426 0.476241053 LSALGNVTTCNDYVALVHPDLDRETEEILADVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSALGNVTTCNDYVALVHPDLDRETEEILADVLK 34 1 P56537 P56537 EIF6 Eukaryotic translation initiation factor 6 0 296.94 4.27E-90 121440000 86048 60905 81588 65560 83919 88976 93744 71589 85569 55506 FALSE TRUE 89445.24148 71364.95997 83714.25031 78527.57232 69654.47836 68312.67244 86396.10033 70629.46655 82489.3884 66381.33797 1.347445596 1.075075649 1.261111223 1.182976643 1.049308141 1.02909454 1.301511885 1.063995826 1.242659321 1 16.01849009 7.999975744 0.016765175 5.23E-07 2.573218799 0.198032092 0.107442327 7910.803898 10.2318639 611.0976962 1004.469722 99994415.12 -7.999975744 2.573218275 LSAQAQVAEDILDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSAQAQVAEDILDKYR 16 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 0 156.83 1.14E-07 364170000 425440 125750 186370 121690 211040 224350 162560 182300 144030 131070 FALSE TRUE 442236.6997 147346.5843 191226.9553 145759.9188 175167.4962 172248.1126 149818.1224 179856.5667 138846.3884 156750.657 2.821274935 0.940006167 1.219943565 0.929883942 1.117491304 1.098866926 0.955773489 1.147405504 0.88577867 1 17.25811196 4.740631278 24.99977388 1.045700226 2.821275542 0.963493388 0.104412804 27.60093422 333212.0716 0.022318772 0.147102165 55034.02514 -4.740631278 1.775575316 LSAS(ph)SEDISER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSASSEDISER 11 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 LSAS(0.975)S(0.025)EDISER;LSAS(0.979)S(0.021)EDISER;LSAS(0.984)S(0.016)EDISER 193.81 8.26E-07 232010000 324256 365033 388620 356929 428880 458880 370336 390530 377397 359447 TRUE FALSE 337057.8773 427724.5782 398747.7565 427528.4909 355979.1308 352312.0744 341308.0966 385295.5841 363814.5557 429873.7576 0.784085726 0.99500044 0.927592693 0.99454429 0.828101563 0.819571021 0.79397286 0.896299384 0.846328833 1 18.71355352 3.219698702 24.97887423 0.854731802 0.930447351 0.125787387 0.076317647 384.7632869 509541.7171 0.020914248 0.025036547 1658.435944 -3.219698702 0.075715549 LSASETSLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSASETSLHR 10 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 148.32 2.53E-05 147280000 60455 101860 92561 88450 112290 124900 102260 105520 80271 96935 FALSE TRUE 62841.81008 119353.6626 94973.2157 105945.146 93202.98591 95893.86788 94244.59399 104105.677 77382.06239 115927.5573 0.542078273 1.029553847 0.819246242 0.913890954 0.803976104 0.827187858 0.812961095 0.898023554 0.667503605 1 16.82286403 -2.344153033 2.343893025 2.103464354 0.827822785 0.15471713 0.126983057 18791755.45 2300272.239 110039398.9 0.028982534 0.00452738 2.344153033 -1.275641568 LSASSS(ph)ISSADLFEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 LSAS(0.002)S(0.013)S(0.985)ISSADLFEEPR 138.39 4.00E-06 44324000 56226 66165 95560 65813 101120 84787 75484 75117 91542 70256 TRUE FALSE 58445.8459 77528.32406 98050.3721 78830.61497 83931.65852 65096.50421 69567.36684 74110.17948 88247.4213 84021.31807 0.695607344 0.922722064 1.166970173 0.938221594 0.998932895 0.774761759 0.82797281 0.882040192 1.050297988 1 16.3584678 1.238940605 24.99915046 1.025149027 0.905884823 0.142472501 0.121435721 21.29463591 1401813.443 0.098032382 0.030723925 17.33566896 -1.238940605 -0.119264204 LSASTASELS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 LSASTAS(0.009)ELS(0.991)PK;LSASTAS(0.001)ELS(0.999)PK 130.06 0.00023417 210470000 748780 301620 358290 286469 554950 634980 488230 394630 429350 277310 TRUE FALSE 778342.4126 353420.8887 367627.3317 343131.7132 460619.7972 487515.5182 449961.2568 389340.6303 413897.7774 331643.5851 2.346924372 1.065664782 1.108501259 1.034639983 1.388900066 1.469998336 1.356761527 1.173973048 1.24801985 1 18.33927409 4.743383363 24.99328686 1.220926201 2.346924833 0.834703051 0.152282153 203.3235116 1053664.142 0.038449043 0.315267741 55383.8781 -4.743383363 1.125998632 LSCS(ph)ELSLYQPLQNSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSCSELSLYQPLQNSSK 17 0 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 LS(0.012)CS(0.988)ELSLYQPLQNSSK;LS(0.006)CS(0.994)ELSLYQPLQNSSK 311.24 4.20E-58 225783000 593190 449990 596850 518450 815910 684150 504670 572070 560630 435860 TRUE FALSE 616609.5992 527272.2821 612404.4013 620997.8626 677221.9096 525266.5309 465112.6467 564402.3374 540453.0358 521258.422 1.182924962 1.011537195 1.174857567 1.191343557 1.299205694 1.007689293 0.892288023 1.082768764 1.036823604 1 18.99163926 2.646717603 12.44268147 1.005644045 1.164279115 0.529245467 0.0790769 0.834401219 110.8595708 0.026812237 0.025275704 443.3202846 -2.646717603 0.15863507 LSCS(ph)LEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSCSLEDLR 9 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.015)CS(0.985)LEDLR;LS(0.027)CS(0.973)LEDLR;LS(0.09)CS(0.91)LEDLR;LS(0.004)CS(0.996)LEDLR;LS(0.009)CS(0.991)LEDLR;LS(0.33)CS(0.67)LEDLR 159.12 6.95E-05 3650770000 4066750 3940820 4149700 4722240 4455530 5075620 5091430 4556500 4167140 3405610 TRUE FALSE 4227308.43 4617625.18 4257844.591 5656284.978 3698180.602 3896884.177 4692350.413 4495427.57 4017165.445 4072874.075 1.037917783 1.13375103 1.045415231 1.388769914 0.908002687 0.956789752 1.152098083 1.103748235 0.986322035 1 21.95761578 LSCS(ph)LEDLRSESVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSCSLEDLRSESVDK 15 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2;E9PI79 E9PP16 PPFIBP2 Liprin-beta-2 1 LS(0.17)CS(0.83)LEDLRSESVDK;LS(0.311)CS(0.688)LEDLRS(0.001)ESVDK;LS(0.001)CS(0.999)LEDLRSESVDK;LS(0.003)CS(0.997)LEDLRSESVDK;LS(0.069)CS(0.931)LEDLRSESVDK;LS(0.007)CS(0.993)LEDLRSESVDK 200.45 4.18E-09 2155167000 3760165 2761731 3458282 2386298 4651103 4211691 3319382 3241884 3717916 2634961 TRUE FALSE 3908619.218 3236036.816 3548407.67 2858300.622 3860510.173 3233589.594 3059200.165 3198431.848 3584108.929 3151231.159 1.240346716 1.026911913 1.12603852 0.907042511 1.22507997 1.02613532 0.970795226 1.014978491 1.137367825 1 21.58748416 4.742158589 24.47106983 1.046499548 1.240346814 0.304992121 0.08695288 308.5980569 2098760.376 0.019570273 0.143700019 55227.90749 -4.742158589 0.193847265 LSDDFDS(ph)PVKGPLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSDDFDSPVKGPLCK 15 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK;LSDDFDS(1)PVKGPLCK 197.09 5.21E-09 1220170000 1592960 759300 1036530 692150 1528110 1380790 1373630 1093650 1186310 632810 TRUE FALSE 1655851.291 889703.8685 1063542.823 829055.2041 1268362.408 1060122.449 1265961.291 1078991.411 1143614.935 756797.0036 2.187972842 1.175617589 1.405321134 1.095478973 1.675961192 1.400801593 1.672788456 1.425734253 1.511125083 1 19.52954685 -1.520064244 2.599049427 0.972548916 1.485530625 0.214204105 0.28823324 14318980.6 13780215.09 2771990.957 0.067778716 0.03019505 1.520064244 0.512981709 LSDDNTIGKEEIQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSDDNTIGKEEIQQR 15 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 160.81 1.54E-06 465690000 585280 577210 601390 457270 719090 692870 626190 532580 496250 528840 FALSE TRUE 608387.3063 676341.3274 617062.7174 547716.6412 596859.3387 531961.443 577107.5916 525441.6362 478390.0594 632456.0727 0.961943971 1.069388621 0.975660989 0.866015309 0.94371667 0.841104175 0.912486442 0.830795464 0.756400452 1 19.27060576 3.845173756 3.500202065 0.871968009 1.017433991 0.41841282 0.06729822 0.208151237 4.716475224 0.017129459 0.0333229 7001.220512 -3.845173756 0.145465982 LSDEHEPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDEHEPEQR 10 0 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 0 77.64 0.032393 48212000 63476 81485 82872 79220 88163 102380 81079 86195 77057 89077 FALSE TRUE 65982.08149 95479.41488 85031.7124 94889.47955 73177.08475 78603.79658 74723.81612 85039.69701 74283.73362 106529.9327 0.61937598 0.896268424 0.798195496 0.890730682 0.686915714 0.737856437 0.701434932 0.798270447 0.697303863 1 16.70089933 -0.992544384 4.302714702 1.000010259 0.764912533 0.420272798 0.084794956 8847861.331 4112687.805 849.5206922 0.018895016 0.101731539 0.992544384 -0.235097726 LSDETLIDIMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSDETLIDIMTR 12 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;; 183.03 3.75E-05 136429000 191646 221787 225217 217024 222521 270014 216851 202495 177020 189769 FALSE TRUE 199212.3321 259877.192 231086.34 259950.6994 184696.9599 207307.3406 199853.652 199780.8857 170649.0848 226950.6022 0.877778381 1.145082628 1.018223075 1.14540652 0.813820092 0.913446973 0.880604193 0.880283567 0.751921709 1 17.79201879 3.231373244 24.99999983 0.870695073 1.05162697 0.458466566 0.092166843 133.302429 463668.5164 0.024629791 0.030025414 1703.622016 -3.231373244 0.180931897 LSDFLITGGGKGS(ph)GFSLDVIDGPISQR ddPTM_MDA-MB-175_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(1)GFSLDVIDGPISQR;LSDFLIT(0.002)GGGKGS(0.997)GFS(0.001)LDVIDGPISQR;LSDFLIT(0.005)GGGKGS(0.989)GFS(0.005)LDVIDGPISQR 234.62 3.36E-45 1304114000 930761 769810 932808 764748 1082124 1043474 926341 929819 912037 683069 TRUE FALSE 967508.163 902018.8792 957117.7428 916012.8719 898184.949 801142.9775 853731.9719 917356.2972 879212.9665 816903.2924 1.184360709 1.104192978 1.171641431 1.121323516 1.099499729 0.980707245 1.04508328 1.12296805 1.07627546 1 19.63980577 3.168304698 2.927071512 1.057452098 1.146533237 0.536060324 0.043173254 0.24073935 4.184040819 0.013802702 0.017536606 1473.34583 -3.168304698 0.089081139 LSDGFNGADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDGFNGADLR 11 0 A0A087X2I1;P62333;H0YJC0 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 77.379 0.076255 256310000 124400 158590 154220 166350 190540 219400 161880 144360 150240 198150 FALSE TRUE 129311.4081 185826.5988 158239.0999 199253.5335 158152.0789 168447.675 149191.4226 142425.0903 144832.8917 236973.6987 0.545678313 0.7841655 0.667749631 0.84082552 0.667382413 0.710828569 0.629569541 0.601016447 0.611177074 1 17.85436742 -1.166348645 4.77579573 1.000029877 0.67480628 0.581635941 0.083149475 3.01E-05 5.25E-06 0.080585014 0.01899209 0.068179114 1.166348645 -0.325223597 LSDGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDGIR 6 0 P37837 P37837 TALDO1 Transaldolase 0 100.27 0.088053 284590000 573050 777660 761790 743460 860660 950610 775630 773920 752010 897220 FALSE TRUE 595674.4565 911217.0556 781642.8732 890514.169 714365.3206 729845.2341 714834.0939 763546.8683 724945.307 1073013.081 0.55514184 0.849213371 0.728456053 0.829919211 0.665756395 0.680182979 0.666193271 0.711591389 0.675616467 1 20.03323623 -1.541446222 6.841224191 1.000210334 0.71161137 0.545914213 0.080091431 0.000242167 1.62E-05 0.073089866 0.017215081 0.028744435 1.541446222 -0.288598964 LSDGIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDGIRK 7 1 P37837 P37837 TALDO1 Transaldolase 0 80.098 0.04944 984420000 743640 681450 765520 624630 1041700 960780 805200 814150 875210 799440 FALSE TRUE 772999.4814 798483.7366 785470.0801 748179.9497 864632.2061 737653.4058 742086.32 803237.6509 843711.3631 956074.9618 0.808513466 0.835168547 0.821557003 0.782553649 0.904356082 0.771543483 0.776180059 0.840140871 0.88247407 1 19.86676421 0.906583041 1.910966826 0.999376743 0.815997309 0.705477976 0.036368701 0.231594737 1.734130028 0.033590702 0.009422871 8.064603893 -0.906583041 -0.183379433 LSDLDSETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 111.82 0.0047988 204040000 557680 474610 522490 485700 687660 662200 591640 558580 526710 540760 FALSE TRUE 579697.637 556120.5755 536106.5186 581770.0103 570771.7988 508414.0857 545265.7108 551093.1488 507753.81 646711.5685 0.896377404 0.859920562 0.828973138 0.899581883 0.88257552 0.786152762 0.843135854 0.852146731 0.785131788 1 19.30276289 4.712628299 4.205903627 0.852789683 0.898886349 0.023110236 0.05868293 0.658834428 25.50145119 0.012962351 0.086372268 51597.45713 -4.712628299 0.046096666 LSDPPT(ph)SPSSPSQMMPHVQTHF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPT(0.488)S(0.488)PS(0.023)S(0.001)PSQMMPHVQTHF 113.93 0.00089962 193960000 39609 53995 48199 46439 43055 57034 44066 50812 51524 60569 TRUE FALSE 41172.7939 63268.22123 49455.10554 55624.49559 35736.52648 43788.71786 40611.99177 50130.94825 49669.6613 72436.33589 0.568399732 0.873432104 0.682738917 0.767908742 0.493350831 0.604513154 0.560657732 0.692069079 0.685700908 1 16.14442595 0.501135948 1.854722031 0.999955079 0.657134303 0.495787752 0.103706737 3.245711152 11.07274037 0.100098595 0.02787228 3.170559794 -0.501135948 -0.342820776 LSDPPTSPSS(ph)PSQMMPHVQTHF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSDPPTSPSSPSQMMPHVQTHF 22 0 Q13496-2;Q13496 Q13496-2 MTM1 Myotubularin 1 LSDPPTSPS(0.021)S(0.977)PS(0.002)QMMPHVQTHF;LSDPPTSPS(0.003)S(0.996)PS(0.001)QMMPHVQTHF;LSDPPTSPS(0.034)S(0.96)PS(0.006)QMMPHVQTHF 237.63 1.02E-30 1073340000 359581 494860 475430 511670 565900 665150 486730 560140 581840 541970 TRUE FALSE 373777.5355 579848.3555 487820.0964 612876.7988 469708.5201 510678.9929 448578.8308 552632.2395 560899.6921 648158.6449 0.576676001 0.894608689 0.752624531 0.945566033 0.724681409 0.787891972 0.692081845 0.85261879 0.865374082 1 19.30598745 0.993438667 1.561866325 0.996971128 0.779429329 0.338409516 0.098253725 0.457697223 2.285946556 0.086153442 0.025245682 9.850055268 -0.993438667 -0.217541799 LSDQCTGLQGFLVFHSFGGGTGSGFTSLLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSDQCTGLQGFLVFHSFGGGTGSGFTSLLMER 32 0 P68366-2;P68366;C9JEV8;C9JQ00;C9JJQ8 P68366-2 TUBA4A Tubulin alpha-4A chain 0 ; 205.03 5.24E-27 81238000 18362.3 15541.2 19662.3 21857.6 24170.5 32870 21624.5 19982.4 23289.4 19824.7 FALSE TRUE 19087.25778 18210.28021 20174.71569 26180.96804 20062.00704 25236.44065 19929.51518 19714.56861 22451.21904 23708.9704 0.805064811 0.768075539 0.850931751 1.104264234 0.846177911 1.064425837 0.840589652 0.831523608 0.946950402 1 14.53314539 3.994006115 23.8365033 0.932403147 0.792303451 0.348595467 0.088621789 176.7457377 702904.7113 0.0225751 0.046302717 9862.933738 -3.994006115 -0.140099696 LSDQFHDILIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSDQFHDILIR 11 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;;;; 201 4.49E-08 3268670000 2292730 3512090 3238150 3347700 3678580 4044610 3215020 3494670 3244450 3545720 FALSE TRUE 2383248.751 4115264.137 3322538.849 4009865.068 3053296.286 3105310.624 2963018.332 3447829.665 3127682.878 4240435.947 0.562029183 0.970481382 0.783537092 0.945625666 0.720043015 0.732309287 0.698753234 0.813083774 0.737585219 1 22.01578116 -1.010816467 4.430054307 1.000008728 0.781199425 0.264490088 0.112583855 1.43869E+11 32121319973 13984724.49 0.024558875 0.097540176 1.010816467 -0.218809303 LSDSFSLYPQFMFHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSDSFSLYPQFMFHLR 16 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ; 222.16 9.90E-15 1026240000 633670 839130 846130 846500 1246170 1196060 939170 793160 929020 1181960 FALSE TRUE 658687.7809 983244.05 868180.8429 1013935.173 1034346.469 918293.1915 865555.4013 782528.9875 895584.7517 1413542.432 0.465983734 0.695588634 0.614188031 0.71730084 0.731740657 0.649639636 0.612330682 0.553594268 0.633574721 1 20.43088376 -1.131798554 4.348161337 1.000061858 0.631465642 0.687060345 0.074821211 4.53E-05 9.05E-06 0.073142904 0.017237061 0.073824658 1.131798554 -0.368596217 LSDVDANTAIKHEEQS(ph)NEDIPIAEQSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSDVDANTAIKHEEQSNEDIPIAEQSSK 28 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LSDVDANT(0.001)AIKHEEQS(0.999)NEDIPIAEQSSK 94.503 0.0014188 70099000 164050 88254 124440 69773 188390 153330 152110 123750 162270 75271 TRUE FALSE 170526.8207 103410.938 127683.0086 83573.89115 156367.5351 117721.4312 140187.2207 122091.3337 156429.9344 90018.9113 1.894344402 1.148769036 1.418402053 0.928403709 1.737052058 1.307741113 1.557308556 1.356285384 1.737745238 1 16.4579405 LSDYKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSDYKGK 7 1 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 ; 67.981 0.058086 1659820000 1567640 1202020 1545340 835520 2404200 1731920 1235360 1421000 1825090 1377510 FALSE TRUE 1629531.638 1408457.585 1585612.83 1000783.362 1995534.943 1329707.828 1138529.255 1401953.819 1759405.367 1647406.71 0.989149569 0.854954381 0.96249021 0.607490158 1.211318935 0.807152125 0.691103932 0.8510065 1.067984825 1 20.65176534 1.242703857 24.9038013 1.033992445 0.865017765 0.144265887 0.157276056 166.0224476 997964.0008 0.109386513 0.036734036 17.48653885 -1.242703857 -0.16897468 LSEAVWQPEEHYSSS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEAVWQPEEHYSSSPEK 18 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 LSEAVWQPEEHYS(0.004)S(0.153)S(0.843)PEK;LSEAVWQPEEHYS(0.001)S(0.18)S(0.819)PEK 170.5 1.00E-11 481150000 146983 213266 302485 260122 363376 398601 325864 334235 313495 237394 TRUE FALSE 152786.0023 249892.7765 310368.0076 311573.3552 301609.4773 306031.9586 300321.9282 329755.1265 302212.3762 283906.8091 0.53815547 0.880192966 1.093203818 1.097449393 1.062353799 1.077931028 1.057818688 1.161490728 1.064477379 1 18.11505792 4.654532642 2.032737617 1.087160964 0.434552749 0.942316565 0.040848528 0.117867355 0.611090726 0.010385118 0.133424845 45136.995 -4.654532642 -0.652608214 LSEDYGVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSEDYGVLK 9 0 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;; 152.47 0.00018705 265975000 360043 289247 329265 290337 534150 448040 391440 337030 357602 353911 FALSE TRUE 374257.7757 338922.9222 337845.9164 347764.792 443355.3738 343989.5001 360757.91 332512.6641 344731.9739 423253.0844 0.884241106 0.800757123 0.798212532 0.82164739 1.047494726 0.812727687 0.852345614 0.78561191 0.814481894 1 18.69116106 LSEEAECPNPST(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSEEAECPNPSTPSK 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 LSEEAECPNPS(0.021)T(0.906)PS(0.073)K;LSEEAECPNPS(0.024)T(0.953)PS(0.024)K;LSEEAECPNPS(0.063)T(0.936)PSK 292.44 6.68E-43 826270000 1326790 912830 1131060 939090 1639090 1656000 1547470 1399500 1532030 1066140 TRUE FALSE 1379172.694 1069601.452 1160536.353 1124839.199 1360478.067 1271419.097 1426175.258 1380741.992 1476892.54 1275029.721 1.081678859 0.838883545 0.910203373 0.882206258 1.067016749 0.997168204 1.118542756 1.082909653 1.158320089 1 20.28209945 3.227271138 23.89673946 1.075187735 0.920571653 0.468281881 0.074071026 99.02135292 209600.6323 0.020636241 0.024897093 1687.6063 -3.227271138 -0.154616082 LSEELSGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSEELSGGR 9 0 B4DXW1;P61158;Q9P1U1-2;Q9P1U1 B4DXW1 ACTR3;ACTR3B Actin-related protein 3;Actin-related protein 3B 0 ;; 197.5 6.49E-05 254960000 189179 230790 226540 238286 247943 283230 254733 232949 212311 231700 FALSE TRUE 196647.933 270426.3872 232443.8185 285418.2596 205797.7374 217454.1249 234766.3618 229826.6997 204669.9686 277097.1788 0.709671364 0.975926165 0.838853068 1.030029468 0.742691565 0.784757628 0.84723476 0.829408299 0.738621625 1 18.0800325 3.192554931 24.99997754 0.816239751 0.891303646 0.081530316 0.104629971 271.104473 147320.0509 0.028111796 0.033600143 1557.955079 -3.192554931 0.075063895 LSEEPLQVLEHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEEPLQVLEHPR 13 0 Q9NZ08-2;Q9NZ08;D6RAL9 Q9NZ08-2 ERAP1 Endoplasmic reticulum aminopeptidase 1 0 ; 125.53 0.0001991 185365000 181943 233439 192457 226666 259148 276970 192610 192609 198076 217031 FALSE TRUE 189126.2501 273530.3323 197472.5875 271499.8583 215098.1155 212647.915 177512.7249 190027.3914 190947.2835 259554.0691 0.72865839 1.053847213 0.76081484 1.04602428 0.828721801 0.819281762 0.683914244 0.732130273 0.735674398 1 17.98567558 2.764962398 2.72698794 0.761030208 0.900059831 0.096903341 0.127452248 0.425519075 6.305871114 0.039653619 0.040234266 582.0528206 -2.764962398 0.139029624 LSEGFSIHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSEGFSIHTR 10 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;; 205.53 1.67E-07 1962110000 501061.3 1778820.9 1657780 1796749 1651075 2200489 1534188 1873232 1509514 1848555 FALSE TRUE 520843.587 2084319.552 1700983.109 2152140.589 1370425.861 1689458.778 1413934.336 1848124.389 1455186.886 2210743.96 0.235596522 0.942813637 0.769416604 0.973491562 0.619893523 0.764203729 0.63957399 0.835973963 0.658234021 1 21.07610052 -4.999999985 0.031525979 2.050378638 1.94E-10 0.162825879 0.196107314 3010.538131 7.138731014 370.0175307 143.3400761 1.00E-05 4.999999985 -2.050378638 LSEGS(ph)QPAEEEEDQETPSR ddPTM_MDA-MB-175_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 348.88 1.13E-90 457360000 230162 313420 324100 292750 345960 396450 282700 277590 289600 292280 TRUE FALSE 239248.9735 367247.4469 332546.3123 350655.0762 287153.8428 304380.4958 260541.2353 273869.3601 279177.3526 349546.67 0.684455021 1.050639238 0.951364555 1.003170982 0.821503586 0.870786427 0.745368953 0.783498696 0.798684057 1 18.41512557 3.208492304 21.40961296 0.818504703 0.933635026 0.109376632 0.111166668 65.59861567 46707.39151 0.030647397 0.036642565 1616.189586 -3.208492304 0.115130322 LSEHATAPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSEHATAPTR 10 0 P33316-2;H0YNJ9;H0YNW5;P33316;A0A0C4DGL3;H0YKC5;H0YMM5;H0YKI0 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 ;; 112.13 0.0016617 901870000 267903 660650 599190 591890 647560 815680 544940 666730 532270 820490 FALSE TRUE 278480.0173 774111.4984 614805.3836 708964.0754 537487.9825 626250.6817 502226.1789 657793.5749 513113.7067 981249.3063 0.283801492 0.788903996 0.6265537 0.72251167 0.547758841 0.638217706 0.511823219 0.670363353 0.522918797 1 19.9042602 -2.239299826 2.330701289 2.434371439 0.60294854 0.4611499 0.13222329 5392027.515 1011945.543 40746453.81 0.030494006 0.005763684 2.239299826 -1.831422899 LSEHS(ph)S(ph)PEEEASPHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 2 LSEHS(1)S(1)PEEEASPHQR;LS(0.001)EHS(0.999)S(1)PEEEASPHQR 210.47 5.07E-12 1603440000 477290 778250 818370 683450 957790 1102650 774250 886690 900730 817420 TRUE FALSE 496133.7777 911908.3836 839697.3945 818634.3701 794985.1979 846576.2483 713562.2619 874805.3709 868312.9032 977577.7985 0.507513344 0.932824359 0.858957104 0.837410968 0.813219366 0.865993734 0.729928874 0.894870334 0.888228952 1 19.898852 7.999930317 0.048974848 1.290142164 5.90E-21 0.327030989 0.104885857 697.4922871 2.579740975 16.24122521 68.53254239 99983956.17 -7.999930317 -1.290142164 LSEHSS(ph)PEEEASPHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 LSEHS(0.187)S(0.813)PEEEASPHQR;LSEHS(0.118)S(0.882)PEEEASPHQR;LS(0.001)EHS(0.143)S(0.856)PEEEASPHQR;LSEHS(0.127)S(0.873)PEEEASPHQR;LSEHS(0.237)S(0.763)PEEEASPHQR;LSEHS(0.046)S(0.954)PEEEASPHQR 282.57 2.30E-35 3073380000 1160334 1625598 1654006 1635480 1862535 2250506 1583999 1768892 1575902 1625256 TRUE FALSE 1206144.882 1904781.811 1697110.755 1958973.063 1545941.966 1727860.088 1459841.019 1745182.896 1519185.595 1943693.796 0.620542641 0.979980394 0.87313689 1.007860943 0.795362916 0.88895694 0.751065329 0.897869253 0.781597183 1 20.89036953 -2.401411217 2.097744581 2.022596623 0.852935743 0.153654764 0.108006834 4628724.615 523669.6295 22390912.03 0.024546208 0.003968156 2.401411217 -1.169660881 LSEHSSPEEEASPHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSEHSSPEEEASPHQR 16 0 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ;; 264.87 2.77E-27 1563647000 162295 892147 690353 868808 722063 1065797 620233 881014 674228 992301 FALSE TRUE 168702.5319 1045366.307 708344.1663 1040655.629 599326.9892 818281.7991 571617.5168 869205.4484 649962.666 1186723.382 0.142158261 0.880884562 0.596890713 0.87691508 0.505026696 0.689530358 0.481677133 0.732441495 0.547695171 1 20.17855226 -2.202287056 2.089651786 1.995303337 0.623959018 0.246130088 0.20472798 9965029.917 1813035.714 46882775.37 0.045554956 0.006276434 2.202287056 -1.371344319 LSELLR ddPTM_MDA-MB-175_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 15057640000 5215930 5807940 5557910 5728060 6627680 6758050 5915780 6053140 5505640 5768110 FALSE TRUE 5421858.944 6805408.515 5702753.7 6861053.171 5501109.321 5188595.307 5452085.706 5972007.559 5307493.092 6898260.717 0.785974779 0.986539766 0.826694428 0.994606242 0.797463237 0.752159931 0.790356574 0.865726566 0.769395839 1 22.71780123 3.185436527 24.99999823 0.819423455 0.899621518 0.12310851 0.088270634 163.1410335 76772.79433 0.023580801 0.028184472 1532.627192 -3.185436527 0.080198063 LSELSNSQQSVQTLSLWLIHHR ddPTM_MDA-MB-175_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 ; 188.19 1.49E-17 622640000 309000 320800 341370 320201 336660 418610 418070 375890 334550 261458 FALSE TRUE 321199.5586 375894.9045 350266.3826 383535.8021 279434.6535 321394.1716 385300.581 370851.8094 322509.6109 312685.6892 1.027228203 1.202149371 1.120186803 1.226585723 0.893659874 1.027850595 1.232229662 1.18602105 1.031417881 1 18.25435367 LSEMEAYLENIEKEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSEMEAYLENIEKEEER 17 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 101.62 0.0019403 0 28442 23997 31020 28919 40196 40953 44327 38468 28335 24769 FALSE TRUE 29564.91212 28118.29808 31828.40668 34639.09189 33363.49828 31442.2864 40852.53391 37952.39938 27315.22888 29622.01132 0.998072406 0.949236626 1.074484995 1.169370017 1.126307661 1.061450084 1.379127618 1.281222905 0.92212607 1 14.85438198 3.993944708 2.784875787 1.16470943 0.973015175 0.173787719 0.12627848 0.368250239 5.735798067 0.034656788 0.08188663 9861.539264 -3.993944708 -0.191694254 LSEMTEAEQQQLIDDHFLFDKPVS(ph)PLLTAAGMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 1 LSEMTEAEQQQLIDDHFLFDKPVS(0.992)PLLT(0.008)AAGMAR;LSEMTEAEQQQLIDDHFLFDKPVS(0.968)PLLT(0.032)AAGMAR 128 3.68E-08 744770000 131397 110578 127036 101287 141397 158957 125228 105839 108447 85082 TRUE FALSE 136584.655 129568.9113 130346.6625 121321.2663 117362.3884 122041.6458 115412.3021 104420.4013 104544.0137 101752.1889 1.342326455 1.27337714 1.281020722 1.192320948 1.153413894 1.199400692 1.134248839 1.026222654 1.027437491 1 16.6347003 2.947358749 0.36610188 0.975089835 1.380703003 0.920195444 0.031587594 0.508148867 0.127769358 0.037085557 0.079690471 885.8470615 -2.947358749 0.405613168 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMAR 34 1 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 312.14 1.34E-104 2355070000 746030 802420 904990 796610 1016540 1103750 880830 794090 826940 728590 FALSE TRUE 775483.8405 940229.393 928574.7829 954177.0804 843748.8939 847420.79 811788.243 783446.5224 797178.5909 871343.2608 0.889986616 1.079057399 1.065681947 1.095064509 0.968331233 0.972545297 0.931651485 0.899125015 0.914884669 1 19.73288165 2.797624577 1.986533191 0.928148761 1.036311213 0.304028498 0.06026226 0.341188918 2.659753805 0.02149711 0.022082246 627.5156722 -2.797624577 0.108162452 LSESSAS(ph)PQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSESSASPQPK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2;A0A3B3IU80;A0A3B3IUB0;A0A3B3IS72;A0A3B3ISB4;A0A3B3IRI6;A0A3B3ITV8;A0A3B3IRT2;A0A3B3ITF8;A0A3B3IT49;Q8N5Y2-5;A0A3B3ITX5 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 LSES(0.034)S(0.382)AS(0.583)PQPK;LSESS(0.001)AS(0.999)PQPK;LSES(0.001)S(0.028)AS(0.972)PQPK;LSES(0.006)S(0.34)AS(0.654)PQPK 218.12 1.14E-11 295842000 779710 556456 640890 483398 756210 796730 712410 642440 683820 506847 TRUE FALSE 810493.5529 652022.9894 657592.1199 579012.6816 627669.6943 611701.5321 656569.4427 633829.1426 659209.4518 606153.9655 1.33710839 1.075672233 1.084859883 0.955223779 1.035495485 1.009152075 1.083172725 1.045657009 1.087528069 1 19.20932476 4.882422002 2.021386393 1.037496461 1.512618105 0.833488784 0.039902257 0.454772304 1.443702912 0.010035627 0.4530307 76281.98789 -4.882422002 0.475121645 LSETSIKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSETSIKDR 9 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;F8VRN8 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 150.27 7.81E-05 1135270000 1965350 2041100 2112520 1785860 2583280 2715190 2002900 2162460 2245180 2399960 FALSE TRUE 2042943.536 2391643.047 2167574.007 2139097.778 2144174.988 2084628.272 1845907.464 2133475.761 2164376.41 2870186.212 0.711780834 0.833271039 0.755203268 0.745281881 0.747050829 0.72630419 0.643131605 0.743323117 0.754089195 1 21.45271291 0.633255096 3.14393179 0.999996573 0.7379364 0.759392188 0.043997697 2.986163332 25.02641588 0.044148548 0.011487674 4.297888022 -0.633255096 -0.262060173 LSEVLQAVTDHDIPQQLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSEVLQAVTDHDIPQQLVER 20 0 Q93009;A0A669KBL1;Q93009-3;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 ; 109.65 0.00019431 510211000 329638 286041 300857 250639 378815 346104 287910 257316 351375 267315 FALSE TRUE 342652.3628 335166.3167 308697.5806 300214.6461 314424.1616 265726.5913 265342.8619 253867.0999 338729.0824 319690.2562 1.071826107 1.048409547 0.965614605 0.939079751 0.98352751 0.831200157 0.829999841 0.794103339 1.059553977 1 18.28631525 3.989101084 0.895559003 0.884404947 1.093731727 0.29457307 0.081117755 0.949243881 1.181554668 0.030644212 0.156824419 9752.165969 -3.989101084 0.20932678 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 LSFASET(0.013)PLEKEPHS(0.986)PADQPEQQAESTLTSAETR;LSFASETPLEKEPHS(1)PADQPEQQAESTLTSAETR 263.17 5.15E-60 350590000 183193 176662 191932 154133 221440 225490 177030 185786 196289 182341 TRUE FALSE 190425.6011 207002.3243 196933.9056 184620.0474 183799.7079 173123.3648 163153.926 183295.8426 189224.5972 218067.2278 0.873242637 0.949259209 0.903088041 0.846619867 0.842858002 0.793899049 0.748181777 0.840547405 0.867735144 1 17.73441345 3.709627212 3.045878688 0.83241017 0.914723266 0.126379727 0.064047372 0.364817701 6.842813061 0.016797974 0.029965533 5124.213454 -3.709627212 0.082313096 LSFDKDAMVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSFDKDAMVAR 11 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;; 170.68 1.41E-05 10346390000 10101580 8854990 10869330 9045290 13825450 13580990 12136590 11235300 11365830 9495270 FALSE TRUE 10500398.18 10375765.65 11152593.67 10834421.36 11475404.95 10427010.89 11185292.36 11084709.18 10956776 11355686.36 0.924681948 0.913706607 0.982115331 0.954096566 1.010542611 0.918219345 0.984994831 0.976137314 0.964871312 1 23.43691157 4.241288763 24.99992891 0.972454202 0.919194259 0.448180293 0.024227714 56.61469727 518771.717 0.005494381 0.013719764 17429.65387 -4.241288763 -0.053259943 LSFFFDFR ddPTM_MDA-MB-175_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 ; 101.99 0.011752 1275050000 790480 757850 807260 1034030 1589540 1431670 1247260 836620 907010 1205220 FALSE TRUE 821688.7608 888004.8422 828297.8588 1238558.048 1319350.559 1099186.34 1149496.502 825406.4773 874366.8873 1441359.784 0.570078873 0.616088261 0.574664194 0.859298325 0.915351305 0.762603725 0.797508377 0.572658185 0.606626393 1 20.45899907 3.756784757 24.01551264 0.763384692 0.589858184 0.346628048 0.12316858 686.4821326 904631.8528 0.034184806 0.061458849 5711.954736 -3.756784757 -0.173526508 LSFQHDPETSVLVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSFQHDPETSVLVLR 15 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 142.1 4.65E-06 251030000 101300 243490 199270 218510 224170 281300 203370 206080 199790 214550 FALSE TRUE 105299.4022 285307.5134 204463.1399 261730.6258 186065.6635 215972.3381 187429.328 203317.8347 192599.5969 256586.9647 0.410384847 1.111933 0.796857082 1.020046463 0.725156337 0.841712043 0.730470966 0.792393468 0.750621128 1 17.96908835 LSFS(ph)PENILIQNQDIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 LS(0.001)FS(0.999)PENILIQNQDIVR;LS(0.001)FS(0.999)PENILIQNQDIVR;LSFS(1)PENILIQNQDIVR 184.22 6.79E-10 314619000 220978 241188 271199 245247 277214 305604 260163 249674 247626 262010 TRUE FALSE 229702.3821 282610.1628 278266.6687 293756.1246 230093.2633 234632.1025 239770.7443 246327.5284 238713.9886 313345.843 0.733063442 0.90191132 0.888049658 0.937482118 0.734310885 0.748795964 0.765195229 0.786120301 0.76182274 1 18.25739633 3.230994403 24.9999966 0.784119319 0.869391474 0.105127067 0.087074514 278.992459 921835.2415 0.023481248 0.028578581 1702.136571 -3.230994403 0.085272155 LSFSDTYQDYEEYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSFSDTYQDYEEYWR 15 0 Q9UHI6;E9PJ60 Q9UHI6 DDX20 Probable ATP-dependent RNA helicase DDX20 0 74.987 0.026127 0 8003.4 9499.6 11814 10318 10467 13878 12107 10053 11866 11605 FALSE TRUE 8319.380412 11131.0824 12121.88255 12358.8696 8687.823079 10655.04482 11158.0217 9918.255978 11438.94498 13878.77756 0.599431785 0.802021818 0.873411401 0.8904869 0.625978984 0.767722141 0.80396286 0.714634696 0.824204072 1 13.76059288 0.930828119 6.810291825 0.999996473 0.764863372 0.396745137 0.089255555 0.883649046 86.14064312 0.085136075 0.02135969 8.527625496 -0.930828119 -0.2351331 LSGAEPDDEEYQEFEEMLEHAESAQDFASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSGAEPDDEEYQEFEEMLEHAESAQDFASR 30 0 Q96GC9;K7EPE7;Q96GC9-2 Q96GC9 VMP1 Vacuole membrane protein 1 0 ; 219.67 1.39E-34 52864000 12862.6 17856 12498.4 20605.7 16802.3 19805.7 14213.2 13626.7 13565.8 16667.1 FALSE TRUE 13370.42538 20922.6291 12824.11857 24681.44596 13946.25105 15206.12633 13099.13224 13444.05638 13077.56951 19932.69913 0.670778468 1.049663619 0.6433709 1.238239026 0.699666962 0.762873419 0.657168011 0.674472448 0.656086234 1 14.28284946 LSGAQADLHIEDGDSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSGAQADLHIEDGDSIR 17 0 M0QXB5;O95571 M0QXB5 ETHE1 "Persulfide dioxygenase ETHE1, mitochondrial" 0 ;;; 240.61 2.50E-20 1327840000 890240 1124760 986670 1065820 1109330 1425740 1049990 1058150 1079240 1243900 FALSE TRUE 925387.3626 1317928.781 1012383.431 1276636.015 920766.4828 1094633.492 967689.0402 1043967.23 1040398.363 1487618.389 0.622059642 0.885932031 0.680539739 0.858174398 0.618953415 0.735829498 0.650495481 0.701770856 0.699371809 1 20.50457306 -1.327144471 8.815946703 1.000000329 0.718582779 0.494116442 0.085887498 5.11E-07 3.89E-08 0.076387386 0.018004658 0.047082068 1.327144471 -0.28141755 LSGEHS(ph)ESS(ph)TPRPR ddPTM_MDA-MB-175_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 2 LS(0.069)GEHS(0.881)ES(0.23)S(0.503)T(0.318)PRPR 51.798 0.091987 185090000 108110 134320 143120 130590 158650 161830 118250 138860 122930 129920 TRUE FALSE 112378.2663 157388.4151 146849.8248 156420.3122 131682.7297 124247.4351 108981.256 136998.8088 118505.7733 155375.3365 0.723269656 1.01295623 0.945129569 1.006725493 0.847513721 0.799659958 0.701406404 0.881728155 0.762706463 1 17.24539799 3.048816333 8.827150751 0.816979363 0.930080006 0.145000935 0.10489733 0.459708032 76.86297668 0.028795106 0.034409248 1118.964562 -3.048816333 0.113100642 LSGEHS(ph)ESSTPRPR ddPTM_MDA-MB-175_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(0.894)ES(0.103)S(0.002)TPRPR;LSGEHS(0.877)ES(0.107)S(0.014)T(0.002)PRPR;LS(0.009)GEHS(0.917)ES(0.021)S(0.027)T(0.027)PRPR;LSGEHS(0.528)ES(0.269)S(0.167)T(0.036)PRPR;LSGEHS(0.724)ES(0.182)S(0.034)T(0.06)PRPR 161.48 2.78E-06 2677871000 485344 893245 801460 761873 881690 950516 728907 822016 738523 896757 TRUE FALSE 504505.7559 1046652.88 822346.706 912569.2054 731820.6487 729773.0642 671773.3647 810998.2201 711943.7015 1072459.365 0.470419461 0.975937098 0.766785888 0.850912618 0.682376109 0.680466867 0.626385844 0.756204148 0.663842123 1 20.03249155 -0.983989267 4.333196244 1.000010274 0.72795995 0.299895778 0.128064121 13213500.7 6098731.532 1265.775571 0.028147753 0.103755406 0.983989267 -0.272050325 LSGEHSES(ph)STPRPR ddPTM_MDA-MB-175_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 1 LSGEHS(0.256)ES(0.351)S(0.042)T(0.351)PRPR;LSGEHS(0.07)ES(0.414)S(0.414)T(0.102)PRPR 156.11 3.43E-06 1384875000 225284 379108 349584 346903 429139 517834 434084 385090 415209 390180 TRUE FALSE 234178.3863 444216.8499 358694.4462 415519.378 356194.1061 397574.9014 400059.3618 379928.4984 400265.7092 466628.3006 0.501852087 0.951971514 0.768694153 0.890471876 0.763335841 0.852016264 0.857340546 0.814199434 0.857782755 1 18.83191428 7.999999994 0.050532748 1.269239816 3.29E-08 0.33251664 0.105069695 628.6610807 2.395501003 14.04483777 61.98389786 99999998.73 -7.999999994 -1.269239783 LSGEHSESST(ph)PRPR ddPTM_MDA-MB-175_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 LSGEHSES(0.041)S(0.152)T(0.807)PRPR 82.482 0.017121 489590000 315010 356200 394620 364970 405500 494370 443330 448670 380240 299510 TRUE FALSE 327446.838 417374.5791 404904.1214 437159.9767 336573.2548 379560.0597 408580.6362 442656.3125 366555.2367 358193.25 0.914162503 1.165221788 1.1304069 1.220458444 0.939641534 1.059651626 1.140670954 1.235803055 1.023344903 1 18.45037863 2.230616766 24.4526144 1.132807144 1.079288956 0 0.10833735 478.3921697 1472562.196 0.040204089 0.030226596 170.0657138 -2.230616766 -0.053518188 LSGEMPPAS(ph)PSFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGEMPPASPSFPR 14 0 Q96JM7-2;Q96JM7 Q96JM7-2 L3MBTL3 Lethal(3)malignant brain tumor-like protein 3 1 LSGEMPPAS(0.844)PS(0.156)FPR 109.07 0.00082742 50142000 63856 83286 74811 77005 74726 103410 72213 82056 69837 73743 TRUE FALSE 66377.08419 97589.72262 76760.63612 92236.35916 62024.10121 79394.59469 66552.75637 80956.17354 67323.58001 88191.52895 0.752646938 1.106565719 0.870385592 1.045864158 0.703288649 0.900251936 0.754638877 0.917958612 0.763379214 1 16.42835247 3.251397229 24.99950013 0.838439009 0.950238429 0.149807996 0.120900642 387.6405271 754931.4036 0.030338572 0.040821891 1784.00977 -3.251397229 0.111799421 LSGFS(ph)FK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 116.52 0.005704 2193500000 2545920 1621940 2797750 1748660 4747140 3028600 3393420 2728770 3038130 1500200 TRUE FALSE 2646434.887 1900495.578 2870661.663 2094539.729 3940222.838 2325253.549 3127434.873 2692195.302 2928788.295 1794135.467 1.475047418 1.059282096 1.600025035 1.167436778 2.196167966 1.296030089 1.743143108 1.500552969 1.632423164 1 20.77485739 4.216797952 24.94526091 1.547769018 1.26716461 0.079706136 0.326377872 414.9872132 475676.4863 0.074190239 0.160484867 16473.95791 -4.216797952 -0.280604408 LSGFS(ph)FKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 LSGFS(1)FKK;LSGFS(1)FKK 147.74 0.00056394 10878400000 6814800 3650700 7458200 3485680 13392800 7195600 8158300 7286800 8880600 4685830 TRUE FALSE 7083853.566 4277679.326 7652566.819 4175137.1 11116296.64 5524530.95 7518831.128 7189132.365 8560988.941 5603928.673 1.264087032 0.763335791 1.365571774 0.745037516 1.983661336 0.985831775 1.341707143 1.282873638 1.527676286 1 22.41800716 LSGIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGIEER 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 90.986 0.038936 90642000 136320 213910 148240 159280 190980 219310 149280 159510 142000 231800 FALSE TRUE 141702.0189 250647.3785 152103.2562 190785.1086 158517.2878 168378.5762 137579.0435 157372.0294 136889.4477 277216.7719 0.511159617 0.904156616 0.548679848 0.688216327 0.57181709 0.607389571 0.496286868 0.567685816 0.493799299 1 18.08065502 -1.040726908 4.634491687 1.000012974 0.601429929 0.517894389 0.116102173 1.66E-05 3.44E-06 0.108904686 0.025668161 0.091048562 1.040726908 -0.398583045 LSGINEIPRPFS(ph)PPVT(ph)SNTSPPPAAPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 LS(0.001)GINEIPRPFS(0.999)PPVT(0.428)S(0.093)NT(0.271)S(0.208)PPPAAPLAR 61.776 0.05799 266750000 127660 153650 136570 145340 161940 185850 167300 145730 141770 158040 TRUE FALSE 132700.1154 180038.1923 140129.1264 174087.8182 134413.4966 142689.1541 154186.5888 143776.7277 136667.7254 189004.9121 0.702098765 0.952558271 0.74140468 0.921075628 0.711164039 0.754949448 0.815780855 0.760703656 0.723090865 1 17.5280642 5.0360726 16.28866949 0.806968742 0.296387988 0.101769758 0.098445194 9750078.123 121350195.8 0.021522646 144274313.2 108660.7253 -5.0360726 -0.510580755 LSGINEIPRPFS(ph)PPVTSNTSPPPAAPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.942)PPVT(0.012)S(0.008)NT(0.037)SPPPAAPLAR 179.44 7.15E-18 1632300000 556310 607510 650940 545940 657230 714180 658130 601630 540380 648540 TRUE FALSE 578273.5484 711845.1167 667904.0312 653925.3025 545514.2794 548322.5185 606544.0509 593566.1339 520931.8294 775608.996 0.745573545 0.917788629 0.861134972 0.843112065 0.70333671 0.706957399 0.78202297 0.76529042 0.671642325 1 19.56497001 3.326229003 8.628739375 0.758316046 0.849347292 0.107991005 0.093704694 0.449788128 39.60904284 0.024003863 0.032502481 2119.478439 -3.326229003 0.091031246 LSGINEIPRPFSPPVTSNT(ph)SPPPAAPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 LSGINEIPRPFS(0.168)PPVT(0.097)S(0.134)NT(0.543)S(0.058)PPPAAPLAR 129.59 2.51E-05 1568400000 280690 308570 381660 366440 327110 428230 351260 370260 337600 343940 TRUE FALSE 291771.8579 361564.4972 391606.3731 438920.7383 271507.959 328780.0724 323727.3234 365297.2703 325449.8419 411328.4579 0.709340315 0.87901649 0.95205271 1.067080893 0.660075795 0.79931273 0.787028753 0.88809141 0.791216449 1 18.64993136 4.742445616 22.95461072 0.863262341 0.709340122 0.153333677 0.111966109 248.5825178 1468550.054 0.026885017 0.198166116 55264.41991 -4.742445616 -0.153922219 LSGLANVVLHELSGDDDTDQNMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGLANVVLHELSGDDDTDQNMR 23 0 Q14789;Q14789-2;E7EU81;F8WF12;C9J8Q0 Q14789 GOLGB1 Golgin subfamily B member 1 0 100.79 0.0022355 127440000 65563 76661 65726 76265 83136 102420 74786 71912 72822 86799 FALSE TRUE 68151.47787 89826.93041 67438.87355 91349.98937 69004.57242 78634.50719 68924.0779 70948.13726 70201.15044 103805.6022 0.656529864 0.865337983 0.649665068 0.880010206 0.664748058 0.757516989 0.663972622 0.683471179 0.676275162 1 16.66352478 -1.172533129 5.220942497 1.000013271 0.722624905 0.511243326 0.081558223 1.16E-05 1.85E-06 0.072982811 0.017201391 0.067215103 1.172533129 -0.277388366 LSGLS(ph)FK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSGLSFK 7 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FK;LSGLS(1)FK;LSGLS(1)FK 112.11 0.0067433 1550919000 2776520 1863707 3339880 1993282 4850660 3589220 3817260 3098190 3660350 1893122 TRUE FALSE 2886139.154 2183784.18 3426920.017 2387547.23 4026146.546 2755678.05 3518053.187 3056663.831 3528614.719 2264043.01 1.274772229 0.96455066 1.513628496 1.054550298 1.778299497 1.217149161 1.553880899 1.350090885 1.558545798 1 21.11046993 3.299189418 24.99999734 1.422611469 1.207192211 0.152653208 0.238525744 123.5642914 50949.77326 0.05994389 0.081164387 1991.541762 -3.299189418 -0.215419258 LSGLS(ph)FKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSGLSFKR 8 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR;LSGLS(1)FKR 136.02 0.00049537 11629110000 9072190 7358480 12015940 6359410 18707200 11175090 11329410 10306680 12575260 8198800 TRUE FALSE 9430367.066 8622241.699 12329085.27 7617282.317 15527356.83 8579844.708 10441381.24 10168535.81 12122678.85 9805197.884 0.961772233 0.879354175 1.257403003 0.776861661 1.583584239 0.875030245 1.064882256 1.037055645 1.236352289 1 23.22511532 4.266906848 24.99436305 1.097298288 0.920563047 0.10590551 0.212384008 470.4929044 414850.4176 0.047358129 0.129641369 18488.72012 -4.266906848 -0.176735241 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSGLTTNVVDIILAHHFGQEELQANLDLIQTYR 33 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 0 ; 299.95 4.59E-90 747850000 198145 235437 238070 250270 276300 337530 264640 219932 235590 196005 FALSE TRUE 205967.9176 275871.4733 244274.2998 299772.659 229334.6247 259143.7728 243896.8253 216984.1713 227111.1619 234408.427 0.878671131 1.17688377 1.042088388 1.27884762 0.978354864 1.105522426 1.04047806 0.92566711 0.968869442 1 17.83866491 1.938013836 4.521248624 0.959926936 1.083951552 0.189451366 0.102508182 0.315447181 12.51091448 0.044419059 0.026407038 86.69894961 -1.938013836 0.124024616 LSGPDDDPLHKQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSGPDDDPLHKQPR 14 1 Q86TI2;Q86TI2-4;Q86TI2-2;M0R1L4 Q86TI2 DPP9 Dipeptidyl peptidase 9 0 ; 114.56 0.00028254 304870000 157441 617180 526290 409970 512570 726980 284360 509370 453640 945140 FALSE TRUE 163656.8923 723175.864 540005.5498 491060.8424 425443.5345 558149.9125 262071.1202 502542.7283 437313.585 1130322.087 0.144787839 0.639796278 0.477744844 0.434443286 0.376391419 0.493797227 0.231855259 0.444601352 0.386892895 1 20.1083025 -1.240074011 3.941738129 1.000572325 0.410344182 0.653027057 0.130380622 100591156.5 197006254.9 748211.2001 0.029077725 0.057534188 1.240074011 -0.590228143 LSGPLKEQYAQEHGLNFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSGPLKEQYAQEHGLNFQR 19 1 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 145.52 7.48E-08 211530000 182360 165050 173860 129370 266720 227810 127580 197290 214030 227600 FALSE TRUE 189559.7136 193396.0536 178390.9344 154958.9999 221383.0297 174904.58 117579.9462 194645.6503 206327.1021 272193.8623 0.696414357 0.710508503 0.655381914 0.569296451 0.813328514 0.642573563 0.431971336 0.715099336 0.758015263 1 18.05427501 0.885379011 2.13795195 0.998508911 0.649452232 0.55262017 0.094772767 0.345292315 3.209526486 0.090853809 0.024984431 7.68031462 -0.885379011 -0.34905668 LSGS(ph)RQDLIPSYSLGSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSGSRQDLIPSYSLGSNK 18 1 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 LS(0.3)GS(0.7)RQDLIPSYSLGSNK;LS(0.245)GS(0.755)RQDLIPSYSLGSNK;LS(0.004)GS(0.995)RQDLIPSYS(0.001)LGSNK;LS(0.006)GS(0.994)RQDLIPSYSLGSNK 323.63 4.12E-62 19628610000 8157590 7110750 8002300 5755390 8607490 8501290 7168670 7026320 6787110 5218260 TRUE FALSE 8479657.952 8331965.999 8210846.512 6893788.964 7144391.924 6526994.236 6606770.914 6932143.673 6542843.237 6240678.137 1.358771878 1.335105868 1.315697803 1.104653823 1.14481019 1.045879004 1.058662339 1.110799743 1.048418632 1 22.57327138 3.729245015 1.794390137 1.071371393 1.357226481 0.910982037 0.03784291 0.093866231 0.585613785 0.010635573 0.023115448 5360.990224 -3.729245015 0.285855088 LSHIAEDVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSHIAEDVGR 10 0 P98171-2;P98171;E7EQN5;E9PCM6;A0A0B4J1X7;S4R352;S4R314;C9JLA8;C9J5M2;F8WAR0 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 0 ; 94.297 0.0082002 196670000 116361 161997 162168 147250 174210 192869 136948 164225 157537 181223 FALSE TRUE 120955.0221 189818.7246 166394.2313 176375.6105 144597.8464 148078.0977 126213.6579 162023.8325 151867.2741 216730.1771 0.558090358 0.875829693 0.767748329 0.813802733 0.667179109 0.6832371 0.582353872 0.747583168 0.700720482 1 17.72554052 -1.910375751 6.227917918 1.07882714 0.714997784 0.468688589 0.092296969 0.055292929 0.000795705 0.048914229 0.020547228 0.012292048 1.910375751 -0.363829356 LSIPTYGLQCTR ddPTM_MDA-MB-175_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 ; 155.97 0.00016933 1947120000 587180 631250 572320 586770 763790 782800 526280 546270 527720 690350 FALSE TRUE 610362.3198 739662.2771 587235.1294 702831.3547 633961.2486 601006.5634 485028.7984 538948.1442 508727.4603 825610.865 0.739285716 0.895896976 0.7112735 0.851286465 0.767869314 0.727953796 0.587478701 0.652787127 0.616183098 1 19.65510243 2.675741169 3.006640257 0.677277694 0.799423362 0.058216688 0.118850098 0.428707715 7.67183945 0.037641541 0.036116031 473.9594304 -2.675741169 0.122145667 LSIVPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSIVPVRR 8 1 P15880;H0YEN5;E9PPT0;E9PMM9;I3L404;E9PM36 P15880 RPS2 40S ribosomal protein S2 0 ; 146.58 0.00088346 1569880000 885620 1077980 959710 855020 1848050 1330510 1006730 931590 993280 1790130 FALSE TRUE 920584.9614 1263114.679 984720.831 1024140.404 1533919.121 1021519.217 927819.872 919103.5598 957532.0468 2140871.699 0.430004732 0.590000176 0.459962562 0.478375423 0.716492783 0.477151067 0.433384155 0.42931277 0.447262695 1 21.02976691 -2.033269873 2.638923518 1.617837211 0.495310535 0.754340202 0.086323684 11884314.9 5180356.126 44374349.44 0.02143269 0.009262541 2.033269873 -1.122526676 LSKDDIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LSKDDIDR 8 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;;;;;; 108.67 0.0034351 7570450000 10853830 8851850 10058870 7831520 13363870 12478110 11576210 10200840 11096360 7924320 FALSE TRUE 11282347.59 10372086.38 10321012.42 9380571.281 11092284.15 9580258.06 10668836.41 10064114.43 10697004.17 9476938.784 1.190505484 1.094455353 1.089066064 0.989831368 1.170450121 1.010902178 1.12576821 1.061958366 1.128740453 1 23.17598969 -4.999901559 0.011077698 2.53E-06 1.980194627 0.183081751 0.060228384 20039.65278 16.85754714 1779.101746 1273.48124 1.00E-05 4.999901559 1.980192093 LSKDPNIVIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSKDPNIVIAK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 138.63 0.001402 0 3870200 3138700 3627300 3142500 5048200 4542700 4337300 3792800 4154000 3179400 FALSE TRUE 4022998.484 3677747.309 3721830.418 3764077.121 4190108.767 3487726.77 3997331.093 3741963.72 4004498.351 3802342.557 1.058031575 0.967231977 0.978825648 0.989936352 1.101980872 0.91725738 1.05128116 0.984120621 1.053166118 1 21.85845708 LSKEDIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 LSKEDIER 8 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;; 123.75 0.0012169 47449200000 57743300 46964350 56153840 43629340 68290910 65624480 61298890 55151590 55266710 46111160 FALSE TRUE 60023050.07 55030111.78 57617255.2 52259093.23 56682845.51 50384189.07 56494122.83 54412373.15 53277671.9 55145758.95 1.08844363 0.997902882 1.044817522 0.947653894 1.02787316 0.913654831 1.024450908 0.986700957 0.966124556 1 25.7167466 7.999988165 0.767137179 0.98347232 21.21208301 0.409472808 0.03663657 388.9537139 1.546291615 0.011507929 13626.67532 99997274.91 -7.999988165 20.22861069 LSKEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 127.76 0.0010601 62302680000 46823000 37949410 46168310 35133720 58229760 53972250 49991480 44851630 47460360 35368260 FALSE TRUE 48671608.2 44466925.96 47371494.09 42083064.95 48331886.19 41438012.89 46073017.17 44250467.26 45752270.91 42297993.38 1.150683621 1.051277434 1.119946605 0.994918709 1.142651987 0.979668528 1.089248295 1.046159965 1.081665281 1 25.33408589 7.999994972 0.888261261 1.054404136 42.38089085 0.231543216 0.051275398 1220.737436 2.805763053 0.014249888 102204.867 99998842.19 -7.999994972 41.32648671 LSLDELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLDELHR 8 0 P05023-4;P05023;P05023-3;P05023-2;Q5TC02;Q5TC01 P05023-4 ATP1A1 Sodium/potassium-transporting ATPase subunit alpha-1 0 178.83 0.00024754 106200000 79085 124140 110170 170060 115570 182270 134580 117130 102820 141250 FALSE TRUE 82207.33687 145460.0793 113041.1207 203697.3604 95925.45268 139940.5548 124031.2679 115560.0639 99119.52828 168925.2331 0.486649243 0.861091482 0.669178421 1.205843299 0.567857453 0.828417118 0.73423766 0.684090007 0.586765674 1 17.36602532 LSLDGNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSLDGNPK 8 0 B8ZZZ7;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F8VT91 B8ZZZ7 SPATS2L SPATS2-like protein 0 ;;; 89.298 0.014004 1743860000 82171 3873460 2655970 3618370 1795610 3865340 1806210 2868200 2136460 4894070 FALSE TRUE 85415.17453 4538696.624 2725186.76 4334072.786 1490392.854 2967673.365 1664634.541 2829756.47 2059569.222 5852969.314 0.014593477 0.775451977 0.46560756 0.740491288 0.254638761 0.507037233 0.284408554 0.483473656 0.351884507 1 22.48073728 -1.308917059 3.778509139 1.001358421 0.444757912 0.387459911 0.214045145 136764766.6 203545694 2052782.497 0.047011162 0.049100164 1.308917059 -0.556600509 LSLDSQEGDSGLDS(ph)GTERFPSLSESLMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLDSQEGDSGLDSGTERFPSLSESLMNR 29 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 LSLDSQEGDS(0.008)GLDS(0.923)GT(0.051)ERFPS(0.005)LS(0.007)ES(0.007)LMNR 106.94 0.00027728 26864000 8109 9488.8 6587 8419.9 9755 12473 7347.4 9222.8 9355.1 10906 TRUE FALSE 8429.149582 11118.42759 6758.662631 10085.33109 8096.848584 9576.33478 6771.491589 9099.183451 9018.411778 13042.82189 0.646267322 0.852455679 0.518190211 0.773247628 0.620789631 0.734222614 0.519173814 0.697639171 0.691446364 1 13.67096842 -1.654080972 3.304956951 1.0236042 0.671723936 0.495985402 0.099007155 9727240.716 10046176.95 1558402.558 0.021003553 0.022177829 1.654080972 -0.351880264 LSLEEETLWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLEEETLWLR 11 0 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 109.66 0.002681 0 10604 13713 12261 12534 13326 15853 11802 11951 11678 11161 FALSE TRUE 11022.65411 16068.10108 12580.53173 15013.18779 11060.85128 12171.381 10876.9284 11790.81639 11257.71106 13347.78426 0.825804036 1.203802876 0.94251836 1.124770037 0.828665722 0.911865278 0.81488644 0.883353833 0.843414221 1 13.70431265 3.227253493 24.99992666 0.872233443 1.031214805 0.303483042 0.106130073 220.9480397 488512.9291 0.027654737 0.033331682 1687.537734 -3.227253493 0.158981362 LSLEGDHST(ph)PPSAYGSVK ddPTM_MDA-MB-175_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(0.118)T(0.879)PPS(0.003)AYGSVK;LS(0.001)LEGDHS(0.124)T(0.875)PPSAYGSVK 110.38 0.0012337 277140000 290180 390040 412360 397150 418400 500890 466670 386270 351510 349110 TRUE FALSE 301636.5305 457026.3359 423106.4404 475705.0846 347280.5174 384565.8886 430091.186 381092.6825 338859.2238 417511.4204 0.722462945 1.094643915 1.013400879 1.139382209 0.83178687 0.921090705 1.030130351 0.912771876 0.811616658 1 18.67145614 3.214076658 24.99997352 0.921382108 1.001265536 0.082684949 0.119929518 562.8132915 574673.2255 0.033882599 0.040513951 1637.105463 -3.214076658 0.079883429 LSLFPAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSLFPASPR 9 0 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR;LSLFPAS(1)PR 229.86 1.17E-07 531737000 769610 932250 843997 797036 1024737 1064536 807819 821312 792294 941132 TRUE FALSE 799994.7971 1092356.686 865992.2552 954687.3419 850552.5708 817313.6472 744500.0359 810303.656 763779.4937 1125528.796 0.710772394 0.970527533 0.769409239 0.848212276 0.755691523 0.726159695 0.661466893 0.719931519 0.678596137 1 20.10217154 3.12257492 4.206497568 0.731362207 0.831145213 0.058894132 0.10868775 0.391939284 12.42696673 0.029571585 0.036001184 1326.095864 -3.12257492 0.099783007 LSLFSDGDS(ph)SESEDTLSSSER ddPTM_MDA-MB-175_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(0.989)S(0.01)ES(0.001)EDTLSSSER 228.01 3.41E-35 0 144310 81870 98412 79830 138590 148330 109010 111310 110780 77860 TRUE FALSE 150007.4702 95930.53564 100976.6976 95620.13573 115032.5213 113882.6055 100465.5114 109818.0715 106793.0494 93115.17628 1.610988415 1.030235236 1.084427927 1.026901731 1.235378871 1.223029478 1.0789381 1.179378871 1.146891986 1 16.5067287 4.745181376 24.9553905 1.122121731 1.610988642 0.78108295 0.079127024 345.9832808 1304067.468 0.018970505 0.184135547 55613.64695 -4.745181376 0.488866911 LSLFSDGDSS(ph)ESEDTLSSSER ddPTM_MDA-MB-175_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(0.229)S(0.764)ES(0.007)EDTLSSSER;LSLFSDGDS(0.326)S(0.656)ES(0.019)EDTLSSSER 279.5 6.61E-45 165119000 395656 434350 432867 453446 523960 551760 444540 455520 446180 480888 TRUE FALSE 411276.8044 508946.2337 444147.8696 543136.2654 434897.4664 423622.102 409695.7932 449414.4995 430122.069 575108.7964 0.715128697 0.884956441 0.772284953 0.944406117 0.756200338 0.736594718 0.712379633 0.781442576 0.74789687 1 19.13347538 LSLGTYASLHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLGTYASLHGR 12 0 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 178.53 2.19E-05 461180000 94166 250300 207010 217880 324850 315300 209600 260260 201680 415530 FALSE TRUE 97883.74639 293287.0779 212404.8507 260976.0137 269632.113 242076.3534 193171.0043 256771.6404 194421.5762 496945.1477 0.196970927 0.590179981 0.427421118 0.525160604 0.542579225 0.487128921 0.388716954 0.516700166 0.391233473 1 18.92272709 -1.172170652 3.974348062 1.000259234 0.462376939 0.705623151 0.106028738 70109205.39 137678439 248922.7543 0.023150696 0.067271227 1.172170652 -0.537882295 LSLLSS(ph)TSK ddPTM_MDA-MB-175_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(0.206)S(0.627)T(0.134)S(0.033)K 68.536 0.058376 0 304380 248090 275620 197220 451960 330500 343720 287990 305510 252840 TRUE FALSE 316397.1574 290697.5276 282802.8836 236229.5274 375136.0006 253746.3838 316778.3283 284129.9651 294514.7548 302379.1571 1.046359017 0.96136761 0.935259184 0.781236146 1.240614612 0.839166251 1.047619589 0.939647983 0.973991586 1 18.20599917 4.741345898 21.58500116 0.966868655 1.046359204 0.038326653 0.116251324 143.4098623 1110898.462 0.025489231 0.172188439 55124.65674 -4.741345898 0.079490549 LSLPGLLSQVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLPGLLSQVSPR 13 0 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 1 LSLPGLLS(0.016)QVS(0.984)PR 79.885 0.020236 90768000 168230 146010 167880 169010 204200 213720 169680 154040 186450 143680 TRUE FALSE 174871.8503 171086.0817 172255.0907 202439.6736 169490.1569 164086.769 156380.0382 151975.3458 179739.7009 171831.3451 1.017694707 0.995662821 1.002466056 1.178130064 0.986375081 0.9549292 0.910078648 0.884444836 1.046023942 1 17.39063371 3.00658493 24.99947406 0.945198199 1.046530935 0.292756399 0.063927499 190.2712554 722350.9961 0.019056579 0.022727564 1015.277893 -3.00658493 0.101332737 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 40 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 LSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(1)LVEK 123.02 9.06E-09 288640000 138690 88853 111150 97061 153800 170210 154120 135510 151710 111450 TRUE FALSE 144165.5883 104112.8116 114046.6603 116259.3761 127657.1309 130681.3071 142039.6717 133693.7101 146249.9867 133286.4937 1.081621883 0.781120492 0.85565054 0.872251741 0.957764942 0.980454234 1.065671906 1.003055197 1.097260365 1 17.02417107 2.794400603 1.763117851 1.03765517 0.887262686 0.397996329 0.076951105 0.330388128 2.043221784 0.027790844 0.028311977 622.8745743 -2.794400603 -0.150392485 LSLS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LSLSPLR 7 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 LS(0.011)LS(0.989)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR;LSLS(1)PLR 203.19 0.00030614 6207340000 1754100 2883740 1953470 2390510 3545200 3317170 2099110 2128910 1930230 4453900 TRUE FALSE 1823353.222 3378999.913 2004379.033 2863345.743 2942588.17 2546807.54 1934576.273 2100375.444 1860761.399 5326556.43 0.342313697 0.634368556 0.376299221 0.537560388 0.552437247 0.478133964 0.363194551 0.394321448 0.349336654 1 22.34477171 -1.663363491 3.001724365 1.05366173 0.449813666 0.751667299 0.09525342 81149323.67 78511886.15 33387013.1 0.02350656 0.021708835 1.663363491 -0.603848063 LSLSHS(ph)PSVFSSAQPQDTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLSHSPSVFSSAQPQDTPK 20 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 LS(0.063)LS(0.042)HS(0.653)PS(0.242)VFSSAQPQDTPK;LS(0.002)LS(0.044)HS(0.941)PS(0.012)VFSSAQPQDTPK 161.64 1.43E-11 625980000 145804 293830 308710 283432 381750 436610 311430 349210 313970 303831 TRUE FALSE 151560.4545 344293.0168 316755.2362 339494.0036 316860.2714 335213.9444 287019.3028 344529.4111 302670.281 363360.8673 0.417107257 0.947523654 0.871737341 0.934316362 0.872026407 0.922537275 0.789901524 0.948174232 0.832974347 1 18.47104353 4.742195357 24.99955896 0.89745526 0.417107074 0.859365992 0.058835511 109.4220644 752568.0929 0.012501298 0.092760857 55232.58335 -4.742195357 -0.480348185 LSLT(ph)RSPVSPLAAQGIPLPAQLTK ddPTM_MDA-MB-175_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(0.027)LT(0.637)RS(0.323)PVS(0.013)PLAAQGIPLPAQLTK 166.97 1.99E-11 321790000 443760 398050 505770 293280 589500 629980 321030 463240 532970 601950 TRUE FALSE 461279.9875 466411.9911 518950.7817 351289.9086 489297.0006 483676.6924 295866.8297 457031.0255 513788.5138 719890.5775 0.64076403 0.647892896 0.72087453 0.487976812 0.679682463 0.671875293 0.410988613 0.634861797 0.713703624 1 19.45741811 0.850679336 2.57801748 0.999491659 0.608534405 0.6362311 0.088530732 0.355957826 4.455673662 0.083591594 0.022320026 7.090540397 -0.850679336 -0.390957254 LSLTRS(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLTRSPVSPLAAQGIPLPAQLTK 24 1 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 2 LS(0.081)LT(0.343)RS(0.733)PVS(0.843)PLAAQGIPLPAQLTK;LS(0.039)LT(0.187)RS(0.799)PVS(0.975)PLAAQGIPLPAQLTK 120.37 0.00010063 464640000 477090 449240 541770 266790 759620 649340 375580 513620 553440 686540 TRUE FALSE 495925.8816 526393.4754 555888.9713 319560.2657 630500.0637 498540.6258 346141.0582 506735.764 533521.8025 821054.3684 0.604011014 0.641118902 0.677042828 0.389207193 0.76791512 0.607195632 0.421581166 0.617176869 0.649800821 1 19.64711823 0.704604196 2.378297799 0.999880579 0.588434207 0.572015553 0.10566286 1.134651478 8.187652489 0.097419458 0.026205857 5.065288614 -0.704604196 -0.411446372 LSLTRS(ph)PVSPLAAQGIPLPAQLTK ddPTM_MDA-MB-175_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(0.011)LT(0.053)RS(0.922)PVS(0.014)PLAAQGIPLPAQLTK 202.62 7.80E-25 312920000 499630 487280 582960 326180 693360 710970 392900 522960 596200 743230 TRUE FALSE 519355.7782 570966.5495 598152.4165 390697.4304 575502.9149 545857.9924 362103.4713 515950.5766 574742.8785 888851.6885 0.584299704 0.642364251 0.672949632 0.439553005 0.647467876 0.614115942 0.407383454 0.580468692 0.646612799 1 19.76158319 0.774074125 2.839369202 0.999892406 0.571441905 0.706121536 0.082157404 0.657003804 7.450874191 0.078673789 0.020715095 5.943936004 -0.774074125 -0.428450502 LSLTSDPEEGDPLALGPES(ph)PGEPQPPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSLTSDPEEGDPLALGPESPGEPQPPQLK 29 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 LSLTSDPEEGDPLALGPES(1)PGEPQPPQLK;LSLTSDPEEGDPLALGPES(1)PGEPQPPQLK 92.275 0.00092602 118680000 45116 39052 48387 38727 57585 54882 48946 43936 50396 42737 TRUE FALSE 46897.21452 45758.87722 49648.00497 46387.08501 47796.72227 42136.48724 45109.48462 43347.10978 48582.2578 51110.4969 0.917565224 0.895293139 0.971385684 0.907584309 0.9351645 0.82441944 0.882587479 0.848105818 0.950533858 1 15.641332 4.770062974 19.67520728 0.90376243 0.917565583 0 0.051899821 5571.550588 3478719.611 0.012282348 0.865751133 58892.90458 -4.770062974 0.013803153 LSMEDSKS(ph)PPPK ddPTM_MDA-MB-175_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(0.002)KS(0.998)PPPK;LSMEDS(0.032)KS(0.968)PPPK;LSMEDS(0.001)KS(0.999)PPPK;LSMEDS(0.002)KS(0.998)PPPK;LSMEDS(0.001)KS(0.999)PPPK;LS(0.001)MEDS(0.01)KS(0.989)PPPK;LSMEDS(0.058)KS(0.942)PPPK;LSMEDS(0.012)KS(0.988)PPPK 139.21 3.68E-05 7871520000 11096570 4098100 6686780 4730540 9320280 9221570 10465460 6973190 7949000 3012453 TRUE FALSE 11534671.15 4801916.796 6861042.98 5666226.693 7736022.135 7080000.122 9645149.899 6879725.794 7662917.043 3602685.488 3.201686961 1.332871496 1.90442463 1.572778615 2.147293223 1.965200722 2.677211189 1.909610433 2.12700139 1 21.78064128 LSMEDSKS(ph)PPPKATEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 LSMEDS(0.021)KS(0.973)PPPKAT(0.006)EEK 89.483 0.002107 331070000 960620 278440 469550 210480 823380 649860 623030 425950 562150 196620 TRUE FALSE 998546.0194 326259.904 481786.8587 252112.3158 683422.1617 498939.8637 574195.2806 420240.837 541918.3313 235143.9245 4.246531232 1.387490256 2.048902007 1.072161725 2.906399403 2.121848841 2.441888651 1.787164342 2.304623998 1 17.84318453 -1.72650411 0.254755171 3.69E-31 2.356835539 0.181172608 0.823483546 49.29522328 2.128922839 33.86058412 1.196873677 0.018771367 1.72650411 2.356835539 LSMPQSAAVST(ph)TPPHNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.015)T(0.608)T(0.377)PPHNRR;LSMPQSAAVS(0.215)T(0.745)T(0.04)PPHNRR;LSMPQSAAVS(0.016)T(0.607)T(0.376)PPHNRR 128.26 1.81E-05 860370000 665998 425904 506706 407469 565623 634734 480649 343756 483392 410059 TRUE FALSE 692292.1153 499049.6989 519911.1746 488065.152 469478.6045 487326.648 442974.4754 339148.5131 465994.8163 490402.21 1.411682291 1.017633462 1.060172985 0.995234406 0.957333786 0.993728491 0.90328809 0.691572155 0.950229846 1 18.90360595 8 0.50637719 0.875168723 17.21306843 0.689465421 0.093615393 63.10535666 0.657973943 0.051864742 1100.132049 100000000 -8 16.33789971 LSMPQSAAVSTT(ph)PPHNR ddPTM_MDA-MB-175_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(0.025)T(0.431)T(0.544)PPHNR;LSMPQSAAVST(0.008)T(0.992)PPHNR;LSMPQSAAVST(0.026)T(0.973)PPHNR;LSMPQSAAVST(0.038)T(0.962)PPHNR 189.11 1.37E-09 2690750000 674710 757110 742450 898840 830220 990210 729180 731880 654930 679490 TRUE FALSE 701348.0718 887137.753 761798.8569 1076627.869 689099.5009 760248.7343 672024.9662 722070.3457 631359.1972 812623.0559 0.863066912 1.091696509 0.937456612 1.324879797 0.847994031 0.935549058 0.826982401 0.888567387 0.776939803 1 19.63222677 LSMPQSAAVSTT(ph)PPHNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSMPQSAAVSTTPPHNRR 18 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 LSMPQSAAVS(0.235)T(0.235)T(0.529)PPHNRR;LSMPQSAAVS(0.011)T(0.189)T(0.8)PPHNRR 112.16 0.00021637 435220000 119926 147884 146607 144213 174481 188163 118608 132851 134481 166314 TRUE FALSE 124660.7711 173281.9266 150427.6989 172737.901 144822.7819 144464.9949 109311.195 131070.3496 129641.0551 198900.044 0.626750847 0.871201047 0.756297967 0.868465876 0.728118401 0.726319572 0.549578536 0.658975971 0.651789977 1 17.60168407 2.80753185 2.834756629 0.677656832 0.785119095 0.004437665 0.128245479 0.550466234 8.704485664 0.03970743 0.041377605 641.9953021 -2.80753185 0.107462263 LSMWDRPDDLIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSMWDRPDDLIGR 13 1 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 ; 142.38 3.68E-05 332620000 118593 146172 135966 124736 148257 170614 145955 139793 131013 148412 FALSE TRUE 123275.1432 171275.9039 139509.3857 149408.4085 123056.3281 130991.4842 134514.6657 137919.3035 126297.8677 177490.4899 0.694545062 0.964986372 0.786010483 0.841782614 0.693312234 0.738019734 0.757869708 0.777051793 0.711575408 1 17.4373822 5.03869201 16.33005945 0.794720098 0.265438672 0.094808289 0.097725547 11275251.57 129701392.7 0.022040561 176970223.3 109318.0837 -5.03869201 -0.529281426 LSNHISSLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSNHISSLFR 10 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 194.17 4.93E-07 3678900000 63730 1535850 988950 1342290 1822200 2384700 896820 1432600 911360 3859500 FALSE TRUE 66246.10961 1799620.29 1014722.849 1607790.956 1512463.095 1830889.565 826524.905 1413398.34 878560.3316 4615695.13 0.014352358 0.389891498 0.219841827 0.348331272 0.327678292 0.396666052 0.179068349 0.306215705 0.190341933 1 22.13811651 -1.841315188 2.553167631 1.285938887 0.273158679 0.796960564 0.11141441 14170453.57 8997734.134 24760946.39 0.024725113 0.014410691 1.841315188 -1.012780207 LSNRPAFMPSEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSNRPAFMPSEGK 13 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 179.56 1.24E-05 3814200000 2497600 2183300 2189300 2115800 3114400 3251100 3195600 2244700 2219400 2682400 FALSE TRUE 2596207.177 2558264.791 2246354.957 2534298.925 2585015.4 2496081.296 2945120.522 2214613.468 2139524.228 3207964.922 0.809300363 0.797472807 0.700242992 0.790002069 0.805811617 0.778088712 0.918065064 0.690348405 0.666941279 1 21.61322694 3.508315328 24.31400735 0.793943207 0.767397209 0.019600646 0.09606734 3005.336162 2342478.652 0.025062703 0.038771631 3223.408363 -3.508315328 -0.026545999 LSPDAIPGKWTSQDSLLGMEFSGR ddPTM_MDA-MB-175_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 ; 195.27 4.01E-19 522730000 224869 317710 334714 180265 501600 392310 138785 287964 321490 644710 FALSE TRUE 233747.0018 372274.2211 343436.9218 215920.879 416338.2112 301201.948 127906.6691 284104.3136 309919.6377 771028.5808 0.303162564 0.482828043 0.445426966 0.28004264 0.539977663 0.390649524 0.165890957 0.368474426 0.401956095 1 19.55642481 0.675866883 3.951519975 0.99999838 0.371470405 0.775404577 0.100962575 4.060612031 49.07637979 0.097950148 0.025039715 4.740966461 -0.675866883 -0.628527975 LSPEDYTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPEDYTLK 9 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;H7C469;H7C1V0;A0A1B0GVF1 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 96.367 0.017254 320480000 253530 148010 173770 167440 286030 265180 229080 193190 204680 166350 FALSE TRUE 263539.5602 173429.5661 178298.589 200559.1322 237410.7228 203595.9638 211124.111 190600.604 197313.6068 198943.0975 1.324698185 0.871754629 0.896229078 1.0081231 1.193359939 1.023387925 1.061228631 0.958065931 0.991809262 1 17.60199632 1.184521326 0.009322415 2.00E-07 2.019000468 0.038271053 0.126129888 6738.021961 51.0839271 5572.216177 5483.961943 15.29400846 -1.184521326 2.019000268 LSPFFTLDLS(ph)PTEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPFFTLDLSPTEDK 15 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 LSPFFTLDLS(0.993)PT(0.007)EDK;LSPFFTLDLS(0.983)PT(0.017)EDK 157.42 2.05E-06 141963000 408660 234189 317913 264524 400720 457900 474910 354930 380970 232051 TRUE FALSE 424794.2124 274409.139 326198.0739 316846.0577 332605.7575 351559.6645 437685.3133 350172.7439 367258.9641 277516.9506 1.530696455 0.988801363 1.175416757 1.141717856 1.198506098 1.266804294 1.577148035 1.261806687 1.323374891 1 18.08221637 2.594808515 4.642757714 1.327181411 1.190486926 0.024106236 0.182732107 0.509897348 17.21765133 0.057226257 0.0534301 393.3765935 -2.594808515 -0.136694485 LSPFVLSAGSGS(ph)PSATSILQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPFVLSAGSGSPSATSILQK 21 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-4 SYNRG Synergin gamma 1 LSPFVLSAGS(0.065)GS(0.934)PS(0.001)ATSILQK 146.78 1.11E-07 153380000 475350 289920 375240 350420 524420 566500 498160 438430 473150 280290 TRUE FALSE 494117.1851 339711.5047 385019.0627 419732.0301 435279.2757 434938.9604 459112.9175 432553.563 456121.4239 335207.459 1.474063813 1.013436592 1.148599329 1.252155997 1.298536963 1.297521725 1.36963813 1.290405542 1.360713826 1 18.35469473 3.504924528 4.788023842 1.291406965 1.192429108 0.011850943 0.144657853 0.487668004 28.33622231 0.036913146 0.055520479 3198.339251 -3.504924528 -0.098977857 LSPLEACAHSFFDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSPLEACAHSFFDELR 16 0 P49840;A8MT37 P49840 GSK3A Glycogen synthase kinase-3 alpha 0 ;;; 230.16 2.51E-15 773861000 365898 577190 500886 514756 509897 668634 437493 461162 472882 709410 FALSE TRUE 380343.9356 676317.8926 513939.5006 616573.2004 423224.8901 513353.8867 403201.1555 454980.8777 455863.0692 848405.307 0.448304522 0.797163675 0.6057712 0.726743686 0.498847528 0.605080947 0.475245914 0.536277737 0.53731756 1 19.69439412 -1.588049714 5.53435676 1.002190303 0.582761904 0.592325081 0.104226918 0.002773677 0.000206459 0.099373116 0.023318388 0.025819646 1.588049714 -0.419428398 LSPS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 LS(0.14)PS(0.855)PS(0.004)SR;LSPS(0.847)PS(0.152)S(0.001)R;LS(0.003)PS(0.969)PS(0.028)SR;LS(0.003)PS(0.988)PS(0.009)SR;LS(0.004)PS(0.986)PS(0.01)SR 168.9 0.00031902 7797710000 4973360 5975120 5393610 5535300 5789250 6753810 5739160 5604240 4957060 5517510 TRUE FALSE 5169712.093 7001300.38 5534171.907 6630165.819 4805195.353 5185339.982 5289309.643 5529124.329 4778656.379 6598560.445 0.783460595 1.061034515 0.838693826 1.004789738 0.728218737 0.785828974 0.801585389 0.837928875 0.724196803 1 22.65371989 3.238058016 24.99998991 0.805286621 0.925976021 0.212382746 0.10211141 17.86651321 888724.1007 0.026353401 0.033373947 1730.047454 -3.238058016 0.1206894 LSPS(ph)PTSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;LS(0.001)PS(0.999)PTSQR;LSPS(1)PTSQR;LSPS(1)PTSQR;LS(0.003)PS(0.989)PT(0.007)S(0.001)QR;LS(0.019)PS(0.98)PT(0.001)SQR 267.31 1.25E-15 60686190000 5876450 6109730 5960290 5764410 6209920 6949710 5686060 5618700 5327860 5841670 TRUE FALSE 6108456.784 7159028.6 6115620.054 6904593.093 5154360.017 5335745.176 5240371.759 5543390.517 5136111.359 6986233.391 0.874356243 1.024733673 0.875381584 0.988314118 0.737788122 0.763751349 0.750099727 0.793473422 0.735176034 1 22.73608341 3.238203839 24.9999904 0.782429559 0.942033733 0.405687136 0.084310526 7.881468669 552286.948 0.021649972 0.027441978 1730.628451 -3.238203839 0.159604173 LSPS(ph)PTTEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSPSPTTEDPR 11 0 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 LS(0.003)PS(0.905)PT(0.068)T(0.024)EDPR 77.74 0.033346 304240000 162630 169010 206660 217420 207970 246500 221370 178830 204280 167870 TRUE FALSE 169050.758 198036.1528 212045.7294 260425.0271 172619.3337 189254.1107 204018.441 176433.0764 196928.0027 200760.9124 0.842050158 0.986427838 1.056210229 1.297189896 0.859825409 0.942684054 1.01622591 0.878821849 0.980908088 1 17.61511888 LSPWIRPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSPWIRPDSK 10 1 O14744-2;O14744;G3V580;O14744-4;G3V5L5;G3V2L6;G3V2X6;C9JSX3 O14744-2 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 0 ; 105.46 0.0023221 1527780000 1870250 1550690 1740310 1508070 2442700 2464000 2113910 1970600 2045420 1693240 FALSE TRUE 1944088.914 1817008.945 1785663.908 1806361.745 2027490.727 1891773.342 1948216.211 1944187.33 1971805.734 2024997.959 0.960044876 0.897289272 0.881810226 0.89203139 1.001230998 0.93421 0.962083049 0.960093476 0.973732208 1 20.94948902 3.250992911 24.99982975 0.966891704 0.905187618 0.571819137 0.026927438 168.0591365 337944.504 0.007326601 0.009850352 1782.349676 -3.250992911 -0.061704087 LSQELEYLTEDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSQELEYLTEDVKR 14 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ;;; 245.19 1.96E-17 302270000 324223 265602 290922 240316 385120 376923 348688 308844 350025 254881 FALSE TRUE 337023.5744 311217.0774 298503.6663 287849.7875 319657.44 289388.3456 321356.9234 304704.4513 337427.6686 304820.052 1.105647651 1.020986236 0.979278313 0.944326942 1.048675892 0.949374373 1.054251259 0.999620758 1.106973332 1 18.21759829 LSQSSQDSS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSQSSQDSSPVR 12 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 LSQSSQDSS(1)PVR;LSQSSQDSS(1)PVR;LSQSSQDSS(1)PVR;LSQSSQDSS(1)PVR;LSQSSQDS(0.177)S(0.823)PVR;LSQSSQDS(0.028)S(0.971)PVR 297.72 2.53E-36 4551230000 4308719 4794040 4585080 4450640 4850650 5536510 4405210 4714080 4302530 4486760 TRUE FALSE 4478830.553 5617379.078 4704570.951 5330963.308 4026138.246 4250739.459 4059918.129 4650895.468 4147682.786 5365854.718 0.834690984 1.046874985 0.876760777 0.993497511 0.750325616 0.792183106 0.756620957 0.866757621 0.772977094 1 22.35537656 3.24175336 24.99889172 0.814118262 0.941364898 0.289644824 0.087335759 90.3386087 707336.9763 0.022501814 0.029234661 1744.830965 -3.24175336 0.127246636 LSQSVIDGVTVLGGQFHDYGLLTTPQLHYMVYCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSQSVIDGVTVLGGQFHDYGLLTTPQLHYMVYCR 34 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 129.9 2.94E-08 499270000 48237 46181 51568 51284 57715 64586 44113 60710 50955 58435 FALSE TRUE 50141.43401 54112.22751 52911.90444 61427.82213 47904.62492 49586.88031 40655.30779 59896.28175 49121.1395 69884.21944 0.717492939 0.774312541 0.757136659 0.87899418 0.685485583 0.709557618 0.581752334 0.857078783 0.702893155 1 16.0926791 -1.339553632 3.094751052 1.002299607 0.744858983 0.479896926 0.080925265 65305791.19 81423733.24 1358629.984 0.019015387 0.045755823 1.339553632 -0.257440624 LSQYLDSSQVKPLFQFFVPDALNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSQYLDSSQVKPLFQFFVPDALNDR 25 1 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 164.96 1.46E-11 444990000 377980 280260 388550 434690 410470 472320 473730 371970 379170 263750 FALSE TRUE 392902.9423 328392.4749 398675.9322 520670.3846 340698.456 362630.8381 436597.8047 366984.3506 365523.7458 315426.7627 1.245623355 1.041105301 1.263925511 1.650685503 1.080119052 1.149651459 1.384149528 1.163453435 1.158822868 1 18.26694555 0.967132846 1.429193766 1.002506955 1.25454052 0.18576914 0.163045456 0.806697589 3.352649312 0.155629096 0.046389165 9.271133749 -0.967132846 0.252033565 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSQYLDSSQVKPLFQFFVPDALNDRHPDVR 30 2 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 289.88 4.75E-81 244840000 202660 170620 224810 197680 234890 264310 180900 182440 228370 195560 FALSE TRUE 210661.1733 199922.6578 230668.7333 236780.514 194963.4817 202928.0082 166720.5853 179994.6902 220151.0083 233876.2378 0.900737823 0.854822447 0.986285462 1.012418005 0.833618172 0.867672621 0.712858163 0.769615126 0.941314134 1 17.83538576 3.146072708 9.744423385 0.828554887 0.935887732 0.146206053 0.087585912 0.452917803 43.74052068 0.025835955 0.030909047 1399.821657 -3.146072708 0.107332845 LSS(ph)ATANALYSSNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSATANALYSSNLR 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LSS(1)ATANALYSSNLR;LSS(1)ATANALYSSNLR;LS(0.005)S(0.995)ATANALYSSNLR;LSS(1)ATANALYSSNLR 405.46 6.69E-133 657650000 738670 746880 834230 994310 1181820 1277800 1103140 1025600 916640 989490 TRUE FALSE 767833.262 875150.8301 855970.7191 1190981.55 980934.6585 981050.3152 1016673.004 1011853.51 883650.3055 1183361.621 0.648857668 0.739546403 0.723338246 1.006439223 0.828939051 0.829036787 0.859139748 0.855067033 0.746728887 1 20.17445958 3.943066631 14.9327833 0.863945054 0.703506418 0.506838158 0.077062608 3.146445176 824.8984606 0.018788816 0.033885316 8771.353831 -3.943066631 -0.160438636 LSS(ph)ATANALYSSNLRDDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSATANALYSSNLRDDTK 19 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 LS(0.025)S(0.962)AT(0.006)ANALYS(0.003)S(0.003)NLRDDTK;LS(0.048)S(0.95)AT(0.003)ANALYSSNLRDDTK 110.94 0.00013679 247680000 177242 138017 162233 130068 262734 203523 177694 195937 194755 151291 TRUE FALSE 184239.651 161720.3461 166460.9253 155795.0622 218074.5685 156257.8677 163765.88 193310.785 187745.8056 180933.5748 1.01827232 0.893810595 0.920011255 0.861062201 1.205274194 0.863620076 0.905116036 1.068407482 1.037650452 1 17.46510062 1.719227515 10.21227859 1.038707381 0.95177582 0.133017634 0.09676756 0.204938758 60.58387816 0.045390601 0.024582909 52.38748087 -1.719227515 -0.086931561 LSS(ph)GFDDIDLPSAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSGFDDIDLPSAVK 15 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 LS(0.024)S(0.976)GFDDIDLPSAVK;LS(0.021)S(0.979)GFDDIDLPSAVK;LS(0.096)S(0.904)GFDDIDLPSAVK;LS(0.022)S(0.978)GFDDIDLPSAVK 331.42 7.32E-69 2339620000 834950 458598 1032330 496039 1794790 873370 908240 836800 1198030 864240 TRUE FALSE 867914.4707 537358.6391 1059233.368 594154.0337 1489712.237 670543.0536 837049.7756 825584.0647 1154913.134 1033571.281 0.839723865 0.51990477 1.02482856 0.574855401 1.441325107 0.64876324 0.809861681 0.798768387 1.117400566 1 19.97920646 4.232423625 24.99966398 0.90413553 0.679814312 0.134407862 0.245475842 265.4295474 1081271.436 0.057370073 0.129090532 17077.47367 -4.232423625 -0.224321219 LSS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSLPR 6 0 Q63ZY3-3;Q63ZY3;Q63ZY3-2;K7ES05 Q63ZY3-3 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 LS(0.376)S(0.624)LPR 107.59 0.032658 123350000 213640 235040 235500 268300 352520 381870 309960 319010 298520 280410 TRUE FALSE 222074.6722 275406.2916 241637.3235 321368.9392 292598.7763 293186.4798 285664.5253 314734.1927 287776.3235 335350.9707 0.662215683 0.821247933 0.720550541 0.958306274 0.872515072 0.874267575 0.851837478 0.938521788 0.858134756 1 18.35531225 6.070554815 0.438618435 0.91760554 6.55E-15 0.611092193 0.061021864 10.31610183 0.621712531 0.03724717 6.308373635 1176399.456 -6.070554815 -0.91760554 LSS(ph)LRAS(ph)TSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.453)S(0.547)LRAS(0.915)T(0.059)S(0.025)K;LS(0.307)S(0.693)LRAS(0.954)T(0.038)S(0.008)K;LS(0.15)S(0.85)LRAS(0.971)T(0.025)S(0.004)K 141 2.18E-05 4340570000 5073760 2983100 4377030 3569510 6341810 5579420 5857330 4450010 4230490 2077940 TRUE FALSE 5274075.963 3495424.22 4491098.998 4275548.424 5263831.401 4283684.262 5398217.169 4390364.895 4078235.491 2485072.558 2.122302604 1.406568274 1.80723053 1.720492389 2.118180165 1.723766273 2.172257366 1.766694852 1.641093125 1 21.24485655 0.803428316 2.149805301 1.001062174 1.851128072 0.577487568 0.220413662 0.503556259 4.00312928 0.200030532 0.054760473 6.359578264 -0.803428316 0.850065898 LSS(ph)LRAS(ph)TSKSESSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSLRASTSKSESSQK 16 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 LS(0.016)S(0.984)LRAS(0.912)T(0.077)S(0.012)KSESSQK;LS(0.461)S(0.539)LRAS(0.811)T(0.141)S(0.026)KS(0.016)ES(0.003)S(0.003)QK;LS(0.46)S(0.54)LRAS(0.781)T(0.149)S(0.036)KS(0.033)ESSQK;LS(0.457)S(0.543)LRAS(0.846)T(0.137)S(0.017)KS(0.001)ESSQK 175.85 1.66E-08 2290150000 2995320 1526530 2549350 1202230 4530590 3062050 2322900 2365280 2761950 1310120 TRUE FALSE 3113577.546 1788699.653 2615788.155 1440027.506 3760481.93 2350935.293 2140825.028 2333577.29 2662547.959 1566812.93 1.987204398 1.141616602 1.66949615 0.919080688 2.400083544 1.500456913 1.366356498 1.489378371 1.699340047 1 20.57940151 -0.989361688 7.175598698 0.999999969 1.553409839 0.158768179 0.394163148 1.78E-07 2.55E-08 0.351412905 0.082828811 0.10247981 0.989361688 0.55340987 LSS(ph)PAAFLPACNS(ph)PSK ddPTM_MDA-MB-175_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 2 LS(0.094)S(0.906)PAAFLPACNS(0.998)PS(0.002)K;LS(0.441)S(0.559)PAAFLPACNS(0.973)PS(0.027)K 188.96 1.60E-09 65354000 163707 94572 120627 108389 141338 169059 177185 129916 131004 64970 TRUE FALSE 170170.2788 110814.0053 123770.6387 129828.0207 117313.4172 129797.6094 163296.7767 128174.6885 126289.1916 77699.62757 2.190104175 1.426184511 1.592937348 1.670896306 1.509832427 1.67050491 2.101641691 1.649617798 1.625351312 1 16.24562006 0.680194388 2.420625677 1.000177219 1.715403451 0.472676424 0.228744626 1.764776722 12.23930407 0.211794151 0.056812569 4.788443731 -0.680194388 0.715226232 LSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSPER 6 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061;Q8TDZ2-3;Q8TDZ2-2;Q8TDZ2;Q8TDZ2-4 O14579;Q8TDZ2-2 COPE;MICAL1 Coatomer subunit epsilon;Protein-methionine sulfoxide oxidase MICAL1 1 LS(0.074)S(0.926)PER;LS(0.081)S(0.919)PER;LS(0.065)S(0.935)PER;LS(0.061)S(0.939)PER 108.09 0.032216 1080660000 1231480 1400950 1452740 1360690 1592510 1852650 1532750 1472790 1474770 1501670 TRUE FALSE 1280099.781 1641552.265 1490599.598 1629830.421 1321815.719 1422400.115 1412609.05 1453049.659 1421693.316 1795893.485 0.712792708 0.914058811 0.830004457 0.907531785 0.736021223 0.792029219 0.786577301 0.809095679 0.791635655 1 20.77627036 -1.242927539 3.510734982 1.00041094 0.811708088 0.470418844 0.060773271 19419419.87 27216128.12 84412.97667 0.014008574 0.0571574 1.242927539 -0.188702852 LSS(ph)PGPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSPGPSR 8 0 Q86VQ6;H0YBI6;H0YBQ0 Q86VQ6 TXNRD3 Thioredoxin reductase 3 1 LS(0.031)S(0.969)PGPSR;LS(0.025)S(0.975)PGPSR 120.33 0.0020606 226320000 1703780 1604730 1865260 1712420 2192100 2400400 2066870 1864070 1920930 1622540 TRUE FALSE 1771046.55 1880329.894 1913870.208 2051131.565 1819487.625 1842943.478 1904863.329 1839085.191 1851796.105 1940445.648 0.912700931 0.969019615 0.986304466 1.057041493 0.937664823 0.949752692 0.981662811 0.947764341 0.954314854 1 20.88795659 3.056551643 0.001363721 1.937206558 9.94E-06 0.024882103 0.037415956 1778058.805 789.2910113 558024.6363 563175.6476 1139.073222 -3.056551643 -1.93719662 LSS(ph)PISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSPISK 7 0 A0A494C142;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 LS(0.04)S(0.96)PISK;LSS(1)PISK;LS(0.031)S(0.969)PISK 138.26 0.0029403 240172000 1449900 1020370 1294110 1082030 1518030 1686400 1736950 1371680 1412770 867600 TRUE FALSE 1507143.172 1195610.61 1327835.57 1296052.304 1259995.803 1294759.158 1600803.32 1353294.873 1361924.684 1037589.609 1.452542661 1.152296245 1.279730983 1.249099156 1.214348903 1.247852857 1.542809707 1.304267951 1.312585122 1 19.98480451 LSS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSSPVK 6 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 LS(0.063)S(0.937)PVK;LS(0.024)S(0.976)PVK;LSS(1)PVK;LS(0.056)S(0.944)PVK;LS(0.009)S(0.991)PVK 134.3 0.014784 2282600000 8497940 4778030 6853740 5053290 7261650 8228030 9722680 7176570 7234810 3527010 TRUE FALSE 8833445.233 5598619.485 7032354.095 6052815.679 6027317.327 6317194.73 8960590.936 7080379.818 6974430.601 4218060.081 2.094196162 1.327297236 1.667201026 1.434976165 1.428931123 1.497654042 2.124339332 1.678586763 1.653468767 1 22.00814821 LSS(ph)PVLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSSPVLHR 8 0 Q16643;Q16643-3;Q16643-2;D6R9W4;D6RCR4 Q16643 DBN1 Drebrin 1 LS(0.049)S(0.951)PVLHR;LS(0.117)S(0.883)PVLHR;LS(0.042)S(0.958)PVLHR;LS(0.022)S(0.978)PVLHR;LS(0.003)S(0.997)PVLHR 152.37 0.00029512 6760150000 1206900 1378000 1410160 1285129 1549110 1666380 1408280 1409630 1359730 1267528 TRUE FALSE 1254549.344 1614660.781 1446909.928 1539323.68 1285792.836 1279388.499 1297895.334 1390736.216 1310793.583 1515875.843 0.827606924 1.065166905 0.954504245 1.015468178 0.848217775 0.843992933 0.856201607 0.917447311 0.864710384 1 20.53172016 3.234957026 24.99799617 0.882437437 0.971993566 0.216714998 0.071009074 117.8467396 817500.9063 0.018982848 0.023549641 1717.738406 -3.234957026 0.089556129 LSS(ph)SASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSASR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.097)S(0.736)S(0.167)ASR 91.069 0.017492 89243000 188880 243230 226540 235930 246250 276400 285310 244560 230070 256480 TRUE FALSE 196337.1282 285002.8604 232443.8185 282596.2498 204392.513 212210.2889 262946.6567 241282.0732 221789.8256 306732.3454 0.640092678 0.929158156 0.757806674 0.921312193 0.666354612 0.691841901 0.857251153 0.786620899 0.723072832 1 18.22662078 -1.855133485 3.626675797 1.065127939 0.781650995 0.328540578 0.096125614 0.047379938 0.001892578 0.08711696 0.020471841 0.013959392 1.855133485 -0.283476944 LSS(ph)SLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LS(0.016)S(0.8)S(0.184)LGR 118.5 0.005238 242520000 489680 511100 551080 470900 654580 631410 538470 535180 536580 585950 TRUE FALSE 509012.9445 598877.4492 565441.5975 564042.6145 543314.7254 484774.5966 496263.3144 528006.7875 517268.5906 700755.6838 0.72637719 0.854616613 0.80690262 0.804906228 0.775326891 0.691788319 0.708183074 0.75348199 0.738158252 1 19.41855202 -1.171451987 3.835104767 1.000145243 0.762742883 0.694846932 0.047276764 3315092.246 1518921.232 4157.643398 0.012025852 0.067382639 1.171451987 -0.23740236 LSS(ph)SSATLLNSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LS(0.002)S(0.493)S(0.493)S(0.012)ATLLNSPDR 169.8 3.43E-06 114420000 203240 245470 240110 249480 307090 260420 192350 216830 233570 293200 TRUE FALSE 211264.0721 287627.563 246367.4639 298826.3994 254890.9515 199941.4017 177273.1044 213923.7485 225163.8613 350646.9263 0.602498001 0.820276869 0.702608366 0.852214512 0.726916258 0.570207199 0.505560126 0.610083056 0.642138414 1 18.41965956 -1.256359016 3.554064745 1.000751957 0.668146651 0.479774436 0.102980642 30686161.69 54114443.9 259184.2268 0.027513984 0.055416741 1.256359016 -0.332605306 LSS(ph)TDDGYIDLQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSTDDGYIDLQFK 14 0 Q96A57;Q96A57-2;Q5JWB9;A0A087WTT2 Q96A57 TMEM230 Transmembrane protein 230 1 LSS(0.999)T(0.001)DDGYIDLQFK;LS(0.012)S(0.985)T(0.003)DDGYIDLQFK 305.98 1.97E-44 203436000 258020 190527 266730 216380 404710 358630 353090 258432 336210 211423 TRUE FALSE 268206.8288 223248.5302 273681.2029 259179.3182 335917.5388 275343.6176 325413.8832 254968.1417 324109.8678 252847.2889 1.060746311 0.8829382 1.082397221 1.0250429 1.328539215 1.088971999 1.286997715 1.00838788 1.281840391 1 17.94790678 3.442993097 24.88129881 1.161593083 1.005718472 0.291250339 0.11700317 205.3589637 149717.335 0.030299291 0.041025633 2773.276024 -3.442993097 -0.155874611 LSS(ph)TDSLESLLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSTDSLESLLSK 13 0 Q9Y450-2 Q9Y450-2 HBS1L HBS1-like protein 1 LS(0.024)S(0.952)T(0.024)DSLESLLSK 107.65 0.0013413 7489500 58940 23113 34080 24620 51772 52826 43062 33511 45662 27261 TRUE FALSE 61266.99671 27082.47796 34968.1528 29489.76252 42971.81393 40557.96209 39686.68792 33061.83986 44018.63354 32602.27101 1.879224815 0.830692989 1.072568006 0.90453093 1.318061982 1.244022604 1.217298265 1.014096222 1.350170776 1 14.99268484 4.751836163 24.95012864 1.110432262 1.87922533 0.663161007 0.165351285 1319.069373 2479020.69 0.038959889 0.754054925 56472.38937 -4.751836163 0.768793068 LSS(ph)TS(ph)SEETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.003)S(0.997)T(0.009)S(0.968)S(0.024)EETQLFHIPR 228.33 6.15E-15 37314000 84981 97430 82461 87522 102890 128430 87278 87310 84271 96891 TRUE FALSE 88336.1155 114162.8446 84610.0014 104833.5904 85400.79455 98604.07888 80436.9223 86139.75226 81238.10317 115874.9364 0.762340143 0.985224658 0.7301838 0.904713251 0.73700834 0.850952604 0.694170153 0.743385541 0.701084339 1 16.82220902 3.227075345 24.99857139 0.769567028 0.847342437 0.049799278 0.107283522 471.1065195 1025397.542 0.028633908 0.03450617 1686.845648 -3.227075345 0.077775409 LSS(ph)TSS(ph)EETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 LS(0.162)S(0.832)T(0.011)S(0.13)S(0.865)EETQLFHIPR;LS(0.384)S(0.615)T(0.022)S(0.501)S(0.478)EETQLFHIPR 155.49 1.34E-07 335030000 170041 220683 212668 229767 242943 318036 236172 226113 215334 228151 TRUE FALSE 176754.35 258583.5886 218210.3028 275214.2268 201647.6356 244176.9589 217660.2215 223082.3251 207584.1714 272852.8202 0.647801074 0.947703558 0.799736292 1.008654507 0.739034456 0.894903555 0.797720256 0.817592154 0.760791738 1 18.05776343 -2.499978122 2.247100639 3.26223721 0.829789054 0.219318565 0.099163287 2969067.143 407209.4166 34343352.18 0.022429039 0.003162437 2.499978122 -2.432448157 LSS(ph)TSSEETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LS(0.002)S(0.984)T(0.013)SSEETQLFHIPR;LS(0.045)S(0.899)T(0.045)S(0.01)S(0.001)EETQLFHIPR 149 9.20E-07 79250000 68718 79084 75156 84851 87829 114363 85199 82753 86506 82778 TRUE FALSE 71431.0397 92666.06181 77114.6271 101634.2745 72899.85795 87803.92644 78520.87975 81643.83139 83392.66596 98996.76422 0.721549237 0.936051421 0.778961087 1.026642389 0.73638627 0.886937337 0.793166124 0.824712121 0.842377694 1 16.59509375 0.893172685 17.68799625 1 0.840356018 0.232911509 0.087861116 6915.68855 1145079.571 0.075554589 0.018888647 7.819386584 -0.893172685 -0.159643982 LSSAGPRS(ph)PYCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSAGPRSPYCK 12 1 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 LSS(0.001)AGPRS(0.945)PY(0.054)CK;LSS(0.001)AGPRS(0.995)PY(0.004)CK;LSS(0.001)AGPRS(0.998)PYCK;LSSAGPRS(1)PYCK 112.68 0.00075538 1593090000 1294570 1064730 1173400 934650 1442230 1531660 1324010 1266580 1229840 976470 TRUE FALSE 1345680.623 1247589.095 1203979.768 1119520.98 1197080.26 1175955.178 1220230.637 1249603.567 1185578.299 1167790.601 1.152330411 1.068332879 1.030989432 0.95866586 1.025081259 1.006991473 1.044905341 1.070057908 1.015231924 1 20.15535017 4.644519001 2.204337082 1.023030001 1.171379738 0.683721182 0.027834044 0.332996039 2.167217533 0.007953578 0.089203528 44108.16605 -4.644519001 0.148349737 LSSAHNGGSAFGAAGYGGAQPT(ph)PPMPTRPVSFHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.884)PPMPT(0.041)RPVS(0.076)FHER;LSSAHNGGSAFGAAGYGGAQPT(0.799)PPMPT(0.126)RPVS(0.075)FHER 324.47 2.11E-105 715680000 61578 184216 154674 146226 159665 204229 126599 158951 122602 179018 TRUE FALSE 64009.14699 215853.665 158704.9315 175149.0664 132525.2003 156799.9099 116675.8396 156820.5218 118189.578 214093.1496 0.298978025 1.008223128 0.741289162 0.818097481 0.619007197 0.732391065 0.544976987 0.732487341 0.552047453 1 17.70787911 -1.334986477 3.107834492 1.002678536 0.686394038 0.22840754 0.17912384 33342971.13 43264193.84 819688.1636 0.042183241 0.046239542 1.334986477 -0.316284499 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVS(ph)FHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 35 1 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 LSSAHNGGSAFGAAGYGGAQPT(0.085)PPMPT(0.108)RPVS(0.807)FHER;LSSAHNGGSAFGAAGYGGAQPT(0.004)PPMPT(0.177)RPVS(0.819)FHER 262.55 2.61E-60 771350000 37194 140410 127165 132117 119592 171818 110394 155373 123838 153795 TRUE FALSE 38662.44784 164524.3253 130479.0244 158249.3483 99263.79456 131915.8734 101741.0298 153290.4791 119381.0946 183928.1857 0.210204041 0.894503062 0.709402009 0.860386611 0.539687782 0.71721402 0.553156274 0.833425712 0.649063623 1 17.48878305 -5 0.18029843 2.296175373 0.614252446 0.239479786 0.187322602 201.5815701 1.942725459 93.72676059 0.543120189 1.00E-05 5 -1.681922927 LSSCDSFTSTINELNHCLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSCDSFTSTINELNHCLSLR 21 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 297 6.47E-55 660750000 364600 414250 409590 462780 486330 517400 493990 496170 437210 346830 FALSE TRUE 378994.6895 485394.2151 420264.2519 554316.5027 403663.8003 397241.6913 455269.773 489519.6527 421474.8975 414784.698 0.913714251 1.170231731 1.013210598 1.336395738 0.973188746 0.957705752 1.097605035 1.180177704 1.01612933 1 18.66200315 1.026166529 24.78676373 0.999999723 1.087953031 0.052936453 0.119654876 458.5350164 434354.4541 0.110688102 0.027672026 10.62102739 -1.026166529 0.087953308 LSSERPS(ph)SDGEGVVENGITTCNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSERPSSDGEGVVENGITTCNGK 24 1 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 LS(0.027)S(0.027)ERPS(0.473)S(0.473)DGEGVVENGITTCNGK 110.17 0.0012212 231290000 66102 67410 70454 52509 80005 99635 82551 70638 85598 50930 TRUE FALSE 68711.758 78987.14312 72290.08912 62895.12348 66405.77868 76496.28123 76080.43691 69691.21315 82517.3447 60908.75839 1.128109648 1.296810922 1.186858689 1.032612142 1.09025008 1.255915951 1.249088619 1.144190343 1.354769772 1 15.89436208 2.730396281 24.83635016 1.208111265 1.151122566 0.057219422 0.106607354 1805.402801 5492122.03 0.033967438 0.032556131 537.522046 -2.730396281 -0.0569887 LSSESHHGGS(ph)PIHWVLPAGMSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LSSESHHGGSPIHWVLPAGMSAK 23 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.004)S(0.004)ES(0.013)HHGGS(0.979)PIHWVLPAGMSAK;LS(0.008)S(0.008)ES(0.034)HHGGS(0.95)PIHWVLPAGMSAK;LS(0.003)S(0.003)ES(0.018)HHGGS(0.976)PIHWVLPAGMSAK;LS(0.005)S(0.005)ES(0.031)HHGGS(0.958)PIHWVLPAGMSAK;LS(0.001)S(0.001)ES(0.004)HHGGS(0.994)PIHWVLPAGMSAK;LSSESHHGGS(1)PIHWVLPAGMSAK;LS(0.011)S(0.011)ES(0.093)HHGGS(0.885)PIHWVLPAGMSAK;LS(0.014)S(0.014)ES(0.119)HHGGS(0.854)PIHWVLPAGMSAK 229.76 8.09E-33 14031040000 1336927 7810740 8322990 8295560 8659700 10929450 7825220 9807760 8508110 8139600 TRUE FALSE 1389709.91 9152173.836 8539893.957 9936397.008 7187727.287 8391250.875 7211858.809 9676303.019 8201904.783 9734398.778 0.142762788 0.940188916 0.877290334 1.020750971 0.738384306 0.862020456 0.740863301 0.994031911 0.84256922 1 23.21466045 4.741077307 24.92686431 0.886562334 0.142762514 0.84672016 0.095450951 76.66776724 759319.079 0.021754167 0.147786474 55090.57525 -4.741077307 -0.743799819 LSSFTSY(ph)ENPT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSFTSYENPT 11 0 Q13882 Q13882 PTK6 Protein-tyrosine kinase 6 1 LSSFT(0.022)S(0.047)Y(0.931)ENPT;LSSFT(0.007)S(0.441)Y(0.552)ENPT;LSS(0.001)FT(0.141)S(0.094)Y(0.764)ENPT 198.25 5.60E-07 588998000 511905 630020 621970 632460 716070 815470 648130 683350 635290 657860 TRUE FALSE 532115.4047 738221.0341 638179.0492 757558.7003 594352.6772 626089.4511 597327.877 674190.811 612426.037 786755.0715 0.676341881 0.938311122 0.811153397 0.962890139 0.755448168 0.795786991 0.759229776 0.856925917 0.778420196 1 19.58555505 -1.766609768 2.36751058 1.050208175 0.82078533 0.313732527 0.081698637 7058665.387 4662723.805 2057881.763 0.020028056 0.017115525 1.766609768 -0.229422845 LSSGLVS(ph)PAPSFYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSGLVSPAPSFYSK 15 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 LSSGLVS(1)PAPSFYSK 248.06 2.55E-18 336600000 475840 415760 480750 424660 581190 589350 573890 507690 542750 444690 TRUE FALSE 494626.5306 487163.5458 493278.7399 508656.4805 482399.5314 452482.3942 528907.0022 500885.246 523216.5335 531818.4914 0.930066439 0.916033485 0.927532133 0.956447526 0.907075514 0.850821101 0.994525408 0.941834957 0.983825388 1 19.02057442 2.201297791 24.99993271 0.972314822 0.916864267 0.536437669 0.029384457 157.0146645 105341.5454 0.011251682 0.00831012 158.9636372 -2.201297791 -0.055450555 LSSGPEQITLEASS(ph)TEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_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 LSSGPEQITLEAS(0.121)S(0.439)T(0.439)EGHPGAPSPQHTDQTEAFQK 134.64 2.61E-08 345130000 37515 52100 58115 53004 58908 64205 59119 58848 50341 48613 TRUE FALSE 38996.12117 61047.76972 59629.52464 63488.033 48894.8392 49294.36179 54485.0983 58059.23882 48529.23724 58137.7866 0.670753454 1.050053215 1.025658666 1.092027005 0.841016524 0.847888519 0.937171872 0.998648938 0.834727981 1 15.82718853 5.049896326 0.005115723 1.85035685 2.34E-06 0.015621399 0.121686408 247336.1127 179.3795658 31126.64353 33796.21861 112175.0639 -5.049896326 -1.85035451 LSSGPEQITLEASSTEGHPGAPS(ph)PQHTDQTEAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 LSSGPEQITLEASSTEGHPGAPS(1)PQHTDQTEAFQK;LSSGPEQITLEASSTEGHPGAPS(0.998)PQHT(0.002)DQTEAFQK 349.58 5.03E-132 1269150000 162704 177383 212414 192836 224406 244959 226573 211471 202563 185470 TRUE FALSE 169127.6796 207847.1504 217949.6833 230978.3852 186261.5483 188070.9846 208813.6162 208636.5771 195272.7972 221809.2955 0.762491397 0.937053382 0.982599412 1.041337717 0.839737342 0.847894964 0.941410574 0.940612415 0.880363453 1 17.7589603 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 35 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;; 322.42 1.69E-105 565900000 81320 147290 183475 157101 180530 232048 159147 197403 186015 174644 FALSE TRUE 84530.57639 172585.9117 188256.5092 188175.1089 149843.5751 178158.3687 146672.6423 194757.1357 179320.3565 208862.148 0.404719463 0.826314932 0.901343355 0.900953623 0.717428105 0.852995004 0.702246164 0.932467359 0.858558423 1 17.67219153 4.737185272 5.140970842 0.849355772 0.384974135 0.71114762 0.086095876 0.082083669 7.237393021 0.019711131 0.135263192 54599.07338 -4.737185272 -0.464381637 LSSLIILMPHHVEPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSLIILMPHHVEPLER 17 0 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;;; 137.44 4.03E-06 8810790000 2046023 2887230 2532800 3050300 3116850 3430420 2630640 2577290 2495700 2584270 FALSE TRUE 2126801.568 3383089.293 2598806.849 3653640.236 2587048.95 2633756.944 2424443.563 2542745.643 2405880.245 3090608.228 0.688149843 1.094635439 0.8408723 1.182175147 0.837067904 0.852180784 0.784455157 0.822733085 0.778448793 1 21.55945936 3.054746947 24.99990233 0.831807973 0.960765653 0.117734426 0.137663552 150.9789017 68942.50062 0.036678967 0.043839746 1134.349665 -3.054746947 0.12895768 LSSLRAS(ph)TSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSLRASTSK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 1 LSSLRAS(0.996)T(0.003)S(0.001)K;LSSLRAS(0.983)T(0.016)SK 95.264 0.0045665 278410000 646440 380350 478520 324010 494050 582970 498400 422800 453870 226100 TRUE FALSE 671961.9504 445672.1538 490990.6243 388098.2109 410071.5575 447584.0525 459334.1057 417133.0576 437535.3074 270399.9661 2.485066696 1.648196042 1.815793957 1.435274629 1.516537015 1.655266674 1.698721018 1.542652034 1.61810415 1 18.04473544 LSSPAAFLPACNS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-5;H0YFE9;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 LSSPAAFLPACNS(0.999)PS(0.001)K;LSSPAAFLPACNS(1)PSK;LSSPAAFLPACNS(1)PSK;LSSPAAFLPACNS(1)PSK 310.75 1.24E-57 2363517000 1864520 984414 1258206 1116972 1529660 1640660 1886470 1346205 1417540 778009 TRUE FALSE 1938132.689 1153479.447 1290995.882 1337905.728 1269648.94 1259641.579 1738603.552 1328161.324 1366523.012 930444.9677 2.083017004 1.23970733 1.38750375 1.437920322 1.364561026 1.35380557 1.868572148 1.42744748 1.46867688 1 19.8275613 0.563775055 2.200246292 1.000080347 1.505525606 0.284026597 0.245584899 4.923015921 23.2721371 0.222101872 0.060286099 3.662478259 -0.563775055 0.505445259 LSSPAAFLPACNS(ph)PSKEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSPAAFLPACNSPSKEMK 19 1 Q86YS7;Q86YS7-5;H0YFE9;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 LSSPAAFLPACNS(0.981)PS(0.019)KEMK;LSSPAAFLPACNS(0.887)PS(0.113)KEMK 185.17 1.41E-14 560650000 771380 346720 495200 282910 828970 674400 524300 534980 647930 329350 TRUE FALSE 801834.678 406266.4629 508105.3188 338868.7536 688061.9755 517780.8206 483203.996 527809.4682 624611.1259 393879.8267 2.035734312 1.031447755 1.290000869 0.860335388 1.746883006 1.314565473 1.226780259 1.340026659 1.585791106 1 18.587396 -1.088129308 4.326121981 0.99995986 1.353560111 0.106210536 0.322930243 0.000115413 2.43E-05 0.288629427 0.068022897 0.081633928 1.088129308 0.353600251 LSSS(ph)ASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSASR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 LS(0.006)S(0.04)S(0.954)ASR 112.41 0.0066717 104040000 425020 497990 495350 495330 554800 618300 553870 546600 493680 553770 TRUE FALSE 441800.1178 583515.9087 508259.2279 593304.7956 460495.2942 474709.1954 510456.2221 539273.7211 475912.5532 662270.6289 0.667099066 0.881083779 0.767449447 0.895864575 0.695327973 0.716790349 0.770766813 0.81427999 0.718607368 1 19.33706135 -1.862731353 3.552426143 1.072933141 0.775838178 0.476242672 0.0721976 0.038436749 0.001485227 0.064428935 0.015516151 0.0137173 1.862731353 -0.297094963 LSSS(ph)LGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSSLGR 7 0 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 LSS(0.007)S(0.993)LGR;LS(0.014)S(0.128)S(0.858)LGR;LS(0.05)S(0.162)S(0.788)LGR 128 0.0039868 971990000 1435950 1596610 1657590 1612730 2014940 2044120 1650660 1725230 1670510 1694820 TRUE FALSE 1492642.415 1870815.348 1700788.157 1931723.18 1672441.219 1569404.109 1521276.956 1702106.114 1610388.671 2026887.53 0.736420937 0.922999091 0.839113238 0.953049023 0.825127785 0.774292646 0.750548283 0.839763474 0.794513089 1 20.95083461 3.025415451 24.99960536 0.815100159 0.868439755 0.014225785 0.083352695 561.8647723 552667.6162 0.022471905 0.026858246 1060.267504 -3.025415451 0.053339595 LSSS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSSSPGK 7 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 LSS(0.006)S(0.994)PGK;LSS(0.009)S(0.991)PGK;LSS(0.001)S(0.999)PGK 154.35 0.0017667 609280000 2431330 1671820 2133070 1636960 2961450 3220790 2828010 2337550 2540620 1744550 TRUE FALSE 2527320.786 1958942.08 2188659.557 1960745.802 2458063.787 2472810.334 2606343.187 2306218.966 2449183.582 2086361.171 1.211353442 0.938927597 1.049031964 0.939792127 1.178158327 1.185226397 1.249229147 1.105378588 1.173902015 1 20.99255749 3.217647728 24.99079022 1.15900912 1.028948193 0.257904517 0.093436178 270.0027622 322651.1178 0.025391694 0.030378968 1650.622375 -3.217647728 -0.130060927 LSSS(ph)PGLFGAFSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.022)S(0.978)PGLFGAFSVR 169.3 3.52E-06 504510000 584780 636710 665270 606080 823440 779440 592020 621880 689890 835380 TRUE FALSE 607867.5659 746059.9896 682607.4827 725960.815 683471.9629 598426.8725 545615.9254 613544.7158 665060.9937 999056.7167 0.608441499 0.7467644 0.683251983 0.726646248 0.684117279 0.598991892 0.546131082 0.614124009 0.665688927 1 19.93020706 0.936948603 20.88351535 1 0.649569778 0.762222026 0.058241928 2013.541574 666915.3095 0.062626733 0.015656683 8.648655602 -0.936948603 -0.350430223 LSSS(ph)SATLLNSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.061)S(0.938)S(0.001)ATLLNSPDR;LSSS(0.855)S(0.145)ATLLNSPDR;LSS(0.001)S(0.859)S(0.14)ATLLNSPDR;LSS(0.093)S(0.79)S(0.116)ATLLNSPDR 344.61 8.19E-70 1557710000 1905340 2280420 2161810 1942770 2745880 2328180 1736830 2032080 1907610 2263170 TRUE FALSE 1980564.294 2672064.396 2218148.545 2327044.107 2279136.298 1787495.479 1600692.726 2004843.291 1838955.489 2706594.83 0.731754998 0.987242112 0.81953476 0.859768179 0.842067779 0.660422261 0.591404634 0.740725309 0.679435085 1 21.36804751 2.801885872 6.869184961 0.708751321 0.855659787 0.173637933 0.117021874 0.325480224 29.91060443 0.033347458 0.035320292 633.7031595 -2.801885872 0.146908467 LSSSDRYS(ph)DAS(ph)DDSFSEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 LSSSDRYS(1)DAS(0.999)DDS(0.001)FSEPR 214.11 1.95E-18 447320000 406410 467250 486100 434210 574490 577730 506620 488750 489040 457060 TRUE FALSE 422455.3806 547496.5528 498768.1653 520095.442 476838.395 443560.9631 466909.8006 482199.1057 471439.5459 546612.1561 0.772861298 1.00161796 0.912471777 0.951488979 0.872352343 0.811472921 0.854188469 0.882159499 0.862475415 1 19.06015802 4.78633296 22.9061201 0.896445568 0.772859722 0.295200098 0.060013274 20585.2938 9869584.459 0.014440299 9.368307798 61141.05949 -4.78633296 -0.123585846 LSSSS(ph)ATLLNSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSS(0.017)S(0.35)S(0.626)AT(0.006)LLNSPDR 171.21 3.20E-06 664430000 871140 932290 974710 930720 1306300 1092500 789130 936380 979470 1008900 TRUE FALSE 905533.2799 1092403.555 1000111.743 1114813.638 1084255.593 838783.432 727275.9286 923829.3577 944219.066 1206574.638 0.750499183 0.905375864 0.828885103 0.923949172 0.898622893 0.69517741 0.602760828 0.765662835 0.782561672 1 20.20248573 2.7424823 24.86639421 0.742043697 0.865567046 0.136092764 0.105360941 443.0147523 2809048.893 0.031329976 0.032135373 552.6908819 -2.7424823 0.123523348 LSSSSATLLNS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSSSSATLLNSPDR 14 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR 319.53 4.74E-56 1366292000 1018567 1355785 1110959 1138624 1121118 1429013 1157304 1198467 1171958 1378324 TRUE FALSE 1058780.812 1588630.527 1139911.504 1363840.429 930550.7628 1097146.388 1066591.488 1182403.51 1129779.461 1648380.198 0.642315901 0.963752494 0.691534335 0.827382196 0.564524352 0.665590614 0.647054296 0.717312372 0.685387668 1 20.65261761 -1.15222047 4.733384528 1.0000278 0.713644696 0.402873324 0.105289629 3.02E-05 5.40E-06 0.099540718 0.023459697 0.070433542 1.15222047 -0.286383104 LSST(ph)PPLSALGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSTPPLSALGR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 LSS(0.003)T(0.996)PPLSALGR 143.42 0.00069525 140300000 302090 283610 361260 362920 423910 438960 351460 332980 345330 318550 TRUE FALSE 314016.7465 332317.8113 370674.7324 434704.4928 351853.9296 337018.1925 323911.6468 328516.9477 332901.6408 380963.7735 0.824269309 0.872308168 0.972992075 1.14106517 0.923588945 0.8846463 0.850242646 0.862331199 0.873840674 1 18.53929429 2.883516586 5.000838676 0.880942874 0.957301362 0.077552815 0.08649266 0.481382812 17.855505 0.028309841 0.030268687 764.7448941 -2.883516586 0.076358487 LSSTSS(ph)EETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSSTSSEETQLFHIPR 16 0 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 1 LSST(0.009)S(0.113)S(0.878)EETQLFHIPR 302.96 4.72E-46 99253000 39406 58506 51997 52800 57912 75432 47550 49990 49810 57235 TRUE FALSE 40961.77931 68553.95039 53352.08454 63243.68241 48068.13893 57914.06118 43822.90675 49319.96582 48017.34783 68449.10242 0.598426829 1.001531765 0.779441697 0.923951961 0.702246446 0.846089417 0.640226171 0.72053488 0.701504419 1 16.062744 3.219480465 24.97830473 0.747253182 0.835073634 0.025727532 0.1358827 575.9366568 753971.5346 0.036306827 0.043459473 1657.602776 -3.219480465 0.087820452 LSSWDQAET(ph)PGHT(ph)PSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 LSSWDQAET(1)PGHT(0.97)PS(0.03)LR;LSSWDQAET(1)PGHT(0.997)PS(0.003)LR 170.27 3.17E-09 405020000 319920 334260 324310 390640 338650 377840 339110 331970 307340 261860 TRUE FALSE 332550.6886 391666.5548 332761.785 467907.4261 281086.394 290092.3862 312529.6721 327520.4851 296278.8934 313166.4534 1.061897547 1.250665742 1.062571618 1.494117333 0.897562274 0.926320119 0.997966636 1.045835151 0.946074812 1 18.25657015 3.189238486 24.99999992 0.976324196 1.208645963 0.510018747 0.119001114 90.70436777 45975.12296 0.03286735 0.039284062 1546.103227 -3.189238486 0.232321766 LSSWDQAET(ph)PGHTPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR 148.56 1.32E-06 487040000 221516 226312 247175 284716 245978 297903 291841 247331 223339 193762 TRUE FALSE 230261.6227 265179.3255 253616.5836 341031.975 204166.7474 228719.543 268965.7398 244015.9325 215301.073 231725.9541 0.993680762 1.144366096 1.09446775 1.471703834 0.881069832 0.987026006 1.160706149 1.053036693 0.929119372 1 17.82206011 LST(ph)TPSPTS(ph)SLHEDGVEDFRR ddPTM_MDA-MB-175_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 2 LS(0.072)T(0.425)T(0.154)PS(0.264)PT(0.148)S(0.802)S(0.134)LHEDGVEDFRR 156.58 1.18E-08 362890000 240620 327480 355530 351350 400700 425020 298610 380150 370140 386810 TRUE FALSE 250119.8634 383722.1426 364795.4039 420845.9813 332589.1571 326315.5462 275204.1679 375054.7111 356818.7337 462598.0136 0.540685122 0.82949371 0.788579702 0.909744463 0.718959328 0.705397638 0.594909965 0.810757288 0.771336502 1 18.81939955 0.595758348 1.58250061 0.999668041 0.741511162 0.367425629 0.103059644 1.96111159 6.326004693 0.097600761 0.027999815 3.942378778 -0.595758348 -0.258156879 LSTDHIPILYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LSTDHIPILYR 11 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 81.017 0.022826 958290000 541170 857700 795480 824860 929490 1043840 785710 813440 714630 897190 FALSE TRUE 562535.8095 1005003.303 816210.8623 988014.846 771495.6218 801423.9795 724123.9971 802537.1673 688910.6059 1072977.203 0.52427564 0.93664926 0.760697301 0.920816252 0.719023312 0.74691613 0.674873609 0.747953605 0.642055212 1 20.03318799 LSTIQNS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSTIQNSPTK 10 0 Q5VYV7 Q5VYV7 SLX4IP Protein SLX4IP 1 LSTIQNS(1)PTK 155.66 1.29E-05 195220000 381640 221170 305990 211000 423110 414990 377220 311300 308910 217540 TRUE FALSE 396707.4419 259154.227 313964.3508 252735.1702 351189.9133 318614.8617 347652.5107 307127.5327 297792.3894 260162.7979 1.524843079 0.996123308 1.206799563 0.971450078 1.349885211 1.224674951 1.33628833 1.180520563 1.144638633 1 17.98905515 0.903019873 2.196367298 1.000941173 1.216149475 0.16573979 0.153937117 0.767713456 7.761403574 0.137359712 0.0376479 7.998708554 -0.903019873 0.215208302 LSTTPS(ph)PT(ph)SSLHEDGVEDFRR ddPTM_MDA-MB-175_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 2 LS(0.003)T(0.013)T(0.065)PS(0.899)PT(0.728)S(0.174)S(0.118)LHEDGVEDFRR 110.13 0.00024185 345790000 164550 211010 243780 201160 242070 275180 222830 245100 214810 244500 TRUE FALSE 171046.5611 247249.3261 250133.1071 240948.8476 200923.0279 211273.6154 205364.0023 241814.8354 207079.0301 292405.0938 0.584964369 0.8455712 0.85543348 0.824024112 0.687139288 0.722537397 0.702327034 0.826985715 0.70819228 1 18.15760892 -1.719186716 2.435698799 1.049871157 0.759088466 0.447535416 0.082602938 12092132.55 8734895.882 3663975.923 0.020571213 0.019090323 1.719186716 -0.290782691 LSTTPS(ph)PTSS(ph)LHEDGVEDFRR ddPTM_MDA-MB-175_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 2 LS(0.013)T(0.077)T(0.092)PS(0.808)PT(0.221)S(0.151)S(0.638)LHEDGVEDFRR 112.48 0.00078328 304160000 146860 204100 210450 206860 235130 294930 209190 254380 232610 255870 TRUE FALSE 152658.1462 239152.5873 215934.4999 247776.2906 195162.6866 226436.9772 192793.1412 250970.4522 224238.4115 306002.8276 0.498878221 0.781537181 0.70566178 0.809718958 0.637780664 0.739983284 0.630037123 0.820157298 0.732798495 1 18.22318546 -5 0.180577211 2.192240307 0.653381783 0.529322504 0.087411025 103.2844019 0.995889779 44.02856314 0.253224852 1.00E-05 5 -1.538858524 LSTTPS(ph)PTSSLHEDGVEDFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 1 LS(0.001)T(0.002)T(0.013)PS(0.972)PT(0.009)S(0.002)S(0.001)LHEDGVEDFRR;LSTT(0.012)PS(0.944)PT(0.041)S(0.001)SLHEDGVEDFRR;LS(0.008)T(0.007)T(0.156)PS(0.541)PT(0.222)S(0.053)S(0.013)LHEDGVEDFRR;LSTT(0.045)PS(0.942)PT(0.01)S(0.003)SLHEDGVEDFRR 144.26 6.08E-08 640048000 48904.9 105133 104203 96860 92376 118792 104839 114176 93598 104988 TRUE FALSE 50835.70321 123188.7749 106918.6158 116018.6189 76673.96052 91204.35831 96621.44523 112645.6575 90229.42626 125558.3885 0.404876997 0.981127398 0.851544983 0.924021249 0.610663783 0.726390004 0.769533971 0.89715756 0.718625234 1 16.93799889 -5 0.227530844 2.158951927 0.755580311 0.163114452 0.159471025 309.2454987 3.09520329 164.8247971 0.271776676 1.00E-05 5 -1.403371616 LSTTPSPT(ph)SSLHEDGVEDFRR ddPTM_MDA-MB-175_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 LSTT(0.001)PS(0.383)PT(0.499)S(0.097)S(0.019)LHEDGVEDFRR 180.66 3.11E-17 239440000 53363 99354 96285 96578 92473 121770 105050 106420 109670 105700 TRUE FALSE 55469.81245 116417.2766 98794.2662 115680.8401 76754.47249 93490.76294 96815.9065 104993.614 105722.9981 126409.8913 0.438809115 0.92095069 0.781539049 0.915124908 0.607187236 0.739584237 0.765888694 0.830580684 0.836350677 1 16.94774983 -5 0.12944823 1.799672079 0.666802272 0.284994193 0.131062289 201.9555256 1.652817746 41.62144642 0.966889204 1.00E-05 5 -1.132869807 LSVDYGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 74.376 0.065961 5370200000 10202000 6453000 8493000 6292400 15473000 11762000 10650000 8386600 9886500 7747200 FALSE TRUE 10604782.84 7561252.553 8714334.557 7537017.939 12842904.99 9030453.755 9815225.171 8274191.345 9530686.796 9265115.511 1.14459262 0.816099113 0.940553256 0.813483429 1.386157029 0.974672549 1.059374291 0.893047835 1.02866357 1 23.14337753 5.071486549 18.53704497 0.989816333 4.418214307 0.083028957 0.153892289 392.6974358 107261.466 0.035164031 2926.786072 117892.6008 -5.071486549 3.428397974 LSVHDMKPLDS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LSVHDMKPLDSPGR 14 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR;LSVHDMKPLDS(1)PGR 141.13 5.91E-06 1374770000 887070 1509300 1759960 1425410 2091190 2216920 1961020 1839180 1825920 1422710 TRUE FALSE 922092.2086 1768510.534 1805826.003 1707351.844 1735730.271 1702073.928 1807310.128 1814528.8 1760205.496 1701462.785 0.541940862 1.039405945 1.06133735 1.003461174 1.020140015 1.000359187 1.062209614 1.066452241 1.034524828 1 20.69834417 4.738832654 24.99936476 1.035541591 0.541940715 0.972469625 0.024729353 3.318542793 304811.8786 0.006294811 0.036726026 54806.57396 -4.738832654 -0.493600876 LSVHDMKPLDS(ph)PGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LSVHDMKPLDSPGRR 15 2 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR;LSVHDMKPLDS(1)PGRR 207.56 1.74E-09 4235915000 1519423 2623774 3101785 2543507 3888138 3838870 3107436 3394633 3089895 2640057 TRUE FALSE 1579410.993 3074386.774 3182620.065 3046605.093 3227233.692 2947350.621 2863867.047 3349133.497 2978690.283 3157325.622 0.500236967 0.973731297 1.008011351 0.964932179 1.022141546 0.933495931 0.9070547 1.060750109 0.943421946 1 21.59027163 4.73842198 6.789465911 0.982303004 0.492166049 0.917487705 0.043097028 0.027623625 8.864064914 0.010166799 0.062325139 54754.77265 -4.73842198 -0.490136955 LSVNSVTAGDYSRPLHISTFINELDSGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LSVNSVTAGDYSRPLHISTFINELDSGFR 29 1 E9PGT1;Q15631 E9PGT1 TSN Translin 0 217.84 1.46E-34 163030000 25204 108600 126620 117140 139720 166500 116900 154820 115360 156240 FALSE TRUE 26199.07338 127251.2052 129919.8212 140309.9424 115970.4443 127832.8983 107737.0725 152744.8911 111208.2161 186852.2366 0.14021279 0.68102586 0.69530782 0.750913904 0.620653231 0.684138979 0.576589687 0.817463542 0.595166631 1 17.51153831 3.487301263 0.096747626 1.210889354 2.49E-25 0.431120994 0.157068815 40.97109541 1.04992814 4.055717911 9.288889121 3071.151654 -3.487301263 -1.210889354 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_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(0.001)VPT(0.999)S(1)DEEDEVPAPKPR 116.21 0.00038232 270940000 363190 297470 329470 277690 422010 384730 421790 338550 362960 280720 TRUE FALSE 377529.0216 348558.1585 338056.2589 332616.2532 350276.8909 295382.2881 388728.9977 334012.291 349897.1405 335721.7093 1.124529666 1.038235386 1.006953824 0.99074991 1.043354902 0.879842679 1.157890559 0.994908228 1.042223755 1 18.35690631 4.719494535 2.944941544 1.016310529 1.140348791 0.206765611 0.06446661 0.566855109 7.309874054 0.014828141 0.16267911 52419.70042 -4.719494535 0.124038263 LSVPTS(ph)DEEDEVPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LSVPTSDEEDEVPAPKPR 18 1 Q5STZ8;F5GYK6;Q8NE71;Q8NE71-2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 LSVPT(0.016)S(0.984)DEEDEVPAPKPR;LSVPT(0.189)S(0.811)DEEDEVPAPKPR;LSVPT(0.002)S(0.998)DEEDEVPAPKPR;LSVPT(0.011)S(0.989)DEEDEVPAPKPR 289.14 2.42E-49 4195710000 2747611 2087963 2797209 2117178 3216328 2852286 2880491 2554715 2829162 1867732 TRUE FALSE 2856088.804 2446554.403 2870106.564 2535949.489 2669617.715 2189885.803 2654710.589 2520473.224 2727341.012 2233678.326 1.278648215 1.095302925 1.284923855 1.135324393 1.195166594 0.980394437 1.188492792 1.128395792 1.221008854 1 21.09099001 3.286868373 2.223966036 1.120690835 1.204989302 0.195035645 0.088932583 0.565097799 5.725540493 0.025772323 0.036253987 1935.835158 -3.286868373 0.084298467 LSVQSNPS(ph)PQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSVQSNPSPQLR 12 0 O75152;E9PBY7;E9PQ61;A0A1W2PPR9 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR;LSVQSNPS(1)PQLR 249.58 6.24E-17 479930000 670580 705620 619470 638370 630710 790840 645650 646590 664980 720150 TRUE FALSE 697055.0162 826804.746 635613.8971 764637.6807 523502.1395 607179.3953 595042.2659 637923.5187 641047.4997 861249.6044 0.809353076 0.960005952 0.738013572 0.887823549 0.607840209 0.70499817 0.690905706 0.740695282 0.744322548 1 19.71607189 3.26865571 24.99997709 0.72997174 0.848829171 0.159195938 0.108637703 298.6200063 248061.5104 0.027787679 0.037620042 1856.332253 -3.26865571 0.118857431 LSVVHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSVVHEK 7 0 P20810-6;P20810-10;P20810;P20810-8;B7Z574;E7ES10;E9PDE4;H0YA91;E7EQK6;D6RBZ8;P20810-5;E9PCH5;P20810-2;F8W7E0;A0A0C4DGB5;H0Y944;E7EN75;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ;;;; 86.953 0.019698 2012940000 2379590 3046850 3301080 3027820 4242980 4411020 3865770 3695430 3669150 3156340 FALSE TRUE 2473538.051 3570122.786 3387108.857 3626713.759 3521759.775 3386627.455 3562760.846 3645898.805 3537098.008 3774764.391 0.655282766 0.94578692 0.897303383 0.960778842 0.932974726 0.897175851 0.943836615 0.96586129 0.937038088 1 21.84795517 4.739263578 24.99999999 0.940026713 0.655282678 0.897496433 0.029090736 16.2093665 576356.27 0.006689212 0.040174831 54860.98206 -4.739263578 -0.284744035 LSYAGGRPPSYAGS(ph)PVHHAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSYAGGRPPSYAGSPVHHAAER 22 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPS(0.001)YAGS(0.999)PVHHAAER;LSYAGGRPPSYAGS(1)PVHHAAER;LSYAGGRPPS(0.005)YAGS(0.995)PVHHAAER 191.4 8.69E-18 3192565000 494349 665501 630211 582087 700374 790082 648610 669577 683132 719269 TRUE FALSE 513866.2802 779795.6199 646634.8164 697222.0712 581324.6776 606597.4293 597770.2534 660602.4155 658546.2128 860195.9893 0.59738279 0.906532499 0.751729634 0.810538621 0.675804915 0.70518514 0.694923321 0.767967328 0.765576939 1 19.71430588 0.448321808 1.60681324 0.99998197 0.742454775 0.497418936 0.078300474 2.988143406 7.818958011 0.070873149 0.020212829 2.807513206 -0.448321808 -0.257527195 LSYLEEAVMHLDHSDPITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LSYLEEAVMHLDHSDPITR 19 0 Q6P2E9;Q6P2E9-2;I3L0V0;I3L3M2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 ;;;; 161.86 1.66E-11 192332000 81826.4 105907.2 107096.2 111914.8 116561.9 133298.5 118464.7 107126.9 102061.5 101113.5 FALSE TRUE 85056.96946 124095.9378 109887.215 134051.2134 96748.74987 102341.9435 109179.1273 105691.0391 98388.32655 120924.7544 0.703387573 1.026224435 0.908723904 1.108550636 0.800073983 0.846327487 0.902868299 0.874023186 0.813632635 1 16.88375008 LSYLPATVEPAS(ph)PTPAHSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LSYLPATVEPASPTPAHSLPR 21 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4 M0R344 SPHK2 Sphingosine kinase 2 1 LSYLPATVEPAS(0.913)PT(0.087)PAHSLPR;LSYLPATVEPAS(0.992)PT(0.008)PAHSLPR;LSYLPATVEPAS(0.989)PT(0.011)PAHSLPR 223.44 2.29E-25 995750000 493800 582530 580280 623090 649680 709490 589900 634560 571880 660310 TRUE FALSE 513295.6053 682574.996 595402.5735 746335.3423 539247.6257 544721.6999 543662.0966 626054.7611 551298.1505 789685.1021 0.650000366 0.864363522 0.753974682 0.945105005 0.682864124 0.689796095 0.68845429 0.792790391 0.698124036 1 19.59091795 -1.034195347 4.306688855 1.00001527 0.756866066 0.415171686 0.088212392 0.30753324 49157305.5 1841.291989 0.020044653 0.092428234 1.034195347 -0.243149204 LT(ph)QTSSTEQLNVLETETEVLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.412)QT(0.249)S(0.152)S(0.094)T(0.094)EQLNVLETETEVLNK;LT(0.438)QT(0.18)S(0.18)S(0.101)T(0.101)EQLNVLETETEVLNK 264.91 5.91E-37 512098000 246498 190232 219847 184266 259439 263136 256135 222475 243873 152251 TRUE FALSE 256229.9314 222902.8662 225576.3934 220713.2648 215339.6514 202026.6519 236058.4694 219493.0865 235096.0584 182081.6684 1.407225305 1.224191694 1.238874816 1.212166314 1.182654208 1.109538668 1.296442808 1.205465044 1.291157207 1 17.47422616 -2.242820311 2.413147017 0.09741119 1.234136131 0.477465658 0.075295655 1381108.014 596513.1096 6880479.708 0.017681205 0.005717151 2.242820311 1.136724941 LT(ph)T(ph)T(ph)S(ph)LNKHLQELMDGLT(ph)AK ddPTM_MDA-MB-175_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 46.621 0.051465 939160000 19671 424380 145050 287930 60888 228260 42570 134290 64960 420900 TRUE FALSE 20447.62627 497263.9638 148830.1222 344881.6946 50538.27951 175250.0743 39233.25216 132490.0622 62622.10229 503367.2964 0.040621682 0.987874992 0.295669034 0.685149188 0.100400403 0.348155463 0.077941599 0.263207529 0.124406378 1 18.94125196 -1.212196111 4.583127533 1.000163675 0.332290531 0.336654729 0.284151097 0.000456993 7.86E-05 0.264575893 0.062346044 0.061348492 1.212196111 -0.667873144 LTADFREDPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTADFREDPDPR 12 1 P17174 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 64.878 0.056781 1680310000 1866530 2425000 2288600 1933820 2783600 2741100 1774260 2207000 2186200 2798700 FALSE TRUE 1940222.046 2841474.886 2348242.796 2316323.824 2310444.666 2104521.067 1635188.865 2177418.775 2107519.089 3347051.681 0.579680934 0.848948614 0.701585461 0.692049017 0.690292498 0.62876862 0.488546046 0.650548298 0.62966434 1 21.6744594 -1.180765281 4.998240776 1.00002758 0.656974598 0.579079887 0.087812107 2.80E-05 4.59E-06 0.088306019 0.020812257 0.065953025 1.180765281 -0.343052982 LTAEDLFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 143.03 8.07E-05 271958000 400390 422670 436540 456015 477641 538776 498587 469236 453736 355934 FALSE TRUE 416197.7064 495260.2846 447916.591 546213.4059 396451.7534 413653.4392 459506.4481 462946.6589 437406.13 425672.4525 0.977741698 1.163477415 1.052256467 1.283177717 0.931354028 0.971764644 1.079483639 1.087565465 1.027565038 1 18.6993842 3.202971421 24.99998609 1.027413825 1.117550423 0.253034761 0.085297691 278.5529967 195671.5924 0.024598471 0.029401733 1595.774132 -3.202971421 0.090136599 LTAEEMDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTAEEMDER 9 0 P46940;H0YLE8;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 152.34 0.00019977 4471400000 3605370 4496660 4614100 4251960 5246130 5439620 4692430 4444100 4375750 4149250 FALSE TRUE 3747712.792 5268926.376 4734347.237 5092984.997 4354394.696 4176350.693 4324625.075 4384534.109 4218267.612 4962216.095 0.755249816 1.061809134 0.954079215 1.026352924 0.877510091 0.841630153 0.871510831 0.883583871 0.850077371 1 22.24255313 3.193771334 24.5763244 0.87867229 0.957740138 0.103457118 0.085755916 186.5785977 102376.7268 0.023171212 0.027695049 1562.324825 -3.193771334 0.079067848 LTAIIEEAEEAPGARPQLQDAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;;; 258.06 1.13E-43 2949179000 862990 838721 919268 964357 922341 1104689 951952 871741 896204 925265 FALSE TRUE 897061.5116 982764.8074 943224.8793 1155103.936 765561.8063 848141.7215 877335.5148 860056.7378 863949.7931 1106552.961 0.810681045 0.88813174 0.852399218 1.043875871 0.6918438 0.766471873 0.792854518 0.777239561 0.780757743 1 20.07764107 3.219524755 24.99993939 0.787561626 0.894699713 0.199575284 0.092770042 330.3735809 433881.1332 0.025173937 0.030134366 1657.771828 -3.219524755 0.107138088 LTALADLEDWEELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTALADLEDWEELEK 15 0 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 196.57 2.06E-08 5802600 10212 9824.5 12534 7029.6 12681 14557 12694 10236 12114 6812.7 FALSE TRUE 10615.17765 11511.78145 12860.64634 8420.033899 10525.48815 11176.35736 11699.01111 10098.80316 11678.01951 8147.518128 1.302872541 1.41291879 1.578474099 1.033447704 1.291864343 1.371749923 1.435898752 1.239494408 1.43332231 1 12.99214494 -1.261322563 3.874704129 0.99953719 1.340032434 0.360793129 0.137429733 10224808.16 3328541.692 39961.70925 0.031488832 0.05478699 1.261322563 0.340495244 LTALDYHNPAGFNCKDETEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTALDYHNPAGFNCKDETEFR 21 1 Q9Y224;G3V4C6;G3V4E7 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 64.203 0.016277 394370000 159380 351920 306200 378490 287480 452940 259950 315500 301610 436300 FALSE TRUE 165672.4455 412359.5224 314179.8235 453354.1923 238614.2523 347751.5494 239574.4397 311271.2386 290755.115 521784.6315 0.317511164 0.79028683 0.602125484 0.868853096 0.457304102 0.66646568 0.459144301 0.596551182 0.557232041 1 18.99309493 -1.83465938 2.608326544 1.149086544 0.597543088 0.390870502 0.153099848 15957280.62 10676953.3 14892350.63 0.035749487 0.014633244 1.83465938 -0.551543456 LTAT(ph)PTPLGGMTGFHMQTEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTATPTPLGGMTGFHMQTEDR 21 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 LT(0.008)AT(0.885)PT(0.107)PLGGMTGFHMQTEDR 220.49 1.72E-24 159150000 100440 123170 113940 116600 132680 142580 114400 116640 107960 109350 TRUE FALSE 104405.4488 144323.4894 116909.37 139663.132 110127.101 109467.9558 105433.0291 115076.6316 104074.5407 130775.0389 0.798359149 1.103601197 0.893973124 1.067964752 0.842111017 0.837070719 0.806216767 0.879958688 0.795828788 1 16.99672767 3.205507581 24.8656135 0.851356772 0.970662121 0.224121619 0.095411513 216.6177168 162959.6526 0.024991803 0.029872714 1605.120277 -3.205507581 0.119305349 LTATEGPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTATEGPGSPR 11 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 LTATEGPGS(1)PR;LTATEGPGS(1)PR 173.57 1.26E-05 1663670000 985270 1068870 1045670 1060990 1080590 1278950 1061460 1119810 1060220 1041340 TRUE FALSE 1024169.22 1252440.108 1072921.019 1270850.655 896911.6978 981933.2452 978259.9916 1104800.779 1022062.889 1245370.635 0.822381058 1.005676601 0.861527475 1.020459789 0.7201966 0.788466676 0.78551715 0.887126087 0.820689729 1 20.24814374 3.24357987 24.99999997 0.826843018 0.928381324 0.21017723 0.088525603 177.4365445 883773.6612 0.023332242 0.030646976 1752.184644 -3.24357987 0.101538306 LTDCVVMRDPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LTDCVVMRDPASK 13 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 143.21 3.71E-05 4722310000 3122490 2666190 2966870 2575210 3670930 3661180 3410290 3186110 3271300 2569340 FALSE TRUE 3245768.316 3124087.392 3044189.07 3084578.852 3046946.63 2810926.431 3142982.559 3143405.407 3153566.552 3072752.98 1.056306295 1.016706326 0.990704131 1.003848624 0.991601554 0.914790889 1.022855589 1.022993201 1.026300055 1 21.55110036 -0.808458005 5.396653182 0.999999998 1.004103831 0.001149901 0.035210446 5.23E-10 1.45E-10 0.035121869 0.008278301 0.155432558 0.808458005 0.004103832 LTDDHVQFLIYQILR ddPTM_MDA-MB-175_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 ; 195.54 9.38E-09 979340000 340070 377500 391380 384690 522800 520890 432100 414480 428010 473490 FALSE TRUE 353496.2262 442332.6885 401579.6843 460780.5338 433934.6427 399921.1917 398230.8729 408924.5736 412606.0037 566261.3 0.624263438 0.781145892 0.709177343 0.813724219 0.766315202 0.706248496 0.703263446 0.722148191 0.728649483 1 19.11110841 -0.979803603 4.85243757 1.00000302 0.730602331 0.735086174 0.048910233 1.52E-06 3.20E-07 0.045178418 0.010648536 0.104760219 0.979803603 -0.269400688 LTDEDFS(ph)PFGSGGGLFSGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTDEDFSPFGSGGGLFSGGK 20 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 LTDEDFS(1)PFGSGGGLFSGGK;LTDEDFS(1)PFGSGGGLFSGGK 367.48 5.24E-112 309390000 818040 631560 876140 682790 1034150 1028520 1112550 915720 1018780 677130 TRUE FALSE 850336.8509 740025.5171 898972.9282 817843.8241 858365.5524 789661.8174 1025345.424 903446.2712 982114.3068 809800.6591 1.050057 0.913836645 1.110116321 1.009932278 1.059971417 0.975131112 1.266170152 1.115640326 1.212785265 1 19.62720729 2.255896616 24.99997546 1.157569539 1.020499581 0.376401908 0.080894321 222.0566794 320223.839 0.025847394 0.021578335 180.2588584 -2.255896616 -0.137069959 LTDEEAQHVLEVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTDEEAQHVLEVVQR 15 0 Q9BV36-2;Q9BV36-5;C9JKV5;C9JI01;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 117 0.0004048 371620000 240899 273096 282940 263811 336180 349640 300970 305410 314810 264062 FALSE TRUE 250409.8785 319998.1136 290313.6488 315992.0284 279036.2437 268441.4088 277379.185 301316.4785 303480.0496 315799.8931 0.792938452 1.013293926 0.919296223 1.000608408 0.883585618 0.850036414 0.878338438 0.954137367 0.960988449 1 18.26865116 1.341687095 2.219183119 0.98904796 0.911462905 0.192860454 0.062415435 0.535044067 4.482203521 0.054869148 0.016505482 21.96276906 -1.341687095 -0.077585055 LTDEGAVHVNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTDEGAVHVNDR 12 0 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 0 126.95 0.00027843 156450000 76729 100870 86143 100700 93443 122260 92849 90750 87480 93044 FALSE TRUE 79758.32017 118193.6378 88387.95735 120618.1594 77559.59224 93866.96787 85571.25276 89533.64469 84331.61189 111274.1904 0.716772864 1.062183759 0.794325774 1.083972474 0.697013314 0.8435646 0.769012585 0.804621848 0.757872168 1 16.76375948 3.216989559 24.99999973 0.801131479 0.916305454 0.132857316 0.126170572 394.2710336 456943.3156 0.03287194 0.03932287 1648.12277 -3.216989559 0.115173975 LTDHGLEEISSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTDHGLEEISSCR 13 0 O95630 O95630 STAMBP STAM-binding protein 0 ; 188.09 6.40E-06 440360000 124896 166362 127773 125402 156079 177345 118048 155311 146083 179153 FALSE TRUE 129826.9905 194933.3794 131102.8693 150206.1413 129548.7473 136159.3114 108795.0893 153229.3101 140825.5014 214254.6003 0.605947272 0.909821209 0.611902238 0.701063786 0.604648615 0.635502394 0.507784146 0.715173956 0.657281109 1 17.70896666 -0.985494458 4.656035415 1.000006373 0.662775654 0.51025703 0.099617157 6.39E-06 1.39E-06 0.093578952 0.022056354 0.10339643 0.985494458 -0.337230719 LTDIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTDIFR 6 0 O75340-2;O75340;A0A024QZ42;H0Y9X3;A0A087WZ38 O75340-2 PDCD6 Programmed cell death protein 6 0 ;;; 124.32 0.042818 643756000 1029425 1171090 1144324 1191710 1239050 1395230 1275624 1204160 1102226 1054772 FALSE TRUE 1070067.494 1372215.598 1174146.024 1427426.681 1028436.724 1071208.977 1175637.258 1188020.205 1062557.102 1261434.379 0.848294221 1.087821627 0.930802302 1.131590121 0.815291498 0.84919913 0.931984475 0.941801036 0.84234037 1 20.26663373 3.220943683 24.99869286 0.897433113 1.001010693 0.244021661 0.088673544 329.9383905 468186.5366 0.024249901 0.029042836 1663.19696 -3.220943683 0.10357758 LTDIHGNVLQYHK ddPTM_MDA-MB-175_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 ; 129.71 8.71E-05 1866580000 2266000 2317300 2263300 2050500 3749600 3299200 2660200 2417100 2612600 3289600 FALSE TRUE 2355463.43 2715278.249 2322283.457 2456082.78 3112244.331 2533010.8 2451686.573 2384702.728 2518573.036 3934134.137 0.598724738 0.690184461 0.590290869 0.624300721 0.791087498 0.643854712 0.623183269 0.606156945 0.640184841 1 21.90761472 -1.211822418 5.583627187 1.000014111 0.644827491 0.785270981 0.055638731 9.86E-06 1.39E-06 0.054350726 0.01281008 0.061401302 1.211822418 -0.355186619 LTEDFVSHLETELEQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTEDFVSHLETELEQSR 17 0 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 0 ;; 256.98 4.09E-27 52810000 77692.5 97608.8 93480.1 95985.5 106204 113469 100914 103375.1 91966.6 102604.4 FALSE TRUE 80759.85989 114372.3521 95916.2682 114971.1454 88151.48202 87117.54439 93004.09699 101989.5259 88656.74003 122707.7677 0.658147902 0.932071003 0.781664193 0.936950835 0.718385508 0.709959492 0.757931619 0.831157862 0.722503079 1 16.90486705 -1.183329605 4.082030299 1.000096201 0.790003822 0.349246419 0.088344185 12208989.65 3539238.36 10528.30688 0.01964134 0.065564748 1.183329605 -0.210092379 LTEDKADVQSIIGLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTEDKADVQSIIGLQR 16 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 230.93 1.64E-15 3318100000 1928370 1468580 1826310 1436570 2281800 2221230 1803970 1848150 1931990 1465320 FALSE TRUE 2004503.537 1720797.191 1873905.139 1720719.258 1893940.451 1705382.996 1662570.118 1823378.572 1862458.057 1752421.399 1.1438479 0.981953994 1.06932336 0.981909522 1.080756291 0.973158052 0.948727354 1.040490931 1.062791209 1 20.74091831 4.748279509 24.46579806 1.016082286 1.143847993 0.441471191 0.043318796 900.3887243 2266524.481 0.010013803 0.128252269 56011.79735 -4.748279509 0.127765707 LTEDLEYHELLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 ;;;;; 257.02 6.92E-24 3890930000 2946070 3698740 3659370 3727490 4166710 4331740 3690440 3913880 3711110 3675040 FALSE TRUE 3062383.118 4333969.823 3754736.188 4464776.397 3458454.123 3325759.033 3401173.67 3861420.84 3577547.876 4395093.725 0.696773109 0.986092697 0.854301734 1.01585465 0.786889732 0.756698091 0.773856915 0.878575312 0.813986709 1 22.0674625 LTEEELLDREFDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTEEELLDREFDLLR 15 1 H0Y9P1;Q9NSY1;Q9NSY1-2;Q9NSY1-3 H0Y9P1 BMP2K BMP-2-inducible protein kinase 0 113.59 0.00061404 32740000 33365 61864 50576 56624 58141 68855 40710 51065 39922 59733 FALSE TRUE 34682.27596 72488.66076 51894.05211 67824.05819 48258.21359 52864.46976 37519.04382 50380.5572 38485.21502 71436.53769 0.485497717 1.01472808 0.726435712 0.949430927 0.675539649 0.740020044 0.525208038 0.705249146 0.538732927 1 16.12437454 3.085034816 25 0.674693586 0.805902871 0.054418779 0.180288508 52.58818381 15453.45259 0.047804663 0.057137739 1216.283502 -3.085034816 0.131209285 LTEEETVCLDLDKVEAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTEEETVCLDLDKVEAYR 18 1 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 78.501 0.010775 27519000 15673 11900 12686 14080 16592 18888 17348 12555 14323 10516 FALSE TRUE 16291.78214 13943.73243 13016.60758 16864.98198 13771.69777 14501.54825 15988.21843 12386.72076 13807.51803 12576.40886 1.295424022 1.108721304 1.035001941 1.341001407 1.095042148 1.153075446 1.27128647 0.984917149 1.097890358 1 13.61843241 1.705484632 9.736394298 1.032746065 1.178029715 0.366737763 0.094621372 0.1268228 24.94145431 0.04357242 0.023481508 50.75567788 -1.705484632 0.145283651 LTEGCS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 76.143 0.038356 683940000 1459430 1590560 1719610 1543480 1851460 1979560 1716610 1783290 1856570 1416490 TRUE FALSE 1517049.423 1863726.307 1764424.449 1848775.737 1536749.491 1519837.191 1582057.623 1759387.914 1789752.408 1694024.095 0.895530015 1.100176977 1.041558059 1.0913515 0.907159169 0.897175663 0.93390503 1.038584941 1.056509417 1 20.69202296 6.560671728 12.01513606 0.997910331 0.503598959 0 0.076908479 0 0 0.017565301 0 3636400.66 -6.560671728 -0.494311372 LTEGCSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTEGCSFR 8 0 P42677;C9J1C5;H0YMV8;Q71UM5 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 0 ;;;; 173.68 0.00064297 2896100000 831153 997750 887480 889740 985290 1145830 979240 965920 948860 989030 FALSE TRUE 863967.5622 1169105.801 910608.4579 1065727.916 817810.7577 879728.3477 902484.61 952973.4223 914710.7139 1182811.492 0.730435549 0.988412616 0.76986778 0.90101248 0.69141259 0.743760399 0.762999528 0.805684954 0.773336005 1 20.17378874 6.886634737 13.96340451 0.809314296 0.312820871 0 0.103089515 0 0 0.021132687 0 7702553.748 -6.886634737 -0.496493425 LTEHQVAEPPEDWPALIWQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTEHQVAEPPEDWPALIWQQQR 22 0 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 0 106.03 0.00049997 64730000 34796 31887 38519 25259 42912 32851 31522 34659 33282 31646 FALSE TRUE 36169.77295 37363.3442 39522.83678 30255.15481 35617.83357 25221.85311 29051.22327 34194.4528 32084.18732 37846.4278 0.955698465 0.987235688 1.044295039 0.799419035 0.941114806 0.666426254 0.767608067 0.903505424 0.84774678 1 15.20786951 3.736214413 24.96563626 0.838276068 0.994892329 0.363113247 0.090081415 203.6135292 2166628.061 0.023430325 0.038282481 5447.715428 -3.736214413 0.156616261 LTELMFEHYNIPAFFLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTELMFEHYNIPAFFLCK 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 65.949 0.032619 221490000 207430 141340 205950 178130 244860 253760 258250 203050 219470 139660 FALSE TRUE 215619.4966 165614.0455 211317.2262 213363.5823 203238.7847 194828.0858 238007.6902 200328.4469 211571.3176 167023.703 1.29095148 0.991560135 1.265193037 1.277444928 1.216826001 1.166469682 1.424993494 1.199401302 1.266714327 1 17.34969333 LTEVSISSDAFFPFRDNVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTEVSISSDAFFPFRDNVDR 20 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 197.45 1.51E-21 666950000 218390 294230 285530 168281 333900 311330 170922 276890 265560 418400 FALSE TRUE 227012.2058 344761.7137 292971.1464 201566.4795 277143.7973 239028.3258 157524.687 273178.7425 256002.5475 500377.4692 0.45368191 0.689003272 0.585500276 0.402828848 0.553869457 0.47769602 0.314811711 0.54594533 0.511618854 1 18.9326573 0.309742873 2.178134922 1.000000795 0.502941586 0.701471536 0.097117357 10.91553762 33.44398151 0.094975323 0.025774054 2.040529479 -0.309742873 -0.49705921 LTEYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTEYSR 6 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;; 148.07 0.025152 2062210000 1839740 2072800 2037470 1974170 2273680 2561710 2111160 2050270 2062110 2171280 FALSE TRUE 1912374.356 2428787.276 2090568.142 2364654.934 1887200.686 1966791.676 1945681.763 2022789.484 1987895.064 2596700.744 0.736463129 0.935335842 0.80508628 0.910638216 0.726768647 0.75741946 0.749289947 0.778984443 0.765546461 1 21.30824833 6.267427242 8.934703248 0.807980046 0.729777534 0 0.091646304 0 0 0.019019367 0 1851088.752 -6.267427242 -0.078202512 LTFDEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTFDEYR 7 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 89.55 0.066542 0 314640 411520 380500 312680 529380 470810 352800 356750 366900 530930 FALSE TRUE 327062.2302 482195.3588 390416.1426 374527.1707 439396.1767 361471.5127 325146.6141 351968.3498 353695.3407 634955.5682 0.515094672 0.759415907 0.614871594 0.589847841 0.692010904 0.56928631 0.512077743 0.554319652 0.557039513 1 19.27629612 -1.88613188 2.574168765 1.20548244 0.596423352 0.731655732 0.0734002 14388412.14 8443145.146 17979418.57 0.018614164 0.012997748 1.88613188 -0.609059088 LTFLEEDDKDLYILWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTFLEEDDKDLYILWK 16 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 200.71 3.18E-11 154743000 431306 202368 319193 206474 394264 431898 432152 287268 357378 151414 FALSE TRUE 448334.2939 237123.1298 327511.4318 247313.9409 327247.1461 331596.235 398278.797 283417.6423 344516.0356 181080.6743 2.475881513 1.309488882 1.808649283 1.365766622 1.807189792 1.831207202 2.199455014 1.56514572 1.902555515 1 17.46627306 -0.351417344 8.002799657 0.999965171 1.78139909 0.34179379 0.334344009 0 0 0.297467105 0.070113669 0.445228192 0.351417344 0.781433919 LTFS(ph)TLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTFSTLELR 9 0 Q3KR16-2;Q3KR16;Q3KR16-3 Q3KR16-2 PLEKHG6 Pleckstrin homology domain-containing family G member 6 1 LT(0.004)FS(0.773)T(0.223)LELR 90.05 0.0098829 0 19304 30500 31788 22958 49927 32583 21725 27679 27803 38781 TRUE FALSE 20066.13683 35738.13774 32616.42139 27499.02388 41440.42637 25016.09205 20022.13773 27308.00828 26802.37546 46379.39444 0.43265198 0.77056068 0.70325242 0.592914681 0.893509432 0.539379445 0.431703302 0.588796137 0.577894036 1 15.50119636 -1.687128052 2.593491042 1.059114652 0.616976339 0.419846076 0.135913806 18767128.25 15530096.07 7287698.569 0.0332984 0.020552845 1.687128052 -0.442138313 LTFSCLGGSDNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTFSCLGGSDNFK 13 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 158.31 0.00011049 92664000 111190 108460 97619 107450 122420 117280 136940 114720 129300 118990 FALSE TRUE 115579.8671 127087.1613 100163.0313 128703.2893 101611.0921 90043.4974 126206.285 113182.366 124646.5183 142303.8123 0.812204994 0.893069267 0.703867519 0.904426151 0.714043359 0.632755342 0.886879156 0.795357231 0.875918334 1 17.11861479 0.872956185 1.270340817 0.999723311 0.788201893 0.367732067 0.08447892 0.651165573 2.047854344 0.07849088 0.023920177 7.463734547 -0.872956185 -0.211521417 LTGFHETSNINDFSAGVANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTGFHETSNINDFSAGVANR 20 0 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;; 340.15 2.78E-80 751550000 174558 357340 357960 374360 369100 472060 358950 389670 358220 400800 FALSE TRUE 181449.6846 418710.3653 367288.7317 448407.2906 306360.5138 362431.2191 330814.5611 384447.111 345327.7322 479329.0862 0.378549289 0.873534232 0.766255882 0.935489424 0.639144426 0.756121899 0.690161667 0.80205254 0.720439761 1 18.87065696 -5 0.248852829 2.545209249 0.71754409 0.251758131 0.142008142 261.9630683 2.599274496 206.0069387 0.194472131 1.00E-05 5 -1.82766516 LTGIKHELQANCYEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTGIKHELQANCYEEVK 17 1 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 174.59 8.02E-10 1425800000 2653600 1274830 1835990 1391040 2305200 2275500 2569800 2048960 2066920 1051590 FALSE TRUE 2758366.177 1493772.136 1883837.408 1666183.56 1913362.927 1747049.611 2368372.361 2021497.043 1992531.953 1257628.927 2.19330688 1.187768589 1.497927861 1.324861034 1.521404992 1.38916144 1.883204426 1.607387521 1.584356014 1 20.26227488 LTGIKHELQANCYEEVKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTGIKHELQANCYEEVKDR 19 2 G3V1A4;P23528;E9PP50;E9PK25 G3V1A4;P23528 CFL1 Cofilin-1 0 ;; 234.04 2.39E-24 15254140000 16535880 9585490 13477570 8662470 20034100 16274200 13865750 13483670 15432050 10592850 FALSE TRUE 17188729.31 11231723.34 13828806.55 10375880.71 16628710.84 12494763.69 12778916.28 13302943.46 14876653.53 12668316.15 1.356828257 0.886599546 1.091605734 0.81904182 1.312622029 0.986300274 1.008730453 1.050095633 1.174319725 1 23.59472144 2.312371267 0.006138913 3.03E-05 2.11554373 0.01545601 0.161567218 39586.3109 134.9921027 23005.34475 23502.57042 205.2916412 -2.312371267 2.115513477 LTGMAFR ddPTM_MDA-MB-175_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 ;;;;;;; 150.02 0.0045995 30003680000 9555676 11677322 9230463 7974871 22510270 15233666 12077611 9492464 9219384 25165080 FALSE TRUE 9932941.467 13682811.22 9471016.449 9552276.681 18683982.35 11695877.94 11130936.29 9365233.047 8887580.171 30095695.61 0.330045253 0.454643461 0.314696712 0.317396773 0.620819089 0.388622948 0.369851438 0.31118181 0.295310675 1 24.84305383 -1.497337711 3.062626544 1.017908371 0.378794864 0.80134202 0.092898478 35743299.15 42571144.06 5404734.815 0.022489727 0.031817224 1.497337711 -0.639113507 LTGRDPNDVRPIQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTGRDPNDVRPIQAR 15 2 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 0 ;; 101.3 0.0010252 352521000 315127 394550 367560 358335 396710 426890 335491 365838 336538 416020 FALSE TRUE 327568.4573 462310.8933 377138.9156 429212.5935 329277.3759 327751.2671 309194.3388 360934.54 324426.0631 497531.1538 0.658387831 0.929209939 0.758020704 0.862684859 0.661822628 0.658755265 0.621457242 0.725451135 0.652071856 1 18.92442734 5.038212859 16.5587557 0.746753327 0.279273206 0.046965483 0.122908797 1097501701 12755989384 0.028633073 15440521559 109197.5412 -5.038212859 -0.467480121 LTGS(ph)QLSITQVASIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTGSQLSITQVASIK 15 0 Q9UJF2;Q9UJF2-2;H0Y638 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 LTGS(1)QLSITQVASIK;LT(0.003)GS(0.997)QLSITQVASIK 272.42 2.12E-33 541260000 407650 339150 353350 331710 489620 491330 384210 364200 379260 338280 TRUE FALSE 423744.3368 397396.3743 362558.5913 397321.2479 406394.5673 377226.0537 354094.6163 359318.4947 365610.5067 404559.4892 1.047421573 0.982294038 0.896181157 0.982108339 1.004535991 0.932436548 0.875259698 0.888172208 0.903724956 1 18.62599234 2.518250606 5.552937239 0.904022415 0.977243679 0.288974872 0.04753518 0.225777296 17.92465178 0.015780985 0.014460098 329.7999653 -2.518250606 0.073221264 LTGS(ph)T(ph)SSLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LT(0.006)GS(0.971)T(0.668)S(0.238)S(0.117)LNK;LT(0.003)GS(0.922)T(0.615)S(0.178)S(0.281)LNK 102.62 0.015506 644100000 3805800 2340590 2803700 2496020 3759500 4087100 3617100 2879600 3068900 1856890 TRUE FALSE 3956055.923 2742568.125 2876766.725 2989725.306 3120461.533 3137932.966 3333582.25 2841003.672 2958450.888 2220712.043 1.781435794 1.234994935 1.295425372 1.346291301 1.405162611 1.413030102 1.501132153 1.279321054 1.332208243 1 21.0825909 -3.558614035 0.232136535 2.31E-10 1.438996691 0.436347723 0.142296092 74.64660094 1.364611336 35.67730626 0.239518864 0.000276303 3.558614035 1.438996691 LTGS(ph)TS(ph)SLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 2 LTGS(0.999)T(0.33)S(0.575)S(0.096)LNK 147.55 3.90E-05 282040000 1372400 869130 1045400 949930 1385400 1462500 1259200 1038600 1077500 863320 TRUE FALSE 1426583.412 1018396.317 1072643.983 1137823.319 1149910.203 1122856.539 1160500.614 1024679.266 1038720.985 1032471.025 1.381717625 0.986367939 1.038909526 1.102038984 1.113745737 1.087542907 1.124003082 0.99245329 1.006053401 1 19.97766986 4.745954756 24.95199047 1.05478587 1.381717783 0.793080581 0.050762136 407.8516435 1376287.518 0.012792602 0.13368942 55712.77058 -4.745954756 0.326931914 LTGS(ph)TSSLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.868)T(0.126)S(0.006)SLNK;LTGS(0.886)T(0.066)S(0.045)S(0.002)LNK;LTGS(0.931)T(0.065)S(0.005)SLNK;LTGS(0.997)T(0.003)SSLNK 269.34 2.66E-18 1620030000 2129880 1599220 1879040 1596890 2298900 2406990 2215880 1856920 1991180 1375540 TRUE FALSE 2213969.307 1873873.595 1928009.326 1912750.076 1908133.799 1848003.051 2042193.535 1832031.025 1919517.821 1645050.727 1.345836497 1.139097758 1.172006002 1.162730149 1.159923988 1.123371469 1.241416755 1.11366233 1.166844152 1 20.64970064 -5 0.110479879 0.459149196 1.272635349 0.499188881 0.059557124 143.5216547 1.053639993 17.73122178 0.698927135 1.00E-05 5 0.813486154 LTGSTSS(ph)LNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTGSTSSLNK 10 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 LTGS(0.001)T(0.071)S(0.06)S(0.868)LNK;LTGS(0.013)T(0.054)S(0.018)S(0.915)LNK;LTGSTS(0.04)S(0.96)LNK 210.44 8.08E-08 1467580000 3065030 2049700 2518590 2019390 3313900 3405160 3293840 2673060 3007660 1841480 TRUE FALSE 3186039.751 2401720.031 2584226.524 2418819.315 2750604.462 2614363.196 3035660.214 2637232.003 2899414.904 2202282.749 1.446698773 1.090559344 1.173430853 1.09832369 1.248978799 1.187115141 1.37841529 1.197499279 1.316549796 1 21.07056828 LTGVFAPRPSTGPHK ddPTM_MDA-MB-175_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 ; 149 2.06E-06 2711700000 1213500 1751700 1693820 1540450 2758600 2383800 1856910 1998380 1875990 2254100 FALSE TRUE 1261409.917 2052540.849 1737962.341 1845146.412 2289694.157 1830198.577 1711360.542 1971594.985 1808473.486 2695747.738 0.4679258 0.761399451 0.64470511 0.684465533 0.84937256 0.678920565 0.63483705 0.731372212 0.670861543 1 21.36225407 -5 0.27360358 3.179666941 0.665941306 0.523419272 0.092163181 171.4422076 1.657182208 211.6661611 0.105347602 1.00E-05 5 -2.513725635 LTHDVELNLDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTHDVELNLDYER 13 0 P02786;G3V0E5;H7C3V5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 ;;; 218.16 2.46E-11 1352020000 711800 917070 869650 1034540 1142180 1148580 824140 789190 718850 800960 FALSE TRUE 739902.4136 1074569.639 892313.7934 1239168.924 948032.6516 881839.7019 759541.7533 778612.1989 692978.7289 957892.7767 0.772427177 1.121805765 0.931538284 1.293640535 0.989706442 0.92060377 0.792929827 0.812838574 0.723440813 1 19.86950465 2.554369539 2.657213457 0.816488485 1.037868453 0.280479917 0.141238074 0.313851339 4.375091546 0.049467013 0.044154666 358.401269 -2.554369539 0.221379967 LTHVNTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTHVNTGR 8 0 Q99470;K7ELI9 Q99470 SDF2 Stromal cell-derived factor 2 0 ; 105.52 0.004372 288840000 217165 285640 237590 282620 311510 329830 254030 281760 241180 285300 FALSE TRUE 225738.8419 334696.448 243781.7906 338521.3925 258559.6415 253231.9811 234118.4648 277983.4681 232499.9789 341199.0726 0.6616045 0.980941846 0.714485502 0.992152147 0.757797023 0.742182501 0.686163837 0.814725157 0.681420313 1 18.3802542 LTIAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTIAEER 7 0 P62701;Q8TD47 P62701 RPS4X;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2" 0 ;;; 149.99 0.0046034 1372720000 1866590 2227940 2161030 2075540 2295160 2556000 2102230 2207210 2116010 2309380 FALSE TRUE 1940284.415 2610571.364 2217348.217 2486075.617 1905029.523 1962407.737 1937451.719 2177625.96 2039855.213 2761858.795 0.702528463 0.945222605 0.802846337 0.900145808 0.689763548 0.710538765 0.701502815 0.788463901 0.738580559 1 21.39720813 5.039287683 16.95990838 0.794601604 0.275541395 0.07315117 0.102948402 98243032.13 1098027943 0.02392354 1595764921 109468.1259 -5.039287683 -0.519060209 LTICPQAENRNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTICPQAENRNDR 13 1 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 99.669 0.0013848 0 91295 93108 78858 68432 101720 112320 67621 79190 86163 99583 FALSE TRUE 94899.3971 109098.5747 80913.10426 81967.64535 84429.67073 86235.38223 62320.68933 78128.58758 83062.01046 119094.3822 0.796841928 0.916068186 0.679403199 0.688257866 0.708930759 0.724092779 0.523288237 0.656022443 0.697446923 1 16.86174584 4.227261116 24.74375674 0.68595319 0.856455052 0.181366688 0.116297687 209.0094716 457694.5754 0.026995534 0.05916698 16875.67358 -4.227261116 0.170501861 LTIFGNSAVSQPASSSNHSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTIFGNSAVSQPASSSNHSSR 21 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 1 LTIFGNSAVSQPAS(0.018)S(0.063)S(0.044)NHS(0.425)S(0.45)R;LTIFGNSAVSQPAS(0.004)S(0.003)S(0.002)NHS(0.171)S(0.82)R 108.13 0.00021054 206498000 39293 142402 103373 131395 121652 155317 83708 130237 111413 149720 TRUE FALSE 40844.31798 166858.4358 106066.9853 157384.5388 100973.6365 119246.9806 77146.74823 128491.386 107403.2679 179054.7674 0.228110754 0.93188491 0.592371746 0.8789743 0.563925987 0.665980484 0.430855594 0.71760941 0.599834729 1 17.45004141 -1.934014209 2.270028227 1.257685012 0.636169103 0.253842264 0.192625587 11505044.23 5145751.147 15697954.66 0.044441621 0.011640879 1.934014209 -0.621515909 LTIQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTIQNR 6 0 P30050 P30050 RPL12 60S ribosomal protein L12 0 121.14 0.046022 149210000 108470 128690 130590 112450 162370 147270 144210 131550 119550 116990 FALSE TRUE 112752.4794 150791.5064 133993.2827 134692.2744 134770.4054 113068.7744 132906.4434 129786.7874 115247.4189 139911.9506 0.805881691 1.077760018 0.957697195 0.962693135 0.963251565 0.808142363 0.949929172 0.927631892 0.823713903 1 17.09415967 LTISPDYAYGATGHPGIIPPHATLVFDVELLK ddPTM_MDA-MB-175_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 0 214.91 5.47E-36 181650000 49728 74403 76439 79043 98683 108330 124510 92961 79495 63479 FALSE TRUE 51691.29984 87181.13648 78431.06314 94677.46948 81908.89891 83171.99926 114750.5809 91715.00985 76633.99048 75916.49467 0.68089682 1.148382006 1.033122821 1.247126463 1.078934153 1.095572176 1.511536872 1.208103855 1.009451119 1 16.21212576 5.098250948 1.531817303 1.180417274 1.37E-17 0.461778771 0.147422674 2.559361101 2.71634756 0.039307088 5.947823917 125386.5486 -5.098250948 -1.180417274 LTIYDWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTIYDWDR 8 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ;; 137.9 0.0016941 257398000 314460 382959 366916 427247 451652 508610 403875 361386 354608 445431 FALSE TRUE 326875.1236 448729.2292 376478.1324 511755.1814 374880.3544 390493.0356 372218.2222 356542.2118 341845.7273 532704.6762 0.613614144 0.842360222 0.706729543 0.960673342 0.703730174 0.733038498 0.698732785 0.669305579 0.641717151 1 19.02297642 LTKEEIVDKYDLFVGSQATDFGEALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 320.35 1.16E-82 1334890000 1421300 1060610 1355190 945910 2034660 1597480 1403450 1242070 1336490 1015680 FALSE TRUE 1477414.021 1242761.517 1390507.365 1133008.175 1688809.22 1226489.48 1293443.922 1225422.083 1288389.986 1214683.05 1.216295907 1.02311588 1.14474913 0.93276034 1.390329124 1.009719762 1.064840678 1.008841017 1.060679974 1 20.21214849 LTLALAPGPPPPPS(ph)RSPSSTLSGPDLAGHSSSATSTPEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTLALAPGPPPPPSRSPSSTLSGPDLAGHSSSATSTPEELR 41 1 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 LTLALAPGPPPPPS(0.192)RS(0.192)PS(0.05)S(0.05)T(0.05)LS(0.05)GPDLAGHS(0.056)S(0.063)S(0.063)AT(0.072)S(0.082)T(0.082)PEELR;LTLALAPGPPPPPS(0.466)RS(0.466)PS(0.017)S(0.017)T(0.017)LS(0.017)GPDLAGHSSSATSTPEELR 111.42 3.23E-06 116969000 11555.6 73668 56298 65255 57444 97563 45552 79065 53346 88980 TRUE FALSE 12011.82401 86319.90594 57765.17213 78162.24423 47679.6894 74905.47183 41981.51521 78005.263 51426.08788 106413.9274 0.112878307 0.811171132 0.542834698 0.734511414 0.448058732 0.703906657 0.394511473 0.733036219 0.483264636 1 16.69932746 -5 0.297491863 4.500346707 0.547301461 0.314638508 0.197745142 305.9463498 2.843337589 667.2526055 0.180336339 1.00E-05 5 -3.953045247 LTLDDIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTLDDIER 8 0 Q5HY81;P11441 Q5HY81 UBL4A Ubiquitin-like protein 4A 0 ; 107.47 0.0093006 84173000 190717 214107 201692 193124 226310 272240 205446 217350 213160 240780 FALSE TRUE 198246.6544 250878.2117 206948.2592 231323.3508 187841.907 209016.3858 189342.6057 214436.7788 205488.4132 287956.231 0.688461068 0.871237309 0.718679566 0.803328165 0.652327982 0.725861653 0.657539533 0.744685323 0.713609886 1 18.13549001 -1.408649285 5.728521304 1.000109853 0.731851354 0.626195563 0.062428474 8.42E-05 8.69E-06 0.058102949 0.013689417 0.039025701 1.408649285 -0.268258499 LTLDKLDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 106.29 0.0034565 0 11251000 5859300 7810800 5057600 13588000 10952000 10560000 8792400 9613700 6854500 FALSE TRUE 11695198.17 6865589.196 8014355.865 6057978.185 11278316.61 8408563.979 9732279.607 8674552.259 9267704.815 8197508.038 1.426677243 0.837521496 0.977657579 0.739002409 1.375822575 1.025746354 1.187224162 1.05819381 1.130551476 1 22.96675398 3.239901826 24.99999995 1.126576437 0.982696866 0.102302924 0.193465519 78.89062199 1470489.161 0.051908217 0.066617845 1737.408037 -3.239901826 -0.14387957 LTLEDLEDSWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ; 185.08 3.14E-05 114877000 127487 168365 196371 186672 193227 225540 183685 176460 166090 185783 FALSE TRUE 132520.2852 197280.3791 201488.5896 223595.1644 160382.3436 173161.7531 169287.2897 174094.8423 160112.4533 222183.6218 0.596444887 0.887915938 0.906856176 1.006353045 0.721845932 0.779363266 0.761925152 0.783562897 0.720631215 1 17.76139295 LTLEGLEEDDDDRVS(ph)PTVLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTLEGLEEDDDDRVSPTVLHK 21 1 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 1 LTLEGLEEDDDDRVS(0.995)PT(0.005)VLHK;LTLEGLEEDDDDRVS(0.748)PT(0.252)VLHK;LTLEGLEEDDDDRVS(0.955)PT(0.045)VLHK 276.52 4.99E-45 780550000 244853 178016 215296 174736 248654 255095 280374 216244 221375 158565 TRUE FALSE 254519.9855 208588.8632 220906.7906 209298.2593 206387.8819 195853.0523 258397.5533 213345.6029 213407.757 189632.7758 1.342172968 1.099962084 1.164918826 1.103702977 1.088355539 1.032801695 1.36262074 1.125046037 1.125373797 1 17.53284881 4.744519661 24.01506946 1.13396089 1.34217313 0.330098269 0.092588849 465.6955159 1876664.64 0.021536201 0.193057187 55528.9755 -4.744519661 0.20821224 LTLEGLEEDDDDRVSPTVLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTLEGLEEDDDDRVSPTVLHK 21 1 Q9NPB8 Q9NPB8 GPCPD1 Glycerophosphocholine phosphodiesterase GPCPD1 0 202.95 3.67E-22 71405000 37905 26988 28936 23808 36733 39935 46651 33023 36492 30089 FALSE TRUE 39401.51867 31622.97906 29690.09593 28517.15134 30489.13778 30660.70147 42994.37272 32580.3807 35178.66005 35984.36346 1.094962225 0.878797789 0.82508326 0.792487308 0.847288512 0.852056241 1.194807094 0.905403836 0.977609624 1 15.13508252 LTLNS(ph)PIFDKPLSR ddPTM_MDA-MB-175_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 LTLNS(1)PIFDKPLSR;LTLNS(1)PIFDKPLSR 200.45 1.16E-08 2631200000 3264700 2851400 3367300 2775600 4304500 4488400 4228300 3485600 4097700 3417100 TRUE FALSE 3393592.877 3341105.769 3455054.604 3324605.396 3572822.628 3446037.122 3896874.797 3438881.233 3950224.577 4086615.321 0.830416521 0.817572858 0.845456284 0.813535196 0.87427427 0.843249695 0.953570251 0.84149864 0.966625011 1 21.96247502 1.277831159 0.342833633 1.015006689 0.811446799 0.697054459 0.03572533 0.734510286 0.282722182 0.057403698 0.040750957 18.95968679 -1.277831159 -0.20355989 LTNSMMMHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTNSMMMHGR 10 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ; 146.71 2.82E-05 768650000 344190 545100 431510 454290 1007430 779870 536310 574510 574420 1179640 FALSE TRUE 357778.887 638716.6847 442755.5051 544147.2061 836187.4084 598757.0115 494272.6208 566809.6332 553746.7364 1410767.872 0.25360578 0.452743997 0.313840082 0.38570995 0.592717927 0.424419228 0.350357157 0.401773845 0.392514422 1 20.4280492 -0.992359628 4.317462361 1.000024663 0.40006802 0.819679857 0.084914935 55802785065 1.20452E+11 22332385.72 0.020173342 0.101774827 0.992359628 -0.599956643 LTPAEEENNSFQRLS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTPAEEENNSFQRLSP 16 1 Q5HYI7-5;Q5HYI7 Q5HYI7-5 MTX3 Metaxin-3 1 LTPAEEENNSFQRLS(1)P;LTPAEEENNSFQRLS(1)P;LTPAEEENNSFQRLS(1)P;LTPAEEENNSFQRLS(1)P 234.36 2.97E-19 665065000 703250 795600 686490 707420 702170 895150 637684 627171 539743 688270 TRUE FALSE 731014.853 932238.1111 704380.4934 847345.5646 582815.3942 687264.9786 587700.6618 618764.7986 520317.7549 823123.3288 0.888098815 1.132561888 0.855741137 1.029427225 0.708053549 0.834947759 0.713988586 0.751727933 0.632126118 1 19.65074908 3.238710797 24.99999997 0.759444639 0.978985034 0.421387157 0.115811972 3.365919505 560222.7659 0.030131961 0.038338074 1732.649818 -3.238710797 0.219540395 LTPEEEEILNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTPEEEEILNK 11 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;; 136.96 0.00020556 322774000 351556 258255 323052 265580 419296 416403 373538 313463 347689 249894 FALSE TRUE 365435.7023 302608.2873 331471.0005 318110.9313 348024.2157 319699.7139 344259.1155 309261.5412 335175.7408 298855.9448 1.222782109 1.01255569 1.109133033 1.06442899 1.164521642 1.069745205 1.151923264 1.034818101 1.121529441 1 18.18909072 -4.999999966 0.212299071 0.509326769 1.114199018 0.222582678 0.060009246 220.9693242 2.205425393 46.12139497 0.113683178 1.00E-05 4.999999966 0.604872248 LTPEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 ;; 183.04 0.00052435 1846010000 1372180 1353350 1360520 1257490 1782390 1635470 1257530 1282460 1252920 1347470 FALSE TRUE 1426354.726 1585777.335 1395976.269 1506217.769 1479419.984 1255656.878 1158961.513 1265270.721 1207827.654 1611480.948 0.88512044 0.984049695 0.866269174 0.934679228 0.918049938 0.779194368 0.719190329 0.785160211 0.749514076 1 20.6199557 2.740717678 23.42450342 0.785603491 0.919416876 0.322252696 0.077545744 73.59823909 799239.0192 0.022265912 0.022573161 550.4497492 -2.740717678 0.133813385 LTPGCEAEAETEAICFFVQQFTDMEHNR ddPTM_MDA-MB-175_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 ;;;;;;; 336.34 4.25E-96 19068430000 3466139 3897512 4027950 4651606 4814788 5065311 4612778 4263395 4422910 3605231 FALSE TRUE 3602984.844 4566879.368 4132921.686 5571679.783 3996372.056 3888969.286 4251216.407 4206251.164 4263730.333 4311606.988 0.835647788 1.059205855 0.958557145 1.292251311 0.926886905 0.901976756 0.985993487 0.975564604 0.988895868 1 22.03979425 LTPHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTPHEK 6 0 O00148;O00148-2;O00148-3;K7EQN7 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ;;; 117.7 0.022498 500451000 1724220 1436380 1576280 1473200 2031430 2131400 1842690 1686350 1585500 1421560 FALSE TRUE 1792293.537 1683067.092 1617359.152 1764594.563 1686128.254 1636414.652 1698255.143 1663747.237 1528438.165 1700087.465 1.054236076 0.989988531 0.95133879 1.0379434 0.991789122 0.962547331 0.998922219 0.978624495 0.899035018 1 20.69717754 2.29716798 0.864479397 0.959157281 1.004204333 0.20046177 0.037011966 1.095219705 1.578590593 0.027912883 0.017085689 198.2293605 -2.29716798 0.045047051 LTPIHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTPIHDR 7 0 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;; 157.58 0.0014664 2547510000 2979550 3363380 3273950 3607030 3532660 4025580 3738430 3482960 3136130 3138350 FALSE TRUE 3097184.935 3941014.352 3359271.827 4320489.768 2932179.715 3090700.053 3445402.088 3436276.618 3023261.294 3753249.595 0.825200898 1.05002725 0.895030224 1.15113308 0.781237602 0.823473093 0.917978408 0.915547056 0.805504994 1 21.8397088 3.204538944 24.99970287 0.873660602 0.979231538 0.212314158 0.100381173 277.7840932 204119.6681 0.027494105 0.032863324 1601.544255 -3.204538944 0.105570937 LTPLSHEVISR ddPTM_MDA-MB-175_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 ;;; 248.05 3.50E-16 2370470000 1227200 1634380 1557570 1673680 1777440 1885510 1521020 1537160 1494910 1733900 FALSE TRUE 1275650.804 1915072.051 1598161.554 2004728.909 1475311.384 1447628.878 1401798.478 1516556.884 1441108.481 2073624.507 0.615179267 0.923538492 0.770709233 0.966775277 0.71146506 0.698115243 0.676013653 0.731355595 0.694970799 1 20.98372324 LTPPVLEEMGHCDSVYLSEVGDTQVVVFKHEKEDGAISTIVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTPPVLEEMGHCDSVYLSEVGDTQVVVFKHEKEDGAISTIVLR 43 2 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 85.468 6.48E-05 110680000 103000 98155 140580 72460 183760 140660 95062 105340 146360 144190 FALSE TRUE 107066.5195 115012.3577 144243.6303 86792.37173 152524.5408 107993.8467 87610.79204 103928.0896 141092.5322 172441.2698 0.620886866 0.666965384 0.83647975 0.503315545 0.884501378 0.626264506 0.508061627 0.602686873 0.818206293 1 17.39574557 0.994592205 4.128305838 0.999124942 0.655105687 0.466563528 0.116394165 0.153177843 7.515952355 0.109844564 0.028065509 9.876252968 -0.994592205 -0.344019255 LTPRPS(ph)PSPMIESTPMSIAGDATPLLDEMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTPRPSPSPMIESTPMSIAGDATPLLDEMDR 31 1 Q7KZ85;Q7KZ85-3;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 LT(0.008)PRPS(0.916)PS(0.074)PMIES(0.001)T(0.001)PMSIAGDATPLLDEMDR;LT(0.007)PRPS(0.415)PS(0.415)PMIES(0.052)T(0.052)PMS(0.06)IAGDATPLLDEMDR 142.91 1.32E-08 155977000 16476.7 18481.2 25252.6 19425.9 20373.2 31362 18950.5 25971.4 23193.8 23937 TRUE FALSE 17127.21284 21655.20234 25910.7035 23268.28504 16910.17074 24078.6508 17465.11029 25623.29586 22359.05967 28626.99685 0.598288844 0.756460849 0.905114275 0.812809152 0.590707116 0.841116898 0.610092298 0.895074534 0.781048036 1 14.80508871 0.755967084 0.908013121 0.997737525 0.744438954 0.325435165 0.110305728 1.091352197 1.699231237 0.103023783 0.034586797 5.701210603 -0.755967084 -0.253298572 LTPS(ph)PDIIVLSDNEASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPS(1)PDIIVLSDNEASSPR;LT(0.001)PS(0.999)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LTPS(1)PDIIVLSDNEASSPR 205.18 4.44E-16 143168000 36016.1 54354.2 45145.2 49125.2 53772.5 62608.9 46863.4 53118.4 43173.5 59838.3 TRUE FALSE 37438.04344 63689.11103 46321.721 58842.01794 44632.26966 48068.93182 43190.12425 52406.43473 41619.69417 71562.46921 0.523151924 0.889979227 0.647290703 0.822246893 0.623682639 0.671705887 0.60353038 0.732317307 0.581585496 1 16.12691555 -0.86779047 5.048055129 1.000000606 0.685485154 0.453898047 0.105852202 6.52E-07 1.46E-07 0.092482586 0.021798312 0.13558434 0.86779047 -0.314515451 LTPSGYEWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTPSGYEWGR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 78.113 0.053196 0 59538 69176 66447 53139 68685 87252 78484 72929 66864 67447 FALSE TRUE 61888.60621 81056.43989 68178.66341 63649.7356 57009.94823 66989.04532 72332.219 71951.50604 64457.5777 80661.9483 0.767259005 1.004890678 0.845239482 0.789092465 0.706776236 0.830491288 0.896732853 0.892012994 0.799107622 1 16.29960063 -0.202047439 7.215463007 0.999999997 0.842956384 0.279867592 0.077962124 10507974.4 1456313.409 0.077546099 0.018807692 0.627989758 0.202047439 -0.157043613 LTPSPDIIVLS(ph)DNEASSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLS(0.96)DNEAS(0.02)S(0.02)PR 81.317 0.0042153 0 12219 13164 12162 11809 15389 20227 13076 14633 13552 12101 TRUE FALSE 12701.41556 15424.8146 12478.95171 14144.78495 12773.18328 15529.58579 12051.06895 14436.86857 13064.26617 14471.95926 0.877656945 1.065841488 0.862284884 0.977392535 0.882616033 1.073081088 0.832718551 0.997575263 0.902729612 1 13.82097263 5.068406444 15.68923952 0.951794887 0.000109062 0.078332564 0.078851832 5154930.283 23606521.72 0.016616721 160159501.4 117059.4404 -5.068406444 -0.951685825 LTPSPDIIVLSDNEASS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR34;A0A0U1RRK3 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 LTPSPDIIVLSDNEAS(0.389)S(0.611)PR 214.3 4.54E-19 73509000 142170 158910 159010 147810 153700 189900 149190 154520 144760 147440 TRUE FALSE 147782.9814 186201.5564 163153.9312 177046.3768 127574.1289 145798.603 137496.098 152448.9121 139550.1159 176328.0451 0.838113876 1.055995127 0.925286339 1.004073837 0.723504471 0.826859975 0.779774414 0.864575525 0.791423258 1 17.42790243 3.253819781 24.99984156 0.823471503 0.960834944 0.336027095 0.085464926 236.021436 386683.2853 0.021676723 0.029240707 1793.989021 -3.253819781 0.137363441 LTPVRPAAAS(ph)PIVSGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 234.72 2.33E-20 2780850000 900600 982970 1007280 981438 1131250 1178390 984690 1014660 1005050 1050670 TRUE FALSE 936156.3834 1151787.451 1033530.544 1175563.507 938960.5291 904726.7812 907507.4248 1001060.142 968878.4468 1256528.67 0.745033843 0.916642396 0.822528422 0.935564412 0.747265503 0.720020802 0.722233759 0.796687068 0.771075479 1 20.26101216 5.043254989 16.75309169 0.812727275 0.385990359 0.049006277 0.09171446 15100366.77 149520350.9 0.021642249 203800860.9 110472.7051 -5.043254989 -0.426736917 LTPVS(ph)PESSSTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LTPVSPESSSTEEK 14 0 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 LTPVS(0.999)PES(0.001)SSTEEK;LTPVS(0.987)PES(0.012)S(0.002)STEEK;LTPVS(1)PESSSTEEK;LTPVS(0.693)PES(0.245)S(0.059)S(0.002)T(0.001)EEK;LTPVS(1)PESSSTEEK;LTPVS(1)PESSSTEEK 336.06 1.35E-68 3006650000 3952904 2592755 3262137 2506434 4212130 4617740 4424190 3462839 3737350 2418583 TRUE FALSE 4108967.702 3038040.502 3347150.97 3002199.164 3496153.647 3545339.868 4077410.427 3416425.307 3602843.504 2892458.032 1.420579886 1.050331748 1.157199494 1.037940441 1.208713699 1.225718689 1.409669693 1.181149482 1.245599232 1 21.4638646 3.013400675 24.91760465 1.234411117 1.153271257 0.009778915 0.135671938 617.5378213 1148258.219 0.037307311 0.044569865 1031.337181 -3.013400675 -0.08113986 LTPYEVDELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 LTPYEVDELRR 11 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 219.33 1.60E-11 8751591000 2823402 3435587 3454105 3142180 3863988 3924328 3296898 3313428 3225964 3520847 FALSE TRUE 2934872.091 4025622.342 3544121.814 3763693.826 3207188.7 3012962.296 3038478.52 3269016.917 3109862.186 4210689.559 0.697005099 0.95604824 0.841696298 0.893842629 0.761677786 0.715550803 0.721610671 0.776361418 0.738563635 1 22.00562508 5.036579003 15.69138699 0.808478133 0.279045978 0.119721688 0.095466928 4842672.454 59438287.68 0.022796774 71037979.63 108787.5017 -5.036579003 -0.529432154 LTQDQDVDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTQDQDVDVK 10 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 125.75 0.00093265 58652000 94340 68957 73044 67890 100670 104820 93134 79702 80058 70072 FALSE TRUE 98064.61605 80799.82834 74947.58665 81318.43937 83558.14936 80477.14356 85833.91372 78633.72506 77176.72822 83801.26679 1.170204459 0.964183853 0.894349089 0.970372436 0.997098881 0.960333258 1.024255563 0.938335756 0.920949422 1 16.35468443 4.738197017 8.318845302 0.962093134 1.17158373 0.741224027 0.03666758 0.043215358 43.50611732 0.008788826 0.051444758 54726.41717 -4.738197017 0.209490596 LTQEPESIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTQEPESIRK 10 1 P09497-2;P09497;H0Y9Q6 P09497-2 CLTB Clathrin light chain B 0 ;;;; 150.09 3.56E-05 2302890000 2615110 2331750 2580620 2067760 3533110 3287190 2830660 2770440 2946620 2500370 FALSE TRUE 2718356.562 2732209.924 2647873.077 2476756.756 2932553.224 2523789.94 2608785.473 2733306.783 2840571.722 2990269.629 0.909067375 0.913700189 0.885496429 0.82827205 0.980698595 0.844000794 0.87242483 0.914066998 0.949938325 1 21.51184415 1.090789868 1.928319275 0.998686826 0.890796188 0.439197437 0.039464387 0.279307867 2.044168369 0.035510461 0.010111768 12.32508343 -1.090789868 -0.107890638 LTQT(ph)SSTEQLNVLETETEVLNK ddPTM_MDA-MB-175_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(0.358)S(0.236)S(0.164)T(0.164)EQLNVLETETEVLNK 111.66 0.0011696 85017000 17669 16050 17116 14786 19307 20993 16499 18147 18013 15630 TRUE FALSE 18366.58576 18806.46265 17562.05702 17710.62667 16025.20304 16117.6939 15205.76527 17903.76915 17364.71565 18692.39925 0.982569734 1.006102127 0.939529313 0.947477444 0.85731119 0.862259237 0.81347317 0.957810119 0.928972007 1 14.19016414 3.84271921 1.775549852 0.89870919 0.993288603 0.286375908 0.052125896 0.432911136 2.626853456 0.015253963 0.037775672 6961.762604 -3.84271921 0.094579413 LTQTSS(ph)TEQLNVLETETEVLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 LT(0.004)QT(0.001)S(0.008)S(0.493)T(0.493)EQLNVLETETEVLNK;LT(0.034)QT(0.023)S(0.096)S(0.423)T(0.423)EQLNVLETETEVLNK;LT(0.018)QT(0.009)S(0.011)S(0.481)T(0.481)EQLNVLETETEVLNK 286.03 2.77E-46 681260000 395282 298575 344291 269881 416357 413770 377534 355728 373016 239678 TRUE FALSE 410888.0386 349852.9337 353263.5063 323262.6563 345584.7859 317678.1882 347941.8986 350960.048 359591.227 286638.3152 1.433472138 1.220537922 1.232436445 1.127771966 1.205647562 1.108289337 1.213870861 1.224400331 1.254512073 1 18.12887194 8 0.020168462 2.34E-11 2.75195288 0.445666962 0.079270581 3400.864245 5.284611476 266.5575008 484.5195626 100000000 -8 2.75195288 LTQYHGGS(ph)LPNVSQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTQYHGGSLPNVSQLR 16 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR;LTQYHGGS(1)LPNVSQLR 244.22 3.11E-20 2349490000 2163520 2617970 2408910 2401720 2838530 2785040 2125220 2455380 2162220 2438500 TRUE FALSE 2248937.44 3067585.983 2471688.174 2876773.048 2356037.684 2138256.668 1958639.703 2422469.647 2084402.125 2916277.387 0.771167191 1.051884158 0.847549065 0.986453847 0.807892176 0.733214432 0.671623252 0.830671889 0.714747552 1 21.47569652 3.088467285 6.17840201 0.773821812 0.918645323 0.222244142 0.109183732 0.254658828 14.45381343 0.029208795 0.035044816 1225.93455 -3.088467285 0.144823511 LTRDETNYGIPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTRDETNYGIPQR 13 1 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 ;;; 161.21 3.88E-05 2692530000 1357800 1182410 1277510 987660 1512160 1601570 1211960 1206490 1211660 1390760 FALSE TRUE 1411406.992 1385479.72 1310802.96 1183016.2 1255123.583 1229629.64 1116963.408 1190318.975 1168052.593 1663252.794 0.848582367 0.832994073 0.788096052 0.711266624 0.754619856 0.739292093 0.671553604 0.715657283 0.702270032 1 20.66557603 4.065707402 2.71818097 0.737531328 0.843349252 0.101641942 0.087291037 0.419647896 6.212185923 0.020890113 0.054044778 11633.41985 -4.065707402 0.105817924 LTRPAAS(ph)PAVGEK ddPTM_MDA-MB-175_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 145.94 0.0001106 42835000 106350 86288 101430 71547 120500 135290 109540 97687 104180 82253 TRUE FALSE 110548.7801 101107.2928 104073.3491 85698.78305 100017.453 103870.9478 100953.9686 96377.66555 100430.5822 98368.90052 1.123818397 1.027837988 1.057990367 0.871197936 1.016758879 1.055932793 1.026279322 0.979757475 1.020958673 1 16.58591466 4.806345217 1.615052003 1.000273787 1.180736671 0.351589048 0.049473834 1.383587264 3.042078244 0.013192447 0.411396405 64024.3558 -4.806345217 0.180462884 LTS(ph)DEEGEPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTSDEEGEPSGK 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 LT(0.022)S(0.978)DEEGEPSGK;LT(0.03)S(0.97)DEEGEPSGK 172.76 3.66E-05 321909000 1091990 642460 907850 738790 1113910 1240540 1373150 969130 1056230 551770 TRUE FALSE 1135102.608 752797.5074 931509.3168 884920.4569 924567.9761 952443.3856 1265518.915 956140.3975 1018216.489 659878.7672 1.720168408 1.140811835 1.411637051 1.3410349 1.401117936 1.443361164 1.917805175 1.448963726 1.54303569 1 19.33184147 2.466733369 24.99244105 1.541993197 1.389113607 0 0.248568071 564.3146701 1357686.885 0.08018489 0.067152404 292.9094403 -2.466733369 -0.15287959 LTSEEFNAIFTFYDKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTSEEFNAIFTFYDKDR 17 1 P22676;H3BMN5 P22676 CALB2 Calretinin 0 ;; 209.73 3.66E-12 820191000 779462 679768 825888 623112 1030600 1035501 956522 842233 976533 677222 FALSE TRUE 810235.7616 796512.8661 847411.3198 746361.6938 855418.9801 795021.5859 881547.3062 830944.2443 941387.7681 809910.6847 1.000401374 0.983457659 1.046302186 0.921535804 1.056189277 0.981616369 1.088450027 1.025970221 1.162335287 1 19.62740329 2.240629791 24.99976745 1.06710123 0.998908766 0.302715328 0.052700472 67.48263635 815334.616 0.017493903 0.013969841 174.0322724 -2.240629791 -0.068192464 LTSS(ph)CPDLPSQTDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTSSCPDLPSQTDKK 15 1 P56962 P56962 STX17 Syntaxin-17 1 LTS(0.013)S(0.987)CPDLPSQTDKK 243.95 3.23E-18 254090000 360320 179480 249240 154570 352840 314590 297300 237960 287650 135720 TRUE FALSE 374545.7118 210304.2938 255735.3992 185143.4847 292864.3828 241531.2402 273996.8492 234770.5354 277297.5327 162311.7355 2.307570126 1.295681383 1.575581694 1.140666041 1.804332767 1.488070098 1.688090195 1.446417505 1.708425653 1 17.30840779 -1.988369546 2.792327074 0.463578687 1.578250483 0.262583034 0.301475652 112957793.9 103821332.6 391136135.6 0.066102432 0.010271419 1.988369546 1.114671796 LTSVVTPRPFGSQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTSVVTPRPFGSQTR 15 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 0 ; 97.065 0.0031533 283060000 470130 389290 406160 398350 499500 491030 400180 406930 418570 404020 FALSE TRUE 488691.0954 456147.5292 416744.8633 477142.441 414595.1684 376995.7241 368812.8459 401475.769 403505.7475 483179.9836 1.011405919 0.944053034 0.862504403 0.987504568 0.858055347 0.780238704 0.763303238 0.830903147 0.835104436 1 18.88220116 3.082757802 5.526405728 0.824465345 0.943829068 0.340640854 0.070592432 0.204081191 10.36355858 0.019678159 0.023622358 1209.923195 -3.082757802 0.119363723 LTTPTYGDLNHLVS(ph)ATMSGVTTCLR ddPTM_MDA-MB-175_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 LTTPTYGDLNHLVS(0.999)AT(0.001)MSGVTTCLR 110.16 0.0018774 104750000 95302 68670 66412 54490 65678 91365 64532 62737 46076 75308 TRUE FALSE 99064.59655 80463.53832 68142.75128 65267.95936 54514.07702 70146.8634 59473.81322 61896.11313 44417.73376 90063.16074 1.099945813 0.89341233 0.756610702 0.72469097 0.605287185 0.778862998 0.660356718 0.687252286 0.493184265 1 16.45864949 4.65928266 1.254728219 0.688379179 1.249951607 0.496273178 0.12332521 0.910241658 1.375179304 0.032056876 0.63722508 45633.38239 -4.65928266 0.561572428 LTTPTYGDLNHLVSATMS(ph)GVTTCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.03)MS(0.97)GVTTCLR;LTTPTYGDLNHLVS(0.002)AT(0.165)MS(0.831)GVT(0.001)TCLR 192.87 2.86E-18 295920000 166872 237864 195258 211948 219149 257390 201976 200538 217585 219016 TRUE FALSE 173460.2354 278715.2917 200346.5839 253870.6818 181898.1313 197615.0733 186144.5934 197850.1161 209754.1584 261927.9919 0.662243978 1.064091278 0.764891841 0.969238454 0.694458542 0.754463362 0.710670868 0.755360718 0.800808485 1 17.99881072 5.035290317 16.11333174 0.816826708 0.089725922 0.133703448 0.124412886 7982148.375 101619072.1 0.028770287 164828407.9 108465.1738 -5.035290317 -0.727100786 LTTPTYGDLNHLVSATMSGVTTCLR ddPTM_MDA-MB-175_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 ;;; 327.05 9.46E-88 10452970000 2519703 3314339 3069090 3360444 3517783 4032405 3321912 3363449 3244589 3399936 FALSE TRUE 2619182.82 3883550.941 3149073.007 4025129.793 2919831.502 3095940.05 3061531.857 3318367.468 3127816.876 4066088.363 0.644152951 0.955107365 0.774472349 0.989926788 0.71809347 0.76140501 0.752942775 0.816108055 0.769244688 1 21.95521014 -1.321640554 3.725160527 1.000583909 0.803140268 0.273638322 0.098434583 14265561.73 5061423.964 66957.52209 0.021341305 0.047682547 1.321640554 -0.197443641 LTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLR 35 1 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 92.343 0.00029866 131720000 7010.7 10191 8280.4 9677.8 14046 15665 9670 9093.1 10261 12703 FALSE TRUE 7287.487849 11941.22498 8496.194026 11592.03995 11658.46594 12027.04116 8912.040132 8971.221868 9891.708614 15191.90964 0.479695313 0.786025277 0.559257804 0.763040344 0.767412802 0.791674085 0.58663067 0.590526279 0.651116868 1 13.89101561 -1.777822904 2.623473085 1.08745342 0.665272508 0.484349826 0.104019091 19669804.98 13897587.95 11013074.28 0.024589188 0.016679272 1.777822904 -0.422180912 LTTTGQVT(ph)SPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.5)S(0.5)PVK 203.76 1.36E-06 171600000 917420 493790 688220 613760 805200 985730 1038900 756900 732590 441550 TRUE FALSE 953640.45 578594.5913 706155.5786 735159.8961 668332.3916 756809.1464 957468.3033 746754.9935 706224.229 528063.2685 1.805920818 1.095691797 1.33725563 1.392181468 1.265629388 1.433178923 1.813169672 1.414139248 1.337385634 1 19.01035127 2.493958806 24.33146227 1.461397777 1.360698713 0 0.251649372 2113.612792 3054324.38 0.078671982 0.072461872 311.8593766 -2.493958806 -0.100699064 LTTTGQVTS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LTTTGQVTSPVK 12 0 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.159)S(0.841)PVK;LTTTGQVT(0.013)S(0.987)PVK;LTTTGQVT(0.014)S(0.986)PVK;LTTTGQVT(0.018)S(0.982)PVK;LTTTGQVT(0.021)S(0.979)PVK 239.61 3.71E-16 2583910000 4118600 2336270 3052640 2768040 3586560 4093040 4517170 3357560 3308700 1883570 TRUE FALSE 4281205.508 2737506.199 3132194.306 3315550.05 2976917.812 3142493.491 4163102.412 3312557.4 3189620.533 2252619.478 1.900545365 1.215254607 1.390467558 1.471864237 1.321536034 1.395039651 1.848116139 1.470535717 1.415960647 1 21.1031722 4.756220211 24.1990955 1.429816028 1.900545974 0.341555216 0.205877102 2915.753534 3995381.459 0.048048152 1.440324938 57045.34496 -4.756220211 0.470729946 LTTTGQVTS(ph)PVKGASFVTSTNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTTTGQVTSPVKGASFVTSTNPR 23 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5;K7ENR9 P49916-3 LIG3 DNA ligase 3 1 LTTTGQVT(0.025)S(0.975)PVKGASFVTSTNPR;LTTTGQVT(0.138)S(0.862)PVKGASFVTSTNPR;LTTTGQVT(0.216)S(0.784)PVKGASFVTSTNPR 223 9.28E-33 3254100000 2401116 1816517 2370027 1669219 2882536 2853510 2271007 2313534 2453636 2117538 TRUE FALSE 2495913.914 2128489.664 2431791.851 1999385.536 2392563.56 2190825.548 2092999.537 2282524.861 2365330.12 2532429.028 0.985580992 0.840493313 0.960260613 0.789512959 0.944770232 0.86510837 0.82647905 0.901318392 0.934016351 1 21.27209041 0.983499232 2.383371679 0.999179807 0.884913852 0.255510751 0.058688108 0.366423502 4.670128657 0.050632079 0.013778083 9.627183107 -0.983499232 -0.114265956 LTVAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LTVASPK 7 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK;LTVAS(1)PK 131.52 0.0036277 1675540000 6689770 3056050 3824820 2953310 5464640 6782280 5362200 4216410 4381080 2508850 TRUE FALSE 6953887.285 3580902.815 3924497.951 3537465.903 4535762.445 5207198.256 4941896.752 4159895.921 4223405.787 3000411.123 2.317644816 1.193470717 1.307986736 1.178993731 1.511713648 1.735494918 1.647073201 1.386441974 1.407609029 1 21.51672876 0.723163245 1.397863193 1.001807726 1.516456265 0.209611256 0.313219338 1.554117402 4.987887831 0.289935687 0.085680755 5.286439239 -0.723163245 0.514648539 LTVDEAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 99.755 0.015327 104670000 219720 213460 191330 204050 260440 253290 222360 215370 199330 221080 FALSE TRUE 228394.7153 250120.0945 196316.217 244410.481 216170.5018 194467.2361 204930.8422 212483.3174 192156.1522 264396.3932 0.863834459 0.946004185 0.742507167 0.924409286 0.817600041 0.735513952 0.775089402 0.803654372 0.726772971 1 18.01234297 3.011857675 24.12637944 0.792398802 0.866299149 0.087103858 0.087251021 280.3079714 570325.6431 0.023332273 0.027865097 1027.679457 -3.011857675 0.073900347 LTVEDLEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LTVEDLEKER 10 1 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 ;;;;; 151.79 1.75E-05 3938030000 4631460 3246148 4035167 2480566 5821540 5125610 3873490 3915870 4262330 3574950 FALSE TRUE 4814313.617 3803648.667 4140326.767 2971214.551 4831996.71 3935264.757 3569875.732 3863384.168 4108929.576 4275393.006 1.126051713 0.889660591 0.968408462 0.694957059 1.130187729 0.92044515 0.83498189 0.903632523 0.961064765 1 22.02762561 4.743044851 24.15335715 0.91575197 1.126051851 0.244156466 0.106784948 383.1205948 2063474.351 0.023981392 0.188198509 55340.72582 -4.743044851 0.210299881 LTVEDPVTVEYITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTVEDPVTVEYITR 14 0 O14818;H0Y586;O14818-2;O14818-4;Q8TAA3-2;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 122.7 0.00024941 35342000 49978 48792 54794 48822 57168 57994 53310 53928 51063 52892 FALSE TRUE 51951.17003 57171.64645 56221.97665 58478.84588 47450.60378 44525.77241 49131.4229 53205.18337 49225.2526 63255.17472 0.821295179 0.903825603 0.888812289 0.924491097 0.750145802 0.703907192 0.776717844 0.841119855 0.778201196 1 15.94889589 3.241702329 24.99826505 0.796457239 0.886279315 0.177099273 0.078009599 118.0949697 939660.4779 0.021099886 0.027409019 1744.625954 -3.241702329 0.089822077 LTVENS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTVENSPK 8 0 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PK;LTVENS(1)PK;LTVENS(1)PK 113.22 0.0030312 883200000 3903620 1484120 1747900 1718500 2570590 3572980 3211320 2158840 2120160 1116930 TRUE FALSE 4057737.932 1739006.065 1793451.71 2058414.171 2133642.03 2743209.544 2959608.347 2129904.281 2043855.856 1335771.049 3.037749573 1.30187435 1.342634063 1.540993251 1.59731118 2.053652493 2.215655408 1.594512984 1.530094441 1 20.34924132 4.746881731 24.65680063 1.62866297 3.037750428 0.627293815 0.335938652 610.0941204 1807757.57 0.082944231 0.940624979 55831.81301 -4.746881731 1.409087458 LTVENS(ph)PKQEAGISEGQGTAGEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTVENSPKQEAGISEGQGTAGEEEEK 26 1 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LTVENS(1)PKQEAGISEGQGTAGEEEEK;LTVENS(1)PKQEAGISEGQGTAGEEEEK 314.78 4.34E-82 575110000 674860 164956 271613 156648 442260 599200 426020 268730 342160 122405 TRUE FALSE 701503.9939 193285.9098 278691.4579 187632.5069 367084.8032 460044.881 392627.4392 265128.1139 329845.7284 146387.9162 4.792089486 1.32036793 1.903787315 1.281748602 2.507616836 3.14264246 2.682102796 1.811133875 2.253230574 1 17.15943694 4.74835696 24.68838881 2.061608098 4.792091247 0.627933904 0.645102089 779.8748625 1965364.748 0.157509938 2.074875913 56021.78721 -4.74835696 2.730483149 LTVENS(ph)PKQEAGISEGQGTAGEEEEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LTVENSPKQEAGISEGQGTAGEEEEKKK 28 3 O43583;F8VVL1 O43583 DENR Density-regulated protein 1 LT(0.018)VENS(0.98)PKQEAGIS(0.001)EGQGTAGEEEEKKK;LTVENS(1)PKQEAGISEGQGTAGEEEEKKK;LTVENS(1)PKQEAGISEGQGTAGEEEEKKK 248.2 6.20E-46 2260260000 2451400 271354 676116 214216 1184570 1156652 899720 581184 779387 194127 TRUE FALSE 2548183.165 317956.9387 693736.1384 256587.2854 983217.2145 888037.1022 829197.5954 573394.1791 751337.0141 232162.4689 10.97586176 1.369544958 2.988149384 1.105205707 4.23503945 3.825067448 3.571626368 2.469797043 3.236255273 1 17.82477524 4.744545557 24.95530569 2.76727793 10.97586544 0.83725136 1.100765891 240.4341593 1002505.485 0.254340393 2.322571967 55532.28666 -4.744545557 8.208587509 LTVIDTPGFGDHINNENCWQPIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTVIDTPGFGDHINNENCWQPIMK 24 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52;K7ELJ9;K7EJZ2 Q9UHD8 9-Sep Septin-9 0 300.41 3.63E-62 326260000 163010 216540 249600 225930 251340 293220 254900 235220 245410 198080 FALSE TRUE 169445.7607 253729.0606 256104.781 270618.2797 208617.3166 225124.0988 234920.2719 232067.2606 236577.742 236889.9835 0.715293058 1.071083955 1.081112748 1.142379579 0.880650644 0.950331861 0.991685121 0.979641508 0.998681913 1 17.85385767 4.746193298 24.83142166 1.008170832 0.715292904 0.619692572 0.069382871 609.8483839 1983969.229 0.017675628 0.187956481 55743.3799 -4.746193298 -0.292877928 LTVNADVGYYSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTVNADVGYYSWR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 182.1 2.67E-05 992670000 205292 242267 199771 210908 227582 270280 253302 184553 223666 229236 FALSE TRUE 213397.0867 283874.4727 204977.1964 252624.9729 188897.6929 207511.5661 233447.5274 182079.3689 215616.3044 274150.4052 0.778394205 1.035469827 0.747681537 0.921483128 0.689029414 0.756925987 0.851530849 0.664158671 0.786489096 1 18.06460808 3.250070434 24.99981223 0.769955493 0.873731245 0.086032378 0.11453273 389.7658488 846583.0978 0.029553988 0.039680857 1778.567834 -3.250070434 0.103775752 LTWFVNEGLVDGWDDPRFPTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LTWFVNEGLVDGWDDPRFPTVR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 192.63 9.14E-18 691330000 71138 67754 64893 78748 71231 80740 92534 73921 87538 76427 FALSE TRUE 73946.58317 79390.22245 66584.16489 94324.11936 59123.18006 61989.35863 85280.94329 72930.20991 84387.52448 91401.40737 0.809031122 0.868588622 0.72848074 1.031976663 0.646851966 0.678210111 0.933037529 0.797911236 0.923262857 1 16.47992876 1.023954195 1.435870379 1.001662133 0.807995557 0.240691133 0.109350842 0.609333766 2.561982084 0.099911273 0.029889032 10.56706053 -1.023954195 -0.193666576 LTWHAYPEDAENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTWHAYPEDAENK 13 0 P45973 P45973 CBX5 Chromobox protein homolog 5 0 62.081 0.079348 113250000 76787 56098 73712 55070 82105 81418 85187 66185 67153 53092 FALSE TRUE 79818.61005 65732.39512 75632.99528 65962.68163 68148.82143 62509.9034 78509.82035 65297.89833 64736.17665 63494.36089 1.257097621 1.035247764 1.191176574 1.038874645 1.073305101 0.984495356 1.236484929 1.028404687 1.01955789 1 15.95434085 6.931951034 1.57290167 1.072225686 199.8925083 0.326113984 0.079322075 1877.364433 5.308196404 0.019396797 1346106.414 8549703.112 -6.931951034 198.8202826 LTWHAYPEDAENKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTWHAYPEDAENKEK 15 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 94.487 0.002675 490760000 934130 448190 621430 428400 952000 924990 842400 607770 729470 400890 FALSE TRUE 971010.1737 525163.1461 637624.9763 513136.2414 790179.38 710175.0909 776370.4868 599623.8373 703216.5172 479436.72 2.025314569 1.095375311 1.329946059 1.070289821 1.648141135 1.481269709 1.619338808 1.250684005 1.466755649 1 18.87098088 1.612530215 25 1.269029598 1.43944072 0.112257804 0.282731524 1.207933512 6440.78915 0.131355584 0.069812205 40.9760617 -1.612530215 0.170411122 LTWHS(ph)CPEDEAQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 1 LTWHS(1)CPEDEAQ 134.56 0.00015027 890530000 781560 1013600 842550 909730 992730 1191900 843420 974000 992120 1087400 TRUE FALSE 812416.5923 1187677.915 864507.5452 1089671.879 823986.1092 915099.2884 777310.5365 960945.1231 956413.795 1300455.21 0.624717088 0.913278601 0.664773026 0.837915731 0.633613601 0.703676129 0.597721883 0.738929811 0.735445394 1 20.31058528 -1.808966363 5.686423942 1.023119448 0.717982729 0.454812471 0.093050191 0.025183727 0.000846039 0.083193146 0.019782546 0.015525073 1.808966363 -0.305136719 LTWHSCPEDEAQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LTWHSCPEDEAQ 12 0 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;;;;; 188.91 2.00E-05 2348480000 2004340 2522730 2278290 2385390 2557120 2937270 2211320 2404870 2295270 2576000 FALSE TRUE 2083472.891 2955989.253 2337664.109 2857213.022 2122461.656 2255133.557 2037990.96 2372636.651 2212663.681 3080717.88 0.676294608 0.959513129 0.758804993 0.927450398 0.688950348 0.732015603 0.661531188 0.770157069 0.718229896 1 21.55483514 5.032505483 17.7220009 0.786407796 0.261440214 0.08525215 0.11366836 36135915.15 502912062.7 0.025950795 596120296.8 107771.8859 -5.032505483 -0.524967582 LVALHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVALHK 6 0 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 69.439 0.0935 273150000 407380 378060 397700 383660 562090 520850 463920 435850 450540 447850 FALSE TRUE 423463.677 442988.8641 408064.3887 459546.8029 466546.1426 399890.4811 427556.7382 430008.1437 434325.1534 535597.6329 0.790637693 0.827092647 0.761886094 0.858007532 0.871075811 0.74662481 0.798279738 0.802856692 0.810916865 1 19.03079006 -2.201741884 1.615864536 1.407695511 0.807537985 0.716993451 0.036284672 177181.6255 29652.97423 263154.6342 0.009828826 0.006284317 2.201741884 -0.600157525 LVALLNTLDR ddPTM_MDA-MB-175_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 95.311 0.017468 24921000 56403 99642 91401 83501 115000 144530 79928 98514 101350 157210 FALSE TRUE 58629.83399 116754.7384 93782.98515 100017.2486 95452.34108 110965.0979 73663.03451 97193.58097 97702.4333 188012.2895 0.311840434 0.620995248 0.498813058 0.531971866 0.507692031 0.590201301 0.39179904 0.51695334 0.519659824 1 17.52046744 0.45600314 2.493637648 0.999997421 0.501151974 0.760399193 0.084448299 5.184790445 23.12070475 0.073723459 0.019664106 2.857611202 -0.45600314 -0.498845447 LVASMEEARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 208.63 1.77E-07 565757000 155066 230149 191523 169534 259751 238466 149303 196047 190186 295668 FALSE TRUE 161188.1254 269675.3004 196514.2467 203067.3192 215598.6178 183085.8855 137600.2407 193419.3106 183341.243 353598.4837 0.455850726 0.762659663 0.555755343 0.574287868 0.609727212 0.517779046 0.389142621 0.547002659 0.518501214 1 18.43175256 -1.536585256 6.235872886 1.00058129 0.548987466 0.68104512 0.092824125 0.000753415 5.60E-05 0.090266748 0.021250177 0.029067973 1.536585256 -0.451593825 LVDEPGHCADFHPSGTVVAIGTHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVDEPGHCADFHPSGTVVAIGTHSGR 26 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 ; 225.26 6.38E-35 510690000 69383 330940 271790 338440 286630 389010 265035 363990 270540 288490 FALSE TRUE 72122.29442 387776.3706 278873.0707 405382.4219 237908.735 298668.323 244260.8642 359111.3094 260803.3182 345014.092 0.20904159 1.123943571 0.808294725 1.174973519 0.68956237 0.865669925 0.707973587 1.040859831 0.75592077 1 18.39629576 4.750108367 24.79978924 0.903064863 0.20904113 0.621922219 0.163334232 974.8015255 2093426.748 0.036085809 0.573795954 56248.16601 -4.750108367 -0.694023733 LVDLDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVDLDWR 7 0 Q9P000;Q9P000-2 Q9P000 COMMD9 COMM domain-containing protein 9 0 ; 105.39 0.018466 170743000 549020 677270 635660 625490 763460 821720 645620 665400 645590 842370 FALSE TRUE 570695.7335 793585.8541 652225.8218 749210.0551 633687.3419 630887.9833 595014.6174 656481.4014 622355.342 1007416.273 0.566494456 0.787743731 0.647424346 0.743694613 0.62902234 0.62624359 0.590634312 0.651648597 0.617773763 1 19.94222851 -1.788670842 2.85374215 1.086384858 0.653645578 0.73067108 0.063516559 15880508.13 12015010.36 9512461.253 0.01481027 0.016267813 1.788670842 -0.43273928 LVDMMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 94.662 0.032653 51536000 58891 68639 62398 68837 73042 81628 66425 67033 68656 85983 FALSE TRUE 61216.06215 80427.21431 64024.14314 82452.75314 60626.34693 62671.13408 61218.43493 66134.53228 66185.08397 102829.7226 0.595314862 0.782139758 0.62262293 0.801837747 0.589579991 0.609465167 0.595337937 0.643146073 0.643637679 1 16.64989781 -1.489850504 4.280878931 1.002263483 0.654326781 0.67275147 0.072461606 0.001518508 0.00018096 0.068059839 0.015945526 0.032370507 1.489850504 -0.347936702 LVDPERDMSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVDPERDMSLR 11 1 Q14444-2;Q14444;G3V153 Q14444-2 CAPRIN1 Caprin-1 0 ;; 99.539 0.0042863 1063760000 1647920 2454780 2083730 1688690 2574820 2489430 1535660 2001810 2027900 3066450 FALSE TRUE 1712981.154 2876369.369 2138033.716 2022707.842 2137153.016 1911297.61 1415290.956 1974979.011 1954916.275 3667262.167 0.467100817 0.78433699 0.583005419 0.551558015 0.582765267 0.52117834 0.385925765 0.538543175 0.533072408 1 21.80627198 -1.481207508 6.264789744 1.000253128 0.549737478 0.664526704 0.095978952 0.000347856 2.88E-05 0.095266094 0.022442119 0.033021173 1.481207508 -0.45051565 LVDQNIFSFYLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 147.62 9.97E-05 2805500000 375540 425550 375540 380260 540820 594730 453320 406770 421580 555310 FALSE TRUE 390366.6092 498634.9022 385326.8809 455474.293 448891.6096 456612.9707 417787.5939 401317.9135 406407.4182 664112.3624 0.587802052 0.750829122 0.580213384 0.685839203 0.6759272 0.687553788 0.629091728 0.604292189 0.611955809 1 19.34106783 -1.253209429 4.407811053 1.000180566 0.646534561 0.812110836 0.051089217 8.65E-05 1.47E-05 0.047201818 0.011119933 0.055820095 1.253209429 -0.353646005 LVDQNIFSFYLSRDPDAQPGGELMLGGTDSK ddPTM_MDA-MB-175_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 ; 222.56 4.78E-35 985410000 559940 569600 558770 381310 912110 732550 464180 522570 649520 836680 FALSE TRUE 582046.8636 667424.3691 573332.0052 456731.9799 757069.868 562426.3644 427796.3587 515565.8039 626143.9021 1000611.427 0.581691202 0.667016537 0.572981669 0.456452892 0.756607258 0.562082692 0.427534952 0.515250766 0.625761295 1 19.9324504 0.876531946 6.345422029 0.999998323 0.564249403 0.673391028 0.089814367 1.500390898 76.95050696 0.089130744 0.022387573 7.525440838 -0.876531946 -0.43574892 LVEAEVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVEAEVHR 8 0 F8VZX1;H0YIC9;F8VYY9;P54619-2;P54619;P54619-3;H0YHF8 F8VZX1 PRKAG1 5-AMP-activated protein kinase subunit gamma-1 0 ;;; 152.63 0.00045401 319659000 455009 527560 504113 550820 581130 608650 527510 533680 518890 548120 FALSE TRUE 472973.1067 618164.3262 517250.5989 659770.552 482349.7302 467300.2617 486162.3878 526526.8925 500215.2503 655513.6196 0.721530556 0.943022857 0.789076815 1.006494041 0.735834795 0.71287651 0.741651086 0.803227998 0.763089027 1 19.32226623 5.037201295 15.1542775 0.819867359 0.361422781 0.079543653 0.105602825 3610068.023 43528751.51 0.024565415 44020866.8 108943.4929 -5.037201295 -0.458444578 LVEALCAEHQINLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVEALCAEHQINLIK 15 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;; 202.82 5.72E-09 2367509000 2679478 2255017 2437903 1987984 2901314 3151415 2805416 2683027 2815444 2413713 FALSE TRUE 2785265.86 2642298.628 2501436.755 2381201.302 2408149.683 2419546.626 2585520.163 2647065.412 2714116.72 2886633.849 0.964883669 0.915356351 0.866558381 0.824905903 0.834241476 0.838189654 0.895686914 0.917007681 0.940235881 1 21.46095669 1.204254942 1.244541003 0.99612553 0.872498549 0.4905922 0.039913807 0.378361361 1.173423011 0.040844838 0.012963397 16.00497286 -1.204254942 -0.123626981 LVEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVEALR 6 0 O75688;O75688-3 O75688 PPM1B Protein phosphatase 1B 0 102.81 0.08195 293460000 172520 188380 179920 174350 199490 219000 194720 203440 182940 226840 FALSE TRUE 179331.2228 220732.7996 184608.863 208835.9096 165580.7611 168140.569 179457.3376 200713.2196 176356.0251 271284.9549 0.661043746 0.813656621 0.680497977 0.76980277 0.610357331 0.619793195 0.661508625 0.739861227 0.650076689 1 18.04944951 -1.275978822 4.983832376 1.000075584 0.693217179 0.690183826 0.062343369 5.23E-05 7.59E-06 0.060239589 0.014195121 0.052968927 1.275978822 -0.306858405 LVEDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVEDEER 7 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 157.9 0.0033611 376430000 573040 606140 650830 721230 715110 795840 730030 646390 663690 574620 FALSE TRUE 595664.0617 710239.8299 667791.1645 863887.1413 593555.8576 611018.2211 672808.341 637726.1993 639803.9265 687205.7872 0.866791393 1.033518406 0.971748459 1.257101086 0.863723602 0.889134277 0.979049294 0.927998878 0.93102232 1 19.39038266 LVEDEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVEDEERR 8 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 144.12 0.00094678 799600000 578890 639010 678350 698380 737190 782540 603580 674680 629630 691020 FALSE TRUE 601745.0242 748754.9967 696028.3583 836517.4795 611882.7071 600806.9445 556269.8224 665637.0182 606969.7393 826412.1386 0.72814156 0.906030976 0.842229108 1.012227968 0.740408664 0.727006437 0.673114293 0.805454067 0.734463727 1 19.65650192 LVEDKPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVEDKPGSR 9 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 ;; 117.52 0.0010381 700515000 685669 515115 649034 488449 783689 725521 704508 615992 662500 525029 FALSE TRUE 712739.7416 603581.9942 665948.3592 585062.7543 650477.8237 557029.7431 649286.8221 607735.6348 638656.7544 627898.3803 1.135119573 0.961273374 1.060598944 0.931779365 1.035960347 0.887133588 1.03406354 0.967888521 1.017133942 1 19.26017157 LVEEHLDSEIQKLDQMDEDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVEEHLDSEIQKLDQMDEDELER 23 1 F8WCJ3;B8ZZX4;O14530-2;O14530;F8WBV5;G3XAJ4 F8WCJ3 TXNDC9 Thioredoxin domain-containing protein 9 0 ;; 318.64 1.08E-73 131129000 164772 151043 193608 134564 244363 236329 205208 195962 207765 169048 FALSE TRUE 171277.3258 176983.4603 198653.5835 161180.3576 202826.2645 181445.1714 189123.2607 193335.4499 200287.5782 202169.719 0.847195746 0.875420222 0.982608001 0.797252716 1.003247497 0.897489358 0.935467793 0.956302709 0.990690294 1 17.6252074 8 0.116210829 1.040432121 0.475144599 0.360354359 0.05420327 104.9252975 0.842208675 0.378118614 9.571783946 100000000 -8 -0.565287522 LVEGILHAPDAGWGNLVYVVNYPK ddPTM_MDA-MB-175_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 ; 277.14 4.48E-52 501900000 394080 353630 435300 378470 520030 464290 464410 406380 405360 382360 FALSE TRUE 409638.5827 414363.2016 446644.2756 453330.2364 431635.4864 356465.6839 428008.3307 400933.1408 390771.1728 457276.1213 0.895823253 0.906155345 0.976749615 0.991370892 0.943927457 0.779541435 0.935995366 0.876785649 0.854562822 1 18.80270606 2.936929672 24.99982883 0.883004073 0.945532394 0.164083544 0.059283597 336.7044138 133462.4432 0.017454684 0.018513504 864.8278612 -2.936929672 0.062528321 LVEHFCAEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVEHFCAEFK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 140.49 3.92E-05 1121760000 2690300 2252700 2756300 2043400 4339300 3691100 3161700 2634800 3017500 2968300 FALSE TRUE 2796515.121 2639583.701 2828131.442 2447578.421 3601707.336 2833897.964 2913877.692 2599484.816 2908900.764 3549881.553 0.787777023 0.743569514 0.796683326 0.689481715 1.014599299 0.798307752 0.820838005 0.732273676 0.819436007 1 21.75933946 -1.985520176 1.850936591 1.190292471 0.797596609 0.348069013 0.081902298 806403.6381 255471.8731 655621.1982 0.021358049 0.010339031 1.985520176 -0.392695862 LVEINGHNVESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVEINGHNVESK 12 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 97.86 0.0046841 52906000 70555 52834 77384 64762 95544 88988 77673 69396 77205 64299 FALSE TRUE 73340.56588 61907.82851 79400.69061 77571.7303 79303.46501 68321.88563 71584.7873 68465.86013 74426.40713 76897.15797 0.953748719 0.805073037 1.032556894 1.008772396 1.031292535 0.888483885 0.930915904 0.890356184 0.967869413 1 16.23064266 3.897270123 0.003321512 1.881352877 6.59E-08 0.019397146 0.068901397 363916.3023 252.3845881 70200.30298 72764.43441 7893.509267 -3.897270123 -1.881352811 LVEIVHPSQEEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVEIVHPSQEEDR 13 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PK08 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ;;; 220.19 2.12E-11 1626180000 737730 1684160 1495370 1858190 1496000 1979600 1742230 1764460 1446010 1541860 FALSE TRUE 766856.1501 1973401.379 1534340.571 2225734.436 1241710.454 1519867.901 1605669.46 1740810.3 1393968.383 1843957.946 0.415875075 1.07019869 0.832090869 1.207041864 0.673394129 0.824242171 0.870773362 0.944061823 0.755965387 1 20.81437432 4.751049212 24.66295011 0.904011425 0.415874707 0.500386712 0.147650249 1345.63852 2657360.049 0.033264625 0.581134374 56370.15274 -4.751049212 -0.488136718 LVEKPSPLTLAPHDFANIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVEKPSPLTLAPHDFANIK 19 1 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 211.33 8.06E-17 1035930000 2247130 1361200 1865710 1523070 2135340 2245760 2179050 1739990 2047100 1403270 FALSE TRUE 2335848.428 1594975.511 1914331.935 1824328.7 1772375.67 1724216.275 2008250.367 1716668.28 1973425.271 1678213.889 1.391865746 0.950400614 1.140696039 1.087065667 1.056108331 1.027411515 1.196659365 1.022913879 1.175908079 1 20.67849517 4.753656712 24.67153447 1.077501348 1.391866018 0.619550337 0.074883292 1426.6777 2331570.774 0.016146631 0.373362688 56709.61669 -4.753656712 0.31436467 LVELIHPSQDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 97.86 0.0016412 0 33101 68066 55926 64353 63028 77771 57508 58834 55968 69873 FALSE TRUE 34407.85304 79755.80602 57383.4775 77081.83133 52314.52307 59709.86388 53000.37269 58045.42646 53953.72261 83563.27655 0.411758065 0.954436079 0.686706887 0.922436679 0.626046814 0.714546705 0.634254362 0.694628416 0.645663081 1 16.35058144 -1.312315221 3.517043409 1.001112287 0.707321028 0.277171882 0.1452867 58016210.26 95339607.52 691910.7655 0.031942534 0.048717476 1.312315221 -0.293791259 LVELLMHNDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVELLMHNDYK 11 0 C9JYI4;P52294;Q5TFJ7;O60684;O15131 C9JYI4;O60684;O15131 KPNA1;KPNA6;KPNA5 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed;Importin subunit alpha-7;Importin subunit alpha-6" 0 ; 189.52 7.38E-06 371280000 1176830 931930 1119590 952770 1531650 1468480 1320020 1158600 1201180 972830 FALSE TRUE 1223292.157 1091981.728 1148767.435 1141225.062 1271300.68 1127447.775 1216553.383 1143070.862 1157949.766 1163437.413 1.051446467 0.93858227 0.987390832 0.980907997 1.092710847 0.969066116 1.045654343 0.982494503 0.995283248 1 20.14996217 LVEPHS(ph)PSPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 LVEPHS(0.993)PS(0.007)PSSK;LVEPHS(0.993)PS(0.006)PSSK;LVEPHS(0.992)PS(0.008)PSSK;LVEPHS(0.988)PS(0.012)PSSK 151.56 4.03E-05 1973180000 3255260 3240180 3712940 3159890 4463760 4740750 4206610 3762720 3871770 3086480 TRUE FALSE 3383780.178 3796655.71 3809702.267 3784906.811 3705011.67 3639782.659 3876884.916 3712286.893 3732425.754 3691216.662 0.916711342 1.028564849 1.032099336 1.025381915 1.003737252 0.98606584 1.050300015 1.005708208 1.011164095 1 21.81566499 4.742729306 24.9620696 1.016649101 0.916711302 0.739401438 0.017658919 202.502354 1212536.135 0.004147243 0.03218787 55300.53152 -4.742729306 -0.0999378 LVEQANS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 LVEQANS(1)PK 129.74 0.00039938 414520000 1936000 809080 1008600 852910 1429500 1646300 1334900 1091000 1148100 712150 TRUE FALSE 2012434.775 948033.1962 1034884.945 1021613.052 1186514.101 1263971.775 1230267.05 1076376.93 1106780.105 851682.1576 2.362894135 1.113130277 1.215106992 1.19952384 1.393141902 1.484088593 1.444514293 1.263824679 1.299522475 1 19.6999556 4.744337942 24.99709943 1.289904512 2.362894598 0.841682538 0.14216168 242.4220837 1048872.036 0.034270689 0.307224189 55505.74579 -4.744337942 1.072990086 LVEQLKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVEQLKEER 9 1 O95232;J3KPP4 O95232 LUC7L3 Luc7-like protein 3 0 ;;; 152.54 7.32E-05 1270890000 1756980 1364280 1571380 1279430 2040800 1963220 1826670 1714820 1784310 1387200 FALSE TRUE 1826346.927 1598584.477 1612331.454 1532497.435 1693905.545 1507291.908 1683490.832 1691835.643 1720093.032 1658995.28 1.1008753 0.96358591 0.971872237 0.923750328 1.021043016 0.90855708 1.014765293 1.019795332 1.036828165 1 20.66187835 2.033433218 24.99999438 1.020125703 0.978026057 0.107273249 0.050640598 363.5842424 271872.1699 0.018304241 0.013518511 108.0023532 -2.033433218 -0.042099646 LVES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVESPK 6 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PK;LVES(1)PK 89.698 0.052312 208532000 1087230 492610 580400 557000 761660 1146200 830300 655640 619490 405380 TRUE FALSE 1130154.68 577211.9355 595525.7008 667172.9375 632193.3053 880012.4208 765218.9164 646852.2182 597194.6759 484806.4495 2.331146133 1.19060284 1.228378256 1.376163494 1.304011747 1.81518299 1.578400859 1.334248377 1.231820815 1 18.88704937 -2.485816124 0.075684115 2.06E-33 2.039704585 0.244120564 0.317272836 268.3057148 2.501072423 64.19314151 16.14564782 0.003267261 2.485816124 2.039704585 LVES(ph)PKEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVESPKEGK 9 1 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 LVES(1)PKEGK;LVES(1)PKEGK 66.498 0.064972 385700000 2697100 725140 1190530 573520 1925670 2194400 1461650 1113110 1354000 582430 TRUE FALSE 2803583.591 849677.1542 1221556.19 686960.5442 1598345.301 1684783.856 1347082.054 1098190.581 1305269.804 696546.0072 4.024979774 1.21984355 1.753733676 0.986238579 2.294672979 2.418768953 1.933945554 1.57662318 1.873917575 1 19.40985912 4.746288302 24.76371545 1.71968007 4.024981049 0.691101957 0.470784325 480.2429689 1538919.006 0.11213348 1.201373598 55755.57533 -4.746288302 2.305300979 LVEVDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 169.06 0.00070539 211160000 379900 564750 487050 517370 513310 606870 459730 525340 458600 585810 FALSE TRUE 394898.7453 661741.4194 499742.9231 619704.2418 426057.7495 465933.6397 423695.1613 518298.6766 442095.0756 700588.2535 0.56366738 0.94455112 0.713319015 0.884548433 0.608142868 0.665060594 0.604770576 0.739804977 0.631034097 1 19.41820727 -1.160212147 3.797784582 1.000181983 0.712138542 0.359885618 0.117340757 35278788.4 61932733.2 79302.89347 0.027064989 0.06914931 1.160212147 -0.288043441 LVFHTQLAHGSPTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVFHTQLAHGSPTGR 15 0 O14908 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 149.59 1.93E-06 766700000 101730 164900 149600 146720 204320 191900 137610 156980 139810 199060 FALSE TRUE 105746.379 193220.2923 153498.6989 175740.7781 169589.7594 147334.1333 126823.7686 154875.9399 134778.2654 238061.9958 0.444196809 0.811638547 0.644784559 0.738214336 0.71237645 0.618889768 0.532734207 0.650569779 0.566147759 1 17.8609778 -1.122923521 4.728407728 1.000025514 0.641946835 0.542761742 0.100207308 2.55E-05 4.73E-06 0.091833414 0.021643803 0.075348824 1.122923521 -0.358078679 LVFVHSAEGNEFWSALLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVFVHSAEGNEFWSALLEK 19 0 P07384;E9PRM1;E9PL37 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;; 209.23 2.33E-16 516497000 376307 304902 376852 319053 446685 456638 408537 385780 432446 296786 FALSE TRUE 391163.8909 357266.5467 386673.0727 382160.7311 370757.6433 350590.7449 376514.8024 380609.2501 416882.3529 354935.5344 1.102070244 1.006567424 1.089417754 1.076704624 1.044577416 0.987758934 1.060797711 1.072333461 1.174529774 1 18.43719749 1.568801763 4.41198816 1.097180025 1.050695868 0.058257552 0.051418419 0.330871209 14.29090104 0.02871283 0.012594475 37.051156 -1.568801763 -0.046484156 LVGATATSS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 LVGATAT(0.012)S(0.03)S(0.958)PPPK;LVGAT(0.001)AT(0.027)S(0.014)S(0.958)PPPK;LVGATATS(0.001)S(0.999)PPPK;LVGAT(0.001)AT(0.005)S(0.028)S(0.966)PPPK 223.06 1.72E-11 751871000 2418810 1773460 2164620 1721030 2675590 2530430 2408770 2136300 2244410 1654290 TRUE FALSE 2514306.487 2078037.959 2221031.775 2061444.597 2220794.167 1942775.982 2219964.313 2107666.393 2163634.123 1978416.452 1.270868165 1.050354164 1.122631068 1.041966971 1.122510968 0.981985355 1.122091515 1.065329997 1.093619152 1 20.91591471 4.742229772 24.65837866 1.071088945 1.270868258 0.621753577 0.047659169 179.634731 1207164.892 0.010118522 0.076031732 55236.96034 -4.742229772 0.199779313 LVGGPMDASVEEEGVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVGGPMDASVEEEGVRR 17 1 P01034 P01034 CST3 Cystatin-C 0 161.94 4.66E-09 810480000 559260 384020 484200 439080 633800 573140 527620 458840 540150 501400 FALSE TRUE 581340.0166 449972.4477 496818.6498 525928.7135 526066.9024 440036.921 486263.7657 452690.0003 520710.107 599639.7301 0.969482153 0.75040466 0.828528573 0.877074495 0.877304948 0.7338355 0.81092653 0.754936635 0.868371592 1 19.19373645 4.757517766 23.8763539 0.821312464 0.969482399 0.209899908 0.075917185 3092.621051 3895010.993 0.017043345 0.567641888 57216.03605 -4.757517766 0.148169934 LVGIISS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LVGIISSR 8 0 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 LVGIIS(0.002)S(0.998)R;LVGIIS(0.004)S(0.996)R;LVGIIS(0.002)S(0.998)R;LVGIIS(0.004)S(0.996)R;LVGIIS(0.005)S(0.995)R;LVGIIS(0.004)S(0.996)R 143.39 0.00063163 902025000 2054390 2384920 2296940 2602700 2404190 2745090 2477530 2460500 2159690 2237570 TRUE FALSE 2135498.904 2794511.458 2356800.143 3117506.292 1995526.643 2107584.45 2283334.725 2427521.022 2081963.179 2675979.001 0.798025285 1.044294988 0.880724454 1.164996546 0.745718349 0.787593792 0.853270793 0.907152493 0.778019251 1 21.35163536 3.203961955 24.99998447 0.843211206 0.970653868 0.233069485 0.11256144 253.5539309 183210.0165 0.030793323 0.036806633 1599.41791 -3.203961955 0.127442662 LVGLNLS(ph)PPMSPVQLPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.982)PPMS(0.018)PVQLPLR;LVGLNLS(0.981)PPMS(0.019)PVQLPLR 219.66 7.56E-19 564310000 269480 349710 314860 310570 355850 353970 288920 318370 283540 329980 TRUE FALSE 280119.2785 409769.9721 323065.5103 371999.819 295362.7441 271765.832 266273.6954 314102.7709 273335.4508 394633.2632 0.709821763 1.038356394 0.818647439 0.942646892 0.748448678 0.688654144 0.674737079 0.795935873 0.692631555 1 18.59015304 3.222728094 24.59785952 0.749628206 0.88467294 0.164379976 0.118033409 268.0001845 416371.7709 0.031315475 0.037551133 1670.044693 -3.222728094 0.135044734 LVGLNLSPPMS(ph)PVQLPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVGLNLSPPMSPVQLPLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 LVGLNLS(0.086)PPMS(0.914)PVQLPLR 74.786 0.070258 75788000 118170 135750 117810 110990 125690 145540 117910 127300 123500 132730 TRUE FALSE 122835.4428 159064.0065 120880.2254 132943.4907 104325.2587 111740.5407 108667.9061 125593.7517 119055.2591 158735.9022 0.773835289 1.002066982 0.761517865 0.837513687 0.657225349 0.703939935 0.684583037 0.791212007 0.750020994 1 17.27626894 4.132653713 12.51710158 0.75853551 0.887874418 0.148916451 0.105091697 0.644420492 71.24393499 0.024209663 0.052332388 13572.3082 -4.132653713 0.129338908 LVGSQEELASWGHEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVGSQEELASWGHEYVR 17 0 Q13200;Q13200-3;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ;;; 247.4 9.57E-21 1469970000 348076 607386 507418 532058 530872 659840 580939 569004 544590 611632 FALSE TRUE 361818.3093 711699.8207 520641.7299 637297.4844 440634.5671 506602.16 535403.4832 561377.4321 524990.3123 731469.58 0.494645737 0.972972548 0.711774958 0.871256306 0.602396298 0.69258131 0.731955912 0.767465179 0.717719953 1 19.48043834 -1.412317114 2.967577939 1.004727875 0.737663411 0.297140864 0.124335556 67602319.03 81085874.61 2703902.565 0.028046333 0.038697498 1.412317114 -0.267064464 LVGYLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 170.44 0.0022673 2986125000 2458710 2569070 2248390 2245690 3867010 3366690 2602350 2346520 2268985 3952330 FALSE TRUE 2555781.769 3010287.788 2306984.89 2689880.779 3209697.021 2584827.27 2398371.007 2315068.738 2187324.673 4726713.392 0.540710121 0.636867002 0.488073784 0.569080576 0.679054716 0.546855089 0.50740775 0.489784031 0.46275805 1 22.17240596 -1.596880679 5.470093859 1.002829148 0.546313228 0.816870261 0.064383862 0.002349846 0.000173172 0.06594371 0.015466461 0.02529993 1.596880679 -0.456515919 LVHDMNHPPSGEYFGQCGGCGEDVVGDGAGVVALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVHDMNHPPSGEYFGQCGGCGEDVVGDGAGVVALDR 36 0 Q15654;H7BZE2 Q15654 TRIP6 Thyroid receptor-interacting protein 6 0 ; 198.39 2.75E-30 224315000 25418 30600 26816 33436 28187 34105 33869 28489 29402 28930 FALSE TRUE 26421.52227 35855.31197 27514.84699 40049.541 23395.78381 26184.63062 31214.25928 28107.15155 28343.82776 34598.2796 0.763665783 1.036332222 0.795266334 1.157558742 0.676212346 0.756818863 0.902191081 0.812385814 0.819226507 1 15.07841268 3.209456086 24.9999742 0.820071644 0.935005436 0.143249725 0.13136042 373.2939469 320647.9834 0.035428658 0.042351839 1619.7802 -3.209456086 0.114933793 LVHDS(ph)LEDLQMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVHDSLEDLQMTR 13 0 A0A087WYY3;A0A2R8Y635;A0A2R8YDN7;Q9H7F0-2;Q9H7F0 A0A087WYY3 ATP13A3 Probable cation-transporting ATPase 13A3 1 LVHDS(1)LEDLQMTR;LVHDS(1)LEDLQMTR;LVHDS(1)LEDLQMTR 177.04 1.02E-05 176035000 107926 156939 128621 191291 141826 204634 148566 150017 115865 163093 TRUE FALSE 112187.0018 183892.0524 131972.9689 229127.7889 117718.4672 157110.8548 136921.0087 148006.2675 111695.0413 195047.9507 0.575176521 0.94280433 0.676618075 1.174725435 0.603536037 0.805498618 0.7019864 0.758819905 0.572654267 1 17.57346932 LVHGDIFRPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVHGDIFRPPR 11 1 Q99805 Q99805 TM9SF2 Transmembrane 9 superfamily member 2 0 137.17 5.05E-05 288950000 300110 349210 305050 431630 308350 380450 341260 325710 287100 267880 FALSE TRUE 311958.5745 409184.101 312999.8536 517005.1257 255936.7771 292096.2533 314511.1495 321344.3902 276767.3271 320365.9571 0.973756941 1.277239644 0.977007221 1.613795456 0.798888807 0.91175809 0.981724626 1.003054111 0.863909916 1 18.28936133 LVHLWSSDSHQPLWSR ddPTM_MDA-MB-175_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 ; 254.56 8.02E-27 2007500000 315140 1022430 887720 880040 912450 1197760 864270 977190 877430 1282610 FALSE TRUE 327581.9705 1198024.399 910854.7125 1054109.285 757352.0749 919598.3922 796526.2591 964092.3664 845851.4657 1533912.872 0.213559698 0.781025064 0.593811245 0.687202842 0.493738653 0.59951149 0.519277381 0.628518336 0.55143384 1 20.54878511 -4.575286968 0.513764837 9.999999999 0.572124031 0.461282783 0.141233219 1486.21451 10.52289644 15266.12012 0.058606522 2.66E-05 4.575286968 -9.427875968 LVHNLTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVHNLTSPK 9 0 Q7Z7G8-2;Q7Z7G8-6;Q7Z7G8 Q7Z7G8-2 VPS13B Vacuolar protein sorting-associated protein 13B 1 LVHNLT(0.162)S(0.838)PK 54.416 0.087075 135120000 51324 36809 41764 37985 50242 67591 49487 51318 47762 42120 TRUE FALSE 53350.31115 43130.65942 42852.40415 45498.31963 41701.88279 51894.0146 45608.07963 50630.16615 46043.05495 50372.60756 1.059113549 0.856232415 0.850708475 0.903235346 0.827868256 1.030203063 0.905414308 1.005113068 0.914049464 1 15.62035179 2.736169121 24.98836063 0.968624655 0.894536132 0.208213541 0.069336692 325.1927019 3397872.799 0.021019841 0.020700209 544.7147321 -2.736169121 -0.074088523 LVHSGSGCRS(ph)PSLGSDLTFATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVHSGSGCRSPSLGSDLTFATR 22 1 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 LVHSGS(0.017)GCRS(0.979)PS(0.004)LGSDLTFATR;LVHS(0.035)GS(0.138)GCRS(0.826)PSLGSDLTFATR 203.82 7.50E-23 366400000 37512 64856 52634 47745 67710 77887 57644 65062 59395 73875 TRUE FALSE 38993.00273 75994.51349 54005.68528 57188.8185 56200.67839 59798.92464 53125.71266 64189.95031 57257.38555 88349.39183 0.441349985 0.860158875 0.61127399 0.647302911 0.636118452 0.676845911 0.601313847 0.726546601 0.648079001 1 16.43093258 -5 0.338948367 4.681057012 0.64566911 0.532611966 0.098758628 281.5981547 2.37877194 749.5760184 0.071348705 1.00E-05 5 -4.035387902 LVIASTLYEDGTLDDGEYNPTDDRPSR ddPTM_MDA-MB-175_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 ; 205.13 2.93E-25 175900000 39614 39806 37051 40247 41609 51565 41737 42327 36211 35601 FALSE TRUE 41177.99131 46642.37085 38016.5795 48207.73647 34536.31704 39589.81023 38465.54488 41759.6758 34907.77318 42576.33433 0.967156801 1.09549992 0.892904006 1.132266017 0.811162294 0.929854833 0.903448958 0.980818956 0.819886769 1 15.37776412 3.234246455 24.9999932 0.91239052 1.017991719 0.312001704 0.082972426 136.2810059 789730.839 0.022070417 0.027266046 1714.930227 -3.234246455 0.105601199 LVIEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVIEEAER 8 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 ;; 189.53 0.00044487 1109070000 887910 848460 649870 812240 1775180 1612360 1522650 1119230 1580170 882500 FALSE TRUE 922965.3724 994176.4049 666806.1461 972898.6477 1473435.538 1237913.826 1403300.714 1104228.553 1523299.99 1055408.979 0.874509684 0.941982137 0.631798819 0.921821462 1.396080162 1.172923341 1.329627417 1.046256546 1.443326731 1 20.00937073 3.389702077 6.051875088 1.223459721 0.82052699 0.619503162 0.150768457 0.129074489 7.15993246 0.039704771 0.054054108 2453.02558 -3.389702077 -0.402932731 LVIGDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 ;;; 145.04 0.0023131 2075240000 1387640 1377902 1418530 1335179 1703630 1825440 1513220 1538800 1533620 1455783 FALSE TRUE 1442425.099 1614545.95 1455498.057 1599273.421 1414047.581 1401509.225 1394609.862 1518174.903 1478425.316 1741015.806 0.828496268 0.927358582 0.836005079 0.918586388 0.812196866 0.804995118 0.801032281 0.872005238 0.849173977 1 20.73149787 0.010275449 1.646113254 1.00007188 0.850500991 0.533664241 0.042061943 25.85757129 41.33031146 0.045788756 0.011485786 1.023942215 -0.010275449 -0.149570889 LVIIEGDLER ddPTM_MDA-MB-175_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 ;;;;; 221.94 1.20E-08 479347000 549609 601255 571514 579883 604990 689915 633313 593230 522859 627024 FALSE TRUE 571307.9877 704515.8691 586408.1243 694582.1266 502154.0159 529692.697 583672.2722 585278.7222 504041.4067 749877.3477 0.761868577 0.939508136 0.782005385 0.92626098 0.6696482 0.706372447 0.778356986 0.78049927 0.672165132 1 19.51629512 3.243738571 24.99898609 0.756649192 0.853603039 0.136616715 0.101830488 214.3985635 1035101.228 0.02620868 0.034450264 1752.825049 -3.243738571 0.096953847 LVIIEGDLERTEER ddPTM_MDA-MB-175_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 ;;; 218.16 5.01E-12 353388000 205061 312399 289145 181918 350825 344796 153511 242965 291502 495841 FALSE TRUE 213156.9666 366051.0981 296680.3562 217900.8374 291191.8918 264722.3544 141478.4067 239708.4516 281010.9 592991.5505 0.359460378 0.617295639 0.500311271 0.367460274 0.491055718 0.446418426 0.238584187 0.404235864 0.473886853 1 19.17765202 0.779460201 4.75844787 0.999997682 0.427365415 0.763373164 0.094973867 2.249731194 48.24626532 0.095088086 0.02408061 6.018111099 -0.779460201 -0.572632267 LVIIESDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 164.68 1.42E-05 61382000 126439 141829 139774 147635 154723 167105 160126 148279 140440 155366 FALSE TRUE 131430.9094 166187.0275 143416.6253 176836.7624 128423.2397 128297.3963 147574.9057 146291.5625 135385.5918 185806.993 0.707351791 0.894406743 0.77185806 0.951722857 0.691164728 0.690487447 0.79423763 0.787330768 0.728635611 1 17.50344527 -1.197216523 3.508931042 1.000312213 0.783636392 0.394401407 0.081767999 143012773.9 227910715.7 519993.9417 0.019170346 0.063501426 1.197216523 -0.216675821 LVIIESDLERAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 195.87 2.34E-08 317233000 249568 346482 346778 238190 386687 394315 220763 303991 325167 490857 FALSE TRUE 259421.1373 405987.5882 355815.3196 285303.2711 320958.0819 302741.3172 203459.0192 299916.4979 313464.3032 587031.0311 0.441920654 0.691594765 0.606126935 0.486010544 0.546748068 0.515716037 0.346589888 0.510903993 0.53398251 1 19.16307724 0.712135197 5.074333136 0.999999866 0.517990474 0.734684053 0.086589455 9.056341701 159.4168523 0.086905157 0.021954215 5.153890615 -0.712135197 -0.482009391 LVILEGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LVILEGELER 10 0 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YGX3;A0A2R8YE05;K7ENT6;A0A2R8YEU4;A0A5F9UN72;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;;;;; 204.91 4.15E-07 741088000 396012 460402 446843 483434 472895 515050 504126 428963 414050 433911 FALSE TRUE 411646.8595 539472.4621 458488.0957 579055.8023 392512.4768 395437.4432 464611.2868 423213.4526 399148.4214 518927.5527 0.793264604 1.039591094 0.883530067 1.11587022 0.756391667 0.762028227 0.895329771 0.815554022 0.769179473 1 18.98517361 3.210689333 24.999993 0.824516254 0.95856374 0.248966249 0.105717557 264.4407715 237197.4854 0.02847392 0.034039533 1624.386357 -3.210689333 0.134047486 LVILEGELERAEER ddPTM_MDA-MB-175_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 ;;;;;;; 222.74 3.45E-12 1335531000 869954 1225640 1099662 792793 1377393 1369837 742365 1044636 1076048 1654491 FALSE TRUE 904300.4557 1436134.136 1128320.095 949605.0891 1143264.23 1051713.117 684176.4915 1030634.363 1037321.243 1978656.834 0.457027434 0.725812638 0.570245469 0.479924094 0.577798136 0.531528812 0.345778247 0.52087575 0.524255255 1 20.91608999 -1.283623864 7.147720702 1.000003598 0.525163985 0.706598401 0.091646485 5.35E-06 5.37E-07 0.090405414 0.021308599 0.052044655 1.283623864 -0.474839614 LVINGNPITIFQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 386.44 1.51E-113 10004000000 381510 424430 414910 436440 391620 487610 478580 406520 417320 352450 FALSE TRUE 396572.3094 497322.5509 425722.8955 522766.5294 325052.5723 374369.9673 441067.6491 401071.2643 402300.7347 421505.8294 0.940846559 1.17987111 1.010004763 1.240235586 0.771169814 0.888172692 1.046409369 0.951520089 0.954436942 1 18.68519306 3.243408543 24.99999447 0.939623355 1.09305353 0.35973851 0.102809216 136.4247555 703516.8587 0.027945376 0.036666877 1751.493552 -3.243408543 0.153430175 LVINGNPITIFQERDPS(ph)K ddPTM_MDA-MB-175_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 228.6 1.41E-19 4874410000 3499300 1410871 1786733 1670791 2439730 2686840 2839970 2056996 2156475 1193787 TRUE FALSE 3637455.066 1653177.119 1833296.73 2001268.473 2025025.566 2062862.129 2617365.731 2029425.333 2078863.886 1427686.706 2.547796411 1.157941103 1.284102963 1.401756047 1.418396317 1.444898324 1.833291379 1.421478063 1.456106495 1 20.445248 7.999999999 0.035231355 6.47E-09 3.803841391 0.206148499 0.361908072 2106.293935 5.668731741 180.1304468 509.9062834 99999999.83 -7.999999999 3.803841385 LVINGNPITIFQERDPS(ph)KIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 LVINGNPITIFQERDPS(1)KIK;LVINGNPITIFQERDPS(1)KIK;LVINGNPITIFQERDPS(1)KIK 235.23 8.09E-30 25772920000 13797200 4673420 7199650 4219260 9733860 8294830 9306730 6756380 8261950 3818270 TRUE FALSE 14341924.11 5476043.531 7387278.794 5053817.035 8079301.954 6368481.442 8577244.184 6665821.777 7964604.033 4566386.901 3.140759734 1.199207086 1.617751398 1.106743065 1.769298601 1.394643419 1.878343725 1.459758431 1.744180729 1 22.12262167 4.744900926 24.99755144 1.496033155 3.140760467 0.760490734 0.28187324 319.2480648 1258646.186 0.06111471 0.577207764 55577.74549 -4.744900926 1.644727313 LVINGNPITIFQERDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 303.05 9.18E-50 1.14026E+11 30718431 22249221 27829967 19998639 31974292 28823573 27673746 25643592 26762054 21983102 FALSE TRUE 31931218.38 26070351.63 28555238.8 23954310.1 26539313.27 22129735 25504605.48 25299881.59 25798892.9 26290269.94 1.214564112 0.991634992 1.086152362 0.911147362 1.009472832 0.841746207 0.97011577 0.962328711 0.981309548 1 24.64802562 8 0.780889995 0.95369977 56.35178982 0.616666048 0.058449172 275.9043947 1.03249756 0.018528467 26988.18144 100000000 -8 55.39809005 LVKPGNQNTQVTEAWNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVKPGNQNTQVTEAWNK 17 1 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3;H0YIN7 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 230.82 6.05E-16 530720000 919830 627640 847030 617400 1023800 1013500 964620 916070 928700 702020 FALSE TRUE 956145.5987 735432.2876 869104.2976 739519.8772 849774.8417 778129.9847 889010.5638 903791.58 895276.2684 839567.378 1.13885511 0.875965773 1.035181119 0.880834459 1.012158004 0.926822558 1.058891266 1.076496781 1.066354282 1 19.67928659 2.216698682 24.24731478 1.058993967 0.973345028 0.175059556 0.075345754 233.5228685 259000.4044 0.0257227 0.019016394 164.7019274 -2.216698682 -0.085648938 LVLEVAQHLGESTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVLEVAQHLGESTVR 15 0 P06576 P06576 ATP5B "ATP synthase subunit beta, mitochondrial" 0 ; 150.76 3.12E-06 997690000 421510 633160 476300 630040 452240 810200 510270 514890 493470 706250 FALSE TRUE 438151.5403 741900.3047 488712.7693 754660.0315 375368.4063 622043.3287 470273.7041 507988.7417 475710.1111 844626.1655 0.518752033 0.878377127 0.57861429 0.893484079 0.444419581 0.736471772 0.556783253 0.601436189 0.563219718 1 19.68795342 -1.139730668 5.111591402 1.000014259 0.644022398 0.364877358 0.141938597 2.10E-05 3.53E-06 0.125025739 0.02946767 0.072488537 1.139730668 -0.355991861 LVLTQEQLHQLHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVLTQEQLHQLHSR 14 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 ; 141.34 5.61E-06 1186370000 897710 1223610 1211560 1273460 1363630 1448320 1020760 1176510 1100950 1356460 FALSE TRUE 933152.284 1433755.499 1243134.249 1525346.587 1131840.66 1111969.63 940750.1639 1160740.808 1061327.025 1622232.366 0.575227263 0.883816357 0.766310841 0.940276263 0.697705633 0.685456444 0.579910858 0.715520681 0.654238595 1 20.62954905 3.084730812 24.99999769 0.697322484 0.799063673 0.039181907 0.136391721 52.78387712 15566.97431 0.036692512 0.043855945 1215.432408 -3.084730812 0.101741189 LVLTSR ddPTM_MDA-MB-175_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 ; 129.96 0.037149 990730000 486090 570350 494930 600190 811610 699430 544860 502430 498500 745410 FALSE TRUE 505281.2085 668303.1758 507828.2824 718905.7906 673652.8221 536997.9825 502152.4495 495695.7477 480559.0824 891458.8178 0.566802637 0.749673639 0.569659834 0.806437467 0.755674641 0.602381144 0.56329293 0.556050081 0.539070423 1 19.76580863 2.709746011 23.8158362 0.612080447 0.692806435 0 0.145796465 1142.732903 944488.9653 0.044095371 0.041582271 512.5615346 -2.709746011 0.080725988 LVLVS(ph)PTSEQYDSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVLVSPTSEQYDSLLR 16 0 O00178 O00178 GTPBP1 GTP-binding protein 1 1 LVLVS(0.857)PT(0.124)S(0.018)EQYDSLLR;LVLVS(0.74)PT(0.229)S(0.03)EQY(0.001)DSLLR 146.78 1.14E-06 39429000 37045 50414 46543 44064 55782 50761 46237 48951 44403 53925 TRUE FALSE 38507.5652 59072.21233 47755.94882 52779.72768 46300.19556 38972.52704 42612.82312 48294.89191 42804.9447 64490.57129 0.5971038 0.915982153 0.740510556 0.818409988 0.717937439 0.604313565 0.660760515 0.748867485 0.66373958 1 15.97680063 -1.092024168 4.303825721 1.000034132 0.723981623 0.455833487 0.092062154 1.254673747 51981154.41 3709.375958 0.02121022 0.080905088 1.092024168 -0.276052509 LVNACLAEELPHIHAFEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVNACLAEELPHIHAFEQK 19 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;; 215.75 2.31E-19 2164413000 1552671 1196585 1304665 1176551 1705936 1763797 1700464 1485058 1545412 1160013 FALSE TRUE 1613971.65 1402089.166 1338665.642 1409269.276 1415961.608 1354181.877 1567177.188 1465153.227 1489792.924 1387295.338 1.163394417 1.010663791 0.9649464 1.015839409 1.020663423 0.976130922 1.129663703 1.056122072 1.073883032 1 20.40384352 2.248965008 24.99965399 1.070295969 1.021228561 0.094150629 0.058509329 415.6295849 998674.4839 0.020072563 0.016612658 177.4046538 -2.248965008 -0.049067408 LVNHFVEEFK ddPTM_MDA-MB-175_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 ;;; 177.57 2.31E-06 16305320000 8895450 6603750 7736800 6051990 10615070 9900490 9560270 8089530 8730840 6456040 FALSE TRUE 9246649.235 7737892.692 7938427.364 7249055.559 8810724.193 7601251.241 8810911.056 7981103.082 8416618.774 7720977.43 1.197600863 1.002190819 1.028163524 0.938877963 1.141141037 0.98449339 1.141165239 1.033690767 1.090097575 1 22.88035206 2.260724893 24.99962657 1.067833696 1.044898955 0.010275777 0.078239447 1283.265075 1447421.791 0.025777836 0.021551608 182.2740709 -2.260724893 -0.022934741 LVNHFVEEFKR ddPTM_MDA-MB-175_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 ; 221.6 5.38E-12 10990600000 3906500 3228680 3859400 3242520 5175900 4994000 4329000 4017800 4087800 3512260 FALSE TRUE 4060731.636 3783180.674 3959979.135 3883880.778 4296102.367 3834219.185 3989681.668 3963947.963 3940680.877 4200420.101 0.966744168 0.900667215 0.942757876 0.924641032 1.022779213 0.912818026 0.949829201 0.943702741 0.938163513 1 22.00210219 LVPDSDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVPDSDVR 8 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 81.297 0.054034 92546000 115630 148020 125930 132060 129520 162800 117500 123500 100840 137410 FALSE TRUE 120195.1617 173441.2836 129211.8393 158181.0738 107504.2367 124992.1673 108290.043 121844.6845 97210.7881 164332.8586 0.731412833 1.055426681 0.786281212 0.962565096 0.654185886 0.760603621 0.658967682 0.741450526 0.591548087 1 17.32626145 3.236856852 24.99974909 0.719224945 0.88919753 0.230761551 0.131797557 54.40250659 798264.8072 0.03386339 0.042525332 1725.269132 -3.236856852 0.169972585 LVPFDHAESTYGLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVPFDHAESTYGLYR 15 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 197.19 8.55E-09 465610000 359550 661820 499120 533880 694850 683030 460950 639420 472310 851850 FALSE TRUE 373745.3116 775482.4368 512127.4772 639479.8705 576739.6452 524406.6339 424819.5345 630849.6208 455311.6554 1018753.698 0.366865232 0.761206991 0.502699993 0.627708024 0.56612275 0.51475311 0.416999256 0.619236644 0.446930064 1 19.95837387 -1.534576899 3.198140249 1.014775116 0.544823543 0.616922997 0.109522859 127607160.4 153884347.2 16325846.96 0.024041135 0.029202706 1.534576899 -0.469951573 LVPGWTKPITIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVPGWTKPITIGR 13 1 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 139.61 4.37E-06 0 984430 859380 830150 844260 863440 1168400 947270 841750 812470 836900 FALSE TRUE 1023296.057 1006971.83 851784.391 1011252.108 716672.7772 897056.8073 873020.5022 830467.7181 783229.3634 1000874.532 1.022401934 1.006091971 0.85104013 1.010368509 0.716046572 0.896272988 0.872257685 0.829742082 0.782545003 1 19.9328297 4.333074752 0.985684455 0.850993527 1.069493622 0.292100909 0.085865962 1.224238058 1.469245265 0.026194503 0.247949002 21531.52311 -4.333074752 0.218500095 LVPLLDRPFDETTYEETED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVPLLDRPFDETTYEETED 19 1 O15270 O15270 SPTLC2 Serine palmitoyltransferase 2 0 ;; 161.1 2.46E-10 118389000 94960 132074 98342 148950 110189 155933 109479 107104 93615 142920 FALSE TRUE 98709.09413 154756.6821 100904.8733 178411.8654 91459.11314 119719.9239 100897.7499 105668.4461 90245.81444 170922.4376 0.577508111 0.905420519 0.590354752 1.043817698 0.535091322 0.700434218 0.590313076 0.618224544 0.527992788 1 17.38298227 LVPLLDTGDIIIDGGNSEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVPLLDTGDIIIDGGNSEYR 20 0 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 187.57 6.67E-17 73419000 33196 37293 42603 31015 33516 37038 28610 25655 29148 35248 FALSE TRUE 34506.60371 43697.78265 43713.26918 37149.67443 27818.96229 28436.48582 26367.47344 25311.13669 28098.96917 42154.17074 0.818581011 1.036618249 1.036985627 0.881281111 0.659933805 0.674582973 0.625500941 0.60044205 0.666576253 1 15.36338776 3.352325534 3.682376099 0.671968386 0.970311691 0.476898628 0.121568672 0.160378759 4.146904453 0.032739359 0.045261018 2250.741059 -3.352325534 0.298343305 LVPLLDTGDIIIDGGNSEYRDTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LVPLLDTGDIIIDGGNSEYRDTTR 24 1 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 303.9 1.73E-62 1715889000 283166.8 327917.4 334094.4 271765.7 348618.1 337214 205000.1 306236.6 298426.5 432912.1 FALSE TRUE 294346.4439 384234.6626 342801.1745 325520.1443 289360.1199 258901.159 188931.6565 302131.9993 287686.1886 517732.9374 0.568529492 0.742148384 0.662119695 0.628741424 0.558898418 0.500067004 0.364921068 0.583567275 0.555665224 1 18.98184858 -1.099037877 4.695898996 1.000014485 0.572006908 0.647577175 0.094303634 2.73E-05 5.24E-06 0.1004612 0.023677542 0.079608992 1.099037877 -0.428007578 LVPLLDTGDIIIDGGNSEYRDTTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVPLLDTGDIIIDGGNSEYRDTTRR 25 2 P52209-2;P52209;K7EM49;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 155.01 3.79E-08 37657000 27767 42487 31545 25935 46940 40095 18077 29131 33512 63917 FALSE TRUE 28863.2626 49783.81175 32367.08861 31064.86559 38961.15557 30783.5439 16660.0775 28740.54659 32305.90967 76440.31239 0.377592159 0.651276927 0.42342957 0.406393755 0.50969383 0.402713476 0.217948841 0.375986776 0.422629221 1 16.22204605 0.896231697 19.38149123 1 0.417003931 0.738795827 0.1032918 7815.991859 1459849.674 0.105350004 0.02633706 7.874657925 -0.896231697 -0.582996069 LVPVS(ph)PLPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;LVPVS(1)PLPPK 150.46 2.26E-05 1639708000 2176220 1697806 1941500 1682170 2408340 2342340 2102100 1981410 1992350 1648177 TRUE FALSE 2262138.846 1989390.973 1992097.085 2014898.205 1998971.227 1798367.034 1937331.909 1954852.44 1920645.713 1971105.727 1.147649675 1.009276644 1.010649534 1.022217214 1.014136989 0.912364572 0.982865547 0.991754229 0.974400148 1 20.91057373 7.999999933 0.871560129 0.982113166 66.94014057 0.731840237 0.028815286 398.6373298 0.996676318 0.009457354 52210.91387 99999984.49 -7.999999933 65.9580274 LVQAEYWHDPIKEDVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVQAEYWHDPIKEDVYR 17 1 A0A2C9F2P4;A0A286YFF7;P50897;Q5T0S4;A0A286YFE3;A0A286YFL8;P50897-2 A0A2C9F2P4 PPT1 Palmitoyl-protein thioesterase 1 0 ;;; 220.34 2.43E-15 2256440000 1798600 1540030 1584070 1459180 1963160 1980430 1894110 1631480 1599880 1417540 FALSE TRUE 1869610.117 1804518.173 1625352.166 1747801.449 1629462.764 1520505.146 1745644.709 1609612.679 1542300.631 1695279.823 1.102832755 1.064436767 0.958751555 1.030981096 0.961176286 0.896905116 1.029708893 0.949467255 0.909761687 1 20.69309199 4.866261987 0.804968067 0.959358332 1.225024843 0.538873259 0.043045164 2.219558259 0.962979608 0.014756774 0.553047683 73495.70947 -4.866261987 0.265666511 LVQAFQFTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ; 229.48 3.73E-09 1327930000 1520380 991710 1246610 992890 1569540 1606890 1392900 1142100 1224880 1147540 FALSE TRUE 1580405.776 1162028.478 1279097.681 1189280.679 1302750.151 1233714.15 1283720.858 1126792.018 1180796.808 1372378.492 1.151581568 0.846725947 0.932029821 0.866583589 0.949264477 0.898960569 0.935398555 0.821050479 0.860401715 1 20.38824699 4.745220101 24.90521801 0.895111997 1.151581691 0.676932038 0.051749131 403.0855835 1507422.712 0.011838022 0.115633994 55618.60612 -4.745220101 0.256469694 LVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQK 32 3 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 188.48 4.85E-20 537250000 276160 180640 254150 83152 482800 293890 174300 236510 324220 244370 FALSE TRUE 287063.01 211663.5148 260773.3578 99599.21742 400733.8285 225638.5014 160637.9106 233339.9703 312551.3855 292249.6228 0.982252799 0.724255904 0.892296645 0.340801868 1.37120392 0.772074569 0.549659942 0.798426934 1.069467199 1 18.15684164 1.244419688 24.19234077 1.034733632 0.794239992 0.114913082 0.255165887 174.4049978 720161.8435 0.173633308 0.059496077 17.55576216 -1.244419688 -0.24049364 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSK 34 2 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 228.79 6.12E-37 1856460000 2182570 759820 1269620 887800 1738290 1700780 2191550 1355400 1704930 506830 FALSE TRUE 2268739.549 890313.1744 1302707.34 1063404.19 1442816.087 1305799.621 2019770.584 1337233.08 1643569.902 606133.6347 3.742969238 1.468839747 2.149208138 1.754405513 2.380359716 2.154309786 3.332219941 2.206168745 2.711563603 1 19.20927638 3.030393279 24.88272257 2.413060947 2.193692654 0 0.784925259 1105.733488 905247.5906 0.213202059 0.254822402 1072.490067 -3.030393279 -0.219368293 LVQDLPEELVHAGWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVQDLPEELVHAGWEK 16 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 0 147.17 1.05E-06 26208000 62124 65420 67345 55888 75713 82971 67733 67676 68470 62462 FALSE TRUE 64576.70349 76655.3761 69100.06602 66942.47959 62843.3313 63702.24269 62423.91047 66768.91392 66005.77807 74700.23299 0.864477939 1.026173186 0.925031466 0.896148203 0.841273565 0.852771673 0.835658846 0.893824708 0.883608731 1 16.18882512 3.750916766 3.240208026 0.875627172 0.9501458 0.136944752 0.05720215 0.336260381 7.337524834 0.014362109 0.02630429 5635.296434 -3.750916766 0.074518628 LVQGAESGCHSEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVQGAESGCHSEKEK 15 1 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 ; 202.33 3.58E-09 143893000 229510 187938 258590 139978 366140 302030 216350 231060 259050 193490 FALSE TRUE 238571.232 220214.8895 265329.0678 167665.2306 303903.6536 231888.1098 199391.9217 227963.0186 249726.8411 231400.6609 1.030987686 0.95166059 1.14662191 0.724566775 1.313322323 1.002106515 0.861673951 0.985144199 1.07919675 1 17.82003346 -1.616037141 7.043840468 0.999990156 1.004985879 0 0.149577481 2.14E-05 1.17E-06 0.134308132 0.031594349 0.02420822 1.616037141 0.004995723 LVQS(ph)PNSYFMDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVQSPNSYFMDVK 13 0 P42677;H0YMV8;Q71UM5;C9JLI6 P42677;H0YMV8 RPS27;RPS27L 40S ribosomal protein S27;40S ribosomal protein S27-like 1 LVQS(0.994)PNS(0.004)Y(0.002)FMDVK;LVQS(0.932)PNS(0.038)Y(0.03)FMDVK 103.85 0.0061681 69040000 176682 119354 162999 124673 183919 195530 195280 161678 154240 138811 TRUE FALSE 183657.5418 139852.1211 167246.8878 149332.9473 152656.5141 150121.1208 179973.4433 159510.9709 148688.9325 166008.3578 1.106315033 0.842440242 1.007460649 0.899550778 0.919571256 0.904298572 1.084122786 0.960861086 0.895671366 1 17.34089635 LVQSDHSAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVQSDHSAVQR 11 0 O75843;H0YJ08 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 86.114 0.014711 119990000 10687 98113 95476 78061 73334 101550 62572 82595 75543 101050 FALSE TRUE 11108.93101 114963.1445 97964.18299 93501.23281 60868.71287 77966.55151 57667.44314 81487.94912 72824.22219 120848.8128 0.091924205 0.951297261 0.810634219 0.77370419 0.503676548 0.645157778 0.477186675 0.674296646 0.602606021 1 16.88284377 -1.589978702 2.667590853 1.029810755 0.629928948 0.212312386 0.220968151 21764429.61 20439457.78 4561619.802 0.053567921 0.025705218 1.589978702 -0.399881807 LVREDENDAS(ph)DDEDDDEKRR ddPTM_MDA-MB-175_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 244.67 4.68E-30 1902300000 836760 393637 540573 376697 805880 758120 596858 529979 664210 468949 TRUE FALSE 869795.9309 461241.0927 554660.7765 451206.5423 668896.8055 582058.1194 550074.7104 522875.4984 640305.2118 560830.578 1.550906753 0.822425008 0.988998814 0.804532706 1.192689614 1.037850186 0.980821539 0.932323448 1.14170881 1 19.09720549 4.748975309 24.89830148 0.986181254 1.550907087 0.682003112 0.115084674 788.2789856 1884491.636 0.026573194 0.374853708 56101.60795 -4.748975309 0.564725832 LVRLS(ph)SDSFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.552)S(0.292)DS(0.156)FAR;LVRLS(0.5)S(0.5)DSFAR;LVRLS(0.754)S(0.245)DS(0.001)FAR 216.88 7.12E-12 980400000 239003 308310 265863 291666 287525 343599 230737 253842 242587 345535 TRUE FALSE 248439.023 361259.8442 272791.6082 349356.6643 238651.6032 263803.3395 212651.231 250439.6632 233856.3413 413235.9676 0.601203773 0.874221686 0.6601352 0.845416884 0.577518953 0.638384265 0.514600005 0.606045172 0.565914779 1 18.6566063 4.040450006 24.99918315 0.651860829 0.745079287 0.006008431 0.15168303 438.5124552 271007.1741 0.035817109 0.077373682 10976.14932 -4.040450006 0.093218458 LVRLSS(ph)DSFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVRLSSDSFAR 11 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 LVRLS(0.239)S(0.76)DS(0.001)FAR 198.48 3.24E-08 629950000 123510 163640 141930 154970 142040 168800 138830 132780 124430 167990 TRUE FALSE 128386.2702 191743.8971 145628.8124 185622.6035 117896.0915 129598.7582 127948.1418 131000.3013 119951.7886 200904.4241 0.639041528 0.954403557 0.72486613 0.923934872 0.586826756 0.645076676 0.636860748 0.652052845 0.59705897 1 17.61614981 3.23085315 24.99837847 0.662914908 0.814714858 0.14718612 0.13972963 245.9701515 797778.2504 0.036376887 0.044249158 1701.583048 -3.23085315 0.15179995 LVS(ph)PEPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVSPEPPPK 9 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 LVS(1)PEPPPK;LVS(1)PEPPPK;LVS(1)PEPPPK;LVS(1)PEPPPK 115.78 0.0014898 250011000 723150 541360 639160 643380 782630 893530 970400 740330 735560 485780 TRUE FALSE 751700.5204 634334.3688 655817.0347 770638.6437 649598.8321 686021.1991 894337.5123 730407.0873 709087.3393 580959.2902 1.293895344 1.091874043 1.128851962 1.326493365 1.118148626 1.180842119 1.539415115 1.257243149 1.220545658 1 19.14807755 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVSPETEASEESLQFNLEKPATGER 25 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 LVS(1)PETEASEESLQFNLEKPATGER;LVS(0.877)PET(0.123)EASEESLQFNLEKPATGER 239.26 9.54E-39 356490000 202157 163613 210463 177548 250680 235232 237460 226662 222402 171668 TRUE FALSE 210138.3145 191712.26 215947.8387 212666.4645 208069.5031 180602.933 218847.2647 223623.9666 214397.7955 205303.0578 1.0235518 0.933801289 1.05184911 1.035866035 1.013474935 0.879689445 1.065971774 1.089238363 1.044299085 1 17.64739559 LVS(ph)PGSANETSSILVESVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.618)PGS(0.382)ANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR 339.53 3.28E-80 506821000 113366 119800 106449 131156 129470 142124 130722 130425 130008 127300 TRUE FALSE 117841.7772 140374.7181 109223.1484 157098.2653 107462.7356 109117.8549 120475.6681 128676.8662 125329.0375 152241.9977 0.774042505 0.922049896 0.71743113 1.031898344 0.705867877 0.716739511 0.79134319 0.845212676 0.823222497 1 17.21600687 0.310303602 1.32108141 1.000093716 0.813596913 0.252197901 0.096244694 6.384350211 10.84587628 0.088704159 0.025980334 2.043165759 -0.310303602 -0.186496803 LVS(ph)SPELGHDEFSTQALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVSSPELGHDEFSTQALAR 19 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 LVS(0.592)S(0.408)PELGHDEFSTQALAR;LVS(0.5)S(0.5)PELGHDEFSTQALAR 275.5 1.25E-39 242590000 120760 154929 128981 132782 157548 185099 129702 137316 122467 165706 TRUE FALSE 125527.698 181536.8506 132342.3508 159045.8833 130768.0472 142112.5625 119535.6183 135475.5036 118059.4366 198172.9181 0.633425088 0.91605277 0.667812495 0.802561141 0.659868404 0.717113942 0.603188465 0.683622691 0.595739507 1 17.59640029 -1.079928138 4.342713104 1.000028681 0.700427825 0.491258814 0.09224939 12094920.13 3007715.762 3467.091408 0.020884351 0.083190141 1.079928138 -0.299600856 LVSAELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVSAELK 7 0 S4R3K6;Q86VQ0 S4R3K6 LCA5 Lebercilin 0 83.843 0.021982 233930000 10669 556740 404100 501830 242400 557250 232720 390800 261820 717770 FALSE TRUE 11090.22036 652355.7642 414631.178 601090.4762 201196.9346 427837.1327 214478.7983 385561.9652 252397.1493 858403.289 0.012919592 0.759964195 0.483026083 0.700242513 0.234385093 0.498410407 0.249857848 0.449161799 0.294030967 1 19.71129608 -1.599254617 4.939054316 1.006054047 0.422769862 0.409515 0.212291842 0.013089845 0.001062085 0.190120597 0.044558212 0.025162013 1.599254617 -0.583284185 LVSDSLSEHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVSDSLSEHEK 11 0 Q96KR1;H0Y8W1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 111.86 0.00094394 0 41858 80926 73800 67847 99162 99724 71630 95637 80168 76676 FALSE TRUE 43510.58616 94824.41098 75723.28863 81266.9341 82306.47866 76564.61233 66015.45343 94355.14245 77282.76934 91699.19415 0.474492569 1.034081181 0.825779216 0.886233896 0.89757036 0.834954037 0.719913125 1.028963704 0.842785698 1 16.48462144 4.751100853 24.70088573 0.891401766 0.47449226 0.639226573 0.095080807 1050.117521 2068404.521 0.021666358 0.37930766 56376.85609 -4.751100853 -0.416909506 LVSFHDDS(ph)DEDLLHI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI 369.51 1.02E-97 5938142800 1097589.1 2096148.8 1817600.5 2095258 1980357.3 2354021.4 1728891.8 1929237.9 1698018.9 2172167.8 TRUE FALSE 1140922.765 2456146.051 1864968.662 2509693.779 1643736.874 1807335.605 1593376.743 1903379.622 1636907.531 2597762.492 0.43919441 0.945485224 0.717913461 0.966098243 0.632751023 0.695727809 0.613365059 0.732699632 0.63012209 1 21.3088381 -1.226052298 4.978790658 1.000039601 0.717495647 0.258534996 0.147512108 6.02E-05 9.36E-06 0.13262842 0.031256444 0.05942206 1.226052298 -0.282543954 LVSGWVKPIIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVSGWVKPIIIGR 13 1 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 175.74 5.79E-07 0 576980 651310 664520 666460 730570 798010 724890 708080 744910 736070 FALSE TRUE 599759.6159 763167.426 681837.9371 798283.7988 606387.9724 612684.2715 668071.2277 698589.3458 718100.8346 880288.8236 0.681321403 0.866951171 0.77456162 0.906843047 0.688851154 0.696003692 0.758922765 0.793591066 0.815755938 1 19.74761743 0.647352772 1.581792725 0.999849786 0.77249938 0.492782496 0.069687909 1.173252779 4.118579317 0.065750849 0.018889984 4.439691278 -0.647352772 -0.227350406 LVSPGS(ph)ANETSSILVESVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 LVS(0.456)PGS(0.544)ANETSSILVESVTR 337.91 4.22E-80 396390000 34053 33857 28752 32928 40573 37502 43812 35805 36619 30867 TRUE FALSE 35397.43873 39671.67638 29501.30074 39441.06012 33676.41595 28792.72885 40377.90096 35325.09254 35301.08934 36914.79767 0.958895645 1.074682211 0.79917276 1.068434953 0.912274158 0.779977967 1.093813417 0.95693583 0.956285598 1 15.17191163 LVSQKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LVSQKPK 7 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ; 73.26 0.05882 0 1114260 947920 971900 869370 1567690 1416120 1233800 1017690 1200120 956210 FALSE TRUE 1158251.845 1110717.886 997228.5124 1041328.791 1301214.614 1087247.592 1137091.532 1004049.53 1156927.916 1143561.042 1.012846541 0.971279928 0.87203785 0.910601842 1.137861965 0.950756061 0.994342663 0.878002567 1.011688815 1 20.12510195 4.710575867 5.293807325 0.962665389 1.01409332 0.023353459 0.073323425 0.574290844 48.23736362 0.017836499 0.094804524 51354.18801 -4.710575867 0.05142793 LVTDQNISENWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVTDQNISENWR 12 0 P24666;F2Z2Q9;G5E9R5;P24666-4 P24666 ACP1 Low molecular weight phosphotyrosine protein phosphatase 0 ;;; 281.41 5.84E-21 292352000 300528 339546 310205 333611 310083 383425 340142 310461 289936 358346 FALSE TRUE 312393.0775 397860.3842 318289.1971 399598.2601 257375.2024 294380.3546 313480.7812 306299.7781 279501.26 428557.0378 0.728941658 0.92837207 0.742699732 0.93242725 0.600562305 0.68691056 0.731479718 0.714723482 0.652191506 1 18.7091277 3.243100757 24.99999263 0.71493371 0.833456688 0.146084399 0.117176652 178.4873956 982822.2274 0.029890783 0.039151476 1750.252704 -3.243100757 0.118522978 LVTFYEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LVTFYEDR 8 0 Q14894;I3NI53;I3L2W5;I3L325 Q14894 CRYM Ketimine reductase mu-crystallin 0 ;;; 161.68 0.00080522 428129000 525848 1145660 648340 585053 823505 780638 595134 604347 510100 874310 FALSE TRUE 546608.8851 1342418.193 665236.273 700774.7372 683525.9142 599346.6552 548485.842 596246.717 491741.6006 1045614.305 0.522763396 1.283855994 0.636215735 0.670203854 0.653707501 0.573200512 0.524558472 0.570235807 0.470289665 1 19.99591935 4.042502897 24.99940956 0.61186892 0.917491915 0.18502523 0.218341194 170.5067765 100286.8149 0.048906681 0.105650385 11028.1559 -4.042502897 0.305622995 LVTISKDPYEACDGAHAVVICTEWDMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVTISKDPYEACDGAHAVVICTEWDMFK 28 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 141.78 7.38E-08 218400000 258220 192180 219830 158090 324650 292720 276850 264490 260190 161560 FALSE TRUE 268414.725 225185.42 225558.9504 189359.7301 269466.109 224740.2162 255149.7736 260944.9442 250825.8127 193214.5887 1.38920527 1.165467999 1.167401239 0.980048822 1.394646805 1.163163805 1.320551286 1.350544728 1.298172226 1 17.5598445 3.205116738 24.99999323 1.277344859 1.174230553 0.057112669 0.139792814 409.1356892 305836.3296 0.038934223 0.046537811 1603.676401 -3.205116738 -0.103114305 LVTSGAESGNLNTS(ph)PSSNQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 LVTSGAESGNLNT(0.064)S(0.935)PS(0.001)SNQTR 284.27 3.30E-45 239350000 308930 360220 371490 370650 364900 451160 371200 374790 341060 423450 TRUE FALSE 321126.7949 422084.9829 381171.3346 443963.4637 302874.4283 346384.9274 342104.374 369766.5531 328785.3172 506416.9201 0.634115454 0.833473303 0.752682858 0.87667581 0.59807328 0.683991616 0.675538989 0.73016232 0.649238412 1 18.94996608 -0.970508911 4.333656043 1.000009164 0.719040758 0.513970824 0.083088958 8964130.37 4136982.973 773.1895751 0.019094919 0.107026442 0.970508911 -0.280968406 LVTSIGDVVNHDPVVGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LVTSIGDVVNHDPVVGDR 18 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;;; 256.49 1.36E-30 3672750000 1775610 1922334 1853277 2053097 2025766 2254320 2003744 2052968 1956698 1821144 FALSE TRUE 1845712.454 2252479.911 1901574.921 2459193.459 1681427.019 1730788.345 1846685.309 2025451.322 1886276.821 2177962.299 0.847449221 1.034214372 0.873098181 1.129125816 0.772018423 0.794682417 0.847895903 0.929975382 0.866074138 1 21.05454755 LVTYYS(ph)CSYWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVTYYSCSYWK 11 0 J3KN75;Q0IIM8;D6RFZ2;Q0IIM8-2;Q0IIM8-3 J3KN75 TBC1D8B TBC1 domain family member 8B 1 LVTY(0.283)Y(0.283)S(0.37)CS(0.036)Y(0.028)WK 60.973 0.094677 405290000 76840 45944 56891 59418 73876 64411 57240 61114 51261 67793 TRUE FALSE 79873.70253 53834.52461 58373.6262 71170.70305 61318.58391 49452.52141 52753.37923 60294.86679 49416.12662 81075.74037 0.98517389 0.664002874 0.719988814 0.877829826 0.756312352 0.609954608 0.650667869 0.743685676 0.609505709 1 16.30698267 4.747385885 24.17205603 0.726327787 0.985174104 0.286184118 0.11657137 865.3193451 2369991.531 0.026221231 0.307956795 55896.66345 -4.747385885 0.258846317 LVVADTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVVADTR 7 0 P22314;P22314-2;Q5JRR9;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 99.919 0.02367 357338000 701230 815940 778570 771140 910590 991540 808500 821370 745560 873020 FALSE TRUE 728915.1019 956071.3479 798860.1738 923669.1904 755808.2371 761269.8619 745127.6574 810360.8786 718727.4412 1044071.554 0.698146692 0.915714392 0.765139296 0.884679969 0.723904635 0.729135718 0.713674896 0.776154542 0.688389065 1 19.99378916 LVVHLY(ph)HLCQMFPES(ph)AS(ph)DAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LVVHLYHLCQMFPESASDAIK 21 0 P78316;E9PFK5;P78316-2 P78316 NOP14 Nucleolar protein 14 3 LVVHLY(1)HLCQMFPES(1)AS(1)DAIK 40.142 0.07736 144100000 17324 346100 244310 302240 206250 336490 180990 269250 244350 387900 TRUE FALSE 18007.9649 405539.9827 250676.9193 362022.1699 171191.6987 258345.2971 166803.5309 265641.1442 235555.8912 463901.5782 0.038818503 0.874194014 0.540366602 0.780385726 0.369025903 0.556896784 0.359566638 0.572623929 0.507771265 1 18.82345923 -1.238373882 2.951820883 1.002614394 0.524742414 0.308275107 0.21885642 13053438.14 17003856.75 318081.7099 0.049407681 0.057759858 1.238373882 -0.47787198 LVVLDEELEGISPDELKDELPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LVVLDEELEGISPDELKDELPER 23 1 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;;;;; 296.69 9.69E-62 973963000 630169 408504 466792 437499 623774 684348 643220 493878 525824 363084 FALSE TRUE 655048.5587 478661.3843 478956.983 524034.9964 517745.1183 525418.5484 592802.7357 487258.3732 506899.697 434223.3581 1.5085521 1.102339096 1.103019849 1.206832812 1.19234746 1.21001908 1.365202319 1.122137637 1.167370864 1 18.72807781 0.876031378 1.389476218 1.002766134 1.222790983 0.257288307 0.118391943 0.810502542 3.044249955 0.10767462 0.032105654 7.516772004 -0.876031378 0.220024849 LVVLDEELEGISPDELKDELPERQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LVVLDEELEGISPDELKDELPERQPR 26 2 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;; 268.36 9.83E-54 285511000 210588 164717 196535 133186 296249 280536 186136 193605 228305 191103 FALSE TRUE 218902.1768 193005.8634 201656.8636 159529.7933 245892.7008 215385.7656 171546.1739 191010.0416 220088.3476 228545.974 0.957803688 0.844494699 0.88234704 0.69802058 1.075900382 0.942417676 0.750598101 0.835762006 0.962993764 1 17.80212488 1.098783953 5.074875006 0.997959354 0.868632393 0.158313892 0.100683434 0.341177585 12.97719314 0.095848219 0.024284597 12.55405286 -1.098783953 -0.129326961 LWAHVYAGAPVSSPEYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWAHVYAGAPVSSPEYTK 18 0 D6RDM7;P61086;P61086-2 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ; 163.7 3.25E-11 948200000 1427720 1060120 1367000 1076700 1603070 1715880 1601590 1330880 1515210 1075270 FALSE TRUE 1484087.488 1242187.363 1402625.143 1289668.046 1330580.734 1317392.874 1476053.191 1313041.73 1460677.888 1285948.569 1.154079971 0.965969708 1.090731913 1.0028924 1.034707582 1.024452226 1.147832212 1.02106862 1.135875822 1 20.29440151 LWDEESAQLLPHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWDEESAQLLPHWK 14 0 Q8TE77;Q8TE77-2;Q8TE77-3;A0A087WWG1;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ; 206.49 1.08E-08 3581800000 3253400 3071000 3710500 3067400 4522400 4538700 4220200 3628000 3921300 3351900 FALSE TRUE 3381846.744 3598420.361 3807198.678 3674122.565 3753684.063 3484655.71 3889409.697 3579372.594 3780173.179 4008640.629 0.843639293 0.897665991 0.949748064 0.916550747 0.936398248 0.869286133 0.970256517 0.892914313 0.943006253 1 21.93468166 -5 0.115486256 1.269513163 0.869587233 0.427398892 0.034024902 164.0519139 1.243399226 10.4652527 0.358554812 1.00E-05 5 -0.399925929 LWDFQGFECIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWDFQGFECIR 11 0 P43034;I3L3N5;P43034-2 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ; 114.83 0.0028017 162671000 169489 176649 206665 201340 263690 272150 228630 217780 222670 226190 FALSE TRUE 176180.5566 206987.0916 212050.8597 241164.4511 218868.068 208947.287 210709.3832 214861.0153 214656.1502 270507.5998 0.651296144 0.765180319 0.783899823 0.891525603 0.809101364 0.772426679 0.778940715 0.794288277 0.793530941 1 18.0453096 -5 0.253087986 2.314931618 0.767019835 0.602615296 0.053919429 136.8435969 1.353300764 93.31427632 0.078906946 1.00E-05 5 -1.547911783 LWDVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWDVDR 6 0 Q9BZK7;A0A0D9SF63 Q9BZK7 TBL1XR1 F-box-like/WD repeat-containing protein TBL1XR1 0 ; 125.86 0.041275 412420000 560440 612170 589260 597580 699590 754260 665510 636420 604570 717700 FALSE TRUE 582566.604 717305.4355 604616.5997 715779.5404 580673.9417 579094.5459 613345.5872 627889.8309 582811.6438 858319.5738 0.678729254 0.83570905 0.704418981 0.833931279 0.676524175 0.674684073 0.714588838 0.73153386 0.679014742 1 19.71115537 -0.776631087 5.743601879 1.000000026 0.728149673 0.666584298 0.058221683 1.80E-08 3.84E-09 0.053758645 0.012671033 0.167251073 0.776631087 -0.271850352 LWDWDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWDWDKK 7 1 P35606;P35606-2;D6RBT6 P35606 COPB2 Coatomer subunit beta 0 ; 87.616 0.030803 911850000 1954880 816550 1254010 903950 1877230 1375550 1808490 1198330 1456750 637540 FALSE TRUE 2032060.172 956786.1106 1286690.531 1082748.612 1558139.115 1056099.359 1666735.828 1182268.346 1404321.852 762453.7566 2.665158581 1.254877561 1.687565337 1.420084304 2.043585072 1.385132344 2.186015629 1.550609904 1.841845279 1 19.54029031 -1.2865491 3.364291451 0.997051038 1.751428191 0.246895087 0.406476415 38118721.82 54934252.91 1151882.953 0.086017269 0.051695281 1.2865491 0.754377153 LWEAGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWEAGWK 7 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 119.89 0.01089 543080000 1941300 1823730 1882860 1632690 2541100 2485500 2213090 1819860 1908250 1983810 FALSE TRUE 2017944.023 2136941.441 1931928.878 1955631.209 2109164.73 1908280.293 2039622.223 1795467.753 1839572.455 2372499.587 0.850556111 0.900713093 0.814301039 0.824291485 0.889005309 0.804333246 0.859693394 0.756783168 0.77537314 1 21.17797641 2.716449595 24.37367254 0.82055816 0.854217049 0 0.067806682 1905.96981 2101006.415 0.020882366 0.019704973 520.5345913 -2.716449595 0.033658889 LWEISTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWEISTGR 8 0 Q05048;A0A0A0MSZ9 Q05048 CSTF1 Cleavage stimulation factor subunit 1 0 ; 101.6 0.012282 43658000 131722 112559 157773 153482 106188 142431 156348 151096 142486 79466 FALSE TRUE 136922.4863 131890.1327 161884.694 183840.2815 88138.20169 109353.5588 144093.0352 149070.8053 137357.9567 95035.84123 1.44074577 1.387793605 1.703406756 1.934431043 0.92742065 1.150655978 1.516196767 1.568574585 1.445327941 1 16.53618408 -1.967344202 2.437973022 0.617938325 1.458974974 0.212015933 0.261588936 9966719.712 4560660.875 21506380.54 0.065861091 0.010780919 1.967344202 0.841036648 LWGDVTEIKS(ph)PILSGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LWGDVTEIKSPILSGPK 17 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 LWGDVT(0.008)EIKS(0.992)PILSGPK 127.5 2.43E-05 199730000 549590 259950 409650 300250 574740 591300 516180 435850 511310 292040 TRUE FALSE 571288.2376 304594.3904 420325.8155 359638.5538 477045.9001 453979.5362 475720.4628 430008.1437 492908.053 349259.6466 1.635712122 0.872114467 1.20347661 1.029716881 1.365877521 1.299833922 1.362082529 1.231199046 1.411294027 1 18.41394044 3.220587406 24.99484972 1.292355281 1.164189316 0.03894187 0.209987936 614.8836532 855100.2597 0.056059603 0.067130891 1661.833104 -3.220587406 -0.128165965 LWGIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWGIDR 6 0 P10644;P10644-2;K7EPB2;K7EM13;P31321;H7BYW5;C9JSK5 P10644;P31321 PRKAR1A;PRKAR1B "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed;cAMP-dependent protein kinase type I-beta regulatory subunit" 0 ; 112.27 0.06314 385400000 299542 359970 344630 329058 385600 422800 363820 355750 330740 401470 FALSE TRUE 311368.1495 421792.0473 353611.3409 394144.6903 320055.8497 324611.1076 335302.8377 350981.7531 318836.732 480130.3599 0.648507521 0.878494848 0.736490275 0.820911826 0.666601982 0.676089526 0.698357916 0.731013455 0.664062843 1 18.87306664 -1.004541979 4.355736448 1.000011396 0.728201377 0.581236532 0.070089652 8705748.135 2007763.523 1037.186575 0.016028679 0.098959621 1.004541979 -0.27181002 LWHLDPDTEYEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LWHLDPDTEYEIR 13 0 Q5TG12;E9PGC5;Q15262;Q15262-2;Q15262-3;Q15262-4;H0YDP9 Q5TG12 PTPRK Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase kappa 0 ;; 132.47 0.00011842 202343000 98612 129712 118870 111555 137612 144406 113960 123399 122071 123601 FALSE TRUE 102505.2779 151989.027 121967.8499 133620.246 114220.7614 110869.895 105027.5174 121745.0382 117677.6886 147818.2495 0.693454822 1.028215579 0.825120378 0.90394959 0.772710824 0.750041997 0.710517935 0.823613043 0.79609716 1 17.17346487 5.037289187 16.57836814 0.831364278 0.120949261 0.161826399 0.099225645 8127475.971 97483377.3 0.023324613 172828981.4 108965.5428 -5.037289187 -0.710415018 LWLDNTENDLNQGDDHGFSPLHWACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LWLDNTENDLNQGDDHGFSPLHWACR 26 0 A0A0A0MTH3;Q13418;Q13418-2;A0A087WWY6 A0A0A0MTH3 ILK Integrin-linked protein kinase 0 56.681 0.049502 26660000 6802.8 8257.2 7592.6 5576.3 9889.3 9139.9 9285.1 9859.6 9246.2 8629.5 FALSE TRUE 7071.379797 9675.309868 7790.469393 6679.275496 8208.320318 7017.296742 8557.3096 9727.448189 8913.431068 10320.2853 0.685192278 0.937504108 0.754869576 0.647198726 0.795357888 0.679951817 0.829173744 0.942556131 0.863680684 1 13.33319523 1.937111361 3.970954727 0.924864578 0.755663584 0.503036423 0.081999272 0.204625004 6.075945425 0.038468181 0.022391644 86.51897405 -1.937111361 -0.169200994 LWLFGYDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWLFGYDEQR 10 0 Q9NT62;Q9NT62-2 Q9NT62 ATG3 Ubiquitin-like-conjugating enzyme ATG3 0 ; 161.79 1.62E-05 566420000 549100 663380 672420 660180 736920 833320 678440 651630 667290 730150 FALSE TRUE 570778.892 777310.3546 689943.8176 790761.6336 611658.6016 639794.0591 625262.1 642895.9657 643274.3632 873208.9129 0.653656741 0.890176844 0.790124571 0.905581267 0.700472238 0.732693001 0.716050982 0.736245309 0.73667865 1 19.73596733 -1.326249612 3.524036053 1.000992627 0.764410458 0.468182156 0.075940137 27276119.77 35416643.09 273556.5215 0.018160702 0.04717918 1.326249612 -0.236582169 LWPSGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LWPSGDR 7 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;;;; 154.35 0.003919 3687818000 1213000 1552540 1418000 1398820 1523460 1809690 1360710 1501380 1305490 1788430 FALSE TRUE 1260890.177 1819176.668 1454954.245 1675502.421 1264502.813 1389416.924 1254053.995 1481256.457 1258505.67 2138838.617 0.589520952 0.850544147 0.680254337 0.783370193 0.591210016 0.649612791 0.586324739 0.692551764 0.588406091 1 21.0283962 -1.127401993 9.160519264 1.000000003 0.672256753 0.575872295 0.085410901 5.80E-09 5.19E-10 0.079767309 0.018801335 0.074575815 1.127401993 -0.327743251 LWS(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LWSLER 6 0 O60437;K7EKI8;K7EQ71;M0QZ12;Q96CP6-2;Q96CP6-3;Q96CP6 O60437;M0QZ12 PPL;GRAMD1A Periplakin;GRAM domain-containing protein 1A 1 LWS(1)LER;LWS(1)LER;LWS(1)LER;LWS(1)LER 98.523 0.041788 76838000 139227 135415 146412 132313 192012 207884 166777 153834 156417 124692 TRUE FALSE 144723.7895 158671.4729 150227.617 158484.1165 159373.8688 159606.0915 153704.5829 151772.1069 150787.5827 149123.01 0.970499385 1.064030781 1.007407354 1.062774393 1.06874096 1.070298215 1.030723447 1.017764507 1.011162413 1 17.18614336 1.696572679 2.482789263 1.007575341 1.042702979 0.177140147 0.029827083 0.425761346 5.728490874 0.019264857 0.008171153 49.72475813 -1.696572679 0.035127638 LWSLGQDDMAIPSKPPAAS(ph)PEKPSALLGNSLALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LWSLGQDDMAIPSKPPAASPEKPSALLGNSLALPR 35 2 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 LWSLGQDDMAIPSKPPAAS(0.991)PEKPS(0.009)ALLGNS(0.001)LALPR 110.91 7.13E-06 229700000 189890 82714 135400 97924 184520 178150 156860 159900 174080 91636 TRUE FALSE 197387.0038 96919.48607 138928.6352 117293.0749 153155.3563 136777.3624 144564.9033 157756.802 167814.8948 109590.3197 1.801135395 0.884379992 1.267709006 1.070286821 1.397526321 1.24807887 1.319139352 1.439514023 1.531293049 1 16.74176084 2.041240349 4.660179909 1.374306608 1.256603306 0 0.256705121 0.725114914 35.88619342 0.096700767 0.067156976 109.9614225 -2.041240349 -0.117703302 LWSNSHRPELVRPALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWSNSHRPELVRPALER 17 2 S4R3P0;P52895;B4DK69;P52895-2 S4R3P0 AKR1C2 Aldo-keto reductase family 1 member C2 0 ; 116.96 0.00014466 1596400000 424740 453060 481400 383150 712810 727660 533980 550180 568160 455710 FALSE TRUE 441509.0632 530869.5307 493945.6795 458935.9264 591646.8108 558671.9928 492125.2523 542805.737 547712.0326 544997.6494 0.810111867 0.974076735 0.906326257 0.842087901 1.085595161 1.025090647 0.902986009 0.995978125 1.004980541 1 19.05589048 3.252657301 24.99999828 0.996063941 0.891300808 0.499504883 0.05805868 228.9360926 406008.1546 0.016300255 0.021963697 1789.193454 -3.252657301 -0.104763133 LWSWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWSWGR 6 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 177.91 0.0083285 967030000 393130 463760 433660 423290 521350 542680 500300 438810 411900 442790 FALSE TRUE 408651.076 543407.1724 444961.5359 507015.4986 432731.1132 416650.7944 461085.1787 432928.4697 397075.7995 529546.2228 0.771700483 1.026175146 0.840269492 0.957452771 0.817173449 0.786807226 0.870717529 0.817546139 0.749841624 1 19.01439709 3.216943734 24.97994593 0.830136656 0.903802752 0.087282618 0.088595983 435.3782617 503111.2302 0.023452729 0.02805491 1647.948874 -3.216943734 0.073666096 LWTFLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LWTFLEDR 8 0 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 ; 163.67 0.00077834 207780000 262250 290460 282000 302850 378720 386310 345430 278190 281170 320290 FALSE TRUE 272603.8325 340344.2455 289349.1517 362752.8261 314345.3097 296595.3571 318354.294 274461.3181 271050.7466 383044.6932 0.711676307 0.888523589 0.755392665 0.947024806 0.82064917 0.774310054 0.831115271 0.716525573 0.707621725 1 18.54715321 2.8347665 5.820478295 0.784949027 0.831780529 0 0.097962555 0.800468163 39.55586312 0.028491515 0.030269595 683.5440393 -2.8347665 0.046831502 LYADS(ph)DSGDDS(ph)DKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYADSDSGDDSDKR 14 1 O43896 O43896 KIF1C Kinesin-like protein KIF1C 2 LYADS(0.954)DS(0.083)GDDS(0.963)DKR 221.78 2.77E-12 111070000 613610 317390 368630 294440 547690 600200 524880 391380 440270 273860 TRUE FALSE 637835.7966 371899.2635 378236.8006 352679.3532 454593.8494 460812.6461 483738.5341 386134.1913 424424.7687 327517.6236 1.947485419 1.135509166 1.154859383 1.076825574 1.387998131 1.406985801 1.476984746 1.178972255 1.295883757 1 18.32121301 1.701652916 0.032393997 1.20E-10 2.51662535 0.194782239 0.232611185 200.6339468 6.375511606 242.9454791 248.2774463 50.30983764 -1.701652916 2.51662535 LYANMFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LYANMFER 8 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 168.23 0.00071658 1685280000 1357213 1904280 1399919 1308633 3062110 2279950 1615239 1397854 1562380 3670080 FALSE TRUE 1410796.817 2231325.277 1436402.039 1567476.702 2541613.636 1750466.165 1488632.347 1379118.054 1506150.249 4389161.908 0.321427381 0.508371603 0.327261119 0.357124375 0.579065819 0.398815583 0.339160955 0.314209884 0.343152128 1 22.06551406 -1.703166904 2.771256325 1.092225596 0.386963087 0.828159179 0.083684554 32917578.51 28519366.64 21170702.83 0.020533856 0.019807657 1.703166904 -0.705262509 LYAVHQEGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LYAVHQEGNK 10 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ;;;;; 121.83 0.00050465 2666000000 5154710 4109220 4350770 3799690 6954370 6234110 5462310 4560810 4859130 4714390 FALSE TRUE 5358221.931 4814946.57 4464154.64 4551257.341 5772268.671 4786332.431 5034159.869 4499679.802 4684250.86 5638084.458 0.950362126 0.854003981 0.791785698 0.807234687 1.02379961 0.848928828 0.892884792 0.798086626 0.830823109 1 22.42677366 4.74241972 23.77343574 0.863203958 0.950362168 0.07565917 0.076938551 469.0881739 2889499.428 0.017961927 0.135496714 55261.12478 -4.74241972 0.087158209 LYAYEPADTALLLDNMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYAYEPADTALLLDNMKK 18 1 O95994 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;; 225.68 6.30E-19 2118740000 2678320 1839580 2469190 1741720 3330500 2853520 2645920 2246680 2651670 1811080 FALSE TRUE 2784062.142 2155513.555 2533539.12 2086227.017 2764382.8 2190833.226 2438525.877 2216566.929 2556236.915 2165926.451 1.285390896 0.995192406 1.16972537 0.963203075 1.276305019 1.011499363 1.125858118 1.023380516 1.180204856 1 21.04655282 3.607199684 0.012899534 3.32E-06 2.229174798 0.098337988 0.10856687 6163.316753 18.8734303 1532.417118 1730.820059 4047.619541 -3.607199684 2.229171477 LYDAYELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LYDAYELK 8 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 123.92 0.0030874 474821000 965090 780400 903510 635130 1277890 1237520 874280 849880 964110 814860 FALSE TRUE 1003192.498 914427.6293 927056.2128 760756.8183 1060674.714 950124.7348 805751.6491 838488.7487 929411.8694 974516.2156 1.029426173 0.938340086 0.951298909 0.780650754 1.08841156 0.974970677 0.826822208 0.860415389 0.953716167 1 19.89432667 2.27039536 24.97900368 0.891950675 0.956727097 0.058256767 0.086634317 434.4858325 340915.8696 0.029992183 0.025091396 186.378306 -2.27039536 0.064776422 LYDDIDFDIEEFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYDDIDFDIEEFAK 14 0 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 226.29 5.72E-12 90399000 279780 165182 238976 213722 307890 293700 316960 236176 272180 130967 FALSE TRUE 290825.9304 193550.7236 245203.9109 255995.5737 255554.9678 225492.6261 292115.847 233010.447 262384.295 156627.4761 1.856800209 1.235739273 1.565522965 1.634423155 1.631610073 1.439674772 1.865035779 1.487672871 1.67521243 1 17.25697779 -1.161478596 4.250876449 0.999839472 1.588855019 0.50383528 0.178089915 0.00024721 4.88E-05 0.157331492 0.037073377 0.068947957 1.161478596 0.589015547 LYDEVQEVVYFPAVVHDNLGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYDEVQEVVYFPAVVHDNLGER 22 0 H9KVC8;F8WBX0;C9JNS3;F8W0M9;C9JID8;Q0VDG4-2;Q0VDG4 H9KVC8 SCRN3 Secernin-3 0 ; 125.73 2.08E-05 93380000 91845 112685 105950 104481 120538 125227 109603 112600 109402 117674 FALSE TRUE 95471.11152 132037.7722 108711.144 125147.03 100048.9938 96144.92708 101012.0305 111090.7812 105464.6434 140729.9673 0.678399302 0.938234938 0.772480419 0.889270653 0.71092885 0.683187305 0.717772003 0.789389661 0.749411411 1 17.10257005 -1.418112823 3.171204651 1.003234342 0.773096054 0.420400886 0.080975788 25914573.34 33212749.46 756866.4698 0.019683026 0.038184506 1.418112823 -0.230138288 LYDLNHNEIGELIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ;;; 220.21 4.72E-12 1179640000 503508 628920 662180 589190 647510 714500 568630 595680 557500 619950 FALSE TRUE 523386.8846 736932.1177 679436.9548 705730.0234 537446.4815 548568.2034 524059.2948 587695.8839 537435.6839 741417.3328 0.705927501 0.993950485 0.916402847 0.951866098 0.724890635 0.739891258 0.706834426 0.792665423 0.724876072 1 19.49992632 3.236031324 24.99985545 0.765876353 0.901056728 0.196409756 0.106101532 83.06264444 821004.882 0.028122415 0.035123595 1721.992773 -3.236031324 0.135180375 LYEEGSNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYEEGSNKR 9 1 P25788-2;P25788 P25788-2 PSMA3 Proteasome subunit alpha type-3 0 123.86 0.00087512 1624300000 1120700 965720 1054300 879530 1281900 1282800 1085900 984500 1159300 760730 FALSE TRUE 1164946.101 1131574.898 1081775.924 1053498.409 1064003.096 984889.141 1000784.321 971304.3878 1117577.019 909780.4784 1.280469442 1.243788941 1.18905159 1.157969899 1.169516297 1.082556907 1.100028352 1.067625005 1.228402945 1 19.79515895 8 0.212562035 1.048266175 2.273944193 0.615639306 0.05195497 32.02120069 0.401554754 0.081980782 13.33153657 100000000 -8 1.225678019 LYEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 LYEIAR 6 0 Q7Z5M8-2;Q7Z5M8 Q7Z5M8-2 ABHD12B Abhydrolase domain-containing protein 12B 0 ;;;;;; 130.84 0.036268 3160780000 2918300 2434010 2625720 2147190 2463290 2746590 2203670 2741590 2892930 1582634 FALSE TRUE 3033516.737 2852032.284 2694148.42 2571897.773 2044580.846 2108736.097 2030940.587 2704843.47 2788814.014 1892720.831 1.602728035 1.50684255 1.4234262 1.358836301 1.08023371 1.114129492 1.073027017 1.429076822 1.473441814 1 20.8520302 3.850980148 1.711431561 1.221266113 1.561517679 0.477637494 0.148795817 0.380758019 2.140089801 0.046636266 0.119195135 7095.453335 -3.850980148 0.340251566 LYELDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 113.5 0.01015 113780000 375200 451400 385630 416150 630030 597730 522900 442400 416530 641010 FALSE TRUE 390013.1857 528924.4386 395679.8346 498463.2279 522937.7256 458916.2662 481913.7317 436470.3516 401539.1667 766603.6366 0.508754677 0.689958165 0.516146566 0.650222885 0.682148767 0.59863565 0.62863481 0.569355963 0.523789802 1 19.54812132 -1.418548884 3.228747911 1.005284589 0.600177667 0.784224499 0.063483056 13562113.5 18075167.88 662510.5223 0.014417151 0.038146185 1.418548884 -0.405106922 LYENFISEFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 LYENFISEFEHR 12 0 Q9UNM6;J3KNQ3;A0A087WUL9;E9PQG3;E9PPD2 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;;;; 215.34 4.17E-11 1426413000 908726 876952 1043251 1211765 1139221 1309830 1485921 1143768 1101417 763106 FALSE TRUE 944603.2042 1027561.684 1070438.978 1451448.5 945576.6213 1005641.833 1369450.629 1128437.661 1061777.217 912622.0102 1.035043198 1.125944447 1.17292698 1.590415839 1.036109814 1.101925904 1.500567172 1.236478683 1.163435908 1 19.79965792 4.241562709 3.176893579 1.251584251 1.06492943 0.093377288 0.17945291 0.484709676 9.920588388 0.044510699 0.132907668 17440.65171 -4.241562709 -0.186654821 DKQS(ph)PSQANGCSDHRPIDILEMLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 DKQSPSQANGCSDHRPIDILEMLSR 25 2 Q9NPI6-2;Q9NPI6;A0A087WVE6;A0A087WT55 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 DKQS(0.79)PS(0.206)QANGCS(0.004)DHRPIDILEMLSR;DKQS(0.986)PS(0.014)QANGCSDHRPIDILEMLSR;DKQS(0.874)PS(0.126)QANGCSDHRPIDILEMLSR;DKQS(0.982)PS(0.018)QANGCSDHRPIDILEMLSR 221.77 5.22E-34 315401000 110543 194758 218082 200307 285407 292991 235729 253886 256482 193912 TRUE FALSE 114907.323 228206.1715 223765.3961 239927.1267 236893.6201 224948.2806 217251.945 250483.0734 247251.2629 231905.3437 0.495492347 0.984048784 0.964899698 1.034590764 1.021509967 0.970000419 0.936813018 1.080109106 1.066173202 1 17.82317654 4.742825661 4.486352919 1.010077203 0.459143162 0.929258517 0.042342205 0.050550641 2.569150323 0.010933673 0.088595917 55312.80219 -4.742825661 -0.550934042 down LYFHSDTCLPLRPQEMEVDS(ph)EDEKDPEWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYFHSDTCLPLRPQEMEVDSEDEKDPEWLR 30 2 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 LYFHSDTCLPLRPQEMEVDS(1)EDEKDPEWLR;LY(0.001)FHS(0.007)DT(0.063)CLPLRPQEMEVDS(0.93)EDEKDPEWLR 83.917 0.00068342 438820000 148994 80954 117538 95223 148273 164565 118221 95945 127017 85870 TRUE FALSE 154876.3982 94857.21977 120601.1368 114057.8252 123069.6084 126347.2728 108954.5291 94659.01421 122445.683 102694.5824 1.508126276 0.923682803 1.17436708 1.110650849 1.198404098 1.230320722 1.060956932 0.921752754 1.192328554 1 16.64800055 4.75322655 24.84332627 1.08961622 1.508126596 0.578753839 0.106944859 1904.189256 3225537.679 0.026626507 0.611881384 56653.47454 -4.75322655 0.418510376 LYFLQCETCHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYFLQCETCHSR 12 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 ; 237.27 4.23E-16 1772140000 1219770 1495910 1297400 1418230 1749070 1649700 1334350 1320800 1364700 1709030 FALSE TRUE 1267927.461 1752820.906 1331211.31 1698751.661 1451763.706 1266582.176 1229760.16 1303096.836 1315584.714 2043881.707 0.620352664 0.857594106 0.651315243 0.831139911 0.710297324 0.619694463 0.601678735 0.637559812 0.643669694 1 20.96288027 -0.980951417 4.783471569 1.000002989 0.685732348 0.551297626 0.085004808 3.88E-06 8.27E-07 0.084005735 0.019800077 0.10448371 0.980951417 -0.314270641 LYGDVPFIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGDVPFIEER 11 0 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 ; 125.68 0.00075193 56518000 60393 66550 65241 64092 73702 81210 69822 68478 57684 74286 FALSE TRUE 62777.36227 77979.44481 66941.23406 76769.2063 61174.16037 62350.20825 64349.16919 67560.16442 55607.96411 88840.91941 0.706626661 0.877742434 0.753495512 0.864119899 0.688580901 0.701818584 0.724319037 0.760462238 0.625927382 1 16.4389367 4.080205112 24.99981159 0.753248517 0.798043432 0.000471177 0.105742287 124.8254845 38898.87258 0.024347679 0.052596993 12028.32383 -4.080205112 0.044794915 LYGKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYGKPIR 7 1 Q5SZ64;Q15427 Q5SZ64 SF3B4 Splicing factor 3B subunit 4 0 64.803 0.09676 0 212020 351360 295440 324020 340180 427470 257760 314680 290240 434460 FALSE TRUE 220390.7133 411703.3468 303139.4091 388110.1889 282356.3251 328196.5709 237556.0977 310462.2293 279794.3191 519584.1188 0.424167532 0.792370921 0.58342701 0.746963148 0.543427551 0.631652429 0.457204308 0.597520629 0.538496673 1 18.98699781 -1.787249009 2.992869938 1.093458961 0.595087214 0.561728372 0.108426243 35499574.79 20653978.22 23762512.64 0.024391352 0.016321159 1.787249009 -0.498371748 LYGPS(ph)SVSFADDFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGPSSVSFADDFVR 15 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 1 LYGPS(0.972)S(0.024)VS(0.004)FADDFVR;LYGPS(0.961)S(0.036)VS(0.003)FADDFVR 125.97 0.00047709 25750000 9824.6 55425 40425 62377.2 31324.8 58646.6 27747.9 45277.8 32249.3 66747 TRUE FALSE 10212.48279 64943.8126 41478.50871 74715.22398 26000.22168 45026.81595 25572.94709 44670.92515 31088.65399 79824.7967 0.127936221 0.81357943 0.519619347 0.935990157 0.325716103 0.564070537 0.320363448 0.559612138 0.389461111 1 16.28454935 -1.305445669 3.480560744 1.001816821 0.51965546 0.298825707 0.226057389 225261532.2 348311518.1 4339309.429 0.050458603 0.049494203 1.305445669 -0.482161361 LYGPSSVSFADDFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGPSSVSFADDFVR 15 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1;E9PJH8 P50454 SERPINH1 Serpin H1 0 ; 193.73 1.88E-07 38001000 21165.2 25791.3 21888.6 28164 29249.5 37979 23858.2 22199.9 24359.1 29552 FALSE TRUE 22000.81844 30220.75515 22459.0349 33734.75514 24277.68044 29158.95283 21988.13194 21902.34665 23482.42075 35342.14859 0.622509364 0.855091056 0.63547452 0.954519079 0.686932782 0.825047542 0.622150402 0.619723122 0.664431046 1 15.10910213 2.240197589 24.99720208 0.684235485 0.766851834 0 0.141063662 117.9631912 1801371.66 0.046579675 0.037089485 173.8591649 -2.240197589 0.082616348 LYGPTNFAPIINHVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGPTNFAPIINHVAR 16 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;H0Y524 Q99829 CPNE1 Copine-1 0 ; 183.6 1.96E-09 2235330000 754840 959200 915740 878930 1076170 1093170 941500 940400 917240 1144290 FALSE TRUE 784641.6661 1123935.138 939604.9367 1052779.731 893243.0078 839297.8347 867702.7698 927795.4762 884228.7116 1368491.717 0.573362379 0.821294806 0.686598921 0.769299308 0.6527208 0.613301363 0.634057743 0.677969377 0.64613377 1 20.38415527 -1.801559955 4.612082341 1.039122819 0.678151129 0.665837302 0.069044706 0.025800107 0.001110078 0.062098134 0.015302216 0.015792106 1.801559955 -0.36097169 LYGS(ph)PTQIGPSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGSPTQIGPSYR 13 0 E7EWD6;Q76L83;Q76L83-2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 LYGS(0.727)PT(0.273)QIGPSYR;LYGS(0.774)PT(0.226)QIGPSYR 196.37 1.49E-07 248070000 156520 151697 173019 148999 201333 224440 175070 181593 187392 171390 TRUE FALSE 162699.5305 177749.7797 177528.0173 178470.5575 167110.4886 172317.2114 161347.5559 179159.0429 180647.7985 204970.589 0.793770127 0.867196511 0.866114588 0.870713005 0.815290083 0.840692376 0.787174183 0.874071952 0.881335217 1 17.64505739 0.791276076 1.515686601 0.999459968 0.838653813 0.734486063 0.029383452 0.367347572 1.496408039 0.027701073 0.008068498 6.184093913 -0.791276076 -0.160806155 LYGS(ph)VCDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYGSVCDLR 9 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 LYGS(1)VCDLR;LYGS(1)VCDLR 138.76 0.00013372 394960000 634020 811800 722100 876940 973560 952500 641100 690150 600790 815840 TRUE FALSE 659051.5992 951220.3351 740918.5192 1050396.115 808074.6189 731296.3103 590848.9068 680899.6681 579167.6853 975688.2278 0.675473558 0.974922427 0.759380403 1.076569425 0.828209869 0.749518432 0.605571421 0.697866028 0.593599132 1 19.8960607 2.713996214 3.352338964 0.695393523 0.877761464 0.158733849 0.147403069 0.332479652 7.815457244 0.045773207 0.044951035 517.6023197 -2.713996214 0.182367941 LYHDIAQQAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYHDIAQQAFK 11 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 89.548 0.012151 410300000 566050 461030 499150 410120 858500 649870 593490 470280 529820 680920 FALSE TRUE 588398.0911 540208.3162 512158.2591 491240.5119 712572.4766 498947.5414 546970.703 463976.6658 510751.8817 814333.237 0.722551978 0.663375006 0.628929578 0.603242616 0.875037938 0.612706836 0.671679207 0.569762653 0.627202549 1 19.63525976 -0.945182941 5.059890476 1.000001567 0.659407847 0.606089453 0.08123283 1.43E-06 2.99E-07 0.078435007 0.018487223 0.113453281 0.945182941 -0.340593719 LYHEADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYHEADK 7 0 O75663 O75663 TIPRL TIP41-like protein 0 81.297 0.027584 59111000 230420 154000 192850 170700 262330 259430 256820 224750 230680 140610 FALSE TRUE 239517.1595 180448.302 197875.8294 204463.9505 217739.2403 199181.3142 236689.7773 221737.5939 222377.8719 168159.8374 1.424342241 1.073076098 1.176712778 1.215890511 1.294834984 1.184476135 1.407528581 1.318612086 1.322419642 1 17.35947365 3.287878613 6.46554912 1.2807099 1.207879453 0 0.131742699 0.599426176 56.84890614 0.034854833 0.046877684 1940.343466 -3.287878613 -0.072830447 LYHEADKTYMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYHEADKTYMLR 12 1 O75663 O75663 TIPRL TIP41-like protein 0 119.69 0.00029466 400720000 542230 434680 501180 415490 785580 705710 568350 525430 561600 633370 FALSE TRUE 563637.6591 509332.9087 514241.1625 497672.6819 652047.3922 541819.5476 523801.2419 518387.4703 541388.1257 757466.7249 0.744108804 0.672416216 0.678896043 0.657022501 0.860826451 0.715304752 0.691517165 0.684369957 0.714735193 1 19.53082299 0.907387889 19.86622972 1 0.710611405 0.710756758 0.054861985 6126.990484 1314305.141 0.053394306 0.013348577 8.079563317 -0.907387889 -0.289388595 LYHNEVEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYHNEVEIEK 10 0 G8JLG1;Q14683;H0Y7K8 G8JLG1 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 65.241 0.08293 0 620270 387130 490900 369140 843510 690240 558920 595860 645130 426920 FALSE TRUE 644758.7386 453616.566 503693.2573 442154.7902 700130.4715 529942.2207 515110.3899 587873.4713 621911.8973 510566.8001 1.262829347 0.88845684 0.986537427 0.86600772 1.371280842 1.037948845 1.008899109 1.151413431 1.21808135 1 18.9617402 3.285837286 24.99995529 1.126943845 0.991892315 0.163299273 0.143720815 212.316041 112271.4479 0.038395101 0.051987067 1931.244614 -3.285837286 -0.13505153 LYHS(ph)LGPVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYHSLGPVTR 10 0 Q86X27 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 LYHS(1)LGPVTR;LYHS(1)LGPVTR;LYHS(1)LGPVTR 166.62 3.54E-06 1675930000 483076 585160 577064 524597 861110 674375 552713 605325 496870 681908 TRUE FALSE 502148.2135 685656.6781 592102.7619 628360.7208 714738.8298 517761.6265 509389.9108 597211.6085 478987.7458 815514.8167 0.615743826 0.840765445 0.726047829 0.770508037 0.876426541 0.634889294 0.624623735 0.732312395 0.587344014 1 19.63735156 -1.096081268 4.828113168 1.000012197 0.717842697 0.462581352 0.092916252 1.20E-05 2.24E-06 0.088353302 0.020824173 0.080152806 1.096081268 -0.282169501 LYHSCADPTGCGTGPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYHSCADPTGCGTGPDAR 18 0 Q9UHL4;R4GMU5 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 163.91 3.20E-11 239400000 109930 123170 118430 108890 123350 142780 111610 101350 113270 101020 FALSE TRUE 114270.1213 144323.4894 121516.3831 130428.117 102383.0111 109621.5089 102861.7166 99991.56903 109193.4348 120812.9349 0.945843435 1.194602958 1.005822624 1.079587357 0.84745074 0.907365664 0.85141311 0.827656154 0.903822384 1 16.8824154 3.240688796 24.99999999 0.875761347 1.062713935 0.541308715 0.074501486 36.15160052 424672.9761 0.019535217 0.02520023 1740.559186 -3.240688796 0.186952588 LYKDDQLLDDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;; 162.93 5.60E-05 1704110000 2998830 1314940 1943680 1461590 2747860 2529650 2765260 2071100 2416210 1100590 FALSE TRUE 3117226.124 1540770.716 1994333.898 1750688.14 2280779.739 1942177.125 2548511.696 2043340.292 2329251.074 1316229.538 2.368299778 1.17059424 1.515187009 1.330078143 1.732813063 1.475561115 1.936221321 1.552419417 1.769638962 1 20.32797967 LYKEELEQTYHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYKEELEQTYHAK 13 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 157.75 2.51E-05 1374050000 1423120 931040 1248920 882140 1706290 1480450 1425090 1165020 1340110 940010 FALSE TRUE 1479305.876 1090938.878 1281467.881 1056624.659 1416255.435 1136637.924 1313387.722 1149404.812 1291879.703 1124186.962 1.315889551 0.970424773 1.139906372 0.939901186 1.259804181 1.011075526 1.168300084 1.022432079 1.149168018 1 20.10045056 0.868205381 0.011705752 1.68E-06 2.13600962 0.079565134 0.116364895 3713.14357 25.75146095 2390.85789 2303.816287 7.382532724 -0.868205381 2.136007939 LYKS(ph)EPELTTVAEVDESNGEEKSEPVSEIETSVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYKSEPELTTVAEVDESNGEEKSEPVSEIETSVVK 35 2 Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;A0JP02;B4DJX4;Q9HAU0-8 Q9HAU0 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 LY(0.428)KS(0.478)EPELT(0.047)T(0.047)VAEVDESNGEEKSEPVSEIETSVVK 138.32 1.80E-09 68944000 94120 33594 54273 31374 94226 77815 65064 55448 66202 32012 TRUE FALSE 97835.93028 39363.50817 55687.39897 37579.68356 78209.49818 59743.64555 59964.11367 54704.81025 63819.40295 38284.13849 2.555521271 1.028193652 1.454581484 0.9815993 2.042869482 1.560532583 1.566291316 1.428915797 1.666993315 1 15.22445917 -1.736420394 2.724987539 0.894540994 1.551277712 0.136718603 0.434320364 28070804.09 22086840.1 19980383.24 0.095248782 0.018347614 1.736420394 0.656736718 LYLEDDDPVQAEAYINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYLEDDDPVQAEAYINR 17 0 D6RFN0;Q9BT78;D6RAX7;Q9BT78-2;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ; 167.98 5.01E-09 98228000 68845 55443 68980 61755 73502 76690 73931 74772 66881 56617 FALSE TRUE 71563.05376 64964.90396 70777.67547 73969.95468 61008.15629 58879.90975 68136.09504 73769.80364 64473.96587 67710.01715 1.056904972 0.959457798 1.045305827 1.092452163 0.901021132 0.869589349 1.006292686 1.089496159 0.9522072 1 16.04708166 -0.895117972 5.681467125 0.999999978 1.000532988 0 0.072560707 5.51E-10 6.60E-20 0.073889736 0.017415969 0.127315719 0.895117972 0.00053301 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYNLDVFQYELYNPMALYGSVPVLLAHNPHR 31 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 169.13 5.52E-13 1457470000 207409 223346 257907 342371 355308 392356 304140 311004 255341 254126 FALSE TRUE 215597.6675 261703.9381 264628.2683 410090.9619 294912.8731 301237.2652 280300.7121 306835.5001 246151.3273 303917.1242 0.709396248 0.86110297 0.8707251 1.349351285 0.970372676 0.991182271 0.92229325 1.009602539 0.809929115 1 18.21331844 4.286145511 2.464550183 1.003742003 0.745624696 0.311374527 0.133834123 0.354907151 4.1480746 0.034544502 0.128949609 19326.15735 -4.286145511 -0.258117307 LYNNHEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 LYNNHEIR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;; 161.79 0.00034549 2835570000 1570370 2047610 1861740 1718080 2038480 2215750 1845330 1861030 1607080 2180560 FALSE TRUE 1632369.42 2399271.089 1910258.474 2057911.096 1691979.898 1701175.643 1700688.213 1836085.937 1549241.505 2607798.983 0.625956767 0.920036822 0.732517532 0.789137165 0.648815307 0.652341555 0.652154642 0.704074949 0.594080109 1 21.31440124 -1.187502181 3.695446702 1.000285665 0.706628118 0.494461574 0.090254879 28652323.87 45856867.91 95886.79997 0.021769176 0.064937837 1.187502181 -0.293657546 LYPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYPLRK 6 1 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 106.05 0.052039 2243600000 1448860 1421160 1508780 1273000 1980760 1749990 1562680 1609190 1545120 1574020 FALSE TRUE 1506062.112 1665233.175 1548100.046 1524795.6 1644071.123 1343581.344 1440193.058 1587621.44 1489511.433 1882419.083 0.800067384 0.884624041 0.822399252 0.810019201 0.873382095 0.713752509 0.765075679 0.843394255 0.791275145 1 20.84415642 -1.306801735 3.529738103 1.000666804 0.813117915 0.585761904 0.047525007 13013872.14 22528478.99 93717.25775 0.01153334 0.0493399 1.306801735 -0.187548889 LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 LYPPGDEEEAELADSSGLYHEGSPS(0.002)PGS(0.998)PWK;LYPPGDEEEAELADSSGLYHEGSPSPGS(1)PWK;LYPPGDEEEAELADSSGLYHEGSPS(0.001)PGS(0.999)PWK 286.54 1.32E-72 222342000 105069 119633 126133 106027 161204 167334 146596 136050 138775 113702 TRUE FALSE 109217.2053 140179.0371 129420.1296 126998.8241 133802.6017 128473.2145 135105.4225 134226.4723 133780.5149 135979.7299 0.803187396 1.030881862 0.951760455 0.933954084 0.983989317 0.944796806 0.99357031 0.987106478 0.98382689 1 17.05303208 4.749832954 24.99786332 0.976537674 0.803187295 0.78825852 0.027292856 753.7195163 1671438.828 0.006367468 0.100628119 56212.50692 -4.749832954 -0.173350379 LYPPSAEYPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYPPSAEYPDLR 12 0 P12532;F8WCN3;C9JSQ1;C9J8F6;C9JJX8;C9J995 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 73.067 0.09352 79462000 47755 68921 67259 67792 70872 98686 55281 57329 54107 84454 FALSE TRUE 49640.40427 80757.64562 69011.82479 81201.05526 58825.20275 75767.6721 50947.93077 56560.59853 52159.69964 101001.1443 0.491483583 0.799571591 0.683277652 0.803961735 0.582421151 0.750166472 0.504429243 0.559999581 0.516426819 1 16.62401211 -1.037802164 4.788067194 1.000009026 0.634757081 0.480715699 0.114590591 1.11E-05 2.23E-06 0.111601564 0.026304091 0.091663795 1.037802164 -0.365251946 LYQHAVEYFLHAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYQHAVEYFLHAIK 14 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 206.2 6.46E-09 239680000 421260 365830 398620 369560 609980 554690 498140 441530 440370 432490 FALSE TRUE 437891.6701 428658.4567 409008.3647 442657.865 506295.8175 425871.6539 459094.4852 435612.0125 424521.1697 517228.135 0.84661224 0.828760904 0.790769753 0.85582712 0.978863645 0.823372947 0.887605399 0.84220479 0.820761944 1 18.98044123 -2.609216379 2.216753816 4.275824636 0.853856963 0.452550439 0.048571735 1585763.175 199964.3162 26535614.74 0.011872075 0.002459142 2.609216379 -3.421967673 LYQHAVEYFLHAIKYEAHSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYQHAVEYFLHAIKYEAHSDK 21 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 ; 246.31 9.26E-31 249131000 435810 348100 453020 201357 774980 566650 307610 447940 563110 536330 FALSE TRUE 453016.1153 407883.4672 464826.0734 241184.8136 643249.1764 435054.1252 283498.7244 441936.097 542843.7811 641413.5948 0.706277695 0.635913349 0.724690086 0.376020738 1.002861775 0.678273938 0.441990514 0.689003321 0.846324096 1 19.29089541 1.07318471 2.886154212 0.99507983 0.651291069 0.331245593 0.159201353 0.261045488 4.422889961 0.145929569 0.039000653 11.83544823 -1.07318471 -0.343788761 LYQPEYQEVSTEEQREEISGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYQPEYQEVSTEEQREEISGK 21 1 A0A494C039;Q9Y4L1;A0A087X054 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 136.96 3.71E-06 358610000 158708 86778 114449 88140 151230 167980 126951 114580 118936 75600 FALSE TRUE 164973.9144 101681.4465 117431.635 105573.8289 125523.9786 128969.1908 117000.2489 113044.2425 114655.5166 90412.37255 1.824682947 1.124640838 1.298844745 1.167692274 1.388349571 1.426455109 1.294073428 1.250318284 1.268139673 1 16.46423259 -5 0.090494461 0.010822516 1.577972283 0.309738093 0.17440852 289.0198477 1.816625272 55.93300743 3.877953129 1.00E-05 5 1.567149767 LYQTDPSGTYHAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 170.45 3.17E-06 4354700000 3553560 3790870 3918950 3134300 5672300 5019060 4355760 3683560 3951730 4638320 FALSE TRUE 3693857.293 4441922.434 4021081.056 3754255.185 4708124.472 3853459.38 4014344.15 3634187.903 3809508.009 5547109.998 0.665906624 0.800763359 0.724896578 0.676794797 0.848752679 0.694678739 0.723682089 0.655149782 0.686755448 1 22.4033049 -1.884966683 2.585581174 1.141396684 0.719484 0.676044816 0.058208162 20779539.51 12448384.72 17960615.26 0.014657411 0.013032668 1.884966683 -0.421912684 LYRPGSVAYVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYRPGSVAYVSR 12 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 131.79 0.00017546 673850000 223581 246700 206560 228641 438270 308050 217870 215293 255160 530950 FALSE TRUE 232408.1505 289068.8059 211943.1233 273865.5074 363773.0219 236510.056 200792.7801 212407.3495 245976.8414 634979.4868 0.366008911 0.455241172 0.333779481 0.431298196 0.572889407 0.372468813 0.316219318 0.334510569 0.387377619 1 19.27635046 -1.405413843 3.268261846 1.006899062 0.394046192 0.863807342 0.071865962 32790536.67 43899473.29 2118721.592 0.019123154 0.039317524 1.405413843 -0.61285287 LYSESLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 LYSESLAR 8 0 P50395;P50395-2;Q5SX87;Q5SX91;P31150 P50395;P31150 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 ;; 138.83 0.0016023 779560000 961100 1635390 1620900 1527410 1684610 2012680 1598540 1567780 1659870 1783260 FALSE TRUE 999044.9701 1916255.511 1663141.986 1829527.139 1398260.594 1545265.572 1473242.258 1546766.473 1600131.603 2132655.654 0.468451139 0.8985302 0.779845533 0.857863357 0.655642926 0.724573407 0.69080175 0.725277177 0.750300031 1 21.02421961 0.732279809 4.290874154 0.999999263 0.732784731 0.351581289 0.110924799 6.586950729 104.7370179 0.099369071 0.025284899 5.398583327 -0.732279809 -0.267214532 LYSGS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LYSGSPTR 8 0 Q6PJI9-4;Q6PJI9-3;Q6PJI9;H3BMH3 Q6PJI9-4 WDR59 WD repeat-containing protein 59 1 LYS(0.003)GS(0.995)PT(0.002)R;LYS(0.004)GS(0.987)PT(0.008)R;LYS(0.001)GS(0.999)PTR;LYS(0.055)GS(0.941)PT(0.004)R 116.12 0.0024477 785117000 579460 755910 727640 759510 866730 968660 782820 759970 765720 789870 TRUE FALSE 602337.5282 885731.6623 746602.8962 909738.8111 719403.5442 743703.3952 721460.5229 749783.8452 738161.8868 944629.9035 0.637643934 0.9376494 0.790365511 0.963063743 0.761571851 0.787296054 0.763749401 0.793732913 0.781429726 1 19.84938968 -0.691396678 7.878509466 1 0.806094736 0.317968147 0.086867118 0 0 0.077770484 0.018330679 0.203518232 0.691396678 -0.193905264 LYSILQGDS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYSILQGDSPTK 12 0 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 LY(0.013)S(0.015)ILQGDS(0.969)PT(0.003)K 56.225 0.078458 8288700 14253 19371 29481 21774 30131 34396 28106 30176 28187 23765 TRUE FALSE 14815.71945 22697.81856 30249.29908 26080.83221 25009.34338 26408.05028 25902.97828 29771.54008 27172.55538 28421.29674 0.521289355 0.79862009 1.064318048 0.917651029 0.87995082 0.929164159 0.91139326 1.047508154 0.956063181 1 14.79468476 4.61124586 2.950362712 0.960733322 0.500863808 0.842741829 0.058447348 0.113857792 1.58472479 0.014978521 0.104580855 40855.06073 -4.61124586 -0.459869515 LYSLLGIDLTAPSNNS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPR 19 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.12)NNS(0.44)S(0.44)PR 187.75 1.86E-14 203400000 159410 199330 171860 209510 189900 243640 179740 185730 173160 188160 TRUE FALSE 165703.6299 233563.3769 176338.8128 250950.4527 157620.8658 187058.3024 165651.5091 183240.5931 166928.0054 225026.3495 0.736374341 1.037937901 0.783636286 1.115204745 0.700455152 0.831272884 0.736142721 0.814307274 0.741815373 1 17.77973442 3.195078564 24.99993357 0.792874417 0.917218829 0.157639197 0.127875916 212.1744273 121988.6271 0.033351866 0.039863333 1567.034522 -3.195078564 0.124344412 LYSLLGIDLTAPSNNSSPRDS(ph)PCKENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYSLLGIDLTAPSNNSSPRDSPCKENK 27 2 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 LYSLLGIDLTAPS(0.154)NNS(0.154)S(0.154)PRDS(0.539)PCKENK 76.573 0.0080284 118600000 110180 53034 90454 57452 137650 107400 112270 85910 104880 56002 TRUE FALSE 114529.9915 62142.17695 92811.30555 68815.83412 114252.3022 82457.97766 103469.984 84758.51697 101105.3893 66974.51968 1.710053197 0.927848042 1.385770379 1.027492761 1.705907003 1.231184308 1.544915657 1.265533779 1.509609771 1 16.03132471 3.27049041 24.99998554 1.385630084 1.247651155 0.039565867 0.267197322 591.4171915 463056.5963 0.066915013 0.090595813 1864.191013 -3.27049041 -0.137978929 LYTDFDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 112934000 191999 203738 195262 231590 222554 259670 268630 217518 195324 189401 FALSE TRUE 199579.2688 238728.4166 200350.6881 277397.8108 184724.3506 199365.5778 247574.0787 214602.527 188294.3274 226510.4996 0.88110383 1.053939738 0.884509497 1.224657626 0.815522242 0.880160426 1.092991623 0.947428606 0.831282999 1 17.7892184 LYTDFDEIRQEIENETER ddPTM_MDA-MB-175_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 ;;;;; 268.55 1.58E-31 929309000 469057 581500 583346 543533 630853 710520 544318 575416 564481 683650 FALSE TRUE 487575.7326 681368.1016 598548.476 651042.2051 523620.8324 545512.498 501652.9328 567703.4897 544165.4391 817598.1282 0.596351332 0.833377766 0.732081515 0.79628632 0.640437905 0.667213487 0.613569082 0.694355173 0.665565906 1 19.64103237 -1.777260681 8.33768197 1.004229076 0.695648722 0.620399656 0.07196183 0.005673687 0.000151571 0.069880942 0.01635244 0.016700879 1.777260681 -0.308580354 LYTLQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 1675650000 1797600 1363570 1587310 1541090 2182220 2111710 1988980 1512410 1672060 1359650 FALSE TRUE 1868570.636 1597752.54 1628676.603 1845913.002 1811287.024 1621297.356 1833078.55 1492138.618 1611882.887 1626047.385 1.149148944 0.982599003 1.001616938 1.135214766 1.113920197 0.997078788 1.127321729 0.917647684 0.991289 1 20.63293787 1.73177678 14.64031591 0.966371338 1.067348107 0.368541584 0.061345639 0.096020138 138.1436483 0.028126596 0.015506932 53.92333944 -1.73177678 0.100976769 LYTLVLTDPDAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYTLVLTDPDAPSR 14 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 190.15 1.48E-06 234987000 160711 193875 142875 156575 205516 216143 150737 155461 139769 296976 FALSE TRUE 167055.9944 227171.5231 146598.4399 187545.0677 170582.4637 165947.0639 138921.8401 153377.2996 134738.741 355162.7613 0.470364612 0.639626526 0.412764107 0.528053862 0.480293776 0.467242296 0.391149792 0.431850735 0.379371814 1 18.4381208 -1.642515497 4.285025013 1.015676467 0.466569018 0.832954653 0.071640949 0.010945453 0.00091314 0.070764664 0.01659318 0.02277637 1.642515497 -0.549107449 LYTYEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LYTYEPR 7 0 Q8TD06;B5MC62;H7C040 Q8TD06 AGR3 Anterior gradient protein 3 homolog 0 ; 81.784 0.061099 400330000 1059910 1122900 1148300 1111140 1478650 1445890 1305920 1195420 1145390 1144100 FALSE TRUE 1101756.065 1315749.34 1178225.641 1330920.176 1227309.601 1110103.96 1203558.578 1179397.35 1104167.638 1368264.49 0.805221559 0.961619153 0.861109566 0.972706802 0.896982718 0.811322641 0.879624215 0.861965913 0.806984063 1 20.3839157 2.976518647 24.67849621 0.863117345 0.905899343 0.030067543 0.066749063 1579.043739 1659548.764 0.018678726 0.01992863 947.3678594 -2.976518647 0.042781997 LYVELHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYVELHR 7 0 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 105.12 0.020593 0 37034 40897 36411 40880 44572 44213 38630 40176 41441 45418 FALSE TRUE 38496.13092 47920.74162 37359.90057 48965.94199 36995.66736 33945.2008 35602.07966 39637.50643 39949.54651 54316.78752 0.708733573 0.882245505 0.687814988 0.901488181 0.681109268 0.624948609 0.655452601 0.729746884 0.735491702 1 15.72911054 -0.803551219 2.7197556 1.000140111 0.733506612 0.463362442 0.085838983 131435.3965 197223.283 202.8463389 0.022039887 0.157198639 0.803551219 -0.266633499 LYVYNTDTDNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 LYVYNTDTDNCR 12 0 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;;; 329.18 9.64E-58 614790000 476383 579324 459624 546260 544131 633190 465724 564030 461257 622510 FALSE TRUE 495190.9687 678818.3905 471602.179 654308.5976 451639.807 486141.2186 429219.3359 556470.1004 444656.4507 744478.9158 0.665151099 0.911803378 0.633466132 0.8788813 0.606652247 0.652995281 0.576536591 0.747462539 0.597272053 1 19.50587147 -1.171534221 3.838603565 1.000193538 0.700775595 0.404791143 0.110238008 5929360902 9714752532 14019435.48 0.025328148 0.067369881 1.171534221 -0.299417942 MAADDVEEYMIERPEPEFQDLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MAADDVEEYMIERPEPEFQDLNEK 24 1 C9J363;Q9BUL8;C9J6F3;C9J5C3;H7C5M9;C9JSA3;C9JND6 C9J363 PDCD10 Programmed cell death protein 10 0 70.533 0.028352 195330000 27840 22759 29447 20647 40844 36924 35204 29831 28239 30518 FALSE TRUE 28939.1447 26667.68121 30214.41301 24730.91497 33901.35147 28348.96059 32444.61849 29431.16424 27222.68391 36497.4178 0.792909374 0.730673095 0.827850704 0.677607252 0.928869863 0.776738802 0.888956547 0.806390315 0.745879724 1 15.15550678 -5 0.222986107 2.010200472 0.775934933 0.419261792 0.070485795 145.2622729 1.453906364 66.21386045 0.123054494 1.00E-05 5 -1.23426554 MAAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MAAVGR 6 0 Q9Y6G9;E9PHI6;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 97.908 0.094307 145010000 167360 173560 160460 187000 190800 212940 198730 202790 173320 138750 FALSE TRUE 173967.502 203367.5799 164641.7194 223988.0419 158367.8842 163487.9121 183153.0233 200071.9317 167082.2471 165935.406 1.048404956 1.225582803 0.992203674 1.349850808 0.954394773 0.985250322 1.103760962 1.205721772 1.006911371 1 17.34026222 MADKDGDLIATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MADKDGDLIATK 12 1 O43852;O43852-3;O43852-15;O43852-6;O43852-10;O43852-2;O43852-4;O43852-8 O43852;O43852-2 CALU Calumenin 0 ; 70.889 0.042013 305840000 716520 489540 518820 471790 820730 744160 689540 532550 636440 414140 FALSE TRUE 744808.7629 573614.6869 532340.8754 565108.6538 681222.6078 571340.1179 635492.053 525412.0383 613534.6487 495282.8038 1.503805012 1.158155871 1.074822044 1.140981777 1.375421481 1.153563406 1.283089274 1.060832386 1.23875621 1 18.91789301 -5 0.0484468 0.195494726 1.624673125 0.258717036 0.12591856 907.171667 3.256532282 97.35011809 22.82115443 1.00E-05 5 1.429178399 MAGNEALS(ph)PTSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALS(1)PTSPFR;MAGNEALS(0.991)PT(0.007)S(0.002)PFR 195.6 2.73E-08 349680000 333260 413990 403860 370510 498290 525400 435460 442460 437150 482650 TRUE FALSE 346417.3621 485089.5621 414384.9234 443795.7721 413590.8438 403383.8125 401327.5073 436529.5474 421417.0569 577216.0266 0.600152016 0.840395172 0.717902664 0.768855596 0.716526958 0.69884375 0.695281296 0.756267199 0.73008551 1 19.13875183 -0.223543778 1.09024331 1.00314351 0.727481798 0.669901941 0.057917609 10.42419993 8.43102502 0.197650777 0.015685345 0.597662796 0.223543778 -0.275661711 MAGNEALSPTS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MAGNEALSPTSPFR 14 0 Q86WR7;Q86WR7-2;D3DRR9 Q86WR7 PROSER2;C10orf47 Proline and serine-rich protein 2 1 MAGNEALSPT(0.001)S(0.999)PFR;MAGNEALS(0.002)PT(0.015)S(0.983)PFR 221.69 4.37E-12 224480000 510760 600800 614650 617150 700000 854410 695380 687110 682200 746730 TRUE FALSE 530925.1992 703982.7264 630668.2839 739220.428 581014.25 655986.2262 640874.2986 677900.4143 657647.7553 893037.4465 0.594516166 0.788301464 0.706205867 0.827759721 0.650604577 0.734556237 0.717634295 0.759095172 0.736416774 1 19.76836115 -4.999999998 0.30701093 3.373473042 0.714729142 0.649610043 0.061378143 165.6391399 1.510308431 253.7671089 0.05387559 1.00E-05 4.999999998 -2.658743901 MAGTAFDFENMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MAGTAFDFENMKR 13 1 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ; 177.81 2.43E-05 1525720000 1560200 1248940 2026780 921860 2559570 1814100 1552450 1510220 1917690 1527270 FALSE TRUE 1621797.901 1463435.73 2079599.552 1104201.157 2124495.206 1392802.768 1430764.912 1489977.971 1848672.712 1826509.315 0.887922053 0.801219965 1.138564985 0.60454176 1.163145015 0.762548954 0.78333294 0.815751641 1.012134291 1 20.80065768 MALIQLGSVEEAIQALIELHNHDLGENHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MALIQLGSVEEAIQALIELHNHDLGENHHLR 31 0 O95758-1;O95758-6;O95758;O95758-5;O95758-4;O95758-7 O95758-1 PTBP3 Polypyrimidine tract-binding protein 3 0 ;; 200.01 3.35E-26 871057000 335846 355252 376206 415084 409948 494405 474819 391707 396035 397540 FALSE TRUE 349105.4594 416263.7675 386010.2374 497186.3763 340265.1854 379586.9315 437601.4461 386456.8084 381781.7777 475430.3516 0.734293589 0.875551521 0.811917531 1.045760698 0.715699333 0.798407023 0.920432287 0.81285683 0.803023569 1 18.85887448 -1.311427503 3.036870501 1.00130071 0.839276492 0.229942589 0.090145268 19919535.26 26302097.94 235813.1918 0.02027084 0.048817158 1.311427503 -0.162024217 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 20 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A6NLN1;P26599;P26599-2;P26599-3;A0A0U1RRM4;A0A0D9SF20 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 ;;;;;;;;;;;;;;;;;;; 285.36 1.10E-72 28775124600 4372489.7 5043899.3 5235483.7 5710300.8 5263261.6 6428120.4 5937501.8 5338562 5130102.9 4765076.3 FALSE TRUE 4545118.97 5910149.769 5371924.706 6839781.255 4368614.273 4935286.856 5472104.894 5267007.309 4945471.499 5698701.768 0.797570948 1.037104591 0.942657631 1.200234989 0.766598157 0.866037048 0.960237106 0.924246876 0.867824234 1 22.44220186 MALLQEFASRPLGAAPQAEHQGLPVPGS(ph)PGGQK ddPTM_MDA-MB-175_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 228.04 1.13E-36 2113580000 2884000 1976030 2367300 1782460 3077600 3385300 2935800 2714800 2934200 2149600 TRUE FALSE 2997862.547 2315397.781 2428993.783 2135025.268 2554470.651 2599115.38 2705684.325 2678412.547 2828598.715 2570772.963 1.166132751 0.900662102 0.944849591 0.830499347 0.993658595 1.011024862 1.052478909 1.041870513 1.10029114 1 21.29377077 2.654220556 2.452534083 1.049711531 0.953092022 0.169976143 0.08339797 0.460624377 5.449597739 0.029540224 0.027865221 451.0457091 -2.654220556 -0.096619509 MALNHPYFNDLDNQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MALNHPYFNDLDNQIK 16 0 P06493;A0A024QZP7;P06493-2 P06493 CDK1;CDC2 Cyclin-dependent kinase 1 0 134.88 2.59E-05 529060000 381100 414100 314770 493170 405910 480030 383160 385310 356440 358550 FALSE TRUE 396146.1223 485218.4537 322973.1648 590717.554 336913.5632 368550.3074 353126.918 380145.5497 343611.794 428801.0076 0.923846062 1.131570227 0.753200573 1.377602999 0.785710754 0.859490302 0.823521661 0.886531381 0.801331592 1 18.70994877 MALPPQEDATAS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.004)AS(0.996)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDAT(0.004)AS(0.996)PPR;MALPPQEDAT(0.001)AS(0.999)PPR;MALPPQEDAT(0.005)AS(0.995)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.018)AS(0.982)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDATAS(1)PPR;MALPPQEDAT(0.003)AS(0.997)PPR 211.9 1.67E-11 6274073000 3205441 3509649 3440262 3761155 3662845 4462720 3892192 3585814 3477385 3207692 TRUE FALSE 3331994.286 4112403.914 3529918.054 4505100.233 3040235.915 3426320.913 3587111.821 3537752.029 3352234.593 3836177.832 0.868571383 1.072005547 0.920165385 1.174372104 0.79251694 0.893160084 0.935074435 0.922207516 0.873847548 1 21.87123817 3.217061036 24.99976176 0.902350508 1.006965466 0.245261793 0.091051273 325.2249437 378171.3926 0.024611556 0.029441378 1648.394041 -3.217061036 0.104614958 MALPPQEDATAS(ph)PPRQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MALPPQEDAT(0.288)AS(0.712)PPRQK;MALPPQEDAT(0.036)AS(0.964)PPRQK;MALPPQEDAT(0.008)AS(0.992)PPRQK;MALPPQEDAT(0.098)AS(0.902)PPRQK 206.01 4.46E-12 1928270000 773878 980260 1004090 753888 1171850 1272120 778394 995240 1033420 1179450 TRUE FALSE 804431.301 1148612.03 1030257.41 903004.7963 972659.3556 976689.4092 717381.4443 981900.4357 996227.4161 1410540.646 0.570299979 0.814306226 0.730398953 0.640183464 0.689564926 0.692422024 0.508586156 0.696116371 0.706273456 1 20.42781681 0.656060196 2.427879006 0.999944361 0.669272639 0.60986929 0.079257918 1.641723157 10.75820327 0.075230941 0.020165392 4.529603593 -0.656060196 -0.330671721 MANSS(ph)PVLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MANSSPVLSK 10 0 Q9NXE8 Q9NXE8 CWC25 Pre-mRNA-splicing factor CWC25 homolog 1 MANS(0.02)S(0.98)PVLSK;MANS(0.011)S(0.989)PVLSK;MANS(0.021)S(0.979)PVLSK;MANS(0.239)S(0.761)PVLSK;MANS(0.109)S(0.891)PVLSK 127.78 0.0013569 1151050000 2682470 2420760 2672420 2389710 3153970 3299030 3108380 2881080 2930210 2467580 TRUE FALSE 2788375.987 2836506.699 2742065.461 2862387.505 2617859.306 2532880.28 2864737.053 2842463.835 2824752.314 2951055.056 0.944874268 0.961183931 0.929181397 0.969953949 0.887092669 0.858296518 0.970750121 0.963202577 0.957200818 1 21.49279941 MAPALSGANLTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MAPALSGANLT(0.058)S(0.942)PR;MAPALSGANLT(0.004)S(0.996)PR;MAPALSGANLT(0.059)S(0.941)PR;MAPALSGANLT(0.002)S(0.998)PR;MAPALS(0.002)GANLT(0.256)S(0.741)PR 213.94 3.51E-10 1483871000 1351230 1477580 1482690 1486240 1489570 1757300 1546350 1492130 1469750 1532200 TRUE FALSE 1404577.604 1731342.871 1521330.119 1780213.836 1236373.423 1349193.707 1425143.046 1472130.438 1416853.985 1832405.254 0.766521271 0.944847144 0.830236715 0.971517535 0.674727067 0.736296572 0.777744466 0.803386933 0.77322087 1 20.80530717 5.083153566 13.60324874 0.823199271 7.56E-05 0.028358005 0.10131985 1952930.11 6864623.092 0.023724773 45877426.62 121102.6276 -5.083153566 -0.8231237 MAPPVDDLS(ph)PK ddPTM_MDA-MB-175_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 166.48 2.14E-05 192006000 815850 385830 447620 376150 681660 897050 619630 504120 527610 365960 TRUE FALSE 848060.388 452093.3012 459285.3449 450551.3473 565791.6767 688723.7324 571061.7815 497363.096 508621.4192 437662.8553 1.937702452 1.032971603 1.049404443 1.029448448 1.292756901 1.573639901 1.304798373 1.136406917 1.162130652 1 18.73946042 1.650327143 3.927195366 1.101244624 1.293800099 0.120640844 0.265494923 0.475717709 17.17657037 0.155867681 0.07099258 44.70201942 -1.650327143 0.192555475 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPT(0.011)PIPT(0.388)RS(0.211)PS(0.388)DS(0.001)S(0.001)TASTPVAEQIER;MAPTPIPT(0.515)RS(0.425)PS(0.06)DSSTASTPVAEQIER 205.42 5.03E-25 1495370000 122315 156245 171236 151148 152384 209364 154060 183591 168648 203054 TRUE FALSE 127144.0906 183078.8633 175698.5508 181044.6233 126481.8221 160742.3839 141984.3746 181130.2629 162578.3914 242838.5436 0.523574589 0.753911882 0.723520032 0.745534957 0.520847392 0.661931099 0.584686321 0.745887618 0.669491708 1 17.8896379 0.104656425 0.897534938 1.004164962 0.657100928 0.599616095 0.083954256 3.267992903 2.692468537 0.118894209 0.026094796 1.272495997 -0.104656425 -0.347064034 MAPTPIPTRS(ph)PSDSSTASTPVAEQIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643;Q16643-3;Q16643-2;D6R9Q9 Q16643 DBN1 Drebrin 1 MAPTPIPT(0.007)RS(0.982)PS(0.004)DS(0.007)STASTPVAEQIER;MAPTPIPT(0.2)RS(0.795)PS(0.005)DSSTASTPVAEQIER 260.53 2.93E-53 1014070000 106054 166771 127376 125239 145416 164563 134048 143060 149669 168641 TRUE FALSE 110241.0938 195412.622 130695.5232 150010.9004 120698.2403 126345.7372 123540.9675 141142.5147 144282.4419 201682.9751 0.546605849 0.968909854 0.64802457 0.743795555 0.598455275 0.626457127 0.612550303 0.699823645 0.715392273 1 17.62172978 0.594455129 2.235274169 0.999972526 0.684162357 0.428529284 0.109940554 3.007107528 15.43917621 0.100805331 0.027309785 3.930566325 -0.594455129 -0.315810169 MAQYLEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MAQYLEEER 9 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ;;; 168.74 0.00013725 1115510000 1326600 1171060 1298000 1064960 1359030 1559270 1325340 1312190 1248040 1384730 FALSE TRUE 1378975.192 1372180.445 1331826.946 1275605.909 1128022.566 1197153.173 1221456.388 1294602.239 1203123.284 1656041.331 0.832693705 0.8285907 0.804223253 0.770274199 0.681156047 0.722900541 0.737576028 0.781745126 0.72650559 1 20.65930725 -1.943831006 5.391941931 1.117215234 0.764579643 0.697793413 0.046380072 0.03428181 0.000357121 0.023556934 0.011522726 0.0113807 1.943831006 -0.352635591 MASCLEVLDLFLNQPHMVLSSFVLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 252.43 8.84E-53 1385023000 189910.3 152492.3 213589 198980.5 294001 279579 261691 216946.1 232890 186775 FALSE TRUE 197408.1053 178681.6663 219155.3048 238338.249 244026.815 214651.0143 241178.9756 214038.2924 224508.3344 223369.9852 0.883771851 0.799935883 0.981131393 1.067011079 1.092478091 0.960966238 1.079728664 0.958223157 1.005096249 1 17.76907581 4.123991815 5.022970164 1.021574074 0.843290681 0.69137409 0.04767251 0.104738669 4.121402482 0.011853638 0.026937403 13304.29342 -4.123991815 -0.178283394 MASNIFGT(ph)PEENQASWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MASNIFGTPEENQASWAK 18 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK;MASNIFGT(1)PEENQASWAK 170.06 1.74E-10 370665000 760890 659470 795480 662710 943870 1027480 924910 893430 937590 815640 TRUE FALSE 790930.5247 772728.8425 816210.8623 793792.06 783431.3145 788863.3416 852413.1374 881455.0322 903846.319 975449.0416 0.810837359 0.792177561 0.836753974 0.813770916 0.803149402 0.808718147 0.87386742 0.903640267 0.926595117 1 19.89570698 1.467370931 0.829867134 0.995276692 0.807169022 0.945973482 0.014990755 0.115417428 0.165150673 0.014332233 0.00573918 29.3339759 -1.467370931 -0.18810767 MATEVAADALGEEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MATEVAADALGEEWK 15 0 P62753;A2A3R5;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 160.15 4.01E-06 22628000 39308 42131 42233 33087 49599 57902 47681 41592 47287 42037 FALSE TRUE 40859.91019 49366.67152 43333.62667 39631.50985 41168.1797 44455.13801 43943.63863 41034.52727 45585.15011 50273.3453 0.812754949 0.981965119 0.861960278 0.788320523 0.818886817 0.884268547 0.874094182 0.816228302 0.906745907 1 15.61750607 0.958036811 6.259597736 0.999986557 0.855998178 0.429062113 0.051425189 0.2853975 38.53663308 0.050019605 0.012567738 9.078974804 -0.958036811 -0.143988379 MATGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MATGLER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 115.69 0.013082 367227000 276291 382550 321934 346180 394530 436650 337287 331731 340557 403040 FALSE TRUE 287199.182 448249.9867 330323.8645 414653.3708 327467.9315 335244.655 310849.5636 327284.6885 328300.4201 482007.9713 0.595839071 0.929963846 0.685307887 0.860262476 0.679382813 0.695516827 0.644905442 0.679002647 0.681109939 1 18.87869748 -1.052660567 4.424382524 1.000015896 0.718588097 0.44115399 0.095601425 12160630.3 2893288.922 2129.375726 0.021435575 0.088580766 1.052660567 -0.281427799 MATHTLITGLEEYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MATHTLITGLEEYVR 15 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 240.59 7.58E-18 459730000 339800 397610 392660 405470 415640 466140 357090 387940 404450 377810 FALSE TRUE 353215.5664 465896.4245 402893.0422 485670.7558 344989.6613 357886.0494 329100.3527 382740.2988 389893.9235 451834.6359 0.781736366 1.031121538 0.89168251 1.074886069 0.763530801 0.792073075 0.728364598 0.847080477 0.862912872 1 18.78543534 3.216154704 24.99999505 0.817463934 0.947220335 0.22237408 0.100777846 287.8825115 321211.8016 0.027302786 0.032655579 1644.957586 -3.216154704 0.129756401 MAVTFIGNSTAIQELFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MAVTFIGNSTAIQELFKR 18 1 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 153.23 5.57E-08 90428000 39295 46337 39136 35057 64966 53937 47191 39228 46942 57756 FALSE TRUE 40846.39694 54295.0193 40155.91631 41991.16997 53923.10253 41410.94917 43492.04611 38702.21282 45252.56659 69072.18239 0.591358135 0.786062021 0.581361627 0.60793171 0.780677556 0.599531501 0.629660807 0.560315477 0.655148933 1 16.07581719 0.938778932 22.26204397 1 0.640196764 0.671310784 0.074863232 4770.504781 1734719.119 0.070922695 0.017730674 8.68518216 -0.938778932 -0.359803237 MAYLLIEEDIRDLAASDDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MAYLLIEEDIRDLAASDDYR 20 1 H7C1M5;Q9H147 H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 0 95.814 0.0010693 20113000 16754 26716 23339 22013 25204 29861 18255 22507 24828 30165 FALSE TRUE 17415.46086 31304.26518 23947.23351 26367.1057 20919.83308 22926.2353 16824.1254 22205.33048 23934.44513 36075.25421 0.482753656 0.867748984 0.663813299 0.730891751 0.579894267 0.6355114 0.466361936 0.615528039 0.663458807 1 15.13872194 -1.663348154 6.053122999 1.003352376 0.634280809 0.501100502 0.109559522 0.004904068 0.000272746 0.10495631 0.024567362 0.021709601 1.663348154 -0.369071567 MCDHLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MCDHLIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;; 152.63 0.0018005 1811150000 1317114 1538438 1582446 1463543 1935089 1976058 1535180 1539115 1485455 1574181 FALSE TRUE 1369114.678 1802652.759 1623685.843 1753027.437 1606163.263 1517148.477 1414848.58 1518485.681 1431993.765 1882611.627 0.72724223 0.957527688 0.862464578 0.931167858 0.853156987 0.805874379 0.751535027 0.806584671 0.760642155 1 20.84430398 2.858918599 4.146282276 0.806687935 0.876891206 0.03247904 0.086427959 0.473967181 13.77004676 0.025047127 0.026752452 722.6343457 -2.858918599 0.070203271 MCDLVSDFDGFSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MCDLVSDFDGFSER 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ;;; 397.39 3.98E-114 1739810000 947150 1250320 1150170 1199660 1303740 1465460 1185820 1245340 1129180 1169480 FALSE TRUE 984544.2134 1465052.734 1180144.375 1436949.167 1082130.74 1125129.124 1092872.33 1228648.254 1088541.032 1398617.215 0.703941152 1.047500859 0.843793686 1.027407036 0.77371473 0.804458226 0.781394879 0.878473567 0.778298037 1 20.41556974 3.205558424 24.99993519 0.828261513 0.911373411 0.084996545 0.10947139 383.3551437 290399.4742 0.029020266 0.034687917 1605.3082 -3.205558424 0.083111898 MCEDLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MCEDLWR 7 0 Q14376;Q14376-2;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 92.925 0.035623 349200000 599980 813670 673420 669230 883040 933080 739530 761280 713550 877650 FALSE TRUE 623667.6737 953411.493 690969.8784 801601.6965 732941.1762 716386.311 681563.7062 751076.2868 687869.4749 1049608.714 0.59419064 0.908349445 0.658311873 0.763714788 0.698299439 0.682527023 0.649350274 0.715577412 0.655358007 1 20.00142017 -0.503899873 6.474223761 1.000000203 0.706978006 0.547347786 0.080988641 9668469.167 1493379.122 0.160916328 0.017384055 0.313400819 0.503899873 -0.293022197 MCHNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MCHNVNR 7 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;; 121.87 0.0043958 376325000 158469 198690 176183 183945 222627 237198 179292 187446 173152 214977 FALSE TRUE 164725.4785 232813.4619 180774.4737 220328.772 184784.9421 182112.3593 165238.6245 184933.593 166920.2933 257097.6272 0.640711781 0.905544965 0.70313552 0.856984852 0.718734529 0.708339323 0.6427077 0.719312718 0.649248673 1 17.97195677 -1.12296595 4.835393849 1.000015493 0.730256742 0.486891141 0.083964209 1.35E-05 2.46E-06 0.078466695 0.018493716 0.075341463 1.12296595 -0.269758751 MCINTEWGAFGDDGSLEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MCINTEWGAFGDDGSLEDIR 20 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 173.03 1.28E-11 78124000 58862 66588 60961 76331 64200 83227 68544 66835 56755 53195 FALSE TRUE 61185.91721 78023.97102 62549.69374 91429.04397 53287.30693 63898.79057 63171.34217 65939.18615 54712.39864 63617.54177 0.961777452 1.226453724 0.983214566 1.437167194 0.837619711 1.004420932 0.992986218 1.036493777 0.860020634 1 15.95713701 MCINTEWGAFGDDGSLEDIRTEFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MCINTEWGAFGDDGSLEDIRTEFDR 25 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 255.67 6.52E-45 650470000 98515.2 117451.1 108909 106135.4 97890.2 127971.5 100549 100035.7 83920.8 83543.3 FALSE TRUE 102404.6562 137622.4128 111747.258 127128.6653 81250.85877 98252.05855 92667.70664 98694.88507 80900.5068 99912.0101 1.024948413 1.377436132 1.118456709 1.272406242 0.813224143 0.983385866 0.927493167 0.987818031 0.809717538 1 16.60837049 3.244556729 24.99957506 0.927685764 1.205402553 0.62044581 0.10638335 88.09754466 367302.3882 0.0273071 0.03603598 1756.130271 -3.244556729 0.277716789 MCINTEWGAFGDDGSLEDIRTEFDREIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MCINTEWGAFGDDGSLEDIRTEFDREIDR 29 2 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;; 190.19 2.19E-18 325795000 129932 189128 179760 120645 203621 209090 111890 152919 153920 230087 FALSE TRUE 135061.8157 221609.2628 184444.6933 144508.2209 169009.5752 160532.0163 103119.7694 150869.3709 148380.4493 275168.1424 0.490833766 0.805359446 0.670298137 0.525163341 0.614204732 0.583396083 0.374751846 0.548280661 0.539235567 1 18.06995393 -1.757623079 7.00858973 1.008568355 0.571828386 0.587891846 0.107404059 0.014998277 0.000518683 0.108466963 0.025543864 0.01747338 1.757623079 -0.436739969 MCIVLRPS(ph)RVHNSEENTMRALTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK;MCIVLRPS(0.333)RVHNS(0.333)EENT(0.333)MRALTLK 62.684 0.05274 840366000 23171.7 162960 136373 177875 97918 184673 131285 162464 131573 196353 TRUE FALSE 24086.53661 190947.1123 139926.9924 213058.1441 81273.93334 141785.4945 120994.5387 160286.4358 126837.7134 234824.6109 0.102572454 0.813147785 0.595878736 0.907307557 0.346104835 0.603793163 0.515254931 0.682579373 0.540138075 1 17.84122409 -5 0.368895158 6.433664105 0.573856922 0.266140059 0.214718904 710.1603091 5.500285433 3074.584972 0.139364192 1.00E-05 5 -5.859807183 MCIVLRPSRVHNS(ph)EENTMRALTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.055)RVHNS(0.472)EENT(0.472)MRALTLK 62.684 0.027884 122360000 7496.6 59012 58474 69048 44247 70081 41165 51045 53746 65725 TRUE FALSE 7792.571557 69146.85195 59997.88048 82705.48831 36725.91074 53805.74984 37938.37974 50360.82527 51811.69196 78602.55537 0.099138909 0.879702341 0.763306997 1.052198468 0.467235583 0.68452927 0.482660895 0.640702138 0.659160402 1 16.26228859 0.758969215 6.191622479 0.999999974 0.648219576 0.165710267 0.243527799 43.33304239 1113.499972 0.223189503 0.05608504 5.740757671 -0.758969215 -0.351780398 MCIVLRPSRVHNSEENT(ph)MRALTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MCIVLRPSRVHNSEENTMRALTLK 24 3 F8WF29;C9J131 F8WF29 FAP 1 MCIVLRPS(0.02)RVHNS(0.14)EENT(0.84)MRALTLK 70.453 0.018076 90263000 5087.8 51744 55281 58817 40546 58136 43809 50768 47872 52647 TRUE FALSE 5288.670273 60630.62949 56721.66827 70450.82705 33654.0054 44634.79506 40375.13611 50087.538 46149.09607 62962.17166 0.083997584 0.962969159 0.900884877 1.118938963 0.534511509 0.708914478 0.641260221 0.795517954 0.732965443 1 15.94219768 -4.999999802 0.030298238 2.035606993 1.44E-11 0.104270965 0.263060933 4735.204779 10.80015975 568.123051 228.3067345 1.00E-05 4.999999802 -2.035606993 MCSFLEWR ddPTM_MDA-MB-175_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 ; 93.429 0.025766 598210000 647900 795350 695130 635150 1239810 1062260 824250 744590 739450 1156300 FALSE TRUE 673479.5923 931945.1755 713245.6589 760780.7743 1029067.539 815566.2137 759643.1312 734609.989 712837.3389 1382854.846 0.487021175 0.673928416 0.515777676 0.5501523 0.744161646 0.589769936 0.549329623 0.531227114 0.515482403 1 20.3992183 -1.682555318 3.529048988 1.032226503 0.574900085 0.743517019 0.075232607 13450948.61 6911642.311 3359597.858 0.017478399 0.020770391 1.682555318 -0.457326418 MCTLIDKFDEHDGPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MCTLIDKFDEHDGPVR 16 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;; 222.64 5.68E-15 2414510000 2812470 2046450 2567560 2203420 3313510 3333820 3223580 2633670 2900950 1978400 FALSE TRUE 2923508.487 2397911.868 2634472.723 2639249.899 2750280.754 2559590.83 2970907.376 2598369.961 2796545.376 2366029.601 1.235617883 1.013475008 1.113457212 1.115476281 1.162403358 1.081808456 1.255650975 1.098198416 1.181957054 1 21.17403669 3.442163395 19.96783557 1.138696635 1.110838192 0 0.080796867 95.22141892 54387.22642 0.020651099 0.027962644 2767.982852 -3.442163395 -0.027858443 MDADGFLPITLIASFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDADGFLPITLIASFHR 17 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 130.01 9.85E-05 0 64933 127740 118810 142060 143660 152150 128480 136080 108240 128880 FALSE TRUE 67496.60498 149678.3513 121906.2862 170159.044 119240.7245 116815.4684 118409.4019 134256.0702 104344.4635 154131.5684 0.437915514 0.97110769 0.790923543 1.103985677 0.773629476 0.757894502 0.768235885 0.871048491 0.676983077 1 17.23380285 4.749359232 24.374966 0.849936272 0.437915178 0.501786345 0.125121206 912.6674605 2060043.894 0.028596448 0.413199669 56151.22457 -4.749359232 -0.412021094 MDAEHPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MDAEHPELR 9 0 Q12765;Q12765-2;Q12765-3;C9K052 Q12765 SCRN1 Secernin-1 0 ;;;; 157.66 6.80E-05 2490610000 2785520 3799990 3591850 3477390 3822100 4412950 3780540 3559600 3618840 3918450 FALSE TRUE 2895494.48 4452608.723 3685456.562 4165207.363 3172420.807 3388109.241 3484211.396 3511889.384 3488598.655 4686195.254 0.617877473 0.950154332 0.786449638 0.888824971 0.676971538 0.722997882 0.743505383 0.749411664 0.744441592 1 22.15998564 -1.121185651 3.520626455 1.000177931 0.768224695 0.376391834 0.09081986 18932476.29 29621197.9 39814.99076 0.021597853 0.075650944 1.121185651 -0.231953236 MDATANDVPSPYEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDATANDVPSPYEVR 15 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 144.27 9.93E-06 122220000 46143 45921 48071 50498 57868 69269 41983 50968 43799 53441 FALSE TRUE 47964.76127 53807.57453 49323.76975 60486.35368 48031.61803 53182.32453 38692.26276 50284.85733 42222.68255 63911.74076 0.750484351 0.841904381 0.771748182 0.946404416 0.75153043 0.832121358 0.605401485 0.786785913 0.660640471 1 15.96379336 MDDPTVNWSNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDDPTVNWSNER 12 0 P15170-2;P15170-3;P15170;H3BR35 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 184.44 3.33E-05 271600000 187728 218820 226900 209922 224380 259280 240720 202397 194268 174639 FALSE TRUE 195139.6464 256400.6328 232813.2004 251443.945 186239.9677 199066.1494 221851.7374 199684.1993 187276.3326 208856.1684 0.934325512 1.227642137 1.114705887 1.203909595 0.891713992 0.953125546 1.062222577 0.956084758 0.896676091 1 17.67215023 3.23774699 24.99993412 0.964370008 1.127435531 0.452032174 0.086165127 19.03290456 584827.3858 0.023561365 0.029780576 1728.8089 -3.23774699 0.163065524 MDEFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MDEFSR 6 0 O00422;O00422-2;H7BZW6;U3KQ12;U3KPY7 O00422 SAP18 Histone deacetylase complex subunit SAP18 0 ;;; 170.31 0.013437 605260000 672839 824630 761300 766450 870850 964940 777640 760165 757830 748280 FALSE TRUE 699403.2033 966253.7878 781140.1034 918051.5224 722823.2281 740847.3088 716686.5448 749976.2316 730555.8463 894891.1393 0.781551155 1.079744502 0.87288841 1.025880671 0.807721963 0.827863051 0.8008645 0.838064205 0.816362811 1 19.77135267 3.220445231 24.99935657 0.836224983 0.945201958 0.181783067 0.092722416 313.9688088 433278.2992 0.024261262 0.029051699 1661.28916 -3.220445231 0.108976975 MDEISDHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDEISDHAK 9 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 130.66 0.00035508 114870000 93869 137190 142800 120080 197460 205570 190610 169120 134870 130640 FALSE TRUE 97575.0206 160751.3153 146521.4853 143831.4656 163895.8197 157829.4829 175669.4901 166853.223 130016.055 156236.4067 0.624534464 1.028897929 0.937819093 0.920601469 1.049024508 1.010196575 1.124382555 1.067953536 0.832175149 1 17.25337115 4.740717736 24.7535435 1.00550741 0.624534313 0.665432288 0.078967587 101.7076447 1167033.207 0.019434782 0.128533135 55044.98222 -4.740717736 -0.380973097 MDELQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 MDELQLFR 8 0 P55072;C9IZA5;C9JUP7 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;;;;;;; 198.07 0.00032321 2006123000 1611005.3 1912489 1753196 1633794 2328785 2329133 1838652 1702668 1760847 2005950 FALSE TRUE 1674609.033 2240944.109 1798885.728 1956953.577 1932938.958 1788227.159 1694533.652 1679846.52 1697474.46 2398977.496 0.698051164 0.934124689 0.749855191 0.815744866 0.80573451 0.745412227 0.706356627 0.70023438 0.707582486 1 21.19398819 2.736152353 7.427809592 0.743740856 0.806200072 0 0.100793975 0.332408209 151.994163 0.029475107 0.029335463 544.693701 -2.736152353 0.062459216 MDEQEDLAKDMLEQLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDEQEDLAKDMLEQLLK 17 1 A0A0J9YYF7;Q86T65-4;Q86T65 A0A0J9YYF7 DAAM2 Disheveled-associated activator of morphogenesis 2 0 80.534 0.01177 75652000 4888.9 179850 152250 175410 115920 181110 114510 163830 150280 226330 FALSE TRUE 5081.917547 210737.8385 156217.7601 210105.5745 96215.95981 139049.9472 105534.407 161634.1268 144871.4522 270675.0302 0.018774977 0.778564016 0.577141379 0.776228137 0.3554667 0.513715459 0.389893397 0.597151968 0.535222817 1 18.04620228 0.190435533 1.205940775 1.001004403 0.513631336 0.337149516 0.208512278 6.806608076 9.023643046 0.199786123 0.056208886 1.550370631 -0.190435533 -0.487373067 MDHRS(ph)RLRGT(ph)GLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDHRSRLRGTGLNR 14 3 A6NJJ0 A6NJJ0 PRDX4 2 MDHRS(1)RLRGT(1)GLNR 43.628 0.077754 16435000 8387 31582 25330 33520 19253 32225 22144 24303 26210 27575 TRUE FALSE 8718.125236 37005.96283 25990.12061 40150.15595 15980.38194 24741.23212 20408.29542 23977.25804 25266.70722 32977.79329 0.264363511 1.12214794 0.788109755 1.217490679 0.484580087 0.750239166 0.618849637 0.727072846 0.766173376 1 15.00920724 4.762929098 23.78179336 0.806187243 0.264362253 0.382863371 0.213637272 4081.616688 3983223.827 0.050094228 2.997128026 57933.41077 -4.762929098 -0.54182499 MDIDAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 206.74 4.74E-16 486090000 500700 494890 482030 445980 632260 675390 618420 513770 556960 477240 FALSE TRUE 520468.0226 579883.5078 494592.0978 534193.5129 524788.671 518540.9081 569946.6245 506883.7535 536915.1184 570746.0407 0.911908249 1.01600969 0.866571229 0.935956581 0.919478426 0.908531766 0.998599349 0.88810735 0.940725086 1 19.12248942 MDIDAPDVEVQGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDIDAPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 156.39 1.19E-08 326240000 376090 317020 371020 296630 451010 466660 429570 346110 385820 321280 FALSE TRUE 390938.3236 371465.7189 380689.086 355302.5286 374347.4813 358285.2873 395899.1809 341470.9616 371934.4136 384228.6647 1.017462671 0.966782942 0.990787833 0.924716351 0.974283065 0.932479329 1.030373882 0.888718081 0.968002775 1 18.55160563 7.684090429 0.824573424 0.955793944 10.93327296 0.134378783 0.038724251 545.8885253 3.037647981 0.012000199 10102.96091 48315939.5 -7.684090429 9.977479017 MDIDVPDVEVQGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDIDVPDVEVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 212.76 1.56E-16 154069000 264020 242745 260400 247410 309200 352450 313630 268590 272887 236531 FALSE TRUE 274443.7135 284434.5655 267186.2379 296346.9596 256642.2944 270598.8289 289046.8611 264989.9904 263065.8502 282874.7208 0.970195261 1.00551426 0.944539113 1.047626167 0.907264862 0.956603079 1.021819342 0.936775084 0.929972991 1 18.10980373 3.230842226 24.9999933 0.958571645 0.989548414 0.14351807 0.039590576 366.5393056 1187224.982 0.011079388 0.01347547 1701.540245 -3.230842226 0.03097677 MDKEETKDWILPSDYDHAEAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ;; 184.26 2.04E-17 1886790000 1088390 746790 976630 697820 1491700 1252740 1113140 908150 1038050 610140 FALSE TRUE 1131360.478 875045.3733 1002081.78 835846.7132 1238141.367 961810.1205 1025889.178 895977.7347 1000690.783 729685.2512 1.550477382 1.199209347 1.373306886 1.14548939 1.696815668 1.318116433 1.405933828 1.227896183 1.371400589 1 19.47691477 -1.159421313 5.121671632 0.999982422 1.354931001 0.328211983 0.156186395 2.92E-05 4.79E-06 0.140765689 0.03317715 0.069275343 1.159421313 0.354948579 MDMMSLNSQLLDAIQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MDMMSLNSQLLDAIQQK 17 0 H0YHW1;H0YHP2;Q6ZP65-2;Q6ZP65 H0YHW1 CCDC64 Bicaudal D-related protein 1 0 ;;;;;;; 70.281 0.025008 26028210000 353823.6 11116840 8299310 10618710 4357865 10760630 4747013 8883599 7135366 15318900 FALSE TRUE 367792.8289 13026070.79 8515596.837 12719059.14 3617116.664 8261636.761 4374929.717 8764528.886 6878565.571 18320345.16 0.02007565 0.711016669 0.464816397 0.694258707 0.197437146 0.450954209 0.238801708 0.478404135 0.375460479 1 24.12694335 -1.297315051 3.486130597 1.002067343 0.415732537 0.437834529 0.202353818 214636043.8 327414452.9 4673442.097 0.045237467 0.050429533 1.297315051 -0.586334806 MDPKELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MDPKELGK 8 1 A0A3B3IU97;A0A2R8Y5X9;Q76EJ3 A0A3B3IU97 SLC35D2 UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose transporter 0 ;;; 59.8 0.087855 6564900000 1453020 11114400 7566200 11630100 4594890 12228300 4842440 9212400 5126290 12455400 FALSE TRUE 1510386.352 13023211.74 7763381.388 13930499.07 3813852.239 9388462.647 4462876.899 9088922.846 4941795.824 14895797.16 0.101396813 0.874287667 0.521179317 0.935196614 0.256035457 0.630275946 0.29960645 0.610166932 0.331757728 1 23.828402 -1.36099203 3.353054625 1.003398816 0.524208632 0.250157634 0.254614397 60977708.13 84057594.93 2035281.887 0.05568576 0.043551987 1.36099203 -0.479190184 MDPVNNINVDKDKPYLYCFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDPVNNINVDKDKPYLYCFR 20 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 166.25 8.70E-12 2513100000 1184370 759960 1071640 765250 1344920 1165560 1006130 989140 1135600 603610 FALSE TRUE 1231129.842 890477.2183 1099567.819 916614.166 1116310.979 894876.3542 927266.9016 975882.1962 1094729.978 721875.8227 1.70545931 1.233560109 1.523209095 1.269767094 1.546403057 1.239654143 1.284524114 1.3518699 1.516507332 1 19.46139116 -3.796976147 0.208768207 7.09E-16 1.455656526 0.392454024 0.151681388 84.41627675 1.322236415 36.71528078 0.311851948 0.000159597 3.796976147 1.455656526 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(ph)PTMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFSPTMGR 38 2 D3DQV9;P78344;H0Y3P2;P78344-2;H0YCH5 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.843)PT(0.157)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.997)PT(0.003)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.962)PT(0.038)MGR;MDRDPLGGLADMFGQMPGS(0.003)GIGT(0.02)GPGVIQDRFS(0.95)PT(0.027)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.992)PT(0.008)MGR;MDRDPLGGLADMFGQMPGSGIGTGPGVIQDRFS(0.999)PT(0.001)MGR;MDRDPLGGLADMFGQMPGS(0.004)GIGT(0.161)GPGVIQDRFS(0.732)PT(0.103)MGR 381.03 1.48E-162 12091140000 1865344 2058454 2234909 2155658 2390343 2732254 1992780 2164976 2022208 2016814 TRUE FALSE 1938989.221 2411977.462 2293152.565 2582040.718 1984033.351 2097729.416 1836580.696 2135958.038 1949429.129 2411970.089 0.803902681 1.000003057 0.950738392 1.070511086 0.822577925 0.869716182 0.761444226 0.885565724 0.808231055 1 21.20178059 3.202753542 24.99995469 0.848563692 0.959015022 0.237230622 0.085370429 212.8922993 148637.5546 0.023212997 0.027745772 1594.973758 -3.202753542 0.110451331 MDRT(ph)PEKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MDRTPEKDK 9 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 MDRT(1)PEKDK 99.5 0.0085137 330250000 1028600 341070 531120 363430 796950 832690 923770 576210 670520 218690 TRUE FALSE 1069209.922 399646.1193 544961.4235 435315.3693 661484.7237 639310.367 851362.4936 568486.8474 646388.1162 261538.1184 4.088160948 1.528060696 2.083678765 1.664443301 2.529209614 2.444425198 3.255213805 2.173629033 2.471487216 1 17.9966617 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 MDRTPPPPTLSPAAITVGR 19 1 Q8NDX5-2;Q8NDX5;Q8NDX5-7;E7EX82;H7C4H9 Q8NDX5-2 PHC3 Polyhomeotic-like protein 3 2 MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.313)LS(0.687)PAAITVGR;MDRT(1)PPPPT(0.013)LS(0.987)PAAITVGR;MDRT(1)PPPPT(0.03)LS(0.97)PAAITVGR;MDRT(1)PPPPT(0.052)LS(0.948)PAAITVGR;MDRT(1)PPPPT(0.002)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.082)LS(0.918)PAAITVGR;MDRT(1)PPPPT(0.001)LS(0.999)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR;MDRT(1)PPPPT(0.004)LS(0.996)PAAITVGR 146.2 2.70E-07 5617700000 2495673 2738530 2678480 2597780 3146580 3372720 2799890 2852830 2711950 2587860 TRUE FALSE 2594204.097 3208851.225 2748283.389 3111613.13 2611725.456 2589456.894 2580427.306 2814592.48 2614347.449 3094901.619 0.838218598 1.03681849 0.888003474 1.005399691 0.84387996 0.83668472 0.833767151 0.90942874 0.844727158 1 21.56146212 3.221805641 24.9996484 0.871198655 0.945010212 0.163199203 0.069871731 354.5819026 529060.9393 0.018573948 0.022255521 1666.50124 -3.221805641 0.073811556 MDRT(ph)PPPPTLSPAAITVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.999)PPPPT(0.001)LSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(1)PPPPTLSPAAITVGR;MDRT(0.999)PPPPT(0.001)LSPAAITVGR 113.68 0.00027876 4743440000 1381976 1293125 1238226 1175486 1509142 1795086 1323460 1363891 1361734 1252410 TRUE FALSE 1436537.48 1515209.16 1270495.187 1407993.622 1252618.582 1378204.481 1219723.747 1345610.272 1312725.459 1497795.761 0.959101045 1.011626017 0.848243279 0.940043803 0.836308003 0.920155149 0.81434584 0.898393698 0.876438226 1 20.51440948 4.242411551 24.99998709 0.885526463 0.985363551 0.330508702 0.052708882 89.13543843 578637.257 0.011532857 0.029236981 17474.77333 -4.242411551 0.099837088 MDS(ph)DEDEKEGEEEKVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MDSDEDEKEGEEEKVAK 17 2 Q96ST2;Q96ST2-3;Q96ST2-2 Q96ST2 IWS1 Protein IWS1 homolog 1 MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK;MDS(1)DEDEKEGEEEKVAK 216.44 2.76E-15 856040000 2461720 281033 574180 247541 1218120 1846010 950220 589880 742520 181186 TRUE FALSE 2558910.606 329298.2316 589143.6025 296503.871 1011064.398 1417302.154 875739.2735 581973.6234 715796.8502 216685.9277 11.80930683 1.519702895 2.718882619 1.368357762 4.666036269 6.540813098 4.041514291 2.685793349 3.303384109 1 17.72524594 4.745726058 24.90167244 3.253067554 11.80931106 0.726347536 1.602188767 447.9702457 1556766.345 0.399390819 4.059341396 55683.44006 -4.745726058 8.556243504 MDS(ph)FDEDLARPSGLLAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MDSFDEDLARPSGLLAQER 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER;MDS(1)FDEDLARPSGLLAQER 271.11 1.55E-39 688507000 276353 290534 395479 297771 542500 456713 395193 409050 404433 357608 TRUE FALSE 287263.6298 340430.9545 405785.5076 356669.215 450286.0438 350648.3273 364216.74 403567.3538 389877.5353 427674.4408 0.671687626 0.796004909 0.948818702 0.833973652 1.052871065 0.819895448 0.85162148 0.943632154 0.911622249 1 18.70615346 4.524506561 2.621268747 0.914576955 0.665787326 0.560268326 0.069853045 0.23199998 2.712416086 0.016577751 0.101450152 33458.50726 -4.524506561 -0.248789629 MDYEDDRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MDYEDDRLR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;;; 145.89 8.76E-05 6393990000 3156360 3686400 3461270 3236610 4415220 4735930 3480990 3765010 3540680 3758830 FALSE TRUE 3280975.53 4319510.524 3551473.54 3876801.798 3664722.481 3636082.031 3208140.908 3714546.199 3413251.618 4495300.771 0.729867855 0.960894664 0.790041361 0.862412104 0.815234101 0.808862903 0.713665463 0.826317612 0.759293269 1 22.09998622 5.033837836 17.41015586 0.825382632 0.35908741 0.117043229 0.082885597 25580342.27 339064483.9 0.018365505 370443343.3 108103.0224 -5.033837836 -0.466295222 MDYVEINIDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDYVEINIDHK 11 0 Q00341;A0A024R4E5;Q00341-2;H0Y394;H7C0A4 Q00341 HDLBP Vigilin 0 ; 122.42 0.00039109 292150000 159147 183187 176171 201234 275710 274440 220560 204060 184286 211341 FALSE TRUE 165430.2464 214647.9423 180762.161 241037.4846 228844.9127 210705.4692 203271.9309 201324.9095 177653.5829 252749.2226 0.654523265 0.849252631 0.715183846 0.953662615 0.905422815 0.833654272 0.804243545 0.796540173 0.702884785 1 17.94734713 -2.496661156 2.267107509 3.561686342 0.808360995 0.313905932 0.087450206 2460849.03 517089.9328 31831373.83 0.021047178 0.003186683 2.496661156 -2.753325347 MDYYDSEHHEDFEFISGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MDYYDSEHHEDFEFISGTR 19 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 99.273 0.00047579 131586000 54680 96614 95658 94581 107769 124615 102032 96630 91032 91253 FALSE TRUE 56838.80862 113206.7029 98150.92606 113288.8395 89450.46387 95675.05481 94034.46523 95334.8329 87755.7761 109132.2782 0.520824907 1.037334736 0.899375764 1.038087369 0.81965176 0.876688881 0.861655843 0.873571362 0.804123011 1 16.73571835 4.751323556 24.66799525 0.904167119 0.520824614 0.67696794 0.080947634 1013.275769 1958400.269 0.018876184 0.339955572 56405.77311 -4.751323556 -0.383342505 MEANKENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 MEANKENR 8 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 ;;;;;;;; 121.96 0.0012869 3251476000 4316830 3789600 4469190 3365762 5968465 5361675 4778259 4424018 4724395 4369458 FALSE TRUE 4487261.782 4440434.321 4585660.763 4031499.678 4953947.451 4116507.238 4403726.574 4364721.275 4554364.947 5225569.637 0.858712465 0.849751248 0.877542753 0.771494776 0.94802056 0.787762392 0.842726608 0.835262293 0.871553776 1 22.31715688 0.822306683 3.905821778 0.999992471 0.845976685 0.504316307 0.045450057 0.999354611 21.05897037 0.039376395 0.010077718 6.642119477 -0.822306683 -0.154015786 MECCDVPAETLYDVLHDIEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 19 MECCDVPAETLYDVLHDIEYR 21 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ;;;;;;;;;;;;;;;;;; 249.06 1.32E-30 5289120000 867858.7 1073430 1004764 1097344.9 1154345 1304765 1066088 1085170 1047961.9 1091670 FALSE TRUE 902122.4316 1257783.252 1030948.975 1314396.446 958129.8492 1001753.103 982525.2369 1070625.071 1010245.956 1305561.835 0.690984071 0.963403815 0.789659247 1.006766903 0.733883163 0.767296558 0.752568902 0.820049302 0.773801691 1 20.31623936 4.805092509 21.40886114 0.832319719 0.690974657 0.164148998 0.100699721 34952.67591 11244104.01 0.022847675 64.27576872 63839.94577 -4.805092509 -0.141345062 MECCDVPAETLYDVLHDIEYRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MECCDVPAETLYDVLHDIEYRK 22 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;F5GY07 Q9Y365 STARD10 PCTP-like protein 0 ; 145.75 4.63E-08 28139000 45298 50332 54070 35391 80951 64287 32694 55495 64509 73913 FALSE TRUE 47086.40002 58976.12947 55479.10862 42391.23417 67190.97793 49357.31853 30131.35885 54751.1803 62187.33369 88394.8372 0.532682694 0.667189752 0.627628382 0.479566856 0.760123329 0.558373318 0.340872384 0.619393417 0.703517713 1 16.43167449 0.881871007 2.388098286 0.998888907 0.571312683 0.599079869 0.106245076 0.315549811 3.67850326 0.10198767 0.027565231 7.618526923 -0.881871007 -0.427576224 MEDGEFWMSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MEDGEFWMSFR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 174.41 2.57E-05 159562000 166671 195644 205953 224007 221552 243881 229981 203691 206505 196795 FALSE TRUE 173251.2998 229244.3351 211320.3044 268314.916 183892.6702 187243.3338 211954.4883 200960.8553 199072.9254 235353.2124 0.736133142 0.974043791 0.897885787 1.140052066 0.781347611 0.795584356 0.900580392 0.853869184 0.845847496 1 17.84446802 MEDSVGCLETAEEVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MEDSVGCLETAEEVKR 16 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 284.72 1.48E-35 1446540000 976870 701080 942410 724660 1199470 1161610 968110 932690 1004240 661844 FALSE TRUE 1015437.582 821485.0364 966969.9788 867995.5851 995584.5178 891843.6819 892227.0085 920188.8161 968097.5986 791519.66 1.282896223 1.037858032 1.221662616 1.09661911 1.25781401 1.126748616 1.127232909 1.162559646 1.223087243 1 19.59426566 -1.532695734 2.716267271 0.991141123 1.16520517 0.329522951 0.072673586 7083402.732 7047740.76 460861.3414 0.015506456 0.029329473 1.532695734 0.174064047 MEDTLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEDTLKR 7 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 119.29 0.0077202 180842000 413140 313060 372640 334360 519080 499380 512870 435280 463110 311930 FALSE TRUE 429451.0862 366825.6197 382351.3045 400495.41 430846.967 383406.5632 472669.9093 429445.7836 446442.7616 373046.7112 1.151199229 0.983323559 1.024942167 1.07357979 1.154941068 1.027770924 1.267052878 1.151185014 1.196747614 1 18.50899676 3.026673866 1.278192206 1.157025557 1.047529983 0.128335865 0.083815904 0.632841348 2.171260603 0.031951365 0.039510258 1063.344198 -3.026673866 -0.109495574 MEEADALIESLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEEADALIESLCR 13 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ; 171.62 5.77E-05 33534000 57074 68890 66832 65697 74129 75939 68986 67642 72594 72071 FALSE TRUE 59327.32559 80721.32161 68573.69682 78691.67051 61528.57906 58303.31812 63578.69706 66735.36963 69981.35612 86191.93257 0.688316456 0.936529896 0.795592984 0.912981855 0.71385543 0.676435907 0.737640927 0.774264686 0.811924667 1 16.39526522 0.781490395 3.592040017 0.999989518 0.781858663 0.389317204 0.082352168 1.966090637 31.08496547 0.080086094 0.020615781 6.046309794 -0.781490395 -0.218130855 MEEDPDDVPHGHITSLAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEEDPDDVPHGHITSLAVK 19 0 P41227-2;P41227;F8W808;A8MWP7 P41227-2 NAA10 N-alpha-acetyltransferase 10 0 ; 111.33 0.0001263 993920000 553270 557640 703670 604090 905410 931590 771260 748860 828210 660550 FALSE TRUE 575113.5268 653410.3322 722008.2183 723577.199 751508.7316 715242.3409 710806.6259 738822.7566 798402.8839 789972.1255 0.728017494 0.827130871 0.913966702 0.915952824 0.951310442 0.905401998 0.899786971 0.935251679 1.010672223 1 19.59144222 5.749245924 0.686686143 0.94620047 5.95E-14 0.813042615 0.033694192 4.460773419 0.562416961 0.013060928 4.51871107 561365.7661 -5.749245924 -0.94620047 MEEEGTEDNGLEDDS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEEEGTEDNGLEDDSR 16 0 Q14151;K7ERX3 Q14151 SAFB2 Scaffold attachment factor B2 1 MEEEGTEDNGLEDDS(1)R 258.13 4.19E-26 227210000 281440 287850 253710 378790 288750 360860 401860 295140 307750 176770 TRUE FALSE 292551.4685 337285.9983 260321.891 453713.5314 239668.3781 277055.7339 370361.1631 291184.1311 296674.1376 211404.697 1.383845641 1.595451771 1.231391235 2.146184724 1.13369467 1.310546728 1.751906028 1.377377774 1.403346954 1 17.68964791 0.656491716 1.346466088 1.000682396 1.502020931 0.223873938 0.275202405 1.726741318 4.747329629 0.246101787 0.073153365 4.534106493 -0.656491716 0.501338536 MEEIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 122.51 0.044642 499950000 626360 769960 646490 746940 795380 821430 722560 664700 591290 896890 FALSE TRUE 651089.1765 902194.6405 663338.0605 894682.5026 660181.5917 630665.3314 665923.8591 655790.7837 570009.5884 1072618.424 0.60700913 0.84111425 0.61842874 0.834110699 0.615485971 0.587968021 0.620839475 0.611392429 0.531418793 1 20.03270551 -1.0192674 4.777912513 1.00000526 0.654448625 0.534923723 0.097328292 7.31E-06 1.50E-06 0.09333304 0.021998355 0.09566049 1.0192674 -0.345556635 MEELHNQEMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEELHNQEMQK 11 0 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 155.99 3.13E-05 281970000 479860 445980 429880 374760 569310 594840 512300 476510 484290 353580 FALSE TRUE 498805.2433 522573.5958 441083.026 448886.4095 472538.8896 456697.4249 472144.5874 470123.1629 466860.4975 422857.2313 1.179606748 1.235815677 1.043101532 1.061555476 1.117490383 1.080027468 1.116557912 1.111777517 1.104061756 1 18.68981112 8 0.018160186 0.279574035 2.145928945 0.397748205 0.04931593 4424.639211 6.195859646 242.6258717 415.6047699 100000000 -8 1.86635491 MEELHNQEVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MEELHNQEVQK 11 0 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 170.62 1.55E-05 2022037000 3697950 2940470 3565665 3030084 3993600 4448130 4411610 3657040 3754451 2514088 FALSE TRUE 3843947.921 3445472.849 3658589.159 3629425.571 3314769.298 3415119.22 4065816.481 3608023.361 3619329.042 3006675.408 1.278471201 1.145941075 1.216822125 1.207122512 1.102469954 1.135845662 1.35226319 1.200004281 1.203764474 1 21.5197377 4.758305939 21.9177809 1.187746051 1.278471665 0.096820576 0.086980177 1955.215853 2170139.93 0.019977933 0.603730709 57319.96801 -4.758305939 0.090725614 MEELHNQEVQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEELHNQEVQKR 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 85.288 0.0056117 22637000 36558 34880 40823 33657 44197 47496 38734 35377 42168 35496 FALSE TRUE 38001.33807 40870.36867 41886.88092 40314.25414 36684.40973 36465.77381 35697.92787 34902.82918 40650.38192 42450.76159 0.89518625 0.962771153 0.98671683 0.949670928 0.864163759 0.859013418 0.840925499 0.822195595 0.95758899 1 15.37350282 3.243909989 23.84048244 0.873070562 0.95232314 0.162341816 0.056317577 87.82841433 391417.899 0.01532633 0.020133973 1753.517036 -3.243909989 0.079252578 MEENEKELAACQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEENEKELAACQLR 14 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 203.27 1.39E-08 479240000 292201 253200 323710 221700 388790 375636 311593 324207 357821 257116 FALSE TRUE 303737.3211 296685.1304 332146.1485 265551.5983 322703.6147 288400.2318 287169.5265 319861.5355 344943.0921 307492.9574 0.987786269 0.96485179 1.080174815 0.863602212 1.049466685 0.937908413 0.933906028 1.040223939 1.121791845 1 18.23019384 1.571833275 5.618559227 1.066867561 0.975176946 0.254020872 0.063172923 0.170170612 11.23109503 0.032856281 0.015112579 37.31068952 -1.571833275 -0.091690615 MEGMDDDPEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 96.143 0.0071728 614640000 433270 560020 520370 517630 595730 695600 578930 571990 543400 492710 FALSE TRUE 450375.8342 656199.0786 533931.2697 620015.669 494468.0274 534057.4419 533551.9538 564323.4096 523843.1401 589247.091 0.764324239 1.113622941 0.906124575 1.052216767 0.839152259 0.906338699 0.905480845 0.957702496 0.889004202 1 19.16851321 3.232248407 24.99998109 0.915993278 0.966329504 0.044831409 0.094411981 443.0403722 1754693.587 0.024967709 0.030525224 1707.05851 -3.232248407 0.050336226 MEGMDDDPEDRMS(ph)YLTAMGADYLSCDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MEGMDDDPEDRMSYLTAMGADYLSCDSR 28 1 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 MEGMDDDPEDRMS(1)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(1)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(1)YLTAMGADYLSCDSR;MEGMDDDPEDRMS(0.995)Y(0.004)LT(0.001)AMGADYLSCDSR;MEGMDDDPEDRMS(0.989)Y(0.001)LT(0.01)AMGADYLSCDSR;MEGMDDDPEDRMS(0.934)Y(0.061)LT(0.005)AMGADYLSCDSR 176.22 1.93E-13 547013000 286139 394014 434359 380912 513663 473354 416726 424495 435364 441472 TRUE FALSE 297435.9887 461682.8395 445678.7524 456255.2567 426350.7467 363424.7072 384061.9272 418805.3389 419695.3347 527969.9859 0.56335776 0.874449025 0.844136531 0.864168928 0.807528379 0.688343499 0.727431364 0.793237021 0.794922715 1 19.01009639 0.515649685 1.979541684 0.999980013 0.776509846 0.372119669 0.088694307 4.419685249 16.76446 0.083393079 0.022984367 3.278307484 -0.515649685 -0.223470167 MEHYT(ph)SRDMDELLAEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEHYTSRDMDELLAEIQK 18 1 H3BUS3;A6NCI4 H3BUS3 VWA3A von Willebrand factor A domain-containing protein 3A 1 MEHYT(0.5)S(0.5)RDMDELLAEIQK;MEHYT(0.5)S(0.5)RDMDELLAEIQK 63.69 0.022937 236216000 1699740 145056 294693 113579 484100 895610 526550 181948 329761 94820 TRUE FALSE 1766847.048 169968.2396 302372.9417 136044.5872 401812.8549 687618.1506 485277.6351 179509.2847 317892.966 113398.1636 15.58091412 1.498862365 2.666471239 1.199707146 3.543380618 6.06375032 4.279413527 1.582999927 2.80333434 1 16.79103775 4.742249838 24.99905383 2.845990702 15.58091896 0.868525338 1.498563219 127.0612092 860961.8967 0.37704317 2.815773568 55239.51257 -4.742249838 12.73492826 MEIATKDPLNPIKQDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEIATKDPLNPIKQDVK 17 2 Q15181;Q5SQT6 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 196.31 9.06E-12 1964930000 5169300 2412200 3936400 2131860 5757800 4414700 4474400 3561500 4638200 2275000 FALSE TRUE 5373387.956 2826476.586 4038985.818 2553535.545 4779091.213 3389452.83 4123684.836 3513763.918 4471272.088 2720742.692 1.974971014 1.038862144 1.484515911 0.938543565 1.756539207 1.245782205 1.515646756 1.291472335 1.643401304 1 21.37556909 -1.261725325 3.793901089 0.999368428 1.40654437 0.15084986 0.302157303 20279968.02 6744758.286 106528.62 0.062696926 0.054736204 1.261725325 0.407175943 MEISAELPQT(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MEISAELPQTPQR 13 0 Q8IWV7;H3BS20;H3BNQ6;A0A087WTJ9;Q8IWV7-2 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 MEISAELPQT(1)PQR;MEISAELPQT(1)PQR;MEISAELPQT(1)PQR;MEISAELPQT(1)PQR;MEISAELPQT(1)PQR 196.97 1.54E-06 458130000 952760 1163960 1128650 1107560 1254460 1453970 1152360 1188330 1189580 1143100 TRUE FALSE 990375.7005 1363861.076 1158063.546 1326632.062 1041227.337 1116307.503 1062035.012 1172402.38 1146767.248 1367068.559 0.724452109 0.997653751 0.847114461 0.970421018 0.761649685 0.816570241 0.776870337 0.857603207 0.838851307 1 20.38265417 4.853193461 19.17190505 0.86191963 0.72425101 0.213377039 0.083292543 91878.45103 15312439.93 0.019102856 1944.955668 71317.06485 -4.853193461 -0.13766862 MEITIRNS(ph)PYR ddPTM_MDA-MB-175_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 191.57 1.07E-06 2483300000 2121000 2617650 2424360 2307410 3400780 3405500 2505120 2529420 2497640 3228330 TRUE FALSE 2204738.718 3067211.025 2487540.813 2763808.811 2822716.63 2614624.236 2308762.148 2495517.262 2407750.424 3860859.453 0.571048686 0.794437369 0.644297168 0.715853256 0.731110952 0.677213006 0.597991762 0.646363146 0.623630685 1 21.88049061 -1.772778194 3.163530848 1.063254256 0.668934593 0.715631188 0.062984278 31601770.99 35445539.9 15671793.27 0.014757223 0.016874146 1.772778194 -0.394319663 MEITIRNS(ph)PYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.001)IRNS(0.997)PY(0.002)RR;MEITIRNS(1)PYRR 174.39 1.59E-05 677500000 435740 350860 372870 323620 443660 518540 350160 407420 390910 402710 TRUE FALSE 452943.3517 411117.4757 382587.2985 387631.0701 368246.8317 398116.9435 322713.5442 401959.2013 376841.2255 481613.3142 0.940470993 0.853625644 0.794386881 0.804859539 0.764610987 0.82663193 0.670067738 0.83460982 0.782455996 1 18.87751575 4.638405007 2.028040124 0.79691918 0.965392369 0.192515128 0.078147063 0.758716934 4.009268879 0.018115468 0.218634963 43491.56211 -4.638405007 0.168473188 MEIVDHALHALTDEVIIPHSGWER ddPTM_MDA-MB-175_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 ; 274.3 1.93E-52 612490000 165656 198829 183636 207720 206893 248990 181613 210790 185963 204930 FALSE TRUE 172196.2268 232976.3341 188421.705 248806.396 171725.4018 191165.846 167377.6985 207964.7048 179270.228 245082.1099 0.702606269 0.950605224 0.768810523 1.015196075 0.700685178 0.780007346 0.682945396 0.848551144 0.73147007 1 17.90290565 5.029519568 15.70037082 0.81940395 0.363061343 0.092559126 0.11557338 1302770.719 19457546.57 0.025810099 15542529.34 107033.4608 -5.029519568 -0.456342607 MEKGEHSIVYLKPSYAFGSVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MEKGEHSIVYLKPSYAFGSVGK 22 2 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;; 209.97 3.03E-23 3994710000 2754970 1819100 2655390 1782730 3899840 3055540 2595410 2735520 3464430 2266320 FALSE TRUE 2863738.343 2131516.274 2724591.645 2135348.673 3236946.59 2345937.142 2391974.982 2698854.829 3339745.841 2710362.013 1.056588872 0.786432316 1.005250085 0.787846296 1.194285699 0.865543839 0.882529703 0.995754374 1.232213935 1 21.37005413 1.437265784 6.498007335 1.117898793 0.938278696 0.2269419 0.128522068 0.241300439 21.30981855 0.075301764 0.029802269 27.36943199 -1.437265784 -0.179620098 MELGAPEEMGQVPPLDS(ph)RPSSPALYFTHDASLVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.281)RPS(0.281)S(0.281)PALY(0.049)FT(0.054)HDAS(0.054)LVHK;MELGAPEEMGQVPPLDS(0.377)RPS(0.309)S(0.309)PALY(0.003)FT(0.003)HDASLVHK;MELGAPEEMGQVPPLDS(0.326)RPS(0.326)S(0.326)PALY(0.012)FT(0.005)HDAS(0.006)LVHK 108.58 2.13E-05 1117940000 481290 530232 629632 597018 628005 773551 775204 640577 652231 433814 TRUE FALSE 500291.7008 621295.2214 646040.7272 715106.3785 521256.9344 593905.5035 714441.4849 631991.1131 628757.3337 518811.5474 0.964303326 1.197535453 1.245231974 1.378354784 1.00471344 1.14474226 1.377073214 1.218151593 1.211918541 1 18.98485107 MELGAPEEMGQVPPLDSRPS(ph)SPALYFTHDASLVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MELGAPEEMGQVPPLDSRPSSPALYFTHDASLVHK 35 1 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 MELGAPEEMGQVPPLDS(0.104)RPS(0.444)S(0.444)PALY(0.005)FT(0.001)HDAS(0.001)LVHK;MELGAPEEMGQVPPLDS(0.067)RPS(0.426)S(0.426)PALY(0.059)FT(0.011)HDAS(0.011)LVHK 126.05 2.21E-08 548556000 299944 339268 367261 370481 411756 438720 479460 383103 389559 276611 TRUE FALSE 311786.0207 397534.6399 376832.1234 443761.036 341765.8622 336833.9289 441878.6724 377968.1309 375538.8477 330807.6294 0.942499486 1.201709406 1.139127668 1.341447405 1.033125695 1.01821693 1.335757199 1.142561711 1.135218218 1 18.33563298 0.749611036 3.352276176 1.000018842 1.153052173 0.107867551 0.12183398 4.766264334 61.33993279 0.112504007 0.029120646 5.618379046 -0.749611036 0.153033331 MELLAHLLGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MELLAHLLGEK 11 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 141.08 3.83E-05 494580000 1986010 1645750 1964000 1777350 2966700 2697500 2330700 1978220 2107500 1804180 FALSE TRUE 2064419.208 1928394.76 2015183.453 2128904.525 2462421.394 2071046.506 2148013.644 1951705.197 2031651.487 2157674.528 0.95677971 0.893737557 0.933960812 0.986666199 1.14123857 0.95985121 0.995522548 0.904541056 0.941593118 1 21.04104583 3.778005356 5.29500785 0.986348199 0.923686949 0.181572387 0.059747195 0.38472145 28.18973577 0.017069638 0.030707819 5997.984729 -3.778005356 -0.06266125 MELQEIQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MELQEIQLK 9 0 P06753-2;A0A087WWU8;P06753-6;P06753-5;P06753-7;P06753-3;P06753-4;J3KN67;A0A2R2Y2Q3;A0A494C0P6;P06753 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 114.5 0.0037891 42464000 62384 70957 76692 75534 94071 98812 87297 87582 89171 72493 FALSE TRUE 64846.96849 83143.31278 78690.65652 90474.39975 78080.84502 75864.41051 80454.43303 86408.10655 85961.75313 86696.61539 0.74797578 0.959014518 0.907655462 1.043574762 0.900621606 0.875056196 0.9279997 0.996672202 0.991523749 1 16.40368805 4.739516039 24.66481416 0.953439494 0.747975704 0.605231778 0.050318821 46.74771468 1206604.767 0.012242991 0.074645499 54892.88283 -4.739516039 -0.20546379 MENGVLGNALEGVHVEEEEGEKT(ph)EDESLVENNDNIDEEAREELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MENGVLGNALEGVHVEEEEGEKTEDESLVENNDNIDEEAREELR 44 2 P49321;P49321-3;P49321-4;E9PPR5;E9PNB5 P49321 NASP Nuclear autoantigenic sperm protein 1 MENGVLGNALEGVHVEEEEGEKT(0.99)EDES(0.01)LVENNDNIDEEAREELR 128.4 2.87E-09 70369000 6940.1 4604.5 6786.4 4627.7 8346.2 9089.5 6025.5 4805.3 5748.4 4508.3 TRUE FALSE 7214.100507 5395.287057 6963.259159 5543.045248 6927.515905 6978.601378 5553.205565 4740.892813 5541.516207 5391.615068 1.338022172 1.000681055 1.29149783 1.028086237 1.284868415 1.2943434 1.029970704 0.879308473 1.027802641 1 12.39650178 2.06372926 5.894197025 0.955139616 1.195333502 0.485813832 0.112486189 0.155215394 10.34045851 0.040740318 0.029652224 115.8055197 -2.06372926 0.240193886 MEQELKEPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEQELKEPGR 10 1 C9JVE2;Q96GG9 C9JVE2 DCUN1D1 DCN1-like protein;DCN1-like protein 1 0 ; 122.18 0.00045183 466060000 1077450 797190 1058570 747500 1220750 1161920 1127440 986230 1088430 762930 FALSE TRUE 1119988.558 934101.1812 1086157.204 895353.2689 1013247.351 892081.6891 1039068.307 973011.2 1049257.617 912411.5263 1.227503737 1.02377179 1.190424685 0.981304207 1.110515729 0.977718566 1.13881541 1.066417041 1.14998286 1 19.79932515 4.751087324 24.25443899 1.075031759 1.227503883 0.301033345 0.07130704 1586.664058 3072044.276 0.015279124 0.264905591 56375.09984 -4.751087324 0.152472124 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MEREDSSEEEEEEIDDEEIER 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER 205.32 3.16E-22 677130000 233759 279799 265384 238553 300266 339787 282146 276874 265699 272532 TRUE FALSE 242987.9858 327852.3017 272300.1251 285738.0714 249226.8926 260876.6188 260030.6593 273162.9569 256136.5449 325929.4275 0.745523311 1.005899664 0.835457317 0.876686937 0.764665205 0.800408299 0.79781277 0.838104614 0.785865047 1 18.31420009 5.044128123 19.78041684 0.84542561 2.50E-05 0.132844959 0.080708514 863.59949 153459.8713 0.017791843 40947.52264 110695.0303 -5.044128123 -0.845400633 MES(ph)GALDDFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MESGALDDFDK 11 0 Q5QNY5;E9PS71 Q5QNY5 PEX19 1 MES(1)GALDDFDK 58.699 0.06742 85961000 13303 240930 140100 224910 87453 210670 72921 171290 112210 356920 TRUE FALSE 13828.21271 282307.8533 143751.1211 269396.5267 72587.7703 161745.0852 67205.26148 168994.1377 108171.584 426851.6404 0.032395829 0.661372305 0.336770689 0.631124497 0.170053863 0.378925767 0.157444075 0.395908371 0.253417286 1 18.7033752 -1.685195979 5.010322744 1.017310125 0.346011728 0.525709577 0.189168598 0.032973662 0.002071771 0.165114611 0.039431642 0.020644483 1.685195979 -0.671298397 MES(ph)HS(ph)EDEDLAGAVGGLGWNSR ddPTM_MDA-MB-175_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 167.72 9.64E-12 86943000 51492 48716 53700 43851 65958 72897 54593 56506 59095 52376 TRUE FALSE 53524.94392 57082.59404 55099.46612 52524.59692 54746.48272 55967.77651 50313.85801 55748.6295 56968.18249 62638.0744 0.854511325 0.911308251 0.879648148 0.838541054 0.874012863 0.893510489 0.803247202 0.890011866 0.909481702 1 15.93475224 0.881331793 2.003676304 0.999499598 0.86719382 0.663178389 0.028745902 0.27982834 2.253243851 0.026830419 0.007455424 7.609073738 -0.881331793 -0.132305778 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.02)EGGADDS(0.98)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.004)EGGADDS(0.996)AEEGDLLDDDDNEDRGDDQLELIKDDEK 277.46 1.53E-76 6210670000 1221188 393724.1 562833 525269.7 837657 1142538 1102736 601704 688815 242822 TRUE FALSE 1269401.445 461343.1514 577500.8904 629166.4789 695272.3623 877200.8648 1016300.671 593639.1421 664024.6827 290398.3218 4.371242359 1.588656396 1.988650922 2.166563756 2.394202412 3.020681591 3.499678182 2.044223735 2.286599587 1 18.14767359 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK;MESEGGADDS(1)AEEGDLLDDDDNEDRGDDQVK 263.74 5.55E-59 209070000 376793 248456 264305 260801 386516 427820 347345 304498 279193 246294 TRUE FALSE 391669.0786 291126.3853 271193.0054 312386.6594 320816.1484 328465.2887 320119.1913 300416.7024 269144.8985 294550.5937 1.329717498 0.988374804 0.92070093 1.060553487 1.089171624 1.115140474 1.086805452 1.019915453 0.913747601 1 18.16815594 4.74320378 24.64361778 1.027905668 1.329717648 0.665173605 0.065443624 260.3535804 1381769.398 0.016722284 0.135839031 55360.98139 -4.74320378 0.30181198 MESLSSHRIDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_MDA-MB-175_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 195.21 3.42E-20 135800000 35546 94749 98604 46464 148400 114310 43682 88709 112220 189390 TRUE FALSE 36949.38353 111021.4037 101173.7012 55654.44052 123175.021 87763.23488 40258.0907 87520.00095 108181.2241 226497.3444 0.163133849 0.49016647 0.446688245 0.24571785 0.543825453 0.387480194 0.177741999 0.386406301 0.477626898 1 17.78913461 0.748617563 2.406398388 0.999774656 0.3591317 0.720243481 0.120206649 0.603361701 4.988439196 0.110913374 0.029813258 5.605541383 -0.748617563 -0.640642956 MESMNRPYTSLVPPLS(ph)PQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MESMNRPYTSLVPPLSPQPK 20 1 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 MESMNRPYTSLVPPLS(1)PQPK;MESMNRPYTSLVPPLS(1)PQPK 118.67 3.77E-05 2720400000 1610940 1108490 1560160 1202170 1850680 1897220 1836830 1615220 1926750 1174170 TRUE FALSE 1674541.155 1298864.535 1600819.051 1439955.638 1536102.075 1456619.408 1692854.465 1593570.618 1857406.644 1404226.131 1.192501064 0.924968213 1.140000899 1.025444269 1.093913609 1.037311139 1.205542632 1.134839028 1.322726164 1 20.42134385 2.239996486 24.99914415 1.173513746 1.06485202 0.181813002 0.099778816 55.13258848 959902.3632 0.032576281 0.02591217 173.7786769 -2.239996486 -0.108661726 MESSFGS(ph)PSKQESSESLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MESSFGSPSKQESSESLPK 19 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 MES(0.001)S(0.035)FGS(0.942)PS(0.022)KQESSESLPK;MESSFGS(0.957)PS(0.043)KQESSESLPK;MESSFGS(0.899)PS(0.101)KQESSESLPK 176.1 7.84E-13 1909900000 2239040 840940 1245840 839390 1903490 1865590 1872160 1300450 1553920 627440 TRUE FALSE 2327439.028 985364.9034 1278307.614 1005418.837 1579935.45 1432334.996 1725415.207 1283019.595 1497994.723 750374.8549 3.101701787 1.313163543 1.703558702 1.339888764 2.105528243 1.908825951 2.299404352 1.709838205 1.996328519 1 19.51725196 4.750787993 24.76218018 1.76209155 3.101702729 0.542776009 0.380760231 1314.692133 2662383.637 0.087242213 1.490212396 56336.25756 -4.750787993 1.339611179 METEADAPS(ph)PAPSLGER ddPTM_MDA-MB-175_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 223.71 3.10E-15 1521220000 1465340 1965300 1807430 1724030 1773370 2084600 1720040 1742660 1696830 1879330 TRUE FALSE 1523192.755 2302824.987 1854533.111 2065037.988 1471933.201 1600483.242 1585218.77 1719302.493 1635761.42 2247548.732 0.677712894 1.024594019 0.825135885 0.918795646 0.654906023 0.712101687 0.705310078 0.764967838 0.727797977 1 21.09992097 3.250382484 24.99971723 0.744442593 0.870603236 0.136332989 0.119126687 332.6792161 703512.9318 0.030284072 0.0406821 1779.846233 -3.250382484 0.126160643 METVSNASSSSNPSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 METVSNASSSSNPS(0.002)S(0.998)PGR;METVSNASSSSNPS(0.065)S(0.935)PGR;METVSNASSSSNPS(0.016)S(0.984)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.162)S(0.838)PGR;METVSNASSSSNPS(0.159)S(0.841)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPSS(1)PGR;METVSNASSSSNPS(0.001)S(0.999)PGR;METVSNASSSSNPS(0.05)S(0.95)PGR 423.36 1.08E-168 11458200000 4794354 6389848 6457314 6403599 6690527 7338242 6209964 6331461 6160389 6107717 TRUE FALSE 4983638.798 7487254.688 6625596.908 7670211.769 5553273.61 5634046.508 5723210.795 6246598.121 5938677.803 7304407.207 0.682278336 1.025032487 0.907068393 1.050079979 0.760263421 0.771321525 0.783528442 0.855182076 0.813026661 1 22.80033576 3.211585208 24.99973644 0.819751638 0.923248645 0.117013876 0.112143281 375.4226689 347925.897 0.030625594 0.036613582 1627.740643 -3.211585208 0.103497007 MEVDRS(ph)PGLPMSDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 180.86 3.71E-07 2177190000 3205310 2502780 2949510 2344810 3987610 4056610 3681580 3206150 3534280 2646750 TRUE FALSE 3331858.114 2932612.996 3026376.654 2808606.419 3309797.477 3114523.806 3393008.14 3163176.803 3407081.953 3165329.987 1.052610037 0.92647939 0.95610147 0.887302882 1.045640578 0.983949168 1.071928726 0.99931976 1.076374965 1 21.59392448 3.21134224 24.99972787 1.028262801 0.953575821 0.361966977 0.048025153 222.5303231 204390.6823 0.013156614 0.015728845 1626.830254 -3.21134224 -0.07468698 MEVGPFSTGQES(ph)PTAENAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 MEVGPFST(0.004)GQES(0.996)PTAENAR 205.92 4.08E-16 44595000 32421 45676 39478 48573 38819 54228 47941 42368 36674 38991 TRUE FALSE 33701.00611 53520.49769 40506.82911 58180.59442 32220.56025 41634.36883 44183.25915 41800.12626 35354.1099 46630.53992 0.722723909 1.147756337 0.868675962 1.247692918 0.690975492 0.892856246 0.94751764 0.896410943 0.758175006 1 15.50898751 3.216974323 24.99951798 0.868771279 0.998355971 0.145697421 0.156808289 450.3716302 521583.1991 0.042278648 0.050575322 1648.064949 -3.216974323 0.129584692 MFADYLAHESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MFADYLAHESR 11 0 O14579;M0QXB4;O14579-3;O14579-2;M0R061 O14579 COPE Coatomer subunit epsilon 0 ;;;;; 220.5 9.10E-12 1338640000 472224 1631060 1427960 1674220 1705850 2128770 1491850 1653790 1333510 1912280 FALSE TRUE 490867.7682 1911181.867 1465173.811 2005375.719 1415890.226 1634395.429 1374914.899 1631623.65 1285517.236 2286954.653 0.214638173 0.835688571 0.640665878 0.876876031 0.619116004 0.714660182 0.601199021 0.713448187 0.562108756 1 21.12499633 -2.539723439 2.204247469 6.285651624 0.658545225 0.275560269 0.172257869 4133063.954 253049.973 110531742 0.038024541 0.002885869 2.539723439 -5.627106399 MFDYTDDPEGPVMPGSHSVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MFDYTDDPEGPVMPGSHSVER 21 0 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 172.83 5.09E-12 201390000 623250 715230 632960 704240 701660 773270 662140 724710 642060 828710 FALSE TRUE 647856.3913 838065.1888 649455.4576 843536.5701 582392.0838 593689.7615 610239.7366 714996.4478 618952.386 991079.8579 0.653687376 0.845608134 0.655300834 0.85112876 0.587633861 0.599033223 0.615732155 0.721431721 0.624523222 1 19.91864178 -1.800123615 6.241512928 1.017707727 0.686892228 0.523044117 0.090544469 0.021731874 0.000695935 0.085394271 0.020283671 0.015844421 1.800123615 -0.330815499 MFEELGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MFEELGQR 8 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 200.66 0.00027467 754600000 837790 1018050 1002010 884130 1143890 1241760 967460 933310 978460 1059480 FALSE TRUE 870866.5961 1192892.168 1028123.204 1059008.275 949451.9864 953380.0591 891627.9572 920800.506 943245.4157 1267064.821 0.687310216 0.941461043 0.811421158 0.835796447 0.749331818 0.752431954 0.703695614 0.726719336 0.744433434 1 20.2730589 5.034336445 16.21816823 0.790166049 0.316586744 0.106986025 0.092811511 950574.759 12454580.46 0.021802335 12795219.55 108227.2056 -5.034336445 -0.473579306 MFEHLLQKPNEHILYNLVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MFEHLLQKPNEHILYNLVLR 20 1 Q5W0V3-2;Q5W0V3 Q5W0V3-2 FAM160B1 Protein FAM160B1 0 ; 206.21 5.08E-22 806260000 338050 266250 339830 275680 412130 405350 397450 354250 379630 271400 FALSE TRUE 351396.475 311976.3664 348686.249 330208.6812 342076.2898 311213.6056 366296.8305 349501.8582 365967.1905 324575.6337 1.082633564 0.961182338 1.074283504 1.017355115 1.053918576 0.958832313 1.128540754 1.076796351 1.127525151 1 18.30819517 2.222875174 24.99998605 1.089631992 1.025061611 0.234775144 0.051229648 301.4110872 480396.3024 0.017456373 0.012933082 167.0610373 -2.222875174 -0.064570381 MFEIDYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MFEIDYSR 8 0 P16278-3;P16278;E7EQ29;P16278-2;F8WF40;C9JF15;C9JWX1 P16278-3 GLB1 Beta-galactosidase 0 ; 119.27 0.0086777 0 177181 236235 217999 192095 237950 256440 196937 200113 176902 224075 FALSE TRUE 184176.2427 276806.5236 223680.233 230090.8177 197503.344 196885.6964 181500.5633 197430.8126 170535.3316 267978.2061 0.687280676 1.032944162 0.834695613 0.85861765 0.73701271 0.734707868 0.677295986 0.736742049 0.636377615 1 18.03175615 3.245489376 5.443940445 0.733985034 0.865936804 0.126770572 0.120127329 0.251042148 22.86836757 0.031555261 0.040799844 1759.905612 -3.245489376 0.13195177 MFEIVFEDPKIPGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MFEIVFEDPKIPGEK 15 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 118.47 0.00026325 230810000 513830 273280 419740 272120 632010 507340 495760 409790 509140 237180 FALSE TRUE 534116.4052 320213.7142 430678.7692 325944.5238 524581.1659 389517.9738 456901.0358 404297.4353 490816.1509 283650.8799 1.88300634 1.128900831 1.51834103 1.149104575 1.84939023 1.373230268 1.610786598 1.425334677 1.730352999 1 18.11375681 -0.934781065 5.600900496 0.999999459 1.500106282 0.279277075 0.24837309 1.50E-06 2.86E-07 0.215308049 0.050748539 0.116203427 0.934781065 0.500106823 MFGIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MFGIDR 6 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 140.72 0.027321 1358840000 725750 1034730 956730 943330 2064840 1360190 1030650 986880 853170 1620830 FALSE TRUE 754403.1704 1212436.828 981663.1698 1129917.858 1713859.234 1044306.486 949864.9599 973652.4878 822464.5784 1938400.606 0.389188472 0.625483104 0.506429459 0.582912456 0.884161524 0.538746471 0.490025105 0.502296834 0.42430062 1 20.88643533 -1.891193173 2.746781663 1.223821263 0.554420691 0.520462595 0.129705866 33173530.35 22138267.95 48205779.19 0.03171698 0.012847151 1.891193173 -0.669400572 MFGIDRDAIAQAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MFGIDRDAIAQAVR 14 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 265.95 7.43E-25 2775900000 2172880 3558300 3475300 3456900 2148380 3692000 1832830 2729200 4083100 3234700 FALSE TRUE 2258666.98 4169410.345 3565869.173 4140664.502 1783199.135 2834588.953 1689167.995 2692619.538 3936150.029 3868477.533 0.583864572 1.07779102 0.921775852 1.07036023 0.460956312 0.732740187 0.436649297 0.696041147 1.017493315 1 21.88333446 3.251376014 24.99047293 0.689066233 0.925781531 0.139349449 0.219814016 353.658875 689643.0675 0.058854541 0.079181478 1783.922626 -3.251376014 0.236715299 MFLGDNAHLSIINEYLSQSYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MFLGDNAHLSIINEYLSQSYQK 22 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 206.01 9.79E-23 54878000 14613 54840 53337 55816 54999 80613 55972 65327 56259 60925 FALSE TRUE 15189.93252 64258.3434 54727.00604 66856.23821 45650.28963 61891.85245 51584.76838 64451.39842 54234.24958 72862.08727 0.208475122 0.881917412 0.751104012 0.917572371 0.626530084 0.849438367 0.707978186 0.884567006 0.744341147 1 16.1528807 4.742804515 24.94737946 0.809069869 0.208474878 0.748845134 0.10580807 184.2776913 1083218.908 0.022469265 0.174966379 55310.10908 -4.742804515 -0.600594991 MFLQYYLNEQGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MFLQYYLNEQGDR 13 0 Q9NPE3;H0YM60 Q9NPE3 NOP10 H/ACA ribonucleoprotein complex subunit 3 0 ; 178.81 3.32E-05 312570000 145809 156354 183791 153795 168658 213470 179628 143006 153000 156659 FALSE TRUE 151565.6519 183206.5832 188580.7444 184215.192 139989.5734 163894.8277 165548.288 141089.2385 147493.5599 187353.3316 0.808982955 0.977866695 1.006551326 0.983250153 0.747195538 0.874790036 0.883615394 0.75306501 0.78724813 1 17.51540211 3.253166752 24.99971453 0.8282099 0.951026548 0.248691517 0.085823908 280.6722348 480392.9311 0.023235891 0.031325278 1791.293506 -3.253166752 0.122816647 MFLYADNEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MFLYADNEDR 10 0 A0A087WY55;Q9NP79;Q5TGM0;Q9NP79-2 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ;; 134.77 0.00037683 348691000 261601 301946 323459 340414 384980 406372 376968 323466 330493 371588 FALSE TRUE 271929.2095 353802.8767 331888.6073 407746.8732 319541.2371 311998.2616 347420.2631 319130.4674 318598.6215 444393.5541 0.611910787 0.796147634 0.746834881 0.917535525 0.719050117 0.702076479 0.781785109 0.718125779 0.716928989 1 18.76147837 -1.513080679 2.935394355 1.009315675 0.749467295 0.510999178 0.074572967 14566963.07 16416708.59 1089176.875 0.019005895 0.030684519 1.513080679 -0.25984838 MFS(ph)PMEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MFSPMEEK 8 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK;MFS(1)PMEEK 143.4 0.00063157 699690000 2216210 1453660 1851700 1480970 2626860 2646110 2618020 1998310 2117050 1171370 TRUE FALSE 2303707.682 1703314.797 1899956.823 1773901.446 2180347.275 2031591.055 2412812.751 1971525.923 2040857.784 1400877.524 1.644474725 1.215891302 1.356261907 1.266278754 1.556415345 1.450227461 1.7223581 1.40735067 1.456842407 1 20.4178994 -0.936004745 5.375778576 0.999999143 1.449313628 0.45321928 0.149190044 1.52E-06 3.00E-07 0.14300751 0.03370713 0.115876469 0.936004745 0.449314484 MFVLDEADEMLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 252.42 2.17E-23 434219000 442343 582851 546500 583569 612645 693032 571175 570747 529944 594366 FALSE TRUE 459807.0432 682951.1253 560742.239 698997.2064 508507.8217 532085.821 526404.811 563097.07 510871.419 710820.6379 0.646867886 0.960792483 0.788866008 0.983366505 0.715381342 0.748551453 0.740559268 0.792178842 0.718706509 1 19.43912604 4.792116017 22.26963271 0.813901706 0.646863985 0.19492244 0.106978794 24914.40547 10358738.84 0.024412104 24.44768788 61960.65742 -4.792116017 -0.167037721 MFYEEHLHLDDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MFYEEHLHLDDEIR 14 0 Q9BV57;Q9BV57-2;A0A0G2JQN5 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 194.85 5.57E-08 24907000 15745 17963 17347 18657 17127 18167 18299 16870 12855 17195 FALSE TRUE 16366.62476 21048.00552 17799.07707 22347.29891 14215.75866 13947.98957 16864.67656 16643.88524 12392.35106 20564.03103 0.795886017 1.023535001 0.865544165 1.086717817 0.691292414 0.678271179 0.820105578 0.809368806 0.602622659 1 14.32783547 3.223582878 24.99997544 0.760765152 0.943152043 0.324071419 0.124314353 256.4913179 428119.578 0.033738796 0.04047691 1673.334933 -3.223582878 0.182386891 MGAGLGHGMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;;;;;;;;;;; 164.65 2.25E-05 9466133000 4273561 5490926 5015681 5016506 5754051 6308020 5173437 5326062 5010256 5305996 FALSE TRUE 4442284.488 6433949.827 5146393.767 6008755.914 4775979.466 4843077.954 4767929.49 5254674.851 4829937.865 6345604.327 0.700056962 1.013922315 0.811017123 0.94691626 0.752643755 0.763217765 0.751375164 0.828081075 0.761147027 1 22.59732614 5.041052268 15.76941863 0.835278369 0.099704665 0.158574333 0.098339573 4602426.224 49662557.82 0.022522569 97510524.11 109913.8114 -5.041052268 -0.735573704 MGANSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGANSLER 8 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 142.79 0.0014234 453360000 326000 371720 387180 343330 453490 493070 378870 392440 362460 464280 FALSE TRUE 338870.7317 435560.0184 397270.2289 411239.6493 376405.9318 378561.965 349173.1794 387179.9837 349415.1354 555246.7768 0.610306527 0.784444028 0.715484079 0.740643019 0.677907459 0.681790477 0.628861245 0.697311538 0.629297008 1 19.08276959 -1.193650728 6.252076002 1.000002832 0.688471553 0.773765978 0.05105039 1.95E-06 2.52E-07 0.04791812 0.011294307 0.064024953 1.193650728 -0.311531279 MGAPESGLAEYLFDKHTLGDS(ph)DNES ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MGAPESGLAEYLFDKHTLGDSDNES 25 1 G3V192;P02794;G3V1D1 G3V192 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 MGAPESGLAEYLFDKHTLGDS(0.994)DNES(0.006);MGAPESGLAEYLFDKHTLGDS(0.5)DNES(0.5);MGAPESGLAEYLFDKHT(0.001)LGDS(0.5)DNES(0.5);MGAPESGLAEYLFDKHTLGDS(0.602)DNES(0.398) 179.17 1.69E-17 440604000 303174 336455 349994 218894 454757 435784 280739 375064 434035 437262 TRUE FALSE 315143.5436 394238.529 359115.1312 262190.5799 377457.5676 334579.7704 258733.9436 370036.8806 418414.1651 522935.117 0.602643681 0.753895686 0.686729805 0.501382622 0.721805737 0.639811249 0.494772554 0.707615283 0.800126347 1 18.99627243 1.01237709 2.019214553 0.99660513 0.634311702 0.667726819 0.081003621 0.187515879 1.616504358 0.07590614 0.021265962 10.28909293 -1.01237709 -0.362293428 MGAT(ph)PTPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGATPTPFK 9 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 1 MGAT(0.841)PT(0.159)PFK 138.22 0.0015957 280500000 557730 467250 486370 482880 748540 746150 568550 558190 541580 515010 TRUE FALSE 579749.6111 547496.5528 499045.2018 578392.2227 621303.4382 572867.9705 523985.5654 550708.3761 522088.6416 615916.349 0.941279789 0.888913817 0.810248344 0.939075937 1.008746462 0.930106777 0.850741446 0.894128524 0.847661606 1 19.2323749 3.557713149 0.004957194 1.802348459 1.36E-07 0.050184488 0.060165651 85334.69286 102.595473 18225.7448 19078.59751 3611.712303 -3.557713149 -1.802348323 MGEIEDGEADHITTDVQGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGEIEDGEADHITTDVQGQK 20 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 205.06 9.01E-22 140107000 228540 170110 221011 192542 295260 292710 267880 244080 254520 187425 FALSE TRUE 237562.9357 199325.0692 226770.7282 230626.2329 245071.8107 224732.5386 246882.8656 240808.5068 245359.8749 224147.3403 1.059851682 0.889259132 1.011703855 1.028904615 1.093351411 1.002610775 1.101431163 1.074331315 1.094636566 1 17.77408785 3.714361879 2.485094952 1.064870272 0.972562319 0.285089341 0.051867012 0.295967176 3.58991711 0.013472905 0.025434817 5180.383111 -3.714361879 -0.092307953 MGESDDSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 136.57 0.00026585 1128800000 865380 875470 992860 806520 1088900 996870 1081000 953650 890680 914750 FALSE TRUE 899545.8706 1025825.162 1018734.747 966047.2488 903809.1669 765362.0502 996268.3953 940867.8816 858624.6008 1093977.749 0.82227072 0.937702036 0.931220721 0.883059322 0.826167779 0.69961391 0.910684332 0.860042979 0.784864776 1 20.06115196 5.082139195 15.71733759 0.864339997 0.000113026 0.026021928 0.081045323 8924673.864 25868250.87 0.019239036 261525278.2 120820.101 -5.082139195 -0.864226971 MGFCTDREDINSLCMTVVQNLMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MGFCTDREDINSLCMTVVQNLMER 24 1 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 ;; 284.33 1.61E-52 640128000 177509 249885 297275 240767 303540 340189 268318 283258 265699 314357 FALSE TRUE 184517.1924 292800.8049 305022.2307 288389.994 251944.3792 261185.2604 247286.534 279461.3898 256136.5449 375949.2354 0.490803478 0.778830697 0.811338878 0.767098232 0.670155317 0.694735448 0.657765759 0.743348738 0.6813062 1 18.52017834 -1.459664064 4.13064836 1.001717415 0.707036869 0.527589593 0.085039605 0.001300444 0.000170113 0.079612709 0.018660578 0.034700516 1.459664064 -0.294680546 MGGAGGEGS(ph)DDDTSLT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;MGGAGGEGS(1)DDDTSLT 350.9 1.27E-86 12643080000 5695300 6202520 6306370 5877340 7242490 7978790 6723900 6519160 6448220 5731600 TRUE FALSE 5920154.842 7267754.561 6470719.183 7039860.31 6011414.137 6125836.942 6196863.148 6431781.323 6216149.822 6854597.282 0.863676537 1.060274479 0.943996987 1.027027558 0.876990126 0.893682982 0.904044817 0.938316441 0.906858502 1 22.70864048 3.232833853 24.99996963 0.916146364 0.977799868 0.169701351 0.057607013 204.88885 894435.3373 0.01526034 0.018718488 1709.361244 -3.232833853 0.061653504 MGGDIANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGGDIANR 8 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 105.25 0.010293 179430000 420970 468280 467430 466500 534930 615550 504280 516390 486340 506210 FALSE TRUE 437590.2207 548703.4473 479611.6098 558772.3076 444002.7897 472597.8413 464753.2159 509468.6367 468836.7184 605392.1575 0.722821092 0.906360349 0.792232942 0.922992313 0.733413514 0.780647445 0.767689522 0.841551431 0.77443474 1 19.20751046 -1.184229416 4.907051583 1.000018985 0.808819152 0.456795803 0.063753867 1.23E-05 2.04E-06 0.057264404 0.01349601 0.065429045 1.184229416 -0.191199833 MGGEEAEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGGEEAEIR 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 108.74 0.0064461 299970000 372920 420290 482730 392690 545850 592850 504240 467750 471030 438360 FALSE TRUE 387643.1696 492471.5381 495310.3404 470362.9099 453066.612 455169.5722 464716.3512 461480.5763 454077.7223 524248.2491 0.739426732 0.939386138 0.944801134 0.897214079 0.864221507 0.86823289 0.886443306 0.880271087 0.866150193 1 18.99989061 -1.757032722 2.307852982 1.032813527 0.880628874 0.323612836 0.05333858 7029786.148 4524801.87 1309105.801 0.012725846 0.017497149 1.757032722 -0.152184653 MGIGGLDKEFSDIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGIGGLDKEFSDIFR 15 1 I3L0N3;P46459;P46459-2 I3L0N3 NSF Vesicle-fusing ATPase 0 ; 148.72 3.18E-06 836710000 1327330 1224890 1451540 1107900 1961690 1818800 1466940 1409710 1437720 1261730 FALSE TRUE 1379734.013 1435255.329 1489368.325 1327039.313 1628242.634 1396411.264 1351957.41 1390815.143 1385976.738 1508941.836 0.9143719 0.951166768 0.98702832 0.879450275 1.079062556 0.925424182 0.895963898 0.921715543 0.918509054 1 20.52510577 -0.032946108 7.944718452 1 0.941345675 0.096493159 0.053784547 6852769.299 862556.5119 0.050404709 0.012224938 0.926944842 0.032946108 -0.058654325 MGIISIS(ph)T(ph)IQKM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGIISISTIQKM 12 1 X6RDV4;Q8WWT9-4 X6RDV4 SLC13A3 2 MGIIS(0.001)IS(1)T(1)IQKM 72.928 0.089884 821180000 57383 38691 53043 43880 63479 74292 69450 58783 70498 77305 TRUE FALSE 59648.52515 45335.87828 54425.34416 52559.33303 52688.86225 57038.80891 64006.32753 57995.11003 67960.79075 92451.43466 0.645187664 0.490375065 0.58869118 0.56850749 0.569908541 0.616959695 0.692323789 0.627303516 0.7350972 1 16.49640809 0.152330477 0.394035387 1.062791611 0.555484023 0.890533524 0.043810705 1.019076419 0.238641366 0.146256344 0.02997272 1.420137766 -0.152330477 -0.507307589 MGLAMGGGGGAS(ph)FDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGLAMGGGGGASFDR 15 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 MGLAMGGGGGAS(1)FDR 111.35 0.00089079 76849000 76034 76449 103240 75862 130040 84483 94316 78532 114610 89095 TRUE FALSE 79035.88103 89578.52106 105930.5192 90867.27717 107935.8472 64863.1036 86923.26547 77479.40699 110485.2085 106551.4594 0.741762539 0.840706655 0.994172391 0.852801807 1.012992669 0.608749087 0.815786719 0.727154817 1.036918772 1 16.70119083 1.223351814 24.99951659 1.018459589 0.825194217 0.318626581 0.11358512 332.4733832 546488.9047 0.108524508 0.027552362 16.72444882 -1.223351814 -0.193265372 MGLS(ph)MER ddPTM_MDA-MB-175_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 107.56 0.007814 1262300000 1335300 1054580 1574880 1000190 1988750 1481070 1399820 1276050 1709260 1249840 TRUE FALSE 1388018.675 1235695.912 1615922.667 1198024.597 1650702.985 1137113.938 1290098.451 1258946.637 1647744.066 1494722.218 0.928613128 0.826706057 1.0810856 0.80150317 1.104354351 0.760752683 0.863102478 0.842261272 1.102374773 1 20.51144597 1.237369657 24.99959226 1.051187414 0.898674488 0.23116504 0.109456219 43.13075793 905175.9713 0.081661429 0.024748122 17.27307494 -1.237369657 -0.152512926 MGLSMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGLSMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 116.3 0.012765 147832000 131969 171292 151244 156624 203987 211463 151325 174115 149959 224598 FALSE TRUE 137179.238 200710.0685 155185.5429 187603.7597 169313.3626 162353.923 139463.7511 171781.2732 144562.0049 268603.6779 0.510712434 0.747234997 0.577749136 0.69844077 0.630346404 0.604436709 0.519217578 0.63953433 0.538198159 1 18.03511953 -2.049440432 2.65076152 1.524669448 0.61204116 0.725609321 0.07239027 16401675.89 10001708.34 51929274.17 0.016121494 0.008924 2.049440432 -0.912628288 MGNGALHGDHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGNGALHGDHQR 12 0 E9PGA6;Q9BXJ4-2;Q9BXJ4;Q9BXJ4-3 E9PGA6 C1QTNF3-AMACR;C1QTNF3 Complement C1q tumor necrosis factor-related protein 3 0 62.454 0.044906 15346000 11084 32836 16407 22359 16261 23653 13333 17808 14136 50270 FALSE TRUE 11521.60488 38475.32757 16834.5799 26781.54347 13496.96103 18159.94921 12287.92462 17569.31289 13627.24812 60119.44402 0.191645233 0.639981427 0.280018889 0.445472241 0.224502426 0.30206449 0.204391854 0.292240109 0.226669563 1 15.87554405 -1.605666936 3.973695063 1.018558881 0.315282951 0.717188276 0.12961642 0.020425774 0.002026969 0.120286385 0.028406839 0.024793227 1.605666936 -0.70327593 MGPGAASGGERPNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MGPGAASGGERPNLK 15 1 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ;; 171.26 9.98E-07 1818400000 609210 566290 634870 623610 817570 879050 680280 642780 643440 484880 FALSE TRUE 633262.0812 663545.9024 651415.2338 746958.1967 678599.7434 674903.9596 626957.876 634164.5855 620282.7201 579882.9524 1.092051557 1.144275581 1.123356414 1.28811891 1.170235718 1.163862391 1.081180044 1.093607913 1.069668831 1 19.1454022 1.559394028 0.924674334 1.014300224 1.166811817 0.509048478 0.051087392 0.443335639 0.744724865 0.048377518 0.018853965 36.25718048 -1.559394028 0.152511594 MGPGIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGPGIDR 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2T0 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 97.071 0.028538 300350000 421900 523660 472060 446470 582550 624220 500250 471460 499640 504190 FALSE TRUE 438556.9378 613594.5315 484362.2714 534780.4334 483528.3591 479254.3651 461039.0978 465140.8499 481658.054 602976.3772 0.727320264 1.017609569 0.803285651 0.886901135 0.801902657 0.794814496 0.764605572 0.771408081 0.798800869 1 19.20174196 3.226692496 23.58680921 0.80294716 0.866160359 0.009927095 0.09379546 257.8025041 512357.515 0.024907532 0.030026601 1685.359279 -3.226692496 0.063213199 MGPLGLDHMASSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MGPLGLDHMASSIER 15 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;;;;;; 208.68 2.77E-09 3021060000 1990110 2827690 2674420 2709480 3282580 3551220 2778180 2792610 2626580 3068460 FALSE TRUE 2068681.079 3313323.761 2744117.582 3245407.057 2724608.224 2726502.974 2560418.992 2755179.631 2532049.899 3669665.988 0.563724624 0.902895188 0.747784019 0.884387589 0.742467634 0.742983962 0.697725352 0.750798476 0.68999465 1 21.80721732 -0.930299869 4.353831846 1.000005106 0.753121864 0.408797922 0.091015412 9282768.417 4264540.109 448.7084739 0.019741061 0.11740866 0.930299869 -0.246883242 MGPLINRPHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MGPLINRPHLER 12 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ;;; 138.24 4.69E-05 2780990000 663919 833525 798043 805343 930374 1035282 747390 777514 776576 949260 FALSE TRUE 690131.0348 976676.4348 818840.6562 964637.4417 772229.3598 794853.4454 688807.6189 767092.6966 748627.1815 1135249.322 0.607911426 0.860318888 0.721287069 0.849714175 0.680228867 0.700157604 0.606745677 0.675704166 0.659438563 1 20.11457774 -0.984358446 4.506528622 1.000007727 0.708211246 0.532225915 0.082443597 7698850.557 1708377.371 586.459697 0.020061781 0.103667244 0.984358446 -0.291796481 MGPPVGGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MGPPVGGHR 9 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;; 109.86 0.0023803 1071104000 691290 822019 789451 758776 934781 1005411 824208 829634 756465 821016 FALSE TRUE 718582.663 963194.3688 810024.7416 908859.6281 775887.2595 771919.5324 759604.4233 818514.1132 729239.9724 981878.3659 0.731844888 0.980971169 0.82497463 0.925633622 0.790207104 0.786166148 0.77362375 0.833620682 0.74269889 1 19.90518479 3.216041258 24.99798682 0.809527411 0.871158511 0.046519745 0.089499746 521.554998 578959.0764 0.023553744 0.028171185 1644.527945 -3.216041258 0.061631099 MGPSGGEGMEPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MGPSGGEGMEPERR 14 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;; 245.55 1.85E-17 3896940000 1230128 1713692 1664930 1514352 1792079 2053280 1620887 1645300 1570159 1709556 FALSE TRUE 1278694.403 2008005.27 1708319.444 1813886.306 1487462.052 1576436.838 1493837.642 1623247.445 1513649.284 2044510.767 0.62542806 0.98214463 0.835563926 0.887198216 0.727539358 0.771058223 0.730657752 0.793953972 0.740347915 1 20.96332423 4.7909215 22.99939564 0.814930085 0.625425117 0.28227969 0.095145269 30788.29004 13522553.85 0.022021009 23.96565231 61790.47022 -4.7909215 -0.189504968 MGPSGGEGMEPERRDS(ph)QDGSSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.995)QDGS(0.002)S(0.003)YR;MGPSGGEGMEPERRDS(0.997)QDGS(0.002)SYR;MGPSGGEGMEPERRDS(0.999)QDGSS(0.001)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(0.998)QDGS(0.001)S(0.001)YR;MGPSGGEGMEPERRDS(0.941)QDGS(0.046)S(0.013)YR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR;MGPSGGEGMEPERRDS(1)QDGSSYR 330.48 8.31E-87 30145770000 3724400.7 5166426.4 5181616.5 4243551.6 5895219 6073883.3 4493453.8 4996676.8 5364119.3 5843000.3 TRUE FALSE 3871442.915 6053719.945 5316653.683 5082913.441 4893151.78 4663315.954 4141245.15 4929704.52 5171065.694 6987824.338 0.554026937 0.866324002 0.760845354 0.727395709 0.700239666 0.667348767 0.592637272 0.705470585 0.740010831 1 22.73641191 -1.517161174 4.449271789 1.002109025 0.703268979 0.542187332 0.082250161 0.001697718 0.000184238 0.078574031 0.018398034 0.030397567 1.517161174 -0.298840046 MGPSGGEGMEPERRDSQDGS(ph)SYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.003)QDGS(0.96)S(0.037)YR;MGPSGGEGMEPERRDS(0.026)QDGS(0.761)S(0.212)YR 168.69 7.37E-12 1320190000 232592 276065 343334 284215 379600 390380 262623 313619 337177 366908 TRUE FALSE 241774.9118 323477.0163 352281.5661 340431.8787 315075.7276 299720.1613 242037.923 309415.4503 325042.0656 438796.5977 0.550995411 0.737191259 0.802835683 0.775830716 0.718045056 0.683050331 0.551594803 0.705145509 0.740757944 1 18.74319281 0.749970795 2.813480579 0.999934159 0.693570955 0.579322055 0.078688877 1.134871166 11.72899651 0.078944579 0.020801032 5.623035112 -0.749970795 -0.306363204 MGPSGGEGMEPERRDSQDGSS(ph)YR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGPSGGEGMEPERRDSQDGSSYR 23 2 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 1 MGPSGGEGMEPERRDS(0.156)QDGS(0.217)S(0.627)YR 106.28 0.0011489 241680000 65146 76503 87195 74512 116510 114690 78553 81502 97905 108420 TRUE FALSE 67718.01438 89641.79514 89467.37333 89250.2512 96705.67182 88054.98564 72395.8106 80409.599 94381.41817 129662.8232 0.522262378 0.691345391 0.690000195 0.688325682 0.745824203 0.679107423 0.558338997 0.620143824 0.727898837 1 16.98440536 0.869813423 4.204761429 0.999956749 0.652136956 0.731654603 0.063670681 0.424098044 12.85545674 0.063675739 0.016226831 7.409918357 -0.869813423 -0.347819793 MGQAPSQSLLPPAQDQPRS(ph)PVPSAFSDQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 MGQAPSQSLLPPAQDQPRSPVPSAFSDQSR 30 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MGQAPS(0.172)QS(0.157)LLPPAQDQPRS(0.661)PVPS(0.005)AFS(0.005)DQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.991)PVPS(0.009)AFSDQSR;MGQAPSQSLLPPAQDQPRS(1)PVPSAFSDQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.99)PVPS(0.007)AFS(0.002)DQSR;MGQAPSQSLLPPAQDQPRS(0.999)PVPS(0.001)AFSDQSR;MGQAPSQSLLPPAQDQPRS(0.989)PVPS(0.011)AFSDQSR 297.99 2.62E-81 19471070000 3353130 4225608 3906048 3735640 4249489 4961836 3390170 4223540 3956640 4516435 TRUE FALSE 3485514.162 4951323.303 4007842.82 4474538.442 3527162.378 3809524.786 3124439.617 4166930.355 3814241.299 5401343.966 0.64530498 0.916683576 0.742008442 0.828412053 0.653015694 0.705292018 0.578455961 0.771461766 0.706165229 1 22.36488699 -1.245575756 3.493250388 1.000621676 0.730059703 0.444036651 0.091458066 19531550.18 30375897.18 130873.5624 0.022388493 0.056809929 1.245575756 -0.270561974 MGQTMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGQTMER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 81.119 0.065295 96504000 72191 117780 105200 119600 119520 138860 99390 113700 101140 127650 FALSE TRUE 75041.15642 138007.7988 107941.5984 143256.523 99204.03309 106611.8694 91599.55209 112176.0375 97499.99116 152660.5735 0.491555578 0.904017296 0.707069258 0.938398958 0.649834013 0.698358895 0.600021014 0.734806865 0.638671721 1 17.21996799 -1.220271168 4.942910576 1.000039943 0.714525775 0.324885221 0.126301401 5.19E-05 8.18E-06 0.114092939 0.026888208 0.060218347 1.220271168 -0.285514168 MGS(ph)KSPGNTSQPPAFFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGSKSPGNTSQPPAFFSK 18 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 MGS(0.527)KS(0.472)PGNT(0.001)SQPPAFFSK 175.47 1.98E-12 744830000 652150 477490 639350 348870 1018200 778730 563470 680620 727860 596470 TRUE FALSE 677897.3856 559495.1931 656011.9862 417875.4447 845126.7277 597881.7593 519303.749 671497.4022 701664.4608 713336.8764 0.950318718 0.78433516 0.919638404 0.585803789 1.18475121 0.838147836 0.727992294 0.941346823 0.983636882 1 19.44422403 1.524303107 7.306829828 0.982335378 0.855717745 0.126511038 0.147036313 0.253990648 26.58643882 0.077569807 0.035736577 33.4428366 -1.524303107 -0.126617633 MGS(ph)PAPLLPGDLLGGGSDSI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MGSPAPLLPGDLLGGGSDSI 20 0 Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 Q9UPQ9-1 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI;MGS(1)PAPLLPGDLLGGGSDSI 183.6 4.52E-17 329397000 592460 522635 553337 466449 703144 855739 617207 564320 546397 412105 TRUE FALSE 615850.7783 612393.4957 567757.4168 558711.22 583623.834 657006.5861 568828.7026 556756.2134 526732.2787 492849.0845 1.249572735 1.242557844 1.151990406 1.133635503 1.184183663 1.333078638 1.154164064 1.129668759 1.068749634 1 18.91078642 1.349692883 1.441397188 1.008174678 1.2086714 0.625992193 0.054970342 0.263094548 1.023900636 0.053174539 0.016784956 22.37138555 -1.349692883 0.200496722 MGS(ph)SPLEVPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGSSPLEVPKPR 12 1 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 MGS(0.5)S(0.5)PLEVPKPR 101.45 0.0040389 252380000 445150 353610 495110 379970 667740 630040 693920 593000 611240 419790 TRUE FALSE 462724.8657 414339.7668 508012.9733 455126.9319 554237.7933 483722.7583 639528.7372 585051.805 589241.5918 502039.8131 0.921689582 0.825312567 1.011897782 0.906555456 1.103971794 0.963514737 1.273860599 1.16534942 1.173694947 1 18.93744225 3.017059047 1.026804756 1.161471303 0.896521933 0.507522169 0.093683209 0.361079372 0.825078281 0.041554606 0.052153873 1040.061564 -3.017059047 -0.26494937 MGSGIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MGSGIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 90.777 0.039293 172220000 569560 765930 694550 759650 707490 938560 699450 665010 613390 823540 FALSE TRUE 592046.6686 897472.5194 712650.5436 909906.5027 587231.1025 720593.664 644625.2813 656096.6287 591314.2137 984896.8954 0.60112553 0.911234997 0.72357883 0.923859652 0.596236119 0.731643756 0.654510421 0.666157678 0.600381844 1 19.90961318 3.225311632 24.99968347 0.687526979 0.793872238 0.06613121 0.137776622 457.8730675 863964.9066 0.036219929 0.043529478 1680.009091 -3.225311632 0.106345259 MGSKS(ph)PGNTSQPPAFFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MGSKSPGNTSQPPAFFSK 18 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 MGS(0.13)KS(0.87)PGNTSQPPAFFSK 186.62 2.85E-14 591300000 1749500 1240600 1625800 870860 2303900 2064100 1220500 1610600 1909300 1458900 TRUE FALSE 1818571.611 1453663.399 1668169.684 1043113.509 1912283.901 1584744.057 1124834.021 1589012.541 1840584.666 1744743.523 1.042314579 0.833167386 0.956111693 0.597860657 1.096025792 0.908296283 0.64469878 0.910742766 1.054931365 1 20.73458355 1.353522744 5.677308586 1.024186995 0.863053217 0.15054778 0.147682354 0.359636881 15.34351509 0.099626637 0.035465384 22.56954189 -1.353522744 -0.161133778 MGSS(ph)PLEVPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MGSSPLEVPKPR 12 1 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 MGS(0.335)S(0.665)PLEVPKPR;MGS(0.262)S(0.738)PLEVPKPR 106.66 0.0011497 637140000 444500 322930 442700 352400 622930 603500 618900 517670 503090 354400 TRUE FALSE 462049.2032 378390.7155 454237.1257 422103.6682 517044.5811 463346.2711 570389.0008 510731.4804 484983.8892 423837.8946 1.09015548 0.892772261 1.071723721 0.995908279 1.219911168 1.093215772 1.345771598 1.205016085 1.144267408 1 18.69315306 3.242222728 24.99856161 1.188589075 1.008298198 0.363725401 0.098390427 84.83776181 579120.2271 0.026319039 0.034285569 1746.717728 -3.242222728 -0.180290877 MGVMSS(ph)PTENSFTLDADF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MGVMSSPTENSFTLDADF 18 0 P31350;P31350-2 P31350 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 MGVMS(0.019)S(0.798)PT(0.183)ENSFTLDADF;MGVMS(0.033)S(0.483)PT(0.483)ENS(0.001)FTLDADF;MGVMS(0.008)S(0.834)PT(0.158)ENSFTLDADF;MGVMS(0.06)S(0.47)PT(0.47)ENSFTLDADF;MGVMS(0.089)S(0.792)PT(0.115)ENS(0.004)FTLDADF 205.72 9.77E-16 69436000 76776 92787 95058 98816 109689 118802 107976 101762 112063 127355 TRUE FALSE 79807.17576 108722.4455 97535.28957 118361.5099 91044.10296 91212.03596 99512.55898 100398.0468 108029.8745 152307.7739 0.523986227 0.713833856 0.640382871 0.777120608 0.597763992 0.598866582 0.653364936 0.659178742 0.709286675 1 17.21663005 0.5940755 1.608669968 0.999975252 0.648107361 0.730319829 0.064379163 0.887688879 2.924729168 0.05856972 0.016749654 3.927132012 -0.5940755 -0.351867891 MHAADLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MHAADLEK 8 0 A0A2R8Y6S3;C9J167;Q68D20;P54278-3;P54278 A0A2R8Y6S3 PMS2;PMS2CL Protein PMS2CL;Mismatch repair endonuclease PMS2 0 72.485 0.046033 248210000 40320 138640 137600 155270 141960 196970 157910 163480 145470 133610 FALSE TRUE 41911.86473 162450.3415 141185.969 185981.9426 117829.6899 151226.7026 145532.6016 161288.818 140234.5631 159788.3214 0.26229617 1.016659667 0.883581277 1.163927006 0.737411151 0.946418995 0.910783719 1.009390527 0.877627113 1 17.28580244 4.742010789 24.97643324 0.948776144 0.262295909 0.79052585 0.106128588 133.2055457 964256.5969 0.02341075 0.17127881 55209.1155 -4.742010789 -0.686480235 MHAPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MHAPGK 6 0 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 ;;; 78.002 0.070933 2107620000 6893880 6075420 7325080 6087230 8832700 8844710 7980090 7356710 7402810 6549870 FALSE TRUE 7166055.706 7118826.125 7515977.602 7291265.925 7331320.809 6790660.145 7354589.694 7258105.336 7136384.314 7833191.622 0.914832172 0.908802755 0.959503861 0.930816745 0.935930227 0.866908468 0.938900776 0.926583401 0.911044266 1 22.90116882 -1.299921336 3.872890929 1.000150828 0.922409437 0.507793305 0.023175329 2186661694 395267699.7 3037221.943 0.005332895 0.050127802 1.299921336 -0.077741391 MHAPPINMESVHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MHAPPINMESVHMK 14 0 B0YIW6;P48444;P48444-2 B0YIW6 ARCN1 Coatomer subunit delta 0 73.022 0.021394 266050000 166190 227530 256170 230230 291390 334490 224730 270920 257640 297460 FALSE TRUE 172751.3095 266606.5076 262846.0006 275768.8068 241859.6319 256809.7667 207115.0754 267288.7605 248367.5867 355741.5918 0.485608974 0.749438676 0.738867781 0.775194167 0.679874486 0.721899752 0.582206523 0.751356509 0.698168537 1 18.44047013 0.073680292 1.127388445 1.001375382 0.690003674 0.553567407 0.084420277 5.747227678 6.240095212 0.100231189 0.023641528 1.184896161 -0.073680292 -0.311371708 MHDLNTDQENLVGTHDAPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MHDLNTDQENLVGTHDAPIR 20 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 266.2 7.18E-37 376920000 57988 96202 115182 97274 105626 127497 97282 100751 109513 107217 FALSE TRUE 60277.41102 112723.9452 118183.7375 116514.5069 87671.73025 97887.75399 89656.78264 99400.59764 105571.6485 128224.1184 0.470094174 0.879116555 0.921696628 0.908678557 0.683738218 0.763411402 0.699219334 0.775209835 0.823336903 1 16.96830813 0.817959477 2.740212522 0.999883634 0.771256502 0.243738214 0.125215036 1.181562945 14.78782743 0.118227809 0.031289356 6.575964764 -0.817959477 -0.228627132 MHEGDEGPGHHHKPGLGEGT(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MHEGDEGPGHHHKPGLGEGTP 21 1 P06702 P06702 S100A9 Protein S100-A9 1 MHEGDEGPGHHHKPGLGEGT(1)P 130.83 7.87E-06 110740000 79883 62242 78496 59837 96687 118520 91748 74090 79736 87268 TRUE FALSE 83036.84252 72931.57932 80541.67025 71672.58 80252.17828 90995.52619 84556.55202 73096.94474 76866.31694 104366.4938 0.795627404 0.69880262 0.771719614 0.686739368 0.768945812 0.871884481 0.810188682 0.700387089 0.736503778 1 16.67129909 3.00177166 24.97914081 0.798198657 0.736554647 0.162366247 0.0826459 134.0195949 1889517.405 0.023740463 0.028192162 1004.087729 -3.00177166 -0.061644011 MHS(ph)QPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MHSQPR 6 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 MHS(1)QPR 110.12 0.030398 191100000 122240 143070 140830 130300 151060 186690 141120 136320 118530 138660 TRUE FALSE 127066.1296 167641.1596 144500.1455 156072.9511 125382.8752 143334.0768 130058.6457 134492.8534 114264.1285 165827.7722 0.766253613 1.010935366 0.871386883 0.941174986 0.756102995 0.864355077 0.784299541 0.811039379 0.689053027 1 17.33932612 3.243967237 24.99975352 0.80831604 0.903683916 0.139946504 0.095003079 210.0597252 971291.8947 0.024360107 0.032056839 1753.748195 -3.243967237 0.095367877 MIAPEGSLVFHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MIAPEGSLVFHEK 13 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 155.98 4.70E-05 418730000 287700 268230 313500 242550 386140 399670 314490 297130 338060 286040 FALSE TRUE 299058.6182 314296.416 321670.0675 290525.6661 320504.0607 306852.6996 289839.452 293147.4584 325893.2866 342084.0614 0.874225525 0.918769541 0.940324627 0.849281504 0.936916088 0.897009636 0.847275523 0.856945679 0.952670187 1 18.38399136 1.028117181 5.097836244 0.999690902 0.889720102 0.553417819 0.032364787 0.11685933 7.982414463 0.032558277 0.008231238 10.66883948 -1.028117181 -0.1099708 MIASDSHRPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MIASDSHRPEVK 12 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 ;;; 131.37 0.00012014 660120000 334501 515123 508480 461726 630290 663780 541960 538740 523683 548045 FALSE TRUE 347707.3578 603591.3681 521731.4065 553054.0247 523153.5309 509627.1547 499479.7591 531519.0715 504835.7511 655423.9248 0.530507576 0.920917509 0.796021303 0.843811164 0.798191081 0.777553482 0.762071295 0.810954638 0.770243093 1 19.32206881 -2.52853026 1.894055496 3.133914822 0.787161115 0.328312912 0.094204763 3859865.641 218283.6402 35357855.37 0.020750049 0.002961214 2.52853026 -2.346753707 MIDLS(ph)AFSRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MIDLSAFSRK 10 1 Q8N1W2 Q8N1W2 ZNF710 Zinc finger protein 710 1 MIDLS(0.5)AFS(0.5)RK 66.071 0.071047 32612000 1285.8 43091 26061 46105 16418 42732 20602 29681 20056 42082 TRUE FALSE 1336.564377 50491.54405 26740.17107 55224.43139 13627.27422 32808.14061 18987.16141 29283.17474 19334.18848 50327.16219 0.026557515 1.003266265 0.53132682 1.09730867 0.270773746 0.651897289 0.377274628 0.581856267 0.384170051 1 15.61904963 -1.752515068 5.978175897 1.014412761 0.565233866 0.163542986 0.304779309 0.052843384 0.002187614 0.266353814 0.063159853 0.017680109 1.752515068 -0.449178895 MIDQVFGVLES(ph)PELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MIDQVFGVLESPELSR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.996)PELS(0.004)R;MIDQVFGVLES(1)PELSR;MIDQVFGVLES(0.999)PELS(0.001)R;MIDQVFGVLES(0.997)PELS(0.003)R;MIDQVFGVLES(0.995)PELS(0.005)R;MIDQVFGVLES(0.992)PELS(0.008)R;MIDQVFGVLES(0.983)PELS(0.017)R 220.34 1.21E-14 278865000 289827 324650 305420 331725 326593 367933 328661 311451 291344 307305 TRUE FALSE 301269.5938 380406.1121 313379.4961 397339.2149 271078.8385 282486.1368 302899.692 307276.5088 280858.5864 367515.531 0.819746564 1.035074929 0.852697287 1.081149452 0.737598321 0.768637276 0.824182018 0.83609122 0.764208755 1 18.48744569 3.222093097 24.99999606 0.813058697 0.9466984 0.278626151 0.098232209 273.8897502 415801.9943 0.026054008 0.031224254 1667.604648 -3.222093097 0.133639702 MIDVDSLTDKECDWLNNYHLTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MIDVDSLTDKECDWLNNYHLTCR 23 1 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ; 269.85 2.79E-45 867380000 498270 594170 636190 550910 724850 767380 641860 650210 687180 580810 FALSE TRUE 517942.0843 696214.0755 652769.634 659878.3537 601640.2559 589167.6248 591549.336 641494.9985 662448.526 694608.5992 0.74566034 1.002311339 0.939766128 0.950000266 0.866157224 0.848200879 0.851629733 0.92353449 0.953700439 1 19.40584075 1.142748673 2.148094275 0.997092667 0.893213655 0.232934182 0.066308543 0.447562958 3.826740474 0.061093926 0.017257208 13.89148496 -1.142748673 -0.103879012 MIEYDPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MIEYDPERR 9 1 O60832;O60832-2;C9IYT0;H7C0M1;H7BZF2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 77.677 0.051188 379086000 252734 243492 254000 259077 309051 310750 269445 276495 231284 267684 FALSE TRUE 262712.1335 285309.8569 260619.4487 310321.6573 256518.6214 238583.022 248325.1968 272789.0368 222960.134 320131.5547 0.820638046 0.891226912 0.814101093 0.969356669 0.801291274 0.745265559 0.775697344 0.852115428 0.696464097 1 18.28830536 MIFDVESMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MIFDVESMKK 10 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 130.01 0.0054982 514180000 1322000 843490 1122360 882280 1671850 1238320 1304170 1118930 1248350 869370 FALSE TRUE 1374193.581 988352.8461 1151609.624 1056792.351 1387669.534 950738.9469 1201945.748 1103932.574 1203422.127 1039706.406 1.321713103 0.950607633 1.107629631 1.016433432 1.33467441 0.914430209 1.156043418 1.061773369 1.157463415 1 19.98774477 1.639334312 24.99999588 1.082198034 1.105224515 0.014801477 0.135327106 6.702432218 5298.259633 0.058152022 0.032243054 43.58472523 -1.639334312 0.023026481 MIIEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MIIEEAKR 8 1 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 107.66 0.010639 283110000 413269 341086 421070 371300 545259 503903 494061 414009 448612 390250 FALSE TRUE 429585.1792 399664.8672 432043.4301 444742.0318 452576.0699 386879.165 455335.2078 408459.8865 432466.5418 466712.0157 0.920450224 0.856341499 0.925717392 0.952926037 0.969711631 0.828946228 0.975623495 0.875186138 0.926623972 1 18.83217309 0.968861516 23.02093071 1.000000001 0.912540449 0.245499312 0.045449826 1931.544358 1428009.075 0.041255024 0.010313756 9.308110198 -0.968861516 -0.087459552 MIKPFFHSLSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MIKPFFHSLSEK 12 1 P10599 P10599 TXN Thioredoxin 0 ;;; 174.68 1.79E-05 11848500000 19697840 17615830 18936460 17373360 27023140 26577080 23856440 21567090 21837670 19998580 FALSE TRUE 20475525.93 20641211.77 19429959.7 20809758.75 22429756.32 20404955.95 21986509.9 21278018.44 21051736.52 23916918.86 0.856110524 0.863038082 0.81239393 0.870085268 0.937819644 0.853159894 0.919286888 0.889663864 0.880202699 1 24.51152821 -5 0.123057758 1.405286638 0.818861544 0.630497571 0.030368549 97.04838016 0.768443251 9.758269078 0.270695378 1.00E-05 5 -0.586425094 MILIQDGSQNTNVDKPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MILIQDGSQNTNVDKPLR 18 1 A0A087WTP3;Q92945;M0R0I5;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 179.46 7.62E-14 489020000 178960 177690 177980 169250 221730 252450 183380 180470 192300 170120 FALSE TRUE 186025.479 208206.8753 182618.305 202727.1448 184040.4138 193822.3134 169006.1964 178051.0948 185379.1606 203451.7569 0.914346879 1.023372216 0.89760004 0.996438409 0.904589946 0.952669647 0.83069421 0.875151425 0.911170114 1 17.63432721 2.730061746 1.887417007 0.89248875 0.956009604 0.076227341 0.05580168 0.530401541 3.742198187 0.019746203 0.019288947 537.1081543 -2.730061746 0.063520854 MIMATNRPDTLDPALLRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MIMATNRPDTLDPALLRPGR 20 2 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ; 205.24 4.97E-22 2119600000 962070 1172930 1103870 1190170 1054390 1369150 1119540 1177520 1018190 1145250 FALSE TRUE 1000053.266 1374371.603 1132637.759 1425582.074 875165.1644 1051185.662 1031787.529 1161737.27 981545.5408 1369639.81 0.730157855 1.003454772 0.826960308 1.040844507 0.638974684 0.767490587 0.753327643 0.848206413 0.716645014 1 20.38536511 3.239740493 24.99993137 0.781451427 0.902476215 0.175716583 0.119349843 49.69894817 1053032.132 0.031189096 0.039981093 1736.762737 -3.239740493 0.121024788 MIMFLDELGNVPELPDTTEHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MIMFLDELGNVPELPDTTEHSR 22 0 E9PGC0;P20936-2;P20936-4;P20936 E9PGC0 RASA1 Ras GTPase-activating protein 1 0 83.063 0.0036149 14060000 6497.7 8218.8 8796.8 6597.3 8026.4 8189.8 8672.2 7306.3 8047.3 9175 FALSE TRUE 6754.234213 9630.314967 9026.051835 7902.226249 6662.075395 6287.843068 7992.450303 7208.370999 7757.679245 10972.66558 0.615550903 0.877664128 0.82259427 0.720173798 0.607151958 0.573046086 0.728396418 0.656938913 0.707000426 1 13.42162642 -1.106701731 3.127947815 1.000478629 0.701697852 0.496629321 0.090320112 5712182.552 8387807.945 27976.48199 0.023401502 0.07821648 1.106701731 -0.298780777 MIMQDKLEK ddPTM_MDA-MB-175_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 78.342 0.0274 776530000 1514900 907060 1375500 794640 2307000 1686400 1410900 1185800 1519300 1367400 FALSE TRUE 1574709.422 1062840.499 1411346.66 951817.4202 1914856.964 1294759.158 1300309.971 1169906.291 1464620.69 1635315.85 0.962939008 0.649929798 0.863042244 0.582038889 1.170940136 0.791748675 0.795143013 0.715400814 0.895619455 1 20.64113788 0.996373864 23.18315328 1.000000015 0.809649498 0.118389576 0.156080123 89.31627677 571041.5641 0.140650986 0.035162746 9.91685273 -0.996373864 -0.190350517 MINLSEPDTIDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MINLSEPDTIDER 13 0 Q14651;C9JAM8 Q14651 PLS1 Plastin-1 0 168.94 6.83E-05 25317000 35787 50350 42728 41949 50577 59682 43388 47627 51025 48075 FALSE TRUE 37199.89839 58997.22083 43841.52678 50246.38699 41979.93961 45821.75999 39987.13519 46988.63797 49188.62022 57494.3758 0.647018041 1.026138992 0.762535921 0.87393569 0.730157324 0.796978128 0.695496466 0.817273643 0.855537947 1 15.81113322 0.862421068 2.395207464 0.999595218 0.797050611 0.287507416 0.09858117 0.647839774 7.269516599 0.087421624 0.023597534 7.284857621 -0.862421068 -0.202544607 MINTDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MINTDLSR 8 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 110.38 0.012579 0 81193 131960 104330 111690 159810 171260 120130 106830 107450 200180 FALSE TRUE 84398.56233 154623.1035 107048.9255 133781.9486 132645.5533 131487.4605 110713.8967 105398.1186 103582.8955 239401.4383 0.352539913 0.645873745 0.447152391 0.558818483 0.554071664 0.549234213 0.462461285 0.440256831 0.432674491 1 17.86907229 -1.841419679 2.718902789 1.186512736 0.496631487 0.783181431 0.079908486 16553805.28 11215352.32 20091315.31 0.018435994 0.014407224 1.841419679 -0.689881249 MIPCDFLIPVQTQHPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MIPCDFLIPVQTQHPIR 17 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 131.48 2.68E-05 1165540000 553230 655520 644490 670890 598980 737190 704080 719690 645930 567900 FALSE TRUE 575071.9476 768100.4608 661285.9389 803590.0396 497165.5936 565988.7947 648892.3698 710043.7327 622683.1055 679169.1319 0.846728629 1.130941359 0.973669014 1.183195764 0.732020303 0.83335471 0.95542088 1.04545937 0.916830692 1 19.37341136 3.253372045 24.99999709 0.924063238 1.036300964 0.197758698 0.117065354 438.5850021 740277.0212 0.033182479 0.044745006 1792.140462 -3.253372045 0.112237726 MIPCDFLIPVQTQHPIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MIPCDFLIPVQTQHPIRK 18 1 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ;; 143.14 6.99E-08 3425900000 3579730 3598760 3942900 3173260 4967910 5001230 3496940 4126190 4540340 4456770 FALSE TRUE 3721060.505 4216819.036 4045655.213 3800921.357 4123466.433 3839770.127 3222840.705 4070885.172 4376934.05 5329988.751 0.698136652 0.791149706 0.759036351 0.713119958 0.77363511 0.720408674 0.604661821 0.763769937 0.82119011 1 22.34570106 0.909700666 2.195161194 0.998956613 0.726582673 0.742333473 0.049223474 0.205403139 2.092152889 0.048028078 0.013169916 8.122704717 -0.909700666 -0.27237394 MISTPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MISTPSPK 8 0 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 MIS(0.002)T(0.009)PS(0.989)PK 82.261 0.022169 0 250860 143480 176740 136010 246590 299460 218540 209770 214050 130020 TRUE FALSE 260764.1465 168121.5739 181345.9896 162912.3721 204674.7199 229914.9534 201410.2638 206958.3763 206346.3823 155494.9296 1.676994531 1.081202932 1.16625018 1.04770215 1.316279061 1.478600967 1.295285089 1.330965433 1.327029652 1 17.24650801 -1.111644713 4.694461068 0.999980257 1.292258514 0.209816994 0.175005454 3.53E-05 6.69E-06 0.165621696 0.039034772 0.077331296 1.111644713 0.292278257 MITNSLNHDS(ph)PPSTPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MITNSLNHDSPPSTPPR 17 0 J3QKZ5;J3QS16;Q8N9M1-2;Q8N9M1;Q8N9M1-3 J3QKZ5 C19orf47 Uncharacterized protein C19orf47 1 MITNSLNHDS(0.995)PPS(0.004)T(0.001)PPR 71.527 0.019532 106260000 26036 47213 41606 43180 44382 58434 44226 47138 35917 50139 TRUE FALSE 27063.92138 55321.46548 42690.28654 51720.87512 36837.96349 44863.58908 40759.45056 46506.19221 34624.35419 59962.77708 0.451345363 0.922596787 0.711946454 0.862549696 0.614347188 0.748190649 0.679745878 0.775584362 0.577430797 1 15.87177958 -1.568939809 2.789659403 1.017683801 0.7180395 0.311151523 0.13042223 25566195.22 25372439.79 3349888.642 0.028523509 0.026981133 1.568939809 -0.299644302 MIVDPVEPHGEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MIVDPVEPHGEMK 13 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 115.57 0.00065339 165710000 694570 523820 633600 561900 699880 768500 822290 631330 646710 483880 FALSE TRUE 721992.1599 613782.0102 650112.1365 673042.1429 580914.6476 590027.5217 757836.7611 622868.054 623435.0334 578687.0216 1.247638418 1.060645889 1.123426157 1.16305035 1.003849449 1.019596949 1.309579674 1.076347025 1.077326794 1 19.14242376 1.000149407 2.342309993 1.002377931 1.124228696 0.157287843 0.090836448 0.556149868 6.74781003 0.084194862 0.023007244 10.00344082 -1.000149407 0.121850765 MIYASSK ddPTM_MDA-MB-175_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 ; 146.94 0.0050827 789440000 903510 895490 860250 730280 2044830 1397890 1176560 893480 922610 1743590 FALSE TRUE 939181.2725 1049283.442 882668.8217 874727.2043 1697250.527 1073251.233 1084338.153 881504.362 889405.4463 2085213.077 0.450400625 0.503202024 0.423299101 0.419490561 0.813945848 0.514696193 0.520013117 0.422740665 0.426529766 1 20.99176338 -1.78351225 2.637651501 1.134290928 0.499846075 0.64273942 0.111972763 35904424.97 26788068.65 31078766.09 0.028601538 0.016462195 1.78351225 -0.634444852 MKAENSHNAGQVDTR ddPTM_MDA-MB-175_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 94.385 0.0026987 22586000 21237 25948 26027 17338 35421 32648 16682 22359 31387 31537 FALSE TRUE 22075.45316 30404.36715 26705.285 20767.40465 29400.15107 25065.99679 15374.42125 22059.31418 30257.388 37716.07134 0.585306273 0.806138234 0.708061154 0.550624811 0.779512553 0.664597237 0.407635809 0.584878366 0.802241244 1 15.20289179 0.989098473 4.091485718 0.999068729 0.634213087 0.522013492 0.109821517 0.15106762 7.361263837 0.111549018 0.028514839 9.752107337 -0.989098473 -0.364855642 MKDTDSEEEIREAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 ;;;;;;;;;; 220.59 9.28E-13 13096361000 9664500 9593900 11553630 9038490 11216060 13244750 12808860 11419660 11842230 8952920 FALSE TRUE 10046061.92 11241577.69 11854727.09 10826276.34 9309558.127 10168857.54 11804868.08 11266598.14 11416030.46 10707073.26 0.93826405 1.049920685 1.107186511 1.011133116 0.869477391 0.949732695 1.102529869 1.0522575 1.066213911 1 23.35206084 2.238725879 25 1.060350892 0.991584595 0.203555835 0.064942332 7.921866166 1198661.357 0.025639286 0.020202037 173.270999 -2.238725879 -0.068766298 MKEEMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKEEMDR 7 1 F5H442;Q99816;Q99816-2 F5H442 TSG101 Tumor susceptibility gene 101 protein 0 ; 88.37 0.017016 494510000 943870 728800 952830 720150 1186670 1110440 1025890 844650 968850 603960 FALSE TRUE 981134.7164 853965.7307 977661.5326 862593.5206 984960.2573 852557.1389 945478.0611 833328.8483 933981.2778 722294.3985 1.358358473 1.182295934 1.35354993 1.194240911 1.363654847 1.180345771 1.308992653 1.153724645 1.293075621 1 19.46222746 -4.531749625 0.209363263 2.30E-13 1.298485396 0.52634347 0.076570245 83.84478855 0.998822922 35.20727623 0.14671424 2.94E-05 4.531749625 1.298485396 MKEIAEAYLGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKEIAEAYLGGK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ; 147.68 6.00E-05 965960000 3698100 2562600 3528300 2382000 4760900 4232500 3679700 3417100 3945300 2651800 FALSE TRUE 3844103.844 3002706.616 3620250.397 2853152.49 3951643.919 3249566.019 3391275.499 3371299.364 3803309.424 3171369.438 1.212127416 0.946817037 1.14154168 0.899659452 1.246037081 1.024657039 1.069341042 1.063042143 1.199264071 1 21.59667452 3.239579238 24.99995085 1.095149891 1.049199722 0.048047834 0.10827902 103.5861342 2542225.489 0.028256829 0.036179357 1736.117991 -3.239579238 -0.045950169 MKEIAEAYLGK ddPTM_MDA-MB-175_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 ;;; 141.38 3.48E-05 10281440000 11417770 8280370 10612240 7283620 14591800 12296440 11632230 10546460 11547770 8233940 FALSE TRUE 11868552.38 9702459.135 10888803.69 8724298.297 12111491.05 9440778.164 10720465.42 10405101.95 11132168.01 9847222.895 1.205268988 0.985299027 1.105774065 0.885965352 1.229939769 0.958724939 1.088679065 1.056653441 1.130488071 1 23.23128548 -0.491046572 7.917621147 1.000000787 1.066131486 0.040529306 0.101505575 0 0 0.086681326 0.020430984 0.322814793 0.491046572 0.066130699 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MKEIAEAYLGYPVTNAVITVPAYFNDSQR 29 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ;;;; 175.42 5.85E-13 3879268000 2426880 2320744 2687760 2080536 3370130 3145280 2472756 2628614 2876960 2811490 FALSE TRUE 2522695.096 2719313.729 2757805.234 2492059.811 2797276.506 2414836.387 2278934.923 2593381.729 2773418.772 3362347.636 0.750277892 0.808754484 0.820202291 0.741166614 0.831941491 0.718199499 0.677780875 0.771300891 0.824845933 1 21.68103746 0.8431644 2.710497118 0.999804805 0.764406243 0.714084265 0.044801027 0.347076215 4.645169832 0.044963403 0.011923892 6.968902687 -0.8431644 -0.235398562 MKENQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKENQK 6 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 76.035 0.06942 3058200000 1745700 1121950 1601560 1085350 2219150 1805960 2119410 1644220 1932020 1119230 FALSE TRUE 1814621.584 1314636.185 1643297.969 1300028.991 1841939.676 1386553.16 1953285.106 1622181.92 1862486.978 1338521.69 1.355690833 0.98215531 1.227696183 0.971242379 1.376099984 1.035883968 1.45928536 1.211920534 1.391450727 1 20.35220909 3.22710021 24.99987281 1.258115202 1.130014657 0.088431051 0.17258472 454.3240333 991065.9135 0.045470853 0.054784922 1686.94223 -3.22710021 -0.128100544 MKETAEAYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKETAEAYLGK 11 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 132.79 0.00015976 2345840000 3536600 2667600 3228400 2913400 4540400 4165800 4094900 3269400 3302400 2339100 FALSE TRUE 3676227.699 3125739.549 3312534.756 3489661.824 3768624.43 3198356.083 3773931.038 3225579.041 3183547.269 2797401.86 1.31415788 1.117372371 1.184146905 1.247465326 1.347187361 1.143330935 1.349084338 1.153062449 1.13803716 1 21.41565609 1.023575359 1.596398128 1.003631097 1.235601088 0.474300026 0.077923329 0.326641336 1.698481579 0.070240888 0.020544415 10.55784688 -1.023575359 0.231969991 MKETAEAYLGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKETAEAYLGKK 12 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 105.14 0.0011599 649780000 437210 317880 388460 267130 651700 448790 385900 375760 452760 284540 FALSE TRUE 454471.3884 372473.4172 398583.5867 319967.5167 540924.2668 344565.324 355652.1496 370723.5518 436465.256 340290.1652 1.335540768 1.09457591 1.171305044 0.940278473 1.589597121 1.012563275 1.04514378 1.089433636 1.282626713 1 18.37640593 MKETIMNQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKETIMNQEK 10 1 P20290-2;D6RDG3 P20290-2 BTF3 Transcription factor BTF3 0 ; 158.42 7.29E-06 730770000 1136260 838410 1049570 711880 1507420 1335840 1234480 993280 1139910 900040 FALSE TRUE 1181120.422 982400.3956 1076922.656 852687.7393 1251189.287 1025611.405 1137718.232 979966.7063 1098884.862 1076385.606 1.09730232 0.912684442 1.000498939 0.792176832 1.162398754 0.952828986 1.056980162 0.910423459 1.020902598 1 20.03776357 4.760245256 23.43986187 0.976356325 1.097302613 0.126303068 0.093335483 4622.904188 4996907.84 0.020651251 0.876840725 57576.49929 -4.760245256 0.120946289 MKEVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKEVGK 6 1 P49902-2;P49902;Q5JUV4;Q86YG4 P49902-2 NT5C2;NT5DC4 Cytosolic purine 5-nucleotidase;5-nucleotidase domain-containing protein 4 0 ; 78.496 0.063503 1709400000 2352900 1400580 2070900 1500000 2632200 2359000 2388800 1911780 2248500 1389250 FALSE TRUE 2445794.309 1641118.72 2124869.355 1796695.523 2184779.584 1811158.001 2201559.614 1886155.716 2167576.924 1661446.939 1.472086921 0.98776475 1.278927004 1.081404095 1.314986072 1.090108844 1.325085721 1.135248844 1.304632049 1 20.66400879 -1.97368296 2.807242988 0.823093827 1.209713176 0.181941168 0.13878321 2868746 9184393.278 3181990.648 0.028086847 0.010624709 1.97368296 0.38661935 MKEYGEQIDPSTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKEYGEQIDPSTHR 14 1 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 79.771 0.01091 539350000 446880 509010 548770 527000 704150 678620 516540 551950 562530 515260 FALSE TRUE 464523.1675 596428.508 563071.397 631239.0271 584458.8345 521020.7896 476052.2451 544552.0131 542284.6552 616215.3318 0.753832538 0.967889757 0.913757526 1.024380593 0.948465259 0.845517407 0.772542033 0.883704097 0.880024607 1 19.23307505 2.737210051 24.96615373 0.86185765 0.929500273 0.051099023 0.083712355 253.5595621 4687193.751 0.025845798 0.025604554 546.0218869 -2.737210051 0.067642623 MKFNPFVTSDR ddPTM_MDA-MB-175_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 ; 198.55 4.86E-08 3454300000 3192300 4007700 3919700 3056400 5496200 4605600 3217500 3890700 4124300 5044900 FALSE TRUE 3318334.469 4695991.299 4021850.602 3660946.798 4561957.887 3536019.199 2965303.943 3838551.53 3975867.249 6033351.565 0.549998526 0.778338747 0.666603058 0.606784928 0.756123332 0.586078759 0.491485356 0.636222088 0.658981531 1 22.52452822 -1.541131283 3.539022676 1.008641024 0.636487807 0.636666464 0.082326639 14256939.79 6246122.131 946888.2279 0.0193452 0.028765287 1.541131283 -0.372153217 MKGDYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 119.29 0.0043911 17108780000 8172280 8058149 8095550 7286670 12582930 11537360 9943760 7694620 7901570 10296650 FALSE TRUE 8494927.925 9442073.407 8306526.684 8727951.577 10444088.05 8857982.99 9164342.108 7591486.205 7617194.039 12314081.43 0.689854779 0.766770422 0.674555121 0.708778128 0.84814187 0.719337698 0.744216462 0.616488225 0.618575903 1 23.55380568 -2.264839783 2.478478785 2.317874936 0.709313454 0.641905687 0.06506169 5424428.23 1617289.389 39637933.47 0.016672822 0.005434508 2.264839783 -1.608561482 MKGDYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 119.29 0.0043911 32953140000 16210140 14419960 15070300 13860310 26844890 20798290 19049140 15482420 15450290 19886920 FALSE TRUE 16850128.84 16896475.96 15463044.4 16601837.95 22281805.19 15968202.35 17556018.63 15274903.48 14894237.08 23783381.22 0.708483318 0.710432037 0.650161735 0.698043638 0.936864485 0.67140169 0.738163278 0.642251131 0.626245568 1 24.5034505 -2.293221659 2.431854106 2.502824214 0.709053249 0.524367727 0.083110937 11312273.31 726084.2591 95427284.16 0.021542229 0.00509071 2.293221659 -1.793770965 MKGYPHWPAR ddPTM_MDA-MB-175_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 ; 123.63 0.00027464 2223500000 2843900 3479900 3023500 2306000 7763200 5121900 3159400 3022600 3281900 8146100 FALSE TRUE 2956179.368 4077545.755 3102294.894 2762119.917 6443614.037 3932416.348 2911757.972 2982086.991 3163785.06 9742172.328 0.303441498 0.418545846 0.318439747 0.283521973 0.6614145 0.403648818 0.298881797 0.306100825 0.324751498 1 23.21581207 -1.681008393 2.725485503 1.085333544 0.368205141 0.758545694 0.106843449 21224393.9 18893534.44 12551291.47 0.027308029 0.020844506 1.681008393 -0.717128403 MKLDYILGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKLDYILGLK 10 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 134.2 0.0041194 0 2412400 1596400 2401200 1662100 3567700 2716000 2896900 2297400 2570000 1973600 FALSE TRUE 2507643.415 1870569.282 2463777.245 1990858.419 2961263.628 2085250.161 2669833.408 2266607.111 2477506.202 2360289.133 1.062430606 0.792517008 1.043845523 0.843480738 1.254619015 0.883472339 1.131146761 0.960309091 1.049662165 1 21.17053217 MKLPGR ddPTM_MDA-MB-175_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 982140000 1793280 1675160 1812760 1445970 2494400 2396900 2007220 1918120 1901970 1688290 FALSE TRUE 1864080.079 1962855.699 1860002.015 1731978.55 2070402.779 1840256.3 1849888.852 1892410.739 1833518.471 2019078.101 0.923233271 0.972154419 0.921213505 0.857806614 1.025419858 0.911433936 0.916204703 0.937264753 0.908096854 1 20.94526529 -0.945094935 4.410634977 1.00000153 0.931221695 0.201491352 0.0415823 3.17721E+11 75937890661 5220192.907 0.009175223 0.113476274 0.945094935 -0.068779835 MKPWFEVGDENSGWSAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKPWFEVGDENSGWSAQK 18 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 171.72 3.02E-14 0 186890 170030 221680 162180 216890 226890 194900 205780 210640 158090 FALSE TRUE 194268.5615 199231.3299 227457.1629 194258.7199 180023.1153 174198.2361 179623.2287 203021.8557 203059.1075 189064.7087 1.027524189 1.053773236 1.203065154 1.027472135 0.952177255 0.921368336 0.950062177 1.073822064 1.074019096 1 17.52852057 3.490953475 24.75365918 0.996875533 1.094783194 0.332796957 0.063010314 715.3475033 1280159.888 0.018518452 0.027435892 3097.087501 -3.490953475 0.097907661 MKQEGSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKQEGSAR 8 1 O43242;F5H8K4 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 69.423 0.049208 54695000 28871 41964 50800 32654 52604 57529 36046 41438 43279 50317 FALSE TRUE 30010.84937 49170.99057 52123.88973 39112.86374 43662.39087 44168.76161 33220.62033 40882.59139 41721.39724 60175.65277 0.498720795 0.81712434 0.866195668 0.649978221 0.725582339 0.733997216 0.552060822 0.679387585 0.693326874 1 15.87689227 -0.586736953 11.57128743 1 0.693571099 0.443779234 0.103834968 0 0 0.099099226 0.023357911 0.258978104 0.586736953 -0.306428901 MKS(ph)LEQDALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;MKS(1)LEQDALR;MKS(1)LEQDALR 109.84 0.0011904 810010000 834961 1182160 1144620 1108770 1437500 1611590 1238740 1234280 1261530 1330300 TRUE FALSE 867925.905 1385186.784 1174449.738 1328081.397 1193154.263 1237322.646 1141644.322 1217736.495 1216127.782 1590946.815 0.54554049 0.87066819 0.738208045 0.834774226 0.749964897 0.777727222 0.717587987 0.765416219 0.764405051 1 20.60145418 0.323431533 2.031307064 1.00000307 0.756205541 0.456264224 0.081269559 11.63099174 33.61769141 0.06992126 0.019166046 2.105869882 -0.323431533 -0.243797529 MKSEEQPMDLENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MKSEEQPMDLENR 13 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 0 65.895 0.052298 225080000 75070 103880 109570 93944 109000 135910 98088 111870 112010 132740 FALSE TRUE 78033.82157 121720.5819 112425.4842 112525.8428 90472.21893 104346.9622 90399.60625 110370.5656 107978.782 158747.8615 0.491558254 0.766754152 0.708201566 0.708833755 0.569911418 0.657312554 0.56945401 0.695257023 0.680190466 1 17.27637763 0.390317333 1.396050673 1.000067897 0.649035553 0.650126022 0.077557856 2.191830331 4.412502611 0.071176027 0.020798013 2.456503191 -0.390317333 -0.351032344 MKVVEVLAGHGHLYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 139.88 1.13E-06 237180000 236430 400040 404350 231780 569950 532460 211890 348020 385120 652570 FALSE TRUE 245764.439 468743.7581 414887.6932 277625.3922 473070.1026 408804.2345 195281.5081 343355.3611 371259.6064 780428.5973 0.314909576 0.600623503 0.531615185 0.35573452 0.606167053 0.523820162 0.250223414 0.439957432 0.475712458 1 19.57390712 0.759662847 5.746942504 0.999999887 0.453996298 0.679207066 0.112373346 8.745820974 209.0760586 0.107129619 0.026964812 5.749933835 -0.759662847 -0.546003589 MKYNTEGRVS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MKYNTEGRVSPSPSQESLSSSK 22 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 MKY(0.007)NT(0.144)EGRVS(0.614)PS(0.183)PS(0.052)QESLSSSK;MKYNT(0.001)EGRVS(0.96)PS(0.039)PSQESLSSSK 146.2 7.73E-08 270180000 362830 247030 332970 203070 430250 382000 298540 310320 386920 276900 TRUE FALSE 377154.8086 289455.4809 341647.4717 243236.6399 357116.2587 293286.2893 275139.6547 306160.668 372994.8248 331153.2534 1.138913191 0.874083156 1.031689915 0.734513816 1.078401782 0.885651239 0.830852942 0.924528643 1.12635108 1 18.33713951 1.255043156 24.67751229 1.063175517 0.929166109 0.153061168 0.117159183 288.5403299 432004.0459 0.072963745 0.026464119 17.9904968 -1.255043156 -0.134009408 MLADLDDLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MLADLDDLNR 10 0 Q9BQS8;Q9BQS8-4 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 0 ;;; 218.48 1.57E-08 179807000 142159 175531 162968 171291 179218 215310 156510 165677 162161 197141 FALSE TRUE 147771.5471 205677.0838 167215.08 205171.8485 148754.5884 165307.5156 144242.3372 163456.3708 156324.8573 235767.0045 0.626769413 0.872374335 0.709238684 0.870231392 0.630938959 0.701147796 0.611800356 0.693296211 0.66304807 1 17.8470023 -1.050133956 4.324926038 1.000021874 0.710316885 0.496375468 0.087994936 11404462.5 2769114.329 2428.204862 0.020195849 0.089097608 1.050133956 -0.289704988 MLAEDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MLAEDELR 8 0 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;;;;;;; 206.8 0.00015924 7264350000 7079980 8892610 8067570 8930440 8056050 9458050 9177560 8354960 7774300 7826370 FALSE TRUE 7359503.077 10419846.59 8277817.502 10696854.38 6686685.499 7261561.226 8458198.866 8242975.427 7494504.462 9359797.357 0.786288719 1.113255575 0.884401359 1.142851065 0.714404943 0.77582462 0.903673289 0.880678834 0.800712256 1 23.15804586 3.231153135 24.99999653 0.843587 0.984146225 0.235516291 0.119800816 230.5634305 778143.0016 0.032413247 0.039469885 1702.758805 -3.231153135 0.140559225 MLAEDELRDAVLLVFANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MLAEDELRDAVLLVFANK 18 1 P61204;F5H423;P61204-2;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ;; 270.42 5.68E-39 1117840000 1609310 1673410 1900100 1386270 2333140 2188760 1611540 1849250 2089400 1905140 FALSE TRUE 1672846.801 1960805.15 1949618.167 1660470.068 1936553.696 1680453.661 1485223.284 1824463.829 2014202.902 2278415.707 0.734214918 0.86060026 0.855690277 0.728782752 0.849956261 0.73755358 0.651866681 0.800759854 0.884036612 1 21.11959957 1.019946883 2.685007142 0.998027458 0.77660749 0.555444662 0.063430426 0.192547767 3.112164949 0.062302192 0.016710384 10.47000485 -1.019946883 -0.221419968 MLAES(ph)DES(ph)GDEESVSQTDKTELQNTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 2 MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(0.999)GDEES(0.001)VSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR;MLAES(1)DES(1)GDEESVSQTDKTELQNTLR 197.01 3.47E-25 3132960000 2374430 1942788 2157340 1761480 2758790 2620990 2377720 2206110 2411360 1879492 TRUE FALSE 2468174.33 2276446.726 2213562.053 2109895.487 2289851.861 2012304.794 2191348.093 2176540.704 2324575.625 2247742.472 1.098068111 1.012770259 0.984793445 0.938673141 1.018734081 0.895255937 0.974910658 0.968322987 1.034182364 1 21.10004532 4.733758539 1.795403017 0.972202544 1.139156995 0.49057988 0.037322629 0.674793445 2.210397241 0.009241868 0.190838214 54169.96301 -4.733758539 0.166954451 MLAES(ph)DESGDEESVSQTDKTELQNTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAES(0.777)DES(0.22)GDEES(0.001)VS(0.001)QT(0.001)DKTELQNTLR;MLAES(1)DESGDEESVSQTDKTELQNTLR 140.46 1.35E-07 420840000 58397 58750 59169 49843 70793 78027 57616 65308 63884 59187 TRUE FALSE 60702.55865 68839.85549 60710.99275 59701.79663 58759.63115 59906.41176 53099.90737 64432.65308 61584.82732 70783.55945 0.857579912 0.972540178 0.857699065 0.843441572 0.830131059 0.846332287 0.75017289 0.910277098 0.870044228 1 16.11112669 0.593217611 1.504802896 0.999705198 0.85701937 0.387088462 0.053333962 1.816751963 5.417690921 0.052200936 0.01512265 3.919382154 -0.593217611 -0.142685828 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 MLAESDES(1)GDEESVSQTDKTELQNTLR;MLAESDES(1)GDEESVSQTDKTELQNTLR 248.4 6.32E-46 291370000 122446 113146 125706 99235 154800 165212 138779 129403 139200 114805 TRUE FALSE 127280.2626 132577.9453 128982.0016 118863.3868 128487.1513 126844.0168 127901.1393 127668.5644 134190.2192 137298.8417 0.927030855 0.965615906 0.939425272 0.865727528 0.935821087 0.92385351 0.931552938 0.929859006 0.977358713 1 17.06695993 1.134931785 2.81845983 0.999741966 0.926809252 0.531385937 0.023502972 0.195148462 2.854268885 0.022719715 0.006177948 13.64368817 -1.134931785 -0.072932714 MLDAEDIVGTARPDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLDAEDIVGTARPDEK 16 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;G3V2N5;G3V2W4 P12814-3 ACTN1 Alpha-actinin-1 0 ; 187 1.29E-09 409658000 512480 383848 440260 449280 708920 635580 679050 477070 487440 482760 FALSE TRUE 532713.1061 449770.9081 451733.5373 538146.243 588418.0316 487976.1773 625824.2866 470675.657 469897.1296 577347.579 0.922690465 0.779029694 0.782429084 0.932100978 1.019174676 0.84520347 1.083964512 0.81523795 0.813889495 1 19.1390806 3.725993625 23.8386851 0.925274355 0.823147744 0.204233826 0.091689407 625.9786702 1187437.572 0.024156343 0.037736711 5321.004486 -3.725993625 -0.102126612 MLDAEDIVNTARPDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MLDAEDIVNTARPDEK 16 1 O43707 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 265.77 3.65E-27 1995550000 1743264 1379346 1522497 1675916 3481960 2687843 3006308 1691948 1863329 2470375 FALSE TRUE 1812089.409 1616237.946 1562174.523 2007407.183 2890097.683 2063632.198 2770665.723 1669270.205 1796268.153 2954397.683 0.613353246 0.547061743 0.528762438 0.679464107 0.978235834 0.698495064 0.937810688 0.565012021 0.607998092 1 21.49443261 3.480189751 24.97482669 0.772420674 0.568568355 0.348969805 0.141801604 152.0061065 1237198.242 0.039548775 0.054601551 3021.27148 -3.480189751 -0.203852319 MLDEMKDNLLLDMYLAPHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLDEMKDNLLLDMYLAPHVR 20 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;Q13098-6 Q13098-7 GPS1 COP9 signalosome complex subunit 1 0 ; 205.62 5.08E-22 246840000 439850 363020 504010 433820 569300 593990 567490 509500 548900 361360 FALSE TRUE 457215.6176 425365.8611 517144.9146 519628.3012 472530.5893 456044.8245 523008.6509 502670.9859 529145.1962 432161.5733 1.05797379 0.984275066 1.196647149 1.20239358 1.093411859 1.055264634 1.210215538 1.163155211 1.224415193 1 18.72121127 4.241102484 24.99999813 1.150359699 1.021124406 0.311877005 0.071896215 68.34487613 672152.2508 0.017129351 0.042680163 17422.1795 -4.241102484 -0.129235293 MLDEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLDEQK 6 0 H3BV99 H3BV99 SNAP23 Synaptosomal-associated protein 0 ; 95.445 0.032873 1965640000 49557 1887900 694020 1466430 281053 1182520 324472 700750 410490 3508290 FALSE TRUE 51513.54863 2212132.139 712106.7313 1756485.477 233279.7114 907897.6513 299039.0368 691357.5924 395716.5451 4195672.255 0.012277782 0.527241406 0.169724108 0.418642203 0.05560008 0.216389078 0.071273212 0.164778741 0.094315409 1 22.00047056 -1.297603324 3.747929857 1.001864594 0.197143878 0.709088808 0.15518468 351575826.4 580285073.9 7432782.107 0.035386644 0.050396071 1.297603324 -0.804720716 MLDHEYTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLDHEYTTK 9 0 P11387;E5RJ33;H0YBR3;H0YC03;E5RGE7;E5RGR4;E5RFE3;E5RGR2;E5RJ95;E5RFS0;E5RIC7;Q969P6-2;Q969P6 P11387;Q969P6-2 TOP1;TOP1MT "DNA topoisomerase 1;DNA topoisomerase I, mitochondrial" 0 ; 147.2 9.30E-05 271710000 813550 956880 1067860 952020 1059250 1056740 1089280 934180 1017750 932160 FALSE TRUE 845669.5822 1121216.697 1095689.309 1140326.715 879199.0634 811328.15 1003899.387 921658.8451 981121.3763 1114798.905 0.75858487 1.005756905 0.982858257 1.022899027 0.788661578 0.727779823 0.900520608 0.826748969 0.880088213 1 20.08835206 4.786809329 22.31873034 0.892523287 0.758582552 0.162422354 0.095918639 21382.71558 9890125.244 0.024452458 13.91678905 61208.16064 -4.786809329 -0.133940735 MLDLLEDFLEHEGYKYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLDLLEDFLEHEGYKYER 18 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 ; 245.66 1.89E-24 513510000 776250 757720 888540 648080 1018100 960050 897490 801510 974480 681180 FALSE TRUE 806896.9494 887852.5158 911696.0823 776268.2897 845043.7257 737092.9372 827142.3886 790767.0695 939408.6552 814644.179 0.990490045 1.089865414 1.119134103 0.952892453 1.037316349 0.90480354 1.015341925 0.970690137 1.153152111 1 19.63581053 5.13443307 11.19362931 1.021495958 0.000216431 0.017114794 0.072935565 1312415.444 1677893.331 0.017224163 32984315.12 136280.2964 -5.13443307 -1.021279527 MLDMGFEPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 112.75 0.0034531 57470000 54264 116310 104390 103010 95590 125670 84832 103100 90959 121690 FALSE TRUE 56406.38462 136285.3377 107110.4892 123385.0705 79341.64594 96485.04705 78182.64617 101718.1131 87685.40336 145532.8256 0.387585305 0.936457718 0.735988522 0.847816086 0.545180413 0.6629779 0.537216575 0.698935877 0.60251289 1 17.15098507 -1.081029387 9.196032847 1.000000001 0.670711085 0.312090721 0.150164901 3.77E-09 3.33E-10 0.136884865 0.032264072 0.082979462 1.081029387 -0.329288916 MLDQTLLDLNEM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLDQTLLDLNEM 12 0 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 94.767 0.0043135 0 28764 42556 33335 42228 42413 46862 40963 38667 37565 49772 FALSE TRUE 29899.62493 49864.66196 34203.73749 50580.57236 35203.65341 35979.0107 37752.21302 38148.73211 36213.04299 59523.87046 0.502313185 0.837725463 0.574622202 0.849752746 0.591420772 0.604446761 0.63423653 0.640898043 0.608378499 1 15.86118072 -1.979109086 2.826466714 1.302037618 0.653970846 0.500209713 0.105069841 30381820.44 9890263.034 59837388.83 0.02299387 0.010492788 1.979109086 -0.648066773 MLEDRDLFVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLEDRDLFVMR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 151.1 3.06E-05 184169000 113431 166440 143805 120295 190556 193623 130607 135600 146472 231176 FALSE TRUE 117909.3435 195024.7753 147552.6764 144088.992 158165.3592 148656.9926 120369.6821 133782.5038 141200.5013 276470.5111 0.426480723 0.705408959 0.533701319 0.521173095 0.572087629 0.537695655 0.435379823 0.483894298 0.51072536 1 18.07676608 -1.444575924 3.023379414 1.00992834 0.525347574 0.787828576 0.073923918 20574194.26 25077290.58 1741304.148 0.017617594 0.035927258 1.444575924 -0.484580766 MLEQLDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 132.76 0.0022067 414107000 743220 889310 834700 946540 1071590 1126880 1058250 921910 779360 923770 FALSE TRUE 772562.8995 1042042.075 856452.9677 1133762.787 889441.5146 865179.198 975301.5998 909553.3044 751310.9858 1104765.045 0.699300637 0.943225059 0.775235397 1.026247882 0.805095634 0.783134117 0.882813594 0.82330022 0.680064046 1 20.07530815 MLEVHFVGDDDVLNHILDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLEVHFVGDDDVLNHILDR 19 0 Q13416;C9JK08;B8ZZ80 Q13416 ORC2 Origin recognition complex subunit 2 0 ; 175.21 1.74E-12 36181000 31893.5 21995.9 24771.2 23856.1 27462.6 29101 24631.8 20120.5 22679.2 31194 FALSE TRUE 33152.68001 25773.52472 25416.75782 28574.76538 22794.51706 22342.73378 22701.09515 19850.81761 21862.98002 37305.86705 0.888672014 0.690870545 0.681307253 0.76595902 0.611016949 0.598906701 0.608512734 0.532109804 0.586046693 1 15.18711492 8 0.676001574 0.631283498 26.78183766 0.160634873 0.128892526 347.1430524 2.014117875 0.045724389 13661.45047 100000000 -8 26.15055417 MLGEDS(ph)DEEEEMDTSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 318.09 8.60E-58 1107020000 752560 921180 923080 857170 1010260 1136990 1040170 973790 919730 866470 TRUE FALSE 782271.6499 1079385.499 947136.2231 1026715.668 838536.3661 872941.3038 958638.7574 960737.9378 886629.097 1036238.207 0.754914888 1.041638392 0.914013995 0.990810473 0.809211975 0.84241374 0.925114275 0.927140045 0.855622859 1 19.98292425 -0.941516766 3.942381698 1.000006313 0.90239589 0.126760341 0.080429133 1.04112E+11 2.46246E+11 10127925.57 0.018311102 0.114415071 0.941516766 -0.097610422 MLHDYIGDKDFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLHDYIGDKDFKK 13 2 E9PLK3;P55786;P55786-2;A6NEC2;A6NEC2-2;E9PJ74;E9PRQ5 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ; 130.07 8.79E-05 1404010000 1504540 1481310 1728960 1489120 2198760 2166820 1622250 1734270 1912240 1611530 FALSE TRUE 1563940.401 1735713.47 1774018.118 1783663.491 1825015.561 1663608.893 1495093.806 1711024.947 1843418.856 1927278.449 0.811476101 0.900603372 0.920478366 0.925483026 0.946939225 0.863190731 0.775753917 0.887793328 0.956488076 1 20.87813359 1.114888931 3.494900019 0.997103803 0.879444197 0.405063588 0.049525124 0.233042122 5.125335002 0.050374128 0.013230002 13.02833541 -1.114888931 -0.117659607 MLISAVS(ph)PEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MLISAVSPEIR 11 0 A0AVK6;E9PMT9 A0AVK6 E2F8 Transcription factor E2F8 1 MLISAVS(1)PEIR;MLISAVS(1)PEIR;MLIS(0.001)AVS(0.999)PEIR;MLISAVS(1)PEIR 211.22 1.06E-08 319098000 343519 403880 404800 387174 415876 500730 408245 410579 399539 473599 TRUE FALSE 357081.3954 473243.2482 415349.4205 463755.8616 345185.5461 384443.0461 376245.6902 405075.8601 385159.6694 566391.6564 0.630449604 0.835540642 0.733325457 0.818790066 0.609446736 0.678758315 0.664285368 0.715186842 0.680023558 1 19.11144049 -1.877099495 6.054859669 1.052281657 0.709935448 0.613333251 0.069690249 0.037132596 0.000753711 0.05094319 0.015571115 0.013270904 1.877099495 -0.342346209 MLITILGTVKPNANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLITILGTVKPNANR 15 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ; 160.65 1.55E-06 186926000 284720 288780 294190 278100 301150 356610 293360 282940 287820 368900 FALSE TRUE 295960.9655 338375.7186 301856.8331 333107.35 249960.6306 273792.732 270365.6766 279147.6521 277461.4144 441178.892 0.670841173 0.766980753 0.684205066 0.755039183 0.56657432 0.620593453 0.612825504 0.632731205 0.628909088 1 18.75100424 -1.272397612 5.769392053 1.000021647 0.658626619 0.746204474 0.059507182 1.76E-05 2.22E-06 0.06124325 0.014434258 0.053407517 1.272397612 -0.341395029 MLKPAFIFDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLKPAFIFDGR 11 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 105.17 0.0022815 1643220000 3091800 3268300 3182500 3157100 5629600 4860800 4238400 3568200 3615000 5097300 FALSE TRUE 3213866.651 3829605.101 3265438.564 3781564.957 4672682.603 3731952.866 3906183.133 3520374.115 3484896.856 6096018.341 0.52720751 0.62821417 0.535667444 0.620333592 0.766513869 0.612195151 0.640776145 0.577487455 0.571667712 1 22.53943581 -1.486397227 3.189925625 1.008915491 0.611333228 0.77116127 0.063903028 87636868.53 107673412.5 6890639.612 0.015636212 0.032628926 1.486397227 -0.397582263 MLLVDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLLVDELR 8 0 P18085;C9JPM4;C9JAK5;U3KQF2 P18085 ARF4 ADP-ribosylation factor 4 0 ; 133.12 0.002171 294180000 297880 477430 431720 487300 409550 533680 439320 493190 419200 501860 FALSE TRUE 309640.5324 559424.8886 442970.9779 583686.4856 339934.8373 409740.908 404884.9505 486579.5947 404113.0739 600189.8583 0.515904306 0.932079876 0.738051421 0.97250308 0.566378843 0.682685491 0.674594788 0.810709458 0.673308734 1 19.19505942 -1.660230233 4.01144484 1.011285353 0.739694792 0.256327463 0.137212712 0.013328902 0.001128959 0.127868222 0.029201203 0.021866021 1.660230233 -0.271590561 MLLYTEVTR ddPTM_MDA-MB-175_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 ; 138.54 0.00031079 356850000 575480 508750 537930 451230 721700 667420 576100 556320 587760 586810 FALSE TRUE 598200.3948 596123.855 551948.8977 540481.9472 599025.6918 512421.8198 530943.7766 548863.4404 566606.6324 701784.1843 0.852399367 0.849440424 0.786493783 0.770154072 0.853575366 0.730170088 0.756562756 0.782097193 0.807380168 1 19.42066791 0.919381324 14.78262677 1 0.794999193 0.692262206 0.040281574 104.7128357 19201.69652 0.040124675 0.01003155 8.305797214 -0.919381324 -0.205000807 MLMGLDLLVFAHDHVGHGQSEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLMGLDLLVFAHDHVGHGQSEGER 24 0 A0A0C4DFN3;Q99685-2;Q99685;A0A3B3ITT3;C9J8Q3 A0A0C4DFN3 MGLL Monoglyceride lipase 0 108.08 0.00083193 9954000 6090.1 6804.4 6489.7 7753.7 8515.4 8023.1 6780.1 7775.8 8311.7 8463 FALSE TRUE 6330.541851 7973.002769 6658.826913 9287.358718 7067.95535 6159.856616 6248.658046 7671.57812 8012.563541 10121.16282 0.625475745 0.787755608 0.657911253 0.917617757 0.69833432 0.608611553 0.617385389 0.757973986 0.791664326 1 13.30508743 0.834734254 1.831579148 0.999091319 0.708945966 0.496673228 0.089153179 0.514486753 3.214465596 0.085380894 0.024036741 6.83493288 -0.834734254 -0.290145353 MLMRRDQVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MLMRRDQVLK 10 2 F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 F8VYC4 RGPD1;RGPD2 RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 0 ;;;;; 64.297 0.042062 5870320000 10950690 7198950 9718000 6494590 13147130 11595840 10069420 9709720 11037050 7530720 FALSE TRUE 11383031.7 8435313.662 9971259.063 7779200.518 10912385.54 8902881.897 9280152.549 9579577.085 10639828.73 9006220.4 1.263907743 0.936609731 1.107152459 0.863758622 1.211649844 0.988525875 1.030415883 1.063662298 1.18138667 1 23.10249035 1.450299472 17.01776384 1.101302787 1.050606762 0.008095956 0.119780861 5.164204647 3275.4765 0.059340819 0.027231222 28.20327043 -1.450299472 -0.050696024 MLPDKDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 MLPDKDCR 8 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;;;;;;;;;;;;;;; 107.66 0.0041551 64745930000 95473780 94841260 93161210 80848640 143312250 131732340 104811000 96738620 98761970 118021910 FALSE TRUE 99243158.56 111129508.6 95589067.67 96840259.68 118952084.9 101139500.5 96595639.95 95441997.03 95207545.99 141146043.6 0.703123914 0.787337043 0.67723519 0.686099711 0.842758903 0.716559231 0.684366614 0.676193215 0.674532162 1 27.07261345 -1.919623631 2.667035908 1.17342771 0.715878916 0.720788598 0.052939231 16210175.76 10481762.9 17599587.13 0.01294167 0.012033068 1.919623631 -0.457548794 MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 26 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 262.71 6.02E-60 25134814000 6648451 3527196 4620841 3331399 6019069 7293426 5518710 4580605 5055631 3217682 TRUE FALSE 6910936.979 4132964.475 4741263.913 3990339.779 4995949.801 5599638.344 5086139.09 4519209.482 4873679.828 3848125.182 1.795923119 1.074020277 1.232097109 1.036956853 1.298281518 1.455160131 1.32171872 1.174392534 1.26650761 1 21.8757243 -4.999999998 0.158523122 9.22E-09 1.353942419 0.182640409 0.200199781 257.4954867 2.358185252 81.44120371 0.851203723 1.00E-05 4.999999998 1.35394241 MLPHAPGVQMQAIPEDAVHEDS(ph)GDEDGEDPDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 33 MLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKR 33 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 1 MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR;MLPHAPGVQMQAIPEDAVHEDS(1)GDEDGEDPDKR 367.39 2.05E-148 52498935000 11602875.3 6309138 8767981 6365720.9 11034912 11136745 10003195.4 8564880 9631774.8 6223149.8 TRUE FALSE 12060965.78 7392683.373 8996481.788 7624841.494 9159201.6 8550404.753 9219118.806 8450081.793 9285129.106 7442456.854 1.620562405 0.993312224 1.208805367 1.024505972 1.230669089 1.148868569 1.238719819 1.135388751 1.247589242 1 22.82734752 7.999999997 0.018526377 3.36E-05 2.662255762 0.156137471 0.159020573 8237.845608 11.76648912 640.7158777 1109.456327 99999999.26 -7.999999997 2.662222122 MLQEDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLQEDELR 8 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ; 118.5 0.0043634 274070000 212707 343090 340620 357650 347170 430820 377840 361940 334180 351100 FALSE TRUE 221104.8366 402013.0386 349496.837 428392.1025 288158.1674 330768.5841 348223.9135 357088.7863 322152.9271 419891.3228 0.526576342 0.957421639 0.832350701 1.02024519 0.68626845 0.787748082 0.829319147 0.85043145 0.767229303 1 18.67965645 -2.362578921 2.181511618 2.128484752 0.81741284 0.163188497 0.129376066 6408989.767 493210.8661 35944048.42 0.029329692 0.004339314 2.362578921 -1.311071912 MLQEDELRDAVLLVFANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MLQEDELRDAVLLVFANK 18 1 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ;; 259.38 9.79E-31 951390000 735800 686059 819550 558359 1013540 894451 737041 761612 920160 826657 FALSE TRUE 764849.9522 803884.2965 840908.1463 668800.7437 841258.8328 686728.3108 679269.8005 751403.8369 887043.6213 988624.6118 0.773650527 0.813134011 0.850583868 0.67649615 0.85093859 0.694629997 0.687085667 0.760049697 0.897250191 1 19.9150633 1.057983079 3.237162317 0.997935557 0.761576632 0.623530254 0.06017321 0.137196598 3.000560037 0.057535417 0.015106673 11.42833807 -1.057983079 -0.236358924 MLQHAASNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLQHAASNK 9 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 139.74 0.00011076 1623090000 4094900 3912300 4238200 3457800 8900300 6767500 5967400 5061400 5271700 7534200 FALSE TRUE 4256569.814 4584207.092 4348650.974 4141742.519 7387430.185 5195850.687 5499659.595 4993560.212 5081972.547 9010382.239 0.472407241 0.508769436 0.482626692 0.459663354 0.819879777 0.576651528 0.610369177 0.554200708 0.564012981 1 23.10315688 -5 0.223647241 3.240722415 0.509714951 0.660014255 0.095851145 98.65693489 0.987484356 99.91266713 0.182474993 1.00E-05 5 -2.731007464 MLQHIDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 121.96 0.0014111 2377310000 1598435 1610221 1537075 1404126 2499060 2196003 1661226 1477171 1515171 2735790 FALSE TRUE 1661542.448 1886763.931 1577132.437 1681857.932 2074270.674 1686014.584 1531014.765 1457371.939 1460640.292 3271815.671 0.507834981 0.57667183 0.482035847 0.514044219 0.633981521 0.515314661 0.46794041 0.445432165 0.446431107 1 21.64166004 -1.20597091 4.169877708 1.00024016 0.508516648 0.875801294 0.055358581 34.06060463 33639771.33 14770.92066 0.014167189 0.062234197 1.20597091 -0.491723512 MLRDQS(ph)AVVVQGLPEGVAFQHPENYDLATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLRDQSAVVVQGLPEGVAFQHPENYDLATLK 31 1 A0A087WW90;A0A0D9SF80;A0A494C0I1;A0A494C1N8;Q86UP8-3;Q86UP8;Q6EKJ0;Q86UP8-2;Q6EKJ0-2;Q86UP8-5 A0A087WW90 GTF2IRD2B;GTF2IRD2 General transcription factor II-I repeat domain-containing protein 2A;General transcription factor II-I repeat domain-containing protein 2B 1 MLRDQS(0.848)AVVVQGLPEGVAFQHPENY(0.151)DLATLK 50.144 0.048588 30223000 2240.8 5430.4 4625.6 5423.9 3896.5 5984 2942.8 3669.1 2842.1 9333.7 TRUE FALSE 2329.268514 6363.028957 4746.146936 6496.731231 3234.174322 4594.306688 2712.135646 3619.921716 2739.813376 11162.45981 0.208669823 0.570038241 0.425188266 0.582016092 0.289736705 0.411585508 0.242969354 0.324294266 0.245448891 1 13.44636736 -1.345503787 3.590713227 1.002804768 0.370933221 0.69814888 0.124905385 280373761.2 433022776.2 8344940.19 0.030003452 0.045133209 1.345503787 -0.631871547 MLRPVS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MLRPVSR 7 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 MLRPVS(1)R;MLRPVS(1)R;MLRPVS(1)R;MLRPVS(1)R 64.841 0.043728 1555740000 543780 732050 812740 686270 1090960 860180 691590 810180 797460 971760 TRUE FALSE 565248.8543 857773.8929 833920.6721 822012.1577 905519.0089 660416.2312 637381.3687 799320.8623 768759.5704 1162157.767 0.486378761 0.738087304 0.717562362 0.707315462 0.779170466 0.568267278 0.548446508 0.68779032 0.661493295 1 20.1483745 0.207227962 2.091183999 1.000006911 0.658715618 0.580009199 0.08804071 22.4298155 57.58326369 0.084397164 0.023012475 1.611491289 -0.207227962 -0.341291293 MLS(ph)EEEKEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLSEEEKEELK 11 1 Q16890-5;E9PNQ9;Q16890-4 Q16890-5 TPD52L1 Tumor protein D53 1 MLS(1)EEEKEELK 78.653 0.036919 678120000 7863.1 336910 213170 330000 130800 360940 134790 268500 156090 403810 TRUE FALSE 8173.54126 394771.6717 218725.3853 395273.015 108566.6627 277117.1551 124224.8076 264901.1967 150472.3514 482928.8381 0.016924939 0.817453092 0.452914318 0.818491222 0.224808821 0.573826066 0.257232117 0.548530499 0.311582866 1 18.88145109 -1.326909355 4.185193953 1.000816116 0.464165549 0.314964623 0.243525555 70325280.87 22298497.94 525202.4667 0.051214796 0.047107564 1.326909355 -0.536650567 MLSGGFGYSPFLSITDGNMPGTRPAS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLSGGFGYSPFLSITDGNMPGTRPASR 27 1 Q15773;F5H7L5;F5H800;F5H0Y3 Q15773 MLF2 Myeloid leukemia factor 2 1 MLSGGFGYSPFLS(0.004)IT(0.016)DGNMPGT(0.175)RPAS(0.804)R 66.454 0.014918 469140000 79871 64715 65333 58395 92852 101900 81516 69742 83402 56424 TRUE FALSE 83024.36875 75829.29784 67035.63165 69945.35671 77069.05021 78235.26931 75126.56292 68807.22256 80400.37831 67479.2025 1.230369739 1.123743243 0.993426555 1.036546878 1.142115605 1.15939825 1.113329146 1.019680435 1.191483825 1 16.0421553 -2.372523143 2.336372122 0.236496762 1.10290851 0.166905112 0.072580985 3867025.386 945682.1587 15704275.41 0.018560639 0.004241084 2.372523143 0.866411748 MLSS(ph)TPPTPIACAPSAVNQAAPHQQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLSSTPPTPIACAPSAVNQAAPHQQNR 27 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 MLS(0.089)S(0.495)T(0.402)PPT(0.014)PIACAPSAVNQAAPHQQNR 131.26 3.87E-05 164300000 64668 77751 62169 75305 72150 84123 73141 74268 73207 74553 TRUE FALSE 67221.14257 91104.12943 63789.17521 90200.10424 59885.96877 64586.70815 67408.0173 73272.55894 70572.29437 89160.23295 0.753936372 1.021802281 0.715444241 1.011662949 0.671666805 0.724389181 0.756032315 0.821807621 0.791522095 1 16.44411277 MLSST(ph)PPTPIACAPSAVNQAAPHQQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLSSTPPTPIACAPSAVNQAAPHQQNR 27 0 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 1 MLS(0.015)S(0.083)T(0.451)PPT(0.451)PIACAPSAVNQAAPHQQNR 159.2 5.52E-11 234360000 39244 47648 40599 42735 32972 46677 36188 43828 42245 44802 TRUE FALSE 40793.38342 55831.17335 41657.04329 51187.85545 27367.43122 35836.97415 33351.49 43240.55735 40724.6107 53580.09411 0.761353336 1.04201335 0.77747238 0.9553521 0.510776095 0.66884866 0.622460459 0.807026528 0.760069787 1 15.70940949 3.275752841 24.99998566 0.714892733 0.887718556 0.22177261 0.141649897 226.2939489 152109.5195 0.037258624 0.050447104 1886.917189 -3.275752841 0.172825823 MLTEAIMHDCVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MLTEAIMHDCVVK 13 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 0 123.64 0.00022107 389440000 334730 299390 347920 297010 430400 449340 366650 374230 358940 278710 FALSE TRUE 347945.3989 350807.9036 356987.081 355757.6915 357240.7617 344987.5948 337911.0149 369214.059 346021.8195 333317.8883 1.043884565 1.052472477 1.071010869 1.067322529 1.071771946 1.035010742 1.013780018 1.107693502 1.03811356 1 18.34653922 2.748153172 24.22251364 1.048538736 1.06167739 0.089897829 0.028244205 1660.029033 4191779.162 0.009043844 0.009455214 559.9550579 -2.748153172 0.013138654 MLVLVLGDLHIPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ; 90.731 0.0032592 138251000 40620 42443 44397 39453 52966 53698 53493 45359 43265 50408 FALSE TRUE 42223.70897 49732.25509 45554.02229 47256.68564 43962.85824 41227.4533 49300.07888 44751.0368 41707.9011 60284.48248 0.700407588 0.824959476 0.755650881 0.783894689 0.729256625 0.683881682 0.81779053 0.742330944 0.691851359 1 15.87949907 -1.647717964 6.294398189 1.001506975 0.751395218 0.720449291 0.047084954 0.000953649 5.34E-05 0.043662882 0.010234317 0.022505156 1.647717964 -0.250111758 MLVTFDEELRPLPVSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MLVTFDEELRPLPVSVR 17 1 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 216.19 4.90E-15 995710000 427410 523310 488610 475840 512930 567540 560210 504310 455940 563830 FALSE TRUE 444284.4768 613184.4217 501343.578 569959.7318 425742.3418 435737.4362 516299.2764 497550.5493 439530.8085 674301.6933 0.658880856 0.909362126 0.743500399 0.845259232 0.631382578 0.64620546 0.765679934 0.737875278 0.651831091 1 19.3630347 -1.133691949 4.245738175 1.000047678 0.737190244 0.461426382 0.086640667 12006237.12 3205892.715 6120.058002 0.019923996 0.073503505 1.133691949 -0.262857434 MLWGSDPYPHAEPQQAT(ph)TPK ddPTM_MDA-MB-175_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(0.599)T(0.401)PK 146.5 4.88E-07 515440000 331460 180700 250670 207850 325670 324290 310910 248600 270760 192550 TRUE FALSE 344546.2967 211733.8193 257202.6661 248962.1096 270312.7297 248978.5622 286540.0618 245267.9236 261015.4005 230276.4859 1.496228742 0.919476509 1.116929786 1.081144298 1.173861624 1.081215745 1.24433053 1.065101904 1.133486988 1 17.81300758 6.514693159 0.014722532 5.97E-06 2.412068302 0.120589888 0.138931186 12033.34795 17.76756644 1228.333748 1718.675356 3271095.017 -6.514693159 2.412062336 MLWGSDPYPHAEPQQATT(ph)PK ddPTM_MDA-MB-175_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(0.226)T(0.774)PK;MLWGSDPYPHAEPQQAT(0.19)T(0.81)PK;MLWGSDPYPHAEPQQAT(0.016)T(0.984)PK 184.45 1.47E-16 688200000 643713 341599 443829 328364 629582 646660 545816 483721 559908 376774 TRUE FALSE 669127.2863 400265.971 455395.5483 393313.4191 522565.8765 496483.0152 503033.5157 477237.5112 539757.0205 450595.6515 1.484983896 0.888304114 1.010652337 0.872874423 1.159722414 1.101837121 1.116374546 1.059125869 1.197874455 1 18.78147387 MMLDQCLELQLFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MMLDQCLELQLFHR 14 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 204.35 1.38E-08 410990000 309520 410820 378680 389150 444500 525240 395730 372270 418950 487100 FALSE TRUE 321740.0886 481375.1393 388548.7119 466122.7085 368944.0488 403260.9701 364711.6486 367280.3296 403872.0713 582537.9189 0.552307546 0.826341297 0.666992996 0.800158571 0.633339113 0.692248448 0.626073663 0.630483128 0.69329748 1 19.15199244 -1.986896122 2.35029541 1.297615303 0.680503481 0.604699672 0.077584462 5532015.799 2295921.359 8930675.529 0.017734584 0.010306326 1.986896122 -0.617111823 MMNGGHYTYSENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 MMNGGHYTYSENR 13 0 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;;;; 164.53 3.35E-05 1892751000 658085.2 1209800 1056697 1316662 1416807 1630914 1319505 1224659 1053211.5 1351728 FALSE TRUE 684066.9118 1417573.739 1084235.392 1577093.814 1175978.652 1252158.94 1216078.75 1208244.449 1015306.624 1616573.221 0.423158631 0.876900422 0.670699834 0.975578336 0.727451523 0.774576075 0.752257141 0.747410902 0.628061019 1 20.62450742 -2.4950391 2.107745113 3.839529223 0.743066691 0.247656917 0.139326095 3495085.11 253899.1817 47464679.85 0.032827837 0.003198607 2.4950391 -3.096462532 MMNGGHYTYSENRVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 MMNGGHYTYSENRVEK 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ;;;;;; 131.72 2.58E-05 1239663000 923110 1443484 1682094 1387918 1993280 2092370 1636824 1751847 1835742 1720766 FALSE TRUE 959555.0956 1691391.148 1725930.751 1662444.038 1654462.978 1606448.778 1508525.458 1728366.356 1769674.004 2057917.152 0.466274891 0.821894675 0.838678442 0.807828457 0.803950235 0.780618781 0.733035077 0.839861972 0.859934523 1 20.97275347 5.865551005 0.056860948 1.315417219 1.15E-16 0.476902532 0.092405848 253.0201386 1.657769118 10.71706775 32.65907811 733754.8836 -5.865551005 -1.315417219 MMYGVSPWGDSPIDFEDSAHVPCPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MMYGVSPWGDSPIDFEDSAHVPCPR 25 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 76.049 7.08E-05 0 24620 22616 26160 27820 30899 31123 21884 26431 23731 24053 FALSE TRUE 25592.01661 26500.12207 26841.75109 33322.71297 25646.79902 23895.15492 20168.6749 26076.73568 22876.92595 28765.72483 0.889670494 0.921239504 0.933115757 1.158417289 0.891574927 0.830681482 0.70113564 0.906521071 0.795284182 1 14.8120632 3.00754133 24.99966698 0.837056467 0.975729789 0.273465307 0.098591092 222.760428 738448.207 0.02820117 0.033646724 1017.516195 -3.00754133 0.138673323 MNDFHIS(ph)DDEEKNPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MNDFHISDDEEKNPSK 16 1 E7ETZ8;Q49MG5;A0A0C4DG83;A2VCS9;Q49MG5-2;A8MSM7 E7ETZ8 MAP9 Microtubule-associated protein 9 1 MNDFHIS(1)DDEEKNPSK;MNDFHIS(1)DDEEKNPSK;MNDFHIS(1)DDEEKNPSK 195.39 3.59E-11 775271000 2301610 808320 1213680 778207 1925810 1762120 1772600 1211240 1423680 609848 TRUE FALSE 2392479.34 947142.6721 1245309.498 932134.0219 1598461.504 1352894.335 1633658.98 1195005.309 1372442.035 729336.0394 3.280352555 1.298636871 1.707456413 1.278058359 2.191666691 1.854967069 2.239926306 1.638483833 1.881769117 1 19.47622416 -2.103332503 0.378587324 3.69E-10 1.924546911 0.211472275 0.542528349 75.1171065 4.125682973 65.21505458 0.350992373 0.007882564 2.103332503 1.924546911 MNEEHNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MNEEHNKR 8 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9;G3V200;O75334-2;O75334-4;O75334-3;O75334;O75334-5;O75334-6;F8VYK7;F8W1Y8;O75334-7;H0YHK3;F8VWG6 Q13136-2 PPFIA1;PPFIA2 Liprin-alpha-1;Liprin-alpha-2 0 ;; 105.78 0.0020624 40468700 31632.5 29940.3 35389.5 28442.2 39954.5 38857.3 36274.5 35807.2 30102.4 29473.6 FALSE TRUE 32881.37553 35082.31362 36311.77944 34067.98227 33163.04836 29833.28096 33431.2099 35327.26305 29019.0205 35248.38761 0.932847649 0.995288466 1.030168524 0.966511792 0.940838734 0.846372926 0.948446501 1.002237703 0.823272282 1 15.10526964 3.319688921 3.645551042 0.929647301 0.98817957 0.176810383 0.0581937 0.420533372 10.94791992 0.016952461 0.023137965 2087.800131 -3.319688921 0.058532269 MNESDIWFEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNESDIWFEEK 11 0 Q13596-2;Q13596;H0YK42;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 0 84.479 0.037062 41181000 56756 53815 59289 56079 83669 79067 58453 66389 65545 55615 FALSE TRUE 58996.77071 63057.30763 60834.12005 67171.25882 69446.97327 60704.88752 53871.30112 65499.16405 63186.04825 66511.69444 0.887013497 0.948063467 0.914637953 1.009916518 1.04413177 0.912694948 0.809952319 0.984776656 0.949999076 1 16.0213204 3.535375839 0.004772192 1.879838139 1.13E-07 0.049273995 0.063367931 95786.97897 112.1286539 21605.63114 22565.94684 3430.645468 -3.535375839 -1.879838026 MNGFIDQIDGIVHFETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MNGFIDQIDGIVHFETR 17 0 D6RFN0;Q9BT78;D6RD63 D6RFN0 COPS4 COP9 signalosome complex subunit 4 0 ;;; 175.39 1.24E-09 365731000 424358.6 504965 521730.1 513728 614235 684643 569589 559542.8 588766 534621 FALSE TRUE 441112.6052 591688.8107 535326.815 615341.8651 509827.5541 525645.0391 524943.1258 552043.044 567576.4267 639369.749 0.689917854 0.925425095 0.837272667 0.962419423 0.797390798 0.82212998 0.82103216 0.863417521 0.887712357 1 19.28629096 0.795797556 1.626404277 0.999714272 0.843176636 0.332017287 0.069090957 0.820641486 3.842031497 0.061498402 0.017665621 6.248813399 -0.795797556 -0.156537636 MNGVMFPGNS(ph)PSYTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 MNGVMFPGNS(0.979)PS(0.021)YTER;MNGVMFPGNS(0.987)PS(0.013)YTER;MNGVMFPGNS(0.976)PS(0.024)YTER;MNGVMFPGNS(0.966)PS(0.033)YT(0.001)ER;MNGVMFPGNS(0.976)PS(0.024)YTER;MNGVMFPGNS(1)PSYTER;MNGVMFPGNS(0.998)PS(0.002)YTER;MNGVMFPGNS(0.998)PS(0.002)YTER;MNGVMFPGNS(0.998)PS(0.002)YTER;MNGVMFPGNS(0.5)PS(0.5)YTER;MNGVMFPGNS(1)PSYTER 454.58 1.13E-182 3458910000 2923130 3491740 3394640 3422540 3726660 4194930 3543600 3555540 3344180 3450780 TRUE FALSE 3038537.43 4091419.183 3483107.107 4099508.197 3093203.664 3220721.082 3265843.373 3507883.802 3223823.615 4126894.272 0.736277023 0.991403926 0.844002021 0.993363999 0.749523361 0.780422485 0.791356201 0.850005736 0.781174269 1 21.97662505 5.032463713 16.30448542 0.854189237 0.337463488 0.139697814 0.092333743 8836647.57 122257398.1 0.021353369 128667714.4 107761.521 -5.032463713 -0.516725749 MNLAIS(ph)IALLLT(ph)VLQVS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MNLAISIALLLTVLQVSR 18 0 E9PIM6;E9PNQ8;P04216 E9PIM6 THY1 Thy-1 membrane glycoprotein 3 MNLAIS(1)IALLLT(1)VLQVS(1)R;MNLAIS(1)IALLLT(1)VLQVS(1)R 56.851 0.042842 54056000 10468.6 30524 20818.9 32177 16030.8 32553 19391.4 22161.3 16250.7 34740 TRUE FALSE 10881.90841 35766.25956 21361.45764 38541.51456 13305.89034 24993.0591 17871.4514 21864.26402 15665.84048 41546.63786 0.261920313 0.86087013 0.514156108 0.927668677 0.32026395 0.601566345 0.430153974 0.526258324 0.377066383 1 15.34244411 -1.618021947 5.96999869 1.002381963 0.545699294 0.313621593 0.205637229 0.006023473 0.0003854 0.183959419 0.043179898 0.024097836 1.618021947 -0.456682668 MNLRSVFT(ph)VEQQRILQRY(ph)YENGMT(ph)NQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNLRSVFTVEQQRILQRYYENGMTNQSK 28 3 Q7Z353 Q7Z353 HDX Highly divergent homeobox 3 MNLRS(0.183)VFT(0.913)VEQQRILQRY(0.457)Y(0.457)ENGMT(0.963)NQS(0.028)K 40.638 0.082328 1511100000 162240 43940 73556 47996 107350 126250 102090 47207 71939 23451 TRUE FALSE 168645.3605 51486.35319 75472.92979 57489.46555 89102.68534 96930.35084 94087.91904 46574.26738 69349.92944 28045.77445 6.013218168 1.835797164 2.691062424 2.049844109 3.177044923 3.456148127 3.354798392 1.660651855 2.472740753 1 14.7754958 8 0.081623171 1.81E-10 10.10801487 0.336124358 1.073120395 252.6027347 1.498373262 27.31720987 287.5429173 99999999.93 -8 10.10801487 MNLSEEVDLEDYVARPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MNLSEEVDLEDYVARPDK 18 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;; 252.4 1.60E-30 1382483000 863330 628646 839880 717179 1177325 1163822 1053057 807714 886134 786725 FALSE TRUE 897414.935 736611.0603 861767.9628 859034.8656 977203.717 893541.9784 970515.6407 796887.915 854242.2104 940868.701 0.953815271 0.782905266 0.915927974 0.913023108 1.038618583 0.949698909 1.031510177 0.846970373 0.907929246 1 19.84363388 3.811486155 2.820510745 0.951730941 0.867372043 0.201139586 0.067656091 0.428652369 6.6679833 0.018563411 0.036936163 6478.674415 -3.811486155 -0.084358898 MNNSGYSDAGLGLGDETDEMPSTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNNSGYSDAGLGLGDETDEMPSTEK 25 0 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 0 49.902 0.048858 6337700000 141020 567590 362960 687290 228730 541410 340190 433520 332840 437420 FALSE TRUE 146587.5785 665069.1673 372419.0358 823233.9106 189850.5563 415675.7326 313525.0189 427709.3735 320861.1534 523124.0741 0.2802157 1.27134116 0.711913395 1.57368768 0.362916879 0.794602568 0.599332041 0.817605984 0.61335574 1 18.99679364 MNS(ph)TGGQTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MNSTGGQTPR 10 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 MNS(0.886)T(0.114)GGQTPR 69.795 0.058644 305830000 204580 208280 270780 257170 368460 428760 342320 324600 338170 269680 TRUE FALSE 212656.9764 244050.4698 277836.7492 308037.4584 305829.3008 329186.9879 315488.0639 320249.2679 325999.3278 322518.6327 0.659363382 0.756701924 0.861459529 0.955099728 0.948253123 1.020675876 0.978201046 0.992963617 1.010792229 1 18.29902299 4.371347914 0.893926549 0.998165378 0.56723865 0.982329281 0.015360185 0.145556813 0.132630441 0.005041742 0.054966092 23515.15871 -4.371347914 -0.430926729 MNSEEEDEVWQVIIGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MNSEEEDEVWQVIIGAR 17 0 Q9NR28-2;Q9NR28;Q9NR28-3;H7BZK7;A0A2U3TZH2;H7BZQ7 Q9NR28-2 DIABLO "Diablo homolog, mitochondrial" 0 ; 214.65 1.36E-14 48050000 37330 36242 38239 43278 39437 46464 37061 34015 33563 29004 FALSE TRUE 38803.81723 42466.28158 39235.53975 51838.25923 32733.51283 35673.44017 34156.06198 33559.08456 32355.07419 34686.77848 1.118691874 1.224278628 1.131138188 1.494467388 0.943688467 1.028444892 0.984699746 0.967489229 0.932778298 1 15.08209824 3.18889698 24.99999992 0.977068745 1.232940465 0.632874401 0.099135953 67.95120916 34205.43763 0.027470019 0.032833008 1544.88793 -3.18889698 0.25587172 MNSTGGQT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MNSTGGQTPR 10 0 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 MNSTGGQT(1)PR;MNSTGGQT(1)PR 136.72 0.0012333 662530000 499880 622790 547470 516750 625040 668290 530710 563650 519750 476730 TRUE FALSE 519615.6484 729749.3379 561737.518 618961.6077 518795.9241 513089.7755 489111.5634 556095.1937 501044.299 570136.116 0.911388761 1.279956343 0.985269135 1.085638307 0.909950992 0.899942595 0.857885599 0.975372684 0.878815225 1 19.12094687 3.237971016 24.99935554 0.917777439 1.075141671 0.351834813 0.096183942 15.43370225 654410.0875 0.025335647 0.032051811 1729.70092 -3.237971016 0.157364232 MNTNPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MNTNPSR 7 0 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ; 94.662 0.052561 0 86196 114397 104305 97989 116738 134970 101709 103778 94048 107803 FALSE TRUE 89599.08464 134043.7949 107023.274 117370.9317 96894.91646 103625.263 93736.78281 102387.0257 90663.23085 128924.9338 0.694970957 1.039704197 0.830120837 0.910381943 0.751560723 0.803764329 0.727064812 0.794160002 0.703224955 1 16.97617178 3.238190826 24.99999765 0.782685725 0.878239922 0.08304636 0.110083932 17.94368248 1213129.484 0.028430925 0.036034105 1730.576595 -3.238190826 0.095554197 MNVPETMNEVLDMS(ph)DDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MNVPETMNEVLDMSDDEVR 19 0 Q12955;Q12955-4;Q12955-5;H0Y8Z4 Q12955;Q12955-4 ANK3 Ankyrin-3 1 MNVPETMNEVLDMS(1)DDEVR;MNVPETMNEVLDMS(1)DDEVR;MNVPETMNEVLDMS(1)DDEVR;MNVPETMNEVLDMS(1)DDEVR 264.69 2.47E-31 173872000 91888 141950 132727 132360 138396 167673 142424 143583 129366 140256 TRUE FALSE 95515.80919 166328.8083 136185.9747 158540.4129 114871.4974 128733.4869 131260.4347 141658.5047 124710.1429 167736.4778 0.569439697 0.991607851 0.811904342 0.945175522 0.684833131 0.767474604 0.782539591 0.844530102 0.743488504 1 17.35583694 -1.027829447 4.535203525 1.000007681 0.803030837 0.222444305 0.114600294 8.15E-06 1.75E-06 0.101654906 0.023959357 0.093793027 1.027829447 -0.196976844 MPARAS(ph)PPHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPARASPPHSK 11 1 Q9HCM7;A0A3B3IRR3 Q9HCM7 FBRSL1 Fibrosin-1-like protein 1 MPARAS(1)PPHSK 55.213 0.076765 87026000 66132 62045 63652 49990 84037 96113 61234 74435 72608 77092 TRUE FALSE 68742.94243 72700.74611 65310.82341 59877.87279 69752.42076 73792.21236 56434.31907 73437.32058 69994.85226 92196.70138 0.745611734 0.788539557 0.708385684 0.649457864 0.756560915 0.80037801 0.612107789 0.79652872 0.759190418 1 16.49242751 0.444459562 1.173191502 1.000116247 0.728357817 0.654976509 0.058245088 1.375709595 2.331712756 0.054464255 0.016518252 2.782656262 -0.444459562 -0.271758431 MPFGELMFESSSSCGWVHGVCFSASGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPFGELMFESSSSCGWVHGVCFSASGSR 28 0 A0A1W2PNV4;C9JEY1;C9K057;O15143 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 167.72 5.42E-12 52270000 13841 25283 25295 26745 26390 30366 24328 23743 24611 23970 FALSE TRUE 14387.45337 29625.15858 25954.20848 32035.08117 21904.23723 23313.9567 22421.10779 23424.76392 23725.25492 28666.46257 0.501891482 1.033443122 0.905385812 1.117510788 0.764106739 0.81328335 0.782137236 0.817148745 0.827631064 1 14.80707627 MPGGPKPGGGPGLS(ph)TPGGHPKPPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPGGPKPGGGPGLSTPGGHPKPPHR 25 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 1 MPGGPKPGGGPGLS(0.573)T(0.427)PGGHPKPPHR 90.299 0.006538 634240000 975810 780250 974920 710530 1164900 1070600 1024300 934250 1041800 862580 TRUE FALSE 1014335.732 914251.868 1000327.216 851070.7133 966890.7141 821969.3751 944012.6895 921727.9069 1004305.822 1031586.036 0.983277882 0.886258476 0.969698291 0.825011859 0.937285578 0.796801572 0.915108054 0.893505607 0.973555076 1 19.97643272 1.144132382 3.731242048 0.998814424 0.898090886 0.28550337 0.054824609 0.254234791 6.172025488 0.04816847 0.01267052 13.93581531 -1.144132382 -0.100723538 SSVSHSVLSEMQVIEQETPVS(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVSHSVLSEMQVIEQETPVSAK 23 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 SSVSHSVLSEMQVIEQETPVS(1)AK 80.359 0.0072397 44871000 8350.1 32857 36061 35318 45356 50009 37177 47750 38528 39808 TRUE FALSE 8679.768396 38499.93416 37000.77928 42303.79499 37646.40332 38395.16764 34262.9696 47109.98935 37141.38481 47607.61543 0.182318907 0.808692765 0.777202953 0.888593025 0.790764313 0.80649214 0.719695143 0.989547343 0.780156378 1 15.53890475 4.74296454 4.511501498 0.840880097 0.136409081 0.837282203 0.087105601 0.072074669 3.740548474 0.020080838 0.162230397 55330.493 -4.74296454 -0.704471016 down MPLDLS(ph)PLATPIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MPLDLSPLATPIIR 14 0 B8ZZU6;E9PBF9;P15336-5;P15336;E9PEK8;H7C2N6;P15336-3;P15336-7;P15336-4;C9JCI8 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(1)PLATPIIR;MPLDLS(0.999)PLAT(0.001)PIIR 216.27 6.49E-12 697090000 697718 788925 718534 780373 753957 912919 861228 745680 773730 752541 TRUE FALSE 725264.4454 924416.7318 737259.5863 934728.4502 625799.6584 700907.3977 793722.699 735685.3793 745883.6084 899987.0007 0.805861023 1.027144538 0.81918915 1.038602168 0.695342997 0.778797246 0.881926848 0.817440006 0.828771535 1 19.77954464 3.24354517 24.99976463 0.825096524 0.922765989 0.154478184 0.100787166 204.9601899 1027959.253 0.026155381 0.034345752 1752.044649 -3.24354517 0.097669464 MPLFEHYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPLFEHYTR 9 0 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 124.81 0.00051932 495390000 123270 169030 171260 143930 216400 208590 167320 151050 151820 253030 FALSE TRUE 128136.7948 198059.5876 175723.1763 172398.9244 179616.4053 160148.1337 154205.0212 149025.4218 146356.0279 302606.3839 0.423443792 0.654512258 0.580698841 0.569713441 0.593564494 0.529229197 0.509589451 0.492472828 0.483651488 1 18.2070829 -1.89068196 2.52764056 1.243514172 0.539830883 0.833081695 0.062108039 9521220.942 5435172.345 13828589.35 0.015210961 0.012862282 1.89068196 -0.703683289 MPLLELGGET(ph)TPPLSTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.604)T(0.395)PPLSTER 98.507 0.013513 60665000 18024 26901 20757 22366 27286 26061 17768 24113 24371 23216 TRUE FALSE 18735.60144 31521.03749 21297.94447 26789.92804 22647.93547 20008.72771 16375.29773 23789.80468 23493.89247 27764.7307 0.674798601 1.13529059 0.767086297 0.964890614 0.815708811 0.720652684 0.589787739 0.856835419 0.846177574 1 14.76096578 3.037872167 9.249347318 0.780171022 0.894531511 0.054013222 0.150262774 0.70459287 161.936198 0.041249691 0.049227837 1091.119123 -3.037872167 0.114360488 MPLLELGGETT(ph)PPLSTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MPLLELGGETTPPLSTER 18 0 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.191)T(0.806)PPLS(0.002)T(0.002)ER;MPLLELGGET(0.03)T(0.97)PPLSTER 171.56 1.45E-10 118623000 59522 70580 69561 64582 66390 80358 68478 68592 59080 68890 TRUE FALSE 61871.97452 82701.56596 71373.8168 77356.12684 55105.05151 61696.07234 63110.51543 67672.63643 56953.72234 82387.67652 0.750985792 1.003809908 0.866316661 0.93892837 0.668850656 0.748850738 0.766018877 0.821392704 0.691289338 1 16.33014094 3.258540076 24.98852295 0.774571232 0.896446352 0.201431093 0.103564498 326.2950682 408098.1048 0.026477162 0.035803398 1813.594022 -3.258540076 0.12187512 MPLLELGGETT(ph)PPLSTERS(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 2 MPLLELGGET(0.471)T(0.529)PPLS(0.04)T(0.207)ERS(0.753)PEAVGSECPSR;MPLLELGGET(0.133)T(0.867)PPLS(0.068)T(0.059)ERS(0.873)PEAVGSECPSR;MPLLELGGET(0.147)T(0.852)PPLS(0.074)T(0.065)ERS(0.862)PEAVGSECPSR 140.34 1.27E-07 277037000 144065 168358 172094 163587 173713 200491 164340 175970 162895 198294 TRUE FALSE 149752.7974 197272.1769 176578.911 195944.0203 144185.3263 153930.0037 151458.6014 173611.41 157032.4408 237145.9127 0.631479563 0.831859907 0.744600272 0.826259319 0.608002578 0.649094062 0.63867262 0.732086874 0.662176459 1 17.85541548 -1.367403095 5.500938813 1.000097337 0.706131589 0.580847746 0.075716624 9.09E-05 1.05E-05 0.073755368 0.017378577 0.042913793 1.367403095 -0.293965747 MPLLELGGETTPPLSTERS(ph)PEAVGSECPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MPLLELGGETTPPLSTERSPEAVGSECPSR 30 1 A0A0J9YWL0;Q9Y4K1 A0A0J9YWL0 AIM1 Absent in melanoma 1 protein 1 MPLLELGGET(0.001)T(0.001)PPLS(0.192)T(0.192)ERS(0.614)PEAVGSECPSR;MPLLELGGETTPPLS(0.023)T(0.023)ERS(0.954)PEAVGSECPSR;MPLLELGGETTPPLST(0.001)ERS(0.999)PEAVGSECPSR;MPLLELGGETTPPLS(0.009)T(0.009)ERS(0.982)PEAVGSECPSR;MPLLELGGETTPPLS(0.064)T(0.064)ERS(0.872)PEAVGSECPSR;MPLLELGGETTPPLS(0.008)T(0.005)ERS(0.986)PEAVGSECPSR 331.64 1.43E-105 1650670000 157035 227779 216522 205971 214924 263797 194156 209056 197650 236970 TRUE FALSE 163234.8631 266898.2714 222164.7412 246711.449 178391.2952 202534.1446 178937.5454 206253.9463 190536.6151 283399.7344 0.575988059 0.941773188 0.783927133 0.870542273 0.629468816 0.714658908 0.631396306 0.727784543 0.672324607 1 18.11247888 3.243221149 24.99969109 0.709459741 0.803028008 0.038657737 0.132048609 262.0078165 1405432.493 0.033855997 0.04437383 1750.737963 -3.243221149 0.093568267 MPLPS(ph)PTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MPLPSPTESR 10 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 MPLPS(0.984)PT(0.015)ESR;MPLPS(0.989)PT(0.011)ESR 84.658 0.015494 251130000 138305 191810 159660 174983 164830 181564 193898 175722 141390 181463 TRUE FALSE 143765.3882 224751.8754 163820.8708 209594.1151 136812.2555 139398.5126 178699.7681 173366.734 136301.4015 217017.2005 0.6624608 1.035640838 0.754875053 0.965794944 0.630421253 0.642338544 0.823435966 0.79886172 0.628067274 1 17.72744987 3.242178236 24.99990172 0.747455508 0.860487891 0.10566818 0.142594347 191.0573742 1320309.301 0.037570961 0.048934243 1746.538791 -3.242178236 0.113032382 MPPSHQLDHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MPPSHQLDHSK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;; 138.42 4.05E-05 349659000 233079 220326 255173 210620 344430 321530 277109 253670 261092 248035 FALSE TRUE 242281.1389 258165.2766 261823.018 252280.0074 285883.9116 246859.5303 255388.4725 250269.9686 251695.3499 296632.7093 0.816771486 0.870319653 0.88265053 0.850479396 0.96376395 0.832206033 0.860958567 0.843703208 0.848508415 1 18.17831817 -2.371311321 2.243513126 1.925206419 0.864116642 0.538292956 0.037983803 3597272.907 408880.415 16901464.75 0.008907626 0.004252934 2.371311321 -1.061089778 MPQAFLLGSIHEPAGALMEPQPCPGSLAESFLEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPQAFLLGSIHEPAGALMEPQPCPGSLAESFLEEELR 37 0 D6RD88;D6RIA4;D6RAS0;D6RA25;D6RAI1;D6RI04;A0A0U1RRE6;D6RA78;Q53HV7-2;Q53HV7 D6RD88 SMUG1 Single-strand selective monofunctional uracil DNA glycosylase 0 49.942 0.033441 130530000 1956.5 0 0 0 0 0 0 0 0 0 FALSE TRUE 2033.744131 0 0 0 0 0 0 0 0 0 0 MPS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MPSPFR 6 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 MPS(1)PFR;MPS(1)PFR;MPS(1)PFR;MPS(1)PFR;MPS(1)PFR 86.794 0.055776 918671000 512942 615991 615965 613683 684495 747210 604866 621988 601671 630566 TRUE FALSE 533193.3462 721782.6625 632017.5539 735067.6657 568144.7844 573681.8016 557455.0224 613651.2682 580016.9782 754113.3348 0.707046702 0.957127569 0.838093593 0.974744288 0.753394428 0.760736848 0.739219155 0.813738784 0.769137677 1 19.52442184 3.202746183 24.99697387 0.79148151 0.873304469 0.079322386 0.097877302 322.87148 225349.8869 0.026118808 0.03121895 1594.946732 -3.202746183 0.081822958 MPSGEFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MPSGEFAR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 152.31 0.001068 375380000 557010 487510 538100 504730 620950 671650 665720 557400 528520 460380 FALSE TRUE 579001.1849 571236.0502 552123.3281 604564.0875 515401.1408 515669.4665 613539.1269 549928.9647 509498.6684 550582.6465 1.051615391 1.037511905 1.002798275 1.098044211 0.936101318 0.936588666 1.114345196 0.998812745 0.925380906 1 19.07059961 3.240005008 24.9998669 0.99267386 1.043587098 0.226194199 0.055227072 74.8408234 1295347.093 0.016218757 0.020817149 1737.820866 -3.240005008 0.050913237 MPTQSEEEKLS(ph)PSPTTEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPTQSEEEKLSPSPTTEDPR 20 1 Q9BTC8;F6RRE2;E7EV10;E7EQY4;Q9BTC8-2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 MPTQS(0.001)EEEKLS(0.82)PS(0.163)PT(0.012)T(0.004)EDPR 81.315 0.0031872 334150000 573430 334980 395500 318080 549530 625650 527410 469930 464730 333410 TRUE FALSE 596069.4592 392510.2092 405807.0549 380995.2746 456121.0869 480352.2693 486070.2261 463631.357 448004.4581 398735.306 1.494900126 0.984387897 1.017735447 0.955509254 1.143919488 1.204689583 1.219029814 1.162754715 1.123563555 1 18.60507183 3.019900287 24.97189515 1.160707728 1.091196906 0 0.151900922 876.8519898 1100310.673 0.043039826 0.051437055 1046.888159 -3.019900287 -0.069510822 MPVSSQHRYS(ph)TPHAFTFNTSSPSSEGSLSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MPVSSQHRYSTPHAFTFNTSSPSSEGSLSQR 31 1 P04049;P04049-2 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 MPVS(0.04)S(0.04)QHRYS(0.873)T(0.047)PHAFTFNTSSPSSEGSLSQR 195.07 5.21E-20 130930000 26983 61139 59488 56139 74718 81477 51000 61538 64092 82807 TRUE FALSE 28048.30968 71639.14765 61038.30615 67243.12664 62017.46105 62555.20155 47002.48674 60713.18377 61785.34144 99031.44621 0.283226296 0.723397975 0.61635277 0.679007822 0.626240083 0.63167008 0.474621835 0.613069748 0.623896185 1 16.59559909 0.556129977 2.196815905 0.99997363 0.589371047 0.531373069 0.117151379 2.993404483 13.91042685 0.104570956 0.028388225 3.598570181 -0.556129977 -0.410602583 MQAQMQMQMQGGDGDGGALGHHV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQAQMQMQMQGGDGDGGALGHHV 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3;H7C2Y0;H7C1T1 Q15019-2 2-Sep Septin-2 0 219.66 3.43E-34 0 91053 105790 76076 90401 96226 116340 85023 89722 92592 99492 FALSE TRUE 94647.84275 123958.6096 78058.60306 108282.048 79869.53889 89321.79815 78358.67509 88519.42335 89259.63201 118985.5525 0.795456597 1.04179547 0.656034295 0.910043662 0.671254091 0.750694486 0.658556215 0.743951022 0.750172018 1 16.86042688 3.242149877 24.99952087 0.741922267 0.850558556 0.09224561 0.126365783 172.7453368 1203176.058 0.03291242 0.042881192 1746.424748 -3.242149877 0.108636288 MQAQWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MQAQWER 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 111.04 0.015516 212720000 219750 194774 192097 150995 304280 296700 210750 213080 228410 254210 FALSE TRUE 228425.8997 228224.9194 197103.2056 180861.3603 252558.5943 227795.9215 194230.8643 210224.0111 220189.5687 304017.5824 0.75135753 0.750696449 0.648328311 0.594904278 0.830736803 0.749285353 0.638880366 0.691486359 0.724265903 1 18.21379524 0.78730059 5.362695849 0.999999678 0.704404072 0.645975711 0.064744395 4.256629854 107.102225 0.063613379 0.016041973 6.127743665 -0.78730059 -0.295595606 MQAS(ph)IEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MQASIEK 7 0 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK;MQAS(1)IEK 119.22 0.0050664 1958150000 3435330 1973300 2281440 1699170 2684960 3202960 2841550 2332730 2481320 2023710 TRUE FALSE 3570959.481 2312198.925 2340896.201 2035260.754 2228571.458 2459121.081 2618821.886 2301463.57 2392017.778 2420217.228 1.475470648 0.955368344 0.967225658 0.840941355 0.920814641 1.016074529 1.082060674 0.950932645 0.98834838 1 21.20670511 4.739423338 24.99327832 0.967964036 1.475470807 0.866412396 0.0596503 25.69580426 744294.737 0.015339907 0.093010742 54881.16707 -4.739423338 0.507506771 MQEEVVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQEEVVRR 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 0 111.46 0.0051792 94745000 99067 117310 114020 103660 132960 147340 111120 113530 115170 155820 FALSE TRUE 102978.2417 137457.08 116991.4549 124163.6386 110359.5067 113122.518 102410.124 112008.316 111025.0542 186349.9456 0.552606771 0.737628763 0.627805146 0.666292862 0.592216468 0.607043472 0.549558111 0.601064388 0.595787961 1 17.50765487 -1.622604472 2.965509506 1.029243499 0.615222129 0.831260831 0.052112055 22623764.74 22537312.09 5089745.466 0.012557587 0.023844901 1.622604472 -0.414021369 MQEHSDQVPVGNIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQEHSDQVPVGNIPR 15 0 P33993;P33993-3;P33993-2;C9J8M6 P33993 MCM7 DNA replication licensing factor MCM7 0 133.25 4.25E-05 179850000 152310 138680 149260 133340 161700 194640 175200 163140 149570 140600 FALSE TRUE 158323.3164 162497.2112 153149.8382 159714.254 134214.2918 149437.8098 161467.3662 160953.3751 144187.0049 168147.8781 0.941571896 0.966394659 0.910804466 0.949844006 0.798192004 0.88872849 0.96027002 0.95721324 0.857501186 1 17.35937105 -0.566351152 7.677717384 1 0.917748935 0.198727959 0.051130784 0 0 0.050946296 0.012008157 0.271424376 0.566351152 -0.082251065 MQFS(ph)FEEYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;MQFS(1)FEEYEK;MQFS(1)FEEYEK 196.11 3.56E-07 967009000 1325150 1086700 1373140 874413 1881820 1581430 1542910 1392000 1505870 1083110 TRUE FALSE 1377467.945 1273332.272 1408925.156 1047369.282 1561948.909 1214166.849 1421972.683 1373342.517 1451674.033 1295324.667 1.063415204 0.983021712 1.087700398 0.808576651 1.20583584 0.937345578 1.097773183 1.060230344 1.12070284 1 20.30488232 3.213528227 24.99998447 1.068192839 0.992775658 0.155055887 0.096144543 451.8369821 451250.8848 0.02586284 0.030924142 1635.039416 -3.213528227 -0.07541718 MQFS(ph)FEGPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK;MQFS(1)FEGPEK 175.88 2.80E-06 2031863000 3653897 2912503 4099954 2370120 5829237 4276680 4365452 4089761 4533984 2823102 TRUE FALSE 3798155.675 3412702.734 4206802.169 2838922.662 4838385.377 3283485.884 4023276.465 4034944.443 4370806.802 3376234.785 1.124967876 1.010801366 1.246004036 0.840854633 1.43307136 0.972528895 1.191645937 1.195101852 1.294580229 1 21.6869838 3.246367121 24.99999953 1.182206244 1.066049325 0.133448826 0.155756393 377.3862709 1208555.338 0.040111547 0.053351262 1763.466124 -3.246367121 -0.11615692 MQHLIAR ddPTM_MDA-MB-175_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 ;;;;;;;;;;;;; 146.21 0.0022347 12598562000 6510567 7220734 6633720 6115517 10996128 9671593 7693013 6778604 7094981 9664173 FALSE TRUE 6767609.212 8460838.895 6806600.193 7325148.01 9127010.09 7425512.1 7090014.539 6687747.901 6839634.02 11557682.67 0.585550703 0.732053227 0.588924302 0.633790373 0.789692048 0.642474129 0.613446029 0.5786409 0.591782472 1 23.46234883 -1.731292916 2.588838546 1.072637338 0.639521329 0.729748221 0.065797567 12602919.88 9675942.24 5892567.071 0.017569258 0.018565519 1.731292916 -0.433116009 MQHNLEQQIQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQHNLEQQIQAR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 165.58 5.42E-05 351810000 328970 330170 324440 312230 455090 515950 394270 363860 337550 328870 FALSE TRUE 341957.9896 386874.1291 332895.1729 373988.1621 377733.9644 396128.4318 363366.0872 358983.0519 325401.6414 393305.7799 0.869445625 0.9836472 0.846402951 0.950883972 0.960407865 1.007176736 0.923876805 0.912732714 0.827350266 1 18.58529186 5.906616656 12.01987085 0.927945758 0.67499783 0 0.060490415 0 0 0.012775687 0 806522.8128 -5.906616656 -0.252947928 MQMELSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MQMELSHK 8 0 Q9Y6D9;C9JJ38 Q9Y6D9 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 0 ; 93.551 0.005929 443700000 799070 410200 555750 500000 724010 729010 964390 673960 674640 304490 FALSE TRUE 830617.9006 480648.6591 570233.3016 598898.5076 600943.0388 559708.4758 888798.5918 664926.6686 650359.8382 364148.9857 2.2809837 1.319923103 1.565934065 1.644652412 1.650266958 1.537031539 2.440755369 1.825974243 1.785971851 1 18.4741693 MQMLEDEDDLAYAETEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MQMLEDEDDLAYAETEKK 18 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 220.36 1.09E-18 278150000 289945 192841 238566 173745 318680 305725 283470 236678 307480 180078 FALSE TRUE 301392.2525 225959.9417 244783.2259 208111.2424 264510.8874 234725.0021 261250.8807 233505.7185 296413.8549 215360.8363 1.399475678 1.049215566 1.136619035 0.966337455 1.228221862 1.089914982 1.213084446 1.084253398 1.376359137 1 17.71639639 2.23865302 24.99999872 1.167019037 1.135897627 0.004142759 0.14038067 18.03676083 4881151.011 0.047829883 0.037708556 173.2419325 -2.23865302 -0.03112141 MQNGFGS(ph)PEPSLPGTPHS(ph)PAPPSGGTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQNGFGSPEPSLPGTPHSPAPPSGGTWK 28 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 2 MQNGFGS(0.714)PEPS(0.284)LPGT(0.102)PHS(0.816)PAPPS(0.039)GGT(0.045)WK 42.268 0.082731 113700000 76310 60816 81931 52165 94519 98371 76722 76390 82864 65121 TRUE FALSE 79322.77772 71260.67492 84066.18917 62483.0813 78452.69414 75525.82608 70708.32916 75366.117 79881.74083 77880.21313 1.018522864 0.915003594 1.079429367 0.802297256 1.007350789 0.969769124 0.907911346 0.967718423 1.02570008 1 16.24896921 1.335626145 5.700537278 1.012142577 0.95532616 0.086895639 0.070693689 0.457809203 20.74267352 0.045937566 0.016253813 21.65838878 -1.335626145 -0.056816416 MQNT(ph)DDEERPQLS(ph)DDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQNTDDEERPQLSDDER 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 2 MQNT(1)DDEERPQLS(1)DDER 97.124 0.0010989 328360000 274670 279910 272170 333840 254360 339320 349940 314540 278950 180230 TRUE FALSE 285514.1837 327982.3651 279262.9738 399872.5556 211123.9781 260518.0724 322510.7884 310324.1058 268910.644 215542.6178 1.324629842 1.521659004 1.295627643 1.855190216 0.979499925 1.20866154 1.496273877 1.439734327 1.247598488 1 17.71761363 -3.49515007 0.252435752 4.35E-11 1.425227402 0.222825414 0.217061936 121.6882697 2.396589037 63.50486929 0.309139453 0.000319779 3.49515007 1.425227402 MQQHEQALADCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MQQHEQALADCR 12 0 Q9UNE7;Q9UNE7-2 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 147.26 6.54E-05 218224000 126057 163647 151744 158579 168405 200176 163438 155874 138440 144599 FALSE TRUE 131033.8277 191752.0993 155698.5733 189945.4529 139779.5783 153688.1577 150627.3025 153784.764 133457.5714 172930.4055 0.757725787 1.108839701 0.900353948 1.098392456 0.808299604 0.888728372 0.871028447 0.889287014 0.771741505 1 17.39983203 3.212044376 24.99956716 0.868442895 0.971795127 0.154767773 0.108104579 353.7124439 333479.9308 0.028581008 0.034170083 1629.462521 -3.212044376 0.103352231 MQQNIQELEEQLEEEESAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 229.17 2.01E-19 329649000 277727.5 401435.5 354418.7 385091.9 405001.9 486170.9 386244.9 379676 408421.9 420230.2 FALSE TRUE 288692.3962 470378.9244 363655.1425 461261.9284 336159.8217 373265.0765 355970.0155 374587.0642 393722.8756 502566.2619 0.574436483 0.935954042 0.723596409 0.917813159 0.668886567 0.742718134 0.708304641 0.745348609 0.783424805 1 18.9389543 0.788931617 4.313316805 0.999997052 0.757134915 0.346080612 0.101401529 3.022035496 60.87105415 0.088873226 0.022610094 6.150800157 -0.788931617 -0.242862138 MQS(ph)LSLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.991)LS(0.009)LNK 75.566 0.039922 66724000 74810 84432 94540 99004 107070 135050 82614 85403 82906 103790 TRUE FALSE 77763.55657 98932.53921 97003.79007 118586.6957 88870.27964 103686.6842 76138.49881 84258.31248 79922.22925 124125.6633 0.626490562 0.797035331 0.78149665 0.955376129 0.715970229 0.835336396 0.613398525 0.6788146 0.643881588 1 16.9214419 2.25645694 24.99796265 0.700858527 0.790227006 0.010706827 0.127523552 550.8970515 769503.0013 0.041822563 0.034924887 180.4915773 -2.25645694 0.089368479 MQSLS(ph)LNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQSLSLNK 8 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 MQS(0.032)LS(0.968)LNK 96.64 0.034391 177600000 481690 347890 529680 386740 733990 683430 657160 509050 661860 514580 TRUE FALSE 500707.4931 407637.4013 543483.8959 463236.0177 609226.642 524713.74 605650.082 502227.0174 638039.7879 615402.0988 0.813626561 0.662391958 0.883136241 0.752737143 0.989965168 0.852635604 0.984153423 0.816095718 1.0367852 1 19.23116984 4.609371713 0.247620444 1.000075287 0.534248481 0.44363361 0.086573102 8.650561617 0.479446982 0.121698719 1.239669994 40679.13529 -4.609371713 -0.465826807 MQTEAQHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQTEAQHER 9 0 Q9H2K8;G3V1Q8;F5GWV8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 0 89.827 0.011266 0 137520 66188 81072 50265 117040 100060 103080 71507 116150 68119 FALSE TRUE 142949.3958 77555.27413 83184.80292 60207.26697 97145.58261 76822.58142 95000.32025 70548.56563 111969.7842 81465.61383 1.754720661 0.95200012 1.021103248 0.73905129 1.192473463 0.943006231 1.166140115 0.865991948 1.374442282 1 16.31390361 4.741631213 24.91974381 1.016836768 1.754720945 0.619601025 0.170556975 166.0516955 1347541.089 0.037281353 0.264548444 55160.88342 -4.741631213 0.737884177 MQYDWSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MQYDWSDR 8 0 O60437;K7EKI8 O60437 PPL Periplakin 0 80.676 0.054388 0 176410 391560 313410 399890 323670 414500 260090 326680 289150 425000 FALSE TRUE 183374.803 458807.3841 321577.7221 478987.0484 268652.689 318238.6568 239703.4662 322301.3889 278743.548 508270.6129 0.360781832 0.90268328 0.632689976 0.942385879 0.52856231 0.626120513 0.471605991 0.634113759 0.548415629 1 18.95523729 -1.084158161 4.457111756 1.000025095 0.635200357 0.302326939 0.169402447 31838270.16 95402511.68 14716.52334 0.038678701 0.082383804 1.084158161 -0.364824738 MRAEDGENYDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MRAEDGENYDIK 12 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 110.8 0.00037979 0 179720 141950 158870 108700 232320 191300 210360 181270 167870 133260 FALSE TRUE 186815.4844 166328.8083 163010.2827 130200.5356 192830.3294 146873.4742 193871.4335 178840.3721 161828.3915 159369.7456 1.172214235 1.043666147 1.022843339 0.816971472 1.209955683 0.921589437 1.216488317 1.122172665 1.015427306 1 17.28201825 2.239881024 24.99999742 1.105424316 1.029779906 0.045300848 0.119085643 93.09147845 1762593.31 0.04141329 0.032900752 173.732482 -2.239881024 -0.07564441 MRAEDGENYDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MRAEDGENYDIKK 13 2 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2;E5RIX8;A0A494C144 E5RJD8 TBCA Tubulin-specific chaperone A 0 ; 121.45 0.0011839 352870000 516650 264240 412850 216094 767020 549920 428290 423690 517800 383120 FALSE TRUE 537047.7409 309621.1645 423609.2102 258836.7482 636642.2144 422209.4141 394719.5107 418011.1286 499164.4791 458185.0287 1.172119793 0.675755743 0.924537433 0.564917516 1.38948716 0.921482344 0.861484959 0.912319483 1.08943865 1 18.80557079 3.270429332 24.99999612 1.000780354 0.82944929 0.172664683 0.203109533 387.8743919 304272.6028 0.054417902 0.073676028 1863.928856 -3.270429332 -0.171331064 MRDAGDPS(ph)PPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 86.467 0.0099368 0 85934 63602 86638 61232 112540 119870 97554 83414 95974 68357 TRUE FALSE 89326.74068 74525.14875 88895.85745 73343.50684 93410.491 92032.00915 89907.46257 82295.97177 92519.91449 81750.24538 1.092678563 0.911619878 1.087407836 0.897165587 1.142632546 1.125770433 1.099782174 1.006675532 1.131738676 1 16.31893544 3.220707991 24.99646331 1.082360467 0.997545899 0.24773332 0.074401106 339.2301233 474974.0954 0.020445118 0.024485384 1662.294588 -3.220707991 -0.084814568 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 73.707 0.0014737 76140000 12224 22604 24887 23420 35598 37566 22151 27228 25752 29515 FALSE TRUE 12706.61296 26486.06117 25535.57566 28052.4061 29547.06468 28841.86582 20414.74674 26863.0532 24825.19055 35297.89915 0.359982131 0.750358004 0.723430467 0.794733023 0.837077146 0.817098652 0.578355858 0.761038301 0.703305045 1 15.1072947 4.739650323 5.715611079 0.760734346 0.346920064 0.591801888 0.102647098 0.096183804 13.38102434 0.023270714 0.155078856 54909.85827 -4.739650323 -0.413814282 MREDYDS(ph)VEQDGDEPGPQR ddPTM_MDA-MB-175_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 205.65 6.09E-16 1550540000 404130 514220 524440 453710 483600 590530 479660 505960 473060 487870 TRUE FALSE 420085.3645 602533.2849 538107.3372 543452.4838 401397.8447 453388.3571 442062.9958 499178.4338 456034.663 583458.7857 0.719991497 1.032692111 0.922271376 0.931432514 0.687962637 0.777070066 0.757659336 0.855550462 0.781605615 1 19.15427122 3.282376068 24.9999773 0.801453338 0.912437708 0.14877732 0.104922845 207.7193546 118517.9275 0.02729655 0.0369595 1915.914253 -3.282376068 0.110984371 MREDYDSVEQDGDEPGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ; 139.44 1.94E-07 758390000 126421 170181 163597 144940 143326 183995 129644 155199 138466 156691 FALSE TRUE 131412.1987 199408.2629 167860.4722 173608.6994 118963.4977 141264.9497 119482.1645 153118.8113 133482.6357 187391.6014 0.701270482 1.064125934 0.895773722 0.926448667 0.634839005 0.753848885 0.637606828 0.81710605 0.712319201 1 17.51569677 3.261479891 24.98714878 0.746371995 0.908768363 0.212664641 0.127470887 292.420189 318801.419 0.032564458 0.044063538 1825.912203 -3.261479891 0.162396368 MREEFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MREEFDK 7 1 O43809;H3BND3;H3BV41 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ;;;; 143.73 0.0021903 1768620000 1805540 1425460 1759090 1401920 2082200 2184450 2130530 1778100 1880320 1382700 FALSE TRUE 1876824.113 1670271.666 1804933.331 1679215.592 1728268.388 1677144.593 1963533.491 1754267.478 1812647.651 1653613.592 1.134983483 1.010073741 1.091508524 1.015482456 1.045146458 1.014230048 1.187419783 1.060869049 1.096173652 1 20.65719072 MREESGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MREESGAR 8 1 F8VZX2;F8W1G6;F8W0G4;P57721;P57721-4;E9PFP8;P57721-5;P57721-3;P57721-2;F8VTZ0;J3QT27;F8VXH9;Q15366;Q15366-6;Q15366-2;Q15366-3;Q15366-5;Q15366-4;Q15366-8;Q15366-7 F8VZX2;Q15366;Q15366-2;Q15366-5 PCBP2;PCBP3 Poly(rC)-binding protein 3;Poly(rC)-binding protein 2 0 ; 106.42 0.0038289 122985000 83417 101745 95913 85497 112614 130282 83216 97571 91320 121763 FALSE TRUE 86710.36757 119218.9123 98412.57157 102408.0514 93471.9125 100025.9799 76693.31248 96263.22034 88033.41104 145620.1286 0.59545592 0.818698029 0.67581709 0.70325478 0.641888683 0.68689666 0.526666974 0.661057103 0.604541501 1 17.15185026 -1.39535578 8.591763296 1.000002179 0.658667463 0.664832608 0.073024307 3.01E-06 2.12E-07 0.069872285 0.01646895 0.040238726 1.39535578 -0.341334715 MREEVITLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 MREEVITLIR 10 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;;;;;; 190.53 8.13E-07 3026890000 1424037 1943401 1773385 1900251 1824920 2119500 1679830 1776911 1675422 2007863 FALSE TRUE 1480259.08 2277165.004 1819600.87 2276114.976 1514720.75 1627278.246 1548160.535 1753094.414 1615123.889 2401265.312 0.616449616 0.948318785 0.757767524 0.947881504 0.630801079 0.677675323 0.644726981 0.730071103 0.672613676 1 21.19536338 5.027191596 15.64786093 0.761132117 0.231066378 0.107677881 0.131637776 5424815.029 86190711.7 0.030588509 73247471.92 106461.2587 -5.027191596 -0.530065739 MREHLELFWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MREHLELFWSR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 123.95 0.0002159 605970000 595660 666880 757770 566740 1056380 976640 685370 678460 705890 1053490 FALSE TRUE 619177.1167 781411.4524 777518.1087 678839.4804 876816.9049 749830.1611 631648.9085 669366.3534 680485.1568 1259901.195 0.491448948 0.620216455 0.617126257 0.538803744 0.695941006 0.595149972 0.501347972 0.531284799 0.540109938 1 20.26487917 -1.674923031 2.732822505 1.055517357 0.570604406 0.82412497 0.059570676 15298723.35 13781293.12 5917634.768 0.014872361 0.021138636 1.674923031 -0.484912951 MRHCSDKELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MRHCSDKELK 10 2 Q8NG31-2;Q8NG31;H0YEY7;H0YCZ2 Q8NG31-2 CASC5 Protein CASC5 0 58.699 0.061533 607740000 15202 1480700 600690 1192100 147550 978560 158710 609400 199320 3080400 FALSE TRUE 15802.1867 1734998.707 616344.4749 1427893.822 122469.5037 751304.2702 146269.8955 601231.9898 192146.5121 3683945.402 0.004289474 0.470962112 0.16730554 0.387599073 0.033244115 0.203940121 0.039704686 0.163203285 0.052157807 1 21.81282025 -1.329450055 3.9086385 1.001963313 0.174939857 0.741524602 0.147123548 115480115.8 212197717.3 2692329.803 0.034684554 0.046832781 1.329450055 -0.827023456 MRITRTENEIELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MRITRTENEIELLK 14 2 A0A0A0MTQ8;P0C221 A0A0A0MTQ8 CCDC175 Coiled-coil domain-containing protein 175 0 81.565 0.063147 18156000000 190590 20756000 18454000 18970000 13167000 23532000 11638000 21275000 16556000 27362000 FALSE TRUE 198114.6404 24320681.54 18934926.4 22722209.38 10928878.04 18067049.63 10725783.15 20989843.42 15960152.79 32723060.02 0.006054282 0.743227605 0.578641679 0.694379113 0.333980931 0.552119808 0.327774455 0.641438894 0.487734117 1 24.96380433 -5 0.337926734 6.318312266 0.484129782 0.361992338 0.205802378 414.0252496 3.506957082 1586.840739 0.154943422 1.00E-05 5 -5.834182484 MRPFEGFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MRPFEGFQR 9 1 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 117.31 0.0010689 438050000 99583 138940 113060 107460 165840 164820 112890 111980 99318 189720 FALSE TRUE 103514.6137 162801.8642 116006.4365 128715.2673 137650.576 126543.0529 104041.3868 110479.0913 95743.56458 226892.0016 0.456228571 0.717530204 0.511284821 0.567297509 0.606678839 0.557723728 0.458550262 0.486923693 0.42197858 1 17.79164623 -1.936436192 2.861269701 1.306604232 0.533839954 0.744789058 0.082251053 43093174.81 16935990.45 87799070.9 0.019975376 0.011576141 1.936436192 -0.772764278 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MRPGAYSTGYGGYEEYSGLSDGYGFTTDLFGR 32 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;; 216.26 7.99E-36 1560750000 425807 489746 504591 514759 551930 653653 500664 562456 555410 577109 FALSE TRUE 442618.1892 573856.0658 517741.056 616576.7938 458113.1357 501851.997 461420.6474 554917.1973 535420.9026 690182.4591 0.641306054 0.831455593 0.750150991 0.893353324 0.663756561 0.727129457 0.668548789 0.804015214 0.775767184 1 19.39661828 0.491422802 1.337013477 0.9998682 0.748741628 0.504846816 0.074850677 1.834082607 3.976094468 0.068773778 0.020354615 3.100436221 -0.491422802 -0.251126572 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVK 41 2 A0A2R8Y5Y7;P32969;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;;;; 149.98 8.97E-14 731466000 445430.6 261465.8 443994.8 287027.2 551280 483029.7 446394.1 431365.3 481408.6 283954.8 FALSE TRUE 463016.544 306370.5172 455565.6692 343800.3235 457573.6225 370853.3726 411404.564 425583.5537 464082.7985 339590.3064 1.363456304 0.902176863 1.341515528 1.012397342 1.347428398 1.092061126 1.211473226 1.253226449 1.36659613 1 18.37343575 3.233091072 24.99977691 1.220667836 1.150166472 0.026365535 0.163195627 487.7073428 2229174.618 0.042907528 0.052667603 1710.373945 -3.233091072 -0.070501364 MS(ph)ADMSEIEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MSADMSEIEAR 11 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 MS(1)ADMSEIEAR;MS(0.999)ADMS(0.001)EIEAR;MS(1)ADMSEIEAR 193.14 0.00027364 50175000 608891 657899 754336 724656 885277 961940 823266 673295 753608 716786 TRUE FALSE 632930.4868 770888.0355 773994.6159 867990.7939 734797.9318 738544.0133 758736.2597 664270.5818 726485.7953 857226.493 0.738346857 0.899281627 0.902905617 1.012557126 0.857180614 0.861550616 0.885105939 0.774906734 0.847484068 1 19.70931691 3.046480778 24.99949764 0.854539044 0.895699836 0 0.081861959 416.6321613 224081.2049 0.023651066 0.028268422 1112.963131 -3.046480778 0.041160792 MS(ph)DEFVDSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSDEFVDSFK 10 0 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 MS(1)DEFVDSFK 90.653 0.011207 8098100 25277 19268 26696 19972 32086 35831 35640 25069 26157 18215 TRUE FALSE 26274.95548 22577.12912 27391.71969 23922.40199 26632.03318 27509.79327 32846.44367 24732.99106 25215.61468 21783.8805 1.206165057 1.036414477 1.257430681 1.098169905 1.222556889 1.262850908 1.507832531 1.135380405 1.157535485 1 14.41097335 4.220246449 24.94043061 1.2203016 1.121289694 0.05127294 0.132240665 528.4396443 719636.841 0.032633287 0.070712804 16605.28941 -4.220246449 -0.099011907 MS(ph)GFIYQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 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;MS(1)GFIYQGK;MS(1)GFIYQGK;MS(1)GFIYQGK 170.52 6.05E-05 13678922000 19629420 15820010 18625780 14556720 22970700 22191230 19803320 18457410 19136090 13101490 TRUE FALSE 20404404.66 18536973.65 19111183.13 17435995.77 19066148.62 17037653.14 18251084.03 18210018.61 18447385.86 15668476.12 1.302258401 1.183074443 1.219721878 1.112807374 1.216847667 1.087384185 1.164828276 1.162207382 1.177356733 1 23.90136154 -5 0.055499459 0.397970516 1.459087957 0.58935458 0.05001969 337.4822903 1.376619315 29.41054773 5.603218925 1.00E-05 5 1.061117441 MS(ph)GFIYQGKLPTTGMTITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSGFIYQGKLPTTGMTITK 19 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;Q14155-6;Q14155-2;Q14155-3;Q14155;E9PDQ5;E7EUY6;F6SJA5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 MS(1)GFIYQGKLPTTGMTITK;MS(1)GFIYQGKLPTTGMTITK 167.51 1.08E-11 1087090000 989260 808920 1061960 575340 1632870 1266130 932580 1093010 1228530 1011400 TRUE FALSE 1028316.749 947845.7175 1089635.55 689140.5348 1355315.341 972090.4959 859481.9428 1078359.989 1184315.445 1209564.466 0.850154562 0.783625631 0.900849505 0.569742709 1.120498642 0.803669853 0.710571422 0.891527504 0.979125527 1 20.20605623 1.369731323 3.557561836 0.991002531 0.82183674 0.205936039 0.132167325 0.363785549 7.461523143 0.098684412 0.032413745 23.42779003 -1.369731323 -0.169165791 MS(ph)GGSTMSSGGGNTNNSNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSGGSTMSSGGGNTNNSNSK 20 0 Q86U70-2;Q86U70;A0A6E1WJ75;Q86U70-3 Q86U70-2 LDB1 LIM domain-binding protein 1 1 MS(0.999)GGS(0.001)T(0.001)MSSGGGNTNNSNSK 120.31 4.00E-05 84857000 126700 92850 116500 98860 145510 150890 137250 123700 130140 74110 TRUE FALSE 131702.2138 108796.2652 119536.0857 118414.2129 120776.2622 115848.0843 126491.9864 122042.0038 125456.2868 88630.43558 1.485970513 1.227527141 1.348702451 1.336044578 1.362695121 1.307091447 1.427184528 1.376976239 1.415498931 1 16.43551458 -1.593795112 2.840134975 0.974604692 1.361898639 0.728769949 0.066827493 12888627.06 12535240.38 2438749.682 0.015297476 0.025480321 1.593795112 0.387293948 MS(ph)MLVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSMLVGK 7 0 D6REY2;P23508;P23508-2;A0A096LNU0 D6REY2 MCC Colorectal mutant cancer protein 1 MS(1)MLVGK 47.907 0.075508 0 9572.5 8581.4 12319 10493 15253 14002 9530.7 12674 11768 10533 TRUE FALSE 9950.429692 10055.1887 12640.04326 12568.48408 12660.30051 10750.2477 8783.65883 12504.12576 11344.47198 12596.73968 0.789921038 0.798237397 1.003437681 0.997756911 1.005045816 0.853415088 0.697296209 0.992647786 0.900587951 1 13.62076276 4.290689371 12.67766945 0.924467484 0.793877911 0.257625769 0.092581858 1.512927715 363.8677312 0.023720191 0.064941916 19529.42113 -4.290689371 -0.130589573 MS(ph)PNQLCSVPLQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MSPNQLCSVPLQPGR 15 0 Q86TB9-4 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR;MS(1)PNQLCSVPLQPGR 268.93 9.82E-26 1433410000 543109 592620 595283 553358 670980 796710 605286 627072 585525 580213 TRUE FALSE 564551.3627 694397.8751 610796.564 662810.5608 556927.0593 611686.1768 557842.1017 618667.1255 564452.0696 693894.6285 0.813598116 1.000725249 0.880243972 0.955203476 0.80261042 0.88152603 0.803929125 0.891586561 0.813455021 1 19.40435707 3.24949007 24.99993407 0.858895795 0.916448681 0.089812965 0.070879446 413.1762581 945089.7513 0.017777807 0.023835631 1776.192657 -3.24949007 0.057552886 MS(ph)PSKSPFLPSMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSPSKSPFLPSMK 13 1 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GV63;A0A1B0GWJ2;A0A1B0GTJ8;A0A1B0GVK1;H0Y7H8;Q8NFD5-4 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 MS(0.986)PS(0.014)KSPFLPSMK;MS(0.992)PS(0.008)KSPFLPSMK 130.27 8.72E-05 769680000 1629800 878980 1200660 805500 1696080 1557920 1446920 1232880 1452090 802450 TRUE FALSE 1694145.762 1029937.977 1231950.186 964825.4958 1407780.927 1196116.691 1333506.63 1216355.26 1399829.565 959674.7137 1.765333335 1.073215708 1.283716418 1.005367217 1.466935522 1.246377208 1.389540238 1.267466198 1.458650045 1 19.87218595 -1.655496936 2.834738731 0.967246381 1.311066489 0.185134135 0.20382623 209330230.5 185587152.6 49679334.73 0.044601117 0.022105639 1.655496936 0.343820108 MS(ph)PSQFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MSPSQFAR 8 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 MS(0.948)PS(0.052)QFAR;MS(0.993)PS(0.007)QFAR;MS(0.989)PS(0.011)QFAR;MS(0.772)PS(0.228)QFAR 169.93 0.00031272 549800000 723110 916740 768990 853840 905570 1070050 839760 807400 746200 970610 TRUE FALSE 751658.9412 1074182.964 789030.5111 1022727.004 751641.5349 821547.1043 773937.4169 796578.1236 719344.4078 1160782.446 0.647545062 0.925395596 0.679740216 0.881066911 0.647530067 0.707752867 0.666737699 0.686242393 0.619706484 1 20.14666618 3.219912498 24.99089275 0.700335189 0.786169991 0.039664378 0.12625537 539.9838077 723646.7246 0.033002907 0.039509413 1659.252567 -3.219912498 0.085834802 MS(ph)S(ph)Y(ph)QKELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSSYQKELEK 10 1 K7ES04;Q5JR82;Q9NZQ9-2;Q9NZQ9 K7ES04 TMOD4 Tropomodulin-4 3 MS(1)S(1)Y(1)QKELEK 103.75 0.0019863 141080000 125380 95287 117540 93120 148690 153360 137960 110580 109220 87535 TRUE FALSE 130330.0992 111651.801 120603.189 111538.8581 123415.7269 117744.4642 127146.3347 109097.856 105289.1935 104685.8073 1.244964361 1.066541912 1.152049089 1.065463036 1.178915558 1.124741426 1.214551791 1.042145624 1.005763783 1 16.67570634 1.576623269 5.537267473 1.009593691 1.143332833 0.565464345 0.054086161 0.101320747 6.531785591 0.028314698 0.013038895 37.72448063 -1.576623269 0.133739142 MS(ph)SPEDDSDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.5)S(0.5)PEDDSDTKR 115.06 0.0006064 565710000 422200 301840 417590 287520 538480 551150 459240 371170 410340 256170 TRUE FALSE 438868.782 353678.672 428472.7385 344390.5978 446949.3619 423153.7653 423243.5688 366195.0733 395571.9436 306361.6068 1.432518867 1.154448417 1.398584969 1.12413106 1.458894822 1.381223221 1.38151635 1.19530341 1.291192939 1 18.22487598 0.503912521 0.92336289 0.999996949 1.320557225 0.421552772 0.111676331 1.569897887 1.979602924 0.104188838 0.033423762 3.190895056 -0.503912521 0.320560277 MSAQESTPIMNGVTGPDGEDYS(ph)PWADRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSAQESTPIMNGVTGPDGEDYSPWADRK 28 1 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 MSAQESTPIMNGVTGPDGEDYS(1)PWADRK;MSAQESTPIMNGVTGPDGEDYS(1)PWADRK 164.83 4.38E-12 293600000 87331 72250 97979 82267 101173 117097 98039 88157 82585 71377 TRUE FALSE 90778.89531 84658.37547 100532.4132 98539.16706 83975.6496 89902.99637 90354.447 86975.39961 79612.78198 85361.95655 1.063458465 0.991757674 1.177719177 1.154368656 0.983759663 1.053197466 1.05848613 1.018901196 0.932649452 1 16.38130562 1.553569678 2.657471128 0.966613617 1.070220357 0.322216582 0.059398629 0.300202927 4.654034716 0.04525933 0.016675753 35.77417917 -1.553569678 0.10360674 MSATFIGNSTAIQELFKR ddPTM_MDA-MB-175_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 ; 289.61 6.24E-49 522120000 470800 492080 482630 343050 749360 663370 390390 502060 580120 658730 FALSE TRUE 489387.5475 576590.9121 495207.7343 410904.2661 621984.0549 509312.371 359790.2117 495330.7069 559241.5945 787795.5314 0.621211378 0.731904269 0.628599319 0.521587455 0.789524731 0.64650325 0.456705068 0.628755416 0.709881654 1 19.58746171 0.831633331 3.044670721 0.999830049 0.626400483 0.614470428 0.088325921 0.516474622 8.036206511 0.085754323 0.022426137 6.786304328 -0.831633331 -0.373429566 MSCFSRPS(ph)MS(ph)PTPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MS(0.063)CFS(0.083)RPS(0.862)MS(0.909)PT(0.083)PLDR;MS(0.003)CFS(0.021)RPS(0.973)MS(0.518)PT(0.485)PLDR;MS(0.001)CFS(0.005)RPS(0.99)MS(0.938)PT(0.065)PLDR;MSCFSRPS(1)MS(0.968)PT(0.032)PLDR;MS(0.001)CFS(0.011)RPS(0.989)MS(0.901)PT(0.099)PLDR;MSCFSRPS(0.997)MS(0.789)PT(0.214)PLDR;MS(0.034)CFS(0.038)RPS(0.938)MS(0.941)PT(0.049)PLDR;MS(0.012)CFS(0.015)RPS(0.97)MS(0.617)PT(0.385)PLDR 144.73 1.54E-05 3063593000 1454336 1911217 1664481 1663109 1880610 2190816 1665820 1937619 1787736 2126878 TRUE FALSE 1511754.308 2239453.653 1707858.742 1992066.996 1560944.584 1682032.186 1535248.676 1911648.387 1723395.731 2543599.023 0.594336723 0.880427156 0.671433951 0.783168644 0.613675572 0.661280403 0.603573386 0.751552572 0.677542221 1 21.27843983 -1.163276884 4.450913086 1.000056157 0.697366642 0.538345758 0.085201827 11652175.28 3045378.213 6485.298308 0.018792045 0.068663054 1.163276884 -0.302689515 MSCFSRPS(ph)MSPT(ph)PLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 MSCFS(0.013)RPS(0.963)MS(0.507)PT(0.516)PLDR;MS(0.001)CFS(0.012)RPS(0.987)MS(0.181)PT(0.819)PLDR 133.86 0.00078744 864010000 504979 686030 641180 586310 705780 795410 591910 656290 618160 755190 TRUE FALSE 524915.9608 803850.3159 657889.6775 702280.368 585811.7677 610688.0821 545514.5475 647493.506 595912.5424 903155.0215 0.581202505 0.890046888 0.728434944 0.777585632 0.648628147 0.676171939 0.60400987 0.716923995 0.659812024 1 19.78461411 -0.969167347 9.303057992 0.999999959 0.701878893 0.533992222 0.084544385 0 6.35E-11 0.079301548 0.018691554 0.107357565 0.969167347 -0.298121066 MSCFSRPSMS(ph)PTPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.001)MS(0.969)PT(0.029)PLDR;MSCFSRPS(0.01)MS(0.913)PT(0.077)PLDR;MSCFSRPS(0.013)MS(0.947)PT(0.04)PLDR;MSCFSRPS(0.036)MS(0.818)PT(0.146)PLDR;MS(0.013)CFS(0.054)RPS(0.178)MS(0.695)PT(0.061)PLDR;MSCFSRPS(0.002)MS(0.581)PT(0.418)PLDR;MSCFSRPSMS(0.602)PT(0.398)PLDR;MSCFSRPS(0.012)MS(0.876)PT(0.112)PLDR;MSCFSRPS(0.012)MS(0.494)PT(0.494)PLDR;MSCFSRPSMS(0.837)PT(0.163)PLDR 135.91 1.23E-05 10121270000 3071410 3883460 3517400 3171520 3941560 4375720 3100600 3631700 3534080 4040000 TRUE FALSE 3192671.638 4550414.046 3609066.334 3798837.19 3271575.039 3359525.345 2857566.87 3583023.002 3406889.151 4831560.65 0.660795107 0.941810395 0.746977342 0.786254684 0.677125938 0.69532923 0.591437649 0.74158709 0.705132233 1 22.20405784 -1.421312579 2.980949081 1.005102113 0.728554743 0.464794407 0.087753306 17512124.39 20785887.15 756006.2702 0.023090613 0.037904208 1.421312579 -0.27654737 MSCFSRPSMSPT(ph)PLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSCFSRPSMSPTPLDR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MSCFSRPS(0.001)MS(0.186)PT(0.814)PLDR 97.69 0.0082546 1097800000 387040 530090 448850 384900 499660 547470 388420 490380 417010 454530 TRUE FALSE 402320.6381 621128.834 460547.3997 461032.0712 414727.9717 420328.3895 357974.6255 483807.2582 402001.8916 543586.451 0.740122638 1.142649587 0.847238556 0.848130174 0.762947588 0.773250306 0.658542215 0.890028177 0.739536261 1 19.05214997 4.015172259 24.91506001 0.802205497 0.954775637 0.141601724 0.125404647 329.7562329 541499.4575 0.028587791 0.061724472 10355.52828 -4.015172259 0.15257014 MSDT(ph)GSPGMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MSDT(0.882)GS(0.118)PGMQR;MSDT(0.809)GS(0.191)PGMQR 162.49 0.00028025 930920000 741530 1094830 1098040 1022340 1235460 1296560 1016810 1097660 1059250 1067470 TRUE FALSE 770806.177 1282858.536 1126655.824 1224555.801 1025456.95 995453.5896 937109.7753 1082947.663 1021127.799 1276620.309 0.603786554 1.004886517 0.882530081 0.95921692 0.803259155 0.779756975 0.734055199 0.84829268 0.799868052 1 20.28389807 MSDTGS(ph)PGMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSDTGSPGMQR 11 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 MS(0.001)DT(0.266)GS(0.733)PGMQR 91.245 0.0052923 0 148440 159270 164990 173450 190600 218850 161950 171580 170190 169240 TRUE FALSE 154300.5258 186623.3836 169289.7749 207757.8923 158201.8801 168025.4042 149255.9358 169280.2507 164064.8951 202399.3377 0.762356871 0.922055307 0.836414668 1.026475159 0.7816324 0.830167757 0.737432926 0.836367612 0.81059996 1 17.62684504 MSES(ph)PTPCSGSSFEETEALVNTAAK ddPTM_MDA-MB-175_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(0.165)ES(0.788)PT(0.046)PCSGS(0.001)SFEETEALVNTAAK;MS(0.132)ES(0.737)PT(0.132)PCSGSSFEETEALVNTAAK;MS(0.05)ES(0.36)PT(0.36)PCS(0.057)GS(0.057)S(0.057)FEET(0.057)EALVNTAAK;MS(0.064)ES(0.467)PT(0.467)PCS(0.002)GSSFEETEALVNTAAK 301.55 1.85E-63 902868000 509263 443669 513023 396006 620507 596606 577583 526389 591259 431761 TRUE FALSE 529369.0965 519865.6995 526392.8008 474334.8048 515033.4418 458053.2982 532310.5352 519333.6165 569979.7041 516356.3014 1.025201194 1.006796466 1.019437159 0.918619185 0.997438088 0.88708765 1.030897723 1.005766009 1.103849614 1 18.97800739 1.71082223 2.352003153 1.047792281 0.978316666 0.2206607 0.050100816 0.376780142 4.44369622 0.032354132 0.013703145 51.38332812 -1.71082223 -0.069475615 MSESPT(ph)PCSGSSFEETEALVNTAAK ddPTM_MDA-MB-175_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 1 MS(0.044)ES(0.408)PT(0.547)PCS(0.001)GS(0.001)SFEETEALVNTAAK 213.45 9.93E-26 116300000 83764 61400 74790 57374 98669 89635 81055 74081 86462 55449 TRUE FALSE 87071.0674 71944.97237 76739.08884 68722.40596 81897.27862 68818.62968 74701.6973 73088.06537 83350.24951 66313.16991 1.313028279 1.08492736 1.157222448 1.036331185 1.235007748 1.037782235 1.126498664 1.102165158 1.256918492 1 16.0170078 4.744679682 24.56512148 1.11829601 1.31302839 0.358064373 0.079365417 555.3982361 2229578.194 0.016988212 0.15428679 55549.4396 -4.744679682 0.19473238 MSGSAS(ph)SENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSGSASSENR 10 0 A0A5F9UY30;A0A5H1ZRP2;O43493-4;O43493;O43493-5;O43493-3;O43493-7;O43493-6 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 MSGS(0.038)AS(0.957)S(0.004)ENR;MSGS(0.033)AS(0.966)S(0.001)ENR 130.4 0.0010853 348820000 550830 667230 599060 813460 940610 1058680 876140 718540 607110 919490 TRUE FALSE 572577.1937 781821.5622 614671.9957 974359.9601 780725.4482 812817.6145 807465.8574 708909.1466 585260.2297 1099646.461 0.520692072 0.710975382 0.558972377 0.886066563 0.709978594 0.73916267 0.734295873 0.644670057 0.532225811 1 20.06860834 3.794856027 24.99996842 0.726979908 0.60828946 0.213467135 0.128722009 541.3278038 240393.6449 0.031687257 0.057124996 6235.280948 -3.794856027 -0.118690447 MSMTGAGKS(ph)PPSVQSLAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSMTGAGKSPPSVQSLAMR 19 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;A2ABF9;A0A0G2JK64;Q96KQ7-2;Q96KQ7;Q96KQ7-3 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 MSMTGAGKS(0.999)PPS(0.001)VQSLAMR;MS(0.002)MT(0.092)GAGKS(0.879)PPS(0.022)VQS(0.005)LAMR 148.36 5.83E-08 476760000 588660 526020 609530 431310 754640 767350 593740 522420 668050 506920 TRUE FALSE 611900.7513 616359.8431 625414.8525 516621.8307 626366.5624 589144.5918 547201.1073 515417.8144 644007.011 606241.2684 1.009335364 1.016690673 1.031626986 0.852171994 1.033196839 0.97179889 0.902612765 0.850185959 1.062294906 1 19.20953254 3.842003667 23.14802878 0.942298512 1.018967223 0.155292656 0.06730713 31.15635852 6959.192903 0.017511088 0.031568576 6950.301857 -3.842003667 0.076668711 MSQPGS(ph)PSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 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 MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.992)PS(0.008)PK;MSQPGS(0.999)PS(0.001)PK;MS(0.002)QPGS(0.92)PS(0.078)PK;MS(0.001)QPGS(0.986)PS(0.014)PK;MS(0.001)QPGS(0.964)PS(0.035)PK;MSQPGS(0.838)PS(0.162)PK;MSQPGS(0.939)PS(0.061)PK;MSQPGS(0.939)PS(0.061)PK;MSQPGS(0.961)PS(0.039)PK;MS(0.005)QPGS(0.969)PS(0.026)PK;MSQPGS(0.999)PS(0.001)PK;MSQPGS(0.998)PS(0.002)PK;MSQPGS(0.992)PS(0.008)PK 197.38 3.32E-07 19598098000 19982462 12752278 17436975 13026428 22053561 22269027 21517728 17715598 18625916 11428623 TRUE FALSE 20771385.03 14942382.55 17891396.89 15603016.58 18304904.58 17097382.97 19831112.25 17478149.39 17955572.92 13667842.86 1.519726649 1.093250976 1.309013944 1.141585891 1.339268 1.250920364 1.450932122 1.278778924 1.313709347 1 23.70428223 -1.232717165 5.677510058 0.999987037 1.294415092 0.359093856 0.11992502 1.80E-05 2.43E-06 0.106233736 0.02503843 0.058517105 1.232717165 0.294428055 MSQPGSPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSQPGSPSPK 10 0 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 MSQPGS(0.349)PS(0.651)PK 217.96 7.35E-09 3393500000 2194900 1392500 1913600 1419000 2337100 2251000 2341600 1947600 1972600 1156800 TRUE FALSE 2281556.347 1631651.043 1963469.988 1699673.965 1939840.577 1728239.364 2158059.273 1921495.608 1901606.511 1383452.812 1.649175402 1.179404913 1.419253314 1.228573863 1.402173287 1.249221766 1.559908119 1.388913009 1.374536591 1 20.39984201 0.872242476 14.84596445 1 1.379270007 0.413825063 0.136844142 1405.40385 163319.1033 0.120371574 0.030092576 7.451478895 -0.872242476 0.379270007 MSS(ph)PEDDSDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSSPEDDSDTKR 12 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 MS(0.146)S(0.854)PEDDSDTKR 116.63 9.70E-05 0 576830 418690 518150 380710 720220 679410 587750 467650 553430 326590 TRUE FALSE 599603.6938 490596.7505 531653.4147 456013.3017 597797.2617 521627.3241 541680.6192 461381.9167 533512.1624 390579.0576 1.535166011 1.256075412 1.361192835 1.167531369 1.530541001 1.335523024 1.386865498 1.18127664 1.365951789 1 18.57525507 -3.912964728 0.216918435 2.34E-09 1.386598452 0.455489408 0.116085046 79.75715256 1.220830612 35.11296009 0.224324396 0.00012219 3.912964728 1.386598449 MSS(ph)PLADAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSSPLADAK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 MS(0.03)S(0.97)PLADAK;MS(0.082)S(0.918)PLADAK 131.83 0.000338 222600000 649680 457390 530040 446760 678970 761850 679630 559240 591760 412670 TRUE FALSE 675329.8681 535943.1745 543853.2778 535127.7946 563558.9219 584921.8834 626358.8247 551744.3025 570462.6732 493524.7855 1.368380855 1.085949866 1.101977639 1.08429771 1.141906017 1.185192519 1.269153735 1.117966754 1.155894678 1 18.91276301 0.442143198 1.553221749 1.00006264 1.164037969 0.260351131 0.084906446 5.057125087 12.55263318 0.079214615 0.022729447 2.767854127 -0.442143198 0.163975329 MSSCVPRPPS(ph)HGGPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(0.999)HGGPT(0.001)R;MSSCVPRPPS(0.999)HGGPT(0.001)R;MSSCVPRPPS(0.566)HGGPT(0.434)R;MSSCVPRPPS(0.988)HGGPT(0.012)R 114.53 0.00034915 1372330000 166357 193409 190406 174915 199206 244101 166218 165109 165586 180401 TRUE FALSE 172924.9028 226625.4912 195368.1368 209512.6649 165345.0353 187412.2421 153189.3988 162895.9839 159626.5922 215747.122 0.801516615 1.050421851 0.905542262 0.971102942 0.766383504 0.868666244 0.710041448 0.755032014 0.7398782 1 17.71898179 3.236120104 24.99992756 0.788241473 0.938693948 0.272902377 0.097362645 66.63362674 682578.5514 0.025922859 0.032390154 1722.344825 -3.236120104 0.150452475 MSSCVPRPPSHGGPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSSCVPRPPSHGGPTR 16 1 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 MSSCVPRPPS(0.198)HGGPT(0.802)R 117.65 0.00053856 349970000 57824 77643 63384 67513 72150 87875 59763 81001 77268 71467 TRUE FALSE 60106.93617 90977.58127 65035.83911 80866.86989 59885.96877 67467.36301 55078.6199 79915.31409 74487.13977 85469.59033 0.703255227 1.064443867 0.760923726 0.946147859 0.700669894 0.78937272 0.644423586 0.935014591 0.871504584 1 16.38312359 1.125690079 1.708398954 0.98722689 0.814695744 0.180095301 0.122296329 0.586351466 3.29676114 0.110065927 0.032134098 13.35642037 -1.125690079 -0.172531147 MSSEGPPRMS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MSSEGPPRMSPK 12 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 MSSEGPPRMS(1)PK;MS(0.006)S(0.006)EGPPRMS(0.988)PK;MSSEGPPRMS(0.999)PK 120.7 0.00023575 1061500000 2061820 1110000 1549980 1092730 2096430 2151530 1726670 1508250 1620150 1041630 TRUE FALSE 2143222.246 1300633.865 1590373.752 1308868.733 1740079.577 1651869.764 1591329.094 1488034.376 1561841.118 1245717.455 1.720472196 1.044084162 1.276672929 1.050694704 1.396849318 1.326038868 1.277439829 1.194519969 1.25376835 1 20.24854545 -5 0.158838883 0.020003879 1.341859395 0.209075989 0.177357254 225.1975073 2.064299684 69.71564904 0.722409857 1.00E-05 5 1.321855515 MSSYAFFVQTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MSSYAFFVQTCR 12 0 P26583;D6R9A6;P09429;Q5T7C4;B2RPK0 P26583;P09429 HMGB2;HMGB1;HMGB1P1 High mobility group protein B2;High mobility group protein B1;Putative high mobility group protein B1-like 1 0 ; 165.66 0.00012561 325250000 249670 324900 274580 242010 507670 458850 305290 281370 293220 587650 FALSE TRUE 259527.1644 380699.0476 281735.7804 289878.8557 421376.4347 352289.0414 281360.5721 277598.6954 282667.0695 702788.7663 0.369281891 0.541697685 0.400882589 0.412469393 0.599577647 0.501273012 0.400348704 0.39499592 0.402207723 1 19.42273161 -1.36852142 5.313476385 1.000243747 0.447558802 0.842537104 0.071723535 0.000211328 2.51E-05 0.070863644 0.016695506 0.042803431 1.36852142 -0.552684945 MSTSQNS(ph)IPFEHHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MSTSQNSIPFEHHGK 15 0 P48730-2 P48730-2 CSNK1D Casein kinase I isoform delta 1 MSTS(0.002)QNS(0.998)IPFEHHGK;MSTSQNS(1)IPFEHHGK;MSTSQNS(1)IPFEHHGK;MSTSQNS(1)IPFEHHGK;MS(0.002)T(0.002)S(0.001)QNS(0.995)IPFEHHGK 158.58 3.03E-06 1305484000 878422 808772 1071310 886810 1155740 1171470 1160220 1042630 1098110 815538 TRUE FALSE 913102.7788 947672.2996 1099229.219 1062218.371 959287.7276 899413.8463 1069278.925 1028655.25 1058589.236 975327.0567 0.936201629 0.971645658 1.127036527 1.089089412 0.983554922 0.922166406 1.096328578 1.054677242 1.08536847 1 19.89552655 MSVIEEGDCKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MSVIEEGDCKR 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;; 143 6.00E-05 660410000 521080 442170 486250 478960 621850 659550 540050 499780 515050 418850 FALSE TRUE 541652.6408 518109.2579 498922.0745 573696.8584 516148.1591 506379.5081 497719.4698 493081.2666 496513.4511 500915.6381 1.081325077 1.034324382 0.996020161 1.145296363 1.030409354 1.010907765 0.993619348 0.984359898 0.99121172 1 18.93420813 2.761429753 2.94908509 0.99232569 1.059393398 0.432959551 0.036247482 0.259955105 4.565904541 0.012135761 0.012302341 577.3374805 -2.761429753 0.067067708 MSVQPTVSLGGFEITPPVVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSVQPTVSLGGFEITPPVVLR 21 0 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 140.84 3.09E-08 0 25231 30896 34184 23319 37064 42525 34506 30658 33412 28382 FALSE TRUE 26227.13936 36202.14766 35074.86312 27931.4286 30763.87452 32649.21322 31801.32956 30247.07966 32209.50865 33942.90949 0.772683891 1.066559944 1.033348751 0.822894355 0.906341707 0.961886111 0.936906412 0.891116292 0.948931872 1 15.05082261 2.754563223 23.80120272 0.936092922 0.929349403 0.010736766 0.085432144 9233.491278 13733203.24 0.026430813 0.027909176 568.2811136 -2.754563223 -0.006743519 MSWFVDLAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSWFVDLAGK 10 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 100.45 0.0093162 141580000 138310 117810 135060 113910 168860 156430 137150 136620 138250 98090 FALSE TRUE 143770.5856 138042.9511 138579.7746 136441.058 140157.2375 120101.5032 126399.8246 134788.8324 133274.4095 117308.8575 1.225573147 1.176747895 1.18132405 1.163092549 1.194771141 1.023805924 1.077496 1.149008142 1.136098436 1 16.83995242 2.764041477 24.93384022 1.091554989 1.185871724 0.589431788 0.045533628 620.3103646 606992.2734 0.014290944 0.015151688 580.8198853 -2.764041477 0.094316735 MSYLTAMGADYLS(ph)CDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(0.999)CDS(0.001)R;MSYLTAMGADYLS(0.999)CDS(0.001)R;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.996)CDS(0.004)R;MSYLTAMGADYLS(0.999)CDS(0.001)R;MSYLTAMGADYLS(0.999)CDS(0.001)R;MSYLTAMGADYLS(1)CDSR;MSYLTAMGADYLS(0.998)CDS(0.002)R;MSYLTAMGADYLS(0.769)CDS(0.231)R;MSYLTAMGADYLS(0.999)CDS(0.001)R 328.73 6.40E-72 1329918000 1331608 1921374 1812938 1823328 2127429 2329878 1735376 1917447 1869277 2209864 TRUE FALSE 1384180.912 2251355.038 1860184.654 2183976.836 1765809.378 1788799.144 1599352.695 1891746.759 1802002.086 2642844.54 0.523746626 0.851868131 0.703857009 0.826373554 0.668147275 0.676846147 0.605163365 0.715799484 0.681841878 1 21.33366013 -1.960746438 2.459888908 1.240510098 0.699590728 0.507284414 0.090112109 9595239.765 4665333.276 13172695.15 0.020543202 0.010945953 1.960746438 -0.54091937 MSYYCSGSSDAPS(ph)SPAAPRPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MSYYCSGSSDAPSSPAAPRPASK 23 1 Q8NF50-3;Q8NF50;A2A369;A2A370 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 MSYYCSGSSDAPS(0.499)S(0.499)PAAPRPASK 69.435 0.0056228 0 49352 28041 36253 28329 44075 48630 32025 29206 34910 22699 TRUE FALSE 51300.45507 32856.82362 37197.78296 33932.39165 36583.14724 37336.41949 29514.79682 28814.54134 33653.59592 27146.43445 1.889767703 1.210355035 1.370264041 1.249976004 1.347622551 1.375371029 1.087243957 1.061448471 1.239705936 1 14.7284751 7.04651352 1.205558987 1.202105714 200 0.70653057 0.128679203 263.3684417 1.702124174 0.037818143 143329.8041 11130470.42 -7.04651352 198.7978943 MTDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MTDFDR 6 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 128.38 0.038736 2304500000 3498900 4029800 4189700 3868700 5153700 4984200 4208400 4498700 4548900 4784800 FALSE TRUE 3637039.274 4721886.803 4298887.024 4633917.313 4277675.915 3826695.086 3878534.611 4438402.285 4385185.978 5722289.949 0.635591574 0.825174335 0.751252918 0.809801208 0.747546166 0.668734916 0.677794143 0.775633937 0.76633411 1 22.44816117 0.494755848 1.524682227 0.999925238 0.738412893 0.651644883 0.057549485 1.658115533 4.335606879 0.054688942 0.015765137 3.124322436 -0.494755848 -0.261512346 MTDQEAIQDLWQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;;;;;;;;;;; 324.67 2.70E-56 13572215000 3604828 4472777 4248930 4123424 4349379 5119053 4234025 4221002 4044195 4395791 FALSE TRUE 3747149.393 5240941.656 4359660.606 4939024.96 3610073.111 3930230.521 3902151.057 4164426.372 3898645.212 5257062.084 0.712783934 0.996933567 0.829296009 0.939502878 0.686709241 0.747609684 0.742268399 0.792158492 0.741601516 1 22.32582534 3.245684413 24.99941624 0.771475021 0.875841328 0.126699679 0.104700552 261.4410015 917464.5742 0.026657391 0.035351839 1760.696143 -3.245684413 0.104366307 MTEEEVEMLVAGHEDS(ph)NGCINYEELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR;MTEEEVEMLVAGHEDS(1)NGCINYEELVR 376.36 2.47E-127 1072289000 509799 662298.8 580587.8 615894.6 668266 734952 565013.8 609070.1 600253.7 710254.7 TRUE FALSE 529926.2582 776043.4669 595718.395 737716.7136 554674.384 564270.5363 520726.542 600906.5115 578650.6866 849415.5098 0.623871653 0.913620552 0.701327428 0.868499227 0.65300713 0.664304489 0.61304101 0.707435295 0.681233954 1 19.69611093 -1.252339358 4.024942871 1.000274873 0.715775855 0.451076289 0.094619481 14181688.04 4412600.223 34451.6998 0.021811822 0.055932038 1.252339358 -0.284499017 MTEEEVEMLVAGHEDSNGCINYEAFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MTEEEVEMLVAGHEDSNGCINYEAFVR 27 0 P60660;J3KND3;G3V1Y7 P60660 MYL6 Myosin light polypeptide 6 0 ;;; 282.87 3.23E-61 425250000 162883.2 222707 201085.2 229428 239016 273883 216404 232529 222634 215421 FALSE TRUE 169313.9545 260955.1948 206325.6455 274808.1736 198388.1457 210277.824 199441.689 229412.3291 214621.4458 257628.6205 0.65720165 1.012912286 0.800864613 1.066683403 0.770054761 0.816205217 0.774144148 0.890476876 0.833065229 1 17.97493335 -0.997879391 3.987961861 1.000013989 0.853304257 0.138872594 0.113391399 5519212.966 2768501.117 655.1486061 0.024258978 0.100489482 0.997879391 -0.146709732 MTEEEVEMLVAGHEDSNGCINYEELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 25 MTEEEVEMLVAGHEDSNGCINYEELVR 27 0 P60660-2;G8JLA2;F8VZU9;F8W180;F8VXL3 P60660-2 MYL6 Myosin light polypeptide 6 0 ;;;;;;;;;;;;;;;;;;;;;;;; 414.8 1.07E-165 5083927200 1637746.9 2213512.3 2218059.3 2204249 2467119.8 2794165.1 2253162.5 2334036.1 2272200.3 2344443.3 FALSE TRUE 1702406.412 2593665.819 2275863.748 2640242.873 2047759.658 2145262.602 2076553.736 2302752.164 2190424.255 2803792.078 0.607179978 0.925056405 0.811709173 0.941668569 0.730353607 0.76512899 0.740623298 0.821299191 0.781236338 1 21.41894794 -1.153161331 4.714569258 1.000020601 0.797524064 0.318149353 0.091161274 1.84E-05 3.31E-06 0.082321793 0.01940146 0.070281119 1.153161331 -0.202496537 MTELETAMGMIIDVFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MTELETAMGMIIDVFSR 17 0 P25815 P25815 S100P Protein S100-P 0 ; 205.72 4.63E-17 446100000 304590 147684 183626 156045 237840 275940 213334 139741 158768 128537 FALSE TRUE 316615.4484 173047.5782 188411.4444 186910.2353 197412.0418 211857.1169 196612.3236 137868.0005 153053.9707 153721.3642 2.059671082 1.125722369 1.225668569 1.215902788 1.284219945 1.378189155 1.279017557 0.896869483 0.995658421 1 17.22995816 4.739921367 24.94747282 1.160836027 2.059671381 0.779700343 0.144128986 57.65382415 1056890.114 0.038535799 0.24200486 54944.13835 -4.739921367 0.898835354 MTESWFSSLSRDPLELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTESWFSSLSRDPLELFR 18 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 203.06 1.12E-15 330250000 230910 410140 341420 362290 383490 448090 268780 368570 315020 511650 FALSE TRUE 240026.5051 480578.3546 350317.6857 433949.8807 318304.5068 344027.8884 247712.3213 363629.922 303682.4917 611898.0214 0.392265536 0.78538962 0.572509917 0.709186605 0.520192084 0.562230758 0.404826152 0.594265563 0.49629592 1 19.22293171 -1.673735701 6.448302965 1.003421784 0.565386072 0.567901902 0.115126469 0.005380607 0.000272242 0.105905244 0.024831161 0.021196507 1.673735701 -0.438035712 MTGS(ph)PTLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MTGSPTLVK 9 0 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 MT(0.001)GS(0.913)PT(0.086)LVK;MT(0.003)GS(0.988)PT(0.009)LVK;MT(0.015)GS(0.943)PT(0.043)LVK 112.83 0.0019913 222590000 1580220 857360 1086430 858640 1463570 1540770 1416580 1086630 1165510 818530 TRUE FALSE 1642608.306 1004604.911 1114743.258 1028476.429 1214792.894 1182949.518 1305544.758 1072065.502 1123563.523 978905.2818 1.678005356 1.026253438 1.138765189 1.050639371 1.240970824 1.208441246 1.333678327 1.095167757 1.147775524 1 19.90080975 4.746910136 24.86022747 1.150068486 1.678005641 0.730666436 0.098115845 516.8540473 1538867.018 0.023193598 0.266324717 55835.46483 -4.746910136 0.527937156 MTGSAPPPS(ph)PTPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 MTGSAPPPS(0.937)PT(0.063)PNK;MTGSAPPPS(0.959)PT(0.041)PNK 227.73 2.01E-12 323700000 632340 497310 592030 523910 698710 709880 746080 636720 615700 392610 TRUE FALSE 657305.2715 582719.124 607458.7882 627537.8343 579943.5238 545021.1283 687600.3001 628185.8099 593541.0773 469534.4125 1.39990862 1.241057329 1.293747108 1.336510845 1.235145941 1.160769294 1.464430043 1.337890883 1.264105594 1 18.84087137 0.859678402 5.509223349 1.000003385 1.308433571 0.561185176 0.08142298 1.530639856 59.67955766 0.078851093 0.019869906 7.238997093 -0.859678402 0.308430186 MTGSEFDFEEMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 MTGSEFDFEEMKR 13 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;;;;;;; 225.23 2.05E-11 6622770000 5111900 4258084 5228307 4141668 6652390 6431630 6092551 5429571 5984560 4245541 FALSE TRUE 5313721.759 4989376.804 5364560.976 4960877.569 5521619.124 4937981.405 5615000.933 5356796.482 5769176.855 5077373.473 1.046549321 0.98266886 1.056562217 0.977055872 1.087495169 0.972546422 1.105886924 1.055032983 1.136252215 1 22.27565095 2.225293623 24.99178245 1.077288731 1.021473435 0.232108393 0.047806783 307.9421685 580084.5891 0.016121318 0.011977224 167.9939428 -2.225293623 -0.055815296 MTKEELNALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTKEELNALK 10 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 90.146 0.010503 0 186860 127860 169220 124930 241270 228220 184890 168880 200030 144180 FALSE TRUE 194237.3771 149818.9604 173630.0122 149640.7811 200259.0116 175219.3637 170397.8387 166616.4398 192830.9594 172429.3105 1.126475403 0.868871771 1.006963443 0.867838424 1.16139774 1.016180852 0.988218524 0.966288384 1.118318915 1 17.39564551 3.259209332 24.9999859 1.030247485 0.963305958 0.135945934 0.088594079 529.0998561 640592.0923 0.023568643 0.031877661 1816.390962 -3.259209332 -0.066941527 MTNHCVFSANEDHETIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTNHCVFSANEDHETIR 17 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;E9PFE3;C9JF98;F8WDX8;E7EMS9;Q9Y6E2-2 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 203.56 5.54E-12 258140000 47722 82183 86989 94614 100110 128230 87253 92441 81676 78982 FALSE TRUE 49606.10141 96297.29096 89256.0048 113328.3668 83093.33796 98450.52584 80413.88187 91201.9796 78736.49671 94457.0107 0.525171197 1.019482728 0.944937852 1.199787776 0.879694766 1.042278653 0.851327829 0.96553955 0.833569643 1 16.52737026 4.742499429 24.83975198 0.9696293 0.525171008 0.634584489 0.101430119 220.9591973 1393398.318 0.023168358 0.17614036 55271.2681 -4.742499429 -0.444458292 MTNNEDSLS(ph)PTSSTLSNLELDAAEKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 MTNNEDS(0.02)LS(0.954)PT(0.026)S(0.001)STLSNLELDAAEKDR;MTNNEDS(0.09)LS(0.523)PT(0.184)S(0.069)S(0.067)T(0.061)LS(0.006)NLELDAAEKDR 128.89 3.37E-05 512700000 183269 159083 155934 150707 208313 215619 184002 171789 191057 157430 TRUE FALSE 190504.6016 186404.2678 159997.7681 180516.3948 172904.0307 165544.755 169579.4424 169486.4494 184180.8959 188275.3943 1.011840142 0.990061757 0.849807107 0.958789094 0.918357023 0.879269198 0.90069891 0.90020499 0.97825261 1 17.52248494 4.408488955 9.452658803 0.917175739 1.006432028 0.336918783 0.043461644 0.269440183 34.40481299 0.009820882 0.027001164 25614.68122 -4.408488955 0.089256289 MTPHEK ddPTM_MDA-MB-175_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 ;;; 114.54 0.025198 1182600000 2239260 1894070 2164130 1859900 2673200 2686350 2467030 2171800 2142440 1799050 FALSE TRUE 2327667.714 2219361.789 2220529.006 2227782.669 2218810.419 2062485.925 2273657.742 2142690.573 2065334.003 2151539.403 1.081861532 1.031522726 1.032065229 1.035436612 1.031266458 0.958609413 1.056758589 0.99588721 0.959933153 1 21.03693783 8 0.270203318 0.989632331 1.583861865 0.457569373 0.027706568 48.04520108 0.673044939 0.031252864 13.31908591 100000000 -8 0.594229535 MTSERAPS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MTSERAPSPSSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 MTSERAPS(0.978)PS(0.019)S(0.002)R;MTSERAPS(0.997)PS(0.002)S(0.001)R 94.007 0.0020562 0 420490 709950 571670 476170 644640 822750 411120 541900 547120 979830 TRUE FALSE 437091.2699 831878.3899 586568.1898 570355.0048 535064.3231 631678.7814 378895.3401 534636.7169 527429.2581 1171808.929 0.373005581 0.709909585 0.500566411 0.48673038 0.456613967 0.539062953 0.323342254 0.456249056 0.450098344 1 20.16030592 -1.140390181 5.603811713 1.000007955 0.477923747 0.721863733 0.097338117 9.53E-06 1.46E-06 0.092828008 0.021879438 0.07237854 1.140390181 -0.522084208 MTSHHFEGAQILSQLQCSGMVSVLDLMQGGYPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MTSHHFEGAQILSQLQCSGMVSVLDLMQGGYPSR 34 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 168.61 1.03E-14 206350000 33183 76551 73233 84837 80073 89631 65647 80274 84041 87457 FALSE TRUE 34493.09046 89698.03877 75141.51214 101617.5054 66462.22006 68815.55862 60501.4166 79198.05833 81016.38083 104592.5247 0.329785427 0.85759512 0.718421439 0.9715561 0.635439485 0.65793955 0.578448764 0.757205724 0.774590546 1 16.67442022 0.80236221 1.738487803 0.999076024 0.696804375 0.256661889 0.160750337 0.985066253 5.283723664 0.146389937 0.041539649 6.343985912 -0.80236221 -0.302271649 MTSSDKDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MTSSDKDFR 9 1 Q86VP6;Q86VP6-2;O75155-2;O75155;A0A3B3ISC4;F8WBB8 Q86VP6 CAND1;CAND2 Cullin-associated NEDD8-dissociated protein 1;Cullin-associated NEDD8-dissociated protein 2 0 ;;;;;;; 90.15 0.010602 3402640000 9501870 8371440 9734020 8390240 13417450 12390480 10910040 9880750 10279790 9218320 FALSE TRUE 9877011.165 9809169.699 9987696.558 10049804.43 11136756.64 9512978.8 10054882.56 9748314.708 9909822.366 11024473.31 0.895916829 0.889763114 0.9059568 0.911590436 1.010184916 0.862896443 0.912051059 0.884243123 0.898893044 1 23.3942064 3.948295825 3.095156492 0.918711962 0.893321441 0.069289599 0.04448491 0.863478534 16.39827934 0.011635723 0.025252519 8877.605159 -3.948295825 -0.025390522 MVDPEKPQLGMIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVDPEKPQLGMIDR 14 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 69.602 0.048844 187050000 346820 282060 335050 281350 417450 417900 365120 342290 345470 284310 FALSE TRUE 360512.7214 330501.6109 343781.6782 337000.1903 346491.9981 320849.0583 336500.9403 337702.1624 333036.6022 340015.1011 1.060284441 0.972020389 1.011077676 0.991133009 1.019048851 0.94363179 0.989664692 0.993197541 0.979475915 1 18.3752393 4.747128495 24.84797321 0.989121524 1.06028448 0.536502353 0.019929417 767.9074268 2226976.808 0.004548453 0.052932608 55863.54545 -4.747128495 0.071162956 MVEGFFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MVEGFFDR 8 0 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ;;;;; 139.97 0.0015286 746029000 730111 1042570 786142 982728 809224 1272881 827409 761116 740732 1168256 FALSE TRUE 758936.346 1221623.287 806629.5063 1177108.665 671672.3935 977273.6784 762554.5205 750914.485 714073.2 1397153.396 0.543201876 0.874365901 0.577337828 0.84250496 0.480743486 0.699474862 0.545791552 0.537460301 0.511091482 1 20.41405899 -1.038179346 4.646909239 1.000011575 0.624241163 0.426195508 0.131037613 1.66E-05 3.44E-06 0.12195468 0.028744019 0.091584221 1.038179346 -0.375770412 MVEKDQDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MVEKDQDGGR 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;;;;; 171.74 3.58E-06 5834380000 5705430 5331190 6493880 4481910 7879020 7169700 5644490 5972660 6520510 5969750 FALSE TRUE 5930684.782 6246780.412 6663115.848 5368418.421 6539746.995 5504645.833 5202060.125 5892606.262 6285838.119 7139408.215 0.830696971 0.874971738 0.933286856 0.751941654 0.916006873 0.771022705 0.728640241 0.825363403 0.880442458 1 22.76737306 3.75193154 24.70942372 0.825525014 0.879183831 0.032550386 0.080443751 1757.668277 3248156.061 0.019764487 0.035372255 5648.479277 -3.75193154 0.053658818 MVEKDQDGGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVEKDQDGGRK 11 2 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 53.528 0.077299 94250000 184230 128600 170240 93236 237240 195950 142100 151860 189410 139280 FALSE TRUE 191503.5427 150686.0496 174676.5943 111677.8025 196914.0295 150443.5822 130961.8307 149824.5651 182593.1711 166569.2493 1.149693256 0.904645066 1.048672519 0.670458701 1.182175163 0.903189411 0.786230539 0.899473136 1.09619976 1 17.34576256 4.743227254 24.02119213 0.932519331 1.149693413 0.156876875 0.141410742 480.9164268 2475329.125 0.031832674 0.254566615 55363.9738 -4.743227254 0.217174082 MVEPENAVTITPLRPEDDYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 MVEPENAVTITPLRPEDDYSPR 22 1 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;A0A669KAX5;H0YDF9 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR;MVEPENAVTITPLRPEDDYS(1)PR 253.21 3.08E-37 2001074000 1139696 1491744 1369582 1603085 1397159 1809510 1532384 1501541 1462556 1574188 TRUE FALSE 1184692.078 1747939.428 1405274.432 1920170.428 1159670.412 1389278.726 1412271.738 1481415.299 1409918.895 1882619.999 0.629278388 0.928461096 0.74644614 1.019945836 0.615987514 0.737949627 0.750162932 0.786890238 0.748913161 1 20.8443104 -1.102094213 4.132730591 1.000041034 0.778704583 0.255031345 0.11571522 12299071.14 6559700.725 4456.53751 0.025172625 0.079050712 1.102094213 -0.221336451 MVGFIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVGFIIGR 8 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 0 159.75 0.00083135 46782000 141580 88867 116780 101220 122110 170310 151830 101430 106140 89878 FALSE TRUE 147169.6877 104129.216 119823.3827 121241.0139 101353.7858 130758.0836 139929.1679 100070.4968 102320.0421 107487.8733 1.369174803 0.968753151 1.114761871 1.127950625 0.942932284 1.216491494 1.301813531 0.930993364 0.951921729 1 16.71381438 8 0.134648751 0.96259765 1.709367165 0.161570006 0.138737785 179.2241109 1.619924511 0.667207152 25.59338205 100000000 -8 0.746769515 MVGGIAQIIAAQEEMLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVGGIAQIIAAQEEMLRK 18 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 89.358 0.0046598 101440000 55118 49040 59999 33060 71605 87054 66145 49006 68057 55974 FALSE TRUE 57294.1012 57462.23852 61562.62323 39599.16933 59433.60768 66837.02782 60960.38206 48349.15473 65607.64186 66941.03361 0.855889103 0.858400826 0.919654506 0.591553001 0.887850164 0.998446307 0.910657914 0.722264837 0.9800811 1 16.03060321 3.042763865 24.9999839 0.894615822 0.808372017 0.17566026 0.111044204 322.1057168 188302.657 0.033598022 0.040157292 1103.478473 -3.042763865 -0.086243806 MVHNGIEYGDMQLICEAYHLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVHNGIEYGDMQLICEAYHLMK 22 0 P52209-2;P52209;K7EM49;K7EPF6;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ; 267.57 4.71E-38 546860000 332820 244040 405940 363520 449900 493060 616070 409750 478660 230307 FALSE TRUE 345959.9906 285951.9716 416519.1299 435423.171 373426.1587 378554.2874 567780.8236 404257.9715 461433.1201 275431.2472 1.256066602 1.03819728 1.512243561 1.580877898 1.355787198 1.374405741 2.061424873 1.467727339 1.675311443 1 18.07133271 4.213675378 12.68171064 1.538589754 1.147178799 0.222943068 0.259564681 1.101542149 560.9774751 0.061616522 0.134639864 16355.93507 -4.213675378 -0.391410955 MVINHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVINHLEK 8 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 ; 109.21 0.0036612 1399580000 1780890 1570970 1802070 1537990 2262900 2305200 2103380 1813690 1831340 1558460 FALSE TRUE 1851200.912 1840771.877 1849033.425 1842199.832 1878253.066 1769852.236 1938511.579 1789380.452 1765430.431 1863810.398 0.993234566 0.987639021 0.992071632 0.988405169 1.007749001 0.949588133 1.040079818 0.960065709 0.947215678 1 20.82982367 1.605345201 25 0.965227796 0.992925454 0.175142989 0.024353577 0.359616986 3521.62791 0.011275165 0.005595561 40.30372633 -1.605345201 0.027697658 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.604)S(0.396)PQGEAMVTDVLEDQK;MVIQGPS(0.634)S(0.366)PQGEAMVTDVLEDQK;MVIQGPS(0.612)S(0.388)PQGEAMVTDVLEDQK;MVIQGPS(0.631)S(0.369)PQGEAMVTDVLEDQK;MVIQGPS(0.95)S(0.05)PQGEAMVTDVLEDQK;MVIQGPS(0.653)S(0.347)PQGEAMVTDVLEDQK 259.2 7.26E-44 524090000 760842 522865 698890 628317 799086 942069 946259 723478 797209 454971 TRUE FALSE 790880.6297 612662.9964 717103.6475 752596.2273 663257.6471 723287.7519 872088.747 713780.9608 768517.6038 544113.8565 1.453520472 1.125983081 1.317929398 1.383159459 1.218968492 1.329294859 1.602768863 1.311822796 1.412420571 1 19.05354904 4.00782632 24.92155744 1.346727427 1.272802927 0 0.16232051 704.9504857 2244742.729 0.037938468 0.081720141 10181.84122 -4.00782632 -0.0739245 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.557)S(0.442)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.863)S(0.137)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.46)S(0.46)PQGEAMVT(0.08)DVLEDQKEGR;MVIQGPS(0.572)S(0.426)PQGEAMVT(0.002)DVLEDQKEGR 236.73 3.61E-45 4796920000 1345940 1036164 1226660 895866 1565090 1439330 1277910 1209340 1395900 1043671 TRUE FALSE 1399078.75 1214117.107 1258627.767 1073065.621 1299056.561 1105067.421 1177744.075 1193130.775 1345661.832 1248158.35 1.120914466 0.972726823 1.008387892 0.859719138 1.040778649 0.885358353 0.943585463 0.955912986 1.078117878 1 20.25136955 4.950366487 1.998742442 0.963352526 1.247713098 0.326828822 0.063202033 1.751722188 4.507304092 0.015081023 1.107363159 89200.33536 -4.950366487 0.284360572 MVIQGPSS(ph)PQGEAMVTDVLEDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVIQGPSSPQGEAMVTDVLEDQK 23 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.142)S(0.858)PQGEAMVTDVLEDQK;MVIQGPS(0.337)S(0.663)PQGEAMVTDVLEDQK 277.82 5.29E-52 94551000 153008 110975 143362 133427 158566 173303 184131 149771 154716 106734 TRUE FALSE 159048.874 130034.093 147098.1315 159818.4624 131613.008 133056.0047 169698.3311 147763.5647 149147.8014 127646.4838 1.246010617 1.018704857 1.152386867 1.252039678 1.031074293 1.042378926 1.329439919 1.157599962 1.168444261 1 16.96179427 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 MVIQGPS(0.026)S(0.974)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.096)S(0.904)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.134)S(0.865)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.201)S(0.799)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.007)S(0.993)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.257)S(0.738)PQGEAMVT(0.006)DVLEDQKEGR;MVIQGPS(0.013)S(0.986)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.05)S(0.95)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.068)S(0.932)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.226)S(0.774)PQGEAMVT(0.001)DVLEDQKEGR;MVIQGPS(0.166)S(0.834)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.142)S(0.858)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.006)S(0.994)PQGEAMVTDVLEDQKEGR;MVIQGPS(0.125)S(0.875)PQGEAMVTDVLEDQKEGR 213.9 6.41E-27 6857240000 4004198 2980161 3642521 2692817 4535289 4210276 3595547 3562067 3924643 3054495 TRUE FALSE 4162286.829 3491980.469 3737448.09 3225448.165 3764382.196 3232503.206 3313718.631 3514323.318 3783395.865 3652964.813 1.139427025 0.955930497 1.023127317 0.882967214 1.030500535 0.884898534 0.907131276 0.962046857 1.035705532 1 21.80063643 MVIQLRPGRS(ph)PEPDGPAPAFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;MVIQLRPGRS(1)PEPDGPAPAFLR 179.47 2.96E-17 4849200000 653108 777770 729422 651760 721490 892420 663416 731210 722130 838680 TRUE FALSE 678893.2081 911345.9473 748431.3365 780676.1827 598851.3875 685168.9798 611415.7204 721409.326 696140.6824 1003003.289 0.676860401 0.908617108 0.746190312 0.778338607 0.597058249 0.683117381 0.609584961 0.719249213 0.694056231 1 19.93589491 -1.138657006 4.773177621 1.000022216 0.712917765 0.513771677 0.083887018 2.05E-05 3.70E-06 0.083867993 0.019766347 0.072667964 1.138657006 -0.287104451 MVMISLEGEDGLDEIYSFSESLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MVMISLEGEDGLDEIYSFSESLRK 24 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ;; 314.27 2.32E-73 132039000 127068 109561.3 140408 108518.8 171434 168031 148212 139256.1 147524 124895.7 FALSE TRUE 132084.7428 128377.601 144067.1478 129983.4947 142293.7099 129008.3468 136594.7562 137389.5998 142214.6401 149366.6211 0.884298927 0.859479849 0.964520364 0.870231205 0.952647311 0.863702652 0.914493179 0.919814606 0.952117943 1 17.18849826 1.036189205 1.307613369 0.999779924 0.901111036 0.46860424 0.033452024 0.372479397 1.306175951 0.029218328 0.008952549 10.86899039 -1.036189205 -0.098668888 MVNHFIAEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;; 158.79 7.88E-06 19852200000 33694200 28742200 34218700 27936900 46308800 45276200 41255700 35582500 36430900 32758000 FALSE TRUE 35024473.03 33678449.27 35110467.43 33462735.44 38437246.72 34761488.72 38021970.43 35105574.79 35119759.03 39176302.91 0.894021907 0.859663796 0.896216969 0.854157563 0.981135122 0.887309065 0.970534931 0.896092081 0.896454142 1 25.22347792 3.258440903 24.99983434 0.930814455 0.876290103 0.381383641 0.038279641 274.3712225 345024.7571 0.009893204 0.013377554 1813.179928 -3.258440903 -0.054524353 MVNHFIAEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVNHFIAEFKR 11 1 P11142;E9PKE3;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 162.26 1.64E-05 1275280000 1619890 1704820 1760900 1286680 3442900 2562800 1679610 1698320 1867210 3115700 FALSE TRUE 1683844.508 1997609.573 1806790.501 1541181.464 2857677.088 1967628.54 1547957.779 1675556.798 1800009.477 3726161.761 0.451897855 0.536103825 0.4848932 0.413610992 0.766922445 0.528057735 0.41542957 0.44967366 0.483073359 1 21.82925888 -1.288964144 3.770846728 1.001036947 0.501830684 0.704256151 0.096558983 1069008286 2085916239 13178515.47 0.023789413 0.051408609 1.288964144 -0.499206263 MVPPVVVGS(ph)PPGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MVPPVVVGSPPGSPSR 16 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 2 MVPPVVVGS(1)PPGS(0.703)PS(0.297)R;MVPPVVVGS(1)PPGS(0.969)PS(0.031)R;MVPPVVVGS(1)PPGS(0.989)PS(0.011)R;MVPPVVVGS(1)PPGS(0.979)PS(0.021)R 137.69 1.56E-05 619060000 437381 479376 428889 452229 514336 593080 448105 494878 443612 513632 TRUE FALSE 454649.1396 561705.099 440066.1997 541678.5464 426909.3504 455346.1582 412981.3592 488244.9699 427646.4908 614268.3563 0.740147421 0.914429489 0.71640708 0.881827203 0.694988348 0.741282134 0.672314234 0.794839853 0.696188378 1 19.22850954 -1.483134554 3.147899663 1.005555163 0.763938268 0.466330325 0.076536226 36926000.04 42624819.94 1773040.697 0.017524017 0.032874976 1.483134554 -0.241616895 MVPPVVVGS(ph)PPGSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVPPVVVGSPPGSPSR 16 0 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 MVPPVVVGS(0.998)PPGS(0.002)PSR 108.71 0.0010791 234920000 53335 54386 51520 51623 61983 67114 56280 54038 63568 65336 TRUE FALSE 55440.70698 63726.37244 52862.65352 61833.87532 51447.1518 51527.79062 51868.62654 53313.709 61280.2001 78137.33827 0.709528994 0.815568765 0.67653512 0.791348627 0.658419559 0.659451573 0.663813584 0.682307718 0.784262703 1 16.25372449 0.883221244 3.688127395 0.999906514 0.706531093 0.742456751 0.051994266 0.270305784 7.290424114 0.051170845 0.013156977 7.64225006 -0.883221244 -0.293375421 MVPTSDKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 MVPTSDKGR 9 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;; 128.27 0.00038494 1644590000 2817650 2234280 2532000 2079770 4265510 3752060 3692940 3152950 3470020 2841090 FALSE TRUE 2928892.998 2618000.21 2597986 2491142.299 3540460.134 2880700.928 3403477.713 3110689.862 3345134.658 3397747.19 0.862010277 0.770510595 0.76462016 0.733174707 1.042002226 0.847826741 1.001686566 0.915515396 0.984515466 1 21.69614708 3.24656734 24.99999979 0.955172015 0.780434123 0.694794354 0.05908135 98.43196949 307339.7722 0.015433778 0.020534859 1764.279306 -3.24656734 -0.174737892 MVQEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVQEAEK 7 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 A0A0G2JIW1;P11142 HSPA1B;HSPA1A;HSPA8 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock cognate 71 kDa protein 0 ; 146.54 0.005146 434630000 853070 662620 731230 595110 1130240 979820 946590 753870 793030 756840 FALSE TRUE 886749.8623 776419.8305 750286.4545 712820.9818 938122.2085 752271.6543 872393.8023 743765.6057 764489.0052 905128.3074 0.979695205 0.857800849 0.828928284 0.78753584 1.036452181 0.831121564 0.963834404 0.821723947 0.844619485 1 19.78776279 4.7466511 23.50091753 0.879416147 0.979695319 0.104853997 0.080409593 915.4735018 2659082.273 0.018048087 0.192400351 55802.17155 -4.7466511 0.100279172 MVQEAEKYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVQEAEKYK 9 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 A0A0G2JIW1;P11142 HSPA1B;HSPA1A;HSPA8 Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock cognate 71 kDa protein 0 ; 140.3 9.98E-05 751620000 929770 604200 673000 504880 1120310 1063660 730970 689340 739490 686070 FALSE TRUE 966478.0375 707966.65 690538.9329 604743.7571 929880.1064 816641.0849 673674.6614 680100.5248 712875.8994 820492.2809 1.177924595 0.862855954 0.841615392 0.737049904 1.13331975 0.995306237 0.821061547 0.828893264 0.868839252 1 19.64613024 2.234473566 24.98088327 0.85993901 0.946320749 0.06588992 0.132251285 279.8685947 1710591.507 0.049526969 0.037906715 171.582727 -2.234473566 0.086381739 MVQEAEKYKAEDEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVQEAEKYKAEDEKQR 16 3 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ; 139.04 1.45E-06 579690000 439461 199997 276567 136374 445981 356264 259416 266117 337817 218341 FALSE TRUE 456811.2596 234344.929 283774.5632 163348.3702 370173.3089 273527.0852 239082.2961 262550.1369 325659.0322 261120.7386 1.749425427 0.897458127 1.08675613 0.625566437 1.417632743 1.047511916 0.915600566 1.00547409 1.24715882 1 17.99435752 4.744698145 24.78929235 1.023353813 1.749425789 0.542051632 0.199175408 450.095124 1817863.579 0.045061801 0.413937748 55551.80118 -4.744698145 0.726071975 MVQEAEKYKAEDEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVQEAEKYKAEDEVQR 16 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 121.26 5.61E-05 279630000 250800 165120 253220 103120 503710 303730 200660 228730 298900 269720 FALSE TRUE 260701.7777 193478.0755 259819.1212 123516.8282 418089.5541 233193.3106 184931.7449 225664.2485 288142.6474 322566.4699 0.808211026 0.599808392 0.805474671 0.382918994 1.296134574 0.722931031 0.573313602 0.699589913 0.893281461 1 18.29923696 1.060166135 4.059356765 0.997479595 0.731329931 0.133015061 0.222618187 0.368347945 12.01899508 0.204178287 0.052366423 11.48592921 -1.060166135 -0.266149664 MVQEAEKYKAEDEVQRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVQEAEKYKAEDEVQRER 18 3 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 113.73 0.00010444 83878000 109910 62643 111430 51294 210180 136870 119170 127120 149310 85458 FALSE TRUE 114249.3317 73401.44796 114333.9573 61439.8001 174453.6787 105084.0168 109829.144 125416.1643 143936.3623 102201.8589 1.117879194 0.718200713 1.118707219 0.601161278 1.70695211 1.02820064 1.074629612 1.227141714 1.408353662 1 16.64106191 3.260164566 24.99999449 1.229265399 0.893196826 0.332661211 0.243805238 281.1885421 325388.0529 0.063418278 0.085792534 1820.390522 -3.260164566 -0.336068573 MVQFEENGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVQFEENGR 9 0 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 160.74 0.00015137 255410000 135210 147240 156550 142480 169370 196630 173940 160420 156720 133460 FALSE TRUE 140548.1952 172527.3246 160629.8216 170662.1187 140580.5479 150965.6625 160306.1283 158269.8323 151079.6778 159608.9318 0.880578509 1.080937782 1.006396195 1.069251682 0.880781209 0.945847208 1.004368155 0.991610122 0.94656155 1 17.28418186 3.262972696 24.99964171 0.965405806 1.014201845 0.125947119 0.060581165 479.6618134 491203.1796 0.016331779 0.022102583 1832.199229 -3.262972696 0.048796039 MVQFEENGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MVQFEENGRK 10 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35;Q5SZW8 P49368 CCT3 T-complex protein 1 subunit gamma 0 ;; 112.13 0.0026653 450320000 723330 588310 652340 597040 989360 849590 738750 768230 788230 659030 FALSE TRUE 751887.6269 689347.6661 669340.5163 715132.73 821188.9406 652285.5982 680844.8446 757933.1334 759861.7563 788154.3106 0.953985301 0.874635407 0.849250594 0.907351163 1.041913911 0.827611534 0.863847137 0.961655761 0.964102773 1 19.58811859 1.593957555 5.711397454 0.975825435 0.902262785 0.250780182 0.057944225 0.210187186 14.48703299 0.032717689 0.015303546 39.26065624 -1.593957555 -0.07356265 MVS(ph)PLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVSPLRR 7 1 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 MVS(1)PLRR 67.838 0.039248 129230000 90113 90583 97908 115300 90381 104960 99254 91954 84520 84485 TRUE FALSE 93670.73082 106139.9256 100459.5629 138105.9959 75018.0699 80584.63068 91474.21213 90721.50704 81478.14171 101038.2182 0.927082173 1.050492848 0.994272907 1.366868877 0.742472217 0.797565833 0.905342689 0.897892982 0.806409131 1 16.62454158 3.199696322 24.99999522 0.856789151 1.075781233 0.437406807 0.125617391 150.1557466 96589.31602 0.03564921 0.042609688 1583.785354 -3.199696322 0.218992082 MVSDINNGWQHLEQAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MVSDINNGWQHLEQAEK 17 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;; 275.74 9.90E-36 1727730000 1800180 1784100 1597930 1860970 2099760 2499180 2727100 1821660 1863890 2056430 FALSE TRUE 1871252.496 2090505.297 1639573.369 2229064.312 1742843.545 1918783.32 2513342.776 1797243.627 1796808.963 2459348.086 0.760873382 0.850024162 0.666669911 0.906363896 0.708660785 0.780199977 1.021954879 0.730780501 0.730603762 1 21.22984451 MVSQSQPGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 MVSQSQPGSR 10 0 E3W994;J3KR49;O75122;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 MVSQSQPGS(1)R;MVSQSQPGS(1)R 113.82 0.0015083 249570000 233770 419790 351780 414120 379220 490330 298960 382070 333940 475270 TRUE FALSE 242999.4201 491885.667 360947.6758 496031.7 314760.3199 376458.2885 275526.734 376948.9766 321921.5646 568390.0569 0.427522292 0.865401604 0.635035169 0.872695949 0.553775204 0.662323846 0.484749391 0.663187141 0.566374377 1 19.11652179 -1.818789567 7.319209434 1.016814774 0.643542184 0.385716076 0.137272292 0.03396319 0.000840867 0.11984985 0.029142374 0.015177856 1.818789567 -0.37327259 MVVNEGSDGGQSVYHVHLHVLGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MVVNEGSDGGQSVYHVHLHVLGGR 24 0 P49773 P49773 HINT1 Histidine triad nucleotide-binding protein 1 0 ;; 200.1 5.46E-25 4035033000 476828 941345 780457 823646 812834 1013961 699657 860151 743623 903184 FALSE TRUE 495653.5376 1103013.681 800796.3506 986560.7205 674668.767 778483.9245 644816.0561 848622.0828 716860.1535 1080145.612 0.458876592 1.021171283 0.741378145 0.913359004 0.624609089 0.720721276 0.596971416 0.785655261 0.663669921 1 20.04279438 -1.161169657 4.315187739 1.000060427 0.735001946 0.226578833 0.151356189 20133622.94 5417740.462 12059.68817 0.032654313 0.068997021 1.161169657 -0.265058482 MVVSFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MVVSFNR 7 0 P46940;H0YLE8;A0A0J9YXZ5;E7EWC2;F5H7S7;Q13576-3;Q13576-2;Q13576 P46940;Q13576 IQGAP1;IQGAP2 Ras GTPase-activating-like protein IQGAP1;Ras GTPase-activating-like protein IQGAP2 0 77.741 0.086604 271000000 274730 270360 257960 273730 343140 382310 307260 302750 250230 330520 FALSE TRUE 285576.5525 316792.2269 264682.6495 327872.977 284813.1854 293524.2965 283176.1583 298692.1314 241224.2712 395279.0658 0.722468193 0.801439424 0.669609581 0.829472151 0.720536983 0.742574859 0.716395536 0.755648749 0.610263209 1 18.59251203 -1.691295244 2.926462556 1.033185479 0.734238173 0.656352442 0.058570209 15705880.33 15238851.89 3869631.646 0.013591313 0.020356577 1.691295244 -0.298947307 MWDPHNDPNAQGDAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MWDPHNDPNAQGDAFK 16 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 157.42 6.87E-08 1182010000 3344280 2398950 2976340 2281960 3716410 3693200 3413930 3088730 3431210 2484170 FALSE TRUE 3476314.757 2810951.001 3053905.865 2733324.877 3084695.956 2835510.271 3146337.246 3047330.626 3307721.422 2970895.549 1.17012352 0.94616285 1.027941176 0.920033987 1.038305085 0.954429472 1.059053472 1.025727958 1.113375199 1 21.50246645 2.185889541 24.99940392 1.049165543 1.004701005 0.069910368 0.070245026 250.2014688 118751.8359 0.024690411 0.018235087 153.4226714 -2.185889541 -0.044464538 MWDVSTGMCLMTLVGHDNWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MWDVSTGMCLMTLVGHDNWVR 21 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 199.12 8.19E-22 83560000 63856 78090 77741 81078 83774 92315 76356 83784 89873 61989 FALSE TRUE 66377.08419 91501.35004 79766.99432 97114.98641 69534.1254 70876.2403 70371.0172 82661.01252 86638.48829 74134.5577 0.89535955 1.234260416 1.075975858 1.309982678 0.937944834 0.956048603 0.949233655 1.115013228 1.168665343 1 16.17785859 3.196296291 24.99993473 1.024915954 1.132642567 0.157098171 0.121953677 268.764835 158977.3886 0.035105378 0.041959259 1571.434528 -3.196296291 0.107726613 MYEEHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 MYEEHLK 7 0 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;;;;; 124.89 0.0041028 3600700000 4534240 3623080 4284760 3726180 5317170 5177600 5354560 4473180 4629710 3216870 FALSE TRUE 4713255.296 4245315.806 4396424.366 4463207.282 4413359.343 3975180.867 4934855.596 4413224.339 4463087.641 3847154.086 1.225127768 1.103495132 1.142773143 1.160132187 1.147175092 1.033278309 1.282728865 1.14714 1.160101088 1 21.87536018 4.756769825 23.21719439 1.141346282 1.225127953 0.115118956 0.0733849 3272.025056 4171729.392 0.016389866 0.479315851 57117.58342 -4.756769825 0.083781671 MYEEHLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MYEEHLKR 8 1 P84090;G3V279 P84090 ERH Enhancer of rudimentary homolog 0 ;; 155.1 0.00026897 1457430000 578490 514640 583540 455090 798770 737890 608060 596470 613230 565250 FALSE TRUE 601329.2319 603025.4167 598747.5318 545105.4437 662995.3607 566526.2303 560398.6683 588475.2953 591159.9721 675999.9151 0.889540396 0.892049545 0.885721312 0.806369101 0.980762491 0.838056659 0.828992217 0.870525694 0.87449711 1 19.36666354 0.8502196 12.37236839 1 0.872744348 0.416046777 0.04474282 467.669998 38635.11281 0.041086632 0.010273299 7.083038461 -0.8502196 -0.127255652 MYPIDFEKDDDSNFHMDFIVAASNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MYPIDFEKDDDSNFHMDFIVAASNLR 26 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 233.43 4.38E-45 783682000 1009514 924579 1221189 925531 1401621 1396860 1314713 1167421 1278038 869664 FALSE TRUE 1049370.392 1083368.251 1253014.189 1108598.269 1163373.963 1072460.435 1211662.36 1151773.631 1232041.662 1040058.01 1.008953714 1.04164214 1.204754135 1.06590042 1.118566418 1.03115444 1.164994979 1.107412875 1.184589369 1 19.98823257 4.458568011 24.94811353 1.112817518 1.017125764 0.236367935 0.061687061 240.0371501 322772.4437 0.013750642 0.037671584 28745.37713 -4.458568011 -0.095691754 MYPPRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 MYPPRSPK 8 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6 Q8WWM7 ATXN2L Ataxin-2-like protein 1 MYPPRS(1)PK;MYPPRS(1)PK;MYPPRS(1)PK 72.2 0.056732 861990000 1077146 602624 724181 561545 1038256 979232 853294 741482 761704 545695 TRUE FALSE 1119672.556 706119.9842 743053.7518 672616.925 861773.616 751820.2084 786410.5866 731543.6466 734290.4218 652613.4873 1.715674864 1.081988034 1.138581666 1.030651278 1.320496178 1.152014512 1.205017368 1.120944726 1.125153611 1 19.31586928 4.742126569 24.85368137 1.140475689 1.715675101 0.808999951 0.08517136 126.8825156 884294.3557 0.019282808 0.142086863 55223.83583 -4.742126569 0.575199412 MYS(ph)FDDVLEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 MYSFDDVLEEGK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MY(0.017)S(0.983)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MYS(1)FDDVLEEGK;MY(0.049)S(0.951)FDDVLEEGK;MYS(1)FDDVLEEGK 279.77 5.67E-28 778060000 2596748 1307451 1981429 1696502 2742505 3033202 3482222 2338061 2460025 1003083 TRUE FALSE 2699269.616 1531995.539 2033066.668 2032065.032 2276334.98 2328786.804 3209276.341 2306723.117 2371489.181 1199617.909 2.250107802 1.27706958 1.694761851 1.693926889 1.897550014 1.94127379 2.675248775 1.922881527 1.976870438 1 20.19414353 3.063192264 2.668412619 2.017045966 1.692284857 0.000999784 0.443560477 0.649660745 9.394361387 0.132072309 0.159260783 1156.624172 -3.063192264 -0.324761109 MYS(ph)FDDVLEEGKRPPTMTVSEASYQSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 MYSFDDVLEEGKRPPTMTVSEASYQSER 28 2 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 MYS(1)FDDVLEEGKRPPTMTVSEASYQSER;MYS(1)FDDVLEEGKRPPTMTVSEASYQSER;MYS(1)FDDVLEEGKRPPTMTVSEASYQSER;MY(0.022)S(0.978)FDDVLEEGKRPPTMTVSEASYQSER;MYS(1)FDDVLEEGKRPPTMTVSEASYQSER 165.87 3.40E-12 1335470000 590287 376213 568823 409113 771878 727036 694875 608502 626826 363661 TRUE FALSE 613591.9866 440824.6562 583646.9947 490034.3303 640674.4533 558192.9073 640408.8818 600346.026 604266.6547 434913.4102 1.410837128 1.013591777 1.34198436 1.126739987 1.473108067 1.283457567 1.472497437 1.380380581 1.389395315 1 18.73036867 MYSFDDVLEEGKRPPTMTVS(ph)EASYQSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 MYSFDDVLEEGKRPPTMTVSEASYQSER 28 2 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 MYSFDDVLEEGKRPPT(0.313)MT(0.231)VS(0.427)EAS(0.022)YQS(0.006)ER 100.66 0.0010657 94822000 28963 22586 28106 25638 39723 39341 35950 31767 38874 18703 TRUE FALSE 30106.4816 26464.96981 28838.46545 30709.11988 32970.89865 30204.64897 33132.14506 31341.21533 37474.93233 22367.49476 1.345992563 1.183188823 1.289302435 1.372935155 1.474054158 1.350381404 1.481263119 1.40119471 1.675419296 1 14.44911606 3.688187264 3.056275084 1.41922345 1.259967612 0.094384751 0.163489894 0.459531222 8.553269525 0.041180723 0.072051025 4877.387535 -3.688187264 -0.159255838 NAADKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NAADKER 7 1 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 84.476 0.019624 198167000 253322 185062 231567 141403 384949 299749 273180 241144 266077 207094 FALSE TRUE 263323.3482 216844.9589 237601.8263 169372.0914 319515.5065 230136.8375 251767.4378 237911.8591 256500.9407 247670.1042 1.063201992 0.875539499 0.959348029 0.683861671 1.290085081 0.929207173 1.016543513 0.960599826 1.035655642 1 17.91806021 3.25316659 24.9999903 1.025081694 0.898624499 0.228994178 0.127208367 396.2272666 678189.6797 0.033778477 0.045539485 1791.292839 -3.25316659 -0.126457195 NACDHLSGFNVCNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NACDHLSGFNVCNR 14 0 Q9Y3B4 Q9Y3B4 SF3B6 Splicing factor 3B subunit 6 0 ; 133.48 4.43E-05 253920000 81753 463300 409490 463360 428076 626700 370590 532460 380102 412500 FALSE TRUE 84980.67157 542868.171 420161.6458 555011.225 355311.7944 481158.4227 341542.1874 525323.2446 366422.2033 493321.4772 0.172262258 1.100434901 0.85169948 1.125049791 0.72024392 0.975344567 0.692331883 1.064870006 0.74276556 1 18.91216857 4.747316086 24.87938768 0.917389146 0.172261852 0.683134157 0.152606773 560.2375591 1591924.373 0.032778576 0.391671852 55887.68056 -4.747316086 -0.745127294 NADDDRGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NADDDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 117.7 0.0010118 476561000 1061090 1402520 1367910 1231360 1610860 1858650 1312020 1384970 1375050 1358710 FALSE TRUE 1102982.653 1643391.9 1403558.858 1474919.333 1337046.593 1427006.706 1209180.444 1366406.743 1325562.219 1624923.21 0.678790632 1.011365884 0.863769346 0.907685559 0.822836786 0.878199472 0.744146207 0.840905425 0.815769146 1 20.63194011 3.220842402 24.84173719 0.836466064 0.875712118 0 0.097972833 879.1496849 1232605.029 0.02632174 0.031525037 1662.809135 -3.220842402 0.039246054 NADDLEVS(ph)SDIIEAVAISSNSFITTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NADDLEVSSDIIEAVAISSNSFITTGK 27 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 NADDLEVS(0.5)S(0.5)DIIEAVAISSNSFITTGK 101.49 0.0017124 350850000 42252 30853 39303 37718 53297 51366 50315 40021 45471 36301 TRUE FALSE 43920.14159 36151.76275 40327.26847 45178.50782 44237.59498 39437.02496 46371.17883 39484.58396 43834.50759 43413.48593 1.011670467 0.832731166 0.928911089 1.040656074 1.018982789 0.908404937 1.068128436 0.909500426 1.009697947 1 15.40585565 3.977384222 23.56929348 0.98710753 0.911855917 0.194785865 0.062900747 498.4159996 519433.2809 0.015196752 0.027706185 9492.579037 -3.977384222 -0.075251613 NADGFIDLEEYIGDMYSHDGNTDEPEWVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NADGFIDLEEYIGDMYSHDGNTDEPEWVK 29 0 O43852;O43852-3;O43852-15;H0Y875;O43852-2;O43852-4 O43852;O43852-2 CALU Calumenin 0 ; 184.75 7.90E-18 81667000 53392 41892 55133 61646 68491 68668 75085 56202 59691 29678 FALSE TRUE 55499.95739 49086.62513 56569.81127 73839.39481 56848.92428 52720.89767 69199.6415 55448.70412 57542.73257 35492.83588 1.563694645 1.383000933 1.593837457 2.08040279 1.601701382 1.485395471 1.949679133 1.562250599 1.621249222 1 15.11524023 0.39967312 1.699802279 1.000028789 1.658386755 0.491439692 0.198399924 4.566741885 11.9468439 0.19173739 0.05410167 2.509996526 -0.39967312 0.658357966 NADGTICYDSTHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NADGTICYDSTHYK 14 0 P14550;Q5T621 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 ;;; 187.89 1.03E-07 1046220000 1054830 1119300 1358160 1195130 1747410 1903960 1586220 1549250 1452730 949040 FALSE TRUE 1096475.503 1311531.068 1393554.765 1431523.147 1450385.872 1461794.145 1461887.932 1528484.838 1400446.531 1134986.218 0.966069443 1.155548013 1.227816465 1.26126919 1.277888533 1.287939996 1.288022629 1.34669903 1.233888579 1 20.11424335 4.880120957 1.267518379 1.267898722 0.753300792 0.447732535 0.08956092 1.42783228 1.582326166 0.02296881 1.038025037 75878.88792 -4.880120957 -0.51459793 NADGYKLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NADGYKLDK 9 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 88.441 0.012021 0 333080 158930 243210 162950 434200 331580 309160 258860 298530 154520 FALSE TRUE 346230.2556 186224.9912 249548.2524 195181.0236 360394.8391 254575.5701 284927.2314 255390.4051 287785.9636 184795.2355 1.873588648 1.007736973 1.350404147 1.056201601 1.950238804 1.377608949 1.541853774 1.382018342 1.557323503 1 17.49556804 -1.076538373 4.461219898 0.99996913 1.438915034 0.182950976 0.286744492 1.930227775 79630807.59 5640.51539 0.062691885 0.083841999 1.076538373 0.438945904 NADHSMNYQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NADHSMNYQYR 11 0 Q12906;K7ELV3;Q12906-7 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ;;;;;;;; 221.09 8.66E-12 2563615000 330506 416683 423805 399122 574065 619414 441342 432394 389829 442852 FALSE TRUE 343554.6321 488245.0639 434849.7065 478067.1403 476485.6364 475564.4858 406748.4608 426598.4657 375799.1304 529620.3705 0.648680925 0.921877426 0.821059254 0.902660032 0.899673923 0.897934657 0.768000031 0.805479716 0.709563211 1 19.01459909 -0.20829018 7.705656517 1 0.825935893 0.280005979 0.086297866 0 0 0.080670244 0.019014159 0.619027325 0.20829018 -0.174064107 NADNDWFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NADNDWFR 8 0 Q9Y3C8 Q9Y3C8 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1 0 ;;;; 122.19 0.0032597 2358080000 3373770 3672150 3827960 3591490 4736530 5302030 4386070 3988630 4057760 3201490 FALSE TRUE 3506969.045 4302813.197 3927719.782 4301876.002 3931416.322 4070713.886 4042278.373 3935168.939 3911722.01 3828760.669 0.915954103 1.12381357 1.025846252 1.123568793 1.026811718 1.063193612 1.055766793 1.027791831 1.021667936 1 21.86844605 1.32294049 1.483146466 1.002709981 1.052690282 0.066639283 0.055175943 0.901561165 3.687592583 0.046255934 0.014406632 21.03490186 -1.32294049 0.049980301 NADSGVHLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NADSGVHLNR 10 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V3Y4;A0A3B3IT62;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 69.979 0.055356 167090000 91186 156230 165260 150410 171580 229930 147090 155810 139520 159920 FALSE TRUE 94786.09369 183061.2872 169566.8114 180160.6491 142414.8929 176532.2421 135560.7015 153721.6218 134498.7025 191253.2621 0.495605108 0.957166875 0.886608727 0.942000398 0.744640333 0.923028659 0.708802035 0.803759476 0.703249194 1 17.54512483 2.231364548 24.99624916 0.786516592 0.835343938 0 0.147996029 823.5595963 2860691.609 0.051739431 0.038987468 170.3587904 -2.231364548 0.048827346 NAEAVLQS(ph)PGLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NAEAVLQSPGLSGK 14 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 1 NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK;NAEAVLQS(1)PGLSGK 283.12 2.07E-33 1687490000 3843420 2466460 3297220 2439900 4450860 4699840 3912830 3404190 3484180 1929210 TRUE FALSE 3995161.189 2890055.319 3383148.262 2922504.938 3694304.407 3608373.387 3606132.16 3358562.401 3358785.042 2307201.763 1.731604602 1.252623574 1.466342613 1.266688066 1.601205611 1.563960918 1.562989513 1.455686475 1.455782974 1 21.13771274 0.413889302 2.010952049 1.000005483 1.480535707 0.527063358 0.137757815 5.989184017 19.54437226 0.126012529 0.034614374 2.593518213 -0.413889302 0.480530224 NAEEES(ph)ESEAEEGD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NAEEESESEAEEGD 14 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;H0Y503 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 1 NAEEES(0.982)ES(0.018)EAEEGD;NAEEES(0.993)ES(0.007)EAEEGD 233.78 3.57E-17 544200000 642650 650420 760660 617070 787340 975480 857970 727920 769890 548870 TRUE FALSE 668022.3182 762124.5754 780483.4245 739124.6042 653508.228 748939.5535 790720.0695 718163.423 742181.8093 656410.5677 1.017689768 1.161048607 1.189017153 1.126009605 0.995578469 1.14096206 1.204612035 1.094076571 1.130667064 1 19.32423894 -2.55858607 1.646007721 2.33E-05 1.120380962 0.233131702 0.063901341 2044566.722 120025.6505 7594674.823 0.016777103 0.00276321 2.55858607 1.120357666 NAEQYKDQADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NAEQYKDQADK 11 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 184.1 4.61E-06 10757580000 9570530 3796000 6068950 3888560 9062670 8777760 8410040 6031170 6966140 2414300 FALSE TRUE 9948381.914 4447933.471 6227111.823 4657705.562 7522200.591 6739258.268 7750839.089 5950332.031 6715429.982 2887335.86 3.44552293 1.54049743 2.15669812 1.613149903 2.605239208 2.334074938 2.684425874 2.060838198 2.325822248 1 21.4613075 4.75493969 24.38160308 2.113239256 3.445524382 0.411174077 0.498431242 2291.935963 3411656.343 0.111332562 2.934540625 56877.39405 -4.75493969 1.332285126 NAEQYKDQADKASTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NAEQYKDQADKASTR 15 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 202.34 3.35E-09 901710000 1018830 631830 887470 394712 1880920 1272650 637520 895750 1095040 751950 FALSE TRUE 1059054.195 740341.8875 910598.1973 472784.8555 1561201.89 977096.3247 587549.5166 883743.9364 1055629.724 899280.2055 1.177668749 0.823260518 1.012585612 0.525736976 1.736057216 1.08653156 0.653355331 0.982723662 1.173860736 1 19.77841119 4.80886119 19.99794656 0.993532109 1.177693159 0.02874932 0.30928587 40758.23892 11587490.93 0.072685511 193.3748605 64396.34074 -4.80886119 0.18416105 NAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NAETPEATTQQETDTDLPEAPPPPLEPAVIAR 32 0 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 NAET(0.993)PEAT(0.005)T(0.002)QQETDTDLPEAPPPPLEPAVIAR;NAET(0.912)PEAT(0.043)T(0.043)QQET(0.002)DTDLPEAPPPPLEPAVIAR 107.52 1.76E-05 140651000 11547.6 13131.5 12757.4 15550.4 13614.8 21156 12720.9 20914.9 13886.4 4340.5 TRUE FALSE 12003.50816 15386.73298 13089.86832 18626.22271 11300.56116 16242.83962 11723.80262 20634.56998 13386.63118 5190.937871 2.312396808 2.964152791 2.52167694 3.588219156 2.176978696 3.129076099 2.258513376 3.975114033 2.578846349 1 12.34177951 0.971982371 24.04169453 0.999999961 2.913614364 0.49709378 0.55836529 1503.021241 1289731.783 0.512056162 0.128014041 9.375239499 -0.971982371 1.913614403 NAFACFDEEATGTIQEDYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NAFACFDEEATGTIQEDYLR 20 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 ;; 264.3 3.48E-36 159813000 133577 146848 155142 146466 174623 222705 172696 164316 147711 137212 FALSE TRUE 138850.7231 172068.0017 159185.128 175436.5376 144940.6448 170985.1389 159159.6363 162113.6128 142394.91 164096.0643 0.846155108 1.048580918 0.970072796 1.069108747 0.883267039 1.041981961 0.96991745 0.987918957 0.867753353 1 17.32418111 -1.032091274 4.793994883 1.000000641 0.971998723 0.011850141 0.074183126 4.58E-07 9.23E-08 0.06464571 0.015236791 0.092877117 1.032091274 -0.028001919 NAFMMLIHADQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NAFMMLIHADQDR 13 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 161.76 4.16E-05 1414860000 1667920 1959680 2106400 1983190 2853400 3513700 2269400 2219700 2054470 1733180 FALSE TRUE 1733770.77 2296239.796 2161294.514 2375459.063 2368380.087 2697696.426 2091518.498 2189948.552 1980530.026 2072763.437 0.836453759 1.10781566 1.042711617 1.146034815 1.14261958 1.301497497 1.009048336 1.056535692 0.955502201 1 20.98312404 1.631119443 2.215133275 0.986350135 1.097917608 0.11388937 0.112265621 0.576998684 6.199159732 0.082713911 0.031640574 42.76804942 -1.631119443 0.111567472 NALESYAFNMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NALESYAFNMK 11 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ; 185.18 1.07E-05 807940000 551260 428580 517590 419570 702890 692030 611580 539020 576810 395110 FALSE TRUE 573024.1705 502185.2811 531078.8206 502559.6937 583413.0089 531316.5203 563642.7615 531795.3186 556050.7208 472524.2397 1.212687355 1.062771471 1.123918682 1.063563838 1.234673187 1.124421724 1.19283354 1.125435002 1.176766553 1 18.85002881 3.309713425 24.99998415 1.149545171 1.112537255 0.02708271 0.069622379 134.9943008 47427.78011 0.017573879 0.023795139 2040.391122 -3.309713425 -0.037007916 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(0.999)PT(0.001)PDENSDQNSR;NALFPEVFS(0.999)PT(0.001)PDENSDQNSR 244.74 2.30E-30 250436000 269013 281252 305681 319838 383014 468942 341631 316183 334757 275263 TRUE FALSE 279633.841 329554.8432 313647.298 383101.0018 317909.4171 360037.3274 314853.0695 311945.0841 322709.161 329195.5146 0.849446085 1.001091535 0.952769051 1.163749154 0.965716126 1.093688436 0.956431833 0.947598221 0.980296349 1 18.32858515 4.893933992 2.268963442 1.006696966 0.757967595 0.335771786 0.066161694 1.433471013 5.760702101 0.016690869 0.829775791 78331.05798 -4.893933992 -0.248729372 NALKWDKDNLQILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NALKWDKDNLQILR 14 2 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 61.097 0.049326 342120000 543570 306650 403380 251150 621500 434870 346210 306080 367820 210910 FALSE TRUE 565030.5633 359314.7521 413892.4142 300826.7204 515857.652 333878.033 319073.1555 301977.4982 354582.23 252233.7764 2.240106664 1.424530676 1.640907971 1.192650424 2.045156915 1.323684868 1.264989805 1.197212771 1.405768233 1 17.94440195 8 0.170842418 1.008807699 4.738671437 0.464361917 0.273335004 54.85511728 0.594252624 0.667834263 52.43356486 100000000 -8 3.729863738 NALLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NALLHK 6 0 A0A1B0GVP4;A8MVM7 A0A1B0GVP4 Putative uncharacterized protein ENSP00000382790 0 76.592 0.07465 593360000 1885100 1089800 1601000 1242300 2216400 2340800 1853700 1600900 1767600 1021500 FALSE TRUE 1959525.204 1276964.673 1642723.375 1488023.232 1839657.12 1797184.675 1708402.15 1579442.554 1703984.421 1221643.367 1.604007566 1.045284333 1.344683252 1.218050433 1.505887208 1.471120561 1.398445894 1.292883501 1.394829675 1 20.22039175 -1.059701363 4.302414624 0.999973898 1.353902239 0.349084714 0.148512772 0.880984626 40448304.03 2790.710347 0.033019608 0.08715627 1.059701363 0.35392834 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NALPPVLTTVNGQSPPEHSAPAK 23 0 Q6PKG0;A0A0B4J210;H0YBM7 Q6PKG0 LARP1 La-related protein 1 1 NALPPVLTTVNGQS(0.999)PPEHS(0.001)APAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLTTVNGQS(1)PPEHSAPAK 234.37 2.94E-37 8112320000 5061760 3266830 4408210 3246590 5771860 6229890 5330400 4755120 4713640 2840660 TRUE FALSE 5261602.193 3827882.64 4523091.574 3888755.812 4790761.299 4783092.462 4912589.32 4691385.394 4543997.017 3397232.939 1.548790527 1.126764843 1.331404603 1.1446833 1.410195116 1.407937739 1.446056072 1.380943102 1.337558271 1 21.69592871 0.91652026 19.05363548 1 1.346185617 0.422731808 0.12211004 3722.724738 849688.9185 0.114630886 0.028656881 8.251259775 -0.91652026 0.346185618 NAMS(ph)LPQLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 191.19 2.04E-06 2362881000 5809139 4358479 5361218 3917894 7419395 6987920 5867734 5404231 5812483 3598691 TRUE FALSE 6038488.293 5107013.864 5500935.745 4692841.739 6158248.888 5365081.483 5407805.677 5331796.123 5603292.872 4303785.6 1.403064384 1.186632964 1.278162124 1.090398587 1.430891187 1.2465959 1.256523019 1.238861927 1.301945169 1 22.03717478 -1.38547978 2.891814104 0.995606316 1.264273499 0.432378087 0.09269049 11363186.02 13113139.72 415946.5201 0.020257866 0.041164251 1.38547978 0.268667183 NAPAAVDEGSIS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NAPAAVDEGSISPR 14 0 R4GMW8;A0A1W2PS85;P28715;A0A494C0S2;A0A090HNM7 R4GMW8 BIVM-ERCC5;ERCC5;ERCC5-201 DNA repair protein complementing XP-G cells 1 NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR 335.95 1.37E-68 3651250000 1826870 1928130 2106300 1889510 2453740 3060770 2202590 2158420 1963230 1640990 TRUE FALSE 1898996.238 2259271.329 2161191.908 2263249.438 2036654.151 2349952.554 2029945.24 2129489.91 1892573.736 1962510.572 0.967636183 1.151214858 1.101238352 1.153241909 1.037779964 1.197421603 1.034361429 1.085084555 0.964363588 1 20.904269 1.369789557 2.333032596 0.981247408 1.098861976 0.293756717 0.064989629 0.327923124 3.065764875 0.052165696 0.015959546 23.43093163 -1.369789557 0.117614567 NAPLPSLQNGPNTPNKPS(ph)SPPPPQQFVVQHSLFGSPVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NAPLPSLQNGPNTPNKPSSPPPPQQFVVQHSLFGSPVAK 39 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 NAPLPSLQNGPNTPNKPS(0.5)S(0.5)PPPPQQFVVQHSLFGSPVAK 152.77 8.19E-14 680320000 249320 145880 214910 123360 267790 299870 236600 232110 234930 85886 TRUE FALSE 259163.3461 170933.7552 220510.7312 147760.2398 222271.1515 230229.7371 218054.6738 228998.9451 226474.9152 102713.7173 2.523161978 1.664176506 2.146847928 1.438563842 2.163987024 2.241470206 2.122936249 2.229487464 2.204914018 1 16.64826934 NAPLPSLQNGPNTPNKPSS(ph)PPPPQQFVVQHSLFGSPVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NAPLPSLQNGPNTPNKPSSPPPPQQFVVQHSLFGSPVAK 39 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 NAPLPSLQNGPNTPNKPS(0.214)S(0.785)PPPPQQFVVQHSLFGSPVAK 220.89 8.74E-40 733160000 526620 288760 359370 273320 539100 602540 533360 472420 473570 201830 TRUE FALSE 547411.3642 338352.2838 368735.4774 327381.8802 447463.9746 462609.2166 491553.8495 466087.9826 456526.3082 241374.7242 2.267890169 1.401771809 1.527647431 1.356322131 1.853814545 1.916560311 2.036476069 1.930972616 1.891359212 1 17.88091509 3.115171277 19.37057866 1.84949498 1.612416303 0.002534707 0.362810179 4.681649396 768.7454405 0.098913464 0.118224804 1303.680824 -3.115171277 -0.237078677 NAPWTLTPEFLAEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NAPWTLTPEFLAEHR 15 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 ;; 165.34 1.43E-06 565570000 301807 346557 374320 332094 433330 561700 380359 400690 386381 291352 FALSE TRUE 313722.5734 406075.4689 384075.0867 397781.202 359672.7214 431253.6876 350545.4677 395319.4059 372475.2233 348436.8461 0.900371407 1.165420573 1.102280344 1.141616354 1.032246519 1.237681067 1.006051661 1.134551097 1.068989194 1 18.41053767 4.749689529 24.46184522 1.103699704 0.900371246 0.409552006 0.071239819 1077.155718 2367575.934 0.015097273 0.226609913 56193.94591 -4.749689529 -0.203328457 NAQAIEDMVGYAQETQHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NAQAIEDMVGYAQETQHEK 19 0 A0A087WW66;Q99460-2;Q99460;H7C378 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;; 291.69 1.47E-49 669750000 422169 330555 401737 320451 571237 554948 496040 477600 493826 238271 FALSE TRUE 438836.5581 387325.2499 412206.5963 383835.2513 474138.3388 426069.7373 457159.0886 471198.5532 476053.2987 284955.6405 1.540017097 1.359247528 1.446564088 1.347000013 1.663902276 1.495214261 1.604316685 1.653585633 1.67062248 1 18.12037782 3.246608767 24.99808399 1.559026248 1.420306993 0.021332173 0.193687864 398.5741164 1237990.023 0.049560444 0.065964033 1764.447608 -3.246608767 -0.138719255 NAS(ph)ASFQELEDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.846)AS(0.154)FQELEDKK 60.618 0.055399 158500000 324580 117970 177260 146010 228510 274690 256080 169860 203330 86589 TRUE FALSE 337394.669 138230.4298 181879.5412 174890.3422 189667.9518 210897.4105 236007.7805 167583.3045 196012.193 103554.4567 3.2581376 1.334857371 1.756366138 1.688873157 1.83157691 2.036584587 2.279069274 1.618310886 1.892841692 1 16.66003012 -2.040682925 0.29497095 3.23E-15 2.010541502 0.270796499 0.488787276 47.18001706 2.067180984 32.98125614 0.504343722 0.009105778 2.040682925 2.010541502 NAS(ph)SPEKAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NASSPEKAK 9 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 NAS(0.5)S(0.5)PEKAK 70.54 0.031564 91373000 410600 143810 237800 129130 402770 402390 311830 232460 292600 126880 TRUE FALSE 426810.8051 168508.2488 243997.2634 154671.5286 334307.2993 308941.0208 287387.9498 229344.2539 282069.3832 151739.7067 2.812782588 1.110508597 1.60799878 1.019321389 2.203162946 2.035993264 1.893953507 1.511432036 1.858902915 1 17.21123913 -1.478238439 2.871584847 0.976441602 1.743296208 0.178676354 0.497356887 38547341.99 42937024.44 7231079.293 0.122057991 0.033247696 1.478238439 0.766854607 NASS(ph)PEKAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NASSPEKAK 9 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 NAS(0.033)S(0.967)PEKAK 78.342 0.028422 0 217480 90008 135840 73087 194200 178590 161440 134110 157490 72606 TRUE FALSE 226066.2783 105466.1738 139380.102 87543.39046 161189.9534 137115.1791 148785.911 132312.4748 151821.9657 86831.75557 2.603497728 1.214603726 1.605174294 1.00819556 1.856347972 1.579090255 1.713496519 1.523779796 1.748461316 1 16.40593513 -2.065710326 2.522653586 0.096324195 1.616695763 0.18798924 0.400009334 4992465.546 2832977.873 25909997.37 0.089018008 0.008595867 2.065710326 1.520371568 NASYYGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 76.827 0.080949 29232000 25775 30756 29184 24965 45335 49438 35509 33393 29288 32553 FALSE TRUE 26792.6169 36038.10375 29944.55901 29903.00249 37628.97289 37956.77374 32725.71179 32945.42145 28233.9306 38931.13709 0.688205352 0.925688445 0.769167336 0.7680999 0.966552115 0.974972132 0.840605085 0.846248631 0.725227484 1 15.24863686 4.752479659 24.03285389 0.861911883 0.688205149 0.256547281 0.091461556 2071.738314 3576991.432 0.021696853 0.429384398 56556.12677 -4.752479659 -0.173706734 NAT(ph)SPQVQRPSFMDYFDKQDFK ddPTM_MDA-MB-175_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 172.75 2.16E-10 868450000 1460400 707060 1179800 636190 1721700 1497200 1315100 1296700 1289900 627220 TRUE FALSE 1518057.72 828492.0548 1210546.557 762026.4832 1429046.049 1149497.99 1212019.026 1279319.857 1243476.751 750111.7501 2.023775417 1.104491504 1.613821617 1.015883944 1.90511087 1.532435654 1.615784615 1.705505689 1.657722 1 19.51674602 3.211786125 24.99926583 1.612252205 1.428015548 0.02475952 0.337896493 618.6518959 577631.9107 0.089538422 0.107046266 1628.49386 -3.211786125 -0.184236657 NATVEMT(ph)RRHIGRGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NATVEMTRRHIGRGVR 16 3 Q15796-2;Q15796;B7Z5N5 Q15796-2 SMAD2 Mothers against decapentaplegic homolog 2;Mothers against decapentaplegic homolog 1 NATVEMT(1)RRHIGRGVR 63.408 0.045708 61749000 45384 51045 50267 62230 59205 69706 63961 49277 58364 51852 TRUE FALSE 47175.79536 59811.58168 51576.99931 74538.90826 49141.35525 53517.8379 58947.56969 48616.52242 56263.49104 62011.40663 0.760759962 0.964525479 0.831734065 1.202019311 0.792456709 0.863032155 0.950592365 0.783993221 0.907308737 1 15.92024599 NAVEEYVYDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NAVEEYVYDFR 11 0 O95757;E9PDE8 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ;; 141.88 8.82E-05 164920000 180305 189345 192954 181111 248720 289596 226393 214171 218583 175196 FALSE TRUE 187423.5806 221863.5309 197982.5398 216934.2152 206442.6632 222341.7179 208647.7251 211300.3881 210716.2405 209522.3019 0.894528071 1.058901744 0.944923466 1.035375296 0.985301619 1.061184017 0.995825854 1.008486382 1.005698385 1 17.67674429 4.754690775 24.60369546 1.009671452 0.894527962 0.528267796 0.032903606 1853.139911 2826578.189 0.007038338 0.182799417 56844.80425 -4.754690775 -0.11514349 NAVEEYVYEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NAVEEYVYEFR 11 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;;;;;; 243.82 1.79E-15 2729963000 1177986 1329431 1407121 1298516 1796523 1978955 1495153 1466631 1444142 1201212 FALSE TRUE 1224493.797 1557750.433 1443791.729 1555358.589 1491150.662 1519372.693 1377959.001 1446973.21 1392167.612 1436566.493 0.852375301 1.084356652 1.005029518 1.08269168 1.037996271 1.057641745 0.959203078 1.00724416 0.969093751 1 20.45419334 2.234275924 24.99989533 0.986023926 1.025924891 0.067714887 0.063242482 284.2406911 1658437.427 0.022076328 0.016888497 171.5046596 -2.234275924 0.039900965 NAVEEYVYEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NAVEEYVYEMR 11 0 P34932;A0A087WYC1 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 194.17 1.47E-06 1275830000 510845 866110 883811 867504 893630 1126350 877880 1075660 898859 835047 FALSE TRUE 531013.5551 1014857.655 906843.8407 1039093.702 741731.0918 864772.2825 809069.4717 1061242.537 866509.2402 998658.4717 0.531726882 1.016220944 0.908062032 1.040489548 0.742727482 0.865933957 0.810156319 1.062668136 0.867673248 1 19.92963185 4.747072669 24.89977389 0.922673908 0.531726674 0.58110286 0.099854004 746.227471 2182841.732 0.023625904 0.275312476 55856.3649 -4.747072669 -0.390947234 NAVIHIPGHTGGKIS(ph)PVPYEDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NAVIHIPGHTGGKISPVPYEDLK 23 1 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 NAVIHIPGHT(0.259)GGKIS(0.741)PVPYEDLK;NAVIHIPGHT(0.202)GGKIS(0.798)PVPYEDLK 138.09 3.00E-06 746400000 906100 301990 526370 337450 926340 882930 718530 623520 682930 199748 TRUE FALSE 941873.5277 353854.4333 540087.6346 404196.6028 768881.0577 677882.8884 662209.7411 615162.7343 658351.4827 238884.7962 3.942793944 1.481276494 2.260870693 1.692014767 3.218627012 2.837697916 2.772088269 2.575143936 2.755937143 1 17.86595551 3.238719457 24.99999486 2.632371412 2.276644061 0 0.826998272 15.90677984 2503273.184 0.218155477 0.277487924 1732.684367 -3.238719457 -0.355727351 NAYAVLYDIILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NAYAVLYDIILK 12 0 Q06323;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 190.15 1.63E-05 28958000 78788 86123 101940 88589 121360 142890 129550 116860 107440 65986 FALSE TRUE 81898.61108 100913.9553 104596.6401 106111.6398 100731.2705 109705.963 119395.5325 115293.6828 103573.2554 78914.69332 1.037811941 1.278772698 1.325439354 1.344637295 1.276457733 1.390184241 1.512969606 1.460991331 1.312471113 1 16.26800632 5.503159328 1.000847756 1.367772498 5.52E-12 0.266086902 0.133155461 8.275149538 2.184419037 0.038309705 17.55365383 318536.5914 -5.503159328 -1.367772498 NCCFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NCCFEHR 7 0 Q9BTY7 Q9BTY7 HGH1 Protein HGH1 homolog 0 143.89 0.0023914 42936000 39924 44757 45692 37952 62475 78755 59700 50457 41262 46611 FALSE TRUE 41500.23035 52443.66659 46882.77106 45458.79232 51855.52182 60465.34479 55020.558 49780.70645 39776.98868 55743.53303 0.744485111 0.940802704 0.841044127 0.815498944 0.930251798 1.084706001 0.987030334 0.893031061 0.71357136 1 15.76651682 3.200834745 9.436590593 0.937563351 0.843413802 0.189042953 0.100129276 0.641737459 152.6954309 0.030061426 0.036148257 1587.942398 -3.200834745 -0.094149549 NCEEVGLFNELAS(ph)PFENEFKK ddPTM_MDA-MB-175_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 68.231 0.007298 21498000 26041 14126 14022 9277.5 23942 25531 22729 17047 18061 13408 TRUE FALSE 27069.11879 16552.03061 14387.42484 11112.56181 19872.34739 19601.81218 20947.44159 16818.51285 17410.98814 16035.04089 1.688122842 1.032241248 0.897249027 0.693017367 1.23930756 1.222436058 1.306354111 1.048859991 1.085808777 1 13.96894041 4.740412128 24.66589988 1.064985685 1.688123089 0.554959989 0.169092418 113.0551668 1505980.912 0.04382048 0.28409184 55006.26139 -4.740412128 0.623137404 NCES(ph)DTEEDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCESDTEEDIAR 12 0 Q9UIK4 Q9UIK4 DAPK2 Death-associated protein kinase 2 1 NCES(0.99)DT(0.01)EEDIAR;NCES(0.999)DT(0.001)EEDIAR 279.55 5.81E-28 337730000 475000 451780 510400 478220 604300 730130 622270 532400 537120 403660 TRUE FALSE 493753.3668 529369.7006 523701.4433 572810.4887 501581.3019 560568.3727 573494.8514 525264.0488 517789.1561 482749.4485 1.022794264 1.096572357 1.084830744 1.186558556 1.03900958 1.161199406 1.187976192 1.088067631 1.072583631 1 18.88091509 4.899726529 1.732679875 1.111791282 0.963246566 0.12785783 0.058641098 2.613188314 5.584917713 0.01444893 0.727576928 79382.8211 -4.899726529 -0.148544717 NCGSFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCGSFTR 7 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 94.114 0.033589 258540000 226398 216993 244600 207768 265850 323390 269340 244300 252410 202039 FALSE TRUE 235336.3679 254259.8598 250974.4769 248863.8903 220660.912 248287.5735 248228.427 241025.5581 243325.8134 241624.6738 0.973974902 1.052292615 1.038695565 1.029960585 0.913238323 1.027575411 1.027330625 0.99752047 1.007040422 1 17.88240826 NCHLNENIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NCHLNENIEK 10 0 Q13907;Q13907-2;Q9BXS1 Q13907 IDI1;IDI2 Isopentenyl-diphosphate Delta-isomerase 1;Isopentenyl-diphosphate delta-isomerase 2 0 127.83 0.00034568 315510000 277210 211670 257900 222910 394700 406430 351550 301510 301990 189930 FALSE TRUE 288154.4649 248022.6759 264621.0859 267000.9327 327609.035 312042.792 323994.5924 297468.7516 291121.4389 227143.1471 1.268602943 1.091922337 1.164997004 1.175474304 1.442302087 1.373771545 1.426389467 1.309609185 1.281665076 1 17.79324225 3.32412526 9.73898432 1.331199431 1.16780528 0.194595851 0.123202377 0.407008271 42.84820624 0.031829634 0.043096284 2109.236412 -3.32412526 -0.163394151 NCIVLIDSTPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCIVLIDSTPYR 12 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 155.97 0.00016933 115272000 192298 175484 207090 183357 244850 319800 215880 203320 209028 189392 FALSE TRUE 199890.0735 205622.0119 212486.9355 219624.4673 203230.4845 245531.2966 198958.7615 200594.828 201505.1231 226499.7363 0.882517908 0.907824509 0.938133258 0.969645576 0.897265877 1.084024647 0.878406151 0.885629411 0.889648379 1 17.78914984 4.451975783 2.907009807 0.937011522 0.884228538 0.090945772 0.060473217 0.779601756 12.41407766 0.015456968 0.070289875 28312.34119 -4.451975783 -0.052782984 NCLECQQHSQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NCLECQQHSQLK 12 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 110.92 0.0014375 227870000 278220 181450 256430 208110 349380 363570 315480 250320 279560 152260 FALSE TRUE 289204.3404 212612.626 263112.7765 249273.5369 289992.5124 279136.3775 290751.8532 246964.8698 269498.6902 182092.4318 1.588228229 1.167608252 1.444940758 1.368939579 1.592556646 1.532937831 1.59672673 1.356261034 1.480010386 1 17.47431144 -0.786257018 1.210959592 0.984659473 1.452542431 0.535893402 0.127913094 143.1167901 88.7225168 9.917209466 0.036588344 0.163584813 0.786257018 0.467882957 NCLTNFHGMDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NCLTNFHGMDLTR 13 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 178.67 1.44E-05 5234900000 1865070 1851350 2028530 1764860 2750890 3252520 2165220 2238440 2004140 1845890 FALSE TRUE 1938704.404 2169304.961 2081395.158 2113944.04 2283294.7 2497171.522 1995504.399 2208437.373 1932011.393 2207556.804 0.878212692 0.982672318 0.942850102 0.957594403 1.03430847 1.13119242 0.903942492 1.000398889 0.875180829 1 21.07401913 4.738603703 20.17110145 0.982566938 0.878212808 0.172836599 0.067307693 0.450593387 197135.6556 0.015962326 0.091923394 54777.68868 -4.738603703 -0.104354129 NCPAVTLTS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCPAVTLTSPAK 12 0 Q9UGU0;Q9UGU0-2 Q9UGU0 TCF20 Transcription factor 20 1 NCPAVTLTS(1)PAK;NCPAVTLT(0.092)S(0.908)PAK 193.51 2.85E-06 268050000 1004620 493380 664970 515350 987250 1190340 929750 706350 739040 383770 TRUE FALSE 1044283.173 578114.177 682299.6645 617284.6918 819437.5976 913901.5748 856873.7656 696882.5336 712442.0948 458962.3838 2.275313207 1.259611239 1.486613476 1.344957046 1.785413416 1.991234156 1.86698038 1.518387036 1.552288641 1 18.80801639 0.693035623 1.471109374 1.001848634 1.679315777 0.338818199 0.290553046 1.287089583 4.319418763 0.276054659 0.080592195 4.932142582 -0.693035623 0.677467144 NCPHIVVGTPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NCPHIVVGTPGR 12 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;F6WLT2;F6UJC5;A0A140T9X9;A0A140TA18;A0A140T996;F6S4E6;A0A0A0MT12;F6TRA5;A0A140T9K1;A0A140T973;A0A140T9L4 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;; 122.34 0.00036017 1310360000 977060 948740 937450 852160 1275980 1528660 1051680 1097970 867500 703730 FALSE TRUE 1015635.083 1111678.715 961880.7171 1020714.705 1059089.375 1173651.882 969246.5735 1083253.508 836278.8445 841612.4198 1.206772927 1.320891528 1.142902237 1.21280851 1.258405117 1.394527759 1.151654314 1.287116828 0.99366267 1 19.68279647 1.233436272 24.9974076 0.996831146 1.247279054 0.659291421 0.071902357 75.50159753 368288.9402 0.059484334 0.016647502 17.11733978 -1.233436272 0.250447907 NCPS(ph)PVLIDCPHPNCNKK ddPTM_MDA-MB-175_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 237.01 3.64E-24 2466120000 4114020 2299490 3076810 2138620 4403280 4011580 3717980 3158660 3438220 1690100 TRUE FALSE 4276444.686 2694409.52 3156994.196 2561632.653 3654812.038 3079951.341 3426555.012 3116323.329 3314479.134 2021242.736 2.115750182 1.333045988 1.561907504 1.26735528 1.808200457 1.523790926 1.695271405 1.54178579 1.63982241 1 20.94681116 -1.371138298 4.667943147 0.999311895 1.593123932 0.39238452 0.226758429 0.001473362 0.00019849 0.199210729 0.046902619 0.042546291 1.371138298 0.593812037 NCQHANAERPTVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCQHANAERPTVAR 14 1 Q9Y5J1;F6VJE8 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 0 ; 132.51 3.00E-05 37250100 69494 92738 88284 87781 88022 106034 94163 87397 76753 84674 FALSE TRUE 72237.67678 108665.0301 90584.75357 105143.8198 73060.05188 81409.21046 86782.25801 86225.58617 73990.67452 101264.2491 0.713358144 1.073083848 0.894538343 1.038311356 0.721479224 0.803928446 0.856988115 0.851490896 0.730669265 1 16.6277654 3.238867356 24.99999999 0.823263904 0.937535504 0.157170102 0.115373698 13.28929481 1083039.973 0.030333015 0.038642753 1733.274534 -3.238867356 0.114271601 NCSASTS(ph)QER ddPTM_MDA-MB-175_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 NCSAST(0.006)S(0.994)QER;NCSAS(0.002)T(0.109)S(0.888)QER;NCSAS(0.002)T(0.008)S(0.99)QER;NCS(0.001)AS(0.002)T(0.015)S(0.982)QER;NCSAST(0.002)S(0.998)QER;NCSAST(0.001)S(0.999)QER 162.48 7.09E-06 1494266000 2658281 2790611 2974578 2777942 3591800 4657300 3241723 3398350 3122585 2709529 TRUE FALSE 2763231.987 3269876.731 3052097.946 3327410.636 2981267.119 3575712.657 2987628.281 3352800.677 3010203.776 3240409.33 0.852741646 1.009093728 0.941886544 1.026848863 0.920027939 1.103475608 0.921991013 1.034684305 0.928957878 1 21.62774464 4.743830888 24.61302321 0.98890688 0.852741575 0.336091953 0.056761399 473.7589431 2212444.025 0.011940802 0.102078146 55440.97873 -4.743830888 -0.136165305 NCSS(ph)PEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCSSPEFSK 9 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57;Q5JX53 Q99829 CPNE1 Copine-1 1 NCS(0.008)S(0.99)PEFS(0.002)K;NCS(0.002)S(0.998)PEFSK 228.28 1.77E-07 1583130000 4603600 3091200 3981600 3188700 5235600 5437400 5243600 4264700 4583700 2154220 TRUE FALSE 4785353.683 3622089.554 4085363.767 3819415.343 4345654.582 4174646.255 4832592.93 4207538.672 4418733.532 2576298.164 1.857453361 1.405927934 1.585749594 1.482520694 1.686782471 1.620404933 1.875789456 1.633172251 1.715148345 1 21.29686814 -1.48473141 6.82153322 0.999802524 1.646301321 0.664470041 0.138831405 0.000406227 3.07E-05 0.13096598 0.030859847 0.03275432 1.48473141 0.646498796 NCSVELTPDYSMESHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NCSVELTPDYSMESHQR 17 0 Q96HU1 Q96HU1 SGSM3 Small G protein signaling modulator 3 0 70.337 0.025426 0 52226 92400 89421 78136 104750 124590 91887 100520 91237 76140 FALSE TRUE 54287.92281 108268.9812 91751.38472 93591.06759 86944.63242 95655.86068 84684.65684 99172.69382 87953.39819 91058.17521 0.596189444 1.189008905 1.00761282 1.0278162 0.954825113 1.050491737 0.930006083 1.089113565 0.965903369 1 16.47450093 4.75276358 24.96475916 1.023613888 0.596189147 0.766937387 0.070727849 1083.501334 1904453.192 0.015693454 0.335304463 56593.11255 -4.75276358 -0.427424742 NCVAIAADRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NCVAIAADRR 10 1 P49720;A0A087WXQ8;A0A087WY10;A0A087WUL2 P49720 PSMB3 Proteasome subunit beta type-3 0 202.56 3.55E-07 462460000 204530 188280 227960 192890 361230 389240 270510 232610 225510 196880 FALSE TRUE 212605.0023 220615.6254 233900.8249 231043.0663 299828.2536 298844.909 249306.7194 229492.2434 217393.9392 235454.8665 0.902954377 0.936976282 0.993399832 0.98126265 1.273400113 1.269223752 1.058830183 0.974676153 0.923293463 1 17.84509102 3.455679498 24.98873072 1.08529556 0.95096909 0.255478111 0.109531531 370.6628783 431977.9499 0.034493667 0.046708381 2855.482469 -3.455679498 -0.13432647 NCVLLSRPEISTDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NCVLLSRPEISTDER 15 1 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 ;; 118.33 0.00027296 1309980000 1052750 1206690 1299010 1246340 1631600 2062510 1472770 1473050 1302390 985950 FALSE TRUE 1094313.383 1413929.621 1332863.268 1492862.332 1354261.215 1583523.31 1357330.439 1453306.174 1255517.238 1179128.025 0.928070031 1.199131553 1.13038045 1.266073149 1.148527713 1.342961304 1.151130674 1.232526191 1.064784494 1 20.16928894 4.740464032 24.43372227 1.185367672 0.928069909 0.366266313 0.093923866 114.5473447 1470260.373 0.020294297 0.13182894 55012.83574 -4.740464032 -0.257297763 NCVVLSDIHIDIMDYIQPATCTDAEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCVVLSDIHIDIMDYIQPATCTDAEFR 27 0 P53618 P53618 COPB1 Coatomer subunit beta 0 ; 162.07 1.25E-11 255201000 86341 85021 82506 97036 119089 140311 116856 102453 96546 66492 FALSE TRUE 89749.80935 99622.69538 84656.17414 116229.4312 98846.29432 107725.8967 107696.5214 101079.7851 93071.32832 79519.83433 1.128646835 1.252803105 1.064591933 1.461640761 1.24303949 1.354704742 1.354335334 1.271126706 1.170416527 1 16.27902713 3.766852683 24.9648095 1.283571385 1.159092898 0.141896913 0.124671443 1195.792544 1055158.617 0.029640159 0.053421958 5845.91751 -3.766852683 -0.124478487 NCWQNYLDFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NCWQNYLDFHR 11 0 P14854;A0A494C160 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 234.61 1.68E-15 2860300000 2072100 2599300 1939840 2377400 3185000 4367600 2423800 2173500 1788000 2293300 FALSE TRUE 2153908.108 3045709.555 1990393.824 2847642.624 2643614.838 3353291.092 2233816.223 2144367.788 1723650.229 2742628.227 0.785344542 1.110507624 0.725724983 1.038289695 0.963898355 1.222656085 0.81448014 0.78186601 0.628466597 1 21.38712764 2.028896537 24.99999367 0.783948369 0.975617577 0.209116692 0.158995549 277.3284704 239931.0858 0.056609921 0.041808578 106.8800226 -2.028896537 0.191669209 NDAPTPGTSTT(ph)PGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NDAPTPGTSTTPGLR 15 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 NDAPTPGT(0.005)S(0.031)T(0.422)T(0.543)PGLR;NDAPTPGT(0.003)S(0.004)T(0.06)T(0.933)PGLR;NDAPTPGT(0.002)S(0.016)T(0.21)T(0.772)PGLR 163.02 1.75E-05 1489490000 2202450 1798490 1940870 1631230 2557360 3200830 2293530 2110290 2036200 1593200 TRUE FALSE 2289404.427 2107366.667 1991450.667 1953882.425 2122660.861 2457485.742 2113757.126 2082005.014 1962917.56 1905357.036 1.201561903 1.10602193 1.045185038 1.025467872 1.114048874 1.289777031 1.109375873 1.092711221 1.030209836 1 20.86162993 1.270258707 2.151916544 1.002251888 1.124276747 0.285878864 0.07076037 0.435107174 3.413964872 0.069587932 0.02033361 18.63196705 -1.270258707 0.12202486 NDEELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 128.61 0.0087036 11429790000 7329510 4126510 6296790 4866870 8054730 8505020 8364310 6112370 6196300 2864480 FALSE TRUE 7618884.714 4835205.993 6460889.52 5829522.36 6685589.872 6529858 7708693.526 6030443.678 5973296.373 3425720.012 2.224024347 1.411442259 1.885994622 1.70169259 1.951586775 1.906127172 2.250240387 1.760343419 1.743661581 1 21.70797581 0.669519444 1.92795122 1.000580158 1.880390623 0.572603527 0.228984305 1.059351649 5.228817288 0.209118115 0.058030631 4.67217869 -0.669519444 0.879810465 NDEELNKLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDEELNKLLGK 11 1 A0A0U1RR32;A0A0U1RRH7;P20671;Q99878;Q96KK5;Q6FI13;P0C0S8;Q16777;Q9BTM1;Q9BTM1-2;H0YFX9 A0A0U1RR32;Q99878 HIST1H2AD;HIST1H2AJ;HIST1H2AH;HIST2H2AA3;HIST1H2AG;HIST2H2AC;H2AFJ Histone H2A type 1-D;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 2-C;Histone H2A.J;Histone H2A 0 ; 158.2 2.75E-05 15859300000 18890900 10276900 15697200 6079760 24074000 18922700 13395300 13197500 16935500 7695700 FALSE TRUE 19636727.32 12041877.63 16106281.93 7282318.382 19981910.08 14528189.7 12345341.38 13020609.1 16325994.66 9203525.072 2.133609369 1.308398417 1.750012284 0.791253169 2.171114863 1.578546219 1.341370973 1.414741525 1.773884956 1 23.13375511 -2.853373503 0.286594967 3.77E-18 1.598874934 0.163191083 0.389192121 111.9958993 3.221842468 69.58002995 0.411313179 0.001401608 2.853373503 1.598874934 NDEELNKLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NDEELNKLLGR 11 1 Q7L7L0;P04908 Q7L7L0 HIST3H2A;HIST1H2AB Histone H2A type 3;Histone H2A type 1-B/E 0 ;;; 186.46 3.66E-06 7105440000 7322900 5978800 7357500 3393200 12184700 9515800 5336500 6604600 7974900 6256700 FALSE TRUE 7612013.747 7005612.391 7549242.494 4064364.832 10113549.05 7305899.663 4918211.186 6516076.14 7687884.907 7482580.573 1.017297932 0.936256192 1.008908948 0.543176888 1.351612448 0.976387704 0.657288102 0.87083274 1.027437638 1 22.83510448 NDEWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NDEWAR 6 0 Q13409-2;Q13409-3;Q13409-6;Q13409;Q13409-5;Q13409-7 Q13409-2 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 ;;; 130.05 0.037058 1503320000 2037530 2487960 2379670 2532320 2923940 3677660 2491010 2735020 2410120 2758770 FALSE TRUE 2117973.258 2915247.776 2441686.155 3033205.338 2426929.723 2823579.2 2295758.127 2698361.53 2323380.252 3299298.162 0.641946606 0.883596339 0.740062291 0.919348658 0.735589693 0.855812073 0.695832269 0.817859253 0.704204391 1 21.65372773 -1.140052908 4.759723402 1.000017473 0.783487786 0.377620716 0.085484123 1.40E-05 2.52E-06 0.072951124 0.017193358 0.072434771 1.140052908 -0.216529687 NDFEQGELYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDFEQGELYLR 11 0 P83111;P83111-2 P83111 LACTB "Serine beta-lactamase-like protein LACTB, mitochondrial" 0 89.548 0.016978 0 23103 18333 24817 28034 22410 31519 21921 16868 27137 15483 FALSE TRUE 24015.12428 21481.55014 25463.75141 33579.04153 18600.7562 24199.18993 20202.77474 16641.91205 26160.34467 18516.59741 1.296951257 1.160124059 1.375185238 1.81345637 1.004545046 1.306891833 1.091063023 0.898756488 1.412805176 1 14.17653139 NDFTEEEEAQVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDFTEEEEAQVRK 13 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 80.706 0.018141 0 35499 31213 32496 21602 41887 47797 28389 30815 32098 49902 FALSE TRUE 36900.52793 36573.58995 33342.87246 25874.81112 34767.0627 36696.87112 26163.796 30401.97533 30942.79925 59679.34147 0.618313256 0.612835012 0.558700408 0.433563952 0.582564449 0.614900738 0.438406245 0.509422098 0.518484261 1 15.864944 -1.603821132 2.760148834 1.037162992 0.538758343 0.81601609 0.065068212 10119080.48 9955085.263 2729105.886 0.017983695 0.024898826 1.603821132 -0.498404649 NDHQEDFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NDHQEDFWK 9 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 185.08 4.33E-05 3749480000 5619850 3322646 4906490 3859873 6802570 7184670 5926800 4866610 5207730 2655264 FALSE TRUE 5841726.017 3893284.604 5034357.16 4623344.359 5646271.581 5516139.277 5462241.929 4801381.053 5020304.815 3175512.143 1.839616967 1.226033606 1.585368575 1.455936602 1.778066443 1.737086501 1.720113696 1.512002108 1.580943353 1 21.59855786 0.204285111 1.345862555 0.999438225 1.601286684 0.531279814 0.170384724 5.736168567 8.851483315 0.165328634 0.047158993 1.600608473 -0.204285111 0.601848459 NDHSAYKR ddPTM_MDA-MB-175_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 0 105.57 0.0028322 57372000 39762 30296 36457 26448 59681 51645 39066 37121 31638 27938 FALSE TRUE 41331.83446 35499.10233 37407.09937 31679.33546 49536.44494 39651.23144 36003.90484 36623.45371 30499.35456 33411.91619 1.237038733 1.062468316 1.119573602 0.948144826 1.482598144 1.186739222 1.077576773 1.096119525 0.912828656 1 15.0280751 1.529561072 1.924413206 0.960212869 1.163165368 0.260713616 0.133637987 0.452724821 3.36356445 0.11162716 0.037744151 33.85018699 -1.529561072 0.202952499 NDIASHPPVEGSYAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NDIASHPPVEGSYAPR 16 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 124.29 8.33E-05 2707660000 776410 708960 782130 711560 1032900 1202020 981630 891700 960980 605770 FALSE TRUE 807063.2663 830718.3651 802512.9503 852304.4442 857328.0269 922869.0718 904687.2756 879748.22 926394.5175 724459.0333 1.114021952 1.146674038 1.107740967 1.176470173 1.183404427 1.273873372 1.248776306 1.214351923 1.278739687 1 19.46654459 3.379497247 2.103064875 1.219133339 1.125527124 0.146558122 0.075769001 0.446046884 4.011554352 0.021198411 0.032154594 2396.057562 -3.379497247 -0.093606214 NDIHTLLK ddPTM_MDA-MB-175_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 0 118.18 0.0044469 0 347020 196010 231360 230800 329780 323280 368430 261190 258750 133960 FALSE TRUE 360720.6176 229673.1928 237389.4317 276451.5511 273724.1134 248203.1194 339551.4939 257689.1753 249437.638 160206.8972 2.251592309 1.433603651 1.481767863 1.72559082 1.708566349 1.549266129 2.119456152 1.608477411 1.556971906 1 17.28957673 0.78823402 2.034633947 1.00126007 1.72386812 0.441962005 0.248790299 0.715748815 4.986279927 0.226058047 0.0623973 6.140928204 -0.78823402 0.722608049 NDKS(ph)EEEQSSSSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NDKSEEEQSSSSVK 14 1 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(0.579)EEEQS(0.42)S(0.001)SSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK;NDKS(1)EEEQSSSSVK 294.93 3.61E-43 5229145000 9236628 2322055 3372463 2369535 6025285 7900532 6103759 3721548 3624068 1237124 TRUE FALSE 9601297.206 2720849.883 3460352.156 2838221.951 5001109.208 6065753.177 5625330.42 3671666.736 3493638.501 1479514.762 6.489490646 1.83901503 2.338842603 1.918346491 3.3802361 4.099826061 3.802145518 2.481669552 2.361340753 1 20.49669266 1.016808201 1.498504188 1.039851972 3.252024779 0.245086519 1.282775262 0.616473762 2.823900291 1.184895182 0.350917801 10.39461004 -1.016808201 2.212172807 NDKS(ph)EEEQSSSSVKK ddPTM_MDA-MB-175_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 1 NDKS(1)EEEQSSSSVKK 162.32 8.36E-07 266910000 551600 109270 157620 106310 331580 347500 286710 191580 191710 50384 TRUE FALSE 573377.5939 128036.2725 161727.7067 127337.8007 275218.15 266798.3914 264236.921 189012.1835 184810.3945 60255.78014 9.515727663 2.124879509 2.684019795 2.113287728 4.567497913 4.427764287 4.385254334 3.136830741 3.067098196 1 15.87881202 4.744724688 24.96446897 3.227424251 9.515730489 0.751583062 1.110167147 343.2025628 1389930.446 0.266574286 2.471426562 55555.19647 -4.744724688 6.288306238 NDKSEEEQSS(ph)SSVKK ddPTM_MDA-MB-175_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 1 NDKS(0.013)EEEQS(0.321)S(0.572)S(0.086)S(0.007)VKK 125.51 7.09E-05 141470000 231140 40823 71321 49886 128730 151560 109470 75124 79072 19396 TRUE FALSE 240265.5857 47834.03269 73179.68385 59753.30191 106848.5206 116362.4869 100889.4554 74117.08566 76226.21417 23196.27484 10.35793839 2.062142866 3.154803276 2.575986977 4.606279298 5.01642991 4.349381788 3.195215015 3.286140326 1 14.50160552 4.745568764 24.78649775 3.429551387 10.35794202 0.771255846 1.157628144 346.5692487 1225715.339 0.274286529 2.753880856 55663.27611 -4.745568764 6.928390629 NDKSEEEQSSS(ph)SVKKDETNVK ddPTM_MDA-MB-175_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 NDKSEEEQSS(0.053)S(0.474)S(0.474)VKKDETNVK 232 1.83E-25 476690000 460890 47697 93948 52976 237750 276880 195030 102080 126460 25163 TRUE FALSE 479086.2931 55888.58872 96396.36206 63454.49468 197337.3399 212578.8162 179743.039 100711.7846 121908.7293 30093.20808 15.92008043 1.857182809 3.203259746 2.108598542 6.557537482 7.064013103 5.972877286 3.346661623 4.051037995 1 14.87715029 4.745427856 24.81792802 4.139496561 15.92008645 0.770862186 1.961221777 355.382865 1284303.085 0.485500911 4.789212709 55645.21902 -4.745427856 11.78058989 NDKSEEEQSSSS(ph)VKKDETNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDKSEEEQSSSSVKKDETNVK 21 3 B4DY08;G3V4W0;P07910;G3V2Q1;P07910-3;G3V5V7;P07910-2;G3V4C1;B2R5W2;G3V2D6;P07910-4 B4DY08;P07910;P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 NDKSEEEQSS(0.003)S(0.204)S(0.794)VKKDETNVK;NDKSEEEQS(0.002)S(0.013)S(0.213)S(0.772)VKKDETNVK 243.87 2.22E-29 1554210000 1954950 227420 415840 199152 1010810 1131130 819080 510280 533810 116321 TRUE FALSE 2032132.936 266477.6159 426677.132 238543.6712 838992.8773 868442.1999 754878.3693 503440.5312 514598.2824 139111.8728 14.60790437 1.915563427 3.067151087 1.71476141 6.031065933 6.242761183 5.426412238 3.618961638 3.699168675 1 17.08588603 4.744943482 24.96137272 3.864420507 14.60790928 0.781652169 1.736026017 337.6684191 1320478.426 0.426996309 4.055156122 55583.19184 -4.744943482 10.74348878 NDKSEEEQSSSSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 256.35 2.38E-24 3035579000 2698082 974780.8 1395817 975676 2332333 2434060 2145478 1477358 1456365 704505.7 FALSE TRUE 2804604.361 1142191.82 1432193.138 1168661.801 1935883.87 1868786.454 1977309.828 1457556.432 1403950.708 842540.1033 3.328748803 1.355652764 1.699851594 1.387069643 2.297675638 2.218038579 2.346843575 1.729954962 1.666331018 1 19.68438583 0.932949523 1.553438457 1.010009741 2.024449939 0.266607172 0.54116281 0.646978509 3.158514131 0.495209019 0.144630572 8.569382391 -0.932949523 1.014440198 NDKSEEEQSSSSVKK ddPTM_MDA-MB-175_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 0 ; 225.7 5.42E-13 262730000 594100 170760 260021 167032 483720 442010 403540 284372 279721 109752 FALSE TRUE 617555.5267 200086.7017 266797.3609 200070.4311 401497.4472 339359.8762 371909.4803 280560.4585 269653.8959 131255.8031 4.70497694 1.524402708 2.032651926 1.524278747 3.058892923 2.585484743 2.833470762 2.137508986 2.054415039 1 17.00202168 0.833494452 1.359053896 1.00743934 2.510067009 0.233540993 0.864756658 0.983621919 3.411319152 0.780390507 0.23332886 6.815448675 -0.833494452 1.502627669 NDLAVVDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NDLAVVDVR 9 0 P19338 P19338 NCL Nucleolin 0 ;;; 126.39 0.0011049 1023930000 1693320 1821810 2003680 1771120 2536040 3104180 2321940 2204030 1993180 1604480 FALSE TRUE 1760173.581 2134691.696 2055897.547 2121442.25 2104964.827 2383281.239 2139940.276 2174488.583 1921445.841 1918847.136 0.917307871 1.112486584 1.071423308 1.105581685 1.096994537 1.242038094 1.115221862 1.133226583 1.001354305 1 20.87180835 4.739492651 24.15189612 1.107556409 0.917307773 0.396876485 0.065647292 45.55995715 1180301.208 0.015135388 0.091842101 54889.92678 -4.739492651 -0.190248636 NDLSPTTVMSEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDLSPTTVMSEGAR 14 0 P30043;M0R192;A0A2R8Y7Y9;M0QZL1 P30043 BLVRB Flavin reductase (NADPH) 0 244.16 4.33E-12 0 37711 34961 44319 39170 51324 60558 45347 38763 42632 40867 FALSE TRUE 39199.8594 40965.27979 45473.98955 46917.70909 42599.96481 46494.32227 41792.58365 38243.44539 41097.68265 48874.1062 0.802057827 0.838179621 0.930431124 0.959970682 0.871626473 0.951307878 0.855106863 0.782488896 0.84088868 1 15.5767827 -0.1239694 7.787176797 1 0.869071457 0.31635061 0.057208379 0 0 0.061536335 0.014504253 0.751675855 0.1239694 -0.130928543 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 41 0 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ;; 371.48 1.65E-176 4293570000 1685310 1209140 1592390 1332800 1992440 2245520 1994030 1818360 1738840 922040 FALSE TRUE 1751847.34 1416800.389 1633888.992 1596423.862 1653765.76 1724032.011 1837732.718 1793987.858 1676259.488 1102696.084 1.588694623 1.284851202 1.481721949 1.447746015 1.499747559 1.563469786 1.66658134 1.626910518 1.520146404 1 20.07260379 0.89733401 19.92826618 1 1.524823481 0.704270061 0.101046666 12621.5287 2449943.292 0.107726272 0.026931568 7.894670523 -0.89733401 0.524823481 NDPYHPDHFNCANCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDPYHPDHFNCANCGK 16 0 P48059;P48059-4;P48059-2;P48059-5;P48059-3;A0A0J9YXC7 P48059 LIMS1 LIM and senescent cell antigen-like-containing domain protein 1 0 ; 120.63 5.96E-05 259440000 238360 173826 176488 188745 261808 301598 223577 216817 225499 131564 FALSE TRUE 247770.6369 203679.2633 181087.4223 226078.1977 217305.9697 231556.4353 206052.4505 213910.9228 217383.335 157341.4469 1.574732162 1.294504833 1.150920027 1.436863599 1.381110788 1.471681111 1.309587872 1.359533213 1.381602492 1 17.26353923 -1.264964994 2.942715162 0.997495829 1.366108435 0.521246947 0.107150276 7404391.119 9556542.722 166871.1005 0.026460396 0.054329412 1.264964994 0.368612606 NDQCYDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDQCYDDIR 9 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;F8W1H8;F8VUX3;F8VSA4;F8VRE9;F8VTT6;F8VVB7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 85.807 0.033884 231220000 198330 446760 427070 447360 451770 628210 434070 465710 485910 460510 FALSE TRUE 206160.2215 523487.5547 438199.795 535846.4728 374978.2968 482317.7481 400046.4592 459467.9192 468422.194 550738.1175 0.374334398 0.950519926 0.7956591 0.97296057 0.680864979 0.875766054 0.72638237 0.834276591 0.850535271 1 19.07100694 4.746983431 24.93874283 0.840041481 0.374334157 0.678979894 0.098541699 573.0707264 1696741.481 0.021437929 0.248118908 55844.8889 -4.746983431 -0.465707324 NDQDTWDYTNPNLSGQGDPGSNPNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NDQDTWDYTNPNLSGQGDPGSNPNKR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 237.2 9.25E-45 3189230000 431241 276836 378790 343937 481056 522033 447142 367998 415423 238822 FALSE TRUE 448266.7277 324380.4295 388661.5786 411966.7121 399286.2729 400798.7472 412093.8417 363065.5887 400472.0074 285614.5984 1.569481148 1.135727765 1.360790312 1.442386749 1.397989722 1.40328523 1.442831858 1.27117308 1.402141241 1 18.12371019 -0.761459919 0.658890512 0.942539975 1.376881247 0.524195017 0.1084914 16.09974291 4.405912549 2.131304093 0.038350409 0.173196887 0.761459919 0.434341272 NDQEPPPEALDFS(ph)DDEKEKEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDQEPPPEALDFSDDEKEKEAK 22 2 Q96HR8-2;Q96HR8 Q96HR8-2 NAF1 H/ACA ribonucleoprotein complex non-core subunit NAF1 1 NDQEPPPEALDFS(1)DDEKEKEAK 121.86 1.39E-05 70912000 218820 26304 56888 20296 116980 159100 72910 59956 66438 21356 TRUE FALSE 227459.1826 30821.50738 58370.54801 24310.48822 97095.78138 122151.4362 67195.12369 59152.38789 64046.90936 25540.29931 8.905893379 1.206779412 2.285429285 0.951848211 3.801669675 4.782693996 2.630945035 2.316041295 2.507680453 1 14.64048781 4.745690899 24.94020993 2.500218332 8.905896465 0.741087046 1.154199465 433.5779635 1516524.457 0.28408873 2.89280348 55678.93237 -4.745690899 6.405678133 NDRGDQVPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDRGDQVPNR 10 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6;F5H3E1 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 115.41 0.0011185 256110000 83592 87968 78929 77568 132350 136900 81319 87933 81391 80295 FALSE TRUE 86892.27671 103075.8197 80985.95458 92910.71888 109853.1943 105107.0497 74945.00429 86754.40196 78461.75381 96027.26791 0.904870862 1.073401565 0.843364144 0.967545166 1.14397917 1.094554203 0.780455447 0.903435075 0.817077852 1 16.55115651 2.238062742 24.99999999 0.867980045 1.005065241 0.288588636 0.099250738 16.84710346 845883.1062 0.036267413 0.028437346 173.006628 -2.238062742 0.137085196 NDRGNDLDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDRGNDLDTK 10 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 122.7 0.00043924 551620000 886360 572700 705580 445650 1165780 1068250 695310 708860 778840 481880 FALSE TRUE 921354.1772 671056.77 723967.9944 533798.2399 967621.132 820165.127 640809.7853 699358.8912 750809.7005 576295.1599 1.598753974 1.164432424 1.256245141 0.926258412 1.679037409 1.423168515 1.111947193 1.213542885 1.302821458 1 19.13644838 -4.491971102 0.189937162 2.43E-11 1.339765903 0.161898737 0.210844921 220.21502 2.566494884 83.5836031 0.580223792 3.22E-05 4.491971102 1.339765903 NDRGPGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDRGPGGPR 9 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 88.496 0.011624 42533000 13572 23544 24250 18386 28643 37782 21883 23956 20378 21886 FALSE TRUE 14107.83304 27587.49885 24881.97492 22022.69592 23774.27309 29007.70309 20167.75328 23634.909 19644.59976 26174.14267 0.538998859 1.053998185 0.950631898 0.8413913 0.908311435 1.108258003 0.77052202 0.90298694 0.750534602 1 14.67585466 4.752471568 24.44882247 0.914169002 0.538998515 0.523998362 0.108988935 1403.912452 2467350.733 0.02529168 0.504993655 56555.0731 -4.752471568 -0.375170487 NDS(ph)GEENVPLDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NDSGEENVPLDLTR 14 0 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 NDS(1)GEENVPLDLTR 139.29 1.09E-05 85156000 75094 72930 79350 75222 109500 128220 88599 92128 95827 61749 TRUE FALSE 78058.76911 85455.16018 81417.92619 90100.68708 90887.22911 98442.84819 81654.37887 90893.17485 92378.20499 73847.53429 1.057026072 1.157183662 1.102513807 1.220090663 1.230741554 1.333055316 1.105715711 1.230822068 1.250931475 1 16.17226213 3.739875741 24.78610083 1.208211385 1.110735423 0.171025317 0.088055696 159.9060105 3013703.487 0.021469053 0.036149099 5493.836632 -3.739875741 -0.097475961 NDS(ph)PTQIPVSSDVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDSPTQIPVSSDVCR 15 0 Q8TC07-2;Q8TC07-3;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 NDS(0.997)PT(0.003)QIPVSSDVCR;NDS(1)PTQIPVSSDVCR 357.45 1.21E-82 1769620000 689600 587160 602150 594010 846340 1105390 735530 708400 643110 519170 TRUE FALSE 716825.9405 688000.1625 617842.5237 711503.4051 702479.4291 848679.9248 677877.2367 698905.0567 619964.5967 620891.4214 1.154510943 1.108084504 0.995089483 1.145938534 1.13140463 1.36687333 1.091780645 1.125647791 0.998507268 1 19.24398147 1.277885587 2.965253584 0.992156386 1.141739757 0.291993789 0.087443503 0.342602225 5.031328989 0.08032086 0.023598441 18.96206307 -1.277885587 0.149583371 NDS(ph)WGSFDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NDS(1)WGSFDLR;NDS(0.996)WGS(0.004)FDLR;NDS(1)WGSFDLR;NDS(0.983)WGS(0.017)FDLR;NDS(1)WGSFDLR 253.72 4.54E-17 1809440000 1287350 1162170 1332490 1100220 1723610 2046630 1538570 1316560 1398190 1030030 TRUE FALSE 1338175.572 1361763.657 1367215.784 1317840.232 1430631.388 1571331.199 1417972.863 1298913.667 1347869.415 1231844.657 1.086318444 1.105467032 1.109893018 1.069810405 1.161373213 1.275592008 1.151097141 1.054445996 1.094187816 1 20.2323889 1.702537187 5.981186096 1.055567863 1.138447734 0.322264472 0.057847406 0.1962289 16.36328103 0.032413585 0.016421972 50.41237838 -1.702537187 0.082879872 NDSDPTYGQQGHPNTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NDSDPTYGQQGHPNTWK 17 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 ;;; 229.4 1.12E-15 1410990000 1535470 1103500 1388350 1043904 1790780 1941300 1658520 1467390 1502580 876742 FALSE TRUE 1596091.541 1293017.541 1424531.542 1250385.095 1486383.855 1490462.496 1528520.869 1447722.037 1448502.439 1048522.809 1.522228728 1.233180175 1.358608062 1.192520644 1.417598018 1.42148791 1.457785044 1.380725365 1.381469652 1 19.99992681 -1.148989063 5.764481323 0.999995389 1.371074905 0.593015435 0.092911346 5.38E-06 7.94E-07 0.087868165 0.020710468 0.070959564 1.148989063 0.371079516 NDSWGSFDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 0 ; 96.015 0.016352 120852000 182729 203636 196006 184466 270330 323470 243980 217870 190909 186741 FALSE TRUE 189943.282 238608.8989 201114.0774 220952.8242 224379.4032 248348.9947 224856.2101 214949.809 184038.2224 223329.3236 0.850507578 1.068417237 0.900526962 0.989358767 1.004701933 1.11203039 1.006836928 0.962479112 0.824066537 1 17.76881317 -4.489201864 4.234554427 1.028369383 0.97758501 0 0.086279102 0 0 0 0.018416223 3.24E-05 4.489201864 -0.050784373 NDSYTLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDSYTLHK 8 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QQM1;J3QLH6;J3QRW1;J3QSE0 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 93.111 0.011301 943250000 635880 633600 728890 612730 920400 1026800 910770 827550 706250 579320 FALSE TRUE 660985.0334 742415.8713 747885.4722 733926.1652 763950.7368 788341.2613 839381.4675 816458.0458 680832.2005 692826.6622 0.954040988 1.071575203 1.07946982 1.05932148 1.10265782 1.137862187 1.211531705 1.178444899 0.982687644 1 19.40213493 6.136924472 0.690363209 1.11992386 8.83E-10 0.228794328 0.069724321 21.90668164 1.739003647 0.026744524 29.57834907 1370643.376 -6.136924472 -1.119923859 NDTKEDVFVHQTAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NDTKEDVFVHQTAIK 15 1 P67809;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 260.12 4.13E-25 651420000 948690 761480 1124420 795200 1633340 1571690 1490330 1250370 1304320 584310 FALSE TRUE 986145.0137 892258.2665 1153723.309 952488.1866 1355705.45 1206688.817 1373514.04 1233610.835 1257377.778 698794.3572 1.411209183 1.276853852 1.651019784 1.363045046 1.940063534 1.726815342 1.965548271 1.765341724 1.799353079 1 19.41450843 3.251186905 24.9982205 1.758175368 1.431018317 0.179059105 0.270338193 298.1592188 590308.5748 0.068679259 0.092373796 1783.146006 -3.251186905 -0.327157052 NEDEEEEEEEKDEAEDLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 159.04 2.38E-11 232930000 389650 178120 236840 183320 333590 462590 344380 231250 270780 113890 FALSE TRUE 405033.6829 208710.7244 243012.245 219580.1488 276886.491 355160.4831 317386.5957 228150.472 261034.6807 136204.5649 2.973715918 1.532332815 1.784171074 1.612135019 2.032872328 2.607551981 2.330219959 1.675057456 1.916489956 1 17.05541553 0.633168514 1.157818073 1.004536675 2.059090221 0.354607296 0.434633127 1.423807287 2.966054379 0.414421927 0.12769538 4.29703127 -0.633168514 1.054553546 NEDS(ph)PGPPVGSHHAFFSDDQEPYPVTDISDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEDSPGPPVGSHHAFFSDDQEPYPVTDISDLIR 33 0 J3KQ40;O95759-2;O95759 J3KQ40 TBC1D8 TBC1 domain family member 8 1 NEDS(0.66)PGPPVGS(0.17)HHAFFS(0.17)DDQEPYPVTDISDLIR 77.077 0.0034712 20774000 7691.8 13849 11882 18850 14940 19575 20515 15310 13816 14278 TRUE FALSE 7995.478203 16227.45802 12191.65468 22578.47374 12400.50414 15029.00291 18906.98069 15104.79449 13318.76486 17075.50073 0.468242679 0.950335705 0.713985193 1.322273009 0.726216135 0.880150055 1.10725776 0.884588671 0.779992638 1 14.05964027 5.002477447 2.023312938 0.935390022 3.93E-10 0.375113054 0.176276864 2.101177949 4.762943241 0.0420725 4.673226209 100572.0833 -5.002477447 -0.935390021 NEEDAAELVALAQAVNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;; 285.75 2.55E-39 145124000 150853 166216 177243 163046 212110 240334 186323 181501 178201 137755 FALSE TRUE 156808.7929 194762.305 181862.0982 195296.0122 176055.618 184520.0708 171718.5164 179068.276 171787.5808 164745.4548 0.951824699 1.182201386 1.103897515 1.185440973 1.068652353 1.12003133 1.042326276 1.086939098 1.042745495 1 17.32987914 1.216193594 0.727260224 1.001591567 1.107870575 0.186345484 0.063478771 0.946857505 1.162513345 0.056710502 0.02307981 16.45104891 -1.216193594 0.106279008 NEEDDMVEMEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEEDDMVEMEEER 13 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 292.73 3.23E-40 100680000 44826 52021 62990 74954 82503 87799 79187 61597 60824 46515 FALSE TRUE 46595.76509 60955.20208 64631.57115 89779.67748 68479.16953 67409.01286 72980.11602 60771.39297 58634.95612 55628.72367 0.837620604 1.095750506 1.16183811 1.613908635 1.231003788 1.211766304 1.311914263 1.092446293 1.054041011 1 15.76354238 1.555860162 4.881451153 1.039840286 1.21939681 0.1437358 0.181865662 0.316049978 16.33571512 0.11141366 0.049513902 35.96335188 -1.555860162 0.179556523 NEEDEGHS(ph)NS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.999)NS(0.562)S(0.439)PR 86.548 0.01283 33340000 103480 97006 94568 99422 122850 142940 131460 108470 105670 59961 TRUE FALSE 107565.4703 113666.0259 97032.51977 119087.3749 101968.0009 109744.3513 121155.8217 107016.1371 101866.9573 71709.20993 1.500023085 1.585096615 1.353138877 1.660698465 1.421965198 1.530408038 1.689543391 1.492362518 1.420556124 1 16.1298708 0.756826326 2.145752949 1.000359037 1.53250204 0.735529411 0.09509882 0.465230003 3.294159154 0.085509142 0.023380479 5.71250148 -0.756826326 0.532143003 NEEDEGHSNS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.902)S(0.097)PR;NEEDEGHS(0.079)NS(0.46)S(0.46)PR;NEEDEGHS(0.017)NS(0.491)S(0.491)PR 168.64 1.92E-05 347016000 217186 210069 228773 233467 260197 338062 328061 263350 249787 152985 TRUE FALSE 225760.671 246146.7166 234735.0123 279646.0758 215968.8069 259552.2239 302346.7216 259820.224 240797.2147 182959.4817 1.233938077 1.345361904 1.282989054 1.528459051 1.180418773 1.418632265 1.652533768 1.420097071 1.316123179 1 17.48116466 NEEDEGHSNSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 NEEDEGHSNS(0.044)S(0.956)PR;NEEDEGHSNS(0.041)S(0.959)PR;NEEDEGHSNS(0.041)S(0.959)PR;NEEDEGHSNS(0.02)S(0.98)PR;NEEDEGHSNS(0.029)S(0.971)PR;NEEDEGHS(0.001)NS(0.295)S(0.704)PR;NEEDEGHSNS(0.022)S(0.978)PR;NEEDEGHSNS(0.056)S(0.944)PR;NEEDEGHSNS(0.042)S(0.958)PR 199.41 7.61E-08 28429663000 18687594 18283481 20067275 21138552 23226231 28971796 28202413 22183400 20312469 12850956 TRUE FALSE 19425394.64 21423526.64 20590244.67 25319694.49 19278244.55 22243535.45 25991834.18 21886067.81 19581427.21 15368854.78 1.263945487 1.393957256 1.339738384 1.647467873 1.254370923 1.447312488 1.691201755 1.424053263 1.274098004 1 23.87350633 0.943569808 2.900894018 1.001370946 1.441417971 0.489621954 0.13576221 0.24527863 4.927099935 0.128669313 0.033957424 8.781522281 -0.943569808 0.440047025 NEEDEGHSNSS(ph)PRHS(ph)EAATAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEEDEGHSNSSPRHSEAATAQR 22 1 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 2 NEEDEGHS(0.002)NS(0.452)S(0.546)PRHS(0.998)EAAT(0.002)AQR 131.95 1.50E-05 39413000 14318 18893 20209 23848 22872 26021 25960 22036 20070 15141 TRUE FALSE 14883.2857 22137.72578 20735.66314 28565.06322 18984.22561 19978.0171 23925.18737 21740.64346 19347.68462 18107.58906 0.821936352 1.222566169 1.14513661 1.577518858 1.04841266 1.103295256 1.321279563 1.200637114 1.068484852 1 14.14430685 1.096836562 3.827623934 1.003288266 1.193668931 0.093930305 0.182905547 0.453327506 11.81456403 0.168427049 0.043601988 12.49788608 -1.096836562 0.190380665 NEEDEGHSNSSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NEEDEGHSNSSPR 13 0 Q14103-3;Q14103;D6RAF8;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 ;;; 216.15 2.80E-11 1758370000 1714210 1899200 2061790 2265870 2227400 2862230 2805910 2319710 1949910 1322810 FALSE TRUE 1781888.334 2225372.826 2115521.941 2714052.323 1848787.344 2197520.46 2585975.442 2288618.082 1879733.12 1581989.293 1.126359289 1.406692723 1.337254273 1.715594622 1.168647191 1.38908681 1.634635237 1.446671031 1.188208497 1 20.5933084 1.036378669 3.714118369 1.002876715 1.415190657 0.366457234 0.17066717 0.195005296 6.040191402 0.159159947 0.041079031 10.87373309 -1.036378669 0.412313942 NEEKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEEKLR 6 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 0 83.843 0.051552 56388000 276650 235080 268210 243760 309720 346680 294730 260330 285070 221270 FALSE TRUE 287572.3556 275453.1613 275199.7729 291975.0004 257073.905 266168.824 271628.2925 256840.7022 274810.3864 264623.62 1.086722174 1.040924318 1.039966776 1.103359558 0.971469988 1.005839252 1.026470322 0.970588726 1.038495303 1 18.01358232 3.23274736 24.99999956 1.000482151 1.063843542 0.591982836 0.026580041 98.05846954 421701.8787 0.007386537 0.009053179 1709.020847 -3.23274736 0.063361391 NEEPS(ph)EEEIDAPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 175.32 5.22E-07 3798400000 5529000 1861160 3266600 1920550 4872360 4572990 4832820 3237310 3866820 1327680 TRUE FALSE 5747289.189 2180799.752 3351730.28 2300429.058 4044157.988 3510982.377 4454010.94 3193919.155 3727653.904 1587813.476 3.619624897 1.373460917 2.110909329 1.448803082 2.546998151 2.211205806 2.805122269 2.011520372 2.347664861 1 20.59861002 4.755342172 24.59699751 2.062395751 3.619626428 0.45004278 0.536167804 2557.338319 3748255.504 0.121027849 3.407359509 56930.12947 -4.755342172 1.557230677 NEEPVRS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NEEPVRSPERR 11 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR;NEEPVRS(1)PERR 86.641 0.011276 4458240000 1792410 1871630 1915510 1802660 2397460 2846260 2149960 2128390 1988080 1643180 TRUE FALSE 1863175.731 2193067.893 1965429.764 2159220.768 1989940.606 2185259.25 1981440.517 2099862.413 1916529.389 1965129.66 0.948118472 1.115991447 1.000152714 1.098767583 1.012625602 1.112017845 1.008300143 1.068561762 0.975268669 1 20.90619307 1.234071242 24.99952408 0.98763431 1.048389212 0.163555134 0.052092755 182.7925867 1017833.691 0.038735472 0.010943639 17.14238489 -1.234071242 0.060754902 NEFSHDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEFSHDSR 8 0 P57735 P57735 RAB25 Ras-related protein Rab-25 0 140.75 0.00064449 748300000 2620700 1393300 1505400 1271900 2054200 2196500 1736900 1196700 1601000 1284100 FALSE TRUE 2724167.26 1632588.437 1544631.961 1523478.024 1705027.818 1686396.163 1600757.239 1180660.194 1543380.323 1535694.809 1.773898852 1.063094325 1.005819614 0.992044783 1.110264753 1.098132359 1.042366771 0.768811737 1.005004584 1 20.55046011 4.744456003 3.717502988 0.993099939 1.862018793 0.871477236 0.088266228 0.101956643 2.641055309 0.024992326 0.246254795 55520.83681 -4.744456003 0.868918854 NEFWFS(ph)DGSLSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NEFWFSDGSLSDK 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 NEFWFS(0.999)DGS(0.001)LSDK;NEFWFS(0.999)DGS(0.001)LSDK;NEFWFS(1)DGSLSDK 185.99 8.59E-06 161262000 463721 282533 371343 251759 532587 551169 446293 376229 385786 188453 TRUE FALSE 482029.0632 331055.8449 381020.5036 301556.1788 442058.052 423168.3528 411311.3885 371186.2656 371901.6372 225376.7572 2.138770072 1.468899673 1.690593601 1.338009219 1.961418105 1.877604231 1.824994705 1.646958942 1.650133056 1 17.78197921 0.456230136 1.387990898 1.000020458 1.734665886 0.507125199 0.218838095 2.244027233 4.889031241 0.202753172 0.059472228 2.859105201 -0.456230136 0.734645428 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEGIDLTHNPEFTTCEFYMAYADYHDLMEITEK 33 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 165.04 2.30E-14 65694000 26155 17774 18986 20200 26717 25658 32153 21967 24161 8026.7 FALSE TRUE 27187.6196 20826.54624 19480.79076 24195.49971 22175.65388 19699.31835 29632.76384 21672.5683 23291.45033 9599.378185 2.832227158 2.169572428 2.029380485 2.520527814 2.310113578 2.052145251 3.086946183 2.257705435 2.426349903 1 13.22872524 3.039048865 24.92236291 2.305318408 2.355294742 0.003392595 0.528326582 2623.812606 1674591.358 0.144563264 0.172785869 1094.079461 -3.039048865 0.049976335 NEGSES(ph)APEGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NEGSESAPEGQAQQR 15 0 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NEGSES(1)APEGQAQQR;NEGS(0.109)ES(0.891)APEGQAQQR 182.09 5.89E-07 423620000 103887 99430 100825 119332 128062 162630 160741 130410 109785 68875 TRUE FALSE 107988.539 116506.329 103452.5823 142935.5134 106294.067 124861.6472 148141.7004 128662.0673 105833.8593 82369.73756 1.311022011 1.414431228 1.255953769 1.735291597 1.290450475 1.515867974 1.798496691 1.562006522 1.284863379 1 16.32982677 3.806030346 24.99997229 1.498850748 1.335865221 0.040155828 0.223879332 431.0276879 159709.0051 0.055001621 0.099155568 6397.795379 -3.806030346 -0.162985527 NEKAPVDFGYVGIDSILEQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 231.89 3.41E-26 405720000 657260 556100 635660 396500 963510 933680 583180 715240 757120 580590 FALSE TRUE 683209.1323 651605.8491 652225.8218 474926.5166 799732.9144 716846.9701 537468.8277 705653.3777 729871.3991 694345.4944 0.983961353 0.93844614 0.939339028 0.683991644 1.151779511 1.032406742 0.774065407 1.016285672 1.051164593 1 19.40529418 3.219079941 24.99998156 0.991423774 0.893928362 0.19203341 0.116242119 496.239551 636833.7464 0.034496799 0.041287631 1656.074771 -3.219079941 -0.097495412 NEKDNALLSAIEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NEKDNALLSAIEESR 15 1 H3BVG0;Q8N1F7;H3BM93;H3BNN5;H3BV11;H3BRI8 H3BVG0 NUP93 Nuclear pore complex protein Nup93 0 ; 195.92 8.38E-09 685790000 467420 307260 412000 356260 584040 560740 509980 446950 461340 295249 FALSE TRUE 485874.1025 360029.5148 422737.0585 426727.1647 484765.0894 430516.6331 470006.435 440959.3663 444736.4635 353097.3887 1.376034256 1.019632335 1.197225106 1.208525405 1.372893442 1.219257482 1.331095755 1.248832137 1.259529177 1 18.42970663 5.065049771 21.37914526 1.224535108 5.101788203 0.151349797 0.113406993 1295.223546 438001.3441 0.025244561 6872.845646 116158.1726 -5.065049771 3.877253096 NELMYQLEQDHDLQAILQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 138.04 1.91E-06 72815000 20801.5 37309 35389 34122 33920 44840 35711 40473 36227 34078 FALSE TRUE 21622.75928 43716.53053 36311.26641 40871.22976 28154.29052 34426.58956 32911.87851 39930.52564 34923.19735 40754.93164 0.530555651 1.072668479 0.890966196 1.002853596 0.690819231 0.844722054 0.807555728 0.979771626 0.856907273 1 15.31468703 1.186418384 0.997729423 0.985836462 0.850445774 0.086962887 0.148060298 1.347395123 2.864071542 0.131659837 0.045025449 15.36096089 -1.186418384 -0.135390688 NENEEILERPAQLANAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NENEEILERPAQLANAR 17 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ; 312.09 3.45E-58 1501620000 509060 452910 583750 478250 631540 715080 584760 539400 534320 369220 FALSE TRUE 529158.0819 530693.7693 598963.0046 572846.4226 524191.0564 549013.5071 538924.9832 532170.2253 515089.9276 441561.5899 1.198378876 1.201856732 1.356465368 1.297319413 1.187130105 1.243345254 1.220497878 1.205200447 1.166518872 1 18.75225516 0.490033552 0.582299892 0.99114963 1.255483953 0.709063933 0.047325517 1.009844314 0.593193991 0.067677508 0.021633801 3.090534185 -0.490033552 0.264334323 NENLAANFLLQQNFDED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NENLAANFLLQQNFDED 17 0 P54727;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;;; 198.74 3.24E-11 471988000 903070 910730 951320 987920 1102560 1490670 1131190 1088660 1007120 673560 FALSE TRUE 938723.9009 1067140.793 976112.1807 1183327.627 915147.245 1144484.484 1042524.372 1074068.293 970873.9479 805531.1859 1.165347683 1.324766578 1.211762124 1.469002874 1.136079225 1.420782341 1.294207338 1.333366494 1.205259293 1 19.61958092 -0.629734501 7.979508304 1 1.292190062 0.407745125 0.102491335 0 0 0.088203282 0.020789713 0.234566236 0.629734501 0.292190062 NENLAANFLLSQNFDDE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725;K7EQ16;P54725-3 P54725-2;P54725-3 RAD23A UV excision repair protein RAD23 homolog A 0 ;; 156.24 1.97E-08 76467000 151420 156049 156204 173007 191334 261873 218527 187804 156311 100027 FALSE TRUE 157398.1785 182849.2019 160274.8046 207227.2682 158811.115 201056.9645 201398.2827 185286.7946 150685.3976 119625.3755 1.315759118 1.528515176 1.339806073 1.732301924 1.327570462 1.6807217 1.683574926 1.548892062 1.259644093 1 16.86816393 1.019169393 3.296138022 1.002759763 1.528650711 0.565182758 0.145462138 0.144570526 3.690691099 0.133976901 0.034973659 10.45127784 -1.019169393 0.525890949 NENTFLDLTVQQIEHLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NENTFLDLTVQQIEHLNK 18 0 A0A087WYS1;E7EUC7;Q16851;Q16851-2;C9JVG3;C9JQU9;C9JNZ1;C9JWG0 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 ;; 183.56 6.27E-14 1158720000 1243848 850075 1199919 880063 1542235 1505061 1453797 1217512 1301418 698405 FALSE TRUE 1292956.079 996068.7686 1231189.875 1054136.835 1280086.446 1155533.392 1339844.592 1201193.243 1254580.22 835244.088 1.547997882 1.192548122 1.474047997 1.262070393 1.532589651 1.383467909 1.60413538 1.438134385 1.502052201 1 19.67183834 -1.106533611 4.683479209 0.999971563 1.434927635 0.537280296 0.121768618 8001017.18 1890345.87 2343.047917 0.026813559 0.078246765 1.106533611 0.434956072 NEQEEQEEKREIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEQEEQEEKREIK 13 2 Q9C0D0;Q4VY13;Q4VY12 Q9C0D0 PHACTR1 Phosphatase and actin regulator 1;Phosphatase and actin regulator 0 53.252 0.082297 1233300000 13994 485570 509300 497210 437740 647000 387080 551150 504010 558010 FALSE TRUE 14546.49393 568962.8703 522572.7764 595556.654 363333.1112 496744.0554 356739.6582 543762.7357 485870.7786 667341.3758 0.02179768 0.852581439 0.783066651 0.892431783 0.54444865 0.744362741 0.53456847 0.814819454 0.728069315 1 19.34806543 4.743528724 24.90659335 0.74959579 0.021797364 0.725283479 0.137075805 251.7299302 1261953.36 0.03099726 0.258110148 55402.41856 -4.743528724 -0.727798426 NEQLPLQYLADVDT(ph)SDEESIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NEQLPLQYLADVDTSDEESIR 21 0 Q9BV36-2;H7C2D8;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 NEQLPLQYLADVDT(0.498)S(0.498)DEES(0.003)IR 63.69 0.07223 0 12554 13420 13027 10705 18558 20631 14416 15034 13327 10213 TRUE FALSE 13049.64161 15724.78061 13366.49432 12822.41705 15403.51779 15839.76292 13286.03625 14832.49382 12847.36387 12214.04181 1.068413046 1.287434647 1.094354721 1.049809494 1.261131903 1.296848591 1.087767379 1.214380469 1.051851965 1 13.57625307 1.091161282 4.651714556 1.001590522 1.172318579 0.306104687 0.088145145 0.224139028 7.810544611 0.081944935 0.02085449 12.33562851 -1.091161282 0.170728057 NES(ph)SPIRFDILLDDLDTVPVSTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NESSPIRFDILLDDLDTVPVSTLQR 25 1 A0A0A0MTP3;Q99550-2;Q99550;F5H1U6 A0A0A0MTP3 MPHOSPH9 M-phase phosphoprotein 9 1 NES(0.5)S(0.5)PIRFDILLDDLDTVPVSTLQR;NES(0.5)S(0.5)PIRFDILLDDLDTVPVSTLQR 90.616 0.0081942 33278000 24427 26040 27588 24704 31924 34605 32670 28860 25589 23386 TRUE FALSE 25391.39682 30512.16744 28306.96594 29590.37747 26497.56988 26568.51319 30109.24003 28473.17891 24668.05689 27968.03895 0.907871906 1.090965566 1.012118368 1.058006874 0.947423233 0.949959818 1.076558857 1.018061329 0.882008815 1 14.77149148 3.243175593 24.97604363 0.987817619 1.022140852 0.065015538 0.065099603 378.9446708 2050809.343 0.018177136 0.023814063 1750.554328 -3.243175593 0.034323233 NESEDNKFS(ph)DDS(ph)DDDFVQPR ddPTM_MDA-MB-175_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 211.94 1.26E-22 613170000 1419370 610810 773250 641950 1249630 1604660 1051750 935330 876910 461468 TRUE FALSE 1475407.824 715711.8661 793401.5302 768925.794 1037218.339 1232002.034 969311.0868 922793.4312 845350.1804 551883.8193 2.673402938 1.296852419 1.437624193 1.393274757 1.879414295 2.232357592 1.756368012 1.672079157 1.531753878 1 19.07400506 0.826237464 1.54254232 1.0021761 1.77297989 0.279193643 0.38991442 0.885134508 3.896820711 0.366189952 0.106450251 6.702509898 -0.826237464 0.77080379 NESSDSALGDS(ph)ESEDTGHDMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NESSDSALGDSESEDTGHDMTR 22 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 NESSDSALGDS(0.999)ES(0.001)EDTGHDMTR 114.24 1.70E-05 0 34746 52181 52550 57066 56401 69880 52798 55948 49751 62118 TRUE FALSE 36117.79891 61142.68084 53919.49617 68353.48447 46813.97817 53651.42904 48659.5548 55198.10857 47960.47123 74288.83278 0.486180729 0.823039999 0.725808902 0.920104435 0.630161714 0.722200458 0.655004972 0.74302027 0.645594626 1 16.18085774 -1.571904296 5.963707351 1.000799606 0.714297832 0.3867642 0.11070376 0.001093702 7.85E-05 0.099607217 0.023414954 0.026797588 1.571904296 -0.286501774 NESSFASHK ddPTM_MDA-MB-175_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 85.958 0.015816 0 61491 99159 114900 93430 149400 182730 121310 127860 95958 81087 FALSE TRUE 63918.71216 116188.7869 117894.3884 111910.1751 124005.0414 140293.7268 111801.4052 126146.2458 92504.49032 96974.44515 0.659129445 1.198138197 1.215726352 1.154017174 1.278739375 1.446708219 1.152895539 1.300819465 0.953905848 1 16.565317 4.738659549 6.079975886 1.212026357 0.644879275 0.571701823 0.136333135 0.084262851 15.65379733 0.03090515 0.197596268 54784.73296 -4.738659549 -0.567147082 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NETLDATHLAEFHQIEGVVADHGLTLGHLMGVLR 34 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 206.39 6.49E-28 148350000 79814 75061 126700 92580 122080 144620 120420 121900 109980 81790 FALSE TRUE 82965.11835 87952.14286 130001.9061 110892.0477 101328.8852 111034.1967 110981.1657 120266.1299 106021.8413 97815.18454 0.848182404 0.899166559 1.329056493 1.1336895 1.035921832 1.135142742 1.134600586 1.229524132 1.083899619 1 16.57777082 4.370397738 7.834414308 1.143870277 0.861398133 0.584299561 0.088404419 0.135191025 8.758286573 0.020956065 0.0579072 23463.76703 -4.370397738 -0.282472144 NFAELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFAELAR 7 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 101.28 0.021339 77136000 123760 144070 126240 135340 193380 192580 155000 163860 148970 145580 FALSE TRUE 128646.1404 168812.9018 129529.9181 162109.8481 160509.3367 147856.2136 142850.695 161663.7247 143608.5988 174103.6137 0.73890563 0.969611705 0.74398179 0.931111334 0.921918467 0.849242646 0.820492418 0.928548933 0.824845595 1 17.40958662 -5 0.225431394 1.696213773 0.849132366 0.237942542 0.075391307 225.6777138 2.25897054 71.67552672 0.124895909 1.00E-05 5 -0.847081407 NFAFLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFAFLEFR 8 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 108.74 0.0087288 389260000 522350 547760 554480 594270 777630 963560 711800 619130 538800 591130 FALSE TRUE 542972.7813 641833.519 568930.2043 711814.8323 645448.7304 739787.7929 656007.2561 610831.575 519408.6932 706950.6056 0.768049107 0.907890189 0.804766556 1.006880575 0.913003999 1.046449055 0.927939308 0.864037134 0.734717092 1 19.43124989 5.684774779 1.027093227 0.916628667 0.041265708 0.194821537 0.089239539 19.22693055 3.781906383 0.02672622 29.25690863 483921.3454 -5.684774779 -0.875362959 NFDEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 NFDEILR 7 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;;;;;;;; 195.6 0.0010794 21316420000 21702330 23407500 25071730 23083200 30618210 34454630 27292510 27713290 25657730 20579360 FALSE TRUE 22559154.75 27427556.04 25725119.88 27648988.06 25413737.6 26453064.35 25153251.75 27341838.68 24734313.31 24611491.58 0.916610628 1.114420715 1.045248306 1.123417814 1.0325964 1.074825728 1.022012488 1.110937896 1.004990422 1 24.55282876 4.751207235 24.56983843 1.0638765 0.916610509 0.484791523 0.043658191 1224.233885 2378385.21 0.009339363 0.16715651 56390.66745 -4.751207235 -0.147265991 NFDFEGSLS(ph)PVIAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 NFDFEGS(0.402)LS(0.598)PVIAPK;NFDFEGS(0.064)LS(0.936)PVIAPK;NFDFEGS(0.155)LS(0.845)PVIAPK;NFDFEGSLS(1)PVIAPK;NFDFEGS(0.168)LS(0.832)PVIAPK 276.14 1.64E-33 1129698000 1043949 674080 986656 780261 1270177 1282664 1123394 1082005 1055044 647203 TRUE FALSE 1085164.913 789847.9964 1012369.066 934594.297 1054272.767 984784.725 1035339.443 1067502.493 1017073.173 774010.0364 1.402003671 1.020462215 1.307953409 1.207470515 1.362091856 1.272315188 1.337630514 1.379184303 1.314030988 1 19.56199275 3.257157761 24.88950857 1.305567293 1.224434626 0 0.13586388 616.4402243 825007.9452 0.03467619 0.046867407 1807.830717 -3.257157761 -0.081132666 NFDKLNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFDKLNVR 8 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 80.455 0.025008 0 235270 214310 230890 201270 350430 344060 231100 288690 255930 204300 FALSE TRUE 244558.6413 251116.0754 236907.1831 241080.6053 290864.0338 264157.2793 212985.7781 284820.5828 246719.1293 244328.6734 1.000941223 1.027779801 0.969624972 0.986706152 1.190462133 1.08115546 0.871718309 1.16572721 1.009783771 1 17.89846366 NFDKLSFLYLITGNLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFDKLSFLYLITGNLEK 17 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 182.7 6.68E-10 103890000 402310 251310 330510 279530 504930 514380 353120 365760 424930 235390 FALSE TRUE 418193.5095 294470.5376 339123.3621 334820.1997 419102.179 394923.0405 325441.5317 360857.5855 409636.8523 281510.1637 1.485536096 1.046038742 1.204657614 1.189371621 1.488763935 1.402873116 1.156056064 1.281863435 1.455140542 1 18.10282748 4.820969447 21.01810183 1.261726654 1.485571768 0.167895903 0.156193212 72827.3077 18563977.17 0.036531609 431.8404124 66216.99173 -4.820969447 0.223845114 NFDLRPGVIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFDLRPGVIVR 11 1 P31153;P31153-2;Q00266 P31153 MAT2A;MAT1A S-adenosylmethionine synthase isoform type-2;S-adenosylmethionine synthase isoform type-1 0 72.887 0.041102 790530000 1120200 1079800 1239700 1173300 1707700 2040500 1480500 1369100 1342800 1117800 FALSE TRUE 1164426.361 1265247.25 1272007.6 1405375.238 1417425.764 1566624.799 1364454.541 1350749.454 1294472.89 1336811.508 0.871047529 0.946466456 0.951523526 1.051289003 1.060303382 1.171911514 1.020678333 1.010426261 0.968328655 1 20.35036463 4.065243413 1.734715562 1.043941385 0.892513443 0.512779233 0.053585512 0.335481523 1.909718331 0.01608292 0.054572699 11620.99765 -4.065243413 -0.151427941 NFEATLGWLQEHACSR ddPTM_MDA-MB-175_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 ; 237.4 9.28E-20 1067990000 621990 610860 677880 669710 872420 985520 693130 748190 719680 562780 FALSE TRUE 646546.6455 715770.4532 695546.1097 802176.6391 724126.36 756647.9157 638800.6594 738161.7368 693778.8574 673045.9659 0.96062777 1.063479301 1.033430323 1.19186011 1.075894362 1.124214324 0.949118919 1.096747881 1.03080457 1 19.36034551 1.002283512 13.44379178 1.000000018 1.063865733 0.078277245 0.067824634 0.499155693 2792.164697 0.063217047 0.015805533 10.05271828 -1.002283512 0.063865715 NFEDVAFDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFEDVAFDEK 10 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 167.67 1.20E-05 510460000 1519760 1093010 1250760 1094440 1902510 1879700 1723580 1358500 1459300 804250 FALSE TRUE 1579761.298 1280725.965 1283355.833 1310916.965 1579122.03 1443168.162 1588481.296 1340291.53 1406780.078 961827.3892 1.642458217 1.331554892 1.334289133 1.3629441 1.641793577 1.500444028 1.65152429 1.39348447 1.462611789 1 19.87541848 0.277774061 1.462583209 0.999853183 1.479120569 0.586700611 0.121065637 4.754988067 8.830682167 0.118456861 0.034083384 1.89571943 -0.277774061 0.479267386 NFEDVAFDEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 169.62 2.67E-05 8873360000 11000800 5156200 6985070 4953390 12374800 10644550 9826940 7266730 8407270 3980720 FALSE TRUE 11435120.08 6041737.24 7167106.662 5933155.758 10271335.92 8172514.582 9056678.765 7169331.37 8104693.995 4760665.869 2.402000139 1.269094998 1.505484077 1.246286953 2.157541865 1.716674685 1.902397483 1.505951388 1.702428656 1 22.18273194 -1.048885623 7.660677934 0.999999964 1.687142722 0.270617503 0.348523279 1.99E-07 2.44E-08 0.317814549 0.074909604 0.089354078 1.048885623 0.687142758 NFEHLNSDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 ; 146.5 3.57E-05 469700000 240670 320230 318340 315070 421040 497660 361080 343960 330630 299630 FALSE TRUE 250171.8374 375227.0115 326636.2019 377389.9056 349471.7712 382086.0071 332777.6061 339349.7788 318730.6909 358336.7617 0.698147285 1.04713513 0.911534168 1.053171056 0.975260728 1.06627633 0.928672806 0.947013578 0.889472488 1 18.45095653 4.747476304 24.98004254 0.977129244 0.69814714 0.674709941 0.05865011 680.0631756 1905365.14 0.013592181 0.166782574 55908.3022 -4.747476304 -0.278982103 NFEWVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NFEWVAER 8 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;; 105.36 0.010244 784390000 506140 1461530 1117090 1491820 1134360 1631730 951590 1258600 926750 1601260 FALSE TRUE 526122.798 1712536.408 1146202.283 1786897.543 941541.8924 1252785.437 877001.8893 1241730.526 893396.4485 1914996.239 0.274738293 0.894276643 0.598540227 0.933107599 0.49166775 0.654197335 0.457965332 0.648424524 0.466526477 1 20.86891013 -1.928633418 2.54641591 1.253322796 0.614948094 0.281520031 0.189682267 15544087.73 8927261.874 23460470.13 0.042404258 0.011786004 1.928633418 -0.638374702 NFGEDMDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NFGEDMDDER 10 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;;;;; 226.39 7.10E-09 7252910000 4733000 4920410 5088930 5296690 5963610 7144960 6786250 5696520 5035500 3570760 FALSE TRUE 4919862.495 5765452.142 5221551.696 6344359.473 4949917.702 5485651.323 6254325.992 5620167.467 4854273.339 4270382.056 1.152089539 1.350102185 1.222736427 1.485665542 1.1591276 1.284580923 1.464582305 1.316080715 1.136730455 1 22.02593372 1.052313754 3.38723463 1.002868028 1.311658744 0.463739196 0.106264099 0.170342393 4.131197211 0.096675167 0.025228042 11.28012088 -1.052313754 0.308790717 NFGEDMDDERLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NFGEDMDDERLK 12 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YBN4 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;;;;;; 198.14 1.70E-07 4671450000 4922355 3033630 4187767 2790820 6107550 5876130 4458032 4177938 4569644 2602150 FALSE TRUE 5116693.376 3554632.354 4296903.648 3342835.866 5069390.833 4511487.861 4108599.803 4121939.575 4405183.405 3111991.471 1.644186182 1.142237177 1.380756884 1.074178993 1.628986094 1.449710869 1.320247771 1.324534342 1.415551246 1 21.56940668 -1.358747522 3.341479158 0.997394801 1.364131839 0.298483015 0.171937779 40275381.99 60864067.59 1046594.116 0.038751707 0.043777653 1.358747522 0.366737039 NFGEEVDDESLKELFSQFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFGEEVDDESLKELFSQFGK 20 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YCC8 B1ANR0 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 ; 317.99 1.42E-66 476770000 1415240 696140 1039970 629830 1581130 1444840 1360390 1030370 1249680 513360 FALSE TRUE 1471114.768 815696.6298 1067072.473 754408.4941 1312370.087 1109297.807 1253759.077 1016559.575 1204704.261 613943.0631 2.396174591 1.328619344 1.738064222 1.228792276 2.137608788 1.806841503 2.042142264 1.655788031 1.962241018 1 19.22774534 -1.445123171 6.236418921 0.999727403 1.786984048 0.341355088 0.336384849 0.001180473 0.000105032 0.30156659 0.071056411 0.035882015 1.445123171 0.787256645 NFGIWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFGIWLR 7 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ; 132.96 0.0077193 550120000 618860 561290 604680 556400 1399440 1230230 933030 729980 608110 856810 FALSE TRUE 643293.0707 657687.1913 620438.4576 666454.2593 1161563.689 944527.7268 859896.6706 720195.8121 586224.2399 1024685.515 0.627795613 0.641842967 0.605491586 0.650398829 1.133580666 0.921773279 0.839181054 0.702845704 0.572101617 1 19.96674977 3.440567736 24.99968228 0.842920315 0.626926387 0.375261167 0.14458064 206.2012614 141024.5832 0.043041603 0.058278762 2757.831555 -3.440567736 -0.215993928 NFHQYSVEGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFHQYSVEGGK 11 0 Q9HCY8 Q9HCY8 S100A14 Protein S100-A14 0 ; 148.18 3.49E-05 304460000 818700 749830 755330 847810 1004770 1420500 1262820 895700 905300 608650 FALSE TRUE 851022.9082 878607.4696 775014.5203 1015504.288 833979.5543 1090610.403 1163836.869 883694.6066 872718.4298 727903.3142 1.169142785 1.207038699 1.064721791 1.395108757 1.145728475 1.498290201 1.598889366 1.214027453 1.198948285 1 19.47338731 3.736497888 24.99405299 1.316553806 1.152974853 0.125739334 0.168408908 331.906462 4021724.036 0.044203975 0.072366442 5451.272448 -3.736497888 -0.163578953 NFIQYFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFIQYFHK 8 0 B0QY89;Q9Y262-2;Q9Y262;H7C3A0;C9JHP4;C9K0Q7 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 71.379 0.048894 238090000 811950 604780 831000 684830 1290500 992540 1004200 928030 919620 875280 FALSE TRUE 844006.413 708646.2605 852656.5427 820287.33 1071141.271 762037.6271 925488.18 915591.2758 886523.0558 1046774.358 0.806292595 0.676980913 0.8145562 0.783633382 1.023278095 0.727986525 0.884133408 0.87467874 0.846909412 1 19.99751906 8 0.050085287 1.293291802 1.09E-08 0.355445876 0.082783857 513.5767879 1.940488338 11.77559193 51.30446794 99999999.99 -8 -1.293291792 NFLEGDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFLEGDWK 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39 B7ZC38 SH3GLB2 Endophilin-B2 0 ; 93.551 0.025564 570250000 1789730 1164720 1421210 1143380 2166660 1952030 1891230 1655330 1614830 1036170 FALSE TRUE 1860389.922 1364751.6 1458247.9 1369537.151 1798371.907 1498700.616 1742990.451 1633143.009 1556712.584 1239187.673 1.501297958 1.101327611 1.176777281 1.105189457 1.451250643 1.209421824 1.406558901 1.317914183 1.256236338 1 20.24096327 3.260938705 24.9996078 1.297190629 1.209420213 0.010981531 0.15576732 678.0430258 757468.4281 0.040321312 0.054556609 1823.6383 -3.260938705 -0.087770416 NFLIEPFVPHSQAEEFYVCIYATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NFLIEPFVPHSQAEEFYVCIYATR 24 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ;; 254.75 8.11E-44 1871750000 917873 1025628 1175804 1121255 1494903 1712740 1316152 1321643 1213300 920143 FALSE TRUE 954111.3348 1201771.631 1206446.418 1343035.892 1240799.922 1314982.092 1212988.567 1303928.537 1169633.57 1100427.404 0.867037055 1.092095332 1.096343488 1.220467509 1.127561816 1.19497396 1.102288586 1.184929177 1.062890261 1 20.06963254 4.875657512 1.884637312 1.138215283 0.70754102 0.588332966 0.063181999 0.753736816 2.065858129 0.014723746 0.639085435 75103.03916 -4.875657512 -0.430674263 NFLYAWCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFLYAWCGK 9 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 133.55 0.0027829 0 437450 364300 425210 313030 622110 575130 505560 426930 424930 345260 FALSE TRUE 454720.8638 426865.6911 436291.3219 374946.3997 516363.9644 441564.7737 465932.8862 421207.7017 409636.8523 412907.0866 1.101266795 1.033805679 1.056633165 0.908064821 1.250557283 1.069404687 1.128420658 1.020102864 0.992079975 1 18.65545765 -1.103208361 4.542597905 0.999994744 1.062287821 0.045773856 0.085279309 4.36E-06 8.60E-07 0.079227645 0.01867256 0.078848174 1.103208361 0.062293077 NFPNAIEHTLQWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 278.16 3.63E-33 5410700000 1089320 1043970 1169990 1089490 1481810 1696660 1313090 1189230 1077610 988380 FALSE TRUE 1132327.195 1223263.727 1200480.901 1304987.87 1229932.465 1302636.428 1210166.575 1173290.317 1038827.027 1182034.137 0.957947964 1.034880202 1.015605948 1.104018766 1.04052195 1.102029448 1.023800021 0.992602735 0.878846891 1 20.17284027 1.564450643 3.197940512 0.938390173 1.043628421 0.402381808 0.048365309 0.18760362 4.362568142 0.031509419 0.012464599 36.6818004 -1.564450643 0.105238248 NFQAATESVPNSGNIHNGSLEQTEEPETSSHS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFQAATESVPNSGNIHNGSLEQTEEPETSSHSPSR 35 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 NFQAATESVPNSGNIHNGSLEQTEEPETS(0.001)S(0.004)HS(0.953)PS(0.041)R 183.8 4.96E-20 119100000 8712.4 20710 21464 24962 23400 30683 24032 27591 22081 19068 TRUE FALSE 9056.372279 24266.7814 22023.36947 29899.4091 19422.47636 23557.33826 22148.30904 27221.18777 21286.30912 22804.00952 0.397139471 1.064145381 0.965767421 1.311147019 0.851713219 1.033034925 0.971246264 1.193701825 0.933445897 1 14.47699989 4.739515197 24.96991458 1.04633508 0.397139263 0.699723097 0.125393174 40.3998415 1056624.402 0.028189839 0.171652192 54892.7764 -4.739515197 -0.649195817 NFQLLVITHDEDFVELLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NFQLLVITHDEDFVELLGR 19 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494BZX8 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 120.92 3.62E-05 37975800 38807.1 35455.3 43509.2 42545.8 50944 59292 54423 48040.3 47538.9 29131.3 FALSE TRUE 40339.23427 41544.47197 44643.0855 50961.23225 42284.55708 45522.33158 50157.18305 47396.39836 45827.98428 34839.02048 1.157875099 1.192469576 1.281410467 1.462763061 1.21371257 1.306647861 1.439684077 1.360440038 1.315421147 1 15.08841644 4.202979335 3.577191845 1.324894332 1.169007648 0.114793286 0.123472452 0.337613235 8.882452803 0.029039073 0.077937679 15958.03212 -4.202979335 -0.155886683 NFRNPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFRNPLAK 8 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 163.77 0.00030456 3646100000 2606700 1935860 2565400 1732180 3928700 3306900 2143800 2257400 2624500 2217190 FALSE TRUE 2709614.529 2268328.896 2632256.431 2074800.034 3260900.977 2538922.592 1975763.354 2227143.245 2530044.758 2651605.93 1.02187678 0.855454753 0.992702725 0.782469224 1.229783408 0.957503739 0.745119526 0.839922411 0.954155642 1 21.33843495 2.445584486 24.82658236 0.862036284 0.973238771 0.095629317 0.126690277 350.0334645 275553.7893 0.043127865 0.036083681 278.9873337 -2.445584486 0.111202487 NFTKPQDGDVIAPLIT(ph)PQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFTKPQDGDVIAPLITPQKK 20 2 Q9Y3Z3-4;Q9Y3Z3;Q9Y3Z3-3 Q9Y3Z3-4 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 NFTKPQDGDVIAPLIT(1)PQKK 218.86 4.58E-23 2260800000 2941000 1006900 1772700 1033100 2896100 2527700 2602800 1957600 2292000 664410 TRUE FALSE 3057112.951 1179827.242 1818898.018 1237444.097 2403821.956 1940679.983 2398785.735 1931361.574 2209511.368 794588.4186 3.847416951 1.484828138 2.289107135 1.557339709 3.025241622 2.442371342 3.018903471 2.430644002 2.780699185 1 19.59984824 3.211500661 24.99963213 2.551859446 2.236427828 0 0.809546939 871.2161317 804880.2523 0.216884934 0.259288994 1627.423791 -3.211500661 -0.315431618 NFWNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NFWNGR 6 0 P47755;P52907 P47755;P52907 CAPZA2;CAPZA1 F-actin-capping protein subunit alpha-2;F-actin-capping protein subunit alpha-1 0 ;;;; 137.2 0.029866 2389480000 970883 951747 1022543 986453 1310904 1603968 1276136 1101991 1083108 951653 FALSE TRUE 1009214.211 1115202.144 1049191.311 1181570.459 1088077.006 1231470.74 1176109.126 1087220.613 1044127.155 1138111.185 0.886744831 0.979870999 0.921870661 1.038185438 0.95603753 1.082030259 1.033386844 0.955285061 0.917421047 1 20.11821007 5.736142684 0.865532917 0.994512276 0.441388558 0.283098192 0.049470444 14.7899481 2.347554218 0.016253018 11.65853996 544681.5743 -5.736142684 -0.553123718 NFWSHETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NFWSHETR 8 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 110.76 0.0033646 1181570000 270485 385620 443490 428550 561770 572160 445720 444110 463170 354470 FALSE TRUE 281163.9567 451847.2353 455047.7137 513315.9109 466280.5361 439284.5112 410783.3017 438157.4319 446500.6022 423921.6098 0.663245162 1.065874503 1.073424197 1.210874603 1.099921602 1.036239958 0.969007695 1.033581261 1.053262188 1 18.69343799 4.738964569 24.65454497 1.061308333 0.663245024 0.789712055 0.061456304 13.00837438 793613.0454 0.016145492 0.09516609 54823.22365 -4.738964569 -0.398063308 NFYELSPHIFALSDEAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NFYELSPHIFALSDEAYR 18 0 E9PDF6;O43795;O43795-2;E7EQD9;C9JUP5;C9JYW1 E9PDF6 MYO1B Unconventional myosin-Ib 0 139.98 1.30E-07 284600000 97016 103060 119610 99742 116110 164560 109670 103900 111500 116960 FALSE TRUE 100846.2666 120759.7533 122727.1349 119470.6699 96373.66367 126343.4339 101073.7788 102507.3904 107487.1368 139876.0727 0.720968674 0.863333886 0.877399061 0.854117989 0.688993205 0.903252654 0.722595201 0.732844356 0.768445487 1 17.09378967 NFYES(ph)DDDQKEK ddPTM_MDA-MB-175_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;NFYES(1)DDDQKEK 207.85 1.18E-07 1565500000 3586530 752490 1245338 934710 2102500 2899730 2345820 1391410 1596820 439647 TRUE FALSE 3728128.974 881724.3039 1277792.531 1119592.848 1745117.801 2226311.653 2161948.499 1372760.425 1539350.76 525787.4121 7.090563387 1.676959706 2.430245574 2.129364116 3.319055879 4.23424297 4.111830084 2.6108659 2.927705618 1 19.00412008 4.748615918 24.7237712 2.856724357 7.090566103 0.646963755 0.964483906 793.9706124 1952153.23 0.234126598 3.171236399 56055.20153 -4.748615918 4.233841746 NFYNEHEEITNLTPQQLIDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NFYNEHEEITNLTPQQLIDLR 21 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;; 217.82 5.66E-25 642838000 290052 311299 350208 308667 401511 473981 379188 392159 362313 296188 FALSE TRUE 301503.4769 364762.1817 359334.7082 369720.4113 333262.3036 363906.096 349466.2537 386902.75 349273.4259 354220.3677 0.851174874 1.029760609 1.014438301 1.043758194 0.940833261 1.027343793 0.986578654 1.092265678 0.986034282 1 18.43428764 4.741131907 24.62645253 1.017645415 0.851174801 0.615954884 0.03831065 123.6604137 1184268.097 0.00912201 0.062136677 55097.50173 -4.741131907 -0.166470614 NFYQEHPDLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NFYQEHPDLAR 11 0 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4;X6RLV5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;;;;; 196.78 5.93E-08 6290650000 1784270 2036581 2114138 1878919 2555590 3103160 2246050 2274630 2121230 1777760 FALSE TRUE 1854714.357 2386347.944 2169234.173 2250563.57 2121191.725 2382498.119 2069998.732 2244142.305 2044887.347 2126078.035 0.872364197 1.122417854 1.020298473 1.058551725 0.997701726 1.12060709 0.973623121 1.055531485 0.961811991 1 21.01976312 1.235595407 24.99587401 0.980905989 1.032081119 0.064700906 0.069444192 195.4305548 1647276.68 0.051320186 0.015003143 17.20265212 -1.235595407 0.051175129 NFYVEHPEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;; 147.71 3.52E-05 7240510000 2110160 2472850 2631620 2431920 3065470 3676340 2729810 2722380 2585560 2191720 FALSE TRUE 2193470.746 2897542.751 2700202.179 2912946.517 2544402.504 2822565.75 2515840.359 2685890.949 2492506.201 2621145.571 0.836836676 1.105449 1.03016109 1.111325731 0.970721555 1.076844332 0.959824737 1.024701176 0.950922462 1 21.32176605 -0.437862167 7.865611216 1 1.013787556 0 0.07893616 0 0 0.069434951 0.016365975 0.364869728 0.437862167 0.013787556 NGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGAAGPHSPDPLLDEQAFGDLTDLPVVPK 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;NGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 216.94 1.65E-34 1265570000 216145 128579 206609 161275 313661 315096 329239 248078 295003 168871 TRUE FALSE 224678.5715 150661.443 211993.4003 193174.7136 260345.0153 241919.7293 303432.3869 244752.9202 284385.8997 201958.0392 1.112501252 0.746003693 1.049690327 0.956509156 1.289104491 1.197871252 1.502452629 1.211899864 1.408143497 1 17.62369605 3.238816732 24.5132228 1.286805255 0.956414763 0.480257157 0.153083483 3.958200011 378794.2592 0.040051894 0.050998014 1733.072505 -3.238816732 -0.330390491 NGALDQQKDELDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGALDQQKDELDVR 14 1 P12270 P12270 TPR Nucleoprotein TPR 0 ; 81.311 0.012641 424820000 935730 581370 824580 576920 1133090 1221970 973380 840700 837400 472460 FALSE TRUE 972673.3429 681215.7751 846069.2322 691033.0541 940487.7665 938185.9866 897083.9321 829431.7916 807262.1376 565029.4912 1.721455885 1.205628707 1.497389509 1.223003515 1.664493236 1.660419502 1.5876763 1.467944248 1.42870797 1 19.10796664 0.640686542 2.053441094 1.000114663 1.497735778 0.451711072 0.165491155 1.828194627 9.280828658 0.155563018 0.042710167 4.372064314 -0.640686542 0.497621115 NGDECAYHHPIS(ph)PCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGDECAYHHPISPCK 15 0 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;G3V411;Q6PJT7-8;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6;Q6PJT7-6;H0YJ51 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK;NGDECAYHHPIS(1)PCK 185.61 6.95E-07 618120000 645270 430301 460758 462047 697650 848400 646320 571900 542250 304241 TRUE FALSE 670745.7579 504201.8495 472765.732 553438.5175 579063.7022 651371.9576 595659.7496 564234.6159 522734.5284 363851.1989 1.843461722 1.385736397 1.299338118 1.521057287 1.591484937 1.79021523 1.637097119 1.550729028 1.436671172 1 18.47298904 0.784582255 2.222091347 1.000318702 1.570375783 0.558636618 0.154294688 0.666836476 5.358499003 0.153725939 0.041843459 6.0895087 -0.784582255 0.570057081 NGDGFVSLEEFLGDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGDGFVSLEEFLGDYR 16 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 193.06 1.01E-09 120115000 82554 93482 89882 106565 112901 136299 124892 93849 83780 51859.5 FALSE TRUE 85813.29567 109536.8063 92224.39876 127643.2389 93710.12835 104645.6229 115102.6387 92591.10766 80764.77417 62020.37611 1.383630688 1.766142245 1.487001604 2.058085535 1.510957111 1.687278108 1.855884242 1.49291432 1.302229674 1 15.92045465 1.127095648 1.831292382 1.011201813 1.681948361 0.575239913 0.186333302 0.210101835 1.34503533 0.162461599 0.046880659 13.39971768 -1.127095648 0.670746548 NGDLDEVKDYVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NGDLDEVKDYVAK 13 1 P58546;C9JL85 P58546 MTPN Myotrophin 0 ;; 198.74 1.13E-07 2215480000 3227850 1140280 1925100 1167290 3044190 2932820 2851620 2095130 2274420 721520 FALSE TRUE 3355288.01 1336114.22 1975269.687 1398176.478 2526739.671 2251717.002 2628102.573 2067048.209 2192564.068 862888.0297 3.88843963 1.548421318 2.289137895 1.620345201 2.928235859 2.609512387 3.045705216 2.395499924 2.540960117 1 19.71881384 NGDLDEVKDYVAKGEDVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NGDLDEVKDYVAKGEDVNR 19 2 P58546 P58546 MTPN Myotrophin 0 ;; 222.06 1.42E-19 1094370000 1753200 614870 1377280 510950 2458700 1775640 1453080 1319640 1645690 597470 FALSE TRUE 1822417.69 720469.1395 1413173.048 612014.385 2040771.052 1363274.52 1339183.793 1301952.384 1586461.938 714532.8072 2.55050247 1.008307991 1.977758101 0.856523842 2.856091465 1.90792432 1.874208964 1.822103018 2.220278652 1 19.44664073 -0.884205014 7.34207713 1.000000011 1.866507588 0.176284448 0.578357677 4.61E-08 7.32E-09 0.515472119 0.121497942 0.130555444 0.884205014 0.866507578 NGEELHGGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGEELHGGKR 10 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 88.441 0.0079146 65436000 114966 74956 99781 84756 126643 152052 135766 100739 96596 57677 FALSE TRUE 119504.9465 87829.10992 102381.3748 101520.4838 105116.2681 116740.2274 125124.3062 99388.75848 93119.52883 68977.70386 1.732515578 1.273297095 1.484267656 1.471786942 1.523916602 1.692434234 1.813981898 1.440882386 1.349994616 1 16.07384248 0.941501005 2.011246584 1.00392954 1.555048141 0.575447081 0.147719864 0.282903039 2.432463692 0.144538727 0.040287003 8.739790145 -0.941501005 0.551118602 NGEFELMHVDEFIDELLHSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 ;;;;;; 245.44 1.85E-30 210450200 74966 78810.1 94594.9 81150.6 116708.7 135537.5 108115.5 92236.9 91980.7 74129.4 FALSE TRUE 77925.71557 92345.12162 97060.1208 97201.94647 96870.59686 104060.9697 99641.1246 91000.61522 88670.33257 88653.63664 0.878990626 1.041639408 1.094823907 1.096423679 1.092686104 1.173792454 1.12393725 1.026473574 1.000188328 1 16.43589219 4.727815116 2.863317846 1.081162001 0.845748624 0.558704517 0.052113829 0.299381624 3.517629139 0.013517058 0.161900441 53433.68384 -4.727815116 -0.235413378 NGGCNHMQCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGGCNHMQCSK 11 0 O95376 O95376 ARIH2 E3 ubiquitin-protein ligase ARIH2 0 ; 66.289 0.070972 0 45615.4 28856.1 35432.1 26314.4 60598.2 54729 41951.6 37281.2 34692.1 25057.9 FALSE TRUE 47416.33121 33811.91071 36355.48963 31519.30978 50297.73961 42019.01918 38663.32397 36781.50649 33443.5381 29967.51574 1.582257656 1.128285407 1.213163278 1.051782538 1.678408716 1.402152235 1.290174478 1.227379233 1.11599301 1 14.87111187 1.24233872 1.563793533 1.006978401 1.327691564 0.282757618 0.179960102 0.499100645 2.261048032 0.168916225 0.051091549 17.47184306 -1.24233872 0.320713163 NGGS(ph)FEDDLSLGAEANHLHESDAQIENCNNILAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NGGSFEDDLSLGAEANHLHESDAQIENCNNILAK 34 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 NGGS(0.979)FEDDLS(0.021)LGAEANHLHESDAQIENCNNILAK;NGGS(0.836)FEDDLS(0.158)LGAEANHLHES(0.006)DAQIENCNNILAK;NGGS(0.688)FEDDLS(0.156)LGAEANHLHES(0.156)DAQIENCNNILAK 196.19 8.14E-27 240531000 39139 74070 81871 66844 109944 111086 95175 114774 104406 65255 TRUE FALSE 40684.23794 86790.94632 84004.62552 80065.54369 91255.75815 85287.96002 87714.93481 113235.6423 100648.4485 78040.46787 0.521322322 1.112127447 1.076423909 1.025949048 1.169338942 1.092868384 1.123967311 1.450986204 1.289695605 1 16.25193481 4.952780129 1.704842662 1.182324968 8.23E-31 0.676927673 0.128836059 1.135763648 2.074873098 0.037669606 2.595785461 89697.45666 -4.952780129 -1.182324968 NGHDGDTHQEDDGEKS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGHDGDTHQEDDGEKSD 17 1 K7EQH5;Q08117;Q08117-2 K7EQH5 AES Amino-terminal enhancer of split 1 NGHDGDTHQEDDGEKS(1)D;NGHDGDTHQEDDGEKS(1)D 201.64 6.85E-12 222052000 499179 149649 231324 179286 314045 527998 377225 196802 237610 96007 TRUE FALSE 518886.9724 175350.0516 237352.4935 214748.2357 260663.7431 405378.4664 347657.1188 194164.1911 229058.4625 114817.7335 4.519223265 1.527203563 2.067211103 1.870340314 2.270239406 3.530625924 3.027904386 1.691064483 1.994974605 1 16.80898596 4.748944408 24.45813337 2.189606649 4.519225035 0.520401609 0.690279475 938.1173395 2209595.336 0.168948377 2.342600832 56097.61637 -4.748944408 2.329618386 NGHLAVVAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGHLAVVAPR 10 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 0 100.48 0.003987 265430000 56042 37663 45039 33033 63182 72420 54916 50223 46269 35883 FALSE TRUE 58254.58143 44131.32727 46212.75334 39566.82881 52442.34621 55601.55254 50611.54042 49549.84283 44603.78773 42913.58683 1.357485723 1.028376571 1.0768793 0.922011692 1.222045279 1.295663137 1.179382666 1.154642306 1.039386148 1 15.38914687 1.145326271 4.027370303 1.003164738 1.14882217 0.17103443 0.119467835 0.406208251 11.23347136 0.115366247 0.030086817 13.97417799 -1.145326271 0.145657431 NGHVGISFVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGHVGISFVPK 11 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 74.611 0.02569 0 352010 260030 319590 264120 439350 460500 399230 395740 365710 206560 FALSE TRUE 365907.6266 304688.1297 327918.7779 316362.1477 364669.4439 353555.8539 367937.3094 390435.7526 352548.1685 247031.4772 1.481218632 1.233397999 1.327437223 1.280655208 1.476206385 1.431217827 1.489434924 1.580510132 1.427138649 1 17.91433536 3.234751929 24.99140662 1.446825884 1.32349731 0 0.159899869 202.0123726 1325543.146 0.042847983 0.053079982 1716.927392 -3.234751929 -0.123328574 NGLHRPVS(ph)TDFAQYNSYGDVSGGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.5)T(0.5)DFAQYNSYGDVSGGVR 201.63 3.67E-25 183450000 74138 87039 90471 85976 114410 145890 115520 121680 103030 93931 TRUE FALSE 77065.02549 101987.2712 92828.74858 102981.7962 94962.62907 112009.2585 106465.2405 120049.0786 99321.97043 112334.981 0.68602874 0.90788524 0.826356561 0.916738448 0.845352251 0.997100435 0.947747884 1.068670485 0.884158875 1 16.77744773 6.417835017 0.32268908 1.005078386 1.16E-16 0.595141878 0.064983382 13.6984455 0.48849334 0.059930334 6.678354064 2617188.582 -6.417835017 -1.005078386 NGMVLKPHFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGMVLKPHFHK 11 1 P26373;P26373-2;J3QSB4;H3BTH3 P26373 RPL13 60S ribosomal protein L13 0 ; 112.75 0.00095758 1629220000 3826800 2194300 2851900 2075590 5307000 4171700 3732500 3274100 3259600 2329600 FALSE TRUE 3977885.019 2571153.956 2926222.857 2486135.507 4404918.036 3202885.898 3439936.897 3230216.045 3142287.633 2786040.517 1.427791518 0.922870267 1.050315973 0.892354397 1.581067471 1.149619282 1.234704548 1.159428955 1.127868605 1 21.40978481 4.776067124 22.95187049 1.140549274 1.427793602 0.191319836 0.184499869 12365.09425 7566300.042 0.043770531 9.487465573 59712.7571 -4.776067124 0.287244328 NGPFKPNYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGPFKPNYYR 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 ; 119.68 0.00060212 385470000 661190 455210 529530 464460 957960 907050 776240 644610 590790 493180 FALSE TRUE 687294.2917 533388.7765 543329.9868 556328.8017 795126.3014 696401.384 715396.2805 635970.0573 569527.5833 589809.1785 1.165282462 0.904341261 0.921196222 0.943235239 1.348107711 1.180723206 1.212928362 1.07826409 0.965613293 1 19.16988875 3.342583248 20.3771101 1.139429485 0.973380359 0.255748128 0.122184557 3.954489749 761.0332143 0.034112476 0.046188477 2200.813534 -3.342583248 -0.166049126 NGPLNES(ph)QEDEEDSEHGTSLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGPLNESQEDEEDSEHGTSLNR 22 0 Q9H2K8 Q9H2K8 TAOK3 Serine/threonine-protein kinase TAO3 1 NGPLNES(1)QEDEEDSEHGTSLNR;NGPLNES(1)QEDEEDSEHGTSLNR 349.05 3.64E-96 430390000 138073 158610 228280 178419 301020 286930 235520 226849 231875 194429 TRUE FALSE 143524.2287 185850.0337 234229.1643 213709.7457 249852.7279 220294.856 217059.327 223808.4602 223529.864 232523.64 0.61724575 0.799273716 1.007334843 0.919088251 1.074526134 0.947408427 0.933493588 0.962519167 0.961321026 1 17.82701787 4.524032556 2.518478579 0.972570013 0.605944011 0.870073352 0.043931088 0.107888743 1.145125279 0.010753207 0.068438522 33422.00936 -4.524032556 -0.366626002 NGQLDLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGQLDLSGK 9 0 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 65.224 0.067163 156140000 2602.3 279650 203850 274490 169740 320250 131970 195470 159990 263370 FALSE TRUE 2705.040813 327677.7121 209162.4985 328783.3027 140887.6554 245876.7909 121625.8466 192850.0444 154231.9912 314972.309 0.008588186 1.040338159 0.664066308 1.043848279 0.44730172 0.780629865 0.386147744 0.612276187 0.489668415 1 18.26486547 -1.810621746 2.323625629 1.136010277 0.6251303 0.136106664 0.293392822 16714345.55 9951250.618 12758757.15 0.075036396 0.015466009 1.810621746 -0.510879978 NGS(ph)EADIDEGLYSR ddPTM_MDA-MB-175_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 80.609 0.010674 0 62571 57029 74721 43084 96442 93724 62100 55872 84295 45599 TRUE FALSE 65041.3514 66823.28713 76668.29064 51605.88661 80048.82329 71958.0214 57232.43973 55123.12723 81261.23942 54533.251 1.192691618 1.225367751 1.405899873 0.946319643 1.467890174 1.319525612 1.049496201 1.010816817 1.490122777 1 15.73484854 -4.999999939 0.185093646 0.109316148 1.2588464 0.09817885 0.183882944 315.5809668 3.065956939 103.8676531 0.529050709 1.00E-05 4.999999939 1.149530252 NGS(ph)GTLDLEEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 1 NGS(0.967)GT(0.033)LDLEEFLR;NGS(0.976)GT(0.024)LDLEEFLR;NGS(0.998)GT(0.002)LDLEEFLR;NGS(0.994)GT(0.006)LDLEEFLR 147.64 4.12E-05 86709000 153144 140512 145468 120800 186653 233898 169697 146399 163194 123404 TRUE FALSE 159190.2434 164643.843 149259.0156 144693.8794 154925.7897 179578.7343 156395.7057 144436.7609 157320.6798 147582.6511 1.078651469 1.115604319 1.011358818 0.980426076 1.04975611 1.216801114 1.059716061 0.978683875 1.06598356 1 17.17116361 1.98004168 24.26364125 1.014190488 1.074643995 0.15661084 0.062887601 1039.729054 1264012.178 0.02747367 0.018004797 95.5084242 -1.98004168 0.060453507 NGS(ph)PPPGAPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR 171.11 4.13E-05 1452080000 630046 552253 675948 538928 799598 1209650 787586 677768 645840 463849 TRUE FALSE 654920.7026 647098.1568 693563.7602 645526.3499 663682.6176 928727.1199 725852.9513 668683.6286 622596.3446 554731.3306 1.180608822 1.166507318 1.250269675 1.163673862 1.196403702 1.674192656 1.308476575 1.205418897 1.122338527 1 19.08142968 1.137723982 2.023836294 1.007202133 1.276912483 0.279984258 0.142207211 0.418925336 3.212247606 0.141660585 0.040317773 13.73168972 -1.137723982 0.26971035 NGSGTLDLEEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NGSGTLDLEEFLR 13 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;;;; 292.08 3.37E-40 805803000 874897 958101 1020827 933786 1313502 1542873 1154041 1161230 1035018 809398 FALSE TRUE 909438.6091 1122647.394 1047430.59 1118486.084 1090233.399 1184564.128 1063584.251 1145665.611 997767.9044 967984.0412 0.939518185 1.159778825 1.082074234 1.15547988 1.126292741 1.223743448 1.098762175 1.183558367 1.030768961 1 19.88462374 4.744435139 24.50614145 1.128706042 0.939518075 0.390743488 0.065541702 436.2500265 1819790.869 0.014174572 0.126602154 55518.16952 -4.744435139 -0.189187967 NGSLDS(ph)PGKQDTEEDEEEDEKDKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 NGS(0.01)LDS(0.967)PGKQDT(0.023)EEDEEEDEKDKGK 100.68 0.0042691 120060000 697560 86271 125740 68699 224030 470680 245310 147910 155320 51201 TRUE FALSE 725100.2074 101087.3732 129016.8877 82287.45715 185949.4606 361371.7032 226081.9612 145927.5084 149730.0635 61232.85565 11.84168531 1.650868183 2.106987929 1.343844841 3.036759574 5.901598078 3.692167527 2.383156997 2.445256912 1 15.90201835 4.742792027 24.98912559 2.751977997 11.84168891 0.811093512 1.334016334 187.011198 1104377.355 0.336992624 2.63130598 55308.51864 -4.742792027 9.089710913 NGSTAVAESVAS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGSTAVAESVASPQK 15 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 NGSTAVAESVAS(1)PQK 129.12 0.00021247 0 167710 85627 117550 88833 168320 196260 163680 142980 136190 73306 TRUE FALSE 174331.3203 100332.7712 120613.4496 106403.9023 139709.0265 150681.5893 150850.3339 141063.587 131288.5485 87668.90717 1.988519373 1.144451031 1.375783655 1.213701707 1.593598358 1.718757473 1.720682267 1.609049223 1.497549733 1 16.41977764 3.134716667 21.37954409 1.579167932 1.405806439 0 0.287816425 10.52912661 2132.243233 0.078520053 0.093849627 1363.693175 -3.134716667 -0.173361493 NGVAAEVS(ph)PAKEENPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NGVAAEVSPAKEENPRR 17 2 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR;NGVAAEVS(1)PAKEENPRR 145.55 2.45E-07 897580000 586123 337519 397900 302342 617440 737670 541827 454585 432312 255982 TRUE FALSE 609263.5886 395485.2627 408269.6009 362144.3452 512487.7693 566357.322 499357.1839 448492.0316 416753.1756 306136.7718 1.99016794 1.291858081 1.333618299 1.182949513 1.674048388 1.850014027 1.631157149 1.465005425 1.361330013 1 18.22381682 0.882460812 1.829644534 1.002027902 1.543326394 0.340544221 0.2363967 0.607376997 4.04099303 0.23163416 0.065381844 7.628880491 -0.882460812 0.541298493 NGVGPAPSLSELDLRPPS(ph)PINLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGVGPAPSLSELDLRPPSPINLSR 24 1 Q5FWE3-2;Q5FWE3 Q5FWE3-2 PRRT3 Proline-rich transmembrane protein 3 1 NGVGPAPSLSELDLRPPS(0.967)PINLS(0.033)R;NGVGPAPSLSELDLRPPS(0.997)PINLS(0.003)R 113.47 0.00086083 156466000 65357 74161 67209 81869 75548 109757 74525 71619 65668 77241 TRUE FALSE 67937.34483 86897.57486 68960.52175 98062.44385 62706.37795 84267.60013 68683.53577 70659.06445 63304.62151 92374.89508 0.735452471 0.940705532 0.746528824 1.061570287 0.678824889 0.912234867 0.743530325 0.764916316 0.685301147 1 16.4952132 NGVMPSHFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NGVMPSHFSR 10 0 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ;;;; 131.82 0.00018208 637669000 341316 841667 809806 770896 996177 1156263 849585 1010350 788711 744158 FALSE TRUE 354791.4192 986216.76 830910.2096 923376.9279 826847.1894 887738.4416 782992.3077 996807.9108 760325.4452 889961.5123 0.398659284 1.108156641 0.933647352 1.037547034 0.929081964 0.99750206 0.879804685 1.120057325 0.854335198 1 19.76338342 4.745731879 24.99984743 0.988177223 0.398659009 0.813930233 0.084009291 316.9002549 1104723.702 0.018262609 0.1873083 55684.1864 -4.745731879 -0.589518214 NGYGFINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NGYGFINR 8 0 P67809;C9J5V9;P16989;P16989-3;P16989-2;Q9Y2T7 P67809;P16989;P16989-2;Q9Y2T7 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 3;Y-box-binding protein 2 0 ; 102.77 0.011401 171728000 220986 222439 219659 197103 436790 436390 269100 247340 220224 277190 FALSE TRUE 229710.6979 260641.1679 225383.494 236089.3851 362544.5918 335045.0361 248007.2388 244024.8119 212298.1813 331500.0734 0.692943128 0.786247693 0.679889726 0.712185016 1.093648602 1.010693701 0.748136301 0.73612295 0.640416695 1 18.33864966 6.153702945 13.25166879 0.803842842 0.703944274 0 0.153630551 0 0 0.035309649 0 1424632.82 -6.153702945 -0.099898568 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 NGY(0.001)GFVEFEDS(0.999)RDADDAVYELNGK 77.522 0.00011478 0 30241 23816 28580 26298 37701 39943 37242 27935 31711 20394 TRUE FALSE 31434.93803 27906.21274 29324.81828 31499.66591 31292.59749 30666.84359 34322.87473 27560.57702 30569.7273 24389.81383 1.288855185 1.144174897 1.20233875 1.291509075 1.28301912 1.257362758 1.407262678 1.130003583 1.25338092 1 14.57399113 -0.907315715 6.374697724 0.999999973 1.24688968 0.497257393 0.075581825 2.81E-08 4.91E-09 0.072444581 0.01707535 0.123789636 0.907315715 0.246889707 NGYGFVEFEDSRDADDAVYELNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;;; 232.59 2.17E-34 1967479000 1976040 1411545 1852184 1341027 2402019 2445542 2200308 1983641 1983764 1137232 FALSE TRUE 2054055.585 1653966.873 1900453.437 1606278.138 1993724.668 1877601.933 2027842.11 1957053.537 1912368.721 1360050.837 1.510278535 1.216106655 1.39734 1.181042719 1.465919225 1.380538052 1.491004641 1.438956166 1.406100911 1 20.37522915 -1.191559464 6.987307067 0.999999131 1.387130687 0.557896797 0.103478373 1.36E-06 1.58E-07 0.097620567 0.023009337 0.064333997 1.191559464 0.387131556 NHAAPFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 124.23 0.0013137 2132300000 2745360 2059690 2577140 2016030 3817830 4013520 3009560 2605510 2729060 1783660 FALSE TRUE 2853748.933 2413425.735 2644302.386 2414794.717 3168876.62 3081440.805 2773662.823 2570587.4 2630841.664 2133134.027 1.337819798 1.131399014 1.239632556 1.132040784 1.485549703 1.444560336 1.300275927 1.205075428 1.233322253 1 21.02454318 0.710112587 1.205507703 1.001699746 1.288162235 0.377413558 0.110593227 1.117398341 2.725629354 0.112269669 0.034367474 5.129943557 -0.710112587 0.286462489 NHAVVCQGCHNAIDPEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NHAVVCQGCHNAIDPEVQR 19 0 Q9UGI8-2;Q9UGI8 Q9UGI8-2 TES Testin 0 ;;; 208.17 1.64E-16 1240840000 273671 265080 263948 234197 353872 457332 296254 256605 276547 226415 FALSE TRUE 284475.7424 310605.428 270826.7017 280520.4676 293720.9638 351123.5739 273032.8374 253165.6297 266594.1275 270776.6843 1.05059172 1.147090743 1.000184718 1.035984573 1.084735064 1.296727504 1.008332154 0.934960964 0.984553483 1 18.04674399 2.014144189 24.9969177 0.96737028 1.100791573 0.372925209 0.07748829 239.8987621 423969.3418 0.029879393 0.022057813 103.3104348 -2.014144189 0.133421293 NHDEESLECLCR ddPTM_MDA-MB-175_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 ;;; 213.73 5.17E-09 2738620000 1567600 1551300 1506980 1486980 1857740 2279130 1711520 1533700 1534380 1327870 FALSE TRUE 1629490.058 1817723.708 1546253.137 1781100.206 1541962.018 1749836.598 1577366.59 1513143.26 1479157.964 1588040.703 1.02610094 1.144632946 0.973686086 1.121570878 0.97098394 1.101883972 0.993278439 0.952836572 0.931435801 1 20.59881646 2.043537253 5.689058529 0.959897833 1.055687766 0.374060714 0.056268024 0.177199736 13.92869702 0.0199769 0.014350686 110.5445289 -2.043537253 0.095789933 NHEESSETMNDLLAQVATNTDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHEESSETMNDLLAQVATNTDTSR 24 0 O75843 O75843 AP1G2 AP-1 complex subunit gamma-like 2 0 ; 159.59 2.16E-11 291400000 129656 155368 173349 169564 191554 249870 183107 154359 166505 139237 FALSE TRUE 134774.919 182051.2454 177866.6173 203103.2531 158993.7195 191841.4793 168754.5949 152290.0701 160512.5176 166517.8243 0.809372327 1.093283834 1.068153623 1.219708785 0.954815019 1.152077744 1.01343262 0.91455717 0.963935953 1 17.34531709 1.99483383 24.76170118 0.953501755 1.058071067 0.122483497 0.10611603 349.3911372 1674652.944 0.039366724 0.028236378 98.81749258 -1.99483383 0.104569312 NHEGDEDDSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NHEGDEDDSHVR 12 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 184.98 7.88E-06 869490000 229012 184389 229179 152645 320816 367801 252551 135586 189062 195929 FALSE TRUE 238053.5706 216056.3764 235151.593 182837.7254 266283.8109 282384.7918 232755.3927 133768.6914 182257.6956 234317.5363 1.015944322 0.92206661 1.003559515 0.780298941 1.136422886 1.205137252 0.99333322 0.570886386 0.77782354 1 17.8381054 1.767759396 25 0.739916636 1.008376029 0.322050034 0.145786735 21.7683046 18648.55483 0.067733312 0.037567373 58.5813527 -1.767759396 0.268459393 NHETDGGS(ph)AHGDDDDDGPHFEPVVPLPDKIEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NHETDGGSAHGDDDDDGPHFEPVVPLPDKIEVK 33 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NHET(0.077)DGGS(0.923)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.002)DGGS(0.998)AHGDDDDDGPHFEPVVPLPDKIEVK;NHET(0.002)DGGS(0.998)AHGDDDDDGPHFEPVVPLPDKIEVK 249.44 6.81E-48 2552260000 1345310 509610 916190 446757 1434720 1228180 1190170 603825 859270 402393 TRUE FALSE 1398423.878 597131.5533 940066.6641 535124.2012 1190846.807 942953.8082 1096881.365 595731.7135 828345.0405 481234.2041 2.905911229 1.240833566 1.953449393 1.11198289 2.474568093 1.959448851 2.279308819 1.237924712 1.721292945 1 18.87637966 1.213794451 1.181340947 1.078352823 1.926687245 0.220683935 0.537241975 0.663532885 1.877232502 0.473155866 0.15282575 16.36042011 -1.213794451 0.848334422 NHFTVAQSEAFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHFTVAQSEAFDR 13 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 ; 214.58 3.06E-11 993940000 305960 515310 559600 532100 698350 872880 564010 570490 542840 483030 FALSE TRUE 318039.5371 603810.4839 574183.6357 637347.7918 579644.7164 670166.8486 519801.4224 562843.5147 523303.2944 577670.4803 0.550555287 1.045250717 0.993963956 1.103306839 1.003417582 1.160119604 0.899823412 0.974333178 0.90588547 1 19.13988725 4.741320933 24.96325897 1.008961132 0.550555119 0.768445513 0.075589428 118.8979534 1075209.714 0.018175381 0.126451762 55121.48805 -4.741320933 -0.458406013 NHKEDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHKEDEAK 8 1 O14617-5;O14617-2;O14617;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 ; 156.92 0.00023148 77436000 235410 76769 141329 76203 216260 224480 207552 123671 162527 67213 FALSE TRUE 244704.1686 89953.47857 145012.1498 91275.72596 179500.2024 172347.922 191283.5319 122013.3925 156677.685 80382.10048 3.044261933 1.119073501 1.804035338 1.135523026 2.233086737 2.144108216 2.379678197 1.517917444 1.949161369 1 16.29458666 NHKPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NHKPSR 6 1 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 1 NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R;NHKPS(1)R 85.38 0.033175 10277680000 8659240 4630880 6404150 5709100 8906900 9278780 11182580 6551390 7295080 3159380 TRUE FALSE 9001113.482 5426197.617 6571047.41 6838342.94 7392908.319 7123923.966 10306060.16 6463579.333 7032531.496 3778400.021 2.382255302 1.436109884 1.739108452 1.809851499 1.956624041 1.885434027 2.727625477 1.710665704 1.861245886 1 21.84934402 3.244955974 21.43397801 1.939923749 1.805513606 0 0.451602338 142.9781596 479164.6214 0.120343791 0.158417467 1757.745415 -3.244955974 -0.134410143 NHLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHLEGK 6 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 92.692 0.046466 83163000 343270 210108 274131 209974 382200 409860 357910 251120 309050 187140 FALSE TRUE 356822.5647 246192.4146 281275.0791 251506.2305 317233.7805 314676.2265 329856.079 247754.1471 297927.3509 223806.5 1.594335127 1.100023523 1.256777971 1.123766425 1.417446681 1.406019157 1.473844946 1.107001571 1.331182744 1 17.77189241 0.411615805 0.903741978 0.999864143 1.309588418 0.254790995 0.159043298 3.04011536 3.380582341 0.158970766 0.049588678 2.579976825 -0.411615805 0.309724275 NHLS(ph)PQQGGATPQVPSPCCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHLSPQQGGATPQVPSPCCR 20 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 NHLS(1)PQQGGATPQVPSPCCR;NHLS(1)PQQGGATPQVPSPCCR 148.1 7.36E-08 425410000 131364 137182 138763 130003 164723 204180 141103 126779 130897 120809 TRUE FALSE 136550.3522 160741.9414 142379.2778 155717.2054 136723.4433 156762.2894 130042.9782 125079.7349 126186.0425 144479.2105 0.945121112 1.112561045 0.985465502 1.077782781 0.946319147 1.085016237 0.900080902 0.865728255 0.873385466 1 17.14050239 2.219235519 23.80968125 0.8951388 1.026314797 0.434794919 0.063680529 106.870617 131669.5394 0.021747212 0.016090767 165.6668134 -2.219235519 0.131175997 NHLVTLPEAIHFLTEIEVLDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NHLVTLPEAIHFLTEIEVLDVR 22 0 Q13045-3;Q13045;Q13045-2;J3KS54;J3QQQ2 Q13045-3 FLII Protein flightless-1 homolog 0 149.73 3.54E-08 74344000 43678 11587 23472 13718 32078 25705 30913 21480 25637 14650 FALSE TRUE 45402.44117 13576.97712 24083.6996 16431.37946 26625.39302 19735.40331 28489.95828 21192.09573 24714.32938 17520.38701 2.591406294 0.774924498 1.374610024 0.937843408 1.519680644 1.126425079 1.626103252 1.209567787 1.410604079 1 14.09674702 4.751281325 24.95663913 1.245909117 2.591407162 0.719984405 0.25612231 1014.852853 1990993.975 0.056081401 1.026906127 56400.28844 -4.751281325 1.345498045 NHS(ph)GS(ph)RT(ph)PPVALNSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 NHS(1)GS(1)RT(1)PPVALNSSR 99.021 0.060851 0 137180 131220 125160 104930 166780 234760 132350 105980 122770 121280 TRUE FALSE 142595.9723 153756.0143 128421.7724 125684.8408 138430.7952 180240.5478 121976.0612 104559.5114 118351.5317 145042.494 0.98313238 1.060075638 0.885407917 0.866538056 0.954415436 1.242674081 0.840967759 0.720888814 0.815978328 1 17.14611611 2.025601955 24.99751522 0.806189422 0.992783756 0.270432046 0.118718471 241.5679258 235863.6926 0.044883732 0.033147866 106.0722925 -2.025601955 0.186594334 NHSGS(ph)RTPPVALNSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.036)GS(0.482)RT(0.482)PPVALNSSR 116.06 0.00027605 252500000 57987 64557 82474 61923 92176 106220 55990 71449 65536 69300 TRUE FALSE 60276.37154 75644.16257 84623.34019 74171.18458 76507.95644 81552.01478 51601.3575 70491.34302 63177.37216 82878.00817 0.727290301 0.912716947 1.021059049 0.894944102 0.923139421 0.98400066 0.622618215 0.850543402 0.762293563 1 16.33870171 2.285955956 24.99998389 0.795999904 0.915514101 0.158336499 0.11293187 179.8045312 94842.05535 0.037319544 0.031223689 193.1772396 -2.285955956 0.119514197 NHSGSRT(ph)PPVALNSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NHSGSRTPPVALNSSR 16 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 NHS(0.03)GS(0.171)RT(0.799)PPVALNSSR;NHS(0.017)GS(0.181)RT(0.802)PPVALNSSR;NHS(0.039)GS(0.28)RT(0.681)PPVALNSSR 167.51 9.24E-09 944190000 232437 273613 312068 240147 413792 503930 252913 274526 288897 317842 TRUE FALSE 241613.7922 320603.9043 320200.7484 287647.3598 343455.7836 386899.8946 233089.0182 270846.428 278499.6534 380117.0544 0.635629971 0.843434675 0.842374065 0.756733634 0.903552681 1.017844083 0.613203263 0.71253427 0.732668135 1 18.53608423 -0.553398531 7.698832321 1.000019184 0.784416779 0.236094496 0.116441739 0 0 0.116428519 0.027442465 0.279641401 0.553398531 -0.215602405 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_MDA-MB-175_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 297.13 1.26E-70 3006700000 361220 416120 476020 344740 537320 673380 523960 447770 436120 427420 TRUE FALSE 375481.2445 487585.373 488425.4723 412928.5431 445986.5383 516997.7002 482890.6461 441768.3756 420424.1264 511164.7655 0.734560106 0.953871248 0.955514748 0.80781887 0.872490767 1.011411066 0.944686877 0.864238706 0.822482602 1 18.96342887 2.932184498 24.999173 0.919499336 0.871559885 0.128216033 0.080426336 515.219135 189926.8359 0.02503656 0.0265553 855.4300417 -2.932184498 -0.047939451 NHVQPYIPSILEALMVPTSQGFTEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NHVQPYIPSILEALMVPTSQGFTEVR 26 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 125.82 0.00010853 327920000 222105 221500 259012 242985 352680 405840 295752 246759 279413 209295 FALSE TRUE 230873.8769 259540.902 265762.0655 291046.7078 292731.5796 311589.8106 272570.1854 243451.5992 269356.9807 250302.3481 0.922379988 1.036909578 1.061764173 1.162780573 1.16951192 1.244853726 1.088963757 0.972630106 1.076126464 1 17.9333123 4.660266003 1.76259304 1.100010146 0.881971089 0.335632413 0.075889932 1.004226126 3.559040207 0.022725326 0.347886263 45736.82392 -4.660266003 -0.218039057 NIAVGKDPLEGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIAVGKDPLEGQR 13 1 O00170 O00170 AIP AH receptor-interacting protein 0 82.069 0.010061 0 95703 89486 94825 76603 124510 151740 113110 105180 96110 77424 FALSE TRUE 99481.42834 104854.5244 97296.2174 91754.84476 103345.8347 116500.6846 104244.1426 103770.2341 92651.01987 92593.75043 1.074385991 1.132414703 1.050786008 0.990939932 1.116121058 1.258191661 1.125822663 1.120704515 1.000618502 1 16.4986272 1.235118247 24.91495128 1.00030917 1.110198246 0.309773148 0.064668598 113.8810868 824171.8238 0.058325377 0.016878177 17.18376191 -1.235118247 0.109889075 NICFTVWDVGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NICFTVWDVGGQDR 14 0 P18085;C9JPM4;C9JAK5 P18085 ARF4 ADP-ribosylation factor 4 0 ;;; 217.21 1.36E-11 631479000 513372 434559 483461 525205 621207 766660 579470 577919 572501 401499 FALSE TRUE 533640.323 509191.1279 496060.3908 629088.9814 515614.456 588614.8338 534049.6272 570172.9411 551896.8008 480165.0419 1.111368543 1.060450227 1.033103928 1.310151566 1.073827561 1.225859408 1.112220967 1.187452004 1.149389799 1 18.87317085 NIDDGTSDRPYSHALVAGIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;;;;;; 232.56 7.47E-27 13777820000 4157851 4562573 5136758 4744243 5399214 6121106 5856554 5228723 5092922 3512565 FALSE TRUE 4322006.168 5346159.421 5270626.133 5682640.105 4481457.533 4699571.898 5397501.994 5158640.521 4909628.732 4200784.86 1.028856824 1.272657277 1.254676521 1.352756757 1.066814341 1.11873663 1.284879415 1.228018262 1.168740818 1 22.00222747 3.228341647 24.99982306 1.168985023 1.232441156 0.098460642 0.107921447 599.507439 1466639.884 0.03149999 0.038050747 1691.771275 -3.228341647 0.063456132 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 293.07 4.36E-62 5395520000 875465 1181906 1170852 920295 1554670 1581600 1027473 1278610 1147639 1295333 FALSE TRUE 910029.0342 1384889.162 1201365.365 1102326.604 1290407.749 1214297.369 946936.9815 1261472.324 1106335.697 1549128.701 0.587445726 0.89397941 0.775510366 0.711578453 0.832989375 0.783858287 0.611270698 0.81431086 0.714166419 1 20.56302558 -1.132178719 5.297709155 1.000006228 0.753497996 0.409921264 0.090699826 6.13E-06 1.00E-06 0.080624613 0.019002923 0.073760063 1.132178719 -0.246508232 NIDEHANEDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIDEHANEDVER 12 0 P61026 P61026 RAB10 Ras-related protein Rab-10 0 67.964 0.053946 271820000 91047 101470 109510 89207 113900 140440 92310 83706 98589 96883 FALSE TRUE 94641.60586 118896.6832 112363.9206 106851.8783 94539.31868 107824.9384 85074.50099 82584.05799 95040.80115 115865.3689 0.816823929 1.026162384 0.969780027 0.922207208 0.815941118 0.930605403 0.734253054 0.712758771 0.820269266 1 16.8220899 2.944448814 1.298299807 0.793691033 0.945168762 0.137086828 0.096884646 0.538409079 1.889105362 0.039196008 0.044800068 879.9313964 -2.944448814 0.151477729 NIDLATPLHHTWTYQALVHDVLDFHLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIDLATPLHHTWTYQALVHDVLDFHLNR 28 0 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 ; 231.68 7.65E-36 900351000 67971.2 205186.4 217110.2 221489.7 262457.7 285205 222685.5 263111.7 173470.3 184056.8 FALSE TRUE 70654.75546 240425.5681 222768.2702 265299.7016 217845.2339 218970.4611 205230.8286 259585.118 167227.1378 220119.206 0.320984056 1.09225166 1.01203468 1.205254673 0.989669361 0.99478126 0.932362207 1.17929336 0.759711707 1 17.7479255 4.74158125 24.99123562 1.030723343 0.320983796 0.752243631 0.119880216 126.6674183 1047932.269 0.026817875 0.189306007 55154.53789 -4.74158125 -0.709739547 NIDNPALADIYTEHAHQVVVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIDNPALADIYTEHAHQVVVAK 22 0 O75083;D6RD66 O75083 WDR1 WD repeat-containing protein 1 0 ; 208.39 4.01E-23 950420000 693370 523760 709950 562240 892270 825350 791900 696120 685560 499910 FALSE TRUE 720744.783 613711.7057 728451.8802 673449.3939 740602.2641 633674.9708 729828.8088 686789.65 660886.8295 597857.7931 1.205545518 1.026517866 1.218436706 1.126437426 1.238759907 1.059909193 1.22073981 1.148750853 1.105424797 1 19.18944284 -1.608760165 4.491156588 0.99736399 1.150683727 0.303212634 0.06823688 0.001633993 0.000142343 0.059941739 0.013895778 0.024617267 1.608760165 0.153319737 NIDPKPCTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIDPKPCTPR 10 1 K7EQ55;K7EK33;Q96EP5;Q96EP5-2 K7EQ55 DAZAP1 DAZ-associated protein 1 0 76.143 0.033636 297530000 1014200 609180 737250 620470 1024800 1093000 911890 754040 817020 473530 FALSE TRUE 1054241.399 713801.9262 756463.3407 743197.1141 850604.862 839167.3146 840413.679 743933.3272 787615.6098 566309.1372 1.861600546 1.260445717 1.335778095 1.312352327 1.502015076 1.481818426 1.484019282 1.313652347 1.390787395 1 19.11123028 -3.379722397 0.236489852 9.83E-12 1.47903877 0.427636203 0.157922321 69.99375336 1.392866945 34.41877468 0.257135528 0.000417136 3.379722397 1.47903877 NIEDVIAQGIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIEDVIAQGIGK 12 0 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 0 174.84 6.82E-05 89392000 257820 202540 239690 199890 310760 320650 276800 265390 244630 200870 FALSE TRUE 267998.9327 237324.6695 245936.5183 239427.6454 257937.1262 246183.897 255103.6927 261832.8811 235825.8141 240226.6306 1.115608757 0.987919902 1.023768754 0.996674036 1.073724114 1.024798526 1.061929279 1.089941113 0.981680563 1 17.87403657 3.231048111 24.99461554 1.04721663 1.027400214 0 0.04479752 624.0297864 2076188.489 0.012474128 0.015205917 1702.347083 -3.231048111 -0.019816416 NIEDYIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 ;;; 179.37 0.00024469 893260000 734474 840662 848060 818802 1056550 1133320 915530 899920 873096 880680 FALSE TRUE 763471.6007 985039.1591 870161.1403 980758.5917 876958.0084 870123.6056 843768.3663 887858.0444 841673.4455 1053232.384 0.724884282 0.935253391 0.826181528 0.931189172 0.832634869 0.82614589 0.801122695 0.842983996 0.799133656 1 20.00639236 NIEVPFKPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIEVPFKPAR 10 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 134.68 0.0041779 0 276170 242450 283790 253270 370700 374000 325300 326810 317020 256460 FALSE TRUE 287073.4048 284088.9015 291185.8005 303366.0501 307688.5464 287144.168 299802.136 322429.6465 305610.5121 306708.4268 0.935981472 0.926250721 0.949389632 0.989102429 1.003195607 0.93621219 0.977482553 1.051257867 0.996420331 1 18.22650828 3.901435299 0.406682387 1.016284251 0.895693255 0.476971471 0.026997102 2.500758908 0.534213872 0.026250396 0.138629887 7969.577506 -3.901435299 -0.120590996 NIGRDT(ph)PTSAGPNSFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 NIGRDT(0.997)PT(0.003)SAGPNSFNK;NIGRDT(0.965)PT(0.028)S(0.006)AGPNSFNK;NIGRDT(0.974)PT(0.024)S(0.002)AGPNSFNK;NIGRDT(0.824)PT(0.176)SAGPNSFNK 215.59 9.00E-15 2674560000 1248010 903830 986100 838790 1433210 1482290 1090800 1092080 1072490 752380 TRUE FALSE 1297282.398 1059055.772 1011798.576 1004700.158 1189593.476 1138050.612 1005300.246 1077442.454 1033891.294 899794.4558 1.441754159 1.176997441 1.124477451 1.116588519 1.322072467 1.264789536 1.117255435 1.197431754 1.149030523 1 19.77923595 -5 0.109559763 0.332829971 1.327992173 0.385925486 0.092515692 197.616908 1.441891654 29.59517321 1.197088196 1.00E-05 5 0.995162203 NIGS(ph)DFIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIGSDFIPR 9 0 Q5T853;Q5T857;P41279-2;P41279 Q5T853 MAP3K8 Mitogen-activated protein kinase kinase kinase 8 1 NIGS(1)DFIPR 128.28 0.00044236 66125000 65252 76533 78014 75844 96572 101230 76385 71801 72429 71605 TRUE FALSE 67828.19935 89676.94741 80047.10893 90845.71683 80156.72593 77720.86666 70397.7441 70838.62504 69822.29444 85634.62879 0.792065083 1.047204252 0.934751631 1.060852579 0.936031686 0.907586893 0.82207099 0.827219386 0.815351166 1 16.38590669 2.56543098 2.683458557 0.848800379 0.964787687 0.173691335 0.085390723 0.352968811 4.99537059 0.02910055 0.026167157 367.6469603 -2.56543098 0.115987308 NIHESCMSQIGWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NIHESCMSQIGWNR 14 0 P11413;P11413-3;P11413-2;E9PD92 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;;; 254.45 2.96E-24 4465290000 1463359 2653489 2522260 2731666 2924616 3737270 2627623 3107800 2582948 2543484 FALSE TRUE 1521133.543 3109205.094 2587992.168 3271981.382 2427490.817 2869345.681 2421663.043 3066145.024 2489988.206 3041830.992 0.500071683 1.022149193 0.850800776 1.075661794 0.798036059 0.943295564 0.796120182 1.007993223 0.818582036 1 21.53650857 4.747101117 24.87169144 0.921172765 0.500071455 0.630519948 0.097253242 603.6707269 1757971.741 0.020776981 0.243281784 55860.02382 -4.747101117 -0.421101311 NIHLNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIHLNLDR 8 0 Q9Y5S9;Q9Y5S9-2;A0A0J9YW13 Q9Y5S9 RBM8A RNA-binding protein 8A 0 ;;; 128.36 0.0011368 798610000 601880 615780 594460 540010 1169730 1095650 791280 618910 590180 810730 FALSE TRUE 625642.6872 721535.4249 609952.116 646822.3662 970899.7124 841201.8922 729257.406 610614.5238 568939.5371 969577.0211 0.64527384 0.744175459 0.629090936 0.667118086 1.001364194 0.86759677 0.752139737 0.629774129 0.586791482 1 19.88699598 NIIEATHMYDNAAEACSTTEEVFNS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 338.1 1.01E-95 3241617000 557054 680352 676732 687091 780449 894240 672007 719886 693466 641280 TRUE FALSE 579046.9221 797197.1636 694368.1919 822995.549 647788.5577 686566.3123 619333.3354 710237.1057 668508.2941 766926.538 0.75502267 1.039470046 0.905390748 1.073108712 0.844655291 0.895217832 0.80755236 0.926082318 0.871671876 1 19.54872887 NIIGSS(ph)PVADFSAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 NIIGS(0.001)S(0.999)PVADFSAIK;NIIGS(0.002)S(0.998)PVADFSAIK;NIIGSS(1)PVADFSAIK;NIIGSS(1)PVADFSAIK 287.16 2.38E-34 783879000 1820340 1283950 1658120 1393010 2097850 2158230 2253400 1736740 1845810 1029540 TRUE FALSE 1892208.429 1504458.425 1701331.969 1668543.22 1741258.206 1657013.791 2076772.62 1713461.841 1779379.659 1231258.651 1.53680823 1.221886582 1.381782753 1.355152484 1.414209926 1.345788547 1.686707028 1.391634357 1.445171294 1 20.23170243 -0.684298361 6.064476446 0.999999996 1.418483065 0.537210772 0.116913925 6.59E-09 1.36E-09 0.110537206 0.026053869 0.206871965 0.684298361 0.418483069 NIIHGS(ph)DSVK ddPTM_MDA-MB-175_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(0.959)DS(0.041)VK 127.71 0.00022464 141490000 190510 127220 153660 149280 269910 274270 255940 177540 207500 134150 TRUE FALSE 198031.4819 149069.0454 157664.5058 178807.1384 224030.7946 210574.9491 235878.754 175160.3667 200032.1155 160434.124 1.234347637 0.929160465 0.982736726 1.114520614 1.396403639 1.312532171 1.470253012 1.091789965 1.246817762 1 17.29162151 3.439946258 7.83637431 1.263476746 1.038567288 0.28735059 0.146780623 0.246726514 44.12993486 0.040048027 0.054599221 2753.887903 -3.439946258 -0.224909458 NIIHGSDS(ph)VK ddPTM_MDA-MB-175_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(0.303)DS(0.697)VK 118.73 0.00050641 150550000 119800 82595 103760 94622 162880 166170 145160 108470 125170 90849 TRUE FALSE 124529.7965 96780.04875 106464.0708 113337.9492 135193.7158 127579.5358 133781.9799 107016.1371 120665.1562 108649.1221 1.146164774 0.890757761 0.979888919 1.043155683 1.244314847 1.174234392 1.231321315 0.984970103 1.110594856 1 16.72931699 3.466956521 24.65192523 1.125309127 0.997019707 0.232604647 0.098609265 239.2188732 580160.6253 0.027801128 0.037684684 2930.599834 -3.466956521 -0.12828942 EDALDDSVSSSSVHASPLAS(ph)SPVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 EDALDDSVSSSSVHASPLASSPVRK 25 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;O14715;Q99666;J3KQ37 P49792 RANBP2;RGPD3;RGPD4;RGPD8;RGPD5 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 8;RANBP2-like and GRIP domain-containing protein 5/6 1 EDALDDSVSSSSVHASPLAS(0.5)S(0.5)PVRK;EDALDDSVSSSSVHASPLAS(0.876)S(0.124)PVRK 279.93 1.51E-53 638090000 34867 292600 287660 370990 338500 507800 356240 433730 310960 238882 TRUE FALSE 36243.57608 342851.7739 295156.6559 444370.7147 280961.8909 389871.1458 328316.9779 427916.5588 299768.6103 285686.3542 0.126864919 1.20009853 1.033149297 1.555449563 0.983462762 1.364682422 1.149221771 1.497854386 1.049292715 1 18.1240726 4.743030495 4.90110669 1.235920629 0.065354549 0.726149064 0.197591127 0.083508969 5.986215452 0.04381894 0.333265674 55338.89655 -4.743030495 -1.17056608 down NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIIHGSDSVESAEKEIGLWFHPEELVDYTSCAQNWIYE 38 1 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;; 166.27 3.84E-18 1056440000 92952.9 411811 399539 276010 478462 518941 273318 397262 387203 492181 FALSE TRUE 96622.75227 482536.3358 409951.3146 330603.9542 397133.2001 398424.8174 251894.621 391937.3527 373267.6397 588614.4436 0.164152873 0.819783376 0.696468323 0.561664699 0.674691565 0.6768859 0.427945022 0.665864314 0.634146246 1 19.16696342 -4.999999942 0.344782323 5.439134927 0.589050129 0.343892623 0.170927782 461.9463911 3.840924484 1512.33661 0.124487172 1.00E-05 4.999999942 -4.850084798 NIIHGSDSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIIHGSDSVK 10 0 Q32Q12;P22392-2;P22392;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;; 184.24 1.58E-06 8045800000 2436810 9539510 10549980 9185210 13796700 14885000 10821900 13335600 10746500 8578480 FALSE TRUE 2533017.14 11177846.64 10824921.15 11002017.12 11451541.86 11428184.33 9973651.2 13156858.09 10359735.56 10259268.91 0.246900355 1.089536373 1.055135726 1.072397772 1.116214222 1.113937497 0.972160033 1.282436225 1.009792769 1 23.29042459 4.738595912 8.962327501 1.093075739 0.243056712 0.900183267 0.083014967 0.022048525 34.81981376 0.019346766 0.113179171 54776.70593 -4.738595912 -0.850019027 NIIIALIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIIIALIDR 9 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 76.064 0.056208 0 288190 149640 185680 150230 217850 225430 226400 190790 195230 132980 FALSE TRUE 299567.9637 175339.506 190518.9733 179945.0456 180819.9348 173077.2989 208654.1764 188232.7721 188203.7104 159034.8849 1.883661964 1.102522293 1.1979697 1.131481597 1.136982838 1.088297696 1.312002561 1.18359423 1.183411492 1 17.27898374 4.741403811 24.99870365 1.161485535 1.883662224 0.88766633 0.078337317 78.27288937 688176.1537 0.017911962 0.12534367 55132.00811 -4.741403811 0.722176689 NIILEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIILEEGK 8 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ; 107.47 0.014301 221400000 665760 413180 489830 444430 681890 729680 716640 563860 535930 319720 FALSE TRUE 692044.7189 484140.4509 502595.3722 532336.9275 565982.5814 560222.8784 660467.8842 556302.379 516641.984 382363.0126 1.809915437 1.266180135 1.314445581 1.392229138 1.480223146 1.465159704 1.727332044 1.45490636 1.351181906 1 18.54458345 0.856575095 2.684336675 1.000589325 1.481337986 0.464778846 0.158554236 0.504961627 6.935786738 0.150292 0.039922274 7.187454279 -0.856575095 0.480748661 NIILEEGKEILVGDVGQTVDDPYATFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIILEEGKEILVGDVGQTVDDPYATFVK 28 1 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;E9PS23 G3V1A4;P23528 CFL1 Cofilin-1 0 ;;; 325.65 5.35E-84 3106561000 4919562 2776994 4402759 2687140 6022951 5257868 4526607 4304817 4795364 2364850 FALSE TRUE 5113790.106 3253921.117 4517498.516 3218648.272 4999171.94 4036807.841 4171799.715 4247117.969 4622779.786 2828197.08 1.808144893 1.15052842 1.597306832 1.138056571 1.767617956 1.42734319 1.475073907 1.501705097 1.634532409 1 21.43145123 -1.100799907 4.335094993 0.999943422 1.487462622 0.329704975 0.213213349 4.304112752 54823393.83 6996.005185 0.044417201 0.079286654 1.100799907 0.4875192 NIIQHFENNQQYDAPEPGT(ph)QRLSTGSFPEDLLESDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIIQHFENNQQYDAPEPGTQRLSTGSFPEDLLESDSSR 38 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 NIIQHFENNQQYDAPEPGT(0.823)QRLS(0.146)T(0.026)GS(0.005)FPEDLLESDSSR;NIIQHFENNQQYDAPEPGT(0.458)QRLS(0.458)T(0.072)GS(0.012)FPEDLLESDSSR;NIIQHFENNQQYDAPEPGT(0.674)QRLS(0.282)T(0.031)GS(0.012)FPEDLLESDSSR;NIIQHFENNQQYDAPEPGT(0.839)QRLS(0.102)T(0.019)GS(0.04)FPEDLLESDSSR 320.52 4.54E-110 273127000 95596 103847 114901 100647 131480 155341 107297 109141 108756 120453 TRUE FALSE 99370.2039 121681.9144 117895.4145 120554.6762 109131.0766 119265.407 98886.78077 107678.1434 104841.8928 144053.4591 0.689814771 0.844699705 0.818414324 0.836874567 0.757573454 0.827924631 0.686458912 0.747487385 0.727798509 1 17.13624478 NIITHAPNLDNIELYWNSYNNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIITHAPNLDNIELYWNSYNNRR 23 1 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4;G3V5H8;G3V4S9;G3V5L7;A0A0U1RR50;G3V2I9;H7C0X0 Q9UN36 NDRG2 Protein NDRG2 0 147.21 7.77E-08 136790000 63521 73914 87613 51178 84601 90291 63320 66084 88809 62901 FALSE TRUE 66028.85813 86608.15453 89896.26675 61300.85565 70220.55224 69322.28362 58356.81294 65198.25207 85612.78144 75225.24664 0.877748643 1.151317655 1.195027877 0.81489737 0.933470548 0.921529496 0.775761005 0.866707056 1.138085753 1 16.19892931 3.73415908 24.98589006 0.905260112 1.082360017 0.239644364 0.122466635 447.1864139 2538516.239 0.031998926 0.05150029 5421.994597 -3.73415908 0.177099905 NILFVITKPDVYK ddPTM_MDA-MB-175_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 ; 185.87 7.56E-06 1045040000 3208700 1793710 2551300 2041390 3727500 3631500 3388500 2874900 2983500 1388170 FALSE TRUE 3335381.954 2101765.739 2617788.974 2445170.849 3093900.881 2788139.161 3122900.516 2836366.668 2876124.418 1660155.333 2.009078239 1.266005474 1.576833758 1.472856666 1.863621325 1.679444751 1.881089349 1.708494748 1.732442959 1 20.6628868 3.260950459 24.99231508 1.69852714 1.55836872 0 0.290930869 774.3583788 864359.6087 0.073760354 0.099796163 1823.68766 -3.260950459 -0.140158419 NILGGTVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NILGGTVFR 9 0 O75874;C9J4N6;P48735;P48735-2 O75874;P48735 IDH1;IDH2 "Isocitrate dehydrogenase [NADP] cytoplasmic;Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 107.57 0.0069919 0 364250 385990 380210 409350 552560 565370 457730 448720 435440 458020 FALSE TRUE 378630.8713 452280.7799 390118.5849 490318.2082 458636.0486 434071.3858 421851.9265 442705.6424 419768.5995 547760.2497 0.691234662 0.825691131 0.712206819 0.895132877 0.837293412 0.792447765 0.770139722 0.808210604 0.766336367 1 19.06318505 -2.50573038 2.188066295 3.650614151 0.792627446 0.557420362 0.056376752 1598931.073 127676.6524 21235065.84 0.01291762 0.003120826 2.50573038 -2.857986705 NILPFDHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NILPFDHTR 9 0 Q06124;Q06124-1;Q06124-3 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 76.143 0.036267 257820000 234630 311040 295530 268830 407510 459210 352580 313640 325420 284780 FALSE TRUE 243893.3736 364458.7004 303231.7546 322003.7716 338241.5958 352565.4369 324943.8583 309436.1688 313708.1978 340577.1886 0.716117761 1.070120703 0.890346637 0.945464883 0.993142251 1.035199798 0.954097542 0.908563988 0.921107485 1 18.37762228 4.755025479 24.75001388 0.962377637 0.716117542 0.659793035 0.054236285 1824.090369 2741924.308 0.012991783 0.355299361 56888.63055 -4.755025479 -0.246260095 NINDAWVCTNDMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NINDAWVCTNDMFR 14 0 P61970 P61970 NUTF2 Nuclear transport factor 2 0 ;;; 184.98 2.86E-06 1327360000 651975 716394 697261 672483 893521 993767 698074 658202 661699 742120 FALSE TRUE 677715.4764 839429.0967 715432.1945 805498.1302 741640.6196 762979.6749 643357.1358 649379.8788 637884.5822 887524.2053 0.763602246 0.945809806 0.806098797 0.907578774 0.835628612 0.859671962 0.724889678 0.731675683 0.718723589 1 19.75942694 2.254015548 24.75779875 0.765535783 0.856831232 0.058839783 0.090652641 327.473433 524590.1985 0.02887246 0.024071161 179.4797882 -2.254015548 0.091295449 NINMDNDLEVLTSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 NINMDNDLEVLTS(0.003)S(0.859)PT(0.138)R;NINMDNDLEVLTS(0.003)S(0.993)PT(0.004)R;NINMDNDLEVLTS(0.002)S(0.998)PTR;NINMDNDLEVLTS(0.008)S(0.725)PT(0.267)R;NINMDNDLEVLTS(0.168)S(0.829)PT(0.003)R;NINMDNDLEVLTS(0.001)S(0.995)PT(0.004)R 401.85 3.65E-140 1419544000 1399112 1650602 1687088 1531489 1889290 2230900 1762701 1735706 1619574 1486426 TRUE FALSE 1454350.022 1934080.054 1731054.899 1834412.953 1568149.161 1712807.285 1624535.89 1712441.7 1561285.848 1777662.715 0.818124839 1.087990448 0.973781406 1.031924075 0.882140997 0.963516459 0.913860585 0.963310804 0.878280134 1 20.76155019 3.24217961 24.99957903 0.933905061 0.985516715 0.078280721 0.072868226 211.0255447 1457726.381 0.018900759 0.024622161 1746.544315 -3.24217961 0.051611654 NINTFVET(ph)PVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NINTFVET(1)PVQK 124.3 0.0036376 77075000 222610 120600 141850 128300 163590 211460 181850 151310 155380 107790 TRUE FALSE 231398.8147 141312.1119 145546.7275 153677.3571 135783.0302 162351.6197 167596.1218 149281.9369 149787.9042 128909.3867 1.795050155 1.096212739 1.129062291 1.192134731 1.053321513 1.259424343 1.300107976 1.158037756 1.161962739 1 16.97599779 4.742224902 24.99369739 1.162646803 1.795050397 0.836140215 0.085498621 134.632204 918273.7257 0.020034328 0.149362342 55236.34094 -4.742224902 0.632403594 NIQFEAFHVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIQFEAFHVFK 11 0 Q9Y376;A0A087X0K1 Q9Y376 CAB39 Calcium-binding protein 39 0 ; 114.71 0.0012209 371530000 1060820 974210 1095320 958780 1658680 1593500 1277400 1177630 1155810 1060110 FALSE TRUE 1102701.993 1141522.989 1123864.939 1148423.822 1376738.166 1223433.775 1177274.05 1161845.796 1114212.624 1267818.257 0.869763459 0.900383775 0.886455872 0.905826853 1.085911295 0.964991447 0.92858266 0.916413523 0.878842545 1 20.27391652 3.458299918 24.9812893 0.956869235 0.888539587 0.311444745 0.052535907 334.907523 444516.707 0.015590802 0.021113264 2872.76379 -3.458299918 -0.068329649 NIQVSHQEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NIQVSHQEFSK 11 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 196.38 6.07E-08 1042940000 3015040 2215310 2691570 2205350 3855940 3719230 3026040 2943870 3081290 1958540 FALSE TRUE 3134076.107 2595772.26 2761714.525 2641561.648 3200508.696 2855495.198 2788851.078 2904412.238 2970394.975 2342278.414 1.338045933 1.108225326 1.179071842 1.127774406 1.366408313 1.219110068 1.190657379 1.239994452 1.268164773 1 21.15948114 -1.055199538 4.915683208 0.99999496 1.222192212 0.428058117 0.078369158 4.15E-06 7.97E-07 0.072715485 0.017138815 0.088064417 1.055199538 0.222197251 NIRDDEGFIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NIRDDEGFIIR 11 1 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;; 228.93 2.65E-12 1190410000 355827 375634 411750 376722 466252 546025 437565 433258 406585 347732 FALSE TRUE 369875.3247 440146.2175 422480.5433 451236.4872 386998.6516 419218.9688 403267.5119 427450.8852 391952.0853 415863.4277 0.889415371 1.058391261 1.015911752 1.085059318 0.930590732 1.008068854 0.969711413 1.027863613 0.942501935 1 18.66575029 3.220154792 24.99809488 0.984932057 1.015759777 0.071132525 0.054930183 693.527617 941919.5702 0.015231544 0.018239267 1660.178528 -3.220154792 0.030827721 NIRDNEEKDSAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NIRDNEEKDSAFR 13 2 O14787-2;O14787;Q92973-2;Q92973;Q92973-3;S4R398 O14787-2;Q92973-2 TNPO2;TNPO1 Transportin-2;Transportin-1 0 111.66 0.00054107 127420000 159730 130720 150550 92612 201970 195270 111690 136020 136340 121190 FALSE TRUE 166036.2637 153170.1431 154473.4567 110930.3772 167639.2115 149921.5018 102935.446 134196.8744 131433.15 144934.8602 1.145592327 1.056820581 1.06581299 0.765380924 1.156652108 1.034406089 0.710218686 0.925911642 0.906842908 1 17.14504511 5.650682508 0.466269725 0.904355911 1.629982037 0.240284572 0.123962191 14.81744562 1.305474825 0.076642789 7.079448896 447386.1217 -5.650682508 0.725626126 NISFNDKK ddPTM_MDA-MB-175_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 ; 136.63 0.0012547 4571500000 3797000 1979840 2761200 1858800 4383200 4227800 3777800 3171300 3197700 1488860 FALSE TRUE 3946908.492 2319862.119 2833159.14 2226465.092 3638145.23 3245957.523 3481686.165 3128793.911 3082615.402 1780573.611 2.216649998 1.30287347 1.591149685 1.250420133 2.043243372 1.822984179 1.955373338 1.75718313 1.731248505 1 20.76391065 0.782518018 13.71950055 1 1.731986656 0.37397414 0.287484924 19842.78102 1251792.848 0.270666099 0.067662047 6.060633443 -0.782518018 0.731986656 NISFTVWDVGGQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NISFTVWDVGGQDK 14 0 P61204;F5H423;F5H0C7;P84077 P61204;P84077 ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 1 0 ; 228.8 3.54E-12 559280000 1029470 677850 867580 689410 1131580 1185140 1060090 948180 925620 469450 FALSE TRUE 1070114.271 794265.4646 890189.8475 825773.2403 939234.4358 909909.196 976997.3758 935471.198 892307.117 561429.7393 1.906051988 1.414719259 1.585576583 1.470839862 1.672933174 1.620700031 1.740195268 1.66623022 1.589347793 1 19.09874596 0.882424114 10.03473285 1.000000002 1.628295952 0.684170654 0.128604619 15.44427987 1318.691389 0.117729074 0.029448108 7.628235887 -0.882424114 0.62829595 NISHYEEQLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NISHYEEQLVK 11 0 P13861-2;P13861;H7C330 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 118.61 0.00069774 380740000 360670 290570 338890 277270 462000 463740 414790 358670 386470 239210 FALSE TRUE 374909.5301 340473.1372 347721.7518 332113.1784 383469.405 356043.413 382277.6759 353862.6153 372561.0202 286078.6195 1.310512232 1.190138353 1.215476194 1.160915761 1.340433639 1.244564916 1.336267899 1.236941844 1.302302915 1 18.12605215 -0.868121991 6.318959128 0.999999982 1.257248516 0.639913384 0.058423185 1.47E-08 2.59E-09 0.054975174 0.012957772 0.13548088 0.868121991 0.257248534 NIYAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIYAEK 6 0 H0Y7V4;A0A075B6F3;Q96JB1-2;Q96JB1 H0Y7V4 DNAH8 "Dynein heavy chain 8, axonemal" 0 ; 82.263 0.059704 201585000 362190 391600 428030 386550 461900 539140 486410 424020 442360 439170 FALSE TRUE 376489.5409 458854.2538 439184.8134 463008.4363 383386.403 413932.9057 448283.9132 418336.7055 426439.55 525216.9531 0.716826711 0.873647073 0.836196948 0.881556533 0.729958164 0.788117945 0.853521408 0.79650267 0.811930284 1 19.00255396 -2.061413044 2.197720635 1.25600377 0.812383012 0.541064678 0.052501218 3516934.122 1084219.674 4517002.385 0.012590593 0.008681344 2.061413044 -0.443620758 NIYAFMGT(ph)PVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NIYAFMGTPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 NIYAFMGT(1)PVQK;NIYAFMGT(1)PVQK 176.4 0.00028062 254270000 1072420 638310 726440 580040 889470 987730 828960 693430 676780 560430 TRUE FALSE 1114759.97 747934.7771 745371.6232 694770.1808 738278.2071 758344.6767 763983.9491 684135.7051 652422.82 670235.5284 1.663236165 1.115928275 1.112104017 1.036606016 1.101520549 1.131459979 1.139873845 1.020739242 0.973423211 1 19.35430864 4.74841063 3.745162635 1.070807635 1.731544534 0.915605867 0.054181157 0.074642975 1.967413868 0.013637624 0.138378652 56028.71086 -4.74841063 0.6607369 NIYSEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NIYSEELR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 234.82 3.33E-08 6964820000 3885780 4609100 4662020 4167620 5688430 6294070 4906910 5023940 4495870 4055310 FALSE TRUE 4039193.595 5400677.071 4783516.071 4991962.797 4721512.7 4832367.63 4522293.572 4956602.302 4334064.517 4849870.351 0.832845685 1.113571432 0.986318339 1.029298195 0.973533798 0.996391095 0.932456591 1.022007176 0.893645439 1 22.20951475 2.371215358 19.77943794 0.968395728 0.995408636 0.023398694 0.072699713 10.78132888 1968.242916 0.023462226 0.01962985 235.0798248 -2.371215358 0.027012907 NKAGT(ph)PVSELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKAGTPVSELTK 12 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 NKAGT(0.935)PVS(0.065)ELTK;NKAGT(0.991)PVS(0.009)ELTK 103.67 0.003591 1360030000 1608680 811340 1190950 672020 1816230 1662850 1288520 1129120 1256010 637860 TRUE FALSE 1672191.929 950681.3337 1221987.135 804943.5502 1507507.873 1276678.288 1187522.435 1113985.993 1210806.445 762836.4544 2.19207134 1.246245284 1.601899238 1.055198064 1.97618751 1.673593705 1.556719568 1.460320868 1.587242506 1 19.54101426 -2.635179483 0.354038311 1.07E-10 1.598110344 0.255521326 0.306112606 95.04413267 3.600468056 72.68273048 0.219417938 0.002316437 2.635179483 1.598110344 NKDEEIQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKDEEIQQLR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 0 138.99 4.56E-05 176230000 115110 96419 108620 84209 147580 150530 143370 113550 136220 87392 FALSE TRUE 119654.6317 112978.2132 111450.7264 100865.2889 122494.4043 115571.6888 132132.2848 112028.048 131317.4688 104514.7892 1.144858375 1.080978243 1.066363213 0.965081494 1.172029387 1.10579268 1.264244858 1.07188704 1.256448679 1 16.67334758 3.180824503 24.99999717 1.14968581 1.065653446 0.177203199 0.084870504 126.7833715 54897.04417 0.023038532 0.027536323 1516.437456 -3.180824503 -0.084032364 NKDEMSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKDEMSTK 8 1 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 69.825 0.055533 67712000 96422 44195 64457 42332 95115 83701 75014 66613 75772 34404 FALSE TRUE 100228.815 51785.14746 66136.80237 50705.14325 78947.38627 64262.71125 69134.20667 65720.16169 73044.98052 41144.8051 2.436001696 1.258607188 1.60741562 1.232358329 1.918769237 1.56186695 1.680265747 1.597289416 1.775314778 1 15.32842267 -1.316145258 4.883163167 0.999703783 1.647119621 0.277497735 0.323721705 0.000943426 0.00013212 0.283257016 0.066734527 0.048289726 1.316145258 0.647415839 NKDLPESALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKDLPESALR 10 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 95.507 0.0067259 162990000 340150 279700 339920 267090 498460 466990 386210 371590 375890 256070 FALSE TRUE 353579.3847 327736.2992 348778.5944 319919.6048 413731.9472 358538.6498 355937.851 366609.4438 362361.7923 306242.0137 1.154575038 1.070187252 1.13889858 1.044662687 1.350996691 1.170768979 1.162276354 1.19712328 1.183253035 1 18.2243127 NKDQEVNFQEYVTFLGALALIYNEALKG ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NKDQEVNFQEYVTFLGALALIYNEALKG 28 2 P06703 P06703 S100A6 Protein S100-A6 0 ;;;; 210.79 4.34E-25 13392490000 4703570 2423770 3785380 2547950 5343390 4961600 5699590 3938470 4552440 1761450 FALSE TRUE 4889270.576 2840033.643 3884030.113 3051926.905 4435122.476 3809343.594 5252841.243 3885681.252 4388598.574 2106572.403 2.320960139 1.348177561 1.843767681 1.448764306 2.105373863 1.808313633 2.493548874 1.844551484 2.083288744 1 21.00646607 3.218196947 24.9986357 1.962056584 1.719782272 0.01034758 0.432324721 662.0595262 812748.5705 0.114948764 0.137539884 1652.711113 -3.218196947 -0.242274312 NKDQGTYEDYVEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 ;;;;;;;;; 284.53 4.98E-34 49191947000 16807069 12972700 16457620 12074052 21530881 20383713 18190211 16772160 17514104 10797661 FALSE TRUE 17470625.06 15200660.31 16886519.1 14462263.45 17871069.54 15649904.57 16764414.73 16547356.63 16883774.82 12913255.94 1.352921768 1.177136145 1.307688717 1.119954837 1.38393211 1.211925532 1.298232979 1.281424043 1.307476201 1 23.62234947 -1.193492379 6.396795619 0.999998137 1.268711775 0.532069032 0.076263644 1.80E-06 2.27E-07 0.065622962 0.015467373 0.064048302 1.193492379 0.268713638 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPS(0.005)T(0.002)T(0.063)PS(0.421)VDS(0.508)DDES(0.001)VVK;NKDSGSDTASAIIPSTTPS(0.002)VDS(0.997)DDESVVK;NKDSGSDTASAIIPSTTPS(0.016)VDS(0.983)DDES(0.001)VVK;NKDSGSDTASAIIPSTTPS(0.008)VDS(0.991)DDESVVK 195.42 2.00E-20 2257150000 2532280 1064290 1625610 1094790 2496220 2389780 2168760 1652660 1851650 718330 TRUE FALSE 2632256.37 1247073.528 1667974.732 1311336.194 2071913.416 1834789.812 1998766.924 1630508.796 1785009.478 859073.0102 3.064065962 1.451650225 1.941598342 1.526454887 2.411801315 2.135778671 2.326655477 1.89798629 2.077832101 1 19.71242122 -0.16633078 1.210606009 0.993607797 2.066203837 0.359621765 0.436037236 23.3929679 22.50346304 1.100501838 0.117490917 0.68181919 0.16633078 1.07259604 NKDSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NKDSGSDTASAIIPSTTPSVDSDDESVVKDK 31 2 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 NKDSGSDTASAIIPSTTPS(0.001)VDS(0.895)DDES(0.104)VVKDK;NKDSGSDTASAIIPSTTPS(0.008)VDS(0.602)DDES(0.39)VVKDK;NKDSGSDTASAIIPSTTPS(0.022)VDS(0.947)DDES(0.03)VVKDK 186.24 1.07E-18 1228130000 4628300 1207860 2201130 1123550 3995700 3567060 3077140 2234350 2745010 766010 TRUE FALSE 4811028.858 1415300.559 2258493.256 1345784.837 3316512.341 2738664.374 2835945.726 2204402.193 2646217.626 916094.9934 5.251670288 1.544927731 2.465348324 1.469045073 3.620271222 2.989498244 3.095689581 2.406303068 2.888584312 1 19.80513768 4.751184184 24.51665838 2.48948406 5.251672575 0.53988152 0.788353201 1204.355674 2338964.779 0.180248974 3.172057446 56387.67447 -4.751184184 2.762188515 NKDTPACSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKDTPACSR 9 1 P42695 P42695 NCAPD3 Condensin-2 complex subunit D3 0 58.676 0.097829 7850200 11243 9391.4 14428 11077 20802 15348 15004 13830 11742 10468 FALSE TRUE 11686.88232 11004.2999 14804.00553 13267.99754 17266.08347 11783.6596 13827.94727 13644.63147 11319.40771 12519.00418 0.933531306 0.879007606 1.182522613 1.05982851 1.379189848 0.941261736 1.104556487 1.089913485 0.904177964 1 13.61183219 4.251017719 24.99923037 1.091541684 0.906269361 0.235335082 0.126393165 295.5627978 593131.9584 0.029547805 0.079695544 17824.51488 -4.251017719 -0.185272322 NKDVYPSCSSTTASTVGNSSSHNTASQS(ph)PDFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKDVYPSCSSTTASTVGNSSSHNTASQSPDFVR 33 1 Q6PIJ6-2;Q6PIJ6 Q6PIJ6-2 FBXO38 F-box only protein 38 1 NKDVYPSCSSTTASTVGNSSSHNT(0.002)AS(0.005)QS(0.994)PDFVR 344.09 1.85E-118 170750000 13160 28116 43534 36398 48229 61176 33354 53539 33935 29103 TRUE FALSE 13679.56696 32944.70429 44668.5318 43597.41576 40031.05181 46968.80113 30739.62633 52821.39728 32713.68598 34805.17564 0.393032551 0.946546129 1.283387628 1.252613008 1.150146525 1.349477492 0.883191243 1.517630534 0.939908659 1 15.08701423 4.665931963 2.568801374 1.199333209 0.290118185 0.611480358 0.186370477 0.235884969 2.222779555 0.042574532 0.430473237 46337.43217 -4.665931963 -0.909215024 NKEDEDIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKEDEDIAK 9 1 O75886;O75886-2 O75886 STAM2 Signal transducing adapter molecule 2 0 87.298 0.012363 139680000 165790 95845 126320 85281 194110 190100 182700 120770 126210 80297 FALSE TRUE 172335.5172 112305.6332 129612.003 102149.3273 161115.2515 145952.156 168379.4966 119151.2757 121667.7268 96029.65977 1.794607183 1.169489025 1.349708031 1.063726848 1.677765515 1.519865387 1.753411363 1.240775777 1.266980712 1 16.55119245 1.090475356 1.7939069 1.017118348 1.447873838 0.276094136 0.231644896 0.453549035 2.876094826 0.216413545 0.062368117 12.31616095 -1.090475356 0.430755491 NKEDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKEDFEK 7 1 O15042-2;O15042;E7ET15;E7EW00;H0Y8D9 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 85.676 0.01882 92514000 358680 178470 250480 175650 404510 360130 363460 274020 309230 158200 FALSE TRUE 372840.9634 209120.8342 257007.7146 210393.0457 335751.5347 276495.2653 334971.0555 270347.2101 298100.8727 189196.2611 1.970657143 1.105311664 1.358418571 1.11203596 1.774620348 1.461420346 1.770495112 1.428924697 1.575617145 1 17.52952405 -1.489852188 6.18622455 0.999656375 1.492010118 0.243766609 0.266494616 0.001194238 9.85E-05 0.24398592 0.057469282 0.032370381 1.489852188 0.492353744 NKEDQYDHLDAADMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKEDQYDHLDAADMTK 16 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ; 249.19 2.12E-20 628010000 939490 455890 676740 434760 991670 866510 896750 674660 757730 309070 FALSE TRUE 976581.7906 534185.5612 694376.4003 520754.2304 823106.2876 665276.1846 826460.3918 665617.2862 730459.4453 369626.349 2.642078394 1.445204225 1.878590101 1.408866635 2.226860422 1.799861364 2.235934733 1.800784192 1.976210428 1 18.49570808 -0.953190994 5.587151463 0.999998707 1.9127338 0.387203355 0.351853935 5.14E-06 9.63E-07 0.309017317 0.072835978 0.11138046 0.953190994 0.912735093 NKEEAAEYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NKEEAAEYAK 10 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;; 147.58 2.43E-05 5777390000 7620440 3995440 6173010 3876850 8740670 7825350 7872720 6242230 6941950 3153740 FALSE TRUE 7921300.855 4681625.74 6333883.712 4643679.359 7254934.035 6008031.057 7255635.635 6158563.117 6692110.576 3771654.971 2.100218847 1.241265645 1.679338052 1.231204708 1.923541281 1.592942913 1.9237273 1.632854321 1.774316746 1 21.84676627 -1.165300896 6.25046519 0.999995969 1.664840244 0.36734405 0.266335521 1.37E-05 1.83E-06 0.236120478 0.055653793 0.068343797 1.165300896 0.664844276 NKEFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NKEFER 6 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ;; 91.041 0.04409 846710000 1248130 896760 1112180 821540 1545460 1496330 1273020 1189230 1176870 690660 FALSE TRUE 1297407.136 1050771.554 1141164.324 984038.1599 1282763.261 1148830.035 1173237.366 1173290.317 1134514.679 825981.6035 1.570745802 1.272148859 1.381585643 1.191356025 1.553016745 1.39086637 1.420415855 1.420479962 1.373535045 1 19.65575012 0.923367651 16.06088916 0.999999999 1.39547601 0.555647725 0.106712006 251.4736504 52706.27 0.096222446 0.024056296 8.382385911 -0.923367651 0.395476011 NKEGLHNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKEGLHNAK 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 102.61 0.0021371 509670000 553970 392690 505060 351680 701050 654850 530390 492240 468330 342040 FALSE TRUE 575841.1634 460131.4528 518222.2785 421241.2543 581885.7714 502771.0118 488816.6459 485642.3279 451474.8948 409056.1892 1.407731208 1.124861241 1.26687309 1.029788243 1.422508171 1.229100121 1.194986554 1.187226451 1.10369897 1 18.6419395 1.090599309 1.185510355 1.000434393 1.237527485 0.335262133 0.109977032 0.524502927 1.528657315 0.096632087 0.030624187 12.31967665 -1.090599309 0.237093093 NKEIFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKEIFLR 7 1 P14625;Q96GW1;A0A1W2PRR1;F8W026 P14625 HSP90B1 Endoplasmin 0 131.06 0.0031944 2816300000 2400300 2133300 2309900 1907900 3453600 3367400 2229400 2455500 2464800 1688700 FALSE TRUE 2495065.697 2499677.68 2370097.892 2285276.925 2866558.306 2585372.383 2054653.803 2422588.039 2376092.329 2019568.433 1.235444988 1.237728635 1.173566517 1.131566967 1.419391519 1.280160821 1.017372707 1.199557291 1.176534695 1 20.9456156 0.639394016 0.492962838 0.9925512 1.235074174 0.33010982 0.095050836 1.995180418 0.99027562 0.145619375 0.053876425 4.359071738 -0.639394016 0.242522974 NKELEIAQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKELEIAQDR 10 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 116.24 0.0010185 238370000 312050 247010 298120 225710 425410 453570 344520 302480 309990 218470 FALSE TRUE 324369.975 289432.046 305889.2521 270354.7643 353098.9602 348235.2414 317515.6222 298425.7504 298833.5205 261275.0136 1.241488692 1.107767796 1.170755855 1.034751699 1.351445572 1.332830249 1.215254447 1.142190163 1.143750856 1 17.99520964 0.880369731 1.360404768 1.002319304 1.202548791 0.317302774 0.090118934 0.746188082 2.696419153 0.090218184 0.027041723 7.592236559 -0.880369731 0.200229487 NKELYEINPPEISEEIIGS(ph)PIPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKELYEINPPEISEEIIGSPIPEPR 25 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NKELYEINPPEISEEIIGS(1)PIPEPR;NKELYEINPPEISEEIIGS(1)PIPEPR;NKELYEINPPEISEEIIGS(1)PIPEPR;NKELYEINPPEISEEIIGS(1)PIPEPR 203.64 3.09E-25 399062000 280233 248562 302714 232581 395598 414811 303373 321563 331155 253454 TRUE FALSE 291296.8152 291250.59 310602.9755 278584.8276 328354.3933 318477.4318 279593.8315 317252.974 319236.7962 303113.4586 0.961015775 0.960863273 1.024708625 0.919077724 1.083272233 1.050687202 0.922406523 1.0466476 1.053192417 1 18.20949839 3.244169231 24.99945103 1.023615177 0.970183449 0.274937652 0.047173878 210.6521039 938942.4219 0.013259997 0.017482216 1754.564069 -3.244169231 -0.053431728 NKESKDPADETEAD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKESKDPADETEAD 14 2 P16949 P16949 STMN1 Stathmin 0 ;;; 110.98 0.0026932 1962240000 3915170 1566080 2491170 1420390 4096090 3756680 3264410 2524760 2991620 1252480 FALSE TRUE 4069743.935 1835042.058 2556091.937 1701338.903 3399838.085 2884248.003 3008537.014 2490919.722 2883952.181 1497879.476 2.717003604 1.225093265 1.706473704 1.135831641 2.269767454 1.925554125 2.008530768 1.662964052 1.925356631 1 20.51449011 -1.386603907 4.29897686 0.998131261 1.810073672 0.245817117 0.439207238 0.007333312 0.001046346 0.396433359 0.093257717 0.04105784 1.386603907 0.811942412 NKEVTWEVLEGEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKEVTWEVLEGEVEK 15 1 P05455 P05455 SSB Lupus La protein 0 ; 182.15 5.09E-07 215587000 819890 372460 576490 409370 885460 794670 824830 634860 751560 297080 FALSE TRUE 852259.8903 436427.1077 591513.803 490342.1642 734949.8255 610119.9358 760177.6693 626350.7401 724511.5024 355287.1381 2.398791847 1.228378573 1.664889436 1.38012923 2.068608026 1.71725872 2.139614942 1.762942344 2.039228063 1 18.43862594 3.2335557 24.99433291 1.841681468 1.63641682 0.007582857 0.415162423 392.876195 1962007.623 0.10928892 0.134523201 1712.20476 -3.2335557 -0.205264649 NKFDVDAADEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKFDVDAADEK 11 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 93.958 0.0036624 0 507250 213160 314010 244430 611130 511670 589770 354690 400520 210040 FALSE TRUE 527276.6217 249768.5718 322193.3586 292777.5244 507250.3409 392842.3969 543542.2863 349935.9607 386105.3634 251193.3165 2.099086986 0.994328095 1.282651 1.165546633 2.019362409 1.563904655 2.163840558 1.393094233 1.53708454 1 17.93843855 3.263206237 24.99820371 1.651103009 1.350129877 0.063249501 0.404447622 503.409616 510607.8492 0.106055704 0.143536011 1833.184755 -3.263206237 -0.300973132 NKFDVDAADEKFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKFDVDAADEKFR 13 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 80.469 0.0099584 59016000 131840 79451 103150 63467 160300 126970 113440 108570 111550 68796 FALSE TRUE 137045.145 93096.09121 105838.1737 76020.58317 133052.2633 97483.14175 104548.2764 107114.7967 107535.3373 82275.25902 1.665690836 1.13151988 1.286391255 0.923978655 1.617160065 1.184841505 1.270713427 1.301907742 1.307019128 1 16.32817104 -1.773238198 2.412470165 0.918248721 1.288122181 0.159038702 0.2048094 15816537.27 10415280.54 7627302.705 0.044912165 0.016856283 1.773238198 0.369873461 NKFEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NKFEEAER 8 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 150.35 0.0004474 9330140000 7765640 6718530 7082760 6400680 11175080 10644410 8716320 7391390 7349890 4885050 FALSE TRUE 8072233.464 7872385.265 7267342.544 7666715.4 9275543.893 8172407.095 8033112.063 7292320.507 7085368.895 5842182.018 1.381715503 1.347507702 1.243943191 1.312303413 1.587684852 1.398862115 1.375019135 1.248218642 1.212794958 1 22.47807588 1.065533848 1.182554353 1.006710496 1.378097876 0.655457909 0.08496194 0.305274093 0.887241596 0.085719722 0.027106873 11.6287718 -1.065533848 0.37138738 NKGNECFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKGNECFQK 9 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 106.4 0.0026831 487870000 497560 625070 460610 566070 519020 722350 437940 530360 402870 722450 FALSE TRUE 517204.053 732420.9101 472613.875 678036.9564 430797.1658 554595.1598 403613.1185 523251.3917 388370.7874 864000.2454 0.598615632 0.847709146 0.547006644 0.784764773 0.498607689 0.641892364 0.46714468 0.605614865 0.449503099 1 19.7206722 -1.113090639 4.632072251 1.00003062 0.607147541 0.483069118 0.122699026 24001060.13 72798881.14 11450.54589 0.028399786 0.07707426 1.113090639 -0.392883079 NKHEAMITDLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 NKHEAMITDLEER 13 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;;;;;;;; 281.48 1.12E-32 12553387000 9569941 7670387 9730576 7747198 12249010 12690160 11114697 10124003 10136922 6690339 FALSE TRUE 9947769.66 8987716.3 9984162.804 9279570.641 10166927.66 9743062.661 10243498.01 9988307.299 9772096.157 8001182.833 1.243287382 1.123298453 1.247835853 1.159774853 1.270678082 1.21770279 1.280247961 1.248353838 1.221331441 1 22.93178186 0.913306865 20.3154689 1 1.225159276 0.679798165 0.046036852 6246.79777 1463864.674 0.043662015 0.010915504 8.19043305 -0.913306865 0.225159276 NKIFMEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NKIFMEFR 8 1 F5H5U2;Q8NHQ9 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 0 ;; 60.973 0.05342 360089000 9773.3 536293 295101 551320 147185 463094 137343 338917 163056 612230 FALSE TRUE 10159.15743 628397.151 302791.5745 660369.4505 122166.5463 355547.4368 126577.6968 334374.372 157187.6464 732184.7466 0.013875128 0.858249443 0.413545319 0.901916427 0.166852078 0.485597984 0.172876719 0.45668033 0.214683039 1 19.48184819 -1.503506349 5.438229016 1.001148262 0.424444627 0.290105839 0.276273628 0.003557078 0.00032475 0.24738829 0.058206004 0.031368493 1.503506349 -0.576703635 NKKS(ph)PEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 NKKSPEIHR 9 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR;NKKS(1)PEIHR 115.78 0.00074116 33989460000 14220550 5757014 8521000 5034298 13655180 13018730 12200820 9279190 9836810 3808115 TRUE FALSE 14781988.29 6745736.371 8743064.26 6030067.119 11334077.38 9995327.258 11244487.85 9154817.636 9482785.13 4554242.223 3.245762427 1.481198417 1.919762681 1.324054985 2.488685675 2.194728951 2.469014008 2.010173633 2.082187258 1 22.11877959 4.752455352 24.28465857 1.957811899 3.245763728 0.427712906 0.465312272 1587.71729 2774876.176 0.107029415 2.136600024 56552.96137 -4.752455352 1.287951829 NKKS(ph)PEIHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKKSPEIHRR 10 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NKKS(1)PEIHRR;NKKS(1)PEIHRR;NKKS(1)PEIHRR;NKKS(1)PEIHRR 161.25 5.09E-06 7785420000 5605940 2310340 3186390 1844230 5777540 4909870 3823130 3616670 3912880 1839700 TRUE FALSE 5827266.84 2707122.923 3269429.941 2209013.19 4795475.814 3769627.102 3523463.081 3568194.454 3772056.213 2200153.992 2.648572264 1.230424294 1.486000504 1.004026626 2.179609169 1.713346937 1.601462031 1.621793051 1.714451001 1 21.06917307 -1.183994208 5.151604732 0.999958873 1.657476134 0.180055602 0.436399635 0.00019251 3.05E-05 0.394602629 0.093002936 0.06546449 1.183994208 0.657517261 NKLDLETLTDILQHQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKLDLETLTDILQHQIR 17 1 P18440;F5H5R8 P18440 NAT1 Arylamine N-acetyltransferase 1 0 ; 214.22 3.61E-15 315240000 740160 564810 798150 629090 1092150 1016340 843530 856320 815100 545040 FALSE TRUE 769382.0883 661811.7239 818950.4447 753522.1244 906506.7331 780310.4378 777411.9144 844842.4311 785764.7102 651830.1526 1.180341359 1.015313148 1.256386256 1.156009923 1.390710033 1.197106999 1.192660253 1.296108239 1.205474627 1 19.31413656 4.223075314 24.9933657 1.228548576 1.097827228 0.14942521 0.102741436 291.9405674 471195.4023 0.023482971 0.051008684 16713.80434 -4.223075314 -0.130721348 NKNDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKNDLTR 7 1 P42574;A8MVM1;C9JXR7 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 91.853 0.014682 249710000 727310 585810 668980 621060 883820 939820 830090 710720 676520 501000 FALSE TRUE 756024.7604 686418.3105 686414.1684 743903.8143 733588.5921 721561.0481 765025.3768 701193.9609 652172.1774 599161.3578 1.261804939 1.14563181 1.145624896 1.241575086 1.224358985 1.204285021 1.276826963 1.170292362 1.088475031 1 19.19258506 1.11020761 2.263482341 1.002946819 1.210630615 0.737144125 0.041487501 0.140566451 1.385756004 0.039639122 0.011047707 12.88865533 -1.11020761 0.207683796 NKPEWFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKPEWFFK 8 1 Q5TA02;P78417-3;P78417;Q5TA01;P78417-2 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 123.86 0.0012125 2038790000 5451400 3413700 4594700 3562400 6219800 6284200 6262400 5660500 5523600 2517710 FALSE TRUE 5666625.481 3999976.42 4714441.657 4267032.087 5162560.618 4824789.788 5771536.724 5584630.256 5324806.715 3011007.07 1.881970168 1.328451354 1.565735831 1.417144493 1.714562768 1.602384078 1.916812744 1.85473834 1.768447098 1 21.52181466 3.210638742 23.73176237 1.712967621 1.533863798 0 0.276278012 296.8177758 252274.1339 0.075145467 0.089840399 1624.197143 -3.210638742 -0.179103823 NKPGPNIES(ph)GNEDDDASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 332.67 1.53E-75 38069988000 11609875 4136885 7119417 4140252 10914377 10294744 10020561 7160352 7759908 2800548 TRUE FALSE 12068241.83 4847362.818 7304954.856 4959181.488 9059155.096 7903945.724 9235123.245 7064379.193 7480630.427 3349261.761 3.603254296 1.447292915 2.18106418 1.48067898 2.704821463 2.359906836 2.757360847 2.10923472 2.233516208 1 21.6754117 4.755803421 24.41648146 2.116389075 3.603255957 0.424142072 0.541524984 2532.251214 3585685.675 0.122507833 3.534284485 56990.62512 -4.755803421 1.486866882 NKPLFFADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKPLFFADK 9 1 E5RK69;P08133;P08133-2;E7EMC6 E5RK69;P08133 ANXA6 Annexin;Annexin A6 0 85.958 0.014743 0 237530 88390 117930 108980 268230 244930 226760 104560 179610 151930 FALSE TRUE 246907.8678 103570.2949 121003.3527 130535.9187 222636.3604 188048.7195 208985.9587 103158.5442 173145.8712 181697.7746 1.358893186 0.570014108 0.665959464 0.718423321 1.225311432 1.034953344 1.15018447 0.567747978 0.952933362 1 17.47118122 4.764006246 23.69726424 0.866055208 1.358894456 0.293640487 0.224114064 5307.082058 4942270.045 0.056303555 3.755940029 58077.27697 -4.764006246 0.492839247 NKPLS(ph)PIKLTPTSVLDYFGTGSVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NKPLSPIKLTPTSVLDYFGTGSVQR 25 2 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 NKPLS(1)PIKLTPTSVLDYFGTGSVQR;NKPLS(0.993)PIKLT(0.005)PT(0.001)S(0.001)VLDYFGTGSVQR;NKPLS(1)PIKLTPTSVLDYFGTGSVQR 227.15 2.96E-34 1653080000 1685290 728218 1201150 630741 1871390 1495780 1355960 1205280 1222140 540457 TRUE FALSE 1751826.551 853283.7768 1232452.956 755499.6872 1553291.796 1148407.764 1249676.312 1189125.193 1178155.42 646349.2015 2.710340705 1.320159095 1.906791179 1.168872315 2.403177404 1.776760552 1.933438317 1.839756575 1.822784677 1 19.30195429 0.363879532 2.10678531 0.999995522 1.856541762 0.276197008 0.424665436 15.54650137 49.59223263 0.369701051 0.100827235 2.311423542 -0.363879532 0.85654624 NKPRPPPLSPLGGPVPSALPNGPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKPRPPPLSPLGGPVPSALPNGPPSPR 27 2 Q15642 Q15642 TRIP10 Cdc42-interacting protein 4 1 NKPRPPPLSPLGGPVPSALPNGPPS(1)PR;NKPRPPPLSPLGGPVPSALPNGPPS(1)PR 111.79 0.00064519 2265100000 1286930 819070 1158160 928190 1532590 1600430 1259870 1199370 1216960 678810 TRUE FALSE 1337738.99 959738.901 1188342.601 1111783.212 1272080.899 1228754.387 1161118.097 1183294.407 1173161.847 811809.8229 1.64784775 1.182221345 1.463818948 1.369511898 1.56696909 1.513598817 1.43028338 1.457600504 1.445119059 1 19.63078227 0.861696603 16.00099065 1 1.447829999 0.575838398 0.116562188 4052.689465 468882.7564 0.104266839 0.02606671 7.272715573 -0.861696603 0.447829999 NKPRS(ph)PVVELSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKPRSPVVELSK 12 2 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 NKPRS(1)PVVELSK;NKPRS(0.99)PVVELS(0.01)K;NKPRS(1)PVVELSK;NKPRS(1)PVVELSK 150.39 3.55E-05 2767940000 8262410 3727240 5757000 3828820 8856690 8525980 8039880 6422670 6596020 2866670 TRUE FALSE 8588616.327 4367364.476 5907032.149 4586149.168 7351232.997 6545950.357 7409693.197 6336584.614 6358630.529 3428339.101 2.505182852 1.273900961 1.723001131 1.337717487 2.144254924 1.909364904 2.161306971 1.848295757 1.854726251 1 21.70907838 3.223404727 24.9980697 1.887541321 1.679736237 0 0.435498085 782.0745703 1289948.745 0.116859559 0.140172199 1672.648661 -3.223404727 -0.207805084 NKPSDLGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKPSDLGTK 9 1 P31948;P31948-2;P31948-3;F5H783 P31948 STIP1 Stress-induced-phosphoprotein 1 0 61.833 0.078965 590620000 690530 386970 563980 370950 873330 683420 711330 597820 623990 344930 FALSE TRUE 717792.6576 453429.0873 578677.7821 444322.8028 724881.6785 524706.0623 655574.0959 589807.2007 601532.7218 412512.4294 1.740050981 1.099188909 1.40281296 1.077113733 1.757235969 1.271976369 1.589222649 1.429792556 1.458217205 1 18.65407806 -1.005182268 5.637606611 0.999998972 1.417874369 0.248910494 0.221197918 2.61E-06 4.60E-07 0.194947814 0.045949527 0.09881383 1.005182268 0.417875397 NKPYPK ddPTM_MDA-MB-175_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 ; 79.027 0.062227 2544500000 2052860 1186280 1585400 1100990 2672240 2243180 2305390 1859420 1824960 1021900 FALSE TRUE 2133908.498 1390014.362 1626716.826 1318762.536 2218013.599 1722235.441 2124687.508 1834497.516 1759280.046 1222121.74 1.746068684 1.137377985 1.331059561 1.079076244 1.814887607 1.40921758 1.738523618 1.501075921 1.439529295 1 20.22095657 3.248985492 24.99925019 1.521790703 1.310656165 0.069928764 0.264323373 421.4286266 1010595.883 0.068050745 0.091162149 1774.130214 -3.248985492 -0.211134538 NKQDDDLNCEPLS(ph)PHNITPEPVSK ddPTM_MDA-MB-175_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 301.85 1.76E-62 2468690000 2623260 1264280 1773040 1301220 2683560 2490670 2283150 1890830 2149830 910060 TRUE FALSE 2726828.33 1481410.255 1819246.879 1558597.432 2227409.43 1912249.639 2104190.737 1865486.517 2072458.038 1088368.833 2.505426697 1.361128884 1.671535259 1.432048939 2.04655753 1.756986769 1.933343434 1.714020523 1.904187235 1 20.05373612 -1.068365869 5.740569518 0.999996457 1.789695268 0.384906192 0.307299731 1.28E-05 2.07E-06 0.272815726 0.064302995 0.085434667 1.068365869 0.789698811 NKQPT(ph)PVNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKQPTPVNIR 10 1 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3;A0A087X1B7 X6R700 CHTOP Chromatin target of PRMT1 protein 1 NKQPT(1)PVNIR 115.12 0.0020453 124280000 198940 103570 137100 105920 189940 217580 171960 153980 139540 89261 TRUE FALSE 206794.3048 121357.3418 140672.9386 126870.6599 157654.0666 167050.3425 158481.3259 151916.15 134517.9827 106749.9839 1.937183475 1.136837097 1.317779483 1.188484112 1.476853305 1.564874638 1.484602808 1.423102321 1.260121807 1 16.70387633 0.940079956 2.640267672 1.000870071 1.426660281 0.298689374 0.209402689 0.407466939 6.534522106 0.191432034 0.051150778 8.711239533 -0.940079956 0.42579021 NKS(ph)EDEDEDEGDATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKSEDEDEDEGDATR 15 1 Q9BZI1 Q9BZI1 IRX2 Iroquois-class homeodomain protein IRX-2 1 NKS(1)EDEDEDEGDATR;NKS(1)EDEDEDEGDATR 234.23 7.24E-18 487220000 611060 269505 406040 272170 591210 677180 522380 440540 457900 219496 TRUE FALSE 635185.1206 315790.3873 416621.736 326004.4137 490716.3354 519915.2078 481434.4906 434635.2819 441420.2684 262502.0387 2.419734048 1.203001656 1.587118096 1.241911931 1.869381045 1.980613981 1.834021911 1.655740596 1.681587963 1 18.0019691 0.313615879 1.966523523 0.999990902 1.702423453 0.293865322 0.333760193 16.80739906 46.21770108 0.307630124 0.084722942 2.05880815 -0.313615879 0.702432551 NKS(ph)NEDQSMGNWQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NKSNEDQSMGNWQIK 15 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 NKS(0.999)NEDQS(0.001)MGNWQIK;NKS(1)NEDQSMGNWQIK;NKS(0.978)NEDQS(0.022)MGNWQIK;NKS(1)NEDQSMGNWQIK 240.46 4.64E-18 1601990000 2390120 1068798 1530950 1125441 2009400 2174010 2212100 1549800 1666950 794283 TRUE FALSE 2484483.783 1252355.742 1570847.815 1348049.871 1667842.906 1669129.125 2038709.822 1529027.466 1606956.795 949907.5464 2.615500627 1.318397508 1.653684951 1.419137974 1.755794985 1.757149031 2.146219208 1.609659247 1.691698104 1 19.85742758 0.525376101 1.659390594 1.000346252 1.762298447 0.308345783 0.349731925 3.238056821 9.952573515 0.314042458 0.089168101 3.352556461 -0.525376101 0.761952196 NKS(ph)NEDQSMGNWQIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 75.533 0.015253 821450000 550570 252721 364950 202624 563320 502000 362700 359980 393270 184928 TRUE FALSE 572306.9287 296123.8659 374460.8968 242702.4224 467567.0676 385418.1079 334270.6263 355155.0569 379116.2895 221161.1009 2.587737745 1.338950948 1.693158947 1.097401041 2.114146953 1.742702972 1.511434989 1.605865839 1.714208728 1 17.75473813 -2.624166248 0.217428495 1.88E-17 1.800869662 0.251138672 0.382551077 69.19210558 1.741948563 34.51049953 0.77385445 0.002375931 2.624166248 1.800869662 NKS(ph)TSSAMSGSHQDLSVIQPIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKSTSSAMSGSHQDLSVIQPIVK 23 1 J3KPG1;Q96QF0-5;Q96QF0-7;Q96QF0-6;Q96QF0-3;Q96QF0-4;Q96QF0-2;Q96QF0;H0YI02;Q96QF0-8 J3KPG1 RAB3IP Rab-3A-interacting protein 1 NKS(0.167)T(0.167)S(0.167)S(0.167)AMS(0.167)GS(0.167)HQDLSVIQPIVK 104.44 0.0009884 471750000 96550 144500 195200 127960 324970 262940 229130 237880 246850 115640 TRUE FALSE 100361.8686 169316.7509 200287.0724 153270.1061 269731.7155 201876.1699 211170.1919 234691.6077 237965.9167 138297.4439 0.725695759 1.224294145 1.448234086 1.1082642 1.95037383 1.459724519 1.526927656 1.697006112 1.720681959 1 17.07741497 4.987815726 0.861028603 1.566628681 6.63E-11 0.433745466 0.265484662 2.804911749 1.210555122 0.08264196 4.587213995 97233.45678 -4.987815726 -1.566628681 NKSNEDQSMGNWQIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 112.34 0.00041999 335930000 263850 169850 303940 106970 483440 351580 165530 249210 340580 213060 FALSE TRUE 274267.0017 199020.4163 311860.9261 128128.3467 401265.0415 269930.8732 152555.3261 245869.7476 328322.5923 254805.0277 1.076379867 0.781069424 1.22391983 0.502848581 1.57479248 1.05936243 0.598713956 0.964932873 1.28852478 1 17.95903422 1.28591496 20.45530666 1.144260265 0.963546163 0.049879391 0.297253508 52.85120897 22829.15544 0.190294896 0.069497332 19.3159005 -1.28591496 -0.180714102 NKTEDLEATSEHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NKTEDLEATSEHFK 14 1 C9JXZ5;Q9BV40 C9JXZ5 VAMP8 Vesicle-associated membrane protein 8 0 ;; 204.43 8.21E-09 991080000 1088690 758980 1203620 903960 1988740 1676700 1536680 1307960 1365020 642222 FALSE TRUE 1131672.322 889328.911 1234987.326 1082760.59 1650694.685 1287311.836 1416231.006 1290428.936 1315893.197 768053.1048 1.473429786 1.157900288 1.60794523 1.409747039 2.149193428 1.676071391 1.843923288 1.680129834 1.713284132 1 19.55084654 3.787942837 2.009286188 1.712188218 1.338909198 0.123808395 0.293861658 0.492433324 3.854772114 0.076928689 0.168437204 6136.812259 -3.787942837 -0.37327902 NKTHTLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKTHTLCR 8 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 85.666 0.0099625 119280000 247190 255120 281420 181230 452340 421630 279050 282720 281720 348150 FALSE TRUE 256949.2521 298934.8754 288754.0364 217076.7531 375451.4084 323712.8224 257177.3318 278930.6008 271580.9522 416363.3268 0.617127484 0.717966392 0.693514577 0.521363768 0.901739861 0.777476789 0.617675274 0.669921155 0.652269148 1 18.66748348 -1.918101131 2.571679956 1.192871934 0.68668168 0.486661734 0.096909244 24595833.38 13507805.98 28585029.53 0.023022546 0.012075326 1.918101131 -0.506190253 NKYNTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NKYNTPK 7 1 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 72.547 0.046793 1563000000 457450 270390 375790 288170 611810 525730 462180 441070 474680 277030 FALSE TRUE 475510.4792 316827.3792 385583.3961 345169.1659 507814.7547 403637.175 425953.1239 435158.1781 457596.3595 331308.7244 1.435248891 0.95629048 1.163819023 1.041835425 1.532753946 1.218311337 1.285668298 1.313452215 1.381178115 1 18.33781667 3.280048399 24.99998275 1.301116361 1.136549412 0.134432071 0.170121667 240.8308444 145119.8644 0.043347016 0.05869157 1905.673081 -3.280048399 -0.16456695 NKYQELINDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NKYQELINDIAR 12 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 154.47 6.52E-05 3564300000 3413300 2763940 3099400 2336800 5061800 4378600 3384300 3431200 3543000 2579700 FALSE TRUE 3548059.72 3238625.195 3180172.91 2799012.065 4201397.044 3361736.508 3119029.723 3385210.376 3415488.122 3085142.824 1.150047153 1.049748871 1.030802492 0.907255263 1.36181606 1.089653446 1.0109839 1.097262127 1.107076177 1 21.55690585 4.754400204 21.31426003 1.076851576 1.15004759 0.040273607 0.111607108 1486.262588 1999689.434 0.026210809 0.524012987 56806.78408 -4.754400204 0.073196014 NLAPDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLAPDEKR 8 1 O95232;J3KPP4;D6RDI2;C9JL41;O95232-2;E7EN55 O95232 LUC7L3 Luc7-like protein 3 0 83.948 0.02854 185500000 163240 180780 183440 129720 240070 237820 193770 175060 182350 125440 FALSE TRUE 169684.8412 211827.5587 188220.5971 155378.2288 199262.9872 182589.9092 178581.8011 172713.607 175787.2591 150017.5663 1.131099813 1.412018365 1.254657049 1.035733565 1.328264363 1.217123526 1.190405934 1.151289221 1.171777835 1 17.19477192 -1.441241762 0.188007656 0.778027319 1.2833135 0.328509572 0.096443404 29.29849304 1.00620028 3.369339027 0.32215127 0.03620414 1.441241762 0.505286181 NLAPHHAS(ph)PDPPAPPASASDPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLAPHHASPDPPAPPASASDPHR 23 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR;NLAPHHAS(1)PDPPAPPASASDPHR 128.88 6.79E-05 1407750000 455628 516390 530578 552854 622580 755450 569950 581610 560517 417711 TRUE FALSE 473616.5453 605075.9655 544405.2986 662206.8711 516754.074 580008.1865 525275.8297 573814.4693 540344.1027 499553.4729 0.948079777 1.211233628 1.089783833 1.325597573 1.034431952 1.161053256 1.051490698 1.14865475 1.081654181 1 18.93027959 0.362023102 0.640480536 0.996094512 1.131926502 0.116890892 0.098230716 4.378308185 2.706121105 0.127023091 0.035812573 2.301564245 -0.362023102 0.13583199 NLDDGIDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 237.51 8.27E-12 6538800000 3526990 4571620 4655740 4727200 5108420 6351960 5396750 5014420 4648810 3844170 FALSE TRUE 3666238.289 5356760.173 4777072.409 5662226.051 4240092.593 4876813.555 4973738.633 4947209.902 4481500.236 4597361.51 0.797465738 1.165181411 1.039090008 1.231625148 0.92228827 1.06078531 1.081868072 1.076097647 0.974798311 1 22.13237469 4.752394162 24.58117031 1.065354042 0.79746551 0.465904635 0.084646152 1584.265355 2815058.752 0.018868969 0.379655627 56544.99396 -4.752394162 -0.267888532 NLDDGIDDERLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLDDGIDDERLR 12 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ;;; 224.43 1.83E-11 8557700000 6528060 7627230 7455900 5786090 10041200 10490600 6985200 7751800 7815300 7178520 FALSE TRUE 6785792.85 8937147.421 7650206.879 6930561.332 8334400.411 8054317.137 6437681.772 7647899.8 7534028.88 8585013.553 0.790423079 1.041017276 0.8911118 0.807286009 0.970808067 0.938183392 0.749874387 0.890843067 0.877579148 1 23.03338898 NLDDTIDDEKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLDDTIDDEKLR 12 1 B1ANR0;Q13310-2;Q13310;Q13310-3;H0Y5F5;H0YEU6;P0CB38 B1ANR0;P0CB38 PABPC4;PABPC4L Polyadenylate-binding protein;Polyadenylate-binding protein 4;Polyadenylate-binding protein 4-like 0 ; 196.58 1.87E-07 403660000 335620 225817 271890 221318 379170 396470 385330 307630 350040 186812 FALSE TRUE 348870.5368 264599.3131 278975.6768 265094.0398 314718.8188 304395.8511 355126.8277 303506.723 337442.1288 223414.2347 1.561541221 1.184344021 1.248692489 1.186558413 1.408678455 1.362472949 1.58954432 1.35849322 1.510387775 1 17.76936158 3.202826451 24.71477026 1.401443391 1.284031723 0.025578196 0.17593251 363.9034276 251684.9276 0.047523648 0.056803568 1595.241543 -3.202826451 -0.117411668 NLDIERPTYTNLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 272.74 4.97E-33 1.53675E+11 31411744 35382996 34445973 34968493 44304044 48816824 39157441 37447018 33510208 27740788 FALSE TRUE 32651903.91 41459750.32 35343663.35 41885156.54 36773258.43 37479856.45 36088178.46 36945101.97 32304182.16 33176064.28 0.984200646 1.24968863 1.065336233 1.262511315 1.108427393 1.129725821 1.087777566 1.113607137 0.973719543 1 24.98363941 1.31226653 3.336110245 0.984005831 1.132057379 0.331205258 0.077841849 0.247334969 4.55434314 0.05953193 0.018328493 20.5242138 -1.31226653 0.148051548 NLDKDMYGDDLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLDKDMYGDDLEAR 14 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 182.57 1.37E-06 133320000 264720 215140 240330 191710 355000 326360 305040 252500 267900 170870 FALSE TRUE 275171.35 252088.6214 246593.1972 229629.6658 294657.2268 250567.836 281130.1677 249115.6505 258258.3313 204348.705 1.34657741 1.233619863 1.206727477 1.123714808 1.441933419 1.226177754 1.375737457 1.219071344 1.26381193 1 17.64067358 -0.824931832 4.975499623 0.999999618 1.26821034 0.458328043 0.088283359 3.54E-07 8.38E-08 0.081085566 0.019112024 0.149647053 0.824931832 0.268210722 NLDSAT(ph)SPQNGDQQNGYGDLFPGHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLDSATSPQNGDQQNGYGDLFPGHKK 26 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 NLDS(0.017)AT(0.597)S(0.386)PQNGDQQNGYGDLFPGHKK 164.66 1.03E-11 64941000 99032 71263 90769 64351 120940 118250 96257 93852 99999 61408 TRUE FALSE 102941.8598 83501.8659 93134.51471 77079.43573 100382.662 90788.2296 88712.12482 92594.06745 96400.05552 73439.72187 1.401719086 1.137012284 1.268176299 1.049560562 1.366871489 1.236227852 1.207958344 1.26081724 1.312641893 1 16.16427297 -1.178404137 4.343802348 0.999934446 1.242910674 0.365538394 0.098118752 6571450.48 1782730.724 4087.591012 0.021027679 0.066312571 1.178404137 0.242976227 NLDSLEEDLDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLDSLEEDLDFLR 13 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;; 253.76 2.01E-23 452600000 213608 234047 254090 262701 275961 327758 322854 282562 246362 205024 FALSE TRUE 222041.4088 274242.7516 260711.7941 314662.4737 229053.2478 251641.1717 297547.8599 278774.7186 237495.4797 245194.5274 0.90557245 1.118470117 1.063285535 1.283317687 0.934169495 1.026291959 1.213517541 1.136953265 0.968600247 1 17.90356725 4.743234435 24.01254542 1.094221816 0.905572316 0.19998512 0.104043007 419.0676009 2152896.716 0.024194338 0.192708642 55364.88915 -4.743234435 -0.1886495 NLDSLEEDLDFLRDQFTTTEVNMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NLDSLEEDLDFLRDQFTTTEVNMAR 25 1 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 ;;;; 380.52 1.44E-120 1931841000 401659 528871 526647 383038 589259 651942 460468 573757 539443 512218 FALSE TRUE 417516.8075 619700.4802 540371.8535 458801.7731 489096.9657 500538.3508 424375.315 566066.7259 520028.5518 612577.3101 0.681574065 1.011628198 0.882128418 0.748969584 0.798424881 0.817102336 0.692770215 0.924073936 0.848919056 1 19.2245324 0.854045536 1.256826374 0.996824366 0.818444909 0.250913219 0.095319039 0.917035349 2.785837405 0.088316548 0.026957307 7.145712458 -0.854045536 -0.178379457 NLDSTTVAVHGEEIYCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLDSTTVAVHGEEIYCK 17 0 P21291;E9PS42;E9PND2 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 270.42 1.39E-35 1945430000 2356600 2144800 2095150 2403900 2888100 3275700 2682800 2604100 2565900 1775980 FALSE TRUE 2449640.388 2513152.716 2149751.33 2879384.245 2397181.794 2514968.319 2472515.126 2569196.299 2473553.76 2123949.278 1.153342226 1.183245166 1.012148149 1.355674674 1.128643616 1.18409999 1.164112134 1.209631664 1.164601145 1 21.01831788 -0.692737895 6.659968152 1.000017153 1.175015425 0.297573034 0.07959866 1.05E-09 0 0.070779285 0.016682837 0.202890684 0.692737895 0.174998272 NLEAQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NLEAQHK 7 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 ;;;;; 124.83 0.0041079 2340910000 3677740 2675790 3339630 2703600 4505810 4638550 4092370 3491420 3566020 2078960 FALSE TRUE 3822940.015 3135336.118 3426663.501 3238364.011 3739914.026 3561317.06 3771599.346 3444623.226 3437679.637 2486292.408 1.537606761 1.261048824 1.378222244 1.302487189 1.504213267 1.43238062 1.516957271 1.38544574 1.382652992 1 21.24556455 0.503427639 2.091865409 1.000020678 1.411865772 0.67942733 0.085001811 2.835840472 11.25314853 0.07967253 0.021772691 3.187334469 -0.503427639 0.411845094 NLEELEEKST(ph)TPPPAEPVSLPQEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLEELEEKSTTPPPAEPVSLPQEPPK 26 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 NLEELEEKS(0.1)T(0.527)T(0.373)PPPAEPVSLPQEPPK 124.28 0.00019532 94554000 137120 64437 103720 36289 202540 136550 73986 92216 123210 84816 TRUE FALSE 142533.6035 75503.5535 106423.0284 43466.85589 168112.3231 104838.3319 68186.78399 90979.99535 118775.6962 101434.0713 1.405184685 0.744360869 1.049184234 0.42852323 1.657355571 1.033561313 0.672227617 0.896937234 1.170964496 1 16.6301828 4.756812216 23.61775439 0.952313319 1.40518552 0.154956697 0.310204284 3363.688445 4352494.771 0.071612952 2.159545714 57123.15896 -4.756812216 0.452872202 NLEELEEKSTT(ph)PPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 NLEELEEKS(0.02)T(0.109)T(0.871)PPPAEPVSLPQEPPKPR;NLEELEEKS(0.028)T(0.149)T(0.824)PPPAEPVSLPQEPPKPR 190.97 2.12E-16 2275500000 5700800 3035000 4565800 1565760 8034600 5880200 3023600 4047300 5282000 3937700 TRUE FALSE 5925871.986 3556237.641 4684788.499 1875462.655 6668881.562 4514612.665 2786602.331 3993052.564 5091901.852 4709216.923 1.258356131 0.755165391 0.994812636 0.398253613 1.416133865 0.958675877 0.591733695 0.847922835 1.081262965 1 22.16705575 NLEQILNGGES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NLEQILNGGESPK 13 0 Q13033-2;Q13033;G3V340;G3V3G7 Q13033-2 STRN3 Striatin-3 1 NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK;NLEQILNGGES(1)PK 295.22 1.21E-40 1453982000 4932070 1554090 1944870 1765960 3038690 4396870 3441850 2388590 2403130 973960 TRUE FALSE 5126791.932 1820992.868 1995554.91 2115261.617 2522174.559 3375763.578 3172068.803 2356574.858 2316641.821 1164788.814 4.401477649 1.563367407 1.713233236 1.816004404 2.165349227 2.898176507 2.723299506 2.023177789 1.988894289 1 20.15163698 4.746362547 24.63829223 2.070887176 4.401479041 0.65529348 0.522037294 506.8068378 1600436.565 0.127217221 1.363603214 55765.10789 -4.746362547 2.330591864 NLEQILNGGES(ph)PKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLEQILNGGESPKQK 15 1 Q13033-2;Q13033;G3V340 Q13033-2 STRN3 Striatin-3 1 NLEQILNGGES(1)PKQK 138.04 7.89E-06 252690000 142160 42309 71098 34773 113490 119140 76061 72462 93189 45738 TRUE FALSE 147772.5866 49575.24163 72950.87229 41650.99561 94199.01034 91471.54058 70099.14007 71490.76541 89835.14609 54699.48539 2.701535225 0.906320074 1.333666519 0.761451325 1.722118767 1.672255962 1.281531985 1.306973272 1.642339877 1 15.73923964 4.749022558 24.84439499 1.310564622 2.701536075 0.647239158 0.311937718 864.8351741 2053715.268 0.073249156 1.042819435 56107.71185 -4.749022558 1.390971453 NLETFCEETRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NLETFCEETRR 11 1 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;; 210.15 2.20E-08 869660000 526290 702510 657640 664350 768960 932700 601470 700840 638050 647280 FALSE TRUE 547068.3356 823160.6277 674778.6387 795756.4471 638252.4539 716094.5602 554325.2098 691446.3861 615086.7051 774102.1231 0.70671339 1.063374719 0.871692014 1.027973472 0.824506786 0.925064715 0.716087959 0.89322373 0.794580827 1 19.56216438 NLFPNTYLIVGVCSDELTHNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLFPNTYLIVGVCSDELTHNFK 22 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;C9JPY0 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 163.62 1.46E-13 0 25257 26018 25425 22992 30421 42654 32838 31270 34321 26597 FALSE TRUE 26254.16586 30486.38911 26087.59639 27539.74898 25250.04929 32748.25493 30264.07175 30850.8768 33085.79391 31808.17292 0.825390566 0.958445151 0.820153878 0.865807321 0.793822687 1.029554731 0.951455836 0.969904083 1.040166438 1 14.95710988 2.732095268 24.99915273 0.990288181 0.857514731 0.697288994 0.047736444 313.1619808 1210880.596 0.015028405 0.014485697 539.6289839 -2.732095268 -0.132773451 NLFQQYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLFQQYDR 8 0 Q9UBV8 Q9UBV8 PEF1 Peflin 0 86.833 0.039407 0 50084 48253 46824 47606 65159 72668 62259 45146 50768 49563 FALSE TRUE 52061.35499 56540.07739 48044.27191 57022.32471 54083.29645 55791.95829 57378.9769 44540.89171 48940.8696 59273.92091 0.878318056 0.953877802 0.810546547 0.962013713 0.912429879 0.941256415 0.968030729 0.751441629 0.82567289 1 15.85510987 1.752861285 25 0.834253988 0.917674988 0.092305388 0.073365252 6.841222719 11975.95031 0.031845197 0.017659799 56.60584596 -1.752861285 0.083421 NLGS(ph)INTELQDVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLGSINTELQDVQR 14 0 O75396;A0A087X1A9 O75396 SEC22B Vesicle-trafficking protein SEC22b 1 NLGS(0.998)INT(0.002)ELQDVQR 121.45 0.00012012 104240000 30418 41609 44047 58576 60966 60246 56203 41000 39108 63237 TRUE FALSE 31618.92613 48755.02208 45194.90101 70162.15797 50603.0211 46254.77954 51797.662 40450.46206 37700.51072 75627.0794 0.418090007 0.644676781 0.597602094 0.927738563 0.669112459 0.611616631 0.68490893 0.534867436 0.498505443 1 16.20661528 4.854432964 2.174017322 0.671041742 0.295098506 0.214331112 0.152163063 1.69638198 6.908129672 0.037563251 1.377619516 71520.8989 -4.854432964 -0.375943236 NLGSGS(ph)PKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLGSGSPKPR 10 1 A0A1C7CYX9 A0A1C7CYX9 1 NLGS(0.022)GS(0.978)PKPR;NLGS(0.001)GS(0.999)PKPR 143.31 2.07E-05 1009950000 1349150 719840 969180 750950 1458640 1557370 1187410 1012900 1029350 557160 TRUE FALSE 1402415.484 843466.9204 994437.627 899485.6686 1210700.894 1195694.42 1094337.701 999323.7323 992303.8946 666324.8345 2.104702408 1.265849443 1.492421677 1.349920672 1.816982995 1.794461737 1.642348664 1.499754595 1.489219436 1 19.34586614 0.633152256 1.213577457 1.001016061 1.613876644 0.399160159 0.229926978 1.279993597 2.879696717 0.213463617 0.064985421 4.296870412 -0.633152256 0.612860583 NLHNPIVQS(ph)LEDLEDQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLHNPIVQSLEDLEDQKR 18 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 NLHNPIVQS(1)LEDLEDQKR 80.412 0.0040657 66121000 93893 79155 100680 87295 113940 143210 122460 116040 99536 72871 TRUE FALSE 97599.96814 92749.25551 103303.8035 104561.6905 94572.5195 109951.6479 112861.2652 114484.6736 95953.7188 87148.67725 1.119924837 1.064264639 1.185374314 1.199808118 1.085185943 1.261655958 1.295042779 1.313670812 1.101034713 1 16.41119115 4.144478262 5.278896804 1.204522339 1.092723182 0.079643068 0.095835252 0.335237314 14.71574892 0.024397991 0.055316774 13946.91846 -4.144478262 -0.111799158 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLHTHHFPSPLSNNQEVSAFGEDGEGDDLDLWTVR 35 0 Q9HCN8 Q9HCN8 SDF2L1 Stromal cell-derived factor 2-like protein 1 0 79.163 0.00072835 176100000 16568 35276 21882 30381 36407 38894 27630 33490 33391 33352 FALSE TRUE 17222.11743 41334.37859 22452.2629 36390.27112 30218.55114 29861.45794 25464.2884 33041.12133 32189.26443 39886.68584 0.431776094 1.036295138 0.562901189 0.912341308 0.757609977 0.748657285 0.638415749 0.828374698 0.807017774 1 15.28361964 -5 0.209608717 2.188106612 0.719219654 0.200087009 0.160989662 234.3898532 2.336203738 116.7375298 0.309020081 1.00E-05 5 -1.468886958 NLIQHNNS(ph)TQTDIFYTDRLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLIQHNNSTQTDIFYTDRLEDR 22 1 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLIQHNNS(0.814)T(0.078)QT(0.108)DIFYTDRLEDR 125.83 1.25E-05 160700000 21441 52419 42659 61972 64260 85080 32730 59469 37227 111940 TRUE FALSE 22287.50724 61421.55549 43770.72858 74229.87663 53337.10815 65321.4594 30164.53708 58671.91533 35887.20754 133872.4998 0.166483089 0.458806369 0.326958327 0.55448189 0.398417212 0.487937848 0.225322879 0.438267123 0.268070049 1 17.03050011 -1.518349199 3.27070351 1.016468899 0.378735781 0.723207549 0.1169055 65869917.14 83048219.69 9711876.514 0.026814933 0.030314527 1.518349199 -0.637733118 NLKPIKPMQFLGDEETVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NLKPIKPMQFLGDEETVR 18 2 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;; 242.98 2.58E-24 8219030000 5298270 3404450 4441880 3294310 5739910 5863030 5719920 4512210 4626450 2634000 FALSE TRUE 5507449.791 3989137.805 4557639.042 3945914.685 4764242.148 4501430.138 5271577.724 4451731.205 4459944.968 3150081.869 1.748351319 1.266360041 1.446831934 1.252638772 1.512418517 1.428988301 1.673473244 1.413211272 1.415818748 1 21.58695789 0.598817875 2.182215076 1.000078788 1.460817421 0.474853793 0.146610582 2.490917888 12.5256092 0.132420137 0.036001194 3.970250187 -0.598817875 0.460738633 NLKPIKPMQFLGDEETVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLKPIKPMQFLGDEETVRK 19 3 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ; 241.52 1.00E-24 5325800000 4359600 1989930 3098940 1999910 4821400 3923700 3780700 3292000 3243100 1588160 FALSE TRUE 4531720.374 2331684.998 3179700.922 2395486.229 4001860.15 3012480.139 3484358.855 3247876.125 3126381.465 1899329.545 2.385957922 1.227635828 1.674117549 1.261227276 2.106985679 1.586075543 1.834520431 1.7100119 1.64604477 1 20.85705881 0.687717767 3.320036776 1.000009449 1.703462254 0.299066883 0.329015177 5.000366372 51.86195226 0.287510681 0.07445839 4.872117646 -0.687717767 0.703452805 NLLDDVEEFHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLLDDVEEFHER 12 0 P29375;P29375-2;E7EV89 P29375 KDM5A Lysine-specific demethylase 5A 0 140.82 6.00E-05 18479000 27092 51501 48829 47639 44679 56992 41729 44658 44310 64764 FALSE TRUE 28161.61308 60345.89613 50101.52385 57061.85201 37084.47954 43756.47172 38458.17194 44059.43256 42715.29176 77453.26582 0.363594908 0.779126554 0.646861347 0.736726223 0.478798139 0.564940306 0.496533897 0.568851837 0.55149762 1 16.24103845 -1.319970375 3.433650534 1.001926968 0.581504875 0.546222731 0.115761772 41803208.4 59236332.88 818614.9098 0.02701374 0.047866274 1.319970375 -0.420422093 NLLDEELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLLDEELQR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 128.86 0.00094353 185546000 313940 413700 418120 415860 492360 561880 439070 450950 415580 432450 FALSE TRUE 326334.5936 484749.7569 429016.5507 498115.8668 408668.8231 431391.8854 404654.5461 444905.7529 400623.357 517180.2977 0.630988062 0.937293549 0.829529958 0.963137747 0.790186372 0.834122814 0.78242452 0.86025271 0.774629967 1 18.98030779 -1.605495597 2.763712218 1.013769874 0.830173224 0.266164888 0.087586408 19987415.83 19354051.74 1996485.847 0.019160445 0.024803011 1.605495597 -0.183596649 NLLEDDS(ph)DEEEDFFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR 290.92 1.66E-45 2368857000 878201 980395 998544 1036414 1157929 1336111 1074713 1033114 956300 890307 TRUE FALSE 912873.0536 1148770.215 1024566.877 1241413.596 961104.6422 1025819.469 990474.1868 1019266.797 921882.9498 1064745.611 0.857362589 1.078915192 0.962264476 1.165925065 0.902661286 0.9634409 0.930244912 0.957286686 0.865824607 1 20.02207735 NLLHVTDTGVGMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NLLHVTDTGVGMTR 14 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;; 197.47 1.77E-08 3221040000 2195130 2803170 2699790 2690450 3667530 3976300 2816750 2948810 2762760 2255750 FALSE TRUE 2281795.427 3284592.642 2770148.745 3222612.98 3044124.561 3052864.586 2595965.775 2909286.025 2663328.807 2697721.024 0.845823348 1.21754348 1.026847743 1.194568657 1.128405989 1.131645771 0.962281034 1.078423603 0.987251381 1 21.36330973 2.249496066 24.9863644 1.018647678 1.100085039 0.133427385 0.101300712 419.1852252 957793.5421 0.033104158 0.027444093 177.621718 -2.249496066 0.081437361 NLLQQS(ph)WEDMKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLLQQSWEDMKR 12 1 Q8TDM6-4;Q8TDM6;Q8TDM6-2;R4GMQ2 Q8TDM6-4 DLG5 Disks large homolog 5 1 NLLQQS(1)WEDMKR;NLLQQS(1)WEDMKR 168.41 2.85E-05 293390000 382901 270066 272414 239317 434796 448834 388486 341296 344062 212438 TRUE FALSE 398018.2271 316447.7347 279513.3326 286653.1883 360889.5312 344599.1056 358035.4522 336721.4854 331679.2758 254061.1587 1.566623679 1.245557315 1.100181287 1.128284189 1.420482899 1.356362804 1.409249072 1.325356017 1.305509577 1 17.95481631 0.898893268 15.94893513 0.999999999 1.312939256 0.346142868 0.1308207 1296.039058 204446.3849 0.130400342 0.032602981 7.923065895 -0.898893268 0.312939256 NLLSVAYK ddPTM_MDA-MB-175_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 ; 152.47 0.0010624 1476840000 2145000 1429890 1868670 1453040 3522800 2765800 2546500 1987020 2038500 1804550 FALSE TRUE 2229686.256 1675462.484 1917369.075 1740446.975 2923995.714 2123484.866 2346898.676 1960387.247 1965134.783 2158117.022 1.033162814 0.776353862 0.88844537 0.806465524 1.354882837 0.983952605 1.08747517 0.908378566 0.910578418 1 21.04134167 5.075927598 20.85364993 0.969306091 3.479963443 0.015334807 0.155318115 3975.946273 1099296.346 0.036542294 3121.323174 119104.343 -5.075927598 2.510657352 NLNHVSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLNHVSYGR 9 0 P00367;P00367-2;P00367-3;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 69.954 0.053781 68021000 9578.1 43968 36505 46771 25214 51259 26781 32953 30853 41280 FALSE TRUE 9956.250784 51519.16198 37456.35029 56022.1642 20928.13329 39354.87409 24681.83524 32511.31894 29742.60656 49368.02565 0.201674073 1.043573473 0.758716797 1.134786402 0.423920807 0.797173344 0.499955891 0.658550114 0.602467005 1 15.59128933 3.206823196 24.99996863 0.642713099 0.801325713 0.040034195 0.274392101 529.6764842 417231.4414 0.074014498 0.088471502 1609.990066 -3.206823196 0.158612614 NLNIINTHAYNQPEDLVYS(ph)QPEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLNIINTHAYNQPEDLVYSQPEMR 24 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 NLNIINTHAYNQPEDLVYS(1)QPEMR;NLNIINTHAYNQPEDLVYS(1)QPEMR 217.83 7.85E-33 304520000 65345 82517 77819 67260 109091 126407 74966 82476 83628 86655 TRUE FALSE 67924.87106 96688.65286 79847.02707 80563.82725 90547.75079 97050.88997 69089.96903 81370.54412 80618.24462 103633.3881 0.655434241 0.932987472 0.770475891 0.777392583 0.873731453 0.936482843 0.666676737 0.785176916 0.777917678 1 16.66112935 4.770162225 23.07198062 0.820104842 0.655433418 0.226578813 0.096099784 7227.259706 5276281.362 0.022136441 2.606333799 58906.36513 -4.770162225 -0.164671424 NLNNSNLFS(ph)PVNR ddPTM_MDA-MB-175_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;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR 287.44 4.09E-33 5939070000 2541780 2619560 2808310 2757740 3164610 4077610 3223920 3127430 2880400 2227540 TRUE FALSE 2642131.437 3069449.053 2881496.866 3303212.741 2626690.723 3130646.874 2971220.726 3085511.916 2776734.967 2663983.814 0.991797106 1.152202591 1.081649539 1.239952256 0.986001007 1.175174886 1.115329872 1.158232231 1.042324263 1 21.34515389 -0.297685373 8.11304847 0.999977322 1.111987414 0.135016744 0.077605605 0 0 0.067497832 0.015909391 0.503865505 0.297685373 0.112010092 NLPFDFTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLPFDFTWK 9 0 A0A087X0X3;P52272-2;P52272;M0R2I7;M0QY96 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 153.24 0.00018273 542860000 905190 617830 800550 691020 1104150 1058410 842630 887610 903270 636620 FALSE TRUE 940927.6002 723937.4964 821412.9907 827701.6935 916466.9774 812610.3179 776582.4588 875713.0398 870761.4891 761353.5002 1.235861659 0.950855938 1.078885157 1.087145056 1.203733847 1.067323284 1.020002481 1.150205574 1.143701958 1 19.53820693 3.468744938 24.9219619 1.104942538 1.076141175 0 0.086121001 930.6187284 2768851.448 0.022938659 0.031117928 2942.692874 -3.468744938 -0.028801363 NLPIMS(ph)TASVEIDDALYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLPIMSTASVEIDDALYSR 19 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NLPIMS(0.384)T(0.384)AS(0.231)VEIDDALYSR 62.765 0.04593 11114000 7423.6 6221.4 8156.8 4376.6 11204 10083 8781.9 8583.5 10918 5233.7 TRUE FALSE 7716.68946 7289.877054 8369.372909 5242.278417 9299.548082 7741.376059 8093.551731 8468.452222 10525.06331 6259.14331 1.232866716 1.164676489 1.337143519 0.837539286 1.485754139 1.236810802 1.293076597 1.352973051 1.681550141 1 12.61174949 NLPIMSTAS(ph)VEIDDALYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NLPIMSTASVEIDDALYSR 19 0 A0AVT1;A0AVT1-4;A0AVT1-3 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 1 NLPIMSTAS(1)VEIDDALYSR;NLPIMS(0.008)T(0.209)AS(0.783)VEIDDALYSR;NLPIMST(0.005)AS(0.995)VEIDDALYSR;NLPIMST(0.002)AS(0.998)VEIDDALYSR;NLPIMS(0.051)T(0.168)AS(0.781)VEIDDALYSR 226.72 1.51E-19 420140000 104540 127322 160876 114899 181805 172084 151543 141905 166324 131669 TRUE FALSE 108667.3199 149188.5631 165068.5607 137625.6793 150901.851 132120.099 139664.6637 140002.9956 160338.0317 157467.0196 0.690095743 0.947427363 1.048273862 0.873996851 0.95830766 0.839033464 0.886945495 0.889094084 1.018232466 1 17.26469017 7.999999976 0.017311601 1.650019174 8.84E-14 0.168268132 0.090311761 9947.898857 13.28339595 488.6236029 816.2444286 99999994.37 -7.999999976 -1.650019174 NLPIYSEEIVEMYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLPIYSEEIVEMYK 14 0 P35579;Q5BKV1 P35579 MYH9 Myosin-9 0 126.76 0.00019424 24620000 16337 11335 13355 12015 19183 20159 19510 15188 15900 8736.2 FALSE TRUE 16981.99737 13281.69808 13703.04227 14391.53114 15922.28051 15477.37776 17980.75522 14984.4297 15327.76211 10447.89113 1.625399535 1.271232435 1.311560592 1.377457993 1.523970754 1.481387734 1.72099374 1.43420615 1.467067557 1 13.35092415 0.144212847 2.920862555 0.999999751 1.466004748 0.544948197 0.128322735 227.4183859 770.3543081 0.127642272 0.033430576 1.393839754 -0.144212847 0.466004997 NLPLGWDGKPIPYWLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLPLGWDGKPIPYWLYK 17 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 125.52 4.25E-05 486720000 929150 620640 839310 676640 1276090 1161850 1017320 922940 1037470 625510 FALSE TRUE 965833.5595 727230.0921 861183.1081 810477.3724 1059180.678 892027.9455 937579.8001 910569.4989 1000131.657 748066.7084 1.291106192 0.972146045 1.151211648 1.083429276 1.415890676 1.192444384 1.253337155 1.217230347 1.336955175 1 19.5128074 NLQEEIDALESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLQEEIDALESR 12 0 Q9NQP4;E9PQY2 Q9NQP4 PFDN4 Prefoldin subunit 4 0 203.61 2.86E-07 57299000 101680 117840 109750 107650 131140 154740 125120 126580 111570 107430 FALSE TRUE 105694.4049 138078.1033 112610.1752 128942.8487 108848.8696 118803.9801 115312.7675 124883.4021 107554.6175 128478.8516 0.822659944 1.074714644 0.876488027 1.003611466 0.847212349 0.924696778 0.897523336 0.972015243 0.83713869 1 16.97117138 5.045522853 19.07508237 0.934053059 2.05E-05 0.183367576 0.072168953 335.5041281 77153.10298 0.015109777 18775.24439 111051.097 -5.045522853 -0.934032553 NLQLDYVDLYLIHFPVSVKPGEEVIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLQLDYVDLYLIHFPVSVKPGEEVIPK 27 1 S4R3P0;P52895;H0Y804;Q04828;A6NHU4 S4R3P0 AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C2;Aldo-keto reductase family 1 member C1 0 198.24 3.41E-25 460310000 269320 135710 258760 170460 301340 297690 333840 228650 241900 128910 FALSE TRUE 279952.9616 159017.1368 265503.4982 204176.4792 250118.3344 228556.009 307672.7485 225585.3207 233194.0663 154167.4464 1.815901918 1.031457292 1.722176143 1.324381275 1.622380991 1.482517966 1.995705032 1.463248734 1.512602509 1 17.23413864 0.582598575 2.297095796 1.000092031 1.552951361 0.303178902 0.252085666 4.45089559 23.04433372 0.225261728 0.060785493 3.824710558 -0.582598575 0.55285933 NLQLLMDRVDEMSQDIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLQLLMDRVDEMSQDIVK 18 1 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 181.14 6.84E-14 140290000 249240 194170 232350 176860 357450 332460 272200 245790 297200 176020 FALSE TRUE 259080.1877 227517.1871 238405.2319 211842.3801 296690.7767 255251.2035 250864.2527 242495.5871 286503.8301 210507.7489 1.230739434 1.080801957 1.132524732 1.006340057 1.409405489 1.212550155 1.191710301 1.151955633 1.361013224 1 17.68351382 3.273259912 24.99999814 1.220905502 1.111753363 0.171694882 0.11674639 318.183491 229241.4904 0.030716613 0.041588661 1876.11697 -3.273259912 -0.109152139 NLQPLMRS(ph)PISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLQPLMRSPISR 12 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 NLQPLMRS(0.999)PIS(0.001)R 70.47 0.071586 120500000 175800 106160 117840 109370 167600 207200 97082 130600 128730 128960 TRUE FALSE 182740.7197 124392.1542 120911.0072 131003.0596 139111.4119 159080.9401 89472.45916 128849.5206 124097.0324 154227.2429 1.184879638 0.806551111 0.783979568 0.849415817 0.901989877 1.031471076 0.580133947 0.835452402 0.80463756 1 17.2346981 2.269745104 24.99974241 0.788525758 0.909854353 0.133661524 0.145351514 389.2201771 312025.695 0.049055904 0.041039244 186.099456 -2.269745104 0.121328595 NLQS(ph)PTQFQTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLQSPTQFQTPR 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 NLQS(0.963)PT(0.037)QFQTPR;NLQS(1)PTQFQTPR;NLQS(0.967)PT(0.033)QFQTPR;NLQS(0.998)PT(0.002)QFQTPR 278.53 6.43E-28 876300000 634730 590110 682130 680960 901090 1036280 797430 816180 747850 663930 TRUE FALSE 659789.6305 691456.8021 699906.8682 815651.8555 747923.0437 795619.675 734925.3529 805240.4421 720935.0246 794014.3718 0.830954267 0.870836633 0.881478841 1.027250746 0.941951519 1.002021756 0.925581928 1.014138372 0.907962186 1 19.5988056 3.896323588 5.170368057 0.973796142 0.85631972 0.651996181 0.038182264 0.122035092 4.885604531 0.009039633 0.016863717 7876.324269 -3.896323588 -0.117476421 NLRPGDSQTAAQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLRPGDSQTAAQAR 14 1 Q8WZA9;M0QZP8 Q8WZA9 IRGQ Immunity-related GTPase family Q protein 0 ;;; 231.58 4.45E-13 494628000 303779 306449 341242 298677 449475 494684 362114 361001 357189 279927 FALSE TRUE 315772.4295 359079.2319 350135.0469 357754.4191 373073.4 379801.138 333730.5585 356162.3721 344333.8377 334773.3361 0.943242473 1.072604037 1.0458869 1.068646695 1.114405957 1.134502354 0.996885123 1.063891098 1.028558133 1 18.3528251 4.74185968 24.52726401 1.061607008 0.943242416 0.402082702 0.041953386 242.8084458 1805078.365 0.009980701 0.072047899 55189.90923 -4.74185968 -0.118364592 NLS(ph)FEIK ddPTM_MDA-MB-175_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 144.77 0.002446 4603798000 4518230 2398010 4162980 2425481 6358960 5110370 5210250 3869260 4792500 2021760 TRUE FALSE 4696613.209 2809849.564 4271470.679 2905233.902 5278066.251 3923564.016 4801856.991 3817398.899 4620018.861 2417885.163 1.942446763 1.162110429 1.766614372 1.20155992 2.182926771 1.622725544 1.985973968 1.578817289 1.910768523 1 21.2053143 3.260011043 24.99921464 1.74510785 1.510494487 0.059729009 0.366599759 582.2922664 678623.1081 0.091568449 0.123872393 1819.747131 -3.260011043 -0.234613363 NLS(ph)NEELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;NLS(1)NEELTK;NLS(1)NEELTK 185.37 4.50E-05 4224160000 7896270 4679340 6219230 4341730 8505150 8561150 7665930 6102770 6953490 3482800 TRUE FALSE 8208020.837 5482980.245 6381308.243 5200511.235 7059447.641 6572952.658 7065054.375 6020972.35 6703235.253 4165187.978 1.970624347 1.316382424 1.532057683 1.248565794 1.694868918 1.578068671 1.696215012 1.445546367 1.609347595 1 21.98995018 -1.498563551 5.618468989 0.999162226 1.550087843 0.429142752 0.194999508 0.001888691 0.000168561 0.174260887 0.041016079 0.031727544 1.498563551 0.550925617 NLS(ph)PGAVESDVR ddPTM_MDA-MB-175_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 169.64 4.54E-05 6012680000 848333 948950 971170 950855 1113630 1299990 1070400 986096 929869 848910 TRUE FALSE 881825.8419 1111924.781 996479.488 1138931.281 924335.5704 998087.024 986499.251 972878.996 896403.1963 1015237.661 0.868590553 1.095235946 0.981523368 1.121837107 0.910462255 0.983106776 0.971692924 0.958277094 0.882949117 1 19.95338606 3.189369409 24.99999497 0.95253655 1.019881882 0.169221278 0.071157252 183.7437079 93381.62899 0.019207022 0.022956827 1546.569387 -3.189369409 0.067345332 NLS(ph)SDEATNPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 NLS(0.875)S(0.125)DEATNPISR;NLS(0.927)S(0.073)DEATNPISR 258.96 6.21E-24 412810000 360470 350100 389920 354900 491890 558150 442060 439360 393220 339560 TRUE FALSE 374701.6339 410226.9516 400081.6355 425098.1607 408278.7135 428528.1213 407410.1821 433471.0978 379068.089 406090.2807 0.92270525 1.010186579 0.985203671 1.04680703 1.00538903 1.055253331 1.003250266 1.067425443 0.933457674 1 18.63144097 5.869473655 1.124643845 1.02052036 4.86E-11 0.327908461 0.037088314 18.02712831 2.538893172 0.009815208 38.71759092 740412.352 -5.869473655 -1.02052036 NLS(ph)STTDDEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.498)S(0.498)T(0.004)T(0.001)DDEAPR 206.45 9.44E-08 276980000 257250 318720 324550 315440 467630 480540 379620 395380 375750 332790 TRUE FALSE 267406.4286 373457.6807 333008.0396 377833.0905 388142.4196 368941.8677 349864.3924 390080.5778 362226.8309 397993.8289 0.671885867 0.938350431 0.836716591 0.949344093 0.975247332 0.927003991 0.879069893 0.980117151 0.910131778 1 18.60238654 5.28880168 1.451726359 0.936509229 3.96E-17 0.721644902 0.048018766 2.610950081 1.637330407 0.012174558 5.256486279 194447.1938 -5.28880168 -0.936509229 NLSDIGWPVFEIPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLSDIGWPVFEIPSPR 16 0 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(1)PR;NLSDIGWPVFEIPS(1)PR 118.24 0.00030177 25018000 27281 23060.8 24958 31759 25555 39474 29474 26168 23897 20282.5 TRUE FALSE 28358.07495 27021.31301 25608.42598 38040.83541 21211.17023 30306.76173 27163.75086 25817.26076 23036.95164 24256.46754 1.169093352 1.113983846 1.055735999 1.56827598 0.874454213 1.249430144 1.119856006 1.064345446 0.949724093 1 14.56608185 1.598403284 2.048127223 0.975518824 1.168999512 0.178887906 0.164845176 0.502494667 4.476425636 0.121052558 0.04396453 39.66461871 -1.598403284 0.193480688 NLSDIGWPVFEIPS(ph)PRPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLSDIGWPVFEIPSPRPSK 19 1 F5H4R1;J3KNB8;F5H538;Q9Y6R4-2;Q9Y6R4;F5H1X6 F5H4R1 MAP3K4 Mitogen-activated protein kinase kinase kinase 4 1 NLSDIGWPVFEIPS(1)PRPSK;NLSDIGWPVFEIPS(0.998)PRPS(0.002)K 181.37 1.91E-14 710010000 875600 720880 933240 817830 1168350 1276170 994770 933960 1036410 681440 TRUE FALSE 910169.3641 844685.5323 957561.0011 979594.333 969754.2843 979798.858 916797.3281 921441.7939 999109.8066 814955.121 1.116833726 1.036481041 1.174986176 1.202022428 1.189948083 1.202273392 1.124966645 1.13066569 1.225969113 1 19.63636109 -1.728159714 6.539908215 0.997436756 1.153674005 0.437164448 0.053048056 0.002101582 8.74E-05 0.054446363 0.012641334 0.018699943 1.728159714 0.156237249 NLSEMQDLEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLSEMQDLEEIR 12 0 Q8N139;Q8N139-2 Q8N139 ABCA6 ATP-binding cassette sub-family A member 6 0 60.49 0.091578 506590000 318450 350020 373950 371110 425980 397740 344480 382250 359690 378340 FALSE TRUE 331022.6519 410133.2122 383695.4442 444514.4503 353572.0718 305370.9128 317478.7575 377126.564 346744.8272 452468.4792 0.731592734 0.906434881 0.848004804 0.982420811 0.781429178 0.674899859 0.701659391 0.833486931 0.766340293 1 18.78745777 4.824051257 19.70875045 0.820793734 0.731574289 0.069264813 0.103182811 58887.32501 13561282.77 0.025176212 248.0937353 66688.54728 -4.824051257 -0.089219445 NLSFDIPTGSLRDS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLSFDIPTGSLRDSR 15 1 Q5THJ4-2;Q5THJ4 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 NLSFDIPTGSLRDS(1)R;NLSFDIPT(0.002)GS(0.002)LRDS(0.996)R 115.57 0.00031315 310910000 298570 342490 307090 355020 412420 453900 314230 321320 287330 283910 TRUE FALSE 310357.7741 401309.9933 315093.0177 425241.8964 342316.9957 348488.6039 289599.8315 317013.231 276989.0494 339536.7287 0.91406245 1.181933969 0.92800864 1.252417958 1.008188413 1.026364969 0.852926376 0.933664031 0.815785233 1 18.37320812 2.375443016 4.122621028 0.897975331 1.063833456 0.324475569 0.106961243 0.235049321 7.349502183 0.035654626 0.029372724 237.3793934 -2.375443016 0.165858125 NLSS(ph)TTDDEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.019)S(0.859)T(0.092)T(0.03)DDEAPR;NLS(0.073)S(0.529)T(0.274)T(0.123)DDEAPR 243.92 2.38E-16 916560000 756770 782330 867740 848240 1197500 1276350 1060330 1060980 977080 875600 TRUE FALSE 786647.864 916689.0918 890354.0173 1016019.34 993949.3777 979937.0558 977218.5639 1046759.299 941915.0817 1047157.056 0.751222426 0.875407454 0.850258338 0.970264522 0.949188445 0.935807146 0.933211077 0.999620155 0.899497431 1 19.99804641 6.003754206 0.567691877 0.962411335 5.06E-12 0.760747323 0.035331195 6.348548738 0.513075338 0.015564488 5.531831703 1008681.85 -6.003754206 -0.962411335 NLSSTT(ph)DDEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLSSTTDDEAPR 12 0 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NLS(0.11)S(0.11)T(0.379)T(0.401)DDEAPR 228.17 1.25E-10 603570000 536630 585500 656150 588040 860430 967370 774180 751940 695280 638260 TRUE FALSE 557816.5668 686055.0704 673249.808 704352.5569 714174.4159 742712.9781 713497.7487 741861.4742 670257.0086 763314.8268 0.730781779 0.898783891 0.882008032 0.922754979 0.935622355 0.973010024 0.93473587 0.97189449 0.878087239 1 19.54191869 5.686262749 0.817344274 0.947503642 6.20E-15 0.772186823 0.034186846 4.259976778 0.690652369 0.010627715 5.253610948 485582.1895 -5.686262749 -0.947503642 NLSYQVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLSYQVHR 8 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 0 118.5 0.0018756 95275000 55536 77855 66882 60770 108020 109970 75534 76966 63762 91206 FALSE TRUE 57728.60416 91225.99062 68624.99986 72790.12462 89658.79898 84431.13411 69613.44771 75934.39666 61467.21808 109076.0695 0.529250865 0.836352016 0.629148082 0.667333586 0.821984139 0.774057358 0.638210086 0.696160001 0.563526155 1 16.73497509 -2.292373719 2.362390018 2.51348302 0.691518255 0.485069125 0.097397024 3757405.549 816237.6321 30221812.86 0.022390842 0.005100659 2.292373719 -1.821964765 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 NLTANDPSQEYVAS(1)EGEEDPEVEFLK;NLTANDPSQEYVAS(1)EGEEDPEVEFLK 286.54 1.52E-61 209580000 272170 189377 245220 173423 298510 314860 280500 257450 274070 156972 TRUE FALSE 282915.4818 221901.0266 251610.6347 207725.5518 247769.3768 241738.5367 258513.677 253999.3039 264206.2742 187727.658 1.507052742 1.182036941 1.34029603 1.106526092 1.319834166 1.287708691 1.377067609 1.353020149 1.407391309 1 17.51828169 -2.171725771 2.546715528 0.13863608 1.314648747 0.447994788 0.106442628 5508689.363 1742480.016 28115747.26 0.025155342 0.006734017 2.171725771 1.176012667 NLTEQNSYSNIPHEGKHT(ph)PLYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 NLTEQNS(0.003)Y(0.016)S(0.114)NIPHEGKHT(0.691)PLY(0.176)ER;NLTEQNSYSNIPHEGKHT(1)PLYER 227.59 1.20E-32 405710000 121219 116271 137506 126722 171815 194564 154440 137036 141422 100114 TRUE FALSE 126004.8197 136239.6398 141089.5193 151787.2334 142609.9477 149379.4596 142334.5892 135199.2566 136332.2498 119729.4215 1.052413167 1.137896083 1.178403082 1.267752165 1.191101952 1.24764204 1.188802113 1.12920663 1.138669578 1 16.86941819 0.76890206 1.121630809 1.001279569 1.182788241 0.462757431 0.056789679 0.759191169 1.733962662 0.056733555 0.017780045 5.873568791 -0.76890206 0.181508672 NLVLTGFSHIDLIDLDTIDVSNLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NLVLTGFSHIDLIDLDTIDVSNLNR 25 0 Q9UBT2 Q9UBT2 UBA2 SUMO-activating enzyme subunit 2 0 ;;;;; 267.18 1.53E-45 609685400 213871.4 244719.4 258390.5 247437.8 311475.2 377492 280186.4 258919 276556.4 226854.6 FALSE TRUE 222315.208 286748.0533 265124.3687 296380.2583 258530.7568 289825.2039 258224.6578 255448.6143 266603.1892 271302.4155 0.819436892 1.056931442 0.977228191 1.092435015 0.952924641 1.068273585 0.951796383 0.941564099 0.98267901 1 18.04954237 0.121150024 11.39408365 0.999999999 0.984977949 0.003999251 0.074259591 0 0 0.066940022 0.015777914 1.321752146 -0.121150024 -0.01502205 NLVPGESVYGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLVPGESVYGEKR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 150.26 7.08E-05 335180000 212220 149090 225380 146400 255730 261190 184770 172620 197910 146600 FALSE TRUE 220598.6095 174695.0477 231253.588 175357.483 212261.1059 200532.5809 170287.2446 170306.3112 190787.2578 175323.4632 1.258237805 0.99641568 1.319011065 1.000194041 1.210682826 1.143786332 0.971274703 0.971383454 1.088201512 1 17.41965956 2.247290037 24.29936391 1.000476784 1.150513081 0.341507964 0.099698896 138.3334033 385067.66 0.031986592 0.026363101 176.7217638 -2.247290037 0.150036297 NLVS(ph)PAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLVSPAMR 8 0 Q14686 Q14686 NCOA6 Nuclear receptor coactivator 6 1 NLVS(1)PAMR 71.153 0.051902 93472000 102280 103840 102380 109010 98607 138640 129590 113900 101760 86087 TRUE FALSE 106318.0934 121673.7122 105048.1069 130571.8526 81845.81736 106442.9611 119432.3972 112373.3568 98097.67748 102954.0994 1.032674697 1.181824842 1.020339234 1.26825307 0.794973856 1.033887545 1.1600548 1.091489872 0.952829251 1 16.65164175 7.999999922 0.068511102 0.928224574 1.370635148 0.045634603 0.122459375 1002.846172 5.07874447 5.847880205 42.95934542 99999982.08 -7.999999922 0.442410574 NLVS(ph)PAYCTQESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NLVSPAYCTQESR 13 0 Q9NUQ3 Q9NUQ3 TXLNG Gamma-taxilin 1 NLVS(1)PAYCTQESR 117.53 0.00052368 146400000 2259200 109670 164230 103680 374510 1795600 309310 171520 190780 73408 TRUE FALSE 2348394.96 128504.9694 168509.9687 124187.5945 310850.924 1378599.113 285065.474 169221.055 183913.8651 87790.89212 26.7498701 1.463761972 1.919447048 1.414584037 3.540810629 15.70321339 3.24709622 1.92754682 2.09490826 1 16.42178365 4.742082009 24.84605536 3.770637162 26.74987958 0.738428243 4.133937136 166.0619512 1171635.784 1.030532474 7.559137356 55218.16988 -4.742082009 22.97924242 NLYSDDIPHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NLYSDDIPHALR 12 0 P60228;H0YBR5;E5RIT4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ;;; 146.79 6.26E-05 2737000000 1601920 1812640 1920170 1915430 2205770 2665740 2171040 2059320 1872410 1640140 FALSE TRUE 1665165.039 2123946.82 1970211.208 2294296.337 1830834.003 2046662.285 2000868.212 2031718.184 1805022.33 1961494.031 0.848926896 1.082820945 1.004444152 1.169667764 0.933387497 1.043420093 1.020073567 1.03580136 0.920228306 1 20.90352151 1.254544353 24.98445652 0.960114134 1.02291187 0.068748215 0.082176263 498.7398721 779595.6401 0.051159286 0.018554205 17.96984591 -1.254544353 0.062797736 NMADRYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMADRYER 8 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 0 96.665 0.0080072 58394000 60313 79051 77040 64570 97429 107560 79334 73243 81602 79840 FALSE TRUE 62694.20381 92627.39432 79047.72569 77341.75328 80868.05338 82580.82009 73115.59378 72261.29739 78665.15996 95483.11937 0.65659987 0.970091833 0.827871211 0.810004468 0.846935604 0.864873505 0.765743665 0.756796572 0.823864579 1 16.54295808 2.256713923 24.96231524 0.808148378 0.835637832 0 0.096603024 1324.653476 1821504.006 0.031432461 0.026251073 180.5984101 -2.256713923 0.027489454 NMAPS(ph)QQSPVR ddPTM_MDA-MB-175_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(0.782)QQS(0.218)PVR 77.64 0.018282 0 51956 50677 51010 48133 59546 72784 57538 47757 46951 49435 TRUE FALSE 54007.263 59380.38054 52339.36251 57653.56374 49424.39219 55881.01905 53028.02121 47116.89553 45261.24268 59120.84176 0.913506327 1.004389971 0.885294609 0.975181713 0.835989318 0.94519999 0.896942933 0.796959145 0.765571689 1 15.85137919 1.939315483 5.691899753 0.834122775 0.926048701 0.150413355 0.072430716 0.295292108 19.50780268 0.029908984 0.018304629 86.95918936 -1.939315483 0.091925926 NMDDDRLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NMDDDRLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 105.86 0.0027624 229850000 471314 668200 627090 483150 751460 766860 508329 602740 603180 698230 FALSE TRUE 489921.8407 782958.1521 643432.4806 578715.6279 623727.0976 588768.3869 468484.8447 594661.2562 581471.6696 835034.8001 0.586708291 0.937635356 0.770545707 0.693043725 0.74694743 0.705082455 0.561036312 0.712139489 0.696344236 1 19.6714768 -1.062192901 4.359965203 1.000023312 0.71398908 0.440341744 0.097329496 52787268386 11353858891 12925788.36 0.022699251 0.086657688 1.062192901 -0.286034232 IALESEGRPEEQMESDNCS(ph)GGDDDWTHLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 IALESEGRPEEQMESDNCSGGDDDWTHLSSK 31 1 Q13501;Q13501-2 Q13501 SQSTM1 Sequestosome-1 1 IALESEGRPEEQMES(0.004)DNCS(0.996)GGDDDWTHLSSK;IALESEGRPEEQMESDNCS(1)GGDDDWTHLSSK 195.66 8.60E-26 296402000 62917 112643 136033 137275 142725 163369 154474 145177 141996 127397 TRUE FALSE 65401.01174 131988.559 139578.1317 164427.5853 118464.6555 125429.0256 142365.9242 143231.1398 136885.5917 152358.003 0.429258788 0.866305389 0.916119462 1.079218565 0.777541404 0.823251967 0.934417106 0.940095938 0.898447006 1 17.21710576 4.743179182 3.560792053 0.917177405 0.369635936 0.77431704 0.079143961 0.133791173 3.009692468 0.019328418 0.197445426 55357.84581 -4.743179182 -0.547541469 down NMFHPMDFEDDPLVLNEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NMFHPMDFEDDPLVLNEIR 19 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ;;;; 208.47 2.69E-16 321471000 254273 307703 338410 336344 384575 457077 366511 349505 337249 301773 FALSE TRUE 264311.8944 360548.5967 347229.2426 402871.8393 319205.0789 350927.7938 337782.9101 344820.4571 325111.4744 360899.6416 0.732369512 0.999027306 0.962121329 1.116298807 0.884470479 0.972369472 0.935946926 0.955446937 0.900836235 1 18.46123818 4.743207548 24.88147535 0.967863246 0.73236941 0.579680274 0.060588905 318.9676476 1707814.348 0.014013607 0.113253785 55361.46173 -4.743207548 -0.235493836 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 NMGGPYGGGNYGPGGS(0.064)GGS(0.935)GGYGGR;NMGGPYGGGNYGPGGS(0.007)GGS(0.993)GGYGGR;NMGGPYGGGNYGPGGS(0.161)GGS(0.839)GGYGGR;NMGGPYGGGNYGPGGS(0.06)GGS(0.94)GGYGGR;NMGGPYGGGNYGPGGS(0.209)GGS(0.791)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR;NMGGPYGGGNYGPGGS(0.002)GGS(0.998)GGYGGR;NMGGPYGGGNYGPGGSGGS(1)GGYGGR 433.1 4.65E-181 3921880000 2424300 2478502 2601073 2451592 3016135 3856532 2672021 2790701 2653168 2191549 TRUE FALSE 2520013.236 2904165.438 2668859.099 2936509.58 2503453.45 2960910.889 2462581.012 2753296.218 2557681.002 2620941.067 0.961491759 1.108062091 1.018282758 1.120402751 0.955173499 1.129712883 0.939578933 1.050499095 0.975863607 1 21.32165348 2.22321666 24.99998812 0.999561613 1.049149946 0.162851242 0.062658327 476.1999406 775869.7806 0.021294765 0.015785493 167.1924491 -2.22321666 0.049588333 NMGGPYGGGNYGPGGSGGSGGYGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 387.38 6.58E-138 63175000 19392 23202 20924 19948 25204 34403 22925 23917 22330 16131 FALSE TRUE 20157.61113 27186.76301 21469.29663 23893.65486 20919.83308 26413.42463 21128.0786 23596.43174 21526.34766 19291.5606 1.044892715 1.409256803 1.112885425 1.238554794 1.084403357 1.369169927 1.095198 1.223147895 1.115842731 1 14.23568224 0.945981643 2.602889882 0.999822925 1.20144688 0.221615697 0.114388642 0.426359225 6.647841148 0.096802931 0.025927203 8.830425753 -0.945981643 0.201623955 NMKELKVHYET(ph)ALAESEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMKELKVHYETALAESEKK 19 3 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 NMKELKVHY(0.307)ET(0.347)ALAES(0.347)EKK 55.864 0.061032 32062000 2736 29733 34239 37545 29870 44687 34801 34198 39191 31765 TRUE FALSE 2844.019393 34839.41146 35131.29647 44971.28894 24792.70807 34309.12149 32073.20668 33739.63175 37780.52357 37988.74357 0.074864792 0.917098282 0.924781742 1.183805641 0.65263301 0.903139148 0.84428185 0.888148135 0.994518903 1 15.21328438 4.738689635 24.73998696 0.914010977 0.074864559 0.800954339 0.126790385 3.693465996 707376.4334 0.0292293 0.16937798 54788.52835 -4.738689635 -0.839146419 NMLAFSSPAAGGVCEPLKS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NMLAFSSPAAGGVCEPLKSPQR 22 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 NMLAFSSPAAGGVCEPLKS(1)PQR;NMLAFSSPAAGGVCEPLKS(1)PQR 243.19 5.75E-31 3370100000 2274500 1327640 1461220 1632530 2289700 2700400 2371700 1938990 1951250 855680 TRUE FALSE 2364299.016 1555651.842 1499300.594 1955439.561 1900497.612 2073273.025 2185799.957 1913001.011 1881024.894 1023334.113 2.310388158 1.520179795 1.46511347 1.910851536 1.857162375 2.025998155 2.135959242 1.869380671 1.838133675 1 19.96484582 0.619647983 3.468529451 1.000002929 1.876432721 0.548882814 0.239946882 7.772563686 69.97076346 0.234666828 0.060540097 4.165316274 -0.619647983 0.876429791 NMMAACDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 96.711 0.016712 820080000 969350 1062380 981670 997890 1803400 1855010 1204080 1076760 1017130 1272180 FALSE TRUE 1007620.687 1244835.501 1007253.127 1195269.664 1496858.712 1424212.04 1109701.063 1062327.793 980523.69 1521439.314 0.662281221 0.818195961 0.662039634 0.785617706 0.98384385 0.936095201 0.729375831 0.69823869 0.644471114 1 20.53700536 6.433918795 11.74140368 0.783840206 0.421824001 0 0.130545499 0 0 0.029322148 0 2715931.391 -6.433918795 -0.362016204 NMPGLSAATLASLGGT(ph)SSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R;NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R;NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R;NMPGLSAATLASLGGT(0.333)S(0.333)S(0.333)R 239 3.20E-23 436203000 547843 600190 590223 534921 744420 898230 557907 611642 572254 550686 TRUE FALSE 569472.2647 703267.9637 605604.6963 640726.7772 617883.7543 689629.6953 514176.7915 603443.9394 551658.6903 658582.3782 0.864694051 1.067851171 0.919558003 0.972887825 0.938202683 1.047142648 0.78073269 0.916277082 0.83764569 1 19.32900438 2.245897722 24.99996803 0.877501814 0.969523115 0.228489237 0.07591658 214.6332658 731328.5526 0.024273276 0.019925038 176.1561145 -2.245897722 0.092021301 NMPGLSAATLASLGGTS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMPGLSAATLASLGGTSSR 19 0 Q32MZ4-2;Q32MZ4;C9JTC6;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 NMPGLSAATLASLGGT(0.083)S(0.458)S(0.458)R 225.84 1.72E-19 240200000 207240 208370 203930 197960 256670 288110 205840 206370 192880 165480 TRUE FALSE 215421.9952 244155.9266 209244.5833 237115.8971 213041.3251 221200.8188 189705.7229 203603.9477 185938.2865 197902.6377 1.088525134 1.233717395 1.057310735 1.198144198 1.076495632 1.117725471 0.958581074 1.028808661 0.939544256 1 17.59443132 2.287990442 6.475608745 0.988073955 1.131825994 0.629022629 0.055180654 0.122674395 11.67836328 0.01812098 0.014944961 194.0843164 -2.287990442 0.143752038 NMPGLSAATLASLGGTSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.001)S(0.08)S(0.919)R;NMPGLSAATLASLGGT(0.019)S(0.244)S(0.736)R 402.38 1.90E-147 6744500000 1918040 1964100 1954930 1790070 2568360 2792490 1749260 2050420 1708900 1613610 TRUE FALSE 1993765.7 2301418.896 2005877.082 2144140.503 2131791.085 2143976.518 1612148.43 2022937.474 1647397.023 1929765.985 1.033164495 1.192589627 1.039440584 1.111088349 1.104688911 1.111003373 0.835411362 1.048281237 0.853677096 1 20.87999448 2.265747653 24.9964489 0.946465546 1.101078858 0.556379475 0.071535097 155.693452 143147.9684 0.022827169 0.01909418 184.3943685 -2.265747653 0.154613313 NMQNVEHVPLSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NMQNVEHVPLSLDR 14 0 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ;;;;; 120.92 8.92E-05 3063580000 2560190 7091100 6705130 7389340 6497770 8986020 6417420 7376440 6595820 7086490 FALSE TRUE 2661268.278 8308941.264 6879871.196 8850929.397 5393281.376 6899153.039 5914405.852 7277570.887 6358437.727 8474952.036 0.314015733 0.980411597 0.811788806 1.044363361 0.636378985 0.814063963 0.697868947 0.858715289 0.750262385 1 23.01477377 -4.999999925 0.026354919 2.058294154 2.56E-13 0.136937834 0.18835219 4793.32815 9.533352822 550.534485 248.9467493 1.00E-05 4.999999925 -2.058294154 NMSVHLSPCFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMSVHLSPCFR 11 0 P62280;M0QZC5;M0R1H5 P62280 RPS11 40S ribosomal protein S11 0 85.522 0.012371 0 46217 414420 303310 313500 480280 590020 245830 427200 273980 674320 FALSE TRUE 48041.68285 485593.4113 311214.5078 375509.3643 398642.1772 452996.7968 226561.2022 421474.0828 264119.5133 806440.0934 0.059572538 0.602144431 0.385911502 0.465638263 0.494323361 0.561724052 0.280939904 0.522635328 0.327512875 1 19.62120784 -2.128945651 2.277652498 2.128803673 0.426081842 0.572354883 0.15220572 15398163.52 4001705.316 89811628.26 0.03301778 0.007431121 2.128945651 -1.702721831 NMSVIAHVDHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 212.17 1.35E-08 9037850000 7389210 6601120 8532410 7118070 11518580 11406200 10151080 9299000 8786590 5326810 FALSE TRUE 7680941.717 7734811.01 8754771.614 8526003.001 9560655.886 8757282.913 9355411.825 9174362.115 8470362.342 6370496.432 1.205705364 1.214161423 1.374268349 1.338357708 1.500770935 1.374662557 1.468553028 1.440132996 1.329623591 1 22.60297437 4.235412772 4.993374099 1.383994668 1.206431375 0.126088494 0.132862018 0.235602229 16.14501949 0.030170782 0.077082597 17195.41937 -4.235412772 -0.177563293 NMTVADSGTNHDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMTVADSGTNHDSR 14 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 67.646 0.039446 59968000 9153.3 22009 21622 25809 28017 32678 23655 30930 23947 24426 FALSE TRUE 9514.679352 25788.87454 22185.48708 30913.94317 23254.68035 25089.02974 21800.85929 30515.43394 23085.15215 29211.80704 0.325713481 0.882823665 0.759469863 1.058268772 0.796071271 0.858866064 0.746303002 1.044626712 0.790267857 1 14.83426399 4.738565574 20.32035609 0.882758409 0.325714964 0.696644876 0.110095858 0.028231637 62300.16365 0.024675377 0.141754686 54772.87963 -4.738565574 -0.557043445 NMTVEQLLTGSPTS(ph)PTVEPEKPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 NMTVEQLLTGSPT(0.002)S(0.988)PT(0.009)VEPEKPTR;NMTVEQLLTGS(0.001)PT(0.236)S(0.738)PT(0.025)VEPEKPTR;NMTVEQLLTGSPT(0.024)S(0.966)PT(0.01)VEPEKPTR;NMTVEQLLTGSPT(0.03)S(0.934)PT(0.036)VEPEKPTR;NMTVEQLLTGS(0.001)PT(0.064)S(0.914)PT(0.022)VEPEKPTR;NMTVEQLLTGSPT(0.207)S(0.793)PTVEPEKPTR 223.76 4.47E-33 1889430000 1111955 772864 1076710 804625 1354350 1440160 1211030 1126080 1176180 753608 TRUE FALSE 1155855.842 905597.38 1104769.947 963777.4234 1124138.071 1105704.666 1116106.304 1110986.739 1133849.512 901263.0589 1.282484432 1.004809163 1.225801875 1.069363061 1.247291853 1.226838995 1.238380175 1.232699741 1.258067221 1 19.78158873 NMVDLVNTHHLHSS(ph)SDDEDDRLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHS(0.169)S(0.415)S(0.415)DDEDDRLK;NMVDLVNTHHLHS(0.041)S(0.863)S(0.097)DDEDDRLK 300.44 3.52E-62 1302630000 289420 419660 629350 527010 694300 766410 749500 636780 581290 348260 TRUE FALSE 300846.5251 491733.3405 645751.378 631251.005 576283.134 588422.8926 690752.2315 628245.0057 560369.4864 416494.8792 0.722329469 1.180646786 1.550442539 1.51562729 1.383649987 1.412797424 1.658489134 1.508409916 1.34544148 1 18.66793923 4.614155278 2.632422243 1.455807546 0.666809576 0.606091448 0.169942953 0.209551765 2.226056724 0.03937798 0.317252328 41129.67502 -4.614155278 -0.78899797 NMVDLVNTHHLHSSS(ph)DDEDDRLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NMVDLVNTHHLHSSSDDEDDRLK 23 1 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 NMVDLVNTHHLHSS(0.096)S(0.904)DDEDDRLK 279.93 3.35E-52 681690000 286000 530820 720380 559700 811610 811860 795200 769910 691780 339880 TRUE FALSE 297291.5008 621984.2058 739153.6946 670406.9895 673652.8221 623317.8189 732870.1461 759590.6158 666882.9729 406472.9786 0.731393024 1.530198165 1.818457151 1.649327322 1.657312681 1.533479104 1.80299844 1.868735822 1.640657579 1 18.63279992 4.725756468 3.541608833 1.671560852 0.632733963 0.553516511 0.234668498 0.172640612 3.878764658 0.052401273 0.469791267 53180.99619 -4.725756468 -1.038826888 NNASTDYDLSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NNASTDYDLSDK 12 0 P39023;G5E9G0;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 139.89 0.00013774 317020000 420200 232540 347670 245550 485220 495070 498860 373070 378730 189640 FALSE TRUE 436789.8205 272476.9361 356730.5658 294119.0571 402742.4777 380097.4954 459758.0497 368069.6069 365099.5813 226796.3271 1.925912231 1.201416882 1.572911565 1.296842241 1.775789241 1.675942023 2.027184723 1.622908146 1.609812583 1 17.79103775 3.221534094 24.99325662 1.677677247 1.483255444 0.013149106 0.302787453 587.8606916 862919.7107 0.081377236 0.097497691 1665.459567 -3.221534094 -0.194421803 NNAYLAQS(ph)PQLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NNAYLAQSPQLYK 13 0 P14868;P14868-2 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 1 NNAYLAQS(1)PQLYK;NNAYLAQS(1)PQLYK 183.23 1.10E-05 168834000 370520 220940 294740 240920 422960 457090 380790 310630 339910 172103 TRUE FALSE 385148.4157 258884.7263 302421.1665 288573.2569 351065.4103 350937.7748 350942.6848 306466.5129 327676.7055 205823.2877 1.871257718 1.257800947 1.469324341 1.402043763 1.705664185 1.705044063 1.705067918 1.488978805 1.592029304 1 17.6510467 -1.223237235 3.006552991 0.997392672 1.566987766 0.508623249 0.169997253 8137329.105 10989710.71 199027.1614 0.043507197 0.05980848 1.223237235 0.569595094 NNDLCYWVPELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NNDLCYWVPELVR 13 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ;; 136.27 0.00017288 80153000 134384 150950 172389 156215 200491 226292 178766 169109 159500 153579 FALSE TRUE 139689.5841 176874.4883 176881.599 187113.8607 166411.6114 173739.1125 164753.8538 166842.3705 153759.6262 183669.8646 0.760547107 0.963002225 0.963040939 1.018751014 0.906036555 0.945931511 0.897010809 0.908381845 0.837152172 1 17.48675541 2.230376873 24.62945122 0.903363889 0.932852672 0.001994941 0.073188997 635.0700308 1911262.944 0.026556317 0.019948413 169.9717999 -2.230376873 0.029488783 NNFEGEVTKENLLDFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NNFEGEVTKENLLDFIK 17 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 90.422 0.0034714 425500000 407940 509420 571020 511390 752470 856480 608490 639400 593270 480180 FALSE TRUE 424045.7862 596908.9223 585901.2503 612541.4157 624565.4182 657575.5001 560794.9638 630829.8888 571918.3286 574262.0774 0.738418577 1.039436428 1.020268051 1.066658308 1.087596487 1.145079095 0.976548837 1.098505219 0.995918677 1 19.13134977 4.743770619 4.447761544 1.054865066 0.715299571 0.773978116 0.050085716 0.087833032 4.312402636 0.01143437 0.09430392 55433.28537 -4.743770619 -0.339565496 NNLAGAEELFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NNLAGAEELFAR 12 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 181.44 4.22E-05 698020000 388322 397035 445482 421093 550380 660750 459280 468720 427768 332570 FALSE TRUE 403653.2524 465222.6727 457091.6269 504383.9386 456826.6042 507300.8263 423280.4335 462437.5751 412372.7132 397730.7241 1.014890799 1.16969257 1.149248975 1.268154327 1.148582638 1.275488152 1.064238712 1.162690099 1.036813825 1 18.60143249 1.18006696 1.449018381 0.996130112 1.16691197 0.343253289 0.075485245 0.405564368 1.647736378 0.067652458 0.020568351 15.13794627 -1.18006696 0.170781857 NNQITNNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NNQITNNQR 9 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 184.04 0.00010347 475754000 296700 303145 303353 299539 408587 493979 348210 340546 287559 264888 FALSE TRUE 308413.9451 355207.7956 311258.6284 358786.9202 339135.5277 379259.8636 320916.3903 335981.5379 277209.8078 316787.732 0.973566568 1.12128015 0.982546345 1.132578329 1.070545016 1.197205022 1.013032886 1.060588855 0.875064845 1 18.27315694 1.336148596 6.44124018 0.938748817 1.072000557 0.351235592 0.071328826 0.202492384 10.80762599 0.046241845 0.016602995 21.68445923 -1.336148596 0.133251739 NNRPSEGPLQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NNRPSEGPLQTR 12 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;;;; 199.31 1.58E-07 4805850000 1383315 1412730 1492826 1622988 1811702 2596590 1768414 1608121 1435977 1069786 FALSE TRUE 1437929.344 1655355.388 1531730.272 1944010.182 1503749.541 1993571.324 1629801.09 1586566.768 1384296.468 1279390.084 1.123917843 1.293862918 1.197234753 1.519481983 1.175364386 1.558220084 1.273889105 1.240096189 1.081997184 1 20.28702478 1.243745497 1.96526316 1.002374342 1.313175021 0.394121444 0.131419852 0.299992345 2.016258846 0.115555772 0.033771793 17.52853003 -1.243745497 0.310800679 NNRQPYAVSELAGHQTSAESWGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NNRQPYAVSELAGHQTSAESWGTGR 25 1 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;; 182.39 1.34E-17 392363000 64784 153018 133091 106669 206620 211407 94891 156015 139839 170577 FALSE TRUE 67341.72234 179297.6512 136559.4608 127767.8098 171498.8062 162310.9282 87453.19547 153923.8741 134806.2217 203998.2973 0.330109237 0.878917391 0.669414709 0.626318021 0.84068744 0.795648446 0.428695713 0.754535093 0.660820328 1 17.63819758 -1.640950262 1.377625468 1.104015192 0.67487251 0.268966389 0.164958318 10911.23411 4104.071345 3954.786526 0.042988209 0.022858606 1.640950262 -0.429142682 NNSLWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NNSLWDR 7 0 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 110.22 0.015943 513030000 559920 579550 589100 605540 820610 948970 647340 608650 619690 452460 FALSE TRUE 582026.074 679083.2042 604452.43 725314.0046 681123.0053 728586.0993 596599.7993 600492.0423 597387.4779 541110.8741 1.075613339 1.254979777 1.117058368 1.340416612 1.258749432 1.346463607 1.102546313 1.109739373 1.104001983 1 19.04556471 2.107449513 9.336424037 1.089147439 1.234026041 0.436289464 0.08508293 0.283277206 22.66580126 0.031565335 0.023304268 128.0706203 -2.107449513 0.144878603 NNSQIASGQNQPQAAAGSHQLS(ph)MGQPHNAAGPSPHTLRR ddPTM_MDA-MB-175_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(0.002)HQLS(0.808)MGQPHNAAGPS(0.127)PHT(0.063)LRR 223.78 4.45E-40 140050000 6990.4 11788 10632 7981.3 20841 21620 11054 11234 13964 9549.4 TRUE FALSE 7266.38639 13812.4973 10909.07865 9559.977318 17298.45426 16599.08265 10187.5586 11083.42661 13461.43837 11420.4221 0.636262507 1.209455937 0.955225522 0.83709492 1.514694826 1.453456143 0.892047466 0.970491853 1.17871636 1 13.47932835 4.746744143 24.15512001 1.104656511 0.63626213 0.300182639 0.217792329 892.4665524 2634173.152 0.055022247 0.608212137 55814.12783 -4.746744143 -0.46839438 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHTLR 38 0 Q68EM7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7-7;Q68EM7-2 Q68EM7;Q68EM7-2 ARHGAP17 Rho GTPase-activating protein 17 1 NNSQIASGQNQPQAAAGS(0.004)HQLS(0.155)MGQPHNAAGPS(0.654)PHT(0.187)LR;NNSQIASGQNQPQAAAGS(0.262)HQLS(0.262)MGQPHNAAGPS(0.465)PHT(0.011)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.999)PHT(0.001)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(0.743)PHT(0.257)LR;NNSQIASGQNQPQAAAGS(0.041)HQLS(0.305)MGQPHNAAGPS(0.576)PHT(0.078)LR;NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(1)PHTLR;NNSQIASGQNQPQAAAGS(0.003)HQLS(0.14)MGQPHNAAGPS(0.716)PHT(0.14)LR 335.58 3.67E-129 2314359000 245979.2 428231 415956 422739 478968 671736 476273 490965 425010 302976.2 TRUE FALSE 255690.6488 501776.3431 426796.1551 506355.5124 397553.1904 515735.4943 438941.4778 484384.4172 409713.9731 362338.5856 0.705667734 1.384827239 1.177893197 1.397465058 1.097187013 1.423352397 1.211412461 1.33682814 1.130748944 1 18.46697892 4.746805271 24.90601417 1.25688912 0.705667446 0.577681085 0.136362261 608.9075927 1839385.882 0.028463932 0.322464445 55821.98435 -4.746805271 -0.551221674 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPS(ph)PHTLRR ddPTM_MDA-MB-175_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(0.009)HQLS(0.037)MGQPHNAAGPS(0.665)PHT(0.289)LRR 102.86 6.99E-06 138410000 7740.8 12539 11620 11071 16134 17695 6933.6 14540 8504.4 10220 TRUE FALSE 8046.412761 14692.47571 11922.82675 13260.81076 13391.54844 13585.60442 6390.126314 14345.11508 8198.328305 12222.41333 0.658332569 1.202092853 0.975488754 1.084958461 1.095655014 1.111532073 0.522820342 1.173672883 0.670761828 1 13.57724155 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHT(ph)LR ddPTM_MDA-MB-175_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(0.234)HQLS(0.234)MGQPHNAAGPS(0.234)PHT(0.298)LR 118.3 1.32E-06 102150000 5952.2 10493 6013.7 11234 12563 14360 10282 11626 8384.5 8496.6 TRUE FALSE 6187.197452 12295.09113 6170.421962 13456.05167 10427.54575 11025.10763 9476.069973 11470.17249 8082.743483 10161.34609 0.608895455 1.209986454 0.607244543 1.324239087 1.026197283 1.085004637 0.932560498 1.12880443 0.795440231 1 13.31080391 4.756601153 24.64499655 1.017410845 0.608895037 0.281310679 0.193208094 3919.604018 5354426.426 0.041900387 1.331988431 57095.40437 -4.756601153 -0.408515808 NNSQIASGQNQPQAAAGSHQLSMGQPHNAAGPSPHT(ph)LRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.007)HQLS(0.047)MGQPHNAAGPS(0.409)PHT(0.538)LRR;NNSQIASGQNQPQAAAGS(0.003)HQLS(0.188)MGQPHNAAGPS(0.267)PHT(0.543)LRR 192.27 1.73E-24 781530000 87696 133331 142378 109707 165241 214206 104262 164881 132915 140014 TRUE FALSE 91158.3058 156229.5621 146088.4876 131406.7172 137153.3938 164459.9028 96089.672 162671.0399 128131.4151 167447.0626 0.544400746 0.933008676 0.872445807 0.784765735 0.819085099 0.982160572 0.573851046 0.971477417 0.765205511 1 17.35334554 -5 0.173597966 1.70518859 0.775957683 0.149274476 0.142214151 266.1018296 2.531201666 65.00857519 0.451346743 1.00E-05 5 -0.929230907 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(1)DGEDRGGGTSGVR 240.64 8.47E-39 472310000 110572 129942 138685 123550 194170 195555 155791 155190 152493 112869 TRUE FALSE 114937.4679 152258.5277 142299.245 147987.8212 161165.0528 150140.3149 143579.6943 153109.9319 147004.8067 134983.5195 0.851492599 1.127978647 1.054197175 1.096339922 1.193960961 1.112286266 1.063683143 1.134286114 1.089057444 1 17.04242375 4.742023253 24.95016066 1.103040983 0.851492502 0.685153416 0.049742046 173.5575935 1250519.609 0.011262181 0.082617722 55210.69999 -4.742023253 -0.251548481 NNWEVSALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NNWEVSALSR 10 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 89.827 0.023868 0 187350 102940 162750 112100 194010 181130 175590 155280 170580 89006 FALSE TRUE 194746.7227 120619.1442 166991.3987 134273.0454 161032.2495 139065.3026 161826.797 153198.7256 164440.8591 106445.0216 1.829552193 1.133159094 1.568804217 1.261430957 1.512820864 1.306451918 1.520285257 1.439228658 1.544843119 1 16.69974895 -1.053914379 4.498675838 0.999979491 1.444747095 0.358967418 0.182666991 0.654752869 47716720.4 2563.30669 0.037253732 0.088325402 1.053914379 0.444767604 NPDDITNEEYGEFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NPDDITNEEYGEFYK 15 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;;; 361.61 9.45E-83 6114258000 3149878 2633994 3232595 2513089 3934502 3913598 3739516 3272149 3490317 2419571 FALSE TRUE 3274237.616 3086361.98 3316839.081 3010170.503 3265716.755 3004724.176 3446402.965 3228291.195 3364701.173 2893639.612 1.131529166 1.066602063 1.146251616 1.040271391 1.12858448 1.038389219 1.19102702 1.115650747 1.162792063 1 21.46445382 2.247322776 24.99957875 1.128074995 1.09257244 0.031296583 0.058109756 475.2473991 1355945.086 0.018409235 0.015190144 176.7350862 -2.247322776 -0.035502555 NPDDITQEEYGEFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;; 278.97 2.84E-33 3252860000 2032064 1614085 2078417 1581310 2508840 2506140 2301626 1997120 2174693 1664867 FALSE TRUE 2112291.456 1891291.543 2132582.254 1894088.398 2082388.273 1924126.966 2121218.54 1970351.873 2096426.224 1991065.813 1.0608848 0.949889015 1.071075723 0.951293717 1.045866118 0.966380395 1.06536837 0.989596557 1.052916589 1 20.92510948 2.240955359 24.99925366 1.023594287 1.007013366 0.039447918 0.04566396 263.9594589 2755575.658 0.014631622 0.01169256 174.1627844 -2.240955359 -0.016580921 NPDELAEALDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPDELAEALDER 12 0 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 142.08 0.00014206 399784000 264453 279019 303100 315700 325660 360220 294260 305760 292460 285320 FALSE TRUE 274893.8086 326938.3428 310999.035 378144.5177 270304.4295 276564.3642 271195.1323 301661.7873 281934.4217 341222.9912 0.805613384 0.958136911 0.91142462 1.108203513 0.792163589 0.810509172 0.794773914 0.884060556 0.82624685 1 18.38035533 NPDTQWITKPVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPDTQWITKPVHK 13 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 205.61 4.12E-08 5164200000 6871800 4479200 6137300 4753500 8019400 7914600 6876500 6339800 7125900 3980400 FALSE TRUE 7143103.97 5248467.757 6297243.08 5693728.112 6656265.252 6076554.097 6337501.962 6254825.351 6869440.251 4760283.171 1.500562827 1.102553686 1.32287153 1.196090213 1.398291869 1.276511056 1.331328775 1.313960772 1.443073869 1 22.18261597 -1.532255302 5.913180432 0.999464979 1.31205409 0.435115322 0.109193495 0.000698541 5.53E-05 0.09589239 0.022564571 0.029359232 1.532255302 0.312589111 NPDVDTSFLPDRDREEEENRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPDVDTSFLPDRDREEEENRLR 22 3 Q14320;B0S8I6;Q9Y247 Q14320 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 ; 236.04 7.70E-31 437860000 112477 141957 151589 123929 173331 175510 148942 143448 132347 146914 FALSE TRUE 116917.6788 166337.0105 155539.5339 148441.7863 143868.2585 134750.4624 137267.5369 141525.3142 127583.8573 175698.9855 0.665443107 0.946715828 0.885261423 0.84486422 0.818833747 0.766939331 0.781265393 0.805498756 0.726150222 1 17.42274634 3.109830498 3.984050966 0.800749474 0.846986644 0 0.095511053 0.774378604 22.77840952 0.026605328 0.032341073 1287.746856 -3.109830498 0.046237169 NPEAALS(ph)PTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NPEAALSPTFR 11 0 Q86U44;F5H6D8;B4DTN4;B4E349 Q86U44 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 NPEAALS(0.981)PT(0.019)FR;NPEAALS(0.534)PT(0.466)FR;NPEAALS(0.957)PT(0.043)FR;NPEAALS(0.951)PT(0.049)FR 153.7 3.39E-05 538230000 410391 453647 455716 436406 496706 624520 510909 482864 457227 431071 TRUE FALSE 426593.5536 531557.3434 467592.3333 522725.8043 412276.0915 479484.6947 470862.6176 476391.9979 440771.4896 515531.1091 0.82748363 1.031086842 0.907010896 1.013955889 0.799711374 0.93007907 0.913354421 0.924080021 0.854985241 1 18.97569996 5.090094703 10.29050332 0.925354828 8.37E-05 0.168805191 0.067708208 56880.0248 228001.1603 0.015025872 1076014.977 123053.7073 -5.090094703 -0.925271122 NPEHFVVCNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPEHFVVCNR 10 0 Q2TAY7;Q2TAY7-2 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 101.93 0.0030146 344740000 211020 328370 275410 314200 347580 428640 315420 338270 305570 307220 FALSE TRUE 219351.2325 384764.9931 282587.4109 376347.8222 288498.4758 329094.8561 290696.5562 333736.0439 294572.5954 367413.8769 0.597014012 1.047224989 0.769125579 1.024315754 0.78521388 0.895706114 0.791196453 0.908338157 0.801745971 1 18.48704659 -2.599474214 2.040539166 3.397730821 0.856635252 0.114914541 0.124939244 3949596.053 260795.9174 43747934.59 0.027682785 0.002514929 2.599474214 -2.541095569 NPEISHLLNNPDIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPEISHLLNNPDIMR 15 0 Q9UHD9 Q9UHD9 UBQLN2 Ubiquilin-2 0 143.14 3.39E-06 127240000 69553 91222 92084 92504 117200 128250 106470 96133 82141 86952 FALSE TRUE 72299.00615 106888.6689 94483.78469 110801.0151 97278.38586 98465.88115 98124.60319 94844.49438 79184.76146 103988.5796 0.695259099 1.027888536 0.908597704 1.065511381 0.93547182 0.946891298 0.943609419 0.912066447 0.761475556 1 16.66606557 -0.216271839 7.457139513 1 0.921395966 0.052752653 0.105078426 0 0 0.094840477 0.022354115 0.607754469 0.216271839 -0.078604034 NPEISHMLNNPDIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NPEISHMLNNPDIMR 15 0 Q9UMX0;Q9UMX0-2 Q9UMX0 UBQLN1 Ubiquilin-1 0 ;;;; 245.76 4.02E-18 959640000 414263 494290 513032 488640 612974 689102 536206 530543 537771 477911 FALSE TRUE 430618.4231 579180.4625 526402.0354 585291.5336 508780.8984 529068.5039 494176.7726 523431.9389 518416.7268 571548.5103 0.753424102 1.013353114 0.921010248 1.024045244 0.89017973 0.925675589 0.864627873 0.91581367 0.907038891 1 19.12451643 0.943366486 0.005777996 1.863600957 3.24E-05 0.071964139 0.073264239 22016.35863 80.93169389 13154.99788 12941.68579 8.777412032 -0.943366486 -1.86356851 NPEVGLKPVWYSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPEVGLKPVWYSPK 14 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 143.28 8.36E-06 460800000 629950 454120 569640 458640 808590 708890 704220 604670 628720 332670 FALSE TRUE 654820.9124 532111.5774 584485.2864 549357.6231 671146.1606 544261.0408 649021.3963 596565.3877 606092.49 397850.3171 1.645897676 1.337466767 1.469108509 1.380814843 1.68693132 1.368004542 1.631320545 1.499471942 1.523418391 1 18.60186622 -0.321102794 9.096567214 1.000013636 1.501813618 0.632965071 0.115281463 0 0 0.101776914 0.023989049 0.47741626 0.321102794 0.501799982 NPEYDYLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPEYDYLFK 9 0 Q9H0U4;E9PLD0 Q9H0U4 RAB1B Ras-related protein Rab-1B 0 ; 111.65 0.0048624 183660000 349390 253460 309940 258910 327580 384180 312000 306670 323840 171177 FALSE TRUE 363184.187 296989.7834 318017.291 310121.6252 271898.0686 294960.0173 287544.6247 302559.5903 312185.0617 204715.8558 1.774089191 1.450741479 1.553457058 1.514888156 1.328172982 1.440826438 1.404603584 1.47794898 1.52496767 1 17.64326332 -3.361913427 0.203399314 7.25E-18 1.574957455 0.668143798 0.107115565 41.59735287 0.751289921 18.1488603 0.257615812 0.000434597 3.361913427 1.574957455 NPFDTFFGQR ddPTM_MDA-MB-175_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 99.34 0.011254 0 150140 159360 150540 157360 173030 190880 164920 152840 159990 155830 FALSE TRUE 156067.6431 186728.8404 154463.1961 188485.3383 143618.4224 146551.0128 151993.1395 150791.4298 154231.9912 186361.905 0.837443914 1.00196894 0.828834606 1.011394139 0.770642597 0.786378594 0.815580521 0.809132262 0.827593983 1 17.50774746 3.222774141 24.99726491 0.820934727 0.919266339 0.196399464 0.081363506 303.9234153 481249.6596 0.021361212 0.025612218 1670.221772 -3.222774141 0.098331612 NPFRGS(ph)PK ddPTM_MDA-MB-175_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 64.439 0.040564 595940000 715058 504581 603296 462951 861447 981840 719317 584794 593184 508180 TRUE FALSE 743289.042 591238.8617 619018.3894 554521.326 715018.5466 753822.5399 662935.054 576955.793 571835.4237 607748.1413 1.223021498 0.972835327 1.018544274 0.912419617 1.176504703 1.240353509 1.090805564 0.949333702 0.940908552 1 19.21311405 1.736466687 6.525286792 0.95981971 1.085639 0.251061043 0.100247935 0.213529717 25.28928094 0.053038613 0.027756676 54.5088082 -1.736466687 0.12581929 NPGFEIIHGLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPGFEIIHGLLDR 13 0 Q9NSD9;Q9NSD9-2 Q9NSD9 FARSB Phenylalanine--tRNA ligase beta subunit 0 ; 155.28 4.55E-05 381730000 419190 416960 469550 465820 581000 645970 568490 502020 466850 396750 FALSE TRUE 435739.9449 488569.6365 481786.8587 557957.8057 482241.8275 495953.2573 523930.2683 495291.243 450048.1597 474485.5663 0.918341833 1.029682821 1.015387807 1.175921557 1.016346675 1.045244139 1.104206968 1.043848914 0.94849705 1 18.85600468 4.833751893 1.996122352 1.051567896 0.856397171 0.284679553 0.058372342 1.230475128 4.280139878 0.014500249 0.476677589 68194.89944 -4.833751893 -0.195170725 NPHNDRFVLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPHNDRFVLSK 11 1 P29401;P29401-2;E9PFF2;F8W888 P29401 TKT Transketolase 0 113.35 0.00084356 458830000 941480 861110 955010 620440 1329500 1190200 816050 973920 1058500 895160 FALSE TRUE 978650.3574 1008998.944 979898.3451 743161.1802 1103512.065 913794.0877 752085.8687 960866.1954 1020404.792 1070549.463 0.914157067 0.942505675 0.915322812 0.694186682 1.030790358 0.853574841 0.702523232 0.897544886 0.953159874 1 20.02992002 1.185706866 3.351278107 0.992301588 0.86426817 0.172754125 0.097436769 0.397965381 7.994256712 0.089312298 0.024376796 15.33581518 -1.185706866 -0.128033418 NPHPSSAFLNLIGFVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPHPSSAFLNLIGFVSR 17 0 P53004;C9J1E1 P53004 BLVRA Biliverdin reductase A 0 161.08 3.01E-09 288280000 73198 502640 423850 541870 330560 645140 367190 562480 381410 473080 FALSE TRUE 76087.91356 588964.51 434895.8792 649050.2687 274371.5293 495316.0122 338408.6883 554940.8756 367683.1286 565770.9683 0.134485362 1.040994577 0.768678323 1.147196136 0.484951588 0.875470888 0.598137245 0.980857815 0.649879809 1 19.10985862 4.749435153 24.80471951 0.831298425 0.134484919 0.522189189 0.201915227 1083.367843 2471099.392 0.044066009 0.655526064 56161.04143 -4.749435153 -0.696813506 NPISGLLEYAQFASQTCEFNMIEQSGPPHEPR ddPTM_MDA-MB-175_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 ; 188.47 8.09E-20 259040000 96178 122016 138063 131629 145030 177663 127321 138056 124142 119030 FALSE TRUE 99975.18171 142971.2988 141661.0352 157664.8233 120377.8524 136403.4608 117341.2473 136205.5851 119674.1537 142351.6495 0.702311368 1.004352948 0.995148533 1.107572858 0.845637215 0.958214824 0.824305498 0.956824776 0.840693832 1 17.11909969 NPLFDHAALSAPLPAPSS(ph)PPALP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NPLFDHAALSAPLPAPSSPPALP 23 0 Q5SPY9;Q9NQX5 Q5SPY9 NPDC1 Neural proliferation differentiation and control protein 1 1 NPLFDHAALSAPLPAPS(0.077)S(0.923)PPALP;NPLFDHAALSAPLPAPS(0.14)S(0.86)PPALP;NPLFDHAALSAPLPAPS(0.154)S(0.846)PPALP;NPLFDHAALSAPLPAPS(0.033)S(0.967)PPALP;NPLFDHAALSAPLPAPS(0.12)S(0.88)PPALP 167.99 1.07E-11 646263000 545180 1040531 961081 1037344 1127932 1442440 837625 1003089 932109 1105624 TRUE FALSE 566704.1274 1219234.105 986127.5604 1242527.547 936206.5215 1107455.17 771969.7638 989644.2327 898562.5792 1322249.854 0.428590803 0.922090557 0.745795174 0.939707078 0.708040556 0.837553634 0.583830477 0.748454787 0.679570942 1 20.33456339 -2.416853868 2.141931387 3.02305273 0.741138101 0.233674066 0.144520617 8202526.704 808019.3017 80306153.69 0.033970722 0.003829536 2.416853868 -2.281914629 NPLPNIDHELQELLIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NPLPNIDHELQELLIDR 17 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 0 ;;; 169.28 1.99E-09 116535000 70972.8 86525 86777 93735 91798 119517 108842 98456 88791 73551 FALSE TRUE 73774.86095 101384.9957 89038.47991 112275.5032 76194.20875 91760.98805 100310.6796 97136.35836 85595.42925 87961.91023 0.83871372 1.152601114 1.012239044 1.276410471 0.866218214 1.043190033 1.14038769 1.104300238 0.973096526 1 16.42459131 2.44093566 24.9342913 1.072992208 1.039460182 0 0.126818207 1052.899784 725511.564 0.042468917 0.035532086 276.016891 -2.44093566 -0.033532026 NPLPNIDHELQELLIDRGEDVPS(ph)EEEEEEENGFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDR 36 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR;NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR;NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR;NPLPNIDHELQELLIDRGEDVPS(1)EEEEEEENGFEDR 295.97 2.89E-92 248205000 78954 90153 105853 74567.7 123677 118043 77369 95333 97538 97842 TRUE FALSE 82071.16489 105636.0765 108611.6161 89316.9685 102654.4277 90629.30221 71304.61561 94055.21707 94027.62643 117012.2666 0.701389412 0.902777799 0.928207096 0.763312865 0.877296293 0.774528217 0.60937727 0.803806471 0.803570678 1 16.83630025 2.701920358 16.21729724 0.772077587 0.839624344 0 0.108908833 24.97680872 11052.71651 0.033927011 0.032001939 503.4082843 -2.701920358 0.067546758 NPLPPILGS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPLPPILGSPTK 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 NPLPPILGS(0.974)PT(0.026)K 83.729 0.013254 389770000 1552100 862840 1226200 1068500 1995700 2108200 1764000 1532100 1525800 862180 TRUE FALSE 1613378.106 1011026.058 1258155.779 1279846.111 1656471.627 1618602.5 1625733.071 1511564.706 1470886.756 1031107.664 1.564703826 0.98052424 1.220198262 1.241234214 1.606497251 1.569770604 1.576686051 1.465962051 1.426511322 1 19.97576355 3.28538728 11.83081616 1.478872217 1.229839316 0.146042539 0.209966251 1.059367152 264.6875369 0.054162125 0.073273695 1929.244541 -3.28538728 -0.249032901 NPLPSKETIEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPLPSKETIEQEK 13 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ; 157.38 4.34E-05 1090610000 967170 484550 717980 487010 1020260 952210 918630 759790 830650 355190 FALSE TRUE 1005354.618 567767.6932 736691.1486 583339.1244 846836.5696 731073.6584 846625.3802 749606.2578 800755.0688 424782.68 2.366750496 1.336607447 1.734277746 1.373264853 1.993576032 1.721053359 1.993078862 1.764681785 1.8850935 1 18.69636542 NPPGFAFVEFEDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 129.84 0.00015255 1111660000 681220 697630 746150 840670 843850 1092600 1029660 855690 814310 584420 FALSE TRUE 708115.0916 817442.5257 765595.282 1006952.017 700412.6784 838860.2085 948952.5587 844220.8752 785003.1422 698925.9096 1.013147577 1.169569642 1.095388326 1.440713533 1.002127219 1.200213352 1.357729833 1.207883216 1.123156448 1 19.41478 4.966335159 1.448026234 1.200130097 0.85030866 0.107816689 0.133416576 4.010326593 5.057915183 0.034081191 2.361429783 92541.20679 -4.966335159 -0.349821438 NPPGFAFVEFEDPRDAADAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NPPGFAFVEFEDPRDAADAVR 21 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;; 189.84 1.84E-17 5385980000 648583 851427 814492 574319 1117112 1144511 703182 852143 832318 926583 FALSE TRUE 674189.5577 997652.9641 835718.3306 687917.584 927225.7013 878715.6655 648064.7574 840721.4169 802363.0378 1108129.198 0.608403387 0.900303832 0.754170481 0.620791858 0.836748732 0.792972216 0.584827797 0.758685375 0.724069936 1 20.07969467 -0.826842204 7.628324961 1 0.733940642 0.409536902 0.096771282 6.60E-10 8.66E-11 0.088619872 0.020887904 0.148990232 0.826842204 -0.266059359 NPPGFAFVEFEDPRDAEDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NPPGFAFVEFEDPRDAEDAVR 21 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;;;; 183.09 4.05E-17 3996312000 402057.3 440806 489621 398386 564072 647541 449117 518013 523068 426073 FALSE TRUE 417930.8327 516511.0015 502380.9255 477185.5617 468191.2429 497159.4163 413914.036 511069.883 504242.8849 509553.8467 0.820189731 1.013653424 0.985923134 0.936477204 0.918825843 0.975675916 0.812306763 1.002975223 0.989577231 1 18.95887508 1.599190497 25 0.997219859 0.92982091 0.227029601 0.061944939 1.150579309 3305.988197 0.031562935 0.014965298 39.736581 -1.599190497 -0.067398949 NPPPNSDPNLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NPPPNSDPNLRR 12 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;; 141.13 9.66E-05 360543000 99387 110146 109357 101439 130802 151347 97853 116982 113865 104907 FALSE TRUE 103310.8755 129062.7187 112206.9333 121503.3314 108568.3228 116198.9529 90183.02617 115414.0476 109767.0209 125461.5181 0.82344672 1.028703627 0.894353384 0.96845099 0.865351579 0.926172062 0.718810258 0.919915918 0.874905888 1 16.9368854 3.221813899 24.97460562 0.873620187 0.933422944 0.054967267 0.082969613 523.1980969 780250.3065 0.022536658 0.027002769 1666.53293 -3.221813899 0.059802756 NPPS(ph)PRPSQLPVLDR ddPTM_MDA-MB-175_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 124.82 5.71E-05 1043480000 830370 878342 977187 1000200 1048128 1248070 1058456 1025172 968106 754054 TRUE FALSE 863153.6488 1029190.406 1002653.296 1198036.575 869967.5769 958224.6572 975491.453 1011431.246 933264.0542 901796.4441 0.957149093 1.141266871 1.111839931 1.328499999 0.964705043 1.062573116 1.081720226 1.12157378 1.03489436 1 19.7824423 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPQNSAQTADGSHCAVSDVEMQEHYDEFFEEVFTEMEEK 39 0 Q01081-2 Q01081-2 U2AF1 Splicing factor U2AF 35 kDa subunit 0 ; 337.92 5.59E-130 158303000 48033 40757.6 54383 37956.7 67832 72442 61926 53486 57319 32284.5 FALSE TRUE 49929.37993 47757.40075 55800.26566 45464.42197 56301.94087 55618.44337 57072.07831 52769.10766 55256.10039 38610.02965 1.29317124 1.236916966 1.445227216 1.177528802 1.458220607 1.440518018 1.478167171 1.366720205 1.431133332 1 15.23668804 4.255323126 24.94887481 1.3700955 1.265044067 0.037381242 0.144714043 599.5662514 892362.6368 0.032283253 0.08789711 18002.09818 -4.255323126 -0.105051432 NPS(ph)PTTRPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NPSPTTRPVSR 11 1 H0Y5D5;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-2;Q9ULV3;A0A494C0L7;Q9ULV3-3;Q9ULV3-4;A0A0U1RQR2 H0Y5D5 CIZ1 Cip1-interacting zinc finger protein 1 NPS(0.957)PT(0.043)TRPVSR;NPS(0.976)PT(0.024)TRPVSR;NPS(0.967)PT(0.033)TRPVSR 136.14 6.39E-05 1699880000 152891 188269 229479 210469 223274 296325 209282 207493 210121 214741 TRUE FALSE 158927.2547 220602.7362 235459.4113 252099.14 185321.9652 227508.0096 192877.93 204711.8957 202558.7863 256815.3875 0.618838522 0.858993452 0.916843082 0.981635651 0.721615504 0.885881535 0.75103728 0.79711694 0.788733059 1 17.97037212 NPSDSAVHS(ph)PFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NPSDSAVHSPFTK 13 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK;NPSDSAVHS(0.993)PFT(0.007)K;NPSDSAVHS(1)PFTK;NPSDSAVHS(1)PFTK 229.68 5.63E-12 2788530000 3941150 2992810 3804180 3571600 4299380 5128850 5273850 4378770 4197290 2500320 TRUE FALSE 4096749.645 3506801.837 3903320.056 4278051.82 3568572.923 3937752.316 4860471.856 4320079.75 4046230.353 2990209.832 1.370054235 1.172761122 1.305366605 1.430686159 1.193418898 1.316881602 1.6254618 1.444741337 1.353159336 1 21.5118153 2.45345694 24.99597426 1.414813438 1.291798678 0 0.164495016 502.2889799 530551.2166 0.053884451 0.045084948 284.0906499 -2.45345694 -0.123014761 NPSDSAVHS(ph)PFTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NPSDSAVHSPFTKR 14 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 NPSDSAVHS(0.995)PFT(0.005)KR;NPSDSAVHS(0.99)PFT(0.01)KR;NPSDSAVHS(0.5)PFT(0.5)KR;NPSDSAVHS(1)PFTKR;NPSDSAVHS(1)PFTKR;NPSDSAVHS(0.999)PFT(0.001)KR;NPSDSAVHS(0.998)PFT(0.002)KR 232.84 8.16E-15 3823950000 2066220 2036350 2350670 1846480 2845580 2990020 2407440 2433450 2417890 1955010 TRUE FALSE 2147795.961 2386077.272 2411930.391 2211708.233 2361889.328 2295633.169 2218738.562 2400833.583 2330870.611 2338056.779 0.918624381 1.020538634 1.031596159 0.945960018 1.010193315 0.981855184 0.948966929 1.026849991 0.996926436 1 21.15687853 1.69634332 15.52734758 1.00882243 0.983208915 0.118986615 0.034264735 0.355795881 117.0196995 0.01551948 0.008567036 49.69850451 -1.69634332 -0.025613515 NPSPT(ph)TRPVSR ddPTM_MDA-MB-175_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(0.307)PT(0.687)T(0.006)RPVSR 117.83 0.0012976 263850000 47670 56681 49116 52803 54855 87605 61989 50194 57053 58873 TRUE FALSE 49552.04841 66415.52083 50396.00331 63247.2758 45530.76669 67260.06642 57130.1402 49521.23153 54999.67367 70408.03716 0.703783977 0.943294594 0.715770604 0.898296251 0.646670019 0.955289611 0.811415039 0.703346287 0.781156185 1 16.1034525 -0.949769921 5.427307492 1.00000041 0.794774363 0.266158186 0.101890817 4.63E-07 8.95E-08 0.090440002 0.02131687 0.112261303 0.949769921 -0.205226047 NPTDAYQLNYDMHNPFDICAASYRPIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NPTDAYQLNYDMHNPFDICAASYRPIYR 28 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 242.97 1.32E-45 1360780000 429720 496770 486310 483910 594110 661120 582140 527540 459680 384970 FALSE TRUE 446685.6774 582086.3832 498983.6381 579625.9537 493123.3944 507584.8994 536510.3457 520469.1892 443136.2066 460397.5008 0.970217424 1.264312648 1.083810484 1.258968506 1.071081823 1.102492734 1.165319848 1.130477877 0.962507846 1 18.81252048 1.244333702 24.11688763 0.981253877 1.13638774 0.340839637 0.082919436 78.88556034 329559.8198 0.053199704 0.018207017 17.55228661 -1.244333702 0.155133864 NPVAS(ph)PT(ph)QPS(ph)GT(ph)EKGGHVLKDK ddPTM_MDA-MB-175_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 60.218 0.034279 861060000 0 473680 341050 453640 234110 456730 222830 378080 301920 548550 TRUE FALSE 0 555030.8553 349938.0432 543368.638 194316.0658 350661.3793 205364.0023 373012.456 291053.9582 656027.8699 0 0.846047677 0.533419477 0.828270662 0.296200931 0.534522077 0.313041582 0.568592392 0.443660966 1 19.32339758 -1.276248542 3.411530206 1.00169059 0.500576985 0.295407691 0.237559675 70547690.18 107056372.4 1242069.447 0.051792506 0.052936041 1.276248542 -0.501113605 NPVWYQALTHGLNEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 192.62 1.76E-10 347260000 119160 128770 118380 128470 168910 179540 116200 141450 126330 105880 FALSE TRUE 123864.5288 150885.2458 121465.0801 153880.9826 140198.7385 137844.556 107091.9404 139554.0941 121783.408 126625.1588 0.978198408 1.191589785 0.959249182 1.215248091 1.107194967 1.088603223 0.845739831 1.102104001 0.961763121 1 16.95020455 2.431719586 24.99994348 0.990080757 1.095816793 0.247069047 0.095044385 184.1119375 101378.2828 0.030869986 0.025827689 270.2213045 -2.431719586 0.105736036 NPWGEVEWTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NPWGEVEWTGR 11 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ;;; 180.19 1.58E-05 483457000 327346 296924 332817 287901 296113 347774 276909 327446 293939 215873 FALSE TRUE 340269.8728 347918.3873 341490.4844 344846.9585 245779.818 267008.7591 255204.149 323057.122 283360.1928 258169.1812 1.318011202 1.34763718 1.322739154 1.335740218 0.952010681 1.034239477 0.988515158 1.251338833 1.097575595 1 17.97795726 3.255600874 24.99919964 1.073472669 1.331625791 0.746905511 0.078525949 142.5662588 209153.0042 0.024262478 0.032769422 1801.36149 -3.255600874 0.258153122 NPYYGGESASITPLEDLYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NPYYGGESASITPLEDLYKR 20 1 P50395;P50395-2;Q5SX87;V9GYF8;Q5SX90;V9GYJ7 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 230.62 2.49E-25 1253260000 503038 374064 519503 323356 690121 627195 548943 482053 523964 324458 FALSE TRUE 522898.3287 438306.5822 533041.675 387314.8517 572814.4789 481538.4665 505915.4133 475591.868 505106.638 388029.333 1.347574228 1.129570744 1.373714896 0.998158693 1.476214374 1.240984703 1.303807136 1.225659577 1.301722821 1 18.56580619 -0.973715955 4.925225844 0.99999769 1.261964571 0.287370391 0.125670808 2.83E-06 5.89E-07 0.107926349 0.02543826 0.106239017 0.973715955 0.261966881 NQALNTDNYGHDLASVQALQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQALNTDNYGHDLASVQALQR 21 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 290.98 1.01E-54 1698960000 526740 611590 639310 607610 724950 1044530 697980 715640 642030 566050 FALSE TRUE 547536.1019 716625.825 655970.9438 727793.4445 601723.2579 801953.7375 643270.5038 706048.0164 618923.4657 676956.6598 0.808820024 1.058599269 0.968999912 1.07509607 0.888865261 1.184645613 0.950238829 1.042973736 0.914273398 1 19.36870395 4.746804827 24.73028566 1.011808109 0.808819906 0.348793344 0.082115525 915.2227783 2745335.317 0.017504956 0.196515585 55821.9273 -4.746804827 -0.202988203 NQDECVIALHDCNGDVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQDECVIALHDCNGDVNR 18 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5;Q5VU81;Q5VU80;Q5VU79;Q5VU78;Q5VU77 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 0 ;;; 266.78 3.47E-31 2018770000 805040 843600 800000 954970 1022280 1331880 964620 969120 871850 793900 FALSE TRUE 836823.6008 988481.7377 820848.6572 1143860.216 848513.2107 1022571.055 889010.5638 956130.5316 840472.2888 949449.5049 0.881377679 1.041110383 0.864552199 1.204761506 0.893689666 1.07701468 0.936343175 1.007036737 0.88522063 1 19.85673175 4.757709196 22.45188602 0.990920924 0.881377273 0.099876374 0.097762631 2223.261509 2606620.827 0.020916135 0.629136664 57241.26144 -4.757709196 -0.109543651 NQEIPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQEIPHK 7 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ;;; 87.616 0.019211 1420660000 2116260 2040160 2368970 2050890 2982290 3504170 2703910 2573760 2440850 1860950 FALSE TRUE 2199811.579 2390541.61 2430707.304 2456549.921 2475361.411 2690379.624 2491970.469 2539262.957 2353004.285 2225567.522 0.988427247 1.07412675 1.092174144 1.103785842 1.112238288 1.208851044 1.11970113 1.14095076 1.057260344 1 21.08574184 5.115516238 1.041946935 1.118571218 0.818423898 0.295376656 0.051767881 3.775191707 1.957810314 0.01468476 1.513579254 130471.6752 -5.115516238 -0.30014732 NQEQMKPLEEKQEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQEQMKPLEEKQEEER 16 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 178.12 1.60E-09 446050000 451400 198639 325920 167730 566710 475510 339100 297290 352190 165132 FALSE TRUE 469221.6206 232753.7031 334413.7429 200906.4934 470380.8366 365080.0089 312520.4559 293305.3138 339514.7507 197486.4538 2.375968638 1.178580599 1.693350286 1.017317844 2.381838489 1.848633169 1.582490596 1.485192064 1.719179945 1 17.59139417 -0.259209556 0.611552321 0.941468811 1.692906371 0.200723963 0.417495252 11.78640814 4.126303775 2.027337388 0.159413194 0.550541985 0.259209556 0.75143756 NQESLGS(ph)PHICDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQESLGSPHICDLGK 15 0 A4D1E1;A0A087WUA7 A4D1E1 ZNF804B Zinc finger protein 804B 1 NQES(0.001)LGS(0.999)PHICDLGK;NQES(0.002)LGS(0.998)PHICDLGK 84.687 0.0086353 213550000 764890 383830 509070 410300 836770 846720 711850 480990 580180 264271 TRUE FALSE 795088.4478 449749.8167 522336.7824 491456.1154 694536.1343 650082.1122 656053.3369 474543.1158 559299.4351 316049.8427 2.515705881 1.423034458 1.65270382 1.554995602 2.197552539 2.05689744 2.07579074 1.501481892 1.769655794 1 18.26979257 0.628928422 0.969035237 1.004068127 1.877826857 0.398053983 0.325473331 1.268311867 1.961963485 0.310296539 0.100452656 4.255282746 -0.628928422 0.87375873 NQEYETLDHLECDLNLMFENAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NQEYETLDHLECDLNLMFENAK 22 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;H0Y5B5;Q86U86-6 Q86U86-8 PBRM1 Protein polybromo-1 0 190.57 1.73E-17 19691000 23919 16913 24097 16245 28979 33767 23978 25314 25345 12535 FALSE TRUE 24863.34059 19817.67619 24724.98762 19458.21251 24053.15993 25925.12599 22098.54171 24974.70724 24432.8384 14990.99325 1.658551916 1.32197219 1.649322843 1.297993548 1.604507422 1.729380139 1.474121249 1.66598082 1.629834527 1 13.87180835 -1.4135653 4.6811989 0.998997418 1.557619556 0.587915933 0.140414202 0.001400542 0.000175452 0.129599369 0.030495654 0.038586439 1.4135653 0.558622139 NQGGYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQGGYDR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ; 127.31 0.0089977 260880000 394810 386060 378870 349490 475480 599420 441140 437900 375410 333540 FALSE TRUE 410397.4037 452362.8019 388743.6634 418618.0789 394658.0794 460213.7893 406562.2941 432030.6668 361899.0674 398890.777 1.02884656 1.134051796 0.974561674 1.049455397 0.989388831 1.153733844 1.019232125 1.08308011 0.907263563 1 18.60563424 1.244824781 24.99194017 0.953631772 1.05474097 0.322692574 0.058182386 143.1761077 571242.8043 0.038078232 0.013135235 17.5721451 -1.244824781 0.101109198 NQGGYDRYS(ph)GGNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYR 182.31 9.31E-07 627570000 139890 138200 157960 179890 188520 263150 219210 197800 166450 131680 TRUE FALSE 145412.9652 161934.775 162076.5674 215471.7051 156475.4377 202037.4006 202027.7474 195148.8145 160459.497 157480.1748 0.923373151 1.028286736 1.029187119 1.368246545 0.993619914 1.282938635 1.282877338 1.239196075 1.018918713 1 17.26481069 3.973944723 22.8886519 1.187631837 0.989056541 0.285305593 0.126727819 264.8244067 232640.6826 0.030913667 0.056069037 9417.697214 -3.973944723 -0.198575296 NQGGYDRYS(ph)GGNYRDNYDN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NQGGYDRYSGGNYRDNYDN 19 2 P98179 P98179 RBM3 RNA-binding protein 3 1 NQGGYDRYS(1)GGNYRDNYDN 114.2 0.00012767 324340000 52733 55420 56230 45338 71499 97279 59855 62145 56173 57346 TRUE FALSE 54814.93956 64937.95389 57695.39999 54305.72108 59345.62552 74687.42653 55163.4087 61312.04792 54151.3447 68581.85074 0.799263055 0.946867913 0.841263386 0.791838081 0.865325518 1.089026116 0.804344125 0.893998153 0.789587101 1 16.06553922 2.983979041 24.8629864 0.906336474 0.848936996 0.117768211 0.090393908 1814.895172 2816547.375 0.027061445 0.029474178 963.7825098 -2.983979041 -0.057399478 NQGGYGGSSSS(ph)SSYGSGR ddPTM_MDA-MB-175_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 NQGGYGGSSS(0.002)S(0.713)S(0.26)S(0.026)YGSGR 277.03 4.21E-39 210120000 262380 310620 332090 302480 399210 458760 267920 321490 252240 249650 TRUE FALSE 272738.965 363966.5687 340744.5382 362309.6412 331352.4268 352219.9426 246919.7303 317180.9524 243161.9317 298564.1377 0.913502094 1.219056554 1.141277519 1.2135069 1.109819918 1.179712826 0.827024077 1.062354491 0.814437841 1 18.18768136 2.251937001 24.99958059 0.941489096 1.137013127 0.466060747 0.106017365 199.3667416 372602.9458 0.034682533 0.02886196 178.6228446 -2.251937001 0.195524031 NQGGYGGSSSSS(ph)SYGSGR ddPTM_MDA-MB-175_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 NQGGYGGSSSS(0.023)S(0.89)S(0.087)YGSGR 278.46 3.71E-39 127600000 211960 241090 267630 240570 355260 388220 219480 267560 226560 217420 TRUE FALSE 220328.3445 282495.3321 274604.6577 288154.028 294873.0321 298061.7885 202276.5841 263973.7958 218406.1499 260019.2862 0.847353855 1.086439918 1.056093421 1.108202519 1.134042926 1.146306464 0.777929157 1.015208524 0.839961347 1 17.98825911 2.253244992 24.9893703 0.916163034 1.069095271 0.356197483 0.101539308 257.2097249 437710.2098 0.03439382 0.028662111 179.1616246 -2.253244992 0.152932237 NQGGYGGSSSSSS(ph)YGSGR ddPTM_MDA-MB-175_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 NQGGYGGSSSSS(0.005)S(0.995)YGSGR 214.42 1.52E-18 0 151660 184530 177280 162700 226760 303340 187340 195800 181240 159500 TRUE FALSE 157647.6539 216221.5921 181900.0624 194881.5744 188215.4162 232893.8822 172655.8013 193175.6213 174717.2078 190750.9712 0.826457936 1.133528132 0.953599666 1.021654428 0.986707512 1.220931567 0.905137207 1.012711076 0.915944001 1 17.54133088 NQGGYGGSSSSSSYGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 311.26 8.52E-61 578520000 58536.7 61229.7 66820 60989 81363.2 96132.3 72881.3 72410.5 60548.1 44261 FALSE TRUE 60847.77412 71745.42467 68561.38409 73052.44217 67533.11233 73807.03022 67168.67327 71439.95569 58368.98571 52933.09552 1.149522308 1.355398243 1.295246073 1.38009012 1.275820196 1.394345626 1.268935297 1.349627393 1.102693601 1 15.6918824 1.097391619 3.890551456 1.003127231 1.313622484 0.707314721 0.067494899 0.095965421 2.559272941 0.058630556 0.015153684 12.51386944 -1.097391619 0.310495253 NQIGDKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NQIGDKEK 8 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 144.77 0.00052903 3507310000 6104360 3097780 3926120 2776351 7327680 6493200 5631090 4284440 4732880 2403765 FALSE TRUE 6345364.846 3629799.618 4028437.913 3325504.941 6082123.571 4985252.705 5189710.452 4227014.09 4562544.573 2874736.729 2.207285552 1.262654622 1.401324119 1.156803302 2.115714984 1.734159742 1.805281993 1.470400419 1.587117362 1 21.45499841 0.404732575 1.222057202 0.999965893 1.631745288 0.261716668 0.323194858 4.024277609 6.891543264 0.306664778 0.091932374 2.539408533 -0.404732575 0.631779395 NQKDPGVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 NQKDPGVLDR 10 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ;;;;;;;;;; 164.33 5.64E-06 67548050000 48425590 38906230 47061310 31163510 70331760 64752780 46607710 50961050 51692160 34102890 FALSE TRUE 50337469.69 45588072.35 48287766.4 37327559.26 58376792.56 49714928.18 42954475.9 50278000.48 49831769.26 40784698.36 1.234224396 1.117773925 1.183967722 0.915234408 1.43134055 1.218960301 1.053200775 1.23276627 1.221825127 1 25.28152465 4.768907204 21.24290002 1.162836106 1.234225124 0.02649264 0.136357525 6770.651069 4738908.061 0.031040714 2.51511534 58736.38371 -4.768907204 0.071389019 NQKPEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQKPEVR 7 1 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ;;; 112.17 0.0058498 1912460000 4481470 3093330 3976190 2994430 5361710 5395500 4725940 4352010 4313460 2479240 FALSE TRUE 4658401.896 3624585.365 4079812.778 3586719.317 4450328.449 4142476.895 4355508.474 4293678.424 4158219.417 2964999.61 1.571130694 1.222457282 1.375991 1.209686269 1.500954143 1.397125612 1.468974383 1.448121076 1.402435064 1 21.49960048 -0.683437652 5.905618602 0.999999993 1.397794587 0.555691638 0.107196971 8.91E-09 2.01E-09 0.099615545 0.023479609 0.207282362 0.683437652 0.397794594 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NQKPSQVNGAPGSPTEPAGQK 21 1 Q9BQG0;Q9BQG0-2;I3L1L3 Q9BQG0 MYBBP1A Myb-binding protein 1A 1 NQKPSQVNGAPGS(0.973)PT(0.027)EPAGQK 205.89 2.73E-22 404830000 915450 433830 599140 428810 844550 905820 752140 641310 646140 274160 TRUE FALSE 951592.6729 508336.9278 614754.0806 513627.3381 700993.6927 695457.0328 693185.3014 632714.2884 622885.5476 327876.4029 2.902290816 1.550391926 1.874956768 1.566527306 2.137981527 2.121095104 2.114166483 1.92973414 1.899757171 1 18.32279255 0.450093504 1.592985938 1.00000798 1.999421131 0.422569263 0.356417306 3.391582173 8.799186088 0.320287424 0.091491479 2.8189898 -0.450093504 0.999413151 NQLNPIGSLQELAIHHGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQLNPIGSLQELAIHHGWR 19 0 O75569;O75569-3;O75569-2 O75569 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 0 ; 153.21 2.78E-08 455920000 232838 227030 277071 239716 328490 410850 270780 299012 284247 227119 FALSE TRUE 242030.624 266020.6365 284291.6979 287131.1093 272653.3871 315436.314 249555.556 295004.2332 274017.006 271618.6196 0.891067867 0.979390282 1.04665762 1.05711129 1.003809634 1.161320658 0.918771903 1.086097241 1.008829978 1 18.05122285 4.602277435 2.349639561 1.038818479 0.876832475 0.354157766 0.05987791 0.419171316 3.407306872 0.013803334 0.122189704 40020.03228 -4.602277435 -0.161986004 NQLS(ph)QNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQLSQNR 7 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 1 NQLS(1)QNR;NQLS(1)QNR 60.76 0.061557 974850000 5891.8 7512.7 19213.5 7350.3 5553.3 12578 12618 11387 7786.6 10464 TRUE FALSE 6124.412813 8802.947784 19714.21959 8804.167402 4609.35205 9656.950121 11628.96819 11234.37589 7506.361787 12514.22045 0.48939627 0.703435569 1.575345397 0.703533027 0.368329139 0.771678121 0.929260295 0.897728782 0.599826558 1 13.6112808 -1.778146568 10.25056241 1.001052667 0.802114809 0.038756738 0.311521962 0.007608064 0.000164662 0.306210302 0.071836837 0.016666846 1.778146568 -0.198937857 NQLTSNPENTVFDAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQLTSNPENTVFDAKR 16 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 199.01 6.29E-11 579460000 152357 137677 148762 120383 229918 224540 136384 155398 151511 138231 FALSE TRUE 158372.172 161321.9538 152638.8599 144194.3981 190836.6205 172393.9879 125693.8657 153315.144 146058.1487 165314.7179 0.958004067 0.975847498 0.923322871 0.872241746 1.154383729 1.042822987 0.760330764 0.92741376 0.8835157 1 17.33485565 -0.860005816 4.539170484 1.000000284 0.942258299 0.027320339 0.099255311 3.17974E+12 7.98743E+11 13650805.76 0.02396808 0.138036578 0.860005816 -0.057741985 NQMAEKDEYEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NQMAEKDEYEHK 12 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;;; 170.18 2.51E-05 1586750000 1835880 630995 1012026 867345 1548140 1588230 1758990 1135215 1225329 350762 FALSE TRUE 1908361.96 739363.4828 1038400.229 1038903.252 1284987.716 1219387.652 1621115.768 1119999.3 1181229.649 419487.0982 4.549274503 1.762541652 2.475404449 2.476603588 3.063235369 2.906853769 3.864518777 2.669925499 2.815890295 1 18.67826691 3.226039516 24.69797685 2.879077933 2.716386962 0 0.947064774 1815.634878 3581347.201 0.257875455 0.310284305 1682.827172 -3.226039516 -0.162690971 NQNYLVPS(ph)PVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQNYLVPSPVLR 12 0 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 NQNYLVPS(1)PVLR;NQNYLVPS(1)PVLR 161.87 6.74E-05 348020000 424280 463320 454530 412630 572000 694250 505040 504660 464680 362260 TRUE FALSE 441030.902 542891.6059 466375.4252 494246.9824 474771.6443 533020.959 465453.6451 497895.8582 447956.2576 433237.9111 1.017987786 1.253102722 1.076488029 1.140821174 1.095868187 1.230319289 1.074360376 1.149243511 1.033972896 1 18.72479997 1.131836325 4.111389456 1.001504975 1.132843 0.311670837 0.067558126 0.219626403 6.179731344 0.057016639 0.014762218 13.5467877 -1.131836325 0.131338024 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8;Q9NYJ8-2 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 NQPTVYIAAS(0.889)PPNT(0.111)DELMSR;NQPTVYIAAS(0.999)PPNT(0.001)DELMSR;NQPTVYIAAS(0.992)PPNT(0.008)DELMSR;NQPTVYIAAS(0.889)PPNT(0.111)DELMSR 231.93 6.87E-26 635697000 384839 444091 496930 479477 647936 790410 560065 586136 560820 449120 TRUE FALSE 400032.7409 520360.1747 509880.404 574316.1195 537800.0702 606849.2563 516165.6418 578279.8056 540636.1978 537116.4651 0.744778399 0.968803246 0.949292076 1.069258079 1.001272732 1.129828065 0.960993891 1.076637644 1.006553016 1 19.03487542 5.41079217 1.012864449 1.037181197 5.46E-12 0.738849994 0.050308872 2.800523193 0.873538402 0.013581738 4.371825802 257508.8562 -5.41079217 -1.037181197 NQQFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQQFHK 6 0 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;; 136.44 0.013169 2953570000 4644810 3292590 4079700 3321530 5482990 5876200 4688400 4479930 4244400 2680010 FALSE TRUE 4828190.685 3858066.72 4186020.334 3978518.72 4550993.318 4511541.605 4320910.957 4419883.866 4091644.873 3205106.648 1.506405626 1.203724913 1.306047128 1.24130619 1.419919466 1.407610448 1.348133286 1.379013041 1.276601787 1 21.61194093 0.856772151 4.123612216 1.00002736 1.346576874 0.616448353 0.083005343 0.604122769 16.46238794 0.077223854 0.019700396 7.19071624 -0.856772151 0.346549514 NQS(ph)PTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 2 NQS(0.973)PT(0.027)EAEKPASSSLPS(0.556)S(0.444)PPPQLLTR;NQS(0.98)PT(0.02)EAEKPAS(0.025)S(0.006)S(0.006)LPS(0.475)S(0.424)PPPQLLT(0.064)R 170.47 4.00E-12 321050000 354300 238540 302410 245200 422640 417070 365320 319250 346910 205091 TRUE FALSE 368288.0376 279507.3894 310291.053 293699.8282 350799.8038 320211.8133 336685.2638 314970.9759 334424.7769 245274.6547 1.501533201 1.139568985 1.265075894 1.197432439 1.430232586 1.305523449 1.37268673 1.28415623 1.363470584 1 17.90403864 -1.069552422 4.741704337 0.999987964 1.310730398 0.469287533 0.101122147 1.20E-05 2.35E-06 0.09129302 0.021517138 0.085201566 1.069552422 0.310742434 NQS(ph)PTEAEKPASSSLPSSPPPQLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 NQS(0.964)PT(0.036)EAEKPASSSLPSSPPPQLLTR;NQS(0.998)PT(0.002)EAEKPASSSLPSSPPPQLLTR;NQS(0.967)PT(0.033)EAEKPASSSLPSSPPPQLLTR 259.43 5.91E-53 1859080000 741058 394502 572647 409691 731425 778993 731752 621739 629133 315367 TRUE FALSE 770315.5421 462254.6497 587570.6513 490726.657 607097.6398 598083.6815 674395.3662 613405.6057 606490.6262 377157.1256 2.04242606 1.225628838 1.557893545 1.301119941 1.609667692 1.585767949 1.788101882 1.626392726 1.608058247 1 18.52480616 NQS(ph)PVLEPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQSPVLEPVGR 11 0 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 NQS(1)PVLEPVGR;NQS(1)PVLEPVGR;NQS(1)PVLEPVGR;NQS(1)PVLEPVGR 182.72 5.94E-06 541110000 734230 775070 886200 805690 1038980 1199490 839400 829410 741200 583637 TRUE FALSE 763217.9673 908182.2433 909295.1 965053.0773 862374.5507 920926.6259 773605.6346 818293.1156 714524.3568 697989.4957 1.093451939 1.301140273 1.302734648 1.382618339 1.235512219 1.319398976 1.108334208 1.17235735 1.023689269 1 19.4128458 1.613241898 1.051926253 1.001600419 1.278431964 0.593373908 0.080882891 0.3224735 0.680477669 0.069969846 0.026447649 41.04326467 -1.613241898 0.276831545 NQSFCPTVNLDKLWTLVSEQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQSFCPTVNLDKLWTLVSEQTR 22 1 P46776;E9PLL6;E9PJD9 P46776 RPL27A 60S ribosomal protein L27a 0 ; 313.65 2.57E-67 2533760000 1380520 1129300 1418570 1009770 1884400 1897860 1172430 1556760 1422460 1305400 FALSE TRUE 1435023.996 1323248.49 1455539.1 1209499.492 1564090.361 1457110.777 1080531.873 1535894.179 1371265.942 1561168.137 0.919198875 0.847601523 0.932339743 0.774740058 1.001871819 0.933346475 0.692130366 0.983810867 0.87835891 1 20.57419449 0.643422578 1.237825958 0.998980806 0.8813098 0.12826842 0.089509462 2.448675345 5.763611119 0.080673969 0.024450777 4.399695069 -0.643422578 -0.117671006 NQSLGQS(ph)APSLTAGLK ddPTM_MDA-MB-175_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 202.35 3.21E-11 92246000 209272 159756 217305 157114 306670 283470 212568 194989 223076 141791 TRUE FALSE 217534.2202 187192.8503 222968.1468 188190.6803 254542.3429 217638.3885 195906.3647 192375.4914 215047.5383 169572.2317 1.282841052 1.10391217 1.314885961 1.109796565 1.501085056 1.283455353 1.155297437 1.1344752 1.268176612 1 17.37154042 0.347920786 0.56914504 0.992091389 1.251868642 0.278344912 0.11511266 3.108601066 1.563314876 0.189788218 0.050848152 2.228028725 -0.347920786 0.259777253 NQTAEKEEFEHQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;; 231.17 3.85E-13 10615140000 8934820 4199630 5751200 4430430 7771820 8523680 9015420 6488950 6084480 2704340 FALSE TRUE 9287573.593 4920883.784 5901080.997 5306755.83 6450768.812 6544184.498 8308767.823 6401976.239 5865500.753 3234203.645 2.871672477 1.521513276 1.824585476 1.640823032 1.994546269 2.023429943 2.569030505 1.979459843 1.813584238 1 21.62497909 3.051633299 24.99952263 1.998838124 1.909828449 0 0.501364051 932.8864237 451673.077 0.138637941 0.165704022 1126.246098 -3.051633299 -0.089009675 NQTYSFS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NQTYSFSPSK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 NQTYSFS(1)PSK;NQTYS(0.001)FS(0.775)PS(0.225)K;NQTYS(0.002)FS(0.99)PS(0.008)K;NQTYSFS(1)PSK 253.97 4.47E-17 1957950000 2808080 1364320 1865810 1454420 2657770 3010380 2748460 1932200 1900520 840890 TRUE FALSE 2918945.167 1598631.347 1914434.541 1742099.935 2206003.205 2311264.868 2533028.523 1906302.019 1832120.656 1005646.296 2.902556475 1.589655681 1.903685769 1.732318751 2.193617392 2.298288054 2.518806597 1.895598908 1.821834043 1 19.93969154 0.808285579 1.718024221 1.003555405 2.115946019 0.470678329 0.363781471 0.601561435 3.184550109 0.338189015 0.096198225 6.43110468 -0.808285579 1.112390614 NQVALNPQNTVFDAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NQVALNPQNTVFDAKR 16 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 262.24 1.14E-26 958390000 793420 558040 662950 407720 1066750 1045390 570350 664110 706050 579920 FALSE TRUE 824744.8343 653879.0291 680227.0216 488365.7991 885424.216 802614.0155 525644.4767 655208.6917 680639.3984 693544.2208 1.189174114 0.942807985 0.980798342 0.704159568 1.276665841 1.15726437 0.757910543 0.944725184 0.981392935 1 19.40362835 2.247259588 24.99171896 0.91377529 1.029865532 0.117178588 0.159953025 450.1878583 1293368.476 0.057434143 0.047370512 176.7093739 -2.247259588 0.116090242 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_MDA-MB-175_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 293.06 1.41E-81 929320000 519246 160835 316456 175555 479108 432555 473915 317770 347227 104671 TRUE FALSE 539746.233 188457.1601 324703.1033 210279.255 397669.3933 332100.6567 436768.304 313510.8129 334730.3681 125179.2784 4.311785784 1.505498055 2.593904578 1.67982479 3.176798895 2.653000248 3.489142209 2.504494489 2.67400781 1 16.93363624 NQVIIPLVLS(ph)PDRDEDLMR ddPTM_MDA-MB-175_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 199.46 4.20E-16 86829000 63726 74607 72647 64965 86389 113410 72625 78323 73191 57746 TRUE FALSE 66241.95169 87420.17189 74540.2405 77814.8831 71704.62864 87072.24625 66932.46273 77273.2083 70556.87021 69060.22309 0.959191105 1.265854177 1.079351285 1.126768487 1.038291298 1.260816174 0.969189784 1.118924974 1.021671623 1 16.07556737 1.350838005 0.911650955 1.001258586 1.116932871 0.117753592 0.098150986 1.016166864 1.776164885 0.08319284 0.030684786 22.43045094 -1.350838005 0.115674284 NQYDNDVTVWSPQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 0 ;; 301.93 5.28E-44 955630000 355117 366461 354828 347746 420228 530376 400827 405261 379263 320830 FALSE TRUE 369137.2934 429397.8261 364075.1092 416529.1209 348797.7947 407204.2119 369409.1324 399829.1392 365613.3987 383690.4958 0.962070464 1.119125521 0.948877059 1.085586235 0.909060293 1.06128303 0.962778949 1.042061619 0.952886253 1 18.5495835 NQYVTLHDMILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NQYVTLHDMILK 12 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 107.14 0.0018461 633050000 230550 152920 216470 171130 286170 286750 260230 225050 230760 120870 FALSE TRUE 239652.292 179182.8204 222111.386 204979.0032 237526.9256 220156.6582 239832.4926 222033.5729 222454.9927 144552.1623 1.657894896 1.239572052 1.536548347 1.418027928 1.643191785 1.5230257 1.659141508 1.536010042 1.538925389 1 17.14123066 -1.445917797 6.449436046 0.999859492 1.526281003 0.637083578 0.119554825 0.000231631 1.99E-05 0.111009406 0.026158299 0.035816422 1.445917797 0.526421511 NRAEVSQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRAEVSQPR 9 1 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 113.44 0.0016409 74780000 49430 38581 42903 42153 79944 76456 58055 49776 46619 41041 FALSE TRUE 51381.53457 45206.98663 44021.08743 50490.73759 66355.14744 58700.2527 53504.4974 49108.83414 44941.1913 49082.19817 1.046846647 0.921046496 0.896885002 1.028697562 1.35191882 1.195958105 1.090099861 1.000542681 0.915631185 1 15.58291224 3.478315554 24.99959136 1.098980527 0.953413601 0.213116959 0.118126321 69.45601635 1453904.453 0.035698116 0.048983931 3008.261284 -3.478315554 -0.145566926 NRDEAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRDEAIK 7 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;; 117.4 0.0047788 10512200000 10410300 9487200 10728600 9769200 13773300 15046000 12079600 11129400 11393100 9027900 FALSE TRUE 10821306.68 11116552.8 11008196.13 11701518.6 11432119.39 11551794.52 11132769.39 10980228.6 10983064.56 10796744.16 1.002274994 1.029620841 1.019584791 1.083800675 1.058848781 1.069933154 1.03112283 1.016994423 1.017257091 1 23.36409299 -0.490503841 6.217673565 1 1.03720198 0.163742356 0.024783433 0 0 0.025687481 0.006054597 0.323218462 0.490503841 0.03720198 NRDNDPNDYVEQDDILIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRDNDPNDYVEQDDILIVK 19 1 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 0 170.19 1.16E-11 106410000 123960 102950 122500 93973 172460 169570 132130 138260 143330 90829 FALSE TRUE 128854.0365 120630.8617 125692.4506 112560.5789 143145.3108 130189.9374 121773.3053 136406.8508 138171.5813 108625.2035 1.186225962 1.110523688 1.157120508 1.036228935 1.317790956 1.19852422 1.121040987 1.255756918 1.272002968 1 16.72899935 3.249473171 24.99995501 1.205219382 1.124138713 0.124061631 0.090436958 391.5753629 897069.3509 0.023718111 0.031809911 1776.123545 -3.249473171 -0.081080669 NRDSDKTDTDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRDSDKTDTDWR 12 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;; 119.25 0.0003023 1557110000 2608050 1955820 2512730 1357020 4035320 3388190 1931820 2439700 2819800 2159570 FALSE TRUE 2711017.828 2291716.871 2578213.808 1625434.506 3349397.748 2601334.221 1780398.901 2406999.812 2718315.949 2582696.394 1.049685063 0.887334987 0.998264377 0.629355626 1.296860814 1.007216422 0.689356637 0.931971647 1.052510839 1 21.30044663 4.755788367 21.9405435 0.93453752 1.049685545 0.028951161 0.177287583 2506.929219 3192426.562 0.041189884 0.984128871 56988.64977 -4.755788367 0.115148026 NRDVITLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NRDVITLR 8 1 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 160.59 0.00032147 259340000 174242 191948 204646 163136 261080 301260 202913 209927 197886 180461 FALSE TRUE 181121.2087 224913.5759 209979.2429 195403.8139 216701.7149 231296.9306 187008.1488 207113.2719 190764.1215 215818.8778 0.839227831 1.042140419 0.972941964 0.905406496 1.004090639 1.071717789 0.866505056 0.959662445 0.883908412 1 17.71946154 -0.96875152 4.093028813 1.000002705 0.95366706 0.03907051 0.072527524 8657131.167 2115204.655 213.3248983 0.016110106 0.107460407 0.96875152 -0.046335645 NRDYPLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 87.001 0.012546 127290000 262050 214000 268380 206280 365660 341220 244220 275710 267660 234310 FALSE TRUE 272395.9363 250752.8353 275374.2033 247081.5683 303505.2438 261976.8262 225077.3982 272014.5584 258026.9689 280218.5584 0.972083855 0.894847353 0.982712226 0.881745912 1.083101867 0.93490177 0.803220884 0.970722853 0.920806139 1 18.09619298 2.482455515 24.99754923 0.915674375 0.961039138 0.06210832 0.069980751 627.7780718 2941935.548 0.023142357 0.019893957 303.7074988 -2.482455515 0.045364763 NREEEIEQLNEVIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NREEEIEQLNEVIEK 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;A0A6I8PUA5;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ; 157.8 1.29E-08 50189000 197129 152313 182133 142760 260610 243690 211798 197496 201477 121771 FALSE TRUE 204911.8051 178471.5729 186879.5356 170997.5019 216311.6053 187096.6907 195196.7193 194848.8892 194225.8821 145629.696 1.407074318 1.225516346 1.283251567 1.174193908 1.485353683 1.284742712 1.340363433 1.337974977 1.333696955 1 17.15194505 -0.29360797 8.860368851 1.000003924 1.317362347 0.571688587 0.082855629 0 0 0.075938643 0.01789891 0.508618357 0.29360797 0.317358424 NREEEWDPEYT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 NREEEWDPEY(0.036)T(0.964)PK 79.347 0.033555 504270000 613210 290310 396130 262850 488170 594650 438620 357110 390010 231280 TRUE FALSE 637420.0043 340168.4842 406453.4732 314840.9455 405191.0378 456551.5495 404239.8183 352323.5246 375973.6163 276594.8879 2.304525616 1.229843714 1.469490186 1.138274637 1.464925982 1.650614561 1.461486947 1.273788996 1.359293439 1 18.07741497 4.743390578 24.960569 1.360093042 2.30452601 0.722486259 0.179143946 255.2691648 1319150.957 0.041261131 0.338255848 55384.79822 -4.743390578 0.944432968 NREEEWDPEYTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 100.18 0.0022969 374840000 785130 510760 776960 477000 946290 950570 801720 743000 768420 471580 FALSE TRUE 816127.5387 598479.0568 797208.2159 571349.1763 785439.9638 729814.5235 738879.0915 733041.3003 740764.7143 563977.0721 1.447093471 1.061176219 1.413547209 1.013071638 1.392680665 1.294049988 1.310122571 1.299771456 1.31346601 1 19.10527699 -0.936311061 4.864918999 0.999998138 1.278446553 0.284797624 0.13427643 2.41E-06 5.25E-07 0.115290375 0.027174021 0.115794769 0.936311061 0.278448415 NREELDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NREELDK 7 1 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 127.46 0.0035135 4371400000 3300540 1749210 2235100 2276970 3091910 3763150 4669700 2843200 2968240 1069430 FALSE TRUE 3430847.868 2049623.211 2293348.542 2727347.87 2566348.243 2889215.444 4303676.712 2805091.555 2861413.622 1278964.333 2.682520364 1.602564792 1.793129396 2.132465933 2.006583121 2.259027378 3.364970078 2.19325237 2.237289617 1 20.2865446 2.657133096 5.060058943 2.377836226 2.010282383 0 0.60112696 0.610931656 27.41608596 0.188562509 0.177979665 454.0807549 -2.657133096 -0.367553844 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 24 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELR 38 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;;;;;;;;;;;; 279.72 7.79E-77 10458406700 1203948.2 905925.2 1137998.7 1038938.1 1375378.1 1472876 1510959.4 1184443.8 1266057.6 719944.5 FALSE TRUE 1251481.005 1061510.806 1167655.881 1244436.955 1141591.822 1130822.871 1392526.454 1168568.268 1220492.434 861003.8406 1.453513847 1.232875808 1.356156414 1.445332641 1.325884703 1.313377267 1.617328969 1.357216093 1.417522637 1 19.71566015 -1.188031609 6.565338301 0.999998178 1.390285713 0.587998698 0.098192229 2.55E-06 3.16E-07 0.092737075 0.021858236 0.064858723 1.188031609 0.390287535 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 NREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRR 39 3 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;; 248.49 3.83E-51 12202208000 1047621 914355 1132558 824736 1533028 1408387 1204996 1098497.9 1255873 889409 FALSE TRUE 1088981.886 1071388.359 1162073.392 987866.3192 1272444.448 1081310.464 1110545.265 1083774.332 1210674.376 1063671.665 1.023795145 1.00725477 1.092511374 0.928732382 1.19627559 1.016582936 1.044067734 1.018899317 1.13820309 1 20.02062146 NREELGFRPEYSASQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NREELGFRPEYSASQLK 17 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 188.58 2.27E-10 1464790000 423070 340330 370680 343650 538070 527460 483470 345480 387900 291080 FALSE TRUE 439773.1303 398779.0301 380340.2253 411622.9443 446609.0536 404965.4087 445574.3581 340849.4057 373939.5548 348111.5529 1.263310932 1.145549542 1.09258145 1.182445514 1.282948095 1.163320796 1.279975785 0.979138448 1.074194613 1 18.40919017 1.708961259 8.804110888 1.022094 1.195908409 0.643910955 0.06237541 0.074119806 12.95417024 0.030415531 0.016239077 51.16361938 -1.708961259 0.173814408 NRENS(ph)PSSQSAGLSSINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRENSPSSQSAGLSSINK 18 1 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2 H3BSS6 ZNF106 Zinc finger protein 106 1 NRENS(0.555)PS(0.222)S(0.222)QSAGLSSINK 112.47 0.00016645 1034200000 278300 144610 181710 135720 308640 321490 231710 188960 227590 112180 TRUE FALSE 289287.4989 169445.6426 186445.5119 162565.0109 256177.483 246828.8197 213547.9647 186427.3003 219399.0804 134159.5232 2.156294924 1.263016136 1.389729983 1.211729194 1.909499057 1.839815869 1.591746599 1.389594237 1.635359721 1 17.03358994 -0.338964741 0.725861297 0.964025531 1.584744185 0.278816184 0.286640568 14.42070837 6.154659078 1.757991835 0.100645066 0.458179083 0.338964741 0.620718654 NRENS(ph)SPCQGNGEQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRENSSPCQGNGEQAGR 17 1 Q5T5X7 Q5T5X7 BEND3 BEN domain-containing protein 3 1 NRENS(0.826)S(0.174)PCQGNGEQAGR 73.405 0.015952 113910000 14917 24378 26572 11896 25646 28648 16929 20163 15471 17044 TRUE FALSE 15505.93468 28564.73187 27264.48815 14248.99329 21286.70208 21994.93616 15602.06074 19892.74797 14914.20173 20383.44547 0.760712152 1.40136916 1.337579958 0.699047338 1.044313245 1.079058798 0.765428041 0.975926665 0.731682078 1 14.31511031 3.74618704 24.99700213 0.907603816 1.190035292 0.266551362 0.201667898 719.5836941 2358560.429 0.049989067 0.087968526 5574.257673 -3.74618704 0.282431475 NRENSS(ph)PCQGNGEQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRENSSPCQGNGEQAGR 17 1 Q5T5X7 Q5T5X7 BEND3 BEN domain-containing protein 3 1 NRENS(0.004)S(0.996)PCQGNGEQAGR 109.83 0.00035609 115610000 13870 23443 24893 19787 24452 31966 18149 21816 23052 19310 TRUE FALSE 14417.59831 27469.15289 25541.73203 23700.80954 20295.65777 24542.38095 16726.43396 21523.5922 22222.36302 23093.42479 0.624316161 1.189479393 1.106017503 1.026301199 0.878850061 1.062743234 0.724294214 0.93202253 0.962280962 1 14.49519452 3.246497376 24.78873219 0.916355176 1.009559989 0.021967883 0.161072264 463.7603402 1448444.069 0.043369739 0.057669296 1763.995105 -3.246497376 0.093204812 NREPVQLETLSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NREPVQLETLSIR 13 1 P62314;J3QLI9 P62314 SNRPD1 Small nuclear ribonucleoprotein Sm D1 0 219.84 1.99E-11 1310900000 380500 388330 482530 403920 667040 658930 491040 510150 468490 442520 FALSE TRUE 395522.4338 455022.6567 495105.1282 483814.1704 553656.7791 505903.4937 452551.0017 503312.2737 451629.1364 529223.3214 0.747363954 0.859793282 0.935531576 0.914196618 1.04616852 0.955935752 0.855122938 0.951039482 0.853381017 1 19.01351711 4.638223226 1.878906607 0.938003889 0.709609389 0.536129824 0.055439976 0.506537754 2.194208311 0.014374169 0.188725793 43473.36188 -4.638223226 -0.2283945 NRGPS(ph)PEPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NRGPSPEPLK 10 1 Q92674-2;Q92674 Q92674-2 CENPI Centromere protein I 1 NRGPS(1)PEPLK;NRGPS(1)PEPLK 74.769 0.02483 275833000 493380 343470 442150 343430 621820 614870 570530 474020 467600 272000 TRUE FALSE 512859.0234 402458.3007 453672.7922 411359.429 516123.2585 472075.7609 525810.3678 467666.5372 450771.1673 325293.1922 1.576605461 1.237217102 1.394658121 1.264580504 1.586640209 1.451231603 1.616419834 1.437676989 1.385738091 1 18.3113811 0.738429277 3.05937141 1.000041284 1.443325416 0.548796673 0.120485101 1.518491475 16.82132218 0.115153486 0.030062582 5.47556927 -0.738429277 0.443284132 NRHS(ph)PDHPGMGSSQASSSSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 252.73 3.16E-37 2272720000 158964 416728 403867 408565 476572 574490 460923 469058 408079 357578 TRUE FALSE 165240.0215 488297.7923 414392.1058 489377.9376 395564.4617 441073.404 424794.6509 462771.0447 393392.3165 427638.5629 0.386401124 1.141846958 0.969024176 1.144372795 0.924997173 1.031416346 0.99334973 1.082154616 0.919917778 1 18.70603243 4.744919483 24.99793917 1.026072366 0.38640084 0.864691005 0.075539778 218.4721662 858833.6861 0.016243791 0.153478635 55580.12032 -4.744919483 -0.639671526 NRLENDGATALAEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NRLENDGATALAEAFR 16 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 ;; 233.14 1.10E-19 583483000 299683 333825 371474 345184 503977 547680 383956 421490 385140 405576 FALSE TRUE 311514.7162 391156.847 381154.9176 413460.3649 418311.1696 420489.6202 353860.5254 415840.616 371278.8866 485040.852 0.642244287 0.806441036 0.785820238 0.852423797 0.862424614 0.866915886 0.72954788 0.857331118 0.765459002 1 18.88774674 -5 0.179500239 1.765731581 0.762957689 0.46123967 0.066811535 126.9366211 1.221575612 34.98083922 0.207109643 1.00E-05 5 -1.002773892 NRNEQESAVHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NRNEQESAVHPR 12 1 Q9UJU6-2;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ;;;;; 158.01 3.86E-05 2616851000 972727 1512794 1551479 1318802 1869519 2184466 1352715 1537079 1492565 1277904 FALSE TRUE 1011131.013 1772604.602 1591911.817 1579657.099 1551738.828 1677156.877 1246685.664 1516476.97 1438847.877 1528284.822 0.661611631 1.159865345 1.041632943 1.033614335 1.01534662 1.097411198 0.815741703 0.992273789 0.941478877 1 20.54348201 -0.380002057 7.833374238 0.999998543 0.9813638 0.000263295 0.135731015 0 0 0.121664399 0.028676574 0.416867409 0.380002057 -0.018634743 NRPCLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NRPCLSPK 8 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9 A0A0G2JQJ7 MAPT Microtubule-associated protein tau 1 NRPCLS(1)PK;NRPCLS(1)PK 65.278 0.039175 378660000 394690 175494 244450 171529 370480 428710 346630 259680 265370 136465 TRUE FALSE 410272.666 205633.7293 250820.5678 205456.9242 307505.9419 329148.5997 319460.2349 256199.4144 255819.3855 163202.704 2.513883998 1.25998972 1.536865271 1.258906374 1.884196367 2.016808494 1.957444497 1.569823343 1.567494774 1 17.31630543 0.756652179 1.577738073 1.002345516 1.732841278 0.287738256 0.356403664 1.123603275 4.690175106 0.333209324 0.096129866 5.7102113 -0.756652179 0.730495762 NRPDSGVEEAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRPDSGVEEAWK 12 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 93.228 0.0066487 292440000 769140 313960 378170 280450 567930 446050 524950 349370 498700 256580 FALSE TRUE 799506.2411 367880.1877 388025.4209 335922.1729 471393.4615 342461.6475 483803.0473 344687.2666 480751.8844 306851.9385 2.605511456 1.198885005 1.264536319 1.094737008 1.536224486 1.116048506 1.576666094 1.123301578 1.566722657 1 18.22718317 4.740769674 24.98755763 1.282828348 2.605511916 0.796349121 0.201782525 75.66586688 855831.7493 0.042715674 0.283702925 55051.56558 -4.740769674 1.322683569 NRPDYVS(ph)EEEEDDEDFETAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRPDYVSEEEEDDEDFETAVK 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 NRPDYVS(1)EEEEDDEDFETAVK 288.98 1.85E-47 183670000 152840 97304 139020 97436 177550 181430 152990 133420 142610 67491 TRUE FALSE 158874.2412 114015.2051 142642.9754 116708.55 147370.1144 139295.6321 140998.244 131631.7231 137477.494 80714.56926 1.968346516 1.4125728 1.767251894 1.445941557 1.825818012 1.72578053 1.746874763 1.630829779 1.703255004 1 16.30054149 -1.269532767 5.282827166 0.999905615 1.682076776 0.63470441 0.157303055 0.000155852 2.16E-05 0.135746736 0.031991428 0.053760987 1.269532767 0.682171161 NRPEDYQGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NRPEDYQGGR 10 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;;;;; 212.28 3.97E-08 5696607000 915649.9 1044858 1045139 997324 1308988 1602995 1032725 1001589 917941 828568 FALSE TRUE 951800.4651 1224304.234 1072376.181 1194591.71 1086486.687 1230723.705 951777.316 988164.3377 884904.4827 990910.0357 0.960531664 1.235535205 1.082213463 1.205550118 1.09645341 1.242013564 0.960508302 0.997229115 0.893022021 1 19.91839456 2.216981336 24.99076397 0.966114573 1.140302017 0.514390229 0.082931647 179.250204 207586.7068 0.028456772 0.021035317 164.8091563 -2.216981336 0.174187444 NRPLLDFVSMEELNDMDDYDS(ph)EDDNDWRPTVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVK 33 2 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVSMEELNDMDDYDS(1)EDDNDWRPTVVK;NRPLLDFVS(0.001)MEELNDMDDY(0.117)DS(0.878)EDDNDWRPT(0.004)VVK 197.35 6.26E-27 189067000 61778 62408 66820 52328 76278 81725 71270 68524 56420.2 58932 TRUE FALSE 64217.04314 73126.08853 68561.38409 62678.32222 63312.29281 62745.6073 65683.67117 67605.54786 54389.64802 70478.59708 0.91115666 1.037564474 0.972797231 0.889324204 0.898319425 0.890278892 0.931966212 0.959235153 0.771718653 1 16.10489759 3.795102329 6.687471291 0.908005548 0.980922539 0.196189652 0.062542394 0.363572273 35.26010171 0.015336133 0.027758672 6238.818178 -3.795102329 0.072916991 NRPLSDEELDAMFPEGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NRPLSDEELDAMFPEGYK 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 186.23 4.47E-14 441440000 787480 511240 753440 530550 1064960 1072460 932860 832420 849350 447320 FALSE TRUE 818570.3185 599041.4931 773075.2654 635491.2065 883938.4796 823397.4183 859739.9956 821262.7715 818782.0594 534963.7895 1.530141543 1.119779516 1.445098305 1.187914433 1.652333292 1.53916477 1.607099419 1.535174506 1.530537347 1 19.02908172 3.239882162 24.99990836 1.517303548 1.315262812 0.10662906 0.203059912 55.55212314 1050875.108 0.051985047 0.066707183 1737.329373 -3.239882162 -0.202040737 NRPPFGQGYTQPGPGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRPPFGQGYTQPGPGYR 17 1 Q92734-2;Q92734 Q92734-2 TFG Protein TFG 0 151.44 2.28E-07 321760000 41182 35426 39554 46759 51360 63570 38381 51779 50239 35239 FALSE TRUE 42807.89716 41510.13992 40584.80973 56007.79064 42629.84555 48806.83091 35372.59693 51084.9872 48430.9082 42143.40736 1.015767349 0.984973511 0.96301681 1.328981071 1.01154245 1.158113071 0.839338799 1.212170311 1.149192987 1 15.36301934 NRPT(ph)SISWDGLDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.65)S(0.35)ISWDGLDSGK;NRPT(0.499)S(0.499)IS(0.001)WDGLDSGK;NRPT(0.74)S(0.205)IS(0.046)WDGLDS(0.009)GK;NRPT(0.61)S(0.39)ISWDGLDSGK;NRPT(0.864)S(0.112)IS(0.024)WDGLDSGK 187.47 5.48E-07 3439459000 2021330 1521030 1674610 1106910 2803290 2501650 1657320 1875620 1797990 1376190 TRUE FALSE 2101133.669 1782255.071 1718251.712 1325853.494 2326787.767 1920679.7 1527414.928 1850480.382 1733280.691 1645828.082 1.276642252 1.082892612 1.044004372 0.80558444 1.413748977 1.166998985 0.928052538 1.124346098 1.053135932 1 20.65038221 1.286110219 0.013969265 7.30E-07 2.132195317 0.057935114 0.158151081 2184.846507 27.32176373 2100.048228 2063.876187 19.3245869 -1.286110219 2.132194586 NRPTS(ph)ISWDGLDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.183)S(0.815)IS(0.002)WDGLDSGK 163.62 9.25E-07 742500000 755250 586780 678110 482310 1161800 1012600 675670 763100 723000 579520 TRUE FALSE 785067.8532 687554.9005 695782.1037 577709.4784 964317.651 777438.9961 622709.2199 752871.8927 696979.3712 693065.8484 1.132746412 0.99204845 1.003919188 0.833556407 1.391379554 1.121739006 0.898484929 1.086292009 1.005646683 1 19.4026329 NRPTSIS(ph)WDGLDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 NRPT(0.018)S(0.303)IS(0.679)WDGLDSGK;NRPT(0.032)S(0.255)IS(0.713)WDGLDSGK 232.73 5.49E-14 1819170000 1207420 957090 1044800 749760 1837350 1647600 1078980 1182730 1140640 854090 TRUE FALSE 1255089.874 1121462.762 1072028.346 898060.2902 1525037.903 1264969.87 994406.7282 1166877.439 1099588.589 1021432.583 1.228754491 1.09793126 1.049534119 0.879216412 1.493038237 1.238427176 0.973541225 1.142393006 1.076516069 1 19.96216256 1.066623668 0.975796212 1.004909186 1.142402893 0.074591712 0.157082793 1.708740365 3.516217058 0.151687031 0.051390788 11.65798972 -1.066623668 0.137493707 NRPTSISWDGLDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ;;; 207.79 2.93E-09 5199370000 7650410 6704630 6795750 4972740 11265800 11135200 7610050 7791820 7138010 7723790 FALSE TRUE 7952454.094 7856098.048 6972852.828 5956333.13 9350843.34 8549218.556 7013554.396 7687383.398 6881114.414 9237118.77 0.860923659 0.850492263 0.754873138 0.644825868 1.012311693 0.925528703 0.759279443 0.832227407 0.744941641 1 23.13901149 4.457147414 24.87784577 0.825921352 0.858315968 0.001851088 0.111290254 1330.750895 1657479.179 0.02695388 0.073835017 28651.50331 -4.457147414 0.032394617 NRS(ph)AEEGELAESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.982)AEEGELAES(0.018)K;NRS(1)AEEGELAESK;NRS(1)AEEGELAESK 209.33 1.02E-07 461000000 1178040 700300 949660 658670 1498120 1474190 1274840 1071080 1178570 631710 TRUE FALSE 1224549.929 820571.0774 974408.9198 788952.9601 1243470.098 1131831.714 1174914.71 1056723.925 1136153.496 755481.4797 1.620886761 1.086156444 1.289785317 1.044304832 1.645930616 1.498159445 1.555186647 1.398742329 1.503880011 1 19.52703686 3.235197139 24.99999715 1.460613266 1.249953003 0.125128984 0.216993109 142.3231724 1057858.848 0.057491839 0.07144176 1718.688372 -3.235197139 -0.210660264 NRSAEEGELAES(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 NRS(0.062)AEEGELAES(0.938)K 191.46 9.32E-06 389270000 661780 387790 569910 377430 840160 822740 738090 604330 642610 375060 TRUE FALSE 687907.5854 454389.9159 584762.3228 452084.5275 697349.9033 631671.1037 680236.5772 596229.9448 619482.5916 448545.826 1.533639476 1.013028969 1.303684682 1.007889275 1.55469043 1.408264367 1.516537526 1.329250904 1.381090974 1 18.77489586 3.232087563 24.9995958 1.38980454 1.20653149 0.113642628 0.198146436 259.4153921 1001887.884 0.052374173 0.064022191 1706.426406 -3.232087563 -0.18327305 NRT(ph)PSDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRTPSDVK 8 1 P39687;H0YN26;H7BZ09;O95626 P39687 ANP32A;ANP32D Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member D 1 NRT(1)PSDVK;NRT(0.999)PS(0.001)DVK;NRT(1)PSDVK;NRT(0.999)PS(0.001)DVK 96.113 0.014827 1814650000 1944040 1100330 1414030 1119300 2131380 2254620 1907980 1497280 1656940 828690 TRUE FALSE 2020792.2 1289303.118 1450880.783 1340694.199 1769088.789 1731018.674 1758427.542 1477211.411 1597307.053 991055.9393 2.039029403 1.300938794 1.463974662 1.352793668 1.785054424 1.746640735 1.774296962 1.490542917 1.611722396 1 19.91860697 0.009856365 1.269461143 0.99834385 1.607535977 0.427993012 0.214067082 12.97065303 15.36891523 0.274626048 0.060052032 1.022954612 -0.009856365 0.609192127 NRT(ph)SVDFKDTDYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRTSVDFKDTDYKR 14 3 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 NRT(0.462)S(0.462)VDFKDT(0.075)DYKR 66.152 0.057776 154100000 105290 59569 78541 33461 183210 133780 81171 77116 127120 73763 TRUE FALSE 109446.9305 69799.51237 80587.84298 40079.48593 152068.0296 102711.6225 74808.60492 76082.38616 122544.976 88215.44757 1.240677608 0.791239112 0.913534366 0.454336367 1.723825405 1.164326944 0.848021599 0.862461034 1.389155521 1 16.42874369 3.276334157 24.99989904 1.11617949 0.8502962 0.196793282 0.302079083 333.6443306 220815.698 0.08604723 0.116505979 1889.444578 -3.276334157 -0.265883289 NRTPSDVK ddPTM_MDA-MB-175_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 ;; 128.6 0.0010274 1036890000 1021690 691170 844540 592590 1407720 1312830 988420 942650 930430 647650 FALSE TRUE 1062027.11 809873.0709 866549.4062 709802.5333 1168436.257 1007945.129 910945.0576 930015.3186 896944.006 774544.6175 1.371163244 1.045611902 1.118785654 0.916412712 1.508546094 1.301339014 1.176104045 1.200725301 1.15802755 1 19.56298882 0.723860835 2.041991155 1.00003147 1.199643396 0.132355521 0.156925405 2.56466905 15.53732925 0.149941767 0.041280119 5.294937462 -0.723860835 0.199611926 NRTS(ph)VDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NRTSVDFK 8 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 NRT(0.296)S(0.704)VDFK;NRTS(1)VDFK;NRT(0.016)S(0.984)VDFK;NRT(0.402)S(0.598)VDFK;NRT(0.226)S(0.774)VDFK;NRT(0.149)S(0.851)VDFK;NRT(0.126)S(0.874)VDFK 156.01 0.0002421 2207110000 5178580 3002150 4635510 3488680 6354930 6184890 6513060 4611550 5618560 2413920 TRUE FALSE 5383034.337 3517745.909 4756315.199 4178730.491 5274721.269 4748543.03 6002549.338 4549739.715 5416349.123 2886881.407 1.864653783 1.218528028 1.647561686 1.447489489 1.827134726 1.64486945 2.079250407 1.576005064 1.876193844 1 21.46108041 3.24456314 24.96669024 1.714278101 1.528627764 0.022792824 0.305956274 370.1958457 1539768.906 0.077930949 0.10281524 1756.156197 -3.24456314 -0.185650336 NRVPS(ph)AGDVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 1 NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK;NRVPS(1)AGDVEK 125.39 0.00019945 1935440000 3798530 2181850 2893160 2125880 4173750 4670250 3873150 3080370 3048660 1794740 TRUE FALSE 3948498.898 2556565.765 2968558.126 2546372.719 3464297.466 3585655.216 3569562.382 3039082.679 2938939.322 2146384.941 1.839604268 1.191103104 1.383050202 1.186354167 1.614014989 1.670555522 1.663057877 1.415907567 1.369250812 1 21.03347741 0.793452559 1.950233167 1.000957164 1.487672821 0.360093249 0.199366956 0.856535445 5.593850548 0.191209277 0.053158667 6.215163511 -0.793452559 0.486715658 NRVPSAGDVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NRVPSAGDVEK 11 1 Q15785 Q15785 TOMM34 Mitochondrial import receptor subunit TOM34 0 68.171 0.056609 0 125840 107690 117720 87210 178350 190690 160170 141140 126640 94513 FALSE TRUE 130808.2604 126184.9198 120787.8799 104459.8777 148034.1307 146405.1374 147615.4569 139248.2492 122082.2511 113031.0128 1.15727761 1.116374318 1.068626007 0.924170059 1.309677115 1.2952652 1.305973053 1.231947284 1.080077477 1 16.78635914 3.22356979 24.99995661 1.227405146 1.070310267 0.255110704 0.110467576 279.9362542 466844.2009 0.031661607 0.03798244 1673.284507 -3.22356979 -0.157094878 NS(ph)FTPLSSSNTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.999)FT(0.001)PLSSSNTIR;NS(1)FTPLSSSNTIR 110.29 0.0011225 1484380000 553300 560110 560990 489470 725560 913130 648540 683860 615870 512140 TRUE FALSE 575144.7112 656304.5354 575609.8603 586285.7051 602229.5704 701069.3961 597705.7402 674693.9753 593704.959 612484.0275 0.939036261 1.071545552 0.939795708 0.957226113 0.983257593 1.144632945 0.975871555 1.10156991 0.969339497 1 19.2243127 2.950314712 24.99374842 1.045993233 0.979664541 0.187302448 0.061573181 542.7954979 273048.2017 0.017549366 0.018614178 891.8970176 -2.950314712 -0.066328692 NS(ph)LESISSIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLESISSIDR 11 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 NS(1)LESISSIDR 166.79 0.00082763 0 51086 45928 50697 61796 65343 89470 97907 66291 62060 40214 TRUE FALSE 53102.91473 53815.77673 52018.20547 74019.06436 54236.0202 68691.94843 90232.79351 65402.47758 59826.47272 48093.16336 1.104167641 1.118990164 1.081613307 1.539076642 1.127728276 1.428310047 1.876208326 1.359912158 1.243970422 1 15.5535442 3.752948225 24.04289345 1.403682645 1.103330292 0.21548779 0.225714532 659.1850036 1101547.699 0.058096281 0.104054635 5661.717885 -3.752948225 -0.300352353 NS(ph)PATLFEVPDTW ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPATLFEVPDTW 13 0 A0A494C0Q6;A0A494C0K5;A0A494C0W0;O95453-2;O95453-3;O95453;O95453-4 A0A494C0Q6 PARN Poly(A)-specific ribonuclease PARN 1 NS(0.5)PAT(0.5)LFEVPDTW 65.347 0.061717 6525700 16495 13684 15193 14464 17357 24869 19567 15629 13942 10382 TRUE FALSE 17146.23534 16034.12055 15588.94206 17324.93603 14406.66334 19093.55164 18033.28741 15419.51882 13440.23014 12416.15412 1.380961863 1.291391875 1.255537093 1.39535446 1.160316085 1.537799181 1.452405248 1.241891705 1.082479326 1 13.59993075 1.280905292 2.614409905 1.012250132 1.348079933 0.607783195 0.099733264 0.183098881 2.07267795 0.089959369 0.026298386 19.09436816 -1.280905292 0.335829801 NS(ph)PEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 NS(1)PEDKR 60.342 0.060077 670900000 758000 415190 562820 444660 682580 888340 896830 567990 555240 269670 TRUE FALSE 787926.4253 486495.6528 577487.5516 532612.4208 566555.2954 682036.4979 826534.1212 560377.0231 535257.0209 322506.6734 2.443132159 1.508482438 1.790622022 1.651477209 1.756724255 2.114798093 2.562843468 1.737567218 1.65967735 1 18.29896949 NS(ph)PEDLGLSLTGDSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.999)PEDLGLS(0.001)LTGDSCK 360.57 8.64E-88 3652650000 5352700 2577010 3553310 2700730 5093300 5639080 4850100 3739990 4136380 1839549 TRUE FALSE 5564028.729 3019591.421 3645912.178 3234926.333 4227542.685 4329489.131 4469936.489 3689861.551 3987512.492 2199973.406 2.52913454 1.372558147 1.657252841 1.470438835 1.92163354 1.967973394 2.031813874 1.677230071 1.812527588 1 21.06905465 -0.024627166 1.356389246 0.998337928 1.807860677 0.391134464 0.308589099 19.10989765 23.73107647 0.400213572 0.082920788 0.944871683 0.024627166 0.809522748 NS(ph)PFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPFTR 6 0 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;H3BSK8 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 NS(0.999)PFT(0.001)R 79.906 0.069141 95272000 186730 177360 195960 182530 218650 313580 249560 206400 180970 122280 TRUE FALSE 194102.2446 207820.2003 201066.8786 218633.8892 181483.9511 240755.7974 229998.8351 203633.5456 174456.9251 146238.4248 1.327299886 1.421105298 1.374925084 1.495050904 1.241014127 1.646323787 1.572766087 1.392476334 1.192962283 1 17.15796291 1.076836005 2.584593137 1.004805266 1.441910563 0.624594227 0.110085765 0.16046928 2.171486921 0.104593342 0.02842425 11.93537326 -1.076836005 0.437105297 NS(ph)PGSQVASNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NSPGSQVASNPR 12 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 1 NS(1)PGSQVASNPR;NS(1)PGSQVASNPR;NS(0.999)PGS(0.001)QVASNPR;NS(1)PGSQVASNPR;NS(0.966)PGS(0.034)QVASNPR 291.13 4.20E-36 4631940000 1534740 1363999 1461516 1425724 1940823 2480113 1744883 1698105 1581357 1050758 TRUE FALSE 1595332.72 1598255.218 1499604.308 1707727.952 1610922.6 1904144.342 1608114.511 1675344.68 1524444.27 1256633.912 1.269528623 1.271854279 1.193350182 1.358970131 1.281934686 1.51527372 1.279700075 1.333200277 1.213117246 1 20.26113299 0.894608617 2.930835003 1.000169088 1.314082107 0.587259658 0.079801214 0.293115966 5.391805816 0.07662154 0.02015597 7.845283046 -0.894608617 0.313913019 NS(ph)PGVPTGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPGVPTGAK 10 0 Q08379;B7ZC06;R4GND7 Q08379 GOLGA2 Golgin subfamily A member 2 1 NS(1)PGVPTGAK;NS(0.998)PGVPT(0.002)GAK 113.76 0.0015166 254930000 1026090 537510 669320 542170 900760 1066420 875360 690540 699340 443660 TRUE FALSE 1066600.826 629823.1613 686763.0291 649409.6078 747649.1369 818760.1168 806746.9959 681284.4408 674170.89 530586.6826 2.010229168 1.187031605 1.294346525 1.223946301 1.409098949 1.543122252 1.520481049 1.284020996 1.270614043 1 19.01722894 -3.895785607 0.155474817 1.12E-15 1.530728726 0.289697496 0.219540522 130.2522192 1.623821034 42.26080728 1.046004791 0.00012712 3.895785607 1.530728726 NS(ph)PLDCGSASPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPLDCGSASPNK 13 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 1 NS(0.999)PLDCGS(0.001)ASPNK;NS(0.995)PLDCGS(0.005)ASPNK 203.53 5.00E-07 186000000 405650 204610 260090 245030 403000 432810 427060 291390 305860 128214 TRUE FALSE 421665.3752 239750.1759 266868.1591 293496.2027 334498.2039 332296.4368 393585.9213 287484.3937 294852.1583 153335.0785 2.749960279 1.563570308 1.740424707 1.914083884 2.181485197 2.16712601 2.56683549 1.874876881 1.922926973 1 17.22632825 4.757674043 24.05959693 1.951016294 2.749961483 0.286043468 0.398233366 3507.761579 4415380.217 0.091464599 3.160413607 57236.62838 -4.757674043 0.79894519 NS(ph)PPFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPPFLK 7 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 NS(1)PPFLK;NS(1)PPFLK 68.626 0.064974 397120000 1654440 944540 1267430 969070 1712790 1935630 1675400 1404360 1357290 708450 TRUE FALSE 1719758.569 1106757.397 1300460.267 1160749.154 1421650.568 1486109.267 1544077.77 1385536.851 1308441.398 847257.2134 2.029795134 1.306282649 1.534906102 1.370007992 1.677944484 1.754023741 1.822442755 1.635320218 1.544326065 1 19.69244049 0.757080076 3.206268581 1.000050619 1.630967838 0.479875542 0.198976351 1.600061314 20.04189603 0.187934941 0.04884569 5.715840162 -0.757080076 0.630917218 NS(ph)PQALR ddPTM_MDA-MB-175_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 85.355 0.021894 673680000 740484 1009870 1087140 1165460 1073730 1564640 1287560 1095500 967840 755850 TRUE FALSE 769718.8801 1183307.317 1115471.761 1395984.509 891217.7581 1201276.072 1186637.683 1080816.614 933007.6275 903944.3359 0.85151137 1.309048876 1.234004924 1.544325744 0.98592106 1.328927042 1.312733136 1.195667224 1.032151639 1 19.78587441 1.250978836 3.607951732 1.002823283 1.235860955 0.170123257 0.180403898 0.358741638 8.552217619 0.148784573 0.043433212 17.82291909 -1.250978836 0.233037673 NS(ph)PQALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPQALRR 8 1 Q7L7X3-3;Q7L7X3 Q7L7X3-3 TAOK1 Serine/threonine-protein kinase TAO1 1 NS(1)PQALRR;NS(1)PQALRR 83.182 0.011237 737060000 145189 143371 153715 134643 187522 264310 161836 157305 141642 147241 TRUE FALSE 150921.1738 167993.854 157720.9392 161274.9835 155647.0774 202928.0082 149150.8714 155196.5838 136544.3321 176090.0549 0.857068129 0.954022384 0.895683401 0.915866507 0.883906122 1.152410386 0.847014737 0.881347808 0.775423304 1 17.42595391 NS(ph)PQSS(ph)PTSTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 2 NS(0.999)PQS(0.011)S(0.418)PT(0.418)S(0.138)T(0.016)PK 69.92 0.059959 0 275500 172480 227240 198100 295460 391170 331090 244000 239350 121200 TRUE FALSE 286376.9527 202102.0983 233162.0611 237283.5887 245237.8147 300326.6957 305138.3007 240729.5791 230735.8403 144946.8195 1.975738093 1.394318958 1.60860419 1.637038947 1.691915805 2.071978515 2.105174172 1.660813117 1.591865493 1 17.14516415 2.994388906 24.21168835 1.768159078 1.63618609 0 0.318294382 678.3205636 2926961.74 0.090040906 0.104514393 987.163083 -2.994388906 -0.131972988 NS(ph)PVT(ph)KTPPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.865)PVT(0.567)KT(0.567)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;NS(0.948)PVT(0.46)KT(0.391)PPRDLPT(0.2)IPGVT(0.001)SPSSDEPPMEASQSHLR;NS(0.997)PVT(0.612)KT(0.375)PPRDLPT(0.016)IPGVTSPSSDEPPMEASQSHLR;NS(0.994)PVT(0.497)KT(0.497)PPRDLPT(0.011)IPGVTSPSSDEPPMEASQSHLR;NS(0.998)PVT(0.536)KT(0.458)PPRDLPT(0.004)IPGVT(0.003)S(0.001)PSSDEPPMEASQSHLR;NS(0.971)PVT(0.511)KT(0.511)PPRDLPT(0.006)IPGVTSPSSDEPPMEASQSHLR;NS(0.99)PVT(0.561)KT(0.447)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.599)KT(0.393)PPRDLPT(0.009)IPGVTSPSSDEPPMEASQSHLR 150.94 4.46E-13 3318200000 679746 469881 705188 472195 1137382 1144962 876192 885129 871737 467899 TRUE FALSE 706582.897 550579.4066 723565.7786 565593.7616 944050.2139 879061.9276 807513.7815 873265.2935 840363.3557 559574.8506 1.26271382 0.983924503 1.293063435 1.010756222 1.68708478 1.570946097 1.443084479 1.5605871 1.501789001 1 19.0939716 3.244761568 24.99989663 1.49670523 1.137740116 0.392733095 0.193644583 126.8219993 511294.9921 0.049450454 0.065309375 1756.958763 -3.244761568 -0.358965113 NS(ph)PVTKT(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLR 36 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 NS(0.989)PVT(0.177)KT(0.829)PPRDLPT(0.006)IPGVTSPSSDEPPMEASQSHLR;NS(0.999)PVT(0.174)KT(0.827)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;NS(0.617)PVT(0.497)KT(0.542)PPRDLPT(0.132)IPGVT(0.132)S(0.056)PS(0.017)S(0.006)DEPPMEASQSHLR 171.37 1.18E-16 726386000 117785 85815.6 133923 96628.4 221599 218781 169868 170299 165380 88109.7 TRUE FALSE 122435.2427 100553.7617 137413.1434 115741.2091 183931.6811 167972.4284 156553.3023 168016.4205 159428.0061 105373.1088 1.161921141 0.954263976 1.304062726 1.098394177 1.745527709 1.594073008 1.485704504 1.594490496 1.512985694 1 16.68514721 3.256246601 24.99770711 1.527600011 1.12958934 0.429044002 0.199978657 195.3691524 276136.7581 0.051269662 0.069269723 1804.041822 -3.256246601 -0.398010672 NS(ph)QKHSPTSEPTPPGDALPPVSSPHTHR ddPTM_MDA-MB-175_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 1 NS(0.476)QKHS(0.476)PT(0.037)S(0.01)EPTPPGDALPPVSSPHTHR;NS(0.324)QKHS(0.324)PT(0.172)S(0.172)EPT(0.009)PPGDALPPVSSPHTHR 113.64 0.0002315 684540000 125912 328486 375648 305045 468150 460416 417155 464800 366762 234453 TRUE FALSE 130883.103 384900.9152 385437.6955 365381.9905 388574.0302 353491.3617 384457.3011 458570.1163 353562.3073 280389.5765 0.466790188 1.372736177 1.374650586 1.303122588 1.385836218 1.26071506 1.371154042 1.635474906 1.260968085 1 18.09707319 4.738914726 24.88310046 1.363638714 0.4667899 0.739929413 0.152209726 12.64565907 888241.6396 0.035687463 0.209156163 54816.93205 -4.738914726 -0.896848814 NS(ph)RDGDPLPSSLSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSRDGDPLPSSLSCK 15 1 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK;NS(1)RDGDPLPSSLSCK 231.39 1.22E-13 2602180000 2119570 1276650 1704370 1281910 2294820 2424260 2194310 1747510 1962490 1028470 TRUE FALSE 2203252.26 1495904.707 1748787.282 1535467.972 1904747.316 1861262.355 2022314.248 1724087.487 1891860.368 1229979.005 1.791292576 1.216203448 1.421802547 1.248369253 1.548601487 1.513247256 1.64418599 1.40172107 1.538124114 1 20.23020226 -1.570738377 6.103527133 0.998874617 1.469151357 0.436242404 0.16338367 0.002359523 0.000165946 0.149184896 0.035087883 0.026869626 1.570738377 0.470276741 NS(ph)RFAQDFLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSRFAQDFLIR 11 1 A0A087WVD4;Q9HBK9-2;Q9HBK9 A0A087WVD4 AS3MT Arsenite methyltransferase 1 NS(1)RFAQDFLIR 60.255 0.057415 271380000 46304 51051 52900 33209 79442 79321 46368 61866 78789 57226 TRUE FALSE 48132.11767 59818.61213 54278.61746 39777.64108 65938.47722 60899.89987 42733.555 61036.78746 75953.39928 68438.33904 0.703291727 0.874051197 0.793102495 0.58121868 0.963472786 0.889850641 0.624409587 0.891850801 1.109807753 1 16.06251713 1.437884645 5.009708624 1.046835352 0.782630508 0.484268862 0.114501541 0.164801278 7.796112697 0.07541516 0.028630487 27.40846066 -1.437884645 -0.264204844 NS(ph)SEASSGDFLDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.737)S(0.263)EASSGDFLDLK;NS(0.789)S(0.211)EASSGDFLDLK 206.63 1.11E-08 113534000 262240 156411 201042 188579 266210 307150 342550 223354 247090 134231 TRUE FALSE 272593.4377 183273.3725 206281.3197 225879.3633 220959.7193 235819.0674 315700.0359 220360.305 238197.2792 160530.9944 1.698073563 1.141669702 1.28499372 1.407076335 1.376430265 1.468993998 1.966598644 1.372696318 1.483808656 1 17.29249235 2.687438784 4.881608494 1.516250668 1.363919139 0 0.257181934 0.59909841 32.02968707 0.080777615 0.077125748 486.8988891 -2.687438784 -0.152331529 NS(ph)SEKLPTELSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSEKLPTELSK 12 1 P38432 P38432 COIL Coilin 1 NS(0.848)S(0.152)EKLPTELSK 167.28 3.01E-05 250180000 586190 219130 359860 244110 587960 513550 549890 388480 422020 128930 TRUE FALSE 609333.2338 256763.8729 369238.2472 292394.2294 488018.7692 394285.7954 506788.1849 383273.061 406831.5826 154191.365 3.951798688 1.665228613 2.394675261 1.896307419 3.165020099 2.55711982 3.286748159 2.485697309 2.638484864 1 17.23436245 3.239666449 24.99999246 2.640940661 2.413138272 0 0.813009567 168.6496107 3812667.357 0.213286192 0.273158034 1736.46666 -3.239666449 -0.227802389 NS(ph)TELAPPLPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSTELAPPLPVR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 NS(0.908)T(0.092)ELAPPLPVR;NS(0.795)T(0.205)ELAPPLPVR;NS(0.753)T(0.247)ELAPPLPVR 243.49 2.51E-16 719930000 669880 583810 718300 857660 831520 1160630 1218580 874610 798610 448870 TRUE FALSE 696327.3797 684074.8261 737019.4881 1027302.588 690178.5274 891091.272 1123064.515 862887.2835 769868.1821 536817.4824 1.297139908 1.274315477 1.37294241 1.913690634 1.285685638 1.659952035 2.092078877 1.607412783 1.434133961 1 19.03407213 3.977821326 22.66115775 1.620278026 1.295202776 0.128978173 0.290209077 343.1646514 350633.7271 0.071635803 0.130893524 9502.137834 -3.977821326 -0.32507525 NS(ph)TPFMAEHLEETLSAVTNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSTPFMAEHLEETLSAVTNNR 21 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 NS(0.5)T(0.5)PFMAEHLEETLSAVTNNR 104.14 0.00027142 42822000 21389 44551 47471 42570 43059 67897 38555 45279 41585 44407 TRUE FALSE 22233.45424 52202.28769 48708.13326 50990.21894 35739.84656 52128.95074 35532.95836 44672.10907 40088.36397 53107.70143 0.4186484 0.982951367 0.917157624 0.960128523 0.672969185 0.981570457 0.669073551 0.841160658 0.754850293 1 15.69663347 -2.560258343 2.13344286 3.954401444 0.811578313 0.107362719 0.170143297 4475395.293 288094.4525 64608106.63 0.038716753 0.002752591 2.560258343 -3.142823131 NS(ph)TPSEPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.556)T(0.444)PSEPGSGR 140.16 4.06E-05 1972200000 737790 693020 699240 669870 937210 1159900 899330 787590 790410 557720 TRUE FALSE 766918.5189 812040.7941 717462.7688 802368.2866 777903.379 890530.8035 828838.1646 777033.6443 761963.2985 666994.5558 1.149812262 1.217462402 1.075665105 1.202960773 1.166281452 1.335139539 1.242646072 1.164977491 1.142383085 1 19.34731546 0.827257882 1.796811385 1.000635759 1.197456525 0.463353807 0.063397363 0.573424892 3.409922942 0.062263532 0.017582283 6.718276633 -0.827257882 0.196820766 NS(ph)WDSPAFSNDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(0.998)WDS(0.002)PAFSNDVIR;NS(0.999)WDS(0.001)PAFSNDVIR;NS(1)WDSPAFSNDVIR;NS(1)WDSPAFSNDVIR 308.42 1.23E-55 2350180000 1341030 1271180 1439430 1330200 1774140 2129690 1647970 1486540 1432090 1080300 TRUE FALSE 1393974.9 1489495.277 1476942.728 1593309.59 1472572.317 1635101.773 1518797.805 1466615.363 1380549.361 1291964.101 1.07895792 1.152892155 1.14317629 1.233246023 1.139793524 1.265593813 1.175572761 1.135182751 1.068566347 1 20.30113455 1.14282176 1.870248183 1.002085809 1.172526901 0.565049038 0.048623942 0.226168651 1.486323476 0.045491668 0.013113578 13.89382293 -1.14282176 0.170441092 NSASATT(ph)PLSGNSSR ddPTM_MDA-MB-175_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(0.006)T(0.787)PLS(0.204)GNS(0.001)S(0.001)R 131.72 0.00057975 131910000 185190 189550 197040 159680 214180 313540 214010 198350 187840 155700 TRUE FALSE 192501.4442 222103.738 202175.0243 191264.2274 177773.7601 240725.0867 197235.337 195691.4427 181079.6751 186206.4339 1.033806621 1.192782297 1.085757457 1.027162292 0.954713306 1.292786085 1.059229441 1.050938136 0.972467338 1 17.5065434 1.515591756 2.578628928 0.988472231 1.095669864 0.182465074 0.088679979 0.443188022 6.113825452 0.067861664 0.023785078 32.77870232 -1.515591756 0.107197633 NSASATTPLSGNS(ph)SR ddPTM_MDA-MB-175_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(0.007)GNS(0.646)S(0.347)R 139.08 6.93E-06 137090000 175840 187310 192640 173920 245130 302450 200030 205450 192850 159730 TRUE FALSE 182782.299 219479.0354 197660.3567 208320.8569 203462.8902 232210.5712 184351.1259 202696.2788 185909.3662 191026.0353 0.956844959 1.148948284 1.034729933 1.090536463 1.065105549 1.215596454 0.965057594 1.061092424 0.973214808 1 17.54340975 NSASATTPLSGNSS(ph)R ddPTM_MDA-MB-175_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 NSASATTPLSGNS(0.04)S(0.96)R;NSASATTPLSGNS(0.08)S(0.92)R;NSASATTPLS(0.003)GNS(0.199)S(0.798)R 227.34 7.80E-13 1072280000 1259000 1332200 1346110 1140630 1722870 2131870 1393410 1486870 1259810 1052520 TRUE FALSE 1308706.292 1560994.987 1381190.732 1366243.21 1430017.173 1636775.501 1284190.883 1466940.94 1214469.684 1258741.142 1.039694539 1.24012391 1.097279406 1.085404428 1.136069303 1.300327324 1.020218407 1.165403188 0.964828783 1 20.2635502 1.236179616 24.99996999 0.982414315 1.137224952 0.362048292 0.081294635 64.04320727 672364.088 0.06247369 0.01845597 17.22580853 -1.236179616 0.154810637 NSATCHS(ph)EDS(ph)DLEID ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 2 NSATCHS(1)EDS(1)DLEID;NSATCHS(1)EDS(1)DLEID 197.79 1.21E-08 249093000 307820 396650 357540 348950 466530 587200 421810 449260 406310 351150 TRUE FALSE 319972.9713 464771.552 366857.7861 417971.2685 387229.3972 450831.6991 388747.43 443238.4045 391686.9825 419951.1193 0.761929083 1.106727737 0.873572588 0.995285521 0.92208207 1.073533748 0.925696854 1.055452371 0.932696603 1 18.67986189 4.759822035 24.34863503 0.986670368 0.761928759 0.474770654 0.071088383 3129.417543 3583735.283 0.015240106 0.690299742 57520.41821 -4.759822035 -0.224741608 NSATCHSEDS(ph)DLEID ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSATCHSEDSDLEID 15 0 Q13371-2;Q13371 Q13371-2 PDCL Phosducin-like protein 1 NSATCHSEDS(1)DLEID;NSATCHSEDS(1)DLEID 213.51 3.55E-10 709550000 644820 861490 902770 905970 1121910 1322280 963650 960580 938470 789130 TRUE FALSE 670277.9915 1009444.206 926296.9278 1085168.162 931208.1389 1015200.509 888116.595 947704.9963 904694.648 943744.9147 0.710232162 1.069615518 0.981511967 1.149853255 0.986715928 1.075714945 0.941055767 1.004196136 0.958622011 1 19.84803744 4.744463135 24.81790034 1.018168433 0.710232013 0.705915556 0.059707384 309.1413973 1299784.014 0.013700736 0.122701295 55521.74851 -4.744463135 -0.30793642 NSATFKS(ph)FEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 NSATFKSFEDR 11 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6 O43399 TPD52L2 Tumor protein D54 1 NS(0.001)AT(0.009)FKS(0.99)FEDR;NSAT(0.022)FKS(0.978)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSAT(0.02)FKS(0.98)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NS(0.002)AT(0.03)FKS(0.969)FEDR;NSATFKS(1)FEDR;NSATFKS(1)FEDR;NSAT(0.097)FKS(0.903)FEDR;NSATFKS(1)FEDR 255.15 4.90E-20 36927178000 21665795 12767776 24410055 9683830 35123108 26679139 23169778 22772275 27953137 10679323 TRUE FALSE 22521177.32 14960542.21 25046201.09 11599262.67 29152894.65 20483313.29 21353670.26 22467049.9 26947109.06 12771731.87 1.763361268 1.17137929 1.96106537 0.908198104 2.28261092 1.603800761 1.671947898 1.759123205 2.109902504 1 23.60645084 4.235175433 24.9995677 1.686342829 1.467370353 0.028982674 0.432957919 284.9144731 2104161.461 0.098690932 0.227820581 17186.02476 -4.235175433 -0.218972476 NSATFKS(ph)FEDRVGTIK ddPTM_MDA-MB-175_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 NS(0.12)AT(0.222)FKS(0.658)FEDRVGTIK;NSAT(0.001)FKS(0.999)FEDRVGTIK;NS(0.136)AT(0.184)FKS(0.68)FEDRVGTIK 94.384 0.0032372 839252000 1147429 573552 1018977 371802.7 1884694 1173370 685451 896385 1202868 783992 TRUE FALSE 1192730.383 672055.0944 1045532.378 445344.1643 1564334.387 900872.6001 631723.5595 884370.4253 1159577.016 937600.222 1.272109749 0.716782141 1.115115327 0.474982998 1.668444984 0.960828058 0.673766436 0.943227619 1.236749937 1 19.83861339 4.786481111 21.77054453 0.969346592 1.27211615 0.073885004 0.312847863 19240.28446 8739794.359 0.071120743 35.79133759 61161.9201 -4.786481111 0.302769558 NSDDAPWS(ph)PK ddPTM_MDA-MB-175_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 83.204 0.017746 0 378020 187430 228970 180350 374510 396450 309000 250510 268230 145710 TRUE FALSE 392944.5215 219619.6445 234937.1463 216022.6917 310850.924 304380.4958 284779.7726 247152.3232 258576.4547 174259.0847 2.254944252 1.26030528 1.348206016 1.239663872 1.783843433 1.746712352 1.634232 1.418303807 1.483862119 1 17.41087435 0.575203341 1.064893293 1.000915148 1.575198389 0.27576534 0.286290088 1.981350759 3.374340354 0.269661946 0.084600037 3.760134162 -0.575203341 0.57428324 NSDEINALQDYGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSDEINALQDYGKR 14 1 J3KNC9;O75596 J3KNC9 CLEC3A C-type lectin domain family 3 member A 0 134.14 6.49E-05 522480000 58035 121650 107510 105790 117110 140760 79324 127960 100210 134080 FALSE TRUE 60326.26661 142542.4412 110311.7989 126714.9462 97203.68403 108070.6232 73106.37761 126244.9055 96603.46167 160350.4089 0.376215234 0.888943422 0.687942112 0.79023775 0.606195424 0.673965374 0.455916378 0.787306415 0.602452232 1 17.29086851 -1.624668969 2.787225566 1.030149166 0.66408188 0.332894396 0.146859946 25183059.02 24653836.81 5524021.831 0.03242384 0.023731819 1.624668969 -0.366067286 NSDGGS(ph)DPETQKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSDGGSDPETQKEK 14 1 O75554-2;O75554 O75554-2 WBP4 WW domain-binding protein 4 1 NSDGGS(1)DPETQKEK;NS(0.004)DGGS(0.994)DPET(0.002)QKEK 132.79 2.93E-05 666770000 2494490 790950 1257340 741130 2041660 2062380 1875180 1269840 1438390 433490 TRUE FALSE 2592974.391 926789.5098 1290107.313 887723.3019 1694619.362 1583423.501 1728198.492 1252819.872 1386622.625 518424.0658 5.00164742 1.787705415 2.488517409 1.712349716 3.268789923 3.054301691 3.333561471 2.416592814 2.674687994 1 18.98377317 4.749313105 24.6970651 2.522803013 5.001649092 0.539611448 0.710490991 1034.406796 2375843.241 0.162961632 2.36992344 56145.26099 -4.749313105 2.47884608 NSEGWEQNGLYEFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSEGWEQNGLYEFFR 15 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ;;; 364.53 5.07E-97 217424000 125128 151233 141968 129500 195828 216142 150031 160718 163130 150047 FALSE TRUE 130068.1501 177206.0913 145667.8027 155114.7135 162541.2265 165946.2962 138271.1782 158563.8381 157258.9832 179445.8368 0.724832364 0.987518543 0.811764738 0.864409653 0.905795472 0.924770945 0.770545478 0.883630631 0.87635905 1 17.45318893 0.607272034 2.114067492 0.999960343 0.86258328 0.253424385 0.071959618 3.493919935 17.17477765 0.062611017 0.01710428 4.048293897 -0.607272034 -0.137377063 NSFLGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSFLGSPR 8 0 Q8IWQ3-6;Q8IWQ3-3;Q8IWQ3-2;Q8IWQ3-4;Q8IWQ3;Q8IWQ3-5;H0YES6;J3KNK0;Q8TDC3;Q8TDC3-2 Q8IWQ3-6;J3KNK0 BRSK2;BRSK1 Serine/threonine-protein kinase BRSK2;Serine/threonine-protein kinase BRSK1 1 NSFLGS(1)PR 73.781 0.044767 131380000 103600 120930 110810 112430 141680 167130 119360 126640 99159 107230 TRUE FALSE 107690.208 141698.7868 113697.7996 134668.3184 117597.2842 128316.5904 110004.2513 124942.5979 95590.28696 128239.6655 0.8397574 1.104952873 0.886603994 1.050129989 0.917011782 1.000599853 0.857802076 0.974289799 0.745403434 1 16.96848304 2.244552881 24.99948296 0.899793675 0.970721197 0.115939585 0.096705319 306.9408352 1280548.539 0.031096126 0.025385375 175.611471 -2.244552881 0.070927522 NSGSSQGLGGS(ph)PGSHSHTTMANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSGSSQGLGGSPGSHSHTTMANK 23 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 NSGSSQGLGGS(0.936)PGS(0.052)HS(0.004)HT(0.004)T(0.004)MANK;NSGSSQGLGGS(0.978)PGS(0.006)HS(0.006)HT(0.006)T(0.006)MANK;NSGSSQGLGGS(0.89)PGS(0.034)HS(0.034)HT(0.034)T(0.007)MANK 87.091 0.0074949 99812000 33485.3 60764 66404 61304 89689 112263 89969 83161 79610 54045 TRUE FALSE 34807.3255 71199.74432 68134.54279 73429.74823 74443.69582 86191.61961 82916.99469 82046.36282 76744.85165 64634.083 0.53852896 1.10158203 1.05415811 1.136084011 1.151771517 1.333532025 1.282867968 1.269397801 1.18737434 1 15.98000751 4.973567199 1.29017489 1.212092018 6.69E-32 0.780423491 0.099990772 1.018058614 0.999776037 0.02758654 1.874894332 94095.1414 -4.973567199 -1.212092018 NSGTQS(ph)DGEEKQPGLVMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSGTQSDGEEKQPGLVMER 19 1 J3QRV5;Q6P1M3;Q6P1M3-2 J3QRV5 LLGL2 Lethal(2) giant larvae protein homolog 2 1 NSGT(0.008)QS(0.992)DGEEKQPGLVMER;NS(0.001)GT(0.211)QS(0.788)DGEEKQPGLVMER 188.69 9.47E-15 584800000 484220 273910 335390 252120 487130 578800 446420 366240 364040 182249 TRUE FALSE 503337.3795 320951.9118 344130.5389 301988.5835 404327.8166 444382.4718 411428.4339 361331.1518 350938.2715 217957.2022 2.309340432 1.472545567 1.578890422 1.385540741 1.855078945 2.038851973 1.887656979 1.657807809 1.610124685 1 17.73368535 0.683260515 1.604211162 1.000899297 1.761144575 0.446944466 0.258298878 1.125802849 4.291874373 0.247218839 0.070908131 4.822369844 -0.683260515 0.760245278 NSHLINVLMWELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSHLINVLMWELEK 14 0 A0A087WZK9;B3KS98;O15372;E5RJT0 A0A087WZK9 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 ; 149.22 7.55E-06 285380000 557130 340610 465480 338780 656810 758310 629190 518060 492070 225170 FALSE TRUE 579125.9226 399107.1179 477610.7912 405789.6728 545165.6708 582203.9948 579872.4437 511116.2531 474360.4968 269287.7504 2.150583982 1.482084192 1.773607565 1.506899858 2.024472595 2.162014403 2.153356188 1.89803009 1.761537598 1 18.03878908 3.22010004 24.96918672 1.915243464 1.713944081 0 0.358044353 670.3314339 906666.8638 0.097148406 0.116317809 1659.969238 -3.22010004 -0.201299383 HKSETDTSLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKSETDTSLIR 11 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 222.49 4.59E-12 679980000 99094 548020 639560 670440 667910 888110 622990 815120 679180 628910 FALSE TRUE 103006.3076 642138.172 656227.459 803051.0309 554378.8968 681859.9119 574158.4159 804194.6497 654736.4445 752132.8733 0.136952274 0.853756291 0.872488735 1.067698354 0.737075743 0.906568422 0.763373649 1.069218855 0.870506353 1 19.52062803 4.744699929 3.935301088 0.911141714 0.059842932 0.825402723 0.106189281 0.093563045 2.944194227 0.02474774 0.23042421 55552.02936 -4.744699929 -0.851298782 down NSKYEYDPDIS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 NSKYEYDPDIS(1)PPR 78.661 0.012873 166050000 327080 216110 266990 192930 388100 395970 253600 280100 277810 200440 TRUE FALSE 339993.371 253225.2114 273947.9787 231090.9782 322130.9006 304011.9685 233722.1693 276345.7177 267811.6724 239712.3803 1.418338804 1.056371019 1.142819484 0.964034389 1.343822543 1.268236409 0.97501084 1.15282205 1.117220863 1 17.8709449 2.567490232 0.020873343 2.29E-06 2.281323182 0.168154667 0.135519756 1035.700574 9.649038084 500.5737406 551.5921434 369.3943362 -2.567490232 2.281320892 NSLDASRPAGLS(ph)PTLTPGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLDASRPAGLSPTLTPGER 20 1 Q14135-4;G5E9M7;Q14135;Q14135-2;A0A0A6YYI5;A0A075B6E4;Q14135-6;E7ERW0;G5E9M9;E7EWF5;F8W708;E7EQU6;Q14135-5 Q14135-4 VGLL4 Transcription cofactor vestigial-like protein 4 1 NSLDASRPAGLS(0.974)PT(0.026)LTPGER 142.23 1.10E-07 313180000 118910 134240 137320 122520 186420 201820 155020 148260 141360 132320 TRUE FALSE 123604.6586 157294.6758 140898.672 146754.0903 154732.395 154950.3636 142869.1273 146272.8172 136272.4812 158245.5706 0.781093955 0.993991018 0.890379879 0.927381978 0.977799217 0.979176624 0.902831762 0.924340673 0.861145628 1 17.27180559 4.7526134 24.56626205 0.93561698 0.781093821 0.528097639 0.044823774 1539.207034 2690693.779 0.010329079 0.213590412 56573.54585 -4.7526134 -0.154523159 NSLEDNSWVFPS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLEDNSWVFPSPPK 15 0 Q9H6S1 Q9H6S1 AZI2 5-azacytidine-induced protein 2 1 NSLEDNSWVFPS(1)PPK 117.37 0.00039325 11586000 50004 18176 27349 18227 31684 40621 38605 28854 29578 12358 TRUE FALSE 51978.19653 21297.58661 28061.73741 21832.2462 26298.365 31187.38837 35579.03922 28467.25933 28513.49356 14779.31349 3.516956086 1.441040318 1.898717246 1.47721653 1.779403692 2.110205483 2.407353985 1.926155727 1.929284034 1 13.85129164 4.747028246 24.97549905 1.841179242 3.516956936 0.655498119 0.37619171 670.6815341 1978148.561 0.087894079 1.021158467 55850.65183 -4.747028246 1.675777695 NSLESYAFNMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 118.28 0.0017258 168010000 61229 655740 634070 822240 411240 894230 396150 708200 500560 783240 FALSE TRUE 63646.3682 768358.2441 650594.3851 984876.6179 341337.5717 686558.6347 365098.7279 698707.7374 482544.9434 936700.882 0.067947377 0.820281329 0.694559381 1.051431291 0.364404025 0.732953975 0.389770881 0.745924073 0.515153719 1 19.8372289 -1.883297706 2.478499973 1.195971879 0.618343739 0.16958464 0.263416015 18806326.95 10926017.18 21614322.21 0.064565198 0.013082848 1.883297706 -0.57762814 NSLFTGDTLGAGQFSFQRPLLVLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLFTGDTLGAGQFSFQRPLLVLVDR 26 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3;H0YJY1 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 71.085 0.027238 122050000 44338 44287 46635 57354 83624 75889 57864 70101 54471 48259 FALSE TRUE 46088.49848 51892.94774 47850.34641 68698.45002 69409.62235 58264.92986 53328.46848 69161.41076 52510.59935 57714.42708 0.798561136 0.899133031 0.82908813 1.190316763 1.202639026 1.009538391 0.924005854 1.19833834 0.909834889 1 15.81664438 3.755143853 24.5702437 1.073001994 0.847947957 0.477868538 0.104820164 554.210579 821133.0149 0.026965234 0.048431279 5690.413855 -3.755143853 -0.225054037 NSLLAGGDDDTMSVISGIS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 NSLLAGGDDDTMSVIS(0.002)GIS(0.499)S(0.499)R;NSLLAGGDDDTMSVISGIS(0.5)S(0.5)R;NSLLAGGDDDTMSVISGIS(0.5)S(0.5)R 302.66 3.21E-55 123380000 70937 85422 83660 82097 96699 130239 96479 84920 84202 64966 TRUE FALSE 73737.64754 100092.564 85840.24833 98335.54156 80262.13852 99992.96604 88916.72388 83781.7863 81171.58647 77694.84385 0.949067453 1.288278077 1.104838417 1.265663675 1.033043308 1.286996165 1.144435325 1.078344227 1.044748692 1 16.24553124 1.535255098 2.199237983 1.020558599 1.161630283 0.207084743 0.104158972 0.406895675 4.075987721 0.075445913 0.026079354 34.29691821 -1.535255098 0.141071684 NSLS(ph)PVQATQKPLVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSLSPVQATQKPLVSK 16 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 NSLS(1)PVQATQKPLVSK;NSLS(1)PVQATQKPLVSK 273.51 2.01E-35 1502140000 1041910 642590 840740 573820 1084660 1107770 1096740 844380 1044290 424120 TRUE FALSE 1083045.411 752949.8338 862650.3751 687319.8833 900289.8806 850507.2059 1010774.653 833062.4672 1006706.207 507218.1937 2.135265305 1.484469294 1.700748092 1.355077345 1.774955811 1.676807371 1.992780751 1.642414404 1.984759654 1 18.95224697 NSLTSKDPDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSLTSKDPDIK 11 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 88.087 0.0091097 0 523880 227950 315260 251570 564270 568300 433950 353360 376950 159350 FALSE TRUE 544563.1869 267098.6393 323475.9346 301329.7951 468355.587 436320.9377 399935.8651 348623.7872 363383.6431 190571.5816 2.857525673 1.401565948 1.697398594 1.58118956 2.45763604 2.289538315 2.0986123 1.829358734 1.90680919 1 17.53997347 0.399397578 1.177885547 0.999395827 2.008527183 0.358610486 0.41022343 3.114114124 5.034320876 0.390591726 0.117788616 2.508404542 -0.399397578 1.009131356 NSMDRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSMDRPK 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 71.379 0.049681 115965000 184647 154004 167488 131119 240160 249680 202364 182986 186975 168000 FALSE TRUE 191937.0061 180452.989 171852.8749 157053.9468 199337.689 191695.6039 186502.1809 180533.372 180245.8063 200916.3834 0.955307889 0.898149698 0.855345253 0.781688104 0.99214253 0.954106383 0.928257705 0.898549779 0.897118509 1 17.61623569 3.216214739 24.99913457 0.9365178 0.87321189 0.313864398 0.051529662 338.2918431 378458.2124 0.015647897 0.018715749 1645.184992 -3.216214739 -0.063305911 NSMFHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 129.55 0.0036491 155167000 122598.4 233738 243549 222079 429999 404626 281638 278843 233110 307852 FALSE TRUE 127438.6795 273880.6833 249896.087 266005.5634 356907.9236 310657.7437 259562.4776 275105.5657 224720.4166 368169.7052 0.346141135 0.743897935 0.678752443 0.722508016 0.969411439 0.843789533 0.705007701 0.747224885 0.61037183 1 18.49001139 4.955751057 1.752659405 0.779638221 1.79E-17 0.551094129 0.117617933 1.384661091 2.662850372 0.030182002 2.145063598 90313.16381 -4.955751057 -0.779638221 NSMPTVSFLDQDQS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSMPTVSFLDQDQSPPR 17 0 A7KAX9;A7KAX9-2 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 NSMPTVSFLDQDQS(1)PPR;NSMPTVSFLDQDQS(1)PPR 369.41 1.04E-104 334720000 136274 136508 131915 144225 168231 217811 157039 155433 137711 97634 TRUE FALSE 141654.2027 159952.1871 135352.8133 172752.2745 139635.1547 167227.6962 144729.8728 153349.6749 132754.808 116763.513 1.213171813 1.369881593 1.159204702 1.479505627 1.195880041 1.432191375 1.239512834 1.31333557 1.136954556 1 16.83323 1.038008137 2.689918892 1.000388863 1.303804976 0.493037516 0.098662169 0.181219925 2.853356943 0.082475692 0.02215962 10.91460787 -1.038008137 0.303416113 NSNILEDLETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSNILEDLETLR 12 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;; 244.27 5.04E-16 163109000 191943 207410 224415 199697 275496 313565 238427 241655 224206 172023 FALSE TRUE 199521.0579 243031.0541 230263.4393 239196.4706 228667.2883 240744.2809 219738.4687 238416.01 216136.8699 205727.6133 0.969831199 1.181324423 1.11926365 1.162685294 1.111505085 1.170208885 1.068103913 1.158891634 1.050597275 1 17.65037592 1.033958224 4.950409875 1.000337077 1.121923885 0.295925701 0.059237843 0.17177567 10.21868208 0.051199539 0.012960984 10.81329929 -1.033958224 0.121586808 NSNLVGAAHEELQQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSNLVGAAHEELQQSR 16 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;; 286.85 4.66E-36 14570670000 4830590 5869120 6339420 5745690 8194480 10172060 6927020 7115760 6325460 4782670 FALSE TRUE 5021305.423 6877095.705 6504630.493 6882170.333 6801585.217 7809753.224 6384062.072 7020384.876 6097807.93 5719742.617 0.877890101 1.202343561 1.137224335 1.203230773 1.189141832 1.365402912 1.116144991 1.227395243 1.066098309 1 22.4475188 4.741032396 24.61465367 1.181136808 0.877889967 0.452398952 0.094494674 148.3008227 1476709.511 0.020834278 0.140984075 55084.87852 -4.741032396 -0.303246841 NSNS(ph)PPS(ph)PSSMNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 NS(0.019)NS(0.981)PPS(0.93)PS(0.055)S(0.014)MNQR;NSNS(1)PPS(0.998)PS(0.002)SMNQR;NSNS(1)PPS(1)PSSMNQR 305.64 3.29E-44 1786840000 919380 958360 982210 909019 1176860 1484930 1096890 1056090 997920 770841 TRUE FALSE 955677.8323 1122950.875 1007807.199 1088820.245 976817.7576 1140077.512 1010912.896 1041934.841 962005.0541 921872.5353 1.036670251 1.21811946 1.093217512 1.181096305 1.059601756 1.236697557 1.096586412 1.130237426 1.043533696 1 19.81420776 1.127702096 2.21429455 0.999143196 1.136258702 0.34390404 0.061741318 0.280230903 2.586734804 0.051524518 0.014451331 13.41844209 -1.127702096 0.137115506 NSNS(ph)PPSPSSMNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNS(1)PPSPSSMNQR;NSNS(1)PPSPSSMNQR;NSNS(1)PPSPSSMNQR 141 3.83E-05 402350000 628780 616080 640900 604640 802430 966540 725950 706760 650450 485320 TRUE FALSE 653604.7199 721886.9476 657602.3805 724235.9873 666033.2352 742075.7331 669048.1421 697287.0382 627040.4316 580409.162 1.126110273 1.243755259 1.132997932 1.247802472 1.147523642 1.278538972 1.152718093 1.201371522 1.080342063 1 19.14671077 1.060064503 2.89280447 1.000468829 1.193746103 0.611911494 0.050034239 0.133340918 2.333652648 0.041812041 0.011148768 11.48324163 -1.060064503 0.193277274 NSNSPPS(ph)PSSMNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 NSNSPPS(0.999)PS(0.001)SMNQR;NSNS(0.013)PPS(0.987)PSSMNQR;NSNSPPS(0.998)PS(0.002)SMNQR;NSNS(0.003)PPS(0.996)PS(0.001)SMNQR;NSNSPPS(1)PSSMNQR;NSNSPPS(0.981)PS(0.018)S(0.001)MNQR;NSNSPPS(0.997)PS(0.003)SMNQR;NSNSPPS(0.971)PS(0.021)S(0.008)MNQR 312.93 9.26E-56 2994790000 1505284 1601351 1756029 1607492 1993810 2626110 1870490 1856480 1759124 1371867 TRUE FALSE 1564713.775 1876370.577 1801792.558 1925449.12 1654902.888 2016235.752 1723876.106 1831596.922 1695813.471 1640658.073 0.953711075 1.143669488 1.098213326 1.173583425 1.008682379 1.228918923 1.05072235 1.116379429 1.033617851 1 20.64584317 1.088297241 3.913438998 1.000658564 1.10079708 0.15732084 0.075185311 0.325569297 8.959463398 0.064798109 0.016716674 12.25454642 -1.088297241 0.100138516 NSPEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPEDKR 7 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 81.635 0.04276 150400000 165010 116020 159230 119070 205300 198910 176770 155950 163640 94997 FALSE TRUE 171524.7222 135945.5325 163379.6646 142621.6906 170403.1793 152716.167 162914.3055 153859.7453 157750.6284 113609.8433 1.509769904 1.196599947 1.438076665 1.255363853 1.499898022 1.344215981 1.433980549 1.35428182 1.388529583 1 16.79372831 -1.077888348 4.555012306 0.999976294 1.375916078 0.593770536 0.094256534 1.99E-05 4.03E-06 0.080131677 0.018886028 0.083581787 1.077888348 0.375939784 NSPGLGSLVS(ph)PHGPHMPPAASIPPPPGLGGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPGLGSLVSPHGPHMPPAASIPPPPGLGGVK 32 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 NS(0.127)PGLGS(0.081)LVS(0.396)PHGPHMPPAAS(0.396)IPPPPGLGGVK;NS(0.209)PGLGS(0.34)LVS(0.436)PHGPHMPPAAS(0.015)IPPPPGLGGVK 101.49 1.88E-05 999720000 350451 402394 461360 382250 685450 709780 566530 562820 489020 323273 TRUE FALSE 364287.0761 471502.0393 473383.4206 457857.9091 568937.4538 544944.3518 522123.8982 555276.3185 471420.2657 386612.1549 0.942254586 1.21957376 1.224440087 1.184282241 1.471597431 1.409537556 1.35051082 1.436261927 1.219362246 1 18.56052747 5.491474092 0.814589134 1.336248482 7.54E-11 0.348524382 0.135834672 6.838234507 1.436148567 0.043426086 11.00202071 310080.2404 -5.491474092 -1.336248482 NSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 43 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 NS(0.014)PMAQT(0.985)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 132.49 1.61E-09 150960000 103300 70229 74488 71509 136920 126210 108060 108230 108060 69060 TRUE FALSE 107378.3638 82290.28444 76429.21847 85653.26677 113646.3873 96899.64023 99589.97484 106779.3539 104170.9417 82590.98477 1.30012209 0.996359163 0.925394202 1.037077679 1.376014436 1.173247183 1.205821375 1.292869363 1.261287076 1 16.33369669 3.269001487 24.99054326 1.233721434 1.049900771 0.247593447 0.128339654 235.3909875 193243.5373 0.034305911 0.04644506 1857.810818 -3.269001487 -0.183820662 NSPNNISGISNPPGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPNNISGISNPPGTPR 17 0 Q9BWW4-2;Q9BWW4;Q9NW25;A0A087WVT6;Q9BWW4-3 Q9BWW4-2 SSBP3 Single-stranded DNA-binding protein 3 1 NSPNNISGISNPPGT(1)PR;NSPNNISGIS(0.006)NPPGT(0.994)PR 138.55 3.68E-05 169430000 104381 94902 92268 87957 111348 144301 95843 102977 91798 75798 TRUE FALSE 108502.0425 111200.6803 94672.57988 105354.6321 92421.10673 110789.2797 88330.57522 101596.7618 88494.20791 90649.16686 1.196944729 1.226714863 1.044384446 1.162223942 1.019547227 1.22217648 0.974422361 1.120768842 0.976227482 1 16.46800614 8 0.164772249 0.98381744 1.873092367 0.380744428 0.07670835 62.10994138 0.655272389 0.192765269 13.522851 100000000 -8 0.889274926 NSPNNMSLSNQPGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPNNMSLSNQPGTPR 16 0 H0Y9V4;A0A087X159;P81877-4;P81877-5;P81877-3;P81877 H0Y9V4 SSBP2 Single-stranded DNA-binding protein 2 1 NSPNNMSLSNQPGT(1)PR;NSPNNMSLS(0.001)NQPGT(0.999)PR 173.87 7.41E-12 0 62052 73553 71671 74467 76251 109862 72999 74725 64398 67047 TRUE FALSE 64501.86087 86185.15559 73538.80514 89196.35034 63289.88226 84348.21547 67277.14763 73723.4336 62080.32856 80183.57596 0.804427342 1.074847992 0.917130525 1.112401752 0.789312294 1.05193881 0.839039003 0.919433097 0.774227488 1 16.29101914 2.213554866 24.99055182 0.879728651 0.961085003 0.094599454 0.113534352 500.4008999 500093.4681 0.038959142 0.02878499 163.5139709 -2.213554866 0.081356352 NSPQSS(ph)PTSTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 NSPQS(0.004)S(0.936)PT(0.048)S(0.011)TPK;NSPQS(0.064)S(0.917)PT(0.019)S(0.001)TPK;NSPQS(0.024)S(0.9)PT(0.076)S(0.001)TPK 209.22 6.06E-08 316650000 1162650 800620 1042610 854810 1416520 1585330 1326480 1129320 1115840 599580 TRUE FALSE 1208552.32 938120.257 1069781.273 1023888.867 1175740.436 1217161.133 1222507.031 1114183.313 1075681.136 717056.2213 1.685435931 1.308293867 1.491907108 1.42790598 1.63967678 1.697441703 1.704897043 1.553829783 1.500135002 1 19.45172671 0.690021628 2.8597138 1.000031725 1.561235588 0.657039903 0.121405207 1.727361821 15.16702831 0.122672948 0.032242017 4.898032111 -0.690021628 0.561203863 NSPRPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPRPSPK 8 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 NSPRPS(1)PK 55.401 0.075196 250630000 93995 39132 63254 52569 94204 114840 92987 66482 80052 27283 TRUE FALSE 97705.99518 45852.6166 64902.4512 62966.9913 78191.23773 88170.15042 85698.43596 65590.91753 77170.94416 32628.58149 2.994491048 1.405289918 1.989128802 1.929810872 2.39640322 2.702236702 2.626483655 2.010228902 2.365133286 1 14.99384865 3.242796333 24.98027615 2.271317807 2.02504147 0 0.57922199 408.7694354 2410709.355 0.152880873 0.199925233 1749.02627 -3.242796333 -0.246276337 NSPTFKS(ph)FEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSPTFKSFEEK 11 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEK;NSPT(0.002)FKS(0.998)FEEK 152.94 1.98E-05 1283670000 1733170 490090 1347970 510690 1885480 1619940 1832530 1133240 1755260 350900 TRUE FALSE 1801596.89 574259.1451 1383099.206 611702.9577 1564986.783 1243733.485 1688891.51 1118050.771 1692088.535 419652.1366 4.293072125 1.368417065 3.295823099 1.457642901 3.729247742 2.963724897 4.024503542 2.664232286 4.032121817 1 18.6788344 3.186298311 24.99997332 3.177387673 2.564901067 0.032992109 1.13934869 279.4148098 133658.4629 0.298410622 0.356669308 1535.671451 -3.186298311 -0.612486606 NSPTFKS(ph)FEEKVENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSPTFKSFEEKVENLK 16 2 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 1 NSPTFKS(1)FEEKVENLK 171.06 2.64E-09 760760000 1746400 408990 1226900 318410 1982100 1348300 1302300 946650 1640400 336760 TRUE FALSE 1815349.221 479230.851 1258874.022 381390.5476 1645183.35 1035177.759 1200222.323 933961.7052 1581362.324 402741.6743 4.50747796 1.189921187 3.125760511 0.946985554 4.084959305 2.570326898 2.980129447 2.319009342 3.926492899 1 18.61949524 3.220428508 24.9954128 2.840035568 2.401864287 0.020818215 1.225679798 1044.610725 1440009.785 0.32537091 0.389603021 1661.225191 -3.220428508 -0.438171282 NSPTFKS(ph)FEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NSPTFKSFEER 11 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 NSPT(0.154)FKS(0.845)FEER;NSPTFKS(1)FEER;NSPT(0.002)FKS(0.998)FEER;NSPT(0.004)FKS(0.996)FEER;NSPT(0.082)FKS(0.918)FEER 157.68 1.85E-05 1894440000 3293649 1877954 4064243 1762977 6526740 4355320 3907102 3531580 4861160 2028481 TRUE FALSE 3423684.806 2200477.991 4170160.511 2111688.589 5417327.066 3343862.936 3600853.136 3484244.947 4686207.801 2425923.014 1.411291614 0.907068352 1.718999526 0.870468097 2.233099333 1.378387903 1.484322921 1.436255366 1.931721565 1 21.21010234 4.233808155 24.9977253 1.515294732 1.15917999 0.109602643 0.395544094 215.3157808 1132575.377 0.090488037 0.206021509 17132.00353 -4.233808155 -0.356114742 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NS(0.013)QEDS(0.987)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NS(0.087)QEDS(0.913)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK;NSQEDS(1)EDS(1)EDKDVK 221.13 1.89E-11 46246690000 31145200 4290760 7200660 4414130 13662430 27116900 13277880 7836290 8454760 2386811 TRUE FALSE 32374836.55 5027664.653 7388315.115 5287231.739 11340095.03 20819410.94 12237125.07 7731257.35 8150474.839 2854460.917 11.34183914 1.761335957 2.588339911 1.852269795 3.972762409 7.293640214 4.287017908 2.708482468 2.855346447 1 21.44478688 4.745439111 24.84385133 3.319597931 11.34184316 0.680595162 1.680507047 462.1189554 1669041.858 0.422051818 4.180555797 55646.66111 -4.745439111 8.022245231 NSQEDS(ph)EDSEDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.978)EDS(0.022)EDKDVK;NSQEDS(1)EDSEDKDVK;NSQEDS(0.91)EDS(0.09)EDKDVK;NSQEDS(1)EDSEDKDVK;NSQEDS(0.994)EDS(0.006)EDKDVK;NS(0.001)QEDS(0.94)EDS(0.059)EDKDVK;NSQEDS(0.999)EDS(0.001)EDKDVK;NSQEDS(0.916)EDS(0.084)EDKDVK;NSQEDS(0.995)EDS(0.005)EDKDVK 268.09 9.08E-26 21112060000 17862730 3355096 6040654 3308653 10531426 15347724 9968991 6263975 7084158 1902821.8 TRUE FALSE 18567964.37 3931307.639 6198078.406 3963094.688 8741297.97 11783447.7 9187595.436 6180016.661 6829200.537 2275643.3 8.159435345 1.727558813 2.723659901 1.741527193 3.841242593 5.17807325 4.037361847 2.715722917 3.0009978 1 21.11784301 4.747769924 24.6350653 3.036126057 8.159438646 0.63988951 1.182129326 672.4432762 1798751.241 0.289579997 3.584552781 55946.11381 -4.747769924 5.123312589 NSQEDSEDS(ph)EDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 NSQEDS(0.029)EDS(0.971)EDKDVK 201.27 3.94E-09 4950100000 601390 91215 176220 94590 313400 532780 275130 163620 208420 44792 TRUE FALSE 625133.3416 106880.4667 180812.438 113299.6197 260128.3799 409049.9194 253564.5917 161426.9415 200919.0049 53568.13481 11.66987322 1.995224719 3.375373039 2.115056275 4.856028325 7.636067988 4.733496744 3.013488189 3.7507187 1 15.70908744 4.746708378 24.80878503 3.795378019 11.66987754 0.649279369 1.772677995 607.8329989 1850719.051 0.437182026 4.885699106 55809.53161 -4.746708378 7.874499526 NSQEDSEDSEDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;;;; 209.31 2.23E-09 4128880000 4021800 944861 1641381 829934 2690755 3335470 2370655 1543497 1805260 529023 FALSE TRUE 4180583.77 1107133.527 1684156.737 994092.4681 2233381.426 2560857.642 2184836.867 1522808.947 1740289.045 632674.9281 6.607791117 1.749924768 2.66196219 1.571253141 3.530061532 4.047667338 3.453332461 2.406937401 2.750684385 1 19.2711049 4.747239048 24.55623449 2.691875173 6.607793685 0.638693988 0.906178594 574.9382306 1626782.478 0.215954943 2.532972978 55877.76767 -4.747239048 3.915918512 NSQKHS(ph)PTSEPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 2 NS(0.258)QKHS(0.36)PT(0.175)S(0.207)EPTPPGDALPPVS(0.69)S(0.301)PHT(0.009)HR;NS(0.256)QKHS(0.732)PT(0.008)S(0.003)EPTPPGDALPPVS(0.696)S(0.277)PHT(0.027)HR;NS(0.202)QKHS(0.3)PT(0.212)S(0.277)EPT(0.009)PPGDALPPVS(0.492)S(0.447)PHT(0.062)HR;NS(0.304)QKHS(0.474)PT(0.103)S(0.115)EPT(0.004)PPGDALPPVS(0.461)S(0.412)PHT(0.127)HR 155.3 2.75E-08 1492370000 442964 642903 819733 621225 1146077 1242356 1012383 1073182 866906 552909 TRUE FALSE 460452.5608 753316.5892 841095.9154 744101.4508 951267.2409 953837.6471 933029.7751 1058797.751 835706.2224 661240.9325 0.696346125 1.139246759 1.271996143 1.125310631 1.438609127 1.442496373 1.411028461 1.601228385 1.263845266 1 19.33481651 5.077033297 0.820775207 1.395106469 4.45E-16 0.549977851 0.166798981 2.672108013 0.949106601 0.055478459 3.844895134 119407.9649 -5.077033297 -1.395106469 NSQKHS(ph)PTSEPTPPGDALPPVSSPHT(ph)HR ddPTM_MDA-MB-175_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(0.061)QKHS(0.309)PT(0.309)S(0.309)EPT(0.013)PPGDALPPVS(0.311)S(0.311)PHT(0.377)HR 60.943 0.056079 275120000 31641 60851 80397 55582 92964 102230 85100 82004 75965 45163 TRUE FALSE 32890.21111 71301.68589 82492.21187 66575.9537 77162.01249 78488.63181 78429.63963 80904.87051 73231.03449 54011.82515 0.608944634 1.320112507 1.527299099 1.232618108 1.428613313 1.453174959 1.452082751 1.497910324 1.355833362 1 15.72098768 4.733029465 4.206775101 1.397562515 0.5501257 0.696102464 0.148746969 0.10006951 4.034712422 0.032554668 0.253694957 54079.10119 -4.733029465 -0.847436816 EKDHSSSRPS(ph)SPRPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 EKDHSSSRPSSPRPQK 16 3 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 EKDHS(0.011)S(0.011)S(0.011)RPS(0.484)S(0.484)PRPQK 76.539 0.01886 92583000 35456 213330 263750 222870 276520 357230 258660 341870 286310 231590 TRUE FALSE 36855.83026 249967.768 270623.5417 266953.0208 229517.2292 274268.7464 238385.5533 337287.7918 276005.759 276965.6264 0.133070052 0.902522711 0.977101546 0.963848923 0.828684888 0.990262763 0.860704472 1.217796577 0.996534345 1 18.07934741 4.745372998 3.571377084 0.986131245 0.027328976 0.869900225 0.097562334 0.102902372 2.328767987 0.025742349 0.267152482 55638.1906 -4.745372998 -0.958802268 down NSQKHSPTS(ph)EPTPPGDALPPVS(ph)SPHTHR ddPTM_MDA-MB-175_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(0.133)QKHS(0.224)PT(0.293)S(0.335)EPT(0.015)PPGDALPPVS(0.549)S(0.367)PHT(0.085)HR 86.632 0.0048087 478930000 338230 177710 240190 148760 319250 422480 268900 248140 261630 149500 TRUE FALSE 351583.5816 208230.3101 246449.5487 178184.284 264983.999 324365.4227 247822.9154 244814.0892 252213.9874 178791.6626 1.966442822 1.164653357 1.378417456 0.996602869 1.482082526 1.814208884 1.386098835 1.369270164 1.410658549 1 17.44791994 0.201313971 1.159452856 0.998968401 1.429482234 0.198520306 0.265409008 9.196371121 11.72128642 0.269587725 0.076012971 1.589695595 -0.201313971 0.430513833 NSQPNRYT(ph)NR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSQPNRYTNR 10 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRYT(1)NR;NSQPNRY(0.002)T(0.998)NR 138.31 0.00011022 1304400000 725410 817690 1034020 714009 1501400 1336320 1004940 1033730 950050 700342 TRUE FALSE 754049.7469 958121.8968 1060967.411 855237.8491 1246192.564 1025979.932 926170.1769 1019874.54 915857.8861 837560.606 0.900292757 1.143943363 1.266735091 1.021105629 1.48788345 1.22496202 1.105794817 1.217672528 1.093482525 1 19.67583406 4.718868721 3.704864395 1.190448078 0.874790147 0.272153498 0.133400607 0.293614417 7.609990243 0.030574593 0.246866331 52344.21864 -4.718868721 -0.315657931 NSRPEANEALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 ;;; 197.25 1.80E-07 2641990000 1204340 1310380 1384730 1242920 1679660 2197220 1468830 1534350 1406470 1048690 FALSE TRUE 1251888.273 1535427.572 1420817.201 1488765.866 1394151.993 1686948.954 1353699.267 1513784.548 1355851.419 1254160.727 0.998188068 1.224266985 1.132882868 1.187061462 1.111621472 1.345081948 1.079366653 1.207010007 1.081082664 1 20.25829082 -0.58929655 8.158403593 0.999986698 1.159366003 0.195619415 0.0912288 0 0 0.079293154 0.018689576 0.257456257 0.58929655 0.159379305 NSS(ph)PAPPQPAPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSSPAPPQPAPGK 13 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 NS(0.023)S(0.977)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NSS(1)PAPPQPAPGK;NS(0.003)S(0.997)PAPPQPAPGK;NSS(1)PAPPQPAPGK 212.55 1.36E-08 1380460000 3213670 1911270 2407480 2283100 2926760 3500770 3674370 2718520 2568250 1133305 TRUE FALSE 3340548.173 2239515.755 2470220.907 2734690.366 2429270.381 2687769.222 3386363.278 2682082.686 2475819.184 1355354.416 2.464704533 1.652346964 1.822564546 2.01769392 1.792350659 1.983074825 2.498507577 1.978879217 1.826695036 1 20.37023873 0.784943546 2.790490015 1.000377912 2.017355666 0.589611076 0.256104842 0.753637589 8.654948675 0.243303272 0.064204992 6.094576688 -0.784943546 1.016977754 NSSLGS(ph)PSNLCGS(ph)PPGSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 2 NS(0.003)S(0.003)LGS(0.992)PS(0.002)NLCGS(0.995)PPGS(0.004)IR;NSS(0.001)LGS(0.999)PS(0.002)NLCGS(0.98)PPGS(0.018)IR 144.48 2.80E-07 103820000 254200 301390 312510 295900 387970 482810 331460 341690 324510 283860 TRUE FALSE 264236.0123 353151.388 320654.2673 354428.1368 322022.998 370684.6946 305479.2991 337110.2044 312830.9485 339476.9322 0.778362202 1.040280957 0.944553921 1.044041887 0.948585802 1.091928963 0.899852892 0.993028311 0.921508706 1 18.37295402 4.748006755 24.8071835 0.985670735 0.778362079 0.546765975 0.056997454 815.9531107 2142783.378 0.012352574 0.158136505 55976.63085 -4.748006755 -0.207308657 NSSLGSPSNLCGS(ph)PPGSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSSLGSPSNLCGSPPGSIR 19 0 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 NSSLGSPSNLCGS(0.999)PPGS(0.001)IR;NSSLGSPSNLCGS(0.991)PPGS(0.009)IR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(0.996)PPGS(0.004)IR;NSSLGSPSNLCGS(1)PPGSIR;NSSLGSPSNLCGS(1)PPGSIR 346.53 1.31E-90 2681960000 996183 1004497 1110234 1030179 1405075 1827180 1162843 1254264 1137413 843453 TRUE FALSE 1035513.074 1177011.546 1139167.61 1233945.331 1166240.853 1402845.136 1071696.327 1237452.643 1096477.728 1008711.466 1.026570143 1.166846601 1.129329494 1.223288693 1.156168927 1.39072984 1.062440909 1.226765714 1.087008292 1 19.94408213 1.00414763 4.933417274 1.000212275 1.176083071 0.254517421 0.094281611 0.190936241 15.21832979 0.085374915 0.021607243 10.0959602 -1.00414763 0.175870796 NSSNTSVGS(ph)PSNTIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSSNTSVGSPSNTIGR 16 0 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 NSSNT(0.007)S(0.235)VGS(0.737)PS(0.021)NTIGR;NSSNTSVGS(1)PSNTIGR;NSSNTSVGS(0.999)PS(0.001)NTIGR 269.71 5.55E-28 243630000 542720 509190 533090 445130 664750 831160 546950 545390 502410 387400 TRUE FALSE 564147.0047 596639.4216 546982.7633 533175.3854 551756.0324 638135.6864 504078.6298 538079.9391 484328.3622 463303.6128 1.21766157 1.287793587 1.180614069 1.150812061 1.190916749 1.377359616 1.088009279 1.161398108 1.045380068 1 18.82159841 1.408339583 1.23625264 1.002931428 1.223785675 0.544637165 0.071187982 0.321465228 0.949123231 0.064162569 0.021400198 25.60587278 -1.408339583 0.220854247 NSSQSGGKPGS(ph)SPITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.904)S(0.096)PITK 139.98 1.06E-06 275760000 649940 269350 468260 273970 727310 669650 556090 494980 501590 234590 TRUE FALSE 675600.1331 315608.7672 480463.2403 328160.4483 603682.106 514133.9361 512502.2127 488345.6027 483537.8739 280553.419 2.408098021 1.124950708 1.712555284 1.169689713 2.151754586 1.83257056 1.826754472 1.740651048 1.723514458 1 18.09791597 0.824153168 13.35897327 0.999999999 1.726701782 0.269858443 0.365916789 3823.559548 290488.5541 0.327300577 0.081832375 6.670419822 -0.824153168 0.726701783 NSSQSGGKPGSS(ph)PITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 NSSQSGGKPGS(0.233)S(0.767)PITK;NSSQSGGKPGS(0.189)S(0.811)PITK 136.68 9.76E-06 862250000 1044600 443130 665960 418170 1034540 971520 868320 686870 744650 284800 TRUE FALSE 1085841.615 519234.1304 683315.4647 500882.7779 858689.2603 745899.2035 800258.8095 677663.6311 717850.192 340601.1072 3.188015516 1.524464012 2.006204473 1.470584703 2.521099439 2.189949439 2.349548468 1.98961077 2.10759794 1 18.3777236 0.028402695 1.330334458 0.997791171 2.124479489 0.353942533 0.465030886 15.47864782 19.72924704 0.522153383 0.122801305 1.067585569 -0.028402695 1.126688318 NSSS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 NSS(0.004)S(0.996)PVSPASVPGQR;NSS(0.003)S(0.997)PVSPASVPGQR;NSS(0.004)S(0.996)PVSPASVPGQR;NSS(0.015)S(0.985)PVSPASVPGQR 290.77 6.95E-44 3124840000 1800580 1785780 1767320 1697410 2160700 2702190 2178550 1975200 1935030 1324530 TRUE FALSE 1871668.289 2092473.824 1813377.811 2033152.632 1793424.986 2074647.325 2007789.558 1948725.675 1865388.648 1584046.294 1.181574236 1.320967595 1.144775767 1.283518442 1.132179655 1.309713821 1.267506869 1.230220154 1.177609932 1 20.59518307 0.807783472 2.340973217 1.000138967 1.236125178 0.564995112 0.061651128 0.49409682 4.610006662 0.053477054 0.014454284 6.423673699 -0.807783472 0.235986211 NSSTETDQQPHS(ph)PDSSSSVHSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(0.998)PDS(0.001)S(0.001)SSVHSIR 113.92 0.0012032 66859000 8523.1 20418 25806 28830 24361 37452 20886 25215 25909 16540 TRUE FALSE 8859.598569 23924.63267 26478.52556 34532.48795 20220.12592 28754.34059 19248.90074 24877.03417 24976.54015 19780.69632 0.447891137 1.209493957 1.33860432 1.745767054 1.022215072 1.453656642 0.973115427 1.257641984 1.262672443 1 14.27180559 4.736956153 4.57272333 1.266773283 0.396727796 0.544589967 0.220659322 0.13655705 7.518246452 0.050999916 0.381709069 54570.27629 -4.736956153 -0.870045486 NSSTETDQQPHSPDS(ph)SSSVHSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(0.228)PDS(0.548)S(0.22)S(0.003)SVHSIR 156.11 1.37E-08 373070000 28739 120300 139800 144490 123550 217520 110030 150020 109490 105300 TRUE FALSE 29873.63791 140960.5892 143443.3028 173069.6907 102549.0151 167004.2765 101405.5611 148009.2273 105549.4763 125931.5189 0.237221294 1.119343199 1.13905799 1.374315916 0.814323658 1.326151531 0.805243691 1.175315192 0.838149791 1 16.94227989 4.740379389 24.84663074 1.075756056 0.237220986 0.624234808 0.192710782 86.84238179 1186269.839 0.041811237 0.270075667 55002.11491 -4.740379389 -0.838535071 NSSTETDQQPHSPDSS(ph)SSVHSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSTETDQQPHSPDSSSSVHSIR 23 0 Q92613 Q92613 JADE3 Protein Jade-3 1 NSSTETDQQPHS(0.078)PDS(0.243)S(0.385)S(0.191)S(0.095)VHS(0.006)IR 86.659 0.0043274 269990000 60917 117490 101690 106710 118370 240260 108380 132400 92156 86006 TRUE FALSE 63322.0502 137667.9936 104340.1249 127816.9195 98249.50968 184463.2562 99884.8924 130625.3946 88839.32356 102857.229 0.615630528 1.338437705 1.014417032 1.242663454 0.955202766 1.793391266 0.971102307 1.26996805 0.863714922 1 16.65028367 4.749254093 24.24027649 1.175998252 0.615630038 0.285083427 0.258103289 1204.25824 2729764.136 0.056700509 0.802524035 56137.63251 -4.749254093 -0.560368213 NSSYFVEWIPNNVK ddPTM_MDA-MB-175_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 ; 242.94 3.85E-17 1081230000 2247520 1408170 1926290 1524480 2665900 2864100 2325400 2184150 2090660 1165160 FALSE TRUE 2336253.825 1650012.243 1976490.7 1826017.594 2212751.27 2198956.181 2143129.072 2154875.042 2015417.555 1393450.794 1.676595855 1.18411949 1.41841442 1.310428472 1.58796513 1.578065182 1.538001257 1.546430668 1.44635 1 20.41023063 0.943450904 20.56572249 0.999999999 1.477014202 0.521905157 0.137063622 1677.020471 609899.4214 0.131994128 0.032998532 8.779118348 -0.943450904 0.477014204 NSSYVHGGLDSNGKPADAVYGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSSYVHGGLDSNGKPADAVYGQK 23 1 Q13283;E5RH42;E5RIZ6;E5RJU8;Q13283-2;E5RIF8;E5RI46 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 128.29 2.58E-05 57186000 19177 20548 22581 28314 49259 38799 33934 30917 33599 15331 FALSE TRUE 19934.12277 24076.95916 23169.47941 33914.42469 40885.97277 29788.52025 31274.16441 30502.60819 32389.77855 18334.81592 1.087227865 1.313182486 1.263687594 1.849728126 2.229963636 1.624696991 1.705725574 1.663644092 1.766572334 1 14.16229816 3.752683583 18.68044536 1.734359515 1.230544667 0.347831671 0.290786616 28.465364 37647.01097 0.07158524 0.127371579 5658.268902 -3.752683583 -0.503814849 NSSYVHGGVDASGKPQEAVYGQNDIHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSSYVHGGVDASGKPQEAVYGQNDIHHK 28 1 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 220.67 8.50E-35 315360000 333070 328470 481140 320820 673210 626870 545940 553740 523110 249978 FALSE TRUE 346219.8608 384882.1674 493678.9037 384277.2384 558778.0047 481288.9428 503147.7963 546318.021 504283.3733 298956.403 1.158094817 1.287419047 1.651340793 1.285395578 1.86909529 1.609896754 1.683013949 1.827417027 1.686812419 1 18.18957558 4.607627228 0.897206443 1.651817955 0.923263676 0.20671949 0.252642382 2.198980962 1.595143486 0.078511068 1.510854175 40516.06206 -4.607627228 -0.728554279 NST(ph)PSEPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.087)T(0.898)PS(0.016)EPGSGR;NS(0.029)T(0.747)PS(0.224)EPGSGR;NS(0.208)T(0.78)PS(0.012)EPGSGR;NS(0.207)T(0.767)PS(0.026)EPGSGR 168.18 0.00020535 2894367000 2369500 2283690 2471540 2136770 3112680 3965080 2851080 2617870 2506640 1792080 TRUE FALSE 2463049.69 2675895.993 2535950.363 2559416.728 2583587.765 3044250.261 2627604.9 2582781.735 2416426.516 2143203.765 1.149237292 1.248549502 1.183252104 1.194201303 1.205479296 1.420420359 1.226017303 1.205103209 1.127483329 1 21.03133759 -0.565312705 8.282701625 1.000000001 1.221747712 0.426733184 0.075586598 0 0 0.073538282 0.017333139 0.272074159 0.565312705 0.221747711 NSTFSEIFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 132.32 0.00036348 3361100000 3432780 2180310 2789090 1967920 8198400 4706800 3990900 3541240 3443010 2638030 FALSE TRUE 3568308.805 2554761.282 2861775.977 2357168.702 6804838.896 3613717.032 3678082.83 3493775.47 3319096.743 3154901.47 1.131036528 0.809775299 0.90708886 0.74714495 2.156910116 1.145429442 1.165831283 1.107411912 1.052044501 1 21.58916352 NSTPS(ph)EPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NSTPSEPGSGR 11 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 1 NS(0.001)T(0.183)PS(0.812)EPGS(0.005)GR;NST(0.032)PS(0.967)EPGS(0.001)GR;NST(0.001)PS(0.999)EPGSGR 128.41 0.00027939 287583000 321459 352554 380276 363731 449791 541607 446203 406176 389083 333123 TRUE FALSE 334150.4495 413102.407 390186.305 435675.9062 373335.6865 415826.9824 411228.4429 400731.8751 375079.9788 398392.0738 0.838747735 1.036924262 0.979402781 1.093585778 0.93710621 1.043763191 1.032220443 1.005873112 0.941484541 1 18.60382942 4.744204702 24.7756377 1.009645659 0.838747652 0.557525309 0.045159171 377.6161699 1657552.378 0.009939719 0.087955004 55488.71943 -4.744204702 -0.170898007 NSTWSGESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NSTWSGESK 9 0 P19338 P19338 NCL Nucleolin 0 88.596 0.026029 0 94378 111700 111190 103360 154880 162080 144760 118470 111960 83566 FALSE TRUE 98104.11632 130883.6061 114087.7027 123804.2995 128553.5529 124439.3763 133413.3329 116882.1034 107930.5815 99939.15773 0.981638414 1.309632871 1.141571585 1.238796707 1.286318154 1.245151342 1.334945541 1.169532604 1.079962889 1 16.60876244 -0.477748099 8.216299143 0.999999999 1.20862141 0.241735305 0.104182906 0 0 0.094826183 0.022350746 0.33285256 0.477748099 0.20862141 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(1)PRT(0.51)S(0.49)PVIMAR;NSVLSDPGLDS(1)PRT(0.543)S(0.457)PVIMAR;NSVLSDPGLDS(1)PRT(0.62)S(0.38)PVIMAR;NSVLSDPGLDS(1)PRT(0.639)S(0.361)PVIMAR;NSVLSDPGLDS(1)PRT(0.544)S(0.456)PVIMAR;NSVLSDPGLDS(1)PRT(0.549)S(0.451)PVIMAR 197.32 2.10E-21 2552780000 401377 431681 452733 398753 524438 614000 437669 443903 455977 319123 TRUE FALSE 417223.6739 505818.8537 464531.5939 477625.1532 435294.2161 471407.8053 403363.3601 437953.2064 439566.4768 381649.0419 1.093212947 1.325350776 1.217169554 1.251477407 1.140561533 1.23518666 1.056896038 1.147528641 1.151755746 1 18.54188704 1.145461783 0.339755183 0.987483692 1.240344406 0.426550228 0.070179296 1.289035532 0.46950676 0.123250513 0.07887661 13.97853901 -1.145461783 0.252860714 NSVLSDPGLDS(ph)PRTS(ph)PVIMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 NSVLSDPGLDS(0.999)PRT(0.042)S(0.958)PVIMAR;NSVLSDPGLDS(1)PRT(0.338)S(0.662)PVIMAR;NSVLSDPGLDS(1)PRT(0.383)S(0.617)PVIMAR;NSVLSDPGLDS(1)PRT(0.11)S(0.89)PVIMAR 184.95 2.15E-17 2723600000 252034 295555 291471 307357 396941 471844 296822 302950 311977 241866 TRUE FALSE 261984.4969 346314.2722 299066.9737 368151.2972 329469.1106 362265.3819 273556.316 298889.4508 300749.0087 289255.0119 0.905721547 1.197262823 1.033921493 1.272756848 1.139026454 1.252408314 0.945727143 1.033307768 1.039736552 1 18.14198243 2.224011676 24.99994148 1.00803196 1.138466384 0.27373587 0.102549659 309.4152217 531675.1193 0.036793317 0.027292031 167.4987907 -2.224011676 0.130434424 NSWGEPWGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSWGEPWGER 10 0 Q9UBR2 Q9UBR2 CTSZ Cathepsin Z 0 ;;; 229.38 3.84E-09 1486050000 1074440 1235690 1126720 1060760 1419720 1770120 1276360 1218450 1111090 997630 FALSE TRUE 1116859.721 1447910.145 1156083.249 1270575.162 1178396.502 1359036.456 1176315.568 1202118.671 1071102.088 1193096.498 0.936101751 1.213573376 0.968977154 1.064939143 0.987679122 1.139083435 0.985934977 1.007561981 0.897749755 1 20.1862793 1.732421733 2.119428178 0.955012151 1.051882856 0.168652668 0.082069505 0.459424773 4.246942672 0.051287919 0.021508961 54.00347828 -1.732421733 0.096870705 NSYNNSQAPS(ph)PGLGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NSYNNSQAPSPGLGSK 16 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NSYNNSQAPS(1)PGLGSK;NS(0.002)YNNS(0.008)QAPS(0.99)PGLGSK 426.84 4.08E-160 602395000 1285370 719168 1015423 728345 1447045 1604381 1230494 1060528 1118512 572750 TRUE FALSE 1336117.4 842679.5096 1041885.758 872409.4671 1201076.808 1231787.827 1134044.665 1046313.357 1078256.972 684969.3965 1.950623498 1.230244028 1.521069062 1.273647365 1.753475139 1.798310747 1.655613624 1.527532999 1.574168097 1 19.38568001 0.028266742 1.588986887 0.999660304 1.577548103 0.410959595 0.21062219 26.10415921 40.81455926 0.220832654 0.056237233 1.067251423 -0.028266742 0.577887799 NSYVAGQYDDAASYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NSYVAGQYDDAASYQR 16 0 E7EUI8;E7EM57;P11413;P11413-3;P11413-2;E9PD92 E7EUI8;P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;; 492.3 2.14E-231 2461710000 889104 944505 986770 978776 1201715 1603660 1029283 1037722 1009351 760894 FALSE TRUE 924206.5125 1106716.387 1012486.037 1172374.971 997447.9135 1231234.269 948605.1089 1023813.034 973024.6547 909976.6111 1.015637656 1.216203112 1.112650616 1.288357258 1.096124781 1.353039467 1.04244999 1.125098185 1.069285345 1 19.79546994 1.386816063 1.166610836 1.012337981 1.17419927 0.227232968 0.098291718 0.597903425 1.595030767 0.083639745 0.028199269 24.36778547 -1.386816063 0.161861289 NT(ph)FVGTPFWMAPEVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTFVGTPFWMAPEVIK 16 0 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 NT(1)FVGTPFWMAPEVIK 132.64 0.00010488 0 12852 14456 24799 14577 37893 29169 23744 22217 26809 16549 TRUE FALSE 13359.40688 16938.70555 25445.28231 17460.28709 31451.9614 22394.94181 21882.88324 21919.21745 25844.14933 19791.4597 0.67500867 0.855859336 1.285669814 0.882213205 1.589168352 1.131545735 1.105673031 1.107508884 1.305823306 1 14.2725904 4.399087512 4.157909018 1.174536113 0.708572018 0.459673568 0.182214202 0.16435284 5.283957665 0.042575904 0.135708261 25066.14293 -4.399087512 -0.465964096 NT(ph)PSQHSHSIQHS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.997)PS(0.003)QHS(0.001)HS(0.013)IQHS(0.986)PER;NT(1)PSQHSHSIQHS(1)PER;NT(0.995)PS(0.005)QHSHSIQHS(1)PER;NT(0.999)PS(0.001)QHSHSIQHS(1)PER;NT(0.942)PS(0.058)QHS(0.003)HS(0.009)IQHS(0.989)PER;NT(0.995)PS(0.005)QHSHSIQHS(1)PER 224.39 1.66E-14 1655368000 275780.7 886911 809282 877991 989451 1224651 823293 1004235 769326 728301 TRUE FALSE 286668.735 1039231.065 830372.5538 1051654.999 821264.4724 940244.365 758761.1434 990774.8724 741638.1075 870997.6368 0.32912688 1.193150269 0.953357987 1.207414297 0.942900919 1.079502774 0.871140301 1.137517291 0.851481194 1 19.73230928 4.746791646 24.89032188 1.030678671 0.32912651 0.752745474 0.11984142 422.9958085 1279092.732 0.02557246 0.287994785 55820.23319 -4.746791646 -0.70155216 NTADHDES(ph)PPRT(ph)PTGNAPSSESDIDISSPNVSHDESIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTADHDESPPRTPTGNAPSSESDIDISSPNVSHDESIAK 39 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 2 NT(0.004)ADHDES(0.7)PPRT(0.622)PT(0.622)GNAPS(0.022)S(0.022)ES(0.008)DIDISSPNVSHDESIAK 88.634 0.0070362 181160000 20416 18924 25223 15098 28763 26988 21840 21480 23553 14195 TRUE FALSE 21222.03944 22174.04979 25880.3321 18084.33934 23873.87553 20720.44601 20128.12373 21192.09573 22705.33213 16976.23847 1.250102576 1.306181568 1.524503331 1.065273639 1.406311273 1.220555781 1.185664526 1.248338716 1.337477214 1 14.05122921 -4.465253471 0.204473899 2.18E-13 1.32485972 0.334512776 0.118786703 125.3205514 1.518339711 51.68715296 0.258185774 3.43E-05 4.465253471 1.32485972 NTAEWLLSHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTAEWLLSHTK 11 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 113.77 0.0013475 203750000 336660 320600 366400 353870 489860 549720 491610 382670 350670 338300 FALSE TRUE 349951.5968 375660.5561 375948.685 423864.4298 406593.7722 422055.8611 453076.3236 377540.9346 338049.4552 404583.4079 0.864967742 0.928512017 0.929224179 1.047656482 1.004968974 1.043186282 1.119858884 0.933159708 0.835549478 1 18.62607763 4.113972823 2.139799567 1.000047467 0.886004625 0.24686956 0.072510427 0.478142084 4.282392611 0.020554402 0.064481241 13000.88218 -4.113972823 -0.114042842 NTAS(ph)LNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTASLNSR 8 0 C9JXI9;C9JSG7;C9JJM9;C9JD81;C9J3W7;C9JBN7;C9JEW7;C9J718;C9JF32;A0A0C4DG23;A0A3B3ITR4;O00522-3;O00522 C9JXI9 KRIT1 Krev interaction trapped protein 1 1 NT(0.015)AS(0.984)LNS(0.001)R 82.008 0.022438 0 124850 193990 199280 187600 204480 294530 167350 203770 179000 215600 TRUE FALSE 129779.1744 227306.2735 204473.4005 224706.7201 169722.5626 226129.8711 154232.6697 201038.7965 172557.825 257842.6921 0.503326945 0.881569579 0.793016078 0.871487643 0.658240733 0.877007098 0.598165759 0.779695538 0.669236826 1 17.97613163 -1.111892529 4.537056199 1.000022281 0.745084645 0.293099335 0.121996486 2.67E-05 5.22E-06 0.107202168 0.025265434 0.077287182 1.111892529 -0.254937636 NTASQEDKDDSVVLPLGADTLTHNLGIPVLVVCTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTASQEDKDDSVVLPLGADTLTHNLGIPVLVVCTK 35 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 134.03 1.06E-08 136330000 255310 126720 172490 120100 258200 233780 223220 176560 207370 81479 FALSE TRUE 265389.8359 148483.1743 176985.2311 143855.4215 214311.2562 179488.138 205723.4331 174193.502 199906.7942 97443.25004 2.72353227 1.523791275 1.816290313 1.476299502 2.199344297 1.841976103 2.111212763 1.787640518 2.051520184 1 16.57227463 -1.440372092 2.987580434 0.98046969 1.919123436 0.407257228 0.341499516 39655098.38 47298902.46 6528570.888 0.075206731 0.036276711 1.440372092 0.938653746 NTCEHIYEFPQLSEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTCEHIYEFPQLSEDVIR 18 0 A6NIH7 A6NIH7 UNC119B Protein unc-119 homolog B 0 ; 161.22 3.86E-11 181664000 139434 149345 165005 152855 188876 227708 155769 175872 146270 139292 FALSE TRUE 144938.962 174993.842 169305.1659 183089.2628 156770.925 174826.2679 143559.4188 173514.7235 141005.7713 166583.6005 0.870067411 1.050486611 1.016337535 1.099083357 0.941094589 1.049480666 0.861786024 1.041607475 0.846456499 1 17.34588685 2.274318079 24.99942141 0.948889745 1.008484187 0.135485749 0.080438715 374.2806389 261672.6448 0.026312561 0.022013999 188.0693742 -2.274318079 0.059594442 NTDDDRPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTDDDRPPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 100.48 0.004226 623468000 789060 881600 910050 942320 1066190 1281840 1041660 936530 892640 664095 FALSE TRUE 820212.6981 1033007.942 933766.6506 1128708.083 884959.4046 984152.0865 960011.9673 923977.3472 860514.0608 794211.7004 1.03273812 1.300670768 1.175715052 1.421167786 1.114261354 1.239155865 1.208760796 1.163389241 1.083481974 1 19.59916409 1.165898338 1.338413103 1.000031222 1.222401851 0.337822052 0.097886106 0.420185503 1.493901125 0.084972639 0.026279236 14.65204817 -1.165898338 0.222370629 NTDDDRPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTDDDRPPRR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 169.21 2.65E-06 1472580000 2121040 2122770 2376970 2027880 2840760 3285480 2318580 2446990 2279580 2054910 FALSE TRUE 2204780.297 2487339.235 2438915.791 2428988.611 2357888.63 2522477.062 2136843.641 2414192.102 2197538.361 2457530.271 0.897152854 1.012129643 0.992425534 0.98838604 0.959454562 1.026427667 0.869508574 0.982365153 0.894206019 1 21.22877776 2.258951658 24.99874578 0.93777897 0.98092383 0.159116953 0.048093379 416.624795 510767.3505 0.015431526 0.012896786 181.5313586 -2.258951658 0.043144859 NTDEMVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTDEMVELR 9 0 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 190.03 8.73E-05 4572440000 3179590 3525390 3605020 3495950 4345560 4938610 4256740 3803620 3712300 3107170 FALSE TRUE 3305122.668 4130848.309 3698969.783 4187438.476 3606903.263 3791692.673 3923085.596 3752638.695 3578695.048 3715960.471 0.889439674 1.111650229 0.995427646 1.126879177 0.970651677 1.02038025 1.055739324 1.009870456 0.96306058 1 21.82530372 1.45081371 5.995166995 0.982339514 1.028525039 0.06138356 0.064705687 0.432941543 34.21801379 0.037084981 0.014999162 28.23668506 -1.45081371 0.046185525 NTDKNGEELHGGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTDKNGEELHGGKR 14 2 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ; 157.09 3.24E-06 744520000 347570 177500 268620 171775 431360 393030 292460 255338 307630 152767 FALSE TRUE 361292.332 207984.2442 275620.4579 205751.5823 358037.5813 301754.7389 269536.221 251915.6118 296558.4564 182698.7687 1.977530196 1.138399813 1.508605995 1.126179359 1.959715349 1.651651738 1.475303982 1.378857742 1.623209934 1 17.47910739 -1.108722267 6.438286226 0.999999058 1.515639303 0.253097639 0.274771148 3.50E-06 4.84E-07 0.250454951 0.05903269 0.077853427 1.108722267 0.515640245 NTDVAQS(ph)PEAPKQEAPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;NTDVAQS(1)PEAPKQEAPAK 263.54 4.03E-31 1940760000 4573510 1862330 2843050 1760730 4187500 4219960 3544360 2838100 3184400 1364110 TRUE FALSE 4754075.706 2182170.691 2917142.219 2108997.139 3475710.246 3239938.244 3266543.802 2800059.912 3069794.066 1631381.237 2.914141464 1.337621545 1.788142558 1.292767804 2.130532194 1.98600926 2.002317869 1.716373738 1.881714707 1 20.63766253 -0.423753055 0.898172341 0.966750975 1.867668073 0.279511363 0.428693105 25.88042947 14.0080965 3.493474248 0.126603049 0.376918058 0.423753055 0.900917098 NTEDLTEEWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NTEDLTEEWLR 11 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ;; 267.39 8.36E-21 744720000 625221 751328 722341 703486 814946 1002650 727965 740542 696556 685339 FALSE TRUE 649905.2079 880362.7395 741165.7999 842633.4311 676421.77 769799.7328 670905.2011 730616.2458 671487.0856 819618.0554 0.792936665 1.074113404 0.904281933 1.028080611 0.825289006 0.939217636 0.818558348 0.891410628 0.819268294 1 19.64459224 3.228809379 24.99849461 0.876218801 0.955473806 0.120985619 0.087789189 344.0427821 881994.8051 0.022961436 0.027766021 1693.594284 -3.228809379 0.079255005 NTEEEGLKYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTEEEGLKYK 10 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 103.44 0.0025666 381210000 450180 248480 342400 221690 582790 442140 402010 357250 400550 233970 FALSE TRUE 467953.454 291154.5071 351323.2253 265539.6203 483727.564 339459.6857 370499.4057 352461.6481 386134.2837 279811.9419 1.67238557 1.040536387 1.25556909 0.948993165 1.72875954 1.21317083 1.324101478 1.259637619 1.379977856 1 18.09409801 -1.058948321 4.185160245 0.999968011 1.299768608 0.140470617 0.23047999 1.474676514 59194841.25 4430.301318 0.049677027 0.087307525 1.058948321 0.299800597 NTEESSS(ph)PVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 NTEESS(0.006)S(0.994)PVRK;NTEES(0.001)S(0.037)S(0.961)PVRK;NTEESS(0.036)S(0.964)PVRK;NTEES(0.001)S(0.181)S(0.818)PVRK 176.98 5.01E-06 5250280000 2638800 1834200 2237360 1723820 3075830 3035440 2893190 2377020 2479110 1475240 TRUE FALSE 2742981.862 2149209.582 2295667.44 2064786.451 2553001.515 2330505.063 2666414.208 2345159.935 2389887.315 1764285.033 1.554727162 1.218175942 1.301188525 1.170324756 1.447045952 1.320934554 1.511328475 1.329240962 1.354592524 1 20.75065223 -0.929006126 3.780727367 0.999970929 1.351956693 0.466546013 0.114239825 10012369.3 18874523.52 4199.911532 0.025830696 0.117758936 0.929006126 0.351985764 NTEISFILGQEFDEVTADDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NTEISFILGQEFDEVTADDRK 21 1 P15090 P15090 FABP4 "Fatty acid-binding protein, adipocyte" 0 ;; 250.39 1.00E-30 223054000 103734 89019 98521 74512 167317 144205 123625 108252 115553 70827 FALSE TRUE 107829.4984 104307.3208 101088.5382 89250.2512 138876.5161 110715.5742 113934.9495 106801.059 111394.2701 84704.19459 1.273012499 1.231430407 1.193430133 1.053669793 1.639547094 1.307084906 1.345092177 1.260870958 1.315097448 1 16.37014579 NTETS(ph)KSPEKDVPMVEK ddPTM_MDA-MB-175_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(0.023)ET(0.105)S(0.499)KS(0.373)PEKDVPMVEK 73.405 0.020744 102850000 162710 30976 55515 35349 104960 109420 111690 60102 66953 17372 TRUE FALSE 169133.9164 36295.88704 56961.76651 42340.92669 87118.93669 84008.86328 102935.446 59296.431 64543.37461 20775.71079 8.140944881 1.74703467 2.741748144 2.038001352 4.193307154 4.043609584 4.954605259 2.854122855 3.106674677 1 14.34261022 4.748535271 24.81503869 3.135917426 8.140947905 0.644065456 1.148120076 821.5987434 2043935.641 0.274098397 3.708131812 56044.79316 -4.748535271 5.005030479 NTETSKS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTETSKSPEK 10 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NTET(0.017)S(0.012)KS(0.971)PEK 59.248 0.064094 93325000 259500 80923 110270 80586 190180 237450 191830 129390 146820 63916 TRUE FALSE 269745.2604 94820.89576 113143.7268 96525.67027 157853.2715 182305.8361 176793.8633 127655.7387 141535.9769 76439.11645 3.528890349 1.240476083 1.480180986 1.262778467 2.065084983 2.384980944 2.312871623 1.670031583 1.851617123 1 16.22202348 NTETSKS(ph)PEKDVPMVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NTETSKSPEKDVPMVEK 17 2 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NT(0.012)ET(0.09)S(0.09)KS(0.808)PEKDVPMVEK;NTET(0.003)S(0.05)KS(0.947)PEKDVPMVEK;NTET(0.031)S(0.031)KS(0.938)PEKDVPMVEK;NT(0.001)ET(0.028)S(0.028)KS(0.944)PEKDVPMVEK;NT(0.008)ET(0.03)S(0.03)KS(0.932)PEKDVPMVEK 135.21 1.28E-05 3142950000 3851400 717104 1416910 800050 2476980 2770820 2771260 1601480 1675850 421326 TRUE FALSE 4003456.246 840261.0337 1453835.839 958297.5021 2055943.824 2127339.047 2554041.4 1580014.78 1615536.486 503876.7629 7.945308338 1.667592347 2.885300426 1.901848969 4.080251315 4.221943149 5.068781868 3.1357167 3.206213512 1 18.9427114 NTETSKS(ph)PEKDVPMVEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTETSKSPEKDVPMVEKK 18 3 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 NT(0.045)ET(0.275)S(0.275)KS(0.405)PEKDVPMVEKK;NT(0.001)ET(0.031)S(0.163)KS(0.806)PEKDVPMVEKK 139.79 7.29E-07 1050720000 2341990 302633 668190 300145 1509710 1400290 1060240 742930 908900 169476 TRUE FALSE 2434453.574 354607.8636 685603.5803 359512.7852 1253090.033 1075093.869 977135.6184 732972.2385 876188.8665 202681.5774 12.01122275 1.749581132 3.382663531 1.773781267 6.182555167 5.304349231 4.821038157 3.616373269 4.322982275 1 17.62885544 4.747340428 24.84973641 3.775759159 12.01122732 0.714027786 1.597479333 575.4958142 1628802.993 0.377710275 4.513212994 55890.8131 -4.747340428 8.235468165 NTFDHPYPTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTFDHPYPTTK 11 0 P61962 P61962 DCAF7 DDB1- and CUL4-associated factor 7 0 62.088 0.083192 125720000 378420 260840 328870 305270 438250 445870 403280 343530 360960 262580 FALSE TRUE 393360.3138 305637.2409 337440.6224 365651.4949 363756.4215 342323.4497 371669.8598 338925.5423 347969.1201 314027.5236 1.252630054 0.973281697 1.074557473 1.164393142 1.158358406 1.090106516 1.183558229 1.079286103 1.108084782 1 18.26053149 0.50893556 1.228073254 1.000131816 1.119443738 0.207208939 0.07146292 3.122637683 6.121133032 0.065044046 0.019625338 3.228015119 -0.50893556 0.119311922 NTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 NT(0.001)FT(0.024)AWS(0.97)DEES(0.972)DY(0.033)EIDDRDVNK;NTFTAWS(1)DEES(0.999)DY(0.001)EIDDRDVNK;NTFT(0.007)AWS(0.993)DEES(1)DYEIDDRDVNK 123.28 1.39E-05 888600000 1282320 726070 1040580 746980 1462990 1498550 1219660 1062320 1162520 701290 TRUE FALSE 1332946.984 850766.8745 1067698.37 894730.4145 1214311.482 1150534.473 1124059.862 1048081.338 1120681.132 838694.3485 1.58931199 1.014394429 1.273048246 1.066813454 1.447859384 1.371816175 1.340249716 1.249658281 1.336221156 1 19.67778561 -1.278809157 5.135699444 0.999942996 1.288238068 0.238154867 0.159328493 9.69E-05 1.36E-05 0.143690294 0.033861446 0.052624847 1.278809157 0.288295072 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 NTFTAWS(0.995)DEES(0.004)DYEIDDRDVNK;NTFTAWS(1)DEESDYEIDDRDVNK;NTFTAWS(0.999)DEES(0.001)DYEIDDRDVNK 322.45 5.33E-68 1578950000 636170 401531 511252 342886 713600 804940 606530 532747 612190 357223 TRUE FALSE 661286.4828 470490.8258 524575.6471 410707.8274 592302.5269 618004.884 558988.5937 525606.3979 590157.4015 427214.0074 1.547904496 1.101300092 1.227898987 0.961363205 1.386430493 1.446593214 1.308450997 1.230311714 1.381409297 1 18.70459943 -1.015378172 4.464677656 0.99998891 1.276028591 0.219177517 0.161649166 1.74E-05 3.85E-06 0.15299251 0.036059232 0.096521003 1.015378172 0.276039681 NTGKEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTGKEEQR 8 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 88.496 0.013292 93431000 301150 196430 273540 183061 378740 359270 313760 295110 300360 203383 FALSE TRUE 313039.6345 230165.3245 280668.6771 219269.9194 314361.9101 275834.9873 289166.6713 291154.5332 289550.1023 243232.0048 1.287000182 0.946278943 1.15391343 0.901484653 1.292436455 1.134040676 1.188851243 1.197023942 1.190427643 1 17.89197355 3.220044385 24.99990556 1.178100741 1.069015888 0.125711281 0.120505329 411.4501791 555522.9597 0.031794493 0.038064204 1659.756526 -3.220044385 -0.109084853 NTGVSPASRPSPGTPTS(ph)PSNLTSGLK ddPTM_MDA-MB-175_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(0.007)PGT(0.039)PT(0.184)S(0.764)PS(0.007)NLTSGLK 233.58 4.37E-45 286150000 254050 152990 216880 162520 277370 322360 234510 241650 234200 129270 TRUE FALSE 264080.0902 179264.8424 222532.071 194665.9709 230222.7465 247496.7754 216128.4934 238411.077 225771.1877 154597.9815 1.708172951 1.159554871 1.439424169 1.259175373 1.489170455 1.600905607 1.398003333 1.542135769 1.460376038 1 17.23816196 -1.140120152 5.19723485 0.999984838 1.44642585 0.449994596 0.149435304 2.48E-05 4.10E-06 0.136477882 0.032167054 0.072423557 1.140120152 0.446441011 NTHEAEVLLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTHEAEVLLSPK 12 0 A0A0U1RR07;Q9HCH5-7;Q9HCH5-8;A0A0U1RQP0;A0A0U1RRJ3;Q9HCH5-11 A0A0U1RR07 SYTL2 Synaptotagmin-like protein 2 1 NTHEAEVLLS(1)PK 96.096 0.0036565 184190000 556040 319720 410820 326790 618510 800880 598380 509360 514330 291000 TRUE FALSE 577992.8886 374629.4229 421526.3067 391428.0866 513375.8911 614887.7575 551477.412 502532.8623 495819.3638 348015.8785 1.660823325 1.076472213 1.211227225 1.124742033 1.47515077 1.766838226 1.584632904 1.443994063 1.424703281 1 18.40879361 3.163348143 8.516259209 1.493651776 1.250900885 0.106586967 0.234517369 0.434402488 44.1349913 0.065179062 0.078087431 1456.626287 -3.163348143 -0.242750891 NTIQWLENELNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTIQWLENELNR 12 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 223.08 5.42E-11 338439000 227525 221639 241424 233425 280711 358155 263200 245359 242969 207609 FALSE TRUE 236507.8627 259703.7741 247715.7078 279595.7683 232995.8445 274978.9291 242569.6963 242070.3639 234224.5932 248286.0086 0.952562184 1.045986343 0.997703049 1.126103601 0.938417133 1.107508758 0.976976905 0.974965787 0.943366058 1 17.92164344 2.039089278 24.99958348 0.971489395 1.02906415 0.178296612 0.057031031 241.9488644 154737.5811 0.019706837 0.014554444 109.4181274 -2.039089278 0.057574755 NTKDEFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTKDEFEER 9 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 104.43 0.0029739 307590000 539510 470600 534570 414160 726890 709150 624910 542150 584300 377120 FALSE TRUE 560810.2714 551421.8892 548501.3334 496079.6119 603333.4974 544460.6598 575927.9213 534883.366 563271.1571 451009.4436 1.243455718 1.222639342 1.216163744 1.099931762 1.337740276 1.207204566 1.276975304 1.185969326 1.248912113 1 18.78279812 -1.547152775 2.599591155 0.985076055 1.224473404 0.576490854 0.058229912 4650193.761 4418681.768 484199.7003 0.01334942 0.028369209 1.547152775 0.239397349 NTLQLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;; 108.09 0.0073315 1784640000 1138050 2126560 1829350 1988320 2650950 3120130 1902780 2030260 1614310 2423390 FALSE TRUE 1182981.093 2491780.138 1877024.364 2381603.761 2200342.466 2395527.094 1753635.132 2003047.686 1556211.298 2898206.872 0.408176899 0.859766141 0.647650236 0.821750781 0.759208215 0.826554901 0.6050759 0.69113344 0.536956597 1 21.46672915 4.753138507 24.44067183 0.733379416 0.408176587 0.37861497 0.129767632 2022.587308 3390904.889 0.028975469 0.625522661 56641.99055 -4.753138507 -0.325202829 NTNPNFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTNPNFVR 8 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 160.63 0.00081944 159770000 61309 73255 67572 77653 106890 118100 76918 69333 69774 72138 FALSE TRUE 63729.52666 85835.97641 69332.98183 93012.53163 88720.87598 90673.06482 70888.96617 68403.70454 67262.84737 86272.05993 0.738704126 0.994945252 0.80365511 1.078130413 1.02838481 1.051013096 0.821690895 0.792883636 0.779659688 1 16.39660578 -0.92432904 5.109974314 1.000000315 0.901057644 0.058569507 0.121430051 4.55E-07 9.59E-08 0.122749571 0.028932259 0.119033981 0.92432904 -0.098942671 NTPS(ph)QHSHSIQHS(ph)PER ddPTM_MDA-MB-175_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(0.15)PS(0.844)QHS(0.006)HSIQHS(1)PER 124.7 3.83E-05 296980000 17930 114230 97155 106660 83159 95842 97269 80254 101480 124340 TRUE FALSE 18637.89024 133848.1139 99686.93911 127757.0297 69023.66288 73584.148 89644.80161 79178.3264 97827.75462 148702.0424 0.12533715 0.900109452 0.67038043 0.85914778 0.464174276 0.494842887 0.602848489 0.532462938 0.65787768 1 17.18206494 0.938599625 11.9799777 1.000000002 0.594990188 0.269731824 0.204999604 17.25711067 3368.199289 0.185240843 0.046318542 8.681597051 -0.938599625 -0.405009813 NTPSQHSHSIQHS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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(0.022)IQHS(0.978)PER;NTPSQHS(0.002)HS(0.027)IQHS(0.971)PER;NTPSQHSHS(0.249)IQHS(0.751)PER;NTPSQHSHS(0.004)IQHS(0.996)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHS(0.001)HS(0.072)IQHS(0.927)PER;NTPSQHSHS(0.001)IQHS(0.999)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER;NTPSQHSHSIQHS(1)PER 290.96 2.64E-45 23173186000 757209.2 4008228.4 3686570 3531476 4250117 5578173 3008539 4834837 3446030.2 3783498.8 TRUE FALSE 787104.4039 4696610.448 3782645.043 4229991.412 3527683.63 4282726.859 2772721.852 4770033.918 3322008.246 4524802.95 0.1739533 1.037970161 0.83598006 0.934845442 0.779632543 0.946500191 0.612782895 1.054197049 0.73417744 1 22.10942354 4.746599278 24.94100193 0.878231841 0.173952943 0.712513038 0.134868502 478.9443221 1485952.414 0.029036579 0.323065288 55795.51344 -4.746599278 -0.704278898 NTSLPPLWS(ph)PEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER;NTSLPPLWS(1)PEAER 231.37 5.92E-13 1076000000 566303 652649 665481 592518 779754 907925 681047 719350 636943 527315 TRUE FALSE 588661.0797 764736.3888 682823.9816 709716.2919 647211.6936 697073.1785 627664.7566 709708.2899 614019.5459 630632.2782 0.933445845 1.212650248 1.082760913 1.125404323 1.026290147 1.105356009 0.995294371 1.125391634 0.973657022 1 19.26643949 1.210887211 0.703178222 0.99362258 1.087307351 0.111914372 0.077014282 1.338553376 1.553227896 0.068582188 0.028504354 16.25126645 -1.210887211 0.093684771 NTVDLVT(ph)T(ph)CHIHSSSDDEIDFK ddPTM_MDA-MB-175_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 2 NT(0.309)VDLVT(0.359)T(0.366)CHIHS(0.341)S(0.32)S(0.305)DDEIDFK 60.481 0.056313 22526000 31060 28288 36656 34520 44869 53580 48392 43580 39055 17685 TRUE FALSE 32286.27278 33146.24395 37611.28547 41347.95297 37242.18341 41136.85701 44598.90859 42995.88138 37649.41818 21150.03715 1.526535039 1.567195543 1.778308246 1.954982522 1.760856643 1.945001643 2.108691738 2.032898622 1.780111208 1 14.36837258 4.172575777 3.003092192 1.873239603 1.532765273 0.062865633 0.296201486 0.425819256 7.636638964 0.070523744 0.19697281 14879.06966 -4.172575777 -0.34047433 NTVDLVTTCHIHSS(ph)SDDEIDFK ddPTM_MDA-MB-175_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 NTVDLVTTCHIHS(0.003)S(0.596)S(0.401)DDEIDFK 137.03 2.33E-06 63056000 35686 52372 65228 57833 82088 90556 89892 82425 64879 41704 TRUE FALSE 37094.91084 61366.4836 66927.89527 69272.19479 68134.71108 69525.74139 82846.03015 81320.2277 62544.01746 49875.10033 0.743756115 1.230403211 1.341909988 1.388913392 1.366106747 1.393997023 1.661069945 1.630477476 1.254012865 1 15.60603212 5.040416226 1.145114847 1.441926098 6.25E-15 0.513079442 0.180459637 2.125219728 1.474599158 0.051564019 4.32190411 109752.9559 -5.040416226 -1.441926098 NTVDLVTTCHIHSSS(ph)DDEIDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NTVDLVTTCHIHSSSDDEIDFK 22 0 Q5H9R7-2;Q5H9R7;Q5H9R7-5;E9PQP7;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 NTVDLVTTCHIHS(0.019)S(0.07)S(0.911)DDEIDFK;NTVDLVTTCHIHS(0.014)S(0.119)S(0.867)DDEIDFK;NTVDLVTTCHIHS(0.001)S(0.023)S(0.976)DDEIDFK;NTVDLVTTCHIHS(0.009)S(0.216)S(0.775)DDEIDFK 308.77 2.51E-67 1470120000 531339 841840 1077640 970670 1319880 1398940 1496520 1340830 1134230 604950 TRUE FALSE 552316.674 986419.4714 1105724.184 1162665.629 1095527.269 1074057.386 1379218.852 1322858.367 1093409.284 723478.37 0.763418365 1.363440169 1.528344494 1.607049605 1.514250203 1.484574288 1.906371924 1.828469823 1.5113227 1 19.46459036 4.966541277 1.322905089 1.616940644 1.33E-13 0.487795371 0.234410821 1.680231606 1.758523193 0.063152109 4.206468867 92585.13784 -4.966541277 -1.616940644 NTVELLTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NTVELLTDR 9 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 68.371 0.05826 9154800000 99024 5465200 2292540 4830100 1124330 3984300 1132750 2549170 1174080 5998000 FALSE TRUE 102933.544 6403805.587 2352285.476 5785479.364 933216.7882 3059006.708 1043962.095 2515002.546 1131825.09 7173193.261 0.014349752 0.892741259 0.327927241 0.806541683 0.130097818 0.426449783 0.145536591 0.35061129 0.157785389 1 22.77418407 -1.550589447 3.532276815 1.016204 0.373186481 0.328091939 0.273716444 448579922.4 609294210.7 69274872.66 0.061592867 0.028145603 1.550589447 -0.643017519 NTVGNVPLEWYDDFPHVGYDLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NTVGNVPLEWYDDFPHVGYDLDGR 24 0 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 84.404 0.012924 26172000 15001 12611 16216 18453 19849 25040 24154 21215 18352 9680.8 FALSE TRUE 15593.25106 14776.84115 16638.60228 22102.94832 16475.07407 19224.83948 22260.74637 20930.64763 17691.5151 11577.56741 1.34685038 1.276333847 1.437141473 1.909118517 1.423016899 1.660524945 1.922748154 1.807862298 1.528085692 1 13.49904454 3.969314236 9.520259656 1.663981882 1.32251616 0.155706972 0.258437373 0.564132865 171.9927715 0.062658176 0.115894394 9317.818269 -3.969314236 -0.341465721 NVADHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVADHKK 7 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 0 51.995 0.096317 17113000 59395 43070 63121 48889 74893 71079 72545 63125 68570 50018 FALSE TRUE 61739.96046 50466.93746 64765.98511 58559.09828 62162.71461 54571.97946 66858.73334 62278.91263 66102.17909 59818.06945 1.032128938 0.843673792 1.082716071 0.97895333 1.039196269 0.912299243 1.117701289 1.041138793 1.105053702 1 15.86829373 2.230119138 24.99955863 1.068098491 0.982338288 0.25828269 0.070087648 246.4228983 729778.0968 0.02444208 0.01834073 169.8709587 -2.230119138 -0.085760203 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_MDA-MB-175_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 162.02 1.16E-11 1360170000 1334980 842460 1042370 815910 1399560 1551710 1242830 1118760 1142390 712860 TRUE FALSE 1387686.041 987145.9516 1069535.019 977294.5628 1161663.291 1191348.869 1145413.737 1103764.852 1101275.607 852531.2685 1.62772451 1.157899995 1.254540517 1.146344538 1.362604909 1.397425424 1.343544547 1.294691342 1.291771514 1 19.70139322 0.38289344 1.662816513 0.999987137 1.313833573 0.358549559 0.12843281 6.059893139 15.07070976 0.11754078 0.033281509 2.414868243 -0.38289344 0.313846437 NVALLSQLYHS(ph)PAR ddPTM_MDA-MB-175_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 202.97 1.01E-08 385120000 392670 411230 408720 417490 492420 676030 492670 471250 425950 366990 TRUE FALSE 408172.9148 481855.5536 419371.579 500068.2759 408718.6243 519032.2778 454053.238 464933.6646 410620.1427 438894.6641 0.930001999 1.097884283 0.955517607 1.139381079 0.931245371 1.182589629 1.034538069 1.059328588 0.935577888 1 18.7435152 4.758979976 23.5529538 1.041677932 0.930001759 0.134676913 0.080954872 3918.13612 4519259.453 0.017399189 0.644144146 57408.99926 -4.758979976 -0.111676173 NVALLSQLYHS(ph)PARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 NVALLSQLYHS(1)PARR;NVALLSQLYHS(1)PARR;NVALLSQLYHS(1)PARR 162.81 9.64E-07 761810000 634700 591770 589330 514740 827780 919620 574390 690980 659050 631750 TRUE FALSE 659758.4461 693401.8942 604688.4239 616554.0357 687074.2513 706052.192 529367.8109 681718.5433 635330.9192 755529.3169 0.873240034 0.917769673 0.800350708 0.81605574 0.909394561 0.934513296 0.7006582 0.902305878 0.840908361 1 19.52712821 -0.696869664 5.412204777 1.000000013 0.854734037 0.299154785 0.066569976 9.21E-09 2.38E-09 0.061780593 0.014561824 0.200969585 0.696869664 -0.145265976 NVALLSQLYHSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 ; 287.54 4.96E-34 677320000 794950 1045080 1032260 1047870 1422880 1675950 1131710 1272190 1099800 768860 FALSE TRUE 826335.2398 1224564.36 1059161.544 1255135.558 1181019.366 1286736.012 1043003.613 1255138.374 1060218.413 919503.3963 0.898675571 1.331767088 1.151884319 1.365014598 1.284410009 1.399381467 1.134311866 1.36501766 1.15303371 1 19.81049538 4.745561248 24.6089365 1.260857781 0.89867536 0.402136096 0.12410942 570.861048 2006652.582 0.026407801 0.261951037 55662.31282 -4.745561248 -0.362182421 NVATETQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVATETQLK 9 0 Q5T3J3 Q5T3J3 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1 0 66.273 0.064195 933670000 33358 1167800 917310 921640 527740 1013000 577340 734760 911340 2304700 FALSE TRUE 34674.9996 1368360.566 941215.8522 1103937.641 438034.9433 777746.1022 532086.5822 724911.744 878541.0514 2756261.839 0.012580445 0.496455216 0.341482743 0.400519873 0.15892356 0.282174245 0.193046457 0.263005399 0.318743684 1 21.39428152 0.682303569 3.749842518 0.999997758 0.275718381 0.750132638 0.12592357 3.110351442 36.25851171 0.114432938 0.029354465 4.811755693 -0.682303569 -0.724279377 NVDAAVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVDAAVSPR 9 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 NVDAAVS(1)PR 102.87 0.0036861 292160000 440540 490810 494760 449510 552610 676500 533220 569590 487550 414170 TRUE FALSE 457932.8594 575102.7995 507653.852 538421.7363 458677.5496 519393.1275 491424.8231 561955.5777 470003.1707 495318.6817 0.924521679 1.161076335 1.024903503 1.087020854 0.926025136 1.048603953 0.99213868 1.134533379 0.948890458 1 18.91799751 NVDHEVNLLVEEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVDHEVNLLVEEIHR 15 0 Q9P1F3;Q5SZC9 Q9P1F3 ABRACL Costars family protein ABRACL 0 140.84 2.82E-06 20636000 12056 16113 12533 13527 10224 20581 11435 13268 13405 9595.7 FALSE TRUE 12531.98019 18880.28241 12859.62028 16202.60023 8486.128132 15801.37466 10538.69482 13090.16416 12922.55667 11475.79369 1.09203603 1.645226719 1.120586568 1.411893648 0.739480715 1.376930875 0.918341258 1.140676149 1.126070842 1 13.48630632 3.30036819 24.99999997 1.068654805 1.326789193 0.274978104 0.211058407 87.11357428 35234.79244 0.053164196 0.071984639 1996.954592 -3.30036819 0.258134388 NVDILKDPETVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVDILKDPETVK 12 1 O14980 O14980 XPO1 Exportin-1 0 92.856 0.0028558 0 297980 127280 229410 122860 327500 279790 270760 203800 238390 114380 FALSE TRUE 309744.4805 149139.3499 235388.6131 147161.3413 271831.667 214813.0128 249537.1237 201068.3943 229810.3905 136790.5711 2.26437011 1.090275073 1.720795602 1.075814949 1.987210557 1.570378799 1.824227516 1.469899517 1.68001631 1 17.06160926 -1.607023791 4.767090743 0.991855242 1.608459177 0.226267543 0.347971431 0.026951447 0.002221748 0.301463479 0.070680938 0.024715887 1.607023791 0.616603935 NVDLLSDMVQEHDEPILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 318.1 2.01E-61 2315738000 3468609 2867100 3619751 2786997 4527214 4699675 4222213 3837395 3887875 2586655 FALSE TRUE 3605552.362 3359502.122 3714084.685 3338256.688 3757679.781 3608246.706 3891264.912 3785960.997 3747951.138 3093460.523 1.165540124 1.086001291 1.200624562 1.079133438 1.214717225 1.166411105 1.257900298 1.223859483 1.211572319 1 21.56079019 3.214557493 24.99909875 1.19710417 1.134323117 0.054138717 0.074481525 424.4762337 442087.9731 0.019915167 0.023815572 1638.91901 -3.214557493 -0.062781054 NVEDIELWLYEVEGHLASDDYGKDLTNVQNLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVEDIELWLYEVEGHLASDDYGKDLTNVQNLQK 33 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 291.83 9.74E-90 336260000 400700 268820 391740 247840 495570 449270 394340 380900 414910 248850 FALSE TRUE 416519.9454 314987.7439 401949.0662 296862.0123 411333.1884 344933.8513 363430.6004 375794.6585 399977.4701 297607.393 1.399561823 1.058400266 1.350601752 0.997495423 1.382133637 1.159023127 1.221174638 1.2627195 1.343976929 1 18.18305084 -1.096005522 4.760842894 0.999988322 1.235041005 0.236641432 0.129727257 1.42E-05 2.69E-06 0.110556181 0.026057048 0.080166787 1.096005522 0.235052683 NVFEVGPGDS(ph)PTFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 NVFEVGPGDS(0.999)PT(0.001)FPR;NVFEVGPGDS(0.999)PT(0.001)FPR;NVFEVGPGDS(1)PTFPR;NVFEVGPGDS(1)PTFPR;NVFEVGPGDS(0.998)PT(0.002)FPR 287.48 1.96E-34 783164000 974194 1074332 1061687 1053852 1158116 1391439 1040249 1071349 944208 873331 TRUE FALSE 1012655.931 1258840.164 1089355.435 1262300.78 961259.856 1068298.38 958711.5652 1056989.319 910226.1385 1044443.489 0.969565077 1.2052736 1.04300084 1.20858696 0.920356024 1.02283981 0.917916168 1.012011976 0.871493909 1 19.994303 3.22412202 24.99945557 0.9619817 1.109111006 0.460063317 0.079057582 194.0240989 335939.0201 0.02074715 0.024902204 1675.413535 -3.22412202 0.147129306 NVFIIGATNRPDIIDPAILRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVFIIGATNRPDIIDPAILRPGR 23 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ; 180.45 2.56E-17 4815900000 1641860 1773560 1818930 1836580 2461800 2920000 2173680 2185020 1914150 1309090 FALSE TRUE 1706681.901 2078155.134 1866332.81 2199850.042 2043344.115 2241874.253 2003301.282 2155733.381 1845260.115 1565581.121 1.090126776 1.327401758 1.192102271 1.40513322 1.305166553 1.431975783 1.279589575 1.376954124 1.178642288 1 20.57826683 0.972191585 4.738934444 1.000229291 1.307798314 0.486989915 0.095814976 0.141835363 10.95680524 0.087520598 0.02218269 9.379756943 -0.972191585 0.307569023 NVGSAGVTVVIVRDDLLGFALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVGSAGVTVVIVRDDLLGFALR 22 1 Q9Y617;Q9Y617-2 Q9Y617 PSAT1 Phosphoserine aminotransferase 0 ; 100.94 0.0007102 26542000 18374.7 18940.7 24967 17255 27428 35266 19338.5 22309.6 22734.2 22741.6 FALSE TRUE 19100.14734 22193.61789 25617.66053 20667.9875 22765.79836 27076.00596 17822.69784 22010.5763 21916.00058 27197.38111 0.702278917 0.816020403 0.941916445 0.759925649 0.837058475 0.995537249 0.655309339 0.809290285 0.805812902 1 14.73118012 4.715349518 4.643783806 0.83610205 0.696396105 0.148270937 0.101841989 0.336687924 18.51308769 0.023510211 0.144002447 51921.7735 -4.715349518 -0.139705944 NVHMNDNVLHSAFEVGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVHMNDNVLHSAFEVGAR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 205.65 5.43E-16 309320000 72686 85413 96413 82740 106760 124120 81305 88004 84894 68511 FALSE TRUE 75555.69941 100082.0183 98925.60198 99105.72505 88612.97333 95295.01106 74932.10165 86824.45033 81838.68152 81934.41873 0.922148477 1.221489331 1.207375405 1.209573786 1.081510978 1.163064467 0.914537539 1.059682264 0.998831539 1 16.322182 2.256481667 24.998612 1.001830594 1.142519883 0.373918404 0.088671093 251.767784 351197.7827 0.03011646 0.025148745 180.501854 -2.256481667 0.140689288 NVHSEDFENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVHSEDFENR 10 0 A0A669KBJ7;Q9H2P0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 148.28 2.54E-05 491730000 68564 152490 104200 95001 103610 135430 113300 74632 104880 129340 FALSE TRUE 71270.95966 178678.9713 106915.5376 113791.9143 85998.40921 103978.435 104419.2499 73631.68011 101105.3893 154681.6966 0.460758844 1.155139717 0.691197084 0.735652095 0.55597017 0.672209041 0.675058861 0.476020639 0.65363512 1 17.23894297 3.743270489 2.612271065 0.638659085 0.818412249 0.015049793 0.205707229 0.58376525 7.875222255 0.052833644 0.100927168 5536.948566 -3.743270489 0.179753164 NVIGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVIGAR 6 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4 P62258 YWHAE 14-3-3 protein epsilon 0 ; 114.6 0.058509 334590000 354610 370130 379600 406940 455280 548550 447020 423040 367870 266990 FALSE TRUE 368610.2766 433696.9483 389492.6878 487431.5174 377891.6682 421157.5759 411981.4043 417369.8408 354630.4306 319301.5787 1.154426728 1.358267473 1.219827003 1.526555301 1.183494519 1.318996222 1.290257963 1.307133659 1.11064415 1 18.28456016 1.090402509 3.166868696 1.002055232 1.300350369 0.500347379 0.09849125 0.164601849 3.193552865 0.085481613 0.022620501 12.31409525 -1.090402509 0.298295137 NVIIWGNHSSTQYPDVNHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVIIWGNHSSTQYPDVNHAK 20 0 A0A5K1VW95;P40925;P40925-3;B9A041;P40925-2;B8ZZ51;C9JF79 A0A5K1VW95 MDH1 "Malate dehydrogenase, cytoplasmic;Malate dehydrogenase" 0 47.088 0.096141 763820000 536800 134520 199890 106770 324750 348690 239570 152270 226200 112330 FALSE TRUE 557993.2785 157622.7636 205099.2976 127888.7873 269549.111 267712.0319 220791.8774 150229.0697 218059.1062 134338.9128 4.153623599 1.173321715 1.526730367 0.951986172 2.006485726 1.992810768 1.643543727 1.118284096 1.623201362 1 17.03551773 4.742361111 24.99923908 1.466121466 4.153624627 0.833237463 0.362980518 146.089465 960921.7695 0.087902732 0.665410309 55253.6676 -4.742361111 2.687503161 NVITEPIYPEVVHMFAVNMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVITEPIYPEVVHMFAVNMFR 21 0 H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2;G3V2U3 H0YJ75 PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 ; 213.13 5.73E-23 183664000 182949 192420 187396 196272 273100 311710 238981 211986 212135 167443 FALSE TRUE 190171.9678 225466.6382 192279.6937 235094.0158 226678.5595 239320.0765 220249.0448 209144.6744 204500.3028 200250.25 0.949671563 1.125924378 0.960197022 1.17400111 1.131976412 1.195105008 1.099869013 1.044416546 1.021223708 1 17.61144452 4.748886395 23.957384 1.087654824 0.949671423 0.232656865 0.07265733 1203.812999 2792928.866 0.017430756 0.234000149 56090.12335 -4.748886395 -0.137983402 NVKDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVKDLR 6 1 A0A0A0MSQ3 A0A0A0MSQ3 UHRF2 0 ; 68.485 0.087566 1912580000 4040000 3731700 3864400 2913500 5262600 4744800 3345300 3679100 3902300 4106000 FALSE TRUE 4199502.32 4372590.446 3965109.439 3489781.604 4368065.132 3642892.108 3083086.645 3629787.682 3761856.985 4910492.086 0.855210078 0.89045871 0.807477004 0.710678592 0.889537149 0.74185887 0.627856962 0.739190211 0.766085541 1 22.22743618 2.703147638 23.52413819 0.745263058 0.826038836 0.030654909 0.100917091 605.724888 402369.779 0.031407653 0.029613028 504.8328864 -2.703147638 0.080775778 NVKLPDAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NVKLPDAYER 10 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;; 107.97 0.002019 1753380000 2617500 2422960 2642170 1688560 4689830 4045490 2272900 2945370 3319840 3018390 FALSE TRUE 2720840.921 2839084.532 2711027.121 2022552.128 3892654.372 3105986.257 2094744.159 2905892.133 3200359.607 3609785.73 0.753740284 0.786496691 0.751021618 0.560297004 1.078361616 0.860435076 0.580295983 0.80500405 0.886578829 1 21.78348177 1.048186544 2.756851903 0.996760258 0.769406324 0.225162842 0.136003302 0.366924677 5.969475278 0.129065384 0.03459691 11.17343082 -1.048186544 -0.227353933 NVLFSHLDDNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 161.21 5.89E-05 1350920000 561443 814790 841510 840170 1003420 1102100 882500 929380 804620 800090 FALSE TRUE 583609.2032 954723.8443 863440.4419 1006353.118 832859.0268 846153.9775 813327.344 916923.1813 775661.8834 956852.3169 0.609926101 0.997775547 0.90237587 1.051732959 0.870415436 0.884309901 0.850003004 0.958270326 0.810639082 1 19.86793675 4.747178733 24.86978246 0.922237673 0.609925931 0.631954427 0.072118641 649.8160626 1875166.333 0.016353183 0.19323594 55870.00789 -4.747178733 -0.312311741 NVLS(ph)DSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 1 NVLS(0.705)DS(0.19)RPAMAPGS(0.052)S(0.052)HLGAPASTTTAADATPSGSLAR;NVLS(0.912)DS(0.079)RPAMAPGS(0.004)S(0.004)HLGAPASTTTAADATPSGSLAR 91.707 0.00032542 610930000 37980 58011 65443 64787 71189 78939 77431 76470 61348 58891 TRUE FALSE 39479.47973 67973.93799 67148.49834 77601.67523 59088.31921 60606.61358 71361.75589 75445.04473 59140.09746 70429.56391 0.560552665 0.965133592 0.953413519 1.101833817 0.838970397 0.860528026 1.013235805 1.07121272 0.839705575 1 16.10389353 4.738598586 8.560342698 0.967337409 0.558199032 0.652505033 0.087420239 0.053026257 62.74366026 0.021297977 0.125205751 54777.04316 -4.738598586 -0.409138377 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVLSDSRPAMAPGSSHLGAPASTTTAADATPSGSLAR 37 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ; 238.21 1.25E-49 346050000 69148 155101 162933 152814 176408 228700 163527 199747 153792 132212 FALSE TRUE 71878.01643 181738.3902 167179.1678 183040.1531 146422.2312 175587.891 150709.3264 197069.7182 148257.056 158116.41 0.454589226 1.149396133 1.057316997 1.157629072 0.926040701 1.110497582 0.953154239 1.246358415 0.937644966 1 17.27062758 4.743008718 24.99999999 1.070918418 0.454588981 0.759797123 0.101910452 198.2391634 1114139.144 0.0226477 0.179862498 55336.12176 -4.743008718 -0.616329437 NVMEEGKDFQPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NVMEEGKDFQPSR 13 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 0 ;;;; 227.63 8.02E-12 2577460000 2392110 1737569 2247020 1732066 2961390 2946320 2556190 2249690 2445100 1518209 FALSE TRUE 2486552.35 2035982.959 2305579.187 2074663.485 2458013.986 2262081.832 2355829.148 2219536.585 2357101.329 1815672.986 1.369493499 1.121337915 1.269820725 1.1426416 1.35377571 1.245864123 1.297496392 1.222431904 1.298197058 1 20.79207296 -1.418412437 5.637125114 0.999866891 1.252748367 0.504512586 0.076520633 0.000115425 1.19E-05 0.06680695 0.015738308 0.038158172 1.418412437 0.252881475 NVMNDAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVMNDAWR 8 0 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 107.69 0.0091985 347590000 463390 318750 370150 353320 527640 534960 464170 391790 361130 329660 FALSE TRUE 481684.995 373492.833 379796.4131 423205.6414 437951.9413 410723.6474 427787.1425 386538.6959 348133.0018 394250.5653 1.221773759 0.947348884 0.96333765 1.073443335 1.110846705 1.041783281 1.08506412 0.980439167 0.883024737 1 18.5887533 1.566019591 4.542058684 0.938497986 1.056075761 0.299439827 0.076985173 0.199427292 9.068229238 0.04441167 0.01957463 36.81455806 -1.566019591 0.117577775 NVMSAFGLTDDQVSGPPS(ph)APAEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NVMSAFGLTDDQVSGPPSAPAEDR 24 0 Q92734-2;Q92734;Q92734-4;Q92734-3 Q92734-2 TFG Protein TFG 1 NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVSGPPS(1)APAEDR;NVMSAFGLTDDQVS(0.191)GPPS(0.809)APAEDR 243.24 7.34E-38 182878000 130991 137166 159450 166097 166973 224999 177270 177400 155387 115588 TRUE FALSE 136162.6258 160723.1935 163605.398 198950.4908 138590.9891 172746.3921 163375.1142 175022.2432 149794.6522 138235.2555 0.985006504 1.162678746 1.183528741 1.439216718 1.002573392 1.2496551 1.181862858 1.266118708 1.083621191 1 17.07676608 -1.33210654 8.129270364 0.999999314 1.184403601 0.138472616 0.126223038 1.48E-06 1.21E-07 0.115136335 0.027137794 0.046547189 1.33210654 0.184404287 NVMVEPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVMVEPHR 8 0 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R2U2;M0R1H0;M0R2B0;M0QXC9 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 85.731 0.020558 0 112000 116500 131170 149480 147360 187870 150090 149590 123750 104560 FALSE TRUE 116421.8465 136507.9688 134588.398 179046.6978 122311.7998 144240.0397 138325.5536 147584.9907 119296.2617 125046.5301 0.931028205 1.091657391 1.076306539 1.431840594 0.978130299 1.153490941 1.106192659 1.180240592 0.95401497 1 16.9321055 -3.150023557 9.782422026 1.008594099 1.106578682 0 0.140183096 0 0 0 0.029360168 0.000707907 3.150023557 0.097984583 NVNHSWIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVNHSWIER 9 0 Q4G0J3;Q4G0J3-3;D6RFF0 Q4G0J3 LARP7 La-related protein 7 0 76.943 0.034002 103960000 66963 58350 65793 60534 92157 85724 72934 62832 66585 56697 FALSE TRUE 69606.75095 68371.1586 67507.61963 72507.44452 76492.18606 65815.90016 67217.2425 61989.83981 64188.61886 67805.69162 1.026562067 1.008339521 0.995604027 1.069341567 1.128108633 0.970654507 0.991321538 0.914227675 0.946655322 1 16.04911876 2.506522407 23.78531708 0.956238698 1.042795806 0.493440811 0.040820845 328.8488187 266035.9867 0.014174787 0.013338884 321.0128422 -2.506522407 0.086557108 NVNVQNFHISWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVNVQNFHISWK 12 0 O43707 O43707 ACTN4 Alpha-actinin-4 0 ; 100.02 0.0034676 1328840000 1049880 1112740 1166850 1439200 2265900 2810500 1802170 1593210 1305890 1788260 FALSE TRUE 1091330.073 1303844.439 1197259.07 1723869.464 1880743.127 2157803.969 1660911.206 1571855.626 1258891.274 2138635.309 0.510292741 0.609661888 0.559823858 0.806060508 0.879412736 1.008963033 0.776621989 0.734980676 0.588642331 1 21.02825906 3.728520767 6.520077409 0.818752761 0.564138654 0.518267475 0.118130347 0.130141471 29.1117472 0.032735215 0.053935911 5352.057457 -3.728520767 -0.254614107 NVPESSPHS(ph)PCEGLPSEAALTPRPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVPESSPHSPCEGLPSEAALTPRPEGK 27 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 NVPES(0.006)S(0.035)PHS(0.959)PCEGLPSEAALTPRPEGK;NVPESS(0.003)PHS(0.997)PCEGLPSEAALTPRPEGK 240.46 2.20E-45 642100000 220540 225130 273580 236810 307470 370550 311200 297300 296700 197197 TRUE FALSE 229247.0895 263794.3262 280709.7195 283650.3112 255206.3592 284495.3782 286807.3308 293315.1798 286021.825 235833.9766 0.972069813 1.118559463 1.190285317 1.202754223 1.082144155 1.206337536 1.216140842 1.243735886 1.212810084 1 17.84741206 4.696845517 2.242588339 1.183016992 0.92916806 0.399867731 0.071057285 0.490409192 3.076844926 0.017227865 0.237892944 49756.00657 -4.696845517 -0.253848932 NVPHEDICEDSDIDGDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVPHEDICEDSDIDGDYR 18 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 168.27 2.11E-11 494070000 164350 207870 197970 181090 249300 270570 231570 231190 223950 196530 FALSE TRUE 170838.6649 243570.0555 203129.2608 216909.0615 206924.075 207734.218 213418.9383 228091.2762 215890.0832 235036.2907 0.726860794 1.036308286 0.864246369 0.922874765 0.880392021 0.883838906 0.90802547 0.97045131 0.918539357 1 17.84252401 7.999981846 0.019368739 1.633340785 3.88E-07 0.228044647 0.070907581 5199.260482 7.761420908 244.8871916 434.7333891 99995820 -7.999981846 -1.633340397 NVPLPEFPEHPFQEEHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVPLPEFPEHPFQEEHLK 18 0 A0A3B3ISG5;P14735 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 209.73 2.84E-16 411570000 472890 336130 440010 349390 587310 647690 536910 487370 484150 278820 FALSE TRUE 491560.0624 393857.7128 451477.0221 418498.2992 487479.256 497273.8133 494825.5912 480837.6023 466725.5361 333449.4407 1.474166702 1.181161714 1.353959452 1.255057733 1.461928546 1.491301987 1.483959878 1.442010523 1.399689066 1 18.3471085 3.235804412 24.99946771 1.41631537 1.30915414 0.006597727 0.153323078 163.0508061 1478914.538 0.040157349 0.050064301 1721.093291 -3.235804412 -0.10716123 NVPNLHVMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 87.476 0.014031 0 392110 279840 317210 234490 842720 613730 523730 345620 354500 518400 FALSE TRUE 407590.8056 327900.3431 325476.7532 280871.4221 699474.7554 471200.5087 482678.6741 340987.5292 341741.6142 619970.5546 0.657435748 0.52889664 0.524987438 0.453039939 1.128238672 0.760036917 0.778550966 0.550006007 0.551222331 1 19.24184017 NVPNWHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ;;;;;; 140.12 0.002646 10829910000 3330540 3376170 3728760 3655520 4450520 5371020 4328570 4026310 3791730 2785280 FALSE TRUE 3462032.291 3956000.935 3825934.549 4378570.945 3694022.2 4123682.004 3989285.373 3972343.9 3655266.378 3331002.289 1.039336509 1.187630807 1.148583585 1.314490524 1.108982186 1.23797033 1.197623126 1.192537127 1.097347303 1 21.66752491 0.993425099 3.140106931 1.000550077 1.183227687 0.394439146 0.069355041 0.213536994 5.165316672 0.062220608 0.016306586 9.849747543 -0.993425099 0.18267761 NVPQEESLEDS(ph)DVDADFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 1 NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK 367.18 1.73E-107 1024750000 964940 490853 649330 476847 841340 994350 951460 679700 737400 365112 TRUE FALSE 1003036.576 575153.1844 666252.0732 571165.9134 698329.3273 763427.282 876882.079 670589.7333 710861.118 436648.7059 2.297124812 1.317198876 1.525830866 1.308067345 1.599293248 1.748378666 2.008209499 1.535764848 1.627993186 1 18.73611354 0.389252479 1.859196095 1.000038195 1.650036476 0.326452091 0.285497736 8.561793856 24.56353702 0.265351056 0.073765841 2.450487429 -0.389252479 0.649998281 NVQRPESVSDHMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVQRPESVSDHMYR 14 1 Q7Z4H3-2;Q7Z4H3;V9GYS5;V9GZ04;Q7Z4H3-3 Q7Z4H3-2 HDDC2 HD domain-containing protein 2 0 83.633 0.0050787 83443000 78049 63056 69468 64249 92060 101330 89627 91071 92756 65076 FALSE TRUE 81130.43479 73885.37749 71278.39315 76957.26044 76411.67408 77797.64317 82601.80154 89850.34221 89417.72968 77826.39624 1.042453958 0.949361413 0.915863982 0.988832378 0.981822078 0.999630549 1.061359713 1.154497016 1.148938329 1 16.24797193 2.16375308 2.549022288 1.117061043 0.973223902 0.54188313 0.050570894 0.180619948 2.361604862 0.022330902 0.014711567 145.7985081 -2.16375308 -0.143837141 NVRS(ph)DIS(ph)DQEEDEESEGCPVSINLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVRSDISDQEEDEESEGCPVSINLSK 26 1 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;H0YBA1 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 NVRS(1)DIS(1)DQEEDEESEGCPVSINLSK 118.74 2.49E-10 0 133720 108630 115130 98566 140750 169270 137120 136150 122370 76485 TRUE FALSE 138999.3689 127286.3575 118130.3824 118062.0606 116825.3653 129959.6078 126372.1761 134325.1319 117965.9276 91470.77136 1.519604206 1.391552248 1.291454971 1.290708047 1.277187932 1.420777434 1.381558002 1.468503326 1.289657077 1 16.4810232 0.974136819 20.06766834 0.999999997 1.377322798 0.701355141 0.074544616 99.17970519 76956.06558 0.076422385 0.019105596 9.421863737 -0.974136819 0.377322801 NVS(ph)ES(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNR;NVS(1)ES(1)PNR 118.61 0.0027106 445690000 963830 910350 935780 967790 1028870 1249500 1161360 1025490 981670 742110 TRUE FALSE 1001882.753 1066695.531 960167.1956 1159215.973 853983.0449 959322.5614 1070329.569 1011744.984 946339.8885 887512.2459 1.128866398 1.201893873 1.081863602 1.306140821 0.96222114 1.080911915 1.205988507 1.139978618 1.066283753 1 19.7594075 -4.999999999 0.177796504 0.447293532 1.163740734 0.189456166 0.087436822 227.0982601 2.178530994 44.15014251 0.273681461 1.00E-05 4.999999999 0.716447202 NVS(ph)ES(ph)PNRK ddPTM_MDA-MB-175_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 89.613 0.0080124 383509000 2134380 1172710 1531470 1357800 2010410 2293090 2404560 1717920 1711700 839030 TRUE FALSE 2218646.971 1374113.82 1571381.366 1626368.787 1668681.226 1760554.6 2216084.304 1694894.092 1650096.251 1003421.864 2.211080952 1.369427824 1.566022649 1.620822553 1.662990698 1.754550765 2.208527024 1.689114173 1.644469101 1 19.93649685 2.748096469 14.15107211 1.745865196 1.658180619 0 0.343938504 13.15032309 19496.845 0.101377772 0.104726882 559.881953 -2.748096469 -0.087684576 NVS(ph)ES(ph)PNRKNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 NVS(1)ES(1)PNRKNEK;NVS(1)ES(1)PNRKNEK;NVS(1)ES(1)PNRKNEK 124.68 0.001568 1336280000 4489200 1940390 3043510 1556390 4752900 4227000 3342670 3042190 3458490 1794090 TRUE FALSE 4666437.082 2273636.888 3122826.371 1864239.297 3945003.756 3245343.311 3080662.791 3001414.419 3334019.62 2145607.586 2.174879094 1.059670419 1.455450844 0.868863118 1.838641783 1.512552124 1.435799729 1.398864564 1.553881354 1 21.03295481 -1.37965157 3.521597846 0.997051111 1.452273566 0.14431729 0.343952872 10800573.45 6351239.011 232105.9695 0.073994025 0.041720397 1.37965157 0.455222456 NVSES(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVSESPNR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.01)ES(0.99)PNR;NVS(0.015)ES(0.985)PNR 113.99 0.0028764 400640000 498660 544630 535230 524410 619250 733380 616810 544230 508080 475030 TRUE FALSE 518347.4818 638165.9659 549178.5335 628136.7328 513990.1062 563063.6095 568462.8205 536935.487 489794.3 568103.0335 0.912418085 1.123327862 0.966688261 1.105673964 0.90474804 0.991129384 1.000633313 0.945137511 0.862157516 1 19.11579308 2.656006115 0.896218511 0.940791801 1.023682056 0.126004697 0.074074986 1.054390526 1.778824129 0.044009386 0.037603615 452.9039573 -2.656006115 0.082890256 NVSES(ph)PNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 NVSESPNRK 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.035)ES(0.965)PNRK;NVSES(1)PNRK;NVS(0.001)ES(0.999)PNRK;NVS(0.003)ES(0.997)PNRK;NVS(0.267)ES(0.733)PNRK 133.88 0.00016209 2073369000 1891900 1336609 1580106 1256461 1953900 2111920 2041048 1645303 1618729 987341 TRUE FALSE 1966593.673 1566161.198 1621284.86 1504985.236 1621776.776 1621458.586 1881065.324 1623250.404 1560471.259 1180791.565 1.665487569 1.326365503 1.373049155 1.274556221 1.373465753 1.373196281 1.593054507 1.374713753 1.321546753 1 20.17132289 0.786751791 2.261401862 1.000398022 1.413621548 0.552335162 0.113412269 0.633643623 5.272464991 0.106063622 0.028795795 6.120005192 -0.786751791 0.413223526 NVSES(ph)PNRKNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NVSESPNRKNEK 12 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 NVS(0.007)ES(0.993)PNRKNEK 124.68 0.00016634 80217000 140600 74459 100690 45283 173600 137580 83004 93572 109180 81798 TRUE FALSE 146150.9966 87246.75404 103314.0641 54239.84224 144091.534 105629.13 76497.92959 92317.82039 105250.6331 97824.75198 1.494008353 0.891867879 1.056113734 0.554459287 1.472955782 1.079779176 0.781989507 0.943706153 1.075910043 1 16.57791193 4.744681281 24.0458436 0.978408887 1.49400875 0.319475451 0.223130176 473.6225952 1860597.235 0.051645047 0.46727288 55549.64415 -4.744681281 0.515599863 NVSKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NVSKPR 6 1 Q9Y3U8;J3QSB5;J3KTD3 Q9Y3U8 RPL36 60S ribosomal protein L36 0 ;; 118.01 0.020275 634722000 672310 515170 666150 501090 845430 874150 730430 762740 666970 471820 FALSE TRUE 698853.3179 603646.44 683510.4162 600204.1064 701724.1106 671141.9104 673176.988 752516.7179 642965.88 564264.0955 1.238521684 1.069794171 1.21133069 1.063693599 1.24360936 1.189410979 1.193017584 1.333625024 1.13947686 1 19.10601103 3.205982773 24.999214 1.209564509 1.145081594 0 0.095640901 451.8324445 346720.5712 0.026272299 0.031403411 1606.877513 -3.205982773 -0.064482915 NVSSFPDDATS(ph)PLQENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NVSSFPDDATSPLQENR 17 0 P52292;J3QLL0;J3KS65 P52292 KPNA2 Importin subunit alpha-1 1 NVSSFPDDATS(1)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDATS(1)PLQENR;NVSSFPDDATS(1)PLQENR 383.24 1.16E-121 1472430000 1304080 1253690 1270590 1188220 1373710 1800390 1342410 1346600 1287900 1271520 TRUE FALSE 1355566.085 1469001.505 1303702.619 1423246.37 1140207.265 1382276.708 1237188.396 1328551.03 1241548.731 1520649.999 0.891438586 0.966035252 0.85733247 0.935946056 0.749815714 0.909003853 0.813591817 0.87367312 0.816459232 1 20.5362567 NVTELNEPLSNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ; 308.58 2.71E-55 420250000 260460 316380 306680 297870 364580 413050 326820 323120 288680 322130 FALSE TRUE 270743.1619 370715.8039 314672.3327 356787.7969 302608.8218 317125.3973 301202.9944 318789.1049 278290.4632 385245.2059 0.702781392 0.962285314 0.816810509 0.926131699 0.785496658 0.82317805 0.781847482 0.827496618 0.722372294 1 18.55541748 NVTFHGVLLDAFFNESSADWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 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 ;;;;;;;;;;;;; 286.05 1.97E-45 7086241000 3180399.9 2608702 3980857 4592854 3759697 5342069 5099682 3981801 3964542 2201252 FALSE TRUE 3305964.544 3056726.276 4084601.404 5501306.813 3120625.047 4101454.435 4699955.599 3928431.471 3821858.908 2632545.184 1.255805433 1.161129653 1.55157884 2.089729303 1.185402274 1.557980642 1.785327609 1.492256047 1.451773338 1 21.32802686 0.71713891 2.725591733 1.00009334 1.520859734 0.24520219 0.266230022 2.757296381 24.68991359 0.258083171 0.068226532 5.213614427 -0.71713891 0.520766394 NVVGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 141.59 0.027066 1397000000 1258570 1318670 1401580 1384800 1597230 1924180 1572500 1482750 1341560 1070250 FALSE TRUE 1308259.315 1545141.315 1438106.326 1658709.307 1325733.415 1477318.356 1449243.341 1462876.162 1293277.518 1279944.996 1.022121512 1.207193527 1.123568849 1.295922334 1.035773739 1.154204564 1.132270016 1.142921114 1.01041648 1 20.28765038 1.228538556 5.993196324 1.002130899 1.143157662 0.345507318 0.073669049 0.157652633 20.0674141 0.057668127 0.016728162 16.92538498 -1.228538556 0.141026762 NVVHELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NVVHELR 7 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 90.657 0.016978 490730000 640760 730790 743320 768230 869750 998800 839020 757520 722440 661480 FALSE TRUE 666057.6996 856297.4977 762691.5298 920183.6011 721910.2057 766843.837 773255.42 747366.6835 696439.5255 791084.3412 0.841955358 1.08243515 0.964108996 1.163192789 0.912557825 0.969357876 0.97746268 0.944737046 0.880360651 1 19.59347199 NVYS(ph)SSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.882)S(0.107)S(0.011)R 93.178 0.024305 0 124480 168870 168410 168710 195420 245350 191480 172370 168670 184940 TRUE FALSE 129394.5665 197872.1089 172798.903 202080.3345 162202.5782 188371.1808 176471.2973 170059.6621 162599.5996 221175.4521 0.585031319 0.894638654 0.781275233 0.913665294 0.733366098 0.851682133 0.79787922 0.768890311 0.73516115 1 17.75483175 -2.532719488 2.194118006 4.08247955 0.791067784 0.343800584 0.088865838 2894490.969 208091.9319 44786343.58 0.01958103 0.002932787 2.532719488 -3.291411766 NWDDVLTVDYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NWDDVLTVDYTR 12 0 Q13045-3;Q13045;Q13045-2 Q13045-3 FLII Protein flightless-1 homolog 0 ; 169.82 9.96E-05 103791000 87358 102513 114014 109941 121135 133469 119573 112472 105398 93398 FALSE TRUE 90806.9613 120118.8103 116985.2985 131687.0017 100544.516 102472.8475 110200.5558 110964.4968 101604.7466 111697.5499 0.812971828 1.075393421 1.04733988 1.178960521 0.9001497 0.917413565 0.98659779 0.993437161 0.909641677 1 16.76923801 NWGGPDFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NWGGPDFER 9 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 0 ; 82.645 0.04036 0 171612 391900 378590 396080 391440 462500 326020 411770 343650 410010 FALSE TRUE 178387.3743 459205.7764 388456.3664 474423.4418 324903.1686 355091.3843 300465.7005 406250.8967 331282.1036 490343.6094 0.363800753 0.936497933 0.792212561 0.96753263 0.662603045 0.724168476 0.612765609 0.82850248 0.675612157 1 18.90343355 -1.538406815 2.415637726 1.019673335 0.743458492 0.192076891 0.164260881 5309732.827 4615874.992 677862.0338 0.040094026 0.028946308 1.538406815 -0.276214842 NWQWWR ddPTM_MDA-MB-175_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 ; 119.7 0.04836 4291400000 2770800 2766900 2783600 2506400 4399500 4429600 3458200 3228100 2747000 2827300 FALSE TRUE 2880193.324 3242093.552 2856142.903 3002158.439 3651674.561 3400892.531 3187137.248 3184832.6 2648136.007 3381255.303 0.851811847 0.958843169 0.844698979 0.887882804 1.079975995 1.005807674 0.942589944 0.941908349 0.783181324 1 21.68912752 4.747282489 23.24643547 0.938873116 0.851811728 0.094840003 0.080160651 1103.040681 2939756.64 0.019455889 0.219894594 55883.35728 -4.747282489 -0.087061388 NWRDPDQTDGLGLSYLSSHIANVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NWRDPDQTDGLGLSYLSSHIANVER 25 1 P06396-2;A0A0A0MS51;A0A0A0MT01;P06396-4;P06396-3;P06396 P06396-2 GSN Gelsolin 0 ;;; 249.78 1.40E-39 1668940000 426487 800244 786068 719433 834080 1065900 700948 789760 752275 770949 FALSE TRUE 443325.0361 937679.682 806553.5778 861734.7001 692303.3795 818360.8789 646005.8642 779174.559 725200.7697 922001.6958 0.480828873 1.017004292 0.874785352 0.934634615 0.750869963 0.887591512 0.700655831 0.845090158 0.786550364 1 19.81440988 -2.430903525 2.129094784 2.501687368 0.818406323 0.14130654 0.13965209 7546776.622 512226.4502 54863764.2 0.030971293 0.003707631 2.430903525 -1.683281045 NWTEDMEGGIS(ph)SPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.5)S(0.5)PVKK 94.707 0.0017169 590180000 627110 251300 425760 283290 555720 580390 607040 431580 520360 230210 TRUE FALSE 651868.787 294458.8202 436855.6554 339323.9165 461258.9129 445603.2184 559458.6186 425795.376 501632.3452 275315.2419 2.367717757 1.069533304 1.586747077 1.232492303 1.675384587 1.618519975 2.032065551 1.546573932 1.822028965 1 18.07072496 NWTEDMEGGISS(ph)PVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.134)S(0.866)PVKK;NWTEDMEGGIS(0.195)S(0.805)PVKK;NWTEDMEGGIS(0.087)S(0.913)PVKK;NWTEDMEGGIS(0.02)S(0.98)PVKK;NWTEDMEGGIS(0.092)S(0.908)PVKK 274.27 1.93E-35 3487380000 7086210 2951650 4811640 2809600 6598920 6169940 6577530 4905290 5489080 2185560 TRUE FALSE 7365979.043 3458572.927 4937035.291 3365330.494 5477237.935 4737064.941 6061966.011 4839542.611 5291529.083 2613778.637 2.818134229 1.323208048 1.888849814 1.287534624 2.095524792 1.812343584 2.319234661 1.851550297 2.024474838 1 21.31770553 NYAGAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NYAGAYR 7 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 ;;; 164.1 0.0028154 1753040000 1276170 1406650 1377210 1200460 2534970 2284290 1560470 1513420 1243570 1598640 FALSE TRUE 1326554.177 1648231.195 1413101.224 1437907.405 2104076.705 1753798.266 1438156.284 1493135.08 1198814.159 1911862.9 0.693854239 0.862107422 0.739122677 0.752097551 1.100537442 0.917324284 0.752227727 0.78098439 0.627039815 1 20.86654764 4.747914816 23.25929009 0.828947306 0.693854048 0.092572068 0.132233745 1303.404085 3240734.724 0.032083968 0.382832667 55964.78189 -4.747914816 -0.135093258 NYDTTIHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYDTTIHGK 9 0 J3QRN6;O94832;K7EIG7;J3KRL0 J3QRN6 MYO1D Unconventional myosin-Id 0 73.067 0.044971 107490000 57313 43956 43785 46332 61218 68082 52336 52478 54503 37081 FALSE TRUE 59575.7615 51505.10107 44926.07307 55496.33131 50812.18623 52270.98729 48233.76757 51774.61825 52541.44768 44346.31199 1.34342088 1.161429187 1.01307349 1.251430588 1.145804103 1.17869976 1.087661305 1.167506742 1.184798585 1 15.43652651 -5 0.170506399 0.38430644 1.202043992 0.292783136 0.082057243 181.7870528 1.717482416 38.16888958 0.288113978 1.00E-05 5 0.817737552 NYDYYASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 ;;; 118.18 0.0045056 2151960000 1653910 1172430 1425560 1024250 2076790 1971400 1564290 1353400 1546890 1166920 FALSE TRUE 1719207.644 1373785.732 1462711.265 1226843.593 1723777.978 1513572.227 1441676.862 1335259.887 1491217.731 1395555.632 1.231916238 0.98440055 1.048121072 0.879107622 1.235191158 1.084566027 1.03304865 0.956794452 1.068547679 1 20.41240821 4.746906921 24.66153314 1.031114018 1.231916359 0.315177846 0.088305399 1086.042311 3208933.879 0.020964613 0.237608667 55835.05152 -4.746906921 0.200802342 NYEIKNEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYEIKNEADR 10 1 O15145;C9JZD1;F8VR50 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 89.403 0.010521 152040000 195530 146840 171120 133760 215820 245680 227400 195210 265040 130000 FALSE TRUE 203249.6754 172058.6277 175579.5278 160217.3288 179134.9935 188624.5433 209575.7938 192593.5292 255501.2622 155471.011 1.307315583 1.106692667 1.129339332 1.030528635 1.152208327 1.21324575 1.348005602 1.238774534 1.643401304 1 17.24628608 2.466805324 2.722285941 1.31944799 1.136092191 0.181722562 0.160174799 0.41222655 6.226232049 0.056914311 0.048117218 292.9579743 -2.466805324 -0.183355799 NYGFVHIEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYGFVHIEDK 10 0 Q9BWF3;E9PB51;Q9BQ04;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2;E9PLB0;E9PM61;U3KQD5 Q9BWF3 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 100.72 0.0038198 381970000 825410 535970 615880 521780 849530 958890 829940 719170 680130 339880 FALSE TRUE 857997.8242 628018.6782 631930.3388 624986.5266 705127.194 736202.3296 764887.1342 709530.7025 655652.2542 406472.9786 2.110836069 1.545044102 1.554667523 1.537584439 1.734745558 1.811196238 1.881766254 1.745579017 1.613027898 1 18.63279992 0.780072445 3.198004364 1.000074872 1.729884029 0.637699381 0.166467775 0.921448421 12.53131854 0.160750714 0.041799495 6.026601078 -0.780072445 0.729809156 NYGYNPS(ph)PVKPEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR 182.09 3.40E-07 1554880000 1111300 610870 850550 631790 1139440 1401800 1100070 929520 976960 491487 TRUE FALSE 1155174.982 715782.1706 872716.0317 756756.1763 945758.3958 1076253.194 1013843.639 917061.3048 941799.4004 587784.4676 1.965303688 1.21776299 1.484755178 1.287472225 1.609022436 1.831033744 1.724856125 1.560199963 1.602286982 1 19.16492771 -1.27993609 6.149580507 0.999978474 1.576830852 0.401657145 0.214601657 6.25E-05 7.32E-06 0.20501723 0.048321226 0.05248847 1.27993609 0.576852377 NYHIFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYHIFYR 7 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 84.244 0.021688 405580000 145560 176107 162870 173316 228554 295560 201183 179069 164395 199363 FALSE TRUE 151306.8212 206352.0073 167114.526 207597.3875 189704.4727 226920.6693 185413.7508 176668.873 158478.4561 238424.3628 0.634611411 0.865482054 0.700912122 0.870705431 0.795658927 0.951751183 0.777662771 0.740984985 0.664690698 1 17.86317214 4.751274376 24.07064878 0.807103787 0.634611225 0.222186784 0.101248519 1916.800042 3628919.934 0.023127285 0.399298812 56399.38602 -4.751274376 -0.172492562 NYILDQTNVYGS(ph)AQR ddPTM_MDA-MB-175_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 NYILDQT(0.002)NVYGS(0.998)AQR;NYILDQTNVYGS(1)AQR 144.97 4.34E-06 258150000 187956 218723 223105 185782 278677 315626 228651 241604 202930 203780 TRUE FALSE 195376.648 256286.9738 228919.2996 222529.1251 231307.5831 242326.6449 210728.7372 238365.6936 195626.5889 243706.7894 0.801687341 1.051620164 0.939322619 0.91310187 0.949122442 0.994336865 0.864681438 0.978083927 0.802712922 1 17.89478692 2.240581167 24.9996311 0.915284679 0.945488218 0.031784666 0.078601842 224.1855719 2773817.638 0.026175965 0.020889491 174.0127885 -2.240581167 0.030203539 NYILSAS(ph)ASALWNDEVDKAEQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYILSASASALWNDEVDKAEQELR 24 1 B7ZC38;Q9NR46;Q9NR46-2 B7ZC38 SH3GLB2 Endophilin-B2 1 NYILS(0.001)AS(0.842)AS(0.157)ALWNDEVDKAEQELR;NYILS(0.054)AS(0.766)AS(0.179)ALWNDEVDKAEQELR 156.37 1.70E-08 97090000 69870 37900 66390 47309 99362 93747 66592 55684 65510 37316 TRUE FALSE 72628.52155 44409.03018 68120.17794 56666.579 82472.48273 71975.68 61372.34503 54937.64706 63152.3079 44627.35574 1.627443982 0.995107809 1.526422007 1.269772274 1.848025306 1.612815252 1.375218048 1.231030747 1.415103065 1 15.44564071 0.764678392 0.84805327 1.008405966 1.452936612 0.257946818 0.225133538 1.33730441 1.862328725 0.219961059 0.07584473 5.816723121 -0.764678392 0.444530647 NYISQYSEIAIQMMMHMQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYISQYSEIAIQMMMHMQPK 20 0 P07602 P07602 PSAP Prosaposin;Saposin-A;Saposin-B-Val;Saposin-B;Saposin-C;Saposin-D 0 164.99 1.73E-11 189090000 85237 64301 98678 58972 98040 98248 88148 83306 65527 46187 FALSE TRUE 88602.22258 75344.19656 101249.6297 70636.48559 81375.19582 75431.39096 81238.72943 82189.41933 63168.69607 55236.45835 1.604053287 1.364030186 1.833021754 1.278801858 1.473215305 1.365608752 1.470744719 1.487955995 1.143605111 1 15.7533332 0.075896548 0.292126038 0.853427238 1.564420146 0.521048095 0.153211482 4.282895481 0.589493656 0.880531001 0.197675138 1.190958279 -0.075896548 0.710992908 NYIVEDGDIIFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYIVEDGDIIFFK 13 0 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 94.767 0.0039046 0 14375 9137 12017 10568 16429 17113 15412 12175 14405 12547 FALSE TRUE 14942.5361 10706.20867 12330.17289 12658.31886 13636.40445 13138.7651 14203.96717 12011.81404 13886.56686 15005.34442 0.99581427 0.713493031 0.821718752 0.843587358 0.90876984 0.8756057 0.946593878 0.800502388 0.925441394 1 13.87318881 3.340592093 5.111147997 0.893867421 0.83109277 0.114099968 0.080872473 0.456702342 18.99251877 0.021643664 0.029430371 2190.746332 -3.340592093 -0.062774651 NYLPAINGIVFLVDCADHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYLPAINGIVFLVDCADHER 20 0 Q9Y6B6;D6RD69;D6RDB2;Q9H029;D6R9R5 Q9Y6B6 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 ; 173.21 5.22E-12 758150000 241340 274840 308300 278670 334960 435940 317430 298070 292460 240260 FALSE TRUE 250868.2896 322041.632 316334.5513 333790.0943 278023.6188 334699.5417 292549.0072 294074.8592 281934.4217 287334.3469 0.873088415 1.120790589 1.100928429 1.161678365 0.967596188 1.164843484 1.018148405 1.023458777 0.981206823 1 18.13237093 2.029184154 24.99665102 1.008322084 1.070865086 0.103583124 0.084432838 450.9596662 386251.8414 0.030345359 0.022411355 106.9508288 -2.029184154 0.062543002 NYLPAINGIVFLVDCADHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYLPAINGIVFLVDCADHSR 20 0 Q9NR31;Q5SQT8;Q9NR31-2 Q9NR31 SAR1A GTP-binding protein SAR1a 0 ; 171 8.48E-12 1439580000 398230 461120 524350 492940 631110 722090 567950 543600 556820 401500 FALSE TRUE 413952.4279 540313.773 538014.9918 590442.0607 523834.1476 554395.5409 523432.5949 536313.9312 536780.157 480166.2378 0.862102321 1.125263982 1.120476513 1.229661759 1.090943316 1.154590842 1.090107037 1.116933864 1.117904831 1 18.87317444 4.738946048 24.99994188 1.122376889 0.862102242 0.661101793 0.054419547 17.04460827 1105168.903 0.011964854 0.070273576 54820.88571 -4.738946048 -0.260274646 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNS(1)ESGEKNEGSESAPEGQAQQR;NYQQNYQNS(0.916)ES(0.084)GEKNEGSESAPEGQAQQR;NYQQNY(0.003)QNS(0.98)ES(0.017)GEKNEGSESAPEGQAQQR 496.43 4.18E-301 3885160000 1136847 654317 885764 676359 1318223 1531375 1070950 991569 1009472 567905 TRUE FALSE 1181730.597 766690.8549 908847.7375 810140.7915 1094151.925 1175736.364 987006.1406 978278.6394 973141.2999 679175.1116 1.739949797 1.128855934 1.338164079 1.192830505 1.611001208 1.731124042 1.453242505 1.440392357 1.43282827 1 19.37342407 0.36183476 2.349281842 0.999999494 1.445191441 0.330846588 0.192724201 22.9001806 82.14114525 0.186759371 0.050178101 2.300566334 -0.36183476 0.445191947 NYQQNYQNSES(ph)GEKNEGSESAPEGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNY(0.001)QNS(0.133)ES(0.867)GEKNEGSESAPEGQAQQR;NYQQNYQNS(0.299)ES(0.701)GEKNEGSESAPEGQAQQR 447.05 2.90E-220 2472100000 932690 547260 758630 537020 1040160 1182500 918180 809990 840640 414744 TRUE FALSE 969513.3214 641247.6479 778400.521 643240.9532 863353.9747 907882.296 846210.6524 799133.4089 810385.5306 496005.146 1.954643675 1.292824587 1.569339607 1.296843306 1.740614955 1.830388864 1.706052163 1.611139351 1.633824844 1 18.91999556 3.181291503 24.99999227 1.635607753 1.514496545 0 0.27418554 287.294293 125412.4339 0.073848956 0.088266439 1518.068969 -3.181291503 -0.121111208 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 1 NYQQNYQNSESGEKNEGS(0.985)ES(0.015)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.991)ES(0.009)APEGQAQQR;NYQQNYQNSES(0.002)GEKNEGS(0.964)ES(0.034)APEGQAQQR;NYQQNYQNSESGEKNEGS(0.996)ES(0.004)APEGQAQQR 389.69 5.39E-155 5081160000 771729 463120 628508 432850 820316 952807 717916 640157 656422 319084 TRUE FALSE 802197.4568 542657.2574 644887.4348 518466.4381 680878.9793 731532.0142 661643.868 631576.7425 632797.5004 381602.4006 2.102181369 1.422048857 1.689945959 1.358656123 1.78426283 1.917000556 1.733856671 1.655064909 1.65826394 1 18.54171072 0.275367071 1.540537762 0.999815655 1.696165812 0.518715802 0.203287173 5.995923618 11.82357973 0.187856958 0.05364435 1.885241847 -0.275367071 0.696350158 NYQQNYQNSESGEKNEGSESAPEGQAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 201.21 2.95E-25 607090000 135291 74706 94006 87904 137831 148829 132309 109306 111259 66055 FALSE TRUE 140632.3931 87536.17437 96455.87359 105291.1488 114402.5359 114265.7203 121938.2749 107840.9319 107254.8103 78997.21255 1.780219689 1.108091938 1.221003507 1.332846381 1.448184463 1.446452559 1.54357693 1.365123254 1.357703732 1 16.26951413 0.603542548 2.297652159 1.000044895 1.395037991 0.331680556 0.171224744 3.792371239 20.54241532 0.159114055 0.042944358 4.013678181 -0.603542548 0.394993096 NYS(ph)SPPPCHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NY(0.005)S(0.571)S(0.425)PPPCHLSR;NY(0.001)S(0.58)S(0.418)PPPCHLSR 65.943 0.038255 274615000 72999 395000 335460 365060 362670 500010 308330 398780 329590 410750 TRUE FALSE 75881.05689 462838.1773 344202.3632 437267.7784 301023.4829 383890.2552 284162.2889 393435.0064 317728.1203 491228.5982 0.154471985 0.942205277 0.700696915 0.890151306 0.612797146 0.781490037 0.578472609 0.800920402 0.646802978 1 18.90603503 -5 0.038306811 2.111262672 6.41E-10 0.20139632 0.204425245 1750.636616 5.017683959 242.8961987 76.88090736 1.00E-05 5 -2.111262672 NYS(ph)VGSRPLKPLS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 2 NY(0.007)S(0.948)VGS(0.051)RPLKPLS(0.994)PLR 49.66 0.098004 323650000 148040 117750 172100 123690 317910 248130 213260 188930 223750 151570 TRUE FALSE 153884.7335 137972.6465 176585.0674 148155.5128 263871.7718 190505.5679 196544.1239 186397.7024 215697.2812 181267.2395 0.848938473 0.761155998 0.974169783 0.817331986 1.455705799 1.05096524 1.084278243 1.02830331 1.189940785 1 17.46775868 NYS(ph)VGSRPLKPLSPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYS(0.997)VGS(0.003)RPLKPLSPLR 149.94 4.11E-07 1961000000 1141100 990870 1316100 1024900 3090900 1959900 1492000 1408500 1314100 1712600 TRUE FALSE 1186151.509 1161044.215 1350398.647 1227622.161 2565509.922 1504742.928 1375053.141 1389621.361 1266805.798 2048151.18 0.579132791 0.566874275 0.659325669 0.599380638 1.252597927 0.734683524 0.671363108 0.678475971 0.618511861 1 20.96589078 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_MDA-MB-175_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 115.87 0.00034222 24611000 106140 76600 94738 77448 118450 120140 106010 100450 95497 64428 TRUE FALSE 110330.4892 89755.45413 97206.95011 92766.98324 98315.91131 92239.30574 97700.65919 99103.63205 92060.08162 77051.43305 1.431907036 1.164877155 1.261585233 1.203961816 1.275977713 1.197113436 1.267992759 1.286201024 1.194787403 1 16.23353417 0.885722652 4.348208096 1.000031952 1.255949279 0.567616865 0.068523818 0.448346836 15.84185845 0.05971269 0.01519002 7.686394174 -0.885722652 0.255917327 NYSHHNGLDELTCCVS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYSHHNGLDELTCCVSD 17 0 Q9BTC8;F6RRE2 Q9BTC8 MTA3 Metastasis-associated protein MTA3 1 NYSHHNGLDELTCCVS(1)D 104.06 0.00055972 59080000 15039 48780 38701 47800 44743 61414 30987 45499 44302 43920 TRUE FALSE 15632.75133 57157.58554 39709.57985 57254.69733 37137.60084 47151.52924 28558.15797 44889.16033 42707.57967 52525.2831 0.297623362 1.088191861 0.756008869 1.090040719 0.707042374 0.897692053 0.543703076 0.854620055 0.81308614 1 15.68072441 -3.14823427 0.941484906 3.466350847 0.795368983 0.074766019 0.225233011 45546.90112 1034.576426 236794.6251 0.063692323 0.00071083 3.14823427 -2.670981863 NYSS(ph)PPPCHLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYSSPPPCHLSR 12 0 Q12986;Q12986-2;Q12986-3 Q12986 NFX1 Transcriptional repressor NF-X1 1 NYS(0.248)S(0.752)PPPCHLSR;NYS(0.228)S(0.772)PPPCHLSR 101.04 0.0018654 359840000 70734 330480 277220 298640 284980 423330 268310 354730 265110 319280 TRUE FALSE 73526.63294 387237.3692 284444.5809 357710.1006 236539.2014 325018.0231 247279.1611 349975.4246 255568.7429 381836.803 0.192560362 1.01414365 0.744937572 0.936814099 0.61947722 0.851196167 0.647604315 0.916557602 0.669314065 1 18.54259664 4.750465397 24.67561814 0.812216457 0.192559912 0.648216416 0.138982543 882.8804177 1829948.772 0.029734175 0.489787885 56294.42625 -4.750465397 -0.619656545 NYSVGSRPLKPLS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYSVGSRPLKPLSPLR 16 2 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 NYSVGS(0.001)RPLKPLS(0.999)PLR 79.248 0.01487 408820000 639350 503810 544030 470730 679750 846650 633910 573360 541220 405880 TRUE FALSE 664592.0317 590335.4484 558207.8687 563838.989 564206.3378 650028.3686 584222.4778 565675.047 521741.5979 485404.415 1.369151189 1.216172392 1.14998515 1.161586033 1.162342823 1.339148035 1.20357883 1.165368566 1.074859605 1 18.8888277 -4.999999997 0.11397838 0.288300168 1.321357071 0.5059736 0.073048792 148.0989925 1.112042854 24.04876158 0.859439056 1.00E-05 4.999999997 1.033056903 NYTEEEDRFLICMLHK ddPTM_MDA-MB-175_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 ; 193.69 2.01E-10 129141000 112184 107548 130791 105824 145964 160128 134507 127758 128042 83349 FALSE TRUE 116613.1109 126018.5324 134199.5209 126755.6713 121153.0914 122940.6988 123963.9899 126045.613 123433.7934 99679.64074 1.169878925 1.264235419 1.346308232 1.2716305 1.21542464 1.233358165 1.243623963 1.264507095 1.238304959 1 16.60501125 -3.257412888 0.470719803 1.06E-09 1.25601281 0.754326077 0.042735218 131.0323267 3.646069751 131.5988639 0.022178887 0.000552824 3.257412888 1.256012809 NYVPPKGDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 NYVPPKGDKK 10 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 72.652 0.026628 916600000 1379180 520810 861630 485930 1490660 1202450 1169150 964930 1097820 408170 FALSE TRUE 1433631.091 610255.0662 884084.7856 582045.5036 1237278.146 923199.2108 1077508.968 951996.6917 1058309.673 488143.0966 2.936907438 1.250156092 1.811118075 1.192366557 2.534662795 1.89124709 2.207362914 1.950241022 2.168031628 1 18.8969446 3.232017396 24.99805042 2.015114873 1.759494202 0.010977099 0.57881859 550.8929033 2104657.053 0.154284415 0.188490486 1706.150729 -3.232017396 -0.25562067 NYYEQWGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;; 217.81 1.68E-05 19187300000 4496010 3543770 4333580 3520450 5443470 5471940 4924410 4431750 4309110 2527180 FALSE TRUE 4673515.946 4152384.931 4446516.655 4216784.503 4518190.914 4201164.863 4538421.877 4372349.64 4154025.973 3022332.535 1.546327511 1.373900748 1.471220193 1.395208652 1.494935075 1.390040578 1.501628899 1.446680532 1.37444372 1 21.52723097 0.721084939 2.401623455 1.000065632 1.450257394 0.871814001 0.051816524 0.420619884 3.214511442 0.044104463 0.011851718 5.261201551 -0.721084939 0.450191762 NYYGYQGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 NYYGYQGYR 9 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 132.08 0.00073276 247270000 104550 87581 94219 73692 145390 157570 111260 91441 103010 92366 FALSE TRUE 108677.7147 102622.3555 96674.42454 88268.05765 120676.6597 120976.7555 102539.1505 90215.38296 99302.69022 110463.3492 0.98383505 0.929017237 0.875171948 0.799070988 1.092458816 1.095175516 0.928264 0.816699689 0.898965049 1 16.75320825 -2.67855636 2.177371146 3.101309643 0.930028186 0.037170855 0.095144062 3105078.749 676514.541 32658586.65 0.025359356 0.002096253 2.67855636 -2.171281457 PAAPPRPLDRES(ph)PGVENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PAAPPRPLDRESPGVENK 18 2 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 PAAPPRPLDRES(1)PGVENK 116.35 8.51E-05 197430000 323640 106500 193990 129000 245660 324850 306260 192810 231200 94403 TRUE FALSE 336417.5571 124790.5465 199045.5388 154515.815 203902.8009 249408.5106 282254.5409 190225.6973 222879.1572 112899.4604 2.979797742 1.105324561 1.76303357 1.368614291 1.80605647 2.209120485 2.50005217 1.684912369 1.974138374 1 16.78467907 2.987939803 24.37843649 1.954110327 1.730833745 0 0.585635588 1808.286827 3655276.117 0.165667716 0.184684757 972.6124023 -2.987939803 -0.223276583 PAAS(ph)PRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PAASPRPR 8 1 P20810-6;P20810-10;P20810-7;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 1 PAAS(1)PRPR 99.013 0.0043087 88074000 97239 133700 166210 166380 149080 244430 164480 147990 146040 146780 TRUE FALSE 101078.0708 156661.935 170541.5691 199289.4674 123739.4349 187664.8369 151587.6278 146006.4361 140784.0489 175538.7307 0.575816348 0.892463642 0.971532427 1.135301973 0.704912439 1.069079377 0.863556591 0.831761945 0.802011319 1 17.42142986 4.735587688 4.865787105 0.914950326 0.55840363 0.416057382 0.122148964 0.166312593 11.69832689 0.028558462 0.200265932 54398.59559 -4.735587688 -0.356546696 PANKQEDEVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PANKQEDEVMR 11 1 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 72.29 0.042589 97395000 225940 118920 147890 108960 217780 220560 213750 131600 169620 93258 FALSE TRUE 234860.2857 139343.5849 151744.1349 130511.9628 180761.8334 169338.2826 196995.7165 129836.1173 163515.4093 111530.1196 2.105801433 1.249380754 1.360566415 1.170194772 1.620744549 1.518318848 1.766300594 1.164135014 1.466109872 1 16.76707385 -3.335878152 0.195848472 4.82E-12 1.564106476 0.246720462 0.270915615 101.9429452 1.806697672 42.17764566 0.707752535 0.000461447 3.335878152 1.564106476 PAQPQEHPFASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PAQPQEHPFASSR 13 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 151.99 4.49E-05 1437180000 877000 717970 962420 832460 1272980 1373940 1084230 955270 1043990 772380 FALSE TRUE 911624.6372 841275.7625 987501.4558 997118.1034 1056599.314 1054863.257 999245.2195 942466.1682 1006417.004 923713.0729 0.986913214 0.910754418 1.06905649 1.07946735 1.143860951 1.141981518 1.081770139 1.020301862 1.089534222 1 19.81708526 4.186828197 7.496765705 1.080942949 0.949126392 0.560285314 0.045831214 0.144555129 17.59010298 0.0120485 0.026556234 15375.46281 -4.186828197 -0.131816557 PAS(ph)DGVFLSNSFQPPSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PASDGVFLSNSFQPPSAK 18 0 P55196-1 P55196-1 MLLT4 Afadin 1 PAS(1)DGVFLSNSFQPPSAK 172.93 1.00E-11 39033000 70085 26744 43670 29843 57158 76279 58266 39191 47758 23887 TRUE FALSE 72852.00992 31337.07396 44808.07608 35745.85633 47442.30358 58564.35827 53698.95867 38665.70875 46039.19891 28567.20031 2.550197749 1.096959927 1.568514786 1.251290149 1.660726395 2.050055926 1.879741735 1.35350011 1.611610463 1 14.80207203 0.600243608 1.071956819 1.003361353 1.66325106 0.208159606 0.396345306 2.176989623 3.852958388 0.365815323 0.114805138 3.983305426 -0.600243608 0.659889707 PAS(ph)PSLQLLPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PASPSLQLLPWR 12 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 PAS(0.999)PS(0.001)LQLLPWR;PAS(0.994)PS(0.006)LQLLPWR 199.13 1.84E-07 275820000 300640 179301 235990 184050 309590 382230 317810 216650 232950 162309 TRUE FALSE 312509.4993 210094.552 242140.0933 220454.5407 256966.0024 293462.8753 292899.2218 213746.1611 224566.175 194110.341 1.609958016 1.082346005 1.24743531 1.135717652 1.32381408 1.51183535 1.508931571 1.101158032 1.156899596 1 17.56651745 1.616782315 8.941992772 1.093917085 1.328908608 0.346962911 0.162014149 0.132558065 27.33895799 0.084902128 0.042780679 41.37922145 -1.616782315 0.234991523 PAT(ph)PGASSVEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PATPGASSVEQLRK 14 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 PAT(0.971)PGAS(0.024)S(0.005)VEQLRK;PAT(0.991)PGAS(0.008)S(0.002)VEQLRK;PAT(0.944)PGAS(0.041)S(0.014)VEQLRK 92.439 0.0029055 987960000 1857560 624990 958220 742200 1435670 1608870 1507130 961500 1098190 457800 TRUE FALSE 1930897.903 732327.1708 983192.0004 889004.9448 1191635.326 1235234.325 1388997.212 948612.6652 1058666.356 547497.1449 3.526772552 1.337590849 1.79579384 1.623761791 2.176514229 2.256147519 2.53699444 1.732634908 1.933647264 1 19.06249192 0.627244498 1.241266986 1.003165331 2.095486705 0.25847724 0.572072995 1.791047589 4.149156093 0.517227161 0.156541377 4.238815346 -0.627244498 1.092321375 PAVEASTGGEATQETGKEEAGKEEPPPLT(ph)PPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PAVEASTGGEATQETGKEEAGKEEPPPLTPPAR 33 2 Q9C0C2;E9PKK0;E9PKE7 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 PAVEASTGGEATQETGKEEAGKEEPPPLT(1)PPAR 129.25 3.61E-06 554980000 743150 176930 359020 227210 530320 622250 641910 359350 457170 125280 TRUE FALSE 772490.1358 207316.3512 368376.3561 272151.4598 440176.3958 477741.8678 591595.4169 354533.501 440716.541 149826.2174 5.15590762 1.383712109 2.458690893 1.816447512 2.937913027 3.188639987 3.948544035 2.36629815 2.941518172 1 17.19293057 PCSEETPAIS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PCSEETPAISPSK 13 0 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(1)PSK;PCSEETPAIS(0.998)PS(0.002)K;PCSEETPAIS(0.998)PS(0.002)K 266.6 2.03E-24 533220000 979490 352466 590600 412792 883830 1106870 961800 600230 708730 268759 TRUE FALSE 1018161.022 412999.2937 605991.5212 494441.0255 733596.8923 849816.2173 886411.6028 592184.8986 683222.9457 321417.1803 3.167724328 1.284932228 1.88537377 1.538315485 2.282382328 2.643966375 2.757822721 1.842418311 2.125657829 1 18.29408752 PCSEETPAIS(ph)PSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 PCSEETPAIS(0.967)PS(0.033)KR;PCSEETPAIS(0.994)PS(0.006)KR;PCSEETPAIS(0.994)PS(0.006)KR;PCSEETPAIS(1)PSKR;PCSEETPAIS(0.998)PS(0.002)KR;PCSEETPAIS(0.961)PS(0.039)KR;PCSEETPAIS(0.994)PS(0.006)KR;PCSEETPAIS(0.795)PS(0.204)KR 318.07 5.79E-56 9504290000 5774040 2192840 3373740 2036800 5195860 6172930 4982900 3283580 3897210 1712654 TRUE FALSE 6002003.558 2569443.212 3461662.436 2439672.961 4312669.573 4739360.559 4592327.278 3239568.981 3756950.173 2048215.761 2.930357081 1.254478782 1.690086808 1.191121076 2.105573864 2.313897125 2.242111093 1.581654161 1.834255085 1 20.96593627 PEEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PEEQLRK 7 1 A0A590UK20;Q9BXX2 A0A590UK20 ANKRD30B Ankyrin repeat domain-containing protein 30B 0 ;; 94.662 0.022505 1877810000 1463260 1164090 1267630 1311180 1473390 1595930 1760190 1338750 1347320 961950 FALSE TRUE 1521030.635 1364013.402 1300665.479 1570527.491 1222943.694 1225299.444 1622221.708 1320806.246 1298830.216 1150425.685 1.322145928 1.185659726 1.130594958 1.365170746 1.063035805 1.065083525 1.410105607 1.148102188 1.128999668 1 20.13373636 -4.999999999 0.210290463 0.014966518 1.231580219 0.241358474 0.114490782 221.6838335 2.21037458 91.85646834 0.238797999 1.00E-05 4.999999999 1.216613701 PEINTNHLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PEINTNHLDK 10 0 Q13907 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 ; 142.89 3.49E-05 367580000 1487820 694360 1001550 774720 1700040 1484580 1465880 1096560 1244690 620450 FALSE TRUE 1546560.282 813610.9286 1027651.216 927957.3037 1411067.808 1139808.794 1350980.495 1081862.407 1199893.85 742015.2983 2.084270076 1.096488079 1.38494613 1.250590528 1.901669428 1.536098779 1.820690892 1.458005528 1.617074274 1 19.50108941 -1.372867362 5.464233492 0.999792113 1.555426229 0.263584065 0.285692637 0.000683195 7.84E-05 0.261199269 0.061542651 0.042377237 1.372867362 0.555634116 PEMT(ph)ENETPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PEMTENETPTK 11 0 C9JBW0;Q68DE3 C9JBW0 KIAA2018 Basic helix-loop-helix domain-containing protein KIAA2018 1 PEMT(1)ENETPTK 98.04 0.065029 60439000 4234.8 146300 103220 121140 79879 119080 79809 109080 98041 171260 TRUE FALSE 4401.993174 171425.8869 105909.998 145101.1304 66301.19611 91425.47467 73553.36204 107617.961 94512.52356 204815.118 0.021492521 0.836978679 0.517100491 0.708449317 0.323712413 0.446380499 0.359120766 0.525439538 0.461452868 1 17.64396268 -1.212032145 3.360857021 1.001149961 0.48014674 0.369596558 0.208288361 43624271.3 65623239.95 533546.513 0.046208679 0.061371658 1.212032145 -0.521003221 PERTVLGSRELCDSEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PERTVLGSRELCDSEGK 17 2 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 0 51.147 0.08652 315000000 65803 19402 19067 26930 25851 42311 25334 32397 21583 41616 FALSE TRUE 68400.95325 22734.14257 19563.90168 32256.67362 21456.85625 32484.91148 23348.25488 31962.77121 20806.23205 49769.85841 1.374344944 0.456785358 0.393087349 0.648116644 0.431121505 0.652702509 0.469124398 0.642211415 0.418048849 1 15.60298466 -0.914737894 8.876010235 0.999999888 0.592990316 0.15229972 0.273898523 0 0 0.244895475 0.057722417 0.121692022 0.914737894 -0.407009573 PFPTPS(ph)PASLDVYVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PFPTPSPASLDVYVAR 16 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 PFPT(0.005)PS(0.989)PAS(0.006)LDVYVAR;PFPT(0.004)PS(0.967)PAS(0.028)LDVY(0.001)VAR;PFPT(0.002)PS(0.996)PAS(0.002)LDVYVAR 109.84 0.00098729 68185000 157763 94130 114009 101168 139295 197832 165227 119170 114589 71474 TRUE FALSE 163991.6051 110296.0953 116980.1682 121178.7284 115617.6857 151888.5162 152276.076 117572.7211 110464.9643 85477.96185 1.91852498 1.290345405 1.368541852 1.41766048 1.352602275 1.776931889 1.781465921 1.375474082 1.29232099 1 16.38326489 1.049305901 1.94405209 1.01001629 1.5331909 0.414591202 0.204058854 0.327032408 2.528166188 0.195313677 0.05527067 11.20226651 -1.049305901 0.52317461 PFSAPKPQT(ph)SPSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.798)S(0.2)PS(0.002)PK 86.367 0.011912 493820000 419100 127400 231880 179490 364970 370860 443260 238710 276410 104420 TRUE FALSE 435646.3916 149279.959 237922.9833 214992.5863 302932.5298 284733.3854 408516.123 235510.4829 266462.0581 124879.0998 3.488545261 1.195395861 1.905226605 1.721605831 2.425806483 2.280072374 3.271292985 1.885907917 2.133760242 1 16.93017252 3.221110896 24.90597125 2.267831849 2.002352937 0 0.758385053 1061.219525 1514674.894 0.208587856 0.249855481 1663.837454 -3.221110896 -0.265478912 PFSAPKPQTS(ph)PSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PFSAPKPQT(0.271)S(0.719)PS(0.009)PK 83.252 0.0052107 422810000 537300 169840 296470 203930 441020 469790 542300 297940 332240 95575 TRUE FALSE 558513.0189 199008.6988 304196.2518 244266.7453 366055.5779 360688.3922 499793.109 293946.6016 320282.7473 114301.0914 4.886331462 1.741091852 2.661359119 2.137046483 3.202555405 3.155598848 4.372601373 2.571686745 2.802097018 1 16.80247965 PFVPNVHAAEFVPSFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PFVPNVHAAEFVPSFLR 17 0 P15170-2;P15170-3;Q8IYD1 P15170-2 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 ; 101.15 0.0011588 1063630000 524830 431090 516280 488350 669230 796710 798710 558550 624160 370790 FALSE TRUE 545550.6937 505126.3541 529734.6809 584944.1724 555474.5236 611686.1768 736105.0232 551063.5509 601696.6035 443439.2013 1.230271686 1.139110734 1.194604986 1.319107942 1.25265092 1.379413852 1.659990865 1.242703733 1.35688636 1 18.75837679 3.546588179 1.571273391 1.352569206 1.177799187 0.098562845 0.156530251 0.689248716 3.38469448 0.047669205 0.091727481 3520.368929 -3.546588179 -0.174770019 PGHLQEGFGCVVTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PGHLQEGFGCVVTNR 15 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;; 244.57 4.84E-18 2393300000 919925 776420 983057 940899 1045746 1220563 1144305 962928 1005140 674819 FALSE TRUE 956244.3493 909764.0953 1008676.273 1127006.014 867990.4685 937105.7411 1054611.384 950021.5252 968965.2077 807036.8629 1.184883112 1.127289393 1.249851549 1.396474022 1.07552766 1.161168447 1.30676978 1.177172406 1.200645537 1 19.62227505 0.338137782 1.527208905 0.999972868 1.211807444 0.345343707 0.086419394 6.375596237 13.45327862 0.082595619 0.023700753 2.17840077 -0.338137782 0.211834577 PGHLQEGFGCVVTNRFDQLFDDESDPFEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PGHLQEGFGCVVTNRFDQLFDDESDPFEVLK 31 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 168.95 5.87E-13 320710000 174743 129538 169401 75997 272380 217020 129738 145358 182181 153116 FALSE TRUE 181641.9886 151785.1438 173815.7292 91028.97977 226080.9449 166620.394 119568.7966 143409.7138 175624.3414 183116.1486 0.99194959 0.828900919 0.949210272 0.497110607 1.234631389 0.90991644 0.652966969 0.783162571 0.95908713 1 17.4823995 1.079558673 6.011014813 0.99889203 0.847828642 0.065768628 0.187114954 0.505098336 26.98123415 0.173726637 0.043714093 12.01043324 -1.079558673 -0.151063388 PGMYPDPHS(ph)PFAVS(ph)PIPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PGMYPDPHSPFAVSPIPGR 19 0 P41162 P41162 ETV3 ETS translocation variant 3 2 PGMYPDPHS(1)PFAVS(1)PIPGR;PGMY(0.003)PDPHS(0.997)PFAVS(1)PIPGR;PGMY(0.001)PDPHS(0.999)PFAVS(1)PIPGR 99.366 0.00042668 269926000 510120 325567 447522 392351 594550 874430 675710 508090 555280 336902 TRUE FALSE 530259.9315 381480.5997 459184.791 469956.8567 493488.6034 671356.8846 622746.0846 501279.8846 535295.5813 402911.4965 1.316070492 0.946809915 1.139666639 1.166402202 1.224806459 1.666263908 1.545615079 1.24414391 1.328568646 1 18.62010345 2.988508355 22.19975092 1.383681367 1.136533075 0.224614252 0.185721692 162.6229555 314161.1515 0.054805173 0.061326678 973.886522 -2.988508355 -0.247148292 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 PGPTPS(0.005)GT(0.005)NVGS(0.148)S(0.148)GRS(0.692)PS(0.002)K;PGPTPSGTNVGSS(0.001)GRS(0.998)PSK;PGPTPSGTNVGS(0.01)S(0.158)GRS(0.817)PS(0.015)K 186.69 1.21E-14 1930240000 663173 306722 369777 378668 666659 849210 605659 353951 434308 309989 TRUE FALSE 689355.5821 359399.1175 379413.6924 453567.4002 553340.5413 651993.8474 558185.865 349206.8658 418677.3399 370725.4095 1.859477566 0.969448299 1.023435898 1.223459166 1.492588658 1.758697491 1.505658503 0.941955574 1.12934622 1 18.49999148 1.725977917 9.155612942 1.031429303 1.383175802 0.288895093 0.27205282 0.153855786 40.60565331 0.13878916 0.074559712 53.20812039 -1.725977917 0.351746499 PGPYDRPGTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PGPYDRPGTAR 11 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 81.525 0.01955 87943000 72201 58192 64561 71416 74023 113850 92005 56688 69654 53553 FALSE TRUE 75051.55123 68186.02333 66243.5127 85541.87164 61440.5969 87410.06291 84793.40769 55928.19008 67147.16615 64045.68502 1.171843992 1.06464664 1.034316561 1.335638328 0.959324533 1.364807994 1.323951921 0.873254616 1.048426075 1 15.96681375 1.720455598 12.8432021 0.972181372 1.17390923 0.33028554 0.133793062 0.129302101 68.08698604 0.062286063 0.034182928 52.53583003 -1.720455598 0.201727858 PGS(ph)LPLNAEACWPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PGSLPLNAEACWPK 14 0 Q01581;D6RIW1 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 PGS(1)LPLNAEACWPK 113.4 0.00056434 99586000 217080 98318 138340 80330 178260 222910 184370 116630 159600 89380 TRUE FALSE 225650.486 115203.3517 141945.254 96219.03424 147959.4289 171142.5307 169918.5976 115066.7656 153856.0272 106892.2997 2.111007871 1.077751643 1.327927778 0.900149351 1.384191651 1.601074457 1.589624305 1.076473852 1.439355572 1 16.7057984 7.99999884 0.028872743 2.74E-10 3.247865729 0.130838183 0.320662173 3928.830476 8.701439327 317.2198652 745.2204414 99999732.81 -7.99999884 3.247865729 PGS(ph)WLHRVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PGSWLHRVPR 10 1 Q96KV7-3;Q96KV7-5 Q96KV7-3 1 PGS(1)WLHRVPR 52.278 0.091539 236980000 67858 162000 139160 165470 151680 191550 146560 174560 144020 122960 TRUE FALSE 70537.08624 189822.2398 142786.6239 198199.4721 125897.4878 147065.4155 135072.2442 172220.3087 138836.7483 147051.6578 0.47967556 1.29085413 0.970996356 1.347822086 0.856144634 1.000093557 0.918536018 1.171155166 0.944135894 1 17.16596352 4.753643674 24.53854212 1.058234175 0.479675024 0.555784931 0.154428158 1537.683572 2501594.261 0.034477419 0.797122273 56707.91424 -4.753643674 -0.578559151 PGSGAAAS(ph)GGRGDLPYGPGRRS(ph)SGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PGSGAAASGGRGDLPYGPGRRSSGGGGR 28 3 P54826 P54826 GAS1 Growth arrest-specific protein 1 2 PGS(0.002)GAAAS(0.951)GGRGDLPY(0.142)GPGRRS(0.477)S(0.428)GGGGR;PGS(0.002)GAAAS(0.989)GGRGDLPY(0.109)GPGRRS(0.477)S(0.424)GGGGR 88.744 0.0047102 2594930000 33129 414230 467990 513710 423760 561150 424170 484010 456220 464360 TRUE FALSE 34436.9585 485370.7802 480186.2039 615320.3047 351729.4266 430831.4168 390922.447 477522.6376 439800.7313 555342.4513 0.062010312 0.874002661 0.864666842 1.108001564 0.633355915 0.775794135 0.703930424 0.859870583 0.791945097 1 19.08301816 4.74028041 24.85682887 0.8359439 0.06201003 0.766858818 0.12953729 64.67693235 934716.4719 0.030446361 0.195138701 54989.5809 -4.74028041 -0.773933869 PGWLSS(ph)PTLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 PGWLSSPTLGR 11 0 Q5XPI4;Q5XPI4-2;C9JS59;C9J266 Q5XPI4 RNF123 E3 ubiquitin-protein ligase RNF123 1 PGWLS(0.006)S(0.992)PT(0.002)LGR;PGWLS(0.001)S(0.999)PT(0.001)LGR;PGWLS(0.018)S(0.981)PT(0.002)LGR;PGWLS(0.002)S(0.998)PTLGR;PGWLS(0.238)S(0.761)PT(0.001)LGR;PGWLS(0.028)S(0.971)PT(0.001)LGR;PGWLSS(0.999)PT(0.001)LGR;PGWLS(0.036)S(0.962)PT(0.002)LGR 260.97 1.20E-20 2195474000 3390850 2353370 3115790 2707610 3878380 4965990 3936000 2841780 3087410 1850510 TRUE FALSE 3524723.376 2757542.991 3196990.047 3243167.177 3219134.353 3812714.083 3627486.035 2803690.587 2976294.717 2213082.004 1.592676353 1.246019346 1.44458725 1.46545278 1.454593344 1.722807413 1.639110538 1.266871531 1.344864181 1 21.07762548 -0.105031542 8.181551281 1.000000068 1.458062583 0.473063827 0.146822178 10081906.16 1232273.164 0.148180485 0.035939047 0.785178606 0.105031542 0.458062514 PIPEAEEAQRPEPVGTSSNADS(ph)ASPDLGPRGPDLAVLQAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PIPEAEEAQRPEPVGTSSNADSASPDLGPRGPDLAVLQAER 41 2 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 PIPEAEEAQRPEPVGT(0.003)S(0.003)S(0.003)NADS(0.495)AS(0.495)PDLGPRGPDLAVLQAER 54.52 0.011942 34756000 13340 14512 15719 9208.2 24635 23793 10363 15986 14886 23222 TRUE FALSE 13866.6735 17004.32311 16128.65005 11029.55448 20447.5515 18267.43634 9550.720981 15771.73382 14350.25577 27771.90629 0.499305786 0.612285053 0.580754158 0.397147908 0.736267482 0.657766743 0.343898646 0.567902457 0.516718428 1 14.76133859 -1.345903883 3.328935366 1.003007441 0.54599904 0.605820243 0.109915629 20272290.88 29146174.84 600815.4395 0.02670976 0.045091649 1.345903883 -0.457008401 PIPEAEEAQRPEPVGTSSNADSAS(ph)PDLGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PIPEAEEAQRPEPVGTSSNADSASPDLGPR 30 1 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 PIPEAEEAQRPEPVGTSSNADS(0.001)AS(0.999)PDLGPR;PIPEAEEAQRPEPVGTSSNADS(0.001)AS(0.999)PDLGPR;PIPEAEEAQRPEPVGTSSNADSAS(1)PDLGPR;PIPEAEEAQRPEPVGTSSNADS(0.002)AS(0.998)PDLGPR 278.2 1.18E-71 2553330000 541630 433713 574090 447375 652360 906930 773650 555861 595010 344144 TRUE FALSE 563013.9706 508199.8339 589051.257 535864.4397 541472.0802 696309.2522 713009.2914 548410.5925 573595.7063 411572.4278 1.367958426 1.234776189 1.431221378 1.301993048 1.315617966 1.691826773 1.732402958 1.332476511 1.393668933 1 18.65078681 THKPDPGT(ph)PQHTSSRPPEPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THKPDPGTPQHTSSRPPEPQK 21 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 THKPDPGT(1)PQHTSSRPPEPQK;THKPDPGT(1)PQHTSSRPPEPQK 120.85 3.08E-05 142138000 41806 169403 214605 195018 209871 323030 228351 258774 207423 158745 TRUE FALSE 43456.53316 198496.6475 220197.7826 233591.9783 174197.2024 248011.1781 210452.2519 255305.5578 199957.8867 189848.0434 0.228901665 1.045555403 1.159863324 1.230415516 0.91756122 1.306366785 1.108530002 1.344788986 1.053252292 1 17.5344856 4.747234514 3.224509553 1.160186218 0.085529738 0.821892895 0.126174555 0.12769118 2.07685218 0.029394557 0.348035973 55877.18439 -4.747234514 -1.07465648 down PIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PISPGLSYASHTVGFTPPTSLTR 23 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 PIS(0.98)PGLS(0.008)Y(0.001)AS(0.008)HT(0.004)VGFT(0.993)PPT(0.003)S(0.002)LT(0.002)R 89.396 0.010381 100480000 43576 43044 68523 66294 75083 93773 110600 74666 75803 59550 TRUE FALSE 45296.41413 50436.47216 70308.76567 79406.75533 62320.41848 71995.64189 101930.883 73665.2244 73074.86484 71217.68235 0.636027636 0.708201538 0.987237486 1.114986513 0.875069455 1.010923685 1.431258076 1.034367056 1.026077547 1 16.11994787 4.217089027 2.527353191 1.081139399 0.638108216 0.575046223 0.135411123 0.201907356 2.538032521 0.036674049 0.120102594 16485.00285 -4.217089027 -0.443031183 PIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_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(0.997)PGLS(0.003)YASHTVGFTPPTSLTR 144.29 9.79E-08 2199740000 238874 224089 294610 309430 385230 393420 439990 311180 332280 213369 TRUE FALSE 248304.93 262574.5426 302287.7786 370634.3304 319748.7422 302054.1673 405502.4341 307009.1411 320321.3077 255174.5704 0.973078664 1.028999646 1.184631283 1.452473614 1.253058805 1.183715787 1.58911773 1.203133763 1.255302624 1 17.96112504 4.149503265 3.181525989 1.295077952 0.991364957 0.340035454 0.1499608 0.233831384 4.656719863 0.036275457 0.096076934 14109.22845 -4.149503265 -0.303712995 PIT(ph)PVYTVAPNVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PITPVYTVAPNVQR 14 0 B7Z8Z7;A0AV96;A0AV96-2 B7Z8Z7 RBM47 RNA-binding protein 47 1 PIT(1)PVYTVAPNVQR 145.49 9.57E-05 96007000 136390 90609 117190 80796 181620 169050 109900 120680 142560 102950 TRUE FALSE 141774.7825 106170.3909 120244.0677 96777.20765 150748.2973 129790.6995 101285.7508 119062.482 137429.2934 123121.0814 1.151506963 0.862325036 0.976632647 0.786032794 1.224390621 1.054171211 0.822651569 0.967035707 1.116212527 1 16.90971828 3.278218069 24.99992128 1.011779759 0.940603961 0.08430176 0.131001946 501.3226288 316028.535 0.036739385 0.049744555 1897.658537 -3.278218069 -0.071175798 PKEGDDR ddPTM_MDA-MB-175_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 195930000 239150 236450 290610 360180 445340 424150 554090 318640 286210 275230 FALSE TRUE 248591.8267 277058.4482 298183.5353 431422.529 369641.2659 325647.5906 510658.978 314369.152 275909.358 329156.0489 0.755240037 0.841723702 0.905903253 1.310692999 1.122997032 0.989341049 1.55141909 0.955076332 0.838232683 1 18.32841218 3.945287539 5.952374113 1.120657514 0.814638147 0.311708769 0.191087957 0.238082681 18.85150593 0.049344 0.092358889 8816.323934 -3.945287539 -0.306019367 PKPSS(ph)SPVIFAGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPS(0.075)S(0.467)S(0.458)PVIFAGGQDR 78.413 0.012842 209640000 195540 107240 142220 123740 157620 188770 197980 137890 160160 90838 TRUE FALSE 203260.0702 125657.6358 145926.37 148215.4027 130827.8087 144931.0283 182461.8103 136041.8101 154395.8729 108635.9669 1.871020031 1.15668539 1.343260195 1.364330865 1.204277114 1.33409802 1.679570914 1.252272281 1.42122243 1 16.7291423 PKPSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PKPS(0.026)S(0.118)S(0.856)PVIFAGGQDR 125.04 4.80E-05 179430000 316790 175060 277980 230580 303060 306410 373610 229160 257800 158600 TRUE FALSE 329297.1138 205125.1932 285224.3872 276188.0358 251545.9695 235250.9212 344325.472 226088.485 248521.8284 189674.6334 1.736115726 1.081458229 1.503756101 1.456114773 1.326197209 1.240286679 1.815348029 1.191980609 1.310253374 1 17.53316722 0.942831823 1.492871059 1.008244833 1.420773168 0.267076982 0.215170592 0.607429805 2.740970856 0.188208852 0.055465526 8.766612754 -0.942831823 0.412528335 PLELELCPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PLELELCPGR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;; 152.47 4.18E-05 489560000 446498 335102 430010 358768 592277 645420 520771 407435 449311 344332 FALSE TRUE 464126.0858 392653.1618 441216.4139 429731.2396 491601.9671 495530.9864 479951.6082 401974.0003 433140.3849 411797.2628 1.127074237 0.953510859 1.071440861 1.0435505 1.193796102 1.203337252 1.16550461 0.976145391 1.051829199 1 18.65157471 1.713854807 10.5274274 1.011565009 1.105354618 0.280214182 0.072512451 0.165378734 45.35115267 0.038017856 0.020628748 51.74338154 -1.713854807 0.093789609 PLENLEEEGLPKNPDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PLENLEEEGLPKNPDLR 17 1 Q15008;Q15008-4;C9J7B7 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ; 120.24 7.38E-05 229540000 231170 168605 188071 147256 268650 301440 216892 196556 239260 132950 FALSE TRUE 240296.7701 197561.5972 192972.2848 176382.7973 222984.969 231435.1284 199891.4383 193921.4883 230649.0793 158999.007 1.511309879 1.242533528 1.213669748 1.109332697 1.402429947 1.455575935 1.257186709 1.219639619 1.4506322 1 17.27865823 -1.516436604 5.724265855 0.999481341 1.304037549 0.363555441 0.125009533 0.000827857 6.99E-05 0.121098408 0.028495899 0.030448324 1.516436604 0.304556207 PLHISTFINELDSGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PLHISTFINELDSGFR 16 0 E9PGT1;Q15631 E9PGT1 TSN Translin 0 116.96 0.00038707 104210000 37203 85388 97348 122260 101420 132550 109210 113650 96339 86037 FALSE TRUE 38671.80317 100052.7248 99884.96885 146442.6631 84180.66463 101767.2713 100649.8348 112126.7076 92871.77821 102894.3029 0.375840081 0.972383523 0.970753152 1.42323393 0.818127557 0.989046706 0.978186664 1.089727074 0.902593979 1 16.65080358 4.753107865 3.450734173 1.029355953 0.283004012 0.618803441 0.151042873 0.20543222 4.090500114 0.035455057 0.409220676 56637.99427 -4.753107865 -0.746351941 PLMPY(ph)MRYS(ph)RK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PLMPYMRYSRK 11 2 Q969G3;Q969G3-4;Q969G3-2;B4DGM3;Q969G3-5;A0A2R8Y855;A0A2R8Y7I9;A0A2U3TZQ7;J3QKS7;J3QR61;J3QKX6;A0A2R8YEB8 Q969G3 SMARCE1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 2 PLMPY(0.5)MRY(0.5)S(0.999)RK 66.595 0.018382 265410000 98676 411830 426650 426280 359150 509040 358460 389430 427710 450060 TRUE FALSE 102571.8047 482558.5989 437768.8495 510596.9117 298101.8113 390823.1746 330362.9685 384210.3278 412316.8006 538240.6401 0.190568673 0.896548055 0.813332954 0.948640578 0.553844859 0.726112347 0.613783026 0.713826306 0.766045464 1 19.0378918 -4.999998407 0.327753794 3.967458832 0.690916737 0.180713915 0.20074785 626.7701078 5.449453194 1294.266108 0.162980073 1.00E-05 4.999998407 -3.276542095 PLPKGT(ph)MMETLSR ddPTM_MDA-MB-175_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 55.66 0.06911 924880000 838770 506470 678510 466810 910400 914110 857360 694000 760540 395970 TRUE FALSE 871885.2873 593452.2827 696192.528 559143.6247 755650.5332 701821.806 790157.8829 684698.0652 733168.314 473552.7402 1.841157728 1.253191529 1.470147819 1.180742032 1.595705122 1.482035149 1.668574196 1.445874994 1.548229483 1 18.85316558 -0.92359422 8.244424505 1.000036458 1.487676238 0.406956225 0.180080057 2.42E-09 4.94E-18 0.162343816 0.038264805 0.119235556 0.92359422 0.48763978 PLPPAAIES(ph)PAVAAPAYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PLPPAAIESPAVAAPAYSR 19 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR;PLPPAAIES(1)PAVAAPAYSR 217.67 3.72E-19 614228000 112594 96239 107846 121786 122392 147817 152374 104150 123671 116894 TRUE FALSE 117039.2981 112767.2996 110656.5554 145874.9073 101587.8516 113488.7419 140430.5277 102754.0396 119220.1049 139797.1412 0.837208093 0.80664954 0.791550917 1.043475611 0.726680465 0.811810177 1.004530754 0.735022467 0.852807889 1 17.09297533 -1.801149417 2.30857308 1.054478361 0.843159071 0.181631425 0.098252706 10433200.8 6261377.293 3178411.302 0.02553257 0.015807041 1.801149417 -0.211319289 PLT(ph)SPESLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PLTSPESLSR 10 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 PLT(0.5)S(0.5)PESLSR 108.31 0.024234 87488000 145340 108660 134000 132770 174720 225980 202050 139400 150230 90873 TRUE FALSE 151078.1354 127321.5097 137492.1501 159031.5097 145021.1568 173499.5698 186212.793 137531.571 144823.2516 108677.8245 1.390146851 1.171550041 1.265135282 1.463329897 1.334413506 1.596457884 1.713438725 1.265498014 1.33259248 1 16.72969807 3.751529135 22.56887542 1.414690995 1.265204582 0.053034598 0.188798495 477.8896106 831653.2856 0.047634412 0.084987415 5643.247982 -3.751529135 -0.149486413 PLTS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 PLTSPLR 7 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 PLT(0.025)S(0.975)PLR;PLT(0.03)S(0.97)PLR;PLT(0.026)S(0.974)PLR;PLT(0.021)S(0.979)PLR;PLT(0.192)S(0.808)PLR 145.65 0.0023836 857779000 2166610 1568280 1949130 1768010 2806200 3182820 2881190 1967980 2103560 1498990 TRUE FALSE 2252149.436 1837619.89 1999925.929 2117717.101 2329203.126 2443658.291 2655354.799 1941602.447 2027853.287 1792688.391 1.256297217 1.025063753 1.11560154 1.18130798 1.299279417 1.36312496 1.481213809 1.083067452 1.131180018 1 20.77369331 5.078311415 20.17656477 1.200268919 3.386917855 0.012552706 0.145635584 3073.904175 820701.1598 0.035386259 11035.77945 119759.8973 -5.078311415 2.186648935 PMFIVNTNVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PMFIVNTNVPR 11 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 ; 215.93 2.90E-11 1311650000 443160 293770 334830 243548 476890 748520 474170 333370 295890 248820 FALSE TRUE 460656.299 344222.7123 343555.9449 291721.0675 395828.4081 574687.5739 437003.3164 328901.7204 285240.9767 297571.5151 1.548052403 1.156773061 1.154532364 0.980339356 1.330195896 1.931258689 1.468565687 1.105286305 0.958562773 1 18.18287691 1.570571892 4.491356573 0.993552919 1.355260406 0.299808039 0.245998521 0.235972429 10.52526299 0.160754367 0.070924219 37.20248004 -1.570571892 0.361707487 PMS(ph)SEELPLASSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PMSSEELPLASSWR 14 0 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 PMS(0.947)S(0.053)EELPLASSWR;PMS(0.965)S(0.035)EELPLASSWR 120.54 0.00012935 37515000 50202 43522 60111 47545 54028 101824 66794 72573 55322 51597 TRUE FALSE 52184.01372 50996.56495 61677.54204 56949.25909 44844.33986 78176.91916 61558.51175 71600.27764 53330.97203 61706.44427 0.845681749 0.826438236 0.999531617 0.922906185 0.726736735 1.26691661 0.997602641 1.160337117 0.864269083 1 15.91313354 2.747649292 24.99588143 1.070256843 0.872931098 0.394111379 0.119263272 655.0952808 1801657.58 0.035195342 0.036864226 559.3057602 -2.747649292 -0.197325745 PNWGGGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PNWGGGKK 8 1 P21291;E9PS42;E9PP21;A0A087X134 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ; 81.642 0.035807 1133710000 1448510 750460 1096460 739400 1488150 1339340 1299220 1082240 1301090 722830 FALSE TRUE 1505698.293 879345.6672 1125034.648 885651.1131 1235194.795 1028298.583 1197383.742 1067734.343 1254264.025 864454.6991 1.741789703 1.017225851 1.301438525 1.024519982 1.42887163 1.189534378 1.385131856 1.235153611 1.450930889 1 19.72143084 -2.162481614 2.454048026 0.272867291 1.290304484 0.165587015 0.204050576 10279675.27 3532362.76 41360474.65 0.045607001 0.00687889 2.162481614 1.017437193 PPQDQS(ph)VIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PPQDQSVIK 9 0 Q58EX2-2;Q58EX2-3;Q58EX2;Q58EX2-4 Q58EX2-2 SDK2 Protein sidekick-2 1 PPQDQS(1)VIK;PPQDQS(1)VIK;PPQDQS(1)VIK 78.655 0.030584 40245000 19094.7 147309 148731 152262 145507 179161 140739 153373 155295 173864 TRUE FALSE 19848.5735 172608.1748 152607.052 182378.9691 120773.7721 137553.573 129707.5094 151317.2858 149705.9633 207929.322 0.095458271 0.830129071 0.733937141 0.877120011 0.580840504 0.661540045 0.623805763 0.727734234 0.719984858 1 17.66573369 -5 0.04701784 2.241556111 2.43E-14 0.291172561 0.192971462 942.640731 3.28901168 155.7527067 38.08456206 1.00E-05 5 -2.241556111 PQRS(ph)RPNLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PQRSRPNLIK 10 2 Q9NWF9-1 Q9NWF9-1 RNF216 E3 ubiquitin-protein ligase RNF216 1 PQRS(1)RPNLIK 60.518 0.076841 939070000 1157800 745980 974640 665930 1411700 1172300 995440 999930 1144200 865210 TRUE FALSE 1203510.838 874096.2621 1000039.919 797648.9664 1171739.738 900051.0914 917414.8117 986527.5739 1103020.466 1034731.334 1.163114326 0.844756734 0.966473022 0.770875434 1.132409641 0.869840375 0.886621272 0.953414226 1.065996969 1 19.98082479 1.32592661 6.656486459 1.032065174 0.940190791 0.075266505 0.116264766 0.469004241 28.3179377 0.074085263 0.026616392 21.18003191 -1.32592661 -0.091874383 PQS(ph)PS(ph)IPSS(ph)HLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PQSPSIPSSHLR 12 0 Q9P2P6;H3BN21 Q9P2P6 STARD9 StAR-related lipid transfer protein 9 3 PQS(0.999)PS(0.999)IPS(0.022)S(0.98)HLR 45.14 0.094313 73531000000 773270 19932000 15315000 17183000 11738000 19693000 9329500 16482000 12928000 21834000 TRUE FALSE 803799.2967 23355165.95 15714121.48 20581746.11 9742778.953 15119599.2 8598229.412 16261085.75 12462723.81 26111954.26 0.030782809 0.894424282 0.601797986 0.788211633 0.373115656 0.579029783 0.32928326 0.622744877 0.477280393 1 24.6382071 -1.22010382 3.185073407 1.001458921 0.538260513 0.275639593 0.231162597 23537508.47 33369537.71 352197.9347 0.053609356 0.060241556 1.22010382 -0.463198409 PQS(ph)PSIPSS(ph)HLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PQSPSIPSSHLR 12 0 Q9P2P6;H3BN21 Q9P2P6 STARD9 StAR-related lipid transfer protein 9 2 PQS(0.5)PS(0.5)IPS(0.022)S(0.978)HLR 48.513 0.093209 10703000000 46660 3887900 2598300 3395100 2125600 4068900 1380800 3122000 2057700 3812500 TRUE FALSE 48502.17283 4555616.581 2666013.833 4066640.647 1764291.271 3123959.64 1272569.288 3080154.697 1983643.779 4559486.38 0.01063764 0.999151264 0.584718016 0.89190762 0.386949565 0.685156042 0.279103649 0.675548612 0.435058604 1 22.12043989 -1.516059139 3.137244419 1.012977611 0.569447293 0.190281849 0.275941801 142684120.7 163021303.6 15823067.22 0.060069199 0.0304748 1.516059139 -0.443530318 PQTS(ph)PSPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PQTSPSPKR 9 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 PQT(0.168)S(0.823)PS(0.009)PKR 94.465 0.0092194 46739000 156990 67622 102120 67692 157560 162580 126710 93155 121300 53350 TRUE FALSE 163188.0864 79235.55247 104781.3311 81081.27556 130778.0075 124823.2589 116778.1391 91906.4096 116934.4367 63802.91105 2.557690295 1.241879895 1.64226568 1.270808404 2.049718505 1.956388147 1.830294844 1.44047361 1.832744537 1 15.96133463 -2.315871108 0.408270733 1.24E-13 1.743655042 0.266815909 0.374204589 91.88102672 4.761741881 83.21228118 0.218647811 0.004832022 2.315871108 1.743655042 PQYQTWEEFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PQYQTWEEFSR 11 0 P49458;Q6P2S0;Q659G3;E9PE20;P49458-2 P49458 SRP9;DKFZp564M2223 Signal recognition particle 9 kDa protein 0 ; 193.52 2.13E-06 754080000 355910 270244 344460 230780 479610 429110 432950 342260 417420 222219 FALSE TRUE 369961.6016 316656.3048 353436.9106 276427.5952 398086.0635 329455.7057 399014.2477 337672.5645 402397.1357 265758.5584 1.39209666 1.191518748 1.329917323 1.0401456 1.497923777 1.239680512 1.501416361 1.270599022 1.514145539 1 18.01975663 3.219377442 24.99999475 1.351799854 1.241604916 0.071778709 0.16928152 567.3032776 739321.9519 0.044448151 0.053204844 1657.209607 -3.219377442 -0.110194938 PRPATS(ph)TPDLASHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PRPATSTPDLASHR 14 1 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 PRPAT(0.183)S(0.785)T(0.031)PDLASHR 74.732 0.019515 155240000 56908 41648 48864 39066 66563 68416 56738 50337 56499 55668 TRUE FALSE 59154.77178 48800.72002 50137.43598 46793.1382 55248.64504 52527.42085 52290.7273 49662.31485 54465.61203 66575.07877 0.888542272 0.733017834 0.753096157 0.702862679 0.829869766 0.788995249 0.785439961 0.745959536 0.818108112 1 16.02269461 0.880322614 5.194089554 0.999993925 0.77486574 0.640676633 0.049512441 0.6634726 28.23342881 0.045386697 0.011458099 7.59141291 -0.880322614 -0.225128185 PRPPGRPVS(ph)GHGMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 PRPPGRPVSGHGMDSR 16 2 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR;PRPPGRPVS(1)GHGMDSR 122.19 4.94E-05 4733290000 559598 420324 596870 613881 816948 946430 1020552 658114 767309 435159 TRUE FALSE 581691.3611 492511.3773 612424.9225 735304.8295 678083.4708 726635.9758 940558.4675 649293.0583 739693.699 520420.0744 1.117734288 0.946372751 1.176789583 1.412906353 1.302954102 1.396248937 1.807306278 1.247632615 1.421339674 1 18.98931709 3.911172345 3.187737852 1.396322464 1.032854786 0.328376573 0.19348203 0.251108754 4.877164631 0.049207602 0.102340384 8150.276549 -3.911172345 -0.363467678 PS(ph)DWWVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PSDWWVVK 8 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 PS(1)DWWVVK 63.159 0.078751 292300000 29739 223030 175340 196450 105400 223280 123860 168410 150920 302200 TRUE FALSE 30913.11868 261333.6676 179909.5044 235307.2237 87484.14565 171426.6038 114151.5296 166152.7394 145488.4187 361410.304 0.085534691 0.723094125 0.497798492 0.651080561 0.24206323 0.47432683 0.315850235 0.459734373 0.402557473 1 18.46327811 -1.26029995 3.804923926 1.000858851 0.437988738 0.485702005 0.176308704 9363615.467 6203394.276 61569.66374 0.03870276 0.054916146 1.26029995 -0.562870113 PSATSHSGSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PSATSHSGSGSK 12 0 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ;; 148.28 6.63E-05 119029000 106992 137805 204367 140735 258755 223517 233296 200466 218787 140230 FALSE TRUE 111216.1268 161471.9368 209692.9719 168571.9629 214771.9175 171608.5642 215009.6499 197779.0812 210912.8986 167705.3836 0.663163724 0.962830967 1.250365178 1.005167272 1.280650107 1.023274032 1.282067667 1.17932458 1.257639403 1 17.35556948 4.598031276 2.567915564 1.167354923 0.626697885 0.661276414 0.109370168 0.193177711 1.968190132 0.024814882 0.195007893 39630.65739 -4.598031276 -0.540657038 PSHLTNKFEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PSHLTNKFEDK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 180.18 4.07E-06 335360000 714500 369010 669130 461460 856520 771230 901270 633240 658680 334950 FALSE TRUE 742709.0117 432384.597 686568.0775 552735.4107 710929.0363 592123.5206 830626.1024 624752.4536 634974.2355 400577.0395 1.85409781 1.079404345 1.713947655 1.37984796 1.774762321 1.478176386 2.073573921 1.559631212 1.585148855 1 18.6117202 0.567240699 2.907115005 1.000011379 1.611481085 0.335559785 0.2582053 9.477242289 62.22108689 0.23317523 0.061133812 3.691821541 -0.567240699 0.611469706 PSMS(ph)PTPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PSMSPTPLDR 10 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 PS(0.197)MS(0.79)PT(0.013)PLDR;PS(0.007)MS(0.956)PT(0.037)PLDR 113.69 0.0056885 409460000 546610 386820 482110 462320 585410 774460 716960 498740 492230 311567 TRUE FALSE 568190.5849 453253.326 494674.1827 553765.5161 485902.2173 594603.4021 660762.8018 492055.2061 474514.7385 372612.5883 1.524882955 1.216419789 1.32758312 1.48616964 1.304041335 1.595768422 1.773323882 1.320554435 1.27348016 1 18.50731689 0.985652495 2.100272326 1.005925177 1.447846087 0.449241366 0.153538548 0.315586054 3.007261377 0.152306818 0.042293606 9.675033883 -0.985652495 0.441920911 PSSS(ph)PVIFAGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PSSSPVIFAGGQDR 14 0 Q15366;Q15366-6;H3BSS4;Q15366-2;Q15366-3 Q15366;Q15366-2 PCBP2 Poly(rC)-binding protein 2 1 PSS(0.013)S(0.987)PVIFAGGQDR 161.21 4.86E-06 214680000 310970 206910 280760 249000 328310 470460 389690 273920 277980 174250 TRUE FALSE 323247.3357 242445.183 288076.8362 298251.4568 272503.9835 361202.7949 359145.0795 270248.5504 267975.5541 208390.9513 1.551158214 1.163415117 1.382386493 1.431211168 1.307657467 1.733294045 1.723419742 1.296834382 1.285927016 1 17.66893311 0.991550767 1.857729097 1.007902305 1.453762739 0.405062382 0.170114336 0.380309334 2.750737029 0.169173052 0.047980209 9.807329503 -0.991550767 0.445860435 PSTGAMGDRLTAMKAAFQS(ph)QYKS(ph)HFVAASLSNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PSTGAMGDRLTAMKAAFQSQYKSHFVAASLSNQK 34 3 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 2 PS(0.008)T(0.008)GAMGDRLT(0.032)AMKAAFQS(0.892)QY(0.2)KS(0.779)HFVAAS(0.041)LS(0.04)NQK 41.287 0.081292 650370000 90254 142060 354700 136320 551880 222320 545030 292980 391350 61761 TRUE FALSE 93817.29761 166457.6999 363943.7734 163283.6891 458071.6347 170689.5493 502309.1244 289053.0823 377265.3899 73861.88546 1.270171984 2.253634589 4.927355579 2.210662348 6.201732217 2.310928677 6.800653967 3.913426803 5.107714047 1 16.17254247 4.384624889 4.408959773 4.233821106 1.47054138 0.221026993 1.737148359 0.243999514 8.265251592 0.38478993 1.179198857 24245.15078 -4.384624889 -2.763279726 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_MDA-MB-175_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 307.08 3.84E-63 6045640000 1703550 1282460 1767240 1469608 2302320 2851020 2298210 1726640 1934160 1299558 TRUE FALSE 1770807.469 1502712.529 1813295.726 1760292.076 1910972.469 2188913.813 2118070.295 1703497.215 1864549.959 1554181.509 1.139382665 0.966883546 1.166720693 1.132616793 1.229568399 1.408402944 1.362820419 1.096073532 1.199698973 1 20.56772357 3.717774163 1.79703809 1.227709356 1.061406152 0.181173673 0.12018793 0.544977784 3.413191508 0.036150774 0.077585933 5221.246091 -3.717774163 -0.166303204 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PTGDFDSKPSWADQVEEEGEDDKCVTSELLK 31 2 O75821;K7ENA8;K7ER90;K7EL20;K7EL60;K7ENH0 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 308.03 9.34E-93 88058000 356100 53291 124190 52029 226530 232000 199870 118890 146080 42571 FALSE TRUE 370159.103 62443.3147 127426.4934 62320.18091 188024.5115 178121.516 184203.6671 117296.474 140822.6093 50911.97238 7.270570863 1.22649569 2.502878743 1.224077128 3.693129587 3.49861747 3.618081534 2.303907481 2.766001841 1 15.63571734 0.612373202 0.991342684 1.004615679 3.090078572 0.141179048 1.614583525 2.635769848 4.161871197 1.471073171 0.472251325 4.096125005 -0.612373202 2.085462893 PTRPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 PTRPDK 6 1 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 77.374 0.066201 303830000 345230 180026 275680 213618 372820 371550 423390 271240 327770 167232 FALSE TRUE 358859.947 210944.0651 282864.4473 255871.0028 309448.1896 285263.1434 390203.5855 267604.4715 315973.6217 199997.9085 1.794318499 1.054731355 1.414337026 1.279368393 1.547257128 1.426330632 1.95103833 1.338036349 1.57988463 1 17.60962539 3.226625984 24.66470744 1.510255476 1.364095292 0.010989995 0.280726076 570.9236029 1179896.994 0.075611072 0.091065807 1685.101185 -3.226625984 -0.146160184 PVS(ph)PSSLLDTAISEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PVSPSSLLDTAISEEAR 17 0 A0A0B4J2F2;P57059 A0A0B4J2F2 LOC102724428;SIK1 Serine/threonine-protein kinase SIK1 1 PVS(0.89)PS(0.085)S(0.024)LLDTAISEEAR 90.348 0.0040119 14547000 15736 14158 17675 14292 20861 27635 24093 17363 23130 13343 TRUE FALSE 16357.26943 16589.52637 18135.62502 17118.91494 17315.05467 21217.19006 22204.5277 17130.27739 22297.55582 15957.30538 1.025064636 1.039619533 1.13650924 1.072794844 1.085086376 1.329622361 1.391496069 1.073506897 1.397325882 1 13.96192943 2.823409624 7.595502797 1.241285424 1.072787313 0.318258608 0.121908131 0.348556375 27.74310876 0.035978277 0.038188323 665.9009339 -2.823409624 -0.16849811 PVS(ph)SAASVYAGAGGSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVS(0.5)S(0.5)AASVYAGAGGSGSR;PVS(0.443)S(0.443)AAS(0.115)VYAGAGGSGSR;PVS(0.25)S(0.25)AAS(0.25)VYAGAGGS(0.216)GS(0.033)R 267.46 2.94E-31 85039000 98919 84225 98743 79278 115734 125587 104651 93610 107066 79441 TRUE FALSE 102824.3985 98689.98857 101316.3237 94958.95178 96061.57602 96421.32254 96448.18117 92355.31107 103212.7156 95005.94296 1.082294384 1.038777002 1.066420905 0.999505387 1.011111232 1.0148978 1.015180505 0.972100357 1.086381676 1 16.53573014 3.741973106 24.95153795 1.010636982 1.06012539 0.361343439 0.029129475 289.1485151 2114205.083 0.007269421 0.012432259 5520.432532 -3.741973106 0.049488408 PVSS(ph)AASVYAGAGGSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.681)AAS(0.319)VYAGAGGSGSR 322.02 1.12E-61 258130000 306330 216900 296930 247430 365040 399300 362130 257120 291080 186520 TRUE FALSE 318424.1449 254150.8878 304668.2397 296370.9155 302990.6312 306568.6265 333745.3043 253673.727 280604.0877 223065.0229 1.427494732 1.139357863 1.365827039 1.328630153 1.358306324 1.374346469 1.496179455 1.137218752 1.257947499 1 17.76710479 1.005118782 1.184782697 1.010855359 1.340620659 0.497768569 0.103082991 0.408713503 1.188101432 0.094595676 0.029707457 10.11856165 -1.005118782 0.329765301 PVSSAASVYAGAGGS(ph)GSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 PVSS(0.198)AAS(0.167)VYAGAGGS(0.606)GS(0.029)R;PVSSAASVYAGAGGS(0.998)GS(0.002)R;PVSSAASVYAGAGGS(0.962)GS(0.038)R;PVSSAASVYAGAGGS(0.985)GS(0.015)R;PVSSAASVYAGAGGS(0.965)GS(0.035)R;PVSSAASVYAGAGGS(0.968)GS(0.032)R 347.14 2.95E-90 4262540000 1300701 959483 1241758 1030544 1492722 1730790 1508706 1117268 1314941 819534 TRUE FALSE 1352053.68 1124266.742 1274119.234 1234382.527 1238989.648 1328840.253 1390449.681 1102292.85 1267616.53 980105.9964 1.379497406 1.147086892 1.299981062 1.259437787 1.264138422 1.355812798 1.418672763 1.124666979 1.293346368 1 19.90257826 0.369135164 0.871201423 0.998840631 1.285913258 0.478766818 0.088333821 2.005143911 2.023330873 0.091884272 0.02798908 2.339565261 -0.369135164 0.287072627 PVVLS(ph)GPSGAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PVVLSGPSGAGK 12 0 B1ANH0;B1ANG9;Q16774;Q16774-2;B1ANH2;Q16774-3;B1ANH6;B1ANH5 B1ANH0 GUK1 Guanylate kinase 1 PVVLS(0.5)GPS(0.5)GAGK 60.436 0.096458 581750000 227660 196210 225450 198310 332410 266200 262470 235380 224890 245250 TRUE FALSE 236648.1926 229907.5412 231325.4122 237535.1261 275907.0669 204379.0843 241896.9156 232225.1161 216796.2528 293302.0419 0.806841272 0.783859327 0.788693494 0.809865232 0.940692622 0.696821212 0.824736555 0.791760994 0.739156984 1 18.16202759 -1.20819085 3.775417518 1.000203937 0.799547841 0.509341737 0.059447759 6441792.616 4134789.914 9953.918492 0.013192299 0.061916892 1.20819085 -0.200656096 PWIS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 70.919 0.035893 1704670000 224035 3831740 1915890 3076430 1277290 3135740 1142750 2106950 1333170 4530770 TRUE FALSE 232880.0748 4489811.538 1965819.667 3684938.672 1060176.702 2407511.908 1053178.269 2078709.782 1285189.472 5418487.635 0.042978796 0.828609723 0.362798589 0.680067746 0.195659153 0.444314368 0.194367569 0.383632837 0.237186012 1 22.3694588 -1.442168978 5.552669044 1.000491145 0.385303539 0.413083023 0.223370639 0.00124946 0.000125524 0.198973555 0.046862941 0.036126927 1.442168978 -0.615187606 PYHPPPLFPPS(ph)PQPPDSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 PYHPPPLFPPSPQPPDSTPR 20 0 P54259 P54259 ATN1 Atrophin-1 1 PYHPPPLFPPS(0.988)PQPPDS(0.006)T(0.006)PR 62.1 0.029041 141750000 145630 95820 129000 116630 172280 177020 177350 133930 160180 84220 TRUE FALSE 151379.5849 112276.3396 132361.846 139699.0659 142995.9071 135909.7878 163448.8436 132134.8874 154415.1531 100721.2965 1.502955086 1.114722939 1.314139617 1.386986375 1.41971869 1.349364955 1.622783356 1.311886284 1.533093382 1 16.62000923 5.066505334 21.31390958 1.359996243 5.243102901 0.063682085 0.172511344 1992.267161 657319.3141 0.037373516 10784.52768 116548.1365 -5.066505334 3.883106658 QAAAYGLGVMAQYGGDNYRPFCTEALPLLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAAAYGLGVMAQYGGDNYRPFCTEALPLLVR 31 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 105.84 0.00013377 90553000 3912.2 3004.8 5569 5421.3 6637.8 6758 4499.9 6404 2724.5 5520.3 FALSE TRUE 4066.656677 3520.851026 5714.132715 6493.616959 5509.509127 5188.556918 4147.18608 6318.164855 2626.445777 6601.897092 0.615983045 0.533308983 0.865528898 0.983598634 0.834534233 0.785919084 0.628180964 0.95702262 0.397831978 1 12.68866494 4.240677082 24.97955961 0.80989098 0.574645952 0.223642917 0.172762765 72.8258471 859468.5165 0.040321462 0.099901795 17405.12241 -4.240677082 -0.235245028 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAALGIMQMVEDTLIEHAHTKPLLPSQLVR 30 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 137.32 1.36E-06 427400000 454630 478260 548450 463710 535870 653080 551120 537160 520160 501730 FALSE TRUE 472579.1435 560397.4347 562743.0576 555430.454 444783.0088 501412.0675 507921.7743 529960.2488 501439.5432 600034.3873 0.787586767 0.933942198 0.937851346 0.925664371 0.741262531 0.835638887 0.846487776 0.883216462 0.835684677 1 19.19468566 -1.42197188 3.258588602 1.001789109 0.862059367 0.324843852 0.060974559 29487653.6 41328559.63 497529.7974 0.015045109 0.037846709 1.42197188 -0.139729742 QAAPPIELDAVWEDIRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAAPPIELDAVWEDIRER 18 1 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 271.72 5.28E-39 355333000 169215 209973 191521 167085 229696 251592 150637 177857 213230 275812 FALSE TRUE 175895.7389 246034.2294 196512.1946 200133.9143 190652.356 193163.5709 138829.6783 175473.1178 205555.894 329852.0807 0.533256418 0.74589261 0.595758542 0.606738372 0.577993492 0.585606647 0.420884652 0.531975173 0.623175981 1 18.33145968 0.867981552 6.639693785 0.999999321 0.573165022 0.734366776 0.076244579 1.997014304 100.3915865 0.078453294 0.019690315 7.378728866 -0.867981552 -0.426834299 QAAS(ph)PLEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;QAAS(1)PLEPK 143.55 0.00010666 639110000 2012470 1222420 1527470 1213470 1943010 2097080 1859270 1602740 1688950 1096790 TRUE FALSE 2091923.87 1432361.126 1567277.123 1453490.744 1612737.854 1610064.952 1713535.559 1581257.892 1628165.019 1311685.001 1.594837074 1.092000842 1.194857852 1.108109602 1.229516121 1.227478358 1.30636209 1.205516485 1.241277455 1 20.32298987 -2.529636934 1.19083166 3.43E-05 1.234041935 0.232910081 0.131872507 48819.92601 3487.649304 129614.1047 0.035467652 0.002953677 2.529636934 1.234007655 QAATMSEVEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAATMSEVEWR 11 0 Q9UHB9;Q9UHB9-4;Q9UHB9-2 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 75.416 0.046285 0 45093 41231 33169 36231 44601 48405 34733 31601 29981 39284 FALSE TRUE 46873.30646 48312.10352 34033.41139 43397.38366 37019.73795 37163.67233 32010.5367 31177.44028 28901.98967 46980.94766 0.997708833 1.028333951 0.724408789 0.923723037 0.787973419 0.791037094 0.681351448 0.663618804 0.615185327 1 15.51978819 4.322381944 0.61369409 0.717780741 1.134115676 0.33746161 0.119282318 2.196735505 0.883328801 0.057732387 0.60265076 21007.86624 -4.322381944 0.416334935 QACTAQT(ph)PEPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QACTAQTPEPLRR 13 1 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 QACTAQT(1)PEPLRR;QACT(0.001)AQT(0.999)PEPLRR;QACT(0.001)AQT(0.999)PEPLRR 125.41 0.00011752 736870000 320334 453420 428700 492960 443500 568960 390720 414710 403320 494640 TRUE FALSE 332981.0337 531291.3579 439872.2742 590466.0167 368114.0284 436827.6627 360094.3454 409151.4908 388804.592 591555.2375 0.562890855 0.89812637 0.743586137 0.998158717 0.62228175 0.738439346 0.608724803 0.691653906 0.657258304 1 19.17415336 QADFEAHNILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QADFEAHNILR 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;;;; 211.26 9.94E-09 1353590000 1922129 2287753 2152295 2177499 2483757 2785094 2173601 2245996 2108720 2631856 FALSE TRUE 1998016.137 2680656.782 2208385.576 2608201.803 2061568.872 2138298.127 2003228.474 2215892.097 2032827.579 3147517.793 0.634791054 0.851673273 0.70162767 0.828653553 0.654982436 0.679360139 0.636447069 0.704012572 0.645851021 1 21.5857831 -1.03076744 4.608319235 1.000009133 0.70675543 0.596893554 0.072908559 6783955.294 1517403.722 687.0786845 0.017162997 0.093160661 1.03076744 -0.293253703 QADLYISEGLHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QADLYISEGLHPR 13 0 P40227;Q92526-3;Q92526 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 ;;;; 157.86 3.99E-05 3359680000 2185610 3110320 2930260 3053870 3026330 3745030 2986030 3214220 3019510 3078500 FALSE TRUE 2271899.57 3644493.265 3006624.983 3657916.371 2511915.508 2875303.539 2751977.166 3171138.638 2910838.425 3681673.134 0.617083453 0.989901366 0.816646365 0.993547292 0.682275535 0.780977407 0.747480036 0.861330847 0.790629238 1 21.81193012 -1.777988234 7.669512114 1.003647513 0.816041938 0.202263969 0.113066658 0.006636088 0.000192097 0.103022411 0.023909127 0.016672924 1.777988234 -0.187605576 QADNPHVALYQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QADNPHVALYQAR 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1;Q9BST8;J3QQH7;J3QLE9 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 92.935 0.0026616 0 317840 427817 345485 386830 450849 531132 366289 314071 325520 444162 FALSE TRUE 330388.5686 501291.2418 354488.6229 463343.8194 374213.848 407784.6424 337578.3111 309861.392 313804.5988 531187.0399 0.621981607 0.943718886 0.667351792 0.872279978 0.704486028 0.767685602 0.635516844 0.583337636 0.590761022 1 19.01886042 2.246265934 23.99017891 0.657496354 0.769106776 0.002393106 0.143198053 211.8626788 659626.1699 0.046229559 0.037957906 176.3055299 -2.246265934 0.111610422 QAEEECAHRGS(ph)PLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAEEECAHRGSPLPK 15 1 H7C1J2;F2Z2A4;H7C1M5;Q9H147 H7C1J2;H7C1M5 DNTTIP1 Deoxynucleotidyltransferase terminal-interacting protein 1 1 QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK;QAEEECAHRGS(1)PLPK 186.9 2.20E-07 2095080000 2972340 2314850 2652840 2103270 3333570 3487970 2883600 2728560 2990510 2049790 TRUE FALSE 3089690.278 2712407.48 2721975.19 2519290.528 2766930.962 2677941.828 2657575.897 2691988.116 2882882.129 2451407.105 1.260374204 1.106469617 1.110372563 1.027691616 1.128711325 1.092410079 1.084102225 1.098139967 1.176011167 1 21.22517866 7.631483235 0.011931319 1.50E-07 2.377479315 0.282956957 0.058239605 12499.04137 12.21972016 1029.25441 1436.852203 42803889.6 -7.631483235 2.377479165 QAEELFHNLCTQQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAEELFHNLCTQQHR 15 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 ; 136.63 1.25E-05 84073000 65680 81675 83495 91681 99801 108202 81527 80022 86334 84451 FALSE TRUE 68273.09712 95702.04591 85670.94829 109815.2282 82836.86167 83073.72532 75136.70071 78949.43598 83226.8562 100997.5565 0.675987613 0.947567933 0.848247732 1.087305792 0.82018679 0.822532031 0.743945728 0.781696495 0.824048215 1 16.62396086 3.038203938 24.99968185 0.811476813 0.89878968 0.038070689 0.114621751 349.3472046 228601.7095 0.031791777 0.03799839 1091.95298 -3.038203938 0.087312867 QAEEQIEHLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAEEQIEHLQR 11 0 H3BP71;O75150-4;O75150;O75150-3 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 146.07 3.59E-05 67015000 93701 108820 103270 102060 111740 135420 116680 111760 96084 121830 FALSE TRUE 97400.38783 127508.9885 105961.301 122247.1634 92746.47471 103970.7573 107534.3167 110262.04 92625.95561 145700.2559 0.668498399 0.875145947 0.727255422 0.839031906 0.636556704 0.713593512 0.738051667 0.756773139 0.635729533 1 17.15264389 -1.553229553 8.757251997 1.000032068 0.737847292 0.535779929 0.074595575 4.39E-05 2.24E-06 0.067818932 0.015983127 0.027975023 1.553229553 -0.262184776 QAEILQESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAEILQESR 9 0 E5RJD8;O75347;E5RIW3;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 145.9 0.00022347 131630000 154010 196170 164560 154700 164560 189590 158510 168970 153180 184870 FALSE TRUE 160090.4337 229860.6715 168848.5688 185299.1983 136588.15 145560.5958 146085.572 166705.2335 147667.0817 221091.737 0.724090533 1.039661973 0.76370366 0.838110012 0.617789484 0.65837194 0.660746412 0.754009335 0.667899596 1 17.75428558 3.563613614 2.356474892 0.711384967 0.867573784 0.13039059 0.128739547 0.43681734 4.760505305 0.034286599 0.058139561 3661.117049 -3.563613614 0.156188817 QAEPELDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAEPELDLR 9 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;D6RC54;D6RAA8;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;A0A0C4DGB5;E7EVY3;H0Y9H6 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 96.668 0.016779 724820000 802220 1006420 921940 895520 975070 1142440 872410 937910 857500 1021540 FALSE TRUE 833892.265 1179264.806 945966.5138 1072651.183 809327.9497 877125.6238 804028.2246 925338.8506 826638.7425 1221691.204 0.682572046 0.965272404 0.774309016 0.878005161 0.662465234 0.717960169 0.658127211 0.757424501 0.676634766 1 20.22044824 4.015149915 24.98701454 0.748762222 0.835389346 0.02444639 0.119136452 579.5056981 955774.7918 0.027585479 0.059561719 10354.99552 -4.015149915 0.086627123 QAEREEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QAEREEKR 8 2 P14678-2;P14678;P14678-3 P14678-2 SNRPB Small nuclear ribonucleoprotein-associated proteins B and B 0 ;; 161.79 0.00019432 166837000 139590 159766 180253 146091 133627 201565 94845 144593 189789 118039 FALSE TRUE 145101.121 187204.5677 184950.5413 174987.3638 110913.1303 154754.5835 87410.80107 142654.9673 182958.531 141166.4821 1.027872331 1.326126181 1.31015903 1.23958153 0.785690262 1.096255862 0.619203651 1.010544183 1.296047959 1 17.10703806 3.262306593 24.52427853 0.953393096 1.239107537 0.316742627 0.184474533 206.6015678 213371.3331 0.050572981 0.068435338 1829.391232 -3.262306593 0.285714441 QAFEELRDDLVELSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAFEELRDDLVELSK 15 1 Q15397 Q15397 KIAA0020 Pumilio domain-containing protein KIAA0020 0 ; 148.03 3.29E-06 67734000 65126 53554 63817 58333 76139 67976 76061 63499 64364 52113 FALSE TRUE 67697.22477 62751.48291 65480.12345 69871.09329 63196.91998 52189.60419 70099.14007 62647.89977 62047.55221 62323.54459 1.086222313 1.006866399 1.050648256 1.121102687 1.014013571 0.837397881 1.124761766 1.005204376 0.995571619 1 15.92748967 3.018103819 24.74649512 0.997018596 1.061696889 0.19603078 0.070095706 405.2829929 553985.5154 0.020412095 0.024392734 1042.566627 -3.018103819 0.064678293 QAGAPGGSSGSGGS(ph)PELSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAGAPGGSSGSGGSPELSALR 21 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 QAGAPGGSSGS(0.031)GGS(0.969)PELSALR;QAGAPGGSSGSGGS(1)PELSALR 310.47 1.70E-66 300200000 130533 176924 149656 146460 149357 195942 148866 163655 156435 154665 TRUE FALSE 135686.5436 207309.3207 153556.1583 175429.3509 123969.3505 150437.44 137197.4939 161461.4724 150804.9349 184968.6455 0.733565104 1.120780877 0.830173989 0.948427504 0.670218188 0.813313195 0.741733787 0.87291266 0.81529999 1 17.49692121 QAGEVTFADAHRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAGEVTFADAHRPK 14 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 0 96.673 0.0019697 132090000 243870 186780 237030 171090 251920 288410 246960 240770 257970 176230 FALSE TRUE 253498.1759 218858.0121 243207.1965 204931.0913 209098.7284 221431.1484 227602.6299 237542.872 248685.7101 210758.8944 1.202787558 1.038428355 1.153959349 0.972348484 0.992122914 1.050637265 1.079919453 1.127083498 1.179953571 1 17.68523399 -0.269456582 7.503395552 0.999953268 1.084355712 0.113034789 0.073589286 0 0 0.071611556 0.016879006 0.537704187 0.269456582 0.084402444 QAGEVTYADAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 211.77 2.80E-08 4471940000 3899080 3106670 3743020 3057290 4350510 4631270 4240250 3769210 4114560 2869660 FALSE TRUE 4053018.689 3640216.406 3840566.176 3662012.837 3611011.864 3555727.73 3907888.125 3718689.905 3966477.789 3431914.934 1.180978773 1.060695406 1.119073826 1.067046505 1.052185714 1.036076884 1.138690265 1.083561212 1.155762268 1 21.71058236 4.747038725 24.08197232 1.08325287 1.180978857 0.309026513 0.045285122 798.3249916 2267546.904 0.010217405 0.114849704 55851.99947 -4.747038725 0.097725987 QAGEVTYADAHKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAGEVTYADAHKER 14 1 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 96.247 0.0020712 98202000 177650 191170 177580 96099 290080 220250 110150 171010 198060 280270 FALSE TRUE 184663.7592 224001.9604 182207.8807 115107.0954 240772.3052 169100.2754 101516.1552 168717.8907 190931.8593 335183.5404 0.550933256 0.668296421 0.543606289 0.343415119 0.718329739 0.504500535 0.302867364 0.503359713 0.569633757 1 18.35459178 0.769242805 3.763050946 0.999982956 0.513059091 0.593879373 0.119062082 1.681494159 26.70480052 0.116179439 0.029802532 5.878178978 -0.769242805 -0.486923864 QAGGHKDPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAGGHKDPEK 10 1 Q15813-2;Q15813;A0A2R8Y5Q8;A0A2R8YHI9;A0A2R8Y7E7;A0A2U3TZJ6;A0A2R8Y6Q1 Q15813-2 TBCE Tubulin-specific chaperone E 0 56.936 0.07262 58320000 136910 84050 101910 107390 134680 147910 139940 107650 126040 82461 FALSE TRUE 142315.3125 98484.93368 104565.8583 128631.4215 111787.1417 113560.1441 128971.1371 106207.1278 121503.845 98617.65414 1.443101783 0.998654192 1.060315815 1.304344771 1.133540872 1.151519422 1.307789546 1.076958571 1.232069918 1 16.58955831 -1.196590604 3.488931629 0.999727453 1.178537236 0.159532194 0.12837481 2380804.547 1364350.503 4664.859659 0.027798993 0.063593012 1.196590604 0.178809783 QAGPASVPLRTEEEFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;; 222.3 1.92E-15 2718640000 3582260 2154200 2723430 1959460 4264030 3587650 3193180 2702770 3260360 1914780 FALSE TRUE 3723690.391 2524167.093 2794404.823 2347035.34 3539231.704 2754472.659 2942890.208 2666543.789 3143020.28 2289944.48 1.626105097 1.102283097 1.2202937 1.024931111 1.545553499 1.202855651 1.285136052 1.164457834 1.372531215 1 21.12688119 -2.175341776 2.314173189 0.32350333 1.265755765 0.177676568 0.179142216 11376593.03 2458156.066 40355124.18 0.039790398 0.006678182 2.175341776 0.942252434 QAHDLS(ph)PAAESSSTFSFSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QAHDLSPAAESSSTFSFSGR 20 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(0.967)PAAES(0.008)S(0.013)S(0.005)T(0.005)FSFSGR;QAHDLS(1)PAAESSSTFSFSGR 304.72 2.13E-55 4734880000 969137 1274900 1153292 1220463 1213376 1519680 1106390 1285420 1150678 1212560 TRUE FALSE 1007399.277 1493854.158 1183347.737 1461866.939 1007126.781 1166757.351 1019668.261 1268191.047 1109265.324 1450137.916 0.694692047 1.030146265 0.816024272 1.008088212 0.694504136 0.804583714 0.70315261 0.874531335 0.764937811 1 20.46775868 5.028485259 15.68156857 0.843806335 0.277628728 0.137851628 0.117327196 4561670.525 70074418.24 0.026592976 66779446.74 106778.855 -5.028485259 -0.566177607 QAHELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAHELFR 7 0 E7EPM6;P33121-2;P33121;P33121-3;D6RER0;D6RG07 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 93.162 0.015137 100630000 73593 88647 82180 80040 69938 104280 65555 66289 81748 78181 FALSE TRUE 76498.50847 103871.4327 84321.67831 95871.6731 58049.96374 80062.55038 60416.6278 65400.50438 78805.90545 93499.07008 0.818174003 1.110935463 0.901845101 1.025375686 0.620861402 0.856292478 0.646173569 0.699477592 0.842852291 1 16.5126644 3.2514799 24.99964614 0.75323721 0.970126553 0.329797401 0.127299189 215.6413473 417277.4296 0.032645796 0.043926402 1784.349405 -3.2514799 0.216889344 QAHLTNQYMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAHLTNQYMQR 11 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;H0YB86 P11940-2 PABPC1 Polyadenylate-binding protein 1;Polyadenylate-binding protein 0 ;;; 123.67 0.00027694 331666000 74182.9 533872 312927 534031 257098 548966 208353 346520 231457 624930 FALSE TRUE 77111.69817 625560.3631 321082.1347 639660.7379 213396.5738 421476.9662 192021.7474 341875.4662 223126.9078 747373.0685 0.103176983 0.837012182 0.429614269 0.855878764 0.285528851 0.563944546 0.256928909 0.45743616 0.298548231 1 19.51146905 -1.270485943 5.348650774 1.000066968 0.465699141 0.332190373 0.231634227 0.000169669 2.31E-05 0.20571785 0.048482119 0.053643123 1.270485943 -0.534367828 QAHLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QAHLYR 6 0 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;; 107.55 0.072514 647460000 397160 398880 369696 346334 443230 520880 368940 382660 347585 416700 FALSE TRUE 412840.1835 467384.5371 379330.5815 414837.8315 367889.9229 399913.514 340021.5188 377531.0686 335075.4837 498344.3868 0.828423465 0.937874589 0.761181608 0.832432034 0.738224274 0.802484235 0.682302295 0.757570625 0.672377361 1 18.92678355 4.222886228 24.65334373 0.767674573 0.88314902 0.156648271 0.090967953 249.1059575 391806.3455 0.020740189 0.045052902 16706.52898 -4.222886228 0.115474447 QAHTMDPQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 139.98 3.04E-05 20220990000 3054844 3324952 3391771 3384310 3801832 4537830 2944479 3163252 3098461 3456710 FALSE TRUE 3175451.6 3895986.641 3480163.339 4053716.417 3155597.955 3483987.754 2713683.042 3120853.781 2986947.994 4133986.142 0.768133102 0.942428568 0.841842043 0.980582972 0.76333056 0.842767158 0.656432545 0.754926038 0.722534593 1 21.97910212 3.202093851 24.96600614 0.769759179 0.884516529 0.153332684 0.100808846 232.5800141 159229.0746 0.02725042 0.032571452 1592.552841 -3.202093851 0.11475735 QALDYVELSPLTQAS(ph)PQR ddPTM_MDA-MB-175_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 QALDYVELSPLTQAS(1)PQR;QALDYVELSPLTQAS(1)PQR;QALDYVELSPLTQAS(1)PQR 318.93 1.90E-61 617460000 340892 395055 317258 331983 347414 406011 307944 336903 290019 314883 TRUE FALSE 354350.6794 462902.6231 325526.0041 397648.2465 288360.6924 311721.0984 283806.5446 332387.3663 279581.2728 376578.2951 0.940974783 1.229233414 0.864431138 1.055951051 0.765739014 0.827772345 0.753645519 0.882651419 0.742425351 1 18.52259032 3.243060615 24.99932242 0.821889544 1.02610258 0.418239997 0.111853536 99.92031725 555093.8148 0.029086068 0.038092556 1750.090935 -3.243060615 0.204213036 QALTEFNTAIQEIVVTHWHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QALTEFNTAIQEIVVTHWHR 20 0 Q53H82 Q53H82 LACTB2 Beta-lactamase-like protein 2 0 ; 162.65 1.20E-11 139116000 141774 97357 102139 93818 116425 145946 102737 89933 112470 106575 FALSE TRUE 147371.347 114077.3074 104800.8262 112374.9204 96635.12009 112052.2533 94684.20549 88727.59524 108422.2267 127456.3307 1.156249722 0.895030531 0.822248888 0.881673901 0.758182191 0.879142312 0.742875657 0.696141139 0.85066176 1 16.95964351 QAPQTIHLPSGEILDVFDAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAPQTIHLPSGEILDVFDAAER 22 0 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 ;;; 207.17 8.40E-23 458313000 283187 365274 283412 329206 327309 409282 276846 328518 291497 348177 FALSE TRUE 294367.4414 428006.9681 290797.9495 394321.9642 271673.1331 314232.4582 255146.0871 324114.7536 281006.0799 416395.6169 0.706941739 1.027885383 0.698369382 0.946988749 0.652439944 0.754648813 0.612749214 0.778381761 0.674853597 1 18.66759536 3.231809848 24.99984277 0.729043055 0.847629325 0.107708168 0.135378187 277.1212738 1026250.879 0.035173162 0.042944836 1705.335559 -3.231809848 0.11858627 QAQAQES(ph)EEEEESR ddPTM_MDA-MB-175_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 377.75 1.71E-97 3155774000 762170.6 846143 810924 812623 813004 986821 810507 865396 848689 841813 TRUE FALSE 792261.6838 991461.4782 832057.3456 973357.404 674809.8705 757646.7782 746977.3435 853796.7821 818144.8487 1006750.14 0.786949664 0.984813847 0.8264785 0.966831158 0.670285351 0.752566847 0.741968949 0.848072176 0.812659285 1 19.94127424 3.257724409 24.99283734 0.79374352 0.893322242 0.155437716 0.097481656 385.7202184 503041.5319 0.025397849 0.034335331 1810.191033 -3.257724409 0.099578722 QAQEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAQEEAER 8 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 175.51 0.0006181 352119000 341930 420970 378015 375564 414506 487713 365383 387360 371377 424149 FALSE TRUE 355429.6604 493268.3228 387866.3814 449849.4383 344048.4182 374449.0471 336743.3257 382168.0728 358011.2143 507252.8757 0.70069521 0.972430806 0.76464107 0.886834673 0.678258192 0.738190092 0.663856908 0.753407405 0.705784494 1 18.95234561 3.241885836 24.99963416 0.73799933 0.836491223 0.082802529 0.111176775 152.403988 1145791.505 0.028304785 0.036812675 1745.363286 -3.241885836 0.098491893 QAQEYEALLNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QAQEYEALLNIK 12 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 251.87 1.12E-20 726040000 847340 696650 821340 639430 911640 949250 880910 741160 808470 644490 FALSE TRUE 880793.6375 816294.2183 842744.7951 765907.3455 756679.7584 728801.0735 811861.9724 731225.9625 779373.3226 770765.476 1.142751803 1.059069514 1.093386797 0.993697006 0.981725028 0.945554901 1.053319067 0.94870098 1.011167919 1 19.55593243 3.730407088 4.6750126 0.987190683 1.095650609 0.671222905 0.034529552 0.105200287 6.480040388 0.008642434 0.01469077 5375.354214 -3.730407088 0.108459926 QAQQERDELADEIANSSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 372.9 4.05E-108 6835020000 4114840 3217300 4098290 2969910 4726620 5165890 3840730 3980340 4606620 3466390 FALSE TRUE 4277297.061 3769846.248 4205094.804 3557349.334 3923190.821 3966190.337 3539683.547 3926990.053 4440828.646 4145562.752 1.031777183 0.909368998 1.014360427 0.858110116 0.946359048 0.956731468 0.853848743 0.947275506 1.071224563 1 21.98313653 1.307821084 7.446596501 1.034979139 0.935223869 0.313215664 0.056595123 0.22214816 19.8092098 0.036285873 0.013098154 20.31519914 -1.307821084 -0.09975527 QAQYLGMSCDGPFKPDHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QAQYLGMSCDGPFKPDHYR 19 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;; 205.62 2.42E-16 1611584000 1319946 1030449 1187315 1233291 1301813 1513432 1343454 1304502 1309220 980474 FALSE TRUE 1372058.487 1207420.6 1218257.404 1477232.279 1080531.291 1161960.354 1238150.565 1287017.284 1262101.428 1172579.108 1.170120189 1.029713553 1.038955407 1.259814599 0.921499696 0.990944105 1.055920711 1.097595272 1.076346508 1 20.16125383 4.747676543 23.88690042 1.057395665 1.170120301 0.148600231 0.083806249 1359.444381 3562071.339 0.019775952 0.24124069 55934.08566 -4.747676543 0.112724636 QAQYLGMSCDGPFKPDHYRY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAQYLGMSCDGPFKPDHYRY 20 2 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 190.63 9.89E-18 2238100000 1551600 1772620 1809610 1640390 2121330 2251190 1392690 1786310 1829870 2044510 FALSE TRUE 1612858.366 2077053.696 1856769.923 1964854.246 1760747.084 1728385.24 1283527.319 1762367.436 1764013.336 2445092.59 0.659630794 0.849478545 0.759386344 0.803590937 0.720114687 0.70687926 0.52494017 0.720777382 0.721450526 1 21.22145767 0.607846384 4.57039208 0.999999957 0.717159701 0.515121765 0.081943288 36.1815998 420.8853475 0.083076282 0.021073254 4.053651268 -0.607846384 -0.282840257 QAREEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAREEEAR 8 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 ; 133.23 0.00084645 260130000 140163 187172 163863 148234 192753 178793 139615 160918 154141 220525 FALSE TRUE 145696.7435 219317.335 168133.4044 177554.2428 159988.9139 137271.0354 128671.6115 158761.1574 148593.4955 263732.6515 0.552441052 0.831589618 0.637514557 0.673235725 0.60663294 0.520493138 0.487886542 0.601977633 0.563424721 1 18.00871667 -1.749631705 6.306836919 1.010301564 0.609217435 0.626426656 0.090731068 0.013829016 0.000548983 0.09244017 0.021704189 0.017797881 1.749631705 -0.401084129 QAREQTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QAREQTGK 8 1 Q9Y5B6-2;Q9Y5B6 Q9Y5B6-2 PAXBP1 PAX3- and PAX7-binding protein 1 0 ;;; 72.547 0.041835 3365060000 493198 4222270 1439570 3544110 518520 2315170 602840 1424440 606830 6019000 FALSE TRUE 512669.8379 4947412.028 1477086.377 4245124.38 430382.1556 1777506.854 555587.8256 1405347.712 584990.3068 7198307.809 0.071220883 0.687302094 0.205199113 0.589739213 0.059789351 0.246933988 0.077183116 0.195233067 0.081267754 1 22.77922636 -1.456898497 3.841603781 1.006112478 0.250956302 0.538557028 0.209338825 49754375.13 37855754.51 2411277.984 0.047291553 0.034922193 1.456898497 -0.755156177 QAS(ph)DTGSNDAHNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.997)DT(0.003)GSNDAHNKK;QAS(0.948)DT(0.052)GSNDAHNKK;QAS(0.988)DT(0.012)GSNDAHNKK;QAS(0.996)DT(0.004)GSNDAHNKK;QAS(0.447)DT(0.447)GS(0.107)NDAHNKK;QAS(1)DTGSNDAHNKK;QAS(0.972)DT(0.014)GS(0.014)NDAHNKK 278.07 1.72E-33 1538485000 1629633 863632 2015856 985310 1760044 1565200 2276172 1408168 2315174 757728 TRUE FALSE 1693972.169 1011954.078 2068390.863 1180201.377 1460872.35 1201706.021 2097759.691 1389293.811 2231851.34 906190.294 1.869333826 1.116712554 2.28251271 1.302376979 1.612103285 1.326107804 2.314921827 1.533114866 2.462894775 1 19.78945451 2.273796181 24.99992775 1.851648126 1.583688712 0.055965191 0.484697904 494.9887547 351196.9585 0.153858487 0.128722391 187.8435041 -2.273796181 -0.267959414 QAS(ph)ESSSRPH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QASESSSRPH 10 1 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 QAS(0.797)ES(0.137)S(0.008)S(0.057)RPH;QAS(0.999)ES(0.001)SSRPH;QAS(0.999)ES(0.001)SSRPH;QAS(0.925)ES(0.069)S(0.003)S(0.003)RPH;QAS(0.984)ES(0.013)S(0.003)SRPH;QAS(0.841)ES(0.018)S(0.136)S(0.005)RPH 131.66 0.00014786 1289493000 795325 1188597 1207668 1249046 1401845 1747191 1216453 1425594 1296781 1497022 TRUE FALSE 826725.0451 1392729.289 1239140.82 1496103.571 1163559.888 1341432.369 1121104.235 1406486.244 1250110.105 1790334.799 0.461771198 0.777915555 0.692127987 0.835655751 0.649911898 0.749263417 0.626198092 0.785599568 0.698254933 1 20.77179797 -5 0.224224257 2.525226487 0.67015382 0.474781487 0.097593876 133.9190163 1.340467126 92.45388021 0.166305496 1.00E-05 5 -1.855072667 QAS(ph)LDGLQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR 194.13 6.80E-07 713050000 438943 511774 484182 453382 588578 691049 516234 529619 530003 524476 TRUE FALSE 456272.8086 599667.2035 496800.1807 543059.6064 488531.7218 530563.3427 475770.2302 522520.3236 510928.2956 627237.0305 0.727432831 0.9560456 0.792045362 0.865796469 0.77886301 0.845873756 0.758517446 0.833050822 0.814569725 1 19.25865121 -1.092180409 3.800041224 1.000054378 0.821544792 0.447105362 0.060285219 13236157.28 27398674.25 10917.12455 0.013028878 0.080875986 1.092180409 -0.178509587 QAS(ph)LPVSGSVAGDFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QASLPVSGSVAGDFVK 16 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;H0Y493;H0Y7J9;E9PCD1 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 1 QAS(0.984)LPVS(0.012)GS(0.004)VAGDFVK;QAS(1)LPVSGSVAGDFVK 129.11 6.00E-05 105167000 127101 98914 157253 95112 213901 147448 156289 139992 178000 123773 TRUE FALSE 132119.0456 115901.7101 161351.1424 113924.8697 177542.1844 113205.4366 144038.6598 138115.6362 171593.8148 148023.9496 0.89255182 0.782992957 1.090034031 0.769638089 1.199415263 0.764777841 0.973076723 0.933062769 1.159230079 1 17.17547109 7.999999996 0.193168895 1.028276403 0.242444538 0.102031713 0.142622297 127.5867896 1.505864706 0.257503238 30.07096734 99999999.14 -7.999999996 -0.785831864 QAS(ph)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QASPQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK 37 0 F8VPD4;P27708;H7BZB3 F8VPD4;H7BZB3 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 QAS(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK;QAS(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK;QAS(1)PQNLGTPGLLHPQTSPLLHSLVGQHILSVQQFTK 333.53 6.38E-129 2493100000 409698 647630 825360 758590 787100 1023720 774960 832040 886580 701670 TRUE FALSE 425873.1934 758855.4146 846869.5596 908636.8378 653309.0231 785976.5446 714216.6102 820887.8647 854672.159 839148.8022 0.507506168 0.904315674 1.009200701 1.082807764 0.778537753 0.936635484 0.851120336 0.978238737 1.018498932 1 19.67856713 4.733268468 4.066610456 0.94997711 0.47142709 0.723021497 0.082815345 0.116316801 4.15447338 0.020078107 0.162440193 54108.87048 -4.733268468 -0.47855002 QAS(ph)PTEVVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QASPTEVVER 10 0 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01;A0A0C4DG68 Q8TB72-3 PUM2 Pumilio homolog 2 1 QAS(0.926)PT(0.074)EVVER;QAS(0.565)PT(0.435)EVVER;QAS(0.938)PT(0.062)EVVER;QAS(0.975)PT(0.025)EVVER;QAS(0.999)PT(0.001)EVVER;QAS(0.698)PT(0.302)EVVER 200.81 2.66E-07 4847620000 1359140 1558380 1612580 1492910 1640340 2008640 1476090 1571060 1532550 1539540 TRUE FALSE 1412799.897 1826019.642 1654605.16 1788203.142 1361515.593 1542163.801 1360390.209 1550002.51 1477393.825 1841183.387 0.767332525 0.991764132 0.898663963 0.971224895 0.739478535 0.837593806 0.738867306 0.841851236 0.802415357 1 20.8122019 3.24468024 24.99993047 0.815051889 0.912670324 0.157825633 0.088380429 211.2619609 863042.7473 0.022637017 0.029890789 1756.629776 -3.24468024 0.097618434 QAS(ph)VHDS(ph)GEEGEA ddPTM_MDA-MB-175_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 180.56 1.87E-05 4062200000 4761800 5676000 5713900 5540100 6713500 7348300 5768400 6255200 5954000 6034300 TRUE FALSE 4949799.541 6650808.847 5862808.928 6635915.244 5572341.668 5641768.69 5316257.735 6171359.275 5739716.703 7216605.551 0.685890271 0.921597945 0.812405346 0.919534149 0.7721555 0.781775954 0.736670128 0.855160952 0.795348542 1 22.78288897 -1.40249183 3.112146462 1.002566827 0.813666467 0.395464512 0.070648041 17653856.48 21728679.82 402451.4289 0.016047855 0.039582951 1.40249183 -0.18890036 QAS(ph)VHDSGEEGEA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA;QAS(1)VHDSGEEGEA 219.95 2.27E-11 26892626000 3426231 7056120 6357661 6213965 6790599 7939278 5844219 6900167 6043614 6383485 TRUE FALSE 3561501.246 8267953.721 6523346.869 7443068.73 5636335.408 6095501.005 5386133.844 6807681.548 5826105.513 7634206.667 0.466518841 1.083014134 0.854489164 0.97496296 0.738300082 0.798445899 0.705526334 0.891733987 0.76315795 1 22.86404681 -0.89118555 3.915328118 1.000007921 0.821257911 0.112752375 0.157551375 4.50384E+11 8.81637E+11 51402440.76 0.034864191 0.128473765 0.89118555 -0.17875001 QASALIDRPAPFFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QASALIDRPAPFFER 15 1 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 0 ;; 183.31 4.66E-07 1247711000 400293 470713 374367 436367 498463 601001 447599 470737 483432 539553 FALSE TRUE 416096.8767 551554.2961 384123.3116 522679.0902 413734.4373 461427.626 412515.0208 464427.5405 466033.3768 645268.08 0.644843422 0.854767674 0.595292598 0.810018512 0.641182247 0.715094455 0.639292464 0.719743553 0.722232187 1 19.29953913 -1.702590095 2.553278715 1.051232415 0.705612619 0.574448873 0.07624084 8336098.446 6593070.591 2742049.066 0.017865856 0.019833982 1.702590095 -0.345619796 QASASYDS(ph)EEEEEGLPMSYDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QASASYDSEEEEEGLPMSYDEKR 23 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 1 QASAS(0.001)YDS(0.999)EEEEEGLPMSYDEKR;QASASYDS(1)EEEEEGLPMSYDEKR;QASAS(0.002)YDS(0.998)EEEEEGLPMSYDEKR 271.44 7.90E-52 987270000 364250 302503 348485 270190 437270 424050 335601 350455 408382 313722 TRUE FALSE 378630.8713 354455.5371 357566.8054 323632.7756 362943.0016 325570.814 309295.7167 345757.724 393684.4116 375189.8193 1.009171496 0.944736554 0.953029072 0.862584108 0.967358342 0.867749596 0.824371294 0.92155412 1.049293961 1 18.51726116 1.250468964 21.56886618 1.024646887 0.91456269 0.384772664 0.053310306 36.90587953 66851.13823 0.037496928 0.013359966 17.80200684 -1.250468964 -0.110084197 QASCSGDEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QASCSGDEYR 10 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A087WT27;A0A494C1E2;A0A494C1Q4;J3KN95;A0A494C099;A0A494C163;D6RIS6 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 203.78 4.63E-07 273880000 292220 330720 320150 363950 338460 421970 297300 317400 303630 342110 FALSE TRUE 303757.0712 387518.5874 328493.372 435938.2237 280928.6901 323973.8625 273996.8492 313145.7722 292702.4156 409139.9044 0.742428367 0.947154221 0.802887639 1.065499158 0.68663234 0.791841272 0.669689869 0.765375777 0.715409112 1 18.64223473 3.197385198 24.99993913 0.754393675 0.887426179 0.185909567 0.117720132 200.0540326 121463.5939 0.031117871 0.037193349 1575.37953 -3.197385198 0.133032504 QASDT(ph)GSNDAHNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.089)DT(0.91)GS(0.001)NDAHNKK 105.5 0.00075915 192890000 49313 47111 68506 50512 64014 80030 76578 58576 72089 48392 TRUE FALSE 51259.91532 55201.94778 70291.32264 60503.12284 53132.92315 61444.24537 70575.61626 57790.88453 69494.53097 57873.48588 0.885723653 0.953838307 1.214568668 1.04543768 0.918087486 1.061699402 1.219480997 0.998572726 1.200800849 1 15.82061492 2.480334893 24.95338953 1.102744773 1.012329942 0.163691705 0.107228416 273.5374565 2124009.531 0.037163926 0.031665506 302.2281361 -2.480334893 -0.09041483 QASDTGSNDAHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QASDTGSNDAHNK 13 0 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 0 128.22 0.0001678 60353000 70857 68395 81312 60832 80982 97625 90369 84836 82120 70961 FALSE TRUE 73654.48907 80141.30921 83431.05752 72864.38803 67216.70857 74953.07327 83285.64164 83698.91218 79164.51724 84864.44932 0.867907465 0.944344892 0.983109632 0.858597312 0.792047896 0.883209328 0.981396124 0.986265896 0.932834866 1 16.3728727 2.238436072 24.99826467 0.975560939 0.889352253 0.417396802 0.050296807 3.722980568 747018.2011 0.0201216 0.015819166 173.1554129 -2.238436072 -0.086208686 QASDTGSNDAHNKK ddPTM_MDA-MB-175_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 ;;; 359.59 1.40E-82 1265010000 1143159 810241 1142781 836210 1489450 1299770 1354100 1161740 1355188 735705 FALSE TRUE 1188291.8 949393.5889 1172562.812 1001609.842 1236273.821 997918.1157 1247962.104 1146168.776 1306415.049 879852.3088 1.350558256 1.079037447 1.332681406 1.138384058 1.405092433 1.134188211 1.418376802 1.302683148 1.484811752 1 19.74690185 3.244395885 24.9955201 1.306996286 1.222407336 0.036107034 0.152961651 403.5288123 1728514.843 0.039180396 0.051638214 1755.479997 -3.244395885 -0.08458895 QASEGPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QASEGPLK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 114.89 0.0059752 4109380000 4043110 3267380 3466480 2702020 5863240 4988380 4118730 3647310 3851040 4254920 FALSE TRUE 4202735.105 3828527.098 3556819.317 3236471.491 4866608.559 3829904.345 3795893.18 3598423.775 3712441.823 5088590.109 0.825913468 0.752374826 0.698979332 0.63602519 0.95637661 0.75264548 0.745961671 0.707155361 0.72956197 1 22.27883455 -1.145244836 4.423510321 1.000040941 0.752728169 0.447391533 0.081238396 3.24E-05 6.27E-06 0.077787035 0.018331548 0.071573979 1.145244836 -0.247312772 QASGDTPTT(ph)PKHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QASGDTPTTPKHPK 14 1 A0A087WWW8;Q9Y6J0;Q9Y6J0-2;B5MEB3 A0A087WWW8 CABIN1 Calcineurin-binding protein cabin-1 1 QASGDTPT(0.004)T(0.996)PKHPK 146.76 1.20E-05 130200000 229110 137630 187570 147540 256460 245950 214710 205860 208160 140260 TRUE FALSE 238155.4397 161266.8819 192458.2283 176722.9716 212867.0208 188831.8399 197880.4692 203100.7834 200668.3623 167741.2616 1.419778518 0.961402581 1.14735174 1.053545025 1.26902003 1.125732799 1.179676767 1.210797996 1.196296966 1 17.35587809 3.250496383 24.99088022 1.175764407 1.132499184 0 0.127285107 1048.546307 2195415.65 0.032709369 0.043945763 1780.313081 -3.250496383 -0.043265223 QATENAKEEVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QATENAKEEVRR 12 2 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;; 289.31 2.50E-36 2444694000 1908845 1846711 2014324 1221108 2606720 2457085 1455996 1897817 2172890 2205903 FALSE TRUE 1984207.675 2163869.249 2066818.938 1462639.518 2163630.665 1886464.246 1341871.229 1872379.867 2094688.113 2638107.458 0.752132999 0.820235446 0.783447593 0.554427574 0.820145009 0.715082413 0.508649193 0.709743593 0.794011672 1 21.3310719 -1.591168506 8.858522569 1.000069009 0.71123048 0.409256776 0.101552394 0.000139434 6.43E-06 0.099056807 0.023342381 0.025634892 1.591168506 -0.288838529 QATVGDINTERPGMLDFTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QATVGDINTERPGMLDFTGK 20 1 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ;;; 206.34 7.07E-22 1273200000 1328110 1100400 1130880 1086050 1200780 1373620 1249320 1141390 1160000 898210 FALSE TRUE 1380544.808 1289385.14 1160351.662 1300867.448 996671.8445 1054617.572 1151395.034 1126091.534 1118251.827 1074197.052 1.285187672 1.200324594 1.080203729 1.211013795 0.927829622 0.981772916 1.071865755 1.048310021 1.041011818 1 20.03482724 4.469801917 0.793376221 1.025363816 1.374320765 0.640849363 0.064354482 1.194041548 0.749004313 0.024357428 0.343367516 29498.63476 -4.469801917 0.348956949 QATVS(ph)WDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_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 2 QAT(0.01)VS(0.989)WDS(0.001)GGSDEAPPKPS(0.142)RPGYPS(0.858)PR;QAT(0.048)VS(0.952)WDSGGSDEAPPKPS(0.133)RPGYPS(0.867)PR 168.67 3.70E-12 398840000 311570 237790 296670 251450 401040 413230 381930 313800 362710 261020 TRUE FALSE 323871.0242 278628.5828 304401.4639 301186.0595 332871.364 317263.5951 351993.3286 309594.0243 349656.138 312161.8715 1.037509875 0.892577243 0.975139797 0.964839357 1.066342159 1.016343199 1.127598726 0.991773988 1.120111615 1 18.25193481 3.244916885 24.68135449 1.052440245 0.962708249 0.38071486 0.053691315 123.1483035 478180.4146 0.013844192 0.018291217 1757.587218 -3.244916885 -0.089731996 QATVSWDSGGSDEAPPKPS(ph)RPGYPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.649)RPGYPS(0.351)PR 256.29 3.62E-53 856620000 269600 221910 265540 223240 281140 298710 251880 249740 270400 201910 TRUE FALSE 280244.0162 260021.3163 272460.1905 267396.2057 233351.9232 229339.1295 232136.9874 246392.6438 260668.3568 241470.3987 1.160572963 1.07682481 1.12833785 1.107366398 0.966379003 0.949760843 0.961347597 1.020384466 1.079504396 1 17.88148682 3.265860069 10.18664578 0.994319819 1.116179787 0.69643426 0.039453168 0.236167338 84.99294461 0.011552698 0.015495734 1844.421045 -3.265860069 0.121859968 QATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QATVSWDSGGSDEAPPKPSRPGYPSPR 27 2 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1;E5RJQ2;E5RG80;E5RHK7 E7ESA6 PTK2 Focal adhesion kinase 1 1 QATVSWDSGGSDEAPPKPSRPGYPS(1)PR;QATVSWDSGGSDEAPPKPS(0.001)RPGYPS(0.999)PR;QATVSWDSGGS(0.001)DEAPPKPS(0.346)RPGYPS(0.654)PR;QATVSWDSGGSDEAPPKPS(0.065)RPGYPS(0.935)PR;QATVSWDSGGSDEAPPKPS(0.002)RPGYPS(0.998)PR;QATVSWDS(0.015)GGS(0.042)DEAPPKPS(0.307)RPGYPS(0.635)PR 316.1 1.83E-82 7515500000 2667930 2049183 2267415 2171850 2619978 2825982 2633215 2299980 2513640 1821306 TRUE FALSE 2773261.936 2401114.24 2326505.698 2601435.448 2174635.075 2169690.509 2426816.728 2269152.53 2423174.587 2178156.04 1.273215457 1.102360986 1.068107911 1.19432924 0.998383511 0.996113441 1.114161099 1.041776846 1.112488978 1 21.05467588 7.999999906 0.859410549 1.060487467 79.19590085 0.525843843 0.059157741 563.8938929 1.4817911 0.018486375 86206.62129 99999978.33 -7.999999906 78.13541338 QAVDFLSNEGHIYSTVDDDHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QAVDFLSNEGHIYSTVDDDHFK 22 0 Q5TEJ0;P15927;P15927-2;P15927-3 Q5TEJ0 RPA2 Replication protein A 32 kDa subunit 0 ;; 301.48 4.73E-56 988110000 303425 352150 366250 349831 452440 467990 374659 401467 385010 335056 FALSE TRUE 315404.4533 412629.0232 375794.7759 419026.5277 375534.4104 359306.415 345292.2486 396085.9915 371153.5653 400703.8082 0.787126169 1.029760673 0.937836797 1.045726342 0.937187026 0.896688296 0.861714417 0.988475736 0.92625415 1 18.6121767 QAVDVSPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAVDVSPLRR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 117.14 0.0015998 159690000 214810 239230 238750 226150 290800 304450 217050 211760 221360 282500 FALSE TRUE 223290.8647 280315.8915 244972.0211 270881.795 241369.9199 233746.1015 200037.0538 208921.7036 213393.2968 337850.4662 0.660916254 0.829704025 0.725090079 0.801780143 0.714428258 0.691862599 0.592087547 0.618385127 0.631620549 1 18.36602532 2.867273457 2.921048031 0.668021943 0.757496985 0 0.117513515 0.595061406 9.766122523 0.035554905 0.03825246 736.6708026 -2.867273457 0.089475042 QAVEQQIQSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QAVEQQIQSHR 11 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;;; 219.74 9.66E-12 3259540000 2825470 3437950 3233020 3245980 3405370 4073970 3039530 3261640 3242420 3379580 FALSE TRUE 2937021.737 4028391.169 3317275.157 3888025.156 2826526.424 3127852.209 2801283.696 3217923.051 3125725.938 4041743.995 0.726671887 0.996696271 0.820753408 0.9619672 0.699333364 0.773886771 0.69308786 0.796171914 0.773360693 1 21.94654651 QAVRVS(ph)PCHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.914)PCHS(0.086)R 88.768 0.0085373 0 105990 412260 314150 379330 297210 436130 215630 345720 264520 416010 TRUE FALSE 110174.567 483062.4481 322337.0071 454360.3418 246690.3504 334845.4171 198728.3572 341086.1889 254999.9769 497519.1945 0.221447872 0.970942334 0.647888585 0.913251884 0.49584087 0.673030148 0.399438573 0.685573929 0.512542993 1 18.92439266 -1.057029412 4.843453162 1.000007698 0.62705328 0.22686749 0.212789914 2.13E-05 4.14E-06 0.18881576 0.044503096 0.087694143 1.057029412 -0.372954419 QAVRVSPCHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAVRVSPCHSR 11 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 QAVRVS(0.233)PCHS(0.767)R 68.044 0.057732 0 116950 372710 309030 339970 255960 410400 223120 351780 269270 381100 TRUE FALSE 121567.2763 436720.0432 317083.5757 407215.0513 212452.0106 315090.8197 205631.2714 347064.9645 259579.0253 455769.2484 0.266729879 0.958204277 0.695710772 0.893467589 0.466139415 0.691338481 0.45117408 0.76149272 0.569540455 1 18.79794406 -1.426068854 3.213714606 1.004933048 0.65407629 0.224301118 0.199533291 70291491.32 95828386.07 3199899.517 0.043457777 0.037491356 1.426068854 -0.350856758 QAWRKGPDGPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAWRKGPDGPQK 12 2 Q9BYZ6-2;E5RI44 Q9BYZ6-2 RHOBTB2 Rho-related BTB domain-containing protein 2 0 ; 68.069 0.030182 3747200000 9574600 4598000 6718900 4549900 9244000 7297800 8116500 5290900 7697300 4430500 FALSE TRUE 9952612.601 5387670.733 6894000.054 5449856.64 7672708.182 5602996.549 7480307.521 5219984.14 7420275.677 5298571.648 1.878357652 1.01681568 1.301105376 1.028552033 1.448071045 1.057454145 1.411759247 0.985168171 1.400429431 1 22.33717207 4.747437274 24.62402702 1.187170802 1.878358093 0.573096698 0.179948452 611.9780254 1697593.669 0.037833463 0.452483869 55903.27801 -4.747437274 0.691187291 QAYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QAYSPR 6 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 QAY(0.001)S(0.999)PR 73.573 0.08665 1343500000 202070 252790 236570 233780 228730 281290 232190 246550 212860 235840 TRUE FALSE 210047.8796 296204.7161 242735.2085 280020.9862 189850.5563 215964.6605 213990.3411 243245.4005 205199.2102 282048.3326 0.744722997 1.050191339 0.860615648 0.992812061 0.673113557 0.765700894 0.758700961 0.86242453 0.72753208 1 18.10558288 3.251270851 24.99995705 0.791919518 0.91827378 0.198643474 0.111679238 323.4077824 636112.0648 0.028690028 0.038594321 1783.490707 -3.251270851 0.126354261 QAYVDKLEELMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QAYVDKLEELMK 12 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 161.63 5.91E-05 786780000 1266100 799900 934040 768000 1527710 1381160 1240220 1112110 1340610 830290 FALSE TRUE 1316086.606 937276.6026 958381.8497 919908.1077 1268030.4 1060406.522 1143008.316 1097203.984 1292361.708 992969.4286 1.32540496 0.943912849 0.965167529 0.926421379 1.277008499 1.067914571 1.151101215 1.104972573 1.301512082 1 19.92138978 3.246504307 24.9973962 1.148387488 1.027985782 0.13665273 0.13422571 330.2866856 1039347.533 0.035960042 0.047812017 1764.023258 -3.246504307 -0.120401706 QCEGITS(ph)PEGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QCEGITSPEGSK 12 0 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 1 QCEGIT(0.179)S(0.821)PEGSK 115.68 0.00096855 69477000 240340 158330 193280 150620 257930 267580 259550 214070 243390 154750 TRUE FALSE 249828.8088 185521.9459 198317.0356 180412.1864 214087.1507 205438.6002 239205.7928 211200.7418 234630.4414 185070.2996 1.349913029 1.002440404 1.071576779 0.974830574 1.156788265 1.110057101 1.292513133 1.141191981 1.267790898 1 17.49771386 2.605695841 2.685119173 1.185529664 1.093687955 0.039699822 0.12208576 0.645889261 9.079747796 0.041468544 0.038163584 403.3627984 -2.605695841 -0.09184171 QCVENADLPEGEKKPIDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QCVENADLPEGEKKPIDQR 19 2 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 165.3 1.24E-11 2380930000 3812700 1908000 2682710 1822300 3850420 3437170 3111790 2657940 3321830 1668130 FALSE TRUE 3963228.34 2235684.158 2752623.626 2182745.501 3195926.984 2638939.358 2867879.769 2622314.662 3202277.987 1994968.135 1.986612352 1.120661588 1.379783255 1.094125496 1.601994 1.322797749 1.43755668 1.314464435 1.605177512 1 20.92793427 -2.143186486 2.541728581 0.06547542 1.404204928 0.207536297 0.247314422 61227129.36 47313352.36 320300570.8 0.055696578 0.007191401 2.143186486 1.338729508 QDAAGKDS(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDAAGKDSPNR 11 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QDAAGKDS(1)PNR;QDAAGKDS(1)PNR 118.16 0.00045867 318800000 841350 515400 657800 510000 771650 851780 748150 643500 682660 400870 TRUE FALSE 874567.1477 603915.9407 674942.8084 610876.4778 640485.2086 653967.0039 689508.0481 634874.9351 658091.2 479412.8014 1.824246547 1.259699238 1.40785312 1.274218119 1.335978528 1.364100003 1.438234536 1.324276142 1.372702602 1 18.87090891 -4.269498306 0.145071841 2.08E-24 1.519220215 0.44144712 0.144337132 106.5429516 1.137025671 32.39055317 0.791187286 5.38E-05 4.269498306 1.519220215 QDAKDPTSLLGVLQAEADS(ph)TSEGLEDAVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 1 QDAKDPTSLLGVLQAEADS(0.333)T(0.333)S(0.333)EGLEDAVHS(0.001)R 76.611 0.0016856 21729000 10928 13355 14133 10343 15471 16305 12765 13064 10270 13378 TRUE FALSE 11359.44588 15648.61736 14501.31759 12388.81453 12841.24495 12518.41085 11764.44594 12888.89845 9900.384706 15999.16296 0.710002511 0.978089754 0.906379767 0.774341418 0.802619798 0.782441612 0.73531634 0.805598298 0.618806417 1 13.96570881 3.728726046 23.65055822 0.779207812 0.876150583 0.088127663 0.107978498 580.1822896 1395247.003 0.026499997 0.041675073 5354.587825 -3.728726046 0.096942771 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDAKDPTSLLGVLQAEADSTSEGLEDAVHSR 31 1 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ;; 297.66 1.22E-81 157740000 157673.4 139261 177096.9 131464.8 214609.1 207802.8 155305.3 162959.4 190101.9 155593 FALSE TRUE 163898.4676 163177.9934 181712.1907 157468.1451 178129.9218 159543.749 143132.0648 160775.1958 183260.1698 186078.4693 0.880802965 0.876931082 0.976535283 0.846245918 0.957283895 0.857400373 0.76920272 0.864018263 0.984854241 1 17.50555161 1.223883613 10.7280402 0.992704355 0.876540393 0.411623122 0.054417435 0.371840034 252.9391913 0.049851315 0.013676135 16.74494065 -1.223883613 -0.116163962 QDAPPWGSGVELTHLGS(ph)PSAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDAPPWGSGVELTHLGSPSAQR 22 0 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 1 QDAPPWGSGVELTHLGS(0.99)PS(0.01)AQR;QDAPPWGSGVELTHLGS(1)PSAQR;QDAPPWGSGVELTHLGS(0.986)PS(0.014)AQR 326.55 7.93E-81 554565000 318932 370888 373939 380624 340095 446490 375855 374333 344714 329958 TRUE FALSE 331523.6816 434585.1289 383684.1575 455910.2912 282285.7734 342799.4641 346394.503 369315.6784 332307.8105 394606.9527 0.840136443 1.101311383 0.972319811 1.15535291 0.715359351 0.868711161 0.877821591 0.935907682 0.842123557 1 18.59005685 3.244384453 24.99999936 0.874771946 1.020070881 0.320204331 0.102714108 164.6351279 706724.5522 0.027305959 0.035996028 1755.433789 -3.244384453 0.145298935 QDATVWIPS(ph)PSRQPVYYDELDAASSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDATVWIPSPSRQPVYYDELDAASSSLR 28 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.904)PS(0.096)RQPVYYDELDAASSSLR 177.71 1.06E-17 120990000 40157 50415 40243 40071 43942 53861 41614 45612 52574 47895 TRUE FALSE 41742.42937 59073.38408 41291.76564 47996.9242 36472.75454 41352.59902 38352.18594 45000.64575 50681.87201 57279.10824 0.728754875 1.031325136 0.72088702 0.837948175 0.63675493 0.721949072 0.669566743 0.78563803 0.884822993 1 15.80572141 1.034162988 2.701679403 0.998029474 0.765775514 0.344137325 0.1035251 0.285078452 4.561782942 0.099262644 0.026640915 10.81839884 -1.034162988 -0.23225396 QDATVWIPS(ph)PSRQPVYYDELDAASSSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDATVWIPSPSRQPVYYDELDAASSSLRR 29 2 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QDATVWIPS(0.814)PS(0.182)RQPVY(0.001)Y(0.001)DELDAAS(0.001)S(0.001)S(0.001)LRR 64.668 0.0054532 47070000 50808 56681 47689 45126 57712 57307 37405 49243 53016 68762 TRUE FALSE 52813.93907 66415.52083 48931.81452 54051.78811 47902.13485 43998.31775 34473.09836 48582.97813 51107.96452 82234.59737 0.64223503 0.807634778 0.595027106 0.657287685 0.58250586 0.535034148 0.419204319 0.59078514 0.621489813 1 16.32745787 -1.801391013 6.453397232 1.020856618 0.601024182 0.61938895 0.092664759 0.028896304 0.000889309 0.093238276 0.022891017 0.01579825 1.801391013 -0.419832436 QDDMWEHIATFNALGYVQASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDDMWEHIATFNALGYVQASK 21 0 Q96RS6-2;Q96RS6;Q96RS6-3 Q96RS6-2 NUDCD1 NudC domain-containing protein 1 0 139.26 2.86E-07 12002000 33246 20016 25844 23030 29976 35243 29449 31925 31413 16229 FALSE TRUE 34558.57775 23453.5923 26517.51587 27585.26526 24880.69023 27058.34736 27140.71043 31497.09759 30282.45227 19408.76183 1.780565811 1.208402293 1.366265201 1.421278983 1.281930834 1.394130527 1.39837413 1.622828796 1.560246477 1 14.24442046 1.954168724 24.93158548 1.475321583 1.392837426 0 0.212853892 1764.601972 959916.648 0.081840719 0.052829407 89.9847106 -1.954168724 -0.082484157 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDDSPPRPIIGPALPPGFIK 20 1 A0A0A0MRI1;Q8IXQ4;Q8IXQ4-4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK 190.24 1.15E-17 2057330000 1047980 850450 999550 790970 1245080 1252840 1066740 992650 1085080 788260 TRUE FALSE 1089355.06 996508.1719 1025599.094 947421.5052 1033441.746 961886.897 983126.1314 979345.1504 1046028.183 942704.4549 1.155563712 1.057073791 1.087932797 1.005003742 1.096252109 1.02034831 1.042878419 1.038867638 1.109603521 1 19.84644602 7.535620083 1.096767127 1.04787881 65.78347836 0.440222962 0.035579387 857.6112366 2.264849722 0.009436826 139160.2014 34325753.81 -7.535620083 64.73559955 QDEEKPLHALLHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDEEKPLHALLHGR 14 1 P24593;C9JXX4 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 ; 179.41 1.21E-06 94614000 97206 74353 94846 75736 117178 111082 102841 101877 113583 84343 FALSE TRUE 101043.7679 87122.54936 97317.76468 90716.35475 97260.12541 85284.88896 94780.0537 100511.5055 109495.17 100868.396 1.001738621 0.863724941 0.964799368 0.899353597 0.964227937 0.845506545 0.939640734 0.99646182 1.085525044 1 16.6221147 1.618460113 3.068860101 1.042367069 0.921637931 0.490054829 0.048845413 0.155045606 3.43536753 0.028891341 0.011972388 41.53938987 -1.618460113 -0.120729138 QDEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDEFKR 6 1 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 ; 108.09 0.049246 1180330000 2117100 1534300 1766560 1699050 2312150 2373810 2253190 1856050 1873370 1123850 FALSE TRUE 2200684.743 1797804.09 1812598.005 2035117.019 1919131.569 1822528.603 2076579.08 1831172.686 1805947.78 1344046.89 1.637357118 1.337605186 1.348612179 1.514171145 1.427875458 1.356000759 1.545019817 1.362432144 1.343664267 1 20.35815204 0.636636764 1.243738832 1.000251828 1.441227999 0.676624968 0.092154011 0.685526099 1.612338641 0.082527496 0.024975616 4.331484497 -0.636636764 0.44097617 QDEHGYIS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 1 QDEHGYIS(1)R 84.169 0.016441 105770000 67868 107250 90979 58195 103050 113840 66917 99513 77990 129600 TRUE FALSE 70547.48105 125669.3532 93349.98748 69705.79731 85533.59781 87402.38526 61671.87068 98179.19101 75183.15513 154992.6387 0.455166656 0.810808528 0.602286588 0.44973618 0.551855872 0.563913138 0.397901934 0.633444219 0.485075651 1 17.24184017 -1.60002618 4.655206736 1.006103728 0.555823057 0.59348919 0.111630236 0.006922055 0.000594741 0.105799882 0.024705187 0.02511735 1.60002618 -0.450280671 QDEHGYISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;;;; 149.94 8.64E-05 3.33705E+11 90615194 104715900 102287800 100849560 111923250 134540140 103558260 109313390 106420120 100159760 FALSE TRUE 94192751.83 122700041.2 104953504.1 120797302 92898575.94 103295231.5 95441092.98 107848222.8 102590080.7 119784147.3 0.786354071 1.024342904 0.876188598 1.00845817 0.775549837 0.862344758 0.79677566 0.900354723 0.856457912 1 26.83586175 5.04086359 15.33833903 0.89113132 0.342708967 0.138411555 0.082440671 2733339.699 29754589.85 0.018878854 41585665.11 109866.0702 -5.04086359 -0.548422353 QDELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDELKR 6 1 Q86VP6;Q86VP6-2;A0A0C4DGH5;O75155-2;O75155;P56385 Q86VP6 CAND1;CAND2;ATP5I "Cullin-associated NEDD8-dissociated protein 1;Cullin-associated NEDD8-dissociated protein 2;ATP synthase subunit e, mitochondrial" 0 ;; 121.52 0.031454 1029460000 2768890 1952700 2443360 2196150 3013690 3215620 3016650 2507230 2649200 1607000 FALSE TRUE 2878207.915 2288061.035 2507035.969 2630541.915 2501424.05 2468840.988 2780197.09 2473624.683 2553855.809 1921860.882 1.49761512 1.190544569 1.304483583 1.368747311 1.301563539 1.284609626 1.446617243 1.287098721 1.328845305 1 20.87407248 0.048021884 1.503737875 0.999730955 1.33091911 0.596964333 0.082409098 12.60408006 18.87402971 0.081508615 0.020959135 1.116919529 -0.048021884 0.331188155 QDENDDDDDWNPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QDENDDDDDWNPCK 14 0 Q14974;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 360.32 4.15E-82 2796850000 4552880 2468440 3392330 2630390 4441960 4691840 3947560 3370620 3918530 2070210 FALSE TRUE 4732631.218 2892375.368 3480736.907 3150673.291 3686917.226 3602231.266 3638139.932 3325442.352 3777502.871 2475828.013 1.911534724 1.168245675 1.405888005 1.272573569 1.489165324 1.454960218 1.469463918 1.343163715 1.525753344 1 21.23947967 -1.433369475 2.90859304 0.990344023 1.429866209 0.338447086 0.186598911 19187975.73 22062023.76 1520165.626 0.040335002 0.036866382 1.433369475 0.439522186 QDFVQHFSQIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDFVQHFSQIVR 12 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ; 200.16 1.63E-07 3383200000 894100 5562300 4655700 5688200 4784700 7572500 3493600 6215000 4507400 6697300 FALSE TRUE 929399.7584 6517581.756 4777031.367 6813308.982 3971398.403 5813901.637 3219762.503 6131698.091 4345179.554 8009507.707 0.116037064 0.81373063 0.596420097 0.850652653 0.495835518 0.725875029 0.401992559 0.76555243 0.5425027 1 22.93328214 -5 0.274454842 3.746999668 0.581525372 0.257125647 0.209325434 299.3552849 2.890205201 467.4353111 0.227610794 1.00E-05 5 -3.165474297 QDGGQNESFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDGGQNESFKR 11 1 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 68.359 0.092123 71045000 86516 88527 105240 84508 118800 138680 115040 100590 111580 100250 FALSE TRUE 89931.71848 103730.8236 107982.6409 101223.4302 98606.41843 106473.6717 106022.8642 99241.75558 107564.2576 119892.0681 0.750105657 0.865201721 0.900665428 0.844287965 0.822459901 0.888079365 0.884319254 0.827759143 0.897175762 1 16.87137669 -5 0.196773118 1.653474162 0.829016731 0.577781381 0.040147025 104.8606886 1.03444966 26.88617165 0.100157872 1.00E-05 5 -0.824457431 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPK 38 2 O43809;H3BND3 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 280.84 7.31E-77 339840000 265180 175984 254580 202716 308100 309270 272160 274110 293020 174029 FALSE TRUE 275649.5112 206207.883 261214.5639 242812.6198 255729.2721 237446.7295 250827.388 270436.0038 282474.2674 208126.6506 1.324431592 0.99078077 1.255075038 1.16665799 1.228719491 1.140876139 1.205167082 1.299381906 1.357222954 1 17.66710219 1.988182895 22.12298218 1.25216836 1.179454144 0 0.119694682 332.6952241 622841.8333 0.043638466 0.029921883 97.31569635 -1.988182895 -0.072714216 QDHAQQLATAAEER ddPTM_MDA-MB-175_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 ; 184.48 1.29E-06 1385800000 1220040 1500340 1332100 1427050 1427060 1731890 1179440 1548790 1205630 1359000 FALSE TRUE 1268208.121 1758011.724 1366815.62 1709316.231 1184488.851 1329684.795 1086992.411 1528031.003 1162239.612 1625270.03 0.780306101 1.081673624 0.840977557 1.051712146 0.72879511 0.818131615 0.668807269 0.940170541 0.715105546 1 20.632248 3.230562218 24.99983104 0.808399967 0.941904253 0.197323887 0.12513558 261.6728601 817885.1392 0.033168519 0.040316063 1700.443545 -3.230562218 0.133504286 QDHPSSMGVYGQESGGFSGPGENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDHPSSMGVYGQESGGFSGPGENR 24 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;Q01844-4 B0QYK0 EWSR1 RNA-binding protein EWS 0 ;; 301 3.33E-62 518360000 153384 432725 416654 432397 409497 559875 356247 456450 397407 504939 FALSE TRUE 159439.7188 507042.1526 427512.3455 517923.836 339890.8462 429852.5162 328323.4293 450332.0344 383104.3997 603872.1294 0.264028941 0.839651522 0.707951774 0.857671369 0.562852348 0.71182705 0.543696941 0.745740716 0.634413117 1 19.20388356 QDIAFAYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 111.61 0.0048794 90473000 138910 136800 146480 124020 183770 206550 156380 136430 139520 165220 FALSE TRUE 144394.2741 160294.3358 150297.3891 148550.7858 152532.841 158581.8928 144122.527 134601.379 134498.7025 197591.6957 0.730770965 0.811240246 0.760646284 0.751806827 0.771959776 0.802573672 0.729395669 0.681209696 0.680690056 1 17.59216279 2.211906942 24.80905927 0.738686302 0.771938494 0 0.089302295 873.4373316 812983.4646 0.031093103 0.022970624 162.8946955 -2.211906942 0.033252192 QDKDDIINIFSVASGHLYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDKDDIINIFSVASGHLYER 20 1 Q9NYU2-2;Q9NYU2 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 90.968 0.0011184 61565000 64508 131100 147610 140920 137900 184640 134930 124980 101180 167770 FALSE TRUE 67054.82565 153615.4052 151456.8379 168793.5554 114459.8073 141760.1582 124353.834 123304.8475 97538.55156 200641.3193 0.334202476 0.765621985 0.754863646 0.841270163 0.57046977 0.706535218 0.61978178 0.614553612 0.486133922 1 17.61425921 -1.490478246 3.094503249 1.009425787 0.644030977 0.378348902 0.140595769 151513911.4 178880272.3 12164170.41 0.03280469 0.032323751 1.490478246 -0.36539481 QDLECDKISLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDLECDKISLER 12 1 Q0VF96;Q0VF96-2;Q9P2M7 Q0VF96;Q9P2M7 CGNL1;CGN Cingulin-like protein 1;Cingulin 0 80.632 0.018074 373430000 271690 220660 275930 188800 315060 354410 237460 247130 266500 199760 FALSE TRUE 282416.531 258556.6385 283120.9625 226144.0765 261506.2137 272103.6486 218847.2647 243817.6266 256908.7171 238899.1474 1.18215797 1.082283639 1.185106626 0.946608973 1.094630168 1.138989618 0.916065491 1.020588099 1.075385659 1 17.86604218 7.999999946 0.299747314 1.005170194 2.481704656 0.309114444 0.073078671 63.90223744 0.913605425 0.072391492 50.57177843 99999987.55 -7.999999946 1.476534462 QDLPALEEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QDLPALEEKPR 11 1 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 179.67 6.38E-06 1700910000 2216600 1529640 1906610 1727490 2319160 2350420 2485760 2038180 2196870 1225240 FALSE TRUE 2304113.08 1792343.771 1956297.823 2069182.366 1924950.012 1804570.576 2290919.636 2010861.531 2117805.078 1465302.319 1.57244894 1.223190428 1.335081367 1.412119764 1.313687958 1.231534648 1.563445035 1.372318534 1.445302481 1 20.48276692 -2.189956168 2.208289009 0.000106099 1.380526827 0.508495765 0.113596082 1618313.681 378865.2852 8070262.773 0.026069019 0.006457194 2.189956168 1.380420728 QDLPDAMKPHEIQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QDLPDAMKPHEIQEK 15 1 P62330 P62330 ARF6 ADP-ribosylation factor 6 0 ;;; 233.14 7.63E-18 1329420000 3098340 1429910 2281230 1461500 2870600 2823980 3005100 2285970 2678440 1114540 FALSE TRUE 3220664.856 1675485.919 2340680.728 1750580.338 2382656.437 2168153.443 2769552.41 2255330.311 2582043.468 1332912.774 2.416260778 1.257010925 1.756064443 1.31334951 1.787556158 1.626628153 2.077819692 1.692031433 1.937143614 1 20.34615094 QDLPNAMNAAEITDKLGLHSLR ddPTM_MDA-MB-175_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 ;; 202.17 1.31E-22 6699360000 893590 865320 1041930 831210 1205990 1225900 946180 1031600 1127540 863730 FALSE TRUE 928869.6232 1013931.979 1069083.552 995620.8571 1000996.251 941203.3037 872015.9392 1017773.089 1086960.056 1032961.356 0.89922979 0.981577842 1.034969552 0.96385102 0.969054887 0.911169908 0.844190282 0.985296384 1.052275624 1 19.97835485 1.477409935 11.9816174 1.023725613 0.946599922 0.304913017 0.050199051 0.099447883 86.59917156 0.029195012 0.013512971 30.01994796 -1.477409935 -0.077125691 QDLPSLDEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QDLPSLDEKPR 11 1 Q92598-2;Q92598;Q92598-4;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 166.48 1.86E-05 2161090000 2220550 1556300 2029990 1908940 2406570 2581380 2510850 2225410 2293430 1288420 FALSE TRUE 2308219.029 1823582.419 2082893.207 2286522.634 1997502.091 1981893.616 2314043.016 2195582.019 2210889.902 1540861.231 1.498005779 1.183482576 1.351772091 1.483925086 1.296354306 1.286224597 1.501785476 1.424905744 1.434840373 1 20.55530551 QDPGTELLHCENEDLICFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDPGTELLHCENEDLICFK 19 0 Q9NQE9 Q9NQE9 HINT3 Histidine triad nucleotide-binding protein 3 0 ;; 223.44 2.20E-19 335205000 230471 173006 223668 205668 259210 271583 226101 241579 259395 183893 FALSE TRUE 239570.173 202718.4347 229496.9718 246348.5165 215149.5768 208511.9641 208378.6128 238341.0286 250059.4246 219923.3125 1.089335052 0.92176874 1.043531808 1.120156448 0.978293635 0.948112148 0.947505794 1.083746084 1.137030094 1 17.74664102 1.62356524 9.195719395 1.083423218 1.006261969 0.164256484 0.06772498 0.164258526 34.5944339 0.034114984 0.01748452 42.03056619 -1.62356524 -0.077161249 QDPSVLHTEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 QDPSVLHTEEMR 12 0 P50502;Q3KNR6;Q8NFI4;F8WAQ7 P50502 ST13;ST13P5 Hsc70-interacting protein;Putative protein FAM10A5 0 ;;;;;;;; 216.34 3.93E-11 12461720000 6301040 8333220 8000310 7889060 8175880 9899010 7637010 8454210 7853450 8202650 FALSE TRUE 6549809.925 9764385.712 8208804.651 9449492.522 6786146.838 7600114.948 7038401.201 8340895.143 7570805.869 9809802.218 0.66768012 0.995370293 0.836796142 0.963270442 0.691772034 0.774747011 0.717486555 0.850261296 0.771759277 1 23.22579262 4.990277429 12.6583842 0.831563369 0.544315891 0.191764194 0.105965632 65969.92929 1860486.533 0.024509092 242433.2095 97786.16835 -4.990277429 -0.287247478 QDS(ph)DEDDGPQRVEEVDQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDSDEDDGPQRVEEVDQGR 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 QDS(1)DEDDGPQRVEEVDQGR;QDS(1)DEDDGPQRVEEVDQGR 149.04 5.42E-08 700070000 341760 304690 319350 298100 350690 497090 399820 327430 353380 233090 TRUE FALSE 355252.9487 357018.1373 327672.5233 357063.2903 291079.8391 381648.381 368481.0637 323041.3364 340661.9228 278759.5227 1.274406504 1.280738803 1.175466654 1.280900781 1.044196934 1.369095403 1.321860003 1.158853098 1.222063804 1 18.08866156 0.446048396 1.111613856 1.000025321 1.240368304 0.400695613 0.087403887 2.210269612 3.470811116 0.082191405 0.02519683 2.792855051 -0.446048396 0.240342983 QDS(ph)DSDVVDIEEAEHDFMGEAHPVVFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 QDS(1)DSDVVDIEEAEHDFMGEAHPVVFSR;QDS(0.999)DS(0.001)DVVDIEEAEHDFMGEAHPVVFSR 244.61 2.98E-45 148292000 69019 80030 74100 71173 86946 119311 87865 82882 79112 68829 TRUE FALSE 71743.92341 93774.52995 76031.10687 85250.80697 72166.94998 91602.82843 80977.91171 81771.10236 76264.77457 82314.72474 0.871580676 1.139219383 0.923663501 1.03566898 0.876719812 1.112836479 0.983759734 0.993395806 0.926502212 1 16.32886291 1.42098498 19.37811194 0.962147572 0.995921491 0.016316498 0.085746992 42.17297061 14557.00498 0.049566155 0.018956997 26.36240209 -1.42098498 0.033773919 QDS(ph)LEPVLRDPCYLINEGICNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDSLEPVLRDPCYLINEGICNR 22 1 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;E7EWD5 D6RD37 TSC22D3 1 QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR;QDS(1)LEPVLRDPCYLINEGICNR 212.82 9.90E-24 287948000 77826 69795 94964 65115 115565 106571 90959 90387 106159 67794 TRUE FALSE 80898.63057 81781.74832 97438.83985 77994.55265 95921.30258 81821.50035 83829.3959 89175.51011 102338.3583 81076.93631 0.997800784 1.008693126 1.201807127 0.961981991 1.183089877 1.009183426 1.033948737 1.099887516 1.26223761 1 16.30700395 1.490777154 6.762194247 1.147047587 1.06059783 0.08725327 0.094676325 0.245666735 27.63182097 0.049528289 0.022205282 30.95830356 -1.490777154 -0.086449758 QDS(ph)WEVVEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDSWEVVEGLR 11 0 Q9H4L5-5;Q9H4L5;Q9H4L5-7;Q9H4L5-3;C9J8P4;C9JEF2;C9JZ19;Q9H4L5-6;Q9H4L5-2;Q9H4L5-8;Q9H4L5-4 Q9H4L5-5;Q9H4L5-6 OSBPL3 Oxysterol-binding protein-related protein 3 1 QDS(1)WEVVEGLR 115.82 0.0011249 17827000 22926 25208 21996 25437 31817 36567 28272 22993 27539 20116 TRUE FALSE 23831.13618 29537.27791 22569.23383 30468.36268 26408.7577 28074.86843 26055.96676 22684.81644 26547.87677 24057.34506 0.990597097 1.227786268 0.938143165 1.266488992 1.097741985 1.166997786 1.083077401 0.942947627 1.103524795 1 14.55418982 1.984225618 19.90229144 1.010116619 1.118479273 0.164632854 0.099424869 72.97338828 92067.54102 0.036678171 0.024583683 96.4329868 -1.984225618 0.108362654 QDSDS(ph)DVVDIEEAEHDFMGEAHPVVFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 QDS(0.463)DS(0.537)DVVDIEEAEHDFMGEAHPVVFSR 85 0.0044264 19672000 12923 14413 14143 10923 16102 18431 15243 14683 12549 12252 TRUE FALSE 13433.21002 16888.32063 14511.5782 13083.5368 13364.98779 14150.67957 14048.21383 14486.1984 12097.36394 14652.54482 0.916783411 1.152586178 0.990379376 0.892919077 0.912127412 0.965748936 0.958755902 0.988647268 0.825615215 1 13.83886363 4.00082999 24.99216514 0.93937029 1.043884294 0.241099624 0.071404942 34.64818374 1043151.931 0.016625231 0.035440218 10019.12951 -4.00082999 0.104514004 QDSGEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QDSGEWR 7 0 Q96G03-2;Q96G03 Q96G03-2;Q96G03 PGM2 Phosphoglucomutase-2 0 ;; 84.568 0.049902 1487120000 1862540 1884890 1869640 1818520 2180190 3066100 2041510 1899670 1828320 1780310 FALSE TRUE 1936074.517 2208605.195 1918364.354 2178217.828 1809602.083 2354044.742 1881491.112 1874208.031 1762519.12 2129127.658 0.909327588 1.037328685 0.90100955 1.023056471 0.84992653 1.105638139 0.883691076 0.880270388 0.827812796 1 21.02183102 2.100016174 21.18944337 0.886907625 0.969982851 0.1595348 0.080588728 6.437461691 1348.136113 0.027478269 0.020294055 125.8972298 -2.100016174 0.083075226 QDVEALWENMAVIDCFASDHAPHTLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QDVEALWENMAVIDCFASDHAPHTLEEK 28 0 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 ; 220.13 1.53E-34 52824000 26704 33976 44546 43632 51772 62597 47055 45680 49109 37530 FALSE TRUE 27758.29454 39811.1137 45706.90535 52262.27937 42971.81393 48059.79542 43366.70614 45067.73432 47341.57668 44883.28494 0.618455057 0.886991978 1.01835027 1.164404063 0.957412408 1.070772682 0.96621061 1.004109534 1.054770762 1 15.45389065 4.65760435 2.188079166 1.028718167 0.550816488 0.833236212 0.056291064 0.194853331 1.219586692 0.014180983 0.169329677 45457.37469 -4.65760435 -0.47790168 QDYINLDESEAAAFDDEWRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QDYINLDESEAAAFDDEWRR 20 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 84.946 0.0052105 0 10410 10486 7059.2 7767.5 9317.1 12755 9984.1 9277.9 9191 9751.4 FALSE TRUE 10820.99484 12286.88893 7243.168551 9303.888316 7733.38267 9792.844554 9201.520153 9153.544926 8860.217705 11662.00013 0.927884987 1.05358333 0.621091448 0.797795251 0.663126615 0.839722556 0.789017326 0.784903518 0.759751124 1 13.50952762 4.253859656 24.99999387 0.773755078 0.990734225 0.408801182 0.100057342 200.081309 326944.8952 0.022000383 0.059769353 17941.53744 -4.253859656 0.216979147 QEAEDLSLSAPSSPEISPQS(ph)SPRPHRPNNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEAEDLSLSAPSSPEISPQSSPRPHRPNNDR 31 2 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 QEAEDLSLSAPS(0.053)S(0.053)PEIS(0.262)PQS(0.316)S(0.316)PRPHRPNNDR 68.516 0.0027533 173220000 8724.6 15435 21526 19723 19987 21708 15075 16744 23007 26159 TRUE FALSE 9069.053945 18085.84118 22086.98524 23624.15053 16589.61688 16666.64599 13893.38211 16519.57407 22178.98256 31284.35521 0.28989103 0.578111362 0.706007367 0.755142638 0.530284763 0.532746987 0.444099999 0.528045854 0.708948048 1 14.93315375 0.925575829 3.295725691 0.999467724 0.552466 0.567713843 0.121617184 0.24754409 6.462480798 0.121650486 0.031619884 8.425114827 -0.925575829 -0.447001724 QEAGDS(ph)PPPAPGTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEAGDSPPPAPGTPK 15 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 QEAGDS(1)PPPAPGTPK 218.36 2.04E-12 165360000 256380 166500 223330 179840 260210 289580 254370 202730 234130 133560 TRUE FALSE 266502.0804 195095.0798 229150.1633 215411.8152 215979.5971 222329.4336 234431.8147 200012.7359 225703.707 159728.5248 1.668468926 1.221416651 1.434622673 1.348612062 1.35216673 1.391920659 1.467689099 1.252204239 1.413045712 1 17.28526245 -3.51283068 0.252467385 1.50E-14 1.422444379 0.520203763 0.115183694 61.10169794 1.194098422 31.90570964 0.152106339 0.000307022 3.51283068 1.422444379 QEAGISEGQGTAGEEEEKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QEAGISEGQGTAGEEEEKKK 20 2 O43583;F8VVL1 O43583 DENR Density-regulated protein 0 ;; 207.37 3.79E-22 602190000 1271670 324142 553221 262181 932520 881080 713480 543610 697720 209192 FALSE TRUE 1321876.514 379810.867 567638.3937 314039.6193 774010.5835 676462.5229 657555.5733 536323.7971 672609.1935 250179.1672 5.283719378 1.518155454 2.268927506 1.255258872 3.093825086 2.703912282 2.628338645 2.143758824 2.688510003 1 17.93260213 -1.45110138 0.275640127 5.26E-39 2.720973142 0.187361094 1.032629421 39.89717266 2.152141503 32.52410361 1.286665108 0.035391472 1.45110138 2.720973142 QEALEWLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEALEWLIR 9 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 130.66 0.0027162 0 138180 149710 161980 137040 171480 198790 151670 153380 152080 171270 FALSE TRUE 143635.4531 175421.5279 166201.3319 164146.103 142331.8909 152624.0352 139781.7091 151324.192 146606.6705 204827.0773 0.701252271 0.856437197 0.81142266 0.801388689 0.694888062 0.74513603 0.682437649 0.738789978 0.71575825 1 17.64404692 -1.080993098 3.852181498 1.000067143 0.750623234 0.65991111 0.053897286 8342456338 14854967797 7579447.051 0.013695536 0.082986396 1.080993098 -0.249443909 QEALKNDLVEALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEALKNDLVEALKR 14 2 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 163.8 2.37E-06 1101190000 2326400 1363740 1830790 1249880 2496920 2307350 2268170 2042920 2352840 1203780 FALSE TRUE 2418248.068 1597951.737 1878501.891 1497102.533 2072494.43 1771502.931 2090384.909 2015537.999 2268161.748 1439637.643 1.679761626 1.109968015 1.304843549 1.039916218 1.439594498 1.230520012 1.452021568 1.400031465 1.575508781 1 20.4572743 2.239317217 24.99997287 1.393483919 1.286733366 0.002192259 0.215620628 65.42256724 2161821.807 0.072267108 0.05717801 173.5070862 -2.239317217 -0.106750553 QEARPEPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QEARPEPAR 9 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ;; 147.3 8.46E-05 895120000 1191330 1583390 1255490 1314790 1859510 1980050 1377980 1365270 1321000 1718410 FALSE TRUE 1238364.628 1855324.915 1288209.101 1574851.538 1543431.154 1520213.395 1269970.327 1346970.789 1273457.468 2055099.539 0.602581337 0.90279078 0.62683538 0.766313995 0.751025011 0.739727379 0.617960494 0.655428491 0.619657318 1 20.97077684 -1.028678611 5.131834304 1.000003108 0.699976808 0.5071475 0.089285022 3.05E-06 5.77E-07 0.083056574 0.019576419 0.093609816 1.028678611 -0.300026301 QEASTGQSPEDHASLAPPLS(ph)PDHSSLEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEASTGQSPEDHASLAPPLSPDHSSLEAK 29 0 P48681 P48681 NES Nestin 1 QEASTGQSPEDHASLAPPLS(0.996)PDHS(0.003)S(0.001)LEAK 137.91 3.91E-06 67204000 22946 35843 37648 35094 34671 54400 42766 44824 40598 34920 TRUE FALSE 23851.9258 41998.75643 38629.13781 42035.48845 28777.6358 41766.42444 39413.88917 44223.2076 39136.88591 41761.90542 0.571140746 1.005671461 0.924985041 1.006551019 0.68908819 1.000108209 0.943776123 1.058936539 0.937143206 1 15.34989992 QEDKDDLDVTELTNEDLLDQLVK ddPTM_MDA-MB-175_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 ;;; 305 2.41E-62 534319000 750520 329637 506061 312191 689250 738155 659414 474974 592734 248445 FALSE TRUE 780151.1091 386249.5905 519249.3654 373941.448 572091.5312 566729.6881 607727.4076 468607.7504 571401.6191 297123.041 2.625683645 1.299965123 1.747590371 1.258540727 1.925436443 1.907390575 2.045372872 1.577150493 1.923114469 1 18.18070096 -1.40655426 4.617875984 0.998582107 1.78001647 0.296296061 0.372559722 0.005031792 0.000646639 0.333748983 0.078540789 0.039214415 1.40655426 0.781434363 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 229.6 1.45E-25 1030340000 428245 470264 476430 518740 453980 584010 505010 502910 511120 391611 TRUE FALSE 445152.4433 551028.1839 488846.1572 621345.2237 376812.6418 448382.5283 465425.9966 496169.314 492724.891 468339.6776 0.950490562 1.176556696 1.043785484 1.326697808 0.804571254 0.957387447 0.993778701 1.059421906 1.052067366 1 18.83719574 3.232728113 24.99998089 0.986285962 1.12235241 0.291436433 0.11143615 194.4748345 833581.009 0.031608676 0.038749161 1708.945108 -3.232728113 0.136066448 QEEEEAMRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEEEEAMRR 9 1 A0A024R7W5;A0A087X0Q1;A0A087WY31;Q7Z739 A0A024R7W5 YTHDF3 YTH domain-containing family protein 3 0 70.977 0.053399 60854000 13582 38244 29343 22486 17550 31842 19600 23418 22086 37919 FALSE TRUE 14118.22785 44812.1095 30107.70269 26933.66369 14566.85727 24447.17807 18063.70078 23104.12001 21291.12917 45348.50205 0.311327325 0.988171769 0.663918351 0.593926204 0.321220252 0.539095603 0.398330705 0.509479232 0.469500165 1 15.46876728 -1.274684369 3.44932907 1.001450217 0.53784542 0.362564974 0.185744934 55576803.95 84338189.36 847013.8184 0.045811373 0.053127041 1.274684369 -0.463604797 QEEEMMAKEEELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEEEMMAKEEELVK 14 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 160.48 4.33E-06 173204000 318663 186233 294100 90765 492410 360190 212471 243165 355690 232358 FALSE TRUE 331244.0613 218217.0691 301764.4876 108718.0461 408710.3241 276541.3312 195816.9678 239905.7709 342888.7864 277884.1013 1.192022356 0.785280871 1.085936497 0.391235215 1.470794198 0.995167877 0.704671361 0.863330323 1.233927327 1 18.08412377 4.76415182 22.23640267 0.933808773 1.192023816 0.06212429 0.279934163 4651.522368 4041449.259 0.063444641 3.587564826 58096.74761 -4.76415182 0.258215042 QEES(ph)ESPVERPLKENPPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.562)ES(0.438)PVERPLKENPPNK 81.373 0.0031146 185120000 157510 104370 135790 112910 174940 151570 179980 133010 149160 81896 TRUE FALSE 163728.6164 122294.7356 139328.799 135243.261 145203.7613 116370.1646 165872.6973 131227.2185 143791.7607 97941.95321 1.671690334 1.248645056 1.422565044 1.380851173 1.482549168 1.18815442 1.693581676 1.33984686 1.46813246 1 16.57963935 -1.675896416 2.633605056 0.940518995 1.425022311 0.41746592 0.153154953 18951785.56 16149845.36 7559680.262 0.036334137 0.021091311 1.675896416 0.484503316 QEESES(ph)PVERPLKENPPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEESESPVERPLKENPPNK 19 2 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 QEES(0.259)ES(0.741)PVERPLKENPPNK 80.786 0.0035498 101990000 122910 110200 130940 100340 147680 143320 160740 143920 151020 78958 TRUE FALSE 127762.5817 129125.9928 134352.404 120186.9525 122577.4063 110036.102 148140.7788 141990.9878 145584.8197 94428.30836 1.353011443 1.367450026 1.422797954 1.272785191 1.298100204 1.165287232 1.568817459 1.503690898 1.541749738 1 16.5269318 2.228132442 24.99836934 1.456172125 1.318155875 0.029967814 0.164556363 407.1406322 975988.44 0.0576428 0.043026594 169.0956527 -2.228132442 -0.13801625 QEETAVLEEDS(ph)ADWEKELQQELQEYEVVTESEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR 34 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 QEETAVLEEDS(1)ADWEKELQQELQEYEVVTESEKR 199.85 2.02E-27 16510000 52731 26168 36920 20714 45588 45104 42248 38757 39121 19863 TRUE FALSE 54812.8606 30662.15044 37882.16553 24811.16737 37838.96804 34629.27956 38936.49137 38237.52581 37713.04285 23754.77455 2.307446046 1.290778423 1.594717957 1.044470758 1.592899481 1.457781865 1.639101701 1.609677487 1.587598433 1 14.53592989 4.745600533 24.88570167 1.459523369 2.307446466 0.570979807 0.227853674 568.7114606 2010308.609 0.051738586 0.522666842 55667.34815 -4.745600533 0.847923097 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEETAVLEEDSADWEKELQQELQEYEVVTESEKR 34 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 165.37 1.40E-14 33735000 31841 15403.3 19467.5 15757.1 32718 28470 24202 23665 29938 11828.5 FALSE TRUE 33098.10727 18048.69695 19974.83904 18873.80735 27156.60605 21858.27397 22304.984 23347.80938 28860.53723 14146.0681 2.339739002 1.275880819 1.41204177 1.334208715 1.919728213 1.545183708 1.576762096 1.650480488 2.040180848 1 13.78811349 3.260736225 24.99191651 1.64697908 1.555252636 0 0.377587612 1598.397121 1801382.546 0.099201012 0.134215073 1822.788271 -3.260736225 -0.091726444 QEFAQHANAFHQWIQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEFAQHANAFHQWIQETR 18 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 314.21 1.71E-61 991040000 393670 579450 453670 453830 553640 668290 365030 467090 363200 679740 FALSE TRUE 409212.3956 678966.03 465493.0129 543596.2195 459532.4706 513089.7755 336417.9948 460829.4226 350128.5029 812922.0386 0.503384551 0.83521666 0.572617042 0.66869416 0.565284798 0.63116726 0.413837956 0.566880218 0.430703667 1 19.63275748 -1.087259176 4.903346614 1.000014058 0.579841565 0.550392325 0.114814035 1.73E-05 3.23E-06 0.109271386 0.025754651 0.08179765 1.087259176 -0.420172493 QEFEFWYPVDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QEFEFWYPVDLR 12 0 A0A6I8PL42;A0A6I8PIT3;A0A6I8PIV1;Q9P2J5;A0A6I8PLB3;A0A6I8PRS0;B4DER1;Q9P2J5-2;A0A6I8PS05;A0A6I8PLB8;A0A6I8PIP7;A0A6I8PTV8;A0A6I8PRP1 A0A6I8PL42 LARS "Leucine--tRNA ligase, cytoplasmic" 0 ;;; 164.13 0.0001352 212619000 218682 242516 228718 279536 229831 280758 274590 254490 233362 197789 FALSE TRUE 227315.7342 284166.2365 234678.579 334827.3865 190764.4087 215556.2094 253066.9183 251078.9778 224963.3472 236541.9677 0.960995364 1.201335388 0.992122376 1.415509433 0.806471725 0.911281036 1.069860544 1.061456368 0.95105046 1 17.85173665 3.2098297 24.99999511 0.980457987 1.135953929 0.283037554 0.135860691 303.0040198 263655.8465 0.038593142 0.046135457 1621.174262 -3.2098297 0.155495942 QEGHLDSES(ph)PTNIPLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEGHLDSESPTNIPLTK 17 0 H7BXC7;Q9H7P9-3;Q9H7P9;E7ESZ3 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 QEGHLDS(0.024)ES(0.765)PT(0.212)NIPLTK 59.356 0.056014 119570000 127450 104290 127330 129680 159540 174430 167640 155770 158160 118920 TRUE FALSE 132481.8244 122200.9962 130648.3244 155330.3169 132421.4478 133921.276 154499.9388 153682.1579 152467.8525 142220.0971 0.931526747 0.859238594 0.918634757 1.09218261 0.931102217 0.941648042 1.086343927 1.080593819 1.072055606 1 17.11776582 3.556247251 0.555295786 1.063684541 0.866491587 0.42111707 0.061887769 1.255395876 0.686527559 0.044803514 0.139508192 3599.542048 -3.556247251 -0.197192954 QEIFQEQLAAVPEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEIFQEQLAAVPEFR 15 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 177.84 1.71E-06 30632000 26383 34564 31762 32333 31344 35847 29326 38197 32349 35877 FALSE TRUE 27424.62121 40500.09813 32589.74381 38728.3709 26016.15808 27522.07752 27027.35149 37685.03169 31184.76581 42906.41124 0.639173038 0.943917167 0.759554175 0.902624335 0.606346635 0.641444407 0.629914055 0.878307707 0.726808999 1 15.38890562 -1.566522355 7.331451884 1.000162632 0.754966628 0.292461479 0.117283214 0.00031039 1.84E-05 0.113056767 0.026630262 0.02713174 1.566522355 -0.245196003 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.774)S(0.121)PT(0.091)AT(0.003)DS(0.009)T(0.002)S(0.001)GDSSR;QEKPAEKPAETPVAT(0.896)S(0.09)PT(0.015)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.606)S(0.335)PT(0.054)AT(0.005)DSTSGDSSR 210.59 1.44E-25 15202700000 2166051 1220991 1804930 1175090 2381204 2027256 2220902 1742964 1985254 1001184 TRUE FALSE 2251568.366 1430686.706 1851967.959 1407519.295 1976447.795 1556456.517 2046821.898 1719602.418 1913805.096 1197346.836 1.880464623 1.194880767 1.546726398 1.175531811 1.650689454 1.299921185 1.70946449 1.436177361 1.598371532 1 20.19140969 -1.062559446 4.98210457 0.999989619 1.48608535 0.3227888 0.216149207 2.20E-05 4.15E-06 0.18500713 0.043605668 0.08658458 1.062559446 0.486095731 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 QEKPAEKPAETPVAT(0.037)S(0.962)PTATDSTSGDSSR;QEKPAEKPAETPVAT(0.024)S(0.976)PTATDSTSGDSSR;QEKPAEKPAETPVAT(0.024)S(0.929)PT(0.045)AT(0.002)DSTSGDSSR;QEKPAEKPAETPVAT(0.122)S(0.822)PT(0.047)AT(0.008)DSTSGDSSR;QEKPAEKPAETPVAT(0.01)S(0.961)PT(0.028)AT(0.001)DSTSGDSSR;QEKPAEKPAETPVAT(0.175)S(0.82)PT(0.005)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.154)S(0.754)PT(0.091)ATDSTSGDSSR;QEKPAEKPAETPVAT(0.001)S(0.996)PT(0.003)ATDSTSGDSSR;QEKPAEKPAET(0.043)PVAT(0.083)S(0.83)PT(0.04)AT(0.003)DSTSGDSSR;QEKPAEKPAETPVAT(0.067)S(0.929)PT(0.003)ATDSTSGDSSR 186.05 3.62E-18 52819680000 11856293 6510601 9458879 6266022 11891910 11455870 11450129 9467227 10919847 5266277 TRUE FALSE 12324388.6 7628746.076 9705385.157 7505422.449 9870527.386 8795417.808 10552637.97 9340334.307 10526843.84 6298103.149 1.956841339 1.211276776 1.541001303 1.191695701 1.56722225 1.396518539 1.67552638 1.483039272 1.67143084 1 22.58648596 -1.885184788 2.572622008 0.743745689 1.505896099 0.344098225 0.215064966 17638163.69 11217648.12 27531818.14 0.048463937 0.013026124 1.885184788 0.76215041 QEKPAEKPAETPVATSPTATDSTSGDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;P54727-2;H0Y579 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 ;; 179.81 6.49E-18 1934040000 855710 491045 687830 456465 890380 822340 822770 655800 814180 418015 FALSE TRUE 889494.0916 575378.159 705755.4149 546752.4146 739033.5256 631363.9977 758279.1375 647010.0737 784877.8208 499917.0359 1.779283417 1.150947293 1.411745078 1.093686303 1.478312345 1.262937552 1.516809957 1.294234897 1.570016152 1 18.93132917 -2.210814581 2.008105051 2.95E-05 1.377287513 0.265388262 0.195253236 2960893.121 526181.0377 13436167.09 0.045023317 0.006154396 2.210814581 1.377257968 QEKPVNGEDKGDSGVDTQNS(ph)EGNADEEDPLGPNCYYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK 38 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 QEKPVNGEDKGDSGVDT(0.028)QNS(0.972)EGNADEEDPLGPNCYYDK 213.09 9.10E-32 280900000 328670 114340 193000 115210 269270 266180 255960 203830 240570 91049 TRUE FALSE 341646.1454 133977.0056 198029.7386 137998.1941 223499.5816 204363.729 235897.1864 201097.9922 231911.9327 108888.3083 3.13758337 1.230407632 1.818650153 1.267337112 2.052558122 1.876819763 2.166414283 1.846828143 2.129814819 1 16.73248953 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDK 38 2 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 151.13 1.09E-13 104610000 56238 23834 35195 25593 57210 47738 52975 41208 51501 17592 FALSE TRUE 58458.31967 27927.3041 36112.21061 30655.21901 47485.46463 36651.57298 48822.68108 40655.67416 49647.48907 21038.81558 2.778593664 1.327418076 1.716456446 1.457079126 2.257040776 1.742092982 2.320600268 1.932412688 2.359804376 1 14.36076587 3.229039317 24.99627935 1.994994399 1.777322569 0.001258378 0.517385926 741.1682374 1945786.355 0.138374479 0.167412433 1694.491196 -3.229039317 -0.21767183 QEKS(ph)PQDPGDPVQYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEKSPQDPGDPVQYNR 16 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 QEKS(1)PQDPGDPVQYNR 58.366 0.066991 348710000 251230 165200 202400 152460 243820 266250 243740 217040 229990 157790 TRUE FALSE 261148.7544 193571.8149 207674.7103 182616.133 202375.5635 204417.4726 224635.0219 214130.9338 221712.7048 188705.9294 1.38389268 1.025785546 1.100520322 0.967728643 1.072438816 1.083259404 1.190397263 1.134733468 1.174911173 1 17.52578023 2.300656911 24.99895896 1.13801343 1.093970357 0 0.113325344 279.5588262 112543.2752 0.038043483 0.031829445 199.8282619 -2.300656911 -0.044043072 QELEEICHDLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QELEEICHDLEAR 13 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 184.31 9.62E-06 99281000 90625 92527 93225 94322 91109 120864 101955 97750 85767 88727 FALSE TRUE 94202.94498 108417.7925 95654.52009 112978.6101 75622.32472 92795.16771 93963.50069 96439.82114 82680.26242 106111.3569 0.887774389 1.021735992 0.901454122 1.06471742 0.712669472 0.874507409 0.885517851 0.908854848 0.779183915 1 16.69521955 3.257246524 24.99888116 0.861687293 0.967873939 0.276709644 0.086144031 320.5447658 428837.0898 0.022431235 0.030320237 1808.200244 -3.257246524 0.106186646 QELEQS(ph)LASWTQNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QELEQSLASWTQNLK 15 0 Q8WXH0-13 Q8WXH0-13 SYNE2 Nesprin-2 1 QELEQS(0.333)LAS(0.333)WT(0.333)QNLK;QELEQS(0.412)LAS(0.294)WT(0.294)QNLK 73.156 0.064532 3618500000 206661 4462500 4440100 4628600 3465700 5319300 2921800 4192100 3912600 5415100 TRUE FALSE 214820.1359 5228899.662 4555812.654 5544123.265 2876601.552 4083973.19 2692781.681 4135911.756 3771786.29 6476085.167 0.033171296 0.807416754 0.703482511 0.856091778 0.444188345 0.630623762 0.415803933 0.638643818 0.582417648 1 22.62669053 -2.189803675 1.023126011 1.651858737 0.583185687 0.251244741 0.222352286 5213.683826 660.0438872 7818.815055 0.06328055 0.006459462 2.189803675 -1.06867305 QELGS(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 133.15 0.00029906 6351220000 2719090 3070040 3058290 2915810 3284690 3808920 3311340 3234190 3226410 3267810 TRUE FALSE 2826441.773 3597295.488 3137991.55 3492548.515 2726359.567 2924356.055 3051788.518 3190840.973 3110292.134 3908074.803 0.723231237 0.920477644 0.802950739 0.89367494 0.697622155 0.748285589 0.780893067 0.816473874 0.795862999 1 21.89802665 -1.202169891 3.810761521 1.000181595 0.800387558 0.460787596 0.065588453 22364764.39 44559748.31 49983.63489 0.015400899 0.062781272 1.202169891 -0.199794037 QELQDDKRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QELQDDKRR 9 2 P12270 P12270 TPR Nucleoprotein TPR 0 79.974 0.0143 62496000 41657 49530 50041 42691 54911 63035 29899 51509 54039 55227 FALSE TRUE 43301.65053 58036.39221 51345.10957 51135.15238 45577.24783 48396.07655 27555.43825 50818.60611 52094.14695 66047.67327 0.655612051 0.878704568 0.777394676 0.774215803 0.690065911 0.732744609 0.417205284 0.769423109 0.788735536 1 16.01122012 0.865552639 2.414680128 0.999003821 0.710364534 0.369549985 0.113907869 0.568379786 6.53027863 0.111542146 0.030076625 7.337576439 -0.865552639 -0.288639287 QELS(ph)FAARSFYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.278)FAARS(0.278)FY(0.222)Y(0.222)K 54.023 0.084833 1481400000 901240 656040 769940 624140 902110 869170 888150 844040 863370 504170 TRUE FALSE 936821.6511 768709.7667 790005.2689 747593.0291 748769.6644 667318.4399 818534.4823 832727.0244 832297.4824 602952.4586 1.553723909 1.274909416 1.310228124 1.239887189 1.241838645 1.106751337 1.357543983 1.381082393 1.380369995 1 19.20168473 4.738896663 7.362566777 1.272317998 1.557092734 0.363946009 0.116514461 0.117913922 57.78684471 0.027455628 0.166267104 54814.65223 -4.738896663 0.284774736 QELSFAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 138.4 0.0016451 2146230000 2148710 2325340 2302730 2425170 3120460 3311850 2481520 2386930 2270460 2948220 FALSE TRUE 2233542.73 2724699.056 2362741.036 2904861.388 2590045.324 2542723.029 2287011.978 2354937.108 2188746.588 3525867.262 0.633473289 0.772774144 0.670116275 0.823871454 0.7345839 0.721162438 0.648638139 0.667902939 0.620768289 1 21.74954673 -1.195017543 5.138813048 1.00002181 0.701252649 0.684062397 0.06130237 1.54E-05 2.42E-06 0.059828053 0.014100579 0.06382377 1.195017543 -0.29876916 QELSHALYQHDAACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QELSHALYQHDAACR 15 0 Q9UMS4;F5GY56;F5H2I0 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 ; 174.59 5.23E-07 609230000 150042 145064 126636 158037 158028 203658 148669 161273 172360 150854 FALSE TRUE 155965.774 169977.6136 129936.2382 189296.2469 131166.457 156361.516 137015.9353 159111.3992 166156.7973 180410.953 0.8645028 0.942169035 0.720223667 1.049250302 0.727042648 0.866696358 0.759465725 0.881938688 0.92099063 1 17.4609274 1.041769461 2.270797817 0.997865074 0.848716216 0.201269875 0.094584709 0.423121411 4.598207184 0.081866583 0.022579153 11.00954727 -1.041769461 -0.149148858 QELVDAFVEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QELVDAFVEHR 11 0 K7EIG1;A0A494C0R8;O75153;I3L2B0 K7EIG1 CLUH Clustered mitochondria protein homolog 0 109 0.0019879 63842000 79601 83174 89235 90258 88323 111010 87340 93418 87587 80250 FALSE TRUE 82743.70895 97458.4875 91560.53741 108110.763 73309.88801 85229.60987 80494.06258 92165.88451 84434.76098 95973.45102 0.862152065 1.015473409 0.954019434 1.126465307 0.763855913 0.888054029 0.838711766 0.960326877 0.879772063 1 16.55034775 3.233932687 24.99999953 0.888140969 0.988844526 0.252450221 0.085203121 161.9142561 874658.404 0.023554579 0.029053185 1713.691677 -3.233932687 0.100703556 QEMQEVQSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QEMQEVQSSR 10 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;; 272.82 2.09E-23 3720464000 1773951 2148389 2003961 1966721 2072754 2569870 1970101 2066997 1985909 1999555 FALSE TRUE 1843987.955 2517358.099 2056185.87 2355732.544 1720428.015 1973056.639 1815679.336 2039292.286 1914436.523 2391329.518 0.771114119 1.052702306 0.859850495 0.985114149 0.719444143 0.825087728 0.759276094 0.85278598 0.800574119 1 21.18938151 3.250441461 24.99999955 0.816703218 0.922778275 0.167147784 0.097834198 322.9091324 679470.3191 0.024686478 0.033163005 1780.087954 -3.250441461 0.106075057 QENESGYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QENESGYER 9 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0QYZ0;M0R0K8;M0QZV6;M0R203 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 74.772 0.06245 0 27738 34885 43964 33318 37490 52877 32083 36115 43906 30340 FALSE TRUE 28833.11766 40876.22738 45109.73796 39908.20096 31117.46319 40597.11811 29568.25063 35630.9375 42325.83164 36284.54211 0.794639149 1.126546596 1.243221916 1.09986784 0.857595587 1.118854359 0.814899373 0.981986693 1.16649761 1 15.14706744 QENGDLS(ph)PFSGTSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QENGDLSPFSGTSLR 15 0 P19174-2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 QENGDLS(0.999)PFS(0.001)GTSLR;QENGDLS(1)PFSGTSLR 164.93 4.83E-09 91794000 209177 197214 209515 213151 216386 263700 233140 228172 214528 174406 TRUE FALSE 217435.4695 231083.9704 214975.133 255311.6316 179604.785 202459.6714 214865.8776 225113.7276 206807.1792 208577.5165 1.042468398 1.107904506 1.030672609 1.224061135 0.861093698 0.970668722 1.030148797 1.07928089 0.991512329 1 17.67022413 3.242958514 24.99999959 1.000554891 1.096706894 0.365454596 0.071515839 148.861291 846201.5744 0.020738399 0.02713589 1749.679544 -3.242958514 0.096152003 QENKRPS(ph)PR ddPTM_MDA-MB-175_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 96.067 0.0060002 855510000 465880 319382 403361 299155 485831 498150 412257 391379 427884 283818 TRUE FALSE 484273.3021 374233.3741 413872.919 358326.9661 403249.6202 382462.212 379943.2191 386133.2047 412484.5384 339426.7031 1.426738962 1.102545471 1.219329285 1.0556829 1.188031515 1.126788814 1.119367497 1.137604087 1.215238915 1 18.37274054 4.742532037 24.84568764 1.13548998 1.426739086 0.651946324 0.065039756 202.1082741 1264359.145 0.013769556 0.104930266 55275.41824 -4.742532037 0.291249106 QENLPDEIYHVYSFALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 0 175.51 1.22E-09 99683000 146330 183760 148470 156370 183890 226150 164010 159280 171590 181810 FALSE TRUE 152107.2214 215319.3505 152339.2502 187299.5193 152632.4435 173630.0898 151154.4676 157145.1121 165414.5094 217432.1885 0.699561654 0.990282773 0.700628785 0.861415785 0.701977221 0.798548232 0.695179811 0.722731594 0.760763669 1 17.73020601 5.048613735 16.73081693 0.786016632 0.137143456 0.054646 0.109819559 27350589.78 226964315.8 0.024433944 578320828.7 111844.269 -5.048613735 -0.648873176 QENSADDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QENSADDLHR 10 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 119.03 0.00074673 59700000 110750 70781 86112 56897 119720 106390 89632 85901 93834 76969 FALSE TRUE 115122.4955 82937.08615 88356.14946 68151.05678 99370.03716 81682.53486 82606.40963 84749.6376 90456.93267 92049.60189 1.25065718 0.90100429 0.959875411 0.740373183 1.079527072 0.887375211 0.897411916 0.920695319 0.982697707 1 16.49012386 4.741071165 24.59359418 0.924173153 1.250657326 0.565298269 0.084253132 122.5315459 1200242.401 0.018518811 0.125516679 55089.79612 -4.741071165 0.326484173 QEPAEEYETPES(ph)PVPPARS(ph)PS(ph)PPPKVVDVPSHASQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEPAEEYETPESPVPPARSPSPPPKVVDVPSHASQSAR 38 2 P54259 P54259 ATN1 Atrophin-1 3 QEPAEEY(0.019)ET(0.019)PES(0.964)PVPPARS(0.997)PS(1)PPPKVVDVPSHASQSAR 78.621 0.0014005 45749000 6400.6 16696 16795 15410 18062 23784 14573 21524 16194 20967 TRUE FALSE 6653.30063 19563.40812 17232.6915 18458.05201 14991.82769 18260.52645 13430.73018 21235.50599 15611.1811 25075.08221 0.265335147 0.78019318 0.687243669 0.736111326 0.597877509 0.728233961 0.535620584 0.846876824 0.622577464 1 14.61396681 -5 0.102715008 2.040817959 0.445642487 0.384059908 0.146542202 193.9990685 1.348449824 43.46025607 2.131279007 1.00E-05 5 -1.595175472 QEPCAQHNGSEPAS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QEPCAQHNGSEPASPKR 17 1 M0QZ09;Q8N6T7;Q8N6T7-2 M0QZ09 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 QEPCAQHNGSEPAS(1)PKR;QEPCAQHNGSEPAS(1)PKR;QEPCAQHNGS(0.003)EPAS(0.997)PKR;QEPCAQHNGS(0.002)EPAS(0.998)PKR;QEPCAQHNGS(0.001)EPAS(0.999)PKR 183.25 3.30E-10 1976626000 1415630 1567620 1743410 1493330 2045200 2293270 1931000 1900620 1916230 1404230 TRUE FALSE 1471520.166 1836846.541 1788844.697 1788706.217 1697557.635 1760692.797 1779643.174 1875145.298 1847265.257 1679361.983 0.876237631 1.093776422 1.065193041 1.065110581 1.01083486 1.048429591 1.059713863 1.116581962 1.099980395 1 20.6794818 4.743669304 24.89849661 1.066160469 0.876237547 0.716681247 0.03499267 279.4069415 1361714.449 0.008724197 0.073623867 55420.35511 -4.743669304 -0.189922922 QEPES(ph)EEEEEEKQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QEPESEEEEEEKQEK 15 1 P49756 P49756 RBM25 RNA-binding protein 25 1 QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK;QEPES(1)EEEEEEKQEK 273.27 1.16E-33 4160360000 5829800 1659150 2534230 1664420 3716120 5020450 4428120 2701700 3091380 1008095 TRUE FALSE 6059965.006 1944096.106 2600274.116 1993637.308 3084455.25 3854526.573 4081032.384 2665488.131 2980121.838 1205611.914 5.026464101 1.612538897 2.156808576 1.653631061 2.558414705 3.197153684 3.385029905 2.210900622 2.471874907 1 20.20133415 4.748425677 24.91677201 2.350290046 5.026465619 0.590178294 0.689617447 972.0032369 2454994.987 0.166055778 2.231183732 56030.65211 -4.748425677 2.676175572 QEPIES(ph)DEEEAEPPREVEPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEPIESDEEEAEPPREVEPGQR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 QEPIES(1)DEEEAEPPREVEPGQR 123.36 1.48E-05 897840000 33069 32676 34374 29531 36531 36189 25919 32046 30049 37497 TRUE FALSE 34374.58965 38287.84882 35269.81468 35372.14366 30321.47367 27784.6532 23887.40105 31616.47579 28967.54236 44843.81923 0.766540189 0.85380437 0.786503364 0.788785261 0.676157254 0.619587129 0.532679898 0.705035305 0.645965104 1 15.45262153 3.256395609 4.331143725 0.668210708 0.804204859 0.130201712 0.116991348 0.290852318 12.64647447 0.031394556 0.041168999 1804.660901 -3.256395609 0.135994151 QEPLLIGSTK ddPTM_MDA-MB-175_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 ; 126.19 0.00090509 159090000 368500 309440 358390 314480 429960 460530 350680 347340 370060 325100 FALSE TRUE 383048.6645 362583.9129 367729.9378 376683.2054 356875.5528 353578.8869 323192.7853 342684.4754 356741.6129 388797.1206 0.985214767 0.932578699 0.945814458 0.96884258 0.917896594 0.909417452 0.83126332 0.881396639 0.917552096 1 18.56865801 2.976474676 2.632923711 0.892725883 0.955300091 0.197942043 0.042519081 0.334808973 4.653913053 0.013205149 0.015127851 947.2719477 -2.976474676 0.062574208 QEPQGQEIQSENLIMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEPQGQEIQSENLIMEK 17 0 Q4VCS5 Q4VCS5 AMOT Angiomotin 0 58.09 0.06809 2268500000 68866 1897900 1926500 1960300 1737800 2099700 1407100 1839400 1724300 2259900 FALSE TRUE 71584.88286 2223849.561 1976706.173 2348041.489 1442409.377 1612076.496 1296807.825 1814745.852 1662242.78 2702684.137 0.026486589 0.82282999 0.731386308 0.868781319 0.533695136 0.596472401 0.479822191 0.671460578 0.615034053 1 21.36596148 0.138974068 1.396380365 1.000375529 0.608205563 0.229103306 0.222170754 15.93093791 23.98295241 0.213357265 0.058993288 1.377127238 -0.138974068 -0.392169965 QEPS(ph)PKPNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 89.013 0.0071477 381500000 1844400 614720 977750 597080 1182000 1384300 1356900 957870 1076200 522930 TRUE FALSE 1917218.336 720293.3781 1003230.968 715180.6419 981084.0622 1062817.304 1250542.632 945031.3194 1037467.772 625388.1214 3.06564559 1.151754172 1.604173367 1.143578871 1.568760308 1.699452337 1.999626455 1.511111719 1.658918257 1 19.25439229 4.747133076 24.93121022 1.523685596 3.065646398 0.727080901 0.290074224 556.7726944 1619220.437 0.067730598 0.794077715 55864.1347 -4.747133076 1.541960802 QEPVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEPVSPK 7 0 Q15596;E7EWM1 Q15596 NCOA2 Nuclear receptor coactivator 2 1 QEPVS(1)PK 62.823 0.087208 359390000 561260 267040 314490 310760 466550 602780 414440 361680 415610 290310 TRUE FALSE 583418.9782 312902.0427 322685.8678 372227.4005 387245.9976 462793.4802 381955.1099 356832.2712 400652.2773 347190.6862 1.680399277 0.901239737 0.929419713 1.072112287 1.115369775 1.332966288 1.100130634 1.027770287 1.153983368 1 18.40536872 2.824073545 0.018978913 1.03E-05 2.245713575 0.073952376 0.208416746 2593.880513 18.15572778 1013.420593 1132.008845 666.9196982 -2.824073545 2.245703309 QEQEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEQEEAR 7 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 143.61 0.0056069 54543000 94248 113700 107200 105690 115500 127030 116580 106920 112120 104480 FALSE TRUE 97968.98382 133227.0905 109993.7201 126595.1665 95867.35126 97529.20766 107442.155 105486.9123 108084.8231 124950.8556 0.784060128 1.06623592 0.880295853 1.013159661 0.767240455 0.780540535 0.859875304 0.844227211 0.865018671 1 16.93100125 3.239690896 24.99991217 0.842346733 0.941270453 0.157837291 0.091846481 44.80318091 990954.0531 0.024026001 0.030775231 1736.564408 -3.239690896 0.09892372 QEQEEARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEQEEARR 8 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ; 183.43 0.00035808 424480000 257750 293550 317520 306670 283430 329470 242720 300760 285360 317020 FALSE TRUE 267926.169 343964.929 325794.832 367328.4107 235252.6698 252955.5857 223694.9722 296728.8041 275089.9493 379133.9993 0.706679352 0.907238416 0.859313152 0.968861699 0.620500061 0.667193093 0.590015595 0.782648891 0.725574467 1 18.53234831 3.235466923 24.99997079 0.71211978 0.863773527 0.201462158 0.122875416 105.9309439 856024.3434 0.033341978 0.041488512 1719.756354 -3.235466923 0.151653747 QEQINTEPLEDTVLS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 QEQINTEPLEDT(0.023)VLS(0.866)PT(0.111)K;QEQINTEPLEDTVLS(0.998)PT(0.002)K 185.92 5.31E-14 116898000 366540 306950 289990 233180 323330 400340 331830 292950 320820 232770 TRUE FALSE 381011.2822 359666.2748 297547.3776 279302.308 268370.4821 307367.1022 305820.2975 289023.4844 309273.7509 278376.8248 1.368688943 1.292012275 1.068865477 1.00332457 0.964054685 1.104140412 1.098583899 1.038245495 1.110989577 1 18.08667958 4.287265475 3.39928587 1.047380852 1.353749181 0.858165118 0.04636637 0.079190773 1.82451984 0.012136561 0.037551465 19376.06019 -4.287265475 0.30636833 QEQLS(ph)PK ddPTM_MDA-MB-175_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 109.15 0.007441 796363000 2945060 1287070 1565300 1170460 2054640 2638930 1996320 1685890 1889670 1024500 TRUE FALSE 3061333.243 1508114.26 1606093.004 1401973.495 1705393.027 2026078.501 1839843.222 1663293.402 1821661.146 1225231.16 2.498576059 1.230881412 1.31084897 1.144252236 1.39189492 1.65362959 1.501629474 1.357534363 1.486789763 1 20.22462253 4.742663778 24.97236246 1.364096697 2.49857651 0.789370701 0.178911612 181.3695611 1103795.694 0.042619926 0.329851567 55292.18831 -4.742663778 1.134479813 QEQLS(ph)PR ddPTM_MDA-MB-175_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 80.706 0.041104 0 590650 692950 671510 667270 625890 761400 631070 647230 669230 667200 TRUE FALSE 613969.3181 811958.7721 689010.1023 799254.0144 519501.4414 584576.3891 581605.0844 638554.9405 645144.543 797925.0657 0.769457364 1.01758775 0.863502266 1.001665506 0.651065449 0.732620661 0.728896872 0.800269308 0.808527731 1 19.60589374 3.247534307 24.99999459 0.772308145 0.916980607 0.244303346 0.106776931 229.5886369 639611.7685 0.02765912 0.036915627 1768.211893 -3.247534307 0.144672462 QEQSYFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEQSYFVR 8 0 O60664-4;O60664;O60664-3;O60664-2 O60664-4 PLIN3 Perilipin-3 0 ; 114.64 0.0060897 413340000 223505 234582 200113 178884 277840 284540 224894 228559 199506 240270 FALSE TRUE 232329.15 274869.6337 205328.1092 214266.7213 230612.856 218459.8972 207266.2206 225495.5405 192325.818 287346.3063 0.808533623 0.956579666 0.714566726 0.74567418 0.802560712 0.760266941 0.721311589 0.784751833 0.669317175 1 18.13243098 4.231474009 24.99995921 0.764923208 0.882556651 0.1783141 0.090553945 197.0710735 695231.7367 0.020122773 0.044983351 17040.17337 -4.231474009 0.117633443 QERLS(ph)PEVAPPAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QERLSPEVAPPAHR 14 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR 142.58 5.67E-06 2560871000 1219933 1397871 1430220 1262866 1450502 1775280 1295198 1547288 1387200 1472657 TRUE FALSE 1268096.897 1637944.47 1467492.708 1512657.126 1203946.188 1362998.125 1193676.996 1526549.135 1337274.943 1761195.943 0.720020337 0.930018307 0.83323648 0.858880655 0.683595822 0.773904874 0.677765016 0.866768482 0.759299354 1 20.748124 -1.513844482 3.229213616 1.005552014 0.793713135 0.389726535 0.078931728 33153292.95 33548043.52 1572073.819 0.018773099 0.030630601 1.513844482 -0.211838879 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK;QES(1)DPEDDDVKKPALQSSVVATSK 185.47 1.85E-17 1833860000 2710980 648830 1120850 700090 1847410 1757910 1779450 1125050 1391530 394440 TRUE FALSE 2818011.584 760261.5053 1150060.272 838565.7124 1533387.908 1349662.044 1639972.059 1109970.545 1341449.107 471722.966 5.973869807 1.611669476 2.437999323 1.777665649 3.250611097 2.861132786 3.476557593 2.35301358 2.843722277 1 18.84758032 4.747817923 24.81831997 2.50770278 5.973871819 0.679646997 0.732543539 641.5510731 1719922.267 0.166917655 2.088018079 55952.29739 -4.747817923 3.46616904 QES(ph)LQSVKNTTEQEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QESLQSVKNTTEQEILK 17 1 A0A494BZZ1;A0A499FIV7;Q9NPP4 A0A494BZZ1 NLRC4 NLR family CARD domain-containing protein 4 1 QES(0.498)LQS(0.498)VKNT(0.002)T(0.002)EQEILK 63.128 0.034057 2447600000 1471100 1113700 1566400 1029600 1621700 1449200 1547000 1438000 1651000 1211000 TRUE FALSE 1529180.164 1304969.312 1607221.671 1233251.807 1346044.013 1112645.263 1425742.098 1418725.962 1591580.833 1448272.264 1.055865117 0.901052478 1.109751054 0.851533125 0.929413652 0.768256971 0.984443418 0.979598931 1.0989514 1 20.46590141 1.553743502 2.761822687 1.047102266 0.936753024 0.160598013 0.0942488 0.408514993 6.885623271 0.066893867 0.024933368 35.78850044 -1.553743502 -0.110349242 QESCLGNS(ph)PPFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QESCLGNSPPFEK 13 0 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 QES(0.001)CLGNS(0.999)PPFEK;QES(0.002)CLGNS(0.998)PPFEK 115.38 0.00070112 159042000 538400 383890 475340 446400 500360 633670 653300 536710 530900 341300 TRUE FALSE 559656.4477 449820.1213 487727.7509 534696.5876 415308.9859 486509.7459 602092.6389 529516.2803 511793.0127 408171.2004 1.371131641 1.102037872 1.194909759 1.309981172 1.017487235 1.191925705 1.475098288 1.297289666 1.253868505 1 18.63881487 2.407825049 24.9999749 1.295410624 1.190137145 0.008950175 0.143526387 109.1118219 39362.29007 0.047208047 0.039497089 255.7555395 -2.407825049 -0.105273478 QESCSPHHPQVLAQQGSGSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QESCSPHHPQVLAQQGSGSSPK 22 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 QESCSPHHPQVLAQQGSGS(0.002)S(0.998)PK;QESCSPHHPQVLAQQGSGS(0.033)S(0.967)PK 160.47 3.09E-11 320785000 60041.6 125790 140613 125193.1 148463 200244 144618 163290 136628.2 100270 TRUE FALSE 62412.08873 147393.454 144277.4903 149955.9215 123227.3123 153740.3657 133282.4633 161101.3646 131710.9778 119915.9867 0.520465123 1.229139317 1.203154761 1.250508173 1.027613712 1.282067303 1.111465343 1.343451937 1.098360455 1 16.87166448 4.740664369 24.81046686 1.189013386 0.520464866 0.76862677 0.106822076 70.52288442 831643.5161 0.023433894 0.15473755 55038.21857 -4.740664369 -0.66854852 QESEQGPCRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QESEQGPCRR 10 1 P24593 P24593 IGFBP5 Insulin-like growth factor-binding protein 5 0 77.744 0.051441 87984000 33616 79490 53468 66406 61446 77031 32873 64748 49475 98574 FALSE TRUE 34943.18564 93141.78915 54861.42 79540.9086 51001.43087 59141.71767 30296.32836 63880.15897 47694.40441 117887.688 0.296410815 0.790089201 0.465370226 0.674717691 0.432627289 0.501678493 0.256993151 0.541873032 0.404574941 1 16.84705353 -1.051892647 5.574345858 1.000002637 0.491601659 0.508788127 0.151702135 4.66E-06 7.92E-07 0.137553795 0.032421572 0.088737533 1.051892647 -0.508400978 QESRPGEWLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QESRPGEWLVR 11 1 Q9BUP3-3;Q9BUP3;E9PI87 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 ;; 145.23 3.31E-05 694900000 256081 316599 283231 299405 309414 365508 267343 284008 282385 343463 FALSE TRUE 266191.2756 370972.4155 290612.2325 358626.4154 256819.9188 280624.3063 246387.9571 280201.3373 272222.019 410757.9989 0.648048915 0.903141062 0.707502309 0.873084435 0.625234127 0.683186468 0.599837271 0.68215674 0.662730902 1 18.64792914 QETHCQST(ph)PLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QETHCQSTPLKK 12 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 QETHCQS(0.189)T(0.811)PLKK 171.81 2.85E-05 362670000 854370 435840 618080 434270 779370 761360 700410 620310 682360 421210 TRUE FALSE 888101.1873 510692.1296 634187.6726 520167.3098 646892.9658 584545.6785 645510.034 611995.7591 657801.9969 503738.0349 1.7630219 1.013804982 1.258963248 1.03261472 1.284185273 1.160416006 1.281439934 1.214908775 1.305841432 1 18.94231414 4.749351466 24.93949481 1.186827477 1.763022237 0.709258113 0.113095964 783.9898584 1811898.464 0.024709733 0.36592356 56150.22046 -4.749351466 0.57619476 QETVADFT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QETVADFTPK 10 0 O75400-3;O75400;O75400-2;F5H578 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 QETVADFT(1)PK;QETVADFT(1)PK;QETVADFT(1)PK 175.15 3.23E-05 414880000 1357180 597750 710230 800410 852180 1080080 1313480 819170 841560 412880 TRUE FALSE 1410762.514 700408.9127 728739.1773 958728.709 707326.748 829247.7888 1210526.005 808190.366 811272.42 493775.9309 2.857090486 1.418475201 1.475849938 1.94162706 1.43248527 1.679400993 2.451569487 1.636755288 1.642997095 1 18.91349699 4.746713726 24.81533466 1.68635549 2.857091127 0.503544209 0.361484584 787.804499 2397752.631 0.083643751 0.938470856 55810.21891 -4.746713726 1.170735637 QEVPSWLENMAYEHHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 159.88 1.83E-09 1029290000 769496 700412 772613 660950 913360 939160 863347 805734 822785 657027 FALSE TRUE 799876.2963 820702.3126 792747.9295 791683.9373 758107.3934 721054.3231 795675.6062 794934.4536 793173.1286 785758.8611 1.017966625 1.044470961 1.008894673 1.007540578 0.964809219 0.917653442 1.012620596 1.011677364 1.009435805 1 19.58372711 3.789624811 2.258383516 0.987583229 1.029906703 0.266423801 0.02819667 0.457081284 4.540604023 0.008747549 0.018284761 6160.625521 -3.789624811 0.042323475 QEVPVPGDGVEFPSSTGAEGQTGHPAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEVPVPGDGVEFPSSTGAEGQTGHPAEK 28 0 A0A087WUJ4;Q92618 A0A087WUJ4 ZNF516 Zinc finger protein 516 0 55.67 0.064952 147840000 6383.1 139860 75486 126910 43120 145880 45817 100140 55984 252400 FALSE TRUE 6635.109717 163879.867 77453.22717 152012.4192 35790.4778 112001.5808 42225.74382 98797.7871 53969.14678 301852.9475 0.021981265 0.542912926 0.256592582 0.503597598 0.118569251 0.371046835 0.139888459 0.327304364 0.178792843 1 18.20348636 -1.675630967 2.695970735 1.095628335 0.283413085 0.65191944 0.159126257 24972546.69 21843752.19 16390789.95 0.036342488 0.021104207 1.675630967 -0.81221525 QEWDNTVTDLTVHRAT(ph)PEDLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QEWDNTVTDLTVHRATPEDLVR 22 1 Q8N0Z3;C9IZF0;C9J5T2 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 QEWDNTVTDLT(0.001)VHRAT(0.999)PEDLVR 120.85 4.13E-05 40588000 8065.9 12202 10831 9640.3 9774.3 14374 8469.5 10085 8406.3 9798.5 TRUE FALSE 8384.34796 14297.59858 11113.26476 11547.12257 8112.867977 11035.85634 7805.638459 9949.827071 8103.758905 11718.32847 0.715490096 1.220105633 0.948366039 0.985389904 0.692322971 0.941760283 0.666105109 0.849082452 0.691545635 1 13.51647917 3.261601806 24.53886576 0.799366988 0.984037755 0.205899571 0.152631544 248.3837995 264526.5283 0.038662582 0.052312952 1826.424844 -3.261601806 0.184670767 QEYDESGPSIVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 257.04 6.91E-24 2.0862E+11 35975734.8 48867458.7 52675883.2 55295186.6 46092485.9 64647392.4 61604964.6 57161906.1 53901963.2 45111133.1 FALSE TRUE 37396084.59 57260064.6 54048659.99 66232409.47 38257701.61 49634015.26 56776206.5 56395744.25 51962042.07 53949795.93 0.693164524 1.061358317 1.00183252 1.22766747 0.709135242 0.920003763 1.052389643 1.04533749 0.963155489 1 25.68511417 4.745890511 24.11648508 0.999800207 0.693164282 0.35351864 0.123593202 603.4559909 1985380.972 0.029377063 0.297432573 55704.52958 -4.745890511 -0.306635925 QEYDESGPSIVHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 203.85 9.39E-09 7333000000 3873720 5725710 6145700 4167550 7632160 7418230 4568000 6011170 6564160 7597170 FALSE TRUE 4026657.457 6709056.153 6305861.991 4991878.951 6334848.169 5695458.507 4209948.224 5930600.098 6327917.164 9085690.005 0.443186754 0.738420103 0.694043269 0.549422108 0.69723358 0.626860316 0.46336032 0.652740749 0.696470731 1 23.11516465 0.767815349 2.08459395 0.999605571 0.611242207 0.617585388 0.092663056 0.577113844 4.001157449 0.085109782 0.023384773 5.858890059 -0.767815349 -0.388363365 QEYLDTLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QEYLDTLYR 9 0 P60228;E5RGA2;H0YBR5 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 ; 117.31 0.0027268 354010000 368530 380830 409010 401980 417210 484220 413190 400910 405350 354080 FALSE TRUE 383079.849 446234.5901 419669.1366 481490.4442 346292.7932 371767.2434 380803.0881 395536.4572 390761.5327 423455.1967 0.90465261 1.053794105 0.991059125 1.137051683 0.817779061 0.87793761 0.899275983 0.934069201 0.922793098 1 18.69184981 3.230120986 24.99992283 0.905344989 1.02175185 0.39153831 0.068934726 179.3064744 531141.9164 0.019177699 0.02327123 1698.716817 -3.230120986 0.116406861 QFAAQEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QFAAQEEKR 9 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 145.99 0.0001537 105672000 68251 59748 64253 52156 89542 85900 74657 69476 70018 64648 FALSE TRUE 70945.60218 70009.25423 65927.48596 62472.30113 74321.68282 65951.02683 68805.18926 68544.78786 67498.06586 77314.53784 0.917623052 0.905512161 0.852717843 0.808027867 0.96128988 0.853022325 0.88993857 0.886570492 0.873032003 1 16.2384521 -1.503440936 2.910343701 1.004199037 0.882641854 0.443534206 0.039285217 23642224.39 25207402.11 788317.9453 0.008972286 0.031373218 1.503440936 -0.121557183 QFCQEGQPHVLEALS(ph)PPQTSGLS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 2 QFCQEGQPHVLEALS(0.972)PPQT(0.039)S(0.053)GLS(0.861)PS(0.075)R;QFCQEGQPHVLEALS(0.972)PPQT(0.027)S(0.001)GLS(0.997)PS(0.003)R;QFCQEGQPHVLEALS(0.999)PPQT(0.002)S(0.003)GLS(0.946)PS(0.051)R;QFCQEGQPHVLEALS(0.999)PPQT(0.019)S(0.052)GLS(0.903)PS(0.028)R 172.67 2.41E-12 1488580000 350760 384666 374276 439880 457864 573300 431030 506525 497025 522995 TRUE FALSE 364608.2756 450729.3932 384029.94 526886.9511 380036.4408 440159.7634 397244.7423 499735.8609 479137.1673 625465.8569 0.582938735 0.720629892 0.613990253 0.842391228 0.607605414 0.703731081 0.635118189 0.798981839 0.766048477 1 19.25457161 0.715047689 0.749145985 1.001806523 0.674281673 0.627794817 0.07505655 0.655068543 0.708815834 0.069888121 0.024958142 5.18857011 -0.715047689 -0.32752485 QFCQEGQPHVLEALSPPQTSGLS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QFCQEGQPHVLEALSPPQTSGLSPSR 26 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 QFCQEGQPHVLEALSPPQTS(0.001)GLS(0.949)PS(0.05)R;QFCQEGQPHVLEALSPPQT(0.002)S(0.005)GLS(0.936)PS(0.057)R;QFCQEGQPHVLEALSPPQT(0.001)S(0.005)GLS(0.977)PS(0.017)R;QFCQEGQPHVLEALSPPQT(0.002)S(0.004)GLS(0.985)PS(0.01)R;QFCQEGQPHVLEALSPPQTS(0.016)GLS(0.753)PS(0.231)R 215.12 2.75E-34 2504280000 775707 945227 813899 784157 754898 990141 647658 800536 732461 816540 TRUE FALSE 806332.5113 1107562.384 835109.8766 939260.9141 626580.7076 760195.7585 596892.8736 789806.1243 706099.8717 976525.3794 0.825715878 1.134186994 0.85518502 0.961839737 0.641643034 0.778470047 0.611241537 0.808792215 0.723073754 1 19.89729801 3.255658862 24.9886501 0.745771578 0.951439713 0.335067037 0.125580797 234.2687064 342375.6489 0.031938072 0.043139203 1801.602029 -3.255658862 0.205668135 QFDVDILISGHTHKFEAFEHENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QFDVDILISGHTHKFEAFEHENK 23 1 Q9UBQ0;F8VXU5;Q9UBQ0-2;Q05DG7 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;; 149.73 3.09E-08 810531000 643607 418951 721272 523984 881175 887751 819587 723935 889318 362688 FALSE TRUE 669017.1013 490902.5753 740068.9409 627626.4713 731393.1882 681584.2842 755345.6293 714231.8354 857311.6189 433749.7695 1.542403359 1.131764464 1.706211721 1.446978224 1.686209976 1.571376706 1.741431771 1.646644876 1.976511987 1 18.72650347 4.222475711 24.94524352 1.625314038 1.337083814 0.133800642 0.25643205 321.4338615 498497.0778 0.057940662 0.125786419 16690.74459 -4.222475711 -0.288230224 QFEDEKANWEAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QFEDEKANWEAQQR 14 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2;Q5JXL7 E7EPK1 SEPT7;DKFZp586I031 Septin-7 0 73.707 0.021642 0 68638 68904 77095 64788 85869 107630 58122 73418 84127 91717 FALSE TRUE 71347.88124 80737.726 79104.15903 77602.87303 71273.01805 82634.56365 53566.24577 72433.9518 81099.2857 109687.1901 0.650466852 0.736072516 0.721179556 0.707492579 0.649784336 0.753365672 0.488354617 0.660368378 0.739368796 1 16.74303552 0.843723241 3.529436849 0.999910185 0.669293313 0.663370744 0.07020393 0.502215 10.29332881 0.068809665 0.01774681 6.977875897 -0.843723241 -0.330616872 QFEDELHPDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 ;;;; 128.54 0.00026367 1619047000 7077670 5024420 6170160 4754900 7530660 7991900 6740260 6467650 6822050 4488430 FALSE TRUE 7357101.877 5887325.05 6330959.438 5695405.028 6250601.103 6135902.343 6211940.809 6380961.731 6576525.753 5367851.922 1.370585848 1.096774862 1.179421402 1.061021263 1.164451105 1.143083385 1.157248914 1.188736542 1.225168997 1 22.35591344 -2.243914651 2.332181646 0.37086549 1.169776214 0.308270525 0.078676572 3036532.428 529729.5592 10165908.04 0.017585719 0.005702763 2.243914651 0.798910724 QFEEIWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QFEEIWER 8 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 169.09 0.00070498 832572000 890993 1027306 1030859 1011808 1166838 1335025 1011422 1049833 1050469 1121898 FALSE TRUE 926170.0916 1203737.814 1057724.032 1211940.602 968499.2935 1024985.676 932144.1008 1035761.706 1012662.826 1341712.433 0.690289565 0.897165283 0.788338847 0.903278954 0.721838204 0.76393842 0.694742091 0.771969969 0.754754 1 20.35564406 -1.432258129 2.911700808 1.004917144 0.77793177 0.481171315 0.069680405 24464175.54 28291831.56 992071.7572 0.016280342 0.036960843 1.432258129 -0.226985374 QFFDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 138.37 0.028694 1551630000 2700770 3124880 2955250 3123000 3117500 3606380 3101890 3175990 3129950 3131180 FALSE TRUE 2807398.485 3661553.832 3032266.243 3740720.079 2587588.464 2768852.9 2858755.757 3133421.049 3017303.711 3744674.771 0.749704222 0.977802895 0.809754232 0.998943916 0.691004859 0.739410782 0.76341897 0.836767207 0.805758549 1 21.83640899 QFGFIVLTTSAGIMDHEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QFGFIVLTTSAGIMDHEEAR 20 0 P62244 P62244 RPS15A 40S ribosomal protein S15a 0 ;;; 205.63 8.46E-22 1172840000 1006812 1238264 1275521 1221613 1390828 1474815 1189275 1255151 1270610 1218215 FALSE TRUE 1046561.715 1450926.21 1308762.125 1463244.405 1154415.553 1132311.567 1096056.518 1238327.754 1224880.994 1456900.905 0.718347907 0.995899038 0.898319248 1.004354105 0.792377539 0.777205617 0.752320569 0.849973907 0.840744206 1 20.47447132 3.206220389 24.98442226 0.821294836 0.910355828 0.096371056 0.096870583 329.8740721 254843.1464 0.026486372 0.03165957 1607.756925 -3.206220389 0.089060992 QFHDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QFHDSK 6 0 Q02543;M0R3D6;M0R1A7;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;; 104.45 0.033822 2065623000 1378975 6328370 6480170 6251500 6868240 8929230 5750820 8262800 6477860 6673300 FALSE TRUE 1433417.998 7415218.32 6649048.554 7488028.041 5700779.018 6855551.656 5300055.701 8152050.681 6244723.084 7980805.367 0.179608189 0.929131582 0.833130022 0.938254687 0.714311245 0.859004993 0.664100358 1.021457147 0.782467783 1 22.92810291 4.742308924 24.97156967 0.856472589 0.179607926 0.772077281 0.110920065 156.9847696 1045803.325 0.024771352 0.185265911 55247.02852 -4.742308924 -0.676864663 QFHHQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QFHHQLR 7 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 93.262 0.015064 9818300 7687.5 20043 13552 21998 13863 21653 12594 18853 15648 30832 FALSE TRUE 7991.008436 23485.22934 13905.17625 26349.13874 11506.57221 16624.4189 11606.84937 18600.30637 15084.83154 36872.94009 0.21671742 0.636923155 0.377110592 0.714592834 0.312060069 0.450856885 0.314779601 0.504443267 0.409103031 1 15.17027483 -1.430627188 3.90807457 1.003301872 0.445405046 0.58010158 0.14345047 31730569.57 11629170.39 892584.106 0.031236711 0.037099906 1.430627188 -0.557896826 QFLEVELDQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QFLEVELDQAR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 134.3 0.00033416 201320000 126077 137264 127304 132343 147482 163888 125812 135964 125145 162253 FALSE TRUE 131054.6173 160838.0242 130621.6468 158520.0504 122413.0623 125827.4957 115950.5267 134141.625 120641.0559 194043.3688 0.675388281 0.828876685 0.673156973 0.816931036 0.630854139 0.648450377 0.597549545 0.691297135 0.621722126 1 17.56601961 -1.038311737 4.422729005 1.000016122 0.688208757 0.61878216 0.073666272 9721580.331 2282308.179 1634.777589 0.017348544 0.091556306 1.038311737 -0.311807365 QFLIHELNAFEES(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QFLIHELNAFEESK 14 0 I3L2N4;I3L269;I3L0U4;I3L4V2;I3NI25;Q96NB1 I3L2N4 FOPNL LisH domain-containing protein FOPNL 1 QFLIHELNAFEES(1)K 61.353 0.084663 0 294000 215850 233000 218540 270680 340570 296970 261250 325240 223670 TRUE FALSE 305607.347 252920.5584 239072.1714 261766.5597 224669.9103 261477.7789 273692.7154 257748.3711 313534.6759 267493.8541 1.142483621 0.945519138 0.893748278 0.978589062 0.839906812 0.977509483 1.023173846 0.963567451 1.172119176 1 18.02914622 1.268808248 24.72535056 1.086059572 0.96590238 0.229504632 0.08430372 208.2837577 170257.9037 0.054413246 0.019864027 18.56984369 -1.268808248 -0.120157192 QFLIS(ph)PPAS(ph)PPVGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QFLISPPASPPVGWK 15 0 V9GYW9;E9PD55;E9PDJ2;P53805-4;P53805-3;P53805-2;P53805;H0YF64;Q9UKA8-6;Q9UKA8-5;Q9UKA8-2;Q9UKA8 V9GYW9 RCAN1;RCAN3 Calcipressin-1;Calcipressin-3 2 QFLIS(1)PPAS(1)PPVGWK;QFLIS(1)PPAS(1)PPVGWK 126.19 0.00012549 831630000 1092670 777820 986760 886020 986110 1191350 1140600 1020520 1120520 761050 TRUE FALSE 1135809.455 911404.5344 1012475.776 1061272.111 818491.3744 914677.0176 1051196.792 1006841.599 1080192.704 910163.1763 1.247918489 1.001363885 1.112411271 1.166024004 0.899279817 1.004959376 1.154954209 1.106220978 1.186812137 1 19.79576569 -1.044205192 7.535275257 0.999999997 1.092273739 0.079651467 0.098115156 9.27E-09 1.10E-09 0.092812395 0.02187609 0.090322263 1.044205192 0.092273742 QFLISPPAS(ph)PPVGWK ddPTM_MDA-MB-175_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 1 QFLIS(0.004)PPAS(0.996)PPVGWK 159.04 1.88E-06 314110000 746180 559680 621010 619550 612510 835860 700530 631120 675860 536880 TRUE FALSE 775639.7626 655800.6863 637194.0308 742095.1408 508395.769 641744.1826 645620.6281 622660.8687 651535.9306 642071.3568 1.208027355 1.021382872 0.992403763 1.155782972 0.791805714 0.999490439 1.005527846 0.969768955 1.014740688 1 19.29237412 7.999999116 0.936513877 0.982227804 144.0149112 0.37885455 0.082674432 1157.052939 2.103417838 0.023990274 354361.6125 99999796.39 -7.999999116 143.0326834 QFS(ph)PTMS(ph)PTLSSITQGVPLDTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QFSPTMSPTLSSITQGVPLDTSK 23 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 2 QFS(0.491)PT(0.491)MS(0.476)PT(0.476)LS(0.031)S(0.031)IT(0.003)QGVPLDTSK 57.826 0.041754 23593000 46790 34184 45850 35643 57181 64086 53706 49380 48208 37225 TRUE FALSE 48637.30533 40054.83609 47044.88867 42693.07902 47461.39404 49202.99773 49496.38339 48718.14187 46473.0035 44518.52603 1.092518321 0.899734103 1.056748569 0.958995789 1.066104345 1.10522522 1.111815412 1.094334117 1.043902565 1 15.44211821 3.105955172 6.398653468 1.081974341 0.998956245 0.240139856 0.057722856 0.238378448 12.76498919 0.015460934 0.018560573 1276.30706 -3.105955172 -0.083018096 QFVEMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QFVEMTR 7 0 B0YIW6;P48444;Q6P1Q5;E9PK34 B0YIW6 ARCN1 Coatomer subunit delta 0 90.657 0.039498 84470000 136480 138080 149760 139340 177570 201250 162540 168980 154730 160720 FALSE TRUE 141868.3358 161794.1659 153662.8686 166901.0361 147386.7148 154512.7375 149799.6901 166715.0995 149161.2975 192210.0068 0.73809027 0.841757245 0.799453011 0.868326467 0.766800424 0.803874575 0.779354273 0.867359105 0.776032944 1 17.55232392 -4.999999859 0.375672267 3.613468032 0.804589767 0.665995498 0.041308945 323.2497442 2.450547369 687.1745971 0.026368687 1.00E-05 4.999999859 -2.808878265 QFYINVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 110.41 0.0079835 1108690000 1055200 1077010 1096490 1225900 1096970 1421070 1170590 1141940 1176360 994460 FALSE TRUE 1096860.111 1261978.09 1125065.43 1468379.361 910507.4312 1091048.029 1078836.097 1126634.162 1134023.033 1189305.397 0.922269514 1.061105157 0.945985306 1.234652903 0.765579164 0.917382559 0.907114438 0.947304338 0.9535171 1 20.1816878 3.223286312 24.99998578 0.914500411 1.035652165 0.288867468 0.096588826 305.926486 500719.4468 0.026620065 0.031926261 1672.192656 -3.223286312 0.121151753 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 200.97 4.63E-22 9146350000 1363020 1649910 1505190 1447460 1662020 1930840 1256250 1539170 1530630 1628140 TRUE FALSE 1416833.082 1933269.208 1544416.488 1733763.268 1379510.434 1482431.672 1157781.842 1518539.944 1475542.925 1947142.86 0.727647216 0.992874867 0.793170609 0.890414003 0.708479312 0.761336881 0.594605494 0.779881114 0.757799007 1 20.89292731 QGANINEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGANINEIR 9 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 ;; 140.83 0.00025161 262360000 271969 321697 301850 302311 321950 409670 304689 317060 296310 348870 FALSE TRUE 282706.5461 376945.9573 309716.459 362107.2135 267225.054 314530.3511 280806.68 312810.3293 285645.861 417224.397 0.677588722 0.903460967 0.742325859 0.867895588 0.64048281 0.753863756 0.673035139 0.749741222 0.684633648 1 18.670464 -1.150130983 3.884030793 1.000117301 0.746417163 0.477379106 0.080414284 4898827.134 2175949.274 5016.151687 0.017911389 0.07077323 1.150130983 -0.253700137 QGDETPS(ph)TNNGSDDEKTGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;Q9Y3P9-3;Q9Y3P9-4;C9JGR5;B5MCD9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 QGDETPS(0.396)T(0.396)NNGS(0.207)DDEKTGLK 96.338 0.00066502 1325600000 271430 118720 169820 132790 225590 306990 213780 176880 189960 98455 TRUE FALSE 282146.266 139109.2365 174245.6487 159055.4657 187244.2924 235696.225 197023.365 174509.2129 183123.3767 117745.3722 2.396240809 1.181441222 1.479851356 1.350842608 1.590247573 2.001745126 1.673300286 1.482089781 1.555249037 1 16.84531083 0.476992983 1.134367921 1.000195857 1.627730028 0.261504374 0.323845267 2.84234654 4.765892115 0.299392086 0.091718258 2.999114059 -0.476992983 0.627534171 QGDETPSTNNGS(ph)DDEKTGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;Q9Y3P9-3;Q9Y3P9-4;C9JGR5;B5MCD9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 QGDET(0.002)PS(0.007)T(0.007)NNGS(0.983)DDEKTGLK;QGDETPSTNNGS(1)DDEKTGLK;QGDETPSTNNGS(1)DDEKTGLK 258.83 1.73E-36 3106300000 2766300 874850 1385280 779910 2037920 2404460 2008870 1386040 1688440 562490 TRUE FALSE 2875515.66 1025098.682 1421381.535 934173.8702 1691515.086 1846060.605 1851409.52 1367462.401 1627673.374 672699.146 4.274593891 1.523859051 2.112952786 1.388694895 2.51451945 2.74425888 2.752210303 2.032799371 2.419615639 1 19.3596019 4.748724466 24.8582724 2.130513855 4.274595167 0.578044994 0.565727278 969.6964836 2371587.718 0.132115097 1.817855797 56069.21379 -4.748724466 2.144081312 QGDTGDWIGTFLGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 201.3 6.48E-09 1528570000 1371060 1233330 1481150 1166220 1770930 1834460 1561140 1572590 1596090 1235810 FALSE TRUE 1425190.507 1445144.834 1519749.986 1396894.835 1469907.951 1408434.467 1438773.768 1551512.003 1538647.033 1477943.308 0.964306614 0.977808029 1.028287064 0.945161311 0.994563149 0.95296921 0.973497264 1.049777752 1.041073107 1 20.4951595 1.755291965 11.31265292 1.033661835 0.977247674 0.493634145 0.024810219 0.119936219 69.94130582 0.011226546 0.006151956 56.92354842 -1.755291965 -0.056414162 QGFDFLCMPVFHPR ddPTM_MDA-MB-175_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 ; 145.29 8.62E-06 345330000 394940 479000 420730 425040 565880 591590 416680 452900 410850 638960 FALSE TRUE 410532.5362 561264.5239 431694.5694 509111.6434 469691.9197 454202.1881 384019.5328 446829.6163 396063.5888 764151.9784 0.537239381 0.73449332 0.564932869 0.666243964 0.614657729 0.594387244 0.502543399 0.5847392 0.518304735 1 19.54350007 -1.918673886 2.711052697 1.245047877 0.592861215 0.77561861 0.066013501 13964321.1 8308041.44 21739183.2 0.016537805 0.012059411 1.918673886 -0.652186662 QGFGELLQAVPLADSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGFGELLQAVPLADSFR 17 0 P27695;G3V3M6;G3V5Q1 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 166.09 4.12E-09 0 54216 55021 53353 55422 63185 72630 58290 59349 52101 62099 FALSE TRUE 56356.48954 64470.42875 54743.42301 66384.30618 52444.83627 55762.78322 53721.07749 58553.52373 50225.89519 74266.11009 0.758845313 0.86810025 0.737125224 0.893870786 0.706174542 0.750851003 0.723359247 0.78842858 0.676296296 1 16.18041639 -1.302794528 3.69803224 1.000605732 0.770038496 0.537846734 0.064738417 7096743.188 5000426.902 31820.53046 0.014315344 0.049797263 1.302794528 -0.230567236 QGGDVLQNEEGETTSHLMGMFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGGDVLQNEEGETTSHLMGMFYR 23 0 P39748;F5H1Y3 P39748 FEN1 Flap endonuclease 1 0 ; 226.81 9.42E-33 113529000 81657 81413 90861 93397 91148 99885 112080 96097 101943 86602 FALSE TRUE 84880.88141 95395.04944 93228.9123 111870.6478 75654.69552 76688.22252 103294.8767 94808.9769 98274.09134 103570.0038 0.819550819 0.92106832 0.900153605 1.080145252 0.730469178 0.740448196 0.997343564 0.915409611 0.948866349 1 16.6602467 QGGLGPMNIPLVSDPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGGLGPMNIPLVSDPKR 17 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 ; 151.39 4.04E-07 1148600000 646620 467600 538300 452630 730250 762730 632080 549310 589640 455720 FALSE TRUE 672149.0569 547906.6626 552328.5402 542158.863 606122.3658 585597.5168 582535.918 541947.3979 568418.9716 545009.6087 1.233279278 1.005315601 1.013428995 0.994769366 1.112131522 1.074471913 1.068854399 0.994381364 1.042952202 1 19.05592214 4.743907627 24.87149889 1.035380966 1.233279368 0.710315667 0.038163391 307.6360418 1430914.422 0.009576797 0.082126254 55450.77589 -4.743907627 0.197898402 QGGSQPSSFS(ph)PGQSQVTPQDQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGGSQPSSFSPGQSQVTPQDQEK 23 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 1 QGGSQPSS(0.001)FS(0.999)PGQSQVTPQDQEK 298.5 5.73E-62 109750000 136860 93991 112290 95261 144100 171470 139620 135170 139080 82779 TRUE FALSE 142263.3385 110133.2231 115216.3696 114103.3415 119605.9335 131648.6912 128676.2196 133358.2672 134074.538 98997.96015 1.437033028 1.112479721 1.163825694 1.152582753 1.208165636 1.329812159 1.299786575 1.34708096 1.354316167 1 16.59511118 2.764491372 15.61938314 1.295019696 1.202839087 0.010591352 0.127115712 16.36575063 9855.528799 0.036503596 0.03861176 581.4218817 -2.764491372 -0.092180609 QGIAVMTPTVPGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.001)VPGS(0.999)PK;QGIAVMTPT(0.001)VPGS(0.999)PK;QGIAVMTPT(0.001)VPGS(0.999)PK;QGIAVMTPT(0.001)VPGS(0.999)PK 168.41 1.32E-06 502167000 1271430 604999 699994 632320 945807 1203720 888528 740591 793423 556309 TRUE FALSE 1321627.038 708902.872 718236.4187 757391.0087 785039.064 924174.2726 818882.8536 730664.589 764867.8612 665307.0974 1.986491717 1.065527295 1.079556225 1.13840813 1.179964962 1.389094264 1.230834387 1.098236577 1.149646328 1 19.3436609 4.742456418 24.99555745 1.158019731 1.986492037 0.859986859 0.101434415 139.789682 896858.7157 0.025298796 0.192170979 55265.79454 -4.742456418 0.828472305 QGIETPEDQNDLRK ddPTM_MDA-MB-175_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 0 185.67 1.85E-06 315500000 191560 124050 153160 122640 182600 187650 179430 172380 177170 124920 FALSE TRUE 199122.9367 145354.6225 157151.4754 146897.826 151561.7172 144071.1314 165365.8077 170069.5281 170793.6863 149395.6823 1.332856035 0.972950626 1.05191444 0.983280264 1.014498645 0.964359406 1.106898173 1.138383155 1.143230405 1 17.18877893 -0.210007489 7.545463583 1.000014094 1.072733944 0.044949189 0.105659255 0 0 0.099657617 0.023489526 0.616584369 0.210007489 0.072719849 QGLAET(ph)ASPVAVSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAET(0.794)AS(0.205)PVAVSLR 168.64 1.39E-05 95395000 225330 252150 243310 258550 224120 297820 258580 246010 228990 221880 TRUE FALSE 234226.2024 295454.801 249650.8585 309690.4183 186024.1625 228655.8185 238311.8239 242712.6383 220748.6946 265353.1379 0.882696185 1.113440012 0.940824972 1.167087832 0.701043764 0.861703843 0.898093107 0.914677853 0.831905349 1 18.01755408 3.24459565 24.99998417 0.868991359 1.026172248 0.363426936 0.102506008 154.6995434 640834.9383 0.026971974 0.035599948 1756.287662 -3.24459565 0.157180889 QGLAETAS(ph)PVAVSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGLAETASPVAVSLR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 1 QGLAETAS(1)PVAVSLR 235.53 1.16E-17 91221000 158020 170850 171420 183590 183850 215310 187200 166510 166050 175360 TRUE FALSE 164258.7516 200192.1585 175887.346 219903.554 152599.2427 165307.5156 172526.7748 164278.2058 160073.8929 209718.4345 0.783234683 0.954575877 0.838683287 1.048565685 0.727638669 0.788235502 0.822659082 0.783327447 0.76328003 1 17.67809416 3.210088003 24.99960178 0.8016348 0.90488869 0.178016786 0.094629186 299.6019789 263056.5592 0.025192463 0.030115968 1622.138764 -3.210088003 0.10325389 QGLGPASTTSPSPGPRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QGLGPASTTSPSPGPRSPK 19 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QGLGPASTTSPS(0.007)PGPRS(0.992)PK;QGLGPASTTSPS(0.003)PGPRS(0.997)PK;QGLGPASTTSPSPGPRS(1)PK;QGLGPASTT(0.001)S(0.013)PS(0.054)PGPRS(0.932)PK;QGLGPASTTSPSPGPRS(0.999)PK 203.24 3.12E-16 3029370000 2046410 1033304 1356660 874555 1870390 1884650 1260930 1324480 1428540 1001368 TRUE FALSE 2127203.847 1210765.924 1392015.674 1047539.369 1552461.776 1446968.6 1162095.012 1306727.512 1377127.124 1197566.887 1.77627143 1.011021545 1.162369876 0.874723057 1.296346611 1.208257021 0.970380047 1.091152007 1.149937543 1 20.19167481 4.742506205 24.99763239 1.088756164 1.776271696 0.754029661 0.118442204 183.5760833 1163017.45 0.027166395 0.206823877 55272.13051 -4.742506205 0.687515532 QGMSMRES(ph)PVSAPLEGLICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGMSMRESPVSAPLEGLICR 20 1 O75376;O75376-2;A0A088AWL3 O75376 NCOR1 Nuclear receptor corepressor 1 1 QGMS(0.228)MRES(0.769)PVS(0.003)APLEGLICR 59.282 0.041081 75640000 23428 33647 25861 18115 29685 36564 21985 32018 27356 33248 TRUE FALSE 24352.95553 39425.61051 26534.95891 21698.09293 24639.1543 28072.56513 20261.75825 31588.85108 26371.4629 39762.30903 0.612463313 0.991532219 0.667339487 0.545694993 0.619661054 0.70600943 0.509571973 0.79444207 0.663227653 1 15.27911392 -0.056805576 1.074756005 1.00252526 0.680585469 0.356343481 0.129201425 12.31266422 11.20417748 0.244187953 0.038511052 0.877393524 0.056805576 -0.321939791 QGNFFAS(ph)PMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGNFFASPMLK 11 0 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 QGNFFAS(1)PMLK 86.756 0.01493 82093000 316460 252420 254120 217380 314110 350930 295040 281410 308260 223670 TRUE FALSE 328954.0852 295771.1714 260742.576 260377.1152 260717.6944 269431.8259 271913.9939 277638.1592 297165.7828 267493.8541 1.229763152 1.105712026 0.974760997 0.973394757 0.97466798 1.007244921 1.016524267 1.037923507 1.110925647 1 18.02914622 4.557659423 2.929994549 1.012338092 1.232599123 0.747025614 0.039428127 0.152945196 2.231838791 0.010484361 0.063397627 36112.6553 -4.557659423 0.220261031 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGPPHINHDDPSLVPNVPYFDLPAGLMAPLVK 32 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 ; 156.03 4.37E-11 826070000 826700 699900 883350 727350 905170 1033100 925580 925120 905900 686460 FALSE TRUE 859338.7544 820102.3805 906370.8267 871217.6591 751309.5267 793178.1818 853030.621 912720.2796 873296.836 820958.6939 1.046750294 0.998956935 1.104039501 1.061219846 0.91516118 0.966160889 1.039066432 1.111773694 1.063752467 1 19.64695011 -0.751537613 5.953616047 0.999999999 1.036228221 0.029778593 0.057238301 9.05E-10 3.04E-10 0.060762399 0.014321834 0.177199457 0.751537613 0.036228222 QGPPS(ph)PCQQLVLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGPPSPCQQLVLTK 14 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 QGPPS(1)PCQQLVLTK;QGPPS(1)PCQQLVLTK 210.83 4.93E-09 175689000 340120 256700 301910 256430 356330 407820 317710 317580 356680 296850 TRUE FALSE 353548.2002 300786.2282 309778.0226 307151.0886 295761.1539 313109.9856 292807.06 313323.3596 343843.1565 355012.074 0.995876552 0.847256334 0.872584471 0.865184908 0.833101676 0.881969963 0.824780568 0.882570996 0.968539331 1 18.43750857 1.18755257 3.508343049 0.997016476 0.870055824 0.491425224 0.044717383 0.170816946 3.79827469 0.039031239 0.010624988 15.40112942 -1.18755257 -0.126960652 QGPVSQSATQQPVTADKQQGHEPVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.004)ADKQQGHEPVS(0.996)PR;QGPVSQSATQQPVTADKQQGHEPVS(1)PR 277.24 3.73E-61 5929000000 2629760 2299600 2624840 1722670 2951050 3204980 2156420 2603150 2879460 2338520 TRUE FALSE 2733584.955 2694538.412 2693245.487 2063408.984 2449431.575 2460671.967 1987394.166 2568259.032 2775828.797 2796708.22 0.977429442 0.963467834 0.963005532 0.737799163 0.875826644 0.879845795 0.71061906 0.918314972 0.992534286 1 21.41529832 3.950019992 24.98481743 0.862964718 0.968645957 0.187042693 0.088351893 503.9802409 251937.9558 0.022317597 0.040234473 8912.919672 -3.950019992 0.105681239 QGQDVAPPPNPVPQRT(ph)SPTGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGQDVAPPPNPVPQRTSPTGPK 22 1 Q9UPY8-2 Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 QGQDVAPPPNPVPQRT(0.714)S(0.284)PT(0.002)GPK;QGQDVAPPPNPVPQRT(0.594)S(0.4)PT(0.006)GPK;QGQDVAPPPNPVPQRT(0.571)S(0.284)PT(0.145)GPK 189.45 3.44E-17 1376080000 1415310 903450 1219640 784577 1499560 1503830 1013430 1220160 1292520 988300 TRUE FALSE 1471187.532 1058610.51 1251424.82 939763.9889 1244665.327 1154588.273 933994.7085 1203805.751 1246002.458 1181938.463 1.244724305 0.895656198 1.058790165 0.795103991 1.053071176 0.976859887 0.790222789 1.018501207 1.054202479 1 20.17272349 4.746235002 24.57363479 0.957136355 1.244724482 0.439276321 0.096356224 658.937845 2109876.253 0.021707471 0.229290064 55748.73309 -4.746235002 0.287588127 QGQEHIGSSCSFAEQALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGQEHIGSSCSFAEQALR 18 0 O75382;O75382-2;O75382-4;A0A1W2PPI7;E9PMK8 O75382 TRIM3 Tripartite motif-containing protein 3 0 152.18 4.23E-08 205420000 91881 108190 112100 108260 135330 146500 111680 121330 114740 110470 FALSE TRUE 95508.53283 126770.7909 115021.4181 129673.5049 112326.6549 112477.5952 102926.2298 119703.7698 110610.5298 132114.4814 0.722922512 0.959552575 0.870619306 0.981523778 0.850222123 0.85136462 0.779068492 0.906060929 0.837232441 1 17.01142909 -0.981140491 4.364933148 1.000002327 0.867298272 0.241009515 0.07290417 8677281.512 1987953.047 391.1001518 0.016038138 0.104438231 0.981140491 -0.132704055 QGQQQAGGDGKTEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGQQQAGGDGKTEQK 15 1 Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 ; 238.49 8.23E-18 323080000 318310 156892 221050 124265 282860 281060 217160 199091 246830 128412 FALSE TRUE 330877.1246 183836.9805 226810.7446 148844.2461 234779.5582 215788.0745 200138.4318 196422.5108 237946.6365 153571.8728 2.154542486 1.19707455 1.476902902 0.969215543 1.528792701 1.405127583 1.303223228 1.279026603 1.549415477 1 17.22855448 4.743439225 24.80334423 1.313493401 2.154542873 0.639552079 0.192032469 269.529626 1370265.5 0.041749 0.343625043 55391.00249 -4.743439225 0.841049472 QGQSQAASSSSVT(ph)SPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 QGQSQAASSSS(0.004)VT(0.498)S(0.498)PIK 218.14 5.30E-14 155480000 310760 181810 225210 189520 285290 334280 291310 265440 263060 153710 TRUE FALSE 323029.0448 213034.4532 231079.1576 227006.4903 236796.5077 256648.5361 268476.361 261882.211 253592.522 183826.5315 1.757249305 1.158888499 1.257050088 1.23489514 1.288151964 1.396145235 1.460487552 1.424615961 1.37952079 1 17.48798548 -1.325143511 3.155941906 0.997293199 1.36551155 0.337678523 0.156399824 16964994.66 23153067.12 431516.8935 0.036327068 0.047299493 1.325143511 0.368218351 QGQSQAASSSSVTS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 QGQSQAASSSSVT(0.032)S(0.968)PIK 152.37 2.26E-07 189350000 275430 174820 220110 169350 263370 305780 270050 239730 253010 138640 TRUE FALSE 286304.1891 204843.9751 225846.2474 202846.9245 218602.4615 234767.2291 248882.7754 236516.8115 243904.2195 165803.8536 1.726764384 1.235459675 1.362129061 1.223415018 1.318440173 1.415933491 1.501067496 1.426485612 1.471040716 1 17.33911801 -1.698115091 2.535925018 0.931331473 1.400427769 0.441923996 0.137574097 8657757.29 6685795.475 3791873.453 0.03220053 0.020039409 1.698115091 0.469096296 QGRPTLQEGPGLQQKPRPEAEPPS(ph)PPSGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QGRPTLQEGPGLQQKPRPEAEPPSPPSGDLR 31 3 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1;B0QYI1;Q8WUA7-2 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 QGRPTLQEGPGLQQKPRPEAEPPS(0.998)PPS(0.002)GDLR;QGRPTLQEGPGLQQKPRPEAEPPS(0.999)PPS(0.001)GDLR;QGRPTLQEGPGLQQKPRPEAEPPS(0.92)PPS(0.08)GDLR;QGRPTLQEGPGLQQKPRPEAEPPS(0.986)PPS(0.014)GDLR 165.52 1.00E-12 2447080000 912920 776270 929330 768420 1038120 1160390 943520 953040 1062220 758597 TRUE FALSE 948962.7865 909588.334 953549.1033 920411.1825 861660.7332 890907.0084 869564.437 940266.0577 1023990.91 907229.5579 1.046000737 1.002599977 1.051056036 1.014529536 0.949771451 0.982008358 0.958483362 1.036414708 1.128701 1 19.79110812 1.494900485 6.790150539 1.070302901 1.000475277 0.270916946 0.042286198 0.143990995 15.97817429 0.023622885 0.010639018 31.25363131 -1.494900485 -0.069827624 QGRPVVICDKEDTETIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGRPVVICDKEDTETIK 17 2 Q06210-2;Q06210;A0A6I8PRN4 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 148.52 2.02E-07 363640000 645380 319230 482500 353660 597250 653040 578640 499700 517450 284048 FALSE TRUE 670860.1007 374055.2692 495074.3464 423612.8924 495729.6583 501381.3569 533284.6848 493002.3388 498827.0756 339701.7672 1.974850194 1.101128417 1.457379367 1.247014097 1.459308447 1.475945683 1.569861379 1.451279877 1.468426496 1 18.3739092 -1.205282066 5.049117905 0.999955916 1.453870823 0.300866878 0.212799902 9.54E-05 1.50E-05 0.186176093 0.043877876 0.062332986 1.205282066 0.453914908 QGS(ph)FTIEKPSPNIPIELIPHINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGSFTIEKPSPNIPIELIPHINK 23 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QGS(0.937)FT(0.063)IEKPSPNIPIELIPHINK 169.91 4.80E-12 587900000 627510 324060 507990 327050 691950 652270 571320 458000 575610 245920 TRUE FALSE 652284.5793 379714.7842 521228.6367 391739.5139 574332.5862 500790.1777 526538.4455 451861.2591 554893.9085 294103.3156 2.21787564 1.291093177 1.772263722 1.331979251 1.952825948 1.702769575 1.790317952 1.536403145 1.886731224 1 18.16596352 -0.967150444 5.533407938 0.999998661 1.695116538 0.393188301 0.266791019 3.93E-06 7.33E-07 0.230338626 0.05429123 0.107857303 0.967150444 0.695117877 QGS(ph)PVEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGSPVEPK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 QGS(1)PVEPK 84.821 0.018022 271760000 1268800 568010 775040 562170 1192200 1373100 1107400 799090 911390 422280 TRUE FALSE 1318893.204 665561.299 795238.1791 673365.5481 989550.2698 1054218.335 1020599.094 788379.5056 878589.2519 505017.681 2.611578274 1.317897024 1.574673935 1.333350442 1.959436881 2.087487972 2.02091755 1.561092879 1.739719786 1 18.94597437 0.410000134 1.190414637 1.000023711 1.790335079 0.298133374 0.370347781 3.482281964 5.785047738 0.350011306 0.105486342 2.570396576 -0.410000134 0.790311369 QGSES(ph)PAQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGSESPAQAGR 11 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 1 QGS(0.114)ES(0.886)PAQAGR;QGS(0.134)ES(0.866)PAQAGR 184.51 5.11E-06 1033040000 235010 348180 304240 295330 331600 427370 267850 293090 299300 312740 TRUE FALSE 244288.3763 407977.2065 312168.7443 353745.3925 275234.7504 328119.7944 246855.2171 289161.6079 288528.2515 374015.4152 0.653150556 1.090803186 0.834641385 0.945804312 0.735891461 0.877289494 0.660013484 0.773127513 0.771434117 1 18.51273821 3.237057893 24.99801488 0.784245304 0.892760207 0.063843792 0.132699656 77.479063 1288881.201 0.034797489 0.043745268 1726.067967 -3.237057893 0.108514903 QGSFT(ph)IEKPSPNIPIELIPHINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGSFTIEKPSPNIPIELIPHINK 23 1 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QGS(0.36)FT(0.636)IEKPS(0.004)PNIPIELIPHINK 121.23 0.00010301 774940000 566630 316020 442560 281700 686820 649400 554770 436620 528670 292010 TRUE FALSE 589000.9899 370293.9767 454093.4772 337419.4192 570074.5817 498586.6918 511285.6778 430767.8231 509643.27 349223.7686 1.68660052 1.060334404 1.300293731 0.966198322 1.632404873 1.427699763 1.464063227 1.233500872 1.459360203 1 18.41379223 -1.106810277 4.376679123 0.999969347 1.343281829 0.193927106 0.217439562 8.49E-05 1.73E-05 0.199103593 0.046923393 0.078196934 1.106810277 0.343312483 QGSGRES(ph)PSLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QGSGRESPSLASR 13 1 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;Q8WWM7-7;H3BSK9 Q8WWM7 ATXN2L Ataxin-2-like protein 1 QGSGRES(0.984)PS(0.016)LASR;QGSGRES(0.99)PS(0.01)LASR;QGSGRES(0.997)PS(0.003)LASR;QGSGRES(0.999)PS(0.001)LASR;QGS(0.012)GRES(0.676)PS(0.312)LASR;QGS(0.004)GRES(0.988)PS(0.009)LASR 202.76 2.40E-07 8034720000 3393409 3708760 3682600 3477900 3889240 4774030 3457342 3671559 3513824 3400310 TRUE FALSE 3527383.408 4345710.68 3778571.581 4165818.24 3228148.374 3665333.884 3186346.5 3622347.757 3387362.161 4066535.642 0.86741731 1.068651811 0.929186884 1.02441454 0.793832554 0.901340651 0.783553073 0.890769952 0.832984747 1 21.95536883 3.243829283 24.99990821 0.859592639 0.976203597 0.310874502 0.076262413 132.9955785 631061.7135 0.019249311 0.025312545 1753.191204 -3.243829283 0.116610959 QGSIT(ph)SPQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.018)IT(0.553)S(0.429)PQANEQS(0.001)VT(0.999)PQRR;QGS(0.001)IT(0.566)S(0.434)PQANEQS(0.035)VT(0.965)PQRR;QGS(0.03)IT(0.542)S(0.428)PQANEQS(0.012)VT(0.988)PQRR 174.26 3.00E-12 2626470000 799510 859590 779600 883300 832120 1064410 899390 882780 824040 691650 TRUE FALSE 831075.2722 1007217.896 799917.0164 1058014.104 690676.5396 817216.9088 828893.4617 870947.778 794382.9614 827165.5751 1.00472662 1.217673857 0.967057915 1.27908382 0.834991881 0.987972582 1.002088925 1.052930398 0.960367531 1 19.65781662 3.234016437 24.99999986 0.983567568 1.113597018 0.330223363 0.099800341 141.0846379 776184.1394 0.026912437 0.033201153 1714.022178 -3.234016437 0.13002945 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QGS(0.008)IT(0.201)S(0.791)PQANEQS(0.003)VT(0.997)PQRR 165.34 1.91E-11 1328900000 321720 341780 378480 369110 320420 455980 425740 410360 347090 288900 TRUE FALSE 334421.754 400478.0563 388343.4997 442118.8563 265955.1229 350085.5554 392369.3863 404859.7954 334598.2987 345504.4237 0.967923219 1.159111227 1.12398995 1.279632983 0.769758951 1.013259256 1.135642149 1.171793377 0.968434196 1 18.39834466 1.205942489 24.80387014 0.984216851 1.083445013 0.073134048 0.131741208 556.7951742 423391.1107 0.1272308 0.031817092 16.06728469 -1.205942489 0.099228162 QGSITSPQANEQSVT(ph)PQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQSVT(1)PQRR;QGSITSPQANEQS(0.002)VT(0.998)PQRR 328.62 1.96E-75 5772900000 315979 301728 343936 306970 302880 432865 347436 338856 305813 268333 TRUE FALSE 328454.0949 353547.4369 352899.2547 367687.7498 251396.5658 332338.6639 320203.0585 334314.1896 294806.8499 320907.7138 1.023515736 1.101710622 1.099690782 1.145774109 0.783392094 1.035620677 0.997804181 1.041776733 0.918665514 1 18.29179894 QGTEIDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGTEIDGR 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 126.82 0.0057422 0 771050 887000 821920 813600 958480 1000100 750580 879290 766840 882390 FALSE TRUE 801491.6494 1039335.35 843339.9104 974527.6516 795557.912 767841.9317 691747.5783 867504.5558 739241.5782 1055277.426 0.759508002 0.984893 0.799164172 0.923480051 0.753885085 0.72762092 0.655512533 0.822063028 0.700518707 1 20.00919089 3.222926297 24.86180946 0.761129435 0.870370916 0.140689702 0.104915597 333.5557678 530421.6979 0.027866615 0.033416407 1670.807043 -3.222926297 0.109241481 QGTLHVGDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGTLHVGDEIR 11 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8Y3B3;Q5JS79;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 77.078 0.0336 81561000 60233 91631 73436 88344 61150 96037 65504 70755 69903 88843 FALSE TRUE 62611.04535 107367.9115 75349.80249 105818.1795 50755.74484 73733.8622 60369.62532 69806.64496 67387.20468 106250.0848 0.589279956 1.010520713 0.709174045 0.995935012 0.477700746 0.693965208 0.568184255 0.657003193 0.634232008 1 16.69710447 3.239817657 25 0.649182095 0.831030254 0.155218076 0.171473784 49.39263597 982303.9633 0.043732182 0.056084976 1737.071347 -3.239817657 0.181848159 QGTQYTFSSIEREEYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QGTQYTFSSIEREEYGK 17 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 245.67 1.23E-20 353130000 122110 102490 108030 71280 127700 135910 89406 115020 122080 106220 FALSE TRUE 126930.9971 120091.8602 110845.3505 85378.97125 105993.5996 104346.9622 82398.1241 113478.345 117686.3646 127031.7753 0.999206669 0.945368668 0.872579717 0.672107204 0.83438651 0.821424104 0.648641837 0.893306771 0.926432496 1 16.95482989 4.206951284 3.12855908 0.815257853 0.982272845 0.233437488 0.101369172 0.305024171 6.01753211 0.025249659 0.072286539 16104.64975 -4.206951284 0.167014991 QGTTPPIWHLTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 123.88 0.00021827 307950000 452890 856860 742890 700430 712390 991110 713880 761790 743190 719820 FALSE TRUE 470770.4469 1004019.04 762250.3237 838972.9634 591298.2023 760939.7229 657924.2202 751579.4511 716442.7371 860854.9472 0.546863846 1.166304547 0.885457331 0.974581102 0.686873212 0.88393489 0.764268385 0.873061662 0.832245594 1 19.71541064 4.785594316 23.39030163 0.88117891 0.546860615 0.405580325 0.125717181 20381.17914 10135153.73 0.029034249 19.70362297 61037.15969 -4.785594316 -0.334318295 QGVLTHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 QGVLTHGR 8 0 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;;;;;;; 147.51 0.00053616 3669790000 3847910 4552730 4220720 4161100 5327780 5805580 4338880 4660010 4623800 5594670 FALSE TRUE 3999828.458 5334625.962 4330715.431 4984153.16 4422165.859 4457322.029 3998787.248 4597550.188 4457390.341 6690838.47 0.597806759 0.797303056 0.647260497 0.744922058 0.660928504 0.666182878 0.597651141 0.687141112 0.666193088 1 22.67375558 -1.894734224 2.241727018 1.188316298 0.675752592 0.743053259 0.057513944 3670184.549 1758116.646 3647866.601 0.01335142 0.012742827 1.894734224 -0.512563706 QGVSYSVHAYTGQPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGVSYSVHAYTGQPSPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 QGVSYS(0.001)VHAYT(0.235)GQPS(0.764)PR;QGVSYSVHAYT(0.057)GQPS(0.943)PR;QGVSYSVHAYT(0.041)GQPS(0.958)PR 188.84 1.27E-14 353760000 75978 200485 187503 207622 180812 282397 178959 225611 187389 245148 TRUE FALSE 78977.67011 234916.7392 192389.4822 248689.0119 150077.6408 216814.5765 164931.726 222587.0536 180644.9065 293180.057 0.269382819 0.801271211 0.656216129 0.848246687 0.511895803 0.739527029 0.562561204 0.759216216 0.616156871 1 18.16142744 -5 0.225223246 2.790445194 0.613339797 0.32436723 0.158195393 185.079023 1.852589809 150.8818517 0.264359159 1.00E-05 5 -2.177105397 QGVTEAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QGVTEAAEK 9 0 O76070;F8W754;G4Y816;Q16143 O76070 SNCG;SNCB Gamma-synuclein;Beta-synuclein 0 ;;; 153.97 0.0001787 352331000 581624 630900 662680 660030 794950 892730 761090 748710 741560 686260 FALSE TRUE 604586.9646 739252.1673 679949.9852 790581.964 659824.6829 685406.987 701433.7771 738674.7671 714871.4005 820719.5078 0.7366548 0.900736683 0.82848035 0.963279119 0.803958815 0.835129396 0.854657128 0.900033154 0.871030107 1 19.64652972 -5 0.165962501 1.546058103 0.823004888 0.406874686 0.055941873 133.7765535 1.250208971 23.97472151 0.204688477 1.00E-05 5 -0.723053216 QGYACPYYHNS(ph)KDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QGYACPYYHNSKDR 14 1 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYY(0.005)HNS(0.994)KDR;QGYACPY(0.027)Y(0.153)HNS(0.819)KDR;QGYACPY(0.002)Y(0.02)HNS(0.978)KDR 79.97 0.010631 276352000 474880 290297 319838 309570 435050 543750 375510 334141 356955 251072 TRUE FALSE 493628.6291 340153.2516 328173.241 370802.022 361100.3564 417472.3031 346076.545 329662.3864 344108.2593 300264.7513 1.643977946 1.132844432 1.092946273 1.23491692 1.202606549 1.390347356 1.152571334 1.097905715 1.146016167 1 18.1958756 4.74121718 24.91209784 1.168967719 1.643978124 0.685599288 0.097964017 137.9895963 1293931.261 0.023787048 0.162835038 55108.32108 -4.74121718 0.475010405 QGYACPYYHNS(ph)KDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGYACPYYHNSKDRR 15 2 Q9C0B0 Q9C0B0 UNK RING finger protein unkempt homolog 1 QGYACPYYHNS(1)KDRR;QGYACPYYHNS(1)KDRR 142.98 2.34E-06 200513000 214357 127657 139450 146790 208065 216872 158387 172005 168911 137733 TRUE FALSE 222819.9799 149581.0967 143084.1816 175824.6239 172698.1856 166506.7647 145972.2131 169699.5543 162831.9261 164719.1443 1.352726672 0.908097825 0.868655445 1.067420697 1.048440279 1.010852536 0.88618851 1.030235769 0.988542812 1 17.32964871 4.745370705 24.98591497 0.980163021 1.352726844 0.746938407 0.06530474 407.0478241 1493402.203 0.01610515 0.159033377 55637.8968 -4.745370705 0.372563822 QGYGEGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QGYGEGFR 8 0 Q9Y6B6;Q9H029;Q9NR31;Q9NR31-2;H0Y5E8 Q9Y6B6;Q9NR31 SAR1B;DKFZp434B2017;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 ;;;;; 153.73 0.0016199 1439900000 2926550 3161040 3118170 3125120 3366080 3764020 3149720 3116650 3195830 3102280 FALSE TRUE 3042092.454 3703924.031 3199432.072 3743259.408 2793914.924 2889883.399 2902836.716 3074876.405 3080812.703 3710112.369 0.819946177 0.998332035 0.862354493 1.008934241 0.75305399 0.77892072 0.782412075 0.828782554 0.830382586 1 21.82303145 3.231112036 24.99995947 0.815688687 0.923527672 0.226219052 0.082523715 203.3986277 682673.9772 0.021838699 0.02659208 1702.597676 -3.231112036 0.107838986 QGYVIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QGYVIYR 7 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 122.79 0.010019 131070000 332120 373750 354080 334920 412150 441770 365690 389290 336920 360540 FALSE TRUE 345232.3541 437938.6551 363307.6157 401166.1764 342092.8902 339175.6126 337026.2622 384072.2043 324794.315 431180.91 0.800667066 1.015672644 0.842587432 0.930389465 0.793385983 0.786620197 0.781635398 0.890744918 0.753266918 1 18.71793378 3.241131865 24.99987969 0.827404355 0.901872138 0.113409588 0.084695917 122.9813052 1195717.63 0.022060018 0.028546248 1742.335819 -3.241131865 0.074467783 QHDYS(ph)DYEDSSLEFLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHDYSDYEDSSLEFLER 17 0 A0A0A0MQS0;F8W9L8;A8MW92 A0A0A0MQS0 PHF20L1 PHD finger protein 20-like protein 1 1 QHDY(0.049)S(0.95)DYEDSSLEFLER 104.18 0.00055576 39057000 13585 17764 19427 17947 18575 23480 16310 16360 17282 19505 TRUE FALSE 14121.34629 20814.82882 19933.28358 21496.86303 15417.62813 18027.12584 15031.57958 16140.72096 16660.0242 23326.6313 0.605374437 0.892320393 0.854529028 0.921558829 0.660945335 0.772813083 0.644395643 0.691943931 0.714206178 1 14.50969036 3.227168962 24.99564486 0.723735413 0.826299835 0.052696693 0.12373665 418.1020286 917401.0881 0.033649065 0.04055202 1687.209305 -3.227168962 0.102564422 QHEAEEGVR ddPTM_MDA-MB-175_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 0 157.78 0.0013379 0 99577 106580 104580 95854 112560 129280 113320 115400 104290 95331 FALSE TRUE 103508.3769 124884.2859 107305.4407 114813.6351 93427.09141 99256.67926 104437.6823 113853.2518 100536.6233 114009.2842 0.907894279 1.095386983 0.941199144 1.007055135 0.819469151 0.870601723 0.916045417 0.998631406 0.881828388 1 16.79879179 QHEAEEGVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHEAEEGVRR 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 0 123.67 0.00029594 100560000 38723 38471 37224 33654 51980 48220 33751 38692 35563 38857 FALSE TRUE 40251.81394 45078.09499 38194.08802 40310.66075 43144.45817 37021.63578 31105.50843 38173.39703 34283.09458 46470.28519 0.866183923 0.970041281 0.821903456 0.867450255 0.928431104 0.796673307 0.669363407 0.821458204 0.737742289 1 15.50402088 2.663808461 6.835777927 0.784509681 0.889932915 0.175106144 0.08771134 0.344145505 26.7359459 0.026621815 0.025099301 461.1141627 -2.663808461 0.105423234 QHEAPSNRPLNELLT(ph)PQGPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 QHEAPSNRPLNELLT(1)PQGPS(1)PR;QHEAPSNRPLNELLT(1)PQGPS(1)PR;QHEAPSNRPLNELLT(1)PQGPS(1)PR 191.98 1.88E-16 527670000 232183 329121 338185 350131 347878 464360 311154 343120 353125 399602 TRUE FALSE 241349.7641 385644.9715 346998.3789 419385.8668 288745.8218 356519.4274 286764.9364 338521.0376 340416.1002 477896.3611 0.505025323 0.806963608 0.726095462 0.877566562 0.604201759 0.746018293 0.600056748 0.708356592 0.712322018 1 18.86633826 0.56583543 3.2252076 0.999999038 0.701770878 0.442389638 0.101555205 11.40302884 83.50836082 0.091373738 0.023715834 3.679895025 -0.56583543 -0.298228161 QHEAPSNRPLNELLT(ph)PQGPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLT(1)PQGPSPR;QHEAPSNRPLNELLT(1)PQGPSPR 185.02 5.42E-17 332240000 200726 219951 235730 232560 278720 310920 251790 244490 262220 265500 TRUE FALSE 208650.8175 257725.8733 241873.3175 278559.6739 231343.274 238713.542 232054.0419 241213.0115 252782.7534 317519.6417 0.657127277 0.81168482 0.761758599 0.877299031 0.728595159 0.751807166 0.73083366 0.759679024 0.796116902 1 18.27648631 0.738888906 2.948315711 0.999983165 0.762831588 0.638608466 0.053859164 1.118442819 11.847301 0.049450016 0.012959814 5.481367316 -0.738888906 -0.237151577 QHEAPSNRPLNELLTPQGPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QHEAPSNRPLNELLTPQGPSPR 22 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLT(0.027)PQGPS(0.973)PR;QHEAPSNRPLNELLT(0.012)PQGPS(0.988)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR;QHEAPSNRPLNELLTPQGPS(1)PR 156.27 7.85E-09 5412310000 895864 1090126 1103333 1173050 1151263 1464888 1026943 1065459 1071048 1061409 TRUE FALSE 931233.4025 1277346.66 1132086.764 1405075.789 955571.7265 1124689.963 946448.5242 1051178.265 1032501.192 1269371.772 0.733617545 1.006282548 0.89184807 1.10690644 0.752791064 0.886020934 0.745603885 0.82810906 0.813395425 1 20.27568323 3.191301938 24.99999879 0.825111898 0.93672359 0.149464302 0.110932702 184.9561132 97841.71269 0.029833899 0.035658427 1553.466665 -3.191301938 0.111611692 QHELLSQEQSVNQLEDDGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHELLSQEQSVNQLEDDGER 20 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 86.371 0.0031029 0 26515 55119 39703 53365 38968 69561 31505 45224 31666 51938 FALSE TRUE 27561.83267 64585.25948 40737.6928 63920.43772 32344.23328 53406.51196 29035.55578 44617.84625 30526.34685 62114.25669 0.443727964 1.039781572 0.655850926 1.029078365 0.52072157 0.859810852 0.467453968 0.718318928 0.491454756 1 15.92263682 2.270671446 24.99999184 0.647228548 0.767833869 0.030906537 0.227024092 558.5937504 434893.0895 0.071646032 0.05993891 186.4968267 -2.270671446 0.120605321 QHFISFDTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 ;;;;; 166.87 5.41E-06 5262600000 1136164 1443020 1375830 1426710 1565960 1819350 1278530 1313100 1332790 1681280 FALSE TRUE 1181020.632 1690847.46 1411685.26 1708908.98 1299778.679 1396833.535 1178315.478 1295500.042 1284823.148 2010694.626 0.587369468 0.84092703 0.702088344 0.849909756 0.646432662 0.694701979 0.586024085 0.644304722 0.63899467 1 20.93926256 -1.185131208 5.242589309 1.000016636 0.688780996 0.53431923 0.087416541 1.71E-05 2.66E-06 0.085187171 0.020077737 0.065293326 1.185131208 -0.31123564 QHFPATPLLDYALEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QHFPATPLLDYALEVEK 17 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 145.61 4.68E-07 564900000 629330 570150 678500 518080 748250 795560 699040 672690 704660 509080 FALSE TRUE 654176.4343 668068.8273 696182.2674 620554.6777 621062.7323 610803.2468 644247.4182 663673.6908 679299.4242 608824.4791 1.074491018 1.097309406 1.143485999 1.019266963 1.020101447 1.003250145 1.058182515 1.090090352 1.115755768 1 19.21566684 3.732192165 24.95444849 1.048299724 1.104316868 0.34250973 0.038558689 643.6271887 2522020.753 0.011165949 0.017762596 5397.493964 -3.732192165 0.056017144 QHGCTANDANTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QHGCTANDANTK 12 0 Q8N6H7;G5E9L0;Q8N6H7-2;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48;H0YDX1 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 ;; 189.3 8.11E-06 195659000 238587 217812 244510 201400 286583 329952 267796 264991 274122 205783 FALSE TRUE 248006.599 255219.5167 250882.1315 241236.3189 237869.724 253325.6485 246805.4498 261439.2291 264256.4028 246102.2389 1.007738085 1.037046708 1.019422386 0.980228055 0.966548395 1.029351255 1.002857393 1.062319588 1.073766756 1 17.90889826 1.753797768 10.2888037 1.050629167 1.006231377 0.30484105 0.026758886 0.145124106 69.85714574 0.012825194 0.006997935 56.72803867 -1.753797768 -0.04439779 QHGDVVSAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QHGDVVSAIR 10 0 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 ;;;;; 170.02 4.45E-06 3191000000 549949 774744 716848 755866 860981 909688 726534 725811 771731 886235 FALSE TRUE 571661.4112 907800.2553 735529.6478 905374.0388 714631.7572 698426.7485 669586.3666 716082.6907 743956.5521 1059875.78 0.539366426 0.856515709 0.69397722 0.854226557 0.674259918 0.658970383 0.631759286 0.675628884 0.701928062 1 20.01546376 -1.931400772 4.144248979 1.155395012 0.700959952 0.499979835 0.090419478 0.059007877 0.00097675 0.03979343 0.019683547 0.011711141 1.931400772 -0.454435061 QHHHLLQSPVSHHEPES(ph)PQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR;QHHHLLQSPVSHHEPES(1)PQLR 302.8 1.35E-55 1502890000 425426 498288 598709 464953 684875 899640 555272 455678 483864 461854 TRUE FALSE 442222.147 583865.0879 614311.8484 556919.3157 568460.1921 690712.2442 511748.3297 449570.3817 466449.8292 552345.4486 0.800626036 1.057065084 1.112187762 1.008280809 1.029175118 1.250507714 0.926500492 0.81392973 0.844489314 1 19.07521132 2.01233244 24.99927477 0.866652648 1.048218538 0.285071601 0.113755611 239.8185737 486137.8562 0.041922456 0.030941701 102.8803516 -2.01233244 0.18156589 QHHHLLQSPVSHHEPESPQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHHHLLQSPVSHHEPESPQLR 21 0 Q9Y6D6 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 34.689 0.088838 83676000 8420 21065 14644 24452 13523 16189 14986 26809 23896 15889 FALSE TRUE 8752.428102 24682.74989 15025.63467 29288.53262 11224.36529 12429.3501 13811.35816 26449.66921 23035.98763 19002.14534 0.460602103 1.298945432 0.790733594 1.541327682 0.590689372 0.654102465 0.726831519 1.391930687 1.21228352 1 14.21387469 1.739116327 23.85848999 1.226445679 0.887134452 0.182413674 0.321795632 0.114544891 4348.147169 0.146383955 0.081168353 54.84238425 -1.739116327 -0.339311228 QHHPPYHQQHHQGPPPGGPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QHHPPYHQQHHQGPPPGGPGGR 22 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;;; 179.78 1.93E-17 3876782000 588327.7 601502.4 619044.6 613519.7 670842 810674.4 552251.9 551795.2 583853.3 555609.2 FALSE TRUE 611555.3319 704805.7582 635177.4108 734872.0655 556812.5165 622407.5565 508964.953 544399.2879 562840.5338 664470.185 0.920365346 1.060703361 0.955915593 1.105951903 0.837979685 0.936697493 0.765971092 0.819298292 0.847051601 1 19.34184494 3.218840333 24.98342966 0.852495158 1.010387688 0.44068003 0.077725113 188.24741 238488.2318 0.021370704 0.025576341 1655.161337 -3.218840333 0.15789253 QHIAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QHIAEK 6 0 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 ; 71.715 0.087502 357150000 1276950 1060610 1311820 1064040 1503060 1586130 1402020 1267070 1444030 1110230 FALSE TRUE 1327364.972 1242761.517 1346007.107 1274503.936 1247570.398 1217775.346 1292126.009 1250086.999 1392059.642 1327758.312 0.999703756 0.935984739 1.013744064 0.959891514 0.939606544 0.917166426 0.973163562 0.941501919 1.04842849 1 20.34056113 1.242261605 24.99999925 1.024214254 0.958771219 0.421896621 0.029990402 78.52136776 530437.634 0.021230166 0.007077039 17.46874098 -1.242261605 -0.065443035 QHIIPLENVTIDSIKDEGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHIIPLENVTIDSIKDEGDLR 21 1 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 0 93.006 0.0010721 99268000 105270 72009 85155 68864 96938 116750 86289 87655 88949 68225 FALSE TRUE 109426.1409 84375.9856 87374.20926 82485.09366 80460.51339 89636.58186 79525.44271 86480.1281 85747.74287 81592.3825 1.341131825 1.034115968 1.070862335 1.010941109 0.98612776 1.098590078 0.974667491 1.059904435 1.050928288 1 16.31614685 4.738616859 9.642267326 1.033377515 1.342060792 0.860427866 0.037371631 0.024123854 61.6139112 0.008287836 0.04822341 54779.34797 -4.738616859 0.308683278 QHLVEVR ddPTM_MDA-MB-175_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 88464000 39812 49022 47714 55212 60454 69997 46318 49391 53832 60695 FALSE TRUE 41383.8085 57441.14716 48957.46604 66132.76881 50178.05067 53741.25756 42687.47413 48728.99443 51894.59684 72587.02317 0.570126817 0.791341822 0.674465819 0.911082531 0.691281285 0.740370044 0.588086854 0.671318265 0.714929399 1 16.14742403 0.923909421 19.65475263 1 0.705826983 0.477439566 0.092357498 3291.043594 850104.2088 0.087239473 0.021809868 8.392849227 -0.923909421 -0.294173017 QHMDITGEENPLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QHMDITGEENPLNK 14 0 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 ; 246.5 9.73E-18 583010000 570250 440260 521820 422510 623950 678300 589270 515810 582790 402650 FALSE TRUE 592763.9103 515871.2303 535419.0579 506081.2169 517891.2019 520775.1047 543081.4776 508896.4106 561815.5017 481541.5583 1.23097145 1.071291193 1.111885462 1.050960625 1.075485995 1.081474892 1.127797733 1.056806836 1.166702005 1 18.87730079 3.557612723 0.010592994 1.29E-06 2.216247502 0.246411534 0.053853084 5735.385939 14.75492465 1468.678317 1619.231193 3610.877234 -3.557612723 2.216246211 QHMENEMAHYACDCWDAESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHMENEMAHYACDCWDAESK 20 0 P41250 P41250 GARS Glycine--tRNA ligase 0 109.89 0.00011032 178360000 76298 38585 75734 65264 81888 80923 82544 67722 76754 49667 FALSE TRUE 79310.30395 45211.6736 77707.69026 78173.02441 67968.70701 62129.85965 76073.98559 66814.29736 73991.63853 59398.29772 1.335228567 0.7611611 1.308247765 1.316081898 1.14428712 1.045987209 1.280743532 1.124852057 1.245686179 1 15.85813397 -1.171616267 4.28720913 0.999956836 1.166551022 0.089515458 0.164712772 6.90E-05 1.33E-05 0.149424881 0.0352099 0.067357155 1.171616267 0.166594186 QHPDPDSSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QHPDPDSSVK 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;; 128.28 0.00033372 1180390000 1175650 1135290 1364240 1140570 1591300 1849070 1411230 1403490 1338860 1106030 FALSE TRUE 1222065.57 1330267.226 1399793.215 1366171.342 1320811.394 1419651.515 1300614.105 1384678.512 1290674.69 1322735.402 0.923892691 1.005694127 1.058256408 1.032837965 0.998545433 1.073269463 0.983276098 1.046829555 0.97576181 1 20.33509307 4.709474283 3.76570249 1.023814271 0.916336576 0.468064025 0.030736325 0.177935946 4.800425473 0.006766506 0.050420075 51224.09371 -4.709474283 -0.107477694 QHQNTMEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHQNTMEDK 9 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 79.974 0.019286 15792000 19068 18721 19477 19559 20728 25421 20931 18846 19548 16596 FALSE TRUE 19820.81936 21936.18612 19984.58662 23427.71182 17204.66196 19517.35801 19290.37353 18593.4002 18844.4713 19847.66845 0.998647242 1.105227356 1.006898451 1.180376016 0.866835417 0.983357721 0.971921391 0.93680526 0.949455164 1 14.27668192 3.230781443 24.99999976 0.950380821 1.070398077 0.512099726 0.058023431 133.0339446 427531.5347 0.015445203 0.018782378 1701.302118 -3.230781443 0.120017256 QHREPS(ph)EQEHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHREPSEQEHRR 12 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 QHREPS(1)EQEHRR 79.771 0.010512 2210000 873.22 2124.1 0 884.29 1599.2 1720.5 827.82 760.91 1648.8 1528.6 TRUE FALSE 907.6953999 2488.897652 0 1059.199923 1327.368555 1320.939949 762.9333053 750.711246 1589.46001 1828.099903 0.496523958 1.361466979 0 0.579399365 0.726091913 0.722575362 0.417336768 0.410651105 0.869460147 1 10.8361292 1.059910686 5.96171073 0.998399624 0.587691997 0.159222724 0.324143772 0.305473802 19.86214707 0.299911271 0.075465035 11.47917524 -1.059910686 -0.410707627 QHS(ph)ITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 1 QHS(0.996)IT(0.004)K 101.65 0.038064 78646000 148760 97040 197850 128100 260860 192490 200050 149100 244510 138060 TRUE FALSE 154633.1597 113705.8651 203006.1335 153437.7977 216519.1104 147787.1147 184369.5583 147101.5584 235710.1329 165110.2137 0.936545088 0.688666453 1.229518932 0.929305306 1.311361094 0.895081603 1.116645386 0.890929489 1.427592683 1 17.33306984 4.241707048 24.99991073 1.081311443 0.81260577 0.283254062 0.180945796 96.61074036 767582.5469 0.04086013 0.102650138 17446.44913 -4.241707048 -0.268705673 QHSITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QHSITK 6 0 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ; 82.305 0.059593 286330000 652550 539450 601540 499690 732130 800320 692490 679850 698110 592510 FALSE TRUE 678313.1779 632096.3412 617216.6266 598527.1906 607682.8041 614457.809 638210.8243 670737.7228 672985.1575 708600.9902 0.957256887 0.892034234 0.871035512 0.844660393 0.857581082 0.867142182 0.900663184 0.946566166 0.949737817 1 19.43461396 1.524565136 1.334859621 0.987720888 0.878543918 0.624661733 0.030022042 0.269950005 0.922213983 0.027992968 0.009598091 33.46302022 -1.524565136 -0.10917697 QHSLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHSLLK 6 0 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841;K7EQJ5;S4R456;K7EJ78 K7EM56 RPS15 40S ribosomal protein S15 0 81.635 0.06136 116420000 158410 183930 186720 189330 244960 279610 216800 222240 236800 226170 FALSE TRUE 164664.1491 215518.5467 191586.0766 226778.9089 203321.7867 214674.815 199806.6495 219261.2363 228277.6143 270483.6812 0.608776649 0.796789462 0.708309188 0.838419929 0.751697055 0.793670117 0.738701309 0.810626487 0.843960764 1 18.04518203 -5 0.115876766 1.771034 0.643377878 0.691342112 0.053705836 88.14074658 0.6696408 15.91424069 0.539325837 1.00E-05 5 -1.127656121 QHTFVETESVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QHTFVETESVR 11 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 141.38 3.82E-05 1794550000 205513 248091 207204 215366 243919 284688 222346 213649 218673 223768 FALSE TRUE 213626.8119 290698.6994 212603.9065 257964.752 202457.7355 218573.5265 204917.9395 210785.3846 210803.0014 267611.0553 0.798273493 1.086273133 0.794451134 0.963954018 0.756537264 0.81675821 0.765730471 0.787655743 0.787721573 1 18.02977819 3.237940336 24.99999994 0.803531956 0.914969974 0.153550763 0.101390923 23.77222319 958141.803 0.026198191 0.033147431 1729.578729 -3.237940336 0.111438018 QHVIDGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QHVIDGEK 8 0 Q9UQ80;Q9UQ80-2;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ;;; 104.17 0.0046324 2083840000 5085050 3717040 4379550 3589550 5323230 6105950 5158880 4548300 4918210 3382240 FALSE TRUE 5285811.701 4355412.705 4493684.671 4299552.276 4418389.266 4687935.649 4754513.505 4487337.478 4741204.583 4044925.171 1.30677614 1.076759772 1.110943832 1.062949769 1.092329049 1.158967212 1.175426814 1.109374658 1.172136537 1 21.94768158 4.745131896 24.92655763 1.112894989 1.306776231 0.573847134 0.051504522 526.0805922 1995505.398 0.01185556 0.114297258 55607.31121 -4.745131896 0.193881242 QHVPEQHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QHVPEQHPK 9 0 Q9H3U1;A0A1W2PNX8;Q9H3U1-2 Q9H3U1;Q9H3U1-2 UNC45A Protein unc-45 homolog A 0 95.573 0.0045993 66109000 188380 156390 189280 168500 243530 239480 206170 157780 192950 164160 FALSE TRUE 195817.3879 183248.766 194212.7923 201828.7971 202134.8576 183864.3994 190009.8567 155665.2172 186005.7672 196324.009 0.997419464 0.933399674 0.989246263 1.028039302 1.029598258 0.936535477 0.967838104 0.792899544 0.947442792 1 17.58287709 1.970714864 23.2728538 0.887919369 0.98447388 0.19947674 0.058450883 313.3129608 248988.3257 0.023537679 0.015227005 93.4791736 -1.970714864 0.096554511 PIRPGQHPAAS(ph)PTHPSAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 PIRPGQHPAASPTHPSAIR 19 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 1 PIRPGQHPAAS(0.993)PT(0.007)HPSAIR;PIRPGQHPAAS(0.942)PT(0.058)HPSAIR;PIRPGQHPAAS(0.793)PT(0.207)HPSAIR;PIRPGQHPAAS(0.998)PT(0.002)HPSAIR 168.68 9.41E-12 1755030000 281017 624962 752097 760232 798018 1004190 960410 836265 738428 546369 TRUE FALSE 292111.7682 732294.362 771697.2657 910603.6205 662371.1854 770982.0911 885130.5546 825056.2355 711852.1205 653419.5447 0.447050858 1.120710833 1.181013442 1.393597158 1.013699683 1.179918932 1.354612916 1.262674559 1.089425816 1 19.31765008 4.750490936 3.262972391 1.205340536 0.329831515 0.756254398 0.124369719 0.15726518 2.636891447 0.029450879 0.35322838 56297.73673 -4.750490936 -0.875509021 down QHYIDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QHYIDLK 7 0 Q32Q12;P22392-2;J3KPD9;P22392;F6XY72;O60361 Q32Q12;O60361 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 ;;;;;; 136.16 0.0030076 14581030000 26444250 19792360 24024450 19982410 28949140 31715180 27291760 25185640 26048430 17580510 FALSE TRUE 27488289.41 23191543.87 24650546.9 23934871.06 24028375.52 24349810.09 25152560.54 24848067.69 25110952.09 21025074.34 1.3074051 1.103042182 1.17243566 1.138396501 1.142843785 1.158131938 1.196312562 1.181830195 1.19433357 1 24.32560757 -2.372845549 2.039861 9.83E-06 1.173558036 0.516656068 0.051307185 791686.6101 82722.24679 3657342.877 0.011516802 0.004237937 2.372845549 1.173548206 QHYNCEHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 QHYNCEHSK 9 0 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5;E9PQ34;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 ;;;;;;; 198.25 1.54E-05 2333291000 2210356 2153751 1925915 1744605 3837400 3319000 2146034 1761776 1981880 2666147 FALSE TRUE 2297622.562 2523640.98 1976105.927 2089682.662 3185120.119 2548212.55 1977822.247 1738162.274 1910552.526 3188527.458 0.720590489 0.79147538 0.619755029 0.655375464 0.998931375 0.799181623 0.620293309 0.545130094 0.599195883 1 21.60445887 2.234517749 24.99341446 0.640487823 0.764612064 0.010833357 0.152358552 216.7484071 1339943.112 0.055331306 0.042367922 171.600184 -2.234517749 0.124124241 QIANS(ph)QDGYVWQVTDMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 383.65 2.11E-126 160731000 115014 122817 98204 117656 122409 155270 107209 109805 114998 128804 TRUE FALSE 119554.8415 143909.8644 100763.2769 140928.0056 101601.9619 119210.8956 98805.67844 108333.2436 110859.2444 154040.6777 0.776125133 0.93423287 0.654134209 0.914875264 0.659578778 0.773892308 0.641425888 0.703276856 0.719675128 1 17.23295185 3.225753081 24.99916883 0.726716839 0.816176416 0.057680362 0.118672196 467.4842176 912485.8279 0.031449192 0.037819893 1681.717644 -3.225753081 0.089459576 QIAQSKEDDDVIVNKPHVS(ph)DEEEEEPPFYHHPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 232.47 6.49E-38 1597700000 1359700 664190 923260 454040 1472200 1121800 970520 872960 1152800 562650 TRUE FALSE 1413382.006 778259.4658 947320.9141 543847.7568 1221955.97 861278.951 894448.1064 861259.3991 1111310.953 672890.4949 2.100463622 1.156591558 1.407838157 0.808226243 1.815980429 1.279968966 1.329262507 1.279939909 1.651548003 1 19.36001222 7.999999998 0.028206391 7.06E-10 3.312587495 0.115896947 0.342572412 4214.832451 9.123027258 350.7527124 808.0083157 99999999.5 -7.999999998 3.312587495 QIATLHAQVADMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 ; 161.04 4.28E-05 2844100000 3926300 3280400 3705900 3310800 4597400 4622600 4326600 3917900 4134900 2947800 FALSE TRUE 4081313.356 3843783.182 3802478.798 3965666.358 3815935.59 3549071.206 3987469.787 3865386.959 3986085.757 3525364.971 1.157699526 1.090322056 1.078605713 1.124895264 1.082422847 1.006724477 1.131079993 1.096450152 1.130687401 1 21.74934119 4.737299744 5.138845277 1.08667491 1.160862986 0.202976767 0.044106014 0.262544698 23.1068559 0.010052678 0.069096318 54613.46658 -4.737299744 0.074188075 QICLVMLETLSQS(ph)PQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.002)QS(0.998)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.006)QS(0.994)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLS(0.001)QS(0.999)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLET(0.002)LS(0.113)QS(0.885)PQGR;QICLVMLETLS(0.004)QS(0.996)PQGR;QICLVMLETLS(0.038)QS(0.962)PQGR;QICLVMLETLS(0.006)QS(0.994)PQGR;QICLVMLETLSQS(1)PQGR;QICLVMLETLSQS(1)PQGR 467.64 2.31E-206 8708392000 2171912 2519321 2174835 2311645 2392123 2845073 2030255 2303785 2128953 2541765 TRUE FALSE 2257660.763 2951994.784 2231512.987 2768881.481 1985510.787 2184347.913 1871118.308 2272906.53 2052332.397 3039775.187 0.742706491 0.971122732 0.734104613 0.910883638 0.653176852 0.718588639 0.615544964 0.747721917 0.67515927 1 21.5355332 3.236635226 24.99988591 0.715535719 0.841548554 0.145996279 0.118487572 74.63929115 969145.0781 0.030607413 0.038378437 1724.388929 -3.236635226 0.126012835 QIDNPDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 ;;; 173.48 0.00064568 1347880000 3742330 2898160 3014660 2965230 3957810 4313840 3560340 2988000 3206380 2365080 FALSE TRUE 3890080.078 3395896.435 3093224.516 3551743.644 3285062.87 3312016.037 3281271.248 2947950.747 3090983.01 2828472.144 1.375329111 1.200611589 1.093602609 1.255711021 1.16142663 1.170955862 1.16008611 1.042241393 1.09281013 1 21.43159153 8 0.126882878 0.94697614 2.081999421 0.647715272 0.060954061 56.15680389 0.484105934 0.351423916 11.36814952 100000000 -8 1.135023281 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QIDS(0.001)S(0.999)PVGGETDETTVSQNYR;QIDS(0.001)S(0.999)PVGGETDETTVSQNYR;QIDS(0.001)S(0.999)PVGGETDETTVSQNYR;QIDS(0.099)S(0.901)PVGGETDETTVSQNYR;QIDSS(1)PVGGETDETTVSQNYR;QIDS(0.19)S(0.81)PVGGETDETTVSQNYR;QIDS(0.251)S(0.749)PVGGETDETTVSQNYR;QIDS(0.005)S(0.995)PVGGETDETTVSQNYR;QIDS(0.017)S(0.983)PVGGETDETTVSQNYR;QIDS(0.152)S(0.848)PVGGETDETTVSQNYR 406.43 1.49E-151 10858180000 2676620 3166637 3026673 2920406 2939235 3807307 2923631 3047827 2952816 3229326 TRUE FALSE 2782295.024 3710482.272 3105550.585 3498053.59 2439624.885 2923117.65 2694469.163 3006975.864 2846544.729 3862050.601 0.720419102 0.960754443 0.8041196 0.905750326 0.63169159 0.756882276 0.697678369 0.778595667 0.737055265 1 21.88093564 QIEAQEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QIEAQEKPR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;; 115.7 0.0013074 457081000 383873 318857 426331 428615 452694 504910 541578 435093 464054 318920 FALSE TRUE 399028.6025 373618.2094 437441.5361 513393.7677 375745.2356 387652.3045 499127.7012 429261.29 447352.7872 381406.2679 1.046203579 0.979580675 1.146917534 1.346054879 0.985157474 1.016376334 1.308651019 1.125469941 1.172903607 1 18.54096903 4.229344565 24.32317567 1.147627773 1.012892128 0.152528836 0.115788149 205.1889641 541545.9773 0.028484732 0.062971097 16956.82605 -4.229344565 -0.134735645 QIEEELWEEEFIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QIEEELWEEEFIER 14 0 Q9BPZ3;D6RA77 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 0 ; 182.08 3.64E-06 44804000 28683 34469 34926 37404 37455 46858 32391 34495 34927 37785 FALSE TRUE 29815.42699 40388.78262 35836.20025 44802.39956 31088.41248 35975.93964 29852.10878 34032.65095 33669.98409 45188.24731 0.6598049 0.893789536 0.793042492 0.991461325 0.68797562 0.796134875 0.660616655 0.753130581 0.745104891 1 15.46365998 QIEETLAHFHLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QIEETLAHFHLTK 13 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 244.67 2.72E-17 2001150000 1896390 1997290 2112640 2043070 2373900 2633700 2213200 2091060 1847340 1768810 FALSE TRUE 1971260.942 2340309.021 2167697.134 2447183.148 1970385.326 2022063.089 2039723.601 2063032.761 1780854.594 2115374.454 0.931873285 1.106333215 1.024734477 1.156855773 0.931459356 0.955888961 0.964237607 0.975256536 0.84186258 1 21.01248163 3.202767026 24.99997279 0.947568207 1.056461418 0.395732189 0.066626625 169.6726992 118507.1028 0.018230604 0.021790447 1595.023281 -3.202767026 0.108893211 QIEHCEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIEHCEGR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 73.499 0.042213 0 19475 22722 24131 23096 22897 24936 19541 17520 20218 22570 FALSE TRUE 20243.88804 26624.32675 24759.87368 27664.31987 19004.97612 19144.99191 18009.32536 17285.17306 19490.35813 26992.15937 0.749991424 0.986372612 0.917298736 1.024902065 0.704092468 0.709279745 0.667205803 0.640377556 0.722074802 1 14.72025278 3.222150403 24.98762217 0.710914651 0.92424041 0.346750286 0.116204195 206.7440438 314805.8563 0.031580134 0.037848633 1667.824707 -3.222150403 0.213325759 QIEYEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIEYEYK 7 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 112.94 0.01452 122400000 234150 182860 211370 169580 278570 268920 242630 226230 215970 184540 FALSE TRUE 243394.4228 214264.7825 216878.4758 203122.4179 231218.7709 206467.4055 223612.0266 223197.7569 208197.2819 220697.0798 1.102843876 0.970854634 0.982697533 0.920367492 1.047674809 0.935523958 1.013207909 1.011330812 0.943362196 1 17.75170801 4.742003702 24.79320385 0.982631196 1.102843927 0.488217571 0.037506743 246.0204182 1771474.398 0.008410513 0.060861667 55208.21448 -4.742003702 0.12021273 QIEYYFSVDNLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIEYYFSVDNLER 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 0 91.202 0.015448 35386000 25149 16194 30082 23251 30660 33252 25390 23193 29091 24445 FALSE TRUE 26141.90194 18975.19353 30865.96163 27849.9784 25448.42415 25529.72694 23399.86546 22882.13577 28044.02059 29234.52972 0.894213185 0.649067856 1.055804965 0.952639863 0.870491997 0.87327305 0.80041874 0.782709214 0.959277295 1 14.83538576 QIFDEYENETFLCHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QIFDEYENETFLCHR 15 0 S4R3N1;Q9Y3A3-2;Q9Y3A3-3;Q9Y3A3;B4DM50 S4R3N1 HSPE1-MOB4;MOB4 MOB-like protein phocein 0 ;;; 290.39 6.78E-44 709360000 681456 676337 734033 792030 737925 865617 845567 784946 751591 597050 FALSE TRUE 708360.4091 792492.6186 753162.503 948691.17 612492.7721 664590.5703 779289.2491 774425.0828 724541.3867 714030.5163 0.992059013 1.109886203 1.054804362 1.328642332 0.857796352 0.930759338 1.091394879 1.084582613 1.014720478 1 19.44562621 3.215858335 24.99989688 1.009866867 1.115776441 0.254353299 0.103006765 399.2487266 439654.0058 0.030985252 0.037057834 1643.835423 -3.215858335 0.105909574 QIGLDQIWDDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QIGLDQIWDDLR 12 0 A0A590UJ56;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;Q13616;A0A590UJC4;A0A590UK34;A0A590UJ50;A0A590UJM8;A0A590UJ59;A0A590UJ97 A0A590UJ56 CUL1 Cullin-1 0 ;;; 208.72 1.48E-07 203293000 130769 180367 150408 166419 161117 183978 134548 158108 146217 192601 FALSE TRUE 135931.8611 211343.6292 154327.756 199336.1815 133730.3899 141251.8977 124001.7762 155988.8209 140954.6787 230337.4784 0.590142178 0.917539042 0.670007144 0.865409237 0.580584588 0.613238882 0.53834824 0.677218584 0.611948519 1 17.81338965 -1.352140751 3.246318592 1.002545789 0.676129359 0.409988795 0.117356212 25227323.99 33179188.04 607641.6793 0.027781733 0.044448719 1.352140751 -0.326416429 QIGNVAALPGIVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIGNVAALPGIVHR 14 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 79.466 0.019008 327940000 310750 331000 301000 321550 334740 395780 333480 346710 293840 370350 FALSE TRUE 323018.65 387846.6752 308844.3073 385151.6303 277841.0144 303866.0931 307340.9662 342062.9196 283264.7558 442912.9917 0.729304979 0.875672384 0.697302434 0.869587566 0.627303826 0.686062723 0.693908221 0.772302746 0.63954944 1 18.75666379 -1.155679657 4.231622128 1.000060103 0.736125864 0.495175401 0.080997343 11152898.16 3045921.223 7249.559113 0.018211495 0.069874762 1.155679657 -0.263934239 QIHIDIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIHIDIPR 8 0 Q9NU19;A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;B0QYI1;Q8WUA7-2 Q9NU19;A0A0A0MRY0 TBC1D22B;TBC1D22A TBC1 domain family member 22B;TBC1 domain family member 22A 0 102.07 0.0050364 91676000 47763 50973 47846 52583 63466 63514 52421 51670 48675 57667 FALSE TRUE 49648.72012 59727.21624 49092.90607 62983.76046 52678.07199 48763.83606 48312.10504 50977.44817 46923.19626 68965.74455 0.719904069 0.866041781 0.711844792 0.913261517 0.763829526 0.707073292 0.700523214 0.739170562 0.680384103 1 16.07359233 4.20715721 24.98842676 0.76437126 0.792973636 0 0.10304136 1132.282698 900984.4377 0.02436603 0.052644897 16112.28777 -4.20715721 0.028602376 QIILEKEETEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIILEKEETEELKR 14 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 107.07 0.00050889 64415000 129480 69547 94283 60200 127500 119770 105520 105170 113550 68627 FALSE TRUE 134591.9704 81491.15625 96740.09243 72107.38032 105827.5955 91955.23263 97249.06667 103760.3682 109463.3577 82073.14671 1.639902645 0.992908881 1.17870578 0.878574579 1.289430219 1.120405837 1.184907251 1.264242597 1.333729266 1 16.32462265 1.984575597 20.60936258 1.227657017 1.164363196 0 0.204794225 378.9835199 506373.9208 0.078084507 0.05238001 96.5107291 -1.984575597 -0.063293821 QILGVIDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QILGVIDKK 9 1 Q14444-2;Q14444;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 107.83 0.0051546 0 411330 383350 393580 317970 444350 507760 391580 383830 460590 421550 FALSE TRUE 427569.626 449187.3805 403837.0181 380863.517 368819.5457 389840.4352 360886.9364 378685.3867 444013.4559 504144.6514 0.848109019 0.890989083 0.801034023 0.755464758 0.731574846 0.773270993 0.715840058 0.751144311 0.880726305 1 18.94347821 0.987152541 3.936040366 0.999491743 0.7804216 0.644861152 0.050484532 0.129461722 5.681582165 0.054853608 0.014060364 9.708509068 -0.987152541 -0.219070143 QILIACS(ph)PVSSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 QILIACS(0.994)PVS(0.004)S(0.001)VR;QILIACS(0.999)PVS(0.001)SVR 102.15 0.0017956 276420000 372400 473750 383150 422500 379170 490390 380310 423620 392840 486590 TRUE FALSE 387102.6396 555112.8772 393135.2038 506069.239 314718.8188 376504.3544 350500.3084 417942.0668 378701.7651 581927.9942 0.665207111 0.953920215 0.675573624 0.869642368 0.540820895 0.646994745 0.602308725 0.718202374 0.650770832 1 19.15048112 5.062039626 15.6288386 0.72293952 0.127063492 0.011386281 0.145807132 11377744.52 64341912.84 0.03317661 215401420 115355.8505 -5.062039626 -0.595876028 QINWTVLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QINWTVLYR 9 0 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 162.97 0.00014743 1050560000 712180 710290 751940 615830 972020 992650 784510 768420 736550 1010390 FALSE TRUE 740297.4163 832276.7822 771536.1741 737639.3359 806796.3876 762122.0813 723018.0563 758120.5868 710041.7094 1208356.575 0.612648147 0.688767537 0.638500414 0.610448398 0.667680719 0.630709591 0.598348262 0.627398073 0.587609422 1 20.20461481 -1.502516245 3.209332108 1.009358672 0.630234887 0.936173309 0.029050541 44136551.47 49847425.93 3587602.545 0.007166039 0.031440088 1.502516245 -0.379123786 QIPFHDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QIPFHDVR 8 0 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3;Q8IXW7;A0A087WY29 Q06787 FMR1 Fragile X mental retardation protein 1 0 ;; 139.96 0.00065716 315072000 285987 352030 319749 336153 337690 392382 313576 323567 301256 368430 FALSE TRUE 297277.9876 412488.4141 328081.9216 402643.0601 280289.5744 301257.2271 288997.0937 319230.1136 290413.8554 440616.8045 0.674685996 0.936161331 0.744596934 0.913816849 0.636130015 0.683717062 0.655892128 0.724507351 0.659107534 1 18.74916499 5.052666338 15.64757053 0.756833544 0.126902543 0.039130886 0.125212524 6432302.634 48972909.58 0.0288511 123701386.6 112892.8241 -5.052666338 -0.629931001 QIQEEEDEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIQEEEDEKQR 11 1 A0A087WV26;O43805 A0A087WV26 SSNA1 Sjoegren syndrome nuclear autoantigen 1 0 78.324 0.027536 502430000 103080 105780 118570 93583 129080 161930 104700 112400 118300 119020 FALSE TRUE 107149.678 123946.8921 121660.0316 112093.4381 107139.0277 124324.2116 96493.34042 110893.4618 114042.4061 142339.6902 0.752774422 0.870782365 0.854716147 0.787506548 0.752699599 0.873433203 0.677908883 0.779076178 0.80119892 1 17.11897848 0.922906574 17.75040139 1 0.792693586 0.535322565 0.057484317 871.8840798 200749.5219 0.055366327 0.013841582 8.373491311 -0.922906574 -0.207306414 QIQELVEAIVLPMNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QIQELVEAIVLPMNHK 16 0 P17980;E9PM69;R4GNH3;E9PN50;E9PMD8 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ; 145.55 1.21E-06 359300000 556360 540480 602930 550090 644180 729890 618510 589420 631270 557510 FALSE TRUE 578325.5224 633303.2356 618642.8511 658896.1601 534682.5137 560384.1091 570029.57 581519.789 608550.716 666743.4103 0.867388434 0.949845512 0.927857466 0.98823048 0.801931456 0.840479411 0.854945938 0.872179282 0.912721006 1 19.34677214 5.077299325 13.64646695 0.89675504 0.534255365 0.016532789 0.061301368 3761317.256 15551915.43 0.014905004 38451092.83 119481.131 -5.077299325 -0.362499675 QIS(ph)LPDLSQEEPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QISLPDLSQEEPQLK 15 0 H0YBZ4;Q15390-2;Q15390 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 QIS(1)LPDLSQEEPQLK;QIS(1)LPDLSQEEPQLK 244.88 4.85E-18 156535000 286908 230793 273008 216954 287937 305110 261434 236118 251025 215011 TRUE FALSE 298235.3494 270429.9024 280122.8128 259866.8537 238993.5716 234252.8265 240942.1199 232953.2244 241990.6593 257138.2888 1.159824742 1.051690527 1.089385848 1.010611274 0.929435957 0.910999399 0.93701378 0.905945301 0.941091505 1 17.97218492 3.555257389 1.771580624 0.928260792 1.104495699 0.813337375 0.034857419 0.131924986 0.819773892 0.009893915 0.018254075 3591.34716 -3.555257389 0.176234908 QIS(ph)QDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;QIS(1)QDVK 117.52 0.0054678 1015380000 2953860 1920850 2428260 1647270 3486240 3001360 3209100 2813690 3140780 1483840 TRUE FALSE 3070480.674 2250741.045 2491542.45 1973095.089 2893650.17 2304339.626 2957562.357 2775977.088 3027743.941 1774570.038 1.730267393 1.268330354 1.404025988 1.111872198 1.630620436 1.298534054 1.666636026 1.56430968 1.706184527 1 20.75903808 2.245487164 24.98785883 1.539677352 1.39753639 0.002275894 0.246755246 441.0283271 1591033.038 0.080647839 0.066097563 175.9896649 -2.245487164 -0.142140962 QIS(ph)QDVKLEPDILLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 250.79 3.35E-19 648476000 1264667 969390 1195206 561828 1853038 1441272 967392 1238487 1474409 1085429 TRUE FALSE 1314597.03 1135875.192 1226354.05 672955.9015 1538059.263 1106558.421 891565.2872 1221887.108 1421345.308 1298098.031 1.012710133 0.875030363 0.944731462 0.518416857 1.184856017 0.852445959 0.686824312 0.941290318 1.094944507 1 20.30796791 1.462187718 8.33057301 1.038727946 0.86546038 0.150757865 0.169486945 0.235527214 52.51304262 0.092529351 0.041114719 28.98596197 -1.462187718 -0.173267566 QISLAPETLDSSGDVS(ph)PGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QISLAPETLDSSGDVSPGPR 20 0 Q8TER5;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 QISLAPETLDSSGDVS(1)PGPR 228.68 3.03E-25 87992000 142140 167990 166920 180470 157590 208730 159250 167300 157590 214290 TRUE FALSE 147751.797 196840.9757 171270.0723 216166.4274 130802.9081 160255.6208 146767.5689 165057.6171 151918.3667 256276.0227 0.57653383 0.768081905 0.668303147 0.843490644 0.510398541 0.625324286 0.57269333 0.644061881 0.592791964 1 17.96733898 -1.917824974 5.20038201 1.13197974 0.646939772 0.568350421 0.092889499 0.054704824 0.000864431 0.034615243 0.020732613 0.012083007 1.917824974 -0.485039968 QISSLRDEVEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QISSLRDEVEAK 12 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ;;; 211.22 3.14E-08 1849480000 1754040 1327560 1590830 1258640 1973510 2069590 1716300 1566630 1745990 1293900 FALSE TRUE 1823290.854 1555558.103 1632288.337 1507595.235 1638053.475 1588959.087 1581771.921 1545631.887 1683152.161 1547414.932 1.178281802 1.005262435 1.054848511 0.974266956 1.058574169 1.026847457 1.022202829 0.998847727 1.087718702 1 20.56142867 4.742920681 24.95086948 1.024431382 1.178281864 0.672459333 0.032003681 231.5275874 1324889.62 0.006984634 0.05508281 55324.90558 -4.742920681 0.153850483 QIT(ph)MEELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QITMEELVR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR;QIT(1)MEELVR 161.87 0.00071777 1341401000 1017887 1210959 1193882 1021231 1428082 1411756 1161531 1250320 1191498 1157674 TRUE FALSE 1058073.965 1418931.788 1224995.546 1223227.444 1185337.132 1083897.064 1070487.165 1233561.506 1148616.22 1384498.055 0.764229289 1.024870915 0.884793981 0.88351691 0.856149366 0.782880886 0.773195138 0.890981032 0.829626459 1 20.4009316 QIT(ph)QEEDDSDEEVAPENFFSLPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.547)QEEDDS(0.453)DEEVAPENFFSLPEK;QIT(0.824)QEEDDS(0.176)DEEVAPENFFSLPEK 96.54 0.023519 376200000 76087 108343 91652 111754 82753 128120 86676 93398 79990 119916 TRUE FALSE 79090.97351 126950.0675 94040.52641 133858.6076 68686.67462 98366.07168 79882.10863 92146.15258 77111.17553 143411.2443 0.551497715 0.885216972 0.655740259 0.933389905 0.478949018 0.685902087 0.557014264 0.642530877 0.537692675 1 17.12979862 -1.157936253 4.394141443 1.000067235 0.662912448 0.347350994 0.140257952 8.78E-05 1.68E-05 0.129073027 0.030416752 0.069512634 1.157936253 -0.337154787 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 QIT(0.109)QEEDDS(0.891)DEEVAPENFFSLPEK;QIT(0.408)QEEDDS(0.592)DEEVAPENFFSLPEK;QIT(0.385)QEEDDS(0.615)DEEVAPENFFSLPEK 110.89 0.0012155 441167000 142589 111319 132609 115989 146199 157318 145924 134325 140455 111901 TRUE FALSE 148218.5238 130437.1723 136064.8995 138931.278 121348.1462 120783.2787 134486.0956 132524.5931 135400.052 133825.8585 1.107547715 0.97467839 1.016731004 1.038149724 0.906761575 0.90254066 1.004933554 0.990276428 1.011763 1 17.02999738 7.588923099 1.201833327 0.978643331 163.3842149 0.415827948 0.043353835 2012.109906 2.818958183 0.012607842 901022.7638 38808164.19 -7.588923099 162.4055715 QITT(ph)SPITVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 QIT(0.004)T(0.796)S(0.2)PITVR;QIT(0.005)T(0.879)S(0.115)PITVR;QIT(0.004)T(0.603)S(0.392)PITVR;QIT(0.02)T(0.656)S(0.277)PIT(0.046)VR 154.67 0.00015728 1695720000 2591380 2838880 2798390 2978020 2868840 3514190 2759580 2918850 2712280 2817220 TRUE FALSE 2693689.683 3326435.557 2871318.342 3567063.467 2381195.602 2698072.631 2543276.909 2879727.59 2614665.573 3369200.32 0.799504163 0.987307147 0.852225475 1.058727036 0.70675394 0.80080505 0.754860699 0.854721393 0.776049307 1 21.68397478 3.227865851 24.99988827 0.806794146 0.923773168 0.225626748 0.098042236 276.029592 645240.5786 0.026029568 0.031409001 1689.918851 -3.227865851 0.116979022 QITVNDLPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 ;;; 157.78 7.08E-05 1633020000 1899700 2211130 1926990 2022090 2186240 2576340 2000520 2081010 2054920 2268500 FALSE TRUE 1974701.623 2590874.377 1977208.942 2422053.367 1814623.706 1978024.08 1843714.015 2053117.465 1980963.831 2712969.142 0.727874708 0.954995889 0.728798906 0.892768491 0.668870013 0.729099365 0.679592697 0.756778775 0.730182957 1 21.37144121 5.066599007 15.84525772 0.778805613 0.149588301 0.015559054 0.110773315 10852579.02 52171833.19 0.025015271 224354519.2 116573.2775 -5.066599007 -0.629217312 QIVWNGPVGVFEWEAFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QIVWNGPVGVFEWEAFAR 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 297.83 4.95E-49 306820000 64273 85525 47342 63784 64365 85758 32365 58842 55067 104185 FALSE TRUE 66810.54767 100213.2535 48575.77141 76400.28482 53424.26029 65842.00418 29828.14673 58053.31924 53085.14943 124598.056 0.536208588 0.804292271 0.389859786 0.613173971 0.428772824 0.528435244 0.239394961 0.465924759 0.426051185 1 16.92692203 -1.185511346 4.527687765 1.000104135 0.488466089 0.538080432 0.141032535 0.000150238 2.70E-05 0.137266197 0.032347354 0.0652362 1.185511346 -0.511638046 QIYVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 136.58 0.030496 976060000 570590 693180 602530 645020 646430 744430 559970 622430 569690 753430 FALSE TRUE 593117.3338 812228.2728 618232.4268 772603.0308 536550.0595 571547.4144 516078.0882 614087.3439 549186.9682 901050.1832 0.658251166 0.901424014 0.686124301 0.857447282 0.595471894 0.634312522 0.572751771 0.681524021 0.609496539 1 19.78124793 3.233775743 24.98668942 0.658087297 0.778377757 0.090350112 0.132633414 203.0036742 1060088.793 0.034471916 0.04246742 1713.072499 -3.233775743 0.120290459 QIYYSDKYDDEEFEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QIYYSDKYDDEEFEYR 16 1 P61024;Q5T179 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;; 177.67 2.66E-09 3318980000 2082590 1552120 1685460 1388820 2039480 2275620 1881410 1840190 1827470 1611980 FALSE TRUE 2164812.261 1818684.536 1729384.472 1663524.451 1692809.918 1747141.742 1733940.168 1815525.263 1761699.712 1927816.618 1.122934745 0.943390839 0.897068972 0.862905961 0.878096963 0.906280051 0.89943211 0.941752056 0.913831583 1 20.87853639 4.734188219 3.090537381 0.908528092 1.155081833 0.754819191 0.035722821 0.161518815 2.357244131 0.008546236 0.096736213 54223.58394 -4.734188219 0.246553741 QIYYSDKYFDEHYEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QIYYSDKYFDEHYEYR 16 1 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 209.25 7.66E-12 189490000 253730 265280 277890 233370 299880 350320 245280 281730 267160 319120 FALSE TRUE 263747.4563 310839.7764 285132.0417 279529.8895 248906.5047 268963.4892 226054.3127 277953.8702 257544.9638 381645.4541 0.69107978 0.814472629 0.747112375 0.732433431 0.652193029 0.704747001 0.592314962 0.728303894 0.674827804 1 18.54187348 -1.938163195 7.616896598 1.099797146 0.704795704 0.713404569 0.056250662 0.032336598 0.000262521 0.018474913 0.013201637 0.011530199 1.938163195 -0.395001442 QKAEADKNDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 158.05 4.56E-06 11146570000 13626030 4065500 7158530 3913770 12132370 9348600 11494510 8038980 10886120 3599440 FALSE TRUE 14163996.19 4763718 7345087.173 4687902.025 10070114.08 7177529.329 10593540.27 7931230.622 10494330.67 4304681.353 3.290370419 1.106636615 1.706302179 1.089024167 2.339340187 1.667377616 2.46093483 1.842466369 2.43788792 1 22.03747502 QKAHEEANAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKAHEEANAAR 11 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 0 139.31 2.37E-05 12417000 24449 20283 26940 17055 30730 30945 22837 24299 28909 22271 FALSE TRUE 25414.2654 23766.44747 27642.07853 20428.4281 25506.52558 23758.49273 21046.97627 23973.31165 27868.57074 26634.57605 0.954183215 0.892315591 1.037826864 0.766989047 0.95764714 0.892016929 0.79021255 0.900082344 1.046330555 1 14.7010127 -1.711600837 5.50242977 1.002376596 0.908198138 0.074245426 0.086535866 0.00245264 0.00012855 0.081453204 0.018730907 0.019426706 1.711600837 -0.094178458 QKDEEDKAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QKDEEDKAR 9 2 O00170 O00170 AIP AH receptor-interacting protein 0 ;; 97.813 0.0036203 509290000 820830 338127 531900 310769 741560 658290 695510 504900 609130 313806 FALSE TRUE 853237.0022 396197.682 545761.751 372238.1806 615509.8961 505412.124 640994.1088 498132.6413 587207.5303 375290.2775 2.273538787 1.055709955 1.454238982 0.99186737 1.640090173 1.346723201 1.70799551 1.327326262 1.564675574 1 18.51764739 -2.054149555 2.480989197 0.37713092 1.457095446 0.147629507 0.34368137 10850627.45 3643456.895 38351852.65 0.075660915 0.008827759 2.054149555 1.079964526 QKDFLDGVYAFEYYPST(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.085)T(0.915)PGR;QKDFLDGVYAFEYYPS(0.004)T(0.996)PGR;QKDFLDGVYAFEYYPS(0.045)T(0.955)PGR;QKDFLDGVYAFEYYPS(0.155)T(0.845)PGR;QKDFLDGVYAFEYYPS(0.015)T(0.985)PGR;QKDFLDGVYAFEYYPS(0.001)T(0.999)PGR 265.89 1.78E-36 2310603000 2662092 3190762 2832531 2329451 3791560 3624890 2578255 2793014 2851914 4286570 TRUE FALSE 2767193.448 3738750.553 2906349.085 2790209.455 3147071.986 2783064.233 2376164.636 2755578.216 2749274.172 5126441.32 0.539788379 0.729307198 0.566933064 0.544278044 0.61389018 0.542884246 0.463511525 0.537522629 0.536292918 1 22.28952625 -1.749881113 6.978252347 1.007858159 0.562766421 0.799933563 0.065438193 0.008381092 0.0003004 0.066376963 0.015614187 0.017787663 1.749881113 -0.445091738 QKDFLDGVYAFEYYPSTPGR ddPTM_MDA-MB-175_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 ; 178.22 5.72E-17 1181970000 1532410 1666820 1589560 1258760 2116880 2069240 1509790 1589500 1692380 2255330 FALSE TRUE 1592910.73 1953083.369 1630985.239 1507738.971 1757053.494 1588690.37 1391448.715 1568195.352 1631471.574 2697218.733 0.590575288 0.724110116 0.604691499 0.558997664 0.651431592 0.58901058 0.515882786 0.581412005 0.604871809 1 21.36304109 -1.43532941 2.988146208 1.008206913 0.600515156 0.838599312 0.052332635 11327381.41 13658295.04 785312.2196 0.013656773 0.036700382 1.43532941 -0.407691758 QKDYDFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKDYDFEER 9 1 Q96NC0 Q96NC0 ZMAT2 Zinc finger matrin-type protein 2 0 ; 94.616 0.0078445 682920000 1293140 1047270 1225010 970860 1372780 1505070 1403350 1151180 1367760 935580 FALSE TRUE 1344194.166 1227130.476 1256934.767 1162893.21 1139435.346 1155540.302 1293351.76 1135750.315 1318534.585 1118888.988 1.201365086 1.096740149 1.123377547 1.039328497 1.018363178 1.032756881 1.155925006 1.015069705 1.178431997 1 20.09363547 5.128988038 1.11589014 1.06576383 1.384627287 0.319548488 0.058485822 4.106756053 2.354071876 0.016016765 1.891426131 134582.3284 -5.128988038 0.318863457 QKEEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QKEEEAR 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ;; 128.69 0.003405 1615290000 3042560 2262270 2772060 2263290 3071770 3204820 3372610 2842270 2987120 2133640 FALSE TRUE 3162682.618 2650797.274 2844302.161 2710962.007 2549631.633 2460549.125 3108256.016 2804174.02 2879614.135 2551685.907 1.239448245 1.038841523 1.114675655 1.062419947 0.999194934 0.964283699 1.218118581 1.098949527 1.128514339 1 21.28301932 4.746858035 24.36681475 1.076180016 1.239448361 0.335454049 0.07121811 917.8651846 2695384.428 0.017444186 0.193449794 55828.7668 -4.746858035 0.163268345 QKEEESQQQAVLEQERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKEEESQQQAVLEQERR 17 2 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 141.22 3.55E-07 347610000 112480 87578 106600 74699 117490 121230 99143 102160 118710 90903 FALSE TRUE 116920.7973 102618.8402 109378.0836 89474.23925 97519.09177 93076.16976 91371.9126 100790.7123 114437.6503 108713.7024 1.075492736 0.943936578 1.006111292 0.823026328 0.897026682 0.856158586 0.840482024 0.927120594 1.052651577 1 16.73017427 4.93900142 1.184809318 0.908890312 1.205558886 0.273146223 0.072148237 2.843249967 2.482823384 0.02052344 1.16036197 86896.32712 -4.93900142 0.296668574 QKEELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKEELQR 7 1 P80303-2;P80303;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 104.06 0.0075122 87842000 118180 133570 137760 144660 213880 214390 160730 122470 134310 166870 FALSE TRUE 122845.8377 156509.6085 141350.1388 173273.3162 177524.754 164601.1716 148131.5626 120828.49 129476.2093 199564.9816 0.615568106 0.784253867 0.708291293 0.868255116 0.889558642 0.824799874 0.742272324 0.60545938 0.64879223 1 17.60649906 4.742391382 23.22317168 0.768617944 0.615567952 0.15592263 0.112607764 303.9439856 1842372.06 0.028398026 0.209782741 55257.51907 -4.742391382 -0.153049992 QKEIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QKEIEER 7 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 0 ;; 117.04 0.0048531 775030000 1428200 1344280 1473350 1341000 1741300 1955550 1617420 1586930 1638330 1458130 FALSE TRUE 1484586.439 1575149.633 1511746.711 1606245.798 1445314.448 1501403.149 1490642.394 1565659.799 1579366.823 1743822.656 0.851340263 0.903273981 0.866915398 0.921106164 0.82881963 0.860983853 0.854813068 0.897832009 0.905692341 1 20.7338219 0.75057284 1.289177473 0.999637337 0.87165426 0.697493325 0.025439457 0.457576634 1.316439248 0.023461991 0.007074611 5.630835501 -0.75057284 -0.127983077 QKELSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKELSEK 7 1 Q15046;Q15046-2;H3BVA8;H3BRC9;H3BSN6;H3BQK5 Q15046 KARS Lysine--tRNA ligase 0 64.711 0.06617 147420000 139490 115700 126160 107060 160290 177210 158050 128500 140960 109470 FALSE TRUE 144997.1729 135570.575 129447.8332 128236.1485 133043.9631 136055.6631 145661.628 126777.6677 135886.8771 130918.5506 1.107537261 1.03553373 0.988766166 0.979510909 1.016234617 1.039238997 1.112612593 0.968370541 1.037949752 1 16.99831001 QKEQEQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKEQEQVR 8 1 Q9NQA3;Q6VEQ5 Q9NQA3 WASH6P;WASH2P WAS protein family homolog 6;WAS protein family homolog 2 0 75.294 0.035351 28574000 51785 37834 45212 33775 61935 60755 52560 49895 48947 41172 FALSE TRUE 53829.51179 44331.69519 46390.26186 40455.59419 51407.31082 46645.572 48440.20986 49226.23914 47185.40703 49238.86511 1.093232179 0.9003395 0.94214726 0.821619144 1.044039311 0.947332395 0.983779982 0.999743577 0.958295991 1 15.58750989 QKETS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKETSPR 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QKET(0.01)S(0.99)PR 90.964 0.044068 200270000 975530 715970 928040 688300 1095000 1101100 1100500 915710 1037400 739760 TRUE FALSE 1014044.678 838932.278 952225.4848 824443.6856 908872.2911 845386.2123 1014239.934 903436.4052 1000064.177 884701.8084 1.146199395 0.948265585 1.076323656 0.931888776 1.027320485 0.955560624 1.146420099 1.021176171 1.130396894 1 19.75483175 2.249070015 24.99945776 1.072866437 1.010930652 0.140544603 0.072652727 384.5244397 914696.1137 0.023252296 0.019263928 177.4475532 -2.249070015 -0.061935785 QKFDNLYCCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKFDNLYCCR 10 1 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 97.452 0.0055169 236970000 210350 205540 179830 181410 299610 283370 181140 177620 170270 313350 FALSE TRUE 218654.7804 240839.8961 184516.5175 217292.3565 248682.3992 217561.612 166941.7735 175239.2944 164142.016 374744.9331 0.583476283 0.642676858 0.492378952 0.579840679 0.663604434 0.580559183 0.445481069 0.467622852 0.438009968 1 18.51554945 -1.37411135 3.408236266 1.003376203 0.541035824 0.764402937 0.075977012 154369525.4 210141107.3 5114459.232 0.02027497 0.042256026 1.37411135 -0.462340379 QKFNDS(ph)EGDDTEETEDYR ddPTM_MDA-MB-175_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(0.998)EGDDT(0.002)EETEDYR 336.14 2.58E-75 16530790000 11576200 7648800 9670450 7224420 11594630 12575250 11401990 9903810 10612570 6438260 TRUE FALSE 12033237.31 8962421.901 9922469.871 8653388.713 9623778.934 9654838.767 10508272.23 9771065.626 10230625.68 7699713.779 1.562816185 1.163994164 1.288680353 1.123858492 1.24988788 1.253921775 1.36476141 1.269016733 1.328702075 1 22.87637339 4.747400204 24.81671659 1.243073561 1.562816366 0.486673008 0.102277989 887.539005 2491663.089 0.022814395 0.274215511 55898.50648 -4.747400204 0.319742805 QKGESRPET(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKGESRPETPK 11 2 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 QKGES(0.063)RPET(0.937)PK 70.889 0.081251 62163000 186680 56958 92173 60660 118160 137350 130740 99049 99972 39220 TRUE FALSE 194050.2705 66740.09343 94575.1041 72658.36695 98075.20541 105452.5441 120492.2572 97721.41017 96374.02725 46904.40809 4.137143575 1.422895974 2.016337226 1.549073315 2.090959238 2.248243787 2.568889835 2.083416339 2.054690192 1 15.51743589 4.747591482 24.97489725 1.972647261 4.13714471 0.70267207 0.435206905 657.5569553 1818437.372 0.100714412 1.244697024 55923.13143 -4.747591482 2.16449745 QKGYNHGQGSYSYSNSYNS(ph)PGGGGGSDYNYESK ddPTM_MDA-MB-175_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 186.64 4.52E-20 574740000 185800 246250 242290 177610 321140 291990 199570 258690 289880 230030 TRUE FALSE 193135.5275 288541.5219 248604.2764 212740.7279 266552.7375 224179.7477 183927.1819 255222.6837 279447.2754 275099.9743 0.702055782 1.048860592 0.903687022 0.773321511 0.968930434 0.81490283 0.668583057 0.927745211 1.015802623 1 18.06959648 1.483462184 8.960538253 0.996332688 0.848350276 0.276543704 0.108934324 0.137306047 35.79034803 0.059244747 0.027233211 30.44122911 -1.483462184 -0.147982412 QKHLPHFKPWLHPEQSPLPSLALSELSVQHADS(ph)LENIDESAVAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKHLPHFKPWLHPEQSPLPSLALSELSVQHADSLENIDESAVAESR 46 2 Q9Y365;F5H8H3;F5GY11 Q9Y365 STARD10 PCTP-like protein 1 QKHLPHFKPWLHPEQS(0.005)PLPS(0.005)LALS(0.065)ELS(0.058)VQHADS(0.867)LENIDESAVAESR 60.065 0.0043079 489610000 105510 129750 188870 98738 175910 167180 138970 138930 195520 216920 TRUE FALSE 109675.6163 152033.5532 193792.1074 118268.0817 146008.881 128354.9786 128077.1683 137067.8706 188483.2734 259421.3208 0.422770249 0.586048798 0.747016886 0.455891911 0.562825294 0.494774208 0.493703323 0.528360083 0.726552747 1 17.98493753 0.95335715 2.855373766 0.999105811 0.538999541 0.744680061 0.08437849 0.140907635 2.749898513 0.080771518 0.021370752 8.981671152 -0.95335715 -0.460106269 QKIDDRDS(ph)DEEGASDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QKIDDRDSDEEGASDR 16 2 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR;QKIDDRDS(1)DEEGASDR 157.73 2.03E-08 357165000 318153 230606 266003 205837 335385 366892 270027 258577 245218 204553 TRUE FALSE 330713.9261 270210.7866 272935.2567 246550.9442 278376.3775 281686.8933 248861.5782 255111.1983 236392.6521 244631.2439 1.351887522 1.104563678 1.115700727 1.007847323 1.13794286 1.151475538 1.017292698 1.042839803 0.966322405 1 17.90024915 7.935008389 0.962595719 1.05169078 199.9997217 0.704935656 0.057791139 636.283829 1.186296079 0.018029993 278653.2908 86101038.37 -7.935008389 198.9480309 QKIPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QKIPAR 6 1 A0A3B3ISL2;A0A3B3IRU6;Q9GZU2-2;Q9GZU2-4;Q9GZU2 A0A3B3ISL2 PEG3 Paternally-expressed gene 3 protein 0 ;;; 92.279 0.042807 3262760000 2227030 2305720 2603930 1976810 3264990 2748830 2601240 2297320 2666360 2335940 FALSE TRUE 2314954.864 2701709.474 2671790.555 2367817.118 2710008.166 2110455.891 2397348.012 2266528.183 2570398.224 2793622.719 0.828656944 0.967098906 0.956389185 0.847579418 0.97006949 0.755454871 0.858150242 0.811322219 0.920094975 1 21.41370577 2.767556286 24.9994829 0.852810944 0.915580509 0.061500443 0.075424263 1366.468721 1178139.132 0.021614579 0.022922039 585.5396198 -2.767556286 0.062769564 QKKPLVGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKKPLVGKK 9 3 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 57.59 0.050111 364290000 640170 425130 554910 363530 820550 683330 600520 598740 661870 458450 FALSE TRUE 665444.4059 498142.7704 569371.4105 435435.149 681073.2041 524636.9635 553449.6732 590714.8696 638049.428 548274.4999 1.213706649 0.908564543 1.038478737 0.794191867 1.242212075 0.956887405 1.009439019 1.077407156 1.163740842 1 19.06453885 1.64805464 4.809886795 1.093168645 1.016691048 0.035504711 0.129885844 0.466561276 24.16078107 0.067204626 0.031778572 44.46872118 -1.64805464 -0.076477597 QKLDILDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QKLDILDQER 10 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 176.78 2.19E-06 1706980000 2735600 2375870 2538820 2301620 3172140 3433700 2853350 2666720 2940530 2352850 FALSE TRUE 2843603.6 2783907.191 2604983.735 2756873.566 2632940.776 2636275.213 2629696.971 2630976.98 2834700.9 2813845.909 1.010575451 0.989360214 0.925773414 0.979752856 0.935708941 0.936893952 0.93455614 0.935011036 1.007411561 1 21.4241119 4.418309281 5.987013524 0.951982808 1.005709046 0.271845416 0.028201143 0.18297634 12.98114909 0.006525551 0.018737946 26200.48203 -4.418309281 0.053726237 QKLDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKLDPK 6 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 0 ; 81.958 0.055182 2169100000 2425000 1488460 1937930 1237700 2193020 2065600 1800350 1782660 2161600 1354030 FALSE TRUE 2520740.873 1744091.426 1988434.048 1482513.366 1820251.244 1585895.704 1659233.863 1758766.359 2083804.438 1619326.254 1.556660288 1.077047582 1.227939115 0.915512462 1.124079375 0.979355272 1.024644576 1.086109951 1.286834221 1 20.62696225 QKLDSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKLDSQR 7 1 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 82.426 0.022365 160104000 333830 482560 366440 373620 522240 599000 370410 389110 351270 576950 FALSE TRUE 347009.8662 565435.9262 375989.7274 447520.9209 433469.8313 459891.3279 341376.2963 383894.6169 338627.8613 689992.3061 0.502918457 0.819481494 0.544918725 0.648588277 0.628224152 0.666516603 0.494753772 0.556375214 0.490770489 1 19.39622075 -1.712886633 2.628090067 1.070847042 0.597178873 0.613919154 0.096398991 9466328.74 7653212.638 4418409.989 0.024194332 0.019369275 1.712886633 -0.473668169 QKLEEDAEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QKLEEDAEMK 10 1 P05455 P05455 SSB Lupus La protein 0 ;;; 122.18 0.00045183 1038455000 2839630 1312980 1822090 1249200 3074850 2866500 2672710 2089400 2504210 1197690 FALSE TRUE 2951740.785 1538474.101 1869575.162 1496288.032 2552188.095 2200798.817 2463216.006 2061395.011 2414083.971 1432354.424 2.060761453 1.074087583 1.305246195 1.044635326 1.781813252 1.536490396 1.719697279 1.439165458 1.685395689 1 20.44995709 3.225836898 24.99940301 1.554619758 1.34525174 0.044601334 0.330860448 570.1488164 1120219.044 0.08984919 0.108064402 1682.042239 -3.225836898 -0.209368018 QKLQLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 90.657 0.015484 957750000 1946890 2215030 1941820 2080610 3950400 3980500 3082350 3286800 3840500 2894120 FALSE TRUE 2023754.721 2595444.172 1992425.424 2492148.448 3278912.419 3056089.2 2840747.353 3242745.822 3702281.155 3461167.403 0.58470293 0.749875366 0.575651274 0.72003118 0.947342916 0.882964863 0.820748326 0.936893668 1.069662552 1 21.72282729 3.250443937 0.467558804 1.011773358 0.554262673 0.755534833 0.079385092 0.765859884 0.311962186 0.071763657 0.166538484 1780.098103 -3.250443937 -0.457510685 QKLYTLQDK ddPTM_MDA-MB-175_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 ; 125.54 0.00045482 3931600000 5957400 4041100 4815800 3359200 7529900 6184500 4351900 4380100 5187800 4923800 FALSE TRUE 6192602.752 4735127.49 4941303.704 4023639.734 6249970.288 4748243.602 4010786.706 4321391.924 5001092.091 5888524.338 1.051639154 0.804128032 0.839141255 0.683301877 1.061381414 0.806355435 0.681119152 0.7338667 0.849294629 1 22.48947471 2.493164926 24.64276058 0.778471385 0.875654157 0.040063222 0.132087776 1353.570798 2079060.324 0.042118044 0.038664439 311.2898252 -2.493164926 0.097182772 QKPQAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 QKPQAER 7 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;;;;; 109.21 0.0064555 6959670000 3655870 3519210 3674820 3186500 4278140 4638150 4026920 3972500 4058300 3453120 FALSE TRUE 3800206.571 4123606.942 3770588.828 3816780.189 3550943.291 3561009.954 3711279.488 3919255.135 3912242.576 4129692.75 0.920215328 0.998526329 0.913043429 0.92422861 0.859856533 0.862294163 0.898681745 0.949042791 0.947344709 1 21.97760302 1.099180674 1.481521321 0.996712764 0.912494644 0.343749699 0.037201939 0.482784456 2.110902244 0.038495426 0.011522904 12.56552602 -1.099180674 -0.08421812 QKQPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKQPER 6 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 87.989 0.047254 140720000 152090 123920 145650 124600 173660 174990 156340 166520 157240 126250 FALSE TRUE 158094.6306 145202.296 149445.7587 149245.5081 144141.3352 134351.2245 144085.6623 164288.0718 151580.9631 150986.2703 1.047079515 0.961692052 0.989797008 0.988470725 0.954665182 0.889824116 0.954296454 1.088099411 1.003938721 1 17.20405784 1.758376035 25 1.038540794 0.966997015 0.289137014 0.043393662 9.767232557 12334.07169 0.020480817 0.011357505 57.32922026 -1.758376035 -0.07154378 QKREEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKREEEER 8 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 176.6 0.00014587 218968000 244379 228353 271804 197418 311369 304307 260023 272104 291929 214708 FALSE TRUE 254027.2716 267570.8514 278887.4355 236466.6912 258442.6086 233636.3111 239641.7178 268456.891 281422.5323 256775.9218 0.98929553 1.042040272 1.0861121 0.920906795 1.006490822 0.909884032 0.933271765 1.045490905 1.095984898 1 17.9701504 1.594900393 7.97390053 1.055026731 0.985711162 0.20961931 0.055778839 0.1753346 25.39594173 0.030995982 0.014883178 39.3459824 -1.594900393 -0.069315568 QKS(ph)AEPS(ph)PTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QKSAEPSPTVMSTSLGSNLSELDR 24 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 2 QKS(0.999)AEPS(0.957)PT(0.044)VMSTSLGSNLSELDR;QKS(1)AEPS(0.598)PT(0.402)VMSTSLGSNLSELDR;QKS(0.999)AEPS(0.942)PT(0.059)VMSTSLGSNLSELDR 162 1.06E-11 734740000 530244 354392 431028 315314 524071 599191 493266 424339 474454 302355 TRUE FALSE 551178.4426 415256.0692 442260.9438 377682.1681 434989.5986 460037.9711 454602.522 418651.4298 457378.4932 361595.6733 1.524294905 1.148398888 1.223081404 1.04448752 1.202972355 1.272244125 1.257212283 1.157788825 1.264889287 1 18.46401789 -4.999999992 0.206634695 2.59E-08 1.253456498 0.266415932 0.116851472 211.1061364 2.100315787 87.97702393 0.252023381 1.00E-05 4.999999992 1.253456473 QKS(ph)AEPSPT(ph)VMSTSLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSAEPSPTVMSTSLGSNLSELDR 24 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 2 QKS(0.999)AEPS(0.132)PT(0.869)VMSTSLGSNLSELDR 132.57 0.00011052 135660000 139340 94390 128070 79245 140490 180080 132840 127470 155710 84984 TRUE FALSE 144841.2508 110600.7482 131407.6094 94919.42448 116609.56 138259.1491 122427.6537 125761.4731 150106.0275 101634.9877 1.425112101 1.088215296 1.292936738 0.933924691 1.147336785 1.360349937 1.204581773 1.237383661 1.476912931 1 16.63303761 2.777760463 24.85499639 1.263223206 1.165425178 0.050072926 0.164944656 1367.022056 866769.4088 0.048031029 0.050943741 599.4603497 -2.777760463 -0.097798027 QKS(ph)DAEEDGGTVS(ph)QEEEDRKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 2 QKS(1)DAEEDGGT(0.031)VS(0.969)QEEEDRKPK;QKS(1)DAEEDGGT(0.036)VS(0.964)QEEEDRKPK;QKS(1)DAEEDGGT(0.002)VS(0.998)QEEEDRKPK;QKS(1)DAEEDGGT(0.189)VS(0.811)QEEEDRKPK 182.56 6.56E-17 2059600000 2783433 606041 913470 789695 1758459 2195306 1712364 944185 1188830 459403 TRUE FALSE 2893325.084 710123.8274 937275.7786 945894.314 1459556.767 1685479.452 1578144.435 931529.7445 1146044.241 549414.222 5.266199832 1.292510821 1.705954708 1.721641479 2.656568958 3.067775431 2.872412784 1.695496234 2.085938431 1 19.06753473 4.747530076 24.76705759 2.088064611 5.266201705 0.69563474 0.644159322 622.581541 1719070.939 0.159564876 1.945530176 55915.22487 -4.747530076 3.178137093 QKS(ph)DAEEDGGTVSQEEEDRKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 197.01 1.14E-21 2059790000 2443220 571511 913620 758663 1620220 1919330 1566020 948290 1128330 468405 TRUE FALSE 2539680.212 669663.5685 937429.6877 908724.277 1344815.583 1473594.695 1443271.26 935579.7236 1087721.624 560179.9916 4.533686048 1.195443569 1.673443718 1.622200526 2.400684786 2.630573597 2.576442004 1.670141272 1.941735942 1 19.09553093 0.911250302 1.112402006 1.021554988 2.264345705 0.176077861 0.868934736 1.113375476 2.785581516 0.789496117 0.250692073 8.151739676 -0.911250302 1.242790717 QKS(ph)EEPSVSIPFLQTALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKSEEPSVSIPFLQTALLR 19 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 QKS(0.953)EEPS(0.046)VS(0.001)IPFLQTALLR;QKS(0.998)EEPS(0.002)VSIPFLQTALLR 82.885 0.0023143 135741000 285680 188593 283360 180864 395870 347320 319000 300000 331370 191176 TRUE FALSE 296958.867 220982.3807 290744.5944 216638.3594 328580.1588 266660.1937 293995.9464 295978.9907 319444.0584 228633.2769 1.298843594 0.966536384 1.271663505 0.947536432 1.437149322 1.166322756 1.285884323 1.294557794 1.397189695 1 17.80267587 3.235803368 24.99894877 1.276129767 1.120852849 0.1671717 0.154142661 111.1436867 1007700.852 0.039912831 0.049753817 1721.089156 -3.235803368 -0.155276918 QKS(ph)FSEDVISHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSFSEDVISHK 12 1 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 QKS(1)FSEDVISHK 174.49 1.83E-05 142590000 326000 244070 258780 169790 393060 344290 325670 283050 322360 156520 TRUE FALSE 338870.7317 285987.1239 265524.0194 203373.9552 326247.8016 264333.8653 300143.1344 279256.1777 310758.3266 187187.0972 1.810331677 1.5278143 1.418495309 1.086474219 1.742896847 1.41213721 1.603439227 1.491855912 1.660148221 1 17.51412147 -1.331249293 3.170887627 0.996099709 1.516205425 0.401719815 0.192873678 20646136.47 26636472.22 749718.7638 0.045909826 0.046639159 1.331249293 0.520105716 QKS(ph)PAQSDSTTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QKSPAQSDSTTQR 13 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR;QKS(1)PAQSDSTTQR 216.17 1.69E-11 1920630000 588090 468731 561431 493167 614672 711272 624536 578839 660663 421754 TRUE FALSE 611308.2473 549231.903 576062.3531 590713.9606 510190.273 546089.8574 575583.2364 571080.61 636885.8677 504388.6213 1.211978664 1.088906212 1.142100215 1.171148467 1.011502344 1.082676798 1.14115032 1.13222342 1.262688809 1 18.9441762 -2.404993706 2.167001318 2.07E-05 1.132548439 0.277888108 0.066291 621354.8399 198388.7224 3050051.763 0.01583745 0.003935558 2.404993706 1.132527718 QKS(ph)PEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 130.56 0.00063137 44785327000 14971884 9625532 12613945 9942519 14316630 15779586 15022202 12964030 12584894 8175121 TRUE FALSE 15562985.54 11278642.24 12942674.77 11909119.58 11883094.35 12115016.29 13844722.55 12790268.38 12131966.12 9776879.438 1.591815225 1.15360349 1.323804272 1.218090052 1.215428136 1.239149605 1.416067636 1.308215823 1.24088327 1 23.22094263 0.826061012 3.381446239 1.000064252 1.300499871 0.380574805 0.117574697 0.974370912 17.29270361 0.105368279 0.027270716 6.699787243 -0.826061012 0.30043562 QKS(ph)PEIHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 129.74 0.00019866 14062480000 5442380 3726360 4478420 3195910 5671400 5687160 4187060 4375810 4594100 3605440 TRUE FALSE 5657249.365 4366333.343 4595131.304 3828051.459 4707377.454 4366403.28 3858867.296 4317159.424 4428759.238 4311856.938 1.312021583 1.012634094 1.065696606 0.887796491 1.09172858 1.012650314 0.894943258 1.001229745 1.027111823 1 22.03987788 5.130432792 1.661985982 0.990918525 1.846408186 0.695728259 0.061774782 1.734669697 1.952952985 0.015494542 3.27625664 135030.7848 -5.130432792 0.855489661 QKSDAEEDGGT(ph)VSQEEEDRKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.5)VS(0.5)QEEEDRKPK 109.26 0.00040656 122590000 115880 26995 38928 39305 80123 90160 67382 43079 58458 24761 TRUE FALSE 120455.0319 31631.18126 39942.49566 47079.41169 66503.72108 69221.70639 62100.42277 42501.59647 56354.108 29612.44387 4.06771668 1.068171928 1.348841583 1.589852289 2.245803196 2.337588437 2.09710563 1.43526136 1.903054954 1 14.85391594 7.999999952 0.055124248 1.32E-10 5.572418867 0.183639119 0.764852151 879.2366852 3.637792628 80.0961457 403.2089183 99999988.87 -7.999999952 5.572418867 QKSDAEEDGGTVS(ph)QEEEDRKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSDAEEDGGTVSQEEEDRKPK 22 3 P27824;P27824-2;P27824-3 P27824 CANX Calnexin 1 QKSDAEEDGGT(0.001)VS(0.999)QEEEDRKPK 171.31 4.40E-12 138060000 223700 76677 99499 81112 165350 198910 179680 91141 116500 64652 TRUE FALSE 232531.8487 89845.67829 102092.0257 97155.7115 137243.8661 152716.167 165596.2121 89919.40397 112307.1878 77319.32156 3.007422259 1.162008104 1.320394742 1.256551526 1.775026776 1.97513589 2.14171838 1.162961627 1.452511293 1 16.23854136 8 0.046799699 4.03E-10 4.475727249 0.192144194 0.524086602 1197.215803 4.239904936 100.1479548 396.8851468 99999999.99 -8 4.475727249 QKSFS(ph)EDVISHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSFSEDVISHK 12 1 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 QKS(0.228)FS(0.772)EDVISHK 167.28 3.01E-05 291430000 512440 303740 383160 229300 545660 509030 511880 391380 442360 268020 TRUE FALSE 532671.5269 355904.9822 393145.4644 274654.8556 452908.9081 390815.4969 471757.5081 386134.1913 426439.55 320533.3874 1.661828526 1.110352295 1.226535144 0.856868165 1.412985124 1.219266112 1.471788982 1.204661375 1.330406025 1 18.29011511 -1.954314931 2.573333743 0.79811085 1.264706084 0.137719679 0.205955519 16203577.21 6470332.479 19514207.93 0.048244063 0.011109258 1.954314931 0.466595234 QKSLDS(ph)DLSDGPVTVQEFMEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QKSLDSDLSDGPVTVQEFMEVK 22 1 Q14161-3;Q14161;Q14161-6;R4GNG3;Q14161-9;Q14161-5;Q14161-11;Q14161-7;Q14161-2 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 QKS(0.335)LDS(0.623)DLS(0.042)DGPVTVQEFMEVK 70.452 0.01058 31833000 46035 23712 28951 21770 47154 44389 39429 29881 37633 15114 TRUE FALSE 47852.49735 27784.35155 29705.48684 26076.04102 39138.77992 34080.32747 36338.45195 29480.49407 36278.59568 18075.29892 2.647397288 1.537144789 1.643429908 1.442634013 2.165318542 1.885464114 2.010392863 1.630982381 2.007081367 1 14.14173189 -1.318495797 3.608133952 0.997042152 1.852127011 0.378973243 0.337649491 6813389.101 4152529.915 148351.3843 0.074659778 0.048029073 1.318495797 0.85508486 QKT(ph)VDIDDAQILPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;QKT(1)VDIDDAQILPR 238.68 3.99E-17 1434160000 1917230 1432820 1736670 1239430 2771870 2301540 1808080 2066140 2040570 1333830 TRUE FALSE 1992923.721 1678895.689 1781929.047 1484585.555 2300708.527 1767042.215 1666357.965 2038446.773 1967130.284 1595168.451 1.249350011 1.052488023 1.117078918 0.930676352 1.442298164 1.107746467 1.044628211 1.277888095 1.233180285 1 20.60527735 3.294625523 24.99998859 1.190311262 1.087025618 0.105015343 0.137896686 190.6805611 85024.9015 0.036876928 0.049931571 1970.722716 -3.294625523 -0.103285643 QKVDDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKVDDDR 7 1 Q13618;Q13618-2;Q13618-3;A0A087WTG3 Q13618 CUL3 Cullin-3 0 ; 75.738 0.038902 172237000 901880 608980 743910 607800 888370 949470 966700 792410 893130 502880 FALSE TRUE 937486.9188 713567.5778 763296.9057 728021.0259 737365.1847 728969.9819 890927.528 781789.0401 860986.4258 601409.7078 1.55881574 1.186491619 1.269179556 1.210524234 1.226061328 1.21210212 1.481398648 1.299927537 1.431613781 1 19.19798863 QKVDSLLENLEK ddPTM_MDA-MB-175_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 ; 210.38 4.04E-08 4028500000 3964500 2201500 2377900 2283400 3766800 3708100 3414800 2863100 2778100 1810600 FALSE TRUE 4121021.521 2579590.5 2439870.027 2735049.705 3126520.681 2846949.972 3147139.053 2824724.828 2678116.724 2165352.404 1.90316436 1.191302854 1.126777343 1.263096806 1.443885381 1.31477443 1.453407329 1.304510445 1.236804097 1 21.04617041 -4.207523839 0.174903485 2.29E-16 1.431278264 0.262579087 0.199515875 151.5028246 1.858734966 54.00534239 0.679792186 6.20E-05 4.207523839 1.431278264 QKWDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QKWDQK 6 1 O15371-2;O15371;B0QYA5;B0QYA6 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 123.96 0.01693 709470000 1363560 986070 1231950 900240 1744380 1643570 1502270 1445630 1550120 1000970 FALSE TRUE 1417394.402 1155419.852 1264055.629 1078304.785 1447870.911 1261875.776 1384518.152 1426253.694 1494331.484 1197090.907 1.184032385 0.965189732 1.055939546 0.90077101 1.209491194 1.054118588 1.156568932 1.19143307 1.248302427 1 20.19110128 3.218697749 24.9999882 1.152149877 1.02420903 0.259429606 0.095982482 290.0118831 365016.6385 0.026516226 0.031731765 1654.618015 -3.218697749 -0.127940846 QKYNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 131.65 0.013895 2182407000 2591413 2482950 2595802 2055652 3129725 3131353 2404360 2733487 2724552 2868798 FALSE TRUE 2693723.986 2909377.348 2663450.733 2462253.83 2597735.462 2404143.722 2215899.981 2696849.078 2626495.906 3430884.042 0.78513991 0.847996409 0.776316162 0.717673288 0.757162128 0.700735931 0.645868515 0.78605078 0.765544936 1 21.71014894 0.459304379 1.836822618 0.999969143 0.750098097 0.669284752 0.052062432 2.962090247 9.323061621 0.053818944 0.015001863 2.879415774 -0.459304379 -0.249871046 QLAAENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLAAENR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 120.46 0.010592 243100000 347660 408320 361460 377250 413090 499510 382480 395910 359710 436160 FALSE TRUE 361385.8853 478445.7837 370879.9445 451868.924 342873.1094 383506.3726 352500.2182 390603.474 346764.1074 521617.2012 0.69281819 0.917235441 0.711019391 0.866284553 0.657327075 0.735225701 0.675783347 0.748831659 0.664786565 1 18.99263192 -1.206078814 3.546504193 1.000372129 0.743910614 0.472840415 0.081980143 18192066.26 26756432.65 77169.70805 0.019378352 0.062218736 1.206078814 -0.256461515 QLAEDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLAEDFLR 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;; 128.38 0.0026425 576720000 1028750 1237410 1108670 1087020 1397120 1462400 1101410 1119520 1047310 1660590 FALSE TRUE 1069365.844 1449925.542 1137562.851 1302029.312 1159638.041 1122779.763 1015078.606 1104514.666 1009617.518 1985950.817 0.538465422 0.730091365 0.572805148 0.655620119 0.583920826 0.565361314 0.511129781 0.556164159 0.50837992 1 20.92139846 -1.732417634 3.91905994 1.037421288 0.581408833 0.79574747 0.063800834 0.020685074 0.001412318 0.061254884 0.014768693 0.018517501 1.732417634 -0.456012454 QLAELETEDGMQES(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLAELETEDGMQESP 15 0 Q96QG7-2;Q96QG7 Q96QG7-2 MTMR9 Myotubularin-related protein 9 1 QLAELETEDGMQES(1)P 172.1 4.09E-06 52436000 86961 107530 95609 98719 104690 116360 95428 89216 96686 97325 TRUE FALSE 90394.28743 125997.441 98100.64908 118245.3236 86894.83119 89337.15345 87948.10401 88020.20545 93206.28975 116393.9704 0.776623455 1.082508318 0.842832741 1.01590592 0.746557841 0.767541078 0.755607045 0.756226505 0.800782802 1 16.8286568 3.228205693 24.99989349 0.785075612 0.934210889 0.239311937 0.105726516 226.3294151 546426.2373 0.0276726 0.033416986 1691.241756 -3.228205693 0.149135277 QLALEVIVTLSETAAAMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLALEVIVTLSETAAAMLR 19 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 166.09 4.79E-11 47053000 82143 84761 93339 101900 90706 123770 101350 89781 98043 80883 FALSE TRUE 85386.06907 99318.0424 95771.49102 122055.5159 75287.82652 95026.29325 93405.92217 88577.63255 94514.45158 96730.47525 0.882721488 1.026750278 0.990086018 1.261810361 0.778325821 0.98238216 0.965630758 0.915715883 0.977090739 1 16.56168287 3.209300447 24.99999988 0.935343496 1.035782143 0.188757557 0.10525173 354.8468173 303181.4629 0.029544724 0.035317818 1619.199822 -3.209300447 0.100438647 QLAPIWDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLAPIWDK 8 0 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 ; 124.23 0.0030562 870890000 1750240 1614060 1667980 1656080 2087200 2191700 1882130 1600390 1615700 1400950 FALSE TRUE 1819340.827 1891262.249 1711448.929 1983647.681 1732418.49 1682710.891 1734603.733 1578939.39 1557551.273 1675439.33 1.085888814 1.128815718 1.021492631 1.183956737 1.034008489 1.004340092 1.03531277 0.942403202 0.929637526 1 20.67610801 2.52429662 1.138220741 0.958295196 1.100486694 0.585881718 0.047974856 0.322010188 0.847179301 0.026221906 0.019609424 334.4233708 -2.52429662 0.142191499 QLCAEHGISPEGIVEEFATEGTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLCAEHGISPEGIVEEFATEGTDR 24 0 P23258;K7EIS0;Q9NRH3;K7EKE5 P23258 TUBG1;TUBG2 Tubulin gamma-1 chain;Tubulin gamma chain;Tubulin gamma-2 chain 0 ;; 178.39 4.02E-17 75005000 45215.5 62939 56002 53887.9 59836 65467 57264 59615 62157 57171 FALSE TRUE 47000.64285 73748.28365 57461.45813 64546.76578 49665.09809 50263.28141 52775.49805 58815.95844 59919.98171 68372.56285 0.687419645 1.078623948 0.840416912 0.944044849 0.7263893 0.73513818 0.771881232 0.860227495 0.876374663 1 16.06112988 6.968437184 11.16049 0.847225381 0.286288887 0 0.12070791 0 0 0.025519826 0 9299020.051 -6.968437184 -0.560936494 QLDDKDEEINQQSQLVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLDDKDEEINQQSQLVEK 18 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 293.25 2.83E-49 1108780000 1885950 743280 1173620 719730 1523470 1563840 1475410 1153350 1384720 659240 FALSE TRUE 1960408.762 870932.5581 1204205.501 862090.4458 1264511.114 1200661.86 1359763.509 1137891.23 1334884.198 788405.4561 2.486548954 1.104675965 1.527393668 1.093460781 1.603884275 1.522898974 1.724700785 1.44328178 1.693144292 1 19.58857823 4.750445681 24.64509027 1.443623971 2.486549725 0.62616502 0.247901655 962.3522884 1995506.899 0.05569722 0.912490064 56291.87058 -4.750445681 1.042925754 QLDDLKVELSQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLDDLKVELSQLR 13 1 P42766;F2Z388 P42766 RPL35 60S ribosomal protein L35 0 ;;; 194.48 8.99E-07 4544236000 5133700 3873440 4821360 3702740 6069280 5840910 5353670 4936340 5729450 4731350 FALSE TRUE 5336382.44 4538673.189 4947008.602 4435130.92 5037625.953 4484447.172 4934035.356 4870176.437 5523248.214 5658367.445 0.943095777 0.802117083 0.874281964 0.783818118 0.890296716 0.79253375 0.87198921 0.86070346 0.976120456 1 22.43195444 1.216729416 2.959658688 1.001729594 0.847655325 0.58010461 0.046348502 0.153771271 2.330146041 0.038124463 0.010716159 16.47135837 -1.216729416 -0.154074269 QLDWRPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLDWRPER 8 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ;; 77.677 0.029725 919990000 1777170 2223450 1998560 2037330 2024850 2524280 1940010 2023860 2002510 2304480 FALSE TRUE 1847334.044 2605310.241 2050644.115 2440307.793 1680666.72 1938054.226 1787946.947 1996733.467 1930440.056 2755998.734 0.670295679 0.945323454 0.744065696 0.885453162 0.609821296 0.703213032 0.648747376 0.724504494 0.70045027 1 21.39414379 5.049285005 16.11481632 0.756313749 0.134845093 0.043606473 0.123254804 9869838.307 82768396.52 0.028257628 191072623.1 112017.2753 -5.049285005 -0.621468656 QLDYEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLDYEWK 7 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 ; 81.594 0.062294 82726000 362920 294930 354540 282240 392890 431040 388280 319940 345790 286930 FALSE TRUE 377248.3618 345581.9333 363779.6037 338066.2296 326106.6981 330937.4925 357845.599 315651.7276 333345.0854 343148.4399 1.099373676 1.007091664 1.060123146 0.98518947 0.950337114 0.96441497 1.042830325 0.919869336 0.971431155 1 18.38847327 5.26495789 0.578430625 0.968501895 1.255901082 0.498198695 0.036509899 5.2751895 0.860921688 0.017220244 1.157326041 184059.3524 -5.26495789 0.287399187 QLEAIDQLHLEYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;F5GXS2;O43707-3 O43707 ACTN4 Alpha-actinin-4 0 ;;; 182.35 1.53E-06 1822010000 1672792 1815400 1421220 1639920 1868670 2193700 2116190 1621600 1561660 2253550 FALSE TRUE 1738835.12 2127180.828 1458258.161 1964291.281 1551034.141 1684246.421 1950317.498 1599865.104 1505456.162 2695089.976 0.645186296 0.789280079 0.541079583 0.728840706 0.575503658 0.624931426 0.723655802 0.593622149 0.558592171 1 21.36190201 -2.055939558 2.675936228 1.503084236 0.643645838 0.656958893 0.077537981 13168938 7168989.289 40367392.46 0.017947135 0.008791449 2.055939558 -0.859438399 QLEEAEEEAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QLEEAEEEAQR 11 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;; 389.36 8.39E-102 4344170000 1758400 2160623 1882197 1960191 1967867 2388210 1874170 1958735 1920740 2094547 FALSE TRUE 1827822.99 2531693.193 1931248.6 2347910.929 1633369.67 1833584.421 1727267.658 1932481.361 1851612.943 2504933.382 0.729689262 1.010682843 0.770978028 0.937314719 0.652061121 0.731989295 0.689546345 0.771470162 0.739186501 1 21.25634081 3.245843292 24.99989652 0.747624747 0.866261092 0.140811828 0.114332883 254.035584 872045.6287 0.028977263 0.038454548 1761.34038 -3.245843292 0.118636344 QLEEAEEESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLEEAEEESQR 11 0 P35749;P35749-2;P35749-4;P35749-3 P35749 MYH11 Myosin-11 0 173.71 2.76E-05 73059000 70390 78434 73587 82040 78680 108640 86578 81823 74581 87199 FALSE TRUE 73169.05155 91904.42937 75504.73767 98267.26714 65306.0017 83410.00646 79791.79013 80726.29652 71896.84438 104283.9745 0.701632747 0.881290052 0.724030111 0.942304583 0.626232381 0.799835323 0.765139519 0.774100689 0.689433297 1 16.67015795 -1.196091603 9.049264711 1.000000012 0.771351377 0.387074748 0.087771907 1.95E-08 1.70E-09 0.076379284 0.018002769 0.063666122 1.196091603 -0.228648635 QLEEEDGSRDSPLFDFIESCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLEEEDGSRDSPLFDFIESCLR 22 1 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;;; 205.84 9.12E-23 108227000 78937 105128 88896 87882 109454 114733 61874 84813 99662 135666 FALSE TRUE 82053.49371 123182.9162 91212.70279 105264.7973 90849.04818 88087.99955 57024.1542 83676.22046 96075.18409 162247.1552 0.505731479 0.759230053 0.56218368 0.648792869 0.559942318 0.542924771 0.35146474 0.515733052 0.592153274 1 17.30783366 0.90128429 10.36776072 0.999999995 0.553514089 0.646079795 0.098061349 12.61166977 1325.143164 0.100358889 0.025100907 7.966806882 -0.90128429 -0.446485906 QLEEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 98.904 0.025406 305120000 413640 541370 465630 446670 504630 614950 458740 503580 487680 556400 FALSE TRUE 429970.8266 634346.0862 477764.7003 535019.9928 418853.1728 472137.1822 422782.7601 496830.3338 470128.4921 665415.9271 0.646168523 0.953307639 0.717994086 0.804038453 0.629460696 0.709536942 0.635366157 0.746646291 0.706518244 1 19.34389687 -1.058942509 3.721055373 1.000082498 0.730030942 0.446046019 0.091012144 26158739217 45938376036 27522275.18 0.021274128 0.087308694 1.058942509 -0.270051557 QLEGDCCSFITQLVNHFWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLEGDCCSFITQLVNHFWK 19 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 ; 187.06 1.92E-14 109742000 154965 124557 160056 145470 173865 204522 164731 162570 177536 137078 FALSE TRUE 161083.1379 145948.6958 164227.1908 174243.5318 144311.4894 157024.8651 151818.9538 160391.0151 171146.514 163935.8096 0.982598849 0.890279532 1.001777411 1.062876575 0.880292657 0.957843594 0.926087803 0.978376936 1.043984926 1 17.3227715 1.418881106 5.46120293 1.020627426 0.957346537 0.199299295 0.051137299 0.322537584 16.5778773 0.034548079 0.012879098 26.23500224 -1.418881106 -0.06328089 QLFHPEQLITGK ddPTM_MDA-MB-175_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 ;; 147.73 6.54E-05 14835497000 8588890 7775130 8172460 8253540 9236360 10763210 8809960 8377880 8572780 7112630 FALSE TRUE 8927986.009 9110448.095 8385441.021 9886065.578 7666366.826 8263617.596 8119412.315 8265588.222 8264247.322 8506213.669 1.049584028 1.071034475 0.985801832 1.162216935 0.901266665 0.971480134 0.9545272 0.971711803 0.971554165 1 23.02008566 3.223615276 24.99999846 0.961098661 1.061624895 0.551663445 0.046440882 172.8054733 289061.7038 0.012525466 0.015026738 1673.459768 -3.223615276 0.100526235 QLFHPEQLITGKEDAANNYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 215.58 3.91E-25 7205150000 5678560 6956740 6696250 4484234 8617540 7786520 4195588 6086280 6886060 9078720 FALSE TRUE 5902753.934 8151505.979 6870759.776 5371202.101 7152733.629 5978218.736 3866726.849 6004703.372 6638232.046 10857521.36 0.543655751 0.75077043 0.632811076 0.494698737 0.658781447 0.550606215 0.356133478 0.553045504 0.611394795 1 23.37219146 0.777098131 4.115542695 0.999991375 0.565388712 0.6307689 0.09863026 1.924524209 34.93510903 0.100135116 0.025540531 5.985468243 -0.777098131 -0.434602663 QLGEAHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLGEAHGR 8 0 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ; 136.99 0.0007674 94031000 128229 154010 135365 137351 145136 155446 131010 144311 136718 153088 FALSE TRUE 133291.5799 180460.0195 138892.7231 164518.6178 120465.8346 119346.0223 120741.0939 142376.7471 131797.5459 183082.6626 0.728040428 0.985675088 0.758633948 0.898602935 0.657986031 0.651869602 0.659489502 0.777663735 0.719879993 1 17.48213565 3.243499648 24.99438112 0.726633171 0.846940446 0.134761193 0.116636631 191.8969103 971103.1476 0.030357167 0.039852761 1751.861015 -3.243499648 0.120307275 QLHDDYFYHDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLHDDYFYHDEL 12 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ;;; 202 1.42E-07 2111270000 1506380 2008270 1642910 1926990 1945700 2154380 1486120 1682890 1620240 1936230 FALSE TRUE 1565853.046 2353174.75 1685725.584 2308142.871 1614970.609 1654057.895 1369634.031 1660333.612 1561927.879 2315597.197 0.676219961 1.016228018 0.727987401 0.996780819 0.697431579 0.714311581 0.591481987 0.717021775 0.674524862 1 21.14295288 3.192385577 24.99726564 0.708109111 0.856847752 0.141527465 0.139419069 177.0591326 95851.89684 0.036639134 0.043792284 1557.34767 -3.192385577 0.148738641 QLHDEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLHDEAR 7 0 P18206;P18206-2 P18206 VCL Vinculin 0 138.54 0.0027753 273190000 121400 108100 115550 120290 117500 140540 129890 119520 107580 145970 FALSE TRUE 126192.9657 126665.3341 118561.3279 144083.003 97527.39197 107901.7149 119708.8824 117918.0299 103708.2168 174570.0267 0.722878767 0.725584663 0.679161997 0.825359345 0.558672034 0.618099893 0.685735602 0.675476954 0.594078026 1 17.41344635 -1.835450004 6.782861866 1.024706391 0.67720321 0.649647538 0.071350906 0.024692054 0.000599021 0.063991038 0.016095531 0.014606629 1.835450004 -0.347503181 QLHEQAMQFGQLLTHLDTTQQMIANSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLHEQAMQFGQLLTHLDTTQQMIANSLK 28 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 229.76 3.74E-35 114770000 79926 69815 91831 73306 86692 120640 95968 78268 99418 60496 FALSE TRUE 83081.5402 81805.18316 94224.1913 87805.708 71956.12481 92623.18832 88445.77739 77218.94548 95839.9656 72349.03293 1.148343479 1.130701819 1.302355919 1.213640382 0.994569269 1.280227041 1.222487348 1.06731137 1.324688966 1 16.14268611 -1.384522787 4.316081109 0.999603186 1.179902241 0.237987798 0.099707858 0.000365199 5.21E-05 0.092605657 0.021779666 0.041255059 1.384522787 0.180299055 QLHFQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLHFQEK 7 0 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 73.931 0.047556 61015000 46238 47514 46499 36837 62094 58912 49013 52683 52996 43307 FALSE TRUE 48063.51194 55674.15989 47710.80214 44123.24865 51539.28406 45230.58082 45171.23299 51976.87056 51088.68431 51792.17749 0.928007168 1.074953064 0.92119707 0.85192882 0.99511715 0.873309118 0.872163234 1.003566042 0.986416999 1 15.66044659 1.61868343 15.89685714 0.996277939 0.933586957 0.190896246 0.061805154 0.197459829 249.3142561 0.03061146 0.016406286 41.56075511 -1.61868343 -0.062690982 QLHLEGASLELS(ph)DDDTESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK 349.6 6.62E-91 2680260000 2084680 1237790 1617470 1437820 1920060 2343460 2085900 1731340 1782890 1118460 TRUE FALSE 2166984.776 1450370.804 1659622.597 1722216.505 1593688.887 1799226.93 1922401.708 1708134.219 1718724.137 1337600.823 1.620053411 1.084307649 1.240745796 1.287541451 1.19145328 1.345115 1.437201349 1.277013433 1.284930532 1 20.35121621 0.52773047 2.402668502 1.000011769 1.301695285 0.314634168 0.136197654 7.449811586 36.38099688 0.122586884 0.032864673 3.37078048 -0.52773047 0.301683516 QLHVLVPQS(ph)PPTDLPGLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLHVLVPQSPPTDLPGLTR 19 0 O95402 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 QLHVLVPQS(0.956)PPT(0.042)DLPGLT(0.002)R 51.39 0.087539 46648000 70708 57730 70214 58439 83067 81094 81564 63848 64980 65894 TRUE FALSE 73499.60644 67644.67842 72043.83452 69998.05978 68947.30101 62261.14749 75170.80055 62992.22199 62641.38249 78804.66768 0.932680875 0.858384159 0.914207707 0.888247636 0.874913924 0.790069286 0.953887666 0.799346331 0.794894317 1 16.26599346 3.148707994 3.775839524 0.856073283 0.896990652 0.029813909 0.066947574 0.631478258 17.31564905 0.018804241 0.023233738 1408.341555 -3.148707994 0.040917369 QLICDPSYIPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLICDPSYIPDR 12 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 77.593 0.033653 0 56690 43052 40464 40832 55242 59906 53199 43870 56479 41729 FALSE TRUE 58928.16497 50445.8461 41518.52508 48908.44773 45851.98457 45993.73938 49029.12337 43281.99441 54446.33182 49904.9986 1.180806866 1.010837542 0.831951232 0.980031041 0.918785409 0.921625903 0.982449148 0.867287759 1.090999566 1 15.60689671 4.656883007 3.508886961 0.940575728 1.191472875 0.495869308 0.069478915 0.177710953 3.613590713 0.015511617 0.100913234 45381.93471 -4.656883007 0.250897147 QLIYNYPEQLFGAAGVMAIEHADFAGVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLIYNYPEQLFGAAGVMAIEHADFAGVER 29 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 223.56 1.50E-34 101195000 75507 110146 71544 91932 92083 105805 62704 90216 84237 118759 FALSE TRUE 78488.07466 129062.7187 73408.49541 110115.8752 76430.76455 81233.39224 57789.09663 89006.80208 81205.32682 142027.5523 0.552625694 0.908716067 0.516860949 0.775313476 0.538140405 0.571955166 0.406886521 0.626686869 0.571757561 1 17.1158113 -1.619353247 9.07628771 1.000137472 0.608190587 0.437540392 0.13344925 0.000359358 1.51E-05 0.125080297 0.029471612 0.024024079 1.619353247 -0.391946885 QLKDSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLKDSEER 8 1 A0A2R8Y430;P48637;A0A2R8Y5T7;P48637-2 A0A2R8Y430 GSS Glutathione synthetase 0 73.985 0.038441 109380000 189270 185490 169670 154940 369120 281290 197840 184220 202560 291540 FALSE TRUE 196742.5257 217346.4646 174091.7396 185586.6696 306377.1142 215964.6605 182332.7838 181750.8322 195269.9052 348661.6811 0.564279175 0.623373535 0.499314232 0.532282954 0.878723217 0.619410369 0.522950452 0.521281351 0.560055537 1 18.41146829 -1.148848357 4.905069482 1.000027468 0.589048495 0.582536956 0.103779338 3.25E-05 5.64E-06 0.104792753 0.02469824 0.070982558 1.148848357 -0.410978973 QLKPWCWYCNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLKPWCWYCNR 11 1 J3QRS9;O43670-2;O43670;O43670-4;O43670-3 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 73.499 0.039573 83618000 321270 209100 275570 177980 502760 362970 311810 276750 240490 326550 FALSE TRUE 333953.9877 245011.2984 282751.5806 213183.9128 417301.0348 278675.7184 287369.5174 273040.6189 231834.8119 390531.2203 0.855127504 0.627379543 0.724017866 0.54588187 1.068547182 0.713581153 0.735842623 0.699151834 0.593639637 1 18.57507836 QLLCGAAIGTHEDDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLLCGAAIGTHEDDKYR 17 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 185.33 3.52E-10 398890000 473440 353440 342500 429720 553750 604830 544910 406200 400420 374470 FALSE TRUE 492131.7768 414140.5706 351425.8314 514717.3334 459623.7728 464367.3988 502198.5303 400755.5534 386008.9624 447840.2268 1.098900338 0.924750716 0.784712516 1.149332513 1.026311942 1.03690417 1.121378787 0.894862787 0.861934546 1 18.7726246 1.614221482 24.99999999 0.908795136 1.01304701 0.160870595 0.104435504 0.987780481 3871.375032 0.050881755 0.02734929 41.13594531 -1.614221482 0.104251874 QLLDS(ph)DEEQEEDEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR 361.2 5.04E-83 976400000 304400 329900 326740 363330 338070 400340 372010 342280 332000 335100 TRUE FALSE 316417.947 386557.7587 335255.1128 435195.5896 280604.9822 307367.1022 342850.8841 337692.2965 320051.3849 400756.4291 0.789551768 0.964570324 0.836555794 1.085935391 0.700188348 0.766967364 0.85550938 0.842637253 0.798618217 1 18.61236614 5.05499502 13.6329229 0.863516941 0.373895324 0.043668901 0.109428634 2236646.152 17058738.33 0.025306768 28285881.74 113499.7801 -5.05499502 -0.489621616 QLLEEELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLLEEELAR 9 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 77.677 0.074269 74251000 96338 130080 107210 127660 119380 135810 107540 115400 109550 128420 FALSE TRUE 100141.4986 152420.2281 110003.9807 152910.767 99087.83024 104270.1857 99110.7338 113853.2518 105607.3169 153581.4403 0.652041669 0.992439112 0.716258296 0.99563311 0.64518102 0.678924391 0.645330149 0.741321683 0.687630724 1 17.22864436 5.039983188 16.16000622 0.772498373 0.118780639 0.066513271 0.142265609 9573085.417 105885062.2 0.032780034 184757239.9 109643.5751 -5.039983188 -0.653717734 QLLEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLLEELER 8 0 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 187.3 0.00047221 148575000 195740 237450 222440 235460 244780 273350 204080 237790 221444 237150 FALSE TRUE 203467.9663 278230.1904 228236.9691 282033.2852 203172.383 209868.6052 188083.6763 234602.814 213474.2737 283615.002 0.71740904 0.981013657 0.80474223 0.994423014 0.716366841 0.739977095 0.663165471 0.827187604 0.752690345 1 18.11357432 QLLGHMEDLEGDAQSVLDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLLGHMEDLEGDAQSVLDAR 20 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 ; 215.58 1.19E-24 119405000 55128.8 68386 63878 59836 64466 74381 57493 69089 56462 61982 FALSE TRUE 57305.32759 80130.76353 65542.71316 71671.38221 53508.09235 57107.14 52986.54843 68162.97496 54429.94365 74126.18618 0.773078052 1.081004806 0.884204578 0.966883444 0.721851414 0.7704044 0.714815521 0.919553244 0.734287658 1 16.17769567 3.253209294 24.99609049 0.805647606 0.934337307 0.205823886 0.111104643 333.48305 569042.7685 0.028964302 0.039050674 1791.468986 -3.253209294 0.128689701 QLLHSCTVIATNILLVDEIMR ddPTM_MDA-MB-175_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 ;;;; 252.91 2.38E-36 1949294000 645482 754408 641253 783231 728049 857204 674455 719927 738254 749783 FALSE TRUE 670966.1278 883971.7055 657964.58 938151.7541 604295.491 658131.3621 621589.4547 710277.5561 711684.3828 896688.6234 0.748271039 0.985817911 0.733771526 1.046240277 0.67391899 0.733957524 0.693205466 0.792111707 0.79368062 1 19.77424757 QLLLTADDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QLLLTADDR 9 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;; 229.55 2.86E-07 1253841000 1518990 1872120 1489290 1829860 1986290 2219810 1826030 1600190 1517860 2224600 FALSE TRUE 1578960.898 2193642.047 1528102.121 2191800.846 1648661.135 1704292.769 1682900.997 1578742.07 1463232.515 2660467.777 0.593489954 0.824532462 0.574373474 0.823840403 0.619688443 0.640598914 0.632558309 0.593407702 0.549990692 1 21.3432485 -0.995176249 4.576377957 1.00000783 0.652023097 0.566717823 0.091726526 1.20835E+11 26531778304 11707783.85 0.020559775 0.101116901 0.995176249 -0.347984733 QLLLTADDRVNPCIGGVILFHETLYQK ddPTM_MDA-MB-175_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 ;;; 278.24 3.40E-61 5846422000 2616016 5433256 4833244 4183124 5080963 5937870 3330977 5051848 5094365 6338990 FALSE TRUE 2719298.332 6366375.453 4959202.309 5010533.442 4217302.724 4558889.682 3069886.319 4984136.241 4911019.799 7580993.723 0.358699457 0.839781127 0.654162566 0.660933596 0.556299461 0.601357797 0.404945108 0.657451572 0.647806868 1 22.85395554 0.622908464 1.914254513 0.999800321 0.597012751 0.474027118 0.128382237 1.693972922 7.528922422 0.117203489 0.032529772 4.19670521 -0.622908464 -0.402787571 QLLNCLHVVTLYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLLNCLHVVTLYNR 14 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 121.45 0.0001145 196550000 211210 250020 190620 226960 290780 309430 190920 211380 192180 293170 FALSE TRUE 219548.7339 292958.9901 195587.7138 271852.0106 241353.3195 237569.572 175955.1915 208546.7968 185263.4793 350611.0484 0.626188863 0.835566909 0.557848119 0.775366355 0.688379104 0.677587238 0.501852957 0.594809541 0.528401715 1 18.41951193 -1.159356751 4.692137257 1.000040623 0.642570928 0.532485837 0.10038438 4.32E-05 7.73E-06 0.098315313 0.023170512 0.069285642 1.159356751 -0.357469695 QLLNPAQVFDLMNGGPHLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLLNPAQVFDLMNGGPHLGLR 21 0 Q86XP1-2;Q86XP1;A0A0D9SFR6;Q86XP1-5;Q86XP1-3;Q16760;H7BZR7;Q16760-2 Q86XP1-2 DGKH;DGKD Diacylglycerol kinase eta;Diacylglycerol kinase delta 0 30.152 0.089081 154520000 2381.3 60615 42602 42347 32362 57965 19600 44516 30179 84512 FALSE TRUE 2475.315563 71025.15473 43712.24312 50723.11021 26861.1188 44503.50722 18063.70078 43919.33583 29092.86369 101070.5083 0.024490978 0.702728777 0.432492562 0.501858663 0.265766139 0.440321395 0.178723755 0.434541555 0.287847209 1 16.62500256 -1.7561295 3.679209219 1.079167501 0.375108893 0.535437391 0.17763687 56969607.9 40466824.72 36410083.48 0.038142212 0.017533576 1.7561295 -0.704058608 QLLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLLSER 6 0 A0A087X1E4;P53365;P53365-2;P53365-3;E9PRV8;E9PPY7 A0A087X1E4 ARFIP2 Arfaptin-2 0 107.32 0.072981 315910000 161320 176070 170780 150810 184610 188710 152080 163400 177910 169970 FALSE TRUE 167689.0382 206308.6529 175230.6671 180639.7679 153230.0581 144884.9624 140159.5722 161209.8903 171507.0539 203272.3672 0.824947534 1.014937031 0.862048637 0.888658751 0.753816469 0.712762706 0.689516111 0.793073316 0.843730292 1 17.63305458 3.306105932 5.439086037 0.777730231 0.90569402 0.191743985 0.093315072 0.249458606 13.75831307 0.025039046 0.033806547 2023.51269 -3.306105932 0.127963789 QLLTLS(ph)SELSQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLLTLSSELSQAR 13 0 P15311;E7EQR4 P15311 EZR Ezrin 1 QLLT(0.007)LS(0.955)S(0.036)ELS(0.001)QAR;QLLTLS(0.95)S(0.049)ELSQAR 182.04 1.21E-05 99627000 135933 141576 152443 157869 152487 194964 162081 155289 164504 180214 TRUE FALSE 141299.7398 165890.5767 156415.7898 189095.017 126567.3142 149686.5657 149376.6677 153207.605 158583.5332 215523.4829 0.655611806 0.769709985 0.725748247 0.87737547 0.587255331 0.694525551 0.693087666 0.7108627 0.735806285 1 17.71748554 -1.377797822 2.989930266 1.003887921 0.717259775 0.587879517 0.071167249 10683979.34 13486496.36 362137.3087 0.017881659 0.041898857 1.377797822 -0.286628146 QLMEQDASS(ph)SPSAQVIGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 QLMEQDAS(0.088)S(0.561)S(0.345)PS(0.006)AQVIGLK;QLMEQDAS(0.002)S(0.498)S(0.484)PS(0.017)AQVIGLK 197.72 8.12E-16 133638000 340936 301494 355581 345864 373682 429509 393095 348220 383882 322327 TRUE FALSE 354396.4165 353273.2492 364847.733 414274.8669 310163.6671 329762.044 362283.1867 343552.6805 370066.1618 385480.8043 0.919362035 0.916448356 0.946474452 1.074696489 0.804615077 0.855456459 0.939821601 0.891231617 0.960011906 1 18.55629949 1.004074634 5.572369792 0.999928314 0.918566623 0.136303165 0.06583138 0.273743586 33.14136132 0.06374086 0.016062431 10.09426342 -1.004074634 -0.081361691 QLMEQDASSS(ph)PSAQVIGLK ddPTM_MDA-MB-175_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(0.063)S(0.936)PS(0.001)AQVIGLK 292.02 1.51E-49 146400000 260400 234320 262480 252860 308090 342220 269590 266400 281270 246210 TRUE FALSE 270680.7931 274562.6372 269320.4444 302874.9533 255720.9718 262744.5914 248458.8314 262829.3437 271147.1476 294450.1355 0.919275492 0.932458858 0.914655529 1.028612036 0.868469534 0.892322875 0.843806137 0.892610707 0.920859307 1 18.16766381 QLNDLWDQIEQAHLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLNDLWDQIEQAHLELR 17 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 182.09 7.67E-10 145840000 126240 151640 176840 133540 142930 177440 143940 141680 124230 162670 FALSE TRUE 131224.0527 177682.9904 181448.5957 159953.8134 118634.8097 136232.2491 132657.6067 139781.0113 119758.9866 194542.072 0.674527887 0.913339663 0.932695914 0.822206795 0.609815699 0.7002714 0.68189675 0.718513018 0.615594279 1 17.56972266 3.400354491 7.951028845 0.70476579 0.852408189 0.168630498 0.121112638 0.326333663 29.46309943 0.031201358 0.042308874 2513.937583 -3.400354491 0.147642399 QLNENKQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLNENKQER 9 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 94.363 0.008001 900750000 116260 105240 122060 78569 154800 148540 117500 120080 120840 107910 FALSE TRUE 120850.0346 123314.1513 125240.9839 94109.71369 128487.1513 114043.8361 108290.043 118470.524 116490.992 129052.8984 0.936437973 0.955531823 0.970462387 0.729233631 0.995616161 0.883698371 0.839113606 0.917999715 0.902660796 1 16.97760302 QLNTITLPDFSDPETGS(ph)VHATSVAASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLNTITLPDFSDPETGSVHATSVAASR 27 0 Q86TV6;H0YK02 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 QLNTITLPDFSDPET(0.041)GS(0.959)VHATSVAASR 135.17 1.44E-05 82277000 15815 27421 22613 20137 24649 29445 21603 25243 21654 24768 TRUE FALSE 16439.38841 32130.34344 23202.31336 24120.0385 20459.17178 22606.84499 19909.70041 24904.65887 20874.67677 29620.81539 0.554994459 1.084721775 0.783311096 0.814293536 0.690702518 0.763208058 0.672152341 0.840782353 0.704729985 1 14.85432373 -1.55749924 3.163969694 1.008855241 0.777030826 0.216136788 0.13165737 44329148.64 51524493.35 3324102.65 0.029427066 0.027701339 1.55749924 -0.231824415 QLNVNAKPFVPNVHAAEFVPSFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLNVNAKPFVPNVHAAEFVPSFLR 24 1 P15170-2;P15170-3 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 ; 109.11 0.001326 1615640000 2031690 1830690 2023820 1883430 2388700 2509000 1852190 2128190 2128380 2344400 FALSE TRUE 2111902.69 2145096.767 2076562.412 2255966.833 1982669.627 1926322.774 1707010.508 2099665.094 2051780.02 2803740.294 0.753244762 0.765083974 0.740640072 0.804627603 0.707151669 0.687054639 0.608833319 0.748880022 0.731801025 1 21.41892129 0.386938326 2.313609887 0.999997797 0.725080823 0.729436454 0.049795251 8.061909381 29.54707204 0.051067884 0.013749659 2.437464651 -0.386938326 -0.274916974 QLPAHDQDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLPAHDQDPSK 11 0 Q9UGI8-2;Q9UGI8;F8W7T0 Q9UGI8-2 TES Testin 0 ;; 142.12 3.78E-05 864250000 1086640 799600 903820 782600 1115090 1129340 997900 919880 980820 764540 FALSE TRUE 1129541.386 936925.08 927374.2917 937395.9442 925547.4001 867067.9003 919681.9905 907550.5132 945520.4798 914336.975 1.235366629 1.024704355 1.014258766 1.025219334 1.012260715 0.948302348 1.005845783 0.992577724 1.034105046 1 19.80236644 4.752770151 3.397745821 1.002875911 1.269327085 0.908121867 0.021933107 0.091075972 1.72701759 0.005478748 0.064089893 56593.96877 -4.752770151 0.266451174 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 QLPALDGSLMGPES(1)PPAQEEEAPVSPHK;QLPALDGSLMGPES(1)PPAQEEEAPVSPHK 213.06 1.21E-25 266040000 173597 153482 187689 175081 195902 236810 227138 197118 209402 153757 TRUE FALSE 180450.7436 179841.3396 192580.3295 209711.4992 162602.648 181814.4664 209334.33 194475.9556 201865.6629 183882.7403 0.98133595 0.978021859 1.04729965 1.140463204 0.884273574 0.988752213 1.138412065 1.057608535 1.097795598 1 17.48842655 2.262766426 24.90975496 1.078191172 1.005022605 0.199756728 0.068421534 350.5997734 360794.7738 0.024021539 0.020088563 183.1329226 -2.262766426 -0.073168567 QLPDKWQHDLFDSGFGGGAGVETGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLPDKWQHDLFDSGFGGGAGVETGGK 26 1 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 309 6.43E-82 778330000 616490 469660 592650 409980 703450 603790 635130 590980 625140 418150 FALSE TRUE 640829.5012 550320.4516 608094.9459 491072.8203 583877.8203 463568.923 585346.851 583058.8797 602641.3335 500078.4865 1.281457848 1.100468159 1.215999013 0.981991494 1.167572363 0.926992333 1.170509963 1.165934739 1.2050935 1 18.93179502 QLPFRGDEGIFEESFIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLPFRGDEGIFEESFIEER 19 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 207.07 3.05E-16 44350000 15427 25997 24772 15973 25623 30017 15934 20995 21582 36357 FALSE TRUE 16036.06987 30461.78252 25417.57867 19132.41173 21267.61161 23046.00666 14685.05144 20713.59637 20805.26804 43480.45805 0.368810969 0.700585594 0.584574768 0.440023233 0.489130349 0.530031368 0.337739115 0.476388642 0.478496984 1 15.40807952 -1.19063541 6.796455703 1.000001608 0.49053524 0.710429976 0.09776833 2.39E-06 2.84E-07 0.094831785 0.022351995 0.064471027 1.19063541 -0.509466368 QLPLEPES(ph)PSGQVGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 QLPLEPES(0.968)PS(0.032)GQVGPR;QLPLEPES(0.994)PS(0.006)GQVGPR 215.49 1.68E-14 131539000 111977 119404 110334 124538 106849 138189 124147 119649 111291 102520 TRUE FALSE 116397.9384 139910.7082 113209.3947 149171.2447 88686.84515 106096.699 114416.0337 118045.3009 107285.6586 122606.8311 0.949359325 1.141133058 0.923353076 1.216663405 0.723343425 0.865340846 0.933194608 0.962795464 0.875038182 1 16.90367984 3.241185161 24.99999992 0.897784512 1.054000874 0.370157362 0.104879892 76.7711028 731273.4638 0.028335816 0.036681236 1742.549649 -3.241185161 0.156216362 QLQDIATLADQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLQDIATLADQRR 13 1 O95373 O95373 IPO7 Importin-7 0 135.13 9.26E-06 0 83611 98620 101940 87164 103990 123170 86735 89294 95908 129200 FALSE TRUE 86912.02684 115557.2178 104596.6401 104404.779 86313.81694 94565.63416 79936.48406 88097.15999 92456.28981 154514.2663 0.562485451 0.7478741 0.6769384 0.675696695 0.5586139 0.612018789 0.517340476 0.570155508 0.598367335 1 17.23738052 -1.582842798 5.832996545 1.001430823 0.611972592 0.758135797 0.06552532 0.001321408 9.45E-05 0.068761182 0.016153611 0.02613107 1.582842798 -0.38945823 QLQEFTDLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLQEFTDLGHR 11 0 O75864 O75864 PPP1R37 Protein phosphatase 1 regulatory subunit 37 0 126.34 0.00030943 202840000 94301 129990 115300 129520 108880 152430 121720 122710 113440 130970 FALSE TRUE 98024.0763 152314.7713 118304.8127 155138.6694 90372.61649 117030.4426 112179.2683 121065.2732 109357.3166 156631.0639 0.625827814 0.972442934 0.755308748 0.990471912 0.576977607 0.747172621 0.716200641 0.772932713 0.698184088 1 17.25701084 5.019191819 17.79282093 0.787886605 0.270151637 0.126664513 0.134426384 44653146.52 930135193.6 0.030159279 636103235.1 104518.1753 -5.019191819 -0.517734968 QLQGPEKEPPKPEQVESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLQGPEKEPPKPEQVESR 18 2 O60664-4;O60664;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;; 169.51 1.02E-11 2645640000 2413230 1263900 1796650 1188960 2379090 2194510 2126370 1810450 2211070 1181670 FALSE TRUE 2508506.184 1480964.993 1843472.175 1424132.739 1974693.132 1684868.311 1959699.563 1786183.879 2131494.023 1413195.612 1.77505942 1.047954707 1.304470633 1.007739288 1.397324698 1.192239982 1.386715007 1.263932511 1.508279536 1 20.43052974 -2.156413611 2.547372063 0.24619374 1.30113279 0.16596387 0.211547858 50832085.48 40122523.05 213878024.8 0.050330975 0.006975677 2.156413611 1.054939049 QLRDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLRDELR 7 1 A0A0U1RRM1;Q8WXI9;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 0 100.19 0.0090994 85886000 91954 112260 94518 100110 122590 124740 86919 101950 95971 124930 FALSE TRUE 95584.41492 131539.7817 96981.21673 119911.4592 101752.1956 95771.02545 80106.06166 100583.527 92517.02246 149407.6416 0.639755865 0.880408662 0.649104796 0.802579158 0.681037426 0.641004867 0.536157728 0.673215412 0.619225506 1 17.18889441 -1.154369503 4.3779339 1.000060107 0.680802175 0.523564285 0.091497021 5.73E-05 1.11E-05 0.089623579 0.021120296 0.070085874 1.154369503 -0.319257933 QLS(ph)EEQPSGNGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLSEEQPSGNGVK 13 0 Q9H4Z3 Q9H4Z3 PCIF1 Phosphorylated CTD-interacting factor 1 1 QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK;QLS(1)EEQPSGNGVK 260.25 5.50E-24 299820000 1045650 801430 994510 827940 1228960 1313730 1088630 1063990 1190080 832820 TRUE FALSE 1086933.069 939069.3682 1020427.748 991704.0608 1020061.818 1008636.117 1003300.336 1049728.954 1147249.253 995995.1337 1.091303594 0.942845338 1.024530857 0.995691673 1.024163456 1.012691813 1.007334576 1.053949883 1.151862308 1 19.92577917 1.574379694 4.422501291 1.083486988 1.011681246 0.21094982 0.048434348 0.192737993 8.370795345 0.02586269 0.011403137 37.53009761 -1.574379694 -0.071805742 QLS(ph)ES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(0.979)ES(0.376)ES(0.332)S(0.312)LEMDDERYFNEMSAQGLRPR 46.608 0.062328 50373000 18046 24987 26020 22133 26068 36719 25112 25112 28110 27303 TRUE FALSE 18758.47001 29278.32288 26698.10258 26510.84134 21636.97067 28191.56873 23143.65582 24775.41471 27098.32659 32652.5001 0.574488016 0.896664047 0.817643442 0.811908468 0.662643614 0.863381629 0.70878664 0.758760114 0.829900513 1 14.99490584 0.870379766 3.180124346 0.999877174 0.767148125 0.386238517 0.090646674 0.540690916 10.61899835 0.080240601 0.020904233 7.419587581 -0.870379766 -0.232729049 QLS(ph)ESES(ph)SLEMDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(1)ES(0.055)ES(0.527)S(0.418)LEMDDER;QLS(0.987)ES(0.353)ES(0.399)S(0.261)LEMDDER 155.08 5.28E-06 170094000 195112 201567 214410 247740 260690 298390 284090 262810 252550 193355 TRUE FALSE 202815.1724 236184.5643 219997.7007 296742.2326 216378.0069 229093.4446 261822.2835 259287.4618 243460.7748 231239.2102 0.877079507 1.021386313 0.951385799 1.28326953 0.935732338 0.990720581 1.132257298 1.121295396 1.052852475 1 17.81902652 4.760089789 1.315994202 1.073358016 0.793959967 0.243880393 0.096826059 1.940122893 2.83514313 0.026474211 0.738163189 57555.89201 -4.760089789 -0.279398049 QLS(ph)ESESS(ph)LEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 QLS(0.999)ES(0.057)ES(0.167)S(0.778)LEMDDERYFNEMSAQGLRPR;QLS(0.999)ES(0.035)ES(0.156)S(0.809)LEMDDERYFNEMSAQGLRPR 116.73 0.00014987 132075000 58354 82176 81672 83845 91334 102112 72350 93017 81619 95842 TRUE FALSE 60657.86098 96289.08876 83800.43941 100429.2907 75809.0793 78398.03552 66679.01795 91770.25926 78681.54813 114620.4049 0.52920648 0.840069348 0.73111275 0.876190333 0.661392528 0.683979747 0.581737763 0.800645045 0.686453238 1 16.80650437 -1.639568369 2.447005685 1.037007374 0.717759038 0.413682814 0.103179861 5982863.843 4818097.393 1396450.808 0.024929551 0.022931456 1.639568369 -0.319248335 QLS(ph)ESESSLEMDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.995)ES(0.005)ESSLEMDDER;QLS(0.734)ES(0.266)ESSLEMDDER;QLS(0.996)ES(0.004)ESSLEMDDER;QLS(0.994)ES(0.006)ESSLEMDDER;QLS(0.989)ES(0.011)ESSLEMDDER;QLS(0.72)ES(0.28)ESSLEMDDER;QLS(0.96)ES(0.04)ESSLEMDDER 313.56 3.24E-56 4155504000 1673267 1865042 1801867 1883212 1817792 2152906 2233176 2105753 1972422 1495841 TRUE FALSE 1739328.873 2185348.455 1848825.134 2255705.713 1508804.365 1652926.209 2058133.83 2077528.825 1901434.918 1788922.404 0.972277427 1.221600473 1.033485371 1.26092988 0.84341521 0.923978706 1.15048804 1.161329759 1.062894015 1 20.77065938 -1.993426046 2.551160573 0.92507124 1.077879521 0.023806695 0.125859154 46886522.9 14134525.61 20652614.71 0.030265529 0.010152522 1.993426046 0.152808281 QLS(ph)ESESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(1)ESESSLEMDDERYFNEMSAQGLRPR;QLS(0.499)ES(0.499)ES(0.002)SLEMDDERYFNEMSAQGLRPR;QLS(0.99)ES(0.003)ES(0.003)S(0.003)LEMDDERYFNEMSAQGLRPR;QLS(0.988)ES(0.012)ESSLEMDDERYFNEMSAQGLRPR;QLS(0.515)ES(0.143)ES(0.171)S(0.171)LEMDDERYFNEMSAQGLRPR;QLS(0.988)ES(0.007)ES(0.002)S(0.003)LEMDDERYFNEMSAQGLRPR;QLS(0.565)ES(0.122)ES(0.144)S(0.169)LEMDDERYFNEMSAQGLRPR 318.6 3.00E-83 1100720000 57861.3 88114.9 94362.4 58464.6 85664.7 103127.1 91344.6 84033.9 74631.8 96372.3 TRUE FALSE 60145.7088 103247.9486 96821.56166 70028.72338 71103.44489 79177.39393 84184.77157 82907.56302 71945.8161 115254.607 0.521850799 0.895824916 0.840066737 0.60760021 0.616924969 0.686978126 0.730424351 0.719342724 0.624233755 1 16.81446489 -1.827753359 3.341860846 1.079182144 0.701975779 0.426724077 0.106118651 0.056850275 0.002930184 0.093304209 0.023814115 0.014867798 1.827753359 -0.377206365 QLS(ph)KPLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSKPLSER 9 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 QLS(0.999)KPLS(0.001)ER 74.46 0.024847 123020000 122540 106370 153500 100480 216860 167390 160420 125700 179320 131110 TRUE FALSE 127377.9738 124638.2201 157500.3361 120354.6441 179998.2147 128516.2093 147845.8612 124015.1971 172866.3082 156798.4942 0.812367328 0.794894241 1.004476075 0.767575254 1.147958821 0.819626553 0.942903578 0.790920842 1.102474288 1 17.25855218 4.259899399 24.51334058 0.928487479 0.803630618 0.170790124 0.120977646 346.1261544 397610.2815 0.02736406 0.074768276 18192.79389 -4.259899399 -0.124856861 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.992)LEGS(0.008)GLGVEDLKDNTPSGK;QLS(1)LEGSGLGVEDLKDNTPSGK 224.06 4.37E-26 392970000 293466 201870 230608 188216 409921 354244 291222 257977 338163 194015 TRUE FALSE 305052.2643 236539.6022 236617.8339 225444.563 340242.7748 271976.1996 268395.2587 254519.2403 325992.5797 232028.5246 1.314718804 1.019441909 1.019779074 0.971624344 1.466383392 1.172167086 1.156733893 1.096930822 1.404967688 1 17.82394265 QLS(ph)LPLTQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 QLS(0.997)LPLT(0.003)QSK;QLS(0.975)LPLT(0.025)QSK;QLS(0.997)LPLT(0.003)QSK;QLS(0.996)LPLT(0.004)QSK;QLS(0.998)LPLT(0.002)QSK;QLS(0.998)LPLT(0.002)QSK 182.37 1.87E-06 1616224000 2647200 2124220 3006770 2146150 3819990 3330420 3050070 2756220 3069160 2283940 TRUE FALSE 2751713.5 2489038.261 3085128.896 2570652.064 3170669.464 2556980.428 2810997.544 2719277.379 2958701.531 2731434.314 1.007424372 0.911256862 1.129490422 0.941136329 1.16080751 0.936131034 1.029128736 0.995549249 1.08320435 1 21.3812273 4.270821291 24.99982887 1.029899601 0.959340694 0.14257552 0.072984069 362.5452975 280942.3021 0.015971497 0.043731725 18656.11846 -4.270821291 -0.070558907 QLS(ph)LSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSLSSSR 8 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 QLS(0.993)LS(0.006)SSR 87.942 0.015699 103530000 41174 46994 70804 54083 82315 61063 63496 66889 68250 65696 TRUE FALSE 42799.58131 55064.85394 72649.21041 64780.45598 68323.1257 46882.04367 58519.0176 65992.46236 65793.69583 78567.87337 0.544746593 0.700857126 0.924668154 0.824515838 0.869606402 0.596707556 0.744821198 0.839942072 0.837412202 1 16.26165189 -5 0.115786254 1.73675485 0.650576588 0.345971321 0.109095445 209.3249787 1.58944956 36.37256623 1.235771023 1.00E-05 5 -1.086178262 QLS(ph)MSSADSADAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSMSSADSADAKR 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 QLS(0.904)MS(0.074)S(0.022)ADSADAKR 89.344 0.0029172 0 126260 103550 111890 105860 169450 164860 115500 129320 143190 111090 TRUE FALSE 131244.8423 121333.907 114805.9453 126798.792 140646.9495 126573.7635 106446.8082 127586.6769 138036.6199 132855.9586 0.98787321 0.913274108 0.864138474 0.954408018 1.05864239 0.952714239 0.801219677 0.960338387 1.038994573 1 17.01950341 1.466731469 25 1.012887686 0.931421318 0.211515476 0.065582182 3.822509196 9202.590826 0.037319548 0.017276398 29.29081592 -1.466731469 -0.081466368 QLS(ph)MTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QLSMTLR 7 0 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 QLS(0.983)MT(0.017)LR;QLS(0.921)MT(0.079)LR;QLS(0.968)MT(0.032)LR;QLS(0.996)MT(0.004)LR;QLS(0.909)MT(0.091)LR 121.73 0.0046253 1009816000 745403 969004 962123 895135 1056865 1127432 933026 964171 936815 1038597 TRUE FALSE 774832.086 1135422.899 987196.7158 1072190.031 877219.4648 865603.0044 859892.9841 951247.8648 903099.2111 1242090.197 0.62381306 0.914122744 0.794786657 0.863214309 0.706244576 0.696892228 0.692295122 0.765844435 0.727080218 1 20.24433851 -1.197211498 4.330787645 1.000080807 0.757810954 0.449839678 0.081570401 6.24E-05 1.16E-05 0.077492367 0.018259046 0.063502161 1.197211498 -0.242269853 QLS(ph)PQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QLSPQSK 7 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 QLS(0.999)PQS(0.001)K;QLS(0.999)PQS(0.001)K;QLS(0.958)PQS(0.042)K;QLS(0.99)PQS(0.01)K;QLS(0.975)PQS(0.025)K;QLS(0.962)PQS(0.038)K 132.39 0.0035386 7323110000 9231690 7225770 8747820 7096830 9439440 10518060 9633390 8677710 9051220 6444690 TRUE FALSE 9596164.25 8466739.789 8975795.376 8500561.792 7834927.36 8075399.968 8878299.72 8561399.491 8725468.36 7707403.614 1.245057964 1.098520359 1.164567969 1.102908608 1.016545617 1.047745826 1.151918358 1.110802018 1.132089196 1 22.87781351 7.999995919 0.941322314 1.090691189 100.3656147 0.447567634 0.051637092 1228.482566 2.198538452 0.016143206 262512.4643 99999060.32 -7.999995919 99.27492351 QLS(ph)SGVSEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 27 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.918)S(0.081)GVSEIR;QLS(0.967)S(0.033)GVSEIR;QLS(0.499)S(0.499)GVS(0.002)EIR;QLS(0.916)S(0.084)GVSEIR;QLS(0.984)S(0.016)GVSEIR;QLS(0.939)S(0.059)GVS(0.002)EIR;QLS(0.945)S(0.051)GVS(0.003)EIR;QLS(0.953)S(0.047)GVS(0.001)EIR;QLS(0.498)S(0.498)GVS(0.003)EIR;QLS(0.951)S(0.048)GVS(0.001)EIR;QLS(0.75)S(0.25)GVSEIR;QLS(0.945)S(0.055)GVSEIR;QLS(0.972)S(0.026)GVS(0.001)EIR;QLS(0.963)S(0.037)GVS(0.001)EIR;QLS(0.977)S(0.022)GVSEIR;QLS(0.976)S(0.024)GVSEIR;QLS(0.978)S(0.022)GVSEIR;QLS(0.967)S(0.033)GVSEIR;QLS(0.959)S(0.04)GVS(0.001)EIR;QLS(0.8)S(0.2)GVS(0.001)EIR;QLS(0.909)S(0.091)GVS(0.001)EIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.493)S(0.493)GVS(0.013)EIR;QLS(0.5)S(0.5)GVSEIR;QLS(0.693)S(0.304)GVS(0.003)EIR;QLS(0.477)S(0.477)GVS(0.046)EIR;QLS(0.499)S(0.499)GVS(0.001)EIR 219.16 6.76E-09 3.51898E+11 16701586 19454399 20387683 18293679 22884989 23563751 21347972 21617426 22534958 20587381 TRUE FALSE 17360977.51 22795540.69 20919002.77 21912114.11 18995006.74 18091426.94 19674662.17 21327679.76 21723929.26 24621084.14 0.705126444 0.925854465 0.84963776 0.889973568 0.771493515 0.734794083 0.799098125 0.866236419 0.882330329 1 24.55339095 0.932929074 1.422110522 0.998134004 0.817320206 0.441292153 0.064128391 0.478057487 1.945969428 0.061248534 0.018232172 8.568978903 -0.932929074 -0.180813798 QLS(ph)TEQAVLQESLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSTEQAVLQESLEK 15 0 Q9ULD2;Q9ULD2-2;Q9ULD2-4;Q9ULD2-7;Q9ULD2-3;Q9ULD2-6 Q9ULD2 MTUS1 Microtubule-associated tumor suppressor 1 1 QLS(0.879)T(0.121)EQAVLQESLEK;QLS(0.959)T(0.041)EQAVLQESLEK 223.18 1.37E-12 72998000 50693 54894 52378 47037 51926 69345 52583 53388 62740 63722 TRUE FALSE 52694.39878 64321.61748 53743.01371 56340.77821 43099.63707 53240.67468 48461.40706 52672.42119 60481.99966 76207.10587 0.691463062 0.844037006 0.70522313 0.739311349 0.565559295 0.698631369 0.63591717 0.691174669 0.793653019 1 16.21763791 0.896876328 2.868590743 0.999676792 0.695751493 0.656451345 0.066855713 0.25570993 4.530843231 0.066042395 0.017419643 7.886355096 -0.896876328 -0.303925299 QLSES(ph)ESSLEMDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSES(0.713)ES(0.254)S(0.032)LEMDDER;QLS(0.001)ES(0.999)ESSLEMDDER 252.82 4.62E-24 406460000 472210 504920 571450 734120 640180 771200 749300 718240 668740 647200 TRUE FALSE 490853.2154 591636.0823 586342.4565 879326.7449 531362.4323 592100.4876 690567.9081 708613.1676 644672.178 774006.4486 0.634171997 0.764381335 0.757542082 1.136071601 0.686509051 0.764981337 0.892199166 0.915513261 0.832902851 1 19.56198606 4.310829129 2.147120236 0.876413675 0.656957491 0.293068535 0.120612204 0.450655112 3.836098249 0.031004031 0.13604008 20456.39634 -4.310829129 -0.219456184 QLSES(ph)ESSLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSES(0.881)ES(0.073)S(0.046)LEMDDERYFNEMSAQGLRPR;QLS(0.129)ES(0.517)ES(0.179)S(0.152)LEMDDERY(0.004)FNEMS(0.02)AQGLRPR;QLS(0.051)ES(0.948)ES(0.001)SLEMDDERYFNEMSAQGLRPR;QLS(0.172)ES(0.585)ES(0.172)S(0.071)LEMDDERYFNEMSAQGLRPR;QLS(0.001)ES(0.912)ES(0.071)S(0.016)LEMDDERYFNEMSAQGLRPR;QLS(0.005)ES(0.935)ES(0.027)S(0.034)LEMDDERYFNEMSAQGLRPR;QLS(0.319)ES(0.465)ES(0.108)S(0.108)LEMDDERYFNEMSAQGLRPR 382.12 3.27E-129 1383050000 138050.3 157888.1 173623 138138.6 163710.9 209849.6 164177.5 169079.7 181088.1 194347.6 TRUE FALSE 143500.6324 185004.153 178147.758 165462.0028 135883.3797 161115.2107 151308.8386 166813.4632 174570.7747 232426.2912 0.617402755 0.795969131 0.766469908 0.711890217 0.584629987 0.693188408 0.650997087 0.717704793 0.751080154 1 17.82641374 0.659384235 1.693116301 0.999859702 0.69308462 0.702830011 0.059940155 0.779722046 3.104779442 0.058746533 0.016668988 4.564405658 -0.659384235 -0.306775083 QLSESES(ph)SLEMDDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSESESSLEMDDER 15 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSES(0.013)ES(0.644)S(0.343)LEMDDER 161.19 1.75E-06 69596000 52930 49275 52603 68130 57640 66270 56306 61375 48063 45675 TRUE FALSE 55019.71727 57737.59794 53973.87739 81605.91065 47842.37339 50879.79683 51892.58859 60552.36851 46333.22202 54624.14175 1.007241771 1.056997805 0.98809566 1.493953187 0.875846683 0.931452563 0.949993665 1.108527596 0.848218764 1 15.73725109 QLSESES(ph)SLEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLS(0.007)ES(0.026)ES(0.511)S(0.445)LEMDDERY(0.001)FNEMS(0.009)AQGLRPR 48.085 0.084946 77186000 32146 35889 40365 23989 37446 42828 38653 37840 33047 34724 TRUE FALSE 33415.1489 42052.65657 41416.94506 28733.9526 31080.9423 32881.84606 35623.27686 37332.81669 31857.64493 41527.50297 0.804651051 1.012645923 0.997337718 0.691925845 0.748442359 0.791808891 0.857823715 0.898990164 0.76714569 1 15.34177951 3.763869885 24.84085635 0.820879681 0.945655001 0.233146327 0.096020794 985.6325127 967387.334 0.024590053 0.044309826 5805.904458 -3.763869885 0.12477532 QLSESESS(ph)LEMDDERYFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSESES(0.01)S(0.989)LEMDDERYFNEMS(0.001)AQGLRPR 145.01 7.76E-08 537370000 16876 37814 34832 24941 33613 40107 34171 30162 35099 43864 TRUE FALSE 17542.27751 44308.26035 35739.75053 29874.25536 27899.47427 30792.75708 31492.58773 29757.72773 33835.79385 52458.31097 0.334404162 0.844637571 0.681298156 0.569485651 0.53184088 0.586994825 0.600335526 0.567264313 0.645003494 1 15.67888374 0.824395847 4.967112681 0.99999734 0.597608781 0.509972482 0.119781085 2.090938732 58.64348042 0.108332808 0.027390113 6.674148216 -0.824395847 -0.402388559 QLSESESSLEMDDERYFNEMS(ph)AQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSESESSLEMDDERYFNEMSAQGLRPR 28 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 QLSESES(0.01)S(0.01)LEMDDERYFNEMS(0.98)AQGLRPR 138.84 1.14E-06 150680000 25922 38336 48659 42642 46902 56439 33661 42976 55402 61825 TRUE FALSE 26945.42058 44919.90979 49927.09351 51076.46033 38929.61479 43331.89759 31022.56286 42399.97701 53408.09284 73938.42504 0.364430546 0.607531331 0.675252326 0.690797245 0.526513985 0.586053836 0.419572947 0.573449827 0.722332033 1 16.17403669 0.92947339 2.666788685 0.998973547 0.559388952 0.669792023 0.09624479 0.203862469 3.302970877 0.093789665 0.025011145 8.501066033 -0.92947339 -0.439584595 QLSILVHPDKNQDDADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSILVHPDKNQDDADR 17 1 O75937 O75937 DNAJC8 DnaJ homolog subfamily C member 8 0 ; 208.34 3.16E-12 574640000 699980 689790 728360 617800 825600 927880 712880 753210 833170 649460 FALSE TRUE 727615.7509 808256.0667 747341.66 739998.9961 685264.8069 712393.9322 657002.6028 743114.452 803184.3745 776709.2523 0.936792949 1.040615989 0.962189722 0.952736167 0.882266826 0.917195115 0.845879717 0.956747264 1.034086271 1 19.56701513 5.100339866 19.15943332 0.947989862 0.000236834 0 0.058900269 4925.448192 898052.8472 0.014246381 9182.978087 125991.0995 -5.100339866 -0.947753027 QLSLARPQAPALHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSLARPQAPALHLR 15 1 Q99988 Q99988 GDF15 Growth/differentiation factor 15 0 103.66 0.00087443 510110000 155040 252590 164970 190240 217870 221610 139930 213470 207760 287670 FALSE TRUE 161161.0989 295970.3676 169269.2537 227868.9042 180836.5352 170144.436 128961.921 210608.7838 200282.7582 344033.4287 0.468446045 0.860295375 0.492013972 0.662345241 0.525636523 0.494557859 0.374852878 0.612175348 0.582160748 1 18.39218923 0.438010421 2.067065598 0.999981143 0.56271348 0.524211519 0.124902156 5.722671363 20.0321817 0.116977827 0.032006526 2.741639957 -0.438010421 -0.437267663 QLSQQSDGDRDLQEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSQQSDGDRDLQEHR 16 1 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 0 171.56 2.93E-09 511940000 87286 115010 96186 110850 106640 136270 93921 94537 104820 143190 FALSE TRUE 90732.11868 134762.0728 98692.68618 132775.7991 88513.37089 104623.3577 86559.2266 93269.88615 101047.5487 171245.339 0.529837012 0.786953231 0.576323343 0.775354237 0.516880468 0.610955944 0.505469096 0.544656495 0.590074739 1 17.3857052 -1.724624091 6.061858014 1.008508845 0.602661828 0.610044478 0.094963084 0.010792706 0.000490287 0.090873703 0.021266212 0.018852802 1.724624091 -0.405847018 QLSS(ph)GVSEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.08)S(0.92)GVSEIR;QLS(0.079)S(0.92)GVS(0.001)EIR 225.1 3.84E-09 1.2087E+11 6399500 7602700 7822900 6856500 8660500 9920600 8503900 8164800 8773400 8276700 TRUE FALSE 6652157.201 8908404.584 8026771.201 8212695.235 7188391.303 7616690.998 7837342.097 8055364.211 8457647.048 9898360.898 0.672046339 0.899987854 0.81091923 0.829702546 0.726220369 0.769490128 0.791781809 0.813807891 0.85444925 1 23.23875821 0.774556171 1.374197953 0.99975451 0.790110977 0.560002207 0.057112231 0.563661054 1.873477009 0.051653858 0.015358101 5.950537154 -0.774556171 -0.209643533 QLSSGVS(ph)EIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLS(0.02)S(0.127)GVS(0.853)EIR 96.551 0.0055097 0 519540 723360 570740 548870 605630 696720 553340 673880 590400 672950 TRUE FALSE 540051.8404 847591.453 585613.9533 657434.8478 502685.2289 534917.3389 509967.7649 664847.7408 569151.6193 804801.6681 0.671037178 1.053168112 0.727650024 0.816890513 0.624607588 0.664657344 0.633656446 0.826101345 0.70719488 1 19.61827377 QLSSGVSEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;; 268.69 9.84E-18 15347900000 6663087 8258950 7685080 7834830 8024210 9169390 7644050 7868090 7746200 8534870 FALSE TRUE 6926150.82 9677360.417 7885359.498 9384535.989 6660257.65 7039938.136 7044889.387 7762631.123 7467415.775 10207114.37 0.678561107 0.948099538 0.772535627 0.919411271 0.652511318 0.68970895 0.690194029 0.76051182 0.731589312 1 23.28307173 5.034958651 17.67151646 0.780307994 0.25669411 0.072055904 0.114566493 36943856.58 473443104.3 0.026518051 618127018.9 108382.3719 -5.034958651 -0.523613884 QLSSGVSEIRHT(ph)ADRWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLSSGVSEIRHTADRWR 17 2 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 QLSSGVSEIRHT(1)ADRWR 192.27 9.35E-09 107620000 41066 63026 55731 36651 57875 65682 50145 43903 54740 60470 TRUE FALSE 42687.31739 73850.22523 57183.39564 43900.45841 48037.42817 50428.35092 46214.50387 43314.5521 52769.91809 72317.93873 0.590272872 1.021188194 0.790722145 0.607047977 0.664253282 0.69731455 0.639046199 0.598946165 0.729693338 1 16.14206594 5.03228225 16.93067165 0.724204794 0.11883629 0.075020108 0.144810744 16156858.32 225066500.6 0.034810392 289056747.4 107716.504 -5.03228225 -0.605368504 QLSSTS(ph)PLAPYPTSQMVSSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QLSSTSPLAPYPTSQMVSSDR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 QLS(0.001)S(0.011)T(0.096)S(0.891)PLAPYPTSQMVSSDR;QLSST(0.001)S(0.999)PLAPYPTSQMVSSDR;QLSST(0.002)S(0.998)PLAPYPTSQMVSSDR;QLSSTS(1)PLAPYPTSQMVSSDR 291.08 1.05E-54 1218360000 639660 770930 677870 725440 683880 885160 627120 757130 699350 837310 TRUE FALSE 664914.2707 903331.2305 695535.8491 868929.8668 567634.3219 679595.0047 577964.6957 746981.9108 674180.5301 1001364.863 0.664007991 0.902099987 0.694587832 0.867745513 0.566860635 0.678668715 0.577176928 0.745963772 0.67326162 1 19.93353631 -1.096481508 3.426521101 1.000229654 0.709771013 0.420388411 0.102900891 19865123.31 33082513.15 52483.64406 0.024411936 0.080078972 1.096481508 -0.290458642 QLT(ph)QPETHFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 164.7 8.27E-05 7265030000 2038840 2504650 3369000 2567430 3542650 3169990 2958850 2912660 3438120 2299070 TRUE FALSE 2119334.978 2934804.154 3456798.908 3075259.991 2940471.618 2433807.864 2726927.605 2873620.557 3314382.733 2749528.748 0.770799352 1.067384422 1.25723323 1.118468026 1.069445672 0.885172729 0.991779994 1.045132028 1.205436653 1 21.39075294 -1.268831578 4.156078596 0.999956032 1.048076679 0.00997494 0.13449587 5.51E-05 9.69E-06 0.130846475 0.030812635 0.053847857 1.268831578 0.048120648 QLT(ph)QPETHFGREPAAAISRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 202.58 3.01E-20 537980000 193966 153955 186412 100262 244140 201850 121176 146057 204352 230190 TRUE FALSE 201623.9275 180395.5736 191270.0499 120093.5243 202641.17 154973.3966 111677.9085 144099.3448 196997.4114 275291.3232 0.732402043 0.655289718 0.694791422 0.436241589 0.736097192 0.562943266 0.405671734 0.523443104 0.715596151 1 18.07059961 0.927254673 4.576352358 0.999857023 0.585951704 0.558049138 0.10961715 0.267684019 14.16692743 0.108977484 0.027657134 8.457746669 -0.927254673 -0.413905319 QLTEMLPSILNQLGADS(ph)LTSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLTEMLPSILNQLGADSLTSLRR 23 1 P20290-2;D6RDG3;H0Y9Y1;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 1 QLTEMLPSILNQLGADS(0.982)LT(0.018)SLRR;QLTEMLPSILNQLGADS(0.996)LT(0.004)SLRR 204.86 1.01E-24 415860000 109936 175627 156978 117534 147592 177443 119001 146336 150576 190045 TRUE FALSE 114276.3582 205789.5711 161068.9756 140781.8744 122504.3646 136234.5524 109673.3907 144374.6053 145156.7992 227280.6791 0.502798384 0.905442433 0.708678697 0.619418575 0.539000345 0.599411058 0.482546036 0.635226038 0.638667571 1 17.79411552 -1.358603394 5.162422919 1.000182127 0.627150074 0.493762911 0.113694636 0.000242267 3.01E-05 0.111905616 0.026363654 0.043792184 1.358603394 -0.373032053 QLTEMLPSILNQLGADSLTSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLTEMLPSILNQLGADSLTSLRR 23 1 P20290-2;D6RDG3;H0Y9Y1;P20290 P20290-2;P20290 BTF3 Transcription factor BTF3 0 80.309 0.018117 205530000 135550 158530 178700 179950 215490 204190 147870 187060 173710 216480 FALSE TRUE 140901.6187 185756.2943 183357.0688 215543.5729 178861.0868 156769.967 136279.563 184552.7667 167458.211 258895.1112 0.544242099 0.717496338 0.708229166 0.832551731 0.69086313 0.605534675 0.526389094 0.712847631 0.646818745 1 17.9820082 -1.764909402 2.261973594 1.097274783 0.668924859 0.578612588 0.085707356 3197998.215 1981731.289 1725044.903 0.023274829 0.017182668 1.764909402 -0.428349924 QLTQPETHFGR ddPTM_MDA-MB-175_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 ;;; 174.23 1.13E-05 2736600000 1792410 1963910 1657990 2006840 1681120 2215990 1786520 1882520 1773100 1730690 FALSE TRUE 1863175.731 2301196.265 1701198.581 2403786.962 1395363.823 1701359.906 1646487.894 1857287.899 1709286.477 2069785.569 0.900178143 1.111804189 0.821920206 1.161370046 0.674158639 0.821998149 0.795487184 0.897333485 0.825827807 1 20.98104988 3.236562888 24.9999725 0.831953585 0.994252991 0.313671256 0.117972447 61.20046504 765878.1207 0.031114601 0.038997584 1724.101733 -3.236562888 0.162299407 QLVAGNS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLVAGNSPK 9 0 Q96EU6-2;Q96EU6 Q96EU6-2 RRP36 Ribosomal RNA processing protein 36 homolog 1 QLVAGNS(1)PK 95.094 0.0086832 80802000 384340 143080 179180 131410 231000 338070 249950 202940 195870 128550 TRUE FALSE 399514.04 167652.877 183849.578 157402.5058 191734.7025 259558.366 230358.2659 200219.9212 188820.677 153736.9113 2.598686527 1.090518052 1.195871418 1.023843295 1.247161147 1.688328222 1.498392702 1.30235426 1.228206521 1 17.23010406 4.74355665 24.98684441 1.278903098 2.598687075 0.800356632 0.201285371 240.9199189 1204882.337 0.051130992 0.427189901 55405.98122 -4.74355665 1.319783977 QLVARPDVVEMHDVTAQDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLVARPDVVEMHDVTAQDPK 20 1 Q13435;E9PPJ0 Q13435 SF3B2 Splicing factor 3B subunit 2 0 ;; 150.29 5.36E-08 409626000 663729 438669 486461 383577 610446 706700 608184 526197 563451 461645 FALSE TRUE 689933.5334 514006.9884 499138.5733 459447.3857 506682.607 542579.6351 560512.9489 519144.1899 543172.5086 552095.499 1.249663391 0.93101101 0.904080135 0.832188247 0.917744499 0.982764098 1.015246366 0.940315925 0.983837958 1 19.07455831 4.739830766 24.70730561 0.942117673 1.249663509 0.759775668 0.05132531 47.06465807 915392.5961 0.01325846 0.082537631 54932.67733 -4.739830766 0.307545836 QLVEILTTHCDSYWVEMASLQVFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QLVEILTTHCDSYWVEMASLQVFEK 25 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;A0A0G2JLQ8;F5H5B1;K7ELX1;K7EJ90;F5H7Q5 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 ;; 243.87 9.87E-39 119437000 127378 118773 144141 120883 158044 166259 154322 145051 151950 112290 FALSE TRUE 132406.9818 139171.3388 147897.4329 144793.2966 131179.7373 127647.8669 142225.8384 143106.8286 146481.3492 134291.0756 0.985970075 1.036340935 1.101319892 1.078204907 0.976831385 0.950531272 1.0590863 1.065646604 1.090775009 1 17.03500391 -1.070889208 4.69254534 0.999998266 1.039724819 0.051993176 0.048723397 9.39E-07 1.86E-07 0.050096069 0.011807241 0.084939714 1.070889208 0.039726554 QLVHELDEAEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QLVHELDEAEYR 12 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;; 203.93 1.19E-07 5823600000 2613744 2923532 2912732 3259482 2740750 3627376 3227140 3048300 2948230 2438491 FALSE TRUE 2716936.631 3425625.879 2988640.189 3904197.811 2274878.294 2784972.897 2974188.334 3007442.525 2842123.778 2916266.624 0.931648913 1.174661415 1.024817198 1.338765729 0.780065264 0.954978833 1.019861596 1.031264597 0.974576109 1 21.4756912 3.230329585 24.99993932 0.970235135 1.114939896 0.29739728 0.117843962 244.8573813 743699.8672 0.033050653 0.040145877 1699.532934 -3.230329585 0.144704761 QLVHELDEAEYRDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QLVHELDEAEYRDIR 15 1 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 107.98 0.00067002 24489000 23410 28746 27060 21862 26196 34565 19114 28226 26382 39348 FALSE TRUE 24334.24488 33682.90189 27765.20583 26186.23835 21743.21328 26537.80259 17615.79473 27847.67664 25432.51697 47057.48724 0.517117388 0.715781991 0.590027378 0.556473367 0.462056403 0.563944319 0.374346268 0.591779933 0.540456333 1 15.52213667 -0.277454002 1.992237805 1.000167915 0.546143873 0.72430191 0.084069432 194.0693995 297.4566802 0.356997212 0.022493472 0.527893115 0.277454002 -0.454024042 QLVYVEQAGSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLVYVEQAGSSPK 13 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 QLVYVEQAGS(0.067)S(0.933)PK;QLVYVEQAGS(0.008)S(0.992)PK 163.26 4.10E-05 352070000 992870 471580 494050 422500 752660 979690 689720 602700 578270 414120 TRUE FALSE 1032069.274 552570.1966 506925.3489 506069.239 624723.122 752171.8448 635657.9442 594621.7923 557458.1757 495258.8852 2.083898553 1.115719906 1.023556294 1.021827683 1.261407197 1.518744776 1.283486199 1.200628217 1.125589449 1 18.91782333 4.741394957 24.92188111 1.188388665 2.083898891 0.769528772 0.149428009 129.1144595 1135220.125 0.038598778 0.268432975 55130.88408 -4.741394957 0.895510226 QLWGLLIEETEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QLWGLLIEETEKR 13 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 198.33 2.03E-07 576190000 603880 491040 585160 489260 739850 776630 656180 560710 725740 533060 FALSE TRUE 627721.6487 575372.3002 600409.7503 586034.1677 614090.5613 596269.4524 604746.897 553194.5996 699620.7592 637502.9009 0.984656929 0.902540678 0.94181493 0.9192651 0.963274928 0.935320375 0.948618267 0.867752286 1.097439334 1 19.28207238 1.234413207 24.99999994 1.048719676 0.930515697 0.603348606 0.037521414 67.93640716 409483.9769 0.030126802 0.008590095 17.1558882 -1.234413207 -0.118203979 QMDTVLSS(ph)SPDVLFDPINGLTPDEEALSNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDT(0.002)VLS(0.082)S(0.518)S(0.398)PDVLFDPINGLTPDEEALSNER 115.18 3.83E-05 48821000 14922 14679 13134 15296 15018 18518 13654 16292 14411 18778 TRUE FALSE 15511.13208 17200.00406 13476.28283 18321.50315 12465.24572 14217.47514 12583.7638 16073.63239 13892.35093 22457.18957 0.690697829 0.765901896 0.600087682 0.815841318 0.555067039 0.63309236 0.560344551 0.7157455 0.618614848 1 14.45488977 -1.02064519 5.508656329 1.000001358 0.662945832 0.607601707 0.081552087 1.29E-06 2.29E-07 0.074688552 0.017604189 0.09535749 1.02064519 -0.337055526 QMDTVLSSS(ph)PDVLFDPINGLTPDEEALSNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QMDTVLSSSPDVLFDPINGLTPDEEALSNER 31 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 QMDT(0.001)VLS(0.157)S(0.126)S(0.715)PDVLFDPINGLTPDEEALSNER;QMDTVLS(0.029)S(0.136)S(0.834)PDVLFDPINGLTPDEEALSNER;QMDT(0.001)VLS(0.012)S(0.049)S(0.938)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.004)S(0.996)PDVLFDPINGLTPDEEALSNER;QMDTVLSS(0.001)S(0.999)PDVLFDPINGLTPDEEALSNER 205.42 4.34E-26 308976000 155016 205735 175957 181495 188836 233547 166924 196702 190404 210163 TRUE FALSE 161136.1514 241068.3859 180542.584 217394.1693 156737.7242 179309.2487 153840.0607 194065.5314 183551.3972 251340.416 0.641107204 0.959131005 0.718318951 0.864939164 0.623607324 0.71341192 0.612078484 0.772122265 0.730290019 1 17.93928315 -1.155109528 3.282339634 1.000437374 0.739801409 0.370226425 0.102768036 17470973.63 26734534.32 80719.84345 0.023907257 0.069966552 1.155109528 -0.260635966 QMEDGHTLFDYEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QMEDGHTLFDYEVR 14 0 A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WVR3 UHRF1 E3 ubiquitin-protein ligase UHRF1 0 151.72 6.86E-06 88274000 100460 115550 109800 103720 105590 145050 115630 120360 116230 136950 FALSE TRUE 104426.2384 135394.8136 112661.4782 124235.5064 87641.84952 111364.3358 106566.6185 118746.7711 112046.905 163782.7304 0.637590044 0.826673321 0.687871535 0.758538499 0.535110443 0.679951638 0.650658456 0.725026202 0.684119166 1 17.32142372 -1.334921633 4.817137433 1.000194021 0.689814348 0.623903613 0.072815249 0.000147308 2.03E-05 0.068450161 0.016123848 0.046246446 1.334921633 -0.310379672 QMEKDETVSDCSPHIANIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QMEKDETVSDCSPHIANIGR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;;;; 289.96 1.17E-54 3316830000 2407470 2413606 2732670 2123837 3254630 3518350 2766570 2817570 3251450 2552950 FALSE TRUE 2502518.775 2828124.055 2803885.625 2543925.62 2701409.155 2701266.534 2549719.014 2779805.083 3134430.95 3053151.673 0.819650984 0.926296613 0.918357791 0.833212985 0.884793631 0.884746918 0.835110498 0.910470681 1.026621434 1 21.54186783 1.346180263 4.050609602 1.013296451 0.875193831 0.726017007 0.034167043 0.109383518 2.822126259 0.025515244 0.008480305 22.19117319 -1.346180263 -0.13810262 QMEQISQFLQAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QMEQISQFLQAAER 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 127.71 0.00018135 19024000 17588 20487 16790 18995 24247 26820 17263 18256 18755 22239 FALSE TRUE 18282.38782 24005.48288 17227.56119 22752.15431 20125.5036 20591.46146 15909.88095 18011.30818 18080.01121 26596.30626 0.687403267 0.902587098 0.647742624 0.855462939 0.756702957 0.774222603 0.598198893 0.677210888 0.679794068 1 14.69893828 QMGFPLIYVEAEQVEDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QMGFPLIYVEAEQVEDDR 18 0 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ; 135.58 1.88E-05 58684000 31637 37227 36038 44608 36104 40536 38010 39494 34907 34177 FALSE TRUE 32886.05319 43620.44766 36977.17989 53431.32926 29967.05498 31122.12833 35030.67688 38964.64753 33650.70389 40873.32879 0.804584656 1.067210549 0.904677475 1.307241931 0.733168936 0.761428767 0.857054659 0.953302525 0.823292472 1 15.31887212 QMGFPLIYVEAEQVEDDRLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QMGFPLIYVEAEQVEDDRLLR 21 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;;;; 194.92 1.78E-18 324682000 99558 145114 132256 117775 159553 158607 106496.2 134968 140885 175542 FALSE TRUE 103488.6267 170036.2007 135702.7 141070.5435 132432.2381 121772.928 98148.74957 133158.9747 135814.5764 209936.0939 0.492952997 0.809942671 0.646400042 0.671968983 0.630821673 0.580047602 0.46751727 0.634283377 0.646932949 1 17.6795907 0.624186623 2.823547351 0.999987931 0.6191454 0.618144044 0.089847701 3.10677267 22.55019032 0.086112201 0.022653821 4.209074594 -0.624186623 -0.380842531 QMGYTEAIEVIQAASS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QMGYTEAIEVIQAASSPVK 19 0 P19838;P19838-2;P19838-3 P19838 NFKB1 Nuclear factor NF-kappa-B p105 subunit;Nuclear factor NF-kappa-B p50 subunit 1 QMGYTEAIEVIQAAS(0.201)S(0.799)PVK;QMGYTEAIEVIQAAS(0.155)S(0.845)PVK 171 1.17E-11 47656000 195407 122559 139175 123851 159367 186016 165551 147597 154610 112258 TRUE FALSE 203121.8192 143607.5549 142802.0148 148348.3581 132277.8543 142816.6031 152574.68 145618.7036 149045.6163 134252.8058 1.512980068 1.069680101 1.063679928 1.104992609 0.985289309 1.063788591 1.136472934 1.084660412 1.11018623 1 17.03459271 4.73884238 25 1.073245911 1.512980199 0.899627813 0.044491998 6.501888515 576618.6447 0.010491605 0.061584875 54807.80134 -4.73884238 0.439734288 QMIAVADENQNHHLEPEEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QMIAVADENQNHHLEPEEVLK 21 0 A0A5F9UP49;Q9BRK5;Q9BRK5-2;Q9BRK5-5 A0A5F9UP49 SDF4 45 kDa calcium-binding protein 0 91.811 0.0011336 112100000 54144 41276 40892 38068 59407 57002 47282 44027 48890 42614 FALSE TRUE 56281.64693 48364.83192 41957.67911 45597.73678 49309.01936 43764.14937 43575.91329 43436.89008 47130.45845 50963.39741 1.104354297 0.949011141 0.823290464 0.894715406 0.967537917 0.85873689 0.855043335 0.852315432 0.924790356 1 15.63717384 4.667506643 3.236953124 0.888619811 1.119510727 0.574958271 0.052951994 0.180001103 3.055762989 0.012483814 0.093287713 46505.74899 -4.667506643 0.230890916 QMKDKQDEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QMKDKQDEEQR 11 2 P27797;K7EL50 P27797 CALR Calreticulin 0 73.881 0.023817 74119000 84169 131750 128060 106470 176800 177270 85310 122860 117310 160170 FALSE TRUE 87492.05711 154377.0376 131397.3488 127529.4482 146747.5992 136101.7291 78623.17928 121213.2627 113088.036 191552.2449 0.456752972 0.805926538 0.685960892 0.665768487 0.766096995 0.710520146 0.410452925 0.632794791 0.590376981 1 17.54737841 -1.31064842 5.849372699 1.00003351 0.639052546 0.459870529 0.118282866 5.12E-05 6.03E-06 0.113457162 0.026739633 0.048904811 1.31064842 -0.360980964 QMKEMELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QMKEMELLR 9 1 Q6ZUX3 Q6ZUX3 FAM179A Protein FAM179A 0 ; 81.594 0.019006 835240000 433370 584220 548830 527630 731690 674130 550500 590890 608340 754750 FALSE TRUE 450479.7822 684555.2404 563132.9607 631993.6392 607317.5952 517573.524 507350.3715 582970.0861 586445.9622 902628.8119 0.499075341 0.758401717 0.623880994 0.700170027 0.672832051 0.573406828 0.562080852 0.645858052 0.649708889 1 19.7837733 0.469266672 2.378951449 0.999996387 0.633019703 0.715824378 0.06969421 4.703920683 20.37697616 0.063803964 0.017121853 2.946230164 -0.469266672 -0.366976683 QMNMS(ph)PPPGNAGPVIMSIEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QMNMSPPPGNAGPVIMSIEEK 21 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 1 QMNMS(1)PPPGNAGPVIMSIEEK;QMNMS(1)PPPGNAGPVIMSIEEK;QMNMS(1)PPPGNAGPVIMSIEEK;QMNMS(1)PPPGNAGPVIMSIEEK 170.87 2.56E-11 404488000 606380 475453 547638 405713 607471 699250 566706 557509 627770 498185 TRUE FALSE 630320.3506 557108.3542 561909.8962 485961.8205 504213.2964 536859.7847 522286.1029 550036.5038 605176.6803 595794.8124 1.057948706 0.935067481 0.943126534 0.81565299 0.846286819 0.90108167 0.876620763 0.923197873 1.01574681 1 19.18445604 -0.365502283 8.406409465 0.999999996 0.916898062 0.090880588 0.069161433 0 0 0.067916323 0.016008031 0.431020293 0.365502283 -0.083101934 QMNPHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QMNPHIR 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;;; 154.46 0.0016769 870825000 781166 1090429 938920 908678 1237092 1258913 792342 973980 899957 1501127 FALSE TRUE 812007.0369 1277701.698 963389.0265 1088411.796 1026811.544 966549.5348 730236.1636 960925.3912 867567.7234 1795244.095 0.4523101 0.711714748 0.536634004 0.606275102 0.571962078 0.538394493 0.40676149 0.535261692 0.483258921 1 20.77574859 -1.335057386 3.247305828 1.003184594 0.540027632 0.751188841 0.079748867 28654600.23 38202798.05 869327.9913 0.019676819 0.046231993 1.335057386 -0.463156962 QMQVLHPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QMQVLHPAAR 10 0 P50991 P50991 CCT4 T-complex protein 1 subunit delta 0 ;;;;;; 86.898 0.013244 1310490000 1528699 1392918 1521013 1175370 1959364 1976187 1466724 1505895 1623257 1540915 FALSE TRUE 1589053.217 1632140.831 1560651.848 1407854.678 1626312.007 1517247.519 1351758.34 1485710.941 1564836.298 1842827.792 0.862290673 0.885671921 0.846878832 0.763964318 0.882508943 0.82332572 0.733523961 0.806212576 0.8491495 1 20.81348983 4.000026092 21.42231892 0.821733955 0.872054969 0.010460234 0.069185647 0.393898473 302886.1299 0.01624892 0.034333275 10000.60082 -4.000026092 0.050321014 QMVEHGGFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QMVEHGGFYR 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 143.24 3.43E-05 559470000 315660 358670 363740 365290 320050 436200 369060 325440 361350 379590 FALSE TRUE 328122.5005 420268.7824 373219.3632 437543.2717 265648.0153 334899.1607 340132.1128 321078.0091 348345.0841 453963.3928 0.722795066 0.925776812 0.822135373 0.963829416 0.585174971 0.737722834 0.74925009 0.707277314 0.767341794 1 18.79221644 3.25426536 24.99999944 0.739549609 0.860822969 0.147930043 0.113558409 359.4583831 572209.57 0.028983148 0.039110778 1795.830568 -3.25426536 0.12127336 QMVIDVLHPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 ; 114.82 0.0012066 1763630000 2476500 2203530 2481800 2074200 2945800 2862300 2496700 2751000 2706500 2411200 FALSE TRUE 2574274.132 2581969.136 2546477.747 2484470.569 2445073.968 2197574.204 2301002.13 2714127.345 2609093.594 2883628.475 0.892720458 0.895388972 0.88308108 0.861577901 0.847915739 0.762086456 0.797953741 0.941219498 0.904795336 1 21.45945387 1.276478401 1.642519684 0.982355792 0.851505375 0.483104843 0.046123667 0.3237953 1.582842195 0.046528352 0.014054306 18.9007223 -1.276478401 -0.130850417 QNAQCLHGDIAQSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QNAQCLHGDIAQSQR 15 0 Q9BQ39;A0A087WVC1 Q9BQ39 DDX50 ATP-dependent RNA helicase DDX50 0 90.754 0.0058921 31093000 24094 27328 25074 24803 21629 30077 21536 28202 26573 22554 FALSE TRUE 25045.24972 32021.37142 25727.44904 29708.95937 17952.51031 23092.07257 19847.95205 27823.99832 25616.64292 26973.02448 0.928529529 1.187162806 0.95382144 1.101432262 0.665572758 0.856117288 0.735844512 1.03154907 0.949713405 1 14.71922968 3.290312466 24.99999215 0.875231922 1.046701777 0.308399608 0.124345232 126.7427328 61225.15719 0.034396411 0.046572907 1951.247977 -3.290312466 0.171469855 QNAVLQAAQDDLGHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QNAVLQAAQDDLGHLR 16 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ;; 152.94 4.99E-07 276191000 159840 310792 234991 293266 220865 336741 194510 255535 237612 293660 FALSE TRUE 166150.6066 364168.1084 241115.0585 351273.1395 183322.4462 258538.0061 179263.7979 252109.9713 229060.3905 351197.0545 0.47309795 1.036933834 0.686552052 1.000216645 0.52199312 0.736162228 0.510436507 0.717859014 0.652227539 1 18.42192122 QNEEFRPFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QNEEFRPFIR 10 1 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 0 ;; 81.625 0.01865 1083140000 423570 837720 651053 770902 598872 949540 542917 657712 527776 978420 FALSE TRUE 440292.8707 981591.8934 668019.976 923384.1147 497075.9514 729023.7254 500361.7469 648896.4464 508781.4449 1170122.666 0.376279243 0.83887948 0.57089739 0.789134457 0.424806703 0.623031881 0.42761478 0.554554206 0.434810349 1 20.15822835 -1.247690248 6.352701717 1.000007207 0.566516196 0.441412225 0.148326892 1.42E-05 1.68E-06 0.134571002 0.031718162 0.056534005 1.247690248 -0.433491011 QNGDDPLLTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 190.57 5.14E-06 1032610000 819380 923110 883000 898380 964080 1140270 941730 934330 888640 876450 FALSE TRUE 851729.7551 1081646.962 906011.7054 1076076.883 800206.026 875459.5735 867914.7418 921806.8346 856658.02 1048173.597 0.812584631 1.031934944 0.864371806 1.026620863 0.763428909 0.835223837 0.828025763 0.879440998 0.817286395 1 19.99944624 3.235967599 24.99999978 0.847549224 0.935917383 0.176206348 0.083999843 101.3181854 976839.3138 0.021858503 0.027287369 1721.740116 -3.235967599 0.088368159 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QNGSNDSDRYSDNEEDSKIELK 22 2 P42167;G5E972;H0YJH7;P42167-3;P42167-2 P42167;P42167-2 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGSNDS(0.003)DRYS(0.996)DNEEDS(0.001)KIELK;QNGS(0.001)NDS(0.004)DRYS(0.995)DNEEDSKIELK;QNGSNDSDRYS(1)DNEEDSKIELK;QNGS(0.001)NDS(0.009)DRY(0.011)S(0.976)DNEEDS(0.002)KIELK 190.79 8.64E-18 1209411000 1328656 551606 708947 589723 1027779 1201036 1094053 762300 873000 488989 TRUE FALSE 1381112.365 646340.0396 727422.7412 706368.4493 853077.4927 922113.5909 1008298.267 752082.6154 841580.9005 584797.0323 2.361695235 1.105238235 1.243889249 1.207886515 1.458758245 1.576809628 1.724184993 1.28605751 1.43909913 1 19.15757646 0.51396102 1.189265444 1.000800979 1.47467447 0.158517625 0.339663878 3.595531518 6.761094189 0.311281889 0.094634063 3.26558521 -0.51396102 0.473873491 QNGSNDSDRYS(ph)DNEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QNGSNDSDRYSDNEEGK 17 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK;QNGSNDSDRYS(1)DNEEGK 233.85 2.45E-20 612840000 913970 419458 606854 542389 736440 878570 938090 647900 645880 318622 TRUE FALSE 950054.2413 491496.6486 622669.1138 649671.9253 611260.1918 674535.4324 864560.0546 639215.9603 622634.905 381049.8805 2.493254269 1.289848583 1.634088201 1.704952445 1.604147444 1.770202451 2.268889452 1.677512559 1.633998426 1 18.53962034 4.757092662 24.30609996 1.67827721 2.493255306 0.401217853 0.312782767 2959.57097 3881596.572 0.072209849 2.394151723 57160.05813 -4.757092662 0.814978095 QNGSNDSDRYS(ph)DNEEGKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QNGSNDSDRYSDNEEGKKK 19 3 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 QNGSNDS(0.001)DRYS(0.999)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDS(0.005)DRYS(0.994)DNEEGKKK;QNGSNDS(0.001)DRYS(0.999)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK;QNGSNDSDRYS(1)DNEEGKKK 195.71 6.20E-16 1680300000 2097700 473144 871002 411048 1474600 1417040 1191780 845103 1144354 342406 TRUE FALSE 2180518.816 554402.8015 893701.0277 492352.0675 1223948.019 1087953.935 1098365.169 833775.7766 1103168.923 409493.8999 5.324911595 1.353873163 2.182452603 1.202342862 2.988928575 2.656825744 2.682250382 2.036112813 2.693981335 1 18.64348244 7.999999984 0.057204023 7.31E-11 7.189677898 0.182895891 1.061926034 839.4686843 3.596343861 95.41771396 509.6896633 99999996.34 -7.999999984 7.189677898 QNLFQEAEEFLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 QNLFQEAEEFLYR 13 0 A0A087X1Z3;Q9UL46 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ;;;;;;;; 257.09 1.60E-23 2538951000 754189 1016521 836169 929380 934728 1131941 760865 912251 894708 1080722 FALSE TRUE 783964.9641 1191100.574 857960.2511 1113208.59 775843.2684 869064.8575 701226.4131 900023.7675 862507.6339 1292468.784 0.606563945 0.92157009 0.663815066 0.861304044 0.600280083 0.672406845 0.542548046 0.696360159 0.667333435 1 20.30169801 -1.077361057 3.707103647 1.000114286 0.693628992 0.412468806 0.110104508 32277349.24 59268735.08 46705.70389 0.025829774 0.083683328 1.077361057 -0.306485294 QNLLSQSHAYQQFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QNLLSQSHAYQQFLR 15 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 174.62 9.03E-07 449030000 78767 156100 124690 137530 125660 161070 115330 127970 115580 161050 FALSE TRUE 81876.78198 182908.9607 127939.5238 164733.0235 104300.3581 123663.9335 106290.1332 126254.7715 111420.2984 192604.664 0.4251028 0.94966008 0.664259739 0.855290937 0.54152561 0.64206095 0.551856487 0.655512535 0.578492213 1 17.55528311 -1.079195768 4.558716835 1.000020382 0.658629095 0.341608519 0.144831247 2.98E-05 6.02E-06 0.131225007 0.030928071 0.083330547 1.079195768 -0.341391287 QNLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNLNDR 6 0 K7EMD9 K7EMD9 KRT13 0 ; 117.6 0.052539 398060000 525610 577410 613470 648380 263760 557910 543930 626320 617200 182747 FALSE TRUE 546361.4887 676575.6759 629457.5322 776627.6288 218926.1694 428343.8577 501295.3453 617925.2049 594987.0926 218552.7757 2.499906427 3.095708456 2.880116851 3.553501556 1.001708483 1.959910398 2.29370386 2.827350066 2.722395497 1 17.73762218 3.266382548 24.99999947 2.131091817 3.004537262 0.37687036 0.634416981 280.0184564 251614.7646 0.181783099 0.246082483 1846.641315 -3.266382548 0.873445445 QNLWFANPGGSNS(ph)MPSQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QNLWFANPGGSNSMPSQSR 19 0 M0QZ22;Q5PRF9;M0QX45 M0QZ22 SAMD4B Protein Smaug homolog 2 1 QNLWFANPGGS(0.012)NS(0.971)MPS(0.009)QS(0.009)R 88.282 0.010092 41188000 97973 114620 96835 102420 108010 131630 89051 109680 108830 115810 TRUE FALSE 101841.0497 134305.0934 99358.59965 122678.3703 89650.49878 101060.9274 82070.94993 108209.919 104913.2296 138500.7522 0.735310445 0.969706599 0.717386715 0.885759596 0.647292505 0.729677823 0.592566817 0.781294811 0.757492128 1 17.07953429 6.142641829 11.17396109 0.769509192 0.393219144 0 0.125984463 0 0 0.026391984 0 1388806.784 -6.142641829 -0.376290048 QNPHDGVVT(ph)PAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.962)PS(0.038)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.983)PS(0.017)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.999)PS(0.001)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.974)PS(0.026)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(0.999)PAAS(0.947)PS(0.053)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVT(1)PAAS(0.997)PS(0.003)LPQPGLQMPGQWGPVQGGPQPSGQHR 305.05 1.07E-96 4605920000 183408.5 323144.1 298456 312156.7 301398 412054 254510.4 367951 289661.2 316790.6 TRUE FALSE 190649.6092 378641.5855 306234.0085 373900.3636 250166.4756 316360.7032 234561.2098 363019.2187 279236.35 378859.6527 0.503219617 0.999424411 0.808304622 0.986909957 0.660314377 0.835034032 0.61912428 0.958189177 0.737044306 1 18.53130398 -1.630477074 0.618474654 1.116798653 0.802257299 0.133373657 0.156921023 173.5547157 23.09397828 31.17906763 0.056074574 0.023416551 1.630477074 -0.314541353 QNPHDGVVTPAAS(ph)PSLPQPGLQMPGQWGPVQGGPQPSGQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNPHDGVVTPAASPSLPQPGLQMPGQWGPVQGGPQPSGQHR 41 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 QNPHDGVVTPAAS(0.991)PS(0.009)LPQPGLQMPGQWGPVQGGPQPSGQHR;QNPHDGVVTPAAS(0.815)PS(0.185)LPQPGLQMPGQWGPVQGGPQPSGQHR 265.29 7.64E-67 486170000 14284.6 27350.2 18614.9 12640 20525.3 38336 21378.1 15078.2 17469.9 22181.3 TRUE FALSE 14848.56704 32047.38409 19100.01959 15140.15427 17036.41684 29433.04499 19702.42866 14876.10139 16841.16171 26527.30105 0.559746618 1.20809064 0.720013678 0.570738585 0.642222019 1.109537866 0.7427227 0.560784581 0.634861484 1 14.69519028 1.999780063 24.99991914 0.675248617 0.809348884 0.001777135 0.229009463 23.23477166 2641235.55 0.085718511 0.062630296 99.94937047 -1.999780063 0.134100267 QNRDEVLDNLLAFVCDIRPEIHENYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNRDEVLDNLLAFVCDIRPEIHENYR 26 2 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 ; 195.3 1.41E-19 1005480000 415430 606650 459480 434120 499990 613520 391320 486510 484490 602100 FALSE TRUE 431831.4972 710837.4184 471454.4263 519987.6403 415001.8784 471039.278 360647.3159 479989.1292 467053.2995 720069.9671 0.599707691 0.987178262 0.654734189 0.722134881 0.576335491 0.654157651 0.500850379 0.666586792 0.648622107 1 19.45777757 -1.295172797 3.030972669 1.002422126 0.667866813 0.403929917 0.121060055 24786863.11 32696354.4 548517.9709 0.031430329 0.050678903 1.295172797 -0.334555313 QNS(ph)PAGNKENIKPNETSPSFSK ddPTM_MDA-MB-175_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 139.93 6.96E-08 201217000 444000 152716 278440 145188 385190 373500 366790 244310 331080 120527 TRUE FALSE 461529.4628 178943.785 285696.3751 173905.7531 319715.5414 286760.2854 338040.0414 241035.4241 319164.4955 144141.958 3.201909209 1.241441337 1.982048663 1.20648946 2.218060208 1.989429652 2.345188355 1.672208616 2.214237269 1 17.13713082 -1.080799931 7.590416501 0.999999919 1.959689214 0.230016909 0.54685371 8.47E-07 1.03E-07 0.479978213 0.11313194 0.083023315 1.080799931 0.959689294 QNS(ph)SSSDSGGSIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNSSSSDSGGSIVR 14 0 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 QNS(0.804)S(0.093)S(0.093)S(0.009)DSGGSIVR;QNS(0.456)S(0.456)S(0.067)S(0.021)DSGGSIVR 153.22 6.77E-06 176680000 424750 460720 474980 535210 555030 666600 616290 559360 516430 438470 TRUE FALSE 441519.458 539845.0761 487358.369 641072.9406 460686.1989 511792.2524 567983.5794 551862.6941 497843.7852 524379.8015 0.841984105 1.029492506 0.929399583 1.222535534 0.878535362 0.975995359 1.083153046 1.052410281 0.949395426 1 19.00025259 4.74082322 24.21210683 1.018381545 0.841984008 0.24346538 0.090290591 179.3110555 1918607.626 0.020443347 0.135304068 55058.35351 -4.74082322 -0.176397537 QNSPAGNKENIKPNET(ph)SPSFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QNSPAGNKENIKPNETSPSFSK 22 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 QNSPAGNKENIKPNET(0.89)S(0.109)PSFSK 105.46 0.024705 501240000 148670 60869 103990 70417 178570 143960 131020 117950 141120 54233 TRUE FALSE 154539.6064 71322.77725 106700.0648 84345.27243 148216.7352 110527.4717 120750.31 116369.0732 136041.1188 64858.918 2.382704047 1.099660301 1.645110158 1.300442176 2.285217512 1.704121425 1.861737966 1.794187704 2.097492881 1 15.98501734 3.270475728 24.99995172 1.827749649 1.573466075 0.033780934 0.44088629 536.8828248 420551.0026 0.111918379 0.151525607 1864.127992 -3.270475728 -0.254283574 QNTASPGS(ph)PVNSHLPGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNTASPGSPVNSHLPGSPK 19 0 Q8NDX1-2;Q8NDX1 Q8NDX1-2 PSD4 PH and SEC7 domain-containing protein 4 2 QNT(0.001)AS(0.013)PGS(0.987)PVNSHLPGS(1)PK;QNTAS(0.008)PGS(0.992)PVNSHLPGS(1)PK 167.06 9.88E-12 291370000 631730 316680 385890 286810 536710 690240 527040 452770 453630 256520 TRUE FALSE 656671.1882 371067.3266 395946.6104 343540.162 445480.2259 529942.2207 485729.2276 446701.3587 437303.9449 306780.1826 2.140526753 1.209554422 1.290652502 1.119825143 1.452115394 1.727433031 1.583313575 1.456095876 1.425463474 1 18.22684577 0.631518914 2.340581775 1.000051204 1.477721406 0.224815929 0.273651536 4.32630649 25.53412275 0.257833011 0.06943363 4.280740618 -0.631518914 0.477670201 QNVAYEYLCHLEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNVAYEYLCHLEEAK 15 0 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 168.64 1.24E-06 212480000 396570 247920 315390 290170 360550 447770 455480 339730 363580 163705 FALSE TRUE 412226.8898 290498.3315 323609.3225 347564.7599 299263.8398 343782.2035 419778.2874 335176.475 350494.8268 195779.8604 2.105563304 1.483800892 1.652924472 1.775283521 1.528573159 1.755963064 2.144134164 1.712006916 1.790249651 1 17.57887284 2.518466135 24.89872994 1.761959831 1.691749074 0 0.312974761 3361.243396 2024205.939 0.094713332 0.089287583 329.9636769 -2.518466135 -0.070210757 QNVAYEYLCHLEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QNVAYEYLCHLEEAKR 16 1 P46940;A0A0J9YXZ5;A0A087X225 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 206.74 1.25E-11 4491500000 5070200 4151400 4856900 3903300 6425100 6422300 5117600 5048400 5804000 3890400 FALSE TRUE 5270375.411 4864370.657 4983474.804 4675361.09 5332963.797 4930818.156 4716469.14 4980734.456 5595115.174 4652649.394 1.132768658 1.045505527 1.071104737 1.004881454 1.146220862 1.059787175 1.013716861 1.07051575 1.202565399 1 22.14962104 1.442009552 25 1.113035346 1.064877405 0.035898616 0.062189609 74.42713592 52999.76964 0.031339056 0.014384229 27.67002506 -1.442009552 -0.048157941 QPAIMPGQSYGLEDGSCSYKDFSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QPAIMPGQSYGLEDGSCSYKDFSESR 26 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;; 150.22 1.28E-07 465010000 115327 104151 123253 92290 152177 151610 108935 133893 134011 137867 FALSE TRUE 119880.199 122038.1241 126465.0744 110544.6865 126310.0079 116400.8752 100396.3901 132098.3833 129187.9703 164879.399 0.727078093 0.740165993 0.76701562 0.670457845 0.766075135 0.705975858 0.60890803 0.801181858 0.78353009 1 17.33105163 0.760650629 1.368424327 0.998762029 0.718436633 0.740762534 0.049649789 0.395595306 1.283006924 0.046163616 0.013730149 5.763026661 -0.760650629 -0.280325396 QPAQELS(ph)PTPGGTAHQALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPAQELSPTPGGTAHQALK 19 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 QPAQELS(0.966)PT(0.034)PGGTAHQALK;QPAQELS(0.996)PT(0.004)PGGTAHQALK 257.2 3.55E-31 1588830000 1046100 951430 1104400 939720 1317070 1433480 1219960 1109820 1170520 928400 TRUE FALSE 1087400.836 1114830.701 1133181.571 1125593.811 1093194.912 1100575.995 1124336.347 1094944.678 1128393.214 1110302.205 0.979373752 1.004078616 1.020606432 1.013772472 0.984592219 0.991240034 1.012639931 0.986168156 1.01629377 1 20.08252098 1.212539199 24.99995659 1.008146862 0.999684888 0.065175815 0.013602947 846.0827185 812847.6138 0.013080667 0.003274009 16.31320145 -1.212539199 -0.008461974 QPAQSQNLS(ph)PLSGFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPAQSQNLSPLSGFSR 16 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 QPAQSQNLS(0.998)PLS(0.002)GFSR;QPAQSQNLS(1)PLSGFSR;QPAQSQNLS(0.999)PLS(0.001)GFSR;QPAQSQNLS(0.999)PLS(0.001)GFSR 371.19 2.59E-104 5485200000 1797990 1908340 1804840 1899530 1908480 2219450 1754300 1878320 1879490 2045890 TRUE FALSE 1868976.034 2236082.55 1851875.613 2275251.364 1584077.251 1704016.374 1616793.382 1853144.193 1811847.522 2446742.975 0.763862838 0.913901694 0.756873784 0.929910247 0.647422826 0.696442737 0.660794125 0.757392261 0.740514039 1 21.22243113 -0.949179184 5.175831913 1.000000626 0.761960188 0.388784654 0.089134536 9.12E-07 1.85E-07 0.088296117 0.020811519 0.112414107 0.949179184 -0.238040438 QPASAQSTPSTTPHSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 QPASAQSTPSTTPHS(0.204)S(0.796)PK;QPASAQSTPSTTPHS(0.298)S(0.702)PK;QPASAQSTPSTTPHS(0.008)S(0.992)PK 232.02 3.06E-20 663840000 320171 266921 277626 252511 355062 433350 328586 282488 278968 205286 TRUE FALSE 332811.5983 312762.6054 284861.1616 302456.9221 294708.6881 332711.03 302830.5707 278701.7104 268927.9962 245507.8613 1.35560465 1.273941306 1.160293443 1.231964307 1.200404283 1.355195016 1.233486248 1.135204832 1.095394644 1 17.9054097 1.387654569 1.478124347 1.015390022 1.257191158 0.685890939 0.059433004 0.224972556 0.91862479 0.055907731 0.017774904 24.41487861 -1.387654569 0.241801137 QPCT(ph)PPPQPQQQQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPCTPPPQPQQQQVK 15 0 P35321 P35321 SPRR1A Cornifin-A 1 QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK;QPCT(1)PPPQPQQQQVK 163.34 1.73E-05 1361170000 752330 627470 704850 593360 832460 914980 776210 733250 804510 560470 TRUE FALSE 782032.5693 735233.0915 723218.97 710724.837 690958.7465 702489.7617 715368.632 723421.9831 775555.8423 670283.3657 1.166719345 1.096898907 1.078974964 1.060334887 1.030845732 1.048048926 1.067262994 1.07927784 1.157056675 1 19.35441161 4.799256874 1.605095893 1.066102344 1.214192021 0.398895255 0.038069056 1.245446829 2.734076563 0.00995219 0.300922696 62987.86302 -4.799256874 0.148089677 QPDISCILGTGGKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPDISCILGTGGKSPR 16 1 P57740;P57740-2;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 QPDISCILGTGGKS(1)PR;QPDISCILGTGGKS(1)PR;QPDISCILGT(0.009)GGKS(0.991)PR;QPDISCILGT(0.001)GGKS(0.999)PR 225.74 3.99E-15 2943130000 2672610 1847860 2317910 1915400 2792990 3045500 2557570 2311130 2638670 2008330 TRUE FALSE 2778126.707 2165215.581 2378316.639 2294260.403 2318238.557 2338228.78 2357100.98 2280153.083 2543704.782 2401823.812 1.156673813 0.901488098 0.990212782 0.955215945 0.965199257 0.973522191 0.981379637 0.949342359 1.059072181 1 21.19569889 1.239052692 24.99999848 1.029536087 0.978150735 0.068155397 0.064182106 29.26330864 1487464.528 0.044919924 0.014132502 17.34014367 -1.239052692 -0.051385352 QPDKEFSFMDEEEEDEIRV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPDKEFSFMDEEEEDEIRV 19 2 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 0 ; 167.16 7.36E-11 162610000 118686 120896 143507 111872 167542 176810 149420 147570 163577 124475 FALSE TRUE 123371.8149 141658.9476 147246.9103 133999.9477 139063.2707 135748.5571 137708.07 145592.0655 157689.8957 148863.493 0.828758028 0.951603007 0.989140503 0.900153187 0.934166382 0.911899582 0.925062735 0.978023977 1.059291922 1 17.18363047 1.537440274 3.156495443 1.02881586 0.92348267 0.534756361 0.04105306 0.167029534 3.651697726 0.027779406 0.010603025 34.46991985 -1.537440274 -0.10533319 QPDPDENKPMEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPDPDENKPMEDK 13 1 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;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 147.35 3.90E-05 313320000 998430 338610 551870 369080 745170 849740 914320 587910 697110 255040 FALSE TRUE 1037848.787 396763.6335 566252.1856 442082.9224 618506.2696 652400.7629 842653.2093 580030.0281 672021.1473 305010.205 3.40266906 1.300820848 1.856502426 1.449403709 2.02782156 2.138947328 2.76270497 1.901674169 2.203274305 1 18.21849799 3.006581922 24.86138009 2.104240764 1.916421128 0 0.67190478 926.470705 3499447.49 0.184492348 0.220001704 1015.270861 -3.006581922 -0.187819636 QPDPDENKPMEDKVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPDPDENKPMEDKVK 15 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;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 117.4 0.00020973 542410000 1325130 403980 630020 347210 1117160 888780 769700 656440 850800 324350 FALSE TRUE 1377447.156 473360.4225 646438.8388 415887.1017 927265.5422 682374.3146 709368.9028 647641.4955 820179.8742 387900.1724 3.551035172 1.220315061 1.666508253 1.072149824 2.390474684 1.759149294 1.82874088 1.669608682 2.114409666 1 18.56532589 8 0.045880192 3.74E-13 4.985269351 0.168659144 0.647898056 1335.210526 4.639568718 126.2556929 487.2229644 99999999.96 -8 4.985269351 QPEDDSSQAFISTQNGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPEDDSSQAFISTQNGSPR 19 0 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QPEDDSSQAFIST(0.001)QNGS(0.999)PR 214.86 3.00E-25 0 60952 68248 59961 68666 62580 76614 49253 54320 52144 60572 TRUE FALSE 63358.43203 79969.0631 61523.63292 82247.92985 51942.67395 58821.5596 45392.42116 53591.92925 50267.34763 72439.92368 0.874634163 1.103936325 0.849305601 1.135395037 0.717044846 0.812004715 0.626621604 0.739812061 0.693917733 1 16.14449741 3.219985076 24.98169838 0.744075862 0.988789675 0.43704315 0.124262195 187.0836476 251602.7459 0.032753432 0.039213177 1659.52988 -3.219985076 0.244713813 QPEWLEEQQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPEWLEEQQGR 11 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 137.78 0.0001658 183800000 236888 168846 167753 174054 222295 258993 201912 184199 230956 147019 FALSE TRUE 246240.5212 197843.9871 172124.781 208481.3617 184509.3753 198845.8008 186085.6098 181730.1137 222643.9387 175824.5582 1.400489918 1.125235229 0.978957563 1.185735166 1.04939479 1.130933033 1.058359604 1.033587774 1.266284647 1 17.42377707 4.724880301 4.261855556 1.086434415 1.420979164 0.55898179 0.082679469 0.132586074 5.555364898 0.018369463 0.131753408 53073.8143 -4.724880301 0.334544749 QPEYSPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 164.13 6.56E-06 1289330000 615840 633874 621045 603753 580911 739450 604417 581837 515426 556021 TRUE FALSE 640153.8387 742736.9286 637229.9429 723173.5414 482167.9557 567723.944 557041.2162 574038.4267 496875.9189 664962.6693 0.962691394 1.116960339 0.958294311 1.08754006 0.7251053 0.853768144 0.83770299 0.86326414 0.747223779 1 19.34291383 3.248214858 24.99983068 0.834076179 1.032265232 0.566405724 0.08291105 133.3192395 345230.4346 0.021093387 0.028204531 1770.984899 -3.248214858 0.198189053 QPGTCS(ph)PDLAAPLDENGAVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPGTCSPDLAAPLDENGAVDR 21 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 QPGT(0.003)CS(0.997)PDLAAPLDENGAVDR;QPGT(0.043)CS(0.957)PDLAAPLDENGAVDR 147.25 4.05E-09 62799000 98225 98293 96785 124543 100542 137357 127591 111265 108012 84869 TRUE FALSE 102102.9988 115174.0581 99307.29661 149177.2337 83451.90675 105457.9184 117590.084 109773.6747 104124.6692 101497.4556 1.005966093 1.13474823 0.978421538 1.469763284 0.822206884 1.039020316 1.158552037 1.081541148 1.025884527 1 16.63108404 QPGVDSLS(ph)PVASLPK ddPTM_MDA-MB-175_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 255.22 1.07E-24 257250000 317630 220740 286920 242350 319520 338780 333820 285890 300560 189136 TRUE FALSE 330170.2777 258650.3779 294397.3709 290286.1067 265208.1045 260103.4793 307654.3161 282058.1122 289742.9043 226193.578 1.459680158 1.143491253 1.301528423 1.283352557 1.17248291 1.149915403 1.360137272 1.246976659 1.280951064 1 17.78719844 -2.323765283 1.800640821 3.07E-05 1.261221367 0.425399695 0.092736633 1026802.049 120093.6011 4167859.925 0.021866057 0.004744984 2.323765283 1.261190704 QPGYQPPNPHPGPS(ph)SPPAAPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.726)S(0.274)PPAAPASK 172.32 3.32E-12 333230000 200120 210370 216200 181430 223820 256280 225510 231700 216090 199390 TRUE FALSE 208020.8921 246499.411 221834.3496 217316.3125 185775.1563 196762.854 207833.9369 228594.4405 208312.9631 238456.6529 0.872363549 1.033728386 0.930292138 0.911345143 0.779073069 0.825151454 0.871579528 0.958641487 0.873588388 1 17.86336751 3.732141862 3.446557783 0.882335678 0.956733221 0.126123512 0.069044814 0.424732449 10.79441751 0.019019532 0.033815711 5396.868824 -3.732141862 0.074397543 QPGYQPPNPHPGPSS(ph)PPAAPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 QPGYQPPNPHPGPS(0.174)S(0.826)PPAAPASK 149.84 5.83E-08 287740000 334100 309690 351330 326060 413640 475060 410710 377560 378860 320370 TRUE FALSE 347290.526 362876.8484 360485.9484 390553.6948 343329.6205 364734.5146 378517.477 372499.4258 365224.9026 383140.3676 0.906431573 0.947112022 0.940871751 1.019348854 0.896093572 0.951960549 0.987934212 0.972227041 0.953240466 1 18.54751351 8 0.127985649 1.003238898 0.752308717 0.256856577 0.031775479 127.1160715 1.103453015 0.173323037 5.746474598 100000000 -8 -0.250930182 QPHRPDPGRPVGLEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPHRPDPGRPVGLEQLR 17 2 Q9BV57 Q9BV57 ADI1 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase" 0 81.428 0.0055971 87886000 48822 45487 45804 49916 35106 51434 46542 45545 50045 45574 FALSE TRUE 50749.53026 53299.03841 46997.68987 59789.23582 29138.69466 39489.23299 42893.91643 44934.54377 48243.89023 54503.35273 0.93112676 0.977903849 0.862289887 1.096982714 0.534622059 0.724528511 0.786995924 0.824436324 0.885154542 1 15.73405736 3.264501151 24.99990946 0.783332731 0.96036444 0.319932787 0.12400651 265.6762096 256040.7536 0.033653347 0.045552035 1838.658828 -3.264501151 0.177031709 QPHVGDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QPHVGDYR 8 0 Q06323;Q06323-3;Q06323-2;H0YKK6 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 116.3 0.0022971 7745390000 5253970 6005880 5424130 5729310 5989010 6732140 5335350 5524470 5320940 5660240 FALSE TRUE 5461400.793 7037343.171 5565487.284 6862550.418 4971000.219 5168702.512 4917151.326 5450423.516 5129440.409 6769255.656 0.806794878 1.039603692 0.822171235 1.01378213 0.734349605 0.763555518 0.726394684 0.805173241 0.757755456 1 22.69056577 3.227440521 24.98060945 0.783080275 0.922059347 0.258956034 0.099822883 234.6526779 527131.8879 0.026080981 0.031445778 1688.264626 -3.227440521 0.138979072 QPLLLS(ph)EDEEDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPLLLSEDEEDTK 13 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 1 QPLLLS(1)EDEEDTK;QPLLLS(1)EDEEDTK 211.57 2.19E-08 292660000 447290 286700 364270 274890 604660 585420 405860 357220 429590 260830 TRUE FALSE 464949.3546 335938.4948 373763.1755 329262.4215 501880.1092 449465.0771 374047.6327 352432.0502 414129.1398 311934.6446 1.490534516 1.076951536 1.198209888 1.055549383 1.608927119 1.440895024 1.199121801 1.129826572 1.327615085 1 18.25088427 -0.512107667 5.726776977 0.999999999 1.266296524 0.182254297 0.176057141 0 68218046.58 0.394700677 0.041838187 0.307533431 0.512107667 0.266296524 QPLLLS(ph)EDEEDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.993)EDEEDT(0.007)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(0.993)EDEEDT(0.007)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR 242.9 1.76E-17 36530580000 7612760 4939870 6286380 4983650 8662550 9149970 7429030 6452190 6983480 4550110 TRUE FALSE 7913317.643 5788254.246 6450208.227 5969401.095 7190092.845 7025028.137 6846723.216 6365708.947 6732145.919 5441616.937 1.454221739 1.063701159 1.18534772 1.096990318 1.321315507 1.290981746 1.258214846 1.169819379 1.237159101 1 22.37560397 -0.414510776 0.925866582 0.992398259 1.223993728 0.292338382 0.107104651 27.13458653 15.40216235 0.874262472 0.032026348 0.385025261 0.414510776 0.231595469 QPLLLSEDEEDT(ph)KR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 QPLLLS(0.012)EDEEDT(0.988)KR 195.38 6.80E-08 444950000 374690 226080 332830 265060 401450 434890 359780 303830 325500 196660 TRUE FALSE 389483.0505 264907.4813 341503.8232 317488.0769 333211.6724 333893.3883 331579.5035 299757.6558 313785.3186 235191.7617 1.656023356 1.126346771 1.452022897 1.349911555 1.416765919 1.419664472 1.409826182 1.274524472 1.334167984 1 17.843478 0.307755751 0.665153453 0.989378013 1.395198703 0.473995602 0.124577892 2.022596135 1.268592616 0.162100175 0.043089308 2.031214326 -0.307755751 0.40582069 QPPGPVPT(ph)PPLPSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPPGPVPTPPLPSER 15 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QQI0 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 QPPGPVPT(1)PPLPSER;QPPGPVPT(1)PPLPSER 122.96 0.0011815 451170000 293980 370540 361630 364130 397770 452210 353820 410520 372450 383010 TRUE FALSE 305586.5574 434177.3626 371054.3749 436153.8272 330157.1975 347191.0808 326086.6639 405017.6509 359045.5973 458053.4763 0.667141662 0.947874833 0.810067807 0.952189755 0.720783084 0.757970627 0.711896494 0.884214774 0.783850829 1 18.80515651 -1.278168939 3.82805419 1.000326592 0.81042326 0.284153599 0.092825569 494827.7811 44958931.66 25863.14463 0.020670301 0.052702481 1.278168939 -0.189903332 QPPGTQQSHS(ph)SPGEITSSPQGLDNPALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGT(0.001)QQS(0.004)HS(0.565)S(0.429)PGEIT(0.001)SSPQGLDNPALLR 122.35 1.74E-05 624970000 22853 30384 20603 24901 24159 31033 27189 23648 25104 30776 TRUE FALSE 23755.25409 35602.21565 21139.93111 29826.34348 20052.46181 23826.05606 25057.85513 23331.03724 24200.51194 36805.96796 0.64541854 0.967294643 0.574361504 0.810367045 0.544815499 0.647342194 0.680809568 0.633892777 0.657515976 1 15.16765209 -0.975758198 4.041760829 1.000021843 0.684321679 0.401046692 0.115615414 29285791.09 59151231.29 9412.44351 0.026462877 0.105740608 0.975758198 -0.315700164 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0;Q5TDH0-3;Q5TDH0-2 Q5TDH0 DDI2 Protein DDI1 homolog 2 1 QPPGT(0.215)QQS(0.154)HS(0.112)S(0.519)PGEITSSPQGLDNPALLR 55.413 0.038756 210480000 5650.7 7754.2 8908.2 10844 14519 11050 8418.2 10990 8192.2 7928.3 TRUE FALSE 5873.793999 9085.923531 9140.35501 12988.91083 12051.06557 8483.804964 7758.359487 10842.69703 7897.364322 9481.698589 0.619487526 0.958259055 0.963999744 1.369892822 1.270981718 0.894755817 0.818245741 1.143539517 0.832906071 1 13.21092982 4.774415252 2.088291804 1.049546231 0.475957981 0.346053647 0.1713689 0.915335943 4.088398242 0.045731632 1.023134704 59486.06653 -4.774415252 -0.57358825 QPPGVPNGPSS(ph)PTNESAPELPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QPPGVPNGPSSPTNESAPELPQR 23 0 Q8TF74;Q8TF74-2 Q8TF74 WIPF2 WAS/WASL-interacting protein family member 2 1 QPPGVPNGPS(0.208)S(0.762)PT(0.03)NES(0.001)APELPQR;QPPGVPNGPS(0.247)S(0.734)PT(0.019)NESAPELPQR;QPPGVPNGPS(0.13)S(0.678)PT(0.188)NES(0.004)APELPQR 124.08 3.82E-05 1042540000 409670 483740 423540 519840 457790 585530 468240 508820 459640 568590 TRUE FALSE 425844.0879 566818.582 434577.8003 622662.8004 379975.0193 449549.5313 431538.1253 502000.1002 443097.6462 679994.3242 0.626246533 0.833563696 0.639090335 0.915688232 0.558791457 0.66110777 0.634620187 0.738241603 0.651619624 1 19.37516318 -1.46872618 4.569052316 1.00112305 0.699519003 0.447212916 0.101490347 0.001077312 0.000125266 0.091180152 0.021414364 0.033983947 1.46872618 -0.301604047 QPPMFS(ph)PLISAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPPMFSPLISAR 12 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3;F8W719;E7EPJ2 A0A087WVF7 ITSN2 Intersectin-2 1 QPPMFS(1)PLISAR 132.65 0.00018593 60702000 25441 32132 31516 32285 31819 40239 29173 30635 27105 30930 TRUE FALSE 26445.43032 37650.42105 32337.33285 38670.87664 26410.41775 30894.10208 26886.34403 30224.38793 26129.49634 36990.14131 0.714931855 1.017850155 0.874214904 1.045437386 0.713985316 0.835198271 0.726851617 0.817093065 0.706390823 1 15.17485319 3.22356818 24.99968581 0.789398449 0.917812035 0.183953147 0.115353431 329.3536941 549191.7396 0.030472683 0.036557334 1673.278305 -3.22356818 0.128413586 QPPTAAGRPVDASPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPPTAAGRPVDASPR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 63.754 0.064114 45126000 13153 17660 15692 20074 18385 26087 13222 15611 16640 22968 FALSE TRUE 13672.2906 20692.96762 16100.94641 24044.57729 15259.92427 20028.6896 12185.62509 15401.76008 16041.12965 27468.13985 0.497750873 0.753344338 0.586168066 0.875362417 0.55554997 0.729160755 0.443627605 0.560713618 0.583990388 1 14.74547159 -0.921093326 4.252371301 1.000009367 0.620105975 0.461616229 0.122909597 1.03015E+11 2.50309E+11 15998493.02 0.028900738 0.119924157 0.921093326 -0.379903392 QPS(ph)ATRLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.995)AT(0.005)RLPK;QPS(0.806)AT(0.194)RLPK 74.46 0.024847 1586540000 846460 1461290 1255730 995610 1687190 1788100 750110 1287140 1291120 2144020 TRUE FALSE 879878.8944 1712255.19 1288455.355 1192538.686 1400402.046 1372840.874 691314.4182 1269887.994 1244652.843 2564099.669 0.343153156 0.667780278 0.502498156 0.465090613 0.546157415 0.535408545 0.269612927 0.495256877 0.485415157 1 21.29002091 0.446195036 3.406726402 0.999999866 0.479853554 0.69618175 0.103272717 28.02130149 171.1566195 0.096622156 0.024958203 2.79379822 -0.446195036 -0.520146312 QPS(ph)EEEIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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;QPS(1)EEEIIK 144.57 0.00010409 64783026000 11405420 8130977 13972340 8484208 14862620 13320200 15620130 12146470 15694630 7007231 TRUE FALSE 11855714.79 9527409.05 14336470.66 10162359.02 12336277.16 10226785.42 14395783.39 11983666.44 15129783.33 8380163.753 1.414735456 1.136900105 1.710762591 1.21266831 1.472080681 1.220356275 1.717840345 1.430003851 1.805428125 1 22.998547 2.250619638 24.99926911 1.520981953 1.365223761 0.051835618 0.250802817 556.188614 1153020.656 0.079841091 0.066322464 178.0818415 -2.250619638 -0.155758192 QPS(ph)SPGPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPSSPGPTPR 10 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 QPS(0.644)S(0.356)PGPTPR 78.903 0.02247 0 196680 237880 228950 253690 230150 295330 230940 255190 233450 266840 TRUE FALSE 204445.0783 278734.0396 234916.6251 303869.1248 191029.1852 226744.0833 212838.3194 251769.5955 225048.1801 319122.189 0.64064827 0.873439858 0.736133786 0.95220306 0.598608282 0.710524342 0.666949296 0.788944185 0.705210066 1 18.2837494 -1.971592034 6.280697872 1.16832249 0.746157699 0.368677442 0.101345985 0.054425802 0.000246171 0.022358316 0.021849412 0.010675985 1.971592034 -0.422164791 QPS(ph)SPSHNTNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.721)S(0.279)PS(0.001)HNTNLR 77.42 0.018338 234060000 62975 114420 107830 121630 118240 140390 108990 112300 112450 127810 TRUE FALSE 65461.30163 134070.7449 110640.1384 145688.051 98141.60703 107786.5501 100447.079 110794.8022 108402.9465 152851.9224 0.428266132 0.877128287 0.72383871 0.953131951 0.642069825 0.705169738 0.657152867 0.724850564 0.709202375 1 17.22177517 -1.696501381 6.06252269 1.004030822 0.721156266 0.295784448 0.132172247 0.006736576 0.000337243 0.119722683 0.027904936 0.020114008 1.696501381 -0.282874556 QPS(ph)SPYEDKDK ddPTM_MDA-MB-175_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 126.1 0.00082752 71802000 158940 46180 68242 61690 99584 126970 138630 77384 85412 28373 TRUE FALSE 165215.0739 54111.05577 70020.44258 73892.09787 82656.74725 97483.14175 127763.8184 76346.79405 82338.0388 33932.14612 4.868983923 1.594684155 2.063543 2.177642924 2.435942217 2.872884651 3.76527373 2.249984242 2.426549695 1 15.05036506 0.692533056 1.701310944 1.003523878 2.70133802 0.255764656 0.895176677 1.668166127 7.106319813 0.819971219 0.23267619 4.926438389 -0.692533056 1.697814142 QPSGS(ph)FSTPGSATYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPSGSFSTPGSATYVR 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 QPS(0.009)GS(0.952)FS(0.035)T(0.003)PGSATYVR;QPS(0.004)GS(0.911)FS(0.023)T(0.059)PGS(0.002)ATYVR;QPS(0.01)GS(0.975)FS(0.009)T(0.005)PGSATYVR;QPS(0.016)GS(0.964)FS(0.018)T(0.002)PGSATYVR 195.74 5.00E-11 1096060000 307452 384080 376129 434966 455647 554300 430511 432985 383915 498874 TRUE FALSE 319590.4424 450042.7523 385931.2307 521000.9766 378196.2857 425572.2255 396766.4229 427181.5443 370097.9741 596618.8088 0.535669405 0.754322099 0.646864003 0.873256037 0.633899368 0.713306753 0.665024999 0.716004152 0.62032569 1 19.18644993 -1.517368544 4.949614853 1.001261127 0.691255935 0.548812289 0.08566612 0.001087592 0.00010605 0.075669355 0.017766578 0.030383056 1.517368544 -0.310005192 QPSLTLELFPNHT(ph)DNLNSSQRLSPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPSLTLELFPNHTDNLNSSQRLSPSSR 27 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 QPSLTLELFPNHT(0.271)DNLNS(0.271)S(0.271)QRLS(0.178)PS(0.004)S(0.004)R 71.44 0.029431 45955000 16377 25434 22368 21020 29348 31516 14225 21901 26696 43317 TRUE FALSE 17023.57661 29802.09165 22950.92846 25177.69326 24359.43744 24196.88663 13110.00733 21607.45292 25735.21617 51804.1368 0.328614232 0.575284012 0.443032736 0.486017041 0.470221858 0.467084062 0.253068734 0.417098986 0.496779172 1 15.66077969 0.764065574 3.696363933 0.999982299 0.431039846 0.806623189 0.083194071 1.014423504 15.45988475 0.080870339 0.020771098 5.808521135 -0.764065574 -0.568942453 QPSLTLELFPNHTDNLNSSQRLS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPSLTLELFPNHTDNLNSSQRLSPSSR 27 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 QPSLTLELFPNHT(0.002)DNLNS(0.253)S(0.253)QRLS(0.363)PS(0.065)S(0.065)R 125.02 4.61E-05 190890000 41429 84447 69394 58088 78179 96469 38725 65212 58413 136770 TRUE FALSE 43064.64891 98950.11534 71202.46465 69577.63302 64890.1615 74065.53675 35689.63331 64337.93981 56310.72754 163567.4629 0.263283713 0.60494987 0.435309464 0.425375755 0.396718029 0.452813386 0.218195188 0.393341919 0.344266069 1 17.31952627 -1.316066478 4.243118948 1.000755605 0.395238174 0.766381194 0.100582316 31458738.4 9758168.047 221277.9691 0.023008116 0.048298487 1.316066478 -0.605517431 QPSS(ph)PSHNTNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 QPS(0.03)S(0.969)PS(0.001)HNTNLR;QPS(0.231)S(0.768)PS(0.001)HNTNLR;QPS(0.252)S(0.747)PSHNTNLR 147.39 0.00031253 628570000 178237 402590 352253 345848 348398 405360 338218 379700 346690 419750 TRUE FALSE 185273.9344 471731.7008 361433.0026 414255.7021 289177.4324 311221.2833 311707.5894 374610.7426 334212.6946 501991.9759 0.369077482 0.939719604 0.71999757 0.825223753 0.57605987 0.619972626 0.620941378 0.746248467 0.665772982 1 18.93730478 -1.367650581 2.59411843 1.007126632 0.686862426 0.307741013 0.144994597 3780777.401 4010002.553 203667.3015 0.03419091 0.042889345 1.367650581 -0.320264205 QPSS(ph)PYEDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.149)S(0.851)PYEDKDK;QPS(0.149)S(0.851)PYEDKDK;QPS(0.017)S(0.983)PYEDKDK;QPS(0.284)S(0.716)PYEDKDK;QPS(0.315)S(0.685)PY(0.001)EDKDK 145.69 2.19E-05 1465300000 2010300 768532 1105780 954237 1447053 1646950 1957270 1103654 1284480 601001 TRUE FALSE 2089668.196 900521.3927 1134597.535 1142982.23 1201083.448 1264470.822 1803854.063 1088861.323 1238251.816 718755.6391 2.907341637 1.252889499 1.578558099 1.59022367 1.671059513 1.75924995 2.50969031 1.514925608 1.722771619 1 19.45514184 4.751241736 24.44677572 1.674971934 2.907342701 0.5139691 0.371751435 1253.292634 2416049.344 0.086528598 1.525628848 56395.14739 -4.751241736 1.232370767 QPSS(ph)PYEDKDKDK ddPTM_MDA-MB-175_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(0.026)S(0.974)PYEDKDKDK 118.24 0.00023129 170640000 433110 81927 137770 103420 231830 336560 284940 142830 171590 40606 TRUE FALSE 450209.5172 95997.32495 141360.3994 123876.1673 192423.6194 258399.0406 262605.6582 140915.5975 165414.5094 48561.96825 9.270825163 1.976800538 2.910928129 2.55088852 3.962434521 5.321016629 5.407640335 2.901768659 3.406256282 1 15.56753928 4.747628301 24.86270762 3.453657373 9.27082842 0.651347543 1.310795663 728.8701979 1998445.458 0.318928507 3.925686126 55927.87275 -4.747628301 5.817171047 QPSS(ph)PYEDKDKDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPSSPYEDKDKDKK 14 3 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QPS(0.019)S(0.981)PYEDKDKDKK;QPS(0.287)S(0.713)PYEDKDKDKK;QPS(0.251)S(0.749)PYEDKDKDKK;QPS(0.046)S(0.954)PYEDKDKDKK 223.11 2.01E-11 3728120000 7489510 777060 1746800 732073 3226860 3437910 3424560 1735220 2149450 402608 TRUE FALSE 7785201.638 910514.0103 1792323.043 876874.8544 2678359.49 2639507.505 3156134.039 1711962.214 2072091.714 481491.3292 16.16893424 1.891028883 3.722440954 1.821164372 5.56263286 5.481941926 6.554913552 3.555541108 4.30348708 1 18.87715029 4.744642631 24.99838924 3.999672159 16.16893958 0.822728164 1.724121738 274.1490084 1126780.349 0.410069884 3.784750499 55544.70075 -4.744642631 12.16926742 QPSVETLDS(ph)PTGSHVEWCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPSVETLDSPTGSHVEWCK 19 0 F8WA39;Q13613;Q13613-2;E9PPP8;Q8NEC6 F8WA39 MTMR1 Myotubularin-related protein 1 1 QPSVET(0.004)LDS(0.988)PT(0.007)GS(0.001)HVEWCK;QPSVETLDS(0.993)PT(0.006)GSHVEWCK 217.71 2.28E-19 847420000 539730 627770 701020 604870 891300 835290 725560 766120 770820 620720 TRUE FALSE 561038.9572 735584.6141 719289.1571 724511.4806 739797.1444 641306.5564 668688.7113 755851.4145 743078.3388 742338.1996 0.755772716 0.990902279 0.968950752 0.975985718 0.996576957 0.863900789 0.90078715 1.018203583 1.000997038 1 19.50171708 4.742674494 24.89217179 0.966206375 0.755772628 0.654846503 0.046300806 257.62526 1558772.136 0.011696768 0.090332359 55293.55259 -4.742674494 -0.210433747 QPT(ph)PPFFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QPTPPFFGR 9 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 QPT(1)PPFFGR 99.539 0.058898 2950100000 859780 958250 857700 908030 987190 1122000 891330 963320 958090 926390 TRUE FALSE 893724.7783 1122821.983 880052.3666 1087635.624 819387.7964 861432.5041 821465.2255 950408.2711 923608.5281 1107898.384 0.806684793 1.013470188 0.794343939 0.981710633 0.739587501 0.777537468 0.741462609 0.857847872 0.83365816 1 20.07939413 5.086454981 14.72714597 0.849694344 2.77E-05 0.015921663 0.099636422 3785076.547 10606240.64 0.022989815 101835585.3 122026.7321 -5.086454981 -0.849666667 QPVYYDELDAASS(ph)SLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QPVYYDELDAASSSLRR 17 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 QPVYYDELDAAS(0.106)S(0.552)S(0.341)LRR;QPVYYDELDAAS(0.028)S(0.899)S(0.073)LRR 130.71 1.80E-05 523830000 141937 191929 184224 175731 230460 214250 130005 184469 144775 207630 TRUE FALSE 147540.7824 224891.3127 189025.0288 210490.0673 191286.4915 164493.6845 119814.8684 181996.4948 139564.576 248311.1232 0.594177097 0.905683603 0.761242696 0.847686824 0.770350072 0.662449923 0.482519135 0.732937343 0.562055273 1 17.92178936 2.762872165 5.29927935 0.659460818 0.78716164 0.063430478 0.147613345 0.349356845 30.03364672 0.042871359 0.044140123 579.2581656 -2.762872165 0.127700822 QPYAVSELAGHQTSAESWGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QPYAVSELAGHQTSAESWGTGR 22 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ;;; 349.37 5.53E-96 5871160000 775741 1899820 1631470 1998420 1682900 2288860 1543549 1900520 1619090 1891240 FALSE TRUE 806367.8537 2226099.306 1673987.448 2393701.511 1396841.259 1757306.953 1422561.596 1875046.638 1560819.267 2261792.268 0.356517203 0.984219169 0.74011547 1.058320671 0.617581587 0.776953294 0.628953249 0.829009217 0.690080733 1 21.109035 -2.181916125 2.273175497 1.630772681 0.756622078 0.14232935 0.186786364 9722833.526 1959083.282 31596566.62 0.04129143 0.006577849 2.181916125 -0.874150602 QQAAYYAQTS(ph)PQGMPQHPPAPQGQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 QQAAYYAQTS(1)PQGMPQHPPAPQGQ;QQAAYYAQT(0.015)S(0.985)PQGMPQHPPAPQGQ 207.88 4.52E-25 528980000 203903 213499 190086 183579 161215 232029 167319 213180 205845 215059 TRUE FALSE 211953.2479 250165.7925 195039.7973 219890.3783 133811.7319 178143.7812 154204.0996 210322.6708 198436.6787 257195.6935 0.8240933 0.972667112 0.758332283 0.854953577 0.520272055 0.692639051 0.599559415 0.81775347 0.771539663 1 17.97250696 3.8748251 2.019081729 0.724233589 0.891225196 0.131550658 0.132673043 0.527979709 4.17093307 0.035744436 0.085639861 7495.922717 -3.8748251 0.166991606 QQALTVSTDPEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQALTVSTDPEHR 13 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 115.83 0.00063356 258000000 84710 97630 93133 126420 81519 113570 119030 104420 104470 89620 FALSE TRUE 88054.41621 114397.193 95560.12249 151425.4987 67662.4295 87195.08867 109700.1176 103020.4207 100710.1451 107179.3231 0.8215616 1.067343866 0.891591024 1.412823801 0.631301146 0.813543939 1.02351941 0.961196784 0.939641548 1 16.70966708 5.954351837 10.85159841 0.959005065 0.684460191 0 0.193880203 0 0 0.040908138 0 900226.5899 -5.954351837 -0.274544874 QQASKS(ph)PYNGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QQASKSPYNGVR 12 1 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 QQAS(0.002)KS(0.998)PYNGVR;QQAS(0.048)KS(0.952)PYNGVR;QQASKS(1)PYNGVR;QQAS(0.084)KS(0.916)PYNGVR;QQAS(0.001)KS(0.999)PYNGVR;QQAS(0.001)KS(0.999)PYNGVR 262.83 1.18E-21 3931720000 4056980 3155650 3753680 3132460 4568470 4839300 3667190 3865380 4176760 3306880 TRUE FALSE 4217152.703 3697608.34 3851503.984 3752051.239 3791923.101 3715445.915 3379746.065 3813570.904 4026439.223 3954799.822 1.066337841 0.934967257 0.973880894 0.948733541 0.958815432 0.939477618 0.85459346 0.964289237 1.018114546 1 21.91517324 4.74306371 24.62221223 0.949768726 1.066337899 0.386160692 0.041776561 377.6631381 2064915.966 0.009982139 0.078348603 55343.12906 -4.74306371 0.116569173 QQDLHLES(ph)PQRQPEYSPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 QQDLHLES(1)PQRQPEYSPES(1)PR;QQDLHLES(0.999)PQRQPEY(0.003)S(0.016)PES(0.982)PR 204.86 2.89E-22 440280000 325266 338762 327450 322461 328268 401720 311504 325977 346174 315127 TRUE FALSE 338107.7528 396941.7383 335983.616 386242.8233 272469.1226 308426.6181 287087.5025 321607.8115 333715.2654 376870.1022 0.897146658 1.053258765 0.891510401 1.024869898 0.722978875 0.818389722 0.761767784 0.853365151 0.885491482 1 18.52370782 3.25100685 24.99282672 0.828201504 0.967509026 0.347224666 0.083893729 219.7523457 441274.0495 0.021726339 0.029214175 1782.40688 -3.25100685 0.139307522 QQDS(ph)QPEEVMDVLEMVENVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQDSQPEEVMDVLEMVENVK 20 0 Q9H307 Q9H307 PNN Pinin 1 QQDS(1)QPEEVMDVLEMVENVK 109.89 0.00063899 4973900 7943.2 6105.4 5861.4 4264 7568 8450.9 8591 6497.5 7299.5 4511.9 TRUE FALSE 8256.803669 7153.954957 6014.152899 5107.406473 6281.594063 6488.30655 7917.614972 6410.41164 7036.792421 5395.920419 1.530193744 1.325808092 1.114574054 0.946531097 1.16413764 1.202446672 1.467333533 1.188010783 1.304094922 1 12.39765336 -4.999999999 0.020592922 2.21E-07 2.082219724 0.130795397 0.16526577 9589.869935 14.94810762 1027.274109 552.20045 1.00E-05 4.999999999 2.082219503 QQDVIYELIQTELHHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QQDVIYELIQTELHHVR 17 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 0 ;; 112.56 0.00026307 286202000 241288 264719 272666 297710 278587 329882 292124 293710 284591 253953 FALSE TRUE 250814.2366 310182.429 279771.9 356596.1494 231232.8812 253271.9049 269226.5576 289773.2979 274348.6255 303710.2281 0.825834013 1.021310448 0.921180369 1.174132829 0.761360204 0.833926162 0.886458646 0.954111093 0.903323629 1 18.21233597 4.782779231 21.51830316 0.934499262 0.825831726 0.09155318 0.106388298 12470.79729 6067874.439 0.025243712 8.405974586 60642.79802 -4.782779231 -0.108667536 QQEGFKPNYMENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QQEGFKPNYMENR 13 1 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;;;; 133.48 9.74E-05 1117210000 817762 714153 793210 659993 944170 1088670 874703 815940 861430 766810 FALSE TRUE 850047.8752 836803.2224 813881.7042 790537.6455 783680.3206 835842.8915 806141.4932 805003.6589 830427.3026 917051.738 0.92693557 0.912492925 0.887498132 0.862042579 0.854565002 0.911445731 0.879057811 0.877817058 0.905540296 1 19.8066436 0.842728725 4.559942341 0.999996861 0.887592718 0.701907461 0.021567947 0.843447838 23.90649949 0.021785546 0.005527931 6.96191513 -0.842728725 -0.112404143 QQEIILWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQEIILWR 8 0 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 101.43 0.012562 137150000 124300 125880 124570 119010 131640 158230 127600 124730 123360 125380 FALSE TRUE 129207.46 147498.9108 127816.3965 142549.8228 109263.8798 121483.4805 117598.3786 123058.1984 118920.2977 149945.8105 0.861694365 0.98368144 0.852417258 0.950675596 0.728689114 0.810182559 0.78427252 0.820684473 0.793088499 1 17.19408169 3.255051303 24.99949898 0.811320623 0.912964626 0.24573299 0.075032325 280.508915 425242.6199 0.018867766 0.025473758 1799.083428 -3.255051303 0.101644004 QQEKEDKDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQEKEDKDEK 10 2 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 89.403 0.0064884 373520000 696530 140210 257110 131590 448510 442560 413120 249780 341360 99305 FALSE TRUE 724029.5422 164289.9768 263810.4978 157618.1092 372272.4304 339782.1471 380738.5749 246432.1077 329074.5203 118761.9134 6.096479261 1.383355758 2.221339234 1.327177246 3.134611254 2.861036314 3.205897951 2.075009576 2.77087587 1 16.85771272 -0.807806107 7.181386807 0.999999995 2.670867724 0.144415473 1.276816725 8.52E-08 1.19E-08 1.142981894 0.269403416 0.155666045 0.807806107 1.670867729 QQELTHQEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQELTHQEHR 10 0 P18206;P18206-2;P18206-3 P18206 VCL Vinculin 0 ; 134.13 0.0001034 1621150000 376620 463440 390610 456960 448680 479720 442770 460330 383790 553150 FALSE TRUE 391489.2484 543032.2149 400789.6175 547345.3241 372413.5339 368312.3002 408064.5304 454160.0293 369977.4729 661529.1518 0.591794401 0.820874203 0.605853297 0.82739411 0.562958613 0.556758987 0.616850413 0.686530636 0.559276144 1 19.33544521 -1.520065204 5.429727768 1.000860362 0.652786496 0.544959883 0.096503183 0.000963115 8.51E-05 0.089537111 0.021054386 0.030194983 1.520065204 -0.348073866 QQEQADSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQEQADSLER 10 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 138.23 0.010126 0 73354 86379 79427 79176 77851 90535 73331 79913 75879 93324 FALSE TRUE 76250.07256 101213.9213 81496.93287 94836.77648 64617.91483 69509.61832 67583.12461 78841.89695 73148.12961 111609.051 0.68318897 0.90686123 0.730200034 0.84972299 0.578966618 0.622795532 0.605534444 0.706411319 0.655396036 1 16.7680945 5.07349393 15.21714823 0.722603373 0.165802975 0.001561812 0.13273817 9000329.507 36416091.28 0.030937824 159979953.7 118438.7813 -5.07349393 -0.556800398 QQFHDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQFHDAK 7 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 107.9 0.0073747 473530000 623230 551210 631380 523270 734780 795680 630610 561170 626350 558800 FALSE TRUE 647835.6016 645876.0297 647834.2815 626771.2442 609882.3581 610895.3786 581181.1404 553648.434 603807.7859 668286.1611 0.969398499 0.966466264 0.969396524 0.937878533 0.912606595 0.914122444 0.869659098 0.828460121 0.903516818 1 19.35010647 3.183338079 1.266261107 0.882672579 0.969883977 0.265917325 0.042428093 0.426796596 1.445538238 0.01585854 0.022917561 1525.239624 -3.183338079 0.087211397 QQFLNDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQFLNDLR 8 0 O94855;O94855-2;E9PDM8;E9PC44 O94855 SEC24D Protein transport protein Sec24D 0 83.313 0.042456 61081000 168050 227150 207130 225970 231090 272790 222480 226590 207400 260100 FALSE TRUE 174684.7438 266161.2455 212527.978 270666.1915 191809.4043 209438.6567 205041.4363 223552.9317 199935.7145 311061.6151 0.56157602 0.855654419 0.683234342 0.870136907 0.61662833 0.673302801 0.659166629 0.718677332 0.642752769 1 18.24684085 -1.008369986 6.181961108 1.00000022 0.703549687 0.488154458 0.092639921 2.59E-07 4.15E-08 0.082738528 0.019501644 0.098091192 1.008369986 -0.296450533 QQFS(ph)PSMTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQFSPSMTER 10 0 Q8TDB6 Q8TDB6 DTX3L E3 ubiquitin-protein ligase DTX3L 1 QQFS(0.994)PS(0.006)MTER;QQFS(0.999)PS(0.001)MTER 255.24 4.13E-17 576760000 573410 674830 635060 667360 675810 801620 624090 700370 636710 714120 TRUE FALSE 596048.6696 790726.8031 651610.1853 799361.8161 560936.0576 615455.9037 575172.195 690982.6857 613794.9315 854038.1413 0.697918091 0.925868254 0.762975509 0.935979059 0.656804457 0.720642175 0.673473663 0.80907708 0.718697329 1 19.70394098 5.039699946 15.42973318 0.787323809 0.331561886 0.0587705 0.112580347 5918013.418 66522635.17 0.025432935 74801727.67 109572.09 -5.039699946 -0.455761923 QQFVEYDKNSDDTVTWDEYNIQMYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQFVEYDKNSDDTVTWDEYNIQMYDR 26 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 201.6 4.46E-25 243310000 129210 139130 126980 114280 152950 159560 114120 136830 146510 148210 FALSE TRUE 134311.3106 163024.4952 130289.2031 136884.2429 126951.6136 122504.6082 105174.9762 134996.0177 141237.1337 177248.9118 0.757755346 0.91974892 0.735063486 0.772271274 0.716233529 0.691144486 0.593374454 0.761618315 0.796829342 1 17.43541725 0.803490767 2.59602648 0.999791754 0.741324477 0.502739844 0.076471464 0.742946941 8.12810375 0.078294241 0.020857188 6.360492827 -0.803490767 -0.258467278 QQGHEPVS(ph)PR ddPTM_MDA-MB-175_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 157.22 1.00E-05 1292570000 1098640 1241150 1162980 1261710 1222760 1483910 1290050 1281680 1120690 1088640 TRUE FALSE 1142015.156 1454307.858 1193288.214 1511272.472 1014915.692 1139294.391 1188932.51 1264501.176 1080356.586 1301938.165 0.877165434 1.117032972 0.916547534 1.160786674 0.779542162 0.875075654 0.91320198 0.971245187 0.829806373 1 20.3122295 3.231578792 24.99997615 0.899073008 1.017727027 0.274937157 0.097764373 213.9582857 766124.4912 0.026490225 0.032314453 1704.428519 -3.231578792 0.118654019 QQGNEPSQILSLTGDRVPLHCVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQGNEPSQILSLTGDRVPLHCVDR 24 1 Q8NFH3 Q8NFH3 NUP43 Nucleoporin Nup43 0 105.24 0.0017455 67641000 42623 45795 48372 63431 42000 57877 50364 59670 51042 60958 FALSE TRUE 44305.78895 53659.93501 49632.61406 75977.46248 34860.855 44435.94388 46416.33808 58870.22125 49205.00839 72901.55299 0.607748218 0.736060246 0.680816965 1.042192647 0.478190842 0.60953357 0.636698893 0.807530414 0.674951443 1 16.15366193 -0.206330773 0.851493636 1.008762525 0.699469692 0.288905686 0.141949881 13.21618299 7.827554711 0.537300741 0.04536799 0.621826502 0.206330773 -0.309292833 QQGVLALRPYLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQGVLALRPYLQK 13 1 P56192;P56192-2;H0YHV5 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 66.492 0.061618 0 220610 131140 131610 110910 160240 165050 124990 131780 129120 119740 FALSE TRUE 229319.8531 153662.2749 135039.8647 132847.667 133002.462 126719.6389 115192.9572 130013.7046 124472.9964 143200.7604 1.601387119 1.07305488 0.943010807 0.927702245 0.928783211 0.88490898 0.80441582 0.907912111 0.86922022 1 17.12767963 5.044283945 1.387368601 0.893439441 2.428060305 0.949328087 0.048136391 0.488046657 0.484763271 0.012748804 1.279604076 110734.7539 -5.044283945 1.534620863 QQHNQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQHNQLK 7 0 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 74.415 0.046243 61928000 41527 50427 48026 49582 57757 66863 56918 53874 54150 59323 FALSE TRUE 43166.51803 59087.44498 49277.59701 59389.17161 47939.48577 51335.08157 52456.61843 53151.90715 52201.15208 70946.20604 0.608440119 0.832848552 0.694576916 0.837101445 0.675715989 0.723577545 0.739385816 0.74918604 0.73578497 1 16.11443792 QQHQGILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQHQGILSR 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 0 ; 115.78 0.0021097 71948000 69769 135290 125262 130708 128709 157474 120599 137771 113060 128642 FALSE TRUE 72523.53399 158525.0051 128526.4306 156561.6523 106831.0902 120903.05 111146.1353 135924.4051 108990.9927 153846.9369 0.471400572 1.030407288 0.835417547 1.01764556 0.694398552 0.785865825 0.722446202 0.883504136 0.708437847 1 17.23113619 -1.108624304 4.077066854 1.000040531 0.808464862 0.129435918 0.156176546 29135567.09 78084970.47 17820.24137 0.03463665 0.07787099 1.108624304 -0.19157567 QQHVIETLIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQHVIETLIGK 11 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ; 141.73 3.80E-05 699600000 1628890 1243220 1514100 1351030 1667610 1923460 1730900 1615730 1594260 1039280 FALSE TRUE 1693199.835 1456733.364 1553558.69 1618259.702 1384150.248 1476765.565 1595227.535 1594073.782 1536882.894 1242907.018 1.362290027 1.172037283 1.249939591 1.301995788 1.113639418 1.188154499 1.283464903 1.282536633 1.236522823 1 20.24528694 -1.741422984 2.402199245 0.9419901 1.242473573 0.537968975 0.067664939 6534175.725 4517772.764 2252626.844 0.016427252 0.018137483 1.741422984 0.300483473 QQKPTLSGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQKPTLSGQR 10 1 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80;C9JFN4;C9J188;C9JWF5;C9JV57 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 61.233 0.097455 0 160330 153400 151040 133970 266620 270210 184120 147200 178130 260600 FALSE TRUE 166659.9522 179745.2567 154976.2265 160468.8661 221300.0276 207457.8226 169688.1933 145227.0248 171719.1361 311659.5805 0.534749973 0.576735862 0.49726123 0.514885074 0.710069709 0.665655207 0.544466475 0.465979658 0.550983017 1 18.24961154 -2.108582732 2.378049439 1.798983089 0.559128179 0.775876145 0.070553958 4217633.838 1138806.533 18228565.85 0.019691998 0.007787844 2.108582732 -1.23985491 QQLQMLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQLQMLDR 8 0 Q6ZU80;H0YJE3;Q6ZU80-1 Q6ZU80 CEP128 Centrosomal protein of 128 kDa 0 ; 60.973 0.06744 161587000 113431 170698 120216 165239 134762 167774 129144 130544 102937 170906 FALSE TRUE 117909.3435 200014.0537 123348.9277 197922.781 111855.2034 128811.0311 119021.3558 128794.2712 99232.31748 204391.7585 0.576879148 0.978581794 0.603492668 0.968350106 0.547258873 0.630216365 0.582319741 0.630134366 0.485500581 1 17.6409775 3.209520738 24.99924933 0.62296917 0.78314213 0.115327369 0.177723184 350.6792206 301884.5662 0.046326272 0.05537899 1620.02135 -3.209520738 0.16017296 QQLS(ph)PSPGQEAGILPETEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QQLSPSPGQEAGILPETEK 19 0 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 QQLS(1)PSPGQEAGILPETEK;QQLS(0.999)PS(0.001)PGQEAGILPETEK;QQLS(0.973)PS(0.027)PGQEAGILPETEK 277.27 1.76E-39 626180000 892170 675145 828870 673270 974890 1090600 954530 889600 930440 642396 TRUE FALSE 927393.5605 791095.9019 850471.0331 806440.7965 809178.546 837324.6782 879711.4444 877676.3671 896953.6462 768261.1968 1.207133153 1.02972258 1.107007664 1.049696119 1.053259685 1.089895835 1.145068172 1.142419233 1.167511323 1 19.55123736 2.329768895 6.614095311 1.127973814 1.08365449 0.01085909 0.062636646 0.493220178 29.83923169 0.020466341 0.017022249 213.6824701 -2.329768895 -0.044319324 QQLSAEELDAQLDAYNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQLSAEELDAQLDAYNAR 18 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ; 192.32 4.21E-14 150996000 77957 115445 105064 98299 115827 133794 86001 113439 115994 130873 FALSE TRUE 81034.80256 135271.7807 107802.0542 117742.2488 96138.76791 102722.3712 79260.0169 111918.5358 111819.3986 156515.0586 0.517744447 0.864273265 0.688764743 0.752274253 0.614246123 0.656309828 0.506405055 0.715065609 0.714432206 1 17.25594194 0.659903874 1.988550429 0.999804595 0.667266204 0.502271408 0.099810339 1.368272853 6.920684191 0.092324968 0.025486454 4.569870298 -0.659903874 -0.332538391 QQLTGHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQLTGHSK 8 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 ; 89.08 0.01416 85201000 124176 111440 120328 107516 136085 151005 135957 132565 136002 123022 FALSE TRUE 129078.5644 130578.9531 123463.8465 128782.3439 112953.3203 115936.3773 125300.3351 130788.183 131107.3146 147125.8055 0.877334632 0.88753263 0.839171933 0.875321249 0.767732893 0.788008445 0.851654369 0.888954746 0.891123852 1 17.16669079 0.900128229 1.118678381 0.998012858 0.840536464 0.618146513 0.037309182 0.436148077 1.096154002 0.038480826 0.012185896 7.945628019 -0.900128229 -0.157476395 QQLVASHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQLVASHLEK 10 0 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VX93 Q13561 DCTN2 Dynactin subunit 2 0 ; 116.55 0.0028105 0 1123250 1078360 1221040 1093540 1518380 1531150 1292940 1279220 1327400 1242830 FALSE TRUE 1167596.777 1263559.942 1252861.305 1309838.948 1260286.31 1175563.617 1191595.984 1262074.148 1279627.133 1486338.743 0.785552273 0.850115727 0.842917748 0.881251972 0.847913247 0.790912316 0.801698798 0.849116094 0.86092564 1 20.50333152 0.6464392 1.701021549 0.999902422 0.83180549 0.759514394 0.028433683 0.737938338 2.891154065 0.028370555 0.008040424 4.430361861 -0.6464392 -0.168096932 QQNDELTTLADEAQSLKDEIDVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQNDELTTLADEAQSLKDEIDVLR 24 1 Q86VS8 Q86VS8 HOOK3 Protein Hook homolog 3 0 ; 260.41 4.71E-44 62947000 49173 40551 45419 38034 55793 52320 49118 45321 48174 33642 FALSE TRUE 51114.38801 47515.31881 46602.65645 45557.01168 46309.32579 40169.47292 45268.00281 44713.54613 46440.22715 40233.50579 1.270443304 1.180988777 1.15830464 1.132315238 1.151013934 0.998408469 1.12513195 1.111350981 1.154267475 1 15.29610983 8 0.421421822 1.08616289 4.529724838 0.569124711 0.050298985 58.75371045 0.751817821 0.032048708 170.6987922 99999999.97 -8 3.443561948 QQNELAELHANLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QQNELAELHANLAR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;;; 196.37 2.49E-08 2161920000 1310570 1642210 1510580 1568760 1543850 1840270 1454320 1538830 1458500 1530380 FALSE TRUE 1362312.316 1924246.793 1549946.956 1879056.046 1281426.928 1412895.182 1340326.598 1518204.501 1406008.87 1830228.66 0.744339953 1.05136961 0.846859734 1.026678298 0.70014581 0.771977411 0.732327401 0.829516297 0.768214869 1 20.80359247 3.234288111 24.99999021 0.788672945 0.921855149 0.206138913 0.110875765 140.6590077 823047.9999 0.028978742 0.035804696 1715.094722 -3.234288111 0.133182204 QQPGPSEHIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QQPGPSEHIER 11 0 P50552;K7EQD0 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ;;;; 223.31 7.03E-12 3642526000 636472 1113516 1023122 1005430 1068245 1233358 914258 1007398 1007815 1120893 FALSE TRUE 661600.406 1304753.711 1049785.4 1204301.053 886665.0965 946929.2962 842596.069 993895.4776 971543.935 1340510.523 0.493543613 0.973325975 0.78312358 0.898389854 0.661438371 0.706394527 0.628563562 0.741430568 0.724756664 1 20.35435111 -1.10391482 4.586914467 1.000015853 0.740333173 0.28022523 0.127324847 2.49E-05 4.86E-06 0.116962025 0.027566076 0.078720017 1.10391482 -0.25968268 QQPPEPEWIGDGEST(ph)SPSDKVVK ddPTM_MDA-MB-175_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(0.099)T(0.524)S(0.373)PS(0.005)DKVVK 163.19 2.54E-11 171110000 157260 86535 128340 76225 171510 150990 131750 122560 151610 76942 TRUE FALSE 163468.7462 101396.7131 131684.6458 91302.07749 142356.7915 115924.8608 121423.0907 120917.2837 146153.5857 92017.31176 1.776499912 1.101930834 1.431085557 0.992227177 1.547065316 1.259815773 1.319567899 1.31407103 1.588327054 1 16.48961769 -2.018132738 2.451742732 0.612628709 1.349678493 0.197989958 0.220026938 16966909.91 5823597.353 37010967.34 0.047334042 0.009591074 2.018132738 0.737049784 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q5STZ8;Q8NE71;Q8NE71-2;A0A0G2JIC2 Q5STZ8;Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 QQPPEPEWIGDGES(0.214)T(0.139)S(0.643)PS(0.004)DKVVK;QQPPEPEWIGDGES(0.003)T(0.017)S(0.957)PS(0.023)DKVVK;QQPPEPEWIGDGES(0.052)T(0.232)S(0.692)PS(0.024)DKVVK 193.05 4.43E-18 2688360000 860110 485074 680860 441454 894230 804290 682800 670290 827070 413449 TRUE FALSE 894067.8069 568381.6861 698603.7709 528772.2836 742229.104 617505.8366 629280.3518 661305.8589 797303.9123 494456.4156 1.808183247 1.149508163 1.412872296 1.069401199 1.50110117 1.248857972 1.272671022 1.337440142 1.612485726 1 18.91548383 4.749643966 24.55947238 1.302878019 1.808183622 0.427633066 0.179455321 1173.767226 2600874.278 0.038921008 0.583104519 56188.05079 -4.749643966 0.505305603 QQPPLGPS(ph)SSLLSLPGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 QQPPLGPS(0.521)S(0.239)S(0.239)LLSLPGLK 172.95 9.98E-12 662970000 209450 319370 319610 316260 353660 416340 292020 321320 279970 277110 TRUE FALSE 217719.2477 374219.3131 327939.2992 378815.2841 293544.9995 319651.3447 269130.7093 317013.231 269893.9344 331404.3989 0.656959438 1.129192353 0.989544195 1.143060519 0.885760722 0.964535612 0.812091542 0.956575205 0.814394544 1 18.33823323 QQPPLGPSSS(ph)LLSLPGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 QQPPLGPSS(0.084)S(0.916)LLSLPGLK 230.05 1.62E-19 659490000 321490 339840 348280 293960 454040 438700 311820 352580 362620 339260 TRUE FALSE 334182.6734 398204.8764 357356.4629 352104.4106 376862.443 336818.5736 287378.7336 347854.2418 349569.377 405731.5015 0.823654738 0.981449247 0.880770809 0.867826159 0.928846889 0.830151399 0.708297809 0.857350836 0.861578102 1 18.63016579 2.721377115 22.75057631 0.832108772 0.898760538 0.050420771 0.077259378 481.029149 636869.1059 0.023878409 0.022584118 526.4742263 -2.721377115 0.066651766 QQQQEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQQQEALRR 9 1 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 ; 143.04 0.00016499 99138000 37208 47741 41457 40019 48875 53256 33943 47261 38577 58462 FALSE TRUE 38677.00057 55940.14538 42537.40348 47934.63876 40567.24496 40888.1011 31282.45897 46627.5436 37188.62131 69916.50958 0.553188379 0.800099229 0.608402847 0.685598281 0.580224116 0.584813249 0.447425925 0.666903195 0.531900427 1 16.09334554 -1.273979759 5.017372556 1.000088704 0.610366709 0.628202858 0.090772255 8.78E-05 1.27E-05 0.085679492 0.020190275 0.053213306 1.273979759 -0.389721995 QQQQQQGEDGS(ph)PQAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QQQQQQGEDGSPQAHR 16 0 A0A087WUX9;E9PEG3;A0A087WZ66;F5GZG9;P10275-3;P10275-4;P10275 A0A087WUX9 AR Androgen receptor 1 QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR;QQQQQQGEDGS(1)PQAHR 235.54 6.76E-20 796821300 253352.8 263510.3 256545.3 287584.1 252185.8 333345.6 206216.1 230682.8 221604.1 239116.7 TRUE FALSE 263355.3642 308766.1442 263231.0813 344467.3766 209319.3478 255931.1363 190052.3432 227590.8744 213628.6117 285967.0392 0.920929086 1.079726339 0.920494481 1.204570211 0.731970189 0.894967256 0.664595276 0.795864009 0.747039282 1 18.12548934 3.219280327 24.99987563 0.790219433 1.026955847 0.475882022 0.115307496 181.955516 235932.9204 0.03064343 0.036677265 1656.839068 -3.219280327 0.236736414 QQQQQQQHQQPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQQQQQQHQQPNR 13 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JH18;Q6Y7W6-4;Q6Y7W6-5 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 188.96 5.67E-06 97971000 41279 58892 54324 55098 46998 59848 44930 52180 47601 56506 FALSE TRUE 42908.72679 69006.24288 55739.72807 65996.21995 39009.29675 45949.20901 41408.2692 51480.61245 45887.84931 67577.26883 0.63495799 1.02114578 0.824829547 0.976603836 0.57725471 0.679950667 0.612754406 0.761803686 0.679042674 1 16.04425042 3.242750006 24.99999766 0.701636816 0.872756188 0.190563495 0.144444195 143.2950128 855099.7239 0.037322511 0.048790452 1748.839711 -3.242750006 0.171119371 QQQQQQQQHSENKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QQQQQQQQHSENKR 14 1 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 0 ;;;; 128.54 4.75E-05 90271700 140301 107712 132951 108365 136375 160729 131906 130876 140164 100835.4 FALSE TRUE 145840.1918 126210.6981 136415.8123 129799.2736 113194.0262 123402.1256 121566.863 129121.8213 135119.525 120592.166 1.209367048 1.046591186 1.131216204 1.076349135 0.938651572 1.023301344 1.00808259 1.070731421 1.120466855 1 16.87977666 7.999999821 0.802556737 1.037279128 42.55850742 0.453666328 0.054269026 498.3882553 1.693490125 0.018648102 37636.15738 99999958.87 -7.999999821 41.5212283 QQQS(ph)PPKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQQSPPKGK 9 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QQQS(1)PPKGK;QQQS(1)PPKGK 94.191 0.0053832 470500000 1927640 926750 1227060 816230 1622990 1803570 1581960 1355800 1513300 709080 TRUE FALSE 2003744.716 1085912.103 1259038.192 977677.8578 1347114.74 1384718.201 1457961.842 1337627.719 1458836.629 848010.6498 2.362876829 1.280540644 1.484696203 1.152907523 1.588558752 1.632901899 1.719273032 1.577371368 1.720304608 1 19.69372286 -2.06945796 2.481980814 0.123079148 1.589450987 0.263638035 0.305150462 4752700.852 2494433.885 23506348.92 0.069688589 0.00852201 2.06945796 1.466371838 QQS(ph)GSELEELMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQSGSELEELMNK 13 0 Q9H6S3;Q9H6S3-3;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 QQS(0.99)GS(0.01)ELEELMNK;QQS(0.922)GS(0.078)ELEELMNK 272.12 4.38E-32 97758000 222473 177652 194092 161260 192073 285550 242830 181015 222090 137702 TRUE FALSE 231256.4058 208162.3491 199150.197 193156.7467 159424.5001 219235.3401 223796.3501 178588.79 214097.0243 164682.0704 1.404259767 1.264025577 1.209301027 1.172906961 0.968074421 1.331264171 1.358960022 1.084445863 1.300062743 1 17.32932397 4.674516358 1.752796244 1.181902107 1.460584241 0.239085465 0.125024262 1.181387081 4.032395386 0.03226787 0.526146734 47262.46387 -4.674516358 0.278682135 QQS(ph)LFS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQSLFSSPR 9 0 Q5T7B8-4;Q5T7B8-2;Q5T7B8 Q5T7B8-4 KIF24 Kinesin-like protein KIF24 2 QQS(0.989)LFS(0.996)S(0.015)PR;QQS(0.933)LFS(0.977)S(0.09)PR 74.533 0.059678 3073000000 15526.4 109149 20805.7 18455.3 23296 30653 22693 25920.1 9803.4 25284 TRUE FALSE 16139.39426 127894.4917 21347.91363 22105.70326 19336.15424 23534.3053 20914.26336 25572.68346 9450.577549 30237.91571 0.533746916 4.229606727 0.705998186 0.731059094 0.639467165 0.778304481 0.691656911 0.845715813 0.312540641 1 14.88407108 4.104399376 24.96369069 0.71355335 2.403382643 0.385423411 0.842707951 8.199300835 1943.836337 0.184358244 0.39825938 12717.43058 -4.104399376 1.689829293 QQS(ph)PQEPK ddPTM_MDA-MB-175_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 192.44 0.0001845 25100738000 11946480 6980633 8788786 6899863 10360040 11933850 11164850 9013980 9727860 5356845 TRUE FALSE 12418136.26 8179502.416 9017828.983 8264635.307 8599044.101 9162394.197 10289719.88 8893162.342 9377756.219 6406416.215 1.938390488 1.27676725 1.407624588 1.290055942 1.342254985 1.430190279 1.606158504 1.388164934 1.463806894 1 22.6110861 -2.225006646 1.558389022 1.49E-05 1.44602317 0.359056427 0.18362989 254095.2486 39386.03891 891382.9804 0.047073487 0.00595653 2.225006646 1.446008265 QQS(ph)PS(ph)PIR ddPTM_MDA-MB-175_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 56.043 0.063436 681270000 416280 467580 510790 522860 580320 689730 562120 543620 566480 551580 TRUE FALSE 432715.0558 547883.2277 524101.607 626280.1474 481677.4137 529550.6605 518059.5656 536333.6631 546092.4955 659651.5404 0.655975207 0.830564615 0.794512822 0.949410574 0.730199786 0.802773325 0.785353378 0.813056031 0.827849951 1 19.3313446 0.46383659 1.332436725 1.000066051 0.798446921 0.432403577 0.070058333 2.352923444 4.893931904 0.06373362 0.018855471 2.909622123 -0.46383659 -0.201619129 QQSFCAKPPPS(ph)PLS(ph)PVPSVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQSFCAKPPPSPLSPVPSVVK 21 1 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 2 QQS(0.001)FCAKPPPS(0.999)PLS(0.996)PVPS(0.004)VVK 79.017 0.0045931 415280000 447440 306980 366160 303180 452000 539850 496190 432420 465970 332900 TRUE FALSE 465105.2767 359701.427 375702.4304 363148.0991 375169.2015 414478.019 457297.3312 426624.1172 449199.8307 398125.3812 1.168238195 0.903487806 0.94367867 0.912145058 0.942339321 1.04107409 1.14862642 1.071582314 1.128287348 1 18.60286332 2.532782576 4.502877954 1.09336815 0.965875821 0.310331289 0.078986015 0.228670051 9.630117382 0.02570537 0.023488687 341.0221406 -2.532782576 -0.127492329 QQSFCAKPPPS(ph)PLSPVPSVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQSFCAKPPPSPLSPVPSVVK 21 1 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 QQSFCAKPPPS(0.997)PLS(0.003)PVPSVVK;QQSFCAKPPPS(0.997)PLS(0.003)PVPSVVK 123.35 1.43E-05 582770000 1278790 841320 1027340 898530 1348100 1424840 1287720 1184300 1301300 847910 TRUE FALSE 1329277.617 985810.1654 1054113.324 1076256.552 1118950.444 1093942.504 1186785.142 1168426.396 1254466.467 1014041.73 1.310870724 0.972159366 1.039516711 1.061353315 1.103456012 1.078794364 1.170351383 1.152246856 1.237095506 1 19.95168559 2.244119876 24.83595571 1.153205293 1.085224395 0.037276261 0.098760855 293.9633128 1313280.998 0.032935996 0.026828142 175.4364682 -2.244119876 -0.067980898 QQSHFAMMHGGTGFAGIDSS(ph)SPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.01)S(0.549)S(0.441)PEVK;QQSHFAMMHGGTGFAGIDS(0.065)S(0.494)S(0.44)PEVK 140.11 1.87E-07 858970000 358250 299360 359620 325170 490330 512190 453280 475290 473390 404600 TRUE FALSE 372393.9866 350772.7513 368991.9926 389487.6555 406983.8817 393241.6348 417750.7292 468919.515 456352.7864 483873.6235 0.769610015 0.724926374 0.762579266 0.804936737 0.841095406 0.812694918 0.863346768 0.969095012 0.943123916 1 18.88427077 2.163777665 0.567434228 1.00752297 0.744395087 0.916839642 0.025595072 0.220315028 0.144572411 0.024964909 0.018602393 145.8067618 -2.163777665 -0.263127884 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 QQSHFAMMHGGTGFAGIDS(0.006)S(0.054)S(0.94)PEVK;QQSHFAMMHGGTGFAGIDS(0.078)S(0.373)S(0.548)PEVK;QQSHFAMMHGGTGFAGIDS(0.012)S(0.114)S(0.873)PEVK;QQSHFAMMHGGTGFAGIDSS(0.127)S(0.873)PEVK;QQSHFAMMHGGT(0.001)GFAGIDS(0.076)S(0.33)S(0.593)PEVK 127.83 5.51E-05 2520320000 996980 834930 950050 903923 1345250 1478070 1199890 1214680 1350090 1063120 TRUE FALSE 1036341.54 978322.7326 974809.0835 1082716.271 1116584.886 1134810.643 1105839.486 1198399.201 1301500.525 1271418.009 0.815106859 0.76947371 0.766710143 0.85158167 0.878220127 0.892555111 0.869768619 0.942569 1.023660602 1 20.278007 2.348762007 0.473205945 1.016906318 0.769268323 0.859821441 0.031163122 0.377603707 0.180262162 0.032085488 0.032964301 223.2348562 -2.348762007 -0.247637995 QQSSSSKGDS(ph)PELKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QQSSSSKGDSPELKPR 16 2 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 QQS(0.005)S(0.003)S(0.002)S(0.001)KGDS(0.989)PELKPR 138.75 2.56E-06 202930000 371110 153970 222090 125690 299890 298410 258510 201490 237640 110350 TRUE FALSE 385761.7094 180413.1498 227877.8478 150551.1069 248914.8049 229108.7999 238247.3107 198789.3561 229087.3828 131970.9697 2.923080054 1.36706694 1.726727085 1.140789578 1.886133029 1.736054531 1.805300902 1.506311248 1.735892244 1 17.00986108 7.999999977 0.047815427 1.79E-11 4.690084185 0.282257864 0.423009662 829.458622 2.998441909 71.53169487 291.9182977 99999994.66 -7.999999977 4.690084185 QQTEKPES(ph)EDEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QQTEKPESEDEWER 14 1 O60231;A0A140T947;A2AB15 O60231 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 QQTEKPES(1)EDEWER;QQT(0.006)EKPES(0.994)EDEWER;QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER 241.64 5.00E-17 4385700000 2629250 1392990 1733380 1454930 2187300 2609730 2114760 1954590 1799770 1109290 TRUE FALSE 2733054.82 1632225.197 1778553.307 1742710.811 1815503.527 2003659.758 1948999.585 1928391.918 1734996.629 1326634.137 2.060142088 1.230350668 1.340650943 1.313633324 1.368503551 1.510333334 1.469131188 1.453597389 1.307818472 1 20.33933912 -3.491908343 0.209091969 1.03E-14 1.513490799 0.318864894 0.212758755 93.44871327 1.640799814 41.01621308 0.462019464 0.000322175 3.491908343 1.513490799 QQVAPTDDETGKELVLALYDYQEKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QQVAPTDDETGKELVLALYDYQEKSPR 27 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 QQVAPTDDETGKELVLALYDYQEKS(1)PR;QQVAPTDDETGKELVLALYDYQEKS(1)PR 140.24 1.18E-07 380880000 529940 249338 330290 207493 451750 445860 379330 338172 379420 252045 TRUE FALSE 550862.4404 292159.8619 338897.6287 248534.4961 374961.6964 342315.7721 349597.1234 333639.3575 365764.7483 301428.3921 1.827506814 0.969251304 1.124305598 0.824522516 1.243949496 1.135645417 1.159801574 1.106861086 1.213438276 1 18.20145579 4.744520126 24.83835749 1.093194228 1.827507166 0.778141543 0.118663671 268.3027666 1118211.875 0.02736126 0.248505718 55529.03501 -4.744520126 0.734312938 QRDEKDEHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRDEKDEHGR 10 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 107.03 0.0013153 64581000 44622 38319 44207 29843 52897 51777 41366 44264 45322 32882 FALSE TRUE 46383.71102 44899.99017 45359.07074 35745.85633 43905.58683 39752.57644 38123.62483 43670.71348 43690.87007 39324.59834 1.179508831 1.141778736 1.153452868 0.908994824 1.116491679 1.010883216 0.969459993 1.110518996 1.111031566 1 15.26314441 3.941513704 24.99865481 1.039373185 1.157387295 0.444411063 0.064128932 237.001947 101301.0527 0.016236219 0.029270352 8740.045716 -3.941513704 0.11801411 QRDELNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QRDELNR 7 1 P43034;I3L495 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 ;;; 172.15 0.00083115 946115000 309862 357632 326984 351509 356219 390611 321314 343389 312050 387079 FALSE TRUE 322095.591 419052.514 335505.4717 421036.4311 295669.0216 299897.515 296128.5691 338786.4321 300819.3815 462919.719 0.695791468 0.905237986 0.724759516 0.909523647 0.638704746 0.647839145 0.639697461 0.731847053 0.649830563 1 18.82040249 5.065104932 15.36048329 0.745926078 0.194643332 0.011246848 0.1260875 7903941.005 41267946.66 0.028982976 137003169.7 116172.927 -5.065104932 -0.551282746 QREESYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QREESYSR 8 1 P23246;P23246-2;H0Y9K7;H0Y9U2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;; 193.38 0.00015591 2658040000 742649 884399 818599 734309 995406 1097790 836221 801930 800278 1094546 FALSE TRUE 771969.356 1036287.649 839932.3624 879553.1285 826207.2437 842844.9097 770675.813 791181.44 771476.1511 1309001.332 0.589739167 0.791662791 0.641658906 0.67192684 0.631173722 0.64388392 0.588750977 0.604416069 0.589362388 1 20.32003514 -1.16200806 6.88365327 1.000000614 0.639783254 0.779748859 0.057529877 5.50E-07 6.69E-08 0.056469832 0.013310045 0.068863952 1.16200806 -0.360217359 QREEYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QREEYER 7 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 157.68 0.0013313 305890000 187648 227790 190251 202785 203630 259720 195380 217775 210463 211670 FALSE TRUE 195056.4879 266911.1605 195209.0974 242895.2677 169017.0453 199403.9661 180065.6051 214856.0823 202888.4777 253142.6838 0.770539701 1.054390182 0.77114256 0.959519209 0.667675015 0.787713724 0.711320597 0.848754857 0.801478734 1 17.94959126 3.261154349 24.99493384 0.792154951 0.892307664 0.116881188 0.113505873 424.6637654 469792.6577 0.028937759 0.039154228 1824.544033 -3.261154349 0.100152713 QREFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QREFESR 7 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;H0YAB0;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ; 139.97 0.0024222 4114090000 324000 318865 338229 345214 409042 445751 348249 377748 327923 383420 FALSE TRUE 336791.7702 373627.5833 347043.5256 413496.2988 339513.1869 342232.0857 320952.3334 372684.9059 316121.1153 458543.808 0.734481121 0.814813278 0.756838321 0.901759639 0.740416032 0.746345452 0.699938213 0.812757471 0.689402211 1 18.80670005 -1.155550581 4.931645156 1.000015724 0.770339693 0.579942834 0.059577586 9.84E-06 1.68E-06 0.055096406 0.012985459 0.069895533 1.155550581 -0.229676031 QRELEIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRELEIEER 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 185.77 3.87E-05 617240000 401100 387890 452070 354380 465820 514200 418520 447960 416100 494540 FALSE TRUE 416935.7377 454507.0901 463851.3156 424475.3063 386640.0828 394784.8428 385715.3088 441955.8289 401124.6423 591435.6445 0.704955377 0.768481059 0.784280285 0.717703287 0.653731452 0.667502621 0.652167843 0.747259373 0.67822196 1 19.17386167 -1.134292879 4.978454442 1.000014206 0.710028019 0.795062857 0.044427593 7.57E-06 1.32E-06 0.046462168 0.010950702 0.073401869 1.134292879 -0.289986187 QRELEQLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 125.97 0.00044384 288510000 151980 122080 144710 121190 195850 173510 134700 147980 156140 148170 FALSE TRUE 157980.2878 143046.2903 148481.2615 145161.0203 162559.487 133214.9321 124141.862 145996.5701 150520.5519 177201.0746 0.891531206 0.807254079 0.837925288 0.819188149 0.917373031 0.75177271 0.700570594 0.823903413 0.849433629 1 17.43502783 2.726026085 24.72966185 0.804869755 0.84912127 0 0.079594445 1963.810197 3874440.75 0.024754802 0.023497696 532.1402205 -2.726026085 0.044251515 QRHS(ph)YPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRHSYPER 8 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 QRHS(1)YPER;QRHS(1)YPER 103.34 0.0029016 951220000 358940 418740 421690 374570 434250 511470 401470 413990 435090 425510 TRUE FALSE 373111.2284 490655.3377 432679.5878 448658.828 360436.3401 392688.8439 370001.7324 408441.1412 419431.1959 508880.5376 0.733200036 0.964185701 0.850257685 0.881658454 0.708292641 0.771671964 0.727089572 0.802626768 0.8242233 1 18.95696749 5.042933732 15.70288222 0.822124921 0.313290652 0.087059995 0.090042263 927607.8043 9460337.794 0.02126713 13691199.24 110391.0164 -5.042933732 -0.508834269 QRIDEFEAL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRIDEFEAL 9 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 102.51 0.029133 1518630000 1486080 1791470 1622690 1645630 1943910 2226570 1700670 1652910 1612780 2082720 FALSE TRUE 1544751.586 2099141.037 1664978.634 1971130.702 1613484.873 1709482.861 1567367.042 1630755.445 1554736.363 2490789.108 0.620185619 0.842761449 0.668454278 0.791367963 0.647780604 0.686321799 0.629265254 0.654714379 0.6241943 1 21.24817144 -1.076143228 5.077443734 1.000006389 0.686458524 0.641913783 0.070572261 4.97E-06 9.05E-07 0.066551833 0.015686098 0.083918318 1.076143228 -0.313547866 QRLEAEAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 135.87 0.00019021 1435240000 744550 900710 822150 769000 942680 1114490 812340 897440 827320 900190 FALSE TRUE 773945.4089 1055399.936 843575.9044 921105.9048 782443.5903 855666.5878 748666.6681 885411.2847 797544.9148 1076564.995 0.718902632 0.980340194 0.783581027 0.855597116 0.726796425 0.794811824 0.695421708 0.822441087 0.740823748 1 20.03800399 5.044239011 15.69557106 0.809964232 0.268432636 0.081435856 0.096500022 3747373.11 36778251.88 0.021479142 59320744.36 110723.2974 -5.044239011 -0.541531596 QRPDLGS(ph)AQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRPDLGSAQK 10 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 QRPDLGS(1)AQK;QRPDLGS(1)AQK 83.204 0.041467 304962000 436820 290233 353906 255376 423690 483930 354920 325345 359554 292569 TRUE FALSE 454065.9909 340078.2601 363129.0811 305888.6106 351671.3251 371544.5915 327100.443 320984.2824 346613.7218 349892.294 1.297730755 0.971951272 1.037831034 0.874236489 1.005084511 1.061882751 0.93486038 0.917380257 0.990629767 1 18.41655137 4.738594082 23.40596624 0.972245445 1.297730881 0.763869727 0.053419746 0.519040976 358998.843 0.012969471 0.074513979 54776.47517 -4.738594082 0.325485436 QRPDLGSAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QRPDLGSAQK 10 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 79.693 0.023931 85527000 51391 47717 49855 50604 64353 70762 57086 52183 56934 60526 FALSE TRUE 53419.95636 55912.02356 51154.26226 60613.32016 53414.30005 54328.59791 52611.45015 51483.57224 54884.95646 72384.91086 0.73799851 0.772426503 0.706697869 0.837375075 0.737920368 0.750551424 0.726828969 0.711247298 0.758237536 1 16.14340137 -1.769593265 2.095449648 1.083227888 0.746977279 0.820381465 0.03525145 583282.7529 323969.185 248564.4804 0.009137408 0.016998349 1.769593265 -0.336250609 QRPQATAEQIR ddPTM_MDA-MB-175_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 ;;; 237.49 1.27E-15 912970000 182570 200690 142282 171519 310486 268341 161166 163534 160776 356347 FALSE TRUE 189778.0046 235156.9463 145989.9858 205444.9463 257709.7006 206022.8695 148533.3878 161342.0942 154989.7032 426166.372 0.445314359 0.55179611 0.34256571 0.48207686 0.60471618 0.483432957 0.348533806 0.378589454 0.36368356 1 18.70105723 -1.475025122 3.747713915 1.006005789 0.442666365 0.797244144 0.084033786 21744981.45 17164966.37 1002557.401 0.020987668 0.033494606 1.475025122 -0.563339424 QRPVPQPSSAS(ph)LDEYTLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QRPVPQPSSASLDEYTLMR 19 1 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 QRPVPQPS(0.004)S(0.021)AS(0.975)LDEYTLMR 66.609 0.016313 144670000 36854 44735 40443 46490 42977 56661 40067 45525 33656 49002 TRUE FALSE 38309.02438 52417.88826 41496.9778 55685.58324 35671.78489 43502.34146 36926.44384 44914.81184 32444.72713 58603.0037 0.65370411 0.894457365 0.708103257 0.95021722 0.60870233 0.742322726 0.630111795 0.766425081 0.553635907 1 15.83868699 3.217440596 24.99997256 0.704870342 0.801572029 0.078845012 0.138320878 519.0806066 614439.2458 0.036215617 0.04332551 1649.835318 -3.217440596 0.096701687 QRQEEPPPGPQRPDQSAAAAGPGDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRQEEPPPGPQRPDQSAAAAGPGDPK 26 2 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 ; 120.08 0.00014452 173919000 102273 62890 80128 66915 98573 93588 79188 75757 77844 57403 FALSE TRUE 106310.817 73690.86828 82216.20151 80150.58728 81817.59667 71853.60534 72981.03764 74741.60133 75042.40965 68650.0188 1.548591229 1.073428232 1.197613678 1.167524622 1.191807345 1.046665487 1.063088385 1.08873388 1.093115646 1 16.0669725 QRQEEPPPGPQRPDQSAAAAGPGDPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QRQEEPPPGPQRPDQSAAAAGPGDPKR 27 3 Q9BQ61;K7EN60;K7ELS0;K7ERU7 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 80.729 0.0050768 63095000 14134 15754 17707 14971 22842 24467 15432 17538 16572 18502 FALSE TRUE 14692.02123 18459.62695 18168.45897 17932.21912 18959.325 18784.91005 14222.39952 17302.9318 15975.57696 22127.11266 0.663982756 0.834253761 0.821094882 0.810418395 0.856836827 0.848954418 0.642758942 0.781978745 0.721991034 1 14.43352759 4.74782036 23.83786367 0.800330906 0.663982615 0.191284394 0.088550232 1123.265878 2891562.833 0.020324098 0.245282242 55952.61126 -4.74782036 -0.136348291 QRQELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QRQELEK 7 1 P35579 P35579 MYH9 Myosin-9 0 ;;; 155.75 0.0014498 4167230000 2179524 1800040 2066878 1658411 2579090 2642890 2311852 2080415 2237200 1624780 FALSE TRUE 2265573.29 2109182.868 2120742.539 1986439.746 2140697.203 2029118.851 2130642.999 2052530.44 2156683.609 1943124.533 1.165943434 1.08545944 1.091408452 1.022291527 1.101677822 1.044255691 1.096503576 1.056304115 1.109904987 1 20.88994693 4.835730023 0.009770248 2.95E-07 2.209553627 0.354623708 0.036535653 8068.834391 11.89275641 1248.232142 1446.593998 68506.22283 -4.835730023 2.209553332 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.991)DDES(0.009)PSTSSGSSDADQRDPAAPEPEEQEER 249.44 7.09E-48 774540000 47230.9 72550 71381.3 51440.7 67522 103094 60325.5 65497.1 60851 59692.7 TRUE FALSE 49095.6124 85009.89814 73241.55532 61615.51692 56044.63456 79151.9809 55597.02968 64619.21851 58660.9844 71388.34168 0.687725912 1.190809257 1.025959612 0.863103351 0.785067047 1.1087522 0.778797047 0.905178871 0.821716586 1 16.12340087 3.735212804 24.8171146 0.888954126 0.990429361 0.04156933 0.149018711 646.5204105 4792621.134 0.037015515 0.060063802 5435.165894 -3.735212804 0.101475235 QRS(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;QRS(1)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR 171.16 7.38E-15 312824000 57680.8 77370.2 73626.8 64254.4 106735 104103 68817.6 83128.4 77747.9 110844 TRUE FALSE 59958.08252 90657.92999 75545.57489 76963.72854 88592.22282 79926.65595 63423.49669 82014.19977 74949.76827 132561.7596 0.452303007 0.683892024 0.569889651 0.580587711 0.668309044 0.602939009 0.478444892 0.618686717 0.565395092 1 17.01630513 -1.969205699 2.596331057 1.345879073 0.584203971 0.768723989 0.069069553 5031965.807 2814030.845 10472362.02 0.016061669 0.010734808 1.969205699 -0.761675101 QRS(ph)PIALPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QRSPIALPVK 10 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 QRS(1)PIALPVK;QRS(1)PIALPVK;QRS(1)PIALPVK;QRS(1)PIALPVK 96.229 0.0041681 2883110000 6405700 5579010 6642650 5876530 8848400 9036500 8324100 7455900 8021600 5864510 TRUE FALSE 6658601.982 6537161.569 6815762.916 7038890.094 7344352.129 6937909.824 7671635.291 7355965.856 7732904.183 7013548.452 0.949391314 0.932076197 0.971799505 1.003613241 1.047166378 0.989215355 1.093830797 1.048822277 1.102566588 1 22.74171312 3.580985222 0.830136578 1.059451701 0.928482245 0.628685447 0.033439261 0.441869099 0.589404926 0.014060784 0.039328547 3810.528567 -3.580985222 -0.130969456 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_MDA-MB-175_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 173.59 2.43E-12 1311800000 1729500 1238420 1707430 1049690 2129420 2033390 1691170 1613870 1831920 1248410 TRUE FALSE 1797781.995 1451109.001 1751927.028 1257315.549 1767461.949 1561165.989 1558611.676 1592238.712 1765989.557 1493012.037 1.204130945 0.971933893 1.173417886 0.842133565 1.183822973 1.045648628 1.043937783 1.066460734 1.182836784 1 20.50979437 1.442784316 24.99904266 1.102495165 1.06146949 0.00475773 0.110225984 142.135056 103495.0633 0.054341672 0.024976877 27.71943131 -1.442784316 -0.041025675 QRS(ph)PLLNQPVPELSHASLIANQSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QRSPLLNQPVPELSHASLIANQSPFR 26 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR;QRS(1)PLLNQPVPELSHASLIANQSPFR 312.13 5.31E-82 2099300000 240901 753720 722307 767931 678760 1003670 636047 793440 662266 857860 TRUE FALSE 250411.9575 883165.5469 741130.9138 919825.4598 563384.6176 770582.8533 586191.9741 782805.2346 638431.176 1025941.242 0.244080214 0.860834432 0.722391189 0.896567388 0.549139263 0.751098427 0.571369928 0.763011762 0.622288246 1 19.96851668 -2.024725568 2.502400018 1.368839734 0.680193265 0.238880092 0.177674241 11885820.71 4686328.859 25163238.64 0.039145183 0.009446576 2.024725568 -0.688646469 QRS(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QRSPSPAPAPAPAAAAGPPTR 21 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR;QRS(1)PS(1)PAPAPAPAAAAGPPTR 133.36 5.70E-06 4168240000 793670 880700 865510 792370 863160 1092280 866800 844560 882480 910820 TRUE FALSE 825004.7044 1031953.374 888065.9016 949098.421 716440.3715 838614.5237 798857.951 833240.0546 850719.7172 1089277.74 0.757386912 0.947373967 0.815279583 0.871309847 0.657720566 0.769881264 0.73338316 0.764947289 0.78099431 1 20.05494042 5.085538671 14.43539699 0.801501666 0.000102503 0.013179102 0.096857158 2360861.677 7076381.123 0.0225089 58370929.38 121769.5415 -5.085538671 -0.801399163 QRS(ph)SPVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.534)S(0.466)PVTK;QRS(0.585)S(0.415)PVTK 53.798 0.081337 120737000 145462 110176 126612 94293 152292 165904 146794 137708 151433 110056 TRUE FALSE 151204.9521 129097.8709 129911.6127 112943.874 126405.4602 127375.3103 135287.9027 135862.2495 145982.9559 131619.3661 1.148804744 0.980842522 0.98702506 0.858109846 0.960386484 0.967755081 1.027872317 1.032236012 1.10912976 1 17.00601225 2.00713624 2.381826845 1.05146613 0.977160258 0.135733089 0.071180961 0.560537003 5.977781476 0.038815987 0.021408928 101.6567544 -2.00713624 -0.074305872 QRSDDES(ph)PSTSSGSSDADQRDPAAPEPEEQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GN77;R4GND1;A0A1B0GX65;Q969T4;R4GMM6;R4GNG6 R4GN77 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 QRS(0.3)DDES(0.692)PS(0.003)T(0.004)SSGSSDADQRDPAAPEPEEQEER 132.43 2.72E-08 444140000 32907 34177 34772 34147 37943 49321 39455 30067 31918 35888 TRUE FALSE 34206.19377 40046.63389 35678.18689 40901.17468 31493.46241 37866.94522 36362.414 29664.00104 30769.27741 42919.56648 0.796983674 0.933062404 0.831280225 0.952972689 0.73377867 0.882276973 0.847222304 0.691153324 0.716905597 1 15.38934788 1.947392231 17.07828867 0.768570497 0.857152302 0.020643964 0.098644876 19.77944586 6419.367126 0.037925611 0.024442392 88.59153586 -1.947392231 0.088581805 QRSS(ph)PVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QRSSPVTK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QRS(0.059)S(0.941)PVTK;QRS(0.158)S(0.842)PVTK;QRS(0.024)S(0.976)PVTK;QRS(0.295)S(0.705)PVTK;QRS(0.209)S(0.791)PVTK;QRS(0.149)S(0.851)PVTK 125.23 0.00076976 6322020000 4503150 3196690 3944280 3006280 4600590 4987020 4802230 4125660 4419940 3201680 TRUE FALSE 4680937.839 3745696.641 4047071.177 3600913.211 3818583.355 3828860.184 4425818.664 4070362.276 4260867.223 3828987.896 1.222500036 0.978247188 1.056955855 0.940434733 0.997282692 0.999966646 1.155871678 1.06303869 1.112792032 1 21.86853167 2.26744125 24.95999927 1.087902942 1.025412811 0.081170222 0.080191903 428.1867895 370057.5389 0.026744128 0.02237195 185.1148461 -2.26744125 -0.06249013 QRT(ph)LEDEEEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRTLEDEEEQER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQER;QRT(1)LEDEEEQER 252.37 7.55E-21 1436210000 404380 430450 457840 377130 397640 468480 546120 466160 502780 334270 TRUE FALSE 420345.2346 504376.4391 469771.6865 451725.1884 330049.2948 359682.6199 503313.6874 459911.8877 484685.046 399763.8065 1.051483971 1.261686103 1.175123107 1.129980206 0.825610747 0.89973783 1.259027654 1.150459047 1.212428534 1 18.60878833 3.469566682 24.98731501 1.069242077 1.169305794 0.111264205 0.133584972 459.6067472 1520177.223 0.040810428 0.05536815 2948.266119 -3.469566682 0.100063717 QRT(ph)LEDEEEQERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRTLEDEEEQERER 14 2 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 1 QRT(1)LEDEEEQERER;QRT(1)LEDEEEQERER 225.08 1.39E-10 1031200000 1099820 327720 461890 347380 642850 819270 677200 510400 585690 365018 TRUE FALSE 1143241.743 384003.3607 473927.2328 416090.7272 533578.5866 629006.9587 624119.2945 503558.9228 564611.1313 436536.2884 2.6188928 0.879659655 1.085653691 0.95316412 1.222300644 1.440904171 1.429707704 1.15353279 1.293388766 1 18.73574206 4.745911604 24.98672185 1.179569136 2.618893483 0.853044931 0.18127172 333.481043 1133506.839 0.045930253 0.476438292 55707.23514 -4.745911604 1.439324347 QRWDEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRWDEAFR 8 1 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ; 193.1 0.00015724 1028660000 282780 269930 239990 202664 533220 388330 334210 266830 285400 521310 FALSE TRUE 293944.3728 316288.3777 246244.3366 242750.3343 442583.4549 298146.2427 308013.7469 263253.5803 275128.5097 623450.7134 0.471479728 0.507318976 0.394970013 0.389365717 0.709893253 0.478219427 0.494046667 0.422252433 0.441299535 1 19.24991599 -1.611723691 2.914964168 1.038514342 0.477861269 0.767331676 0.086105137 34604295.62 34979787.25 10157101.58 0.022559628 0.024449856 1.611723691 -0.560653073 QRYDENEDLS(ph)DVEEIVSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRYDENEDLSDVEEIVSVR 19 1 Q8NHM5-4;Q8NHM5-2;Q8NHM5-3;Q8NHM5;S4R3G4;F6SRV7;F5H0A1;F8WBN2 Q8NHM5-4;F8WBN2 KDM2B Lysine-specific demethylase 2B 1 QRYDENEDLS(1)DVEEIVSVR;QRYDENEDLS(1)DVEEIVSVR 203.25 3.12E-16 66838000 48110 51073 45994 43778 52816 63613 45602 48623 49435 56996 TRUE FALSE 50009.41995 59844.39046 47192.64142 52437.15774 43838.35519 48839.84481 42027.59608 47971.28822 47655.84401 68163.27495 0.733671027 0.877956502 0.692347037 0.769287535 0.643137455 0.716512592 0.61657243 0.703770296 0.699142523 1 16.05670703 -1.058442565 3.986467559 1.000047666 0.715019937 0.612538201 0.067524142 19895072.15 36848236.02 13110.88154 0.016702987 0.087409258 1.058442565 -0.285027729 QRYEILTPNSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QRYEILTPNSIPK 13 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 134.13 9.04E-05 1752610000 2500550 1750070 2054020 1707010 2906000 2977300 2401390 2437730 2547840 1993130 FALSE TRUE 2599273.645 2050630.909 2107549.449 2044651.483 2412039.158 2285867.196 2213162.777 2405056.217 2456143.736 2383645.663 1.090461424 0.860291838 0.884170614 0.857783317 1.011911794 0.958979446 0.928478092 1.008982272 1.030414786 1 21.18473836 1.682820443 4.754182095 1.016559344 0.936466144 0.188328186 0.06724342 0.250609869 13.12600433 0.036259334 0.017527812 48.17485801 -1.682820443 -0.0800932 QS(ph)FAVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSFAVLR 7 0 Q8TE77;Q8TE77-2;A0A087WWG1;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 QS(1)FAVLR 99.568 0.010943 42439000 41950 76733 72596 60711 72131 73738 57575 71627 66011 67302 TRUE FALSE 43606.21839 89911.29585 74487.9114 72719.4546 59870.19838 56613.46701 53062.12106 70666.95722 63635.277 80488.53833 0.541769292 1.117069557 0.925447436 0.9034759 0.74383508 0.703373029 0.659250648 0.877975407 0.790612904 1 16.29649574 4.799458441 22.40125984 0.841854851 0.541759666 0.330384877 0.133265796 33286.00045 12242473.03 0.032971559 71.17767395 63017.10402 -4.799458441 -0.300095185 QS(ph)PALQHRPMGQSQANHIPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSPALQHRPMGQSQANHIPGDR 22 1 Q5TCQ9;Q5TCQ9-1;Q5TCQ9-3;Q5TCQ9-2 Q5TCQ9 MAGI3 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3" 1 QS(1)PALQHRPMGQSQANHIPGDR;QS(0.998)PALQHRPMGQS(0.002)QANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR;QS(1)PALQHRPMGQSQANHIPGDR 117.03 8.70E-05 806440000 94607 127165 126184 142651 134260 181169 129869 140457 126772 118840 TRUE FALSE 98342.15741 149004.5995 129472.4587 170866.942 111438.5332 139095.2454 119689.5284 138574.4037 122209.5005 142124.4227 0.691944112 1.048409533 0.910979663 1.202234907 0.784091369 0.978686441 0.842146101 0.975021752 0.859876847 1 17.11679496 QS(ph)PECENFLDVGLGR ddPTM_MDA-MB-175_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 69.485 0.051943 36777000 20744 22786 19423 26040 31101 35925 27110 27894 25630 23048 TRUE FALSE 21562.98914 26699.31825 19929.17934 31190.63428 25814.46313 27581.9632 24985.04736 27520.12656 24707.58131 27563.81432 0.782293368 0.968636559 0.723019648 1.13157903 0.936534502 1.000658431 0.906443755 0.998415032 0.89637744 1 14.75048792 3.748522435 24.99998846 0.977035415 0.839048542 0.413861354 0.084871893 708.9749945 1779225.304 0.020186232 0.035846717 5604.313676 -3.748522435 -0.137986873 QS(ph)PLTYEDHGAPFAGHLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSPLTYEDHGAPFAGHLPR 19 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 QS(0.982)PLT(0.018)YEDHGAPFAGHLPR;QS(0.974)PLT(0.026)YEDHGAPFAGHLPR 171.29 6.80E-12 898900000 260140 262350 284130 287670 288150 352280 252390 259950 243187 232350 TRUE FALSE 270410.5281 307406.5717 291534.6612 344570.2674 239170.3659 270468.3089 232607.0123 256465.7954 234434.7474 277874.5339 0.973138935 1.106278317 1.049159335 1.240021036 0.860713512 0.973346874 0.837093666 0.922955378 0.843671221 1 18.0840741 3.21569862 24.99998028 0.902259863 1.090087956 0.569672793 0.079078774 155.5806874 170129.6533 0.021485925 0.025696488 1643.231003 -3.21569862 0.187828093 QS(ph)PSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSPSFK 6 0 Q6IN85-2;Q6IN85;Q6IN85-4 Q6IN85-2 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 QS(0.992)PS(0.008)FK 94.114 0.047046 666610000 1628600 1233100 1340300 1112400 1713400 1840900 1682300 1499400 1531100 918220 TRUE FALSE 1692898.386 1444875.333 1375229.319 1332429.4 1422156.88 1413378.874 1550436.93 1479302.996 1475996.01 1098127.629 1.541622614 1.315762663 1.25234015 1.21336479 1.295074309 1.287080697 1.411891377 1.347113903 1.344102426 1 20.06661431 -1.48497719 2.963446092 0.990191515 1.329841757 0.572708262 0.086541235 20883040.55 25488122.5 1695684.024 0.021772157 0.032735789 1.48497719 0.339650242 QS(ph)PSPSTRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.5)PS(0.5)PSTRPIR;QS(0.996)PS(0.004)PSTRPIR 83.633 0.01003 654510000 1238300 1156980 1344160 1170620 1597950 1771540 1432720 1406610 1391550 1363210 TRUE FALSE 1287189.04 1355682.315 1379189.914 1402165.142 1326331.03 1360126.683 1320419.663 1387756.694 1341468.387 1630304.899 0.789538841 0.831551396 0.845970539 0.860063135 0.81354784 0.834277492 0.809921913 0.851225249 0.822832826 1 20.63671037 -4.999996347 0.512866232 6.893232671 0.829454934 0.867905789 0.020028075 921.9477036 4.078899399 6251.331692 0.008977775 1.00E-05 4.999996347 -6.063777737 QS(ph)SFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSSFPK 6 0 B4E059;A0A087X1G4;Q86X67-3;Q86X67 B4E059 NUDT13 Nucleoside diphosphate-linked moiety X motif 13 1 QS(0.975)S(0.025)FPK 76.478 0.07862 650960000 800160 547250 711660 588210 872840 895380 797240 756340 735820 474910 TRUE FALSE 831750.9347 641235.9305 730206.4442 704556.1824 724474.9686 687441.5646 734750.2456 746202.4994 709337.9819 567959.5218 1.464454601 1.129016956 1.285666348 1.240504218 1.275575003 1.210370701 1.293666568 1.313830424 1.248923479 1 19.11542859 0.951313887 21.13389988 0.999999999 1.272187861 0.512055617 0.080422759 1307.848652 567719.05 0.069975887 0.017493972 8.939513549 -0.951313887 0.272187862 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_MDA-MB-175_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(0.982)PT(0.018)GGGGGGGSGGTR;QSAGPNS(0.876)PT(0.124)GGGGGGGSGGTR 268.31 2.87E-37 362620000 312150 330810 320060 374700 351330 433520 323360 332360 328150 290920 TRUE FALSE 324473.923 387624.0442 328401.0265 448814.5416 291611.0521 332841.5501 298014.1983 327905.2578 316339.9456 347920.204 0.932610177 1.114117662 0.943897545 1.289992753 0.838154981 0.956660597 0.856559047 0.942472596 0.909231318 1 18.40839693 QSAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSAPSPTR 8 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 QSAPS(0.992)PT(0.008)R 97.633 0.0084895 338620000 603240 770130 665880 689360 659600 856460 651890 686460 622880 657450 TRUE FALSE 627056.381 902393.8367 683233.3798 825713.3505 547481.4276 657560.1448 600793.1584 677259.1265 600462.6705 786264.7399 0.797513038 1.147697195 0.868960981 1.050172173 0.696306727 0.83630883 0.764110519 0.861362709 0.763690192 1 19.58465563 3.247370551 24.99965441 0.813691737 0.97212059 0.273702226 0.115879886 218.5574585 620189.265 0.029172827 0.038915685 1767.545291 -3.247370551 0.158428854 QSDEVGDRDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSDEVGDRDHR 11 1 P40222 P40222 TXLNA Alpha-taxilin 0 ;;; 136.7 5.63E-05 565678000 226692 282048 252563 286115 276918 333470 219888 282608 255103 298935 FALSE TRUE 235641.9752 330487.55 259144.9993 342707.693 229847.5773 256026.6463 202652.604 278820.102 245921.8929 357505.5898 0.659128086 0.924426245 0.724869783 0.958607929 0.642920234 0.716147254 0.566851568 0.779904175 0.687882651 1 18.44760627 QSDS(ph)VKGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSDSVKGK 8 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 1 QS(0.005)DS(0.995)VKGK 107.06 0.0024689 320110000 713770 299130 627060 290070 1160400 589890 733130 504420 708530 390440 TRUE FALSE 741950.1908 350503.2506 643401.6987 347444.9802 963155.6225 452896.9874 675665.3549 497659.075 683030.1437 466939.2426 1.588965165 0.750639952 1.377913099 0.744090341 2.0627001 0.969927018 1.447009147 1.065789785 1.462781624 1 18.83287532 5.056584318 20.20386613 1.221438159 6.702187676 0.082620961 0.377804981 742.3925352 271721.7189 0.079394763 4426.629288 113915.8928 -5.056584318 5.480749517 QSFDDNDS(ph)EELEDKDSK ddPTM_MDA-MB-175_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 298.15 1.91E-46 6320650000 14125810 3705709 5606900 3287365 9047280 9695160 8407730 5836060 6899960 2449531 TRUE FALSE 14683507.89 4342135.694 5753020.42 3937595.985 7509426.577 7443606.022 7748710.153 5757837.162 6651631.787 2929469.7 5.012343321 1.482225842 1.963843633 1.344132689 2.563408175 2.540939755 2.645089708 1.96548787 2.270592451 1 21.4822081 7.999999957 0.061113659 2.50E-10 7.031359184 0.224316959 0.927781469 639.6593663 2.915014769 66.7666839 398.489292 99999990.02 -7.999999957 7.031359184 QSFTMVADT(ph)PENLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QSFTMVADTPENLR 14 0 Q14847;Q14847-2;C9J9W2;F6S2S5 Q14847 LASP1 LIM and SH3 domain protein 1 1 QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR;QSFTMVADT(1)PENLR 234.82 3.58E-16 369492000 591210 497230 394447 440230 390270 538010 416710 423670 444560 600770 TRUE FALSE 614551.4273 582625.3846 404726.6129 527306.18 323932.0448 413065.3311 384047.1813 417991.3966 428560.3724 718479.3791 0.855350126 0.810914553 0.563309991 0.733919714 0.450857818 0.574916056 0.534527771 0.581772294 0.596482495 1 19.45458723 -1.070576833 6.541928552 1.000000312 0.624897027 0.449777431 0.121248313 5.71E-07 8.11E-08 0.121679166 0.028680031 0.08500083 1.070576833 -0.375103285 QSHAASAAPQASS(ph)PPDYTMAWAEYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 QSHAASAAPQAS(0.319)S(0.681)PPDYTMAWAEYYR;QSHAASAAPQAS(0.04)S(0.96)PPDYTMAWAEYYR 230.88 3.10E-35 641040000 254860 393630 371690 388550 344030 472130 342220 396160 354980 382380 TRUE FALSE 264922.0696 461232.8905 381376.5467 465404.0303 285551.9035 362484.9627 315395.9022 390850.1232 342204.3391 457300.0399 0.579317836 1.008600154 0.833974445 1.017721386 0.624430087 0.792663309 0.689691394 0.85469077 0.748314693 1 18.80278152 4.772367436 23.67410645 0.827950344 0.579316818 0.264580642 0.129276015 11397.75842 7981280.369 0.029669832 4.879721405 59206.23387 -4.772367436 -0.248633526 QSHSES(ph)PSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.001)ES(0.499)PS(0.499)LQSK;QSHSES(1)PSLQSK;QSHSES(1)PSLQSK;QSHSES(0.995)PS(0.005)LQSK;QSHS(0.001)ES(0.999)PSLQSK;QSHSES(1)PSLQSK;QS(0.001)HS(0.006)ES(0.993)PSLQSK 302.15 1.41E-36 7708050000 5874120 5169450 6051180 4781554 6895610 7530460 6497880 6206580 6526400 4431596 TRUE FALSE 6106034.793 6057262.825 6208878.722 5727331.11 5723496.675 5781624.79 5988559.187 6123390.947 6291516.139 5299882.388 1.152107603 1.14290514 1.171512548 1.080652492 1.079928998 1.09089681 1.129941902 1.155382421 1.18710486 1 22.33752891 3.751573926 24.42570541 1.112535274 1.154248101 0.179646089 0.048314482 1231.715126 2311898.101 0.01261502 0.022529854 5643.830035 -3.751573926 0.041712827 QSHSGS(ph)ISPYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.002)GS(0.703)IS(0.296)PYPK 188.63 9.40E-06 94955000 109690 75804 102080 85088 117870 129630 130940 103180 106230 62729 TRUE FALSE 114020.6459 88822.74733 104740.2887 101918.1524 97834.4995 99525.39706 120676.5807 101797.0409 102406.8031 75019.54653 1.519879167 1.183994724 1.396173311 1.358554632 1.304120113 1.32665954 1.608601841 1.356940232 1.365068276 1 16.19497892 0.558208555 2.98562195 1.000003854 1.379964333 0.520204266 0.109582861 7.945807395 52.65380961 0.101856257 0.026630852 3.615834592 -0.558208555 0.379960478 QSHSGSIS(ph)PYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(0.999)PYPK;QSHSGSIS(0.999)PYPK;QSHSGSIS(1)PYPK;QSHSGS(0.013)IS(0.987)PYPK 168.1 3.85E-05 10318139000 8448030 6325670 7956560 6990820 9435730 11190170 10472930 8858490 8414470 4643240 TRUE FALSE 8781564.748 7412054.616 8163914.49 8373583.33 7831847.985 8591422.606 9652034.381 8739756.431 8111634.868 5552993.978 1.581410818 1.334785279 1.470182486 1.507940287 1.410382942 1.547169444 1.73816763 1.573881849 1.460767813 1 22.4048344 0.870171828 6.714511302 1.000000801 1.522607841 0.698359327 0.101978391 2.219751729 114.7621943 0.106588081 0.02674696 7.41603597 -0.870171828 0.52260704 QSHSS(ph)SS(ph)PHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 QS(0.032)HS(0.092)S(0.869)S(0.195)S(0.812)PHPK;QS(0.016)HS(0.119)S(0.757)S(0.269)S(0.839)PHPK 77.222 0.017539 1346300000 1618940 1556570 2013750 1506600 2363800 2515100 2428100 2061750 2192800 1399570 TRUE FALSE 1682857.001 1823898.789 2066229.979 1804600.983 1962002.12 1931006.142 2237779.177 2034115.614 2113881.556 1673788.945 1.005417682 1.089682659 1.234462675 1.078153245 1.172192065 1.153673614 1.33695421 1.215276048 1.262931962 1 20.67468619 2.811762055 1.961637138 1.223460401 1.110938484 0.135460187 0.098213687 0.523155304 3.980204667 0.033974692 0.035220083 648.279151 -2.811762055 -0.112521916 QSHSS(ph)SSPHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.023)S(0.431)S(0.431)S(0.115)PHPK 87.447 0.022928 397990000 147700 669040 735500 686930 827900 937990 634990 882920 678050 678360 TRUE FALSE 153531.31 783942.4156 754667.7342 822802.7037 687173.8537 720156.0379 585217.8246 871085.9016 653647.1129 811271.654 0.189247719 0.966313086 0.930228155 1.014213549 0.847032989 0.887687909 0.721358649 1.073729 0.80570683 1 19.62982556 4.740909006 24.99963146 0.91718629 0.189247465 0.826392045 0.099964666 79.3380358 844536.6169 0.022808937 0.153440197 55069.23019 -4.740909006 -0.727938825 QSHSSS(ph)SPHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHS(0.002)S(0.075)S(0.461)S(0.461)PHPK;QSHS(0.007)S(0.057)S(0.468)S(0.468)PHPK 90.444 0.019192 474565000 137607 662441 704030 601489 685888 846500 629545 840870 619205 622540 TRUE FALSE 143039.8306 776210.0887 722377.6002 720461.7289 569301.0028 649913.2038 580199.6179 829599.513 596919.933 744514.7938 0.1921249 1.042571746 0.970266281 0.967692966 0.764660431 0.872935245 0.779298978 1.114282107 0.801756981 1 19.50594099 4.744156079 24.96740441 0.925605971 0.192124582 0.795266713 0.111356196 258.0209546 1151275.746 0.026595872 0.233790051 55482.50729 -4.744156079 -0.733481389 QSHSSSS(ph)PHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSHSSSSPHPK 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 QSHSS(0.003)S(0.014)S(0.983)PHPK;QSHS(0.001)S(0.016)S(0.047)S(0.937)PHPK;QSHSS(0.001)S(0.067)S(0.932)PHPK;QSHSSS(0.125)S(0.875)PHPK 155.06 2.04E-05 2334449000 503792 2715963 2984115 2773063 3138779 4043728 2878833 3884390 2963337 2800653 TRUE FALSE 523682.0972 3182408.518 3061883.488 3321566.585 2605250.467 3104633.455 2653182.547 3832326.106 2856687.08 3349387.334 0.156351609 0.95014646 0.914162258 0.99169378 0.77782896 0.926925777 0.792139661 1.144187197 0.852898395 1 21.67546579 4.739349854 24.84569398 0.932624593 0.156351344 0.837967839 0.101745604 22.14338901 696955.7937 0.024055496 0.145283581 54871.8817 -4.739349854 -0.776273248 QSHVWEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QSHVWEQK 8 0 Q8TE77;Q8TE77-3;E9PIT5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;;; 116.52 0.0022561 757890000 2050517 1596461 1937362 1620953 2313420 2511180 2192979 1959736 2148935 1527653 FALSE TRUE 2131472.995 1870640.758 1987851.245 1941572.665 1920185.695 1927996.502 2021087.576 1933468.944 2071595.249 1826967.357 1.16667273 1.023904861 1.088060626 1.062729806 1.051023538 1.055298824 1.106252703 1.058294193 1.133898338 1 20.80101943 QSIAIDDCTFHQCVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSIAIDDCTFHQCVR 15 0 A0A087WY71;Q96CW1-2;Q96CW1;E9PFW3;C9JJ47 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 166.48 1.37E-06 214230000 166840 213150 169340 171920 200620 242260 166620 204440 196200 190600 FALSE TRUE 173426.972 249756.8544 173753.1395 205925.2629 166518.6841 185998.7865 153559.889 201699.8162 189138.8003 227944.4207 0.760830081 1.095691895 0.762260989 0.903401198 0.730523184 0.815983062 0.673672505 0.884864019 0.829758411 1 17.79832257 5.064072181 15.0132036 0.843883875 0.00012779 0.045972315 0.119358303 714645.6342 3947399.388 0.027154574 18350213.05 115896.9963 -5.064072181 -0.843756084 QSIDALKDWFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSIDALKDWFR 11 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 ; 93.766 0.0082128 500670000 767470 750660 708070 688710 1014390 999330 774610 791120 794390 882240 FALSE TRUE 797770.3082 879580.0157 726522.8859 824934.7824 841964.3501 767250.7525 713894.0441 780516.3304 765800.0591 1055098.036 0.756110125 0.833647666 0.688583298 0.781856049 0.79799632 0.727184324 0.676613944 0.739757163 0.725809387 1 20.00894563 -1.849762864 7.268782635 1.02050357 0.746562675 0.735106817 0.045467526 0.01475638 0.000304997 0.043000438 0.01047979 0.01413309 1.849762864 -0.273940895 QSIRNS(ph)QK ddPTM_MDA-MB-175_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 110.66 0.0020487 233650000 254780 176280 251320 157191 408230 294540 265900 255030 298420 223180 TRUE FALSE 264838.9111 206554.7187 257869.6057 188282.9106 338839.2104 226137.5488 245058.0632 251611.74 287679.9225 266907.848 0.992248498 0.773880275 0.966137218 0.705422909 1.269498866 0.84724953 0.918137346 0.942691427 1.077824892 1 18.0259822 QSLGHPPPEPGPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSLGHPPPEPGPDR 14 0 P13861-2;P13861;C9J830 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 67.605 0.052116 281940000 55817 163080 124330 141170 118370 173170 116910 150300 107240 140230 FALSE TRUE 58020.69826 191087.7214 127570.1419 169093.0046 98249.50968 132953.8919 107746.2887 148285.4743 103380.4533 167705.3836 0.345968012 1.139425087 0.760680064 1.008274159 0.58584589 0.792782492 0.642473643 0.884202231 0.616440875 1 17.35556948 -1.15426536 4.278457054 1.000054907 0.771930586 0.100810118 0.214728799 27666696.68 7464075.173 14167.63422 0.045156252 0.070102683 1.15426536 -0.228124321 QSMAFSILNT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSMAFSILNTPK 12 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 QSMAFSILNT(1)PK;QSMAFSILNT(1)PK 228.9 1.06E-10 2109090000 3119400 1811930 1831450 1422700 2603100 2445500 1740100 2082100 2026200 1630680 TRUE FALSE 3242556.321 2123114.883 1879179.092 1704105.814 2160625.992 1877569.687 1603706.415 2054192.855 1953277.458 1950180.525 1.662695468 1.088676077 0.963592379 0.873819522 1.107910762 0.96276712 0.822337417 1.053334719 1.001588024 1 20.89517625 4.745595001 2.820888575 0.972923423 1.79507858 0.877460168 0.076925821 0.135086954 1.47299205 0.018813271 0.257861 55666.63911 -4.745595001 0.822155157 QSMDMS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QSMDMSPIK 9 0 Q14562;F5H658 Q14562 DHX8 ATP-dependent RNA helicase DHX8 1 QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK;QSMDMS(1)PIK 167.3 6.30E-05 983550000 2381070 1591920 1814840 1382080 2927640 2700740 2372400 1827240 1980940 1734290 TRUE FALSE 2475076.482 1865319.877 1862136.221 1655451.299 2430000.799 2073534.065 2186445.089 1802748.837 1909646.356 2074090.921 1.193330754 0.89934335 0.897808386 0.798157536 1.171598012 0.999731518 1.05417032 0.869175415 0.920714872 1 20.98404771 1.733443334 24.99999949 0.920043262 0.992656442 0.066350199 0.118591173 1.616375578 7828.770256 0.055368414 0.030704614 54.13066139 -1.733443334 0.07261318 QSNASS(ph)DVEVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QSNAS(0.003)S(0.997)DVEVEEK;QSNAS(0.006)S(0.994)DVEVEEK;QSNAS(0.114)S(0.886)DVEVEEK;QSNAS(0.127)S(0.873)DVEVEEK 349.81 6.73E-76 1856490000 3527790 1953770 2465530 2283910 2988110 3498810 3856880 2783140 2898350 1456710 TRUE FALSE 3667069.873 2289314.799 2529783.737 2735660.581 2480192.13 2686264.402 3554567.668 2745836.561 2794038.95 1742124.434 2.104941416 1.314093732 1.452125742 1.570301482 1.423659574 1.541947492 2.040363821 1.576142615 1.603811355 1 20.73241624 QSNASS(ph)DVEVEEKETSVSKEDTDHEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSNASSDVEVEEKETSVSKEDTDHEEK 27 2 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 QS(0.011)NAS(0.173)S(0.816)DVEVEEKETSVSKEDTDHEEK 127.31 3.04E-05 351390000 278280 167180 244570 159500 342380 358060 244490 245040 284310 190220 TRUE FALSE 289266.7093 195891.8645 250943.6951 191048.6239 284182.3699 274905.9915 225326.2349 241755.6396 274077.7386 227489.967 1.271558096 0.861101116 1.103097857 0.839811208 1.249208366 1.208431277 0.99048867 1.062709019 1.204790445 1 17.79544339 3.224584106 24.99956838 1.113537231 1.013635925 0.109396842 0.139414171 531.1038098 949975.5384 0.038759245 0.04655038 1677.197112 -3.224584106 -0.099901307 QSNVIADHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSNVIADHR 9 0 P49750;P49750-1;H0YIQ2;P49750-3;F8VU51;H0YI23 P49750 YLPM1 YLP motif-containing protein 1 0 71.221 0.050193 96133000 89505 105320 103810 90069 110260 139660 95649 86571 92456 115780 FALSE TRUE 93038.72651 123407.8907 106515.3739 107884.3794 91518.04458 107226.0816 88151.78145 85410.65735 89128.52662 138464.8743 0.67193017 0.891257739 0.769259167 0.779146191 0.660947732 0.774391933 0.636636417 0.616839887 0.643690518 1 17.07916051 3.286471985 8.875867548 0.694083048 0.785677304 0.018110355 0.117189353 0.642703517 110.2099489 0.03064138 0.041375065 1934.069095 -3.286471985 0.091594256 QSPAS(ph)PPPLGGGAPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSPASPPPLGGGAPVR 16 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 QS(0.298)PAS(0.702)PPPLGGGAPVR;QS(0.021)PAS(0.979)PPPLGGGAPVR 185.28 1.77E-09 392680000 337610 403490 383690 405940 395470 549710 424000 417060 424860 446010 TRUE FALSE 350939.1035 472786.2688 393689.2766 486233.7204 328248.1507 422048.1834 390765.7721 411469.9929 409569.3716 533397.1201 0.65793213 0.886368244 0.738079119 0.911579201 0.615391681 0.791245711 0.732598204 0.771413975 0.767850737 1 19.02485051 -1.708186593 3.41156184 1.023609373 0.7663187 0.408849365 0.085219323 13875206.11 7214727.376 2458862.062 0.017978364 0.019580032 1.708186593 -0.257290673 QSPGSTS(ph)PKPPHTLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSPGSTSPKPPHTLSR 16 1 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 QS(0.001)PGS(0.003)T(0.059)S(0.937)PKPPHTLSR 73.294 0.021421 190900000 93355 61032 81900 58505 104190 108520 98253 84993 89802 56740 TRUE FALSE 97040.72749 71513.77124 84034.38128 70077.11438 86479.82102 83317.87464 90551.67312 83853.80786 86570.04356 67857.11665 1.430074431 1.053887562 1.238401887 1.032715769 1.27443996 1.227842837 1.334446225 1.235740804 1.275769556 1 16.05021251 QSPS(ph)PS(ph)TRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 QS(0.358)PS(0.67)PS(0.822)T(0.15)RPIR;QS(0.131)PS(0.881)PS(0.967)T(0.021)RPIR 127.27 0.0034696 254070000 399390 413020 420110 418220 456010 550980 472090 457570 442350 358010 TRUE FALSE 415158.2256 483952.9722 431058.4117 500942.6677 378497.5831 423023.2452 435086.3522 451437.0226 426429.9099 428155.205 0.969644234 1.130321357 1.006780734 1.170002518 0.884019577 0.988013786 1.016188399 1.054377051 0.995970398 1 18.70777434 3.245240646 24.99985186 0.998361212 1.069096292 0.248898132 0.066595505 250.5236026 937570.7375 0.018127022 0.023995225 1758.897962 -3.245240646 0.07073508 QSPS(ph)PSTRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSPSPSTRPIR 11 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 QS(0.484)PS(0.516)PSTRPIR 60.937 0.0548 469640000 542750 598360 559970 552250 738540 758800 628050 598560 622140 599240 TRUE FALSE 564178.1891 701123.6754 574563.2782 661483.4017 613003.2346 582580.1997 578821.7999 590537.2822 599749.3029 716649.6049 0.787244122 0.978335397 0.801735289 0.92302207 0.855373715 0.812921958 0.807677554 0.824025128 0.836879416 1 19.45090838 3.004981078 24.78523486 0.839219346 0.876842317 0 0.07339994 387.7600044 1929417.81 0.019404281 0.023115914 1011.53538 -3.004981078 0.037622972 QSPSS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 QSPS(0.113)S(0.789)S(0.097)PT(0.001)R 127.03 0.0004793 243380000 433030 511970 568820 656370 619400 747360 701300 689310 649670 628260 TRUE FALSE 450126.3588 599896.8649 583643.9165 786198.0269 514114.6092 573796.9664 646330.2735 680070.9269 626288.5036 751355.5182 0.599085716 0.798419457 0.776787955 1.046372866 0.684249462 0.763682375 0.860218975 0.905125351 0.833544825 1 19.51913618 8 0.099112793 1.06036605 0.064250185 0.338905141 0.104433006 166.8147215 1.171897479 1.357642313 22.60269378 100000000 -8 -0.996115864 QSPSSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSPSSSPTR 9 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 QSPS(0.011)S(0.095)S(0.894)PTR 127.7 0.00045962 263090000 292930 367660 405520 466370 466020 578460 503190 496530 463180 451240 TRUE FALSE 304495.1026 430802.745 416088.1843 558616.594 386806.0869 444121.4316 463748.653 489874.8275 446510.2423 539651.8385 0.564243612 0.798297558 0.771030792 1.035142576 0.716769701 0.822977705 0.859347861 0.907760879 0.827404283 1 19.04166941 5.110546004 1.256745891 0.868421893 0.146502005 0.512800772 0.089897154 2.550749682 1.861997339 0.023696983 2.976374072 128987.0185 -5.110546004 -0.721919888 QSQESLPGAVS(ph)PLSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSQESLPGAVSPLSGR 16 0 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 QSQESLPGAVS(1)PLSGR 140.35 1.79E-06 201770000 168100 224960 224100 212470 259060 257390 193560 213680 235100 193380 TRUE FALSE 174736.7178 263595.1301 229940.2301 254495.9318 215025.0737 197615.0733 178388.2614 210815.9691 226638.7969 231269.1085 0.755555806 1.139776651 0.994253974 1.100432018 0.929761329 0.854481061 0.771344961 0.9115613 0.979978685 1 17.81921305 3.011730082 23.97587442 0.888613046 1.008392504 0.126688145 0.112275337 214.4222894 438266.0487 0.031224144 0.037288035 1027.377576 -3.011730082 0.119779458 QSQQPMKPIS(ph)PVKDPVS(ph)PASQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 QS(0.019)QQPMKPIS(0.98)PVKDPVS(0.936)PAS(0.065)QK 46.415 0.087698 304990000 418220 122010 205580 114090 273280 277630 243790 185790 237890 88348 TRUE FALSE 434731.6485 142964.2684 210937.5837 136656.6615 226827.9632 213154.64 224681.1028 183299.7889 229328.3854 105658.0991 4.114513249 1.353083859 1.996416607 1.293385577 2.146810942 2.017399914 2.126492003 1.734838981 2.170476162 1 16.68904383 4.745519374 24.99600625 1.808751775 4.114514314 0.761321007 0.394666699 364.8100682 1310372.954 0.086371828 0.864882739 55656.9462 -4.745519374 2.305762538 QSQQPMKPISPVKDPVS(ph)PASQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSQQPMKPISPVKDPVSPASQK 22 2 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 QSQQPMKPIS(0.014)PVKDPVS(0.963)PAS(0.023)QK;QSQQPMKPIS(0.002)PVKDPVS(0.959)PAS(0.038)QK 69.782 0.0094993 801300000 1022540 410270 560560 337520 906240 768470 697940 576100 739640 267106 TRUE FALSE 1062910.669 480730.681 575168.6541 404280.4486 752197.6485 590004.4888 643233.6391 568378.3218 713020.5009 319440.3066 3.327415629 1.504915538 1.800551283 1.265589972 2.354736183 1.846994498 2.01362704 1.779294316 2.232093089 1 18.28518684 -1.995690015 2.816233485 0.065056742 1.961586567 0.239402185 0.534901066 99897266.89 96189051.13 606585710.1 0.119227482 0.010099735 1.995690015 1.896529825 QSS(ph)PSGSEQLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QSSPSGSEQLVR 12 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 QSS(0.998)PS(0.002)GSEQLVR;QSS(0.937)PS(0.062)GSEQLVR;QSS(0.996)PS(0.003)GSEQLVR;QSS(0.999)PSGSEQLVR;QSS(0.946)PS(0.017)GS(0.037)EQLVR;QS(0.004)S(0.961)PS(0.018)GS(0.018)EQLVR 335.95 2.51E-58 4859680000 3351730 3629420 3469410 3679870 3639980 4563640 4054750 3802650 3679010 3229120 TRUE FALSE 3484058.888 4252744.652 3559825.675 4407737.303 3021257.5 3503803.773 3736928.1 3751681.697 3546603.149 3861804.239 0.902184231 1.101232582 0.921803762 1.141367358 0.782343514 0.907297096 0.967663783 0.971484173 0.918379837 1 21.8808436 3.246995829 24.99985397 0.928591286 1.015914243 0.212229456 0.086729953 304.7037154 903059.515 0.0230447 0.030707964 1766.020861 -3.246995829 0.087322957 QSS(ph)TPSAPELGQQPDVNISEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.098)S(0.449)T(0.449)PS(0.003)APELGQQPDVNISEWK 151.95 2.89E-08 84880000 106160 74990 103490 82163 113800 131910 102320 94672 103330 67318 TRUE FALSE 110351.2788 87868.94916 106187.0344 98414.59617 94456.31665 101275.9016 94299.89104 93403.07669 99611.17348 80507.67322 1.370692685 1.091435706 1.318967872 1.222425046 1.173258559 1.257965826 1.171315569 1.16017608 1.237287944 1 16.29683867 -4.999999986 0.167226017 0.167211448 1.269358878 0.464606583 0.0744226 112.0993307 1.050915485 30.9269854 0.255147967 1.00E-05 4.999999986 1.10214743 QSSLAEPVS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSSLAEPVSPSK 12 0 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 QSSLAEPVS(0.936)PS(0.064)K;QSSLAEPVS(0.974)PS(0.026)K;QSSLAEPVS(0.998)PS(0.002)K;QSSLAEPVS(0.994)PS(0.006)K 228.51 1.09E-11 807100000 1784190 1019680 1383480 1172310 1799930 2100930 1947470 1534560 1642500 895150 TRUE FALSE 1854631.199 1194802.108 1419534.625 1404189.419 1493978.542 1613020.847 1794822.213 1513991.733 1583386.746 1070537.504 1.732429917 1.116076834 1.32600177 1.311667657 1.395540592 1.506739224 1.676561733 1.414235118 1.479057707 1 20.02990391 -0.475707814 6.423635703 1.000000073 1.432816337 0.37867178 0.168798099 0 0 0.161194764 0.03799397 0.334419956 0.475707814 0.432816264 QSST(ph)PSAPELGQQPDVNISEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 QS(0.27)S(0.27)T(0.437)PS(0.024)APELGQQPDVNISEWK 174.15 1.09E-11 82051000 108600 80780 99228 89971 123220 132940 114710 104730 106490 76183 TRUE FALSE 112887.6119 94653.33662 101813.9632 107766.9953 102275.1084 102066.6997 105718.7305 103326.2657 102657.4457 91109.60024 1.239030921 1.038895313 1.117488859 1.182828099 1.122550293 1.120262842 1.160346771 1.134087576 1.126746747 1 16.47531546 0.579205878 2.576318593 1.000002518 1.136469229 0.422052656 0.048559513 4.814405643 28.33389859 0.043069674 0.011448895 3.794948425 -0.579205878 0.136466711 QSTIVCHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QSTIVCHNR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;;;; 140.16 0.00010975 1499500000 635245 866130 775400 772350 965750 1048420 771900 827810 762090 952840 FALSE TRUE 660324.9631 1014881.09 795607.561 925118.5248 801592.16 804940.344 711396.461 816714.561 734662.5298 1139530.755 0.579470945 0.890613163 0.698188757 0.811841647 0.703440567 0.70637878 0.624288952 0.716711293 0.644706189 1 20.12000843 -1.028157259 4.966171985 1.000004282 0.712933207 0.514482342 0.084877968 3.76E-06 7.36E-07 0.076804266 0.018102669 0.093722258 1.028157259 -0.287071075 QSVDHFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSVDHFAK 8 0 E7ETZ4;Q9Y6E2;Q75MG1;B5MCH7;B5MCE7;E9PFD4 E7ETZ4 BZW2 Basic leucine zipper and W2 domain-containing protein 2 0 ; 87.913 0.014987 499910000 316480 479560 535840 479620 625500 669250 531210 522530 498230 472470 FALSE TRUE 328974.8748 561920.6995 549804.4306 574487.4045 519177.7334 513826.8301 489572.3721 515526.34 480298.7996 565041.4505 0.582213702 0.994476952 0.973033801 1.016717276 0.918831234 0.909361304 0.866436209 0.912369065 0.85002401 1 19.10799718 4.744761529 24.80098723 0.933007947 0.582213528 0.79459643 0.054203266 289.7795024 1158957.826 0.013693323 0.12659123 55559.90943 -4.744761529 -0.35079442 QSVEHFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSVEHFTK 8 0 Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3;C9IZ80 Q7L1Q6-2 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 ; 75.378 0.032862 95120000 389900 683250 608080 642240 713030 895890 594470 717520 669450 999820 FALSE TRUE 405293.5531 800592.8726 623927.0643 769273.1551 591829.4153 687833.1248 547873.888 707902.818 645356.6253 1195715.586 0.338954813 0.669551256 0.521802234 0.643357972 0.494958351 0.575248105 0.458197496 0.592032776 0.539724189 1 20.18944284 -0.576449201 0.970371328 1.019039209 0.541688825 0.704003702 0.090002362 18.81007265 10.12446019 1.432462821 0.024809776 0.265186126 0.576449201 -0.477350385 QSVENDIHGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QSVENDIHGLR 11 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 190.46 2.26E-06 722296000 634530 1061590 1121300 1079830 434527 940970 537400 740910 1390490 922480 FALSE TRUE 659581.7344 1243909.824 1150521.999 1293417.151 360666.2557 722443.978 495277.1838 730979.3133 1340446.537 1103222.294 0.597868388 1.127524191 1.042874138 1.172399396 0.326920746 0.654848966 0.448936888 0.662585698 1.215028507 1 20.07329209 3.260182591 24.99989994 0.67771261 0.999456869 0.171121201 0.278960854 352.210821 407232.8208 0.076082954 0.102925561 1820.46608 -3.260182591 0.321744259 QSVFPFESGKPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QSVFPFESGKPFK 13 1 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 ; 145.43 3.81E-05 1184010000 1342430 1108790 1101200 884190 1388940 1431500 1283080 1341430 1209990 1133250 FALSE TRUE 1395430.173 1299216.057 1129898.177 1059080.143 1152848.475 1099055.82 1182508.837 1323450.325 1166442.696 1355288.64 1.029618438 0.958626833 0.8336956 0.7814425 0.850629483 0.810938561 0.872514387 0.976508093 0.860659982 1 20.37016871 -0.884242346 7.799797402 1 0.886368789 0.173951348 0.074478639 0 7.40E-11 0.077469514 0.01825974 0.130544222 0.884242346 -0.11363121 QSYVDT(ph)SPAAPVSYADMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QSYVDTSPAAPVSYADMR 18 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 QSYVDT(0.623)S(0.377)PAAPVSYADMR 108.75 0.0042717 53459000 104890 118030 130170 110500 166080 173560 128980 145540 149840 161190 TRUE FALSE 109031.1382 138300.7344 133562.3371 132356.5702 137849.7809 133253.3203 118870.2106 143589.2744 144447.2877 192772.0943 0.565596066 0.717431301 0.692850994 0.686596111 0.715091992 0.691247978 0.616635987 0.744865458 0.749316379 1 17.5565367 0.605290392 1.063554118 1.000109761 0.675938243 0.810408099 0.047112368 0.510158399 0.89647636 0.042827304 0.013474686 4.029864022 -0.605290392 -0.324171518 QTDDLRGEIAVLEATVQNNQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 QTDDLRGEIAVLEATVQNNQDER 23 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;;;; 197.12 2.76E-24 283622000 126520 170950 148406 144434 165572 188647 143317 154824 147349 160109 FALSE TRUE 131515.1073 200309.3327 152273.5823 173002.6141 137428.1306 144836.5932 132083.4391 152748.8375 142045.9383 191479.2931 0.68683723 1.046114854 0.7952483 0.903505603 0.717717976 0.756408648 0.689805341 0.797730319 0.741834462 1 17.54682886 3.243397685 24.9713649 0.76799694 0.866891511 0.077167054 0.116268684 221.4399601 1143176.232 0.029707206 0.038976332 1751.449762 -3.243397685 0.098894571 QTDFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QTDFEHR 7 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 ;; 106.6 0.010525 1365020000 1226210 1420590 1329700 1327920 1467920 1708450 1428350 1389650 1403920 1324630 FALSE TRUE 1274621.718 1664565.282 1364353.074 1590578.613 1218403.483 1311688.379 1316392.195 1371024.015 1353393.193 1584165.887 0.804601165 1.050751879 0.861243816 1.004048014 0.769113571 0.827999384 0.830968654 0.865454828 0.854325424 1 20.59529199 3.242623208 24.99999129 0.849167049 0.933852151 0.144772172 0.084143397 162.7080992 1001249.867 0.021549887 0.028156976 1748.329186 -3.242623208 0.084685102 QTDPST(ph)PQQESSKPLGGIQPSSQTIQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7W5;A0A2R8YF61 A0A2R8Y4Z0 CDK13 Cyclin-dependent kinase 13 1 QTDPS(0.003)T(0.997)PQQESSKPLGGIQPSSQTIQPK 260.9 1.63E-53 249540000 143260 96194 131800 86782 155900 162900 122300 121780 133460 91148 TRUE FALSE 148916.0154 112714.5712 135234.8163 103947.2206 129400.1737 125068.9438 112713.8064 120147.7383 128656.8007 109006.7055 1.366117935 1.034015024 1.240610068 0.953585563 1.18708453 1.14735092 1.034008008 1.102205023 1.180265013 1 16.73405736 4.747945733 24.43356953 1.102133179 1.366118129 0.458700049 0.087361619 770.94604 2007052.363 0.018922735 0.233535921 55968.76615 -4.747945733 0.263984949 QTDVGITHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QTDVGITHFR 10 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;; 124.1 0.00044442 347234000 362408 454079 420275 456900 447995 553190 409409 427451 433371 474760 FALSE TRUE 376716.1477 532063.536 431227.7118 547273.4563 371844.9699 424720.0062 377318.4528 421721.7185 417774.0624 567780.1322 0.663489485 0.937094318 0.759497713 0.963882717 0.654910147 0.748036048 0.664550292 0.742755328 0.735802538 1 19.11497284 5.025611097 16.84394598 0.783339507 0.3399344 0.092561435 0.118112127 38797786.55 658273839.1 0.027032053 474335462.3 106074.5252 -5.025611097 -0.443405108 QTELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QTELKR 6 1 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YAR2;Q9H361;H0YAP2;H0YAW6 P11940-2 PABPC1;PABPC3 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3 0 ; 146.21 0.017715 1624170000 1529740 1294500 1470180 1199570 1708240 1840010 1674350 1582170 1578710 1182370 FALSE TRUE 1590135.316 1516820.305 1508494.099 1436841.366 1417873.975 1412695.563 1543110.072 1560963.599 1521892.535 1414032.764 1.124539231 1.072691061 1.066802791 1.016130179 1.002716494 0.999054336 1.09128311 1.103909074 1.076278128 1 20.43138412 -0.874324891 7.71144891 1.000009921 1.061509815 0.171449652 0.040551998 0 0 0.043669695 0.010293046 0.1335596 0.874324891 0.061499893 QTFLSHGDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTFLSHGDDFR 11 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 0 102.73 0.0028291 153410000 73639 111800 93979 93466 95673 126600 88160 100990 91605 120430 FALSE TRUE 76546.32458 131000.7803 96428.16994 111953.2958 79410.53763 97199.06864 81249.78884 99636.39424 88308.15394 144025.9527 0.531475912 0.909563713 0.669519403 0.77731335 0.551362696 0.674871902 0.564132973 0.691794724 0.613140564 1 17.13596928 -1.81474476 6.479222754 1.020828028 0.669662307 0.462915815 0.108203448 0.029597729 0.000846264 0.095251439 0.023157968 0.015319876 1.81474476 -0.351165722 QTFPFPTIYEGEKQHES(ph)EEPFMPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QTFPFPTIYEGEKQHESEEPFMPEER 26 1 H7BZ15;Q9BSF0 H7BZ15 C2orf88 Small membrane A-kinase anchor protein 1 QT(0.008)FPFPT(0.016)IY(0.002)EGEKQHES(0.974)EEPFMPEER;QT(0.012)FPFPT(0.052)IY(0.013)EGEKQHES(0.923)EEPFMPEER 48.422 0.068315 2064480000 2689200 260530 369970 216317 913420 2186310 946850 393110 433730 136527 TRUE FALSE 2795371.693 305274.0009 379611.7221 259103.857 758157.1947 1678572.636 872633.4229 387841.0034 418120.142 163276.8517 17.12044092 1.869671039 2.324957385 1.586898904 4.643384453 10.28053039 5.34450177 2.375358169 2.560804779 1 17.31696074 4.743537932 24.8168816 3.757330488 17.12044705 0.711156794 2.59087766 278.6410383 1389253.231 0.66392226 5.511938694 55403.59329 -4.743537932 13.36311656 QTFT(ph)PPPQLQQQQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QTFTPPPQLQQQQVK 15 0 B1AN48;Q9UBC9 B1AN48 SPRR3 Small proline-rich protein 3 1 QTFT(1)PPPQLQQQQVK;QTFT(1)PPPQLQQQQVK;QTFT(1)PPPQLQQQQVK 262.36 6.00E-24 735230000 824310 666401 797612 662059 950706 1025670 853838 832143 910338 680236 TRUE FALSE 856854.3953 780850.1879 818398.424 793012.2942 789105.3337 787473.6867 786911.9465 820989.4842 877575.1132 813515.2203 1.053273957 0.959847054 1.006002597 0.97479712 0.969994555 0.96798888 0.96729837 1.009187614 1.078744554 1 19.63380981 1.481553123 5.451886795 1.041270264 0.984028859 0.317284907 0.0313378 0.156415702 10.503652 0.017660452 0.007442934 30.30770999 -1.481553123 -0.057241404 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSER 39 1 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 131.24 5.52E-09 39594000 9878.4 9794 12053 12447 10451 17551 12957 14690 15375 14479 FALSE TRUE 10268.40686 11476.04331 12367.11108 14908.97945 8674.542753 13475.04624 11941.39648 14493.10458 14821.65675 17315.88283 0.593005102 0.662746648 0.714206212 0.86100025 0.500958735 0.778189964 0.689621003 0.83698329 0.855957325 1 14.07980832 1.273787621 0.882210342 0.996507522 0.678462104 0.560131289 0.092284344 0.386221647 0.652039442 0.083120503 0.03061579 18.78398015 -1.273787621 -0.318045418 QTGYGWICQECDSS(ph)SSKEDENEAERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTGYGWICQECDSSSSKEDENEAERK 26 2 A0A0U1RRH6;O94880-2 A0A0U1RRH6 PHF14 PHD finger protein 14 1 QTGYGWICQECDS(0.154)S(0.437)S(0.334)S(0.075)KEDENEAERK 108.52 0.0013494 74377000 53068 23959 30896 18298 46064 50411 28363 28362 36109 26735 TRUE FALSE 55163.16562 28073.77187 31701.17514 21917.28979 38234.05773 38703.80924 26139.83395 27981.85378 34809.44414 31973.21138 1.725293245 0.878040418 0.991491745 0.685489159 1.195815374 1.210507408 0.817554222 0.875165571 1.088706534 1 14.96457603 4.742426019 24.99165278 0.962525294 1.72529354 0.674387256 0.157041263 225.8651237 1460266.257 0.038080976 0.288322722 55261.92632 -4.742426019 0.762768245 QTLENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QTLENER 7 0 P35579 P35579 MYH9 Myosin-9 0 ;;; 125.5 0.0094068 1768980000 1108164 1734660 1581340 1921220 1481380 2089850 1688550 1600570 1555310 1808050 FALSE TRUE 1151915.17 2032574.361 1622551.019 2301231.582 1229575.557 1604514.009 1556197.039 1579116.977 1499334.697 2162302.78 0.53272612 0.940004508 0.750381045 1.064250392 0.568641713 0.74203947 0.719694324 0.730294107 0.693397202 1 21.04413712 -1.098913036 3.736201772 1.000103078 0.755413348 0.203891554 0.148285021 40676646.69 69068888.16 51777.94224 0.03349867 0.079631879 1.098913036 -0.24468973 QTLPS(ph)SPTTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTLPSSPTTTK 11 0 F8VW64;F8VWX1;F8W659;J3KQU3;P51513-2;P51513 F8VW64 NOVA1 RNA-binding protein Nova-1 1 QTLPS(0.649)S(0.331)PT(0.015)T(0.003)T(0.001)K 110.92 0.001814 111210000 426680 359090 398180 362450 503960 578480 487830 476740 459130 343170 TRUE FALSE 443525.6559 420760.9142 408556.8979 434141.5282 418297.0592 444136.7869 449592.6099 470350.0801 442606.001 410407.5911 1.080695546 1.025226929 0.995490597 1.057830161 1.019223495 1.08218463 1.095478299 1.146055995 1.078454713 1 18.64669789 2.598953886 4.077784744 1.097273765 1.03422198 0.183186674 0.040946162 0.264555976 7.487183721 0.013404502 0.012481685 397.1493777 -2.598953886 -0.063051785 QTLPSS(ph)PTTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QTLPSSPTTTK 11 0 F8VW64;F8VWX1;F8W659;J3KQU3;P51513-2;P51513 F8VW64 NOVA1 RNA-binding protein Nova-1 1 QTLPS(0.403)S(0.487)PT(0.081)T(0.022)T(0.006)K;QTLPS(0.023)S(0.849)PT(0.117)T(0.009)T(0.002)K;QTLPS(0.412)S(0.581)PT(0.006)T(0.001)TK 175.21 1.06E-05 435010000 1772630 1394870 1609410 1382270 1960130 2023020 1804100 1654960 1765260 1244720 TRUE FALSE 1842614.801 1634428.072 1651352.547 1655678.88 1626947.803 1553204.264 1662689.928 1632777.968 1701728.637 1488599.052 1.237818067 1.097963934 1.109333332 1.112239644 1.092938895 1.043400009 1.116949474 1.09685544 1.143174607 1 20.50552379 8 0.012608536 3.61E-09 2.397432475 0.422189922 0.044578553 8528.189766 8.306089001 654.1890801 950.8108734 99999999.96 -8 2.397432472 QTMEELKDLLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QTMEELKDLLKR 12 2 O14964-2;O14964;I3L2H4;I3L165 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ; 113.25 0.00066691 248760000 513660 293090 370720 268700 516910 463190 434700 377140 443750 247050 FALSE TRUE 533939.6934 343425.9276 380381.2677 321848.058 429045.8228 355621.1422 400627.0781 372085.0552 427779.5242 295454.7174 1.807179449 1.162364001 1.287443541 1.089331255 1.452154247 1.203640088 1.355967783 1.259364069 1.447868316 1 18.17257751 -2.242776877 2.030020675 3.58E-05 1.321478719 0.215424521 0.191900418 1937795.027 345376.3835 8868508.884 0.042624335 0.005717723 2.242776877 1.321442954 QTPMAS(ph)SPRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QTPMASSPRPK 11 1 Q5SSJ5;Q5SSJ5-2;Q5SWC8;B0QZK4 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 QTPMAS(0.709)S(0.291)PRPK 76.759 0.020877 171020000 243110 105560 198730 114450 243760 192300 219730 158220 197250 94564 TRUE FALSE 252708.1705 123689.1089 203909.0671 137087.8684 202325.7623 147641.2393 202506.9884 156099.3197 190151.011 113092.0053 2.234536119 1.093703384 1.803036975 1.212180013 1.789036827 1.305496697 1.790639294 1.380286072 1.681383318 1 16.78713742 -2.550204134 0.447596236 6.31E-24 1.572184268 0.221877813 0.326970028 152.2376386 7.248050491 148.4577998 0.153309676 0.002817058 2.550204134 1.572184268 QTPS(ph)PDVVLR ddPTM_MDA-MB-175_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(0.006)PS(0.994)PDVVLR;QT(0.001)PS(0.999)PDVVLR;QTPS(1)PDVVLR;QT(0.001)PS(0.999)PDVVLR;QT(0.002)PS(0.998)PDVVLR;QT(0.024)PS(0.976)PDVVLR 239.48 3.21E-12 5771940000 2391590 2837000 2597520 2595540 2891310 3391670 2642680 2738410 2818750 2901770 TRUE FALSE 2486011.82 3324232.681 2665213.505 3108930.065 2399846.159 2604006.044 2435539.836 2701706.093 2717303.738 3470316.274 0.716364626 0.957904819 0.768003056 0.89586361 0.691535287 0.750365626 0.701820711 0.778518694 0.783013283 1 21.72663572 QTQDWVLQSFEEPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QTQDWVLQSFEEPRR 15 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 0 ; 156.67 3.34E-06 229760000 119100 197966 174392 150140 164597 219578 139156 164086 168952 181396 FALSE TRUE 123802.16 231965.1205 178936.7988 179837.2439 136618.8607 168584.3372 128248.5891 161886.6956 162871.4505 216937.0732 0.570682356 1.069273763 0.824832732 0.828983452 0.629762625 0.777111698 0.591178756 0.746238037 0.750777394 1 17.7269171 5.031351674 13.84265549 0.780766242 7.31E-05 0.183354216 0.140148916 893042.4864 12321826.5 0.033208102 15735104.5 107485.9439 -5.031351674 -0.780693168 QTS(ph)IETDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 QT(0.01)S(0.99)IETDR;QT(0.012)S(0.988)IETDR;QT(0.056)S(0.944)IETDR 186.46 0.00021751 666540000 1164910 1261430 1376370 1340990 1558510 1827760 1563840 1538950 1469100 1307690 TRUE FALSE 1210901.546 1478070.79 1412239.333 1606233.82 1293595.027 1403290.44 1441262.134 1518322.892 1416227.378 1563906.818 0.774279856 0.945114359 0.903020127 1.027064913 0.827156076 0.897297987 0.921578011 0.970852531 0.905570179 1 20.57672312 8 0.098532397 1.024189987 0.577826247 0.231857839 0.06312149 222.2184824 1.553306679 0.817519079 13.41105798 100000000 -8 -0.44636374 QTVEDEKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QTVEDEKLR 9 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;; 192.12 3.20E-05 2939520000 2390100 1849840 2065780 1591550 2656100 2540020 2205570 1982230 2216610 1644630 FALSE TRUE 2484462.994 2167535.63 2119615.924 1906353.84 2204617.071 1950138.849 2032691.66 1955661.449 2136834.639 1966863.76 1.263159678 1.102026319 1.077662809 0.969235327 1.1208794 0.99149666 1.033468459 0.99430448 1.08641721 1 20.9074656 5.107569924 1.140900434 1.027436253 1.577013559 0.710774858 0.044723721 1.645820079 1.016387473 0.011927154 1.320605947 128106.1337 -5.107569924 0.549577306 QVAEQGGDLS(ph)PAANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QVAEQGGDLSPAANR 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR 263.15 5.07E-25 2104980000 1490210 1709330 1541800 1695960 1704680 2089790 1596640 1706880 1614090 1812130 TRUE FALSE 1549044.641 2002894.131 1581980.575 2031415.826 1414919.102 1604467.944 1471491.185 1684002.065 1555999.216 2167182.178 0.714773616 0.924192784 0.7299712 0.937353512 0.652884246 0.740347517 0.678988227 0.777046841 0.717982656 1 21.047389 5.047293409 16.13505461 0.781581298 0.327712285 0.031298163 0.113060689 11695911.96 103811255.3 0.025124213 163821260.4 111504.7605 -5.047293409 -0.453869013 QVAGDAPVEQATAETAS(ph)PVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVAGDAPVEQATAETASPVHR 21 0 Q92766;Q92766-2;A0A087X055;Q92766-4 Q92766 RREB1 Ras-responsive element-binding protein 1 1 QVAGDAPVEQATAET(0.012)AS(0.988)PVHR 211.49 9.46E-23 323200000 80158 148390 151630 149790 123490 134980 138240 131160 125630 111620 TRUE FALSE 83322.69974 173874.8282 155581.6024 179418.0149 102499.2139 103632.9406 127404.3876 129402.0147 121108.6008 133489.8019 0.624187755 1.302532671 1.165494294 1.344057841 0.76784303 0.776336013 0.95441289 0.969377532 0.907249836 1 17.02637 3.224667172 24.99901101 0.898048065 1.126917527 0.219740258 0.195634125 330.9768206 595538.1179 0.0555537 0.06671614 1677.517935 -3.224667172 0.228869462 QVAPESHWPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVAPESHWPELR 12 0 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 0 114.7 0.0010289 224980000 273270 210040 234530 203880 267330 286470 237270 224000 232360 186150 FALSE TRUE 284058.9106 246112.7361 240642.0445 244206.8555 221889.3421 219941.684 218672.1574 220997.6464 223997.409 222622.5284 1.2759666 1.105515861 1.080942015 1.096954819 0.996706594 0.987957892 0.982255295 0.992701179 1.006175837 1 17.76424007 8 0.480700141 0.98776258 8.822208373 0.91730824 0.025105995 25.50089414 0.285165809 0.014234093 199.6821328 100000000 -8 7.834445793 QVDEAEEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVDEAEEEIER 11 0 Q9P2M7 Q9P2M7 CGN Cingulin 0 ; 157.68 7.09E-05 161492000 147601 172351 161510 180977 156116 199079 177810 192325 159909 161534 FALSE TRUE 153428.4015 201950.9435 165719.0833 216773.7104 129579.4581 152845.9193 163872.7876 189747.198 154153.9063 193183.4945 0.794210716 1.045384048 0.857832517 1.122112999 0.670758433 0.79119554 0.848275304 0.982212266 0.797966238 1 17.55961231 5.067530863 13.03757096 0.898797748 0.000129302 0.058403924 0.129048422 2133702.337 12008982.93 0.029954084 49381895.59 116823.6748 -5.067530863 -0.898668446 QVDEAEEEIERLDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVDEAEEEIERLDGLR 16 1 Q9P2M7 Q9P2M7 CGN Cingulin 0 79.652 0.016194 29091000 22163 25500 21584 16699 29562 28560 18366 22640 19337 32391 FALSE TRUE 23038.01235 29879.42664 22146.49677 20002.01236 24537.0618 21927.37283 16926.42493 22336.54783 18641.06515 38737.39629 0.594722789 0.771332859 0.57170845 0.51634891 0.633420523 0.566051798 0.436953088 0.576614589 0.481216265 1 15.24143937 -1.48215283 5.944555456 1.000357125 0.572248235 0.691156568 0.08582303 0.000417885 3.64E-05 0.085487237 0.020133211 0.032949374 1.48215283 -0.42810889 QVDLESNPQNRS(ph)PESRPSVVYPSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVDLESNPQNRSPESRPSVVYPSTK 25 2 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 QVDLES(0.064)NPQNRS(0.884)PES(0.052)RPSVVYPSTK 82.492 0.010529 315340000 74271 53032 57026 41862 81512 86044 64843 65766 80851 50665 TRUE FALSE 77203.27643 62139.83347 58512.14441 50142.17865 67656.61936 66061.58501 59760.43622 64884.51434 77941.1883 60591.83671 1.274153098 1.025547942 0.965677022 0.827540167 1.116596278 1.090272033 0.986278672 1.070845808 1.286331502 1 15.88683582 1.447126162 11.38898367 1.155030709 1.034489419 0.09041074 0.125911006 0.591950664 210.5465115 0.070020228 0.03097405 27.99794541 -1.447126162 -0.12054129 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVDVPTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSK 40 1 P30049 P30049 ATP5D "ATP synthase subunit delta, mitochondrial" 0 178.19 4.43E-24 95518000 28884 33227 35808 35720 36850 48918 37826 38185 32810 36583 FALSE TRUE 30024.36262 38933.47878 36741.1859 42785.30939 30586.25016 37557.53586 34861.09928 37673.19253 31629.17451 43750.73843 0.686259563 0.889893067 0.839784361 0.977933423 0.69910249 0.858443473 0.796811678 0.86108701 0.722940358 1 15.41701975 -2.040411445 2.751555715 1.229309908 0.822496059 0.285044117 0.087258739 25299522.25 9471355.561 36625369.79 0.019583393 0.009111472 2.040411445 -0.406813849 QVEDLQATFSSIHSFQDLSSSILAQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QVEDLQATFSSIHSFQDLSSSILAQSR 27 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;; 332.36 2.85E-95 782941000 141960.9 223930 209724 234845 218937 287626 174953 244819 215045 221600 FALSE TRUE 147565.6259 262388.2356 215189.5797 281296.6401 181722.1669 220829.2205 161239.7267 241537.6017 207305.5725 265018.2772 0.556813015 0.990075999 0.811980147 1.061423548 0.685696733 0.833260343 0.608409836 0.911399788 0.782231228 1 18.01573233 -1.0059498 4.271710495 1.000008447 0.813817303 0.128474176 0.150975402 35235.23712 79423126.32 1923.341077 0.03265457 0.09863935 1.0059498 -0.186191144 QVEEALHQLHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QVEEALHQLHAR 12 0 F5H169;F5H5V4;F5GX23;J3KN29;O00233-2;O00233 F5H169 PSMD9 26S proteasome non-ATPase regulatory subunit 9 0 ;;;;; 207.66 4.39E-08 2778785000 708812 888455 711851 768150 788121 915217 744285 772663 722289 899405 FALSE TRUE 736796.4451 1041040.235 730402.4219 920087.7773 654156.4739 702671.722 685945.9969 762306.7163 696293.96 1075626.19 0.684993032 0.967845749 0.679048566 0.855397336 0.608163394 0.653267584 0.637717828 0.708709702 0.647338236 1 20.03674536 4.175224795 24.99999233 0.707136735 0.826434295 0.079664621 0.1302448 106.9825336 42227.45589 0.029741336 0.064248684 14970.10324 -4.175224795 0.11929756 QVEEELTHLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVEEELTHLQK 11 0 P67936-2;A0A2R8YHD2;K7ELP0 P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ; 139.89 3.89E-05 305210000 449980 434680 483210 427810 558700 660480 568030 480740 560100 450980 FALSE TRUE 467745.5579 509332.9087 495802.8496 512429.5411 463732.3736 507093.5297 523506.3243 474296.4666 539942.1104 539340.8965 0.867254015 0.944361742 0.919275458 0.950103255 0.85981311 0.940209676 0.970640884 0.879400153 1.00111472 1 19.04083791 1.22109201 24.98871614 1.000557484 0.918187492 0.476062283 0.035281858 229.5107297 328304.6196 0.031629581 0.007980812 16.637651 -1.22109201 -0.082369992 QVEELFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QVEELFER 8 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 161.79 0.00080376 480695000 439082 557192 529212 565582 559687 650533 509837 552494 503502 604894 FALSE TRUE 456417.2964 652885.3916 543003.6995 677452.4315 464551.6037 499456.5697 469874.6437 545088.7216 485381.0614 723411.3979 0.630923563 0.90250913 0.75061535 0.936469115 0.642167935 0.690418441 0.649526183 0.753497558 0.670961313 1 19.4644568 -1.401285404 3.064284923 1.003769177 0.740596636 0.379044057 0.101106698 21696561.02 26783837.83 721048.073 0.023755856 0.039693061 1.401285404 -0.263172541 QVEELYHSLLELGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVEELYHSLLELGEK 15 0 A0A0D9SGF6;Q13813;Q13813-2 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 191.86 1.58E-07 714740000 1161890 949820 1181640 1035850 1665750 1384850 1833880 1523020 1348380 853650 FALSE TRUE 1207762.314 1112944.196 1212434.509 1240738.038 1382606.41 1063239.575 1690135.694 1502606.408 1299852.067 1020906.373 1.183029459 1.09015305 1.187605975 1.215329898 1.354293054 1.041466292 1.655524677 1.471835662 1.273233375 1 19.96141913 3.029422939 1.108785414 1.375181371 1.148754786 0.055857928 0.185921789 0.811786802 2.139290419 0.081041007 0.102062791 1070.096488 -3.029422939 -0.226426584 QVELALWDTAGQEDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QVELALWDTAGQEDYDR 17 0 Q5JR08;P08134;E9PQH6;Q5JR07;C9JNR4;C9JX21;Q5JR05;U3KQA9;U3KQV3;Q5JR06;E9PN11;P62745;P61586 Q5JR08;P61586 RHOC;RHOA;RHOB Rho-related GTP-binding protein RhoC;Rho-related GTP-binding protein RhoB;Transforming protein RhoA 0 ;;;;; 323.24 1.97E-58 870454000 964196 1078605 1040533 1135100 1149363 1405302 1073214 1110818 1076159 1184478 FALSE TRUE 1002263.203 1263847.018 1067650.145 1359619.392 953994.6878 1078941.908 989092.6824 1095929.302 1037428.248 1416553.786 0.707536285 0.892198398 0.753695451 0.959807814 0.673461677 0.761666743 0.698238706 0.7736588 0.732360647 1 20.43395395 QVEPPAKKPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 214.53 1.58E-39 2632460000 684810 343850 502600 131210 859460 647190 269760 405110 572630 408760 TRUE FALSE 711846.8276 402903.5627 515698.1689 157162.9464 713369.2962 496889.9308 248615.5063 399680.1631 552021.1582 488848.6958 1.456170045 0.824188683 1.054923892 0.321496094 1.459284442 1.016449333 0.508573529 0.817594823 1.129227024 1 18.89902848 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR 37 1 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 250.33 5.27E-51 76886000 140130 119900 133180 113300 141960 174560 142000 140650 136540 111250 FALSE TRUE 145662.4406 140491.8923 136650.7802 135710.4018 117829.6899 134021.0855 130869.669 138764.8168 131625.9521 133047.3075 1.094816899 1.055954419 1.027084146 1.020016146 0.885622506 1.007319036 0.9836326 1.042973506 0.989316917 1 17.02157979 4.221540084 1.611072664 0.991324189 1.092369389 0.449615876 0.038890726 0.466316066 2.114795167 0.011451147 0.054793051 16654.82538 -4.221540084 0.1010452 QVFEQDAS(ph)GDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVFEQDASGDER 12 0 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 QVFEQDAS(1)GDER;QVFEQDAS(1)GDER 119.56 0.00052935 207144000 128374 133132 131102 148777 153467 176932 125557 142583 129957 158809 TRUE FALSE 133442.3046 155996.3854 134518.6258 178204.6465 127380.7342 135842.2244 115715.5143 140671.9081 125279.873 189924.583 0.702606806 0.821359631 0.708273904 0.93829163 0.670691135 0.715242979 0.609270861 0.74067246 0.65962958 1 17.53506713 -1.028223293 4.50402148 1.000010132 0.731043436 0.462910035 0.087378026 9.71E-06 2.10E-06 0.082936711 0.01954755 0.093708008 1.028223293 -0.268966696 QVFGEATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVFGEATK 8 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;A0A1B0GU92;A0A1B0GU03;C9JH19;F8WD96;F8W787 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ; 122.13 0.0032649 279090000 621090 525170 540830 507880 621340 753630 659640 551020 553600 509140 FALSE TRUE 645611.1128 615363.8622 554924.4741 608337.1481 515724.8487 578610.8539 607935.6932 543634.4782 533676.0441 608896.2349 1.06029743 1.010621888 0.911361316 0.999081803 0.846983146 0.950261836 0.998422487 0.892819576 0.876464681 1 19.21583687 4.412598884 3.416201041 0.931700183 1.054026541 0.395027454 0.051395049 0.215382528 4.875676291 0.012379637 0.045320885 25858.23534 -4.412598884 0.122326358 QVGETSAPGDTLDGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVGETSAPGDTLDGTPR 17 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 QVGETSAPGDT(0.086)LDGT(0.914)PR 80.382 0.015508 0 1190300 315590 477360 318060 712990 973340 721640 451300 507490 299410 TRUE FALSE 1237293.963 369790.1276 489800.3938 380971.3187 591796.2145 747296.5361 665075.9711 445251.0617 489225.534 358073.6569 3.455417451 1.032720839 1.36787609 1.063946792 1.652722011 2.086991103 1.857371963 1.243462212 1.366270667 1 18.44989686 4.745826066 24.75984721 1.443539243 3.455418537 0.759617026 0.345016091 389.2848499 1326602.23 0.086665906 0.88834985 55696.26422 -4.745826066 2.011879293 QVHPDTGISSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 208.56 4.09E-08 1.09584E+11 50318619 55131090 61178355 54495130 67149421 72133080 64928698 62263527 58813764 49577600 FALSE TRUE 52305236.93 64599425.85 62772713.19 65274104.06 55735386.4 55381265.36 59839416.99 61428986.26 56697068.12 59291381.5 0.88217268 1.08952472 1.058715645 1.100903747 0.940025093 0.934052538 1.009243089 1.036052538 0.95624468 1 25.82131908 3.226919437 24.99977687 0.984768297 1.038727922 0.140354278 0.063406583 442.3010247 949852.8595 0.018557335 0.022353832 1686.240194 -3.226919437 0.053959624 QVHQCIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVHQCIER 8 0 E7EQY1;Q96C01;C9JF51 E7EQY1 FAM136A Protein FAM136A 0 ; 147.51 0.00053616 234570000 146104 220390 164281 185739 179536 241240 164570 176133 158524 197568 FALSE TRUE 151872.2987 258240.2681 168562.2978 222477.6198 149018.5348 185215.666 151670.5734 173772.2252 152818.7522 236277.6669 0.642770435 1.092952506 0.713407661 0.941593942 0.630692425 0.783889855 0.641916671 0.735457682 0.646776118 1 17.85012375 QVIDVLETDKHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVIDVLETDKHFR 13 1 P80303-2;P80303;E9PKG6;Q2L696;E9PLR0;E9PLE9;A0A2R8Y6G7;E9PM22 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 152 2.70E-05 294890000 837370 835590 823810 833810 1358300 1264390 909580 884640 889410 1063270 FALSE TRUE 870430.0142 979096.0825 845279.1654 998735.1293 1127416.651 970754.5845 838284.7429 872782.8478 857400.3078 1271597.399 0.684516982 0.769973329 0.664738042 0.78541772 0.886614468 0.763413471 0.659237541 0.68636728 0.674270259 1 20.27821054 5.924017397 1.135123603 0.751538507 7.88E-16 0.034459214 0.104000217 98.06557823 12.24483446 0.029288878 159.9766948 839493.6148 -5.924017397 -0.751538507 QVKPYVEEGLHPQIIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVKPYVEEGLHPQIIIR 17 1 Q99832-3;Q99832;Q99832-4;F8WAM2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 149.73 1.89E-07 2092030000 3058010 2058070 2773480 2104100 3570400 3144700 3057570 2691030 3205800 2185710 FALSE TRUE 3178742.596 2411527.513 2845759.167 2520284.7 2963504.683 2414391.083 2817909.674 2654961.144 3090423.884 2613958.027 1.216064896 0.922557856 1.088678218 0.964164181 1.133723133 0.923653348 1.078024071 1.015686219 1.182277547 1 21.31780454 QVLDLEDLVFTQGSHFMANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVLDLEDLVFTQGSHFMANK 20 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 86.8 0.0030157 0 40255 66617 59502 52586 56991 71675 64438 43583 49093 43133 FALSE TRUE 41844.29848 78057.95154 61052.671 62987.35385 47303.69018 55029.5675 59387.18118 42998.84117 47326.15252 51584.08552 0.811186203 1.513217706 1.183556331 1.221061752 0.91702101 1.066793507 1.151269439 0.833567965 0.917456461 1 15.65463842 3.245834786 24.97260544 0.978906484 1.205988621 0.230084633 0.178212332 216.2873531 742520.9355 0.047882309 0.063535037 1761.305886 -3.245834786 0.227082137 QVLEDFPTISLEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVLEDFPTISLEFR 14 0 E9PNM1;P37268;A0A1W2PQ47;P37268-4;P37268-3;P37268-2;E9PJG4;E9PS69 E9PNM1 FDFT1 Squalene synthase 0 80.69 0.024235 0 46962 48977 69086 60889 67647 67922 59763 71461 65164 52972 FALSE TRUE 48816.09602 57388.41876 70886.43791 72932.66246 56148.3871 52148.14487 55078.6199 70503.18218 62818.76037 63350.84919 0.770567351 0.905882391 1.118950082 1.151249958 0.886308358 0.823164102 0.869421967 1.112900349 0.99160092 1 15.95107634 4.564374851 4.01258148 0.994589115 0.780499337 0.296333927 0.105741742 0.317051716 8.745849796 0.028233193 0.136637315 36675.39931 -4.564374851 -0.214089778 QVLGQMVIDEELLGDGHSYSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVLGQMVIDEELLGDGHSYSPR 22 0 P28070 P28070 PSMB4 Proteasome subunit beta type-4 0 ; 255.2 4.49E-37 411780000 286630 331040 310270 353130 362320 409090 309880 364560 370200 326340 FALSE TRUE 297946.3737 387893.5449 318355.8911 422978.06 300732.9758 314085.0473 285590.7959 359673.6695 356876.5743 390280.0748 0.76341682 0.993885084 0.815711361 1.083780821 0.770556826 0.804768338 0.731758586 0.921578355 0.914411463 1 18.57415028 1.045781965 2.002467873 0.995737372 0.860653395 0.150095129 0.104767734 0.612614271 5.058031065 0.096551485 0.027179585 11.11173729 -1.045781965 -0.135083977 QVLIRPCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVLIRPCSK 9 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 84.17 0.014294 781560000 924200 1004100 892460 759540 1434520 1385460 946980 1048590 1163370 1174320 FALSE TRUE 960688.1296 1176546.364 915718.2408 909774.745 1190680.803 1063707.912 872753.2331 1034535.366 1121500.541 1404405.52 0.684053228 0.837754016 0.652032641 0.647800604 0.847818373 0.757407954 0.62143962 0.736635787 0.79855891 1 20.42152814 0.84816514 2.521685479 0.999693099 0.723027875 0.570920066 0.072524258 0.417508253 4.979738559 0.06865295 0.018385381 7.049610786 -0.84816514 -0.276665223 QVNELVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVNELVR 7 0 M0R1K3;Q15102;M0R389 M0R1K3 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 0 87.435 0.045003 52714000 51697 68106 67778 65634 86637 86455 68201 73501 66634 86815 FALSE TRUE 53738.03748 79802.67571 69544.35036 78616.2093 71910.47369 66377.13649 62855.22741 72515.83932 64235.85536 103824.7371 0.517584142 0.768628729 0.669824478 0.75720114 0.69261407 0.639319091 0.605397415 0.698444719 0.618695093 1 16.66379069 -1.161263521 5.210607199 1.000014108 0.669025613 0.672859612 0.070368279 1.07E-05 1.73E-06 0.063478577 0.014961407 0.068982111 1.161263521 -0.330988495 QVQDESQR ddPTM_MDA-MB-175_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 75.825 0.08698 49915000 99513 145930 135690 129650 163210 175900 137380 128830 130590 157990 FALSE TRUE 103441.8501 170992.3423 139226.1929 155294.383 135467.6225 135049.8908 126611.7966 127103.2446 125890.0914 188945.1156 0.547470358 0.90498419 0.736860503 0.821902077 0.71696811 0.714757248 0.670098278 0.672699287 0.666278623 1 17.5276077 -1.144774278 5.130430351 1.000011447 0.720511772 0.466578261 0.090738713 1.14E-05 1.90E-06 0.08425845 0.019859094 0.071651572 1.144774278 -0.279499675 QVQEFLKDGDDVIIIGVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QVQEFLKDGDDVIIIGVFK 19 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ;;; 239.72 2.46E-24 657961500 2623550 1316318 1587854 1404471 2194446 2380610 1775606 1735737 1837593 1029898 FALSE TRUE 2727129.78 1542385.377 1629234.78 1682271.172 1821434.853 1827749.406 1636429.362 1712472.285 1771458.387 1231686.795 2.214142258 1.252254537 1.322767108 1.365827075 1.478813332 1.483940085 1.328608352 1.390347199 1.438237704 1 20.23220401 QVQPEGPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QVQPEGPYR 9 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 219.56 1.14E-06 3820460000 2812880 3076610 2906080 3255250 3403000 3853910 2896730 2705500 2708580 3317940 FALSE TRUE 2923934.674 3604993.835 2981814.832 3899128.734 2824559.276 2958897.809 2669676.733 2669237.198 2611098.735 3968026.817 0.736873718 0.908510451 0.751460353 0.982636689 0.711829684 0.745684932 0.672797049 0.67268628 0.658034548 1 21.91999035 QVRPVTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVRPVTEK 8 1 P38606;P38606-2;C9JVW8 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 66.621 0.055823 180010000 156070 135750 155820 153770 188820 210930 200390 172620 199680 135970 FALSE TRUE 162231.7641 159064.0065 159880.7972 184185.247 156724.4438 161944.7042 184682.9082 170306.3112 192493.5558 162610.7182 0.997669563 0.978188943 0.983211925 1.132675934 0.963801437 0.995904243 1.135736378 1.047325251 1.183769175 1 17.31106283 2.251895577 24.98237399 1.091905269 1.009647005 0.292754756 0.063287272 287.6155756 538832.5517 0.021262575 0.017692587 178.6058077 -2.251895577 -0.082258264 QVS(ph)ASELHTSGILGPETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.991)AS(0.009)ELHTSGILGPETLR;QVS(0.997)AS(0.003)ELHTSGILGPETLR;QVS(1)ASELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.999)AS(0.001)ELHTSGILGPETLR;QVS(0.998)AS(0.002)ELHTSGILGPETLR;QVS(0.995)AS(0.005)ELHTSGILGPETLR;QVS(0.822)AS(0.178)ELHTSGILGPETLR 271.11 1.65E-39 19586150000 675618 5010390 4694123 4727005 4117895 6705620 3667591 6067400 4340130 5843730 TRUE FALSE 702291.9203 5870885.507 4816455.702 5661992.48 3417936.679 5148341.38 3380115.634 5986076.427 4183929.569 6988697.009 0.100489679 0.840054376 0.689177925 0.810164251 0.48906637 0.736666846 0.483654625 0.856536837 0.598670906 1 22.73659207 -5 0.050577857 2.272943208 1.58E-11 0.268004402 0.208353381 805.2866324 3.010902013 141.2465102 31.09625636 1.00E-05 5 -2.272943208 QVSDDLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVSDDLTER 9 0 P35232;C9JW96;C9JZ20;E7ESE2;E9PCW0 P35232 PHB Prohibitin 0 102.06 0.009568 0 125350 181950 129690 174380 127650 184780 122470 117960 130370 151430 FALSE TRUE 130298.9148 213198.4971 133069.8279 208871.8435 105952.0986 141867.6454 112870.4814 116378.9391 125678.0092 181099.8092 0.719486759 1.17724308 0.734787234 1.153352091 0.585048096 0.783367172 0.62325014 0.642623201 0.693970964 1 17.4664255 3.224784245 24.99987659 0.69588996 0.947617027 0.272849606 0.17689936 249.8319951 453367.3165 0.046202649 0.055492696 1677.970204 -3.224784245 0.251727067 QVVEAEKVVES(ph)PDFSKDEDYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVVEAEKVVESPDFSKDEDYLGK 23 2 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 1 QVVEAEKVVES(1)PDFSKDEDYLGK;QVVEAEKVVES(0.999)PDFS(0.001)KDEDYLGK 132.76 1.34E-05 111355000 476370 135584 233840 118362 366570 341150 321810 230040 297100 109127 TRUE FALSE 495177.4554 158869.4973 239934.0625 141773.6503 304260.5623 261923.0827 296585.6913 226956.6901 286407.429 130508.3463 3.794220596 1.217312929 1.838457611 1.086318648 2.331349458 2.006945074 2.272541946 1.739020503 2.194552587 1 16.99378255 -1.418067168 2.654442751 0.971780195 1.991080742 0.161814524 0.706548542 11269522.16 11892085.65 2397899.237 0.170736086 0.03818852 1.418067168 1.019300547 QVVGAGLQTAGESGSSPEGLLAS(ph)ELVHRPEPCTSPEAMGPSGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPSGHR 44 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QVVGAGLQTAGES(0.024)GS(0.021)S(0.019)PEGLLAS(0.316)ELVHRPEPCT(0.273)S(0.273)PEAMGPS(0.075)GHR 64.072 0.0015606 147320000 8312.8 10558 11472 16981 14280 18436 9431.1 14656 14326 15072 TRUE FALSE 8640.995763 12371.25437 11770.96974 20339.79112 11852.6907 14154.5184 8691.865738 14459.56029 13810.41006 18025.06983 0.479387644 0.686336002 0.65303324 1.128416772 0.657566978 0.785268436 0.482209823 0.802191638 0.766177895 1 14.13771723 -4.99999995 0.280444973 3.047498216 0.702567516 0.202026542 0.173335327 393.5269857 3.766265493 469.0904007 0.195872743 1.00E-05 4.99999995 -2.344930699 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPS(ph)GHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVVGAGLQTAGESGSSPEGLLASELVHRPEPCTSPEAMGPSGHR 44 1 P98171-2;P98171;E7EQN5;E9PCM6 P98171-2 ARHGAP4 Rho GTPase-activating protein 4 1 QVVGAGLQTAGESGS(0.006)S(0.191)PEGLLAS(0.15)ELVHRPEPCT(0.15)S(0.191)PEAMGPS(0.312)GHR 139.85 6.28E-14 235800000 0 0 0 0 0 0 0 2939.7 0 0 TRUE FALSE 0 0 0 0 0 0 0 2900.29813 0 0 0 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(ph)PDDDDIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLTPDDDDIVR 39 1 P41743 P41743 PRKCI Protein kinase C iota type 1 QVVPPFKPNISGEFGLDNFDSQFTNEPVQLT(1)PDDDDIVR 130.15 1.42E-08 54502000 37992 37284 38996 36056 49248 47450 39642 51163 42129 39964 TRUE FALSE 39491.9535 43687.23697 40012.2678 43187.76918 40876.84255 36430.45661 36534.75645 50477.24367 40612.78552 47794.18064 0.826292092 0.914070215 0.837178653 0.903619826 0.855268194 0.762236241 0.764418512 1.05613786 0.849743315 1 15.54454735 1.741664048 25 0.968413185 0.840831275 0.44694868 0.066731914 0.489030205 3961.961477 0.030685309 0.017016525 55.16505408 -1.741664048 -0.12758191 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEAS(0.004)PES(0.994)PPPAS(0.002)PDGVTEIR;QVVSVVQDEEVGLPFEASPES(0.99)PPPAS(0.01)PDGVTEIR 212.84 2.32E-28 599390000 142653 162202 164688 166848 157479 202873 159113 166753 174477 197564 TRUE FALSE 148285.0506 190058.9317 168979.9046 199850.0364 130710.7758 155758.8203 146641.3073 164517.9488 168197.6069 236272.8832 0.6276008 0.804404336 0.715189582 0.845844151 0.55321954 0.659232741 0.620643831 0.696304826 0.71187859 1 17.85009454 -1.192424837 4.416146865 1.000083289 0.693127038 0.559821454 0.081745987 6.61E-05 1.21E-05 0.078089368 0.01840086 0.064205933 1.192424837 -0.306956251 QVVSVVQDEEVGLPFEASPESPPPAS(ph)PDGVTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 1 QVVSVVQDEEVGLPFEASPES(0.08)PPPAS(0.918)PDGVT(0.001)EIR;QVVSVVQDEEVGLPFEAS(0.003)PES(0.033)PPPAS(0.96)PDGVT(0.004)EIR;QVVSVVQDEEVGLPFEAS(0.004)PES(0.239)PPPAS(0.737)PDGVT(0.02)EIR 143.54 1.66E-10 3367170000 153462 190554 190650 207409 197447 244962 191073 210243 213039 229993 TRUE FALSE 159520.7983 223280.1672 195618.4956 248433.8811 163885.0295 188073.2879 176096.199 207425.0365 205371.768 275055.7249 0.57995811 0.811763388 0.71119587 0.903212908 0.595824826 0.68376431 0.640220083 0.754120048 0.74665513 1 18.06936441 0.523238029 1.532134217 0.999890885 0.712622363 0.469296605 0.092121732 2.054271729 5.643590214 0.084305226 0.024295349 3.336092076 -0.523238029 -0.287268521 QWADDWLVHLISPNVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QWADDWLVHLISPNVYR 17 0 Q9H7Z7;A6NHH0;X6RJ95 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 76.713 0.019321 310580000 110330 136460 123380 120560 123510 145270 118540 116950 111550 148430 FALSE TRUE 114685.9136 159895.9435 126595.3842 144406.4082 102515.8143 111533.2441 109248.5251 115382.4765 107535.3373 177512.0166 0.646074084 0.900761236 0.713165151 0.813502156 0.577514786 0.628313768 0.615442983 0.649998117 0.605791874 1 17.43755717 3.249985032 24.99143544 0.654893546 0.77388817 0.083185815 0.129411555 371.9180519 813582.9422 0.032577137 0.043730328 1778.218123 -3.249985032 0.118994624 QWIQISDAVYHMVYEQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QWIQISDAVYHMVYEQAK 18 0 Q96TA1;Q96TA1-2 Q96TA1 FAM129B Niban-like protein 1 0 ; 195.78 2.03E-15 528160000 776530 691400 725520 712360 883130 918090 743820 793540 902460 672280 FALSE TRUE 807188.004 810142.5717 744427.6472 853262.6818 733015.878 704877.5113 685517.4448 782903.8943 869980.6409 804000.3944 1.003964687 1.00763952 0.92590458 1.061271472 0.911710844 0.876712892 0.85263322 0.973760585 1.082064943 1 19.61683668 3.209057122 24.9982869 0.940032351 0.994991898 0.103993436 0.068383896 450.507281 381713.3255 0.020640725 0.024673873 1618.292874 -3.209057122 0.054959547 QWLQEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QWLQEIDR 8 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 ;;; 129.77 0.0025041 2608680000 1043870 1263560 1063850 1335600 1295820 1529140 1147370 1126650 1100850 1329120 FALSE TRUE 1085082.794 1480566.601 1091574.805 1599777.694 1075556.979 1174020.409 1057436.141 1111549.1 1061230.624 1589535.616 0.682641384 0.931446006 0.686725603 1.00644344 0.676648556 0.738593333 0.665248473 0.699291723 0.667635637 1 20.60017391 QWLQEIDRYASENVNK ddPTM_MDA-MB-175_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 0 244.88 4.01E-20 361410000 249570 227880 275630 180920 287830 301330 175440 190130 235760 220010 FALSE TRUE 259423.2163 267016.6173 282813.1442 216705.436 238904.7594 231350.6742 161688.5544 187581.6183 227275.0437 263116.7472 0.985962388 1.014821824 1.074858014 0.823609437 0.907980058 0.879270045 0.614512592 0.712921623 0.863780227 1 18.00534355 3.309280663 1.166390971 0.773934113 1.024620106 0.348048283 0.109465044 0.437059377 1.252475927 0.041797445 0.070758871 2038.358943 -3.309280663 0.250685992 QWTEILHFTEHSGLTTGVAFGHHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QWTEILHFTEHSGLTTGVAFGHHAK 25 0 Q9UMS4;H0YGZ5 Q9UMS4 PRPF19 Pre-mRNA-processing factor 19 0 58.015 0.027408 32283000 13132 15020 19004 19540 22412 24043 26109 24708 22383 18711 FALSE TRUE 13650.4615 17599.56816 19499.25985 23404.95368 18602.41625 18459.37763 24062.50836 24376.82967 21577.4402 22377.06221 0.610020269 0.78650039 0.871394988 1.04593505 0.831316286 0.824924088 1.07532026 1.089366846 0.964265997 1 14.44973302 5.452235923 0.51348883 1.013234752 6.86E-20 0.647580361 0.085861016 5.737232951 0.670856344 0.051886219 4.084331924 283293.0521 -5.452235923 -1.013234752 QWTSLS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QWTSLSLR 8 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 QWTS(0.002)LS(0.998)LR;QWTS(0.011)LS(0.989)LR;QWTSLS(1)LR;QWTS(0.002)LS(0.998)LR 102.53 0.0051894 811600000 442912 485768 828260 577330 960640 608850 754220 698590 795880 653780 TRUE FALSE 460398.5078 569194.8752 849845.136 691524.1508 797350.7559 467453.8147 695102.2656 689226.5437 767236.4343 781875.6736 0.588838511 0.727986423 1.086931292 0.884442596 1.019792254 0.597862078 0.889018918 0.881504013 0.981276768 1 19.5765797 4.45544371 10.11599157 0.902501413 0.623308138 0.418786938 0.125868141 0.270530643 122.8411948 0.03014658 0.084096068 28539.32586 -4.45544371 -0.279193275 QWYESHYALPLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QWYESHYALPLGR 13 0 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ;;; 197.19 1.36E-07 9410050000 5331050 5594620 5392150 5698430 4990130 6379260 5400320 5520580 5083900 6040070 FALSE TRUE 5541523.97 6555452.465 5532673.859 6825562.446 4141909.485 4897773.544 4977028.807 5446585.655 4900931.432 7223506.072 0.767151563 0.90751671 0.76592638 0.944909906 0.573393231 0.67803273 0.689004586 0.754008594 0.678469899 1 22.78426782 3.249849968 24.99999322 0.714331268 0.844996882 0.194051129 0.115105587 305.9255024 677460.5479 0.029455312 0.03953571 1777.665188 -3.249849968 0.130665614 QY(ph)T(ph)FKMNEDT(ph)QEEPGKSEEEK ddPTM_MDA-MB-175_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(0.999)T(0.992)FKMNEDT(0.698)QEEPGKS(0.311)EEEK 68.361 0.021639 158810000 215560 27526 63209 33603 60078 139280 91428 43094 59461 23505 TRUE FALSE 224070.4752 32253.37638 64856.27847 40249.57311 49865.96302 106934.3308 84261.63446 42516.39542 57321.01023 28110.35472 7.971100951 1.147384183 2.307202421 1.431841523 1.773935744 3.80409041 2.997530102 1.51248164 2.039142188 1 14.77881404 4.74409048 24.99828616 2.077511555 7.97110346 0.826191874 0.820744543 242.6975532 1097105.556 0.199424403 1.750378363 55474.12746 -4.74409048 5.893591905 QYAENYTRPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QYAENYTRPSSR 12 1 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 QYAENYTRPS(0.097)S(0.903)R;QYAENYTRPS(0.052)S(0.948)R;QYAENYTRPS(0.283)S(0.716)R 97.2 0.0030615 1026360000 523530 550460 522550 617370 516140 760470 613520 602080 573470 496570 TRUE FALSE 544199.3687 644997.223 536168.0823 739483.9433 428406.7072 583862.3675 565430.6993 594010.1024 552830.9267 593863.3841 0.916371312 1.086103707 0.902847518 1.245208853 0.721389327 0.983159399 0.952122516 1.000247057 0.930905898 1 19.17977156 3.240328757 24.99998209 0.939792454 1.031467465 0.163783089 0.116426856 97.27315419 1375342.143 0.031014219 0.039919518 1739.116828 -3.240328757 0.091675011 QYDISDPQRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QYDISDPQRPR 11 1 Q13228;Q13228-4;Q13228-2;Q13228-3;H0Y532 Q13228 SELENBP1 Selenium-binding protein 1 0 ;;; 122.33 0.00035853 2412920000 1914000 2187730 2074950 2022200 2087300 2589680 1943000 2175700 2138640 2118850 FALSE TRUE 1989566.198 2563455.609 2129024.902 2422185.124 1732501.492 1988266.067 1790702.583 2146538.3 2061670.764 2533998.09 0.785149052 1.011624918 0.840184099 0.955874882 0.683702762 0.784635977 0.70667085 0.847095469 0.813603914 1 21.27298401 3.25878091 24.99994898 0.794068498 0.902164841 0.166207299 0.098949394 354.0591621 437748.4349 0.025402768 0.034354276 1814.600016 -3.25878091 0.108096343 QYDPPAESQQS(ph)ESPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.639)ES(0.361)PPRR 89.028 0.0025421 912820000 260880 341610 256220 328560 295860 378150 277380 278110 294660 305920 TRUE FALSE 271179.7438 400278.8601 262897.3037 393548.1873 245569.8229 290330.3934 255638.2308 274382.3903 284055.2442 365859.1668 0.741213474 1.094079079 0.718575145 1.075682183 0.671214077 0.793557794 0.698733977 0.749967242 0.776405978 1 18.48092888 3.217987324 24.99999964 0.763009751 0.907236107 0.154371677 0.140159163 352.6834918 428568.5802 0.036505102 0.043677989 1651.913582 -3.217987324 0.144226356 QYDPPAESQQSES(ph)PPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 QYDPPAESQQS(0.011)ES(0.989)PPRR;QYDPPAES(0.005)QQS(0.039)ES(0.956)PPRR;QYDPPAESQQS(0.018)ES(0.982)PPRR 183.05 4.37E-10 1507390000 1014056 1218885 1094455 1165500 1077681 1360106 1048637 1203092 1089857 1103099 TRUE FALSE 1054091.714 1428219.017 1122977.396 1396032.421 894497.1686 1044241.994 966442.0918 1186966.52 1050633.259 1319230.129 0.799020346 1.082615524 0.851236924 1.058217509 0.67804483 0.791554082 0.732580367 0.899741822 0.796398776 1 20.33126482 3.244817861 24.99999263 0.810669946 0.950508788 0.240819119 0.113970715 196.4571302 784913.1214 0.029636228 0.039153217 1757.186511 -3.244817861 0.139838841 QYECSLEQALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QYECSLEQALR 11 0 Q8TE77;Q8TE77-2;Q8TE77-3;E9PIT5;Q8TE77-5 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 90.827 0.014325 0 163320 142400 194490 141710 238610 246120 187290 203710 218590 172380 FALSE TRUE 169767.9997 166856.0923 199558.5692 169739.815 198051.1574 188962.36 172609.7204 200979.6007 210722.9886 206154.5606 0.823498637 0.809373762 0.96800463 0.823361921 0.960692584 0.916605286 0.837283056 0.974897669 1.022160208 1 17.65336685 8 0.124038487 1.049602174 0.306609868 0.460412814 0.05743857 80.71186544 0.683191538 0.343414054 10.4193042 100000000 -8 -0.742992306 QYEMGECTR ddPTM_MDA-MB-175_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 ; 89.886 0.027461 749800000 271610 302720 278620 272620 320940 377240 299020 269980 279590 327630 FALSE TRUE 282333.3725 354709.8052 285881.0661 326543.4223 266386.7334 289631.7271 275582.0311 266361.3597 269527.6105 391822.8256 0.720563872 0.905281117 0.729618203 0.833395609 0.679865276 0.739190543 0.703333275 0.679800518 0.68788134 1 18.57984192 3.244436721 24.99922902 0.725632027 0.800105409 0.024180771 0.102491254 309.8583856 1318249.693 0.0261718 0.034517938 1755.645069 -3.244436721 0.074473382 QYHES(ph)EEES(ph)EEEEAA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QYHESEEESEEEEAA 15 0 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 QYHES(1)EEES(1)EEEEAA;QYHES(1)EEES(1)EEEEAA 116.35 0.00066636 297980000 218670 211240 215300 216987 233020 263770 225540 220920 216840 197441 TRUE FALSE 227303.2605 247518.8268 220910.8949 259906.381 193411.3436 202513.415 207861.5855 217958.9288 209035.9708 236125.7837 0.962636341 1.04824989 0.935564475 1.100711565 0.819103025 0.857650578 0.880300246 0.923062807 0.885273804 1 17.84919606 3.232424635 24.99997336 0.890087703 1.008950085 0.472532408 0.060723247 120.4425373 490721.4132 0.016436334 0.020111053 1707.751341 -3.232424635 0.118862382 QYLVFHDGDSVVFAGPAGNSVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QYLVFHDGDSVVFAGPAGNSVETR 24 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 193.19 5.34E-18 194720000 55633 105330 84684 115090 144090 155980 123280 75510 82223 211960 FALSE TRUE 57829.4338 123419.6081 86890.93461 137854.4585 119597.6333 119756.0089 113616.9915 74497.91196 79263.81029 253489.5038 0.228133445 0.486882519 0.342779221 0.543827087 0.471805071 0.472429853 0.448211819 0.293889533 0.3126907 1 17.95156649 -1.073294752 4.25036712 1.000067199 0.403519807 0.777321774 0.096313468 7861833.573 3308761.292 4798.661816 0.022712921 0.084470536 1.073294752 -0.596547392 QYMEGFNDELEAFKER ddPTM_MDA-MB-175_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 ;;; 263.2 5.72E-27 820820000 506305 418097 501346 312927 627754 630594 447244 485600 578638 453321 FALSE TRUE 526294.3124 489901.9074 514411.4886 374823.0266 521048.5993 484148.1002 412187.8466 479091.3263 557812.9314 542140.5706 0.970770942 0.903643693 0.948852598 0.691376088 0.961095014 0.893030565 0.760296995 0.883703143 1.028908297 1 19.04830745 1.258730178 8.509024237 1.01465468 0.871792249 0.299579797 0.084083396 0.198495265 72.1558187 0.058510079 0.020173242 18.14388056 -1.258730178 -0.142862432 QYNEEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 125.5 0.0094053 406810000 370520 651970 500950 557850 497250 702040 481780 527440 432300 659170 FALSE TRUE 385148.4157 763940.7759 514005.1685 668191.065 412727.6226 539001.8495 444016.8247 520370.5295 416741.6074 788321.7409 0.488567543 0.969072317 0.652024601 0.847612124 0.523552252 0.683733331 0.563243155 0.660099173 0.528644062 1 19.58842504 -1.123431913 4.369930117 1.000046952 0.66446536 0.337632732 0.143653448 18918778.13 4863685.995 8949.196483 0.031527869 0.075260671 1.123431913 -0.335581592 QYPWGVAEVENGEHCDFTILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 QYPWGVAEVENGEHCDFTILR 21 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4 E7EPK1 7-Sep Septin-7 0 ;;;;; 295.17 7.57E-55 1979740000 752747 960234 796545 851668 796256 1025673 728577 856558 839133 977483 FALSE TRUE 782466.0328 1125146.72 817303.6171 1020125.388 660908.6895 787475.99 671469.231 845077.2411 808932.7672 1169002.079 0.669345288 0.96248479 0.699146419 0.872646342 0.565361432 0.673630958 0.574395241 0.722904823 0.691985739 1 20.15684606 5.056630137 15.96307662 0.73330926 0.156748079 0.015108546 0.142500814 11454379.74 75824209.48 0.032746589 210753977.2 113927.9116 -5.056630137 -0.57656118 QYPWGVVQVENENHCDFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QYPWGVVQVENENHCDFVK 19 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2;E7EW69;E7EX04;B5ME97;Q9P0V9;Q9P0V9-2;Q9P0V9-3;A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3 D6RGI3;E7EW69;A0A087X142 SEPT11;SEPT10;SEPT8 Septin-11;Septin-10;Septin-8 0 ; 298.26 8.69E-50 663220000 473450 407970 449590 417360 489350 550490 492710 464880 511910 422290 FALSE TRUE 492142.1716 478035.6739 461306.6847 499912.5623 406170.4618 422647.0403 454090.1027 458649.044 493486.4591 505029.6403 0.974481758 0.946549739 0.913424971 0.989867767 0.80425074 0.836875713 0.899135549 0.908162625 0.977143557 1 18.94600854 1.165839763 3.656956826 0.998477561 0.906446314 0.264318524 0.05349397 0.310003657 7.385724799 0.052813325 0.014088659 14.65007213 -1.165839763 -0.092031247 QYQDFLEDLEEDEAIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 QYQDFLEDLEEDEAIRK 17 1 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 0 ;;; 328.8 9.74E-72 240397000 283685 220046 261366 236716 296337 329243 314406 294610 299013 198891 FALSE TRUE 294885.1029 257837.1888 268177.4127 283537.7183 245965.7426 252781.303 289762.0362 290661.2348 288251.5805 237859.8835 1.239742905 1.083987703 1.127459615 1.192036733 1.034078294 1.062731972 1.218204735 1.221985106 1.211854544 1 17.85975245 2.223525903 24.97609836 1.187157018 1.120803354 0.019883851 0.083263869 492.833653 818703.7959 0.029964644 0.022216324 167.3115425 -2.223525903 -0.066353664 QYTS(ph)PEEIDAQLQAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 QYT(0.247)S(0.752)PEEIDAQLQAEK;QYT(0.079)S(0.921)PEEIDAQLQAEK 232.01 8.53E-16 122927000 382960 267110 353410 295520 400630 433280 400560 358180 395570 278330 TRUE FALSE 398079.5565 312984.0647 362620.1549 353972.974 332531.0557 332657.2864 369163.0605 353379.183 381333.513 332863.4346 1.19592456 0.9402777 1.089396183 1.063418018 0.999001456 0.999380683 1.109052609 1.061634131 1.145615509 1 18.34457087 2.22179033 24.99917657 1.082679875 1.043376768 0.039654644 0.072290951 713.5111065 1063610.347 0.025217382 0.018672574 166.6442488 -2.22179033 -0.039303107 QYVETHWCAQSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 QYVETHWCAQSEK 13 0 Q96P70 Q96P70 IPO9 Importin-9 0 169.04 2.92E-05 133910000 162360 109290 167090 122310 163430 183390 147730 144850 164220 117280 FALSE TRUE 168770.0982 128059.7073 171444.5027 146502.5529 135650.227 140800.4518 136150.5366 142908.5227 158309.7543 140258.7705 1.203276612 0.913024596 1.222344257 1.044516164 0.967142564 1.003862013 0.970709611 1.018891882 1.128697718 1 17.09773146 3.486521964 24.31926716 1.011946918 1.099651784 0.192438292 0.088439967 527.7324528 1365220.807 0.022640533 0.032459282 3065.645716 -3.486521964 0.087704867 QYYTLLNQAPDMLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 QYYTLLNQAPDMLHR 15 0 Q13283;E5RH42;E5RJU8;Q13283-2;E5RIF8;E5RI46;E5RH00 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 ; 195.2 2.03E-08 1874310000 848340 1050940 922030 937300 963310 1165840 818300 1027910 959520 1155960 FALSE TRUE 881833.1183 1231430.77 946058.8593 1122695.142 799566.9103 895091.3285 754159.5078 1014132.548 924987.0626 1382448.23 0.63787786 0.890760857 0.684335832 0.812106463 0.578370237 0.647468245 0.545524593 0.733577233 0.669093455 1 20.39879402 -1.7749068 9.001555325 1.002912673 0.69062822 0.477205185 0.097703785 0.005679874 0.000142031 0.094083513 0.022048929 0.016791643 1.7749068 -0.312284453 RAAATQPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAAATQPDAK 10 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 99.343 0.0076321 302820000 316390 245070 279180 207231 426160 364230 329980 298170 333270 252560 FALSE TRUE 328881.3215 287158.8661 286455.6601 248220.6733 353721.4754 279643.1025 304115.3054 294173.5189 321275.6778 302044.2964 1.088851289 0.950717724 0.948389569 0.82180222 1.171091392 0.925834739 1.00685664 0.973941645 1.063670732 1 18.20440062 3.25527432 24.99999863 1.013416393 0.952027933 0.137081443 0.085166373 566.2421565 846967.6881 0.02293321 0.030969217 1800.007522 -3.25527432 -0.061388459 RAADEDWDS(ph)ELEDDLLGEDLLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RAADEDWDSELEDDLLGEDLLSGK 24 1 Q96EV2;A8MTF7;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK;RAADEDWDS(1)ELEDDLLGEDLLSGK 246.32 4.41E-38 163684000 73713.2 58114.6 70203.5 53514.8 91399.5 77942.7 76293.3 68884 71839.5 56556.5 TRUE FALSE 76623.45405 68095.33048 72033.06088 64099.86771 75863.44564 59841.68916 70313.23179 67960.72265 69254.01043 67637.66334 1.13285188 1.006766454 1.064984468 0.947694887 1.121615412 0.884739156 1.039557376 1.004776323 1.023897146 1 16.0455392 7.604685297 1.158929248 1.00743799 129.229891 0.265006183 0.060464104 2033.469902 3.489870808 0.015234046 692557.7528 40242531.94 -7.604685297 128.222453 RAAEDDEDDDVDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;; 269.87 1.31E-25 8281660000 7335330 4306120 6086020 4265560 7744370 8227470 7881140 6132000 6560090 3884050 FALSE TRUE 7624934.493 5045662.613 6244626.681 5109275.037 6427984.754 6316764.781 7263395.653 6049810.57 6323993.642 4645055.233 1.641516432 1.086243836 1.344360049 1.09993849 1.383833869 1.359890134 1.563683377 1.302419512 1.361446382 1 22.14726432 -1.323635781 5.535869144 0.999938405 1.341828791 0.290510827 0.163371269 0.000116845 1.43E-05 0.148819929 0.035070896 0.047463987 1.323635781 0.341890386 RAAEDDEDDDVDTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 ;;;;;; 186.85 2.05E-07 9831588000 5528943 2241752 3482887 1907172 4681052 4757933 4573571 3187766 3729743 1765752 FALSE TRUE 5747229.939 2626755.468 3573653.896 2284404.929 3885368.453 3652975.168 4215082.554 3145039.211 3595510.278 2111717.297 2.721590597 1.243895417 1.692297497 1.081775924 1.839909375 1.729859945 1.996044906 1.489327769 1.702647548 1 21.00998528 -2.355633643 0.429655499 4.47E-10 1.705828969 0.207736943 0.422317456 124.7975918 6.590209207 118.5335605 0.224577484 0.004409267 2.355633643 1.705828968 RAAEEAEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 169.65 7.32E-06 919740000 557480 617090 608810 588630 1075520 852230 1011460 678570 613920 679400 FALSE TRUE 579489.7409 723070.4072 624676.0887 705059.2571 892703.4946 654312.4982 932179.1222 669474.8791 591825.1391 812515.4221 0.713204605 0.889915917 0.768817516 0.867748769 1.098691139 0.805292405 1.147275605 0.823953442 0.728386346 1 19.63203567 3.477166787 24.99999998 0.931805252 0.803524675 0.198639178 0.128363316 2.760232382 1515706.854 0.034580611 0.047315222 3000.314539 -3.477166787 -0.128280577 RAAPT(ph)TPPPPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAAPTTPPPPVK 12 1 Q9NZQ3-5;Q9NZQ3-4;Q9NZQ3-3;Q9NZQ3-2;Q9NZQ3;C9JC20;C9JMQ4;C9JSC3 Q9NZQ3-5 NCKIPSD NCK-interacting protein with SH3 domain 1 RAAPT(0.5)T(0.5)PPPPVK;RAAPT(0.6)T(0.4)PPPPVK 67.136 0.032919 1561410000 1114920 850100 1052260 832070 1245460 1377510 1214140 1123530 1133380 994460 TRUE FALSE 1158937.903 996098.0621 1079682.76 996650.9625 1033757.154 1057604.179 1118972.534 1108470.918 1092589.875 1189305.397 0.974466193 0.837546071 0.907826335 0.838010964 0.869210849 0.88926207 0.940862235 0.932032194 0.918678985 1 20.1816878 2.269349356 4.450000987 0.941565196 0.881217356 0.339671624 0.041668075 0.232626345 10.49330945 0.014433563 0.011431562 185.9299516 -2.269349356 -0.060347841 RAAS(ph)SDQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAASSDQLR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAAS(0.918)S(0.082)DQLR;RAAS(0.991)S(0.009)DQLR;RAAS(0.954)S(0.046)DQLR;RAAS(0.984)S(0.016)DQLR 131.49 0.00020317 3018285000 695822 800368 815484 830548 745680 961390 878307 772330 725179 760217 TRUE FALSE 723293.5899 937824.978 836736.183 994827.9155 618929.58 738121.7425 809463.0023 761978.1796 699079.9494 909166.9659 0.795556391 1.031521176 0.920332804 1.094219162 0.680765583 0.811865994 0.890334815 0.83810588 0.768923614 1 19.79418574 3.242570283 24.99998947 0.827846396 0.962624439 0.263696578 0.105247938 130.9691518 816577.3636 0.027929618 0.036468396 1748.116142 -3.242570283 0.134778042 RAAS(ph)SDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 RAAS(0.94)S(0.062)DQLRDNS(0.999)PPPAFKPEPPK;RAAS(0.791)S(0.21)DQLRDNS(1)PPPAFKPEPPK 90.323 0.0079753 2982730000 586330 307040 451320 263850 632460 520810 483040 401800 517810 293960 TRUE FALSE 609478.7611 359771.7316 463081.77 316038.7425 524954.6751 399859.7705 445178.0626 396414.5282 499174.1192 351555.8338 1.733661349 1.023370108 1.317235345 0.898971691 1.493232723 1.13740047 1.266308278 1.127600484 1.419899974 1 18.42339431 7.999997077 0.02159994 3.17E-07 2.840069997 0.111215437 0.22915076 6986.039726 11.61898366 552.6778964 1047.968632 99999326.97 -7.999997077 2.84006968 RAASS(ph)DQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAASSDQLR 9 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAAS(0.285)S(0.715)DQLR 117.95 0.00065463 72675000 55773 62852 67198 63356 80755 72994 75673 71524 75244 69871 TRUE FALSE 57974.96111 73646.34208 68949.23508 75887.6277 67028.29394 56042.24973 69741.55253 70565.33777 72535.98314 83560.88469 0.693805018 0.881349478 0.825137687 0.908171664 0.802149166 0.670675639 0.834619604 0.844478108 0.868061455 1 16.35054015 0.832908601 1.249047339 0.998894592 0.807198338 0.420039673 0.069788566 0.6815642 2.011000863 0.066488422 0.02030122 6.80626103 -0.832908601 -0.191696253 RAASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAASSDQLRDNSPPPAFKPEPPK 23 3 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RAASSDQLRDNS(1)PPPAFKPEPPK;RAAS(0.063)S(0.068)DQLRDNS(0.869)PPPAFKPEPPK 122.78 0.00035506 354750000 343486 177869 243468 137801 385575 330140 260381 259027 311821 202419 TRUE FALSE 357047.0925 208416.6171 249812.9761 165057.6265 320035.0992 253469.9883 239971.6568 255555.1667 300598.6231 242079.1275 1.47491895 0.860944185 1.031947606 0.681833367 1.32202682 1.047054287 0.99129429 1.055667911 1.241737056 1 17.88511917 RAAVAASSS(ph)S ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAAVAASSSS 10 1 P61927 P61927 RPL37 60S ribosomal protein L37 1 RAAVAASS(0.044)S(0.928)S(0.028);RAAVAAS(0.014)S(0.028)S(0.802)S(0.157);RAAVAAS(0.002)S(0.112)S(0.651)S(0.236);RAAVAASS(0.018)S(0.963)S(0.019) 98.04 0.0059828 913180000 1015110 1108140 1076810 1014780 1302300 1429850 1181930 1152800 989700 1297540 TRUE FALSE 1055187.327 1298454.425 1104872.553 1215500.455 1080935.511 1097789.007 1089287.238 1137348.602 954080.8903 1551768.12 0.679990337 0.836758023 0.712008798 0.783300314 0.696583141 0.707443975 0.701965213 0.732937213 0.614834702 1 20.56548156 -1.589418021 8.18714748 1.00012061 0.72274584 0.691844103 0.056309933 0.000117076 5.87E-06 0.051491645 0.012131483 0.025738426 1.589418021 -0.27737477 RADAGEKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RADAGEKPK 9 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RQX9 P47897 QARS Glutamine--tRNA ligase 0 ;;; 146.11 5.38E-05 658830000 1426710 867890 1242750 902020 1741280 1604320 1572530 1277990 1468220 890190 FALSE TRUE 1483037.612 1016943.356 1275137.086 1080436.864 1445297.848 1231740.994 1449270.99 1260860.634 1415379.049 1064605.687 1.393039349 0.955230062 1.197755283 1.014870461 1.357589825 1.156992687 1.361321856 1.184345199 1.329486651 1 20.02188775 3.238282806 24.99999992 1.242229402 1.131119362 0.07903654 0.148959445 15.60915423 1404729.764 0.03825164 0.048501078 1730.943158 -3.238282806 -0.111110041 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RADDFPVRDDPSDVTDEDEGPAEPPPPPK 29 2 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 2 RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK;RADDFPVRDDPS(1)DVT(1)DEDEGPAEPPPPPK 186.05 7.66E-18 3782770000 1899960 1390720 1596150 1546350 1742160 1956290 2142270 1653190 1712010 1156608 TRUE FALSE 1974971.888 1629565.342 1637746.98 1852213.415 1446028.265 1501971.295 1974353.28 1631031.692 1650395.095 1383223.193 1.427804202 1.178092841 1.18400775 1.339056071 1.045404872 1.085848837 1.42735698 1.179152938 1.193151693 1 20.39960253 -4.484639515 0.249150012 3.24E-12 1.246757723 0.249803741 0.122708149 206.6585488 2.601794306 104.993007 0.176934377 3.28E-05 4.484639515 1.246757723 RADDFPVRDDPS(ph)DVT(ph)DEDEGPAEPPPPPKLPLPAFR ddPTM_MDA-MB-175_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 173.96 1.96E-18 409700000 129196 135312 132363 110164 130661 143504 105813 116258 111820 149281 TRUE FALSE 134296.7578 158550.7834 135812.4885 131954.1104 108451.2899 110177.3708 97519.10057 114699.7517 107795.62 178529.7538 0.7522374 0.888091649 0.760727473 0.739115512 0.607468994 0.617137303 0.546234443 0.642468548 0.603796385 1 17.44580501 3.564168381 2.22004218 0.641183327 0.814404989 0.159293423 0.123862537 0.393061233 3.80877948 0.03306781 0.056995205 3665.796744 -3.564168381 0.173221662 RADDNATIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RADDNATIR 9 1 O75821;K7ENA8;K7ER90;K7EL20 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 77.662 0.039274 0 24378 38430 34671 30127 32822 34267 29877 29788 25818 36275 FALSE TRUE 25340.46226 45030.05356 35574.55474 36086.03068 27242.92816 26309.00857 27535.16267 29388.74058 24888.81522 43382.39172 0.584118608 1.037979968 0.820022902 0.831812845 0.62797202 0.606444401 0.634708267 0.677434771 0.57370777 1 15.40482197 3.246803425 24.41388883 0.664222518 0.834271909 0.140161052 0.1519606 194.469152 575981.8243 0.038900077 0.051767836 1765.238638 -3.246803425 0.170049391 RADLNQGIGEPQS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.996)PS(0.004)R;RADLNQGIGEPQS(0.98)PS(0.02)R;RADLNQGIGEPQS(0.991)PS(0.009)R;RADLNQGIGEPQS(0.999)PS(0.001)R;RADLNQGIGEPQS(0.978)PS(0.022)R 269.7 2.24E-22 2169770000 1336486 1250327 1441843 1133552 1665564 1870970 1574304 1404009 1471918 1247795 TRUE FALSE 1389251.499 1465060.936 1479418.613 1357765.202 1382452.026 1436465.572 1450905.939 1385190.556 1418943.959 1492276.54 0.930961161 0.981762359 0.991383684 0.909861655 0.926404717 0.962600117 0.972276854 0.928239853 0.950858585 1 20.50908348 RADLNQGIGEPQS(ph)PSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RADLNQGIGEPQSPSRR 17 2 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 RADLNQGIGEPQS(0.859)PS(0.141)RR 108.37 0.00051878 268410000 83491 83812 92418 62003 115820 103170 89779 92351 90242 90199 TRUE FALSE 86787.28915 98206.05903 94826.489 74267.00834 96132.95777 79210.33106 82741.88739 91113.1859 86994.20805 107871.7671 0.804541276 0.910396313 0.879066799 0.68847494 0.891178112 0.734300857 0.767039325 0.844643491 0.806459469 1 16.7189578 -1.302136953 3.33413819 1.000870026 0.815107958 0.409421262 0.067001771 20076006.47 28377810.25 173815.1763 0.015692805 0.049872719 1.302136953 -0.185762069 RADS(ph)GEEENTK ddPTM_MDA-MB-175_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 212.5 3.51E-09 1164030000 1423770 1074000 1198960 1018380 1516530 1624640 1541790 1297450 1273170 884290 TRUE FALSE 1479981.539 1258451.145 1230205.883 1219812.524 1258750.772 1247341.982 1420940.471 1280059.805 1227348.86 1057549.695 1.399443966 1.189968804 1.163260591 1.153432818 1.190252126 1.179464178 1.343615792 1.210401564 1.160559042 1 20.01229403 0.867732205 2.64041808 1.000337933 1.224671479 0.452584658 0.076244351 0.475541836 6.549065171 0.072627275 0.019341496 7.374493641 -0.867732205 0.224333547 RAEATAASTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAEATAASTSR 11 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 162.22 4.07E-05 270571000 80848.7 81963.5 67362 62028.3 95092 97171 80882 75316 70336.8 100899 FALSE TRUE 84040.6691 96040.09354 69117.50906 74297.3126 78928.29581 74604.50789 74542.25749 74306.51221 67805.39231 120668.2272 0.696460626 0.795902084 0.572789629 0.615715622 0.65409344 0.618261407 0.617745526 0.615791861 0.561915874 1 16.88068633 -1.172726143 6.188281476 1.00000275 0.638024676 0.743874692 0.06359263 2.48E-06 3.31E-07 0.063222912 0.01490167 0.067185237 1.172726143 -0.361978074 RAEDGSVIDYELIDQDAR ddPTM_MDA-MB-175_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 ;;;;; 278.07 5.88E-39 5428800000 1367104 2248150 2013420 2037090 1695361 2286520 1863910 1866560 1673658 2161170 FALSE TRUE 1421078.322 2634252.274 2065891.379 2440020.322 1407184.143 1755510.383 1717811.864 1841541.816 1613423.376 2584609.883 0.54982314 1.019206918 0.799304913 0.944057491 0.544447405 0.679216772 0.664631005 0.712502814 0.624242516 1 21.30151511 3.24769544 24.99997197 0.687842804 0.839692064 0.121074407 0.158758808 323.2591957 884683.0589 0.040496742 0.054070843 1768.868061 -3.24769544 0.15184926 RAEEQMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAEEQMLK 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 100.02 0.010266 1398530000 1426060 1098490 1331570 1190510 1707340 1749170 1821220 1404490 1437060 982140 FALSE TRUE 1482361.95 1287147.112 1366271.808 1425989.325 1417126.957 1342951.776 1678468.018 1385665.109 1385340.491 1174571.529 1.262044851 1.095843957 1.163208689 1.214050647 1.206505455 1.143354614 1.429004515 1.179719647 1.179443276 1 20.16370314 3.738445931 25 1.211496171 1.165913643 0 0.106259417 42.28717328 9218901.395 0.026582183 0.044300617 5475.779243 -3.738445931 -0.045582528 RAELGS(ph)WSSQEHLEWEPACQTPQPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAELGSWSSQEHLEWEPACQTPQPSAR 27 1 B7Z896;F5H3M2;Q9BVG8-5;Q9BVG8-2;Q9BVG8;Q9BVG8-6;H3BTL6 B7Z896 KIFC3 Kinesin-like protein;Kinesin-like protein KIFC3 1 RAELGS(0.399)WS(0.301)S(0.301)QEHLEWEPACQTPQPSAR;RAELGS(0.333)WS(0.333)S(0.333)QEHLEWEPACQTPQPSAR 105.71 0.00095022 579190000 68699 75320 86402 69571 89634 109433 91980 92978 89998 104829 TRUE FALSE 71411.28957 88255.62409 88653.7071 83331.93615 74398.0447 84018.84422 84770.36725 91731.78199 86758.98956 125368.2355 0.569612305 0.703971175 0.707146485 0.664697368 0.593436164 0.670176492 0.676171017 0.731698756 0.692033267 1 16.93581233 -0.871250212 0.39558499 1.125324354 0.64878219 0.845465297 0.043453658 4.794707871 0.574461912 0.747030263 0.029271771 0.134508518 0.871250212 -0.476542164 RAELGSWS(ph)SQEHLEWEPACQTPQPSAR ddPTM_MDA-MB-175_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(0.119)WS(0.441)S(0.441)QEHLEWEPACQTPQPSAR 160.86 8.32E-12 195150000 25206 33052 34711 30949 35459 45742 26372 45989 36462 43982 TRUE FALSE 26201.15234 38728.42389 35615.59718 37070.61983 29431.69185 35119.11373 24304.89373 45372.59268 35149.73974 52599.43081 0.498126157 0.73628979 0.677109935 0.704772262 0.559543923 0.667670984 0.462075223 0.862606153 0.668253234 1 15.68275957 0.713569397 0.85810659 0.997081864 0.633178216 0.499960861 0.108348987 0.81957748 1.11744876 0.100092138 0.034084123 5.170938786 -0.713569397 -0.363903648 RAELPGSSS(ph)PLLAQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RAELPGS(0.005)S(0.026)S(0.97)PLLAQPR;RAELPGSS(0.083)S(0.917)PLLAQPR;RAELPGSS(0.02)S(0.98)PLLAQPR;RAELPGS(0.113)S(0.113)S(0.775)PLLAQPR;RAELPGSS(0.076)S(0.924)PLLAQPR 219.34 7.66E-15 1703236000 894135 1020243 959429 978958 1039109 1221772 957682 997221 879956 1027794 TRUE FALSE 929436.1402 1195461.799 984432.5079 1172592.971 862481.6233 938033.9691 882616.3824 983854.8836 848286.5555 1229170.556 0.756149044 0.972576013 0.80089171 0.953970924 0.701677745 0.763143865 0.718058514 0.800421779 0.690129251 1 20.22925368 3.233294429 24.99982362 0.766435439 0.873159342 0.157677936 0.101687301 190.8037366 905789.6919 0.026337148 0.032383248 1711.17501 -3.233294429 0.106723903 RAELYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAELYEK 7 1 Q99614;H0YB37 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 86.67 0.031918 325030000 109900 108500 110900 101400 165550 167880 152870 141250 149090 115820 FALSE TRUE 114238.9369 127134.031 113790.1451 121456.6174 137409.8701 128892.4142 140887.6499 139356.7748 143724.28 138512.7115 0.824754173 0.917851002 0.821514097 0.876862607 0.992037977 0.930545745 1.017145996 1.006093761 1.0376252 1 17.07965885 3.042664335 1.016329023 1.014778195 0.852015736 0.767338065 0.036730165 0.238267018 0.5346636 0.016547556 0.021414336 1103.225611 -3.042664335 -0.162762459 RAEPPKPEVVDSTESIPVS(ph)DEDSDAMVDDPNDEDFVPFRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAEPPKPEVVDSTESIPVSDEDSDAMVDDPNDEDFVPFRPR 41 3 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 RAEPPKPEVVDSTESIPVS(1)DEDSDAMVDDPNDEDFVPFRPR;RAEPPKPEVVDSTES(0.001)IPVS(0.999)DEDSDAMVDDPNDEDFVPFRPR 169.92 3.66E-19 352350000 129075 103829 135334 108385 144348 169106 154701 139040 132257 99091 TRUE FALSE 134170.9807 121660.8231 138860.9152 129823.2295 119811.7785 129833.6943 142575.1314 137176.3962 127497.0964 118505.9842 1.132187387 1.026621768 1.171762895 1.095499357 1.011018805 1.095587663 1.203104909 1.157548263 1.075870533 1 16.85460039 2.454734603 24.79123941 1.131480427 1.085588028 0 0.067024319 525.2329201 581645.0532 0.022649533 0.018950866 284.9276548 -2.454734603 -0.045892399 RAEVLGHKT(ph)PEPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;RAEVLGHKT(1)PEPAPR;RAEVLGHKT(1)PEPAPR 163.11 7.42E-05 8526300000 5848120 3633090 4396120 3275060 5777090 6244350 4822860 4441340 4454860 3309820 TRUE FALSE 6079008.293 4257044.946 4510686.499 3922857.093 4795102.305 4794194.347 4444831.631 4381811.102 4294530.459 3958315.859 1.535756243 1.075468734 1.139546883 0.991041956 1.211399615 1.211170234 1.12290979 1.106988744 1.0849388 1 21.91645531 4.741641864 24.95002385 1.112805569 1.535756403 0.769220707 0.070689108 130.5583639 1057127.3 0.016497507 0.116881735 55162.23626 -4.741641864 0.422950834 RAFS(ph)TEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RAFSTEK 7 1 Q9NZ32;H0YJD9 Q9NZ32 ACTR10 Actin-related protein 10 1 RAFS(0.968)T(0.032)EK;RAFS(0.985)T(0.015)EK;RAFS(0.895)T(0.105)EK 95.483 0.0082278 1213940000 867390 709610 901240 614830 1430270 1090130 1025480 847160 1081190 791360 TRUE FALSE 901635.227 831479.9975 924727.0548 736441.5389 1187153.216 836963.8286 945100.198 835805.2059 1042278.183 946411.8405 0.952688025 0.878560434 0.977087369 0.778140665 1.254372743 0.884354773 0.998614089 0.883130546 1.10129453 1 19.8521086 RAGAES(ph)PTMSVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAGAESPTMSVDGR 14 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 RAGAES(0.946)PT(0.05)MS(0.004)VDGR;RAGAES(0.795)PT(0.204)MSVDGR;RAGAES(0.938)PT(0.059)MS(0.003)VDGR;RAGAES(0.652)PT(0.341)MS(0.007)VDGR 150.27 7.69E-06 430890000 705520 835430 811477 664662 980980 1019910 731140 829989 769095 941980 TRUE FALSE 733374.4744 978908.6038 832624.7573 796130.1598 814233.37 783051.3594 673831.3363 818864.355 741415.4212 1126542.946 0.650995576 0.868949211 0.739097218 0.706702006 0.722771709 0.695092329 0.598140833 0.726882502 0.658133295 1 20.10347088 -0.977684689 4.736017099 1.000002966 0.709647889 0.628764939 0.067425258 2.97E-06 6.42E-07 0.065226192 0.01537374 0.105272591 0.977684689 -0.290355077 RAGDLLEDS(ph)PK ddPTM_MDA-MB-175_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 175.6 5.90E-06 38653170000 45123440 16372420 21353590 18551450 31161580 55589470 37392090 24351080 25920950 11334260 TRUE FALSE 46904948.25 19184255.78 21910082.1 22220871.44 25864745.76 42679658.06 34461200.28 24024693.6 24988060.07 13554991.24 3.460345154 1.415290902 1.616384822 1.639312859 1.908134451 3.148630442 2.542325529 1.772387247 1.843458224 1 23.69232084 0.884055062 1.527143654 1.01314409 2.1675897 0.244953234 0.640775209 0.819683351 3.747418617 0.615380719 0.17981374 7.656936788 -0.884055062 1.15444561 RAGDLLEDS(ph)PKRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 185.33 2.88E-06 63206300000 20072940 7501760 12435960 6674300 18728200 16923010 14802060 12164050 13932110 6787750 TRUE FALSE 20865435.17 8790128.924 12760051.33 7994456.619 15544787.25 12992897.4 13641835.86 12001010.81 13430696.08 8117679.653 2.570369374 1.082837621 1.57188407 0.984820412 1.914929871 1.60056789 1.680509264 1.478379453 1.654499396 1 22.95263598 -1.199021316 3.807435951 0.999483167 1.583004013 0.161627542 0.414614577 12348061.83 5856159.674 50675.24821 0.088369581 0.063238081 1.199021316 0.583520846 RAGDLLEDSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAGDLLEDSPK 11 1 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ; 114.24 0.002059 501110000 518650 364710 438550 351590 615310 641490 506290 455510 545850 400100 FALSE TRUE 539126.7025 427346.1055 449978.9733 421133.4526 510719.826 492513.6694 466605.6669 449404.6335 526204.9651 478491.9346 1.126720564 0.893110363 0.94041078 0.880126544 1.06735305 1.029304015 0.975158896 0.939210467 1.099715433 1 18.86813508 3.229154351 24.99838649 1.007831536 0.953901842 0.113318403 0.075809596 465.2880191 1236562.246 0.021786725 0.026359702 1694.940085 -3.229154351 -0.053929693 RAGELTEDEVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 209.19 9.32E-08 5645290000 2476880 3012950 2934090 2832500 3353380 3528160 2918560 3002560 2813060 3328330 FALSE TRUE 2574669.135 3530400.725 3010554.796 3392760.046 2783373.665 2708798.31 2689795.641 2962315.594 2711818.52 3980452.539 0.646828246 0.886934511 0.756334805 0.852355357 0.699260609 0.680525212 0.675751215 0.744215781 0.681283973 1 21.92450103 -1.112654535 4.596477978 1.000017217 0.739445719 0.528379561 0.07477551 0.46449083 45454036.86 2018.86981 0.017366057 0.077151694 1.112654535 -0.260571497 RAHT(ph)PTPGIYMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAHTPTPGIYMGR 13 1 Q13595;Q13595-3;Q13595-4;Q13595-2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.997)PT(0.003)PGIYMGR;RAHT(0.995)PT(0.005)PGIYMGR 114.96 0.00041113 647900000 138617 152725 161641 152344 161905 208040 140948 186600 144858 175999 TRUE FALSE 144089.7062 178954.3307 165853.4972 182477.1885 134384.4459 159725.8629 129900.1275 184098.9322 139644.5889 210482.6343 0.684568143 0.850209478 0.787967605 0.866946525 0.63845859 0.758855301 0.617153657 0.874651407 0.663449454 1 17.68334168 -1.920717018 4.99451096 1.097756061 0.756710472 0.402973541 0.091185234 0.057921131 0.000919441 0.051521043 0.019569709 0.012002811 1.920717018 -0.341045589 RAHT(ph)PTPGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 34 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RAHT(0.889)PT(0.092)PGIY(0.004)MGRPT(0.01)HS(0.004)GGGGGGGGGGGGGGGGR;RAHT(0.962)PT(0.028)PGIYMGRPT(0.009)HS(0.001)GGGGGGGGGGGGGGGGR;RAHT(0.985)PT(0.015)PGIYMGRPTHSGGGGGGGGGGGGGGGGR;RAHT(0.996)PT(0.004)PGIYMGRPTHSGGGGGGGGGGGGGGGGR 204.53 2.62E-27 713757000 76118 60681 70403 61328 82164 84534 61707 65666 68499 70825 TRUE FALSE 79123.19742 71102.48972 72237.76002 73458.49535 68197.79263 64902.25963 56870.2441 64785.85468 66033.73437 84701.80272 0.934138293 0.839444822 0.852847964 0.867260117 0.805151608 0.766244136 0.671417163 0.764869844 0.779602467 1 16.37010505 3.115439169 2.764088988 0.770835862 0.87090539 0.133021532 0.082402921 0.380516639 5.885409062 0.024014243 0.029768476 1304.485237 -3.115439169 0.100069528 RALIVLAHSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RALIVLAHSER 11 1 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 194.39 3.46E-07 770540000 153560 134400 123250 79893 447650 248420 251420 158410 136840 397170 FALSE TRUE 159622.6674 157482.1545 126461.9963 95695.59694 371558.6129 190728.2198 231713.0434 156286.7731 131915.1551 474987.8572 0.336056312 0.331549854 0.266242588 0.201469565 0.782248656 0.401543359 0.487829404 0.329033197 0.277723216 1 18.85753111 -2.048718732 2.605917434 1.826866944 0.382735265 0.594793606 0.153670943 17856257.76 6145716.462 88036740.13 0.037095712 0.008938842 2.048718732 -1.444131679 RALS(ph)SAGPIPIRPPIVPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RALSSAGPIPIRPPIVPVK 19 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RALS(0.941)S(0.059)AGPIPIRPPIVPVK 128.38 1.13E-05 136020000 192980 158610 233960 137190 312680 236580 203630 227320 248680 191420 TRUE FALSE 200598.9994 185850.0337 240057.1898 164325.7725 259530.7653 181637.8804 187668.9485 224273.1472 239730.0554 228925.084 0.876264828 0.811837787 1.048627724 0.717814621 1.133693 0.793438085 0.819783246 0.979679218 1.047198722 1 17.80451603 1.554378983 5.395649779 1.020599218 0.888932403 0.194851223 0.116587898 0.227651043 14.00718834 0.061911765 0.028005838 35.84090629 -1.554378983 -0.131666815 RALS(ph)SDSILS(ph)PAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 RALS(0.825)S(0.009)DS(0.178)ILS(0.988)PAPDAR;RALS(0.973)S(0.027)DSILS(1)PAPDAR 202.86 1.96E-11 484890000 304388 369564 329844 332125 371662 454260 339382 354914 337886 429530 TRUE FALSE 316405.4733 433033.7422 338440.0056 397818.3337 308487.026 348764.9994 312780.352 350156.9584 325725.5489 513688.1797 0.615948519 0.842989501 0.658843281 0.774435444 0.600533628 0.678943011 0.608891472 0.681652746 0.634091968 1 18.97053335 -0.659818237 6.05294981 1.000000002 0.67950563 0.63642103 0.073140514 2.99E-09 3.30E-10 0.06697216 0.015785489 0.218867745 0.659818237 -0.320494373 RALS(ph)SDSILSPAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RALS(0.953)S(0.046)DS(0.001)ILSPAPDAR;RALS(0.931)S(0.06)DS(0.009)ILSPAPDAR;RALS(0.826)S(0.174)DS(0.001)ILSPAPDAR;RALS(0.979)S(0.019)DS(0.002)ILSPAPDAR;RALS(0.98)S(0.02)DSILSPAPDAR;RALS(0.357)S(0.319)DS(0.319)ILS(0.005)PAPDAR 344.71 5.11E-73 10518190000 2044920 2526100 2384630 1999150 2575780 2743340 1943830 2193550 2134780 2879890 TRUE FALSE 2125655.021 2959938.025 2446775.417 2394575.903 2137949.836 2106240.861 1791467.525 2164149.05 2057949.685 3444149.307 0.617178534 0.859410485 0.710415025 0.695259029 0.620748302 0.611541682 0.520148044 0.628355178 0.597520462 1 21.71571626 -1.109013613 3.826527061 1.000133421 0.650839299 0.599904006 0.085460971 98558666.32 192845264.3 171926.1515 0.022323268 0.077801216 1.109013613 -0.349294122 RALSS(ph)DS(ph)ILSPAPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 RALS(0.473)S(0.491)DS(0.518)ILS(0.519)PAPDAR 97.713 0.0019917 88136000 55650 60746 64016 61725 71109 87696 59049 66757 68728 77610 TRUE FALSE 57847.10497 71178.65296 65684.30955 73934.02077 59021.91758 67329.93305 54420.58508 65862.23161 66254.49271 92816.19357 0.623243668 0.766877527 0.70768157 0.79656381 0.635901078 0.725411488 0.586326405 0.709598499 0.713824713 1 16.50208891 0.566761922 2.607631337 0.999992301 0.695141325 0.691562469 0.061005439 3.208693715 18.63717305 0.056037235 0.01487294 3.687753821 -0.566761922 -0.304850976 RALVEFESNPEETREPGS(ph)PPSVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RALVEFESNPEETREPGSPPSVQR 24 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RALVEFESNPEETREPGS(1)PPSVQR;RALVEFESNPEETREPGS(1)PPSVQR;RALVEFESNPEETREPGS(1)PPSVQR;RALVEFESNPEETREPGS(1)PPSVQR 224.12 3.70E-33 687773000 120675 165823 185038 147023 242071 233879 148194 185066 172495 241099 TRUE FALSE 125439.3422 194301.8103 189860.2423 176103.7106 200923.8579 179564.1467 136578.167 182585.493 166286.9386 288337.7329 0.435043103 0.673868829 0.658464781 0.610754995 0.696835117 0.622756324 0.473674277 0.633234822 0.576708906 1 18.13740012 -2.141415952 2.180234313 1.80788488 0.602786154 0.694609944 0.079921921 4201488.826 940552.0881 16793136.91 0.018629759 0.007220779 2.141415952 -1.205098726 RAPFDLFENK ddPTM_MDA-MB-175_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 ; 165.39 9.41E-06 4187100000 3078000 2001980 2540200 2054100 4302400 3521000 3658900 2682800 2823900 2385900 FALSE TRUE 3199521.817 2345804.492 2606399.699 2460394.849 3571079.585 2703301.111 3372105.857 2646841.454 2722268.391 2853371.424 1.12131277 0.822116768 0.913445644 0.862276403 1.251529876 0.947405966 1.181797024 0.927618967 0.954053289 1 21.44423612 5.06394801 20.0948965 0.988626691 3.679955198 0.093168916 0.127483633 777.019633 263287.2417 0.029167595 7202.621074 115863.8645 -5.06394801 2.691328506 RAPFDLFENKK ddPTM_MDA-MB-175_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 ; 144.57 2.06E-05 3627200000 7689900 4303700 6528100 4669900 9245000 8017700 8458200 6480100 7694500 3847700 FALSE TRUE 7993503.19 5042826.997 6698227.649 5593592.282 7673538.202 6155710.684 7795224.183 6393244.859 7417576.448 4601583.146 1.737120234 1.095889575 1.455635471 1.215579965 1.667586558 1.337737576 1.694030931 1.389357674 1.611961843 1 22.13369887 3.253594032 24.99994326 1.475191047 1.361728711 0.01413742 0.244427457 805.1002504 1338839.755 0.061200796 0.082553496 1793.056736 -3.253594032 -0.113462337 RAPFDLFENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RAPFDLFENR 10 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;;;; 234.9 6.76E-12 27976250000 4974690 5518880 4921680 4474930 9015570 7272460 5885550 5155120 5125900 8438420 FALSE TRUE 5171094.602 6466704.709 5049943.024 5360057.798 7483106.632 5583541.38 5424225.212 5086024.048 4941419.86 10091766.84 0.512407261 0.640790143 0.500402269 0.531131752 0.741506096 0.553276891 0.537490144 0.503977562 0.489648635 1 23.26667544 -1.068739168 4.688072964 1.000019065 0.55736607 0.763847354 0.073938685 0.393962899 46827086.09 1914.327797 0.017541091 0.085361263 1.068739168 -0.442652994 RAPFDLFENRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RAPFDLFENRK 11 2 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ; 176.18 5.03E-06 2893400000 2533400 2011490 2209800 1928040 3603800 2905500 2598800 2416300 2826800 3254700 FALSE TRUE 2633420.588 2356947.76 2267389.203 2309400.557 2991227.363 2230741.658 2395099.265 2383913.451 2725064.02 3892396.15 0.676555131 0.605526177 0.582517585 0.59331077 0.768479684 0.573102421 0.615327724 0.612453964 0.700099351 1 21.89222712 0.801944411 3.018673631 0.99994776 0.626771294 0.807529458 0.054239981 0.409146078 5.594553171 0.050788332 0.013287617 6.337885821 -0.801944411 -0.373176466 RAPS(ph)PDGFSPYSPEETNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RAPSPDGFSPYSPEETNR 18 1 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 RAPS(1)PDGFSPYSPEETNR;RAPS(1)PDGFSPYSPEETNR;RAPS(0.999)PDGFS(0.001)PYSPEETNR 130.83 1.12E-05 374850000 179132 161977 169368 164001 202259 217672 177720 184560 168610 171113 TRUE FALSE 186204.2697 189795.2897 173781.8692 196439.9083 167879.0874 167120.9769 163789.842 182086.2751 162541.759 204639.3162 0.909914444 0.92746249 0.849210564 0.959932392 0.820365756 0.816661138 0.80038306 0.88979126 0.794284119 1 17.64272382 3.223017614 24.99887247 0.845734994 0.908302351 0.166339157 0.062015116 371.7562898 597919.7858 0.016632277 0.019943924 1671.158391 -3.223017614 0.062567357 RAPS(ph)PGAYK ddPTM_MDA-MB-175_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 124.21 0.00032839 3753980000 2688710 2112240 2375490 1947920 3077040 3163030 2754610 2540250 2730150 2156180 TRUE FALSE 2794862.347 2475000.789 2437397.221 2333212.762 2554005.84 2428464.219 2538696.47 2506202.104 2631892.435 2578642.188 1.083850392 0.959807762 0.945225061 0.904822225 0.990446 0.941760834 0.984509011 0.971907663 1.020650498 1 21.29818017 1.251639015 21.41840101 1.010325153 0.96948976 0.099571199 0.044266765 76.40738228 125141.9604 0.029557835 0.010579439 17.85003266 -1.251639015 -0.040835394 RAPS(ph)PLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RAPSPLPK 8 1 Q9BSL1 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 1 RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK;RAPS(1)PLPK 81.017 0.01467 2235440000 2696930 2145380 2674910 2233230 3375490 3401180 3091070 2660900 2840250 2086710 TRUE FALSE 2803406.879 2513832.326 2744620.352 2674956.228 2801725.415 2611307.49 2848783.856 2625234.988 2738029.957 2495560.872 1.123357443 1.007321582 1.099801004 1.071885787 1.122683661 1.046381004 1.14154052 1.051961913 1.097160157 1 21.25093266 -1.174701323 3.410756116 0.999876918 1.082682439 0.29578292 0.039088168 929371.0018 641689.9893 769.7824993 0.008192468 0.066880372 1.174701323 0.082805521 RAPS(ph)PVVSPTEMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RAPSPVVSPTEMNK 14 1 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(0.999)PVVS(0.001)PTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK;RAPS(1)PVVSPTEMNK 219.74 3.00E-12 2691100000 2448858 1885025 2065229 2044548 2367875 2716970 2783545 2153802 2278419 1687170 TRUE FALSE 2545540.805 2208763.38 2119050.564 2448953.492 1965384.453 2085994.894 2565363.469 2124933.807 2196419.145 2017738.659 1.261581025 1.094672678 1.050210618 1.213711935 0.97405303 1.033828085 1.271405223 1.053126379 1.088554821 1 20.9443079 7.989281181 0.012901371 2.81E-07 2.401925733 0.159888179 0.093169482 16573.65994 16.54327419 1270.572944 1861.573459 97562109.3 -7.989281181 2.401925452 RAPS(ph)SPVAKPGPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAPSSPVAKPGPVK 14 2 Q9GZR2;A0A0C4DG31;Q9GZR2-2 Q9GZR2 REXO4 RNA exonuclease 4 1 RAPS(0.579)S(0.421)PVAKPGPVK 56.817 0.063523 289820000 414880 282740 344890 241340 467350 437780 405880 379100 391990 273790 TRUE FALSE 431259.7828 331298.3956 353878.1167 289076.3317 387910.0139 336112.2296 374066.065 374018.7846 377882.3565 327433.9085 1.317089561 1.011802342 1.080761972 0.882853987 1.184697137 1.026504039 1.142417005 1.142272608 1.154072155 1 18.32084421 2.211549472 24.93104715 1.124512529 1.075965535 0.002504437 0.11439184 832.0996528 768015.7888 0.041129042 0.03038249 162.7606713 -2.211549472 -0.048546995 RAPS(ph)VANVGSHCDLSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAPSVANVGSHCDLSLK 17 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 RAPS(1)VANVGSHCDLSLK 165.58 1.15E-09 229220000 147100 123170 135980 146720 173140 206660 214690 161550 163710 142020 TRUE FALSE 152907.6216 144323.4894 139523.7505 175740.7781 143709.7246 158666.347 197862.0368 159384.6865 157818.1091 169846.0999 0.900271609 0.849730959 0.821471618 1.034705997 0.846117307 0.934177159 1.164948957 0.938406514 0.929183003 1 17.37386856 2.467373167 24.99824918 1.00782702 0.89215476 0.321486772 0.080656509 252.3724185 647185.3926 0.027840874 0.023318556 293.3412691 -2.467373167 -0.115672261 RAPS(ph)WR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAPSWR 6 1 Q13136-2;A0A2R8Y7R9;Q13136;O75335;B1APN9;M0QZB5;O75335-1;O75335-2 Q13136-2 PPFIA1;PPFIA4 Liprin-alpha-1;Liprin-alpha-4 1 RAPS(1)WR 60.074 0.080362 2565500000 559230 734500 658710 625710 716270 688340 672510 643770 606750 780070 TRUE FALSE 581308.8322 860644.6614 675876.5237 749473.5704 594518.6812 528483.4669 619796.9089 635141.3161 584913.186 932909.7812 0.623113664 0.922537933 0.724482193 0.803371972 0.6372735 0.566489362 0.664369612 0.680817512 0.626977225 1 19.83137804 -1.348852818 3.412634523 1.001809154 0.697251446 0.468612473 0.097590637 23959660.29 34720732.13 434963.4481 0.023918098 0.044786506 1.348852818 -0.304557708 RAQQQAEAER ddPTM_MDA-MB-175_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 ;;; 217.14 1.19E-08 657960000 238803 298320 247689 221602 321504 342979 237452 237905 239960 381162 FALSE TRUE 248231.1268 349554.1394 254143.9788 265434.2142 266854.8649 263327.3251 218839.8918 234716.2726 231323.8865 455843.3961 0.544553522 0.766829447 0.557524757 0.582292551 0.585409084 0.577670593 0.480076916 0.514905502 0.507463503 1 18.79817875 -1.616148046 5.435759686 1.003544336 0.567424533 0.752801973 0.07417282 0.003371001 0.000238047 0.075988527 0.017800211 0.024202039 1.616148046 -0.436119803 RAQS(ph)TDSLGTSGSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 1 RAQS(0.527)T(0.396)DS(0.077)LGTSGSLQSK;RAQS(0.451)T(0.402)DS(0.147)LGTSGSLQSK;RAQS(0.998)T(0.002)DSLGTSGSLQSK;RAQS(0.662)T(0.328)DS(0.009)LGTSGSLQSK;RAQS(0.499)T(0.499)DS(0.001)LGTSGSLQSK 241.79 2.37E-20 1310610000 1034940 1023688 1161038 739667 1386200 1329520 928098 1101007 1246950 1035408 TRUE FALSE 1075800.23 1199498.451 1191295.604 885970.9249 1150574.219 1020759.129 855351.2536 1086249.802 1202072.513 1238276.374 0.868788465 0.968683952 0.962059545 0.715487224 0.929174007 0.824338694 0.690759569 0.87722727 0.970762698 1 20.23990192 RAQST(ph)DS(ph)LGTSGSLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RAQSTDSLGTSGSLQSK 17 1 Q15276-2;Q15276;I3L456 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 2 RAQS(0.441)T(0.559)DS(1)LGTSGSLQSK 128.38 3.21E-05 124950000 189540 136170 180900 120100 211420 214420 171010 175900 176790 147400 TRUE FALSE 197023.1856 159556.1382 185614.4026 143855.4215 175482.9039 164624.2046 157605.7893 173542.3482 170427.3624 176280.2079 1.117670486 0.905127922 1.052950895 0.816061107 0.995477065 0.933877981 0.894064009 0.984468707 0.966798057 1 17.42751098 4.747797575 24.61637656 0.948444472 1.117670596 0.387675656 0.063243441 970.9162873 2587411.624 0.013754459 0.171457591 55949.67583 -4.747797575 0.169226124 RAS(ph)AAAAAGGGATGHPGGGQGAENPAGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASAAAAAGGGATGHPGGGQGAENPAGLK 29 1 Q07617 Q07617 SPAG1 Sperm-associated antigen 1 1 RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK;RAS(1)AAAAAGGGATGHPGGGQGAENPAGLK 271.04 2.38E-71 1263770000 500500 369790 440270 335577 601900 525750 440840 413448 455800 371047 TRUE FALSE 520260.1265 433298.5559 451743.7979 401953.129 499589.253 403652.5303 406285.8089 407906.4058 439395.847 443746.5555 1.172426287 0.976455029 1.018022095 0.905816899 1.125843675 0.909646566 0.915580761 0.919232839 0.99019551 1 18.7593764 2.702055751 24.99949923 0.93752334 1.027554834 0.264902591 0.075127531 795.2075626 544578.2652 0.023397425 0.022059665 503.5652475 -2.702055751 0.090031494 RAS(ph)AGPAPGPVVTAEGLHPSLPS(ph)PTGNSTPLGSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 2 RAS(0.953)AGPAPGPVVT(0.051)AEGLHPS(0.062)LPS(0.273)PT(0.22)GNS(0.22)T(0.22)PLGSSK 63.116 0.012601 68138000 20931 34308 35552 34229 45312 47474 39191 44878 45839 42089 TRUE FALSE 21757.37204 40200.13212 36478.51433 40999.39404 37609.88243 36448.88298 36119.10701 44276.48382 44189.26334 50335.53371 0.432246774 0.798643208 0.724707014 0.81452189 0.747183543 0.724118337 0.717566783 0.879626788 0.877894006 1 15.61928959 5.864828177 0.098554845 1.149781672 7.59E-16 0.597281169 0.089934042 60.98585947 0.6957088 1.491151457 9.692565397 732534.6573 -5.864828177 -1.149781672 RAS(ph)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASAGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 35 1 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK;RAS(1)AGPAPGPVVTAEGLHPSLPSPTGNSTPLGSSK 245.39 5.52E-48 1219040000 185938 539130 506780 498970 617700 718120 504650 622540 543940 579920 TRUE FALSE 193278.9758 631721.3837 519987.1031 597664.7767 512703.5746 551347.5132 465094.2143 614195.8696 524363.7057 693544.2208 0.278682988 0.91085956 0.74975335 0.86175439 0.739251455 0.794970957 0.670604989 0.885590062 0.756063838 1 19.40362835 4.745403554 24.98246632 0.808004666 0.278682744 0.752031241 0.092852843 356.0020987 1299672.99 0.019972084 0.197394263 55642.10532 -4.745403554 -0.529321923 RAS(ph)AILPGVLGSETLSNEVFQES(ph)EEEKQPEVPSSLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASAILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 37 2 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 2 RAS(1)AILPGVLGSETLSNEVFQES(1)EEEKQPEVPSSLAK 185.17 1.80E-23 69011000 75495 26572 45781 22218 76948 55574 54500 44437 47151 31263 TRUE FALSE 78475.60089 31135.5343 46974.09047 26612.65409 63868.40645 42667.78073 50228.14759 43841.3947 45454.04472 37388.38628 2.098929874 0.832759512 1.256381864 0.711789321 1.708241858 1.141204127 1.343415766 1.172593927 1.215726305 1 15.19030258 4.752150903 24.7289201 1.173840113 2.098930588 0.539273771 0.261538291 1486.540726 2704858.276 0.058270011 1.141660544 56513.33065 -4.752150903 0.925090475 RAS(ph)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASAILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 37 2 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 1 RAS(0.99)AILPGVLGS(0.005)ET(0.005)LSNEVFQESEEEKQPEVPSSLAK;RAS(1)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK;RAS(1)AILPGVLGSETLSNEVFQESEEEKQPEVPSSLAK 184.55 1.86E-23 3000190000 1237362 537144 737725 484184 1166450 968971 888367 692804 814010 390779 TRUE FALSE 1286214.007 629394.3036 756950.7195 579954.1501 968177.2456 743942.1701 818734.4732 683518.0956 784713.9391 467344.6631 2.752174377 1.346745461 1.619684099 1.240955971 2.071655722 1.591849076 1.751885788 1.462556758 1.679090404 1 18.83412739 8 0.046502303 1.03E-10 4.56252872 0.296345166 0.386686508 836.6098962 2.944802234 71.68159686 281.6418072 100000000 -8 4.56252872 RAS(ph)APHGPLDMAPFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASAPHGPLDMAPFAR 16 1 Q8N4B1-2;Q8N4B1;Q8N4B1-4 Q8N4B1-2 FAM109A Sesquipedalian-1 1 RAS(1)APHGPLDMAPFAR;RAS(1)APHGPLDMAPFAR 131.25 2.79E-05 702030000 239411 262605 271280 249193 341040 344760 309380 264772 264270 255030 TRUE FALSE 248863.1311 307705.366 278349.7797 298482.6316 283070.1426 264694.7149 285129.9872 261223.1644 254758.9743 304998.2457 0.815949386 1.008875855 0.912627478 0.978637208 0.928104167 0.867856516 0.934857794 0.856474318 0.83528013 1 18.21844142 2.870895779 6.463515195 0.890539971 0.93585361 0.03995943 0.063846343 0.55497228 26.8399171 0.018293194 0.019459711 742.8408521 -2.870895779 0.04531364 RAS(ph)CTSSTSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RASCTSSTSGSK 12 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 RAS(0.998)CT(0.002)SSTSGSK;RAS(0.99)CT(0.01)SSTSGSK;RAS(0.996)CT(0.004)SSTSGSK;RAS(0.916)CT(0.042)S(0.035)S(0.007)TSGSK;RAS(0.968)CT(0.031)SSTSGSK 155 4.41E-05 1046965000 1463060 1114827 1474700 1312890 1847900 1706630 1721570 1425280 1515900 1031491 TRUE FALSE 1520822.739 1306289.865 1513131.893 1572575.723 1533794.618 1310291.047 1586628.845 1406176.453 1461343.055 1233591.912 1.232841042 1.05893193 1.226606529 1.274794126 1.243356577 1.062175452 1.28618616 1.139904079 1.184624381 1 20.23443378 -0.144982635 0.766484672 0.99276976 1.192497994 0.360148396 0.076301478 7.891825345 4.22426897 0.244533453 0.025155643 0.716172046 0.144982635 0.199728234 RAS(ph)DDGKLTDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASDDGKLTDPSK 13 2 P04049;P04049-2;A0A0B4J1W9 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 RAS(0.507)DDGKLT(0.48)DPS(0.013)K;RAS(0.998)DDGKLT(0.002)DPSK 68.41 0.039774 728560000 1947810 913180 1311730 819890 2245200 1885420 1727700 1315570 1721890 855330 TRUE FALSE 2024711.043 1070011.561 1345914.761 982061.7949 1863561.706 1447559.779 1592278.359 1297936.936 1659919.515 1022915.537 1.979353103 1.046040971 1.315763338 0.960061471 1.821813863 1.415131285 1.556607854 1.26886032 1.622733701 1 19.9642556 -1.369781296 5.214467296 0.999784098 1.417360312 0.156439995 0.303375365 0.000707435 8.55E-05 0.272901482 0.064290676 0.042679439 1.369781296 0.417576214 RAS(ph)DGGANIQLHAQQLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASDGGANIQLHAQQLLK 18 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2;H7C3X8 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RAS(1)DGGANIQLHAQQLLK 241.6 2.50E-24 342510000 131770 128660 132830 122280 186780 158430 136820 145580 147200 129890 TRUE FALSE 136972.3813 150756.3542 136291.6589 146466.619 155031.2023 121637.0335 126095.6909 143628.7382 141902.3008 155339.4586 0.881761676 0.970496199 0.877379515 0.942880968 0.998015596 0.783040154 0.811742825 0.924612069 0.913498103 1 17.24506482 4.19722055 24.99990001 0.900219644 0.926129888 0.006559826 0.069375239 676.1266416 408878.4539 0.017623431 0.038071651 15747.82392 -4.19722055 0.025910243 RAS(ph)DTSLTQGIVAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASDTSLTQGIVAFR 15 1 Q9H0K1 Q9H0K1 SIK2 Serine/threonine-protein kinase SIK2 1 RAS(0.998)DT(0.002)SLTQGIVAFR;RAS(0.997)DT(0.003)SLTQGIVAFR 190.24 1.38E-07 470740000 144313 173519 150267 142525 172361 182982 141311 146597 145516 175983 TRUE FALSE 150010.5887 203319.5385 154183.0815 170716.0196 143063.1388 140487.2036 130234.6746 144632.107 140278.9076 210463.4995 0.712762969 0.966056057 0.732588225 0.81114312 0.679752732 0.667513388 0.61879934 0.687207556 0.666523687 1 17.68321052 3.243298556 23.84075179 0.694232782 0.81187829 0.087405499 0.11866197 106.5371068 536074.0319 0.0305792 0.040044471 1751.050035 -3.243298556 0.117645508 RAS(ph)FAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 130.01 0.0022082 26476600000 14266030 11470690 14274460 10981930 17694240 17642010 16962660 14015630 14915850 10657830 TRUE FALSE 14829263.88 13440691.78 14646464.15 13154122.98 14686579.41 13544920.54 15633082.39 13827773.4 14379031.47 12746027.73 1.163441991 1.054500434 1.149100289 1.032017445 1.152247564 1.062677787 1.226506227 1.084869239 1.12811864 1 23.60354437 -1.114204554 4.743988236 0.999992741 1.115636522 0.279924859 0.05628008 3.87E-06 7.23E-07 0.048792497 0.01149978 0.076876826 1.114204554 0.115643782 RAS(ph)FAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 86.67 0.032655 3073200000 3478400 2711800 3444000 2802700 4095300 4168600 3592700 3259400 3475700 2617800 TRUE FALSE 3615729.918 3177530.555 3533753.469 3357065.695 3399182.369 3200505.826 3311094.786 3215713.074 3350610.236 3130707.789 1.154924113 1.014955968 1.128739476 1.07230247 1.085755234 1.022294651 1.057618599 1.027152098 1.070240489 1 21.57805743 2.753836265 21.67449665 1.038123654 1.088112791 0.340350115 0.038675076 169.1353303 239983.0799 0.010783689 0.011378783 567.3306736 -2.753836265 0.049989136 RAS(ph)GQAFELILS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR;RAS(1)GQAFELILS(1)PR 174.99 8.59E-06 776963000 307906 328666 306979 331027 391870 450411 396435 413297 420709 527536 TRUE FALSE 320062.3666 385111.8288 314979.1249 396503.1526 325260.0774 345809.8713 365361.3888 407757.4297 405567.7653 630896.5789 0.507313524 0.610419904 0.499256353 0.628475674 0.515552134 0.548124499 0.579114551 0.646314219 0.642843501 1 19.267044 0.154175971 0.574656188 1.025642424 0.548726308 0.909069108 0.041647541 0.798546985 0.34847766 0.084036115 0.016526844 1.42618535 -0.154175971 -0.476916115 RAS(ph)GQAFELILSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.905)GQAFELILS(0.095)PR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR 214.59 4.18E-12 8293429000 1121999 1347475 1265130 1418567 1747015 1818125 1588248 1575970 1520390 1973636 TRUE FALSE 1166296.387 1578893.349 1298100.327 1699155.319 1450058.014 1395893.023 1463756.972 1554846.7 1465671.461 2360332.187 0.494123833 0.668928449 0.5499651 0.719879739 0.614344889 0.591396851 0.620148715 0.658740625 0.620959825 1 21.17055848 -5 0.311682059 4.414863634 0.602142526 0.799363199 0.05812923 117.8053591 1.063456529 264.2523628 0.04985434 1.00E-05 5 -3.812721108 RAS(ph)HTLLPSHR ddPTM_MDA-MB-175_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(0.537)HT(0.463)LLPSHR 84.173 0.0075983 148790000 152730 164640 166520 187570 257070 213070 203080 191440 184180 237880 TRUE FALSE 158759.8983 192915.6393 170859.648 224670.7862 213373.3332 163587.7216 187162.0589 188874.0599 177551.3978 284488.0315 0.558054754 0.678115133 0.600586419 0.789737217 0.750025694 0.575024969 0.657890801 0.663908632 0.624108497 1 18.11800843 -1.228980306 4.650259966 1.000088514 0.659234821 0.691482383 0.069033451 6.26E-05 1.04E-05 0.066029023 0.015559163 0.059022784 1.228980306 -0.340853693 RAS(ph)ISEPSDTDPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 RAS(0.986)IS(0.012)EPSDT(0.002)DPEPR;RAS(0.994)IS(0.006)EPSDTDPEPR;RAS(0.97)IS(0.03)EPSDTDPEPR;RAS(0.779)IS(0.188)EPS(0.009)DT(0.024)DPEPR;RAS(1)ISEPSDTDPEPR;RAS(0.933)IS(0.061)EPS(0.005)DT(0.001)DPEPR 206.81 3.93E-09 2439007000 1397132 1554552 1504428 1500101 1510754 1717336 1343774 1485389 1443804 1590851 TRUE FALSE 1452291.85 1821534.213 1543634.63 1796816.5 1253956.575 1318510.74 1238445.483 1465479.79 1391841.776 1902547.795 0.763340534 0.957418372 0.811351302 0.944426471 0.659093337 0.693023715 0.650940537 0.77027226 0.731567312 1 20.85950127 3.238574861 25 0.732263939 0.871312836 0.215608754 0.10707388 0.469980528 819835.9347 0.027955518 0.035539058 1732.107576 -3.238574861 0.139048896 RAS(ph)LSDIGFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RASLSDIGFGK 11 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44 Q07002 CDK18 Cyclin-dependent kinase 18 1 RAS(0.5)LS(0.5)DIGFGK;RAS(0.6)LS(0.4)DIGFGK;RAS(0.686)LS(0.314)DIGFGK;RAS(1)LSDIGFGK;RAS(1)LSDIGFGK 184.87 2.89E-06 3085610000 7327400 6323520 7534930 6611590 9576870 9071270 8740150 7606220 8346380 6552810 TRUE FALSE 7616691.41 7409535.37 7731296.466 7919342.768 7948997.058 6964605.019 8055074.205 7504271.062 8045995.414 7836707.658 0.971924913 0.945490848 0.986549046 1.010544621 1.014328645 0.888715686 1.027864577 0.957579559 1.026706082 1 22.90181625 7.999077884 0.057669302 1.037166696 0.867120722 0.056295346 0.040089195 1305.756354 5.637537827 3.485087301 18.85965167 99787900.21 -7.999077884 -0.170045974 RAS(ph)LSDLTDLEDIEGLTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;J3KSU7;K7EN88;Q8WZ73-3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 RAS(0.499)LS(0.499)DLT(0.002)DLEDIEGLTVR;RAS(0.917)LS(0.083)DLTDLEDIEGLTVR;RAS(0.993)LS(0.007)DLTDLEDIEGLTVR;RAS(0.995)LS(0.005)DLTDLEDIEGLTVR;RAS(0.997)LS(0.003)DLTDLEDIEGLTVR;RAS(0.487)LS(0.487)DLT(0.026)DLEDIEGLTVR;RAS(0.993)LS(0.007)DLTDLEDIEGLTVR;RAS(0.751)LS(0.249)DLTDLEDIEGLTVR 354.06 4.32E-91 851968000 221541.4 263562 267802 302783.9 298500 325601.8 252549.2 270226.2 256081.6 295377.7 TRUE FALSE 230288.0255 308826.7233 274781.1401 362673.6517 247761.0766 249985.7165 232753.7338 266604.2598 246865.2732 353251.305 0.651909907 0.874240856 0.777863057 1.026673211 0.701373422 0.707671035 0.658889948 0.754715569 0.698837541 1 18.43033536 RAS(ph)LSEIGFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RASLSEIGFGK 11 1 Q00537;Q00537-2;F5H6Z0 Q00537 CDK17 Cyclin-dependent kinase 17 1 RAS(0.992)LS(0.008)EIGFGK;RAS(0.998)LS(0.002)EIGFGK;RAS(0.993)LS(0.007)EIGFGK;RAS(0.997)LS(0.003)EIGFGK 192.4 8.62E-07 1701700000 4644490 3868450 5037200 3828320 6161000 5926400 5581900 4903900 5668000 4223310 TRUE FALSE 4827858.052 4532826.195 5168473.57 4585550.27 5113755.421 4550083.415 5144376.092 4838171.242 5464009.787 5050786.734 0.955862582 0.897449533 1.023300694 0.907888317 1.012467105 0.900866272 1.018529659 0.95790448 1.081813601 1 22.2680767 1.256700056 24.90559033 1.040906786 0.960294643 0.3102307 0.048664977 217.0622067 298030.3079 0.029444595 0.010705273 18.05926437 -1.256700056 -0.080612143 RAS(ph)LTLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RASLTLEEK 9 1 Q6P3W7;A0A0U1RQQ9 Q6P3W7 SCYL2 SCY1-like protein 2 1 RAS(1)LTLEEK;RAS(1)LTLEEK;RAS(1)LTLEEK;RAS(1)LTLEEK 212.1 2.49E-06 800900000 1508570 1109200 1261840 1138870 1878780 1942140 1734840 1421470 1624580 1164200 TRUE FALSE 1568129.508 1299696.472 1294724.587 1364135.087 1559425.647 1491107.418 1598858.708 1402417.52 1566111.683 1392302.7 1.126284901 0.933487001 0.929916021 0.979769045 1.120033486 1.070964969 1.148355676 1.007264814 1.124835629 1 20.40904147 3.253172339 24.99412816 1.078455646 0.983698106 0.276863739 0.06767974 283.6499483 485195.7337 0.018152686 0.024475951 1791.316551 -3.253172339 -0.09475754 RAS(ph)MQPIQIAEGTGITTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASMQPIQIAEGTGITTR 18 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RAS(1)MQPIQIAEGTGITTR 179.44 5.12E-14 308220000 52847 53220 58787 53140 91993 66072 48406 71927 70375 78573 TRUE FALSE 54933.44037 62360.12101 60319.03751 63650.93339 76356.06272 50727.77933 44611.81123 70962.93621 67842.2175 93967.87498 0.584598091 0.663632343 0.641911265 0.677369084 0.812576242 0.539841721 0.474755987 0.755182941 0.721972456 1 16.51988 0.786409134 1.461270541 0.997983241 0.639897133 0.58645463 0.090824191 0.537925069 2.033237689 0.088413099 0.025945577 6.115178432 -0.786409134 -0.358086109 RAS(ph)PPGT(ph)PTPEADATLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RASPPGTPTPEADATLLK 18 1 Q8IYK8;Q8IYK8-2 Q8IYK8 REM2 GTP-binding protein REM 2 2 RAS(1)PPGT(0.985)PT(0.015)PEADATLLK;RAS(1)PPGT(0.999)PT(0.001)PEADATLLK;RAS(0.995)PPGT(0.868)PT(0.138)PEADATLLK;RAS(1)PPGT(0.988)PT(0.012)PEADATLLK 182.02 6.10E-14 554616000 888322 657069 823148 703573 1024314 973175 911387 805162 897971 649138 TRUE FALSE 923393.6385 769915.4895 844599.9131 842737.6394 850201.4722 747169.8549 839950.1055 794370.1204 865653.1991 776324.1626 1.189443383 0.991744849 1.087947476 1.085548641 1.095162966 0.962445704 1.081957958 1.02324539 1.11506667 1 19.56629967 RAS(ph)PPGTPTPEADATLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASPPGTPTPEADATLLK 18 1 Q8IYK8;Q8IYK8-2 Q8IYK8 REM2 GTP-binding protein REM 2 1 RAS(0.99)PPGT(0.01)PTPEADATLLK 176.34 6.83E-13 296050000 233720 159600 197070 180840 208040 268900 233760 153990 236700 152010 TRUE FALSE 242947.4461 187010.0585 202205.8061 216609.6122 172677.4351 206452.0502 215437.2804 151926.0159 228181.2132 181793.4491 1.336392743 1.028695255 1.112283237 1.191514949 0.949855102 1.135640757 1.185066247 0.835706769 1.255167413 1 17.47194069 4.743907635 24.50446524 1.068763219 1.336392894 0.292996256 0.120206397 531.4924374 2435638.806 0.027813731 0.235153 55450.77684 -4.743907635 0.267629675 RAS(ph)PS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 99.752 0.0034249 605440000 1488900 1190030 1294300 1142680 1555550 1649480 1562770 1369610 1446140 1108450 TRUE FALSE 1547682.922 1394408.395 1328030.521 1368698.693 1291138.167 1266413.268 1440276.004 1351252.618 1394093.704 1325629.555 1.167507858 1.051883907 1.00181119 1.032489573 0.973981126 0.955329687 1.08648453 1.019328977 1.051646517 1 20.33824624 4.713598979 2.732917515 1.016835158 1.191825406 0.625545684 0.035370799 0.27234334 2.858834518 0.008930285 0.104623056 51712.9102 -4.713598979 0.174990248 RAS(ph)PS(ph)PPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 59.185 0.05698 1044960000 226322 217244 226506 172740 245623 293524 265641 238381 209292 193642 TRUE FALSE 235257.3673 254553.9671 232408.9324 206907.4564 203872.0902 225357.4994 244819.3643 235185.8926 201759.6218 231582.4424 1.015868754 1.099193723 1.00356888 0.893450532 0.880343467 0.97311997 1.057158573 1.015560118 0.871221582 1 17.82116635 4.00761151 13.88847754 0.962416939 1.056010807 0.308684956 0.060508166 1.15861969 2092.545544 0.016469284 0.034917592 10176.80635 -4.00761151 0.093593868 RAS(ph)PSKPASAPASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.926)PS(0.074)KPASAPASR 78.225 0.017699 299440000 300410 218310 280650 234230 337370 367450 336340 280730 287140 239330 TRUE FALSE 312270.4188 255803.0443 287963.9696 280559.9949 280023.9679 282115.3063 309976.7919 276967.2735 276805.8875 286222.1313 1.091007245 0.8937221 1.006085617 0.980217685 0.978344919 0.985651616 1.082993794 0.967665471 0.967101622 1 18.1267757 2.426483861 24.99997794 1.005161692 0.984606653 0.014708171 0.053888701 450.0836534 222206.6322 0.017774234 0.014870995 266.9831552 -2.426483861 -0.020555039 RAS(ph)PSPPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RAS(0.949)PS(0.051)PPPKR 51.726 0.080743 35613000 15640 416040 348680 437980 229360 437300 209330 391590 271310 590230 TRUE FALSE 16257.47928 487491.6337 357766.8872 524611.1368 190373.4691 335743.7023 192922.1676 386341.3766 261545.6061 705874.2679 0.023031693 0.690621058 0.506842229 0.743207623 0.269698837 0.47564236 0.273309535 0.547323219 0.370527186 1 19.4290517 -1.30505947 3.696178687 1.001487069 0.44902488 0.411986924 0.202309638 270836677.1 473520461.3 4555376.703 0.045108679 0.049538235 1.30505947 -0.55246219 RAS(ph)QEANLLTLAQK ddPTM_MDA-MB-175_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(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK;RAS(1)QEANLLTLAQK 261.8 1.68E-24 2635447000 2858697 2319276 2787385 2428127 3542570 3537280 3572510 3070520 3170520 2414321 TRUE FALSE 2971560.565 2717593.612 2860026.543 2908403.273 2940405.217 2715800.328 3292487.331 3029364.702 3056413.605 2887360.975 1.029161435 0.941203277 0.990533074 1.007287727 1.018371185 0.940582197 1.140310256 1.049181148 1.058549184 1 21.46132005 2.250377577 24.99984074 1.066944995 0.988127822 0.425530602 0.042052307 189.0342191 399918.5613 0.013854202 0.011504256 177.9826124 -2.250377577 -0.078817173 RAS(ph)RLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASRLEK 7 2 Q14161-3;Q14161;F8VXI9;Q14161-6;Q14161-4 Q14161-3 GIT2 ARF GTPase-activating protein GIT2 1 RAS(1)RLEK 60.518 0.076409 102790000 97929 103170 113210 84924 161940 146730 106340 107700 115120 131250 TRUE FALSE 101795.3125 120888.6449 116160.3456 101721.7137 134413.4966 112654.1812 98004.79293 106256.4577 110976.8537 156965.9246 0.648518542 0.770158525 0.740035431 0.648049658 0.856322778 0.717698325 0.624369864 0.676939648 0.707012391 1 17.26009188 -1.29798265 3.162892015 1.001749749 0.709124558 0.643006984 0.064844717 11482664.17 15781160.69 191061.0522 0.015907223 0.050352072 1.29798265 -0.292625192 RAS(ph)SASVPAVGASAEGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASSASVPAVGASAEGTR 18 1 V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23;A0A2R8YFI4 V9GYZ0 PANK2 "Pantothenate kinase 2, mitochondrial" 1 RAS(0.394)S(0.394)AS(0.211)VPAVGASAEGTR;RAS(0.48)S(0.48)AS(0.039)VPAVGASAEGTR;RAS(0.825)S(0.146)AS(0.028)VPAVGAS(0.002)AEGTR 108.64 0.0002361 406310000 99746 154144 141915 151702 180730 187828 140291 154014 141171 177217 TRUE FALSE 103684.0491 180617.0329 145613.4215 181708.2028 150009.5792 144207.7936 129294.6248 151949.6942 136090.2833 211939.2781 0.489215826 0.85221123 0.68705255 0.857359733 0.707795084 0.68042033 0.61005504 0.716949192 0.642119217 1 17.69329146 -1.393503955 3.334765845 1.002836006 0.700606363 0.445023399 0.102358121 29591316.34 40811336.96 806473.4178 0.02378722 0.040410669 1.393503955 -0.302229643 RAS(ph)SLNFLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.665)S(0.335)LNFLNK 99.844 0.0046802 532070000 1208300 898460 1176400 828710 1622500 1408800 1294500 1131100 1205400 1152700 TRUE FALSE 1256004.617 1052763.516 1207057.95 992626.3645 1346708.03 1081627.551 1193033.707 1115939.455 1162017.889 1378549.495 0.911105928 0.763674804 0.875600009 0.720051306 0.976902196 0.784612779 0.865426821 0.809502639 0.842927942 1 20.39471964 0.93160634 19.35743282 1.000000001 0.835479279 0.318192749 0.07068808 2114.009788 598330.6151 0.060112434 0.015028109 8.542920016 -0.93160634 -0.164520722 RAS(ph)SLNVLNVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 168.68 1.83E-05 1162200000 1497000 1326920 1559640 1105390 1965980 1807780 1639430 1530760 1676930 1475670 TRUE FALSE 1556102.716 1554808.188 1600285.5 1324032.843 1631803.422 1387950.492 1510927.193 1510242.666 1616577.617 1764799.283 0.881744871 0.881011344 0.906780457 0.750245569 0.924639667 0.786463654 0.856146763 0.855758885 0.916012168 1 20.75107268 0.957145728 2.400382262 0.999745345 0.853938383 0.45201172 0.049648918 0.270690193 3.512726148 0.043989216 0.011932709 9.060365705 -0.957145728 -0.145806962 RAS(ph)SLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RAS(0.392)S(0.392)LS(0.216)R 76.85 0.041991 186630000 341660 417550 410240 401300 438280 490820 399110 419490 415270 487940 TRUE FALSE 355149.0006 489260.9644 420931.1914 480675.9422 363781.3221 376834.4934 367826.7153 413867.4227 400324.5138 583542.5008 0.608608628 0.838432443 0.721337676 0.823720537 0.623401589 0.645770433 0.630334063 0.709232699 0.686024605 1 19.15447821 -1.947725904 5.008771251 1.163685528 0.700884265 0.588100601 0.075663943 0.046633624 0.000486692 0.024702561 0.017116342 0.011279091 1.947725904 -0.462801263 RAS(ph)TAFCPPAASSEAPDGPSSTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASTAFCPPAASSEAPDGPSSTAR 24 1 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RAS(0.784)T(0.216)AFCPPAASSEAPDGPSSTAR;RAS(0.793)T(0.207)AFCPPAASSEAPDGPSSTAR;RAS(0.804)T(0.196)AFCPPAASSEAPDGPSSTAR 124.06 1.88E-07 685380000 390773 371604 383622 414677 457834 509577 407439 374167 396333 408963 TRUE FALSE 406201.0198 435424.0963 393619.5045 496698.8729 380011.5402 391235.4645 375502.8665 369151.9034 382069.0527 489091.4698 0.830521579 0.890271295 0.804797321 1.015554152 0.776974377 0.799922895 0.76775591 0.754770684 0.781181183 1 18.89974478 RAS(ph)VCAEAYNPDEEEDDAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RASVCAEAYNPDEEEDDAESR 21 1 P31323 P31323 PRKAR2B cAMP-dependent protein kinase type II-beta regulatory subunit 1 RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR;RAS(1)VCAEAYNPDEEEDDAESR 260.49 8.23E-37 6221400000 983117 1392194 1378929 1213288 1793172 1676961 1274340 1382603 1334277 1609196 TRUE FALSE 1021931.218 1631292.49 1414865.023 1453272.745 1488369.264 1287512.222 1174453.901 1364071.468 1286256.631 1924487.146 0.531014832 0.847650499 0.735190685 0.755148065 0.773384882 0.669015756 0.610268509 0.708797391 0.668363327 1 20.8760426 -1.437049816 2.942327641 1.006493553 0.704563553 0.534931315 0.083850943 29513970.46 33935352.31 1589728.928 0.019154633 0.036555286 1.437049816 -0.30193 RAS(ph)WASENGETDAEGTQMTPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASWASENGETDAEGTQMTPAK 22 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 RAS(0.92)WAS(0.076)ENGET(0.004)DAEGTQMTPAK;RAS(0.951)WAS(0.049)ENGET(0.001)DAEGTQMTPAK 139.16 4.08E-09 217270000 121042 112518 134568 106154 157881 181902 144581 137690 150730 118212 TRUE FALSE 125820.8316 131842.0912 138074.9526 127150.9444 131044.444 139658.0173 133248.3634 135844.4908 145305.2567 141373.3781 0.889989567 0.932580752 0.976668695 0.899398077 0.92693862 0.987866451 0.942527973 0.960891595 1.027812016 1 17.10915095 1.817008315 0.633707365 1.010109164 0.925286536 0.516377866 0.029234307 0.638968911 0.525479359 0.027533031 0.015316221 65.61578291 -1.817008315 -0.084822628 RASEDTTS(ph)GSPPKK ddPTM_MDA-MB-175_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(0.006)T(0.135)S(0.493)GS(0.365)PPKK 62.475 0.040043 939990000 68685 28697 44901 25958 61578 63975 54929 41790 49916 26783 TRUE FALSE 71396.73684 33625.48652 46071.15695 31092.41492 51110.99356 49117.7758 50623.52145 41229.8734 48119.53291 32030.61606 2.229015412 1.049792063 1.438347513 0.970709239 1.595691867 1.53346335 1.580472925 1.287202011 1.502298077 1 14.96716393 -2.662363997 0.537711031 5.04E-09 1.44077546 0.149018483 0.327975207 439.899071 21.44572582 512.4594474 0.133449026 0.002175885 2.662363997 1.440775455 RASEDTTSGS(ph)PPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASEDTTSGSPPKK 14 2 Q9BZZ5-2;G3V1C3;Q9BZZ5;Q9BZZ5-5;Q9BZZ5-6;Q9BZZ5-1;H0YER7 Q9BZZ5-2 API5 Apoptosis inhibitor 5 1 RASEDT(0.001)T(0.02)S(0.077)GS(0.902)PPKK;RASEDTTS(0.002)GS(0.998)PPKK;RASEDTT(0.002)S(0.468)GS(0.53)PPKK 137.69 1.03E-05 1086490000 1133050 378938 634410 402421 894200 977970 892210 663700 755020 339331 TRUE FALSE 1177783.689 444017.6538 650943.2458 482018.6727 742204.2034 750851.2888 822276.2488 654804.1871 727846.9777 405816.4126 2.902257406 1.094134293 1.604033808 1.187775205 1.828916181 1.850224056 2.026227189 1.613547818 1.793537558 1 18.63046769 RASGQAFELILS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR;RASGQAFELILS(1)PR 172.55 1.74E-06 1096140000 398246 398318 439460 400165 487580 591280 534450 539380 533110 660310 TRUE FALSE 413969.0596 466726.018 450912.6886 479316.4426 404701.3258 453964.1809 492558.4125 532150.4933 513923.4752 789685.1021 0.524220425 0.591028015 0.57100316 0.606971616 0.512484438 0.574867349 0.623740287 0.67387683 0.650795455 1 19.59091795 -0.079676093 0.429279992 1.065989096 0.554327813 0.9404585 0.032074385 1.047654178 0.238537395 0.147683039 0.020248029 0.832384351 0.079676093 -0.511661282 RASS(ph)LNFLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RAS(0.099)S(0.901)LNFLNK;RAS(0.176)S(0.824)LNFLNK 120.55 0.00057709 670390000 1263260 1121250 1317560 965540 1893340 1593910 1498620 1380720 1423710 1409810 TRUE FALSE 1313134.48 1313815.965 1351896.696 1156520.93 1571510.743 1223748.558 1381154.248 1362213.707 1372470.955 1686035.277 0.778829778 0.779233972 0.801819935 0.685941122 0.932074651 0.725814326 0.819172806 0.80793903 0.81402268 1 20.68520329 -4.999999994 0.246432821 2.232831186 0.774559715 0.524844002 0.059842969 130.3727858 1.295760193 80.69500174 0.081130763 1.00E-05 4.999999994 -1.458271471 RASS(ph)LNVLNVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASSLNVLNVGGK 13 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;H0YG16;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 RAS(0.05)S(0.95)LNVLNVGGK;RAS(0.264)S(0.736)LNVLNVGGK;RAS(0.228)S(0.772)LNVLNVGGK 199.61 7.13E-08 2421810000 4538900 4061200 5015100 3580100 6215400 5951100 4928400 5032300 5465000 4715000 TRUE FALSE 4718099.277 4758679.508 5145797.626 4288233.094 5158908.528 4569047.215 4542099.13 4964850.25 5268315.718 5638813.976 0.836718377 0.843914967 0.912567368 0.760484938 0.914892485 0.810285148 0.805506113 0.880477751 0.934295002 1 22.42696032 1.133775692 2.009687426 0.997451393 0.842346378 0.574688358 0.044460732 0.2012535 1.528788023 0.038876216 0.011068584 13.60741695 -1.133775692 -0.155105014 RASS(ph)PSLIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RASSPSLIER 10 1 A1L170;A1L170-2 A1L170 C1orf226 Uncharacterized protein C1orf226 1 RAS(0.194)S(0.806)PSLIER 101.38 0.0020649 146600000 87205 100060 95346 116120 109820 138330 112420 111120 92076 83127 TRUE FALSE 90647.92074 117244.5266 97830.79509 139088.1894 91152.83563 106204.9539 103608.2266 109630.6182 88762.20275 99414.14409 0.911821166 1.179354585 0.984073202 1.399078478 0.91690007 1.068308286 1.042187986 1.102766806 0.892852859 1 16.6011635 RASSLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RASSLSR 7 1 Q9Y259;Q9Y259-2 Q9Y259 CHKB Choline/ethanolamine kinase 1 RASS(0.002)LS(0.998)R;RAS(0.003)S(0.048)LS(0.949)R;RAS(0.006)S(0.006)LS(0.987)R 112.11 0.0068096 942580000 964290 1168930 1182030 1121050 1289030 1460930 1226480 1238070 1123530 1384680 TRUE FALSE 1002360.914 1369684.634 1212834.673 1342790.344 1069921.141 1121651.148 1130345.293 1221475.697 1083094.375 1655981.535 0.605297156 0.827113471 0.732396254 0.810872776 0.64609485 0.677333125 0.682583271 0.737614322 0.65404979 1 20.65925516 -1.447799995 6.126352289 1.000118667 0.713382951 0.627467736 0.067354602 0.000103789 9.36E-06 0.062001992 0.014608003 0.035661533 1.447799995 -0.286735716 RASVFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RASVFVK 7 1 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2;H7C3I1 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ; 91.064 0.026743 379850000 897470 811200 924310 872590 1301830 1187920 1067680 948980 906020 967960 FALSE TRUE 932902.8086 950517.2897 948398.2779 1045185.698 1080545.402 912043.5831 983992.4517 936260.4753 873412.5172 1157613.229 0.805884716 0.821100922 0.819270421 0.902879883 0.933425236 0.78786555 0.850018319 0.808785224 0.754494243 1 20.14272188 -2.433153446 2.279467959 2.615616684 0.833686281 0.50366284 0.050132295 1782056.975 337406.6139 14788948.18 0.012790143 0.003688473 2.433153446 -1.781930403 RAT(ph)SLPSIPNPFPELCSPPSQS(ph)PILGGPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.542)S(0.458)LPSIPNPFPELCS(0.001)PPS(0.144)QS(0.854)PILGGPSSAR 175.49 5.07E-15 151910000 58358 75753 70277 72582 89842 109170 65109 85426 83549 114120 TRUE FALSE 60662.0189 88762.98847 72108.47635 86938.50296 74570.68893 83816.92199 60005.58645 84281.0042 80542.08781 136479.629 0.444476728 0.650375364 0.528346075 0.637007175 0.546386955 0.614135037 0.439666981 0.617535414 0.590139997 1 17.0583261 0.314091161 1.415798292 1.000170946 0.561418844 0.779379867 0.069976352 2.121184802 3.952775019 0.060863429 0.017655217 2.061062497 -0.314091161 -0.438752102 RAT(ph)SLPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.5)S(0.5)LPSIPNPFPELCSPPSQSPILGGPSSAR 169.44 1.99E-14 359240000 77375 89992 84453 70318 102750 130810 75466 85317 96072 99004 TRUE FALSE 80429.82475 105447.426 86653.91456 84226.69052 85284.5917 100431.3599 69550.77773 84173.46517 92614.38749 118401.9383 0.679294832 0.890588681 0.731862297 0.71136243 0.72029726 0.848223952 0.587412493 0.710912899 0.782203306 1 16.85333317 -1.510665261 8.294537157 1.000022933 0.737422501 0.481451692 0.080827016 3.35E-05 1.97E-06 0.076381006 0.018001607 0.030855653 1.510665261 -0.262600431 RATS(ph)LPSIPNPFPELCSPPS(ph)QSPILGGPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 2 RAT(0.201)S(0.798)LPS(0.001)IPNPFPELCS(0.002)PPS(0.684)QS(0.314)PILGGPSSAR 119.53 1.97E-06 118340000 31723 42877 34795 34613 44357 54023 36578 49929 37538 48051 TRUE FALSE 32975.44854 50240.79121 35701.78628 41459.34809 36817.21298 41476.97698 33710.92078 49259.78342 36187.01471 57465.67346 0.573828628 0.874274818 0.62127152 0.721462842 0.640681833 0.721769614 0.58662709 0.857203622 0.629715316 1 15.81041281 -2.632374255 0.378641632 1.534978581 0.691489938 0.455155938 0.100208042 66.17238549 2.640809737 28.92415016 0.062719215 0.002331448 2.632374255 -0.843488643 RATS(ph)LPSIPNPFPELCSPPSQSPILGGPSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RATSLPSIPNPFPELCSPPSQSPILGGPSSAR 32 1 Q14451;Q14451-3;Q14451-2;J3QL76 Q14451 GRB7 Growth factor receptor-bound protein 7 1 RAT(0.126)S(0.852)LPS(0.022)IPNPFPELCSPPSQSPILGGPSSAR 230.43 7.94E-37 426520000 67916 86643 100830 93425 115540 136010 87087 81645 92394 116080 TRUE FALSE 70597.37612 101523.2613 103457.7126 111904.1862 95900.55207 104423.7388 80260.89338 80550.68232 89068.75799 138823.6535 0.508539967 0.731310974 0.745245569 0.806088756 0.690808444 0.752204225 0.578149986 0.580237447 0.641596412 1 17.08289388 -1.531944883 3.052407559 1.012264247 0.67072283 0.554568123 0.088600288 106633458.3 129011528.1 10902075.54 0.022871473 0.029380225 1.531944883 -0.341541417 RATVVESSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RATVVESSEK 10 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 153.74 2.52E-05 544980000 561630 474740 504040 435810 714610 682230 635550 522000 534490 459250 FALSE TRUE 583803.5861 556272.902 517175.6965 522011.9172 593140.8475 523792.4218 585733.9303 515003.4438 515253.8093 549231.2446 1.062946786 1.012820934 0.941635607 0.950441043 1.079947387 0.953682856 1.066461415 0.937680529 0.938136376 1 19.06705417 1.621198 24.99999992 0.953434142 1.005236419 0.173481365 0.050074536 1.36589334 2555.283555 0.022851799 0.012579467 41.80209038 -1.621198 0.051802277 RAVS(ph)PSNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RAVSPSNPK 9 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 1 RAVS(0.988)PS(0.012)NPK;RAVS(0.999)PS(0.001)NPK;RAVS(0.5)PS(0.5)NPK;RAVS(0.994)PS(0.006)NPK;RAVS(1)PSNPK;RAVS(0.989)PS(0.011)NPK 177.47 5.52E-05 8363020000 4820630 3873700 4359540 3662030 5662910 5576910 5345760 4711790 4803570 3915770 TRUE FALSE 5010952.195 4538977.842 4473153.194 4386368.604 4700330.581 4281757.171 4926745.363 4648636.162 4630690.454 4682990.16 1.070032612 0.969247786 0.955191671 0.936659795 1.003702852 0.914321198 1.052051188 0.992664089 0.988831985 1 22.15899858 2.22278598 24.99962193 1.007737659 0.973284975 0.129300586 0.042491596 501.6638783 795030.4436 0.015529251 0.011508008 167.0267304 -2.22278598 -0.034452684 RAVSEGCAS(ph)EDEVEGEA ddPTM_MDA-MB-175_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 204.81 8.95E-12 311230000 257650 318600 272260 297870 295540 344020 274310 287060 265820 304900 TRUE FALSE 267822.2209 373317.0716 279355.3193 356787.7969 245304.2164 264126.5687 252808.8654 283212.4302 256253.1901 364639.3173 0.734485307 1.023798186 0.766114091 0.978467708 0.67273112 0.724350217 0.69331214 0.776691971 0.70275798 1 18.4761106 3.231485415 24.99521974 0.746162671 0.878464871 0.174929246 0.118484494 225.2286609 795685.5228 0.030828916 0.037592286 1704.062091 -3.231485415 0.1323022 RCDDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RCDDLTR 7 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;; 143.61 0.015098 0 382576 489400 422272 375305 544329 515659 403710 450501 387308 608984 FALSE TRUE 397680.3959 573450.643 433276.7552 449539.2088 451804.151 395905.0121 372066.1553 444462.771 373368.8607 728302.7551 0.546037198 0.787379478 0.59491297 0.617242219 0.62035211 0.543599498 0.510867428 0.610271989 0.512656115 1 19.47417878 -1.398323761 4.792713516 1.000527036 0.596817345 0.721372672 0.07573038 0.000423852 5.32E-05 0.07287463 0.01715488 0.039964671 1.398323761 -0.403709691 RCDIIIISGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RCDIIIISGR 10 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 ; 166.65 8.79E-06 567390000 110896 161827 136560 150782 145649 171675 136834 150096 133029 182505 FALSE TRUE 115274.2597 189619.5284 140118.8658 180606.2296 120891.635 131806.083 126108.5935 148084.2086 128241.3123 218263.3605 0.528142971 0.868764817 0.641971541 0.827469297 0.553879656 0.60388552 0.577781783 0.678465723 0.587553092 1 17.73571044 -1.823235361 6.61768507 1.02318196 0.657293084 0.48434688 0.107598995 0.033105612 0.000884282 0.09371942 0.023271289 0.015023276 1.823235361 -0.365888876 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDR 38 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 199.21 9.79E-31 1738847000 257601.8 341633.5 376530.3 311384.5 476225 454151 335167.7 345580.3 387389.4 461584.9 FALSE TRUE 267772.118 400306.3961 386342.9889 372975.4247 395276.4446 348681.313 308896.3799 340948.3613 373447.3312 552023.6236 0.485073657 0.725161712 0.699866767 0.675651202 0.716049871 0.631642013 0.559570943 0.617633642 0.676506068 1 19.07437048 0.829661956 5.717568234 0.999999235 0.642254279 0.702694186 0.070013275 2.317214662 77.61282056 0.06726713 0.016933794 6.755569337 -0.829661956 -0.357744956 RCPT(ph)PEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RCPTPEIQK 9 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK;RCPT(1)PEIQK 136.38 0.00011396 2320160000 3428740 2735460 3289240 2935560 3683430 4343380 4284500 3371600 3436780 2421950 TRUE FALSE 3564109.303 3205253.976 3374960.297 3516205.006 3057321.884 3334695.82 3948669.695 3326409.217 3313090.959 2896484.731 1.230494766 1.106601371 1.165191813 1.213955996 1.055528397 1.15129066 1.363262734 1.148429743 1.143831667 1 21.46587163 0.795025195 2.49806952 1.000240292 1.17962425 0.324765992 0.077527801 1.049467278 10.51696263 0.074401206 0.019918297 6.237710222 -0.795025195 0.179383957 RCPT(ph)PEIQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RCPTPEIQKK 10 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RCPT(1)PEIQKK 112.42 0.077335 1579400000 3800400 2253500 3255200 2202900 4503200 4110300 3523000 2965600 3497200 1893800 TRUE FALSE 3950442.727 2640521.095 3340033.186 2638627.045 3737747.673 3155745.117 3246858.054 2925850.983 3371336.455 2264853.851 1.744237371 1.165868206 1.474723495 1.165031926 1.65032621 1.393354859 1.433583917 1.291849795 1.488544814 1 21.11098653 -2.900132905 0.425375247 2.46E-12 1.415673323 0.334661034 0.177545145 147.0452953 5.271189715 133.4930535 0.092445271 0.00125854 2.900132905 1.415673323 RCQYVTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 182.76 0.00036371 1092060000 1732270 1329630 1498340 1526450 2407200 2277910 2547260 1840910 1930310 1454270 FALSE TRUE 1800661.357 1557983.609 1537387.971 1828377.254 1998025.004 1748899.925 2347599.105 1816235.613 1860838.52 1739206.363 1.035335079 0.895801466 0.883959491 1.051271024 1.148814222 1.005573555 1.349810555 1.044289885 1.069935437 1 20.72999769 3.544169294 4.438568954 1.112978475 0.935555556 0.342243821 0.101327265 0.222581438 8.509083876 0.026718603 0.041419447 3500.816071 -3.544169294 -0.177422919 RCS(ph)DGGAHGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RCSDGGAHGYGR 12 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RCS(1)DGGAHGYGR;RCS(1)DGGAHGYGR;RCS(1)DGGAHGYGR 132.63 0.00010873 654465000 93229.2 190509 151923 186456 158770 220283 112355 161801 138421 203555 TRUE FALSE 96909.9608 223227.4388 155882.2382 223336.4403 131782.3321 169125.6117 103548.3215 159632.3222 133439.2552 243437.705 0.398089363 0.916979721 0.640337281 0.91742748 0.541339034 0.69473877 0.425358601 0.655741978 0.548145388 1 17.89319311 -1.060160959 4.80910425 1.000010741 0.644519111 0.296046183 0.167353575 1.81E-05 3.53E-06 0.151903561 0.035802931 0.087064085 1.060160959 -0.35549163 RCS(ph)DPSLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RCSDPSLNEK 10 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 RCS(0.991)DPS(0.009)LNEK;RCS(0.998)DPS(0.002)LNEK;RCS(1)DPSLNEK;RCS(1)DPSLNEK;RCS(1)DPSLNEK;RCS(0.998)DPS(0.002)LNEK 148.57 1.52E-05 2605120000 3287110 2549870 2889200 2424050 3786440 3894840 3372800 2985600 3246620 2406690 TRUE FALSE 3416887.641 2987790.337 2964494.926 2903519.855 3142822.281 2990322.437 3108431.123 2945582.915 3129774.78 2878234.827 1.187146931 1.038063437 1.029969792 1.008784908 1.091926987 1.038943178 1.079978289 1.023399095 1.087393826 1 21.45675287 4.740362813 24.95373869 1.045396132 1.18714698 0.662740048 0.030566802 87.06523242 1205428.528 0.006762334 0.044065827 55000.01567 -4.740362813 0.141750847 RCS(ph)EDFSPLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RCSEDFSPLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR 40 2 Q7Z3T8 Q7Z3T8 ZFYVE16 Zinc finger FYVE domain-containing protein 16 1 RCS(0.998)EDFS(0.002)PLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR;RCS(0.944)EDFS(0.056)PLSPDVPMTVNTVDHSHSTTVEKPNNETGDITR 97.541 5.90E-05 694260000 77336 94195 126274 100355 166310 152352 160389 141632 132919 106713 TRUE FALSE 80389.285 110372.2585 129564.8042 120204.9195 138040.6856 116970.5569 147817.2911 139733.6547 128135.2712 127621.3692 0.62990458 0.864841517 1.015228131 0.941887085 1.081642412 0.916543661 1.158248748 1.094907973 1.00402677 1 16.96151039 5.211283402 0.876051686 1.050309423 1.67E-17 0.768269177 0.067732139 2.060624558 0.694135655 0.021879653 2.521440488 162660.9866 -5.211283402 -1.050309423 RCS(ph)SSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.332)S(0.332)S(0.332)LGVPLT(0.002)EVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.333)S(0.333)S(0.333)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR;RCS(0.333)S(0.333)S(0.333)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 70.073 0.0025877 415442000 14742.3 16219.2 14310.8 17093.7 18129.3 18069.7 13148 15458 16040 14081.5 TRUE FALSE 15324.33739 19004.72143 14683.7512 20474.78284 15047.68806 13873.28602 12117.4254 15250.81079 15462.72353 16840.50032 0.909969247 1.128512875 0.871930817 1.21580609 0.893541627 0.823804861 0.719540701 0.905603189 0.918186707 1 14.03964738 3.023493676 24.99371082 0.858103552 1.030528092 0.303526746 0.114014627 246.6667095 262414.1885 0.031010211 0.037062512 1055.586132 -3.023493676 0.17242454 RCS(ph)VTSMESTVSSGTQTTVQDDPEQFEVIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RCSVTSMESTVSSGTQTTVQDDPEQFEVIK 30 1 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 RCS(0.988)VT(0.012)SMESTVSSGTQTTVQDDPEQFEVIK;RCS(0.993)VT(0.005)S(0.001)MESTVSSGTQTTVQDDPEQFEVIK;RCS(0.841)VT(0.027)S(0.035)MES(0.046)T(0.046)VS(0.002)S(0.002)GT(0.002)QTTVQDDPEQFEVIK 235.05 1.25E-45 791470000 361234 310156 412940 335017 477690 494270 397098 360940 429410 337310 TRUE FALSE 375495.7973 363422.8803 423701.5556 401282.3627 396492.4244 379483.2832 365972.4211 356102.1897 413955.618 403399.4363 0.93082876 0.900900813 1.050327585 0.994751917 0.982877983 0.940713469 0.907220953 0.882753315 1.026168063 1 18.62184954 2.66571653 5.886582829 0.935092562 0.973560081 0 0.054382597 0.581388851 36.29213326 0.018385729 0.017355386 463.1445203 -2.66571653 0.038467519 RCSSS(ph)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RCSSSLGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 36 2 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 RCS(0.33)S(0.285)S(0.385)LGVPLTEVVEPLDFEDVLLSRPPDAEPGPLR 176.89 4.14E-23 330170000 35036 39621 40341 47943 49214 45878 40427 43110 46731 46036 TRUE FALSE 36419.24833 46425.59854 41392.3196 57425.9823 40848.62186 35223.52979 37258.2261 42532.18096 45049.16044 55055.87279 0.661496158 0.843245165 0.751823875 1.043049168 0.741948493 0.639777884 0.676734819 0.772527594 0.818244415 1 15.74860884 0.816548099 2.906941089 0.999896845 0.768705626 0.293040283 0.108821809 1.145428882 15.65162318 0.107177171 0.028164824 6.554628756 -0.816548099 -0.231191219 RDDFCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDDFCK 6 1 P32456;H3BNS1;Q9H0R5-4;P32455;Q9H0R5 P32456 GBP2;GBP3;GBP1 Interferon-induced guanylate-binding protein 2;Guanylate-binding protein 3;Interferon-induced guanylate-binding protein 1 0 ;;; 132.09 0.024125 1123630000 1388180 1215260 1438410 1246050 1923740 1784550 1626090 1484880 1528780 1229740 FALSE TRUE 1442986.418 1423971.452 1475896.146 1492514.971 1596743.362 1370115.308 1498632.817 1464977.612 1473759.506 1470684.008 0.981166865 0.96823753 1.003544023 1.014844088 1.085714778 0.931617737 1.019003952 0.996119904 1.002091203 1 20.48805587 4.187880671 6.507210576 1.007135566 0.974743592 0.116551855 0.0351681 0.373761923 35.21498251 0.00856604 0.019186476 15412.76905 -4.187880671 -0.032391974 RDDGLSAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RDDGLSAAAR 10 1 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 ;;;; 206.36 2.43E-07 1807870000 657901 792459 696348 658162 983981 923920 701253 720191 683040 965967 FALSE TRUE 683875.4395 928557.6688 714495.4009 788344.4792 816724.2611 709353.5821 646286.9575 710538.0176 658457.5238 1155229.739 0.591982197 0.803786154 0.618487714 0.682413595 0.706979948 0.614036809 0.559444529 0.61506209 0.569979721 1 20.13974836 -1.711587306 7.118452826 1.003173977 0.641362347 0.705675849 0.069698215 0.003571824 0.000144717 0.068657017 0.016084104 0.019427311 1.711587306 -0.361811629 RDDGSWEVIEGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDDGSWEVIEGYR 13 1 P00367;P49448 P00367 GLUD1;GLUD2 "Glutamate dehydrogenase 1, mitochondrial;Glutamate dehydrogenase 2, mitochondrial" 0 ; 166.64 7.68E-06 126670000 153597 187599 176710 194497 192018 253490 192176 167226 165184 231790 FALSE TRUE 159661.1282 219817.6689 181315.2078 232967.9261 159378.8489 194620.7892 177112.743 164984.609 159239.0601 277204.8126 0.575968096 0.792979266 0.65408391 0.840418043 0.574949791 0.70208301 0.638923766 0.595172239 0.574445511 1 18.08059278 -0.970017407 4.606042719 1.000005578 0.662719477 0.569012433 0.088497984 0.049161791 52883387.31 762.4531324 0.020162538 0.107147636 0.970017407 -0.337286102 RDDGTGQLLLPLSDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 183.74 3.10E-09 2239500000 1529246 1695550 1635925 1690672 1874120 2046260 1659866 1695320 1683720 1644306 FALSE TRUE 1589621.813 1986747.523 1678558.549 2025081.875 1555557.752 1571047.126 1529761.366 1672597.008 1623123.246 1966476.279 0.808360533 1.01030841 0.853586981 1.029802341 0.791038147 0.798914863 0.777920071 0.850555395 0.825396809 1 20.90718135 3.210173872 24.99988641 0.828348142 0.926433718 0.185894596 0.084696861 281.0384625 247506.7134 0.022405087 0.026783944 1622.459527 -3.210173872 0.098085576 RDDMESLGYVLMYFNR ddPTM_MDA-MB-175_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 414150000 229701 222717 246217 208296 343610 296522 307920 268958 248605 296677 FALSE TRUE 238769.7728 260966.9123 252633.6173 249496.3271 285203.2949 227659.2593 283784.4258 265353.0579 239657.7546 354805.1779 0.672960226 0.735521713 0.712034753 0.703192463 0.803830701 0.64164582 0.799831692 0.747883837 0.675462957 1 18.43666754 -2.202696463 2.478252998 1.870562272 0.726188196 0.73363314 0.050291494 6509657.437 1101500.393 31937157.41 0.011408846 0.00627052 2.202696463 -1.144374076 RDDNSAANNSANEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 161.19 4.79E-09 126588000 54107 52332 60089 32670 71992 80049 43607 43636 66182 69099 FALSE TRUE 56243.18614 61319.61391 61654.9687 39132.02849 59754.82555 61458.8329 40188.96939 43051.13079 63800.12275 82637.62607 0.680600216 0.742030197 0.746088333 0.473537665 0.723094653 0.743714889 0.486327734 0.520962821 0.772046897 1 16.33451119 -1.711356967 8.000387142 1.001754564 0.642377072 0.462899357 0.111061373 0.003619463 0.000130585 0.111981927 0.026292988 0.019437618 1.711356967 -0.359377492 RDEFEFLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDEFEFLEK 9 1 Q14258;A0A3B3IUA7 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 150.04 0.00013819 368420000 625810 546730 606550 506770 802000 798610 729310 640290 674270 519400 FALSE TRUE 650517.462 640626.6245 622357.1913 607007.5934 665676.3265 613144.9306 672144.7765 631707.9599 650003.1544 621166.4855 1.047251385 1.031328379 1.001916887 0.977205963 1.071655252 0.987086304 1.082068644 1.016970449 1.046423414 1 19.24462047 3.237413861 24.99999997 1.034783066 1.014739515 0.080916114 0.032308693 81.3955481 1774527.256 0.008744348 0.011038602 1727.483313 -3.237413861 -0.020043551 RDEGS(ph)SPSLALNTYPSYLSQLDSWGDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDEGSSPSLALNTYPSYLSQLDSWGDPK 28 1 Q9NYD6 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 RDEGS(0.462)S(0.462)PS(0.033)LALNT(0.039)Y(0.002)PS(0.001)YLSQLDSWGDPK 70.525 0.0071111 41013000 33899 21093 26570 18830 32449 30575 31370 25860 34098 24785 TRUE FALSE 35237.3587 24715.55867 27262.43603 22554.5178 26933.33057 23474.41962 28911.13743 25513.389 32870.81964 29641.14621 1.188798788 0.83382601 0.919749723 0.760919218 0.90864673 0.791953842 0.975371776 0.860742321 1.108959127 1 14.85531362 1.242689519 24.99998908 1.054479586 0.896540364 0.209421667 0.115237458 132.4812285 802197.1328 0.077984962 0.026204932 17.48596154 -1.242689519 -0.157939222 RDELLAQHAAGALGLPDLVAVLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 175.48 1.03E-12 1068180000 367030 398310 390190 464120 426580 499440 498350 427400 371150 355720 FALSE TRUE 381520.6278 466716.6441 400358.6719 555921.5507 354070.084 383452.6291 459288.0248 421671.4021 357792.384 425416.5233 0.896816665 1.097081609 0.941098077 1.306770001 0.83229039 0.9013581 1.079619619 0.991196578 0.841040167 1 18.69851654 RDELTLEGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDELTLEGIK 10 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 ;; 139.76 6.49E-05 680170000 791190 632140 739710 640640 904520 927170 866550 791240 815760 669760 FALSE TRUE 822426.7921 740705.1276 758987.4503 767356.6799 750770.0135 711848.8189 798627.5467 780634.722 786400.9569 800986.6487 1.026767167 0.924740917 0.94756567 0.95801432 0.937306527 0.888714962 0.997054755 0.974591428 0.981790344 1 19.61141867 RDEQDDDDKGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RDEQDDDDKGDSK 13 2 Q9H4A6;D6REM1 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ;;;;; 180.11 7.41E-06 3191605000 5840520 1562894 2605734 1535693 3976690 5051940 4137080 2592144 2994185 1096259 FALSE TRUE 6071108.239 1831308.887 2673641.569 1839448.492 3300733.654 3878703.498 3812804.859 2557400.55 2886424.867 1311049.962 4.630722258 1.396826162 2.039313258 1.403034625 2.517626139 2.958471157 2.908207139 1.950650718 2.201613173 1 20.32229123 0.664202787 1.252725526 1.005652549 2.429633506 0.201143532 0.884492051 1.89763144 4.67647138 0.810079281 0.245023803 4.615330299 -0.664202787 1.423980957 RDETALQEEEELQLALALSQSEAEEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDETALQEEEELQLALALSQSEAEEKER 28 2 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 85.185 0.0021692 19956000 14626 11424 12496 9236.2 14260 15043 12974 10112 12848 9782.9 FALSE TRUE 15203.44577 13385.98313 12821.65603 11063.09279 11836.09029 11549.49123 11957.06398 9976.46518 12385.60299 11699.67195 1.299476245 1.144133202 1.095898764 0.945589999 1.011660014 0.987163681 1.021999936 0.85271324 1.058628228 1 13.51418046 4.730838437 0.884623792 0.967228015 1.483842789 0.760402053 0.056050466 0.993613942 0.610295735 0.018652164 0.498799078 53806.95768 -4.730838437 0.516614774 RDFVDHIDLVDPVDGVVLVDPEYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDFVDHIDLVDPVDGVVLVDPEYLK 25 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ; 177.7 1.97E-17 113734000 178843 123278 155091 132238 209509 172938 196375 171806 175638 108721 FALSE TRUE 185903.8597 144450.0375 159132.7989 158394.2817 173896.735 132775.7704 180982.6144 169503.2216 169316.8227 130022.7984 1.429778947 1.110959304 1.223883818 1.218203913 1.337432644 1.021172995 1.391929851 1.303642313 1.302208727 1 16.98840508 RDGLLTMLPGPPPVYAADSNS(ph)PLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDGLLTMLPGPPPVYAADSNSPLLR 25 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 RDGLLTMLPGPPPVY(0.01)AADS(0.371)NS(0.619)PLLR 56.648 0.059875 159230000 69521 75166 85143 71490 82137 100830 77321 67177 93188 81796 TRUE FALSE 72265.74276 88075.17579 87361.89653 85630.50862 68175.38208 77413.76059 71260.37798 66276.60219 89834.18208 97822.36012 0.738744625 0.90035832 0.893066743 0.875367437 0.696930456 0.791370812 0.728467171 0.677519967 0.918339958 1 16.57787665 5.041646865 14.67102036 0.809072851 0.45159183 0.030245062 0.102405164 959802.7605 10269455.75 0.025079569 9027740.945 110064.3987 -5.041646865 -0.357481021 RDGPEETDWWWAALHGQEGYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDGPEETDWWWAALHGQEGYVPR 23 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 ; 160 1.26E-11 72880000 43856 51200 49398 43739 55213 61592 50138 53158 57027 51158 FALSE TRUE 45587.46874 59993.20172 50685.35246 52390.44365 45827.91398 47288.19144 46208.05255 52445.50396 54974.60941 61181.43062 0.745119365 0.980578602 0.828443401 0.856312824 0.749049401 0.772917386 0.755262701 0.857212776 0.898550571 1 15.90080622 1.010899211 1.958447116 0.998066139 0.81766578 0.427017489 0.066960681 0.327977301 2.645367752 0.06418714 0.018071814 10.25413926 -1.010899211 -0.18040036 RDGSDVIYPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDGSDVIYPAR 11 1 P25685;P25685-2;M0R080 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 136.7 0.0021979 0 36319 42098 46036 43289 51687 54308 39275 46179 39365 45825 FALSE TRUE 37752.90216 49328.00402 47235.73598 51851.435 42901.2622 41695.79005 36196.52287 45560.04604 37948.26134 54803.53138 0.68887718 0.900088056 0.861910442 0.946133099 0.782819302 0.760823053 0.660477928 0.831334129 0.692441899 1 15.74198124 3.033667972 24.98295812 0.772396228 0.855123636 0.062771657 0.105980167 379.1522781 281343.4211 0.028755536 0.034369281 1080.607487 -3.033667972 0.082727408 RDHALLEEQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDHALLEEQSK 11 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 96.64 0.004454 1708940000 894410 864572 719946 721718 1067050 1136740 1207960 817248 756236 957370 FALSE TRUE 929721.9974 1013055.516 738708.3842 864471.6663 885673.2221 872749.3625 1113276.939 806294.1273 729019.2141 1144948.322 0.812020927 0.884804577 0.645189281 0.755031166 0.773548644 0.762260921 0.972338155 0.704218795 0.636726742 1 20.12685105 RDHALLEEQSKQQSNEHLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDHALLEEQSKQQSNEHLRR 20 3 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 127.17 1.32E-05 76788000 44889 55309 56675 43118 56740 68704 53675 53108 51893 44943 FALSE TRUE 46661.25238 64807.89051 58151.99706 51646.61171 47095.35507 52748.53722 49467.81325 52396.17413 50025.38107 53748.72036 0.868136991 1.205756901 1.081923377 0.960890071 0.876213513 0.981391498 0.92035332 0.97483575 0.930726922 1 15.71394279 3.696245463 6.078463377 0.945965393 1.067345962 0.234720721 0.083642674 0.232298059 23.44492288 0.020901694 0.033175226 4968.730742 -3.696245463 0.121380569 RDHHSTHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RDHHSTHYR 9 1 P05060 P05060 CHGB Secretogranin-1;PE-11;GAWK peptide;CCB peptide 0 ;;;;; 96.331 0.01193 4209410000 2324310 2327810 2332990 1825240 3604180 2887140 2296670 2407150 2485800 3207720 FALSE TRUE 2416075.554 2727593.26 2393789.636 2186267.024 2991542.771 2216645.49 2116651.004 2374886.092 2396336.544 3836211.318 0.629807733 0.711012255 0.623998377 0.569902657 0.779816992 0.577821529 0.551755581 0.619070717 0.624662289 1 21.87125076 -1.975311366 2.473858066 1.320903326 0.630594619 0.745388235 0.064521735 4215175.663 1840444.186 7738755.654 0.015976299 0.010584946 1.975311366 -0.690308707 RDHRPPCAQEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDHRPPCAQEAPR 13 2 Q13501;Q13501-2;E7EMC7;C9JRJ8;E9PFW8;E3W990 Q13501 SQSTM1 Sequestosome-1 0 ;; 133.16 6.21E-05 54810000 24832.8 36170 24255.4 30193.6 32930 37268 30137.5 28596.5 30112.6 32336.7 FALSE TRUE 25813.21812 42381.91614 24887.51565 36165.80396 27332.57036 28613.0718 27775.244 28213.21069 29028.85341 38672.45724 0.667483267 1.095919917 0.643546271 0.935182467 0.706770976 0.739882434 0.718217718 0.729542747 0.750633797 1 15.23901882 3.216933463 24.99716 0.753464047 0.84041878 0.029714111 0.144185201 602.4683748 696345.0516 0.037965761 0.045415866 1647.909899 -3.216933463 0.086954733 RDIEDIPYV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDIEDIPYV 9 1 Q96EI5;Q96EI5-2;A2RQR6 Q96EI5 TCEAL4 Transcription elongation factor A protein-like 4 0 98.299 0.0051233 0 62338 88039 84029 75589 90528 100100 82287 86695 84193 93906 FALSE TRUE 64799.15238 103159.0134 86218.86477 90540.27859 75140.0829 76853.29203 75837.12992 85532.99533 81162.91038 112305.0828 0.576992161 0.918560504 0.767720059 0.806199295 0.669071079 0.684326035 0.675277806 0.76161286 0.722700241 1 16.7770637 -1.746953387 4.888414005 1.015274172 0.73639461 0.459078162 0.08732118 0.014240969 0.000737177 0.082831996 0.018999744 0.017907981 1.746953387 -0.278879562 RDINVSVGSQQPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDINVSVGSQQPDTK 15 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 105.39 0.0042845 0 56635 42509 50070 26294 95257 67403 35802 49626 72872 70862 FALSE TRUE 58870.99353 49809.59008 51374.86533 31494.87472 79065.24916 51749.67475 32995.74569 48960.84464 70249.35095 84746.05217 0.694675351 0.587751155 0.60622134 0.371638252 0.932966754 0.610644076 0.389348469 0.577735993 0.82893951 1 16.37085854 1.062112351 3.518065506 0.995826378 0.590069211 0.445647072 0.147708791 0.18232116 4.587678232 0.139683956 0.036330886 11.53751693 -1.062112351 -0.405757167 RDINVSVGSQQPDTKDS(ph)PVCPHFTTNGNENSSIEK ddPTM_MDA-MB-175_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 119.5 7.66E-07 1001700000 259540 121880 213520 128940 283540 302460 206120 217740 212170 87420 TRUE FALSE 269786.8396 142811.9419 219084.5066 154443.9472 235343.9721 232218.2488 189963.7758 214821.5515 204534.0431 104548.2752 2.580500147 1.365990415 2.095534394 1.477250072 2.25105552 2.221158104 1.816995788 2.054759401 1.956359803 1 16.67380974 0.890518496 18.53762222 1 1.965278494 0.424349202 0.342040889 9738.003113 1648866.506 0.299648609 0.074912152 7.771744165 -0.890518496 0.965278494 RDLFAFQES(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDLFAFQESPPR 12 1 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 RDLFAFQES(1)PPR 137.21 5.90E-05 80618000 37898 42176 44129 45005 51273 53405 43827 47841 42948 46051 TRUE FALSE 39394.2423 49419.39992 45279.03799 53906.85467 42557.63377 41002.49811 40391.72522 47199.76965 41402.30987 55073.81175 0.715298997 0.897330298 0.822151882 0.978811035 0.77273812 0.744500822 0.733410743 0.857027472 0.751760384 1 15.74907884 4.763980056 22.70316048 0.830414081 0.715298488 0.137754504 0.090740849 4561.769445 4074074.919 0.020978097 1.239518323 58073.77474 -4.763980056 -0.115115592 RDNYVPEVSALDQEIIEVDPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDNYVPEVSALDQEIIEVDPDTK 23 1 H3BNC9;P08708;H0YN88;A0A075B716 H3BNC9 RPS17 40S ribosomal protein S17 0 ;;; 208.97 1.48E-24 572084000 636607 394340 579207 422072 655135 640928 689066 558846 629928 359641 FALSE TRUE 661740.7359 462064.8275 594301.6102 505556.5818 543775.3867 492082.1854 635055.2064 551355.5835 607257.0143 430105.7682 1.538553502 1.074305117 1.381756894 1.175423859 1.264282944 1.144095759 1.476509392 1.281906973 1.411878331 1 18.71433195 4.770682032 23.3529229 1.265163798 1.538554711 0.260484658 0.144746949 7945.743149 5776468.276 0.031809748 4.1959605 58976.91242 -4.770682032 0.273390912 RDPFIGEHTEEILEEFGFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDPFIGEHTEEILEEFGFSR 20 1 D6RB81;Q9UHK6;Q9UHK6-5 D6RB81 AMACR Alpha-methylacyl-CoA racemase 0 ;; 219.91 5.77E-25 100285000 55831 77532 63026 72061 72107 95137 65281 71212 62605 72451 FALSE TRUE 58035.25099 90847.51788 64668.50934 86314.45072 59850.2779 73042.87357 60164.10464 70257.51962 60351.85828 86646.38629 0.669794246 1.048485941 0.746349757 0.996169078 0.690741766 0.842999653 0.694363691 0.810853431 0.696530587 1 16.40285196 3.222778746 24.99997176 0.778097579 0.869802394 0.067789492 0.133776568 530.0695895 839678.3824 0.034728607 0.041639081 1670.239483 -3.222778746 0.091704815 RDPHLACVAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDPHLACVAYER 12 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ;;; 96.591 0.003504 3334990000 986099 1265294 1119706 1125881 1338910 1445500 987158 1173899 1105153 1320213 FALSE TRUE 1025030.95 1482598.402 1148886.458 1348576.901 1111322.556 1109804.532 909781.9765 1158164.804 1065378.759 1578883.46 0.649212545 0.939016995 0.727657542 0.854133275 0.703866108 0.702904654 0.576218574 0.733534066 0.674767192 1 20.59047326 RDPMYNEYLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDPMYNEYLDR 11 1 Q7L5D6;Q7L5D6-2 Q7L5D6 GET4 Golgi to ER traffic protein 4 homolog 0 ; 176.51 1.37E-05 436280000 149812 196851 179941 182532 220666 247370 164363 165308 162537 262750 FALSE TRUE 155726.6934 230658.628 184630.4103 218636.2848 183157.2721 189922.0664 151479.7986 163092.3166 156687.3251 314230.8318 0.495580566 0.734041999 0.587563 0.695782408 0.582874924 0.604403029 0.482065358 0.519020733 0.498637655 1 18.26146522 -1.832885637 3.839049894 1.096218682 0.578478451 0.712273775 0.080505586 0.04893467 0.002130132 0.0575331 0.019024472 0.014693131 1.832885637 -0.517740231 RDPSSNDINGGMEPTPSTVS(ph)TPSPSADLLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPT(0.001)PS(0.005)T(0.005)VS(0.411)T(0.368)PS(0.198)PS(0.013)ADLLGLR 56.952 0.018267 91527000 16812 20397 17295 25340 24845 29903 21935 20852 18873 21257 TRUE FALSE 17475.75074 23900.02608 17745.72191 30352.17637 20621.85577 22958.48143 20215.67738 20572.51305 18193.76442 25421.90216 0.68742892 0.94013524 0.698048549 1.193938053 0.811184609 0.903098489 0.795207111 0.809243656 0.71567282 1 14.63378436 -0.284314924 7.85093534 0.999999999 0.845116586 0.101840402 0.142213276 0 0 0.128906724 0.030383606 0.519619064 0.284314924 -0.154883413 RDPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 RDPSSNDINGGMEPTPSTVST(0.003)PS(0.996)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPST(0.001)VS(0.004)T(0.05)PS(0.945)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPS(0.048)T(0.036)VS(0.064)T(0.203)PS(0.646)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.004)T(0.012)PS(0.978)PS(0.005)ADLLGLR;RDPSSNDINGGMEPTPST(0.001)VS(0.261)T(0.129)PS(0.608)PS(0.001)ADLLGLR;RDPSSNDINGGMEPTPSTVS(0.022)T(0.022)PS(0.954)PS(0.002)ADLLGLR;RDPSSNDINGGMEPTPS(0.001)T(0.002)VS(0.004)T(0.076)PS(0.915)PS(0.003)ADLLGLR;RDPSSNDINGGMEPTPSTVST(0.004)PS(0.996)PSADLLGLR 258.17 1.88E-59 4868650000 578956 719253 728543 758646 766528 922364 784862 755371 673854 725410 TRUE FALSE 601813.6299 842779.1077 747529.4291 908703.9145 636233.8444 708158.9396 723342.4656 745246.4873 649602.1262 867540.2007 0.693701144 0.971458276 0.861665463 1.047448768 0.733376786 0.816283717 0.833785529 0.859033952 0.748786195 1 19.72657109 3.198798553 24.99996947 0.826743097 0.896854578 0.071059884 0.108059359 374.6613195 235563.1274 0.02931406 0.03503749 1580.514751 -3.198798553 0.07011148 RDPTEEIEILLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDPTEEIEILLR 12 1 B4DG22;B1AXG1;B7ZB17;P51812;A0A2R8Y603 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 0 ; 159.08 0.00011498 67898000 36497 40230 39452 37099 40161 45453 41654 43897 34997 40386 FALSE TRUE 37937.92974 47139.18955 40480.15153 44437.07147 33334.44757 34897.2296 38389.05064 43308.63252 33737.46481 48298.86346 0.785482867 0.975989623 0.838118097 0.920043833 0.690170434 0.722526931 0.794823064 0.896680158 0.698514673 1 15.55970162 3.281292702 24.99964303 0.798390776 0.883786515 0.131704259 0.099663087 273.9290638 160255.4047 0.026685268 0.036131776 1911.140878 -3.281292702 0.085395739 RDQALTEEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDQALTEEHAR 11 1 P12814-3;P12814;P12814-2;P12814-4;H9KV75;H0YJ11 P12814-3 ACTN1 Alpha-actinin-1 0 ;;; 189.24 1.81E-06 2081450000 832458 1134540 783083 1021176 1025711 1239382 1049084 850625 765740 1433414 FALSE TRUE 865324.0846 1329388.42 803490.7863 1223161.565 851361.0106 951554.3135 966854.0548 839223.7632 738181.167 1714264.029 0.504778768 0.775486388 0.468708888 0.713519939 0.496633538 0.555080371 0.564005333 0.489553388 0.430611128 1 20.7091579 -1.855295752 3.466621493 1.139364743 0.557623717 0.624400905 0.103440308 14753882.36 17896566.92 15581825.75 0.023031226 0.013954178 1.855295752 -0.581741026 RDRS(ph)PIRGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDRSPIRGSPR 11 3 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 RDRS(1)PIRGS(1)PR;RDRS(1)PIRGS(1)PR;RDRS(1)PIRGS(1)PR 82.529 0.026827 892203000 463115 490177 467616 406370 582185 583314 448641 477692 467898 447585 TRUE FALSE 481399.1378 574361.0867 479802.4571 486748.7731 483225.4017 447848.1637 413475.3461 471289.3201 451058.4424 535280.7112 0.899339595 1.073009123 0.89635671 0.909333669 0.902751382 0.836660381 0.772445817 0.880452649 0.842657755 1 19.02993614 4.057165227 8.930823461 0.869168627 0.986468053 0.278092841 0.067959267 0.327992151 47.20763596 0.016197682 0.035107363 11406.83677 -4.057165227 0.117299426 RDS(ph)ASYR ddPTM_MDA-MB-175_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(0.556)AS(0.444)YR;RDS(0.748)AS(0.252)YR;RDS(1)ASYR;RDS(1)ASYR;RDS(0.854)AS(0.145)Y(0.001)R;RDS(1)ASYR 147.3 0.0013234 5611466000 776700 824310 940946 959403 1220952 1230669 1075608 1117772 1124134 1112118 TRUE FALSE 807364.7157 965878.8303 965467.8258 1149170.05 1013415.015 944864.7757 991299.0344 1102790.095 1083676.637 1330016.229 0.607033732 0.726215823 0.725906801 0.864027088 0.761956879 0.710415975 0.745328525 0.829155367 0.814784521 1 20.34301242 -5 0.098574861 1.787338039 0.58463112 0.696743648 0.055389789 114.6562327 0.771888585 18.55448364 1.022799604 1.00E-05 5 -1.202706919 RDS(ph)AYGSFSTSSSTPDHTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDSAYGSFSTSSSTPDHTLSK 21 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 RDS(1)AYGSFSTSSSTPDHTLSK;RDS(1)AYGSFSTSSSTPDHTLSK;RDS(0.798)AY(0.084)GS(0.102)FS(0.002)T(0.002)S(0.002)S(0.002)S(0.002)T(0.002)PDHT(0.003)LSK;RDS(1)AYGSFSTSSSTPDHTLSK 298.97 2.48E-55 1224350000 253790 293626 331500 293183 501587 508341 374114 400038 419720 364403 TRUE FALSE 263809.8252 344053.9814 340139.1623 351173.7223 416327.4209 390286.5067 344789.9671 394676.1449 404614.3592 435800.7909 0.605344989 0.789475349 0.780492302 0.805812494 0.955315891 0.895561722 0.791164161 0.905634302 0.92843879 1 18.73330929 5.747297002 0.494351708 0.909843234 7.83E-26 0.722826175 0.057309943 6.458123387 0.567610135 0.032458051 4.227227098 558852.2479 -5.747297002 -0.909843234 RDS(ph)DGVDGFEAEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDSDGVDGFEAEGK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK 190.79 3.44E-07 1492360000 1457100 885030 1224210 986350 1711820 1705610 1742040 1294700 1470200 792430 TRUE FALSE 1514627.433 1037027.018 1256113.918 1181447.086 1420845.448 1309507.926 1605494.353 1277346.664 1417287.789 947691.4865 1.598228384 1.09426647 1.32544603 1.246657908 1.499270035 1.381787158 1.694110769 1.347850732 1.495516008 1 19.85405795 3.24142816 24.99721049 1.434008376 1.300964917 0.027316582 0.202199758 180.7205677 1575380.262 0.052426829 0.067970336 1743.524922 -3.24142816 -0.133043459 RDS(ph)DGVDGFEAEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSDGVDGFEAEGKK 15 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK;RDS(1)DGVDGFEAEGKK 153.95 1.34E-06 296220000 1053890 731010 831720 717600 1209640 1207740 1074820 870340 981230 683090 TRUE FALSE 1095498.391 856555.281 853395.3065 859539.1382 1004025.825 927260.6885 990572.7999 858674.5159 945915.724 816928.407 1.340996814 1.048507156 1.04463904 1.052159688 1.229025477 1.135057467 1.212557663 1.051101307 1.157893049 1 19.63985013 -0.18443543 0.707454106 0.993133741 1.136166423 0.165590669 0.093592005 13.64227982 6.297373904 0.355785497 0.032649932 0.653980156 0.18443543 0.143032682 RDS(ph)DTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSDTYR 7 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 RDS(0.964)DT(0.036)YR;RDS(0.955)DT(0.043)Y(0.002)R 80.916 0.030312 246200000 485590 539610 562230 534280 658400 741710 646420 589920 571240 526610 TRUE FALSE 504761.4682 632283.8199 576882.1757 639958.9893 546485.4032 569459.0932 595751.9113 582013.0873 550681.184 629789.1469 0.801476924 1.003961124 0.915992564 1.016148012 0.867727565 0.904205949 0.945954554 0.924139595 0.874389765 1 19.26450937 -1.575068196 2.733478835 1.005356436 0.922202894 0.140936327 0.060223634 17637094.85 17477786.59 686824.9046 0.013145733 0.026603073 1.575068196 -0.083153542 RDS(ph)EEFGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSEEFGVK 9 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RDS(1)EEFGVK 96.067 0.002435 0 190870 123250 149140 122260 217260 224430 220040 157250 195220 120640 TRUE FALSE 198405.695 144417.2287 153026.7109 146442.6631 180330.2228 172309.5338 202792.6898 155142.321 188194.0703 144277.0982 1.375171094 1.00097126 1.060644502 1.015009762 1.249888063 1.194295809 1.405577825 1.075308021 1.304393231 1 17.13848279 3.222142771 24.95973336 1.212696435 1.101214664 0.086138769 0.143396933 487.3669249 740932.8255 0.039471554 0.047303707 1667.795397 -3.222142771 -0.111481771 RDS(ph)FDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDR;RDS(1)FDDR;RDS(1)FDDR 132.55 0.0020565 217110000 328525 306479 366142 387984 445650 474380 456240 390580 399064 339389 TRUE FALSE 341495.4207 359114.3842 375683.9613 464726.0772 369898.5722 364212.4343 420478.7166 385344.914 384701.7646 405885.7766 0.841358432 0.884767107 0.925590358 1.144967634 0.911336621 0.897327414 1.035953317 0.949392505 0.947807947 1 18.63071426 4.151145221 3.614212142 0.979770425 0.860049842 0.332544058 0.067706234 0.25752711 6.472041925 0.01713756 0.043201388 14162.67279 -4.151145221 -0.119720584 RDS(ph)FDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.988)FDDRGPS(0.012)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR;RDS(0.998)FDDRGPS(0.002)LNPVLDYDHGSR;RDS(0.999)FDDRGPS(0.001)LNPVLDYDHGSR;RDS(0.987)FDDRGPS(0.013)LNPVLDYDHGSR;RDS(1)FDDRGPSLNPVLDYDHGSR 263.01 1.13E-37 14254670000 1401423 2755992 2757230 2651807 3350560 3618620 2714383 3104710 2902050 3082180 TRUE FALSE 1456752.262 3229312.187 2829085.679 3176326.51 2781033.008 2778250.346 2501622.568 3063096.441 2797605.787 3686074.159 0.395204274 0.876084432 0.767506446 0.861709877 0.754470173 0.753715261 0.67866854 0.83099154 0.758966224 1 21.81365367 -5 0.126044145 1.768814435 0.647797394 0.313246293 0.124493805 195.9438886 1.576313627 38.72732782 0.988737101 1.00E-05 5 -1.121017041 RDS(ph)FIGTPYWMAPEVVMCETMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSFIGTPYWMAPEVVMCETMK 22 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 RDS(0.871)FIGT(0.129)PYWMAPEVVMCETMK 153.01 2.27E-08 186020000 98286 69458 96496 92388 124330 121010 118820 110770 128310 76911 TRUE FALSE 102166.4072 81386.87119 99010.76503 110662.0706 103196.431 92907.26142 109506.5779 109285.3093 123692.1482 91980.2379 1.110743019 0.884829971 1.076435192 1.203107028 1.121941336 1.010078508 1.190544626 1.188139016 1.344768735 1 16.48903631 4.00091754 24.87420108 1.155123731 0.993497988 0.252563317 0.106004702 36.0280455 976571.0227 0.02576078 0.054902687 10021.14948 -4.00091754 -0.161625743 RDS(ph)FIGTPYWMAPEVVMCETSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 RDS(0.989)FIGT(0.011)PYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.898)FIGT(0.1)PY(0.002)WMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.999)FIGT(0.001)PYWMAPEVVMCETSK;RDS(0.998)FIGT(0.002)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.971)FIGT(0.028)PY(0.001)WMAPEVVMCETSK;RDS(0.997)FIGT(0.003)PYWMAPEVVMCETSK;RDS(1)FIGTPYWMAPEVVMCETSK;RDS(0.992)FIGT(0.005)PY(0.003)WMAPEVVMCETSK 318.8 1.03E-67 7103272000 3177664 2441174 3111793 2644831 4537496 4064722 3595455 3221610 3468598 2375218 TRUE FALSE 3303120.628 2860426.645 3192888.882 3167970.678 3766214.051 3120751.917 3313633.842 3178429.587 3343763.836 2840596.491 1.162826413 1.006980982 1.124020568 1.115248395 1.325853236 1.098625562 1.166527472 1.118930337 1.177134396 1 21.43776248 -2.472019897 1.796934185 4.22E-05 1.141841379 0.243819691 0.07600026 1264984.825 85512.28891 5142399.504 0.018962816 0.003372719 2.472019897 1.141799193 RDS(ph)FLGGGPGPEEPEDLALQLQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSFLGGGPGPEEPEDLALQLQQK 24 1 A0A2R8Y2X6;A1A5D9 A0A2R8Y2X6 CCDC64B Bicaudal D-related protein 2 1 RDS(1)FLGGGPGPEEPEDLALQLQQK;RDS(1)FLGGGPGPEEPEDLALQLQQK;RDS(1)FLGGGPGPEEPEDLALQLQQK 179.41 2.32E-17 241732000 199464 147947 192110 145409 257644 255133 235364 206337 235328 164726 TRUE FALSE 207338.9927 173355.7464 197116.5444 174170.4662 213849.7649 195882.2273 216915.5547 203571.39 226858.5912 197000.9058 1.052477357 0.879974362 1.000586995 0.884109976 1.08552681 0.994321455 1.101089123 1.033352558 1.151561158 1 17.58784274 3.223935715 24.99852653 1.060313187 0.952286236 0.396261248 0.064492104 217.7151276 372142.458 0.017060783 0.020474156 1674.694968 -3.223935715 -0.108026951 RDS(ph)GDNSAPSGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSGDNSAPSGQER 14 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER;RDS(1)GDNSAPSGQER 196.3 1.53E-08 418336000 100559 100424 97047 114850 110635 146236 131782 114744 108412 95373 TRUE FALSE 104529.147 117671.0408 99576.12454 137566.9872 91829.30222 112274.9052 121452.5825 113206.0444 104510.2733 114059.5133 0.916443915 1.031663536 0.87301902 1.206098318 0.805099895 0.984353711 1.064817646 0.992517336 0.916278443 1 16.79942726 2.476960131 24.99984078 0.998982107 0.96986043 0.01309028 0.104986963 34.46151422 5345214.967 0.034468832 0.029107315 299.8887206 -2.476960131 -0.029121677 RDS(ph)ICSSVSLESSAAETQEEMLQVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSICSSVSLESSAAETQEEMLQVLK 26 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 1 RDS(0.805)ICS(0.044)S(0.044)VS(0.061)LES(0.023)S(0.023)AAETQEEMLQVLK;RDS(0.584)ICS(0.123)S(0.123)VS(0.158)LES(0.006)S(0.006)AAETQEEMLQVLK 145.16 1.42E-07 171500000 32252 22695.3 28541 30303 38936 40308 31723 34957 29483 28009 TRUE FALSE 33525.33386 26593.04123 29284.80191 36296.84295 32317.67263 30947.07787 29236.46837 34488.45859 28421.91259 33496.82729 1.000851023 0.793897315 0.87425599 1.083590474 0.96479802 0.923880868 0.872813061 1.029603738 0.84849566 1 15.03173683 RDS(ph)IVAELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR 135.61 8.54E-05 1000780000 583655 507148 546221 573078 696482 701243 674610 542979 588198 422191 TRUE FALSE 606698.1501 594246.7239 560455.968 686431.1179 578094.2384 538389.9407 621732.3054 535701.2546 567028.8689 504911.2431 1.201593663 1.176933039 1.110008889 1.359508483 1.144942297 1.066306104 1.231369501 1.060981038 1.123026822 1 18.94567028 1.240284546 0.50423265 0.999065359 1.200376737 0.364178544 0.07715259 0.952216459 0.640761927 0.082983729 0.044823222 17.38939792 -1.240284546 0.201311378 RDS(ph)IVAELDREMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSIVAELDREMSR 14 2 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 1 RDS(1)IVAELDREMSR 93.754 0.0034938 53082000 10676 11593 13152 8720.5 20172 18602 10792 12622 15126 14923 TRUE FALSE 11097.49672 13584.00757 13494.75192 10445.38887 16743.17065 14281.96742 9946.09484 12452.82274 14581.61821 17846.87613 0.621817322 0.761142032 0.756140841 0.585278275 0.938156937 0.800250268 0.557301724 0.697759241 0.817040366 1 14.12338395 0.935848905 3.609071654 0.999612416 0.715698043 0.406969431 0.105697733 0.290174958 9.660984296 0.101456374 0.02615531 8.62678361 -0.935848905 -0.283914374 RDS(ph)LDKSGLFPEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSLDKSGLFPEWK 14 2 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 RDS(1)LDKSGLFPEWK 175.32 1.89E-06 356390000 483780 276690 375670 245240 567530 477260 446580 344190 423600 219200 TRUE FALSE 502880.008 324209.3552 385460.2688 293747.74 471061.4533 366423.5979 411575.8927 339576.696 408354.7187 262148.0432 1.918305404 1.236741466 1.470391555 1.120541418 1.796929123 1.397773539 1.570013217 1.295362315 1.557725604 1 18.00002225 -2.858004829 0.374925832 2.10E-11 1.480270965 0.278839087 0.232162903 119.2135343 4.105334326 95.34993843 0.147907043 0.00138674 2.858004829 1.480270965 RDS(ph)LEEGELR ddPTM_MDA-MB-175_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 96.059 0.0074137 138580000 167054 124343 146286 148205 163933 189953 185129 149575 152675 131262 TRUE FALSE 173649.4209 145697.943 150098.3333 177519.5067 136067.7272 145839.2945 170618.1052 147570.1918 147180.2566 156980.2757 1.10618624 0.928128979 0.956160464 1.130839565 0.866782318 0.92902942 1.08687607 0.940055629 0.937571653 1 17.26022377 3.227575664 24.99979777 0.963201299 1.017731106 0.155191841 0.07793836 518.1603808 1179239.172 0.022536589 0.027189747 1688.790058 -3.227575664 0.054529807 RDS(ph)LGAYASQDANEQGQDLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDSLGAYASQDANEQGQDLGK 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGK;RDS(0.996)LGAY(0.004)ASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK;RDS(1)LGAYASQDANEQGQDLGK 354.91 9.64E-96 1433070000 1186258 673924 925885 890377 1116189 1338544 1418924 997894 1077900 501199 TRUE FALSE 1233092.382 789665.2046 950014.3237 1066490.913 926459.5925 1027687.442 1307705.029 984518.8632 1039106.59 599399.348 2.057213419 1.317427533 1.584943872 1.779266055 1.545646647 1.714528795 2.181692445 1.642509066 1.733579779 1 19.19315799 2.500685136 23.50076583 1.735417655 1.639765251 0 0.325288248 1948.778018 1943559.016 0.099505715 0.093184425 316.7270355 -2.500685136 -0.095652404 RDS(ph)LGAYASQDANEQGQDLGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RDSLGAYASQDANEQGQDLGKR 22 2 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(1)LGAYASQDANEQGQDLGKR;RDS(0.594)LGAYAS(0.406)QDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(1)LGAYASQDANEQGQDLGKR;RDS(0.997)LGAYAS(0.003)QDANEQGQDLGKR 257.19 2.04E-37 3323230000 1885330 1248935 1618760 1294720 2039550 2032460 1904340 1628170 1806570 1113328 TRUE FALSE 1959764.284 1463429.871 1660946.215 1550811.752 1692868.02 1560451.967 1755072.855 1606347.044 1741551.899 1331463.306 1.471887566 1.099113933 1.247459249 1.164742389 1.271434228 1.171982706 1.318153379 1.206452358 1.307998419 1 20.34458124 -0.987049393 4.302658451 0.999989823 1.242382393 0.36764378 0.098178418 0.065103413 24982145.41 618.8131084 0.020392793 0.103026894 0.987049393 0.24239257 RDS(ph)LGTYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RDS(0.88)LGT(0.118)YS(0.001)SR;RDS(1)LGTYSSR;RDS(1)LGTYSSR;RDS(1)LGTYSSR 175.6 1.68E-06 2452990000 654127 728622 705884 766313 769738 968210 766940 764574 731385 745220 TRUE FALSE 679952.4391 853757.1606 724279.9169 917887.4242 638898.2097 743357.9009 706825.2388 754326.1361 705062.5967 891231.5909 0.762935746 0.957952085 0.812673074 1.029908986 0.716871144 0.834079389 0.793088178 0.846386219 0.791110418 1 19.76544085 5.037954161 13.34017891 0.85461941 0.468773711 0.084067094 0.095698923 710472.7203 8324684.243 0.021239968 6205708.912 109132.5142 -5.037954161 -0.385845698 RDS(ph)LSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSLSGK 7 1 Q92845-2;Q92845-3;Q92845 Q92845-2 KIFAP3 Kinesin-associated protein 3 1 RDS(1)LSGK 106.35 0.0085741 0 219100 146170 197680 157410 252600 251850 239290 214060 228360 157150 TRUE FALSE 227750.2372 171273.5605 202831.7032 188545.2282 209663.1422 193361.6543 220533.8245 211190.8758 220141.3682 187940.5337 1.211820743 0.911317836 1.079233411 1.003217478 1.11558235 1.028844872 1.173423424 1.123711164 1.17133523 1 17.51991672 2.248381731 24.96941014 1.128671366 1.052700048 0.093483045 0.085666802 350.7725296 891811.764 0.02748402 0.022727669 177.166551 -2.248381731 -0.075971317 RDS(ph)LTGSSDLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 RDS(0.981)LT(0.019)GSSDLYK;RDS(1)LTGSSDLYK;RDS(0.961)LT(0.039)GSSDLYK;RDS(1)LTGSSDLYK;RDS(1)LTGSSDLYK;RDS(0.994)LT(0.006)GSSDLYK;RDS(0.932)LT(0.067)GSS(0.001)DLYK 238.01 2.46E-16 2308560000 3934700 2716890 3302840 2827290 5177700 4940440 5062080 3689450 4159080 2478120 TRUE FALSE 4090044.994 3183494.723 3388914.724 3386519.523 4297596.403 3793097.683 4665300.942 3639998.957 4009395.523 2963660.168 1.380065447 1.074176708 1.143489649 1.142681459 1.450097569 1.279869306 1.574168656 1.228210642 1.352852654 1 21.4989486 3.258763764 24.83299742 1.33487481 1.174207534 0.128023783 0.158658817 355.3233105 436748.0141 0.040915532 0.055330016 1814.528376 -3.258763764 -0.160667276 RDS(ph)LTGSSDLYKR ddPTM_MDA-MB-175_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(0.966)LT(0.024)GS(0.005)S(0.005)DLYKR;RDS(0.999)LT(0.001)GSSDLYKR;RDS(0.983)LT(0.011)GS(0.003)S(0.003)DLYKR;RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR;RDS(1)LTGSSDLYKR 160.64 2.27E-05 1885616000 1818720 1491025 1861780 1220190 2663550 2198350 1733496 1760890 2064660 1685849 TRUE FALSE 1890524.47 1747096.945 1910299.516 1461539.94 2210800.722 1687816.529 1597620.054 1737288.15 1990353.29 2016158.834 0.937686277 0.866547276 0.947494555 0.724913095 1.09654095 0.837144624 0.792407834 0.861682185 0.987200639 1 20.94317787 1.230042603 22.0841604 0.993600892 0.879594556 0.179481126 0.094315253 77.3779078 200577.5945 0.079720341 0.021476181 16.98410253 -1.230042603 -0.114006336 RDS(ph)PPPPAR ddPTM_MDA-MB-175_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 132.5 0.00018574 9524334000 1948735 1833343 2056555 1988058 2285360 2508570 2163380 2001069 1989946 1832329 TRUE FALSE 2025672.563 2148205.399 2110150.513 2381289.939 1896895.324 1925992.635 1993808.623 1974247.943 1918328.232 2191338.785 0.924399539 0.980316423 0.962950378 1.086682696 0.865633071 0.878911398 0.909858684 0.900932323 0.875413809 1 21.06338111 3.203189349 24.99995016 0.899467175 0.98616557 0.380620312 0.051821592 169.1662772 119564.0312 0.014293077 0.017084102 1596.575089 -3.203189349 0.086698396 RDS(ph)QDGSSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RDSQDGSSYR 10 1 Q14847;Q14847-2;C9J9W2;Q14847-3;J3KSN1 Q14847 LASP1 LIM and SH3 domain protein 1 1 RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR;RDS(1)QDGSSYR 179.65 1.28E-06 7275779000 675574 663489 744280 722402 809773 897167 949621 751009 758969 623724 TRUE FALSE 702246.1832 777438.0745 763676.5482 865290.9594 672128.0747 688813.5609 875187.2246 740942.9528 731653.8539 745930.7759 0.94143613 1.042238904 1.023790106 1.160015094 0.901059584 0.923428263 1.173282097 0.99331329 0.980860259 1 19.50868223 1.511328175 25 0.989203632 1.026319143 0.028205476 0.08567411 2.659825973 1931.50287 0.046152031 0.021365869 32.45847975 -1.511328175 0.037115511 RDS(ph)SASTISSAYLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSASTISSAYLSSR 16 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RDS(0.927)S(0.073)ASTISSAYLSSR 130.3 6.11E-05 0 48572 53863 61962 62802 87403 62535 52238 55646 48566 66001 TRUE FALSE 50489.66007 63113.55125 63576.78062 75224.04815 72546.26928 48012.19398 48143.44906 54900.15639 46818.11915 78932.63228 0.639655091 0.799587565 0.805456233 0.953015831 0.919090966 0.608267995 0.60993087 0.695531807 0.593140223 1 16.26833424 2.73331525 24.99807123 0.676352139 0.828248705 0.157355274 0.134838767 647.002338 3083439.867 0.041754491 0.04043104 541.1469935 -2.73331525 0.151896566 RDS(ph)SDDWEIPDGQITVGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.839)S(0.161)DDWEIPDGQITVGQR;RDS(0.992)S(0.008)DDWEIPDGQITVGQR;RDS(0.795)S(0.205)DDWEIPDGQITVGQR;RDS(0.733)S(0.267)DDWEIPDGQITVGQR;RDS(0.688)S(0.312)DDWEIPDGQITVGQR 219.96 3.19E-19 3502040000 1764470 1727450 1880540 1638660 2139030 2370800 2047810 1905330 2002700 1755840 TRUE FALSE 1834132.638 2024126.1 1929548.417 1962782.057 1775438.445 1820217.63 1887297.301 1879792.168 1930623.218 2099863.23 0.873453381 0.963932351 0.918892426 0.934718999 0.845501945 0.866826755 0.898771536 0.89519743 0.919404269 1 21.00186393 0.81472335 3.340560365 0.999989314 0.900510347 0.462532712 0.032343988 1.004666223 16.67526833 0.032237735 0.008351634 6.527146339 -0.81472335 -0.099478967 RDS(ph)SDTTPLLNGSSQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.943)S(0.027)DT(0.027)T(0.003)PLLNGSSQDR 277.07 9.44E-36 448240000 195510 209620 221550 211030 227400 299260 245090 185850 209000 199860 TRUE FALSE 203228.8858 245620.6044 227323.775 252771.1041 188746.6292 229761.4003 225879.2054 183358.9847 201478.1308 239018.7404 0.850263395 1.027620696 0.951070927 1.057536759 0.789672931 0.961269396 0.945027176 0.767132252 0.842938635 1 17.86676421 3.238679025 24.99999999 0.873398278 0.974154772 0.19202192 0.085908879 4.632952684 977956.7212 0.024116874 0.030682351 1732.523066 -3.238679025 0.100756494 RDS(ph)SESQLASTESDKPTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSSESQLASTESDKPTTGR 20 2 Q96B23-2;Q96B23;A0A087WVF1;K7EQH1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RDS(0.717)S(0.185)ES(0.004)QLAS(0.09)T(0.004)ESDKPTTGR;RDS(0.857)S(0.141)ES(0.002)QLASTESDKPTTGR 224.08 4.75E-25 707140000 433650 328870 426110 304476 474790 515810 504110 405550 474910 290749 TRUE FALSE 450770.8369 385350.8642 437214.7767 364700.444 394085.3654 396020.9447 464596.541 400114.2656 457818.0819 347715.6998 1.296377578 1.108235448 1.257391532 1.048846642 1.13335511 1.138921668 1.336139096 1.150693701 1.31664484 1 18.40754868 RDS(ph)SGGTKDGDRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSSGGTKDGDRPK 14 3 Q9Y478;F5H4Y8 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 RDS(0.923)S(0.077)GGTKDGDRPK;RDS(0.958)S(0.04)GGT(0.001)KDGDRPK 154.52 3.37E-05 830660000 1111480 577170 869130 331490 1736180 1132280 668120 737110 1060810 760720 TRUE FALSE 1155362.089 676294.4577 891780.2418 397057.7326 1441064.744 869325.1299 615751.0086 727230.2461 1022631.655 909768.5191 1.269951712 0.743369817 0.980227633 0.436438197 1.583990557 0.955545407 0.676821626 0.799357453 1.124056981 1 19.79513999 2.457528102 24.42871149 0.86061747 0.987075314 0.016996426 0.304192197 757.9927496 945056.7336 0.103970665 0.087000151 286.7662931 -2.457528102 0.126457844 RDS(ph)SSHEETPGSHPLYGHGECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.446)S(0.446)S(0.105)HEET(0.002)PGSHPLYGHGECK;RDS(0.331)S(0.331)S(0.331)HEET(0.006)PGSHPLYGHGECK;RDS(0.333)S(0.333)S(0.333)HEETPGSHPLYGHGECK 160.05 7.15E-12 1277500000 375571 585608 669330 591017 824540 847860 675910 718730 732200 615420 TRUE FALSE 390398.8331 686181.6186 686773.2897 707918.3986 684384.9853 650957.3644 622930.408 709096.6 705848.265 735999.7661 0.530433366 0.932312278 0.933116179 0.961845956 0.9298712 0.884453222 0.846373106 0.963446774 0.959033274 1 19.48934578 4.738765027 24.96302501 0.929965275 0.530433246 0.896395922 0.041184516 4.743855643 578939.4278 0.009966441 0.057923136 54798.04027 -4.738765027 -0.399532029 RDS(ph)TEAPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSTEAPKPK 10 2 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 RDS(0.878)T(0.122)EAPKPK 126.95 0.00019257 97973000 290510 127720 191500 149490 256220 245780 253130 178350 210040 114100 TRUE FALSE 301979.5591 149654.9165 196490.6473 179058.6758 212667.8159 188701.3198 233289.0092 175959.51 202480.7014 136455.7104 2.213022512 1.096728865 1.439959139 1.312210938 1.558511661 1.382875947 1.709631707 1.289499057 1.483856563 1 17.05807324 -3.257789222 0.226802244 1.38E-15 1.542566732 0.231140831 0.282661196 99.93147802 2.031147411 48.0076007 0.487393129 0.000552345 3.257789222 1.542566732 RDSFDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSFDDR 7 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 74.173 0.075202 156270000 190580 198420 204340 237640 233430 244980 273960 224330 211530 176560 FALSE TRUE 198104.2456 232497.0915 209665.2683 284644.4827 193751.652 188087.1077 252486.2993 221323.2233 203917.0766 211153.5516 0.938199922 1.101080658 0.992951654 1.348044968 0.917586517 0.890759859 1.195747348 1.048162447 0.96572885 1 17.68793299 RDSFDDRGPS(ph)LNPVLDYDHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RDS(0.463)FDDRGPS(0.537)LNPVLDYDHGSR 62.051 0.022297 89421000 6659.7 25082 22805 24046 22824 25858 24895 26522 21914 28357 TRUE FALSE 6922.630098 29389.63839 23399.31703 28802.22703 18944.38463 19852.87138 22943.66485 26166.51597 21125.31942 33913.01122 0.20412903 0.866618367 0.689980518 0.849297246 0.558617001 0.585405739 0.676544607 0.771577487 0.622926678 1 15.04955127 -5 0.188354033 2.4128786 0.602260506 0.277733538 0.175762484 187.1447583 1.827037598 99.32253834 0.463506969 1.00E-05 5 -1.810618094 RDSFDDRGPSLNPVLDYDHGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSFDDRGPSLNPVLDYDHGSR 22 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 229.78 1.52E-26 437060000 52607 229640 207508 189949 198559 254550 162791 229420 187922 248810 FALSE TRUE 54683.96498 269078.8836 212915.8289 227520.3453 164808.0121 195434.6202 150031.016 226345.0002 181158.7239 297559.5557 0.183774858 0.904285809 0.715540217 0.764621202 0.553865634 0.656791612 0.504205001 0.760671253 0.60881501 1 18.18281892 -4.999999544 0.416188211 7.403310686 0.638525429 0.264854796 0.184715078 1200.009099 7.908700152 7017.556062 0.100398503 1.00E-05 4.999999544 -6.764785257 RDSIVAELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RDSIVAELDR 10 1 O14579;M0QXB4;O14579-3 O14579 COPE Coatomer subunit epsilon 0 ; 167.71 8.27E-06 491510000 168860 181228 165395 171395 230000 236080 203962 183743 175715 190564 FALSE TRUE 175526.7232 212352.4992 169705.3296 205296.4194 190904.6822 181253.9978 187974.9255 181280.2256 169391.0515 227901.3672 0.770187232 0.931773696 0.744643754 0.900812584 0.837663611 0.795317729 0.824808239 0.795432813 0.743264744 1 17.79805005 2.964587409 22.22119551 0.816762295 0.841071561 0 0.081287316 823.1413339 516514.8136 0.022739174 0.02413566 921.6953773 -2.964587409 0.024309265 RDSS(ph)ASTISSAYLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSASTISSAYLSSR 16 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RDS(0.421)S(0.579)ASTISSAYLSSR 95.835 0.0022159 341630000 60487 66246 73744 71052 68635 82428 53152 63968 56919 55119 TRUE FALSE 62875.07347 77623.23518 75665.82922 85105.87353 56968.44722 63285.34621 48985.80735 63110.61359 54870.49631 65918.51273 0.95383028 1.177563509 1.147869181 1.291076968 0.864225312 0.960054218 0.743126708 0.957403482 0.832398882 1 16.00839607 3.220709794 24.99931617 0.888176252 1.145460898 0.584775411 0.103029274 156.1555359 218688.7046 0.028490949 0.034119892 1662.30149 -3.220709794 0.257284646 RDSS(ph)DDWEIPDGQITVGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSDDWEIPDGQITVGQR 19 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 RDS(0.383)S(0.617)DDWEIPDGQITVGQR 208.11 1.75E-16 2107700000 621170 697690 675730 748520 783570 950040 756550 682680 735380 755870 TRUE FALSE 645694.2712 817512.8302 693340.0789 896575.0219 650379.0513 729407.608 697249.6341 673529.7912 708913.8174 903968.2545 0.714288658 0.90436011 0.766996048 0.991821358 0.719471119 0.806895159 0.771320929 0.745081244 0.78422424 1 19.78591258 RDSS(ph)SHEETPGSHPLYGHGECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSSHEETPGSHPLYGHGECK 22 1 B7ZBM3;Q8IVH2-3;Q8IVH2-2;Q8IVH2 B7ZBM3 FOXP4 Forkhead box protein P4 1 RDS(0.254)S(0.373)S(0.373)HEET(0.001)PGSHPLYGHGECK 171.99 2.04E-12 683630000 132880 194660 213700 201710 291000 288670 257400 236640 253460 220680 TRUE FALSE 138126.205 228091.3408 219269.1976 241607.636 241535.9239 221630.7673 237224.3154 233468.2279 244338.0241 263918.0208 0.523367842 0.864250725 0.830823135 0.915464716 0.915192995 0.839771254 0.898856072 0.884624048 0.925810308 1 18.00973034 5.08696255 1.649901254 0.898011438 7.41E-11 0.860842382 0.045192973 0.900507394 1.117618497 0.010885366 1.704110144 122169.4308 -5.08696255 -0.898011438 RDSSDT(ph)TPLLNGSSQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDSSDTTPLLNGSSQDR 17 1 B4DQA8;E9PCW1 B4DQA8 GOSR1 Golgi SNAP receptor complex member 1 1 RDS(0.025)S(0.236)DT(0.714)T(0.025)PLLNGSSQDR 296.85 6.92E-46 465750000 166640 177190 156880 183990 211010 233530 167920 181890 178580 163140 TRUE FALSE 173219.0759 207621.0042 160968.4217 220382.6728 175142.5956 179296.1967 154757.9916 179452.0621 172152.9407 195104.1595 0.887828718 1.064154679 0.82503839 1.129564195 0.897687656 0.918976803 0.793207034 0.919775686 0.882364277 1 17.57388501 3.047207318 24.99997764 0.892443374 0.977262699 0.131478472 0.092133373 204.2734411 108177.4707 0.024527008 0.029315374 1114.826588 -3.047207318 0.084819325 RDTDS(ph)DTQDANDSSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDTDSDTQDANDSSCK 16 1 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 RDT(0.009)DS(0.987)DT(0.004)QDANDSSCK 120.4 7.32E-05 250810000 151660 123270 153010 117820 208570 204600 169790 141530 151600 126270 TRUE FALSE 157647.6539 144440.6636 156997.5663 141124.4443 173117.3459 157084.7507 156481.4161 139633.0218 146143.9456 151010.1889 1.043953756 0.956496145 1.039648831 0.93453591 1.146395135 1.040226172 1.036230848 0.924659606 0.967775398 1 17.20428637 1.751538707 25 0.958238653 1.027298616 0.212994435 0.056072481 5.598283836 10800.61518 0.025656183 0.014227543 56.43372368 -1.751538707 0.069059963 RDTFNHLTTWLEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RDTFNHLTTWLEDAR 15 1 P61019;P61019-2;E9PKL7 P61019 RAB2A Ras-related protein Rab-2A 0 149.44 2.18E-06 433190000 105920 193280 161460 193700 190090 233520 156120 171750 159150 214900 FALSE TRUE 110101.8034 226474.3365 165667.7802 232013.2819 157778.5697 179288.519 143882.9065 169447.9722 153422.2226 257005.5405 0.428402451 0.881204102 0.644607816 0.902755954 0.613911161 0.697605657 0.559843598 0.659316417 0.596960759 1 17.97143994 -1.073470384 4.797398568 1.000011784 0.671721247 0.359233437 0.133966751 1.56E-05 3.01E-06 0.119788331 0.028233367 0.084436382 1.073470384 -0.328290538 RDVQEIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 185.81 0.00033798 468970000 51968 58101 46891 45477 92150 76948 50379 49305 46383 94568 FALSE TRUE 54019.73677 68079.39479 48113.01798 54472.21486 76486.37592 59077.99316 46430.16234 48644.14712 44713.68489 113096.789 0.477641649 0.60195692 0.425414536 0.481642453 0.676291313 0.522366671 0.410534753 0.430110771 0.395357687 1 16.78719844 -1.579115154 6.129205406 1.001340736 0.490630589 0.76506677 0.084574337 0.001633965 0.000112202 0.086353403 0.020307558 0.026356324 1.579115154 -0.510710147 RDVYLS(ph)PR ddPTM_MDA-MB-175_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 RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR;RDVYLS(1)PR 126.12 0.00075513 2553950000 1477642 1721530 1628020 1600353 2173550 2170100 1673150 1618230 1623710 1905900 TRUE FALSE 1535980.447 2017189.386 1670447.539 1916898.047 1804090.747 1666127.163 1542004.131 1596540.274 1565272.994 2279324.614 0.673875251 0.884994341 0.732869521 0.840993878 0.791502332 0.730974058 0.676518001 0.700444449 0.686726666 1 21.12017497 2.737672665 20.4783113 0.730548829 0.790642352 0 0.103325055 17.59761503 405823.6233 0.02990362 0.029752591 546.6038237 -2.737672665 0.060093523 RDYDDMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 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;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR;RDYDDMS(1)PR 140.91 6.61E-05 17984560000 7544432 9246080 9131193 8418680 11551210 11394510 9957862 9428770 9582760 9703410 TRUE FALSE 7842292.001 10834022.32 9369159.391 10083869.78 9587739.45 8748307.738 9177338.756 9302392.761 9237878.339 11604607.41 0.675791238 0.933596626 0.807365477 0.868953979 0.826201104 0.753865032 0.790835781 0.801612018 0.796052638 1 23.46819438 -1.755070384 6.981343126 1.003714398 0.809530211 0.452819826 0.063862989 0.003465372 0.000121577 0.058037232 0.013465602 0.017576387 1.755070384 -0.194184186 RDYDDMSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RDYDDMSPR 9 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;; 184.71 7.01E-05 1308659000 256048 439852 401414 391545 402136 484274 368832 414191 380927 569277 FALSE TRUE 266156.9728 515393.1594 411875.1786 468991.4324 333781.0664 371808.7027 339921.9841 408639.4471 367217.5117 680815.9287 0.390938228 0.757022769 0.604972888 0.688866715 0.490266241 0.546122215 0.49928618 0.600220162 0.539378555 1 19.37690527 -1.489668153 3.394029408 1.007880444 0.574665343 0.634065385 0.098228574 24957598.07 41958640.89 1916492.783 0.022339397 0.032384101 1.489668153 -0.433215101 RDYEVDGR ddPTM_MDA-MB-175_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 ; 138.08 0.0011555 577970000 541960 680700 647180 652990 660360 788290 603150 636450 597850 689020 FALSE TRUE 563356.9993 797604.9299 664046.0425 782149.473 548112.2431 605221.5942 555873.527 627919.4288 576333.4953 824020.2769 0.683668855 0.967943329 0.805861289 0.949187168 0.665168393 0.734474152 0.674587195 0.76201939 0.699416642 1 19.65232031 3.233011305 24.99989372 0.739018222 0.856699038 0.131434441 0.115450397 206.1320123 928633.5656 0.030132487 0.036983106 1710.059829 -3.233011305 0.117680816 RDYYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RDYYDR 6 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;; 117.18 0.03679 948960000 773920 855370 867930 821300 846990 939610 798453 850210 869940 752420 FALSE TRUE 804474.9592 1002273.144 890548.9688 983750.6887 703018.9423 721399.8174 735868.1675 838814.3256 838631.0293 899842.293 0.894017724 1.113832003 0.989672274 1.093247891 0.78126906 0.801695834 0.817774596 0.932179263 0.931975565 1 19.77931265 3.243699275 24.99999326 0.870613128 1.026843856 0.415064169 0.084155547 117.0910603 569653.3673 0.023246473 0.030547691 1752.666456 -3.243699275 0.156230728 REALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REALEK 6 1 O43707;O43707-2;F5GXS2;O43707-3;Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3;Q4VCS5;E7ERM3;Q4VCS5-2;A6NP16 O43707;Q9Y2J4;Q4VCS5 ACTN4;AMOTL2;AMOT Alpha-actinin-4;Angiomotin-like protein 2;Angiomotin 0 96.19 0.068129 174810000 392550 380560 389910 332670 466330 433000 495580 414510 356490 352220 FALSE TRUE 408048.1771 445918.2197 400071.3749 398471.1331 387063.3932 332442.3122 456735.1446 408954.1715 343659.9945 421230.7653 0.968704593 1.058607909 0.949767699 0.945968732 0.918886807 0.789216599 1.084287242 0.97085542 0.815847328 1 18.68425128 4.098940968 7.078774239 0.936868457 1.013141976 0.130384654 0.08233028 0.449514884 27.80535349 0.020616046 0.045107078 12558.59248 -4.098940968 0.076273518 RECPSDECGAGVFMASHFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RECPSDECGAGVFMASHFDR 20 1 P62979 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;; 168.64 7.76E-12 1875940000 618045 1361610 1764021 1324370 2348810 1835130 1446150 1604690 1867040 1667650 FALSE TRUE 642445.8938 1595455.926 1809992.836 1586326.433 1949560.115 1408948.869 1332796.984 1583181.755 1799845.595 1994394.088 0.322125851 0.799970244 0.907540213 0.795392667 0.977520003 0.706454596 0.668271628 0.793815909 0.902452332 1 20.92751908 4.736693719 5.270601673 0.825715494 0.30160115 0.691253347 0.103431763 0.08746128 8.571944228 0.024771403 0.16627739 54537.31081 -4.736693719 -0.524114345 REDEGEPGDEGQLEDEGS(ph)QEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REDEGEPGDEGQLEDEGSQEK 21 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEK;REDEGEPGDEGQLEDEGS(1)QEK 283.41 2.27E-45 519090000 542840 268250 352610 320170 404410 522290 508820 345800 368450 198046 TRUE FALSE 564271.7424 314319.8508 361799.3063 383498.6704 335668.5327 400996.0629 468937.3588 341165.1166 355189.5565 236849.3219 2.382408098 1.327087822 1.527550526 1.619167272 1.417223955 1.6930429 1.97989741 1.440431047 1.499643544 1 17.85361002 -2.601786166 0.256363709 3.01E-12 1.712286541 0.335704291 0.290787817 56.2206166 1.657283519 31.68325448 0.403567807 0.002501577 2.601786166 1.712286541 REDEGEPGDEGQLEDEGS(ph)QEKQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REDEGEPGDEGQLEDEGSQEKQGR 24 2 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 REDEGEPGDEGQLEDEGS(1)QEKQGR 148.3 8.53E-08 291080000 165480 108780 126240 106340 186140 175290 140750 135710 139670 83281 TRUE FALSE 172013.2782 127462.1188 129529.9181 127373.7346 154499.9893 134581.554 129717.6472 133891.0294 134643.304 99598.31744 1.727070121 1.279761768 1.300523156 1.278874361 1.551230917 1.351243249 1.302408018 1.344310154 1.351863239 1 16.60383375 -3.902898876 0.188124508 5.03E-13 1.456495263 0.470930764 0.130096277 78.82211505 1.116923682 30.47317073 0.365786149 0.000125055 3.902898876 1.456495263 REDIFYTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 REDIFYTSK 9 1 S4R3P0;P52895;B4DK69;H0Y804;Q04828;A6NHU4;P52895-2;S4R3D5;P17516;A0A0A0MSS8;P42330;S4R3Z2 S4R3P0;A0A0A0MSS8 AKR1C2;AKR1C1;AKR1C3;AKR1C4 Aldo-keto reductase family 1 member C2;Aldo-keto reductase family 1 member C1;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C3 0 ;;; 193.21 5.43E-05 2016110000 2150680 2148680 2236130 1990950 3298880 3125220 2694220 2468930 2484550 2704520 FALSE TRUE 2235590.507 2517699.076 2294405.385 2384753.968 2738137.556 2399435.018 2483039.996 2435838.032 2395131.531 3234418.913 0.691187681 0.778408469 0.709371744 0.737305226 0.846562437 0.741844233 0.767692764 0.753099118 0.740513704 1 21.62507511 -1.736216714 2.572754634 1.051531205 0.754048198 0.7770289 0.039873876 7057336.742 5291018.476 2320445.429 0.009636439 0.018356221 1.736216714 -0.297483007 REDLVEEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REDLVEEIK 9 1 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 ; 152.54 0.00012864 551370000 945750 621370 788280 620150 1042400 986970 906700 756460 885050 552460 FALSE TRUE 983088.9403 728085.4639 808823.2244 742813.819 865213.2203 757761.1752 835630.4848 746320.891 853197.2234 660703.9595 1.487941651 1.101984411 1.224184013 1.124276324 1.309532368 1.146899703 1.264757798 1.129584408 1.29134571 1 19.33364447 -5 0.198185285 0.042899213 1.254696345 0.282568168 0.110599727 181.1915388 1.790054775 68.9512047 0.247357427 1.00E-05 5 1.211797132 REDLVEEIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REDLVEEIKR 10 2 B3KWE1;P12081-4;P12081;B4DDD8;P12081-3;P12081-2;B4E1C5 B3KWE1 HARS "Histidine--tRNA ligase, cytoplasmic" 0 71.153 0.029155 560160000 278110 318760 314880 307320 398120 414350 348980 320500 327840 336240 FALSE TRUE 289089.9975 373504.5504 323086.0315 368106.9787 330447.7046 318123.492 321626.0357 316204.2217 316041.1024 402119.7903 0.718915121 0.928839016 0.803457177 0.915416221 0.821764341 0.791116229 0.799826429 0.786343347 0.785937698 1 18.61726581 3.020031182 24.87156665 0.813407459 0.848084952 0 0.081680093 841.7809047 1045182.378 0.021644443 0.025867649 1047.203733 -3.020031182 0.034677493 REDS(ph)FESLDSLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 REDSFESLDSLGSR 14 1 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 REDS(0.902)FES(0.056)LDS(0.013)LGS(0.03)R;REDS(0.906)FES(0.009)LDS(0.023)LGS(0.062)R;REDS(1)FESLDSLGSR;REDS(1)FESLDSLGSR 219.96 2.95E-12 1326150000 948706 1053420 1188352 1005064 1320611 1292048 1145366 1192855 1199818 1087523 TRUE FALSE 986161.6454 1234336.691 1219321.429 1203862.659 1096134.014 991989.4332 1055589.22 1176866.73 1156636.785 1300602.31 0.758234579 0.949050052 0.9375052 0.925619346 0.842789533 0.762715417 0.811615674 0.904862863 0.889308573 1 20.31074846 -1.980403338 7.052383075 1.09613589 0.867843443 0.273905975 0.065933135 0.052130151 0.000144856 0.033392723 0.015584008 0.010461565 1.980403338 -0.228292447 REDS(ph)MEDRGEEDDSLAIKPPQQMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REDSMEDRGEEDDSLAIKPPQQMSR 25 3 P21127-2;P21127;P21127-9;P21127-3;P21127-8;P21127-6;Q9UQ88-9;A0A087X1I0;A0A087WYI9;Q5QPR3;Q9UQ88-4;Q9UQ88-3;Q9UQ88-2;Q9UQ88;Q5QPR4;J3KS35;E7ESP2;E9PFJ2 P21127-2;Q5QPR3 CDK11B;CDK11A Cyclin-dependent kinase 11B;Cyclin-dependent kinase 11A 1 REDS(1)MEDRGEEDDSLAIKPPQQMSR 107.52 0.019908 136740000 60120 62792 73784 59863 91832 102630 68116 68174 76730 70160 TRUE FALSE 62493.58402 73576.03755 75706.87165 71703.72273 76222.42944 78795.73787 62776.88993 67260.23904 73968.50229 83906.50871 0.744800195 0.87688117 0.902276508 0.854566872 0.908420939 0.939089697 0.748176642 0.801609316 0.881558575 1 16.35649511 4.741565157 24.15671943 0.866717103 0.744800121 0.249138568 0.0669088 278.8285463 2241614.019 0.016412948 0.114431456 55152.49414 -4.741565157 -0.121916982 REDS(ph)PGPEVQPMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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 241.51 1.18E-17 28579900000 18330120 14325231 18041995 14242322 21018111 20982543 19798933 17853872 18106548 12597219 TRUE FALSE 19053807.29 16785477.99 18512184.21 17059410.78 17445460 16109665.38 18247040.9 17614570.05 17454896.87 15065402.87 1.264739314 1.114173854 1.228787864 1.13235676 1.157981645 1.069315273 1.21118838 1.169206705 1.158608039 1 23.84473592 -4.169829544 0.355055539 3.89E-22 1.171083677 0.471209547 0.053547368 203.4838691 2.942443054 152.119786 0.037561466 6.76E-05 4.169829544 1.171083677 REEAAVDAQQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 143.21 9.94E-05 682150000 1261430 1046120 1247690 1088000 1550450 1530120 1293450 1246440 1290270 1064200 FALSE TRUE 1311232.23 1225782.972 1280205.826 1303203.153 1286905.063 1174772.819 1192066.009 1229733.511 1243833.435 1272709.615 1.030268189 0.963128555 1.005889962 1.023959541 1.011153721 0.923048593 0.936636288 0.966232593 0.977311258 1 20.27947186 2.762518822 24.55819291 0.95723456 1.005343226 0.440829034 0.025864748 573.0207776 587369.7341 0.007907754 0.008383288 578.7870726 -2.762518822 0.048108666 REEAEESGPQLAPLGAPAPEPKPEPEPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REEAEESGPQLAPLGAPAPEPKPEPEPPAR 30 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 114.79 7.67E-05 161770000 443430 292460 378640 290030 405840 446990 431080 341770 356730 222070 FALSE TRUE 460936.9588 342687.73 388507.6695 347397.0683 336855.4618 343183.3467 397290.8232 337189.1322 343891.357 265580.3647 1.735583725 1.290335339 1.462862926 1.308067593 1.268374874 1.292201504 1.495934474 1.269631257 1.294867402 1 18.01878896 -3.036992704 0.061122769 1.62E-17 1.961385493 0.537410177 0.123432733 215.548913 1.418065676 41.7815847 11.66931224 0.000918348 3.036992704 1.961385493 REEDEENDNDNES(ph)DHDEADS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.997)DHDEADS(0.003);REEDEENDNDNES(1)DHDEADS;REEDEENDNDNES(1)DHDEADS 370.87 2.37E-112 3682139000 1899843.4 2232229 2248610 2086654.2 2183745 2537422.9 2158969.5 2183514.4 2125136.9 2024457 TRUE FALSE 1974850.684 2615596.966 2307210.624 2499388.173 1812552.805 1948144.886 1989743.829 2154247.961 2048653.638 2421110.589 0.815679669 1.080329407 0.952955489 1.032331272 0.748645193 0.804649278 0.821831038 0.889776771 0.846162768 1 21.20723755 3.249803228 24.99999531 0.845228761 0.976940888 0.299428525 0.088204236 237.9996192 529232.3231 0.023122418 0.031030304 1777.473882 -3.249803228 0.131712126 REEDEPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REEDEPEER 9 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 180.19 7.85E-05 220720000 153683 175034 159802 166392 181383 210566 163768 162409 175485 158619 FALSE TRUE 159750.5235 205094.7279 163966.5714 199303.841 150551.5824 161665.2377 150931.4362 160232.173 169169.3291 189697.3561 0.842133632 1.081168089 0.864358759 1.050641111 0.793640911 0.852227153 0.795643331 0.844672674 0.891785382 1 17.53334005 3.22792219 24.99999912 0.849603738 0.961459412 0.217933304 0.087420733 253.4869912 595686.4964 0.022935027 0.02767934 1690.138093 -3.22792219 0.111855673 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 REEDEPEERS(0.981)GDET(0.018)PGSEVPGDK;REEDEPEERS(0.988)GDET(0.007)PGS(0.005)EVPGDK 161.5 1.39E-11 527980000 374380 232890 304810 216240 398930 363190 367140 311080 333970 196413 TRUE FALSE 389160.8115 272887.0459 312753.599 259011.6266 331120.0211 278844.6267 338362.6075 306910.4814 321950.4849 234896.3668 1.65673406 1.161733787 1.33145354 1.102663401 1.409643008 1.18709638 1.440476122 1.30657824 1.370606491 1 17.84166487 -1.57165393 2.735760931 0.978465817 1.320019585 0.297712496 0.151246785 14590123.33 14515935.24 2288107.602 0.034379009 0.026813041 1.57165393 0.341553767 REEEEDFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REEEEDFIR 9 1 Q96A65 Q96A65 EXOC4 Exocyst complex component 4 0 134.84 0.00038079 157520000 78156 127120 105930 115300 103650 127840 100390 96890 97866 146740 FALSE TRUE 81241.65923 148951.8711 108690.6228 138105.9959 86031.61002 98151.09743 92521.16948 95591.34803 94343.82178 175490.8935 0.462939459 0.848772652 0.619351926 0.786969586 0.490234042 0.559294534 0.527213507 0.54470831 0.53759953 1 17.42103664 -0.90020974 9.444027753 1 0.599679567 0.506687293 0.119141155 0 0 0.114072271 0.026887092 0.125831757 0.90020974 -0.400320433 REEEKEGEDKSQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REEEKEGEDKSQPK 14 3 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2;H0YIL7 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 ; 103.21 0.0004945 157228000 174840 49775 80351 44029 113110 123984 112463 83225 91710 45480 FALSE TRUE 181742.8182 58323.46905 82445.01307 52737.80479 93883.6026 95190.595 103647.8562 82109.505 88409.37501 54390.93523 3.341417415 1.072301272 1.515785907 0.969606508 1.72608914 1.750118739 1.905609009 1.509617451 1.625443185 1 15.73107861 4.746675619 24.91854248 1.494640322 3.341418365 0.760834872 0.316893358 474.1746287 1456001.86 0.075372688 0.844573477 55805.32213 -4.746675619 1.846778043 REEGDPS(ph)PHSGGVCKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REEGDPSPHSGGVCKPK 17 2 O75376;O75376-2;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 REEGDPS(1)PHSGGVCKPK 106.03 0.00040338 92779000 194330 114830 154550 114670 204710 190810 200440 148660 174100 123450 TRUE FALSE 202002.2985 134551.1592 158577.7 137351.3837 169913.4673 146497.2693 184728.989 146667.4559 167834.175 147637.6639 1.368230119 0.911360663 1.074100577 0.930327534 1.150881576 0.99227572 1.251232132 0.993428452 1.136797824 1 17.17170129 REELITNWEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REELITNWEQIR 12 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 202.13 2.25E-07 177970000 70004 75655 62456 71124 63597 76876 55782 62416 61174 70754 FALSE TRUE 72767.81197 88648.15774 64083.65467 85192.11492 52786.80466 59022.71407 51409.66108 61579.41561 58972.35969 84616.89163 0.859967916 1.047641387 0.757338794 1.006797972 0.623832944 0.697528743 0.607557901 0.727743769 0.696933657 1 16.36865807 3.236777314 24.99779461 0.70404618 0.91572989 0.352574937 0.125649795 44.16403046 619081.2967 0.032737543 0.041093775 1724.953189 -3.236777314 0.21168371 REEQT(ph)DT(ph)SDGESVTHHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.925)S(0.075)DGESVTHHIR 131.33 7.59E-06 205170000 53022 85038 70613 81620 90360 97887 69595 73344 72046 82835 TRUE FALSE 55115.3495 99642.615 72453.23279 97764.19239 75000.63948 75154.22774 64139.96205 72360.94365 69453.07853 99064.93228 0.556355799 1.005831354 0.731371143 0.986869825 0.757085658 0.758636038 0.647453752 0.730439541 0.701086418 1 16.59608683 3.027224636 24.97034333 0.741292319 0.832652649 0.014027058 0.147696356 544.9899996 499859.3115 0.039197914 0.046849622 1064.693581 -3.027224636 0.09136033 REEQT(ph)DTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 2 REEQT(1)DT(0.272)S(0.728)DGESVTHHIR 148.53 7.42E-08 218330000 45607 83022 80190 97117 99054 114590 84975 90493 74691 98120 TRUE FALSE 47407.59958 97280.38268 82279.81728 116326.4527 82216.83646 87978.20913 78314.43746 89280.08935 72002.8855 117344.7354 0.404002782 0.82901361 0.701180304 0.991322298 0.700643588 0.749741425 0.667387738 0.760835917 0.613601328 1 16.84039359 -2.491930008 2.198168464 4.307486504 0.72578499 0.262815341 0.142739409 4438828.243 369258.1165 73278289.31 0.032359565 0.003221588 2.491930008 -3.581701513 REEQTDT(ph)SDGESVTHHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.021)DT(0.49)S(0.49)DGESVTHHIR;REEQT(0.084)DT(0.458)S(0.458)DGESVTHHIR 143.98 7.74E-08 2758940000 226740 442610 413540 399970 489700 546250 400800 432690 428840 428830 TRUE FALSE 235691.8703 518624.8245 424317.1921 479082.8722 406460.9689 419391.716 369384.2487 426890.4983 413406.1322 512851.0281 0.4595718 1.011258233 0.827369292 0.934156014 0.792551729 0.817765185 0.720256426 0.832386941 0.806093991 1 18.96818029 -2.728098836 1.614851796 3.852996401 0.809685309 0.15749807 0.137077144 2907830.606 96688.80995 30385512.64 0.033343547 0.001870256 2.728098836 -3.043311092 REEQTDTS(ph)DGESVTHHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REEQTDTSDGESVTHHIR 18 1 P36915;A2AB27 P36915 GNL1 Guanine nucleotide-binding protein-like 1 1 REEQT(0.079)DT(0.205)S(0.716)DGESVTHHIR;REEQT(0.077)DT(0.296)S(0.627)DGESVTHHIR 145.67 4.20E-08 2115330000 258485 542560 593110 611880 560080 666330 506940 589070 548680 604800 TRUE FALSE 268690.1874 635740.4595 608566.9338 732908.0377 464877.8017 511584.9558 467204.7182 581174.4802 528933.114 723298.9804 0.371478731 0.878945604 0.841376734 1.013285042 0.642718729 0.707293899 0.645935817 0.803505184 0.731278667 1 19.46423259 -2.029722911 2.630807689 1.300366517 0.74913172 0.186873095 0.162713943 24227514.56 8001329.226 43938531.07 0.03734966 0.009338499 2.029722911 -0.551234798 REERPENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 REERPENK 8 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ;;; 126.31 0.00068871 215712000 161066 122123 148064 127997 177611 184206 193115 161922 165709 121690 FALSE TRUE 167425.0101 143096.6753 151922.6695 153314.4246 147420.7457 141426.9482 177978.1417 159751.7004 159745.1655 145532.8256 1.150427811 0.983260475 1.043906547 1.053469717 1.012972469 0.971787276 1.222941566 1.097702184 1.09765728 1 17.15098507 2.260818983 24.99999101 1.115045054 1.03368557 0.189152921 0.068123366 314.6949463 353455.7656 0.022347778 0.018683758 182.3135648 -2.260818983 -0.081359484 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 REESPMDVDQPS(0.995)PS(0.005)AQDTQSIASDGTPQGEK;REESPMDVDQPS(0.995)PS(0.005)AQDTQSIASDGTPQGEK 315.7 5.94E-93 619800000 504620 357143 449680 384978 520070 533000 519960 454932 488950 302656 TRUE FALSE 524542.7873 418479.5321 461399.0302 461125.4994 431668.6872 409218.8277 479204.1765 448834.3807 471352.785 361955.6485 1.449190776 1.156162457 1.274739135 1.273983432 1.192601052 1.130577267 1.323930649 1.240025905 1.302239064 1 18.4654534 -2.314944839 1.889669762 3.83E-05 1.254010419 0.447401165 0.086553753 1319039.102 170949.577 5615694.816 0.019745975 0.004842339 2.314944839 1.253972137 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 177.42 7.98E-20 99075000 38359 20976 35998 23554 45320 39746 38322 32171 35530 23187 TRUE FALSE 39873.44294 24578.46483 36936.13745 28212.9109 37616.52259 30515.59386 35318.2215 31739.80037 34251.28224 27730.04871 1.437914638 0.886347698 1.331989635 1.017412959 1.356525659 1.100452227 1.273644409 1.144599517 1.235168485 1 14.75916253 -1.645406681 6.119207514 0.998719294 1.189357202 0.121510226 0.158290883 0.002391221 0.000138565 0.132512542 0.031033775 0.022625246 1.645406681 0.190637907 REFDRHS(ph)GSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REFDRHSGSDR 11 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 REFDRHS(0.804)GS(0.196)DR 74.301 0.021496 61526000 34960 42326 45964 39212 55295 51772 52491 58681 47059 48317 TRUE FALSE 36340.24779 49595.16125 47161.8596 46968.01656 45895.97565 39748.73761 48376.61826 57894.47718 45365.35578 57783.79107 0.628900374 0.858288464 0.81617801 0.812823383 0.79427076 0.687887328 0.837200491 1.001915522 0.78508791 1 15.81837724 1.993368655 23.97699503 0.926800011 0.775070547 0.427743774 0.083939562 164.7430552 595663.1468 0.030866901 0.02194381 98.48467485 -1.993368655 -0.151729464 REFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REFEER 6 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ; 143.85 0.018194 1066130000 435960 588740 540180 531930 598030 636690 555740 593320 531030 571070 FALSE TRUE 453172.0374 689851.5152 554257.5346 637144.1663 496377.0742 488828.3966 512179.6466 585367.5159 511918.334 682960.2327 0.663540885 1.010090313 0.811551695 0.93291547 0.726802309 0.715749429 0.749940659 0.857103368 0.749558041 1 19.38144205 5.022157468 16.18295796 0.827485531 0.289284499 0.194325067 0.104909625 7826807.813 143861349.3 0.024195683 106411506.9 105234.3367 -5.022157468 -0.538201033 REFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REFITGDVEPTDAESEWHSENEEEEKLAGDMK 32 2 Q99733;Q99733-2;C9JZI7;E9PNJ7;C9J6D1;A8MXH2;E9PKT8 Q99733 NAP1L4 Nucleosome assembly protein 1-like 4 1 REFITGDVEPTDAESEWHS(1)ENEEEEKLAGDMK 261.49 1.06E-59 308840000 203840 93058 150230 84467 207740 170680 171710 117630 189600 85815 TRUE FALSE 211887.7606 109039.9876 154145.1172 101174.3205 172428.429 131042.1567 158250.9215 116053.3623 182776.333 102628.8062 2.064603189 1.062469609 1.501967361 0.985827705 1.680117263 1.27685551 1.541973714 1.1308069 1.780945718 1 16.6470762 -2.185843373 2.089224517 7.26E-05 1.408997673 0.135786974 0.325883746 4631119.67 895731.3549 21897981.64 0.071243063 0.006518634 2.185843373 1.408925054 REFQLDLDEIENDNGTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REFQLDLDEIENDNGTVR 18 1 Q14008;Q14008-3;Q14008-2;H0YEK7;H0YCF6 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 85.054 0.00594 53942000 32800 35884 36429 38780 39179 47363 34656 36150 35612 37282 FALSE TRUE 34094.96933 42046.79786 37378.36967 46450.56825 32519.36757 36363.66104 31939.57216 35665.46838 34330.33108 44586.69409 0.764689332 0.943034659 0.838330144 1.041803372 0.729351396 0.81557204 0.716347619 0.799912824 0.769968076 1 15.44432561 3.200217523 24.99999949 0.790151447 0.896067706 0.160830123 0.099180512 233.3191153 152125.2476 0.0263549 0.031500747 1585.687207 -3.200217523 0.105916259 REGDVAACYANPSLAQEELGWTAALGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REGDVAACYANPSLAQEELGWTAALGLDR 29 1 Q14376;Q14376-2;Q5QPP4;Q5QPP9 Q14376 GALE UDP-glucose 4-epimerase 0 ; 165.34 7.66E-12 108131000 34218 37630 44497 34912 47019 47493 37844 34865 42584 46290 FALSE TRUE 35568.95306 44092.65978 45656.62837 41817.4894 39026.72717 36463.47051 34877.68839 34397.6917 41051.41016 55359.63922 0.642506952 0.796476646 0.824727708 0.755378647 0.704967152 0.658665248 0.630020153 0.621349636 0.741540421 1 15.75654692 0.963881266 22.70373433 1.000000002 0.702424601 0.638897122 0.066283476 1267.495022 796731.3212 0.073362624 0.018340656 9.201979603 -0.963881266 -0.297575401 REGGDGEEQDVGDAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REGGDGEEQDVGDAGR 16 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 ; 138.56 9.55E-06 553150000 251630 318820 284730 306930 312430 358050 267370 298390 300210 320850 FALSE TRUE 261564.5467 373574.8549 292150.2977 367639.8379 259323.2602 274898.3138 246412.8408 294390.5701 289405.5007 383714.4145 0.681664636 0.973575245 0.76137431 0.958107968 0.675823608 0.716413831 0.642177702 0.767212695 0.754221082 1 18.54967344 5.036444348 16.49415262 0.788749576 0.254296572 0.070236007 0.122205991 9907430.485 121971223.5 0.028437578 156437261.3 108753.7769 -5.036444348 -0.534453004 REGS(ph)YDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 REGSYDR 7 1 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 REGS(0.999)Y(0.001)DR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR;REGS(1)YDR 112.71 0.0038545 3259445000 2413580 2771749 2557097 2489703 3095090 3215654 2756211 2798576 2545143 2687215 TRUE FALSE 2508870.002 3247775.33 2623737.048 2982158.822 2568987.707 2468867.092 2540171.98 2761065.666 2453543.801 3213723.329 0.780673924 1.010595809 0.816416592 0.927945102 0.799380483 0.768226396 0.790414021 0.859148528 0.763458316 1 21.6158143 3.228566858 24.99377571 0.820163723 0.888136195 0.077908014 0.086234468 401.1135996 1003158.589 0.022842574 0.027604934 1692.6488 -3.228566858 0.067972472 REGT(ph)PPPPPPSR ddPTM_MDA-MB-175_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 65.716 0.035161 348580000 157164 196286 183556 197810 200255 240926 187233 198202 177697 214187 TRUE FALSE 163368.9561 229996.5936 188339.6202 236936.2276 166215.7266 184974.5878 172557.1882 195545.4264 171301.7197 256152.8418 0.637779206 0.89788812 0.735262661 0.924979891 0.648892768 0.722125847 0.673649322 0.763393547 0.668748074 1 17.96664537 -1.113596342 4.323690928 1.000037308 0.746285151 0.404016102 0.09405313 1.448279296 51204352.58 3899.161104 0.020797258 0.076984565 1.113596342 -0.253752156 REGTGTEMPMIGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REGTGTEMPMIGDR 14 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ; 160.63 7.57E-06 750860000 187359 204609 220390 232240 229930 260630 256630 224020 229180 205933 FALSE TRUE 194756.078 239749.0041 226133.5445 278176.3788 190846.5807 200102.6324 236514.67 221017.3783 220931.8566 246281.6285 0.790786057 0.973474983 0.918190877 1.129505195 0.774911965 0.812495165 0.960342318 0.897417236 0.897069984 1 17.90994949 -0.933653205 3.952520996 1.000004979 0.909867116 0.074496736 0.098537877 32281024.74 50616019.03 2288.564809 0.023140861 0.116505598 0.933653205 -0.090137863 REHS(ph)AFGDRPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REHSAFGDRPEKR 13 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 REHS(1)AFGDRPEKR;REHS(1)AFGDRPEKR 104.2 0.0011067 84999000 73766 81631 86348 74223 108629 110007 84155 71819 84474 83502 TRUE FALSE 76678.33864 95650.48925 88598.29982 88904.08787 90164.28138 84459.54142 77558.7112 70856.38378 81433.79724 99862.61816 0.767838257 0.957820764 0.887201852 0.89026394 0.902883211 0.845757331 0.776654094 0.709538615 0.815458264 1 16.60765711 2.438596808 3.992270341 0.791088994 0.885748426 0.029297447 0.084013213 0.328304169 11.38615426 0.028524689 0.024131723 274.5344237 -2.438596808 0.094659431 REIEIAEQDMSALISLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REIEIAEQDMSALISLR 17 1 O43865-2;O43865 O43865-2 AHCYL1 Putative adenosylhomocysteinase 2 0 90.718 0.0059861 9863100 7514.5 8539.4 9790.9 9268.4 10155 12243 8008.1 8186.9 8676.8 10391 FALSE TRUE 7811.178262 10005.97552 10046.0589 11101.66186 8428.856727 9399.748794 7380.404197 8077.167997 8364.523663 12426.9175 0.628569254 0.80518564 0.808411168 0.893356044 0.678274136 0.756402285 0.593904659 0.649973575 0.673097223 1 13.60118086 2.448065715 24.90065452 0.688944938 0.769150951 0 0.124034834 505.0160268 432796.9624 0.040926764 0.034242306 280.5858175 -2.448065715 0.080206013 RELDDLEQWIQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RELDDLEQWIQER 13 1 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 ; 132.05 0.00019775 57105000 24007.3 31892 30819 33874 29913 38256 25406 29958 28512 29706 FALSE TRUE 24955.12674 37369.20291 31622.16846 40574.1761 24828.39894 29371.62378 23414.61133 29556.46201 27485.85869 35526.32194 0.702440483 1.051873678 0.890105328 1.142087722 0.698873331 0.826756674 0.659077834 0.831959527 0.773675888 1 15.11660071 3.212131727 24.99846338 0.784831921 0.950107433 0.217349018 0.136292169 283.0617918 267740.744 0.036510651 0.043650848 1629.790292 -3.212131727 0.165275512 RENIRDFLSELELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RENIRDFLSELELK 14 2 A6ND36 A6ND36 FAM83G Protein FAM83G 0 53.001 0.085542 1559500000 40206 2658000 2231600 2371400 1644000 2907200 1358700 2561800 1956100 3314400 FALSE TRUE 41793.36393 3114490.824 2289757.329 2840455.842 1364553.467 2232046.859 1252201.544 2527463.261 1885700.343 3963793.222 0.01054378 0.785734939 0.577668208 0.716600408 0.344254453 0.563108804 0.315909906 0.637637515 0.47573126 1 21.91845027 -0.684873843 0.871643362 1.035208766 0.50654859 0.334386372 0.213929338 40.43804808 17.44817701 4.718287489 0.063139485 0.206598021 0.684873843 -0.528660175 REPAEQPGDGER ddPTM_MDA-MB-175_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 ;;; 157.33 0.00011856 1588210000 981387 986965 982184 974396 1207830 1350460 1181450 1017467 1021802 961095 FALSE TRUE 1020132.917 1156468.561 1007780.522 1167128.621 1002523.488 1036836.131 1088844.862 1003829.519 985027.5456 1149403.164 0.88753272 1.006147014 0.87678593 1.015421444 0.872212222 0.902064797 0.947313263 0.873348491 0.856990459 1 20.13245349 3.1857316 24.99975946 0.902827024 0.945758807 0.091651351 0.056547898 197.6727449 93541.84401 0.015125154 0.018078034 1533.668862 -3.1857316 0.042931783 REPEDEGEDDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REPEDEGEDDD 11 1 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 133.32 0.0033644 280750000 235960 258730 259840 229300 298160 347940 283630 252080 244720 222810 FALSE TRUE 245275.883 303164.8649 266611.6439 274654.8556 247478.8697 267136.2081 261398.3395 248701.2799 235912.575 266465.3535 0.920479453 1.137727141 1.000549003 1.030733834 0.928746895 1.002517605 0.980984342 0.933334396 0.885340521 1 18.02358844 3.250439178 24.55897104 0.954550064 1.029053203 0.231567363 0.059485143 236.9476856 489886.5698 0.015780515 0.021193648 1780.078595 -3.250439178 0.074503138 REPHPAEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 REPHPAEAEK 10 1 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WWC8;Q9P2K5-4 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ;; 126.19 0.00025255 340815000 1046240 877597 988370 824167 1290490 1176250 1158160 994405 1026590 960752 FALSE TRUE 1087546.363 1028317.458 1014127.734 987184.7727 1071132.971 903083.7637 1067380.393 981076.6275 989643.2264 1148992.96 0.946521346 0.89497281 0.882623105 0.859173909 0.932236322 0.785978501 0.928970351 0.853857823 0.861313569 1 20.13193853 -1.630489479 2.840248943 1.010604637 0.881111887 0.380765301 0.044769789 15990203.38 14928173.48 1243403.708 0.010214428 0.023415882 1.630489479 -0.12949275 REPLGVCVGIGAWNYPFQIASWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REPLGVCVGIGAWNYPFQIASWK 23 1 P49189-3;P49189;P49189-2 P49189-3 ALDH9A1 4-trimethylaminobutyraldehyde dehydrogenase 0 ; 175.47 2.38E-12 311460000 219264 189232 187407 201621 270546 270681 211624 201556 227272 218596 FALSE TRUE 227920.712 221731.124 192290.9804 241501.032 224558.6876 207819.44 195036.3579 198854.4715 219092.5251 261425.7009 0.871837433 0.848161153 0.735547346 0.923784583 0.858977089 0.794946477 0.746048905 0.760653871 0.838068041 1 17.99604145 2.733475676 23.79959381 0.802214438 0.845689772 0 0.08027191 674.5985817 3157381.48 0.024718323 0.023973735 541.3469278 -2.733475676 0.043475334 REPLPSR ddPTM_MDA-MB-175_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 ;;;;; 122.19 0.0069993 4052880000 1216110 1325420 1298390 1344110 1403720 1572800 1493370 1386720 1184480 1289190 FALSE TRUE 1264122.962 1553050.575 1332227.11 1609970.946 1165116.176 1207541.036 1376315.757 1368133.287 1141850.796 1541782.097 0.819910261 1.007308735 0.864082617 1.044227293 0.755694451 0.783211219 0.892678518 0.887371366 0.740604524 1 20.55616745 3.229323012 24.99934099 0.841788093 0.934141301 0.185980227 0.092849097 315.5096825 853849.4823 0.025388395 0.03074068 1695.598455 -3.229323012 0.092353207 REPLQMEDSNMEQGVEGVEPGMPES(ph)PGHLTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REPLQMEDSNMEQGVEGVEPGMPESPGHLTGR 32 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 REPLQMEDSNMEQGVEGVEPGMPES(1)PGHLTGR 120.23 1.48E-07 83033000 20867 31274 38250 33061 37685 39161 28852 33196 38251 36711 TRUE FALSE 21690.84527 36645.06622 39246.82642 39600.36712 31279.31716 30066.45124 26590.50485 32751.06192 36874.35398 43903.81758 0.49405374 0.834666966 0.893927421 0.90198004 0.712450964 0.684825441 0.605653593 0.745972987 0.839889468 1 15.42205877 -1.405260955 3.210261451 1.003098838 0.748375709 0.277671264 0.122875874 217209097.6 264775359 6102889.912 0.030213361 0.039331367 1.405260955 -0.254723128 REPPS(ph)PQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 REPPSPQGR 9 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 REPPS(1)PQGR;REPPS(1)PQGR;REPPS(1)PQGR 94.747 0.0052142 587048000 168055 157029 155117 135646 157920 206172 147341 132886 146199 148951 TRUE FALSE 174689.9412 183997.5092 159159.4765 162476.3739 131076.8148 158291.6776 135792.0274 131104.8805 140937.3265 178135.0966 0.980659873 1.032909925 0.893476241 0.912096364 0.735828129 0.888604663 0.762297997 0.735985682 0.79118225 1 17.44261226 3.791914353 1.37681721 0.800703485 1.009761759 0.40305393 0.081773776 0.37236383 1.336954195 0.02401262 0.06576419 6193.189268 -3.791914353 0.209058273 REPWLLPSQHNDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REPWLLPSQHNDIIR 15 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 140.84 3.16E-06 217780000 20200 72781 47438 67690 60707 82814 42100 55379 45679 82441 FALSE TRUE 20997.5116 85280.57059 48674.27325 81078.87997 50388.04582 63581.70356 38800.09199 54636.73509 44035.02171 98593.73552 0.212970038 0.864969464 0.493685253 0.822353261 0.511067418 0.644885836 0.393535064 0.55416031 0.446631031 1 16.58920836 -1.544150055 3.221815238 1.014965094 0.55959549 0.350600701 0.183516829 139619133.9 180598769.5 18338707.22 0.040187645 0.028566034 1.544150055 -0.455369605 REQEVAEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REQEVAEERR 10 2 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 59.198 0.059705 92126000 104790 116240 104340 104290 140820 152290 104320 100460 109470 147030 FALSE TRUE 108927.1901 136203.3158 107059.1861 124918.2507 116883.4667 116922.9555 96143.12581 99113.49802 105530.1961 175837.7134 0.619475697 0.774596718 0.608852242 0.710417852 0.664723536 0.664948111 0.546771929 0.563664621 0.600156781 1 17.42388501 -0.960724185 9.279037584 0.999999912 0.636491121 0.73649188 0.064708605 0 0 0.067821269 0.015985626 0.109465134 0.960724185 -0.363508791 REQEVNILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 REQEVNILK 9 1 P35579 P35579 MYH9 Myosin-9 0 ; 90.827 0.017905 427370000 391340 247070 318890 238883 402210 350200 312390 303370 356970 223895 FALSE TRUE 406790.4054 289502.3506 327200.5354 286133.3444 333842.4879 268871.3573 287904.0555 299303.8214 344122.7194 267762.9385 1.519218483 1.081189025 1.221978431 1.068606977 1.246783777 1.004139553 1.075219958 1.117794057 1.285176811 1 18.03059676 4.742501594 24.62300234 1.125043807 1.519218674 0.617559408 0.093678522 197.1203705 1231535.17 0.020836887 0.157745421 55271.54361 -4.742501594 0.394174867 REQGGSGLGSGSS(ph)GGGGSTSGLGSGYIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REQGGSGLGSGSSGGGGSTSGLGSGYIGR 29 1 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 REQGGSGLGS(0.007)GS(0.075)S(0.913)GGGGS(0.002)T(0.001)S(0.001)GLGSGYIGR 64.127 0.00083226 0 12644 12693 13281 12573 16225 16761 17118 13469 13398 15869 TRUE FALSE 13143.19488 14872.92401 13627.11377 15059.90187 13467.0803 12868.51177 15776.24643 13288.47009 12915.8086 18978.22672 0.692540725 0.783683546 0.71803936 0.793535776 0.709606882 0.678067132 0.831281376 0.70019556 0.680559295 1 14.21205758 -1.386165665 4.890735789 1.000264194 0.734524239 0.719447468 0.050193886 0.000135832 1.70E-05 0.045654878 0.010750356 0.041099291 1.386165665 -0.265739955 REREEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REREEIEK 8 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 126.07 0.00069462 103150000 146010 135640 152450 114180 185790 204200 145420 145860 159530 156330 FALSE TRUE 151774.5875 158935.1149 156422.9722 136764.4632 154209.4822 156777.6447 134021.6004 143904.9853 153788.5465 186959.8704 0.811803021 0.85010283 0.836666028 0.731517747 0.824826642 0.83856308 0.716846883 0.769710553 0.822575166 1 17.51236911 0.906650094 8.727173897 0.999999952 0.795393531 0.661870333 0.043133668 3.375322726 315.7948225 0.04355612 0.010901434 8.065849129 -0.906650094 -0.204606421 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RES(0.992)AAS(0.008)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.996)AAS(0.004)GLGGLLEEEGAGAGAAQEEVLEPGR;RES(0.966)AAS(0.034)GLGGLLEEEGAGAGAAQEEVLEPGR 244.53 2.65E-46 512100000 116455 133403 112143 127972 146795 149816 113396.4 125375 120471 124458 TRUE FALSE 121052.7333 156313.9275 115065.5387 153284.4796 121842.8383 115023.5045 104508.0939 123694.5532 116135.2722 148843.1622 0.813290524 1.050192197 0.773065669 1.029838908 0.818598829 0.772783262 0.702135673 0.831039541 0.780252653 1 17.18343342 3.028664404 24.46698079 0.799040863 0.916928685 0.161574933 0.106670934 235.4880066 201002.7656 0.02819332 0.033696882 1068.229099 -3.028664404 0.117887823 RES(ph)CGSSVLTDFEGK ddPTM_MDA-MB-175_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(0.985)CGS(0.015)SVLTDFEGK;RES(0.995)CGS(0.005)SVLTDFEGK;RES(0.695)CGS(0.094)S(0.211)VLTDFEGK;RES(0.971)CGS(0.029)SVLTDFEGK;RES(0.999)CGS(0.001)SVLTDFEGK;RES(0.812)CGS(0.187)S(0.002)VLTDFEGK 246.12 3.99E-18 3938420000 4165320 2835410 3525290 3218430 4814070 4800670 5055480 3900270 4325780 2706020 TRUE FALSE 4329770.05 3322369.611 3617161.953 3855025.848 3995776.101 3685787.147 4659218.268 3847993.26 4170096.023 3236212.809 1.337912648 1.026622724 1.117714491 1.191215187 1.234707461 1.138919893 1.43971319 1.189042096 1.288572869 1 21.62587505 3.442044605 3.444324033 1.233795462 1.147588643 0.019466061 0.127643854 0.603535981 14.962087 0.034199925 0.049917389 2767.225846 -3.442044605 -0.086206819 RES(ph)CGSSVLTDFEGKDVATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.991)CGS(0.005)S(0.005)VLTDFEGKDVATK;RES(0.998)CGS(0.002)SVLTDFEGKDVATK;RES(0.998)CGS(0.002)SVLTDFEGKDVATK;RES(0.751)CGS(0.104)S(0.144)VLT(0.001)DFEGKDVATK;RES(0.999)CGS(0.001)SVLTDFEGKDVATK 247.69 1.93E-30 3225090000 2306320 1454390 1938940 1105963 3072890 2520610 2137780 1913980 2302420 1494810 TRUE FALSE 2397375.294 1704170.169 1989470.369 1324719.18 2550561.255 1935236.528 1970215.218 1888326.229 2219556.354 1787689.4 1.341046881 0.953280905 1.112872499 0.741023122 1.426736242 1.082535103 1.102101527 1.056294359 1.241578293 1 20.76966467 4.759053592 23.28233712 1.082538869 1.341047528 0.176882558 0.169088817 3276.372922 3722175.739 0.038019661 1.429873006 57418.73121 -4.759053592 0.258508659 RES(ph)DESGESAPDEGGEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RESDESGESAPDEGGEGAR 19 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 RES(1)DESGESAPDEGGEGAR;RES(1)DESGESAPDEGGEGAR 227.24 8.06E-20 1469520000 713320 560320 663640 635640 946250 1190670 875680 572130 701440 556090 TRUE FALSE 741482.4244 656550.6013 680935.0036 761367.6948 785406.763 914154.9373 807041.9134 564461.5332 676195.3114 665045.1885 1.114935402 0.987227053 1.023892835 1.144836032 1.180982551 1.374575673 1.213514401 0.84875666 1.016765963 1 19.34309285 1.744309156 25 0.947632571 1.147361936 0.402390667 0.107877929 1.234437767 5387.873466 0.056106053 0.031113588 55.50206678 -1.744309156 0.199729365 RES(ph)EDDPES(ph)EPDDHEK ddPTM_MDA-MB-175_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 135.54 7.81E-05 362340000 632680 374390 502970 351630 686690 702150 644840 507140 542190 341960 TRUE FALSE 657658.6949 438688.5702 516077.8114 421181.3645 569966.6791 539086.3037 594295.7558 500342.6178 522676.6878 408960.5148 1.608122719 1.07269175 1.261925767 1.029882713 1.393696111 1.318186681 1.45318615 1.223449697 1.278061497 1 18.64160203 0.365822886 1.696773962 1.000019366 1.286417485 0.228941187 0.161178793 9.476315965 23.58626037 0.146276357 0.041264007 2.321789731 -0.365822886 0.286398119 RES(ph)FLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 112.75 0.0038493 222070000 31584 37217 38593 26633 62354 46259 32342 35825 43360 39035 TRUE FALSE 32830.96071 43608.73024 39598.76528 31900.92791 51755.08935 35516.04831 29806.94953 35344.82447 41799.48207 46683.16088 0.703272017 0.934142621 0.84824516 0.683349784 1.108645781 0.760789279 0.638494673 0.757121493 0.895386715 1 15.51061463 RES(ph)LTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RESLTKK 7 2 Q8IYK8 Q8IYK8 REM2 GTP-binding protein REM 2 1 RES(1)LTKK 80.688 0.015253 57742000 137050 63126 86107 51357 138750 139980 102080 97760 110100 67111 TRUE FALSE 142460.8398 73967.39945 88351.01916 61515.26131 115165.3246 107471.7664 94078.70286 96449.6871 106137.5225 80260.11553 1.77498922 0.921595975 1.100808522 0.766448701 1.434901056 1.339043256 1.172172532 1.201713784 1.322419259 1 16.29239561 RES(ph)PS(ph)PAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RES(1)PS(1)PAPKPR;RES(1)PS(1)PAPKPR 87.566 0.0073095 542981000 378919 303381 380447 298900 435880 411745 375199 370204 348749 294867 TRUE FALSE 393879.0147 355484.3268 390361.7614 358021.5279 361789.2733 316123.4638 345789.922 365242.0209 336197.5916 352640.5431 1.116941947 1.008064256 1.1069679 1.015259121 1.025943501 0.896446736 0.980573359 1.035734626 0.95337192 1 18.42783883 3.363392555 2.213966093 0.981468457 1.06973633 0.465472089 0.045481977 0.297527603 2.968297679 0.013803397 0.020479214 2308.83318 -3.363392555 0.088267873 RES(ph)PSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RESPSEER 8 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(1)PSEER;RES(0.968)PS(0.032)EER 116.84 0.0013442 125016000 57270 64809 53619 61936 48382 67064 79276 50802 50705 51209 TRUE FALSE 59531.06382 75939.44161 55016.35519 74186.75594 40158.04492 51489.40236 73062.13997 50121.08229 48880.13695 61242.42309 0.972055984 1.239981009 0.898337336 1.211362193 0.655722666 0.840747308 1.192998844 0.818404625 0.798141786 1 15.90224374 3.25975269 24.99979897 0.890650009 1.078823364 0.259720818 0.161970232 350.1133467 413017.9862 0.044087128 0.059635516 1818.664919 -3.25975269 0.188173355 RES(ph)PSEERLEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RESPSEERLEPK 12 2 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 RES(0.853)PS(0.147)EERLEPK;RES(0.802)PS(0.198)EERLEPK;RES(0.995)PS(0.005)EERLEPK 92.439 0.0060911 1019584000 335617 306498 343469 300974 436842 482724 343557 357953 354286 311252 TRUE FALSE 348867.4183 359136.6473 352420.0843 360505.7589 362587.7529 370618.6668 316628.1046 353155.2255 341535.3161 372235.8701 0.937221387 0.964809348 0.946765512 0.968487424 0.974080635 0.995655434 0.850611481 0.948740446 0.917523924 1 18.50585756 RES(ph)PSPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RESPSPAPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.999)PS(0.001)PAPK;RES(0.999)PS(0.001)PAPK;RES(0.997)PS(0.003)PAPK 104.24 0.0020161 719060000 1301730 896320 1096850 1061330 1227520 1398320 1619960 1150850 1138800 677320 TRUE FALSE 1353123.306 1050255.988 1125434.812 1271257.906 1018866.589 1073581.372 1492983.302 1135424.738 1097814.81 810027.8859 1.67046509 1.296567693 1.389377862 1.569400175 1.257816683 1.325363473 1.843125809 1.401710679 1.355280268 1 19.62761205 0.827574025 2.464725406 1.000779304 1.466975968 0.403096174 0.171998984 0.671640035 7.244828587 0.160997347 0.043223124 6.723168949 -0.827574025 0.466196664 RES(ph)PSPAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.67)PS(0.33)PAPKPR;RES(0.998)PS(0.002)PAPKPR;RES(0.88)PS(0.12)PAPKPR;RES(0.994)PS(0.006)PAPKPR;RES(0.887)PS(0.113)PAPKPR;RES(0.997)PS(0.003)PAPKPR;RES(0.828)PS(0.172)PAPKPR;RES(0.958)PS(0.042)PAPKPR;RES(0.675)PS(0.325)PAPKPR 153.05 2.57E-05 55214140000 10110880 8391250 9437850 7965910 11457900 11595690 10878940 9690640 9979610 7574090 TRUE FALSE 10510065.35 9832381.913 9683808.124 9541543.222 9510290.251 8902766.732 10026220.26 9560752.821 9620445.786 9058087.921 1.160296239 1.085480953 1.069078619 1.053372776 1.049922493 0.982852762 1.10688043 1.055493489 1.062083507 1 23.11077511 5.135471761 1.083398345 1.048522932 1.316961635 0.540146296 0.032270354 2.871073062 1.546548915 0.009263986 1.083322128 136606.6247 -5.135471761 0.268438703 RES(ph)QEEPR ddPTM_MDA-MB-175_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 160.72 0.00021542 1843300000 1707320 1870870 1911300 1799220 2163160 2194390 2018710 1912220 1954210 1950280 TRUE FALSE 1774726.312 2192177.369 1961110.048 2155100.346 1795466.836 1684776.179 1860478.235 1886589.819 1883878.364 2332400.026 0.760901343 0.939880529 0.840812051 0.923984017 0.769793696 0.72233586 0.797666873 0.80886203 0.807699513 1 21.15338381 5.044964457 16.11493477 0.833596509 0.375339107 0.072215096 0.081382737 830756.0989 7888955.771 0.019114741 11570472.55 110908.4043 -5.044964457 -0.458257402 RES(ph)VNLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RESVNLGK 8 1 P46013 P46013 MKI67 Antigen KI-67 1 RES(1)VNLGK 76.927 0.021153 158110000 81205 72578 79481 67713 88479 94842 76000 76363 76616 83191 TRUE FALSE 84411.0361 85042.70692 81552.34015 81106.4293 73439.37118 72816.38284 70042.92141 75339.47889 73858.60513 99490.68366 0.848431562 0.854780606 0.819698259 0.815216323 0.738153247 0.731891471 0.704014877 0.757251595 0.742367048 1 16.60227382 3.478975255 2.670099646 0.75940523 0.842674274 0.077562133 0.079651427 0.455084472 6.525234609 0.021149726 0.032864321 3012.834356 -3.478975255 0.083269045 RESPS(ph)PAPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RESPSPAPKPR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RES(0.423)PS(0.577)PAPKPR 88.706 0.010064 3006100000 1131800 957340 1135000 888210 1268100 1265600 1120700 1053000 1125200 837450 TRUE FALSE 1176484.338 1121755.698 1164579.032 1063895.287 1052548.815 971683.5804 1032856.606 1038886.257 1084704.272 1001532.294 1.174684377 1.120039469 1.162797286 1.062267581 1.050938469 0.970196954 1.031276387 1.037296814 1.083044729 1 19.93377751 3.577588268 2.490422426 1.028495691 1.150831932 0.758332416 0.031126864 0.141070124 1.708418433 0.008896607 0.015039575 3780.839727 -3.577588268 0.122336241 RET(ph)DDEGEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RETDDEGEDD 10 1 Q92688 Q92688 ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member B 1 RET(1)DDEGEDD;RET(1)DDEGEDD 181.66 3.60E-06 269420000 535870 565660 549590 515820 593780 668750 579280 521880 531800 500000 TRUE FALSE 557026.5614 662807.7048 563912.7669 617847.6564 492849.4877 513442.9475 533874.5199 514885.0522 512660.6219 597965.4269 0.9315364 1.108438172 0.94305246 1.033249798 0.824210674 0.858649889 0.892818374 0.861061575 0.857341577 1 19.18970255 3.244881182 24.9997454 0.874217163 1.007165812 0.466709499 0.06335218 113.5246456 449021.2743 0.016177083 0.021382316 1757.442731 -3.244881182 0.132948649 REVS(ph)PAPAVAGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 REVSPAPAVAGQSK 14 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 REVS(1)PAPAVAGQSK 117.2 0.00033631 30077000 100850 72450 85706 70836 112530 114520 99232 89908 90429 68893 TRUE FALSE 104831.6359 84892.72392 87939.56877 84847.14938 93402.19079 87924.46557 91453.93655 88702.93032 87174.47795 82391.26431 1.272363481 1.030360738 1.067340931 1.02980759 1.133641917 1.06715762 1.109995548 1.07660601 1.058054864 1 16.33020376 RFDAMPFTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFDAMPFTLR 10 1 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 199.82 4.35E-07 1202190000 268420 394510 283130 282100 682030 538090 332340 299690 314810 996820 FALSE TRUE 279017.4289 462264.0236 290508.6004 337898.538 566098.7842 413126.7523 306290.3224 295673.1457 303480.0496 1192127.794 0.234049932 0.387763817 0.243689143 0.28344154 0.474864177 0.346545693 0.256927423 0.248021351 0.254570065 1 20.18510747 -1.638082364 2.782889732 1.068484231 0.303649117 0.888598905 0.074002506 15352552.77 14525693.42 7566995.721 0.019935446 0.023010054 1.638082364 -0.764835114 RFDAQTGADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RFDAQTGADR 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ;;;;; 197.07 5.16E-07 2113440000 1124252 1495210 1336341 1217401 1680340 1595530 1333470 1348450 1310880 1739550 FALSE TRUE 1168638.337 1752000.686 1371167.144 1458199.284 1394716.407 1224992.338 1228949.137 1330376.233 1263701.685 2080381.517 0.561742319 0.842153553 0.659094081 0.700928783 0.670413766 0.58883062 0.590732578 0.639486663 0.60743747 1 20.98841669 -0.733751207 6.173608345 1.000000005 0.653574884 0.657463307 0.075511357 5.38E-09 1.05E-09 0.072216023 0.01702148 0.184607267 0.733751207 -0.346425121 RFDDAVVQSDMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 RFDDAVVQSDMK 12 1 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;;;;;;;;;;; 302.63 1.97E-36 39762250000 21472750 17307560 20919750 16788560 26824340 26394500 24868660 21016050 21832950 17487620 FALSE TRUE 22320510.75 20279998.8 21464935.87 20109287.06 22264748.27 20264777.39 22919389.45 20734364.23 21047186.39 20913984.32 1.067252916 0.969686048 1.026343692 0.961523484 1.064586639 0.968958238 1.095888239 0.991411484 1.006369044 1 24.3179646 3.237674137 24.99991988 1.021498185 1.005032021 0.02704175 0.043835116 100.6655194 2839004.493 0.011511385 0.014569004 1728.518919 -3.237674137 -0.016466163 RFDDAVVQSDMKHWPFMVVNDAGRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFDDAVVQSDMKHWPFMVVNDAGRPK 26 3 P11142;E9PKE3;E9PNE6;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 155.56 2.67E-08 724550000 479010 510400 603850 278200 987540 723530 370850 480380 641970 837720 FALSE TRUE 497921.6847 598057.2296 619586.8271 333227.1297 819678.3035 555501.1227 341781.808 473941.2918 618865.6251 1001855.195 0.496999653 0.596949771 0.618439501 0.332610073 0.818160456 0.554472468 0.34114891 0.473063667 0.617719635 1 19.93424257 0.876651416 5.028569811 0.999980147 0.526819117 0.53125986 0.132278517 0.858553883 34.20304841 0.126650119 0.032009404 7.527511296 -0.876651416 -0.47316103 RFDEATQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RFDEATQLR 9 1 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ;; 153.97 0.00012317 544760000 179944 306713 228146 236334 251883 303960 200185 221633 200065 391882 FALSE TRUE 187048.3281 359388.5719 234091.6722 283080.1598 209068.0176 233369.8966 184493.9766 218662.3722 192864.6997 468663.7749 0.399109848 0.766836677 0.499487447 0.604015448 0.446093829 0.497947375 0.393659563 0.466565551 0.411520391 1 18.83819376 -1.495094665 5.971647624 1.000482171 0.500749788 0.662417845 0.107420757 0.000681648 5.76E-05 0.102813202 0.024210993 0.031981979 1.495094665 -0.499732383 RFDEDDDKSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFDEDDDKSFR 11 2 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 77.593 0.018106 103580000 50883 58640 58512 55589 75449 87653 52311 57228 74530 84131 FALSE TRUE 52891.90013 68710.96384 60036.87079 66584.33828 62624.20593 67296.91914 48210.72713 56460.95227 71847.67986 100614.8587 0.525686771 0.682910703 0.596699847 0.661774406 0.622415086 0.668856668 0.479161108 0.561159187 0.714086178 1 16.61848385 0.901850365 3.962516136 0.999847148 0.600557273 0.795118789 0.061449236 0.197232694 6.709050972 0.060626818 0.015510712 7.977197873 -0.901850365 -0.399289875 RFDEILEASDGIMVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 39 RFDEILEASDGIMVAR 16 1 P14618;P14618-3;B4DNK4;P14618-2;H3BTN5;H3BR70 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 297.73 1.51E-45 17358734500 5338089.5 6822580.5 6236996.2 6461319.6 6950202.5 7513069.4 6331423.4 6277648.5 6248203.8 7661035.2 FALSE TRUE 5548841.395 7994305.629 6399537.445 7739349.332 5768809.562 5768272.894 5835149.89 6193506.89 6023332.166 9162068.368 0.605631957 0.872543765 0.698481739 0.844716392 0.629640528 0.629581953 0.636881287 0.675994398 0.657420565 1 23.1272419 -1.015522095 4.296284311 1.000017173 0.696470835 0.525907322 0.086988334 9572138.133 4525174.446 1510.487472 0.020252232 0.096489022 1.015522095 -0.303546338 RFDSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RFDSEK 6 1 P17980;E9PM69;E9PKD5;R4GNH3 P17980;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 ;;; 160.03 0.014329 1710004000 1925780 1695870 1844630 1544130 2354480 2317200 2233550 1920750 1904930 1728630 FALSE TRUE 2001811.281 1987122.48 1892702.573 1849554.305 1954266.331 1779065.418 2058478.515 1895005.488 1836371.941 2067321.952 0.968311336 0.961206105 0.915533534 0.894661958 0.945313007 0.860565243 0.995722274 0.916647495 0.888285417 1 20.97933165 -1.18280345 3.879386066 1.000044954 0.927811697 0.238791185 0.038900206 10894628457 2294982238 4957565.504 0.008705711 0.065644229 1.18280345 -0.072233256 RFDVSGYPTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFDVSGYPTLK 11 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 152.96 5.24E-05 3322700000 3167600 3277700 3427200 3184000 4379100 4335900 3578600 3456000 3489100 3351300 FALSE TRUE 3292659.294 3840619.478 3516515.647 3813785.697 3634742.146 3328952.936 3298099.981 3409677.973 3363527.973 4007923.07 0.821537549 0.958256785 0.877391004 0.951561602 0.9068892 0.830593022 0.822895031 0.850734386 0.839219694 1 21.93442339 2.758562049 22.62042933 0.855083611 0.907451011 0.051669341 0.059765582 430.75298 487153.9289 0.016798815 0.017786166 573.5378043 -2.758562049 0.0523674 RFEDLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFEDLGSR 8 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ; 128.6 0.0018062 331850000 125370 282700 209427 247090 189170 272730 156533 229150 168073 317020 FALSE TRUE 130319.7044 331251.5259 214884.8397 295963.6645 157014.951 209392.5908 144263.5344 226078.6191 162024.0856 379133.9993 0.343729934 0.873705673 0.566778079 0.780630767 0.414141046 0.552291779 0.380508039 0.596302678 0.427353089 1 18.53234831 -1.387291512 4.652266717 1.000624925 0.557094148 0.40755793 0.163046282 0.000995812 0.000131149 0.148754117 0.035013875 0.040992885 1.387291512 -0.443530777 RFEEALQTIFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFEEALQTIFNR 12 1 J3QRN6;O94832;K7EIG7 J3QRN6 MYO1D Unconventional myosin-Id 0 215.93 6.46E-11 121230000 177770 158340 166450 132970 205320 199300 179300 158150 166940 147400 FALSE TRUE 184788.4969 185533.6633 170787.8237 159271.0691 170419.7797 153015.5954 165245.9975 156030.2579 160931.862 176280.2079 1.048265708 1.052492878 0.968842877 0.903510786 0.966755042 0.868024818 0.937405279 0.885126356 0.912932109 1 17.42751098 4.086381656 2.782814013 0.918347408 1.053223669 0.643650569 0.036668082 0.138714042 2.145594976 0.008876869 0.023272742 12200.61313 -4.086381656 0.134876261 RFEEELAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFEEELAAR 9 1 Q02818 Q02818 NUCB1 Nucleobindin-1 0 ; 177.78 8.29E-05 168370000 75149 100526 94675 120180 142143 145838 112488 87956 94173 142163 FALSE TRUE 78115.94055 117790.5585 97142.30828 143951.2453 117981.5836 111969.3347 103670.8966 86777.09369 90783.73213 170017.118 0.459459268 0.692815876 0.57136781 0.846686775 0.69393944 0.658576831 0.609767404 0.510402098 0.533968186 1 17.37532048 4.745451885 23.65918704 0.65628825 0.459459072 0.16034592 0.142396323 747.4655984 2566061.131 0.033034969 0.317618242 55648.29788 -4.745451885 -0.196829177 RFEELGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RFEELGVK 8 1 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 137.13 0.0012207 2438780000 1444090 1731890 1687690 1242890 2153460 2095760 1521240 1660130 1649610 2333170 FALSE TRUE 1501103.788 2029328.635 1731672.588 1488729.932 1787415.638 1609051.502 1402001.234 1637878.673 1590240.858 2790309.99 0.537970259 0.727277128 0.620602225 0.533535678 0.640579593 0.576656897 0.502453576 0.586988069 0.56991548 1 21.41199398 -1.476929405 2.895989414 1.012555117 0.589103853 0.806934114 0.060392125 12013863.29 13356773.08 1208004.249 0.015668221 0.033348062 1.476929405 -0.423451264 RFEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFEELK 6 1 P53990-2;P53990;P53990-4;P53990-5;J3KR23;P53990-6 P53990-2 IST1 IST1 homolog 0 ; 120.65 0.032061 234629000 407750 293130 367140 283520 456970 476730 464720 344420 425480 290730 FALSE TRUE 423848.2849 343472.7973 376707.97 339599.4098 379294.4026 366016.6824 428294.0321 339803.6133 410167.0579 347692.9771 1.219030331 0.987862338 1.08345004 0.976722086 1.090888881 1.052700821 1.231816747 0.977309395 1.179681745 1 18.4074544 RFEELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFEELKK 7 2 P53990-2;P53990;P53990-4;P53990-5;J3KR23;P53990-6 P53990-2 IST1 IST1 homolog 0 81.548 0.015131 201250000 288100 147920 207530 135230 312180 304990 261420 182440 240780 146830 FALSE TRUE 299474.4105 173324.1093 212938.4023 161978.0904 259115.7551 234160.6947 240929.2173 179994.6902 232114.3748 175598.5273 1.705449443 0.987047625 1.212643441 0.922434219 1.475614626 1.333500333 1.372045774 1.025035306 1.321846934 1 17.42192122 0.070335538 0.61344737 0.988036748 1.252474707 0.100139868 0.227316013 9.59673516 4.347381666 0.51890993 0.087987068 1.175805638 -0.070335538 0.264437958 RFEETGQELAELLEEEKLSCVPVLIFANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFEETGQELAELLEEEKLSCVPVLIFANK 29 2 P36405 P36405 ARL3 ADP-ribosylation factor-like protein 3 0 176.89 7.70E-18 50715000 177130 127530 164130 123270 227150 211760 188260 162380 194190 139390 FALSE TRUE 184123.2292 149432.2855 168407.3626 147652.4381 188539.1241 162581.9493 173503.6893 160203.5617 187201.1398 166700.8017 1.104513159 0.896410119 1.010237269 0.885733221 1.131003104 0.975291946 1.040808967 0.961024542 1.122976842 1 17.34690152 3.248984046 24.99977946 1.02874469 0.971237805 0.134458499 0.07742417 455.2692904 1091921.976 0.020074778 0.026893167 1774.124305 -3.248984046 -0.057506885 RFEIACYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFEIACYK 8 1 Q9Y3A5;A0A087X020;F8WE72 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 135.71 0.0013181 1143380000 1579790 1411970 1680560 1296330 3249840 2394240 2077890 1709210 1697790 2901650 FALSE TRUE 1642161.329 1654464.864 1724356.774 1552740.205 2697433.358 1838214.045 1915019.552 1686300.836 1636686.87 3470172.762 0.473221779 0.47676729 0.496908048 0.447453286 0.777319616 0.529718308 0.551851358 0.485941465 0.471644204 1 21.72657606 -1.582096543 3.009599981 1.026200055 0.525090925 0.71719569 0.089773905 25834780.42 27029604.05 5377657.007 0.022546094 0.026176011 1.582096543 -0.50110913 RFEIPDEEHCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFEIPDEEHCLK 12 1 Q01968-2;Q01968 Q01968-2 OCRL Inositol polyphosphate 5-phosphatase OCRL-1 0 99.011 0.0026204 65413000 78979 79243 73392 80291 100050 110510 94675 76657 88370 99534 FALSE TRUE 82097.15191 92852.36883 75304.65581 96172.32016 83043.53674 84845.7273 87254.12611 75629.5383 85189.58096 119035.7816 0.689684654 0.780037461 0.632622013 0.807927825 0.697635078 0.712774984 0.733007546 0.635351298 0.715663642 1 16.86103578 -2.217130241 2.3000176 1.918199863 0.709250008 0.733182695 0.05216966 2438954.06 503918.3386 11638251.15 0.012807855 0.006065544 2.217130241 -1.208949855 RFEKPLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFEKPLEEK 9 2 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 159.09 3.73E-05 1973200000 2518900 1324980 1792600 1356420 2526500 2289600 2644500 1848150 2217100 1062930 FALSE TRUE 2618348.117 1552535.008 1839316.629 1624715.827 2097046.432 1757875.099 2437217.18 1823378.572 2137307.004 1271190.782 2.05976015 1.221323368 1.446924139 1.278105419 1.649670892 1.382857022 1.917270966 1.434386244 1.681342434 1 20.27774914 RFESIPDMLELDHLTVSGDVTFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFESIPDMLELDHLTVSGDVTFGK 24 1 A0A087WYS1;E7EUC7;Q16851;Q16851-2 A0A087WYS1 UGP2 UTP--glucose-1-phosphate uridylyltransferase 0 145.25 1.39E-07 299100000 170880 163850 198220 186870 231510 243030 226680 209190 197630 187810 FALSE TRUE 177626.4743 191989.9629 203385.776 223832.3282 192158.0129 186589.9657 208912.2293 206386.1502 190517.3349 224607.7737 0.790829594 0.854778799 0.905515302 0.996547558 0.855526992 0.8307369 0.930120209 0.918873585 0.848222356 1 17.77704833 RFFPYYVYNIIGGLDEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFFPYYVYNIIGGLDEEGK 19 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 ; 211.13 2.30E-16 491380000 756520 460950 641270 442300 902340 935420 712730 615620 724950 385430 FALSE TRUE 786387.9938 540114.5768 657982.023 529785.6199 748960.5691 718182.8814 656864.3602 607368.6209 698859.1911 460947.629 1.706024599 1.171748248 1.427455055 1.149340156 1.624827902 1.558057437 1.425030348 1.317652121 1.516135776 1 18.81424332 -1.36801859 3.359900873 0.99685856 1.418108877 0.358745501 0.172620999 27637477.62 42708587.03 866263.9066 0.040731535 0.042853018 1.36801859 0.421250317 RFLDNFDSSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFLDNFDSSEK 11 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 96.734 0.01089 339900000 335220 250020 334460 279690 393460 417950 424810 350320 336760 270280 FALSE TRUE 348454.7444 292958.9901 343176.3024 335011.8472 326579.8097 320887.4466 391512.2822 345624.5334 324640.0734 323236.1912 1.078018966 0.90633103 1.061688981 1.0364305 1.010344196 0.992733658 1.211226629 1.069263105 1.004343209 1 18.30222921 RFPEEPHVPLEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFPEEPHVPLEQR 13 1 Q8TCD5;J3KSX6;J3KRC4;Q8TCD5-2 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 ; 80.3 0.011791 136235000 95756 143266 122389 135401 120957 153494 125138 138487 108644 135593 FALSE TRUE 99536.52082 167870.821 125578.5579 162182.9137 100396.7723 117847.3447 115329.3566 136630.8083 104733.9237 162159.8523 0.613817288 1.035218142 0.774412138 1.000142214 0.619122248 0.726735644 0.71120783 0.842568653 0.645868396 1 17.30705715 5.023177193 16.4508657 0.805792516 0.151942682 0.148941306 0.143554675 7842562.064 141213352.6 0.032450192 133729914.9 105481.7175 -5.023177193 -0.653849834 RFPELESLVPNALDYIR ddPTM_MDA-MB-175_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 0 100.77 0.0020066 113620000 111250 125170 121910 131590 142070 149220 110430 145610 115210 145880 FALSE TRUE 115642.2359 146666.9738 125087.0748 157618.1092 117920.9921 114565.9165 101774.208 143658.3361 111063.6146 174462.393 0.662849076 0.840679595 0.716985894 0.903450346 0.675910666 0.656679726 0.583359005 0.823434401 0.636604902 1 17.41255656 -1.119006099 4.357815031 1.000031873 0.728533099 0.42340282 0.096997528 1.728527164 54955921.94 4382.198007 0.022146212 0.07603156 1.119006099 -0.271498774 RFPGYDSESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RFPGYDSESK 10 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;; 185.99 2.23E-06 7499870000 11425710 8810880 10482350 8058320 13181400 13556330 12243750 10620980 11664870 8596490 FALSE TRUE 11876805.85 10324080.1 10755528.65 9652231.644 10940830.34 10408077.81 11284052.88 10478623.14 11245053.61 10280807.63 1.15524055 1.004209054 1.046175461 0.93885928 1.0641995 1.012379395 1.097584284 1.019241242 1.093790879 1 23.29345027 RFS(ph)DFLGLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSDFLGLYEK 11 1 Q13596-2;Q13596;Q13596-3 Q13596-2 SNX1 Sorting nexin-1 1 RFS(1)DFLGLYEK;RFS(1)DFLGLYEK 124.68 0.00021081 259240000 717630 619620 806050 591830 1092990 915120 921350 740790 926560 807210 TRUE FALSE 745962.5865 726034.915 827056.3252 708892.2076 907203.9502 702597.2488 849132.1795 730860.9217 893213.2866 965367.3445 0.772724073 0.752081494 0.856727058 0.73432379 0.939749988 0.727802999 0.879594886 0.757080635 0.925257408 1 19.8807185 1.053900726 4.48506791 0.999035596 0.804343659 0.499042598 0.066114192 0.130591471 5.292374192 0.056622992 0.01441507 11.32141541 -1.053900726 -0.194691937 RFS(ph)DGAASIQAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFSDGAASIQAFK 13 1 H0Y4E8;Q9Y2K2-8;Q9Y2K2-7;Q9Y2K2 H0Y4E8 SIK3 Serine/threonine-protein kinase SIK3 1 RFS(0.657)DGAAS(0.343)IQAFK 125.45 0.00021188 265420000 384210 317890 332290 278970 408440 419840 391660 366580 394280 345000 TRUE FALSE 399378.9075 372485.1347 340949.7504 334149.4334 339013.5147 322338.5227 360960.6658 361666.5947 380089.9398 412596.1446 0.96796568 0.902783847 0.826352245 0.80987047 0.821659434 0.781244631 0.874852251 0.876563195 0.921215442 1 18.65437081 1.012444401 1.415609593 0.998984507 0.850263796 0.448992057 0.049969448 0.410857308 1.681248022 0.050244324 0.015064711 10.29068776 -1.012444401 -0.148720711 RFS(ph)DQAGPAIPTSNSYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 208.12 4.09E-16 2136570000 2411000 2274390 2401680 2216960 3069130 3019260 2786400 2471020 2797130 2244940 TRUE FALSE 2506188.142 2664998.79 2464269.754 2655468.071 2547440.379 2318082.622 2567994.687 2437900.019 2696461.838 2684793.011 0.933475367 0.992627282 0.917862101 0.989077393 0.948840513 0.863412044 0.956496339 0.908040213 1.004346267 1 21.35637943 1.22161207 24.75022074 1.002173231 0.938691186 0.332227262 0.035978937 282.0967601 411937.5555 0.033555627 0.008480801 16.65758622 -1.22161207 -0.063482045 RFS(ph)DSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.723)DS(0.277)EER;RFS(0.871)DS(0.129)EER 101.79 0.0054528 689660000 1010400 1246990 1220010 1285580 1251030 1510920 1146580 1269070 1183790 1344320 TRUE FALSE 1050291.372 1461150.832 1251804.463 1539863.887 1038380.367 1160031.728 1056708.064 1252060.192 1141185.629 1607713.765 0.653282565 0.90883767 0.778623963 0.95779729 0.645873905 0.721541205 0.657273755 0.778783027 0.709818908 1 20.61657914 3.222130811 24.99965322 0.736103748 0.827363355 0.071404265 0.119604384 490.6493216 746572.2124 0.03186545 0.038190024 1667.749468 -3.222130811 0.091259607 RFS(ph)DSEGEETVPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RFSDSEGEETVPEPR 15 1 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 1 RFS(0.996)DS(0.004)EGEETVPEPR;RFS(0.996)DS(0.004)EGEETVPEPR;RFS(0.999)DS(0.001)EGEETVPEPR;RFS(0.976)DS(0.024)EGEETVPEPR;RFS(0.989)DS(0.011)EGEETVPEPR 261.28 3.73E-25 2348740000 703023 846449 813123 939904 940963 1118190 907790 819628 747222 810935 TRUE FALSE 730778.8909 991820.0313 834313.6534 1125814.206 781018.4454 858507.3188 836635.0477 808642.2273 720329.6262 969822.187 0.753518429 1.022682348 0.860274867 1.160845999 0.80532128 0.885221364 0.862668496 0.833804627 0.742744016 1 19.88736073 RFS(ph)EGVLQSPSQDQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(0.781)EGVLQS(0.191)PS(0.029)QDQEK;RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK;RFS(0.869)EGVLQS(0.027)PS(0.104)QDQEK;RFS(1)EGVLQSPSQDQEK 301.04 3.87E-46 8963150000 4958000 3549440 3805770 3260280 5656950 5219330 3960120 3806830 4191730 3214960 TRUE FALSE 5153745.668 4159028.709 3904951.493 3905153.653 4695383.66 4007219.707 3649715.447 3755805.671 4040870.456 3844869.858 1.340421356 1.081708579 1.015626442 1.015679021 1.221207436 1.042225057 0.949242908 0.976835578 1.050977174 1 21.87450334 4.736971781 3.05911687 1.032259578 1.388612284 0.636196185 0.069121165 0.249139896 3.510532465 0.018391255 0.21499887 54572.24003 -4.736971781 0.356352706 RFS(ph)FCCSPEPEAEAEAAAGPGPCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSFCCSPEPEAEAEAAAGPGPCER 25 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 1 RFS(0.973)FCCS(0.027)PEPEAEAEAAAGPGPCER;RFS(0.976)FCCS(0.024)PEPEAEAEAAAGPGPCER 200.01 4.21E-25 1359840000 221487 262640 213794 279140 249400 259790 252530 266380 271840 324070 TRUE FALSE 230231.4778 307746.3769 219365.6473 334353.0589 207007.0771 199457.7097 232736.0387 262809.6118 262056.5315 387565.3118 0.594045625 0.794050364 0.566009497 0.862701198 0.534121787 0.514642832 0.600507919 0.678104061 0.676160955 1 18.56407993 0.446243173 1.574549452 0.999972346 0.64356432 0.506705794 0.105138765 2.904724554 7.382021902 0.098228742 0.028117063 2.794107898 -0.446243173 -0.356408027 RFS(ph)FFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSFFK 6 1 O15020;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 RFS(1)FFK;RFS(1)FFK 119.86 0.012647 543630000 494390 425600 564150 536140 808340 713130 648970 538460 592390 437910 TRUE FALSE 513908.899 498693.4893 578852.2125 642186.8918 670938.6555 547516.3651 598102.0356 531242.8244 571069.9996 523710.0802 0.981285101 0.952231985 1.105291333 1.226225952 1.281126106 1.045456992 1.142047973 1.014383424 1.09043156 1 18.99840885 1.727928296 11.24550083 1.040042487 1.108115632 0.096766604 0.097038143 0.263016148 133.0475655 0.050607203 0.027597086 53.44761079 -1.727928296 0.068073145 RFS(ph)FSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR;RFS(1)FSQR 169.77 0.00061219 10177295000 1351886 1649608 1508151 1493446 1805493 1877265 1437245 1456605 1532917 1816294 TRUE FALSE 1405259.503 1932915.342 1547454.654 1788845.161 1498595.945 1441298.654 1324589.981 1437081.593 1477747.617 2172162.034 0.646940459 0.889857806 0.712402956 0.8235321 0.689909832 0.663531832 0.609802566 0.66159042 0.680311871 1 21.0507003 -1.274773511 3.568066253 1.000752867 0.707820943 0.540128695 0.080646057 1356413088 2270382767 11277243.23 0.020362772 0.053116138 1.274773511 -0.292931924 RFS(ph)IPESGQGGTEMDGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSIPESGQGGTEMDGFR 18 1 Q9Y572 Q9Y572 RIPK3 Receptor-interacting serine/threonine-protein kinase 3 1 RFS(1)IPESGQGGTEMDGFR;RFS(1)IPESGQGGTEMDGFR 144.48 6.00E-08 259020000 55366 75755 69591 63156 80625 110349 83083 83040 73602 76130 TRUE FALSE 57551.89243 88765.33196 71404.59863 75648.0683 66920.3913 84722.11711 76570.73736 81926.98463 70953.0784 91046.2159 0.632117347 0.974948064 0.784267615 0.83087548 0.735015625 0.930539685 0.841009553 0.899839535 0.779308373 1 16.47431144 2.729821111 24.97688985 0.881289143 0.803431308 0.199167089 0.096670645 1255.58325 3588362.251 0.028903319 0.027633674 536.8106346 -2.729821111 -0.077857835 RFS(ph)LFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSLFGK 7 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RFS(1)LFGK;RFS(1)LFGK 104.95 0.0049221 859760000 625070 598330 825760 670660 1219090 880140 853400 659120 786600 791620 TRUE FALSE 649748.2463 701088.5231 847279.984 803314.5463 1011869.517 675740.8237 786508.2781 650285.5745 758290.4197 946722.7825 0.686313098 0.740542571 0.894961017 0.848521406 1.068812894 0.713768419 0.830769358 0.686880665 0.800963528 1 19.85258251 -2.339045416 2.04818611 1.956006174 0.806793351 0.215619259 0.109870468 7367958.904 800633.0549 32625935.49 0.027491734 0.00458094 2.339045416 -1.149212823 RFS(ph)LSVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;RFS(1)LSVPR;RFS(1)LSVPR;RFS(0.999)LS(0.001)VPR 158.47 0.00022344 4094960000 672681 818594 782092 797893 993123 977968 756152 777797 711074 937720 TRUE FALSE 699238.9653 959181.1517 802473.96 955713.8539 824312.3072 750849.7532 696882.8304 767371.9034 685482.5856 1121448.28 0.623514234 0.85530574 0.715569299 0.852213937 0.735042642 0.669535784 0.621413259 0.684268652 0.611247614 1 20.09693166 -1.465204149 5.65522712 1.000273773 0.7104109 0.525624328 0.083303726 0.000293475 2.78E-05 0.082321819 0.01938536 0.03426067 1.465204149 -0.289862873 RFS(ph)MEDVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RFSMEDVSK 9 1 Q07002 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK;RFS(1)MEDVSK 150.26 5.25E-05 4117940000 5965250 4445280 5689230 4454380 7781470 7444790 7004900 5727180 6516270 4861440 TRUE FALSE 6200762.676 5208722.261 5837496.008 5335443.069 6458778.509 5715850.349 6455837.634 5650416.52 6281750.716 5813946.09 1.066532537 0.895901369 1.004050591 0.917697376 1.110911317 0.983127511 1.110405486 0.971872878 1.080462498 1 22.47108626 3.24976697 24.99582727 1.038579871 0.968035555 0.234379548 0.063161806 305.7796507 682038.5197 0.015970774 0.021428416 1777.32549 -3.24976697 -0.070544316 RFS(ph)MEDVSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFSMEDVSKR 10 2 Q07002 Q07002 CDK18 Cyclin-dependent kinase 18 1 RFS(0.92)MEDVS(0.08)KR 57.106 0.094315 249510000 338700 293530 296200 218890 334160 333040 337340 268010 265090 213470 TRUE FALSE 352072.1375 343941.4942 303919.2153 262185.7887 277359.6026 255696.5073 310898.4093 264417.7643 255549.4627 255295.3594 1.379077702 1.347229715 1.190461182 1.02699003 1.086426339 1.001571309 1.217798906 1.035732749 1.000995331 1 17.96180779 4.091367865 2.440957456 1.062000691 1.375711069 0.797382801 0.062372846 0.120824971 1.429778079 0.01623944 0.045630901 12341.49767 -4.091367865 0.313710377 RFS(ph)NVGLVHTSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RFSNVGLVHTSER 13 1 A0A087X165;Q9C0H9;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER;RFS(1)NVGLVHTSER 161.33 2.53E-05 3613600000 182528 950870 686881 928350 652784 1205910 593393 953530 619176 1125450 TRUE FALSE 189734.3464 1114174.526 704781.6831 1111974.859 541824.0088 925855.6782 546881.3061 940749.49 596891.9767 1345960.379 0.140965774 0.827791473 0.523627362 0.826157201 0.40255569 0.687877364 0.406313079 0.698942929 0.443469203 1 20.36020451 -2.087156272 2.367921238 1.69258976 0.569387116 0.298481909 0.204804379 22831417.77 6896798.283 85259577.82 0.043537828 0.008181703 2.087156272 -1.123202645 RFS(ph)TEEFVLL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFSTEEFVLL 10 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 1 RFS(0.546)T(0.454)EEFVLL 63.727 0.081253 65525000 151390 158150 166980 143090 202140 221350 182850 177640 182180 200830 TRUE FALSE 157366.9941 185311.0323 171331.636 171392.7749 167780.315 169944.8171 168517.7392 175259.0264 175623.3774 240178.7934 0.655207697 0.771554514 0.71335039 0.713604946 0.698564235 0.70757628 0.701634548 0.729702335 0.731219334 1 17.87374925 -0.030359485 1.009040672 1.002953346 0.711661394 0.911051158 0.026935374 2.100387534 1.802357388 0.045623001 0.007555719 0.932482124 0.030359485 -0.291291952 RFSDIQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 206.38 0.00011524 1078708000 399957 569891 444386 452320 558847 591931 487856 511211 474956 602372 FALSE TRUE 415747.6112 667765.3461 455967.0642 541787.546 463854.3866 454463.9961 449616.5719 504359.0527 457862.4263 720395.2603 0.57711042 0.926943003 0.632940122 0.752069837 0.643888726 0.630853673 0.624124834 0.700114341 0.635571125 1 19.45842916 -1.873566205 5.905532203 1.056527971 0.68455602 0.509504044 0.09399447 0.048485679 0.001038048 0.06307762 0.020048206 0.013379312 1.873566205 -0.371971951 RFSDS(ph)EER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSDSEER 8 1 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RFS(0.194)DS(0.806)EER;RFS(0.013)DS(0.987)EER 135.16 0.00089577 1091420000 869490 1001720 957220 956640 1047970 1133490 983020 1001180 940600 1041680 TRUE FALSE 903818.1366 1173757.618 982165.9396 1145860.537 869836.4337 870254.1257 905968.3238 987760.8197 906747.9897 1245777.252 0.725505411 0.942188996 0.78839611 0.919795682 0.698227899 0.698563186 0.727231391 0.792887186 0.727857238 1 20.2486147 5.030100111 17.6113942 0.798088534 0.479510622 0.045869071 0.103100641 66234570.79 990276951.2 0.023794308 643844725.3 107176.6334 -5.030100111 -0.318577913 RFSDS(ph)EGEETVPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RFSDSEGEETVPEPR 15 1 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 1 RFSDS(0.996)EGEET(0.003)VPEPR 259.4 7.80E-25 351780000 126550 133340 121780 146640 146410 164030 141680 127510 123580 105650 TRUE FALSE 131546.2917 156240.1078 124953.6868 175644.9543 121523.2805 125936.5184 130574.7514 125800.937 119132.3799 126350.0947 1.041125391 1.236565023 0.988948106 1.390145015 0.961798096 0.996726743 1.033436118 0.995653682 0.942875272 1 16.94706722 RFSEGTSADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RFSEGTSADR 10 1 A0A087X2I1;P62333;H0YJX2 A0A087X2I1;H0YJX2 PSMC6 26S protease regulatory subunit 10B 0 ;; 132.62 0.00035069 486730000 224112 674620 642410 657900 645400 753770 647230 664630 599450 678890 FALSE TRUE 232960.1148 790480.7372 659151.7323 788030.6564 535695.1385 578718.341 596498.4214 655721.722 577875.9116 811905.4974 0.286930087 0.973611756 0.811857703 0.970594064 0.659799866 0.712790273 0.734689472 0.807633061 0.711752677 1 19.63095229 -2.658211924 2.002325637 6.049953747 0.757187414 0.148309765 0.182505722 5625459.833 152264.5771 130055467.7 0.041284091 0.002196788 2.658211924 -5.292766333 RFSFS(ph)QR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RFS(0.442)FS(0.558)QR;RFS(0.458)FS(0.542)QR 102.55 0.0090848 2413720000 990000 1307760 1206580 1152600 1472700 1485630 1171150 1228510 1215860 1446830 TRUE FALSE 1029085.964 1532357.607 1238024.466 1380580.84 1222370.98 1140614.947 1079352.203 1212043.833 1172101.436 1730308.637 0.594741275 0.885597849 0.715493432 0.797881262 0.706446789 0.659197396 0.623791721 0.700478404 0.677394432 1 20.72259797 -1.023066049 4.640076507 1.00000774 0.709293556 0.550976681 0.079382116 0.084191007 48268333.31 924.9665669 0.018268005 0.094827423 1.023066049 -0.290714184 RFST(ph)EEFVLL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFSTEEFVLL 10 1 Q96DT6 Q96DT6 ATG4C Cysteine protease ATG4C 1 RFS(0.445)T(0.555)EEFVLL;RFS(0.449)T(0.551)EEFVLL 76.655 0.068372 110228000 202969 230889 234114 227079 272820 307070 253600 250970 247880 266370 TRUE FALSE 210982.3728 270542.3897 240215.2032 271994.5484 226446.1538 235757.6462 233722.1693 247606.1577 238958.8472 318560.1015 0.662300055 0.849266397 0.754065566 0.853824905 0.710842798 0.740072737 0.73368312 0.777266696 0.750121707 1 18.28120606 -2.062512096 2.015377154 1.317567046 0.762391518 0.632153628 0.055087502 1634913.892 461947.9753 2388293.51 0.012865091 0.008659402 2.062512096 -0.555175528 RFTDEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFTDEESR 8 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2 E9PK91;Q9NYF8 BCLAF1 Bcl-2-associated transcription factor 1 0 ; 77.049 0.054871 203350000 167299 386637 294720 340712 263503 393147 247527 305043 238805 400178 FALSE TRUE 173904.0937 453038.8971 302400.6453 408103.8167 218712.8542 301844.5675 228125.1869 300954.3975 230210.4547 478585.2172 0.363371219 0.946621168 0.63186374 0.852729675 0.456998767 0.63070182 0.476665761 0.628841817 0.481022912 1 18.86841631 -1.086290612 4.57747469 1.00002516 0.617013027 0.319891438 0.171137695 4.10E-05 8.19E-06 0.154746359 0.036471673 0.081980278 1.086290612 -0.383012132 RFVEVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ;; 133.55 0.0052287 685070000 415616 487630 474339 461640 563650 584050 491090 502667 465303 610590 FALSE TRUE 432024.8406 571376.6593 486700.664 552951.0141 467840.9743 448413.2389 452597.0826 495929.5711 448556.8359 730223.42 0.591633778 0.782468274 0.66650925 0.757235387 0.640681963 0.61407677 0.619806309 0.67914772 0.614273418 1 19.47797841 -1.848207729 3.044621477 1.115141404 0.666279139 0.740794495 0.059795618 96988816 23662887.43 77434376.49 0.014044304 0.014183789 1.848207729 -0.448862265 RFVNVVPTFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RFVNVVPTFGK 11 1 P62861;E9PR30 P62861 FAU 40S ribosomal protein S30 0 ; 118.28 0.0011895 648360000 1149030 1021760 1234880 1053470 1460630 1614030 1415360 1313600 1376550 1216080 FALSE TRUE 1194394.592 1197239.332 1267061.987 1261843.222 1212352.634 1239195.993 1304420.385 1295993.341 1327008.234 1454347.593 0.821257997 0.823214022 0.871223629 0.867635239 0.833605831 0.852063152 0.896911021 0.89111664 0.912442281 1 20.47194069 -0.062582339 0.21167791 1.07463437 0.810061607 0.897498913 0.016201041 2.81117448 0.221560408 0.197174858 0.051535985 0.865800159 0.062582339 -0.264572763 RGAAAADLLS(ph)SSPESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.303)S(0.303)S(0.303)PES(0.073)QHGGT(0.018)QS(0.001)PGGGQPLLQPTK 81.967 0.00049175 151430000 36499 62415 65147 71173 76516 98559 62589 72467 70347 59936 TRUE FALSE 37940.0087 73134.29073 66844.78434 85250.80697 63509.83765 75670.16593 57683.11063 71495.6984 67815.22521 71679.31166 0.529302079 1.020298452 0.93255338 1.189336295 0.886027449 1.055676515 0.804738624 0.997438406 0.946092026 1 16.12926916 4.741830474 24.94708008 0.97825827 0.529301908 0.659536663 0.097413901 175.5040713 1338928.976 0.021839187 0.157623535 55186.19795 -4.741830474 -0.448956362 RGAAAADLLSS(ph)SPESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.194)S(0.406)S(0.333)PES(0.031)QHGGT(0.031)QS(0.005)PGGGQPLLQPTK 65.504 0.0026165 760680000 97655 172530 216810 187290 209940 297060 219280 201210 210190 156190 TRUE FALSE 101510.4948 202160.6854 222460.2467 224335.403 174254.4738 228072.317 202092.2606 198513.1091 202625.303 186792.4401 0.54344006 1.08227445 1.190948877 1.200987593 0.93287755 1.220993296 1.081908136 1.06274702 1.084761797 1 17.51107654 4.737549875 5.97937503 1.100894288 0.528456489 0.789581201 0.085470242 0.052916271 9.122475148 0.019498463 0.1236155 54644.9301 -4.737549875 -0.572437799 RGAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTK 34 1 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.228)S(0.185)S(0.582)PES(0.004)QHGGT(0.001)QSPGGGQPLLQPTK 91.751 0.00018576 662900000 84428 144970 169910 158720 154350 203090 153570 179710 160820 130180 TRUE FALSE 87761.28263 169867.4698 174337.9942 190114.3423 128113.6421 155925.4254 141532.7821 177301.2814 155032.1196 155686.2786 0.563705957 1.091088254 1.119803208 1.221137431 0.822896169 1.001536081 0.909089635 1.138836916 0.995798224 1 17.24828227 4.742531641 24.82059359 1.037548751 0.563705753 0.621842641 0.109828861 236.5247501 1478316.406 0.026505335 0.201776693 55275.36781 -4.742531641 -0.473842998 RGAAAADLLSSS(ph)PESQHGGTQSPGGGQPLLQPTKVDAAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAAAADLLSSSPESQHGGTQSPGGGQPLLQPTKVDAAEGR 41 2 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 1 RGAAAADLLS(0.038)S(0.178)S(0.697)PES(0.086)QHGGT(0.001)QSPGGGQPLLQPTKVDAAEGR 112.45 2.26E-06 461990000 31421 87409 88061 60441 101840 104000 48932 88260 85444 125510 TRUE FALSE 32661.52534 102420.8158 90355.942 72396.0494 84529.27318 79847.57614 45096.58198 87077.01906 82368.88713 150101.2815 0.217596579 0.682344713 0.601966493 0.482314666 0.563148245 0.531957991 0.300441019 0.580121757 0.548755389 1 17.19557677 0.504981751 1.651189985 0.999861574 0.501271251 0.565797593 0.132029756 2.068471905 6.113473879 0.119448287 0.033933492 3.198760695 -0.504981751 -0.498590323 RGAAGDWGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAAGDWGER 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 127.7 0.00055999 107300000 136290 179850 170020 146510 208700 223020 185040 183070 157520 199270 FALSE TRUE 141670.8344 210737.8385 174450.8609 175489.2407 173225.2485 171226.9849 170536.0813 180616.2461 151850.886 238313.1412 0.594473447 0.884289626 0.732023673 0.73638088 0.726880807 0.718495774 0.715596632 0.757894614 0.637190569 1 17.86249898 -1.82704504 3.095124054 1.078745805 0.729885564 0.569749232 0.072071919 5661369.926 8699206.6 2904396.569 0.015313146 0.014892066 1.82704504 -0.348860241 RGADDDRPSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGADDDRPSWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 150.33 1.91E-05 1230490000 142002 169590 152506 154664 204614 243047 142957 194239 190851 242875 FALSE TRUE 147608.3486 198715.7633 156480.4316 185256.0776 169833.7854 186603.0177 131751.6568 191635.5439 183982.3098 290461.7061 0.508185229 0.684137561 0.538729989 0.637798628 0.584702843 0.642435866 0.453593896 0.65976182 0.633413307 1 18.14798845 0.457080584 1.357330233 0.999982515 0.588084157 0.767685443 0.067667876 1.119640621 2.368230772 0.058787422 0.017321868 2.864709474 -0.457080584 -0.411898358 RGAEDDRGPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGAEDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;;; 113.61 0.00076982 1238408000 170060 297549 228599 242464 234620 333296 191186 239757 222028 380789 FALSE TRUE 176774.1001 348650.7261 234556.4777 290422.6555 194739.3762 255893.0551 176200.3417 236543.4496 214037.2557 455397.3139 0.388175544 0.7655968 0.515058984 0.63773467 0.427625219 0.561911648 0.386915637 0.519422145 0.470001138 1 18.79676626 -1.334007497 5.630553687 1.00008496 0.522338375 0.629978484 0.110529297 0.000110899 1.31E-05 0.10068129 0.023726617 0.046343892 1.334007497 -0.477746585 RGAEEEEEEEDDDS(ph)GEEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAEEEEEEEDDDSGEEMK 19 1 Q08495;Q08495-2;Q08495-3;Q08495-4;E5RFK4 Q08495 DMTN Dematin 1 RGAEEEEEEEDDDS(1)GEEMK 74.662 0.0066519 222890000 236580 163270 204620 182240 289100 296670 249130 217710 250670 152110 TRUE FALSE 245920.3611 191310.3524 209952.5653 218286.5281 239958.8853 227772.8886 229602.5396 214791.9536 241648.4357 181913.0422 1.351856679 1.051658255 1.154136959 1.199949852 1.31908566 1.252097628 1.262155461 1.180739715 1.328373341 1 17.47288945 5.076390367 18.19223056 1.206068138 4.928418243 0.17046122 0.101330313 241.997904 59423.1029 0.02245551 1127.09714 119231.3242 -5.076390367 3.722350104 RGALLY(ph)MYCHS(ph)LTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGALLYMYCHSLTK 14 1 A6NDU8 A6NDU8 C5orf51 UPF0600 protein C5orf51 2 RGALLY(0.5)MY(0.5)CHS(0.998)LT(0.001)K 51.147 0.086477 173670000 24103 191430 215880 197310 222620 251300 206070 222270 227720 182810 TRUE FALSE 25054.60505 224306.6134 221506.0101 236337.3291 184779.1319 192939.3835 189917.6949 219290.8342 219524.4017 218628.1194 0.114599188 1.025973301 1.013163406 1.081001519 0.845175508 0.882500312 0.868679178 1.003031242 1.004099575 1 17.73811944 4.741064686 24.99996914 0.964803237 0.114598889 0.923882646 0.073587597 60.05207841 599509.4016 0.018757048 0.127561919 55088.97427 -4.741064686 -0.850204348 RGAS(ph)SS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGASSSPQR 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RGAS(0.999)S(0.008)S(0.993)PQR 89.44 0.016134 0 9466.4 9267.8 9816.4 8540.9 10760 10890 10839 12250 9978.2 9750.3 TRUE FALSE 9840.140782 10859.47256 10072.22345 10230.26453 8931.019043 8360.96254 9989.410858 12085.80879 9619.086531 11660.6846 0.843873333 0.93128945 0.863776338 0.877329666 0.765908636 0.717021583 0.856674475 1.036457909 0.824916105 1 13.50936487 -1.026051533 4.699805527 1.000003541 0.866200685 0.205675807 0.082438084 3.42E-06 7.09E-07 0.089288988 0.021045059 0.094177784 1.026051533 -0.133802856 RGAT(ph)PPAPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGATPPAPPR 10 1 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 RGAT(1)PPAPPR;RGAT(1)PPAPPR 65.563 0.040197 602420000 236120 252380 237270 283900 303030 320670 274530 244350 260860 218490 TRUE FALSE 245442.1999 295724.3018 243453.4511 340054.5726 251521.0688 246199.2523 253011.6212 241074.8879 251471.6996 261298.9323 0.93931574 1.131747073 0.93170473 1.301400544 0.96257978 0.942213006 0.968284176 0.922601887 0.962390842 1 17.9953417 3.042275503 24.99998152 0.952508904 1.077496041 0.249647719 0.098502616 178.5938065 105611.8704 0.02656794 0.031754737 1102.238314 -3.042275503 0.124987137 RGAYGGGYGGYDDYGGYNDGYGFGSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGAYGGGYGGYDDYGGYNDGYGFGSDR 27 1 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 92.412 0.0095814 169980000 25691 46601 44288 40674 40187 38624 29827 42726 36930 63637 FALSE TRUE 26705.30052 54604.35924 45442.18166 48719.1958 33356.02809 29654.16135 27489.0818 42153.32786 35600.89651 76105.45175 0.350898653 0.717482887 0.59709496 0.640153822 0.438286973 0.389645691 0.361197275 0.553880529 0.467783788 1 16.21571218 -0.943215814 4.582146386 1.000006244 0.507178759 0.617798961 0.117482893 25228.65206 73660823.58 1271.853774 0.028232921 0.11396833 0.943215814 -0.492827485 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_MDA-MB-175_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 ; 267.81 1.98E-53 821800000 171586 218886 197404 186769 210033 258910 189706 201059 212596 242944 FALSE TRUE 178360.3478 256477.9678 202548.5104 223711.3508 174331.6657 198782.0763 174836.348 198364.133 204944.7115 290544.2254 0.613883644 0.882750182 0.697134869 0.769973488 0.600017658 0.684171493 0.601754682 0.682733008 0.705382154 1 18.14839826 0.783195117 6.266924236 0.999999964 0.692506354 0.565158469 0.080840651 11.59894893 335.3717851 0.076649315 0.019256658 6.070089819 -0.783195117 -0.30749361 RGDDSFGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGDDSFGDK 9 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 190.57 5.92E-05 1187940000 1102940 758560 984280 846530 1245140 1309080 1395900 974480 1024390 592060 FALSE TRUE 1146484.923 888836.7792 1009931.145 1013971.107 1033491.548 1005066.009 1286485.71 961418.6895 987522.404 708062.8213 1.619185316 1.255307795 1.426329861 1.432035516 1.459604313 1.419458809 1.816908997 1.357815522 1.394681904 1 19.43351784 0.711160135 1.872840692 1.000804349 1.472878178 0.49478636 0.143388517 0.956760301 4.92457079 0.133326723 0.037218562 5.142332272 -0.711160135 0.472073829 RGDDSFGDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGDDSFGDKYR 11 2 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 215.72 7.09E-12 4833164000 1938129 1803376 2026835 1416884 3352289 2650545 2049901 1762850 2019026 2547447 FALSE TRUE 2014647.829 2113091.8 2079655.985 1697139.426 2782468.113 2034996.093 1889224.403 1739221.879 1946361.649 3046570.466 0.661283844 0.69359689 0.682621987 0.557065541 0.913311589 0.667962916 0.620115118 0.570878599 0.638869729 1 21.53875468 -1.179665173 3.939664173 1.000196293 0.663584632 0.53611048 0.092785949 10946614.26 6555578.261 17145.19461 0.022140113 0.066120302 1.179665173 -0.336611662 RGDDWNDREWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGDDWNDREWDR 12 2 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ;; 198.14 1.05E-07 1603080000 441770 624190 535980 628500 635230 735860 520810 565410 617790 655590 FALSE TRUE 459211.4207 731389.777 549948.0791 752815.4241 527253.8315 564967.6671 479987.5513 557831.6038 595555.8586 784040.3085 0.58569874 0.932847162 0.701428323 0.960174389 0.672483067 0.720584976 0.612197544 0.711483323 0.759598521 1 19.5805683 0.939458782 17.71570024 1.000000002 0.739259164 0.315940898 0.115332455 520.4794238 152306.1095 0.106367352 0.026591838 8.69878871 -0.939458782 -0.260740837 RGDIIGVQGNPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGDIIGVQGNPGK 13 1 Q15046;Q15046-2;H3BVA8;J3KRL2;H3BPV7 Q15046 KARS Lysine--tRNA ligase 0 ; 145.6 6.72E-05 404200000 544760 468130 558660 479420 662720 689920 603990 596700 628970 493680 FALSE TRUE 566267.5454 548527.686 573219.1385 574247.8451 550071.0911 529696.5358 556647.6856 588702.2125 606333.4926 590407.1439 0.959113641 0.929066817 0.970887877 0.972630245 0.931680954 0.897171623 0.942820037 0.997112278 1.026975196 1 19.17135065 1.65394954 3.826458191 1.012832882 0.942662262 0.653405671 0.021765101 0.116398711 4.003710257 0.013669978 0.006210469 45.07643279 -1.65394954 -0.07017062 RGDLIIEFEVIFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDLIIEFEVIFPER 15 1 P25685;P25685-2 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 123.97 0.00015952 11223000 8920.7 10704 12361 10856 12906 12442 11137 10976 8744 9596.5 FALSE TRUE 9272.896124 12542.32873 12683.13781 13003.2844 10712.24273 9552.53406 10264.05284 10828.88467 8429.305148 11476.75044 0.807972272 1.09284669 1.105115763 1.133010992 0.933386396 0.832337874 0.894334411 0.943549721 0.734467931 1 13.48642659 3.048197418 7.328246807 0.883946359 1.04338808 0.319098257 0.10576735 0.24840276 30.99524327 0.030179767 0.03603601 1117.371058 -3.048197418 0.159441721 RGDLPFVVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGDLPFVVPR 10 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 223.14 7.33E-09 18327570000 2502446 2826638 2727697 2824143 3137285 3380220 2849211 2921750 2687083 3044463 FALSE TRUE 2601244.5 3312091.088 2798783.025 3382750.056 2604010.416 2595215.133 2625882.397 2882588.72 2590375.408 3640967.235 0.714437767 0.909673412 0.768692175 0.92908006 0.715197432 0.712781787 0.721204622 0.791709602 0.711452546 1 21.79589033 5.042312227 16.26416519 0.794175736 0.325596175 0.059076258 0.099794022 899728.386 9271160.595 0.022521915 12750908.22 110233.1524 -5.042312227 -0.468579561 RGDQGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDQGPK 7 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 77.058 0.062659 87189000 114460 78291 108470 69082 152180 134340 137540 114320 126800 102650 FALSE TRUE 118978.9692 91736.87023 111296.8173 82746.21341 126312.498 103141.5709 126759.2554 112787.7274 122236.4928 122762.3021 0.969181639 0.747272319 0.906604188 0.674036019 1.028919267 0.840172994 1.032558474 0.918748878 0.99571685 1 16.90550808 3.214178602 24.99998921 0.960646916 0.824654069 0.370215048 0.092281216 238.1355348 244170.554 0.024376213 0.029148082 1637.489796 -3.214178602 -0.135992848 RGDQLLSVNGVSVEGEHHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDQLLSVNGVSVEGEHHEK 20 1 Q9NUP9;G3V1D4;O14910 Q9NUP9 LIN7C;LIN7A Protein lin-7 homolog C;Protein lin-7 homolog A 0 150.98 3.30E-08 416830000 198770 245610 244280 233220 297350 345580 292070 278010 272950 222730 FALSE TRUE 206617.5931 287791.6069 250646.1375 279350.2199 246806.5532 265324.2823 269176.7902 274283.7307 263126.5828 266369.6791 0.775679851 1.080421795 0.940970978 1.0487313 0.926556484 0.996075391 1.010538403 1.029710783 0.98782483 1 18.02307034 4.751190415 24.90176254 1.001909076 0.775679701 0.710538345 0.043395254 967.7188027 1907983.655 0.009513151 0.169873542 56388.48349 -4.751190415 -0.226229375 RGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(1)ES(0.999)EEDEQDS(0.001)EEVR 156.15 4.94E-08 340540000 263760 263720 290870 275090 314830 375200 315340 290440 275940 256050 TRUE FALSE 274173.4485 309011.8585 298450.3112 329501.9809 261315.3091 288065.4862 290622.8268 286547.1269 266008.9733 306218.0951 0.895353517 1.009123443 0.974633165 1.076036936 0.853363381 0.940719999 0.949071369 0.935761575 0.868691229 1 18.22420001 3.230127533 24.99999876 0.924843364 0.989228419 0.237010104 0.056414816 263.2360551 780366.1381 0.015557867 0.018880718 1698.742425 -3.230127533 0.064385055 RGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RGDS(1)ES(0.019)EEDEQDS(0.982)EEVR 215.2 3.80E-15 319550000 199890 199980 201020 186220 227250 271540 221720 191750 203800 175200 TRUE FALSE 207781.8115 234325.0094 206258.7463 223053.7602 188622.1262 208478.9502 204341.007 189179.9049 196465.2778 209527.0856 0.991670413 1.118351877 0.984401352 1.064558119 0.90022789 0.994997614 0.975248648 0.902889974 0.937660528 1 17.67677723 3.247761388 24.99929961 0.947644066 1.041407048 0.45275827 0.047197758 163.564544 444416.5035 0.012571949 0.016788378 1769.136685 -3.247761388 0.093762982 RGDS(ph)QECSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.609)QECS(0.391)PR 62.408 0.090341 44035000 47274 52950 50006 47206 51068 65044 42110 55208 45516 55917 TRUE FALSE 49140.41402 62043.75061 51309.19744 56543.2059 42387.4796 49938.51675 38809.30817 54468.02706 43877.88805 66872.86555 0.734833383 0.927786631 0.767264824 0.84553287 0.633851701 0.74676801 0.580344626 0.814501167 0.656138894 1 16.02913332 3.268610348 24.99485062 0.724924986 0.822950369 0.092213431 0.118516981 390.3355959 324671.8497 0.029971585 0.040576328 1856.138369 -3.268610348 0.098025383 RGDSQECS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGDSQECSPR 10 1 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 RGDS(0.171)QECS(0.829)PR 88.092 0.013167 38929000 31499 39624 34544 35880 39273 49042 38154 37521 37130 43709 TRUE FALSE 32742.60484 46429.11377 35444.24502 42976.95691 32597.38949 37652.73874 35163.38978 37018.09237 35793.69855 52272.94169 0.626377697 0.88820549 0.678061036 0.822164499 0.623599676 0.720310308 0.672688176 0.708169297 0.684746207 1 15.67377673 -0.724250202 6.441155948 1.000000002 0.716243435 0.543462516 0.07866238 1.04E-09 4.84E-10 0.06972536 0.016434425 0.188690397 0.724250202 -0.283756566 RGDTVATLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGDTVATLSER 11 1 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ;; 163.99 3.74E-05 340148000 170446 409370 361720 323997 335516 417720 276854 301118 323605 444280 FALSE TRUE 177175.3397 479676.113 371146.7204 388082.6396 278485.1102 320710.8606 255153.4601 297082.0057 311958.5193 531328.1597 0.333457462 0.90278692 0.698526351 0.730401038 0.524130154 0.603602227 0.480218214 0.559130926 0.587129655 1 19.01924365 -1.842344324 5.657440997 1.050461874 0.606548616 0.402145748 0.14543783 0.070837949 0.001974038 0.10776229 0.032236437 0.014376583 1.842344324 -0.443913258 RGDTWHDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGDTWHDRDR 10 2 Q9UBU9;Q9UBU9-2;E9PIN3;E9PMV7;E9PLA7 Q9UBU9 NXF1 Nuclear RNA export factor 1 0 ; 128.51 0.00018425 31418000 6651.8 16110.3 12574.5 11495.2 19714.6 15719.2 9151.5 12569.5 11438.3 21786.9 FALSE TRUE 6914.4182 18877.1187 12902.2018 13768.91625 16363.51933 12068.65403 8434.181517 12401.02641 11026.63782 26055.62592 0.26537141 0.724493004 0.495179116 0.52844312 0.6280225 0.463188029 0.323699056 0.475944291 0.423196044 1 14.66930729 -1.282383875 3.340927371 1.002035918 0.486037355 0.604539438 0.125905868 51055989.17 75402503.46 1064570.158 0.031200685 0.052193464 1.282383875 -0.515998563 RGEAHLAVNDFELAR ddPTM_MDA-MB-175_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 ;;;;; 207.55 2.17E-09 7125860000 2205272 2395186 2471540 2153980 3026400 3115320 2424154 2491093 2554173 2596400 FALSE TRUE 2292337.841 2806540.564 2535950.363 2580030.815 2511973.609 2391834.143 2234142.475 2457703.973 2462248.813 3105114.869 0.738245746 0.903844361 0.816700982 0.83089706 0.808979286 0.770288458 0.71950397 0.791501789 0.792965451 1 21.56621521 -1.543915313 2.780000768 1.010911713 0.797430607 0.614009548 0.048286441 16449819.61 17057328.61 1346637.46 0.012920416 0.028581478 1.543915313 -0.213481106 RGEDVETSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGEDVETSKK 10 2 O60869;O60869-2;O60869-3 O60869 EDF1 Endothelial differentiation-related factor 1 0 ;;; 155.99 6.60E-06 1704420000 2379640 1403938 1894600 1280293 2857796 2415568 2520823 1927832 2288480 1313621 FALSE TRUE 2473590.025 1645053.43 1943974.832 1533531.134 2372028.857 1854588.94 2323234.306 1901992.565 2206118.052 1570999.884 1.574532277 1.047137843 1.237412461 0.976149744 1.509884807 1.180515008 1.478825256 1.210689182 1.404276394 1 20.58325164 4.763506047 23.80142488 1.243635153 1.574533062 0.245256895 0.180730442 5743.748731 5480168.175 0.040250248 2.569167918 58010.42497 -4.763506047 0.330897908 RGEEGHDPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGEEGHDPKEPEQLR 15 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 216.68 1.31E-12 3011780000 1496160 1143060 1425860 1009170 1738700 1786810 1447010 1366100 1468890 994980 FALSE TRUE 1555229.552 1339371.663 1463019.083 1208780.814 1443156.395 1371850.457 1333589.575 1347789.664 1416024.936 1189927.281 1.306995458 1.125591189 1.229502934 1.015844273 1.212810579 1.152885961 1.120731995 1.132665572 1.19000964 1 20.18244198 -5 0.106188416 0.541215158 1.249570225 0.341503978 0.072014429 206.1468029 1.469552018 21.24495394 0.944729335 1.00E-05 5 0.708355067 RGEEGHDPKEPEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGEEGHDPKEPEQLRK 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 143.67 8.33E-07 1058990000 1507410 825900 1192930 684490 1838650 1563720 1285620 1171680 1396940 754190 FALSE TRUE 1566923.711 967741.9004 1224018.736 819880.079 1526116.93 1200569.728 1184849.745 1155975.546 1346664.402 901959.0907 1.737244768 1.072933252 1.357066799 0.908999186 1.692002382 1.331068937 1.313640228 1.281627469 1.493043771 1 19.78270247 -1.07631236 4.51279286 0.999977194 1.336096665 0.162229875 0.238290688 5.00E-05 1.02E-05 0.210882721 0.049702164 0.083885644 1.07631236 0.336119471 RGEFCIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGEFCIAK 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 82.749 0.031212 568720000 275700 254460 204930 168260 498240 332070 270950 189040 242670 317800 FALSE TRUE 286584.8489 298161.5256 210270.6442 201541.3258 413549.3428 254951.7751 249712.231 186506.228 233936.3541 380066.8254 0.754038053 0.784497635 0.553246509 0.530278657 1.088096396 0.670807758 0.657021909 0.490719567 0.615513743 1 18.53589358 2.488479006 24.85998978 0.635806533 0.737869915 0 0.18889761 1653.336919 3618852.619 0.063065889 0.056311348 307.9491473 -2.488479006 0.102063382 RGEGDAPFSEPGT(ph)TSTQRPSSPETATK ddPTM_MDA-MB-175_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(0.01)EPGT(0.429)T(0.064)S(0.01)T(0.133)QRPS(0.075)S(0.279)PET(0.001)ATK 236.27 8.05E-45 1486600000 883540 595200 858820 699560 821740 1089500 985050 743540 856770 532680 TRUE FALSE 918422.8414 697420.97 881201.5547 837930.88 682060.9283 836480.1365 907839.2071 733574.0625 825935.0151 637048.4472 1.441684452 1.094769123 1.383256734 1.315333055 1.070657862 1.313055766 1.425070905 1.151520054 1.296502674 1 19.28104357 -3.528370222 0.364635729 1.27E-07 1.277603013 0.307036813 0.124591309 187.4929988 4.151716221 143.2117607 0.084584555 0.000296231 3.528370222 1.277602887 RGEGDAPFSEPGTT(ph)STQRPSSPETATK ddPTM_MDA-MB-175_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(0.008)EPGT(0.121)T(0.483)S(0.121)T(0.121)QRPS(0.121)S(0.023)PET(0.001)ATK 119.65 0.00036012 1618600000 743410 466840 623170 499870 734930 774930 797870 667950 684740 397390 TRUE FALSE 772760.4008 547016.1385 639410.3221 598742.794 610006.8611 594964.2517 735330.8646 658997.2228 660096.3412 475250.962 1.626004917 1.1510048 1.345416155 1.259845517 1.28354682 1.251894892 1.547247504 1.386629961 1.388942672 1 18.85833002 -1.972865097 2.734376752 0.700273396 1.355576502 0.394238921 0.133791743 13002992.52 4073202.94 24564242.78 0.031945573 0.010644736 1.972865097 0.655303106 RGEGDAPFSEPGTTSTQRPS(ph)S(ph)PETATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGEGDAPFS(0.004)EPGT(0.03)T(0.095)S(0.099)T(0.101)QRPS(0.79)S(0.813)PET(0.061)AT(0.007)K;RGEGDAPFSEPGT(0.118)T(0.24)S(0.245)T(0.254)QRPS(0.498)S(0.526)PET(0.108)AT(0.01)K 58.21 0.033895 293500000 111868 90708 124008 87273 127602 132975 118974 103703 105825 89305 TRUE FALSE 116284.635 106286.3934 127239.7504 104535.3389 105912.2576 102093.5715 109648.507 102313.0309 102016.3789 106802.6049 1.088780888 0.995166677 1.191354373 0.978771436 0.991663618 0.955909002 1.026646373 0.957963816 0.955186243 1 16.70458731 3.602220205 22.22359869 0.980020877 1.082615014 0.516789756 0.048892539 5.224683451 909.0562933 0.012154887 0.018830302 4001.475893 -3.602220205 0.102594136 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFSEPGT(0.04)T(0.122)S(0.122)T(0.122)QRPS(0.292)S(0.292)PET(0.008)AT(0.001)K;RGEGDAPFS(0.013)EPGT(0.111)T(0.111)S(0.111)T(0.037)QRPS(0.504)S(0.109)PET(0.004)ATK;RGEGDAPFSEPGTTSTQRPS(0.499)S(0.499)PET(0.001)ATK 152.19 3.86E-08 6398970000 771565 556802 718438 582968 865097 908907 906447 747765 770989 446962 TRUE FALSE 802026.982 652428.4122 737161.0845 698277.3304 718048.1209 697827.1239 835397.3156 737742.4333 743241.2565 534535.6463 1.500418143 1.220551738 1.379068149 1.306325098 1.343311949 1.305482859 1.562846784 1.380155727 1.390442829 1 19.02792663 -1.105467705 5.779801746 0.999997463 1.375422475 0.598183413 0.09257166 2.93E-06 4.54E-07 0.086868656 0.020475 0.078439045 1.105467705 0.375425012 RGEGDAPFSEPGTTSTQRPSS(ph)PETATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RGEGDAPFS(0.021)EPGT(0.04)T(0.04)S(0.003)T(0.004)QRPS(0.04)S(0.812)PET(0.038)AT(0.002)K;RGEGDAPFSEPGTTSTQRPS(0.199)S(0.8)PETATK 201.85 2.29E-25 2194800000 975090 725160 984270 768050 1071550 1180890 1194660 930300 1021340 606320 TRUE FALSE 1013587.306 849700.589 1009920.885 919967.9976 889408.3137 906646.1941 1101019.428 917830.8502 984582.1729 725116.7953 1.397826271 1.171812037 1.392769953 1.26871699 1.226572491 1.250345048 1.518402876 1.265769675 1.357825635 1 19.46785386 -1.23258419 4.923290156 0.999947685 1.313954665 0.491716829 0.096552899 5.23E-05 8.16E-06 0.088236689 0.020794129 0.058535025 1.23258419 0.31400698 RGEIIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGEIIAK 7 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 137.88 0.0045531 1193220000 1929680 1595370 1915600 1507970 2321200 2327420 2232810 1837330 1905920 1477030 FALSE TRUE 2005865.256 1869362.387 1965522.11 1806241.965 1926643.253 1786911.977 2057796.518 1812703.597 1837326.312 1766425.749 1.135550281 1.058273968 1.112711423 1.022540555 1.090701522 1.01159756 1.164949344 1.026198581 1.040137867 1 20.75240168 1.384285591 0.010405076 3.55E-07 2.104668325 0.253546001 0.046475687 1359.581315 13.63805869 1383.814247 1372.44216 24.22621633 -1.384285591 2.10466797 RGES(ph)LDNLDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(0.999)LDNLDS(0.001)PR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(1)LDNLDSPR 236.24 4.81E-16 12479850000 5905580 6249610 7304350 6246120 8360120 8614040 8078330 7504050 7283580 5890250 TRUE FALSE 6138736.859 7322931.902 7494707.362 7481583.893 6939069.789 6613559.757 7445129.386 7403470.484 7021445.379 7044331.712 0.871443468 1.039549556 1.063934475 1.062071492 0.985057217 0.938848428 1.056896479 1.05098266 0.996751099 1 22.74803142 4.741985918 24.3678651 1.024852567 0.871443385 0.570030725 0.039020463 176.6990895 1256969.16 0.009937237 0.071947961 55205.95384 -4.741985918 -0.153409182 RGESLDNLDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RGES(0.134)LDNLDS(0.866)PR 74.769 0.0083039 0 63154 86223 83754 81478 107080 120240 101140 91678 104590 94934 TRUE FALSE 65647.36869 101031.1295 85936.69804 97594.10521 88878.57985 92316.08225 93212.38252 90449.20636 100825.8263 113534.4997 0.578215158 0.889871623 0.756921449 0.859598673 0.782833237 0.813110398 0.821004917 0.796667151 0.888063334 1 16.79277123 -5 0.091600441 1.631518758 0.643413638 0.486448748 0.07443142 185.5430845 1.177854336 22.91159238 1.53929322 1.00E-05 5 -0.98810512 RGESLDNLDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGESLDNLDSPR 12 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 127.79 0.0004224 178310000 133200 163520 149950 123480 178460 173120 140800 140700 124500 137510 FALSE TRUE 138458.8389 191603.288 153857.8202 147903.9754 148125.4329 132915.5037 129763.7281 138814.1466 120019.2693 164452.4517 0.841938429 1.165098398 0.935576324 0.899372274 0.900718909 0.8082306 0.78906533 0.844098979 0.729811371 1 17.32731099 3.450255212 1.41829712 0.825714352 1.003466056 0.271976723 0.099866218 0.443503978 1.814303421 0.030806922 0.056254327 2820.039631 -3.450255212 0.177751704 RGEVPAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGEVPAELR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ;;;; 145.99 0.0001537 1589445000 991307 1102063 1012202 1158745 1163168 1369850 1280617 1141124 991681 1031200 FALSE TRUE 1030444.566 1291333.747 1038580.816 1387941.302 965453.1188 1051723.098 1180238.893 1125829.099 955990.5945 1233243.896 0.835556185 1.047103295 0.842153623 1.125439426 0.782856596 0.8528103 0.957019854 0.912900605 0.775183723 1 20.23402672 3.195091199 24.99999896 0.882404921 0.960003311 0.131922006 0.103411523 287.0173082 165067.5722 0.02813355 0.033626217 1567.080113 -3.195091199 0.07759839 RGFAFVTFDDHDSVDKIVIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGFAFVTFDDHDSVDKIVIQK 21 2 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" 0 178.75 3.60E-17 20378000 14089 24539 32436 17523 42733 37321 20506 32849 30600 34935 FALSE TRUE 14645.2446 28753.38236 33281.30881 20988.9971 35469.25992 28653.76336 18898.68614 32408.71289 29498.71198 41779.84438 0.350533728 0.688211811 0.796587668 0.502371357 0.848956248 0.685827431 0.452339793 0.775702097 0.706051265 1 15.3505195 -5 0.173108706 2.376086103 0.573221586 0.37161219 0.147538199 148.5252446 1.411322994 70.13688667 0.493434285 1.00E-05 5 -1.802864517 RGFEGSCSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGFEGSCSQK 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 0 ; 148.28 4.07E-05 209650000 239840 185801 210870 164561 269040 283000 228960 215420 229650 220920 FALSE TRUE 249309.0684 217710.8764 216365.4454 197110.6746 223308.6769 217277.5389 211013.5169 212532.6473 221384.9414 264205.0442 0.943619639 0.824022407 0.818930032 0.746051898 0.845209741 0.822382251 0.798673309 0.804423125 0.837928519 1 18.01129849 0.904332595 10.24773446 0.999999998 0.820982205 0.550505114 0.046934824 11.47107093 1229.351734 0.044028071 0.011012246 8.022922457 -0.904332595 -0.179017793 RGFEVVYMTEPIDEYCVQQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGFEVVYMTEPIDEYCVQQLK 21 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 122.01 4.61E-05 128660000 53892 58019 65415 51995 90417 74893 52416 59827 61107 56634 FALSE TRUE 56019.69777 67983.31192 67119.76864 62279.45581 75047.95064 57500.23576 48307.49696 59025.11692 58907.77101 67730.34798 0.827098922 1.003734869 0.990985144 0.919520683 1.108040234 0.848958222 0.71323267 0.871472223 0.869739678 1 16.04751479 2.525235482 24.98861779 0.841301281 0.970968988 0.24355456 0.093227775 454.3379027 235964.2577 0.028839097 0.027189271 335.1471128 -2.525235482 0.129667707 RGFGFVTFDDHDPVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGFGFVTFDDHDPVDK 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 119.46 0.00012516 2600070000 3236290 2155730 2790680 2165730 3597620 3781860 3428240 2888760 2978660 2018980 FALSE TRUE 3364061.228 2525959.858 2863407.413 2594104.93 2986097.837 2903580.33 3159525.591 2850040.897 2871458.608 2414560.475 1.393239582 1.046136506 1.185891777 1.074359063 1.236704513 1.202529553 1.30853032 1.18035598 1.189226212 1 21.20332917 0.520714281 2.513043567 1.000005934 1.198400398 0.288093708 0.09519181 9.611709559 48.72482835 0.085838353 0.022880054 3.316761789 -0.520714281 0.198394465 RGGADVNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ;; 128.03 0.00068734 756040000 521242 765780 616360 610380 730270 847770 593580 636480 623500 775790 FALSE TRUE 541821.0366 897296.7581 632422.8479 731111.3422 606138.9662 650888.2656 547053.6486 627949.0267 601060.3568 927791.1971 0.583990275 0.967132218 0.68164351 0.788012803 0.653313987 0.701546067 0.589630135 0.676821497 0.647840116 1 19.82344063 -1.214223666 4.426234629 1.00009944 0.701053871 0.424548683 0.105144515 12976448034 2303647084 13565817.54 0.023820941 0.061062746 1.214223666 -0.299045569 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942;P31942-3;P31942-4;P31942-5 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;; 205.58 7.90E-27 1510852000 331994 390330 380927 349655 387542 497876 373196 370118 399897 393498 FALSE TRUE 345101.3795 457366.1412 390854.2706 418815.7154 321667.7493 382251.8444 343943.9224 365157.1736 385504.7851 470596.3991 0.73332771 0.97188619 0.830550916 0.889967956 0.683532109 0.812271078 0.730868156 0.775945533 0.819183457 1 18.84413076 RGGGS(ph)GGGEES(ph)EGEEVDED ddPTM_MDA-MB-175_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 205.63 2.69E-16 655310000 578520 675130 665010 648050 775480 936030 670390 686510 647160 645440 TRUE FALSE 601360.4163 791078.3257 682340.7069 776232.3558 643664.1866 718651.2182 617843.0801 677308.4564 623868.838 771901.6103 0.77906356 1.024843471 0.88397368 1.005610489 0.833868174 0.931014016 0.800416882 0.87745439 0.808223263 1 19.55805744 3.206011316 24.9991634 0.867191166 0.927806688 0.067792768 0.083892054 406.1159946 311912.2929 0.022173042 0.026503812 1606.983123 -3.206011316 0.060615523 RGGGSGGGEES(ph)EGEEVDED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 RGGGSGGGEES(1)EGEEVDED;RGGGS(0.024)GGGEES(0.976)EGEEVDED;RGGGS(0.002)GGGEES(0.998)EGEEVDED;RGGGS(0.02)GGGEES(0.98)EGEEVDED;RGGGSGGGEES(1)EGEEVDED 275.96 1.98E-39 2649181000 1368649 1374158 1449670 1317759 1896960 1988591 1577875 1573778 1473736 1337025 TRUE FALSE 1422684.319 1610158.947 1487449.591 1578407.797 1574515.417 1526770.878 1454197.034 1552684.08 1420696.529 1598989.45 0.889739654 1.006985348 0.930243531 0.987128337 0.984694062 0.954834866 0.909447548 0.971040853 0.8884965 1 20.60872899 2.467623975 24.53909698 0.94084769 0.963012951 0.034521257 0.04191091 501.1093008 1294754.613 0.013378536 0.011206917 293.5107246 -2.467623975 0.022165261 RGGMIVDPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGGMIVDPLR 10 1 Q5QPM7;H0Y555;F5H4Z3;Q92530 Q5QPM7;Q92530 PSMF1 Proteasome inhibitor PI31 subunit 0 91.855 0.015818 316120000 187640 221690 253730 216120 297010 291080 223580 214330 209760 280540 FALSE TRUE 195048.1721 259763.533 260342.4122 258867.8909 246524.3463 223481.0814 206055.2154 211457.2569 202210.7786 335506.4417 0.581354477 0.774243057 0.775968446 0.771573534 0.734782751 0.666100717 0.614161726 0.630262882 0.602703118 1 18.35598094 -1.172423891 4.195800746 1.000083906 0.685361679 0.633682165 0.072187702 11447580.43 3198779.04 11080.55888 0.018485616 0.067232012 1.172423891 -0.314722227 RGGPNYQEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGGPNYQEGLR 11 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 ;;;;; 179.95 1.10E-05 3860650000 985690 1270940 1167250 1066330 1427140 1506500 1098210 1243280 1222700 1494300 FALSE TRUE 1024605.802 1489214.058 1197669.494 1277246.891 1184555.253 1156638.206 1012129.431 1226615.865 1178695.266 1787079.475 0.573340927 0.833322793 0.670182558 0.714711858 0.662844193 0.64722259 0.566359496 0.686380143 0.659565107 1 20.76917236 -1.56248661 4.26455013 1.004488972 0.670432294 0.665743342 0.070512862 0.002927978 0.000300391 0.06642508 0.015476403 0.027385041 1.56248661 -0.334056678 RGGSDT(ph)NLNFDVPDGILDFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGGSDTNLNFDVPDGILDFHK 21 1 G3V207;Q9ULS5;F8VQF2 G3V207 TMCC3 Transmembrane and coiled-coil domains protein 3 1 RGGS(0.255)DT(0.745)NLNFDVPDGILDFHK 133.15 7.91E-06 11755000 12168 12385 9544.1 12594 15665 15661 11937 9300.8 8020.2 11224 TRUE FALSE 12648.40204 14512.02741 9792.827087 15085.05561 13002.2689 12023.97009 11001.34675 9176.137989 7731.554569 13423.1279 0.942284252 1.081121145 0.729548817 1.123810763 0.968646726 0.895765144 0.819581459 0.683606538 0.575987551 1 13.71243327 2.203176732 2.186572386 0.723018071 0.967832277 0.305685847 0.140303445 0.319504036 3.078613449 0.063133016 0.04112498 159.6528709 -2.203176732 0.244814207 RGILTLK ddPTM_MDA-MB-175_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 ; 143.61 0.0038644 21340000000 3514800 3227800 3402800 2694100 6131900 5010100 4713000 3768900 3668100 4728000 FALSE TRUE 3653567.018 3782149.541 3491479.763 3226984.939 5089601.828 3846580.204 4343582.745 3718384.06 3536085.798 5654361.077 0.646150284 0.6688907 0.617484401 0.570707264 0.900119706 0.680285562 0.768182768 0.657613479 0.625373185 1 22.43093258 3.282075933 24.99999672 0.744151632 0.62829094 0.277270008 0.11019896 215.4197739 123759.3816 0.029251886 0.039607015 1914.590648 -3.282075933 -0.115860692 RGKNENESEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGKNENESEKR 11 3 P47813;O14602;A6NJH9 P47813 EIF1AX;EIF1AY "Eukaryotic translation initiation factor 1A, X-chromosomal;Eukaryotic translation initiation factor 1A, Y-chromosomal" 0 ;; 137.59 3.30E-05 104423000 94989 60886 80011 45558 128297 94151 68472 70603 93535 76182 FALSE TRUE 98739.23907 71342.69687 82096.15239 54569.23642 106489.1218 72285.85712 63104.98572 69656.68227 90168.69362 91108.40431 1.083755553 0.783052863 0.901082101 0.598948438 1.168817768 0.79340493 0.692636274 0.764547275 0.989685796 1 16.47529652 RGLDDDRGPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGLDDDRGPWR 11 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 94.767 0.0046448 401849000 94834 136132 131312 100772 150403 163029 76894 113630 106158 192971 FALSE TRUE 98578.11955 159511.612 134734.0986 120704.4008 124837.5518 125167.9855 70866.84735 112106.9757 102337.3943 230779.9728 0.427151968 0.691184812 0.583820584 0.523028057 0.540937544 0.542369357 0.307075378 0.485774283 0.4434414 1 17.81615851 -1.507007397 6.040175372 1.000520693 0.505298313 0.702751316 0.096584133 0.000705652 5.76E-05 0.097441352 0.022944209 0.031116633 1.507007397 -0.49522238 RGLDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGLDEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 139.97 0.0042586 631628000 667030 782019 743047 756071 877264 958511 810318 787701 735579 801507 FALSE TRUE 693364.8595 916324.68 762411.4152 905619.5872 728146.9786 735911.3466 746803.1578 777143.1565 709105.6555 958546.9509 0.723349919 0.955951797 0.795382443 0.944783755 0.759636216 0.76773636 0.779099195 0.810751269 0.739771437 1 19.87048957 3.198916358 24.99999708 0.797011233 0.857838969 0.043908321 0.092961319 361.0180809 227659.8751 0.024412352 0.029178705 1580.943531 -3.198916358 0.060827736 RGLEVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGLEVSK 7 1 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;; 111.95 0.010365 1360780000 1830690 1588070 1812390 1437740 2454170 2271680 2127660 1811660 1892380 1749820 FALSE TRUE 1902967.055 1860808.669 1859622.372 1722120.681 2037011.06 1744116.748 1960888.45 1787377.661 1824273.613 2092663.727 0.909351575 0.889205774 0.888638891 0.822932351 0.973405824 0.833443389 0.937029884 0.854116043 0.871747137 1 20.99690907 -1.001788998 4.857974104 1.000001616 0.885779827 0.381075258 0.043323022 6.78E-07 1.39E-07 0.037473405 0.008832441 0.099588915 1.001788998 -0.114221789 RGLKPSCTIIPLMK ddPTM_MDA-MB-175_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 ; 93.958 0.0024497 2225600000 5329100 3693900 5138200 3822700 7168500 6361700 5197300 4861400 5853700 4375900 FALSE TRUE 5539496.983 4328298.59 5272105.713 4578818.65 5950000.931 4884291.587 4789922.045 4796240.885 5643026.48 5233273.823 1.058514645 0.82707283 1.007420191 0.874943449 1.136955782 0.933314738 0.915282136 0.916489572 1.078297576 1 22.31928232 3.511436528 0.005327539 1.920884369 1.51E-08 0.008053336 0.092454142 87395.03183 115.6167343 20345.08464 21343.93061 3246.657887 -3.511436528 -1.920884354 RGLLYDS(ph)DEEDEERPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 261.46 2.14E-27 4764660000 597848 590712 667100 523788 885385 821369 651597 753124 654044 686299 TRUE FALSE 621451.5007 692162.1909 684485.174 627391.703 734887.574 630618.4977 600523.1245 743029.6046 630505.0842 820766.1491 0.757160248 0.843312302 0.833958826 0.764397635 0.895367791 0.768329077 0.731661662 0.905287828 0.768190897 1 19.64661171 -5 0.41478958 4.338321518 0.80971419 0.498703379 0.057447222 721.72723 4.781119526 2192.07311 0.032438694 1.00E-05 5 -3.528607328 RGLLYDS(ph)DEEDEERPARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGLLYDSDEEDEERPARK 18 3 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 RGLLYDS(1)DEEDEERPARK;RGLLYDS(1)DEEDEERPARK 129.92 0.00011145 514300000 202793 157465 192203 135386 281430 263750 188423 181186 200494 164637 TRUE FALSE 210799.4242 184508.3888 197211.9681 162164.9467 233592.6291 202498.0597 173653.9129 178757.498 193278.2601 196894.468 1.070621366 0.937092803 1.001612539 0.823613524 1.186384927 1.028459874 0.881964408 0.907884817 0.981633776 1 17.58706305 2.250364983 24.96566529 0.93036737 1.004184498 0.099457105 0.092541454 461.566714 976190.4009 0.032257229 0.026785871 177.9774511 -2.250364983 0.073817128 RGMDDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGMDDDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 61.962 0.092687 27354000 9317.9 8314.2 10182 9944.2 11416 13231 7575 9413.9 10833 6869.3 FALSE TRUE 9685.777887 9742.099175 10447.35128 11911.13308 9475.512398 10158.30077 6981.251706 9287.722069 10443.12245 8215.207814 1.179005827 1.185861562 1.271708704 1.449888225 1.153411163 1.236523895 0.849796118 1.130552297 1.271193947 1 13.00408136 2.434334655 24.9999897 1.068263911 1.250851379 0.33979325 0.125051721 166.701881 97402.18705 0.044047037 0.036852425 271.8533284 -2.434334655 0.182587467 RGMDDDRGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGMDDDRGPR 10 2 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 82.417 0.071817 51609000 27713 34950 36765 33589 39846 50488 31326 35117 34280 42010 FALSE TRUE 28807.13064 40952.39063 37723.1261 40232.80395 33072.99115 38762.92715 28870.58626 34646.31405 33046.2695 50241.05517 0.573378297 0.815118044 0.750842632 0.800795362 0.658286157 0.771538874 0.57464132 0.68960164 0.657754288 1 15.61657914 -1.114620929 5.246214247 1.000006759 0.701622695 0.550283838 0.081575229 6.25E-06 1.05E-06 0.076494287 0.018029468 0.076803157 1.114620929 -0.298384064 RGNDPLT(ph)SSPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLT(0.785)S(0.175)S(0.04)PGR 77.597 0.054151 1235500000 1202800 1464500 1407700 1293200 1561500 1834900 1247900 1533800 1407800 1465500 TRUE FALSE 1250287.473 1716016.483 1444385.818 1548991.1 1296076.788 1408772.283 1150086.337 1513241.92 1357133.553 1752636.666 0.713375166 0.979105662 0.824121648 0.88380617 0.739501126 0.803801672 0.656203513 0.863408799 0.774338218 1 20.74109552 5.021641521 19.08588427 0.823872263 0.427355491 0.11042232 0.099177321 3458.30319 27288.50305 0.021853232 43858.69354 105109.3913 -5.021641521 -0.396516772 RGNDPLTSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RGNDPLTS(0.001)S(0.999)PGR;RGNDPLT(0.015)S(0.137)S(0.848)PGR;RGNDPLT(0.067)S(0.183)S(0.75)PGR 197.13 2.10E-07 4478500000 809060 943210 1016810 877000 1110810 1290190 1116260 1065560 957216 950660 TRUE FALSE 841002.3135 1105198.98 1043308.904 1050467.982 921994.913 990562.9255 1028764.624 1051277.911 922765.9831 1136923.626 0.73971751 0.972096063 0.917659622 0.923956508 0.810955892 0.871266023 0.90486696 0.924668894 0.8116341 1 20.11670391 -1.7987351 2.669883234 1.033864833 0.883204764 0.233945536 0.0663411 13484312.46 10641693.67 2973719.057 0.014951148 0.01589516 1.7987351 -0.150660069 RGNGLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGNGLIK 7 1 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ; 128.86 0.0059592 1589470000 1509550 1347240 1657690 1303710 2108400 1980720 1848050 1689360 1749810 1371520 FALSE TRUE 1569148.2 1578617.99 1700890.763 1561579.947 1750014.921 1520727.798 1703195.012 1666716.892 1686834.68 1640243.085 0.956655885 0.962429292 1.036974811 0.952041781 1.066924127 0.927135625 1.038379633 1.016140173 1.028405299 1 20.64547821 7.347815799 0.512707602 1.012399464 3.92E-09 0.152973406 0.04039401 95.21804948 1.954248232 0.019030081 97.88795572 22274901.83 -7.347815799 -1.01239946 RGNVAGDSK ddPTM_MDA-MB-175_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 ;;;;;;;; 164.66 9.96E-05 14240412000 5203990 3792140 4789530 3808310 5723250 5744850 6611820 4980770 5137450 3208900 FALSE TRUE 5409447.544 4443410.546 4914349.086 4561582.351 4750414.009 4410695.652 6093568.272 4914010.925 4952554.178 3837622.517 1.409583022 1.157855033 1.280571256 1.188648006 1.237853381 1.149330251 1.587849833 1.280483139 1.290526662 1 21.87178138 RGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACK 50 2 P68104;A0A087WVQ9;A0A087WV01 P68104 EEF1A1 Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 ; 292.25 6.02E-103 601970000 1594930 1343800 1742870 1040230 2357220 2201710 1510150 1770540 2060630 1527210 FALSE TRUE 1657899.068 1574587.197 1788290.624 1245984.389 1956540.586 1690396.22 1391780.497 1746808.807 1986468.329 1826437.559 0.907722829 0.862108419 0.979114022 0.682193806 1.071233219 0.925515472 0.762019205 0.956402149 1.087619075 1 20.800601 1.465097236 6.611927361 1.038445895 0.886275196 0.276605526 0.10316092 0.183589582 20.31277027 0.058094927 0.024882129 29.18080284 -1.465097236 -0.152170699 RGNVCGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGNVCGDSK 9 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;; 157.75 0.00010873 3459730000 2591290 2008670 2400070 1683510 3209350 3153420 2987160 2395850 2725900 2228190 FALSE TRUE 2693596.13 2353643.447 2462617.796 2016503.253 2663825.833 2421085.996 2753018.594 2363737.55 2627795.391 2664761.169 1.010820842 0.883247427 0.92414203 0.75672945 0.999648998 0.908556468 1.033120201 0.887035422 0.986127921 1 21.34557481 RGPAEESSSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPAEESSSWR 11 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 143.55 5.95E-05 902440000 341540 481350 492330 449830 642140 642950 524410 501670 600550 547250 FALSE TRUE 355024.2629 564018.1181 505160.5243 538805.0314 532989.2722 493634.6065 483305.3739 494945.9342 578936.3228 654473.1598 0.542458094 0.861789532 0.771858275 0.823265283 0.814379114 0.754247289 0.738464774 0.756250928 0.884583751 1 19.3199745 -5 0.193546202 2.008476329 0.732620481 0.445212466 0.083726279 132.7227773 1.304555383 51.49285015 0.209102324 1.00E-05 5 -1.275855848 RGPCIIYNEDNGIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPCIIYNEDNGIIK 15 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 222.16 2.31E-12 2266800000 1258250 978800 1196630 935050 1564890 1582000 1404340 1241750 1342730 1021830 FALSE TRUE 1307926.682 1146901.286 1227815.161 1120000.099 1298890.557 1214604.475 1294264.161 1225106.372 1294405.41 1222038.024 1.07028313 0.938515221 1.00472746 0.916501841 1.062888822 0.993917089 1.059103019 1.002510845 1.059218603 1 20.22085775 3.212781935 24.99974131 1.028261981 0.980951739 0.207546083 0.044999977 328.5595698 318630.7946 0.011957267 0.014296347 1632.232175 -3.212781935 -0.047310242 RGPEEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPEEDR 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 113.26 0.009894 132259000 104092 159501 145655 152269 137678 186337 137091 145771 141929 156588 FALSE TRUE 108201.6325 186894.056 149450.889 182387.3537 114275.5427 143063.0557 126345.4492 143817.1782 136821.003 187268.4205 0.577788995 0.99800092 0.79805708 0.973935452 0.610223242 0.763946507 0.674675681 0.767973467 0.730614391 1 17.51474811 4.807533696 21.31421362 0.795011424 0.577771971 0.216452421 0.130276078 34664.56157 10708795.12 0.030003675 110.6636819 64199.80305 -4.807533696 -0.217239453 RGPEVTSQGVQT(ph)SSPACKQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPEVTSQGVQTSSPACKQEK 21 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.468)S(0.063)S(0.468)PACKQEK 120.08 0.0020796 79398000 143900 72490 97208 65763 140010 130560 112550 94234 131300 66206 TRUE FALSE 149581.2831 84939.59361 99741.32034 78770.72512 116211.1502 100239.4187 103728.0369 92970.94737 126574.5386 79177.79811 1.889182153 1.072770343 1.259713237 0.994858748 1.467723945 1.26600412 1.310064682 1.174204759 1.598611501 1 16.27280833 4.748212962 24.60612872 1.244728324 1.889182586 0.530805141 0.183514665 791.3155251 2017200.063 0.040574966 0.52426205 56003.21528 -4.748212962 0.644454262 RGPEVTSQGVQTS(ph)SPACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPEVTSQGVQTSSPACK 18 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.017)S(0.656)S(0.327)PACK;RGPEVTSQGVQT(0.004)S(0.661)S(0.334)PACK 178.19 5.51E-14 919680000 833730 548670 721230 640060 846130 1059990 999280 816410 885860 515800 TRUE FALSE 866646.3042 642899.8044 740025.8463 766661.9576 702305.1248 813823.3868 920953.8225 805467.3593 853978.0716 616861.1344 1.404929336 1.042211559 1.199663595 1.242843672 1.138514141 1.319297556 1.492967819 1.305751513 1.384392733 1 19.23458623 2.65097122 6.953885336 1.33494015 1.198525573 0.071533824 0.146006976 0.446681082 30.47730523 0.04403063 0.041474299 447.6836363 -2.65097122 -0.136414577 RGPEVTSQGVQTSS(ph)PACKQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPEVTSQGVQTSSPACKQEK 21 2 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB05;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 1 RGPEVTSQGVQT(0.161)S(0.024)S(0.815)PACKQEK 110.68 0.00013897 97936000 153920 69682 102020 65918 147020 137710 118720 104400 112910 60453 TRUE FALSE 159996.8805 81649.34145 104678.725 78956.38365 122029.5929 105728.9395 109414.4162 103000.6888 108846.3912 72297.60791 2.213031455 1.129350525 1.447886424 1.092102297 1.687878706 1.462412694 1.513389161 1.424676303 1.5055324 1 16.14166029 -2.04538537 2.287792962 0.397354184 1.47444959 0.201755676 0.293623617 10449771.54 3627057.684 32945419.39 0.065354493 0.009007715 2.04538537 1.077095407 RGPFELEAFYSDPQGVPYPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPFELEAFYSDPQGVPYPEAK 22 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ; 157.73 3.64E-09 419950000 1152790 897870 1148880 918640 1501330 1513110 1355320 1194840 1283880 949210 FALSE TRUE 1198303.039 1052072.188 1178820.757 1100344.25 1246134.463 1161713.134 1249086.477 1178825.124 1237673.41 1135189.526 1.055597336 0.926781092 1.038435195 0.969304442 1.097732524 1.023364916 1.100332983 1.038439042 1.090279096 1 20.11450175 3.24487869 24.99363946 1.060018532 0.99539789 0.304121702 0.044988902 163.6752648 647477.8673 0.011294554 0.014928644 1757.432649 -3.24487869 -0.064620641 RGPGLYYVDSEGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGPGLYYVDSEGNR 14 1 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ; 242.07 2.92E-17 2092400000 961300 1036280 1040330 1050820 1234590 1392830 1085900 1171740 1097860 1072320 FALSE TRUE 999252.8663 1214253.029 1067441.854 1258669.06 1024734.833 1069366.341 1000784.321 1156034.742 1058348.233 1282420.573 0.779192791 0.946844627 0.832364886 0.981479154 0.799063002 0.833865553 0.780386982 0.901447439 0.825273904 1 20.29043804 -0.961701189 4.181178126 1.000006239 0.857154759 0.309108162 0.065560655 17833552.73 34157001.73 1608.815496 0.014762049 0.109219155 0.961701189 -0.14285148 RGPGYTSGTNSEASNAS(ph)ETESDHRDELSDWSLAPTEEERESFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLR 44 3 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;A0A087WXC0 Q06787 FMR1 Fragile X mental retardation protein 1 1 RGPGYTSGTNS(0.001)EAS(0.052)NAS(0.628)ET(0.158)ES(0.158)DHRDELS(0.002)DWSLAPTEEERESFLR 55.834 0.011163 115200000 3841.8 5534 4717.8 6634.5 6210 7059.8 5393.9 6159.6 4981.2 5985.1 TRUE FALSE 3993.477231 6484.421451 4840.749744 7946.784298 5154.426418 5420.268442 4971.112024 6077.040637 4801.927585 7157.765753 0.557922314 0.905928145 0.676293401 1.110232518 0.720116667 0.757257031 0.694506106 0.849013623 0.670869619 1 12.80529362 -2.355828389 2.234296045 2.358678001 0.782237204 0.177245356 0.146103796 8277189.69 894086.2822 56951335.97 0.033247244 0.00440729 2.355828389 -1.576440797 RGPLT(ph)SGSDEENVALPLGDNVLTHNLGIPVLVVCTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTK 36 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 RGPLT(0.333)S(0.333)GS(0.333)DEENVALPLGDNVLTHNLGIPVLVVCTK 209.44 1.08E-30 237690000 258550 217710 265660 190280 315320 298110 262280 262920 253770 232490 TRUE FALSE 268757.7536 255099.999 272583.3178 227916.8161 261722.019 228878.4704 241721.8083 259395.9875 244636.8673 278041.9642 0.9666086 0.9174874 0.980367545 0.819720925 0.941304021 0.823179591 0.869371675 0.932938264 0.879855917 1 18.08494312 3.771339812 24.99629067 0.892307587 0.951087802 0.204769381 0.0534836 992.3837508 756755.0229 0.01279848 0.023070731 5906.630614 -3.771339812 0.058780215 RGPLTS(ph)GSDEENVALPLGDNVLTHNLGIPVLVVCTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTK 36 1 O43237;O43237-2;B4E2E0 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 RGPLT(0.269)S(0.366)GS(0.366)DEENVALPLGDNVLTHNLGIPVLVVCTK 183.1 2.48E-23 212880000 127810 106780 119010 104820 167270 152230 133820 125760 162340 119440 TRUE FALSE 132856.0375 125118.6344 122111.4984 125553.0831 138837.5051 116876.8896 123330.8387 124074.3929 156497.4151 142841.9812 0.930090975 0.875923404 0.854871218 0.878964868 0.971965692 0.818225067 0.863407506 0.868612938 1.095598183 1 17.12406052 1.246092763 24.99999258 1.047799107 0.880755169 0.68123578 0.045141804 79.70202508 264545.9575 0.030384604 0.010616731 17.62352435 -1.246092763 -0.167043937 RGPNYTSGYGTNSELSNPS(ph)ETESER ddPTM_MDA-MB-175_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(0.999)ET(0.001)ESER;RGPNYTSGYGTNSELSNPS(0.998)ET(0.002)ESER 221.59 6.85E-34 555170000 140844 137825 151791 164991 162031 184987 169677 147716 135859 142674 TRUE FALSE 146404.6299 161495.3716 155746.7982 197625.7274 134489.0285 142026.5728 156377.2734 145736.1086 130969.4611 170628.2386 0.858032826 0.946475055 0.912784422 1.158224037 0.788199126 0.832374371 0.916479445 0.854114828 0.767572016 1 17.3804969 RGPNYTSGYGTNSELSNPSETESER ddPTM_MDA-MB-175_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 ; 257.38 1.01E-44 369090000 65553 74532 75330 87614 75202 94654 81116 79249 72752 57609 FALSE TRUE 68141.08306 87332.29122 77293.16168 104943.7877 62419.1909 72672.043 74757.91596 78186.79678 70133.66973 68896.38056 0.989037196 1.267588958 1.121875504 1.523211914 0.905986503 1.054802043 1.085077552 1.134846216 1.017958696 1 16.07214057 3.182674951 24.99999696 1.050706987 1.221057165 0.313659453 0.137840303 112.9983239 50548.27317 0.038662565 0.046210631 1522.912497 -3.182674951 0.170350177 RGPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGPPEK 6 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 119.56 0.033528 371682000 499350 394340 486520 443500 552060 591750 627550 498870 503290 384490 FALSE TRUE 519064.7236 462064.8275 499199.1109 531222.9763 458221.0384 454325.0306 578360.9912 492183.4636 485176.6912 459823.454 1.128834815 1.004874422 1.085632119 1.155275947 0.99651515 0.988042316 1.257789237 1.070374857 1.055136894 1 18.81072053 RGPPPPPR ddPTM_MDA-MB-175_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 ;;; 121.62 0.0022857 242622000 144847 157952 167312 141369 182716 180369 166965 161796 173141 157972 FALSE TRUE 150565.6714 185079.0273 171672.2882 169331.3663 151657.9996 138481.0333 153877.847 159627.3893 166909.6892 188923.5888 0.796965971 0.979650177 0.908686359 0.89629552 0.802747823 0.733000226 0.814497798 0.84493096 0.883477231 1 17.52744332 RGPRT(ph)PPITTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPRTPPITTK 11 2 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RGPRT(1)PPITTK 127.36 0.013742 202810000 274580 221550 285650 227960 315550 347860 331250 269240 281830 228510 TRUE FALSE 285420.6304 259599.4891 293094.2737 273049.8076 261912.9237 267074.7869 305285.7594 265631.2782 271686.9934 273282.1594 1.044417356 0.949932076 1.072496918 0.999149773 0.958397446 0.977285848 1.117108267 0.97200373 0.994162934 1 18.06003175 RGPWWDDWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGPWWDDWER 10 1 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 96.334 0.010921 71990000 37782 47816 46644 49252 49316 59097 47071 51538 43033 46509 FALSE TRUE 39273.66253 56028.02604 47859.58096 58993.8986 40933.28394 45372.61737 43381.45202 50847.21741 41484.25074 55621.54808 0.706087189 1.007307922 0.860450358 1.060630289 0.735924931 0.815738126 0.779939673 0.91416401 0.745830567 1 15.76335628 4.783042701 21.60102983 0.873177062 0.706083769 0.184960913 0.108675428 8512.773215 4133347.607 0.024816395 8.558129794 60679.5989 -4.783042701 -0.167093293 RGQAALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGQAALDR 8 1 P40429;M0QYS1;Q8J015 P40429 RPL13A;RPL13a 60S ribosomal protein L13a 0 ;;;;; 144.5 0.00093712 1673190000 1767030 2093710 1913120 1783730 3187160 2844860 2132590 2044510 2005950 3179940 FALSE TRUE 1836793.709 2453288.406 1962977.479 2136546.47 2645407.682 2184184.379 1965432.023 2017106.688 1933756.251 3802988.359 0.48298694 0.645094903 0.516167102 0.56180726 0.695612879 0.574333701 0.516812527 0.530400437 0.508483347 1 21.85870209 -1.024473883 4.493640464 1.000017094 0.560814806 0.817297527 0.062536238 8112246.791 1849454.911 1448.422817 0.014628509 0.094520523 1.024473883 -0.439202288 RGQPAS(ph)PSAHMVSHSHSPSVVS ddPTM_MDA-MB-175_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(0.829)PS(0.168)AHMVS(0.004)HSHSPSVVS;RGQPAS(0.956)PS(0.044)AHMVSHSHSPSVVS;RGQPAS(0.989)PS(0.011)AHMVSHSHSPSVVS;RGQPAS(0.987)PS(0.013)AHMVSHSHSPSVVS 152.88 1.79E-08 1103213000 47254 283447 230013 263233 238136 357591 195225 287818 229866 303087 TRUE FALSE 49119.62441 332126.8173 236007.3277 315299.7017 197657.7278 274545.9096 179922.7544 283960.2705 221593.1676 362471.0947 0.135513218 0.916284973 0.651106616 0.869861642 0.545306179 0.757428423 0.496378213 0.783401145 0.611340244 1 18.46750643 -5 0.257327179 3.144715415 0.630733553 0.208592245 0.211407181 304.3876257 2.99873925 345.0163006 0.261368286 1.00E-05 5 -2.513981862 RGQS(ph)SPPPAPPICLR ddPTM_MDA-MB-175_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(0.5)S(0.5)PPPAPPICLR;RGQS(0.609)S(0.391)PPPAPPICLR 88.385 0.0041687 1194370000 491890 422610 493130 465850 544040 631750 493520 492830 518760 513860 TRUE FALSE 511310.197 495189.9801 505981.3729 557993.7396 451564.2751 485035.6368 454836.6128 486224.42 500089.9289 614541.0286 0.832019626 0.805788315 0.823348401 0.907984518 0.734799231 0.789264857 0.740124079 0.791199281 0.813761662 1 19.22914981 0.814248597 6.27284692 0.999999924 0.80105234 0.619189129 0.046098846 5.853653929 197.6823694 0.0454246 0.011411892 6.520015033 -0.814248597 -0.198947584 RGQSS(ph)PPPAPPICLR ddPTM_MDA-MB-175_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(0.075)S(0.925)PPPAPPICLR 69.747 0.029853 235400000 253890 247760 252340 214390 286910 362460 259050 242030 245560 235580 TRUE FALSE 263913.7732 290310.8527 258916.1877 256795.7021 238141.1407 278284.1581 238744.9841 238785.9837 236722.3436 281737.3905 0.93673677 1.030430686 0.918998317 0.911471855 0.845259269 0.987743081 0.847402553 0.847548078 0.840223384 1 18.10399152 4.044446025 4.737744559 0.888489627 0.983669713 0.240167344 0.059050515 0.229095175 11.56146708 0.014510633 0.032176645 11077.60881 -4.044446025 0.095180086 RGRS(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGRSPQPPAEEDEDDFDDTLVAIDTYNCDLHFK 33 2 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;M0QYZ0;M0R0K8;M0QYI8 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 RGRS(0.975)PQPPAEEDEDDFDDT(0.025)LVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;RGRS(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK 165.31 1.84E-14 1492050000 147506 165859 154695 110975.6 233270 216135 115097.9 164088.9 159743.3 225967 TRUE FALSE 153329.6508 194343.993 158726.4788 132926.2425 193618.8487 165940.9218 106076.2258 161889.5567 153994.1698 270240.9073 0.56738135 0.719150905 0.587351783 0.491880537 0.71646758 0.614048123 0.392524681 0.599056443 0.569840338 1 18.04388655 -1.653594051 2.781680691 1.045338179 0.583012006 0.653249614 0.090880066 21921414.45 19990634.2 7089316.378 0.021877096 0.022202708 1.653594051 -0.462326173 RGS(ph)ALGPDEAGGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGSALGPDEAGGELER 16 1 O75145-2;O75145;R4GN36;R4GNF1 O75145-2 PPFIA3 Liprin-alpha-3 1 RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER;RGS(1)ALGPDEAGGELER 158.92 9.86E-09 2922970000 970510 825712 947840 794636 1215152 1204584 1050267 932656 1090175 831445 TRUE FALSE 1008826.484 967521.6129 972541.4891 951812.629 1008600.897 924837.6216 967944.3282 920155.2718 1050939.815 994350.7288 1.014557997 0.973018458 0.978066854 0.957220226 1.014331129 0.930091963 0.973443575 0.925383011 1.056910589 1 19.92339529 2.758799584 24.98249145 0.968395009 0.984438302 0 0.038586444 3121.682426 3853324.426 0.011376286 0.012055327 573.8515825 -2.758799584 0.016043293 RGS(ph)ASGSEPAGDSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RGSASGSEPAGDSDR 15 1 P50747;A0A0C4DG27 P50747 HLCS Biotin--protein ligase;Biotin--[methylmalonyl-CoA-carboxytransferase] ligase;Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase;Biotin--[methylcrotonoyl-CoA-carboxylase] ligase;Biotin--[acetyl-CoA-carboxylase] ligase 1 RGS(0.898)AS(0.09)GS(0.006)EPAGDS(0.006)DR;RGS(0.983)AS(0.016)GS(0.001)EPAGDSDR;RGS(0.937)AS(0.03)GS(0.03)EPAGDS(0.003)DR;RGS(0.971)AS(0.014)GS(0.014)EPAGDSDR;RGS(0.491)AS(0.491)GS(0.018)EPAGDSDR;RGS(0.999)AS(0.001)GSEPAGDSDR;RGS(0.992)AS(0.008)GSEPAGDSDR 213.5 2.09E-10 1253633000 756211.9 773879.9 793443.8 751859.7 994964.9 1045781 890082.9 833777.7 860292.2 689098.8 TRUE FALSE 786067.7297 906787.7529 814121.5972 900575.3046 825841.1217 802914.2117 820315.8765 822602.2737 829330.4518 824114.5163 0.953833131 1.100317656 0.987874356 1.092779325 1.002095104 0.97427505 0.995390641 0.998165009 1.006329139 1 19.6524853 3.026072745 24.9792161 0.994367383 1.036717501 0.166773794 0.041276337 332.9355803 318969.4158 0.010807388 0.012916858 1061.873408 -3.026072745 0.042350118 RGS(ph)DAS(ph)DFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 2 RGS(1)DAS(1)DFDISEIQSVCSDVETVPQTHRPTPR 132.7 3.47E-08 174920000 7855.2 15602 7142.6 12663 14049 10543 8785.8 15816 8567.9 17130 TRUE FALSE 8165.329362 18281.52213 7328.742024 15167.7036 11660.956 8094.548031 8097.146039 15604.01239 8259.542953 20486.29553 0.398575201 0.892378132 0.357738763 0.740382935 0.569207643 0.395120144 0.39524696 0.761680528 0.403174061 1 14.32237151 -1.231860769 4.029044475 1.000343355 0.560900347 0.3574674 0.181631219 25295019.19 7733956.022 77992.99437 0.039431086 0.058632611 1.231860769 -0.439443009 RGS(ph)DASDFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(1)DASDFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.5)DAS(0.5)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.79)DAS(0.21)DFDISEIQSVCSDVETVPQTHRPTPR;RGS(1)DASDFDISEIQSVCSDVETVPQTHRPTPR;RGS(0.68)DAS(0.32)DFDISEIQSVCSDVETVPQTHRPTPR 253.47 2.22E-59 1573550000 186943.5 197462 194238.6 163714.5 189080 250565 199465.6 187400.3 214230 185237.1 TRUE FALSE 194324.1737 231374.5625 199300.6175 196096.7395 156940.2491 192375.0761 183830.9651 184888.5055 206519.9041 221530.7632 0.877188211 1.04443536 0.899652105 0.885189653 0.708435465 0.868389895 0.829821387 0.834595173 0.932240296 1 17.75714753 3.887540924 3.121382674 0.849171236 0.961907632 0.149834625 0.081484183 0.339832291 6.265319999 0.020407904 0.041928922 7718.642465 -3.887540924 0.112736396 RGS(ph)DELTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGSDELTVPR 10 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RGS(1)DELTVPR;RGS(1)DELTVPR;RGS(1)DELTVPR;RGS(0.998)DELT(0.002)VPR;RGS(1)DELTVPR 159.75 4.65E-06 3182760000 781229 977967 1007687 846292 1096975 1311020 1001283 959014 1041723 1074450 TRUE FALSE 812072.5242 1145925.225 1033948.151 1013686.032 910511.5813 1006555.474 922799.8221 946159.986 1004231.593 1284967.906 0.631978838 0.891792876 0.804649008 0.788880428 0.708587022 0.783331217 0.718150094 0.736329664 0.781522704 1 20.2933009 0.944315467 18.3778513 1.000000001 0.760820833 0.552582756 0.064898292 362.8061735 119740.1602 0.059717504 0.014930112 8.796612611 -0.944315467 -0.239179168 RGS(ph)DPASGEVEASQLR ddPTM_MDA-MB-175_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 153.56 2.69E-07 520560000 185021 216490 196842 255230 271210 320310 273120 217990 215710 239570 TRUE FALSE 192325.7719 253670.4734 201971.8642 305713.7322 225109.8211 245922.8568 251712.1407 215068.2006 207946.6392 286509.1547 0.671272693 0.885383484 0.704940352 1.067029543 0.785698528 0.858342056 0.878548335 0.750650362 0.725794048 1 18.12822171 4.748462092 23.77619407 0.840577029 0.67127251 0.185558105 0.110965022 1185.589535 2846811.899 0.025020573 0.319293989 56035.35039 -4.748462092 -0.169304518 RGS(ph)DPASGEVEASQLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSDPASGEVEASQLRR 17 2 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(1)DPASGEVEASQLRR 98.543 0.00094022 338120000 9987.5 16882 14317 15499 13668 17593 21651 16591 13136 16542 TRUE FALSE 10381.81421 19781.35218 14690.11278 18564.65594 11344.71824 13507.29237 19953.93805 16368.62478 12663.23793 19783.08818 0.524782285 0.999912248 0.742559132 0.938410412 0.573455374 0.682769659 1.008636157 0.827404934 0.640104205 1 14.27198003 -1.581155148 6.359272307 1.00046216 0.787018795 0.143592673 0.163644157 0.001014018 6.68E-05 0.149840658 0.035242926 0.026232812 1.581155148 -0.213443366 RGS(ph)FDATGSGFSMTFSSSSYSSSGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.934)FDAT(0.032)GS(0.032)GFS(0.002)MT(0.001)FSSSSYSSSGYGR;RGS(0.667)FDAT(0.161)GS(0.161)GFS(0.011)MTFSSSSYSSSGYGR;RGS(0.782)FDAT(0.091)GS(0.091)GFS(0.027)MT(0.006)FSSSSYSSSGYGR;RGS(0.998)FDAT(0.001)GS(0.001)GFSMTFSSSSYSSSGYGR 103.09 3.23E-06 460440000 173613 163292 192686 174254 222714 221459 191377 177182 180480 189794 TRUE FALSE 180467.3753 191336.1308 197707.5555 208720.9211 184857.1538 170028.5035 176376.3707 174807.1651 173984.5601 226980.5005 0.795078762 0.842962855 0.871033217 0.919554414 0.814418655 0.749088592 0.777055167 0.770141773 0.766517651 1 17.79220884 3.012106884 24.37326361 0.792142693 0.858366071 0.045805676 0.073873977 303.5640143 611121.2021 0.019979931 0.023862303 1028.269335 -3.012106884 0.066223379 RGS(ph)FSSENYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;Q6P6C2-1;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 RGS(0.876)FS(0.062)S(0.062)ENYWR;RGS(0.85)FS(0.149)S(0.001)ENYWR;RGS(0.99)FS(0.01)SENYWR;RGS(1)FSSENYWR;RGS(0.993)FS(0.007)SENYWR 203.93 2.14E-08 2444920000 712819 701726 778750 665751 968390 1055660 837680 869360 794900 745654 TRUE FALSE 740961.6445 822241.9818 799044.8648 797434.5607 803783.4137 810498.9637 772020.4527 857707.6512 766291.7043 891750.6249 0.830906785 0.922053721 0.896040712 0.894234933 0.901354472 0.908885221 0.865735814 0.961824559 0.859311654 1 19.7662808 -4.999999997 0.190216177 1.43484437 0.879597876 0.458041296 0.034434734 118.0736665 1.155682182 19.47349131 0.086451522 1.00E-05 4.999999997 -0.555246494 RGS(ph)GDTSISIDTEASIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 24 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(0.894)GDT(0.047)S(0.057)IS(0.002)IDTEASIR;RGS(0.983)GDT(0.016)S(0.001)ISIDTEASIR;RGS(0.97)GDT(0.03)S(0.001)ISIDTEASIR;RGS(0.978)GDT(0.02)S(0.002)ISIDTEASIR;RGS(0.997)GDT(0.003)SISIDTEASIR;RGS(0.99)GDT(0.008)S(0.002)ISIDTEASIR;RGS(0.989)GDT(0.011)S(0.001)ISIDTEASIR;RGS(0.99)GDT(0.01)S(0.001)ISIDTEASIR;RGS(0.965)GDT(0.015)S(0.02)ISIDTEASIR;RGS(0.916)GDT(0.076)S(0.009)ISIDTEASIR;RGS(0.927)GDT(0.036)S(0.035)IS(0.001)IDTEASIR;RGS(0.714)GDT(0.242)S(0.037)IS(0.008)IDTEASIR;RGS(0.971)GDT(0.026)S(0.003)ISIDTEASIR;RGS(0.955)GDT(0.044)S(0.001)ISIDTEASIR;RGS(0.978)GDT(0.022)SISIDTEASIR;RGS(0.978)GDT(0.017)S(0.005)ISIDTEASIR;RGS(0.63)GDT(0.114)S(0.114)IS(0.14)IDT(0.001)EASIR;RGS(0.969)GDT(0.029)S(0.001)ISIDTEASIR;RGS(0.954)GDT(0.044)S(0.002)ISIDTEASIR;RGS(0.993)GDT(0.006)SISIDTEASIR;RGS(0.985)GDT(0.004)S(0.005)IS(0.006)IDTEASIR;RGS(0.998)GDT(0.001)SISIDTEASIR;RGS(0.97)GDT(0.029)S(0.001)ISIDTEASIR;RGS(0.97)GDT(0.028)S(0.003)ISIDTEASIR 128.95 2.16E-05 581705800 289518.1 343630.1 336972.6 324198.9 370428.8 440000 328610.9 342563.4 330248.9 367182.6 TRUE FALSE 300948.4981 402645.8966 345754.3828 388324.4748 307463.4449 337816.6683 302853.519 337971.8979 318363.3066 439125.0003 0.685336744 0.916927746 0.78737121 0.884314203 0.700172945 0.769295003 0.689674964 0.7696485 0.72499472 1 18.74427215 3.237170595 24.99943081 0.758603965 0.823296326 0.024962798 0.100307926 89.97268202 1618162.403 0.025909011 0.032609415 1726.515952 -3.237170595 0.06469236 RGS(ph)GDTSSLIDPDTSLSELR ddPTM_MDA-MB-175_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(0.984)GDT(0.012)S(0.003)S(0.001)LIDPDTSLSELR;RGS(0.971)GDT(0.024)S(0.003)S(0.002)LIDPDTSLSELR;RGS(0.497)GDT(0.142)S(0.161)S(0.2)LIDPDTSLSELR;RGS(0.867)GDT(0.04)S(0.071)S(0.022)LIDPDTSLSELR;RGS(0.991)GDT(0.008)S(0.001)SLIDPDTSLSELR;RGS(0.912)GDT(0.026)S(0.026)S(0.026)LIDPDT(0.003)S(0.004)LS(0.004)ELR;RGS(0.97)GDT(0.03)SSLIDPDTSLSELR 132.79 7.31E-06 6379870000 2945860 2632411 2897010 2533293 3379540 3877138 3519091 2993043 3123504 2217866 TRUE FALSE 3062164.827 3084507.112 2972508.461 3034370.794 2805086.998 2976731.458 3243255.452 2952926.154 3011089.701 2652414.379 1.154482064 1.162905441 1.120680269 1.144003297 1.057559867 1.122272403 1.222755946 1.113297446 1.135225976 1 21.33887475 0.308260928 1.895839527 0.999999691 1.137365928 0.518072096 0.039658717 9.784284969 25.62903153 0.038437951 0.010644034 2.033578435 -0.308260928 0.137366237 RGS(ph)GDTSSLIDPDTSLSELRDIYDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGSGDTSSLIDPDTSLSELRDIYDLK 26 2 C9JSU1;Q9Y608-4;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.974)GDT(0.026)SSLIDPDTSLSELRDIYDLK;RGS(0.997)GDT(0.003)SSLIDPDTSLSELRDIYDLK;RGS(0.998)GDT(0.002)SSLIDPDTSLSELRDIYDLK;RGS(0.997)GDT(0.003)SSLIDPDTSLSELRDIYDLK 214.44 2.32E-34 524378000 937100 672364 858020 512381 1310090 1157050 840880 836350 1001750 647916 TRUE FALSE 974097.4316 787837.2867 880380.7061 613728.4325 1087401.37 888342.6728 774969.6284 825140.0962 965697.2132 774862.7351 1.257122568 1.016744323 1.13617634 0.792047939 1.403347097 1.146451665 1.000137951 1.064885507 1.246281657 1 19.56358124 -1.212668921 3.731712288 0.999886059 1.106854811 0.043215411 0.158974451 0.000153763 3.24E-05 0.145233874 0.03419256 0.061281739 1.212668921 0.106968752 RGS(ph)GHLPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSGHLPSAR 10 1 Q8N4Y2 Q8N4Y2 CRACR2B EF-hand calcium-binding domain-containing protein 4A 1 RGS(1)GHLPSAR;RGS(0.986)GHLPS(0.014)AR 87.914 0.007688 226750000 149314 142359 143477 134970 247199 275610 214713 152337 145096 156665 TRUE FALSE 155209.032 166808.0509 147216.1285 161666.6632 205180.2023 211603.7544 197883.234 150295.1717 139874.0233 187360.5072 0.8283978 0.890305291 0.785737244 0.862864141 1.095109131 1.129393582 1.056162993 0.802171033 0.746550196 1 17.51545736 3.452612434 24.84927639 0.965216693 0.83768559 0.234052391 0.115438232 371.0964389 376250.0948 0.036483231 0.049400587 2835.387591 -3.452612434 -0.127531103 RGS(ph)GSALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.5)GS(0.5)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.876)GS(0.124)ALGGPLDPQFVGPSDTSLGAAPGHR;RGS(0.5)GS(0.5)ALGGPLDPQFVGPSDTSLGAAPGHR 232.47 2.07E-36 922880000 173927 207536 231545 211289 282203 318892 234976 251622 243979 218925 TRUE FALSE 180793.7723 243178.6936 237579.2529 253081.3336 234234.2349 244834.1659 216557.9671 248249.4187 235198.2434 261819.1622 0.690529183 0.928804032 0.90741736 0.966626474 0.894641297 0.935126993 0.827128027 0.948171313 0.898323261 1 17.99821116 4.740115746 24.9119631 0.91863673 0.690529104 0.711312813 0.044338164 64.54726538 1033897.467 0.009691912 0.061384483 54968.73542 -4.740115746 -0.228107626 RGS(ph)GSPEDT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSGSPEDTPR 11 1 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 RGS(0.94)GS(0.213)PEDT(0.847)PR 82.941 0.038908 61492000 114450 116360 127580 112630 164200 184940 137290 113390 133420 112270 TRUE FALSE 118968.5744 136343.9248 130904.8396 134907.8778 136289.3427 141990.4878 126528.8511 111870.1925 128618.2403 134267.157 0.886058639 1.01546743 0.974958006 1.004771985 1.015060911 1.057522115 0.942366353 0.833191043 0.957927785 1 17.03474693 -0.809236062 4.863824781 1.000000049 0.961841122 0.02419864 0.062901907 4.77E-08 1.16E-08 0.068821507 0.016221358 0.155154344 0.809236062 -0.038158928 RGS(ph)GVFCANCLTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 238.65 1.51E-17 2443070000 2054770 1243770 1845670 1369300 2765560 2358940 2219390 1993640 2131720 1421510 TRUE FALSE 2135893.906 1457377.822 1893769.676 1640143.453 2295471.099 1811111.935 2045428.413 1966918.517 2054999.814 1700027.668 1.256387732 0.85726712 1.113964032 0.964774564 1.350255141 1.065342623 1.203173602 1.156992062 1.208803746 1 20.6971268 3.279180993 24.99994593 1.168922802 1.039172292 0.16054346 0.129016364 234.6462718 144412.2818 0.032349139 0.043800417 1901.870721 -3.279180993 -0.12975051 RGS(ph)HPKAELDDAGSSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSHPKAELDDAGSSLLR 18 2 Q5FWE3-2;Q5FWE3 Q5FWE3-2 PRRT3 Proline-rich transmembrane protein 3 1 RGS(1)HPKAELDDAGSSLLR 139.04 3.81E-07 185650000 117500 106270 105260 98882 143590 157640 102630 107730 107220 122750 TRUE FALSE 122138.9907 124521.0458 108003.1621 118440.5645 119182.6231 121030.4991 94585.59243 106286.0556 103361.1731 146800.5123 0.83200657 0.848233047 0.735713795 0.806813019 0.811867896 0.824455563 0.644313776 0.724016925 0.704092728 1 17.16349748 RGS(ph)HPYIDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGSHPYIDFR 10 1 Q13946-3;Q13946-2;Q13946;E5RG23 Q13946-3 PDE7A "High affinity cAMP-specific 3,5-cyclic phosphodiesterase 7A" 1 RGS(1)HPYIDFR;RGS(0.999)HPY(0.001)IDFR;RGS(1)HPYIDFR;RGS(1)HPYIDFR;RGS(0.999)HPY(0.001)IDFR;RGS(0.999)HPY(0.001)IDFR 107.99 0.0013537 3037300000 2482780 2146910 2481010 2255520 3060650 3342410 3007250 2399510 2610290 2006990 TRUE FALSE 2580802.072 2515625.092 2545667.159 2701655.124 2540401.806 2566185.932 2771533.887 2367348.493 2516346.173 2400221.264 1.075235067 1.048080495 1.060596869 1.125585863 1.058403175 1.06914557 1.154699331 0.986304275 1.048380918 1 21.19473598 1.668073687 11.19571 1.013473779 1.082086463 0.486310418 0.034242785 0.101355268 16.89678002 0.01581895 0.008591133 46.5665096 -1.668073687 0.068612684 RGS(ph)IGENQIKDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGSIGENQIKDEK 13 2 Q05682-5;Q05682-4;C9J813;E9PGZ1 Q05682-5 CALD1 Caldesmon 1 RGS(1)IGENQIKDEK;RGS(1)IGENQIKDEK;RGS(1)IGENQIKDEK 149.86 3.12E-05 1297860000 1409600 556770 840230 479044 1466230 1251650 1293990 887480 1175560 435827 TRUE FALSE 1465252.096 652390.9164 862127.0841 573797.4734 1217000.748 960973.2564 1192563.683 875584.7822 1133251.825 521218.9562 2.811202622 1.251663833 1.654059343 1.100876065 2.334912677 1.843703582 2.288028224 1.679879006 2.174233711 1 18.99153003 3.213327355 24.99625498 1.928986765 1.668508135 0.020287305 0.555707013 756.7247259 749615.0145 0.150710056 0.180199231 1634.283346 -3.213327355 -0.260478631 RGS(ph)ISSMSSVSSVLDEKDDDRIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGSISSMSSVSSVLDEKDDDRIR 23 3 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 RGS(0.998)IS(0.001)S(0.001)MSSVSSVLDEKDDDRIR;RGS(0.992)IS(0.007)S(0.002)MSSVSSVLDEKDDDRIR;RGS(0.998)IS(0.002)SMSSVSSVLDEKDDDRIR;RGS(0.989)IS(0.009)S(0.001)MSSVSSVLDEKDDDRIR 229.86 2.59E-32 2216580000 349555 226940 294276 164301 427165 412172 329068 253854 315391 189446 TRUE FALSE 363355.7013 265915.1797 301945.0743 196799.2474 354555.6459 316451.2995 303274.7903 250451.5024 304040.1395 226564.3165 1.60376403 1.173685176 1.332712401 0.868624197 1.564922717 1.396739365 1.338581445 1.105432251 1.341959511 1 17.78956113 -4.337712355 0.20701089 9.60E-15 1.332821701 0.16972559 0.203452888 201.9412483 2.576933493 84.08887207 0.445589757 4.60E-05 4.337712355 1.332821701 RGS(ph)KGHMNYEGPGMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 87.208 0.0058045 52857000 35898 20620 25833 19423 46116 35419 31077 26988 36034 21074 TRUE FALSE 37315.28076 24161.3246 26506.2292 23264.81143 38277.21879 27193.47403 28641.10354 26626.27 34737.14338 25203.04681 1.480586099 0.958666814 1.051707335 0.923095196 1.518753628 1.078975658 1.136414329 1.056470283 1.378291428 1 14.62131053 4.756958381 23.76685403 1.124278037 1.480586708 0.267755278 0.177635711 2749.325919 3551558.81 0.040839536 1.284781048 57142.38733 -4.756958381 0.356308671 RGS(ph)LCSGCQKPITGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSLCSGCQKPITGR 15 2 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 RGS(1)LCSGCQKPITGR 66.152 0.031006 112340000 63240 52702 53372 56144 74673 78486 72246 58258 73502 48970 TRUE FALSE 65736.76403 61753.15854 54762.91817 67249.11563 61980.11013 60258.81597 66583.16974 57477.1468 70856.67738 58564.73391 1.122463292 1.054442741 0.935083531 1.148286881 1.058317967 1.028926658 1.136915773 0.981429317 1.209886439 1 15.83774455 3.694825677 24.99665943 1.074518454 1.039040469 0.055525756 0.078881566 1633.259357 933487.3625 0.020013952 0.031005678 4952.513603 -3.694825677 -0.035477985 RGS(ph)LEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 98.233 0.024603 3186700000 3249160 1921130 2617530 1792150 3717090 3362870 3542270 2760650 2955890 1663710 TRUE FALSE 3377439.346 2251069.133 2685744.982 2146631.921 3085260.37 2581894.407 3264617.621 2723648.002 2849508.096 1989682.121 1.697476853 1.131371242 1.349836215 1.078881847 1.55062979 1.297641659 1.640773462 1.368886001 1.432142384 1 20.92410653 -1.294647976 3.786398697 0.999174209 1.387073731 0.279352636 0.189625141 315.9511677 32694843.69 43866.05888 0.042889579 0.050740182 1.294647976 0.387899522 RGS(ph)LEMSSDGEPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSLEMSSDGEPLSR 15 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 RGS(1)LEMSSDGEPLSR 99.409 0.0015551 0 70550 69420 64306 59394 71528 83096 70539 69619 60130 66545 TRUE FALSE 73335.36848 81342.34499 65981.86719 71141.95593 59369.69611 63798.21333 65009.96886 68685.87118 57965.93305 79583.21867 0.921492869 1.022104237 0.829092719 0.893931624 0.746007728 0.801654097 0.816880367 0.863069782 0.728368795 1 16.28017663 4.22562247 24.85560236 0.828720102 0.97179854 0.340097752 0.075904668 178.3118277 342558.7263 0.017422214 0.038015704 16812.11956 -4.22562247 0.143078438 RGS(ph)LGEEGSEPPPPPPLPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGSLGEEGSEPPPPPPLPLAR 21 1 Q14934-2;Q14934-11;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-14;Q14934-15;Q14934-16;Q14934-17;Q14934-12;Q14934-13;Q14934-18 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 RGS(0.997)LGEEGS(0.003)EPPPPPPLPLAR;RGS(1)LGEEGSEPPPPPPLPLAR;RGS(0.972)LGEEGS(0.028)EPPPPPPLPLAR;RGS(1)LGEEGSEPPPPPPLPLAR 151.05 4.02E-08 1175960000 316701 308150 317841 295990 394254 406779 312873 342546 324200 280957 TRUE FALSE 329204.6 361072.3654 326124.1976 354535.9386 327238.8459 312310.742 288349.1967 337954.7312 312532.1053 336005.1449 0.979760593 1.074603681 0.970592869 1.055150327 0.973910224 0.929482024 0.858168993 1.005802251 0.930140833 1 18.3581238 3.029478551 5.742765542 0.943583862 1.020236656 0.353641371 0.047982255 0.189128684 18.06224029 0.013675142 0.016137561 1070.233524 -3.029478551 0.076652794 RGS(ph)LPAGASWQNTDLFEMIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSLPAGASWQNTDLFEMIEK 21 1 J3KPC5;P47736-3 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 RGS(1)LPAGASWQNTDLFEMIEK;RGS(0.999)LPAGAS(0.001)WQNTDLFEMIEK 247.69 1.25E-30 160599000 198936 135873 180035 125771 236872 225191 196366 165159 189639 118085 TRUE FALSE 206790.1469 159208.1308 184726.86 150648.1284 196608.582 172893.8031 180974.3198 162945.3138 182813.9294 141221.4949 1.464296544 1.127364718 1.308064754 1.066750699 1.39220012 1.22427399 1.281492736 1.153827991 1.294519149 1 17.10760017 -4.285440912 0.251987616 2.06E-15 1.270074492 0.313924914 0.114177304 145.9541392 2.015525315 74.94284267 0.14854459 5.18E-05 4.285440912 1.270074492 RGS(ph)LPDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 RGS(1)LPDQK;RGS(1)LPDQK 119.39 0.0010438 537480000 1274720 728390 1066570 738200 1404240 1455170 1336290 1026680 1146930 599470 TRUE FALSE 1325046.93 853485.3164 1094365.69 884213.7567 1165547.786 1117228.821 1231548.098 1012919.034 1105652.213 716924.669 1.848237322 1.190481167 1.526472359 1.23334263 1.625760469 1.55836292 1.717820786 1.41286676 1.542215328 1 19.45146201 -1.250399558 4.817092272 0.999876088 1.505833246 0.397383587 0.190633586 0.000234522 3.65E-05 0.170635361 0.040209368 0.05618242 1.250399558 0.505957157 RGS(ph)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER ddPTM_MDA-MB-175_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(1)LQAYTFEEQPTLPVLLPTSSGLPPGWEEKQDER;RGS(0.996)LQAYT(0.004)FEEQPTLPVLLPTSSGLPPGWEEKQDER 154.77 5.67E-14 662890000 192300 128201 163373 115726 236297 233152 180684 157076 187055 128026 TRUE FALSE 199892.1525 150218.5245 167630.6346 138616.2574 196131.3203 179005.9815 166521.516 154970.6531 180322.9271 153110.2435 1.305543953 0.981113484 1.094836183 0.905336274 1.280981049 1.169131322 1.087592261 1.012150785 1.177732613 1 17.22421128 -1.659285649 2.730214543 0.988172278 1.101011596 0.065507865 0.120634883 24280659.95 20322227.06 1997360.619 0.028532174 0.021913631 1.659285649 0.112839318 RGS(ph)LSNAGDPEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RGSLSNAGDPEIVK 14 1 O43847;O43847-2;F5H7V1 O43847 NRD1 Nardilysin 1 RGS(0.992)LS(0.008)NAGDPEIVK;RGS(0.998)LS(0.002)NAGDPEIVK;RGS(1)LSNAGDPEIVK;RGS(0.998)LS(0.002)NAGDPEIVK;RGS(0.991)LS(0.009)NAGDPEIVK;RGS(0.712)LS(0.288)NAGDPEIVK 211.33 2.44E-09 12423400000 14581600 9594410 13223640 10537480 17153000 16517900 17443100 13296230 14365400 7756960 TRUE FALSE 15157292.83 11242175.28 13568258.92 12621762.09 14237339.19 12681868.06 16075864.24 13118015.79 13848392.06 9276787.796 1.633894529 1.211860779 1.462603136 1.360574627 1.534727268 1.367053805 1.732912792 1.414068757 1.492800349 1 23.14519391 -1.696232058 7.152473655 0.996882577 1.463968023 0.504704228 0.138988094 0.006445532 0.000273744 0.125542539 0.029470748 0.020126485 1.696232058 0.467085446 RGS(ph)LTLTISGESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RGSLTLTISGESPK 14 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.984)LT(0.016)LTISGESPK;RGS(0.98)LT(0.02)LTISGESPK;RGS(0.856)LT(0.144)LTISGESPK;RGS(0.995)LT(0.005)LTISGESPK;RGS(1)LTLTISGESPK;RGS(0.995)LT(0.005)LTISGESPK;RGS(0.97)LT(0.03)LTISGESPK;RGS(0.993)LT(0.007)LTISGESPK 264.35 1.18E-24 4429660000 6364780 3772671 4990130 3723911 7346790 7110760 6452650 5107240 5947310 3273759 TRUE FALSE 6616066.429 4420597.897 5120176.887 4460489.481 6097985.26 5459393.755 5946874.432 5038785.802 5733267.475 3915189.396 1.689845818 1.129089158 1.307772465 1.139278086 1.557519865 1.394413706 1.51892382 1.286983921 1.464365295 1 21.90065067 -1.185198229 4.796644987 0.999953726 1.374680423 0.315627393 0.170263063 7.89E-05 1.34E-05 0.154447427 0.036399122 0.065283251 1.185198229 0.374726696 RGS(ph)MEQAPAVALPPTHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSMEQAPAVALPPTHK 17 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 RGS(1)MEQAPAVALPPTHK;RGS(1)MEQAPAVALPPTHK 119.18 6.23E-05 756910000 162346 169983 193974 138815 360820 224826 213136 204925 183466 161410 TRUE FALSE 168755.5454 199176.258 199029.1218 166272.1927 299487.9453 172613.5688 196429.8434 202178.3156 176863.0945 193035.1991 0.874221625 1.031813156 1.031050931 0.861356858 1.551468057 0.894207738 1.017585623 1.047365022 0.916221991 1 17.55850442 5.542950992 1.283190647 1.049772707 5.88E-06 0.066458664 0.182512803 27.172667 8.335668398 0.04844821 61.73044124 349100.9189 -5.542950992 -1.049766829 RGS(ph)MFYDEDGDLAHEFYEETIVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RGSMFYDEDGDLAHEFYEETIVTK 24 1 O75896 O75896 TUSC2 Tumor suppressor candidate 2 1 RGS(0.546)MFY(0.454)DEDGDLAHEFYEETIVTK;RGS(0.548)MFY(0.452)DEDGDLAHEFYEETIVTK;RGS(0.554)MFY(0.446)DEDGDLAHEFYEETIVTK;RGS(0.559)MFY(0.441)DEDGDLAHEFYEETIVTK;RGS(0.534)MFY(0.449)DEDGDLAHEFY(0.017)EETIVTK;RGS(0.541)MFY(0.45)DEDGDLAHEFY(0.008)EETIVTK;RGS(0.99)MFY(0.01)DEDGDLAHEFYEETIVTK;RGS(1)MFYDEDGDLAHEFYEETIVTK 194.23 1.78E-18 899152000 728126 539064 820586 515247 1110906 924330 963757 782910 882207 582592 TRUE FALSE 756872.9767 631644.0487 841971.1453 617161.3187 922074.5949 709668.3659 888215.208 772416.372 850456.5424 696739.748 1.086306586 0.906570998 1.208444254 0.885784571 1.323413222 1.018555878 1.274816329 1.108615339 1.220622973 1 19.41026034 3.244152323 24.99999299 1.160926813 1.026881075 0.213432576 0.1275614 202.8750596 907030.0257 0.032108082 0.042301567 1754.49576 -3.244152323 -0.134045737 RGS(ph)MNNELLS(ph)PEFGPVRDPLADGVEGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 2 RGS(1)MNNELLS(1)PEFGPVRDPLADGVEGLGR 63.97 0.0071252 22092000 5253.3 6148.9 5432.9 6547.8 8379.9 9318.5 10399 7068.1 7216 4640.9 TRUE FALSE 5460.70434 7204.925743 5574.485837 7842.935297 6955.487591 7154.419598 9583.899207 6973.363681 6956.29757 5550.1955 0.983876035 1.298139091 1.004376483 1.413091719 1.253196863 1.289039206 1.72676786 1.256417667 1.2533428 1 12.43832287 3.732441765 24.6444864 1.34034617 1.11573139 0.206168082 0.189300948 573.7354399 2310797.236 0.048229543 0.07687981 5400.596927 -3.732441765 -0.22461478 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR;RGS(0.5)MNNELLS(0.5)PEFGPVRDPLADGVEGLGR;RGS(1)MNNELLSPEFGPVRDPLADGVEGLGR 186.88 3.30E-18 572198000 104024 123270 108729.8 106657.8 116466 143669.6 130723.5 122172.6 110509.9 92358.9 TRUE FALSE 108130.9478 144440.6636 111563.3879 127754.3945 96669.15092 110304.5127 120477.0505 120535.0761 106532.6703 110454.8581 0.978960543 1.307689549 1.010036044 1.156620873 0.875191481 0.998638852 1.090735641 1.091260975 0.964490581 1 16.75309735 RGS(ph)MNNELLSPEFGPVRDPLADGVEGLGRGS(ph)PEPSALPPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSMNNELLSPEFGPVRDPLADGVEGLGRGSPEPSALPPQR 41 3 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 2 RGS(1)MNNELLSPEFGPVRDPLADGVEGLGRGS(0.997)PEPS(0.003)ALPPQR 157.51 4.97E-15 70845000 10124 14002 13299 9647.2 14347 17640 9506.1 11951 12818 14107 TRUE FALSE 10523.70334 16406.73458 13645.58287 11555.38737 11908.30206 13543.37734 8760.987042 11790.81639 12356.68268 16870.99656 0.62377485 0.972481651 0.808819018 0.684926188 0.705844615 0.802760957 0.5192928 0.698880849 0.732421623 1 14.04225757 3.779528692 7.746855261 0.710294054 0.819275431 0.021563593 0.138575716 0.623087118 105.0959698 0.033410407 0.060013747 6019.060275 -3.779528692 0.108981377 RGS(ph)PSAAFTFPDTDDFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGSPSAAFTFPDTDDFGK 18 1 Q9ULT0;Q9ULT0-4;H7C055;Q9ULT0-3 Q9ULT0 TTC7A Tetratricopeptide repeat protein 7A 1 RGS(0.992)PS(0.008)AAFTFPDTDDFGK;RGS(0.985)PS(0.015)AAFTFPDTDDFGK;RGS(0.996)PS(0.004)AAFTFPDTDDFGK;RGS(0.94)PS(0.06)AAFTFPDTDDFGK 263.54 4.07E-31 654480000 999520 644390 884140 688630 1162500 1219010 1081450 842780 900890 529946 TRUE FALSE 1038981.821 755058.9698 907181.4147 824838.9586 964898.6652 935913.4018 996683.1232 831483.9126 868467.1449 633778.7723 1.639344621 1.19136046 1.431384979 1.301461953 1.522453429 1.47671939 1.572604143 1.311946611 1.370300147 1 19.27361981 0.575570348 1.26074363 1.000707529 1.429733783 0.5118417 0.126438814 1.226555231 2.724739686 0.114626105 0.034485938 3.763313062 -0.575570348 0.429026254 RGS(ph)PTTGFIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.998)PT(0.002)TGFIEQK;RGS(0.95)PT(0.034)T(0.017)GFIEQK;RGS(0.765)PT(0.234)T(0.001)GFIEQK;RGS(0.824)PT(0.174)T(0.002)GFIEQK;RGS(0.979)PT(0.011)T(0.011)GFIEQK 209.21 6.12E-08 6648240000 6802720 4442910 5724640 4248500 7470480 7623110 7291680 5809950 6165490 3509290 TRUE FALSE 7071296.638 5205945.231 5873828.821 5088840.619 6200650.478 5852758.232 6720139.068 5732077.123 5943595.219 4196868.186 1.684898435 1.240435725 1.399574292 1.212532868 1.47744704 1.394553742 1.601227098 1.365798703 1.416197735 1 22.00088172 0.100612999 1.996001824 0.999974609 1.414981356 0.46158412 0.136375404 40.60757153 87.80036498 0.124013216 0.033767092 1.260703618 -0.100612999 0.415006747 RGS(ph)PVPPVPER ddPTM_MDA-MB-175_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 85.469 0.0093059 7466950000 2494900 2304040 2579060 2290460 3110650 3413060 2786560 2597850 2574970 2081740 TRUE FALSE 2593400.578 2699740.947 2646272.422 2743506.152 2581902.824 2620428.54 2568142.146 2563030.07 2482297.333 2489617.096 1.041686524 1.084400068 1.062923462 1.101979158 1.037068242 1.052542797 1.031541015 1.029487657 0.997059884 1 21.24749244 1.960551094 0.774781743 0.997999067 1.071056919 0.680068702 0.017871649 0.353491076 0.399364437 0.014892468 0.007628356 91.31688611 -1.960551094 0.073057851 RGS(ph)PVPPVPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(1)PVPPVPERR 101.67 0.0013259 406020000 30723 17192 16471 15167 10277 30808 7174.2 13754 24621 23806 TRUE FALSE 31935.96776 20144.59226 16900.24779 18166.98733 8530.119211 23653.3089 6611.867458 13569.65013 23734.89502 28470.32991 1.121728054 0.707564413 0.593609131 0.638102452 0.299614344 0.830805578 0.232237121 0.476624267 0.833671232 1 14.79717159 4.874482504 1.641698068 0.563818637 1.472540279 0.287258042 0.229653547 1.555511988 3.105520286 0.056636343 2.481311469 74900.11832 -4.874482504 0.908721642 RGS(ph)QNSSEHRPPASSTSEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSQNSSEHRPPASSTSEDVK 21 2 O15014 O15014 ZNF609 Zinc finger protein 609 1 RGS(0.944)QNS(0.047)S(0.009)EHRPPASSTSEDVK 136.53 2.50E-06 92879000 54840 54646 80355 60601 110770 105780 94597 88319 88215 60910 TRUE FALSE 57005.12555 64031.02541 82449.11731 72587.69692 91941.35497 81214.19811 87182.23996 87135.22827 85040.15938 72844.14831 0.782562867 0.879013989 1.131856425 0.996479451 1.262165282 1.11490353 1.196832443 1.196187069 1.167426092 1 16.15252546 4.496703664 1.066109338 1.162185567 0.658416429 0.680310161 0.082634677 0.603759958 0.746681679 0.023375779 0.314558808 31383.66535 -4.496703664 -0.503769139 RGS(ph)RPEMTPVSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSRPEMTPVSLR 13 2 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 RGS(0.991)RPEMT(0.005)PVS(0.004)LR 87.275 0.0066488 285640000 316230 214320 294420 194360 394190 420430 313810 263870 276550 195580 TRUE FALSE 328715.0046 251127.7928 302092.8271 232803.8279 327185.7246 322791.5042 289212.7522 260333.2543 266597.0195 233900.1564 1.405364621 1.073653805 1.291546067 0.995312836 1.398826446 1.380039711 1.236479516 1.113010176 1.13978983 1 17.8355333 1.680625255 3.236746762 1.084364957 1.250153924 0.265076859 0.130792779 0.314832715 7.628690829 0.077742039 0.034876516 47.93196732 -1.680625255 0.165788967 RGS(ph)RS(ph)SPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.988)RS(0.593)S(0.419)PEPK 101.39 0.088382 169530000 933940 453130 618260 382270 901610 1040300 861990 585320 657940 357230 TRUE FALSE 970812.6724 530951.5526 634372.3635 457881.865 748354.6542 798706.0909 794424.9714 577474.7428 634260.8679 427222.3789 2.272382535 1.242799017 1.484876249 1.071764701 1.751674751 1.869532427 1.859511605 1.351695911 1.484615271 1 18.7046277 0.802293104 1.326982424 1.006100469 1.604666846 0.243028662 0.329307298 1.087188564 3.49254223 0.30955836 0.092928425 6.342976521 -0.802293104 0.598566377 RGS(ph)RSS(ph)PEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSRSSPEPK 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RGS(0.995)RS(0.151)S(0.855)PEPK 83.823 0.075457 826190000 2675700 1253400 1695500 1200700 2532200 2763600 2290800 1724600 1910400 939410 TRUE FALSE 2781338.702 1468661.7 1739686.123 1438194.876 2101777.548 2121795.783 2111241.11 1701484.558 1841645.077 1123469.403 2.475669292 1.307255627 1.548494438 1.280137111 1.870791979 1.888610207 1.879215494 1.514491229 1.639248093 1 20.0995294 0.441036776 1.141974364 0.99996145 1.704747477 0.300629335 0.328669558 2.928028204 4.754221779 0.30580685 0.09320695 2.760811629 -0.441036776 0.704786027 RGS(ph)SDPTVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGSSDPTVQR 10 1 H7BXG1;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3;Q2KHT3-2 H7BXG1;Q2KHT3 CLEC16A Protein CLEC16A 1 RGS(0.997)S(0.003)DPTVQR;RGS(0.958)S(0.042)DPTVQR;RGS(0.968)S(0.032)DPTVQR;RGS(0.908)S(0.092)DPTVQR 130.1 0.00017494 1287360000 1039900 978387 995680 883944 1395000 1419820 1112098 1059942 1056301 987429 TRUE FALSE 1080956.055 1146417.356 1021628.239 1058785.485 1157878.398 1090088.323 1024928.853 1045735.211 1018284.933 1180896.807 0.915368768 0.970802317 0.86512914 0.896594418 0.980507688 0.9231021 0.867924146 0.885543262 0.862297982 1 20.17145147 2.35841135 9.203476167 0.892570075 0.9260303 0.024686237 0.047725058 0.651613994 49.58650808 0.01598513 0.013359562 228.2502966 -2.35841135 0.033460225 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 RGS(0.587)S(0.198)GS(0.198)VDET(0.016)LFALPAASEPVIR 131.95 1.76E-05 44002000 26939 21964 25682 36670 26292 38761 32848 23796 26938 20645 TRUE FALSE 28002.57252 25736.14614 26351.29402 43923.21655 21822.89523 29759.34518 30273.28793 23477.05354 25968.50664 24689.99248 1.134166912 1.042371567 1.067286434 1.778988657 0.883876139 1.20532014 1.226135972 0.950873256 1.051782687 1 14.59163878 1.74544512 10.31957537 1.00310432 1.19201171 0.1348405 0.220748078 0.204139737 111.8903282 0.10318669 0.056120707 55.64743099 -1.74544512 0.18890739 RGS(ph)SPGSLEIPK ddPTM_MDA-MB-175_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 1 RGS(0.753)S(0.247)PGSLEIPK;RGS(0.748)S(0.252)PGSLEIPK 159.81 4.27E-05 967560000 2236000 1202710 1768050 1348410 2498500 2343700 2282800 1786850 2012710 1016340 TRUE FALSE 2324279.007 1409266.087 1814126.835 1615121.473 2073805.862 1799411.194 2103868.171 1762900.198 1940272.96 1215472.364 1.912243401 1.15943902 1.492528246 1.328801478 1.70617278 1.480421314 1.730905805 1.45038279 1.596311868 1 20.21308566 -1.194883684 5.527278548 0.999981317 1.52670274 0.38829147 0.202627138 4.25E-05 6.19E-06 0.178762527 0.042133239 0.063843445 1.194883684 0.526721423 RGSDAS(ph)DFDISEIQSVCSDVETVPQTHRPTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSDASDFDISEIQSVCSDVETVPQTHRPTPR 32 2 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A0U1RQJ2;A0A494C073;H0YC65;A0A494C1U5 F6QMI7 DST Dystonin 1 RGS(0.416)DAS(0.584)DFDISEIQSVCSDVETVPQTHRPTPR 118.68 4.08E-07 120000000 18189 14439 14915 17233 20480 21214 20217 18320 19091 13218 TRUE FALSE 18907.11576 16918.78593 15303.69715 20641.63596 16998.81692 16287.37 18632.33871 18074.45037 18403.91864 15807.81403 1.196061374 1.07027992 0.96810964 1.305786868 1.075342668 1.030336641 1.178679018 1.143387083 1.164229198 1 13.94835026 RGSDPAS(ph)GEVEASQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSDPASGEVEASQLR 16 1 Q8WWA1-3;Q8WWA1-2;Q8WWA1 Q8WWA1-3 TMEM40 Transmembrane protein 40 1 RGS(0.051)DPAS(0.832)GEVEAS(0.117)QLR;RGS(0.015)DPAS(0.985)GEVEASQLR 261.3 8.41E-27 1213970000 731020 885380 847400 1170150 1037930 1434230 1111910 784770 878130 844160 TRUE FALSE 759881.2341 1037437.128 869483.9401 1401602.177 861503.0293 1101151.818 1024755.589 774251.4418 846526.2728 1009556.99 0.752687805 1.02761621 0.861252955 1.388333885 0.853347595 1.090727745 1.015054721 0.766921976 0.838512616 1 19.94529092 1.755620074 25 0.847418446 1.007244006 0.103068986 0.17097121 11.84830643 17382.41315 0.075557412 0.041900659 56.96657039 -1.755620074 0.15982556 RGSGDT(ph)SISIDTEASIR ddPTM_MDA-MB-175_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(0.005)GDT(0.924)S(0.046)IS(0.025)IDTEASIR 115.53 0.00084847 0 24757 27742 27931 26638 33533 36076 29097 26529 29954 26186 TRUE FALSE 25734.42548 32506.4727 28658.90481 31906.91689 27833.07264 27697.89574 26816.30111 26173.42215 28875.96139 31316.64534 0.821749111 1.037993449 0.915133294 1.018848492 0.888762903 0.884446448 0.856295456 0.835767109 0.922064323 1 14.93464206 3.04107329 23.95940042 0.882139493 0.952619606 0.086878969 0.069653423 151.7272225 88506.05484 0.018795071 0.022464373 1099.191319 -3.04107329 0.070480113 RGSGDTSS(ph)LIDPDTSLSELRESLSEVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSGDTSSLIDPDTSLSELRESLSEVEEK 29 2 Q9Y608-2;Q9Y608-5 Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 RGS(0.248)GDT(0.209)S(0.247)S(0.292)LIDPDT(0.003)S(0.001)LSELRESLSEVEEK 66.461 0.0076025 32113000 49604 40555 49654 17512 94977 69252 25340 42814 59014 60228 TRUE FALSE 51562.40422 47520.00578 50948.02403 20975.82133 78832.84346 53169.27252 23353.78459 42240.14836 56890.09767 72028.52347 0.715860908 0.659738719 0.707331229 0.291215484 1.09446702 0.738169686 0.324229673 0.586436405 0.789827348 1 16.13628071 -1.820125325 2.377085495 1.133175867 0.643477408 0.18147259 0.217398 24464138.37 14503788.72 18635089.01 0.053696043 0.015131245 1.820125325 -0.489698458 RGSGS(ph)ALGGPLDPQFVGPSDTSLGAAPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSGSALGGPLDPQFVGPSDTSLGAAPGHR 30 1 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 RGS(0.364)GS(0.636)ALGGPLDPQFVGPSDTSLGAAPGHR 259.47 1.40E-58 610410000 94024 109160 124660 100110 142790 163810 126960 127100 128880 110070 TRUE FALSE 97736.14012 127907.3809 127908.742 119911.4592 118518.6068 125767.6101 117008.5435 125396.4324 124241.634 131636.1091 0.742472113 0.971673971 0.971684311 0.910931355 0.900350273 0.955418775 0.888878775 0.95259905 0.943826393 1 17.00619576 4.74434663 24.83486444 0.93939086 0.74247202 0.766104064 0.033309372 270.177148 1159623.604 0.007676596 0.068781687 55506.85616 -4.74434663 -0.19691884 RGSMNNELLS(ph)PEFGPVRDPLADGVEGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RGSMNNELLSPEFGPVRDPLADGVEGLGR 29 2 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 RGS(0.011)MNNELLS(0.989)PEFGPVRDPLADGVEGLGR;RGS(0.285)MNNELLS(0.715)PEFGPVRDPLADGVEGLGR 145.9 4.65E-08 681730000 249010 234910 258590 246460 306990 353720 332390 262350 272150 224670 TRUE FALSE 258841.1071 275253.9652 265329.0678 295209.0524 254807.9495 271573.8907 306336.4033 258833.6274 262355.3747 268689.7849 0.963345544 1.02443033 0.987492204 1.098698458 0.948335083 1.010733961 1.140111833 0.963317706 0.976424819 1 18.03558195 4.74297334 23.20384106 1.018010439 0.963345486 0.072717882 0.056872245 466.5383218 2452978.714 0.013148091 0.101945802 55331.61415 -4.74297334 -0.054664953 RGSMNNELLS(ph)PEFGPVRDPLADGVEGLGRGS(ph)PEPSALPPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSMNNELLSPEFGPVRDPLADGVEGLGRGSPEPSALPPQR 41 3 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 2 RGS(0.384)MNNELLS(0.616)PEFGPVRDPLADGVEGLGRGS(0.96)PEPS(0.04)ALPPQR 72.529 0.0030727 58469000 12295 15820 17167 11624 19909 21913 12750 14285 15332 13167 TRUE FALSE 12780.41609 18536.96194 17614.38612 13923.19251 16524.87529 16824.03784 11750.62168 14093.53294 14780.20431 15746.82155 0.81161878 1.177187528 1.118599462 0.884190658 1.049410209 1.06840849 0.74622181 0.895008106 0.938615089 1 13.94277303 2.265431915 24.98023751 0.882154604 1.025346988 0.207649891 0.116407944 289.1486644 268798.9264 0.039308713 0.032879975 184.26036 -2.265431915 0.143192384 RGSPT(ph)TGFIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGSPTTGFIEQK 12 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RGS(0.083)PT(0.913)T(0.004)GFIEQK 182.52 3.24E-05 1479000000 1454100 860450 1206900 831480 1592900 1508000 1557300 1249200 1342900 790340 TRUE FALSE 1511508.991 1008225.594 1238352.805 995944.2623 1322139.427 1157789.854 1435234.757 1232456.517 1294569.291 945191.991 1.599155521 1.066688677 1.31016007 1.053695198 1.398805152 1.224925586 1.518458441 1.303921879 1.369636332 1 19.85024788 -0.760474163 12.21719751 1 1.3091141 0.248448313 0.164554296 0 0 0.147515396 0.034769712 0.173590453 0.760474163 0.3091141 RGT(ph)FEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGTFEK 6 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RGT(1)FEK 76.827 0.043382 104430000 107740 81150 96943 87993 122330 139790 111840 107680 104950 77958 TRUE FALSE 111993.6584 95086.88124 99469.41422 105397.7528 101536.3903 107325.891 103073.6886 106236.7257 101172.87 93232.3775 1.20123139 1.019891199 1.066897755 1.130484447 1.089067908 1.151165442 1.105556796 1.139483177 1.08516883 1 16.50854344 3.737525667 24.92041884 1.109617548 1.088395225 0 0.058303583 408.4975795 9836455.791 0.014151593 0.023847459 5464.188427 -3.737525667 -0.021222323 RGT(ph)FSDQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGTFSDQELDAQSLDDEDDNMHHAVYPAVNR 31 1 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RGT(0.5)FS(0.5)DQELDAQSLDDEDDNMHHAVYPAVNR 142.91 1.67E-08 291160000 25249 17472 19166 18359 18475 32510 23832 23975 18572 16520 TRUE FALSE 26245.85002 20472.68009 19665.48171 21990.3554 15334.6261 24960.04519 21963.98557 23653.65434 17903.59735 19756.77771 1.328447908 1.036235787 0.995379004 1.113053744 0.776170402 1.263366201 1.111719021 1.197242521 0.906200273 1 14.27006004 7.999837035 0.009823174 0.070641177 2.218389226 0.051738873 0.15355843 69360.00647 52.66415615 4972.886908 6655.132032 99962483.05 -7.999837035 2.147748048 RGT(ph)GQSDDSDIWDDTALIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 RGT(0.617)GQS(0.378)DDS(0.005)DIWDDTALIK;RGT(0.625)GQS(0.375)DDSDIWDDTALIK;RGT(0.715)GQS(0.28)DDS(0.005)DIWDDTALIK;RGT(0.74)GQS(0.26)DDSDIWDDTALIK 220.23 1.73E-19 2138430000 238744 190756 243385 153389 265140 301213 263376 251463 268056 167675 TRUE FALSE 248169.7975 223516.8591 249727.813 183728.8864 220071.5975 231260.8457 242731.9009 248092.5498 258408.7169 200527.7059 1.237583586 1.114643276 1.245353164 0.91622694 1.097462301 1.153261314 1.210465655 1.237198364 1.288643461 1 17.61344205 2.401979263 3.688107346 1.207427414 1.117670749 0.047840804 0.110576664 0.49968524 13.56983117 0.039463285 0.032697157 252.3360283 -2.401979263 -0.089756665 RGTGGVDTAATGGVFDISNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RGTGGVDTAATGGVFDISNLDR 22 1 P12532;P12532-2 P12532 CKMT1A "Creatine kinase U-type, mitochondrial" 0 124.19 3.70E-05 209230000 34803 40538 37275 44908 52226 51135 32967 31494 35840 44554 FALSE TRUE 36177.04931 47500.08616 38246.41712 53790.66836 43348.64317 39259.67121 30382.9604 31071.87444 34550.1254 53283.50326 0.678954031 0.891459518 0.717790963 1.009518239 0.813547168 0.736807244 0.570213266 0.583142484 0.64842068 1 15.70140132 2.554261463 3.56348031 0.653199653 0.829845903 0.104721312 0.14299558 0.332721514 8.113013356 0.046724436 0.042531944 358.3120905 -2.554261463 0.17664625 RGTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 RGT(0.002)GQS(0.998)DDS(1)DIWDDTALIK;RGT(0.095)GQS(0.907)DDS(0.998)DIWDDTALIK;RGT(0.479)GQS(0.574)DDS(0.947)DIWDDTALIK;RGT(0.209)GQS(0.794)DDS(0.998)DIWDDTALIK 217.26 1.27E-18 716643000 540343 363444 471121 334602 620012 618068 506699 475003 496689 335827 TRUE FALSE 561676.1589 425862.6798 483398.8003 400785.2769 514622.5817 474531.0739 466982.6084 468636.3617 478813.2599 401625.8709 1.398505922 1.060346732 1.203604736 0.997907022 1.281348188 1.181525166 1.162730397 1.166848044 1.192187293 1 18.61549268 -1.665163888 2.71242558 0.978313203 1.175582169 0.216590934 0.103473127 13618208.82 12050367.92 2045293.882 0.023363798 0.021619025 1.665163888 0.197268966 RGTLVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RGTLVAER 8 1 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ;; 106.2 0.0068009 385550000 475960 541210 460640 437250 1156490 780720 507250 487530 441450 1269180 FALSE TRUE 494751.2683 634158.6075 472644.6568 523736.7449 959910.2429 599409.6119 467490.4195 480995.4578 425562.3007 1517851.521 0.325954984 0.417800159 0.311390574 0.345051369 0.632413796 0.394906619 0.307994829 0.316892299 0.280371495 1 20.53359924 -1.484522842 5.861908514 1.000598421 0.370947608 0.794212318 0.096158627 0.000783174 6.89E-05 0.096960826 0.022833666 0.032770054 1.484522842 -0.629650813 RGVTIKPTVDDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 116.82 0.0031804 2767810000 1505640 1143020 1438590 1210060 1788710 1653470 1654490 1407950 1613250 1114500 FALSE TRUE 1565083.83 1339324.794 1476080.837 1449406.256 1484665.713 1269476.651 1524806.751 1389078.733 1555189.448 1332864.937 1.174225375 1.004846595 1.107449672 1.087436706 1.113890592 0.952442079 1.14400695 1.042175163 1.16680198 1 20.34609916 RHDS(ph)LHDPAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHDSLHDPAAPSR 13 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 RHDS(1)LHDPAAPSR;RHDS(1)LHDPAAPSR 77.221 0.012479 864670000 319010 383800 326720 413180 421080 422670 389880 367420 327260 455500 TRUE FALSE 331604.7611 449714.6645 335234.5916 494905.7708 349504.972 324511.2981 359320.1868 362495.3359 315481.9765 544746.5039 0.608732243 0.82554851 0.615395582 0.908506557 0.641591951 0.595710658 0.6596099 0.665438572 0.579135385 1 19.05522551 -1.151889536 5.025030446 1.000017424 0.681632572 0.477501859 0.101056491 1.89E-05 3.18E-06 0.093510704 0.022039479 0.070487233 1.151889536 -0.318384852 RHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 19 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 ;;;;;;;;;;;;;;;;;; 399.86 8.39E-181 18232864000 2692140.4 2906400 3338590.12 3589112.7 3474344 4064297.7 3009066 3052329.2 3245041.3 3200389.1 FALSE TRUE 2798428.182 3405551.591 3425596.521 4299028.48 2883776.248 3120426.154 2773207.544 3011417.72 3128252.897 3827444.069 0.731148028 0.889771746 0.895008904 1.123211313 0.753446999 0.815276748 0.724558607 0.786796009 0.817321649 1 21.86794986 RHEHPPNPPVS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RHEHPPNPPVSPGK 14 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK;RHEHPPNPPVS(1)PGK 121.44 5.39E-05 641772000 743119 440366 559665 476528 676092 839236 719198 604100 594814 356340 TRUE FALSE 772457.9119 515995.4349 574250.3297 570783.8161 561170.1233 644336.1577 662825.3815 596003.0276 573406.7603 426158.0005 1.812609199 1.210807809 1.347505688 1.339371349 1.316812362 1.511965414 1.555351257 1.398549428 1.345526213 1 18.70102889 0.744226654 2.275916289 1.000210443 1.426121271 0.409197184 0.156851523 1.12771234 8.477785982 0.143017637 0.038746375 5.549152427 -0.744226654 0.425910827 RHEHPPNPPVS(ph)PGKTVNDVNSNNNMSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHEHPPNPPVSPGKTVNDVNSNNNMSYR 28 2 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 RHEHPPNPPVS(0.771)PGKT(0.228)VNDVNS(0.001)NNNMSYR;RHEHPPNPPVS(0.931)PGKT(0.069)VNDVNSNNNMSYR 88.744 0.0021527 236718000 43247 29651 39636 24298.7 55019 58516 41095 39629 46464 31608 TRUE FALSE 44954.42495 34743.3286 40668.94672 29104.91034 45666.89003 44926.54582 37873.86652 39097.83807 44791.76972 37800.98243 1.189239593 0.919111789 1.075870099 0.769951162 1.208087386 1.188502069 1.0019281 1.034307459 1.184936656 1 15.20613611 RHEHPPNPPVSPGKT(ph)VNDVNSNNNMSYR ddPTM_MDA-MB-175_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(0.123)PGKT(0.877)VNDVNSNNNMSYR 100.86 0.0013268 191570000 79462 50618 67164 41483 100530 90601 67615 69867 73744 62783 TRUE FALSE 82599.22112 59311.24775 68914.34902 49688.21359 83441.94651 69560.29082 62315.15962 68930.54714 71089.96785 75084.1268 1.100088989 0.789930579 0.917828467 0.661767216 1.111312738 0.926431375 0.829937861 0.9180442 0.946804217 1 16.19622033 3.222624182 24.99999259 0.939274458 0.865471657 0.10132422 0.122841435 655.6405624 1028522.133 0.034540036 0.041408252 1669.645157 -3.222624182 -0.073802801 RHES(ph)EEGDSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RHESEEGDSHR 11 1 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHR;RHES(1)EEGDSHR;RHES(1)EEGDSHR 155.37 1.48E-05 284850600 146578.7 170881.7 159478.1 159137.6 165038.4 201224.6 175117.3 160339.9 149246 148327.2 TRUE FALSE 152365.7403 200229.3027 163634.2303 190614.5423 136985.2317 154493.2362 161391.1484 158190.8059 143874.6656 177389.0749 0.858935311 1.128757804 0.92245946 1.074556268 0.772230374 0.870928699 0.909814477 0.891773104 0.811068357 1 17.43655763 3.246343309 24.99999852 0.874205825 1.000381689 0.302236158 0.089363375 198.5009502 637632.0442 0.022906029 0.030449418 1763.369435 -3.246343309 0.126175865 RHES(ph)EEGDSHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHESEEGDSHRR 12 2 Q6UN15;Q6UN15-5;Q6UN15-3;H0Y8P7 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 RHES(1)EEGDSHRR 91.207 0.0040021 48664000 5853.3 9057.2 10034 7224.7 8021.3 10180 6865.3 9440.9 7382.9 10109 TRUE FALSE 6084.392804 10612.70364 10295.49428 8653.724096 6657.842291 7815.849279 6327.179847 9314.360178 7117.190871 12089.665 0.503272241 0.877832731 0.85159467 0.715795193 0.550705275 0.646490145 0.523354439 0.77043989 0.588700421 1 13.56148665 -1.934659087 5.923589498 1.131726695 0.678836234 0.378698633 0.126407222 0.073509785 0.000810859 0.040913881 0.028849395 0.011623607 1.934659087 -0.452890461 RHGAPAAPS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RHGAPAAPSPPPR 13 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR 118.55 0.00025661 1669068000 410455 497272 516792 509829 576174 647335 500969 547321 441609 508651 TRUE FALSE 426660.0803 582674.5978 530260.0241 610671.6545 478236.1493 497001.2567 461701.7407 539985.0572 425715.5784 608311.4247 0.701384296 0.957855753 0.871691707 1.003879969 0.786169928 0.817017791 0.7589891 0.887678638 0.699831634 1 19.21445057 RHNS(ph)SDGFDSAIGRPNGGNFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHNSSDGFDSAIGRPNGGNFGR 22 2 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 RHNS(0.919)S(0.081)DGFDSAIGRPNGGNFGR 168.26 5.02E-12 330430000 14094 22946 20280 18567 28376 27722 14807 19895 21646 22195 TRUE FALSE 14650.442 26886.797 20808.51346 22239.49718 23552.65766 21283.98563 13646.38865 19628.34007 20866.96469 26543.6853 0.551936999 1.012926302 0.783934605 0.837845119 0.887316791 0.801847422 0.51411055 0.739473055 0.786136682 1 14.69608107 2.457101275 24.99933309 0.721303565 0.827287554 0.000238663 0.155244399 568.6775328 710114.3613 0.050331133 0.042114344 286.4845957 -2.457101275 0.10598399 RHNS(ph)WSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.999)WS(0.001)SSSR;RHNS(1)WSSSSR 185.2 9.03E-07 2326710000 191037 413116 368469 357848 398114 493634 357489 444532 379269 498583 TRUE FALSE 198579.2883 484065.4594 378071.6048 428629.2663 330442.7245 378994.9846 329468.0781 438573.7756 365619.1828 596270.7929 0.33303541 0.811821517 0.634060245 0.718850011 0.554182308 0.635608836 0.552547738 0.735527852 0.613176408 1 19.18560815 -5 0.299759834 4.062196482 0.612913158 0.465520015 0.122532924 229.4495742 2.123096704 441.2550608 0.112580154 1.00E-05 5 -3.449283324 RHPKGEEGS(ph)DDDETENGPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHPKGEEGSDDDETENGPKPK 21 3 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 RHPKGEEGS(1)DDDETENGPKPK;RHPKGEEGS(1)DDDETENGPKPK 229.56 8.93E-26 655230000 662410 168977 347590 144303 639080 504430 399990 312150 384590 153105 TRUE FALSE 688562.4583 197997.4853 356648.4809 172845.7027 530449.4099 387283.7772 368637.7386 307966.1398 370748.681 183102.9934 3.760519943 1.081344885 1.947802569 0.943980759 2.897000208 2.115114396 2.013280787 1.681928483 2.024809503 1 17.48229585 -1.918259835 0.270207246 2.32E-12 2.113035061 0.152674657 0.76753274 60.7927114 2.568826888 40.37774061 0.960382517 0.012070914 1.918259835 2.113035061 RHPT(ph)GTTPPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHPTGTTPPVK 11 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 RHPT(0.436)GT(0.282)T(0.282)PPVK 53.034 0.082371 210100000 279760 228510 270600 217940 299810 329300 319800 265700 282210 237770 TRUE FALSE 290805.1408 267754.8149 277652.0583 261047.8815 248848.4033 252825.0656 294733.2404 262138.7261 272053.3172 284356.4791 1.02267809 0.941616719 0.976422479 0.918030362 0.875128304 0.889113082 1.036492087 0.921866549 0.956733316 1 18.11734115 -3.462955783 8.330782613 0.999751961 0.949314688 0 0.05221128 0 0 0 0.011379936 0.000344385 3.462955783 -0.050437273 RHQDGLPYIDDS(ph)PSSSPHLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHQDGLPYIDDSPSSSPHLSSK 22 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RHQDGLPYIDDS(0.98)PS(0.018)S(0.002)SPHLSSK 138.78 4.52E-07 275520000 48580 113620 123970 108280 133740 180010 101340 141050 119480 144800 TRUE FALSE 50497.97591 133133.3512 127200.76 129697.4608 111006.9226 138205.4056 93396.706 139159.4555 115179.9381 173170.7876 0.291607936 0.768797977 0.734539363 0.748956926 0.641025684 0.798087296 0.539332917 0.803596596 0.665123372 1 17.40183606 -5 0.113202267 1.967430822 0.511859531 0.372273349 0.14083214 185.1869706 1.383734622 42.04982073 1.535754101 1.00E-05 5 -1.455571291 ALSDHHIYLEGTLLKPNMVTPGHACTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 ALSDHHIYLEGTLLKPNMVTPGHACTQK 28 1 P04075;J3KPS3;P04075-2;H3BQN4;H3BU78 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 ;;;; 281.28 5.67E-62 16137490000 3207296 6887819 8274493 7106330 9615569 10680950 8112051 9720100 9289201 9052150 FALSE TRUE 3333922.523 8070748.333 8490133.085 8511940.864 7981118.016 8200461.234 7476207.246 9589817.958 8954884.471 10825745.48 0.307962397 0.745514325 0.784253898 0.786268334 0.737234958 0.757496216 0.690595143 0.885834419 0.827184094 1 23.36796304 4.750608916 3.328313542 0.797187133 0.234980233 0.768594066 0.081708953 0.152365021 2.718568141 0.018961851 0.22265841 56313.03257 -4.750608916 -0.5622069 down RHS(ph)DENDGGQPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSDENDGGQPHK 13 1 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RHS(1)DENDGGQPHK;RHS(1)DENDGGQPHK 167.99 1.46E-05 826160000 582977 446124 495200 488652 631648 706882 627308 538398 567146 386859 TRUE FALSE 605993.3821 522742.3266 508105.3188 585305.9071 524280.6986 542719.3684 578137.9598 531181.6555 546734.5262 462656.6142 1.309812426 1.129871076 1.098234205 1.265097892 1.13319616 1.173050059 1.249604873 1.148112097 1.181728542 1 18.81958229 0.010541142 1.068753722 0.998708835 1.185727164 0.437361762 0.063892897 7.86196267 7.530450001 0.092138701 0.017976702 1.024568835 -0.010541142 0.187018329 RHS(ph)DENDGGQPHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 141.6 4.57E-06 324794000 148786.4 108670.2 134971.5 105140.9 165188.1 161189.7 158132.7 138798.2 136735 104535.7 TRUE FALSE 154660.602 127333.4615 138488.9682 125937.4562 137109.4858 123755.835 145737.8458 136937.8372 131813.9341 125017.469 1.237111927 1.018525351 1.107756934 1.00735887 1.096722617 0.989908339 1.165739852 1.09534962 1.054364123 1 16.93177017 -3.640240439 0.009509405 1.34E-06 2.020294002 0.147785403 0.069987655 29103.96557 26.49752308 3151.587068 2510.244503 0.00022896 3.640240439 2.020292657 RHS(ph)GSYLVTSV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSGSYLVTSV 11 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 RHS(0.972)GS(0.028)YLVTSV;RHS(0.992)GS(0.008)YLVTSV 101.53 0.0010744 0 259280 395730 355270 367630 405250 487370 354630 385770 358870 438940 TRUE FALSE 269516.5746 463693.5491 364528.6281 440346.1167 336365.7498 374185.7037 326833.1739 380599.3841 345954.3388 524941.889 0.513421733 0.883323581 0.694417107 0.838847358 0.640767591 0.712813573 0.622608294 0.72503146 0.659033592 1 19.0017982 -2.028916502 2.741256338 1.353841749 0.705207032 0.448111057 0.100020554 39383418.87 12395219.75 87682863.74 0.021859534 0.009355855 2.028916502 -0.648634716 RHS(ph)HSHS(ph)PMSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSHSHSPMSTR 12 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 RHS(0.975)HS(0.026)HS(0.996)PMS(0.002)T(0.001)R;RHS(0.998)HS(0.01)HS(0.991)PMST(0.001)R 86.367 0.0046772 95376000 46126 63929 57670 52747 50214 66841 53326 48868 46089 58989 TRUE FALSE 47947.0901 74908.30845 59172.92758 63180.19917 41678.64222 51318.19074 49146.16878 48213.00439 44430.26589 70546.76514 0.679649733 1.061824852 0.838775916 0.895578969 0.59079452 0.727435066 0.696646667 0.683419067 0.62979877 1 16.10629231 3.259908507 24.99070581 0.702965222 0.880577876 0.214229834 0.135048532 285.9145958 334700.9966 0.034134542 0.04617496 1819.317543 -3.259908507 0.177612654 RHS(ph)LENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RHSLENK 7 1 O14578-4 O14578-4 CIT Citron Rho-interacting kinase 1 RHS(1)LENK;RHS(1)LENK;RHS(1)LENK 112.71 0.0038545 347970000 322035 227004 296548 229389 385497 411376 358585 303208 305138 229772 TRUE FALSE 334749.1905 265990.1712 304276.2845 274761.4595 319970.3576 315840.1585 330478.1707 299143.9927 294156.143 274791.4241 1.218193732 0.967971151 1.107299056 0.999890955 1.16441173 1.149381424 1.202650962 1.088622011 1.070470608 1 18.06797745 3.219908882 24.96051714 1.122796492 1.068238165 0.042705902 0.081570493 565.5905787 756895.1678 0.022306102 0.026706838 1659.238752 -3.219908882 -0.054558328 RHS(ph)MQTEQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RHSMQTEQIR 10 1 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 RHS(1)MQTEQIR;RHS(1)MQTEQIR;RHS(1)MQTEQIR 219.97 3.71E-09 841850000 125020 179562 172896 162383 189990 229696 153298 150709 160682 220639 TRUE FALSE 129955.8861 210400.3767 177401.8118 194501.8727 157695.5677 176352.5851 141282.1022 148688.9924 154899.0862 263868.9877 0.492501553 0.797366824 0.6723102 0.737115318 0.597628274 0.668333883 0.535425187 0.56349552 0.587030282 1 18.00946228 -0.955452071 4.880447264 1.000002963 0.628840339 0.615360719 0.08825015 2.87E-06 6.15E-07 0.086321364 0.020345978 0.110802084 0.955452071 -0.371162624 RHS(ph)MREEDFIQPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RHSMREEDFIQPSSR 15 2 Q14289 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RHS(1)MREEDFIQPSSR;RHS(1)MREEDFIQPSSR;RHS(1)MREEDFIQPSSR;RHS(1)MREEDFIQPSSR 98.391 0.002612 1025280000 425421 529850 539160 535830 547450 722690 444080 483164 509402 648680 TRUE FALSE 442216.9496 620847.6158 553210.9525 641815.5747 454394.6445 554856.2 409271.8492 476687.9769 491068.7215 775776.4263 0.570031435 0.800291933 0.713106165 0.827320286 0.585728864 0.715226941 0.527564174 0.614465664 0.633002892 1 19.56528141 -1.086544514 5.275241506 1.00000509 0.664705547 0.536207214 0.093412856 5.68E-06 9.84E-07 0.091919959 0.021665413 0.081932364 1.086544514 -0.335299543 RHS(ph)PESPSIAVVESELVAEYITTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.714)PES(0.128)PS(0.158)IAVVESELVAEYITTER;RHS(0.854)PES(0.059)PS(0.087)IAVVESELVAEYITTER 196.93 5.12E-25 27620000 18210.5 21559.3 25409.8 24156.4 23896.2 28689.6 26246.1 23813.9 23060.6 22459.4 TRUE FALSE 18929.4646 25261.94207 26072.00026 28934.46382 19834.33246 22026.8752 24188.8621 23494.71362 22230.65351 26859.88942 0.704748419 0.940508044 0.970666701 1.077236893 0.738436862 0.820065744 0.900557025 0.874713714 0.827652458 1 14.71316574 3.222227694 24.99865632 0.856452915 0.927904007 0.076540739 0.1063259 603.7642744 924100.7687 0.030706459 0.036803957 1668.121554 -3.222227694 0.071451092 RHS(ph)PESPSIAVVESELVAEYITTVSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RHSPESPSIAVVESELVAEYITTVSHR 27 1 Q7Z589-4;E9PMC9 Q7Z589-4 EMSY;C11orf30 Protein EMSY 1 RHS(0.993)PES(0.005)PS(0.001)IAVVESELVAEYITTVSHR;RHS(0.706)PES(0.221)PS(0.057)IAVVES(0.016)ELVAEYITTVSHR;RHS(0.926)PES(0.057)PS(0.017)IAVVES(0.001)ELVAEYITTVSHR 179.78 8.91E-18 73207000 11368.4 17908.1 17396.5 16361 17258.7 28179.1 15475.4 17006.3 18106.8 22525.9 TRUE FALSE 11817.23321 20983.67687 17849.86708 19597.15697 14325.07234 21634.93108 14262.39771 16778.35837 17455.1398 26939.41882 0.438659545 0.778920919 0.662592879 0.727452849 0.53175135 0.803095688 0.529424848 0.622818127 0.647940474 1 14.71743111 -2.015858713 2.175212013 1.388446906 0.641193493 0.497574861 0.109065467 7138986.39 2493345.757 13854488.95 0.024510789 0.009641426 2.015858713 -0.747253413 RHS(ph)PPIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RHSPPIEK 8 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK;RHS(1)PPIEK 169.65 0.00018362 3790713000 4829860 3767195 4492080 3895557 5586790 5707190 5162640 4615830 4878090 3827951 TRUE FALSE 5020546.602 4414181.437 4609147.295 4666086.548 4637149.431 4381781.616 4757978.787 4553962.349 4702528.494 4577964.708 1.096676563 0.964223562 1.006811452 1.01924913 1.012928174 0.95714622 1.039321858 0.99475698 1.027209425 1 22.12627491 4.754147347 24.68759426 1.003145607 1.096676645 0.572562409 0.024428228 1659.407552 2628257.214 0.005461014 0.128367083 56773.71945 -4.754147347 0.093531038 RHS(ph)SAS(ph)FENVWLRPGELGGAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSSASFENVWLRPGELGGAPK 22 2 P35568 P35568 IRS1 Insulin receptor substrate 1 2 RHS(0.826)S(0.214)AS(0.96)FENVWLRPGELGGAPK 58.877 0.036068 74670000 48372 51888 55250 47500 64331 66696 60576 49898 56970 48697 TRUE FALSE 50281.76391 60799.36037 56689.86039 56895.35823 53396.0396 51206.86479 55827.89483 49229.19893 54919.66083 58238.24479 0.863380483 1.043976524 0.973412928 0.9769415 0.916855235 0.879265249 0.958612249 0.84530705 0.943017102 1 15.82967926 3.211382489 7.091846994 0.911605287 0.970796952 0.079818479 0.057802432 0.281270619 50.00574186 0.015711693 0.019233689 1626.98103 -3.211382489 0.059191665 RHS(ph)SDINHLVTQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSSDINHLVTQGR 14 1 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5;A0A075B6Q2 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 1 RHS(0.556)S(0.444)DINHLVTQGR 61.015 0.041545 91928000 40184 139890 109440 131780 112890 153370 119790 121190 127020 194590 TRUE FALSE 41770.49535 163915.0193 112292.0963 157845.6907 93700.99812 117752.1418 110400.5468 119565.6463 122448.575 232716.1848 0.179491149 0.704355906 0.482528091 0.678275517 0.402640659 0.505990342 0.474399951 0.513783115 0.526171289 1 17.82821202 0.280222649 1.731897809 1.000051694 0.50222392 0.549746763 0.136818634 7.227797049 16.45776771 0.118335318 0.033208956 1.906437837 -0.280222649 -0.497827774 RHS(ph)VADPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSVADPR 8 1 A0A0D9SGD0;A0A0D9SF89;Q9H2X9 A0A0D9SGD0 SLC12A5 Solute carrier family 12 member 5 1 RHS(1)VADPR 51.268 0.092071 382100000 426910 521260 484340 529920 603310 584700 452430 472430 472180 554240 TRUE FALSE 443764.7364 610782.3502 496962.2983 634736.5943 500759.5817 448912.2862 416967.3544 466097.8486 455186.334 662832.7164 0.669497334 0.921472847 0.749755234 0.957612047 0.755484105 0.67726332 0.629068759 0.703190771 0.686728827 1 19.33828529 3.009021954 24.97302215 0.711154115 0.82995855 0.07772705 0.121995575 325.6356084 901360.5396 0.032444526 0.038727358 1020.991095 -3.009021954 0.118804434 RHS(ph)VSEMTSCPEPQGFSDPPGQGPTGTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.299)VS(0.193)EMT(0.253)S(0.253)CPEPQGFS(0.001)DPPGQGPTGTFR;RHS(0.636)VS(0.099)EMT(0.132)S(0.132)CPEPQGFSDPPGQGPTGTFR;RHS(0.25)VS(0.25)EMT(0.25)S(0.25)CPEPQGFS(0.001)DPPGQGPTGTFR 104.51 0.00022864 444062000 54737 68455 71195 61477 99206 84784 66566 70002 78559 71173 TRUE FALSE 56898.05903 80211.61374 73050.40019 73636.96711 82342.99956 65094.20091 61348.38298 69063.73769 75731.67694 85117.98666 0.668461053 0.942357977 0.858225189 0.865116411 0.967398347 0.764752592 0.720745231 0.811388291 0.889725896 1 16.37717641 RHS(ph)VTDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSVTDKR 8 2 Q17R89-3;Q17R89 Q17R89-3 ARHGAP44 Rho GTPase-activating protein 44 1 RHS(0.999)VT(0.001)DKR;RHS(0.991)VT(0.009)DKR 98.156 0.0040293 73929000 112175 86018 102615 85054 130718 125298 110117 106366 109232 86525 TRUE FALSE 116603.7556 100790.9224 105289.2312 101877.4273 108498.6011 96199.43841 101485.7418 104940.3377 105300.7617 103477.9171 1.12684676 0.974033158 1.017504354 0.98453303 1.048519376 0.929661527 0.980747822 1.014132683 1.017615783 1 16.65896339 4.744677409 24.95176436 0.996673968 1.126846819 0.622990272 0.030464076 428.3360432 1747229.334 0.007048609 0.065168229 55549.14889 -4.744677409 0.130172851 RHS(ph)VTLPSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RHSVTLPSSK 10 1 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 RHS(0.998)VT(0.002)LPSSK;RHS(0.998)VT(0.002)LPSSK;RHS(0.996)VT(0.004)LPSSK;RHS(0.978)VT(0.022)LPSSK;RHS(0.999)VT(0.001)LPSSK;RHS(1)VTLPSSK 138.77 3.43E-05 4060410000 4284870 4025130 4705120 4100440 6456970 6293180 5301580 5116750 5715020 4656840 TRUE FALSE 4454039.976 4716414.766 4827739.292 4911494.793 5359416.546 4831684.319 4886028.306 5048168.336 5509337.547 5569258.637 0.799754557 0.846865817 0.866854928 0.881893823 0.96232136 0.867563285 0.877321135 0.90643453 0.989240742 1 22.40905386 8 0.090296543 1.07274379 0.36899676 0.682551631 0.034619395 99.65449976 0.646057831 0.655359667 8.688914542 99999999.9 -8 -0.70374703 RHS(ph)VVAGGGGGEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 195.18 3.56E-08 1582230000 501393 565521 561237 629301 651348 671930 511778 493940 503944 584309 TRUE FALSE 521188.3828 662644.8326 575863.2973 753774.8595 540632.0996 515884.4407 471663.5031 487319.5422 485807.1539 698793.1613 0.745840703 0.948270346 0.824082617 1.078680933 0.773665413 0.738250557 0.674968688 0.697373084 0.695208798 1 19.41450596 3.020380826 24.98626734 0.734260223 0.900957742 0.224947415 0.118671736 272.728189 334354.0518 0.032035504 0.038286053 1048.047161 -3.020380826 0.166697519 RHS(ph)WGPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;RHS(1)WGPGK 134.38 0.0005384 898930000 1065990 930260 1099540 929440 1359960 1460710 1187810 1086310 1132500 967050 TRUE FALSE 1108076.108 1090024.919 1128194.916 1113280.458 1128794.485 1121482.24 1094706.348 1071749.791 1091741.546 1156524.932 0.958108275 0.942500147 0.975504189 0.962608265 0.976022612 0.969700011 0.946547989 0.926698389 0.943984445 1 20.14136494 2.225085438 23.2801461 0.945836585 0.964089348 0 0.020278373 189.4813711 327348.7428 0.007313722 0.005438428 167.9134319 -2.225085438 0.018252762 RHS(ph)YAGEQPETVPYLLLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHSYAGEQPETVPYLLLNR 19 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RHS(1)YAGEQPETVPYLLLNR;RHS(1)YAGEQPETVPYLLLNR 107.56 0.00017888 1811910000 176768 214971 200996 202576 224319 254556 183821 210708 184470 239700 TRUE FALSE 183746.9371 251890.597 206234.1209 242644.9282 186189.3365 195439.2268 169412.6297 207883.8039 177830.9607 286664.6257 0.640982251 0.878694385 0.719426474 0.846441822 0.64950231 0.681769599 0.590978497 0.725181223 0.620344977 1 18.12900436 -1.245911433 4.395638106 1.00014084 0.709311667 0.496668605 0.088753468 0.0001209 2.07E-05 0.084813156 0.019981013 0.056766036 1.245911433 -0.290829173 RHSLAMPGET(ph)VLNGNQEWVVQADLPLTAAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSLAMPGETVLNGNQEWVVQADLPLTAAIR 31 1 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 RHS(0.453)LAMPGET(0.547)VLNGNQEWVVQADLPLTAAIR 96.158 0.00027769 18155000 6098 6774 6759.6 8862.2 8590.7 12359 7158.7 4195.4 7518.3 9172.4 TRUE FALSE 6338.753749 7937.381806 6935.760729 10615.11671 7130.455883 9488.809552 6597.582388 4139.167525 7247.717852 10969.55616 0.57784961 0.723582767 0.632273597 0.967688806 0.650022278 0.865013079 0.601444789 0.37733227 0.660712042 1 13.42121753 2.07144055 11.33467596 0.58001264 0.737224362 0 0.183747472 1.023608528 157.7381964 0.065991102 0.048731811 117.8801148 -2.07144055 0.157211723 RHSPES(ph)PSIAVVESELVAEYITTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSPESPSIAVVESELVAEYITTER 25 1 Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-7 EMSY Protein EMSY 1 RHS(0.274)PES(0.363)PS(0.363)IAVVESELVAEYITTER 103.9 0.0027841 18981000 5786.3 8713.6 6695.8 8257.4 9737.1 10803 8483.1 8776.4 7929.9 9258.5 TRUE FALSE 6014.747592 10210.09302 6870.298049 9890.689074 8081.99122 8294.166971 7818.172456 8658.766713 7644.504448 11072.52581 0.543213689 0.922110564 0.620481556 0.893264034 0.729913965 0.749076328 0.706087535 0.782004654 0.690402947 1 13.43469674 -1.96719827 2.359910963 1.212904882 0.745518197 0.346852499 0.107589432 7737227.899 3365423.877 9005846.826 0.023925423 0.010784543 1.96719827 -0.467386685 RHSVSEMTS(ph)CPEPQGFSDPPGQGPTGTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHSVSEMTSCPEPQGFSDPPGQGPTGTFR 29 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 RHS(0.164)VS(0.189)EMT(0.297)S(0.347)CPEPQGFS(0.003)DPPGQGPTGTFR 62.942 0.011586 482890000 27921 33402 36501 37018 31210 42781 33239 26965 30479 36544 TRUE FALSE 29023.34264 39138.53367 37452.24605 44340.04991 25904.93535 32845.7611 30633.64033 26603.57828 29382.06674 43704.09712 0.664087455 0.895534658 0.856950458 1.014551331 0.59273471 0.751548785 0.700932918 0.608720464 0.672295475 1 15.41548091 3.227385141 24.99984105 0.695611213 0.860418367 0.187069484 0.133429811 279.7753389 625863.9099 0.036469787 0.043964296 1688.049358 -3.227385141 0.164807154 RHT(ph)MDKDSR ddPTM_MDA-MB-175_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 134.56 0.011696 613090000 897850 706550 768500 755950 1304820 1227350 1067130 895340 937190 803410 TRUE FALSE 933297.8113 827894.4663 788527.7413 905474.6537 1083027.162 942316.5632 983485.5622 883339.4318 903460.715 960822.8073 0.971352683 0.861651555 0.820679667 0.942395046 1.127187192 0.980739171 1.02358682 0.919357269 0.94029899 1 19.87391087 3.479788614 24.99995451 0.994066796 0.882148154 0.398601538 0.062796277 109.3750327 1025126.519 0.018096781 0.024941118 3018.482163 -3.479788614 -0.111918642 RHT(ph)PLSK ddPTM_MDA-MB-175_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 60.518 0.056855 597260000 599230 510010 648500 530530 777830 839950 805020 628580 701180 506310 TRUE FALSE 622888.0631 597600.2502 665400.4427 635467.2505 645614.7344 644884.3421 741920.4289 620154.9132 675944.6688 605511.7506 1.028696904 0.986934192 1.098905912 1.049471377 1.066229902 1.065023662 1.225278334 1.024183119 1.116319655 1 19.20779543 4.235895739 24.99924252 1.083844541 1.007815538 0.195638432 0.058815365 92.87558269 871302.7288 0.013909621 0.032366612 17214.55256 -4.235895739 -0.076029004 RHT(ph)VEDAVVSQGPEAAGPLSTPQEVSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHTVEDAVVSQGPEAAGPLSTPQEVSASR 29 1 Q96NW4 Q96NW4 ANKRD27 Ankyrin repeat domain-containing protein 27 1 RHT(0.815)VEDAVVS(0.185)QGPEAAGPLSTPQEVSASR;RHT(0.947)VEDAVVS(0.053)QGPEAAGPLSTPQEVSASR 116.34 0.00012452 161372000 54985 58595 64016 61745 66898 74326 51141 61598 62533 67748 TRUE FALSE 57155.85026 68658.23544 65684.30955 73957.97671 55526.70186 57064.91292 47132.43479 60772.37956 60282.44955 81021.92349 0.705436847 0.847403178 0.810697978 0.912814378 0.685329346 0.704314468 0.581724461 0.750073276 0.744026394 1 16.30602472 3.215969124 24.99460212 0.720385819 0.820511363 0.075372994 0.110869304 410.9945206 454711.8955 0.030226503 0.036151684 1644.254822 -3.215969124 0.100125544 RHVTLPS(ph)SPR ddPTM_MDA-MB-175_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(0.009)LPS(0.613)S(0.378)PR 76.868 0.021259 183720000 89176 115850 107450 129000 137690 157880 131600 123440 106930 119010 TRUE FALSE 92696.73734 135746.3363 110250.2353 154515.815 114285.503 121214.7627 121284.8481 121785.4887 103081.6102 142327.7309 0.651290769 0.953758874 0.774622307 1.085633938 0.80297425 0.85165949 0.852151913 0.855669432 0.724255277 1 17.11885726 -2.523475252 2.231057984 3.232132646 0.848391645 0.148412156 0.113678142 3518028.18 472919.574 39934536.9 0.026095203 0.002995882 2.523475252 -2.383741 RHYNGEAYEDDEHHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RHYNGEAYEDDEHHPR 16 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 ; 133.23 1.05E-05 250280000 82584 94199 87783 68129 104685 120340 80593 82473 85172 116421 FALSE TRUE 85844.48009 110376.9455 90070.69709 81604.71286 86890.68109 92392.85877 74275.91007 81367.58433 82106.67636 139231.4659 0.616559479 0.792758625 0.646913372 0.586108264 0.624073592 0.663591798 0.533470718 0.58440514 0.589713509 1 17.08712577 -1.140109702 7.51993205 1.000000128 0.624651336 0.745045138 0.065557389 1.50E-07 1.71E-08 0.067565496 0.015925335 0.072425299 1.140109702 -0.375348792 RIDFIPVS(ph)PAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 RIDFIPVS(1)PAPS(0.976)PT(0.024)R;RIDFIPVS(1)PAPS(0.94)PT(0.06)R;RIDFIPVS(1)PAPS(0.977)PT(0.023)R;RIDFIPVS(1)PAPS(0.635)PT(0.365)R 136.46 2.59E-05 810740000 836540 836650 786070 709080 813330 866710 683710 725360 735900 837580 TRUE FALSE 869567.2451 980338.1293 806555.63 849333.9076 675080.4571 665429.7376 630119.0237 715637.7356 709415.1028 1001687.765 0.868102093 0.978686337 0.805196648 0.847902847 0.673943 0.664308541 0.629057323 0.714431943 0.708219794 1 19.93400145 3.599360773 1.709186288 0.708780828 0.909822824 0.28451579 0.105967592 0.364082113 2.092121947 0.029814308 0.058197971 3975.216376 -3.599360773 0.201041995 RIDFIPVSPAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RIDFIPVSPAPS(0.837)PT(0.163)R 207.1 2.18E-09 317410000 190430 247600 238880 258040 273790 355070 277030 257950 281770 315300 TRUE FALSE 197948.3234 290123.3739 245105.409 309079.5418 227251.2736 272610.3736 255315.6647 254492.6022 271629.1527 377076.9982 0.52495465 0.769400879 0.650014215 0.819672224 0.602665436 0.722956783 0.677091591 0.674908847 0.720354607 1 18.52449962 -4.999999999 0.413092935 6.516039759 0.681967352 0.597791475 0.077988974 541.5991696 3.610207492 2705.517509 0.041714142 1.00E-05 4.999999999 -5.834072407 RIDFTPVS(ph)PAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 2 RIDFT(0.045)PVS(0.955)PAPS(0.66)PT(0.34)R;RIDFT(0.01)PVS(0.99)PAPS(0.995)PT(0.005)R;RIDFT(0.012)PVS(0.988)PAPS(0.984)PT(0.016)R 151.41 2.01E-06 676660000 806860 871940 912260 803060 1017700 1059330 893260 892960 920000 875130 TRUE FALSE 838715.4558 1021688.912 936034.245 961902.8711 844711.7175 813316.6618 823243.9471 880991.3318 886889.3797 1046594.968 0.801375395 0.976202775 0.894361499 0.91907844 0.8071047 0.777107369 0.786592686 0.841769126 0.84740459 1 19.9972718 RIDFTPVSPAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RIDFTPVSPAPS(0.886)PT(0.114)R 155.86 1.36E-06 173290000 59389 72584 79428 95319 101570 97958 96597 79657 95694 98623 TRUE FALSE 61733.72358 85049.73737 81497.95893 114172.8137 84305.16768 75208.73907 89025.47473 78589.32821 92249.99163 117946.2886 0.523405393 0.721088712 0.690975188 0.968006836 0.714775926 0.637652443 0.754796745 0.66631455 0.782135604 1 16.8477705 0.910586713 5.755857371 0.999991264 0.715755596 0.405927443 0.105525797 0.83573091 52.66526269 0.100551414 0.025310027 8.139293567 -0.910586713 -0.284235669 RIDIS(ph)PSTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.999)PS(0.001)TFR;RIDIS(0.609)PS(0.366)T(0.025)FR;RIDIS(0.692)PS(0.197)T(0.11)FR;RIDIS(0.953)PS(0.041)T(0.006)FR;RIDIS(0.944)PS(0.039)T(0.017)FR;RIDIS(0.952)PS(0.037)T(0.011)FR;RIDIS(0.998)PS(0.002)TFR 143.94 2.03E-05 31466340000 474176 635297 615287 524264 729756 704332 591328 625437 613974 653249 TRUE FALSE 492896.8346 744404.3178 631321.8847 627961.8544 605712.3358 540761.5673 544978.1662 617054.04 591877.1957 781240.6343 0.630915512 0.95284895 0.8081017 0.80380081 0.775321084 0.692183104 0.697580415 0.78983864 0.757611893 1 19.57540746 -1.283730294 3.67090945 1.000535056 0.771606366 0.418535946 0.082061647 9190919.014 6476429.691 35927.90428 0.018706434 0.052031903 1.283730294 -0.228928689 RIDIS(ph)PSTFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RIDISPSTFRK 11 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 RIDIS(0.991)PS(0.008)T(0.001)FRK;RIDIS(0.911)PS(0.083)T(0.006)FRK;RIDIS(0.903)PS(0.036)T(0.061)FRK 123.72 0.00028673 3043130000 975268 1007837 1042422 734971 1478650 1288910 770055 1003800 1186300 1329900 TRUE FALSE 1013772.334 1180925.165 1069588.374 880346.0701 1227309.601 989580.1861 709696.0769 990345.7029 1143605.295 1590468.443 0.637404872 0.742501475 0.67249896 0.553513699 0.771665484 0.622194166 0.44621827 0.622675481 0.719036772 1 20.60102032 0.857106342 3.381764656 0.999843164 0.631239868 0.619400868 0.086230589 0.451921616 9.265159726 0.086203937 0.02231944 7.196251656 -0.857106342 -0.368603296 RIDIS(ph)PSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(1)PSTLR;RIDIS(0.988)PS(0.011)TLR;RIDIS(0.885)PS(0.099)T(0.015)LR;RIDIS(0.918)PS(0.072)T(0.01)LR;RIDIS(0.978)PS(0.016)T(0.007)LR;RIDIS(0.982)PS(0.013)T(0.005)LR;RIDIS(0.849)PS(0.101)T(0.05)LR;RIDIS(0.793)PS(0.151)T(0.056)LR;RIDIS(1)PSTLR;RIDIS(0.997)PS(0.002)T(0.001)LR 141.07 2.34E-05 36457790000 933217 1021980 1012574 942426 1030454 1136884 1001231 986337 879505 1085364 TRUE FALSE 970061.1278 1197497.115 1038962.51 1128835.05 855297.7971 872859.9206 922751.898 973116.7658 847851.7869 1298020.295 0.747338952 0.922556542 0.800420852 0.869659014 0.658924826 0.672454756 0.710891734 0.749693028 0.65318839 1 20.30788151 3.249643941 24.99370393 0.724931048 0.838778833 0.155976362 0.103216122 308.8843095 696552.5679 0.026210709 0.035164034 1776.822074 -3.249643941 0.113847785 RIDIS(ph)PSTLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.715)PS(0.094)T(0.191)LRK;RIDIS(0.845)PS(0.14)T(0.015)LRK;RIDIS(0.993)PS(0.004)T(0.004)LRK;RIDIS(0.996)PS(0.002)T(0.002)LRK 110.98 0.000898 6182010000 1684100 1505760 1669270 1197890 2139200 2047600 1560670 1694240 1731990 1894750 TRUE FALSE 1750589.568 1764362.567 1712772.548 1434829.067 1775579.548 1572075.932 1438340.607 1671531.484 1669656.018 2265989.985 0.772549561 0.778627698 0.755860599 0.633201857 0.783577844 0.693770026 0.634751529 0.737660579 0.73683292 1 21.11171005 -1.492629636 4.968200188 1.000835664 0.722828184 0.712382806 0.052362532 0.000485942 4.96E-05 0.050832102 0.011946327 0.032164023 1.492629636 -0.27800748 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_MDA-MB-175_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(0.978)PS(0.022)LEEPSDLEELEQFAK;RIDT(0.912)PS(0.086)LEEPS(0.002)DLEELEQFAK;RIDT(0.497)PS(0.497)LEEPS(0.006)DLEELEQFAK;RIDT(0.918)PS(0.069)LEEPS(0.013)DLEELEQFAK;RIDT(0.976)PS(0.024)LEEPSDLEELEQFAK;RIDT(0.968)PS(0.032)LEEPSDLEELEQFAK 255.68 1.17E-36 797277000 451797 380364 419838 351838.8 515339 499911 452030 424781 438206 410750 TRUE FALSE 469634.2944 445688.5582 430779.3232 421431.4645 427741.8609 383814.2465 416598.7074 419087.5055 422435.0517 491228.5982 0.956040215 0.90729359 0.87694268 0.857913131 0.870759281 0.781335305 0.848075029 0.853141505 0.859956145 1 18.90603503 4.578109504 1.314363626 0.856232647 0.981757306 0.202879531 0.051577849 1.277876267 2.418168763 0.013457183 0.199054862 37853.80183 -4.578109504 0.125524658 RIEELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RIEELNK 7 1 Q9BTC8;E7EV10;E7EQY4;Q9BTC8-2;E9PCS8;H7C3F3;H0YIT0;E9PF88;E7ESY4;Q13330-3;Q13330;Q13330-2;O94776 Q9BTC8;E7ESY4;O94776 MTA3;MTA1;MTA2 Metastasis-associated protein MTA3;Metastasis-associated protein MTA1;Metastasis-associated protein MTA2 0 ;;; 128.61 0.0059987 654140000 705000 632960 701250 531397 938100 872010 758220 709900 727960 701490 FALSE TRUE 732833.9444 741665.9563 719525.1511 636505.7405 778642.0971 669498.8929 698788.7352 700384.9517 701760.8618 838933.5347 0.873530398 0.884058064 0.857666456 0.758708186 0.928133237 0.798035679 0.832948865 0.834851538 0.836491608 1 19.67819699 -1.39853687 7.497360269 1.000004834 0.843789607 0.527217161 0.044040231 3.34E-06 2.68E-07 0.040040122 0.009437255 0.039945065 1.39853687 -0.156215227 RIENAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RIENAK 6 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;;; 117.62 0.036181 2569850000 2475570 2138410 2502970 2018180 3064300 2982180 2904140 2562990 2746020 2455940 FALSE TRUE 2573307.415 2505665.283 2568199.454 2417369.98 2543431.381 2289613.89 2676505.918 2528637.311 2647191.277 2937134.421 0.876128582 0.853098607 0.874389485 0.82303689 0.865956751 0.779540042 0.91126436 0.860919845 0.901283665 1 21.48597786 0.692896799 0.922735865 1.000180898 0.850563534 0.648811014 0.032568401 0.604033771 0.915305641 0.029448897 0.009754671 4.930566258 -0.692896799 -0.149617364 RIEQHYFEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 ; 122.51 0.00031589 399870000 296060 377410 255120 370950 341670 417670 316280 295400 261520 372990 FALSE TRUE 307748.6774 442227.2317 261768.6368 444322.8028 283593.0554 320672.4724 291489.1472 291440.6462 252107.9463 446070.2492 0.689910789 0.991384726 0.586832763 0.996082576 0.635758731 0.718883344 0.653460184 0.653351455 0.565175433 1 18.7669114 4.231809558 24.99379837 0.713097586 0.840647758 0.070361128 0.160873121 323.9832132 1199469.354 0.037343162 0.083639918 17053.34419 -4.231809558 0.127550172 RIEYIEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIEYIEAR 8 1 Q8WUW1;Q8WUW1-2 Q8WUW1 BRK1 Protein BRICK1 0 ; 107.79 0.0063107 1221260000 1119790 1398300 1291600 1316850 1712060 1923530 1418070 1394430 1318910 1873630 FALSE TRUE 1164000.174 1638447.148 1325260.157 1577319 1421044.653 1476819.309 1306917.968 1375739.947 1271442.687 2240731.926 0.519473196 0.731210695 0.591440744 0.703930257 0.634187712 0.659078979 0.583254941 0.613969003 0.567422935 1 21.09553863 -1.108955425 4.320209368 1.000051578 0.626154408 0.77930608 0.060215132 7662401.152 1966864.264 3816.380716 0.012933528 0.077811641 1.108955425 -0.37389717 RIILLAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIILLAEGR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 161.17 0.0001038 209880000 87624 80416 49765 53784 274750 134720 85206 50907 63982 312050 FALSE TRUE 91083.46318 94226.82245 51061.91678 64422.31467 228048.0931 103433.3217 78527.33108 50224.67493 61679.30032 373190.2229 0.244067121 0.252490062 0.136825441 0.172625944 0.611077352 0.277159784 0.210421727 0.134581969 0.165275767 1 18.50955166 -1.415115739 3.348740388 1.008324642 0.242106711 0.749066181 0.13109536 124261083.2 167989694 9873036.841 0.033310555 0.03844893 1.415115739 -0.766217931 RIILLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIILLVK 7 1 P52209-2;P52209;K7EM49;K7EPF6;K7EMN2 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 117.93 0.022747 0 78544 69372 83862 54837 142920 114220 97875 88689 92728 113920 FALSE TRUE 81644.97777 81286.10136 86047.51261 65683.59493 118626.5094 87694.13602 90203.30175 87500.26902 89390.73739 136240.4429 0.59927123 0.59663709 0.631585679 0.482115248 0.870714356 0.643671836 0.662089023 0.642248859 0.65612483 1 17.0557955 -5 0.253598235 3.206906614 0.612126216 0.59492101 0.089411012 127.5300924 1.260649576 146.1880877 0.12199069 1.00E-05 5 -2.594780398 RINPPSSGGTSS(ph)SPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RINPPSSGGTSSSPIK 16 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 RINPPSS(0.001)GGT(0.002)S(0.013)S(0.572)S(0.412)PIK 79.511 0.011116 222400000 213010 165180 202880 147430 248100 269530 217470 197160 236440 193720 TRUE FALSE 221419.7993 193548.3801 208167.2195 176591.214 205928.0506 206935.7423 200424.1331 194517.3927 227930.5706 231675.725 0.955731548 0.835427968 0.898528404 0.762234429 0.888863305 0.893212883 0.865106317 0.839610592 0.983834498 1 17.82174736 1.228630666 22.78631702 0.991917729 0.86410903 0.518607212 0.047929173 55.35364579 127006.3416 0.041120523 0.010872047 16.92897508 -1.228630666 -0.127808699 RIPADTFAALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIPADTFAALK 11 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 121.02 0.0006739 271720000 784340 663230 672610 696070 1108430 972560 939670 734300 738560 789920 FALSE TRUE 815306.3488 777134.5933 690138.7692 833750.5684 920019.4645 746697.6793 866016.21 724457.9096 711979.3699 944689.7001 0.863041429 0.822634769 0.730545458 0.882565533 0.973885356 0.790415815 0.916720284 0.766873937 0.753664796 1 19.849481 -2.349975797 2.30786931 2.071718994 0.833148732 0.319177256 0.073007343 4512286.525 774156.8122 25150632.58 0.017732452 0.004467085 2.349975797 -1.238570261 RIPADTFAALKNPNAMLVNLEEPLASTYQDILYQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIPADTFAALKNPNAMLVNLEEPLASTYQDILYQAK 36 2 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 304.51 7.38E-93 484210000 343350 310750 370600 256760 464370 420040 373240 335880 399380 358610 FALSE TRUE 356905.7231 364118.8952 380258.1405 307546.3616 385436.5533 322492.0758 343984.4735 331378.078 385006.3918 428872.7635 0.832194892 0.849013801 0.886645581 0.717103971 0.898720054 0.751952801 0.802066493 0.772672238 0.897717049 1 18.71019017 0.985131585 4.561217843 0.999761343 0.812872959 0.540359559 0.054033003 0.120185302 8.222456869 0.049278029 0.012514625 9.663436229 -0.985131585 -0.186888384 RIPEEILGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIPEEILGK 9 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ; 104.22 0.0052837 714690000 1452950 1142330 1398810 1269260 1769690 1845590 1709520 1479530 1506300 1155540 FALSE TRUE 1510313.588 1338516.291 1435264.138 1520315.84 1468878.726 1416979.693 1575523.355 1459699.32 1452088.557 1381945.939 1.092889053 0.968573555 1.038581972 1.100126855 1.062906069 1.025351031 1.140075969 1.056263693 1.050756413 1 20.39826975 3.988230092 24.85345739 1.067292116 1.023942924 0.067712011 0.045712713 938.3536494 1981455.859 0.010845392 0.021049363 9732.627283 -3.988230092 -0.043349192 RIPHS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIPHSPAR 8 1 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 RIPHS(1)PAR 65.179 0.039777 956140000 45357 76891 57580 64059 97207 96792 60297 63011 68065 134990 TRUE FALSE 47147.72938 90096.43112 59080.5821 76729.679 80683.78886 74313.5249 55570.76358 62166.44061 65615.35395 161438.706 0.292047245 0.558084448 0.365962932 0.475286757 0.499779705 0.46032037 0.344222058 0.385077669 0.406441278 1 17.30062699 -1.624581765 2.686294595 1.056652763 0.422225798 0.842205273 0.075209394 11104488.03 10143859.19 4388417.51 0.018425209 0.023736585 1.624581765 -0.634426966 RIPSIVS(ph)SPLNSPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 RIPS(0.005)IVS(0.595)S(0.4)PLNSPLDR 70.99 0.025656 99274000 63639 68600 76069 61146 72614 72564 61580 58384 61369 81131 TRUE FALSE 66151.51686 80381.51637 78051.42063 73240.4963 60271.09822 55712.11072 56753.19869 57601.45798 59160.34168 97027.0661 0.681784161 0.828444264 0.804429359 0.754846037 0.621178199 0.574191439 0.584921311 0.593663812 0.609730295 1 16.56609963 3.28953852 5.063837277 0.631040576 0.776886371 0.109162902 0.124929915 0.276572061 15.14071846 0.032473824 0.043549098 1947.773802 -3.28953852 0.145845795 RIPSIVSS(ph)PLNSPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 RIPSIVS(0.082)S(0.918)PLNSPLDR;RIPSIVS(0.064)S(0.936)PLNSPLDR 105.46 0.00078503 550980000 218454 243510 241300 227160 277070 286310 225018 260300 247000 289360 TRUE FALSE 227078.7326 285330.9483 247588.4762 272091.57 229973.7404 219818.8416 207380.5012 256811.1043 238110.5182 346054.5519 0.656193457 0.824525921 0.715460828 0.786267854 0.664559212 0.63521442 0.599271127 0.74211162 0.688072204 1 18.40063996 -1.590201132 5.312121247 1.001974972 0.70320122 0.653077031 0.065298972 0.001571129 0.000121203 0.065038008 0.015237194 0.025692056 1.590201132 -0.298773752 RIQLVEEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 272.65 7.26E-27 11204490000 3866540 4412670 4259650 4268300 4691980 5212940 4454110 4643930 4305660 5027530 FALSE TRUE 4019193.985 5170511.747 4370659.978 5112557 3894438.916 4002313.688 4104985.22 4581685.714 4150700.138 6012578.246 0.668464313 0.859949182 0.726919435 0.850310265 0.647715299 0.665656815 0.682732939 0.762016813 0.690336153 1 22.51955233 -1.2056892 5.087924068 1.000024389 0.731722113 0.56553204 0.071401835 1.93E-05 3.02E-06 0.067607538 0.015933802 0.062274579 1.2056892 -0.268302275 RIQLVEEELDRAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 293.52 3.13E-44 511608000 149416 246490 221560 127781 284131 264685 114779 178497 224986 483505 FALSE TRUE 155315.0591 288822.7401 227334.0356 153055.7004 235834.5141 203215.9201 105782.3221 176104.5397 216888.7978 578238.5475 0.26860032 0.499487178 0.393149223 0.264693008 0.407849866 0.351439594 0.182938897 0.304553442 0.375085332 1 19.14130526 0.792357689 5.664774664 0.999999574 0.333565795 0.85057348 0.083316864 2.903387842 79.13019389 0.082806892 0.020850412 6.199514625 -0.792357689 -0.666433779 RIQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIQPQPPDEDGDHSDKEDEQPQVVVLK 27 2 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK;RIQPQPPDEDGDHS(1)DKEDEQPQVVVLK 92.343 0.0028495 262070000 561690 174950 296758 164045 415840 453460 333546 280107 346756 180463 TRUE FALSE 583865.9549 204996.3016 304491.7573 196492.6114 345155.6653 348150.7873 307401.793 276352.6238 334276.3193 215821.2697 2.705321657 0.949842904 1.410851478 0.910441365 1.599266216 1.613144005 1.424335022 1.280469827 1.548857162 1 17.71947753 4.748357681 24.80320714 1.32597071 2.705322489 0.731750529 0.254201058 612.6290158 1550956.36 0.05859909 0.775807479 56021.88021 -4.748357681 1.379351779 RIS(ph)ACLSDYSLASDSGVFEPLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RISACLSDYSLASDSGVFEPLTK 23 1 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 RIS(0.988)ACLS(0.012)DYSLASDSGVFEPLTK;RIS(0.999)ACLS(0.001)DYSLASDSGVFEPLTK;RIS(0.982)ACLS(0.018)DYSLASDSGVFEPLTK 220.14 1.21E-32 148463000 181291 173162 186164 161160 224215 234283 199940 183040 193802 177436 TRUE FALSE 188448.5087 202901.2265 191015.5868 193036.967 186103.0144 179874.3238 184268.1804 180586.6482 186827.1039 212201.187 0.88806529 0.956173853 0.900162669 0.909688441 0.877012127 0.847659367 0.868365455 0.851016202 0.880424405 1 17.6950732 3.30809978 3.174348063 0.87479233 0.917370357 0.033404193 0.044402578 0.435489777 8.845486138 0.012012496 0.016438045 2032.824004 -3.30809978 0.042578027 RIS(ph)AVEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RISAVEPK 8 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;E9PLU6;E9PRJ0;E9PRE3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RIS(1)AVEPK 63.944 0.042944 242010000 282250 248880 270110 201820 382200 352300 259740 254450 249690 261310 TRUE FALSE 293393.4479 291623.204 277149.2885 241739.3936 317233.7805 270483.6642 239380.9001 251039.5139 240703.7057 312508.6914 0.938832922 0.933168299 0.886853058 0.773544545 1.015119865 0.865523653 0.765997576 0.803304103 0.770230436 1 18.25353679 2.473158277 24.5456638 0.815086017 0.905838273 0.133487836 0.083901016 142.6134538 883295.1977 0.027631751 0.023218707 297.2749241 -2.473158277 0.090752255 RIS(ph)FSASHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RISFSASHR 9 1 E9PKY8;E9PJM0;Q03393 E9PKY8 PTS 6-pyruvoyl tetrahydrobiopterin synthase 1 RIS(1)FSASHR;RIS(1)FSASHR 151.16 5.12E-05 770200000 222051 353670 299490 285870 368460 367210 294490 290490 264750 416690 TRUE FALSE 230817.7449 414410.0713 307294.9554 342414.2328 305829.3008 281931.0426 271407.1043 286596.4567 255221.6992 498332.4275 0.463180263 0.831593628 0.616646516 0.687120111 0.613705398 0.56574894 0.544630631 0.575110992 0.512151498 1 18.92674893 -1.873034553 5.441234942 1.080382484 0.605533388 0.605597466 0.096515268 0.054591755 0.001273841 0.054206631 0.021367807 0.013395701 1.873034553 -0.474849097 RIS(ph)GLIYEETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 1 RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR 163.02 1.50E-05 591162000 501127 727097 522999 675799 556092 705887 530423 507293 509045 615783 TRUE FALSE 520911.8809 851970.2537 536628.7836 809470.0251 461567.6805 541955.4421 488847.0593 500493.5671 490724.5699 736433.889 0.707343712 1.156886268 0.728685618 1.099175414 0.626760511 0.735918662 0.663803047 0.679617783 0.666352509 1 19.49019649 3.222749201 24.99992626 0.70672841 0.925846108 0.246792712 0.16355465 271.5761979 429396.7412 0.042535961 0.05099785 1670.125861 -3.222749201 0.219117698 RIS(ph)HEGSPVKPVAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 121.26 6.06E-05 121530000 108020 86797 91003 74939 119090 122710 112160 98004 127640 103900 TRUE FALSE 112284.713 101703.7096 93374.61294 89761.71053 98847.12434 94212.46219 103368.6061 96690.41668 123046.2613 124257.2157 0.903647425 0.818493389 0.751462299 0.722386302 0.795504098 0.758205161 0.831892181 0.778147298 0.990254454 1 16.92297011 1.235353809 24.87204549 0.995127385 0.791885145 0.738707772 0.047588992 39.06352591 302950.1472 0.040370018 0.011727508 17.19308495 -1.235353809 -0.20324224 RIS(ph)IVENCFGAAGQPLTIPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RISIVENCFGAAGQPLTIPGR 21 1 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 RIS(1)IVENCFGAAGQPLTIPGR;RIS(1)IVENCFGAAGQPLTIPGR 265.75 3.82E-37 1649730000 326810 416110 403550 435400 463120 526540 432450 457660 456890 646920 TRUE FALSE 339712.7112 487573.6556 414066.8445 521520.8205 384399.0278 404259.0648 398553.439 451525.8163 440446.6181 773671.588 0.43909162 0.630207524 0.53519717 0.674085527 0.496850387 0.522520241 0.515145503 0.583614318 0.569294033 1 19.56136177 0.022913899 1.230584765 1.001436126 0.551941597 0.818664014 0.063366732 4.347496787 5.021281321 0.077165972 0.017106013 1.054177879 -0.022913899 -0.44949453 RIS(ph)LDQQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 86.344 0.021339 2175870000 2177390 2613980 2430310 2481990 2780460 3240360 2483680 2675070 2543950 3432280 TRUE FALSE 2263355.039 3062910.731 2493645.875 2972920.214 2307838.402 2487835.498 2289002.672 2639215.062 2452393.736 4104769.551 0.551396372 0.746183359 0.607499604 0.724259956 0.562233366 0.606084085 0.557644624 0.642963029 0.597449797 1 21.9688698 -1.501731283 2.799768888 1.015111575 0.624368816 0.762250326 0.063359462 8261269.497 8815871.72 958480.105 0.015413957 0.031496966 1.501731283 -0.39074276 RIS(ph)LSDMPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RISLSDMPR 9 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-18;Q9ULU4-15;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 1 RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(1)LSDMPR;RIS(0.997)LS(0.003)DMPR;RIS(0.997)LS(0.003)DMPR;RIS(0.941)LS(0.059)DMPR;RIS(1)LSDMPR 200.27 1.43E-05 4251891000 1271700.3 1459562 1508415 1658706 1860716 1838511 1753856 1793908 1737280 1920987 TRUE FALSE 1321908.01 1710230.42 1547725.534 1986793.096 1544432.159 1411544.683 1616384.184 1769863.598 1674755.632 2297367.623 0.575401166 0.744430453 0.673695197 0.864812874 0.672261654 0.614418289 0.703580989 0.77038763 0.728988959 1 21.1315503 -4.999999996 0.258991454 2.875646055 0.686302791 0.589821217 0.075003082 138.3117511 1.360385932 137.7630094 0.099959609 1.00E-05 4.999999996 -2.189343264 RIS(ph)QSQPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RISQSQPVR 9 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RIS(1)QSQPVR;RIS(1)QSQPVR;RIS(0.991)QS(0.009)QPVR;RIS(1)QSQPVR;RIS(0.974)QS(0.026)QPVR;RIS(1)QSQPVR 184.43 2.70E-05 4288332000 1538587 1884069 1800001 1814995 1835503 2079900 1743342 1806686 1714563 2056730 TRUE FALSE 1599331.603 2207643.195 1846910.505 2173995.594 1523504.856 1596874.746 1606694.299 1782470.329 1652856.213 2459706.865 0.650212278 0.897522882 0.750866102 0.883843366 0.619384723 0.649213436 0.6532056 0.724667786 0.671972842 1 21.23005496 -1.32431281 2.985676097 1.002637757 0.724860427 0.44603291 0.092798536 9841777.859 12486775.11 230167.3636 0.022516762 0.047390053 1.32431281 -0.27777733 RIS(ph)QVSSGETEYNPTEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RISQVSSGETEYNPTEAR 18 1 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764;H7C3Y7 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 RIS(1)QVSSGETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR;RIS(0.999)QVS(0.001)SGETEYNPTEAR;RIS(1)QVSSGETEYNPTEAR 299.94 1.03E-49 2380170000 687895 525830 488207 466957 628550 754730 470298 478277 534950 535428 TRUE FALSE 715053.6258 616137.2121 500930.0755 559319.7009 521709.2955 579455.3955 433434.8139 471866.4791 515697.254 640334.8652 1.11668701 0.962210939 0.782293926 0.873480004 0.814744478 0.904925574 0.676887731 0.736905805 0.805355576 1 19.28846704 4.530174918 2.256780197 0.806776068 1.136855819 0.521989392 0.086726513 0.293924304 2.362496474 0.022085307 0.161098352 33898.06579 -4.530174918 0.330079751 RIS(ph)SSSVQPCSEEVSTPQDSLAQCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RISSSSVQPCSEEVSTPQDSLAQCK 25 1 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 RIS(0.661)S(0.219)S(0.119)S(0.001)VQPCSEEVSTPQDSLAQCK;RIS(0.604)S(0.202)S(0.102)S(0.091)VQPCSEEVSTPQDSLAQCK 231.94 5.75E-35 1239420000 724060 641500 663830 568710 950640 911330 708530 761690 832840 838660 TRUE FALSE 752646.4479 751672.6348 681129.9551 681199.1406 789050.5524 699687.4188 652993.5672 751480.7914 802866.2511 1002979.37 0.750410697 0.749439777 0.679106645 0.679175625 0.786706662 0.697608984 0.651053837 0.749248503 0.800481321 1 19.9358605 0.834706452 1.811860517 0.999431855 0.71429663 0.82902766 0.038961677 0.230447071 1.409257705 0.037543046 0.010589509 6.834495346 -0.834706452 -0.285135226 RISAVSVAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RISAVSVAER 10 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;; 155.47 2.03E-05 760800000 288156 345046 304406 287568 623250 485130 361592 318078 316756 657480 FALSE TRUE 299532.6214 404304.9664 312339.0704 344448.0921 517310.1876 372465.9097 333249.4742 313814.6847 305356.0134 786300.6178 0.380939064 0.51418625 0.397226027 0.438061581 0.65790383 0.473694032 0.423819423 0.399102681 0.388345127 1 19.58472146 -1.544408822 2.847795256 1.027522585 0.453733098 0.811530442 0.079139894 37053576.8 38755511.71 7810977.727 0.019758263 0.028549018 1.544408822 -0.573789487 RISEQFTAMFR ddPTM_MDA-MB-175_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 0 225.79 8.36E-12 289050000 111250 120560 115540 90544 251580 188850 100210 130720 116670 301450 FALSE TRUE 115642.2359 141265.2422 118551.0673 108453.333 208816.5215 144992.4495 92355.27835 128967.9122 112471.0695 360513.3559 0.320771017 0.391844684 0.328839599 0.300830278 0.579219932 0.402183296 0.256177134 0.357734076 0.311974765 1 18.45969318 -1.799870687 2.492126139 1.202301734 0.361951189 0.840063486 0.08363581 8289332.252 5506801.079 10137968.46 0.021216327 0.015853652 1.799870687 -0.840350545 RITEAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RITEAEK 7 1 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 89.698 0.028352 254194000 329980 380170 363110 368320 436130 531040 459520 418530 371180 434400 FALSE TRUE 343007.8652 445461.2402 372572.9449 441172.5967 361996.7784 407714.008 423501.6217 412920.2899 357821.3043 519512.3629 0.660249668 0.857460326 0.717158958 0.849205194 0.696801085 0.784801358 0.815190652 0.794822837 0.688763791 1 18.98679856 -1.67272479 2.847218555 1.026935131 0.769684211 0.535619609 0.065995784 28359731 25960450.98 5536157.182 0.014544612 0.021245904 1.67272479 -0.257250921 RITEAEKNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RITEAEKNER 10 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;; 153.54 9.05E-06 1063880000 709910 670250 718780 477020 1011750 933040 725620 691200 773270 801500 FALSE TRUE 737937.795 785360.2237 737511.9973 571373.1322 839773.0964 716355.6004 668744.0083 681935.5946 745440.1638 958538.5794 0.769857167 0.819330844 0.769412951 0.596087778 0.876097337 0.747341438 0.697670415 0.711432601 0.777684049 1 19.87047697 0.954207146 18.55394899 1.000000001 0.746256783 0.532253558 0.070297112 228.9595088 92769.05091 0.066463339 0.016615835 8.999267175 -0.954207146 -0.253743219 RIVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RIVDGK 6 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;; 106.42 0.051536 16451960000 29531400 28732900 32386400 30390200 39999600 42343200 38283100 35505300 35351100 34612100 FALSE TRUE 30697322.48 33667552.06 33230416.19 36401290.85 33200482.28 32509633.52 35282370.59 35029409.53 34078820.82 41393678.31 0.741594459 0.813350092 0.802789642 0.879392515 0.80206649 0.785376774 0.852361327 0.846250224 0.823285637 1 25.30290712 -5 0.191110335 1.785834008 0.786220471 0.7438754 0.033393172 68.75290844 0.673734413 20.54372643 0.089044225 1.00E-05 5 -0.999613537 RIVNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RIVNAK 6 1 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 122.51 0.030768 1091270000 1465800 1149500 1395900 1183550 1775120 1763880 1713310 1491050 1565120 1258050 FALSE TRUE 1523670.916 1346917.683 1432278.301 1417652.657 1473385.736 1354245.602 1579016.285 1471064.914 1508791.637 1504540.811 1.012714913 0.89523506 0.951970389 0.942249388 0.979292636 0.900105595 1.049500468 0.97775009 1.002825331 1 20.52089181 2.238142895 24.99999998 1.004239504 0.946065976 0.401529165 0.036141233 11.21133657 670911.6318 0.012126271 0.009518344 173.038561 -2.238142895 -0.058173527 RIVSQLLTLMDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RIVSQLLTLMDGLK 14 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 137.68 3.18E-05 28765000 77234 59440 58745 45918 141160 109510 78321 63456 68879 120950 FALSE TRUE 80283.25796 69648.35762 60275.94296 55000.44335 117165.6736 84077.96214 72181.99537 62605.47611 66400.05824 144647.8368 0.555025638 0.481502933 0.416708223 0.380236888 0.810006401 0.581259727 0.499018838 0.432813083 0.459046327 1 17.14218522 -1.751484289 2.719491589 1.103375379 0.50964248 0.617657778 0.114959626 25944813.49 20882995.26 18037703.44 0.028680845 0.017722122 1.751484289 -0.5937329 RKADSEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKADSEEER 9 2 H0YGZ1;H0YGK7;J3KQH6;P78364 H0YGZ1 PHC1 Polyhomeotic-like protein 1 0 61.78 0.048895 10205000 10150 9621.2 13659 8610.7 13890 12665 12584 11421 13160 9483.6 FALSE TRUE 10550.72984 11273.56626 14014.96476 10313.87076 11528.98276 9723.74569 11597.6332 11267.92018 12686.37417 11341.72985 0.930257552 0.993990018 1.235699047 0.909373693 1.016510084 0.857342383 1.022562991 0.993492204 1.118557252 1 13.46935308 -1.537450436 3.201240258 0.999757721 1.007329053 0.000500466 0.101607868 3592967089 519148591.2 6550545.226 0.02300705 0.029010123 1.537450436 0.007571331 RKAEDS(ph)DS(ph)EPEPEDNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKAEDSDSEPEPEDNVR 17 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 2 RKAEDS(1)DS(1)EPEPEDNVR 87.748 0.021969 171280000 496540 433840 477930 386350 616050 757870 491780 477130 479900 471870 TRUE FALSE 516143.7826 508348.6452 490385.2484 462768.8769 511334.041 581866.1781 453232.9986 470734.8528 462628.4927 564323.892 0.914623304 0.900810071 0.868978357 0.820041263 0.906100288 1.031085493 0.803143381 0.834157227 0.819792497 1 19.10616391 -1.080937532 4.672176419 1.000006333 0.875369979 0.249080919 0.063628487 4.35E-06 8.56E-07 0.063834528 0.015045178 0.082997014 1.080937532 -0.124636354 RKAEGDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKAEGDAK 8 2 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 49.813 0.08972 21042000 41496 46804 44059 40333 55830 52325 52041 41625 46767 55758 FALSE TRUE 43134.29412 54842.22292 45207.21373 48310.74702 46340.03654 40173.31174 47961.89044 41067.08496 45083.86481 66682.71255 0.646858721 0.822435393 0.677945033 0.72448683 0.694933286 0.602454672 0.71925524 0.615858045 0.676095244 1 16.02502517 -0.791435409 7.479646135 1 0.685604183 0.7168878 0.059061599 8.44E-10 0 0.056616829 0.013344714 0.161645862 0.791435409 -0.314395818 RKAS(ph)PEPPDSAEGALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RKAS(1)PEPPDSAEGALK;RKAS(0.994)PEPPDS(0.006)AEGALK;RKAS(1)PEPPDSAEGALK;RKAS(1)PEPPDSAEGALK 155.49 1.32E-07 1894800000 2652320 1334830 1906730 1210720 2908240 2450740 2364790 1974830 2312300 1222890 TRUE FALSE 2757035.642 1564076.669 1956420.95 1450196.802 2413898.404 1881592.776 2179431.581 1948360.634 2229080.775 1462491.882 1.88516304 1.069460069 1.337731152 0.991593061 1.650537985 1.286566305 1.4902179 1.332219794 1.524166255 1 20.47999719 -0.922617001 5.189995205 0.999999032 1.377909211 0.181934892 0.249412034 2.54E-06 5.27E-07 0.219551249 0.051748593 0.119504153 0.922617001 0.377910179 RKAS(ph)VHSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKASVHSSGR 10 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 1 RKAS(1)VHSSGR;RKAS(1)VHSSGR 79.633 0.013786 27583000 3303 18637.1 19558 20209.5 32324 35257 18351.8 29630 24297 36128 TRUE FALSE 3433.40499 21837.87695 20067.69755 24206.87878 26829.57803 27069.09608 16913.33796 29232.85831 23422.55572 43206.58989 0.079464846 0.505429311 0.464459185 0.560258952 0.620960323 0.626503877 0.391452739 0.676583327 0.542106095 1 15.39896375 -5 0.077729984 2.607757466 2.38E-17 0.626100006 0.134706958 178.505229 0.986890611 49.88506054 4.983498048 1.00E-05 5 -2.607757466 RKCEEEIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKCEEEIAK 9 2 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 147.95 5.13E-05 285960000 410580 254310 325690 213530 557060 439610 388430 316840 383690 290570 FALSE TRUE 426790.0154 297985.7642 334177.749 255765.5967 462371.1402 337517.2399 357983.8416 312593.278 369881.0718 347501.6282 1.228166952 0.857508973 0.961658081 0.736012657 1.330558198 0.971268082 1.030164502 0.899544787 1.064400975 1 18.40666021 4.758674118 23.62754247 0.980792785 1.228167452 0.200757367 0.146392272 3534.919362 4152365.56 0.033634094 1.235782789 57368.58236 -4.758674118 0.247374667 RKDDAPPHYPPPSTAAAS(ph)PAGLDLSNGHLDTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKDDAPPHYPPPSTAAASPAGLDLSNGHLDTFR 33 2 O15156;O15156-2 O15156 ZBTB7B Zinc finger and BTB domain-containing protein 7B 1 RKDDAPPHYPPPSTAAAS(1)PAGLDLSNGHLDTFR 129.25 3.60E-08 134290000 42432 48569 51648 55172 71440 56270 61938 62063 54861 41811 TRUE FALSE 44107.24812 56910.34794 52993.98931 66084.85693 59296.65432 43202.14528 57083.13772 61231.147 52886.56333 50003.06493 0.882090892 1.138137192 1.059814821 1.321616125 1.185860395 0.863989944 1.141592776 1.224547877 1.057666433 1 15.60972891 4.740847658 23.74605816 1.123079912 0.882090726 0.238875825 0.12032493 145.6862725 1512430.533 0.028979359 0.192870295 55061.45173 -4.740847658 -0.240989186 RKDDEDSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKDDEDSFR 9 2 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 147.78 5.15E-05 272195000 215073 185919 233970 193721 268800 273520 273350 242310 236000 205257 FALSE TRUE 223564.2481 217849.142 240067.4504 232038.4356 223109.472 209999.1252 251924.1127 239062.2308 227506.4061 245473.1793 0.910748167 0.887466169 0.977978332 0.945270014 0.908895516 0.855487047 1.026279586 0.973883304 0.926807592 1 17.90520588 2.229610155 24.999958 0.980625667 0.917142986 0.425154282 0.038320565 208.1705024 581446.3337 0.014737814 0.011043972 169.6719907 -2.229610155 -0.063482681 RKDDSYFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKDDSYFDR 9 2 Q9HCD5;Q5JY17 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 0 ;; 164.97 3.48E-05 771060000 329584 321075 366710 324414 477700 485030 396050 346931 386520 395300 FALSE TRUE 342596.2308 376217.1336 376266.7639 388582.1209 396500.7246 372389.1332 365006.5661 342280.9574 372609.2207 472751.4665 0.724685707 0.795803208 0.79590819 0.821958573 0.838708608 0.787705929 0.77208976 0.724018817 0.788171475 1 18.85072241 0.933539219 22.83280408 1 0.781737476 0.779384583 0.034608018 8542.608683 2934842.655 0.037071118 0.00926778 8.581026016 -0.933539219 -0.218262524 RKDGVFLYFEDNAGVIVNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKDGVFLYFEDNAGVIVNNK 20 2 J3KTJ3;P62829;J3KT29 J3KTJ3 RPL23 60S ribosomal protein L23 0 ; 148.44 6.21E-08 66240000 130263 89351 139477 98616 150761 137060 152179 126028 144676 86147 FALSE TRUE 135405.8838 104696.3392 143111.8852 118121.9505 125134.6991 105229.8922 140250.8123 124338.8008 139469.139 103025.8553 1.314290316 1.01621422 1.389087087 1.146527249 1.214595101 1.021393046 1.361316652 1.206869872 1.353729495 1 16.65264691 RKDNPIEDELVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKDNPIEDELVFR 13 2 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 154.72 2.61E-05 186000000 44860 49285 57965 41262 66326 65204 50504 52100 62161 64261 FALSE TRUE 46631.10744 57749.31537 59475.61552 49423.50045 55051.93021 50061.35918 46545.36451 51401.68472 59923.83775 76851.7126 0.606767317 0.751438236 0.773900978 0.643102135 0.716339667 0.651401999 0.605651624 0.668842411 0.779733278 1 16.22978979 0.897971108 3.063651564 0.999698061 0.67856619 0.771573407 0.053436935 0.193102394 3.932966171 0.052893922 0.013844605 7.906260284 -0.897971108 -0.321131872 RKDPELWGSVLLESNPYR ddPTM_MDA-MB-175_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 2114900000 1167810 1244490 1433270 1032600 1690680 1674000 1235950 1315850 1461290 1504620 FALSE TRUE 1213916.041 1458221.477 1470622.194 1236845.198 1403298.817 1285238.87 1139073.009 1298213.183 1408698.458 1799421.481 0.674614621 0.810383499 0.817275001 0.687357137 0.779861101 0.714251154 0.633021791 0.721461423 0.782861866 1 20.77910172 0.827246246 3.475602046 0.999950828 0.730382607 0.676739936 0.055869737 0.59226402 10.97978727 0.055557838 0.014345022 6.718096633 -0.827246246 -0.269568221 RKDREDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 180.28 1.11E-05 3225270000 1030413 837946 999024 680435 1149524 1206043 972682 908798 992331 758814 TRUE FALSE 1071094.501 981856.7072 1025059.386 815023.0121 954128.3211 925957.791 896440.6432 896617.0493 956617.2012 907489.0749 1.180283631 1.081948791 1.129555622 0.898107795 1.051393727 1.020351447 0.987825273 0.988019662 1.054136328 1 19.79152075 3.776172813 24.90412136 1.000885955 1.125731355 0.623671286 0.046447059 341.3681383 226028.5268 0.01124592 0.020273311 5972.729048 -3.776172813 0.1248454 RKDS(ph)AQDDQAK ddPTM_MDA-MB-175_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 182.57 2.99E-06 7163133000 5155560 2098300 3350245 2080736 4685790 4395430 4559500 3333291 3918460 1885991 TRUE FALSE 5359105.49 2458666.702 3437555.137 2492299.37 3889301.09 3374657.996 4202114.476 3288613.686 3777435.39 2255514.827 2.376001002 1.09006896 1.524066743 1.104980265 1.724351817 1.496180808 1.863040059 1.458032396 1.674755291 1 21.10502534 -0.612881094 7.021932736 0.999905711 1.564270047 0.198753894 0.352044954 0 0 0.310210828 0.073117393 0.243847836 0.612881094 0.564364336 RKDS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKDSPSR 7 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKDS(0.881)PS(0.119)R;RKDS(0.72)PS(0.28)R 85.533 0.016334 1195920000 678330 533000 662530 451980 749130 685720 792030 648520 684640 572310 TRUE FALSE 705110.9922 624538.6038 679796.0761 541380.295 621793.1502 526471.9222 729948.619 639827.6502 659999.9401 684443.187 1.030196524 0.912476909 0.993210377 0.790979157 0.908465687 0.769197403 1.066485331 0.934814843 0.964287398 1 19.38457127 -0.580483504 7.808999725 1 0.928373209 0.052053412 0.089353899 0 0 0.083721028 0.019733236 0.262734132 0.580483504 -0.071626791 RKDVPSPGGLSAPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKDVPSPGGLSAPSSPR 17 2 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 RKDVPSPGGLS(0.01)APS(0.166)S(0.824)PR 81.665 0.0069425 246790000 71362 81935 89998 65119 107470 101310 76007 98276 116780 109860 TRUE FALSE 74179.42686 96006.69888 92343.42181 77999.34384 89202.28779 77782.28787 70049.37273 96958.77097 112577.1106 131384.9636 0.564596015 0.730728207 0.702846195 0.593670247 0.67893833 0.592018186 0.53316126 0.737974638 0.856849273 1 17.00344065 1.171907602 2.033613859 0.991685698 0.634670783 0.796410325 0.06163039 0.128461411 0.961709674 0.058086534 0.016625689 14.85619538 -1.171907602 -0.357014915 RKEDEVEEWQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RKEDEVEEWQHR 12 2 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;; 217.09 2.25E-11 20645520000 13239689 9867640 11878810 9689660 15096680 15606330 14440600 12613680 13362130 9868770 FALSE TRUE 13762402.14 11562330.41 12188381.55 11606245.83 12530551.73 11981996.37 13308708.04 12444614.25 12881229.55 11802366.53 1.166071407 0.979662035 1.032706577 0.983382934 1.061698236 1.015219816 1.127630463 1.054416859 1.091410737 1 23.49257283 RKEDQDRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKEDQDRSPR 10 3 O60318 O60318 MCM3AP Germinal-center associated nuclear protein 1 RKEDQDRS(1)PR;RKEDQDRS(1)PR 89.231 0.064399 193843000 121718 98731 130578 83584 127210 141073 142924 112635 118879 116401 TRUE FALSE 126523.5206 115687.2812 133980.97 100116.6657 105586.8896 108310.9337 131721.2434 111125.3121 114600.568 139207.5473 0.908884059 0.831041732 0.962454784 0.719189927 0.758485382 0.778053603 0.946221997 0.798270742 0.823235307 1 17.08687791 -1.979059038 12.39366751 1.091050231 0.834492997 0.293358825 0.076223145 0.037975831 6.42E-05 0.014615398 0.017166159 0.010493998 1.979059038 -0.256557234 RKEEEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKEEEERR 8 3 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;Q5JVM0;O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6;Q9H3P7;A0A0J9YYF7;Q86T65-4;Q86T65 Q9UM54-1;O95819-3;Q9H3P7;A0A0J9YYF7 MYO6;MAP4K4;ACBD3;DAAM2 Unconventional myosin-VI;Mitogen-activated protein kinase kinase kinase kinase 4;Golgi resident protein GCP60;Disheveled-associated activator of morphogenesis 2 0 ; 115.71 0.0029478 50564000 59985 52592 58633 40845 79002 72405 56019 56064 65383 57785 FALSE TRUE 62353.25412 61624.26689 60161.02415 48924.01909 65573.26826 55590.03606 51628.0844 55312.55378 63029.8786 69106.86439 0.902272946 0.891724251 0.870550627 0.707947315 0.948867654 0.804406864 0.747076066 0.8003916 0.912063934 1 16.0765414 3.989107441 24.35840938 0.829129499 0.893033351 0.029795242 0.085647021 870.643702 1946992.762 0.020646298 0.040454507 9752.308718 -3.989107441 0.063903852 RKEEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKEEWER 7 2 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 0 151.5 0.0010559 121420000 148200 136540 150530 137530 185240 178760 171680 149300 161420 143600 FALSE TRUE 154051.0504 159989.6829 154452.9355 164733.0235 153752.971 137245.6991 158223.273 147298.8777 155610.5257 171735.6706 0.897024188 0.931604263 0.899364325 0.959224271 0.8952885 0.799168272 0.921318631 0.857706947 0.90610486 1 17.3898302 3.014342423 24.88519881 0.883679909 0.921695789 0.024806488 0.050873052 483.004881 838044.2677 0.013684353 0.016349579 1033.576017 -3.014342423 0.03801588 RKEQEEEEQKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 193.81 1.02E-06 278680000 252836 119200 163011 111227 231161 202704 212110 154559 197602 107214 FALSE TRUE 262818.1605 139671.6728 167259.2006 133227.3686 191868.3358 155629.068 195484.264 152487.3894 190490.3426 128220.5306 2.0497354 1.08930818 1.304465048 1.039048646 1.496393245 1.213760911 1.524594097 1.189258762 1.485646189 1 16.96826776 7.999999982 0.02762311 6.55E-11 3.199366474 0.158275459 0.274072832 3687.758876 7.819700074 299.128913 677.3663664 99999995.95 -7.999999982 3.199366474 RKFS(ph)NSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKFSNSLK 8 2 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 RKFS(1)NSLK;RKFS(0.996)NS(0.004)LK 122.7 0.0010862 2690500000 3977500 2363900 3151200 1995580 5143700 3868100 3959700 3083400 4136600 2543700 TRUE FALSE 4134534.771 2769881.436 3233322.861 2390299.768 4269375.711 2969792.397 3649328.367 3042072.066 3987724.574 3042089.313 1.359110252 0.910519433 1.062862569 0.785742798 1.40343536 0.976234453 1.1996125 0.999994331 1.310850591 1 21.53663108 3.248863009 24.99933801 1.133910061 1.023434925 0.084344449 0.187743344 575.0114244 1395288.944 0.048837145 0.065397231 1773.629932 -3.248863009 -0.110475135 RKGDEVDGVDEVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKGDEVDGVDEVAK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 92.935 0.0026781 116320000 278550 139360 193530 112480 283830 253220 246130 188280 225480 115890 FALSE TRUE 289547.3691 163293.9959 198573.5508 134728.2083 235584.678 194413.4926 226837.6875 185756.4146 217365.0188 138596.4267 2.089140219 1.178197735 1.43274654 0.972090057 1.699788975 1.402730917 1.636677748 1.340268426 1.568330614 1 17.08053054 -1.127317039 3.887433174 0.99984956 1.456976543 0.195576075 0.288663132 8376732.655 3643767.691 12522.64684 0.062072895 0.074590404 1.127317039 0.457126983 RKGS(ph)GS(ph)EQEGEDEEGGER ddPTM_MDA-MB-175_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 137.85 1.60E-05 1820720000 2898400 1929580 2326520 1633840 3047030 3185620 2754740 2347170 2480810 1682460 TRUE FALSE 3012831.07 2260970.355 2387151.022 1957008.675 2529096.929 2445808.034 2538816.281 2315710.025 2391526.133 2012105.824 1.497352194 1.123683619 1.18639437 0.972617171 1.256940315 1.215546421 1.261770753 1.150888784 1.188568764 1 20.94027475 -5 0.206335665 0.091524861 1.226516813 0.212799776 0.123525818 246.2813143 2.449783999 92.75143022 0.267819798 1.00E-05 5 1.134991952 RKHDNEGSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKHDNEGSGSK 11 2 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 168.98 9.80E-06 79957000 65570 50905 70062 44915 90641 79566 74303 67432 84378 52113 FALSE TRUE 68158.75423 59647.53776 71887.87328 53799.05294 75233.8752 61088.00233 68478.93671 66528.18434 81341.25226 62323.54459 1.093627692 0.957062666 1.153462528 0.86322197 1.207150134 0.980175353 1.098765116 1.067464708 1.305144834 1 15.92748967 1.430312379 16.28360524 1.163831032 1.051243968 0.105918687 0.116143655 4.936025677 1715.84069 0.06214552 0.025609707 26.93471465 -1.430312379 -0.112587065 RKHS(ph)PS(ph)PPPPTPTESR ddPTM_MDA-MB-175_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 182.39 1.15E-09 108268000 127310 95344 119193 89642 157312 144142 130962 116351 114688 109035 TRUE FALSE 132336.2971 111718.5903 122299.2675 107372.92 130572.1624 110667.205 120696.8562 114791.5052 110560.4013 130398.3206 1.014861974 0.856748689 0.937889897 0.823422568 1.00133316 0.848685815 0.925601309 0.880314291 0.847866757 1 16.99256576 4.752468974 23.8745679 0.899003136 1.014862122 0.239019605 0.059904375 1629.675256 2797347.681 0.012667125 0.245048553 56554.73526 -4.752468974 0.115858986 RKLEEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RKLEEQAR 8 2 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 0 ;;;; 169.21 0.00017005 1486300000 1058462 972455 806446 622461 2350890 1507490 1214286 924914 1025687 2077920 FALSE TRUE 1100250.897 1139466.582 827462.6453 745581.9279 1951286.558 1157398.294 1119107.09 912517.0407 988772.7252 2485048.64 0.442748234 0.458528885 0.332976438 0.300027096 0.78521061 0.465744724 0.450336091 0.367202889 0.397888681 1 21.24484266 -1.226672429 4.889810354 1.000092181 0.442721946 0.636970931 0.125799608 0.000127936 2.02E-05 0.123265096 0.029049089 0.059337271 1.226672429 -0.557370235 RKLEGDSTDLSDQIAELQAQIAELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKLEGDSTDLSDQIAELQAQIAELK 25 2 P35579 P35579 MYH9 Myosin-9 0 128.98 5.95E-05 271890000 606240 291430 437000 295690 631640 527870 590160 437330 532990 274130 FALSE TRUE 630174.8233 341480.8355 448388.579 354176.5995 524274.0584 405280.1924 543901.7171 431468.3067 513807.794 327840.525 1.922199287 1.041606542 1.367703334 1.080331968 1.599174045 1.236211394 1.659043577 1.316092044 1.56724918 1 18.32263467 -1.110429676 4.671300552 0.999971894 1.402018246 0.188644354 0.259278499 6.82E-05 1.30E-05 0.225753863 0.053206981 0.07754795 1.110429676 0.402046352 RKLESTESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKLESTESR 9 2 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;; 178.84 2.84E-05 588440000 516580 456650 517920 389380 703480 636960 572630 513590 543660 570500 FALSE TRUE 536974.9773 535076.0853 531417.4207 466398.2018 583902.7209 489035.6932 527745.7643 506706.1661 524093.7828 682278.5521 0.787031888 0.784248726 0.778886305 0.68358913 0.855812804 0.716768381 0.773504843 0.742667587 0.768152218 1 19.38000134 -2.337453827 2.012320226 2.126671784 0.764117124 0.72389883 0.043413994 1466182.97 163347.9873 7512234.161 0.010327833 0.004597759 2.337453827 -1.36255466 RKLS(ph)GDQPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 65.472 0.051468 75739000 49565 53678 63609 48893 77154 75006 55649 59209 64861 61166 TRUE FALSE 51521.86447 62896.77894 65266.7028 58563.88947 64039.39064 57586.99323 51287.08597 58415.4002 62526.66528 73150.30661 0.704328756 0.859829328 0.892227331 0.800596637 0.875449381 0.787241994 0.701119221 0.798566717 0.854769695 1 16.15857629 0.872647299 3.432039711 0.999895684 0.804329475 0.490226033 0.060734306 0.501226575 11.34382647 0.059920225 0.015497207 7.45842796 -0.872647299 -0.19556621 RKPAAPPPS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKPAAPPPSPAAR 13 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RKPAAPPPS(1)PAAR;RKPAAPPPS(1)PAAR 105.28 0.00076469 123932000 86695 69947 83199 82045 104335 116634 106547 97644 88407 96862 TRUE FALSE 90117.78554 81959.85314 85367.23429 98273.25612 86600.17397 89547.52111 98195.56773 96335.24189 85225.24934 115840.2544 0.777948789 0.707524803 0.736939286 0.848351522 0.747582733 0.773025936 0.847680871 0.831621464 0.735713589 1 16.82177715 -5 0.178225638 1.877288659 0.735604601 0.665034484 0.047100584 78.68307066 0.755414963 24.45410855 0.149844458 1.00E-05 5 -1.141684059 RKPDTIEVQQMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKPDTIEVQQMK 12 2 P15311;E7EQR4;A0A2R8Y5S7;P35241;P35241-5;A0A2R8Y7M3;P35241-4;P26038 P15311;A0A2R8Y5S7 EZR;RDX;MSN Ezrin;Radixin;Moesin 0 ;; 171.05 2.22E-05 2834890000 3888720 2769640 3625170 2702870 4796820 4384250 4391510 3585770 4093770 2608530 FALSE TRUE 4042249.668 3245304.125 3719644.908 3237489.619 3981458.25 3366074.381 4047291.971 3537708.618 3946436.017 3119621.51 1.295750031 1.040287777 1.192338524 1.037782823 1.276263238 1.079000889 1.29736635 1.134018536 1.265036802 1 21.57293957 RKPEEES(ph)PR ddPTM_MDA-MB-175_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 71.548 0.038802 299436000 444750 365320 418920 392670 437150 536760 576020 437890 435800 258170 TRUE FALSE 462309.0734 428060.8682 429837.3993 470338.954 362843.3991 412105.6247 530870.0473 432020.8008 420115.6431 308753.4685 1.497340502 1.386416387 1.392170269 1.52334792 1.175188091 1.334740065 1.719397841 1.399241935 1.360683153 1 18.23609582 0.757876199 2.775018821 1.000143687 1.429371927 0.483037719 0.132347775 1.19003291 12.38734666 0.127754063 0.033719965 5.726327715 -0.757876199 0.42922824 RKPFTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKPFTFK 7 2 Q9Y2J8 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 95.909 0.0073791 1670420000 1568660 1302630 1528520 1340190 1986900 1958220 1727160 1645110 1631400 1450220 FALSE TRUE 1630591.908 1526346.569 1568354.487 1605275.582 1649167.448 1503453.082 1591780.686 1623059.991 1572686.233 1734362.843 0.94016769 0.880061848 0.9042828 0.925570787 0.950877986 0.866861907 0.917789892 0.935824933 0.9067804 1 20.72597432 -4.99999891 0.320671311 1.815604924 0.910906333 0.511424495 0.025014766 260.2567013 2.301893578 144.0306477 0.021665986 1.00E-05 4.99999891 -0.904698591 RKPNAGGS(ph)PAPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKPNAGGSPAPVR 13 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR;RKPNAGGS(1)PAPVR 121.32 0.00012941 1704990000 1689750 1522010 1664800 1315380 1876260 1983120 1644820 1596060 1630730 1424800 TRUE FALSE 1756462.635 1783403.378 1708186.056 1575558.238 1557333.995 1522570.434 1515894.71 1574667.426 1572040.346 1703962.281 1.030810749 1.046621394 1.002478796 0.924643847 0.913948632 0.89354703 0.889629265 0.924121058 0.92257931 1 20.70046197 3.839100006 2.663388372 0.916575715 1.038149543 0.726091624 0.029178035 0.124113528 1.707460438 0.007427368 0.01537287 6903.987647 -3.839100006 0.121573828 RKPQEESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKPQEESER 9 2 P26358;P26358-2;K7EJL0;K7ENQ6;K7ERQ1;K7ELB1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;; 228.64 8.77E-08 228001000 186923 171672 189718 156241 234161 221713 206229 182109 198877 174127 FALSE TRUE 194302.8644 201155.3306 194662.2069 187145.0035 194358.3969 170223.5158 190064.2321 179668.1267 191719.4556 208243.8518 0.933054507 0.965960478 0.934780092 0.898682011 0.933321177 0.817423969 0.912700329 0.862777581 0.920648816 1 17.66791438 3.759761649 1.948145816 0.894987598 0.950791737 0.096013775 0.045934137 0.533252723 3.923779673 0.012332115 0.026602754 5751.242093 -3.759761649 0.055804138 RKPS(ph)PEPEGEVGPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RKPSPEPEGEVGPPK 15 2 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK;RKPS(1)PEPEGEVGPPK 160.97 8.76E-07 15574560000 23519310 10958800 17027430 11844275 22442690 20749700 22957680 17021139 19669430 9609465 TRUE FALSE 24447870.52 12840888.65 17471178.81 14187037.24 18627889.57 15930896.64 21158197.05 16792998.47 18961531.06 11492255.68 2.127334372 1.117351459 1.52025671 1.234486739 1.620908034 1.386228873 1.841083042 1.461244767 1.649939888 1 23.45415866 -1.875122807 2.619874838 0.749296766 1.532513055 0.262643662 0.275397505 16199966.76 9543587.133 25178730.1 0.061011211 0.013331444 1.875122807 0.783216289 RKPS(ph)SEEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKPSSEEGKR 10 3 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 RKPS(0.905)S(0.095)EEGKR;RKPS(0.969)S(0.031)EEGKR 116.51 0.0059714 475830000 737830 340206 517070 337660 732570 607520 623890 481070 580090 310012 TRUE FALSE 766960.0981 398633.7341 530545.269 404448.1402 608048.0131 466432.6871 574987.8716 474622.0435 559212.6742 370752.9159 2.068655607 1.075200537 1.430994191 1.090883235 1.640035687 1.25806883 1.550865406 1.280157278 1.508316321 1 18.50009851 -2.211726178 1.832789987 6.85E-05 1.409205833 0.175314073 0.277652035 2184273.153 378390.5257 9033226.68 0.069315277 0.006141491 2.211726178 1.409137327 RKPS(ph)VPDSASPADDSFVDPGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(0.996)VPDS(0.002)AS(0.002)PADDSFVDPGER;RKPS(0.953)VPDS(0.039)AS(0.008)PADDSFVDPGER 218.88 5.97E-26 1795470000 800530 670600 773800 680000 1039330 1007200 928320 821270 956580 840630 TRUE FALSE 832135.5425 785770.3335 793965.8637 814501.9704 862665.0578 773293.0643 855555.8527 810262.219 922152.8727 1005335.354 0.827719367 0.78160022 0.789752256 0.810179377 0.858086861 0.769189168 0.851015385 0.805962126 0.917258972 1 19.9392454 1.046432104 2.623290464 0.999877836 0.810584993 0.835191065 0.027279643 0.087504122 1.287167581 0.024513138 0.006617569 11.12838403 -1.046432104 -0.189292843 RKPSVPDSAS(ph)PADDSFVDPGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKPSVPDSASPADDSFVDPGER 22 2 P16333-2;P16333;C9JAB9;C9K098;C9JVV5;H7C5C7;C9J869 P16333-2 NCK1 Cytoplasmic protein NCK1 1 RKPS(0.218)VPDS(0.158)AS(0.623)PADDS(0.002)FVDPGER 131.5 9.46E-06 1191400000 825510 641110 786910 624350 1061700 991160 958520 839400 990830 818430 TRUE FALSE 858101.7722 751215.6554 807417.5211 747844.5665 881232.6132 760978.1112 883388.6978 828149.216 955170.2218 978785.6887 0.876700367 0.767497588 0.824917579 0.764053434 0.900332548 0.777471636 0.902535364 0.846098615 0.975872689 1 19.90063348 1.276659775 1.034273979 1.006652666 0.818280718 0.614140514 0.049152588 0.285623283 0.633503428 0.041529053 0.01423737 18.90861741 -1.276659775 -0.188371948 RKPVEGYDISFLITNFHTEQMYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKPVEGYDISFLITNFHTEQMYK 23 2 F8WCF6;P59998;P59998-3;R4GN08;P59998-4 F8WCF6 ARPC4-TTLL3;ARPC4 Actin-related protein 2/3 complex subunit 4 0 162.11 1.02E-11 513040000 254690 147390 267670 148600 325640 292290 286480 262270 294440 165400 FALSE TRUE 264745.3579 172703.086 274645.7001 177992.6365 270287.8291 224410.0772 264024.949 258754.6996 283843.1619 197806.9632 1.33840262 0.873089011 1.388453144 0.899829984 1.366422216 1.134490281 1.334760641 1.308117244 1.434950304 1 17.59373369 3.186737647 24.99999851 1.279233878 1.125770932 0.108473161 0.190735779 191.0738774 92175.44713 0.050262422 0.060075146 1537.225738 -3.186737647 -0.153462946 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 RKPVLPALTINPTIAEGPS(0.941)PT(0.046)S(0.013)EGASEANLVDLQK 183.93 1.53E-20 2924000000 548020 337040 502260 341880 662310 572840 556350 514070 586340 363370 TRUE FALSE 569656.2528 394923.9982 515349.3082 409502.8436 549730.7828 439806.5915 512741.8332 507179.7325 565237.7379 434565.3944 1.31086428 0.908779216 1.185895874 0.94232732 1.265012792 1.012060779 1.179895684 1.167096458 1.300696616 1 18.72921377 RKPYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKPYHK 6 2 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 90.939 0.027256 595380000 731040 647970 748160 561240 938950 901180 749950 715840 735320 741040 FALSE TRUE 759902.0237 759253.807 767657.6642 672251.5969 779347.6144 691894.6025 691166.9594 706245.3357 708855.9768 886232.5999 0.857452122 0.856720693 0.866203369 0.75854984 0.879393981 0.780714456 0.779893404 0.796907421 0.799853195 1 19.75732587 RKQDAPSQSENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKQDAPSQSENK 12 2 C9J470;E9PHA2;Q15003;Q15003-2 C9J470 NCAPH Condensin complex subunit 2 0 138.75 3.87E-05 19700000 23594 12895 16261 12165 26849 21855 20862 15276 21218 12849 FALSE TRUE 24525.50934 15109.61594 16684.77502 14571.20069 22285.21657 16779.50747 19226.78193 15071.25021 20454.36832 15366.51554 1.596035827 0.983281857 1.085787795 0.948243644 1.450245276 1.091952656 1.251212864 0.980785147 1.331099967 1 13.90750244 7.987935179 0.017086145 1.01E-06 2.58841842 0.071223522 0.205453871 14179.28495 18.72347957 1098.928522 1821.840398 97260204.58 -7.987935179 2.588417414 RKQEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RKQEEEER 8 2 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;Q5JVM0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;;;;; 185.81 0.00011855 634747400 652641 546319.9 610994.2 481850.3 767617.2 734597.9 693398.4 616415.2 656473.2 522193.1 FALSE TRUE 678407.7706 640146.093 626917.2108 577158.8512 637137.9025 563998.6707 639048.0215 608153.1625 632846.8578 624506.84 1.086309592 1.025042565 1.003859639 0.924183394 1.020225659 0.903110478 1.023284263 0.973813453 1.013354566 1 19.25235785 4.563746495 1.806188325 0.979306489 1.099978642 0.422323688 0.037980091 0.528068742 2.302577702 0.009235179 0.096486845 36622.37417 -4.563746495 0.120672153 RKQEELQQLEQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKQEELQQLEQQR 13 2 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 254.4 4.66E-24 1365990000 872760 804220 926920 652200 1044800 1090210 874940 872130 946970 765190 FALSE TRUE 907217.2387 942338.529 951076.2967 781203.2134 867205.2692 837025.2498 806359.9166 860440.5239 912888.7347 915114.3301 0.991370377 1.029749506 1.039297785 0.853667337 0.947646912 0.914667405 0.881157567 0.940254672 0.997567959 1 19.80359247 3.763265127 24.9614718 0.928445106 1.021100264 0.441010671 0.044400145 639.7483746 646400.3336 0.011021158 0.019857129 5797.825323 -3.763265127 0.092655157 RKQGGS(ph)PDEPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKQGGSPDEPDSK 13 2 Q9ULX6;Q9ULX6-2;V9GZ50 Q9ULX6 AKAP8L A-kinase anchor protein 8-like 1 RKQGGS(1)PDEPDSK 94.544 0.0040214 39839000 139160 54953 87097 49115 139330 115710 104780 89844 101830 46352 TRUE FALSE 144654.1443 64390.75027 89366.81937 58829.80041 115646.7364 88838.1061 96567.06981 88639.78814 98165.15819 55433.78694 2.609494178 1.161579496 1.612136286 1.06126252 2.086213892 1.602598542 1.742025489 1.599020977 1.770854268 1 15.75847795 -1.639819448 4.966441676 0.989217255 1.663053843 0.198366961 0.414324529 0.044970691 0.003261402 0.364699731 0.08587727 0.022918202 1.639819448 0.673836588 RKREPEDEGEDDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKREPEDEGEDDD 13 3 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 96.745 0.0050095 53282000 124360 104240 130740 77190 177820 163050 109970 113620 134360 129060 FALSE TRUE 129269.8288 122142.4091 134147.1918 92457.95161 147594.2199 125184.1085 101350.264 112097.1097 129524.4098 154346.836 0.837528207 0.791350262 0.869128226 0.599027191 0.956250376 0.811057174 0.656639726 0.726267623 0.839177616 1 17.23581638 RKRET(ph)DDEGEDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 107.75 0.0041713 5885130000 3054890 1742510 2477430 1437737 3274350 2996880 2684010 2233350 2542740 1585500 TRUE FALSE 3175499.416 2041772.538 2541993.861 1722117.087 2717777.157 2300900.038 2473630.283 2203415.596 2451227.284 1896148.369 1.674710412 1.076799986 1.340609154 0.908218532 1.433314608 1.213459915 1.304555236 1.162048093 1.292740233 1 20.85464043 7.999948876 0.023029801 2.16E-06 2.881436285 0.172398558 0.191800084 4821.570562 8.544373405 378.4847247 748.5925382 99988229.01 -7.999948876 2.881434128 RKS(ph)ELPQDPHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;RKS(1)ELPQDPHTK;RKS(1)ELPQDPHTK 88.507 0.00519 1294730000 935530 626390 802210 584370 1545360 1050810 833060 822960 923230 661760 TRUE FALSE 972465.4468 733967.6099 823116.2516 699956.6418 1282680.259 806775.3027 767762.5804 811929.5673 890003.1326 791419.2018 1.228761502 0.927406876 1.040050898 0.88443222 1.620734317 1.019403245 0.970108608 1.025915931 1.124566008 1 19.59408254 RKS(ph)ELPQDVYTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.99)ELPQDVYT(0.01)IK;RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK;RKS(1)ELPQDVYTIK 197.45 1.05E-07 1833050000 3237460 2038150 3251180 2073030 4723990 3247590 3392170 2836870 3572710 2441600 TRUE FALSE 3365277.421 2388186.408 3335908.422 2483069.147 3921007.867 2493386.44 3126282.852 2798846.398 3444128.865 2919984.773 1.152498277 0.817876323 1.142440349 0.850370581 1.342817916 0.853903919 1.070650395 0.958514039 1.179502338 1 21.47752942 RKS(ph)EPAVGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKSEPAVGPPR 11 2 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 RKS(1)EPAVGPPR;RKS(1)EPAVGPPR;RKS(1)EPAVGPPR;RKS(1)EPAVGPPR 121.48 0.00032353 1515700000 1244780 1047720 1112290 993440 1511690 1423380 1307970 1216070 1342520 1106640 TRUE FALSE 1293924.876 1227657.76 1141277.191 1189939.467 1254733.474 1092821.567 1205447.894 1199770.571 1294202.967 1323464.92 0.977679768 0.92760884 0.862340341 0.899109186 0.948067043 0.825727641 0.910827235 0.906537493 0.977889892 1 20.33588852 1.171003982 3.479752031 0.999077 0.90448272 0.405712905 0.039841068 0.215480116 4.662457046 0.036664402 0.009869205 14.82531679 -1.171003982 -0.094594281 RKS(ph)EPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSEPSSR 8 2 H0YD71;Q9ULL1 H0YD71 PLEKHG1 Pleckstrin homology domain-containing family G member 1 1 RKS(0.847)EPS(0.141)S(0.012)R 107.06 0.0032106 54745000 58703 43697 55783 42463 71626 65003 70218 59629 63496 52583 TRUE FALSE 61020.63977 51201.61983 57236.75081 50862.05466 59451.0381 49907.03838 64714.12968 58829.77079 61210.79136 62885.63209 0.970343109 0.814202197 0.910172148 0.808802472 0.945383486 0.793615914 1.029076556 0.935504166 0.973366878 1 15.94044281 2.229423299 24.99998076 0.976224388 0.873005373 0.454407878 0.059162548 175.9687617 481451.9424 0.019976038 0.014961347 169.5990047 -2.229423299 -0.103219015 RKS(ph)HEAEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 152 9.81E-06 2558043000 1646285 865062 1240528 831700 1905491 1691899 1756102 1285953 1623499 1098320 TRUE FALSE 1711281.603 1013629.669 1272857.179 996207.7776 1581596.32 1298981.098 1618454.137 1268716.903 1565069.588 1313514.775 1.302826306 0.771692628 0.969046715 0.758429061 1.204094807 0.988935277 1.232155258 0.965894657 1.191512739 1 20.325001 3.221979968 24.99922819 1.090894654 0.939051598 0.157906425 0.16463316 409.7442209 617784.5983 0.044315604 0.053104952 1667.170311 -3.221979968 -0.151843056 RKS(ph)ISGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKSISGK 7 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0-6;D6RD46 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 RKS(1)ISGK;RKS(1)ISGK;RKS(1)ISGK 130.41 0.0028082 3309720000 3496080 2210980 3082410 1897670 4740230 3466620 3432610 3016950 3779100 2537750 TRUE FALSE 3634107.938 2590698.616 3162740.137 2273023.462 3934487.398 2661550.042 3163553.059 2976512.72 3643090.929 3034973.524 1.197410096 0.853614898 1.042098098 0.748943424 1.296382774 0.876959888 1.042365949 0.980737623 1.200369921 1 21.5332525 1.277679145 24.99646727 1.100185809 0.999005981 0.053941017 0.158274158 380.2265287 242961.9902 0.095658068 0.034929433 18.95305159 -1.277679145 -0.101179828 RKS(ph)LS(ph)DSESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.995)LS(0.618)DS(0.343)ES(0.038)DDS(0.006)K 106.31 0.0068095 1672700000 5578900 1604600 2509000 1349200 3949600 4608600 3707800 2569600 2975600 1279600 TRUE FALSE 5799159.28 1880177.568 2574386.601 1616067.733 3278248.403 3538322.494 3417172.947 2535158.715 2868508.737 1530313.121 3.789524642 1.228622785 1.68226134 1.056037298 2.142207604 2.312155889 2.232989381 1.656627445 1.874458697 1 20.54539545 0.487587309 1.093705974 1.000560891 1.970398836 0.151990583 0.712709824 3.794643173 6.099530597 0.658199835 0.203447749 3.073175126 -0.487587309 0.969837944 RKS(ph)LSDS(ph)ESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.998)LS(0.044)DS(0.938)ES(0.018)DDS(0.002)K 108.71 0.0058756 1634600000 3604700 952470 1478200 1010300 2438600 2841500 2456000 1652000 1904400 804070 TRUE FALSE 3747016.339 1116049.313 1516723.106 1210134.325 2024087.643 2181604.688 2263492.302 1629857.642 1835861.016 961612.1216 3.896598488 1.160602376 1.577271201 1.258443293 2.1048899 2.268695079 2.353851674 1.694922106 1.909149203 1 19.87509556 0.461204459 1.223777103 1.000557337 1.990270984 0.151180536 0.730100767 4.573058057 8.403897081 0.667654535 0.201019145 2.89204109 -0.461204459 0.989713647 RKS(ph)LSDSES(ph)DDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 RKS(0.995)LS(0.243)DS(0.154)ES(0.603)DDS(0.006)K;RKS(0.984)LS(0.066)DS(0.076)ES(0.497)DDS(0.377)K 96.391 0.020947 1626760000 7152900 1984520 3294500 1996150 4994400 5932600 5002000 3388600 3937600 1638510 TRUE FALSE 7435302.015 2325345.873 3380357.376 2390982.512 4145453.672 4554843.559 4609930.17 3343181.36 3795886.545 1959544.663 3.794402932 1.186676638 1.725072891 1.220172501 2.11551885 2.324439777 2.352551721 1.706101128 1.937126832 1 20.90208703 0.420980319 1.183213773 1.000045096 2.007896463 0.16680168 0.698610247 4.770629901 7.960294376 0.639945451 0.193311459 2.636211919 -0.420980319 1.007851367 RKS(ph)LSDSESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKSLSDSESDDSK 13 2 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 RKS(0.857)LS(0.124)DS(0.016)ES(0.003)DDSK;RKS(0.998)LS(0.002)DSESDDSK;RKS(0.998)LS(0.002)DSESDDSK;RKS(0.997)LS(0.003)DSESDDSK 263.08 1.97E-24 3146180000 3696630 1425930 2121680 1321620 3131830 3015350 2809330 2111290 2506030 1137730 TRUE FALSE 3842575.807 1670822.385 2176972.724 1583032.491 2599482.655 2315080.661 2589127.374 2082991.611 2415838.47 1360646.41 2.824081097 1.227962219 1.599954777 1.163441493 1.910476253 1.701456486 1.902865692 1.530883847 1.775507914 1 20.37586077 -2.241972961 0.633993602 9.21E-15 1.702920249 0.20057638 0.436267946 400.9556916 32.32514736 567.7067768 0.154546603 0.005728317 2.241972961 1.702920249 RKS(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_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(1)LVGTPYWMAPELISR;RKS(0.5)LVGT(0.5)PY(0.001)WMAPELISR;RKS(0.348)LVGT(0.348)PY(0.305)WMAPELISR;RKS(0.416)LVGT(0.416)PY(0.168)WMAPELISR 208.88 4.59E-16 7635069000 2603996 1649399 1860367 1452674 2678985 2402017 1762796 1840847 1957818 1855011 TRUE FALSE 2706803.773 1932670.448 1908849.692 1740008.581 2223612.087 1844184.955 1624623.443 1816173.457 1887356.513 2218464.889 1.220124684 0.871174684 0.860437189 0.784330007 1.002320162 0.831288773 0.732318754 0.81866225 0.850748877 1 21.08113029 4.74171802 4.306021646 0.847582039 1.249027057 0.635807781 0.081083304 0.12854455 5.614297969 0.019167833 0.158969418 55171.91017 -4.74171802 0.401445018 RKS(ph)NFSNSADDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSNFSNSADDIK 13 2 P45973 P45973 CBX5 Chromobox protein homolog 5 1 RKS(0.931)NFS(0.068)NS(0.001)ADDIK 106.28 0.00072361 182530000 247590 130270 161560 124200 227290 203160 206870 168920 191900 136350 TRUE FALSE 257365.0444 152642.8591 165770.3863 148766.3893 188655.327 155979.1689 190654.9888 166655.9037 184993.5565 163065.1719 1.578295606 0.936084986 1.016589774 0.912312467 1.156932071 0.956544963 1.169195032 1.022020225 1.134476199 1 17.31508915 4.745128257 24.99837447 1.037167337 1.578295851 0.77919582 0.086939387 324.227115 1234071.21 0.01949296 0.188190386 55606.84531 -4.745128257 0.541128513 RKS(ph)NLPIFLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKSNLPIFLPR 11 2 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 RKS(1)NLPIFLPR;RKS(1)NLPIFLPR 187.16 2.92E-06 1939260000 1115530 912050 1215810 952130 1461640 1310680 1194540 939090 1192890 1146830 TRUE FALSE 1159571.986 1068687.493 1247495.007 1140458.472 1213190.955 1006294.434 1100908.833 926503.0346 1149958.122 1371529.381 0.845459092 0.779194021 0.909564917 0.83152318 0.884553384 0.733702425 0.802687021 0.675525473 0.838449499 1 20.3873541 2.743908575 24.87407622 0.780218749 0.848398105 0 0.086864886 867.2209183 4033569.247 0.025449532 0.026286773 554.5089691 -2.743908575 0.068179356 RKS(ph)PENTEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RKSPENTEGK 10 2 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.989)PENT(0.011)EGK;RKS(0.999)PENT(0.001)EGK;RKS(0.996)PENT(0.004)EGK;RKS(0.987)PENT(0.013)EGK;RKS(0.957)PENT(0.043)EGK;RKS(0.994)PENT(0.006)EGK;RKS(1)PENTEGK;RKS(1)PENTEGK 226.51 1.56E-09 5272250000 4521505 2027548 3076706 1977416 4017243 3793994 4314844 2886896 3496062 1681425 TRUE FALSE 4700017.509 2375763.597 3156887.486 2368542.983 3334393.47 2912896.392 3976635.253 2848201.881 3370239.412 2010868.036 2.337307782 1.181461714 1.569912809 1.17787092 1.658186122 1.448576605 1.977571467 1.416404175 1.676012225 1 20.93938698 4.752264712 24.25846735 1.490585365 2.337308641 0.479391455 0.273351586 1308.236323 2315728.527 0.060649449 1.178221703 56528.14218 -4.752264712 0.846723276 RKS(ph)PENTEGKDGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKSPENTEGKDGSK 14 3 Q15651;A0A087WZE9;Q15651-2 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 RKS(0.997)PENT(0.003)EGKDGSK;RKS(0.98)PENT(0.02)EGKDGSK;RKS(0.992)PENT(0.008)EGKDGSK;RKS(0.5)PENT(0.5)EGKDGSK 136.66 0.00014243 1488880000 2556830 857790 1519490 553725 2538770 1781550 1427010 1246560 1707310 830010 TRUE FALSE 2657775.623 1005108.76 1559089.158 663250.1523 2107230.782 1367812.012 1315157.227 1229851.902 1645864.247 992634.568 2.677496541 1.012566751 1.57065773 0.668171524 2.122866612 1.377961292 1.324915805 1.238977507 1.658076698 1 19.92090317 4.747439746 24.98052711 1.345501657 2.67749723 0.528600457 0.381380754 871.936601 2453052.027 0.084085977 1.020457505 55903.59621 -4.747439746 1.331995573 RKS(ph)PPKEYIDEEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RKSPPKEYIDEEGVR 15 3 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR;RKS(1)PPKEYIDEEGVR 107.39 0.006417 3460870000 1733010 824870 1142390 748320 1671860 1620260 1421870 1209590 1360390 757960 TRUE FALSE 1801430.573 966535.0059 1172161.622 896335.4625 1387677.834 1243979.17 1310420.114 1193377.425 1311429.83 906467.75 1.987307958 1.066265188 1.293109018 0.988822231 1.530862884 1.372336931 1.445633465 1.316513935 1.446747366 1 19.78989617 -1.689359325 6.038328502 0.995172898 1.362609117 0.161298582 0.258285942 0.015617599 0.000803444 0.232698474 0.054371204 0.020447522 1.689359325 0.367436219 RKS(ph)QEALHEQSSYILSSAETPARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKSQEALHEQSSYILSSAETPARPR 25 3 Q9NVE5;Q9NVE5-3 Q9NVE5 USP40 Ubiquitin carboxyl-terminal hydrolase 40 1 RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR;RKS(1)QEALHEQSSYILSSAETPARPR 218.4 1.02E-33 2477470000 287340 278278 350579 299527 412791 394524 364629 368062 353970 297293 TRUE FALSE 298684.4051 326070.0818 359715.3767 358772.5466 342624.9333 302901.7801 336048.4262 363128.7309 341230.6888 355541.8713 0.840082221 0.917107402 1.011738436 1.009086624 0.963669713 0.851944045 0.945172575 1.021338864 0.95974825 1 18.43965995 4.569867847 3.40106915 0.969432832 0.84143846 0.425847344 0.046670515 0.269076151 5.318233615 0.012436392 0.068085847 37142.21905 -4.569867847 -0.127994372 RKS(ph)QMEEVQDELIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSQMEEVQDELIHR 15 2 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RKS(1)QMEEVQDELIHR 92.681 0.0026864 222010000 103620 84576 100260 82168 139280 113370 115520 117620 117330 74120 TRUE FALSE 107710.9976 99101.27009 102872.858 98420.58515 115605.2353 87041.53564 106465.2405 116043.4963 113107.3162 88642.39489 1.215118316 1.117989538 1.16053789 1.110310538 1.304175451 0.981940253 1.201064577 1.309119597 1.275995717 1 16.43570924 2.007433733 24.9992601 1.235811842 1.147759767 0.005021752 0.110248419 362.5550744 1219248.564 0.038722004 0.028543931 101.7264134 -2.007433733 -0.088052075 RKS(ph)QVNGEAGSYEMTNQHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKSQVNGEAGSYEMTNQHVK 20 2 Q05D32-2;Q05D32;H0YMH7 Q05D32-2 CTDSPL2 CTD small phosphatase-like protein 2 1 RKS(1)QVNGEAGSYEMTNQHVK;RKS(1)QVNGEAGSYEMTNQHVK 223.64 3.31E-25 467608000 154584 135066 214776 147432 274094 250702 223534 213983 234444 170113 TRUE FALSE 160687.0957 158262.5348 220373.239 176593.6096 227503.5998 192480.2599 206012.821 211114.9079 226006.4062 203443.3853 0.789836914 0.777919295 1.083216535 0.868023353 1.118264914 0.946112156 1.012629733 1.03770839 1.11090565 1 17.63426785 4.24731193 24.99948575 1.019206608 0.783877964 0.638634523 0.071654179 106.0938105 303066.7576 0.016270512 0.043125606 17673.06724 -4.24731193 -0.235328644 RKS(ph)TDSVPISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.494)T(0.494)DS(0.013)VPISK 69.451 0.02842 62293000 164790 103780 134390 95605 200070 180290 173780 145200 184720 122700 TRUE FALSE 171296.0364 121603.4077 137892.3138 114515.3836 166062.1729 138420.3798 160158.6695 143253.8315 178071.9633 146740.7158 1.167338155 0.828695751 0.939700431 0.780392702 1.13167073 0.943299064 1.091439882 0.976237786 1.213514343 1 17.1629097 3.220682427 24.99976396 1.049524472 0.922626881 0.217794085 0.119889051 362.9273356 507494.1785 0.032664858 0.039118756 1662.196741 -3.220682427 -0.126897592 RKS(ph)TITALLFGEDDLEALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKSTITALLFGEDDLEALK 19 2 Q96HU1;Q96HU1-2 Q96HU1 SGSM3 Small G protein signaling modulator 3 1 RKS(0.899)T(0.078)IT(0.023)ALLFGEDDLEALK;RKS(0.644)T(0.196)IT(0.16)ALLFGEDDLEALK 187.78 1.39E-14 1548460000 1419330 679170 1348470 752150 1938400 1322170 1487140 1088890 1438950 746480 TRUE FALSE 1475366.244 795812.1643 1383612.236 900923.0251 1608911.46 1015116.055 1370574.081 1074295.211 1387162.471 892738.4638 1.652629862 0.891428113 1.549851711 1.009167927 1.802220388 1.137081123 1.535247036 1.203370589 1.553828503 1 19.76787806 -1.102637358 4.64276233 0.999975934 1.352931168 0.130577438 0.283579701 6.15E-05 1.19E-05 0.238855317 0.056294903 0.07895191 1.102637358 0.352955234 RKS(ph)VEEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSVEEESK 9 2 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RKS(1)VEEESK 119.69 0.00061935 135110000 152440 59529 85229 64027 129980 127060 130980 84890 107900 57341 TRUE FALSE 158458.4489 69752.64268 87450.13776 76691.3495 107886.046 97552.24061 120713.4453 83752.1884 104016.7001 68575.87109 2.310702677 1.017160141 1.275231891 1.11834306 1.573236246 1.42254468 1.760290368 1.221306956 1.51681194 1 16.06541342 -1.81336073 0.856073277 0.696931634 1.437886539 0.13187013 0.352597128 1027.633761 173.7608423 636.5470056 0.106046101 0.015368776 1.81336073 0.740954905 RKS(ph)YTSDLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKSYTSDLQK 10 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RKS(0.994)Y(0.001)T(0.005)SDLQK;RKS(1)YTSDLQK 212.55 2.00E-08 597350000 1216520 731040 1008560 652110 1633700 1254570 1104480 987260 1191500 932510 TRUE FALSE 1264549.149 856590.4333 1034843.902 781095.4116 1356004.258 963215.1307 1017907.972 974027.3945 1148618.148 1115217.481 1.13390363 0.768092725 0.92793013 0.700397389 1.215910153 0.863701608 0.912743917 0.873396814 1.029949914 1 20.08889365 RKSLVGT(ph)PYWMAPELISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKSLVGTPYWMAPELISR 18 2 O96013;O96013-4;O96013-2;O96013-3;M0R1R1 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RKS(0.365)LVGT(0.584)PY(0.051)WMAPELISR 158.15 6.21E-11 679390000 347870 367710 442140 325900 592680 501210 397810 465080 484800 463770 TRUE FALSE 361604.1762 430861.3321 453662.5316 390362.0473 491936.4653 384811.5734 366628.6127 458846.3633 467352.1427 554636.8521 0.651965651 0.776835024 0.817945165 0.703815561 0.886952361 0.693808159 0.661024617 0.827291518 0.842627281 1 19.08118395 0.962465737 1.563436482 0.997158484 0.750236947 0.544377743 0.071064389 0.325866287 1.627225824 0.065454411 0.019130897 9.17203572 -0.962465737 -0.246921537 RKT(ph)DTVVESSVSGDHSGTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RKTDTVVESSVSGDHSGTLR 20 2 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 RKT(0.992)DT(0.008)VVESSVSGDHSGTLR;RKT(0.986)DT(0.014)VVESSVSGDHSGTLR;RKT(0.991)DT(0.009)VVESSVSGDHSGTLR;RKT(0.987)DT(0.013)VVESSVSGDHSGTLR 286.44 1.48E-43 1658090000 315381 464151 542885 458779 627068 665277 569848 586196 553634 435757 TRUE FALSE 327832.4854 543865.3237 557033.0291 549524.1169 520479.2053 510776.4991 525181.8247 578339.0014 533708.8205 521135.2411 0.629073721 1.043616476 1.068883824 1.054475064 0.998741141 0.980122738 1.00776494 1.109767592 1.024127287 1 18.99129829 4.739144405 24.92167899 1.03678784 0.629073591 0.913968067 0.03705417 12.8678614 549190.6368 0.009694763 0.05749995 54845.92994 -4.739144405 -0.407714249 RKT(ph)SDANETEDHLESLICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKTSDANETEDHLESLICK 19 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RKT(0.412)S(0.412)DANET(0.175)EDHLESLICK;RKT(0.362)S(0.362)DANET(0.276)EDHLESLICK 220.23 1.41E-17 783250000 867430 549170 802680 515730 1271610 1031900 837880 917530 1023720 667070 TRUE FALSE 901676.8062 643485.6756 823598.5002 617739.8547 1055462.186 792256.8636 772204.7762 905232.0111 986876.5172 797769.5947 1.130247144 0.806605917 1.032376398 0.774333666 1.323016311 0.993089821 0.967954634 1.134703575 1.237044535 1 19.60561261 3.25185295 24.99999131 1.102236736 0.933548045 0.265972536 0.1408152 319.7753881 601424.2924 0.037278635 0.050185124 1785.882783 -3.25185295 -0.16868869 RKT(ph)SQSEEEEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RKTSQSEEEEAPR 13 2 Q7RTP6;A0A5F9ZHV5;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;J3KSK6;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RKT(0.971)S(0.029)QS(0.001)EEEEAPR;RKT(0.956)S(0.044)QSEEEEAPR 162.61 6.46E-05 989800000 240950 256460 279350 235240 348290 372720 297930 288960 311320 315310 TRUE FALSE 250462.8921 300505.01 286630.0905 281769.7699 289087.7902 286161.4286 274577.4681 285086.9638 300115.654 377088.9575 0.664201078 0.796907478 0.76011266 0.747223604 0.766630219 0.758869818 0.728150381 0.756020451 0.795874947 1 18.52454538 0.695298959 2.014100432 0.999950624 0.749241849 0.844822441 0.032397389 0.456780444 2.541567094 0.028471857 0.007849993 4.957913651 -0.695298959 -0.250708775 RKTPEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKTPEELLR 9 2 O43633;M0R1L7;M0QXX8 O43633 CHMP2A Charged multivesicular body protein 2a 0 128.91 0.00022735 419490000 227900 188500 200890 179420 318190 259030 228080 253680 220560 232730 FALSE TRUE 236897.668 220873.4087 206125.3584 214908.7405 264104.1775 198874.2081 210202.4936 250279.8345 212622.0887 278328.9876 0.851142635 0.793569547 0.740581713 0.772139267 0.9488921 0.714529269 0.755230332 0.899223026 0.763923623 1 18.08643165 -4.999999876 0.329508337 2.949272866 0.799664561 0.402079797 0.070813107 358.065651 3.099594877 488.6280521 0.058884074 1.00E-05 4.999999876 -2.149608305 RKVDWLTEK ddPTM_MDA-MB-175_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 ; 156.83 3.94E-05 2604500000 1972990 1101370 1683200 1160730 2778900 2086630 2332600 1579090 1771450 1355790 FALSE TRUE 2050885.169 1290521.73 1727065.575 1390318.93 2306543.571 1602041.806 2149764.717 1557924.881 1707695.861 1621431.092 1.264861133 0.795915248 1.065148919 0.857464086 1.422535673 0.988041868 1.32584402 0.960833235 1.053202858 1 20.62883628 5.047351297 20.25793232 1.060882552 3.121946533 0.107724522 0.182121882 313.7399782 244178.7958 0.039884072 22263.2377 111519.6242 -5.047351297 2.061063981 RKVMDS(ph)DEDDDY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 168.1 3.74E-05 1887660000 3297650 2416900 2989600 1946990 4296820 3984080 3224860 3191130 3413420 2694120 TRUE FALSE 3427843.768 2831983.774 3067511.432 2332098.811 3566448.071 3058837.799 2972087.047 3148358.122 3290571.681 3221981.232 1.063893152 0.878957253 0.952057511 0.723808937 1.106911498 0.949365493 0.922440831 0.97714974 1.021288283 1 21.61951666 3.202877654 24.99995723 0.986698438 0.90622499 0.191717301 0.090784205 322.5862445 226007.2612 0.02553062 0.030515963 1595.429632 -3.202877654 -0.080473448 RKVMDSDEDDDY(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKVMDSDEDDDY 12 2 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 RKVMDS(0.008)DEDDDY(0.992) 131.28 0.00019868 1161700000 1898300 1335600 1686400 1174500 2406700 2292700 1898300 1744600 1851700 1479400 TRUE FALSE 1973246.35 1564978.91 1730348.969 1406812.594 1997609.994 1760255.171 1749506.286 1721216.491 1785057.679 1769260.105 1.115294661 0.884538631 0.978007114 0.79514176 1.129065188 0.994910339 0.988834983 0.972845364 1.008928915 1 20.75471473 3.224311278 24.99999939 1.008819524 0.941535102 0.145036777 0.085220921 482.7621752 846988.5032 0.023683773 0.028432737 1676.143813 -3.224311278 -0.067284422 RKVS(ph)LVLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKVSLVLEK 9 2 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 RKVS(1)LVLEK 117.07 0.00095364 1235300000 1101500 649040 845620 555270 1161300 943020 1090000 883150 989760 648050 TRUE FALSE 1144988.071 760507.5712 867657.5519 665100.7487 963902.6408 724017.8966 1004562.952 871312.8188 954138.7309 775022.9898 1.477360137 0.981270983 1.119524922 0.858169057 1.243708449 0.934188929 1.29617181 1.124241255 1.23111023 1 19.56387958 2.222127428 24.99589252 1.172375551 1.09296998 0.024470495 0.177428348 875.7009054 1331987.067 0.062195961 0.046065858 166.7736477 -2.222127428 -0.079405571 RKVTGTEGSSSTLVDYTSTSSTGGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RKVTGTEGSSSTLVDYTSTSSTGGSPVR 28 2 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 RKVTGTEGSSSTLVDYT(0.001)S(0.003)T(0.003)S(0.002)S(0.004)T(0.003)GGS(0.985)PVR 55.117 0.035522 117000000 58146 55217 70492 54680 78633 72358 54405 59753 67565 77295 TRUE FALSE 60441.64898 64700.09022 72329.07943 65495.5408 65266.99075 55553.9511 50140.59394 58952.10877 65133.34885 92439.47535 0.65385106 0.699918406 0.782447966 0.708523502 0.706051073 0.600976486 0.542415389 0.63773738 0.70460535 1 16.49622145 -1.903275492 6.925027669 1.071203089 0.667096217 0.709119893 0.063228523 0.041566834 0.00058058 0.036610938 0.016260251 0.012494662 1.903275492 -0.404106872 RLAAAEETAVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEET(0.004)AVS(0.996)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR 192.85 1.45E-06 5882890000 1984990 2172580 2045710 2175710 2003510 2417810 2128140 2125680 2048600 2406540 TRUE FALSE 2063358.938 2545703.715 2099022.883 2606058.944 1662954.086 1856310.27 1961330.826 2097188.737 1974871.286 2878055.437 0.716928142 0.884522126 0.729319823 0.905492963 0.577804744 0.64498767 0.681477779 0.728682537 0.686182504 1 21.45666295 -1.269814446 3.445033193 1.000814008 0.729229033 0.425905087 0.094602138 29229947.84 43708206.41 251991.2195 0.023582449 0.053726129 1.269814446 -0.271584974 RLAEDEAFQR ddPTM_MDA-MB-175_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 ; 205.52 2.68E-07 478250000 249510 338130 286430 274570 351050 358320 252870 296340 285920 407660 FALSE TRUE 259360.8475 396201.1972 293894.6011 328879.1265 291378.6464 275105.6104 233049.3886 292368.047 275629.7951 487533.1719 0.531986052 0.812665107 0.602819701 0.674577948 0.59765912 0.564280804 0.478017501 0.599688521 0.565355982 1 18.89514086 -1.448080955 5.633257429 1.000307913 0.604150068 0.661080049 0.085272519 0.00033231 3.26E-05 0.083203134 0.019596239 0.03563847 1.448080955 -0.396157845 RLAPEYEAAATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RLAPEYEAAATR 12 1 H7BZJ3;P30101 H7BZJ3;P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 223.03 3.75E-11 3098560000 1007162 1298940 1129717 1078910 1372730 1498860 1015064 1074000 1035330 1468010 FALSE TRUE 1046925.533 1522022.841 1159158.353 1292315.178 1139393.845 1150772.48 935500.6313 1059604.787 998068.6755 1755638.453 0.596321829 0.866934099 0.660248898 0.73609414 0.648991165 0.65547236 0.532854945 0.603543848 0.568493287 1 20.74356434 -1.080811002 4.87362801 1.000008955 0.652298512 0.576632421 0.089428659 1.16E-05 2.20E-06 0.090053322 0.021225069 0.083021198 1.080811002 -0.347710444 RLAVPTEVSTEVPEMDTS(ph)T ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 RLAVPTEVSTEVPEMDT(0.059)S(0.471)T(0.471) 102.78 0.00040851 50597000 35116 50659 48807 51018 55078 66232 50187 55976 47005 61604 TRUE FALSE 36502.4068 59359.28918 50078.95052 61109.20813 45715.86123 50850.62176 46253.2118 55225.73328 45313.29923 73674.12432 0.495457627 0.805700641 0.679735945 0.829452792 0.620514484 0.69021006 0.627808097 0.749594702 0.615050395 1 16.16887039 -1.146055597 4.537522075 1.000041574 0.688385751 0.50961716 0.094001528 3.57E-05 6.72E-06 0.082231773 0.019379633 0.071440486 1.146055597 -0.311655823 RLDECEEAFQGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLDECEEAFQGTK 13 1 K7ESG5;K9J957;P61289;P61289-2;B3KQ25;P61289-3;K7ENH2;K7EMD0;K7EPX6;K7EKR3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ;;; 241.76 1.07E-16 1594310000 1556510 1310330 1453920 1222180 1785110 1820710 1668760 1541590 1587910 1382990 FALSE TRUE 1617962.217 1535368.985 1491810.35 1463923.556 1481677.64 1397877.696 1537958.231 1520927.508 1530761.429 1653960.412 0.978235153 0.928298509 0.90196255 0.885101932 0.895836218 0.845169985 0.929863992 0.919567057 0.925512738 1 20.65749327 0.593676995 1.106275844 0.999859925 0.906919792 0.404377269 0.032474388 1.398271307 2.58422438 0.032128967 0.00999439 3.923530154 -0.593676995 -0.092940133 RLDEEEEDNEGGEWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 ; 239.58 1.26E-19 1758870000 350810 413600 424160 365210 445930 493710 394590 373060 382520 398590 FALSE TRUE 364660.2497 484632.5826 435213.9581 437447.448 370130.9779 379053.3347 363661.0047 368059.7409 368753.1799 476686.079 0.764990348 1.016670308 0.912999094 0.917684546 0.776466933 0.795184402 0.762894116 0.772121858 0.773576566 1 18.86267997 3.242681923 24.99621841 0.795934624 0.911907328 0.182850956 0.087621511 126.3394102 766257.3211 0.022676569 0.029629093 1748.565573 -3.242681923 0.115972703 RLDEELEDAEK ddPTM_MDA-MB-175_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 ;; 189.24 4.48E-06 1486170000 2523970 1465550 1913250 1523570 2462480 2745600 2501320 1951730 2107990 1419910 FALSE TRUE 2623618.285 1717246.812 1963110.867 1824927.599 2043908.529 2107976.01 2305260.002 1925570.252 2032123.852 1698114.179 1.545018773 1.011266989 1.156053516 1.074678971 1.203634334 1.24136294 1.357541225 1.133946278 1.196694473 1 20.69550204 1.557151374 11.39196217 1.121322599 1.212262974 0.111000513 0.146850023 0.335646004 61.60485494 0.076413862 0.035543314 36.07043448 -1.557151374 0.090940374 RLDEVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLDEVSR 7 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 107.01 0.012145 336085000 601714 865364 864890 836804 719236 954016 816412 827896 804937 746127 FALSE TRUE 625470.1333 1013983.535 887429.7439 1002321.334 596980.5216 732460.2423 752419.4941 816799.4083 775967.4746 892316.3002 0.700951146 1.136349897 0.99452374 1.123280314 0.669023441 0.820852698 0.843220609 0.915369817 0.869610333 1 19.76719567 3.253095356 24.99858272 0.851288091 0.99972773 0.192059967 0.135644649 360.8234437 620583.6956 0.036135164 0.048712191 1790.999052 -3.253095356 0.148439639 RLDGESSELQEQMVEQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDGESSELQEQMVEQQQR 19 1 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;Q7Z406-5;A0A0C4DFM8 Q7Z406 MYH14 Myosin-14 0 ; 186.38 3.31E-14 126280000 78099 102228 97128 96595 112301 116143 87229 94742 86830 117616 FALSE TRUE 81182.40883 119784.8638 99659.23547 115701.2027 93212.11613 89170.54841 80391.76305 93472.13846 83705.00526 140660.6033 0.577151007 0.851587872 0.708508517 0.822555854 0.66267394 0.633941177 0.57153006 0.664522519 0.59508493 1 17.10185878 -1.075726398 4.58274641 1.000018628 0.679459344 0.532226826 0.090972647 12596893.27 2956919.139 2358.992111 0.021697472 0.083998901 1.075726398 -0.320559285 RLDINEGAARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RLDINEGAARPR 12 2 Q9BUP0;H7C0I0 Q9BUP0 EFHD1 EF-hand domain-containing protein D1 0 ;;;;; 187.45 5.89E-06 2565030000 919962 1085671 1000399 982229 1156479 1276219 934989 1024370 1014857 1276572 FALSE TRUE 956282.8101 1272126.549 1026470.22 1176510.965 959901.1127 979836.4785 861702.119 1010639.996 978332.4948 1526691.842 0.626375791 0.833256925 0.672349319 0.770627662 0.628745819 0.641803704 0.564424395 0.661980347 0.640818578 1 20.54197746 -1.153773118 4.927772474 1.000022217 0.671375514 0.64642198 0.072962198 1.81E-05 3.11E-06 0.071875509 0.016940076 0.070182185 1.153773118 -0.328646703 RLDLPIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDLPIER 8 1 P17812;B4E1E0;P17812-2;A0A3B3IRI2;A0A3B3IRQ8;A0A3B3ITF6;A0A3B3ITB8;A0A3B3ISY3 P17812 CTPS1 CTP synthase 1;CTP synthase 0 ; 129.83 0.0017223 245130000 100564 127759 118858 131911 104662 126268 118467 127646 117913 138999 FALSE TRUE 104534.3444 149700.6144 121955.5371 158002.6021 86871.59062 96944.17061 109181.247 125935.1142 113669.3342 166233.1928 0.628841585 0.900545865 0.733641309 0.950487682 0.522588715 0.583181788 0.656795705 0.757581035 0.683794447 1 17.34284896 -1.290946305 3.115201971 1.001730004 0.71727683 0.318321392 0.125837927 18254791.96 24586602.83 298960.2468 0.030249069 0.05117451 1.290946305 -0.284453174 RLDLTTSAFHWSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDLTTSAFHWSDR 14 1 Q17RN3;Q17RN3-2 Q17RN3 FAM98C Protein FAM98C 0 89.541 0.0039652 109020000 20786 53184 39186 53456 42978 60988 42779 56722 42816 63217 FALSE TRUE 21606.64733 62317.93829 40207.21935 64029.43725 35672.61491 46824.46128 39425.8702 55961.73437 41275.06052 75603.16079 0.285790265 0.824276891 0.531819291 0.846914819 0.471840258 0.619345287 0.521484417 0.740203634 0.545943583 1 16.20615893 -4.999999811 0.377290675 6.355279237 0.603880854 0.353450422 0.161850881 611.4658942 4.611419424 2676.71089 0.098711958 1.00E-05 4.999999811 -5.751398382 RLDPNKYPVPENWLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDPNKYPVPENWLHK 16 2 P39748;P39748-2;I3L3E9 P39748 FEN1 Flap endonuclease 1 0 80.638 0.0090128 365060000 482770 376240 530680 412070 620710 616520 495830 486830 545590 444450 FALSE TRUE 501830.1324 440856.2933 544509.9568 493576.2161 515201.9359 473342.5735 456965.549 480304.8401 525954.3225 531531.468 0.944121209 0.829407702 1.02441716 0.928592653 0.969278334 0.890525965 0.859714949 0.903624468 0.989507403 1 19.01979558 1.223652276 14.06588051 0.99478795 0.916758652 0.254328937 0.051997384 2.157838014 2017.21302 0.046544958 0.012401526 16.73602346 -1.223652276 -0.078029298 RLDQELDFILSQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDQELDFILSQQK 14 1 P37198;M0QXN5 P37198 NUP62 Nuclear pore glycoprotein p62 0 122.33 0.00017538 142450000 103200 108250 119160 108010 140430 156590 134610 140080 131640 122750 FALSE TRUE 107274.4157 126841.0954 122265.4075 129374.0556 116559.7588 120224.3456 124058.9165 138202.4567 126902.3021 146800.5123 0.7307496 0.864037144 0.832867717 0.881291581 0.794001035 0.818964074 0.845085038 0.941430343 0.864454082 1 17.16349748 -4.999999992 0.077839199 1.559651004 0.673216596 0.619515608 0.043769553 176.3285675 0.976042633 16.77115666 1.670176441 1.00E-05 4.999999992 -0.886434407 RLDQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDQLER 7 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 109.71 0.01117 366160000 97578 129690 107180 114030 135050 147910 109480 109490 97827 131380 FALSE TRUE 101430.4548 151963.2487 109973.1988 136584.7937 112094.2492 113560.1441 100898.6715 108022.4656 94306.22538 157121.3956 0.645554696 0.967170945 0.699925039 0.869294682 0.713424476 0.722754172 0.642170159 0.687509586 0.600212498 1 17.26152012 RLDQVEQELNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDQVEQELNELR 13 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 164.65 5.88E-05 70578000 39263 50995 42625 50350 40985 53797 47487 49128 40391 43240 FALSE TRUE 40813.13356 59752.99456 43735.84252 60309.07972 34018.38434 41303.46205 43764.84486 48469.51952 38937.3358 51712.05012 0.789238359 1.155494598 0.845757274 1.166248091 0.6578425 0.798720259 0.846318116 0.937296421 0.752964458 1 15.65821288 3.239161181 24.99999999 0.83594837 0.990819027 0.230771139 0.140305758 23.63200111 983708.9207 0.037268482 0.047572972 1734.447589 -3.239161181 0.154870656 RLDS(ph)SGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDSSGER 8 1 A0A087X2H1;Q9ULT8;G3V4V5;A0A087WVU6 A0A087X2H1 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 RLDS(0.956)S(0.044)GER;RLDS(0.518)S(0.482)GER 97.749 0.0049067 128696000 101112 78367 95299 81243 109976 215980 99170 91443 93505 93991 TRUE FALSE 105103.9798 91825.92264 97782.57023 97312.62291 91282.3188 165821.9182 91396.79627 90217.35616 90139.77332 112406.7369 0.935032746 0.816907644 0.869899554 0.865718778 0.812071601 1.475195551 0.813090023 0.802597412 0.801907215 1 16.77836898 RLDTEELSLPDISAEIAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDTEELSLPDISAEIAEK 19 1 E9PM06;P35790-2;P35790 E9PM06 CHKA Choline kinase alpha 0 102.98 0.00061202 29233000 39395 55364 87795 59390 97424 80192 95122 86755 87676 63440 FALSE TRUE 40950.34502 64872.33633 90083.00982 71137.16474 80863.90328 61568.62332 87666.08908 85592.19113 84520.55789 75869.85337 0.539744618 0.855047604 1.187336021 0.93762096 1.065823904 0.811503128 1.15547988 1.128144939 1.114020314 1 16.21123913 4.597632523 3.027106111 1.052072645 0.523584602 0.677899011 0.107844111 0.166978649 2.491705141 0.026764 0.174789188 39594.28665 -4.597632523 -0.528488044 RLDVFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLDVFEK 7 1 A0A087WW66;Q99460-2;Q99460;C9J9M4;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 97.431 0.03736 0 275160 248930 283550 228510 344040 353420 317750 301380 285230 266700 FALSE TRUE 286023.5293 291681.7911 290939.5459 273708.596 285560.2037 271343.5611 292843.9247 297340.4941 274964.628 318954.7587 0.896752663 0.914492677 0.912165559 0.858142381 0.895300026 0.850727427 0.918136246 0.932234074 0.862080344 1 18.28299228 -5 0.412677037 2.828470557 0.894198872 0.582315992 0.026815856 639.1445945 4.266920652 1057.198981 0.016465053 1.00E-05 5 -1.934271685 RLDVTVQSFGWSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLDVTVQSFGWSDR 14 1 Q52LJ0;Q52LJ0-1;Q8NCA5;E9PH82 Q52LJ0;Q8NCA5 FAM98B;FAM98A Protein FAM98B;Protein FAM98A 0 ; 162.79 7.03E-06 1258420000 554430 517500 620410 534780 615140 690760 618480 574620 613430 499580 FALSE TRUE 576319.3245 606376.5994 636578.3943 640557.8878 510578.7225 530341.4586 570001.9215 566918.1588 591352.7741 597463.136 0.964610684 1.014918851 1.065468907 1.072129558 0.854577784 0.887655533 0.954036973 0.948875545 0.989772822 1 19.18849017 3.254354418 24.99991383 0.936166159 1.03084084 0.447591783 0.048972548 226.4572254 358455.5515 0.014202819 0.019167629 1796.198867 -3.254354418 0.094674681 RLEAAYLDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLEAAYLDLQR 11 1 E5RJD8;O75347;E5RIW3;E5RHG6;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 ;; 201.38 6.99E-08 2052920000 931840 1167480 868960 851350 1968010 1518070 1129280 950710 942100 2315480 FALSE TRUE 968629.7627 1367985.608 891605.8115 1019744.489 1633488.363 1165521.249 1040764.083 937967.2875 908194.005 2769153.973 0.34979267 0.494008503 0.321977694 0.368251278 0.589887156 0.420894345 0.375841897 0.338719803 0.327968041 1 21.40101384 -1.594410922 6.237763401 1.001773509 0.399100153 0.834709849 0.080286691 0.002024887 0.000131661 0.079491873 0.018693446 0.025444216 1.594410922 -0.602673356 RLEAEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEAEQAR 8 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 ; 179.51 0.00041033 128870000 117445 158332 120378 111050 225407 203205 135832 120751 128879 267940 FALSE TRUE 122081.8193 185524.2893 123515.1496 133015.3585 187092.3987 156013.7184 125185.1329 119132.5304 124240.67 320437.713 0.380984554 0.578971456 0.385457593 0.415105193 0.583865104 0.486876894 0.390669162 0.371780616 0.387721747 1 18.28968443 -1.491904401 3.233988597 1.012690652 0.441945235 0.825741014 0.076848052 52387641.93 64153733.18 5902674.812 0.019081842 0.032217779 1.491904401 -0.570745417 RLEAFEHPNVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEAFEHPNVVR 12 1 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VYY1;Q96BE9 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 75.695 0.021498 48796000 30995 39549 36420 34314 43233 44120 32703 35754 38733 44001 FALSE TRUE 32218.70653 46341.2331 37369.13512 41101.20678 35884.2701 33873.79865 30139.65341 35274.77611 37339.0069 52622.1535 0.612265071 0.880641137 0.710140742 0.781062804 0.681923253 0.643717453 0.572755986 0.670340793 0.709568203 1 15.68338267 0.931698466 18.66032963 1 0.69413472 0.553700996 0.082030443 977.2470772 266991.0582 0.081768809 0.020442202 8.544732397 -0.931698466 -0.305865281 RLEAFLTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEAFLTQK 9 1 P36507;A0A1B0GUL7;Q02750;Q02750-2 P36507;Q02750 MAP2K2;MAP2K1 Dual specificity mitogen-activated protein kinase kinase 2;Dual specificity mitogen-activated protein kinase kinase 1 0 ; 115.39 0.0023795 1124960000 1227860 999620 1217750 976650 1807400 1447920 1259770 1167090 1205970 1333500 FALSE TRUE 1276336.861 1171296.959 1249485.565 1169828.455 1500178.794 1111662.523 1161025.936 1151447.068 1162567.375 1594773.794 0.800324702 0.734459623 0.783487646 0.7335388 0.940684378 0.697065959 0.728019196 0.722012785 0.728985753 1 20.60492037 -0.988499177 4.199077856 1.000012987 0.760889825 0.536766267 0.065971012 7061613.786 3364074.14 817.6314063 0.015213411 0.102683538 0.988499177 -0.239123162 RLEDELGGQFLDLSLHDTVTTLILGGHNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEDELGGQFLDLSLHDTVTTLILGGHNKR 30 2 Q9H269-2;Q9H269 Q9H269-2 VPS16 Vacuolar protein sorting-associated protein 16 homolog 0 145.67 1.25E-08 125860000 36624 75485 84407 69890 93584 102080 68611 88678 82794 86664 FALSE TRUE 38069.9438 88448.96156 86606.71576 83714.0334 77676.62511 78373.46704 63233.09054 87489.41646 79814.26011 103644.1515 0.367313961 0.853390763 0.835616043 0.807706293 0.749454976 0.756178384 0.61009801 0.84413269 0.770079729 1 16.66127918 -5 0.147795953 1.887314361 0.662223484 0.293450406 0.135090733 188.9612839 1.671145953 49.48627622 0.693391088 1.00E-05 5 -1.225090876 RLEDLSESIVNDFAYMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEDLSESIVNDFAYMK 17 1 P49755 P49755 TMED10 Transmembrane emp24 domain-containing protein 10 0 ; 171.98 2.66E-09 430720000 528660 577970 569880 646120 1370710 1114960 808370 651440 712510 1283810 FALSE TRUE 549531.905 677231.8515 584731.541 773920.6075 1137717.204 856027.4374 745007.8471 642708.5123 686866.9043 1535347.989 0.357920099 0.441093391 0.380846261 0.504068532 0.741015855 0.5575462 0.485237127 0.418607714 0.447368876 1 20.55013425 -2.119276652 2.273126711 1.964595455 0.483334919 0.695639843 0.102878864 7281327.963 1881760.648 36264180.42 0.026937843 0.007598421 2.119276652 -1.481260535 RLEEALMADMLAHVEELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEEALMADMLAHVEELAR 19 1 O95983-2;O95983;K7EIE8 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 0 ; 191.8 5.75E-15 127979000 155834 203641 191334 190773 186456 217957 197819 189841 190581 202898 FALSE TRUE 161986.4467 238614.7576 196320.3212 228507.33 154762.2757 167339.7899 182313.4299 187296.4919 183722.027 242651.9784 0.667566973 0.983362094 0.809061284 0.941708085 0.637795236 0.689628789 0.751337084 0.771872923 0.757142094 1 17.8885291 5.054282757 12.9227129 0.800323188 2.51E-05 0.113824292 0.117124879 632898.1829 5014548.126 0.027515544 12153203.84 113313.7877 -5.054282757 -0.800298136 RLEEEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEEEADR 8 1 A0A669KAX4;Q13620-1;K4DI93;Q13620;Q13620-3 A0A669KAX4 CUL4B Cullin-4B 0 ; 72.365 0.074307 142263000 152976 219920 179043 221330 206135 254310 197813 199608 176128 230980 FALSE TRUE 159015.6106 257689.5493 183709.0077 265108.4134 171096.2463 195250.3566 182307.9002 196932.5813 169789.1877 276236.1086 0.575651067 0.932859757 0.665043425 0.959716725 0.619384074 0.706824164 0.659971287 0.712913971 0.614652402 1 18.07554239 -1.034589445 4.616202852 1.000009712 0.722142239 0.321977297 0.123232213 14971949.57 3355532.857 1472.997036 0.026690011 0.092344398 1.034589445 -0.277867472 RLEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEEELR 7 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 99.305 0.017038 212820000 82052 103640 88867 97068 105170 119540 87037 98442 99006 121350 FALSE TRUE 85291.47632 121439.3638 91182.94703 116267.7607 87293.24097 91778.64665 80214.81251 97122.54601 95442.7934 145126.2091 0.587705535 0.83678451 0.628301032 0.801149299 0.601498802 0.632405733 0.552724508 0.669228161 0.657653735 1 17.14694856 -1.595238742 5.56578178 1.001877168 0.664018069 0.582888937 0.085506978 0.001922131 0.000139784 0.079898407 0.018738482 0.025395763 1.595238742 -0.337859099 RLEEFEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEEFEGER 9 1 Q08378;Q08378-4;Q08378-2 Q08378 GOLGA3 Golgin subfamily A member 3 0 96.113 0.0092617 0 135530 176710 158940 149500 166450 192420 162560 150910 116420 144130 FALSE TRUE 140880.8291 207058.5679 163082.107 179070.6538 138156.8885 147733.3712 149818.1224 148887.2983 112230.0669 172369.514 0.817318711 1.201248197 0.946119202 1.038876595 0.801515798 0.857073665 0.869168329 0.863768162 0.651101604 1 17.39514511 3.240463185 24.99693324 0.838551321 1.0112897 0.299860645 0.11966967 56.06007049 736537.4952 0.031387116 0.040436515 1739.655222 -3.240463185 0.172738379 RLEEIPLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEEIPLIK 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 84.817 0.024429 292890000 402440 424450 449290 428380 574650 606760 522890 453810 507490 542660 FALSE TRUE 418328.642 497345.9857 460998.8665 513112.2854 476971.1983 465849.1855 481904.5155 447727.4192 489225.534 648983.8371 0.644590232 0.76634572 0.710339519 0.790639545 0.734950812 0.717813232 0.742552415 0.689889938 0.753833156 1 19.30782302 0.953862017 20.71723644 1.000000001 0.726583504 0.823701191 0.037972789 413.977202 185888.047 0.034236911 0.008559228 8.992118414 -0.953862017 -0.273416497 RLEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEELER 7 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6;Q9NRD5;Q9NRD5-2;F6V107 O95819-3 MAP4K4;PICK1 Mitogen-activated protein kinase kinase kinase kinase 4;PRKCA-binding protein 0 118.06 0.0081639 196320000 87015 105890 95114 110100 120820 116120 103270 107380 101520 121320 FALSE TRUE 90450.41939 124075.7838 97592.74898 131877.4514 100283.0596 89152.88982 95175.42755 105940.7467 97866.31503 145090.3312 0.623407629 0.855162317 0.672634408 0.908933423 0.691176722 0.614464721 0.655973605 0.730170962 0.674519895 1 17.14659186 -1.038025867 9.15546687 1 0.71753029 0.467887972 0.091415742 6.15E-10 6.97E-11 0.085710448 0.020202146 0.091616592 1.038025867 -0.28246971 RLEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLEELLR 7 1 P42285;H0YAC4 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 101.54 0.014404 48000000 21344 21294 16863 19221 30319 27575 22539 18860 20154 25429 FALSE TRUE 22186.6776 24951.07886 17302.46363 23022.85643 25165.38721 21171.12415 20772.33429 18607.21255 19428.66148 30411.32568 0.729553122 0.820453509 0.568948023 0.757048761 0.8275005 0.6961592 0.683045997 0.611851412 0.638862695 1 14.89232109 2.513475345 24.67193309 0.690727235 0.739031083 0 0.121827392 2033.165305 1379818.049 0.037723029 0.035552996 326.1935315 -2.513475345 0.048303848 RLEEPEEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLEEPEEPK 9 1 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ; 141.91 0.0001693 686630000 1259450 814340 1019650 784280 1278670 1543100 1319570 1082410 1165110 728850 FALSE TRUE 1309174.059 954196.5603 1046222.917 939408.2432 1061322.13 1184738.411 1216138.655 1067902.064 1123177.919 871654.2028 1.501942002 1.094696219 1.200272899 1.077730412 1.21759538 1.35918396 1.3952077 1.22514417 1.288559058 1 19.73339639 -1.068140373 4.499102678 0.999983621 1.255170729 0.283892392 0.124500745 2.02E-05 4.19E-06 0.119085666 0.02806696 0.085479038 1.068140373 0.255187108 RLEEPSLR ddPTM_MDA-MB-175_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 ; 155.84 0.00064533 210640000 121987 136898 146833 146562 151325 156733 141961 135572 135945 139618 FALSE TRUE 126803.141 160409.1666 150659.5886 175551.5262 125602.8306 120334.1361 130833.7259 133754.8791 131052.366 166973.474 0.759420871 0.960686526 0.902296545 1.051373742 0.752232241 0.720678161 0.783559944 0.801054658 0.784869374 1 17.3492594 3.20764333 24.99995902 0.792083514 0.920308488 0.229959896 0.097539276 241.1554576 194999.5435 0.026682862 0.031895274 1613.03329 -3.20764333 0.128224974 RLEEQAAQHK ddPTM_MDA-MB-175_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 ;;; 152.69 1.14E-05 1219710000 1265250 1030370 1177590 980770 1507270 1428460 1288260 1168970 1217620 1187910 FALSE TRUE 1315203.047 1207328.032 1208278.963 1174763.379 1251064.784 1096721.814 1187282.815 1153301.869 1173798.094 1420658.221 0.925770201 0.849837079 0.850506438 0.82691485 0.880623338 0.771981464 0.835727269 0.811808113 0.826235387 1 20.43812808 5.058971174 1.636046917 0.83858516 1.036021164 0.106256663 0.057811821 4.384022379 5.739117375 0.013645637 1.764311225 114543.6911 -5.058971174 0.197436004 RLEEWLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 ;; 193.1 0.00027645 1701780000 757394 864187 829829 894579 924910 995770 784846 899820 810160 934107 FALSE TRUE 787296.5 1012604.395 851455.0255 1071524.056 767694.1286 764517.5085 723327.7197 887759.3847 781002.4999 1117127.382 0.704750875 0.906435928 0.762182576 0.959178043 0.687203752 0.684360191 0.647489025 0.794680534 0.699116781 1 20.09136227 5.039994602 15.8958916 0.780110957 0.379010198 0.037986816 0.117837389 15262362.13 169102205.1 0.02721891 176896334.4 109646.4567 -5.039994602 -0.401100759 RLEIS(ph)PDSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLEISPDSSPER 12 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 RLEIS(1)PDS(0.013)S(0.987)PER;RLEIS(1)PDS(0.083)S(0.917)PER;RLEIS(0.997)PDS(0.484)S(0.519)PER;RLEIS(0.998)PDS(0.39)S(0.612)PER 174.18 2.08E-05 1963940000 1809800 2125560 1814870 1900960 2068050 2247200 1718770 1871010 1697560 1956330 TRUE FALSE 1881252.301 2490608.395 1862167.003 2276964.214 1716523.6 1725321.857 1584048.316 1845932.171 1636465.147 2339635.407 0.804079258 1.064528425 0.795921876 0.973213265 0.733671406 0.737431931 0.677049215 0.788982833 0.699453061 1 21.1578523 3.229859423 24.99775176 0.756146717 0.91240563 0.259631592 0.110910148 206.2458729 592525.2255 0.029072604 0.035256093 1697.694036 -3.229859423 0.156258912 RLELLPSAES(ph)PVCWLEQPESHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLELLPSAESPVCWLEQPESHQR 23 1 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 RLELLPS(0.005)AES(0.995)PVCWLEQPESHQR;RLELLPS(0.21)AES(0.79)PVCWLEQPESHQR 208.86 4.43E-25 87200000 30641 38337 28740 32817 40699 42539 30687 34109 36161 43722 TRUE FALSE 31850.73034 44921.08153 29488.98801 39308.10465 33780.99852 32659.96193 28281.67275 33651.82465 34859.57267 52288.48879 0.60913465 0.85910078 0.563967112 0.75175446 0.646050389 0.624610936 0.540877608 0.643579981 0.666677762 1 15.67420575 -1.577884225 5.694999644 1.001360707 0.655083641 0.584221811 0.087006743 0.001447619 0.000107298 0.081129735 0.019053409 0.026431133 1.577884225 -0.346277066 RLESSGAGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLESSGAGGR 10 1 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 0 ; 138.99 8.02E-05 99050000 55694 72917 63979 65818 73966 80285 64990 64010 59855 73121 FALSE TRUE 57892.84213 85439.92753 65646.3453 78836.60395 61393.28574 61640.02548 59895.91398 63152.05065 57700.83024 87447.65996 0.662028488 0.977040753 0.75069299 0.901529029 0.702057502 0.704879073 0.68493444 0.722169703 0.659832753 1 16.41613216 3.220411492 24.97500306 0.725423868 0.828686267 0.075418417 0.119785314 424.0895283 583588.1595 0.031396066 0.037594029 1661.160104 -3.220411492 0.1032624 RLFDANKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 92.538 0.0056289 316520000 733440 575790 728130 462240 1357260 915430 665050 663980 784130 1087120 FALSE TRUE 762396.7775 674677.4535 747105.666 553669.6924 1126553.43 702835.256 612921.6432 655080.4342 755909.3145 1300120.35 0.586404772 0.518934615 0.574643467 0.425860339 0.866499344 0.540592458 0.471434543 0.50386138 0.581414878 1 20.31021375 0.939670697 20.46815594 1.000000001 0.557042438 0.576968943 0.112260415 1742.832049 591299.5087 0.106509905 0.026627476 8.703034341 -0.939670697 -0.442957562 RLFDDEAS(ph)VDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 139.88 2.39E-05 787760000 708128 947306 838020 846702 938256 1007310 678778 858522 762058 1086185 TRUE FALSE 736085.4402 1109998.436 859859.4896 1014177.128 778771.5803 773377.5184 625573.6067 847014.9168 734631.6814 1299002.154 0.566654518 0.854500843 0.661938463 0.780735525 0.599515234 0.595362768 0.481580115 0.652050433 0.565535383 1 20.30897239 -1.089857404 4.584882157 1.000018718 0.642171359 0.523762542 0.103028237 52979600404 10516961870 13970472.11 0.024534189 0.081309744 1.089857404 -0.357847359 RLGDSS(ph)LSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 RLGDS(0.027)S(0.973)LSR;RLGDS(0.147)S(0.853)LSR 121.56 0.00037384 892930000 325370 412430 379780 509020 424680 623150 405440 424920 380570 563660 TRUE FALSE 338215.8588 483261.6442 389677.3788 609702.6367 352493.0453 478432.8564 373660.5534 419224.6424 366873.36 674098.3851 0.501730706 0.71690076 0.578071966 0.904471291 0.522910384 0.709737432 0.554311599 0.621904238 0.544243048 1 19.36259964 -1.303926951 5.185205373 1.000090283 0.632810114 0.482551813 0.115399285 0.000110574 1.48E-05 0.102579275 0.024172252 0.049667586 1.303926951 -0.367280169 RLGDSSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLGDSSLSR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 125.74 0.0024351 0 302833 289837 328553 256707 434421 429511 353718 362044 293829 363673 FALSE TRUE 314789.0807 339614.2501 337115.3611 307482.8784 360578.2736 329763.5796 325992.6589 357191.3924 283254.1517 434927.7614 0.723773253 0.780852087 0.77510656 0.706974596 0.829053249 0.758203106 0.749532883 0.821266022 0.651267123 1 18.73041627 -1.302960621 3.478956554 1.00089045 0.76154835 0.678459024 0.05040073 639078651.7 1134188462 6219629.819 0.011229018 0.049778222 1.302960621 -0.2393421 RLGGLRPES(ph)PESLTSVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLGGLRPESPESLTSVSR 18 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 RLGGLRPES(1)PESLTSVSR;RLGGLRPES(1)PESLTSVSR 179.03 6.75E-14 692670000 147889 190245 169555 107849 207022 212446 102336 162711 146345 279730 TRUE FALSE 153727.7719 222918.0988 173973.7426 129181.2103 171832.4744 163108.6362 94314.63691 160530.1252 141078.072 334537.7377 0.459522961 0.666346644 0.520042204 0.386148394 0.513641527 0.487564235 0.281925255 0.479856552 0.421710486 1 18.35180944 -0.952319333 4.939164141 1.00000278 0.46795964 0.742427464 0.093912056 3.78E-06 8.02E-07 0.093354804 0.022003791 0.111604233 0.952319333 -0.53204314 RLGSLVDEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLGSLVDEFK 10 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 129.82 0.00046984 316270000 368920 259660 347560 273490 498440 446490 392720 339480 386010 316940 FALSE TRUE 383485.2465 304254.5851 356617.6991 327585.5057 413715.3468 342799.4641 361937.5802 334929.8259 372117.5755 379038.3248 1.011732116 0.802701377 0.940848658 0.86425431 1.091486849 0.904392621 0.954883864 0.883630504 0.981741294 1 18.5319842 RLHPPS(ph)PVPQGVCPAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLHPPSPVPQGVCPAHR 17 1 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHR 63.69 0.024291 127620000 42855 62324 46971 53932 54542 61944 58080 59797 55111 58337 TRUE FALSE 44546.94849 73027.66219 48195.10285 64599.58863 45270.97032 47558.44477 53527.53784 58995.51902 53127.56588 69767.01822 0.638510139 1.046736181 0.690800669 0.925933059 0.648887848 0.681675181 0.767232701 0.845607574 0.761499735 1 16.09025756 -1.10419006 4.388289167 1.000025134 0.785543062 0.222712288 0.123495052 2.81E-05 5.74E-06 0.110711395 0.02609187 0.078670143 1.10419006 -0.214482073 RLHPPS(ph)PVPQGVCPAHREPLAAFCGDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLHPPSPVPQGVCPAHREPLAAFCGDELR 29 2 Q96F44-3;Q96F44;Q96F44-2 Q96F44-3 TRIM11 E3 ubiquitin-protein ligase TRIM11 1 RLHPPS(1)PVPQGVCPAHREPLAAFCGDELR 177.6 6.25E-18 271170000 44772 63936 53919 47528 73991 69798 45545 62773 55047 89751 TRUE FALSE 46539.63313 74916.51065 55324.17343 56928.89654 61414.03625 53588.4723 41975.06389 61931.63061 53065.86922 107335.9901 0.433588334 0.697962637 0.515429852 0.530380318 0.5721663 0.499259123 0.391062344 0.576988488 0.494390271 1 16.71177437 -1.263093774 3.149399977 1.002243403 0.527165164 0.764377732 0.079347868 12810942.38 17499377.81 276906.3577 0.018485856 0.054564003 1.263093774 -0.47507824 RLIELYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLIELYK 7 1 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ; 155.75 0.002549 2366500000 2056860 1689100 2001400 1600740 3642300 3005300 2814400 2511190 2432600 2614700 FALSE TRUE 2138066.421 1979189.786 2053558.128 1917361.594 3023183.147 2307364.621 2593799.974 2477531.606 2345051.201 3127000.404 0.683743571 0.632935571 0.656718217 0.613163207 0.96679973 0.737884337 0.829485014 0.792302938 0.749936328 1 21.57634797 3.26215046 24.99993978 0.826913408 0.646381041 0.580561045 0.082079462 170.7690243 180975.6498 0.021207009 0.02869836 1828.733666 -3.26215046 -0.180532367 RLIISDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLIISDR 7 1 P30520;G3V2N1;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 0 ; 113.26 0.009894 853910000 741070 880560 821390 859210 1135100 1124840 897550 934860 905370 1125770 FALSE TRUE 770328.0158 1031789.33 842796.0982 1029159.174 942156.1074 863612.9571 827197.6857 922329.7308 872785.9106 1346343.077 0.572163239 0.766364345 0.625989105 0.764410789 0.699789024 0.641450884 0.614403342 0.685062928 0.64826412 1 20.36061466 -1.073022384 4.305824715 1.000028565 0.671832217 0.736738592 0.059393436 0.750651941 31660267.82 2261.959858 0.012912552 0.084523528 1.073022384 -0.328196348 RLIVDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLIVDVIR 8 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 158.76 0.00058226 607390000 397790 502410 466480 440330 607130 613300 501350 503020 490950 562110 FALSE TRUE 413495.0564 588695.0093 478636.852 527425.9597 503930.2595 470870.3697 462052.877 496277.8397 473280.8054 672244.6923 0.615096052 0.87571537 0.711997964 0.784574376 0.749623263 0.700444905 0.687328412 0.738239878 0.704030557 1 19.35862693 -1.646172486 6.860221503 1.000996848 0.733336126 0.611660166 0.064559984 0.000904133 4.66E-05 0.057418169 0.013486536 0.022585386 1.646172486 -0.267660723 RLKS(ph)EDELRPEVDEHTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLKSEDELRPEVDEHTQK 18 3 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2;H0YCR2;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 RLKS(1)EDELRPEVDEHTQK;RLKS(1)EDELRPEVDEHTQK;RLKS(1)EDELRPEVDEHTQK 218.69 5.52E-19 3601830000 4396410 1689720 2874860 1590350 4403900 3942130 3304030 2931200 3310570 1763780 TRUE FALSE 4569983.662 1979916.266 2949781.213 1904916.483 3655326.651 3026630.051 3045051.495 2891912.058 3191423.232 2109358.921 2.166527287 0.938634125 1.398425457 0.903078402 1.732908807 1.434857776 1.443590972 1.370990982 1.512982547 1 21.00837317 -1.408887411 2.952683999 0.992690031 1.408521044 0.122593215 0.342112997 27341293.95 33520233.99 1699391.796 0.076153641 0.039004309 1.408887411 0.415831013 RLLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLLAEK 6 1 P02545;P02545-6;P02545-3;P02545-5;P02545-4;B5MCA1;Q96G28;Q96G28-2;P02545-2;Q3BDU5;Q5TCI8;A0A3B3ISJ8 P02545;P02545-2;A0A3B3ISJ8 LMNA;CFAP36 Prelamin-A/C;Lamin-A/C;Cilia- and flagella-associated protein 36 0 ; 133.47 0.023172 3032700000 3434100 2861700 3128100 2442500 4701600 4272800 4091200 3292600 3347800 3481500 FALSE TRUE 3569680.92 3353174.714 3209620.856 2925619.21 3902423.711 3280506.955 3770521.054 3248468.083 3227313.332 4163633.268 0.857347583 0.805348238 0.770870211 0.702660158 0.937264034 0.787895269 0.905584333 0.780200338 0.775119499 1 21.98941157 3.242603936 24.99999886 0.84795286 0.784635525 0.18625011 0.077809865 211.8926291 1310128.444 0.021124199 0.02759822 1748.251607 -3.242603936 -0.063317335 RLLEDGEDFNLGDALDSSNSMQTIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 359.82 3.09E-110 6025870000 2857430 2721900 3091050 2079556 3819940 3534060 2589590 3011010 3379340 3398870 FALSE TRUE 2970243.543 3189365.152 3171605.302 2490885.97 3170627.963 2713328.124 2386611.169 2970652.336 3257718.214 4064813.501 0.730720743 0.784627671 0.780258504 0.612792191 0.780018065 0.667516018 0.587139156 0.730821312 0.801443464 1 21.95475773 0.890808048 2.419022129 0.999322237 0.70670631 0.648886188 0.065178753 0.27213164 3.319786884 0.063753767 0.017205941 7.776927464 -0.890808048 -0.292615927 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLS(ph)PQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLLGPAPEDDGGHNDHSQPQASQDQDSHTLSPQV 34 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 RLLGPAPEDDGGHNDHSQPQAS(0.001)QDQDS(0.018)HT(0.057)LS(0.924)PQV 78.366 0.00095656 222010000 71679 46737 59550 48104 62702 107790 61766 69681 44155 44146 TRUE FALSE 74508.94227 54763.71619 61101.92192 57618.82762 52043.93644 82757.40607 56924.61952 68747.04017 42565.87018 52795.56347 1.411272792 1.037278752 1.157330615 1.091357376 0.985763443 1.567506825 1.078208391 1.302136688 0.806239528 1 15.68812908 1.237577871 24.99999991 0.903119708 1.196947483 0.31767363 0.176067193 30.03474593 763860.1104 0.132457331 0.040347666 17.28135815 -1.237577871 0.293827775 RLLS(ph)FQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLLSFQR 7 1 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 RLLS(1)FQR;RLLS(1)FQR;RLLS(1)FQR;RLLS(1)FQR 142 0.0025739 367830000 466868 536714 516353 459227 662992 615617 520076 495356 531267 614777 TRUE FALSE 485300.3091 628890.4544 529809.5834 550060.7299 550296.8567 472649.2815 479311.0842 488716.5631 512146.8044 735230.7825 0.660065276 0.855364696 0.720603103 0.748147035 0.748468195 0.642858396 0.651919228 0.664711781 0.696579654 1 19.48783764 -0.986459556 4.593106543 1.000006059 0.708923661 0.673101349 0.060656377 0.040064044 39169990.35 588.5067393 0.014976174 0.103166915 0.986459556 -0.291082397 RLNDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLNDSGK 7 1 Q9H201;I6L9I8;Q9H201-2;D6RFG3;D6REL6;D6RBR6 Q9H201 EPN3 Epsin-3 0 72.038 0.084482 47840000 85446 84335 93683 74812 123110 135710 136030 130920 133010 117830 FALSE TRUE 88819.47406 98818.88021 96124.45594 89609.59031 102183.8062 104193.4092 125367.6132 129165.2315 128222.9961 140916.5325 0.630298464 0.701258245 0.682137534 0.635905445 0.725137103 0.739398049 0.889658658 0.916608075 0.909921595 1 17.10448135 2.252413058 1.129511728 0.956631424 0.664700757 0.937040736 0.031687533 0.107433307 0.26404725 0.020399093 0.011675536 178.8187516 -2.252413058 -0.291930667 RLNHS(ph)PPQSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLNHSPPQSSSR 12 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 RLNHS(1)PPQSSSR;RLNHS(0.961)PPQS(0.02)S(0.02)SR;RLNHS(0.998)PPQS(0.001)SSR;RLNHS(0.996)PPQS(0.003)S(0.001)SR;RLNHS(1)PPQSSSR 109.07 0.0010028 4377389000 252189 386178 324170 308215 370758 409767 299553 349431 303381 398208 TRUE FALSE 262145.6165 452501.0675 332618.1365 369179.0071 307736.6876 314604.8243 276073.2531 344747.449 292462.3771 476229.2334 0.550460992 0.950174907 0.69844124 0.77521282 0.64619445 0.660616363 0.579706649 0.723910724 0.614121008 1 18.86129666 -1.067579631 4.323487828 1.000027524 0.694624834 0.426859129 0.10800224 13821769.18 3412948.489 3701.454397 0.024122441 0.085589476 1.067579631 -0.30540269 RLNKHEENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLNKHEENLK 10 2 P42766 P42766 RPL35 60S ribosomal protein L35 0 ; 109.66 0.0011944 1631300000 2102610 1363230 1811460 1064320 3096900 2161620 1901540 1744870 2070640 1913850 FALSE TRUE 2185622.666 1597354.148 1858668.136 1274839.319 2570490.044 1659616.515 1752492.326 1721482.872 1996118.071 2288832.265 0.954907312 0.697890436 0.812059566 0.556982414 1.123057414 0.725093114 0.765670929 0.752122774 0.872111994 1 21.12618031 0.957347406 4.658559067 0.999875353 0.792832284 0.155361912 0.144005108 0.379820057 26.22669448 0.12806837 0.032481521 9.064574154 -0.957347406 -0.207043069 RLNNLS(ph)PAPHLASGSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 2 RLNNLS(0.689)PAPHLAS(0.143)GS(0.167)PPPGLPSGLPS(0.018)GLQS(0.251)GS(0.699)PS(0.032)R 90.331 0.00060797 275060000 33415 53528 46029 51201 48976 58417 37716 41267 59340 54554 TRUE FALSE 34734.25 62721.01761 47228.55355 61328.40498 40651.07701 44850.53707 34759.72137 40713.88336 57204.36499 65242.8118 0.53238432 0.961347555 0.723888996 0.940002481 0.623073652 0.687440284 0.532774729 0.624036307 0.87679184 1 15.99353134 1.033839209 4.969565433 0.998918159 0.705463912 0.329817871 0.13952116 0.188089478 11.30782199 0.135660735 0.034336189 10.8103364 -1.033839209 -0.293454247 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLNNLSPAPHLASGSPPPGLPSGLPSGLQSGSPSR 35 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;A0A087WU33 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RLNNLSPAPHLASGSPPPGLPSGLPSGLQS(0.019)GS(0.779)PS(0.202)R;RLNNLSPAPHLASGSPPPGLPSGLPSGLQS(0.043)GS(0.776)PS(0.181)R 156.07 6.06E-12 1453860000 323854 789740 654490 715870 683390 946730 600820 708550 655990 869280 TRUE FALSE 336640.006 925371.7017 671546.5471 857466.9493 567227.6119 726866.3053 553726.1584 699053.0462 632381.048 1039598.773 0.323817241 0.890123888 0.645967045 0.824805658 0.545621664 0.699179649 0.532634487 0.672425809 0.608293377 1 19.9875954 -1.344483707 3.000936972 1.00379794 0.647620015 0.343729322 0.149498995 14756420.61 18440331.27 493239.2283 0.033506353 0.045239343 1.344483707 -0.356177925 RLPDAHSDYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLPDAHSDYAR 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 ;;; 177.83 5.07E-06 2411850000 497553 671746 555939 606156 682350 770469 495751 549756 516073 889907 FALSE TRUE 517196.7766 787113.15 570427.227 726051.8476 566364.3907 591539.2513 456892.7412 542387.42 497499.6335 1064267.238 0.485965139 0.739582242 0.535981196 0.68220821 0.532163699 0.555818341 0.429302646 0.509634611 0.467457435 1 20.02142903 -1.011205217 4.991937524 1.000005222 0.549392632 0.693369084 0.090038206 5.29E-06 1.05E-06 0.088217857 0.020792908 0.097452903 1.011205217 -0.45061259 RLPGAIDVIGQTITISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLPGAIDVIGQTITISR 17 1 Q6UN15;Q6UN15-5;Q6UN15-3;A0A0B4J203;Q6UN15-4 Q6UN15 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 80.238 0.018991 189680000 67166 107700 85771 102930 87893 104650 84658 81203 84594 131590 FALSE TRUE 69817.76554 126196.6372 88006.26272 123289.2468 72952.97925 80346.62349 78022.28475 80114.60661 81549.47846 157372.5411 0.443646427 0.801897436 0.55922248 0.783422864 0.463568668 0.510550462 0.495780803 0.509076145 0.518193822 1 17.26382431 -1.159147024 5.096277447 1.000022483 0.566419467 0.545296712 0.119150655 3.00E-05 4.94E-06 0.113523989 0.026756475 0.06931911 1.159147024 -0.433603016 RLPIFSRLS(ph)ISDD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.002)RLS(0.997)IS(0.001)DD;RLPIFS(0.029)RLS(0.969)IS(0.001)DD;RLPIFS(0.001)RLS(0.997)IS(0.002)DD;RLPIFS(0.001)RLS(0.999)ISDD 130.21 0.00011392 436161000 232706 363348 345351 261477 439576 457633 247847 377950 414575 711823 TRUE FALSE 241893.4126 425750.1925 354351.1308 313196.3702 364857.0285 351354.6712 228420.1045 372884.1985 399654.5267 851291.0882 0.284148884 0.500122929 0.416251428 0.367907493 0.428592562 0.412731528 0.268321973 0.438021969 0.469468707 1 19.699293 0.567566369 1.758164927 0.99988468 0.390556571 0.885338114 0.065576646 0.680983864 2.429620364 0.059781386 0.0168143 3.694591011 -0.567566369 -0.609328109 RLPLSFVLDVLEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLPLSFVLDVLEGR 14 1 C9K0I3;B5MC20;P0C869-8;P0C869-7;P0C869-6;P0C870 C9K0I3 JMJD7 JmjC domain-containing protein 7 0 66.335 0.089249 23524000 61134 92023 74981 80849 100640 107640 82525 84317 81398 126060 FALSE TRUE 63547.61753 107827.2344 76935.06646 96840.69089 83533.24875 82642.2413 76056.47486 83186.86853 78468.50188 150759.0434 0.421517781 0.715228964 0.510318086 0.642354108 0.554084497 0.548174354 0.504490299 0.551786922 0.520489518 1 17.20188502 -1.757826045 2.492031757 1.110655513 0.555880449 0.760051731 0.075479623 6466545.334 4600078.97 4389858.85 0.017381994 0.017465216 1.757826045 -0.554775064 RLPS(ph)SPASPSPK ddPTM_MDA-MB-175_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(0.5)S(0.5)PASPSPK;RLPS(0.5)S(0.5)PASPSPK 153.23 4.32E-05 690220000 1471020 1350340 1347510 1134240 1677970 1893080 1641100 1582900 1446860 1185870 TRUE FALSE 1529097.005 1582250.391 1382627.218 1358589.287 1392749.259 1453440.86 1512466.294 1561683.815 1394787.791 1418218.522 1.078181523 1.115660504 0.974904217 0.957954833 0.982041369 1.024835621 1.066455043 1.101158806 0.983478759 1 20.43564841 2.345353154 6.588901393 1.052672296 1.019204036 0 0.054761236 0.668002549 36.77921519 0.0208629 0.01736632 221.4895057 -2.345353154 -0.03346826 RLPSS(ph)PASPSPK ddPTM_MDA-MB-175_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(0.1)S(0.9)PASPSPK;RLPS(0.057)S(0.943)PASPSPK 162.79 3.78E-05 1249970000 1241800 1192730 1316430 1101230 1643770 1729050 1520410 1383200 1371680 1190750 TRUE FALSE 1290827.223 1397572.099 1350737.247 1319050.007 1364362.563 1327504.342 1401236.291 1364660.466 1322313.505 1424054.664 0.906444995 0.981403407 0.948515026 0.926263605 0.958082998 0.93220041 0.983976477 0.958292193 0.928555299 1 20.4415731 2.252508745 24.99541732 0.964299335 0.944227109 0.187866089 0.025421874 480.4248302 860932.6925 0.008436061 0.00702488 178.8581542 -2.252508745 -0.020072226 RLQEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLQEAK 6 1 Q9BUZ4;F6SA91 Q9BUZ4 TRAF4 TNF receptor-associated factor 4 0 84.064 0.090235 134820000 233900 185340 238010 200170 308210 290770 263150 230920 244210 208100 FALSE TRUE 243134.5526 217170.7033 244212.7361 239763.0286 255820.5743 223243.0742 242523.6154 227824.8951 235420.9298 248873.2107 0.976941439 0.87261583 0.981273699 0.963394284 1.027915273 0.897015286 0.974486626 0.915425547 0.945947252 1 17.92505142 RLQEETGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLQEETGAK 9 1 Q07666-2;Q07666;Q5VWX1 Q07666-2 KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 80.916 0.036492 198650000 94325 168960 199140 145810 255370 235810 197740 196250 209050 142470 FALSE TRUE 98049.02383 197977.5657 204329.752 174650.7828 211962.2986 181046.7012 182240.6221 193619.5898 201526.3313 170384.2687 0.575458195 1.161947445 1.199228975 1.02504054 1.244025051 1.062578738 1.069585963 1.136370107 1.182775457 1 17.37843261 4.740960023 24.98237377 1.124142193 0.575458001 0.823955343 0.075515175 77.94292652 811484.3109 0.016634322 0.112227034 55075.69963 -4.740960023 -0.548684192 RLQSIGTENTEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLQSIGTENTEENR 14 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 311.26 1.59E-55 4377430000 734828 803540 749230 956930 957180 1180570 1040250 805970 776572 851180 FALSE TRUE 763839.5769 941541.7443 768755.5493 1146207.898 794478.8855 906400.5092 958712.4868 795167.2905 748623.3254 1017952.424 0.750368641 0.924936885 0.755197916 1.125993583 0.7804676 0.890415394 0.941804807 0.781143864 0.73542074 1 19.95723871 -0.158247451 7.768696145 1 0.858328515 0.124713086 0.115540682 0 0 0.104971061 0.024741916 0.694628422 0.158247451 -0.141671485 RLQSIGTENTEENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RLQSIGTENTEENRR 15 2 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;;;;; 290.62 3.76E-44 13773020000 2081207 2565980 2401140 1753098 2503450 2470420 1461494 2245970 2163200 3017580 FALSE TRUE 2163374.659 3006667.104 2463715.681 2099855.552 2077914.463 1896702.395 1346938.281 2215866.446 2085346.855 3608817.026 0.599469201 0.83314479 0.682693432 0.581868113 0.575788256 0.525574553 0.373235404 0.614014629 0.577847766 1 21.78309457 -1.209846925 5.050417507 1.000041485 0.59402409 0.551109337 0.109382449 5.54E-05 8.66E-06 0.114800682 0.027056022 0.061681237 1.209846925 -0.406017395 RLQTQVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLQTQVFK 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 ; 136.99 0.0012305 1480040000 1658420 1428050 1658420 1279420 2415200 2208800 1776800 1550540 1753570 2031500 FALSE TRUE 1723895.702 1673306.479 1701639.788 1532485.457 2004665.167 1695839.675 1637529.773 1529757.547 1690459.358 2429533.53 0.709558309 0.688735701 0.700397738 0.630773537 0.825123482 0.698010402 0.67400995 0.629650725 0.695795854 1 21.21224791 0.918360651 22.01684856 1 0.690963482 0.762114218 0.051144703 12749.99295 3438476.49 0.050405244 0.012601311 8.286299969 -0.918360651 -0.309036518 S(ph)PSWQRPNQGVPSTGR ddPTM_MDA-MB-175_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(0.931)PS(0.069)WQRPNQGVPSTGR;S(0.992)PS(0.008)WQRPNQGVPSTGR;S(0.995)PS(0.005)WQRPNQGVPSTGR;S(0.936)PS(0.064)WQRPNQGVPSTGR 187.37 8.17E-10 2464400000 250732 112367 128295 91783 127797 137223 138115 134242 136323 90965 TRUE FALSE 260631.093 131665.1582 131638.4731 109937.4035 106074.1116 105355.0379 127289.1854 132442.7056 131416.7619 108787.8501 2.395773909 1.210292859 1.210047565 1.010566928 0.975054765 0.968444893 1.170068029 1.217440233 1.20800955 1 16.73115791 4.753784737 3.494168886 1.104243318 2.576003983 0.940816053 0.097252473 0.077195295 1.597870237 0.026690464 0.305954408 56726.33652 -4.753784737 1.471760665 up RLS(ph)AEGGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 54.343 0.067607 0 130770 93064 104530 97984 157130 152310 124540 98226 121450 93466 TRUE FALSE 135932.9006 109047.0181 107254.1377 117364.9427 130421.0987 116938.3108 114778.2294 96909.44114 117079.0382 111778.8732 1.216087591 0.975560184 0.959520656 1.049974288 1.166777719 1.046157538 1.026832944 0.866974576 1.047416519 1 16.77028801 1.972934289 11.93708697 0.954216046 1.061141335 0.199653195 0.084593801 1.781074235 781.9890997 0.034850448 0.022749044 93.95811372 -1.972934289 0.106925289 RLS(ph)APLPSSCGDPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 186.06 2.43E-07 3927280000 5355600 3895220 4615750 3786670 6091890 6349760 6221600 4932100 5968520 4337180 TRUE FALSE 5567043.223 4564193.734 4736040.237 4535662.024 5056392.714 4875124.472 5733934.735 4865993.267 5753714.131 5186967.381 1.073275156 0.879934921 0.91306536 0.874434268 0.974826395 0.939879531 1.105450317 0.938119118 1.109263604 1 22.30645987 2.362740425 12.25921035 1.025441141 0.936441476 0.298808705 0.070343271 0.576328201 59.44090983 0.023343253 0.019526173 230.5368875 -2.362740425 -0.088999665 RLS(ph)APLPSSCGDPEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSAPLPSSCGDPEKQR 17 2 H0YKX0;Q96EP0-3;Q96EP0 H0YKX0 RNF31 E3 ubiquitin-protein ligase RNF31 1 RLS(0.999)APLPS(0.001)SCGDPEKQR 58.627 0.048473 333570000 220400 234710 237040 150780 325560 321860 198010 243820 273130 339910 TRUE FALSE 229101.5622 275019.6167 243217.4571 180603.834 270221.4275 247112.8928 182489.4588 240551.9917 263300.1047 406508.8565 0.5635832 0.676540283 0.598307892 0.444280195 0.664736876 0.607890551 0.448918777 0.591750925 0.647710623 1 18.63292726 0.736593146 2.414657225 0.999870583 0.573384578 0.751941718 0.073015404 0.626362365 5.033013916 0.069541208 0.018678841 5.452468253 -0.736593146 -0.426486006 RLS(ph)AQAHPAGK ddPTM_MDA-MB-175_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 112.96 0.0008914 905330000 961300 911120 889410 807950 1225540 1219190 908170 853910 927240 881590 TRUE FALSE 999252.8663 1067597.772 912588.7553 967760.0985 1017223.149 936051.5995 836985.2623 842464.7332 893868.8135 1054320.681 0.947769387 1.012593029 0.865570382 0.917899189 0.964813805 0.887824374 0.79386213 0.799059288 0.847814929 1 20.00788231 2.483809255 5.328372906 0.836867456 0.939286469 0.233663034 0.064835133 0.188002979 17.18020553 0.021453348 0.018901439 304.6556631 -2.483809255 0.102419013 RLS(ph)ASSTGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSASSTGSTR 11 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 RLS(0.843)AS(0.024)S(0.06)T(0.06)GS(0.01)T(0.004)R;RLS(0.894)AS(0.015)S(0.043)T(0.043)GS(0.005)TR 126.17 0.00033154 379850000 373110 445090 385630 390370 431600 477960 399090 412650 384510 462810 TRUE FALSE 387840.6709 521530.7452 395679.8346 467584.0209 358236.7862 366961.0336 367808.283 407119.1017 370671.5602 553488.7585 0.700720051 0.942260773 0.714883236 0.84479407 0.647234078 0.662996363 0.664527106 0.735550805 0.669700251 1 19.07819449 5.050974842 16.51557961 0.749844244 0.359425931 0.011871496 0.11908717 18933370.43 147062411.9 0.027094333 239846311.4 112453.983 -5.050974842 -0.390418313 RLS(ph)DCESTDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSDCESTDVKR 12 2 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 RLS(1)DCESTDVKR;RLS(0.999)DCESTDVKR 100.45 0.0016825 121164000 112474 103400 134988 107564 166456 150867 143198 139099 157759 135861 TRUE FALSE 116914.5604 121158.1457 138505.8982 128839.8382 138161.8686 115830.4257 131973.7666 137234.6054 152081.2844 162480.3617 0.719561177 0.745678705 0.852447008 0.792956372 0.850329647 0.712888773 0.812244416 0.844622722 0.935997943 1 17.30990583 1.247967579 1.552262052 0.999114641 0.784070041 0.730987132 0.045176001 0.18646124 0.832843931 0.042126352 0.012774616 17.69976819 -1.247967579 -0.2150446 RLS(ph)DEHEPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSDEHEPEQR 11 1 Q9UK59;Q9UK59-2 Q9UK59 DBR1 Lariat debranching enzyme 1 RLS(1)DEHEPEQR;RLS(1)DEHEPEQR 122.12 0.00024347 368660000 204000 228890 218134 206650 234020 226070 204950 203400 197875 234700 TRUE FALSE 212054.0775 268200.077 223818.7512 247524.7532 194241.364 173568.6686 188885.4835 200673.7557 190753.5174 280684.9714 0.755487821 0.955519904 0.797401977 0.881859659 0.692026235 0.618375354 0.67294477 0.714943001 0.679600039 1 18.09859229 3.234847902 24.99622523 0.706764449 0.851695007 0.201050433 0.109479945 112.9943826 760746.4341 0.028746679 0.035642022 1717.306847 -3.234847902 0.144930557 RLS(ph)DPLLPSPEDETGSLVHLEDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLSDPLLPSPEDETGSLVHLEDPER 25 1 Q8WYL5-2;Q8WYL5-5;Q8WYL5-4;Q8WYL5 Q8WYL5-2 SSH1 Protein phosphatase Slingshot homolog 1 1 RLS(1)DPLLPSPEDETGSLVHLEDPER;RLS(0.997)DPLLPS(0.003)PEDETGSLVHLEDPER;RLS(1)DPLLPSPEDETGSLVHLEDPER 86.145 0.0079395 93955000 20493.8 25465.9 26785.5 31511.6 26338.4 31953.5 29490.3 29200.8 27286.7 26029 TRUE FALSE 21302.91105 29839.47023 27483.55213 37744.50043 21861.40818 24532.78388 27178.77323 28809.41104 26304.657 31128.88419 0.684345475 0.958578214 0.882895512 1.212523398 0.702286919 0.788103542 0.87310464 0.925488073 0.845024089 1 14.92596624 -1.109082287 4.198388554 1.000021286 0.882911509 0.063702942 0.140980887 2.71E-05 5.74E-06 0.1315573 0.031002718 0.077788915 1.109082287 -0.117109777 RLS(ph)EDYGVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 1 RLS(1)EDYGVLK;RLS(1)EDYGVLK 143.94 2.03E-05 481280000 980570 865940 934590 694350 1438790 1227520 1255290 1206210 1256320 891300 TRUE FALSE 1019283.661 1014658.459 958946.1832 831690.3576 1194224.99 942447.0832 1156897.09 1190042.728 1211105.289 1065933.17 0.956235991 0.95189688 0.899630681 0.780246249 1.120356344 0.88415213 1.085337357 1.116432776 1.136192514 1 20.02368556 2.207894713 11.12846357 1.096393607 0.933181616 0.42634759 0.086159011 0.529358164 188.9917863 0.031459605 0.023361318 161.3967233 -2.207894713 -0.163211991 RLS(ph)EGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSEGR 6 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 1 RLS(1)EGR;RLS(1)EGR 84.522 0.05906 1387070000 1484860 1913870 1839020 1753700 1957080 2263380 1773630 1840760 1858780 2038980 TRUE FALSE 1543483.419 2242562.285 1886946.372 2100576.626 1624416.241 1737744.297 1634608.246 1816087.623 1791882.871 2438479.092 0.632969716 0.919656146 0.773821017 0.861429008 0.666159593 0.712634487 0.67033925 0.744762434 0.734836266 1 21.21755017 -1.212460155 3.549457673 1.000401414 0.748637193 0.451149351 0.083915113 5134470510 7496614686 22372032.46 0.019878908 0.061311204 1.212460155 -0.251764221 RLS(ph)EQLAHTPTAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSEQLAHTPTAFK 14 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(0.942)EQLAHT(0.057)PTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK;RLS(1)EQLAHTPTAFK 149.36 4.60E-06 2767690000 1498340 1546490 1659570 1529300 1986140 2159940 1856830 1703410 1807570 1801920 TRUE FALSE 1557495.62 1812087.627 1702819.758 1831790.975 1648536.632 1658326.669 1711286.813 1680578.575 1742515.909 2154971.724 0.72274527 0.840886963 0.790181949 0.850030167 0.764992233 0.769535234 0.794111029 0.77986108 0.808602679 1 21.03923751 0.791171324 4.971447948 0.999999543 0.791154363 0.768480619 0.034511462 1.994957413 47.26117104 0.031023022 0.007843142 6.182602485 -0.791171324 -0.20884518 RLS(ph)EQLAHTPTAFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSEQLAHTPTAFKR 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RLS(1)EQLAHTPTAFKR;RLS(1)EQLAHTPTAFKR 121.63 5.94E-05 1707830000 715040 763020 789530 569690 1012130 971340 756590 860450 837380 926230 TRUE FALSE 743270.3313 894062.7495 810105.8004 682372.9816 840088.5041 745761.0058 697286.4988 848917.0752 807242.8574 1107707.035 0.670999017 0.807129251 0.731335791 0.616022974 0.75840315 0.673247513 0.629486387 0.766373281 0.728751224 1 20.07914494 0.337608187 1.165115165 1.000373545 0.705141948 0.700227071 0.057452442 1.825473112 2.709144229 0.055276052 0.016522351 2.175745969 -0.337608187 -0.295231597 RLS(ph)ESQLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(0.981)ES(0.009)QLS(0.01)FR;RLS(1)ESQLSFR;RLS(0.92)ES(0.034)QLS(0.045)FR;RLS(0.877)ES(0.11)QLS(0.013)FR;RLS(0.888)ES(0.112)QLS(0.001)FR 163.09 6.96E-06 1353570000 718776 955160 991304 929899 1250976 1187126 908491 982578 964527 1278603 TRUE FALSE 747153.8315 1119201.3 1017138.197 1113830.247 1038335.546 911433.9776 837281.1015 969408.1491 929813.8617 1529120.778 0.488616624 0.731924722 0.665178455 0.728412211 0.679040898 0.596051006 0.547557207 0.633964408 0.608070909 1 20.54427093 -1.596259162 2.901216729 1.024603453 0.634536206 0.700880276 0.072288702 17373632 17230744.19 3252583.042 0.017256431 0.025336163 1.596259162 -0.390067247 RLS(ph)ESSALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RLS(0.529)ES(0.471)SALK;RLS(0.927)ES(0.055)S(0.018)ALK 117.7 0.00067893 492040000 424660 297630 401110 401480 513800 549310 619950 449820 459310 368070 TRUE FALSE 441425.9047 348745.6373 411563.2561 480891.5457 426464.4595 421741.0774 571356.6991 443790.8987 442779.5228 440186.2694 1.002816161 0.792268323 0.934975225 1.092472844 0.968827265 0.958096848 1.297988463 1.008188873 1.005891264 1 18.74775462 3.879430121 4.814826389 1.052956411 0.890220098 0.271107742 0.103578011 0.263782732 9.208833622 0.02664655 0.049944098 7575.828261 -3.879430121 -0.162736313 RLS(ph)FLVSYIASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSFLVSYIASK 12 1 P47897;A0A1B0GVU9;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 1 RLS(1)FLVSYIASK 180.78 1.16E-05 127000000 428090 392200 483590 386130 800750 656680 597180 479080 490150 539880 TRUE FALSE 444991.3238 459557.2991 496192.7527 462505.3615 664638.801 504176.0221 550371.4712 472658.7162 472509.5972 645659.1494 0.689204705 0.711764558 0.768505725 0.716330531 1.029395776 0.780870251 0.852417985 0.732056096 0.73182514 1 19.30041323 -2.663503216 2.172677952 7.026540742 0.782020733 0.329395534 0.094454319 3234327.636 256762.3443 95954943.27 0.023099587 0.002170185 2.663503216 -6.244520009 RLS(ph)GEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSGEER 7 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 RLS(1)GEER 99.788 0.0062912 443930000 98970 137100 117590 138250 130890 147920 134140 136670 117620 144250 TRUE FALSE 102877.412 160645.8585 120654.492 165595.4374 108641.3646 113567.8217 123625.7563 134838.1622 113386.8792 172513.0257 0.596345764 0.931210022 0.699393518 0.959901067 0.629757458 0.658314474 0.716616938 0.781611485 0.657265611 1 17.39634577 -1.137808401 4.442861922 1.000037403 0.744410546 0.313278908 0.116442441 15476052.1 3963388.214 5679.957576 0.02545268 0.072810095 1.137808401 -0.255626856 RLS(ph)GLSSVGHNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSGLSSVGHNWR 13 1 Q14D93;A0A0G2JR24;Q8WYQ4 Q14D93 C22orf15 Uncharacterized protein C22orf15 1 RLS(0.986)GLS(0.007)S(0.007)VGHNWR;RLS(0.989)GLS(0.006)S(0.006)VGHNWR 63.894 0.030846 346030000 386490 140083 190461 115730 234690 490380 229190 103961 199258 114354 TRUE FALSE 401748.9236 164141.1656 195424.5701 138621.0486 194797.4776 376496.6768 211225.4889 102567.5728 192086.7435 136759.4769 2.937631328 1.200217852 1.42896547 1.013612013 1.424380102 2.752984184 1.544503487 0.749985121 1.404558923 1 17.06128128 4.743020213 24.46319232 1.393214141 2.937632168 0.450677942 0.512244832 338.3404807 1855880.877 0.130743539 1.034400993 55337.5864 -4.743020213 1.544418027 RLS(ph)IIGPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 186.69 8.03E-07 1119380000 336986 452406 361320 383409 469039 461977 349380 352021 348826 475471 TRUE FALSE 350290.4675 530103.2113 370736.296 459246.1558 389311.9183 354689.8431 321994.6827 347302.7343 336271.8204 568630.439 0.616024826 0.932245576 0.651981095 0.807635547 0.684648397 0.623761619 0.566263535 0.610770565 0.591371473 1 19.1171318 3.040989221 5.586020517 0.64276335 0.7573551 0.02946567 0.14203322 0.375328369 28.99908126 0.038312841 0.045490158 1098.978564 -3.040989221 0.11459175 RLS(ph)LESEGAGEGAAASPELSALEEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLSLESEGAGEGAAASPELSALEEAFR 27 1 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(0.978)LES(0.022)EGAGEGAAASPELSALEEAFR;RLS(0.97)LES(0.03)EGAGEGAAASPELSALEEAFR;RLS(0.906)LES(0.094)EGAGEGAAASPELSALEEAFR 154.74 2.56E-08 223685000 34710.4 34295.6 39097 42046 42026 46683 50293 42862 43242 40211 TRUE FALSE 36080.79339 40185.60252 40115.89994 50362.57331 34882.43553 35841.58074 46350.90324 42287.505 41685.72887 48089.57556 0.750283049 0.835640615 0.834191183 1.047265914 0.725363764 0.745308735 0.963845131 0.879348684 0.866835034 1 15.55343657 -4.999999996 0.11352453 1.482213096 0.772737548 0.223821709 0.092493662 265.4054035 1.987186397 29.46709856 1.066539258 1.00E-05 4.999999996 -0.709475548 RLS(ph)LESEGAGEGAAASPELSALEEAFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSLESEGAGEGAAASPELSALEEAFRR 28 2 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 RLS(1)LESEGAGEGAAASPELSALEEAFRR;RLS(0.979)LES(0.021)EGAGEGAAASPELSALEEAFRR;RLS(0.999)LES(0.001)EGAGEGAAASPELSALEEAFRR;RLS(0.995)LES(0.005)EGAGEGAAASPELSALEEAFRR 159.49 5.40E-12 188911000 27760.3 36531.1 31965.9 31259.6 35856.6 42338.9 28117 36876.4 27712 45045.7 TRUE FALSE 28856.29808 42805.03225 32798.95761 37442.65558 29761.70794 32506.33213 25913.11607 36382.13218 26714.65053 53871.54246 0.535650118 0.794575954 0.60883643 0.695035892 0.552456948 0.603404518 0.481016783 0.67534974 0.495895408 1 15.71723575 -1.392027804 4.616717412 1.000607117 0.610857629 0.624946758 0.091760033 0.000540801 7.12E-05 0.083794511 0.019720624 0.040548257 1.392027804 -0.389749488 RLS(ph)LGQGDSTEAATEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(0.962)LGQGDS(0.037)T(0.001)EAATEER;RLS(1)LGQGDSTEAATEER;RLS(1)LGQGDSTEAATEER 193.15 1.55E-10 2169970000 660640 752490 766670 771580 806760 863350 887930 751100 787840 749230 TRUE FALSE 686722.5773 881724.3039 786650.05 924196.2211 669627.2234 662850.0467 818331.7264 741032.7331 759485.7923 896027.2736 0.766408119 0.98403735 0.877930922 1.0314376 0.747329064 0.739765481 0.913288859 0.827020287 0.847614592 1 19.77318312 5.02644335 12.93354382 0.874716532 0.528369728 0.113885379 0.095475361 344496.6768 5163707.33 0.022598082 2367304.578 106277.9945 -5.02644335 -0.346346805 RLS(ph)LGQGDSTEAATEERGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSLGQGDSTEAATEERGPR 20 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(1)LGQGDSTEAATEERGPR;RLS(1)LGQGDSTEAATEERGPR 326.79 5.32E-80 526400000 76878 106053 96956 89162 131466 134402 79639 104097 101406 180884 TRUE FALSE 79913.2028 124266.7778 99482.75301 106797.9775 109119.4563 103189.1724 73396.68708 102701.75 97756.41787 216324.7566 0.369413118 0.574445476 0.459876875 0.493692812 0.504424265 0.477010463 0.339289355 0.474757266 0.451896581 1 17.72283925 -1.349376663 3.396838658 1.003313894 0.46221377 0.868714896 0.06291198 36474448.67 52192988.35 1204954.744 0.014608153 0.044732517 1.349376663 -0.541100124 RLS(ph)LLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSLLCR 7 1 O15068-4;O15068-10;A2A3G7;O60423;O60423-3;O60423-1 O15068-4 MCF2L;ATP8B3 Guanine nucleotide exchange factor DBS;Phospholipid-transporting ATPase IK 1 RLS(1)LLCR;RLS(1)LLCR 112.71 0.0038545 181278000 39943 41409 43593 51205 55097 56951 48496 49058 45554 43407 TRUE FALSE 41519.98048 48520.67363 44729.06939 61333.19617 45731.63162 43724.99335 44694.7568 48400.45775 43914.52044 51911.77057 0.799818231 0.93467576 0.861636367 1.181489198 0.880949178 0.842294394 0.860975388 0.932359987 0.845945341 1 15.66377407 RLS(ph)LLSHAGRPGSGGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSLLSHAGRPGSGGDDR 18 2 A0A2R8Y701;Q18PE1-2;Q18PE1;Q18PE1-3 A0A2R8Y701 DOK7 Protein Dok-7 1 RLS(1)LLSHAGRPGSGGDDR;RLS(0.997)LLS(0.003)HAGRPGSGGDDR 101.75 0.00031718 224990000 125927 169798 141262 173516 170788 184909 167121 174588 150133 182779 TRUE FALSE 130898.6952 198959.4857 144943.4038 207836.9469 141757.5168 141966.6871 154021.6193 172247.9334 144729.7427 218591.0455 0.598829174 0.910190466 0.663080244 0.950802657 0.648505598 0.649462501 0.704610836 0.787991718 0.662102797 1 17.73787478 -1.005168822 7.990799755 1.000000003 0.738212916 0.341077834 0.111878166 5.17E-09 6.51E-10 0.09968498 0.023495975 0.098816889 1.005168822 -0.261787087 RLS(ph)LPADIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 107.99 0.0016436 6147032000 3018127 3349007 3262288 3630436 3676042 4143997 3716630 3491920 3296959 3610141 TRUE FALSE 3137284.984 3924172.901 3347305.905 4348525.405 3051189.694 3181616.5 3425310.829 3445116.524 3178302.09 4317479.009 0.72664742 0.908903759 0.775291761 1.007190862 0.706706318 0.736915337 0.793359 0.797946329 0.736147665 1 22.04175773 5.025183631 13.17306083 0.817612182 0.531397337 0.072428634 0.102836806 595838.7969 9254185.495 0.023159414 3424053.123 105970.17 -5.025183631 -0.286214845 RLS(ph)LPADIRLPEGYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;RLS(1)LPADIRLPEGYLEK;RLS(1)LPADIRLPEGYLEK 252.13 2.91E-27 1032340000 1079465 1185154 1371370 987639 1837027 1637419 1108533 1318562 1460440 1707617 TRUE FALSE 1122083.112 1388694.98 1407109.029 1182991.046 1524769.807 1257153.253 1021643.287 1300888.833 1407879.05 2042191.857 0.54945039 0.680002212 0.689019018 0.579275176 0.746633967 0.61559018 0.500268025 0.63700618 0.689396075 1 20.96168698 0.754599101 2.664593576 0.999904685 0.625725511 0.73425283 0.06745343 0.664272524 6.469761266 0.064576752 0.017128053 5.683280623 -0.754599101 -0.374179175 RLS(ph)LPGLLSQVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSLPGLLSQVSPR 14 1 Q96Q42;Q96Q42-3 Q96Q42 ALS2 Alsin 2 RLS(1)LPGLLS(0.052)QVS(0.948)PR;RLS(1)LPGLLS(0.002)QVS(0.998)PR;RLS(1)LPGLLS(0.165)QVS(0.835)PR;RLS(1)LPGLLS(0.002)QVS(0.998)PR 113.42 0.001877 658934000 253375 285041 277898 271860 321573 331121 275709 277760 283499 312177 TRUE FALSE 263378.4406 333994.5744 285140.2502 325633.0966 266912.1363 254223.1659 254098.2081 274037.0815 273295.9264 373342.1062 0.705461389 0.894607302 0.76375058 0.872211013 0.714926422 0.680938908 0.680604207 0.734010649 0.732025458 1 18.5101387 4.027321733 24.99809098 0.754711024 0.8073205 0 0.102677794 757.6167612 693172.9064 0.024303739 0.052500424 10649.31647 -4.027321733 0.052609476 RLS(ph)LPMDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 RLSLPMDIR 9 1 Q07002;A0A0A0MSJ6;Q07002-3;D6R9B0;D6RA44;D6RGH0 Q07002 CDK18 Cyclin-dependent kinase 18 1 RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR;RLS(1)LPMDIR 117.7 0.00067893 2235573000 1844032 2235225 2086646 2187006 2873450 2829440 2270341 2184640 2212718 3073630 TRUE FALSE 1916835.807 2619107.506 2141025.709 2619589.259 2385021.995 2172345.441 2092385.74 2155358.474 2133082.711 3675848.95 0.521467512 0.712517718 0.582457478 0.712648777 0.648835691 0.590977886 0.569225169 0.586356649 0.580296617 1 21.80964605 -1.114297084 4.629661529 1.000030675 0.613375484 0.79675057 0.058838699 1.81E-05 3.46E-06 0.055262465 0.013024456 0.076860449 1.114297084 -0.386655191 RLS(ph)LPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(ph)LVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSLPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHSLVEK 41 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 2 RLS(0.883)LPNT(0.073)AWGS(0.036)PS(0.008)PEAAGYPGAGAEDEQQQLAANRHS(1)LVEK;RLS(1)LPNTAWGSPSPEAAGYPGAGAEDEQQQLAANRHS(1)LVEK 205.16 1.05E-35 464140000 134003 102848 127808 110342 177584 179589 153087 143583 161763 136359 TRUE FALSE 139293.5419 120511.344 131138.7815 132167.3183 147398.3351 137882.1764 141087.6409 141658.5047 155941.1812 163075.9353 0.854163686 0.738989132 0.804157776 0.81046488 0.90386319 0.845509034 0.865165303 0.868665904 0.956248885 1 17.31518438 1.434346041 0.284742502 1.025822508 0.770665256 0.71175921 0.038388398 0.881291897 0.274792488 0.086273549 0.074549496 27.18604561 -1.434346041 -0.255157252 RLS(ph)LQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 134.23 0.0019569 1456040000 441690 497050 606730 444659 737790 582560 481715 493440 603430 633640 TRUE FALSE 459128.2623 582414.471 622541.8822 532611.223 612380.7193 447269.2688 443956.9196 486826.2439 581712.6722 757789.6262 0.605878263 0.768570129 0.821523363 0.702848396 0.808114413 0.590228809 0.585857742 0.64242928 0.767644016 1 19.53143786 0.908848219 5.274607891 0.999977181 0.691398152 0.561160829 0.082315397 0.529379269 29.42887008 0.085012203 0.021452047 8.106776852 -0.908848219 -0.30857903 RLS(ph)LTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSLTLR 7 1 Q00537;Q00537-2;F8VQZ9;F8VZY6;F8VUX2;F8W1S5 Q00537 CDK17 Cyclin-dependent kinase 17 1 RLS(0.996)LT(0.004)LR 130.53 0.0021768 542770000 118190 113990 126420 126560 133380 155970 132510 123880 121820 133350 TRUE FALSE 122856.2325 133566.8958 129714.6091 151593.1903 110708.1152 119748.3312 122123.5199 122219.5912 117435.722 159477.3794 0.770367766 0.837528785 0.813373091 0.950562336 0.694193218 0.750879728 0.765773306 0.766375719 0.736378554 1 17.28299228 5.065795126 12.02374922 0.800742874 0.582672856 0.003724269 0.091677642 1424984.227 8809588.656 0.020832962 7154759.672 116357.6994 -5.065795126 -0.218070018 RLS(ph)MEIEK ddPTM_MDA-MB-175_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 82.774 0.011884 1161090000 878900 776420 966460 772720 1233230 1223120 1071790 999020 1083850 751740 TRUE FALSE 913599.6507 909764.0953 991646.7416 925561.7097 1023606.005 939068.9166 987780.2992 985629.771 1044842.45 899029.0601 1.01620703 1.011940699 1.103019675 1.029512561 1.138568318 1.044536777 1.098718988 1.096326932 1.162189852 1 19.77800822 4.245072241 24.95507407 1.08733776 1.014073825 0.265354957 0.046364136 171.9944677 659131.4509 0.010452235 0.027230355 17582.16055 -4.245072241 -0.073263935 RLS(ph)MSEVKDDNSATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSMSEVKDDNSATK 15 2 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 RLS(0.961)MS(0.039)EVKDDNSATK;RLS(1)MSEVKDDNSATK 308.97 2.19E-56 576200000 352799 170311 252280 168644 409707 372882 328996 278287 316433 185316 TRUE FALSE 366727.7769 199560.5894 258854.6241 202001.2798 340065.1505 286285.8066 303208.4338 274557.018 305044.6381 221625.1221 1.65472115 0.900442096 1.167984124 0.911454793 1.534416077 1.291757017 1.368114007 1.23883527 1.376399188 1 17.7577619 3.237088682 24.9998773 1.312253643 1.140873801 0.080877011 0.231326308 85.00269217 1443727.206 0.061431224 0.077294213 1726.190339 -3.237088682 -0.171379842 RLS(ph)NLPTVDPIAVCHELYNTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSNLPTVDPIAVCHELYNTIR 22 1 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9;Q86U86-6;C9JQF1;C9JPI5;C9JCJ2;C9J053 Q86U86-8 PBRM1 Protein polybromo-1 1 RLS(0.998)NLPT(0.002)VDPIAVCHELYNTIR 126.36 9.32E-06 364400000 272160 155360 162000 144680 230270 235630 176490 189070 198920 135490 TRUE FALSE 282905.087 182041.8715 166221.8531 173297.2722 191128.7877 180908.5035 162656.2526 186535.8259 191760.9081 162036.6714 1.745932476 1.123460942 1.025828608 1.06949415 1.179540323 1.116466427 1.00382371 1.151195123 1.183441417 1 17.30596083 4.737642371 5.497848862 1.096587908 1.769322608 0.902077055 0.064415752 0.039729419 4.673022432 0.015217936 0.100769028 54656.56966 -4.737642371 0.6727347 RLS(ph)NSSLCSIEEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RLS(0.935)NS(0.063)S(0.001)LCSIEEEHR 125.59 4.21E-05 196410000 63109 65987 79141 84874 86592 84300 84195 74275 82359 79030 TRUE FALSE 65600.59205 77319.75394 81203.47948 101661.8239 71873.12277 64722.60258 77595.5759 73279.46511 79394.91568 94514.41538 0.694080282 0.818073662 0.859165019 1.075622417 0.760446144 0.684790805 0.820991968 0.775325804 0.840029697 1 16.52824677 0.960929081 20.147038 1.000000003 0.813924055 0.230359196 0.102950274 784.810794 404692.7556 0.102444688 0.025611172 9.139639818 -0.960929081 -0.186075948 RLS(ph)NVSLTGVSTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSNVSLTGVSTIR 14 1 F8WBA3;Q15139;A0A494C0Q1 F8WBA3 PRKD1 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 1 RLS(0.999)NVS(0.001)LTGVSTIR;RLS(0.944)NVS(0.055)LT(0.001)GVSTIR;RLS(0.999)NVS(0.001)LTGVSTIR;RLS(1)NVSLTGVSTIR;RLS(1)NVSLTGVSTIR 231.4 3.40E-13 2381010000 1658890 1769080 1668480 1752470 1945010 1985360 1647070 1688630 1615190 1769120 TRUE FALSE 1724384.258 2072905.728 1711961.959 2099103.335 1614397.895 1524290.228 1517968.35 1665996.677 1557059.627 2115745.192 0.815024543 0.979752069 0.809153184 0.992134281 0.76303985 0.720450758 0.717462743 0.787427845 0.735939107 1 21.01273446 3.209921466 24.94855255 0.769917004 0.898364119 0.237833426 0.094850355 232.7873801 202788.4945 0.024998652 0.029884128 1621.51685 -3.209921466 0.128447115 RLS(ph)PAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSPAER 7 1 P41212 P41212 ETV6 Transcription factor ETV6 1 RLS(1)PAER 76.927 0.024152 629600000 61443 243070 158130 253510 140840 271800 116960 188930 128190 273980 TRUE FALSE 63868.81708 284815.3817 162250.9977 303653.5213 116900.0671 208678.5692 107792.3696 186397.7024 123576.4669 327661.1353 0.194923383 0.869237608 0.495179257 0.926730358 0.356771233 0.636873119 0.328975145 0.568873395 0.377147161 1 18.32184504 -1.372126959 4.037913837 1.00133887 0.540682493 0.287008819 0.222269171 33192044.04 11281430.71 391418.3508 0.047387264 0.042449545 1.372126959 -0.460656377 RLS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSPEK 6 1 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEK;RLS(1)PEK;RLS(1)PEK;RLS(1)PEK 94.309 0.027335 1637070000 2093160 1610660 1801320 1710800 1972300 2802470 2496030 1844490 1783640 1369050 TRUE FALSE 2175799.573 1887278.326 1848263.879 2049191.134 1637049.15 2151638.814 2300384.646 1819767.629 1719447.145 1637289.135 1.32890369 1.152684816 1.128856131 1.251575601 0.999853425 1.314147128 1.404995976 1.1114516 1.050179292 1 20.64287768 1.501063471 7.271326013 1.042438045 1.21778239 0.356137894 0.109243362 0.143310088 17.67448975 0.061944962 0.028266212 31.70030724 -1.501063471 0.175344345 RLS(ph)PEKQNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSPEKQNCR 10 2 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RLS(1)PEKQNCR;RLS(1)PEKQNCR;RLS(1)PEKQNCR;RLS(1)PEKQNCR 133.16 0.00010673 1142320000 670460 526864 596340 472921 835260 869470 635090 582710 624000 598730 TRUE FALSE 696930.2785 617348.7936 611881.1103 566463.3623 693282.8035 667548.7694 585309.9863 574899.7256 601542.3619 716039.6801 0.973312371 0.862171205 0.854535199 0.791106105 0.968218414 0.932279017 0.817426747 0.802888082 0.840096406 1 19.44968001 2.227471233 24.99860422 0.842654809 0.891858997 0.004869535 0.073148258 550.4336562 1240824.045 0.0270178 0.020143237 168.8384019 -2.227471233 0.049204188 RLS(ph)PGSDIYVTVSSMALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSPGSDIYVTVSSMALAR 19 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 RLS(0.993)PGS(0.007)DIYVTVSSMALAR 102.21 0.00024297 205710000 57587 106320 122850 103780 106610 134620 100510 108340 127730 109330 TRUE FALSE 59860.57923 124579.6329 126051.5719 124307.3742 88488.47028 103356.5452 92631.76357 106887.8795 123133.0223 130751.1203 0.457820775 0.952799737 0.9640573 0.95071747 0.676770265 0.790483057 0.708458661 0.817491118 0.941735887 1 16.99646378 1.163756643 3.372819217 0.995127082 0.798164476 0.201102772 0.146142392 0.387570257 7.857364428 0.135149305 0.036351577 14.57997044 -1.163756643 -0.196962606 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 RLS(0.811)PPS(0.063)S(0.063)S(0.063)AASSYSFSDLNSTR;RLS(0.994)PPS(0.004)S(0.001)S(0.001)AASSYSFSDLNSTR;RLS(0.753)PPS(0.049)S(0.077)S(0.121)AASSYSFSDLNSTR;RLS(0.889)PPS(0.037)S(0.037)S(0.037)AASSYSFSDLNSTR 168.98 5.40E-12 1612880000 537707 631511 615126 819260 642515 940980 761360 651566 597238 744420 TRUE FALSE 558936.0876 739968.1018 631156.6889 981307.1828 533300.5298 722451.6557 701682.6138 642832.8235 575743.521 890274.8462 0.627824194 0.831168155 0.708945885 1.102251947 0.599029089 0.811492831 0.788164034 0.722061087 0.64670312 1 19.76389127 -2.156311908 2.464133823 1.569664328 0.765366881 0.217218192 0.136453191 6288759.989 2554044.141 19875057.88 0.030706027 0.006977311 2.156311908 -0.804297448 RLS(ph)QPAGGLLDSITNIFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSQPAGGLLDSITNIFGR 19 1 Q676U5-3;Q676U5;Q676U5-4 Q676U5-3 ATG16L1 Autophagy-related protein 16-1 1 RLS(1)QPAGGLLDSITNIFGR 139.51 1.13E-07 48746000 44803 34672 35721 37694 38825 47112 34791 32487 38220 41199 TRUE FALSE 46571.85704 40626.64629 36651.91861 45149.76069 32225.54037 36170.95199 32063.99051 32051.5649 36844.46967 49271.15525 0.945215447 0.824552339 0.74388186 0.916352792 0.654044749 0.734120233 0.650765957 0.650513769 0.747789847 1 15.58845568 5.334181455 0.637438293 0.721614297 1.2801574 0.165538953 0.111730076 8.816655716 1.566976246 0.044909387 4.252579879 215864.6139 -5.334181455 0.558543103 RLS(ph)QPESAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(1)QPESAEK;RLS(1)QPESAEK 195.36 2.22E-07 5210030000 7237600 6157610 7366130 6034460 9626190 9921910 9307290 7930250 8430230 6286180 TRUE FALSE 7523346.037 7215131.618 7558097.399 7228058.177 7989933.662 7617696.771 8577760.29 7823957.97 8126827.669 7517836.615 1.000732847 0.959735092 1.005355368 0.961454544 1.062796928 1.013283097 1.140987857 1.040719341 1.081006157 1 22.84188613 3.230119585 24.80945409 1.061042895 0.981923143 0.468521023 0.038764979 131.8738127 387596.0907 0.010502899 0.012751032 1698.711334 -3.230119585 -0.079119752 RLS(ph)QRPTPEELEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSQRPTPEELEQR 14 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RLS(0.996)QRPT(0.004)PEELEQR 111.66 0.00050306 274740000 65487 94643 77320 81415 90416 92184 77261 91938 68601 108300 TRUE FALSE 68072.47733 110897.199 79335.02272 97518.644 75047.12062 70775.66306 71205.08094 90705.72149 66132.06341 129519.3115 0.52557782 0.856221345 0.612534315 0.752927443 0.579428039 0.546448728 0.549764202 0.700325847 0.510596163 1 16.9828077 -1.483427392 5.431773414 1.000572215 0.63401368 0.525604771 0.106353563 0.000702221 6.68E-05 0.098119937 0.02309218 0.032852817 1.483427392 -0.366558535 RLS(ph)QRPTTEELEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSQRPTTEELEQR 14 2 J3KP75;O75167-5;O75167-2;O75167;O75167-4 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 RLS(0.939)QRPT(0.019)T(0.042)EELEQR 140.35 7.85E-06 280660000 104370 120660 110450 99923 114730 131000 103010 125780 126920 126350 TRUE FALSE 108490.6082 141382.4164 113328.4177 119687.4712 95228.23558 100577.2353 94935.80703 124094.1248 122352.174 151105.8634 0.717977488 0.935651425 0.749993516 0.792076948 0.630208739 0.66560776 0.628273483 0.82123964 0.809711624 1 17.20520012 0.856011974 1.560402437 0.997883318 0.739161081 0.446816706 0.087500534 0.565986277 2.635074702 0.087759063 0.025490312 7.178140825 -0.856011974 -0.258722238 RLS(ph)QSDEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RLSQSDEDVIR 11 1 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y917;Q9H7D7-3;Q9H7D7-4 A0A499FIZ0 WDR26 WD repeat-containing protein 26 1 RLS(0.997)QS(0.003)DEDVIR;RLS(0.998)QS(0.002)DEDVIR;RLS(0.97)QS(0.03)DEDVIR;RLS(1)QSDEDVIR;RLS(0.967)QS(0.033)DEDVIR;RLS(0.754)QS(0.246)DEDVIR 224.5 3.77E-12 4923820000 2320160 2842760 2757650 2614320 2976430 3272920 2612890 2628020 2772160 3012190 TRUE FALSE 2411761.708 3330981.916 2829516.624 3131424.693 2470497.492 2512833.932 2408084.854 2592795.69 2672390.503 3602370.959 0.66949288 0.924663771 0.785459537 0.869267693 0.685797637 0.697550019 0.668472204 0.719747 0.741842118 1 21.78051532 5.032729572 17.02779359 0.769797592 0.307562588 0.078694441 0.106275768 1059655.916 14604822.47 0.024930836 14638783.68 107827.509 -5.032729572 -0.462235004 RLS(ph)S(ph)LRAS(ph)TSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.555)T(0.445)S(0.001)K;RLS(1)S(1)LRAS(0.802)T(0.163)S(0.035)K;RLS(1)S(1)LRAS(0.825)T(0.147)S(0.028)K;RLS(1)S(1)LRAS(0.861)T(0.125)S(0.014)K 111.33 0.0011063 1700060000 1294500 829650 1245190 1101440 1855000 1824630 2121180 1615080 1717690 1093000 TRUE FALSE 1345607.86 972135.9337 1277640.674 1319301.545 1539687.763 1400887.335 1954916.369 1593432.494 1655870.672 1307152.423 1.029419244 0.743705108 0.977422871 1.009294342 1.177894586 1.071709244 1.49555349 1.219010473 1.266777036 1 20.31799595 3.279628242 1.275782784 1.252609558 0.888155907 0.466279538 0.140617564 0.329310658 1.125041352 0.048713334 0.077556989 1903.830331 -3.279628242 -0.364453651 RLS(ph)S(ph)LRASTSKS(ph)ESSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSLRASTSKSESSQK 17 3 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 3 RLS(1)S(1)LRAS(0.139)T(0.098)S(0.087)KS(0.468)ES(0.11)S(0.098)QK 65.213 0.085252 261020000 239410 115290 203530 100890 352490 235230 230180 206610 281810 154270 TRUE FALSE 248862.0917 135090.1607 208834.159 120845.7409 292573.8757 180601.3974 212137.8901 203840.7309 271667.7131 184496.2528 1.348873421 0.732210864 1.13191545 0.655003769 1.585798471 0.978889244 1.149822215 1.104850249 1.472483636 1 17.49323199 3.251105412 24.9998427 1.197330957 0.96200993 0.183426161 0.254887057 395.194656 787557.2819 0.065604928 0.088224018 1782.811441 -3.251105412 -0.235321028 RLS(ph)SASTGKPPLSVEDDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 RLS(0.791)S(0.207)AS(0.002)TGKPPLSVEDDFEK;RLS(0.79)S(0.208)AS(0.002)TGKPPLSVEDDFEK;RLS(0.956)S(0.044)ASTGKPPLSVEDDFEK;RLS(0.85)S(0.15)ASTGKPPLSVEDDFEK 305.7 1.17E-55 1363500000 1240910 658904 982920 738908 1591410 1515710 1497190 1195270 1428370 785252 TRUE FALSE 1289902.085 772065.6364 1008535.703 885061.797 1320902.697 1163709.323 1379836.336 1179249.361 1376963.243 939107.0948 1.373540986 0.82212736 1.073930448 0.942450336 1.406551717 1.239165724 1.469306688 1.255713398 1.466247301 1 19.84093017 3.237162537 24.99912155 1.322425636 1.038014643 0.311610898 0.182834564 37.54409334 671331.6744 0.047479238 0.059757435 1726.483916 -3.237162537 -0.284410993 RLS(ph)SSSATLLNSPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSSSATLLNSPDR 15 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 RLS(0.318)S(0.318)S(0.318)S(0.045)AT(0.002)LLNSPDR 105.32 0.00081097 146740000 179450 128170 140510 115110 194090 207020 174950 142310 143550 115200 TRUE FALSE 186534.8246 150182.2005 144171.806 137878.4144 161098.6511 158942.7424 161236.9619 140402.5672 138383.6635 137771.2344 1.353946094 1.090083871 1.046457969 1.000777957 1.169319937 1.15367147 1.170323853 1.019099291 1.004445262 1 17.07191517 4.737408466 5.253020411 1.076782067 1.365483446 0.616076041 0.066619255 0.109158097 10.54159781 0.016803455 0.114005803 54627.14023 -4.737408466 0.288701379 RLS(ph)STSLASGHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.842)S(0.111)T(0.047)SLASGHSVR;RLS(0.656)S(0.288)T(0.056)SLASGHSVR;RLS(0.845)S(0.143)T(0.012)SLASGHSVR;RLS(0.684)S(0.287)T(0.027)S(0.002)LASGHSVR;RLS(0.827)S(0.101)T(0.072)SLASGHSVR 186.38 6.55E-07 7450770000 559094 1291867 1061624 1178086 1346922 1551068 1071505 1314177 1176422 1470109 TRUE FALSE 581167.4628 1513735.108 1089290.794 1411107.895 1117972.68 1190855.964 987517.6382 1296562.607 1134082.802 1758148.712 0.330556488 0.860982406 0.619566926 0.802610089 0.635880612 0.677335174 0.561680381 0.737459009 0.64504373 1 20.74562567 -4.999999114 0.401507218 6.485196808 0.657040649 0.366499005 0.136918474 775.646236 5.389909373 3731.648806 0.076194023 1.00E-05 4.999999114 -5.82815616 RLS(ph)TEHSSVSEYHPADGYAFSSNIYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSTEHSSVSEYHPADGYAFSSNIYTR 27 1 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RLS(0.584)T(0.415)EHS(0.001)SVSEYHPADGYAFSSNIYTR 282.88 1.52E-61 436180000 16697 105340 93177 108210 94402 159050 80440 114760 103390 128070 TRUE FALSE 17356.21045 123431.3256 95605.26917 129613.615 78355.58176 122113.0479 74134.90261 113221.8299 99669.0141 153162.8645 0.113318659 0.805882849 0.624206589 0.846247003 0.511583418 0.797275817 0.484026614 0.739225075 0.65073877 1 17.22470702 -5 0.050559573 2.239258814 5.92E-09 0.299414497 0.196267114 768.1392428 2.871030701 132.7032055 29.23111933 1.00E-05 5 -2.239258808 RLS(ph)TIFEECDEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RLSTIFEECDEELER 15 1 Q5T5P2;Q5T5P2-3;A0A0U1RRK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RLS(0.971)T(0.029)IFEECDEELER;RLS(0.951)T(0.049)IFEECDEELER;RLS(0.992)T(0.008)IFEECDEELER;RLS(0.979)T(0.021)IFEECDEELER;RLS(0.767)T(0.233)IFEECDEELER;RLS(0.955)T(0.045)IFEECDEELER 280.62 6.26E-34 2204263000 451888 493483 434463 444430 559291 586180 459977 507315 473251 576535 TRUE FALSE 469728.8872 578234.8665 445785.4627 532336.9275 464222.9156 450048.5786 423922.8008 500515.2722 456218.789 689495.9948 0.681264127 0.838634119 0.646538147 0.772066744 0.673278625 0.652721092 0.614829969 0.725914691 0.661669962 1 19.39518265 -1.770520677 5.926447106 1.013191327 0.69780619 0.675481523 0.063138279 0.010772 0.000417105 0.05984084 0.013952587 0.016962088 1.770520677 -0.315385137 RLS(ph)TSPDVIQGHQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.447)T(0.447)S(0.106)PDVIQGHQPR 125.23 5.62E-05 606960000 75720 142000 228980 138200 382760 193010 458830 243370 304920 154370 TRUE FALSE 78709.48407 166387.3954 234947.4069 165535.5475 317698.5919 148186.3526 422865.7057 240108.0232 293945.9888 184615.8459 0.426341973 0.901262806 1.272628608 0.896648642 1.720863073 0.802674071 2.290516849 1.300581876 1.592203461 1 17.49416686 4.625797024 0.679921442 1.49106789 7.08E-11 0.353445114 0.410263026 2.807243341 1.087997392 0.162445051 3.168359632 42247.11184 -4.625797024 -1.49106789 RLS(ph)VELTSSLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSVELTSSLFR 12 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0;A0A2R8Y7Z0;A0A2R8YG06 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RLS(1)VELTSSLFR;RLS(0.997)VELT(0.002)S(0.001)S(0.001)LFR;RLS(1)VELTSSLFR;RLS(1)VELTSSLFR 207.21 4.97E-08 331122000 225283.2 305697.1 261103.3 352404 344124 457360 333281.5 290032.1 256057.2 456936 TRUE FALSE 234177.5547 358198.1989 267907.8665 422108.4594 285629.9254 351145.0714 307158.0252 286144.6941 246841.7514 546463.8606 0.428532556 0.655483784 0.490257244 0.772436184 0.522687676 0.642576933 0.562082962 0.523629676 0.451707367 1 19.05976656 -1.05953184 4.523290664 1.000023311 0.566217322 0.638865111 0.098939729 2.24E-05 4.66E-06 0.088982987 0.020972324 0.087190298 1.05953184 -0.433805989 RLS(ph)YNTASNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 1 RLS(0.516)Y(0.337)NT(0.146)AS(0.001)NK;RLS(0.9)Y(0.062)NT(0.038)ASNK;RLS(0.981)Y(0.006)NT(0.012)ASNK;RLS(0.49)YNT(0.49)AS(0.02)NK;RLS(0.862)Y(0.002)NT(0.136)ASNK 103.13 0.0018659 1808840000 1476350 1037817 1723030 1086423 1915370 1759790 2034730 1499320 2459310 1575610 TRUE FALSE 1534637.438 1216053.997 1767933.577 1301314.227 1589796.092 1351105.442 1875242.546 1479224.068 2370799.913 1884320.613 0.8144248 0.645354081 0.938233953 0.69060128 0.843697235 0.717025242 0.995182313 0.785017188 1.258172255 1 20.84561303 1.250647367 24.99851941 1.129086121 0.806056815 0.555400719 0.116437641 128.8881602 266577.3418 0.07286629 0.026170059 17.80932122 -1.250647367 -0.323029306 RLSEDYGVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 0 ;;;; 167.12 8.56E-06 2810810000 2780760 2304660 2584220 1912850 5073740 3630830 3013680 2547570 2917370 4199400 FALSE TRUE 2890546.552 2700467.427 2651566.896 2291206.021 4211307.487 2787624.758 2777459.887 2513423.991 2812374.424 5022192.028 0.575554765 0.537706924 0.527970034 0.456216331 0.838539718 0.555061364 0.553037373 0.500463538 0.559989425 1 22.25988576 -0.930242914 5.264115833 1.000001019 0.56416188 0.643516883 0.096621123 1.15E-06 2.33E-07 0.092849704 0.021884834 0.117424058 0.930242914 -0.435839138 RLSELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSELLR 7 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ; 164.53 0.0019148 4711700000 1867520 2071480 1695130 1723370 3366000 2802800 2112880 1941770 1879070 3929400 FALSE TRUE 1941251.132 2427240.576 1739306.48 2064247.442 2793848.522 2151892.177 1947266.945 1915743.749 1811442.638 4699290.697 0.413094498 0.516512115 0.370121066 0.439267876 0.594525579 0.457918506 0.414374651 0.407666576 0.385471501 1 22.16401158 -1.407882468 3.564422548 1.004294469 0.444886963 0.87370217 0.063380225 39044488.29 61753708.43 1739143.661 0.015653429 0.039094668 1.407882468 -0.559407506 RLSES(ph)QLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSESQLSFR 10 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 RLS(0.208)ES(0.791)QLS(0.001)FR 175.34 3.00E-06 336420000 195640 253180 250470 269810 369210 345420 249230 265730 266650 354280 TRUE FALSE 203364.0183 296661.6955 256997.454 323177.6127 306451.8161 265201.4399 229694.7014 262168.324 257053.3186 423694.3829 0.479978084 0.700178495 0.606563278 0.762761145 0.723285057 0.625926259 0.542123546 0.618767523 0.60669513 1 18.69266448 -1.4090083 3.119560681 1.005261693 0.632712608 0.662712969 0.079248386 20528108.29 25712998.18 960328.8982 0.019794724 0.038993453 1.4090083 -0.372549084 RLSKS(ph)EDKESLTEDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSKSEDKESLTEDASK 17 3 F8WE37;Q9BXW9-4;Q9BXW9-3;Q9BXW9;Q9BXW9-1 F8WE37 FANCD2 Fanconi anemia group D2 protein 1 RLS(0.412)KS(0.559)EDKES(0.028)LT(0.001)EDASK 108.4 0.0036318 99864000 110050 35578 68831 25170 133970 102910 65584 58388 87554 38247 TRUE FALSE 114394.859 41688.24474 70624.79241 30148.55088 111197.8273 79010.71212 60443.35471 57605.40436 84402.94864 45740.76737 2.500938781 0.911402391 1.544022903 0.659117733 2.431044201 1.727358693 1.321432896 1.259388674 1.845245576 1 15.48119295 -0.9865189 4.839864725 0.999993432 1.527872847 0.081037787 0.561500593 3.72E-05 7.80E-06 0.50871069 0.119902766 0.103152819 0.9865189 0.527879415 RLSLGQGDS(ph)TEAATEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSLGQGDSTEAATEER 17 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RLS(0.004)LGQGDS(0.495)T(0.495)EAAT(0.006)EER 62.162 0.067907 473430000 123030 163870 166120 160740 174910 205330 166340 188680 164890 202410 TRUE FALSE 127887.3194 192013.3978 170449.2237 192533.8922 145178.8607 157645.2193 153301.8362 186151.0532 158955.6411 242068.3641 0.528310752 0.793219711 0.704136719 0.795369907 0.599743222 0.651242552 0.633299757 0.769001988 0.656655989 1 17.88505502 -1.470034573 0.621600754 1.146861455 0.686370597 0.570985385 0.082612564 46.53932919 7.050070003 11.0508087 0.03060618 0.033881718 1.470034573 -0.460490858 RLSNS(ph)S(ph)LCSIEEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 2 RLS(0.432)NS(0.802)S(0.766)LCSIEEEHR 77.871 0.015036 0 38186 40606 39577 40113 51330 55141 39063 35638 39172 37400 TRUE FALSE 39693.61277 47579.76463 40608.40913 48047.23167 42604.94493 42335.33842 36001.13999 35160.3309 37762.20737 44727.81393 0.887448084 1.063762354 0.907900601 1.074213726 0.952538056 0.946510341 0.804893797 0.786095447 0.844266778 1 15.44888463 2.362854239 4.242113431 0.834155881 0.980813666 0.319216934 0.078394978 0.195054235 6.275511413 0.026394048 0.021694354 230.5973111 -2.362854239 0.146657785 RLSNSS(ph)LCSIEEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSNSSLCSIEEEHR 15 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RLS(0.279)NS(0.279)S(0.431)LCS(0.011)IEEEHR 116.29 0.00021638 83514000 26382 28487 35390 35001 28534 39071 33062 24491 30373 28714 TRUE FALSE 27423.58173 33379.42065 36312.29247 41924.09333 23683.80087 29997.35238 30470.51405 24162.7382 29279.88166 34339.95854 0.798590997 0.972028566 1.057435536 1.220854512 0.689686356 0.873540728 0.887319477 0.703633296 0.852647554 1 15.06760068 3.223320224 24.99981482 0.817458452 1.012585278 0.310298715 0.128332979 265.5948341 435671.7322 0.03726394 0.044694589 1672.323236 -3.223320224 0.195126826 RLSPS(ph)AS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RLS(0.262)PS(0.749)AS(0.989)PPR;RLS(0.175)PS(0.83)AS(0.995)PPR;RLS(0.394)PS(0.68)AS(0.926)PPR;RLS(0.472)PS(0.545)AS(0.983)PPR 142.08 2.43E-05 5564720000 2223670 2586880 2370710 2541600 2522670 2768890 2341080 2457550 2137930 2506250 TRUE FALSE 2311462.209 3031156.517 2432492.65 3044320.894 2093867.454 2125857.26 2157580.032 2424610.562 2060986.317 2997301.702 0.771181028 1.011295097 0.811560828 1.015687173 0.698584147 0.709257016 0.719840792 0.8089311 0.687613901 1 21.51523288 3.225502472 24.99723604 0.758364854 0.903716326 0.247845856 0.111170393 270.4463557 517715.1834 0.02934832 0.035279695 1680.747493 -3.225502472 0.145351472 RLSQPESAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSQPESAEK 10 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 82.171 0.030166 49879000 74879 53963 63082 51126 80023 87482 78871 66967 73542 61680 FALSE TRUE 77835.28074 63230.72548 64725.96874 61238.5702 66420.71904 67165.6313 72688.88493 66069.4169 70895.23779 73765.01507 1.055178809 0.85719125 0.877461608 0.830184474 0.900436596 0.910535045 0.985411375 0.895674146 0.961095686 1 16.17064912 2.456396063 20.63224649 0.947149009 0.896858337 0.142608927 0.062108532 67.94976331 67641.13953 0.021182216 0.017728001 286.0197766 -2.456396063 -0.050290672 RLSS(ph)AS(ph)TGKPPLSVEDDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.501)S(0.538)AS(0.704)T(0.256)GKPPLSVEDDFEK;RLS(0.472)S(0.53)AS(0.784)T(0.212)GKPPLS(0.001)VEDDFEK 70.091 0.010215 149148000 113957 61965 78433 64106 125182 120167 124240 98482 105415 63740 TRUE FALSE 118456.1104 72607.00673 80477.02841 76785.97546 103903.6084 92260.0354 114501.7442 97162.00987 101621.1347 76228.63262 1.553958221 0.952489953 1.055732284 1.007311463 1.363052239 1.210306839 1.502083144 1.274613049 1.333109768 1 16.21804538 3.227336748 24.9891777 1.304520885 1.122621275 0.097280331 0.194562229 369.4064898 822457.0003 0.053299481 0.06424563 1687.86127 -3.227336748 -0.181899611 RLSS(ph)AST(ph)GKPPLSVEDDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSASTGKPPLSVEDDFEK 20 2 O75152;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 2 RLS(0.419)S(0.572)AS(0.426)T(0.579)GKPPLS(0.004)VEDDFEK 74.274 0.026293 68469000 68229 36372 55779 40667 82558 70172 73236 65721 66203 39590 TRUE FALSE 70922.7336 42618.60807 57232.64656 48710.81122 68524.82065 53875.61647 67495.57095 64840.11749 63820.36696 47346.9025 1.497938194 0.900135084 1.208793892 1.028806715 1.447292579 1.137891047 1.425554099 1.369469048 1.347931197 1 15.53098243 3.242522831 24.99689466 1.31292312 1.143996492 0.088188858 0.191293386 183.1987329 1155758.325 0.049542414 0.064673228 1747.925151 -3.242522831 -0.168926628 RLSS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RLSSLR 6 1 P62753;A2A3R5;Q9Y253-2;Q9Y253 P62753 RPS6;POLH 40S ribosomal protein S6;DNA polymerase eta 1 RLSS(1)LR;RLS(0.001)S(0.999)LR;RLS(0.052)S(0.948)LR 103.35 0.036818 9454200000 4176620 4711100 4375960 4223420 4701800 4764400 4322070 4181440 3748070 3509580 TRUE FALSE 4341516.183 5520194.778 4490001.112 5058799.87 3902589.715 3657940.305 3983294.86 4125394.636 3613177.693 4197215.006 1.03438022 1.315204194 1.069757233 1.20527537 0.929804575 0.871516065 0.949032836 0.982888565 0.860851228 1 22.00100094 3.232345535 24.99933199 0.933389355 1.161343758 0.644153552 0.081452853 84.15038551 338483.4265 0.021806908 0.026686077 1707.440327 -3.232345535 0.227954403 RLSS(ph)LRAST(ph)SK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLSSLRASTSK 11 2 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 2 RLS(0.461)S(0.543)LRAS(0.317)T(0.6)S(0.079)K;RLS(0.462)S(0.564)LRAS(0.17)T(0.691)S(0.114)K 63.827 0.07965 1651100000 2482540 1894100 2511170 2003910 3611400 3134600 2816300 2615940 2515080 1573730 TRUE FALSE 2580552.596 2219396.941 2576613.153 2400277.417 2997535.518 2406636.655 2595551.047 2580877.603 2424562.762 1882072.263 1.371123016 1.179230461 1.369029874 1.275337544 1.592678229 1.278716393 1.379092131 1.371295701 1.288241058 1 20.84389059 -0.540383082 8.801203411 1.000008109 1.347391858 0.506131737 0.10220484 0 0 0.094187734 0.022200262 0.288148868 0.540383082 0.34738375 RLSS(ph)TSLASGHSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 RLS(0.147)S(0.427)T(0.427)SLASGHSVR 233.55 2.11E-17 1451700000 123870 287610 227280 242290 300560 388100 243800 256730 247350 327880 TRUE FALSE 128760.4832 337004.7802 233203.1035 290214.2388 249470.9186 297969.6567 224690.3189 253288.9543 238447.9218 392121.8084 0.328368585 0.859439014 0.594721075 0.740112467 0.636207712 0.75989055 0.573011534 0.645944574 0.608096558 1 18.58094236 -1.653195957 2.762546054 1.038809419 0.64728127 0.39658878 0.133399068 48730321.76 45485263.07 13451173.51 0.029715077 0.022223069 1.653195957 -0.391528149 RLSS(ph)TSS(ph)EETQLFHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSTSSEETQLFHIPR 17 1 Q8N271-3;Q8N271-2;Q8N271 Q8N271-3 PROM2 Prominin-2 2 RLS(0.377)S(0.448)T(0.298)S(0.258)S(0.618)EET(0.001)QLFHIPR 94.384 0.0098978 107220000 60384 81692 62695 83282 74467 101510 65238 76656 68789 115050 TRUE FALSE 62768.00695 95721.96552 64328.8832 99754.93103 61809.12594 77935.8409 60124.47509 75628.5517 66313.29733 137591.8447 0.456189879 0.695695052 0.467534128 0.725006131 0.449220854 0.566427764 0.436977026 0.54965868 0.481956597 1 17.07003544 -1.496121738 3.304425708 1.009954976 0.539430403 0.673409061 0.096812304 36208202.44 52783113.65 3350289.933 0.021885765 0.031906434 1.496121738 -0.470524574 RLSSAHNGGS(ph)AFGAAGYGGAQPTPPMPTRPVSFHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSSAHNGGSAFGAAGYGGAQPTPPMPTRPVSFHER 36 2 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 RLS(0.304)S(0.304)AHNGGS(0.386)AFGAAGY(0.006)GGAQPTPPMPTRPVSFHER 64.347 0.0033838 544040000 19287 64914 71630 67669 71170 85751 49391 61149 75453 110180 TRUE FALSE 20048.46565 76062.47454 73496.73664 81053.72623 59072.54882 65836.62982 45519.60436 60329.39767 72737.46127 131767.6615 0.152150121 0.577246903 0.557775222 0.615126089 0.448308395 0.499641787 0.345453534 0.457846766 0.552012994 1 17.00763682 0.774317767 3.075094585 0.99993572 0.465211669 0.625169575 0.125526187 0.899074529 11.36880033 0.116919405 0.030518867 5.947271531 -0.774317767 -0.534724051 RLST(ph)EHSSVSEYHPADGYAFSSNIYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSTEHSSVSEYHPADGYAFSSNIYTR 27 1 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 RLS(0.33)T(0.669)EHSSVSEYHPADGYAFSSNIYTR 132.68 2.71E-05 333460000 11783 26764 19346 19749 18987 30693 18191 24155 27343 30475 TRUE FALSE 12248.20194 31360.5088 19850.17265 23655.29326 15759.59652 23565.01591 16765.14189 23831.24173 26358.93077 36445.99277 0.336064434 0.860465209 0.544646233 0.649050594 0.432409583 0.646573577 0.459999594 0.653878243 0.723232618 1 15.15347258 0.890082236 1.642801296 0.998315612 0.574288253 0.483507448 0.136649389 0.403991614 2.15862371 0.118015772 0.033995622 7.763941164 -0.890082236 -0.424027359 RLSTS(ph)PDVIQGHQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSTSPDVIQGHQPR 15 1 Q9Y385 Q9Y385 UBE2J1 Ubiquitin-conjugating enzyme E2 J1 1 RLS(0.141)T(0.282)S(0.577)PDVIQGHQPR 168.08 7.80E-07 650030000 77579 156630 194690 161850 271150 219490 291850 180250 233700 163140 TRUE FALSE 80641.87882 183529.9841 199763.7813 193863.4469 225060.0199 168516.7739 268974.0344 177834.0436 225289.1827 195104.1595 0.413327317 0.940676942 1.02388274 0.993640768 1.153537784 0.863727223 1.378617632 0.911482585 1.154712351 1 17.57388501 4.889737125 1.808446146 1.063155169 2.18E-12 0.664092416 0.137496583 0.747475302 1.801258802 0.032250891 1.531041855 77577.74029 -4.889737125 -1.063155169 RLSYNTASNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLSYNTASNK 10 1 P49207 P49207 RPL34 60S ribosomal protein L34 0 86.313 0.024502 0 264130 389630 372960 335380 690400 594840 349280 435880 333790 807900 FALSE TRUE 274558.0564 456545.9216 382679.644 401717.163 573046.0546 456697.4249 321902.5209 430037.7416 321776.9631 966192.5368 0.284164953 0.472520646 0.396069758 0.415773407 0.593097165 0.47267745 0.333166019 0.445084934 0.333036068 1 19.88195118 -1.39822883 3.505625671 1.004488629 0.42220475 0.813041385 0.083943576 197329771.3 285388474.7 8925883.09 0.019832988 0.039973407 1.39822883 -0.582283879 RLT(ph)VMS(ph)LQESGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLTVMSLQESGLK 13 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 2 RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK;RLT(1)VMS(1)LQESGLK 66.498 0.020289 2361110000 41679.1 1990850 1911290 2191920 1883690 2546550 1620640 1821730 1813630 1705870 TRUE FALSE 43324.62305 2332763.001 1961099.788 2625475.234 1563501.047 1955152.356 1493610.002 1797312.689 1748357.811 2040102.566 0.021236493 1.143453785 0.961275095 1.28693296 0.76638355 0.958359834 0.732124956 0.880991338 0.856995055 1 20.96021025 4.746279831 24.99975715 0.942151971 0.021236052 0.758183262 0.157914347 469.7453111 1521300.423 0.038239181 0.412319718 55754.48784 -4.746279831 -0.920915919 RLTAEDLFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLTAEDLFEAR 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 185.57 7.07E-06 270320000 237280 645450 445420 568130 397430 613240 343060 466170 369360 707120 FALSE TRUE 246647.9976 756301.0166 457028.0111 680504.4183 329874.9906 470824.3037 316170.0608 459921.7537 356066.8058 845666.6254 0.291661028 0.894325251 0.540435199 0.804695843 0.39007687 0.556749302 0.373870804 0.543857047 0.421048667 1 19.68972952 -1.257782425 4.809148714 1.000123095 0.543246982 0.375667215 0.179493549 0.00022214 3.43E-05 0.162965382 0.038401032 0.055235409 1.257782425 -0.456876113 RLTAIIEEAEEAPGARPQLQDAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLTAIIEEAEEAPGARPQLQDAWR 24 2 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 112.88 0.00085926 45864000 18160 21911 15990 13854 19588 25640 16656 18998 22713 42115 FALSE TRUE 18876.97082 25674.04381 16406.71254 16594.27985 16258.43876 19685.49858 15350.4592 18743.36288 21895.56357 50366.62791 0.374791238 0.509743155 0.325745701 0.329469741 0.322801812 0.390844085 0.304774408 0.37213853 0.434723635 1 15.62018052 0.619134717 2.324014414 0.9999714 0.365195959 0.922508647 0.054757804 0.730370915 4.153639231 0.053683739 0.01446882 4.160396449 -0.619134717 -0.634775441 RLTELETAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLTELETAVR 10 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18;F8VRV7 Q13561 DCTN2 Dynactin subunit 2 0 ; 158.3 1.29E-05 327050000 145283 201905 178962 166312 216660 224980 174294 186631 163425 259510 FALSE TRUE 151018.885 236580.6131 183625.8967 199208.0172 179832.2106 172731.8046 160632.3808 184129.5167 157543.3662 310356.0159 0.486598865 0.762287828 0.591662115 0.64186936 0.579438456 0.556560195 0.517574568 0.593284832 0.507621435 1 18.24356459 -1.530133871 3.152810123 1.013658067 0.586169023 0.73761222 0.074774523 13451204.11 17171426.32 1584880.811 0.017310012 0.029502997 1.530133871 -0.427489044 RLTLEDLEDSWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 225.21 2.06E-11 474565000 283352 390779 376427 329463 402675 443366 316169 352612 342343 447154 FALSE TRUE 294538.9558 457892.2534 386236.9969 394629.7981 334228.4473 340400.9658 291386.8476 347885.8129 330022.1423 534765.265 0.550781764 0.856249056 0.722255206 0.737949571 0.625000293 0.636542775 0.544887386 0.650539285 0.617134589 1 19.02854623 -0.965105421 4.371509053 1.000009413 0.662380444 0.573118626 0.087972646 9900807.115 4530396.567 897.6727932 0.02102531 0.108366383 0.965105421 -0.33762897 RLVEVDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RLVEVDSSR 9 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 130.01 0.0005986 507250000 142200 209133 185152 186819 203790 260280 174452 180383 157587 247967 FALSE TRUE 147814.1658 245049.9659 189977.2132 223771.2406 169149.8486 199833.9146 160777.9964 177965.2609 151915.4747 296551.386 0.498443686 0.826332223 0.640621566 0.7545783 0.570389675 0.673859317 0.542158978 0.600116099 0.512273696 1 18.17792259 -1.217491882 4.943881063 1.000021655 0.628767512 0.560865655 0.099658909 5.29E-05 8.37E-06 0.092465074 0.021791285 0.060604953 1.217491882 -0.371254144 RLVPDSDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLVPDSDVR 9 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 110.14 0.0037456 248040000 218410 239420 212100 217870 275090 293060 206960 230420 186550 268740 FALSE TRUE 227032.9954 280538.5226 217627.5002 260964.0357 228330.3001 225001.2564 190737.9344 227331.5968 179836.1019 321394.4577 0.706399846 0.872879155 0.6771352 0.811974287 0.710436333 0.700078209 0.593469893 0.707328927 0.559549481 1 18.29398552 4.211437543 24.97955398 0.705364425 0.789639702 0.039598606 0.121107512 484.8206849 446506 0.027914719 0.060326631 16271.87289 -4.211437543 0.084275277 RLVSDGNINSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLVSDGNINSDR 12 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 92.99 0.011904 154130000 90191 120240 94373 100410 119930 132560 89308 104960 84383 124280 FALSE TRUE 93751.81032 140890.2847 96832.43791 120270.7983 99544.34144 101774.949 82307.8056 103553.1829 81346.07231 148630.2865 0.630771914 0.947924464 0.651498696 0.809194419 0.669744665 0.684752424 0.553775462 0.696716566 0.547304821 1 17.1813686 3.220137846 23.49326019 0.668822159 0.765542236 0.036034988 0.143196179 272.6441176 347682.2372 0.037803488 0.045284551 1660.113747 -3.220137846 0.096720077 RLWGDIYFNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLWGDIYFNPK 11 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 75.695 0.059942 299380000 178310 187150 213380 183650 277230 266920 216970 188130 210250 260490 FALSE TRUE 185349.8165 219291.5567 218940.8581 219975.4219 230106.5436 204931.8752 199963.3245 185608.4251 202683.1436 311528.0281 0.594969954 0.703922398 0.702796661 0.706117595 0.738638334 0.65782805 0.641879081 0.595800083 0.650609657 1 18.24900244 -1.105606627 4.119744684 1.000067989 0.664980759 0.830269026 0.045324417 16275661.5 38118937.84 15919.56241 0.012186686 0.078413957 1.105606627 -0.33508723 RLYWDDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLYWDDLKR 9 2 P02786;G3V0E5 P02786 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 57.174 0.06587 259200000 587020 237650 298620 167210 517080 408100 317410 205630 324370 237530 FALSE TRUE 610196.0029 278464.5388 306402.2825 200283.6389 429186.9263 313324.9598 292530.5748 202873.8662 312695.9871 284069.4557 2.148052142 0.980269203 1.078617487 0.705051652 1.510852074 1.102987152 1.029785388 0.71416994 1.100773 1 18.11588419 4.739543778 24.37921053 1.011621417 2.14805266 0.714163805 0.213055346 31.49253297 780751.3063 0.051888612 0.316204766 54896.38892 -4.739543778 1.136431243 RMDEISDHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMDEISDHAK 10 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 113.69 0.00094461 320000000 165500 276890 313630 242680 372980 367310 304560 309130 310510 308800 FALSE TRUE 172034.0678 324443.7036 321803.4554 290681.3797 309580.9928 282007.8191 280687.7914 304986.618 299334.8058 369303.4477 0.465833907 0.87852877 0.871379505 0.787107138 0.838283517 0.763620868 0.760046496 0.825842867 0.810538888 1 18.49444721 -4.999999986 0.027904179 2.102904588 1.87E-10 0.336981346 0.105621469 2298.128008 4.834905477 275.5569176 118.9560357 1.00E-05 4.999999986 -2.102904588 RMDKLEAEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMDKLEAEKR 10 3 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 145.09 1.36E-05 1154930000 1120090 739600 1090810 618750 1782640 1298760 1041510 1060720 1229170 1081430 FALSE TRUE 1164312.018 866620.5467 1119237.405 741136.9032 1479627.49 997142.6729 959873.7247 1046502.783 1184932.412 1293315.503 0.900253662 0.670076671 0.865401676 0.573051897 1.144057645 0.770997232 0.742180638 0.809162792 0.916197485 1 20.30264283 1.062750429 3.091474707 0.998208466 0.805149584 0.15870744 0.143139699 0.385272198 7.623786317 0.127370487 0.033664671 11.55448063 -1.062750429 -0.193058882 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RMEDEGGFPVPQENGQPESPR 21 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR;RMEDEGGFPVPQENGQPES(1)PR 207.31 2.29E-22 3309570000 822280 1110590 1032780 1036577 1001689 1115521 901730 1100412 970581 1118283 TRUE FALSE 854744.2493 1301325.193 1059695.095 1241608.837 831422.2616 856458.1536 831050.0464 1085662.777 935649.9794 1337389.143 0.639114093 0.973034064 0.792361072 0.92838262 0.621675648 0.640395623 0.621397333 0.811777771 0.699609373 1 20.35098788 5.036633224 15.8428537 0.77284503 0.130262643 0.087519342 0.136549808 8737423.974 107020765.4 0.032345155 157597285 108801.0843 -5.036633224 -0.642582387 RMEDEGGFPVPQENGQPES(ph)PRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMEDEGGFPVPQENGQPESPRR 22 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RMEDEGGFPVPQENGQPES(1)PRR;RMEDEGGFPVPQENGQPES(1)PRR 146.03 4.62E-08 787050000 99564 137872 137723 136388 154778 143501 107580 130191 123408 136998 TRUE FALSE 103494.8636 161550.4435 141312.1745 163365.1393 128468.8908 110175.0675 99147.59849 128446.0026 118966.5702 163840.1351 0.631681996 0.986024843 0.862500354 0.997100858 0.784111236 0.672454692 0.605148418 0.783971537 0.726113721 1 17.32192928 3.011589148 24.14079989 0.734364114 0.878853887 0.122552536 0.134331755 224.929809 468534.9095 0.036652678 0.043770964 1027.044233 -3.011589148 0.144489773 RMEDETQKELETMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMEDETQKELETMR 14 2 A0A0A0MSW4;P48739;P48739-3 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 85.178 0.0044094 53680000 34952 45477 44457 44139 40876 54857 44137 38246 39848 45125 FALSE TRUE 36331.93195 53287.32099 45615.58594 52869.56246 33927.91212 42117.29312 40677.42661 37733.37493 38413.87826 53966.37978 0.673232707 0.987417003 0.845259329 0.979675914 0.628686087 0.780435769 0.753754963 0.699201523 0.711811287 1 15.71977329 3.242233648 24.99999866 0.744579136 0.877816496 0.151471978 0.121850705 137.3338724 934737.6256 0.031464689 0.040999842 1746.761648 -3.242233648 0.13323736 RMEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMEEEER 7 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 99.136 0.017237 80152000 81946 85433 72968 70237 81859 99651 89565 81709 80390 64124 FALSE TRUE 85181.29136 100105.4532 74869.60602 84129.66896 67944.63642 76508.56548 82544.66127 80613.8245 77496.7796 76687.87007 1.110753125 1.305362283 0.97629007 1.097040104 0.885989353 0.997661891 1.076371807 1.051193943 1.010548077 1 16.22671078 4.227944155 24.99996027 1.016950641 1.208057718 0.553228384 0.070397961 129.0800276 303963.6238 0.016964568 0.037245507 16902.23575 -4.227944155 0.191107077 RMEEEQHHWDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMEEEQHHWDDR 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 177.42 9.48E-06 245940000 141940 189470 189540 204780 160050 206320 171040 164240 197380 253820 FALSE TRUE 147543.9008 222009.9986 194479.5681 245284.8728 132844.7582 158405.3068 157633.4379 162038.6314 190276.3324 303551.1693 0.486059405 0.731375864 0.640681334 0.808051154 0.437635468 0.521840542 0.519297745 0.53380994 0.626834457 1 18.21158021 0.951008277 19.5611674 1.000000002 0.585768912 0.567602851 0.108035477 509.2180619 203319.4603 0.106457693 0.026614423 8.933225084 -0.951008277 -0.41423109 RMEEEQHHWDDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMEEEQHHWDDRR 13 2 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 ; 94.728 0.0030161 715820000 440960 490230 466050 404160 542700 526830 417390 443880 469790 540890 FALSE TRUE 458369.4413 574423.189 478195.6459 484101.6417 450452.0478 404481.7167 384673.8812 437930.5146 452882.3497 646867.0395 0.708599161 0.888008128 0.739248743 0.748378897 0.696359561 0.62529344 0.594672255 0.677002364 0.700116596 1 19.30310968 3.564590032 1.898421507 0.686317416 0.794081272 0.021537613 0.113756993 0.665217785 4.731578658 0.031712806 0.057487453 3669.357545 -3.564590032 0.107763856 RMEEETKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMEEETKR 8 2 F5GWE5;Q00169 F5GWE5 PITPNA Phosphatidylinositol transfer protein alpha isoform 0 ; 101.65 0.0029511 100532000 39996 41809 50728 41486 112396 83338 73723 42182 51336 74245 FALSE TRUE 41575.07296 48989.37052 52050.01335 49691.80698 93290.96807 63984.0125 67944.39862 41616.61929 49488.42739 88791.88624 0.468230541 0.551732513 0.586202361 0.559643556 1.050669966 0.720606524 0.765209542 0.468698448 0.557353036 1 16.43814023 3.437514401 24.99999298 0.722420547 0.543004787 0.271814215 0.169052595 261.2331477 164890.5992 0.049822474 0.067460047 2738.510441 -3.437514401 -0.17941576 RMEELHNQEMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RMEELHNQEMQK 12 1 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;;;; 170.18 2.72E-05 841804000 1197648 996638 1236822 980817 1439814 1470225 1387994 1196008 1253823 996245 FALSE TRUE 1244932.068 1167802.824 1269054.597 1174819.675 1195074.931 1128787.525 1279199.403 1179977.469 1208698.155 1191440.133 1.044896871 0.980160724 1.065143402 0.98605011 1.003050759 0.947414388 1.073658145 0.990379152 1.01448501 1 20.18427503 4.77875646 21.04742006 1.007915266 1.044897681 0.091247217 0.03597629 6428.331543 3365467.603 0.007996929 1.653011004 60083.67105 -4.77875646 0.036982415 RMEELHNQEVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 ;;;; 124.12 0.00015686 737779000 392646 905717 883453 899869 837004 1119394 745750 932177 797313 1167025 FALSE TRUE 408147.9673 1061266.849 906476.5109 1077860.402 694730.3591 859431.7081 687296.1663 919682.692 768617.8609 1395681.205 0.292436386 0.760393452 0.649486794 0.772282667 0.497771523 0.615779381 0.492444954 0.65894897 0.550711623 1 20.41253801 -1.514138617 2.952832954 1.014718277 0.598681136 0.457102565 0.134294431 24712451.05 28153635.01 2942451.922 0.031275068 0.030609863 1.514138617 -0.416037141 RMGESDDSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 ;;;;; 210.15 2.20E-08 2436080000 1065306 1559688 1317351 1193711 1537793 1650126 1090648 1310412 1255170 1903690 FALSE TRUE 1107365.103 1827552.281 1351682.249 1429823.473 1276399.495 1266909.244 1005160.16 1292848.071 1209996.677 2276681.607 0.486394364 0.802726334 0.593707194 0.628029615 0.560640316 0.556471858 0.441502297 0.567865118 0.531473823 1 21.11850111 -1.519920751 6.583277959 1.000293119 0.575831231 0.662142442 0.091217001 0.000394342 2.88E-05 0.088750723 0.020904715 0.030205028 1.519920751 -0.424461888 RMGS(ph)S(ph)MS(ph)AATARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMGSSMSAATARR 13 2 Q86UX6 Q86UX6 STK32C Serine/threonine-protein kinase 32C 3 RMGS(0.975)S(0.978)MS(0.695)AAT(0.351)ARR 42.317 0.065583 173250000 79899 662770 501300 563150 372400 622940 419920 513320 410260 626560 TRUE FALSE 83053.47422 776595.5919 514364.2898 674539.3892 309099.581 478271.6257 387005.5731 506439.785 395494.8227 749322.4358 0.110838099 1.03639709 0.686439195 0.900199109 0.41250544 0.638272128 0.516474023 0.675863635 0.527803258 1 19.51522712 -1.586242863 3.376976318 1.01485371 0.62923775 0.185585748 0.24154546 24686074.19 23500172.45 2518731.787 0.051771228 0.025927291 1.586242863 -0.385615959 RMHS(ph)QPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMHSQPR 7 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 1 RMHS(1)QPR;RMHS(1)QPR 103.7 0.0050943 409960000 40221 77950 72837 70743 75903 89938 53988 74858 61343 108523 TRUE FALSE 41808.95614 91337.30613 74735.19206 84735.75425 63001.03517 69051.26252 49756.27949 73854.65095 59135.27741 129786.0041 0.322137633 0.703753127 0.575833986 0.652888228 0.485422412 0.53203936 0.383371688 0.569049425 0.455636783 1 16.98577529 -1.335988533 3.312642019 1.002981231 0.527444892 0.631421061 0.109883861 69204901.66 97328961.87 2019215.208 0.024894421 0.046132975 1.335988533 -0.475536339 RMKVT(ph)NEDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RMKVTNEDFK 10 2 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 1 RMKVT(1)NEDFK;RMKVT(1)NEDFK;RMKVT(1)NEDFK 75.294 0.063391 2936550000 285798 3234260 2084310 3365880 1201780 3025540 1176110 2321370 1479940 5180800 TRUE FALSE 297081.5257 3789718.996 2138628.831 4031641.018 997501.8649 2322904.188 1083923.425 2290255.832 1426677.248 6195878.568 0.047948249 0.611651593 0.345169585 0.650697229 0.160994418 0.374911187 0.174942652 0.36964182 0.2302623 1 22.56287744 -1.243889557 4.157986443 1.000456466 0.339683323 0.550900952 0.181388128 3483490.247 185340372.1 168783.8556 0.039287237 0.057030929 1.243889557 -0.660773143 RMNS(ph)TGGQTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMNSTGGQTPR 11 1 Q96ST2;Q96ST2-3;Q96ST2-2;A0A1B0GW95 Q96ST2 IWS1 Protein IWS1 homolog 1 RMNS(0.867)T(0.133)GGQTPR 118.26 0.00045578 57483000 28174 29835 32720 26428 39894 46753 31504 39197 33312 47381 TRUE FALSE 29286.33128 34958.92917 33572.71008 31655.37952 33112.83213 35895.3243 29034.63416 38671.62833 32113.10763 56664.39979 0.516838286 0.61694696 0.592483291 0.558646692 0.584367473 0.633472241 0.512396395 0.682467801 0.56672457 1 15.79015501 -4.999999998 0.32370205 4.990616266 0.57282992 0.86882049 0.048447758 101.2085701 0.888719388 277.0473644 0.038619557 1.00E-05 4.999999998 -4.417786345 RMS(ph)ADMSEIEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMSADMSEIEAR 12 1 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RMS(1)ADMSEIEAR;RMS(1)ADMSEIEAR 215.15 2.58E-11 643500000 164577 237870 196635 237100 227740 270140 209400 219900 219610 316940 TRUE FALSE 171074.627 278722.3221 201759.4696 283997.6723 189028.8361 207404.079 192986.6808 216952.6002 211706.279 379038.3248 0.4513386 0.73534074 0.53229306 0.749258462 0.498706394 0.547184982 0.5091482 0.572376422 0.558535286 1 18.5319842 -1.435334311 3.053054094 1.00800927 0.575555372 0.660515688 0.091883572 24929654.5 30701299.09 1724308.141 0.020866175 0.036699968 1.435334311 -0.432453898 RMS(ph)DEFVDSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMSDEFVDSFK 11 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 RMS(1)DEFVDSFK 128.9 0.00015698 149500000 139920 142030 177790 158040 221350 226670 234990 195670 213330 158540 TRUE FALSE 145444.1496 166422.5477 182423.3535 189299.8403 183725.0061 174029.3277 216570.8698 193047.3637 205652.295 189602.8776 0.767098852 0.877742732 0.962133886 0.998401726 0.968999039 0.917862271 1.142234087 1.018166845 1.084647541 1 17.53262133 5.991696729 0.464816903 1.046346313 4.87E-18 0.697100334 0.054804076 7.865648573 0.533092429 0.032952464 5.795881338 981062.6197 -5.991696729 -1.046346313 RMS(ph)FQKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMSFQKPK 8 2 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;E5RII8 Q8N573-2 OXR1 Oxidation resistance protein 1 1 RMS(1)FQKPK;RMS(1)FQKPK 125.74 0.00065172 2738400000 3355700 2486400 3187500 2177000 4749600 3742500 3421800 3148300 3498600 2607800 TRUE FALSE 3488185.627 2913419.858 3270568.869 2607604.102 3942264.689 2873361.093 3153590.375 3106102.188 3372686.069 3118748.481 1.118456858 0.934163135 1.048679908 0.836105931 1.264053422 0.921318635 1.011171755 0.995945075 1.081422914 1 21.57253578 4.772112749 22.75589201 1.01045179 1.118457489 0.083648449 0.107374783 11127.90659 7546771.992 0.023410622 3.204062581 59171.52323 -4.772112749 0.108005699 RMS(ph)GEPIQTVESIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 80.596 0.005726 131620000 33483 101501 82021 119835 79852 142629 77665 91621 81964 151067 TRUE FALSE 34804.93469 118933.0072 84158.53464 143538.0053 66278.78556 109505.5763 71577.41436 90392.97036 79014.13165 180665.6863 0.192648285 0.65830435 0.465824675 0.794495116 0.366858737 0.606122715 0.3961871 0.500332809 0.437349965 1 17.462963 -1.463044154 2.889068537 1.014008025 0.499752485 0.480858921 0.158452384 33491503.89 37981410.31 3791440.9 0.035576992 0.034431492 1.463044154 -0.51425554 RMS(ph)PKPELTEEQKQEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMSPKPELTEEQKQEIR 17 3 P41208 P41208 CETN2 Centrin-2 1 RMS(1)PKPELTEEQKQEIR;RMS(0.998)PKPELT(0.002)EEQKQEIR 82.406 0.0073938 611700000 866150 320680 487170 346670 704500 683160 766430 515530 633830 283020 TRUE FALSE 900346.2708 375754.2955 499866.0504 415240.2913 584749.3416 524506.4434 706355.2139 508620.1636 611018.5821 338472.3503 2.66002901 1.110147683 1.476829791 1.226807126 1.727613323 1.549628627 2.086891923 1.50269339 1.805224508 1 18.36867846 RMS(ph)VGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RMSVGDR 7 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 RMS(1)VGDR 64.374 0.045199 190340000 161280 620000 438740 600150 304080 510710 288920 424000 365510 923670 TRUE FALSE 167647.4589 726480.1771 450173.9248 718857.8787 252392.5902 392105.3424 266273.6954 418316.9735 352355.3665 1104645.452 0.151765853 0.657659139 0.407527976 0.650758918 0.228482894 0.354960356 0.241049013 0.378688902 0.318975981 1 20.07515196 -1.460660995 4.299505493 1.002962126 0.38270256 0.582803256 0.15814539 0.004307475 0.000540339 0.146887603 0.034486475 0.034620952 1.460660995 -0.620259566 RMSADMS(ph)EIEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RMSADMSEIEAR 12 1 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RMS(0.483)ADMS(0.517)EIEAR;RMS(0.451)ADMS(0.549)EIEAR 175.34 6.14E-05 690020000 571550 768080 755590 791650 839780 957750 789230 782730 772510 944080 TRUE FALSE 594115.2353 899991.7652 775281.2961 948236.0072 697034.4956 735327.0773 727368.0903 772238.7846 744707.516 1129054.4 0.526206031 0.79711993 0.686664253 0.839849707 0.617361303 0.651276924 0.644227674 0.68396951 0.65958515 1 20.10668357 -1.996171334 2.32133363 1.310591959 0.682981074 0.571622756 0.083419847 8150532.669 3081584.051 13539528.79 0.019545655 0.010088548 1.996171334 -0.627610885 RMYS(ph)FDDVLEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RMYSFDDVLEEGK 13 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 RMYS(1)FDDVLEEGK;RMYS(1)FDDVLEEGK;RMYS(1)FDDVLEEGK;RMYS(1)FDDVLEEGK;RMYS(1)FDDVLEEGK;RMY(0.003)S(0.997)FDDVLEEGK 209.45 2.32E-08 764977000 947066 573124 834301 674667 1087380 1066663 1147462 871717 974105 578568 TRUE FALSE 984456.897 671553.5887 856043.5694 808114.1189 902547.536 818946.6837 1057520.93 860033.0595 939047.1513 691927.3222 1.422775002 0.970555096 1.237187118 1.167917631 1.30439644 1.18357327 1.528369955 1.242952882 1.357147089 1 19.40026098 3.236588699 24.9228992 1.292401341 1.185931903 0.028465768 0.162861218 122.4694053 1547890.549 0.043060934 0.053987551 1724.2042 -3.236588699 -0.106469439 RMYS(ph)FDDVLEEGKRPPTMTVSEASYQSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RMYSFDDVLEEGKRPPTMTVSEASYQSER 29 3 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 RMYS(1)FDDVLEEGKRPPTMTVSEASYQSER;RMYS(1)FDDVLEEGKRPPTMTVSEASYQSER;RMYS(1)FDDVLEEGKRPPTMTVSEASYQSER;RMY(0.087)S(0.889)FDDVLEEGKRPPT(0.01)MT(0.01)VS(0.004)EASYQSER 135.82 4.04E-06 994710000 89185 95950 119409 78580 150087 144925 103117 125707 127891 131855 TRUE FALSE 92706.09267 112428.6661 122520.8966 94122.88946 124575.2653 111268.3651 95034.42009 124022.1033 123288.2279 157689.4627 0.587902901 0.712975136 0.776975801 0.596887629 0.79000374 0.705616997 0.602668171 0.78649582 0.781841892 1 17.26672673 0.814806636 1.151546894 0.998663295 0.68977438 0.638284952 0.071015236 0.442049655 1.103789269 0.063972312 0.019954873 6.528398192 -0.814806636 -0.308888915 RNAEQYKDQADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNAEQYKDQADK 12 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 139.3 3.33E-05 685300000 761440 406810 605820 393980 846500 766240 738250 576720 691740 446210 FALSE TRUE 791502.2392 476676.453 621608.1669 471908.0681 702612.2324 588292.3725 680384.0359 568990.0117 666844.4125 533636.3063 1.483224117 0.893260911 1.16485359 0.884325265 1.316649981 1.102421941 1.274995775 1.066250562 1.249623395 1 19.0254973 3.193729493 24.99990117 1.168652737 1.09536074 0.026195022 0.179925714 495.3614037 276234.6331 0.048060908 0.057443973 1562.174315 -3.193729493 -0.073291997 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RNAETPEATTQQETDTDLPEAPPPPLEPAVIAR 33 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.987)PEAT(0.006)T(0.006)QQET(0.002)DTDLPEAPPPPLEPAVIAR;RNAET(0.569)PEAT(0.202)T(0.202)QQET(0.026)DTDLPEAPPPPLEPAVIAR;RNAET(0.999)PEATTQQETDTDLPEAPPPPLEPAVIAR;RNAET(0.999)PEATTQQETDTDLPEAPPPPLEPAVIAR 134.61 2.10E-08 697439000 218801 222042 233679 233078 227631 266393 231619 233542 221924 197782 TRUE FALSE 227439.4324 260175.9863 239768.8667 279180.1327 188938.3639 204527.263 213464.0976 230411.7515 213936.9986 236533.5961 0.961552338 1.099953624 1.013677848 1.18029801 0.798780245 0.86468589 0.902468406 0.974118498 0.904467704 1 17.85168559 3.236824995 24.99988361 0.908511235 1.062862629 0.518513404 0.073850341 37.45336971 539481.0739 0.020821234 0.026138549 1725.142582 -3.236824995 0.154351394 RNAET(ph)PEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNAETPEATTQQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 48 2 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 1 RNAET(0.989)PEAT(0.006)T(0.006)QQETDTDLPEAPPPPLEPAVIARPGCVNLSLHGIVEDR 103.65 1.27E-07 99080000 7369.1 18364 15114 17322 20320 22352 12470 18716 15731 22122 TRUE FALSE 7660.037758 21517.87415 15507.88326 20748.2399 16866.01366 17161.08675 11492.56882 18465.14263 15164.84438 26456.38235 0.289534588 0.813333957 0.586167944 0.784243274 0.637502642 0.648655834 0.434396837 0.69794662 0.573201739 1 14.69132818 -1.024396982 4.281536139 1.000024862 0.618369882 0.386960859 0.147714789 14922462.34 7140673.592 3327.154755 0.031439154 0.094537262 1.024396982 -0.38165498 RNALFPEVFS(ph)PTPDENSDQNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNALFPEVFSPTPDENSDQNSR 22 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 RNALFPEVFS(0.993)PT(0.007)PDENSDQNSR;RNALFPEVFS(0.996)PT(0.004)PDENSDQNSR 185.48 2.16E-17 341690000 137829 149050 169917 163950 200017 225560 158629 159029 158494 193708 TRUE FALSE 143270.5953 174648.1781 174345.1766 196378.8207 166018.1818 173177.1084 146195.2445 156897.4764 152789.8319 231661.3738 0.618448354 0.753894252 0.752586302 0.84769773 0.716641618 0.747544166 0.631073027 0.677270767 0.659539523 1 17.82165799 -1.020556956 4.726376158 1.00000578 0.713117715 0.638401331 0.065099247 0.04812651 43201515.86 656.3839291 0.016051829 0.095376865 1.020556956 -0.286888065 RNDDIS(ph)ELEDLSELEDLKDAK ddPTM_MDA-MB-175_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 153.94 2.01E-08 17319000 39614 17597 23595 19372 42371 39780 35452 22603 31798 16213 TRUE FALSE 41177.99131 20619.14786 24209.90508 23203.72378 35168.79255 30541.69787 32673.1796 22300.04376 30653.59619 19389.62693 2.123712408 1.063411273 1.248600871 1.196708109 1.813794184 1.57515655 1.685085521 1.150101744 1.580927591 1 14.24299743 -0.196874294 0.69265204 0.974276434 1.474577731 0.171283394 0.31803587 13.36133 5.920022638 1.267744923 0.112690407 0.635514854 0.196874294 0.500301298 RNDFQLIGIQDGYLSLLQDSGEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RNDFQLIGIQDGYLSLLQDSGEVR 24 1 P63241;P63241-2;I3L397;I3L504 P63241 EIF5A Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A 0 ;;;;;;; 290.54 1.36E-61 5131556000 1250281 1660942 1692825 1464575 1796221 2067577 1591199 1628609 1669260 1891799 FALSE TRUE 1299643.059 1946195.868 1736941.41 1754263.564 1490899.996 1587413.576 1466476.665 1606780.16 1609183.659 2262460.793 0.574437826 0.860211975 0.767722214 0.775378547 0.658972743 0.701631419 0.648177714 0.710191383 0.711253721 1 21.10946136 -0.364612906 8.408609044 1 0.714877628 0.575170534 0.074217998 0 0 0.069578303 0.016399763 0.431903868 0.364612906 -0.285122372 RNDS(ph)IYEASSLYGISAMDGVPFTLHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNDSIYEASSLYGISAMDGVPFTLHPR 27 1 E9PLZ8;Q96EY5;M0QZK6;E9PQA6;Q96EY5-2;Q96EY5-3 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 RNDS(1)IYEASSLYGISAMDGVPFTLHPR 176.01 2.98E-13 67069000 14463 19594 23693 16596 30852 20081 12111 20832 19791 28370 TRUE FALSE 15034.01041 22959.11708 24310.45904 19878.63927 25607.78806 15417.49208 11161.70817 20552.78111 19078.72578 33928.55832 0.443107846 0.676690028 0.71651907 0.585896963 0.75475615 0.454410468 0.328976789 0.605766414 0.562320556 1 15.05021251 -0.948175187 6.792533725 1.000000031 0.571707965 0.516036753 0.124965065 5.95E-08 9.31E-09 0.12482151 0.02942071 0.112674286 0.948175187 -0.428292065 RNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNDSYTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 39 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RNDS(0.672)Y(0.139)T(0.189)EEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 188.18 4.59E-24 124210000 140660 68966 115630 55643 167650 170480 123600 114790 136820 82691 TRUE FALSE 146213.3654 80810.37402 118643.4128 66649.01932 139152.9129 130888.6036 113911.909 113251.4278 131895.8749 98892.71824 1.478504869 0.817151914 1.199718391 0.673952749 1.407109799 1.323541369 1.151873576 1.145194811 1.333726864 1 16.59357667 3.170254813 25 1.227211752 1.037416166 0.136057853 0.227715395 97.02110403 35508.45534 0.061842379 0.073915806 1479.97648 -3.170254813 -0.189795586 RNEFLGELQK ddPTM_MDA-MB-175_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 ; 150.33 3.49E-05 661320000 492940 437940 486490 398380 782100 703190 550750 525240 557160 613820 FALSE TRUE 512401.6518 513152.7883 499168.3291 477178.375 649158.9214 539884.7794 507580.7759 518200.0169 537107.9204 734086.2767 0.698012847 0.699036073 0.679985916 0.650030371 0.884308755 0.735451399 0.691445668 0.705911598 0.731668657 1 19.48559011 0.826864565 7.480388279 0.99999999 0.718073233 0.665668377 0.05969806 10.8257407 468.0549596 0.058388426 0.014631595 6.712195006 -0.826864565 -0.281926757 RNEIDAEPPAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNEIDAEPPAKR 12 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 ;; 100.22 0.0018868 347578000 620125 567613 613643 531923 764909 759405 618399 589094 607919 572836 FALSE TRUE 644608.0138 665096.1173 629635.0407 637135.7818 634890.0414 583044.6976 569927.2705 581198.1585 586040.1139 685072.2466 0.940934357 0.970840843 0.919078307 0.930027139 0.926749032 0.851070381 0.831922871 0.848374987 0.85544279 1 19.38589661 2.826159099 4.407222609 0.862780066 0.939435858 0.270879473 0.04661317 0.229023653 7.937351306 0.013649747 0.014458986 670.1300596 -2.826159099 0.076655792 RNEIWLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNEIWLLK 8 1 Q9NRV9;A0A3B3IRV5 Q9NRV9 HEBP1 Heme-binding protein 1 0 ; 134.66 0.0013904 1320000000 1427370 1438460 1532420 1443350 1971320 1972330 1895900 1697160 1674500 1513920 FALSE TRUE 1483723.67 1685504.315 1572356.124 1728840.322 1636235.731 1514286.248 1747294.404 1674412.346 1614235.072 1810543.638 0.819490698 0.930938244 0.868444201 0.9548736 0.903726205 0.83637103 0.965066164 0.924811924 0.891574794 1 20.78799152 -4.999999999 0.106837574 1.302138981 0.845510671 0.354116588 0.043665479 196.4765549 1.407036826 13.13844538 0.573674675 1.00E-05 4.999999999 -0.45662831 RNELVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RNELVIR 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ;;;;;;; 170.66 0.0015495 18653880000 7551120 14175840 10126230 12645870 11524470 14187570 10087510 10606010 9460660 21708320 FALSE TRUE 7849244.048 16610430.25 10390127.87 15147185.34 9565544.706 10892721.88 9296824.607 10463853.78 9120172.695 25961649.67 0.302339957 0.639806424 0.400210618 0.58344464 0.368449033 0.419569712 0.358098377 0.403050419 0.351294036 1 24.62987872 -1.501420455 3.419930507 1.011264271 0.428751214 0.747094954 0.100320163 115597982.2 174241778.3 12504727.73 0.022923139 0.031519516 1.501420455 -0.582513057 RNENLQLGPLGRDPPQECSTFSPTDSGEEPGQLS(ph)PGVQFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNENLQLGPLGRDPPQECSTFSPTDSGEEPGQLSPGVQFQR 41 2 Q07002;A0A0A0MSJ6;Q07002-3 Q07002 CDK18 Cyclin-dependent kinase 18 1 RNENLQLGPLGRDPPQECSTFSPTDSGEEPGQLS(1)PGVQFQR 54.361 0.012103 75238000 9058.7 8375.2 6701 4694.3 8370.1 8572.6 4453.8 6469.4 6634.2 9975.1 TRUE FALSE 9416.344471 9813.57545 6875.633565 5622.818529 6947.353392 6581.743569 4104.699518 6382.688275 6395.436438 11929.52986 0.789330726 0.822628852 0.57635411 0.471336138 0.582366067 0.551718605 0.344078901 0.535032675 0.536101298 1 13.54224957 -1.06491643 3.843234856 1.000094237 0.569026276 0.474702768 0.13257595 41026329.39 74340891.08 57408.31405 0.035240731 0.086115945 1.06491643 -0.431067961 RNENMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNENMAK 7 1 Q9UHB9;Q9UHB9-4;Q9UHB9-2;Q9UHB9-3 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 74.486 0.073839 46785000 39245 42143 43248 37111 61731 50016 48450 42674 47301 43754 FALSE TRUE 40794.4229 49380.73242 44375.07841 44451.44503 51237.98667 38400.542 44652.3624 42102.02483 45598.64625 52326.75858 0.77960921 0.943699433 0.848037975 0.849497394 0.979192827 0.733860515 0.853337061 0.804598373 0.87142119 1 15.67526127 2.742579633 24.99697963 0.837841833 0.880074732 0.011714758 0.080936606 1057.953342 6580152.698 0.023288466 0.023895528 552.8147634 -2.742579633 0.042232899 RNEVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNEVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;; 96.948 0.019814 1480870000 805730 1474670 1285230 1288650 1161580 1629830 1215320 1273420 1139720 1384110 FALSE TRUE 837540.8426 1727933.101 1318724.15 1543541.124 964135.0465 1251326.683 1120060.043 1256351.888 1098701.7 1655299.854 0.505975301 1.043879208 0.796667834 0.932484299 0.582453411 0.755951666 0.676650844 0.758987494 0.663747838 1 20.65866115 4.807545568 22.28151705 0.782719672 0.505961984 0.268982671 0.143118921 56347.97139 18196214.06 0.032892125 156.1344696 64201.55816 -4.807545568 -0.276757688 RNGAAGPHS(ph)PDPLLDEQAFGDLTDLPVVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RNGAAGPHSPDPLLDEQAFGDLTDLPVVPK 30 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(0.991)PDPLLDEQAFGDLT(0.009)DLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK;RNGAAGPHS(1)PDPLLDEQAFGDLTDLPVVPK 173.23 5.82E-13 1213932000 567590 424496 618863 462725 828191 856389 906175 765721 888499 675632 TRUE FALSE 589998.8915 497399.8859 634991.0782 554250.6239 687415.3896 657505.6335 835146.6357 755457.7625 856522.0945 808009.1546 0.730188375 0.615586944 0.785871143 0.685945971 0.850751982 0.813735376 1.033585611 0.934961885 1.060040087 1 19.62401211 2.664232604 0.881538023 1.01857618 0.687433076 0.81878265 0.061567798 0.21644595 0.354251954 0.035758414 0.030896967 461.5647177 -2.664232604 -0.331143105 RNLDIERPTYTNLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RNLDIERPTYTNLNR 15 2 P68363;F8VQQ4;F8VVB9;C9JDS9;P68366-2;P68366;Q9BQE3;F5H5D3 P68363;P68366-2;Q9BQE3 TUBA1B;TUBA1A;TUBA4A;TUBA1C Tubulin alpha-1B chain;Tubulin alpha-4A chain;Tubulin alpha-1C chain 0 ;;; 266.42 1.48E-25 6653860000 1230299 1188776 1340029 1138596 1691000 1617880 1240636 1445413 1312606 1464891 FALSE TRUE 1278872.155 1392939.031 1374951.257 1363806.89 1403564.424 1242151.889 1143391.709 1426039.603 1265365.566 1751908.344 0.729988049 0.79509812 0.784830588 0.778469316 0.801163159 0.709027897 0.652654982 0.813992129 0.722278406 1 20.74049587 -1.194852751 4.060445086 1.000130047 0.756807217 0.702561385 0.047958702 5063556227 1004057527 6437057.968 0.011302761 0.063847993 1.194852751 -0.24332283 RNLLEDDS(ph)DEEEDFFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNLLEDDSDEEEDFFLR 17 1 O75379 O75379 VAMP4 Vesicle-associated membrane protein 4 1 RNLLEDDS(1)DEEEDFFLR;RNLLEDDS(1)DEEEDFFLR 228.15 9.34E-16 655350000 234030 240300 266370 245380 303460 350490 252730 254670 244900 269670 TRUE FALSE 243269.6851 281569.6557 273311.821 293915.4316 251877.9776 269094.0092 232920.3622 251256.5652 236086.0968 322506.6734 0.754308996 0.873066138 0.847460979 0.911346821 0.781000824 0.834382763 0.722218737 0.779074004 0.732034765 1 18.29896949 3.183792154 24.99955334 0.791433061 0.848506306 0.026847829 0.082068005 202.0921339 92245.75299 0.02217364 0.026502589 1526.835166 -3.183792154 0.057073245 RNNGVVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNNGVVDK 8 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 ; 82.287 0.033132 182700000 329570 254010 319780 237230 399390 413190 360280 332790 322450 260190 FALSE TRUE 342581.6781 297634.2416 328113.7295 284153.3859 331501.8305 317232.8845 332040.3122 328329.4944 310845.0875 311169.2489 1.100949658 0.956502748 1.054454226 0.913179522 1.065342516 1.019486616 1.067073027 1.055147627 0.998958247 1 18.24733997 RNPAGSVVMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNPAGSVVMER 11 1 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ;; 161.33 4.24E-05 456857000 403194 346845 407893 349025 434425 483324 408632 330669 384763 319851 FALSE TRUE 419112.4105 406412.9307 418523.0267 418061.1033 360581.5937 371079.3258 376602.3561 326236.9229 370915.4548 382519.6795 1.095662349 1.062462802 1.094121555 1.092913974 0.942648478 0.970092117 0.984530669 0.852863108 0.969663718 1 18.54517445 3.236663165 24.94856504 0.942656354 1.085147616 0.731198114 0.039182532 24.53735669 322630.5589 0.011816942 0.01481792 1724.499867 -3.236663165 0.142491262 RNPDELAEALDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNPDELAEALDER 13 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 209.39 6.13E-08 329650000 343760 430850 392350 403650 444410 512160 416910 429860 411680 507920 FALSE TRUE 357331.9102 504845.136 402574.9633 483490.7652 368869.3469 393218.6019 384231.5048 424098.4298 396863.7172 607437.1993 0.588261487 0.831106716 0.662743348 0.795951854 0.607255116 0.647340338 0.632545233 0.698176586 0.653341148 1 19.21237574 -1.513923014 3.980367662 1.003683519 0.683022838 0.627612957 0.073990124 0.002285963 0.000279159 0.067712282 0.015794793 0.030625063 1.513923014 -0.32066068 RNPDTQWITKPVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNPDTQWITKPVHK 14 2 P61313;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 171.08 1.85E-06 5637800000 3255300 2671300 3256500 2526300 3774100 3700600 3549300 3384700 3373500 2575700 FALSE TRUE 3383821.758 3130074.995 3341367.065 3025994.6 3132579.83 2841191.733 3271096.592 3339333.633 3252088.394 3080359.1 1.098515351 1.016139643 1.084732967 0.982351246 1.016952806 0.92235731 1.061920538 1.084072838 1.055749764 1 21.55466712 -0.395555931 6.65684518 1.000000448 1.035943729 0.04230678 0.051191765 0 0 0.050891968 0.011995352 0.402201855 0.395555931 0.035943282 RNPS(ph)PDHSYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RNPSPDHSYKR 11 2 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 RNPS(1)PDHSYKR;RNPS(0.999)PDHS(0.001)YKR;RNPS(1)PDHSYKR;RNPS(1)PDHSYKR 148.57 1.81E-05 2165120000 864609 739891 865710 654175 1039010 1010920 797820 819458 895600 766227 TRUE FALSE 898744.4309 866961.5237 888271.1138 783568.8625 862399.4513 776149.1506 735284.7837 808474.5059 863367.5309 916354.5103 0.98078246 0.946098386 0.969353131 0.855093584 0.941119885 0.846996596 0.8024021 0.882272632 0.942176332 1 19.80554632 3.749678387 24.58388384 0.8849071 0.963480041 0.241265799 0.054278979 716.2569608 1583799.952 0.013721439 0.024429208 5619.250424 -3.749678387 0.078572941 RNQKPEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNQKPEVR 8 2 C9JXB8;C9JNW5;P83731 C9JXB8 RPL24 60S ribosomal protein L24 0 ; 116.05 0.0013194 504420000 784980 701180 923660 730820 1056310 1002030 933080 932480 971540 770770 FALSE TRUE 815971.6165 821602.2106 947731.3384 875374.0147 876758.8035 769323.7184 859942.7514 919981.6308 936574.4652 921787.6242 0.885205654 0.891313996 1.028145002 0.949648261 0.951150548 0.834599747 0.932907677 0.998040771 1.016041483 1 19.81407487 1.713041147 4.248522535 1.00707739 0.925620551 0.370475604 0.047943166 0.210621472 8.822906295 0.027594513 0.013464035 51.64652988 -1.713041147 -0.081456839 RNS(ph)CNVGGGGGGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSCNVGGGGGGFK 14 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RNS(1)CNVGGGGGGFK;RNS(1)CNVGGGGGGFK 170.79 6.65E-08 538580000 509611 332905 441442 483491 686133 697588 714159 611389 624240 372561 TRUE FALSE 529730.8358 390078.8441 452946.3412 579124.0767 569504.3577 535583.759 658181.3515 603194.3305 601773.7243 445557.1948 1.188917701 0.875485456 1.016584058 1.299774941 1.278184629 1.202053889 1.477209568 1.353797756 1.350609375 1 18.76525111 3.737810449 6.704308871 1.306783913 1.010821096 0.405565859 0.13751986 0.110185054 30.36912331 0.034477994 0.057877895 5467.772662 -3.737810449 -0.295962817 RNS(ph)EGSELSCTEGSLTSSLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSEGSELSCTEGSLTSSLDSR 22 1 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 RNS(0.799)EGS(0.195)ELS(0.004)CT(0.001)EGSLTSSLDSR 69.444 0.0038224 0 15986 14214 16809 15990 16378 20542 15292 15339 15844 16855 TRUE FALSE 16617.13962 16655.14393 17247.05635 19152.77427 13594.07341 15771.43182 14093.37308 15133.40579 15273.77753 20157.41454 0.824368601 0.826253977 0.855618478 0.950160262 0.674395686 0.782413428 0.699165712 0.750761253 0.75772503 1 14.29902299 3.236984318 24.99975446 0.759156757 0.860791163 0.16672235 0.089406538 58.76013023 931928.8635 0.023548365 0.029599728 1725.775575 -3.236984318 0.101634406 RNS(ph)FSENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.74)FS(0.26)ENEK;RNS(0.882)FS(0.118)ENEK;RNS(0.796)FS(0.204)ENEK;RNS(1)FSENEK;RNS(0.998)FS(0.002)ENEK 218.4 3.25E-07 3822200000 1878730 1357390 1685880 1349370 2234830 2248780 2095260 1762590 1899590 1250500 TRUE FALSE 1952903.711 1590511.173 1729815.418 1616271.359 1854954.395 1726534.926 1931028.046 1738965.364 1831224.127 1495511.533 1.305843297 1.063523175 1.1566714 1.080748174 1.24034777 1.154477841 1.291215751 1.162789672 1.224480111 1 20.51220761 3.225604008 24.99800682 1.191736762 1.145753748 0.007156056 0.0943694 735.5701349 1419178.353 0.025090948 0.030167993 1681.140488 -3.225604008 -0.045983014 RNS(ph)FTPLSSSNTIR ddPTM_MDA-MB-175_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(1)FTPLSSSNTIR;RNS(0.999)FT(0.001)PLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(0.948)FT(0.026)PLS(0.026)SSNTIR;RNS(0.98)FT(0.02)PLSSSNTIR;RNS(1)FTPLSSSNTIR 247.9 7.47E-18 10825340000 1624440 1686080 1985970 1773020 2265530 2375830 1864410 1901650 1747440 1948560 TRUE FALSE 1688574.146 1975651.124 2037726.01 2123718.064 1880436.02 1824079.489 1718272.672 1876161.492 1684549.976 2330343.025 0.724603257 0.847794124 0.874431785 0.911332813 0.806935288 0.782751496 0.73734753 0.805100997 0.7228764 1 21.1521109 3.016912393 24.92575915 0.792634479 0.844686253 0.009387834 0.084221451 618.811028 912006.8093 0.023027092 0.027516521 1039.710411 -3.016912393 0.052051773 RNS(ph)GSSLVSSSSASSNLSHLEEDTWILWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSGSSLVSSSSASSNLSHLEEDTWILWGR 30 1 Q96CN4;Q96CN4-2 Q96CN4 EVI5L EVI5-like protein 1 RNS(0.798)GS(0.167)S(0.035)LVSSSSASSNLSHLEEDTWILWGR;RNS(0.999)GS(0.001)SLVSSSSASSNLSHLEEDTWILWGR 267.73 3.34E-59 452650000 33347 59208 63118 67038 73580 85206 72283 67142 69823 65312 TRUE FALSE 34663.56531 69376.51343 64762.90693 80297.91631 61072.89788 65418.19781 66617.26958 66242.07131 67310.08387 78108.63593 0.443786592 0.888205415 0.82913888 1.02802866 0.781896869 0.837528361 0.852879695 0.848076151 0.861749576 1 16.25319445 4.739851544 24.96633443 0.872312168 0.44378645 0.763220966 0.072890159 48.87114595 945056.7034 0.016267555 0.101642823 54935.30548 -4.739851544 -0.428525718 RNS(ph)LDGGGR ddPTM_MDA-MB-175_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 177.12 3.22E-05 4335430000 1063082 1232166 1234870 1184084 1408698 1527200 1285319 1134250 1237481 1299171 TRUE FALSE 1105053.298 1443780.926 1267051.727 1418292.281 1169248.017 1172530.945 1184572.338 1119047.234 1192944.301 1553718.683 0.711231261 0.929242173 0.815496229 0.912837244 0.752548083 0.754661032 0.762411079 0.720237998 0.767799418 1 20.56729388 3.212687953 24.99098726 0.771447507 0.846511412 0.033418797 0.092789421 425.0942218 410606.7871 0.024704574 0.029537045 1631.878997 -3.212687953 0.075063905 RNS(ph)LEGYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(1)LEGYSR;RNS(0.661)LEGYS(0.339)R 107.85 0.0028677 932250000 590250 567550 541140 513120 696490 693520 604730 620130 615880 484680 TRUE FALSE 613553.5258 665022.2976 555242.553 614613.6045 578100.8786 532460.4904 557329.6824 611818.1717 593714.5991 579643.7662 1.058501034 1.147294832 0.957903087 1.060329879 0.997338214 0.918599529 0.961503797 1.055507205 1.024274966 1 19.144807 4.237604959 24.99980925 0.999455377 1.102897938 0.459005867 0.045951143 21.61472686 565505.4673 0.011824406 0.028135277 17282.43608 -4.237604959 0.103442561 RNS(ph)LIELPDDYSCLLNQASHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSLIELPDDYSCLLNQASHFR 22 1 Q8IWV7 Q8IWV7 UBR1 E3 ubiquitin-protein ligase UBR1 1 RNS(1)LIELPDDYSCLLNQASHFR 292.27 9.51E-56 46366000 16057 12951 16179 19036 19392 17329 19672 18737 16021 14449 TRUE FALSE 16690.94276 15175.23351 16600.63803 22801.26398 16095.75477 13304.60237 18130.05724 18485.86116 15444.40734 17280.00491 0.965910765 0.878196134 0.960684798 1.319517217 0.931467025 0.769942048 1.049192829 1.069783328 0.893773319 1 14.07681601 7.999522347 0.006993581 1.346127114 0.602056554 0 0.139201791 528543.0039 285.9131955 13705.74204 16865.3808 99890076.7 -7.999522347 -0.74407056 RNS(ph)LILKPKPDPAQQTDSQNSDTEQYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNSLILKPKPDPAQQTDSQNSDTEQYFR 28 3 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 RNS(0.999)LILKPKPDPAQQTDSQNSDTEQYFR;RNS(1)LILKPKPDPAQQTDSQNSDTEQYFR;RNS(0.986)LILKPKPDPAQQT(0.014)DSQNSDTEQYFR 123.56 0.00023794 1249550000 948260 534450 798710 562900 1005520 915920 956690 731690 905510 464900 TRUE FALSE 985698.037 626237.6301 819525.0387 674239.9399 834602.0696 703211.4609 881702.138 721882.8924 872920.872 555988.254 1.77287565 1.126350468 1.473997037 1.212687382 1.501114571 1.264795535 1.585828714 1.298377955 1.570034737 1 19.08469488 -1.199597953 4.157360246 0.999808961 1.406161642 0.308845278 0.188297582 0.000290579 5.59E-05 0.158888101 0.037432807 0.063154172 1.199597953 0.40635268 RNS(ph)LPQIPMLNLEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RNSLPQIPMLNLEAR 15 1 Q14289;Q14289-2;H0YB74 Q14289 PTK2B Protein-tyrosine kinase 2-beta 1 RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR;RNS(1)LPQIPMLNLEAR 194.08 4.08E-08 1434345000 465374.6 609177 572167 581449 683221 760262 612750 569851 575501 646323 TRUE FALSE 483747.9486 713798.411 587078.1421 696457.8767 567087.3385 583702.6724 564721.0539 562213.0794 554788.8314 772957.6172 0.625840198 0.923463842 0.759521776 0.901029838 0.733659034 0.755154823 0.730597695 0.727353049 0.717748062 1 19.56002979 RNS(ph)PAFLSTDLGDEDVGLGPPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.996)PAFLS(0.003)T(0.001)DLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR;RNS(1)PAFLSTDLGDEDVGLGPPAPR 241.77 8.21E-38 1024567000 269704 335426 300557 314994 328096 412380 322615 290905 298802 357689 TRUE FALSE 280352.1222 393032.8062 308389.7623 377298.873 272326.3591 316610.9947 297327.5933 287005.8943 288048.1744 427771.3112 0.655378504 0.918791878 0.720922031 0.882010699 0.636616697 0.740140786 0.695062024 0.670933012 0.673369548 1 18.7064802 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(0.999)PPCHLPNIPGVT(0.001)SPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.999)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSK 201.98 2.13E-25 1981380000 698821 485902 666365 707687 1021621 1134725 1207315 946353 964161 559960 TRUE FALSE 726410.9927 569351.8887 683731.0193 847665.3764 847966.2273 871202.3157 1112682.496 933668.686 929461.0339 669673.4409 1.084724208 0.850193324 1.020991692 1.265789151 1.266238401 1.300936042 1.661529975 1.394214895 1.387931755 1 19.35309823 3.562217647 1.467726017 1.390824624 0.950362891 0.460634785 0.165404967 0.308284393 1.31902319 0.050913388 0.102780371 3649.367894 -3.562217647 -0.440461734 RNS(ph)PMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;RNS(1)PMAQT(1)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 172.77 2.00E-20 1169210000 236112 180890 256031 237458 411642 418399 360749 339204 367566 288315 TRUE FALSE 245433.8841 211956.4504 262703.3782 284426.4837 341671.2399 321232.1731 332472.5507 334657.5252 354337.3715 344804.8041 0.711805291 0.614714319 0.761890133 0.824891302 0.990912063 0.931634853 0.964234102 0.970570947 1.027646272 1 18.39542035 3.60608614 1.508199659 0.979339679 0.662612539 0.916804132 0.038924895 0.09714189 0.434931659 0.011469329 0.023922644 4037.254616 -3.60608614 -0.316727141 RNS(ph)PMAQTPPCHLPNIPGVTSPGTLIEDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSK 30 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.977)PMAQT(0.023)PPCHLPNIPGVTSPGTLIEDSK;RNS(0.832)PMAQT(0.168)PPCHLPNIPGVTSPGTLIEDSK 273.41 1.20E-71 348180000 206672 125593 184580 162044 201440 247860 259400 189401 214900 99256 TRUE FALSE 214831.5701 147162.6208 189390.3064 194095.8195 167199.3008 190298.2714 239067.5502 186862.3894 207165.791 118703.3128 1.809819499 1.23975159 1.595493015 1.635133973 1.408547889 1.603142042 2.013992234 1.57419692 1.745240179 1 16.85700067 2.482114115 24.93392949 1.659994372 1.527415307 0 0.27720119 717.3396916 3582362.671 0.087654618 0.075250677 303.4688475 -2.482114115 -0.132579065 RNS(ph)PSGTTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSPSGTTTK 10 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RNS(0.546)PS(0.402)GT(0.044)T(0.008)TK 94.191 0.0087622 32196000 121760 84528 112390 83662 122500 127540 143720 117680 119390 81002 TRUE FALSE 126567.1788 99045.02646 115318.9757 100210.0939 101677.4938 97920.76789 132454.8509 116102.6921 115093.1772 96872.79102 1.306529702 1.022423587 1.190416571 1.034450364 1.049598062 1.010818072 1.367307058 1.198506731 1.188085695 1 16.56380389 2.264140599 24.99998945 1.210115853 1.097254473 0.100393744 0.118844288 377.0025273 368453.3586 0.039060586 0.032670054 183.7133004 -2.264140599 -0.11286138 RNS(ph)RDGDPLPSSLSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RNSRDGDPLPSSLSCK 16 2 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 RNS(0.999)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK;RNS(1)RDGDPLPSSLSCK 194.77 8.31E-11 3228459000 2067020 1741330 2237190 1366361 2854050 2552850 1808120 2034020 2393690 2116300 TRUE FALSE 2148627.546 2040389.882 2295493.009 1636623.128 2368919.6 1959989.276 1666394.83 2006757.289 2307541.564 2530948.466 0.848941642 0.806175989 0.906969478 0.646644193 0.93598097 0.774409002 0.658407254 0.792887455 0.911729968 1 21.2712467 1.062237563 3.439637187 0.997601535 0.792582814 0.366179562 0.087632609 0.212466018 5.13161689 0.080905493 0.021097457 11.54084378 -1.062237563 -0.205018721 RNS(ph)RTEEPTVASESVENGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNSRTEEPTVASESVENGHR 20 2 Q14686;A0A0D9SFT8;F6M2K2 Q14686 NCOA6 Nuclear receptor coactivator 6 1 RNS(0.491)RT(0.491)EEPT(0.017)VASESVENGHR;RNS(0.497)RT(0.497)EEPT(0.005)VASESVENGHR;RNS(0.493)RT(0.493)EEPT(0.013)VASESVENGHR 207.17 3.61E-22 793441000 250783 317998 352204 311285 375864 460960 308823 365929 335691 379442 TRUE FALSE 260684.1065 372611.6828 361382.7256 372856.2439 311974.7715 353909.0259 284616.6463 361024.3203 323609.5465 453786.395 0.57446435 0.821116911 0.796371882 0.821655845 0.687492562 0.77990224 0.627204009 0.795582072 0.713131883 1 18.79165383 -1.815360699 2.362315137 1.094743632 0.74130738 0.491879472 0.080522615 8535858.005 5167488.952 4607489.041 0.021118102 0.015298164 1.815360699 -0.353436251 RNS(ph)S(ph)SPVSPASVPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.973)S(0.721)S(0.306)PVSPASVPGQR 87.352 0.022743 219570000 103340 111550 106200 96579 114960 136250 112250 118770 106370 99890 TRUE FALSE 107419.943 130707.8448 108967.6592 115682.0379 95419.14026 104608.0024 103451.5517 117178.0824 102541.7645 119461.533 0.899201109 1.0941417 0.91215688 0.968362242 0.798743645 0.875662649 0.865982121 0.980885474 0.858366387 1 16.86618661 4.044128649 24.99244352 0.90536136 0.998291162 0.19167478 0.07324223 188.6282616 106828.1053 0.017446878 0.037689538 11069.51643 -4.044128649 0.092929802 RNS(ph)SEASSGDFLDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(0.999)S(0.001)EASSGDFLDLK;RNS(0.948)S(0.052)EASSGDFLDLK;RNS(0.978)S(0.004)EAS(0.015)S(0.003)GDFLDLK;RNS(0.859)S(0.126)EAS(0.008)S(0.008)GDFLDLK;RNS(1)SEASSGDFLDLK;RNS(0.998)S(0.002)EASSGDFLDLK;RNS(0.912)S(0.087)EASSGDFLDLK;RNS(0.529)S(0.387)EAS(0.042)S(0.042)GDFLDLK;RNS(0.492)S(0.492)EAS(0.013)S(0.003)GDFLDLK;RNS(0.994)S(0.006)EASSGDFLDLK;RNS(1)SEASSGDFLDLK 282.18 5.10E-34 26161159000 10385548 6122735 8328910 7408606 9923213 10847465 13167972 8920345 9204056 4296665.4 TRUE FALSE 10795577.45 7174267.108 8545968.237 8874006.154 8236468.799 8328305.649 12135831.95 8800782.366 8872803.822 5138514.721 2.100913988 1.396175257 1.663120318 1.726959372 1.602889015 1.620761271 2.361739259 1.712709381 1.726725388 1 22.29291998 0.61403406 3.025428165 1.000019346 1.769270328 0.444385441 0.258087535 5.952101511 45.53909427 0.244851297 0.06394487 4.111819671 -0.61403406 0.769250982 RNS(ph)SIVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.995)S(0.005)IVGR;RNS(0.999)S(0.001)IVGR 129.82 0.00065807 473390000 167883 183411 151510 165721 210115 209330 155037 165289 180518 178588 TRUE FALSE 174511.1505 214910.4125 155458.4751 198500.1192 174399.7274 160716.2799 142884.7948 163073.5713 174021.1924 213578.8993 0.817080484 1.006234292 0.727873753 0.929399486 0.816558789 0.752491376 0.669002393 0.763528475 0.814786447 1 17.7044096 3.010602564 9.00436895 0.773990766 0.870205531 0.066258472 0.104607798 0.293847732 190.863192 0.028796213 0.033767172 1024.71375 -3.010602564 0.096214765 RNS(ph)SS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 RNS(0.68)S(0.348)S(0.887)PVS(0.085)PASVPGQR;RNS(0.983)S(0.018)S(0.839)PVS(0.161)PASVPGQR;RNS(0.931)S(0.092)S(0.916)PVS(0.062)PASVPGQR 208.86 9.19E-12 268905000 460733 489680 512838 470099 611930 689920 578890 536536 577260 513230 TRUE FALSE 478923.0946 573778.7308 526202.9796 563083.1791 507914.3572 529696.5358 533515.0892 529344.6125 556484.5254 613787.5921 0.780274969 0.934816438 0.857304687 0.917390945 0.827508349 0.862996487 0.869217782 0.862423124 0.906640233 1 19.22737996 0.868281968 2.655450955 0.999934344 0.866596562 0.509884062 0.040464535 0.383561868 5.34932314 0.034919038 0.009292495 7.383834743 -0.868281968 -0.133337782 RNS(ph)SSPVSPASVPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.333)S(0.333)S(0.333)PVSPASVPGQR;RNS(0.333)S(0.333)S(0.333)PVSPASVPGQR 155.88 1.33E-07 849310000 219783 287092 247007 220968 281476 355536 193810 249523 277805 351127 TRUE FALSE 228460.2025 336397.8177 253444.2053 264674.8109 233630.8101 272968.1522 178618.6658 246178.5523 267806.8523 419923.6129 0.544051812 0.801092883 0.603548354 0.630292755 0.556365022 0.650042398 0.425359899 0.586246033 0.637751353 1 18.67976739 0.773904602 4.255201358 0.999994912 0.598912753 0.641589548 0.089224457 2.094008 38.89547787 0.086183316 0.021940867 5.941616299 -0.773904602 -0.401082159 RNS(ph)SSSSSPSERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RNSSSSSSPSERPR 14 2 G3V1D0;B7WPE2;H0Y3M3;Q32P44;Q32P44-2 G3V1D0 EML3 Echinoderm microtubule-associated protein-like 3 1 RNS(0.952)S(0.038)S(0.009)S(0.001)SSPSERPR;RNS(0.819)S(0.061)S(0.019)S(0.019)S(0.041)S(0.041)PSERPR;RNS(0.944)S(0.051)S(0.003)SS(0.001)S(0.001)PSERPR;RNS(0.974)S(0.025)S(0.001)SSSPSERPR 167.19 2.90E-06 1544030000 265119 365490 317727 382429 414841 453948 303372 338186 354724 381401 TRUE FALSE 275586.1028 428260.0644 326007.2266 458072.3148 344326.475 348525.4566 279592.9099 333653.1698 341957.5525 456129.2236 0.604184272 0.938900737 0.714725586 1.004259958 0.754887995 0.764093679 0.61296864 0.731488255 0.749694461 1 18.79908308 3.029532623 24.99959107 0.742094338 0.824936593 0.003869303 0.13779178 547.3763733 463354.6923 0.037110291 0.04435475 1070.366782 -3.029532623 0.082842255 RNS(ph)TDSRPVSVTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.781)T(0.216)DS(0.003)RPVSVTYR;RNS(0.723)T(0.244)DS(0.031)RPVSVT(0.001)YR;RNS(0.776)T(0.224)DSRPVSVTYR;RNS(0.995)T(0.005)DSRPVSVTYR;RNS(0.945)T(0.054)DS(0.001)RPVSVTYR 167.14 1.93E-06 2369860000 499549 545331 532030 493057 590236 689637 583136 554069 541210 517091 TRUE FALSE 519271.5803 638987.3572 545895.1389 590582.203 489907.8955 529479.2583 537428.2766 546642.6113 521731.9578 618405.0811 0.83969488 1.033282838 0.882746852 0.955008652 0.792211951 0.856201339 0.869055402 0.883955562 0.843673465 1 19.23819265 3.280555796 24.99982989 0.86840729 0.932016409 0.125714429 0.067719724 243.4335266 144914.9096 0.017222614 0.023319346 1907.900826 -3.280555796 0.06360912 RNS(ph)TIPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSTIPTK 8 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 1 RNS(0.899)T(0.101)IPTK 65.842 0.038727 93234000 194000 194750 193830 170310 282450 249210 211960 212400 248720 157740 TRUE FALSE 201659.2698 228196.7976 198881.369 203996.8097 234439.2499 191334.7543 195346.0213 209553.1254 239768.6158 188646.1329 1.068981732 1.209655316 1.054256273 1.081372868 1.242746121 1.014252195 1.035515642 1.11082651 1.270996718 1 17.525323 4.214943716 24.99316018 1.103287019 1.139318768 0.026615775 0.091432699 966.80305 1023144.193 0.022231101 0.048064925 16403.77169 -4.214943716 0.03603175 RNS(ph)TIVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.981)T(0.019)IVLR;RNS(1)TIVLR;RNS(0.976)T(0.024)IVLR;RNS(0.986)T(0.014)IVLR 163.9 0.00020411 1082930000 266142 315041 293324 318342 366310 362955 305389 325098 304312 298681 TRUE FALSE 276649.4917 369146.8411 300968.2644 381309.0974 304044.757 278664.2019 281451.8122 320740.5931 293359.8706 357201.8234 0.774490704 1.033440528 0.842572027 1.067489225 0.851184785 0.780130961 0.787934982 0.897925408 0.821272041 1 18.44637992 3.048136298 24.99999754 0.845990402 0.934291581 0.111710719 0.098110152 203.4614878 105668.0903 0.026305575 0.031441169 1117.213816 -3.048136298 0.088301178 RNS(ph)TTFPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RNS(0.956)T(0.044)TFPSR;RNS(0.968)T(0.031)TFPSR;RNS(0.928)T(0.063)T(0.01)FPSR 132.9 0.00017886 2582980000 259897 276904 270836 242537 350088 355498 328966 295952 285324 346240 TRUE FALSE 270157.9342 324460.108 277894.2087 290510.0947 290580.1668 272938.9771 303180.7853 291985.2475 275055.245 414079.0988 0.652430743 0.783570359 0.671113827 0.70158116 0.701750384 0.659146955 0.732180847 0.705143651 0.664257737 1 18.65954686 -1.677244939 2.940239586 1.033760932 0.69977278 0.854429685 0.037526957 17586289.92 18627601.5 4486689.607 0.00854285 0.021025923 1.677244939 -0.333988153 RNS(ph)TTIMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSTTIMSR 9 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RNS(0.959)T(0.038)T(0.003)IMSR;RNS(0.974)T(0.023)T(0.002)IMSR 63.662 0.032014 286790000 205990 207570 200750 214470 246090 265330 222960 221500 208359 225940 TRUE FALSE 214122.6443 243218.5328 205981.7099 256891.5259 204259.7097 203711.1286 205483.8126 218531.1548 200860.2003 270208.6171 0.792434551 0.900113902 0.762306221 0.95071552 0.755933367 0.753903154 0.760463581 0.808749762 0.743352312 1 18.04371416 5.075348534 14.33822843 0.816238527 0.506211944 0.00175099 0.08820309 1784709.541 7349321.177 0.01959672 16500787.98 118945.6417 -5.075348534 -0.310026584 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;RNS(1)VERPAEPVAGAATPSLVEQQK 222.72 4.29E-33 3303133000 1284253 926357 1224806 934198 1498190 1498460 1418613 1260236 1337578 947106 TRUE FALSE 1334956.3 1085451.609 1256725.451 1118979.576 1243528.199 1150465.374 1307418.406 1243344.598 1289438.829 1132673.287 1.17858902 0.958309533 1.109521576 0.987910273 1.097870156 1.015708049 1.154276719 1.097708061 1.138403142 1 20.11130035 2.244577023 24.99983908 1.106612305 1.05442443 0.062781936 0.070872611 302.1333766 1255449.575 0.022509363 0.018376161 175.6212336 -2.244577023 -0.052187875 RNS(ph)VTPLASPEPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSVTPLASPEPTK 14 1 Q5W015;Q5VX20;A0A1W2PR17;Q16875-3;Q16875-2;Q16875;Q16875-4;Q9H178 Q5W015 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 RNS(0.988)VT(0.012)PLASPEPTK 141.6 5.90E-06 182430000 333890 217340 306240 276960 439330 375620 433310 357030 365730 248910 TRUE FALSE 347072.235 254666.4543 314220.866 331741.8614 364652.8435 288387.9476 399346.03 352244.5968 352567.4487 297679.1488 1.165927262 0.855506525 1.055568948 1.114427607 1.22498618 0.968787867 1.341531752 1.183302889 1.184387452 1 18.18339864 3.720884988 2.899644158 1.16542128 1.002662428 0.160956915 0.123115201 0.364623892 6.158294744 0.032101464 0.058508731 5258.779829 -3.720884988 -0.162758852 RNSFS(ph)ENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 RNS(0.382)FS(0.618)ENEK 196.75 1.78E-05 871240000 645870 459200 569600 428710 732720 749970 711100 589280 605220 421090 TRUE FALSE 671369.4463 538064.0279 584444.2439 513507.5584 608172.5161 575800.8334 655362.1239 581381.6655 583438.2504 503594.5232 1.333154781 1.068446941 1.160545274 1.019684557 1.207663086 1.143381842 1.301368648 1.154463837 1.158547648 1 18.94190307 0.620349482 2.824258829 1.000008582 1.169842265 0.25201561 0.089018038 6.819897464 49.05060698 0.081456899 0.021428056 4.172049783 -0.620349482 0.169833682 RNSFT(ph)PLSSSNTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.248)FT(0.75)PLS(0.002)S(0.001)SNTIR;RNS(0.029)FT(0.969)PLSS(0.002)SNTIR 300.3 1.54E-43 1548350000 1063030 1208210 1221710 1173230 1546970 1607630 1247590 1312030 1258550 1356430 TRUE FALSE 1104999.245 1415710.669 1253548.766 1405291.392 1284016.592 1234282.296 1149800.636 1294444.384 1213255.031 1622196.488 0.681174724 0.872712202 0.772747799 0.866289258 0.791529634 0.76087102 0.708792458 0.797957827 0.747908802 1 20.62951715 -1.108327978 5.063080785 1.000006691 0.781171787 0.574498534 0.057307398 4.10E-06 7.22E-07 0.052523758 0.01237959 0.077924141 1.108327978 -0.218834904 RNSGS(ph)SLVSSSSASSNLSHLEEDSWILWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSGSSLVSSSSASSNLSHLEEDSWILWGR 30 1 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 RNS(0.422)GS(0.527)S(0.051)LVSSSSASSNLSHLEEDSWILWGR 125.62 6.59E-06 60174000 18768 27967 24783 23805 37199 31596 25835 28637 30377 27839 TRUE FALSE 19508.97513 32770.1147 25428.86534 28513.55795 30875.92727 24258.30784 23809.98519 28253.16786 29283.7377 33293.51904 0.585969152 0.984279092 0.763778239 0.856429683 0.927385514 0.728619519 0.715153756 0.848608638 0.879562706 1 15.02295375 0.95547102 1.990806295 0.998384749 0.805714112 0.251077469 0.107072733 0.513147486 4.333131472 0.095156668 0.026594957 9.025494784 -0.95547102 -0.192670637 RNSLEGYS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 RNS(0.059)LEGYS(0.941)R;RNS(0.007)LEGYS(0.993)R 117.83 0.0011522 568570000 453940 519680 528450 529050 641020 694630 634150 635870 569960 558070 TRUE FALSE 471861.9017 608930.9975 542221.8411 633694.5109 532059.6494 533312.7097 584443.666 627347.2027 549447.2509 667413.1316 0.707001225 0.912374912 0.812423094 0.949478638 0.797196855 0.799074343 0.875684997 0.939968324 0.823249087 1 19.34822055 -4.999999983 0.104250642 1.467769586 0.760940393 0.340339332 0.068745687 207.2226099 1.456789762 20.89526684 0.981284535 1.00E-05 4.999999983 -0.706829193 RNSNS(ph)PPSPSSMNQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSNSPPSPSSMNQR 15 1 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RNS(0.059)NS(0.941)PPSPSSMNQR 112.43 0.00046819 129220000 61415 83996 88676 60043 107040 103270 59205 83111 84251 97385 TRUE FALSE 63839.71162 98421.6596 90986.96941 71919.32619 88845.37903 79287.10757 54564.3574 81997.03299 81218.82297 116465.7262 0.548141618 0.845069728 0.781233865 0.617514942 0.762845705 0.680776312 0.468501414 0.70404432 0.69736244 1 16.82954593 -1.976480363 6.149945333 1.229616875 0.679632625 0.455522671 0.105476599 0.048952901 0.000187214 0.015055239 0.023806376 0.010556492 1.976480363 -0.54998425 RNSPMAQT(ph)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 44 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 RNS(0.467)PMAQT(0.533)PPCHLPNIPGVTSPGTLIEDSKVEVNNLNNLNNHDR 55.767 0.010886 36528000 10985 10933 11542 8123.1 13602 18580 11607 13945 13853 6057.4 TRUE FALSE 11418.69628 12810.6577 11842.794 9729.824935 11289.9369 14265.07658 10697.21301 13758.09008 13354.43324 7244.231554 1.576246728 1.768394288 1.634789544 1.343113464 1.558472671 1.96916353 1.476652552 1.899178675 1.843457534 1 12.82261695 RNSSEAS(ph)SGDFLDLK ddPTM_MDA-MB-175_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(0.124)S(0.007)EAS(0.847)S(0.022)GDFLDLK 182.79 5.64E-07 142600000 336360 179280 251560 218050 322620 311390 393660 266880 281950 134890 TRUE FALSE 349639.7525 210069.9454 258115.8603 261179.6392 267781.1676 239074.3917 362803.9006 263302.9101 271802.6746 161319.1129 2.167379589 1.302201219 1.600032728 1.619024767 1.659946939 1.481996692 2.24898274 1.632186698 1.684875832 1 17.29955785 RNSSS(ph)PVSPASVPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RNS(0.133)S(0.133)S(0.653)PVS(0.071)PAS(0.01)VPGQR 142.13 1.63E-06 77860000 74536 91140 88169 75520 97528 102700 69375 81162 87852 110000 TRUE FALSE 77478.73883 106792.586 90466.75657 90457.6306 80950.2254 78849.48143 63937.20622 80074.15614 84690.22368 131552.3939 0.58895727 0.811787478 0.687686129 0.687616758 0.615345894 0.599377017 0.486020849 0.608686423 0.643775618 1 17.00527798 -1.381668195 9.1192299 1.00000084 0.634453359 0.651518206 0.079721925 1.47E-06 9.97E-08 0.083388026 0.019654701 0.041527119 1.381668195 -0.365547481 RNST(ph)DSRPVSVTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RNSTDSRPVSVTYR 14 2 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 RNS(0.348)T(0.649)DS(0.002)RPVSVTYR 144.3 1.43E-05 1129300000 261710 262650 237770 260640 280750 317170 296680 244420 272610 271020 TRUE FALSE 272042.5129 307758.0944 243966.4815 312193.8141 233028.2153 243512.0743 273425.4464 241143.9497 262798.8194 324121.18 0.839323468 0.949515531 0.752701448 0.963200905 0.718953989 0.751299481 0.843590186 0.743993187 0.810804216 1 18.30617377 3.231841266 24.9999944 0.794663237 0.872602932 0.089539565 0.091980858 290.702092 1081583.965 0.024345818 0.029724949 1705.458934 -3.231841266 0.077939695 RNSTIPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RNSTIPTK 8 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1;Q53FA3 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 ;;; 109.79 0.0056931 2022007000 2221238 2060260 2406980 2159130 3278200 3203230 2869750 2668020 2648640 2228880 FALSE TRUE 2308934.191 2414093.628 2469707.876 2586199.47 2720972.735 2459328.378 2644811.496 2632259.556 2553315.964 2665586.362 0.866201232 0.905652003 0.926515798 0.97021785 1.020778308 0.922621909 0.992206268 0.987497383 0.957881538 1 21.34602149 4.131906415 1.479831085 0.979624588 0.869461237 0.694160634 0.025470608 0.264344729 1.020283064 0.007112159 0.030960315 13548.97419 -4.131906415 -0.110163351 RNT(ph)IDSTSSFSQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RNTIDSTSSFSQFR 14 1 Q8TDN4-2;Q8TDN4;Q8TDN4-4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 RNT(0.324)IDS(0.211)T(0.211)S(0.211)S(0.039)FS(0.004)QFR;RNT(1)IDSTSSFSQFR 141.18 5.71E-06 633940000 267990 264532 309230 288440 384890 424420 357520 319020 354230 350970 TRUE FALSE 278570.4521 309963.3132 317288.7878 345492.5711 319466.5353 325854.8871 329496.6482 314744.0587 341481.3315 419735.8518 0.663680386 0.738472332 0.755924914 0.823119039 0.76111329 0.776333224 0.785009541 0.749862223 0.813562459 1 18.67912217 -5 0.204231432 2.10019009 0.726730675 0.813121189 0.035667256 62.00850923 0.615871967 27.86523877 0.085091035 1.00E-05 5 -1.373459415 RPAAAAAAGSAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 RPAAAAAAGS(0.001)AS(0.999)PR;RPAAAAAAGS(0.018)AS(0.982)PR;RPAAAAAAGS(0.15)AS(0.85)PR;RPAAAAAAGS(0.001)AS(0.999)PR;RPAAAAAAGS(0.002)AS(0.998)PR 184.44 1.37E-06 1648990000 615768 686407 599799 705456 636322 709093 642291 592294 547594 616830 TRUE FALSE 640078.9961 804292.0627 615430.2547 844993.0912 528160.2137 544416.8972 591946.5531 584355.2677 527886.1989 737686.0286 0.867684857 1.090290492 0.834271263 1.14546441 0.715968845 0.738006247 0.802436986 0.792146313 0.715597393 1 19.49264739 3.21987029 24.99990506 0.782477025 0.981263972 0.394888916 0.114907684 213.941008 286163.6833 0.03019254 0.036145197 1659.091315 -3.21987029 0.198786947 RPAEAT(ph)SSPTS(ph)PERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.489)S(0.243)S(0.268)PT(0.32)S(0.679)PERPR 123.48 9.68E-05 623630000 293050 330700 308790 285090 307200 343880 287070 315640 285370 329490 TRUE FALSE 304619.8403 387495.1525 316837.3211 341479.9511 254982.2537 264019.0816 264568.7033 311409.3621 275099.5894 394047.257 0.773054081 0.983372287 0.804059197 0.866596442 0.647085468 0.670018829 0.67141364 0.790284304 0.698138572 1 18.58800913 3.263222147 24.77603149 0.731076024 0.862048481 0.192119491 0.108293822 275.9562322 277235.3516 0.027987973 0.037878116 1833.251915 -3.263222147 0.130972456 RPAEAT(ph)SSPTSPERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.241)S(0.241)S(0.241)PT(0.138)S(0.138)PERPR 130.73 7.78E-05 453290000 53860 58978 65913 64406 67537 75178 56768 68552 71568 74186 TRUE FALSE 55986.43439 69107.01271 67630.74693 77145.31457 56057.08486 57719.04883 52318.37582 67633.17257 68992.28166 88721.32632 0.631036941 0.778922223 0.762282866 0.86952391 0.63183326 0.650565667 0.589693346 0.762310206 0.777629061 1 16.43699331 0.780590493 1.836735106 0.999327609 0.709667044 0.540475961 0.080828944 0.635250288 3.630845572 0.080382045 0.022566456 6.033794195 -0.780590493 -0.289660565 RPAEATS(ph)SPT(ph)SPERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.305)S(0.344)S(0.305)PT(0.551)S(0.495)PERPR 69.398 0.051122 89601000 30365 35224 33063 33521 33504 41261 30935 28901 31037 41804 TRUE FALSE 31563.83365 41273.448 33924.64894 40151.35375 27809.00205 31678.75807 28510.23387 28513.62937 29919.98443 49994.69341 0.631343679 0.825556578 0.678564996 0.803112311 0.556239076 0.633642411 0.570265201 0.570333118 0.598463205 1 15.60948735 -1.166722131 4.414501772 1.000073488 0.649469658 0.577059999 0.089368785 6.90E-05 1.30E-05 0.092355668 0.021763889 0.068120507 1.166722131 -0.35060383 RPAEATSS(ph)PTS(ph)PERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 2 RPAEAT(0.166)S(0.236)S(0.596)PT(0.364)S(0.638)PERPR;RPAEAT(0.014)S(0.049)S(0.924)PT(0.051)S(0.962)PERPR;RPAEAT(0.027)S(0.033)S(0.935)PT(0.375)S(0.629)PERPR 154.95 1.51E-06 13316350000 1300930 1536740 1318340 1381460 1504720 1684880 1284300 1449870 1387900 1594610 TRUE FALSE 1352291.721 1800663.141 1352697.023 1654708.665 1248948.232 1293592.155 1183633.21 1430436.864 1337949.75 1907043.299 0.709103837 0.94421723 0.709316366 0.867682798 0.654913411 0.678323432 0.620664046 0.750080958 0.70158331 1 20.86290617 5.067965767 15.80046288 0.754169305 0.175081444 0.007685908 0.12151462 14077520.15 64529588.04 0.02775634 268123856.7 116940.721 -5.067965767 -0.57908786 RPAEATSSPT(ph)SPERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.003)S(0.065)S(0.123)PT(0.575)S(0.233)PERPR;RPAEAT(0.005)S(0.013)S(0.413)PT(0.475)S(0.093)PERPR;RPAEATSS(0.015)PT(0.924)S(0.061)PERPR;RPAEAT(0.001)S(0.004)S(0.02)PT(0.821)S(0.154)PERPR 195.09 1.74E-10 12153900000 699680 845900 765810 880850 970180 909360 930920 946080 797583 1015850 TRUE FALSE 727303.9067 991176.7448 785767.6377 1055079.501 805269.1501 698174.9215 857952.0579 933399.3451 768878.1436 1214886.358 0.598660033 0.815859639 0.646782831 0.868459419 0.66283496 0.574683317 0.706199434 0.768301775 0.632880712 1 20.21238994 -1.674100034 2.851950093 1.034692762 0.704796114 0.501093655 0.090359303 15409255.63 15635679.12 3918746.935 0.02147504 0.021178733 1.674100034 -0.329896649 RPAEATSSPTS(ph)PERPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 RPAEAT(0.035)S(0.035)S(0.035)PT(0.282)S(0.612)PERPR 59.512 0.052767 128730000 17265 22384 24386 18706 20108 29377 24250 20262 23426 25723 TRUE FALSE 17946.63553 26228.27788 25021.51919 22405.99097 16690.04934 22554.63696 22349.22163 19990.42103 22582.90284 30762.92935 0.58338513 0.852593639 0.813365948 0.728343868 0.542537713 0.733175853 0.726498487 0.649821764 0.734094682 1 14.90890527 -1.19675067 5.254815147 1.000017578 0.707660289 0.489993545 0.089647614 1.85E-05 2.82E-06 0.086751702 0.020446344 0.063569578 1.19675067 -0.292357288 RPAEDMEEEQAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPAEDMEEEQAFK 13 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;; 218.11 3.96E-11 1868850000 1308840 1017090 1186150 1112100 1429720 1608750 1703700 1304060 1355260 894050 FALSE TRUE 1360514.014 1191767.296 1217062.043 1332070.061 1186696.705 1235142.193 1570159.542 1286581.209 1306484.457 1069221.98 1.272433638 1.114611669 1.138268822 1.245831161 1.109869351 1.155178454 1.468506607 1.203287281 1.221901983 1 20.02812997 RPAEDMEEEQAFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RPAEDMEEEQAFKR 14 2 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;;;; 254.18 1.69E-24 13944430000 7625610 6308260 7933270 5897320 9908800 9357780 8541130 7968390 8270250 6765780 FALSE TRUE 7926674.971 7391654.584 8140017.533 7063792.294 8224505.715 7184577.414 7871653.913 7861586.766 7972605.318 8091405.052 0.97964135 0.913519288 1.006007916 0.872999467 1.016449635 0.887927049 0.972841412 0.971597234 0.985317787 1 22.94795881 1.629606443 1.864944527 0.99190529 0.947101381 0.135416246 0.044737819 0.603389356 4.354907926 0.031361578 0.011540471 42.61931278 -1.629606443 -0.044803909 RPAEDYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPAEDYVPR 9 1 Q969E4;Q5H9L2 Q969E4 TCEAL3;TCEAL5 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5 0 ;; 111.61 0.003363 923290000 467960 494250 483300 484080 557290 583450 481540 462450 494550 583630 FALSE TRUE 486435.4221 579133.5928 495895.195 579829.5792 462562.0449 447952.5798 443795.6365 456251.6142 476751.2421 697981.1242 0.696917732 0.829726726 0.710470782 0.830723868 0.662714261 0.641783229 0.635827562 0.653673285 0.683043173 1 19.4128285 -1.177859333 4.412827351 1.000070016 0.702721813 0.634007748 0.067223858 5.00E-05 9.31E-06 0.07024616 0.016553289 0.066395809 1.177859333 -0.297348203 RPAEEQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPAEEQKR 8 2 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 98.033 0.0043924 83583000 105626 94771 96455 90304 122737 127047 124131 96795 115977 96998 FALSE TRUE 109796.196 111047.182 98968.69654 108165.8617 101874.2086 97542.25967 114401.2879 95497.62135 111803.0104 116002.901 0.946495261 0.957279353 0.853157082 0.932441006 0.878203974 0.84086052 0.986193336 0.823234769 0.963794953 1 16.82380136 1.009728428 24.94254808 1.000000026 0.900491453 0.293448561 0.050959318 173.2370118 444157.409 0.046160942 0.011540236 10.2265331 -1.009728428 -0.099508572 RPAETNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPAETNLR 8 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ;;;;; 197.66 0.00022807 4399890000 1041120 1467986 1180048 1232542 1559180 1647530 1343249 1283499 1196699 1859390 FALSE TRUE 1082224.222 1720101.176 1210801.02 1476335.129 1294151.141 1264916.126 1237961.633 1266295.795 1153630.037 2223701.87 0.48667685 0.77353048 0.54449791 0.66390875 0.581980506 0.568833504 0.556712053 0.569453942 0.518788086 1 21.08453195 -1.886349219 2.624014391 1.207092717 0.588461119 0.724607732 0.076737648 8871724.264 5390054.253 11391435.96 0.017321914 0.012991245 1.886349219 -0.618631598 RPAGGRPS(ph)PSAMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RPAGGRPSPSAMGK 14 2 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 RPAGGRPS(1)PSAMGK;RPAGGRPS(1)PSAMGK;RPAGGRPS(0.995)PS(0.005)AMGK;RPAGGRPS(0.998)PS(0.002)AMGK;RPAGGRPS(1)PSAMGK;RPAGGRPS(0.953)PS(0.047)AMGK;RPAGGRPS(0.999)PS(0.001)AMGK;RPAGGRPS(0.995)PS(0.005)AMGK 113.33 0.00042669 2367587000 2883258 3491130 3259340 3091970 3579399 4163610 3591031 3056540 3160889 4017110 TRUE FALSE 2997091.252 4090704.42 3344281.078 3703552.437 2970974.037 3196674.678 3309556.607 3015572.081 3047129.222 4804185.792 0.623849989 0.851487556 0.696118182 0.770901168 0.618413643 0.665393641 0.68889022 0.627696807 0.634265483 1 22.19586051 -0.996652039 4.551647081 1.000007195 0.687109489 0.640761165 0.070455901 12965924.76 43015162.2 1836.386921 0.017077278 0.100773876 0.996652039 -0.312897706 RPAPAVS(ph)PGSWKPGPPGS(ph)PRPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPAPAVSPGSWKPGPPGSPRPWK 23 3 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 RPAPAVS(0.984)PGS(0.024)WKPGPPGS(0.991)PRPWK;RPAPAVS(0.999)PGS(0.001)WKPGPPGS(1)PRPWK 130.41 4.99E-05 3130200000 2231800 1393730 1646540 1158140 2335600 2138100 2082700 1718180 2118920 1437110 TRUE FALSE 2319913.187 1633092.286 1689450.185 1387216.635 1938595.546 1641558.678 1919452.532 1695150.607 2042660.483 1718684.189 1.349819357 0.950199167 0.982990473 0.807138766 1.127953325 0.955125257 1.116815145 0.98630721 1.188502516 1 20.71287304 2.231052012 24.99470445 1.064217852 1.017634579 0.017240402 0.143139013 881.7776306 2935249.085 0.051652581 0.038916576 170.2362374 -2.231052012 -0.046583273 RPAS(ph)PS(ph)SPEHLPATPAESPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.999)PS(0.537)S(0.464)PEHLPATPAESPAQR 98.967 0.0037775 383850000 28531 37880 29899 33937 36522 42622 30132 39648 30880 34401 TRUE FALSE 29657.42591 44385.59533 30678.1925 40649.63731 30314.00349 32723.68644 27770.1751 39116.58341 29768.63483 41141.2173 0.720868945 1.078859554 0.745680233 0.988051399 0.736828064 0.795399081 0.674996437 0.950788187 0.723572047 1 15.32829686 5.036769548 16.96692873 0.848268982 0.18504314 0.081587521 0.133249796 34114777.22 413834784.1 0.029361016 695372062.3 108835.2422 -5.036769548 -0.663225842 RPAS(ph)PSHNGSSGGGYGASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPASPSHNGSSGGGYGASK 19 1 K7ELX9;K7EQ79;K7ENM4;K7ENP7;Q6PI98;Q6PI98-3;Q6PI98-4 K7ELX9 INO80C INO80 complex subunit C 1 RPAS(0.878)PS(0.119)HNGS(0.004)SGGGYGASK;RPAS(0.927)PS(0.065)HNGS(0.007)S(0.001)GGGYGASK 147.11 6.66E-08 121744000 47107 65370 73408 72626 100767 86509 90004 80679 76768 67257 TRUE FALSE 48966.82073 76596.78899 75321.07279 86991.20603 83638.66133 66418.59581 82949.2513 79597.62997 74005.13468 80434.72144 0.608777153 0.952285128 0.93642486 1.081513114 1.039832797 0.825745333 1.031261746 0.989592909 0.920064536 1 16.29553079 4.758091466 3.444566169 0.980268568 0.553507603 0.72331739 0.068113957 0.173739908 3.3969846 0.01640777 0.198654142 57291.66796 -4.758091466 -0.426760965 RPAS(ph)PSS(ph)PEHLPATPAESPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.991)PS(0.08)S(0.929)PEHLPATPAESPAQR;RPAS(0.955)PS(0.259)S(0.785)PEHLPAT(0.001)PAESPAQR;RPAS(0.791)PS(0.382)S(0.827)PEHLPATPAESPAQR;RPAS(0.867)PS(0.343)S(0.787)PEHLPAT(0.002)PAESPAQR 177.35 2.24E-16 4966440000 537097 729109 650385 701116 722943 802267 638514 683094 641683 730766 TRUE FALSE 558302.0043 854327.7991 667334.5674 839794.6522 600057.4071 615952.6477 588465.6042 673938.2422 618588.9542 873945.6063 0.638829236 0.977552599 0.763588217 0.96092325 0.68660727 0.704795176 0.673343512 0.771144379 0.707811733 1 19.73718396 5.020911258 17.58968429 0.78909665 0.288333824 0.132267429 0.121700473 19499571.5 384398790.2 0.02807167 270323099.2 104932.7991 -5.020911258 -0.500762826 RPAS(ph)PSSPEHLPATPAESPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 1 RPAS(0.905)PS(0.09)S(0.006)PEHLPATPAESPAQR;RPAS(0.734)PS(0.118)S(0.148)PEHLPATPAESPAQR;RPAS(0.868)PS(0.056)S(0.076)PEHLPATPAESPAQR 171.25 2.93E-12 1408870000 304694 544248 543459 531654 579020 726168 516633 588633 504800 610873 TRUE FALSE 316723.5544 637718.3603 557621.988 636813.5744 480598.3872 557526.4872 476137.9555 580743.3374 486632.3466 730561.8685 0.433534199 0.872914927 0.763278255 0.871676448 0.657847621 0.763147532 0.65174214 0.794926977 0.666106962 1 19.47864693 -1.536601289 2.80041688 1.013512788 0.731092238 0.316346532 0.122654409 27428960.74 28904817.76 2813660.333 0.029635601 0.0290669 1.536601289 -0.28242055 RPAS(ph)TAGLPTAGLPTATGLPSGAPPGVATIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPASTAGLPTAGLPTATGLPSGAPPGVATIR 31 1 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RPAS(0.605)T(0.157)AGLPT(0.237)AGLPTATGLPSGAPPGVATIR 87.226 0.00039559 239080000 42478 49684 43065 50188 51126 59441 46210 46040 44146 60729 TRUE FALSE 44155.06424 58216.84051 44187.30928 60115.0366 42435.62078 45636.72859 42587.93945 45422.90911 42557.19408 72627.68482 0.60796464 0.801579186 0.608408617 0.827715172 0.584289874 0.62836546 0.586387127 0.625421411 0.585963799 1 16.14823197 -0.960299425 9.127505423 0.999977523 0.651716171 0.605327542 0.084615925 0 0 0.079222733 0.018672977 0.109572249 0.960299425 -0.348261352 RPAS(ph)VSSSAAVEHEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 RPAS(0.997)VS(0.003)SSAAVEHEQR;RPAS(0.734)VS(0.264)S(0.002)SAAVEHEQR;RPAS(0.823)VS(0.176)SSAAVEHEQR;RPAS(0.999)VS(0.001)SSAAVEHEQR;RPAS(0.999)VS(0.001)SSAAVEHEQR;RPAS(0.957)VS(0.02)S(0.017)S(0.006)AAVEHEQR 248.92 1.07E-20 10998820000 1041157 1253210 1106918 1124990 1164946 1403590 1166361 1045026 1056298 1141469 TRUE FALSE 1082262.682 1468439.069 1135765.192 1347509.664 966928.895 1077627.494 1074938.577 1031019.136 1018282.041 1365117.996 0.792797901 1.075686551 0.831990492 0.987101238 0.708311588 0.789402453 0.78743272 0.755260087 0.745929688 1 20.38059423 3.241872408 24.99782028 0.782623243 0.926457544 0.248227082 0.103766587 97.12067284 733073.4429 0.026417315 0.034353918 1745.309321 -3.241872408 0.143834302 RPASPS(ph)S(ph)PEHLPATPAESPAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPASPSSPEHLPATPAESPAQR 22 1 Q9H7L9 Q9H7L9 SUDS3 Sin3 histone deacetylase corepressor complex component SDS3 2 RPAS(0.487)PS(0.667)S(0.841)PEHLPAT(0.004)PAESPAQR 104.79 0.0018889 1253800000 116000 198150 179930 164080 181010 197620 181470 171760 191100 212790 TRUE FALSE 120579.7696 232180.7211 184619.1236 196534.5343 150241.9849 151725.75 167245.9072 169457.8381 184222.3483 254482.1264 0.47382412 0.912365534 0.725469903 0.772292094 0.59038325 0.596213778 0.657200997 0.665892888 0.723910755 1 17.95720481 0.781167298 3.628200288 0.999988964 0.680415677 0.433780464 0.110872581 1.771731103 28.31218875 0.10267791 0.02641099 6.041813255 -0.781167298 -0.319573286 RPASVSSSAAVEHEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 ;;;;; 183.36 1.30E-09 625116000 338576 466781 474465 522454 469294 579490 517419 513423 450729 476505 FALSE TRUE 351943.2419 546947.0057 486829.9477 625793.8418 389523.5735 444912.2298 476862.3468 506541.4045 434507.3513 569867.0315 0.617588354 0.959780046 0.854286914 1.098140105 0.683534144 0.780729899 0.836795814 0.888876486 0.762471467 1 19.12026581 -1.729203871 6.610556151 1.002566988 0.841679604 0.128331703 0.129362172 0.00468986 0.000192116 0.12002791 0.027881841 0.018655038 1.729203871 -0.160887384 RPATADS(ph)PKPSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPATADSPKPSAK 13 2 Q03111 Q03111 MLLT1 Protein ENL 1 RPATADS(1)PKPSAK;RPATADS(0.987)PKPS(0.013)AK;RPAT(0.006)ADS(0.994)PKPSAK;RPATADS(0.998)PKPS(0.002)AK;RPATADS(0.999)PKPS(0.001)AK 165.44 2.78E-05 3970530000 10704360 3857260 5730670 3736030 8540210 8802970 8040380 5809480 6693040 3066530 TRUE FALSE 11126976.4 4519714.4 5880015.968 4475005.583 7088548.155 6758613.628 7410154.006 5731613.423 6452158.798 3667357.841 3.034058 1.232417068 1.603338486 1.220226053 1.932876055 1.842910869 2.020570211 1.562872692 1.759348031 1 21.80630961 -2.283350665 0.373112735 9.36E-11 1.793328321 0.199652205 0.483697087 90.96895578 4.428827942 76.04737199 0.320937585 0.00520774 2.283350665 1.793328321 RPDADLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPDADLK 7 1 P27824;P27824-2;P27824-3;D6RGY2;D6RFL1;H0Y9H1 P27824 CANX Calnexin 0 ; 101.72 0.014192 660840000 405250 399270 377760 527820 608990 763780 622130 410110 476740 565810 FALSE TRUE 421249.5829 467841.5166 387604.7359 632221.2206 505474.0973 586403.6702 573365.825 404613.1463 459582.2205 676669.6364 0.622533597 0.69138837 0.572812367 0.934312974 0.747002777 0.866602606 0.847334939 0.597947838 0.679182567 1 19.36809213 3.761891151 24.99189461 0.784485728 0.635159135 0.324211544 0.115795594 1143.762914 1225205.758 0.030726257 0.055351066 5779.511745 -3.761891151 -0.149326592 RPDDVPLSLS(ph)PSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPDDVPLSLSPSKR 14 2 Q9UFC0;F8WDB4 Q9UFC0 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 RPDDVPLS(0.038)LS(0.947)PS(0.015)KR;RPDDVPLS(0.001)LS(0.977)PS(0.022)KR;RPDDVPLS(0.019)LS(0.923)PS(0.058)KR;RPDDVPLS(0.072)LS(0.919)PS(0.009)KR 169.49 1.73E-06 2804880000 1795470 1196680 1505300 1181710 1927540 2065750 1848070 1579070 1643870 1185270 TRUE FALSE 1866356.542 1402200.481 1544529.355 1415448.711 1599897.439 1586010.869 1703213.444 1557905.149 1584707.44 1417500.963 1.316652751 0.989206016 1.089614325 0.998552204 1.128674675 1.11887816 1.201560696 1.099050505 1.117958634 1 20.43491828 RPDHSGGS(ph)PS(ph)PPTSEPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 2 RPDHS(0.01)GGS(0.99)PS(0.957)PPT(0.02)S(0.024)EPAR;RPDHS(0.107)GGS(0.894)PS(0.992)PPT(0.003)S(0.004)EPAR;RPDHS(0.465)GGS(0.537)PS(0.978)PPT(0.01)S(0.011)EPAR 120.63 0.00013983 873500000 353964 398315 406171 388471 388880 482523 393313 381063 390005 427717 TRUE FALSE 367938.772 466722.5028 416756.1499 465309.4043 322778.3165 370464.346 362484.0993 375955.4738 375968.7962 511519.957 0.719304823 0.912422861 0.814740743 0.909660313 0.631018032 0.724242214 0.708641167 0.734977137 0.735003182 1 18.964431 RPDHSGGS(ph)PSPPTSEPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RPDHS(0.018)GGS(0.979)PS(0.003)PPTSEPAR;RPDHS(0.001)GGS(0.999)PSPPTSEPAR;RPDHS(0.051)GGS(0.948)PSPPTSEPAR 232.02 2.91E-20 691762000 198089 264481 259275 246497 268481 300654 252960 254890 242388 306633 TRUE FALSE 205909.7067 309903.5544 266031.9195 295253.3709 222844.6955 230831.665 233132.3342 251473.6165 233664.5032 366711.8655 0.561502711 0.845087338 0.725452172 0.805137217 0.607683352 0.629463311 0.63573709 0.685752603 0.637188281 1 18.48428742 -1.908143701 7.331917811 1.066691101 0.685550632 0.563034115 0.084120378 0.048294522 0.000605047 0.042894009 0.018900481 0.012355385 1.908143701 -0.381140469 RPDLLTMVVDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPDLLTMVVDYR 12 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 ; 138.55 0.00011619 1858960000 1484750 1821730 1615190 1564400 2670900 2319870 1866310 1696180 1681740 2892000 FALSE TRUE 1543369.076 2134597.956 1657283.178 1873833.651 2216901.372 1781115.35 1720023.746 1673445.481 1621214.506 3458632.029 0.446236854 0.617179838 0.479173027 0.541784623 0.640976361 0.514976828 0.497313311 0.48384606 0.468744432 1 21.7217701 -1.989533541 2.879866757 1.445202112 0.52278805 0.850935177 0.060123773 15710476.21 3783510.727 46382859.01 0.014363813 0.010243927 1.989533541 -0.922414062 RPDPDS(ph)DEDEDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W010;Q5W011 H0Y6J6 RBM17 Splicing factor 45 1 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER;RPDPDS(0.995)DEDEDY(0.005)ER 219.87 2.97E-12 2032887000 253105 405312 351168 418029 331638 428606 357776 346491 304911 381386 TRUE FALSE 263097.7808 474921.1831 360319.7266 500713.8885 275266.2912 329068.7521 329732.5822 341846.8549 293937.3127 456111.2846 0.576828045 1.041239713 0.789982048 1.097788863 0.603506864 0.72146593 0.722921343 0.749481248 0.644442097 1 18.79902634 3.214825551 24.99995344 0.727500207 0.88205295 0.138176388 0.164496676 379.9121953 400157.4263 0.043685788 0.052241428 1639.930906 -3.214825551 0.154552743 RPDPDS(ph)DEDEDYERER ddPTM_MDA-MB-175_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 162.81 4.15E-09 4993830000 175154 213240 210867 196780 216868 227159 181193 234004 169614 265187 TRUE FALSE 182069.2152 249862.3112 216362.3672 235702.4967 180004.8548 174404.7649 166990.6192 230867.5591 163509.6253 317145.3153 0.57408767 0.787848028 0.682218393 0.74320031 0.567578476 0.549920672 0.526542916 0.72795513 0.515566894 1 18.27478451 -1.34521547 5.142447418 1.000155455 0.637922876 0.582291327 0.093687206 0.000166832 2.12E-05 0.090633143 0.021353342 0.045163182 1.34521547 -0.362232579 RPDQQLQGEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPDQQLQGEGK 11 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;; 182.1 9.52E-06 2876430000 3201100 2743090 3247900 2542570 3806130 3909290 3501810 3187730 3294710 2657150 FALSE TRUE 3327481.9 3214194.369 3332542.942 3045482.757 3159165.382 3001416.643 3227328.982 3145003.693 3176134.031 3177767.668 1.04711302 1.011462984 1.048705661 0.958371749 0.994146115 0.944504746 1.015596267 0.989689625 0.999485917 1 21.59958222 3.747982897 24.99605272 0.986217407 1.033330799 0.523402583 0.021734573 537.5781664 1426118.445 0.005391538 0.009554477 5597.355583 -3.747982897 0.047113392 RPDS(ph)PTRPTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPDSPTRPTLR 11 2 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 RPDS(0.892)PT(0.084)RPT(0.024)LR;RPDS(0.994)PT(0.005)RPT(0.001)LR;RPDS(0.999)PT(0.001)RPTLR;RPDS(0.996)PT(0.003)RPTLR;RPDS(0.981)PT(0.017)RPT(0.002)LR;RPDS(0.99)PT(0.009)RPT(0.001)LR 108.23 0.0016464 7672710000 2593780 2935090 2768330 2739850 3004290 3308440 2868530 2919990 2692280 2999380 TRUE FALSE 2696184.437 3439168.876 2840474.954 3281784.152 2493621.859 2540104.95 2643687.123 2880852.31 2595385.369 3587051.084 0.751643725 0.95877332 0.791869111 0.914897523 0.695173222 0.708131802 0.737008496 0.803125532 0.723542907 1 21.77436686 RPDTTAPLTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPDTTAPLTDR 11 1 Q96JB2;Q96JB2-2;A0A087WYY9 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 0 ;; 117.21 0.0014195 653570000 252120 263042 295615 257026 309340 349346 290704 277643 292404 287026 FALSE TRUE 262073.8923 308217.4173 303318.9698 307864.9757 256758.4973 268215.6859 267917.8609 273921.6497 281880.4372 343263.2493 0.763477864 0.897903921 0.883633685 0.896877182 0.74799297 0.781370235 0.780502607 0.797992941 0.821178608 1 18.38895588 4.817420215 20.55568114 0.832293115 0.763467037 0.078453523 0.072745638 65174.45817 16978290.44 0.017183862 124.2207616 65678.0447 -4.817420215 -0.068826077 RPDYAPMES(ph)S(ph)DEEDEEFQFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPDYAPMESSDEEDEEFQFIK 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 RPDY(0.001)APMES(0.999)S(0.999)DEEDEEFQFIK;RPDY(0.028)APMES(0.986)S(0.986)DEEDEEFQFIK 103.26 0.00021466 65941000 107211 93174 112716 87779 128252 127291 144820 99476 102489 81944 TRUE FALSE 111443.7731 109175.9097 115653.4716 105141.4242 106451.7709 97729.59436 133468.63 98142.68693 98800.44091 97999.35789 1.137188809 1.114047194 1.180145197 1.072878705 1.086249677 0.997247293 1.361933719 1.001462551 1.00817437 1 16.58048468 1.593781963 25 1.003575655 1.130821634 0.316002863 0.089102611 1.095254167 1938.930827 0.045737447 0.021335953 39.24478583 -1.593781963 0.127245978 RPEDPNADPSSEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPEDPNADPSSEAK 14 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 99.069 0.0052276 0 149180 117280 130870 113540 172000 177900 154690 130310 171900 112740 FALSE TRUE 155069.7416 137421.9277 134280.5797 135997.8731 142763.5014 136585.4211 142564.9936 128563.4076 165713.3526 134829.2445 1.150119488 1.019229383 0.99593067 1.008667472 1.058846706 1.013025191 1.057374416 0.953527613 1.2290609 1 17.04077393 1.256085412 24.99989981 1.114530664 1.027569243 0.1757238 0.070881032 312.6016494 445942.9795 0.043984446 0.015986983 18.03372373 -1.256085412 -0.086961421 RPEGPGAQAPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 RPEGPGAQAPS(0.122)S(0.878)PR;RPEGPGAQAPS(0.034)S(0.966)PR;RPEGPGAQAPS(0.119)S(0.881)PR;RPEGPGAQAPS(0.01)S(0.99)PR;RPEGPGAQAPS(0.023)S(0.977)PR;RPEGPGAQAPS(0.062)S(0.938)PR 155.24 3.61E-06 32698913000 7113351 8461050 7355376 8101470 7954730 9603960 7817150 7652500 7349270 8004440 TRUE FALSE 7394191.59 9914169.52 7547063.141 9703916.586 6602587.836 7373585.839 7204421.357 7549930.754 7084771.208 9572756.764 0.772420294 1.03566504 0.788389732 1.013701364 0.689726899 0.770267753 0.752596304 0.788689292 0.740097276 1 23.19050302 3.232337141 24.99999503 0.777046283 0.903898862 0.196468443 0.109327726 196.643815 789926.9977 0.028311039 0.034641208 1707.407329 -3.232337141 0.126852579 RPEILK ddPTM_MDA-MB-175_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 92.822 0.074269 1155100000 1465300 1214600 1527500 1516900 1807400 1784700 1810300 1500900 1586200 1286800 FALSE TRUE 1523151.175 1423198.102 1567307.905 1816938.293 1500178.794 1370230.472 1668403.956 1480782.89 1529112.972 1538923.823 0.989750859 0.924800878 1.018444111 1.180655121 0.974823296 0.890382261 1.084136805 0.962219746 0.993624863 1 20.55349039 RPELEDSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPELEDSTLR 10 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;;; 184.55 2.48E-06 4205890000 1869090 2392630 2055310 2063610 2390860 2556770 2111620 2060310 2005540 2326400 FALSE TRUE 1942883.116 2803545.59 2108873.067 2471785.899 1984462.471 1962998.916 1946105.707 2032694.914 1933361.007 2782213.538 0.698322789 1.007667295 0.757983899 0.888424222 0.713267491 0.705552931 0.699481071 0.730603488 0.694900294 1 21.40780172 3.231935436 24.9982278 0.736940859 0.844488989 0.090163278 0.114613139 256.8219223 969043.5882 0.029939879 0.036569791 1705.828775 -3.231935436 0.10754813 RPELLTHSTTEVTQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPELLTHSTTEVTQPR 16 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ;;; 183.01 1.33E-09 1161150000 339720 507980 470461 502098 477675 574490 459305 508276 442978 503274 FALSE TRUE 353132.4079 595221.6135 482721.6001 601411.4858 396479.9741 441073.404 423303.4739 501463.3916 427035.3083 601880.9045 0.586714756 0.988935866 0.80202179 0.99922008 0.658734928 0.73282505 0.703301053 0.833160494 0.70950134 1 19.19911852 4.777717258 23.4198969 0.812169299 0.586713351 0.243562305 0.12421313 16200.87364 9689410.19 0.028538583 8.187302134 59940.07175 -4.777717258 -0.225455947 RPENPKPQDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPENPKPQDGK 11 2 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 101.72 0.0017288 117655000 161649 90722 114078 100560 160322 168651 179758 136097 144359 74431 FALSE TRUE 168031.0273 106302.7978 117050.9664 120450.4679 133070.5237 129484.3612 165668.0982 134272.8423 139163.5478 89014.32938 1.887685146 1.194221183 1.314967682 1.353158179 1.494933733 1.454646258 1.861139655 1.508440756 1.563383657 1 16.44174998 2.852539401 2.708287438 1.541582895 1.414120486 0 0.262986787 0.999286613 14.25599047 0.082727474 0.088358297 712.0974023 -2.852539401 -0.127462409 RPENSLLEETLHFDHAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPENSLLEETLHFDHAVR 18 1 O00566;U3KQ48 O00566 MPHOSPH10 U3 small nucleolar ribonucleoprotein protein MPP10 0 133.93 4.73E-06 62497000 22883 23673 20457 21279 22358 25732 25402 22228 21128 20534 FALSE TRUE 23786.43851 27738.6536 20990.12623 25487.92269 18557.59515 19756.13297 23410.92486 21930.07002 20367.60741 24557.24415 0.968611883 1.129550752 0.854742743 1.03789833 0.755687203 0.804493079 0.953320524 0.893018365 0.829393041 1 14.58386105 4.005133252 1.683420926 0.8810447 1.043435974 0.240312465 0.095935556 0.497556173 2.671957559 0.025999985 0.0824194 10118.89879 -4.005133252 0.162391274 RPEQVTWAAQEQELESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPEQVTWAAQEQELESLR 18 1 O60826 O60826 CCDC22 Coiled-coil domain-containing protein 22 0 111.4 0.00049023 128610000 40514 115450 43760 100370 54419 89632 33559 42908 33953 85009 FALSE TRUE 42113.524 135277.6394 44900.42155 120222.8864 45168.87782 68816.32639 30928.55789 42332.88844 32731.03816 101664.886 0.414238639 1.330623038 0.441651226 1.182540907 0.444291826 0.676893755 0.304220652 0.41639636 0.321950277 1 16.63346195 3.199714834 24.99994479 0.484794026 0.848531615 0.175637025 0.326484259 218.5640977 140660.46 0.086145785 0.102965594 1583.852861 -3.199714834 0.363737589 RPERPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPERPEVK 8 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 0 61.765 0.047188 82929000 60315 54222 62351 56468 78529 71352 63211 60963 73604 55908 FALSE TRUE 62696.28277 63534.20671 63975.91828 67637.20186 65180.66863 54781.57935 58256.35665 60145.8907 70955.00642 66862.10218 0.937695357 0.950227478 0.956833785 1.011592511 0.974852218 0.819321822 0.871291131 0.899551297 1.061214112 1 16.02890109 RPES(ph)PSEIS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 RPES(0.989)PS(0.011)EIS(1)PIK;RPES(0.977)PS(0.023)EIS(1)PIK 115.34 0.0033606 192094000 502620 351200 401180 372100 437900 578560 593670 438380 428840 299330 TRUE FALSE 522463.8257 411515.868 411635.0804 445700.2694 363465.9144 444198.2082 547136.5941 432504.2331 413406.1322 357977.9825 1.459485922 1.149556364 1.14988938 1.245049392 1.015330362 1.240853432 1.528408508 1.208186688 1.154836756 1 18.44951133 0.950724784 2.790804599 1.001486434 1.246261623 0.231044208 0.140810418 0.460083682 8.486147901 0.136195871 0.03613851 8.927395674 -0.950724784 0.244775189 RPES(ph)PSEISPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 RPES(0.971)PS(0.029)EISPIK;RPES(0.999)PS(0.001)EISPIK;RPES(0.999)PS(0.001)EISPIK;RPES(0.994)PS(0.003)EIS(0.003)PIK;RPES(0.976)PS(0.024)EISPIK;RPES(0.996)PS(0.004)EISPIK;RPES(0.996)PS(0.004)EISPIK 219.53 1.94E-11 5333530000 3673900 3269360 3800760 3161410 4394280 4475630 4221720 3839380 3942680 3087040 TRUE FALSE 3818948.409 3830847.148 3899810.928 3786727.462 3647341.855 3436232.761 3890810.555 3787919.391 3800783.717 3691886.383 1.034416559 1.037639502 1.056319324 1.025689057 0.98793448 0.930752576 1.053881445 1.026011908 1.029496394 1 21.81592672 3.474703051 21.08392324 1.00726908 1.042064519 0.233913949 0.030952823 17.80877975 155260.7911 0.009286952 0.012695371 2983.342063 -3.474703051 0.034795439 RPFDPNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPFDPNDR 8 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2;F8WEA1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ;;;; 109.44 0.0058013 3631700000 508230 908321 588418 1074051 641570 726977 645554 616567 584043 754434 FALSE TRUE 528295.3128 1064318.066 603752.6565 1286495.082 532516.1606 558147.6092 594953.7906 608302.9279 563023.4065 902250.8978 0.585530382 1.179625389 0.669162711 1.425872876 0.590208513 0.618616851 0.659410583 0.674205955 0.624020888 1 19.78316915 RPFGISALIVGFDFDGTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPFGISALIVGFDFDGTPR 19 1 O14818;H0Y586;O14818-2 O14818 PSMA7 Proteasome subunit alpha type-7 0 ;; 162.09 4.54E-11 1838417000 862730 1028256 1044002 985199 1143229 1221369 1128455 1008949 940455 1097108 FALSE TRUE 896791.2466 1204850.969 1071209.55 1180068.422 948903.3429 937724.5598 1040003.748 995425.689 906608.2083 1312065.307 0.683495891 0.918285822 0.816430054 0.899397625 0.7232135 0.71469351 0.792646328 0.75867084 0.690977959 1 20.3234081 5.024572539 14.48877182 0.799560099 0.420031738 0.128859744 0.095428001 8994355.883 148159060.2 0.02189141 76848246.34 105821.1652 -5.024572539 -0.379528361 RPGAPSLS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPGAPSLSPAPR 12 1 Q5QP82-2;Q5QP82 Q5QP82-2 DCAF10 DDB1- and CUL4-associated factor 10 1 RPGAPS(0.062)LS(0.938)PAPR;RPGAPS(0.005)LS(0.995)PAPR;RPGAPSLS(1)PAPR 136.81 6.33E-05 1076800000 451272 521419 489285 529908 610754 628572 486808 533254 485474 543934 TRUE FALSE 469088.567 610968.6572 502036.1691 634722.2208 506938.2532 482595.6791 448650.7169 526106.6024 468001.8856 650507.4531 0.721111749 0.939218535 0.771760826 0.975733972 0.77929661 0.741875711 0.689693431 0.808763374 0.719441235 1 19.31120606 3.042907787 24.99928559 0.772846771 0.855592883 0.063855549 0.104954537 275.9438977 160770.9424 0.027771683 0.033193488 1103.844217 -3.042907787 0.082746112 RPGFS(ph)PTSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.953)PT(0.045)S(0.002)HR 102.73 0.0017813 321160000 87338 100210 101240 89284 107790 105940 96123 104630 100170 93656 TRUE FALSE 90786.17168 117420.288 103878.3976 106944.1087 89467.8943 81337.04054 88588.62809 103227.606 96564.90127 112006.1 0.810546672 1.048338331 0.92743518 0.95480611 0.79877698 0.726184025 0.790926816 0.921624857 0.862139662 1 16.77321778 3.249501817 24.9844653 0.841617882 0.942796622 0.176335528 0.088682789 323.2047852 738040.7355 0.024592367 0.032978635 1776.240701 -3.249501817 0.10117874 RPGFSPT(ph)SHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 RPGFS(0.104)PT(0.715)S(0.181)HR 86.288 0.0080049 332480000 134000 150280 130900 148560 157010 177230 154710 146130 147130 142650 TRUE FALSE 139290.4235 176089.421 134311.3615 177944.7246 130321.4963 136071.0184 142583.4259 144171.3664 141834.82 170599.5363 0.816475979 1.032179951 0.787290308 1.043055148 0.763902992 0.797604855 0.835778508 0.845086508 0.831390419 1 17.3802542 3.212176394 24.99959606 0.835694523 0.91831981 0.122960513 0.094748021 387.3655847 367035.7613 0.024944187 0.029822214 1629.957926 -3.212176394 0.082625288 RPGQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPGQAAK 7 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 0 ; 81.297 0.044229 198731000 406610 253380 372430 229382 369900 374420 298120 251420 276910 304870 FALSE TRUE 422663.2768 296896.044 382135.8318 274753.075 307024.5301 287466.6294 274752.5754 248050.1261 266944.0632 364603.4394 1.159241058 0.814298528 1.048086196 0.753566876 0.842077986 0.788436417 0.753565506 0.680328541 0.732149054 1 18.47596865 8 0.503519152 0.763161075 12.50098766 0.441124909 0.111701735 88.8363374 0.933820233 0.054529915 1104.817947 100000000 -8 11.73782659 RPGQSFHVNSEVNSVLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;RPGQSFHVNSEVNSVLS(1)PR 275.2 9.31E-40 2258980000 219719 865956 742245 898103 813041 1174420 718110 964490 817320 1019830 TRUE FALSE 228393.6758 1014677.207 761588.5145 1075745.093 674840.5812 901678.7535 661822.6618 951562.5891 787904.8129 1219646.163 0.187262243 0.831943918 0.624433986 0.882014084 0.553308494 0.739295364 0.542634972 0.780195616 0.64601098 1 20.21803123 -5 0.121608877 2.046661906 0.503372173 0.289751212 0.181103451 206.9589219 1.625722224 54.02272633 1.560259908 1.00E-05 5 -1.543289732 RPGRS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 107.57 0.0058647 7917340000 4927010 2953320 4039087 2924616 4919460 5997200 5203590 3910220 4353130 2433040 TRUE FALSE 5121532.159 3460529.736 4144348.925 3503096.316 4083251.946 4604441.188 4795719.019 3857809.897 4196461.702 2909747.605 1.76012935 1.189288628 1.424298423 1.203917587 1.403301077 1.582419445 1.648156359 1.325822862 1.442208147 1 21.47246259 0.076470558 1.456176622 0.999616582 1.433390436 0.368409479 0.173250859 16.97883383 25.19874665 0.177358711 0.046806728 1.192533418 -0.076470558 0.433773854 RPGS(ph)VSSTDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 RPGS(0.723)VS(0.012)S(0.077)T(0.188)DQER;RPGS(0.929)VS(0.018)S(0.018)T(0.035)DQER 130.47 0.00022875 885670000 572480 705210 652800 666030 743480 840660 657500 684840 690990 803940 TRUE FALSE 595081.9525 826324.3317 669812.5043 797768.7461 617103.5352 645429.4553 605963.4319 675660.84 666121.4049 961456.6506 0.618937892 0.85945043 0.696664279 0.829750094 0.641842287 0.67130375 0.630255593 0.702747066 0.692825209 1 19.87486229 -1.856499939 7.776225025 1.022479012 0.70646088 0.575617049 0.076013706 0.026510726 0.000489221 0.065865774 0.016755001 0.01391554 1.856499939 -0.316018132 RPGSVSSTDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPGSVSSTDQER 12 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 0 114.7 0.0016497 121490000 125720 148460 211220 156200 181570 185840 170780 161540 188980 170570 FALSE TRUE 130683.5227 173956.8501 216724.5667 187095.8938 150706.7963 142681.4764 157393.8173 159374.8205 182178.6467 203989.9257 0.64063714 0.852771771 1.062427794 0.917182028 0.73879529 0.699453544 0.771576424 0.781287703 0.893076685 1 17.63813838 4.740230504 23.85502221 0.843475189 0.640637008 0.25072572 0.110071125 126.3753984 1805009.971 0.028259306 0.18004813 54983.26228 -4.740230504 -0.202838181 RPGTEAASYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPGTEAASYR 10 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 0 70.942 0.084135 31384000 11089 11228 11091 12276 16849 16657 11182 13145 12638 17249 FALSE TRUE 11526.80228 13156.32166 11380.04057 14704.15616 13985.013 12788.66419 10305.52562 12968.81278 12183.16085 20628.6113 0.558777424 0.637770593 0.55166295 0.712803976 0.677942533 0.619947897 0.499574376 0.628680845 0.590595299 1 14.33235908 -2.2450212 2.157741053 2.318147138 0.609846079 0.797503408 0.059158906 2427274.642 401728.2878 15599511.28 0.015151553 0.005688252 2.2450212 -1.708301059 RPGTQGHLGPEKEEEES(ph)DGEPEDSSTS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RPGTQGHLGPEKEEEESDGEPEDSSTS 27 2 Q8IYB7;H7C1Q8 Q8IYB7 DIS3L2 DIS3-like exonuclease 2 1 RPGTQGHLGPEKEEEES(0.886)DGEPEDS(0.028)S(0.028)T(0.028)S(0.028);RPGTQGHLGPEKEEEES(0.998)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.998)DGEPEDS(0.001)STS;RPGTQGHLGPEKEEEES(0.607)DGEPEDS(0.098)S(0.098)T(0.098)S(0.098);RPGTQGHLGPEKEEEES(0.892)DGEPEDS(0.027)S(0.027)T(0.027)S(0.027);RPGTQGHLGPEKEEEES(1)DGEPEDSSTS;RPGTQGHLGPEKEEEES(0.998)DGEPEDSSTS 152.44 3.70E-08 3035310000 2585160 1559999 2100828 1517224 2740228 2853429 2420818 2045430 2293468 1422585 TRUE FALSE 2687224.113 1827916.693 2155577.304 1817326.379 2274445.023 2190763.359 2231067.96 2018014.356 2210926.535 1701313.294 1.579499862 1.0744151 1.267007853 1.068190312 1.336876066 1.287689555 1.311379843 1.186150936 1.299541091 1 20.6982174 -1.645941047 2.523796953 0.967362983 1.255524389 0.249118447 0.138025101 10992716.6 9112602.879 2327933.612 0.032401283 0.022597425 1.645941047 0.288161406 RPHFPQFSYSAS(ph)GTA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPHFPQFSYSASGTA 15 1 P31749;P31749-2;G3V2I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 RPHFPQFSYS(0.001)AS(0.978)GT(0.021)A 105.9 0.00078331 201140000 66526 79549 93907 105320 118540 130080 83720 94301 88780 120470 TRUE FALSE 69152.49785 93210.92194 96354.29357 126151.9817 98390.61314 99870.89138 77157.80764 93037.04934 85584.82514 144073.79 0.479979723 0.646966544 0.668784333 0.875606741 0.682918199 0.693192644 0.53554368 0.645759714 0.594034662 1 17.13644838 -1.559312016 3.295680618 1.012298185 0.651487277 0.529587161 0.099733528 36136934.9 45086852.71 3910228.125 0.02472125 0.027585952 1.559312016 -0.360810908 RPHFPQFSYSASGT(ph)A ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPHFPQFSYSASGTA 15 1 P31749;P31749-2;G3V2I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 RPHFPQFSYSAS(0.001)GT(0.999)A 99.044 0.0015789 195270000 39410 60156 62414 69900 72576 86476 62853 64314 66036 70521 TRUE FALSE 40965.93723 70487.32505 64040.56011 83726.01137 60239.55744 66393.25956 57926.41762 63451.97603 63659.37726 84338.23974 0.485733842 0.83576946 0.759330054 0.992740797 0.714261498 0.787226053 0.686834558 0.752351202 0.754810362 1 16.36389929 -2.405012914 1.914891101 2.440317054 0.758545272 0.277216979 0.119672971 4140998.942 376046.4474 25794019.27 0.028359182 0.003935384 2.405012914 -1.681771782 RPHGSTLSVSAS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPHGSTLSVSASPEK 15 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 RPHGS(0.001)T(0.001)LS(0.019)VS(0.204)AS(0.775)PEK 128.55 4.37E-05 104370000 22829 103800 94772 106120 113650 164840 99132 132580 97132 106830 TRUE FALSE 23730.30655 121626.8425 97241.83618 127110.2193 94331.81359 126558.4082 91361.77481 130802.982 93636.23829 127761.2931 0.185739405 0.951985062 0.761121258 0.994903982 0.73834423 0.990584903 0.715097449 1.023807593 0.732899895 1 16.96309129 4.742302686 24.99797461 0.877745672 0.18573914 0.744005359 0.121950497 160.257002 1070513.876 0.025405294 0.190559077 55246.23494 -4.742302686 -0.692006532 RPHS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 101.38 0.0055746 1109650000 1189660 870573 1054119 805901 1299330 1596720 1206940 1076773 1130476 774360 TRUE FALSE 1236628.695 1020087.141 1081590.207 965305.8124 1078470.351 1225905.979 1112336.889 1062340.619 1089790.39 926081.016 1.335335326 1.101509612 1.1679218 1.042355686 1.164552919 1.323756731 1.201122655 1.147135727 1.176776514 1 19.82077888 0.209829716 1.265456635 0.999763857 1.18122488 0.29909522 0.0846674 8.198666909 11.78901009 0.084752496 0.024213229 1.621174321 -0.209829716 0.181461023 RPHT(ph)PAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPHTPAER 8 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 RPHT(1)PAER;RPHT(1)PAER 110.39 0.0020133 554100000 157453 205291 168491 183909 176008 197820 154648 167548 167693 207345 TRUE FALSE 163669.366 240548.1323 172882.0139 220285.6513 146090.223 151879.303 142526.2857 165302.2931 161657.7617 247970.2829 0.660036211 0.970068387 0.697188437 0.888355043 0.589144075 0.612489937 0.574771638 0.666621384 0.651923931 1 17.91980771 4.045153436 24.97719284 0.688064313 0.819696705 0.060175114 0.146840465 254.0299105 140516.7049 0.034726048 0.075016792 11095.66755 -4.045153436 0.131632392 RPHT(ph)PTPGIYMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.981)PT(0.019)PGIYMGR;RPHT(0.985)PT(0.015)PGIYMGR;RPHT(0.981)PT(0.019)PGIYMGR;RPHT(0.877)PT(0.123)PGIYMGR;RPHT(0.996)PT(0.004)PGIYMGR;RPHT(0.911)PT(0.089)PGIYMGR;RPHT(0.996)PT(0.004)PGIYMGR;RPHT(0.997)PT(0.003)PGIYMGR;RPHT(0.942)PT(0.058)PGIYMGR;RPHT(0.955)PT(0.045)PGIYMGR;RPHT(0.974)PT(0.026)PGIYMGR;RPHT(0.983)PT(0.017)PGIYMGR 175.26 1.09E-05 30956590000 2051051 2171315 2073533 2639953 2152060 2597058 2648530 2328045 2051735 1883782 TRUE FALSE 2132028.077 2544221.461 2127570.973 3162127.824 1786253.61 1993930.638 2440931.298 2296841.365 1977893.458 2252873.016 0.946359632 1.129323066 0.944381223 1.403597896 0.792878071 0.885061264 1.08347487 1.019516568 0.877942718 1 21.10333457 RPHTPT(ph)PGIYMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPHTPTPGIYMGR 13 1 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 1 RPHT(0.144)PT(0.856)PGIYMGR;RPHT(0.368)PT(0.632)PGIYMGR 100.58 0.0011349 2057980000 362185 404849 367930 450640 395910 393290 499530 386280 343610 333149 TRUE FALSE 376484.3435 474378.6665 377518.5581 539775.247 328613.3596 301954.3579 460375.5333 381102.5484 331243.5432 398423.168 0.944935871 1.190640265 0.947531641 1.354778764 0.824784767 0.757873493 1.155493883 0.956527077 0.831386249 1 18.60394202 3.196195079 24.99999763 0.930028616 1.103704354 0.271488085 0.150688667 202.5509359 119525.1346 0.042797396 0.051153056 1571.068349 -3.196195079 0.173675738 RPILQLS(ph)PPGPR ddPTM_MDA-MB-175_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 131.24 0.0001239 3599110000 1140631 1248970 1180029 1150011 1231309 1461870 1143134 1150935 1119603 1299158 TRUE FALSE 1185663.993 1463470.882 1210781.525 1377479.743 1022011.536 1122372.847 1053532.17 1135508.599 1079308.707 1553703.136 0.763121323 0.941924392 0.779287559 0.886578466 0.65779074 0.722385648 0.678078164 0.730840128 0.694668551 1 20.56727945 3.2473398 24.99951673 0.728086038 0.845281947 0.157825626 0.102316688 260.6130757 742114.8928 0.025771699 0.034372627 1767.420142 -3.2473398 0.117195909 RPIS(ph)DDDCPSASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPISDDDCPSASK 13 1 Q96PU4 Q96PU4 UHRF2 E3 ubiquitin-protein ligase UHRF2 1 RPIS(1)DDDCPSASK;RPIS(0.995)DDDCPS(0.005)ASK 190.41 4.70E-06 274120000 517650 410520 446420 364540 592880 581030 550610 474590 501000 363310 TRUE FALSE 538087.2217 481023.6166 458054.0719 436644.924 492102.4694 446094.5881 507451.7494 468228.8973 482969.1079 434493.6385 1.238423705 1.107090125 1.054225037 1.004951247 1.132588433 1.02669993 1.167915257 1.077642699 1.111567731 1 18.72897553 7.791402711 0.009921968 3.06E-07 2.322112036 0.200194176 0.064116845 25485.13101 20.19661989 2048.102414 2722.922476 61858973.77 -7.791402711 2.32211173 RPISADSAIMNPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPISADSAIMNPASK 15 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;J3KSQ2;J3QL20 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 149.3 5.42E-06 939030000 664140 504360 646110 576110 689040 768050 691870 672830 667980 495790 FALSE TRUE 690360.76 590979.9066 662948.1574 690062.8385 571917.2269 589682.0274 637639.4215 663811.8144 643939.5303 592930.558 1.164319752 0.996710152 1.118087352 1.163817296 0.964560216 0.994521229 1.075403203 1.119543942 1.086028577 1 19.17750363 1.366694152 0.00676597 1.55E-07 2.120770852 0.094668069 0.067151201 7963.598075 51.38973381 8074.844714 8027.283762 23.264523 -1.366694152 2.120770697 RPKEEDPATGTGDPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPKEEDPATGTGDPPR 16 2 P45974-2;P45974;F5H571 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ; 120.66 5.79E-05 150076000 401580 342060 379020 258726 522480 474580 364180 386270 423570 361830 FALSE TRUE 417434.6885 400806.1441 388897.5726 309901.2306 433669.0362 364365.9873 335634.62 381092.6825 408325.7984 432723.6608 0.964668046 0.926240417 0.898720379 0.716164284 1.002184709 0.842029268 0.775632697 0.880683718 0.943617915 1 18.72308648 1.06706164 3.164367688 0.998173271 0.87142097 0.202502309 0.079855977 0.338353374 6.919288733 0.074804692 0.019721885 11.66975237 -1.06706164 -0.126752301 RPKS(ph)ESQGNATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPKSESQGNATK 12 2 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 RPKS(0.997)ES(0.003)QGNATK;RPKS(0.971)ES(0.029)QGNATK;RPKS(0.994)ES(0.006)QGNATK 243.99 1.17E-16 424020000 166604 103606 170493 124359 285625 242552 220177 205732 253226 160622 TRUE FALSE 173181.6546 121399.5246 174936.1876 148956.839 237074.5645 186222.9739 202918.9514 202974.499 244112.4457 192092.8056 0.901552008 0.631983713 0.910685786 0.77544205 1.234166807 0.96944273 1.056358934 1.056648105 1.270804729 1 17.55144396 3.253997809 24.99357254 1.088993878 0.800118493 0.612743852 0.11395009 154.7628091 250567.0745 0.029920846 0.040366127 1794.724574 -3.253997809 -0.288875385 RPLAPSGRS(ph)PVEGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPLAPSGRSPVEGLGR 16 2 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1 Q9Y5U2-2 TSSC4 Protein TSSC4 1 RPLAPS(0.053)GRS(0.947)PVEGLGR 90.193 0.0028874 89393000 19053 21330 19647 21298 24732 25296 19768 22812 19357 23888 TRUE FALSE 19805.22715 24993.26158 20159.01696 25510.68083 20528.06347 19421.38736 18218.53251 22506.24245 18660.34535 28568.39624 0.693256527 0.874857005 0.705640484 0.892968601 0.718558483 0.679820708 0.63771632 0.787802097 0.653181411 1 14.80213243 -1.189781556 4.352530782 1.000072723 0.742481386 0.469716653 0.083338396 5.138458039 46822426.54 6692.246573 0.018891474 0.064597907 1.189781556 -0.257591336 RPLDDGVGNQLGALVHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPLDDGVGNQLGALVHQR 18 1 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 0 ;;; 195.46 1.36E-15 1495660000 684480 713082 699403 712727 768271 831683 677259 691651 686218 758917 FALSE TRUE 711503.7989 835548.2865 717630.0167 853702.2733 637680.5698 638537.2275 624173.6699 682380.5497 661521.1482 907612.2558 0.783929254 0.920600489 0.790679073 0.940602408 0.702591405 0.703535263 0.687709609 0.751841489 0.728858765 1 19.79171656 3.225340134 24.99951034 0.742650586 0.858479529 0.176465974 0.096651189 296.1014625 559917.3268 0.025492483 0.030640096 1680.11935 -3.225340134 0.115828944 RPLDS(ph)PEAEELPAMK ddPTM_MDA-MB-175_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 201.31 3.97E-09 1200810000 2025370 1792810 2098060 1942770 2517370 2586180 2472010 2271890 2336360 1947990 TRUE FALSE 2105333.172 2100711.171 2152737.167 2327044.107 2089468.347 1985578.889 2278247.397 2241439.031 2252274.86 2329661.344 0.903707819 0.901723839 0.924055839 0.998876559 0.896897891 0.85230366 0.977930721 0.962130842 0.966782089 1 21.15168882 2.13424906 23.27125911 0.972492275 0.916003379 0.432614746 0.035548905 7.374174504 1625.184275 0.014037279 0.010367221 136.2225669 -2.13424906 -0.056488896 RPLEDGDQPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPLEDGDQPDAK 12 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 126.1 0.00047067 202320000 423660 287210 381060 285420 434520 473630 463740 396060 386000 290380 FALSE TRUE 440386.4239 336536.0833 390990.7366 341875.2241 360660.4456 363636.6104 427390.847 390751.4635 372107.9354 347274.4013 1.268122333 0.969078291 1.125884128 0.984452706 1.038546015 1.047116082 1.230700695 1.125195125 1.071509832 1 18.40571654 RPLEEDFRRS(ph)PTEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RPLEEDFRRS(0.993)PT(0.007)EDFR;RPLEEDFRRS(0.993)PT(0.007)EDFR;RPLEEDFRRS(0.858)PT(0.142)EDFR;RPLEEDFRRS(0.997)PT(0.003)EDFR 133.09 0.00019666 5041580000 2457080 3419180 3217530 2508350 3485950 3701840 2561510 3160940 3096620 4301510 TRUE FALSE 2554087.416 4006397.567 3301381.475 3004494.143 2893409.464 2842143.762 2360732.153 3118572.77 2985173.251 5144308.527 0.496487993 0.778801961 0.641754175 0.58404237 0.562448665 0.552483147 0.458901744 0.606218067 0.58028659 1 22.29454574 -1.459781799 5.971289827 1.000245957 0.586325062 0.699891248 0.081596512 0.00027072 2.45E-05 0.080052971 0.018857671 0.03469111 1.459781799 -0.413920895 RPLEMEQQQAYRPEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 140.89 9.32E-07 797010000 1240980 667490 829600 637130 1305370 1202880 1144050 812950 926610 504890 FALSE TRUE 1289974.849 782126.2151 851220.0575 763152.4124 1083483.674 923529.3498 1054376.372 802053.735 893261.4871 603813.5288 2.136379506 1.29531085 1.409739956 1.263887568 1.794401122 1.529494299 1.746195342 1.328313621 1.479366467 1 19.20374356 0.608814723 0.946033535 1.001101112 1.561514203 0.312430087 0.254065066 1.571380404 2.289997527 0.234871173 0.076363465 4.062699707 -0.608814723 0.560413091 RPLFLAPDFDRWLDES(ph)DAEMELR ddPTM_MDA-MB-175_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 236.34 2.11E-37 1092510000 353260 519795 437301 515255 496200 642803 314863 435734 482326 922609 TRUE FALSE 367206.9776 609065.7478 448697.4233 617170.9011 411856.1012 493521.745 290183.2153 429893.6984 464967.1815 1103376.569 0.33280295 0.552001705 0.406658466 0.559347478 0.373268848 0.447283148 0.262995629 0.389616483 0.421403893 1 20.07349382 0.899466029 19.2576449 1 0.414718312 0.807869912 0.0854212 4629.716259 886842.3487 0.081619226 0.020404807 7.933521973 -0.899466029 -0.585281688 RPLPVES(ph)PDTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLPVESPDTQR 12 1 P57682 P57682 KLF3 Krueppel-like factor 3 1 RPLPVES(0.995)PDT(0.005)QR;RPLPVES(0.996)PDT(0.004)QR 107.73 0.0010914 771800000 1669420 1509800 1688480 1655580 1781200 2079740 1958950 1749920 1653520 1446720 TRUE FALSE 1735329.991 1769096.405 1732483.176 1983048.783 1478432.26 1596751.904 1805402.38 1726465.185 1594010.138 1730177.085 1.002978253 1.022494415 1.001332864 1.146153651 0.854497654 0.922883512 1.043478379 0.997854613 0.921298838 1 20.72248828 3.239429749 24.99996787 0.963762586 1.038764606 0.3125471 0.062227066 34.5631997 994167.7024 0.01827611 0.023383518 1735.520504 -3.239429749 0.075002021 RPLQEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLQEDR 7 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 0 ; 90.657 0.027223 58079000 49235 113190 90369 114500 87004 114849 81930 103879 91728 137410 FALSE TRUE 51178.83582 132629.502 92724.09038 137147.7583 72215.09116 88177.0603 75508.11252 102486.6719 88426.7272 164332.8586 0.311433978 0.807078408 0.564245588 0.834572948 0.439444015 0.536575953 0.459482742 0.623652949 0.538095229 1 17.32626145 -1.317665729 3.117699288 1.003147862 0.577056077 0.422817614 0.151007565 25286810.99 33782880.02 740057.6995 0.035267734 0.048120959 1.317665729 -0.426091785 RPLS(ph)ASLGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.5)AS(0.5)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.912)AS(0.088)LGQLNEVGLPSAAILPDEGAVDLPSR 131.57 4.63E-08 273904000 33019 39393 36433 37808 39434 47085 37944 43276 33091 48897 TRUE FALSE 34322.61562 46158.44131 37382.47391 45286.30955 32731.02277 36150.22233 34969.85013 42695.95601 31900.06137 58477.43096 0.586937816 0.789337708 0.639263273 0.774423719 0.5597206 0.618191014 0.598005924 0.730127082 0.54551065 1 15.83559231 -1.466631922 3.515187383 1.00458225 0.656328229 0.616485957 0.082861383 16634094.86 36529057.57 805581.386 0.01877827 0.034148221 1.466631922 -0.34825402 RPLS(ph)GPDVGTPQPAGLASGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPLSGPDVGTPQPAGLASGAK 21 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 RPLS(1)GPDVGTPQPAGLASGAK;RPLS(1)GPDVGTPQPAGLASGAK;RPLS(1)GPDVGTPQPAGLASGAK;RPLS(1)GPDVGTPQPAGLASGAK 277.82 4.54E-45 1705300000 1206557 971996 1201670 1185357 1467110 1678780 1499080 1364930 1411470 1161480 TRUE FALSE 1254192.802 1138928.752 1232986.507 1419817.077 1217731.166 1288908.787 1381578.192 1346635.346 1360671.47 1389049.768 0.90291423 0.819933726 0.887647466 1.022149896 0.876664893 0.927906844 0.994621089 0.969465153 0.979569992 1 20.40566686 4.062379627 0.341819456 0.99882313 0.794744182 0.447505483 0.046072053 3.813924922 0.506282979 0.048196902 0.311217381 11544.61958 -4.062379627 -0.204078948 RPLS(ph)SSHEASEGQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.447)S(0.447)S(0.107)HEASEGQAK;RPLS(0.862)S(0.106)S(0.032)HEASEGQAK 222.13 8.84E-13 492260000 278620 398520 434340 409390 546310 645420 528920 522930 527740 459590 TRUE FALSE 289620.1327 466962.7099 445659.2572 490366.1201 453448.4213 495530.9864 487461.8683 515920.9787 508746.7405 549637.8611 0.526929008 0.849582503 0.810823433 0.892162194 0.82499488 0.901559047 0.886878257 0.938656187 0.925603523 1 19.06812186 5.150263097 1.219904601 0.902063319 2.13E-32 0.829635896 0.050226975 1.370987414 0.883829578 0.013625889 1.986852078 141339.3525 -5.150263097 -0.902063319 RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 RPLS(0.253)AS(0.747)LGQLNEVGLPSAAILPDEGAVDLPSR;RPLS(0.174)AS(0.826)LGQLNEVGLPSAAILPDEGAVDLPSR 221.63 3.63E-36 1425980000 176685 199180 184496 191744 195278 209864 155370 172671 168966 183754 TRUE FALSE 183660.6602 233387.6156 189304.1173 229670.3909 162084.7153 161126.2665 143191.6934 170356.6277 162884.9467 219757.0781 0.835744003 1.062025476 0.861424437 1.045110323 0.737563116 0.733201715 0.651590814 0.775204281 0.741204552 1 17.74555011 3.224348132 24.90163547 0.7529496 0.952597329 0.389927573 0.107269682 185.7570132 325463.3981 0.028334242 0.034018193 1676.286053 -3.224348132 0.19964773 RPLSSS(ph)HEASEGQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPLSSSHEASEGQAK 15 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2;A0A0J9YVR0 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 RPLS(0.176)S(0.295)S(0.523)HEAS(0.006)EGQAK 173.56 5.90E-07 331480000 185330 262260 281380 270250 347090 365870 327310 283260 303360 242760 TRUE FALSE 192646.9715 307301.1149 288712.994 323704.6434 288091.7658 280902.2373 301654.5869 279463.363 292442.1329 290324.1741 0.663558149 1.058475809 0.99445041 1.114976541 0.992310636 0.96754684 1.039026763 0.962590745 1.007295151 1 18.14730518 4.743101403 24.99281437 1.013068241 0.663558008 0.855934546 0.043269834 162.3530166 893571.5566 0.010287959 0.082321905 55347.9326 -4.743101403 -0.349510233 RPLT(ph)PFHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPLTPFHHR 9 1 Q9UHV7;J3QRB7 Q9UHV7 MED13 Mediator of RNA polymerase II transcription subunit 13 1 RPLT(1)PFHHR;RPLT(1)PFHHR 71.085 0.038552 141874000 55898 80701 81197 63365 78586 79898 63305 83121 59764 86751 TRUE FALSE 58104.8962 94560.76898 83313.06052 75898.40787 65227.97979 61342.90037 58342.98868 82006.89895 57613.10531 103748.1975 0.560056922 0.911444934 0.803031402 0.731563629 0.628714343 0.591267143 0.56235183 0.790441674 0.555316687 1 16.66272675 -1.188913809 3.822280175 1.000239403 0.691339419 0.394625696 0.117759168 58198649.22 131286582.9 185162.8608 0.028586965 0.064727106 1.188913809 -0.308899984 RPMEEDGEEKS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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(0.5)PS(0.5)K;RPMEEDGEEKS(0.97)PS(0.03)K;RPMEEDGEEKS(0.973)PS(0.027)K;RPMEEDGEEKS(0.881)PS(0.119)K;RPMEEDGEEKS(0.984)PS(0.016)K;RPMEEDGEEKS(0.86)PS(0.14)K;RPMEEDGEEKS(0.977)PS(0.023)K;RPMEEDGEEKS(0.905)PS(0.095)K;RPMEEDGEEKS(0.999)PS(0.001)K;RPMEEDGEEKS(0.811)PS(0.189)K;RPMEEDGEEKS(0.635)PS(0.365)K;RPMEEDGEEKS(0.892)PS(0.108)K 194.51 1.07E-07 10921310000 11288690 3001977 4604474 2963527 7089370 8945320 7674660 4956566 5327680 2234557 TRUE FALSE 11734376.2 3517543.198 4724470.375 3549703.795 5884321.42 6867904.998 7073100.095 4890131.34 5135937.838 2672375.661 4.390990522 1.316260752 1.76789156 1.328295212 2.20190653 2.569962411 2.646746189 1.829881708 1.921862226 1 21.34969139 4.747163857 24.98874462 1.916508792 4.390991778 0.68888141 0.511625055 666.8340332 1936826.073 0.124741463 1.472515172 55868.09424 -4.747163857 2.474482987 RPMEEDGEEKS(ph)PSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPMEEDGEEKSPSKK 15 3 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 1 RPMEEDGEEKS(0.995)PS(0.005)KK;RPMEEDGEEKS(0.997)PS(0.003)KK;RPMEEDGEEKS(0.884)PS(0.116)KK;RPMEEDGEEKS(0.5)PS(0.5)KK 145.52 2.89E-06 2150180000 4363290 734780 1307240 758002 2395090 2865870 2450400 1421810 1714820 464313 TRUE FALSE 4535556.058 860972.7492 1341307.748 907932.5332 1987973.457 2200315.125 2258331.245 1402752.963 1653103.963 555286.2425 8.167960434 1.550502576 2.415524905 1.635071182 3.580087719 3.962488095 4.066967758 2.526179932 2.977030289 1 19.08287213 0.65940063 1.070386168 1.008730643 3.394903208 0.151672171 1.778496852 2.251614572 4.241036719 1.624222156 0.512231454 4.564577972 -0.65940063 2.386172565 RPMEEDGEEKSPS(ph)K ddPTM_MDA-MB-175_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 1 RPMEEDGEEKS(0.293)PS(0.707)K 80.859 0.013405 416230000 338500 122010 181140 107600 235250 302650 222060 192240 182740 125630 TRUE FALSE 351864.2414 142964.2684 185860.6572 128882.9588 195262.289 232364.1242 204654.357 189663.3372 176163.2231 150244.7932 2.34193967 0.951542249 1.237052235 0.857819803 1.29962766 1.546570229 1.36213943 1.262362131 1.172508008 1 17.19695547 4.746742207 24.92283432 1.21203087 2.341940252 0.756063787 0.19624493 504.7353751 1537493.201 0.048427544 0.546033543 55813.87912 -4.746742207 1.129909382 RPMEEDGEEKSPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPMEEDGEEKSPSK 14 2 Q12906;Q12906-5;Q12906-2;Q12906-3;Q12906-7;Q12906-4;Q12906-6 Q12906;Q12906-7 ILF3 Interleukin enhancer-binding factor 3 0 ; 146.27 4.70E-06 228863000 388084 196814 279261 178897 413382 383224 365088 297683 339340 197488 FALSE TRUE 403405.856 230615.2735 286538.7711 214282.2926 343115.4753 294226.0338 336471.4486 293693.0463 327127.2197 236181.9925 1.708029693 0.976430384 1.213211761 0.907276166 1.452758831 1.245759809 1.424627869 1.243503128 1.385064188 1 17.84953945 RPMS(ph)DPSWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.97)DPS(0.03)WNR;RPMS(0.99)DPS(0.01)WNR;RPMS(0.979)DPS(0.021)WNR;RPMS(0.999)DPS(0.001)WNR 154.74 8.54E-06 1766100000 1247560 1440720 1492640 1554480 1642730 1780700 1663020 1553830 1547920 1631370 TRUE FALSE 1296814.632 1688152.453 1531539.425 1861951.504 1363499.341 1367159.412 1532668.147 1533003.45 1492210.662 1951005.717 0.664690329 0.86527294 0.784999968 0.954354715 0.698869988 0.700745979 0.785578501 0.785750363 0.764841768 1 20.89578657 -1.352939306 5.793102096 1.00003885 0.782286136 0.406838889 0.080165293 3.89E-05 4.34E-06 0.075027888 0.017681092 0.044367064 1.352939306 -0.217752714 RPMS(ph)SPEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPMSSPEMK 9 1 P51610-2;P51610;A6NEM2;P51610-4;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 RPMS(0.5)S(0.5)PEMK;RPMS(0.581)S(0.419)PEMK;RPMS(0.5)S(0.5)PEMK;RPMS(0.5)S(0.5)PEMK 68.44 0.035564 808434000 807373 578491 740031 568575 917262 1046186 892411 729536 793862 615027 TRUE FALSE 839248.7095 677842.3292 759316.8158 681037.438 761346.1329 803225.1566 822461.4939 719757.7632 765291.0617 735529.7652 1.141012572 0.921570222 1.032340024 0.925914178 1.035099011 1.092036236 1.118189274 0.978556949 1.040462396 1 19.4884242 3.019582288 24.9953322 1.046927323 0.998589649 0.070454373 0.068314457 568.1481994 725193.4559 0.019166344 0.022905483 1046.121887 -3.019582288 -0.048337674 RPNEDS(ph)DEDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPNEDSDEDEEK 12 1 Q12996;E9PLP8;H0YE74 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK;RPNEDS(1)DEDEEK 191.44 3.28E-06 1165500000 2565790 1084680 1537690 1258940 1895530 2537750 2373300 1590910 1657850 856600 TRUE FALSE 2667089.37 1270965.352 1577763.465 1507954.574 1573328.488 1948396.022 2187274.545 1569586.454 1598184.302 1024434.369 2.603475098 1.240650832 1.540131327 1.471987488 1.535802131 1.901923716 2.13510461 1.53214935 1.560065096 1 19.96639613 4.751464136 24.72371631 1.595185846 2.60347585 0.524441176 0.298744725 1539.671864 2950018.508 0.071068044 1.314153699 56424.03441 -4.751464136 1.008290004 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 223.46 3.98E-33 15562740000 7379330 3991935 5717764 3604771 7135000 7602790 6349320 5548950 5781650 3973821 TRUE FALSE 7670671.646 4677518.783 5866773.627 4317783.945 5922195.249 5837157.244 5851643.708 5474575.402 5573569.546 4752415.142 1.614057572 0.984240359 1.234482564 0.908545196 1.246144344 1.228250704 1.231298936 1.151956477 1.172786758 1 22.18022944 7.999999988 0.017867514 2.19E-11 2.63830663 0.133194122 0.173149808 10259.98887 14.13710072 798.9100827 1356.701191 99999997.33 -7.999999988 2.63830663 RPNKPLFTALVTQCQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPNKPLFTALVTQCQK 16 2 Q8NCW5-2;Q8NCW5;Q5T3I4;Q5T3I3 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 122.34 5.28E-05 803620000 759870 611200 761680 525300 979610 967720 780290 673540 885350 627220 FALSE TRUE 789870.2543 716168.8455 781530.0065 629202.7721 813096.2421 742981.6959 719128.8309 664512.298 853486.4264 750111.7501 1.053003441 0.954749536 1.041884768 0.838812046 1.083966812 0.990494677 0.958695595 0.8858844 1.137812368 1 19.51674602 2.386724226 14.21278269 0.974385058 0.991355622 0 0.086592821 7.572219035 1162.831341 0.02925632 0.024475767 243.6263316 -2.386724226 0.016970564 RPNKQEESES(ph)PVERPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPNKQEESESPVERPLK 17 3 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBF8 H3BLV9 SRPK1 SRSF protein kinase 1 1 RPNKQEES(0.437)ES(0.563)PVERPLK;RPNKQEES(0.25)ES(0.75)PVERPLK 186.63 2.83E-09 428790000 532690 300554 422670 290845 538410 509210 594020 444490 488830 242507 TRUE FALSE 553721.0125 352171.8115 433685.1274 348373.2729 446891.2605 390953.6947 547459.1602 438532.3386 471237.1038 290021.6036 1.909240573 1.214295098 1.49535456 1.201197665 1.540889558 1.348015768 1.887649587 1.512067836 1.624834488 1 18.14580084 RPNPCAYT(ph)PPSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPNPCAYTPPSLK 13 1 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 RPNPCAY(0.005)T(0.995)PPS(0.001)LK;RPNPCAY(0.006)T(0.994)PPS(0.001)LK;RPNPCAYT(0.999)PPSLK 91.371 0.0038457 1006850000 1209000 850980 1053850 889750 1186290 1215460 1082080 1004750 1051020 848390 TRUE FALSE 1256732.254 997129.1953 1081314.197 1065739.894 984644.8495 933187.8355 997263.7421 991282.9697 1013193.996 1014615.777 1.238628732 0.982765316 1.065737613 1.050387662 0.970460811 0.919745047 0.982897925 0.977003307 0.9985987 1 19.95250207 7.798057966 1.041547377 0.984449244 200 0.749151345 0.041534094 668.9199798 1.165938071 0.012418898 317466.3253 62814219.28 -7.798057966 199.0155507 RPNT(ph)SPDR ddPTM_MDA-MB-175_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(0.621)S(0.379)PDR 94.82 0.005912 673921000 388877 459596 387847 401924 340349 469176 419875 374104 353046 352539 TRUE FALSE 404230.1642 538528.0378 397954.6114 481423.3676 282496.5985 360216.9844 386964.1004 369089.7478 340339.9434 421612.2673 0.958772302 1.277306378 0.943887648 1.141862808 0.67003885 0.854379752 0.917819832 0.875424594 0.807234442 1 18.68555732 3.260129612 24.99974691 0.8542892 1.084763015 0.471070892 0.117443527 197.4389038 228841.9258 0.030553383 0.041332888 1820.244017 -3.260129612 0.230473816 RPNTS(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPNTSPDR 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.211)S(0.789)PDR;RPNT(0.436)S(0.564)PDR 95.618 0.0058326 667316000 213591 247094 239611 231016 198383 255999 264083 254801 203324 209054 TRUE FALSE 222023.7376 289530.4724 245855.4595 276710.2753 164661.9285 196547.112 243383.4844 251385.8094 196006.409 250014.1287 0.888044763 1.158056442 0.983366263 1.106778552 0.658610493 0.786144019 0.973478922 1.005486413 0.783981329 1 17.9316501 RPNTSPDRGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPNTSPDRGSR 11 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RPNT(0.095)S(0.036)PDRGS(0.869)R;RPNT(0.023)S(0.013)PDRGS(0.964)R;RPNT(0.005)S(0.001)PDRGS(0.993)R;RPNT(0.32)S(0.015)PDRGS(0.665)R;RPNT(0.058)S(0.008)PDRGS(0.935)R;RPNT(0.106)S(0.106)PDRGS(0.788)R 113.56 0.0010831 5901820000 1243848 1669310 1447459 1145535 1654534 1760558 992934 1284007 1384025 2052898 TRUE FALSE 1292956.079 1956001.007 1485180.971 1372118.404 1373296.902 1351695.086 915105.2385 1266796.986 1334214.211 2455124.058 0.526635742 0.796701495 0.60493113 0.558879458 0.559359474 0.550560808 0.372732789 0.515980845 0.543440649 1 21.2273645 -1.1777309 5.124671165 1.00002715 0.55575419 0.644464097 0.098286302 3.28E-05 5.26E-06 0.102383221 0.024130484 0.066415447 1.1777309 -0.44427296 RPPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPPDEQR 7 1 B8ZZU8;Q15370;Q15370-2;I3L0M9;A0A0B4J296 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 ;;; 153.71 0.0027702 3488700000 298891 369384 317010 334110 322988 396722 314310 321021 304992 397180 FALSE TRUE 310691.4475 432822.8286 325271.541 400195.9608 268086.6151 304589.3279 289673.5609 316718.2386 294015.3975 474999.8165 0.65408751 0.911206307 0.684782456 0.842518138 0.564393092 0.641240938 0.609839311 0.666775497 0.618980023 1 18.85756743 3.247750909 24.99716488 0.660301142 0.776697989 0.083613036 0.132347771 348.2005204 947083.1065 0.033322072 0.044506917 1769.093999 -3.247750909 0.116396847 RPPEEDFRHS(ph)PEEDFR ddPTM_MDA-MB-175_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 185.87 8.30E-10 4693490000 1286010 1511770 1420310 1344000 1524870 1687050 1458290 1430390 1388720 1562480 TRUE FALSE 1336782.668 1771404.738 1457324.445 1609839.189 1265673.142 1295258.205 1343985.419 1411217.962 1338740.238 1868618.041 0.715385723 0.94797583 0.779894239 0.861513243 0.677331116 0.693163705 0.71924031 0.755220131 0.716433326 1 20.83354027 5.069305801 15.02776878 0.780402536 9.47E-05 0.033864885 0.104682579 3717285.947 17409086.18 0.024196791 90020221.66 117302.1037 -5.069305801 -0.780307856 RPPEEDFRHS(ph)PEEDFRQS(ph)PQEHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPPEEDFRHSPEEDFRQSPQEHFR 24 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 2 RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR;RPPEEDFRHS(1)PEEDFRQS(1)PQEHFR 153.88 3.35E-08 6382210000 882874 1064621 993871 957855 1043965 1162227 962479 1030420 936207 1063725 TRUE FALSE 917730.5472 1247461.375 1019772.095 1147315.86 866512.2022 892317.393 887037.381 1016608.905 902513.0929 1272141.548 0.721406002 0.980599508 0.801618418 0.901877517 0.681144487 0.70142933 0.697278839 0.799131911 0.709443925 1 20.27882777 3.246702348 24.97614282 0.750475581 0.857051591 0.126473657 0.107285479 287.3972286 881634.4718 0.027494305 0.036595529 1764.827848 -3.246702348 0.106576009 RPPEGHPTPRPAS(ph)PEPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPPEGHPTPRPASPEPGR 18 2 Q8WXD9 Q8WXD9 CASKIN1 Caskin-1 1 RPPEGHPT(0.002)PRPAS(0.998)PEPGR 133.48 6.56E-06 146360000 26426 61831 49408 49099 45740 57829 34469 47548 44651 64602 TRUE FALSE 27469.31889 72449.99327 50695.61307 58810.63565 37965.13114 44399.09116 31767.22971 46910.69683 43044.01923 77259.52502 0.355546049 0.937748365 0.656172984 0.761208869 0.491397418 0.574674659 0.411175576 0.607183345 0.557135437 1 16.23742519 -1.769623724 6.373630495 1.013593928 0.600351448 0.368390398 0.159056469 0.029545492 0.001067928 0.148096087 0.035102622 0.016997157 1.769623724 -0.41324248 RPPES(ph)PPIVEEWNSR ddPTM_MDA-MB-175_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 208.87 1.64E-09 2886060000 296215 385827 367937 365155 422090 451509 411577 402121 360518 390563 TRUE FALSE 307909.7969 452089.7859 377525.7405 437381.5691 350343.2926 346652.8774 379316.5193 396731.2257 347543.0276 467086.3421 0.659213874 0.967893396 0.808256861 0.936404107 0.750061094 0.742160167 0.812090796 0.849374495 0.744065917 1 18.83332973 -0.98424289 8.122561291 1.000000001 0.815414171 0.295038232 0.088447914 1.19E-09 2.19E-10 0.079576784 0.018756428 0.103694831 0.98424289 -0.184585829 RPPS(ph)PDVIVLS(ph)DNEQPS(ph)SPR ddPTM_MDA-MB-175_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(0.701)S(0.299)PR 107.95 8.93E-05 254640000 76785 90264 87965 81331 106640 100540 92672 87397 89661 87936 TRUE FALSE 79816.53109 105766.1398 90257.44016 97418.02905 88513.37089 77191.1087 85408.12649 86225.58617 86434.11812 105165.3756 0.75896207 1.005712567 0.858242931 0.926331775 0.841658867 0.733997366 0.812131617 0.819904704 0.8218876 1 16.68230027 3.062238243 7.142051243 0.820473406 0.893039312 0.054344606 0.085311817 0.41946228 39.62250649 0.022878086 0.027369944 1154.086186 -3.062238243 0.072565906 RPPS(ph)PDVIVLS(ph)DNEQPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.36)S(0.64)PR;RPPS(1)PDVIVLS(1)DNEQPS(0.313)S(0.687)PR 193.3 3.20E-18 5352700000 935630 1053680 1042160 1029700 1105160 1237980 1068410 1119520 1076330 1209450 TRUE FALSE 972569.3949 1234641.344 1069319.546 1233371.587 917305.298 950477.9068 984665.2324 1104514.666 1037593.094 1446418.571 0.672398305 0.853585102 0.73928776 0.852707239 0.634190763 0.657125071 0.680760917 0.763620357 0.717353271 1 20.46405368 -1.643871806 4.897617142 1.004815985 0.732782627 0.557394226 0.072113413 0.003846186 0.000279674 0.070818152 0.016444966 0.02270535 1.643871806 -0.272033358 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_MDA-MB-175_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 180.79 1.87E-16 417360000 219022 247397 245680 247520 235591 314210 249561 233614 227621 274560 TRUE FALSE 227669.1577 289885.5103 252082.6226 296478.7172 195545.326 241239.4894 229999.7567 230482.7864 219428.9647 328354.7752 0.693363322 0.882842377 0.767714197 0.902921899 0.595530629 0.734691582 0.700461129 0.70193219 0.668267926 1 18.32489591 5.047244552 15.24490196 0.756824407 0.360160536 0.024183116 0.117053719 5313426.995 48175577.12 0.026625777 60402040.51 111492.2171 -5.047244552 -0.396663871 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JHD7;C9JJK9;C9JMI3;C9JGN4 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 RPPS(1)PDVIVLSDNEQPS(0.13)S(0.87)PR;RPPS(1)PDVIVLSDNEQPS(0.115)S(0.885)PR;RPPS(1)PDVIVLSDNEQPS(0.115)S(0.885)PR;RPPS(1)PDVIVLSDNEQPS(0.033)S(0.967)PR 250.9 2.32E-30 2233560000 652400 721800 702120 695120 708540 767240 713210 662830 612740 747650 TRUE FALSE 678157.2558 845763.5352 720417.824 832612.6613 588102.6239 589060.1376 657306.7366 653945.848 590687.6071 894137.7029 0.758448339 0.945898526 0.805712388 0.931190642 0.657731602 0.658802482 0.735129203 0.731370398 0.660622637 1 19.77013751 3.237880029 24.99999675 0.723676874 0.862525758 0.221421394 0.107146587 22.16554201 814220.2672 0.027824667 0.035194412 1729.338575 -3.237880029 0.138848883 RPPS(ph)PEPSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.989)PEPS(0.01)TK;RPPS(1)PEPSTK;RPPS(0.999)PEPS(0.001)TK;RPPS(0.997)PEPS(0.003)TK;RPPS(0.995)PEPS(0.005)TK;RPPS(0.994)PEPS(0.006)TK;RPPS(0.999)PEPS(0.001)TK;RPPS(0.998)PEPS(0.001)TK 99.844 0.0027062 79044110000 9080860 8529350 9096170 8305100 11119180 12092020 10764640 9259130 9958710 8055780 TRUE FALSE 9439379.365 9994199.513 9333223.663 9947823.992 9229145.755 9283831.611 9920879.389 9135026.507 9600297.972 9634155.854 0.979782714 1.037371583 0.968764031 1.032557926 0.957961019 0.963637266 1.029761148 0.948191689 0.996485641 1 23.19972683 3.230012441 24.99996546 0.980312209 1.004397458 0.114731358 0.029427331 364.109735 1064872.503 0.007966499 0.009660497 1698.292301 -3.230012441 0.024085249 RPPSAFFLFCSEHRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPPSAFFLFCSEHRPK 16 2 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 134.85 1.56E-05 2010420000 872810 1105790 1372380 1052910 1543950 1632420 1399960 1479620 1448690 1337400 FALSE TRUE 907269.2128 1295700.831 1408145.35 1261172.455 1281509.93 1253315.195 1290227.477 1459788.114 1396551.93 1599437.924 0.567242529 0.810097604 0.880400126 0.788509786 0.801225175 0.783597272 0.806675556 0.912688196 0.873151692 1 20.60913357 7.819264804 0.083905014 1.131602861 1.76E-15 0.588829216 0.068536221 132.9677648 0.837098771 1.663658822 17.39938468 65957593.79 -7.819264804 -1.131602861 RPPSAFFLFCSEYRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPPSAFFLFCSEYRPK 16 2 P09429;Q5T7C4 P09429 HMGB1 High mobility group protein B1 0 ; 225.01 4.09E-15 11166500000 2211640 1820900 2293440 1832740 2637600 2630200 2275430 2281410 2314220 2041540 FALSE TRUE 2298957.255 2133625.41 2353208.93 2195250.502 2189261.694 2019375.911 2097075.851 2250831.431 2230931.674 2441540.675 0.941601046 0.873884851 0.963821309 0.899125099 0.896672219 0.827090833 0.858914976 0.921889794 0.913739303 1 21.21936038 0.698146532 1.566353275 0.99970949 0.895517392 0.403050865 0.037241361 1.115992179 4.192828124 0.036511864 0.010526284 4.990528406 -0.698146532 -0.104192098 RPPSGFFLFCSEFRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPPSGFFLFCSEFRPK 16 2 O15347;E7ES08;E7EQU1;E9PES6 O15347 HMGB3 High mobility group protein B3 0 ; 185.71 9.10E-10 1108760000 757260 652640 904790 620170 1034710 1064370 861490 815170 953370 808000 FALSE TRUE 787157.2095 764725.8432 928369.5707 742837.775 858830.3638 817186.1982 793964.1627 804243.9795 919058.3999 966312.1299 0.814599326 0.79138595 0.960734676 0.768734814 0.888771172 0.845675194 0.821643585 0.83228178 0.951098896 1 19.88212975 1.119157535 3.780806806 0.997659293 0.840689122 0.540519406 0.050660405 0.149088446 3.697413223 0.04477261 0.011659446 13.15702 -1.119157535 -0.156970171 RPPSPEPS(ph)TK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPPSPEPSTK 10 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RPPS(0.304)PEPS(0.569)T(0.127)K 73.346 0.047946 2284500000 430370 361570 400410 341020 498100 510940 475190 433910 471460 364740 TRUE FALSE 447361.3399 423666.8349 410845.0135 408472.7382 413433.1399 392281.9284 437943.3661 428094.1462 454492.2467 436203.8196 1.025578685 0.971258884 0.941864778 0.936426321 0.947798074 0.899308788 1.003987921 0.981408523 1.041926334 1 18.73464288 1.809151046 2.103943208 1.013387381 0.953923987 0.329521426 0.034364095 0.355059218 3.033854932 0.022431165 0.0100615 64.43933437 -1.809151046 -0.059463393 RPPT(ph)PCS(ph)DPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPPTPCSDPER 11 1 Q9BW71;Q9BW71-2;Q9BW71-3 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 RPPT(1)PCS(1)DPER;RPPT(1)PCS(1)DPER 99.834 0.0099236 447710000 388950 440100 391630 418140 426270 496640 391200 406120 393300 470850 TRUE FALSE 404306.0463 515683.7515 401836.1995 500846.844 353812.7777 381302.8867 360536.7218 400676.6257 379145.2098 563104.0425 0.717995283 0.915787692 0.713609154 0.889439262 0.628325764 0.677144644 0.64026662 0.711549901 0.673312889 1 19.10304198 4.174211144 24.99875289 0.724504096 0.81689806 0.044268094 0.120066149 124.7577434 48465.31404 0.028038265 0.060569619 14935.20348 -4.174211144 0.092393964 RPPT(ph)PGPDTSVSGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPPTPGPDTSVSGPR 15 1 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 RPPT(0.999)PGPDTSVSGPR;RPPT(0.998)PGPDT(0.001)SVSGPR 76.027 0.013843 179910000 116615 135923 123232 141462 149099 177292 141491 111909 107827 124304 TRUE FALSE 121219.0502 159266.7179 126443.5272 169442.7614 123755.2052 136118.6199 130400.5657 110409.0429 103946.3273 148658.9889 0.815416889 1.071356123 0.850560926 1.139808381 0.832477109 0.915643386 0.877179151 0.74270008 0.699226654 1 17.18164717 2.285543727 1.560715818 0.791508524 0.955669828 0.157163083 0.121980655 0.530875919 2.58048428 0.06155445 0.038976325 192.9939643 -2.285543727 0.164161305 RPQGGSDAPSGHAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPQGGSDAPSGHAAPSR 17 1 Q96IQ9-2;M0R0Q5;M0R398 Q96IQ9-2 ZNF414 Zinc finger protein 414 0 ; 92.211 0.0021843 42418000 8310.5 21316.5 21751 19291.1 21647.2 26923 18121.7 19411.2 17192.3 20970.2 FALSE TRUE 8638.604957 24977.44306 22317.84893 23106.822 17967.61668 20670.54127 16701.2738 19151.02461 16573.55248 25078.90919 0.344456965 0.995954125 0.88990509 0.921364714 0.716443309 0.824220109 0.665948972 0.763630685 0.660856194 1 14.61418698 RPQLDLDILSSLIDLCDSPVS(ph)PAEASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPQLDLDILSSLIDLCDSPVSPAEASR 27 1 Q9BQ89 Q9BQ89 FAM110A Protein FAM110A 1 RPQLDLDILSSLIDLCDSPVS(1)PAEASR 194.99 3.48E-19 186850000 59888 78558 89679 88948 101090 113860 87940 95326 93952 111530 TRUE FALSE 62252.42448 92049.7254 92016.10841 106541.6489 83906.75791 87417.74056 81047.03301 94048.31089 90570.68587 133382.1681 0.466722241 0.690120176 0.689868141 0.798769809 0.62907028 0.655393009 0.607630196 0.70510408 0.679031441 1 17.02520628 -5 0.329604435 4.398914362 0.650423653 0.629625152 0.079298331 230.1038351 1.99141529 547.7835692 0.065854497 1.00E-05 5 -3.748490709 RPQS(ph)PGAS(ph)PSQAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 2 RPQS(1)PGAS(0.962)PS(0.038)QAER 97.256 0.010663 416960000 158860 173590 161820 162140 166590 208730 176460 165730 158880 153410 TRUE FALSE 165131.9155 203402.7322 166037.1621 194210.8081 138273.0913 160255.6208 162628.6041 163508.6604 153161.9398 183467.7523 0.90005962 1.108656587 0.904993712 1.058555553 0.753664279 0.873481137 0.886415199 0.891211989 0.83481668 1 17.48516698 3.254433582 24.9997038 0.870450057 0.9950319 0.340955618 0.081522674 251.2575851 395724.8953 0.020766048 0.028025568 1796.526309 -3.254433582 0.124581843 RPQS(ph)PSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPQSPSPR 8 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 RPQS(1)PSPR;RPQS(0.999)PS(0.001)PR 93.258 0.006858 199532000 86054 134509 86706 107103 75418 112935 82632 98233 81527 136396 TRUE FALSE 89451.47837 157609.8744 88965.62959 128287.6537 62598.4753 86707.5578 76155.08792 96916.34731 78592.8592 163120.1847 0.548377741 0.966219323 0.545399269 0.786460939 0.38375677 0.531556275 0.466864895 0.59414074 0.481809528 1 17.31557579 -0.993194401 4.283821686 1.00001802 0.592022173 0.37135724 0.160235681 9405090.984 3293236.387 1689.476304 0.03708302 0.10157939 0.993194401 -0.407995847 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 RPQYSNPPVQGEVMEGADNQGAGEQGRPVR 30 2 P67809;H0Y449;C9J5V9 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ;;;;;;;;; 213.37 7.31E-27 4661595000 965269 1139006 1074397 1022452 1152036 1394002 1026446 1122839 1061987 1219320 FALSE TRUE 1003378.565 1334621.42 1102396.668 1224689.954 956213.3322 1070266.162 945990.4804 1107789.18 1023766.295 1458222.409 0.688083354 0.915238589 0.755986646 0.839851278 0.655739019 0.733952623 0.648728531 0.75968465 0.702064575 1 20.47577935 -1.35699713 3.667509746 1.001109582 0.746418344 0.491573945 0.077967427 746182160.3 1981419120 10263919.47 0.018526743 0.043954452 1.35699713 -0.254691239 RPS(ph)ANCDPFSVTEALIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPSANCDPFSVTEALIR 17 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 1 RPS(1)ANCDPFSVTEALIR;RPS(1)ANCDPFSVTEALIR;RPS(1)ANCDPFSVTEALIR 156.23 4.34E-08 211576000 154544 188745 152578 186312 179082 202831 173954 165140 165511 158170 TRUE FALSE 160645.5165 221160.4855 156554.308 223163.9575 148641.7056 155726.5742 160319.0309 162926.5684 159554.2914 189160.3832 0.849255609 1.169169156 0.827627357 1.179760549 0.785797233 0.823251526 0.847529637 0.861314434 0.843486827 1 17.52925044 3.207934839 24.99972878 0.851453223 1.005302782 0.265656268 0.118556066 234.3094058 191265.4199 0.030889198 0.036923598 1614.11636 -3.207934839 0.153849559 RPS(ph)ASSPNNNTAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.969)AS(0.031)SPNNNTAAK 170.9 1.90E-06 91421000 41009 39346 50202 43659 71143 64791 60993 53659 54975 47039 TRUE FALSE 42628.06699 46103.36943 51510.30536 52294.61989 59050.13827 49744.27217 56212.20928 52939.78887 52996.46049 56255.39143 0.757759672 0.819536906 0.915650999 0.929593032 1.049679627 0.884257862 0.999232391 0.941061604 0.942069002 1 15.77970375 4.306414783 1.574343181 0.963087351 0.745282185 0.732677623 0.042659877 0.246817065 0.998838564 0.011055086 0.065035937 20249.52233 -4.306414783 -0.217805166 RPS(ph)DSGPPAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSDSGPPAER 11 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 RPS(0.749)DS(0.251)GPPAER;RPS(0.979)DS(0.021)GPPAER 95.822 0.0045763 983820000 160454 219070 202012 209690 213892 249390 198846 211116 183861 241573 TRUE FALSE 166788.8478 256693.5684 207276.5987 251166.0561 177534.7142 191472.952 183259.9309 208286.3353 177243.8785 288904.6042 0.577314606 0.888506326 0.71745689 0.86937367 0.614509813 0.662754935 0.634326793 0.720951942 0.613503129 1 18.14023367 -1.043674069 4.39043137 1.000017072 0.705626833 0.444849202 0.100402966 65202475535 14202333098 12862424.64 0.022588589 0.09043279 1.043674069 -0.294390239 RPS(ph)DSSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 1 RPS(0.993)DS(0.005)S(0.003)RPK 81.494 0.016636 59495000 72148 50091 64957 48674 71447 73093 69413 64025 70014 60011 TRUE FALSE 74996.45875 58693.7396 66649.83278 58301.57192 59302.46446 56118.25849 63972.22768 63166.8496 67494.20982 71769.00647 1.044970001 0.817814576 0.928671526 0.812350272 0.826296299 0.781928875 0.891362871 0.880141062 0.940436731 1 16.13107333 1.067362577 1.753150867 0.999672002 0.864911275 0.24800877 0.071073588 0.447229882 2.75553011 0.064101727 0.018499469 11.67784151 -1.067362577 -0.134760727 RPS(ph)EGPQPLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSEGPQPLVR 11 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 RPS(1)EGPQPLVR;RPS(1)EGPQPLVR 183.06 3.38E-06 604510000 165899 229134 176358 181390 188195 195305 160403 139611 146109 206662 TRUE FALSE 172448.8206 268485.9821 180954.0344 217268.4006 156205.6811 149948.3736 147830.1937 137739.7429 140850.5656 247153.4621 0.697739854 1.086312851 0.732152537 0.879082974 0.632018988 0.60670149 0.598131187 0.557304525 0.569891129 1 17.91504759 3.234384624 24.33277746 0.626786387 0.85745217 0.242707366 0.155774913 80.67828126 470099.2333 0.041102407 0.050847118 1715.47591 -3.234384624 0.230665783 RPS(ph)GRSPTSTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.464)GRS(0.158)PT(0.005)S(0.274)T(0.098)EK;RPS(0.925)GRS(0.075)PTSTEK 84.753 0.0094971 193604000 147292 138268 148549 92343 198289 192731 131315 139563 147006 147072 TRUE FALSE 153107.2019 162014.4534 152420.309 110608.1698 164583.9066 147972.1461 121022.1872 137692.3863 141715.2828 175887.9425 0.87048151 0.921123137 0.866576223 0.628855896 0.935731604 0.841286469 0.688064147 0.782841531 0.80571346 1 17.42429706 3.98444789 24.78945288 0.796754629 0.895314201 0.092148149 0.102062025 1095.319225 1745906.194 0.024766899 0.046510246 9648.235382 -3.98444789 0.098559572 RPS(ph)GS(ph)QHSPSLQTFAPEADGTIFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 2 RPS(0.896)GS(0.605)QHS(0.456)PS(0.032)LQT(0.012)FAPEADGTIFFPER 70.08 0.074609 82867000 13276 15905 18550 16207 20023 23662 18337 17896 16457 15735 TRUE FALSE 13800.14673 18636.56003 19033.42824 19412.69623 16619.49761 18166.8591 16899.69803 17656.13339 15864.71578 18817.97199 0.733349308 0.990359643 1.011449494 1.031604056 0.883171557 0.965399413 0.8980616 0.938259096 0.84306193 1 14.19982354 2.234601468 24.99239933 0.916630462 0.94375387 0.002691104 0.087210486 552.5777768 3488142.472 0.031503883 0.024164342 171.6332665 -2.234601468 0.027123409 RPS(ph)GSQHS(ph)PSLQTFAPEADGTIFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 2 RPS(0.967)GS(0.037)QHS(0.539)PS(0.38)LQT(0.078)FAPEADGTIFFPER 156.65 6.15E-08 122720000 16116 42831 34825 40668 33974 54230 47034 50002 33786 38506 TRUE FALSE 16752.27212 50186.89107 35732.56811 48712.00902 28199.11162 41635.90436 43347.35218 49331.80498 32570.04846 46050.51346 0.363780355 1.089822617 0.775942882 1.057795133 0.612351731 0.904135508 0.941300084 1.071254179 0.707267868 1 15.49092962 4.75062202 24.74117647 0.909409434 0.36377997 0.528121994 0.153925397 1250.428944 2564911.212 0.034917362 0.586539274 56314.73181 -4.75062202 -0.545629464 RPS(ph)GSQHSPSLQTFAPEADGTIFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.247)GS(0.247)QHS(0.247)PS(0.205)LQT(0.053)FAPEADGTIFFPER 174.4 9.43E-13 181540000 20823 56753 47393 63983 39353 71104 52813 49024 46103 47075 TRUE FALSE 21645.10812 66499.88627 48628.10051 76638.64643 32663.79112 54591.17359 48673.37906 48366.91347 44443.76204 56298.44494 0.384470799 1.181202897 0.863755661 1.361292421 0.580189935 0.969674627 0.86455992 0.859116331 0.789431432 1 15.78080745 RPS(ph)HPKQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSHPKQPR 9 2 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 RPS(1)HPKQPR 103.22 0.0018041 6481900 8681 5188.8 8159.2 3972.7 11436 9458.8 7602.8 8063.7 9815.8 8620.3 TRUE FALSE 9023.732583 6079.936037 8371.835455 4758.488203 9492.112805 7262.13705 7006.87267 7955.619291 9462.531275 10309.28274 0.875301688 0.589753544 0.812067693 0.461573159 0.92073455 0.704426994 0.67966636 0.771694743 0.917865143 1 13.33165634 1.195380575 2.313066854 0.997576076 0.716020697 0.364784517 0.12609613 0.2742362 2.561197486 0.107017488 0.03033825 15.68124625 -1.195380575 -0.281555379 RPS(ph)ILPEGSSDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPSILPEGSSDSR 13 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 RPS(1)ILPEGSSDSR;RPS(1)ILPEGSSDSR;RPS(0.988)ILPEGS(0.009)S(0.003)DSR 123.14 0.00013897 945960000 1304954 1468865 1355627 1502448 1706771 1570856 1249050 1399211 1380089 1496062 TRUE FALSE 1356474.592 1721131.138 1390955.753 1799627.73 1416654.675 1206048.501 1151146.197 1380456.865 1330419.866 1789186.705 0.758151504 0.961962848 0.777423479 1.005835626 0.791786945 0.674076382 0.643390762 0.771555513 0.743589175 1 20.77087251 3.009885765 24.87952781 0.742883678 0.877945599 0.15771321 0.113769389 268.7123904 676263.0285 0.030468516 0.036377146 1023.023865 -3.009885765 0.135061922 RPS(ph)LGELLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSLGELLLR 10 1 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 RPS(1)LGELLLR;RPS(1)LGELLLR 143.05 2.12E-05 159745000 111885 129927 120578 131736 133503 147282 128027 128609 128321 120174 TRUE FALSE 116302.3062 152240.9516 123720.3617 157792.9876 110810.2077 113077.9876 117991.9092 126885.2067 123702.7523 143719.7944 0.809229561 1.059290073 0.860844271 1.09792105 0.771015629 0.786794805 0.820985792 0.882865212 0.860721745 1 17.13289925 3.214848181 24.99966789 0.845117569 0.957285093 0.206093795 0.098253126 316.7818452 333977.5722 0.026440244 0.031618375 1640.016362 -3.214848181 0.112167523 RPS(ph)LPALHFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSLPALHFIK 11 1 P00519-2;R4GRW0 P00519-2 ABL1 Tyrosine-protein kinase ABL1 1 RPS(1)LPALHFIK;RPS(1)LPALHFIK 128.71 0.00015938 1327900000 1075650 949010 1076700 853530 1870770 1346020 1102580 1096010 1090980 1354280 TRUE FALSE 1118117.493 1111995.085 1104759.687 1022355.686 1552777.184 1033427.254 1016156.899 1081319.779 1051715.843 1619625.237 0.690355687 0.686575548 0.68210822 0.631229783 0.958726222 0.638065665 0.627402485 0.667635793 0.64935753 1 20.6272286 -1.403582388 2.999453479 1.005008934 0.691701928 0.502057842 0.091903472 76618801.57 93071197.46 3292988.077 0.02304169 0.039483679 1.403582388 -0.313307006 RPS(ph)LPPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSLPPSK 8 1 Q6PJT7-5;Q6PJT7;G3V256;Q6PJT7-10;Q6PJT7-4;A0A087WTC9;H0YJ87;Q6PJT7-9;Q6PJT7-2;H0YJA2;Q6PJT7-3;Q6PJT7-11;G3V5I6 Q6PJT7-5;Q6PJT7-9 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 RPS(1)LPPSK 65.179 0.039777 134350000 67835 78880 80741 83735 112520 108600 89448 97819 94613 86321 TRUE FALSE 70513.17818 92427.0264 82845.17679 100297.5331 93393.89059 83379.29585 82436.83203 96507.8963 91207.89661 103233.9472 0.683042546 0.89531621 0.802499362 0.971555731 0.904681968 0.807673232 0.798543834 0.93484652 0.883506822 1 16.65555794 5.588840167 0.027300867 1.589091792 1.54E-10 0.344784886 0.07325946 1328.31588 4.465915813 100.3473212 166.3725774 388007.542 -5.588840167 -1.589091792 RPS(ph)PAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSPAEK 7 1 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 RPS(1)PAEK 100.69 0.0058869 166410000 524880 352920 432470 358270 521530 554330 548480 421890 473550 331700 TRUE FALSE 545602.6677 413531.2647 443740.5235 429134.7367 432880.5169 425595.2585 505488.7044 416235.2546 456507.028 396690.2642 1.375387089 1.042453778 1.118607043 1.081787922 1.091230504 1.072865399 1.274265466 1.049270154 1.150789594 1 18.59765346 4.74664272 24.90750004 1.104202177 1.375387229 0.57649537 0.07116218 676.1342352 2083666.498 0.015833115 0.177627482 55801.09481 -4.74664272 0.271185052 RPS(ph)PFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPSPFLK 7 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(1)PFLK;RPS(1)PFLK;RPS(1)PFLK;RPS(1)PFLK 112.13 0.0073704 820870000 772220 689370 703890 697590 852320 1019560 838490 757080 730660 611090 TRUE FALSE 802707.8419 807763.9349 722233.9517 835571.2199 707442.9508 782782.6416 772766.9628 746932.5809 704363.6893 730821.3855 1.09836392 1.105282291 0.988249613 1.143331649 0.968010741 1.071099802 1.057395115 1.022045326 0.963797315 1 19.47915933 8 0.153311049 0.978609529 1.431983356 0.277279549 0.050419374 86.20283123 0.861654833 0.155354424 8.74624433 100000000 -8 0.453373827 RPS(ph)PLAHQPVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSPLAHQPVPR 12 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RPS(1)PLAHQPVPR 110.84 0.00088571 134510000 28236 90949 47651 72908 48204 77027 55886 58979 51501 93840 TRUE FALSE 29350.77908 106568.7833 48892.82421 87328.98479 40010.3013 59138.64661 51505.50929 58188.48298 49647.48907 112226.1513 0.261532439 0.949589574 0.435663378 0.778151828 0.356514955 0.526959589 0.458943915 0.518493081 0.442387879 1 16.77604937 -1.527573391 6.038076202 1.000654695 0.533784384 0.358277275 0.190267582 0.001515655 0.000118587 0.166512562 0.039195615 0.029677452 1.527573391 -0.466870311 RPS(ph)PPEPWDEEDGASCSTFFGSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;RPS(1)PPEPWDEEDGASCSTFFGSEER 227.77 3.10E-34 910120000 138654 165549 157449 186156 147934 164829 169150 163059 155683 124803 TRUE FALSE 144128.167 193980.753 161552.2503 222977.1012 122788.2315 126549.9628 155891.581 160873.4608 150079.9992 149255.7584 0.965645604 1.299653394 1.082385377 1.493926289 0.822669979 0.847873236 1.044459408 1.077837549 1.005522339 1 17.18742707 3.215997417 24.99994892 0.977465667 1.207633891 0.391090404 0.148758301 253.5964394 280983.286 0.042765765 0.051149276 1644.361945 -3.215997417 0.230168223 RPS(ph)PQPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR;RPS(1)PQPSPR 103.43 0.002097 1264980000 533885 569397 513358 584643 623651 707277 568591 579361 565386 573274 TRUE FALSE 554963.192 667186.5055 526736.5312 700283.6404 517643.0258 543022.6356 524023.3517 571595.6134 545037.8683 685596.0643 0.809460878 0.973148097 0.768289899 1.021423075 0.75502625 0.792044564 0.764332497 0.833720675 0.794983951 1 19.3869993 3.173247072 24.99999678 0.811053274 0.889901982 0.108990567 0.093618633 105.4738802 40371.01143 0.024591396 0.02939235 1490.208621 -3.173247072 0.078848708 RPS(ph)PTSGDSRPAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPSPTSGDSRPAAGR 15 2 Q8N1G1 Q8N1G1 REXO1 RNA exonuclease 1 homolog 1 RPS(0.907)PT(0.066)S(0.027)GDSRPAAGR;RPS(0.751)PT(0.123)S(0.123)GDS(0.004)RPAAGR;RPS(0.435)PT(0.435)S(0.124)GDS(0.005)RPAAGR;RPS(0.967)PT(0.025)S(0.008)GDSRPAAGR;RPS(0.942)PT(0.045)S(0.013)GDSRPAAGR 146.67 3.03E-06 1783400000 256669 314919 308243 291518 314726 355525 289314 312261 287582 317726 TRUE FALSE 266802.4903 369003.8885 316276.0658 349179.3903 261228.9869 272959.7068 266636.8127 308075.6521 277231.98 379978.3265 0.702151864 0.971118253 0.83235291 0.918945545 0.687483914 0.71835599 0.701715846 0.810771643 0.729599455 1 18.53555761 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RPSQEQSASASSGQPQAPLNR 21 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.999)QEQS(0.001)ASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.98)QEQS(0.011)AS(0.003)AS(0.003)S(0.004)GQPQAPLNR 334.36 2.02E-80 9912628000 762660 957235.1 905392.3 781309.3 850536 1116216.1 911083.3 871951.2 796976.5 891141.3 TRUE FALSE 792770.4057 1121632.782 928987.5671 935849.9476 705962.1945 856991.8272 839670.2103 860264.1204 768293.4714 1065743.376 0.743866135 1.052441711 0.871680358 0.878119413 0.662412932 0.804125877 0.787872793 0.80719631 0.720899129 1 20.02342866 3.452770783 24.99346612 0.787165777 0.900517228 0.138094722 0.106955361 334.3303809 343157.6513 0.027301067 0.036967334 2836.421595 -3.452770783 0.113351451 RPS(ph)QGPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 127.56 0.00027075 7636597000 1058891 1348940 1180581 1213477 1419713 1553684 1160777 1273235 1181355 1521150 TRUE FALSE 1100696.834 1580609.952 1211347.911 1453499.129 1178390.691 1192864.437 1069792.266 1256169.367 1138838.264 1819190.218 0.605047687 0.86885359 0.665872045 0.79898139 0.647755622 0.65571177 0.588059596 0.690510181 0.626013846 1 20.79486497 -1.063665917 4.561665785 1.000013366 0.685721012 0.568029014 0.082906683 1.37E-05 2.81E-06 0.077548895 0.018277472 0.086364265 1.063665917 -0.314292354 HGSGPNIILTGDS(ph)SPGFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HGSGPNIILTGDSSPGFSK 19 0 Q53ET0;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 HGSGPNIILTGDS(0.596)S(0.403)PGFS(0.001)K 101.3 0.00032128 133420000 21898 75879 83377 81447 98791 121530 94253 113240 86164 92525 TRUE FALSE 22762.54995 88910.62799 85549.87311 97556.9735 81998.54111 93306.4993 86865.20358 111722.203 83062.97447 110653.5023 0.205710163 0.80350487 0.773132991 0.881643794 0.741038823 0.843231325 0.785019921 1.009658084 0.750658341 1 16.75568959 4.756598768 3.540323262 0.848763057 0.116084106 0.818912252 0.090098939 0.124220239 2.663975731 0.021339873 0.247901003 57095.09076 -4.756598768 -0.732678952 down RPS(ph)QGPPARSPSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 RPS(0.407)QGPPARS(0.407)PS(0.078)QDFS(0.108)FIEDTEILDSAMYR;RPS(0.58)QGPPARS(0.414)PS(0.006)QDFSFIEDTEILDSAMYR 194.11 3.35E-19 97865000 18681.5 26773 25463 19298.3 26306 30167 19280.7 22996.9 22357.2 34509 TRUE FALSE 19419.06005 31371.05448 26126.5867 23115.44614 21834.51552 23161.17144 17769.42835 22688.66417 21552.56874 41270.37784 0.470532645 0.760134899 0.633059062 0.560097759 0.529060228 0.561205704 0.43056132 0.549756638 0.52222853 1 15.33281903 -1.581824525 6.341226769 1.000983954 0.558713933 0.708313624 0.085203004 0.001217555 8.03E-05 0.084747129 0.019934779 0.026192411 1.581824525 -0.442270021 RPS(ph)QNAISFFNVGHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 RPS(1)QNAISFFNVGHSK;RPS(1)QNAISFFNVGHSK 271.43 2.30E-35 3716300000 1436100 1421320 1490980 1379110 1919540 2133350 1526770 1366130 1607920 1638090 TRUE FALSE 1492798.337 1665420.654 1529836.164 1651893.842 1593257.276 1637911.794 1407097.778 1347819.262 1550051.273 1959042.372 0.762004109 0.850119771 0.780910196 0.843214963 0.813283724 0.836077778 0.71825796 0.687999035 0.791229069 1 20.90171717 2.255045853 24.97694791 0.762256042 0.815652742 0 0.084419924 600.6579959 910061.1669 0.027662736 0.023081918 179.9060849 -2.255045853 0.0533967 RPS(ph)RHDNSAIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPSRHDNSAIGR 12 2 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 RPS(0.996)RHDNS(0.004)AIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR;RPS(1)RHDNSAIGR 178.22 1.16E-05 396068000 65539.9 105395 102709 90381 106969 128705 84273 101380 104618.5 116121 TRUE FALSE 68127.46586 123495.7714 105385.6809 108258.092 88786.44759 98815.21429 77667.46205 100021.1669 100853.3006 138872.6867 0.490574983 0.889273293 0.758865429 0.779549202 0.639337005 0.71155255 0.559270969 0.720236422 0.726228483 1 17.08340335 -1.562144115 3.966656745 1.005477409 0.701187222 0.418903354 0.106894485 0.004977033 0.000549385 0.099484406 0.023084735 0.027406646 1.562144115 -0.304290186 RPS(ph)SEDFVFL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSSEDFVFL 10 1 Q86TL0;K7EQ67;K7EN30;Q86TL0-2 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 RPS(0.5)S(0.5)EDFVFL 65.232 0.073711 48475000 50837 60673 63182 71047 66551 78570 77859 68384 66902 71978 TRUE FALSE 52844.08401 71093.11578 64828.57482 85099.88455 55238.68479 60323.30824 71756.20813 67467.42433 64494.21009 86080.711 0.613889957 0.82588904 0.75311384 0.988605735 0.641708045 0.700776138 0.833592187 0.783769367 0.749229524 1 16.39340237 -2.198426437 2.116237345 1.599710507 0.771989602 0.32554012 0.100834419 7149969.937 1330611.806 20529627.68 0.023337534 0.006332476 2.198426437 -0.827720905 RPS(ph)SMYSTGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.815)S(0.185)MYSTGGK;RPS(0.5)S(0.5)MYSTGGK;RPS(0.98)S(0.02)MYSTGGK;RPS(0.964)S(0.036)MYSTGGK 158.52 1.86E-05 427381000 823061 809733 849156 822202 1190970 1062935 827144 831233 802077 870598 TRUE FALSE 855556.0838 948798.3439 871285.7029 984831.1016 988529.3448 816084.4552 762310.2919 820091.6813 773210.4054 1041175.009 0.821721686 0.911276524 0.836829251 0.945884306 0.949436296 0.783811029 0.732163455 0.787659782 0.742632505 1 19.98978116 2.719917157 24.32910904 0.78923304 0.893857459 0.19428957 0.080273374 713.5611948 931172.5546 0.024326466 0.022976856 524.7073606 -2.719917157 0.104624419 RPS(ph)SNLNNNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSSNLNNNVR 11 1 Q9NW75-2;Q9NW75 Q9NW75-2 GPATCH2 G patch domain-containing protein 2 1 RPS(0.984)S(0.016)NLNNNVR;RPS(0.873)S(0.127)NLNNNVR 155.34 1.93E-05 208496000 50977 61347 55862 64698 60704 72884 55615 61973 56822 73067 TRUE FALSE 52989.61132 71882.87004 57317.80961 77495.0713 50385.55576 55957.79557 51255.75098 61142.3533 54776.98732 87383.0797 0.606405857 0.822617723 0.655937166 0.886842986 0.576605402 0.640373351 0.586563796 0.69970472 0.626860343 1 16.41506633 -1.812745905 8.414609664 1.008473727 0.681033838 0.499648516 0.096627694 0.01469694 0.000327057 0.089516408 0.021107104 0.015390548 1.812745905 -0.32743989 RPS(ph)STALHQHHF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPSSTALHQHHF 12 1 Q9UGP4 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 RPS(0.484)S(0.484)T(0.031)ALHQHHF;RPS(0.333)S(0.333)T(0.333)ALHQHHF;RPS(0.471)S(0.471)T(0.058)ALHQHHF;RPS(0.49)S(0.49)T(0.02)ALHQHHF 109.1 0.00076834 909150000 159624 183268 178898 175191 253212 271479 197487 184509 190484 261710 TRUE FALSE 165926.0788 214742.8534 183560.2288 209843.2569 210171.1147 208432.1166 182007.4529 182035.9587 183628.518 312987.0638 0.530137178 0.68610776 0.586478644 0.670453451 0.671500963 0.665944829 0.581517494 0.58160857 0.58669683 1 18.2557435 -1.339944984 5.417537939 1.000101138 0.619114457 0.840649669 0.049914329 6.06E-05 7.39E-06 0.048061738 0.011325271 0.04571461 1.339944984 -0.380986681 RPS(ph)T(ph)SSASGQWSPTPEWVLSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.72)T(0.492)S(0.357)S(0.333)AS(0.091)GQWS(0.006)PT(0.001)PEWVLSWK;RPS(0.698)T(0.347)S(0.302)S(0.298)AS(0.298)GQWS(0.047)PT(0.01)PEWVLSWK 87.091 0.0024992 49599000 43573 38244 52866 44326 58352 55931 55973 49260 50006 51200 TRUE FALSE 45293.29569 44812.1095 54243.73139 53093.5505 48433.34788 42941.87289 51585.69 48599.75027 48206.29383 61231.65972 0.73970387 0.731845416 0.885877202 0.867093114 0.790985384 0.701301795 0.84246761 0.793702972 0.787277269 1 15.90199017 -1.810002652 2.358124997 1.072801158 0.795717374 0.548141701 0.056247669 7242254.217 4372554.591 3002311.001 0.014819812 0.015488072 1.810002652 -0.277083784 RPS(ph)TFGIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSTFGIPR 9 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 RPS(0.978)T(0.022)FGIPR;RPS(0.5)T(0.5)FGIPR 128.08 0.00026177 227012000 42313 39785 58651 51061 58357 70279 51964 62292 55708 58173 TRUE FALSE 43983.54991 46617.76427 60179.49324 61160.7134 48437.49798 53957.76734 47890.9259 61457.07763 53703.07996 69570.88556 0.632212017 0.670075764 0.865009734 0.879113625 0.696232305 0.775579711 0.688375971 0.883373514 0.771918879 1 16.08619606 -5 0.133781188 1.783503795 0.676419803 0.459246613 0.082273092 138.2998322 1.155329359 28.96826326 0.596916697 1.00E-05 5 -1.107083992 RPS(ph)TSS(ph)ASGQWSPTPEWVLSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 2 RPS(0.594)T(0.289)S(0.382)S(0.733)AS(0.002)GQWSPTPEWVLSWK;RPS(0.44)T(0.53)S(0.363)S(0.597)AS(0.07)GQWSPTPEWVLSWK 199.2 6.28E-22 1093200000 537590 442190 595590 449700 671190 633330 567530 484980 563110 540030 TRUE FALSE 558814.4683 518132.6927 611111.5647 538649.3178 557101.3635 486248.7057 523045.5156 478479.6364 542843.7811 645838.539 0.865254138 0.802263509 0.946229634 0.834030931 0.86260161 0.752895153 0.8098704 0.740865723 0.840525531 1 19.30081401 2.797077502 23.67653503 0.805524426 0.861870286 0.000812431 0.075810148 320.0894981 129510.3957 0.02166362 0.02297773 626.7256969 -2.797077502 0.05634586 RPS(ph)TSSASGQWSPTPEWVLSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RPSTSSASGQWSPTPEWVLSWK 22 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RPS(0.553)T(0.109)S(0.311)S(0.023)AS(0.004)GQWSPTPEWVLSWK;RPS(0.46)T(0.102)S(0.154)S(0.233)AS(0.051)GQWSPTPEWVLSWK;RPS(0.509)T(0.091)S(0.133)S(0.133)AS(0.133)GQWSPTPEWVLSWK 217.84 7.53E-26 20808160000 4380900 3500780 4278580 4212420 4916080 5264890 4457580 4063130 5003930 4251160 TRUE FALSE 4553861.315 4102011.733 4390083.31 5045624.103 4080446.478 4042199.088 4108183.232 4008670.388 4823839.537 5084093.409 0.895707641 0.806832488 0.863493834 0.992433399 0.802590777 0.795067825 0.808046372 0.788473001 0.948810171 1 22.27755911 1.068291661 5.28448764 0.998969159 0.84146495 0.446232952 0.059270391 0.164292795 7.92020191 0.059769461 0.015099209 11.7028506 -1.068291661 -0.157504208 RPS(ph)VGSQSNQAGQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPSVGSQSNQAGQGK 15 1 Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1;H0Y3N9 Q9UPP1-4 PHF8 Histone lysine demethylase PHF8 1 RPS(0.979)VGS(0.021)QSNQAGQGK;RPS(0.992)VGS(0.008)QSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(1)VGSQSNQAGQGK;RPS(0.79)VGS(0.208)QS(0.002)NQAGQGK;RPS(0.778)VGS(0.215)QS(0.007)NQAGQGK 247.79 2.78E-18 561292000 601669 552352 666571 585065 807786 850467 689047 750261 762583 650638 TRUE FALSE 625423.3567 647214.1593 683942.3879 700789.1108 670478.8243 652958.9282 635037.6957 740204.9785 735137.7868 778118.0589 0.803764094 0.831768588 0.878969946 0.900620546 0.86166722 0.83915149 0.816119981 0.951275928 0.944763816 1 19.56962954 1.643277704 5.295783133 0.96449198 0.850518815 0.763516711 0.030073921 0.077492954 4.716950275 0.017481425 0.008378485 43.98227644 -1.643277704 -0.113973165 RPS(ph)VYLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSVYLPTR 9 1 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 RPS(1)VYLPTR;RPS(1)VYLPTR 115.57 0.00089049 423730000 84160 106918 96912 105047 126563 113559 90687 107916 91242 129669 TRUE FALSE 87482.70179 125280.3348 99437.60633 125824.9831 105049.8665 87186.64325 83578.71597 106469.5625 87958.21824 155075.1579 0.564130986 0.807868497 0.641222022 0.811380654 0.677412604 0.562221857 0.538956188 0.686567494 0.567197348 1 17.24260807 -1.211293442 8.921005258 1.000000032 0.655439767 0.555741578 0.093588452 5.86E-08 5.25E-09 0.089875876 0.021183945 0.061476135 1.211293442 -0.344560265 RPSANCDPFSVTEALIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSANCDPFSVTEALIR 17 1 A0A2R8YDT1;P15104 A0A2R8YDT1 GLUL Glutamine synthetase 0 ; 201.12 1.89E-11 3080700000 1292240 1526300 1246580 1482410 1529290 1790210 1509000 1560610 1505210 1670180 FALSE TRUE 1343258.633 1788430.152 1279066.899 1775626.273 1269341.832 1374460.858 1390720.637 1539692.576 1451037.786 1997419.793 0.672496907 0.895370196 0.640359579 0.888959987 0.635490765 0.688118173 0.696258564 0.770840752 0.726456096 1 20.92970614 -1.215131696 3.964368755 1.000202352 0.737856708 0.449595935 0.087932547 11874145.29 3639602.581 20646.00554 0.018772871 0.060935209 1.215131696 -0.262345644 RPSAPVDFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSAPVDFSK 10 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 84.169 0.028528 0 309120 281130 272150 307820 364540 405700 337660 280290 290980 263570 FALSE TRUE 321324.2963 329411.8906 279242.4526 368705.8772 302575.621 311482.3234 311193.3269 276533.171 280507.6866 315211.4951 1.019392697 1.045050373 0.885889179 1.16970949 0.959913029 0.988169303 0.987252469 0.877294056 0.8899031 1 18.26596062 1.904246157 4.65429237 0.911411497 1.010495975 0.219733158 0.073992925 0.296141405 10.28410396 0.032697168 0.019108452 80.21325813 -1.904246157 0.099084479 RPSASS(ph)PNNNTAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 RPS(0.247)AS(0.247)S(0.505)PNNNTAAK;RPS(0.033)AS(0.081)S(0.886)PNNNTAAK 150.68 4.38E-06 284160000 193109 166898 195917 155928 211022 214736 197941 179955 173243 144394 TRUE FALSE 200733.0924 195561.4332 201022.758 186770.093 175152.5558 164866.8184 182425.8672 177542.9976 167008.0183 172685.2397 1.16242183 1.132473358 1.16409925 1.081563736 1.014287939 0.954724438 1.056406833 1.028130707 0.967123876 1 17.39778525 3.451095649 2.680366027 1.007430197 1.150799898 0.847741174 0.028493156 0.105899891 1.538194881 0.00859295 0.013083218 2825.502193 -3.451095649 0.143369701 RPSDSSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSDSSRPK 9 2 Q13573;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 ; 96.342 0.0041806 128019000 114347 112794 126836 103384 156857 167836 136878 131182 132384 119165 FALSE TRUE 118861.5079 132165.4921 130141.4504 123833.0466 130194.5032 128858.6326 126149.1447 129423.7199 127619.5257 142513.1002 0.83403917 0.927391881 0.913189385 0.868923955 0.913561651 0.904187983 0.88517578 0.908153143 0.895493295 1 17.12073502 -4.999999962 0.327493629 2.030895181 0.892301538 0.614225607 0.025227714 220.0758919 1.914684291 157.7505973 0.01999474 1.00E-05 4.999999962 -1.138593644 RPSGRS(ph)PTSTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.089)GRS(0.906)PT(0.002)S(0.002)T(0.001)EK;RPS(0.187)GRS(0.737)PT(0.013)S(0.049)T(0.013)EK 94.461 0.0051953 359870000 236750 229240 247540 161238 343950 348060 231320 239600 261870 248860 TRUE FALSE 246097.0728 268610.1868 253991.0958 193130.3952 285485.5019 267228.3399 213188.534 236388.5539 252445.3499 297619.3523 0.826885318 0.902529304 0.853409208 0.648917463 0.959230304 0.897886303 0.716312741 0.794264728 0.848215507 1 18.18310881 0.956337549 17.69705833 1.000000003 0.822606524 0.268990886 0.085998478 213.0596833 86358.29392 0.082676063 0.020669567 9.04352095 -0.956337549 -0.177393479 RPSGRSPTS(ph)TEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSGRSPTSTEK 12 2 A1L390-3;A1L390;A1L390-2;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RPS(0.016)GRS(0.354)PT(0.019)S(0.478)T(0.134)EK 135.55 9.90E-05 214430000 132270 119910 139200 95767 180230 175690 123960 135000 151060 141130 TRUE FALSE 137492.1217 140503.6097 142827.6664 114709.4268 149594.569 134888.6601 114243.6913 133190.5458 145623.3801 168781.7214 0.814614999 0.832457499 0.846227098 0.67963181 0.886319725 0.799189977 0.676872415 0.789128969 0.862791177 1 17.36479915 0.926184189 3.085598283 0.999586032 0.788414631 0.506572805 0.063243328 0.261762067 5.890392803 0.06014522 0.015744403 8.436925002 -0.926184189 -0.2111714 RPSGSQHS(ph)PSLQTFAPEADGTIFFPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSGSQHSPSLQTFAPEADGTIFFPER 27 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 RPS(0.142)GS(0.142)QHS(0.647)PS(0.02)LQT(0.049)FAPEADGTIFFPER;RPS(0.056)GS(0.056)QHS(0.435)PS(0.435)LQT(0.018)FAPEADGTIFFPER 169.6 2.87E-12 277260000 36625.4 121546 108726 127450 110870 150181 127678 105564 91665 118264 TRUE FALSE 38071.39907 142420.58 111559.4889 152659.2296 92024.357 115303.7388 117670.2647 104149.0872 88365.99456 141435.5665 0.269178397 1.006964397 0.788765454 1.079355309 0.650645091 0.815238639 0.831970824 0.736371267 0.624779161 1 17.10978543 4.750557975 24.74932568 0.82426939 0.269178007 0.580870434 0.144359551 1165.498562 2404253.746 0.033054185 0.554600013 56306.42774 -4.750557975 -0.555091383 RPSGVPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPSGVPDR 8 1 P01709;P01706 P01709 Ig lambda chain V-II region MGC;Ig lambda chain V-II region BOH 0 ; 70.552 0.081833 296330000 433530 616880 518350 631190 772070 792580 585370 618740 572830 815040 FALSE TRUE 450646.0992 722824.3413 531858.6268 756037.4981 640833.8172 608515.3067 539487.1698 610446.8024 552213.9602 974731.4831 0.462328453 0.741562527 0.5456463 0.775636687 0.657446516 0.624290194 0.553472602 0.626271761 0.566529316 1 19.89464532 -1.721080522 3.500690541 1.039886403 0.622222877 0.627260495 0.088485984 0.025345697 0.002019432 0.078833337 0.018550328 0.019007258 1.721080522 -0.417663526 RPSQGPPARS(ph)PS(ph)QDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSQGPPARSPSQDFSFIEDTEILDSAMYR 30 2 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 RPS(0.542)QGPPARS(0.683)PS(0.584)QDFS(0.176)FIEDT(0.015)EILDSAMYR 58.16 0.022554 24362000 10225 10430 11880 10007 12500 14204 9237.2 12238 7485.3 14685 TRUE FALSE 10628.6909 12221.27137 12189.60256 11986.35473 10375.25446 10905.33626 8513.164127 12073.96963 7215.905515 17562.24459 0.605201166 0.695883223 0.694079991 0.682506992 0.590770412 0.620953444 0.484742374 0.687495813 0.41087604 1 14.10018962 -1.703168739 8.091490553 1.001525513 0.615210431 0.626964396 0.090546921 0.00238603 8.75E-05 0.083949017 0.019724771 0.019807573 1.703168739 -0.386315082 RPSRPS(ph)NSNISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSRPSNSNISK 12 2 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 RPS(0.328)RPS(0.671)NS(0.002)NISK 70.529 0.037043 159380000 58432 59605 55761 47957 70414 71794 48239 49973 57627 54877 TRUE FALSE 60738.94048 69841.69509 57214.17747 57442.75146 58445.05343 55120.93155 44457.90113 49303.19367 55553.01553 65629.09747 0.925487974 1.064187956 0.871780653 0.875263468 0.890535687 0.839885564 0.677411436 0.751239855 0.84646929 1 16.00204797 3.568880761 0.981252417 0.795224081 0.991090745 0.255968962 0.090720617 0.63871489 1.21510516 0.034897242 0.088282982 3705.789623 -3.568880761 0.195866664 RPSRPSNS(ph)NISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSRPSNSNISK 12 2 Q6P158-2;Q6P158 Q6P158-2 DHX57 Putative ATP-dependent RNA helicase DHX57 1 RPS(0.075)RPS(0.119)NS(0.807)NISK 83.633 0.0099935 154350000 43504 43784 48437 34672 65089 55405 44067 41113 46214 44473 TRUE FALSE 45221.57151 51303.56141 49699.30801 41530.01811 54025.19503 42538.02842 40612.91339 40561.94748 44550.76717 53186.63286 0.850243173 0.964595024 0.934432306 0.780835633 1.015766408 0.799787957 0.763592489 0.762634243 0.8376309 1 15.69877609 2.625506007 19.60007018 0.807928224 0.906709434 0.130102738 0.0876953 6.54633326 1118.54857 0.02677181 0.02524062 422.1881186 -2.625506007 0.098781211 RPSS(ph)MYSTGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 RPS(0.242)S(0.757)MYSTGGK;RPS(0.032)S(0.697)MYS(0.269)T(0.002)GGK;RPS(0.322)S(0.649)MYS(0.015)T(0.015)GGK;RPS(0.11)S(0.89)MYSTGGK;RPS(0.002)S(0.998)MYSTGGK 155.09 1.94E-05 5008220000 3721730 3404340 3817000 3456820 5132570 4849500 4132260 3975280 4050020 3692780 TRUE FALSE 3868666.774 3989008.913 3916474.156 4140568.678 4260137.585 3723277.12 3808362.664 3921997.874 3904260.571 4416309.538 0.875995385 0.903244865 0.886820573 0.937563059 0.964637453 0.843074311 0.86234052 0.888071327 0.88405501 1 22.07440986 -1.804567167 2.304321115 1.037544787 0.894067687 0.477307722 0.033284287 7557746.086 4422209.659 1580636.079 0.008740118 0.015683133 1.804567167 -0.1434771 RPSS(ph)TSVPLGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSSTSVPLGDK 12 1 Q9NXR1;Q9NXR1-1;I3L533;I3L2R9;I3L2T8 Q9NXR1 NDE1 Nuclear distribution protein nudE homolog 1 1 RPS(0.348)S(0.611)T(0.038)S(0.003)VPLGDK 87.388 0.0064783 500220000 761490 480340 579560 470550 868550 809440 774630 613730 668980 471020 TRUE FALSE 791554.2132 562834.6585 594663.8097 563623.3855 720914.1812 621459.8272 713912.4765 605503.9532 644903.5405 563307.3508 1.405190634 0.999160863 1.055664921 1.000561034 1.279788343 1.10323401 1.267358708 1.074908666 1.144851988 1 19.10356277 0.312356658 1.28217251 0.999974753 1.141429463 0.10864108 0.12568143 10.25204541 16.79565042 0.115440919 0.033953944 2.052847359 -0.312356658 0.14145471 RPSSMYSTGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPSSMYSTGGK 11 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 102.97 0.0037254 0 207610 260690 229890 201810 308790 283140 252640 229110 215900 239420 FALSE TRUE 215806.6031 305461.4796 235881.1223 241727.4157 256301.9861 217385.026 232837.4166 226039.1552 208129.8012 286329.765 0.753699508 1.066817065 0.823809296 0.844227339 0.895128685 0.759212113 0.813179226 0.789436457 0.726888457 1 18.12731813 2.753671593 24.1930394 0.80330604 0.882549972 0.068155489 0.101191108 1075.520917 1721932.71 0.028868436 0.030494646 567.115599 -2.753671593 0.079243931 RPT(ph)PAMLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPTPAMLFR 9 1 Q9UD71;J3KSJ8;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 RPT(1)PAMLFR 69.229 0.032717 107220000 33669 45829 43608 36134 58929 50704 39655 39499 39508 45578 TRUE FALSE 34998.27812 53699.77425 44744.4603 43281.19735 48912.26963 38928.76443 36546.73748 38969.58051 38086.1148 54508.13646 0.642074384 0.98516988 0.820876721 0.794031867 0.897338871 0.714182633 0.670482241 0.71493144 0.69872348 1 15.73418398 2.721872718 24.41277679 0.732667291 0.834364093 0.051765986 0.119429614 1117.539797 1634849.699 0.035704668 0.033750438 527.0753642 -2.721872718 0.101696802 RPT(ph)SRAPS(ph)PSGLMSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPTSRAPSPSGLMSPSR 17 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 RPT(0.922)S(0.119)RAPS(0.791)PS(0.167)GLMS(0.001)PSR;RPT(0.918)S(0.083)RAPS(0.701)PS(0.291)GLMS(0.006)PS(0.001)R 83.992 0.0059521 449540000 230550 270130 256200 218460 275900 308270 201667 219640 219422 299330 TRUE FALSE 239652.292 316522.7262 262876.7825 261670.736 229002.6165 236678.9644 185859.8136 216696.0851 211525.0451 357977.9825 0.669460983 0.884196073 0.734337851 0.730968799 0.639711456 0.661155088 0.519193422 0.605333556 0.590888422 1 18.44951133 3.401215821 2.007812555 0.634520106 0.77596596 0.056861025 0.132296792 0.541181168 4.426431202 0.037538806 0.058502635 2518.928389 -3.401215821 0.141445854 RPTETNPVTSNS(ph)DEECNETVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPTETNPVTSNSDEECNETVK 21 1 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVTS(0.001)NS(0.999)DEECNETVK 168.2 6.81E-12 321960000 107610 73992 93372 88920 97967 114870 107360 81904 85037 75599 TRUE FALSE 111858.5259 86699.55042 95805.35103 106508.1106 81314.60433 88193.18337 98944.84267 80806.21085 81976.53498 90411.17662 1.23722011 0.958947264 1.059662694 1.178041417 0.89938664 0.97546771 1.094387291 0.893763513 0.906707976 1 16.46421351 8 0.325605884 0.950631474 3.111102155 0.340508334 0.092127002 69.60370148 0.995458952 0.083555756 90.05684027 100000000 -8 2.160470681 RPTETNPVTSNS(ph)DEECNETVKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPTETNPVTSNSDEECNETVKEK 23 2 P46100;P46100-4;P46100-2;P46100-5;A0A096LNL9;P46100-6;A0A096LNW1;P46100-3 P46100;P46100-3 ATRX Transcriptional regulator ATRX 1 RPTETNPVT(0.028)S(0.207)NS(0.765)DEECNETVKEK 99.871 0.0013177 108450000 47318 29691 41793 26412 56707 51439 40263 41276 48471 29834 TRUE FALSE 49186.15118 34790.19829 42882.15991 31636.21477 47067.9644 39493.07182 37107.08085 40722.76273 46726.53818 35679.40109 1.378558767 0.975077978 1.201874432 0.886680095 1.319191549 1.106887184 1.040014118 1.141352194 1.309622268 1 15.12280378 1.466779724 25 1.178370063 1.120931401 0 0.156257954 11.13715326 26937.58947 0.077237663 0.03575552 29.29407061 -1.466779724 -0.057438661 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAK 261.13 1.19E-58 6981490000 3023430 1797780 2282670 1903550 2900600 3148090 3011080 2427590 2700900 1921250 TRUE FALSE 3142797.351 2106534.73 2342158.255 2280066.508 2407557.048 2416993.807 2775063.682 2395052.127 2603695.137 2297682.153 1.367812057 0.916808588 1.019356943 0.992333298 1.047819884 1.051926962 1.207766565 1.042377478 1.13318334 1 21.13174781 RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPTPNDDTLDEGVGLVHSNIATEHIPSPAKK 31 2 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK;RPTPNDDTLDEGVGLVHSNIATEHIPS(1)PAKK 182.37 1.82E-18 1917350000 825850 381103 541330 393502 756291 733410 683083 527159 615709 362532 TRUE FALSE 858455.1957 446554.4757 555437.5045 471335.5211 627736.926 563086.6424 629541.1696 520093.2959 593549.7534 433563.2043 1.980000118 1.029963962 1.28109927 1.08712067 1.447855629 1.298741768 1.452017061 1.199578956 1.369003983 1 18.7258828 -4.999999917 0.051350345 2.18E-08 1.843092331 0.174873389 0.245207839 1131.637559 4.291977531 162.5451633 34.98087518 1.00E-05 4.999999917 1.84309231 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 0 147.55 1.33E-08 847300000 93070 88732 100820 87602 121550 145250 118760 105410 106440 102360 FALSE TRUE 96744.47547 103971.0308 103447.452 104929.4141 100888.9744 111517.8888 109451.2809 103997.1514 102609.2452 122415.4822 0.790296078 0.849329095 0.845052032 0.857158035 0.824152081 0.910978634 0.894096718 0.849542472 0.838204803 1 16.90142651 -5 0.191283346 1.621372759 0.827047228 0.688521098 0.030613884 81.56425667 0.799456825 19.39034626 0.083656608 1.00E-05 5 -0.794325531 RPTPQDS(ph)PIFLPVDDTSFR ddPTM_MDA-MB-175_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 1 RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPTPQDS(1)PIFLPVDDTSFR;RPT(0.001)PQDS(0.999)PIFLPVDDTSFR;RPT(0.001)PQDS(0.999)PIFLPVDDTSFR 242.83 1.22E-24 21015260000 2758388 2986630 2860405 3261106 3183238 3403689 2710658 2638684 2809237 3143171 TRUE FALSE 2867291.288 3499560.47 2934949.504 3906143.033 2642152.342 2613233.813 2498189.543 2603316.757 2708133.109 3759015.178 0.762777257 0.93097801 0.780776178 1.03914 0.702884191 0.695191078 0.664586181 0.692552872 0.720436865 1 21.84192331 3.176448135 24.99991039 0.720472584 0.875201213 0.221092294 0.115986769 76.93804091 30966.4936 0.030788477 0.036799283 1501.233111 -3.176448135 0.154728629 RPTPQDSPIFLPVDDTSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 260.98 6.28E-31 21801971000 5415352 6232800 6231716 7125794 6339427 7105242 5891441 6000334 5933239 6732614 FALSE TRUE 5629154.279 7303234.916 6394119.638 8535254.785 5261853.463 5455157.226 5429654.46 5919909.337 5719702.887 8051740.81 0.699122638 0.907038004 0.794128846 1.060050862 0.653505073 0.677512771 0.67434541 0.73523347 0.710368481 1 22.9408693 5.058155406 13.94039927 0.785487324 0.140714733 0.036998963 0.136326338 10441164.22 72437214.73 0.03270173 181739285.2 114328.737 -5.058155406 -0.644772591 RPVDSYDIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPVDSYDIPK 10 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;; 102.4 0.0047334 1010640000 908060 799470 925340 800340 1127110 1200900 1163270 945530 1050310 825040 FALSE TRUE 943910.91 936772.7535 949455.1206 958644.8632 935524.2448 922009.1748 1072089.858 932856.7169 1012509.548 986690.7917 0.956643072 0.949408631 0.962262067 0.971575768 0.948143281 0.93444591 1.086550991 0.945439772 1.026167019 1 19.91223852 RPVS(ph)FPETPYTVSPAGADRVPPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPVSFPETPYTVSPAGADRVPPYR 24 2 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 RPVS(1)FPETPYTVSPAGADRVPPYR 114.24 0.00066913 292230000 171870 46147 80481 53644 106130 116770 85751 66607 84762 45123 TRUE FALSE 178655.5603 54072.38828 82578.40098 64254.62309 88090.06051 89651.93717 79029.61255 65714.24211 81711.43218 53963.98792 3.310644139 1.002008754 1.530250157 1.19069449 1.632386039 1.661328983 1.464487997 1.21774251 1.514184465 1 15.71970935 4.74543672 24.99534494 1.379264644 3.310645027 0.864063134 0.232315691 262.6927771 954891.0501 0.05286897 0.526110809 55646.35479 -4.74543672 1.931380383 RPVS(ph)PYSGYNGQLLTSVYQPTEMALMHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPVSPYSGYNGQLLTSVYQPTEMALMHK 28 1 A8MXZ4;J9JIE0;A0A0C4DFY5;Q9NQ84;Q9NQ84-2 A8MXZ4 GPRC5C G-protein coupled receptor family C group 5 member C 1 RPVS(0.737)PY(0.039)S(0.115)GY(0.108)NGQLLTSVYQPTEMALMHK 75.414 0.0041099 283280000 120900 111690 149630 144440 144870 190270 172900 148850 149360 167480 TRUE FALSE 125673.2254 130871.8887 153529.4807 173009.8009 120245.0491 146082.6761 159347.6462 146854.9092 143984.5628 200294.4994 0.62744222 0.653397318 0.766518707 0.863777095 0.600341245 0.72933943 0.795566761 0.733194919 0.718864288 1 17.61176328 -5 0.235901523 2.529823227 0.695308536 0.569970051 0.073670944 126.1338508 1.260251741 92.41133376 0.122326576 1.00E-05 5 -1.834514692 RPWILTSLHNGVIQLWDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RPWILTSLHNGVIQLWDYR 19 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1;A0A3B3ITX2;A0A3B3IS23;A0A3B3IU84 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 176.42 4.38E-13 71076000 23348 39145 42218 45037 59925 57532 55373 47256 51381 54718 FALSE TRUE 24269.79707 45867.84924 43318.23576 53945.18418 49738.9699 44171.06491 51032.71957 46622.61062 49531.80785 65438.94446 0.370876964 0.700925873 0.661964158 0.824359021 0.760082094 0.674996598 0.779852426 0.712459698 0.756916363 1 15.99786186 4.58546728 0.079829467 1.226978242 5.09E-30 0.575467448 0.097378166 72.92074967 0.972101243 4.142305828 12.26340029 38500.5807 -4.58546728 -1.226978242 RPWRPEEAVEDPDEEDEDNT(ph)SEAENGFSLEEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLR 34 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 RPWRPEEAVEDPDEEDEDNT(0.5)S(0.5)EAENGFSLEEVLR;RPWRPEEAVEDPDEEDEDNT(0.577)S(0.423)EAENGFSLEEVLR 175.37 1.44E-13 142092000 51663 63503 57845 58944 44517 53421 48805 46169 47375 60877 TRUE FALSE 53702.69513 74409.14627 59352.48822 70602.94727 36950.01624 41014.78235 44979.53657 45550.18007 45669.983 72804.68259 0.737626939 1.022037919 0.815228995 0.969758328 0.507522524 0.563353632 0.617811039 0.625649044 0.627294583 1 16.15174362 3.24455243 24.99976477 0.630867508 0.890801695 0.368609745 0.144524158 127.4208587 531637.0252 0.03695278 0.04876301 1756.112889 -3.24455243 0.259934187 RPYDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 93.429 0.023958 1120050000 649010 833270 714356 750442 980665 963080 821939 755405 722118 1024140 FALSE TRUE 674633.4159 976377.6406 732972.7042 898877.1878 813971.9136 739419.2656 757513.2734 745280.0316 696129.1142 1224800.625 0.550810803 0.797172716 0.598442464 0.733896742 0.664575031 0.60370582 0.618478843 0.608490898 0.568361169 1 20.22411549 -2.129446822 2.500408435 1.756331018 0.641070603 0.69462431 0.071941383 2756112.102 779169.6193 11884627.6 0.017190297 0.007422551 2.129446822 -1.115260415 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR 32 1 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 ; 194.98 3.60E-21 1134930000 311234 381567 331721 433518 473970 499130 337622 412766 362236 471830 FALSE TRUE 323521.7586 447098.1641 340365.9218 519266.5665 393404.7487 383214.6219 311158.3054 407233.5469 349199.1971 564276.0548 0.573339513 0.792339424 0.60319044 0.920234984 0.697184907 0.679126145 0.551429221 0.721692057 0.618844614 1 19.1060416 -1.40659876 3.292769551 1.003448931 0.688766494 0.44898673 0.104857121 207702881.6 264498675.7 6699946.633 0.024008275 0.039210397 1.40659876 -0.314682437 RPYPDPEDEIPDEMIQCVVCEDWFHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RPYPDPEDEIPDEMIQCVVCEDWFHGR 27 1 E9PCJ7;Q8N806;H0YJA0;H0YJM2 E9PCJ7 UBR7 Putative E3 ubiquitin-protein ligase UBR7 0 ;;; 229.82 4.45E-35 255086000 79105.8 111705 95216 107742 97124 114671 88777 102393 96159 117725 FALSE TRUE 82228.95807 130889.4648 97697.40718 129053.046 80614.89717 88040.39811 81818.42676 101020.5893 92698.25637 140790.9598 0.584049986 0.929672367 0.693918184 0.916628782 0.572585749 0.625327068 0.581134093 0.717521846 0.658410572 1 17.10319518 -1.327497865 3.243589788 1.001963116 0.701149551 0.352033278 0.122961238 31711468.44 42121139.63 594412.2639 0.029693 0.047043772 1.327497865 -0.300813565 RPYTVILIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RPYTVILIER 10 1 Q9Y3A5;A0A087X020 Q9Y3A5 SBDS Ribosome maturation protein SBDS 0 ; 116.24 0.0017907 1582270000 422650 443330 483100 394360 509320 551190 454330 398570 414900 570900 FALSE TRUE 439336.5484 519468.4789 495689.9829 472363.231 422745.9683 423184.4759 418718.4274 393227.8211 399967.83 682756.9245 0.643474321 0.760839561 0.726012385 0.691846855 0.619174926 0.619817186 0.613275988 0.575941169 0.585812924 1 19.38101252 -1.035736184 4.628860267 1.00001038 0.646834549 0.772887918 0.057161483 0.142993816 40943709.51 1104.303679 0.015533415 0.092100888 1.035736184 -0.353175831 RQAQQERDELADEIANSSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQAQQERDELADEIANSSGK 20 2 P35579;P35579-2 P35579 MYH9 Myosin-9 0 191.21 8.69E-18 522590000 260730 265360 310860 161750 424410 406510 283540 254760 314390 272700 FALSE TRUE 271023.8217 310933.5158 318961.267 193743.6672 352268.9398 312104.2132 261315.3939 251345.3589 303075.1653 326130.3438 0.831029148 0.953402594 0.978017756 0.594068203 1.080147697 0.956992255 0.801260597 0.77068989 0.929306859 1 18.31508915 0.997458133 24.77158833 1.000000022 0.868158097 0.092459859 0.12753275 165.5611518 1613483.719 0.120649541 0.030162385 9.941642285 -0.997458133 -0.131841925 RQAS(ph)ESSSRPH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQASESSSRPH 11 2 A0A2R8Y653;Q9BZX2;Q9BZX2-2 A0A2R8Y653 UCK2 Uridine-cytidine kinase 2 1 RQAS(0.996)ES(0.003)SS(0.001)RPH 70.47 0.040699 276430000 19301 31716 46167 28312 35177 42757 34797 40888 30320 49801 TRUE FALSE 20063.01838 37162.97628 47370.14995 33912.0291 29197.6261 32827.33474 32069.52021 40339.96324 29228.78912 59558.55245 0.336862089 0.6239738 0.795354286 0.569389747 0.490233978 0.551177512 0.538453654 0.677316046 0.490757212 1 15.86202107 -1.973845816 2.631079077 1.361441204 0.576434857 0.557781153 0.116042744 10341842.7 4600245.608 22742879.13 0.028936144 0.010620725 1.973845816 -0.785006346 RQATVS(ph)WDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 2 RQAT(0.196)VS(0.804)WDS(0.001)GGSDEAPPKPS(0.005)RPGYPS(0.995)PR;RQAT(0.073)VS(0.915)WDS(0.012)GGSDEAPPKPS(0.073)RPGYPS(0.927)PR;RQAT(0.065)VS(0.923)WDS(0.011)GGS(0.002)DEAPPKPS(0.245)RPGYPS(0.755)PR 128.05 4.43E-05 475100000 315116 243819 291102 220513 418951 411126 349181 332395 380738 335928 TRUE FALSE 327557.023 285693.0166 298688.3573 264129.8132 347737.8587 315648.2172 321811.2808 327939.7887 367035.3138 401746.6599 0.815332287 0.711127298 0.743474401 0.657453663 0.865565027 0.785689711 0.801030383 0.816285041 0.913598918 1 18.6159265 1.08474546 0.538961611 1.007948159 0.742316183 0.684664828 0.052714384 0.501511347 0.369539389 0.056146403 0.026956154 12.15473403 -1.08474546 -0.265631976 RQATVSWDSGGSDEAPPKPS(ph)RPGYPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.974)RPGYPS(0.026)PR 202.58 2.07E-24 1126700000 623990 588250 715060 517730 882250 835690 672420 752670 761770 682180 TRUE FALSE 648625.607 689277.3616 733695.051 620135.4487 732285.4601 641613.6625 619713.9634 742581.6898 734354.0465 815840.1099 0.795040105 0.844868196 0.899312307 0.760118853 0.897584528 0.786445352 0.759602226 0.91020493 0.900120057 1 19.63792691 1.147714374 1.508490059 0.992653074 0.825661423 0.534246131 0.051246047 0.279153067 1.234390292 0.046318428 0.013894156 14.05123102 -1.147714374 -0.166991651 RQATVSWDSGGSDEAPPKPSRPGYPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.01)RPGYPS(0.99)PR;RQATVSWDSGGSDEAPPKPSRPGYPS(1)PR;RQATVSWDSGGSDEAPPKPS(0.001)RPGYPS(0.999)PR 185.19 5.62E-17 2903000000 1063750 847140 1046620 749220 1325490 1342040 1031950 1093070 1209700 1110500 TRUE FALSE 1105747.671 992629.7052 1073895.777 897413.4798 1100183.683 1030371.549 951063.0625 1078419.185 1166163.133 1328081.213 0.832590402 0.747416419 0.808607009 0.675721839 0.828400908 0.775834745 0.716118151 0.812012981 0.878081191 1 20.34091194 1.018481938 1.846650675 0.998404854 0.768790025 0.702719987 0.046729685 0.171482387 1.212527189 0.041110514 0.011699346 10.43474735 -1.018481938 -0.229614829 RQAVDVSPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RQAVDVSPLR 10 1 M0R0F0;M0R0R2;P46782;M0QZN2 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;; 206.27 2.46E-07 1284650000 605656 696512 668917 712213 989474 925274 774310 681118 658895 1026627 FALSE TRUE 629567.7665 816132.5179 686349.5265 853086.6057 821283.5629 710393.1362 713617.5589 671988.7273 635181.4977 1227774.905 0.512771327 0.664724873 0.559019022 0.694823296 0.668920304 0.578602098 0.581228331 0.547322416 0.517343607 1 20.22761466 -1.19254529 4.421210299 1.000109321 0.593902888 0.801948853 0.060871448 8.244107769 36445793.54 7407.717127 0.014476383 0.064188128 1.19254529 -0.406206433 RQCEEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQCEEVAR 8 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 155.84 0.00064533 278610000 144647 158305 157639 169209 184585 190875 148650 160180 165592 223228 FALSE TRUE 150357.7753 185492.6523 161747.2018 202678.0352 153209.3076 146547.174 136998.4246 158033.0491 159632.3763 266965.2526 0.563211031 0.694819459 0.605873612 0.759192566 0.573892318 0.548937259 0.513169498 0.591961117 0.597951886 1 18.02629245 -0.510084697 7.734237502 0.999999847 0.604983269 0.751399809 0.068083294 0 0 0.068349513 0.016110135 0.308969282 0.510084697 -0.395016578 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 333.38 4.21E-95 327900000 336030 257950 327450 316370 401610 381130 358370 312430 352280 290110 FALSE TRUE 349296.7239 302250.9059 335983.616 378947.0417 333344.4757 292618.3336 330280.023 308242.3869 339601.5116 346951.5 1.006759515 0.871161837 0.968387847 1.092219062 0.960781192 0.843398382 0.951948681 0.888430766 0.978815516 1 18.40437448 2.989345392 24.99741835 0.922047975 0.981758414 0.113582689 0.065380413 994.7894205 2333942.056 0.019537303 0.02199784 975.7653508 -2.989345392 0.059710438 RQDLEDSLQAQQYFADANEAESWMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQDLEDSLQAQQYFADANEAESWMR 25 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 240.75 2.22E-38 696560000 216770 267340 265610 246610 251640 294230 238850 247320 241120 307740 FALSE TRUE 225328.247 313253.5654 272532.0148 295388.7219 208866.3227 225899.5416 220128.3129 244005.0799 232442.1383 368035.761 0.612245523 0.851149803 0.740504168 0.80260875 0.56751638 0.613797803 0.59811664 0.662992855 0.631574871 1 18.48948643 -1.107780092 3.829992106 1.000120943 0.676993177 0.54580532 0.088766475 32206027.47 64527800.23 51427.66861 0.022487837 0.078022508 1.107780092 -0.323127766 RQDLLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RQDLLSR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;;; 125.5 0.0064834 1317270000 396474 814540 643650 744690 612670 843820 577280 682310 578970 953060 FALSE TRUE 412127.0997 954430.9088 660424.0478 891987.4593 508528.5722 647855.5932 532031.2852 673164.7505 558132.9828 1139793.86 0.361580382 0.837371513 0.579424114 0.782586651 0.446158372 0.56839716 0.466778515 0.590602191 0.489678882 1 20.12034149 -1.496598816 5.953818964 1.000426157 0.576620678 0.462483646 0.139129748 0.000733507 6.20E-05 0.125551701 0.029564078 0.031871403 1.496598816 -0.42380548 RQDS(ph)AGPVLDGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQDSAGPVLDGAR 13 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 RQDS(1)AGPVLDGAR 119.48 0.00021171 481160000 190500 235570 236830 196230 300220 274640 225660 239420 223940 246310 TRUE FALSE 198021.0871 276027.315 243001.9844 235043.7083 249188.7116 210859.0222 207972.1795 236210.9665 215880.4431 294569.7286 0.672238414 0.937052549 0.824938752 0.79792214 0.845941342 0.715820404 0.706020203 0.801884727 0.732867033 1 18.16824965 2.76991078 24.89974361 0.77408437 0.821899611 0 0.099175531 2095.985803 1664724.963 0.028116732 0.0298191 588.7226976 -2.76991078 0.047815241 RQDS(ph)MEALQMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQDSMEALQMDR 12 1 Q8TDR0-2;Q8TDR0 Q8TDR0-2 TRAF3IP1 TRAF3-interacting protein 1 1 RQDS(1)MEALQMDR;RQDS(1)MEALQMDR 142.39 0.00013498 0 537670 439240 480970 401540 667480 658930 594230 530870 513670 392240 TRUE FALSE 558897.6268 514676.0532 493504.4733 480963.4135 554021.988 505903.4937 547652.6999 523754.556 495183.117 469091.9181 1.191445866 1.097175273 1.052042157 1.025307397 1.181052085 1.07847412 1.167474175 1.116528629 1.055620653 1 18.83951112 1.016223945 3.438019212 1.000622411 1.111955036 0.332240201 0.051653598 0.242188837 6.865016576 0.049223243 0.012787236 10.38063558 -1.016223945 0.111332625 RQDSDLVQCGVTS(ph)PSSAEATGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQDSDLVQCGVTSPSSAEATGK 22 1 Q9HC52 Q9HC52 CBX8 Chromobox protein homolog 8 1 RQDSDLVQCGVT(0.033)S(0.889)PS(0.033)S(0.046)AEATGK 134.2 5.95E-09 0 59532 41300 46306 35147 60830 68135 56471 49319 56738 42613 TRUE FALSE 61882.36933 48392.95373 47512.7724 42098.9717 50490.13833 52311.67885 52044.65546 48657.95947 54696.01046 50962.20147 1.214279751 0.949585228 0.93231397 0.826082282 0.990736995 1.026479966 1.02124033 0.954785274 1.073266242 1 15.63713998 3.005659147 24.9961607 1.008167817 0.966593909 0.018574411 0.094982442 612.9872305 2707500.493 0.027993191 0.033366447 1013.115938 -3.005659147 -0.041573908 RQEAIAQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQEAIAQNR 9 1 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 111.61 0.003363 77915000 17079 19981 16440 15236 17923 19964 17996 16341 13447 20612 FALSE TRUE 17753.29211 23412.58132 16868.43991 18249.63533 14876.45486 15327.66356 16585.4265 16121.97562 12963.0451 24650.52676 0.7201993 0.949780163 0.684303426 0.740334497 0.6034944 0.621798621 0.672822397 0.654021546 0.525872945 1 14.58933086 4.121462709 8.52201036 0.669649665 0.834347291 0.160677895 0.129657384 0.328381763 22.88331512 0.029321138 0.063717609 13227.04128 -4.121462709 0.164697626 RQEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQEELDR 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 ; 157.68 0.0023406 450640000 292850 381430 363440 339170 368520 425300 358040 354080 338730 374780 FALSE TRUE 304411.9441 446937.6354 372911.545 406256.8137 305879.102 326530.5205 329975.8892 349334.1368 326539.1735 448210.9654 0.679171122 0.997159083 0.832000049 0.906396418 0.682444486 0.728519705 0.736206641 0.779396676 0.728539011 1 18.77381842 3.251001042 24.99846408 0.761210943 0.862381367 0.096740809 0.10995812 390.7081194 785105.6542 0.027966581 0.037606163 1782.383044 -3.251001042 0.101170424 RQEELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQEELER 7 1 A0A087WXB0;O15126-2;O15126;A0A087WZA6 A0A087WXB0 SCAMP1 Secretory carrier-associated membrane protein 1 0 ; 118.74 0.0079175 570490000 257420 341790 311600 324010 299510 391820 301630 307550 249100 348810 FALSE TRUE 267583.1404 400489.7737 319720.552 388098.2109 248599.3972 300825.7431 277987.4524 303427.7953 240134.9397 417152.6411 0.641451387 0.960055707 0.766435401 0.930350602 0.595943481 0.721140689 0.666392646 0.727378339 0.575652449 1 18.67021585 3.23956046 24.99999987 0.699940839 0.830097873 0.130277397 0.136090558 43.73428022 1093507.624 0.034860588 0.04462671 1736.042927 -3.23956046 0.130157034 RQEELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQEELQR 7 1 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 ; 132.08 0.014543 39827000 139983 169284 142529 152758 176549 232780 133257 126618 139278 174437 FALSE TRUE 145509.6369 198357.2102 146243.4228 182973.0765 146539.264 178720.3728 122811.9681 124920.8928 134265.412 208614.5904 0.697504603 0.950830955 0.701022026 0.87708667 0.70244015 0.856701214 0.588702679 0.598811869 0.643605089 1 17.67048054 3.208181185 21.69197935 0.700343679 0.80937028 0.038301344 0.137509122 98.45018451 70295.62864 0.038745079 0.046322278 1615.032198 -3.208181185 0.109026601 RQEENDKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQEENDKLR 9 2 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 106.4 0.0016547 339280000 126090 135070 147860 114390 212110 179950 133710 132480 132030 180370 FALSE TRUE 131068.1306 158267.2218 151713.3531 137016.0006 176055.618 138159.3397 123229.4608 130704.3223 127278.2661 215710.0481 0.607612542 0.733703521 0.703320751 0.635185991 0.816167905 0.640486342 0.571273624 0.60592598 0.590043288 1 17.71873386 -0.952156698 4.846491944 1.000002873 0.655881937 0.676310425 0.071401964 2.33E-06 5.04E-07 0.07268123 0.017130987 0.111646034 0.952156698 -0.344120936 RQEHDISLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQEHDISLDR 10 1 Q92797;A0A087WUE9;M0R3C7;Q92797-2 Q92797 SYMPK Symplekin 0 79.693 0.017034 79006000 8376 19092 15443 11959 11884 13742 9452 11467 9165.2 13627 FALSE TRUE 8706.690948 22370.90248 15845.45727 14324.45451 9863.961925 10550.62876 8711.127542 11313.30362 8835.346242 16296.94975 0.534252795 1.372704882 0.972295891 0.878965373 0.605264303 0.647398987 0.534525029 0.694197614 0.542147235 1 13.99231434 3.403691125 3.317251866 0.647904896 0.995116312 0.250506782 0.225612494 0.267297397 5.918492703 0.06007397 0.085980483 2533.326258 -3.403691125 0.347211416 RQEIAEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQEIAEQK 8 1 O15066;O15066-2;F8WAR6;F8WER6;O14782 O15066 KIF3B;KIF3C "Kinesin-like protein KIF3B;Kinesin-like protein KIF3B, N-terminally processed;Kinesin-like protein;Kinesin-like protein KIF3C" 0 84.615 0.027782 51842000 69690 84446 87629 80607 98280 112790 95857 87631 90768 82799 FALSE TRUE 72441.41501 98948.9436 89912.68373 96550.82401 81574.4007 86596.23185 88343.47786 86456.44978 87501.27741 99021.87877 0.73156979 0.999263444 0.908008259 0.975045366 0.823801787 0.874516147 0.892161197 0.873104518 0.883656001 1 16.5954597 -1.541518286 6.696146086 1.000094912 0.888472712 0.193468458 0.07029913 9.18E-05 6.29E-06 0.062744254 0.014776419 0.028739666 1.541518286 -0.1116222 RQELDAFLAQALSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQELDAFLAQALSPK 15 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 105.31 0.0021242 83277000 364550 306470 368030 299090 441330 445420 366090 328720 371420 336770 FALSE TRUE 378942.7155 359103.8385 377621.1641 358249.1093 366312.8842 341977.9554 337394.9092 324314.0461 358052.6668 402753.6336 0.940879694 0.891621598 0.937598404 0.889499385 0.909520992 0.849099615 0.837720336 0.805241763 0.889011636 1 18.61953808 2.747216372 18.40620106 0.856272482 0.912560146 0.053691057 0.05209375 26.96028246 57327.84965 0.015237825 0.01580862 558.7485021 -2.747216372 0.056287664 RQEQIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQEQIAK 7 1 P62753;A2A3R5 P62753 RPS6 40S ribosomal protein S6 0 ;; 155 0.0026311 2324940000 1250120 1174750 1282550 974770 1567880 1452470 1268870 1170000 1317300 1164870 FALSE TRUE 1299475.703 1376504.174 1315974.307 1167576.597 1301372.318 1115155.855 1169412.654 1154318.064 1269890.63 1393103.974 0.932791613 0.988084307 0.944634666 0.838111597 0.934153044 0.800482861 0.839429559 0.828594337 0.911554812 1 20.40987151 3.845367525 5.194307248 0.866393315 0.961437285 0.251150565 0.057788939 0.240497251 9.618394772 0.014149985 0.026153606 7004.344926 -3.845367525 0.09504397 RQEQIQAMPLADSQAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 184.15 1.04E-09 1286890000 328908 432154 400895 409427 420799 507163 386251 395242 414262 421806 FALSE TRUE 341893.5418 506373.0878 411342.653 490410.4386 349271.7363 389382.0794 355975.6373 389944.4275 399352.7915 504450.8097 0.677753976 1.003810635 0.815426688 0.972167016 0.692380168 0.77189306 0.705669672 0.773007833 0.79165854 1 18.94435407 5.031545893 15.95909362 0.819514362 0.225929931 0.139234571 0.111440582 5575594.733 78952215.19 0.026173913 89983265.27 107534.0229 -5.031545893 -0.59358443 RQEQPSIESTS(ph)PISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 RQEQPSIES(0.011)T(0.011)S(0.978)PISR;RQEQPSIES(0.221)T(0.054)S(0.725)PISR;RQEQPSIES(0.146)T(0.254)S(0.6)PISR 129.98 3.83E-05 1443500000 292103 551630 645640 451660 800860 619690 629310 570200 618150 601110 TRUE FALSE 303635.452 646368.1614 662465.9088 540996.9999 664730.1033 475776.389 579983.0378 562557.4017 595902.9022 718885.9956 0.422369407 0.899124709 0.921517338 0.752549087 0.924666925 0.661824534 0.80678027 0.782540493 0.828925457 1 19.45540347 -5 0.191030643 1.905073215 0.748069863 0.206454804 0.139510986 238.4900296 2.336807204 82.43584218 0.358071369 1.00E-05 5 -1.157003353 RQEQTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQEQTLR 7 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ;; 161.02 0.002124 533763000 286627 370979 299153 337263 344313 422233 326517 309783 271489 410839 FALSE TRUE 297943.2553 434691.7574 306949.1729 403972.6148 285786.7992 324175.7848 300923.7443 305630.8656 261718.1639 491335.0361 0.606395297 0.884715572 0.624724781 0.822193789 0.581653614 0.659785606 0.612461401 0.622041668 0.532667416 1 18.90634759 -1.08665985 4.615057804 1.000020504 0.663521863 0.491641593 0.103459716 2.11E-05 4.18E-06 0.097037331 0.022870526 0.081910608 1.08665985 -0.336498641 RQET(ph)ENKYETDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQETENKYETDLGR 14 2 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 RQET(1)ENKYETDLGR 132.74 0.0023196 61619000 60709 66958 71107 35455 116950 72370 59601 71727 65689 60457 TRUE FALSE 63105.8382 78457.51564 72960.10684 42467.89318 97070.88077 55563.16428 54929.31788 70765.61689 63324.86572 72302.39163 0.872804298 1.085130296 1.009096728 0.587364985 1.342568048 0.768483075 0.759716472 0.978745174 0.875833624 1 16.14175575 RQEYLDQQLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQEYLDQQLQK 11 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 148.18 5.60E-05 182580000 200080 157860 189730 147920 277180 258600 211400 214550 222570 213660 FALSE TRUE 207979.3129 184971.227 194674.5197 177178.1345 230065.0426 198544.0691 194829.9156 211674.3082 214559.7492 255522.5862 0.8139371 0.723893843 0.761868148 0.693395199 0.900370672 0.777011817 0.762476298 0.828397643 0.839689956 1 17.96309129 -0.929893709 0.274720288 1.126736969 0.750745527 0.623683226 0.052116458 8.760110862 0.610655701 0.932097899 0.069483985 0.117518514 0.929893709 -0.375991442 RQGLEQFINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQGLEQFINK 10 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 110.39 0.0030349 283770000 350630 250340 327910 257990 462090 425300 348930 306390 329750 388480 FALSE TRUE 364473.1431 293333.9476 336455.604 309019.652 383544.1069 326530.5205 321579.9548 302283.3432 317882.3619 464595.2181 0.784496114 0.631375305 0.724190846 0.665137393 0.825544672 0.702827984 0.69217233 0.650638085 0.68421359 1 18.82561478 -1.442132997 5.960838154 1.000140572 0.702658857 0.707708263 0.056486703 0.00010239 9.58E-06 0.053068172 0.012502424 0.03612992 1.442132997 -0.297481715 RQGSFS(ph)EDVISHK ddPTM_MDA-MB-175_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(0.105)FS(0.895)EDVISHK 90.754 0.0041931 182420000 170530 149560 141840 120100 167810 184480 184790 149370 155340 131990 TRUE FALSE 177262.6561 175245.7666 145536.4669 143855.4215 139285.7161 141637.3158 170305.6769 147367.9395 149749.3437 157850.9134 1.122975169 1.110197989 0.921986853 0.911337277 0.882387774 0.897285374 1.078902068 0.9335894 0.948675814 1 17.26820308 4.244740384 24.84767358 0.945527687 1.11658669 0.613768288 0.053876848 87.40143455 351414.1059 0.013694286 0.0355589 17568.73062 -4.244740384 0.171059003 RQGSVVS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQGSVVSSR 9 1 Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q9BZ67-2 FRMD8 FERM domain-containing protein 8 1 RQGS(0.07)VVS(0.465)S(0.465)R;RQGS(0.265)VVS(0.367)S(0.367)R 111.86 0.002179 363840000 400250 537960 493150 440410 604170 575750 457210 505860 476480 545200 TRUE FALSE 416052.1791 630350.4453 506001.8941 527521.7835 501473.3992 442040.7881 421372.6855 499079.7741 459331.5779 652021.5015 0.638095796 0.96676328 0.776050932 0.809055809 0.769105617 0.677954311 0.646255813 0.765434534 0.704473053 1 19.31456001 4.009735404 24.99583228 0.751141918 0.819673896 0 0.117878214 635.9652348 1632822.696 0.027295628 0.058856353 10226.69737 -4.009735404 0.068531978 RQHEAEEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 103.22 0.0018457 145080000 22679 22067 20582 21847 27575 29257 24047 19183 20619 24019 FALSE TRUE 23574.38443 25856.83559 21118.38383 26168.27139 22887.81135 22462.50514 22162.1333 18925.88326 19876.92622 28725.06318 0.820690429 0.900148955 0.735190161 0.910990908 0.796788895 0.781982793 0.771526007 0.658863068 0.69197154 1 14.81002245 2.648642975 1.963791927 0.744200151 0.838182617 0.021760355 0.098533511 0.622894529 4.765254249 0.035939157 0.033223942 445.2900336 -2.648642975 0.093982466 RQHIAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQHIAEK 7 1 Q96TA1 Q96TA1 FAM129B Niban-like protein 1 0 73.26 0.07917 12501000 18377 15324 16663 15102 20506 24919 21880 20153 21636 17320 FALSE TRUE 19102.53815 17955.7778 17097.25147 18089.13053 17020.39744 19131.9399 20164.98843 19882.882 20857.32459 20713.52239 0.922225481 0.866862596 0.82541497 0.873300551 0.821704639 0.923644928 0.973518074 0.959898641 1.006942431 1 14.33828529 2.447093192 3.121136767 0.97938444 0.860862194 0.795598224 0.029291542 0.112852234 2.275918608 0.010799144 0.009112174 279.9581995 -2.447093192 -0.118522247 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQIQAAYSILSEVQQAVSQGSSDSQILDLSNR 32 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 181.9 2.52E-19 134270000 60541 59198 75511 75819 78903 92391 70888 71372 69432 71597 FALSE TRUE 62931.20543 69364.796 77478.87869 90815.7719 65491.09624 70934.59045 65331.61333 70415.37508 66933.15588 85625.06134 0.734962457 0.810099227 0.904862169 1.060621394 0.76485897 0.82843258 0.762996397 0.822368755 0.781700531 1 16.3857455 RQLAELETEDGMQES(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQLAELETEDGMQESP 16 1 Q96QG7-2;Q96QG7 Q96QG7-2 MTMR9 Myotubularin-related protein 9 1 RQLAELETEDGMQES(1)P;RQLAELETEDGMQES(1)P 185.02 1.83E-09 103070000 228770 285040 267820 250860 304650 314430 260560 285060 286500 278320 TRUE FALSE 237802.0162 333993.4027 274799.6092 300479.3593 252865.7018 241408.3977 240136.6264 281239.237 276188.921 332851.4752 0.714438823 1.003430742 0.825592283 0.90274306 0.759695301 0.72527363 0.721452793 0.844939133 0.829766252 1 18.34451904 RQLEEAEEEAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 270.21 4.44E-23 4423340000 1558090 1920300 1792630 1766400 1833850 2241190 1718560 1833480 1868590 2095770 FALSE TRUE 1619604.596 2250096.587 1839347.41 2115788.648 1522132.832 1720707.588 1583854.777 1808905.2 1801339.811 2506396.006 0.646188628 0.89774185 0.733861451 0.844155769 0.607299417 0.686526624 0.631925192 0.721715641 0.718697208 1 21.25718294 -0.979252319 3.76441509 1.000038383 0.721836039 0.485683067 0.086157607 14994883.01 29380366.72 7952.366667 0.020228522 0.104893284 0.979252319 -0.278202344 RQLHLEGASLELS(ph)DDDTESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RQLHLEGASLELSDDDTESK 20 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 RQLHLEGASLELS(1)DDDTESK;RQLHLEGAS(0.003)LELS(0.997)DDDTESK;RQLHLEGAS(0.034)LELS(0.966)DDDTESK;RQLHLEGASLELS(1)DDDTESK;RQLHLEGAS(0.008)LELS(0.992)DDDTESK 211.92 1.05E-22 1007508000 819762 553233 721379 622809 917176 1032888 1023914 803188 792367 464544 TRUE FALSE 852126.8368 648246.4642 740178.7294 745998.7613 761274.7511 793015.4156 943656.9452 792422.5786 763849.8665 555562.5026 1.533809126 1.166829045 1.332305053 1.342780979 1.370277417 1.427409899 1.698561261 1.426342806 1.374912567 1 19.0835897 2.919173832 3.061285767 1.437927232 1.331678187 0 0.182222807 0.770870506 14.04192772 0.05552144 0.061220913 830.1829917 -2.919173832 -0.106249045 RQLS(ph)MTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQLSMTLR 8 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4;E5RJQ8;E5RGV7 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RQLS(0.997)MT(0.003)LR;RQLS(0.99)MT(0.01)LR 96.113 0.0044031 0 23570.4 33202 27022.4 30979 35902 38443 28119.5 31941 28473.7 39314 TRUE FALSE 24500.97759 38904.18522 27726.62594 37106.55374 29799.39086 29515.19586 25915.42011 31512.88314 27448.9371 47016.82559 0.521110842 0.827452401 0.589717098 0.78921861 0.633802697 0.627758159 0.551194594 0.670246933 0.583810939 1 15.52088952 -1.962755653 2.477098944 1.284030215 0.648702638 0.569079583 0.09289713 12903820.67 5899389.542 21049345.05 0.021094017 0.010895429 1.962755653 -0.635327577 RQLS(ph)PQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQLSPQSK 8 1 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RQLS(0.998)PQS(0.002)K;RQLS(0.997)PQS(0.003)K 110.74 0.0020628 1428040000 742960 592240 652400 587760 874030 847500 767640 671250 696370 559150 TRUE FALSE 772292.6345 693952.613 669402.08 704017.1737 725462.6928 650680.969 707470.3709 662252.9917 671307.7797 668704.7369 1.154908275 1.037756389 1.001042827 1.052807218 1.084877454 0.973046747 1.057971227 0.990351877 1.003892664 1 19.35100981 4.731046018 3.887250041 1.022005336 1.166737882 0.596168981 0.032953704 0.159574909 4.872635498 0.007790369 0.065004962 53832.68207 -4.731046018 0.144732547 RQMPDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQMPDNR 7 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 79.597 0.051619 61333000 91005 138716 111969 107405 163895 159206 119502 122979 128937 217560 FALSE TRUE 94597.94767 162539.3939 114887.0041 128649.3884 136036.1864 122232.8193 110135.121 121330.6677 124296.5826 260186.7166 0.363577161 0.624702891 0.441555993 0.494450255 0.522840629 0.469788854 0.423292636 0.46632153 0.477720708 1 17.98918778 -1.290959696 3.034629221 1.00368012 0.47796759 0.856420701 0.064357925 5932928.41 7765714.202 199285.4413 0.014806124 0.051172932 1.290959696 -0.525712531 RQNGDDPLLTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 92.969 0.011923 497340000 350180 411160 387380 365120 469180 514110 394410 403980 378780 490660 FALSE TRUE 364005.3768 481773.5316 397475.441 437339.6462 389428.9512 394715.7439 363495.1136 398565.3089 365147.7818 586795.4327 0.620327556 0.821024679 0.677366283 0.745301722 0.663653685 0.672663286 0.61945798 0.679223604 0.62227441 1 19.16249812 -1.873107324 5.688169906 1.060243957 0.682531535 0.72395077 0.059237112 0.032154227 0.000717302 0.040750814 0.013092571 0.013393457 1.873107324 -0.377712423 RQPMPS(ph)PSEGSLSSGGMDQGSDAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQPMPSPSEGSLSSGGMDQGSDAPAR 26 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 RQPMPS(0.96)PS(0.04)EGSLSSGGMDQGSDAPAR;RQPMPS(0.849)PS(0.15)EGS(0.001)LSSGGMDQGSDAPAR 223.42 1.39E-34 404180000 102050 142946 129272 182002 155147 194426 150407 153760 163006 156258 TRUE FALSE 106079.0128 167495.8635 132640.9345 218001.4524 128775.1684 149273.5081 138617.7063 151699.0987 157139.4459 186873.7634 0.567650648 0.896304867 0.709788962 1.166570676 0.689102451 0.798793289 0.741771899 0.811773124 0.840885543 1 17.51170451 0.764098311 2.553549404 0.999930468 0.804437964 0.140932701 0.148966858 2.272696502 21.44729137 0.133204143 0.035530052 5.808958999 -0.764098311 -0.195492504 RQPPVS(ph)PLTLS(ph)PGPEAHQGFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQPPVSPLTLSPGPEAHQGFSR 22 1 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 2 RQPPVS(1)PLT(0.274)LS(0.726)PGPEAHQGFSR 106.17 0.00050504 142900000 45126 58972 60136 54524 59802 76419 43231 52910 52059 60928 TRUE FALSE 46907.60932 69099.98226 61703.19356 65308.68446 49636.8774 58671.84539 39842.44126 52200.82799 50185.40676 72865.67506 0.643754543 0.948320073 0.84680741 0.896288745 0.681210698 0.805205542 0.546793003 0.716398056 0.688738651 1 16.15295174 3.233208327 24.98948147 0.715064904 0.842902845 0.090650942 0.131570473 214.8323393 1003037.01 0.035262473 0.043322594 1710.83579 -3.233208327 0.127837941 RQPQEEVVHEDQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQPQEEVVHEDQGK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDQ3;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 193.96 1.29E-07 443920000 436380 328820 396490 359130 485510 537130 517490 434890 448190 286540 FALSE TRUE 453608.6194 385292.2771 406822.8551 430164.8421 402983.1836 412389.6978 476927.7816 429061.0109 432059.7294 342682.0269 1.323701227 1.124343406 1.187173015 1.255288601 1.175968251 1.203417937 1.391750206 1.252067448 1.26081818 1 18.386511 RQQDPS(ph)PGSNLGGGDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQQDPSPGSNLGGGDDLK 18 1 Q13951-2;J3KTD8 Q13951-2 CBFB Core-binding factor subunit beta 1 RQQDPS(0.993)PGS(0.007)NLGGGDDLK 76.733 0.0090309 201150000 54682 40371 45379 46896 68671 80831 57535 53271 63201 47600 TRUE FALSE 56840.88758 47304.40521 46561.61402 56171.88883 56998.32795 62059.22526 53025.25636 52556.98938 60926.40836 56926.30864 0.998499445 0.830976157 0.817927864 0.986747431 1.001265132 1.09016774 0.931471891 0.923246046 1.070268033 1 15.79680793 3.676989005 9.337829782 0.992679428 0.877407172 0.391795039 0.066789242 0.491483599 72.11493807 0.018389347 0.02853497 4753.231925 -3.676989005 -0.115272255 RQQEEMMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQQEEMMR 8 1 Q15233;Q15233-2;H7C367 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 181.41 0.00037517 388050000 75114 71657 74405 66589 120690 123060 74478 74633 66573 146920 FALSE TRUE 78079.55872 83963.53234 76344.05542 79760.10545 100175.1569 94481.17999 68640.21975 73632.66671 64177.05073 175706.161 0.444375759 0.477863336 0.434498455 0.453940289 0.570128881 0.537722636 0.39065346 0.419067074 0.365252137 1 17.42280525 -1.18156548 4.071835202 1.000252557 0.455230765 0.885338675 0.058857658 81384974.22 214262118.6 295378.6432 0.015307124 0.065831617 1.18156548 -0.545021792 RQQEGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 141.52 0.004091 682520000 653970 577840 623480 547810 888920 875520 714710 589910 697920 653180 FALSE TRUE 679789.2406 677079.525 639728.401 656165.183 737821.6959 672193.7486 658689.1627 582003.2213 672801.9955 781158.1151 0.870232578 0.866763734 0.818948672 0.839990228 0.944522859 0.860509205 0.843221302 0.745051751 0.861287853 1 19.57525507 -0.173877368 8.005101234 0.999997548 0.844716127 0.473155078 0.047163685 0 0 0.050744703 0.011960641 0.670073791 0.173877368 -0.155281421 RQQEQQVPILEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 131.53 0.0003159 25769510000 4832200 3839400 4669140 4239220 5533580 5686600 4606540 4525870 4848080 3975020 FALSE TRUE 5022978.987 4498787.084 4790821.624 5077725.063 4592984.048 4365973.331 4245467.358 4465208.115 4673598.548 4753849.063 1.056613056 0.946346218 1.007777395 1.068129214 0.966161102 0.918408068 0.89305893 0.939282686 0.983118834 1 22.18066467 3.010051316 24.03719532 0.938698487 1.01406325 0.395865696 0.041934207 127.5404995 305002.2553 0.012097221 0.014441322 1023.413912 -3.010051316 0.075364763 RQQEVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQQEVEER 8 1 Q9BUQ8;H0YIL9 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 160.59 0.00056519 88435000 66608 81270 74792 72471 75146 85828 76740 77100 74972 88713 FALSE TRUE 69237.73527 95227.49031 76741.14096 86805.5475 62372.70976 65895.74774 70724.91828 76066.60061 72273.77236 106094.6138 0.652603679 0.897571393 0.723327398 0.818189957 0.587897043 0.621103611 0.666621195 0.716969485 0.681219996 1 16.69499189 -1.893880125 9.02622945 1.0320253 0.709359894 0.503842914 0.087122134 0.04385718 0.000515621 0.065890885 0.020182105 0.012767912 1.893880125 -0.322665406 RQQVLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RQQVLDR 7 1 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;;; 141.52 0.004091 913276000 613023 771184 645171 690238 856087 941692 722292 682841 671224 960540 FALSE TRUE 637225.6214 903628.853 661984.6863 826765.0162 710569.6375 722998.3045 665676.8657 673688.6333 647066.7794 1148739.422 0.554717292 0.786626484 0.576270539 0.71971502 0.618564684 0.62938408 0.579484653 0.586459053 0.563284211 1 20.13162015 -2.133236398 2.389423131 1.779997448 0.625262594 0.718688282 0.070598113 3607146.367 906575.4582 15271364.94 0.016265572 0.007358065 2.133236398 -1.154734853 RQS(ph)FASLALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(1)FASLALR 204.94 1.09E-07 1910660000 413121 611520 474160 488310 944150 657460 433600 457520 454910 957970 TRUE FALSE 429431.3361 716543.803 486516.9991 584896.2605 783663.7202 504774.8789 399613.299 451387.6928 438537.878 1145665.88 0.374831217 0.625438721 0.424658714 0.510529528 0.684024665 0.440595192 0.348804399 0.393995929 0.382779906 1 20.12775493 -1.617007284 2.900921255 1.04137232 0.46528939 0.697967087 0.105566218 56715557.46 57379492.8 17780843.16 0.026848209 0.024154203 1.617007284 -0.57608293 RQS(ph)FAVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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;RQS(1)FAVLR;RQS(1)FAVLR;RQS(1)FAVLR 169.58 0.00018387 32789000900 2867152.72 4306697.2 4035765.9 2811249 5719373.1 4069561 3150653.5 4163723.9 4085527.1 4552004.1 TRUE FALSE 2980350.123 5046338.943 4140941.275 3367305.661 4747196.103 3124467.133 2903697.046 4107915.992 3938489.778 5443882.15 0.547467789 0.926974318 0.76065961 0.618548596 0.87202404 0.573940994 0.533387198 0.754593115 0.723470801 1 22.3762044 -1.937517975 5.0415429 1.142937734 0.704775292 0.331237671 0.127267879 0.078279642 0.000970154 0.047176179 0.028040465 0.011547342 1.937517975 -0.438162441 RQS(ph)GLYDSQNPPTVNNCAQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RQSGLYDSQNPPTVNNCAQDR 21 1 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 1 RQS(0.974)GLYDS(0.026)QNPPTVNNCAQDR;RQS(1)GLYDSQNPPTVNNCAQDR;RQS(1)GLYDSQNPPTVNNCAQDR;RQS(1)GLYDSQNPPTVNNCAQDR 250.45 3.67E-31 949170000 189094 222379 205755 221689 235960 261550 204573 218777 199480 240319 TRUE FALSE 196559.5771 260570.8634 211117.1443 265538.4225 195851.6035 200808.9763 188538.0337 215844.6522 192300.7538 287404.9069 0.683911695 0.906633315 0.734563465 0.923917498 0.681448364 0.698697105 0.656001443 0.751012411 0.669093496 1 18.13272517 RQS(ph)HLLLQSSIPDQQLLK ddPTM_MDA-MB-175_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(0.756)HLLLQS(0.106)S(0.138)IPDQQLLK 97.618 0.00064604 80648000 112190 117630 118810 106450 161380 165850 123150 123820 128750 120170 TRUE FALSE 116619.3478 137832.0375 121906.2862 127505.4923 133948.6852 127333.851 113497.1812 122160.3954 124116.3126 143715.0107 0.811462541 0.959065005 0.848250197 0.887210679 0.932043804 0.886016362 0.789737834 0.850018344 0.863628037 1 17.13285123 2.447414238 24.99614998 0.856613857 0.8913342 0 0.062946119 594.0997326 499885.9405 0.020280257 0.016967859 280.1652315 -2.447414238 0.034720343 RQS(ph)ILFSTEV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSILFSTEV 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 RQS(1)ILFSTEV;RQS(1)ILFSTEV 112.7 0.0016796 282160000 287160 269030 268540 286240 446570 413400 287190 280230 273850 445490 TRUE FALSE 298497.2985 315233.8097 275538.373 342857.4177 370662.1909 317394.1151 264679.2974 276473.9752 263994.192 532775.2361 0.560268718 0.591682549 0.517175639 0.64353107 0.695719631 0.595737365 0.496793543 0.51893173 0.495507625 1 19.0231675 -1.187193668 5.060721374 1.000033307 0.567566931 0.812358888 0.062231942 2.58E-05 4.14E-06 0.066465426 0.015664847 0.064983984 1.187193668 -0.432466376 RQS(ph)KGHLTDSPEEAE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSKGHLTDSPEEAE 15 2 Q86YL5 Q86YL5 TDRP Testis development-related protein 1 RQS(0.999)KGHLT(0.001)DSPEEAE;RQS(0.982)KGHLT(0.017)DS(0.001)PEEAE 128.99 5.40E-05 931510000 460620 490360 529420 298370 849940 682520 404920 540500 609920 632170 TRUE FALSE 478805.6333 574575.5155 543217.1201 357386.6955 705467.5024 524015.0737 373181.3123 533255.4816 587969.0983 756031.6079 0.633314306 0.759988749 0.718511124 0.47271396 0.933119059 0.693112653 0.493605437 0.705334904 0.777704387 1 19.52808703 0.891015679 2.520457508 0.999206537 0.675198141 0.389754264 0.123414998 0.43860528 5.838312924 0.114706333 0.03077361 7.780646413 -0.891015679 -0.324008397 RQS(ph)KSEHETSDAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSKSEHETSDAKK 14 3 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RQS(0.84)KS(0.16)EHETSDAKK;RQS(0.977)KS(0.023)EHETSDAKK 158.65 3.59E-06 70496000 89006 68295 111899 56088 183305 132131 133031 117604 157682 77239 TRUE FALSE 92520.02561 80024.13499 114815.1799 67182.03899 152146.8816 101445.5777 122603.6826 116027.7107 152007.0556 92372.50322 1.001597038 0.86631987 1.242958411 0.727294776 1.647101424 1.098222676 1.327274658 1.256084946 1.645587705 1 16.49517584 3.24620013 24.99999953 1.325098247 0.973127806 0.388807531 0.226669324 179.2019089 586427.4427 0.058522811 0.0777683 1762.788181 -3.24620013 -0.351970441 RQS(ph)LELQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQSLELQK 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 RQS(1)LELQK 77.288 0.020582 257240000 248050 201790 227280 179240 265370 326220 259310 214640 231900 182870 TRUE FALSE 257843.2055 236445.8628 233203.1035 214693.137 220262.5022 250460.3489 238984.6046 211763.1019 223553.9643 218699.8752 1.178981951 1.081143108 1.066315668 0.981679284 1.007145075 1.145224014 1.092751445 0.968281768 1.022195207 1 17.73859287 4.747458556 1.589207332 1.033803718 1.234406413 0.432419024 0.050556131 1.115116387 2.623463932 0.014542691 0.349772388 55906.01744 -4.747458556 0.200602695 RQS(ph)LTSPDSQSARPANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSLTSPDSQSARPANR 17 2 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RQS(0.999)LT(0.001)SPDSQSARPANR;RQS(0.997)LT(0.003)SPDSQSARPANR 189.82 1.74E-10 197976000 74473 64607 72791 59821 89829 92941 69413 69171 80130 64904 TRUE FALSE 77413.25155 75702.74968 74687.99326 71653.41525 74559.89867 71356.86128 63972.22768 68243.87589 77246.13695 77620.69614 0.997327458 0.975290785 0.962217514 0.923122554 0.96056725 0.919302001 0.82416457 0.879196906 0.995174493 1 16.24415375 3.83285276 0.944445147 0.909615613 0.997297439 0.134606776 0.050772895 1.098849571 1.702529378 0.019451737 0.074170315 6805.385945 -3.83285276 0.087681826 RQS(ph)LYENQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSLYENQV 9 1 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 RQS(1)LYENQV;RQS(1)LYENQV 115.92 0.00084737 477440000 606910 633960 552530 593110 718530 731810 483520 553980 501100 663140 TRUE FALSE 630871.2754 742837.6985 566929.3857 710425.3877 596394.5273 561858.2182 445620.439 546554.8042 483065.5089 793069.5864 0.795480354 0.936661437 0.714854529 0.895791996 0.752007816 0.708460175 0.561893239 0.689163742 0.609108604 1 19.59708793 4.22241091 24.9362482 0.723861627 0.86607089 0.124521711 0.125497019 346.5573367 535110.1473 0.030975575 0.067238508 16688.25433 -4.22241091 0.142209263 RQS(ph)MKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQSMKEK 7 2 Q9H307 Q9H307 PNN Pinin 1 RQS(1)MKEK 73.499 0.038374 122790000 201680 121230 186830 75051 304110 226380 171300 188550 238650 163400 TRUE FALSE 209642.4821 142050.3095 191698.9433 89895.8638 252417.4908 173806.6758 157873.0584 186022.7957 230061.0331 195415.1015 1.072805942 0.726915721 0.98098326 0.460025162 1.291698998 0.889422949 0.807885661 0.951936643 1.177294034 1 17.57618244 3.226841851 24.999943 0.992536619 0.816434864 0.202081066 0.199476828 409.034358 872601.8719 0.055797404 0.067202119 1685.938975 -3.226841851 -0.176101755 RQS(ph)MLF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RQSMLF 6 1 Q00537 Q00537 CDK17 Cyclin-dependent kinase 17 1 RQS(1)MLF;RQS(1)MLF;RQS(1)MLF;RQS(1)MLF 102.46 0.037623 559970000 512630 639140 575050 661720 722020 751940 510410 569520 517890 718690 TRUE FALSE 532869.0282 748907.3232 590036.2754 792606.241 599291.2983 577313.3308 470402.7305 561886.5159 499251.2401 859503.5453 0.619973043 0.871325461 0.686484981 0.922167506 0.697252852 0.671682315 0.547295858 0.653733797 0.580860012 1 19.71314407 RQS(ph)PEPSPVTLGR ddPTM_MDA-MB-175_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 164.79 2.23E-05 1310060000 709430 881770 765340 860200 809540 930430 788050 775920 783540 812360 TRUE FALSE 737438.8442 1033207.138 785285.3891 1030344.993 671934.68 714351.7333 726280.5818 765520.0615 755340.5485 971526.3884 0.75905179 1.063488497 0.808300627 1.060542467 0.691627822 0.735288039 0.7475665 0.787956015 0.77747816 1 19.88989366 3.225818663 24.99995085 0.774830801 0.924709973 0.227893405 0.117819331 274.4263624 538428.6387 0.030939842 0.037208141 1681.971616 -3.225818663 0.149879172 RQS(ph)PLPPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 92.611 0.0095378 11737496000 8620180 7837549 8498600 7025738 9827760 10101030 9290150 8722224 8912650 7278823 TRUE FALSE 8960511.363 9183587.073 8720080.498 8415408.007 8157240.866 7755218.865 8561963.768 8605316.854 8591885.467 8704969.005 1.029355918 1.054982168 1.001735962 0.966736125 0.93707868 0.890895632 0.983571999 0.988552268 0.987009312 1 23.05340773 3.969710958 2.889374124 0.9629763 1.041938615 0.505730906 0.030535234 0.221730656 3.700966596 0.00886341 0.020126226 9326.33385 -3.969710958 0.078962315 RQS(ph)PLPPQKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 79.466 0.014637 6114180000 6063410 3869250 5158040 3834780 6468490 6018400 5894280 4981870 5895350 3720270 TRUE FALSE 6302798.109 4533763.589 5292462.76 4593288.038 5368978.38 4620717.81 5432270.932 4915096.181 5683177.505 4449185.678 1.416618358 1.019009751 1.189535152 1.03238848 1.20673282 1.038553602 1.220958469 1.104718152 1.277352288 1 22.08510988 4.752424474 24.64749542 1.127299686 1.416618596 0.47421216 0.093164633 1590.304601 2827221.542 0.019690148 0.397714888 56548.94072 -4.752424474 0.28931891 RQS(ph)PS(ph)PSTRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(1)PS(0.957)PS(0.023)T(0.02)RPIR;RQS(1)PS(0.941)PS(0.054)T(0.005)RPIR;RQS(0.998)PS(0.85)PS(0.141)T(0.012)RPIR 75.535 0.017993 1287660000 41077 74188.2 48741.7 39692 82280 74698 64925.4 29452.9 55826 73073 TRUE FALSE 42698.75168 86929.44625 50011.94874 47542.95913 68294.07499 57350.52156 59836.3775 29058.13205 53816.83317 87390.25528 0.488598546 0.994726997 0.5722829 0.544030441 0.781483871 0.656257627 0.684703086 0.33250998 0.615821901 1 16.4151848 RQS(ph)PSPS(ph)TRPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSPSPSTRPIR 12 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RQS(1)PS(0.008)PS(0.579)T(0.414)RPIR;RQS(1)PS(0.191)PS(0.753)T(0.057)RPIR 119.56 0.0024823 875130000 564270 644660 616340 617230 645690 714810 569690 603400 559350 684370 TRUE FALSE 586547.8153 755375.3402 632402.3267 739316.2518 535935.8444 548806.2106 525036.2092 595312.41 539219.1028 818459.1984 0.716648816 0.922923637 0.772674225 0.903302514 0.654810705 0.670535821 0.641493443 0.727357468 0.658822216 1 19.64255097 3.232597286 24.99846984 0.70501039 0.831588962 0.153339682 0.112943167 198.3705656 831575.1323 0.029490215 0.036122212 1708.430381 -3.232597286 0.126578573 RQS(ph)SGSATNVASTPDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSSGSATNVASTPDNR 17 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 RQS(0.869)S(0.113)GS(0.017)AT(0.001)NVASTPDNR;RQS(0.833)S(0.118)GS(0.045)AT(0.003)NVAST(0.001)PDNR 101.3 0.00068637 755900000 314023 472240 412000 374720 452970 523270 373821 430050 371280 455040 TRUE FALSE 326420.8705 553343.5465 422737.0585 448838.4976 375974.3212 401748.4727 344519.9332 424285.8832 357917.7053 544196.3757 0.599821838 1.016808584 0.776809764 0.824773037 0.69087987 0.738241728 0.633080168 0.779655841 0.657699539 1 19.05376782 5.02353808 18.5396664 0.774998484 0.121344473 0.165752774 0.124067375 39250984.93 731064655.3 0.028238215 782774960.4 105569.4066 -5.02353808 -0.653654011 RQS(ph)SPSCGPVAETSSIGNGDGISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQSSPSCGPVAETSSIGNGDGISK 24 1 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 RQS(0.545)S(0.455)PSCGPVAETSSIGNGDGISK;RQS(0.857)S(0.143)PSCGPVAETSSIGNGDGISK;RQS(0.6)S(0.4)PSCGPVAETSSIGNGDGISK 255.73 4.66E-44 1121630000 525260 421798 471380 374749 651210 604000 536800 473720 553770 474030 TRUE FALSE 545997.6704 494238.5254 483664.55 448873.2337 540517.5568 463730.1537 494724.2133 467370.5582 533839.9259 566907.1026 0.963116651 0.871815723 0.85316368 0.791793279 0.953449964 0.818000254 0.872672456 0.824421772 0.941670908 1 19.11275282 -1.277839788 5.57756993 1.000012169 0.870238891 0.294244232 0.056510763 7.98E-06 1.03E-06 0.051090176 0.012040941 0.052742439 1.277839788 -0.129773278 RQS(ph)SSYDDPWK ddPTM_MDA-MB-175_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(0.503)S(0.422)S(0.075)YDDPWK 91.969 0.0063367 148370000 377080 330340 330650 310000 401800 497470 462630 353130 367410 270030 TRUE FALSE 391967.4096 387073.3253 339267.0106 371317.0747 333502.1795 381940.1317 426367.8517 348396.87 354186.9859 322937.2085 1.213757348 1.198602438 1.050566493 1.149811991 1.032715249 1.182707108 1.320280973 1.078837808 1.096767349 1 18.30089415 1.062385472 1.975550122 1.005759516 1.155504452 0.268632983 0.079967898 0.437933394 3.461021992 0.077024424 0.021771311 11.54477497 -1.062385472 0.149744936 RQS(ph)STPSAPELGQQPDVNISEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 RQS(0.794)S(0.169)T(0.037)PSAPELGQQPDVNISEWK 110.4 0.00064915 108010000 69871 66058 78853 67437 89835 89077 75253 64269 82131 77040 TRUE FALSE 72629.56103 77402.94764 80907.97396 80775.83732 74564.87879 68390.21672 69354.47322 63407.57918 79175.12135 92134.51298 0.78829918 0.840108067 0.878150558 0.876716387 0.809304531 0.742286625 0.752752372 0.688206592 0.859342702 1 16.49145406 3.009905377 7.055465691 0.776376171 0.847366382 0 0.084698792 0.28554851 76.40526465 0.023965394 0.027892273 1023.070063 -3.009905377 0.070990211 RQS(ph)VS(ph)PPYKEPSAYQSSTR ddPTM_MDA-MB-175_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(0.932)PPY(0.065)KEPS(0.002)AY(0.001)QSSTR 60.139 0.034892 351510000 82972 60359 72618 71168 81023 94081 96910 76416 73831 52674 TRUE FALSE 86247.79863 70725.18872 74510.48474 85244.81798 67250.7394 72232.11356 89313.94097 75391.76851 71173.83673 62994.4618 1.369133034 1.122720739 1.182810085 1.353211307 1.067565902 1.146642284 1.417806239 1.196799947 1.129842762 1 15.94293738 0.994870408 2.650061139 1.001987468 1.230444756 0.312313544 0.108468463 0.320818251 5.192738418 0.100385797 0.026912908 9.882581585 -0.994870408 0.228457288 RQS(ph)VSGLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQSVSGLHR 9 1 Q8N1G4;J3KRP5 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 RQS(1)VSGLHR;RQS(1)VSGLHR;RQS(1)VSGLHR 99.752 0.0031388 960340000 123245 158593 165738 157455 156311 200072 176290 162557 155041 193369 TRUE FALSE 128110.8078 185830.1141 170057.2684 188599.129 129741.3121 153608.3101 162471.9292 160378.1893 149461.1047 231255.9533 0.553978421 0.803568995 0.735363851 0.815542806 0.561029069 0.664235052 0.702563229 0.693509451 0.646301652 1 17.81913098 -1.835271881 3.001764963 1.098790668 0.691545439 0.562483694 0.082898728 16693216.15 12937019.98 11698315.16 0.019238626 0.014612621 1.835271881 -0.407245229 RQSS(ph)TPSAPELGQQPDVNISEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQSSTPSAPELGQQPDVNISEWK 23 1 Q93100-4;Q93100-2;I3L213;Q93100-3;Q93100 Q93100-4 PHKB Phosphorylase b kinase regulatory subunit beta 1 RQS(0.082)S(0.772)T(0.145)PS(0.001)APELGQQPDVNISEWK;RQS(0.096)S(0.808)T(0.096)PSAPELGQQPDVNISEWK 317.18 1.31E-73 896130000 603240 471040 616470 450280 750080 741970 512560 523920 618060 566670 TRUE FALSE 627056.381 551937.4558 632535.7146 539344.04 622581.6695 569658.7122 472384.2079 516897.7094 595816.1413 677698.1369 0.925273875 0.814429649 0.933359087 0.795847016 0.918671065 0.840578838 0.697042211 0.762725587 0.879176301 1 19.37028328 2.473634586 24.9850314 0.80061178 0.873281393 0 0.087133487 206.3989069 1479002.761 0.028497151 0.023951602 297.6011368 -2.473634586 0.072669613 RQSSGS(ph)ATNVASTPDNR ddPTM_MDA-MB-175_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 1 RQS(0.079)S(0.109)GS(0.79)AT(0.022)NVASTPDNR 100.19 0.00085513 958960000 260440 285560 215880 234810 345000 299570 264310 242340 248030 284010 TRUE FALSE 270722.3723 334602.7087 221506.0101 281254.7172 286357.0232 229999.4075 243592.6916 239091.8287 239103.4488 339656.3218 0.797047942 0.985121392 0.652147468 0.828056771 0.843078738 0.677153325 0.717174025 0.703922799 0.70395701 1 18.37371618 4.240017092 24.99995344 0.752010913 0.891084644 0.171057872 0.107085199 52.17722558 895522.206 0.024548244 0.060289936 17378.69223 -4.240017092 0.139073732 RQSSIFGGADVGFSGGIPS(ph)PDKGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQSSIFGGADVGFSGGIPSPDKGHR 25 2 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 RQSSIFGGADVGFS(0.001)GGIPS(0.999)PDKGHR 115.67 0.00077115 242150000 98909 65095 98850 72123 118670 138090 101120 118640 107240 76521 TRUE FALSE 102814.0037 76274.55988 101426.1122 86388.71413 98498.51579 106020.6903 93193.95017 117049.8249 103380.4533 91513.82487 1.123480565 0.833475816 1.108314644 0.943996323 1.076323888 1.158521026 1.018359251 1.279039807 1.129670337 1 16.48170209 3.015753488 4.818942823 1.136678261 0.998038224 0.196607324 0.105586044 0.24240175 15.06809544 0.030108209 0.035005135 1036.939667 -3.015753488 -0.138640037 RQT(ph)IEER ddPTM_MDA-MB-175_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 157.78 0.00085147 997110000 481252 589900 457619 395375 393439 645010 492326 490004 492748 491069 TRUE FALSE 500252.2006 691210.7362 469544.9271 473578.9949 326562.3793 495216.2027 453736.2017 483436.2979 475014.0957 587284.5685 0.851805458 1.176960495 0.799518585 0.806387602 0.556054759 0.843230402 0.772600245 0.823172145 0.808831223 1 19.1637002 4.141335894 9.615439081 0.787748182 1.013817124 0.312413714 0.12529946 0.278320145 24.82379187 0.029141775 0.063165896 13846.36876 -4.141335894 0.226068942 RQTIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RQTIEER 7 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;;; 170.24 0.0015748 1380800000 838070 1438180 1201220 1280820 1157550 1481350 1090490 1195620 1050360 1563660 FALSE TRUE 871157.6507 1685176.228 1232524.78 1534162.373 960790.0645 1137328.913 1005014.544 1179594.67 1012557.749 1870029.239 0.465852422 0.901149668 0.659093855 0.820394859 0.513783445 0.60818777 0.53743253 0.630789426 0.541466266 1 20.8346294 -1.053677326 4.394779961 1.00002244 0.636671741 0.420950181 0.129709184 16610333.7 3982436.888 4017.28586 0.029275079 0.088373626 1.053677326 -0.363350699 RQVDEGVWPPPNNLLSQS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQVDEGVWPPPNNLLSQSPK 20 1 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 RQVDEGVWPPPNNLLS(0.018)QS(0.982)PK 125.79 1.50E-05 222190000 136660 56208 63655 50372 90656 124410 88727 73831 67932 50792 TRUE FALSE 142055.4423 65861.28676 65313.90159 60335.43125 75246.3255 95517.66295 81772.3459 72841.41621 65487.14059 60743.71993 2.338602945 1.084248493 1.075237106 0.993278504 1.238750699 1.572469764 1.346186009 1.199159622 1.078089071 1 15.89044764 4.741965654 24.99391353 1.195857987 2.338603374 0.80881102 0.169280856 148.175495 1087600.836 0.043623659 0.317645432 55203.37801 -4.741965654 1.142745387 RQVEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 155.42 0.00065622 1247580000 893131 1233620 1085819 1088970 1404970 1423010 1090350 1070639 1127183 1433910 FALSE TRUE 928392.5015 1445484.639 1114116.335 1304365.016 1166153.701 1092537.493 1004885.518 1056288.835 1086615.904 1714857.211 0.541381811 0.842918366 0.649684608 0.76062602 0.680029622 0.637101146 0.585987866 0.615963142 0.633648036 1 20.70965702 -1.609262553 8.040304848 1.000243946 0.661979758 0.607801853 0.081734097 0.000351272 1.71E-05 0.07777873 0.018319776 0.024588806 1.609262553 -0.338264189 RQVEEEILALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQVEEEILALK 11 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 105.65 0.0039082 548970000 973650 952850 970320 875540 1315930 1257620 1129600 1033340 1064240 1158810 FALSE TRUE 1012090.454 1116494.575 995607.3363 1048719.199 1092248.689 965556.8144 1041059 1019489.768 1025938.21 1385856.633 0.730299535 0.805634976 0.718405723 0.756729934 0.788139742 0.696722007 0.751202524 0.735638697 0.740291734 1 20.40234659 -2.182791305 2.297689371 1.664842059 0.747242428 0.864330344 0.030069694 1747136.224 364129.4139 6046509.689 0.006891481 0.006564606 2.182791305 -0.917599631 RQVS(ph)ASELHTSGILGPETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 1 RQVS(0.849)AS(0.151)ELHTSGILGPETLR;RQVS(0.944)AS(0.054)ELHT(0.002)SGILGPETLR;RQVS(0.965)AS(0.034)ELHTSGILGPETLR;RQVS(0.789)AS(0.18)ELHT(0.03)S(0.001)GILGPETLR;RQVS(0.99)AS(0.01)ELHTSGILGPETLR 250.97 3.66E-31 4696910000 169462 826790 750800 655670 750970 1052410 498631 934470 720670 1303480 TRUE FALSE 176152.4906 968784.751 770366.4648 785359.569 623320.3876 808003.7269 459546.9993 921944.9581 694733.2275 1558871.949 0.112999975 0.621465253 0.494182005 0.503799924 0.399853489 0.518325913 0.294794579 0.591418018 0.445664076 1 20.57207099 -4.999999996 0.309613428 5.83913585 0.428792387 0.59250681 0.139611607 193.3777159 1.753513639 609.9209668 0.12124111 1.00E-05 4.999999996 -5.410343463 RQWTSLS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RQWTSLSLR 9 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 RQWT(0.002)S(0.02)LS(0.978)LR;RQWTSLS(1)LR;RQWTS(0.001)LS(0.999)LR 166.16 3.73E-05 489150000 134767 190492 258216 200546 414415 224766 286106 240283 263620 333510 TRUE FALSE 140087.7052 223207.5192 264945.3211 240213.4002 343972.8863 172567.5029 263680.2641 237062.3994 254132.3677 398854.8991 0.351224732 0.559620854 0.664264929 0.602257615 0.862401056 0.432657348 0.661093206 0.594357497 0.637154936 1 18.60550447 -5 0.225948672 3.072842577 0.5545902 0.488982007 0.127142267 137.6190554 1.377518517 130.3516133 0.224068735 1.00E-05 5 -2.518252377 RQYEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RQYEEK 6 1 Q32MZ4-2;Q32MZ4;Q32MZ4-3;Q32MZ4-4 Q32MZ4-2;Q32MZ4-3;Q32MZ4-4 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 ; 143.02 0.018363 473220000 530570 453830 495650 425800 605890 606020 562750 501070 531890 473260 FALSE TRUE 551517.3133 531771.7722 508567.0462 510021.9691 502901.0342 465281.0393 518640.1845 494353.9762 512747.3828 565986.2359 0.974435911 0.939548947 0.898550201 0.901120799 0.888539336 0.822071298 0.916347698 0.87343816 0.905936135 1 19.11040744 4.474946508 1.72068421 0.891742016 0.983439646 0.221025833 0.042217861 0.677145839 2.916069832 0.010411746 0.08658132 29850.14932 -4.474946508 0.091697631 RQYHES(ph)EEES(ph)EEEEAA ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RQYHESEEESEEEEAA 16 1 Q8N9N8;E9PNH5 Q8N9N8 EIF1AD Probable RNA-binding protein EIF1AD 2 RQYHES(1)EEES(1)EEEEAA 70.335 0.029215 442290000 213510 264270 241860 235540 271940 298540 250710 254270 249470 250980 TRUE FALSE 221939.5397 309656.3168 248163.0703 282129.109 225715.7359 229208.6094 231058.6951 250861.9266 240491.6234 300154.7257 0.739417109 1.031655644 0.826783819 0.939945584 0.751997942 0.763634852 0.769798625 0.835775369 0.801225511 1 18.19534686 RRAS(ph)QEANLLTLAQK ddPTM_MDA-MB-175_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 203.06 4.41E-09 2205030000 1025420 840430 988960 735890 1395840 1258940 965090 1025020 1190380 1192860 TRUE FALSE 1065904.373 984767.3149 1014733.11 881446.8456 1158575.615 966570.2644 889443.724 1011281.283 1147538.456 1426578.078 0.747175629 0.690300328 0.711305694 0.617874941 0.812136141 0.677544594 0.623480577 0.708886039 0.804399334 1 20.44412728 0.913759157 2.453410128 0.99938056 0.695520276 0.75161502 0.053131186 0.175622521 2.301968506 0.04912535 0.013246082 8.198967348 -0.913759157 -0.303860284 RRDDGLSAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRDDGLSAAAR 11 2 F8WBN3;B9A031;C9JQZ0;B8ZZY7;F8WBV6;P84101-4;P84101;P84101-3;P84101-2 F8WBN3 SERF2 Small EDRK-rich factor 2 0 90.685 0.044905 50440000 7841.5 16133 16264 9877.5 16239 11132 12784 9375.2 12875 14920 FALSE TRUE 8151.088475 18903.71725 16687.8532 11831.24002 13478.70058 8546.761707 11781.95668 9249.540779 12411.63126 17843.28834 0.456815376 1.059430128 0.935245392 0.663063881 0.755393307 0.478990282 0.660301871 0.518376468 0.695591027 1 14.12309389 3.643818147 6.660390883 0.646366392 0.840767363 0.067868781 0.197047434 0.417254544 24.83095168 0.049869908 0.077665378 4403.704281 -3.643818147 0.19440097 RRDEDMLYS(ph)PELAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR;RRDEDMLYS(1)PELAQR 225.08 5.46E-13 3173562000 777989 939654 908246 877095 1045323 1052561 853053 877689 890761 1046213 TRUE FALSE 808704.6065 1101032.265 931915.6369 1050581.773 867639.3698 808119.6595 786188.4768 865925.0146 858702.6856 1251198.406 0.646344019 0.879982151 0.744818433 0.839660415 0.693446671 0.64587651 0.628348368 0.692076501 0.686304171 1 20.25487915 -1.332807677 3.701278097 1.00094987 0.717974158 0.535180756 0.07900111 32205046.26 56213501.6 341619.9138 0.020003411 0.046472103 1.332807677 -0.282975712 RRDEDMLYSPELAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 ; 142.1 2.61E-06 188115000 110672 142025 140676 130192 157209 173000 133414 146938 142612 176221 FALSE TRUE 115041.416 166416.6889 144342.1321 155943.589 130486.6703 132823.3718 122956.6621 144968.5365 137479.422 210748.131 0.545871584 0.789647283 0.684903498 0.739952418 0.619159324 0.630246974 0.583429431 0.687875787 0.652339935 1 17.68516031 -1.448428945 2.993880263 1.007519099 0.662750605 0.693171496 0.067972446 10833661.14 13286398.64 688976.5532 0.015877501 0.035609925 1.448428945 -0.344768495 RRDELSEEINNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRDELSEEINNLR 13 2 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2;B4DSP0;A0A087WZG9;Q86TG7-2 A0A087WXK2;B4DSP0 PEG10 Retrotransposon-derived protein PEG10 0 ;; 230.14 2.58E-12 1560690000 546970 697090 603960 587440 704230 746640 586720 642840 610630 780670 FALSE TRUE 568564.798 816809.7849 619699.6938 703633.8787 584525.2361 573244.1754 540731.3533 634223.7813 588653.5456 933627.3397 0.608984735 0.874877749 0.66375487 0.753656035 0.626079819 0.613996775 0.579172578 0.679311492 0.630501615 1 19.83248728 -1.224002983 9.222296935 1.000000023 0.671955829 0.591211575 0.082298234 3.87E-08 3.34E-09 0.079406524 0.018716296 0.059703119 1.224002983 -0.328044194 RRDS(ph)DGVDGFEAEGK ddPTM_MDA-MB-175_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 243.16 4.57E-18 4093430000 4511990 2924910 3791080 2835690 4761020 5618180 4816920 3699020 4161930 2819510 TRUE FALSE 4690126.849 3427240.54 3889878.659 3396581.018 3951743.521 4313442.839 4439357.224 3649440.687 4012142.952 3371939.002 1.390928735 1.016400516 1.153602914 1.007307966 1.171949884 1.27921734 1.316559173 1.082297362 1.189862257 1 21.68514701 -0.001780377 1.271437869 0.999541976 1.171421138 0.166521764 0.118575997 26.67888059 31.33618715 0.15658848 0.033206841 0.995908922 0.001780377 0.171879163 RRDS(ph)DGVDGFEAEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRDSDGVDGFEAEGKK 16 3 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 RRDS(1)DGVDGFEAEGKK;RRDS(1)DGVDGFEAEGKK 195.56 2.66E-10 3752600000 4504900 2131700 3153400 1907070 4912600 4167900 4043400 3125300 4138600 2206000 TRUE FALSE 4682756.931 2497802.893 3235580.195 2284282.754 4077558.007 3199968.39 3726467.743 3083410.465 3989652.594 2638223.464 1.774965993 0.946774573 1.226423857 0.86584127 1.545569609 1.212925453 1.41249132 1.168744994 1.512249682 1 21.33113534 3.208984663 24.9999073 1.309521064 1.186800064 0.033190022 0.272122938 719.1967624 607919.4965 0.073626278 0.088011878 1618.022897 -3.208984663 -0.122721 RRDS(ph)DYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 124.1 0.0072894 60057000 85261 56625 77087 62200 95996 104490 97214 88673 93415 83497 TRUE FALSE 88627.17012 66349.90327 79095.95055 74502.97435 79678.63421 80223.78106 89594.11266 87484.48347 90053.0124 99856.6385 0.887544098 0.6644516 0.792095065 0.746099363 0.797930267 0.803389562 0.897227405 0.876100826 0.901822991 1 16.60757072 1.664372342 0.56825783 0.991689725 0.758779088 0.622736975 0.055344111 0.448616278 0.327067079 0.049892435 0.028802452 46.17132547 -1.664372342 -0.232910637 RRDS(ph)EEFGVK ddPTM_MDA-MB-175_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 199.38 2.20E-07 13038430000 4702960 4162380 4743660 3750270 6144410 6185920 5765520 4757980 5595850 4131080 TRUE FALSE 4888636.492 4877236.386 4867283.677 4492062.213 5099985.383 4749333.829 5313603.477 4694207.061 5394456.452 4940486.032 0.989505174 0.987197688 0.985183167 0.909234878 1.032284142 0.961309029 1.075522417 0.950150862 1.091887806 1 22.23622155 2.699170947 1.715361773 1.017072162 0.973737336 0.167055797 0.048182511 0.725027255 4.254301538 0.018099581 0.017114783 500.2313975 -2.699170947 -0.043334826 RRDS(ph)GDNSAPSGQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRDSGDNSAPSGQER 15 2 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 RRDS(0.993)GDNS(0.007)APSGQER;RRDS(0.878)GDNS(0.122)APSGQER 209.03 2.04E-09 1075120000 249530 295090 298090 273900 306710 358430 269270 280050 289620 292380 TRUE FALSE 259381.6371 345769.412 305858.4703 328076.6025 254575.5438 275190.0646 248163.9138 276296.3878 279196.6328 349666.263 0.741797721 0.988855513 0.874715415 0.938256381 0.72805292 0.787007766 0.709716493 0.790171707 0.79846603 1 18.41561908 3.242134021 24.99996669 0.784875296 0.892460431 0.141699787 0.094750734 129.1536461 903567.188 0.024483458 0.031889008 1746.360988 -3.242134021 0.107585136 RRDS(ph)GIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RRDSGIGEETATGLGSHVEVTPHTAPPGVSAGPDAISEVLSTLSLEVNK 49 2 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 RRDS(0.23)GIGEET(0.23)AT(0.23)GLGS(0.23)HVEVT(0.04)PHT(0.04)APPGVSAGPDAISEVLSTLSLEVNK;RRDS(0.175)GIGEET(0.175)AT(0.175)GLGS(0.175)HVEVT(0.057)PHT(0.175)APPGVS(0.057)AGPDAIS(0.007)EVLS(0.003)T(0.002)LSLEVNK;RRDS(0.162)GIGEET(0.162)AT(0.162)GLGS(0.162)HVEVT(0.162)PHT(0.162)APPGVS(0.013)AGPDAIS(0.013)EVLSTLSLEVNK;RRDS(0.231)GIGEET(0.231)AT(0.231)GLGS(0.231)HVEVT(0.057)PHT(0.015)APPGVS(0.005)AGPDAIS(0.001)EVLSTLSLEVNK;RRDS(0.16)GIGEET(0.16)AT(0.16)GLGS(0.16)HVEVT(0.16)PHT(0.16)APPGVS(0.039)AGPDAIS(0.001)EVLSTLSLEVNK 150.42 7.78E-16 3861965000 175441.8 178111.7 212739.1 213141.3 228717.5 234057 252095.1 229656.2 220254 191481.9 TRUE FALSE 182368.3777 208700.999 218283.2557 255300.013 189840.181 179700.8089 232335.2273 226578.0343 212327.1016 228999.1122 0.796371549 0.911361607 0.953205686 1.114851541 0.828999638 0.784722732 1.014568245 0.989427567 0.927196178 1 17.80498248 4.690836693 2.707460481 0.951586688 0.775237925 0.21896964 0.088273135 0.642068973 6.758877349 0.022818416 0.240683049 49072.33153 -4.690836693 -0.176348763 RRDS(ph)YYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRDSYYDR 8 2 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 1 RRDS(1)YYDR;RRDS(1)YYDR;RRDS(0.999)YYDR 146.16 0.00043924 2298520000 728991 877620 811563 877405 1064091 1189546 872641 996375 987316 1215250 TRUE FALSE 757772.1276 1028344.408 832712.9985 1050953.09 883217.1919 913291.9692 804241.1182 983020.2229 951782.69 1453354.97 0.521395078 0.707565894 0.572959129 0.723122095 0.607709204 0.62840255 0.553368678 0.676379992 0.654886597 1 20.47095568 0.256380116 1.17115075 1.000767354 0.62459777 0.771475183 0.061186122 1.882901868 2.575187679 0.055486957 0.016161587 1.804596521 -0.256380116 -0.376169584 RRDSGIGEETATGLGSHVEVTPHTAPPGVS(ph)AGPDAISEVLSTLSLEVNK ddPTM_MDA-MB-175_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(0.131)GIGEET(0.131)AT(0.131)GLGS(0.131)HVEVT(0.131)PHT(0.131)APPGVS(0.149)AGPDAIS(0.046)EVLS(0.009)T(0.01)LSLEVNK 43.723 0.016701 1953300000 42654 33285 44738 35665 47246 51462 50960 38264 44661 30778 TRUE FALSE 44338.01286 39001.43983 45903.90903 42719.43055 39215.1418 39510.73041 46965.62204 37751.13367 43053.65933 36808.35982 1.204563666 1.05958103 1.247105529 1.160590441 1.06538683 1.073417305 1.275949873 1.025613036 1.169670682 1 15.16774584 -4.999999999 0.178400858 0.437101996 1.167168371 0.224536343 0.080315463 200.73203 1.927813193 39.94575333 0.243617924 1.00E-05 4.999999999 0.730066375 RRDVS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRDVSPER 8 2 A0A087WT53;Q96QZ7-7;Q96QZ7-6;Q96QZ7-2;Q96QZ7 A0A087WT53 MAGI1 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1" 1 RRDVS(1)PER;RRDVS(1)PER 80.69 0.019528 258200000 167292 167792 178154 161946 224870 225690 200085 191211 183118 203201 TRUE FALSE 173896.8173 196608.9708 182796.8396 193978.4354 186646.6777 173276.9179 184401.8149 188648.1293 176527.619 243014.3454 0.715582519 0.809042653 0.752205962 0.798218044 0.768047982 0.713031642 0.758810409 0.776283923 0.726408223 1 17.89068195 -2.153583709 2.549928821 1.590511987 0.760343493 0.846518609 0.030954281 3620794.213 947703.2934 12395239.55 0.007205177 0.00702128 2.153583709 -0.830168493 RRDYYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRDYYDR 7 2 P62995;P62995-3;H7BXF3;H7C2L4 P62995 TRA2B Transformer-2 protein homolog beta 0 ;; 109.86 0.050426 166120000 83361 70254 71930 62938 129193 103815 91116 98460 85455 126287 FALSE TRUE 86652.15665 82319.578 73804.55489 75386.94855 107232.82 79705.53958 83974.08983 97140.30475 82379.49124 151030.5197 0.573739379 0.545052604 0.488673117 0.499150428 0.710007621 0.527744589 0.556007421 0.643183278 0.5454493 1 17.20448059 -5 0.286114824 4.293551049 0.541677132 0.812603033 0.062669398 95.37027419 0.904515669 187.0243444 0.067547384 1.00E-05 5 -3.751873916 RREDS(ph)YHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 142.97 5.38E-05 693219000 64999.3 139513.8 117486 110898.5 122219 147323 87357.4 104499.9 102183 181857 TRUE FALSE 67565.52255 163474.2099 120547.7817 132833.8923 101444.258 113109.466 80510.09872 103099.2498 98505.45379 217488.3973 0.310662653 0.75164566 0.554272242 0.610763121 0.466435264 0.520071265 0.370181121 0.474044827 0.4529228 1 17.73057891 -1.304437525 5.601667484 1.000062861 0.504904671 0.622390115 0.116519975 8.91E-05 1.11E-05 0.109876151 0.025894787 0.049609229 1.304437525 -0.495158189 RREEEGLQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RREEEGLQLR 10 2 C9JYI4;P52294;C9J352;C9JWD9;F2Z3G4;C9J4U1 C9JYI4 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 ;;; 202.56 1.25E-07 426452000 191469 239117 224440 234544 237750 289768 206091 221784 218312 280718 FALSE TRUE 199028.344 280183.4847 230289.0908 280936.1032 197337.3399 222473.7735 189937.0489 218811.3482 210454.9938 335719.3174 0.592841501 0.834576595 0.685957223 0.836818403 0.587804543 0.662677904 0.565761453 0.651768715 0.62687782 1 18.35689603 -0.948937904 4.351247728 1.000008122 0.672809753 0.54503274 0.089986372 5343474.978 1842049.106 428.769409 0.020997849 0.112476578 0.948937904 -0.327198368 RREEEMMIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RREEEMMIR 9 2 P23246;P23246-2;H0Y9K7 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 ;; 163.64 3.54E-05 1201141000 307835.4 399688.9 365609.9 310393.4 442394.5 396817 364795.5 338229.3 335380.7 480750.3 FALSE TRUE 319988.9793 468332.3594 375137.9943 371788.2881 367196.4409 304662.2656 336201.8755 333695.8895 323310.4141 574944.1168 0.556556663 0.814570227 0.652477316 0.646651174 0.638664577 0.529898918 0.584755745 0.580397085 0.562333633 1 19.13306221 -1.232992248 5.653694234 1.000017527 0.619702904 0.692214859 0.076317022 1.74E-05 2.36E-06 0.076281533 0.017978902 0.058480052 1.232992248 -0.380314622 RREEGPPPPS(ph)PDGASS(ph)DAEPEPPSGR ddPTM_MDA-MB-175_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(0.251)S(0.749)DAEPEPPSGR 101.44 0.020579 294630000 127970 160840 165240 149510 175850 191870 146010 170160 164020 159500 TRUE FALSE 133022.3544 188463.0188 169546.2901 179082.6318 145959.0798 147311.1003 134565.3547 167879.2835 158116.9522 190750.9712 0.697361348 0.988005553 0.88883579 0.938829463 0.765181319 0.772269202 0.70545043 0.880096612 0.828918203 1 17.54133088 4.795024941 22.21538799 0.850773299 0.697357072 0.213064825 0.092870374 29386.14521 11560128.89 0.022430368 29.84433042 62377.0657 -4.795024941 -0.153416227 RREEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_MDA-MB-175_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(0.096)PDGAS(0.452)S(0.452)DAEPEPPSGR;RREEGPPPPS(0.049)PDGAS(0.476)S(0.476)DAEPEPPSGR;RREEGPPPPS(0.005)PDGAS(0.497)S(0.497)DAEPEPPSGR 184.97 1.18E-17 1732630000 166215 215540 235653 196757 213647 280289 196374 220240 207094 242316 TRUE FALSE 172777.2965 252557.3183 241794.3108 235674.9473 177331.3593 215196.1276 180981.6928 217288.043 199640.7274 289793.1808 0.596208979 0.871508838 0.834368532 0.813252219 0.611923851 0.742585202 0.624520191 0.749803851 0.688907609 1 18.14466412 -1.088783027 4.318881615 1.000029711 0.730115733 0.448162191 0.091139623 12342319.61 3111479.271 3638.98163 0.021172332 0.081511141 1.088783027 -0.269913979 RREEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_MDA-MB-175_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 1 RREEGPPPPS(0.001)PDGAS(0.161)S(0.838)DAEPEPPSGR 146.78 1.05E-07 227160000 24937 35905 32546 34812 36787 42527 33281 27374 29852 35675 TRUE FALSE 25921.53202 42071.40445 33394.1755 41697.7097 30533.95888 32650.74875 30672.34826 27007.0963 28777.63235 42664.83321 0.607562015 0.986090916 0.782709623 0.977332069 0.715670415 0.765284809 0.718914055 0.633006021 0.674504743 1 15.38075979 3.134691375 19.03977802 0.724898136 0.845330834 0.06944491 0.136424355 3.940371191 705.8728623 0.036892496 0.044095234 1363.61376 -3.134691375 0.120432699 RREPGGYDSSSTLMSSELETTSFFDS(ph)DEDDSTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RREPGGYDSSSTLMSSELETTSFFDSDEDDSTSR 34 2 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 RREPGGYDSSSTLMSSELETTSFFDS(0.958)DEDDS(0.027)T(0.007)S(0.007)R;RREPGGYDSSSTLMSSELETTSFFDS(1)DEDDSTSR 156.9 1.05E-11 290470000 57212 56571 57208 49672 61164 72810 64321 57288 50485 49593 TRUE FALSE 59470.77394 66286.62919 58698.88748 59496.97334 50767.36513 55900.98095 59279.35195 56520.14806 48668.05471 59309.79883 1.00271414 1.117633688 0.989699656 1.003155878 0.855969269 0.942525216 0.999486647 0.952964758 0.820573593 1 15.85598286 3.747436392 2.128170769 0.934801612 1.055764831 0.376480408 0.062413826 0.323765812 2.853372242 0.017309151 0.035531167 5590.316443 -3.747436392 0.120963219 RRES(ph)ASSSSSVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRESASSSSSVKK 13 3 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 RRES(0.994)AS(0.005)S(0.001)SSSVKK;RRES(0.996)AS(0.004)SSSSVKK 92.575 0.03321 77748000 93115 61454 89928 55529 137050 118393 95418 97122 110052 77986 TRUE FALSE 96791.2521 72008.24645 92271.59756 66512.47046 113754.29 90898.02001 87938.88783 95820.23845 106091.25 93265.86357 1.037799345 0.772075052 0.989339443 0.713149141 1.219677657 0.974611895 0.942883971 1.027388101 1.137514263 1 16.50906151 3.241834277 25 1.039256161 0.87846457 0.345193427 0.11562171 99.93194265 763144.0334 0.030733494 0.039958124 1745.156091 -3.241834277 -0.160791591 RRES(ph)EKS(ph)LENETLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(1)EKS(0.997)LENET(0.003)LNK 99.059 0.0038595 259020000 149520 71389 83350 82415 137930 136180 185430 99257 94366 52046 TRUE FALSE 155423.1651 83649.50542 85522.16947 98716.44102 114484.7079 104554.2588 170895.5121 97926.62227 90969.78609 62243.41722 2.497021725 1.34390927 1.373995409 1.585973994 1.839306275 1.679764118 2.745599771 1.573284801 1.461516577 1 15.92563365 3.231897634 24.20724482 1.801354111 1.651471855 0 0.510718166 602.2533625 2188043.057 0.144413759 0.176578562 1705.680303 -3.231897634 -0.149882256 RRES(ph)EKSLENET(ph)LNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRESEKSLENETLNK 15 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 RRES(0.999)EKS(0.001)LENET(1)LNK 188.44 5.67E-07 242500000 275890 106320 154750 117440 214870 257260 274020 184790 208380 80338 TRUE FALSE 286782.3502 124579.6329 158782.9121 140669.2815 178346.4741 197515.2638 252541.5964 182313.1923 200880.4445 96078.69294 2.984869397 1.296641629 1.652633974 1.464104862 1.856254167 2.055765517 2.628487011 1.897540305 2.090790771 1 16.5519289 2.839706518 4.875680249 2.038278899 1.782363615 0 0.570178544 0.846893453 32.09871248 0.16830724 0.178931097 691.3636122 -2.839706518 -0.255915284 RRES(ph)LSYIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRESLSYIPK 10 2 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RRES(0.993)LS(0.007)YIPK;RRES(1)LSYIPK;RRES(0.882)LS(0.118)YIPK 156.6 8.39E-06 2222710000 1883590 2211720 2321840 1955200 2801160 3080350 2489110 2358670 2538990 2346080 TRUE FALSE 1957955.588 2591565.705 2382349.058 2341932.724 2325019.824 2364985.396 2294007.054 2327055.887 2447612.246 2805749.458 0.69783693 0.923662552 0.849095436 0.834690609 0.828662665 0.842906835 0.817609373 0.829388341 0.872355954 1 21.41995476 0.820828472 2.672709645 0.999942209 0.831947239 0.496761843 0.052029456 0.586951766 7.121913071 0.045296118 0.01202641 6.61955008 -0.820828472 -0.167994969 RRES(ph)QEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 152.4 6.34E-05 8059580000 5125940 6487360 5880200 6182330 6891890 7139320 6548070 6462990 6280840 7811830 TRUE FALSE 5328316.069 7601513.615 6033442.843 7405176.422 5720409 5481321.127 6034815.163 6376364.19 6054793.795 9342408.522 0.570336446 0.813656735 0.645812354 0.792641042 0.612305594 0.58671392 0.645959246 0.682518237 0.648097734 1 23.1553631 -1.337789649 3.620170455 1.00131954 0.670013556 0.634248035 0.075944984 4933765.232 2735215.6 48849.86802 0.016933624 0.045942048 1.337789649 -0.331305983 RRET(ph)PS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRETPSPR 8 2 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RRET(1)PS(1)PR;RRET(1)PS(1)PR 76.332 0.039814 385860000 263430 253220 236320 285020 241156 282000 321190 283330 256880 209535 TRUE FALSE 273830.4198 296708.5652 242478.6933 341396.1053 200164.3893 216509.7738 296014.2885 279532.4248 247634.939 250589.3715 1.092745547 1.184042897 0.967633591 1.362372647 0.798774458 0.864002222 1.181272321 1.115499924 0.988210065 1 17.9349657 3.236369064 24.99980577 1.012179014 1.140861431 0.235215345 0.138109907 111.2900139 1269526.788 0.041160973 0.051525224 1723.332444 -3.236369064 0.128682417 RRET(ph)PS(ph)PRPMR ddPTM_MDA-MB-175_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 94.551 0.0044617 9656226000 4060798 4896303 4612248 4140039 5186727 5288630 4349093 4706246 4416232 5304210 TRUE FALSE 4221121.441 5737204.952 4732446.972 4958926.357 4305088.997 4060425.832 4008199.726 4643166.47 4257292.673 6343468.394 0.665427993 0.904427136 0.74603461 0.781737379 0.678664845 0.640095541 0.631862489 0.731960212 0.671130115 1 22.59684044 -1.135659102 3.437736631 1.000296195 0.718963187 0.546639192 0.077345895 16047057.94 25040344.99 53075.84022 0.019964788 0.073171321 1.135659102 -0.281333008 RREVS(ph)PAPAVAGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RREVSPAPAVAGQSK 15 2 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 RREVS(1)PAPAVAGQSK 70.529 0.02422 75626000 34317 17996 28607 20588 41959 40886 33363 32686 37895 32190 TRUE FALSE 35671.86166 21086.67301 29352.52192 24660.24495 34826.82417 31390.84613 30747.92088 32247.89763 36531.16635 38497.01419 0.926613724 0.547748272 0.762462298 0.640575522 0.904662995 0.815409891 0.798709238 0.837672695 0.948935057 1 15.23245893 1.571637823 0.449493761 1.008632662 0.714462709 0.384153053 0.10468239 0.918833824 0.497413273 0.110494454 0.077531068 37.29390182 -1.571637823 -0.294169953 RRFS(ph)DSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRFSDSEER 9 2 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 RRFS(0.832)DS(0.168)EER;RRFS(0.992)DS(0.008)EER 125.82 0.00038661 306730000 247580 262200 264180 277670 332140 353070 274650 288840 288710 314960 TRUE FALSE 257354.6496 307230.8104 271064.7478 332592.2972 275682.9614 271074.8433 253122.2153 284968.5722 278319.3835 376670.3817 0.683235694 0.815648974 0.719633826 0.882979691 0.731894449 0.719660628 0.671999253 0.75654627 0.73889373 1 18.52294307 -1.992957516 3.084368835 1.239635538 0.74807388 0.623918094 0.058984142 20963080.73 23646825.86 35740112.66 0.013853904 0.010163481 1.992957516 -0.491561659 RRFS(ph)DSEGEETVPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRFSDSEGEETVPEPR 16 2 A0A1B0GWH8;H3BQ48;A0A1B0GWD3;A0A1B0GV71;A0A1B0GW34;A0A0D9SFH9;H3BPL0;Q9UBD8;A0A1B0GV41;H3BR84;O95090;H3BR00;Q9UP10;Q9UBH5;A0A0D9SF04;Q13286-5;Q13286-4;Q13286-6;Q13286-2;Q13286-7;Q13286-3;Q13286 A0A1B0GWH8 CLN3 Battenin 1 RRFS(0.82)DS(0.18)EGEETVPEPR;RRFS(0.751)DS(0.248)EGEET(0.001)VPEPR 179.41 2.07E-09 1187360000 382060 479640 439490 423640 534910 569500 351390 433530 434470 620880 TRUE FALSE 397144.0238 562014.4389 450943.4704 507434.7276 443986.1893 437242.2559 323847.1336 427719.2395 418833.5096 742529.5485 0.534852821 0.756891682 0.607307105 0.683386578 0.597937402 0.588855025 0.436140399 0.576029924 0.564063087 1 19.50208891 -1.525608372 5.60955832 1.000887077 0.593473758 0.6974194 0.080238287 0.000925136 7.82E-05 0.080742108 0.018992169 0.029812035 1.525608372 -0.407413319 RRGDDWNDREWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRGDDWNDREWDR 13 3 C9JUL9;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5 C9JUL9;Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 177.21 6.85E-06 1014770000 57452.8 73552 94034 73282 120093 87608 77398 80056 76724 107775 FALSE TRUE 59721.08091 86183.98384 96484.60329 87776.96088 99679.63476 67262.36971 71331.34252 78982.98027 73962.71823 128891.4478 0.463344015 0.668655565 0.748572578 0.681014624 0.773361123 0.521852853 0.553421843 0.612786819 0.573837283 1 16.97579702 -1.466837961 3.113865919 1.008170855 0.626280462 0.596098566 0.093313298 28946427.53 34507210.48 2041823.095 0.023790476 0.034132024 1.466837961 -0.381890393 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 RRGDS(1)ES(0.933)EEDEQDS(0.067)EEVR;RRGDS(1)ES(1)EEDEQDSEEVR 163.61 1.61E-10 2441000000 645970 759770 746620 643410 784700 912480 746660 759810 723400 722260 TRUE FALSE 671473.3944 890254.5873 766077.5306 770674.5776 651316.9743 700570.3488 688134.8382 749625.9897 697364.9753 863773.0185 0.777372504 1.030658018 0.886896805 0.89221886 0.754037184 0.811058384 0.79666165 0.867850666 0.807347486 1 19.72029273 3.45287292 24.5525163 0.830533293 0.907879669 0.09198791 0.084008494 317.9927963 321980.6305 0.02160474 0.029254335 2837.088737 -3.45287292 0.077346377 RRGEEGHDPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RRGEEGHDPKEPEQLR 16 3 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;; 159.34 5.49E-09 1696240000 580380 499039 620899 354485 825591 732902 555391 592863 653277 570597 FALSE TRUE 603293.8506 584745.0663 637080.138 424601.075 685257.3367 562696.6177 511858.0022 584916.6412 629765.6884 682394.5574 0.88408362 0.856901715 0.933594987 0.622222247 1.004195197 0.824591304 0.75009098 0.857153145 0.922876189 1 19.38024661 1.050039863 2.72115647 0.99816567 0.838487815 0.216907557 0.096906892 0.35366665 5.580312364 0.086525745 0.023243553 11.22121447 -1.050039863 -0.159677856 RRGNDPLT(ph)SSPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRGNDPLTSSPGR 13 2 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RRGNDPLT(0.721)S(0.14)S(0.14)PGR 77.324 0.04222 628760000 132720 157490 168800 117070 254660 220650 162000 202480 181300 233240 TRUE FALSE 137959.8881 184537.6824 173199.0667 140226.0966 211372.9842 169407.3815 149302.0167 199766.0868 174775.0484 278938.9124 0.494588177 0.661570237 0.620921137 0.502712567 0.757775179 0.607327891 0.53524987 0.716164285 0.626571054 1 18.08958968 -5 0.244841651 3.258963849 0.581925833 0.690412451 0.078845711 95.40488331 0.949172824 107.428772 0.11258176 1.00E-05 5 -2.677038016 RRGS(ph)QEK ddPTM_MDA-MB-175_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 88.056 0.014875 1181680000 670860 479406 629440 446341 785170 765460 710560 549330 707850 511971 TRUE FALSE 697346.0708 561740.2512 645843.7235 534625.9176 651707.0839 587693.5157 654864.4505 541967.1299 682374.6168 612281.9152 1.138929721 0.917453606 1.054814306 0.873169539 1.064390549 0.959841376 1.069547269 0.885159461 1.114477824 1 19.22383655 4.75707274 23.67388658 0.987823447 1.138929995 0.231330046 0.079144809 2535.763441 3242703.973 0.016874285 0.529193322 57157.43613 -4.75707274 0.151106548 RRHDS(ph)LHDPAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRHDSLHDPAAPSR 14 2 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 RRHDS(1)LHDPAAPSR;RRHDS(1)LHDPAAPSR 62.475 0.036443 93983000 45218 68695 58964 59010 84776 89789 59378 69254 64619 108546 TRUE FALSE 47003.24156 80492.83188 60500.65028 70682.00187 70365.8058 68936.86552 54723.7972 68325.76341 62293.37481 129813.5105 0.362082817 0.620065135 0.466058194 0.544488795 0.542053023 0.531045384 0.421557024 0.526337845 0.479868194 1 16.98608102 -1.482092904 3.245233516 1.010351483 0.50368222 0.828349222 0.068353575 10257878.88 12421222.19 944411.2031 0.014863002 0.032953921 1.482092904 -0.506669263 RRHEGLPGLAVQWGAIGDVGILVETMSTNDTIVSGTLPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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 ;;;;;;;;;;;; 353.56 2.79E-146 2943252000 502924 495561.5 601400.6 552856.2 803735.1 779580.8 569391.3 596610.8 637166.3 706205.2 FALSE TRUE 522779.8279 580670.3327 617073.5937 662209.5062 667116.4948 598534.9739 524760.9221 588614.2081 614234.8093 844572.5878 0.618987445 0.687531588 0.730634172 0.784076485 0.789886511 0.708683875 0.621333121 0.696937382 0.727272964 1 19.6878619 0.756961384 4.55850845 0.999999003 0.706237459 0.728405402 0.053775461 3.055864926 56.94301673 0.056244364 0.014269783 5.714278249 -0.756961384 -0.293761544 RRHS(ph)DENDGGQPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRHSDENDGGQPHK 14 2 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHK 58.29 0.052248 148990000 33910 17236 23363 20020 32463 39008 27322 23082 23150 20267 TRUE FALSE 35248.79298 20196.14892 23971.85897 23979.89625 26944.95086 29948.98317 25180.43025 22772.62354 22316.83602 24237.93061 1.454282279 0.833245595 0.98902251 0.989354109 1.111685287 1.235624594 1.038885318 0.939544877 0.920740156 1 14.56497891 1.856487906 4.441861853 0.949292415 1.083860812 0.145489692 0.156766716 0.478869722 14.24912989 0.073559752 0.041640236 71.86011464 -1.856487906 0.134568396 RRHS(ph)DENDGGQPHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRHSDENDGGQPHKR 15 3 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 1 RRHS(1)DENDGGQPHKR 118.96 0.00010163 76544000 65431 76217 73105 54434 94117 73244 51722 60419 64270 104700 TRUE FALSE 68014.2664 89306.67686 75010.17636 65200.88273 78119.02596 56234.19102 47667.89449 59609.18213 61956.93525 125213.9604 0.543184372 0.713232587 0.599056017 0.520715761 0.623884315 0.449104803 0.380691533 0.476058596 0.494808527 1 16.9340359 -1.055733705 4.738041255 1.000015791 0.529705189 0.708859777 0.08967791 1.67E-05 3.32E-06 0.096714218 0.022794995 0.087956167 1.055733705 -0.470310602 RRHT(ph)MDKDSR ddPTM_MDA-MB-175_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 177.38 1.24E-06 783901000 315966.9 262842.1 324334.7 252369 600299 542905 368051.9 373816.4 349393.5 458068.5 TRUE FALSE 328441.5172 307983.186 332787.1287 302286.835 498260.3904 416823.5416 339203.0304 368806.0026 336818.8962 547818.2523 0.599544677 0.56219957 0.607477256 0.55180132 0.909535942 0.760879251 0.61918899 0.673226934 0.614836937 1 19.06333781 3.316536605 24.99999977 0.732100818 0.580909086 0.353080102 0.116747051 44.55783949 14283.4533 0.03201227 0.04334481 2072.70075 -3.316536605 -0.151191732 RRKDS(ph)AQDDQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRKDSAQDDQAK 12 3 Q13045-3;Q13045;Q13045-2;J3KS54 Q13045-3 FLII Protein flightless-1 homolog 1 RRKDS(1)AQDDQAK;RRKDS(1)AQDDQAK 178.85 0.00011862 399830000 295160 87401 181007 83026 327700 256150 246854 197234 237799 113529 TRUE FALSE 306813.1447 102411.4419 185724.1911 99448.29499 271997.6711 196663.0445 227504.9384 194590.4008 229240.6604 135772.8339 2.25975356 0.75428522 1.367903916 0.732460921 2.003329114 1.448471236 1.675629299 1.43320571 1.688413314 1 17.05083532 3.230554849 24.99987126 1.558730588 1.247528547 0.070401828 0.459991119 416.006418 1299075.038 0.122803882 0.14924292 1700.414693 -3.230554849 -0.311202041 RRKEDEVEEWQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RRKEDEVEEWQHR 13 3 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 208.28 2.83E-08 5961860000 1820440 1413780 1819160 1127470 2780290 2310300 1866930 2020900 2122140 2030020 FALSE TRUE 1892312.377 1656585.717 1866568.804 1350480.201 2307697.299 1773767.838 1720595.148 1993813.141 2045764.596 2427763.552 0.779446736 0.682350518 0.768842914 0.556265127 0.950544503 0.730618036 0.708716113 0.821255076 0.84265397 1 21.21119649 0.594835009 0.496131744 1.015295278 0.724347761 0.421296299 0.093226876 1.58728603 0.770189486 0.134903661 0.047733774 3.93400592 -0.594835009 -0.290947516 RRKS(ph)EPAVGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRKSEPAVGPPR 12 3 O94875-12;O94875-10;O94875-3;H7BXR3;O94875-9;O94875-5;O94875-4;O94875-11;O94875-2;O94875-8;H7BZK1;H7BZX1;H7C1R7;O94875-7;O94875 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 RRKS(1)EPAVGPPR;RRKS(1)EPAVGPPR 117.18 0.0042105 182121000 55275 115054 58324 77469 87469 102157 57299 67876 61878 140483 TRUE FALSE 57457.29968 134813.6295 59843.97135 92792.13698 72601.05062 78432.58495 52807.75466 66966.23324 59651.02287 168007.9541 0.341991544 0.802424089 0.356197251 0.552307999 0.432128651 0.466838522 0.314316991 0.39858966 0.355048802 1 17.35817001 -1.174908459 5.076285706 1.000035755 0.448260463 0.597365153 0.136282177 5.31E-05 8.63E-06 0.127051197 0.029944319 0.066848481 1.174908459 -0.551775292 RRLS(ph)EQLAHTPTAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRLSEQLAHTPTAFK 15 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 RRLS(0.99)EQLAHT(0.01)PTAFK;RRLS(1)EQLAHTPTAFK 133.14 2.25E-05 661800000 583420 437800 544450 458550 818610 700290 621250 581780 638010 570870 TRUE FALSE 606453.8721 512988.7444 558638.8143 549249.8214 679462.9646 537658.2605 572554.8017 573982.1907 615048.1447 682721.0465 0.888289405 0.751388502 0.818253395 0.804501083 0.995227799 0.78752261 0.838636519 0.840727254 0.900877669 1 19.3809367 -4.999999997 0.193485826 1.69917429 0.815484848 0.36523908 0.063234269 146.7647743 1.442472686 39.4219154 0.160343435 1.00E-05 4.999999997 -0.883689442 RRLS(ph)PEKQNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRLSPEKQNCR 11 3 Q9NQT8;E7ERX9 Q9NQT8 KIF13B Kinesin-like protein KIF13B;Kinesin-like protein 1 RRLS(1)PEKQNCR 100.18 0.023315 80959000 50091 34305 45811 25773 64178 62925 44269 42333 49275 50258 TRUE FALSE 52068.63136 40196.61689 47004.87229 30870.82248 53269.04648 48311.62239 40799.0801 41765.59538 47501.60238 60105.09285 0.866293169 0.668772229 0.78204475 0.513614088 0.886265106 0.803785837 0.678795725 0.694876148 0.790309109 1 15.87519962 0.89221728 5.09706893 0.999985457 0.731561851 0.369755766 0.102686473 0.861305976 39.47533075 0.093617066 0.023649938 7.80220362 -0.89221728 -0.268423606 RRNDLDDPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RRNDLDDPER 10 2 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ;;; 147.62 1.49E-05 499749000 109326.3 160256.9 152253.6 163445.3 154204.9 199051.2 133516.5 166643 139356.8 224362.4 FALSE TRUE 113642.5867 187779.7759 156221.4539 195774.2925 127993.2062 152824.5755 123051.1278 164409.4232 134341.376 268321.9166 0.423530766 0.699830183 0.582216525 0.72962468 0.47701361 0.569556812 0.458595144 0.612731995 0.500672393 1 18.03360537 -1.527009081 3.02142944 1.016082623 0.5677578 0.654063003 0.095567701 20744054.04 23630560.19 2735878.089 0.023076187 0.029716039 1.527009081 -0.448324823 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.332)Y(0.306)T(0.332)EEEPEWFS(0.006)AGPT(0.006)S(0.006)QS(0.006)ET(0.006)IELTGFDDK;RRNDS(0.497)Y(0.007)T(0.497)EEEPEWFSAGPTSQSETIELTGFDDK;RRNDS(0.36)Y(0.28)T(0.36)EEEPEWFSAGPTSQSETIELTGFDDK 117.66 1.17E-06 921990000 149406 88936 113047 101647 169032 169620 185740 160001 151147 102084 TRUE FALSE 155304.6642 104210.0662 115993.0977 121752.4732 140300.001 130228.3256 171181.2135 157856.4483 145707.249 122085.4053 1.272098527 0.853583325 0.950097986 0.997272958 1.149195522 1.066698557 1.40214314 1.293000158 1.193486221 1 16.89753122 2.741767909 1.73409272 1.249186739 1.00786966 0.215405391 0.145821448 0.399704589 2.392899514 0.054758672 0.053565597 551.7824828 -2.741767909 -0.241317078 RRNDS(ph)YTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 40 3 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.495)Y(0.009)T(0.495)EEEPEWFSAGPTSQSETIELTGFDDKILEEDHK 136 2.19E-09 135590000 83935 37276 69771 36189 132280 103660 73904 77348 90034 56337 TRUE FALSE 87248.81861 43677.86303 71589.28958 43347.07619 109795.0928 79586.53598 68111.21137 76311.27658 86793.69393 67375.15651 1.294970181 0.648278465 1.062547284 0.643368838 1.629607982 1.181244543 1.010924722 1.132632272 1.288215099 1 16.0399291 3.262962364 24.99957043 1.193504288 0.904165903 0.261536864 0.241888063 316.7199045 324477.0657 0.06385324 0.086417851 1832.155641 -3.262962364 -0.289338385 RRNDSYT(ph)EEEPEWFSAGPTSQSETIELTGFDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRNDSYTEEEPEWFSAGPTSQSETIELTGFDDK 33 2 B1AKL4;Q9NRA8;Q9NRA8-3 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RRNDS(0.339)Y(0.284)T(0.377)EEEPEWFSAGPTSQSETIELTGFDDK 154.48 4.68E-09 284830000 41958 31062 38375 32075 48463 50148 52735 41529 45119 32633 TRUE FALSE 43614.53424 36396.65687 39375.08403 38419.33927 40225.27657 38501.887 48601.4929 40972.37168 43495.176 39026.81155 1.1175531 0.932606468 1.008923928 0.984434488 1.030708761 0.986549643 1.245335987 1.049851885 1.114494735 1 15.25217798 RRNS(ph)RDGDPLPSSLSCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRNSRDGDPLPSSLSCK 17 3 P53602;H3BP35 P53602 MVD Diphosphomevalonate decarboxylase 1 RRNS(1)RDGDPLPSSLSCK 132.59 0.00012774 592860000 125520 124370 135080 79346 183450 167310 124130 147300 143110 173420 TRUE FALSE 130475.6265 145729.58 138600.2958 95040.40198 152267.2345 128454.7881 114400.3662 145325.6844 137959.4991 207398.3287 0.629106451 0.702655518 0.668280678 0.458250568 0.734177732 0.619362697 0.551597339 0.700708079 0.665190987 1 17.66204474 0.278451812 1.014926497 1.001598302 0.628706965 0.678112918 0.07570716 1.901460212 2.190937704 0.076135043 0.022236551 1.898680157 -0.278451812 -0.372891336 RRPENPKPQDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRPENPKPQDGK 12 3 P67809;H0Y449 P67809 YBX1 Nuclease-sensitive element-binding protein 1 0 ; 95.401 0.0026581 592760000 625870 168247 268000 184425 370190 415170 355570 258940 348300 143467 FALSE TRUE 650579.8309 197142.1135 274984.3002 220903.7145 307265.236 318753.0595 327699.4943 255469.3328 335764.751 171576.6118 3.791774555 1.149003418 1.60269105 1.287493162 1.790834035 1.857788519 1.909931026 1.488951962 1.956937764 1 17.38849338 4.745729701 24.99945053 1.595793405 3.791775577 0.817643814 0.315736147 333.5896601 1163238.394 0.071685159 0.734168548 55683.90724 -4.745729701 2.195982171 RRPESAPAESS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRPESAPAESSPSK 14 2 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 RRPESAPAES(0.023)S(0.977)PSK;RRPESAPAES(0.122)S(0.878)PSK 82.707 0.0051989 163231000 183124 106544 136307 113232 195099 174372 156016 140385 144454 101132 TRUE FALSE 190353.8769 124842.1032 139859.2724 135628.9516 161936.1417 133876.7456 143787.0582 138503.3687 139255.1288 120946.8791 1.573863487 1.032206074 1.15636942 1.121392736 1.33890302 1.106905334 1.188844717 1.145158682 1.151374304 1 16.88401402 8 0.089816937 0.930507784 1.913882399 0.264358363 0.134537065 253.9225386 1.638551913 2.350732608 30.77657232 100000000 -8 0.983374615 RRPGAALEDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRPGAALEDSR 11 2 Q9H5N1;Q9H5N1-2 Q9H5N1 RABEP2 Rab GTPase-binding effector protein 2 0 ;; 118.28 0.00041723 52303000 32479.1 34289.2 31575 30150.1 44847 49989 32411.6 34956 31894.6 43880 FALSE TRUE 33761.39995 40178.10337 32397.87044 36113.69979 37223.92296 38379.81234 29871.0941 34487.472 30746.71958 52477.44587 0.64335067 0.765626122 0.617367517 0.688175638 0.709331835 0.731358238 0.569217758 0.657186558 0.585903507 1 15.67940988 -1.618714931 2.940128194 1.02538806 0.664200164 0.743541728 0.059361888 21973438.4 23632400.95 4306597.656 0.014541844 0.024059415 1.618714931 -0.361187896 RRPGGEGPQCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRPGGEGPQCEK 12 2 Q9NWY4 Q9NWY4 C4orf27 UPF0609 protein C4orf27 0 ; 63.537 0.03936 44839000 37018 22268.4 28458 22534.8 32197 42542 37097 26180.3 27481 23640 FALSE TRUE 38479.49922 26092.82448 29199.63886 26992.11618 26724.16544 32662.26523 34189.24021 25829.3959 26491.96418 28271.80538 1.361055606 0.922927423 1.032818331 0.954736205 0.945258539 1.15529464 1.209305162 0.913609709 0.937045364 1 14.78707639 4.747722451 24.6434885 1.011737525 1.361055831 0.552024863 0.095387435 815.3655387 2193111.706 0.02392438 0.296216785 55939.99857 -4.747722451 0.349318305 RRPPS(ph)PEPSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(0.99)PEPS(0.008)T(0.001)K;RRPPS(0.997)PEPS(0.003)T(0.001)K;RRPPS(0.987)PEPS(0.013)T(0.001)K;RRPPS(0.994)PEPS(0.004)T(0.002)K 103.76 0.0021191 644767000 712933 637268 680842 541238 876079 958568 802736 734727 778846 648995 TRUE FALSE 741080.1453 746713.8217 698585.3018 648293.261 727163.4045 735955.1092 739815.4548 724879.1863 750815.4846 776153.1445 0.954811754 0.962070214 0.900061163 0.83526462 0.936881348 0.948208629 0.95318232 0.933938349 0.967354819 1 19.56598182 3.007710972 24.99805849 0.952888092 0.911931294 0.263628761 0.036305948 305.281091 989675.4981 0.011187523 0.013347763 1017.913729 -3.007710972 -0.040956799 RRPPSPEPS(ph)TK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRPPSPEPSTK 11 2 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 RRPPS(0.102)PEPS(0.593)T(0.305)K 100.11 0.0033629 256490000 319370 266450 307800 238770 389110 383810 313460 314950 338290 291590 TRUE FALSE 331978.9742 312210.7148 315821.5209 285997.9933 322969.2212 294675.9442 288890.1861 310728.6104 326115.009 348721.4777 0.951988895 0.895301078 0.90565549 0.820133005 0.926152365 0.845018053 0.828426709 0.891050968 0.935173283 1 18.4117157 -1.958216548 5.287056442 1.069161985 0.884978528 0.375870775 0.042750489 0.032001313 0.000252905 0.03800762 0.009523576 0.011009902 1.958216548 -0.184183457 RRPS(ph)PQPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 101.2 0.017176 6026010000 916070 1048300 919160 933340 985130 1157270 999400 959770 916670 1066360 TRUE FALSE 952237.151 1228337.37 943114.0647 1117951.866 817677.9545 888511.5811 921064.4166 946905.853 883679.2258 1275292.825 0.746681179 0.963180648 0.739527461 0.876623662 0.641168787 0.696711817 0.72223759 0.742500729 0.692922604 1 20.28239712 3.257069262 24.96380575 0.732861095 0.834339071 0.110085598 0.108600014 404.2627044 545251.7631 0.027459156 0.037112885 1807.462359 -3.257069262 0.101477976 RRQEIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRQEIEQK 8 2 Q9H307 Q9H307 PNN Pinin 0 ; 118.74 0.0010281 93228000 40723 40381 46842 37981 65950 59469 47158 40560 42273 47405 FALSE TRUE 42330.77549 47316.12263 48062.741 45493.52844 54739.84256 45658.22601 43461.63274 40016.35954 40751.60299 56693.10213 0.74666536 0.834601051 0.847770526 0.802452622 0.965546786 0.805357694 0.766612359 0.70584177 0.718810604 1 15.79088559 2.47710395 18.55266168 0.768354086 0.842341794 0.006316892 0.092757316 0.118515623 52628.20915 0.030470843 0.025944309 299.9880464 -2.47710395 0.073987709 RRS(ph)AS(ph)PPPATSSSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSASPPPATSSSSSSR 17 2 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 RRS(0.997)AS(0.982)PPPAT(0.013)S(0.002)S(0.002)S(0.001)S(0.002)S(0.001)SR 80.835 0.052023 383850000 78858 90288 98589 71839 102930 104470 90518 84961 90326 118410 TRUE FALSE 81971.37473 105794.2617 101158.3103 86048.53978 85433.99537 80208.42576 83422.96264 83822.23676 87075.1849 141610.1724 0.578852305 0.747080947 0.714343529 0.607643775 0.603304084 0.566402995 0.589102896 0.591922426 0.614893573 1 17.11156538 -1.157310685 4.469258894 1.000064516 0.623413204 0.800820267 0.056295981 3.93E-05 7.41E-06 0.059224394 0.013956939 0.069612834 1.157310685 -0.376651313 RRS(ph)FHIENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSFHIENK 9 2 Q96L93-5;Q96L93-6;Q96L93-4;Q96L93;Q96L93-2;A0A1B0GTU3;H0Y534 Q96L93-5 KIF16B Kinesin-like protein KIF16B 1 RRS(1)FHIENK 71.176 0.026257 12694000 27681 21787 25734 14912 42194 39248 30616 29023 30196 31377 TRUE FALSE 28773.86725 25528.74777 26404.64918 17861.54909 35021.87895 30133.24681 28216.23792 28633.99416 29109.25186 37524.7224 0.766797605 0.680318098 0.70366008 0.47599417 0.93330148 0.803023844 0.751937286 0.763070113 0.775735302 1 15.19555378 3.222226621 24.99979914 0.814536748 0.66173478 0.41946682 0.102150993 266.7779297 408312.861 0.029039019 0.034804738 1668.117434 -3.222226621 -0.152801967 HKSEFFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HKSEFFEK 8 1 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 130.75 0.00062164 296200000 190840 852620 1008700 944190 1275200 1403900 938150 1373100 1000900 974150 FALSE TRUE 198374.5106 999050.8525 1034987.551 1130947.964 1058441.959 1077865.501 864615.3516 1354695.84 964877.8045 1165016.041 0.170276205 0.857542572 0.888389099 0.970757418 0.908521361 0.9251937 0.742148881 1.162813036 0.828209888 1 20.15191839 4.759380175 3.165699323 0.935475571 0.036224084 0.823585991 0.10453792 0.146099623 2.184740065 0.024980278 0.33365491 57461.92557 -4.759380175 -0.899251488 down RRS(ph)GLEEPGKDGDGQTLANGLGPGGDSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSGLEEPGKDGDGQTLANGLGPGGDSNR 29 3 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 RRS(0.944)GLEEPGKDGDGQT(0.056)LANGLGPGGDSNR 65.377 0.05601 60223000 19232 27990 33778 23675 43820 42900 31278 38147 33173 25599 TRUE FALSE 19991.29421 32797.06477 34658.28243 28357.84434 36371.49205 32937.12516 28826.34863 37635.70186 31979.11021 30614.63393 0.652997983 1.071287177 1.13208221 0.92628396 1.18804269 1.075862126 0.941587239 1.229336988 1.044569414 1 14.90193381 4.738261167 7.200626849 1.077841096 0.647463777 0.639491253 0.093136178 0.060763542 26.64279746 0.021234394 0.127826119 54734.50148 -4.738261167 -0.430377319 RRS(ph)IQDLTVTGTEPGQVSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSIQDLTVTGTEPGQVSSR 20 2 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 RRS(0.999)IQDLT(0.001)VTGTEPGQVSSR 167.1 1.12E-11 192690000 14957 15184 15006 9368 20796 22855 11188 21929 18637 32393 TRUE FALSE 15547.51391 17791.73388 15397.06869 11220.96244 17261.10335 17547.27262 10311.05533 21635.07762 17966.25801 38739.78815 0.401331929 0.45926255 0.397448448 0.289649556 0.445565249 0.452952209 0.266161892 0.558471759 0.463767585 1 15.24152844 0.189477529 0.749433383 1.013244381 0.393687322 0.846715034 0.075685726 1.128897396 0.770082162 0.108966176 0.025409463 1.546954462 -0.189477529 -0.61955706 RRS(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_MDA-MB-175_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 135.01 1.67E-08 7790570000 1072695 1192654 1576472 1218524 1862511 1963750 1680913 1697892 1677843 1431024 TRUE FALSE 1115045.827 1397483.047 1617556.155 1459544.41 1545922.045 1507698.823 1549158.647 1675134.535 1617457.758 1711405.754 0.651537968 0.816570263 0.945162275 0.852833647 0.903305392 0.880970991 0.905196587 0.978806184 0.94510478 1 20.70675042 5.390021744 0.944250654 0.929870669 6.15E-17 0.798189179 0.042653724 2.682792525 0.78823069 0.013630463 3.422959986 245483.1818 -5.390021744 -0.929870669 RRS(ph)PGLCSDSLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRSPGLCSDSLEK 13 2 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 RRS(0.999)PGLCS(0.001)DSLEK;RRS(1)PGLCSDSLEK 165.7 2.75E-05 748870000 613810 428300 560490 413940 751920 669960 570810 562680 599390 485310 TRUE FALSE 638043.6928 501857.1933 575096.8298 495816.0965 624108.907 514371.9433 526068.4207 555138.195 577818.071 580397.2027 1.099322481 0.864678863 0.99086768 0.854270307 1.07531343 0.886241252 0.906393791 0.956479791 0.995556264 1 19.14668104 1.255241066 4.94593996 0.999107433 0.948629004 0.043719356 0.078859563 0.523270397 31.68004718 0.057658683 0.017889695 17.99869702 -1.255241066 -0.050478429 RRS(ph)PPADAIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 110.35 0.0014228 20339606000 8971657 7114273 8021970 6672000 10655607 10750651 9722584 8474159 8673775 6744732 TRUE FALSE 9325864.946 8336094.046 8231029.128 7991701.686 8844370.728 8253975.233 8960502.461 8360576.76 8361607.532 8066233.1 1.156161102 1.033455635 1.020430358 0.990760072 1.096468527 1.023275069 1.110865797 1.036490845 1.036618633 1 22.94346367 1.250437617 0.006202878 8.28E-08 2.081012812 0.142607353 0.046634801 7688.434181 41.2109592 6941.182376 6880.631907 17.80072195 -1.250437617 2.081012729 RRS(ph)PQEGPTWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RRSPQEGPTWSR 12 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 RRS(1)PQEGPTWSR;RRS(0.966)PQEGPT(0.032)WS(0.001)R;RRS(1)PQEGPTWSR;RRS(0.996)PQEGPT(0.001)WS(0.003)R;RRS(1)PQEGPTWSR;RRS(0.994)PQEGPT(0.001)WS(0.005)R 141.1 4.74E-05 4998830000 366308 458574 445970 389159 446716 533214 408177 419380 373117 460988 TRUE FALSE 380770.1227 537330.5173 457592.3446 466133.4887 370783.3739 409383.1294 376183.0202 413758.8971 359688.5921 551309.7725 0.690664562 0.974643556 0.830009493 0.845501952 0.672549975 0.742564616 0.68234419 0.750501656 0.652425569 1 19.07250365 3.260639412 24.06740993 0.73379515 0.844793793 0.109890036 0.111837418 245.6178213 267737.6002 0.028196069 0.038140933 1822.381978 -3.260639412 0.110998643 RRS(ph)PS(ph)LSSK ddPTM_MDA-MB-175_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(0.998)LS(0.002)SK;RRS(0.975)PS(0.695)LS(0.328)S(0.002)K 106.54 0.014357 3520700000 4412000 3195290 3949500 2990730 4827500 4843200 4480400 3928080 4080810 3029860 TRUE FALSE 4586189.167 3744056.202 4052427.215 3582287.468 4006923.274 3718440.199 4129214.541 3875430.513 3933942.445 3623503.057 1.265678294 1.033269779 1.118372788 0.988625485 1.105814791 1.026200376 1.139564249 1.06952594 1.085673831 1 21.78895368 4.744836783 24.85294546 1.068332834 1.265678389 0.611628793 0.048282652 411.3256128 1628757.565 0.010407949 0.097399056 55569.53761 -4.744836783 0.197345555 RRS(ph)PS(ph)PKPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.987)PKPT(0.013)K;RRS(1)PS(0.854)PKPT(0.146)K;RRS(1)PS(0.999)PKPT(0.001)K;RRS(1)PS(0.993)PKPT(0.007)K;RRS(1)PS(0.997)PKPT(0.003)K;RRS(1)PS(0.947)PKPT(0.053)K 83.204 0.022629 4480990000 3042480 1231716 1763190 1079484 2426750 2499190 2451290 1771748 1926210 1016960 TRUE FALSE 3162599.46 1443253.642 1809140.18 1293002.713 2014251.902 1918790.998 2259151.485 1748000.616 1856886.078 1216213.841 2.600364634 1.186677534 1.487518164 1.06313764 1.656165909 1.577675679 1.857528181 1.437247758 1.526775979 1 20.21396548 -2.66577982 0.344893944 6.27E-18 1.598227108 0.174795894 0.395697556 122.6150647 4.473934905 91.52622123 0.298863279 0.002158839 2.66577982 1.598227108 RRS(ph)PSLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 RRSPSLSSK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RRS(0.999)PS(0.001)LSSK;RRS(0.995)PS(0.005)LSSK;RRS(0.964)PS(0.036)LSSK;RRS(0.966)PS(0.034)LSSK;RRS(0.966)PS(0.034)LSSK;RRS(0.99)PS(0.01)LSSK;RRS(0.96)PS(0.04)LSSK;RRS(0.89)PS(0.11)LSSK 164.13 4.92E-05 23131580000 2112040 1823670 2127560 1636780 2681140 2610860 2477690 2194750 2132340 2075180 TRUE FALSE 2195424.97 2136871.136 2183005.961 1960530.199 2225400.78 2004527.333 2283482.184 2165332.966 2055597.5 2481771.789 0.884620004 0.861026443 0.879615914 0.78997199 0.896698395 0.807700104 0.920101596 0.872494794 0.828278212 1 21.24293903 -1.728819376 2.861698854 1.023173713 0.861609016 0.543700252 0.038437243 58704542.44 55126898.07 9762666.156 0.008653324 0.018671561 1.728819376 -0.161564697 RRS(ph)PSPYYS(ph)R ddPTM_MDA-MB-175_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(0.78)PS(0.255)PY(0.199)Y(0.095)S(0.671)R 101.2 0.01719 6504400000 730150 920200 852240 833440 977540 1012900 812260 839130 798490 897910 TRUE FALSE 758976.8858 1078237.192 874450.0745 998291.9444 811378.1 777669.3256 748592.9388 827882.8349 769752.5009 1073838.273 0.70678882 1.004096444 0.814321948 0.929648318 0.75558687 0.724195948 0.697118884 0.770956722 0.716823492 1 20.0343453 3.218687211 24.30532303 0.758695946 0.870213205 0.118052301 0.107894186 259.2682081 317085.8616 0.028467575 0.034072871 1654.577868 -3.218687211 0.111517259 RRS(ph)QFFEQGSSDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRSQFFEQGSSDSVVPDLPVPTISAPSR 28 2 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 RRS(0.25)QFFEQGS(0.25)S(0.25)DS(0.25)VVPDLPVPTISAPSR;RRS(0.663)QFFEQGS(0.252)S(0.083)DS(0.001)VVPDLPVPTISAPSR 186.05 7.34E-18 871861000 168943 220008 206545 214989 297764 293170 204658 242574 209171 298761 TRUE FALSE 175613.0001 257792.6626 211927.7324 257513.1825 247150.1816 225085.7105 188616.3712 239322.6923 201642.9766 357297.4978 0.491503582 0.721507047 0.593140824 0.720724842 0.691720998 0.629967218 0.527897263 0.669813513 0.564355972 1 18.44676629 -1.579162899 2.910662596 1.022073762 0.629314843 0.690034921 0.075628018 15022487.26 15704260.31 2558967.397 0.01705497 0.026353427 1.579162899 -0.392758919 RRS(ph)QS(ph)IEQESQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(0.988)QS(0.925)IEQES(0.087)QEK 151.96 0.0002213 276530000 489050 299340 409660 291530 513270 509150 456380 423480 446590 317310 TRUE FALSE 508358.0716 350749.3165 420336.0761 349193.7639 426024.5487 390907.6287 420607.7431 417803.9433 430517.3131 379480.8192 1.339614668 0.924287339 1.107660927 0.920188179 1.122651073 1.030111692 1.108376818 1.100988303 1.134490312 1 18.53366744 2.210336106 24.87696963 1.095587534 1.064014929 0 0.115542586 1183.828117 1043414.125 0.04020596 0.02970096 162.3065722 -2.210336106 -0.031572606 RRS(ph)QSIEQES(ph)QEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSQSIEQESQEK 13 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 RRS(0.992)QS(0.176)IEQES(0.832)QEK 174.81 9.52E-05 235850000 374720 255780 313100 249360 434250 389220 378640 354380 361060 252210 TRUE FALSE 389514.2349 299708.2253 321259.6432 298682.6637 360436.3401 298829.5537 348961.2074 349630.1157 348065.5211 301625.7206 1.291382691 0.993642799 1.065093662 0.990242686 1.194978795 0.99072968 1.156934517 1.159152194 1.153964988 1 18.20239993 RRS(ph)QVIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RRSQVIEK 8 2 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK;RRS(1)QVIEK 107.09 0.003205 959740000 502020 476500 510190 409088 651100 678960 587630 518290 599620 563900 TRUE FALSE 521840.1372 558335.1683 523485.9705 490004.3854 540426.2546 521281.8297 541570.0251 511343.1703 578039.7933 674385.4085 0.77380105 0.827917036 0.776241544 0.726593991 0.801361132 0.772973174 0.803057151 0.758235816 0.857135677 1 19.3632138 0.925729208 3.447662724 0.999849167 0.780529878 0.868957785 0.026159671 0.10202689 2.950984036 0.024756115 0.006406669 8.428090851 -0.925729208 -0.219319289 RRS(ph)S(ph)TTHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSSTTHVK 9 2 Q96A58-2;Q96A58 Q96A58-2 RERG Ras-related and estrogen-regulated growth inhibitor 2 RRS(0.948)S(0.554)T(0.451)T(0.047)HVK 54.023 0.073884 42110000 38477 86212 56747 73825 57213 85373 50531 63817 40851 98943 TRUE FALSE 39996.10167 101018.2404 58225.87344 88427.36465 47487.9547 65546.41459 46570.24818 62961.6375 39380.78049 118328.9865 0.338007642 0.853706631 0.49206771 0.747300956 0.401321402 0.553933711 0.39356585 0.532089722 0.332807553 1 16.852444 -1.164194007 4.644364376 1.000062348 0.525091862 0.443132821 0.162458593 9.74E-05 1.75E-05 0.146138118 0.034440579 0.068518208 1.164194007 -0.474970486 RRS(ph)SPSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.343)S(0.343)PS(0.315)ARPPDVPGQQPQAAK 110.03 0.0015577 363560000 35983 25607 31008 22311 46596 39511 33301 36258 32979 32502 TRUE FALSE 37403.63662 30004.80306 31816.09395 26724.04921 38675.62856 30335.16904 30690.7806 35772.02082 31792.09223 38870.14461 0.96227161 0.771924143 0.818522655 0.687521219 0.994995747 0.780423365 0.789572072 0.920295542 0.81790517 1 15.24637485 -0.249847831 0.484789874 1.023887087 0.827028572 0.220002006 0.090018905 8.859010202 2.171186882 0.471044308 0.043732116 0.562538394 0.249847831 -0.196858515 RRS(ph)TLIT(ph)VLNISEIESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSTLITVLNISEIESR 17 2 C9J3W8;B8ZZ73;B8ZZW4;P14778 C9J3W8 IL1R1 "Interleukin-1 receptor type 1;Interleukin-1 receptor type 1, membrane form;Interleukin-1 receptor type 1, soluble form" 2 RRS(0.534)T(0.534)LIT(0.931)VLNIS(0.001)EIESR 66.965 0.044149 43026000 2682.9 51813 35217 43503 27620 53177 27801 35110 32957 60863 TRUE FALSE 2788.822964 60711.4797 36134.78395 52107.76356 22925.16227 40827.44766 25621.88498 34639.40788 31770.88401 72787.93956 0.038314355 0.834087076 0.496439165 0.71588458 0.314958253 0.560909512 0.352007285 0.475894882 0.436485552 1 16.15141181 -1.268512497 4.075328335 1.000542077 0.480971353 0.370371427 0.207037764 45655666.9 28422985.72 206324.5421 0.043850555 0.053887434 1.268512497 -0.519570724 RRS(ph)VSQDLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRSVSQDLIK 10 2 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 RRS(0.952)VS(0.048)QDLIK;RRS(0.792)VS(0.208)QDLIK 81.128 0.017277 1792850000 1136920 692690 1041750 677140 1700340 1325590 1295060 1034730 1235530 1099620 TRUE FALSE 1181806.479 811654.1191 1068898.861 811076.2709 1411316.814 1017741.812 1193549.813 1020861.137 1191063.517 1315069.486 0.898664666 0.617194854 0.812807895 0.616755449 1.073188018 0.773907252 0.907594486 0.776279237 0.905703866 1 20.3267076 3.258122889 24.99999199 0.881182612 0.733305152 0.325477826 0.116415322 307.1050334 392468.4301 0.0300261 0.040599457 1811.852707 -3.258122889 -0.147877461 RRSPS(ph)PY(ph)YSR ddPTM_MDA-MB-175_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(0.01)PS(0.992)PY(0.593)Y(0.379)S(0.027)R 98.676 0.0085564 6450700000 1951300 2253000 2006700 1860500 2117800 2336000 2056300 2065000 1980400 2065400 TRUE FALSE 2028338.831 2639935.224 2058996.251 2228501.347 1757817.112 1793499.402 1895121.833 2037322.053 1909125.791 2470075.586 0.821164681 1.06876698 0.833576212 0.902199657 0.71164507 0.726090899 0.767232324 0.824801502 0.772901769 1 21.23612376 3.347998518 7.711422576 0.788675267 0.914523864 0.213614399 0.097786648 0.298823591 19.31639832 0.025583081 0.034661822 2228.427546 -3.347998518 0.125848597 RRSPS(ph)PYYS(ph)R ddPTM_MDA-MB-175_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(0.259)PS(0.777)PY(0.132)Y(0.083)S(0.748)R 106.3 0.011976 5454700000 2187100 2138500 2046700 2030800 2201000 2428700 2076300 2146800 2104800 2048400 TRUE FALSE 2273448.397 2505770.74 2100038.683 2432486.179 1826874.806 1864671.232 1913554.181 2118025.657 2029048.659 2449744.761 0.928034803 1.022870129 0.857247954 0.992954947 0.745740877 0.761169597 0.7811239 0.864590341 0.828269415 1 21.22420001 3.246790141 24.99980162 0.819864256 0.948817263 0.357045231 0.078236151 182.9967096 555907.4662 0.02083132 0.027735111 1765.184646 -3.246790141 0.128953008 RRSQFFEQGS(ph)SDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRSQFFEQGSSDSVVPDLPVPTISAPSR 28 2 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 RRS(0.259)QFFEQGS(0.345)S(0.345)DS(0.052)VVPDLPVPTISAPSR;RRS(0.217)QFFEQGS(0.38)S(0.38)DS(0.022)VVPDLPVPTISAPSR;RRS(0.048)QFFEQGS(0.418)S(0.418)DS(0.115)VVPDLPVPTISAPSR 130.56 1.89E-05 1142400000 341159 406508 349482 340426 447720 465410 295316 361900 389172 525720 TRUE FALSE 354628.2208 476322.5868 358589.788 407761.2467 371616.7143 357325.5809 272168.3603 357049.3224 375165.7757 628724.7685 0.564043662 0.757601117 0.570344618 0.64855286 0.591064219 0.56833387 0.432889515 0.567894475 0.596709076 1 19.26206907 0.913805986 18.00464066 1 0.585407308 0.723546098 0.0762976 1173.782832 245187.8364 0.076994715 0.019248546 8.199851467 -0.913805986 -0.414592692 RRSSPS(ph)ARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRSSPSARPPDVPGQQPQAAK 21 3 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RRS(0.098)S(0.38)PS(0.522)ARPPDVPGQQPQAAK 85.376 0.016071 450650000 45088 27658 35903 26765 52866 49285 43625 40725 40277 31402 TRUE FALSE 46868.10906 32408.04635 36838.66167 32059.03711 43879.8562 37839.30567 40205.55851 40179.14799 38827.43864 37554.62067 1.247998468 0.862957627 0.980935528 0.853664251 1.168427624 1.007580559 1.070588859 1.069885603 1.033892446 1 15.19670281 3.231849798 24.99997654 1.060877391 0.977182913 0.090911159 0.109852982 331.160216 1233678.908 0.029761435 0.036339487 1705.492438 -3.231849798 -0.083694478 RRT(ph)AS(ph)PPPPPK ddPTM_MDA-MB-175_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 97.073 0.0072159 390370000 678160 505080 621470 479930 721070 760040 691950 595900 654730 492080 TRUE FALSE 704934.2805 591823.561 637666.0187 574858.7216 598502.779 583532.2285 637713.1509 587912.9352 631166.3952 588493.6546 1.19786216 1.005658356 1.08355632 0.97683079 1.017008041 0.991569279 1.08363641 0.99901321 1.072511811 1 19.16666733 4.742724864 24.69521383 1.025920725 1.197862241 0.651455313 0.037814593 202.0996442 1198455.904 0.008286436 0.064311584 55299.96591 -4.742724864 0.171941516 RRT(ph)PEPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRTPEPLSR 9 2 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 RRT(0.997)PEPLS(0.003)R;RRT(1)PEPLSR 93.839 0.014676 811680000 76407 81519 88708 74386 97919 94478 88171 98831 80846 88776 TRUE FALSE 79423.60736 95519.25412 91019.80335 89099.32878 81274.76336 72536.91633 81259.92663 97506.3321 77936.36825 106169.9575 0.748079864 0.899682513 0.857302814 0.839214133 0.765515644 0.683215083 0.765375899 0.918398523 0.734071767 1 16.69601606 -1.133988639 4.036112846 1.000059219 0.808932196 0.400803356 0.072366594 10586893.87 2974501.482 5646.867705 0.017689297 0.073453308 1.133988639 -0.191127023 RRT(ph)PS(ph)PPPR ddPTM_MDA-MB-175_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 62.891 0.087904 126060000 39551 50326 43964 40125 45849 45701 51345 44321 36121 45510 TRUE FALSE 41112.50402 58969.09902 45109.73796 48061.60524 38055.60336 35087.63536 47320.44473 43726.94949 34821.01227 54426.81316 0.755372245 1.083456767 0.828814611 0.883050145 0.699206901 0.644675544 0.869432583 0.803408228 0.639776798 1 15.73202994 3.354438158 6.870471917 0.769643875 0.899888186 0.153527353 0.127006432 0.356412597 20.05950646 0.033721819 0.045727649 2261.716456 -3.354438158 0.130244311 RRVEHHDHAVVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RRVEHHDHAVVSGR 14 2 O95831-3;O95831;E9PMA0;O95831-5;O95831-2 O95831-3 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 0 ;;; 129.93 3.91E-05 285294000 126217 366002 230294 342793 224384 396482 178636 264390 189402 513117 FALSE TRUE 131200.1446 428859.9964 236295.6508 410596.4323 186243.2878 304405.0642 164634.0435 260846.2845 182585.459 613652.4519 0.213802038 0.698864634 0.385064298 0.669102569 0.303499623 0.496054507 0.268285482 0.425071689 0.297538873 1 19.22706228 -1.511143986 3.374095372 1.012895017 0.424709561 0.558177542 0.155359466 352895541.7 457169148.9 41989643.14 0.034426027 0.030821659 1.511143986 -0.588185455 RRVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 212.37 1.77E-24 7089310000 5115690 3151370 4560860 3816650 6400150 6445780 6460160 5311370 5877210 3694030 TRUE FALSE 5317661.391 3692593.283 4679719.758 4571571.978 5312254.789 4948845.282 5953795.779 5240179.773 5665690.36 4417804.452 1.203688721 0.835843533 1.059286306 1.034806322 1.2024649 1.120204693 1.347682054 1.186150231 1.282467439 1 22.07489813 3.254272209 2.299414573 1.210283958 1.013048246 0.267962093 0.121595557 0.316962114 3.435802921 0.034778192 0.047653775 1795.858891 -3.254272209 -0.197235712 RRVS(ph)HS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RRVSHSPPPK 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK;RRVS(1)HS(1)PPPK 75.102 0.021453 410825000 418076 307353 346846 281471 438073 444129 447061 364000 374427 284238 TRUE FALSE 434581.9633 360138.4869 355885.0917 337145.1237 363609.5079 340986.7706 412019.1906 359121.1754 360951.4454 339928.994 1.278449238 1.059452101 1.046939502 0.991810436 1.069663119 1.003111757 1.21207428 1.056459383 1.061843655 1 18.3748739 4.738827266 23.54163546 1.061024916 1.278449371 0.559315528 0.05914519 7.289205176 642721.0219 0.013996653 0.081964826 54805.8939 -4.738827266 0.217424455 RRWS(ph)APESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRWSAPESR 9 2 P54253 P54253 ATXN1 Ataxin-1 1 RRWS(1)APESR 78.324 0.023701 66359000 53682 65150 59132 61764 58317 70562 55769 60521 59324 77661 TRUE FALSE 55801.40681 76339.0057 60673.0285 73980.73485 48404.29717 54175.04488 51397.68005 59709.81499 57188.94083 92877.18604 0.600808543 0.821934955 0.653260839 0.796543672 0.521164553 0.583297656 0.553394028 0.642890009 0.615747992 1 16.50303664 -1.741403079 6.066935631 1.009608881 0.643906791 0.575022614 0.092012303 0.012199409 0.000519987 0.090882618 0.021234502 0.018138314 1.741403079 -0.36570209 RRYS(ph)DFEWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RRYSDFEWLK 10 2 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RRYS(1)DFEWLK 117.2 0.00077868 496590000 703190 520280 737880 528790 778890 852190 676350 677430 750780 584550 TRUE FALSE 730952.4842 609634.0428 757109.759 633383.0837 646494.556 654281.7876 623335.9197 668350.1589 723759.5745 699081.3806 1.045589976 0.872050179 1.083006614 0.906021962 0.924777249 0.935916484 0.89165001 0.956040566 1.035300888 1 19.41510089 1.290000405 7.437175606 1.017425728 0.94785918 0.146062476 0.063102247 0.335904813 40.26978577 0.040520458 0.014505473 19.4984642 -1.290000405 -0.069566548 RRYS(ph)DFEWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RRYSDFEWLR 10 2 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 RRYS(1)DFEWLR;RRYS(1)DFEWLR 122.97 0.00037374 539330000 119655 143708 147855 120934 193561 202795 146778 168298 145050 204564 TRUE FALSE 124379.0718 168388.7311 151708.2228 144854.3842 160659.5704 155698.9346 135273.1568 166042.2406 139829.6788 244644.3992 0.5084076 0.688299964 0.620117294 0.59210178 0.656706513 0.63642959 0.552937886 0.67870853 0.571562968 1 17.90032673 -1.727455255 2.662687344 1.071886115 0.617656934 0.821070038 0.054316448 10995188.4 8680257.438 5238454.593 0.011797816 0.018730301 1.727455255 -0.454229182 RS(ph)AS(ph)PERMD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 108.72 0.0014553 1966770000 2373740 2403540 2378200 2612520 2586570 2948240 2975530 2557540 2389770 1856960 TRUE FALSE 2467457.088 2816329.298 2440177.846 3129268.658 2146905.755 2263555.941 2742300.183 2523260.36 2303762.645 2220795.758 1.111068894 1.268162229 1.09878535 1.409075394 0.966728141 1.019254442 1.234827729 1.136196496 1.03735908 1 21.08264529 3.216391869 24.99991211 1.086140274 1.216301853 0.321357185 0.108573332 329.4157564 371484.429 0.031285517 0.037421081 1645.856129 -3.216391869 0.13016158 RS(ph)ASASHQADIK ddPTM_MDA-MB-175_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 66.387 0.035645 39418000 60415 62888 66438 72330 94996 113910 86905 80310 73175 85618 TRUE FALSE 62800.23085 73688.5248 68169.42886 86636.65812 78848.61385 87456.12882 80093.15902 79233.57581 70541.44604 102393.2078 0.613324186 0.719662235 0.665761238 0.846117237 0.770057072 0.854120412 0.78221164 0.773816716 0.688927005 1 16.64376049 -5 0.091221628 1.677461202 0.576240946 0.546434329 0.07077361 174.9182421 1.106660698 23.97430966 1.628142538 1.00E-05 5 -1.101220256 RS(ph)ASPDDDLGSSNWEAADLGNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.621)AS(0.379)PDDDLGSSNWEAADLGNEER 239.93 9.75E-38 500760000 108620 110690 131030 120010 129200 145900 136640 130610 129100 126040 TRUE FALSE 112908.4015 129700.1465 134444.7494 143747.6198 107238.6301 112016.9361 125929.7998 128859.3866 124453.7162 150735.1248 0.7490517 0.860450718 0.891927144 0.953643817 0.711437565 0.743137582 0.835437659 0.854872988 0.825645093 1 17.20165611 -1.315921006 2.91984206 1.001724307 0.82854857 0.360030377 0.069829831 14103289.55 17404068.5 210814.5512 0.017368669 0.048314667 1.315921006 -0.173175737 RS(ph)ASPDDDLGSSNWEAADLGNEERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSASPDDDLGSSNWEAADLGNEERK 25 2 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.377)AS(0.377)PDDDLGS(0.199)S(0.048)NWEAADLGNEERK 64.209 0.039206 175030000 80797 59929 57329 39958 97979 75702 43895 68588 73586 65051 TRUE FALSE 83986.92795 70221.33957 58823.04084 47861.57314 81324.56458 58121.35777 40454.3952 67668.69005 70937.65423 77796.49797 1.07957209 0.902628542 0.756114252 0.615215008 1.045349941 0.747094783 0.52000278 0.86981666 0.911836086 1 16.24741759 4.595442684 2.830676811 0.792594711 1.091807153 0.218793801 0.153980013 0.453384284 5.835884305 0.037594654 0.262342125 39395.14324 -4.595442684 0.299212442 RS(ph)ASPHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR;RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHR 154.49 1.57E-08 2211792000 271631 364348 360360 348120 436351 485519 341122 366950 350174 414181 TRUE FALSE 282355.2016 426921.9348 369751.2776 416977.097 362180.2129 372764.5704 314383.9663 362031.6355 337571.3061 495331.837 0.570032412 0.861890763 0.74647186 0.841813641 0.731187026 0.752555242 0.634693639 0.730887071 0.681505369 1 18.91803583 -1.180865305 5.363839699 1.000010809 0.732396881 0.494819308 0.082369285 1.01E-05 1.54E-06 0.075458736 0.017785077 0.065937837 1.180865305 -0.267613927 RS(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSASPHDVDLCLVSPCEFEHRK 22 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK 93.73 0.00089117 582570000 454210 534390 577360 425220 838840 773870 445130 573790 643370 698660 TRUE FALSE 472142.5615 626167.3255 592406.4759 509327.2468 696254.2764 594150.4206 410239.5475 566099.2836 620215.2394 835549.0503 0.565068635 0.749408219 0.709002632 0.60957193 0.833289531 0.711089816 0.490982004 0.677517715 0.742284656 1 19.672365 0.826559974 2.976070513 0.999828079 0.669558752 0.544254967 0.09107417 0.608632118 8.958769473 0.087240099 0.022869388 6.707489079 -0.826559974 -0.330269327 RS(ph)AT(ph)LSGSATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSATLSGSATNLASLTAALAK 21 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 2 RS(0.501)AT(0.415)LS(0.396)GS(0.372)AT(0.314)NLAS(0.001)LTAALAK 87.952 0.0021889 33754000 89629 73278 99169 81100 129930 128880 105360 91748 100010 78852 TRUE FALSE 93167.62213 85862.92648 101753.4256 97141.33794 107844.545 98949.5732 97101.60789 90518.26813 96410.65964 94301.53969 0.98797562 0.910514577 1.07902189 1.030114018 1.14361383 1.049289052 1.029692709 0.959881126 1.0223657 1 16.52499371 4.239875394 24.9999994 1.036973126 0.949245095 0.350732755 0.048903742 40.11030698 762602.6142 0.013177632 0.032292778 17373.02296 -4.239875394 -0.087728031 RS(ph)ATLSGSATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSATLSGSATNLASLTAALAK 21 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.2)AT(0.2)LS(0.2)GS(0.2)AT(0.2)NLAS(0.001)LTAALAK;RS(0.192)AT(0.192)LS(0.192)GS(0.192)AT(0.192)NLAS(0.035)LT(0.007)AALAK 102.37 0.00028385 179940000 126362 107735 141580 103075.7 152310 192362 130711.8 121717 148537 159756 TRUE FALSE 131350.8693 126237.6482 145269.6911 123463.7658 126420.4006 147688.8408 120466.2676 120085.5827 143191.1824 191057.1295 0.687495252 0.660732465 0.760346874 0.646213864 0.661688998 0.773008792 0.630524848 0.62853233 0.749467883 1 17.54364457 0.903915856 5.754104915 0.999991101 0.679585728 0.804988617 0.047044837 0.392722286 23.12485116 0.045719287 0.01150811 8.015227546 -0.903915856 -0.320405373 RS(ph)DSASSEPVGIYQGFEK ddPTM_MDA-MB-175_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(0.799)DS(0.17)AS(0.031)SEPVGIYQGFEK 269.28 6.20E-32 314260000 242530 217540 297420 228680 366790 379710 350250 303380 358830 291500 TRUE FALSE 252105.2717 254900.8028 305171.0095 273912.2215 304443.1668 291528.1071 322796.4898 299313.6873 345915.7784 348613.8439 0.723164831 0.731183822 0.875384081 0.785718141 0.873296262 0.836249369 0.925942832 0.858582333 0.99226059 1 18.41127034 7.759924904 0.129078684 1.054112489 5.62E-19 0.769191668 0.043836217 35.31195376 0.32706058 0.225588686 6.706444391 57534044.32 -7.759924904 -1.054112489 RS(ph)DSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSDSMTFLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 38 1 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 RS(0.333)DS(0.333)MT(0.333)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR;RS(0.448)DS(0.448)MT(0.104)FLGCIPPNPFEVPLAEAIPLADQPHLLQPNAR 233.41 4.14E-50 1374070000 163641 208785 206473 225804 224370 214137 164337 177955 222117 248450 TRUE FALSE 170101.673 244642.1996 211853.856 270467.3572 186231.6675 164406.927 151455.8365 175569.8043 214123.0526 297129.0206 0.572484211 0.823353434 0.713002909 0.91026907 0.626770375 0.553318308 0.509730878 0.590887433 0.720639984 1 18.18072999 0.965797243 19.69843877 1.000000005 0.661429892 0.421339444 0.118148003 280.598226 161606.9479 0.123544283 0.030886039 9.242665657 -0.965797243 -0.338570114 RS(ph)EEKEAGEI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSEEKEAGEI 10 2 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 RS(1)EEKEAGEI;RS(1)EEKEAGEI 148.85 1.92E-05 484150000 964290 536300 667810 463510 986490 1014620 847010 681220 824830 466670 TRUE FALSE 1002360.914 628405.3532 685213.6772 555190.8946 818806.7822 778989.8817 780619.143 672089.3602 795144.5294 558105.0516 1.796007599 1.125962489 1.227750359 0.994778479 1.467119461 1.395776439 1.398695713 1.204234504 1.424721972 1 19.09017718 -1.664362625 6.960780133 0.998536941 1.317365503 0.184279756 0.209126706 0.004514505 0.000217682 0.192519459 0.045193911 0.021658949 1.664362625 0.318828562 RS(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 RS(1)ET(1)PPHWR;RS(1)ET(1)PPHWR 92.039 0.0089555 1264260000 479010 478670 471620 463540 522880 627270 535260 474450 483210 508500 TRUE FALSE 497921.6847 560877.849 483910.8046 555226.8285 434001.0444 481596.0489 493304.9226 468090.7738 465819.3665 608130.8392 0.818773942 0.922297987 0.79573469 0.913005545 0.71366393 0.791928345 0.811182217 0.7697205 0.765985437 1 19.21402223 3.255525656 24.99638656 0.795020167 0.861962062 0.084321265 0.079301067 452.4605036 666653.9914 0.019995573 0.027005873 1801.04953 -3.255525656 0.066941895 RS(ph)FSSQRPVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSFSSQRPVDR 11 2 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 RS(0.435)FS(0.435)S(0.129)QRPVDR;RS(0.568)FS(0.338)S(0.095)QRPVDR 85.163 0.012145 581850000 320320 366590 359550 367730 490660 503450 398090 425000 388830 476350 TRUE FALSE 332966.4809 429548.9808 368920.1684 440465.8964 407257.7885 386531.3674 366886.6656 419303.5702 374836.0843 569681.6622 0.584478145 0.754015811 0.647590036 0.773178997 0.714886603 0.678504142 0.644020494 0.736031363 0.657974636 1 19.11979644 -1.953084326 2.423675555 1.236288789 0.692953481 0.74362069 0.054911739 5889536.104 2608762.871 7833259.132 0.012319118 0.011140782 1.953084326 -0.543335308 RS(ph)GSFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.796)GS(0.204)FGK;RS(0.798)GS(0.202)FGK 69.276 0.033163 0 694800 498500 607530 458270 839360 799400 838300 645520 691980 499790 TRUE FALSE 722231.2405 584113.4972 623362.7309 548914.4382 696685.887 613751.465 772591.8555 636867.8603 667075.775 597714.2814 1.208321874 0.977245342 1.042910886 0.918355902 1.165583471 1.026830852 1.292577205 1.06550551 1.116044565 1 19.18909649 3.201286933 24.99992734 1.119503866 1.032903657 0.108657307 0.102452804 314.5372844 210963.1193 0.028087892 0.03357212 1589.596628 -3.201286933 -0.086600209 RS(ph)GSPLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.51)GS(0.49)PLEK 79.659 0.016822 935210000 679420 489900 513090 476530 728910 727540 645940 561480 598840 404680 TRUE FALSE 706244.0262 574036.5141 526461.5469 570786.2117 605010.1386 558579.861 595309.5349 553954.279 577287.8654 483969.2979 1.45927444 1.186101095 1.087799472 1.179385168 1.250100246 1.154163835 1.230056405 1.144606241 1.192819189 1 18.884556 -4.999999657 0.031919946 7.88E-12 1.869138641 0.404578137 0.087207224 1495.877383 3.590438963 168.511392 64.51589083 1.00E-05 4.999999657 1.869138641 RS(ph)ISSPNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.798)IS(0.19)S(0.012)PNVNR 113.69 0.0015404 159090000 173300 197720 196770 190850 231930 228570 184490 223010 191460 223510 TRUE FALSE 180142.0178 231676.872 201897.9878 228599.5604 192506.6214 175488.0815 170029.1917 220020.9157 184569.392 267302.5051 0.673925662 0.866721664 0.755316482 0.855209195 0.720182631 0.656514915 0.636092773 0.823115801 0.690488822 1 18.02811383 -1.979650978 7.755008014 1.175792341 0.747182705 0.491845484 0.078525597 0.037337916 9.80E-05 0.011894663 0.017865623 0.010479704 1.979650978 -0.428609636 RS(ph)LSVEHLETK ddPTM_MDA-MB-175_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 66.246 0.038731 193860000 193490 147440 172710 135070 238300 246500 203630 190440 201800 170870 TRUE FALSE 201129.1346 172761.6731 177210.9645 161786.4429 197793.8511 189254.1107 187668.9485 187887.4633 194537.2574 204348.705 0.984244723 0.845425828 0.867198862 0.791717485 0.967923193 0.926133154 0.918376011 0.919445334 0.95198674 1 17.64067358 3.207619412 24.99992587 0.938813813 0.869884525 0.339364864 0.050509486 239.5778494 193573.8755 0.014255308 0.017039985 1612.944456 -3.207619412 -0.068929288 RS(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSNSAPLIHGLSDTSPVFQAEAPSAR 26 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RS(0.2)NS(0.2)APLIHGLS(0.2)DT(0.2)S(0.2)PVFQAEAPSAR;RS(0.372)NS(0.372)APLIHGLS(0.086)DT(0.086)S(0.086)PVFQAEAPSAR 117.21 0.00039297 432610000 78134 117104 109157 82452 140656 139787 100761 114334 112656 118008 TRUE FALSE 81218.79065 137215.7011 112001.7211 98760.75951 116747.3434 107323.5877 92863.08953 112801.5397 108601.5326 141129.4082 0.575491612 0.972268663 0.793610081 0.69978866 0.827236115 0.760462253 0.657999567 0.799277352 0.769517381 1 17.10665912 0.260518063 1.836292607 1.00001001 0.765911922 0.33645196 0.100256429 15.61721736 37.08785657 0.089669744 0.024930334 1.821872847 -0.260518063 -0.234098087 RS(ph)NSPDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.691)NS(0.309)PDKFK;RS(0.993)NS(0.007)PDKFK;RS(0.995)NS(0.005)PDKFK 120.53 0.00051214 13790270000 23998500 8596050 12138620 8636690 19989100 19179210 19884510 12715650 14915090 5976700 TRUE FALSE 24945979.31 10072354.72 12454962.41 10345001.5 16591359.92 14725129.14 18325910.15 12545217.51 14378298.82 7147719.934 3.490061102 1.409170311 1.742508454 1.447314892 2.321210131 2.060115572 2.563881953 1.755135571 2.011592362 1 22.76905168 0.353248673 1.239092194 0.999520638 2.063399261 0.24184299 0.579014478 5.076223121 8.33567205 0.530265183 0.15765501 2.255530339 -0.353248673 1.063878623 RS(ph)NSSEALLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSNSSEALLVDR 12 1 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 RS(0.787)NS(0.203)S(0.01)EALLVDR 75.376 0.020811 109680000 10546 31038 22338 29671 20429 31892 17035 21751 16819 41360 TRUE FALSE 10962.36422 36368.53506 22920.14663 35539.83524 16956.48588 24485.56633 15699.75219 21459.46342 16213.68748 49463.70011 0.221624428 0.735257067 0.463373071 0.71850337 0.342806661 0.49502092 0.31739947 0.433842664 0.32778962 1 15.59408254 -1.186892018 5.178848405 1.000033355 0.457847743 0.517757568 0.158922196 5.77E-05 9.06E-06 0.145086439 0.034195103 0.065029136 1.186892018 -0.542185611 RS(ph)PASIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSPASIDR 8 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 RS(1)PASIDR;RS(1)PASIDR;RS(1)PASIDR 72.652 0.02793 1039204000 567559 772633 618201 680092 661164 1355074 560337 620191 588214 745586 TRUE FALSE 589966.6676 905326.7075 634311.8259 814612.1677 548779.5794 1040378.6 516416.3218 611878.3541 567044.293 891669.3016 0.661642906 1.015316672 0.711375647 0.91358104 0.615451915 1.16677629 0.57915678 0.686216687 0.635935646 1 19.76614922 RS(ph)PASPHPPPFTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPASPHPPPFTHR 14 1 E5RJM0;B7ZLQ8;Q17RY0-2;Q17RY0 E5RJM0 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 RS(0.999)PAS(0.001)PHPPPFTHR 72.175 0.018508 46880000 37777 38782 39482 34174 48598 47366 42827 36926 34115 34970 TRUE FALSE 39268.46513 45442.50682 40510.93335 40933.5152 40337.32932 36365.96434 39470.10783 36431.06737 32887.20781 41821.70196 0.938949476 1.086577176 0.968658172 0.978762539 0.96450712 0.86954769 0.943770961 0.871104371 0.786367036 1 15.35196415 3.006380492 1.234002905 0.884539613 1.007270406 0.347626143 0.063254066 0.43975632 1.411078344 0.02484617 0.030219068 1014.800078 -3.006380492 0.122730794 RS(ph)PDVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPDVLK 7 1 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 1 RS(1)PDVLK 62.303 0.052843 105090000 93818 156540 135930 150650 137630 194460 135090 153060 143020 287130 TRUE FALSE 97522.00708 183424.5273 139472.4475 180448.1204 114235.7018 149299.6121 124501.2928 151008.4811 137872.7381 343387.6261 0.283999771 0.534161727 0.406166201 0.525493951 0.332672738 0.434784485 0.36256779 0.439760986 0.40150759 1 18.38947853 -1.385039504 3.203202585 1.006221651 0.417774415 0.850241706 0.073829086 53389178.48 71390485.46 3088292.103 0.015907267 0.041206004 1.385039504 -0.588447235 RS(ph)PERPTGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSPERPTGDLR 11 2 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(1)PERPTGDLR;RS(0.987)PERPT(0.013)GDLR;RS(0.999)PERPT(0.001)GDLR;RS(0.999)PERPT(0.001)GDLR 84.753 0.012385 2714480000 3110824 3625940 3647830 3316390 3952320 4148050 3578060 3584300 3433021 3407730 TRUE FALSE 3233641.734 4248666.989 3742895.447 3972362.044 3280506.058 3184728.252 3297602.308 3536258.321 3309467.245 4075409.449 0.793451989 1.042512916 0.91840967 0.974714834 0.804951281 0.781449887 0.809146259 0.867706268 0.812057607 1 21.95851358 3.23701689 24.9999831 0.835925852 0.939156491 0.20417756 0.081701536 51.94420738 841217.6353 0.021623214 0.027177035 1725.905012 -3.23701689 0.103230639 RS(ph)PESCSKPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(1)PESCSKPEK;RS(0.981)PES(0.019)CSKPEK;RS(1)PESCSKPEK;RS(1)PESCSKPEK;RS(0.946)PES(0.054)CSKPEK 201.3 2.29E-08 3701470000 6883300 3534360 5181330 3414620 7157150 6529490 6768100 5311850 6013520 2877250 TRUE FALSE 7155057.999 4141358.836 5316359.716 4090021.644 5940580.199 5013114.903 6237598.637 5240653.339 5797094.59 3440992.049 2.079359062 1.203536299 1.545007847 1.188616999 1.726414974 1.456880699 1.81273265 1.523006524 1.684716066 1 21.71439313 RS(ph)PGGGSEANGLALVSGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSPGGGSEANGLALVSGFK 19 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.908)PGGGS(0.092)EANGLALVSGFK;RS(1)PGGGSEANGLALVSGFK 242.83 1.22E-24 2023050000 1516290 1148860 1430840 1279980 1811770 1771990 1728150 1587930 1665460 1033750 TRUE FALSE 1576154.3 1346167.768 1468128.866 1533156.224 1503805.983 1360472.177 1592693.087 1566646.396 1605520.42 1236293.52 1.274902986 1.088873917 1.187524517 1.240123157 1.216382645 1.100444316 1.288280705 1.267212333 1.298656342 1 20.23758988 2.2116645 24.99976839 1.241044202 1.184438946 0 0.096353371 602.957065 560440.4855 0.033748312 0.024930871 162.8037859 -2.2116645 -0.056605257 RS(ph)PGGGSEANGLALVSGFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPGGGSEANGLALVSGFKR 20 2 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 RS(0.992)PGGGS(0.008)EANGLALVSGFKR 119.87 3.51E-05 551850000 151880 168660 169140 135800 259550 188960 151070 175980 192030 186180 TRUE FALSE 157876.3397 197626.043 173547.9274 162660.8347 215431.7837 145076.9037 139228.7387 173621.2759 185118.8778 222658.4064 0.709051781 0.887575036 0.779435774 0.730539832 0.967543904 0.651567152 0.625301963 0.779765196 0.831403048 1 17.76447256 0.868810022 2.803321898 0.999675638 0.766584832 0.348995424 0.096506585 0.5905286 9.151008243 0.092795552 0.024523088 7.392818122 -0.868810022 -0.233090806 RS(ph)PLGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 98.997 0.0066472 792240000 1288640 957760 1201250 870410 1414910 1541130 1475420 1192540 1297470 875140 TRUE FALSE 1339516.502 1122247.83 1232555.562 1042574.5 1174404.104 1183225.914 1359772.725 1176555.952 1250774.308 1046606.927 1.279865886 1.072272503 1.177668071 0.996147143 1.122106182 1.130535144 1.29922007 1.124162206 1.195075511 1 19.99728828 2.449547969 24.9992623 1.171571476 1.122145306 0.000565637 0.097392201 689.1958426 624853.9048 0.031868276 0.02666367 281.5450975 -2.449547969 -0.04942617 RS(ph)PLSDPPSQDPTPAATPETPPVISAVVHATDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.988)PLS(0.012)DPPSQDPTPAATPETPPVISAVVHATDEEK 141.65 6.39E-11 133910000 180210 140550 167960 139710 199850 223620 230360 176300 184500 111940 TRUE FALSE 187324.83 164688.3692 172337.1756 167344.221 165879.5684 171687.644 212303.7813 173936.9869 177859.881 133872.4998 1.399277897 1.230188197 1.287323206 1.250026863 1.23908621 1.282471339 1.585865518 1.299273467 1.328576678 1 17.03050011 2.438908474 24.99958013 1.346912377 1.275339368 0 0.141262337 514.6725988 336706.5774 0.045878671 0.038384932 274.7315103 -2.438908474 -0.071573009 RS(ph)PPWEP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RSPPWEP 7 1 F5H8F7;Q9UBL3-2;Q9UBL3-3;Q9UBL3;H0YAQ0 F5H8F7 ASH2L Set1/Ash2 histone methyltransferase complex subunit ASH2 1 RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP;RS(1)PPWEP 112.11 0.0068096 4465290000 2927100 3017510 3142120 3173790 3297100 3854250 3463140 3219650 3087030 2662790 TRUE FALSE 3042664.168 3535743.87 3224006.228 3801556.189 2736660.12 2959158.849 3191690.038 3176495.858 2975928.393 3184512.718 0.955456749 1.110293531 1.012401744 1.193763858 0.859365423 0.929234426 1.00225382 0.997482547 0.934500395 1 21.6026412 3.229619193 24.99999989 0.958855991 1.067031647 0.384625622 0.070571455 207.2074694 579346.7176 0.019875322 0.024083359 1696.755218 -3.229619193 0.108175656 RS(ph)PRPDHPGTPPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSPRPDHPGTPPHK 14 2 P30291 P30291 WEE1 Wee1-like protein kinase 1 RS(1)PRPDHPGTPPHK;RS(1)PRPDHPGTPPHK 113.35 0.00025683 145160000 120900 95556 108178 105000 131771 134940 118178 118952 121514 87247 TRUE FALSE 125673.2254 111966.9997 110997.2075 125768.6866 109372.6125 103602.23 108914.8996 117357.643 117140.7349 104341.3792 1.204442823 1.073083378 1.063788963 1.205357717 1.048218965 0.992916049 1.043832278 1.124746902 1.122668071 1 16.67095188 4.740550442 23.38250205 1.079756888 1.204442933 0.291753276 0.060106789 98.94322037 1162456.202 0.014621583 0.094833749 55023.7825 -4.740550442 0.124686044 RS(ph)PS(ph)PYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.991)PS(0.707)PY(0.249)Y(0.004)S(0.05)R 54.772 0.052586 0 155960 146160 154400 119940 173470 200070 153730 158790 153940 127910 TRUE FALSE 162117.4212 171261.843 158423.7908 143663.774 143983.6314 153606.7746 141680.2409 156661.6798 148399.7295 152971.5155 1.059788292 1.119566884 1.035642422 0.93915376 0.94124472 1.004152793 0.926187078 1.024123212 0.970113481 1 17.22290351 3.983867141 4.724371853 0.973844828 1.088501087 0.682572679 0.032461501 0.098784211 5.880015665 0.0081707 0.016673888 9635.342141 -3.983867141 0.114656259 RS(ph)PSLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSPSLSSK 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RS(0.992)PS(0.008)LSSK;RS(0.997)PS(0.003)LSSK 76.17 0.022354 243707000 274630 153855 195667 132884 197069 250480 202140 166784 227778 112958 TRUE FALSE 285472.6045 180278.3994 200766.2428 159168.0586 163571.2818 192309.8161 186295.7386 164548.5333 219580.3143 135089.9574 2.113203749 1.334506302 1.486167045 1.178237536 1.210832285 1.42356856 1.379049503 1.218066365 1.625437734 1 17.0435609 4.740022337 6.114920919 1.321767143 2.133641241 0.67050612 0.167368368 0.07169779 13.58119268 0.036967986 0.240591481 54956.91385 -4.740022337 0.811874098 RS(ph)PTEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSPTEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 RS(1)PTEDFR;RS(1)PTEDFR 96.015 0.0056602 657710000 576505 585516 649290 630493 575687 763364 752028 607829 598400 476033 TRUE FALSE 599265.8626 686073.8183 666211.0308 755202.6336 477831.9294 586084.2799 693082.0803 599682.0465 576863.7009 569302.5521 1.052631611 1.205112845 1.170223159 1.326540046 0.839328627 1.029477696 1.217423104 1.053362653 1.013281424 1 19.11883604 3.255478109 24.99905888 1.043074457 1.188489856 0.354233138 0.106333917 314.5446248 464801.2856 0.030155997 0.040726271 1800.852359 -3.255478109 0.1454154 RS(ph)PVPAQIAITVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 111.95 0.00038081 3037770000 4671980 3959190 4691050 4079560 5872200 5987700 5284200 4952080 5279460 4089780 TRUE FALSE 4856433.378 4639150.084 4813302.617 4886484.792 4874045.541 4597147.419 4870010.596 4885705.468 5089453.266 4891094.087 0.992913506 0.948489234 0.984095282 0.999057615 0.99651437 0.939901653 0.995689412 0.998898279 1.040555175 1 22.22172579 1.643216003 2.532663766 1.019438926 0.977829354 0.370333077 0.021242938 0.248903497 3.624812931 0.014214108 0.00572017 43.97602821 -1.643216003 -0.041609572 RS(ph)PVSTRPLPSASQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSPVSTRPLPSASQK 15 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 RS(1)PVSTRPLPSASQK;RS(0.911)PVS(0.08)T(0.009)RPLPSASQK;RS(0.974)PVS(0.023)T(0.004)RPLPSASQK 189.25 1.39E-07 1540960000 1063980 862150 1121490 845670 1245860 1290010 1088260 1071880 1167170 871270 TRUE FALSE 1105986.752 1010217.556 1150716.951 1012941.002 1034089.162 990424.7278 1002959.338 1057513.202 1125163.78 1041978.675 1.061429354 0.969518456 1.104357487 0.972132181 0.992428336 0.95052303 0.962552653 1.01490868 1.079833788 1 19.99089432 4.764695558 23.19957127 1.004097224 1.061429555 0.110522696 0.047824248 7572.717692 6721890.982 0.011371045 0.807240967 58169.53049 -4.764695558 0.057332331 RS(ph)QSPINCIRPSVLGPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSQSPINCIRPSVLGPLK 18 2 Q96E09 Q96E09 FAM122A Protein FAM122A 1 RS(0.581)QS(0.419)PINCIRPS(0.001)VLGPLK 58.107 0.068118 383180000 158150 130890 166160 137680 200500 193080 139960 174850 176750 142300 TRUE FALSE 164393.8841 153369.3393 170490.2661 164912.6931 166419.0816 148240.0962 128989.5695 172506.4217 170388.802 170180.9605 0.965994572 0.901213267 1.00181751 0.969043144 0.977894831 0.871073331 0.75795535 1.013664638 1.001221297 1 17.37671011 1.595413267 25 1.005600736 0.922415559 0.25401914 0.06611026 1.322299285 2647.586262 0.037472435 0.017537443 39.39247491 -1.595413267 -0.083185177 RS(ph)S(ph)LSSHSHQSQIYR ddPTM_MDA-MB-175_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 2 RS(1)S(0.999)LS(0.001)SHSHQSQIYR;RS(1)S(0.998)LS(0.002)SHSHQSQIYR 166.11 1.41E-06 529420000 149300 209982 200165 205995 219624 296500 221025 234751 204842 208436 TRUE FALSE 155194.4793 246044.7751 205381.4643 246740.1962 182292.3909 227642.3685 203700.483 231604.5468 197469.7764 249275.0435 0.622583301 0.987041349 0.823915068 0.989831123 0.731290178 0.913217646 0.817171587 0.929112452 0.792176279 1 17.92737893 -5 0.217901564 1.704988759 0.837163377 0.148870351 0.109498085 293.2643757 2.932779387 91.0355393 0.193477375 1.00E-05 5 -0.867825382 RS(ph)S(ph)VKRSDSGDEQLPT(ph)ICR ddPTM_MDA-MB-175_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(1)ICR 63.827 0.027801 287440000 141570 267890 207530 330820 187920 305880 248730 247640 201340 207410 TRUE FALSE 147159.2929 313898.0236 212938.4023 396255.2086 155977.4255 234844.0057 229233.8927 244320.7909 194093.8127 248048.0184 0.593269375 1.265472813 0.858456373 1.59749395 0.628819478 0.94676832 0.924151276 0.984973766 0.782484835 1 17.92025991 RS(ph)SAIGIENIQEVQEK ddPTM_MDA-MB-175_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(0.5)S(0.5)AIGIENIQEVQEK 251.55 1.79E-22 975400000 739200 579830 626350 527250 823600 871040 722760 656540 771450 576460 TRUE FALSE 768384.1868 679411.292 642673.1956 631538.4763 683604.7662 668754.1607 666108.1826 647740.1552 743685.6652 689406.3 1.114559276 0.985502007 0.932212536 0.916061365 0.991584739 0.970043588 0.966205535 0.93956228 1.078733492 1 19.39499496 1.242187357 24.99724304 1.039366745 0.971914061 0.168211899 0.054586789 139.9623148 964743.2758 0.039725856 0.013220157 17.46575473 -1.242187357 -0.067452684 RS(ph)SDGS(ph)LSHEEDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.57)S(0.488)DGS(0.802)LS(0.14)HEEDLAK 84.946 0.028459 251720000 299160 212110 265280 197110 349820 352260 335750 267800 278340 207190 TRUE FALSE 310971.0678 248538.2425 272193.4147 236097.7697 290357.7214 270452.9536 309433.0377 264210.579 268322.5978 247784.9136 1.255004041 1.003040253 1.098506809 0.952833513 1.171813558 1.091482728 1.248796923 1.066290014 1.082885128 1 17.91872883 0.853686579 2.073564841 1.000737989 1.108008671 0.12015081 0.090846458 1.215162649 10.04139407 0.082682039 0.022813565 7.139808757 -0.853686579 0.107270682 RS(ph)SDGSLSHEEDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.499)S(0.499)DGS(0.002)LSHEEDLAK;RS(0.636)S(0.362)DGS(0.001)LS(0.001)HEEDLAK 207.07 1.68E-09 626680000 582330 588740 671520 501190 893570 963600 816370 721350 729660 534340 TRUE FALSE 605320.8381 689851.5152 689020.3629 600323.8861 741681.2906 739818.5035 752380.7862 711681.4831 703399.6791 639033.6924 0.947244011 1.079522916 1.078222277 0.939424467 1.160629399 1.157714393 1.177372641 1.113683819 1.100723933 1 19.28553247 3.221298538 24.99993522 1.129016167 1.020784709 0.395266383 0.063733066 230.7673469 334209.8265 0.017749934 0.021262606 1664.556489 -3.221298538 -0.108231458 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR 279.78 5.39E-61 4032100000 548355 652700 652651 589989 671418 759983 604166 629462 607436 701309 TRUE FALSE 570004.4788 764796.1477 669659.6212 706687.0633 557290.6082 583488.4659 556809.8902 621025.0915 585574.497 838717.0712 0.679614734 0.911864291 0.798433279 0.842580994 0.664456021 0.695691653 0.663882863 0.740446466 0.698178822 1 19.6778247 5.039267222 17.42464905 0.763505216 0.274203875 0.055075814 0.107026364 34718925.22 386451039.6 0.024899718 550572089 109462.9686 -5.039267222 -0.489301341 RS(ph)SDPLGDTASNLGSAVDELMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSDPLGDTASNLGSAVDELMR 22 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 RS(0.497)S(0.497)DPLGDT(0.005)AS(0.001)NLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR;RS(0.5)S(0.5)DPLGDTASNLGSAVDELMR 195.27 4.12E-19 136707000 90724 104768 102352 110854 113939 131856 106774 102133 96842 119140 TRUE FALSE 94305.85357 122761.089 105019.3772 132780.5903 94571.68948 101234.4423 98404.77488 100764.0742 93356.67534 142483.2019 0.661873486 0.861582891 0.737064972 0.93190347 0.663739221 0.710500894 0.690641237 0.707199676 0.655211801 1 17.12043232 RS(ph)SDSWEVWGSASTNR ddPTM_MDA-MB-175_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(0.496)S(0.496)DS(0.008)WEVWGSASTNR;RS(0.499)S(0.499)DS(0.001)WEVWGSASTNR;RS(0.498)S(0.498)DS(0.004)WEVWGSASTNR;RS(0.5)S(0.5)DSWEVWGSASTNR;RS(0.38)S(0.38)DS(0.241)WEVWGSASTNR 257.96 6.67E-27 4185350000 1382771 1582907 1440241 1358107 1871160 2012190 1549296 1555851 1731910 2000350 TRUE FALSE 1437363.867 1854758.964 1477774.864 1626736.511 1553100.892 1544889.368 1427858.131 1534997.362 1669578.897 2392280.283 0.600834224 0.775310057 0.617726474 0.679994114 0.649213599 0.645781089 0.596860719 0.64164612 0.697902712 1 21.189955 0.763880526 3.410692997 0.999984506 0.651911981 0.8248431 0.047964272 0.730775897 10.12353026 0.044030846 0.011381064 5.806046716 -0.763880526 -0.348072525 RS(ph)SEASQSDGLPSLLSLTPAQQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSEASQSDGLPSLLSLTPAQQYR 24 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RS(0.483)S(0.483)EAS(0.017)QS(0.017)DGLPSLLSLTPAQQYR;RS(0.363)S(0.363)EAS(0.137)QS(0.137)DGLPSLLSLTPAQQYR;RS(0.402)S(0.402)EAS(0.146)QS(0.05)DGLPSLLSLTPAQQYR 161.31 1.19E-11 262408000 73163 93340 74258 82198 94564 95519 62528 80923 71156 84860 TRUE FALSE 76051.53173 109370.4189 76193.22448 98456.51906 78490.04506 73336.15985 57626.89197 79838.35955 68595.10946 101486.6923 0.749374426 1.077682369 0.750770597 0.970142162 0.773402338 0.722618485 0.567827079 0.786687966 0.675902504 1 16.63093104 3.068066792 5.997997232 0.728438798 0.890340896 0.17659941 0.136615027 0.277595113 18.17853567 0.036717589 0.043967038 1169.679266 -3.068066792 0.161902098 RS(ph)SGFISELPSEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 RS(0.484)S(0.484)GFIS(0.033)ELPSEEGK;RS(0.5)S(0.5)GFISELPSEEGK;RS(0.497)S(0.497)GFIS(0.006)ELPSEEGK;RS(0.498)S(0.498)GFIS(0.004)ELPSEEGK;RS(0.499)S(0.499)GFIS(0.001)ELPSEEGK;RS(0.5)S(0.5)GFIS(0.001)ELPSEEGK 195.56 5.74E-09 3305540000 4152770 2967980 3872670 3260280 5205870 5284430 4953440 3992410 4409300 3060060 TRUE FALSE 4316724.566 3477707.477 3973594.962 3905153.653 4320978.077 4057201.219 4565176.429 3938898.274 4250610.154 3659620.169 1.179555355 0.95029192 1.085794366 1.067092614 1.180717637 1.108639977 1.247445423 1.076313413 1.161489433 1 21.80326249 3.322075945 8.89489572 1.136047981 1.062721491 0.105779278 0.080445266 0.50824918 48.96909691 0.020630745 0.027932786 2099.306956 -3.322075945 -0.07332649 RS(ph)SGREEDDEELLR ddPTM_MDA-MB-175_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 82.482 0.0055257 272050000 63484 71829 75797 68032 77128 75306 79014 76275 63300 78079 TRUE FALSE 65990.39734 84165.072 77772.33209 81488.52654 64017.81011 57817.32277 72820.67622 75252.65839 61021.84536 93377.08514 0.706708688 0.901346105 0.832884556 0.872682269 0.685583728 0.619181062 0.779855958 0.805900701 0.653499146 1 16.51078093 5.058256192 14.6261764 0.784881727 0.15077294 0.046589046 0.111757895 2131937.652 14290171.34 0.026207013 38851246.8 114355.2722 -5.058256192 -0.634108787 RS(ph)SITEPEGPNGPNIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSITEPEGPNGPNIQK 17 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 RS(0.611)S(0.374)IT(0.015)EPEGPNGPNIQK 176.84 6.50E-10 320980000 105560 132000 124540 111540 224330 203060 133650 138630 138550 202340 TRUE FALSE 109727.5903 154669.9732 127785.6147 133602.2791 186198.4667 155902.3924 123174.1638 136771.8916 133563.6126 241984.649 0.453448559 0.639172666 0.528073228 0.552110556 0.769463962 0.64426563 0.509016437 0.565208959 0.551950767 1 17.884556 -1.406213327 3.376169279 1.004111059 0.581882372 0.697406363 0.083139088 67600473.57 99513007.41 2735609.378 0.020155761 0.039245211 1.406213327 -0.422228687 RS(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.443)S(0.443)LDAEIDS(0.036)LT(0.036)S(0.043)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK;RS(0.5)S(0.5)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 269.43 1.41E-74 11054200000 330276 256283 377360 291884 451172 418095 450935 362965 418568 215752 TRUE FALSE 343315.5515 300297.6116 387194.3116 349617.784 374481.9446 320998.7725 415589.5364 358100.0479 403503.8194 258024.4736 1.330554217 1.163833831 1.5006108 1.354979158 1.451342733 1.244063279 1.610659371 1.387853032 1.56381995 1 17.97714839 4.240288658 24.99937213 1.409199725 1.24719403 0.091990482 0.169302492 81.08035782 1172884.839 0.037440951 0.092306413 17389.56261 -4.240288658 -0.162005695 RS(ph)SLLSLMTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.496)S(0.496)LLS(0.009)LMTGK 56.225 0.073712 13849000 23785 24145 23742 24239 41131 35934 28292 23723 29984 22708 TRUE FALSE 24724.05017 28291.71593 24360.73602 29033.40185 34139.56731 27588.87309 26074.39911 23405.03199 28904.8817 27157.19783 0.910405054 1.041775963 0.897026865 1.069086805 1.25710935 1.015895427 0.960128481 0.861835309 1.064354352 1 14.729047 -0.418960959 6.096994627 1.000013892 1.003014673 0 0.107676058 0 0 0.111213237 0.026213211 0.381100081 0.418960959 0.003000781 NIIHGSDSVESAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 0 ;;;;;; 244.56 1.34E-17 6798440000 2783380 7374200 9229990 8634600 11052480 12441620 10764520 10936330 9300970 5696890 FALSE TRUE 2893269.992 8640661.487 9470531.122 10342498.11 9173783.397 9552242.31 9920768.795 10789746.38 8966229.907 6813086.522 0.424663621 1.26824479 1.39005003 1.518034165 1.346494481 1.4020433 1.456134274 1.583679636 1.316030536 1 22.6998771 4.760607846 2.769133088 1.414068079 0.207774175 0.776889369 0.150993639 0.192038934 1.920855416 0.034688104 0.539939771 57624.58968 -4.760607846 -1.206293904 down NSILQGSVHTGFSLLVQGHVEELWGLATHPSR ddPTM_MDA-MB-175_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 75.436 0.00075405 18488000 2938.1 11871 13707 14598 17745 19987 13498 15983 14897 14471 FALSE TRUE 3054.098457 13909.75191 14064.21568 17485.44083 14728.71124 15345.32216 12439.99149 15768.77403 14360.85988 17306.31539 0.176473061 0.803738496 0.81266378 1.010350293 0.851059911 0.886689154 0.718812249 0.911157209 0.829804586 1 14.07901098 4.761839287 3.160219038 0.870784214 0.052182378 0.86711548 0.081769717 0.125174628 1.850312341 0.019070132 0.260601798 57788.21591 -4.761839287 -0.818601837 down RS(ph)SLPLDHGSPAQENPES(ph)EKSSPAVSR ddPTM_MDA-MB-175_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(0.835)S(0.165)LPLDHGSPAQENPES(0.539)EKS(0.243)S(0.218)PAVSR 120.31 7.42E-05 172440000 22054 50270 58713 49834 74168 84087 54313 76263 65362 57735 TRUE FALSE 22924.70895 58903.48145 60243.10901 59691.01646 61560.94985 64559.0686 50055.80514 75240.81923 63009.63439 69047.06785 0.332015677 0.853091714 0.872493371 0.864497484 0.891579495 0.935000871 0.724951931 1.089703322 0.912560611 1 16.07529253 4.766184154 3.049179076 0.911756481 0.218152745 0.789887813 0.08905296 0.184272449 2.415908591 0.021695971 0.319042555 58369.25546 -4.766184154 -0.693603736 down RS(ph)SLPNGEGLQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLPNGEGLQLK 13 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 RS(0.668)S(0.332)LPNGEGLQLK 90.131 0.0075545 86152000 220800 198060 205860 172200 277890 273440 271610 210720 237940 192610 TRUE FALSE 229517.3545 232075.2643 211224.8807 206260.646 230654.3571 209937.704 250320.4985 207895.6431 229376.5859 230348.2418 0.996392908 1.007497442 0.916980651 0.895429652 1.001328924 0.911392691 1.08670462 0.902527588 0.995781796 1 17.81345706 RS(ph)SLSLEEADSEVEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLSLEEADSEVEGR 16 1 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 RS(0.681)S(0.319)LSLEEADSEVEGR 231.89 5.64E-16 579390000 75937 87915 92777 70750 134030 115470 99199 85528 105450 100530 TRUE FALSE 78935.0514 103013.7174 95194.84484 84744.13883 111247.6285 88653.84246 91423.52317 84381.63706 101654.8751 120226.9287 0.65655051 0.856827322 0.791793035 0.7048682 0.925313735 0.737387567 0.760424675 0.701853054 0.84552501 1 16.87540055 0.959095183 7.497805936 0.999995171 0.769359301 0.479837896 0.074178043 0.390325773 70.01159078 0.067951314 0.017027834 9.101127178 -0.959095183 -0.23063587 RS(ph)SLSSHSHQSQIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.559)S(0.441)LSSHSHQSQIYR;RS(0.5)S(0.5)LSSHSHQSQIYR;RS(0.5)S(0.5)LSS(0.001)HSHQSQIYR;RS(0.499)S(0.499)LS(0.001)SHSHQSQIYR 248.94 8.62E-19 2750560000 41280.1 393454 248204 312376 282089 541883 152163 326181 226853 615885 TRUE FALSE 42909.87022 461026.6639 254672.4001 374163.0405 234139.6125 416038.8856 140236.0665 321809.0772 218688.6048 736555.8739 0.058257454 0.625922188 0.345761142 0.50799003 0.317884387 0.564843619 0.190394336 0.436910611 0.296907014 1 19.49043544 -1.827709226 2.826272274 1.201182548 0.382635603 0.571025522 0.163134104 48043362.44 35531991.75 65730266.58 0.035412053 0.014869309 1.827709226 -0.818546944 RS(ph)SLYGIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLYGIAK 9 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.612)S(0.388)LY(0.001)GIAK 80.469 0.014716 160640000 113650 115720 134870 144560 188880 194100 159030 129800 150550 172910 TRUE FALSE 118136.9898 135594.0098 138384.823 173153.5365 156774.2451 149023.2166 146564.8131 128060.2433 145131.7349 206788.4039 0.571294074 0.655713798 0.669209783 0.837346453 0.758138474 0.720655577 0.708767079 0.61928155 0.701836912 1 17.65779576 -1.879794698 2.472853311 1.154367373 0.693865267 0.635959494 0.069549323 9517802.157 5273293.746 8592112.787 0.01882296 0.013188801 1.879794698 -0.460502106 RS(ph)SMIETGQGAEGGLSLR ddPTM_MDA-MB-175_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(0.5)S(0.5)MIETGQGAEGGLSLR 193.53 7.29E-15 192670000 74463 56041 72564 59463 65480 79563 62660 58034 61005 96313 TRUE FALSE 77402.85674 65665.60581 74455.07745 71224.60392 54349.73299 61085.69904 57748.54547 57256.14915 58809.44197 115183.6883 0.671994949 0.570094662 0.646402963 0.618356687 0.471852688 0.530332896 0.501360447 0.497085568 0.510570922 1 16.8135769 -1.78018889 6.950120325 1.013279709 0.552387495 0.806567455 0.064956353 0.014155549 0.000447697 0.066608565 0.015936388 0.016588653 1.78018889 -0.460892213 RS(ph)SPAAFINPPIGTVTPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSPAAFINPPIGTVTPALK 20 1 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 RS(0.5)S(0.5)PAAFINPPIGTVTPALK;RS(0.5)S(0.5)PAAFINPPIGTVTPALK 201.17 7.87E-22 2058240000 1389850 1234350 1532070 1180520 1808180 1805150 1525530 1525810 1662990 1409470 TRUE FALSE 1444722.351 1446340.011 1571997.003 1414023.332 1500826.209 1385931.27 1405954.972 1505359.013 1603139.315 1685628.661 0.857082218 0.858041895 0.932587965 0.838870011 0.890365858 0.822204381 0.834083452 0.893054946 0.951063157 1 20.68485532 1.16551949 2.242565927 0.997690436 0.863235319 0.701777643 0.029932269 0.152894402 1.384909826 0.027937678 0.007885347 14.63927232 -1.16551949 -0.134455118 RS(ph)SPPGHYYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSPPGHYYQK 11 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 RS(0.712)S(0.288)PPGHYYQK;RS(0.97)S(0.03)PPGHYYQK;RS(0.89)S(0.11)PPGHYYQK 141.59 2.33E-05 813920000 1168270 1402780 1213070 1423950 1386940 1890980 1388720 1267100 1247870 1543350 TRUE FALSE 1214394.202 1643696.553 1244683.601 1705603.06 1151188.434 1451828.553 1279868.498 1250116.597 1202959.402 1845739.883 0.65794439 0.890535317 0.674354828 0.924075529 0.623700254 0.786583508 0.693417588 0.677298361 0.651749151 1 20.81576782 -1.313952935 5.453157094 1.000048543 0.732544403 0.402798714 0.09822152 5.39E-05 6.78E-06 0.088386625 0.020829155 0.048534109 1.313952935 -0.26750414 RS(ph)SPSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.465)S(0.465)PS(0.07)ARPPDVPGQQPQAAK;RS(0.475)S(0.475)PS(0.05)ARPPDVPGQQPQAAK;RS(0.473)S(0.473)PS(0.054)ARPPDVPGQQPQAAK;RS(0.49)S(0.49)PS(0.019)ARPPDVPGQQPQAAK 177.56 3.40E-17 3490080000 1781862 1553038 1813064 1372338 1975815 2008465 1906968 1823450 1732094 1435487 TRUE FALSE 1852211.288 1819760.196 1860313.937 1643782.36 1639966.672 1542029.442 1757494.865 1799009.635 1669756.275 1716743.194 1.078909935 1.060007229 1.083629715 0.957500438 0.955277806 0.898229536 1.02373778 1.047920063 0.9726302 1 20.71124281 3.744613003 24.85276699 0.983646216 1.072764793 0.551895475 0.039025894 413.202475 1696716.269 0.011775095 0.020578169 5554.091147 -3.744613003 0.089118576 RS(ph)SPVPPVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.5)S(0.5)PVPPVPER;RS(0.5)S(0.5)PVPPVPER;RS(0.5)S(0.5)PVPPVPER;RS(0.609)S(0.391)PVPPVPER 106.42 0.0014292 4056030000 2103470 2393430 2338030 2314270 2695600 3065650 2402480 2458670 2445200 2665310 TRUE FALSE 2186516.62 2804482.984 2398960.983 2772025.699 2237402.875 2353699.248 2214167.34 2425715.55 2357197.73 3187526.464 0.685960303 0.879830494 0.752608962 0.869647901 0.701924486 0.73840932 0.694634967 0.761002482 0.739506874 1 21.60400589 -0.982238418 4.390613611 1.000007695 0.759929366 0.56532287 0.063599304 12963.60422 35790854.07 685.572988 0.014316514 0.104174538 0.982238418 -0.240078329 RS(ph)SQPSPTAVPASDSPPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.5)S(0.5)QPSPTAVPASDSPPTK;RS(0.5)S(0.5)QPSPTAVPASDSPPTK;RS(0.5)S(0.5)QPSPTAVPASDSPPTK 215.08 2.54E-19 934330000 1028290 882810 1001130 889270 1306650 1313760 1382720 1132900 1291930 970370 TRUE FALSE 1068887.683 1034425.75 1027220.27 1065164.952 1084546.1 1008659.15 1274338.793 1117715.329 1245433.692 1160495.423 0.921061525 0.891365644 0.885156675 0.917853643 0.934554397 0.869162541 1.09809894 0.963136353 1.073191387 1 20.1463094 2.249650179 24.99999981 1.025726463 0.903926975 0.727251422 0.039005584 109.4746484 246796.498 0.012754381 0.010576053 177.6847595 -2.249650179 -0.121799487 RS(ph)SQPSPTAVPASDSPPTKQEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSQPSPTAVPASDSPPTKQEVK 23 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 RS(0.487)S(0.487)QPS(0.025)PTAVPASDSPPTKQEVK;RS(0.499)S(0.499)QPS(0.003)PTAVPASDSPPTKQEVK 133.44 1.20E-05 633820000 637890 416340 532550 303660 838690 613560 503790 528220 629950 454750 TRUE FALSE 663074.3898 487843.1563 546428.6905 363723.0417 696129.7734 471069.9886 464301.6234 521140.0749 607278.2226 543849.5558 1.219223925 0.89701858 1.004742368 0.668793489 1.280004306 0.866177022 0.853731732 0.958243083 1.116629068 1 19.05284809 RS(ph)SRDMAGGAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSSRDMAGGAGPR 13 2 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.5)S(0.5)RDMAGGAGPR;RS(0.5)S(0.5)RDMAGGAGPR;RS(0.832)S(0.168)RDMAGGAGPR;RS(0.5)S(0.5)RDMAGGAGPR 71.98 0.032127 656251000 188729 294025 262470 151231 357646 316269 136086 218186 255006 441526 TRUE FALSE 196180.1667 344521.5066 269310.1838 181144.0404 296853.4607 242820.3179 125419.2237 215261.5736 245828.3839 528034.5662 0.371529023 0.652460139 0.510023777 0.343053376 0.562185659 0.459856861 0.237520859 0.407665686 0.465553582 1 19.01027285 0.925280029 17.94653141 1.000000001 0.441219503 0.695278548 0.110203968 641.4763282 154073.8898 0.109461524 0.027365345 8.41937841 -0.925280029 -0.558780497 RS(ph)SRSSPELT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.636)S(0.348)RS(0.073)S(0.36)PELT(0.582)R 91.781 0.011572 2221900000 1677600 1826600 1903300 1898400 1872100 2191900 1988100 1868200 1932200 1866100 TRUE FALSE 1743832.943 2140304.341 1952901.562 2273897.854 1553881.111 1682864.444 1832267.527 1843159.835 1862660.499 2231726.566 0.781382885 0.959035203 0.875063097 1.018896261 0.69626859 0.754063902 0.821008969 0.825889633 0.83462756 1 21.08972885 RS(ph)SSPAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSSPAELDLKDDLQQTQGK 20 2 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RS(0.333)S(0.333)S(0.333)PAELDLKDDLQQTQGK 296.84 6.24E-55 141520000 243630 157660 216820 158740 275560 252690 213480 191100 236440 197720 TRUE FALSE 253248.7005 184736.8786 222470.5073 190138.2982 228720.4096 194006.5771 196746.8798 188538.6171 227930.5706 236459.4484 1.07100267 0.78126241 0.940839999 0.804105311 0.96727118 0.820464474 0.832053365 0.797340171 0.963930907 1 17.85123326 4.754704754 24.34532796 0.867526911 1.071002893 0.341866969 0.078759045 2213.910413 3338492.57 0.017268606 0.441072793 56846.63398 -4.754704754 0.203475983 RS(ph)SSSGDQSSDSLNSPTLLAL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 RS(0.444)S(0.444)S(0.089)S(0.022)GDQSSDSLNSPTLLAL 73.11 0.015821 34557000 52009 57627 52772 58363 62628 80291 62363 61302 67678 71375 TRUE FALSE 54062.35548 67523.98897 54147.28167 69907.0272 51982.51493 61644.63207 57474.8251 60480.34696 65242.282 85359.56469 0.633348538 0.791053577 0.634343461 0.818971224 0.608982896 0.722176036 0.673326127 0.708536263 0.76432304 1 16.3812652 0.739506263 2.058002132 0.999909136 0.700020815 0.666887487 0.063824749 0.559171127 3.554729993 0.053802078 0.014800162 5.489164712 -0.739506263 -0.299888321 RS(ph)STS(ph)GDTEEEEEEEVVPFSSDEQK ddPTM_MDA-MB-175_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(0.425)S(0.425)T(0.425)S(0.474)GDT(0.251)EEEEEEEVVPFSSDEQK 133.1 0.00022323 452930000 231080 166040 212720 158610 305530 292650 276290 225050 266740 157190 TRUE FALSE 240203.2168 194556.0784 218263.658 189982.5846 253596.1197 224686.4727 254633.6679 222033.5729 257140.0795 187988.3709 1.277755723 1.034936775 1.161048723 1.010608176 1.348998975 1.195214744 1.35451819 1.181102702 1.367850991 1 17.52028389 3.236153409 24.99999419 1.251036609 1.117788128 0.184244141 0.122796552 90.85041146 943529.3069 0.03175736 0.039681087 1722.47691 -3.236153409 -0.133248481 RS(ph)STSGDTEEEEEEEVVPFSSDEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.442)S(0.331)T(0.067)S(0.118)GDT(0.042)EEEEEEEVVPFSSDEQK;RS(0.381)S(0.381)T(0.129)S(0.09)GDT(0.018)EEEEEEEVVPFSSDEQK;RS(0.429)S(0.429)T(0.112)S(0.029)GDTEEEEEEEVVPFSSDEQK;RS(0.353)S(0.353)T(0.094)S(0.198)GDT(0.003)EEEEEEEVVPFSSDEQK 218.93 8.46E-34 2028270000 1860330 1258270 1579040 1182210 2290250 2266070 2128960 1664850 1995060 1182760 TRUE FALSE 1933777.265 1474368.085 1620191.08 1416047.609 1900954.123 1739809.585 1962086.552 1642535.409 1923258.18 1414499.177 1.367110916 1.042325163 1.145416771 1.001094686 1.343906136 1.229982749 1.387124563 1.161213408 1.359674302 1 20.43185991 3.225500732 24.99979412 1.257245738 1.132541723 0.124279855 0.138425751 397.8385971 761558.3065 0.037092709 0.04458674 1680.740758 -3.225500732 -0.124704015 RS(ph)STSGDTEEEEEEEVVPFSSDEQKR ddPTM_MDA-MB-175_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(0.434)S(0.434)T(0.053)S(0.014)GDT(0.064)EEEEEEEVVPFSSDEQKR 99.414 0.0027928 472560000 67186 54984 77747 57477 103170 97248 85905 67747 71409 54242 TRUE FALSE 69838.55516 64427.07428 79773.15069 68845.77905 85633.20025 74663.62581 79171.54163 66838.96228 68839.00404 64869.68137 1.076597783 0.993176981 1.229744759 1.061293621 1.320080482 1.150978766 1.220470641 1.030357493 1.061189181 1 15.98525673 1.645589619 7.668348434 1.033576658 1.150193947 0.272608744 0.089500439 0.16888353 19.4536394 0.045496388 0.0232702 44.21703513 -1.645589619 0.116617289 RS(ph)STSSEPTPTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.496)S(0.496)T(0.006)S(0.002)SEPTPTVK;RS(0.496)S(0.496)T(0.004)S(0.001)S(0.002)EPTPTVK;RS(0.489)S(0.489)T(0.015)S(0.003)S(0.004)EPTPTVK;RS(0.443)S(0.443)T(0.102)S(0.01)S(0.002)EPTPTVK;RS(0.493)S(0.493)T(0.013)S(0.001)SEPTPTVK 174.88 1.18E-05 5825720000 4400010 3808240 4439910 3622620 5906190 5743430 5221160 4716550 5301540 4509830 TRUE FALSE 4573725.792 4462275.596 4555617.702 4339163.424 4902257.933 4409605.425 4811911.836 4653332.362 5110738.611 5393444.843 0.848015679 0.82735167 0.844658254 0.80452541 0.908928908 0.81758608 0.892177815 0.862775554 0.947583365 1 22.3627756 1.081819199 0.955890361 1.002560199 0.842216023 0.742758245 0.029863933 0.250206475 0.496879913 0.025851785 0.008853936 12.07311115 -1.081819199 -0.160344176 RS(ph)SVAQEDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSVAQEDSK 10 1 A1L390-3;A1L390;A1L390-2;G3V311;A0A0U1RR71 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 RS(0.689)S(0.311)VAQEDSK 144.8 1.93E-05 677860000 682950 493240 643890 530740 825020 876680 770120 667490 739120 543460 TRUE FALSE 709913.3934 577950.1331 660670.3024 635718.7879 684783.3951 673084.3562 709755.9821 658543.3883 712519.2156 649940.5818 1.092274299 0.889235338 1.016508771 0.978118317 1.053609229 1.035609062 1.092032106 1.013236297 1.096283623 1 19.30994831 3.235423918 24.96088487 1.049048139 0.988153873 0.191104784 0.054313062 112.516448 895373.9302 0.014250976 0.017742443 1719.58607 -3.235423918 -0.060894266 RS(ph)SVSTIQVEWPEPDLAPAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSVSTIQVEWPEPDLAPAIK 21 1 Q96B33 Q96B33 CLDN23 Claudin-23 1 RS(0.494)S(0.494)VS(0.009)T(0.002)IQVEWPEPDLAPAIK;RS(0.497)S(0.497)VS(0.005)T(0.001)IQVEWPEPDLAPAIK 181.92 2.98E-17 162075000 168238 178894 170225 210001 221000 279040 220051 181017 186744 203157 TRUE FALSE 174880.1661 209617.6529 174661.2033 251538.571 183434.4989 214237.1889 202802.8276 178590.7632 180023.1199 242961.7245 0.719784841 0.862759981 0.718883617 1.035301225 0.754993402 0.881773412 0.834711015 0.735057193 0.740952594 1 17.89036953 -2.458595235 2.314179268 3.176798882 0.81100203 0.268216501 0.094433897 11047908.73 1384684.407 125207862.5 0.02332062 0.003478602 2.458595235 -2.365796852 RS(ph)TS(ph)PIIGSPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.609)T(0.513)S(0.665)PIIGS(0.213)PPVR 63.727 0.026947 0 236970 261750 281560 269150 312700 367270 297210 308230 309480 299880 TRUE FALSE 246325.7586 306703.5264 288897.6849 322387.0667 259547.3657 281977.1085 273913.9036 304098.681 298341.8753 358635.7445 0.68684107 0.855195086 0.805546266 0.898926199 0.723707466 0.786249315 0.763766322 0.84793188 0.831879922 1 18.45215976 0.563647955 1.026919811 0.999948199 0.79530397 0.52649238 0.05851162 1.133126156 1.798530624 0.053841522 0.017031008 3.661406557 -0.563647955 -0.204644229 RS(ph)TSPIIGSPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.399)T(0.399)S(0.202)PIIGSPPVR 121.45 0.00015102 1052300000 529020 537920 476130 401010 490660 499920 359270 383590 410120 448800 TRUE FALSE 549906.1181 630303.5756 488538.3389 480328.5811 407257.7885 383821.1564 331109.4786 378448.6035 395359.8613 536733.7672 1.024541685 1.174331883 0.910206081 0.894910308 0.758770574 0.71510529 0.616897052 0.705095574 0.736603295 1 19.03384713 3.711284071 1.312715413 0.723649 1.101340384 0.591018718 0.106701017 0.27083363 0.896254952 0.032051455 0.081819537 5143.799964 -3.711284071 0.377691383 RS(ph)WGQQAQEYQEQK ddPTM_MDA-MB-175_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 276.05 2.66E-33 1171080000 716840 485810 630690 497870 784220 845120 730640 661780 641760 461120 TRUE FALSE 745141.3967 569244.0884 647126.2995 596347.2 650918.5645 648853.6879 673370.5276 652909.9216 618663.183 551467.6353 1.351196968 1.032234808 1.173461973 1.081382046 1.180338651 1.176594321 1.221051762 1.183949664 1.121848579 1 19.07291669 0.896523951 3.756346159 1.000075387 1.170001424 0.308970708 0.079159766 0.546023431 16.37221665 0.07004137 0.017986656 7.879958874 -0.896523951 0.169926037 RS(ph)WHEES(ph)PFEKQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSWHEESPFEKQFK 14 2 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 2 RS(1)WHEES(1)PFEKQFK;RS(1)WHEES(1)PFEKQFK 53.448 0.079663 5975900000 14924800 3037800 5185500 2316500 8496700 9664600 6988500 3921600 6759800 2379380 TRUE FALSE 15514042.63 3559518.519 5320638.39 2774696.786 7052433.969 7420143.118 6440723.109 3869037.366 6516516.118 2845573.955 5.451990661 1.250896506 1.869794451 0.975092136 2.478387166 2.6076086 2.263417929 1.359668534 2.290053332 1 21.44028824 4.744096047 24.98752568 1.823821643 5.451992216 0.780293716 0.582942063 270.952715 1223073.013 0.138239578 1.212384009 55474.83853 -4.744096047 3.628170574 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 RS(0.958)Y(0.042)DVPPPPMEPDHPFYSNISK;RS(0.992)Y(0.008)DVPPPPMEPDHPFYSNISK;RS(0.539)Y(0.461)DVPPPPMEPDHPFYSNISK;RS(0.544)Y(0.456)DVPPPPMEPDHPFYSNISK;RS(0.641)Y(0.359)DVPPPPMEPDHPFYSNISK 171.08 3.03E-12 1922270000 1248370 1153646 1350680 1082940 1737050 1693670 1539620 1321400 1550960 1174520 TRUE FALSE 1297656.612 1351775.726 1385879.83 1297142.3 1441786.861 1300340.81 1418940.561 1303688.794 1495141.253 1404644.706 0.923832629 0.962361315 0.986640838 0.923466478 1.026442384 0.925743574 1.010177559 0.928127083 1.064426645 1 20.42177383 7.999999994 0.123703682 1.017597464 0.772612402 0.180177125 0.043137452 174.1822646 1.4711609 0.245467912 7.391161635 99999998.58 -7.999999994 -0.244985062 RS(ph)YSPDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.826)Y(0.001)S(0.173)PDGK;RS(0.644)Y(0.002)S(0.354)PDGK 69.672 0.056474 505480000 516360 317090 430160 334700 503010 535770 547190 451260 430960 245576 TRUE FALSE 536746.2915 371547.7409 441370.323 400902.661 417508.5399 411345.5372 504299.818 445211.5978 415449.8338 293691.9154 1.827582795 1.265093526 1.502834433 1.365044933 1.421586765 1.400602181 1.717104869 1.515913699 1.414577018 1 18.16394403 0.81964193 3.902569974 1.000038449 1.494472643 0.478404318 0.156401772 1.166306272 24.22822721 0.142587169 0.036494257 6.601489389 -0.81964193 0.494434194 RS(ph)YSPDGKESPSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSYSPDGKESPSDK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.476)Y(0.048)S(0.476)PDGKESPSDK 58.158 0.057956 74476000 151180 88677 122560 76406 161480 155100 114520 110680 133300 84306 TRUE FALSE 157148.7031 103906.5849 125754.0143 91518.87875 134031.6873 119080.3756 105543.6232 109196.5156 128502.559 100824.1466 1.558641541 1.030572422 1.247260885 0.907707944 1.32936099 1.181070008 1.046808991 1.083039325 1.274521664 1 16.62148167 4.746316475 24.72759207 1.124830537 1.558641786 0.514243415 0.127214609 635.379536 2025691.342 0.028174982 0.304642381 55759.19246 -4.746316475 0.433811248 RSAPGGGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSAPGGGSK 9 1 P06748;P06748-3;P06748-2;E5RI98 P06748 NPM1 Nucleophosmin 0 ;; 141.71 0.00017006 256776000 337330 235158 297369 220157 419180 398197 421446 337385 342229 288383 FALSE TRUE 350648.0489 275544.5572 305118.6804 263703.3975 347927.9333 305721.7815 388411.9613 332862.9059 329912.2451 344886.1274 1.016706736 0.79894358 0.884693979 0.764610045 1.00881974 0.886442675 1.126203493 0.965138576 0.956583112 1 18.39576057 3.212890504 24.99740404 0.991734456 0.862750008 0.34799934 0.083281701 231.878463 225801.2614 0.023017103 0.027519949 1632.640267 -3.212890504 -0.128984447 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.038)AS(0.962)PDDDLGSSNWEAADLGNEER;RS(0.046)AS(0.954)PDDDLGSSNWEAADLGNEER;RS(0.163)AS(0.837)PDDDLGSSNWEAADLGNEER;RS(0.163)AS(0.837)PDDDLGSSNWEAADLGNEER;RS(0.29)AS(0.71)PDDDLGSSNWEAADLGNEER 350.93 3.93E-102 9590220000 1301373 1496708 1403231 1358391 1534924 1775250 1444483 1529894 1479072 1598701 TRUE FALSE 1352752.211 1753755.956 1439800.353 1627076.685 1274018.167 1362975.092 1331260.648 1509388.273 1425840.488 1911935.852 0.707530124 0.917267153 0.753058923 0.851010082 0.666349849 0.712876999 0.69628939 0.7894555 0.745757493 1 20.86660269 -1.846972893 9.03449698 1.009857779 0.762150622 0.499205959 0.07209776 0.014044314 0.000237884 0.068485979 0.016151194 0.014224176 1.846972893 -0.247707158 RSAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSASPDDDLGSSNWEAADLGNEERK 25 2 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 RS(0.182)AS(0.818)PDDDLGSSNWEAADLGNEERK 178.89 1.48E-17 124110000 98785 69795 96239 61415 126600 123470 87132 80016 94142 94698 TRUE FALSE 102685.1081 81781.74832 98747.0674 73562.70369 105080.5772 94795.96371 80302.36616 78943.5164 90753.84781 113252.26 0.906693677 0.722120232 0.871921385 0.649547335 0.927845301 0.837033748 0.709057516 0.697059082 0.801342488 1 16.78918031 2.26858715 24.95900331 0.765682305 0.814405422 0 0.111800071 734.6955436 610699.3967 0.036773102 0.03076281 185.6039226 -2.26858715 0.048723117 RSAS(ph)PHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSASPHDVDLCLVSPCEFEHR 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.165)AS(0.835)PHDVDLCLVSPCEFEHR 213.05 2.91E-23 770930000 168250 201860 192790 187260 235070 243880 194110 204650 172880 231830 TRUE FALSE 174892.6399 236527.8847 197814.2658 224299.4691 195112.8854 187242.566 178895.151 201907.0015 166658.0826 277252.6498 0.630806018 0.853113162 0.713480163 0.809007485 0.703736774 0.67534996 0.645242349 0.728241918 0.601105463 1 18.08084172 -1.205808091 5.079299643 1.000026657 0.711761271 0.5869674 0.073705599 2.14E-05 3.35E-06 0.068707037 0.016192908 0.062257533 1.205808091 -0.288265386 RSAS(ph)PHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSASPHDVDLCLVSPCEFEHRK 22 2 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 RS(0.43)AS(0.57)PHDVDLCLVSPCEFEHRK;RS(0.359)AS(0.641)PHDVDLCLVSPCEFEHRK 78.324 0.0041892 526210000 282420 285630 335230 234390 524000 400640 269520 353840 357640 404730 TRUE FALSE 293570.1597 334684.7306 343966.3692 280751.6424 434930.6672 307597.4318 248394.3181 349097.3536 344768.6063 484029.0945 0.606513458 0.691455812 0.710631599 0.58003051 0.898563066 0.635493683 0.513180553 0.721232169 0.712289014 1 18.88473424 0.623491456 1.880616322 0.999821113 0.669818067 0.507474271 0.097226433 1.553486424 6.744198178 0.090817399 0.025280448 4.202342603 -0.623491456 -0.330003046 RSASAS(ph)HQADIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSASASHQADIK 12 1 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 RS(0.273)AS(0.273)AS(0.454)HQADIK;RS(0.389)AS(0.206)AS(0.405)HQADIK 136.81 6.33E-05 272507000 299674 312210 339920 377810 468150 636420 432030 369280 387680 431230 TRUE FALSE 311505.3609 365829.6388 348778.5944 452539.6903 388574.0302 488621.1 398166.3597 364330.4056 373727.4725 515721.2621 0.604018845 0.709355355 0.676292835 0.877488914 0.753457456 0.94745192 0.772057289 0.706448294 0.724669507 1 18.976232 3.8214121 7.457450569 0.806415494 0.666479561 0.373237278 0.094278713 0.349086583 27.72140494 0.024267371 0.044002593 6628.451763 -3.8214121 -0.139935933 RSATLSGS(ph)ATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSATLSGSATNLASLTAALAK 21 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.191)AT(0.191)LS(0.191)GS(0.213)AT(0.213)NLASLTAALAK 111.66 0.00014896 71977000 25303 23200 30061 23850 36955 37695 35274 32110 32163 30554 TRUE FALSE 26301.98198 27184.41953 30844.41436 28567.45881 30673.4023 28940.90752 32509.13171 31679.61797 31005.45991 36540.47131 0.719804125 0.743953719 0.844116489 0.781803239 0.839436417 0.792023378 0.889674669 0.866973436 0.848523809 1 15.15720762 2.774873658 0.037089954 1.648657966 2.79E-08 0.813421437 0.032811682 70.63546878 1.005977515 19.93961387 24.53064864 595.4888832 -2.774873658 -1.648657938 RSDAEEVDFAGWLCSTIGLNQPS(ph)TPTHAAGV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.494)T(0.494)PT(0.012)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.52)T(0.459)PT(0.021)HAAGV 195.17 4.03E-20 237980000 66008 79955 77620 77753 97319 107213 83110 90706 87309 91527 TRUE FALSE 68614.04681 93686.64929 79642.84097 93132.31133 80776.75114 82314.40558 76595.62103 89490.23444 84166.76614 109459.9633 0.626841493 0.855898782 0.727597914 0.850834484 0.737957046 0.752004689 0.699759243 0.817561342 0.768927411 1 16.74004375 0.037178625 0.900579474 1.003409933 0.759965112 0.546390442 0.065909068 4.115510953 3.211690252 0.101640399 0.01904578 1.089378062 -0.037178625 -0.243444821 RSDAEEVDFAGWLCSTIGLNQPST(ph)PTHAAGV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV 31 1 Q02750;Q02750-2;H3BRW9 Q02750 MAP2K1 Dual specificity mitogen-activated protein kinase kinase 1 1 RSDAEEVDFAGWLCSTIGLNQPS(0.175)T(0.806)PT(0.019)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.044)T(0.808)PT(0.149)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.033)T(0.962)PT(0.005)HAAGV;RSDAEEVDFAGWLCSTIGLNQPS(0.017)T(0.98)PT(0.003)HAAGV 231.53 4.03E-36 744871000 257561 308932 303256 336146 365366 383762 290504 341767 345835 355240 TRUE FALSE 267729.7072 361988.6678 311159.1005 402634.6755 303261.2178 294639.0915 267733.5374 337186.1724 333388.4659 424842.4765 0.630185826 0.85205385 0.732410523 0.947726976 0.71382038 0.693525501 0.630194842 0.793673399 0.784734306 1 18.69656849 -1.465383649 3.402292537 1.003698798 0.755666383 0.388840179 0.092795034 28293863.77 41209250.71 1001712.892 0.021887124 0.034246512 1.465383649 -0.248032415 RSDLDLGYEPEGSAS(ph)PTPPYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSDLDLGYEPEGSASPTPPYLK 22 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 RSDLDLGYEPEGS(0.002)AS(0.614)PT(0.384)PPYLK;RSDLDLGYEPEGS(0.112)AS(0.869)PT(0.019)PPYLK 151.19 3.09E-08 141332000 106649 93837 111308 85350 132325 131847 108407 111505 128534 95949 TRUE FALSE 110859.5849 109952.7748 114208.7779 102231.9753 109832.4438 101227.5324 99909.77607 110010.4579 123908.0864 114748.3695 0.966110328 0.958207731 0.99529761 0.890923119 0.95715908 0.88216968 0.870685802 0.958710423 1.079824376 1 16.80811413 1.387400874 5.906613638 1.037698036 0.93134795 0.507616804 0.042039344 0.16815016 8.184735934 0.029542114 0.010723698 24.4006207 -1.387400874 -0.106350086 RSDLDLGYEPEGSASPT(ph)PPYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSDLDLGYEPEGSASPTPPYLK 22 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 RSDLDLGYEPEGS(0.002)AS(0.182)PT(0.816)PPYLK 152.16 2.54E-08 101180000 90639 74677 91599 66231 115670 105500 91858 100320 103410 79141 TRUE FALSE 94217.49771 87502.19384 93986.14519 79331.29412 96008.45472 80999.22387 84657.92993 98975.37449 99688.2943 94647.1637 0.995460339 0.924509414 0.993015971 0.838179307 1.014382798 0.855801914 0.894458182 1.045729958 1.053262352 1 16.53027165 1.694580092 7.064058517 1.036604102 0.929881386 0.401560873 0.056943364 0.117185014 12.32539334 0.026984566 0.013961291 49.49713845 -1.694580092 -0.106722716 RSDS(ph)ASSEPVGIYQGFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.076)DS(0.674)AS(0.239)S(0.011)EPVGIYQGFEK;RS(0.013)DS(0.952)AS(0.029)S(0.006)EPVGIYQGFEK;RS(0.045)DS(0.943)AS(0.01)S(0.002)EPVGIYQGFEK;RS(0.039)DS(0.782)AS(0.098)S(0.081)EPVGIYQGFEK;RS(0.021)DS(0.896)AS(0.081)S(0.002)EPVGIYQGFEK 252.13 1.09E-30 2323590000 1191430 1006807 1339710 1089540 1587300 1635010 1551050 1325750 1487550 1294880 TRUE FALSE 1238468.576 1179718.27 1374623.943 1305047.76 1317491.313 1255303.706 1429474.648 1307980.49 1434013.366 1548586.944 0.799741068 0.761803059 0.887663394 0.842734575 0.850769999 0.810612353 0.923083236 0.844628385 0.926014113 1 20.56252095 -5 0.068708848 1.563889483 0.643615116 0.681617211 0.037772906 178.9800048 0.887562736 15.89190835 2.060012661 1.00E-05 5 -0.920274367 RSDS(ph)LLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR;RSDS(1)LLSFR 196.7 1.79E-05 1274530000 119722 128797 132524 144606 188034 183692 142171 154153 134445 180839 TRUE FALSE 124448.717 150916.8828 135977.6843 173208.6352 156072.0478 141032.3169 131027.2655 152086.8312 129606.3507 216270.9397 0.575429677 0.697813969 0.628737659 0.800887236 0.721650574 0.652109419 0.605847765 0.703223611 0.599277697 1 17.7224803 -1.584459007 2.821463518 1.022178051 0.670082287 0.70697452 0.064627782 11646569.68 11709378.87 1926497.006 0.015649003 0.026034006 1.584459007 -0.352095764 RSDS(ph)PEIPFQAAAGPSDGLDAS(ph)SPGNSFVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 RS(0.158)DS(0.842)PEIPFQAAAGPS(0.001)DGLDAS(0.512)S(0.454)PGNS(0.034)FVGLR 100.19 9.08E-05 69563000 31943 40114 30806 33229 42659 42756 34632 37396 36333 38705 TRUE FALSE 33204.13431 47003.26746 31608.82967 39801.59702 35407.83842 32826.56697 31917.45335 36894.76779 35025.38243 46288.5037 0.717330042 1.015441496 0.682865661 0.859859227 0.764938064 0.709173215 0.689533055 0.797061146 0.756675624 1 15.49836631 RSDS(ph)PEIPFQAAAGPSDGLDASS(ph)PGNSFVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 2 RS(0.04)DS(0.96)PEIPFQAAAGPSDGLDAS(0.251)S(0.748)PGNS(0.001)FVGLR 139.93 2.39E-09 85384000 41931 41292 41816 43698 48635 52914 43864 49308 45039 53104 TRUE FALSE 43586.46826 48383.57979 42905.75931 52341.33397 40368.04007 40625.52542 40425.82506 48647.10691 43418.05519 63508.71206 0.686306915 0.761841615 0.67558856 0.824159903 0.635629959 0.639684291 0.636539834 0.76599108 0.683655105 1 15.95466689 -1.255850512 3.728884188 1.000497334 0.703746766 0.687631691 0.060423563 3992606.841 2024614.851 15329.64241 0.013999695 0.055481665 1.255850512 -0.296750568 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RS(0.036)DS(0.964)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.19)DS(0.81)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.159)DS(0.841)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.01)DS(0.99)PEIPFQAAAGPSDGLDASSPGNSFVGLR;RS(0.049)DS(0.951)PEIPFQAAAGPSDGLDASSPGNSFVGLR 259.74 1.64E-59 4722200000 560593 688258 666086 699029 737300 781896 649952 679077 689199 705772 TRUE FALSE 582725.6445 806460.9576 683444.7484 837294.8498 611974.0094 600312.5037 599007.0639 669975.0836 664394.8626 844054.5106 0.690388639 0.955460752 0.809716363 0.99199144 0.725040861 0.711224804 0.709678174 0.793758075 0.787146866 1 19.68697665 5.025551496 16.59710143 0.816244503 0.356230938 0.119927331 0.107764923 8893268.477 150454917 0.025581934 110611439.8 106059.9689 -5.025551496 -0.460013565 RSDS(ph)PENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.019)DS(0.981)PENK;RS(0.005)DS(0.995)PENK 101.93 0.0031012 917640000 408659 248819 355918 310981 481880 508810 493070 388289 401170 292806 TRUE FALSE 424793.1729 291551.7277 365193.5155 372492.1136 399970.2097 390646.5886 454421.885 383084.6211 386731.9701 350175.7296 1.213085708 0.832586907 1.042886427 1.0637291 1.142198548 1.115572998 1.297696689 1.093978219 1.104393987 1 18.41771957 3.458864962 2.392798669 1.139563717 1.010471885 0.122495097 0.110503934 0.45140156 5.194415082 0.03083437 0.04821232 2876.503866 -3.458864962 -0.129091832 RSDS(ph)PENKYSDSTGHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSDSPENKYSDSTGHSK 17 2 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5;Q9BTA9-3;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;E9PMZ7;C9JMU2 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 RSDS(1)PENKYSDSTGHSK;RS(0.033)DS(0.96)PENKYS(0.002)DS(0.002)T(0.003)GHSK;RS(0.003)DS(0.923)PENKYS(0.04)DS(0.014)T(0.019)GHSK;RSDS(0.999)PENKYSDSTGHSK;RSDS(1)PENKYSDSTGHSK 235.99 1.86E-20 1691801000 323648 307915 414282 227226 593620 479239 355057 407746 464738 306325 TRUE FALSE 336425.873 360797.006 425078.5293 272170.6246 492716.6844 367943.0052 327226.7046 402280.8318 448012.1702 366343.5188 0.918334448 0.984859804 1.160327691 0.742938282 1.344958104 1.004366083 0.893223676 1.098097308 1.222929156 1 18.48283757 6.239124611 0.665822244 1.061558951 3.66E-11 0.067440648 0.160062672 60.82820542 4.192656268 0.059932428 76.18868205 1734301.546 -6.239124611 -1.061558951 RSDS(ph)QQAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSDSQQAVK 9 1 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 RSDS(1)QQAVK;RSDS(1)QQAVK;RSDS(1)QQAVK;RS(0.005)DS(0.995)QQAVK 152.31 4.95E-05 1930810000 1716220 1421460 1825050 1316510 2091310 2271380 2058140 1860560 2016520 1494490 TRUE FALSE 1783977.691 1665584.698 1872612.302 1576911.749 1735829.873 1743886.418 1896817.609 1835622.236 1943945.839 1787306.702 0.998137415 0.931896409 1.047728574 0.8822838 0.97119866 0.975706305 1.061271469 1.027032593 1.087639764 1 20.76935579 2.304963806 5.7326858 1.044636784 0.965316329 0.40581125 0.045166549 0.188503086 11.52738156 0.015054744 0.012408198 201.8198162 -2.304963806 -0.079320455 RSDS(ph)VSASER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 RSDS(0.999)VS(0.001)ASER;RS(0.002)DS(0.998)VSASER;RS(0.005)DS(0.993)VS(0.002)ASER;RSDS(0.991)VS(0.009)ASER;RSDS(0.987)VS(0.013)ASER 194.13 3.04E-07 1768895000 307524 435828 436410 377370 488237 532574 402876 462354 470033 506406 TRUE FALSE 319665.285 510678.0687 447783.2031 452012.6597 405246.6491 408891.7597 371297.5264 456156.9009 453116.6041 605626.56 0.527825736 0.843222709 0.739371806 0.74635541 0.66913619 0.675154933 0.613079992 0.753198309 0.748178224 1 19.20806895 0.614995464 1.469606864 0.999683295 0.698760605 0.561134463 0.080640861 1.074542771 3.19712916 0.073342467 0.021362665 4.120932152 -0.614995464 -0.30092269 RSDSASSEPVGIYQGFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSDSASSEPVGIYQGFEK 18 1 Q05655;Q05655-2 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 0 ; 112.44 0.00044227 1516880000 266410 430040 379300 370870 440340 484520 302812 325225 355360 494880 FALSE TRUE 276928.0725 503896.0248 389184.8696 444226.9791 365491.1641 371997.573 279076.8042 320865.8908 342570.663 591842.261 0.467908581 0.851402575 0.657582088 0.750583404 0.61754827 0.628541754 0.471539163 0.54214765 0.578820888 1 19.17485319 -1.560197284 6.211741759 1.00070719 0.61851553 0.511761424 0.111802585 0.001128895 7.99E-05 0.111606128 0.026259839 0.027529778 1.560197284 -0.38219166 RSECNMCNTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSECNMCNTPK 11 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 146.5 5.73E-05 67488000 70597 62580 71541 55600 89855 91437 83093 77233 74985 64049 FALSE TRUE 73384.22407 73327.6282 73405.41723 66597.51405 74581.4792 70202.14249 76579.95354 76197.81796 72286.3045 76598.17526 0.958041413 0.957302546 0.958318093 0.869439955 0.973671748 0.916498889 0.999762113 0.994773279 0.943707918 1 16.2250224 2.232111276 24.99905188 0.985824588 0.939025012 0.33640303 0.031411639 174.0096861 674493.7637 0.011409782 0.008629157 170.6519583 -2.232111276 -0.046799576 RSEEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSEEVVR 7 1 O14907;A0A087X282 O14907 TAX1BP3 Tax1-binding protein 3 0 ; 104.44 0.032132 0 437810 348550 426180 291740 455970 503360 384700 369300 402640 415160 FALSE TRUE 455095.0769 408410.7512 437286.6009 349445.3012 378464.3823 386462.2685 354546.2088 364350.1376 388149.0651 496502.6533 0.9166015 0.822575163 0.880733664 0.703813563 0.762260543 0.778368989 0.714087239 0.733833213 0.781766346 1 18.9214419 3.756262937 24.40258412 0.764182042 0.868230631 0.183127792 0.082328407 788.0180316 1086275.836 0.019270106 0.03464095 5705.095736 -3.756262937 0.10404859 RSEGLPSECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSEGLPSECR 10 1 Q9BPY8;Q9BPY8-3 Q9BPY8 HOPX Homeodomain-only protein 0 108.72 0.0033902 104490000 238330 238710 215910 225870 278120 310940 262030 236700 230180 242410 FALSE TRUE 247739.4524 279706.5856 221536.792 270546.4118 230845.2617 238728.8973 241491.4039 233527.4237 221895.8668 289905.5983 0.85455215 0.964819539 0.764168727 0.933222447 0.796277351 0.823471153 0.83300014 0.805529197 0.765407319 1 18.14522367 4.244642419 24.99855418 0.832650772 0.909685818 0.116025312 0.074534798 248.5687714 1021685.428 0.016506197 0.042830519 17564.76804 -4.244642419 0.077035046 RSELIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSELIAK 7 1 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;; 130.28 0.0057382 3118160000 4129920 3495750 3963060 3304170 5167790 5020750 4608820 4104220 4195880 3547480 FALSE TRUE 4292972.431 4096117.869 4066340.599 3957724.964 4289370.902 3854756.903 4247568.645 4049209.644 4044871.098 4242540.785 1.011887133 0.965486975 0.95846824 0.932866686 1.011038224 0.90859631 1.001185106 0.95443034 0.953407711 1 22.0164971 -1.041970894 4.638428879 1.000001012 0.965455837 0.090742737 0.031813212 3.68E-07 7.61E-08 0.02773293 0.006536479 0.090788137 1.041970894 -0.034545175 RSES(ph)PPAELPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSESPPAELPSLR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 RS(0.247)ES(0.753)PPAELPSLR;RS(0.016)ES(0.984)PPAELPSLR 116.06 0.00037671 249100000 167559 336650 264010 313100 240233 331300 227110 279760 246920 406540 TRUE FALSE 174174.3587 394467.0187 270890.3175 375030.2455 199398.2805 254360.5959 209308.5248 276010.2748 238033.3974 486193.7293 0.358240652 0.811337117 0.557165387 0.771359692 0.410121045 0.523167167 0.430504369 0.567696081 0.489585495 1 18.89117176 -1.378502242 5.643770398 1.000139011 0.552657727 0.489175285 0.138879802 0.000229569 2.53E-05 0.127080953 0.029944062 0.041830953 1.378502242 -0.447481284 RSET(ph)PPHWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 RS(0.119)ET(0.881)PPHWR;RS(0.205)ET(0.795)PPHWR;RS(0.062)ET(0.938)PPHWR;RS(0.031)ET(0.969)PPHWR;RS(0.002)ET(0.998)PPHWR 84.169 0.0091852 2253030000 472036 811882 711634 760880 668740 838736 622492 641347 618703 842608 TRUE FALSE 490672.3458 951316.4179 730179.7667 911379.793 555067.8137 643952.2752 573699.4505 632750.7925 596435.9999 1007700.905 0.486922601 0.944046406 0.724599693 0.904414979 0.550825955 0.639031157 0.569315208 0.627915277 0.591878004 1 19.94263607 3.227132004 24.99451197 0.636349511 0.774899816 0.067926565 0.166418566 403.2774116 881971.0794 0.043917459 0.052920846 1687.065732 -3.227132004 0.138550305 RSFS(ph)KEVEER ddPTM_MDA-MB-175_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(0.171)FS(0.829)KEVEER;RS(0.09)FS(0.91)KEVEER 149.82 1.18E-05 420860000 545500 296270 417680 292990 624280 629040 554240 478670 512710 352960 TRUE FALSE 567036.7612 347152.0678 428565.0839 350942.5475 518165.1086 482954.9932 510797.2206 472254.2116 494257.6673 422115.7542 1.343320536 0.822409646 1.015278581 0.831389362 1.227542691 1.144129278 1.210088028 1.11877893 1.170905521 1 18.68727915 3.218234788 24.99912402 1.153206452 0.991062954 0.182837252 0.145748417 338.7685793 416656.9756 0.039364759 0.047103028 1652.85512 -3.218234788 -0.162143497 RSGKNS(ph)QEDS(ph)EDSEDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSGKNSQEDSEDSEDKDVK 19 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 RS(0.412)GKNS(0.596)QEDS(0.99)EDS(0.002)EDKDVK 77.649 0.016162 77802000 211940 28211 43993 24475 93329 151380 90263 55562 60650 13972 TRUE FALSE 220307.5549 33056.0198 45139.49372 29316.08195 77464.96992 116224.2892 83187.9502 54817.28227 58467.21835 16709.54589 13.18453274 1.978271583 2.701419537 1.754451147 4.635970985 6.955562404 4.97846864 3.28059677 3.499030957 1 14.02838491 4.74459431 24.95049769 3.619644509 13.18453704 0.753082921 1.673795214 342.2547457 1415249.635 0.420002726 3.840833346 55538.52095 -4.74459431 9.564892532 RSGS(ph)FGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSGSFGK 7 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.085)GS(0.915)FGK 85.821 0.021746 121350000 316300 220070 300830 195340 351320 338980 343000 290260 313880 221510 TRUE FALSE 328787.7682 257865.3106 308669.8769 233977.669 291602.7519 260257.0323 316114.7637 286369.5395 302583.5201 264910.6434 1.241127061 0.973404871 1.165184882 0.883232421 1.100758913 0.98243328 1.193288271 1.08100428 1.142209751 1 18.01514628 2.246081261 24.99995089 1.110618699 1.052772988 0.041829936 0.105523978 487.823297 1621613.169 0.034198319 0.028092219 176.230576 -2.246081261 -0.057845711 RSGS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSGSFSK 7 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;G3V3H3;Q07866-5;Q07866-10;H0YG16 Q07866-6 KLC1 Kinesin light chain 1 1 RSGS(1)FSK 91.658 0.0099485 114260000 139240 110520 144820 98808 177240 173660 164980 138720 150950 143810 TRUE FALSE 144737.3027 129500.9503 148594.1282 118351.9275 147112.8081 133330.0968 152048.4365 136860.6853 145517.339 171986.8161 0.841560452 0.752970217 0.863985575 0.688145348 0.855372589 0.775234404 0.884070302 0.795762654 0.846095894 1 17.39193845 -1.055996377 0.345618121 1.097747211 0.792109404 0.526212657 0.055169729 10.83501893 0.963549795 1.070854436 0.041712444 0.087902985 1.055996377 -0.305637807 RSGS(ph)PLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSGSPLEK 8 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 RS(0.489)GS(0.511)PLEK;RS(0.081)GS(0.919)PLEK 111.94 0.0019218 961800000 1061910 754380 946650 691300 1206640 1238230 1060650 916730 1004740 634060 TRUE FALSE 1103835.027 883938.8967 971320.4767 828037.0767 1001535.764 950669.8481 977513.4815 904442.7338 968579.6037 758291.9172 1.455686131 1.165697374 1.280932125 1.091976662 1.320778636 1.253699039 1.289099171 1.192736878 1.277317589 1 19.53239382 -3.660837476 0.354542957 1.85E-11 1.259347563 0.412861403 0.092414357 151.451078 3.066410954 112.3440312 0.064106087 0.000218355 3.660837476 1.259347563 RSIQFVDWCPTGFK ddPTM_MDA-MB-175_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 ; 117.37 0.0004924 1208890000 1710870 492850 840690 607420 2632700 1706420 2278980 1453530 1185800 1377610 FALSE TRUE 1778416.469 577493.1537 862599.072 727565.863 2185194.594 1310129.816 2100347.593 1434047.808 1143123.29 1647526.304 1.07944648 0.350521356 0.523572261 0.441611076 1.326348836 0.795210257 1.274849202 0.870424833 0.693842209 1 20.65187007 3.257211469 24.99986499 0.98934426 0.575681887 0.360370469 0.256810608 250.0118659 335117.3384 0.068103543 0.092052108 1808.0543 -3.257211469 -0.413662373 RSIS(ph)SPNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RS(0.044)IS(0.811)S(0.145)PNVNR;RSIS(0.813)S(0.186)PNVNR;RSIS(0.629)S(0.37)PNVNR;RS(0.06)IS(0.818)S(0.122)PNVNR;RS(0.006)IS(0.847)S(0.147)PNVNR 162.48 4.14E-06 8396640000 1126894 1183464 1118663 987252 1437880 1267990 1061996 1133536 1033140 1254520 TRUE FALSE 1171384.645 1386714.736 1147816.277 1182527.499 1193469.671 973518.5391 978753.9785 1118342.804 995957.4932 1500319.175 0.780756965 0.924279819 0.765048062 0.788183954 0.795477183 0.64887429 0.65236384 0.74540326 0.66383041 1 20.51683802 3.503442633 1.359790627 0.725033413 0.841726458 0.076544238 0.104297597 0.751230945 2.798684121 0.032335003 0.063619978 3187.444513 -3.503442633 0.116693045 RSISS(ph)PNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSISSPNVNR 10 1 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 RSIS(0.316)S(0.684)PNVNR;RSIS(0.275)S(0.725)PNVNR 136.01 7.90E-05 2866270000 286908 409320 351660 313925 402000 464460 359800 343718 282488 333980 TRUE FALSE 298235.3494 479617.5259 360824.5485 376018.428 333668.1836 356596.204 331597.9358 339111.0224 272321.3121 399416.9866 0.74667668 1.200794012 0.903378075 0.941418219 0.835388065 0.892791784 0.830204891 0.849015024 0.681797022 1 18.60753616 3.395396968 1.817200916 0.839654447 0.976405023 0.116778208 0.127347732 0.584055002 3.924951829 0.037099768 0.059080166 2485.403856 -3.395396968 0.136750576 RSLS(ph)GSSPCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.227)LS(0.455)GS(0.159)S(0.159)PCPK 104.41 0.0027581 15506000 74077 44499 56779 42780 80034 77383 70297 63916 64390 43727 TRUE FALSE 77001.61716 52141.3571 58258.70738 51241.75631 66429.84927 59411.971 64786.93745 63059.31057 62072.61648 52294.46845 1.472461992 0.997072131 1.114051048 0.979869532 1.270303557 1.13610431 1.238887006 1.205850493 1.186982454 1 15.67437073 RSLSGS(ph)SPCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSLSGSSPCPK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RS(0.045)LS(0.284)GS(0.335)S(0.335)PCPK 81.904 0.021609 16418000 79114 47213 59234 42097 96668 84962 78487 62889 67883 49879 TRUE FALSE 82237.48181 55321.46548 60777.6867 50423.66095 80236.40789 65230.86311 72334.98385 62046.07582 65439.90409 59651.83506 1.378624509 0.927405929 1.018873713 0.84529941 1.345078618 1.093526512 1.212619591 1.040136917 1.097030863 1 15.8642789 4.757317276 23.83128972 1.072410729 1.378625025 0.332982886 0.132971958 2655.321706 3373617.788 0.031491286 1.032531602 57189.62852 -4.757317276 0.306214296 RSNATNSSYS(ph)PTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSNATNSSYSPTTGR 15 1 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 RSNATNS(0.003)S(0.116)Y(0.001)S(0.871)PT(0.004)T(0.005)GR;RSNATNS(0.021)S(0.261)YS(0.559)PT(0.157)T(0.002)GR 114.75 0.00035628 162940000 34428 41204 39984 40404 56292 52215 43074 37700 42359 49438 TRUE FALSE 35787.24402 48280.46648 41026.01589 48395.79061 46723.50595 40088.85758 39697.74733 37194.69316 40834.50786 59124.42955 0.605286923 0.816590821 0.693892799 0.818541354 0.790257197 0.678042188 0.671427152 0.629091789 0.690653731 1 15.85146674 -1.055085495 5.413192858 1.000002226 0.709959623 0.600354629 0.070878925 1.98E-06 3.45E-07 0.071268516 0.016798022 0.088087545 1.055085495 -0.290042603 RSNS(ph)PDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSNSPDKFK 9 2 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 RS(0.03)NS(0.97)PDKFK;RS(0.191)NS(0.809)PDKFK;RS(0.002)NS(0.998)PDKFK;RS(0.003)NS(0.997)PDKFK 132.14 0.00024676 13617200000 18776300 6822590 10924820 7389770 16093000 16208100 16839300 11423800 12513900 5132260 TRUE FALSE 19517602.82 7994316.76 11209529.78 8851444.45 13357517.61 12444014.41 15519391.66 11270682.65 12063527.18 6137828.084 3.179887503 1.302466711 1.826302339 1.442113453 2.176261281 2.027429612 2.528482625 1.836265613 1.96543908 1 22.54929681 RSNVSSPATPTASS(ph)SSSTTPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSNVSSPATPTASSSSSTTPTR 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 RSNVSSPATPT(0.001)AS(0.03)S(0.157)S(0.157)S(0.157)S(0.157)T(0.157)T(0.157)PT(0.03)R 49.528 0.068072 0 7242.3 9977.6 7602.5 8844.2 13118 13332 10408 12309 8614.6 12056 TRUE FALSE 7528.231596 11691.17519 7800.627396 10593.55636 10888.20705 10235.84505 9592.193764 12144.01799 8304.562229 14418.14237 0.522136028 0.810865567 0.541028601 0.734737949 0.755174055 0.709928144 0.665286381 0.842273413 0.575980041 1 13.81559768 -5 0.190768188 2.283589397 0.642705673 0.440815101 0.105195819 121.4596899 1.189694941 59.43119764 0.259968627 1.00E-05 5 -1.640883724 RSPES(ph)CSKPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPESCSKPEK 11 2 Q03111 Q03111 MLLT1 Protein ENL 1 RS(0.297)PES(0.701)CS(0.002)KPEK 131.96 0.00015161 551510000 296310 144530 216080 146390 289330 242870 287040 221740 240450 105550 TRUE FALSE 308008.5476 169351.9032 221711.2223 175345.5051 240149.7899 186467.1232 264541.0548 218767.938 231796.2515 126230.5016 2.440048512 1.341608415 1.756399756 1.389089822 1.902470376 1.477195455 2.095698356 1.733083012 1.836293515 1 16.94570103 4.754492675 24.17932406 1.664615497 2.440049436 0.385372389 0.306933375 1987.356757 3016037.23 0.06713933 1.652929174 56818.88081 -4.754492675 0.775433939 RSPGPGPSQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPGPGPSQSPR 12 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 RS(0.063)PGPGPS(0.117)QS(0.82)PR 59.345 0.061063 125160000 109810 189900 137910 175760 132460 176980 153070 159110 144360 199100 TRUE FALSE 114145.3836 222513.8478 141504.0479 210524.8034 109944.4965 135879.0772 141071.9734 156977.3907 139164.5118 238109.833 0.479381226 0.934500877 0.594280573 0.884149977 0.461738581 0.570657144 0.592465971 0.659264629 0.584455123 1 17.86126767 -1.81493957 6.318021727 1.023959904 0.646246388 0.348945087 0.147265077 0.044191576 0.00129441 0.126781985 0.031386972 0.015313005 1.81493957 -0.377713515 RSPLSDPPSQDPTPAATPET(ph)PPVISAVVHATDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 RSPLSDPPS(0.004)QDPT(0.046)PAAT(0.046)PET(0.84)PPVIS(0.06)AVVHAT(0.004)DEEK 49.626 0.055496 21096000 32973 22856 30062 23761 37855 34996 37678 31208 33102 21621 TRUE FALSE 34274.7995 26781.3402 30845.44042 28460.85488 31420.42062 26868.70937 34724.69991 30789.70781 31910.66549 25857.22099 1.325540727 1.035739309 1.19291398 1.100692719 1.215150717 1.039118217 1.342940137 1.190758582 1.234110406 1 14.65827961 2.251736375 24.99986817 1.210842464 1.148725666 0.018827812 0.112944444 643.2539763 1220518.406 0.035816582 0.029808729 178.5403471 -2.251736375 -0.062116798 RSPPIPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPPIPLAK 9 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 84.17 0.025131 963480000 535200 484010 500970 466940 755850 684320 644310 525770 559400 561270 FALSE TRUE 556330.1093 567134.9524 514025.6898 559299.3383 627370.887 525397.051 593807.2986 518722.9131 539267.3033 671240.1103 0.828809394 0.844906232 0.765785122 0.833232892 0.934644514 0.782725947 0.884642156 0.772782951 0.803389569 1 19.3564694 -1.161938217 4.885824662 1.000012665 0.82702699 0.521312791 0.049473921 7.26E-06 1.25E-06 0.046404863 0.010936852 0.068875027 1.161938217 -0.172985674 RSPS(ph)PKPT(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSPSPKPTK 9 2 Q15287;H3BTC0;H3BMM9;Q15287-2;Q15287-3;H3BMS0;H3BUL0;H3BV80 Q15287 RNPS1 RNA-binding protein with serine-rich domain 1 2 RS(0.392)PS(0.785)PKPT(0.823)K 61.48 0.098105 107470000 366660 131860 193970 140250 288820 297150 287440 191920 241350 112370 TRUE FALSE 381136.0199 154505.9293 199025.0175 167991.0314 239726.4796 228141.4159 264909.7017 189347.6263 232663.8606 134386.75 2.836113083 1.149711033 1.480986909 1.250056507 1.783855026 1.697648137 1.971248666 1.408975411 1.731300597 1 17.03603138 -2.428337157 0.398124419 3.20E-11 1.681388878 0.177833123 0.449053217 126.178869 5.954386222 110.5765158 0.267214921 0.003729605 2.428337157 1.681388878 RSPTGSTTS(ph)R ddPTM_MDA-MB-175_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(0.025)PT(0.025)GS(0.026)T(0.026)T(0.141)S(0.758)R 86.996 0.013958 166220000 179030 204630 203610 182430 198210 288800 191150 197400 176850 203140 TRUE FALSE 186098.2426 239773.6107 208916.2439 218514.1095 164518.335 221730.5768 176167.1635 194754.1759 170485.203 242941.3936 0.766021137 0.986960711 0.859945029 0.899451947 0.67719351 0.912691631 0.72514264 0.801650855 0.701754446 1 17.8902488 RSQAGVSSGAPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSQAGVSSGAPPGR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 125.22 0.00014835 66042000 25332 24888.5 28671 26327.1 28293.1 33111.6 26113.4 25320.8 24381.8 29900.2 FALSE TRUE 26332.12692 29162.90627 29418.18981 31534.5218 23483.84897 25421.93271 24066.56347 24981.41609 23504.30378 35758.57172 0.736386429 0.815550087 0.822689174 0.881873081 0.656733416 0.710932554 0.673029216 0.698613364 0.657305442 1 15.12600149 3.2344691 24.99998985 0.711675082 0.814838254 0.115203743 0.100737825 159.660789 975560.6818 0.026473584 0.032744844 1715.809625 -3.2344691 0.103163172 RSQS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSQSFSK 7 1 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 RSQS(0.999)FS(0.001)K 85.622 0.012664 120130000 77671 119410 128690 119450 169090 162250 149510 133150 143390 108710 TRUE FALSE 80737.51106 139917.7386 132043.7671 143076.8535 140348.1422 124569.8964 137791.0155 131365.342 138229.4219 130009.6431 0.621011712 1.076210466 1.015645947 1.100509547 1.079521017 0.958158898 1.059852271 1.01042768 1.063224378 1 16.98825911 4.741570061 24.99884059 1.040009817 0.621011559 0.901817659 0.041513305 76.51746434 635583.6302 0.009538427 0.067409922 55153.11691 -4.741570061 -0.418998258 RSQS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSQSPVK 7 1 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3;Q7Z309-5 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 RS(0.098)QS(0.902)PVK 53.17 0.086545 128020000 277330 279720 265230 233290 393580 387810 353380 304760 287350 348830 TRUE FALSE 288279.2025 327759.7341 272142.1117 279434.0657 326679.4122 297747.0048 325681.1522 300675.1907 277008.3296 417176.5597 0.69102445 0.785661913 0.652342768 0.669822067 0.78307231 0.713719402 0.780679414 0.720738459 0.664007416 1 18.67029857 -1.910494303 2.708386344 1.159551897 0.721130231 0.755604385 0.04809985 6464744.03 4634806.932 6580785.667 0.011404362 0.012288693 1.910494303 -0.438421666 RSQS(ph)VTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSQSVTR 7 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 RS(0.005)QS(0.6)VT(0.395)R 85.807 0.021757 9814300 23240 30070 24479 20162 25392 26705 21406 21509 26431 33603 TRUE FALSE 24157.53315 35234.28859 25116.94285 24149.98342 21075.87691 20503.16847 19728.14179 21220.70704 25479.75347 40186.86448 0.601130082 0.876761326 0.625003796 0.600942217 0.52444691 0.510195775 0.490910203 0.528050827 0.634031886 1 15.2944364 0.953644036 20.09375337 1.000000002 0.591182252 0.574861069 0.103897063 619.3726165 268478.7594 0.110230635 0.027557659 8.987606217 -0.953644036 -0.40881775 RSRS(ph)ESETSTMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSRSESETSTMAAK 14 2 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 RS(0.002)RS(0.987)ES(0.011)ETSTMAAK;RS(0.071)RS(0.816)ES(0.103)ET(0.006)S(0.002)T(0.002)MAAK 209.73 4.91E-09 381160000 88979 81845 111710 63976 170148 145513 94908 108304 136529 151813 TRUE FALSE 92491.95963 95901.24208 114621.2544 76630.26185 141226.3037 111719.811 87468.86296 106852.362 131615.348 181557.8507 0.509435198 0.528213138 0.631320838 0.42207077 0.777858425 0.615340017 0.481768553 0.588530662 0.724922373 1 17.47006979 0.912790562 2.364303309 0.999189055 0.569003425 0.67533697 0.091835587 0.219641078 2.647842499 0.085171465 0.023091628 8.180701799 -0.912790562 -0.430185631 RSS(ph)AIGIENIQEVQEK ddPTM_MDA-MB-175_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(0.266)S(0.734)AIGIENIQEVQEK 244.87 2.70E-20 949310000 560390 430560 521820 455970 665380 624620 563250 482160 568810 399100 TRUE FALSE 582514.6299 504505.3307 535419.0579 546159.5051 552278.9453 479561.4712 519100.9932 475697.4339 548338.6392 477296.0038 1.220447323 1.057007238 1.121775698 1.144278395 1.157099454 1.004746462 1.087587135 0.996650779 1.148843977 1 18.86452473 2.746302131 24.99788794 1.046471817 1.134715872 0.39403248 0.057185427 625.2530988 2018987.063 0.016584471 0.017293685 557.5735084 -2.746302131 0.088244055 RSS(ph)DGS(ph)LSHEEDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 RS(0.385)S(0.717)DGS(0.894)LS(0.003)HEEDLAK;RS(0.347)S(0.661)DGS(0.991)LSHEEDLAK;RS(0.086)S(0.914)DGS(0.982)LS(0.017)HEEDLAK;RS(0.112)S(0.902)DGS(0.979)LS(0.007)HEEDLAK 183.07 1.82E-06 2477130000 2726560 1957370 2408490 1850340 3494940 3356720 2892330 2524860 2730240 1938420 TRUE FALSE 2834206.694 2293533.071 2471257.228 2216331.729 2900871.347 2577172.652 2665621.617 2491018.382 2631979.196 2318216.286 1.222580788 0.989352497 1.06601668 0.956050453 1.251337662 1.111705007 1.149858895 1.074540972 1.135346694 1 21.14458374 4.774586096 22.68245463 1.088202278 1.22258182 0.202571723 0.082996102 8795.117079 5537245.563 0.01938054 3.45606196 59509.47191 -4.774586096 0.134379542 RSS(ph)DGSLSHEEDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSDGSLSHEEDLAK 15 1 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 1 RS(0.467)S(0.532)DGSLSHEEDLAK 209.43 1.46E-09 811460000 722490 729100 745640 567080 1015500 1120600 990180 907110 923250 663640 TRUE FALSE 751014.4631 854317.2534 765071.991 679246.7314 842885.6727 860357.6329 912567.1042 894951.6742 890022.4128 793667.5518 0.946258243 1.07641701 0.963970354 0.85583281 1.062013523 1.084027728 1.149810273 1.1276153 1.121404561 1 19.5981753 3.013046314 24.64807952 1.106918435 0.96785427 0.510482897 0.062649504 155.3449275 293486.7882 0.018366807 0.021941199 1030.49601 -3.013046314 -0.139064165 RSS(ph)DPALIGLSTSVSDSNFSSEEPSR ddPTM_MDA-MB-175_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(0.292)S(0.708)DPALIGLSTSVSDSNFSSEEPSR 341.01 1.03E-95 1409900000 193630 242150 214690 237500 224470 282850 217550 244400 239330 247300 TRUE FALSE 201274.6619 283737.3788 220284.9978 284476.7911 186314.6696 217162.3741 200497.8625 241124.2178 230716.5601 295753.7002 0.680548246 0.959370512 0.744825839 0.961870607 0.629965642 0.734267649 0.677921738 0.815287239 0.780096952 1 18.17403669 0.240619642 1.746261704 1.000017844 0.777872677 0.286297693 0.106074585 16.74084527 36.63953757 0.097374814 0.027252832 1.740282055 -0.240619642 -0.222145166 RSS(ph)DSWEVWGSASTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSDSWEVWGSASTNR 16 1 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 RSS(1)DSWEVWGSASTNR;RS(0.016)S(0.961)DS(0.023)WEVWGSASTNR;RS(0.02)S(0.487)DS(0.487)WEVWGS(0.006)AST(0.001)NR 280.35 1.96E-35 1227100000 1165820 1327230 1173029 1192898 1491970 1563350 1248820 1330870 1437670 1660080 TRUE FALSE 1211847.474 1555171.428 1203599.099 1428849.664 1238365.472 1200285.655 1150934.225 1313031.865 1385928.538 1985340.892 0.61039768 0.783327153 0.606243041 0.719699911 0.623754579 0.604574086 0.579716174 0.661363431 0.69808089 1 20.92095532 0.675967315 2.318723415 0.999945943 0.649046269 0.764277418 0.0582132 0.882377335 5.72096795 0.054546924 0.014717992 4.74206295 -0.675967315 -0.350899674 RSS(ph)DTEEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSDTEEESR 10 1 Q96IZ7-2;Q96IZ7;C9J713;C9J8Q2;C9JVB3;F8WDM0;C9J367 Q96IZ7-2 RSRC1 Serine/Arginine-related protein 53 1 RS(0.211)S(0.727)DT(0.061)EEESR;RS(0.261)S(0.736)DT(0.003)EEESR 190.57 5.43E-07 904680000 321240 398020 363640 318370 342890 417000 371340 346250 328980 377500 TRUE FALSE 333922.8033 466376.8388 373116.7571 381342.6358 284605.6803 320158.0697 342233.4005 341609.0851 317140.0741 451463.8973 0.739644532 1.033032412 0.826459789 0.844680246 0.630406289 0.70915542 0.758052643 0.756669774 0.70247051 1 18.7842511 3.456062641 24.42440075 0.745135759 0.875131918 0.156593105 0.112779339 248.6089293 288342.7039 0.028947041 0.039198563 2858.002739 -3.456062641 0.129996159 RSS(ph)GREEDDEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.313)S(0.687)GREEDDEELLR;RS(0.374)S(0.626)GREEDDEELLR 191.97 3.36E-07 2615000000 379126 377232 384148 335025 477943 457950 395116 429033 421563 435947 TRUE FALSE 394094.1872 442018.6615 394159.2125 401291.9451 396702.4196 351598.0528 364145.7755 423282.5144 406391.03 521362.4679 0.755892899 0.847814503 0.756017621 0.769698568 0.760895622 0.67438313 0.698450306 0.81187761 0.779478875 1 18.9919272 0.444812059 1.278756016 0.99993848 0.75752069 0.708834864 0.046150804 1.473644787 2.823809975 0.047042668 0.014021671 2.784915736 -0.444812059 -0.242417789 RSS(ph)ITEPEGPGGPNIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSITEPEGPGGPNIQK 17 1 Q96KQ4;A0A3B3ISJ2;H0YJL1 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 RS(0.373)S(0.627)IT(0.001)EPEGPGGPNIQK;RS(0.341)S(0.596)IT(0.063)EPEGPGGPNIQK;RS(0.38)S(0.615)IT(0.005)EPEGPGGPNIQK 194.25 5.21E-11 925410000 914380 1204460 1173579 830290 1830680 1574050 835657 1269020 1156800 1441490 TRUE FALSE 950480.4285 1411316.636 1204163.433 994518.8838 1519501.668 1208500.742 770156.0208 1252010.863 1115166.994 1723922.367 0.551347582 0.818666004 0.698502123 0.57689308 0.881421169 0.701018077 0.446746348 0.726257102 0.646877734 1 20.71726338 -2.101167331 2.269599418 1.551181378 0.675151394 0.400344677 0.120382784 10344058.38 2891243.077 29425067.73 0.028127171 0.00792196 2.101167331 -0.876029984 RSS(ph)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.179)S(0.821)LDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 169.07 5.58E-22 3279000000 999600 843080 1230100 926700 1525800 1393200 1345600 1240500 1224400 704100 TRUE FALSE 1039064.98 987872.4317 1262157.417 1109998.494 1266445.061 1069650.414 1240128.356 1223873.127 1180334.083 842054.9142 1.233963442 1.173168656 1.498901551 1.318202026 1.503993433 1.270285816 1.472740477 1.453436238 1.401730532 1 19.6835548 4.254275834 24.93559898 1.389768431 1.203565939 0.149274998 0.144638777 324.4702178 514832.7861 0.031441139 0.085473495 17958.7388 -4.254275834 -0.186202492 RSS(ph)LLNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.25)S(0.75)LLNAK 84.053 0.010856 677960000 912650 349050 657190 361860 699940 845290 677350 521710 575560 382550 TRUE FALSE 948682.1267 408996.6223 674316.9113 433434.828 580964.4488 648984.208 624257.5371 514717.3308 554845.708 457503.3481 2.07360696 0.893975146 1.473905959 0.947391598 1.269858354 1.418534336 1.364487363 1.12505697 1.212768628 1 18.80342278 4.751985097 24.64393185 1.208441145 2.073607653 0.660319324 0.189786299 1082.810179 1987721.583 0.04213751 0.815864697 56491.75889 -4.751985097 0.865166508 RSS(ph)LLSLMTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSLLSLMTGK 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 RS(0.035)S(0.884)LLS(0.08)LMTGK;RSS(0.987)LLS(0.012)LMTGK 200.05 5.10E-08 2707300000 3274000 2774800 3262600 3075200 4809400 4031000 3655200 3182500 3303600 2942200 TRUE FALSE 3403260.048 3251350.315 3347626.036 3683465.381 3991899.906 3094861.34 3368695.873 3139843.793 3184704.081 3518667.758 0.967201305 0.924028791 0.951390204 1.046835233 1.134491853 0.879554864 0.957378219 0.892338808 0.905088033 1 21.74659787 RSS(ph)LPLDHGSPAQENPESEKS(ph)SPAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSLPLDHGSPAQENPESEKSSPAVSR 27 2 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 RS(0.461)S(0.539)LPLDHGSPAQENPES(0.103)EKS(0.612)S(0.285)PAVSR;RS(0.458)S(0.542)LPLDHGSPAQENPES(0.196)EKS(0.435)S(0.368)PAVSR 171.2 2.54E-12 577160000 66745 216640 221053 219026 309585 307856 247053 280422 225265 218962 TRUE FALSE 69380.14414 253846.2348 226813.8228 262348.6891 256961.8523 236361.1096 227688.3403 276663.4018 217157.7567 261863.4116 0.264947836 0.969384127 0.866153165 1.00185317 0.981282 0.902612198 0.869492759 1.056517977 0.829278727 1 17.99845497 4.739813037 24.96694787 0.944916392 0.264947612 0.896288225 0.069069628 28.67625323 571595.5353 0.015645625 0.097407029 54930.43479 -4.739813037 -0.679968779 RSS(ph)LS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLSPGR 8 1 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 2 RS(0.039)S(0.962)LS(0.999)PGR 66.538 0.041054 412110000 419770 576380 502630 508480 614760 693730 527330 544110 533280 515840 TRUE FALSE 436342.8437 675368.7814 515728.9507 609055.8263 510263.3148 532621.7211 485996.4967 536817.0954 514087.357 616908.9716 0.707305071 1.094762457 0.835988735 0.987270172 0.827129023 0.863371657 0.787792882 0.870172295 0.833327737 1 19.2346981 3.204360274 24.99970368 0.8529942 0.914766658 0.029006241 0.106874701 482.6889154 352833.7976 0.028095778 0.033578655 1600.885511 -3.204360274 0.061772458 RSS(ph)LSLEEADSEVEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLSLEEADSEVEGR 16 1 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 RS(0.424)S(0.574)LS(0.002)LEEADSEVEGR 223.44 9.68E-14 0 147220 170940 169990 162830 184980 195550 156580 181910 165840 156920 TRUE FALSE 153032.3593 200297.6153 174420.079 195037.288 153537.1657 150136.4761 144306.8505 179471.794 159871.4508 187665.4696 0.815452942 1.06731204 0.929420204 1.039281699 0.818142869 0.80002185 0.768957927 0.956338928 0.851895936 1 17.51780369 3.228940656 24.99675323 0.860471752 0.96793807 0.213214231 0.09069364 276.2394754 717786.6626 0.025305875 0.030611089 1694.106294 -3.228940656 0.107466318 RSS(ph)LSSHSHQSQIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLSSHSHQSQIYR 15 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 RS(0.23)S(0.768)LS(0.001)SHSHQSQIYR 216.9 1.01E-12 261230000 6469.7 43917 30497 39295 41966 68447 18975 51280 33349 87280 TRUE FALSE 6725.128752 51459.40312 31291.77687 47067.43372 34832.63431 52551.22157 17487.68992 50592.67548 32148.776 104380.8449 0.064428763 0.492996614 0.299784667 0.450920222 0.33370715 0.503456564 0.167537348 0.484693102 0.307994978 1 16.67149746 -4.872480296 0.396170096 9.999999994 0.34363004 0.667446103 0.138588504 343.6732944 2.703088775 2662.843897 0.078098018 1.34E-05 4.872480296 -9.656369955 RSS(ph)LYGIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSLYGIAK 9 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 RS(0.219)S(0.78)LY(0.001)GIAK;RS(0.171)S(0.829)LYGIAK;RS(0.194)S(0.806)LYGIAK 126.1 0.00029588 1013760000 1732140 1554770 1826140 1480360 2558170 2386810 2109220 1822840 1913350 1793970 TRUE FALSE 1800526.225 1821789.653 1873730.709 1773170.79 2123333.177 1832509.55 1943893.825 1798407.811 1844488.907 2145464.074 0.839224598 0.849135474 0.87334518 0.82647424 0.989684797 0.854132014 0.906048183 0.838237206 0.859715588 1 21.03285831 -2.483428158 2.238423001 2.558768087 0.870984133 0.4260968 0.045028223 2211834.301 303667.8575 17414757.52 0.010664201 0.003285276 2.483428158 -1.687783954 RSS(ph)NPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSNPPAR 8 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 RS(0.224)S(0.776)NPPAR;RS(0.064)S(0.936)NPPAR 126.03 0.00075756 489950000 100620 161782 145562 129403 149974 162756 139462 169185 146499 171670 TRUE FALSE 104592.5553 189566.8 149355.4653 154998.5272 124481.473 124958.3856 128530.604 166917.3518 141226.5296 205305.4497 0.509448509 0.923340322 0.727479302 0.754965479 0.606323277 0.608646219 0.626045749 0.813019587 0.687884953 1 17.6474124 0.118320235 0.894887978 1.003402368 0.697473959 0.398338229 0.112100771 4.762160331 3.955016409 0.155117068 0.034961568 1.313167832 -0.118320235 -0.305928409 RSS(ph)PESDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSPESDR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 RS(0.019)S(0.981)PESDR;RS(0.267)S(0.733)PESDR 130.01 0.00065316 308080000 53278 74878 60943 54769 57620 71281 59508 56439 61617 64893 TRUE FALSE 55381.45658 87737.71403 62531.22465 65602.14473 47825.77298 54727.06802 54843.60746 55682.52752 59399.41621 77607.5409 0.713609218 1.130530784 0.805736452 0.845306319 0.616251622 0.705177195 0.706678846 0.717488621 0.765382017 1 16.24390922 3.705104741 2.383047865 0.733725454 0.919587785 0.137482802 0.137207189 0.395139976 4.391488654 0.035405431 0.067146985 5071.12997 -3.705104741 0.185862331 RSS(ph)PPGHYYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSPPGHYYQK 11 1 D6RDK6;D6RBN5;Q9NX40;D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;Q9NX40-3;Q9NX40-2;Q9NX40-4 D6RDK6 OCIAD1 OCIA domain-containing protein 1 1 RS(0.17)S(0.824)PPGHY(0.004)Y(0.002)QK 64.374 0.042082 187130000 150230 210040 189400 209700 199370 287860 196080 191550 176610 243980 TRUE FALSE 156161.1964 246112.7361 194335.9196 251178.0341 165481.1586 221008.8776 180710.7372 188982.5856 170253.8406 291783.2097 0.535195965 0.843478062 0.666028452 0.860837861 0.567137358 0.757442067 0.6193322 0.647681495 0.583494303 1 18.15453734 -1.084167459 4.926561333 1.000009841 0.680139142 0.454634642 0.106477988 1.06E-05 1.97E-06 0.095012735 0.022394028 0.08238204 1.084167459 -0.319870699 RSS(ph)PVPPVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSPVPPVPER 11 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.238)S(0.762)PVPPVPER;RS(0.182)S(0.818)PVPPVPER 112.96 0.0008914 3160400000 1636550 1923950 1570130 1762290 1891840 2305540 1804190 1758330 1672600 1876070 TRUE FALSE 1701162.258 2254373.446 1611048.878 2110865.702 1570265.713 1770113.276 1662772.873 1734762.462 1612403.453 2243649.997 0.758211958 1.004779466 0.718048216 0.940817732 0.699871065 0.788943587 0.741101721 0.773187647 0.718651953 1 21.09741621 3.233668443 24.99999772 0.772674247 0.856314268 0.077725657 0.109124623 244.701901 1250476.231 0.028253798 0.034790675 1712.649308 -3.233668443 0.083640021 RSS(ph)PVPPVPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSPVPPVPERR 12 2 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 RS(0.414)S(0.586)PVPPVPERR;RS(0.396)S(0.604)PVPPVPERR 64.454 0.049991 675770000 159535 190778 175886 163475 201945 248750 160121 173340 179715 198306 TRUE FALSE 165833.565 223542.6375 180469.7337 195809.8671 167618.461 190981.5823 147570.2976 171016.6608 173247.0923 237160.2639 0.699246839 0.942580489 0.760961093 0.825643655 0.706772957 0.805284912 0.622238714 0.721101664 0.730506407 1 17.85550278 3.249545786 24.65595649 0.740868686 0.81348843 0.007733542 0.109386913 437.9107459 982873.5412 0.028133724 0.037717127 1776.420538 -3.249545786 0.072619744 RSS(ph)RDMAGGAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSRDMAGGAGPR 13 2 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 RS(0.049)S(0.951)RDMAGGAGPR 133.16 8.70E-05 200430000 50108 79398 77688 45977 93255 82704 31200 58594 71151 140060 TRUE FALSE 52086.30253 93033.98887 79712.6131 55071.11337 77403.54841 63497.24939 28754.46247 57808.64327 68590.28941 167502.0754 0.310959147 0.555419917 0.475890301 0.328778693 0.462105011 0.379083359 0.171666306 0.345121952 0.409489191 1 17.35381945 0.880259789 10.51655334 0.999999999 0.376997993 0.777254175 0.099360485 20.37884097 1790.441137 0.101339799 0.025345308 7.590314817 -0.880259789 -0.623002006 RSS(ph)RSS(ph)PELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSRSSPELTR 11 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 RS(0.396)S(0.603)RS(0.096)S(0.904)PELTR 113.94 0.0065122 2173200000 1552100 1663700 1566100 1720800 1752500 2097700 1736500 1774800 1794900 1691200 TRUE FALSE 1613378.106 1949427.533 1606913.853 2061169.104 1454610.676 1610540.966 1600388.593 1751011.709 1730301.9 2022558.26 0.797691784 0.963842462 0.794495706 1.019090102 0.719193461 0.796289035 0.791269465 0.865741049 0.855501636 1 20.94774983 0.477831616 1.804356238 0.999974404 0.844412678 0.236056706 0.084074927 5.870419354 18.6191114 0.076685429 0.021443794 3.004911015 -0.477831616 -0.155561726 RSS(ph)S(ph)PAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSSPAELDLKDDLQQTQGK 20 2 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 2 RS(0.514)S(0.626)S(0.859)PAELDLKDDLQQTQGK 203.47 5.68E-22 182600000 180500 74226 111140 90854 162340 179600 145010 106720 124010 76253 TRUE FALSE 187626.2794 86973.7381 114036.3997 108824.65 134745.5048 137890.6219 133643.7373 105289.593 119546.9043 91193.3154 2.057456498 0.953729314 1.250490776 1.193340209 1.477580941 1.512069402 1.465499272 1.154575777 1.310917404 1 16.47664046 0.945293293 1.01304481 1.010592599 1.380738945 0.156732504 0.276790466 1.188156561 2.541524576 0.249591228 0.082107566 8.816440746 -0.945293293 0.370146345 RSS(ph)SEGLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSSEGLSK 9 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 RS(0.004)S(0.98)S(0.015)EGLSK;RS(0.026)S(0.972)S(0.003)EGLSK;RS(0.264)S(0.736)SEGLSK 182.37 2.84E-05 669050000 565140 468930 570790 470580 765500 768250 696950 631640 688500 542110 TRUE FALSE 587452.1636 549465.0797 585665.2563 563659.3195 635380.5834 589835.5804 642321.2379 623173.899 663721.0195 648326.0752 0.906106026 0.847513467 0.90334984 0.869407141 0.980032437 0.909782289 0.990737936 0.961204435 1.023745681 1 19.30636007 2.719988925 0.605554959 1.005128577 0.86929158 0.68699243 0.031735146 0.446029127 0.34766607 0.023632542 0.025719232 524.7940776 -2.719988925 -0.135836997 RSS(ph)SLKER ddPTM_MDA-MB-175_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(0.008)S(0.74)S(0.252)LKER 71.159 0.038955 3555300000 653820 432350 656260 389810 757420 720770 711780 621910 742710 498690 TRUE FALSE 679633.3185 506602.7493 673362.6747 466913.2545 628674.0189 553382.0909 655988.8237 613574.3137 715980.0122 596398.7575 1.139561929 0.849436292 1.129047749 0.782887705 1.054116916 0.927872642 1.099916483 1.028798779 1.20050554 1 19.18591773 2.229243988 24.98140383 1.079258415 0.975648106 0.153832101 0.116567895 347.35264 931376.3516 0.039525941 0.029585398 169.528995 -2.229243988 -0.103610309 RSS(ph)SPAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSSPAELDLKDDLQQTQGK 20 2 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RS(0.241)S(0.379)S(0.379)PAELDLKDDLQQTQGK 140.97 1.02E-07 137900000 309340 220770 245970 201130 379620 337980 251200 246800 310450 267340 TRUE FALSE 321552.9821 258685.5301 252380.1803 240912.9137 315092.328 259489.2671 231510.2876 243492.0497 299276.9651 319720.1545 1.005732599 0.809099854 0.789378388 0.753511814 0.985525384 0.81161373 0.724102889 0.761578669 0.936059116 1 18.28645017 4.741675415 24.21910256 0.824786464 1.005732698 0.196302799 0.094765075 274.5808481 2134836.167 0.022036705 0.156193336 55166.49794 -4.741675415 0.180946234 RSS(ph)TSGDT(ph)EEEEEEEVVPFSSDEQKR ddPTM_MDA-MB-175_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(0.276)S(0.336)T(0.138)S(0.251)GDT(1)EEEEEEEVVPFSSDEQKR 172.74 8.49E-12 101090000 94685 75070 95444 69202 140810 122770 111580 87465 120750 79921 TRUE FALSE 98423.23691 87962.68854 97931.34905 82889.94905 116875.1665 94258.5281 102834.068 86292.67474 116404.2311 95579.98977 1.029747305 0.920304436 1.024600958 0.867231198 1.222799529 0.986174285 1.075895366 0.902832015 1.217872395 1 16.54442099 RSS(ph)TSSEPTPTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RSS(0.932)T(0.067)SSEPTPTVK 289.23 1.81E-40 900610000 803780 687870 730020 630460 1072900 992950 968630 840830 992560 792230 TRUE FALSE 835513.8551 806006.3216 749044.9209 755163.1063 890528.8412 762352.4108 892706.2496 829560.0492 956837.9595 947452.3003 0.881853213 0.850709129 0.79058853 0.797046042 0.939919446 0.804634081 0.942217618 0.875569196 1.009906208 1 19.85369379 1.493362938 0.847556956 1.00975639 0.84072046 0.558750413 0.051161104 0.39884009 0.586553955 0.045241483 0.018042518 31.14317869 -1.493362938 -0.16903593 RSS(ph)VTVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSSVTVEER 9 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 RS(0.204)S(0.796)VTVEER;RS(0.185)S(0.815)VTVEER;RS(0.185)S(0.815)VTVEER 188.15 2.43E-05 882900000 309196 346665 346028 324440 390937 446280 357219 348859 374667 415088 TRUE FALSE 321403.2968 406202.0171 355045.7739 388613.2636 324485.6684 342638.2334 329219.2414 344183.1157 361182.8079 496416.5463 0.647446785 0.818268489 0.715217445 0.782837048 0.653656029 0.690223233 0.663191515 0.693335301 0.727580115 1 18.92119168 -1.668209493 4.426580829 1.009852601 0.710099879 0.73458655 0.052259676 0.005091257 0.000381611 0.050697904 0.011673691 0.021467947 1.668209493 -0.299752722 RSSEAS(ph)QSDGLPSLLSLTPAQQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSEASQSDGLPSLLSLTPAQQYR 24 1 A0A2R8YGX0;P10071 A0A2R8YGX0 GLI3 Transcriptional activator GLI3;Transcriptional repressor GLI3R 1 RS(0.176)S(0.176)EAS(0.286)QS(0.286)DGLPS(0.076)LLSLTPAQQYR 75.646 0.014707 85491000 23089 21254 26300 25336 28137 25229 24867 25856 24939 22495 TRUE FALSE 24000.57155 24904.20917 26985.39961 30347.38518 23354.28279 19369.9471 22917.85956 25509.44261 24041.45026 26902.46456 0.892132819 0.925722218 1.003082805 1.128052232 0.868109416 0.720006416 0.85188699 0.948219542 0.893652335 1 14.71545072 RSSLDAEIDS(ph)LTSILADLECS(ph)SPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 2 RS(0.062)S(0.063)LDAEIDS(0.284)LT(0.286)S(0.287)ILADLECS(0.093)S(0.093)PY(0.089)KPRPPQS(0.093)S(0.093)T(0.093)GS(0.093)T(0.093)AS(0.086)PPVS(0.086)T(0.098)PVT(0.007)GHK 43.062 0.02008 761290000 25212 18709 21367 15684 21884 24976 22369 21102 19461 9165.5 TRUE FALSE 26207.38923 21922.12521 21923.84157 18786.24839 18164.1655 19175.70251 20615.65933 20819.16221 18760.60241 10961.30424 2.390900631 1.999955911 2.000112495 1.713869807 1.657117173 1.749399715 1.880767003 1.899332575 1.711530124 1 13.42013185 -2.004631465 0.165816558 5.42E-29 2.185898014 0.738969744 0.171273524 23.9028904 0.576208186 10.874741 0.875295495 0.009893923 2.004631465 2.185898014 RSSLDAEIDSLT(ph)SILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 RS(0.011)S(0.013)LDAEIDS(0.251)LT(0.362)S(0.362)ILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHK 131.25 2.49E-11 8131100000 138520 113630 139910 161750 222630 158650 230580 153780 169750 104650 TRUE FALSE 143988.8766 133145.0686 143556.1695 193743.6672 184787.4321 121805.9419 212506.5371 151718.8306 163640.7307 125154.1639 1.150492098 1.063848493 1.147034706 1.548040123 1.4764785 0.973247219 1.697958186 1.212255557 1.307513275 1 16.93334676 3.971246076 23.22698878 1.33460203 1.106738024 0.147395125 0.214407243 440.3725006 355728.154 0.051787404 0.093667897 9359.358359 -3.971246076 -0.227864006 RSSPS(ph)ARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 RS(0.228)S(0.228)PS(0.544)ARPPDVPGQQPQAAK 159.7 1.31E-11 1517700000 676810 541870 720100 485320 794220 807160 725250 728580 714130 550190 TRUE FALSE 703530.9814 634931.9573 738866.3976 581314.8475 659218.7681 619709.3226 668403.0099 718814.5768 688428.6008 657989.1965 1.069213576 0.964958028 1.122915698 0.88347172 1.001868681 0.941822945 1.015826724 1.092441306 1.046261252 1 19.32770437 1.988098035 24.14727809 1.055912597 0.995150658 0.094853304 0.065296012 661.0790217 1341228.381 0.024740137 0.016936544 97.29668298 -1.988098035 -0.060761939 RSSS(ph)LKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.329)S(0.329)S(0.341)LKER;RSS(0.01)S(0.99)LKER;RS(0.012)S(0.135)S(0.853)LKER;RS(0.132)S(0.132)S(0.736)LKER 139.86 0.00034378 7416660000 2478090 1833950 2543970 1584450 2832160 2865260 2842460 2525200 2913220 1873220 TRUE FALSE 2575926.907 2148916.646 2610267.948 1897849.481 2350750.455 2199846.788 2619660.558 2491353.824 2808373.781 2240241.594 1.149843353 0.959234331 1.165172522 0.847162862 1.049328992 0.981968549 1.169365199 1.112091585 1.253603088 1 21.09522289 2.235290733 24.99856658 1.140720809 1.021774112 0.205350268 0.103871944 119.4424998 913134.2998 0.035379306 0.027214102 171.9058804 -2.235290733 -0.118946697 RSSS(ph)PAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSSSPAELDLKDDLQQTQGK 20 2 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 RS(0.064)S(0.064)S(0.873)PAELDLKDDLQQTQGK;RS(0.241)S(0.241)S(0.518)PAELDLKDDLQQTQGK 277.27 7.39E-45 970800000 468860 254200 355780 251420 457100 458090 375790 358350 382000 315720 TRUE FALSE 487370.9548 297856.8726 365051.9191 301150.1256 379402.3053 351705.5399 346334.5979 353546.9044 368251.8946 377579.2892 1.290777775 0.788859138 0.966821882 0.797581155 1.004828168 0.93147466 0.917249986 0.936351422 0.975296859 1 18.52642011 4.751804655 24.99944261 0.922730861 1.290778014 0.702066161 0.071619693 1135.926239 2144136.535 0.015635244 0.302719971 56468.2924 -4.751804655 0.368047153 RSST(ph)SSEPTPTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSSTSSEPTPTVK 13 1 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 RS(0.265)S(0.265)T(0.369)S(0.05)S(0.05)EPTPTVK 84.14 0.010959 0 122680 102210 137890 112830 167430 179100 157680 147900 162030 147040 TRUE FALSE 127523.5011 119763.7724 141483.5267 135147.4372 138970.3084 137506.7393 145320.6296 145917.6424 156198.572 175849.6727 0.725184751 0.681057693 0.804570884 0.7685396 0.790279028 0.781956185 0.826391243 0.829786261 0.888250569 1 17.42398312 -5 0.057988981 1.88492472 0.406444519 0.896550977 0.026837787 116.4982911 0.494971223 14.59161055 2.584478715 1.00E-05 5 -1.478480201 RSSTS(ph)GDTEEEEEEEVVPFSSDEQKR ddPTM_MDA-MB-175_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(0.216)S(0.216)T(0.059)S(0.426)GDT(0.082)EEEEEEEVVPFSSDEQKR 146.03 1.12E-07 158970000 108020 92239 108810 76100 137960 138750 122280 100350 122570 82578 TRUE FALSE 112284.713 108080.3307 111645.678 91152.35286 114509.6085 106527.4153 112695.3741 99004.97239 118158.7296 98757.57805 1.136973134 1.094400378 1.13050239 0.922990971 1.159501992 1.078675858 1.141131408 1.002505067 1.196452282 1 16.59160384 -1.483706596 3.035708155 0.997605635 1.088706439 0.117851645 0.076466631 22513457.59 31376808.52 466845.807 0.017113006 0.032831703 1.483706596 0.091100804 RST(ph)S(ph)PIIGSPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.232)T(0.678)S(0.792)PIIGS(0.298)PPVR 103.17 0.0036146 233940000 195900 235700 232700 242610 281540 309860 251140 275560 250390 283690 TRUE FALSE 203634.2833 276179.6415 238764.3532 290597.5339 233683.9314 237899.711 231454.9906 271866.5689 241378.5128 339273.6239 0.600206644 0.814032162 0.703751593 0.856528517 0.688777184 0.701203083 0.68220744 0.801319495 0.711456759 1 18.37208975 -4.999997186 0.439184622 6.577419852 0.731504054 0.562912228 0.071516634 822.2988041 4.965468059 4448.375311 0.03659301 1.00E-05 4.999997186 -5.845915798 RST(ph)SPIIGS(ph)PPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 RS(0.384)T(0.461)S(0.155)PIIGS(1)PPVR;RS(0.316)T(0.386)S(0.298)PIIGS(1)PPVR;RS(0.367)T(0.517)S(0.123)PIIGS(0.993)PPVR 114.06 0.0017114 1354180000 470870 524860 550470 552680 608020 680800 558220 592560 579550 695020 TRUE FALSE 489460.3112 615000.6222 564815.7004 661998.4544 504668.9776 522694.5176 514465.2578 584617.7024 558692.1087 831195.862 0.588862786 0.739898561 0.67952179 0.796440989 0.607160118 0.62884639 0.618945884 0.703345299 0.672154584 1 19.66482895 -0.14355191 1.411543366 1.000782046 0.672588497 0.725418383 0.060788747 17.73073484 20.79078707 0.128384462 0.016702366 0.718535268 0.14355191 -0.328193549 RSTAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RSTAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 38 1 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 RSTAPSAAASASASAAAS(0.047)S(0.953)PAGGGAEALELLEHCGVCR;RSTAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;RSTAPSAAASASASAAAS(0.013)S(0.987)PAGGGAEALELLEHCGVCR 168.89 2.26E-18 826561000 186121 219450 236865 157754 270786 284134 155889.1 192245 237357 322606 TRUE FALSE 193469.2008 257138.8304 243037.8965 188957.2704 224757.8924 218148.1846 143670.105 189668.2702 228814.5679 385814.469 0.501456571 0.666483118 0.629934634 0.489762011 0.582554338 0.565422508 0.37238133 0.491604866 0.593068913 1 18.55754772 0.860823353 6.098307104 0.999998419 0.535547212 0.757202174 0.07808652 1.524680298 66.66520501 0.081120264 0.020391277 7.25810677 -0.860823353 -0.464451208 RSTS(ph)PIIGSPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 1 RS(0.021)T(0.059)S(0.92)PIIGSPPVR 107.7 0.00078067 842170000 513870 616430 433170 386940 412410 482270 311420 407220 320810 445550 TRUE FALSE 534157.9844 722297.0573 444458.7661 463475.5771 342308.6955 370270.1014 287010.0867 401761.882 309264.1108 532846.9919 1.002460354 1.355543089 0.834120813 0.869809878 0.642414616 0.694890104 0.538635089 0.753991086 0.580399468 1 19.02336179 3.923057381 1.884206126 0.69162941 1.17627114 0.54265165 0.157555793 0.221400661 1.518251064 0.040309782 0.106118239 8376.399485 -3.923057381 0.484641729 RSVSDNDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 104.22 0.0064198 2908370000 3896040 4119670 3938030 3787710 4921340 5127130 4305170 4389220 4164810 4922520 FALSE TRUE 4049858.668 4827191.276 4040658.297 4536907.733 4084812.385 3936431.76 3967719.526 4330389.685 4014919.302 5886993.547 0.687933261 0.819975636 0.686370431 0.770666334 0.693870709 0.668665887 0.673980614 0.735585941 0.681998251 1 22.48909962 -1.747194481 4.357399451 1.022541856 0.715184054 0.775099659 0.046331249 0.010054939 0.000583363 0.044457667 0.0102071 0.017898042 1.747194481 -0.307357802 RSYDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ; 132.36 5.11E-06 327060000 95927 90699 101686 74640 154114 145270 97812 117495 116233 114517 FALSE TRUE 99714.27203 106275.8477 104336.0207 89403.56922 127917.7573 111533.2441 90145.23986 115920.1717 112049.797 136954.4136 0.72808367 0.775994325 0.761830291 0.652798014 0.93401705 0.814382254 0.65821347 0.846414282 0.818153969 1 17.06333623 -5 0.193895232 1.998162754 0.737343987 0.448888362 0.077725016 128.3855036 1.262447034 49.34339912 0.19851201 1.00E-05 5 -1.260818767 RSYS(ph)PDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSYSPDGK 8 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.041)YS(0.959)PDGK;RS(0.01)YS(0.99)PDGK 95.618 0.0058326 846410000 324870 186230 251200 189243 288700 304380 287070 221250 241960 162556 TRUE FALSE 337696.1185 218213.5538 257746.4784 226674.7006 239626.8771 233692.3579 264568.7033 218284.5056 233251.9069 194405.7359 1.737068698 1.122464586 1.325817251 1.165987719 1.232612176 1.202085715 1.360909965 1.122829554 1.199820087 1 17.56871126 4.744001193 24.99327439 1.205074198 1.737068923 0.732737901 0.098402376 279.5014896 1283953.524 0.02127887 0.184928045 55462.72362 -4.744001193 0.531994725 RSYS(ph)PDGKESPSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RSYSPDGKESPSDKK 15 3 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 RS(0.054)YS(0.946)PDGKESPSDKK 128.05 0.00041127 138720000 230590 69620 122650 50916 232890 171200 135940 122610 170580 73672 TRUE FALSE 239693.8713 81576.69343 125846.3598 60987.03283 193303.441 131441.3946 125284.6676 120966.6135 164440.8591 88106.61786 2.720497927 0.925886107 1.428341739 0.692195823 2.193971868 1.491844742 1.421966597 1.372957179 1.866384877 1 16.42696277 -1.74145094 2.795778498 0.902012881 1.517770103 0.079578429 0.556421919 35599654.84 32975005.84 24353740.29 0.124922358 0.018136315 1.74145094 0.615757221 RSYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RSYSPR 6 1 P11274-2;P11274;O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 P11274-2;O75494-2;O75494-6;Q5JRI1 BCR;SRSF10 Breakpoint cluster region protein;Serine/arginine-rich splicing factor 10 1 RS(0.313)YS(0.687)PR;RS(0.293)YS(0.707)PR 83.429 0.060377 765130000 712250 759700 788410 712700 847390 957070 812500 762840 785960 873900 TRUE FALSE 740370.18 890172.5654 808956.6123 853669.9328 703350.9505 734804.997 748814.1269 752615.3776 757673.4531 1045123.973 0.708404169 0.85173873 0.774029333 0.816812124 0.672983271 0.703079267 0.716483543 0.720120672 0.724960361 1 19.99524266 -1.041328459 4.620939625 1.000007149 0.743319559 0.683560498 0.052421316 5.38E-06 1.12E-06 0.053047442 0.012502938 0.090922536 1.041328459 -0.25668759 RSYS(ph)SPDITQAIQEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RSYSSPDITQAIQEEEKR 18 2 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 RS(0.003)YS(0.868)S(0.129)PDITQAIQEEEKR;RS(0.058)YS(0.901)S(0.041)PDITQAIQEEEKR;RSYS(0.5)S(0.5)PDITQAIQEEEKR;RS(0.102)YS(0.864)S(0.034)PDITQAIQEEEKR;RS(0.002)YS(0.817)S(0.18)PDITQAIQEEEKR;RS(0.03)YS(0.878)S(0.091)PDITQAIQEEEKR 275.2 2.42E-39 1599717000 769556 585828 719762 532660 968833 968518 772719 733480 805060 583105 TRUE FALSE 799938.6651 686439.4019 738519.589 638018.5582 804151.1127 743594.3725 712151.2657 723648.9003 776086.0479 697353.2605 1.147106797 0.984349598 1.059032245 0.914914426 1.153147419 1.066309451 1.021220242 1.037707775 1.1129023 1 19.41153015 4.759642119 23.91758922 1.040242758 1.147106991 0.208915389 0.063149338 4510.14616 5116746.099 0.014336623 0.588875481 57496.594 -4.759642119 0.106864232 RT(ph)ASPPPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.537)AS(0.463)PPPPPK 68.809 0.034494 687240000 919260 762350 869470 782690 1107260 1077940 1048890 931500 933420 798090 TRUE FALSE 955553.0946 893277.6822 892129.1025 937503.7459 919048.3407 827604.7713 966675.261 919014.7661 899826.3965 954460.4551 1.001144772 0.935898054 0.934694672 0.982234246 0.962898291 0.867091734 1.012797603 0.962863114 0.942759222 1 19.8643259 -1.087763605 0.491676536 1.016040079 0.954620029 0.100029945 0.038815836 50.90225641 7.273704238 1.180429267 0.01836914 0.081702697 1.087763605 -0.06142005 RT(ph)GTPSDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTGTPSDPR 9 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 RT(0.497)GT(0.497)PS(0.005)DPR;RT(0.497)GT(0.497)PS(0.005)DPR;RT(0.499)GT(0.499)PS(0.001)DPR;RT(0.5)GT(0.5)PS(0.001)DPR 80.763 0.01359 2271073000 1745428 2176660 1747335 1734741 1861206 2199550 1760029 1873707 1635572 1982350 TRUE FALSE 1814338.845 2550484.423 1792871.986 2077867.592 1544838.869 1688737.847 1622073.328 1848593.022 1576708.083 2370753.528 0.765300494 1.075811717 0.756245626 0.876458716 0.651623566 0.712321136 0.684201588 0.779749139 0.665066218 1 21.17691425 3.727069478 1.809367068 0.739098919 0.906950029 0.144495455 0.12636649 0.503803325 3.196946928 0.033751228 0.072892922 5334.202246 -3.727069478 0.16785111 RT(ph)HS(ph)DASDDEAFTTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.85)HS(0.85)DAS(0.3)DDEAFTTSK 107.45 0.00097533 223540000 165910 131910 148490 136130 219560 226710 194710 159450 194250 140040 TRUE FALSE 172460.2549 154564.5164 152359.7714 163056.1077 182239.2696 174060.0383 179448.1214 157312.8336 187258.9804 167478.1568 1.029747749 0.922893584 0.909729211 0.973596264 1.088137541 1.03929994 1.071471796 0.939303588 1.118109872 1 17.35361342 3.430181927 8.687241093 1.034552559 0.949439806 0.354988995 0.054988896 0.318482182 54.21685565 0.015226078 0.020668116 2692.662529 -3.430181927 -0.085112753 RT(ph)HSEGSLLQEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTHSEGSLLQEPR 13 1 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RT(0.77)HS(0.23)EGSLLQEPR 142.94 2.38E-05 201850000 64866 135270 149360 137890 170780 183110 149350 163740 150460 210460 TRUE FALSE 67426.95977 158501.5702 153252.4443 165164.2304 141750.8766 140585.4776 137643.5567 161545.3331 145044.974 251695.6075 0.267890888 0.629735146 0.608880091 0.656206249 0.563183752 0.55855356 0.546865152 0.641828178 0.576271376 1 17.94132051 -5 0.227031799 3.266439328 0.520323013 0.643114611 0.100388546 99.22364371 0.993150741 103.1706617 0.1723635 1.00E-05 5 -2.746116316 RT(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTNSDSALHQSTMTPTQPESFSSGSQDVHQK 31 1 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 RT(0.238)NS(0.183)DS(0.183)ALHQS(0.183)T(0.183)MT(0.029)PTQPESFSSGSQDVHQK 115.18 2.43E-05 256380000 15895 70571 70321 62973 60892 100860 54990 91477 64143 80334 TRUE FALSE 16522.54687 82691.02028 72153.62303 75428.87144 50541.59959 77436.79355 50679.74011 90250.90044 61834.50596 96073.90921 0.17197746 0.860702151 0.751022037 0.785112962 0.526069981 0.806012727 0.527507838 0.939390321 0.643613927 1 16.55185707 1.664595488 0.064171478 1.526747327 1.62E-11 0.265791529 0.198414072 34.45257785 2.214370421 25.09719761 25.92650344 46.19505492 -1.664595488 -1.526747327 RT(ph)NSSSSSPVVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RT(0.474)NS(0.474)S(0.02)S(0.031)S(0.001)SPVVLK 125.18 0.00011909 101960000 147440 135740 168090 126920 207640 205880 165930 169890 182400 155040 TRUE FALSE 153261.045 159052.2891 172470.5635 152024.3972 172345.427 158067.4901 152923.973 167612.9024 175835.4596 185417.1196 0.826574404 0.857808003 0.930176048 0.819904858 0.929501156 0.852496741 0.824756492 0.90397749 0.948323758 1 17.50041493 1.175377469 2.084357385 0.996830437 0.866038523 0.586742179 0.037760583 0.199662275 1.560064076 0.033684905 0.009617007 14.97536682 -1.175377469 -0.130791913 RT(ph)PDSTFSETFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTPDSTFSETFK 12 1 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 RT(0.996)PDS(0.003)TFSETFK;RT(1)PDSTFSETFK 205.18 6.14E-08 683271000 563624 472500 530700 453880 636700 680670 662960 518090 534890 429540 TRUE FALSE 585876.3107 553648.1995 544530.478 543656.1093 528473.9614 522594.7082 610995.4629 511145.851 515639.4134 513700.139 1.140502535 1.077765329 1.060016217 1.058314118 1.028759623 1.017314711 1.189401008 0.995027667 1.00377511 1 18.97056694 8 0.129158005 0.988338561 1.379763734 0.249925806 0.052851133 137.0622726 1.198508613 0.287071071 9.768567497 100000000 -8 0.391425174 RT(ph)PDYFL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTPDYFL 7 1 P67775;P62714;P67775-2;H0YBN9 P67775 PPP2CA;PPP2CB Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform 1 RT(1)PDYFL;RT(1)PDYFL 128 0.0073519 187412000 336090 321340 398040 326870 512360 447650 508930 403580 366050 295520 TRUE FALSE 349359.0927 376527.6453 408413.2494 391523.9104 425269.2302 343690.0717 469038.7368 398170.6702 352875.932 353421.4859 0.988505528 1.06537848 1.155598246 1.107810153 1.203291953 0.972465131 1.327137018 1.126617045 0.998456365 1 18.43103022 4.550935737 3.03205126 1.125384814 0.988034496 0.108010401 0.101732588 0.528818544 8.422728873 0.023856755 0.137263228 35557.86991 -4.550935737 -0.137350318 RT(ph)PS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 2 RT(1)PS(1)DDEEDNLFAPPK 139.44 1.55E-06 194430000 297060 188720 221940 183610 280610 314310 285600 226350 260700 148940 TRUE FALSE 308788.1582 221131.192 227723.9387 219927.51 232912.0124 241316.2659 263213.9257 223316.1485 251317.4579 178121.9414 1.733577322 1.241459588 1.278472135 1.234701959 1.307598663 1.354781247 1.477717589 1.253726221 1.410929254 1 17.44250572 -2.19603589 2.277682109 0.017622586 1.351299932 0.362988591 0.144249617 2328505.463 679843.0265 11719930.49 0.033597205 0.006367429 2.19603589 1.333677346 RT(ph)PSTKPTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.576)PS(0.352)T(0.071)KPT(0.001)VR 76.073 0.059638 70254000 66008 59989 74404 55836 105270 94935 81372 77033 83920 84262 TRUE FALSE 68614.04681 70291.6441 76343.02936 66880.19415 87376.243 72887.785 74993.85001 76000.49864 80899.73559 100771.5256 0.680887249 0.697534782 0.757585329 0.663681469 0.867072742 0.723297425 0.744196831 0.754186246 0.802803521 1 16.62072852 -5 0.184204042 2.087128887 0.691339495 0.723960728 0.050157578 68.4790421 0.664353524 27.19077274 0.141846615 1.00E-05 5 -1.395789392 RT(ph)PTMPQEEAAACPPHILPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTPTMPQEEAAACPPHILPPEK 22 1 Q9NYV4 Q9NYV4 CDK12 Cyclin-dependent kinase 12 1 RT(0.987)PT(0.013)MPQEEAAACPPHILPPEK 126.42 1.50E-05 237170000 180130 212650 231690 218670 256510 301070 254410 228560 222580 175420 TRUE FALSE 187241.6715 249170.9833 237728.0317 261922.2733 212908.5218 231151.0553 234468.6794 225496.527 214569.3893 209790.1904 0.892518717 1.18771513 1.133170389 1.248496285 1.014864048 1.101820132 1.117634142 1.074866878 1.02278085 1 17.67858769 1.284562971 2.086790681 1.000519561 1.106849083 0.126720127 0.090506946 0.580653754 4.302555072 0.079290835 0.023334028 19.25586229 -1.284562971 0.106329522 RT(ph)QSGNFYTDTLGMAEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTQSGNFYTDTLGMAEFR 18 1 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 RT(0.5)QS(0.5)GNFYTDTLGMAEFR;RT(0.5)QS(0.5)GNFYTDTLGMAEFR;RT(0.5)QS(0.5)GNFYTDTLGMAEFR 163.71 1.90E-11 219192000 54970 73191 77707 59889 97433 101586 52611 76104 82280 115449 TRUE FALSE 57140.25805 85760.9849 79732.10826 71734.86545 80871.37346 77994.19105 48487.21235 75083.95036 79318.75887 138069.0211 0.413852851 0.621145744 0.577480072 0.519558007 0.58573149 0.564892765 0.351180967 0.543814606 0.574486284 1 17.07503013 0.664052039 2.630223116 0.999959357 0.523924584 0.771428374 0.07754632 1.25471978 9.269240662 0.073736216 0.019565004 4.613728549 -0.664052039 -0.476034772 RT(ph)SFSFQK ddPTM_MDA-MB-175_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(0.903)S(0.097)FSFQK 86.014 0.031595 619330000 1851900 1578600 1891300 1607900 2354400 2341900 2058200 1956100 2073800 1686200 TRUE FALSE 1925014.442 1849712.27 1940588.832 1925937.821 1954199.929 1798029.217 1896872.906 1929881.679 1999164.343 2016578.606 0.9545943 0.917252749 0.962317475 0.955052194 0.969067074 0.89162367 0.94063921 0.957007911 0.991364451 1 20.94347821 1.302668028 2.471863008 0.999807108 0.941289965 0.498293977 0.021528922 0.234659964 2.377266984 0.019366861 0.005721166 20.07557662 -1.302668028 -0.058517143 RT(ph)SFSTSDVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.483)S(0.483)FS(0.031)T(0.002)SDVSK;RT(0.477)S(0.477)FS(0.046)TSDVSK;RT(0.462)S(0.462)FS(0.074)T(0.001)SDVSK;RT(0.431)S(0.431)FS(0.13)T(0.007)S(0.001)DVSK 109.14 0.0011537 1614550000 2037740 1665890 2033420 1729380 3036240 2653950 2233640 1982560 2113460 2016120 TRUE FALSE 2118191.549 1951993.649 2086412.596 2071446.202 2520141.009 2037610.334 2058561.46 1955987.026 2037396.987 2411140.113 0.878502057 0.809572881 0.865322004 0.859114819 1.045207201 0.845081678 0.853770981 0.811229101 0.844993195 1 21.20128406 3.753713056 3.551447974 0.884098795 0.845103465 0.061157383 0.071958359 0.850032063 23.19950125 0.020113861 0.036386163 5671.697452 -3.753713056 -0.038995329 RT(ph)SHGEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSHGEPK 8 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 RT(0.615)S(0.385)HGEPK;RT(0.61)S(0.39)HGEPK 72.006 0.027702 74158000 64276 48730 51398 42794 71302 66283 68060 57728 69937 56492 TRUE FALSE 66813.66611 57098.99843 52737.4741 51258.52547 59182.11151 50889.77778 62725.27936 56954.25058 67419.98103 67560.5258 0.988945325 0.845153257 0.780595969 0.758705248 0.875986544 0.753247213 0.928430894 0.843010766 0.997919721 1 16.04389294 1.234712078 5.555475546 1.002552187 0.843005053 0.430488325 0.069862001 0.145830711 14.14608631 0.05752874 0.017033116 17.16769851 -1.234712078 -0.159547135 RT(ph)SLGEVSKGDTMENLDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSLGEVSKGDTMENLDGK 19 2 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 RT(0.5)S(0.5)LGEVSKGDTMENLDGK;RT(0.5)S(0.5)LGEVSKGDTMENLDGK 228.58 4.78E-18 618750000 1032720 565940 731350 460680 1120160 975980 973660 752800 941420 502530 TRUE FALSE 1073492.583 663135.7926 750409.5818 551801.129 929755.6033 749323.4361 897341.985 742709.9473 907538.4781 600991.132 1.786203699 1.103403623 1.248620058 0.918151866 1.547037142 1.2468128 1.493103537 1.235808497 1.510069666 1 19.19698418 -0.883299613 5.188930761 0.99999948 1.323912075 0.155071886 0.236520505 1.32E-06 2.83E-07 0.212001052 0.049969047 0.130827905 0.883299613 0.323912595 RT(ph)SMGGTQQQFVEGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSMGGTQQQFVEGVR 16 1 A0A2R8Y804;A0A2R8Y543;A0A2R8Y5C3;A0A2R8Y750;A0A2R8Y5Z1;B4DGU4;A0A2R8YCH5;A0A2R8Y5A3;P35222;A0A2R8Y6G0 A0A2R8Y804 CTNNB1 Catenin beta-1 1 RT(0.8)S(0.2)MGGTQQQFVEGVR;RT(0.5)S(0.5)MGGTQQQFVEGVR 219.87 7.04E-15 648370000 66990 73969 72770 92907 87841 107714 71191 78629 80263 101675 TRUE FALSE 69634.81693 86672.60035 74666.44598 111283.7273 72909.8182 82699.05592 65610.8634 77575.10687 77374.35031 121596.2696 0.572672313 0.712789962 0.614052111 0.915190307 0.599605715 0.680111785 0.539579575 0.637972753 0.636321744 1 16.89173944 -1.311763567 4.198619198 1.000442271 0.656970553 0.522300597 0.098557398 0.000396268 6.50E-05 0.092678193 0.02181674 0.048779398 1.311763567 -0.343471718 RT(ph)SNERPGSGQGQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.74)S(0.26)NERPGSGQGQGR;RT(0.962)S(0.038)NERPGSGQGQGR;RT(0.755)S(0.244)NERPGSGQGQGR 168.62 2.00E-06 1570040000 290330 306964 316059 275136 339796 380760 314477 323387 313583 348435 TRUE FALSE 301792.4526 359682.6792 324295.7572 329557.0796 282037.5973 292334.2605 289827.471 319052.5262 302297.2091 416704.1671 0.724236704 0.863160745 0.778239775 0.790865812 0.676829318 0.701539086 0.695523333 0.765657153 0.725448011 1 18.668664 -1.969742287 7.925411205 1.14500309 0.748126734 0.67807206 0.052325395 0.02783819 0.000106281 0.010520254 0.012546512 0.010721553 1.969742287 -0.396876356 RT(ph)SPQVLGSILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 RT(0.5)S(0.5)PQVLGSILK;RT(0.532)S(0.468)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK;RT(0.5)S(0.5)PQVLGSILK 178.14 1.31E-05 3145880000 3165660 2758670 2961980 2436510 4297460 3954660 3618350 3049880 3284510 3521140 TRUE FALSE 3290642.701 3232450.113 3039171.632 2918444.406 3566979.284 3036250.148 3334734.272 3009001.347 3166301.127 4211039.967 0.781432313 0.767613259 0.721715219 0.693046 0.847054246 0.721021451 0.791902784 0.71455065 0.751904791 1 22.00574514 -1.270316429 3.28048668 1.000998688 0.752650086 0.745955935 0.042973642 10383510.76 14628344.64 102880.3041 0.010045297 0.053664065 1.270316429 -0.248348602 RT(ph)SPSDGAMANYESTEVMGDGESAHDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTSPSDGAMANYESTEVMGDGESAHDSPR 29 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;F8W9S7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 RT(0.402)S(0.402)PS(0.197)DGAMANYESTEVMGDGESAHDSPR;RT(0.498)S(0.498)PS(0.004)DGAMANYESTEVMGDGESAHDSPR;RT(0.37)S(0.37)PS(0.257)DGAMANYES(0.002)TEVMGDGESAHDSPR;RT(0.499)S(0.499)PS(0.001)DGAMANYESTEVMGDGESAHDSPR 256.66 4.31E-58 1036760000 119040.3 230438 163518 236255 186450 342348 144529 235137 170113 258342 TRUE FALSE 123740.103 270013.9339 167779.4134 282985.5338 154757.2956 262842.8653 133200.4393 231985.3731 163990.6664 308959.1686 0.400506331 0.873946985 0.543047206 0.915931821 0.500898861 0.850736576 0.431126352 0.750860944 0.530784269 1 18.23705666 -1.340161822 3.139419562 1.002866506 0.655608927 0.254536699 0.18172605 214717553.1 284358607.5 5795016.411 0.038384487 0.045691791 1.340161822 -0.347257579 RT(ph)SSEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.494)S(0.494)S(0.013)EELR;RT(0.615)S(0.38)S(0.005)EELR 95.018 0.0058294 1764850000 262210 616310 512080 585660 536950 635950 577540 593420 479980 605840 TRUE FALSE 272562.2533 722156.4483 525425.2255 701501.8 445679.4308 488260.2504 532270.9057 585466.1755 462705.6136 724542.7485 0.376185192 0.996706474 0.725181815 0.968199325 0.615118199 0.67388743 0.734630092 0.808049182 0.63861741 1 19.46671129 -2.183169278 2.328933078 1.689193572 0.741969074 0.185692092 0.169109196 12188011.68 2389116.299 44369668.76 0.037311901 0.006558896 2.183169278 -0.947224498 RT(ph)SSEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.365)S(0.365)S(0.269)EELRDATSLLAAGEGGLLDEVEPLRPDELER;RT(0.2)S(0.2)S(0.2)EELRDAT(0.2)S(0.2)LLAAGEGGLLDEVEPLRPDELER;RT(0.31)S(0.31)S(0.31)EELRDAT(0.035)S(0.035)LLAAGEGGLLDEVEPLRPDELER;RT(0.322)S(0.322)S(0.322)EELRDAT(0.017)S(0.017)LLAAGEGGLLDEVEPLRPDELER;RT(0.333)S(0.333)S(0.333)EELRDAT(0.001)SLLAAGEGGLLDEVEPLRPDELER;RT(0.328)S(0.328)S(0.328)EELRDAT(0.008)S(0.008)LLAAGEGGLLDEVEPLRPDELER;RT(0.295)S(0.295)S(0.295)EELRDAT(0.058)S(0.058)LLAAGEGGLLDEVEPLRPDELER 214.58 2.18E-36 431834000 74920.4 101611.5 116571.3 85901.5 133738.7 117430.7 84189.8 112877.1 107094.6 139488.8 TRUE FALSE 77878.31524 119062.4847 119609.2438 102892.5603 111005.8435 90159.1996 77590.78349 111364.1671 103240.2863 166818.9597 0.46684331 0.713722738 0.717000298 0.616791763 0.665427022 0.540461347 0.465119694 0.667575001 0.618876214 1 17.34792374 0.259466485 1.662404372 1.000046283 0.609948714 0.649035273 0.086525036 6.395867756 13.53418651 0.083866753 0.023661079 1.817466794 -0.259466485 -0.390097568 RT(ph)SSLDTITGPYLTGQWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 RT(0.333)S(0.333)S(0.333)LDT(0.001)ITGPYLTGQWPR;RT(0.47)S(0.265)S(0.265)LDT(0.001)ITGPYLTGQWPR 216.58 2.23E-19 219816000 37282 40486 36441 39476 42400 43346 35834 40729 44210 48483 TRUE FALSE 38753.92215 47439.15556 37390.6824 47284.23498 35192.86314 33279.54841 33025.23745 40183.09437 42618.89074 57982.31559 0.668374861 0.818165937 0.644863559 0.815494078 0.606958566 0.57396032 0.569574311 0.693023277 0.735032575 1 15.82332533 0.752758471 2.34513427 0.999836464 0.672750488 0.585700832 0.082075723 0.816144664 6.567749487 0.081637313 0.022026041 5.659244675 -0.752758471 -0.327085976 RT(ph)SSPHKEESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSPHKEESPK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.46)S(0.46)S(0.08)PHKEESPK 119.96 0.021971 34486000 27294 15971 21445 14725 35056 32865 30030 21196 25993 16401 TRUE FALSE 28371.5882 18713.89501 22003.87432 17637.56105 29097.19364 25232.60182 27676.17013 20911.90229 25057.51701 19614.46193 1.446462732 0.954086585 1.121818911 0.899212077 1.483456122 1.286428448 1.411008379 1.06614713 1.277502136 1 14.25963014 3.245225981 24.99989795 1.256451613 1.095760526 0.127265922 0.190031006 310.4198774 1164290.474 0.051282083 0.067876494 1758.838569 -3.245225981 -0.160691087 RT(ph)SSPHKEESPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSPHKEESPKK 13 3 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.532)S(0.432)S(0.037)PHKEESPKK 54.234 0.073554 123880000 99532 43589 78713 44661 117980 94825 94375 83423 85174 35486 TRUE FALSE 103461.6002 51075.07167 80764.32544 53494.8125 97925.80174 72803.33084 86977.6409 82304.85114 82108.60438 42438.80228 2.43790104 1.203499367 1.903077399 1.260516547 2.307459129 1.715489762 2.049483874 1.939377332 1.934753103 1 15.37309632 -0.995195107 6.313358695 0.999999619 1.849094 0.323017907 0.373686651 1.85E-06 2.93E-07 0.329710541 0.077713485 0.10111251 0.995195107 0.849094381 RT(ph)SSTLDSEGTFNSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.437)S(0.437)S(0.102)T(0.024)LDSEGTFNSYR 136.68 9.45E-06 392210000 80096 93250 80490 65406 95740 103590 76348 78526 89657 118330 TRUE FALSE 83258.25193 109264.9621 82587.63552 78343.11158 79466.149 79532.79242 70363.64426 77473.48741 86430.26208 141514.4979 0.58833726 0.772111435 0.583598407 0.553604844 0.561540691 0.562011621 0.497218626 0.54745972 0.610751996 1 17.11059034 0.938694242 18.22332182 1.000000001 0.581051219 0.769941523 0.067982604 310.0762812 92172.15314 0.07058183 0.017646029 8.683488666 -0.938694242 -0.418948782 RT(ph)SVPS(ph)PEQPQPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 2 RT(0.556)S(0.445)VPS(0.999)PEQPQPYR;RT(0.546)S(0.455)VPS(1)PEQPQPYR 76.573 0.023443 370380000 120556 146177 146304 156296 186834 218150 167283 191458 182309 188287 TRUE FALSE 125315.644 171281.7627 150116.8024 187210.8823 155076.0234 167487.9686 154170.9213 188891.8187 175747.7347 225178.2327 0.556517575 0.760649733 0.666657699 0.831389784 0.688681235 0.743801773 0.684661743 0.838854699 0.780482787 1 17.78070785 -5 0.110401732 1.887527345 0.575818039 0.648442971 0.067666896 100.0133371 0.733850368 19.9081162 0.786456552 1.00E-05 5 -1.311709306 RTAQEVETYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTAQEVETYR 10 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;; 162.68 1.07E-05 625710000 192721 254057 227777 235636 243757 315169 258171 246778 224372 259497 FALSE TRUE 200329.7739 297689.3135 233713.0557 282244.0975 202323.2722 241975.7762 237934.8824 243470.3446 216296.8955 310340.4688 0.645516116 0.959234594 0.753085979 0.909465977 0.6519397 0.779710674 0.766689834 0.784526573 0.696966452 1 18.24349231 -1.171338787 4.318093094 1.000056443 0.777949883 0.338340968 0.095355949 3.267120819 50077886.21 5603.353921 0.020366101 0.067400204 1.171338787 -0.222106559 RTAS(ph)PPPPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTASPPPPPKR 11 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.029)AS(0.971)PPPPPKR;RT(0.088)AS(0.912)PPPPPKR 73.927 0.02203 879110000 273700 247899 292703 269426 360220 351050 308750 303696 314685 287965 TRUE FALSE 284505.8873 290473.7249 300331.0806 322717.6586 298989.9331 269523.9577 284549.3682 299625.4519 303359.5483 344386.2283 0.826124461 0.84345337 0.872076337 0.937080615 0.868182025 0.782621184 0.826250717 0.870027391 0.880870149 1 18.39366793 0.686745036 1.763389271 0.999872933 0.853371754 0.574121021 0.037884171 0.98259856 4.383653903 0.039238513 0.011060896 4.861217313 -0.686745036 -0.146501179 RTDALT(ph)SSPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.333)S(0.333)S(0.333)PGR 98.974 0.009906 19571000 46587 48669 48773 54040 53203 58270 58059 53183 46482 43929 TRUE FALSE 48426.29073 57027.52216 50044.06445 64728.95071 44159.57306 44737.67559 53508.18387 52470.16887 44809.1219 52536.04648 0.921772649 1.085493218 0.952566244 1.232086444 0.840557599 0.85156152 1.018504198 0.998746049 0.852921468 1 15.68102002 3.193390124 24.9999541 0.934684453 1.043846561 0.260882302 0.099122837 194.0244858 107383.6527 0.028401588 0.033946539 1560.95407 -3.193390124 0.109162108 RTDALTS(ph)SPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALTS(0.5)S(0.5)PGR;RTDALT(0.315)S(0.342)S(0.342)PGR;RT(0.111)DALT(0.064)S(0.413)S(0.413)PGR 170.74 9.40E-06 4910504000 1969181 2091325 1963036 2218600 1963107 2373487 2397435 2050010 1903098 1768698 TRUE FALSE 2046925.786 2450493.8 2014194.331 2657432.458 1629418.773 1822280.615 2209517.78 2022532.969 1834605.875 2115240.509 0.967703567 1.158494171 0.952229461 1.256326383 0.770323169 0.861500433 1.044570473 0.956171632 0.867327317 1 21.01239028 3.233302803 24.99999994 0.923566585 1.079641735 0.360345298 0.108740531 149.9066638 712780.234 0.030374554 0.037335073 1711.208005 -3.233302803 0.15607515 RTDALTSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 RTDALT(0.011)S(0.062)S(0.927)PGR;RTDALT(0.002)S(0.031)S(0.967)PGR;RTDALT(0.034)S(0.207)S(0.759)PGR;RTDALT(0.001)S(0.263)S(0.736)PGR 153.2 2.00E-05 10407870000 2809550 2848260 2689130 3344550 2635960 3442500 3503750 2894600 2767520 2462810 TRUE FALSE 2920473.203 3337426.499 2759210.937 4006092.008 2187900.461 2643031.547 3229116.92 2855802.622 2667917.496 2945350.466 0.991553717 1.133116937 0.936802248 1.360141027 0.74283196 0.897357234 1.096343867 0.96959688 0.905806466 1 21.49000788 3.223237008 24.99999893 0.945530733 1.095340188 0.276765265 0.13368951 351.9887266 574257.9108 0.03785443 0.045401473 1672.002831 -3.223237008 0.149809454 RTDDIPVWDQEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTDDIPVWDQEFLK 14 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 213.34 1.89E-09 1569540000 2286490 1817130 2338670 1951710 2734250 2799820 2740980 2331350 2478150 1720790 FALSE TRUE 2376762.391 2129207.942 2399617.661 2337752.413 2269483.162 2149604.237 2526134.825 2300102.067 2388961.866 2057945.854 1.154919789 1.034627776 1.166025655 1.135964004 1.102790512 1.044538773 1.227503056 1.117668894 1.160847775 1 20.97277359 -1.162003657 9.014792157 1.000000004 1.126500896 0.329410731 0.054441878 3.21E-09 4.13E-10 0.049998277 0.011784706 0.06886465 1.162003657 0.126500892 RTDEAAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RTDEAAFQK 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ;;;;; 182.46 7.42E-05 10763170000 6318910 5896670 6701160 5333060 8055750 7384940 6855470 6376750 6637960 6611030 FALSE TRUE 6568385.446 6909377.203 6875797.735 6387923.35 6686436.492 5669899.605 6318120.348 6291280.097 6399061.116 7906334.753 0.830775024 0.873903954 0.869656794 0.807950024 0.845706222 0.717133765 0.79912128 0.795726502 0.809358738 1 22.91457761 3.733037738 23.5599407 0.810608757 0.859691127 0.017544862 0.068802605 460.2483477 1963371.918 0.016836456 0.026958378 5408.013139 -3.733037738 0.04908237 RTDEEGKDVPDHAVLEMK ddPTM_MDA-MB-175_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 94.281 0.0011969 162880000 128270 82940 99285 63802 175370 139280 128940 108990 119290 90274 FALSE TRUE 133334.1986 97184.29982 101872.4487 76421.84517 145560.67 106934.3308 118833.3459 107529.1673 114996.7762 107961.4619 1.23501661 0.900175842 0.943600122 0.707862267 1.348265089 0.990486132 1.100701526 0.995995844 1.065165052 1 16.72015689 3.249145881 24.9999726 1.074244073 0.943124441 0.1576464 0.153920306 416.535793 983756.474 0.041498591 0.055621625 1774.785535 -3.249145881 -0.131119632 RTDLCDHALHISHDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RTDLCDHALHISHDEL 16 1 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;; 148.57 3.74E-07 2648330000 200653 2037363 1323057 1754488 1095673 1820462 895842 1432706 1052042 2116250 FALSE TRUE 208574.9354 2387264.247 1357536.952 2101520.49 909430.8948 1397687.29 825623.5632 1413502.92 1014179.214 2530888.669 0.082411739 0.943251387 0.536387463 0.830348847 0.359332635 0.552251589 0.326218839 0.558500631 0.400720595 1 21.27121262 -1.31235273 5.424099184 1.000088603 0.524317304 0.281007391 0.234152771 0.000229753 2.91E-05 0.207618115 0.048927006 0.048713268 1.31235273 -0.4757713 RTEEGPTLSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RTEEGPTLSYGR 12 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;;;; 255.24 6.29E-21 3268860000 1129867 1576930 1374000 1466000 1566130 1768950 1366240 1336070 1222459 1716280 FALSE TRUE 1174475.022 1847755.461 1409807.569 1755970.424 1299919.782 1358138.171 1259150.539 1318162.167 1178462.939 2052552.206 0.572202265 0.900223368 0.686855888 0.855505852 0.633318743 0.661682644 0.613456035 0.642206402 0.574145172 1 20.96898749 -1.081855322 4.33934096 1.000032606 0.685613213 0.450836843 0.105170306 14125576.34 3521694.405 4359.4722 0.024354522 0.082821802 1.081855322 -0.314419393 RTEEPDRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTEEPDRDER 10 2 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ; 155.33 7.25E-06 93371000 50823 58261 58822 51340 64594 73985 66099 64484 55185 69084 FALSE TRUE 52829.53128 68266.87354 60354.94964 61494.89877 53614.33495 56803.105 60917.98766 63619.69745 53198.90263 82619.68711 0.6394303 0.826278529 0.73051535 0.744312898 0.648929291 0.687525056 0.737330167 0.770030724 0.643901042 1 16.33419798 -1.827073829 2.485772431 1.103705282 0.720927588 0.687040331 0.057699365 6633554.584 4252714.379 4113317.723 0.014259075 0.014891079 1.827073829 -0.382777693 RTEISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTEISK 6 1 Q9H4A5;Q5T5I6;Q9H4A5-2 Q9H4A5 GOLPH3L Golgi phosphoprotein 3-like 0 ; 95.541 0.069313 437260000 538700 473000 531080 469850 649950 650890 545830 576350 569020 450870 FALSE TRUE 559968.292 554234.0706 544920.3811 562784.9276 539471.7312 499730.6618 503046.4183 568624.971 548541.0814 539209.3441 1.038498865 1.027864366 1.010591502 1.043722506 1.000486614 0.926784128 0.932933422 1.054553259 1.017306335 1 19.04048597 3.061411486 6.98617778 0.987979259 1.028135296 0.24880776 0.035880844 0.382490541 35.25338919 0.01178341 0.01409586 1151.891267 -3.061411486 0.040156037 RTELFIAAEGIHTGQFVYCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTELFIAAEGIHTGQFVYCGK 21 1 P62917;E9PKZ0;G3V1A1;E9PKU4 P62917 RPL8 60S ribosomal protein L8 0 ; 169.39 6.21E-12 55910000 80452 72854 83746 64347 96732 94831 82825 79917 89806 83127 FALSE TRUE 83628.30708 85366.10777 85928.48956 77074.64454 80289.52919 72807.93743 76332.96008 78845.84333 86573.8996 99414.14409 0.841211357 0.858691774 0.864348734 0.775288519 0.807626821 0.732370007 0.767827966 0.793104885 0.870840869 1 16.6011635 -1.411750067 8.037797275 1.00000358 0.808521189 0.619444369 0.04402727 3.01E-06 2.21E-07 0.045486981 0.010721184 0.038748057 1.411750067 -0.191482391 RTELSIDISSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTELSIDISSK 11 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ; 136.24 0.00016555 1429850000 1822250 1613890 1808840 1513050 2419600 2282800 2221410 1885480 2075240 1620860 FALSE TRUE 1894193.837 1891063.053 1855979.856 1812326.774 2008317.256 1752654.296 2047290.08 1860208.225 2000552.518 1938436.484 0.977176117 0.97556101 0.957462301 0.934942563 1.036050071 0.904158744 1.056155359 0.95964363 1.0320444 1 20.88646203 2.228300076 24.99955436 1.005051186 0.966366738 0.25398769 0.039270075 339.42443 826993.2707 0.013594645 0.010152752 169.1609348 -2.228300076 -0.038684448 RTES(ph)DSGLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTESDSGLKK 10 2 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7 Q12802-2 AKAP13 A-kinase anchor protein 13 1 RT(0.023)ES(0.977)DSGLKK 69.602 0.044487 45028000 100950 49672 81899 51674 107600 97651 96234 69654 89981 45804 TRUE FALSE 104935.584 58202.77961 84033.35522 61894.96297 89310.19043 74973.03517 88690.92762 68720.40206 86742.60139 54778.41683 1.915637399 1.062512993 1.534059582 1.129915148 1.630390135 1.368660131 1.619085267 1.254516031 1.58351786 1 15.74131995 -1.20468874 3.953506082 0.999694342 1.4329261 0.231480071 0.245874991 38169499.93 57138214.44 137616.7647 0.052232396 0.062418203 1.20468874 0.433231758 RTETVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTETVQK 7 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ;;; 118.06 0.0081639 374780000 759640 869550 774080 507680 1065910 953840 632660 746670 705220 1050930 FALSE TRUE 789631.1738 1018888.448 794253.1607 608097.5887 884726.9989 732325.1156 583070.4561 736662.11 679839.27 1256839.612 0.628267255 0.810674997 0.631944723 0.483830699 0.703929913 0.582671893 0.46391795 0.586122607 0.540911715 1 20.26136913 -1.261743695 9.028466545 1.000000086 0.601973637 0.603483753 0.096390071 1.73E-07 1.42E-08 0.096753483 0.02280501 0.054733889 1.261743695 -0.398026449 RTFQQIQEEEDDDYPGSYS(ph)PQDPSAGPLLTEELIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTFQQIQEEEDDDYPGSYSPQDPSAGPLLTEELIK 35 1 Q9NQG5;A2A2M0 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 RTFQQIQEEEDDDYPGS(0.006)Y(0.005)S(0.981)PQDPS(0.007)AGPLLTEELIK 181.14 1.71E-20 18231000 7737.7 7057.8 8453.2 6731.1 10608 8469.4 8361.8 9028 9282.1 7334.4 TRUE FALSE 8043.190371 8269.922248 8673.497336 8062.49149 8804.855949 6502.510205 7706.380267 8906.994427 8948.039034 8771.435254 0.916975402 0.942824294 0.988834448 0.919175854 1.003810174 0.74132796 0.878576885 1.015454617 1.020133966 1 13.09859721 1.673693581 6.645925065 1.01370533 0.914442994 0.307389481 0.067771003 0.17198699 15.30816823 0.036223396 0.018397383 47.17300914 -1.673693581 -0.099262337 RTGAPAQADSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTGAPAQADSR 11 1 P20290 P20290 BTF3 Transcription factor BTF3 0 ;; 117.09 0.0014451 109585000 123277 160180 130848 111980 200098 194393 127529 138097 126284 223406 FALSE TRUE 128144.0712 187689.669 134258.0064 134129.3098 166085.4134 149248.1718 117532.9437 136246.0356 121739.0635 267178.1283 0.479620364 0.702488898 0.502503731 0.502022043 0.621628029 0.558609242 0.43990481 0.509944569 0.455647565 1 18.02744239 -1.864537888 5.084705989 1.095894522 0.531641065 0.776642279 0.075569592 0.043452707 0.001157627 0.038702718 0.0171097 0.013660359 1.864537888 -0.564253457 RTGCIGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTGCIGAK 8 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ; 98.009 0.01255 760840000 1013360 948090 952410 764140 1217480 1213850 1110870 1130560 1033760 958620 FALSE TRUE 1053368.235 1110917.082 977230.587 915284.6113 1010533.184 931951.7336 1023797.107 1115406.692 996555.1795 1146443.235 0.918814123 0.969011852 0.85240207 0.798368888 0.881450693 0.812907002 0.893020322 0.972927973 0.869258197 1 20.12873349 -0.818119985 5.266874163 1.000000066 0.888624286 0.280362002 0.054879616 4.65E-08 1.06E-08 0.057840578 0.013633147 0.15201275 0.818119985 -0.111375781 RTHEHVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RTHEHVSEK 9 1 P20810-6;P20810-10;P20810-7;P20810-9;H0YA91;P20810-5;F8W7E0;E9PSG1 P20810-6;P20810-5 CAST Calpastatin 0 ;;;; 98.943 0.0036822 238102000 86315 336667 338917 314814 408110 474844 347853 403060 340692 417070 FALSE TRUE 89722.78285 394486.9383 347749.4554 377083.2696 338739.608 364568.6773 320587.3729 397657.64 328430.5615 498786.8812 0.179882002 0.79089277 0.697190461 0.756000777 0.679126939 0.730910718 0.642734172 0.797249597 0.6584587 1 18.928064 4.94935145 0.101256004 1.11059872 3.43E-36 0.399466504 0.15251294 69.75237838 1.063956464 2.553842667 11.58124196 88992.09895 -4.94935145 -1.11059872 RTHS(ph)DAS(ph)DDEAFTTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTHSDASDDEAFTTSK 16 1 Q13017-2;Q13017;H0YK04 Q13017-2 ARHGAP5 Rho GTPase-activating protein 5 2 RT(0.068)HS(0.932)DAS(1)DDEAFTTSK;RT(0.226)HS(0.774)DAS(0.999)DDEAFTTSK;RT(0.01)HS(0.991)DAS(0.999)DDEAFTTSK 154.73 1.14E-06 1855380000 1094490 918920 1063330 804460 1482620 1557060 1254970 1148270 1299980 993750 TRUE FALSE 1137701.31 1076737.362 1091041.253 963579.7869 1230604.782 1195456.412 1156602.172 1132879.319 1253193.974 1188456.286 0.957293359 0.905996606 0.918032296 0.810782692 1.035464911 1.0058901 0.973197067 0.953236002 1.054472082 1 20.18065741 3.21856322 24.99999982 0.996161648 0.900024512 0.581580211 0.043621111 186.8720555 233619.9094 0.012818648 0.015339711 1654.105554 -3.21856322 -0.096137136 RTHS(ph)EGSLLQEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTHSEGSLLQEPR 13 1 P49796-1;P49796-4;P49796-6;P49796;C9J582 P49796-1 RGS3 Regulator of G-protein signaling 3 1 RTHS(0.999)EGS(0.001)LLQEPR 185.2 5.43E-06 441890000 111940 151330 177160 173850 185080 209300 176550 175500 205380 218000 TRUE FALSE 116359.4776 177319.7503 181776.9351 208237.0111 153620.1677 160693.247 162711.5497 173147.7096 197988.4139 260712.9261 0.446312653 0.680134096 0.697230236 0.798721468 0.589231113 0.616360874 0.624102349 0.664131664 0.759411575 1 17.99210259 0.849800542 1.898312727 0.99965027 0.64340793 0.629672379 0.084498215 0.363831245 2.50001102 0.079921319 0.022375971 7.076207221 -0.849800542 -0.35624234 RTIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTIEGQSPEPVFGDADVDVSAVQAK 25 1 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 RT(0.023)IEGQS(0.977)PEPVFGDADVDVSAVQAK 219.93 7.86E-34 178220000 164500 155310 173130 112540 219630 217180 167100 163580 181890 160660 TRUE FALSE 170994.587 181983.2844 177641.91 134800.0761 182297.371 166743.2364 154002.2654 161387.4777 175343.8144 192138.251 0.889955988 0.947147606 0.924552551 0.701578553 0.948782297 0.867829469 0.801517993 0.839954964 0.912591915 1 17.55178523 RTIQEVLEEQS(ph)EDEDREAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTIQEVLEEQSEDEDREAK 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 RTIQEVLEEQS(1)EDEDREAK 113.54 9.14E-05 62590000 39713 33878 41263 23066 49068 61584 49121 38418 50049 38520 TRUE FALSE 41280.89991 39696.28297 42338.34768 27628.38595 40727.43889 47282.04931 45270.76767 37903.06955 48247.74627 46067.25649 0.896100681 0.86170278 0.919055114 0.599740207 0.884086485 1.026369984 0.982710305 0.822776793 1.047332747 1 15.49145406 2.998928748 24.99979273 0.953951681 0.818398821 0.344753077 0.09998744 53.38281025 1245851.848 0.02983401 0.035228412 997.5363901 -2.998928748 -0.13555286 RTIQFVDWCPTGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTIQFVDWCPTGFK 14 1 Q9BQE3;F5H5D3;A0A1W2PQM2 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 ; 130.06 0.00010309 721350000 1381910 811050 1086500 966810 1864810 1676170 1739600 1485000 1337880 1189350 FALSE TRUE 1436468.874 950341.5284 1114815.083 1158042.132 1547830.262 1286904.92 1603245.606 1465096.004 1289729.96 1422380.361 1.009904884 0.668134596 0.783767207 0.814157847 1.088197155 0.904754421 1.127156737 1.030031097 0.906740557 1 20.43987588 3.253151346 24.28764756 1.015509404 0.805699549 0.454353799 0.101722122 135.3199524 225250.9137 0.02691372 0.03627079 1791.229966 -3.253151346 -0.209809855 RTLEGELHDLR ddPTM_MDA-MB-175_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 ; 158.42 1.94E-05 1078530000 529960 636110 608140 583510 678240 737010 602120 638960 612930 684380 FALSE TRUE 550883.23 745356.9443 623988.628 698926.5364 562953.0071 565850.597 554924.2611 630395.7863 590870.769 818471.1578 0.673063705 0.910669774 0.76238316 0.853941559 0.68781044 0.691350687 0.678000997 0.770211363 0.721920087 1 19.64257205 -1.113133877 3.577714049 1.000163412 0.752687245 0.4989621 0.075131722 16281781.82 29213984.59 32162.23467 0.018021467 0.077066587 1.113133877 -0.247476167 RTLS(ph)MDKGF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTLSMDKGF 9 2 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 RTLS(1)MDKGF;RTLS(1)MDKGF;RT(0.01)LS(0.99)MDKGF 166.62 4.77E-05 791450000 772595 620356 945270 520698 1466480 1065020 1000250 847230 1205020 869310 TRUE FALSE 803097.6472 726897.3173 969904.5127 623690.5103 1217208.253 817685.2455 921847.7913 835874.2676 1161651.566 1039634.651 0.772480647 0.69918535 0.932928228 0.599913162 1.170803852 0.786512113 0.886703604 0.804007703 1.117365187 1 19.98764519 7.874156989 0.13252263 1.053315802 2.24E-09 0.217081226 0.152046811 124.4421488 1.145525575 0.717285323 24.46098151 74843999.86 -7.874156989 -1.0533158 RTLSSSTQASLEIDSLFEGIDFYTSITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTLSSSTQASLEIDSLFEGIDFYTSITR 28 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 173.96 2.68E-12 101361000 59884 75135 71527 49335 98391 92362 64605 73368 77660 111160 FALSE TRUE 62248.26656 88038.85178 73391.05238 59093.31575 81666.53296 70912.32526 59541.09129 72384.62197 74865.03177 132939.6737 0.468244466 0.662246637 0.552062829 0.444512267 0.614312723 0.533417326 0.447880528 0.544492249 0.56315041 1 17.02041219 0.555825027 2.588242648 0.999993413 0.534631496 0.818273962 0.065633519 2.441449284 13.73841842 0.061082846 0.016225708 3.59604425 -0.555825027 -0.465361916 RTLTTGSSAYLWKPPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTLTTGSSAYLWKPPSR 17 2 Q9BQS8;Q9BQS8-4;Q9BQS8-3;Q9BQS8-2 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 1 RTLTTGSSAYLWKPPS(1)R;RTLTTGSSAYLWKPPS(1)R 104.06 0.00045341 813360000 524140 290700 342990 302840 535480 514820 475790 356230 397660 365400 TRUE FALSE 544833.4519 340625.4637 351928.6012 362740.8481 444459.3009 395260.8572 438496.3366 351455.3195 383348.2943 436993.134 1.24677806 0.77947555 0.80534126 0.830083633 1.017085318 0.904501299 1.003439877 0.804258219 0.877241001 1 18.73725109 RTNPPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 69.825 0.08485 95930000 90061 82537 92807 75232 105320 111150 106730 95099 98107 79054 FALSE TRUE 93616.67782 96712.0877 95225.62666 90112.66505 87417.74402 85337.09699 98364.22371 93824.35346 94576.14823 94543.11772 0.990200874 1.022941596 1.007219023 0.953138285 0.924633608 0.90262622 1.040416543 0.992397498 1.00034937 1 16.52868482 -0.977572157 7.53465833 1 0.982054065 0.01792745 0.040818296 0 4.19E-11 0.042345859 0.009981014 0.105299872 0.977572157 -0.017945935 RTNS(ph)TGGSSGSSVGGGSGK ddPTM_MDA-MB-175_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(0.157)NS(0.491)T(0.157)GGS(0.073)S(0.094)GS(0.025)S(0.003)VGGGSGK;RT(0.002)NS(0.926)T(0.058)GGS(0.01)S(0.002)GS(0.001)SVGGGSGK 112.44 0.00020828 185595000 135270 110872 153873 105351 182733 195530 150336 127776 143365 133070 TRUE FALSE 140610.5641 129913.4035 157883.0568 126189.1134 151672.1099 150121.1208 138552.2715 126063.3717 138205.3217 159142.5187 0.883551204 0.816333715 0.992085949 0.792931483 0.953058373 0.94331246 0.870617561 0.792141363 0.868437441 1 17.27995981 -0.16745605 8.375927009 1 0.875594721 0.238444921 0.064502218 0 0 0.062027386 0.014619995 0.680054861 0.16745605 -0.124405278 RTNSS(ph)SSSPVVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTNSSSSSPVVLK 13 1 Q7Z589-4;E9PMC9;Q7Z589-6;Q7Z589-7;Q7Z589;Q7Z589-5;Q7Z589-2 Q7Z589-4;Q7Z589-7 EMSY;C11orf30 Protein EMSY 1 RT(0.257)NS(0.257)S(0.32)S(0.1)S(0.049)S(0.016)PVVLK 77.468 0.015844 89828000 120590 108610 114340 102870 148860 156110 123410 121420 156450 122940 TRUE FALSE 125350.9863 127262.9226 117319.7943 123217.379 123556.8304 119855.8184 113736.8017 119792.5635 150819.3951 147027.7392 0.852566917 0.865570833 0.797943266 0.83805532 0.840364077 0.815191875 0.773573765 0.814761651 1.025788711 1 17.16572884 1.239425434 24.99992852 1.012894438 0.822928475 0.893479428 0.025978582 6.593375885 190650.8108 0.021302434 0.006742806 17.35503261 -1.239425434 -0.189965963 RTNSTGGS(ph)SGSSVGGGSGK ddPTM_MDA-MB-175_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(0.204)NS(0.204)T(0.204)GGS(0.332)S(0.055)GS(0.002)SVGGGSGK 76.186 0.0081678 18425000 14275 13218 14694 9841.1 15610 15687 14556 14198 14874 11780 TRUE FALSE 14838.58802 15488.08868 15076.93771 11787.64021 12956.61778 12043.93199 13415.06268 14007.69903 14338.68765 14088.06546 1.053273643 1.099376541 1.070192196 0.836711062 0.919687505 0.854903182 0.952228872 0.994295425 1.017789681 1 13.7821859 3.851399525 8.749612492 0.939144981 1.078154181 0.543093667 0.056705738 0.256405709 18.23713279 0.015622161 0.028255517 7102.308379 -3.851399525 0.1390092 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(1)PAPGEGPSGR 172.74 3.62E-12 1031780000 326423 368898 363514 367340 400977 465780 331891 384680 336982 424910 TRUE FALSE 339310.4321 432253.3619 372987.4735 439998.7556 332819.0728 357609.654 305876.5162 379523.9938 324854.0836 508162.9791 0.6677197 0.850619545 0.733991827 0.865861493 0.654945532 0.703730237 0.601926013 0.746854866 0.639271448 1 18.95493175 -1.129239252 4.343997744 1.000045945 0.721498245 0.515573365 0.081858394 3.58E-05 7.17E-06 0.077792198 0.018332777 0.074260992 1.129239252 -0.2785477 RTPDGTENGDFLALDLGGTNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTPDGTENGDFLALDLGGTNFR 22 1 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ; 193.54 1.09E-17 291500000 206183 235061 227841 218950 264081 282660 188090 216027 186664 243582 FALSE TRUE 214323.264 275430.8982 233778.7236 262257.6565 219192.6059 217016.4988 173347.0143 213131.5114 179945.9991 291307.2292 0.735729301 0.945499701 0.802516039 0.900278572 0.752444787 0.744974642 0.595065954 0.73163825 0.617718961 1 18.15218198 3.066372646 4.355391893 0.713286777 0.849709261 0.150194121 0.115697655 0.29457111 11.11597848 0.031619541 0.037840358 1165.125336 -3.066372646 0.136422484 RTPS(ph)DDEEDNLFAPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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(0.004)PS(0.996)DDEEDNLFAPPK;RT(0.025)PS(0.975)DDEEDNLFAPPK;RT(0.019)PS(0.981)DDEEDNLFAPPK;RT(0.018)PS(0.982)DDEEDNLFAPPK;RT(0.089)PS(0.911)DDEEDNLFAPPK;RT(0.02)PS(0.98)DDEEDNLFAPPK;RT(0.014)PS(0.986)DDEEDNLFAPPK;RT(0.017)PS(0.983)DDEEDNLFAPPK;RT(0.012)PS(0.988)DDEEDNLFAPPK;RT(0.034)PS(0.966)DDEEDNLFAPPK;RT(0.061)PS(0.939)DDEEDNLFAPPK 248.18 2.37E-20 6770240000 5801440 4235904 5357110 4179030 6614290 6506960 6188950 5258040 5823510 3839900 TRUE FALSE 6030485.331 4963387.561 5496720.688 5005629.661 5489995.348 4995817.154 5703843.927 5187564.574 5613923.013 4592254.886 1.31318611 1.08081709 1.196954617 1.090015643 1.195490121 1.087878891 1.242057349 1.129633416 1.222476355 1 22.13077129 -1.712779469 2.884791721 0.975213718 1.16705152 0.335464693 0.072660428 12948767.71 14198229.41 2357344.545 0.015888541 0.019374055 1.712779469 0.191837801 RTPS(ph)EADR ddPTM_MDA-MB-175_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(0.077)PS(0.923)EADR;RT(0.08)PS(0.92)EADR;RT(0.015)PS(0.985)EADR;RT(0.057)PS(0.943)EADR 95.094 0.0060603 505779000 396108 476203 452531 502314 532135 608729 557005 520797 485602 473187 TRUE FALSE 411746.6497 557987.1609 464324.3296 601670.2099 441682.8828 467360.9151 513345.4926 513816.5681 468125.2789 565898.9329 0.727597501 0.986019108 0.820507519 1.063211423 0.780497819 0.825873469 0.907132816 0.907965253 0.827224177 1 19.11018489 -2.130440117 2.003175441 1.220767105 0.87902246 0.139212002 0.094111769 7265733.304 1689030.505 7287054.227 0.022744635 0.007405594 2.130440117 -0.341744645 RTPS(ph)EAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTPSEAER 8 1 A0A0C4DGH3;Q9Y6R0 A0A0C4DGH3 NUMBL Numb-like protein 1 RT(0.012)PS(0.988)EAER 80.014 0.016259 38184000 26218 40769 34762 37278 39318 42485 32368 34120 34310 51694 TRUE FALSE 27253.10688 47770.75861 35667.92628 44651.47714 32634.7404 32618.50262 29830.91158 33662.67721 33075.1898 61822.44956 0.440828648 0.772708926 0.57694133 0.722253444 0.527878475 0.527615823 0.482525552 0.544505717 0.5350029 1 15.9158432 -1.769216224 6.882359962 1.011035449 0.57231203 0.638567873 0.097030675 0.016048277 0.000538141 0.091766727 0.021730775 0.017013113 1.769216224 -0.43872342 RTPS(ph)PGPVESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTPSPGPVESK 11 1 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 RT(0.22)PS(0.78)PGPVESK 93.424 0.0056718 98130000 182970 163690 212560 140510 223400 239230 211570 181200 192230 160190 TRUE FALSE 190193.7969 191802.4842 218099.4882 168302.4586 185426.5478 183672.4581 194986.5906 178771.3104 185311.6799 191576.1635 0.992784245 1.001181361 1.138447938 0.87851461 0.967899891 0.958743795 1.017801939 0.93316051 0.967300297 1 17.54755854 3.730945247 24.99990347 0.959865811 1.039842201 0.361491174 0.050844693 616.0503358 2022380.887 0.013079368 0.020711545 5382.019247 -3.730945247 0.079976389 RTPS(ph)TKPTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTPSTKPTVR 10 2 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 RT(0.293)PS(0.568)T(0.139)KPTVR;RT(0.005)PS(0.991)T(0.005)KPTVR;RT(0.016)PS(0.981)T(0.003)KPTVR;RT(0.017)PS(0.938)T(0.045)KPTVR 130.2 0.00014764 630640000 633980 556060 711030 562220 947020 860790 748060 720810 781360 669090 TRUE FALSE 659010.0199 651558.9795 729560.0259 673425.4379 786045.8787 660884.5679 689425.1025 711148.721 753239.0062 800185.375 0.823571688 0.814260045 0.911738765 0.841586786 0.982329724 0.82591433 0.861581733 0.888729966 0.941330634 1 19.60997474 -4.999999987 0.097590081 1.406772756 0.785098103 0.457784345 0.047226264 180.7683979 1.207380868 14.96598693 0.848304307 1.00E-05 4.999999987 -0.621674653 RTQAPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTQAPTK 7 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 ; 97.635 0.019004 178594000 222660 219320 197206 154116 478140 339510 260270 189353 219890 428310 FALSE TRUE 231450.7887 256986.5039 202345.3504 184599.6848 396865.9336 260663.9478 239869.3573 186815.0328 211976.2019 512229.144 0.451850098 0.50170223 0.395028968 0.36038497 0.774782025 0.508881525 0.468285259 0.364709886 0.413830811 1 18.96642981 -1.063271631 4.722885957 1.000018532 0.468704157 0.663541876 0.112985823 1.385212307 147476196.3 6365.565792 0.027418176 0.086442709 1.063271631 -0.531314375 RTQAPTKAS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTQAPTKASE 10 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPTKAS(1)E;RTQAPT(0.001)KAS(0.999)E 184.11 1.26E-06 1197650000 1162725 730415 971851 709784 1261565 1300272 1188226 1057859 1145433 843159 TRUE FALSE 1208630.281 855858.0944 997178.2354 850177.1567 1047124.632 998303.5338 1095089.741 1043680.13 1104209.09 1008359.863 1.198610065 0.848762556 0.988911075 0.843128716 1.038443388 0.990027044 1.08601084 1.035027443 1.095054584 1 19.94357917 2.655420865 2.007320066 1.053611789 0.965201814 0.093357378 0.097453344 0.640363623 5.11093368 0.034908005 0.032500683 452.2940399 -2.655420865 -0.088409975 RTQS(ph)LSALPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTQSLSALPK 10 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 RT(0.157)QS(0.835)LS(0.009)ALPK 81.803 0.0086536 0 132580 110740 136510 109050 180770 183510 158660 129000 151460 122160 TRUE FALSE 137814.3608 129758.7336 140067.5627 130619.7645 150042.78 140892.5836 146223.8146 127270.966 146008.9842 146094.9131 0.943320735 0.888181052 0.958743599 0.894074693 1.027022617 0.964390755 1.000882313 0.871152618 0.999411828 1 17.15654642 3.275927142 24.99972954 0.96509911 0.921420368 0.249584299 0.04479079 305.0567164 204093.4003 0.012765261 0.017283815 1887.674644 -3.275927142 -0.043678742 RTS(ph)FSFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 RT(0.243)S(0.757)FSFQK;RT(0.024)S(0.976)FSFQK;RT(0.185)S(0.815)FSFQK 168.85 0.00018648 2124550000 1694130 1623860 1761470 1491710 2256070 2238020 1951350 1913230 1805000 1776090 TRUE FALSE 1761015.561 1902745.323 1807375.355 1786765.786 1872584.027 1718273.773 1798398.088 1887586.281 1740038.403 2124080.83 0.82907182 0.895797041 0.850897635 0.841194817 0.881597348 0.808949334 0.846671211 0.888660288 0.819195945 1 21.01840724 -2.123850353 2.54091715 1.300661843 0.85433889 0.717051126 0.027958587 2386341.294 1016286.954 4135249.551 0.006700041 0.007518819 2.123850353 -0.446322953 RTS(ph)FSTSDVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSFSTSDVSK 11 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 RT(0.254)S(0.744)FS(0.002)TSDVSK;RT(0.238)S(0.728)FS(0.008)T(0.008)S(0.017)DVSK 120.29 0.00028889 950849000 850330 805220 881290 794430 1292660 1179110 1015540 899690 880840 849830 TRUE FALSE 883901.685 943510.2713 904257.1414 951565.8829 1072934.115 905279.5721 935939.3212 887631.1271 849138.7405 1016337.918 0.869692717 0.928343079 0.889720954 0.936269194 1.055686398 0.890726949 0.920893834 0.873362207 0.835488597 1 19.95494873 -0.518200554 7.591712082 0.999999999 0.912945684 0.182580374 0.056293411 0 0 0.055927071 0.013182137 0.303249048 0.518200554 -0.087054315 RTS(ph)NERPGSGQGQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSNERPGSGQGQGR 15 2 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 RT(0.358)S(0.642)NERPGSGQGQGR 157.14 1.58E-06 970780000 181120 212200 208150 208060 222810 261390 201100 220710 206260 228530 TRUE FALSE 188270.7575 248643.6993 213574.56 249213.647 184936.8358 200686.1339 185337.2565 217751.7435 198836.7429 273306.078 0.688864144 0.909762787 0.781448263 0.91184817 0.676665653 0.734290783 0.678130753 0.796732166 0.727524043 1 18.06015802 -1.515712904 3.158511377 1.006773077 0.770523402 0.419465757 0.082062299 44837609.5 60357333.14 2664849.62 0.019333811 0.030499105 1.515712904 -0.236249675 RTS(ph)SEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSSEELR 8 1 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.001)S(0.999)SEELR;RTS(1)SEELR 158.56 0.00022311 1047590000 585690 620510 605130 664990 639030 691940 689800 679950 620120 534360 TRUE FALSE 608813.4935 727077.7656 620900.1849 796523.0372 530407.9089 531247.4215 635731.6735 670836.3824 597802.0023 639057.6111 0.952673879 1.137734303 0.971587184 1.246402552 0.829984495 0.831298168 0.994795559 1.049727553 0.935443052 1 19.28558647 3.222597687 24.99925015 0.948707168 1.073894022 0.3037274 0.101000981 335.0000208 524636.1322 0.029924474 0.035872742 1669.543299 -3.222597687 0.125186854 RTS(ph)SEELRDATSLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.11)S(0.743)S(0.147)EELRDATSLLAAGEGGLLDEVEPLRPDELER;RT(0.198)S(0.602)S(0.198)EELRDAT(0.001)S(0.001)LLAAGEGGLLDEVEPLRPDELER;RT(0.242)S(0.724)S(0.034)EELRDATSLLAAGEGGLLDEVEPLRPDELER 373.84 4.16E-148 620329000 29596.5 47692.8 44912.9 40666.8 63144.4 61051.7 37492.8 51032.6 56208 69776.1 TRUE FALSE 30764.99267 55883.6674 46083.36707 48710.57166 52411.13744 46873.36792 34554.01637 50348.59147 54185.08506 83447.39085 0.36867531 0.669687414 0.552244553 0.583727917 0.628074011 0.561711606 0.414081447 0.603357288 0.649332286 1 16.34857932 0.743660791 1.862505823 0.999525661 0.550579478 0.711462674 0.086627604 0.490712622 2.673832373 0.078370323 0.021919915 5.541926877 -0.743660791 -0.448946183 RTS(ph)SPPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.013)S(0.493)S(0.493)PPRK 61.78 0.043728 233220000 8725.3 12226 12343 11394 13899 14153 13244 11613 15793 13349 TRUE FALSE 9069.781581 14325.72039 12664.66872 13647.69919 11536.45294 10866.18024 12205.90067 11457.34673 15224.61301 15964.48097 0.568122547 0.897349586 0.793302879 0.854878979 0.722632509 0.680647261 0.764566083 0.717677371 0.953655371 1 13.96257803 1.167069183 5.307188854 0.99209188 0.755348797 0.523081578 0.086792853 0.158030904 7.70337603 0.078682429 0.020195794 14.69160296 -1.167069183 -0.236743083 RTS(ph)STLDSEGTFNSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 RT(0.003)S(0.887)S(0.098)T(0.011)LDSEGTFNSYR 202.84 3.11E-11 86784000 136180 171480 146570 139180 193320 193790 142580 156920 171750 235350 TRUE FALSE 141556.4916 200930.3561 150389.7346 166709.3886 160459.5355 148785.2094 131404.207 154816.7441 165568.751 281462.3265 0.502932287 0.713880108 0.534315681 0.592297345 0.570092408 0.528615006 0.466862506 0.550044285 0.588244804 1 18.10258231 0.708079871 3.849479878 0.99999763 0.557924712 0.819363891 0.062012688 2.151275364 28.002334 0.059433433 0.015219686 5.105988951 -0.708079871 -0.442072917 RTSS(ph)KSEAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RTSSKSEAGAR 11 2 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 RT(0.035)S(0.191)S(0.739)KS(0.035)EAGAR;RT(0.034)S(0.191)S(0.741)KS(0.034)EAGAR 78.069 0.024327 281010000 356330 218760 281520 174476 444140 374230 279450 278260 318080 273380 TRUE FALSE 370398.1835 256330.3283 288856.6425 208986.832 368645.2414 287320.754 257545.9788 274530.3798 306632.3629 326943.5768 1.132911639 0.784020077 0.883506094 0.639213757 1.127550035 0.878808377 0.787738304 0.839687332 0.937875477 1 18.31868215 4.750068695 23.96788562 0.866032425 1.132911925 0.272872992 0.125285885 1219.407255 2539573.891 0.028427427 0.43302106 56243.02817 -4.750068695 0.266879499 RTSS(ph)PHKEESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSPHKEESPK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 RT(0.097)S(0.097)S(0.806)PHKEESPK 83.966 0.0065233 199410000 112050 65702 88810 59636 127890 133930 130100 97008 105750 55591 TRUE FALSE 116473.8205 76985.80741 91124.46156 71431.8228 106151.3035 102826.7872 119902.422 95707.76643 101944.0782 66482.9921 1.751934094 1.157977476 1.370643208 1.074437545 1.596668563 1.546663049 1.803505201 1.439582718 1.533385832 1 16.02069769 3.182215816 24.99999836 1.527740774 1.328107135 0.061243571 0.253416828 168.1899859 74624.41549 0.068685479 0.082094902 1521.303331 -3.182215816 -0.199633638 RTSS(ph)PPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSPPRK 8 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RT(0.062)S(0.062)S(0.876)PPRK 64.297 0.035416 269460000 4623.9 7769.4 9053.2 10953 8556.8 15014 9642.8 9448.5 8957.8 11664 TRUE FALSE 4806.455142 9103.734012 9289.133829 13119.47071 7102.318192 11527.22604 8886.972139 9321.858312 8635.410528 13949.33748 0.34456512 0.652628415 0.665919356 0.940508517 0.509150933 0.826363693 0.637089192 0.668265308 0.619055245 1 13.76790898 -5 0.254764918 3.070174245 0.632542486 0.325924418 0.151306396 230.4133076 2.275342861 249.7225504 0.202172599 1.00E-05 5 -2.437631759 RTSSEELRDAT(ph)SLLAAGEGGLLDEVEPLRPDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RTSSEELRDATSLLAAGEGGLLDEVEPLRPDELER 35 3 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 RT(0.1)S(0.1)S(0.1)EELRDAT(0.351)S(0.351)LLAAGEGGLLDEVEPLRPDELER 82.988 0.0010331 18882000 2703.9 4172.7 4559 1991.1 3978.1 4773.5 3244.6 3577.1 3145.3 3205.3 TRUE FALSE 2810.65206 4889.328766 4677.811285 2384.933637 3301.903983 3664.926968 2990.279774 3529.154825 3032.101267 3833.317166 0.733216673 1.275482449 1.220303743 0.622159225 0.861369889 0.956071937 0.780076275 0.920652968 0.790986275 1 11.90437766 3.754026913 24.98796345 0.849351466 1.096249099 0.281167683 0.166865573 943.7833421 1524809.626 0.040984963 0.073551733 5675.797773 -3.754026913 0.246897633 RTVQS(ph)LEIDLDSMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 RT(0.031)VQS(0.969)LEIDLDSMR;RT(0.095)VQS(0.905)LEIDLDSMR;RT(0.022)VQS(0.978)LEIDLDSMR;RT(0.131)VQS(0.869)LEIDLDSMR 130.02 3.95E-05 118881000 77427.7 96563 92797 89496 116887 108921 91183 98979 99123 113027 TRUE FALSE 80484.60538 113146.9441 95215.36605 107198.0417 97018.58949 83625.74846 84035.8382 97652.3484 95555.58259 135172.4766 0.595421549 0.837056085 0.704399064 0.793046368 0.717739232 0.618659586 0.621693412 0.722427752 0.706915971 1 17.0444419 -1.548465396 4.128749377 1.004039254 0.704488525 0.605599669 0.072136808 0.002669224 0.000291916 0.06951038 0.016186866 0.028283595 1.548465396 -0.299550728 RTVQSLEIDLDSMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 RTVQSLEIDLDSMR 14 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 256.8 4.04E-24 3315290000 1318930 1689150 1632460 1360980 2019060 2063130 1552610 1674610 1648460 2048730 FALSE TRUE 1371002.375 1979248.373 1675003.249 1630177.782 1675860.902 1583999.325 1430912.371 1652164.592 1589132.247 2450139.418 0.559560964 0.80781051 0.683635893 0.665340825 0.683985936 0.646493548 0.584012632 0.674314523 0.648588499 1 21.22443241 -1.89237258 2.611764783 1.175795647 0.664175053 0.723237415 0.062795068 8129785.159 4947537.187 8808915.206 0.014647547 0.012812309 1.89237258 -0.511620594 RVASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 33 1 Q14764 Q14764 MVP Major vault protein 1 RVAS(0.148)GPS(0.148)PGEGIS(0.669)PQS(0.034)AQAPQAPGDNHVVPVLR 68.807 0.0020008 59626000 16657 17930 15741 15113 19048 20747 14738 13749 15467 18994 TRUE FALSE 17314.63122 21009.33802 16151.22339 18102.30629 15810.22776 15928.82367 13582.79705 13564.71714 14910.34569 22715.51064 0.762238256 0.924889533 0.711021806 0.796913905 0.696010229 0.701231151 0.59795253 0.597156602 0.656394916 1 14.47139012 4.12788907 7.058542115 0.693987631 0.842667275 0.124425667 0.117310994 0.309657609 17.88934675 0.028445599 0.062336125 13424.22028 -4.12788907 0.148679644 RVATPVDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVATPVDWK 9 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ; 161.51 0.00010339 2014740000 3150600 2489000 2983600 2490000 3848100 3972700 3790700 3098900 3279700 2434000 FALSE TRUE 3274988.121 2916466.388 3061355.067 2982514.568 3194001.337 3050100.632 3493575.029 3057364.314 3161664.238 2910895.698 1.125079172 1.001913737 1.051688341 1.024603722 1.097257225 1.047822027 1.200171834 1.05031737 1.086148239 1 21.47303172 3.227009714 24.95680246 1.087228335 1.047389784 0.051741753 0.056589252 490.2815716 1059298.704 0.015483408 0.018655711 1686.59075 -3.227009714 -0.039838551 RVDAENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 169.97 0.0015907 1604954000 776025 953946 852872 891265 935338 1059400 894148 877320 816163 1077598 FALSE TRUE 806663.0662 1117778.805 875098.545 1067554.557 776349.5809 813370.4054 824062.3433 865560.9604 786789.4531 1288732.696 0.625935129 0.867347285 0.679038056 0.828375473 0.602413195 0.63113973 0.639436204 0.671637309 0.610514077 1 20.29752163 -1.041591483 4.33078146 1.000021526 0.686501964 0.545287676 0.086546736 9653204.925 4643363.706 1906.169424 0.020041001 0.090867487 1.041591483 -0.313519562 RVDIIPGFEFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RVDIIPGFEFDR 12 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;;;; 145 0.00010186 2951340000 784481 882867 831348 888327 935745 1031091 820496 843267 758304 876885 FALSE TRUE 815452.9156 1034492.539 853013.6118 1064035.429 776687.3991 791635.7416 756183.3796 831964.3852 731012.7872 1048693.827 0.777589125 0.986458119 0.813405772 1.014629248 0.740623602 0.75487785 0.721071642 0.793333921 0.697069791 1 20.0001621 3.209901768 24.99999508 0.770034082 0.898293723 0.219816603 0.102628227 255.9617548 223282.6074 0.026852776 0.032100456 1621.443306 -3.209901768 0.128259641 RVDPDVAQHWAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVDPDVAQHWAK 12 1 K7ERG2;H7BXP1;Q9NYR9-3;Q9NYR9-2;Q9NYR9 K7ERG2 NKIRAS2 NF-kappa-B inhibitor-interacting Ras-like protein 2 0 94.122 0.0044062 72846000 82008 89007 90438 72912 121860 114740 91603 77261 90145 85971 FALSE TRUE 85245.73916 104293.2599 92794.88858 87333.77598 101146.2807 88093.3739 84422.9175 76225.44267 86900.69906 102815.3714 0.829114732 1.014374197 0.902539059 0.849423338 0.983766136 0.856811318 0.821111827 0.741381776 0.845211157 1 16.64969645 2.50862718 6.902580483 0.822527603 0.917418454 0.090156023 0.0806535 0.290091828 47.81540326 0.025564378 0.023454609 322.5723813 -2.50862718 0.094890851 RVEDVLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVEDVLGK 8 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 76.679 0.056405 120640000 258000 149460 185680 154330 258040 262840 218850 182620 217450 171410 FALSE TRUE 268186.0392 175128.5924 190518.9733 184856.0134 214178.453 201799.3934 201695.9651 180172.2776 209624.017 204994.5077 1.308259632 0.854308705 0.929385746 0.90176081 1.044800934 0.984413659 0.983909118 0.878912707 1.022583577 1 17.64522573 4.74820698 24.98993568 0.950992128 1.308259824 0.756570257 0.059967844 626.6624212 1623402.75 0.014265608 0.186837968 56002.44391 -4.74820698 0.357267696 RVEEELEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVEEELEKR 9 2 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 115.57 0.00081775 191230000 209040 199470 214990 189150 233590 245800 226830 209660 210750 197990 FALSE TRUE 217293.0606 233727.4208 220592.816 226563.3054 193884.4552 188716.6751 209050.4719 206849.8506 203165.1487 236782.3498 0.917691124 0.987098156 0.93162694 0.956842035 0.818829847 0.797004825 0.8828803 0.873586443 0.858024886 1 17.85320202 3.254800199 24.99761457 0.863466831 0.949892876 0.325076102 0.053256921 244.8582931 376908.4068 0.014053768 0.018971774 1798.043519 -3.254800199 0.086426045 RVEELVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVEELVAK 8 1 Q9NWB6;Q9NWB6-2;Q9NWB6-3 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 0 ; 91.867 0.019535 261330000 159154 143094 171756 157680 193686 205605 184004 175937 182641 173720 FALSE TRUE 165437.5228 167669.2814 176232.1025 188868.6334 160763.3229 157856.3547 169581.2857 173578.8523 176067.7861 207757.1079 0.796302588 0.807044741 0.84826028 0.909083859 0.773804201 0.759812053 0.816247816 0.835489356 0.847469373 1 17.66453831 0.541002968 1.35773628 0.999952957 0.817727316 0.659127371 0.039115045 1.21644159 2.884944393 0.039705954 0.011733602 3.475385367 -0.541002968 -0.182225641 RVEIMEEESEQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVEIMEEESEQ 11 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 80.896 0.015797 0 55533 56766 62587 61792 60143 77035 55483 62165 65797 53479 FALSE TRUE 57725.48572 66515.11892 64218.06864 74014.27317 49919.91434 59144.78873 51134.09748 61331.77986 63428.97882 63957.18613 0.9025645 1.039994455 1.004079018 1.157247178 0.780520804 0.924755955 0.799505115 0.958950566 0.991741236 1 15.96481885 3.236162584 25 0.903991429 1.025409194 0.28994202 0.089258937 77.93428081 812483.6039 0.024887991 0.031110866 1722.513299 -3.236162584 0.121417765 RVEIQMPKPAEAPTAPS(ph)PAQTLENSEPAPVSQLQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVEIQMPKPAEAPTAPSPAQTLENSEPAPVSQLQSR 36 2 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;K7EJ51 Q9UHD8 9-Sep Septin-9 1 RVEIQMPKPAEAPT(0.006)APS(0.993)PAQT(0.001)LENSEPAPVSQLQSR;RVEIQMPKPAEAPT(0.001)APS(0.999)PAQTLENSEPAPVSQLQSR;RVEIQMPKPAEAPTAPS(1)PAQTLENSEPAPVSQLQSR 358.4 1.39E-145 926400000 343520 298789 331922 235955 417317 419072 280520 322133 357215 351545 TRUE FALSE 357082.4349 350103.6865 340572.16 282626.1947 346381.6054 321748.8791 258532.1094 317815.334 344358.9019 420423.512 0.849339832 0.832740502 0.810069252 0.672241648 0.823887331 0.765297063 0.614932567 0.755940914 0.819076222 1 18.68148383 0.863520828 3.453289078 0.999887783 0.761061717 0.503763887 0.069715023 0.536667917 11.73297456 0.069771704 0.018032816 7.303328372 -0.863520828 -0.238826066 RVEISAPSNFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVEISAPSNFEHR 13 1 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 141.32 2.58E-05 141310000 71083 100130 93073 93608 105220 97006 83105 82691 82774 98234 FALSE TRUE 73889.41173 117326.5486 95498.55884 112123.383 87334.74198 74477.82664 76591.01295 81582.6624 79794.97991 117481.0715 0.628947377 0.9986847 0.812884643 0.954395305 0.743394156 0.63395597 0.651943432 0.6944324 0.679215629 1 16.8420688 3.05427353 8.472328651 0.703501556 0.85641731 0.132881435 0.134001471 0.389114744 55.07164675 0.035671713 0.042644655 1133.113803 -3.05427353 0.152915754 RVELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVELLK 6 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31;A0A3B3IRR8 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 ; 97.473 0.065792 909570000 839320 761490 858160 699560 1005600 1076000 967990 912230 837630 785430 FALSE TRUE 872457.0017 892269.9839 880524.3546 837930.88 834668.4712 826115.3069 892116.4144 900003.049 807483.8599 939319.9705 0.928817686 0.949910586 0.93740619 0.892061179 0.888588018 0.87948232 0.949747096 0.958143207 0.859647282 1 19.84125716 2.183910527 24.99999352 0.940917485 0.913488801 0.120608134 0.038522052 222.3544615 101715.5502 0.014624492 0.01080091 152.7251383 -2.183910527 -0.027428684 RVELSGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVELSGPK 8 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 ; 105.4 0.0070485 1459860000 2142000 1673580 2128300 1568230 2489200 2377600 2160330 1855940 1985320 1794450 FALSE TRUE 2226567.814 1961004.346 2183765.246 1878421.213 2066086.673 1825438.433 1990997.69 1831064.16 1913868.721 2146038.121 1.03752482 0.913778897 1.017579895 0.875297226 0.962744628 0.850608577 0.927755043 0.853230025 0.891814876 1 21.03324427 5.126332623 0.581483105 0.896932567 1.154465731 0.269008261 0.055427083 6.398285052 1.18765329 0.02439004 1.220933745 133761.9597 -5.126332623 0.257533164 RVEPPELPADLQHWISYNEASSQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVEPPELPADLQHWISYNEASSQLLR 26 1 Q8WUY1;H0YAR9 Q8WUY1 THEM6 Protein THEM6 0 58.477 0.048468 113860000 40431 44216 50784 34972 68050 63214 30805 37724 47179 54155 FALSE TRUE 42027.2471 51809.75405 52107.47276 41889.35722 56482.88531 48533.50652 28390.42361 37218.37148 45481.03701 64765.63539 0.648912758 0.799957473 0.804554336 0.646783699 0.872111961 0.749371271 0.438356289 0.574662338 0.702240266 1 15.9829409 3.730932537 23.91117736 0.679471192 0.756023118 0 0.152053129 1141.74537 3578950.771 0.041685501 0.066053216 5381.861741 -3.730932537 0.076551926 RVES(ph)EES(ph)GDEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVESEESGDEEGK 13 1 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 RVES(1)EES(1)GDEEGK 121.31 6.70E-05 0 321700 166280 193890 179280 258350 335840 274920 204330 215030 132390 TRUE FALSE 334400.9644 194837.2965 198942.9327 214741.0489 214435.7593 257846.2497 253371.052 201591.2906 207291.1123 158329.2857 2.112060083 1.230582805 1.256513801 1.356293928 1.354365734 1.628544261 1.600279132 1.2732407 1.309240494 1 17.27256861 -3.663473244 0.143167987 3.83E-13 1.612164835 0.289689108 0.24361061 128.6287655 1.60678729 39.67920108 1.502521651 0.000217033 3.663473244 1.612164835 RVES(ph)EES(ph)GDEEGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVESEESGDEEGKK 14 2 Q15435;B5MBZ8;C9JD73;Q15435-3;H7C118;C9JRC4 Q15435 PPP1R7 Protein phosphatase 1 regulatory subunit 7 2 RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK;RVES(1)EES(1)GDEEGKK 116.98 0.0016246 1955610000 7561000 1786230 2849970 1868410 4593900 6142900 5133700 3077380 3578130 1253930 TRUE FALSE 7859514.118 2093001.108 2924242.559 2237975.921 3813030.519 4716304.572 4731307.18 3036132.755 3449353.8 1499613.576 5.241026253 1.395693625 1.949997391 1.492368406 2.542675381 3.145013254 3.15501757 2.024610076 2.300161759 1 20.51615936 0.68792882 1.301602519 1.00683597 2.558754962 0.177084781 1.048397048 1.920670784 5.203041845 0.96238679 0.288697887 4.87448592 -0.68792882 1.551918992 RVFIMDNCEELIPEYLNFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVFIMDNCEELIPEYLNFIR 20 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 159.04 4.18E-11 217660000 140330 218180 185520 117530 270760 266670 97177 189790 199260 339510 FALSE TRUE 145870.3368 255650.7178 190354.8036 140777.0832 224736.3119 204739.9339 89560.01282 187246.1755 192088.6715 406030.4842 0.359259569 0.629634295 0.468818995 0.346715551 0.553496155 0.50424769 0.220574603 0.461162851 0.473089285 1 18.63122852 0.599551917 3.013249496 0.999993226 0.443206896 0.701898568 0.10840872 3.899933556 28.68188493 0.103021731 0.026914303 3.976966355 -0.599551917 -0.55678633 RVFIMDSCDELIPEYLNFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVFIMDSCDELIPEYLNFIR 20 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 61.181 0.084193 93863000 95714 134210 116420 91606 151260 179430 114780 139080 122650 193030 FALSE TRUE 99492.86263 157259.5235 119454.0008 109725.3934 125548.8792 137760.1018 105783.2437 137215.8601 118235.8505 230850.5327 0.430983899 0.681217936 0.517451701 0.475309249 0.543853539 0.596750201 0.458232617 0.594392651 0.512174908 1 17.81659954 -1.398908202 2.891744573 1.008400504 0.539417032 0.795375145 0.070795242 9108995.118 10756585.49 635701.0664 0.015714832 0.039910925 1.398908202 -0.468983472 RVFITDDFHDMMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVFITDDFHDMMPK 14 1 P14625 P14625 HSP90B1 Endoplasmin 0 113.63 0.00034043 671090000 878350 753000 902360 723460 1357300 1265700 952420 846620 1046100 818150 FALSE TRUE 913027.9362 882321.8925 925876.2429 866558.2287 1126586.631 971760.3569 877766.8317 835272.4437 1008451.065 978450.8281 0.93313625 0.901753943 0.946267524 0.885643104 1.151398311 0.993162179 0.897098563 0.853668288 1.030660955 1 19.90013982 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 181.86 7.03E-18 4059650000 1165198 1357209 1232391 1361665 1325223 1579120 1262139 1382150 1298286 1326625 TRUE FALSE 1211200.917 1590299.088 1264508.122 1630998.273 1099962.068 1212393.312 1163209.247 1363624.54 1251560.94 1586551.769 0.763417205 1.002361927 0.797016616 1.028014531 0.693303609 0.764168769 0.733168164 0.859489471 0.788856037 1 20.59746317 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.998)PEPQRENAS(0.912)PAPGT(0.045)T(0.042)AEEAMS(0.004)R;RVGDPPQPLPEEPMEVQGAERAS(0.997)PEPQRENAS(0.969)PAPGT(0.024)T(0.008)AEEAMS(0.001)R;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.981)PAPGT(0.01)T(0.009)AEEAMSR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.977)PAPGT(0.018)T(0.005)AEEAMSR;RVGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.995)PAPGT(0.002)T(0.002)AEEAMS(0.001)R 87.423 4.03E-05 1492740000 137797.3 183045.5 171177.6 144892.1 189317.7 217090.6 127948.6 159183 158547.3 226991.7 TRUE FALSE 143237.6438 214482.1407 175638.6289 173551.3249 157137.545 166674.5982 117919.6544 157049.4123 152841.2136 271466.3776 0.527644142 0.790087313 0.646999567 0.639310571 0.578847172 0.613978791 0.434380329 0.578522518 0.563020787 1 18.050414 -1.824702599 6.687178761 1.027117853 0.596818716 0.661089419 0.086569205 0.032933942 0.000863329 0.078873244 0.020455881 0.014972606 1.824702599 -0.430299137 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.966)PEPQRENAS(0.023)PAPGT(0.004)T(0.004)AEEAMS(0.003)R 164.93 1.29E-20 1220210000 54395.9 111422.7 109778.3 78870 117638.6 121760.8 56112.9 92862.8 93554.7 155948 TRUE FALSE 56543.49213 130558.682 112639.2127 94470.2506 97642.43279 93483.6995 51714.62427 91618.12606 90187.68462 186503.0248 0.303177346 0.700035198 0.603953812 0.506534683 0.523543427 0.501244951 0.277285713 0.491242038 0.483572235 1 17.5088395 -0.61210465 6.313432559 1.000000001 0.490308721 0.629636152 0.117826582 8.49E-10 5.38E-10 0.11391305 0.026849563 0.244284184 0.61210465 -0.50969128 RVGFQYEGTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVGFQYEGTYK 11 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 166.04 3.35E-05 1091390000 1088330 1103840 1273670 1042690 1875300 1527090 1308780 1266290 1355980 1490360 FALSE TRUE 1131298.109 1293415.933 1306862.887 1248930.97 1556537.176 1172446.491 1206194.404 1249317.454 1307178.545 1782367.507 0.634716524 0.725672976 0.73321741 0.70071462 0.873297549 0.657802886 0.676737204 0.700931457 0.73339451 1 20.76536341 0.800338261 5.772405412 0.999999832 0.714675178 0.664281437 0.060891478 4.464289764 128.9575369 0.057515099 0.014475263 6.314489725 -0.800338261 -0.285324654 RVHNNS(ph)PDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVHNNSPDTSR 11 1 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 RVHNNS(1)PDTSR;RVHNNS(1)PDTSR 91.441 0.0065779 116282000 55607 79025 66125 61299 71196 83016 71685 70352 61312 74329 TRUE FALSE 57802.4073 92596.92902 67848.27182 73423.75924 59094.12935 63736.79212 66066.14239 69409.04651 59105.3931 88892.34444 0.650251804 1.041674956 0.763263386 0.825985181 0.664783112 0.717011038 0.743215209 0.780821419 0.664909824 1 16.43977156 3.705307459 2.466315798 0.7516708 0.846840927 0.023029308 0.127989934 0.70158772 8.370193258 0.03287237 0.061699024 5073.497599 -3.705307459 0.095170128 RVIHFVSGETMEEYS(ph)T(ph)DEDEVDGLEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVIHFVSGETMEEYSTDEDEVDGLEKK 27 2 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 2 RVIHFVSGETMEEY(0.317)S(0.841)T(0.841)DEDEVDGLEKK 92.49 0.0059915 119990000 90851 39624 46631 31973 93772 78337 70622 50838 60725 23401 TRUE FALSE 94437.86763 46429.11377 47846.24217 38297.16397 77832.66893 60144.41896 65086.4631 50156.59976 58539.51911 27985.97791 3.374470884 1.65901345 1.709650537 1.368441156 2.781130936 2.149091204 2.325681215 1.792204651 2.091744634 1 14.77241654 -0.000491096 0.751727053 0.96564122 2.127754658 0.275798418 0.556241045 6.945480057 4.055972682 1.216473216 0.187259987 0.998869848 0.000491096 1.162113437 RVIISAPSADAPMFVMGVNHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 316.96 1.36E-67 36529140000 10347220 9725600 11512370 9308640 13083620 13647620 12135630 11829840 12444130 10564080 FALSE TRUE 10755736.24 11395896.15 11812391.82 11149861.21 10859670.95 10478167.09 11184407.61 11671280.34 11996268.19 12633909.21 0.851338731 0.902008709 0.934975202 0.882534536 0.859565378 0.82936856 0.885268955 0.923805937 0.949529397 1 23.59079777 1.245432648 1.497616032 0.995685776 0.878837853 0.676666686 0.027697927 0.236707328 0.995445074 0.028281786 0.008634171 17.59675746 -1.245432648 -0.116847923 RVIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVIISAPSADAPMFVMGVNHEKYDNSLK 28 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 316.46 4.39E-83 9155400000 3514300 2786600 3776800 1718770 4871500 4196700 3132700 3107800 4101600 3450500 FALSE TRUE 3653047.278 3265176.873 3875226.511 2058737.576 4043444.17 3222080.027 2887150.788 3066145.024 3953984.217 4126559.411 0.885252559 0.791258903 0.939093837 0.498899294 0.979858465 0.780815131 0.699650847 0.743026991 0.958179399 1 21.97650798 1.160532758 5.599713518 0.992212744 0.784800452 0.260761769 0.127755398 0.262361734 13.31674567 0.113865443 0.029004329 14.47214008 -1.160532758 -0.207412291 RVLQALEGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVLQALEGLK 10 1 P39019;A0A075B6E2 P39019 RPS19 40S ribosomal protein S19 0 ; 180.97 3.11E-06 1476190000 1565410 1353850 1285660 990180 4381900 2407000 1751240 1310470 1359180 3776900 FALSE TRUE 1627213.596 1586363.206 1319165.356 1186034.649 3637066.203 1848010.728 1613973.233 1292905.293 1310263.377 4516911.242 0.360249185 0.351205308 0.292050316 0.262576479 0.805210908 0.409131513 0.357317899 0.286236595 0.290079505 1 22.10690513 -1.826769715 2.705005446 1.21131312 0.378164332 0.60984446 0.148928133 94037423.92 66465647.27 129405768 0.040718031 0.01490151 1.826769715 -0.833148788 RVLVDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVLVDVER 8 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 112.11 0.0049781 392250000 275760 326250 344540 290200 361740 360660 326340 368720 318980 360330 FALSE TRUE 286647.2177 382280.8996 353518.9954 347600.6938 300251.564 276902.1809 300760.6181 363777.9115 307499.9721 430929.7646 0.665183149 0.887107206 0.820363374 0.806629577 0.696752902 0.642569169 0.697934194 0.844169843 0.713573295 1 18.71709322 -1.47871877 3.687313743 1.00287894 0.759266563 0.469498937 0.078584563 0.001944943 0.00027496 0.079537923 0.018536856 0.033210945 1.47871877 -0.243612378 RVNALK ddPTM_MDA-MB-175_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 ; 138.53 0.019664 1561490000 1305230 1284650 1421520 1206910 1749350 1804790 1461020 1373040 1548830 1396060 FALSE TRUE 1356761.488 1505278.644 1458565.979 1445633.196 1451996.112 1385654.874 1346501.435 1354636.645 1493087.911 1669591.228 0.81263094 0.901585142 0.873606638 0.86586056 0.869671622 0.829936604 0.806485691 0.811358267 0.894283514 1 20.67106349 0.941866384 5.894413524 0.999986101 0.846487046 0.709235401 0.029909876 0.239006176 22.71952059 0.031936972 0.008034613 8.747146179 -0.941866384 -0.153499054 RVNNGNTAPEDS(ph)SPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.5)S(0.5)PAKK 80.98 0.0053585 116000000 183040 78961 106200 73326 160490 168830 151840 107680 126290 66293 TRUE FALSE 190266.5605 92521.93752 108967.6592 87829.66394 133209.9671 129621.7911 139938.384 106236.7257 121744.8476 79281.84409 2.399875567 1.167000321 1.374433964 1.107815603 1.680207728 1.634949245 1.765074787 1.339988076 1.535595557 1 16.2747029 0.224735668 1.022197739 0.997726425 1.538283269 0.185430214 0.348156324 7.096374202 7.827849914 0.359672545 0.100839465 1.677782529 -0.224735668 0.540556844 RVNNGNTAPEDSS(ph)PAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVNNGNTAPEDSSPAKK 17 2 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 RVNNGNTAPEDS(0.187)S(0.813)PAKK;RVNNGNT(0.001)APEDS(0.25)S(0.75)PAKK 64.761 0.023313 149261000 366780 149677 213757 148385 303870 328500 308010 236590 251080 131116 TRUE FALSE 381260.7576 175382.8604 219327.683 177735.1101 252218.2859 252210.8535 283867.3714 233418.898 242043.6798 156805.6698 2.431422014 1.118472697 1.398722911 1.133473747 1.608476825 1.608429426 1.810313184 1.488587105 1.543590102 1 17.2586182 0.279486878 2.175946344 0.999997961 1.549221167 0.189457435 0.351873379 39.97504698 117.4334616 0.31900448 0.086569841 1.90321073 -0.279486878 0.549223206 RVNS(ph)GDTEVGSSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVNSGDTEVGSSLLR 15 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 RVNS(0.998)GDT(0.002)EVGSSLLR;RVNS(0.863)GDT(0.095)EVGS(0.031)S(0.011)LLR;RVNS(0.946)GDT(0.054)EVGSSLLR 114.53 0.00036707 400370000 223639 261394 253560 239711 328738 336865 224690 273152 279672 327847 TRUE FALSE 232468.4404 306286.3861 260167.9819 287125.1203 272859.2322 258633.209 207078.2107 269490.8442 269606.6594 392082.3426 0.592907191 0.781178729 0.663554447 0.732308215 0.695923286 0.659640032 0.5281498 0.687332264 0.687627649 1 18.58079715 -1.735311567 3.140726676 1.048624463 0.670250692 0.691618008 0.066137049 3881291.417 11731874.42 1017181.089 0.015343985 0.018394519 1.735311567 -0.378373772 RVNTTQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RVNTTQK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 ;;;; 125.49 0.0064841 1427272000 895582 859080 893781 785699 1315930 1172221 1274312 1016540 1038008 989829 FALSE TRUE 930940.2689 1006620.307 917073.6671 941107.9171 1092248.689 899990.4379 1174428.096 1002914.944 1000650.295 1183767.041 0.786421852 0.850353382 0.77470789 0.795011083 0.922688883 0.760276648 0.992110825 0.847223237 0.84531015 1 20.17495376 -5 0.078602604 1.528855462 0.680152138 0.416027269 0.063129403 241.7716793 1.349634546 22.20915063 2.163706774 1.00E-05 5 -0.848703324 RVPFS(ph)LLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVPFSLLR 8 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 RVPFS(1)LLR;RVPFS(1)LLR 102.4 0.0030456 347520000 118621 188148 156663 117477 326911 231789 130091 132505 162883 500606 TRUE FALSE 123304.2487 220460.9554 160745.7665 140713.6 271342.785 177959.5175 119894.1275 130728.9872 157020.8726 598690.161 0.205956698 0.368238815 0.268495754 0.235035765 0.4532274 0.297248108 0.200260728 0.218358336 0.262274016 1 19.19145004 -1.479942159 3.413644047 1.01210813 0.277661656 0.892816419 0.074965545 594561049.4 720559271.9 67089479.18 0.018655863 0.033117523 1.479942159 -0.734446474 RVPGS(ph)SGHLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.591)S(0.409)GHLHK;RVPGS(0.5)S(0.5)GHLHK 93.716 0.0042517 907770000 650250 914940 891780 829800 863020 1130450 835530 911000 847420 820080 TRUE FALSE 675922.3721 1072073.828 915020.5194 993931.9633 716324.1687 867920.1196 770038.9753 898789.5351 816921.5197 980758.9746 0.689182959 1.093106314 0.932971855 1.013431423 0.730377378 0.884947415 0.785145989 0.916422443 0.832948299 1 19.90353911 4.799489011 22.32260677 0.899957525 0.689175965 0.284192917 0.104022582 33810.38199 12385393.26 0.024426936 52.52922757 63021.53991 -4.799489011 -0.210781559 RVPGSS(ph)GHLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVPGSSGHLHK 11 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 RVPGS(0.384)S(0.616)GHLHK;RVPGS(0.187)S(0.813)GHLHK;RVPGS(0.422)S(0.578)GHLHK;RVPGS(0.133)S(0.867)GHLHK 127.87 0.00013051 2040600000 1171390 1120900 1195620 1116490 1383370 1466030 1224820 1161300 1070090 914940 TRUE FALSE 1217637.382 1313405.856 1226778.839 1337328.39 1148225.262 1125566.75 1128815.408 1145734.673 1031577.67 1094204.975 1.112805561 1.200328901 1.12115999 1.222191838 1.049369439 1.0286617 1.031630666 1.047093277 0.942764558 1 20.06145159 3.105246946 5.680998553 1.019574415 1.163061584 0.761656481 0.040701207 0.098741896 4.634844884 0.011275685 0.013562595 1274.22742 -3.105246946 0.143487169 RVPLS(ph)PLSLLAGPADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVPLSPLSLLAGPADAR 17 1 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 RVPLS(1)PLSLLAGPADAR;RVPLS(0.838)PLS(0.162)LLAGPADAR;RVPLS(1)PLSLLAGPADAR 194.75 3.46E-11 1188835000 275986 924679 1011451 1123215 791109 1466175 767397 1090941 1078059 1196939 TRUE FALSE 286882.1404 1083485.425 1037810.244 1345383.575 656636.5748 1125678.076 707246.4179 1076318.72 1039259.867 1431456.28 0.200412785 0.756911294 0.725003102 0.939870531 0.458719266 0.786386627 0.49407476 0.751904711 0.726015793 1 20.44905218 -5 0.143084638 2.152964046 0.544575177 0.264009559 0.193714623 204.4885546 1.776837147 67.53467792 1.076899973 1.00E-05 5 -1.60838887 RVPPPALS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 103.44 0.0020961 733450000 145973 213109 175165 216525 200378 250351 190067 191148 182015 196092 TRUE FALSE 151736.1268 249708.813 179729.9438 259352.9987 166317.8191 192210.7744 175169.0519 188585.9737 175464.3157 234512.473 0.647027959 1.064799709 0.766398228 1.105924113 0.709206709 0.819618555 0.74694983 0.804161806 0.748208884 1 17.83930513 RVPS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVPSPGK 7 1 D6RIF6;H0Y9L2 D6RIF6 SLAIN2 1 RVPS(1)PGK;RVPS(1)PGK;RVPS(1)PGK 79.148 0.020464 468030000 1276670 942310 1106180 972550 1343170 1831240 1452140 1162200 1141320 781290 TRUE FALSE 1327073.917 1104144.412 1135007.96 1164917.487 1114858.443 1405962.263 1338317.472 1146622.61 1100244.116 934368.8168 1.420289177 1.181700836 1.214732276 1.246742685 1.193167434 1.504718734 1.432322492 1.227162753 1.177526579 1 19.8336326 0.999499304 1.967225738 1.003848099 1.303422069 0.447607077 0.106044583 0.330866293 2.709200442 0.105590271 0.029675854 9.988477684 -0.999499304 0.29957397 RVPS(ph)PTPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 RVPS(0.618)PT(0.382)PAPK;RVPS(0.918)PT(0.082)PAPK;RVPS(0.92)PT(0.08)PAPK;RVPS(0.522)PT(0.478)PAPK;RVPS(0.919)PT(0.081)PAPK;RVPS(0.913)PT(0.087)PAPK;RVPS(0.907)PT(0.093)PAPK;RVPS(0.905)PT(0.095)PAPK;RVPS(0.996)PT(0.004)PAPK 141.58 2.28E-05 64908780000 33768290 27005070 30181890 26387210 38494380 38358100 35752600 31691550 31556100 25729410 TRUE FALSE 35101488.16 31642980.7 30968454.85 31606521.38 31951119.04 29450012.6 32950217.79 31266776.61 30420402.13 30770595.27 1.140747777 1.028351269 1.006430151 1.027166394 1.038365321 0.957082966 1.070834591 1.016125178 0.988619227 1 24.87504902 4.736807304 3.944588166 1.016105476 1.152131167 0.637125521 0.028650956 0.144876308 4.642969958 0.006557149 0.056557068 54551.57623 -4.736807304 0.136025692 RVPVLGK ddPTM_MDA-MB-175_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 85.265 0.033572 214370000 302510 283410 303770 227810 403500 374800 373800 324480 325650 307350 FALSE TRUE 314453.3284 332083.4629 311686.4957 272870.1381 334913.2141 287758.3801 344500.5793 320130.8763 313929.9201 367569.3479 0.855493882 0.903457986 0.847966506 0.742363692 0.911156537 0.782868272 0.937239683 0.870940077 0.854069911 1 18.48765694 -0.62822024 0.400268612 1.042616435 0.846391343 0.385818625 0.054895127 10.03435755 1.42094819 0.606362099 0.035277862 0.235385529 0.62822024 -0.196225091 RVQPQWS(ph)PPAGTQPCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVQPQWSPPAGTQPCR 16 1 P49589-3;P49589;B4DKY1;P49589-2;E9PLP0;C9JLN0;E9PRS8 P49589-3 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 RVQPQWS(1)PPAGTQPCR;RVQPQWS(1)PPAGTQPCR 141.83 9.60E-07 367650000 137726 168880 141446 123824 166924 163935 114780 141337 153853 195634 TRUE FALSE 143163.5288 197883.8263 145132.199 148316.0176 138550.3181 125863.5807 105783.2437 139442.6087 148315.8606 233964.7367 0.611902165 0.845784835 0.620316553 0.633924666 0.592184618 0.537959619 0.45213328 0.5959984 0.633923995 1 17.83593158 -1.819657656 6.388479615 1.027454816 0.610298628 0.605323136 0.093517301 0.03618734 0.001021543 0.089603472 0.02294756 0.015147548 1.819657656 -0.417156188 RVQS(ph)LPSVPLSCAAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVQSLPSVPLSCAAYR 16 1 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 RVQS(0.997)LPS(0.003)VPLSCAAYR;RVQS(1)LPSVPLSCAAYR;RVQS(1)LPSVPLSCAAYR;RVQS(1)LPSVPLSCAAYR 192.64 3.08E-10 2462820000 417715 518650 446524 433440 688500 611910 413455 495249 509177 718510 TRUE FALSE 434206.7107 607724.103 458160.7823 519173.1383 571469.0159 469803.1761 381047.3167 488610.9972 490851.8192 859288.2778 0.50530971 0.707241235 0.533186352 0.604189713 0.66504924 0.546735232 0.443445263 0.568622906 0.571230671 1 19.71278269 -1.545512481 2.439356423 1.033342158 0.571615476 0.763617934 0.071494253 1812722.482 1583524.119 394872.6998 0.018321944 0.02847656 1.545512481 -0.461726682 RVQSS(ph)PNLLAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVQSSPNLLAAGR 13 1 O94875-12;O94875-9;O94875-11;C9JN77;C9IZT7;C9JWC3;C9JG84;C9JI79;C9JEA9;C9J372;C9JZ60;C9JBB0;C9JDX2;C9J4Z9;C9J9D3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 RVQS(0.309)S(0.691)PNLLAAGR 124.48 6.07E-05 0 80978 77134 91922 87642 111350 115090 91828 88601 87143 86793 TRUE FALSE 84175.07397 90381.16448 94317.56283 104977.326 92422.76677 88362.09171 84630.28141 87413.44852 84006.74045 103798.4266 0.810947494 0.870737327 0.908660814 1.011357585 0.89040624 0.851285464 0.815332989 0.842146181 0.80932576 1 16.66342505 2.787867982 4.920576065 0.848919489 0.904396805 0.038409109 0.068545998 0.450762357 24.93916279 0.021277702 0.02226835 613.5754603 -2.787867982 0.055477316 RVS(ph)ADSQPFQHGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVSADSQPFQHGDK 14 1 Q96AX9-14;Q96AX9-12;Q96AX9-4;Q96AX9-6;Q96AX9-5;Q96AX9-9;Q96AX9-3;Q96AX9;Q96AX9-13;Q96AX9-2;Q96AX9-11;D6RAZ0;Q96AX9-10;Q96AX9-7;Q96AX9-8;E9PD12;H0YAM8;F2Z2L2;D6RED3 Q96AX9-14 MIB2 E3 ubiquitin-protein ligase MIB2 1 RVS(0.98)ADS(0.02)QPFQHGDK;RVS(0.988)ADS(0.012)QPFQHGDK 64.723 0.028289 122618000 125926 106376 117546 110493 153287 174350 152122 121206 126932 120064 TRUE FALSE 130897.6557 124645.2505 120609.3453 132348.1856 127231.3305 133859.8548 140198.2801 119581.4318 122363.7421 143588.242 0.911618207 0.868074215 0.839966724 0.921720217 0.886084603 0.932248023 0.97639109 0.832807966 0.852184973 1 17.13157809 3.718274668 24.58926113 0.906509607 0.872705157 0.107732833 0.05091705 1708.657886 2071120.539 0.013820041 0.02143613 5227.266805 -3.718274668 -0.03380445 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 RVS(1)EVEEEKEPVPQPLPSDDTR;RVS(0.882)EVEEEKEPVPQPLPS(0.114)DDT(0.004)R;RVS(0.995)EVEEEKEPVPQPLPS(0.005)DDTR;RVS(1)EVEEEKEPVPQPLPSDDTR 214.47 1.18E-25 1673330000 704420 482721 578777 551473 804330 895040 920990 732320 766280 488172 TRUE FALSE 732231.0455 565624.5767 593860.4041 660552.7134 667610.2739 687180.5245 848800.3972 722504.4482 738701.7325 583819.9568 1.254206947 0.968833919 1.017197849 1.131432226 1.143520817 1.177041854 1.453873557 1.237546678 1.265290307 1 19.155164 2.811708455 2.082514157 1.26428174 1.080676452 0.184641446 0.12641984 0.396907971 3.394457695 0.043018613 0.044680593 648.1991467 -2.811708455 -0.183605287 RVS(ph)GPDPKPGS(ph)NCSPAQSVLSEVPSVPTNGMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 2 RVS(0.986)GPDPKPGS(0.531)NCS(0.413)PAQS(0.058)VLS(0.011)EVPSVPTNGMAK 83.058 0.00035079 65661000 119640 69698 96451 73276 123430 125610 109310 93880 124680 70831 TRUE FALSE 124363.4796 81668.08932 98964.5923 87769.77409 102449.4127 96438.98114 100741.9966 92621.69216 120192.7912 84708.97831 1.468126308 0.964101928 1.168289292 1.036133074 1.209428029 1.138474139 1.18927177 1.093410569 1.418890814 1 16.37022727 RVS(ph)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVSGPDPKPGSNCSPAQSVLSEVPSVPTNGMAK 33 2 P22314;Q5JRR9;Q5JRS0;Q5JRS2;Q5JRS1;Q5JRS3 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 RVS(1)GPDPKPGSNCSPAQSVLSEVPSVPTNGMAK;RVS(0.951)GPDPKPGS(0.012)NCS(0.012)PAQS(0.012)VLS(0.012)EVPSVPTNGMAK 222.29 2.13E-36 2085120000 2582460 1472432 2189400 1526332 2823010 2581580 2775620 2301660 2622930 1526270 TRUE FALSE 2684417.515 1725310.742 2246457.563 1828235.914 2343155.769 1982047.169 2558059.652 2270810.012 2528531.262 1825313.384 1.470661169 0.945213439 1.230724314 1.001601111 1.283700535 1.085866781 1.401435871 1.244065831 1.385258709 1 20.79971275 2.253676067 24.99893962 1.278797449 1.159751896 0.051551065 0.17287883 531.0585344 878298.2127 0.054673305 0.045578391 179.3395463 -2.253676067 -0.119045552 RVS(ph)HDPFAQQRPYENFQNTEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSHDPFAQQRPYENFQNTEGK 22 2 Q13546-2;Q13546 Q13546-2 RIPK1 Receptor-interacting serine/threonine-protein kinase 1 1 RVS(1)HDPFAQQRPYENFQNTEGK 103.12 0.00030995 105160000 73091 63504 72708 61178 77604 85440 72562 61839 80746 62609 TRUE FALSE 75976.68912 74410.31801 74602.83021 73278.8258 64412.8998 65597.85486 66874.40083 61010.14935 77839.96723 74876.03483 1.014699687 0.993780162 0.996351241 0.978668622 0.860260562 0.87608612 0.893134913 0.814815441 1.039584527 1 16.19221642 3.356724607 5.515151871 0.895915581 0.998612982 0.264578301 0.063319022 0.221239593 9.811131933 0.01719563 0.023392591 2273.655215 -3.356724607 0.102697401 RVS(ph)HS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK;RVS(1)HS(1)PPPK 105.03 0.011074 8034590000 2729370 2084560 2456650 2098620 2825140 2960470 2921670 2438300 2545400 1914610 TRUE FALSE 2837127.635 2442566.964 2520672.317 2513720.772 2344923.712 2272945.709 2692661.871 2405618.577 2453791.551 2289741.172 1.23906041 1.066743698 1.100854694 1.097818742 1.024099903 0.992664908 1.175967792 1.050607207 1.071645818 1 21.1267531 RVS(ph)HS(ph)PPPKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 73.156 0.023775 1524612000 263835 328547 313330 222527 407876 397316 238145 306196 328808 398876 TRUE FALSE 274251.4095 384972.3915 321495.6372 266542.1764 338545.3832 305045.3804 219478.5726 302091.9435 316974.2643 477028.1153 0.574916657 0.807022436 0.673955322 0.558755696 0.709696918 0.639470443 0.460095675 0.633279117 0.664477112 1 18.86371477 0.71801877 3.522202407 0.999991242 0.631844811 0.610844501 0.087559243 2.461879752 30.04621344 0.085616196 0.022066605 5.224187671 -0.71801877 -0.368146432 RVS(ph)HSPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSHSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.708)HS(0.292)PPPK 56.783 0.073304 98131000 71379 70607 70966 69038 97082 96172 84085 83566 78421 68313 TRUE FALSE 74197.09804 82733.203 72815.43226 82693.51034 80580.03632 73837.5105 77494.19798 82445.93446 75598.64353 81697.62442 0.908191622 1.012675749 0.891279676 1.012189901 0.986320433 0.903790178 0.948548976 1.009159508 0.9253469 1 16.31800651 -5 0.169517366 1.154978176 0.949813818 0.070023334 0.045340404 388.6009639 3.663068501 20.31544035 0.157511843 1.00E-05 5 -0.205164358 RVS(ph)LSEIGFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSLSEIGFGK 11 1 E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;H0YBX5 E5RJM2 CDK16 Cyclin-dependent kinase 16 1 RVS(0.982)LS(0.018)EIGFGK;RVS(0.96)LS(0.04)EIGFGK;RVS(0.997)LS(0.003)EIGFGK;RVS(0.973)LS(0.027)EIGFGK 176.29 5.40E-06 5094910000 4888930 4229730 5123590 4409600 6360630 6269700 6130070 5141340 5693310 4703860 TRUE FALSE 5081948.731 4956153.225 5257114.964 5281805.719 5279452.385 4813657.193 5649579.095 5072428.747 5488408.885 5625491.306 0.903378648 0.881016956 0.934516592 0.938905676 0.938487342 0.85568654 1.0042819 0.901686354 0.97563192 1 22.42354767 -5 0.078359672 1.271335221 0.841062437 0.345371737 0.037942111 287.790307 1.602232312 13.36565113 1.311260077 1.00E-05 5 -0.430272783 RVS(ph)LTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSLTQR 7 1 Q96I34 Q96I34 PPP1R16A Protein phosphatase 1 regulatory subunit 16A 1 RVS(1)LTQR 73.887 0.029202 247770000 82843 98840 90225 98739 111870 114890 119540 94445 97742 123470 TRUE FALSE 86113.70561 115815.0011 92576.33762 118269.2795 92854.37736 88208.53867 110170.1424 93179.11926 94224.28451 147661.5825 0.583182871 0.784327238 0.62694938 0.800948205 0.628832332 0.597369588 0.746098887 0.631031563 0.638109676 1 17.171935 -1.56319102 3.002661429 1.015903681 0.673491755 0.639461536 0.074139829 370777671.1 419000476.8 47555675.95 0.016461578 0.027340659 1.56319102 -0.342411925 RVS(ph)LVGADDLR ddPTM_MDA-MB-175_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 166.48 1.25E-05 1309630000 1026240 1233570 1201230 1312550 1311140 1530870 1288160 1279350 1299600 1591360 TRUE FALSE 1066756.748 1445426.052 1232535.041 1572168.472 1088272.891 1175348.643 1187190.653 1262202.406 1252827.65 1903156.524 0.560519713 0.759488793 0.647626732 0.826084693 0.571825217 0.617578548 0.623800848 0.663215238 0.658289339 1 20.85996279 -1.512757198 2.512999859 1.020191928 0.661156396 0.641832256 0.076464621 2766474.27 2577674.012 381921.9327 0.018521343 0.030707383 1.512757198 -0.359035532 RVS(ph)PLNLSS(ph)VTP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 2 RVS(1)PLNLS(0.029)S(0.485)VT(0.485)P 64.565 0.042175 70582000 114940 159920 155480 149690 176280 193050 146480 152320 153940 199730 TRUE FALSE 119477.92 187385.016 159531.9365 179298.2352 146315.9886 148217.0632 134998.5148 150278.3995 148399.7295 238863.2694 0.500193773 0.784486524 0.667879733 0.750631253 0.612551226 0.620510066 0.565170673 0.629139842 0.621274798 1 17.8658255 -1.8498275 2.359523572 1.158286351 0.64200494 0.658672219 0.077915916 8123511.024 4556438.315 7236424.176 0.018317253 0.014130987 1.8498275 -0.516281411 RVS(ph)PLNLSSVTP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 RVS(0.989)PLNLS(0.006)S(0.006)VTP;RVS(1)PLNLSSVTP;RVS(0.999)PLNLSSVTP;RVS(1)PLNLSSVTP;RVS(0.998)PLNLS(0.001)SVTP 107.74 0.0018874 2962967000 2995133 3327110 3060892 3077856 3730130 3973260 3226942 3189330 3028150 4207940 TRUE FALSE 3113383.164 3898515.261 3140661.36 3686646.73 3096083.835 3050530.58 2974005.854 3146582.248 2919167.473 5032405.277 0.618667017 0.774682293 0.624087526 0.732581445 0.615229431 0.606177446 0.590971055 0.625264078 0.580074003 1 22.26281668 -1.278118205 6.580206358 1.000006367 0.641821606 0.766347907 0.059489738 5.58E-06 6.12E-07 0.057859683 0.013637416 0.052708638 1.278118205 -0.358184762 RVS(ph)QDLEVEKPDASPTSLQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVSQDLEVEKPDASPTSLQLR 21 2 O94885 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 RVS(1)QDLEVEKPDASPTSLQLR;RVS(1)QDLEVEKPDASPTSLQLR 121.1 2.38E-05 699040000 420470 310210 328110 297130 432500 431370 422280 371010 381590 289230 TRUE FALSE 437070.4803 363486.1544 336660.8161 355901.4272 358983.8045 331190.855 389180.5902 366037.2178 367856.6504 345899.0809 1.263578033 1.050844522 0.973292023 1.02891695 1.037828154 0.957478274 1.125127564 1.058219689 1.063479699 1 18.39999165 4.734112225 5.008393497 1.035016065 1.274112344 0.700372565 0.045370504 0.090965127 7.19176655 0.011130395 0.075156214 54214.09651 -4.734112225 0.239096278 RVS(ph)RT(ph)PEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSRTPEPK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RVS(1)RT(1)PEPK 84.718 0.028926 363190000 532710 408100 466500 370490 634540 697440 521590 461870 504780 363290 TRUE FALSE 553741.8021 478188.0004 478657.3732 443771.8162 526681.1175 535470.1298 480706.4129 455679.3881 486613.0664 434469.7199 1.274523348 1.100624459 1.101704794 1.021410229 1.212238951 1.232468237 1.106420979 1.048817368 1.120016066 1 18.72889611 -5 0.110028281 0.558671318 1.207383393 0.277070984 0.073674649 247.7995769 1.813723826 24.30401126 0.970224407 1.00E-05 5 0.648712076 RVS(ph)RTPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSRTPEPK 9 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RVS(0.65)RT(0.35)PEPK 64.121 0.05638 100410000 114020 89873 123600 66534 191500 157270 96167 112170 146460 145620 TRUE FALSE 118521.5976 105307.9886 126821.1175 79694.22662 158948.8984 120746.4259 88629.17925 110666.5446 141188.9332 174151.4509 0.680566237 0.604691997 0.728223146 0.457614485 0.912704991 0.693341487 0.508920131 0.635461514 0.810724989 1 17.40998297 0.991114845 3.335502396 0.998681314 0.64987202 0.465116591 0.117274923 0.186023295 5.236939473 0.108791291 0.02831344 9.797490354 -0.991114845 -0.348809294 RVS(ph)S(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.483)S(0.517)S(0.517)S(0.483)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.5)S(0.5)S(0.5)S(0.5)ELDLPSGDHCEAGLLQLDVPLLR 95.794 0.0011595 80225000 24451 36740 29908 38343 42623 49070 32852 36064 36331 40155 TRUE FALSE 25416.34436 43049.8092 30687.42705 45927.13096 35377.95768 37674.23616 30276.9744 35580.62107 35023.45441 48022.60344 0.529257944 0.896448883 0.639020479 0.956364871 0.736693872 0.78451049 0.630473407 0.740914039 0.729311864 1 15.551426 -1.6163982 2.548981924 1.027032486 0.742778367 0.305067199 0.118391855 12480869.12 10745083.83 2239627.794 0.026852375 0.024188102 1.6163982 -0.284254118 RVS(ph)SSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 2 RVS(0.742)S(0.275)S(0.093)S(0.885)ELDLPS(0.005)GDHCEAGLLQLDVPLLR;RVS(0.742)S(0.438)S(0.204)S(0.613)ELDLPS(0.002)GDHCEAGLLQLDVPLLR 140.73 2.95E-07 162625000 42289 60518 54121 61046 63649 73159 55732 60112 57621 74038 TRUE FALSE 43958.60237 70911.49574 55531.43772 73120.7166 52829.96571 56168.93099 51363.58021 59306.29696 55547.23147 88544.32856 0.496458701 0.800858699 0.627159736 0.825809149 0.596649911 0.634359443 0.580088878 0.669792159 0.627338107 1 16.43411228 -1.914398008 2.503889826 1.210177474 0.655694304 0.557590779 0.09318926 19863758.1 10482881.82 24504731.82 0.021997418 0.01217873 1.914398008 -0.554483171 RVS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.93)S(0.048)S(0.011)S(0.011)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.835)S(0.055)S(0.055)S(0.055)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.25)S(0.25)S(0.25)S(0.25)ELDLPSGDHCEAGLLQLDVPLLR;RVS(0.956)S(0.04)S(0.002)S(0.003)ELDLPSGDHCEAGLLQLDVPLLR 292.54 4.95E-81 3100587000 154913 248575 234049 227219 274725 287319 226777 245321 236079 293116 TRUE FALSE 161029.0849 291265.8226 240148.5092 272162.24 228027.3426 220593.5166 209001.6262 242032.8733 227582.5629 350546.4682 0.459365874 0.830890764 0.685068974 0.776394187 0.650491057 0.629284665 0.596216608 0.690444478 0.649222239 1 18.41924617 -1.918264571 2.365841519 1.211852863 0.669297281 0.530713091 0.094893532 9841767.891 4865802.015 11552537.15 0.021325111 0.012070783 1.918264571 -0.542555583 RVS(ph)TDLPEGQDVYTAACNSVIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSTDLPEGQDVYTAACNSVIHR 23 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 RVS(0.948)T(0.052)DLPEGQDVYTAACNSVIHR;RVS(0.974)T(0.026)DLPEGQDVYTAACNSVIHR;RVS(0.97)T(0.03)DLPEGQDVYTAACNSVIHR;RVS(0.928)T(0.072)DLPEGQDVYTAACNSVIHR 286.74 1.03E-52 1507840000 481908 597650 596420 654110 601020 744280 577260 611994 575640 661150 TRUE FALSE 500934.1 700291.7384 611963.1952 783491.0057 498858.8351 571432.2497 532012.8528 603791.2215 554922.8288 790689.684 0.633540705 0.885672031 0.773961274 0.990895697 0.630916079 0.722701031 0.672846584 0.763626026 0.701821258 1 19.59275208 -1.381437761 3.040736641 1.003174196 0.756956197 0.324616244 0.106786852 21646679.98 27132380.36 607986.2216 0.024930774 0.041549159 1.381437761 -0.246218 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 261.94 7.02E-37 7556850000 3117700 3583380 3838190 3884250 4737460 4420100 3427920 3823910 3700100 4911030 TRUE FALSE 3240789.203 4198797.64 3938216.385 4652543.057 3932188.241 3393598.762 3159230.673 3772656.741 3566934.124 5873252.301 0.55178784 0.714901629 0.670534175 0.792157874 0.669507802 0.577805718 0.537901406 0.642345424 0.607318389 1 22.48572818 -1.743099515 2.532289553 1.079916973 0.642511209 0.683917635 0.073312964 22000913.79 16014796.89 11010601.06 0.018658864 0.018067601 1.743099515 -0.437405764 RVS(ph)VELTNSLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RVSVELTNSLFK 12 1 P14923 P14923 JUP Junction plakoglobin 1 RVS(1)VELTNSLFK;RVS(0.915)VELT(0.081)NS(0.004)LFK;RVS(1)VELTNSLFK;RVS(1)VELTNSLFK 189.52 4.79E-06 2762360000 2664561 2771736 2678040 2767363 3334775 3854545 3507231 2878216 2782128 2863300 TRUE FALSE 2769759.926 3247760.097 2747831.922 3314739.142 2767931.137 2959385.34 3232325.07 2839638.222 2681999.757 3424308.814 0.808852261 0.948442525 0.802448632 0.968002398 0.8083182 0.864228521 0.943935038 0.829258801 0.783223682 1 21.70738138 -1.678304055 3.027268728 1.014301833 0.865295 0.288653091 0.064856632 22819333.25 24085313.72 2518779.208 0.014376958 0.020974709 1.678304055 -0.149006833 RVSLEPHQGPGT(ph)PESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSLEPHQGPGTPESK 16 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 RVS(0.001)LEPHQGPGT(0.996)PES(0.003)K 67.251 0.030651 152750000 134240 108740 143370 111230 169920 159790 146070 136220 129530 123120 TRUE FALSE 139539.8989 127415.2491 147106.34 133230.962 141037.0591 122681.1941 134620.6517 134394.1937 124868.2406 147243.0067 0.947684389 0.865339903 0.999071829 0.904837282 0.957852344 0.833188597 0.914275351 0.912737363 0.84804191 1 17.16783959 RVSS(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVSSSSELDLPSGDHCEAGLLQLDVPLLR 29 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 RVS(0.184)S(0.272)S(0.272)S(0.272)ELDLPSGDHCEAGLLQLDVPLLR 181.32 4.90E-18 855520000 40704 66033 60414 62396 72684 84610 61591 63184 68630 85136 TRUE FALSE 42311.02535 77373.65408 61988.43847 74737.74257 60329.19964 64960.60978 56763.33648 62337.12183 66160.01971 101816.7692 0.415560479 0.75993036 0.608823468 0.734041584 0.592527146 0.638014841 0.55750479 0.612248084 0.649794923 1 16.63561567 0.715749408 3.756254304 0.999997203 0.620446033 0.623221023 0.089218733 2.757038333 35.85565481 0.078115353 0.020037347 5.196960407 -0.715749408 -0.37955117 RVT(ph)LPAITPIILQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVTLPAITPIILQK 14 1 Q14449-2 Q14449-2 GRB14 Growth factor receptor-bound protein 14 1 RVT(1)LPAITPIILQK;RVT(1)LPAITPIILQK 182.34 8.99E-07 463060000 715240 706580 827250 788430 1182950 1000130 837030 855770 864700 853300 TRUE FALSE 743478.2275 827929.6186 848808.8146 944379.1008 981872.5815 767864.9646 771421.4014 844299.8029 833579.6159 1020487.798 0.728551806 0.81130771 0.831767726 0.925419298 0.962160041 0.752448943 0.755933979 0.827349239 0.816844276 1 19.9608275 4.675910552 2.1488945 0.848457016 0.706367201 0.199817729 0.078262798 1.040132487 6.030935072 0.020459699 0.270004795 47414.43195 -4.675910552 -0.142089815 RVT(ph)QHESDNENEIQIQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVTQHESDNENEIQIQNK 18 1 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 RVT(0.605)QHES(0.395)DNENEIQIQNK 89.507 0.002194 305470000 81417 63746 66276 52638 94174 109090 64932 72882 70679 62313 TRUE FALSE 84631.40603 74693.87962 68003.20701 63049.63929 78166.33712 83755.50077 59842.46017 71905.136 68135.2766 74522.0393 1.135656067 1.002305899 0.912524773 0.846053596 1.048902283 1.123902426 0.803016943 0.96488417 0.914296995 1 16.18537953 4.666867438 3.05586411 0.949438814 1.150997068 0.281367552 0.088386916 0.400365876 5.890052235 0.021939757 0.17657285 46437.35101 -4.666867438 0.201558253 RVTSIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVTSIADR 8 1 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 ; 98.048 0.012505 297090000 234980 499120 329610 460860 380760 517160 314510 366340 288320 581070 FALSE TRUE 244257.1918 584839.9774 338199.9074 552016.7325 316038.5512 397057.4276 289857.8844 361429.8115 277943.4195 694919.5412 0.351489888 0.8415938 0.486674913 0.794360641 0.454784378 0.571371798 0.417109992 0.520103106 0.399964892 1 19.40648642 -1.632813216 5.831945831 1.003292079 0.544085236 0.446962634 0.154183581 0.006172166 0.000388607 0.139616953 0.03273617 0.023290928 1.632813216 -0.459206842 RVVFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RVVFLK 6 1 Q02878;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ; 122.5 0.030777 778640000 1076200 1045800 1170220 977300 1461850 1367060 1254680 1233340 1224830 1090130 FALSE TRUE 1118689.207 1225408.015 1200716.895 1170607.023 1213365.259 1049581.033 1156334.903 1216809.095 1180748.608 1303720.102 0.858074678 0.939931825 0.920992852 0.897897502 0.9306946 0.805066234 0.886950275 0.933336146 0.905676461 1 20.31420274 0.557626502 1.073748438 0.999663963 0.895933619 0.395265621 0.038450425 1.605886063 2.716945678 0.037338606 0.011671215 3.610991795 -0.557626502 -0.103730344 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.136)S(0.263)T(0.287)T(0.314)PGGT(0.364)LFS(0.255)T(0.196)T(0.182)PGGT(0.003)R;RVVLGDGVQLPPGDY(0.037)S(0.304)T(0.321)T(0.34)PGGT(0.316)LFS(0.238)T(0.225)T(0.214)PGGT(0.005)R;RVVLGDGVQLPPGDYS(0.028)T(0.164)T(0.806)PGGT(0.89)LFS(0.065)T(0.011)T(0.035)PGGTR 122.91 9.88E-08 792099000 468975 569781 527230 552261 571961 656967 521887 577577 564179 634808 TRUE FALSE 487490.4951 667636.4545 540970.0469 661496.5775 474739.2735 504396.3707 480980.1332 569835.525 543874.308 759186.4735 0.642122209 0.879410366 0.712565445 0.871322923 0.625326307 0.664390619 0.633546764 0.750587036 0.716390936 1 19.53409476 -1.14640283 3.137402256 1.0005775 0.72407753 0.481689362 0.086562514 11043988.78 15893440.91 64282.8478 0.02113743 0.07138339 1.14640283 -0.27649997 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 38 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.015)S(0.309)T(0.325)T(0.343)PGGT(0.287)LFS(0.246)T(0.234)T(0.222)PGGT(0.006)RIIY(0.011)DRK 66.358 0.008246 136910000 59702 54497 63758 40199 99336 76224 48130 62613 75300 89757 TRUE FALSE 62059.08106 63856.43582 65419.58586 48150.24222 82450.9022 58522.13119 44357.44484 61773.77515 72589.96771 107343.1656 0.578137236 0.594881243 0.609443419 0.44856365 0.768105745 0.545187305 0.413230265 0.57547935 0.6762421 1 16.71187081 0.842342455 2.704144191 0.999658066 0.564446031 0.676473279 0.090240926 0.35836312 4.763511746 0.085361444 0.022643351 6.955725817 -0.842342455 -0.435212035 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.027)S(0.132)T(0.118)T(0.698)PGGT(0.041)LFS(0.549)T(0.094)T(0.34)PGGT(0.001)R 115.77 1.63E-06 714630000 348910 402080 409380 399730 460950 484190 385630 440060 422170 487330 TRUE FALSE 362685.2362 471134.1123 420048.7791 478795.4009 382597.8836 371744.2105 355403.3129 434161.7155 406976.1842 582812.983 0.62230123 0.808379576 0.72072653 0.82152494 0.656467675 0.637844765 0.609806788 0.744941736 0.698296359 1 19.15267349 -0.317687793 1.621580731 1.000551748 0.704866872 0.619651237 0.069948165 91.49149428 109.1242921 0.42702429 0.019268794 0.48118514 0.317687793 -0.295684876 RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 RVVLGDGVQLPPGDY(0.008)S(0.044)T(0.159)T(0.788)PGGT(0.001)LFS(0.036)T(0.097)T(0.839)PGGT(0.027)R;RVVLGDGVQLPPGDY(0.003)S(0.038)T(0.172)T(0.786)PGGT(0.001)LFS(0.002)T(0.072)T(0.926)PGGTR;RVVLGDGVQLPPGDY(0.006)S(0.043)T(0.157)T(0.789)PGGT(0.005)LFS(0.052)T(0.123)T(0.821)PGGT(0.003)R 149.48 2.00E-10 1396000000 624563 817758 783204 758185 852260 972240 725532 831350 738890 920860 TRUE FALSE 649221.2295 958201.5752 803614.9396 908151.73 707393.1496 746451.9944 668662.906 820207.1131 712297.4932 1101284.886 0.589512521 0.870076024 0.729706682 0.82462925 0.642334385 0.677800998 0.607166152 0.744772877 0.646787677 1 20.07075629 -1.309646245 8.991584771 1.000000181 0.708766346 0.512589033 0.086566437 3.01E-07 2.31E-08 0.080409365 0.018952657 0.049017793 1.309646245 -0.291233835 RVVYPLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVVYPLEK 8 1 O60832;O60832-2;C9IYT0;H7C2Q2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 76.17 0.049021 0 399470 339500 403960 325430 521970 544280 483990 429370 415170 431330 FALSE TRUE 415241.3841 397806.4841 414487.5295 389799.0827 433245.7258 417879.2186 446053.5991 423614.9975 400228.1128 515840.8552 0.804979636 0.771180646 0.803518227 0.755657639 0.839882536 0.810093296 0.864711654 0.821212576 0.775875173 1 18.97656652 -5 0.247455983 2.145556518 0.789282778 0.774845356 0.031345921 80.75722225 0.802086425 46.75859824 0.045774892 1.00E-05 5 -1.35627374 RVWGSPGGEGTGDLDEFDF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RVWGSPGGEGTGDLDEFDF 19 1 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 89.507 0.048908 56554000 51402 74428 57982 61898 70229 76938 59094 54511 52988 64619 FALSE TRUE 53431.39065 87210.43003 59493.05855 74141.23965 58291.49967 59070.31551 54462.05787 53780.36921 51080.97223 77279.85584 0.691401272 1.128501458 0.76983915 0.959386361 0.754290999 0.764368863 0.704738088 0.695917049 0.660986898 1 16.23780478 3.166905035 7.399558421 0.740146528 0.895845649 0.147078404 0.139125648 0.325783365 28.41452527 0.037066081 0.044519228 1468.60511 -3.166905035 0.155699122 RVYATILNAGTNTDGFK ddPTM_MDA-MB-175_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 ; 292.2 8.20E-46 5535600000 5064600 3502100 4790600 4346200 5922400 6074400 5361000 4716300 5125500 3557000 FALSE TRUE 5264554.319 4103558.432 4915446.972 5205865.388 4915712.563 4663712.658 4940790.812 4653085.713 4941034.256 4253926.047 1.237575421 0.964652038 1.155508327 1.223779006 1.155570762 1.096331391 1.16146608 1.09383324 1.161523308 1 22.02036352 -1.643539587 6.685145898 0.999445303 1.133981735 0.244669146 0.072760295 0.000570374 3.04E-05 0.066800076 0.015681151 0.022722725 1.643539587 0.134536432 RWDDDVVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RWDDDVVFK 9 1 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 ; 115.42 0.0023715 361230000 594330 518690 606010 487540 694040 708040 659980 593230 637850 512030 FALSE TRUE 617794.6073 607770.9727 621803.1184 583973.9568 576067.3287 543608.4405 608249.0431 585278.7222 614893.9031 612352.4751 1.008887254 0.992518194 1.015433339 0.953656563 0.940744673 0.887737802 0.993298905 0.955787305 1.00415027 1 19.22400279 3.733527532 24.72019842 0.958231754 1.004303457 0.264835883 0.03266295 452.388618 2221930.092 0.008695329 0.013944965 5414.115695 -3.733527532 0.046071702 RWDDSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RWDDSQK 7 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;;; 164.77 0.0019004 1874780000 2418050 1995330 2251620 1834900 2999550 2951530 2693010 2382080 2515260 2100090 FALSE TRUE 2513516.481 2338012.406 2310299.067 2197837.743 2489687.562 2266081.888 2481924.839 2350152.114 2424736.284 2511562.427 1.000778023 0.930899579 0.919865277 0.875087842 0.991290336 0.90225983 0.988199542 0.935733107 0.965429431 1 21.2601537 0.737718577 0.615593154 1.000780457 0.93676766 0.172445728 0.038422196 1.948340203 1.527732127 0.040437361 0.01550781 5.466616113 -0.737718577 -0.064012797 RWDQTADQT(ph)PGAT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 RWDQT(0.216)ADQT(0.784)PGAT(1)PK 55.127 0.031633 0 237740 141140 142960 112950 212250 225070 123280 139750 162430 121050 TRUE FALSE 247126.1588 165379.6971 146685.655 135291.1729 176171.8208 172800.9035 113616.9915 137876.8798 156584.176 144767.4299 1.707056339 1.142381938 1.013250392 0.934541513 1.216929947 1.193644894 0.784824263 0.952402622 1.081625723 1 17.14337753 4.751905838 2.602705417 1.014885776 1.864104419 0.747767595 0.118747311 0.262809035 2.243894614 0.031540567 0.495010499 56481.45011 -4.751905838 0.849218643 RWDQTADQTPGAT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 RWDQTADQTPGAT(1)PK;RWDQTADQT(0.057)PGAT(0.943)PK;RWDQTADQTPGAT(1)PK;RWDQTADQTPGAT(1)PK 178.56 4.14E-07 1601180000 2792710 1372540 1709810 1247410 2185950 2534770 2103630 1810130 1810490 1120280 TRUE FALSE 2902968.347 1608263.068 1754369.053 1494143.975 1814383 1946108.082 1938741.984 1785868.168 1745330.819 1339777.417 2.166754202 1.200395713 1.309448145 1.115218062 1.354242113 1.452560745 1.447062743 1.332958852 1.302702073 1 20.35356191 4.742676082 24.99634126 1.302300747 2.16675454 0.792784391 0.135644212 180.1703523 1094269.819 0.031774995 0.24611422 55293.75474 -4.742676082 0.864453792 RWESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RWESER 6 1 Q9Y2T2;H0YBA0;E7ER80;E5RJ52;P53677-2;P53677 Q9Y2T2 AP3M1;AP3M2 AP-3 complex subunit mu-1;AP-3 complex subunit mu-2 0 103.91 0.054973 51561000 24723 144580 75281 180340 58281 157880 54853 104990 57076 178660 FALSE TRUE 25699.08313 169410.4903 77242.8847 216010.7137 48374.41644 121214.7627 50553.47853 103582.7808 55021.84591 213665.0063 0.120277455 0.792878971 0.36151397 1.010978435 0.226403084 0.56731219 0.236601582 0.484790573 0.25751454 1 17.70499112 -1.594289633 3.714273256 1.016684601 0.463910496 0.278827945 0.264173919 0.033572937 0.003667174 0.235278194 0.054888523 0.025451323 1.594289633 -0.552774105 RWLPAGDALLQMITIHLPSPVTAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RWLPAGDALLQMITIHLPSPVTAQK 25 1 P13639 P13639 EEF2 Elongation factor 2 0 137.16 1.46E-05 63436000 94429 86973 138210 77550 147190 140630 155750 103010 126070 112070 FALSE TRUE 98157.12984 101909.9362 141811.8661 92889.15854 122170.6964 107970.8138 143541.908 101629.3194 121532.7653 134027.9708 0.732363023 0.760363196 1.058076649 0.693058009 0.911531344 0.805584186 1.070984714 0.758269478 0.906771658 1 17.03217459 7.999998166 0.031934137 1.447583835 4.27E-08 0.168682292 0.120494501 2366.022061 5.784793236 81.13207719 208.5230045 99999577.82 -7.999998166 -1.447583792 RWQS(ph)PVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 RWQSPVTK 8 1 A9Z1X7 A9Z1X7 SRRM1 1 RWQS(1)PVTK;RWQS(1)PVTK;RWQS(1)PVTK;RWQS(1)PVTK;RWQS(0.996)PVT(0.004)K 129.69 0.00066154 3231200000 3591510 2984240 3475800 2733880 4088740 4605750 4171180 3489540 3680760 2899290 TRUE FALSE 3733305.588 3496760.006 3566382.203 3274633.304 3393737.435 3536134.363 3844232.012 3442768.424 3548290.167 3467350.365 1.076702725 1.008481877 1.028561244 0.944419502 0.978769688 1.019837626 1.108694423 0.992910454 1.023343416 1 21.72540219 2.478766181 24.99984456 1.033750009 1.004543749 0.06064347 0.04313976 173.9351941 2643607.002 0.015158712 0.012852284 301.1384294 -2.478766181 -0.02920626 RWS(ph)APESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RWSAPESR 8 1 P54253 P54253 ATXN1 Ataxin-1 1 RWS(1)APESR;RWS(1)APESR;RWS(1)APESR;RWS(1)APESR 129.74 0.00066009 1539390000 815616 908509 867862 865889 958530 1004398 842579 866689 806988 999107 TRUE FALSE 847817.1495 1064538.354 890479.1967 1037159.26 795599.413 771141.7863 776535.4563 855072.4516 777944.6595 1194862.888 0.709551831 0.890929298 0.745256385 0.868015293 0.665849966 0.645380984 0.649895033 0.71562391 0.651074418 1 20.18841365 4.01825136 24.62743632 0.724140119 0.804703675 0.02177104 0.115676994 526.9968579 711090.0665 0.027361378 0.059090595 10429.20875 -4.01825136 0.080563557 RWS(ph)EDCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RWSEDCR 7 1 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 RWS(1)EDCR 72.2 0.032003 646970000 147190 144660 165400 134670 209060 242560 223390 181700 205540 176970 TRUE FALSE 153001.1749 169504.2297 169710.4599 161307.3241 173524.0559 186229.116 205880.1081 179264.6087 198142.6556 211643.8832 0.72291801 0.800893591 0.801868012 0.762163884 0.81988694 0.879917308 0.972766635 0.847010582 0.936207806 1 17.69127927 2.770521007 2.230543831 0.920191945 0.776476841 0.737778257 0.044411176 0.173930144 1.705297405 0.015357141 0.015560404 589.5504938 -2.770521007 -0.143715104 RWS(ph)GNEPTDEFSDLPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.999)GNEPT(0.001)DEFSDLPLR;RWS(0.995)GNEPT(0.004)DEFS(0.001)DLPLR 241.25 1.45E-20 251882000 176536 215635 179165 213432 186514 229042 216822 202521 182843 197744 TRUE FALSE 183505.7776 252668.6338 183834.1871 255648.2126 154810.4169 175850.4667 199826.9251 199806.5373 176262.5161 236488.1508 0.775961827 1.068419847 0.77735052 1.08101912 0.654622299 0.743591026 0.84497648 0.844890269 0.745333394 1 17.85140837 3.235958926 24.99994121 0.801069197 0.925287432 0.177221212 0.126570656 111.0137187 1066745.622 0.03358203 0.041911871 1721.705735 -3.235958926 0.124218235 RWS(ph)IVSSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RWSIVSSPER 10 1 Q12923-3;Q12923;Q12923-4;Q12923-2 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 RWS(1)IVSSPER;RWS(1)IVSSPER 134.91 9.68E-05 175970000 181536 196633 179444 170329 364380 258365 181399 177446 183431 320013 TRUE FALSE 188703.1815 230403.1882 184120.4581 204019.5678 302442.8178 198363.6443 167180.4724 175067.6266 176829.3541 382713.4203 0.493066539 0.602025369 0.481092244 0.533087049 0.790259243 0.518308567 0.436829396 0.457437909 0.462041164 1 18.54590497 -1.294519478 3.776750153 1.001016539 0.529057049 0.675280589 0.097675505 55573598.26 52201227.74 575447.9862 0.024976302 0.050755198 1.294519478 -0.47195949 RY(ph)GCVFQGT(ph)NQQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYGCVFQGTNQQIK 14 1 H0YL25;Q13114 H0YL25 TRAF3 TNF receptor-associated factor 3 2 RY(1)GCVFQGT(1)NQQIK;RY(1)GCVFQGT(1)NQQIK 76.391 0.039261 447480000 193884 528070 545540 512510 489390 694170 470600 523530 555620 426520 TRUE FALSE 201538.69 618761.9147 559757.2206 613882.9483 406203.6626 532959.5377 433713.1423 516512.9367 535623.3447 510088.4278 0.395105396 1.213048328 1.097372906 1.203483386 0.796339694 1.044837539 0.8502705 1.012594892 1.050059785 1 18.96038785 4.749583486 24.77583638 1.022145516 0.395104985 0.696972026 0.125455798 827.3381861 1859547.519 0.030190553 0.454778909 56180.22657 -4.749583486 -0.627040531 RYDEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYDEIVK 7 1 A0A2U3TZH3;Q05639;A0A2R8Y488 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 137.9 0.0045498 493100000 627490 570950 696900 595310 874240 875760 887720 743190 823680 689560 FALSE TRUE 652263.7897 669006.2211 715061.7865 713060.5412 725636.9971 672378.0123 818138.1868 733228.7537 794035.9177 824666.0796 0.790942911 0.811244985 0.867092517 0.864665783 0.879916144 0.815333659 0.992084199 0.889122 0.962857498 1 19.65345054 7.999975202 0.101071084 1.07738738 0.235161494 0.686390044 0.039842043 67.92819443 0.485223232 0.453941426 7.941292584 99994290.17 -7.999975202 -0.842225886 RYDLEQGLGDLLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYDLEQGLGDLLTER 15 1 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 ;; 168.41 2.01E-06 195838000 124859 144955 152903 142711 195417 190840 128969 152823 155407 171273 FALSE TRUE 129788.5297 169849.8937 156887.7778 170938.8099 162200.0881 146520.3022 118860.0728 150774.6577 149813.9324 204830.6651 0.633638179 0.829221023 0.765938917 0.8345372 0.791874049 0.715324056 0.580284562 0.736094166 0.731403827 1 17.64407219 -1.272245598 6.672594601 1.000003675 0.736180707 0.522496071 0.075890845 4.30E-06 4.69E-07 0.076224076 0.017965937 0.053426214 1.272245598 -0.263822969 RYDQDLCYTDILFTEQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RYDQDLCYTDILFTEQER 18 1 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 184.7 9.12E-14 368163000 246677 248379 255906 248968 284539 321616 251657 259774 237420 244891 FALSE TRUE 256415.9984 291036.1611 262575.1206 298213.1273 236173.1624 246925.5581 231931.4668 256292.1544 228875.3006 292872.7027 0.875520306 0.993729216 0.896550338 1.018234627 0.8064021 0.843115647 0.79191903 0.875097447 0.781483895 1 18.15991421 3.225588681 24.99999373 0.841490548 0.945884511 0.311016487 0.069609845 233.561682 450127.7792 0.018214886 0.021897354 1681.081161 -3.225588681 0.104393963 RYDSNSGGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYDSNSGGER 10 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;; 179.94 3.29E-06 444630000 155223 303394 349636 284341 375418 317858 342714 264108 331290 283340 FALSE TRUE 161351.3239 355499.5594 358747.8014 340582.8011 311604.5825 244040.2967 315851.1812 260568.0643 319366.9376 338855.0481 0.47616621 1.049119856 1.05870579 1.005098797 0.919580759 0.720190825 0.932112958 0.768966157 0.942488357 1 18.37030874 2.956194723 24.95219497 0.852581566 0.924986271 0 0.173725943 1774.686643 1010889.945 0.051726277 0.054867636 904.0547295 -2.956194723 0.072404705 RYEDLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RYEDLLTR 8 1 Q99988;A0A0A0MTT8 Q99988 GDF15 Growth/differentiation factor 15 0 108.15 0.0062 61434000 23655 41152 26116 35654 33495 42086 27232 36731 37705 50406 FALSE TRUE 24588.91767 48219.53588 26796.60441 42706.25478 27801.53186 32312.16432 25097.48468 36238.68102 36348.00442 60282.09062 0.40789756 0.799898202 0.444520157 0.708440174 0.461190572 0.536015987 0.416334013 0.601151696 0.602965226 1 15.87944183 0.565521728 1.766093064 0.999864989 0.549459731 0.554581771 0.121211905 1.66066296 5.939837617 0.105782249 0.02972835 3.677237902 -0.565521728 -0.450405258 RYEEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 133.68 0.0052081 1187040000 969500 989530 1003420 999090 1252170 1312830 1189090 1078480 1115450 1227580 FALSE TRUE 1007776.609 1159474.08 1029569.95 1196707.02 1039326.591 1007945.129 1095886.019 1064024.74 1075305.172 1468100.798 0.686449194 0.789778251 0.701293774 0.815139548 0.707939531 0.686563981 0.746465107 0.724762728 0.732446419 1 20.48551959 -2.038416242 2.333240572 1.32765903 0.73346764 0.79935465 0.040229924 5948515.904 1972558.473 10413936.48 0.008993418 0.009153428 2.038416242 -0.594191389 RYEPSDKDRQS(ph)PPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYEPSDKDRQSPPPAK 16 3 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 RYEPSDKDRQS(1)PPPAK;RYEPS(0.006)DKDRQS(0.994)PPPAK;RYEPSDKDRQS(1)PPPAK 136.04 1.40E-05 838830000 545021 290570 422283 300663 575421 511617 542759 429564 469121 280824 TRUE FALSE 566538.8499 340473.1372 433288.0419 360133.244 477611.144 392801.7054 500216.1313 423806.3972 452237.4268 335846.0861 1.68690026 1.013777296 1.290138727 1.072316335 1.422113175 1.169588456 1.489420756 1.261906614 1.346561552 1 18.35744069 -0.848084265 4.130682735 0.999995106 1.294861143 0.1893694 0.188613359 18146359.05 46824946.04 1524.306464 0.040968596 0.141878221 0.848084265 0.294866037 RYESQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYESQLR 7 1 O15212 O15212 PFDN6 Prefoldin subunit 6 0 ; 153.71 0.0027702 229480000 95058 129262 102772 103853 214000 179080 127596 107004 92414 258560 FALSE TRUE 98810.96324 151461.743 105450.3227 124394.8134 177624.3564 137491.384 117594.6921 105569.7864 89088.03819 309219.8816 0.319549192 0.489818902 0.341020513 0.402285949 0.574427348 0.444639534 0.380294732 0.341406852 0.28810579 1 18.23827356 -1.245316609 5.087348491 1.000086775 0.40057772 0.829990996 0.081735704 8.26E-05 1.23E-05 0.081246974 0.019147344 0.056843838 1.245316609 -0.599509055 RYGDFFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RYGDFFIR 8 1 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 69.375 0.086716 239310000 108280 97808 108460 90678 191060 149930 124040 107520 109270 175400 FALSE TRUE 112554.978 114605.7632 111286.5567 108613.8378 158583.6894 115111.0297 114317.4207 106078.8703 105337.394 209766.2718 0.536573287 0.546349812 0.530526456 0.517785042 0.75600185 0.548758524 0.544975223 0.505700318 0.502165544 1 17.6784232 -1.062137821 4.525976686 1.000024791 0.554101208 0.787785323 0.069395678 0.622814993 42961786.49 2354.71179 0.016669551 0.086668679 1.062137821 -0.445923584 RYIGIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYIGIVK 7 1 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 146.21 0.0035832 4841400000 3572300 3645100 3690000 3511900 6263500 6634500 6095700 5657900 5836600 5500300 FALSE TRUE 3713337.162 4271117.57 3786164.431 4206543.338 5198832.507 5093737.922 5617903.106 5582065.105 5626541.906 6577978.475 0.564510385 0.649305495 0.57558176 0.639488766 0.790338936 0.774362206 0.854047049 0.848598871 0.85536034 1 22.64921286 2.931420382 0.31690816 0.996772742 0.472262007 0.917850579 0.038802837 0.651159419 0.122366206 0.050809965 0.122488937 853.9262859 -2.931420382 -0.524510735 RYNEDLELEDAIHTAILTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYNEDLELEDAIHTAILTLK 20 1 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ; 176.46 2.75E-13 285710000 253930 257360 287860 214280 354710 359860 281670 292630 319110 284520 FALSE TRUE 263955.3525 301559.578 295361.8681 256663.9444 294416.5209 276287.9687 259591.9694 288707.7735 307625.2934 340266.2465 0.775731813 0.886245936 0.86803164 0.754303276 0.865253383 0.811975832 0.762908376 0.848476087 0.904072316 1 18.37630452 1.010575407 2.153255427 0.998663967 0.820923164 0.632330506 0.043281028 0.191675669 1.908592915 0.040148919 0.011129299 10.24649676 -1.010575407 -0.177740803 RYPS(ph)S(ph)ISSSPQKDLTQAK ddPTM_MDA-MB-175_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 RY(0.076)PS(0.569)S(0.569)IS(0.507)S(0.14)S(0.14)PQKDLTQAK 82.007 0.029529 604920000 333830 184980 225090 147130 322210 306030 226600 200460 242940 163600 TRUE FALSE 347009.8662 216748.8761 230956.0303 176231.8749 267440.8593 234959.1704 208838.4999 197773.1616 234196.6369 195654.2877 1.773586821 1.10781562 1.18042918 0.900730962 1.36690518 1.200889453 1.067385245 1.010829683 1.196992101 1 17.5779472 4.738886943 24.57928298 1.113912904 1.773587038 0.717110607 0.124156121 10.89067272 819853.621 0.029136509 0.170475528 54813.42548 -4.738886943 0.659674134 RYPS(ph)SISSS(ph)PQK ddPTM_MDA-MB-175_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(0.512)S(0.487)IS(0.001)S(0.016)S(0.984)PQK 203.8 8.08E-08 163760000 868420 529670 632370 575950 779390 853070 790220 650150 654820 433150 TRUE FALSE 902705.8922 620636.7022 648850.0817 689871.191 646909.5662 654957.4209 728280.4915 641435.8027 631253.1561 518017.4493 1.742616766 1.198099993 1.252564141 1.331752805 1.248818099 1.264353974 1.405899536 1.238251344 1.218594387 1 18.98264117 7.999999943 0.03017314 1.59E-12 3.169705598 0.433662666 0.135483788 1467.878486 3.394754506 113.3212681 276.5850762 99999986.76 -7.999999943 3.169705598 RYPS(ph)SISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_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 RY(0.038)PS(0.524)S(0.438)IS(0.001)S(0.23)S(0.769)PQKDLTQAK 146.64 4.41E-08 874080000 633070 329130 417190 297970 611610 571610 416510 409820 437740 324910 TRUE FALSE 658064.0924 385655.5172 428062.3141 356907.5766 507648.7507 438862.2403 383862.8579 404327.0332 421985.8229 388569.8937 1.693553986 0.992499737 1.101635307 0.918515774 1.306454151 1.129429344 0.987886257 1.040551622 1.085997216 1 18.5678146 4.74262229 24.98237076 1.065533855 1.693554234 0.778823407 0.10086801 180.284805 1108845.199 0.023693677 0.18241576 55286.90647 -4.74262229 0.628020379 RYPSS(ph)ISSS(ph)PQK ddPTM_MDA-MB-175_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(0.343)S(0.641)IS(0.016)S(0.341)S(0.659)PQK;RYPS(0.06)S(0.94)ISS(0.002)S(0.998)PQK 213.71 3.66E-09 583130000 1164180 702050 793000 774580 1005210 1141550 1065520 781020 794050 546570 TRUE FALSE 1210142.725 822621.6263 813666.2315 927789.6121 834344.7633 876442.3129 982001.7582 770551.7044 765472.2956 653659.9268 1.851333814 1.258485632 1.244785244 1.419376612 1.276420244 1.340823075 1.502312927 1.178826593 1.171055872 1 19.31818073 7.999999999 0.05087787 0.379653001 3.092369932 0.460812153 0.161131832 471.9239726 1.809926011 22.40896022 99.88347837 99999999.81 -7.999999999 2.712716931 RYPSS(ph)ISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_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 RY(0.041)PS(0.439)S(0.52)IS(0.008)S(0.14)S(0.852)PQKDLTQAK;RY(0.025)PS(0.451)S(0.523)IS(0.024)S(0.144)S(0.832)PQKDLTQAK;RY(0.001)PS(0.445)S(0.555)ISS(0.034)S(0.966)PQKDLTQAK 154.79 1.26E-08 1962290000 2068020 1100010 1413700 896600 2022110 1814380 1375760 1302350 1424730 1008900 TRUE FALSE 2149667.026 1288928.161 1450542.183 1073944.804 1678392.464 1393017.742 1267924.336 1284894.128 1373454.246 1206574.638 1.781627889 1.068253981 1.202198469 0.890077389 1.391039071 1.154522644 1.050846169 1.064910605 1.138308565 1 20.20248573 4.740767653 24.80377261 1.110495698 1.78162815 0.721713397 0.125713916 89.64852746 1007439.727 0.028530183 0.189572484 55051.30943 -4.740767653 0.671132452 RYPSSISS(ph)SPQK ddPTM_MDA-MB-175_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 1 RYPSSISS(0.5)S(0.5)PQK;RYPSSIS(0.01)S(0.495)S(0.495)PQK 186.62 7.06E-06 4772600000 1671630 1066240 1287930 1035630 1774260 1965720 2012940 1432010 1466850 1218400 TRUE FALSE 1737627.243 1249358.426 1321494.514 1240474.523 1472671.919 1509211.321 1855160.503 1412816.248 1414058.355 1457122.152 1.192506229 0.857415024 0.906920886 0.851318142 1.01067156 1.035747976 1.273167455 0.969593555 0.970445994 1 20.47469039 3.007846269 23.61249345 1.056350996 0.940675371 0.12397398 0.120412194 170.9365538 514405.3294 0.034861326 0.041576663 1018.230893 -3.007846269 -0.115675625 RYPSSISS(ph)SPQKDLTQAK ddPTM_MDA-MB-175_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 1 RYPSSIS(0.011)S(0.494)S(0.494)PQKDLTQAK 249.99 6.71E-25 2888400000 1857300 1011500 1461300 764480 2014600 1753600 1656700 1283200 1702300 943570 TRUE FALSE 1930627.638 1185217.257 1499382.678 915691.8623 1672159.012 1346352.976 1526843.525 1266000.803 1641034.556 1128444.476 1.710875173 1.050310655 1.328716397 0.811463818 1.481826574 1.193105204 1.353051531 1.121899066 1.454244839 1 20.105904 -2.300238284 1.970912159 5.89E-05 1.256006326 0.102096674 0.239535737 3750968.829 496058.0469 16682884.3 0.053404098 0.005009123 2.300238284 1.25594745 RYPSSISSS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RYPSSISSSPQK 12 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 RYPSSISS(0.024)S(0.976)PQK;RYPSSISS(0.378)S(0.621)PQK;RYPSSIS(0.001)S(0.286)S(0.713)PQK;RYPSSIS(0.001)S(0.233)S(0.767)PQK 172.43 2.19E-05 6479500000 2709860 1666170 2004680 1772770 2990650 2984240 3194500 2350400 2302520 1845780 TRUE FALSE 2816847.365 1952321.736 2056923.608 2123418.615 2482300.381 2291195.487 2944106.743 2318896.732 2219652.755 2207425.251 1.276078256 0.884433906 0.931820276 0.96194361 1.124522962 1.037949296 1.33372885 1.050498417 1.005539261 1 21.07393315 3.232794059 24.94267149 1.105522962 0.998505877 0.06733862 0.133044085 283.0036925 1224105.73 0.037541855 0.046031668 1709.204625 -3.232794059 -0.107017085 RYPSSISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_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 1 RYPSSISS(0.109)S(0.891)PQKDLTQAK 248.45 1.32E-24 3000800000 1856200 985770 1450000 870570 2012500 1790900 1621300 1453000 1696100 963700 TRUE FALSE 1929484.209 1155068.329 1487788.191 1042766.148 1670415.969 1374990.616 1494218.27 1433524.912 1635057.692 1152518.564 1.674145883 1.002212342 1.290901715 0.904771672 1.449361443 1.19303121 1.296480869 1.243819368 1.418682305 1 20.13635856 -2.186015181 2.452430228 0.260259407 1.25874357 0.131763412 0.207985127 14367327.27 4381685.736 58745100.01 0.046083892 0.006516056 2.186015181 0.998484162 RYS(ph)ASLPAPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYSASLPAPVK 11 1 Q5VTQ0-2;Q5VTQ0-3;Q5VTQ0-4;Q5VTQ0;Q5VTQ0-5;Q5VTQ0-6;Q5VTQ0-7 Q5VTQ0-2 TTC39B Tetratricopeptide repeat protein 39B 1 RYS(0.989)AS(0.01)LPAPVK;RYS(0.991)AS(0.008)LPAPVK 107.69 0.0013253 401780000 982150 821360 927650 766340 1574480 1249560 1167300 939430 987440 1065410 TRUE FALSE 1020926.04 962422.1907 951825.3211 917919.7647 1306850.452 959368.6273 1075803.976 926838.4774 951902.2273 1274156.691 0.801256272 0.75534053 0.747023759 0.720413565 1.025659137 0.752943994 0.844326277 0.727413264 0.747084118 1 20.28111128 -2.354485454 2.237274822 2.302399229 0.79029962 0.347435126 0.08580778 5197899.103 476961.3216 34442514.61 0.020674098 0.004420939 2.354485454 -1.512099609 RYS(ph)DFEWLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYSDFEWLK 9 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLK;RYS(1)DFEWLK;RYS(1)DFEWLK 182.55 2.83E-05 1185330000 2051310 1569200 2009040 1755070 2259440 2483460 2659740 2073040 2241020 1368240 TRUE FALSE 2132297.303 1838697.893 2061397.233 2102217.608 1875381.196 1906714.052 2451262.629 2045254.29 2160366.128 1636320.431 1.30310498 1.123678381 1.259776015 1.284722459 1.146096547 1.165244909 1.498033381 1.249910623 1.320258604 1 20.64202386 RYS(ph)DFEWLKNELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYSDFEWLKNELER 14 2 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 RYS(1)DFEWLKNELER;RYS(1)DFEWLKNELER;RYS(1)DFEWLKNELER 144.01 4.68E-06 686479000 566590 425076 568793 394397 746340 661737 550564 563811 660369 541625 TRUE FALSE 588959.4107 498079.4964 583616.2128 472407.5494 619477.3934 508058.6105 507409.355 556254.0358 636602.4487 647746.0487 0.909244312 0.768942547 0.900995404 0.729309813 0.956358429 0.784348452 0.783346122 0.858753267 0.982796344 1 19.30506878 1.256869805 3.768129603 0.999429178 0.831580058 0.46247153 0.067392198 0.171788105 4.558557055 0.0524256 0.015512683 18.06632445 -1.256869805 -0.16784912 RYS(ph)DFEWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 193.28 2.07E-05 794100000 213682 231125 218595 218068 250565 292118 266290 224322 238466 255652 TRUE FALSE 222118.3304 270818.9208 224291.7653 261201.1995 207974.0508 224278.0216 245417.494 221315.3305 229883.6552 305742.1146 0.726489154 0.885775652 0.733597874 0.854318679 0.680227031 0.733552922 0.802694435 0.723862759 0.751887438 1 18.22195577 -1.906422724 7.952727582 1.042159759 0.766066348 0.574938045 0.060405844 0.031492471 0.000370562 0.040792164 0.012994408 0.012404443 1.906422724 -0.27609341 RYS(ph)DHAGPAIPSVVAYPK ddPTM_MDA-MB-175_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 RYS(1)DHAGPAIPSVVAYPK;RY(0.359)S(0.639)DHAGPAIPS(0.002)VVAYPK 151.42 2.93E-08 460780000 611850 592240 616740 582860 764440 750750 723670 631320 682230 619880 TRUE FALSE 636006.3105 693952.613 632812.7511 698147.9683 634500.7619 576399.6902 666946.8544 622858.188 657676.6756 741333.6177 0.857921852 0.936086799 0.853613995 0.941745999 0.855890987 0.77751727 0.899658182 0.840186082 0.887153449 1 19.49976341 0.961605174 21.50014229 1.000000001 0.870288951 0.422357375 0.045220666 996.1076693 557797.2342 0.042803908 0.010700977 9.153879144 -0.961605174 -0.12971105 RYS(ph)FRVPEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;RYS(1)FRVPEEER;RYS(1)FRVPEEER;RYS(1)FRVPEEER 165.86 1.66E-05 5542050000 2176159 2757843 2747786 2737535 3044713 3279556 2615733 2663421 2698002 3311327 TRUE FALSE 2262075.438 3231481.082 2819395.56 3279011.252 2527173.772 2517928.821 2410705.013 2627722.198 2600901.435 3960118.126 0.571214132 0.816006235 0.711947339 0.828008445 0.638156159 0.635821645 0.608745733 0.663546418 0.6567737 1 21.91711203 -1.406651931 8.701621588 1.000002177 0.68312733 0.592643654 0.079292673 3.36E-06 2.29E-07 0.077128731 0.018179291 0.039205597 1.406651931 -0.316874847 RYS(ph)GNMEYVISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYSGNMEYVISR 12 1 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 RYS(1)GNMEYVISR;RYS(1)GNMEYVISR 220.42 1.81E-11 619110000 180108 263550 266780 260020 232540 333520 250240 251610 212270 286200 TRUE FALSE 187218.8029 308812.6624 273732.506 311451.1799 193012.9339 256065.0345 230625.5349 248237.5795 204630.4442 342275.4104 0.546982919 0.902234438 0.799743416 0.909943193 0.56391119 0.74812571 0.673801062 0.725256831 0.597853185 1 18.38479812 -1.162138416 4.393603861 1.000056996 0.726426596 0.322755832 0.121797444 6.50E-05 1.24E-05 0.112803934 0.026582613 0.068843285 1.162138416 -0.2736304 RYS(ph)PPIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 RYSPPIQR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 RY(0.018)S(0.982)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR;RY(0.002)S(0.998)PPIQR;RYS(1)PPIQR;RY(0.001)S(0.999)PPIQR;RYS(1)PPIQR;RYS(1)PPIQR 110.54 0.0020863 54033890000 1566911 1741780 1747170 1670220 1693880 2003340 1727363 1720750 1568276 1616850 TRUE FALSE 1628773.856 2040917.166 1792702.686 2000584.531 1405954.883 1538094.646 1591967.774 1697686.161 1511834.053 1933640.801 0.842335275 1.055478952 0.927112566 1.034620561 0.727102408 0.795439693 0.823300674 0.877973903 0.781858788 1 20.88288839 3.247772497 24.99995232 0.829197807 0.968659539 0.352039336 0.086581653 197.0087405 534655.24 0.022514994 0.030072253 1769.181939 -3.247772497 0.139461732 RYS(ph)PS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 RYSPSPPPK 9 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.014)S(0.987)PS(0.999)PPPK;RY(0.039)S(0.964)PS(0.997)PPPK;RY(0.069)S(0.945)PS(0.986)PPPK 77.279 0.022091 2380320000 1518730 1221400 1368330 1165730 1616060 1732150 1621860 1448220 1536220 1162470 TRUE FALSE 1578690.633 1431165.949 1403989.804 1396307.915 1341362.698 1329884.413 1494734.375 1428808.98 1480931.742 1390233.74 1.135557704 1.029442681 1.009894785 1.004369175 0.964846889 0.956590518 1.075167673 1.027747305 1.065239391 1 20.40689603 4.740439689 3.368313273 1.014107667 1.151791367 0.514822828 0.035467693 0.276574386 5.221743983 0.009251178 0.098570517 55009.75222 -4.740439689 0.137683699 RYS(ph)PS(ph)PPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 RYSPSPPPKR 10 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 RY(0.22)S(0.784)PS(0.997)PPPKR;RY(0.124)S(0.877)PS(0.998)PPPKR 57.159 0.064046 488350000 227880 208780 253060 188719 313710 313060 270300 241710 269630 198782 TRUE FALSE 236876.8784 244636.3409 259654.9515 226047.0549 260385.6863 240356.5595 249113.1797 238470.2728 259926.069 237729.527 0.996413367 1.029053244 1.092228445 0.950858136 1.095302252 1.01105051 1.047884892 1.003115918 1.09336889 1 17.85896158 4.712309697 5.125379219 1.035391806 0.995269863 0.065227348 0.045151699 0.418285922 31.93664234 0.009749616 0.05369271 51559.61865 -4.712309697 -0.040121942 RYSGDS(ph)DSSASSAQSGPLGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RYSGDSDSSASSAQSGPLGTR 21 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 RY(0.049)S(0.37)GDS(0.565)DS(0.007)S(0.007)ASSAQSGPLGTR 78.45 0.0014858 0 49876 108260 108470 85450 93588 109130 85265 95070 96197 119940 TRUE FALSE 51845.14299 126852.8129 111296.8173 102351.755 77679.94519 83786.21138 78581.7065 93795.74215 92734.88876 143439.9466 0.361441455 0.884361824 0.775912289 0.713551262 0.541550294 0.584120486 0.547836975 0.653902517 0.646506716 1 17.13008733 0.374962991 2.685130647 0.999999686 0.640667433 0.39635994 0.135191288 30.90076264 130.5734562 0.127397676 0.033676045 2.371171634 -0.374962991 -0.359332253 RYTCGEAPDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 RYTCGEAPDYDR 12 1 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;; 164.93 8.97E-05 2917260000 1395870 1618080 1682260 1488670 1763780 1927080 1463820 1703420 1655220 1820290 FALSE TRUE 1450980.025 1895972.653 1726101.078 1783124.483 1463973.306 1479544.875 1349081.963 1680588.441 1595648.956 2176940.974 0.666522447 0.870934341 0.792902104 0.819096385 0.672491043 0.679644002 0.619714535 0.771995411 0.732977593 1 21.05387086 -0.650048217 1.99350271 1.000533097 0.738140074 0.531096083 0.074327631 2186.515198 2600.035066 9.658407211 0.020470904 0.22384726 0.650048217 -0.262393022 S(ph)ADNTLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SADNTLER 8 0 A0A087WT53;Q96QZ7-7;Q96QZ7-6;Q96QZ7-2;Q96QZ7 A0A087WT53 MAGI1 "Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1" 1 S(1)ADNTLER 104.14 0.0071362 0 34937 45525 38835 41346 43826 48361 38912 37106 44937 42392 TRUE FALSE 36316.33974 53343.56461 39847.072 49524.11539 36376.47217 37129.89067 35861.97576 36608.65476 43319.72615 50697.90076 0.716328274 1.05218488 0.785970847 0.976847456 0.717514367 0.732375308 0.707366089 0.722094095 0.854467848 1 15.62963839 5.055346357 15.22237384 0.819277051 4.98E-05 0.061417763 0.124080263 3492230.479 24885603.93 0.029834755 85405772.13 113591.6366 -5.055346357 -0.819227244 S(ph)AEDVSTVPTQPDNPFSHPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEDVSTVPTQPDNPFSHPDK 21 0 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5;Q9HCH5-15;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 S(1)AEDVSTVPTQPDNPFSHPDK 132.39 7.49E-06 238700000 114580 145500 142420 145540 146940 210860 138140 147810 154920 172020 TRUE FALSE 119103.7069 170488.4932 146131.5822 174327.3776 121963.1913 161890.9606 127312.2258 145828.8487 149344.4595 205724.0255 0.578948942 0.828724272 0.710328227 0.847384632 0.592848555 0.786932689 0.618849576 0.708856675 0.725945641 1 17.65035076 -2.128325605 1.418827154 1.436673677 0.71286077 0.489492493 0.08852924 46218.35319 8407.845544 64851.9363 0.022492576 0.007441738 2.128325605 -0.723812907 S(ph)AEEGELAESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEEGELAESK 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(1)AEEGELAESK 118.61 0.0007319 100370000 59113 272080 328460 270720 329400 378180 281040 335360 350370 286590 TRUE FALSE 61446.82689 318807.6235 337019.9374 324267.608 273408.7057 290353.4264 259011.3504 330865.0477 337760.2521 342741.8234 0.179280212 0.930168429 0.983305551 0.946098742 0.797710367 0.847149098 0.755703952 0.965347749 0.985465529 1 18.38676272 4.739790446 24.9776239 0.904530519 0.179279976 0.88171389 0.080502725 34.04815807 691433.0176 0.020064371 0.124808258 54927.57761 -4.739790446 -0.725250543 S(ph)AEPS(ph)PTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 2 S(0.991)AEPS(0.505)PT(0.505)VMSTSLGSNLSELDR;S(0.946)AEPS(0.526)PT(0.526)VMS(0.001)T(0.001)SLGSNLSELDR 122.01 1.40E-05 63245000 45739 48253 44315 40145 55511 63745 52667 48687 51336 41471 TRUE FALSE 47544.81104 56540.07739 45469.88531 48085.56118 46075.26005 48941.18981 48538.82292 48034.4304 49488.42739 49596.44844 0.958633381 1.140002544 0.916797205 0.969536382 0.929003215 0.986788195 0.978675378 0.968505446 0.997822 1 15.59794919 4.219912169 24.99994305 0.967199605 1.049318073 0.312921315 0.04794054 216.9170722 290797.9225 0.010802302 0.02339824 16592.51311 -4.219912169 0.082118469 S(ph)AEPSPTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.821)AEPS(0.174)PT(0.004)VMSTSLGSNLSELDR 69.361 0.019582 49071000 26600 21668 17948 20395 25046 27016 27204 25779 21359 21798 TRUE FALSE 27650.18854 25389.31045 18415.73962 24429.07013 20788.68987 20741.94343 25071.6794 25433.47467 20590.29376 26068.90075 1.060658016 0.973930995 0.70642563 0.937096288 0.797451725 0.795658537 0.961746705 0.975625129 0.789841273 1 14.67004213 -2.960687684 10.80730181 0.999076175 0.897043025 0 0.11102801 0 0 0 0.024346428 0.001094743 2.960687684 -0.10203315 S(ph)AGEEEDGPVLTDEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 482 4.84E-231 2329490000 4920700 2547780 3605210 2594720 5158600 5361500 4884100 3746610 4178000 2301060 TRUE FALSE 5114973.036 2985341.396 3699164.734 3107947.872 4281743.015 4116372.879 4501271.48 3696392.821 4027634.596 2751908.651 1.858700155 1.084825761 1.344217852 1.129379012 1.555917568 1.495824681 1.635690734 1.343210582 1.463578595 1 21.39200115 -0.988160868 5.06522915 0.999997439 1.420993396 0.262339041 0.217552795 7.33E-06 1.46E-06 0.199256755 0.046964916 0.102763558 0.988160868 0.420995957 S(ph)AKPETVIDSLLQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAKPETVIDSLLQ 13 1 J3KPF9;A0A087X011;E9PES4;Q9Y496;H7C2F6 J3KPF9 KIF3A Kinesin-like protein;Kinesin-like protein KIF3A 1 S(0.992)AKPET(0.008)VIDSLLQ 74.769 0.087362 14593000 62641 35259 50908 31982 68870 60336 56277 42748 65844 31926 TRUE FALSE 65114.11505 41314.45897 52234.7043 38307.94414 57163.502 46323.8784 51865.86169 42175.03298 63474.2873 38181.28844 1.705393341 1.082060367 1.36807076 1.003317219 1.49716011 1.213261267 1.358410462 1.104599523 1.662444875 1 15.22057817 -2.132068241 2.46787192 0.355917995 1.304087165 0.150291215 0.228383912 5274475.716 2212194.697 19011230.76 0.049274093 0.007377883 2.132068241 0.948169171 S(ph)APAS(ph)PTHPGLMSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.96)PT(0.041)HPGLMSPR;S(1)APAS(0.613)PT(0.387)HPGLMSPR 102.39 0.00082137 1463690000 373650 478660 464660 371310 444550 475320 348500 405370 361490 366930 TRUE FALSE 388401.9905 560866.1315 476769.4213 444754.0098 368985.5498 364934.1335 321183.6594 399936.6782 348480.0455 438822.9082 0.885099623 1.278114978 1.08647341 1.013515934 0.840852979 0.831620516 0.731920903 0.911385141 0.794124552 1 18.74327932 3.382006241 2.81657236 0.841298892 1.099902349 0.476381236 0.110855876 0.197682041 3.165189777 0.030455301 0.043967258 2409.94006 -3.382006241 0.258603457 S(ph)APASPT(ph)HPGLMSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(1)APAS(0.171)PT(0.827)HPGLMS(0.002)PR;S(0.999)APAS(0.201)PT(0.8)HPGLMSPR 161.51 2.92E-06 1253360000 504330 550270 608040 512280 638300 715030 552360 619510 575450 547510 TRUE FALSE 524241.3378 644774.592 623886.0219 613607.455 529801.994 548975.1189 509064.5799 611206.4818 554739.6669 654784.1018 0.800632356 0.984713267 0.952811805 0.937114162 0.809124706 0.838406304 0.777454093 0.933447346 0.847210043 1 19.32065977 5.050397929 12.74518209 0.890654097 0.405621918 0.132264872 0.072619239 463000.2981 4041623.7 0.017638592 5182132.747 112304.6991 -5.050397929 -0.485032179 S(ph)APASPTHPGLMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.658)APAS(0.335)PT(0.209)HPGLMS(0.798)PR 111.34 0.0012425 373600000 197060 237590 212240 211160 252200 273070 241370 238170 238290 224330 TRUE FALSE 204840.081 278394.2343 217771.1488 252926.8178 209331.1341 209653.6309 222450.7887 234977.7207 229713.9894 268283.1684 0.763521924 1.037688037 0.81172125 0.942760663 0.780261898 0.781463974 0.829164163 0.875857111 0.856237053 1 18.03339702 0.106377808 1.486922355 1.000100098 0.855509101 0.233744941 0.079645615 21.52047962 33.72395458 0.076950679 0.020955565 1.277549711 -0.106377808 -0.144590997 S(ph)APELPEGILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK;S(1)APELPEGILK 210.95 1.15E-08 1619602000 1577129 1265053 1631211 1180937 2129470 2031008 1943125 1620076 1760104 1240659 TRUE FALSE 1639395.271 1482316.012 1673721.699 1414522.814 1767503.45 1559337.172 1790817.785 1598361.531 1696758.201 1483742.377 1.104905606 0.999038671 1.128040639 0.953347991 1.191246861 1.050948734 1.206960058 1.077250037 1.143566583 1 20.50080919 3.227564945 24.99999885 1.116565013 1.048791272 0.154979724 0.074115007 356.8619333 811367.8033 0.019282841 0.023257799 1688.748379 -3.227564945 -0.067773742 S(ph)APPMEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPPMEGAR 9 0 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 S(1)APPMEGAR 68.355 0.061158 182450000 49688 58382 62517 61359 84653 97355 81096 72985 50940 64989 TRUE FALSE 51649.72061 68408.65435 64146.24438 73495.62706 70263.7133 74745.77668 74739.48362 72006.75545 49106.67935 77722.35026 0.664541415 0.880167083 0.825325587 0.945617661 0.90403485 0.961702476 0.961621507 0.926461375 0.631821853 1 16.24604191 5.357350204 1.261108488 0.9045806 2.70E-12 0.322846652 0.099024256 6.760996421 3.059740207 0.026509944 11.6222814 227693.2749 -5.357350204 -0.9045806 S(ph)APPNLWAAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 109.51 0.0020131 749930000 77590 94614 98397 94624 126089 114661 119269 115067 97377 92815 TRUE FALSE 80653.31311 110863.2185 100961.3067 113340.3448 104656.4368 88032.72045 109920.3841 113524.7151 93872.42079 111000.3222 0.726604315 0.998764835 0.909558681 1.021081223 0.942848045 0.79308527 0.990270856 1.022742212 0.84569503 1 16.76020434 4.746479378 24.68739519 0.949440397 0.726604185 0.447341672 0.073488711 764.678469 2383882.382 0.017446327 0.18985729 55780.11146 -4.746479378 -0.222836212 S(ph)AQLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAQLER 6 0 Q8N3R9-2;Q8N3R9;G3V2B0;G3V2H1 Q8N3R9-2 MPP5 MAGUK p55 subfamily member 5 1 S(1)AQLER 107.56 0.032685 168860000 113650 98350 84319 113790 101000 111370 115470 90733 77218 98693 TRUE FALSE 118136.9898 115240.8474 86516.42241 136297.3224 83832.05608 85506.00533 106419.1597 89516.87254 74438.93926 118030.0038 1.000906431 0.976369091 0.73300364 1.154768432 0.710260556 0.72444296 0.901628029 0.75842472 0.630678106 1 16.84879412 3.201205116 24.99989704 0.77951134 0.950323297 0.287735107 0.136460552 212.6861799 142338.0735 0.037580255 0.044918062 1589.297193 -3.201205116 0.170811957 S(ph)ARHT(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SARHTPAR 8 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 S(1)ARHT(1)PAR;S(1)ARHT(1)PAR 101.38 0.012457 710140000 70435 55414 70350 87953 75495 84129 82521 77865 63765 45399 TRUE FALSE 73215.82819 64930.92344 72183.37879 105349.8409 62662.38687 64591.31474 76052.78839 76821.34704 61470.11011 54294.06483 1.34850519 1.195911996 1.32948931 1.940356487 1.154129591 1.189657008 1.400756945 1.414912427 1.132169976 1 15.72850688 S(ph)AS(ph)PERMD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASPERMD 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 2 S(1)AS(1)PERMD;S(1)AS(1)PERMD;S(1)AS(1)PERMD;S(1)AS(1)PERMD 111.63 0.0021477 1799888000 2490882 2182182 2306448 2323393 2806227 3282900 3194255 2560071 2372888 1609630 TRUE FALSE 2589223.945 2556954.783 2366555.93 2782953.201 2329225.537 2520496.228 2943880.946 2525757.436 2287488.224 1925006.18 1.345047082 1.328283935 1.229375757 1.445685333 1.209983407 1.309344486 1.529283894 1.312077572 1.188301756 1 20.87643165 0.99369403 2.709559028 1.002173711 1.341454977 0.593434933 0.088207233 0.175684938 2.997581208 0.083036461 0.022188591 9.855848757 -0.99369403 0.339281266 S(ph)ASASHQADIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 S(0.888)AS(0.049)AS(0.063)HQADIK;S(0.924)AS(0.075)AS(0.001)HQADIK 136.17 6.75E-05 620170000 1009590 1043800 1084220 1346130 1575700 2063000 1483760 1231170 1272690 1289250 TRUE FALSE 1049449.393 1223064.53 1112475.664 1612390.496 1307863.077 1583899.515 1367459.014 1214668.18 1226886.136 1541853.853 0.680641288 0.793242841 0.72151823 1.045747943 0.848240625 1.027269551 0.886892757 0.78779722 0.795721419 1 20.55623459 3.778802984 24.93182537 0.898090455 0.737944915 0.454724516 0.089856196 526.663255 326288.1788 0.023845202 0.042986894 6009.010789 -3.778802984 -0.16014554 S(ph)ASDNTLVAMDFSGHAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.5)AS(0.5)DNT(0.001)LVAMDFSGHAGR;S(0.599)AS(0.401)DNTLVAMDFSGHAGR;S(0.453)AS(0.453)DNT(0.095)LVAMDFSGHAGR;S(0.594)AS(0.406)DNTLVAMDFSGHAGR;S(0.59)AS(0.41)DNTLVAMDFSGHAGR 275.2 2.98E-39 1275414700 221066.5 304374.5 300190 329228.8 365851 395441.6 337887 361000.4 342922 296154.7 TRUE FALSE 229794.3761 356648.4527 308013.198 394349.274 303663.7777 303606.2814 311402.534 356161.7801 330580.3042 354180.5432 0.648805759 1.006967942 0.86965025 1.113413149 0.857370015 0.857207679 0.879219765 1.005593861 0.933366642 1 18.43412543 4.746152136 24.74578122 0.944083039 0.648805595 0.553576658 0.080290906 605.6298051 1974093.628 0.018629017 0.198180621 55738.09685 -4.746152136 -0.295277444 S(ph)ASMKLPDNTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 S(0.507)AS(0.493)MKLPDNTVK 64.65 0.095372 361700000 634090 287100 479160 244520 731360 552000 628240 449140 618390 280090 TRUE FALSE 659124.3628 336407.1917 491647.3032 292885.3262 607043.6884 423806.3656 578996.9072 443120.0129 596134.2647 334968.2729 1.96772177 1.004295687 1.467742897 0.874367365 1.812242345 1.265213454 1.728512681 1.322871594 1.779673817 1 18.35366493 3.20920842 24.99998973 1.495031687 1.315314481 0.042057587 0.361068754 640.2894292 545348.5339 0.095597387 0.114276568 1618.856749 -3.20920842 -0.179717207 S(ph)ASPHDVDLCLVS(ph)PCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.82)AS(0.18)PHDVDLCLVS(1)PCEFEHRK 149.66 8.02E-08 75567000 20084 24755 22697 22930 33945 31228 25106 27617 31295 29174 TRUE FALSE 20876.93183 29006.47868 23288.50247 27465.48556 28175.04102 23975.77026 23138.12612 27246.83929 30168.69906 34890.08673 0.598362853 0.831367342 0.667481931 0.787200266 0.807537145 0.687180013 0.663171929 0.78093355 0.864678248 1 15.09052956 1.05187984 1.946890847 0.997394382 0.72738654 0.619259253 0.069174885 0.199065602 1.540298598 0.061622728 0.01743895 11.26885627 -1.05187984 -0.270007842 S(ph)ASPHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_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(0.5)AS(0.5)PHDVDLCLVSPCEFEHR 222.57 4.55E-25 1569700000 97591 96217 112470 130920 121710 141510 134590 122970 108230 113080 TRUE FALSE 101443.968 112741.5213 115401.0606 156815.5852 101021.7777 108646.4471 124040.4841 121321.7883 104334.8234 135235.861 0.750126241 0.833665867 0.8533318 1.15957102 0.747004359 0.803384889 0.917215916 0.897112552 0.771502638 1 17.04511824 -2.665132062 2.17088534 4.695756764 0.867064145 0.116123681 0.11469886 3758851.846 389708.1063 68791696.29 0.02727318 0.002162061 2.665132062 -3.828692619 S(ph)ASPHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.544)AS(0.456)PHDVDLCLVSPCEFEHRK;S(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK;S(0.5)AS(0.5)PHDVDLCLVSPCEFEHRK 142.41 6.90E-08 347392000 239225 256867 277199 221316 331978 355654 235589 268266 278930 272353 TRUE FALSE 248669.7877 300981.9091 284423.0337 265091.6442 275548.4981 273058.7485 217122.9186 264670.3331 268891.3638 325715.3558 0.763457366 0.924064229 0.873225743 0.813875181 0.845979452 0.838335509 0.666603262 0.812581686 0.825540948 1 18.31325221 2.452470172 24.97861744 0.798992052 0.847864392 0 0.08576333 645.0225452 653589.3647 0.028139017 0.023543479 283.4458949 -2.452470172 0.048872339 S(ph)ASPYPS(ph)HSLS(ph)SPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 S(0.872)AS(0.208)PY(0.007)PS(0.912)HS(0.001)LS(0.515)S(0.484)PQR 195.46 6.45E-09 298980000 226740 254410 266760 213720 313130 348590 283920 250190 248210 214530 TRUE FALSE 235691.8703 298102.9385 273711.9847 255993.1781 259904.2744 267635.2554 261665.6085 246836.6123 239276.9706 256563.0461 0.918650889 1.161909102 1.066841032 0.997778838 1.01302303 1.043155901 1.019888143 0.962089498 0.932624453 1 17.96895386 1.812245745 3.214777489 0.959636598 1.038018894 0.208991948 0.059239032 0.337665433 6.336445692 0.031276838 0.015891767 64.90015667 -1.812245745 0.078382296 S(ph)ASQSSLDKLDQELKEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 S(0.333)AS(0.069)QS(0.299)S(0.299)LDKLDQELKEQQK 52.79 0.064995 121330000 128490 56222 83792 55219 141560 104360 99353 71430 113250 48645 TRUE FALSE 133562.8844 65877.69115 85975.68836 66141.15339 117497.6818 80123.97159 91565.45225 70472.59769 109174.1546 58176.05639 2.295839435 1.132384958 1.477853497 1.136913663 2.019691417 1.377267154 1.573937079 1.211367736 1.876616626 1 15.82813788 -2.12342937 2.277528543 0.000263023 1.523306957 0.16338739 0.3732847 5620478.584 1634355.309 29017015.65 0.082369782 0.007526111 2.12342937 1.523043934 S(ph)ASTESGFHNHTDTAEGDVIAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASTESGFHNHTDTAEGDVIAAAR 24 0 Q02410-2;Q02410 Q02410-2 APBA1 Amyloid beta A4 precursor protein-binding family A member 1 1 S(0.586)AS(0.121)T(0.069)ES(0.094)GFHNHT(0.128)DT(0.001)AEGDVIAAAR;S(0.799)AS(0.118)T(0.031)ES(0.049)GFHNHT(0.002)DTAEGDVIAAAR 152.1 1.67E-07 363600000 251920 243060 260060 235610 308580 357610 302950 243710 258600 199987 TRUE FALSE 261865.9961 284803.6643 266837.3772 282212.9548 256127.6818 274560.4971 279203.9874 240443.4661 249293.0365 239170.6237 1.094891973 1.190797013 1.115677892 1.179964957 1.070899419 1.147969148 1.167384117 1.005321901 1.042322977 1 17.86768067 1.713505992 7.150697025 1.018870734 1.138700501 0.697010046 0.036870082 0.065445447 8.175380986 0.017143176 0.008942184 51.70183911 -1.713505992 0.119829767 S(ph)AT(ph)RQKT(ph)QLAS(ph)LPQIIEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SATRQKTQLASLPQIIEEEK 20 2 F8VR31;P51530-2;P51530-3;P51530-4;P51530 F8VR31 DNA2 DNA replication ATP-dependent helicase/nuclease DNA2;DNA replication nuclease DNA2;DNA replication ATP-dependent helicase DNA2 4 S(1)AT(1)RQKT(1)QLAS(1)LPQIIEEEK 48.489 0.093349 1253600000 60557 298810 579720 359230 779480 422650 1109400 532940 661090 135540 TRUE FALSE 62947.83712 350128.2931 594827.9794 430284.6218 646984.268 324495.9428 1022442.329 525796.811 637297.5 162096.4679 0.388335649 2.159999521 3.669592478 2.65449721 3.991353274 2.0018693 6.307616336 3.243727749 3.931593996 1 17.30649313 4.590341081 1.966935988 3.539498914 9.39E-12 0.31245953 1.334396771 0.585439733 3.066691877 0.321968454 3.35776317 38935.0809 -4.590341081 -3.539498914 S(ph)ATLSGSATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.849)AT(0.151)LSGSATNLASLTAALAK 222.06 7.78E-25 23965000 32874 29209 33888 28446 40341 47334 41294 34857 35329 29139 TRUE FALSE 34171.8909 34225.41854 34771.14912 34072.5339 33483.85123 36341.39585 38057.26838 34389.79893 34057.51619 34848.22915 0.980591891 0.982127912 0.997788122 0.977740756 0.960847998 1.042847707 1.092086149 0.986844949 0.977309809 1 15.08879773 2.738982111 24.9999922 1.022361525 0.980830379 0.288524062 0.031257762 53.02264418 3145012.312 0.010509436 0.010536677 548.2543808 -2.738982111 -0.041531145 S(ph)ATPVNCEQPDILVSSTPINEGQTVLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SATPVNCEQPDILVSSTPINEGQTVLDK 28 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.5)AT(0.5)PVNCEQPDILVSSTPINEGQTVLDK;S(0.5)AT(0.5)PVNCEQPDILVSSTPINEGQTVLDK;S(0.558)AT(0.442)PVNCEQPDILVSSTPINEGQTVLDK;S(0.553)AT(0.447)PVNCEQPDILVSSTPINEGQTVLDK 237.28 2.36E-45 772671000 1023124 713852 821087 766461 1103250 1283270 1142740 952750 985820 574419 TRUE FALSE 1063517.726 836450.528 842485.2018 918064.6981 915719.9591 985249.9906 1053169.053 939979.9446 950340.5308 686965.4051 1.548138695 1.217602112 1.22638665 1.336406013 1.332992829 1.434206123 1.533074366 1.368307542 1.383389212 1 19.38987792 -0.547583429 6.046130722 0.999999999 1.372485688 0.538409258 0.104299443 6968870.197 1152616.658 0.144744891 0.025145889 0.283410914 0.547583429 0.372485688 S(ph)ATRPSPS(ph)PER ddPTM_MDA-MB-175_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(0.563)AT(0.02)RPS(0.423)PS(0.994)PER 122.01 0.0047801 341710000 275590 271130 289960 266160 339300 386170 314200 306610 288580 235450 TRUE FALSE 286470.506 317694.4684 297516.5958 318805.6536 281625.9072 296487.87 289572.183 302500.3945 278194.0622 281581.9195 1.017361152 1.12824882 1.056589842 1.132195043 1.000156216 1.052936461 1.028376337 1.074289127 0.987968484 1 18.10319518 3.228265367 24.9997116 1.032381989 1.084858808 0.340014791 0.039664698 249.1170403 604924.6292 0.010736169 0.012963541 1691.474158 -3.228265367 0.052476819 S(ph)AVDLSCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SAVDLSCSR 9 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)AVDLSCSR;S(1)AVDLSCSR;S(1)AVDLSCSR 133.89 0.00027713 1513120000 473520 768830 781560 634460 1125300 833910 600480 712750 746280 845560 TRUE FALSE 492214.9352 900870.5718 801928.0957 759954.2943 934021.9079 640247.0405 553412.8085 703196.7521 719421.5286 1011231.293 0.486748125 0.890865006 0.79302144 0.751513823 0.923648145 0.633136104 0.5472663 0.695386661 0.711431236 1 19.94768158 -0.962635585 4.74299762 1.000003388 0.718072254 0.301603483 0.130120297 0.024587106 82140805.55 664.6498972 0.030413046 0.10898442 0.962635585 -0.281931134 S(ph)AVFPGEGK ddPTM_MDA-MB-175_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 122.7 0.00060679 3463870000 3732550 2673680 3329550 2697510 4979770 4564390 4482710 3646230 4107170 2705360 TRUE FALSE 3879913.956 3132863.742 3416320.808 3231069.427 4133310.474 3504379.596 4131343.477 3597358.251 3959353.754 3235423.495 1.199198177 0.96830098 1.055911479 0.998654251 1.277517605 1.083128562 1.276909648 1.111866269 1.223751314 1 21.62552313 3.257411698 24.99999615 1.168076343 1.049314792 0.21711276 0.098582685 317.2740877 420761.133 0.024812713 0.03354188 1808.888085 -3.257411698 -0.118761551 S(ph)AVLLVDETATTPIFANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 336.71 4.20E-75 862554000 134229.2 128540.4 139504.8 146447 179374.9 186290.3 157903.8 153992.8 152964.1 125530.6 TRUE FALSE 139528.6725 150616.2138 143140.4097 175413.7795 148884.8186 143027.2011 145526.8876 151928.7784 147458.9519 150125.9176 0.929410955 1.003265899 0.953469007 1.168444345 0.991732946 0.952714916 0.969365516 1.012008991 0.982235141 1 17.19581354 4.964248219 1.883469054 1.005787751 0.864272966 0.125771523 0.05846199 3.92844763 8.595756909 0.015186065 1.188339018 92097.58009 -4.964248219 -0.141514785 S(ph)AVLLVDETATTPIFANRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 144.92 7.99E-08 114507000 23078.8 93127 75504 71118 64952 95302 48936 66778 58576 111459 TRUE FALSE 23989.96884 109120.8378 77471.69627 85184.92813 53911.48224 73169.55482 45100.26845 65882.95014 56467.8612 133297.257 0.179973462 0.818627782 0.581194977 0.639059873 0.404445549 0.548920184 0.33834356 0.494255858 0.42362358 1 17.02428757 -1.260235595 5.39841021 1.000050689 0.500576051 0.458496874 0.165372108 9.49E-05 1.30E-05 0.150651 0.035505192 0.054924284 1.260235595 -0.499474639 S(ph)AVS(ph)SAQAST(ph)NRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAVSSAQASTNRK 13 1 F6VGH2 F6VGH2 KIF6 3 S(0.667)AVS(0.667)S(0.667)AQAS(0.107)T(0.894)NRK 52.79 0.081619 3529800000 878740 539570 638070 497410 11817000 1092500 8429700 973350 658810 437390 TRUE FALSE 913433.3337 632236.9502 654698.6284 595796.2134 9808350.561 838783.432 7768958.087 960303.8353 635099.5568 523088.1962 1.746231975 1.208662239 1.251602757 1.138997626 18.75085432 1.603522003 14.85209979 1.835835414 1.214134751 1 18.99669469 S(ph)CETSSQDLGFSYYPAENLIEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SCETSSQDLGFSYYPAENLIEYK 23 0 S5FZ81;Q8WUB8-3;Q8WUB8-2;Q8WUB8 S5FZ81 PHF10 PHD finger protein 10 1 S(0.857)CET(0.142)S(0.001)SQDLGFSYYPAENLIEYK;S(0.854)CET(0.144)S(0.001)SQDLGFSYYPAENLIEYK;S(0.863)CET(0.134)S(0.003)SQDLGFSYYPAENLIEYK;S(0.972)CET(0.028)SSQDLGFSYYPAENLIEYK 252.77 1.15E-43 334532000 285892 174606 236366 217548 297803 329858 319553 241947 268085 127479 TRUE FALSE 297179.2369 204593.2223 242525.8921 260578.3451 247182.5524 253253.4785 294505.6009 238704.0962 258436.6732 152456.0693 1.949277836 1.341981485 1.590791978 1.70920283 1.621336255 1.661157077 1.931740745 1.5657238 1.695155033 1 17.21803406 -1.686284447 6.65307287 0.994560394 1.66487476 0.596162565 0.166274802 0.012609173 0.000594566 0.15131471 0.035621927 0.020592807 1.686284447 0.670314366 S(ph)CHDLDLLGQSPGWGQTQAVETNIVCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 312.1 3.13E-82 633110000 163682 192997 179321 189416 217548 263813 185610 200233 199153 206334 TRUE FALSE 170144.2918 226142.7334 183994.2526 226881.9194 180569.2687 202546.4289 171061.4032 197549.2042 191985.5224 246761.1968 0.689509915 0.916443656 0.745636895 0.919439208 0.731757144 0.820819608 0.69322651 0.80056835 0.778021524 1 17.91275602 -1.266231265 5.59179133 1.000016516 0.790600711 0.406454681 0.076675923 1.42E-05 1.87E-06 0.066884549 0.015763597 0.054171235 1.266231265 -0.209415805 S(ph)CNITECQDPDLLHNWPDAFTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SCNITECQDPDLLHNWPDAFTLR 23 0 Q6ZN28 Q6ZN28 MACC1 Metastasis-associated in colon cancer protein 1 1 S(0.928)CNIT(0.072)ECQDPDLLHNWPDAFTLR;S(0.991)CNIT(0.009)ECQDPDLLHNWPDAFTLR;S(0.995)CNIT(0.005)ECQDPDLLHNWPDAFTLR;S(1)CNITECQDPDLLHNWPDAFTLR 218.63 1.42E-32 567840000 230329 250977 228229 219624 272034 307032 202691 219281 236322 232444 TRUE FALSE 239422.5668 294080.3474 234176.8352 263064.9717 225793.7578 235728.4711 186803.5498 216341.8969 227816.8174 277986.9514 0.861272681 1.057892631 0.842402257 0.946321294 0.812245887 0.847983943 0.671986756 0.778244791 0.819523421 1 18.08465764 3.165240522 1.927091444 0.793872972 0.93540322 0.185181204 0.095733075 0.39971028 3.053032925 0.029490658 0.038946047 1462.987183 -3.165240522 0.141530248 S(ph)CPELTSGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCPELTSGPR 10 0 Q13111;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(1)CPELTSGPR;S(1)CPELTSGPR 213.35 2.51E-08 751330000 99603 113599 111708 115139 110245 144989 131298 117206 97253 107209 TRUE FALSE 103535.4034 133108.7446 114619.2022 137913.1505 91505.59428 111317.5021 121006.5197 115635.0453 93752.88353 128214.5509 0.807516796 1.038171905 0.893964074 1.075643518 0.713691181 0.868212705 0.943781488 0.901887067 0.731218749 1 16.96820048 3.250659773 24.99999898 0.864317077 0.955573145 0.156643008 0.106541225 432.5629134 893782.2028 0.028229321 0.037936414 1780.982994 -3.250659773 0.091256068 S(ph)CSPLAFSAFGDLTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.5)CS(0.5)PLAFSAFGDLTIK 72.315 0.019232 0 25553 17938 24517 17410 28668 27230 30448 28959 32822 18301 TRUE FALSE 26561.85217 21018.71196 25155.93316 20853.64604 23795.0236 20906.24517 28061.4062 28570.85197 31640.74263 21886.73056 1.213605299 0.960340418 1.149369162 0.952798591 1.087189498 0.955201834 1.282119599 1.305396066 1.445658709 1 14.41776884 2.222655247 24.41974296 1.286005352 1.050236927 0.36260859 0.131213023 162.2094976 249040.4221 0.045066889 0.033402224 166.976459 -2.222655247 -0.235768425 S(ph)DEDRYQNGAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDEDRYQNGAER 12 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 S(1)DEDRYQNGAER 119.45 0.00031289 78368000 35721 29110 34108 29013 41645 52244 44420 37692 35038 26871 TRUE FALSE 37131.29266 34109.41606 34996.8825 34751.6848 34566.19778 40111.12277 40938.24433 37186.80039 33776.98922 32135.85797 1.155447373 1.061412958 1.089029038 1.081399004 1.07562704 1.248173389 1.273911665 1.157174656 1.051068537 1 14.97189637 2.786805856 24.98479159 1.166377284 1.090032601 0.07247849 0.080434878 695.3980842 360124.8989 0.024504805 0.025991199 612.0767121 -2.786805856 -0.076344683 S(ph)DSASSEPVGIYQGFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.964)DS(0.035)AS(0.001)SEPVGIYQGFEK;S(0.688)DS(0.312)ASSEPVGIYQGFEK;S(0.902)DS(0.098)ASSEPVGIYQGFEK;S(0.605)DS(0.395)ASSEPVGIYQGFEK;S(0.623)DS(0.377)ASSEPVGIYQGFEK 403.2 3.38E-140 715344000 1060628 746278 1085390 863235 1306040 1325800 1462480 1096460 1204330 798085 TRUE FALSE 1102502.412 874445.4413 1113676.155 1033980.307 1084039.787 1017903.043 1347846.996 1081763.747 1160986.399 954454.4755 1.155112623 0.916173022 1.166819564 1.083320717 1.135768981 1.066476263 1.412164782 1.133384331 1.216387401 1 19.86431686 S(ph)DSEATISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSEATISR 9 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2;H0Y4T4 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.975)DS(0.025)EATISR;S(0.998)DS(0.002)EATISR;S(0.999)DS(0.001)EATISR 190.57 3.87E-05 1196810000 506880 502245 534510 482932 641470 724470 565030 523300 503750 488918 TRUE FALSE 526892.0138 588501.6718 548439.7697 578454.5082 532433.1585 556222.8219 520741.4722 516286.0194 485620.1359 584712.1212 0.901113547 1.006481054 0.937965453 0.989297959 0.910590253 0.951276366 0.890594625 0.882974716 0.830528594 1 19.15736697 2.238628144 9.256721942 0.89030542 0.951603144 0.173410993 0.049507218 0.133161519 154.0873838 0.016612453 0.013059605 173.23201 -2.238628144 0.061297723 S(ph)DSELEVKPAESLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 S(0.986)DS(0.014)ELEVKPAESLLR;S(0.997)DS(0.003)ELEVKPAESLLR;S(0.998)DS(0.002)ELEVKPAESLLR 116.29 0.00027868 122096000 210912 115244 144408 120399 192596 205140 217802 136576 141285 79378 TRUE FALSE 219238.9686 135036.2605 148171.3911 144213.5628 159858.6007 157499.3439 200730.1101 134745.4221 136200.1804 94930.59932 2.309465759 1.422473486 1.560839099 1.519147292 1.683952296 1.659099859 2.114493236 1.419409791 1.434734231 1 16.53458557 1.034792612 1.621832524 1.015786299 1.711543996 0.415332496 0.268883265 0.365672546 1.956835835 0.243022745 0.070931414 10.83409431 -1.034792612 0.695757696 S(ph)DSELEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSELEVR 8 0 Q9BQK8-2;Q9BQK8 Q9BQK8-2 LPIN3 Phosphatidate phosphatase LPIN3 1 S(0.992)DS(0.008)ELEVR;S(0.999)DS(0.001)ELEVR 180.09 0.00025271 273660000 288290 284340 285490 296300 340430 381390 369780 269200 269050 209169 TRUE FALSE 299671.9118 333173.1831 292930.1039 354907.2556 282563.8302 292817.9525 340795.6774 265591.8143 259366.9431 250151.6608 1.197960913 1.331884754 1.171010031 1.418768337 1.129570075 1.170561697 1.362356245 1.06172317 1.036838781 1 17.9324435 1.612181091 6.007516758 1.028864679 1.252227913 0.569558731 0.088656441 0.094727375 7.263469824 0.045618839 0.021778341 40.94313475 -1.612181091 0.223363234 S(ph)DSENVYEVIQDLHVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSENVYEVIQDLHVPPR 18 0 A0A0G2JRG8;A0A0G2JNY3;A0A0G2JP16 A0A0G2JRG8 1 S(0.552)DS(0.434)ENVY(0.013)EVIQDLHVPPR;S(0.47)DS(0.421)ENVY(0.108)EVIQDLHVPPR 133.41 8.20E-06 32629000 31330 39261 41271 36966 45168 49672 49612 38025 36739 27991.9 TRUE FALSE 32566.93259 46003.77134 42346.55616 44277.76447 37490.35949 38136.43079 45723.2818 37515.33707 35416.77057 33476.37687 0.972833253 1.374215959 1.264968319 1.322657008 1.11990493 1.13920425 1.365837229 1.120651056 1.057963074 1 15.03085577 1.443839769 3.708531205 1.033864475 1.227912148 0.304890432 0.117450822 0.260363547 6.590531341 0.081639067 0.029168995 27.78687893 -1.443839769 0.194047673 S(ph)DSLLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.997)DS(0.003)LLSFR;S(0.999)DS(0.001)LLSFR;S(0.998)DS(0.002)LLSFR 156.83 0.00040564 86508000 59420 68962 72239 70836 87044 103776 90772 81597 83418 79673 TRUE FALSE 61765.94748 80805.68705 74121.60768 84847.14938 72248.29197 79675.59674 83657.05345 80503.32568 80415.80247 95283.39892 0.648234091 0.848056303 0.777906839 0.890471481 0.758246377 0.836195997 0.877981415 0.844883018 0.843964462 1 16.53993726 -5 0.02670059 2.155802911 1.13E-13 0.583594923 0.056430552 1299.115001 2.617154035 157.0341809 70.27824011 1.00E-05 5 -2.155802911 S(ph)DSPEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.5)DS(0.5)PEIPFQAAAGPSDGLDASSPGNSFVGLR 121.5 5.41E-06 45393000 46987 35361 42921 42868 52785 56501 51384 46360 48473 34820 TRUE FALSE 48842.08304 41433.97668 44039.55652 51347.16245 43812.62455 43379.49903 47356.38781 45738.62003 46728.4662 41642.31233 1.172895555 0.99499702 1.057567509 1.233052623 1.052117957 1.041716864 1.137218016 1.098368882 1.122139084 1 15.34576256 -1.223321753 3.609015326 0.999845078 1.098928381 0.174127 0.065910867 4.011399879 11134881.39 3100.37541 0.015324832 0.059796842 1.223321753 0.099083304 S(ph)EAEDEDDEDYVPYVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEAEDEDDEDYVPYVPLR 18 0 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR 219.58 7.60E-19 348618000 207265 184232 202171 175378 227099 252055 248012 209687 197434 150524 TRUE FALSE 215447.9822 215872.4129 207439.7423 210067.2449 188496.7931 193519.0462 228572.1714 206876.4887 190328.3889 180016.2958 1.196824883 1.199182618 1.152338689 1.166934604 1.047109609 1.075008489 1.269730445 1.149209786 1.05728422 1 17.45776799 -4.99999999 0.172031946 0.404622702 1.184674025 0.372417292 0.062915191 160.3849154 1.520459339 32.50137697 0.235412519 1.00E-05 4.99999999 0.780051323 S(ph)EAEEGEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEAEEGEVR 9 0 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(1)EAEEGEVR 160.77 6.82E-05 123080000 60710 61216 50717 57992 63782 70921 87528 48495 51482 36926 TRUE FALSE 63106.87768 71729.37181 52038.72668 69462.64451 52940.35842 54450.67257 80667.32665 47845.00385 49629.17288 44160.94271 1.429020166 1.624271752 1.178388039 1.572942973 1.198804989 1.233005213 1.826666772 1.083423517 1.123825033 1 15.43048335 1.604260091 25 1.077655377 1.425250507 0.427649666 0.194920834 0.337919561 2326.226807 0.095638186 0.046976703 40.20315079 -1.604260091 0.347595129 S(ph)EEKEAGEI ddPTM_MDA-MB-175_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 93.345 0.024891 509380000 1783060 830900 1088000 792130 1704400 1919750 1572540 1121690 1296640 611340 TRUE FALSE 1853456.586 973600.6115 1116354.174 948810.9497 1414686.697 1473917.157 1449280.206 1106655.58 1249974.18 731120.3682 2.535090891 1.331655708 1.526908868 1.297749305 1.934957304 2.015970585 1.982273055 1.513643483 1.70966948 1 19.47974942 0.396085958 1.144313569 0.999826721 1.751041686 0.294908559 0.354472622 3.530581767 5.459322888 0.338142542 0.102416181 2.489349976 -0.396085958 0.751214964 S(ph)EETQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.999)EET(0.001)QER;S(1)EETQER 155.06 0.0017169 126350000 86840 78605 92352 95810 118240 121655 136036 97432 100144 74515 TRUE FALSE 90268.51026 92104.79729 94758.76899 114760.932 98141.60703 93402.46995 125373.1429 96126.08341 96539.837 89114.78757 1.012946478 1.033552341 1.063333837 1.287787753 1.101294294 1.048114151 1.406872487 1.078677131 1.08332006 1 16.44337723 3.981596975 23.4207663 1.154490339 1.029547743 0.156751746 0.114272664 511.4316439 650883.9092 0.028329007 0.052405875 9585.107222 -3.981596975 -0.124942595 S(ph)EGEKVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEGEKVR 7 1 A0A0U1RRH1;A0A0X1KG73;A0A087X080;Q15413-3;Q15413-2;Q15413;P21817-3;P21817-2;P21817;H7BY35;Q92736;Q92736-2 A0A0U1RRH1;H7BY35 RYR3;RYR1;RYR2 Ryanodine receptor 3;Ryanodine receptor 1;Ryanodine receptor 2 1 S(1)EGEKVR;S(1)EGEKVR 54.525 0.080626 987700000 794080 639880 937380 546060 1681330 1134170 1284190 957410 1093370 534220 TRUE FALSE 825430.8916 749774.4124 961808.8929 654069.0382 1395538.127 870776.206 1183531.832 944577.485 1054019.827 638890.1807 1.291976174 1.173557577 1.505436962 1.023758164 2.18431613 1.362951306 1.852480861 1.478466117 1.649766829 1 19.28520844 S(ph)EGKRKT(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEGKRKTAK 9 3 P82933 P82933 MRPS9 "28S ribosomal protein S9, mitochondrial" 2 S(1)EGKRKT(1)AK 58.674 0.085469 517030000 16229 1128900 764940 1028200 496510 1058700 444350 710520 548630 1439100 TRUE FALSE 16869.73345 1322779.793 784874.9648 1231574.891 412113.4075 812832.9698 409520.6859 700996.6416 528884.9135 1721064.092 0.009801921 0.76858253 0.456040521 0.715589208 0.239452679 0.472285125 0.237946215 0.407304205 0.307301114 1 20.71486939 -1.814347271 5.437885241 1.05741666 0.413056679 0.412189514 0.213989237 0.099834907 0.003408424 0.138866887 0.045232477 0.015333904 1.814347271 -0.644359981 S(ph)EGSPVLPHEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEGSPVLPHEPAK 13 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 S(0.559)EGS(0.441)PVLPHEPAK;S(0.553)EGS(0.447)PVLPHEPAK 104.41 0.00098779 351950000 795310 532320 641990 512960 728240 769720 750060 577690 595750 352690 TRUE FALSE 826709.4529 623741.8191 658720.7868 614421.957 604454.0249 590964.1952 691268.3373 569947.0105 574309.0739 421792.8528 1.95998924 1.478787075 1.561716332 1.456691247 1.433058955 1.401076835 1.638881106 1.35124862 1.36159034 1 18.68617512 1.858461783 0.055254072 9.92E-19 2.811044574 0.668369879 0.132553693 22.99853115 1.11288427 26.60024541 28.71869637 72.18746364 -1.858461783 2.811044574 S(ph)EPDDELLFDFLNSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPDDELLFDFLNSSQK 17 0 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQK;S(1)EPDDELLFDFLNSSQK 126.88 4.42E-05 29525000 28448 16990.7 21748.7 23734.7 23933.7 27280 35598 23799.9 20927.7 14109.2 TRUE FALSE 29571.14901 19908.72056 22315.48899 28429.35282 19865.45822 20944.63343 32807.73574 23480.90127 20174.51617 16873.6276 1.752506912 1.179871989 1.322506903 1.684839413 1.177308086 1.241264411 1.944320244 1.391573989 1.195624121 1 14.04248255 1.092461968 3.114725889 1.010589182 1.460048644 0.279263449 0.244812714 0.294184364 5.519196033 0.227484511 0.060358317 12.37262835 -1.092461968 0.449459462 S(ph)EPDDELLFDFLNSSQKEPTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEPDDELLFDFLNSSQKEPTGR 22 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 1 S(1)EPDDELLFDFLNSSQKEPTGR;S(1)EPDDELLFDFLNSSQKEPTGR;S(1)EPDDELLFDFLNSSQKEPTGR 150.91 3.18E-08 187862000 135477 78859 96106 82359 126620 143882 123465 108031 96515 65082 TRUE FALSE 140825.7366 92402.41981 98610.60131 98649.36438 105097.1776 110467.5861 113787.4907 106583.0211 93041.444 77833.57183 1.809318694 1.187179486 1.266941745 1.26743977 1.3502808 1.419279412 1.461933302 1.369370808 1.195389622 1 16.24810494 1.009528452 2.740547604 1.001794517 1.380088496 0.378245758 0.160112829 0.263275736 4.524996481 0.145507589 0.038872759 10.22182525 -1.009528452 0.378293979 S(ph)ESELIDELSEDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(1)ESELIDELSEDFDR;S(0.999)ES(0.001)ELIDELSEDFDR;S(0.999)ES(0.001)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(0.5)ES(0.5)ELIDELSEDFDR;S(0.5)ES(0.5)ELIDELSEDFDR;S(1)ESELIDELSEDFDR;S(1)ESELIDELSEDFDR 305.23 1.03E-44 1060081000 492150 511300 567748 567857 659228 790658 740607 634025 639109 467137 TRUE FALSE 511580.462 599111.7976 582543.9793 680177.4197 547172.66 607039.662 682556.2881 625526.9319 616107.5919 558663.5513 0.915721924 1.072401799 1.042745635 1.217508137 0.979431464 1.086592567 1.221766279 1.119684523 1.102824035 1 19.09162017 5.635119523 1.059719896 1.110593045 6.19E-08 0.329752565 0.075887239 10.78118565 2.377874566 0.021537587 21.20238004 431637.8526 -5.635119523 -1.110592984 S(ph)ESELIDELSEDFDRSECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(1)ESELIDELSEDFDRSECK;S(0.982)ES(0.018)ELIDELSEDFDRSECK;S(1)ESELIDELSEDFDRSECK;S(0.992)ES(0.008)ELIDELSEDFDRSECK;S(0.998)ES(0.002)ELIDELSEDFDRSECK;S(1)ESELIDELSEDFDRSECK;S(0.984)ES(0.016)ELIDELSEDFDRSECK;S(0.987)ES(0.013)ELIDELSEDFDRSECK 292.68 8.36E-50 1484280000 816052.2 553823.9 787122.6 491080.2 1092122.9 1063250.4 834253 719743.3 889480.7 581836.2 TRUE FALSE 848270.571 648938.8467 807635.6616 588214.3978 906484.2396 816326.6083 768862.0699 710096.3183 857468.4634 695835.8635 1.219067047 0.932603335 1.160669784 0.845334983 1.302727104 1.173159722 1.10494746 1.020493992 1.232285526 1 19.40838751 5.053846419 19.86929851 1.08774673 2.762011508 0.083495606 0.132314924 310.8784095 221707.9603 0.028949851 20467.80174 113199.9981 -5.053846419 1.674264778 S(ph)ESLDPDSSMDTTLILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESLDPDSSMDTTLILK 17 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.5)ES(0.5)LDPDSSMDTTLILK 82.908 0.0064818 14134000 22375 17704 21534 14089 36810 28103 23576 24395 30135 16051 TRUE FALSE 23258.38228 20744.52428 22095.19373 16875.76215 30553.04935 21576.50416 21728.05152 24068.02493 29050.44724 19195.88614 1.211633686 1.080675523 1.151037966 0.879134312 1.591645686 1.124017094 1.131911878 1.253811611 1.513368387 1 14.22850954 3.267509738 24.99998063 1.26366771 1.085654364 0.200370415 0.1841796 361.6329313 312297.81 0.049059553 0.066416535 1851.440409 -3.267509738 -0.178013345 S(ph)ESNEDLFGLVPFDEITGSQQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SESNEDLFGLVPFDEITGSQQQK 23 0 H0Y9P1;Q9NSY1 H0Y9P1 BMP2K BMP-2-inducible protein kinase 1 S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK;S(0.5)ES(0.5)NEDLFGLVPFDEITGSQQQK 173.55 2.39E-12 236255000 434713 289254 389702 294256 471870 463714 410589 370867 412291 248436 TRUE FALSE 451875.8049 338931.1244 399857.9543 352458.9585 391661.7059 356023.4512 378405.9613 365896.1345 397452.7274 297112.2776 1.5208924 1.140750989 1.345814308 1.186282039 1.318227941 1.198279162 1.27361267 1.231507959 1.337718961 1 18.1806487 -3.824992654 0.301082451 9.70E-27 1.289435676 0.404774706 0.102555737 117.8273885 2.114687872 73.56495303 0.09172799 0.000149626 3.824992654 1.289435676 S(ph)ESPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.756)ES(0.244)PKEPEQLR 138.97 2.81E-05 2567800000 1932900 638750 891100 667880 1302800 1364200 1330300 930230 974080 519140 TRUE FALSE 2009212.385 748450.3437 914322.798 799984.6706 1081350.521 1047385.225 1226027.61 917761.7884 939023.0511 620855.5435 3.236199476 1.205514474 1.472682023 1.288519816 1.741710343 1.687003097 1.974738927 1.478221139 1.512466243 1 19.24389811 4.745184406 24.99583048 1.52735719 3.236200251 0.793135561 0.267570892 335.2834082 1265207.894 0.062797916 0.609781572 55614.03499 -4.745184406 1.708843061 S(ph)ESPKEPEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.585)ES(0.415)PKEPEQLRK 64.136 0.034297 169630000 362220 182380 241470 188800 319640 371070 277280 184090 280090 149380 TRUE FALSE 376520.7253 213702.3463 247762.9066 226144.0765 265307.707 284894.6161 255546.0691 181622.5747 270009.6156 178648.1509 2.107610537 1.196219189 1.386876412 1.265862956 1.485085099 1.594724684 1.430443403 1.016649619 1.51140448 1 17.44676146 8 0.105850857 0.897040032 3.102624381 0.305263293 0.253618773 158.2928398 1.17572295 2.581283244 50.87982853 100000000 -8 2.205584348 S(ph)ET(ph)PPHWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SETPPHWR 8 0 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 S(1)ET(1)PPHWR 69.672 0.094607 230950000 163090 150700 154600 162100 175340 256710 212490 176670 163260 122400 TRUE FALSE 169528.9191 176581.5527 158629.003 194162.8962 145535.7694 197092.993 195834.4786 174302.0276 157384.3045 146381.9365 1.158127315 1.206306987 1.083665149 1.32641295 0.994219457 1.346429742 1.337832271 1.190734539 1.075162061 1 17.15937801 1.121363979 3.256817283 1.004572349 1.209508295 0.295804531 0.106762011 0.271130473 5.255823982 0.097654943 0.025932689 13.22403467 -1.121363979 0.204935946 S(ph)ETEDSILHQLFIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 S(0.988)ET(0.012)EDSILHQLFIVR;S(0.999)ET(0.001)EDSILHQLFIVR;S(0.997)ET(0.003)EDSILHQLFIVR 243.01 3.81E-18 53263000 25438 26737.9 26817.9 32197.1 31333.3 36567.7 40230 33860.4 35299.3 21844.4 TRUE FALSE 26442.31188 31329.92633 27516.79651 38565.59028 26007.27686 28075.40586 37076.66748 33406.55672 34028.88509 26124.39194 1.012169467 1.199259543 1.053299023 1.476229202 0.995517022 1.074681697 1.419235615 1.278749637 1.302571373 1 14.67310984 2.258870954 24.95271623 1.279154499 1.143535128 0.095678988 0.162461919 456.2817705 560573.7815 0.054101739 0.045211045 181.4976282 -2.258870954 -0.13561937 S(ph)FAGNLNTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFAGNLNTYK 10 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 S(1)FAGNLNTYK;S(1)FAGNLNTYK;S(1)FAGNLNTYK;S(1)FAGNLNTYK 175.68 2.86E-06 1729300000 908650 755560 895790 676210 1567220 1157890 1197010 977470 995450 886940 TRUE FALSE 944524.2036 885321.5526 919135.0233 809962.3197 1300824.504 888987.5955 1103185.228 964368.6135 959623.949 1060718.912 0.890456645 0.834642942 0.866520822 0.76359751 1.226361188 0.838099129 1.04003541 0.909165098 0.904692033 1 20.01661096 S(ph)FAGNLNTYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFAGNLNTYKR 11 1 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 S(1)FAGNLNTYKR 56.872 0.071202 516910000 406400 345380 381510 291220 695300 519030 369920 377440 418650 502650 TRUE FALSE 422444.9858 404696.3283 391452.464 348822.4468 577113.1544 398493.1485 340924.7038 372381.0342 403582.8683 601134.6437 0.702746032 0.673220771 0.651189327 0.580273405 0.960039752 0.662901652 0.567135345 0.619463606 0.671368507 1 19.19732864 -1.268408792 3.555794109 1.000820568 0.672000059 0.468637479 0.103247471 20746824.71 34046864.24 185835.4997 0.025304502 0.053900303 1.268408792 -0.328820509 S(ph)FDAVLEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFDAVLEALSR 11 0 Q6P1N0-2;Q6P1N0;K7EJY5 Q6P1N0-2 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 S(1)FDAVLEALSR;S(1)FDAVLEALSR 122.46 0.00040944 45327000 35023 32267.8 42453 30806.8 49052 44988 47549 43824 52386 32865.6 TRUE FALSE 36405.73508 37809.54364 43559.36006 36900.29309 40714.15856 34540.2188 43821.98513 43236.61096 50500.63809 39304.98507 0.926237092 0.961952881 1.108240087 0.938819669 1.035852284 0.878774505 1.114921811 1.100028683 1.284840536 1 15.26242468 2.112842143 8.211224994 1.13137383 0.981754008 0.412235539 0.087563169 0.237602112 16.19897024 0.031432891 0.023193873 129.6707858 -2.112842143 -0.149619822 S(ph)FDAVVFDVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFDAVVFDVLK 11 0 Q86X27;Q86X27-3;Q86X27-2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(1)FDAVVFDVLK;S(1)FDAVVFDVLK 162.32 2.65E-05 60825000 144840 93602 122378 90534 173950 165463 163075 116978 134659 105340 TRUE FALSE 150558.395 109677.4154 125567.2712 108441.355 144382.0411 127036.7259 150292.7554 115410.1012 129812.6489 125979.3561 1.195103703 0.870598317 0.996728949 0.860786706 1.146076989 1.008393198 1.192995106 0.916103279 1.030427944 1 16.94282782 4.770816951 23.55859753 1.00464907 1.195104465 0.245094889 0.101363378 9819.009057 7171090.843 0.023442033 3.281614053 58995.23707 -4.770816951 0.190455395 S(ph)FDEVEGVFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFDEVEGVFGR 11 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JW88;Q6Y7W6-4;Q6Y7W6-5;E7ESB6 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 S(1)FDEVEGVFGR;S(1)FDEVEGVFGR 136.27 0.00010762 77774000 108983 91558 115052 91230 162790 177583 150093 119887 136504 93076 TRUE FALSE 113285.733 107282.3743 118050.3496 109275.0217 135119.0139 136342.0395 138328.3185 118280.1109 131591.2477 111312.4602 1.017727331 0.963794836 1.060531314 0.981696223 1.213871419 1.224858739 1.242702913 1.062595425 1.182178954 1 16.76425557 3.245106997 24.99981787 1.160182913 1.006826781 0.489056269 0.074180182 128.7688926 491749.58 0.020597712 0.027243845 1758.356768 -3.245106997 -0.153356132 S(ph)FDGNTLLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFDGNTLLNR 10 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR;S(1)FDGNTLLNR 186.76 1.37E-06 1525060000 623931 581534 891900 654668 941440 773160 1007790 824100 950840 513805 TRUE FALSE 648564.2777 681407.9408 915143.6467 784159.3764 781414.3651 593605.3074 928796.7864 813054.2875 916619.4541 614475.2524 1.055476645 1.108926581 1.4893092 1.276144765 1.27167752 0.96603615 1.511528386 1.323168483 1.491710936 1 19.22899538 2.212748618 24.99957296 1.360207645 1.211307496 0.102436633 0.187448463 476.0281543 461042.2983 0.068559186 0.05065097 163.2106965 -2.212748618 -0.148900149 S(ph)FDYNYR ddPTM_MDA-MB-175_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(1)FDYNYR;S(1)FDYNYR 177.91 0.00075874 24298520000 4912500 4431792 4820346 5135615 5469040 6246950 6516020 5146847 4844649 3584079 TRUE FALSE 5106449.293 5192917.801 4945968.177 6151424.319 4539414.534 4796190.536 6005277.326 5077861.935 4670291.029 4286310.659 1.191339056 1.211512234 1.153898672 1.435132637 1.059049354 1.118955418 1.401036417 1.1846696 1.089582954 1 22.03130499 1.117961868 2.914750564 1.00558862 1.223915449 0.305228779 0.110108281 0.282593077 4.503865923 0.101017978 0.027212062 13.1208469 -1.117961868 0.218326829 S(ph)FDYNYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SFDYNYRR 8 1 O75494-2;O75494;O75494-5;O75494-6;O75494-3;Q5JRI1;O75494-4 O75494-2;O75494-6;Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR;S(1)FDYNYRR 172.56 0.00017326 4441840000 3471170 4182320 3979880 3123140 5644870 5127770 3323140 4017730 4154290 4949890 TRUE FALSE 3608214.472 4900600.926 4083598.942 3740887.77 4685357.014 3936923.13 3062663.603 3963878.901 4004777.914 5919726.174 0.609523881 0.827842502 0.689829026 0.631935948 0.791482051 0.66505156 0.517365755 0.669605111 0.676514048 1 22.49709901 -1.931321886 6.372755581 1.118699828 0.674823671 0.581314019 0.082626328 0.047524233 0.000512161 0.027284879 0.018968527 0.011713269 1.931321886 -0.443876157 S(ph)FEDRVGTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFEDRVGTIK 10 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 S(1)FEDRVGTIK;S(1)FEDRVGTIK 148.72 1.49E-05 1862810000 1728310 1697760 2527700 1031910 3526100 2314000 1886260 2180400 2858700 2001340 TRUE FALSE 1796545.013 1989337.073 2593573.939 1236018.718 2926734.781 1776608.569 1738410.012 2151175.304 2755815.945 2393464.255 0.750604489 0.831153868 1.083606715 0.516414112 1.222802795 0.742274954 0.726315427 0.8987706 1.151392146 1 21.19066883 1.372815864 5.661469548 1.071460183 0.844614345 0.196844123 0.187936183 0.318970706 13.76181324 0.121780153 0.043684011 23.5947763 -1.372815864 -0.226845838 S(ph)FEEEGEHLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFEEEGEHLGSR 12 0 Q9BXW6-4;Q9BXW6 Q9BXW6-4 OSBPL1A Oxysterol-binding protein-related protein 1 1 S(1)FEEEGEHLGSR 207.4 5.08E-08 672420000 83897 74769 83953 69004 117570 113360 81704 94878 94424 83181 TRUE FALSE 87209.31834 87609.99413 86140.88415 82652.78524 97585.49339 87033.85799 75299.82699 93606.3156 91025.69868 99478.72435 0.876663014 0.880690768 0.865922686 0.830858918 0.980968484 0.874899216 0.756944035 0.940968194 0.915026799 1 16.60210039 1.04578771 1.686372157 0.995612182 0.872096054 0.330442597 0.055389082 0.417032094 2.405045999 0.051661249 0.014982158 11.11188429 -1.04578771 -0.123516129 S(ph)FEEKVENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 173.06 9.28E-06 978220000 1411510 484300 1194560 566460 1527790 1175750 1797490 998350 1609130 369427 TRUE FALSE 1467237.505 567474.7577 1225691.215 678504.0973 1268096.802 902699.8812 1656598.037 984968.7512 1551217.726 441809.1475 3.32097584 1.284434152 2.774254951 1.535740265 2.870236636 2.043189658 3.749578401 2.229398727 3.511058416 1 18.75306376 S(ph)FEERVETTVTSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFEERVETTVTSLK 14 1 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6 Q16890-5 TPD52L1 Tumor protein D53 1 S(1)FEERVETTVTSLK;S(1)FEERVETTVTSLK 228.01 1.10E-12 171694000 151868 87374 194737 87227 280630 171044 164455 168877 248459 121253 TRUE FALSE 157863.8659 102379.8048 199812.0062 104480.2403 232928.6128 131321.6232 151564.5874 166613.48 239517.0091 145010.2038 1.088639708 0.706017936 1.37791687 0.720502678 1.60629119 0.905602639 1.045199464 1.148977628 1.651725208 1 17.1457949 3.902650651 1.034262695 1.186366094 0.925835875 0.073255058 0.302015988 1.842936893 3.383860571 0.098423695 0.393166737 7991.91122 -3.902650651 -0.260530219 S(ph)FEMTEFNQALEEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFEMTEFNQALEEIK 15 0 Q9BVS4-2;Q9BVS4;H0Y919 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 S(0.997)FEMT(0.003)EFNQALEEIK;S(1)FEMTEFNQALEEIK 306.26 6.06E-45 30733000 28998 15148.7 23773 21547.1 28208 31945 34140 22818.2 24024.8 11726.4 TRUE FALSE 30142.86343 17750.37138 24392.54391 25809.05207 23413.21424 24526.25788 31464.01759 22512.35935 23160.15214 14023.96356 2.149382612 1.265717164 1.739347353 1.840353617 1.669514765 1.748882031 2.243589514 1.605277941 1.651469788 1 13.77560653 0.688126296 1.794222559 1.001120187 1.777313741 0.454343689 0.257077619 1.118549519 5.140942877 0.234616102 0.065936631 4.876702872 -0.688126296 0.776193554 S(ph)FEVEEVETPNSTPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 341.5 4.08E-72 6897130000 520237 522090 746089 509663 1182516 775839 754997 663815 808414 657486 TRUE FALSE 540776.3585 611754.8962 765532.6923 610472.8202 981512.3527 595662.1502 695818.3623 654917.6457 779319.3381 786307.7934 0.687741318 0.778009453 0.97357892 0.776378952 1.248254641 0.757543236 0.884918563 0.832902397 0.991112316 1 19.58473463 4.415158475 4.069606437 0.919266631 0.703392922 0.26933258 0.133728696 0.264910936 8.617874899 0.031503821 0.103742199 26011.08537 -4.415158475 -0.21587371 S(ph)FEVEEVETPNSTPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 1 S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR;S(1)FEVEEVETPNSTPPRR 267.56 5.17E-28 4196900000 319281 296330 406967 304592 653305 462205 381099 350161 385080 380245 TRUE FALSE 331886.4604 347222.3724 417572.8943 364839.3885 542256.4495 354864.8935 351227.4646 345467.6645 371221.046 454746.7275 0.729827045 0.763551118 0.918253764 0.8022914 1.192436177 0.780357223 0.772358421 0.75969247 0.816324832 1 18.79470373 -2.599124342 2.018449057 3.645375382 0.836664883 0.12637245 0.128380604 6276691.427 336771.2573 76018671.54 0.032256139 0.002516956 2.599124342 -2.808710499 S(ph)FGHFPGPEFLDVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFGHFPGPEFLDVEK 15 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(1)FGHFPGPEFLDVEK;S(1)FGHFPGPEFLDVEK;S(1)FGHFPGPEFLDVEK;S(1)FGHFPGPEFLDVEK 221.46 9.87E-13 309582000 557887 415763 573906 477924 849507 848514 853645 688734 728225 513324 TRUE FALSE 579912.8095 487167.0611 588862.4618 572455.9407 705108.1036 651459.4829 786734.0743 679502.6473 702016.3245 613900.0096 0.944637238 0.793560928 0.959215593 0.932490523 1.148571579 1.061181744 1.281534553 1.106862089 1.143535288 1 19.22764417 3.337819885 2.238536903 1.138680759 0.887182946 0.622003373 0.081377694 0.172967407 1.76817276 0.023215061 0.033767469 2176.806798 -3.337819885 -0.251497813 S(ph)FGNPFEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFGNPFEGSR 10 0 Q96RR4-6;Q96RR4-5;Q96RR4-2;Q96RR4-3;Q96RR4-4;Q96RR4-7;Q96RR4;F5GZ00 Q96RR4-6 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2 1 S(1)FGNPFEGSR;S(1)FGNPFEGSR;S(1)FGNPFEGSR;S(1)FGNPFEGSR 161.25 7.48E-06 417686000 273635 287327 298753 276962 280775 295407 241788 290415 282492 229815 TRUE FALSE 284438.3211 336673.1772 306538.7486 331744.257 233048.9658 226803.2012 222836.0248 286522.4619 272325.1681 274842.8492 1.034912576 1.224966115 1.115323719 1.20703252 0.847935344 0.825210486 0.810776141 1.042495604 0.990839561 1 18.06824742 3.240406595 24.99930839 0.918153861 1.149071064 0.617723649 0.087081946 33.85848255 458525.5737 0.026063784 0.033556775 1739.428555 -3.240406595 0.230917203 S(ph)FHIENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 74.173 0.03021 140510000 262390 291270 276290 284320 346160 399960 342050 275440 278870 280560 TRUE FALSE 272749.3598 341293.3567 283490.3444 340557.6474 287319.8468 307075.3515 315239.2272 271748.1773 268833.5232 335530.3604 0.812890254 1.017175782 0.844902214 1.014983106 0.856315496 0.915193937 0.939525195 0.809906373 0.801219666 1 18.35608379 1.749365166 25 0.851798355 0.917366595 0.043092378 0.081337004 5.77355866 13384.32842 0.034207113 0.018969508 56.15199178 -1.749365166 0.06556824 S(ph)FLNYYADLETSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFLNYYADLETSAR 14 0 H0YAJ5;G5E9Y1;Q92870-2;Q92870;Q92870-4 H0YAJ5 APBB2 Amyloid beta A4 precursor protein-binding family B member 2 1 S(1)FLNYYADLETSAR;S(1)FLNYYADLETSAR 143.28 9.62E-06 88072000 65437 71490 74287 80050 95199 100526 77315 86587 68929 88743 TRUE FALSE 68020.50329 83767.85138 76222.98025 95883.65107 79017.10798 77180.35999 71254.84827 85426.44289 66448.25875 106130.4918 0.640913861 0.789291089 0.718200575 0.903450549 0.744527861 0.727221355 0.671389033 0.80491894 0.626099603 1 16.69547968 -2.239042475 2.504804279 2.016717019 0.74389197 0.500693702 0.078688553 5929786.253 1409792.082 34248244.37 0.01780862 0.005767101 2.239042475 -1.272825049 S(ph)FNDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFNDFR 6 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)FNDFR;S(1)FNDFR;S(1)FNDFR;S(1)FNDFR 141.2 0.012256 2815700000 3006140 3084900 3461940 3626710 3930900 4394720 3880460 3523210 3380680 2956640 TRUE FALSE 3124824.728 3614707.578 3552161 4344062.413 3262727.022 3374112.883 3576299.406 3475987.133 3259009.987 3535937 0.883733146 1.022277144 1.004588317 1.228546327 0.922733358 0.954234446 1.011414911 0.98304555 0.921682142 1 21.75366114 S(ph)FPLFDNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFPLFDNSK 9 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK;S(1)FPLFDNSK 145.09 0.00010281 235890000 582158 434781 525861 431015 772792 747840 708769 578075 605036 450150 TRUE FALSE 605142.0474 509451.2546 539565.3697 516268.4805 641433.0919 574165.4936 653213.8338 570326.8502 583260.8725 538348.2739 1.124071678 0.946322816 1.002260796 0.958986042 1.191483512 1.066531689 1.213366635 1.05940128 1.083426661 1 19.03818027 3.252233321 24.98759458 1.108077927 1.003107685 0.280343983 0.073641367 264.5100144 483403.3822 0.019158495 0.025803209 1787.447609 -3.252233321 -0.104970242 S(ph)FQGDDSDLLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFQGDDSDLLLK 12 0 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;D6RD46;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK;S(1)FQGDDSDLLLK 226.65 1.55E-11 409018000 762988 567156 787933 605312 1202740 1056190 1120230 847430 1120560 727836 TRUE FALSE 793111.3554 664560.6311 808467.1813 725040.9069 998298.6844 810905.8792 1032423.445 836071.587 1080231.264 870441.5289 0.91115983 0.763475327 0.928801251 0.832957623 1.146887701 0.931602931 1.186091669 0.960514359 1.241015311 1 19.73138786 3.247627594 24.99734159 1.068652831 0.857247005 0.527608109 0.101104382 146.8879598 404962.4965 0.025730226 0.034352942 1768.591747 -3.247627594 -0.211405826 S(ph)FSEDTLMDGPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.943)FS(0.046)EDT(0.011)LMDGPAR;S(0.952)FS(0.048)EDTLMDGPAR 167.22 7.64E-07 0 407940 460210 521170 476760 650990 716810 584420 579150 555570 553990 TRUE FALSE 424045.7862 539247.4876 534752.1183 571061.705 540334.9523 550341.7409 538611.6333 571387.4415 535575.1442 662533.7337 0.640036521 0.813917028 0.807131911 0.861936043 0.815558401 0.830662218 0.812957297 0.862427696 0.808374151 1 19.33763439 -4.858592042 0.026230427 2.116558029 9.36E-07 0.62544376 0.050684421 1274.853356 2.580503896 152.3820998 70.35240049 1.38E-05 4.858592042 -2.116557094 S(ph)FSEDVFQSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFSEDVFQSVK 11 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.849)FS(0.151)EDVFQSVK 152.55 3.45E-05 30181000 61761 47033 56167 45127 87935 96992 71030 68580 73244 55675 TRUE FALSE 64199.37197 55110.55188 57630.75816 54052.98591 72987.84011 74467.07793 65462.483 67660.79727 70607.96275 66583.45029 0.964194131 0.827691441 0.865541781 0.811808125 1.096185911 1.11840221 0.983164476 1.016180402 1.060443135 1 16.02287601 3.23859041 25 1.043487659 0.864352821 0.724503277 0.053876968 0.425063792 356046.0747 0.015628661 0.019867444 1732.16959 -3.23859041 -0.179134838 S(ph)FSEDVISHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFSEDVISHK 10 0 F6QMI7;E9PHM6;F8W9J4;Q03001-8;Q03001-14;Q03001;A0A494C1D7;H0YC82;Q03001-10 F6QMI7 DST Dystonin 1 S(0.995)FS(0.005)EDVISHK;S(0.959)FS(0.041)EDVISHK;S(0.964)FS(0.036)EDVISHK;S(0.999)FS(0.001)EDVISHK 213.99 7.84E-09 861220000 990260 877430 879880 721770 1191010 1158170 1065620 970690 937830 659128 TRUE FALSE 1029356.229 1028121.777 902810.3956 864533.9517 988562.5456 889202.5697 982093.9199 957679.4883 904077.6815 788271.5118 1.305839694 1.304273669 1.145303848 1.096746411 1.25408889 1.128040981 1.245882802 1.214910692 1.146911525 1 19.58833311 -5 0.182984078 0.159391972 1.246058686 0.49258145 0.066243622 126.1644519 1.22155135 38.6557218 0.208379662 1.00E-05 5 1.086666714 HASTSS(ph)PADKAK ddPTM_MDA-MB-175_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(0.208)T(0.208)S(0.259)S(0.324)PADKAK 84.468 0.0074002 25739000 9539 32904 42371 34117 67503 56585 37353 52985 44623 30156 TRUE FALSE 9915.607086 38555.00604 43475.22307 40865.24077 56028.86417 43443.9913 34425.17426 52274.82274 43017.02695 36064.49083 0.274940998 1.069057268 1.205485564 1.1331157 1.553574247 1.204619566 0.954544857 1.449481791 1.192780654 1 15.13829144 4.77543054 2.405333076 1.234866048 8.73E-11 0.724426426 0.171903634 0.312509019 2.031336854 0.04180856 0.830812185 59625.29486 -4.77543054 -1.234866048 down S(ph)FSLDEPPLFIPDNIATIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFSLDEPPLFIPDNIATIR 19 0 Q92576-2;Q92576;E7EVH3;D6R9X2;E9PE34;A0A1B0GX99 Q92576-2 PHF3 PHD finger protein 3 1 S(0.831)FS(0.169)LDEPPLFIPDNIATIR;S(0.879)FS(0.121)LDEPPLFIPDNIATIR;S(0.678)FS(0.322)LDEPPLFIPDNIATIR;S(0.865)FS(0.135)LDEPPLFIPDNIATIR 300.18 7.27E-50 135551000 114409 124741 136252 144028 174894 185564 155737 157567 156361 149865 TRUE FALSE 118925.9557 146164.2964 139802.8391 172516.3085 145165.5804 142469.5732 143529.927 155455.0721 150733.5982 179228.1774 0.66354497 0.815520743 0.78002712 0.962551263 0.809948427 0.79490611 0.800822332 0.867358438 0.84101507 1 17.45143794 -5 0.086682873 1.545868531 0.669412633 0.472434801 0.065272837 218.2560293 1.323905367 22.66170206 1.751554061 1.00E-05 5 -0.876455898 S(ph)FTLDDESLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.99)FT(0.01)LDDESLK;S(1)FTLDDESLK;S(0.999)FT(0.001)LDDESLK;S(1)FTLDDESLK 265.12 1.42E-17 130601000 590907 351859 465994 395996 683729 663632 763130 539032 589554 297023 TRUE FALSE 614236.4646 412288.0462 478138.1865 474322.8269 567508.9888 509513.5254 703313.8765 531807.1577 568336.0667 355218.97 1.729176977 1.160658864 1.346037872 1.335297005 1.597631424 1.434364627 1.979944586 1.49712488 1.599959785 1 18.4383491 3.237313122 24.93862576 1.567007723 1.372872049 0.030639649 0.262799484 70.27538381 1404886.398 0.070091815 0.088293579 1727.082653 -3.237313122 -0.194135674 S(ph)GAEVEAGDAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGAEVEAGDAAER 13 0 A0A087WZ13;Q8IY67-2;E9PAU2;Q8IY67;K7EKR9;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 S(1)GAEVEAGDAAER 95.651 0.0048238 171460000 62505 70506 86082 74682 83772 90969 70595 93869 68921 53479 TRUE FALSE 64972.74566 82614.85704 88325.36764 89453.8767 69532.46536 69842.8284 65061.57943 92610.83959 66440.54667 63957.18613 1.01587874 1.29172126 1.381007717 1.398652475 1.087172053 1.092024722 1.017267697 1.448013041 1.038828483 1 15.96481885 3.222973366 24.98376018 1.149448952 1.281036431 0.176313402 0.155759702 500.0744389 801534.1374 0.047445438 0.056896353 1670.988136 -3.222973366 0.131587479 S(ph)GAKCDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGAKCDFR 8 1 B5MCA9;Q8N7S2 B5MCA9 DNAJC5G DnaJ homolog subfamily C member 5G 1 S(1)GAKCDFR 81.297 0.0611 78673000 4542.5 6116.6 7047.9 9855.8 8903.3 7943.6 6799.6 6904.5 7151.4 8894.2 TRUE FALSE 4721.841408 7167.078469 7231.574064 11805.24782 7389.920246 6098.819286 6266.629585 6811.956471 6894.022511 10636.8482 0.443913584 0.673797194 0.679860606 1.109844533 0.694747176 0.573367145 0.589143463 0.640411177 0.648126436 1 13.37678311 -2.165707611 2.122055339 1.725708317 0.677110925 0.268275602 0.162066958 11329078.92 2368409.433 39515592.52 0.040686908 0.006827982 2.165707611 -1.048597391 S(ph)GCCDDSALAR ddPTM_MDA-MB-175_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 198.97 5.44E-08 462440000 154195 170342 161259 151333 223960 242470 187911 185781 187319 192032 TRUE FALSE 160282.7377 199596.9134 165461.542 181266.2157 185891.3592 186160.0172 173182.0448 183290.9096 180577.4258 229656.9937 0.697922302 0.869108796 0.720472472 0.789291076 0.80943043 0.810600253 0.75409001 0.798107241 0.786291864 1 17.80912119 -4.999999938 0.417853095 4.932269776 0.780486585 0.672484058 0.045787141 484.172851 3.171391816 1746.610232 0.024003136 1.00E-05 4.999999938 -4.151783191 S(ph)GDEEFKGEDELCDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGDEEFKGEDELCDSGR 17 1 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR;S(1)GDEEFKGEDELCDSGR 209.24 2.70E-12 251250000 472420 194505 243193 227692 337153 488800 459380 252299 274808 106814 TRUE FALSE 491071.5064 227909.7207 249530.8094 272728.798 279843.8535 375283.6078 423372.5952 248917.3446 264917.7138 127742.1582 3.844239938 1.784138642 1.953394344 2.134994444 2.190693013 2.9378211 3.314274638 1.948591977 2.073847173 1 16.9628752 4.749019068 24.0828834 2.237442969 3.844241464 0.412081904 0.599200272 932.5021867 2147219.142 0.142519548 1.958717088 56107.26096 -4.749019068 1.606798495 S(ph)GDETPGSEVPGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.997)GDET(0.003)PGSEVPGDK;S(0.998)GDET(0.002)PGSEVPGDK;S(0.891)GDET(0.109)PGSEVPGDK;S(1)GDETPGSEVPGDK;S(1)GDETPGSEVPGDK;S(1)GDETPGSEVPGDK 305.48 2.53E-44 2391640000 4165560 2201230 3058770 2862300 3274180 4388770 4519610 3108540 3622710 1002043 TRUE FALSE 4330019.525 2579274.129 3138484.059 3428454.397 2717636.053 3369544.68 4165351.158 3066875.106 3492329.375 1198374.141 3.613245128 2.152311237 2.618951755 2.860921544 2.267769273 2.81176351 3.475835315 2.559196667 2.91422291 1 20.19264697 4.757313013 23.86956213 2.62217847 3.613246757 0.201600172 0.623601002 3601.010295 4583517.884 0.13598181 4.441251999 57189.06717 -4.757313013 0.991068288 S(ph)GDLGDMEPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGDLGDMEPLK 11 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK;S(1)GDLGDMEPLK 207.47 2.40E-08 293254000 920730 502787 650200 644470 819740 911560 1271660 721320 703980 314404 TRUE FALSE 957081.1314 589136.7561 667144.7461 771944.2424 680400.8876 699864.0048 1171983.966 711651.8852 678643.8973 376005.4442 2.545391686 1.566830388 1.774295443 2.053013472 1.809550628 1.861313488 3.116933503 1.89266378 1.804877849 1 18.52039403 S(ph)GDLGDMEPLKGTTPLMQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGDLGDMEPLKGTTPLMQK 19 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-27;O60716-29;O60716-32;O60716-31 O60716-13 CTNND1 Catenin delta-1 1 S(1)GDLGDMEPLKGTTPLMQK 87.659 0.0016237 45064000 113410 50359 76128 59314 104840 92175 102350 73797 85017 36380 TRUE FALSE 117887.5144 59007.76651 78111.95822 71046.13217 87019.33425 70768.75318 94327.53956 72807.87192 81957.25478 43507.96446 2.709561705 1.356252062 1.795348488 1.63294544 2.000078269 1.626570079 2.168052234 1.673437791 1.883729928 1 15.4089919 -2.120768025 0.586472917 1.15E-11 1.849981586 0.353974488 0.352039348 158.5470204 13.2899737 210.5811011 0.128855162 0.007572373 2.120768025 1.849981586 S(ph)GEGEVSGLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGEGEVSGLMR 11 0 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(1)GEGEVSGLMR;S(1)GEGEVSGLMR 165.35 2.28E-05 563600000 131227 106702 123030 97981 151077 155823 140560 108822 136294 101413 TRUE FALSE 136407.9433 125027.2385 126236.2629 117361.3494 125396.9855 119635.4698 129542.5399 107363.4191 131388.8056 121282.9357 1.124708456 1.030872462 1.040841089 0.967665803 1.033921094 0.986416342 1.068101948 0.885231038 1.083324747 1 16.88801705 7.999999859 0.745533307 0.995181595 23.08460457 0.29267642 0.05346897 415.4105884 1.812663192 0.01800307 15403.00625 99999967.51 -7.999999859 22.08942298 S(ph)GEQIFTQDVRPEQLLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGEQIFTQDVRPEQLLEGK 19 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.997)GEQIFT(0.003)QDVRPEQLLEGK 106.12 0.00019392 78551000 71969 40482 64066 45383 107320 89716 82385 60669 77436 47373 TRUE FALSE 74810.39169 47434.46859 65735.61259 54359.62195 89077.78473 68880.81866 75927.44843 59855.83129 74649.09349 56654.83234 1.320459149 0.837253711 1.160282537 0.959487827 1.572289266 1.215797767 1.340176033 1.056500016 1.317612115 1 15.78991139 5.053348393 22.24458732 1.169313389 3.643788447 0.05095283 0.202855304 2543.223161 1298532.301 0.045817121 67949.95799 113070.2605 -5.053348393 2.474475059 S(ph)GEQITSSPVSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGEQITSSPVSPK 13 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(1)GEQITSSPVSPK 239.19 8.82E-17 153910000 182470 112610 133760 84167 161070 164390 140260 95190 124300 71800 TRUE FALSE 189674.0565 131949.8915 137245.8955 100814.9814 133691.3789 126212.9139 129266.0547 93914.13375 119826.4673 85867.83531 2.20890693 1.536662605 1.598338831 1.174071537 1.556943627 1.469850887 1.505407167 1.093705616 1.39547558 1 16.3898302 7.999999995 0.73541166 1.316364225 140.4247622 0.676304438 0.182483874 201.2666304 0.915991232 0.062900439 46295.32427 99999998.81 -7.999999995 139.108398 S(ph)GGMSNELNNIISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGGMSNELNNIISR 14 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 S(1)GGMSNELNNIISR 98.572 0.002648 22784000 5048.5 7470.3 7836.7 8842.7 8071.7 8897.5 7327.5 7050.3 6402.9 7175.8 TRUE FALSE 5247.818678 8753.265914 8040.93084 10591.75967 6699.675317 6831.190468 6753.151403 6955.80226 6172.46088 8581.760621 0.611508397 1.019984861 0.936979158 1.234217562 0.780687741 0.796012703 0.786919107 0.810533242 0.719253444 1 13.06705794 S(ph)GHFDVTTVASIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGHFDVTTVASIK 13 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0A0MSL1;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 S(0.998)GHFDVT(0.002)TVASIK;S(0.988)GHFDVT(0.01)T(0.002)VASIK 112.43 0.00058061 420870000 333200 326730 380260 329690 466420 502350 476010 381750 433600 409440 TRUE FALSE 346354.9933 382843.3359 390169.888 394901.698 387138.095 385686.8257 438699.0924 376633.2657 417994.8207 489661.9288 0.707334945 0.781852363 0.796814833 0.806478255 0.790623228 0.787659409 0.895922404 0.76917 0.853639616 1 18.90142651 -4.999999999 0.141280587 1.701285396 0.72691345 0.7492306 0.038349359 68.06564253 0.587219177 13.40710903 0.224660492 1.00E-05 4.999999999 -0.974371946 S(ph)GKNSQEDSEDSEDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.5)GKNS(0.5)QEDSEDSEDKDVK 101.71 0.00032108 355310000 761450 176820 268600 152900 469180 605400 417870 272330 311770 113640 TRUE FALSE 791512.634 207187.4595 275599.9367 183143.1636 389428.9512 464805.0249 385116.2575 268679.8618 300549.4586 135905.5822 5.823989133 1.524495581 2.027877973 1.347576462 2.865437496 3.420058377 2.833704482 1.97695972 2.211457791 1 17.05224519 4.74538862 24.85670149 2.219900279 5.823990927 0.706514782 0.71151329 424.2237024 1544303.365 0.174173432 1.718040859 55640.19205 -4.74538862 3.604090648 S(ph)GLSRSSNLRVT(ph)RT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGLSRSSNLRVTRTR 15 3 Q9NSI6-3;Q9NSI6-2;Q9NSI6 Q9NSI6-3 BRWD1 Bromodomain and WD repeat-containing protein 1 3 S(0.25)GLS(0.25)RS(0.25)S(0.25)NLRVT(1)RT(1)R 40.715 0.080893 24636000 7237.1 8203.9 4737 6249 6782.5 10014 6447.7 6530.1 8196.3 6407.5 TRUE FALSE 7522.826296 9612.856008 4860.450111 7485.033549 5629.613073 7688.400264 5942.312426 6442.574691 7901.316764 7662.926946 0.981717084 1.254462698 0.634281149 0.976785189 0.734655715 1.003324228 0.775462492 0.840745936 1.031109499 1 12.90367984 4.252305981 24.9999651 0.86563052 1.11808984 0.327721181 0.139059384 231.8231489 421630.5373 0.030436561 0.08241212 17877.46681 -4.252305981 0.25245932 S(ph)GMSPEQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.504)GMS(0.496)PEQSR 135.16 0.00089364 1710800000 797960 954390 897640 834790 1045400 1099000 957800 949980 923000 852400 TRUE FALSE 829464.077 1118299.058 921033.2358 999908.9704 867703.2814 843773.9055 882725.1333 937247.072 889781.4103 1019411.46 0.813669563 1.097004598 0.903495077 0.980868874 0.851180623 0.827706906 0.865916431 0.919400172 0.872838344 1 19.95930505 3.242183025 24.94125899 0.883464063 0.95611529 0.112611004 0.079351215 159.901516 1100957.272 0.020788806 0.027090605 1746.558049 -3.242183025 0.072651226 S(ph)GNSDSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGNSDSIER 9 0 C9J8U3;A0A0A0MRW7;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-10;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3;A0A5F9ZI51;A0A5F9ZGW5;Q7Z2E3-13;Q7Z2E3-9;Q7Z2E3-11 C9J8U3 APTX Aprataxin 1 S(0.998)GNS(0.002)DSIER;S(0.681)GNS(0.319)DSIER 187.93 4.19E-05 354814000 373591 379550 398820 379810 481630 550930 481390 432150 408730 373141 TRUE FALSE 388340.6612 444734.76 409213.5768 454935.2844 399762.7046 422984.8569 443657.3939 426357.7361 394019.8871 446250.8347 0.870229546 0.99660264 0.917003499 1.019460915 0.895825113 0.947863453 0.994188379 0.955421711 0.882956079 1 18.76749534 4.757521545 24.04926573 0.955528093 0.870229417 0.25461656 0.044295529 3439.414524 4362293.319 0.009778213 0.333039686 57216.53391 -4.757521545 -0.085298675 S(ph)GREGGPGEGQVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGREGGPGEGQVRR 14 2 P35916-3 P35916-3 1 S(1)GREGGPGEGQVRR 58.98 0.082327 916760000 106470 998800 507210 1087200 269940 767500 306450 570600 330410 889240 TRUE FALSE 110673.5178 1170336.13 520428.3093 1302244.915 224055.6952 589259.7566 282429.6482 562952.0403 318518.6086 1063469.552 0.104068346 1.100488611 0.489368321 1.22452487 0.210683695 0.554091798 0.265573798 0.529354168 0.299508912 1 20.0203473 3.194537295 24.99988884 0.447885483 0.738949181 0.104936648 0.355826632 249.3967631 141626.1826 0.093505715 0.111761286 1565.082715 -3.194537295 0.291063698 S(ph)GS(ph)IKGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 133.32 0.000526 1425080000 3826900 1416480 2092910 1184520 3474700 3950000 2902180 2191540 2347500 1232280 TRUE FALSE 3977988.967 1659749.421 2147452.954 1418814.521 2884071.735 3032672.363 2674699.548 2162165.991 2263013.934 1473721.673 2.699281039 1.126229906 1.457163177 0.962742523 1.956998929 2.057832506 1.814928557 1.467146769 1.535577562 1 20.49103265 0.742523373 1.335874878 1.003831389 1.67100943 0.167061863 0.467491403 1.672228303 5.078645814 0.435609505 0.130181497 5.527431555 -0.742523373 0.667178041 S(ph)GSFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSFDSR 7 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.493)GS(0.493)FDS(0.013)R;S(0.5)GS(0.5)FDSR 64.42 0.077112 469860000 751160 611700 683570 588200 863720 967930 786610 704560 689590 597640 TRUE FALSE 780816.3768 716754.7166 701384.3958 704544.2044 716905.1829 743142.9266 724953.4528 695116.5256 664771.7906 714736.1155 1.092454068 1.002824261 0.981319372 0.985740316 1.003034781 1.039744474 1.014295258 0.972549883 0.930094025 1 19.44705116 1.662486611 4.189398934 0.961326775 1.014310582 0.308083776 0.033781245 0.207803845 8.490948846 0.01910641 0.008901753 45.97128154 -1.662486611 0.052983806 S(ph)GSLDDSFSDFQELPASSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.5)GS(0.5)LDDSFSDFQELPASSK 177.64 5.26E-15 0 21543 38129 32115 33886 35567 54667 31355 37731 34275 45950 TRUE FALSE 22393.53427 44677.35915 32951.94328 40588.54966 29521.33404 41971.41774 28897.31317 37225.27766 33041.44945 54953.02273 0.40750323 0.813010039 0.599638412 0.738604496 0.537210377 0.763769046 0.525854843 0.677401821 0.601267188 1 15.74591122 -1.346695247 2.859719767 1.004912253 0.636869372 0.47399094 0.116893374 6873530.901 8212603.662 283324.2153 0.025689877 0.045009559 1.346695247 -0.368042881 S(ph)GSNIEQYIHDLDSNSFELDLQFSEDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSNIEQYIHDLDSNSFELDLQFSEDEKR 29 1 E9PER6;O15530-5;O15530-2;O15530;O15530-3;O15530-4 E9PER6 PDPK1 3-phosphoinositide-dependent protein kinase 1 1 S(0.5)GS(0.5)NIEQYIHDLDSNSFELDLQFSEDEKR;S(0.5)GS(0.5)NIEQYIHDLDSNSFELDLQFSEDEKR 190.22 1.82E-18 42649000 31519 19928.7 33856 23511 43751 37765 39438 28290 29232 22005.9 TRUE FALSE 32763.39446 23351.2992 34738.31517 28161.40563 36314.22065 28994.65108 36346.74651 27910.81882 28179.94603 26317.53478 1.244926424 0.887290523 1.319968434 1.070062446 1.379848871 1.101723673 1.381084772 1.060540779 1.070766934 1 14.68373673 1.586895636 13.9096908 1.048026582 1.191237849 0.191700918 0.144583626 0.212055941 114.47048 0.072372328 0.033997441 38.62741412 -1.586895636 0.143211267 S(ph)GSPKLDPSEVYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.52)GS(0.48)PKLDPSEVYLK 83.758 0.0050889 255380000 961170 283840 502900 286110 857480 758270 614940 506710 526460 216570 TRUE FALSE 999117.7338 332587.312 516005.9871 342701.704 711725.8559 582173.2842 566739.396 499918.3813 507512.8074 259002.745 3.857556543 1.284107286 1.992279993 1.323158579 2.747947153 2.247749475 2.188159805 1.930166343 1.959488141 1 17.98260786 0.424717541 0.865213682 0.992334759 2.170208008 0.215651875 0.689189917 3.152271635 3.321573923 0.667810913 0.209782718 2.658995127 -0.424717541 1.177873249 S(ph)GSPRPTEPTDFLMLFEGSPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.498)GS(0.498)PRPT(0.002)EPT(0.002)DFLMLFEGSPSGK;S(0.552)GS(0.447)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.498)GS(0.498)PRPT(0.002)EPT(0.002)DFLMLFEGSPSGK;S(0.48)GS(0.48)PRPT(0.03)EPT(0.01)DFLMLFEGSPSGK 160.57 1.14E-11 430229000 166977 123891 145575 111783 190220 184896 179857 158957 163341 104381.2 TRUE FALSE 173569.3809 145168.3155 149368.8041 133893.3438 157886.4723 141956.7061 165759.3384 156826.4414 157462.3893 124832.6976 1.390416006 1.162902975 1.19655192 1.072582314 1.26478459 1.137175666 1.327851929 1.256292978 1.261387379 1 16.92963635 2.268201083 24.99735889 1.238661371 1.198639245 0 0.113068419 926.1733566 781087.4438 0.03701258 0.03096304 185.4390026 -2.268201083 -0.040022126 S(ph)GSSGPETFNVGSMPSPQQQVMVGQMHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSGPETFNVGSMPSPQQQVMVGQMHR 28 0 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 1 S(0.421)GS(0.421)S(0.158)GPETFNVGSMPSPQQQVMVGQMHR 152.01 2.94E-08 88901000 21439 17031 21149 12277 20341 24034 20071 19949 20650 11739 TRUE FALSE 22285.42827 19955.94177 21700.16031 14705.35396 16883.44409 18452.46774 18497.78257 19681.61628 19906.81053 14039.03229 1.587390627 1.421461348 1.545702001 1.047462079 1.202607397 1.314368922 1.317596697 1.401921149 1.417961731 1 13.77715587 3.776876439 24.99771165 1.273227942 1.50851241 0.448835419 0.136735053 590.1018141 384987.8115 0.035760665 0.064467187 5982.413655 -3.776876439 0.235284468 S(ph)GSSS(ph)PDSEITELKFPSINHD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.736)GS(0.25)S(0.113)S(0.9)PDSEITELKFPSINHD 101.86 0.00027284 53394000 48182 47789 58402 46455 72088 71058 65526 60159 62520 37364 TRUE FALSE 50084.26256 55996.389 59924.0041 55643.66035 59834.50751 54555.85639 60389.9009 59352.66701 60269.91741 44684.76042 1.120835428 1.253142872 1.341038948 1.245249159 1.339036104 1.220905201 1.35146525 1.328252998 1.34878014 1 15.44749527 4.698753643 3.452387958 1.289603038 1.106598273 0.143861369 0.102291092 0.388124796 7.985844201 0.02216791 0.174322347 49975.09673 -4.698753643 -0.183004765 S(ph)GSTESLNPRPQTTISPADLHGMWYPTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.518)GS(0.45)T(0.031)ES(0.001)LNPRPQTTISPADLHGMWYPTVR 103.17 0.00072602 265360000 44953 55193 68308 64984 75793 103880 64383 65141 64517 61994 TRUE FALSE 46727.77915 64671.96841 70088.1626 77837.64124 62909.73293 79755.44432 59336.49223 64267.89144 62195.04577 74140.53735 0.630259516 0.872288909 0.945341983 1.04986616 0.848520056 1.075733292 0.80032455 0.86683876 0.838880429 1 16.17797495 4.726996877 3.238302767 0.920319743 0.592938345 0.505510465 0.087781384 0.266977327 4.530985249 0.021350474 0.216626186 53333.10606 -4.726996877 -0.327381397 S(ph)GTPTQDEMMDKPTSSSVDTMSLLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGTPTQDEMMDKPTSSSVDTMSLLSK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2;Q5VT52-5 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 S(0.517)GT(0.443)PT(0.04)QDEMMDKPTSSSVDTMSLLSK;S(0.48)GT(0.48)PT(0.037)QDEMMDKPT(0.001)S(0.001)SSVDTMSLLSK;S(0.543)GT(0.456)PTQDEMMDKPTSSSVDTMSLLSK 114.14 0.00086234 428800000 917920 294501 482690 322828 746500 692670 658010 470990 580500 200409 TRUE FALSE 954160.1904 345079.2559 495269.2979 386682.4149 619610.1966 531807.89 606433.4568 464677.1494 559607.9184 239675.3065 3.981053386 1.439778094 2.06641771 1.613359426 2.585206652 2.218868092 2.530229191 1.938777742 2.334858466 1 17.87072175 -1.770678079 0.437090996 5.44E-13 2.2788667 0.257541083 0.661169438 58.41007393 4.607204221 61.96169857 0.343160993 0.016955942 1.770678079 2.2788667 S(ph)HESLLSPCSTVECLDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHESLLSPCSTVECLDLGR 19 0 Q9UJF2;Q9UJF2-2 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 S(0.938)HES(0.058)LLS(0.004)PCSTVECLDLGR;S(0.953)HES(0.047)LLSPCSTVECLDLGR 125.45 1.76E-05 267966000 31510 92001 89348 86538 101772 131484 86840 94734 87745 92614 TRUE FALSE 32754.03913 107801.4561 91676.48228 103654.9581 84472.83179 100948.8337 80033.25389 93464.24568 84587.07459 110759.9401 0.29572099 0.973289223 0.827704332 0.935852421 0.762665922 0.911420082 0.722583037 0.843845217 0.763697367 1 16.75707665 4.746530181 24.99561015 0.848655976 0.29572072 0.779101254 0.089972103 422.9369439 1326462.228 0.019727594 0.218643697 55786.63699 -4.746530181 -0.552935256 S(ph)HGLESVPVLPGSGEAGVSFDLPAQADTLHSANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHGLESVPVLPGSGEAGVSFDLPAQADTLHSANK 34 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 S(0.844)HGLES(0.156)VPVLPGSGEAGVSFDLPAQADTLHSANK 110.4 1.83E-05 37866000 25607 22503 30647 21459 44547 38719 35384 26865 33604 25459 TRUE FALSE 26617.98413 26367.7152 31445.686 25703.52615 36974.91685 29727.09904 32610.50962 26504.91862 32394.5986 30447.20361 0.874234116 0.866014349 1.032793895 0.844199897 1.214394508 0.976349074 1.071051057 0.870520622 1.063959732 1 14.89402211 4.282952087 1.533146823 1.005718859 0.848872596 0.213750775 0.100346524 0.845304245 3.258592097 0.027292338 0.156286301 19184.57077 -4.282952087 -0.156846263 S(ph)HNDFVAILDLPEGEHQYK ddPTM_MDA-MB-175_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 103.63 0.00061659 64041000 145497 108632 133854 127055 192205 180219 181304 139632 159880 91030 TRUE FALSE 151241.3339 127288.701 137342.3452 152186.0998 159534.0628 138365.8685 167092.9187 137760.4614 154125.95 108865.5856 1.389248338 1.169228092 1.261577241 1.397926617 1.465422354 1.270978957 1.534855278 1.265417906 1.415745381 1 16.73218844 -1.12558529 4.644607872 0.999969748 1.348393373 0.504316887 0.10470814 3.19E-05 6.00E-06 0.0985775 0.023232925 0.074888427 1.12558529 0.348423625 S(ph)HNNFVAILDLPEGEHQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHNNFVAILDLPEGEHQYK 19 0 Q9Y478 Q9Y478 PRKAB1 5-AMP-activated protein kinase subunit beta-1 1 S(1)HNNFVAILDLPEGEHQYK;S(1)HNNFVAILDLPEGEHQYK;S(1)HNNFVAILDLPEGEHQYK 145.25 2.13E-07 469180000 673180 560190 769380 630770 1077260 1015680 952290 757120 904050 614680 TRUE FALSE 699757.6662 656398.2748 789430.6749 755534.4233 894147.73 779803.7128 877647.0215 746972.0448 871513.4171 735114.7772 0.951902598 0.892919439 1.073887642 1.027777494 1.216337581 1.06079178 1.193891143 1.016129818 1.185547406 1 19.48761 4.158101901 4.553560482 1.100792336 0.922254519 0.467944204 0.074547796 0.15424002 5.785258045 0.017402135 0.040995489 14391.36212 -4.158101901 -0.178537817 S(ph)HS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_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(0.497)HS(0.523)GT(0.516)S(0.464)PDNTAPPPPPPRPQPSHSR 67.283 0.058086 130890000 10880 12200 12342 9836.8 12213 13811 9407.8 11325 10035 9896.8 TRUE FALSE 11309.5508 14295.2551 12663.64266 11782.48968 10137.03862 10603.60456 8670.392053 11173.2069 9673.84231 11835.88847 0.955530362 1.207788932 1.069935957 0.9954884 0.856466217 0.895885812 0.73255101 0.94401083 0.817331317 1 13.53088039 3.455849126 2.511312131 0.867053339 1.090693773 0.518715544 0.088292674 0.198467346 2.520539782 0.024165721 0.037347372 2856.597988 -3.455849126 0.223640435 S(ph)HSDNDRFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHSDNDRFK 9 1 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.742)HS(0.258)DNDRFK;S(0.954)HS(0.046)DNDRFK 101.35 0.0024485 286670000 489310 317360 379200 277460 499860 498360 415800 369120 428870 321290 TRUE FALSE 508628.3366 371864.1113 389082.2635 332340.7599 414893.9757 382623.4427 383208.5095 364172.5502 413435.0525 384240.624 1.323723482 0.967789682 1.01260054 0.864928743 1.079776447 0.995791228 0.997313885 0.947772118 1.075979547 1 18.55165053 4.740835935 24.88078332 0.989539838 1.323723606 0.741795888 0.058395836 88.77862286 970735.0847 0.013070714 0.086736578 55059.96555 -4.740835935 0.334183768 S(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.352)HS(0.352)DNDRPNCS(0.294)WNT(0.003)QYSSAYYTSR;S(0.435)HS(0.435)DNDRPNCS(0.131)WNTQYSSAYYTSR;S(0.484)HS(0.484)DNDRPNCS(0.032)WNTQYSSAYYTSR 250.13 1.21E-38 2422380000 426385 404438 443891 428789 494526 540675 461021 438053 438005 392830 TRUE FALSE 443219.009 473897.0804 455459.1641 513602.1844 410466.6472 415111.4253 424884.9694 432181.616 422241.2856 469797.5173 0.943425609 1.008726234 0.969479717 1.093241589 0.873709698 0.883596464 0.904400202 0.919931673 0.898772918 1 18.84167956 3.213863926 24.9997937 0.90823903 1.00163046 0.454059688 0.048296093 187.0296477 189324.5617 0.013207855 0.015792945 1636.303751 -3.213863926 0.09339143 S(ph)HSGTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_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(0.25)HS(0.25)GT(0.25)S(0.25)PDNT(0.002)APPPPPPRPQPSHSR 46.839 0.096617 9295600 3108.9 3332.4 5582.1 3768.6 3743.1 4103.3 3096 3116.1 2927 4304.8 TRUE FALSE 3231.641773 3904.713778 5727.574112 4514.017832 3106.849199 3150.370761 2853.32743 3074.333776 2821.657842 5148.24314 0.627717395 0.758455588 1.112529839 0.876807429 0.603477558 0.611931231 0.554233231 0.597161729 0.548081698 1 12.32986447 3.23834438 24.99583895 0.621856423 0.85696547 0.224423051 0.167934522 6.992821322 808375.5046 0.04667682 0.05924017 1731.188587 -3.23834438 0.235109047 S(ph)HSLPSSIIF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHSLPSSIIF 10 0 Q86Z20-2;Q86Z20 Q86Z20-2 CCDC125 Coiled-coil domain-containing protein 125 1 S(0.588)HS(0.412)LPSSIIF;S(0.56)HS(0.439)LPS(0.001)SIIF 80.688 0.024395 38985000 85667 108336 115756 103229 153179 158688 118114 113570 114491 143693 TRUE FALSE 89049.19931 126941.8653 118772.6965 123647.3881 127141.6883 121835.1169 108855.916 112047.7799 110370.4913 171846.8922 0.518189175 0.738691655 0.691154172 0.719520653 0.739854452 0.708974805 0.633447103 0.652020985 0.642260619 1 17.39076424 -1.627009155 3.030003633 1.024039095 0.675298881 0.710031271 0.062924961 95897261.73 101456991.1 18193399.95 0.014759702 0.023604285 1.627009155 -0.348740215 S(ph)HSQASLAGPGPVDPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 S(0.563)HS(0.434)QAS(0.003)LAGPGPVDPSNR;S(0.559)HS(0.439)QAS(0.002)LAGPGPVDPSNR;S(0.561)HS(0.437)QAS(0.002)LAGPGPVDPSNR;S(0.442)HS(0.442)QAS(0.116)LAGPGPVDPSNR 145.61 5.78E-08 6080440000 868054 1096558 1079353 1058424 1467513 1527913 1022649 1100724 1193473 1161822 TRUE FALSE 902325.4422 1284883.306 1107481.826 1267777.108 1218065.664 1173078.361 942491.0992 1085970.595 1150520.14 1389458.776 0.649407854 0.924736544 0.797059866 0.912425132 0.876647573 0.84427 0.678315266 0.781578132 0.828034742 1 20.4060916 S(ph)HSWVNSAYAPGGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SHSWVNSAYAPGGSK 15 0 K7ESB7;K7EKT0 K7ESB7 DOCK6 1 S(0.533)HS(0.43)WVNS(0.037)AYAPGGSK;S(0.543)HS(0.443)WVNS(0.014)AYAPGGSK;S(0.554)HS(0.426)WVNS(0.02)AYAPGGSK;S(0.556)HS(0.431)WVNS(0.013)AYAPGGSK 93.5 0.003113 1223660000 1223240 1040760 1202620 1181080 1510310 1600600 1221710 1256610 1276430 1084530 TRUE FALSE 1271534.46 1219502.434 1233961.265 1414694.099 1253588.046 1228884.907 1125949.178 1239767.198 1230491.534 1297022.889 0.980348512 0.940232007 0.951379714 1.090724081 0.966511891 0.94746586 0.868102782 0.955856068 0.948704563 1 20.30677251 2.807888383 4.12645732 0.936033959 0.988404823 0.153202613 0.048792273 0.383723869 12.81682153 0.015697853 0.01649861 642.5225626 -2.807888383 0.052370864 S(ph)HWIFEARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHWIFEARK 9 1 I3L3Y3;A0A087WYU4;A6NH52-2;A6NH52 I3L3Y3 TVP23A Golgi apparatus membrane protein TVP23 homolog;Golgi apparatus membrane protein TVP23 homolog A 1 S(1)HWIFEARK 63.397 0.080857 321140000 35757 737940 580250 718290 370740 713310 450400 538590 431880 748110 TRUE FALSE 37168.71397 864675.4546 595371.7917 860365.6181 307721.7472 547654.5628 415096.4711 531371.082 416336.7232 894687.8311 0.041543779 0.966454918 0.665451983 0.961637778 0.343943146 0.612118041 0.463956764 0.59391786 0.465343004 1 19.77102487 -1.419889585 3.353237888 1.004665777 0.585373264 0.196035139 0.260228236 87256918.47 128992234.2 3975279.814 0.060155811 0.038028607 1.419889585 -0.419292513 S(ph)IAEELELSILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIAEELELSILK 12 0 Q9UBT7-3;Q9UBT7-2;Q9UBT7 Q9UBT7-3 CTNNAL1 Alpha-catulin 1 S(1)IAEELELSILK;S(1)IAEELELSILK 157.52 7.77E-05 19301800 31402 25255 28871 26010 34047 39329 38419 30488 32234 22588.7 TRUE FALSE 32641.77521 29592.34979 29623.40198 31154.70037 28259.7031 30195.43579 35407.61839 30079.35823 31073.90464 27014.52328 1.208304691 1.095423728 1.09657319 1.153257455 1.046092978 1.117748238 1.310688256 1.11345138 1.150266629 1 14.7214476 2.426312772 24.99999545 1.161914087 1.115400614 0 0.081520321 298.56273 146904.1559 0.026864001 0.02247604 266.8779983 -2.426312772 -0.046513473 S(ph)IAIGS(ph)QPVLTVGT(ph)T(ph)HIS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SIAIGSQPVLTVGTTHISK 19 0 Q96DZ1;Q96DZ1-3 Q96DZ1 ERLEC1 Endoplasmic reticulum lectin 1 5 S(0.996)IAIGS(0.999)QPVLT(0.031)VGT(0.992)T(0.992)HIS(0.99)K;S(0.999)IAIGS(0.999)QPVLT(0.025)VGT(0.993)T(0.993)HIS(0.991)K;S(0.995)IAIGS(0.998)QPVLT(0.043)VGT(0.989)T(0.989)HIS(0.986)K;S(1)IAIGS(1)QPVLT(0.035)VGT(0.99)T(0.99)HIS(0.987)K 45.639 0.056892 1168520000 7478.9 137750 81913 97190 59569.3 107998 48398 101393 62079.6 136454 TRUE FALSE 7774.172747 161407.491 84047.72007 116413.8919 49443.73166 82917.10123 44604.4383 100033.9927 59845.36732 163189.5487 0.047638913 0.989079829 0.515031267 0.7133661 0.302983445 0.508103012 0.273329013 0.612992642 0.366723039 1 17.31618914 -1.175423494 5.314278457 1.000020794 0.498855016 0.281965886 0.246980252 5.54E-05 8.60E-06 0.217925256 0.051363347 0.066769251 1.175423494 -0.501165778 S(ph)IDAALFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIDAALFR 8 0 Q5FWE3-2;Q5FWE3 Q5FWE3-2 PRRT3 Proline-rich transmembrane protein 3 1 S(1)IDAALFR;S(1)IDAALFR;S(1)IDAALFR 132.01 0.0010286 122946000 140478 216113 182582 235709 267509 357190 211972 210396 197264 330654 TRUE FALSE 146024.1799 253228.7266 187340.2369 282331.5367 222037.9157 274238.0358 195357.0808 207575.9858 190164.5072 395439.3205 0.369270764 0.640373158 0.473752172 0.713969305 0.561496807 0.693502192 0.494025431 0.524925001 0.48089428 1 18.59309681 -1.981540286 2.803898451 1.394622859 0.5553631 0.63830018 0.101502593 32180945.56 31737364.34 82525144.52 0.023695596 0.010434213 1.981540286 -0.839259758 S(ph)IDQDYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;S(1)IDQDYER;S(1)IDQDYER 174.87 0.00028261 5689880000 2616772 2946568 3138136 2820262 3676619 4044580 3545618 3278537 3235907 2903643 TRUE FALSE 2720084.179 3452618.133 3219918.402 3378101.406 3051668.616 3105287.591 3267703.196 3234593.574 3119447.339 3472556.252 0.783308889 0.994258374 0.927247298 0.972799621 0.878796021 0.8942368 0.941007995 0.931473341 0.898314415 1 21.72756663 -2.57291784 2.135508391 2.360808061 0.918662824 0.176492058 0.055048459 3045930.355 212917.0223 20425975.3 0.012701154 0.002673512 2.57291784 -1.442145237 S(ph)IEALLEAGQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIEALLEAGQAR 12 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 S(1)IEALLEAGQAR 117.7 0.0007394 8220900 8145 8407.3 7937.4 9515.6 9823.9 12032 9854.5 9178.7 8922.2 6432.8 TRUE FALSE 8466.570889 9851.188375 8144.255165 11397.75728 8154.036987 9237.750347 9082.07854 9055.67454 8601.091765 7693.183997 1.100528844 1.280508614 1.058632572 1.48153967 1.059904065 1.200770754 1.180535724 1.177103595 1.118014566 1 12.9093651 0.730606174 0.811013164 0.998337725 1.203880143 0.208189803 0.116412221 1.485895991 1.865096109 0.104388413 0.036381609 5.377818905 -0.730606174 0.205542418 S(ph)IEDLQPPSALSAPFTNSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIEDLQPPSALSAPFTNSLAR 21 0 F8W1F5;Q8IVF7-3;Q8IVF7 F8W1F5 FMNL3 Formin-like protein 3 1 S(1)IEDLQPPSALSAPFTNSLAR 172.5 5.80E-12 28444000 86949 80397 88278 81021 101690 130360 97558 81548 87886 86475 TRUE FALSE 90381.81366 94204.55935 90578.5972 97046.71198 84404.77012 100085.8656 89911.14904 80454.98245 84723.00003 103418.1206 0.873945621 0.910909605 0.875848417 0.938391758 0.816150687 0.96777881 0.869394537 0.777958273 0.819227806 1 16.65812947 1.99705512 24.99809192 0.836712139 0.896981187 0 0.066972072 215.6782252 1830823.523 0.023584686 0.017099971 99.32421004 -1.99705512 0.060269048 S(ph)IEVENDFLPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK 330.99 2.08E-62 1019339000 1364081 979401 1351386 1017973 1810360 1790790 1758599 1434296 1586848 1087473 TRUE FALSE 1417935.971 1147605.503 1386604.229 1219325.021 1502635.654 1374906.162 1620755.415 1415071.608 1529737.65 1300542.513 1.090264991 0.88240522 1.066173704 0.937551067 1.155391414 1.057178945 1.246214867 1.088062554 1.176230407 1 20.31068213 3.231785709 24.99312501 1.127995111 0.991268844 0.351135874 0.083781433 150.11527 553785.6302 0.021924441 0.02676444 1705.240775 -3.231785709 -0.136726267 S(ph)IGSAVDQGNESIVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SIGSAVDQGNESIVAK 16 0 Q9H0H5;F8VRD2;F8W1E5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 S(0.859)IGS(0.141)AVDQGNESIVAK;S(0.962)IGS(0.038)AVDQGNESIVAK;S(0.999)IGS(0.001)AVDQGNESIVAK;S(1)IGSAVDQGNESIVAK 240.66 7.51E-20 168397000 484132 362159 385704 332703 476365 557404 477269 391992 431537 292440 TRUE FALSE 503245.9052 424356.991 395755.7631 398510.6604 395392.6475 427955.3685 439859.4087 386737.9884 416006.0677 349738.0189 1.438922502 1.213356765 1.131577757 1.139454789 1.130539507 1.223645544 1.257682565 1.105793387 1.189479111 1 18.41591511 8 0.021815743 1.98E-06 2.731325282 0.433062482 0.082630069 2840.100046 4.770279809 215.3568511 410.9627775 100000000 -8 2.731323305 S(ph)IHEVDISNLEAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SIHEVDISNLEAALR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(0.966)IHEVDIS(0.034)NLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(0.996)IHEVDIS(0.004)NLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR 358.89 5.76E-83 2269677000 770418.4 860550.8 930785 937227 1083083 1148745 1108813.4 1002560 1040146 943603.2 TRUE FALSE 800835.1133 1008343.706 955042.0217 1122607.703 898980.9385 881966.3831 1021901.708 989122.3231 1002711.349 1128484.181 0.709655596 0.893538184 0.846305192 0.994792592 0.796626974 0.781549621 0.905552533 0.876505263 0.888547102 1 20.10595476 -4.999999995 0.141400967 1.493120711 0.808236119 0.311181377 0.071468166 182.5430373 1.575607308 25.29993348 0.422545062 1.00E-05 4.999999995 -0.684884592 S(ph)IPLSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIPLSIK 7 0 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 S(1)IPLSIK;S(1)IPLSIK 143.7 0.0025214 130435000 504920 438230 558500 449800 699120 640800 651270 550810 671110 443500 TRUE FALSE 524854.6315 513492.5935 573054.9688 538769.0975 580283.8321 491983.9114 600221.7556 543427.2929 646956.8822 530395.3337 0.989553637 0.968131808 1.080429884 1.015787778 1.094059082 0.927579638 1.131649767 1.024570275 1.219763526 1 19.01670856 2.210753999 24.9988259 1.089657218 1.017501455 0.231406958 0.072176283 351.0455512 315596.2545 0.025529668 0.018859324 162.4628243 -2.210753999 -0.072155763 S(ph)IPQLDLGWPDTIAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIPQLDLGWPDTIAYR 16 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR;S(1)IPQLDLGWPDTIAYR 247.61 2.74E-20 269114000 151110 155907 148737 153271 153907 185203 187480 160374 142748 147848 TRUE FALSE 157075.9395 182682.8145 152613.2084 183587.5463 127745.9431 142192.41 172784.8277 158224.4488 137610.5274 176815.9849 0.888358253 1.033180425 0.863118844 1.038297224 0.722479606 0.804183005 0.977201399 0.89485376 0.778269722 1 17.43188918 3.266320064 24.99978516 0.865367178 0.954654463 0.188178479 0.094437894 387.2039583 348708.0102 0.025664742 0.03474289 1846.37565 -3.266320064 0.089287286 S(ph)IQDLTVTGTEPGQVS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 2 S(1)IQDLTVTGTEPGQVS(0.585)S(0.415)R 172.3 1.63E-11 102630000 114380 173310 177470 178640 189520 234710 161410 167490 161310 181180 TRUE FALSE 118895.8107 203074.6443 182095.014 213974.4588 157305.4581 180202.1596 148758.2624 165245.0705 155504.4846 216678.7521 0.548719289 0.937215312 0.84039165 0.987519343 0.725984697 0.831655886 0.686538301 0.762627018 0.717672975 1 17.72519816 S(ph)IQDLTVTGTEPGQVSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SIQDLTVTGTEPGQVSSR 18 0 O43318;O43318-3;Q9UG54;O43318-2;O43318-4 O43318 MAP3K7;DKFZp586F0420 Mitogen-activated protein kinase kinase kinase 7 1 S(0.994)IQDLT(0.006)VTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(0.929)IQDLT(0.07)VT(0.001)GTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR 370.33 1.38E-107 6477680000 1201801 1175403 1228931 1213252 1337835 1538354 1275517 1251920 1217104 1066528 TRUE FALSE 1249249.031 1377269.322 1260957.951 1453229.624 1110430.285 1181094.597 1175538.645 1235140.06 1173300.665 1275493.742 0.979423882 1.079793085 0.988603793 1.139346731 0.870588579 0.925990116 0.921634192 0.968362305 0.919879594 1 20.28262439 3.228619643 24.99999616 0.934032348 1.04499282 0.523598379 0.052504141 152.6788771 383962.9241 0.014179583 0.017136483 1692.854541 -3.228619643 0.110960472 S(ph)IQEIQELDKDDESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 1 S(1)IQEIQELDKDDESLR 131.56 2.66E-05 44961000 49672 38018 52567 36174 53217 64094 51891 39897 48406 29906 TRUE FALSE 51633.08892 44547.29576 53936.9392 43329.10923 44171.19335 49209.13985 47823.64783 39362.24597 46663.87752 35765.50812 1.443655959 1.245537897 1.508071381 1.211477524 1.235022111 1.375882588 1.33714437 1.100564428 1.304717309 1 15.12628132 -4.854247446 0.088061639 4.01E-13 1.568232182 0.502739906 0.102244063 169.8874042 1.074558629 32.02923592 2.5230504 1.40E-05 4.854247446 1.568232182 S(ph)IQFVDWCPTGFK ddPTM_MDA-MB-175_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 1 S(1)IQFVDWCPTGFK;S(1)IQFVDWCPTGFK 211.57 2.19E-08 709290000 1063550 850530 1076300 823070 1331680 1217480 1120880 970840 1036940 887440 TRUE FALSE 1105539.775 996601.9113 1104349.262 985870.7894 1105321.509 934738.7211 1033022.497 957827.4778 999620.732 1061316.877 1.04166795 0.939023898 1.040546218 0.92891276 1.041462294 0.880734813 0.973340309 0.902489632 0.941868309 1 20.01742403 2.741658372 24.99941131 0.933974097 0.9935179 0.259203898 0.048753778 346.5416042 2796659.532 0.013685072 0.013990295 551.643331 -2.741658372 0.059543803 S(ph)IRDTPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 S(0.91)IRDT(0.09)PAK 105.2 0.011662 615410000 1132500 699190 834650 637740 972760 983360 920090 828510 798800 549710 TRUE FALSE 1177211.974 819270.4436 856401.6647 763883.0685 807410.6027 754989.543 847970.9416 817405.1786 770051.344 657415.1497 1.790667549 1.246199519 1.302680148 1.161949293 1.22815941 1.148421273 1.289856101 1.243362248 1.171331912 1 19.32644518 S(ph)ISCGPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISCGPSSR 9 0 Q5VU43-13;Q5VU43-2 Q5VU43-13 PDE4DIP Myomegalin 1 S(0.616)IS(0.384)CGPSSR 114.89 0.0016408 160020000 57288 73680 65918 68477 102020 88142 64668 69936 73759 77774 TRUE FALSE 59549.77448 86333.96685 67635.87723 82021.54622 84678.67684 67672.3563 59599.15318 68998.62231 71104.428 93012.32623 0.640235299 0.928199201 0.727171118 0.881835231 0.910402742 0.727563314 0.640766182 0.741822349 0.76446242 1 16.5051343 2.684825493 24.99344267 0.746641527 0.822263439 0.003095645 0.118668203 793.5132649 369080.3209 0.036053465 0.033991546 483.9778578 -2.684825493 0.075621912 S(ph)ISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE;S(0.5)IS(0.5)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 140.73 8.66E-11 115705000 31984.3 33626.1 45127 30621.5 76091 58410 47872 41277 53096 42628 TRUE FALSE 33247.06486 39401.1211 46303.04669 36678.3413 63157.079 44845.16271 44119.66755 40723.74933 51185.08533 50980.14044 0.652157185 0.772871961 0.908256554 0.719463324 1.238856513 0.879659458 0.865428521 0.79881595 1.004020093 1 15.63764773 4.639921113 1.153976432 0.921391627 0.551060335 0.321970485 0.131533099 1.759900209 2.226874412 0.038794066 0.756060963 43643.65492 -4.639921113 -0.370331291 S(ph)ISESSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.859)IS(0.141)ESSR;S(0.998)IS(0.002)ESSR 168.54 0.0010966 2270430000 1157050 1345110 1283020 1320160 1426660 1698160 1421840 1398480 1476430 1488900 TRUE FALSE 1202731.227 1576122.179 1316456.555 1581283.708 1184156.843 1303788.076 1310392.466 1379735.663 1423293.573 1780621.448 0.67545588 0.885152866 0.739324215 0.88805159 0.665024474 0.732209576 0.735918612 0.774861869 0.799324064 1 20.76394941 0.638518796 1.973945702 0.999954029 0.764194635 0.501318102 0.07084792 1.501162042 7.18530729 0.063649668 0.017583642 4.350295885 -0.638518796 -0.235759393 S(ph)ISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.5)IS(0.5)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.494)IS(0.494)LLEPS(0.012)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.497)IS(0.497)LLEPS(0.007)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.514)IS(0.456)LLEPS(0.03)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.522)IS(0.466)LLEPS(0.012)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 165.71 6.93E-20 869766000 27114.1 96274 89224.4 82728 100639 125478 75007.2 117203 87094 125148 TRUE FALSE 28184.5856 112808.3106 91549.66116 99091.35148 83532.41873 96337.63614 69127.93967 115632.0855 83959.50395 149668.3545 0.188313593 0.75372186 0.611683488 0.662072833 0.558116771 0.643674052 0.461874121 0.77258874 0.560970315 1 17.19140969 -5 0.173348024 2.594574041 0.503307918 0.423362208 0.153124682 127.3497842 1.210727647 69.8846043 0.488489191 1.00E-05 5 -2.091266123 S(ph)ISQDSLDELSMEDYWIELENIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.499)IS(0.499)QDS(0.001)LDELSMEDYWIELENIKK 82.65 0.0087712 33244000 19511 15845 26484 13772 32429 21549 21286 19806 27014 13150 TRUE FALSE 20281.30935 18566.25549 27174.1948 16496.06049 26916.73016 16544.57133 19617.5477 19540.53297 26041.77142 15726.49073 1.289627145 1.180572056 1.727924892 1.048934615 1.711553495 1.052019272 1.247420549 1.242523415 1.655917513 1 13.94090916 S(ph)ISTVNLSENSSVVIPPPDYLECLSMGAAADR ddPTM_MDA-MB-175_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(0.004)ENS(0.004)S(0.001)VVIPPPDYLECLSMGAAADR 54.324 0.035886 28594000 15180 14755 19263 15022 26997 22717 18114 14777 21559 20663 TRUE FALSE 15779.31812 17289.05647 19765.0096 17993.30676 22408.05958 17441.32103 16694.17735 14578.93849 20783.0958 24711.51923 0.638540997 0.699635514 0.799829805 0.728134381 0.906785996 0.705797198 0.675562566 0.589965285 0.841028656 1 14.59289609 0.994904754 21.64485105 1.00000001 0.717712381 0.537072511 0.082117904 25.17715154 106957.2712 0.085643312 0.021410828 9.883363163 -0.994904754 -0.28228763 S(ph)ISVSEHVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISVSEHVVR 10 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9 P49815 TSC2 Tuberin 1 S(0.7)IS(0.298)VS(0.002)EHVVR 133.05 0.00013361 105930000 40285 109960 117370 129360 143930 155370 101000 115910 102230 142460 TRUE FALSE 41875.48291 128844.7746 120428.7586 154947.0219 119464.83 119287.6722 93083.35609 114356.416 98550.76227 170372.3094 0.24578808 0.7562542 0.706856408 0.909461299 0.70119863 0.700158802 0.546352611 0.671214803 0.578443543 1 17.37833135 -2.4612084 2.089205623 4.136986565 0.658852227 0.29329112 0.163704758 8642410.318 534697.8356 128674828.8 0.039019481 0.003457734 2.4612084 -3.478134338 S(ph)ITS(ph)TPLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(0.995)IT(0.005)S(0.499)T(0.431)PLS(0.07)GK;S(0.994)IT(0.027)S(0.691)T(0.287)PLSGK 196.67 4.81E-07 482000000 1328240 887560 1013120 897150 1467790 1509190 1350160 1100460 1179670 794710 TRUE FALSE 1380679.941 1039991.526 1039522.739 1074603.592 1218295.58 1158703.494 1244330.931 1085710.134 1137213.907 950418.2089 1.452707795 1.094246213 1.093752971 1.130663935 1.281852103 1.219151194 1.309245677 1.142349887 1.19654053 1 19.85820295 0.436439077 1.233979516 1.000085966 1.210142676 0.270784205 0.105573471 3.52514807 6.358639759 0.098895516 0.02967273 2.731738208 -0.436439077 0.21005671 S(ph)ITST(ph)PLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 2 S(1)ITS(0.086)T(0.716)PLS(0.198)GK 194.06 2.68E-06 217240000 782460 534500 638590 569710 940880 951430 801170 729890 694920 462230 TRUE FALSE 813352.125 626296.2172 655232.18 682396.9376 780949.5537 730474.8016 738372.2019 720107.0184 669909.9649 552795.1186 1.471344622 1.13296264 1.185307464 1.234448197 1.412728744 1.321420499 1.335706806 1.302665299 1.211859408 1 19.07638535 -0.127214841 9.001353141 1.000000005 1.288122834 0.440411637 0.097991873 0 0 0.093289864 0.021988632 0.746079589 0.127214841 0.288122829 S(ph)ITSTPLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(0.986)IT(0.012)S(0.002)TPLSGK;S(0.952)IT(0.021)S(0.021)T(0.006)PLSGK 161.99 7.24E-06 309000000 446560 334140 361690 338490 498500 465830 466400 392710 443650 273030 TRUE FALSE 464190.5336 391525.9458 371115.9385 405442.3117 413765.1481 357648.0422 429842.3493 387446.3648 427683.1232 326525.001 1.421607939 1.199068814 1.136562093 1.241688417 1.267177542 1.095315952 1.316414816 1.186574883 1.309802073 1 18.31683393 -1.464353864 3.004409992 0.994264962 1.233430829 0.390137458 0.09009554 9067738.536 11257183.97 439131.7344 0.02021042 0.034327813 1.464353864 0.239165867 S(ph)IVVIHPDTGR ddPTM_MDA-MB-175_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 112.15 0.0010074 1299120000 339837 639281 500946 635521 591570 759032 531948 587235 556549 772260 TRUE FALSE 353254.0272 749072.5388 514001.0643 761225.157 491015.1427 582758.3212 490252.5258 579364.0753 536518.9102 923569.5612 0.382487732 0.811062393 0.556537467 0.824220707 0.531649335 0.630984764 0.530823607 0.627309625 0.580918788 1 19.8168611 -1.678931684 2.794876627 1.048699575 0.615192982 0.469709723 0.12462675 20798881.23 19563672.8 7227011.525 0.027866018 0.020944419 1.678931684 -0.433506592 S(ph)IWDEFISDEADEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIWDEFISDEADEK 14 0 D6RD48;D6RAZ7;D6RCR8;D6RDI6;D6RFX6;D6RCE6;D6R9S8;D6RC11;A0A0R4J2F2;D6RA76;D6RDY1;D6RHU6;H0Y8T9;D6RDP6;D6RIU2;Q9NY35;Q9NY35-2 D6RD48 CLDND1 Claudin domain-containing protein 1 1 S(0.5)IWDEFIS(0.5)DEADEK 72.607 0.040023 2314800000 286190 102930 159380 126210 213930 190370 210970 183690 200670 81906 TRUE FALSE 297489.0022 120607.4268 163533.5737 151173.9613 177566.255 146159.4526 194433.6201 181227.936 193447.9259 97953.91251 3.037030319 1.23126707 1.669495067 1.543317234 1.812753064 1.492124703 1.984950015 1.850134735 1.974887178 1 16.5798155 4.750174247 24.92325062 1.670507036 3.037031166 0.656743818 0.305701137 1031.009239 2212538.024 0.069438527 1.117522469 56256.69928 -4.750174247 1.36652413 S(ph)KDAS(ph)PINRWS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 3 S(1)KDAS(0.998)PINRWS(0.888)PT(0.113)R;S(1)KDAS(0.999)PINRWS(0.966)PT(0.035)R 75.533 0.019803 489450000 957440 464530 612150 395070 855940 1081130 734350 584370 664000 366560 TRUE FALSE 995240.4705 544309.414 628103.1319 473213.6668 710447.6245 830053.9422 676789.7281 576537.476 640102.7697 438380.4138 2.270266735 1.241637165 1.43278101 1.079458963 1.620618993 1.893455812 1.543841164 1.315153364 1.460153669 1 18.74182382 -3.097435646 0.203544543 1.05E-12 1.615649408 0.228407414 0.31627835 98.28735407 1.955699644 42.91213521 0.774550264 0.000799032 3.097435646 1.615649408 S(ph)KDEYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDEYEK 7 1 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(1)KDEYEK;S(1)KDEYEK 106.49 0.0046571 312210000 1196020 319690 427890 411090 752090 919770 1101950 531320 565160 220517 TRUE FALSE 1243239.793 374594.2707 439041.1649 492402.375 624250.0104 706167.3567 1015576.28 524198.5245 544820.002 263723.0841 4.714186463 1.420407591 1.664780944 1.867118977 2.367066245 2.677685039 3.850919168 1.987685402 2.065879079 1 18.00866433 2.99784424 24.59847561 2.476842505 2.269928583 0 1.083614117 627.4129747 7159317.873 0.309923114 0.364856687 995.0484778 -2.99784424 -0.206913922 S(ph)KDRDPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDRDPNR 8 2 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 S(1)KDRDPNR;S(1)KDRDPNR 82.379 0.016085 987400000 1981530 1247190 1569780 1154590 2053860 2165660 2191820 1641960 1674090 1058230 TRUE FALSE 2059762.334 1461385.181 1610689.756 1382964.456 1704745.611 1662718.286 2020019.421 1619952.212 1613839.828 1265569.907 1.627537382 1.154724976 1.272699159 1.092760224 1.347018131 1.31380991 1.596134207 1.280017961 1.275188212 1 20.27135577 0.742575467 2.413568055 1.000241514 1.328894324 0.28460876 0.158919688 1.662224075 13.57171392 0.149028364 0.040036687 5.528094611 -0.742575467 0.32865281 S(ph)KDVEFQDGWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDVEFQDGWPR 12 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 S(1)KDVEFQDGWPR;S(1)KDVEFQDGWPR 94.01 0.0041486 1015010000 925580 506770 667240 534840 1007130 1035810 930800 748690 820540 463290 TRUE FALSE 962122.6131 593803.8054 684628.8225 640629.7557 835938.4023 795258.8254 857841.4638 738655.0352 791008.9257 554062.8053 1.736486557 1.071726526 1.235652016 1.156240321 1.508743042 1.435322526 1.548274773 1.333161201 1.427652097 1 19.07969 3.233900795 24.99223798 1.402277193 1.279121063 0.015985859 0.216835213 329.1468023 1765327.128 0.058426068 0.07201604 1713.565835 -3.233900795 -0.12315613 S(ph)KEDSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKEDSRR 7 2 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 S(0.626)KEDS(0.374)RR;S(0.999)KEDS(0.001)RR 75.652 0.033777 4223400000 4366500 1874400 2936610 1900240 4289500 4255500 3904300 2859280 3530800 1742570 TRUE FALSE 4538892.792 2196313.619 3013140.469 2276101.8 3560372.322 3267224.618 3598270.764 2820956.028 3403727.198 2083993.228 2.177978666 1.053896716 1.445849453 1.092182916 1.708437568 1.567771226 1.72662306 1.353630132 1.633271717 1 20.99091916 -1.161376559 4.06514144 0.999804738 1.503363116 0.203076073 0.310620076 16758047.39 9603163.522 27141.56279 0.067178448 0.068964158 1.161376559 0.503558377 S(ph)KEKTDGGESSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKEKTDGGESSK 12 2 A0A0C4DG89;Q7L014;D6RJA6 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 1 S(0.987)KEKT(0.013)DGGESSK 93.153 0.0057747 34647000 181760 36273 75728 26411 139140 128690 104650 69026 96190 25007 TRUE FALSE 188936.0251 42502.60559 77701.53389 31635.01697 115489.0325 98803.69782 96447.25955 68100.81937 92728.14069 29906.64286 6.317527046 1.421176084 2.598136282 1.057792314 3.861651508 3.30373751 3.224944371 2.277113472 3.100586753 1 14.86817835 -1.337899504 0.421520682 2.50E-12 2.978733181 0.161526909 1.373911398 46.2019047 4.558343471 53.51827264 0.772835432 0.045930428 1.337899504 2.978733181 S(ph)KGRDHENVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKGRDHENVK 10 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)KGRDHENVK 108.59 0.0011116 34334000 44696 29929 37078 15645 62404 47249 23389 29491 40779 37194 TRUE FALSE 46460.63259 35069.07293 38044.28314 18739.5343 51796.59037 36276.13582 21555.70906 29095.72138 39311.37176 44481.45218 1.04449451 0.788397663 0.855284198 0.421288726 1.164453673 0.815533982 0.48459994 0.654109071 0.883769972 1 15.44091627 2.452805831 24.99941982 0.702821458 0.843335816 0.019896355 0.222691982 611.8382791 629045.6969 0.075659881 0.063304231 283.6650507 -2.452805831 0.140514359 S(ph)KPAGSDGERR ddPTM_MDA-MB-175_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 74.46 0.032102 67729000 66632 56211 69211 53758 75567 80347 68943 62586 67566 43643 TRUE FALSE 69262.68281 65864.80199 71014.69552 64391.17195 62722.14833 61687.62692 63539.06751 61747.13704 65134.31286 52194.01025 1.327023589 1.261922617 1.360590903 1.233688916 1.201711615 1.181890922 1.217363203 1.183031094 1.247926966 1 15.67159663 -5 0.082391346 0.219032461 1.47120198 0.768724451 0.044463384 113.0580697 0.657091467 15.99181691 1.397467227 1.00E-05 5 1.25216952 S(ph)KPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 S(0.999)KPLT(0.001)R;S(0.998)KPLT(0.002)R;S(0.999)KPLT(0.001)R;S(1)KPLTR;S(0.991)KPLT(0.009)R;S(0.999)KPLT(0.001)R;S(1)KPLTR;S(0.983)KPLT(0.017)R 104.2 0.020611 12867420000 9157670 6068090 7992170 5904510 10241660 9985870 9820360 8104580 8604500 5594640 TRUE FALSE 9519221.883 7110237.254 8200452.516 7072404.455 8500786.291 7666803.03 9050614.522 7995951.362 8294825.726 6690802.592 1.422732438 1.062688244 1.225630618 1.057033795 1.270518174 1.145871952 1.352694897 1.1950661 1.239735534 1 22.67374785 -1.142059998 3.987221497 0.999922238 1.213732379 0.264611491 0.109250267 10401159.56 26467484.9 11092.29593 0.023990426 0.072100786 1.142059998 0.213810141 S(ph)KS(ph)EMLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSEMLSR 8 1 E9PR23;E9PRA4;E9PNU3;E9PQC8;Q71H61 E9PR23 ILDR2 Immunoglobulin-like domain-containing receptor 2 2 S(1)KS(1)EMLSR 110.31 0.001432 0 9883.6 21519 9332.4 14706 14215 20036 14431 10627 10498 14821 TRUE FALSE 10273.81216 25214.72086 9575.610011 17614.80291 11798.73938 15382.94265 13299.86051 10484.56245 10120.17903 17724.89118 0.579626247 1.42255998 0.540235193 0.993789058 0.665659341 0.867872332 0.750349346 0.591516322 0.570958599 1 14.11348915 3.267961159 0.881271551 0.698883843 0.932848248 0.036231753 0.260144211 1.431245309 2.407454666 0.115526952 0.204397267 1853.365862 -3.267961159 0.233964405 S(ph)KS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSPFR 6 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 2 S(1)KS(1)PFR;S(1)KS(1)PFR;S(1)KS(1)PFR 72.607 0.048452 1067770000 735580 364447 458960 334087 639890 833690 627940 481790 513510 285107 TRUE FALSE 764621.2664 427037.9372 470920.8746 400168.4114 531121.7264 640078.1322 578720.422 475332.3931 495028.8754 340968.2579 2.242499847 1.252427249 1.381128195 1.17362365 1.557686717 1.877236714 1.697285329 1.394066404 1.451832726 1 18.37927791 0.714132524 1.337804549 1.002515855 1.558618506 0.252486618 0.297155947 1.429540393 4.199226779 0.280604575 0.083725809 5.177648026 -0.714132524 0.55610265 S(ph)KS(ph)PTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPTLR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.97)KS(0.673)PT(0.357)LR 54.094 0.057825 0 551350 297910 362390 268960 516060 603220 503850 396140 405770 218410 TRUE FALSE 573117.7237 349073.7251 371834.1811 322159.4852 428340.3055 463131.2969 464356.9204 390830.3913 391166.417 261203.2578 2.194144624 1.336406475 1.423543428 1.233367026 1.639873519 1.773068609 1.77776083 1.496269206 1.497555659 1 17.99481337 0.64946523 1.665208262 1.000617721 1.594227626 0.334267145 0.257113705 1.721006253 6.563544867 0.242549971 0.069014159 4.461339049 -0.64946523 0.593609905 S(ph)KSDATASISLSSNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(0.5)KS(0.5)DATASISLSSNLK;S(0.498)KS(0.498)DAT(0.004)ASISLSSNLK 211.27 4.55E-12 872810000 929750 547020 780220 617600 1022940 919840 1039700 792250 931450 399290 TRUE FALSE 966457.2479 640966.4298 800553.1742 739759.4366 849061.0242 706221.1003 958205.5972 781631.1846 897927.2964 477523.2306 2.023895773 1.342272771 1.676469589 1.549159055 1.778051767 1.478925118 2.00661567 1.636844313 1.880384532 1 18.86521139 3.253841928 24.95231434 1.678337471 1.628152486 0 0.301176977 2226.238103 3635119.726 0.076423159 0.103084712 1794.080511 -3.253841928 -0.050184985 S(ph)KSDLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.624)KS(0.376)DLSER 67.385 0.071712 0 488020 406840 449670 447850 575160 576620 572710 511900 529600 340190 TRUE FALSE 507287.4064 476711.6052 461388.7696 536433.3933 477394.5086 442708.7438 527819.4937 505038.8178 510539.7995 406843.7172 1.246885192 1.171731515 1.134068809 1.318524462 1.173410055 1.088154309 1.29735196 1.241358282 1.254879399 1 18.63411519 -2.244231407 2.445674833 0.152161983 1.214289021 0.467125754 0.068581917 3241484.472 825795.2507 15374817.22 0.018120753 0.005698605 2.244231407 1.062127038 S(ph)KSDSYTLDPDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.5)KS(0.5)DSYTLDPDTLR 138.08 1.06E-05 1259100000 1521900 1109700 1440400 1298900 1983300 1996600 1666500 1545300 1652900 1142600 TRUE FALSE 1581985.787 1300282.343 1477938.007 1555818.543 1646179.374 1532919.909 1535875.375 1524587.781 1593412.452 1366470.594 1.157716671 0.951562623 1.081573225 1.13856716 1.204694329 1.121809658 1.123972504 1.115712104 1.166078845 1 20.38202298 3.93923442 5.342042343 1.130496771 1.045968889 0.144769252 0.067601755 0.281689811 16.50448152 0.016124094 0.030490411 8694.295956 -3.93923442 -0.084527881 S(ph)KSEDMDNVQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.5)KS(0.5)EDMDNVQSK;S(0.5)KS(0.5)EDMDNVQSK;S(0.68)KS(0.32)EDMDNVQSK;S(0.5)KS(0.5)EDMDNVQSK;S(0.818)KS(0.182)EDMDNVQSK 185.02 8.22E-06 1488780000 2979280 1248128 2050420 1335275 2885210 2756410 2880050 2094790 2413310 1007668 TRUE FALSE 3096904.275 1462484.275 2103855.63 1599388.41 2394783.035 2116275.551 2654304.155 2066712.766 2326455.445 1205101.252 2.569829108 1.213577924 1.74579159 1.327181768 1.987204836 1.756097712 2.202556965 1.714970226 1.930506205 1 20.20072293 S(ph)KSEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 S(0.615)KS(0.385)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.678)KS(0.322)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR;S(0.5)KS(0.5)EEAHAEDSVMDHHFR 273.56 2.60E-39 5142850000 2485262 2070147 2720446 1823160 2911759 3041080 3517090 2607899 3359690 1778272 TRUE FALSE 2583382.063 2425678.644 2791343.058 2183775.606 2416819.245 2334835.258 3241411.296 2572944.38 3238775.413 2126690.351 1.214742927 1.14058854 1.31252914 1.026842297 1.136422725 1.097872691 1.524157616 1.20983498 1.522918187 1 21.02017856 2.279838102 24.99999653 1.32552946 1.154698929 0.197043062 0.156969949 209.3388937 126786.7519 0.050126431 0.04193837 190.4750524 -2.279838102 -0.170830531 S(ph)KSERECPHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSERECPHSK 11 2 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 S(0.521)KS(0.479)ERECPHSK 95.631 0.0039728 32972000 29082 21491 30738 20230 42814 36206 29161 28570 33341 29361 TRUE FALSE 30230.17982 25181.91207 31539.05753 24231.43362 35536.49157 27797.70521 26875.28462 28187.06588 32141.06392 35113.7258 0.860922022 0.717152951 0.898197409 0.690084378 1.012039901 0.791647841 0.765378325 0.802736401 0.915341884 1 15.09974746 1.03496749 3.506747055 0.998885849 0.815071685 0.313694803 0.087388567 0.222678886 6.15807999 0.077196538 0.020037304 10.83845776 -1.03496749 -0.183814164 S(ph)KSKDQAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSKDQAEEK 10 2 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 S(0.5)KS(0.5)KDQAEEK 72.891 0.050352 0 111420 16045 35430 18519 74475 69322 66954 34534 45031 13416 TRUE FALSE 115818.9476 18800.60394 36353.33491 22182.00293 61815.7661 53223.01609 61705.97053 34071.12822 43410.34311 16044.60834 7.218558734 1.171770824 2.265766427 1.382520686 3.852743851 3.31719011 3.845900706 2.123525081 2.705603166 1 13.96980095 -0.947637326 0.274264131 2.45E-33 3.285066437 0.149239583 1.612627519 31.445433 2.167124008 29.24858364 2.141829107 0.112813916 0.947637326 3.285066437 S(ph)KSMSDVSAEDVQNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.496)KS(0.496)MS(0.008)DVSAEDVQNLR;S(0.696)KS(0.302)MS(0.001)DVSAEDVQNLR;S(0.5)KS(0.5)MS(0.001)DVSAEDVQNLR 130.49 7.54E-05 1258080000 772050 597751 745280 486015 968850 813920 705570 727990 794170 585000 TRUE FALSE 802531.1302 700410.0844 764702.6091 582147.3164 804165.2231 624899.4151 650265.5797 718232.4848 765587.9768 699619.5495 1.147096491 1.00112995 1.093026359 0.832091266 1.149432179 0.893198904 0.929455988 1.026604367 1.094291858 1 19.41621108 7.02090487 1.117908837 0.994746516 28.65821825 0.18005755 0.092357726 480.4171217 4.315175719 0.024830952 33497.5818 10493125.56 -7.02090487 27.66347173 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.498)KS(0.498)PLPPEEEAKDEEEDQT(0.003)LVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.5)KS(0.5)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.58)KS(0.42)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 232.34 1.01E-40 5355492000 731749 232867 376556 183390 589591 611081 534056 344818 454370 149894 TRUE FALSE 760639.0156 272860.0958 386369.3587 219663.9946 489372.5324 469166.6988 492195.2952 340196.2787 438017.3125 179262.8594 4.243148961 1.522122857 2.155322971 1.225373707 2.729915913 2.617199683 2.745662414 1.897751045 2.443435935 1 17.45171709 -1.735708582 0.494955085 4.53E-10 2.354860046 0.219589205 0.78496534 82.42275928 7.710041796 98.95217597 0.357564504 0.018377711 1.735708582 2.354860045 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_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)PPKVPIVIQDDSLPAGPPPQIR 158.69 1.28E-11 3696900000 2139590 826070 1284660 927420 1762510 1838730 1811830 1349650 1532750 655220 TRUE FALSE 2224062.665 967941.0966 1318139.295 1110860.908 1462919.18 1411712.824 1669814.03 1331560.149 1477586.627 783597.8141 2.838270635 1.235252421 1.682163058 1.417641663 1.86692606 1.801578308 2.130958 1.699290281 1.885644141 1 19.57975385 -1.132580393 5.462082076 0.999985209 1.80892772 0.271164974 0.410225712 6.78E-05 1.08E-05 0.364170236 0.085834183 0.073691875 1.132580393 0.80894251 S(ph)KSPRDPDANWDSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPRDPDANWDSPSR 16 2 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.496)KS(0.496)PRDPDANWDS(0.004)PS(0.004)R 65.454 0.045136 420740000 97284 73676 85440 71070 107540 113370 95056 92896 99086 76572 TRUE FALSE 101124.8474 86329.27988 87666.63659 85127.43388 89260.38921 87041.53564 87605.26234 91650.88107 95519.91422 91574.81734 1.104286641 0.942718559 0.957322538 0.929594362 0.974726369 0.950496416 0.95665233 1.000830618 1.043080587 1 16.4826633 1.545476779 4.413644728 1.021927702 0.969499564 0.141488817 0.047056073 0.281194755 12.09441929 0.027441171 0.011789127 35.11371494 -1.545476779 -0.052428139 S(ph)KSPSPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPSPPR 8 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.611)KS(0.388)PS(0.001)PPR 70.977 0.030241 88146000 85087 73910 102510 82446 106370 107750 101700 95425 94255 79261 TRUE FALSE 88446.30046 86603.46756 105181.4948 98753.57272 88289.26539 82726.69547 93728.48826 94145.98396 90862.78096 94790.67541 0.93306963 0.913628552 1.109618582 1.041806826 0.931412979 0.872730309 0.988794392 0.993198788 0.958562438 1 16.53245753 -1.033846791 3.939060406 1.000003431 0.973995925 0.0161267 0.064191101 5137.081164 35354086.03 320.0829948 0.01576222 0.092502444 1.033846791 -0.026007506 S(ph)KSPTISDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.568)KS(0.367)PT(0.062)IS(0.003)DK 67.456 0.036849 229030000 338950 108420 188420 107550 241960 285410 261230 172820 202020 91645 TRUE FALSE 352332.0077 127040.2916 193330.38 128823.069 200831.7256 219127.8529 240754.11 170503.6306 194749.3397 109601.0831 3.214676331 1.159115294 1.763945889 1.17538135 1.832388147 1.999321966 2.19663988 1.555674686 1.776892474 1 16.74190253 -2.200882651 0.385633438 9.46E-10 1.841182459 0.179483769 0.550334986 94.70142568 4.99803706 82.36453558 0.346023036 0.006296763 2.200882651 1.841182458 S(ph)KSQSSSNCSNPISVPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSQSSSNCSNPISVPLRR 19 2 P35568 P35568 IRS1 Insulin receptor substrate 1 1 S(0.5)KS(0.5)QSSSNCSNPISVPLRR 85.932 0.0015432 748110000 266210 353960 378510 271930 362220 381240 315840 315260 369990 329920 TRUE FALSE 276720.1764 414749.8766 388374.2815 325716.9424 300649.9738 292702.7877 291083.6355 311034.4554 356674.1322 394561.5073 0.701335967 1.051166596 0.984318729 0.825516266 0.76198506 0.741843242 0.737739567 0.788304104 0.903975998 1 18.58989069 5.04998934 13.59523685 0.848004427 1.89E-05 0.1508022 0.109995294 3132221.993 27266566.64 0.028150355 66565204.86 112199.0914 -5.04998934 -0.847985483 S(ph)KSVKEDSNLTLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKSVKEDSNLTLQEK 15 2 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 S(0.5)KS(0.5)VKEDSNLTLQEK;S(0.5)KS(0.5)VKEDSNLTLQEK 188.04 1.65E-07 561410000 574600 189732 396580 197083 613370 469960 539520 322770 487490 200111 TRUE FALSE 597285.6517 222316.9951 406915.2006 236065.4292 509109.5865 360818.9123 497231.0126 318443.7961 469945.3301 239318.9191 2.495772812 0.928957042 1.700305192 0.986405212 2.127326951 1.507690715 2.077692038 1.330625248 1.963678141 1 17.86857493 3.225842209 24.99939064 1.680537599 1.497398626 0.015581896 0.517216562 996.2424452 1958217.337 0.137251264 0.1650647 1682.062811 -3.225842209 -0.183138973 S(ph)KSVPGLNVDMEEEEEEEDIDHLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSVPGLNVDMEEEEEEEDIDHLVK 25 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 S(0.5)KS(0.5)VPGLNVDMEEEEEEEDIDHLVK 196.06 5.30E-25 78463000 28821 23411 35453 17123 64171 40985 31842 34930 33460 27693 TRUE FALSE 29958.87533 27431.65714 36376.9343 20509.87829 53263.23634 31466.85488 29346.14084 34461.82048 32255.78114 33118.91314 0.9045851 0.828277698 1.098373433 0.619279933 1.608242279 0.950117377 0.886084055 1.04054805 0.973938396 1 15.01536771 S(ph)KSYNTPLLNPVQEHEAEGAAAGGTSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSYNTPLLNPVQEHEAEGAAAGGTSIR 28 1 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.5)KS(0.5)YNTPLLNPVQEHEAEGAAAGGTSIR 322.63 1.69E-83 413300000 119730 92421 139680 100700 182550 150970 130460 141450 145950 122850 TRUE FALSE 124457.0329 108293.5878 143320.1755 120618.1594 151520.2162 115909.5055 120234.2043 139554.0941 140697.288 146920.1054 0.847106885 0.737091683 0.975497364 0.820977899 1.031310288 0.788928821 0.818364539 0.949863831 0.957644889 1 17.16467231 7.452747715 0.028037594 1.53968079 1.13E-08 0.231757337 0.084434225 2111.749156 4.974477663 92.87172016 198.4039338 28362709.38 -7.452747715 -1.539680778 S(ph)KTFDWAEFRPIQQALAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.5)KT(0.5)FDWAEFRPIQQALAQER 103.29 0.00022646 603810000 124970 93542 114510 85424 160310 154510 122650 128610 117420 94976 TRUE FALSE 129903.9121 109607.1108 117494.2247 102320.6122 133060.5635 118627.3941 113036.3725 126886.1933 113194.0771 113584.7288 1.143674097 0.96498105 1.034419204 0.900830713 1.171465257 1.044395628 0.995172271 1.117106099 0.996560703 1 16.79340936 3.241110815 24.99999344 1.059273586 1.009365423 0.06669642 0.077539963 172.8014794 1693985.097 0.020771206 0.026890445 1742.251373 -3.241110815 -0.049908164 S(ph)KTLAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKTLAFR 7 1 Q53EV4-2 Q53EV4-2 1 S(0.951)KT(0.049)LAFR;S(0.946)KT(0.054)LAFR 64.836 0.043735 1109310000 13717.4 825940 422210 529670 294400 644700 156180 431610 277640 1293150 TRUE FALSE 14258.97354 967788.7701 433213.1394 634437.1451 244357.9932 494978.1955 143938.2035 425824.9739 267647.7906 1546517.984 0.00922005 0.625785655 0.280121631 0.410235867 0.158005271 0.320059773 0.093072441 0.27534434 0.173064777 1 20.56059218 -1.222979941 4.15391686 1.00043276 0.26824742 0.645588449 0.164275595 109880532.9 169889557.4 575572.3251 0.036952549 0.059843923 1.222979941 -0.732185339 S(ph)KTPTPSVETLPHLRPFPASSHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKTPTPSVETLPHLRPFPASSHPR 24 2 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.493)KT(0.493)PT(0.014)PSVETLPHLRPFPASSHPR 93.384 0.0038421 503110000 36844 38087 60317 52472 67932 65445 46574 55506 71038 40019 TRUE FALSE 38298.62957 44628.14597 61888.91057 62850.80499 56384.9429 50246.39058 42923.40818 54762.03286 68481.35626 47859.95684 0.800222819 0.932473594 1.293125081 1.313223186 1.178123564 1.049862848 0.896854302 1.144214004 1.430869578 1 15.54653148 4.417472311 5.486989099 1.15491421 0.82957636 0.397791888 0.149644434 0.180882388 10.74697068 0.038615947 0.113076507 26150.0372 -4.417472311 -0.325337851 S(ph)LAIPDDDRFEDLEEANPFSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLAIPDDDRFEDLEEANPFSFR 22 1 Q96C92-4 Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 1 S(1)LAIPDDDRFEDLEEANPFSFR;S(1)LAIPDDDRFEDLEEANPFSFR;S(1)LAIPDDDRFEDLEEANPFSFR;S(1)LAIPDDDRFEDLEEANPFSFR 188.22 1.55E-17 151854000 42479.5 61330.9 63363 49390.6 85028 71921 59812.1 63808 61351.3 57178.4 TRUE FALSE 44156.62346 71864.00499 65014.29183 59159.91326 70574.97093 55218.43772 55123.87131 62952.75813 59143.2787 68381.41273 0.645740146 1.050928931 0.950759706 0.865146111 1.032078281 0.807506536 0.80612361 0.920612131 0.864902849 1 16.06131661 S(ph)LALVAHTGYLPHQQDPHHVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLALVAHTGYLPHQQDPHHVHR 22 0 Q9Y485;F5H269;E7EMZ0 Q9Y485 DMXL1 DmX-like protein 1 1 S(0.999)LALVAHT(0.001)GYLPHQQDPHHVHR 115.46 8.84E-05 753820000 159110 166700 180970 175540 226640 228040 182370 167150 174820 170090 TRUE FALSE 165391.7857 195329.4283 185686.2269 210261.2881 188115.8138 175081.166 168075.3629 164909.6277 168528.2623 203415.8789 0.813072148 0.960246709 0.912840373 1.033652285 0.924784313 0.860705501 0.826264713 0.810701842 0.828491184 1 17.63407278 2.720503197 4.166607235 0.845757255 0.936236931 0.137665444 0.071817377 0.290402331 12.15826234 0.022612061 0.022238616 525.4158828 -2.720503197 0.090479676 S(ph)LDADEFR ddPTM_MDA-MB-175_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 150.66 0.00050931 1587020000 1527410 1619870 1593770 1343050 1833110 2018370 1742570 1523380 1736650 1473260 TRUE FALSE 1587713.326 1898070.072 1635304.955 1608701.281 1521518.617 1549634.156 1605982.81 1502961.583 1674148.306 1761917.09 0.901128285 1.077275476 0.928139562 0.913040285 0.863558578 0.879515935 0.911497379 0.853026281 0.950185633 1 20.74871461 4.014477873 24.72196344 0.899876365 0.992578338 0.217234827 0.056858841 222.3986404 379754.4285 0.012945326 0.027945912 10338.98423 -4.014477873 0.092701974 S(ph)LDDLSAPPHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDDLSAPPHHR 12 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(1)LDDLSAPPHHR;S(1)LDDLSAPPHHR 108.66 0.0010833 2129630000 696480 789210 761880 770640 944080 997080 851490 893170 846990 755820 TRUE FALSE 723977.5682 924750.6783 781735.2187 923070.2919 783605.6188 765523.2809 784747.9888 881198.5171 816506.9954 903908.458 0.800941248 1.023057888 0.864838925 1.021198866 0.866908161 0.846903549 0.868171972 0.97487584 0.903307175 1 19.78581715 0.612817203 0.970139087 0.998994501 0.90870425 0.128346193 0.071426249 2.687621528 4.098021062 0.065195891 0.021058564 4.100314818 -0.612817203 -0.090290251 S(ph)LDEIAMDLTETGTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLDEIAMDLTETGTQR 16 0 E9PGA7;Q9Y2L6-2;Q9Y2L6;C9JYK2 E9PGA7 FRMD4B FERM domain-containing protein 4B 1 S(1)LDEIAMDLTETGTQR;S(1)LDEIAMDLTETGTQR;S(1)LDEIAMDLTETGTQR 202.63 3.13E-11 39212000 24718.6 25326.7 28517.7 25609.6 30954.4 34388.5 29119.9 27066 26292 30648.9 TRUE FALSE 25694.50941 29676.36371 29260.89469 30675.10244 25692.78214 26402.29204 26837.40615 26703.22454 25345.75606 36653.96515 0.701002178 0.809635836 0.798300936 0.836883604 0.700955055 0.72031203 0.73218289 0.728522124 0.691487427 1 15.16168165 -1.05250652 4.534553208 1.00001016 0.748430926 0.712983892 0.048222373 6.47E-06 1.35E-06 0.048769801 0.011494572 0.088612192 1.05250652 -0.251579233 S(ph)LDFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLDFFR 6 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR;S(1)LDFFR 173.68 0.0049753 582154000 405261 387586 428199 410456 473664 508821 430266 405800 394188 331044 TRUE FALSE 421261.0172 454150.8805 439358.2177 491642.9717 393150.7625 390655.034 396540.6266 400360.9148 380001.2509 395905.7336 1.064043739 1.147118725 1.109754622 1.241818266 0.993041346 0.986737501 1.001603647 1.011253136 0.959827602 1 18.59479744 3.208122659 24.89743275 0.994302892 1.138934231 0.738707513 0.043281169 93.39514905 76394.48185 0.012046086 0.014399452 1614.814571 -3.208122659 0.144631339 S(ph)LDGAEFSRPASVSENHDAGPDGDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 S(0.598)LDGAEFS(0.262)RPAS(0.07)VS(0.07)ENHDAGPDGDKR 56.68 0.044669 165560000 175340 76516 227260 125740 258650 189780 235340 188680 201100 111470 TRUE FALSE 182262.5586 89657.02779 233182.5823 150610.9967 214684.7654 145706.4711 216893.4359 186151.0532 193862.4503 133310.4123 1.367204223 0.672543324 1.749170063 1.129776693 1.610412583 1.092986427 1.62698046 1.396372947 1.454218369 1 17.02442994 4.238900023 24.99999959 1.398144357 1.019873896 0.209018534 0.280843229 11.10262028 817482.2492 0.061258973 0.148177735 17334.04911 -4.238900023 -0.378270461 S(ph)LDLFNCEVTNLNDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 1 S(1)LDLFNCEVTNLNDYR 65.495 0.059997 12381000 4329 39974 34448 38046 30994 51346 27324 34156 27322 33941 TRUE FALSE 4499.912263 46839.22355 35345.74318 45571.38524 25725.65095 39421.66966 25182.27348 33698.19469 26338.68656 40591.08911 0.110859609 1.153928721 0.870775925 1.122694321 0.633775824 0.971190242 0.620389204 0.830187005 0.648878538 1 15.30887543 -5 0.01623187 1.87981243 9.90E-13 0.037165379 0.288112109 32560.00562 40.07517499 2957.961312 1812.84768 1.00E-05 5 -1.87981243 S(ph)LDLPSIGGSSVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDLPSIGGSSVGK 14 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(1)LDLPSIGGSSVGK;S(1)LDLPSIGGSSVGK 145.43 9.00E-06 114209000 348500 243160 303900 342750 347030 380800 498700 333200 332490 221350 TRUE FALSE 362259.0491 284920.8385 311819.8837 410544.927 288041.9646 292364.9711 459610.5909 328733.999 320523.7498 264719.2945 1.368464848 1.076313077 1.177926544 1.550868922 1.088103401 1.104433931 1.736218706 1.241821076 1.21080615 1 18.01410383 S(ph)LDNFFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDNFFAK 8 0 Q9UKY7;Q9UKY7-2 Q9UKY7 CDV3 Protein CDV3 homolog 1 S(1)LDNFFAK;S(1)LDNFFAK 113.63 0.0029495 42059000 113804 80388 111860 103391 119520 140214 146326 96685 127150 71994 TRUE FALSE 118297.0698 94194.01367 114775.1635 123841.4312 99204.03309 107651.4235 134856.5858 95389.09572 122573.8963 86099.84589 1.373952166 1.094009086 1.333047258 1.438346723 1.152197569 1.250309131 1.566281384 1.107889274 1.423625038 1 16.39372303 -1.641217944 5.329691214 0.996393781 1.294611886 0.276248561 0.147048278 0.005934317 0.000399484 0.134091188 0.031284707 0.022844521 1.641217944 0.298218105 S(ph)LDTITLSGDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDTITLSGDER 12 0 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(1)LDTITLSGDER 100.22 0.001373 0 106830 107870 93653 102550 130960 152540 114300 122400 101360 115220 TRUE FALSE 111047.7309 126395.8334 96093.67412 122834.0839 108699.466 117114.8968 105340.8673 120759.4282 97712.0734 137795.153 0.805889964 0.917273436 0.697366141 0.891425288 0.788848255 0.849920293 0.764474403 0.876369202 0.709111106 1 17.07216562 -2.199268109 2.464902908 1.569483818 0.816236175 0.39034039 0.070537098 7731642.268 1201344.444 24778389.95 0.015256004 0.006320216 2.199268109 -0.753247643 S(ph)LEDLRAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLEDLRAPK 9 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK;S(1)LEDLRAPK 153.34 4.74E-05 1225840000 2631120 1613200 2185980 1590260 3216970 2885850 2385020 2063660 2458550 1455900 TRUE FALSE 2734998.649 1890254.551 2242948.435 1904808.682 2670150.588 2215655.073 2198075.9 2036000.013 2370067.266 1741155.73 1.570794962 1.0856321 1.288195189 1.09399099 1.5335507 1.272519761 1.262423494 1.169338261 1.361203495 1 20.73161381 -3.789949636 0.298466105 4.92E-13 1.295291815 0.238846126 0.15515338 174.7504615 3.190018037 107.7489867 0.148469593 0.0001622 3.789949636 1.295291815 S(ph)LEELLLDANQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLEELLLDANQLR 13 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JPP5;Q14160-3;Q5T0G3;Q9BTT6-2;Q9BTT6 A0A0G2JNZ2 SCRIB;LRRC1 Protein scribble homolog;Leucine-rich repeat-containing protein 1 1 S(1)LEELLLDANQLR;S(1)LEELLLDANQLR 145.71 2.57E-06 22947000 30678 31562 34591 33924 36322 41566 37742 30100 38513 28421 TRUE FALSE 31889.19113 36982.52798 35492.46988 40634.06595 30147.99941 31912.92644 34783.68342 29696.55873 37126.92465 33989.5508 0.938205724 1.088055803 1.044217092 1.195486995 0.88697846 0.938904036 1.023364022 0.873696711 1.092304069 1 15.05280368 3.218078542 24.99998374 0.959269733 1.066440787 0.238868028 0.083956548 304.2323856 371338.6198 0.023343909 0.027931763 1652.260582 -3.218078542 0.107171053 S(ph)LEGGGCPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLEGGGCPAR 10 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 S(1)LEGGGCPAR;S(1)LEGGGCPAR;S(1)LEGGGCPAR 110.74 0.0019364 1782730000 284692 313973 331998 345859 390440 405983 294320 301605 328522 329693 TRUE FALSE 295931.86 367895.4204 340650.1406 414268.8779 324073.1483 311699.601 271250.4293 297562.4783 316698.5574 394290.031 0.750543602 0.93305788 0.863958289 1.050670434 0.821915653 0.790533811 0.687946456 0.754679183 0.803212185 1 18.58889771 3.01253521 24.99416136 0.782009082 0.904018316 0.134070258 0.102540927 320.0033241 638055.051 0.028407022 0.033932697 1029.283972 -3.01253521 0.122009233 S(ph)LEGIFDDIVPDGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLEGIFDDIVPDGKR 15 1 Q13009 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 S(1)LEGIFDDIVPDGKR;S(1)LEGIFDDIVPDGKR 168.32 7.72E-07 93704000 94426 68646 87613 62508 104550 101986 88482 75598 83931 55795 TRUE FALSE 98154.01139 80435.41651 89896.26675 74871.89583 86778.62834 78301.29711 81546.54964 74584.73246 80910.33971 66726.96199 1.470979773 1.205441011 1.34722553 1.12206361 1.300503211 1.173458146 1.222092947 1.117760051 1.212558422 1 16.0259822 8 0.091690844 0.884839773 2.219206937 0.583879063 0.080689088 101.6277066 0.667686503 1.240294154 17.05531915 100000000 -8 1.334367163 S(ph)LEGLNQELEEVFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLEGLNQELEEVFVK 15 0 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK;S(1)LEGLNQELEEVFVK 280.54 1.08E-33 273344000 159313 116058 154423 136389 186377 190757 198602 155516 163280 94768 TRUE FALSE 165602.8003 135990.0587 158447.3902 163366.3371 154696.7041 146456.5777 183035.0563 153431.5624 157403.5847 113335.9752 1.461167119 1.199884313 1.39803262 1.44143408 1.364939102 1.292233799 1.614977557 1.353776347 1.388822785 1 16.79024635 0.28230282 2.526647928 0.999999978 1.390704279 0.564283668 0.102967727 31.90462462 110.4561649 0.095501176 0.025421264 1.915591143 -0.28230282 0.390704301 S(ph)LEGLNQELEEVFVKEQGEEELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLEGLNQELEEVFVKEQGEEELLR 24 1 Q9C073;D6RJ87;D6RFX7;K7ENS5 Q9C073 FAM117A Protein FAM117A 1 S(1)LEGLNQELEEVFVKEQGEEELLR;S(1)LEGLNQELEEVFVKEQGEEELLR 200.4 9.30E-25 84394000 26989 25098 30410 21073 42339 41693 30723 30670 34406 28327 TRUE FALSE 28054.54656 29408.38626 31202.50958 25241.1765 35142.2319 32010.43261 28314.85098 30258.91882 33167.73478 33877.1333 0.828126345 0.868089576 0.92104929 0.74508006 1.037343733 0.944897915 0.835810124 0.893195966 0.979059665 1 15.04802418 1.495124001 0.019015466 1.844671187 2.83E-05 0.250200029 0.073294206 405.9988989 7.831142169 379.7602635 377.7372975 31.26972063 -1.495124001 -1.844642895 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLELSSLAGPGEDPLSADSLGKPTR 25 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(1)LELSSLAGPGEDPLSADSLGKPTR;S(0.884)LELS(0.112)S(0.004)LAGPGEDPLSADSLGKPTR 241.04 8.16E-39 1718627000 411320 296307 380118 295687 494062 490338 498890 383932 435437 278948 TRUE FALSE 427559.2312 347195.4223 390024.1874 354173.0061 410081.5177 376464.4306 459785.6982 378786.0195 419765.7074 333602.5198 1.281642691 1.040745803 1.169128421 1.061661663 1.229251859 1.128481976 1.378244081 1.135441122 1.258280986 1 18.34777066 3.211770544 24.95658453 1.201070501 1.133529198 0.038670484 0.110653511 545.8429591 508484.6405 0.029519668 0.035291227 1628.435435 -3.211770544 -0.067541303 S(ph)LENPT(ph)PPFTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLENPTPPFTPK 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(1)LENPT(1)PPFTPK;S(1)LENPT(1)PPFTPK;S(1)LENPT(1)PPFTPK;S(1)LENPT(0.999)PPFT(0.001)PK 199.58 9.02E-07 530100000 2009990 1215650 1550590 1257250 2069740 2110220 2161450 1537130 1743330 856300 TRUE FALSE 2089345.957 1424428.431 1590999.649 1505930.297 1717926.334 1620153.386 1992029.901 1516527.287 1680587.894 1024075.59 2.040226305 1.390940713 1.553595911 1.470526504 1.677538602 1.582064255 1.945198109 1.480874362 1.641077973 1 19.96589078 0.02844066 1.301225198 0.998600472 1.632794356 0.491856264 0.19561574 10.87469805 13.5019905 0.224220726 0.052086194 1.0676789 -0.02844066 0.634193884 S(ph)LEPAENVHGAGGGAFPASQTPSKPASADGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 257.12 2.01E-59 4167580000 1077850 1328542 1631552 1583537 1920543 2072466 2252761 1969119 1872300 1166211 TRUE FALSE 1120404.35 1556708.754 1674071.585 1896755.892 1594089.787 1591167.18 2076183.706 1942726.181 1804916.289 1394707.717 0.803325555 1.116154112 1.200302805 1.359966586 1.142956167 1.14086067 1.48861563 1.392927104 1.294117948 1 20.41153138 5.219904734 0.992066454 1.292357131 1.47E-12 0.491767416 0.13633637 3.500216195 1.427717441 0.041980965 6.048539317 165922.2905 -5.219904734 -1.292357131 S(ph)LESCLLDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLESCLLDLR 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(1)LESCLLDLR;S(1)LESCLLDLR;S(1)LESCLLDLR;S(1)LESCLLDLR;S(0.999)LES(0.001)CLLDLR;S(0.999)LES(0.001)CLLDLR 240.85 2.85E-12 751733000 414506 414586 451353 419494 567723 601889 505149 479257 461222 452044 TRUE FALSE 430871.0169 485787.9205 463115.63 502468.6611 471221.6472 462109.4015 465554.1014 472833.3438 444622.7103 540613.3669 0.797004002 0.898586587 0.8566485 0.929441801 0.871642612 0.854787228 0.861159065 0.874623849 0.822441208 1 19.04423766 -0.987969647 4.306551841 1.000005576 0.866344709 0.581238074 0.034795873 0.014848844 18735983.03 255.6953665 0.007640129 0.102808815 0.987969647 -0.133660868 S(ph)LESVLSLGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 S(0.995)LES(0.005)VLSLGPR;S(1)LESVLSLGPR;S(0.999)LES(0.001)VLSLGPR 234.3 9.62E-06 0 32722.3 25490.8 32857.3 35506.6 33961.5 41990 41656.5 29430.5 30640 24745.5 TRUE FALSE 34014.20167 29868.64661 33713.58823 42529.6995 28188.73636 32238.45886 38391.35468 29036.03229 29537.27239 29593.90694 1.149365028 1.009283656 1.139207077 1.437109996 0.952518247 1.089361365 1.297272265 0.981149003 0.998086276 1 14.85301255 1.614664883 16.66814111 0.992084528 1.147547521 0.243339177 0.129271761 0.138096283 277.889262 0.062663536 0.033130646 41.17796528 -1.614664883 0.155462993 S(ph)LESVLSLGPRPT(ph)GGGSSPPEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(1)LES(0.029)VLS(0.004)LGPRPT(0.413)GGGS(0.261)S(0.292)PPEIR;S(0.999)LES(0.192)VLS(0.159)LGPRPT(0.317)GGGS(0.188)S(0.146)PPEIR 76.765 0.03572 335574000 175517 173313 204112 188025 229592 260020 196260 188356 204334 208281 TRUE FALSE 182446.5467 203078.1596 209431.3264 225215.7838 190566.0338 199634.2956 180876.6284 185831.3959 196980.0593 249089.6742 0.732453271 0.815281325 0.840786866 0.904155439 0.765049914 0.801455525 0.726150648 0.746042149 0.790799779 1 17.92630569 0.870417634 19.45555896 1 0.790176094 0.598090671 0.051303559 46482.29992 6978903.55 0.053739373 0.013434843 7.420234555 -0.870417634 -0.209823906 S(ph)LESVLSLGPRPTGGGS(ph)SPPEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLESVLSLGPRPTGGGSSPPEIR 23 1 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 2 S(0.999)LES(0.001)VLSLGPRPT(0.128)GGGS(0.459)S(0.412)PPEIR;S(1)LESVLSLGPRPT(0.001)GGGS(0.642)S(0.357)PPEIR;S(1)LES(0.001)VLSLGPRPT(0.158)GGGS(0.455)S(0.386)PPEIR 139.41 1.17E-07 857010000 440740 483230 524120 464070 587550 660420 514540 518500 508020 497790 TRUE FALSE 458140.7555 566220.9935 537778.9978 555861.6609 487678.4609 507047.4638 474209.0103 511550.3556 489736.4594 595322.4197 0.769567448 0.951116529 0.903340744 0.933715315 0.819183764 0.85171908 0.796558293 0.859282867 0.822640712 1 19.1833117 3.230616183 24.99883843 0.847405359 0.894834101 0.030710939 0.069197936 408.4195084 1285176.969 0.018472798 0.022453274 1700.654853 -3.230616183 0.047428742 S(ph)LGDLTSEDIACNFESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGDLTSEDIACNFESK 17 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 S(0.999)LGDLT(0.001)SEDIACNFESK 128.79 0.00015183 0 20037 15635 16873 16069 20561 25124 19955 16531 17922 13184 TRUE FALSE 20828.07623 18320.18963 17312.72424 19247.40024 17066.04856 19289.33176 18390.87496 16309.42898 17276.99072 15767.15238 1.32097894 1.161921264 1.098024794 1.220727737 1.082379884 1.223387159 1.16640434 1.034392806 1.095758467 1 13.94463451 7.999999948 0.079206043 0.863387265 1.860316133 0.513735153 0.064362974 166.8670698 0.963643945 1.849005713 18.23082388 99999988.08 -7.999999948 0.996928868 S(ph)LGGAVGSVASGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLGGAVGSVASGAR 14 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR;S(1)LGGAVGSVASGAR 159.22 5.19E-06 733530000 269405 174295 255693 201715 289358 305438 272761 275328 225170 189199 TRUE FALSE 280041.3174 204228.8104 262356.5696 241613.6249 240173.0305 234504.6535 251381.2801 271637.6785 217066.1757 226268.9216 1.237648173 0.90259329 1.159490078 1.067816222 1.061449486 1.036397981 1.110984568 1.200508124 0.959328281 1 17.78767892 2.190710043 24.99404199 1.097801815 1.072160337 0 0.102294051 763.8042451 398956.8878 0.036329227 0.026830977 155.1350905 -2.190710043 -0.025641478 S(ph)LGLDINMDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGLDINMDSR 11 0 Q96H22-5;Q96H22-4;Q96H22;Q96H22-3 Q96H22-5 CENPN Centromere protein N 1 S(1)LGLDINMDSR;S(1)LGLDINMDSR 127.32 0.0003032 20931000 38875 45456 49047 51782 55632 61393 51506 46936 39741 48943 TRUE FALSE 40409.81502 53262.7144 50325.20511 62024.32505 46175.69251 47135.40617 47468.82513 46306.89969 38310.72917 58532.44378 0.690383186 0.909969087 0.859783085 1.059657193 0.788890563 0.805286831 0.810983141 0.791132177 0.654521265 1 15.83694889 S(ph)LGSVQAPSYGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.998)LGS(0.002)VQAPSYGAR;S(1)LGSVQAPSYGAR 169.83 2.92E-05 154540000 74644 81559 90388 90745 92459 116099 98978 95958 99654 94594 TRUE FALSE 77591.00276 95566.12381 92743.58553 108694.0902 76742.85221 89136.76675 91219.84573 94671.83997 96067.47201 113127.8832 0.685869837 0.844761885 0.819811906 0.960807248 0.678372564 0.787929238 0.806342726 0.836856815 0.849193579 1 16.78759504 0.621825409 1.045341464 0.999938642 0.802289503 0.387937162 0.075345632 1.302290505 2.26533462 0.070136625 0.022202716 4.186252396 -0.621825409 -0.197649138 S(ph)LHS(ph)AHSLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLHSAHSLASR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 S(1)LHS(0.965)AHS(0.034)LASR;S(1)LHS(0.931)AHS(0.069)LASR;S(1)LHS(0.998)AHS(0.002)LASR;S(1)LHS(1)AHSLASR;S(1)LHS(1)AHSLASR 167.03 2.88E-05 2677810000 2036778 2607607 2391664 2535916 2179705 3040826 2916130 2619228 2442427 2423820 TRUE FALSE 2117191.568 3055443.218 2453992.729 3037512.616 1809199.523 2334640.246 2687556.111 2584121.533 2354524.529 2898721.122 0.730388154 1.054065945 0.846577723 1.047880251 0.624137144 0.805403537 0.927152354 0.891469522 0.812263212 1 21.46698511 -0.444004169 6.672251703 0.999999557 0.86709668 0.098832818 0.125217116 0 0 0.114910204 0.027084595 0.359745882 0.444004169 -0.132902877 S(ph)LHSAHSLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 230.96 9.14E-13 1914840000 237856 477108 396962 460315 417079 537740 388491 460999 357119 470038 TRUE FALSE 247246.7385 559047.5876 407307.1558 551363.9331 346184.0606 412858.0345 358040.0603 454820.0624 344266.3569 562132.9467 0.439836768 0.994511336 0.724574424 0.980842586 0.61584019 0.734449096 0.636931285 0.809096967 0.612428713 1 19.10055185 -1.240234652 5.069879876 1.000036432 0.740941419 0.200155239 0.161385697 6.02E-05 9.02E-06 0.141468569 0.033339779 0.057512911 1.240234652 -0.259095013 S(ph)LIYTDTLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLIYTDTLVR 10 0 Q5SYE7-2 Q5SYE7-2 NHSL1 NHS-like protein 1 1 S(1)LIYTDTLVR 74.962 0.042401 24294000 14918 12871 17889 13019 15794 18513 15815 9608.4 10630 17007 TRUE FALSE 15506.97416 15081.49413 18355.20204 15594.11934 13109.34152 14213.63632 14575.37898 9479.615114 10247.42838 20339.19603 0.762418246 0.74149903 0.90245465 0.766702839 0.644535876 0.698829801 0.716615296 0.466076196 0.503826619 1 14.31197503 3.281499056 3.883764375 0.63646632 0.801538315 0.123837771 0.143031043 0.340426687 10.73181581 0.04088249 0.054639035 1912.04917 -3.281499056 0.165071995 S(ph)LLDRAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLDRAEER 9 1 P02549-2;P02549 P02549-2 SPTA1 "Spectrin alpha chain, erythrocytic 1" 1 S(1)LLDRAEER 53.567 0.085239 91183000 11459 88235 59272 89682 40604 90482 53318 70745 50630 93380 TRUE FALSE 11911.41017 103388.6749 60816.67701 107420.8319 33702.14658 69468.92677 49138.79584 69796.77899 48807.83619 111676.0231 0.106660408 0.925791159 0.544581328 0.961897003 0.301784982 0.62205767 0.44001205 0.624993414 0.43704848 1 16.76895995 -1.581796576 3.031273593 1.023200637 0.568697034 0.226952934 0.246441007 82051527.66 92574566.61 15405537.22 0.055735488 0.026194097 1.581796576 -0.454503603 S(ph)LLGLSNSEPNGSVETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLGLSNSEPNGSVETK 17 0 Q13033-2;Q13033;G3V340;G3V3G7 Q13033-2 STRN3 Striatin-3 1 S(1)LLGLSNSEPNGSVETK 125.52 4.89E-05 31325000 49918 32919 49257 37503 65131 66848 69345 46647 59296 36534 TRUE FALSE 51888.80119 38572.58218 50540.67789 44920.98146 54060.05588 51323.56509 63909.5577 46021.77326 57161.94854 43692.13781 1.187600419 0.882826616 1.156745365 1.028125052 1.237294822 1.174663627 1.462724437 1.053319329 1.30828912 1 15.41508608 3.237171342 24.99992562 1.214132824 1.057533197 0.191512995 0.142344344 54.01722451 972045.3522 0.037854762 0.047646676 1726.518921 -3.237171342 -0.156599627 S(ph)LLKKPDGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLKKPDGVK 10 2 E9PF82;E9PBG7;H0Y9C2;Q13557;D6R938;Q13557-8;Q13557-6;Q13557-11;Q13557-12;Q13557-10;Q13557-3;Q13557-4;Q13557-9;Q13557-5;H0Y9J2 E9PF82;Q13557 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 S(1)LLKKPDGVK 88.087 0.0064878 382890000 815370 297560 659220 343260 1001600 686630 772310 506060 738310 224470 TRUE FALSE 847561.4372 348663.6153 676399.8148 411155.8035 831348.3898 527170.5885 711774.3241 499277.0934 711738.3673 268450.5988 3.157234296 1.298799917 2.519643532 1.531588327 3.096839395 1.963752701 2.651416415 1.859847196 2.651282473 1 18.0342971 -1.341314316 6.411202407 0.999924813 2.256349423 0.29626729 0.598698366 0.000564496 5.80E-05 0.508583487 0.119867253 0.045570698 1.341314316 1.25642461 S(ph)LLQSEQQPSWTDDLPLCHLSGVGSASNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLLQSEQQPSWTDDLPLCHLSGVGSASNR 29 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 1 S(0.995)LLQS(0.005)EQQPSWTDDLPLCHLSGVGSASNR;S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR;S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR;S(1)LLQSEQQPSWTDDLPLCHLSGVGSASNR 245.6 7.26E-46 979724000 13111.5 81416 71466 80164 68858 101912 50705.8 84217.3 70847.5 83966.1 TRUE FALSE 13629.15214 95398.56467 73328.46267 96020.19993 57153.54176 78244.48249 46731.3469 83088.50485 68297.71231 100417.6497 0.135724668 0.9500179 0.730234803 0.956208398 0.56915833 0.779190538 0.465369853 0.827429293 0.680136535 1 16.61565334 -5 0.28162554 3.248234645 0.675366531 0.151087275 0.231567646 454.8391512 4.345116673 598.3638236 0.242409573 1.00E-05 5 -2.572868114 S(ph)LNLVDSPQPLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLNLVDSPQPLLEK 14 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 1 S(1)LNLVDSPQPLLEK;S(1)LNLVDSPQPLLEK 168.09 3.72E-06 65593000 151097 104036 131191 112034 170600 172815 159506 133345 164878 110184 TRUE FALSE 157062.4262 121903.3737 134609.9452 134193.9908 141601.4729 132681.3353 147003.5029 131557.7284 158944.073 131772.4452 1.191921619 0.925105196 1.021533334 1.018376722 1.074590919 1.006897421 1.11558606 0.998370548 1.206201135 1 17.0076892 2.188433419 1.295834488 1.075837922 1.033970827 0.026559086 0.084606775 1.739133754 5.603881176 0.0513257 0.028185399 154.3239814 -2.188433419 -0.041867095 S(ph)LPAFPTSSLLTQSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPAFPTSSLLTQSQK 16 0 Q99698 Q99698 LYST Lysosomal-trafficking regulator 1 S(0.999)LPAFPT(0.001)SSLLTQSQK 161.09 8.97E-09 76353000 108590 76465 105120 95629 119720 128470 99876 104760 100630 69757 TRUE FALSE 112877.217 89597.26893 107859.5136 114544.1308 99370.03716 98634.78948 92047.45814 103355.8636 97008.34596 83424.54857 1.353045584 1.073991654 1.292898978 1.373026678 1.191136648 1.182323323 1.103361777 1.238914268 1.162827341 1 16.34818435 3.014270807 24.92583932 1.159403407 1.263121432 0.292782585 0.096037193 359.7784583 628395.2833 0.027237236 0.032541389 1033.405592 -3.014270807 0.103718025 S(ph)LPAGDALYLSFNPPQPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 SLPAGDALYLSFNPPQPSR 19 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.998)LPAGDALY(0.002)LSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(0.998)LPAGDALY(0.002)LSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR 321.6 5.25E-62 5680489000 254624.1 291901 282263.8 277588 341521 362120 320227.7 295720 302970 291136 TRUE FALSE 264676.8561 342032.7261 289619.8265 332494.0779 283469.3824 278023.118 295127.4161 291756.3571 292066.1689 348178.5251 0.760175706 0.982348713 0.831814158 0.954952859 0.81414953 0.798507369 0.84763245 0.837950465 0.838840273 1 18.4094677 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 303.74 2.32E-62 369492800 397087 245117 321551 216347 402486 395011 377960 306113 349340 232598 TRUE FALSE 412764.3014 287213.938 329930.8832 259139.7909 334071.5735 303275.6817 348334.5076 302010.0559 336767.3216 278171.1247 1.48385028 1.032508095 1.186071644 0.931584078 1.20095705 1.090248609 1.252231007 1.085698799 1.210648021 1 18.08561314 4.746718323 24.89660646 1.116802846 1.483850472 0.566973116 0.097854434 680.8203175 2077754.835 0.021343874 0.242708578 55810.80961 -4.746718323 0.367047626 S(ph)LPGPAPCLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPGPAPCLK 10 0 A0A5F9UK94;H0Y360;Q01433-2;Q01433;E9PJF6 A0A5F9UK94 AMPD2 AMP deaminase 2 1 S(1)LPGPAPCLK 63.415 0.082586 87187000 98794 94668 155570 93232 181180 120500 189080 111400 160930 116670 TRUE FALSE 102694.4634 110926.4926 159624.282 111673.0113 150383.0883 92515.7012 174259.4155 109906.8652 155138.1607 139529.2527 0.73600669 0.79500528 1.144020189 0.800355547 1.077788961 0.66305595 1.248909545 0.787697655 1.111868355 1 17.09020809 4.452876191 23.92166068 0.963247684 0.750756215 0.195527367 0.172778536 174.003257 171682.0456 0.037413723 0.102475303 28371.1011 -4.452876191 -0.212491469 S(ph)LPGSALELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPGSALELR 10 0 O75145-2;O75145;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 S(0.911)LPGS(0.089)ALELR 72.187 0.040843 0 51621 74038 66550 69755 77319 87619 69530 59567 57348 76615 TRUE FALSE 53659.03694 86753.45056 68284.34767 83552.3308 64176.344 67270.81513 64080.05692 58768.6018 55284.05668 91626.24237 0.58562957 0.946818819 0.745248805 0.911882105 0.700414448 0.734187209 0.69936358 0.64139487 0.603364879 1 16.48347323 3.129263636 22.4785675 0.705576148 0.804610314 0.037609663 0.136141012 9.508754215 1910.900686 0.036515103 0.043643941 1346.677598 -3.129263636 0.099034166 S(ph)LPGSPEFLHQEACPFVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLPGSPEFLHQEACPFVGR 19 0 Q96S53-3;Q96S53-2;Q96S53 Q96S53-3 TESK2 Dual specificity testis-specific protein kinase 2 1 S(0.999)LPGS(0.001)PEFLHQEACPFVGR;S(0.993)LPGS(0.007)PEFLHQEACPFVGR;S(0.994)LPGS(0.006)PEFLHQEACPFVGR 288.64 3.56E-41 270755000 50386 51234 55582 65924 60950 61351 74918 67369 59817 46464.9 TRUE FALSE 52375.27819 60033.04095 57030.51258 78963.57044 50589.74077 47103.16003 69045.7314 66466.02875 57664.19785 55568.80753 0.94253018 1.080337038 1.026304416 1.421005308 0.910398172 0.847654685 1.242526778 1.196103204 1.037708031 1 15.76198766 S(ph)LPITIEMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPITIEMLK 10 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 S(1)LPITIEMLK 93.839 0.0089288 148490000 247310 233360 268880 222640 360560 357590 369180 308850 325870 179690 TRUE FALSE 257073.9898 273437.7647 275887.2337 266677.5275 299272.14 274545.1418 340242.7069 304710.3709 314142.0024 214896.8151 1.1962671 1.272414226 1.283812575 1.240956165 1.392631807 1.27756729 1.583284083 1.41793805 1.461827167 1 17.71328458 3.134564485 1.621493774 1.399392371 1.247291061 0.061728457 0.14788745 0.649579117 3.533088295 0.047909217 0.06329014 1363.215406 -3.134564485 -0.15210131 S(ph)LPLSPELESSP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 S(1)LPLSPELESSP 113.18 0.0012525 39140000 82527 101250 101910 104600 121930 132450 109120 104140 101460 100030 TRUE FALSE 85785.22968 118638.8999 104565.8583 125289.5678 101204.3822 101690.4948 100566.8893 102744.1736 97808.47442 119628.9633 0.717094149 0.991723882 0.874084799 1.04731801 0.845985615 0.850049118 0.840656698 0.858857009 0.817598613 1 16.8682072 S(ph)LPNLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLPNLSR 7 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(1)LPNLSR;S(0.999)LPNLS(0.001)R;S(1)LPNLSR 110.79 0.007053 2958984000 1294170 1451710 1478770 1341010 1742510 1856370 1460100 1439700 1467270 1571490 TRUE FALSE 1345264.831 1701029.9 1517307.961 1606257.775 1446318.773 1425256.201 1345653.547 1420403.176 1414463.239 1879393.378 0.715797367 0.905095187 0.807339208 0.854668211 0.769566813 0.758359702 0.716004197 0.755777472 0.752616912 1 20.84183564 3.219062343 24.09805744 0.771762929 0.825795305 0 0.086931044 394.9458241 488114.6859 0.023121746 0.027679864 1656.007667 -3.219062343 0.054032375 S(ph)LPRPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 76.465 0.024639 1514250000 1377220 1176010 1440370 1189580 1988580 1838450 1650050 1437520 1564860 1320640 TRUE FALSE 1431593.709 1377980.569 1477907.225 1424875.373 1650561.882 1411497.849 1520714.769 1418252.396 1508540.994 1579394.123 0.906419549 0.872474166 0.935743146 0.902165807 1.045060165 0.893695772 0.962846922 0.897972441 0.955139045 1 20.5909398 7.99999668 0.011333664 1.74442292 9.58E-05 0.218475511 0.045384014 16361.78786 14.32899151 931.1190603 1303.145112 99999235.49 -7.99999668 -1.744327155 S(ph)LPRPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLPRPSK 7 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5;H0YHA8;A0A2R8YFX5;Q8IVL0-3;Q8IVL0-2;Q8IVL0 Q8IVL1-9;Q8IVL0-3 NAV2;NAV3 Neuron navigator 2;Neuron navigator 3 1 S(1)LPRPSK;S(1)LPRPSK;S(1)LPRPSK;S(1)LPRPSK 79.974 0.018877 718250000 864330 748290 902140 712090 1304390 1226400 995030 965370 1016250 886660 TRUE FALSE 898454.4158 876802.9866 925650.5095 852939.2766 1082670.254 941587.1863 917036.9486 952430.7942 979675.361 1060384.051 0.847291521 0.826873043 0.872938921 0.804368263 1.021017105 0.887968077 0.864815863 0.89819419 0.923887303 1 20.01615545 -0.95728721 0.018950817 1.930458663 2.86E-06 0.400546534 0.051548594 1442.71379 5.347455209 303.0208802 243.4093912 0.11033487 0.95728721 -1.9304558 S(ph)LPS(ph)SPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.739)S(0.261)PERR;S(1)LPS(0.669)S(0.331)PERR;S(1)LPS(0.609)S(0.391)PERR;S(1)LPS(0.596)S(0.404)PERR 101.39 0.0086722 5289770000 1940780 1908560 2046640 1973770 2279080 2417440 2165300 2072910 1868170 1818390 TRUE FALSE 2017403.493 2236340.333 2099977.12 2364175.815 1891682.796 1856026.197 1995578.128 2045126.032 1800934.927 2174668.705 0.92768314 1.028359091 0.96565381 1.087142979 0.869871715 0.853475379 0.917646961 0.940431077 0.8281422 1 21.0523642 3.217300982 24.99998705 0.900442057 1.001466464 0.409884514 0.059131067 224.4118546 263893.538 0.016352085 0.019562867 1649.305023 -3.217300982 0.101024407 S(ph)LPS(ph)SPLLTHQSISVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(1)LPS(0.551)S(0.449)PLLTHQSISVR;S(0.999)LPS(0.547)S(0.453)PLLT(0.001)HQSISVR 89.831 0.0029879 202870000 37202 104445 95747 104248 104677 154822 73670 113847 82790 123673 TRUE FALSE 38670.76369 122382.6163 98242.24548 124867.9433 86884.04093 118866.9369 67895.5529 112321.0672 79810.40407 147904.3565 0.261457908 0.827444297 0.664228207 0.844247906 0.587433954 0.803674345 0.459050393 0.759416895 0.539608203 1 17.17430502 -2.50681094 2.068549156 4.86460043 0.654273129 0.271491551 0.175950275 7138848.479 430292.2382 129511241.9 0.038380218 0.003113071 2.50681094 -4.210327301 S(ph)LPSASTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPSASTSK 9 0 C9J0A7;Q9UQN3;Q9UQN3-2 C9J0A7 CHMP2B Charged multivesicular body protein 2b 1 S(0.847)LPS(0.153)ASTSK 111.86 0.0021578 404420000 307280 235790 378400 273270 533580 499250 485440 381460 503270 373730 TRUE FALSE 319411.6517 276285.0983 388261.4149 327321.9904 442882.2622 383306.7537 447389.9443 376347.1526 485157.411 446955.238 0.714639016 0.618149369 0.868680758 0.732337296 0.990887285 0.857595395 1.000972595 0.842024258 1.085472033 1 18.76977083 4.098996638 0.447844247 0.986461078 0.533324482 0.610108541 0.088864119 1.933989405 0.459041236 0.064762851 0.442141596 12560.20241 -4.098996638 -0.453136596 S(ph)LPSHMEEAPNVFQLYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQR 18 0 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(0.999)LPS(0.001)HMEEAPNVFQLYQR;S(0.993)LPS(0.007)HMEEAPNVFQLYQR 230.71 7.64E-20 102948000 35712 35774 40942.9 45420 42321 48446 45066 42509 40520 34584 TRUE FALSE 37121.93734 41917.90622 42009.90561 54403.94043 35127.29154 37195.15071 41533.60916 41939.23639 39061.69312 41360.07265 0.897530758 1.013487248 1.015711601 1.315373425 0.849304396 0.899300904 1.00419575 1.014002967 0.944429993 1 15.3359511 S(ph)LPSHMEEAPNVFQLYQRPTSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSHMEEAPNVFQLYQRPTSASR 24 1 Q5THJ4-2;Q5THJ4;H3BLS7 Q5THJ4-2 VPS13D Vacuolar protein sorting-associated protein 13D 1 S(0.995)LPS(0.005)HMEEAPNVFQLYQRPTSASR;S(0.999)LPS(0.001)HMEEAPNVFQLYQRPTSASR 165.42 8.62E-12 397800000 18635.9 112427 103836 110018 126507 120412 67179 112576 108796 145034 TRUE FALSE 19371.65972 131735.4627 106542.0515 131779.232 105003.3853 92448.13786 61913.33444 111067.1029 104880.4532 173450.6355 0.111683994 0.7594983 0.614249992 0.759750644 0.605379075 0.532993942 0.35695075 0.640338403 0.604670331 1 17.4041656 0.546390454 1.680388622 0.99978768 0.559083802 0.352825992 0.18253438 2.720716946 8.803741996 0.166382587 0.047153816 3.518766546 -0.546390454 -0.440703878 S(ph)LPSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.271)S(0.73)PER;S(1)LPS(0.297)S(0.703)PER 115 0.0037239 910900000 1570760 1665080 1629740 1665370 1819180 2122080 1831110 1788880 1597540 1526640 TRUE FALSE 1632774.818 1951044.537 1672212.363 1994775.215 1509956.433 1629259.08 1687582.813 1764902.99 1540044.847 1825755.879 0.894300731 1.068622898 0.915901399 1.092574992 0.827030848 0.892375098 0.924320077 0.966669756 0.843510825 1 20.80006245 3.231992649 24.99999954 0.911693172 0.992766025 0.236046606 0.073816937 225.7983943 859468.0263 0.019943073 0.024374347 1706.053512 -3.231992649 0.081072854 S(ph)LPSS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 2 S(1)LPS(0.081)S(0.919)PERR;S(1)LPS(0.285)S(0.715)PERR 124.48 0.0018489 3997770000 1036840 991960 1108980 1053010 1193370 1236140 1179600 1073600 1049000 1108740 TRUE FALSE 1077775.244 1162321.414 1137880.93 1261292.235 990521.3937 949065.2189 1087139.87 1059210.148 1011246.695 1325976.375 0.812816325 0.87657777 0.858145704 0.951217728 0.747012852 0.715748212 0.819878763 0.798815249 0.762643071 1 20.33862364 5.123926031 14.14284395 0.827180291 0.000411009 0 0.085157368 4617829.899 4323515.903 0.020066368 121168009.6 133022.7835 -5.123926031 -0.826769282 S(ph)LPSS(ph)PLLTHQSISVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPSSPLLTHQSISVR 16 0 J3QQY7;J3KTM5 J3QQY7 TANC2 2 S(0.995)LPS(0.159)S(0.845)PLLTHQSISVR 70.352 0.023064 134490000 13486 48693 44333 53191 43395 59424 34645 47918 33801 50149 TRUE FALSE 14018.43769 57055.64397 45488.3544 63712.02104 36018.7334 45623.67658 31929.43437 47275.73759 32584.50861 59974.73639 0.233739046 0.951327966 0.758458597 1.062314316 0.600565097 0.760714916 0.532381404 0.788260865 0.543303907 1 15.87206729 -2.17313526 2.31832564 1.728447777 0.710994544 0.142974535 0.221781664 21103412.96 4789755.248 80677678.09 0.05078133 0.006712198 2.17313526 -1.017453233 S(ph)LPSSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSSPER 8 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.999)LPS(0.001)SPER;S(0.905)LPS(0.093)S(0.002)PER 137.28 0.00079199 472840000 226464 238749 279950 262340 326540 329280 284520 286700 243220 246150 TRUE FALSE 235404.9736 279752.2835 287245.727 314230.069 271034.8474 252809.7103 262218.5789 282857.2554 234466.5597 294378.3797 0.799668012 0.950315318 0.97577046 1.067435962 0.920702287 0.858791704 0.890753524 0.960862872 0.796480231 1 18.16731219 3.010894736 24.99727253 0.901922308 0.955862069 0.068452893 0.079667229 561.0207116 1287216.02 0.023037956 0.027514071 1025.403359 -3.010894736 0.053939762 S(ph)LPTTVPES(ph)PNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 305.1 3.56E-41 12981070000 2597437 2811532 3335003 3473117 4159190 4537251 4106118 4063742 3989028 4055109 TRUE FALSE 2699985.818 3294390.75 3421915.918 4160089.176 3452212.369 3483543.218 3784269.742 4009274.185 3845463.661 4849629.969 0.556740583 0.679307653 0.705603508 0.857815793 0.711850676 0.718311137 0.780321337 0.826717546 0.792939603 1 22.20944324 1.525327743 0.051977138 1.624781142 1.14E-12 0.738158241 0.057863472 18.7557047 0.996492124 15.29913967 15.19553259 33.52183185 -1.525327743 -1.624781142 S(ph)LPTTVPESPNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 S(0.998)LPT(0.002)TVPESPNYR;S(0.999)LPT(0.001)TVPESPNYR 212.1 1.74E-08 2211530000 163694 202130 179033 230229 239072 258212 221944 205875 198444 229294 TRUE FALSE 170156.7655 236844.2551 183698.7471 275767.609 198434.6268 198246.1762 204547.4493 203115.5824 191302.0392 274219.7692 0.620512394 0.863702336 0.669896075 1.005644523 0.723633556 0.722946332 0.745925248 0.740703644 0.697623077 1 18.06497306 -1.264284271 4.281647938 1.00014672 0.759117538 0.338231618 0.102833621 0.000155039 2.66E-05 0.092241806 0.021726287 0.054414636 1.264284271 -0.241029182 S(ph)LPVSICR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPVSICR 8 0 O94885;A0A087WW74 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 S(0.999)LPVS(0.001)ICR;S(1)LPVSICR 116.52 0.0023665 779130000 286390 286320 322430 303420 354970 398580 291720 311710 345970 339370 TRUE FALSE 297696.8983 335493.2327 330832.7907 363435.5704 294632.3262 306015.8355 268854.2241 307532.0373 333518.6073 405863.0539 0.733491003 0.826616834 0.81513404 0.895463548 0.725940249 0.75398791 0.662425963 0.757723657 0.821751584 1 18.63063349 0.860955217 3.835401168 0.999950098 0.771126658 0.564556707 0.060211284 0.600310471 15.17847839 0.061996659 0.015890783 7.26031087 -0.860955217 -0.22882344 S(ph)LPVSVPVWGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;S(1)LPVSVPVWGFK;S(1)LPVSVPVWGFK 265.53 1.30E-21 18677720000 4280250 4413250 5517050 4303632 7782798 6445651 5552438 5629002 5727865 5304145 TRUE FALSE 4449237.575 5171191.357 5660828.855 5154877.565 6459880.776 4948746.24 5117223.401 5553554.435 5521720.258 6343390.659 0.701397378 0.815209347 0.892397956 0.812637569 1.018364014 0.780142121 0.806701601 0.875486744 0.870468264 1 22.59682276 -4.825961119 0.020583727 2.069750868 6.50E-07 0.332939099 0.075133878 3981.277068 6.373825361 431.9681737 236.1203496 1.49E-05 4.825961119 -2.069750218 S(ph)LQEEHVAVAQLR ddPTM_MDA-MB-175_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 142.39 2.60E-05 302660000 188943 214715 281840 189056 271470 271090 263400 234260 287860 206880 TRUE FALSE 196402.6155 251590.631 289184.9819 226450.7125 225325.6264 208133.4559 242754.0197 231120.1279 277499.9748 247414.175 0.793821193 1.016880423 1.168829482 0.91526976 0.91072238 0.841234969 0.981164558 0.934142629 1.121600954 1 17.91656863 1.253430429 24.99640241 1.06080049 0.950377925 0.174614057 0.099987909 378.2646692 635875.0204 0.068710538 0.024863979 17.92381404 -1.253430429 -0.110422566 S(ph)LQLMDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SLQLMDNR 8 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR;S(1)LQLMDNR 134.2 0.00093024 5129070000 6099524 5562992 5322255 5712845 6759053 8413289 5538558 5614916 5529327 6798551 TRUE FALSE 6340337.917 6518392.602 5460957.338 6842828.69 5610151.585 6459430.134 5104431.352 5539657.235 5330327.601 8130596.902 0.779812109 0.801711446 0.671655157 0.841614555 0.690004886 0.794459523 0.627805241 0.68133463 0.655588718 1 22.95492984 -1.066702285 5.0091224 1.000005826 0.7243458 0.584560287 0.068980453 4.48E-06 8.34E-07 0.066622034 0.015702632 0.085762556 1.066702285 -0.275660026 S(ph)LQLPASPAPDPSPR ddPTM_MDA-MB-175_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 282.85 7.87E-34 1477169000 756188 717306 835390 880771 907814 1055177 1086239 854328 931100 706265 TRUE FALSE 786042.8861 840497.7256 857160.9497 1054984.875 753504.1005 810128.1331 1001096.749 842877.1306 897589.8929 844644.1045 0.930620225 0.995090975 1.014819076 1.249028874 0.892096561 0.959135485 1.185229073 0.997908025 1.062684139 1 19.68798406 4.459622056 2.472234575 1.048535041 0.933777177 0.117745804 0.098698364 0.713330342 7.693461673 0.024649923 0.133107973 28815.2277 -4.459622056 -0.114757865 S(ph)LQLPASPAPDPSPRPAYK ddPTM_MDA-MB-175_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 202.74 3.26E-16 5114650000 3335950 3140590 3357450 2505860 4356900 4354920 3374320 3512440 4249620 3455680 TRUE FALSE 3467655.882 3679961.902 3444947.905 3001511.629 3616315.694 3343555.829 3109831.981 3465361.487 4096677.006 4132754.333 0.839066541 0.890438097 0.833571906 0.726273905 0.875037663 0.809038128 0.752484114 0.838511367 0.991270392 1 21.97867218 1.252111778 4.817056314 1.000658111 0.81799884 0.691647223 0.046930189 0.098712994 5.534192137 0.038873362 0.011903769 17.86947436 -1.252111778 -0.182659271 S(ph)LQQLAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLQQLAEER 9 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER;S(1)LQQLAEER 177.16 5.50E-05 2578260000 632636 594849 632296 621135 751090 795670 631052 606872 578491 545146 TRUE FALSE 657612.9578 697009.6885 648774.1532 743993.6491 623419.9901 610887.701 581588.4953 598737.8735 557671.2219 651956.9212 1.008675476 1.069103902 0.995118131 1.141169953 0.956228809 0.937006236 0.892065835 0.9183703 0.855380476 1 19.31441711 3.045691422 7.970474951 0.916673749 1.050686499 0.612298516 0.050110542 0.148969601 22.65947139 0.013667069 0.0163191 1110.942094 -3.045691422 0.13401275 S(ph)LQTLPTDSSTFDTDTFCPPRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLQTLPTDSSTFDTDTFCPPRPK 23 1 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(0.996)LQT(0.004)LPTDSSTFDTDTFCPPRPK 150.94 4.75E-08 364450000 191650 137420 162940 163450 193170 211960 206760 165290 176640 106250 TRUE FALSE 199216.49 161020.816 167186.3503 195779.9222 160335.0324 162735.5023 190553.6109 163074.5579 170282.7609 127067.6532 1.567798609 1.267205398 1.315727064 1.540753427 1.261808402 1.280699676 1.49962328 1.283367984 1.340095269 1 16.95523729 -3.493937942 0.268560101 1.44E-17 1.400005168 0.520535169 0.109880219 66.409272 1.351753493 36.84240685 0.13245738 0.000320673 3.493937942 1.400005168 S(ph)LQTLPTDSSTFDTDTFCPPRPKPVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLQTLPTDSSTFDTDTFCPPRPKPVAR 27 2 B0QY95;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 S(1)LQTLPTDSSTFDTDTFCPPRPKPVAR;S(0.989)LQT(0.011)LPTDSSTFDTDTFCPPRPKPVAR 220.78 1.41E-34 619260000 455220 447460 484010 394120 616110 596280 443380 485560 517770 458160 TRUE FALSE 473192.4371 524307.7742 496623.6982 472075.7597 511383.8423 457803.0067 408626.717 479051.8624 499135.5588 547927.68 0.863603819 0.956892293 0.906367239 0.861565818 0.933305363 0.83551721 0.745767611 0.874297612 0.910951531 1 19.06362596 2.732749519 24.64358638 0.85577763 0.905001608 0.019482715 0.066178537 888.6300358 3768473.311 0.020749786 0.020057338 540.4425302 -2.732749519 0.049223978 S(ph)LS(ph)PKPR ddPTM_MDA-MB-175_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 134.68 0.0017931 1330080000 3950520 1538480 2171230 1574680 3279220 3866480 3213370 2324030 2379820 1258500 TRUE FALSE 4106489.58 1802701.972 2227814.037 1886147.004 2721819.356 2968548.617 2961497.663 2292880.179 2294170.743 1505078.98 2.728421323 1.197745764 1.48019743 1.253188058 1.808422942 1.972354047 1.967669274 1.523428478 1.524285951 1 20.52140776 0.836199498 1.543387993 1.004448723 1.720409708 0.229149483 0.415338904 0.959331507 4.277177195 0.38234203 0.111188176 6.858031861 -0.836199498 0.715960985 S(ph)LS(ph)SSPQAQPPRPAELSDEEVAELFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 S(0.86)LS(0.454)S(0.357)S(0.33)PQAQPPRPAELSDEEVAELFQR 67.198 0.013629 43840000 24190 20487 20776 22683 28446 31526 20360 21710 24316 22493 TRUE FALSE 25145.03988 24005.48288 21317.43963 27169.6297 23610.75908 24204.56428 18764.13 21419.01296 23440.87191 26900.0727 0.934757321 0.892394722 0.792467733 1.010020679 0.877721014 0.899795497 0.697549416 0.796243683 0.871405523 1 14.71532245 2.38691142 23.08061905 0.814517751 0.899793206 0.069163639 0.087800439 18.37528625 4692.617206 0.029224621 0.024451075 243.7313646 -2.38691142 0.085275455 S(ph)LS(ph)SSPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.936)LS(0.559)S(0.459)S(0.046)PVKK 61.353 0.059969 187850000 819330 336730 473720 316670 763440 723710 693320 504740 615760 285990 TRUE FALSE 851677.7811 394560.7581 486065.5324 379306.3808 633670.7415 555639.3204 638975.7667 497974.7859 593598.9179 342024.2649 2.490109236 1.153604579 1.421143417 1.109004301 1.852706976 1.624561113 1.868217645 1.455963325 1.735546214 1 18.38373916 -1.474835474 5.696784035 0.999384646 1.603772933 0.197487706 0.379201308 0.002767094 0.000255087 0.342810146 0.080724161 0.033509236 1.474835474 0.604388286 S(ph)LSDS(ph)ESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 S(0.581)LS(0.421)DS(0.998)ESDDSK 226.85 6.48E-12 172280000 956060 445900 583270 433160 838800 1048300 847330 635380 666430 339330 TRUE FALSE 993805.987 522479.8564 598470.4954 518837.7551 696221.0756 804848.2121 780914.0605 626863.7704 642445.3145 405815.2166 2.448912575 1.287482172 1.474736458 1.278507394 1.715611064 1.983287415 1.92430946 1.544702477 1.58309814 1 18.63046344 0.639752933 1.582856532 1.000989548 1.688353637 0.286544676 0.333654929 1.922417846 6.6706728 0.314046684 0.090193541 4.362675723 -0.639752933 0.687364089 S(ph)LSDSESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.957)LS(0.042)DSESDDSK;S(0.706)LS(0.294)DSESDDSK;S(0.759)LS(0.24)DS(0.001)ESDDSK;S(0.706)LS(0.294)DSESDDSK 317.32 8.03E-46 2575820000 4218920 1965690 2760160 2055850 3551930 4132970 3891260 2732450 3024350 1488450 TRUE FALSE 4385486.219 2303281.967 2832092.037 2462490.994 2948174.207 3173150.353 3586252.873 2695825.977 2915504.234 1780083.279 2.463641039 1.293918095 1.590988506 1.383357185 1.656200157 1.782585337 2.014654547 1.514438121 1.637847099 1 20.76351331 0.468494667 1.396150495 1.000355665 1.693762076 0.310647841 0.316416057 3.220456747 7.19159049 0.286635172 0.084013334 2.94099758 -0.468494667 0.693406412 S(ph)LSFEMQQDELIEKPMSPMQYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSFEMQQDELIEKPMSPMQYAR 23 1 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 S(0.524)LS(0.476)FEMQQDELIEKPMSPMQYAR;S(0.521)LS(0.479)FEMQQDELIEKPMSPMQYAR 98.243 0.0046145 327340000 222447 195079 261050 183814 359110 291340 272910 274350 296950 217599 TRUE FALSE 231229.3793 228582.3007 267853.1775 220171.8606 298068.6105 223680.7003 251518.6011 270672.787 286262.8275 260233.3579 0.888546269 0.878374328 1.029280718 0.846055488 1.145389711 0.859538924 0.966511761 1.040115645 1.100023571 1 17.98944638 6.907813708 0.256189388 1.038984828 0.396934219 0.209602547 0.08859896 43.52565419 0.977419911 0.10695092 10.84094297 8087489.098 -6.907813708 -0.642050609 S(ph)LSGSS(ph)PCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)LSGSS(1)PCPK;S(1)LSGS(0.001)S(0.999)PCPK 262.15 3.11E-17 1043030000 2761600 1737440 2180880 1746730 2986400 3165500 2701300 2341740 2497800 1546090 TRUE FALSE 2870630.1 2035831.805 2237715.524 2092227.981 2478772.795 2430360.599 2489565.047 2310352.806 2407904.666 1849016.734 1.552517102 1.101034819 1.210219185 1.131535449 1.340589703 1.314407033 1.346426456 1.24950346 1.302262236 1 20.81832685 -0.958697436 4.238882449 0.999990173 1.274629746 0.33110155 0.120193128 16543007.5 32125344.82 2463.000674 0.027390004 0.109977176 0.958697436 0.274639573 S(ph)LSGSSPCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.988)LS(0.012)GSSPCPK 150.09 2.33E-05 296570000 290730 231000 295120 241760 346770 357730 351080 285200 313600 256330 TRUE FALSE 302208.2449 270672.4531 302811.0696 289579.4064 287826.1593 274652.629 323561.4322 281377.3605 302313.5973 306552.9558 0.985827209 0.882954961 0.987793671 0.944630939 0.938911708 0.89593861 1.055482996 0.917875216 0.986170877 1 18.22577679 2.282302743 24.99999912 0.978645077 0.939202906 0.222023246 0.04439575 243.0389068 138903.2395 0.014614652 0.012227418 191.5590803 -2.282302743 -0.039442171 S(ph)LSKSDSDLLTCSPTEDATMGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.38)LS(0.328)KS(0.284)DS(0.008)DLLTCSPTEDATMGSR;S(0.326)LS(0.326)KS(0.326)DS(0.023)DLLTCSPTEDATMGSR 102.57 0.0027572 170933000 165636 115536 116750 105972 174914 188470 156295 139406 143854 108995 TRUE FALSE 172175.4372 135378.4093 119792.6009 126932.9453 145182.1808 144700.6988 144044.1895 137537.4906 138676.7226 130350.4834 1.320865352 1.038572361 0.919003887 0.97378193 1.113783217 1.110089468 1.105052975 1.055136022 1.063875783 1 16.99203641 2.979104199 0.008378704 1.93E-05 2.140960516 0.074890792 0.098974722 17564.20906 48.94289789 6080.36703 6423.315713 953.0247922 -2.979104199 2.140941229 S(ph)LSLESTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSLESTDR 9 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 S(0.999)LS(0.001)LESTDR 196.07 3.17E-05 389340000 155240 153560 196040 174710 213010 203860 214840 170790 184350 159560 TRUE FALSE 161368.9951 179932.7355 201148.9634 209267.1165 176802.6363 156516.6045 198000.2794 168500.8394 177715.2795 190822.727 0.845648721 0.94293137 1.05411429 1.096657195 0.926528192 0.820219934 1.037613719 0.883022908 0.931310868 1 17.54187348 S(ph)LSLSLADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.548)LS(0.45)LS(0.001)LADSGHLPDVHGFNSYGSHR;S(0.988)LS(0.011)LS(0.001)LADSGHLPDVHGFNSYGSHR;S(0.847)LS(0.153)LSLADSGHLPDVHGFNSYGSHR 282.21 4.02E-53 3569600000 153662 459440 448972 475690 592920 579920 335855 495750 423404 525690 TRUE FALSE 159728.6944 538345.2461 460672.5792 569780.0622 492135.6702 445242.3688 309529.8075 489105.2821 408165.7727 628688.8906 0.254066354 0.856298328 0.732751264 0.906298919 0.782796829 0.708207788 0.49234178 0.777976658 0.649233315 1 19.26198674 -2.478197459 2.036447615 3.838092988 0.698603351 0.212594452 0.18034593 5225433.213 380093.4575 68386304.97 0.041744895 0.003325083 2.478197459 -3.139489637 S(ph)LSPILPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.588)LS(0.412)PILPGR;S(0.84)LS(0.16)PILPGR;S(0.673)LS(0.327)PILPGR;S(0.673)LS(0.327)PILPGR 98.044 0.0065882 960910000 266434 349489 317322 305675 345785 383793 322575 305060 297133 327193 TRUE FALSE 276953.0201 409511.0171 325591.672 366136.6027 287008.5892 294662.8922 297290.7286 300971.1697 286439.2414 391300.2039 0.707776324 1.046539238 0.832076418 0.935692338 0.733474162 0.753035366 0.759751019 0.76915669 0.732019147 1 18.57791634 3.237063668 24.99999712 0.775357396 0.88891919 0.128136715 0.108606011 59.46562028 993121.6505 0.028094114 0.03532523 1726.090922 -3.237063668 0.113561794 S(ph)LSPSHLTEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.622)LS(0.375)PS(0.003)HLTEDR 220.69 5.77E-12 102800000 76889 124290 113920 112550 114070 147060 96577 122990 114640 158540 TRUE FALSE 79924.63709 145635.8407 116888.8488 134812.0541 94680.42214 112907.5437 89007.04238 121341.5202 110514.1288 189602.8776 0.421537047 0.768109865 0.61649301 0.711023249 0.499361736 0.595494885 0.469439301 0.639977208 0.58287158 1 17.53262133 -1.222446452 3.080875111 1.00161632 0.594653007 0.599942173 0.10051275 14300830.5 19798008.62 223175.3672 0.023634994 0.059917481 1.222446452 -0.406963314 S(ph)LSPVFNHTMVYDGFGPADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSPVFNHTMVYDGFGPADLR 21 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 S(0.498)LS(0.498)PVFNHT(0.004)MVYDGFGPADLR 103.14 0.0002867 51504000 14266 43407 40144 42562 37321 54447 36060 49862 41822 60265 TRUE FALSE 14829.2327 50861.81459 41190.18562 50980.63657 30977.18975 41802.5094 33233.52297 49193.68145 40316.83439 72072.77291 0.205753603 0.705700815 0.571508268 0.707349454 0.429804328 0.580004178 0.461110647 0.682555693 0.559390638 1 16.13716673 -4.999999915 0.242664049 3.584725353 0.513435903 0.491449215 0.141753225 143.6076695 1.430535024 183.2234157 0.20323437 1.00E-05 4.999999915 -3.07128945 S(ph)LSS(ph)SPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(0.995)LS(0.257)S(0.714)S(0.034)PVKK 122.34 0.0020592 513810000 2228800 920110 1397900 832670 1921500 1885100 1816600 1251200 1488600 712340 TRUE FALSE 2316794.745 1078131.735 1434330.422 997369.6407 1594884.116 1447314.094 1674210.145 1234429.711 1435025.577 851909.3844 2.719531898 1.265547434 1.68366548 1.17074616 1.872128827 1.698906152 1.965244398 1.449015275 1.684481475 1 19.70034046 -2.522107348 0.256264319 5.19E-15 1.772936226 0.234502932 0.404525471 68.49332799 2.090273117 39.50252747 0.552405624 0.003005333 2.522107348 1.772936226 S(ph)LSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.998)LS(0.002)SLR;S(1)LSSLR;S(0.999)LS(0.001)SLR;S(1)LSSLR;S(1)LSSLR 171.38 0.0057134 1187556000 518358 495265 627683 636535 680281 740556 663306 601137 593712 542796 TRUE FALSE 538823.1741 580322.9111 644040.9346 762439.7231 564647.0786 568573.0922 611314.3425 593079.7418 572344.4211 649146.4837 0.830048668 0.893978363 0.992134981 1.174526462 0.869829989 0.875877951 0.941720178 0.913630061 0.881687624 1 19.30818454 S(ph)LSSS(ph)PVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 S(1)LS(0.053)S(0.152)S(0.795)PVKK 111.79 0.0072341 771700000 1974500 765330 1151000 699250 1743800 1632400 1500400 1099200 1261900 582050 TRUE FALSE 2052454.785 896769.4741 1180996.006 837559.5629 1447389.499 1253299.839 1382794.727 1084467.022 1216484.465 696091.5535 2.94854143 1.288292423 1.696610165 1.203231901 2.079309096 1.80048132 1.986512723 1.557937338 1.747592625 1 19.40891754 -2.310485723 0.274982549 6.27E-12 1.857132305 0.23267315 0.456358632 61.6511857 2.212198411 38.85241328 0.539918629 0.004892313 2.310485723 1.857132305 S(ph)LSTSGESLYHVLGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.41)LS(0.41)T(0.054)S(0.054)GES(0.072)LYHVLGLDK;S(0.555)LS(0.426)T(0.005)S(0.006)GES(0.008)LYHVLGLDK 168.09 1.38E-09 209990000 183551 260910 274330 347730 360690 405180 372820 301820 277910 252670 TRUE FALSE 190797.7352 305719.2629 281479.2652 416509.9561 299380.0426 311083.0856 343597.3942 297774.5966 267908.0734 302175.8488 0.63141292 1.011726331 0.931508147 1.378369442 0.990747751 1.029476997 1.137077617 0.985434798 0.886596578 1 18.20502883 4.907794699 1.989672481 1.052886172 0.352828547 0.47173192 0.129332115 1.174202664 3.361496852 0.032400721 1.743680049 80871.35116 -4.907794699 -0.700057624 S(ph)LSTSGESLYHVLGLDKNATSDDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSTSGESLYHVLGLDKNATSDDIKK 26 2 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.507)LS(0.428)T(0.05)S(0.006)GES(0.01)LYHVLGLDKNATSDDIKK 168.22 4.53E-12 336490000 247820 171570 262390 143370 455410 344270 264230 241480 262400 195870 TRUE FALSE 257604.125 201035.8129 269228.099 171728.1581 377999.5709 264318.51 243518.9622 238243.3556 252956.2753 234246.9763 1.099711633 0.858221592 1.149334361 0.733107256 1.613679616 1.128375333 1.039582094 1.017060537 1.07986997 1 17.8376709 7.576843457 7.961530297 1.072146854 1.158834151 0 0.217533618 0 0 0.046201508 0 37743611.83 -7.576843457 0.086687297 S(ph)LSVEHLETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.795)LS(0.205)VEHLETK 156.36 7.13E-06 535350000 1427800 1261100 1301200 1181900 1731600 1820600 1606500 1345800 1373400 1015900 TRUE FALSE 1484170.647 1477684.115 1335110.341 1415676.292 1437263.251 1397793.241 1480578.332 1327761.752 1323971.602 1214946.154 1.221593765 1.216254819 1.098904948 1.165217312 1.182985143 1.150498099 1.218636996 1.092856459 1.089736856 1 20.21246095 1.184009205 1.277205408 1.004607805 1.176156321 0.680555618 0.038810809 0.238582438 0.777876909 0.03615792 0.0113544 15.27598436 -1.184009205 0.171548516 S(ph)LTAHSLLPLAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLTAHSLLPLAEK 13 0 F2Z2E2;Q86VI3 F2Z2E2 IQGAP3 Ras GTPase-activating-like protein IQGAP3 1 S(0.492)LT(0.37)AHS(0.138)LLPLAEK;S(0.492)LT(0.492)AHS(0.017)LLPLAEK;S(0.62)LT(0.301)AHS(0.079)LLPLAEK 141.55 2.57E-05 504834000 806270 717170 896300 799600 1182590 1222770 1074570 895610 944730 780280 TRUE FALSE 838102.1622 840338.3687 919658.3143 957758.4934 981573.7742 938800.1988 990342.3955 883605.8129 910729.3518 933160.9266 0.898132507 0.900528885 0.985530242 1.026359405 1.051880492 1.006043194 1.061277179 0.946895426 0.975961729 1 19.83176637 4.18382188 3.684175583 1.008420675 0.896695321 0.654945711 0.031569952 0.137845443 3.758110404 0.008700123 0.022521032 15269.39676 -4.18382188 -0.111725355 S(ph)LTNSHLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 S(0.977)LT(0.018)NS(0.006)HLEK;S(0.996)LT(0.004)NSHLEK;S(0.976)LT(0.014)NS(0.011)HLEK;S(0.988)LT(0.012)NSHLEK 153.81 4.97E-05 1821720000 1375900 1372320 1370920 1403550 1849110 2030060 1785060 1444450 1530110 1384560 TRUE FALSE 1430221.594 1608005.285 1406647.301 1681168.001 1534798.943 1558609.331 1645142.333 1425089.51 1475041.64 1655838.023 0.863744868 0.971112671 0.849507791 1.015297377 0.926901618 0.941281278 0.993540618 0.86064548 0.89081276 1 20.65913012 4.76208218 22.84157089 0.933006216 0.863744613 0.135293552 0.055200193 4178.811661 4057792.112 0.012660532 0.6245411 57820.5449 -4.76208218 -0.069261603 S(ph)LTPAVPVESKPDKPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 S(0.999)LT(0.001)PAVPVESKPDKPSGK;S(1)LTPAVPVESKPDKPSGK 233.68 4.97E-24 1071550000 2397850 902570 1769410 1043120 2149840 1837310 2330790 1454960 2097320 680310 TRUE FALSE 2492518.97 1057579.376 1815522.278 1249446.023 1784410.965 1410622.597 2148096.589 1435458.641 2021837.863 813603.7192 3.063554051 1.299870381 2.231457693 1.535693598 2.19321879 1.73379566 2.640224643 1.764321631 2.485040094 1 19.63396675 -1.961628773 2.558166583 0.153518933 2.061297411 0.29251019 0.511573386 34447502.85 29326694.8 173963508.4 0.114382362 0.010923737 1.961628773 1.907778479 S(ph)LTRS(ph)PPAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLTRSPPAIR 10 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.994)LT(0.016)RS(0.99)PPAIR;S(0.982)LT(0.019)RS(0.999)PPAIR 103.13 0.0016243 281560000 303090 253090 291280 298410 312730 400790 336980 298030 343570 280130 TRUE FALSE 315056.2272 296556.2387 298870.9961 357434.6073 259572.2663 307712.5965 310566.6271 294035.3953 331204.9828 335016.1101 0.940421125 0.885199935 0.892109326 1.066917669 0.774805326 0.918500894 0.927019978 0.877675391 0.988624048 1 18.35387095 1.182791841 8.137936739 0.995865692 0.909182537 0.196103105 0.067997992 0.450379071 57.03638928 0.060843626 0.015363204 15.23322443 -1.182791841 -0.086683156 S(ph)LTSCSSDITLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLTSCSSDITLR 12 0 E9PMS6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.798)LT(0.014)S(0.064)CS(0.019)S(0.105)DITLR;S(0.422)LT(0.084)S(0.084)CS(0.168)S(0.243)DITLR 134.18 0.00015733 140398000 198128 199352 220431 209162 255500 264480 220490 213890 230901 214800 TRUE FALSE 205950.2464 233589.1553 226175.6129 250533.6193 212070.2013 203058.5282 203207.4177 211023.1544 222590.9181 256885.9474 0.801718617 0.909310757 0.880451481 0.975271796 0.825542243 0.790461799 0.791041393 0.821466322 0.86649706 1 17.97076845 4.782713517 21.54641156 0.861531868 0.801717376 0.065845424 0.069062281 15026.38159 7331796.652 0.016861029 5.494446196 60633.62275 -4.782713517 -0.059814491 S(ph)LVGTPYWMAPELISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 21 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(0.999)LVGT(0.001)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(0.905)LVGT(0.095)PYWMAPELISR;S(0.997)LVGT(0.003)PYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR;S(1)LVGTPYWMAPELISR 418.24 1.02E-140 17166490600 2166589.5 2265975.3 2487573.1 2510048.5 2822236.5 3036418.8 2628464.8 2568997.8 2413126 2345658.5 TRUE FALSE 2252128.126 2655138.931 2552401.299 3006528.602 2342513.748 2331256.551 2422438.861 2534564.587 2326278.067 2805245.373 0.802827499 0.946490798 0.909867395 1.07175245 0.835047718 0.831034808 0.863539027 0.903509052 0.829260103 1 21.41969554 S(ph)MAHSPGPVSQASPGTSSAVLFLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMAHSPGPVSQASPGTSSAVLFLSK 25 0 Q8TDZ2-2;Q8TDZ2;Q8TDZ2-4;H0Y6Z4 Q8TDZ2-2 MICAL1 Protein-methionine sulfoxide oxidase MICAL1 1 S(0.51)MAHS(0.477)PGPVS(0.01)QAS(0.002)PGTSSAVLFLSK 58.398 0.011044 0 23338 26897 27086 26685 37143 37360 30799 34995 33190 28706 TRUE FALSE 24259.40226 31516.35052 27791.88341 31963.21335 30829.44613 28683.7062 28384.8939 34525.94927 31995.49838 34330.39109 0.706645089 0.918030629 0.809541707 0.931047167 0.89802199 0.835519354 0.826815338 1.005696357 0.931987588 1 15.06719867 7.999999999 0.121091632 1.043251473 0.237652556 0.461887804 0.064245019 87.43779128 0.725839634 0.419794392 11.90688761 99999999.75 -7.999999999 -0.805598917 S(ph)MDELNHDFQALALEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 264.63 1.12E-27 570201000 175526 198456 242657 204840 252311 276706 240502 240216 224188 225862 TRUE FALSE 182455.902 232539.2742 248980.8408 245356.7406 209423.2663 212445.225 221650.8248 236996.2974 216119.5177 270115.3345 0.675474061 0.86088883 0.92175752 0.908340658 0.775310542 0.786498202 0.820578458 0.877389275 0.800100883 1 18.04321602 -2.306109984 2.152236088 1.76537461 0.832115327 0.361993929 0.069083926 3499274.916 494039.2622 13016018.79 0.018892856 0.004941855 2.306109984 -0.933259284 S(ph)MDLGIADETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SMDLGIADETK 11 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(1)MDLGIADETK;S(1)MDLGIADETK;S(1)MDLGIADETK 183.06 7.15E-06 310093000 566920 371750 449840 346700 651030 667850 618030 488310 538980 322709 TRUE FALSE 589302.4394 435595.1707 461563.1999 415276.2252 540368.1531 512751.9589 569587.1937 481765.0032 519582.2151 385937.6499 1.526936902 1.12866721 1.195952766 1.076018951 1.400143659 1.328587555 1.475852884 1.248297499 1.346285378 1 18.55800827 3.210133334 24.99832183 1.32093685 1.221953088 0.029621327 0.162154549 551.16481 484680.7762 0.044426053 0.053107975 1622.308089 -3.210133334 -0.098983761 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 S(0.743)MDS(0.128)S(0.128)DLSDGAVTLQEYLELKK;S(0.987)MDS(0.013)SDLSDGAVTLQEYLELKK;S(0.98)MDS(0.018)S(0.002)DLSDGAVTLQEYLELKK;S(0.997)MDS(0.003)S(0.001)DLSDGAVTLQEYLELKK;S(0.96)MDS(0.032)S(0.007)DLSDGAVTLQEYLELKK 173.59 2.19E-12 367204000 440005 216846 345049 223762 478435 378117 406298 331761 360944 192186 TRUE FALSE 457376.7372 254087.6137 354041.2604 268021.4557 397110.7896 290305.0572 374451.3011 327314.2864 347953.6959 229841.1671 1.989968738 1.105492184 1.540373576 1.166115971 1.727761805 1.263068148 1.629174207 1.424089038 1.513887614 1 17.8102777 -1.245896982 3.738418345 0.999292813 1.469071929 0.246419147 0.252866093 56609109.27 118836613.3 492262.7156 0.053441375 0.056767925 1.245896982 0.469779115 S(ph)MFDLTNSSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMFDLTNSSQR 11 0 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 S(0.996)MFDLT(0.004)NSSQR 77.204 0.034884 75227000 38673 49890 44511 45013 69305 53891 50386 41685 48276 46312 TRUE FALSE 40199.8399 58458.21941 45670.99323 53916.43705 57524.56086 41375.63198 46436.61366 41126.28076 46538.55619 55385.9497 0.725812956 1.0554702 0.824595289 0.973467772 1.038612882 0.747042024 0.838418659 0.742539958 0.840259243 1 15.75723242 2.724116369 24.79801427 0.8121532 0.928189483 0.122136402 0.113129826 1116.816902 1917358.382 0.034066775 0.032250581 529.8053864 -2.724116369 0.116036283 S(ph)MGETESGDAFLDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SMGETESGDAFLDLK 15 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5;B1AKL6 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.994)MGET(0.005)ESGDAFLDLK;S(1)MGETESGDAFLDLK;S(1)MGETESGDAFLDLK;S(1)MGETESGDAFLDLK 265.16 3.65E-25 114742000 198380 127125 167032 126540 215991 217082 228930 174137 193137 112994 TRUE FALSE 206212.1956 148957.7299 171384.9911 151569.2343 179276.927 166667.9954 210985.8684 171802.9783 186186.0371 135133.0109 1.525994235 1.102304528 1.268268871 1.121629965 1.326670114 1.233362554 1.561319969 1.271362025 1.377798333 1 17.04402062 S(ph)MGNLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMGNLLEK 8 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 S(1)MGNLLEK;S(1)MGNLLEK 92.866 0.012036 429822000 324250 305120 352820 288910 434710 416170 387730 346870 337840 251990 TRUE FALSE 337051.6404 357521.9865 362014.779 346055.5357 360818.1495 319520.8246 357338.7095 342220.775 325681.2044 301362.6159 1.11842552 1.186351484 1.201259745 1.1483028 1.197289015 1.060253687 1.185743323 1.135578061 1.080695439 1 18.20114094 0.674687509 0.624725418 0.995263763 1.165511685 0.589622583 0.040800593 0.862252828 0.662039256 0.044162828 0.016306605 4.728109319 -0.674687509 0.170247922 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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(0.997)MGY(0.003)DDLDYGMMSDYGTAR;S(0.924)MGY(0.076)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.953)MGY(0.046)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.808)MGY(0.192)DDLDYGMMSDYGTAR;S(0.998)MGY(0.002)DDLDYGMMSDYGTAR;S(0.98)MGY(0.02)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR;S(0.92)MGY(0.08)DDLDYGMMSDYGTAR;S(1)MGYDDLDYGMMSDYGTAR 382.37 1.06E-109 6543758000 1987798 2360342 2189619 2231638 2650959 2945849 2301080 2324656 2119450 2240129 TRUE FALSE 2066277.8 2765712.378 2246682.27 2673049.336 2200349.936 2261720.215 2120715.337 2293497.789 2043171.409 2679039.388 0.771275633 1.032352264 0.838614871 0.997764105 0.821320488 0.844228056 0.79159543 0.856089612 0.762650754 1 21.35328436 3.188518387 24.99996081 0.836340748 0.913642713 0.101179235 0.090532049 190.8376991 95337.42768 0.023642781 0.028258576 1543.541772 -3.188518387 0.077301965 S(ph)MPVLGSVSSVTK ddPTM_MDA-MB-175_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(0.997)MPVLGS(0.002)VS(0.001)SVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK;S(1)MPVLGSVSSVTK 201.06 1.10E-07 2462579000 2863881 2412801 3225928 2555706 4610048 3663419 3198615 3335968 3567696 2903124 TRUE FALSE 2976949.233 2827180.803 3309998.334 3061217.019 3826433.688 2812645.457 2947899.198 3291254.806 3439295.318 3471935.564 0.857432167 0.814295297 0.953358227 0.881703293 1.102103889 0.810108772 0.849065066 0.947959645 0.990598833 1 21.72730874 8 0.117052292 1.013886604 0.526787484 0.173361792 0.081371228 197.5760239 1.595310733 0.606366468 15.65666738 100000000 -8 -0.48709912 S(ph)MSAPSDLEMIGNEDLEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.5)MS(0.5)APS(0.001)DLEMIGNEDLEFTR 151.63 2.88E-07 15826000 34863 23740 29102 23637 39435 46021 35873 28232 30638 24190 TRUE FALSE 36239.41816 27817.16033 29860.42203 28312.32805 32731.85279 35333.32021 33061.18052 27853.59622 29535.34436 28929.56735 1.252677502 0.961547748 1.032176585 0.978664067 1.131432502 1.221356675 1.142816279 0.962807216 1.020939719 1 14.82025713 1.723241272 10.06874563 0.995165801 1.095626296 0.229442743 0.09024255 0.170568224 54.29486141 0.044945367 0.024323641 52.87389107 -1.723241272 0.100460495 S(ph)MSDVSAEDVQNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SMSDVSAEDVQNLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.998)MS(0.002)DVSAEDVQNLR;S(1)MSDVSAEDVQNLR;S(0.999)MS(0.001)DVSAEDVQNLR;S(0.999)MS(0.001)DVSAEDVQNLR;S(0.969)MS(0.031)DVSAEDVQNLR;S(1)MSDVSAEDVQNLR;S(0.816)MS(0.184)DVSAEDVQNLR 353.49 5.46E-82 4270780000 2089493 2154482 2137692 2353263 2278304 2729474 2473833 2280067 2181167 1814712 TRUE FALSE 2171987.797 2524497.524 2193402.01 2818731.398 1891038.7 2095595.029 2279927.505 2249506.431 2102667.226 2170270.072 1.00079148 1.163218144 1.010658553 1.298792917 0.871337961 0.96559182 1.050527091 1.036509908 0.968850492 1 21.04944315 3.218083502 24.99982022 0.991414095 1.113875869 0.350953962 0.090148138 287.1889607 350618.3724 0.025219913 0.030176137 1652.279453 -3.218083502 0.122461774 S(ph)MSGGHGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSGGHGLR 9 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.719)MS(0.281)GGHGLR 82.417 0.062009 101990000 20746 46021 30569 29802 41573 41100 29463 33974 26402 45582 TRUE FALSE 21565.0681 53924.74876 31365.65325 35696.74665 34506.43631 31555.14788 27153.61307 33518.6341 25451.79718 54512.92018 0.39559554 0.989210422 0.575380169 0.654830938 0.632995558 0.578856311 0.498113346 0.614875042 0.466894767 1 15.73431059 -1.24934056 5.18056509 1.000050462 0.609330203 0.385743261 0.150794862 8.20E-05 1.19E-05 0.13627819 0.032116941 0.056319584 1.24934056 -0.390720259 S(ph)MSIDDTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.987)MS(0.013)IDDTPR;S(0.999)MS(0.001)IDDTPR;S(0.991)MS(0.009)IDDTPR 256.24 5.87E-15 776990000 796700 777110 845730 776170 1057330 1120270 789240 907720 878270 899180 TRUE FALSE 828154.3312 910572.5974 867770.4186 929694.1094 877605.4243 860104.2704 727377.3065 895553.4981 846661.2343 1075357.105 0.770120295 0.84676299 0.806960232 0.864544536 0.816106036 0.799831299 0.676405357 0.832796374 0.787330302 1 20.0363844 -1.013778725 4.950906115 1.000002333 0.80092712 0.599016854 0.049062566 1.41E-06 2.81E-07 0.047499258 0.011195536 0.096877132 1.013778725 -0.199075213 S(ph)MSVDLSHIPLKDPLLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.5)MS(0.5)VDLSHIPLKDPLLFK;S(0.568)MS(0.432)VDLSHIPLKDPLLFK 181.14 4.53E-14 633650000 2157460 1766440 2356060 1623420 3164780 2389920 2327360 1973650 2522620 1547500 TRUE FALSE 2242638.187 2069812.329 2417460.859 1944527.631 2626831.826 1834897.3 2144935.442 1947196.45 2431831.399 1850702.996 1.211776385 1.118392488 1.306239231 1.050696754 1.419369737 0.991459625 1.158984151 1.052138811 1.31400414 1 20.81964196 2.688122877 24.99990074 1.106588047 1.210820807 0.175968153 0.126541753 685.6494394 339847.0531 0.037799799 0.035638032 487.6664489 -2.688122877 0.104232759 S(ph)MVWPGDGLVPDTAEPHVAPSPTLPSTEDVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 211.59 9.55E-28 427032000 18566.4 21676.1 20532 21560.6 22400.6 32172.3 24520.5 23595.8 20646.1 20784.8 TRUE FALSE 19299.41581 25398.80156 21067.08079 25825.22233 18592.95401 24700.7709 22598.51914 23279.5369 19903.05089 24857.18361 0.776412007 1.021789192 0.847524849 1.038944022 0.747991176 0.993707545 0.909134337 0.936531558 0.800696137 1 14.60137522 S(ph)NENLDKIDMSLDDIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNENLDKIDMSLDDIIK 17 1 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK;S(1)NENLDKIDMSLDDIIK 186.55 3.13E-10 101194000 240877 88783 148231 77279 223352 197258 184877 134919 162752 54627 TRUE FALSE 250387.01 104030.7896 152094.0216 92564.55555 185386.7068 151447.819 170385.8577 133110.6315 156894.5873 65330.11475 3.832643045 1.592386452 2.32808441 1.416874222 2.837691431 2.318193065 2.608075285 2.037508001 2.401566076 1 15.99546055 -1.750721322 0.509549371 2.35E-08 2.345081973 0.294112178 0.636796229 71.59631037 6.861491412 88.27778018 0.272837687 0.017753283 1.750721322 2.345081949 S(ph)NFSNSADDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNFSNSADDIK 11 0 P45973 P45973 CBX5 Chromobox protein homolog 5 1 S(1)NFSNSADDIK;S(0.999)NFSNSADDIK 150.05 3.57E-05 55071000 161527 116985 122242 96891 165472 181071 140004 130763 138605 99998 TRUE FALSE 167904.2107 137076.2637 125427.7269 116055.7506 137345.1285 139020.0044 129030.1206 129010.3359 133616.6331 119590.6935 1.403990609 1.146211797 1.048808425 0.970441321 1.148460006 1.162465074 1.078931118 1.07876568 1.117282869 1 16.8677456 4.716376068 3.016805922 1.080770124 1.447887328 0.747682256 0.057047746 0.173685765 2.410665398 0.014299744 0.149089574 52044.64711 -4.716376068 0.367117204 S(ph)NGDLSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNGDLSPK 8 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 S(0.999)NGDLS(0.001)PK;S(1)NGDLSPK 147.72 0.0005588 759550000 2050860 1262010 1565740 1328460 2096140 2240760 2278550 1688530 1740560 1015180 TRUE FALSE 2131829.536 1478750.4 1606544.471 1591225.423 1739838.872 1720377.449 2099951.297 1665898.017 1677917.586 1214085.084 1.755914445 1.21799569 1.323255257 1.310637486 1.433045257 1.417015555 1.729657439 1.372142726 1.38204283 1 20.2114381 0.669788291 2.210954097 1.000203047 1.437815461 0.396330127 0.16380641 1.908927536 11.43795481 0.153106272 0.04159092 4.675071863 -0.669788291 0.437612414 S(ph)NLDITVGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNLDITVGSR 10 0 P42356;P42356-2 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 S(1)NLDITVGSR 143.18 3.61E-05 126460000 44165 53691 65555 62413 68576 68870 63404 56724 63265 61389 TRUE FALSE 45908.6683 62912.01159 67263.41715 74758.10512 56919.47601 52875.98623 58434.2288 55963.70756 60988.10501 73416.99919 0.625313876 0.856913416 0.916183144 1.018266967 0.775290146 0.720214485 0.795922327 0.762271792 0.830708224 1 16.16382653 S(ph)NPSIQATLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNPSIQATLNK 11 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 S(0.981)NPS(0.019)IQATLNK 86.498 0.015132 40939000 69781 67997 77828 72883 95194 106430 72412 71407 73012 83640 TRUE FALSE 72536.00776 79674.95581 79856.26162 87299.03987 79012.95788 81713.24546 66736.15823 70449.90596 70384.31238 100027.6566 0.725159523 0.796529265 0.798341822 0.872749026 0.789911116 0.816906526 0.667177064 0.704304273 0.703648518 1 16.61003942 2.282157362 24.9983635 0.73712387 0.802560182 0 0.093558263 305.5763321 175216.1221 0.030351367 0.025393648 191.494966 -2.282157362 0.065436312 S(ph)NSAPLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 292.77 4.47E-63 6833200000 659292 740833 834477 776712 1082727 1126863 990627 897320 845185 849999 TRUE FALSE 685321.3572 868065.3049 856224.1562 930343.3153 898685.4513 865166.146 912979.0672 885292.8931 814766.9569 1016540.03 0.674170556 0.853941094 0.842292611 0.915205784 0.884063023 0.851089107 0.898124068 0.870888373 0.801509958 1 19.9552356 5.09466401 1.572309267 0.880133215 0.381076243 0.612977084 0.049446899 1.819585491 2.038060342 0.011932429 1.831807048 124355.2169 -5.09466401 -0.499056972 S(ph)NSDNNLNASAPDWAVCSTATSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.649)NS(0.351)DNNLNASAPDWAVCSTATSHR;S(0.5)NS(0.5)DNNLNASAPDWAVCSTATSHR 247.32 3.76E-38 209230000 57789 65242 70703 66247 65612 98312 75557 66756 72072 60335 TRUE FALSE 60070.55434 76446.80599 72545.57826 79350.45887 54459.29568 75480.52793 69634.64491 65861.24501 69478.1428 72156.48807 0.832503853 1.059458519 1.005392311 1.09969957 0.754738723 1.046067096 0.965050362 0.912755689 0.962881435 1 16.1388415 S(ph)NSDVTISDIDAEDVLDQNAVNPNTGAALHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSDVTISDIDAEDVLDQNAVNPNTGAALHR 31 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.5)NS(0.5)DVTISDIDAEDVLDQNAVNPNTGAALHR;S(0.499)NS(0.499)DVT(0.002)ISDIDAEDVLDQNAVNPNTGAALHR 95.097 0.00025621 2589400000 138261 256734 227920 258055 220814 345000 244225 270306 228101 326765 TRUE FALSE 143719.651 300826.0674 233859.7824 309097.5088 183280.1152 264878.9785 225082.0063 266682.9902 219891.6896 390788.3455 0.367768519 0.769792833 0.598430801 0.790958872 0.469000975 0.67780675 0.575969086 0.68242309 0.562687429 1 18.57602792 -1.888579703 2.27576573 1.211218319 0.621125453 0.472599794 0.122970041 5245243.146 2586612.152 5947308.937 0.027864839 0.012924695 1.888579703 -0.590092867 S(ph)NSGRELTDEEILASVMIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.511)NS(0.353)GRELT(0.136)DEEILASVMIK;S(0.613)NS(0.383)GRELT(0.004)DEEILASVMIK;S(0.498)NS(0.498)GRELT(0.003)DEEILASVMIK;S(0.333)NS(0.333)GRELT(0.333)DEEILASVMIK;S(0.497)NS(0.497)GRELT(0.005)DEEILASVMIK;S(0.492)NS(0.492)GRELT(0.016)DEEILASVMIK;S(0.499)NS(0.499)GRELT(0.002)DEEILASVMIK;S(0.498)NS(0.498)GRELT(0.004)DEEILASVMIK;S(0.493)NS(0.493)GRELT(0.014)DEEILASVMIK;S(0.344)NS(0.344)GRELT(0.313)DEEILASVMIK;S(0.457)NS(0.457)GRELT(0.086)DEEILASVMIK;S(0.507)NS(0.484)GRELT(0.009)DEEILASVMIK;S(0.483)NS(0.483)GRELT(0.034)DEEILASVMIK;S(0.497)NS(0.497)GRELT(0.005)DEEILASVMIK;S(0.499)NS(0.499)GRELT(0.002)DEEILASVMIK;S(0.627)NS(0.373)GRELTDEEILASVMIK;S(0.383)NS(0.383)GRELT(0.233)DEEILASVMIK 240.75 1.49E-24 2456756000 3098713 2623466 3345725 2234400 4332921 3994049 3389440 3207156 3648915 2668209 TRUE FALSE 3221052.582 3074025.878 3432917.342 2676357.651 3596412.636 3066491.65 3123766.836 3164169.32 3517591.262 3190993.468 1.009419986 0.96334446 1.075814594 0.838722385 1.127051081 0.960983368 0.978932382 0.991593794 1.102349879 1 21.60557422 1.283992642 24.49232715 1.051175011 0.992477787 0.087110726 0.074996944 204.5645358 110280.0577 0.045307113 0.016544862 19.23059148 -1.283992642 -0.058697224 S(ph)NSLDKHQQSSTLGNSVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNSLDKHQQSSTLGNSVVR 19 1 A0A0A0MSY4;Q9BZ29-5;X6RGR3;Q6ZSL5;A0A088AWN3;Q9BZ29-3;Q9BZ29;Q9BZ29-4 A0A0A0MSY4 DOCK9 Dedicator of cytokinesis protein 9 1 S(0.585)NS(0.415)LDKHQQSSTLGNSVVR;S(0.643)NS(0.357)LDKHQQSSTLGNSVVR;S(0.639)NS(0.361)LDKHQQSSTLGNSVVR 254.33 4.05E-31 1113400000 860250 695860 950340 786440 1225260 1222410 1019550 973130 981580 628150 TRUE FALSE 894213.3343 815368.542 975106.6411 941995.4847 1016990.743 938523.8033 939635.0069 960086.7841 946253.1275 751223.9658 1.190341862 1.085386754 1.298023872 1.253947594 1.353778353 1.249326228 1.250805418 1.278030025 1.259615202 1 19.51888356 -2.293194881 2.058093885 8.60E-05 1.249153125 0.550791979 0.066769799 1305998.468 183960.0632 6068124.403 0.016930128 0.005091024 2.293194881 1.249067161 S(ph)NSLPHSAVSNAGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.682)NS(0.318)LPHSAVSNAGSK 245.66 2.63E-18 395360000 454440 434220 612180 460210 758930 742230 680540 640770 652680 430450 TRUE FALSE 472381.6421 508793.9072 628133.9137 551238.1644 629927.3497 569858.3311 627197.4965 632181.5262 629190.1743 514788.436 0.91762287 0.988355355 1.220178756 1.070805259 1.223662588 1.106975781 1.218359723 1.228041428 1.222230591 1 18.97362012 4.351418495 4.555729545 1.172120308 0.933907515 0.548267668 0.075997686 0.130120262 4.458347592 0.01764666 0.052420329 22460.45217 -4.351418495 -0.238212792 S(ph)NSPPALGPEACPVSLPSPPEASTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSPPALGPEACPVSLPSPPEASTLK 26 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(0.5)NS(0.5)PPALGPEACPVSLPSPPEASTLK;S(0.5)NS(0.5)PPALGPEACPVSLPSPPEASTLK 132.35 3.62E-05 127566000 298470 217520 275480 222100 353410 365980 333690 291850 309840 164840 TRUE FALSE 310253.8261 254877.3679 282659.2351 266030.7171 293337.4944 280986.6915 307534.5059 287938.2281 298688.9189 197137.2419 1.573796118 1.292893039 1.433819568 1.34946961 1.487986194 1.42533541 1.560002072 1.460597832 1.515131874 1 17.58884082 -1.191654547 6.327846839 0.999996531 1.452169352 0.730862652 0.082892754 3.90E-06 4.98E-07 0.077096648 0.018171715 0.064319914 1.191654547 0.452172821 S(ph)NVCINGNHVYLEQPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVCINGNHVYLEQPEAK 18 0 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(1)NVCINGNHVYLEQPEAK 123.29 2.21E-05 228070000 93188 78953 104970 99582 163480 148160 92330 84497 101480 86570 TRUE FALSE 96867.1342 92512.56358 107705.6044 119279.0224 135691.728 113752.0854 85092.93334 83364.45592 97827.75462 103531.734 0.935627468 0.893567218 1.040314889 1.152101078 1.310629338 1.098717089 0.821901943 0.805206797 0.94490598 1 16.65971352 2.242441312 24.99931732 0.86714371 1.076794738 0.337292883 0.120516533 109.5775236 705899.5443 0.047933759 0.038699871 174.7597087 -2.242441312 0.209651028 S(ph)PAFALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPAFALK 7 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 S(1)PAFALK;S(1)PAFALK;S(1)PAFALK;S(1)PAFALK 83.614 0.023235 877480000 1508340 1273150 1378000 1190480 1723280 1716550 1491870 1397400 1389900 1314990 TRUE FALSE 1567890.428 1491803.609 1413911.812 1425953.391 1430357.481 1317907.277 1374933.331 1378670.139 1339877.771 1572637.113 0.996981703 0.948600027 0.899070612 0.906727546 0.909527995 0.838023766 0.874285186 0.876661327 0.851994245 1 20.58475438 4.850390058 0.895526342 0.882481121 1.08258498 0.36802476 0.042229283 2.34144143 1.287059223 0.012755145 0.480713072 70858.19064 -4.850390058 0.200103859 S(ph)PAFRGPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPAFRGPDR 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(1)PAFRGPDR;S(1)PAFRGPDR;S(1)PAFRGPDR 101.89 0.0022275 992440000 135039 159834 164145 151466 197954 186032 158463 156173 163451 216582 TRUE FALSE 140370.444 187284.2462 168422.7535 181425.5227 164305.8498 142828.8873 146042.256 154079.7564 157568.4304 259017.0962 0.541935054 0.72305747 0.650237981 0.700438409 0.634343648 0.551426487 0.563832497 0.594863268 0.608332163 1 17.9826878 -1.524997539 3.21177453 1.01134628 0.619383662 0.798968202 0.057375694 31107748.45 40053644.44 3106206.81 0.014509844 0.029853995 1.524997539 -0.391962618 S(ph)PAGGESATVAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPAGGESATVAAK 13 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 S(1)PAGGESATVAAK 219.97 2.26E-11 210070000 135570 100340 123590 123760 139980 157060 194660 141920 142020 80040 TRUE FALSE 140922.4083 117572.6145 126810.8569 148239.3586 116186.2496 120585.1953 179402.0406 140017.7945 136908.7279 95722.30554 1.472200314 1.228267683 1.324778548 1.548639659 1.213784488 1.259739771 1.87419264 1.462749918 1.430269854 1 16.54656753 S(ph)PALSDANK ddPTM_MDA-MB-175_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 91.701 0.0081389 0 283230 204433 251660 240250 328400 330880 327390 265110 260510 179114 TRUE FALSE 294412.1391 239542.7775 258218.4663 287770.7329 272578.6853 254038.1345 301728.3163 261556.6341 251134.296 214207.959 1.374422036 1.118272069 1.20545692 1.343417557 1.2724956 1.185941623 1.40857659 1.22104069 1.172385458 1 17.70865256 0.917661959 2.141117007 1.001249451 1.265479575 0.485413537 0.084495623 0.333999425 3.247758925 0.077581043 0.021369113 8.272979698 -0.917661959 0.264230123 S(ph)PAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPAMSR 6 0 Q9BQI6 Q9BQI6 ANKRD32 Ankyrin repeat domain-containing protein 32 1 S(1)PAMSR;S(1)PAMSR 117.4 0.023869 2403200000 466310 486570 475300 462120 508770 606170 565810 517030 525360 512010 TRUE FALSE 484720.2789 570134.6125 487686.7085 553525.9567 422289.4571 465396.2041 521460.3337 510100.0585 506452.3962 612328.5565 0.791601623 0.931092641 0.796446129 0.903968876 0.689645212 0.760043279 0.85160218 0.833049599 0.827092565 1 19.22394644 -0.01709916 1.009067997 1.001759457 0.819779698 0.406610687 0.065161087 8.428423797 7.315384825 0.114153816 0.019718116 0.961392744 0.01709916 -0.181979759 S(ph)PAPGLASGDRPPSVSSVHSEGDCNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPAPGLASGDRPPSVSSVHSEGDCNRR 27 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.931)PAPGLAS(0.069)GDRPPSVSSVHSEGDCNRR 56.252 0.038971 87232000 8283.7 9068.6 8665.6 6899.8 10132 10071 7668.8 6946.4 5764.9 9374.3 TRUE FALSE 8610.746872 10626.06151 8891.432655 8264.559846 8409.766259 7732.162877 7067.699417 6853.29487 5557.422375 11211.0146 0.768061338 0.947823358 0.793097946 0.73718215 0.75013427 0.689693409 0.630424602 0.611300147 0.495710921 1 13.45262923 3.351411688 1.073862385 0.651510907 0.856682042 0.171561529 0.130392346 0.660959784 1.603676202 0.048181187 0.088315221 2246.010012 -3.351411688 0.205171134 S(ph)PARTPPSEEDS(ph)AEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPARTPPSEEDSAEAER 17 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(1)PART(0.003)PPS(0.111)EEDS(0.886)AEAER 142.93 6.79E-06 124200000 117420 125690 99895 117610 118820 125370 128190 108700 106860 92144 TRUE FALSE 122055.8323 147276.2798 102498.3458 140872.907 98623.01884 96254.7175 118142.1328 107243.0543 103014.1295 110197.8526 1.107606268 1.336471413 0.930130155 1.278363449 0.894963164 0.873471808 1.072091062 0.973186426 0.93481068 1 16.74973659 3.229050435 24.99539899 0.961824714 1.158879682 0.441379102 0.112925706 183.8055428 483091.3827 0.031100432 0.037630139 1694.534578 -3.229050435 0.197054968 S(ph)PCSDGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPCSDGRR 8 1 A0A087WX19;A0A087WX45;Q6IPM2-2;Q6IPM2-3;Q6IPM2-4;Q6IPM2;C9J5R6 A0A087WX19 IQCE IQ domain-containing protein E 1 S(0.996)PCS(0.004)DGRR 61.48 0.052492 148400000 40067 39680 26850 34489 29150 46304 22163 24366 29857 58274 TRUE FALSE 41648.8761 46494.73133 27549.73306 41310.82126 24195.09341 35550.59774 20425.80615 24039.41362 28782.4524 69691.67458 0.597616234 0.667149005 0.395308812 0.592765513 0.347173368 0.510112549 0.293088181 0.344939532 0.412996998 1 16.0886987 -1.194099593 4.952051389 1.000055892 0.452720581 0.64457622 0.11958021 7.80E-05 1.27E-05 0.122358904 0.028837337 0.063958815 1.194099593 -0.54733531 S(ph)PDALESAQSEEEVDELSLIDHNEIMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPDALESAQSEEEVDELSLIDHNEIMSR 28 0 Q13905-2;Q13905;Q13905-4;Q13905-3;H0Y6R4 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 S(1)PDALESAQSEEEVDELSLIDHNEIMSR 102.53 0.00071889 20546000 7226.4 6760.4 7662.5 6783.9 7136.2 9627.8 6967.7 6757.7 6239.5 6237.6 TRUE FALSE 7511.703852 7921.446111 7862.191045 8125.735172 5923.191273 7391.889361 6421.553467 6667.124085 6014.941614 7459.738294 1.006966137 1.0618933 1.053949983 1.089278853 0.794021323 0.99090465 0.860828251 0.893747719 0.806320728 1 12.8649093 3.251625301 24.99815751 0.888817465 1.053722035 0.594883389 0.06549835 147.0053636 281280.5671 0.016855151 0.022684614 1784.946902 -3.251625301 0.164904571 S(ph)PDKPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPDKPGK 7 1 P55317-2;P55317;P55318;Q9Y261;Q9Y261-2 P55317-2 FOXA1;FOXA3;FOXA2 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma;Hepatocyte nuclear factor 3-beta 1 S(1)PDKPGK 69.954 0.035332 113850000 439830 171890 248480 150440 368950 375210 421820 274440 319070 139540 TRUE FALSE 457194.828 201410.7704 254955.5929 180196.583 306236.0108 288073.1639 388756.6462 270761.5807 307586.733 166880.1913 2.739659059 1.206918381 1.52777625 1.079796119 1.835065075 1.72622743 2.329555372 1.622490833 1.843159039 1 17.34845319 S(ph)PDLEASLDTLENNCHVGSDIDFRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.996)PDLEAS(0.004)LDTLENNCHVGSDIDFRPK;S(0.999)PDLEAS(0.001)LDTLENNCHVGSDIDFRPK 120.15 0.00014757 140690000 306500 142144 210265 163326 258550 299670 302400 228250 239010 98588 TRUE FALSE 318600.8567 166556.1263 215744.6786 195631.3953 214601.7634 230076.184 278697.0978 225190.6821 230408.0768 117904.431 2.702195786 1.412636699 1.829826723 1.659237008 1.820133149 1.951378604 2.363754232 1.909942486 1.954193535 1 16.84725841 -0.028492106 10.83294261 1 1.938988734 0.417147725 0.338450824 0 0 0.309294938 0.072901516 0.936500241 0.028492106 0.938988734 S(ph)PDNSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPDNSIK 7 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK;S(1)PDNSIK 162.34 0.0013382 3284220000 5438190 3363820 4385990 3463850 5286160 6142640 6278790 4541080 4985160 2281390 TRUE FALSE 5652893.94 3941529.918 4500292.503 4148989.191 4387620.411 4716104.953 5786642.033 4480214.25 4805745.065 2728384.691 2.07188303 1.444638629 1.649434744 1.520676027 1.608138481 1.728533725 2.120904011 1.642075718 1.761388371 1 21.37961564 2.725570618 21.63684794 1.724736184 1.638836796 0 0.305064041 740.022665 1232612.744 0.092213048 0.087646146 531.5824294 -2.725570618 -0.085899389 S(ph)PDPFGAVAAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPDPFGAVAAQK 12 0 Q9Y3Q8;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK;S(1)PDPFGAVAAQK 193.15 3.33E-06 1760890000 4048730 2526110 3350230 3338370 4092440 4450560 5206500 3779420 3898100 2126500 TRUE FALSE 4208576.987 2959949.742 3437539.746 3998689.622 3396808.511 3416984.889 4798400.925 3728763.057 3757808.142 2543146.961 1.654869755 1.163892527 1.351687417 1.572339186 1.335671341 1.343604967 1.886796555 1.466200387 1.47762131 1 21.2781834 S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPDPGIVPQEAPVGNSLSELSEENFDGK 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5;A0A0C4DH09 O15027 SEC16A Protein transport protein Sec16A 1 S(1)PDPGIVPQEAPVGNSLSELSEENFDGK;S(1)PDPGIVPQEAPVGNSLSELSEENFDGK 195.09 2.34E-19 361210000 675510 426100 594310 419220 713420 707850 752740 610250 699650 360500 TRUE FALSE 702179.6564 499279.3604 609798.2068 502140.4648 592153.1232 543462.5651 693738.2719 602070.5969 674469.7332 431133.0728 1.628684276 1.158063234 1.414408324 1.164699478 1.373481091 1.260544828 1.609104742 1.396484368 1.564411955 1 18.71777371 S(ph)PDPYR ddPTM_MDA-MB-175_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 90.939 0.050832 479770000 589340 519630 529370 569060 556970 616600 636860 559740 516880 421610 TRUE FALSE 612607.5983 608872.4103 543165.8171 681618.3695 462296.4383 473403.9947 586941.2491 552237.6009 498277.5898 504216.4073 1.214969583 1.207561677 1.077247407 1.351836949 0.916861157 0.9388905 1.164066144 1.095239252 0.988221689 1 18.94368354 3.231805434 24.99993109 1.033314745 1.202832569 0.515034821 0.092029841 152.4636343 564244.8734 0.02755298 0.033637661 1705.318228 -3.231805434 0.169517825 S(ph)PDREASGSGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPDREASGSGGR 12 1 Q8N5F7;A0A494C050 Q8N5F7 NKAP NF-kappa-B-activating protein 1 S(0.952)PDREAS(0.024)GS(0.024)GGR;S(0.971)PDREAS(0.026)GS(0.003)GGR 98.253 0.01174 279360000 534930 587390 577710 579980 649860 719680 611560 606410 581870 538490 TRUE FALSE 556049.4495 688269.6632 592765.5972 694698.3129 539397.0293 552545.2269 563624.3292 598282.0658 560928.6124 643996.8055 0.863435105 1.068747015 0.92044804 1.078729439 0.837577182 0.857993739 0.875197399 0.929014027 0.871011483 1 19.29669401 3.222357474 24.98989908 0.89116848 0.984519594 0.258531746 0.072558226 290.1892566 447554.3233 0.019404472 0.023258948 1668.620113 -3.222357474 0.093351114 S(ph)PEAQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPEAQPK 7 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 S(1)PEAQPK;S(1)PEAQPK 102.62 0.0089785 3129500000 3630300 2272500 3132100 2080900 3734700 3905000 4005800 2924500 3385100 1950380 TRUE FALSE 3773627.047 2662784.197 3213725.099 2492495.809 3099877.028 2998122.931 3691814.929 2885301.861 3263270.912 2332519.619 1.617832929 1.14159134 1.377791241 1.068585142 1.328982189 1.285358077 1.582758361 1.236989322 1.399032568 1 21.15345778 -2.212149971 2.285871701 3.13E-06 1.327380065 0.274500654 0.163916893 2058276.571 523764.9545 10642858.52 0.037117506 0.006135501 2.212149971 1.327376935 S(ph)PEASQTDS(ph)PVESPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPEASQTDSPVESPR 15 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 S(1)PEASQTDS(1)PVESPR;S(1)PEASQT(0.331)DS(0.669)PVESPR 294.22 7.72E-44 464860000 271080 309930 327440 289430 316150 375700 363940 305740 324750 258980 TRUE FALSE 281782.4477 363158.0666 335973.3554 346678.3901 262410.9359 288449.3688 335413.4318 301642.0554 313062.3109 309722.1725 0.909791009 1.172528475 1.084757196 1.119320542 0.847246207 0.931316497 1.082949371 0.973911725 1.010784305 1 18.24061514 3.291021248 24.99999521 0.978595836 1.079748445 0.239201708 0.084248905 139.8138318 66626.84132 0.023005821 0.03115 1954.435076 -3.291021248 0.101152609 S(ph)PEDQLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPEDQLGK 8 0 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 S(1)PEDQLGK;S(1)PEDQLGK;S(1)PEDQLGK 141.1 0.00069111 206420000 933420 594430 765450 603100 932110 1032040 1010420 754360 778530 449180 TRUE FALSE 970272.1424 696518.7285 785398.2558 722391.3799 773670.2751 792364.3507 931220.6402 744249.0381 750510.8574 537188.2209 1.806205171 1.296600896 1.462054128 1.344763999 1.440221965 1.475021826 1.733509046 1.385453011 1.397109669 1 19.03506815 0.708091743 1.731242165 1.000817112 1.487062527 0.487383431 0.151824336 0.916959413 4.134091997 0.137940678 0.03903687 5.106128541 -0.708091743 0.486245414 S(ph)PEIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPEIHR 6 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;Q9Y2W1;A0A3B3ITZ9 E9PK91;Q9NYF8;Q9NYF8-4;Q9Y2W1 BCLAF1;THRAP3 Bcl-2-associated transcription factor 1;Thyroid hormone receptor-associated protein 3 1 S(1)PEIHR;S(1)PEIHR;S(1)PEIHR;S(1)PEIHR 91.516 0.050144 3129740000 401491 465829 432985 505180 394720 542259 549922 476203 434403 389049 TRUE FALSE 417342.1747 545831.5071 444268.9448 605103.0962 327625.6354 416327.5653 506817.6767 469820.2777 418768.9209 465275.7028 0.896978227 1.173135635 0.954850946 1.300525887 0.70415376 0.894797564 1.089284641 1.009767488 0.90004468 1 18.82772632 3.244387235 24.99999632 0.94760399 1.078889821 0.206923239 0.140528965 259.0453891 1111466.176 0.038800877 0.051154475 1755.445031 -3.244387235 0.131285831 S(ph)PEIHRR ddPTM_MDA-MB-175_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 78.816 0.021016 2166710000 894552 1004694 1015333 1063938 1172652 1142260 1000541 991474 1000256 1137433 TRUE FALSE 929869.6037 1177242.379 1041793.412 1274381.761 973325.0319 876987.4261 922115.982 978184.9128 964256.9819 1360291.219 0.683581273 0.86543408 0.765860573 0.936844804 0.715526954 0.644705644 0.677881302 0.71909963 0.708860697 1 20.37548411 S(ph)PEPDGPAPAFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPEPDGPAPAFLR 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR;S(1)PEPDGPAPAFLR 174.05 2.16E-05 995687000 489041 492591 482114 533839 519156 646768 667890 512679 506962 367478 TRUE FALSE 508348.7163 577189.6724 494678.2869 639430.7608 430910.0486 496565.9339 615539.0366 505807.3766 488716.5366 439478.2783 1.156709538 1.313351992 1.125603497 1.454976941 0.980503633 1.129898697 1.400613106 1.150926909 1.11203798 1 18.74543233 1.084816251 2.232357 1.005514531 1.220514662 0.210960635 0.133442738 0.420198278 4.167723352 0.119939349 0.033358462 12.15671545 -1.084816251 0.215000131 S(ph)PEPEATLTFPFLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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(0.883)PEPEAT(0.117)LTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK;S(0.999)PEPEAT(0.001)LTFPFLDK;S(1)PEPEATLTFPFLDK 159.41 1.85E-06 4759149000 1195978 734691 977673 1006484 1207625 1285886 1649190 1101166 1179535 555171.5 TRUE FALSE 1243196.135 860868.4641 1003151.962 1205563.531 1002353.334 987258.4643 1519922.178 1086406.671 1137083.766 663946.726 1.872433565 1.296592679 1.510892248 1.815753409 1.509689399 1.486954338 2.289223094 1.636285907 1.712612957 1 19.34070796 S(ph)PEPEATLTFPFLDKMPEANQLHLPNLNSQESPGTASVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPEPEATLTFPFLDKMPEANQLHLPNLNSQESPGTASVPLR 41 1 Q9UPQ0-4;Q9UPQ0-5 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(0.985)PEPEAT(0.007)LT(0.008)FPFLDKMPEANQLHLPNLNSQESPGTASVPLR 203.42 1.42E-35 307560000 61089 47104 67257 54351 90861 84872 68813 61727 80119 52549 TRUE FALSE 63500.84089 55193.74558 69009.77267 65101.46558 75416.47967 65161.76425 63419.25725 60899.65053 77235.53284 62844.97044 1.010436324 0.878252392 1.098095396 1.03590574 1.200040021 1.036865222 1.009138151 0.969045734 1.228985109 1 15.93950967 4.228860293 24.99779511 1.064778628 0.944344347 0.260161609 0.085542658 245.3412142 632251.206 0.021206045 0.046722431 16937.92842 -4.228860293 -0.120434281 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPEPEVLSTQEDLFDQSNK 19 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK;S(1)PEPEVLSTQEDLFDQSNK 268.98 3.59E-32 347190000 654020 378879 466130 456560 632840 667470 743700 535040 558750 259422 TRUE FALSE 679841.2146 443948.521 478277.7307 546866.2053 525270.0828 512460.2081 685406.8507 527868.6639 538640.6966 310250.774 2.191263557 1.430934451 1.541584327 1.762658634 1.693050032 1.651761256 2.20920271 1.701425776 1.736146182 1 18.24307528 S(ph)PEPGQTWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 129.74 0.0003095 1349440000 335874 342131 326085 343843 358034 448730 448430 319200 345397 280942 TRUE FALSE 349134.5649 400889.3378 334583.043 411854.1191 297175.5086 344519.2581 413280.8848 314921.6461 332966.2294 335987.2059 1.039130534 1.193168462 0.995820784 1.225802983 0.884484597 1.025393979 1.230049471 0.937302494 0.991008656 1 18.35804677 2.528721378 0.373468539 0.984254714 1.116103211 0.081323954 0.110747582 3.843628362 1.161397219 0.121640991 0.186068684 337.8480196 -2.528721378 0.131848497 S(ph)PERPTGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPERPTGDLR 10 1 Q5T200;Q5T200-2;Q5T9K0 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(1)PERPTGDLR;S(1)PERPTGDLR;S(1)PERPTGDLR;S(0.998)PERPT(0.002)GDLR 107.37 0.0013885 4297340000 3601630 3825540 3603680 3346740 3967620 4532690 3696000 3748140 3532250 3579360 TRUE FALSE 3743825.133 4482546.736 3697594.861 4008715.183 3293205.37 3480041.441 3406297.862 3697902.314 3405125.012 4280667.061 0.874589189 1.047160798 0.863789407 0.936469743 0.769320604 0.812967089 0.795739966 0.86386123 0.795465979 1 22.0294042 3.261233449 24.95250024 0.830831582 0.934069888 0.251490344 0.075872537 271.433593 298723.246 0.019456926 0.026327031 1824.876377 -3.261233449 0.103238306 S(ph)PESCSKPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPESCSKPEK 10 1 Q03111 Q03111 MLLT1 Protein ENL 1 S(0.997)PES(0.002)CS(0.001)KPEK;S(0.999)PES(0.001)CSKPEK;S(0.993)PES(0.005)CS(0.002)KPEK;S(0.995)PES(0.005)CS(0.001)KPEK;S(1)PESCSKPEK;S(0.988)PES(0.009)CS(0.002)KPEK 125.54 0.00085709 4176867000 6541190 3273042 4876516 3146550 6777440 6053546 6390730 4987663 5775317 2757433 TRUE FALSE 6799441.232 3835161.503 5003602.013 3768928.198 5625413.17 4647701.684 5889807.884 4920811.536 5567464.469 3297699.202 2.061874299 1.162980996 1.517300914 1.142896295 1.705860003 1.409377084 1.786035512 1.492195387 1.688287539 1 21.65302838 S(ph)PETALEAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPETALEAFK 10 0 Q68DA7-5;Q68DA7-3 Q68DA7-5 FMN1 Formin-1 1 S(1)PETALEAFK;S(0.999)PET(0.001)ALEAFK 113.22 0.0015907 84563000 122129 87874 116977 109495 144146 167931 177513 128491 132455 82290 TRUE FALSE 126950.7472 102965.6759 120025.5167 131152.7842 119644.1144 128931.5703 163599.0672 126768.7883 127687.9704 98413.14996 1.28997748 1.046259326 1.219608526 1.332675402 1.215733004 1.310105106 1.662369991 1.288128552 1.297468585 1 16.58656348 3.633447577 1.452440558 1.340154948 1.162999817 0.060632075 0.16484414 0.803570828 3.319860132 0.050843874 0.111442705 4299.793281 -3.633447577 -0.17715513 S(ph)PFEGAVTESQSLFSDNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SPFEGAVTESQSLFSDNFR 19 0 O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6;O95628-5 O95628-3 CNOT4 CCR4-NOT transcription complex subunit 4 1 S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(0.996)PFEGAVT(0.004)ESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR;S(1)PFEGAVTESQSLFSDNFR 357.96 4.47E-91 2464872800 352488 352736.9 358290.1 361972.7 427330.7 463343 377051.7 368464.1 390508.7 329504.3 TRUE FALSE 366404.4984 413316.7187 367627.4343 433569.8197 354693.1803 355738.6103 347497.4025 363525.4414 376454.3682 394064.3588 0.929808774 1.048855877 0.932912165 1.100251291 0.900089471 0.902742413 0.881829058 0.922502716 0.955311892 1 18.58807175 3.165030752 24.99998013 0.919052857 1.001246188 0.297207881 0.056331235 43.44373068 14769.61526 0.015048506 0.017986412 1462.280713 -3.165030752 0.082193332 S(ph)PFLKPDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPFLKPDER 9 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 S(1)PFLKPDER;S(1)PFLKPDER 78.903 0.017233 787590000 440720 331360 387470 334060 511100 506500 479790 382440 413400 311500 TRUE FALSE 458119.9659 388268.5024 397567.7865 400136.0709 424223.4046 388873.0511 442182.8061 377314.0173 398521.8148 372532.461 1.229745093 1.042240725 1.067203071 1.074097194 1.138755542 1.043863534 1.1869645 1.012835274 1.069763998 1 18.50700662 0.851515119 0.01335766 8.91E-07 2.113821746 0.248827594 0.061794506 1431.084755 11.15086399 900.3337801 862.1709503 7.104199008 -0.851515119 2.113820855 S(ph)PGAAGLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGAAGLTSR 10 0 Q53T59;F6TR53 Q53T59 HS1BP3 HCLS1-binding protein 3 1 S(1)PGAAGLTSR;S(1)PGAAGLTSR 93.614 0.0090896 464450000 77358 150750 137884 101760 160309 163817 96983 116215 122768 193556 TRUE FALSE 80412.15357 176640.1398 141477.3703 121887.8243 133059.7334 125772.9844 89381.21904 114657.328 118349.6037 231479.5923 0.347383338 0.763091632 0.611187228 0.526559698 0.57482274 0.543343727 0.386130017 0.495323699 0.51127446 1 17.82052548 -1.478963845 6.336575452 1.00023423 0.530940526 0.627206671 0.108972926 0.000357088 2.94E-05 0.104487264 0.024615882 0.033192209 1.478963845 -0.469293705 S(ph)PGAFDMSGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SPGAFDMSGVR 11 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR;S(1)PGAFDMSGVR 178.49 7.89E-06 5134840000 1198889 1240972 1326766 1544500 1493820 1674950 1714890 1389069 1425710 1229274 TRUE FALSE 1246222.063 1454099.288 1361342.612 1849997.49 1239901.01 1285968.247 1580472.441 1370450.802 1374398.976 1470126.704 0.847697045 0.989097935 0.926003594 1.258393229 0.843397379 0.874732935 1.075058657 0.932199108 0.934884709 1 20.48750907 2.83122785 0.002555377 1.935681274 0.004318179 0.005780794 0.118020421 705866.0769 657.1454456 246458.4273 250202.8756 677.9971209 -2.83122785 -1.931363095 S(ph)PGAPGPLTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 171.26 1.55E-05 27142600000 20954500 16103200 20005000 16109500 25429100 25492300 26549200 21609500 24472200 18699400 TRUE FALSE 21781799.84 18868799.33 20526346.73 19295911.02 21106670.67 19572099.66 24468204.33 21319860 23591450.3 22363189.41 0.974002386 0.843743662 0.917863117 0.862842534 0.94381308 0.87519268 1.094128565 0.953346126 1.054923333 1 24.41462262 2.255099446 24.99989701 1.016973132 0.900937929 0.592969018 0.049576307 160.200968 242157.4719 0.01584043 0.013218023 179.9282874 -2.255099446 -0.116035203 S(ph)PGASNFSTLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 S(0.97)PGAS(0.03)NFSTLPK;S(0.998)PGAS(0.002)NFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(1)PGASNFSTLPK;S(0.994)PGAS(0.006)NFSTLPK 185.99 1.29E-05 3297100000 1605040 1175910 1349110 1278780 1769340 1814820 1860490 1445980 1498020 1083010 TRUE FALSE 1668408.219 1377863.395 1384268.915 1531718.867 1468588.219 1393355.559 1714659.932 1426599.003 1444106.553 1295205.074 1.288142127 1.063818713 1.068764277 1.182607216 1.1338654 1.07577988 1.323852081 1.101446429 1.114963631 1 20.30474911 0.852219104 2.027990719 1.000897444 1.152710685 0.234430951 0.084875313 0.810984291 6.391877868 0.077382216 0.021427618 7.115724151 -0.852219104 0.151813241 S(ph)PGASNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGASNLK 8 0 Q00653;Q00653-4;Q00653-3 Q00653 NFKB2 Nuclear factor NF-kappa-B p100 subunit;Nuclear factor NF-kappa-B p52 subunit 1 S(1)PGASNLK 64.103 0.072486 126440000 221970 183660 208360 168500 269830 302770 278070 228500 231460 197620 TRUE FALSE 230733.547 215202.1763 213790.0328 201828.7971 223964.393 232456.256 256274.1468 225437.3313 223129.7998 236339.8553 0.976278617 0.91056236 0.904587305 0.853976985 0.947637006 0.983567734 1.084345873 0.953869295 0.94410568 1 17.85050341 2.883627984 3.578103479 0.994807543 0.910067666 0.421369645 0.04494584 0.240610539 5.613669471 0.014677854 0.015842058 764.9410781 -2.883627984 -0.084739877 S(ph)PGDGHNAPVEGPEGEYVELLEVTLPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGDGHNAPVEGPEGEYVELLEVTLPVR 28 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 S(1)PGDGHNAPVEGPEGEYVELLEVTLPVR;S(1)PGDGHNAPVEGPEGEYVELLEVTLPVR 125.52 2.43E-05 71410000 8967.3 9869.5 7150.5 10242.8 10264.6 11025.1 8394.7 9960.5 9874.3 9734.4 TRUE FALSE 9321.335928 11564.50985 7336.847904 12268.79527 8519.826958 8464.687612 7736.701479 9826.99579 9518.925872 11641.6693 0.800687228 0.993372132 0.630223013 1.053869076 0.731838943 0.727102565 0.664569769 0.844122568 0.817659875 1 13.50701032 7.458560051 13.13286139 0.81668164 0.815209823 0 0.139721275 0 0 0.028699715 0 28744850.29 -7.458560051 -0.001471817 S(ph)PGEPGGAAPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 83.438 0.013426 1516830000 87635 107013 88069 96297 112081 132250 99557 98523 113279 119089 TRUE FALSE 91094.89747 125391.6503 90364.15049 115344.2592 93029.51165 101536.9418 91753.4622 97202.46034 109202.1109 142422.2095 0.639611601 0.880422027 0.634480752 0.809875508 0.653195257 0.712929129 0.644235633 0.682495102 0.76674917 1 17.11981461 0.86005822 4.248983173 0.999974456 0.708370971 0.569949473 0.076143237 0.639666713 18.48848842 0.067673105 0.017234473 7.245330823 -0.86005822 -0.291603485 S(ph)PGETSKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPR;S(1)PGETSKPR 83.397 0.0098091 176914000 191697 141346 175676 176260 192994 246670 308080 206851 193299 117605 TRUE FALSE 199265.3456 165621.076 180254.2609 211123.7019 160188.9488 189384.6308 283931.8846 204078.5007 186342.2067 140647.4481 1.416771853 1.177561899 1.281603494 1.501084483 1.138939604 1.346520207 2.018748925 1.450993271 1.324888644 1 17.10172385 2.453969731 24.99996688 1.524126136 1.299679437 0.035929676 0.256857014 441.113476 476329.7298 0.085607745 0.07162823 284.4262867 -2.453969731 -0.224446699 S(ph)PGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PGETSKPRPFAGGGYR;S(0.997)PGET(0.002)S(0.001)KPRPFAGGGYR;S(0.999)PGET(0.001)SKPRPFAGGGYR 198.77 7.25E-12 3336110000 1475490 1040160 1331680 1061960 1532640 1579420 1572340 1358220 1368580 896340 TRUE FALSE 1533743.485 1218799.389 1366384.675 1272012.518 1272122.4 1212623.641 1449095.882 1340015.282 1319325.073 1071960.662 1.430783367 1.136981451 1.274659345 1.186622386 1.186724892 1.131220282 1.351818154 1.250060129 1.230758852 1 20.03182053 -1.947372142 1.990258296 0.812133754 1.239110397 0.401792114 0.088580338 2349003.231 873243.8541 2042247.9 0.023927996 0.011288282 1.947372142 0.426976643 S(ph)PGEYINIDFGEPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPGEYINIDFGEPGAR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR 168.41 6.28E-09 290525000 144044 135055 153472 153149 148777 164815 190201 148069 147959 121354 TRUE FALSE 149730.9683 158249.6457 157471.6064 183441.4151 123487.9387 126539.214 175292.5486 146084.3772 142633.9845 145130.9928 1.031695335 1.090391808 1.085030863 1.263971337 0.850872279 0.871896564 1.207822983 1.00656913 0.982794796 1 17.14699612 3.237599908 24.99958186 0.998178254 1.113477881 0.264015963 0.106106712 42.53636996 1106894.521 0.03156047 0.039846529 1728.223505 -3.237599908 0.115299628 S(ph)PGEYVNIEFGSDQSGYLSGPVAFHSSPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGEYVNIEFGSDQSGYLSGPVAFHSSPSVR 31 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 S(1)PGEYVNIEFGSDQSGYLSGPVAFHSSPSVR 123.89 4.68E-06 55840000 0 3198.2 0 0 4006.2 2978.1 1775.1 1807.6 0 0 TRUE FALSE 0 3747.465971 0 0 3325.227555 2286.481409 1635.963024 1783.372079 0 0 0 S(ph)PGGGSEANGLALVSGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SPGGGSEANGLALVSGFK 18 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK;S(1)PGGGSEANGLALVSGFK 321.3 1.30E-61 10313390000 4725940 3648050 4499800 3788270 5373160 5728940 5576830 4510030 4941070 3483120 TRUE FALSE 4912523.76 4274574.21 4617068.485 4537578.499 4459832.182 4398480.508 5139703.492 4449580.425 4763241.856 4165570.676 1.179315907 1.026167731 1.108387984 1.089305368 1.070641343 1.055913067 1.233853388 1.068180274 1.143478824 1 21.99008273 S(ph)PGGGSEANGLALVSGFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;S(1)PGGGSEANGLALVSGFKR;S(1)PGGGSEANGLALVSGFKR 197.07 4.93E-16 3491612000 1645953 1471649 1689399 1363583 2157956 1820260 1481802 1635779 1797485 1593454 TRUE FALSE 1710936.495 1724393.268 1733426.126 1633295.648 1791147.41 1397532.201 1365654.487 1613854.058 1732793.866 1905660.803 0.897817961 0.904879434 0.909619447 0.857075743 0.939908827 0.733358318 0.716630413 0.846873723 0.909287667 1 20.86185992 2.765227281 24.78842632 0.822809989 0.899971045 0.107160355 0.078921682 1156.780904 1075302.294 0.02388568 0.025328206 582.4079324 -2.765227281 0.077161057 S(ph)PGGPGSHVR ddPTM_MDA-MB-175_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 162.93 4.26E-06 2038282000 716969 755401 721339 780291 795463 902205 789935 768358 710706 741891 TRUE FALSE 745275.4897 885135.2455 740137.6869 934630.2309 660250.4834 692681.5618 728017.8306 758059.4178 685127.8299 887250.3371 0.839983327 0.997616128 0.834192624 1.053400818 0.744153545 0.780705887 0.820532605 0.854391806 0.772192245 1 19.75898169 3.222211824 24.99999856 0.821064225 0.929099153 0.237132079 0.08952986 309.5680089 473379.6625 0.023844872 0.028579946 1668.060598 -3.222211824 0.108034928 S(ph)PGHMVILDQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 SPGHMVILDQTK 12 0 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 1 S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK;S(1)PGHMVILDQTK 300.51 1.12E-36 7432610000 5782390 4288220 5254790 4615430 6738920 6676710 6839700 5470670 5503680 3957710 TRUE FALSE 6010683.222 5024688.427 5391734.144 5528348.278 5593440.785 5126145.289 6303586.442 5397344.617 5305603.632 4733147.5 1.26991251 1.061595572 1.139143486 1.168006761 1.181759239 1.083030962 1.331795902 1.140328844 1.120946185 1 22.17436845 0.880995284 2.449082784 1.000594069 1.17072113 0.323125105 0.075679952 0.535388145 6.563284365 0.06862178 0.018477777 7.603180201 -0.880995284 0.170127061 S(ph)PGIISQASAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGIISQASAPR 12 0 Q08495;Q08495-2;Q08495-3;Q08495-4;E5RGQ0;E5RFK4;E5RGQ7;E5RJC0 Q08495 DMTN Dematin 1 S(1)PGIISQASAPR;S(1)PGIISQASAPR 159.75 7.33E-05 456580000 54291 52143 56313 65256 70469 85017 74008 76351 71648 65063 TRUE FALSE 56434.4506 61098.15463 57780.56304 78163.44203 58490.70455 65273.0902 68207.05958 75327.63973 69069.40248 77810.84914 0.725277403 0.785213827 0.742577207 1.00453141 0.751703717 0.838868756 0.876575186 0.968086592 0.88765774 1 16.2476837 8 0.12789198 1.047400329 0.003427203 0.502702141 0.071527462 68.28088615 0.592376292 0.387816915 12.8311825 99999999.99 -8 -1.043973125 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(0.98)PGKAEAES(0.02)DALPDDTVIESEALPSDIAAEAR;S(0.996)PGKAEAES(0.004)DALPDDTVIESEALPSDIAAEAR;S(0.857)PGKAEAES(0.143)DALPDDTVIESEALPSDIAAEAR 164.58 3.42E-14 700650000 315449 203134 270024 182424 351221 343132 310006 254424 295399 171227 TRUE FALSE 327903.1701 238020.6843 277061.0473 218506.9227 291520.5799 263444.7932 285706.9197 251013.8624 284767.6477 204775.6523 1.601280066 1.162348559 1.352997996 1.067055191 1.423609578 1.286504476 1.39521919 1.225799355 1.390632355 1 17.64368466 -1.678210399 2.737130443 0.959194005 1.310171758 0.313976734 0.142052615 26524552 23016666.69 7518007.238 0.031584331 0.020979233 1.678210399 0.350977753 S(ph)PGKQFTFSYENEVCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGKQFTFSYENEVCK 16 1 Q5SXH7-4;A0A494C1H5 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 S(0.977)PGKQFT(0.023)FSYENEVCK 127.92 3.85E-05 379310000 291980 204400 291010 192600 355290 363210 296880 297160 302370 211860 TRUE FALSE 303507.5959 239504.11 298593.9597 230695.7051 294897.9327 278859.982 273609.7698 293177.0563 291487.7628 253369.9107 1.197883344 0.945274478 1.178490212 0.910509478 1.163902738 1.100604177 1.079882647 1.157110785 1.150443484 1 17.95088568 S(ph)PGLCSDSLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPGLCSDSLEK 11 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK;S(1)PGLCSDSLEK 199.15 5.37E-08 644000000 916680 634113 783350 681233 987760 1111180 1064690 791810 846490 542985 TRUE FALSE 952871.2342 743016.975 803764.7445 815978.8541 819860.908 853125.2851 981236.8158 781197.0821 816024.9903 649372.5147 1.46737229 1.144207613 1.237756028 1.256565124 1.262543285 1.313768701 1.511053815 1.203002998 1.256636171 1 19.3086868 0.664187345 1.63083509 1.000665891 1.297194885 0.41703468 0.106188094 1.283727308 4.863356537 0.099084741 0.028314727 4.6151662 -0.664187345 0.296528994 S(ph)PGLLDTTPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGLLDTTPIR 11 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 S(1)PGLLDTTPIR;S(1)PGLLDTTPIR 123.95 0.00037691 297090000 112024 166385 158004 146933 173833 165453 177312 153167 142500 134585 TRUE FALSE 116446.794 194960.3295 162121.714 175995.9088 144284.9288 127029.0482 163413.8221 151114.0469 137371.4528 160954.354 0.72347713 1.211277139 1.00725274 1.093452302 0.896433835 0.789224057 1.015280532 0.938862747 0.853480813 1 17.29629208 3.220576499 24.98142835 0.915415785 1.023207712 0.106636837 0.129690107 462.1861525 642013.5361 0.035648069 0.042690425 1661.791369 -3.220576499 0.107791927 S(ph)PGLLSSDNPQLSALLMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGLLSSDNPQLSALLMGK 19 0 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 S(0.95)PGLLS(0.025)S(0.025)DNPQLSALLMGK;S(0.967)PGLLS(0.031)S(0.001)DNPQLSALLMGK 149.86 8.53E-08 303710000 333790 280100 332540 355050 371640 396920 397890 328060 338310 252930 TRUE FALSE 346968.2869 328204.9961 341206.2656 425277.8303 308468.7655 304741.3454 366702.3421 323662.8923 326134.2892 302486.7909 1.147052689 1.085022573 1.128003853 1.405938517 1.019775986 1.007453398 1.212292084 1.070006698 1.078176962 1 18.20651262 S(ph)PGLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGLQK 6 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(1)PGLQK 74.335 0.084543 370300000 850040 679550 824380 654120 1018100 1010600 1008000 916880 950500 707040 TRUE FALSE 883600.2356 796257.4263 845864.02 783502.9836 845043.7257 775903.4658 928990.3261 904590.7233 916291.6907 845570.9509 1.044974682 0.941680205 1.000346593 0.926596382 0.999376486 0.917608942 1.098654495 1.069798723 1.083636671 1 19.68956629 2.22973561 24.99415807 1.070006704 0.970897704 0.513744153 0.043277141 131.7493356 373137.171 0.014700641 0.011022136 169.721011 -2.22973561 -0.099109 S(ph)PGLVPPS(ph)PEFAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGLVPPSPEFAPR 14 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 2 S(1)PGLVPPS(1)PEFAPR;S(1)PGLVPPS(1)PEFAPR 120.59 0.00017606 402420000 543590 551570 574510 627300 615810 636680 660750 584170 558420 454610 TRUE FALSE 565051.3529 646297.8569 589482.2026 751378.0677 511134.8362 488820.719 608958.6885 576340.1567 538322.5733 543682.1255 1.039304635 1.188742147 1.084240542 1.382017235 0.940135444 0.899092863 1.120063839 1.060068245 0.990142122 1 19.05240387 3.185992232 24.99997831 1.011721197 1.168283005 0.407211577 0.101137643 106.304863 50554.96692 0.02935598 0.03508714 1534.589535 -3.185992232 0.156561808 S(ph)PGMLEPLGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 203.97 1.25E-07 4471660000 996832 1126180 1036381 1167316 1157852 1402127 1308593 1138316 1103861 1042111 TRUE FALSE 1036187.697 1319592.655 1063389.94 1398207.621 961040.7306 1076504.254 1206022.061 1123058.736 1064133.258 1246292.698 0.831416006 1.058814399 0.853242534 1.121893455 0.771119603 0.863765194 0.967687657 0.901119567 0.853838958 1 20.2492115 3.219905042 24.99997406 0.892758629 0.964868419 0.116452215 0.099039915 522.9551186 700800.7372 0.026800179 0.032086299 1659.22408 -3.219905042 0.072109789 S(ph)PGNLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPGNLTER 8 0 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTER;S(1)PGNLTER;S(1)PGNLTER;S(1)PGNLTER 98.754 0.0076554 2457060000 632210 1033420 873980 1055760 885440 1136700 903690 937940 793740 1086440 TRUE FALSE 657170.139 1210901.846 896756.6368 1264586.177 734933.2251 872718.6519 832856.4164 925368.4485 765173.4524 1299307.117 0.505785068 0.931959681 0.690180655 0.973277342 0.565634726 0.671680037 0.641000427 0.712201478 0.588908844 1 20.30931105 -1.067927375 4.416101155 1.000020826 0.706017265 0.287960309 0.142016821 2.94E-05 6.20E-06 0.128304502 0.030239348 0.085520971 1.067927375 -0.294003561 S(ph)PGNLTEREELAGSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPGNLTEREELAGSLAR 17 1 Q9H0F6-2;Q9H0F6 Q9H0F6-2 SHARPIN Sharpin 1 S(1)PGNLTEREELAGSLAR;S(1)PGNLTEREELAGSLAR;S(0.959)PGNLT(0.041)EREELAGSLAR;S(0.998)PGNLT(0.002)EREELAGSLAR;S(0.998)PGNLT(0.002)EREELAGSLAR 290.44 3.45E-46 6077490000 125595.6 157530.2 135252.3 112022.7 183596 156848.7 123906.2 166085 138700.6 153764 TRUE FALSE 130554.2113 184584.7864 138777.086 134180.4557 152388.4175 120422.9665 114194.1083 163858.9022 133708.7925 183891.1118 0.709953896 1.003772203 0.754669895 0.729673416 0.828688325 0.65486018 0.620987644 0.89106483 0.727108511 1 17.48849222 -1.814941807 9.165107512 1.004533898 0.774809563 0.291839825 0.107617685 0.009935192 0.000200607 0.103836774 0.024210992 0.015312926 1.814941807 -0.229724335 S(ph)PGNTSQPPAFFSK ddPTM_MDA-MB-175_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(0.996)PGNT(0.004)SQPPAFFSK;S(1)PGNTSQPPAFFSK 296.35 1.28E-43 3204100000 4086450 3378820 3829000 3694390 4322970 4761280 4652700 4015190 3997770 2975360 TRUE FALSE 4247786.201 3959106.051 3928786.886 4425129.315 3588153.104 3655544.878 4288009.216 3961372.946 3853891.039 3558324.825 1.193760101 1.112631996 1.104111367 1.243599034 1.008382674 1.02732186 1.205064019 1.113269063 1.083063303 1 21.76276678 -5 0.15448152 0.564257511 1.157029805 0.24745289 0.069363524 209.2645342 1.892985686 28.03774711 0.327195221 1.00E-05 5 0.592772294 S(ph)PGPAADGPIDLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGPAADGPIDLSK 14 0 Q8IX07 Q8IX07 ZFPM1 Zinc finger protein ZFPM1 1 S(1)PGPAADGPIDLSK 140.27 1.05E-05 56407000 153610 124710 138420 117880 183370 205080 179100 152550 166700 112980 TRUE FALSE 159674.6414 146127.9724 142027.3389 141196.3122 152200.8329 157453.278 165061.674 150505.3168 160700.4996 135116.2679 1.181757341 1.081497992 1.051149067 1.04499861 1.126443435 1.165316956 1.221626949 1.113894864 1.189349751 1 17.04384186 3.012787745 19.52341149 1.148975216 1.086393351 0.097321665 0.065325045 29.55878718 45122.71899 0.01809093 0.021583029 1029.882658 -3.012787745 -0.062581865 S(ph)PGPGPGPGAGAEPGATGGSSHFISSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGPGPGPGAGAEPGATGGSSHFISSR 27 0 Q9ULI0-2;Q9ULI0;C9JG15 Q9ULI0-2 ATAD2B ATPase family AAA domain-containing protein 2B 1 S(1)PGPGPGPGAGAEPGATGGSSHFISSR 182.56 1.00E-17 342780000 7139.6 19891 19460 25817 16853 23558 15999 21067 14896 22687 TRUE FALSE 7421.476921 23307.12452 19967.14359 30923.52554 13988.33308 18087.01152 14744.95657 20784.63132 14359.89587 27132.08328 0.273531407 0.859024509 0.735923717 1.139740182 0.515564284 0.666628188 0.543450955 0.766053646 0.529258875 1 14.72771221 -1.832820524 2.589254804 1.115434061 0.68707552 0.163126878 0.221242512 48486787.57 34731351.08 34924978.98 0.050559787 0.014695335 1.832820524 -0.428358541 S(ph)PGPGPSQSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGPGPSQSPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(1)PGPGPSQSPR 144.88 0.0015632 0 11902 17539 18423 19256 13926 22452 15651 16237 15876 19079 TRUE FALSE 12371.90015 20551.18682 18903.11851 23064.77933 11558.86349 17237.86326 14424.23372 16019.36957 15304.62586 22817.16476 0.542218995 0.900689767 0.828460447 1.010852118 0.506586318 0.75547788 0.63216591 0.702075378 0.670750552 1 14.47783191 4.767090021 23.54242035 0.759587907 0.542218334 0.16555937 0.153963527 9171.730853 7568219.335 0.036175074 3.258921866 58491.13128 -4.767090021 -0.217369573 S(ph)PGPPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPGPPALK 8 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK;S(1)PGPPALK 100.02 0.006716 1611510000 2814800 1860610 2313020 2026090 2605160 2879770 3080660 2407040 2451010 1533470 TRUE FALSE 2925930.477 2180155.294 2373299.201 2426844.555 2162335.834 2210987.061 2839189.819 2374777.566 2362798.629 1833924.086 1.595447979 1.188792551 1.294109837 1.323306986 1.179075977 1.205604462 1.548150134 1.294915958 1.288384097 1 20.80650249 4.749256887 24.26009061 1.280253894 1.595448252 0.356652088 0.132970663 1159.559922 2629906.999 0.030496304 0.428730477 56137.99365 -4.749256887 0.315194358 S(ph)PGPPALKHPATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGPPALKHPATK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 S(1)PGPPALKHPATK;S(1)PGPPALKHPATK;S(1)PGPPALKHPATK 142.39 2.43E-05 815060000 1403200 927360 1213610 787970 1690850 1381280 1178090 1167330 1355850 943170 TRUE FALSE 1458599.42 1086626.866 1245237.674 943828.1141 1403439.921 1060498.654 1085748.227 1151683.851 1307053.223 1127966.103 1.29312345 0.963350639 1.103967282 0.836752196 1.244221716 0.940186634 0.96257168 1.021027004 1.158769948 1 20.10529228 4.746805625 24.12600212 1.023943945 1.293123672 0.343186329 0.11098651 681.648585 1994520.169 0.024327204 0.26999896 55822.02989 -4.746805625 0.269179727 S(ph)PGPPPPVGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGPPPPVGVK 11 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 S(1)PGPPPPVGVK;S(1)PGPPPPVGVK 99.752 0.0047631 428360000 272460 267654 311670 302690 365350 389610 385730 311920 360690 266620 TRUE FALSE 283216.9312 313621.4924 319792.3762 362561.1786 303247.9375 299128.9821 355495.4747 307739.2226 347708.8374 318859.0843 0.888219735 0.983573961 1.002926973 1.137057705 0.951040608 0.938122816 1.114898374 0.965126094 1.090478065 1 18.28255946 4.695697899 2.110516535 1.023503883 0.859143004 0.289135427 0.065241704 0.781339486 4.178677954 0.016007535 0.235849026 49624.70059 -4.695697899 -0.164360878 S(ph)PGSISYLPSFFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGSISYLPSFFTK 14 0 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(1)PGSISYLPSFFTK;S(0.996)PGS(0.004)ISYLPSFFTK;S(1)PGSISYLPSFFTK 269.78 1.04E-25 3173700000 1667330 1513900 1641920 1393530 2038000 1990580 1865650 1744870 1817650 1623230 TRUE FALSE 1733157.476 1773900.548 1684709.784 1669166.075 1691581.488 1528297.963 1719415.478 1721482.872 1752233.132 1941270.84 0.892795297 0.913783132 0.867838608 0.859831632 0.871378405 0.787266738 0.88571643 0.886781399 0.902621672 1 20.88856998 0.724110852 1.256428897 0.999661206 0.868011342 0.612218124 0.031174214 0.641590493 1.709721935 0.030988733 0.009392237 5.297986561 -0.724110852 -0.131649864 S(ph)PGSNSKVPEIEVTVEGPNNNNPQTSAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.847)PGS(0.132)NS(0.021)KVPEIEVTVEGPNNNNPQTSAVR;S(0.998)PGS(0.001)NS(0.001)KVPEIEVTVEGPNNNNPQTSAVR;S(0.878)PGS(0.078)NS(0.044)KVPEIEVTVEGPNNNNPQTSAVR 311.88 2.73E-92 2104580000 452955 425103 515520 282030 679760 676330 385916 450830 521500 551190 TRUE FALSE 470838.0132 498111.1334 528954.8747 337814.6922 564214.638 519262.6074 355666.8955 444787.3613 502731.3169 659185.1273 0.71427281 0.755646802 0.802437514 0.512473171 0.855927439 0.787734107 0.539555401 0.674753332 0.762655734 1 19.33032417 0.870641006 4.560842302 0.999974489 0.702545597 0.419952065 0.103544291 0.90885759 30.8002139 0.098402101 0.024970674 7.424052013 -0.870641006 -0.297428892 S(ph)PGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 1 S(0.999)PGVVIS(0.001)DDEPGYDLDLFCIPNHYAEDLER;S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER;S(1)PGVVISDDEPGYDLDLFCIPNHYAEDLER 166.65 1.75E-12 180555000 38719.8 44176.7 38881.6 45480.3 55980 48301 36759.8 45326.7 43080.2 41288.4 TRUE FALSE 40248.4876 51763.70458 39894.88644 54476.16759 46464.5396 37083.82476 33878.47082 44719.16973 41529.75202 49378.07147 0.815108537 1.048313615 0.80794744 1.103246157 0.94099543 0.751018087 0.686103564 0.905648366 0.841056582 1 15.59158287 2.831893118 8.008071569 0.824871007 0.951003378 0.169535485 0.115669935 0.463726749 35.81020855 0.033953992 0.036044284 679.0364977 -2.831893118 0.126132371 S(ph)PGYEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPGYEPR 7 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 S(1)PGYEPR;S(0.998)PGY(0.002)EPR;S(0.998)PGY(0.002)EPR;S(0.999)PGY(0.001)EPR 96.034 0.013666 1144872000 721297 1064360 1206750 1093390 1280260 1472020 1261660 1182211 1229200 1138870 TRUE FALSE 749774.3625 1247155.55 1238198.896 1309659.279 1062641.862 1130165.664 1162767.792 1166365.395 1184961.332 1362009.772 0.550491177 0.915672983 0.909096926 0.96156379 0.78020135 0.829777941 0.853714721 0.856356114 0.870009421 1 20.37730562 7.999999999 0.03155823 1.431562869 2.51E-13 0.252167227 0.101632192 2188.434789 5.288899687 74.65403907 189.7694913 99999999.8 -7.999999999 -1.431562869 S(ph)PHEAGFCVYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPHEAGFCVYLK 12 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK;S(1)PHEAGFCVYLK 163.99 3.77E-05 1508410000 999290 761729 896430 890521 1150800 1113440 1235790 994660 948590 704689 TRUE FALSE 1038742.741 892550.0303 919791.7022 1066663.396 955187.4271 854860.4343 1138925.551 981328.2096 914450.4312 842759.3175 1.232549696 1.059080584 1.091404964 1.265679742 1.133404766 1.014358924 1.351424454 1.164422854 1.085067127 1 19.68476115 1.008859125 3.542321295 1.001113164 1.16430649 0.232273446 0.094780861 0.294553411 9.180466289 0.089261257 0.023108083 10.20608367 -1.008859125 0.163193326 S(ph)PHKDLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 107.93 0.0016271 1608250000 482699 424960 495658 441945 556953 633054 595126 489193 499734 384425 TRUE FALSE 501756.3292 497943.5743 508575.2547 529360.4019 462282.328 486036.8025 548478.469 482636.168 481748.671 459745.7185 1.091377927 1.083084745 1.106209877 1.151419971 1.005517418 1.057186142 1.193003974 1.04978937 1.047858961 1 18.81047661 1.18744069 2.262988257 1.006610809 1.095255737 0.276725716 0.048921013 0.373453243 3.368863478 0.045243355 0.012827124 15.39716238 -1.18744069 0.088644928 S(ph)PHQLLSPSSFSPSATPSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPHQLLSPSSFSPSATPSQK 20 0 A0A3B3ITS5;Q14181;E9PIQ6 A0A3B3ITS5 POLA2 DNA polymerase alpha subunit B 1 S(1)PHQLLSPSSFSPSATPSQK;S(1)PHQLLSPSSFSPSATPSQK 184.03 2.68E-17 468230000 324940 341880 412390 347030 463500 547730 470380 443160 440080 355450 TRUE FALSE 337768.8821 400595.2305 423137.2222 415671.4982 384714.4356 420528.0084 433510.3865 437220.1651 424241.6068 425093.622 0.794575276 0.942369421 0.99539772 0.97783518 0.905011074 0.989259746 1.01979979 1.028526758 0.9979957 1 18.69742109 5.530451454 1.124478972 0.993631909 1.30E-14 0.768702978 0.031968522 4.291183721 1.214189774 0.010434065 7.746107864 339196.5718 -5.530451454 -0.993631909 S(ph)PHS(ph)KSPAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(1)PHS(0.671)KS(0.329)PAEQR 81.327 0.012505 257630000 563890 364060 471420 390710 582920 619760 507020 423500 481860 300640 TRUE FALSE 586152.8126 426584.473 483705.5925 467991.2718 483835.4666 475830.1326 467278.4475 417823.6752 464517.9527 359544.6519 1.630264307 1.186457567 1.345328292 1.301622119 1.34568951 1.323424309 1.299639544 1.162091198 1.291961792 1 18.45581142 -4.349598528 0.069450866 6.51E-09 1.717708594 0.541031847 0.103733928 210.537215 1.189647148 35.84522613 5.586419822 4.47E-05 4.349598528 1.717708588 S(ph)PHSKS(ph)PAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 S(0.999)PHS(0.084)KS(0.917)PAEQR 91.14 0.0062382 263690000 476300 362690 430270 303730 485820 506420 427290 373640 418620 290570 TRUE FALSE 495104.6918 424979.1862 441483.1897 363806.8875 403240.4899 388811.6299 393797.8933 368631.967 403553.948 347501.6282 1.424755027 1.222955957 1.270449269 1.04692139 1.160398851 1.118877146 1.133226038 1.060806445 1.161300884 1 18.40666021 7.999999998 0.494972368 1.088407867 11.29391436 0.746968517 0.058854395 47.93012429 0.515928958 0.02872295 507.2744221 99999999.58 -7.999999998 10.20550649 S(ph)PIALPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPIALPVK 8 0 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(1)PIALPVK 66.962 0.063281 75153000 163540 191980 183120 180400 213990 242430 226150 188600 198010 161260 TRUE FALSE 169996.6855 224951.0716 187892.2576 216082.5816 177616.0562 186129.3066 208423.7721 186072.1255 190883.6588 192855.8095 0.881470389 1.166421028 0.974262887 1.120435947 0.920978511 0.965121596 1.080723327 0.964825099 0.989773963 1 17.55716308 3.23057925 24.99995854 0.989206236 1.040603908 0.07758402 0.081393775 443.5626441 1389365.47 0.021778484 0.026476522 1700.510235 -3.23057925 0.051397672 S(ph)PILLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPILLPK 7 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 S(1)PILLPK;S(1)PILLPK;S(1)PILLPK;S(1)PILLPK 89.355 0.018812 1499650000 2203500 1594200 2008330 1901520 2410820 2573520 2985280 2077590 2190240 1343070 TRUE FALSE 2290495.881 1867991.449 2060668.73 2277634.981 2001029.678 1975858.982 2751285.953 2049743.304 2111413.69 1606218.852 1.426017307 1.162974427 1.282931481 1.418010365 1.24580139 1.230130614 1.712896066 1.276129527 1.314524287 1 20.61523705 0.636165606 2.372705121 1.000104712 1.34522248 0.33284347 0.145535497 3.173990566 19.26326484 0.137281362 0.0369027 4.326787897 -0.636165606 0.345117768 S(ph)PIRQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 103.26 0.0050974 8190930000 1272859 1232974 1271932 1505630 1265887 1461174 1459451 1316741 1245011 1116875 TRUE FALSE 1323112.456 1444727.693 1305079.593 1803439.12 1050711.98 1121838.483 1345055.417 1299092.241 1200203.297 1335705.272 0.99057216 1.081621615 0.977071529 1.350177436 0.786634598 0.839884746 1.007000156 0.972588989 0.898553987 1 20.34917028 3.205212402 24.99999941 0.922538487 1.089788172 0.375413449 0.114862678 214.8433158 161059.9928 0.033064756 0.039522176 1604.029688 -3.205212402 0.167249685 S(ph)PISVPGGSALISNLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPISVPGGSALISNLGK 17 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 S(0.998)PIS(0.002)VPGGSALISNLGK 118.2 0.00018908 89883000 129690 96701 115150 122630 128540 150350 152690 120840 138910 87236 TRUE FALSE 134810.2613 113308.6445 118150.9036 146885.848 106690.8167 115433.4911 140721.7588 119220.3375 133910.6562 104328.224 1.292174411 1.086078534 1.132492236 1.407920526 1.022645768 1.106445473 1.348836906 1.142742902 1.283551575 1 16.67076998 S(ph)PKPGPAPHDQELGFFLETGLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPKPGPAPHDQELGFFLETGLQR 23 1 Q86TV6;Q86TV6-2;G3V3H1 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 S(1)PKPGPAPHDQELGFFLETGLQR;S(1)PKPGPAPHDQELGFFLETGLQR 205.07 9.75E-25 166411000 180825 104118 138799 111623 174494 199943 188891 151393 165633 97482 TRUE FALSE 187964.1106 121999.4566 142416.216 133701.6962 144833.5722 153509.2684 174085.2298 149363.8245 159671.9007 116581.7315 1.612294724 1.046471476 1.221599766 1.146849464 1.242335058 1.316752346 1.49324622 1.281194082 1.369613392 1 16.83098221 2.740874865 5.948927032 1.323898515 1.234322573 0 0.179867169 0.51881344 81.46866195 0.053547317 0.053735833 550.6490126 -2.740874865 -0.089575942 S(ph)PLAQMEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPLAQMEEER 10 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEER 95.428 0.0057404 0 61277 37018 49887 32893 60907 61546 54294 47216 36422 36440 TRUE FALSE 63696.26328 43375.55354 51187.0962 39399.13722 50554.0499 47252.87424 50038.29441 46583.14675 35111.17933 43579.72031 1.461603306 0.995315097 1.174562293 0.904070447 1.160036125 1.084285854 1.148201366 1.068917983 0.805677023 1 15.41136932 4.743341971 24.89044467 1.051198535 1.461603484 0.560286584 0.112051008 344.8943587 1795362.636 0.025342648 0.208099121 55378.59981 -4.743341971 0.410404949 S(ph)PLAQMEEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 1 S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR;S(1)PLAQMEEERR 157.58 1.87E-05 3348210000 433667 649552 535295 587267 596331 706400 585223 643196 545018 611628 TRUE FALSE 450788.508 761107.5032 549245.2274 703426.6598 494966.8696 542349.3056 539351.6921 634575.0097 525402.9086 731464.7963 0.616281891 1.040525131 0.750884021 0.961668509 0.676679004 0.74145647 0.737358373 0.867540055 0.718288715 1 19.48042891 -1.582735406 2.709951655 1.01480593 0.799392981 0.201736976 0.124034847 27271287.99 26369507.89 2901573.808 0.027135178 0.026137533 1.582735406 -0.215412949 S(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPLDPDSGLLSCTLPNGFGGQSGPEGER 28 0 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 S(0.997)PLDPDS(0.002)GLLSCTLPNGFGGQSGPEGER 95.823 0.0013757 18841000 12165 10593 10042 11870 12733 13813 15711 13328 12618 10907 TRUE FALSE 12645.28359 12412.26535 10303.70277 14217.85057 10568.64921 10605.14009 14479.53077 13149.35996 12163.88064 13044.01782 0.96943164 0.951567647 0.78991787 1.089990121 0.81022959 0.813027108 1.11005144 1.008075896 0.932525608 1 13.6711007 2.2390804 24.99999355 1.016226724 0.905190788 0.244441289 0.093470238 19.93624176 958930.46 0.033255032 0.026245075 173.4125004 -2.2390804 -0.111035936 S(ph)PLFIFMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPLFIFMR 8 0 C9J417;O43521-11;O43521-10;O43521-14;O43521-19;O43521-4;O43521-8;O43521-12;O43521 C9J417 BCL2L11 Bcl-2-like protein 11 1 S(1)PLFIFMR 74.376 0.043151 23126000 17446 22144 19331 19018 21853 25356 16529 16232 15032 21354 TRUE FALSE 18134.78155 25947.05974 19834.78174 22779.70364 18138.43487 19467.45327 15233.41379 16014.43659 14491.00126 25537.90745 0.710112275 1.016021371 0.776679991 0.8919957 0.710255329 0.762296336 0.596502036 0.627084918 0.567431035 1 14.6403527 2.993588983 1.681047186 0.667427208 0.85786332 0.151710668 0.138753335 0.468524318 2.692764104 0.045985488 0.054250796 985.3465117 -2.993588983 0.190436112 S(ph)PLSGIPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPLSGIPVR 9 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 S(1)PLSGIPVR;S(1)PLSGIPVR;S(1)PLSGIPVR 136.96 0.00018685 441041000 167863 186942 191868 181418 220800 253706 202187 190703 194567 202673 TRUE FALSE 174490.3609 219047.8343 196868.2377 217301.9389 183268.4949 194786.6265 186339.0546 188146.9382 187564.5717 242382.8939 0.719895526 0.903726458 0.812220015 0.896523411 0.756111506 0.803631904 0.768779725 0.776238517 0.773835846 1 17.88692836 3.220414753 24.99757124 0.79696321 0.836645945 0 0.081858642 768.1132327 1058142.576 0.02164883 0.025922355 1661.172576 -3.220414753 0.039682736 S(ph)PLSPTETFSWPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 S(0.989)PLS(0.011)PTETFSWPDVR;S(0.998)PLS(0.002)PTETFSWPDVR;S(1)PLSPTETFSWPDVR;S(1)PLSPTETFSWPDVR 277.52 1.47E-33 251597000 95088 100656 90965 78203 89815 101005 87951 84521 92139 87399 TRUE FALSE 98842.14766 117942.885 93335.62263 93671.31999 74548.27838 77548.1195 81057.1708 83388.13424 88822.93539 104523.1607 0.945648285 1.128389959 0.892965942 0.896177645 0.71322258 0.741922833 0.775494831 0.797795758 0.849791901 1 16.67346313 3.860570381 2.087060248 0.800448417 1.033361983 0.442746795 0.090188464 0.241935157 2.043954007 0.023534941 0.054629878 7253.880238 -3.860570381 0.232913566 S(ph)PLTQEQLIPNLAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPLTQEQLIPNLAMK 15 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 S(0.999)PLT(0.001)QEQLIPNLAMK;S(1)PLTQEQLIPNLAMK 182.1 5.88E-07 53795000 184126 136582 158937 148638 174470 209271 196373 167917 176279 120143 TRUE FALSE 191395.4367 160038.896 163079.0288 178038.1528 144813.6517 160670.9818 180980.7711 165666.3473 169934.7532 143682.7206 1.332069966 1.113835369 1.134994021 1.23910622 1.007871031 1.118234546 1.259586194 1.153001186 1.182708349 1 17.13252705 -2.462416659 1.681188821 4.32E-05 1.166948602 0.264299332 0.085450165 1286229.764 101728.7991 4870795.211 0.020285597 0.003448128 2.462416659 1.166905395 S(ph)PMDSLLHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPMDSLLHPR 10 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 1 S(1)PMDSLLHPR 156.14 7.39E-06 97172000 78847 79844 82265 67291 100860 97605 85732 76580 83333 70092 TRUE FALSE 81959.94044 93556.5859 84408.89348 80600.95896 83715.85323 74937.71797 79012.10182 75553.57036 80333.86161 83825.18541 0.977748394 1.116091607 1.006963397 0.961536304 0.998695712 0.893976167 0.942581892 0.901323033 0.958349942 1 16.35509615 3.569964848 1.361869822 0.934599382 1.047891479 0.401828424 0.046159268 0.355210249 1.308001137 0.014260494 0.030158526 3715.051579 -3.569964848 0.113292097 S(ph)PNELVDDLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPNELVDDLFK 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK;S(1)PNELVDDLFK 194.77 3.83E-07 813136000 699683 431636 505768 443280 702516 729252 736104 541200 584283 326614 TRUE FALSE 727307.0251 505766.1253 518948.7296 530959.4609 583102.5813 559894.2749 678406.245 533946.0992 563254.769 390607.7599 1.861988163 1.294818427 1.328567384 1.359316213 1.492808493 1.433392606 1.73679664 1.366962344 1.441995851 1 18.57536108 0.462503267 1.570781619 1.000155771 1.475225139 0.411574015 0.172764302 3.239971323 8.405350673 0.158535939 0.045414327 2.900703016 -0.462503267 0.475069367 S(ph)PNSHDSEPWTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPNSHDSEPWTLLR 14 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(0.999)PNS(0.001)HDSEPWTLLR;S(1)PNSHDSEPWTLLR;S(0.991)PNS(0.009)HDSEPWTLLR;S(0.993)PNS(0.007)HDSEPWTLLR 228.63 1.02E-12 1013830000 72376 227569 212292 261336 208263 301132 219720 257320 205175 221484 TRUE FALSE 75233.46037 266652.2055 217824.5039 313027.4808 172862.5296 231198.6567 202497.7723 253871.0463 197790.7918 264879.5492 0.28402895 1.006692311 0.822353045 1.181772929 0.652608063 0.872844496 0.764490021 0.958439589 0.746719754 1 18.01497694 4.745746158 24.81913878 0.885005095 0.284028639 0.607340655 0.146021803 494.2803338 1707216.703 0.032301582 0.328685772 55686.01732 -4.745746158 -0.600976456 S(ph)PPADAIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPADAIPK 9 0 P18754-2;C9JW69;P18754;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;M0R1Q8 P18754-2 RCC1 Regulator of chromosome condensation 1 S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK;S(1)PPADAIPK 115.18 0.0015929 650462000 882040 752800 821430 758670 951950 1105370 911000 845530 919140 762120 TRUE FALSE 916863.6203 882087.544 842837.1406 908732.6616 790137.879 848664.5695 839593.4395 834197.0534 886060.3309 911442.8223 1.005947491 0.967792518 0.924728485 0.997026516 0.866908883 0.931122116 0.921169621 0.915248914 0.972151307 1 19.79779263 5.000200854 1.048407889 0.932984896 1.080753541 0.18876229 0.038830403 3.909984353 2.43274969 0.010926813 0.732138821 100046.259 -5.000200854 0.147768645 S(ph)PPAPGLQPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPAPGLQPMR 11 0 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 S(1)PPAPGLQPMR;S(1)PPAPGLQPMR 97.214 0.0067484 1339060000 37071 42868 34282 47184 61497 55001 46855 51762 38556 56396 TRUE FALSE 38534.59171 50230.24553 35175.41708 56516.85437 51043.76191 42227.8513 43182.38267 51068.21506 37168.37709 67445.71643 0.571342314 0.744750715 0.52153671 0.83796062 0.756812509 0.626101308 0.640253895 0.75717507 0.551085807 1 16.0414392 -1.686166861 4.607299964 1.011578964 0.676709368 0.500977398 0.099184202 0.011254016 0.000766584 0.0916169 0.021162962 0.020598383 1.686166861 -0.334869597 S(ph)PPAS(ph)PESWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 S(1)PPAS(1)PESWK;S(1)PPAS(1)PESWK;S(1)PPAS(1)PESWK;S(1)PPAS(1)PESWK 108.72 0.0030911 308719000 713870 413285 503687 479981 651790 729090 806340 526600 522512 305156 TRUE FALSE 742054.1388 484263.4838 516813.497 574919.8092 540998.9686 559769.897 743136.9638 519541.7883 503706.8952 364945.4756 2.03332878 1.326947493 1.416138934 1.575358095 1.4824104 1.533845285 2.036295867 1.423614822 1.380225071 1 18.47732141 0.961777171 1.985425985 1.006710883 1.599182081 0.401175539 0.229819821 0.364892635 3.066109552 0.211546563 0.059179143 9.157505135 -0.961777171 0.592471197 S(ph)PPEEPPDFCCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPEEPPDFCCPK 13 0 A0A087X0G7;A0A087WUW6;A0A087X1B1;Q9Y6K9;Q9Y6K9-2;Q9Y6K9-3 A0A087X0G7 IKBKG NF-kappa-B essential modulator 1 S(1)PPEEPPDFCCPK 146.79 2.28E-06 0 91342 69356 86864 70959 120630 125540 101970 103490 91927 63809 TRUE FALSE 94948.25269 81267.35349 89127.7472 84994.47841 100125.3557 96385.23758 93977.32495 102102.8858 88618.56523 76311.15185 1.244225128 1.064947279 1.1679518 1.113788435 1.312067152 1.26305573 1.231501854 1.337981191 1.161279355 1 16.21960628 3.25246554 24.99430993 1.244223521 1.143259775 0.070184483 0.099115963 368.5729859 662511.535 0.025538499 0.034400536 1788.403617 -3.25246554 -0.100963747 S(ph)PPEGDTTLFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(1)PPEGDTTLFLSR 194.59 9.28E-07 316540000 11838 19445 32580 26207 25845 26574 21435 40991 12954 21829 TRUE FALSE 12305.37338 22784.52749 33429.06156 31390.66638 21451.87613 20402.59123 19754.86869 40441.58269 12487.78807 26105.97461 0.471362344 0.872770614 1.280513831 1.202432273 0.821722861 0.781529575 0.756718299 1.549131312 0.478349813 1 14.6720924 4.672105102 3.652016087 1.016678267 0.444604885 0.209837553 0.290223315 0.338507406 7.746356308 0.070489132 0.459258499 47000.78393 -4.672105102 -0.572073383 S(ph)PPETAAPVEDMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPETAAPVEDMAR 14 0 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 S(0.999)PPET(0.001)AAPVEDMAR;S(1)PPETAAPVEDMAR 105.14 0.001067 871050000 120188 73260 105015 101312 139137 130912 134083 110262 122210 84572 TRUE FALSE 124933.115 85841.83512 107751.7772 121351.2112 115486.5424 100509.672 123573.2241 108784.1182 117811.686 101142.2642 1.235221656 0.848723685 1.065348675 1.199807145 1.141822792 0.993745521 1.221776328 1.075555497 1.164811634 1 16.62602645 3.996993569 24.99970848 1.118386938 1.020738571 0.059049767 0.112694589 244.6499908 2034436.092 0.025815858 0.054167643 9931.01342 -3.996993569 -0.097648367 S(ph)PPGS(ph)GASTPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(1)GASTPVGPWDQAVQR;S(1)PPGS(0.843)GAS(0.156)TPVGPWDQAVQR;S(1)PPGS(1)GASTPVGPWDQAVQR 191.97 1.85E-17 494140000 276772 274482 274246 289363 327402 342688 305837 277019 265449 203543 TRUE FALSE 287699.1723 321622.1483 281393.0761 346598.1377 271750.325 263103.9055 281864.6968 273306.0134 255895.5423 243423.3538 1.181888129 1.321246065 1.155982249 1.42384916 1.11636916 1.08084907 1.1579197 1.122760036 1.051236615 1 17.89310806 3.037516924 24.95467454 1.098964677 1.266646658 0.555748097 0.079728543 122.5950003 81544.2418 0.021364638 0.025535587 1090.226976 -3.037516924 0.167681981 S(ph)PPGSGAS(ph)TPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(1)PPGS(0.114)GAS(0.874)T(0.011)PVGPWDQAVQR 269.83 2.52E-44 188140000 83081 71643 88609 83145 86386 99891 79969 81634 87531 58440 TRUE FALSE 86361.10203 83947.12794 90918.22333 99590.83284 71702.13858 76692.82911 73700.82082 80539.82976 84380.77641 69890.1991 1.235668279 1.201128757 1.30087229 1.424961355 1.025925516 1.097333104 1.054522977 1.152376596 1.207333467 1 16.09280254 3.225445827 24.9999891 1.098751543 1.284992386 0.612501715 0.078095394 168.5336306 321265.7023 0.023333419 0.028049549 1680.528288 -3.225445827 0.186240843 S(ph)PPGSGAST(ph)PVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 2 S(0.999)PPGS(0.023)GAS(0.244)T(0.734)PVGPWDQAVQR 96.379 0.0027423 0 74045 59015 67790 70388 67649 73522 68308 78110 71148 49831 TRUE FALSE 76968.35378 69150.36718 69556.66309 84310.53631 56150.04714 56447.62974 62953.84047 77063.06321 68587.39738 59594.43038 1.291536026 1.160349495 1.167167177 1.414738521 0.942202934 0.947196397 1.056371209 1.293125259 1.15090281 1 15.86288988 3.233182486 24.99997478 1.087907396 1.244920732 0.380332561 0.118339975 191.566517 890487.1736 0.038253636 0.046998048 1710.733995 -3.233182486 0.157013336 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SPPGSGASTPVGPWDQAVQR 20 0 Q8TE77;Q8TE77-2;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.908)PPGS(0.092)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(0.932)PPGS(0.068)GASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR 280.26 1.11E-44 27559580000 248077 261307 289327 288837 305304 379332 319049 305806 271045 232768 TRUE FALSE 257871.2715 306184.4446 296867.0993 345968.0965 253408.5351 291237.8918 294041.1057 301707.1708 261290.1434 278374.433 0.926346823 1.099901457 1.066430908 1.242815631 0.910315407 1.046209196 1.056279137 1.083817819 0.938628381 1 18.08666719 3.202878903 24.99998429 1.020269325 1.08377364 0.149800767 0.087070376 401.3211561 281179.9552 0.025075423 0.029971767 1595.434222 -3.202878903 0.063504315 S(ph)PPKADEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPKADEKER 10 2 Q13427;E9PG73;C9JM79;Q13427-2 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)PPKADEKER 72.089 0.025584 76365000 153500 74510 99734 72183 143640 177470 122030 112330 118200 70115 TRUE FALSE 159560.2985 87306.51289 102333.15 86460.58196 119224.1241 136255.2821 112464.9697 110824.4001 113946.0051 83852.69182 1.902864357 1.04118915 1.220391949 1.031100852 1.421828227 1.624936292 1.341220744 1.321655843 1.358883092 1 16.35556948 -1.205121364 3.099708051 0.998830334 1.345767466 0.161254895 0.245428917 18633690.05 25547630.57 213548.5994 0.058914662 0.062356056 1.205121364 0.346937132 S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPKVPIVIQDDSLPAGPPPQIR 23 1 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR 165.37 8.00E-12 294062000 249652 154086 199370 161646 244526 295637 277657 207220 215920 128398 TRUE FALSE 259508.4537 180549.0719 204565.746 193619.0963 202961.5579 226979.7872 255893.5188 204442.5548 208149.0814 153555.1298 1.690001852 1.175793164 1.332197409 1.260909333 1.321750424 1.478164797 1.666460243 1.331395149 1.355533232 1 17.22839718 0.636426259 2.103176624 1.000185974 1.400495424 0.374854792 0.156780858 2.330134683 12.10550475 0.148852114 0.040714577 4.329385504 -0.636426259 0.40030945 S(ph)PPLGLISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPLGLISR 9 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 S(1)PPLGLISR 95.483 0.0084069 142070000 38219 45555 45805 38634 42237 49559 54369 49727 39898 43418 TRUE FALSE 39727.91563 53378.71688 46998.71593 46275.68989 35057.56983 38049.67332 50107.41571 49060.4909 38462.07877 51924.92581 0.765102983 1.027997942 0.905128225 0.891203775 0.675158785 0.73278243 0.964997348 0.94483507 0.740724771 1 15.66413963 -0.736475901 8.017708834 1.000012998 0.860712468 0.135066286 0.110983486 0 0 0.111034435 0.026171067 0.183452696 0.736475901 -0.13930053 S(ph)PPLMAK ddPTM_MDA-MB-175_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 69.825 0.061564 378130000 400430 307490 377890 377980 464090 478360 521460 381070 422260 236140 TRUE FALSE 416239.2856 360299.0156 387738.1238 452743.3158 385204.1476 367268.1396 480586.6026 375962.38 407062.9451 282407.1118 1.473898029 1.275814243 1.372975777 1.603158337 1.364002999 1.300491823 1.701751063 1.331278017 1.441404724 1 18.10741689 -0.856493355 5.531771206 0.999999798 1.427544163 0.503202644 0.127991087 3.04E-07 6.25E-08 0.117801543 0.027766077 0.139157509 0.856493355 0.427544365 S(ph)PPLPAVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SPPLPAVIR 9 0 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR;S(1)PPLPAVIR 104.05 0.0034862 8708467000 398005.3 552840.7 457623.6 617010.8 524681.1 634602.7 547204.1 471810.9 430109.7 612149.3 TRUE FALSE 413718.8566 647786.7897 469549.647 739053.6946 435495.994 487225.8404 504312.8128 465487.0466 414630.1359 732088.235 0.565121575 0.884847971 0.641383954 1.009514508 0.594868177 0.665528849 0.688868894 0.635834623 0.566366342 1 19.48165801 -1.362796632 5.468396482 1.000098538 0.69933439 0.310466898 0.136336562 0.000155646 1.81E-05 0.125446556 0.029558396 0.043371393 1.362796632 -0.300764148 S(ph)PPPETIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPPETIK 8 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 S(1)PPPETIK;S(1)PPPETIK 75.294 0.04066 290880000 335980 253890 307350 278490 425290 441510 388190 322800 355230 232720 TRUE FALSE 349244.7498 297493.6325 315359.7935 333574.4908 352999.3577 338975.9936 357762.6535 318473.394 342445.3417 278317.0283 1.254845066 1.068902016 1.133095576 1.198541436 1.268335466 1.21794917 1.285450106 1.14428282 1.230414624 1 18.08636965 5.078019036 20.67361409 1.182540671 4.220426486 0.067112784 0.084791581 1737.970606 457909.9248 0.01892969 1395.841491 119679.2987 -5.078019036 3.037885814 S(ph)PPREGSQGELTPANSQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPREGSQGELTPANSQSR 19 1 Q13098-7;Q13098;Q13098-5;A8K070;A0A096LPJ3;A0A096LP07;C9JFE4;J3QQX0 Q13098-7 GPS1 COP9 signalosome complex subunit 1 1 S(0.993)PPREGS(0.007)QGELTPANSQSR;S(0.981)PPREGS(0.018)QGELT(0.001)PANSQSR 127.03 1.47E-05 1246950000 94642 127480 125140 118710 137810 141710 129430 122330 122680 154470 TRUE FALSE 98378.53924 149373.6983 128401.2512 142190.4837 114385.1054 108800.0001 119284.9384 120690.3664 118264.7708 184735.439 0.532537448 0.808581716 0.695054787 0.769697923 0.619183336 0.588950343 0.64570685 0.653314638 0.640184533 1 17.49510113 -1.591836749 3.843042712 1.009043775 0.665081936 0.635705748 0.076837198 0.005917002 0.000628435 0.073936858 0.017078449 0.025595478 1.591836749 -0.343961839 S(ph)PPRPPR ddPTM_MDA-MB-175_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 80.219 0.018475 6735920000 596891.5 436486.3 498220.9 410509.1 673805.6 585696 505937.2 487947.3 494183.5 513110.5 TRUE FALSE 620457.2373 511449.4266 511204.9459 491706.5747 559272.3648 449676.9803 466280.5202 481407.1646 476397.9324 613644.6784 1.011101797 0.833461846 0.833063439 0.801288746 0.911394467 0.732797002 0.759854256 0.784504749 0.776341667 1 19.227044 S(ph)PPSLALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPSLALR 8 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.996)PPS(0.004)LALR;S(0.999)PPS(0.001)LALR 88.136 0.015897 0 43339 43706 47258 60487 50510 72489 49190 41927 42813 57307 TRUE FALSE 45050.05718 51212.16551 48489.5823 72451.14806 41924.32824 55654.52833 45334.35927 41365.03714 41272.16849 68535.20944 0.657327198 0.747238769 0.707513447 1.057137618 0.611719561 0.812057463 0.661475461 0.603558922 0.602203872 1 16.06455773 2.226562088 24.69069977 0.674382107 0.768299617 0 0.155798612 527.7813346 1086065.014 0.055454214 0.041280977 168.485328 -2.226562088 0.09391751 S(ph)PPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPSSSEIFTPAHEENVR 18 0 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 S(0.986)PPS(0.009)S(0.002)S(0.002)EIFTPAHEENVR;S(0.998)PPS(0.002)SSEIFTPAHEENVR;S(0.969)PPS(0.023)S(0.004)S(0.004)EIFTPAHEENVR;S(0.836)PPS(0.121)S(0.021)S(0.021)EIFTPAHEENVR 213.15 7.35E-17 3705720000 302259 212710 247939 240301 325537 305438 300431 222656 286259 167584 TRUE FALSE 314192.4187 249241.2878 254400.494 287831.8206 270202.337 234504.6535 276882.4332 219671.6605 275956.5945 200418.8762 1.567678777 1.243601863 1.26934398 1.436151255 1.348188066 1.170072689 1.381518739 1.09606273 1.376899221 1 17.61265887 -4.487267976 0.068696894 3.37E-09 1.711137028 0.445114337 0.119287741 260.5850188 1.419792574 43.62724376 6.641812414 3.26E-05 4.487267976 1.711137025 S(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.998)PPS(0.002)TGSTYGSSQK;S(0.999)PPS(0.001)TGSTYGSSQK;S(1)PPSTGSTYGSSQK;S(0.993)PPS(0.006)T(0.001)GSTYGSSQK 150.05 7.68E-06 1088820000 367315 250222 306994 361320 324827 400669 555046 344135 334166 151149 TRUE FALSE 381816.8798 293195.682 314994.5158 432788.0176 269613.0226 307619.6969 511540.0442 339522.4332 322139.4309 180763.7526 2.112242495 1.621982714 1.742575662 2.394219036 1.491521495 1.701777555 2.829881748 1.878266125 1.782101922 1 17.46374589 5.077410505 18.28552065 1.898104986 7.687363613 0.012205341 0.47318785 840.4387805 200836.7437 0.104858122 2297.660745 119511.7223 -5.077410505 5.789258627 S(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.996)PPS(0.004)TGSTYGSSQKEESAASGGAAYTK;S(0.952)PPS(0.046)T(0.002)GSTYGSSQKEESAASGGAAYTK;S(0.854)PPS(0.113)T(0.022)GS(0.006)T(0.002)YGS(0.002)SQKEESAASGGAAYTK 232.68 2.82E-36 1613120000 970390 479590 802270 651350 936750 890180 1128930 785830 857350 340271 TRUE FALSE 1008701.747 561955.8518 823177.8153 780185.0859 777521.5696 683449.1858 1040441.517 775297.2342 826494.141 406940.5876 2.478744508 1.380928492 2.022845203 1.917196539 1.910651317 1.679481494 2.556740587 1.905185322 2.030994613 1 18.63445865 S(ph)PPSTGSTYGSSQKEESAASGGAAYTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPSTGSTYGSSQKEESAASGGAAYTKR 28 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.69)PPS(0.221)T(0.072)GS(0.007)T(0.007)Y(0.002)GSSQKEESAASGGAAYTKR;S(0.997)PPS(0.002)TGSTYGSSQKEESAASGGAAYTKR 147.3 4.24E-08 705850000 561100 388050 541270 338920 694380 591190 468050 509690 618120 351620 TRUE FALSE 583252.6613 454694.5689 555375.9409 405957.3644 576349.5356 453895.0821 431363.018 502858.4392 595873.9819 420513.2068 1.387002006 1.081284872 1.320709866 0.965385529 1.370586051 1.079383655 1.025801356 1.1958208 1.417016094 1 18.68179159 4.753572137 23.22675567 1.16565541 1.387002438 0.164137439 0.152250028 1784.654071 2761199.405 0.0337172 0.708313338 56698.57408 -4.753572137 0.221347029 S(ph)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 S(1)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK;S(1)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 335.18 5.47E-129 3626200000 1608560 1434040 1886450 1548010 1853570 2099560 1873740 1778720 1838430 1160990 TRUE FALSE 1672067.191 1680325.215 1935612.437 1854201.758 1538500.833 1611969.009 1726871.363 1754879.168 1772265.263 1388463.762 1.20425699 1.210204588 1.394067667 1.33543403 1.108059768 1.16097305 1.243728076 1.26389987 1.276421691 1 20.40505809 3.256118443 24.99960924 1.197525531 1.288297284 0.231149951 0.09364395 445.7429303 634664.7535 0.026595354 0.035932634 1803.509535 -3.256118443 0.090771753 S(ph)PPVTLGPNLAPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPVTLGPNLAPTSR 15 0 B4DF95;Q15735;C9K0M5 B4DF95 INPP5J "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A" 1 S(1)PPVTLGPNLAPTSR;S(1)PPVTLGPNLAPTSR 101.01 0.0020314 281210000 119900 90831 111489 92324 133871 146745 116736 100773 109698 100339 TRUE FALSE 124633.7446 106430.5177 114394.4949 110585.4116 111115.6552 112665.6977 107585.9273 99422.30277 105749.9904 119998.5059 1.03862747 0.886932023 0.953299327 0.921556571 0.925975322 0.938892504 0.896560557 0.828529505 0.881260892 1 16.87265692 2.167040216 4.35245426 0.87957553 0.940323228 0.07765456 0.05514811 0.327182568 11.94777194 0.020176687 0.014744727 146.9062306 -2.167040216 0.060747698 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.525)PPY(0.419)T(0.056)AFLGNLPYDVTEESIK;S(0.498)PPY(0.42)T(0.081)AFLGNLPYDVTEESIK;S(0.52)PPY(0.427)T(0.053)AFLGNLPYDVTEESIK;S(0.612)PPY(0.257)T(0.131)AFLGNLPYDVTEESIK 211.33 9.99E-23 431133000 300823 156907 232360 213959 269108 286133 344559 241071 270023 118498.3 TRUE FALSE 312699.7243 183854.5567 238415.4925 256279.4516 223365.1183 219682.9471 317551.5652 237839.8376 260304.925 141715.7731 2.206527315 1.297347167 1.682349729 1.808404569 1.576148606 1.550165817 2.240763736 1.678287691 1.836809829 1 17.11264081 -0.549597612 7.670828335 0.999999938 1.752824836 0.413280432 0.272826043 0 0 0.247743653 0.058393739 0.282099546 0.549597612 0.752824898 S(ph)PPYTAFLGNLPYDVTEESIKEFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPYTAFLGNLPYDVTEESIKEFFR 25 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.969)PPY(0.002)T(0.029)AFLGNLPYDVTEESIKEFFR 89.659 0.0086291 115580000 85636 66502 86714 75333 112950 122090 99553 78281 99728 63746 TRUE FALSE 89016.97541 77923.20119 88973.83808 90233.64255 93750.79934 93736.44779 91749.77573 77231.77124 96138.80876 76235.80821 1.167653069 1.022133864 1.167087228 1.18361233 1.229747563 1.229559311 1.203499745 1.013064242 1.261071549 1 16.21818118 -1.292630668 5.571472706 0.99998218 1.155620478 0.27069645 0.079733869 1.82E-05 2.31E-06 0.079495835 0.018735203 0.05097642 1.292630668 0.155638298 S(ph)PQALSNGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQALSNGTK 10 0 Q8NC74 Q8NC74 RBBP8NL RBBP8 N-terminal-like protein 1 S(1)PQALSNGTK;S(1)PQALSNGTK 125.53 0.0017494 192940000 232000 170049 200263 162647 243620 300300 210400 204416 232200 157303 TRUE FALSE 241159.5391 199253.593 205482.0183 194818.0911 202209.5594 230559.8761 193908.2982 201676.1379 223843.1674 188123.5111 1.281921317 1.059163694 1.092271865 1.035586089 1.074876597 1.225577147 1.030749942 1.072041111 1.18987343 1 17.52132064 1.418509822 0.011639609 1.70E-07 2.169356963 0.140014273 0.082238065 1705.886602 19.53587861 1825.280643 1811.853473 26.21258323 -1.418509822 2.169356793 S(ph)PQGQLDTSESKPDSFFLEPLMPAVLKPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQGQLDTSESKPDSFFLEPLMPAVLKPAK 30 2 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)PQGQLDTSESKPDSFFLEPLMPAVLKPAK;S(0.829)PQGQLDT(0.057)S(0.057)ES(0.057)KPDSFFLEPLMPAVLKPAK 292.18 3.60E-81 2194500000 1185951 526068 951806 566336 1267557 1034280 1187638 858455 1136518 544239 TRUE FALSE 1232773.261 616416.0868 976610.8463 678355.5705 1052098.114 794084.1447 1094547.83 846948.8149 1095614.939 650872.212 1.894032713 0.947061613 1.500464804 1.042225429 1.616443435 1.220030799 1.681663175 1.301252073 1.683302681 1 19.3120148 S(ph)PQHFHRPDQGINIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPQHFHRPDQGINIYR 16 1 O14639-3;O14639-5;J3QSX6;O14639-4;H0Y7N6;F6XFR5 O14639-3 ABLIM1 Actin-binding LIM protein 1 1 S(1)PQHFHRPDQGINIYR;S(1)PQHFHRPDQGINIYR;S(1)PQHFHRPDQGINIYR 226.99 3.29E-15 788150000 502682 482647 523912 342817 688630 621901 454034 483656 553905 568200 TRUE FALSE 522528.2735 565537.8678 537565.5771 410625.1794 571576.9186 477473.9178 418445.6287 477173.3824 533970.0672 679527.9112 0.768957779 0.832251124 0.791086824 0.604280078 0.841138251 0.702655343 0.615788729 0.702213073 0.785795636 1 19.37417328 0.873996049 4.546956955 0.999975982 0.729334719 0.522966009 0.076473183 0.718761627 24.83424997 0.075511101 0.019164798 7.481626934 -0.873996049 -0.270641263 S(ph)PQLSDFGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPQLSDFGLER 11 0 Q8IX90-3;Q8IX90 Q8IX90-3 SKA3 Spindle and kinetochore-associated protein 3 1 S(1)PQLSDFGLER;S(1)PQLSDFGLER;S(1)PQLSDFGLER 162.94 2.57E-05 285425000 176698 169009 171433 177329 189853 210427 198808 189194 179434 165164 TRUE FALSE 183674.1735 198034.981 175900.6848 212404.1469 157581.8549 161558.5183 183224.9095 186658.1639 172976.2054 197524.7235 0.92987941 1.002583259 0.890524901 1.075329423 0.797782941 0.817915425 0.927604941 0.944986332 0.875719263 1 17.59167372 3.234593612 24.99812457 0.893809807 0.970575643 0.235388277 0.07099864 160.0262053 1008407.577 0.020279746 0.025097918 1716.301618 -3.234593612 0.076765836 S(ph)PQPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQPNK 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(1)PQPNK;S(1)PQPNK 74.301 0.084637 406750000 797180 595870 708180 669920 961750 992960 1001160 669990 910120 554500 TRUE FALSE 828653.282 698206.0373 726635.7526 802428.1765 798272.0785 762360.0885 922686.4632 661009.8799 877364.959 663143.6585 1.249583362 1.052872976 1.095744102 1.210036719 1.203769452 1.149615289 1.391382473 0.996782328 1.323039055 1 19.33896191 5.080138134 18.94427314 1.161399357 4.157603138 0.046443208 0.12351373 751.1329291 184031.1041 0.026564484 3470.054582 120264.6894 -5.080138134 2.996203781 S(ph)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;S(1)PQPPAEEDEDDFDDTLVAIDTYNCDLHFK;S(0.999)PQPPAEEDEDDFDDT(0.001)LVAIDTYNCDLHFK 188.48 5.56E-18 86367000 170117 165966 166130 156231 210230 221228 196597 182213 175921 150885 TRUE FALSE 176833.3505 194469.3695 170459.4843 187133.0255 174495.1797 169851.1497 181187.2134 179770.7328 169589.6376 180448.0269 0.979968324 1.077702942 0.944645875 1.037046671 0.967010738 0.94127463 1.004096396 0.996246597 0.939825392 1 17.46122384 3.870636886 1.276628392 0.979187317 1.021001193 0.105867353 0.039900892 1.059081336 3.169642894 0.011894636 0.038369692 7423.981588 -3.870636886 0.041813875 S(ph)PQPPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPQPPSR 7 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 S(1)PQPPSR;S(1)PQPPSR;S(1)PQPPSR 90.696 0.017779 4228630000 1201400 1303640 1321060 1294850 1337030 1513760 1196500 1281750 1194490 1354200 TRUE FALSE 1248832.2 1527530.029 1355487.909 1550967.465 1109762.118 1162212.181 1102715.204 1264570.238 1151500.538 1619529.562 0.771107999 0.943193669 0.83696398 0.957665424 0.685237333 0.71762332 0.680886122 0.780825659 0.711009274 1 20.62714337 3.233936273 24.99997936 0.746261899 0.87906792 0.231470488 0.099677675 136.1450222 736023.0066 0.02614333 0.032232883 1713.705827 -3.233936273 0.132806021 S(ph)PQPPVEEEDEHFDDTVVCLDTYNCDLHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 338.51 1.94E-105 3542791000 470141.8 344700 394590 431887 476401 510470 562910 438200 429375 315333 TRUE FALSE 488703.3613 403899.5436 404873.3396 517312.9595 395422.5282 391921.0787 518787.6433 432326.6458 413921.8776 377116.4639 1.295895056 1.071020712 1.073602927 1.371759149 1.048542204 1.039257408 1.375669569 1.146400879 1.097596942 1 18.52465061 1.008060877 2.794323798 1.00197895 1.176672651 0.174157098 0.122342432 0.435690457 7.843331889 0.11286725 0.030066157 10.18734178 -1.008060877 0.1746937 S(ph)PQQSAALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPQQSAALPR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 S(1)PQQSAALPR;S(1)PQQSAALPR;S(0.997)PQQS(0.003)AALPR;S(1)PQQSAALPR 110.58 0.002629 349830000 184194 337310 246048 358085 253491 373754 278252 288499 251281 430256 TRUE FALSE 191466.1213 395240.3686 252460.213 428913.1442 210402.6904 286955.2978 256441.8812 284632.1428 242237.4459 514556.4255 0.372099369 0.768118614 0.490636596 0.833559009 0.408901104 0.557675084 0.498374655 0.553160215 0.470769451 1 18.97296976 -1.526799563 3.258598723 1.012687205 0.556923201 0.48543738 0.138730063 36038671.89 42128768.94 4014783.984 0.030457269 0.029730378 1.526799563 -0.455764005 S(ph)PQREPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPQREPQR 8 1 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR;S(1)PQREPQR 112.13 0.0018781 4114090000 328497 296724 311133 297114 369014 458226 324332 305320 323122 297092 TRUE FALSE 341466.3152 347684.0388 319241.3816 355882.2624 306289.1321 351809.956 298910.0104 301227.6848 311492.9023 355301.4892 0.961060749 0.978560601 0.898508425 1.001634593 0.862054175 0.990173041 0.841285554 0.847808675 0.876700244 1 18.43868421 2.233153025 24.99990394 0.874110563 0.946215116 0.165994688 0.057665737 171.7128169 793839.0304 0.01974094 0.015003144 171.0617951 -2.233153025 0.072104553 S(ph)PQRPGWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPQRPGWSR 9 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR;S(1)PQRPGWSR 95.273 0.0049396 1766600000 164413 185739 194547 206291 237323 270241 206686 209016 202536 193655 TRUE FALSE 170904.1522 217638.2284 199617.0546 247094.7441 196982.9212 207481.6233 190485.4112 206214.4824 195246.7689 231597.9895 0.737934524 0.93972417 0.861911863 1.066912302 0.850538131 0.895869708 0.822483009 0.890398413 0.843041727 1 17.8212632 S(ph)PQRPS(ph)DWSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPQRPSDWSK 10 1 Q5UIP0-2;Q5UIP0;H7BZN3 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 2 S(1)PQRPS(1)DWSK 54.871 0.076415 227750000 28050 348350 314930 356590 274970 403470 322140 342090 336010 401900 TRUE FALSE 29157.43566 408176.4027 323137.3345 427122.4377 228230.6976 309770.2071 296889.825 337504.8431 323917.0657 480644.6102 0.060663191 0.849227047 0.672299923 0.888645017 0.474842935 0.644489089 0.617690948 0.702192089 0.673922185 1 18.87461103 -5 0.11908749 2.113291726 0.463789301 0.265656905 0.210134007 234.0437235 1.812354542 63.75179859 1.975274942 1.00E-05 5 -1.649502424 S(ph)PQTLAPVGEDAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQTLAPVGEDAMK 14 0 Q92797 Q92797 SYMPK Symplekin 1 S(1)PQTLAPVGEDAMK;S(0.997)PQT(0.003)LAPVGEDAMK 189.81 7.09E-07 211890000 548930 329120 472430 481740 599220 643600 647150 496420 566500 267250 TRUE FALSE 570602.1803 385643.7998 484741.9139 577026.7341 497364.7984 494133.6539 596424.692 489766.3019 546111.7757 319612.5207 1.785293577 1.206597911 1.516654957 1.805394648 1.556149294 1.546039726 1.866086756 1.532375205 1.708668279 1 18.2859644 -0.878697265 5.402465572 0.999999469 1.606407937 0.507071865 0.181394818 1.12E-06 2.33E-07 0.169620907 0.039979997 0.132221699 0.878697265 0.606408468 S(ph)PRPDHPGTPPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPRPDHPGTPPHK 13 1 P30291 P30291 WEE1 Wee1-like protein kinase 1 S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK;S(1)PRPDHPGTPPHK 139.29 2.36E-05 546170000 317332 284468 357186 295763 395643 440830 351124 352218 350992 284195 TRUE FALSE 329860.5124 333323.1661 366494.5606 354264.0386 328391.7442 338453.9133 323601.9834 347497.0938 338359.8665 339877.569 0.970527456 0.9807154 1.078313469 1.042328388 0.966205993 0.995811269 0.952113387 1.02241844 0.995534561 1 18.37465563 3.239630064 24.99997436 0.989830838 1.019620212 0.155282018 0.033314632 59.24557834 1384945.292 0.00998153 0.012773968 1736.321183 -3.239630064 0.029789374 S(ph)PRPTGSDLLPGAPILSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPRPTGSDLLPGAPILSLR 19 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 S(1)PRPTGSDLLPGAPILSLR;S(0.996)PRPT(0.002)GS(0.002)DLLPGAPILSLR;S(0.999)PRPT(0.001)GS(0.001)DLLPGAPILSLR;S(0.913)PRPT(0.073)GS(0.014)DLLPGAPILSLR;S(0.915)PRPT(0.005)GS(0.001)DLLPGAPILS(0.079)LR 111.45 0.0004198 1199443000 287616 326849 332404 398169 376644 430899 408925 367062 311059 334384 TRUE FALSE 298971.3018 382982.7732 341066.7213 476925.6398 312622.1874 330829.2376 376872.39 362142.1343 299864.0474 399900.1426 0.747614892 0.957696016 0.852879719 1.192611827 0.781750627 0.827279619 0.942416243 0.905581408 0.749847313 1 18.60928027 S(ph)PRSPSGHPHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPRSPSGHPHVR 12 1 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.5)PRS(0.5)PSGHPHVR;S(0.499)PRS(0.499)PS(0.001)GHPHVR;S(0.5)PRS(0.5)PS(0.001)GHPHVR;S(0.5)PRS(0.5)PS(0.001)GHPHVR 84.566 0.0073462 110854900 23807.7 67797.4 68419.7 42279.8 79709.8 85716 29409.5 67079.8 58956.8 121535.3 TRUE FALSE 24747.64638 79441.07606 70202.77359 50642.61825 66160.75667 65809.75804 27104.30654 66180.705 56834.95628 145347.8151 0.170265004 0.546558447 0.482998479 0.348423664 0.455189207 0.452774319 0.18647894 0.455326452 0.391027249 1 17.14914986 -0.006288903 1.783300653 1.000167401 0.392745617 0.710714949 0.117154788 25.38962215 43.61485947 0.117997259 0.029666548 0.985623607 0.006288903 -0.607421784 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 182.47 4.27E-14 626970000 212821 244947 277318 215935 314332 341669 309552 250998 262609 218042 TRUE FALSE 221223.3374 287014.7418 284545.1349 258646.2985 260901.9589 262321.5528 285288.5054 247633.7824 253157.7534 260763.1552 0.848368847 1.100672147 1.091201457 0.991882071 1.000532298 1.005976295 1.094052207 0.949650199 0.970834063 1 17.99238051 1.622841772 25 0.970184224 1.022577305 0.078786758 0.07020017 1.921220688 3199.725669 0.031567518 0.017416034 41.96060798 -1.622841772 0.052393082 S(ph)PS(ph)PAPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 90.149 0.016996 1709490000 1344840 1274400 1322490 1207920 1493270 1786070 1608320 1423180 1305830 1050330 TRUE FALSE 1397935.322 1493268.287 1356955.176 1446842.971 1239444.499 1371282.311 1482255.676 1404104.6 1258833.433 1256122.054 1.112897682 1.188792349 1.080273347 1.151833109 0.986722982 1.091679194 1.180025199 1.11780905 1.002158532 1 20.26054522 -4.999999997 0.125661389 0.631271318 1.156050996 0.267188026 0.060258638 218.2650985 1.752388799 20.1229905 0.519243745 1.00E-05 4.999999997 0.524779677 S(ph)PS(ph)PAPPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;S(1)PS(1)PAPPPRR 88.087 0.043513 1416730000 796707 854500 834506 747757 957740 1101700 896250 844070 841910 699183 TRUE FALSE 828161.6076 1001253.728 856253.9119 895661.1028 794943.6969 845846.8714 825999.5831 832756.6223 811609.8236 836174.5222 0.990417174 1.197421951 1.024013396 1.071141346 0.950691125 1.011567381 0.98783156 0.995912456 0.970622522 1 19.67344456 3.288728181 9.462889795 0.987897053 1.07669087 0.384452218 0.052227287 0.34339396 61.41588298 0.013474838 0.018212735 1944.142889 -3.288728181 0.088793817 S(ph)PS(ph)PKPR ddPTM_MDA-MB-175_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 491860000 769790 353840 447940 350210 551080 796610 724870 470970 457910 234320 TRUE FALSE 800181.9036 414609.2675 459613.6844 419480.4927 457407.6184 611609.4002 668052.7953 464657.4175 441429.9085 280230.5177 2.855441692 1.479529321 1.640127165 1.496912243 1.632254839 2.182522465 2.383940196 1.658125679 1.575238529 1 18.09625455 0.94901128 1.901208437 1.008840561 1.899054784 0.317628047 0.417895131 0.485684063 3.692283356 0.394366197 0.11103515 8.892242125 -0.94901128 0.890214224 S(ph)PS(ph)PKPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.988)PS(0.716)PKPT(0.296)K;S(0.999)PS(0.958)PKPT(0.042)K;S(1)PS(0.988)PKPT(0.012)K 64.439 0.038113 4456400000 5078400 1653940 2351990 1578990 3337730 3866020 3845530 2449630 2709820 1194380 TRUE FALSE 5278899.153 1937991.329 2413284.792 1891309.509 2770383.847 2968195.445 3544107.31 2416796.717 2612294.108 1428395.893 3.695683514 1.356760642 1.689506952 1.324079352 1.939507009 2.077992144 2.481179991 1.691965601 1.828830592 1 20.44596446 7.999953881 0.047207235 2.12E-10 5.311472417 0.210736869 0.635951713 1173.642582 4.191076859 115.7499744 464.1442809 99989381.2 -7.999953881 5.311472417 S(ph)PS(ph)PLRGNVVPS(ph)PLPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSPLRGNVVPSPLPTR 17 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(0.998)PLPT(0.002)R;S(1)PS(1)PLRGNVVPS(0.994)PLPT(0.006)R;S(1)PS(1)PLRGNVVPS(0.953)PLPT(0.047)R 81.888 0.014036 276206000 155141 143938 152864 157242 185713 204185 145585 156427 161689 130179 TRUE FALSE 161266.0865 168658.2318 156847.7614 188343.9983 154145.5706 156766.1282 134173.6673 154330.3519 155869.8445 155685.0826 1.035848032 1.08332943 1.007468145 1.209775497 0.990111371 1.006943797 0.861827383 0.991298263 1.001186767 1 17.24827119 3.024283909 24.99963971 0.967590491 1.081246774 0.419731359 0.062852179 211.5559896 217789.7121 0.017700788 0.021155667 1057.508602 -3.024283909 0.113656283 S(ph)PS(ph)PLRGNVVPS(ph)PLPTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPLRGNVVPSPLPTRR 18 2 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 3 S(1)PS(1)PLRGNVVPS(0.903)PLPT(0.097)RR 79.762 0.006421 127050000 91576 95831 102490 77685 132340 132210 84531 98536 87633 91345 TRUE FALSE 95191.49119 112289.2288 105160.9736 93050.86113 109844.8941 101506.2312 77905.23934 97215.28609 84479.10545 109242.3038 0.871379382 1.027891438 0.962639654 0.851784134 1.005516089 0.929184277 0.713141673 0.889905125 0.7733186 1 16.73717212 2.447831923 24.9854183 0.834547177 0.946732428 0.233348347 0.085974402 251.3764353 214436.6222 0.027601889 0.023093699 280.4348113 -2.447831923 0.112185251 S(ph)PS(ph)PLRGNVVPSPLPTR ddPTM_MDA-MB-175_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 77.575 0.0099535 177088000 86825 78688 82215 68554 64010 108492 86612 75873 74460 66945 TRUE FALSE 90252.91804 92202.05189 84357.59044 82113.77659 53129.60306 83296.37721 79823.12512 74856.04654 71780.19914 80061.59101 1.127293586 1.151639016 1.053658682 1.025632585 0.663609134 1.040403721 0.99702147 0.934980752 0.896562237 1 16.28882267 3.74948669 2.651102612 0.927639521 1.128293826 0.409742788 0.100544871 0.271262598 3.775374713 0.02759166 0.052794503 5616.770646 -3.74948669 0.200654306 S(ph)PS(ph)PSPTPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 2 S(0.997)PS(0.771)PS(0.228)PT(0.004)PEAK 112.5 0.002219 101370000 485200 247470 292590 233860 421820 515930 415620 319260 315770 186890 TRUE FALSE 504356.0707 289971.0475 300215.1358 280116.81 350119.1871 396113.0765 383042.6184 314980.8419 304405.4994 223507.5173 2.256550817 1.297365972 1.343199278 1.253276907 1.566476114 1.772258407 1.713779577 1.409262855 1.361947478 1 17.76996383 0.942463299 1.564225615 1.005663788 1.565685028 0.295548775 0.278414971 0.600306601 2.984545449 0.261089783 0.076195162 8.759176937 -0.942463299 0.56002124 S(ph)PS(ph)PYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.999)PS(0.945)PY(0.057)YSR;S(0.998)PS(0.909)PY(0.092)YSR;S(0.999)PS(0.988)PY(0.013)YSR;S(0.999)PS(0.984)PY(0.017)YSR;S(0.999)PS(0.972)PY(0.029)YSR;S(0.999)PS(0.96)PY(0.041)YSR 112.89 0.0043176 4737810000 3340020 3286020 3264150 3020680 3554000 4224710 3600990 3377760 3194130 2731280 TRUE FALSE 3471886.569 3850368.373 3349216.431 3618161.488 2949892.349 3243585.129 3318734.994 3332486.652 3079173.885 3266422.022 1.062902021 1.178772475 1.025347125 1.107683411 0.903095904 0.993008591 1.016015374 1.020225381 0.942674849 1 21.63927977 3.265154074 24.99998519 0.986029773 1.094873965 0.563738634 0.049121553 169.637315 159471.5337 0.013393596 0.018130003 1841.425163 -3.265154074 0.108844192 S(ph)PS(ph)YGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 S(1)PS(1)YGR 85.161 0.080449 447440000 770220 725020 704270 856990 842420 925130 1148700 795320 732980 483860 TRUE FALSE 800628.8803 849536.5451 722623.8548 1026500.064 699225.7493 710282.578 1058661.892 784660.0363 706600.193 578663.1029 1.383583775 1.468102149 1.248781633 1.773916565 1.20834687 1.227454411 1.829496104 1.355987676 1.221090803 1 19.14236413 1.056074496 2.618845385 1.00747489 1.445518286 0.32575094 0.201883796 0.281788974 4.061408669 0.183879991 0.049716947 11.37822444 -1.056074496 0.438043396 S(ph)PSAEFSPAAPPGISSIHSPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSAEFSPAAPPGISSIHSPSLR 23 0 G3V2D8;Q68DK2-5;Q68DK2-2;Q68DK2 G3V2D8 ZFYVE26 Zinc finger FYVE domain-containing protein 26 1 S(0.931)PS(0.069)AEFS(0.001)PAAPPGISSIHSPSLR 118.9 0.00015327 99131000 22624 42480 39988 56188 50730 62718 38559 46499 45519 43283 TRUE FALSE 23517.21299 49775.60955 41030.12013 67301.8187 42106.93272 48152.695 35536.64482 45875.75696 43880.78008 51763.47515 0.454320598 0.961597138 0.792646166 1.300179683 0.813448722 0.930244634 0.686519688 0.886257285 0.847717043 1 15.65964686 4.743076438 24.74631644 0.904052152 0.454320389 0.438640992 0.155419254 382.6704206 2096915.659 0.03627874 0.288151964 55344.75098 -4.743076438 -0.449731763 S(ph)PSAPAATSSASSSTSSYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSAPAATSSASSSTSSYKR 20 1 A0A087X0S7;A0A0C4DH00;A0A087WTU1;A0A0B4J2G4;Q15345-3;Q15345 A0A087X0S7 LRRC41 Leucine-rich repeat-containing protein 41 1 S(0.984)PS(0.016)APAATSSASSSTSSYKR 130.6 9.71E-06 146330000 53863 45188 50868 44217 69413 74263 62239 56713 64587 42049 TRUE FALSE 55989.55283 52948.68749 52193.66187 52962.99063 57614.20305 57016.54372 57360.54455 55952.855 62262.52649 50287.69647 1.113384719 1.052915349 1.037901227 1.053199775 1.145691831 1.133807029 1.140647685 1.112654962 1.238126438 1 15.61791785 3.240325072 24.97298857 1.133599994 1.061644261 0.228005584 0.057269249 59.03343836 835512.9229 0.015030806 0.019363487 1739.102071 -3.240325072 -0.071955733 S(ph)PSFASEWDEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.478)PS(0.478)FAS(0.044)EWDEIEK 110.77 0.00066468 12808000 34000 25372 33229 24328 42575 44911 39117 31708 35598 25329 TRUE FALSE 35342.34625 29729.44363 34094.97504 29140.00579 35338.11671 34481.10088 36050.90733 31283.00612 34316.83493 30291.7326 1.166732413 0.981437544 1.12555381 0.96197884 1.166592785 1.138300715 1.190123649 1.032724227 1.132877917 1 14.88663648 3.202566602 24.99999091 1.113052437 1.058149434 0.093326154 0.077805979 389.7966897 270735.7721 0.021257932 0.025408882 1594.287356 -3.202566602 -0.054903003 S(ph)PSFGDPQLS(ph)PEARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 2 S(0.99)PS(0.014)FGDPQLS(0.996)PEARPR;S(0.965)PS(0.047)FGDPQLS(0.987)PEARPR;S(0.993)PS(0.007)FGDPQLS(1)PEARPR;S(0.998)PS(0.002)FGDPQLS(1)PEARPR 150.36 4.25E-07 292130000 502428 545060 512340 490340 494460 630140 558120 511656 527900 416579 TRUE FALSE 522264.2454 638669.815 525692.0013 587327.7885 410411.8658 483799.5349 514373.096 504798.0882 508900.9821 498199.6792 1.048303054 1.281955492 1.05518334 1.178900375 0.823789904 0.971095637 1.032463724 1.013244507 1.021479948 1 18.92636457 3.274885079 24.99994923 0.983596328 1.145011942 0.486001715 0.082455745 148.3255017 102082.5912 0.022204957 0.030064745 1883.150714 -3.274885079 0.161415614 S(ph)PSFNMQLISQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSFNMQLISQV 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 S(0.629)PS(0.371)FNMQLISQV 68.893 0.053961 12237000 15848 8425.4 10523 9475.5 17202 15415 14391 11486 12693 10459 TRUE FALSE 16473.69128 9872.396909 10797.23802 11349.72562 14278.01018 11835.09987 13262.99582 11332.04896 12236.18141 12508.2408 1.317027034 0.789271415 0.863209959 0.907379847 1.141488273 0.946184204 1.060340621 0.905966645 0.978249588 1 13.61059128 4.755890547 24.93506773 0.955587105 1.317027336 0.570140212 0.094386249 2699.727467 3884421.356 0.02296946 0.697272183 57002.05949 -4.755890547 0.361440231 S(ph)PSGHPHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SPSGHPHVR 9 0 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 1 S(0.998)PS(0.002)GHPHVR;S(0.999)PS(0.001)GHPHVR;S(0.999)PS(0.001)GHPHVR;S(0.896)PS(0.104)GHPHVR;S(0.99)PS(0.01)GHPHVR;S(0.999)PS(0.001)GHPHVR;S(0.805)PS(0.195)GHPHVR 147.62 5.92E-05 5869143400 322293.6 644325.3 639413.1 608186.1 571107 700919 576645.4 583848.9 602911.2 609241.5 TRUE FALSE 335018.0002 754983.1581 656076.7307 728483.4953 474030.4361 538141.1848 531446.4268 576023.3605 581212.5437 728610.7073 0.459803839 1.03619553 0.900448928 0.999825405 0.650594936 0.738585337 0.729396949 0.790577677 0.797699701 1 19.47478867 4.760471821 24.42168104 0.832057865 0.459803306 0.458920518 0.125620982 4225.588889 4709631.933 0.030871631 1.497268385 57606.54394 -4.760471821 -0.372254559 S(ph)PSGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSGLRPR 8 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4 P49815 TSC2 Tuberin 1 S(0.877)PS(0.123)GLRPR;S(0.997)PS(0.003)GLRPR;S(1)PSGLRPR 72.275 0.028207 654630000 144980 174069 160880 171923 197486 213528 168143 169298 178351 202799 TRUE FALSE 150703.9223 203963.9967 165072.665 205928.8563 163917.4003 163939.358 154963.5123 167028.8372 171932.1823 242533.5812 0.621373426 0.840972189 0.680617769 0.849073581 0.67585445 0.675944986 0.638936314 0.688683342 0.708900522 1 17.88782499 -1.813880689 6.533746225 1.017661251 0.709545709 0.589760756 0.072826901 0.017876651 0.000509231 0.067280108 0.016003873 0.015350386 1.813880689 -0.308115541 S(ph)PSGPPAMDLEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSGPPAMDLEGPR 14 0 O96018 O96018 APBA3 Amyloid beta A4 precursor protein-binding family A member 3 1 S(0.968)PS(0.032)GPPAMDLEGPR 71.506 0.032226 0 76892 67030 76109 71437 112970 120800 86896 82717 99328 73891 TRUE FALSE 79927.75553 78541.88108 78092.46306 85567.02538 93767.39975 92746.03074 80084.86446 81608.31391 95753.20468 88368.52672 0.904482156 0.888799259 0.883713534 0.968297521 1.061094976 1.049536913 0.906260039 0.923499768 1.083566834 1 16.43124501 3.651901886 4.510254074 0.991950397 0.892003593 0.45207077 0.053831398 0.24184167 8.695847326 0.016113232 0.02574534 4486.440229 -3.651901886 -0.099946804 S(ph)PSHTRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSHTRPR 8 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 S(0.914)PS(0.062)HT(0.025)RPR 76.143 0.022144 173450000 33522 32235 33770 36646 28591 42785 50283 33466 38767 29547 TRUE FALSE 34845.47444 37771.1105 34650.07394 43894.46942 23731.11203 32848.83216 46341.68707 33017.44301 37371.78324 35336.16894 0.986113534 1.06890791 0.980583775 1.242196614 0.67158135 0.929609325 1.311451933 0.934380947 1.057607102 1 15.10885801 S(ph)PSLAK ddPTM_MDA-MB-175_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(0.989)PS(0.011)LAK;S(0.985)PS(0.015)LAK 86.095 0.056609 403610000 812390 727500 819710 865760 1159200 1160750 996390 902680 896210 831690 TRUE FALSE 844463.7845 852442.4658 841072.316 1037004.744 962159.5981 891183.4038 918290.3482 890581.0511 863955.5772 994643.7318 0.849011317 0.857032964 0.845601585 1.042589131 0.967340936 0.895982527 0.923235445 0.89537693 0.868608075 1 19.92382034 S(ph)PSLSLAPLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPSLSLAPLSPR 12 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 2 S(0.995)PS(0.005)LSLAPLS(1)PR;S(0.987)PS(0.012)LS(0.003)LAPLS(0.998)PR;S(0.995)PS(0.005)LSLAPLS(1)PR;S(1)PSLSLAPLS(1)PR;S(0.998)PS(0.002)LS(0.001)LAPLS(0.999)PR;S(0.989)PS(0.011)LSLAPLS(1)PR 248.42 1.38E-16 1118000000 988440 925027 984920 1060970 1223810 1279750 1210240 1064210 1057990 981890 TRUE FALSE 1027464.374 1083893.192 1010587.824 1270826.699 1015787.213 982547.4573 1115378.226 1049946.006 1019913.147 1174272.546 0.874979474 0.92303375 0.860607555 1.082224654 0.865035308 0.836728629 0.949846124 0.89412463 0.868548916 1 20.16333586 S(ph)PSLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.928)PS(0.072)LSSK;S(0.993)PS(0.007)LSSK;S(0.994)PS(0.006)LSSK 96.034 0.013666 1711180000 2370660 1714920 2157270 1865670 2539490 2693910 2899430 2215390 2215810 1474310 TRUE FALSE 2464255.487 2009444.17 2213490.228 2234693.958 2107828.397 2068290.229 2672165.1 2185696.321 2136063.431 1763172.817 1.397625612 1.139675107 1.255401743 1.267427637 1.195474645 1.173050202 1.515543499 1.239638168 1.211488409 1 20.74974246 0.820191492 2.670087909 1.000315196 1.271619 0.38047409 0.1046281 0.787825754 9.523713873 0.09773579 0.025952324 6.609848289 -0.820191492 0.271303804 S(ph)PSMAQDSGASELLPNGDLEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSMAQDSGASELLPNGDLEKR 22 1 F8WE91;Q9Y6K1;Q9Y6K1-3 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 S(0.975)PS(0.025)MAQDSGASELLPNGDLEKR 118.43 6.06E-05 67873000 87851 56416 60367 67146 96875 95425 79525 70642 74650 53176 TRUE FALSE 91319.42532 66105.00914 61940.21361 80427.27839 80408.2221 73263.98993 73291.6227 69695.15954 71963.36108 63594.81908 1.435956995 1.039471613 0.973982071 1.264682871 1.26438322 1.152043374 1.152477887 1.095925117 1.131591569 1 15.95662162 0.915989098 0.678997737 1.001426197 1.178947073 0.176865002 0.120693277 1.637606959 1.697656483 0.121413405 0.04781517 8.241174266 -0.915989098 0.177520876 S(ph)PSMSISEPISVTLPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSMSISEPISVTLPPR 17 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.881)PS(0.118)MS(0.001)ISEPISVTLPPR 86.497 0.005009 31603000 15115 13536 14693 12171 21710 22565 13834 17054 14302 14287 TRUE FALSE 15711.75187 15860.7027 15075.91165 14578.38747 18019.74195 17324.62073 12749.65493 16825.41902 13787.27381 17086.26411 0.919554548 0.928272126 0.882341017 0.853222646 1.054633233 1.013950189 0.746193249 0.984733639 0.806921497 1 14.06054937 4.558762091 0.002965128 1.824087029 2.41E-07 0.010975821 0.092479878 837072.6418 408.2833208 123028.2265 128174.6137 36204.46143 -4.558762091 -1.824086788 S(ph)PSPAHLPDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.64)PS(0.36)PAHLPDDPK 136.17 7.39E-05 882250000 1665400 1503300 1575000 1595000 1888000 2416100 2039200 1635400 1613200 1202200 TRUE FALSE 1731151.278 1761480.081 1616045.794 1910486.239 1567078.434 1854997.391 1879362.176 1613480.138 1555141.247 1437748.072 1.204071361 1.225166018 1.124011797 1.328804591 1.089953424 1.290210314 1.307156804 1.1222273 1.081650726 1 20.45537947 1.322984158 2.232001411 1.019023603 1.220884533 0.503651941 0.073776087 0.234294535 1.969519014 0.062859587 0.018739805 21.03701703 -1.322984158 0.20186093 S(ph)PSPSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.999)PS(0.001)PSFR;S(0.997)PS(0.003)PSFR 130.56 0.0037251 2188500000 122000 140559 137971 154329 143308 185580 154391 149696 133292 147460 TRUE FALSE 126816.6542 164698.9149 141566.6376 184854.8156 118948.5573 142481.8575 142289.43 147689.57 128494.847 176351.9637 0.719111098 0.933921638 0.80275056 1.048215238 0.674495224 0.807940294 0.806849139 0.837470516 0.728627253 1 17.42809811 4.77926238 22.18405194 0.839945898 0.71910957 0.106539568 0.110045454 12745.17609 6945978.411 0.024507144 6.405886916 60153.70475 -4.77926238 -0.120836328 S(ph)PSPVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.558)PS(0.442)PVLR;S(0.849)PS(0.151)PVLR;S(0.901)PS(0.099)PVLR 104.44 0.0085507 1079930000 758690 734320 739770 745180 868920 980540 808830 778240 755300 808820 TRUE FALSE 788643.667 860433.7478 759049.0139 892574.3799 721221.2888 752824.4452 745431.7911 767808.9657 728116.9005 967292.7932 0.815310186 0.889527715 0.784714845 0.922755122 0.745608045 0.778279804 0.770637181 0.793770998 0.752736819 1 19.88359312 5.761898435 8.463247256 0.816349763 0.05395562 0 0.080315709 33417.04357 16908790.6 0.017320131 22098251.06 577960.8683 -5.761898435 -0.762394144 S(ph)PSPVQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.958)PS(0.042)PVQGK;S(0.885)PS(0.115)PVQGK;S(0.841)PS(0.159)PVQGK 134.51 0.00091634 2601000000 4041500 3163400 3817960 2817250 4516340 4544280 4327720 3774960 3845180 2762140 TRUE FALSE 4201061.541 3706689.342 3917459.174 3374493.641 3748654.14 3488939.839 3988501.998 3724362.836 3706792.723 3303328.449 1.271766222 1.122107414 1.185912704 1.021543481 1.134811206 1.056189202 1.207419141 1.127457622 1.12213871 1 21.65548899 -5 0.017268443 4.23E-06 1.961841751 0.316334305 0.065745846 6261.988784 8.196436973 602.6410153 357.9983605 1.00E-05 5 1.961837522 S(ph)PSPYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPYYSR 8 0 P62995;P62995-3;H7BXF3;H7C2L4;Q13595;Q13595-3;Q13595-4 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 S(0.999)PS(0.001)PYYSR 107.21 0.004246 207940000 72357 74853 85191 78849 90496 102160 94963 75699 74778 80008 TRUE FALSE 75213.71023 87708.42047 87411.14745 94445.09686 75113.52224 78434.88825 87519.55192 74684.37872 72086.75439 95684.03575 0.786063314 0.916646333 0.913539513 0.98705177 0.785016243 0.819728052 0.914672455 0.780531236 0.753383298 1 16.54599062 3.218284068 24.99998364 0.831957224 0.902863531 0.101411593 0.082027804 452.1986452 557537.4281 0.022975656 0.027492193 1653.042684 -3.218284068 0.070906308 S(ph)PSQDFSFIEDTEILDSAMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SPSQDFSFIEDTEILDSAMYR 21 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 S(0.443)PS(0.443)QDFS(0.114)FIEDTEILDSAMYR;S(0.415)PS(0.415)QDFS(0.171)FIEDTEILDSAMYR;S(0.494)PS(0.494)QDFS(0.012)FIEDTEILDSAMYR;S(0.489)PS(0.489)QDFS(0.023)FIEDTEILDSAMYR;S(0.499)PS(0.499)QDFS(0.002)FIEDTEILDSAMYR;S(0.458)PS(0.458)QDFS(0.085)FIEDTEILDSAMYR;S(0.484)PS(0.484)QDFS(0.033)FIEDTEILDSAMYR 256.56 1.21E-36 484551000 200802.1 257962.7 260017.9 244099.3 263794.4 292518 259762.9 274145 276700.1 281499 TRUE FALSE 208729.922 302265.7871 266794.1801 292381.413 218954.7221 224585.1277 239402.0051 270470.5347 266741.7175 336653.3394 0.620014411 0.897854712 0.792489332 0.868494023 0.650386307 0.667110946 0.711123215 0.803409629 0.792333496 1 18.36090425 0.602655905 1.353534494 0.999620694 0.753195453 0.425630377 0.086695711 1.468245705 3.777230157 0.083162399 0.024643169 4.005492334 -0.602655905 -0.246425241 S(ph)PSSDLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.333)PS(0.333)S(0.333)DLDT(0.002)DAEGDDFELLDQSELSQLDPASSR;S(0.329)PS(0.329)S(0.329)DLDT(0.012)DAEGDDFELLDQSELSQLDPASSR 150.62 1.80E-10 190121000 61747 60606 67537 74252 74481 92408 76572 64952 71616 61550 TRUE FALSE 64184.81924 71014.60905 69297.0697 88938.82398 61820.74622 70947.64246 70570.08656 64081.42468 69038.55415 73609.54405 0.871963277 0.964747302 0.941414196 1.208251255 0.839846884 0.963837548 0.958708378 0.870558642 0.937902211 1 16.16760521 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSSKPSLAVAVDSAPEVAVK 21 1 O60508;Q5SRN1 O60508 CDC40 Pre-mRNA-processing factor 17 1 S(0.946)PS(0.015)S(0.015)KPS(0.025)LAVAVDSAPEVAVK 116.08 8.38E-05 113260000 119650 73081 95125 89559 114490 120080 158690 100330 115670 72157 TRUE FALSE 124373.8744 85632.09326 97604.03565 107273.5029 95029.03069 92193.23983 146251.4631 98985.24046 111507.0593 86294.78262 1.441267602 0.992320632 1.131053729 1.243105315 1.101214092 1.06835242 1.694789171 1.147059387 1.292164554 1 16.39698572 S(ph)PSSQTPNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSSQTPNSR 10 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 S(0.999)PS(0.001)SQTPNSR 142.97 3.65E-05 326360000 92559 86779 98382 70629 89981 108530 82592 82150 71544 95023 TRUE FALSE 96213.30079 101682.6182 100945.9157 84599.20539 74686.06176 83325.55229 76118.22323 81048.91362 68969.14542 113640.9375 0.846642969 0.894771025 0.888288305 0.744443043 0.657210891 0.733235347 0.669813404 0.713201733 0.606904052 1 16.79412311 3.667112394 4.269342881 0.711408869 0.878908782 0.291671991 0.100511968 0.220256042 7.752530983 0.024583233 0.03982032 4646.355055 -3.667112394 0.167499913 S(ph)PSSVTGNALWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 S(0.983)PS(0.017)SVTGNALWK 174.94 3.04E-05 118840000 65931 61109 79682 62460 89316 89166 80425 72110 72912 53774 TRUE FALSE 68534.00679 71603.99539 81758.57838 74814.40158 74134.09822 68458.54782 74121.07835 71143.4834 70287.91136 64309.98573 1.065682195 1.11341955 1.271320114 1.163340354 1.152761851 1.064508832 1.152559397 1.106258734 1.092954859 1 15.97275515 2.840444276 6.8927033 1.096962673 1.158748091 0.232026831 0.060887279 0.442754353 25.98845633 0.018951343 0.020131475 692.5390644 -2.840444276 0.061785418 S(ph)PSTLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.938)PS(0.062)TLLPK;S(0.988)PS(0.012)TLLPK;S(0.914)PS(0.086)TLLPK;S(0.851)PS(0.149)TLLPK 140.88 0.00067393 1322200000 1692380 1235880 1478260 1308080 1688530 1898230 2042620 1546230 1624420 1020830 TRUE FALSE 1759196.469 1448132.776 1516784.67 1566814.32 1401514.274 1457394.85 1882514.107 1525505.316 1565957.442 1220842.094 1.440969703 1.186175332 1.242408562 1.283388186 1.147989802 1.19376196 1.541980013 1.249551702 1.282686311 1 20.21944518 -2.333332229 1.643370033 7.54E-05 1.283258956 0.35988283 0.114169709 829858.3771 96038.58844 3066297.247 0.030584664 0.004641601 2.333332229 1.283183605 S(ph)PSTTYLHTPTPSEDAAIPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSTTYLHTPTPSEDAAIPSK 21 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.972)PS(0.024)T(0.003)T(0.001)YLHTPTPSEDAAIPSK;S(0.907)PS(0.025)T(0.043)T(0.025)YLHTPTPSEDAAIPSK;S(0.976)PS(0.019)T(0.002)T(0.004)YLHTPTPSEDAAIPSK 226.56 1.53E-25 3208710000 1472386 1284545 1641200 1187370 1881970 1835170 1556761 1568347 1726470 1379340 TRUE FALSE 1530516.936 1505155.611 1683971.02 1422228.242 1562073.412 1408979.58 1434738.005 1547325.874 1664334.682 1649595.264 0.92781361 0.912439338 1.020838903 0.862167995 0.946943439 0.854136533 0.86975153 0.938003344 1.008935172 1 20.65368067 1.33072416 4.164585516 1.004895132 0.914021522 0.378272538 0.045885333 0.224076547 6.217316153 0.035237041 0.011645263 21.41529989 -1.33072416 -0.09087361 S(ph)PSVAAMASPQLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.992)PS(0.008)VAAMASPQLCR;S(0.539)PS(0.461)VAAMASPQLCR 148.85 1.60E-06 123880000 57529 62489 56864 64723 72920 70729 60021 62055 50886 71440 TRUE FALSE 59800.28934 73220.99965 58345.92255 77525.01622 60525.08445 54303.26166 55316.39718 61223.25423 49054.6228 85437.3002 0.699931871 0.857014436 0.682909249 0.907390754 0.708415227 0.635591967 0.647450201 0.716586948 0.574159327 1 16.38257844 4.208089165 24.91694451 0.721051734 0.778473614 0.011077473 0.126808621 691.7925953 565689.1946 0.03010173 0.065039837 16146.90033 -4.208089165 0.05742188 S(ph)PSVPKSPTPKS(ph)PPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.615)PS(0.152)VPKS(0.23)PT(0.017)PKS(0.98)PPS(0.006)R 72.145 0.020739 135600000 737560 273190 453660 232560 650090 594090 498740 428290 504780 270130 TRUE FALSE 766679.4383 320108.2574 465482.7523 278559.6739 539587.934 456121.601 459647.4556 422549.4731 486613.0664 323056.8015 2.37320321 0.990872985 1.440869686 0.862262217 1.670257154 1.41189289 1.422806929 1.307972688 1.506277113 1 18.30142832 8 0.03239573 1.52E-07 3.452648086 0.135856172 0.378606794 2975.339889 7.377455317 241.5732987 629.3449862 100000000 -8 3.452647933 FNWYVDGVEVHNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 FNWYVDGVEVHNAK 14 0 A0A0A0MS08;P01857 A0A0A0MS08 IGHG1 Ig gamma-1 chain C region 0 ; 144.12 8.94E-06 3267800000 8656900 3667370 1646700 707190 904910 2012650 545240 505280 487140 531940 FALSE TRUE 8998681.097 4297212.269 1689614.355 847070.0712 751093.7214 1545242.54 502502.6641 498507.5481 469607.9266 636163.4584 14.14523418 6.754886991 2.65594374 1.331528965 1.180661529 2.429002356 0.789895517 0.783615502 0.738187521 1 19.27903798 4.776695677 1.289743018 1.108895637 20.86643806 0.986824985 0.464038002 0.155884888 0.211773778 0.139249509 4.164645462 59799.2417 -4.776695677 19.75754242 up S(ph)PSY(ph)GRS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSYGRSR 8 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 S(0.991)PS(0.122)Y(0.89)GRS(0.997)R 60.161 0.08582 0 199340 194430 183660 149210 224590 268440 202830 167560 176480 166110 TRUE FALSE 207210.0971 227821.84 188446.3305 178723.2927 186414.272 206098.8782 186931.6546 165314.1323 170128.5193 198656.0741 1.043059459 1.146815374 0.948605933 0.899661857 0.938376905 1.037465777 0.940981319 0.832162485 0.856397269 1 17.59991338 4.149394413 5.917778202 0.922806041 1.093832854 0.524360069 0.062026329 0.149095489 7.808964592 0.016798042 0.03750276 14105.69254 -4.149394413 0.171026813 S(ph)PSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSYGR 6 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 S(1)PSYGR;S(0.999)PS(0.001)YGR;S(1)PSYGR;S(0.999)PS(0.001)YGR 157.21 0.010126 21820800000 1912724 1887926 2057960 2312610 1896418 2354750 2433490 1993760 2007358 1726480 TRUE FALSE 1988239.82 2212162.604 2111592.128 2770037.356 1574065.546 1807894.999 2242746.695 1967036.908 1935113.578 2064750.701 0.962944253 1.071394529 1.022686239 1.341584412 0.76235138 0.875599654 1.086207015 0.952675259 0.937214152 1 20.97753617 3.221100859 24.99999722 0.942215558 1.092136512 0.306145399 0.120484214 330.5135802 473249.3781 0.03513926 0.042089673 1663.799 -3.221100859 0.149920954 S(ph)PSYTNDSTATFIIDGMHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSYTNDSTATFIIDGMHCK 20 0 Q04656-5;Q04656;Q04656-2;Q04656-3 Q04656-5 ATP7A Copper-transporting ATPase 1 1 S(0.972)PS(0.027)YT(0.001)NDSTATFIIDGMHCK;S(0.814)PS(0.106)Y(0.08)TNDSTATFIIDGMHCK 178.95 3.87E-17 298490000 254950 241130 276250 259520 333040 380810 308380 276420 286530 228570 TRUE FALSE 265015.6229 282542.2018 283449.3019 310852.2814 276429.9798 292372.6487 284208.3698 272715.042 276217.8413 273353.9153 0.969496349 1.033613151 1.036931561 1.137178815 1.011253047 1.069575493 1.039708429 0.997662835 1.010476989 1 18.06041051 1.792721584 5.21081223 1.003140401 1.045755488 0.167539105 0.040336 0.355436444 18.35863575 0.019488631 0.010824444 62.04711375 -1.792721584 0.042615087 S(ph)PTAALNESLVECPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPTAALNESLVECPK 15 0 Q53EZ4 Q53EZ4 CEP55 Centrosomal protein of 55 kDa 1 S(0.985)PT(0.015)AALNESLVECPK;S(1)PTAALNESLVECPK 267.62 1.90E-25 238790000 138158 99756 127130 114731 163157 174278 167918 139154 160998 97909 TRUE FALSE 143612.5845 116888.317 130443.1122 137424.4494 135423.6314 133804.5757 154756.1484 137288.8682 155203.7134 117092.394 1.226489438 0.998257129 1.114018664 1.173641128 1.156553614 1.14272645 1.32165842 1.17248323 1.325480744 1 16.83728784 3.133760316 1.239299771 1.212339535 1.106726672 0.079077018 0.101725942 0.812162907 2.64171945 0.037163577 0.051301483 1360.693517 -3.133760316 -0.105612863 S(ph)PTEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPTEDFR 7 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.989)PT(0.011)EDFR;S(0.989)PT(0.011)EDFR;S(0.987)PT(0.013)EDFR;S(0.901)PT(0.099)EDFR;S(0.972)PT(0.028)EDFR;S(0.986)PT(0.014)EDFR 126.62 0.0041269 3609155000 3741020 4065090 3718370 4344730 4046180 4893950 4747740 4064110 3986520 3348340 TRUE FALSE 3888718.358 4763237.585 3815273.777 5204104.626 3358411.769 3757404.281 4375599.733 4009637.253 3843045.924 4004383.115 0.971115462 1.189505961 0.952774414 1.29960208 0.83868393 0.938322876 1.092702573 1.001312097 0.959709851 1 21.93314858 3.219477367 24.99995182 0.980584196 1.09866259 0.251334529 0.110415373 363.7251025 476495.7489 0.030509837 0.036521589 1657.59095 -3.219477367 0.118078395 S(ph)PTFSEELPVLGDGQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 S(0.92)PT(0.08)FSEELPVLGDGQQLR;S(0.999)PT(0.001)FSEELPVLGDGQQLR;S(0.939)PT(0.06)FSEELPVLGDGQQLR;S(0.5)PT(0.5)FSEELPVLGDGQQLR;S(0.988)PT(0.012)FSEELPVLGDGQQLR 342.42 1.36E-75 583000000 127646 127754 117906 129655 135207 174858 146406 144469 129376 125466 TRUE FALSE 132685.5626 149694.7557 120978.7272 155300.372 112224.5624 134249.8795 134930.3152 142532.6294 124719.783 150048.6605 0.884283553 0.9976414 0.806263294 1.035000056 0.747921121 0.89470895 0.899243717 0.949909375 0.831195578 1 17.19507091 -0.946331929 5.539348089 1.000000148 0.898435416 0.129069293 0.081870361 1.36E-07 2.57E-08 0.071921826 0.016952112 0.113153521 0.946331929 -0.101564732 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.939)PT(0.061)GPSNSFLANMGGTVAHK;S(0.851)PT(0.149)GPSNSFLANMGGTVAHK;S(0.979)PT(0.021)GPSNSFLANMGGTVAHK;S(0.966)PT(0.034)GPSNSFLANMGGTVAHK;S(0.848)PT(0.152)GPSNSFLANMGGTVAHK;S(0.766)PT(0.234)GPSNSFLANMGGTVAHK;S(0.903)PT(0.097)GPSNSFLANMGGTVAHK;S(0.859)PT(0.141)GPSNSFLANMGGTVAHK;S(0.828)PT(0.172)GPSNSFLANMGGTVAHK;S(0.995)PT(0.005)GPSNSFLANMGGTVAHK;S(0.978)PT(0.022)GPSNSFLANMGGTVAHK;S(0.836)PT(0.093)GPS(0.036)NS(0.036)FLANMGGTVAHK 278.95 7.81E-45 19325450000 4797286.4 3908146.6 4717805 4343304.1 5274463 5794957 5939168 4788319.4 5090509 3219008.9 TRUE FALSE 4986686.971 4579340.377 4840754.874 5202396.688 4377911.663 4449166.06 5473640.493 4724139.811 4907302.575 3849712.062 1.295340246 1.189528023 1.25743297 1.351372935 1.137204963 1.155713983 1.421831141 1.227141078 1.274719381 1 21.87631911 -0.975106604 4.966340764 0.999997917 1.25618629 0.466149597 0.082410537 1.84E-06 3.80E-07 0.077382674 0.018239123 0.105899375 0.975106604 0.256188372 S(ph)PTKTDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPTKTDPK 8 1 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.994)PT(0.006)KTDPK;S(0.988)PT(0.009)KT(0.002)DPK;S(0.85)PT(0.15)KTDPK 87.789 0.011396 636797000 2235000 774920 1239730 940110 1638910 1872430 2427810 1353740 1536970 457160 TRUE FALSE 2323239.526 908006.482 1272038.382 1126060.952 1360328.664 1437586.509 2237511.908 1335595.33 1481654.75 546731.7491 4.249322505 1.660789744 2.326622488 2.05962239 2.488109874 2.629418379 4.09252236 2.442871356 2.710021418 1 19.06047363 2.476533582 24.99984938 2.788226407 2.47589811 0 0.950235828 103.8026 4415394.736 0.310640645 0.262174104 299.5943244 -2.476533582 -0.312328296 S(ph)PTKTDPKNEEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPTKTDPKNEEEEK 14 2 Q5BKZ1;A0A0A0MRN4;Q5BKZ1-3 Q5BKZ1 ZNF326 DBIRD complex subunit ZNF326 1 S(0.979)PT(0.02)KT(0.001)DPKNEEEEK 96.487 0.001749 216260000 622100 100420 164160 97554 323110 425790 371270 175720 216430 42381 TRUE FALSE 646660.9884 117666.3538 168438.1445 116849.89 268187.8776 326906.7254 342168.8873 173364.7608 208640.7266 50684.74552 12.75849334 2.321533879 3.323251261 2.305425209 5.291293759 6.449805007 6.75092444 3.420452427 4.116440251 1 15.62926399 4.745902266 24.94820796 4.1171962 12.75849754 0.693508147 1.763398139 510.8501675 1735914.924 0.432482088 4.48599364 55706.03735 -4.745902266 8.641301344 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.973)PT(0.027)MEQAVQTASAHLPAPAAVGR;S(0.977)PT(0.023)MEQAVQTASAHLPAPAAVGR;S(0.971)PT(0.029)MEQAVQTASAHLPAPAAVGR;S(0.945)PT(0.055)MEQAVQTASAHLPAPAAVGR;S(0.974)PT(0.026)MEQAVQTASAHLPAPAAVGR;S(0.956)PT(0.044)MEQAVQTASAHLPAPAAVGR;S(0.8)PT(0.2)MEQAVQTASAHLPAPAAVGR;S(0.839)PT(0.16)MEQAVQTASAHLPAPAAVGR;S(0.806)PT(0.19)MEQAVQT(0.004)ASAHLPAPAAVGR;S(0.958)PT(0.042)MEQAVQTASAHLPAPAAVGR;S(0.819)PT(0.18)MEQAVQTASAHLPAPAAVGR;S(0.96)PT(0.04)MEQAVQTASAHLPAPAAVGR;S(0.982)PT(0.018)MEQAVQTASAHLPAPAAVGR 261.2 5.95E-44 13351310000 1070855 1264363 1389973 1492365 1508993 1687714 1612447 1494525 1551582 1124867 TRUE FALSE 1113133.182 1481507.51 1426196.838 1787550.343 1252494.909 1295768.001 1486059.191 1474493.337 1495740.867 1345263.152 0.827446423 1.101277105 1.060161974 1.328773735 0.931040821 0.96320783 1.104660593 1.096063127 1.111857457 1 20.35945698 4.741340052 24.3480015 1.081513562 0.827446294 0.344108078 0.103409412 202.1800123 1770966.291 0.024452211 0.167834999 55123.91475 -4.741340052 -0.254067268 S(ph)PTPPPSSKPSSIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPTPPPSSKPSSIPR 15 1 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3;H7C5F9 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 S(0.497)PT(0.497)PPPS(0.004)S(0.001)KPSSIPR 61.102 0.055748 240050000 477710 417030 440530 382220 540960 563540 527010 452720 495920 392070 TRUE FALSE 496570.3597 488651.6585 452010.5737 457821.9752 449007.8124 432666.3755 485701.5791 446652.0289 478071.9361 468888.6099 1.059036942 1.042148707 0.964004167 0.976398158 0.95760017 0.922748743 1.035857065 0.952575984 1.019585305 1 18.83888571 4.305228937 5.262062893 0.975951744 1.05393802 0.453117399 0.031642128 0.156502259 8.082568552 0.007364332 0.02080723 20194.30622 -4.305228937 0.077986276 S(ph)PTVEPSTLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPTVEPSTLPR 11 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.999)PT(0.001)VEPSTLPR;S(0.999)PT(0.001)VEPSTLPR 139.32 4.10E-05 786530000 320160 355972 355160 289458 401900 441550 366100 375530 375530 346910 TRUE FALSE 332800.164 417107.4219 364415.7614 346711.9285 333585.1816 339006.7043 337404.1254 370496.6346 362014.7487 414880.3725 0.802159336 1.005367931 0.878363465 0.835691326 0.80405149 0.817119167 0.813256417 0.893020396 0.872576224 1 18.66233588 0.539549006 1.341539227 0.999816242 0.85652738 0.357728972 0.057751718 2.204082031 5.125300135 0.056926257 0.01686528 3.463769678 -0.539549006 -0.143288862 S(ph)PVEMDEDFDVIFDPYAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVEMDEDFDVIFDPYAPK 19 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 S(1)PVEMDEDFDVIFDPYAPK 71.085 0.013256 7599700 22063 16523 20572 15494 22981 24958 29048 23435 21821 13645 TRUE FALSE 22934.06428 19360.69672 21108.12322 18558.66696 19074.69783 19161.88274 26771.14186 23120.89216 21035.66647 16318.4765 1.405404743 1.186427956 1.293510655 1.137279387 1.168901878 1.17424459 1.640541742 1.416853599 1.289070488 1 13.99421875 S(ph)PVFTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPVFTPR 7 0 P52735-3 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 S(1)PVFTPR;S(1)PVFTPR 104.2 0.0086071 266160000 128839 125489 133031 148783 143595 168624 177562 140814 123006 114463 TRUE FALSE 133925.6632 147040.7596 136497.8971 178211.8333 119186.7732 129463.6315 163644.2265 138926.6187 118579.0381 136889.8333 0.978346309 1.074153982 0.99713685 1.301863177 0.870676589 0.945750523 1.195444705 1.014879011 0.866236997 1 17.06265578 1.464698725 25 0.935597961 1.053670357 0.131771378 0.120449552 6.016656542 12113.80506 0.063347505 0.029325012 29.15403867 -1.464698725 0.118072396 S(ph)PVGLDCCNCCLDLAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVGLDCCNCCLDLAHR 17 0 D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7;D6RDZ7 D6RD37 TSC22D3 1 S(1)PVGLDCCNCCLDLAHR 157.15 2.35E-08 79549000 45808 49689 51040 57002 54672 62139 60417 61455 56132 41955 TRUE FALSE 47616.53521 58222.69922 52370.14433 68276.82547 45378.87297 47708.15898 55681.35767 60631.29625 54111.82028 50175.27897 0.949003896 1.160386159 1.043743959 1.360766235 0.904406989 0.95082997 1.109736883 1.208389818 1.078455793 1 15.61468911 0.97127342 23.10853366 0.999999993 1.095469423 0.03334193 0.130040093 4518.089774 3634497.156 0.123867504 0.030966876 9.359947655 -0.97127342 0.09546943 S(ph)PVIGSEVFLPNSNHVASGAGEAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPVIGSEVFLPNSNHVASGAGEAEER 26 0 P29590-2;P29590-5;P29590-9;P29590-3;P29590-8;P29590;H3BVD2;P29590-12;P29590-13;P29590-11 P29590-2;P29590-12 PML Protein PML 1 S(0.968)PVIGS(0.032)EVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER;S(1)PVIGSEVFLPNSNHVASGAGEAEER 296.61 1.32E-70 1131920000 119151.7 159439 135205 182940 173448 186913 185017 171682 152331 118052 TRUE FALSE 123855.9011 186821.408 138728.5534 219124.986 143965.3709 143505.2884 170514.8841 169380.8836 146848.6371 141182.0292 0.877278092 1.323266205 0.982621897 1.552074207 1.019714561 1.016455772 1.207766209 1.199734021 1.040136892 1 17.10719694 S(ph)PVLEEAPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVLEEAPFSR 11 0 K7EL81;Q9BZL4-3 K7EL81 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 S(1)PVLEEAPFSR 67.997 0.061305 122900000 53825 41449 51584 41757 60570 71861 75275 48368 54273 36965 TRUE FALSE 55950.05256 48567.54332 52928.32142 50016.40997 50274.33304 55172.37181 69374.74881 47719.70607 52319.72533 44207.58401 1.265621133 1.098624691 1.197267903 1.131398856 1.137233218 1.248029564 1.569295187 1.079446143 1.183501123 1 15.43200627 0.852107656 1.79460469 1.003037123 1.218892518 0.196535979 0.13171485 0.954033381 5.870224633 0.126989703 0.035910664 7.113898361 -0.852107656 0.215855394 S(ph)PVPAQIAITVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPVPAQIAITVPK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK 196.22 1.51E-07 1204541000 678804 526509 617282 523395 752322 751457 686223 635516 657099 504999 TRUE FALSE 705603.7061 616932.8251 633368.876 626920.9688 624442.5752 576942.5002 632435.0481 626997.9475 633450.1353 603943.8853 1.1683266 1.021506865 1.048721399 1.038045064 1.033941382 0.955291566 1.047175182 1.038172524 1.048855946 1 19.20405498 4.740078178 24.66285848 1.027568329 1.168326657 0.707043384 0.027511008 59.07892368 960015.463 0.006574457 0.041485614 54963.98064 -4.740078178 0.140758327 S(ph)PVPSAFSDQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPVPSAFSDQSR 12 0 Q9UQ35;Q9UQ35-2;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(1)PVPSAFSDQSR;S(0.998)PVPS(0.002)AFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(0.998)PVPS(0.002)AFS(0.001)DQSR;S(0.999)PVPSAFSDQSR 133.98 0.00016119 9963720000 3066430 1727290 1862470 2039980 2317670 2936900 2484250 1799890 2029340 1149055 TRUE FALSE 3187495.024 2023938.621 1911007.498 2443481.955 1923713.281 2254849.484 2289527.994 1775765.419 1956304.45 1374190.327 2.31954407 1.472822637 1.390642519 1.77812484 1.399888533 1.640856757 1.666092351 1.29222669 1.423605167 1 20.3901504 8 0.050395651 1.35E-10 4.391083878 0.498410288 0.235259096 430.6555673 1.636769618 33.3591422 146.6443599 99999999.9 -8 4.391083878 S(ph)PVREPIDNLTPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVREPIDNLTPEER 15 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23;H0Y4X3;Q14498-3 Q14498-2;Q14498-3 RBM39 RNA-binding protein 39 1 S(1)PVREPIDNLTPEER 169.51 7.22E-07 120770000 24693 32196 23821 26607 36470 32779 30631 30963 27269 29657 TRUE FALSE 25667.89871 37725.41255 24441.79483 31869.78519 30270.84243 25166.57402 28230.06218 30547.99163 26287.59402 35467.72133 0.723697428 1.063654814 0.689127858 0.898557449 0.853475817 0.709562754 0.795936731 0.861289941 0.741169521 1 15.11421903 5.043228468 16.90479677 0.836764863 0.115483743 0.087925393 0.114719783 14015068.99 138776311.1 0.025108576 323404497.1 110465.9592 -5.043228468 -0.721281119 S(ph)PVS(ph)PLAAQGIPLPAQLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 72.082 0.010122 124440000 251380 205440 219830 201110 257610 280840 275510 241920 236220 172350 TRUE FALSE 261304.6765 240722.7219 225558.9504 240888.9577 213821.5442 215619.1662 253914.8063 238677.4581 227718.4883 206118.6827 1.267738922 1.16788405 1.094315894 1.168690556 1.037371001 1.046092297 1.231886421 1.157961302 1.104793051 1 17.65311575 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.937)PVS(0.063)PLAAQGIPLPAQLTK 367.55 7.24E-108 327840000 317870 239820 286940 246580 310970 345750 332310 289190 314210 182800 TRUE FALSE 330419.753 281007.2195 294417.8921 295352.788 258111.4305 265454.8024 306262.6739 285313.8811 302901.6435 218616.1601 1.511415043 1.285390885 1.346734349 1.351010776 1.180660343 1.214250595 1.400915073 1.305090534 1.385540956 1 17.73804052 -1.435123092 3.019776864 0.993630669 1.324588099 0.550065409 0.089688417 14481320.75 17409831.17 787925.2714 0.020945935 0.036717822 1.435123092 0.330957431 S(ph)PVSTRPLPSASQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SPVSTRPLPSASQK 14 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.998)PVS(0.001)TRPLPSASQK;S(0.814)PVS(0.174)T(0.011)RPLPSASQK;S(0.987)PVS(0.011)T(0.002)RPLPSASQK;S(1)PVSTRPLPSASQK;S(0.998)PVS(0.001)T(0.001)RPLPSASQK;S(0.994)PVS(0.002)T(0.002)RPLPS(0.002)ASQK;S(0.997)PVS(0.003)TRPLPSASQK;S(0.943)PVS(0.044)T(0.013)RPLPSASQK;S(0.999)PVSTRPLPSASQK 180.11 4.71E-06 76505297000 12330485 9441020 11688662 8845289 13474861 13783174 13340333 11280270 12053207 8564031 TRUE FALSE 12817302.07 11062441.74 11993278.13 10594860.76 11184408.94 10582240.72 12294682.84 11129076.43 11619414.43 10241988.91 1.251446588 1.080106788 1.170991127 1.03445345 1.092015334 1.033221264 1.200419465 1.086612818 1.13448809 1 23.28799257 -4.999903103 0.014333244 7.99E-06 1.972324815 0.244340956 0.066169938 10549.72809 11.47385764 978.3516966 634.896339 1.00E-05 4.999903103 1.972316827 S(ph)PVVELSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPVVELSK 8 0 P25098 P25098 ADRBK1 Beta-adrenergic receptor kinase 1 1 S(1)PVVELSK;S(1)PVVELSK;S(1)PVVELSK;S(1)PVVELSK;S(1)PVVELSK;S(1)PVVELSK 140.49 0.00068056 2143760000 2609769 1864731 2213549 2310070 2671890 2963360 3590280 2521230 2517070 1350743 TRUE FALSE 2712804.695 2184984.044 2271235.905 2766994.951 2217723.092 2275164.55 3308864.472 2487437.036 2426481.142 1615395.229 1.679344253 1.352600283 1.405993941 1.712890382 1.372867179 1.408425944 2.048331215 1.539831857 1.502097504 1 20.62345575 S(ph)PYKFPS(ph)SPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPYKFPSSPLR 11 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 2 S(1)PYKFPS(0.676)S(0.324)PLR 105.28 0.0014153 408040000 714140 452970 607980 526160 739880 770140 874310 613090 627770 393070 TRUE FALSE 742334.7986 530764.0739 623824.4583 630232.8776 614115.4619 591286.6566 805779.2976 604872.5314 605176.6803 470084.5407 1.579151694 1.129082171 1.32704738 1.340679863 1.306393656 1.257830465 1.714115713 1.286731383 1.287378392 1 18.84256071 0.799230272 2.264146515 1.000756646 1.364648363 0.332078759 0.156768749 0.896660402 7.722859207 0.143998449 0.03910336 6.298400492 -0.799230272 0.363891718 S(ph)PYNGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPYNGVR 7 0 Q9UK58;Q9UK58-6 Q9UK58 CCNL1 Cyclin-L1 1 S(0.997)PY(0.003)NGVR 68.371 0.065699 143750000 99057 190000 176390 173670 140780 186400 173240 166590 171790 205690 TRUE FALSE 102967.8468 222631.022 180986.8683 208021.4076 116850.2659 143111.4249 159660.9961 164357.1335 165607.3115 245991.0173 0.418583768 0.905037202 0.735745843 0.845646357 0.475018426 0.581775003 0.64905214 0.668142826 0.673225036 1 17.90824611 0.436717769 3.076793593 0.999999934 0.667467937 0.340280825 0.141248596 39.07481875 211.0712053 0.131736376 0.034334415 2.733491761 -0.436717769 -0.332531997 S(ph)PYSGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPYSGPK 7 0 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 S(0.999)PY(0.001)SGPK 84.244 0.02275 549850000 266770 208880 251450 245830 322950 354580 347100 269530 289120 188350 TRUE FALSE 277302.2856 244753.5151 258002.9936 294454.4403 268055.0744 272234.1687 319893.395 265917.3912 278714.6277 225253.5763 1.231067183 1.086568831 1.145389111 1.307213164 1.190014732 1.208567576 1.420147907 1.180524614 1.237337192 1 17.78119049 2.4683722 24.99328191 1.237758095 1.190925599 0 0.110077102 782.3729169 2234976.944 0.036886004 0.030907533 294.016836 -2.4683722 -0.046832497 S(ph)PYSPAEEDALFMDLPTGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPYSPAEEDALFMDLPTGPR 20 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.861)PYS(0.139)PAEEDALFMDLPTGPR;S(0.971)PY(0.01)S(0.019)PAEEDALFMDLPTGPR 239.93 1.16E-29 76011000 24331.2 25102 24918 23658 26256 31490 28717 21585.8 27313 25511 TRUE FALSE 25291.81456 29413.07323 25567.38355 28337.48179 21793.0145 24176.92474 26466.0865 21296.47766 26330.01047 30509.39201 0.828984549 0.964066187 0.838016816 0.92881175 0.714305106 0.792442036 0.867473416 0.698030221 0.86301328 1 14.89696581 3.260729653 24.99999772 0.802023595 0.891551497 0.095597502 0.089009191 380.0180165 428542.8941 0.022994499 0.031110246 1822.760686 -3.260729653 0.089527902 S(ph)QDDAMVDYFFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;S(1)QDDAMVDYFFQR 133.71 0.00010909 67816000 61720 57039 78195 73518 103514 117231 92201 89417 100409 70745 TRUE FALSE 64156.75326 66835.00455 80232.82594 88059.64097 85918.72725 90005.8769 84974.0447 88218.51137 96795.2997 84606.12826 0.758299128 0.789954651 0.948309864 1.040818706 1.015514231 1.063822193 1.004348579 1.042696471 1.144069605 1 16.36847455 4.137170896 1.980440017 1.044623065 0.751074615 0.885244253 0.038638333 0.101580928 0.766441607 0.01022781 0.035126388 13714.21319 -4.137170896 -0.29354845 S(ph)QDVELWEGEVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 227 1.03E-11 86212000 203817.1 127339.3 231290 157838.6 264239.2 227218 266336.2 195000.1 245676.4 137496 TRUE FALSE 211863.9565 149208.8342 237317.6074 189058.604 219323.9152 174450.063 245460.0727 192386.4426 236834.5544 164435.7087 1.288430343 0.907399223 1.443224281 1.149741777 1.333797366 1.060901336 1.492741903 1.169979709 1.44028664 1 17.3271641 4.235804281 24.99992172 1.26601737 1.09791483 0.115479219 0.18053913 124.203889 1126573.67 0.039770232 0.092454239 17210.92775 -4.235804281 -0.16810254 S(ph)QEADVQDWEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 218.63 3.62E-05 882160000 912593 895944 1250504 957108 1440068 1311342 1290130 1108500 1388258 1107455 TRUE FALSE 948622.8763 1049815.413 1283093.162 1146421.106 1195285.756 1006802.694 1189006.239 1093642.371 1338294.866 1324439.604 0.716244722 0.792648762 0.968781935 0.865589569 0.902484154 0.760172598 0.897742891 0.825739707 1.010461226 1 20.33695063 -4.988649755 0.022140396 2.144583088 1.75E-06 0.369490318 0.076045261 3260.759954 5.470095579 368.1787509 189.1380117 1.03E-05 4.988649755 -2.144581335 S(ph)QEDLNEPIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQEDLNEPIKR 11 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(1)QEDLNEPIKR 84.842 0.009592 247540000 466390 268290 359530 261360 467250 457460 453110 370320 404230 213890 TRUE FALSE 484803.4373 314366.7205 368899.6472 313056.2279 387827.0119 351221.8479 417594.0542 365356.4661 389681.8413 255797.6503 1.895261496 1.228966412 1.442154166 1.223843251 1.516147671 1.373045638 1.632517162 1.428302667 1.52339883 1 17.96464349 -0.802006153 6.21073989 0.999999988 1.460961151 0.368118366 0.185523083 8.12E-07 70227539.61 3.20556945 0.039714403 0.157758892 0.802006153 0.460961163 S(ph)QEELREDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQEELREDK 9 1 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK;S(1)QEELREDK 154.23 4.61E-05 3530020000 3848520 2073480 2728170 2017140 3641310 4073380 3961060 2769970 3045640 1428320 TRUE FALSE 4000462.541 2429584.061 2799268.351 2416124.271 3022361.427 3127399.228 3650581.767 2732843.083 2936028.011 1708171.957 2.341955401 1.422329907 1.638750911 1.414450261 1.769354317 1.830845668 2.137127794 1.599864154 1.718812909 1 20.70402178 0.400971404 1.633912895 1.000092435 1.754562713 0.409361775 0.275632319 4.807199708 12.00051581 0.255548362 0.072601933 2.517511155 -0.400971404 0.754470278 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQEEPKDTFEHDPSESIDEFNK 22 1 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 S(1)QEEPKDTFEHDPSESIDEFNK;S(0.836)QEEPKDT(0.164)FEHDPSESIDEFNK;S(0.795)QEEPKDT(0.181)FEHDPS(0.024)ESIDEFNK 217.02 7.82E-26 445380000 749290 294575 457168 306060 634020 678730 682340 472109 503376 217308 TRUE FALSE 778872.5478 345165.9648 469082.1736 366597.7545 526249.5069 521105.2438 628856.4078 465781.1511 485259.5961 259885.342 2.996985293 1.328147106 1.804958179 1.410613433 2.024929543 2.005135187 2.419745581 1.792256337 1.867206486 1 17.98751574 S(ph)QESDGVEYIFISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQESDGVEYIFISK 14 0 S4R337;Q5T2T1-2;Q5T2T1;U5GXS2 S4R337 MPP7 MAGUK p55 subfamily member 7 1 S(0.988)QES(0.012)DGVEYIFISK;S(1)QESDGVEYIFISK;S(0.995)QES(0.005)DGVEYIFISK;S(1)QESDGVEYIFISK;S(1)QESDGVEYIFISK 225.54 2.87E-12 405400000 589979 429805 555454 401609 661125 727476 675646 556560 629917 417093 TRUE FALSE 613271.8265 503620.6653 569929.5876 481046.0615 548747.2086 558530.724 622687.101 549100.2235 607246.4102 498814.3876 1.229458977 1.009635403 1.142568462 0.964378882 1.100103009 1.119716548 1.248334283 1.100810717 1.217379501 1 18.92814355 2.662002706 3.740919602 1.151100907 1.080486369 0.056945056 0.091896153 0.514636076 13.90714462 0.028668129 0.027240686 459.2008743 -2.662002706 -0.070614538 S(ph)QFFEQGSSDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQFFEQGSSDSVVPDLPVPTISAPSR 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.999)QFFEQGSSDSVVPDLPVPTISAPSR;S(1)QFFEQGSSDSVVPDLPVPTISAPSR;S(1)QFFEQGSSDSVVPDLPVPTISAPSR 173.96 2.01E-12 186778000 88394 96010 94177 95369 117157 137860 105575 111836 105001 108286 TRUE FALSE 91883.86338 112498.9706 96631.32999 114232.7036 97242.69499 105844.1043 97299.75563 110337.0213 101222.0345 129502.5684 0.70951383 0.868700691 0.746173077 0.882088324 0.750893949 0.81731278 0.751334563 0.852006433 0.78162183 1 16.98262119 -5 0.366891861 3.588757023 0.794449393 0.551383914 0.055279467 353.6052122 2.755786358 724.7763364 0.034514059 1.00E-05 5 -2.79430763 S(ph)QGAGSSPRRPQGGSDAPSGHAAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQGAGSSPRRPQGGSDAPSGHAAPSR 26 2 Q96IQ9-2;M0R0Q5;M0R398 Q96IQ9-2 ZNF414 Zinc finger protein 414 1 S(0.329)QGAGS(0.329)S(0.329)PRRPQGGS(0.014)DAPSGHAAPSR;S(0.328)QGAGS(0.328)S(0.328)PRRPQGGS(0.016)DAPS(0.001)GHAAPSR 71.881 0.015063 70891000 10620.2 42425 28274 23301 40680 39262 17211.1 33780 29501 45554 TRUE FALSE 11039.4937 49711.16373 29010.84367 27909.86825 33765.22813 30143.99552 15862.04901 33327.23435 28439.26477 54479.43412 0.202635983 0.912475772 0.532510004 0.512300994 0.619779348 0.55330963 0.29115664 0.611739731 0.522018359 1 15.7334241 -1.256137306 2.970341155 1.002845832 0.5380622 0.378541665 0.180817326 14550356.94 18901655.11 376059.0063 0.041748826 0.055445039 1.256137306 -0.464783632 S(ph)QGGEEEGPLSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQGGEEEGPLSDK 13 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK 260.58 5.32E-24 1412440000 1538590 965860 1396390 1198520 1930400 2003630 2080990 1548350 1679590 957880 TRUE FALSE 1599334.721 1131738.942 1432781.071 1435583.679 1602271.298 1538317.298 1917876.566 1527596.901 1619141.884 1145558.246 1.396118204 0.98793662 1.250727386 1.253173886 1.39868165 1.342853847 1.674185117 1.333495617 1.413408606 1 20.12761938 3.403752566 2.20192345 1.396377628 1.189138236 0.103140851 0.181315233 0.477987374 4.694700324 0.051121533 0.078152365 2533.684683 -3.403752566 -0.207239392 S(ph)QGLSGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQGLSGDK 8 0 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(1)QGLSGDK;S(1)QGLSGDK;S(1)QGLSGDK;S(1)QGLSGDK;S(1)QGLSGDK 121.21 0.0015138 3024409000 3286130 2203830 2829340 2363910 3315650 3392150 3326130 2734230 2777140 1679200 TRUE FALSE 3415868.95 2582320.659 2903074.925 2831484.342 2752056.997 2604374.571 3065419.239 2697582.119 2677191.274 2008207.09 1.700954532 1.285883648 1.445605356 1.409956352 1.37040498 1.29686554 1.526445781 1.343278854 1.333125098 1 20.93747662 -3.592966778 0.210107444 5.91E-14 1.475287241 0.584227162 0.110316484 52.3412402 0.887949471 22.76403577 0.228329422 0.00025529 3.592966778 1.475287241 S(ph)QGLSGDKTSGFRPIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQGLSGDKTSGFRPIAK 17 2 Q9Y446;Q9Y446-2;E9PQ15;E9PK71 Q9Y446 PKP3 Plakophilin-3 1 S(0.981)QGLS(0.009)GDKT(0.009)S(0.002)GFRPIAK 68.42 0.019263 1379500000 244120 162900 210190 153560 334730 251090 183850 212940 223060 169480 TRUE FALSE 253758.0461 190876.8078 215667.7241 183933.7097 277832.7142 192778.1528 169439.3566 210085.8876 215032.1142 202686.3611 1.25197396 0.94173484 1.064046554 0.907479461 1.370751898 0.951115565 0.83596822 1.036507274 1.060910626 1 17.62888949 S(ph)QLDLFDDVGTFASGPPK ddPTM_MDA-MB-175_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 135.38 8.95E-06 23374000 40321 22836 28062 27688 32188 35301 33524 29341 29777 24193 TRUE FALSE 41912.90421 26757.90536 28793.31877 33164.60376 26716.69526 27102.87774 30896.30128 28947.73189 28705.33159 28933.15515 1.448611602 0.924818093 0.995166916 1.146249125 0.923393772 0.936741175 1.067851091 1.000503807 0.992125865 1 14.82043604 4.744636089 24.92493398 1.001915782 1.448611807 0.813819015 0.064563253 262.0620956 1075092.114 0.015238286 0.13908668 55543.86396 -4.744636089 0.446696024 S(ph)QPWDLTPMLSSSEPWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 S(1)QPWDLTPMLSSSEPWGR;S(0.999)QPWDLT(0.001)PMLSSSEPWGR;S(0.991)QPWDLT(0.009)PMLSSSEPWGR;S(0.917)QPWDLT(0.082)PMLSSSEPWGR;S(0.967)QPWDLT(0.033)PMLSSSEPWGR 228.08 2.75E-19 315058000 183389.7 222988.6 266229.8 264056.8 356915 392720 311721 312841 325821 356187 TRUE FALSE 190630.067 261285.1574 273167.9673 316286.4469 296246.7158 301516.7317 287287.4935 308647.8781 314094.7659 425975.023 0.447514658 0.613381403 0.641276959 0.742499982 0.695455601 0.707827256 0.67442333 0.724568018 0.737354889 1 18.70040932 -4.999999998 0.048716694 2.304102612 2.23E-07 0.808289616 0.056956647 267.3649929 0.964843668 46.41695827 10.79496541 1.00E-05 4.999999998 -2.304102388 S(ph)QRYSGAYGASVSDEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQRYSGAYGASVSDEELK 18 1 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 1 S(0.707)QRYS(0.293)GAYGASVSDEELK 143.29 1.46E-06 0 115930 105280 104490 85034 141240 165470 105460 98187 102810 90933 TRUE FALSE 120507.0059 123361.021 107213.0952 101853.4714 117232.0752 127042.1002 97193.76963 96870.96387 99109.88818 108749.5803 1.108114675 1.134358594 0.985871347 0.936587259 1.078000254 1.168207729 0.893739262 0.890770921 0.911358811 1 16.73065031 2.215248523 24.99738663 0.911528784 1.062192606 0.501577563 0.069987188 199.6290477 214059.4586 0.027933107 0.020642101 164.1528862 -2.215248523 0.150663822 S(ph)QS(ph)IEQESQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSIEQESQEK 11 0 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 S(1)QS(1)IEQESQEK 130.23 0.00033412 47971000 230930 99773 131000 95041 186380 253370 184750 127550 152180 77318 TRUE FALSE 240047.2947 116908.2366 134413.9676 113839.8261 154699.1942 194528.6574 170268.8122 125840.4009 146703.0715 92466.98176 2.596032553 1.264324134 1.453642858 1.231140283 1.673020912 2.103763459 1.841401212 1.360922553 1.586545475 1 16.49665068 0.734046085 1.072866003 1.006919292 1.68125598 0.22024112 0.394485788 1.485545076 3.03302955 0.371833649 0.117813759 5.420584083 -0.734046085 0.674336688 S(ph)QS(ph)T(ph)PHQEKVITESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSTPHQEKVITESK 15 1 Q9ULI3-2;Q9ULI3 Q9ULI3-2 HEG1 Protein HEG homolog 1 3 S(0.999)QS(0.999)T(0.999)PHQEKVIT(0.002)ESK 70.335 0.039334 48200000 71927 31807 63011 46043 82086 76816 121200 62153 75051 23675 TRUE FALSE 74766.7335 37269.60483 64653.11842 55150.16798 68133.05104 58976.64816 111700.0273 61319.9407 72349.92917 28313.66296 2.640659161 1.316311665 2.283460056 1.947828794 2.406366535 2.08297486 3.945092779 2.16573676 2.555300925 1 14.78921078 3.011966279 2.060267956 2.531526107 2.008685917 0.011053938 0.750988064 0.814208054 6.975228772 0.238019312 0.281593176 1027.936481 -3.011966279 -0.522840189 S(ph)QSDRTEYNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.598)QS(0.402)DRTEYNQK 99.566 0.0028339 559690000 203370 133470 178810 156560 243470 245550 195230 165660 205480 138020 TRUE FALSE 211399.2046 156392.4342 183469.9355 187527.1007 202085.0564 188524.7338 179927.3625 163439.5987 198084.8149 165062.3764 1.280723137 0.947474752 1.111518805 1.136098394 1.224295086 1.14214237 1.090056779 0.9901687 1.20006036 1 17.33265179 0.465742299 0.410264949 0.992437706 1.130441833 0.113813025 0.096580731 5.450828913 1.729420489 0.222004718 0.068589746 2.922417763 -0.465742299 0.138004127 S(ph)QSESSDEVTELDLSHGKK ddPTM_MDA-MB-175_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(0.582)QS(0.418)ESSDEVTELDLSHGKK 229.77 3.41E-20 492990000 662220 390560 600800 306760 875740 665510 645260 528950 625200 311030 TRUE FALSE 688364.9569 457635.6419 616457.3416 367436.2124 726882.0276 510955.3884 594682.8351 521860.2904 602699.1741 371970.3735 1.850590816 1.230301321 1.657275379 0.987810424 1.954139575 1.373645389 1.598737097 1.402961977 1.620288112 1 18.50482819 -1.289207694 3.856384872 0.999086627 1.503775915 0.246085697 0.271545383 18549652.6 6201831.756 141337.5755 0.056183896 0.051379788 1.289207694 0.504689288 S(ph)QSFTHSPSGDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.652)QS(0.346)FT(0.002)HSPSGDPK;S(0.672)QS(0.328)FTHSPSGDPK;S(0.5)QS(0.5)FT(0.001)HSPSGDPK 178.51 9.36E-06 2545010000 3699700 3011380 3769800 3116880 5333200 5556700 4770000 4370100 4450700 3025060 TRUE FALSE 3845767.013 3528561.09 3868044.085 3733389.561 4426664.569 4266240.638 4396114.936 4311525.958 4290520.176 3617762.589 1.0630236 0.975343462 1.069181294 1.031960907 1.223591781 1.17924837 1.215147437 1.191765864 1.185959573 1 21.78666631 3.248781967 24.97515477 1.18038742 1.033075139 0.491751795 0.064273691 141.6031813 345995.3892 0.01632202 0.021851692 1773.298993 -3.248781967 -0.147312281 S(ph)QSNPILGSPFFSHFDGQDSYAAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSNPILGSPFFSHFDGQDSYAAAVR 26 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 S(0.498)QS(0.498)NPILGS(0.003)PFFSHFDGQDSYAAAVR 101.39 0.0027155 120260000 11186 12726 14671 11190 15827 18118 14834 17541 10795 14880 TRUE FALSE 11627.63192 14911.59151 15053.33831 13403.3486 13136.73219 13910.36908 13671.27232 17305.89159 10406.49006 17795.45111 0.65340473 0.837944001 0.845909341 0.753189594 0.738207316 0.781681172 0.768245336 0.972489626 0.584783718 1 14.11922088 -5 0.315221546 2.928341999 0.777825071 0.282406156 0.103072794 412.3750171 3.693442655 529.8922009 0.091430678 1.00E-05 5 -2.150516928 S(ph)QSSHS(ph)YDDSTLPLIDR ddPTM_MDA-MB-175_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 2 S(0.798)QS(0.212)S(0.245)HS(0.459)Y(0.285)DDSTLPLIDR 61.256 0.037757 51603000 28730 40459 37646 39639 43017 52453 41157 42138 41069 39232 TRUE FALSE 29864.28258 47407.51852 38627.08569 47479.47589 35704.98571 40271.58568 37931.0068 41573.20903 39590.93471 46918.75926 0.636510493 1.01041714 0.823275941 1.011950798 0.760995949 0.858325888 0.808440108 0.886067954 0.843818876 1 15.51787724 -1.819366365 2.193208045 1.057840121 0.85589458 0.154883053 0.104758754 7994510.255 4328457.491 2440399.672 0.024190137 0.015157711 1.819366365 -0.201945541 S(ph)QSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.5)QS(0.5)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.454)QS(0.454)VPAS(0.046)T(0.046)GLGWGSGLVAPLQEGSIDSTLAGTQDTR 186.42 2.49E-23 209316000 41545 30697 51927 40618 84345 58666 49818 53456 55779 58777 TRUE FALSE 43185.22868 35968.97096 53280.26028 48652.11917 70008.06703 45041.71059 45913.13498 52739.50976 53771.52469 70293.2278 0.614358311 0.511698951 0.757971457 0.692130959 0.995943268 0.640768848 0.653165837 0.750278674 0.764960244 1 16.10109808 -5 0.088478821 1.859771111 0.479443861 0.406458266 0.114714276 241.7730408 1.491743486 40.31998477 2.960705272 1.00E-05 5 -1.38032725 S(ph)QVMNVIGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQVMNVIGSER 11 0 A0A096LNH6;Q14185 A0A096LNH6 DOCK1 Dedicator of cytokinesis protein 1 1 S(1)QVMNVIGSER;S(1)QVMNVIGSER;S(1)QVMNVIGSER 128.74 0.0002722 357380000 92586 177324 155551 177592 190376 220432 161443 190778 161912 199491 TRUE FALSE 96241.36677 207778.0176 159604.7868 212719.1675 158015.9555 169240.0087 148788.6758 188220.933 156084.8187 238577.442 0.403396759 0.87090387 0.668985238 0.891614755 0.662325634 0.709371378 0.623649389 0.788930133 0.654231253 1 17.86409811 -1.463150469 2.740048214 1.009794496 0.709200706 0.319064661 0.131700757 17963146.22 19182678.18 1347098.346 0.030658645 0.034423064 1.463150469 -0.30059379 S(ph)RADLTAEMISAPLGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.586)RADLT(0.414)AEMISAPLGDFR;S(0.891)RADLT(0.109)AEMISAPLGDFR;S(1)RADLTAEMISAPLGDFR;S(0.948)RADLT(0.052)AEMISAPLGDFR;S(1)RADLTAEMISAPLGDFR;S(0.909)RADLT(0.091)AEMISAPLGDFR;S(0.999)RADLT(0.001)AEMISAPLGDFR;S(0.645)RADLT(0.355)AEMISAPLGDFR;S(0.88)RADLT(0.12)AEMISAPLGDFR;S(0.848)RADLT(0.152)AEMISAPLGDFR;S(0.941)RADLT(0.059)AEMISAPLGDFR;S(0.888)RADLT(0.112)AEMISAPLGDFR 238.69 4.15E-24 2115691000 890223 1037204 1022332 1024228 1241800 1422912 1112020 1113691 1163209 1153245 TRUE FALSE 925369.6914 1215335.719 1048974.812 1226817.241 1030719.28 1092462.252 1024856.967 1098763.794 1121345.335 1379201.278 0.670946081 0.881188075 0.760566879 0.889512837 0.747330572 0.792097767 0.743080059 0.796666746 0.813039658 1 20.39540159 0.632481498 2.277883746 0.999978168 0.788344429 0.52407799 0.060997939 1.876298069 10.72363037 0.052863402 0.014290181 4.290239114 -0.632481498 -0.211633739 S(ph)RAPGPRDTDDDEEEPDPYGFIVQTAEIAEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRAPGPRDTDDDEEEPDPYGFIVQTAEIAEIAR 33 2 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.5)RAPGPRDT(0.5)DDDEEEPDPYGFIVQTAEIAEIAR;S(0.494)RAPGPRDT(0.494)DDDEEEPDPY(0.011)GFIVQTAEIAEIAR 120.33 1.77E-07 44451000 38318 41714 39137 30095 51542 51974 44561 44601 40241 48065 TRUE FALSE 39830.82423 48878.05501 40156.94237 36047.70118 42780.90925 39903.82617 41068.19238 44003.19655 38792.73427 57482.41649 0.692921882 0.850313157 0.698595237 0.627108312 0.744243403 0.69419187 0.714447911 0.765507076 0.674862621 1 15.81083309 -1.793837755 2.693247455 1.077445052 0.721846275 0.688671027 0.056825273 14112032.41 10289505.25 7155335.556 0.013350059 0.016075417 1.793837755 -0.355598776 S(ph)RAS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RAS(0.996)PVS(0.004)R;S(1)RAS(1)PVSR;S(1)RAS(0.998)PVS(0.002)R 85.402 0.0095412 1282650000 74123.9 67843 70098 65304 100011.3 94867 63911.3 78448.9 59662 46884 TRUE FALSE 77050.36881 79494.5075 71924.81147 78220.93629 83011.41495 72835.57697 58901.7653 77397.42081 57514.77627 56070.02215 1.374181173 1.417772001 1.282767666 1.395058059 1.480495491 1.299011025 1.050503692 1.380370791 1.025766962 1 15.77494202 1.450134076 0.580726739 0.994135875 1.392293275 0.580943877 0.10958115 0.551589443 0.445253486 0.108378209 0.056374825 28.19253162 -1.450134076 0.398157401 S(ph)RDKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 83.438 0.017547 6502690000 6756460 3613460 4795810 2977800 7267250 6639200 6636980 5263760 5948160 3013540 TRUE FALSE 7023210.258 4234043.646 4920792.748 3566799.952 6031965.441 5097346.418 6116756.165 5193207.907 5734086.884 3603985.465 1.948734346 1.17482262 1.365375303 0.989682113 1.673693054 1.414363756 1.697219987 1.4409625 1.591040513 1 21.78116176 S(ph)RDREQDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRDREQDRK 9 3 O95232;J3KPP4;H0YA81;H0YBV7;H0YAR4;H0YAX1;H0YAY6 O95232 LUC7L3 Luc7-like protein 3 1 S(1)RDREQDRK;S(1)RDREQDRK 103.88 0.018515 780130000 208497 141720 148351 129610 215990 210387 189274 170034 174429 105726 TRUE FALSE 216728.6226 166059.3076 152217.1489 155246.4712 179276.0969 161527.8077 174438.2093 167754.9723 168151.3344 126440.9855 1.714069388 1.313334493 1.203859242 1.22781763 1.417863807 1.27749564 1.379601786 1.326745214 1.329879973 1 16.94810466 -3.742867991 0.25020529 7.54E-19 1.380169192 0.403771592 0.132575798 97.76092744 1.718403654 50.47616574 0.193408336 0.000180772 3.742867991 1.380169192 S(ph)RDRHDDYYR ddPTM_MDA-MB-175_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 174.02 1.69E-06 2082360000 97777 201195 138098 137793 179716 236434 149704 165884 158838 257360 TRUE FALSE 101637.3115 235748.6762 141696.9473 165048.0441 149167.9385 181525.7867 137969.8093 163660.5963 153121.4514 307784.7645 0.330222036 0.76595304 0.460376743 0.53624501 0.48465017 0.589781586 0.448267183 0.531737159 0.497495227 1 18.23156229 -1.641324884 2.556559023 1.057925021 0.521470401 0.651984767 0.105999765 6612897.43 5602715.332 2523201.015 0.022960788 0.022838896 1.641324884 -0.536454619 S(ph)RECDITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRECDITK 8 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(1)RECDITK;S(1)RECDITK;S(1)RECDITK 131.17 0.00061555 567220000 1429470 910899 1095635 845985 1643880 1483330 1360260 1176038 1308470 700625 TRUE FALSE 1485906.579 1067338.817 1124188.148 1013318.308 1364453.865 1138849.088 1253639.267 1160275.134 1261378.42 837899.0545 1.77337183 1.273827452 1.341674922 1.20935607 1.628422729 1.359172184 1.496169807 1.384743339 1.505406187 1 19.67641692 -1.402103676 4.038517025 0.998349607 1.428749999 0.404911666 0.159859134 0.002205881 0.000326577 0.143732515 0.03375628 0.039618345 1.402103676 0.430400392 S(ph)REDLSALTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SREDLSALTR 10 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 S(1)REDLSALTR;S(1)REDLSALTR;S(1)REDLSALTR 157.82 5.14E-06 3232110000 213859 232265 223501 183529 287436 302519 253374 236043 210016 187587 TRUE FALSE 222302.3185 272154.707 229325.6197 219830.4884 238577.7314 232263.547 233513.8838 232879.2297 202457.5652 224341.0811 0.990912219 1.213129159 1.022218573 0.979894041 1.063459845 1.035314379 1.040887753 1.038058783 0.902454264 1 17.7753343 2.851794587 0.374865152 0.977296842 1.09686652 0.172353203 0.068149891 3.049185378 0.833432545 0.072411643 0.140724358 710.8772026 -2.851794587 0.119569678 S(ph)REDLSAQPVQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SREDLSAQPVQTK 13 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(0.973)REDLS(0.027)AQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK;S(1)REDLSAQPVQTK;S(0.998)REDLS(0.002)AQPVQTK 268.17 6.76E-25 7823060000 10553260 6843580 8711890 6713830 11148000 11457750 10494640 8777850 9380470 5708930 TRUE FALSE 10969910.85 8018911.629 8938929.01 8041805.535 9253066.942 8796861.206 9672042.694 8660197.278 9042868.717 6827485.529 1.606727807 1.174504376 1.309256383 1.177857573 1.355267163 1.288448166 1.416633203 1.268431437 1.3244801 1 22.70292292 -0.483138701 1.220938575 0.995555561 1.316327589 0.404911826 0.117653007 64.75657305 49.66962576 1.582564704 0.031043255 0.328746622 0.483138701 0.320772027 S(ph)REDLTAVVSVSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.997)REDLT(0.003)AVVSVSTK;S(0.99)REDLT(0.009)AVVS(0.001)VSTK;S(0.995)REDLT(0.005)AVVSVSTK;S(0.676)REDLT(0.324)AVVSVSTK;S(0.992)REDLT(0.007)AVVSVSTK;S(0.998)REDLT(0.002)AVVSVSTK 247.02 2.30E-17 2938093000 7449620 4841320 6574600 5106600 8407360 8481630 8205200 6441630 7232290 4104900 TRUE FALSE 7743736.75 5672779.05 6745939.477 6116670.238 6978279.95 6511899.973 7562054.984 6355290.486 6972001.296 4909176.562 1.577400334 1.155545941 1.374148881 1.245966642 1.42147667 1.326474999 1.540391731 1.294573623 1.420197707 1 22.22704962 -0.50535732 7.149320216 1.000017928 1.364976788 0.459275013 0.121112992 0 0 0.105945438 0.024971579 0.312350841 0.50535732 0.36495886 S(ph)REDLTAVVSVSTKFPAYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(1)REDLTAVVSVSTKFPAYER;S(1)REDLTAVVSVSTKFPAYER 153.84 2.52E-08 242040000 178477 163314 182085 104263 291450 227220 124679 181234 214954 211286 TRUE FALSE 185523.4098 191361.9091 186830.2847 124885.9102 241909.4331 174451.5986 114906.3342 178804.8547 207217.8475 252683.4464 0.734212757 0.757318739 0.739384741 0.49423859 0.957361618 0.690395833 0.45474421 0.707623935 0.820068946 1 17.94697163 0.977451999 2.953585252 0.998322997 0.687483853 0.345744585 0.132087171 0.281743039 5.975487238 0.125078923 0.032996334 9.4940606 -0.977451999 -0.310839144 S(ph)RERPSQPEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRERPSQPEGLR 12 2 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(1)RERPSQPEGLR;S(0.999)RERPS(0.001)QPEGLR 124.5 0.00025354 4453000000 637520 635690 664540 657160 865180 994370 765400 703400 742120 637560 TRUE FALSE 662689.7819 744864.8125 681858.4583 787144.2866 718117.0126 763442.6373 705405.948 693972.0735 715411.2462 762477.6752 0.8691268 0.976900487 0.894266784 1.032350601 0.941820379 1.001265561 0.925149642 0.910153957 0.938271728 1 19.54033557 4.749362131 23.90698949 0.952745591 0.869126711 0.277431781 0.042227707 1183.018236 2618277.386 0.009881459 0.140161236 56151.59934 -4.749362131 -0.08361888 S(ph)RERPSQPEGLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(1)RERPSQPEGLRK;S(0.945)RERPS(0.055)QPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK;S(1)RERPSQPEGLRK 147.09 0.00023546 4766860000 1359740 1072783 1391360 1013143 1861480 1821720 1543780 1402590 1570330 1170200 TRUE FALSE 1413423.585 1257025.135 1427619.985 1213539.661 1545066.295 1398653.138 1422774.49 1383790.575 1513814.13 1399478.285 1.009964642 0.898209818 1.020108707 0.867137186 1.104030202 0.99941039 1.016646349 0.988790316 1.081698906 1 20.41645767 3.23626471 24.9999986 1.025821998 0.950327123 0.350799512 0.054883101 69.8548492 760647.0194 0.014540637 0.018182271 1722.918402 -3.23626471 -0.075494876 S(ph)RES(ph)LNVDVVK ddPTM_MDA-MB-175_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 2 S(1)RES(1)LNVDVVK 65.107 0.024764 0 125670 74255 97840 82482 118620 144590 132170 92567 103260 56790 TRUE FALSE 130631.5486 87007.71863 100389.7908 98796.69342 98457.01477 111011.1638 121810.17 91326.29077 99543.69277 67916.91319 1.923402324 1.281090593 1.478126523 1.45466996 1.449668575 1.63451427 1.793517466 1.344676701 1.465668684 1 16.05148327 0.63601324 1.242514332 1.001841887 1.541848154 0.443162007 0.184113852 1.143384046 2.682770121 0.168253532 0.050930114 4.325270169 -0.63601324 0.540006267 S(ph)RES(ph)SPSHGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.912)RES(0.78)S(0.248)PS(0.06)HGLLK 54.004 0.078266 426780000 610250 516670 605270 447980 814070 787510 699980 563150 602910 389450 TRUE FALSE 634343.1412 605404.0534 621043.8334 536589.1069 675694.6722 604622.7373 645113.7385 555601.8954 581211.3869 465755.271 1.361966639 1.299832962 1.333412356 1.152083809 1.450750457 1.298155437 1.385091654 1.192905223 1.24789009 1 18.82921257 0.743372353 0.9281364 1.001554274 1.319985097 0.590887786 0.079185332 0.618862283 0.99041709 0.072001501 0.023947257 5.538247414 -0.743372353 0.318430823 S(ph)RESASPTIPNLDLLEAHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRESASPTIPNLDLLEAHTK 20 1 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 S(0.384)RES(0.384)AS(0.229)PT(0.003)IPNLDLLEAHTK;S(0.353)RES(0.353)AS(0.242)PT(0.053)IPNLDLLEAHTK 187.95 1.65E-17 149641000 102964 90623 113041 80462 143893 135537 121141 113355 124394 122453 TRUE FALSE 107029.0982 106186.7953 115986.9413 96377.14344 119434.1193 104060.5858 111645.6519 111835.6616 119917.0842 146445.3208 0.730846828 0.725095173 0.792015345 0.658110091 0.815554355 0.710576379 0.762370906 0.763668385 0.818852276 1 17.16000257 0.630097424 1.010728413 1.000643137 0.73974183 0.784133529 0.040756598 0.47923298 0.795653471 0.035003714 0.011195698 4.266752233 -0.630097424 -0.260901307 S(ph)RESLNVDVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SRESLNVDVVK 11 1 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0;H0YGB8 Q07866-6 KLC1 Kinesin light chain 1 1 S(0.957)RES(0.043)LNVDVVK;S(0.997)RES(0.003)LNVDVVK;S(0.995)RES(0.005)LNVDVVK;S(0.992)RES(0.008)LNVDVVK;S(0.999)RES(0.001)LNVDVVK;S(0.999)RES(0.001)LNVDVVK 199.07 3.12E-08 8353470000 6489540 3886370 5372160 3992450 7333290 7154810 7742770 5644390 6186460 3305830 TRUE FALSE 6745752.05 4553823.816 5512162.903 4782144.694 6086779.985 5493213.81 7135871.455 5568736.184 5963810.513 3953544.095 1.706254411 1.151833319 1.394233319 1.209584256 1.539575591 1.38944038 1.804930281 1.408542829 1.508471986 1 21.91471508 3.211502545 24.99991589 1.480503458 1.352270003 0.00791058 0.232697005 618.0396891 571027.2159 0.062562778 0.07479457 1627.430851 -3.211502545 -0.128233455 S(ph)RESMIQLF ddPTM_MDA-MB-175_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(0.803)RES(0.197)MIQLF 94.692 0.022492 59274000 57118 63461 84307 72506 93933 83217 78028 68919 76105 77850 TRUE FALSE 59373.06274 74359.93309 86504.10968 86847.47039 77966.30221 63891.11292 71911.96147 67995.25353 73365.99592 93103.21697 0.637712258 0.798682747 0.929120523 0.932808481 0.837417919 0.686239584 0.772389653 0.730321204 0.788007099 1 16.5065434 2.896075621 24.99739547 0.771945363 0.837120033 0 0.109638777 96.86439773 23266.35931 0.033294577 0.035314235 787.1828444 -2.896075621 0.06517467 S(ph)RGQNRPTNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRGQNRPTNVK 11 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;Q5TBP9;Q9BX40-3 Q9BX40 LSM14B Protein LSM14 homolog B 1 S(1)RGQNRPTNVK;S(1)RGQNRPTNVK 59.248 0.079693 214610000 182969 148298 166347 138424 220900 222220 212270 180229 186630 131829 TRUE FALSE 190192.7574 173767.0279 170682.1395 165803.854 183351.4969 170612.7728 195631.7227 177813.3251 179913.2228 157658.3685 1.20636005 1.102174464 1.082607546 1.051665418 1.162967108 1.082167565 1.240858475 1.127839433 1.141158725 1 17.26644222 S(ph)RGSDSPAADVEIEYVTEEPEIYEPNFIFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRGSDSPAADVEIEYVTEEPEIYEPNFIFFK 31 1 Q13435;E9PPJ0;H0YCG1 Q13435 SF3B2 Splicing factor 3B subunit 2 1 S(0.372)RGS(0.372)DS(0.255)PAADVEIEYVTEEPEIYEPNFIFFK 197.96 7.54E-26 14493000 15761 12913 20872 12958 26259 22983 22683 20612 16783 21141 TRUE FALSE 16383.25645 15130.7073 21415.94147 15521.05372 21795.50456 17645.54656 20905.04719 20335.72985 16178.98311 25283.17418 0.647990491 0.598449672 0.847043228 0.613888652 0.862055706 0.697916584 0.826836339 0.804318703 0.639911073 1 14.62588998 -5 0.116071506 1.799687483 0.603525049 0.418597937 0.096422797 148.8341593 1.132092738 28.5590601 0.962599258 1.00E-05 5 -1.196162434 S(ph)RGSPSSYNSSSSSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.496)RGS(0.496)PS(0.007)S(0.001)YNSSSSSPR 139.38 1.09E-06 539090000 141770 167280 177630 152600 163010 226530 169680 164940 146600 152830 TRUE FALSE 147367.1891 196009.0387 182259.1837 182783.8245 135301.6184 173921.8406 156380.0382 162729.2491 141323.8946 182774.1124 0.806280425 1.072411384 0.997182705 1.000053137 0.740266861 0.951567147 0.855591835 0.890329856 0.773216145 1 17.47970222 3.305286637 24.99999286 0.867890601 0.978384556 0.210337549 0.094680793 75.89865137 28435.44893 0.02437538 0.033004413 2019.698937 -3.305286637 0.110493955 S(ph)RKSPHKDLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.5)RKS(0.5)PHKDLGHR;S(0.5)RKS(0.5)PHKDLGHR 73.834 0.023682 283385000 394644 211933 294038 168768 470245 376414 299716 263871 333174 203045 TRUE FALSE 410224.8499 248330.8441 301700.8718 202149.8067 390312.9229 288997.5531 276223.4768 260334.2409 321183.1328 242827.7802 1.689365399 1.022662415 1.242447926 0.832482208 1.607365197 1.190133818 1.137528319 1.072094143 1.322678701 1 17.88957395 4.748322131 24.30528059 1.162974564 1.689365823 0.391127666 0.198600678 914.7667512 2277615.956 0.044723907 0.57950208 56017.29469 -4.748322131 0.526391259 S(ph)RLPKSPPYTAFLGNLPYDVTEESIKEFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRLPKSPPYTAFLGNLPYDVTEESIKEFFR 30 3 E7EX17;P23588-2;P23588;F8VX11;F8VP89;F8W0K0;F8VSC7;F8VYE9;F8VRU1 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.557)RLPKS(0.419)PPY(0.004)T(0.02)AFLGNLPYDVTEESIKEFFR;S(0.483)RLPKS(0.483)PPY(0.001)T(0.032)AFLGNLPYDVTEESIKEFFR 129.63 7.09E-06 267960000 503080 456750 642290 178082 1211130 755740 301750 524360 652090 859770 TRUE FALSE 522941.9869 535193.2595 659028.605 213306.0881 1005262.555 580230.8384 278098.0465 517331.8119 628621.4083 1028225.47 0.508586883 0.52050185 0.640937833 0.207450695 0.977667432 0.564303118 0.270464071 0.503130711 0.611365334 1 19.97172522 0.834157795 3.743165637 0.999927182 0.521360976 0.343512984 0.196578587 1.160768656 24.59524875 0.182974493 0.046971546 6.82586658 -0.834157795 -0.478566206 S(ph)RLTPVSPESSSTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.639)RLT(0.361)PVSPESSSTEEK 145.52 7.34E-07 412260000 537210 346730 437180 337910 591770 586220 548870 460660 527630 375370 TRUE FALSE 558419.4656 406278.1803 448573.2699 404747.5894 491181.1468 450079.2893 505848.1352 454485.6062 508640.6994 448916.5646 1.243927067 0.905019356 0.999235282 0.901609834 1.094147968 1.002590068 1.126819937 1.012405516 1.133040613 1 18.77608781 S(ph)RNSPLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRNSPLLER 9 1 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 S(0.767)RNS(0.233)PLLER 81.431 0.0129 581330000 103990 298360 215390 301690 165100 330020 149010 222480 170490 346530 TRUE FALSE 108095.6055 349601.0091 221003.2403 361363.3815 137036.361 253377.8565 137330.2068 219498.0195 164354.0982 414425.9188 0.260832155 0.843579017 0.533275624 0.871961345 0.330665518 0.611394812 0.331374561 0.529643561 0.396582575 1 18.66075471 -1.138248798 4.791419667 1.000034797 0.53166596 0.34243981 0.197881371 6.84E-05 1.23E-05 0.178066779 0.041967631 0.072736299 1.138248798 -0.468368837 S(ph)RPTSFADELAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.99)RPT(0.009)S(0.001)FADELAAR;S(0.929)RPT(0.064)S(0.008)FADELAAR;S(0.93)RPT(0.056)S(0.014)FADELAAR 128.59 9.90E-05 387618000 59291 233439 170119 207590 141685 245522 144090 166542 154133 271339 TRUE FALSE 61631.85446 273530.3323 174552.4409 248650.6824 117601.4343 188503.2364 132795.8493 164309.7769 148585.7834 324502.682 0.189927104 0.842921638 0.537907545 0.766251548 0.362405123 0.580898855 0.409228819 0.506343356 0.45788769 1 18.30787088 -1.319854265 3.594971456 1.001699962 0.52587226 0.395553565 0.178791753 63801683.45 118440983.3 1212693.022 0.040911506 0.047879073 1.319854265 -0.475827702 S(ph)RQTPS(ph)PDVVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRQTPSPDVVLR 12 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 S(0.535)RQT(0.467)PS(0.998)PDVVLR 64.507 0.035994 487270000 298640 335220 339900 378250 372880 412600 374820 383330 381940 328420 TRUE FALSE 310430.5378 392791.4274 348758.0732 453066.721 309497.9908 316779.903 345440.629 378192.0884 368194.054 392767.611 0.790366948 1.000060637 0.887950186 1.153523632 0.78799265 0.806532652 0.879503857 0.962890212 0.937434869 1 18.58331644 1.654126076 6.771821109 0.963171997 0.906044607 0.074430257 0.105061439 0.43720172 39.93082436 0.054379127 0.02739265 45.09475961 -1.654126076 -0.057127391 S(ph)RS(ph)FDYNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 143.94 5.73E-05 1677950000 1420930 1172920 1265780 1099430 1620270 2056300 1456420 1311690 1265610 862910 TRUE FALSE 1477029.414 1374359.886 1298767.267 1316893.973 1344857.084 1578755.489 1342261.995 1294108.941 1220060.943 1031980.693 1.431256828 1.331768991 1.258518958 1.276083924 1.30318047 1.52983045 1.300665801 1.254004992 1.182251714 1 19.97698455 1.057092672 1.298859712 1.004515295 1.344810143 0.668776629 0.076695279 0.272376042 0.941603524 0.075160692 0.023118509 11.40493125 -1.057092672 0.340294848 S(ph)RS(ph)KEYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSKEYHR 8 2 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 2 S(1)RS(1)KEYHR;S(0.996)RS(0.997)KEY(0.006)HR 71.268 0.026377 435230000 171451 102356 110325 70297 149810 230189 137746 107655 104169 104532 TRUE FALSE 178220.0179 119934.8468 113200.1601 84201.53678 124345.3497 176731.0933 126949.1086 106212.0608 100419.978 125013.044 1.425611377 0.959378661 0.90550679 0.673542009 0.994659003 1.413701224 1.015486901 0.849607828 0.803276001 1 16.93171911 4.738425706 8.030768263 0.955074346 1.42934116 0.371864029 0.182608114 0.107382485 86.93877781 0.046910362 0.277236357 54755.24247 -4.738425706 0.474266814 S(ph)RS(ph)LS(ph)RDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSLSRDR 8 2 P84103 P84103 SRSF3 Serine/arginine-rich splicing factor 3 3 S(1)RS(1)LS(1)RDR;S(1)RS(1)LS(1)RDR 67.187 0.036927 570370000 670520 880170 824290 874300 975410 1317450 983260 893920 853950 798390 TRUE FALSE 696992.6474 1031332.351 845771.6746 1047233.93 809610.1566 1011492.204 906189.5119 881938.4646 823216.5063 954819.2344 0.729973405 1.080133614 0.885792456 1.096787636 0.847919823 1.059354658 0.949069184 0.92367061 0.862170007 1 19.8648681 4.758519335 24.11176585 0.962862609 0.729973048 0.407522501 0.085671019 2766.662263 3342266.927 0.018615042 0.709423033 57348.13979 -4.758519335 -0.232889561 S(ph)RS(ph)PATAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPATAK 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)RS(1)PATAK 105.25 0.052891 630070000 1436700 749080 1012400 759220 1561600 1518900 1539500 1073900 1220600 524290 TRUE FALSE 1493422.025 877728.663 1038783.976 909391.45 1296159.79 1166158.494 1418829.967 1059506.127 1176670.844 627014.5874 2.381797897 1.399853657 1.656714208 1.450351345 2.0671924 1.859858634 2.262834065 1.689763123 1.876624353 1 19.25813948 3.232074189 24.98812324 1.852151548 1.694479946 0 0.398538465 615.4757674 2371038.709 0.107184972 0.131003126 1706.373859 -3.232074189 -0.157671602 S(ph)RS(ph)PHEAGFCVYLK ddPTM_MDA-MB-175_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 120.9 6.70E-05 143204000 260780 201819 238290 226660 304770 312280 261160 254150 236630 198273 TRUE FALSE 271075.7958 236479.8433 244500.0332 271492.6715 252965.3043 239757.7026 240689.5968 250743.535 228113.7325 237120.7982 1.143197045 0.997296927 1.031120151 1.144955118 1.066820398 1.011120511 1.015050551 1.05745062 0.962014864 1 17.85526268 2.774904949 6.249854018 1.016810868 1.073821779 0.329539271 0.047495177 0.295397571 35.15528068 0.014817301 0.015501688 595.5317892 -2.774904949 0.057010911 S(ph)RS(ph)PLAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 97.463 0.0046738 1635780000 78884 160124 135455 156635 134172 191943 130072 143269 102650 162498 TRUE FALSE 81998.40123 187624.0514 138985.0686 187616.9355 111365.4914 147367.1472 119876.6168 141348.7134 98955.64655 194336.3719 0.421940579 0.965460297 0.71517785 0.965423681 0.573055318 0.758309655 0.616851162 0.727340497 0.509197767 1 17.56819641 -1.137139532 4.887116167 1.000017735 0.707759033 0.225172532 0.168321997 2.98E-05 5.26E-06 0.149220864 0.035169562 0.072922318 1.137139532 -0.292258702 S(ph)RS(ph)PLDKDTYPPSASVVGASVGGHR ddPTM_MDA-MB-175_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(0.827)RS(0.834)PLDKDT(0.143)Y(0.195)PPSASVVGASVGGHR 97.047 0.0046693 1341000000 26572 32712 36161 28711 51482 56171 44844 42231 42430 26119 TRUE FALSE 27621.08308 38330.03154 37103.38537 34389.95011 42731.10803 43126.13653 41329.0101 41664.96252 40902.95259 31236.51797 0.884256149 1.227090407 1.187820787 1.100953382 1.36798564 1.380632008 1.323099141 1.333854259 1.309459416 1 14.93094602 5.491064693 0.818145433 1.29266571 1.98E-16 0.433532958 0.120177428 6.331289931 1.337758779 0.038719845 9.90354658 309788.0725 -5.491064693 -1.29266571 S(ph)RS(ph)PLGFYVHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 2 S(1)RS(1)PLGFYVHLK;S(1)RS(1)PLGFYVHLK 128.99 0.0001378 990960000 1111870 560440 795330 536720 1162770 1092860 1043710 756700 853240 556350 TRUE FALSE 1155767.486 656691.2104 816056.9532 642881.6141 965122.7707 839059.8275 961901.283 746557.6742 822532.0591 665356.1305 1.737065961 0.986977019 1.226496482 0.966221824 1.450535625 1.261068755 1.445693876 1.122042227 1.236228271 1 19.34376722 0.718515655 1.201445651 1.002397342 1.266202778 0.12548685 0.218260812 2.046294459 5.009769615 0.194383096 0.059582749 5.230168189 -0.718515655 0.263805436 S(ph)RS(ph)PLLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRSPLLNDR 9 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR;S(1)RS(1)PLLNDR 65.113 0.038396 642420000 406130 338133 377530 350224 484720 613860 497660 401430 382657 295291 TRUE FALSE 422164.326 396204.7124 387368.7419 419497.2619 402327.4675 471300.3181 458652.1088 396049.4875 368885.2493 353147.6178 1.195433028 1.121923786 1.096903172 1.187880764 1.139261451 1.334570289 1.298754645 1.121484239 1.04456389 1 18.42991184 1.328356391 3.055570405 1.01359676 1.193010153 0.490101773 0.070573892 0.236348728 3.620621698 0.065699788 0.020170191 21.29886156 -1.328356391 0.179413393 S(ph)RS(ph)PPPVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SRSPPPVSK 9 1 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 2 S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK;S(1)RS(1)PPPVSK 103.76 0.0019175 16779095000 10194450 4881688 5938758 5779330 7908828 8695188 10761110 6886078 6733073 2985989 TRUE FALSE 10596934.76 5720079.94 6093526.912 6922464.224 6564488.242 6675862.364 9917626.079 6793781.388 6490751.018 3571036.374 2.967467605 1.601798285 1.706374921 1.93850286 1.838258576 1.869446756 2.777240285 1.902467708 1.817609886 1 21.7679114 0.802775562 2.305526574 1.001589765 2.054813924 0.367986672 0.42373218 0.832634212 7.466698674 0.392025609 0.106181391 6.350026852 -0.802775562 1.053224159 S(ph)RS(ph)PQWR ddPTM_MDA-MB-175_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 88.596 0.010522 1189820000 182668 273610 236406 241756 223420 264996 215870 210448 176009 255713 TRUE FALSE 189879.8737 320600.3891 242566.9346 289574.6152 185443.1482 203454.6951 198949.5453 207627.2888 169674.4705 305815.0664 0.620897708 1.048347267 0.793181766 0.946894535 0.606389837 0.665286696 0.650555081 0.678930869 0.554827048 1 18.22229996 3.235213763 24.99998698 0.673018861 0.862106637 0.2022189 0.151898573 108.1818711 808086.8388 0.039429057 0.048986792 1718.754162 -3.235213763 0.189087776 S(ph)RS(ph)RDKEER ddPTM_MDA-MB-175_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 84.297 0.028412 1614220000 2201440 981568 1355419 759630 2093600 2448340 1530906 1288568 1455324 905643 TRUE FALSE 2288354.551 1150144.668 1390742.333 909882.5467 1737730.62 1879750.14 1410909.587 1271296.854 1402947.174 1083086.406 2.112808856 1.061914047 1.284054831 0.840083064 1.604424734 1.735549564 1.302675003 1.173772329 1.295323407 1 20.04671691 1.174561846 1.092174102 1.028937764 1.391720855 0.118307184 0.338634178 1.122772796 2.797532983 0.314729302 0.103721049 14.94726883 -1.174561846 0.362783092 S(ph)RS(ph)RDS(ph)GDENEPIQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSRDSGDENEPIQER 16 2 Q8WX93-8;Q8WX93-3;Q8WX93-2;Q8WX93-9;Q8WX93-5;Q8WX93;Q8WX93-4;Q8WX93-7 Q8WX93-8 PALLD Palladin 3 S(1)RS(1)RDS(1)GDENEPIQER 55.469 0.088894 87450000 97652 109940 122500 100510 151510 184360 151310 115760 123800 100820 TRUE FALSE 101507.3764 128821.3398 125692.4506 120390.578 125756.3843 141545.184 139449.9268 114208.4265 119344.4622 120573.7487 0.841869623 1.068402875 1.042452872 0.998480841 1.042983118 1.173930358 1.156552967 0.94720806 0.989804692 1 16.87955631 4.742125448 24.64724564 1.0476513 0.841869529 0.448431896 0.068124059 287.9349649 1990677.232 0.017565814 0.12934393 55223.69328 -4.742125448 -0.205781771 S(ph)RS(ph)RS(ph)PPPVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRSRSPPPVSK 11 2 Q01130;Q01130-2 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 3 S(1)RS(1)RS(1)PPPVSK;S(1)RS(1)RS(1)PPPVSK;S(1)RS(0.996)RS(0.999)PPPVS(0.005)K 72.797 0.029922 3414860000 4725090 2476430 2716850 2422200 3860210 3877050 4659320 2855600 2926140 1632800 TRUE FALSE 4911640.202 2901737.589 2787653.343 2901303.93 3204052.883 2976663.895 4294110.324 2817325.353 2820828.793 1952715.898 2.515286636 1.486000903 1.427577532 1.485778824 1.640818762 1.524371209 2.199045098 1.442772784 1.444566921 1 20.89705064 -2.549499162 0.215515962 3.34E-14 1.793893705 0.302132695 0.340963736 60.78407445 1.562459626 29.70485532 0.737489895 0.002821635 2.549499162 1.793893705 S(ph)RS(ph)RSPHEAGFCVYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSRSPHEAGFCVYLK 16 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 2 S(0.667)RS(0.667)RS(0.667)PHEAGFCVYLK 88.311 0.0033107 326400000 126650 128470 144620 93920 189110 177870 138290 134040 151830 139350 TRUE FALSE 131650.2398 150533.7231 148388.916 112497.0957 156965.1497 136562.3881 127450.4684 132243.413 146365.668 166652.9645 0.789966384 0.9032766 0.890406699 0.675038071 0.941868332 0.819441698 0.764765684 0.793525716 0.878266213 1 17.34648746 0.929251114 4.671747669 0.999945427 0.822335402 0.358048961 0.072387275 0.380622871 21.2867494 0.067253013 0.017051701 8.49671622 -0.929251114 -0.177610025 S(ph)RS(ph)VVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSVVR 6 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;H7C1M2;H7C2G8 P18583-7 SON Protein SON 2 S(1)RS(1)VVR 55.064 0.090609 70980000 22296 58111 51534 48105 57717 65362 36194 52971 55033 65241 TRUE FALSE 23176.2633 68091.11221 52877.01838 57620.02542 47906.28496 50182.66607 33357.0197 52261.01039 53052.37308 78023.72484 0.297041231 0.872697533 0.677704358 0.738493651 0.613996385 0.643171884 0.427524061 0.669809221 0.679951812 1 16.25162525 0.689139954 2.218218349 0.999829685 0.625807798 0.365471435 0.150286816 1.734140762 10.93102878 0.135346652 0.036762192 4.888098555 -0.689139954 -0.374021887 S(ph)RSCHDLSVL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSCHDLSVL 10 1 Q8IYK8 Q8IYK8 REM2 GTP-binding protein REM 2 1 S(0.5)RS(0.5)CHDLSVL;S(0.5)RS(0.5)CHDLSVL 63.181 0.048605 351940000 492550 598700 568690 540570 765380 713770 562010 584930 586200 680110 TRUE FALSE 511996.2543 701522.0678 583510.5286 647493.1326 635280.981 548007.7348 517958.1877 577089.9701 565102.7765 813364.533 0.629479444 0.862494047 0.717403458 0.796067576 0.781053212 0.673754156 0.636809409 0.709509632 0.694771844 1 19.63354256 -1.242709801 5.517268821 1.000018312 0.723994138 0.591972936 0.069136086 1.55E-05 2.13E-06 0.066704675 0.015721401 0.057186063 1.242709801 -0.276024174 S(ph)RSDIDVNAAAGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 203.89 8.73E-09 1033200000 2199400 1558800 2029900 1514500 2447500 2353300 2290700 1881400 2159400 1486500 TRUE FALSE 2286234.01 1826511.774 2082800.862 1814063.58 2031474.824 1806781.74 2111148.948 1856182.91 2081683.616 1777751.214 1.286025847 1.027428225 1.171592991 1.020426011 1.142721663 1.016329915 1.187539028 1.044118488 1.17096453 1 20.76162201 8 0.011948464 3.17E-08 2.38393674 0.159965277 0.084761615 17448.4289 16.10673539 1344.360016 1916.097786 99999999.9 -8 2.383936708 S(ph)RSDIDVNAAASAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.5)RS(0.5)DIDVNAAASAK;S(0.5)RS(0.5)DIDVNAAASAK 225.29 1.72E-12 1690040000 2012300 1710050 2017430 1532140 2613800 2303300 2256000 1707360 2014550 1532360 TRUE FALSE 2091747.158 2003737.785 2070005.883 1835192.719 2169507.21 1768393.482 2079168.825 1684475.632 1942046.739 1832596.603 1.141411675 1.093387264 1.12954803 1.001416632 1.1838433 0.964966037 1.134548008 0.919174263 1.059724074 1 20.80545782 2.413940688 0.852114237 0.992942588 1.108930288 0.243569976 0.072397365 0.779286602 1.122253155 0.048885674 0.033245306 259.3825098 -2.413940688 0.1159877 S(ph)RSDNALHLASER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSDNALHLASER 13 1 A0A1X7SBR1;Q7Z3G6 A0A1X7SBR1 PRICKLE2 Prickle-like protein 2 1 S(0.583)RS(0.417)DNALHLASER;S(0.771)RS(0.229)DNALHLASER 177.12 9.52E-06 323040000 83537 109837 111031 93895 105492 139398 102644 111727 99162 122574 TRUE FALSE 86835.10526 128700.6503 113924.5591 112467.1508 87560.50752 107024.9271 94598.49507 110229.4823 95593.17899 146590.0285 0.592367067 0.877963199 0.777164451 0.767222381 0.597315578 0.730096912 0.645326944 0.751957575 0.652112425 1 17.16142744 -1.872414472 6.299768821 1.044639495 0.71589518 0.50940727 0.08516165 0.041754745 0.000845634 0.064483145 0.018635161 0.013414841 1.872414472 -0.328744315 S(ph)RSDVDMDAAAEATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSDVDMDAAAEATR 15 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.578)RS(0.422)DVDMDAAAEATR;S(0.5)RS(0.5)DVDMDAAAEATR 123.99 6.02E-05 1407910000 433920 518690 523840 500660 655060 638140 567360 494550 519510 577500 TRUE FALSE 451051.4967 607770.9727 537491.7007 599689.0537 543713.1352 489941.6561 522888.8407 487921.3662 500812.9366 690650.0681 0.653082534 0.879998426 0.778240278 0.868296524 0.787248363 0.709392033 0.757096632 0.706466833 0.725132683 1 19.3975954 2.987273529 24.20440144 0.754635845 0.803289798 0 0.099371578 1303.661225 2479435.376 0.027429421 0.030446841 971.1214108 -2.987273529 0.048653954 S(ph)RSESETSTMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.411)RS(0.411)ES(0.179)ETSTMAAK 152.71 2.75E-05 830510000 1040300 857540 1129400 918790 1418300 1503500 1447800 1258200 1317400 864760 TRUE FALSE 1081371.847 1004815.824 1158833.092 1100523.92 1177217.873 1154334.911 1334317.653 1241335.887 1269987.031 1034193.165 1.04561883 0.971593952 1.120519001 1.064137684 1.138295932 1.116169541 1.290201577 1.200294035 1.227997896 1 19.98007424 3.27078752 1.024329891 1.194723974 1.024042933 0.321050762 0.079223838 0.501133681 1.126143235 0.031514126 0.053266557 1865.46678 -3.27078752 -0.170681042 S(ph)RSFTLDDESLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.472)RS(0.472)FT(0.056)LDDESLK 167.05 3.04E-05 107420000 193280 189160 229280 187490 306930 348910 316670 265510 298920 235490 TRUE FALSE 200910.8436 221646.7585 235255.2252 224574.9624 254758.1482 267880.9403 291848.5779 261951.2727 288161.9276 281629.7568 0.713386419 0.7870147 0.835335115 0.797412053 0.904585336 0.951181237 1.036284593 0.930126403 1.023194178 1 18.10344025 3.250624734 0.80588801 0.997865938 0.743962024 0.872847778 0.037322015 0.230394304 0.325881201 0.019623953 0.034957561 1780.839311 -3.250624734 -0.253903914 S(ph)RSGS(ph)QGRTDSVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSGSQGRTDSVEK 14 2 Q5VTL8;A0A0A0MRN0 Q5VTL8 PRPF38B Pre-mRNA-splicing factor 38B 2 S(0.734)RS(0.333)GS(0.928)QGRT(0.004)DSVEK 99.409 0.010784 742910000 797060 607840 740270 482830 996100 963470 773520 715760 841120 664100 TRUE FALSE 828528.5443 712231.7917 759562.0443 578332.3329 826783.2778 739718.694 712889.4812 706166.4079 810848.2555 794217.68 1.043200832 0.896771514 0.956365066 0.728178618 1.041003365 0.931380291 0.897599612 0.889134586 1.020939568 1 19.59917495 1.231420032 24.97260878 1.010469843 0.918271931 0.146472986 0.083896637 311.2716885 1088555.865 0.070504159 0.019099006 17.03805561 -1.231420032 -0.092197912 S(ph)RSHSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.446)RS(0.446)HS(0.107)DNDRPNCSWNTQYSSAYYTSR 220.64 1.54E-34 679920000 85440 142350 125310 122210 136130 145800 117480 133540 112160 158010 TRUE FALSE 88813.23717 166797.5052 128575.6815 146382.7732 112990.6712 111940.1596 108271.6106 131750.1147 108123.3835 188969.0342 0.469988311 0.882671099 0.680406089 0.774638945 0.597932205 0.592373031 0.572959538 0.697204784 0.572175139 1 17.52779032 -1.755859134 5.532925871 1.015293176 0.656986668 0.471209308 0.111277032 0.019992887 0.000882188 0.102614145 0.024033511 0.017544495 1.755859134 -0.358306508 S(ph)RSLPAFPTSSLLTQSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSLPAFPTSSLLTQSQK 18 1 Q99698 Q99698 LYST Lysosomal-trafficking regulator 1 S(0.586)RS(0.414)LPAFPTSSLLTQSQK 164.66 1.82E-11 168520000 200140 180680 244520 185390 323770 270430 215770 228610 241300 207540 TRUE FALSE 208041.6817 211710.3845 250892.3921 222059.5887 268735.691 207626.7309 198857.3836 225545.8569 232615.6601 248203.4894 0.838189996 0.852971024 1.01083346 0.894667473 1.082723259 0.836518179 0.801186897 0.908713481 0.937197381 1 17.92116387 1.399846564 0.006977788 1.841713632 2.01E-06 0.061839681 0.083506047 10170.45026 69.02790413 9128.952408 9083.197752 25.10999138 -1.399846564 -1.841711626 S(ph)RSPAPPADKEAEKPVFFPAFAAEAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPAPPADKEAEKPVFFPAFAAEAQK 27 3 C9J0Q5;C9JE98 C9J0Q5 NCOR2 1 S(0.5)RS(0.5)PAPPADKEAEKPVFFPAFAAEAQK;S(0.608)RS(0.392)PAPPADKEAEKPVFFPAFAAEAQK 262.77 2.06E-52 1394970000 904600 349853 629710 354679 822810 735008 730439 599061 721983 296084 TRUE FALSE 940314.3065 409937.5313 646120.7599 424833.4476 682949.0501 564313.5312 673185.2825 591031.5672 695998.9729 354095.9909 2.655535026 1.157701702 1.824705098 1.199769154 1.928711614 1.593673878 1.901137826 1.669128096 1.965565809 1 18.43378098 -1.352497094 3.151271925 0.993375496 1.73380203 0.242783312 0.402301116 69166132.07 94625687.64 4297773.195 0.085905063 0.044412263 1.352497094 0.740426534 S(ph)RSPAPPADKEAFAAEAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPAPPADKEAFAAEAQK 19 2 Q9Y618;Q9Y618-4;Q9Y618-5 Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.568)RS(0.432)PAPPADKEAFAAEAQK;S(0.565)RS(0.435)PAPPADKEAFAAEAQK 157.73 1.62E-09 492810000 468430 225893 354770 245723 446390 441860 473580 354730 398100 176829 TRUE FALSE 486923.9781 264688.3655 364015.5976 294326.276 370512.7872 339244.7115 436459.5621 349975.4246 383772.4588 211475.257 2.302510398 1.25162806 1.721315311 1.39177642 1.752038478 1.604181578 2.063880042 1.654923747 1.814739295 1 17.69012935 S(ph)RSPHEAGFCVYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPHEAGFCVYLK 14 1 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.661)RS(0.339)PHEAGFCVYLK;S(0.5)RS(0.5)PHEAGFCVYLK 160.47 2.88E-06 902150000 506890 576060 634600 509210 715070 790570 608570 577530 610160 587390 TRUE FALSE 526902.4086 674993.8239 651138.1973 609930.2182 593522.6568 606972.0987 560868.6932 569789.155 588200.4608 702477.8242 0.750062693 0.960875633 0.926916374 0.868255477 0.84489878 0.864044498 0.798414802 0.811113369 0.837322461 1 19.42209316 3.399552615 4.093443651 0.843624569 0.888850951 0 0.073455 0.609014094 19.73279765 0.019800344 0.027638265 2509.300167 -3.399552615 0.045226382 S(ph)RSPIIHS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPIIHSPK 10 1 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 2 S(0.5)RS(0.5)PIIHS(0.999)PK;S(0.812)RS(0.193)PIIHS(0.995)PK 66.826 0.036876 671550000 1100790 711490 849820 682440 1140480 1352520 1088630 899620 923030 605200 TRUE FALSE 1144250.039 833682.8729 871967.0073 817424.5951 946621.617 1038417.728 1003300.336 887562.0654 889810.3306 723777.3527 1.580942033 1.151849902 1.204744807 1.129386809 1.307890629 1.43471984 1.386200234 1.226291569 1.229397863 1 19.46518644 0.763506435 1.540963773 1.001110518 1.297206473 0.331895695 0.130003598 0.999176858 4.037858077 0.124093616 0.03597982 5.801047675 -0.763506435 0.296095955 S(ph)RSPITTNHRPS(ph)PDPEQRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.5)RS(0.5)PIT(0.001)T(0.003)NHRPS(0.996)PDPEQRPLR 117.8 0.0001401 310290000 44688 56409 47263 47548 55443 61814 55128 53892 49208 47652 TRUE FALSE 46452.31675 66096.80695 48494.71261 56952.85248 46018.81866 47458.6353 50806.92331 53169.66589 47437.01369 56988.49705 0.815117421 1.159827165 0.85095616 0.999374531 0.807510657 0.832775696 0.891529448 0.932989439 0.832396293 1 15.79838312 3.256049171 24.99124369 0.881552167 0.963329224 0.111474361 0.100775984 482.7082998 689788.4448 0.026094242 0.035253462 1803.221891 -3.256049171 0.081777057 S(ph)RSPITTNHRPSPDPEQRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR;S(0.5)RS(0.5)PITTNHRPSPDPEQRPLR;S(0.498)RS(0.498)PIT(0.001)T(0.001)NHRPS(0.001)PDPEQRPLR 86.791 0.0019266 310335000 112860 128841 124419 121702 124993 160381 127253 114044 122425 119553 TRUE FALSE 117315.7999 150968.4395 127661.4614 145774.2924 103746.7345 123134.9433 117278.5773 112515.4267 118018.9482 142977.1214 0.820521485 1.055892286 0.892880344 1.019563766 0.725617732 0.861221307 0.820261145 0.78694707 0.825439392 1 17.12542479 3.24672359 24.99997982 0.823520026 0.951096155 0.262192121 0.089225684 200.1989373 613126.9235 0.022590313 0.030071919 1764.91417 -3.24672359 0.12757613 S(ph)RSPLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPLAR 7 1 Q8N3Y1 Q8N3Y1 FBXW8 F-box/WD repeat-containing protein 8 1 S(0.764)RS(0.236)PLAR 73.985 0.028712 197220000 41404 59355 64041 50841 47893 71879 62404 57265 56550 67940 TRUE FALSE 43038.66189 69548.75953 65709.96107 60897.19805 39752.16497 55186.19159 57512.61142 56497.45634 54514.77655 81251.54221 0.529696554 0.855968486 0.808722632 0.74948975 0.489248129 0.679201774 0.70783409 0.695340111 0.670938361 1 16.31010758 -1.054599478 4.895754773 1.000007226 0.692834773 0.438666201 0.105929485 8.32E-06 1.61E-06 0.102150221 0.024076472 0.088186178 1.054599478 -0.307172453 S(ph)RSPLGFYVHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 S(0.5)RS(0.5)PLGFYVHLK;S(0.603)RS(0.397)PLGFYVHLK 112.5 0.00076518 742440000 572230 503070 567240 477100 868540 772330 655210 606470 619230 656470 TRUE FALSE 594822.0823 589468.3592 582022.7404 571468.956 720905.881 592968.0623 603852.9281 598341.2616 596944.0333 785092.7276 0.75764564 0.750826416 0.741342672 0.727899948 0.918242974 0.75528411 0.769148544 0.762128142 0.760348443 1 19.58250354 -1.734435725 2.406220559 1.052417239 0.771701105 0.648865474 0.050442604 5862909.86 4077910.036 1833449.613 0.012779032 0.018431653 1.734435725 -0.280716134 S(ph)RSPLHPMSEIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPLHPMSEIPR 13 1 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 S(0.585)RS(0.415)PLHPMSEIPR 63.691 0.040659 191140000 46683 141000 114200 155850 97532 154720 100610 123680 97045 153170 TRUE FALSE 48526.08089 165215.6532 117176.1458 186676.6648 80953.54548 118788.6248 92723.9253 122022.2719 93552.36941 183180.7289 0.26490822 0.901927043 0.639675071 1.019084627 0.441932653 0.648477739 0.50618821 0.666130508 0.510710761 1 17.48290821 -1.917105468 3.890212374 1.173536933 0.635355839 0.229443263 0.206472891 0.124175374 0.002645989 0.079883029 0.043472202 0.012103042 1.917105468 -0.538181094 S(ph)RSPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.5)RS(0.5)PLLK;S(0.5)RS(0.5)PLLK 64.836 0.043735 388660000 572100 528560 585140 523240 742850 776250 693070 599620 614180 594190 TRUE FALSE 594686.9498 619336.0684 600389.2291 626735.3103 616580.6223 595977.7017 638745.3624 591583.0747 592075.7818 710610.154 0.836868072 0.871555331 0.844892556 0.881967851 0.867677754 0.838684472 0.898868893 0.832500171 0.833193529 1 19.43869878 -1.089447161 4.354714073 1.000014934 0.8570266 0.796278173 0.02181048 3.11E-06 6.50E-07 0.020001272 0.004713834 0.081386587 1.089447161 -0.142988333 S(ph)RSPLLVTVVESDPRPQGQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSPLLVTVVESDPRPQGQPR 21 2 A0A2R8YH03;Q5VWN6;Q5VWN6-2 A0A2R8YH03 FAM208B Protein FAM208B 1 S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR;S(0.5)RS(0.5)PLLVTVVESDPRPQGQPR 83.362 0.0016722 1272260000 244163 331084 290240 291022 269004 359045 288955 275973 242861 318631 TRUE FALSE 253802.7438 387945.1015 297803.8928 348585.283 223278.7962 275662.2401 266305.9521 272274.0333 234120.4801 381060.6439 0.66604292 1.018066567 0.78151312 0.914776397 0.585940321 0.723407795 0.698854517 0.714516279 0.614391656 1 18.53966109 3.253797082 24.99931197 0.707695979 0.852912623 0.159492827 0.134337082 347.9644713 570921.2269 0.033762613 0.045543093 1793.895258 -3.253797082 0.145216643 S(ph)RSPNRFDAHDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPNRFDAHDPR 13 2 Q96T58;A0A669KB49;F6WRY4 Q96T58 SPEN Msx2-interacting protein 1 S(0.574)RS(0.426)PNRFDAHDPR;S(0.5)RS(0.5)PNRFDAHDPR 74.12 0.018249 2695900000 729190 888460 844710 779870 1014920 1015770 773430 888370 826980 884740 TRUE FALSE 757978.9843 1041046.094 866723.8365 934125.9583 842404.2609 779872.8116 712806.5356 876462.8532 797217.1513 1058087.864 0.716366769 0.983893805 0.819141648 0.882843467 0.796157191 0.737058649 0.673674238 0.828346004 0.753450804 1 20.013028 5.040057351 15.37906186 0.81779306 0.297409555 0.095716321 0.098503747 4009667.203 44626836.83 0.023084357 57763308.72 109662.3002 -5.040057351 -0.520383505 S(ph)RSPQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPQWR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.631)RS(0.369)PQWR 73.233 0.029946 169570000 22898 45271 39201 37244 33617 34758 29557 31170 27682 49841 TRUE FALSE 23802.03072 53045.94209 40222.61026 44610.75204 27902.79435 26685.98126 27240.24511 30752.21713 26685.73023 59606.38969 0.399320121 0.889937176 0.674803666 0.748422313 0.468117504 0.447703365 0.457002097 0.515921486 0.447699154 1 15.86317937 -1.132878705 4.745155725 1.000033385 0.565307542 0.429971054 0.15156981 5.56E-05 1.02E-05 0.152323959 0.035900349 0.073641274 1.132878705 -0.434725843 S(ph)RSPSDSAAYFCIYTYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPSDSAAYFCIYTYPR 18 1 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;Q9NRA0-3;M0QXX5;M0R0E9;A0A075B7A1 M0R344 SPHK2 Sphingosine kinase 2 1 S(0.606)RS(0.39)PS(0.004)DSAAYFCIYTYPR 142.32 6.87E-08 137030000 41103 30371 39484 41525 52960 49332 36317 32125 53772 37776 TRUE FALSE 42725.77818 35586.983 40512.98548 49738.52106 43957.87812 37875.39063 33470.37864 31694.41692 51836.75622 45177.48393 0.945731689 0.787715027 0.896751699 1.100958193 0.973004123 0.838368748 0.740864159 0.701553388 1.14740246 1 15.4633163 2.725996487 22.80653093 0.841652535 0.938772613 0 0.141584721 612.2306216 1111322.629 0.047194217 0.044847154 532.1039552 -2.725996487 0.097120078 S(ph)RSRDDLYDQDDSRDFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSRDDLYDQDDSRDFPR 18 3 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(0.684)RS(0.316)RDDLYDQDDSRDFPR 133.95 6.39E-05 291630000 90228 105920 89868 89298 106640 134570 92195 87362 92047 137100 TRUE FALSE 93790.27111 124110.9361 92210.03391 106960.8779 88513.37089 103318.1569 84968.51499 86191.05529 88734.24645 163962.1201 0.57202402 0.756948837 0.562386202 0.652351152 0.539840366 0.630134307 0.518220397 0.525676633 0.541187479 1 17.32300302 -0.879467255 6.135341871 1.000000055 0.586930312 0.757719334 0.069756947 5.36E-08 9.91E-09 0.069138836 0.016296178 0.131987482 0.879467255 -0.413069743 S(ph)RSSKEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSKEENR 9 2 Q14696 Q14696 MESDC2 LDLR chaperone MESD 1 S(0.333)RS(0.333)S(0.333)KEENR 72.652 0.036341 220960000 87587 109750 108140 95952 123970 159540 110680 116640 108360 116790 TRUE FALSE 91045.00239 128598.7088 110958.2172 114931.0192 102897.6237 122489.2529 102004.6124 115076.6316 104460.1448 139672.7644 0.651845066 0.92071428 0.794415559 0.8228592 0.736704998 0.876973069 0.730311402 0.823901725 0.747892012 1 17.0916912 -1.492410128 4.380072323 1.001225331 0.795103902 0.421048598 0.0737843 0.000782777 9.07E-05 0.063341376 0.014843235 0.032180284 1.492410128 -0.206121429 S(ph)RSSPSTDHYKQEASVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSPSTDHYKQEASVELR 19 2 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.327)RS(0.327)S(0.327)PS(0.015)T(0.004)DHYKQEASVELR 85.062 0.0016159 388750000 187070 247990 273400 183340 369080 311480 249580 266990 302210 231490 TRUE FALSE 194455.668 290580.3534 280525.0286 219604.1048 306343.9134 239143.4905 230017.2674 263411.4358 291333.5211 276846.0334 0.702396439 1.049609958 1.013288958 0.793235511 1.106549766 0.86381404 0.830849063 0.951472674 1.052330487 1 18.07872433 S(ph)RSSSS(ph)PPPKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.794)RS(0.1)S(0.116)S(0.096)S(0.894)PPPKQK 56.339 0.064893 99690000 117320 83233 107030 59678 146970 131020 93856 107940 124480 81648 TRUE FALSE 121951.8842 97527.62029 109819.2897 71482.13028 121988.0919 100592.5906 86499.32147 106493.2409 119999.9891 97645.36235 1.248926536 0.998794187 1.124674916 0.732058631 1.249297345 1.030182983 0.885851815 1.090612378 1.228936902 1 16.5752639 -0.511668416 6.397459232 0.999999032 1.054397884 0.010957374 0.157648318 0 0 0.142742611 0.033644756 0.307844631 0.511668416 0.054398852 S(ph)RST(ph)PVRDR ddPTM_MDA-MB-175_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(0.999)RS(0.261)T(0.74)PVRDR 81.803 0.022347 782250000 538060 537980 571720 528190 620790 759120 531730 494490 538460 542430 TRUE FALSE 559303.0243 630373.8801 586619.4929 632664.4055 515268.3375 582825.8846 490051.6132 487862.1704 519080.9298 648708.7731 0.862178912 0.971736327 0.904287898 0.975267226 0.794298395 0.898439961 0.755426215 0.752051137 0.800175597 1 19.30721142 3.230731383 24.99765724 0.814221854 0.929745382 0.249115503 0.076531941 190.9698432 609739.5607 0.021310877 0.025916341 1701.106027 -3.230731383 0.115523528 S(ph)RSTTELDDYSTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.25)RS(0.25)T(0.25)T(0.25)ELDDYSTNK;S(0.329)RS(0.224)T(0.224)T(0.224)ELDDYSTNK 110.56 0.00042533 2161710000 1184190 1598600 2085780 1662920 2480500 2655800 2146000 2152500 2172900 1539330 TRUE FALSE 1230942.736 1873147.115 2140137.14 1991840.613 2058865.496 2039030.699 1977790.912 2123649.258 2094697.753 1840932.241 0.668651843 1.017499217 1.162529012 1.081973887 1.118382008 1.107607686 1.074342047 1.153572745 1.137846199 1 20.8120051 4.716200718 2.94587741 1.110205203 0.605693712 0.893531961 0.044935037 0.093464217 1.210998046 0.010103246 0.10866005 52023.63785 -4.716200718 -0.504511491 S(ph)RSTTELDDYSTNKNGNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSTTELDDYSTNKNGNNK 19 2 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(0.272)RS(0.184)T(0.272)T(0.272)ELDDYSTNKNGNNK 170.28 6.53E-12 183020000 121790 97091 123990 60260 204230 138520 79541 98972 128990 114530 TRUE FALSE 126598.3632 113765.624 127221.2813 72179.24814 169515.0575 106350.8293 73306.36858 97645.44223 124347.6751 136969.9607 0.924278306 0.830588133 0.92882615 0.526971372 1.237607551 0.776453675 0.535200333 0.712896768 0.907846322 1 17.0635 2.495382498 24.90970696 0.73933287 0.882263056 0.040064116 0.199453926 1676.623038 2287040.419 0.063063521 0.058424341 312.8833828 -2.495382498 0.142930187 S(ph)RSVDSAFPFGLQGNSEYLIEFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSVDSAFPFGLQGNSEYLIEFSR 24 1 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 S(0.595)RS(0.404)VDS(0.001)AFPFGLQGNSEYLIEFSR 131.56 3.35E-05 90053000 30258 31449 39498 39916 52971 42381 39247 42114 41230 31191 TRUE FALSE 31452.6092 36850.12111 40527.35033 47811.26566 43967.00834 32538.65504 36170.71759 41549.53071 39746.14035 37302.27926 0.843181967 0.987878538 1.086457748 1.281725048 1.178668146 0.872296698 0.96966508 1.113860374 1.065515061 1 15.18697616 4.597830908 2.72397195 1.075170073 0.831310508 0.300147304 0.106494621 0.452527442 5.312505384 0.028749709 0.210979997 39612.37742 -4.597830908 -0.243859565 S(ph)RSVS(ph)PCSNVESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSVSPCSNVESR 13 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.652)RS(0.355)VS(0.813)PCS(0.179)NVES(0.001)R 93.576 0.066364 185890000 422090 359060 340310 285350 397050 479910 342400 327600 382320 340450 TRUE FALSE 438754.4391 420725.7619 349178.7582 341791.3783 329559.5828 368458.1756 315561.7933 323209.0578 368560.3779 407154.6592 1.077611245 1.033331567 0.857607178 0.839463262 0.809421126 0.90495876 0.775041587 0.793823798 0.905209776 1 18.63521739 4.269552971 3.69068935 0.843852812 1.068475566 0.595002607 0.063616464 0.124971673 3.530660867 0.015158039 0.044380849 18601.71437 -4.269552971 0.224622754 S(ph)RSWEDSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.473)RS(0.174)WEDS(0.353)PER 79.82 0.068026 730350000 526170 552190 583570 526760 698470 735350 569720 594710 599830 583280 TRUE FALSE 546943.5979 647024.3371 598778.3136 630951.5558 579744.3189 564576.1068 525063.8577 586738.8852 578242.2355 697562.5484 0.784078215 0.92755028 0.858386556 0.904508932 0.831100122 0.809355531 0.752712225 0.841127275 0.82894679 1 19.41196306 3.132397466 9.57145211 0.828472941 0.872056324 0.000132474 0.069100206 0.742854708 61.67371155 0.018629089 0.022287271 1356.430249 -3.132397466 0.043583382 S(ph)RT(ph)SPAPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.634)RT(0.844)S(0.522)PAPWK;S(0.972)RT(0.67)S(0.358)PAPWK 77.185 0.076351 1639220000 2734300 1844420 2392140 2015130 2761400 2990700 3221700 2476710 2526900 1517250 TRUE FALSE 2842252.275 2161184.787 2454481.134 2413716.699 2292018.214 2296155.249 2969174.736 2443513.754 2435957.363 1814526.088 1.566388212 1.191046412 1.352684401 1.330218791 1.263149772 1.265429726 1.636336207 1.346640189 1.342475801 1 20.79116137 0.651984702 3.22417526 1.00000876 1.365828748 0.421367831 0.128981968 5.275700256 47.79102309 0.120344183 0.031243319 4.487295832 -0.651984702 0.365819988 S(ph)RT(ph)SVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.867)RT(0.82)S(0.313)VQTEDDQLIAGQSAR;S(0.942)RT(0.569)S(0.49)VQTEDDQLIAGQSAR 251.12 2.50E-25 1905290000 229676 291823 227095 287158 264164 372080 297270 228742 220690 197465 TRUE FALSE 238743.7858 341941.3302 233013.2823 343956.9953 219261.4976 285670.0589 273969.2006 225676.0876 212747.41 236154.4861 1.010964432 1.447956107 0.986698522 1.456491473 0.928466367 1.209674496 1.160127022 0.955629052 0.900882357 1 17.84937142 1.736032031 4.098944354 0.94235908 1.179615623 0.262245803 0.168349288 0.233386619 8.709236721 0.082519524 0.041036201 54.45428132 -1.736032031 0.237256543 S(ph)RTGS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.501)RT(0.501)GS(0.648)ES(0.342)S(0.007)QTGTSTTSSR 75.106 0.0099242 191410000 26338 32609 35872 34316 40273 51668 39795 45534 38727 36869 TRUE FALSE 27377.84458 38209.34209 36806.85379 41103.60238 33427.40985 39668.89004 36675.76392 44923.69121 37333.22283 44092.77465 0.620914533 0.866566969 0.834759302 0.932207209 0.758115363 0.899668718 0.831786255 1.018844733 0.846697064 1 15.42825464 5.270718039 1.343858909 0.895279099 3.70E-18 0.532050156 0.075187055 3.735741444 2.204485665 0.020152672 6.478898192 186516.8358 -5.270718039 -0.895279099 S(ph)RTGSESSQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.456)RT(0.456)GS(0.085)ES(0.002)SQTGTSTTSSR;S(0.333)RT(0.333)GS(0.333)ESSQTGTSTTSSR;S(0.333)RT(0.333)GS(0.333)ES(0.002)S(0.001)QTGTSTTSSR;S(0.319)RT(0.319)GS(0.319)ES(0.039)S(0.003)QTGTSTTSSR 178.73 5.28E-14 2516814000 54362.9 59875.8 65110 55369.4 112088.2 98702.3 70632.1 78264.6 85305.3 96869.7 TRUE FALSE 56509.18927 70159.00288 66806.82009 66321.30206 93035.4878 75780.18667 65095.77144 77215.59105 82235.17892 115849.463 0.487781193 0.605604904 0.576669225 0.572478286 0.80307224 0.654126352 0.561899639 0.666516607 0.709845145 1 16.82189183 -5 0.17002834 2.462300653 0.537592408 0.729749158 0.072655922 72.40344724 0.683303658 35.64983242 0.272605243 1.00E-05 5 -1.924708245 S(ph)RTPPSAPSQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR;S(0.5)RT(0.5)PPSAPSQSR 68.257 0.032192 5732048000 1019806 1041468 1051260 966743 1284830 1321610 1025065 1037958 1006560 901319 TRUE FALSE 1060068.728 1220332.028 1078656.699 1157961.88 1066435.056 1014686.107 944717.7268 1024045.871 970334.1022 1077915.201 0.983443528 1.132122477 1.0006879 1.074260646 0.989349676 0.941341309 0.87643047 0.950024519 0.900195211 1 20.03981226 2.940490379 2.64547391 0.926923837 1.05031589 0.544931298 0.048744764 0.18582167 2.574640175 0.014540617 0.016307158 871.9475841 -2.940490379 0.123392053 S(ph)RTPS(ph)ASNDDQQE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 S(0.971)RT(0.029)PS(0.662)AS(0.338)NDDQQE;S(0.998)RT(0.002)PS(1)ASNDDQQE;S(0.997)RT(0.003)PS(0.81)AS(0.19)NDDQQE 284.15 1.44E-31 612690000 769383 945290 881840 846828 1077480 1258730 870055 956491 896630 951350 TRUE FALSE 799758.8349 1107636.204 904821.4748 1014328.051 894330.3345 966409.0337 801857.8156 943670.8026 864360.4614 1137748.818 0.70293093 0.973533162 0.795273492 0.891521955 0.786052528 0.84940456 0.704775785 0.829419278 0.759711149 1 20.11775066 3.215434497 24.93271196 0.807645747 0.847041848 0 0.096948814 851.7561527 918292.3202 0.025609106 0.030627362 1642.23195 -3.215434497 0.039396101 S(ph)RTPSLPTPPTREPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTPSLPTPPTREPK 15 2 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.469)RT(0.469)PS(0.063)LPTPPTREPK;S(0.561)RT(0.423)PS(0.017)LPTPPTREPK 66.533 0.030416 645470000 310820 235930 261510 203502 435300 419820 301280 303920 334700 276790 TRUE FALSE 323091.4136 276449.1422 268325.1654 243754.0882 361307.8615 322323.1674 277664.8864 299846.4495 322654.2124 331021.701 0.976042998 0.83513903 0.810596902 0.736368907 1.091492976 0.973722165 0.838811732 0.905821125 0.974722235 1 18.33656627 3.25280931 24.99997703 0.947736542 0.837155718 0.341761747 0.082812767 321.5783232 564220.2104 0.024120168 0.032508082 1789.819807 -3.25280931 -0.110580824 S(ph)RTPSRHS(ph)CS(ph)GSSPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTPSRHSCSGSSPPR 16 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.494)RT(0.494)PS(0.013)RHS(0.5)CS(0.556)GS(0.491)S(0.452)PPR 61.524 0.055774 50002000 23939 52121 42520 44716 48009 61891 44279 47581 43030 52350 TRUE FALSE 24884.1302 61072.3763 43628.10613 53560.69134 39848.44733 47517.75322 40808.29628 46943.25452 41481.35871 62606.9802 0.397465748 0.975488294 0.6968569 0.855506705 0.636485695 0.75898491 0.651817036 0.749808638 0.662567633 1 15.9340359 -0.907054753 4.884868448 1.000001282 0.720292065 0.267092838 0.143383041 1.77E-06 3.96E-07 0.122550466 0.028885289 0.123864042 0.907054753 -0.279709217 S(ph)RTPSRHS(ph)CSGSS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTPSRHSCSGSSPPR 16 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 S(0.499)RT(0.49)PS(0.017)RHS(0.801)CS(0.201)GS(0.108)S(0.883)PPR 118.04 0.0002 422050000 57188 160710 140700 140150 166860 204210 162330 164810 144610 158180 TRUE FALSE 59445.8264 188310.6923 144366.7576 167871.2517 138497.1968 156785.3223 149606.1504 162600.9915 139405.5143 189172.3425 0.314241636 0.995445158 0.763149389 0.887398493 0.732121805 0.82879622 0.790845789 0.859538923 0.73692334 1 17.52934165 4.749837565 24.9116057 0.833212918 0.314241318 0.749581846 0.091641076 721.763245 1594396.3 0.019517052 0.302286262 56213.10369 -4.749837565 -0.5189716 S(ph)RTS(ph)PAPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.979)RT(0.042)S(0.979)PAPWK;S(0.99)RT(0.015)S(0.995)PAPWK;S(0.994)RT(0.02)S(0.986)PAPWK 104.41 0.0090733 2217230000 3908290 2591650 3218200 2731060 3895780 4118200 4281200 3348330 3476780 1991010 TRUE FALSE 4062592.307 3036745.727 3302068.936 3271255.517 3233576.707 3161810.462 3945628.357 3303451.113 3351651.367 2381110.289 1.706175613 1.275348622 1.38677698 1.373836202 1.358012152 1.327872328 1.657054012 1.387357456 1.40760022 1 21.18320301 0.503692287 2.409052091 1.000013421 1.427452324 0.490164926 0.132039359 6.172161223 28.87349031 0.119835697 0.03211123 3.189277338 -0.503692287 0.427438904 S(ph)RTS(ph)PITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.987)RT(0.021)S(0.992)PITR;S(0.747)RT(0.258)S(0.988)PIT(0.007)R;S(0.927)RT(0.085)S(0.983)PIT(0.004)R 103.43 0.0027166 1550490000 116373 218525 184444 224303 199766 260996 178990 204785 190602 208270 TRUE FALSE 120967.4959 256054.9689 189250.7622 268669.4639 165809.8467 200383.6344 164960.2961 202040.192 183742.2713 249076.5189 0.48566399 1.028017293 0.759809728 1.078662353 0.665698426 0.804506323 0.662287625 0.811157121 0.737694071 1 17.9262295 S(ph)RTS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.668)RT(0.369)S(0.962)PVS(0.001)R;S(0.84)RT(0.164)S(0.995)PVS(0.002)R;S(0.971)RT(0.031)S(0.998)PVSR;S(0.938)RT(0.128)S(0.924)PVS(0.01)R 99.539 0.0038362 1585480000 81364.3 112773.7 64613.6 117129 119148.4 106357.8 79311.9 112069.6 99044.4 114981.6 TRUE FALSE 84576.62539 132141.7057 66297.4835 140296.7666 98895.59753 81657.81282 73095.22603 110567.4903 95479.81139 137510.0431 0.615057806 0.960960398 0.482128301 1.0202656 0.719188179 0.593831629 0.531562818 0.804068473 0.694347913 1 17.06917746 -1.965634824 6.939122188 1.162846975 0.718003413 0.211485045 0.165762571 0.079295715 0.000392703 0.030475425 0.035251649 0.010823437 1.965634824 -0.444843562 S(ph)RTS(ph)PVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.992)RT(0.009)S(0.999)PVTR;S(0.603)RT(0.432)S(0.963)PVT(0.002)R;S(0.988)RT(0.013)S(0.999)PVTR;S(0.996)RT(0.004)S(1)PVTR 106.47 0.0023842 6709110000 206704 170144 226253 181831 262644 260734 200588 217673 175657 226745 TRUE FALSE 214864.8335 199364.9085 232149.339 217796.6291 217999.8667 200182.48 184865.3884 214755.4495 169335.1389 271171.3415 0.792358191 0.735199035 0.856098354 0.803169789 0.803919269 0.738213997 0.681729077 0.791954815 0.624458093 1 18.04884519 2.743886152 23.00008459 0.750641588 0.798150065 0.010747451 0.095981727 466.9522476 2016687.582 0.027371722 0.02821377 554.4803403 -2.743886152 0.047508476 S(ph)RTSPITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.392)RT(0.392)S(0.216)PITR 79.659 0.016633 808110000 89162 140310 104120 165430 229990 186040 210230 187590 175350 173080 TRUE FALSE 92682.18461 164407.151 106833.4527 198151.5602 190896.382 142835.0295 193751.6233 185075.6629 169039.1878 206991.7122 0.447757949 0.794269245 0.516124301 0.957292242 0.922241668 0.690051925 0.936035657 0.894121127 0.81664713 1 17.65921348 5.21997486 0.547605339 0.89491464 1.88E-20 0.519072096 0.124836223 5.325053609 0.828290025 0.061307933 3.39737243 165949.0843 -5.21997486 -0.89491464 S(ph)RTSPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTSPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)RT(0.333)S(0.333)PVSR 83.397 0.011016 470170000 78699 82594 79514 92445 86167 116750 90644 82569 76558 82155 TRUE FALSE 81806.09729 96778.87701 81586.20016 110730.3451 71520.36412 89636.58186 83539.08643 81462.29761 73802.69253 98251.6993 0.832617633 0.985009702 0.830379533 1.127006921 0.727930047 0.912315843 0.850255894 0.82911846 0.751159451 1 16.58419474 3.202705591 24.99999739 0.839674422 0.938603228 0.17057946 0.105887294 289.4531049 201821.0083 0.028303568 0.033830318 1594.797664 -3.202705591 0.098928805 S(ph)RTSVQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_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 2 S(0.692)RT(0.247)S(0.061)VQT(1)EDDQLIAGQSAR 202.52 1.38E-14 594280000 607190 664030 580190 674560 598290 909790 731170 698390 571090 544570 TRUE FALSE 631162.3301 778071.9871 595310.228 807985.9546 496592.8795 698505.0605 673858.9848 689029.2244 550536.5825 651268.0651 0.969128327 1.194703117 0.914078641 1.240634998 0.762501505 1.072530803 1.03468759 1.057980978 0.845330229 1 19.31289196 3.261161626 24.99986485 0.981300172 1.076029628 0.159550004 0.127513932 516.349513 571150.8326 0.033269512 0.045016202 1824.574606 -3.261161626 0.094729457 S(ph)RTSVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 S(0.46)RT(0.27)S(0.27)VQTEDDQLIAGQSAR;S(0.333)RT(0.333)S(0.333)VQTEDDQLIAGQSAR 193.53 3.08E-15 355210000 76649 99980 99784 84181 90693 113222 94199 81426 84679 86853 TRUE FALSE 79675.16171 117150.7873 102384.453 100831.7505 75277.03625 86927.9064 86815.43624 80334.61766 81631.41933 103870.1824 0.767064809 1.127857721 0.985696285 0.970747795 0.724722288 0.836889898 0.835807103 0.773413657 0.785898488 1 16.66442204 3.265173681 21.53041664 0.813378716 0.976261682 0.276485793 0.106282527 49.44378244 39999.34421 0.027384957 0.037055031 1841.5083 -3.265173681 0.162882966 S(ph)RVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALR 34 2 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.803)RVPVRPPQQYS(0.197)DDEDDYEDDEEDDVQNTNSALR 188.41 2.01E-20 73160000 9806.9 7984.4 10644 8638.2 7867.7 7674.7 9898 6966.5 6775.2 8328.1 TRUE FALSE 10194.08398 9355.65859 10921.39138 10346.81018 6530.351164 5892.367236 9122.168896 6873.125462 6531.361875 9959.831744 1.023519699 0.93933902 1.096543763 1.038853913 0.655668824 0.59161313 0.915895884 0.690084495 0.655770302 1 13.28190566 3.246746577 24.99943145 0.737171183 1.023618064 0.541703273 0.122616414 129.944394 396839.9455 0.032868435 0.043757874 1765.007588 -3.246746577 0.286446881 S(ph)RWSGSHQFEQLSGSILWMAPEVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRWSGSHQFEQLSGSILWMAPEVIR 25 1 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.333)RWS(0.333)GS(0.333)HQFEQLSGSILWMAPEVIR;S(0.471)RWS(0.37)GS(0.089)HQFEQLS(0.054)GS(0.017)ILWMAPEVIR;S(0.333)RWS(0.333)GS(0.333)HQFEQLSGSILWMAPEVIR;S(0.463)RWS(0.463)GS(0.075)HQFEQLSGSILWMAPEVIR 142.32 2.12E-07 1576301000 483054 678746 834460 744602 1022103 1009192 899443 855865 903676 783201 TRUE FALSE 502125.3449 795315.3456 856206.7131 891882.0532 848366.2971 774822.4525 828942.3074 844393.5296 871152.8773 936654.2407 0.536083992 0.849102381 0.914111821 0.952199877 0.905741159 0.827223557 0.885003528 0.901499713 0.930068791 1 19.83715706 4.743861211 2.965541977 0.906738539 0.471505032 0.874551058 0.042719213 0.127397718 1.615709352 0.010405781 0.132695089 55444.84974 -4.743861211 -0.435233507 S(ph)RWSGSQQVEQPTGSVLWMAPEVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRWSGSQQVEQPTGSVLWMAPEVIR 25 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.471)RWS(0.471)GS(0.058)QQVEQPTGSVLWMAPEVIR;S(0.442)RWS(0.442)GS(0.115)QQVEQPTGSVLWMAPEVIR 121.19 0.00028089 432740000 88041 102346 106055 115854 118460 130783 100786 103905 87843 108138 TRUE FALSE 91516.92666 119923.1294 108818.8804 138769.5754 98324.21151 100410.6303 92886.12996 102512.3234 84681.54759 129325.5707 0.707647576 0.927296348 0.841433599 1.073025038 0.760284382 0.776417454 0.718234835 0.792668634 0.654793535 1 16.98064803 S(ph)RYMELYDLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRYMELYDLNR 11 1 J3QKP7;J3QLW0;H3BRL0;Q9BXC9 J3QKP7 BBS2 Bardet-Biedl syndrome 2 protein 1 S(0.396)RY(0.302)MELY(0.302)DLNR;S(0.389)RY(0.306)MELY(0.306)DLNR;S(0.401)RY(0.3)MELY(0.3)DLNR 91.855 0.015822 3600800000 716660 745010 825720 766910 822680 1021200 904590 829150 782070 699800 TRUE FALSE 744954.2902 872959.6721 847238.9415 918602.509 682841.1475 784041.7764 833685.8721 818036.6005 753923.4535 836912.4115 0.890122168 1.043071724 1.012338842 1.097608897 0.815905151 0.936826561 0.996144711 0.977445894 0.900839136 1 19.67471712 3.263673162 24.99986997 0.943460899 1.013202455 0.205846621 0.069587725 391.196626 389438.527 0.019226595 0.026022846 1835.156736 -3.263673162 0.069741556 S(ph)S(ph)PLAS(ph)LSKTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPLASLSKTR 11 1 X6RDY0;Q5T130;X6RIY5;Q5T124-7;Q5T124-6;Q5T124-3;Q5T124-2;Q5T124 X6RDY0 UBXN11 UBX domain-containing protein 11 3 S(1)S(1)PLAS(0.333)LS(0.333)KT(0.333)R 59.8 0.079652 170130000 37495 32889 42696 41340 42444 46943 37417 31739 30807 56132 TRUE FALSE 38975.33155 38537.42991 43808.69284 49516.92861 35229.38404 36041.19968 34484.15777 31313.59062 29698.26209 67129.99069 0.58059492 0.57407173 0.652594949 0.737627521 0.524793519 0.536886708 0.513692277 0.466462013 0.442399318 1 16.03466982 -1.811380596 6.706092304 1.024074543 0.556945465 0.722549301 0.082013687 0.030582658 0.000860185 0.082268175 0.020933486 0.015439008 1.811380596 -0.467129078 S(ph)S(ph)SQRSPSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_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(0.394)S(0.402)S(0.41)QRS(0.419)PS(0.354)PGPNHT(0.008)S(0.008)NS(0.003)S(0.003)NASNATVVPQNSSAR 107.52 1.26E-05 297110000 9109.2 101240 76113 93658 67821 151070 60372 99538 82095 109640 TRUE FALSE 9468.83825 118627.1825 78096.56731 112183.2729 56292.81065 115986.282 55639.88489 98203.85592 79140.41699 131121.8588 0.072214033 0.904709432 0.595602961 0.855564998 0.429316753 0.884568622 0.424337219 0.748951066 0.603563873 1 17.00054869 -5 0.196773594 2.60712267 0.56935434 0.197209422 0.242577122 231.8392847 2.287094199 146.9235024 0.547321311 1.00E-05 5 -2.037768329 S(ph)SATLWNSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSATLWNSPSR 11 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.987)S(0.013)ATLWNSPSR;S(0.988)S(0.012)ATLWNSPSR 173.76 1.24E-05 220280000 85187 94607 103772 71609 131283 111581 79152 81798 91711 101605 TRUE FALSE 88550.24854 110855.0163 106476.3836 85773.04647 108967.5626 85668.00378 72947.85941 80701.6316 88410.33902 121512.5544 0.728733331 0.9122927 0.876258294 0.705878062 0.896759706 0.705013603 0.600331873 0.664142335 0.727581931 1 16.89074585 2.710359044 21.44314843 0.70289224 0.825233039 0.074210874 0.118221877 193.9281569 147452.4433 0.03614573 0.034093937 513.2855571 -2.710359044 0.122340798 S(ph)SDEDAAGEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 S(0.836)S(0.164)DEDAAGEPK;S(0.991)S(0.009)DEDAAGEPK 195.77 3.81E-05 133490000 384980 202675 230858 174167 403780 416590 368890 276080 297670 154392 TRUE FALSE 400179.3077 237482.8547 236874.3491 208616.7128 335145.6198 319843.286 339975.4379 272379.5992 286956.9148 184642.1564 2.167323625 1.286178949 1.282883355 1.129843351 1.815108892 1.732233268 1.841266613 1.475175575 1.554124586 1 17.49437245 0.37783624 1.774342856 1.00003225 1.57479128 0.26011978 0.29676953 9.770854442 26.09089806 0.286253788 0.080169352 2.386911077 -0.37783624 0.574759031 S(ph)SDEENGPPSS(ph)PDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.949)S(0.051)DEENGPPSS(1)PDLDR 406.43 1.48E-139 629630000 178460 178760 182580 191950 213430 246410 238230 204960 202630 156360 TRUE FALSE 185505.7386 209460.6394 187338.1848 229917.1371 177151.2448 189185.0119 219556.9101 202212.8464 195337.3859 186995.7483 0.992031852 1.120135839 1.001831253 1.229531362 0.947354399 1.011707558 1.174127819 1.081376707 1.044608702 1 17.51264594 S(ph)SDELDAWTDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSDELDAWTDFR 12 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 S(0.981)S(0.019)DELDAWTDFR;S(0.805)S(0.195)DELDAWTDFR 139.46 6.17E-05 73040000 90334 84121 94417 95029 118850 123450 110740 105786 100692 89333 TRUE FALSE 93900.45607 98568.12738 96877.58458 113825.4526 98647.91945 94780.6084 102059.9094 104368.1117 97068.11459 106836.091 0.878920739 0.922610763 0.906787058 1.065421353 0.923357627 0.887159082 0.955294307 0.976899386 0.908570444 1 16.70503957 S(ph)SDIVSSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSDIVSSVR 9 0 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.984)S(0.016)DIVSSVR;S(0.976)S(0.024)DIVSSVR;S(0.916)S(0.084)DIVSSVR;S(0.936)S(0.064)DIVSSVR 154.05 8.04E-05 899100000 762250 771840 873170 737120 1175030 1087060 949890 864350 978620 760080 TRUE FALSE 792344.2186 904397.5159 895925.5275 882920.1359 975298.8203 834606.7896 875435.1397 852764.802 943399.6574 909003.1234 0.871662812 0.994933343 0.985613255 0.971305943 1.072932309 0.91815613 0.963071652 0.938131872 1.037839841 1 19.79392573 4.742834744 24.17987691 0.981879349 0.871662742 0.389500726 0.042866004 295.5609531 1671963.873 0.010080648 0.078232921 55313.95902 -4.742834744 -0.110216608 S(ph)SDKLNLVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDKLNLVTK 10 1 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.824)S(0.176)DKLNLVTK 98.902 0.0064208 0 158870 81362 117500 83096 179910 169490 160290 121210 135580 71442 TRUE FALSE 165142.3103 95335.29059 120562.1465 99532.14078 149328.9625 130128.5161 147726.051 119585.3782 130700.5023 85439.69206 1.932852358 1.115819689 1.411078898 1.164940303 1.747770373 1.523045238 1.729009637 1.399646643 1.529739857 1 16.38261883 -1.159699695 4.078006881 0.999840098 1.492138737 0.282149477 0.241216342 16262365.67 4624698.465 26481.18966 0.053234875 0.069230952 1.159699695 0.492298639 S(ph)SDPLGDTASNLGSAVDELMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 106.67 0.00037921 53047000 19167.7 16412.7 16044.3 20813.3 21146.1 24430 21641 18273.1 16115.2 17566.1 TRUE FALSE 19924.4556 19231.45355 16462.42764 24930.10862 17551.69348 18756.50274 19944.72187 18028.17898 15535.2171 21007.84097 0.948429476 0.915441695 0.783632533 1.186704938 0.835482975 0.892833431 0.949394176 0.858164292 0.73949613 1 14.35864028 1.648272549 5.718946129 0.847348685 0.928645628 0.054692174 0.115569061 0.352769585 24.50896781 0.058561472 0.028532098 44.49103915 -1.648272549 0.081296943 S(ph)SDSEEAFETPESTTPVK ddPTM_MDA-MB-175_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(0.5)S(0.5)DSEEAFETPESTTPVK 203.9 2.42E-18 0 81962 66995 87320 71028 94188 98892 91826 87668 90407 56551 TRUE FALSE 85197.92305 78500.8701 89595.63093 85077.1264 78177.9574 75925.83172 84628.43818 86492.95386 87153.26973 67631.08572 1.259745014 1.160721719 1.324769963 1.257958903 1.1559471 1.122646944 1.251324554 1.278893469 1.288656966 1 16.04539889 3.28535429 24.96671256 1.204057745 1.249648526 0.09550305 0.089048134 408.4669122 217933.8673 0.024841471 0.033635398 1929.097996 -3.28535429 0.045590781 S(ph)SDSWEVWGSASTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSDSWEVWGSASTNR 15 0 Q8N6T3;F8VWH9;Q8N6T3-5;Q8N6T3-2;Q8N6T3-4;E5RHH7 Q8N6T3 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 S(0.849)S(0.151)DSWEVWGSASTNR;S(0.989)S(0.011)DSWEVWGSASTNR;S(0.5)S(0.5)DSWEVWGSASTNR 363.09 1.48E-83 686580000 305521 312678 322583 359081 404255 408221 405273 350522 347641 328092 TRUE FALSE 317583.205 366378.0142 330989.778 430106.1501 335539.8795 313417.8594 373506.6433 345823.8259 335129.4683 392375.3457 0.809386238 0.933743718 0.843553963 1.096159977 0.855150262 0.798770521 0.9519116 0.881359723 0.854104296 1 18.58187487 -1.582745688 2.549662352 1.009030421 0.895307389 0.133422696 0.082406437 15887443.18 14288768.78 966926.1955 0.019182182 0.026136914 1.582745688 -0.113723032 S(ph)SEDIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSEDIIK 7 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 S(0.987)S(0.013)EDIIK 93.178 0.015867 94213000 203030 307490 292830 313250 279320 418700 232270 254400 254170 280990 TRUE FALSE 211045.7812 360299.0156 300461.3904 375209.915 231841.2862 321463.2705 214064.0705 250990.1841 245022.4713 336044.6106 0.628029061 1.072176146 0.894111618 1.116547932 0.689912228 0.956608915 0.637010872 0.74689543 0.729136738 1 18.35829324 3.21471627 24.99994133 0.775366211 0.935634604 0.136640404 0.161375425 367.181741 384975.8403 0.04389255 0.052488168 1639.518306 -3.21471627 0.160268394 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 S(0.945)S(0.055)EDLAGPLPSSVSSSSTTSSKPK;S(0.831)S(0.169)EDLAGPLPSSVSSSSTTSSKPK;S(0.89)S(0.11)EDLAGPLPSSVSSSSTTSSKPK;S(0.854)S(0.146)EDLAGPLPSSVSSSSTTSSKPK 221.69 5.49E-33 1119590000 733916 356220 525500 403157 780982 739394 776512 561064 654520 251147 TRUE FALSE 762891.5704 417398.014 539194.9617 482900.2513 648230.9586 567680.9491 715646.9604 553543.8548 630963.9531 300354.4462 2.539970958 1.389684819 1.795195539 1.607767947 2.158219953 1.890036776 2.382674768 1.842968739 2.10073119 1 18.19630649 3.239361542 24.99999566 1.963425664 1.798767048 0 0.439758718 91.33461905 2850840.108 0.114576387 0.146513745 1735.247958 -3.239361542 -0.164658616 S(ph)SEMLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSEMLVK 7 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 S(0.992)S(0.008)EMLVK;S(0.991)S(0.009)EMLVK;S(0.993)S(0.007)EMLVK 117.89 0.0053807 473361000 475909 350522 431016 320482 527708 537796 526931 422642 446967 298694 TRUE FALSE 494698.2548 410721.4268 442248.631 383872.3831 438008.3827 412901.0294 485628.7713 416977.1753 430880.745 357217.3705 1.384866179 1.149780108 1.238037866 1.074618467 1.226167647 1.155881722 1.359476922 1.16729255 1.206214425 1 18.44644271 0.411088055 1.70270284 1.000029152 1.215503559 0.34907213 0.089440558 5.51897977 14.70862693 0.080084231 0.02259431 2.576843572 -0.411088055 0.215474407 ADEGS(ph)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ADEGSPVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK 41 0 O15040-2;O15040 O15040-2 TECPR2 Tectonin beta-propeller repeat-containing protein 2 1 ADEGS(1)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK;ADEGS(1)PVEPSQEQDILTSMEASGHLSTNLWHAVTDDDTGQK 245.24 1.45E-54 167475000 34463.8 111128.8 137507 120386 169161 199196 142147 179299 157274 127125 TRUE FALSE 35824.45744 130214.3069 141090.5454 144197.9915 140407.0736 152935.7478 131005.1467 176895.7902 151613.7395 152032.7098 0.235636512 0.856488759 0.928027564 0.94846689 0.923532007 1.005939762 0.861690533 1.163537705 0.997244209 1 17.21402223 4.783475447 2.234492483 0.98659662 1.19E-16 0.897434785 0.074965616 0.220879414 1.155486102 0.020117503 0.449122552 60740.09223 -4.783475447 -0.98659662 down S(ph)SFSQHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.489)S(0.489)FS(0.022)QHAR;S(0.82)S(0.18)FSQHAR;S(0.97)S(0.03)FSQHAR 112.95 0.0030873 3086420000 1216580 2422700 2190850 2195920 2487680 3057950 2171200 2298960 1946930 2271660 TRUE FALSE 1264611.518 2838779.879 2247945.351 2630266.422 2064825.042 2347787.456 2001015.671 2268146.202 1876860.37 2716748.283 0.465487188 1.044918256 0.827439688 0.968167142 0.760035464 0.864190279 0.736548057 0.83487536 0.690848093 1 21.37344947 S(ph)SGASSIFDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSGASSIFDLR 11 0 Q96HP0 Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 S(0.524)S(0.476)GASSIFDLR;S(0.996)S(0.004)GASSIFDLR 158.42 3.13E-05 43475000 82558 88144 96408 105975 133053 137479 115099 110777 107835 100392 TRUE FALSE 85817.45359 103282.0463 98920.47168 126936.5387 110436.6986 105551.5858 106077.2396 109292.2155 103954.0394 120061.8903 0.714776799 0.860240049 0.823912329 1.057259205 0.919831416 0.879143128 0.883521319 0.910298974 0.865837104 1 16.87341876 4.750478774 1.434072199 0.918152094 0.634226921 0.505806038 0.062108512 1.049115796 1.910962013 0.016690257 0.431500314 56296.16016 -4.750478774 -0.283925173 S(ph)SGFISELPSEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.628)S(0.372)GFISELPSEEGK;S(0.5)S(0.5)GFISELPSEEGK 380.78 6.40E-98 393683000 1028090 659030 918430 716800 1255170 1196170 1104770 872600 959010 555040 TRUE FALSE 1068679.787 772213.276 942365.0403 858580.9006 1041816.652 918377.6456 1018175.241 860904.2243 924495.4174 663789.4611 1.609967994 1.163340669 1.419674604 1.293453649 1.569498633 1.383537551 1.533882805 1.29695374 1.392753985 1 19.3403662 0.19099445 1.021704348 0.997933272 1.406798778 0.471670949 0.129633887 3.749201494 3.999228582 0.134283252 0.036339776 1.55236717 -0.19099445 0.408865507 S(ph)SGQLSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGQLSGR 8 0 Q9P206-2;Q9P206;Q9P206-3 Q9P206-2 KIAA1522 Uncharacterized protein KIAA1522 1 S(0.961)S(0.039)GQLSGR 78.683 0.03146 58374000 47405 97182 89668 102820 108470 126220 88261 106330 98239 123020 TRUE FALSE 49276.586 113872.2525 92004.82174 123157.4891 90032.30814 96907.31788 81342.87219 104904.8203 94703.39758 147123.4136 0.334933678 0.77399137 0.625358123 0.83710326 0.611950919 0.658680461 0.552888695 0.713039602 0.643700382 1 17.16666733 -4.999999993 0.356605663 5.233913948 0.638497612 0.419042183 0.127857685 440.7359455 3.543041435 1430.42759 0.087812371 1.00E-05 4.999999993 -4.595416336 S(ph)SGREEDDEELLR ddPTM_MDA-MB-175_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(0.989)S(0.011)GREEDDEELLR;S(0.977)S(0.023)GREEDDEELLR 272.48 2.48E-32 1400890000 426610 402280 411170 414700 505590 547580 492440 478690 458670 437410 TRUE FALSE 443452.8922 471368.4607 421885.428 496726.4222 419649.9924 420412.8437 453841.266 472273.9435 442162.5563 523112.1148 0.847720555 0.901084963 0.806491412 0.949560158 0.802218072 0.803676366 0.867579345 0.902815917 0.845253902 1 18.99676066 -1.416780788 3.934768822 1.000704335 0.86112894 0.456484124 0.046243189 0.000276995 4.11E-05 0.043406787 0.010179865 0.038301802 1.416780788 -0.139575394 S(ph)SGRNSPSAASTSSNDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.332)S(0.332)GRNS(0.332)PS(0.003)AASTSSNDSK 69.133 0.016559 60423000 29465 21394 26910 21572 31348 35619 30713 25572 27836 14283 TRUE FALSE 30628.30095 25068.25308 27611.29671 25838.87721 26019.47816 27347.02706 28305.63481 25229.24917 26834.1878 17081.48039 1.793070639 1.467569116 1.616446355 1.512683715 1.523256625 1.600975234 1.657094945 1.4769943 1.570952118 1 14.06014539 -2.598618841 0.383896147 3.23E-15 1.590871664 0.788784211 0.09039223 31.40354026 1.293064671 26.09934267 0.055926074 0.002519888 2.598618841 1.590871664 S(ph)SIEDAQCPGLPDLIEENHVVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSIEDAQCPGLPDLIEENHVVNK 23 0 Q15398-1;Q15398;Q15398-3 Q15398-1 DLGAP5 Disks large-associated protein 5 1 S(0.5)S(0.5)IEDAQCPGLPDLIEENHVVNK 93.176 0.0015458 42384000 20184 16305 19350 17090 26890 23766 22918 20392 23192 15624 TRUE FALSE 20980.87991 19105.25691 19854.2769 20470.35099 22319.2474 18246.70668 21121.62727 20118.67859 22357.32445 18685.22366 1.122859447 1.022479434 1.062565654 1.095536846 1.1944865 0.97653135 1.130391996 1.076715963 1.196524316 1 14.18961021 3.719608988 7.711534067 1.098848449 1.064591337 0.025973925 0.070771754 0.658847222 213.0298379 0.017639452 0.028285341 5243.351688 -3.719608988 -0.034257112 S(ph)SLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLDAEIDSLTSILADLECSSPYKPRPPQSSTGSTASPPVSTPVTGHKR 49 3 Q93052;A0A087WZF1;C9JUT4 Q93052 LPP Lipoma-preferred partner 1 S(0.492)S(0.492)LDAEIDS(0.003)LT(0.003)S(0.003)ILADLECS(0.003)S(0.003)PY(0.001)KPRPPQSSTGSTASPPVSTPVTGHKR 40.829 0.046043 86858000 19862 20214 23920 15194 42918 30503 30349 22688 29387 23910 TRUE FALSE 20646.1671 23685.59726 24543.37485 18199.32785 35622.81369 23419.14053 27970.16608 22383.90447 28329.36761 28594.70672 0.722027587 0.828321042 0.858318817 0.63645793 1.245783496 0.819002648 0.978158872 0.782798883 0.990720692 1 14.80346049 S(ph)SLETLEDIEENAPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLETLEDIEENAPLR 16 0 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.5)S(0.5)LETLEDIEENAPLR 147.7 1.05E-06 48152000 24237 24724 26683 25880 33409 32941 28441 29930 27237 24473 TRUE FALSE 25193.89548 28970.15467 27378.3809 30998.98676 27730.15011 25290.95198 26211.7201 29528.83731 26256.74569 29268.01579 0.860799572 0.989822982 0.935436864 1.059142068 0.947455759 0.864115701 0.895575576 1.008911486 0.897113965 1 14.83703732 3.005873928 24.98272641 0.933718179 0.96671637 0.040530082 0.062417742 513.5740007 2184286.894 0.018198319 0.021695602 1013.617099 -3.005873928 0.032998191 S(ph)SLETLEDIEENAPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.988)S(0.011)LETLEDIEENAPLRR;S(0.975)S(0.025)LETLEDIEENAPLRR;S(0.965)S(0.035)LETLEDIEENAPLRR;S(0.982)S(0.018)LETLEDIEENAPLRR 162.33 1.75E-09 182725000 37892.7 44571 49570 33380.9 55940 56048 49491 44966.7 39722.5 38275.1 TRUE FALSE 39388.73306 52225.72254 50861.83492 39983.54239 46431.33878 43031.70142 45611.7661 44363.99494 38292.89498 45774.37302 0.860497489 1.14093802 1.111142143 0.873491863 1.014352261 0.940082814 0.996447643 0.969188478 0.836557498 1 15.4822525 3.744302807 24.9978778 0.952401516 1.047867094 0.179779338 0.087118884 747.358176 3253515.796 0.021584851 0.03761996 5550.12554 -3.744302807 0.095465578 S(ph)SLGSHQLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.5)S(0.5)LGSHQLPR;S(0.5)S(0.5)LGSHQLPR;S(0.5)S(0.5)LGSHQLPR 167.84 3.30E-06 511153000 159144 223205 198304 216217 243484 267669 218229 219863 239988 241979 TRUE FALSE 165427.128 261538.7225 203471.9651 258984.0773 202096.6767 205506.9313 201123.6407 216916.0961 231350.8788 289390.1521 0.571640489 0.903758198 0.703106045 0.894930513 0.698353677 0.710137957 0.694991309 0.749562812 0.799442818 1 18.1426563 0.788499438 2.561096894 0.99990522 0.745629915 0.413743099 0.092447188 0.873618181 8.925542336 0.081144849 0.021647363 6.144682367 -0.788499438 -0.254275304 S(ph)SLPSLDDQEQASSGWGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLPSLDDQEQASSGWGSR 19 0 R4GMM2;Q9NPB6-2;Q9NPB6 R4GMM2 PARD6A Partitioning defective 6 homolog alpha 1 S(0.5)S(0.5)LPSLDDQEQASSGWGSR 297.55 9.80E-50 95523000 52791 62239 64980 57119 71894 98941 63430 60185 66929 68292 TRUE FALSE 54875.22944 72928.0641 66673.43218 68416.96772 59673.48356 75963.45222 58458.19086 59378.31852 64520.23836 81672.50987 0.671893511 0.892932814 0.816350964 0.837698851 0.73064344 0.930098173 0.715763369 0.727029433 0.789987212 1 16.31756294 S(ph)SLQVDWHEEEWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLQVDWHEEEWEK 14 0 Q96PE3-2;Q96PE3-4;Q96PE3-3;Q96PE3 Q96PE3-2 INPP4A "Type I inositol 3,4-bisphosphate 4-phosphatase" 1 S(0.5)S(0.5)LQVDWHEEEWEK 250.79 9.89E-19 114520000 227280 158440 190520 184820 260840 285240 293780 206920 254160 139890 TRUE FALSE 236253.1899 185650.8375 195485.1077 221376.8444 216502.51 218997.3329 270752.7559 204146.5759 245012.8312 167298.7671 1.412163365 1.109696387 1.168479069 1.323242533 1.294107026 1.309019406 1.618378668 1.220251526 1.464522635 1 17.35206729 3.627924384 5.68329453 1.338541001 1.218623832 0.045871021 0.166600269 0.533403748 23.38489728 0.041884316 0.065494442 4245.456393 -3.627924384 -0.119917169 S(ph)SLVTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.786)S(0.214)LVTSK;S(0.679)S(0.321)LVTSK;S(0.751)S(0.249)LVTSK 217.2 3.74E-05 5471990000 18265800 12336900 17039900 12203900 22033500 18958900 18803300 15817700 18817300 10262100 TRUE FALSE 18986947.89 14455666.61 17483973.79 14617794.99 18288253.54 14555982.8 17329448.21 15605689.6 18140069.05 12272762.02 1.547080263 1.177865797 1.424616054 1.19107622 1.490149774 1.186039685 1.412025116 1.271571109 1.478075516 1 23.54895663 -1.134072946 4.116293898 0.999909726 1.341728099 0.39058421 0.131646851 5.117562143 31197235.87 5795.270763 0.026619115 0.073439051 1.134072946 0.341818374 S(ph)SLYGIAK ddPTM_MDA-MB-175_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(0.637)S(0.363)LYGIAK 153.05 0.00046926 215090000 327230 249700 307270 276090 437580 419900 391670 354490 338830 267040 TRUE FALSE 340149.2931 292584.0326 315277.7086 330699.778 363200.3079 322384.5886 360969.882 349738.6414 326635.5745 319361.3752 1.065092148 0.916153472 0.987213023 1.035503363 1.137270616 1.009466434 1.130286597 1.095118786 1.02277733 1 18.28483031 3.581899771 3.8022924 1.074720308 0.982724469 0.256440993 0.056052319 0.251915096 6.516580699 0.014505866 0.023029459 3818.56134 -3.581899771 -0.091995839 S(ph)SMEMEGIFNHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSMEMEGIFNHK 12 0 O75962-5;O75962;E7EPJ7;O75962-4;O75962-2;E7EWP2 O75962-5 TRIO Triple functional domain protein 1 S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK;S(0.5)S(0.5)MEMEGIFNHK 195.36 2.24E-07 361794000 311750 284692 378132 294975 429988 412357 382580 340043 351780 235458 TRUE FALSE 324058.1307 333585.6364 387986.4306 353320.1746 356898.7933 316593.3361 352592.3799 335485.2798 339119.5065 281591.487 1.150809402 1.184643897 1.377834375 1.254726051 1.267434599 1.124300097 1.252141475 1.191389993 1.204296018 1 18.10324419 -0.635529102 0.409813865 0.933763236 1.241920879 0.510853234 0.066482192 8.179661772 1.194500448 0.779605196 0.043121677 0.231457308 0.635529102 0.308157644 S(ph)SNAKLPSVPTVDSVSQDPVSNMSITER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSNAKLPSVPTVDSVSQDPVSNMSITER 28 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 S(0.485)S(0.485)NAKLPS(0.028)VPT(0.001)VDSVSQDPVSNMSITER 122.95 2.71E-05 53042000 19507 17924 19315 12335 24961 23354 15317 18295 18352 17265 TRUE FALSE 20277.15142 21002.30757 19818.36477 14774.82618 20718.13814 17930.38743 14116.41352 18049.78545 17691.5151 20647.74619 0.982051563 1.017171917 0.959831867 0.71556605 1.003409183 0.868394413 0.683678179 0.87417703 0.856825483 1 14.33369669 3.979562959 23.36327133 0.848725422 0.996834342 0.274649454 0.096703406 359.5881437 411078.3661 0.023928247 0.043906494 9540.320363 -3.979562959 0.14810892 S(ph)SNKPVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSNKPVSK 8 1 Q711Q0-3;Q711Q0 Q711Q0-3 C10orf71 Uncharacterized protein C10orf71 1 S(0.499)S(0.499)NKPVS(0.002)K 53.472 0.082587 519270000 382100 270450 310860 261890 3146800 466490 2374700 407450 401520 245820 TRUE FALSE 397185.603 316897.6837 318961.267 313691.0603 2611908.06 358154.7672 2188564.809 401988.7992 387069.3736 293983.7225 1.351046241 1.077942959 1.084962338 1.067035473 8.884532919 1.218280945 7.44451016 1.367384547 1.316635392 1 18.16537675 S(ph)SPAAFINPPIGTVTPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPAAFINPPIGTVTPALK 19 0 F6VRR5;Q9BY77-2;Q9BY77;Q6R954;F8WEE2;Q8WUT1;F8WCX5 F6VRR5 POLDIP3;PDIP46 Polymerase delta-interacting protein 3 1 S(0.5)S(0.5)PAAFINPPIGTVTPALK;S(0.5)S(0.5)PAAFINPPIGTVTPALK 151.95 6.35E-08 249460000 384090 302880 359600 292620 444060 454170 375350 371070 382210 280490 TRUE FALSE 399254.1698 354897.2839 368971.4714 350499.3626 368578.8398 348695.9005 345929.0862 366096.4136 368454.3368 335446.6452 1.190216613 1.057984299 1.09994086 1.044873656 1.098770386 1.039497355 1.031249205 1.091370025 1.09839923 1 18.35572379 6.613538263 1.525773621 1.064431947 37.83972966 0.562763662 0.033242359 305.3012454 3.1125622 0.008322664 38901.7484 4107128.237 -6.613538263 36.77529772 S(ph)SPAELSSSSQHLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPAELSSSSQHLLR 15 0 Q9UQC2;Q9UQC2-2;E9PJE2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 S(0.582)S(0.418)PAELSSSSQHLLR;S(0.5)S(0.5)PAELSSSSQHLLR;S(0.5)S(0.5)PAELSSSSQHLLR 127.71 4.93E-05 848340000 76243 137490 122340 131731 139688 168833 140746 143330 123572 129588 TRUE FALSE 79253.13251 161102.838 125528.2809 157786.9986 115943.8837 129624.0944 129713.9607 141408.8958 119124.6679 154978.2875 0.511382167 1.039518765 0.809973338 1.018123256 0.748129854 0.836401644 0.836981508 0.912443272 0.768653918 1 17.24170658 -5 0.017952734 2.024298475 1.63E-13 0.114407379 0.140895595 10809.70011 14.70572984 1084.029138 630.8443681 1.00E-05 5 -2.024298475 S(ph)SPAFGDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 1 S(0.5)S(0.5)PAFGDRR;S(0.5)S(0.5)PAFGDRR;S(0.5)S(0.5)PAFGDRR 147.74 5.61E-05 617880000 458240 518780 523330 544760 415580 605750 516420 528990 466070 383978 TRUE FALSE 476331.669 607876.4295 536968.4097 652511.9021 344939.86 465073.7427 475941.651 521899.7543 449296.2317 459211.1374 1.037282483 1.323740606 1.169327932 1.420940933 0.751157435 1.012766688 1.036433162 1.136513712 0.97840883 1 18.80879811 3.250039723 24.99948632 1.007024526 1.239067399 0.468420264 0.130318834 212.1884453 462106.5781 0.035985926 0.048309315 1778.442069 -3.250039723 0.232042873 S(ph)SPAFTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPAFTKR 8 1 Q5VVQ6-2;Q5VVQ6 Q5VVQ6-2 YOD1 Ubiquitin thioesterase OTU1 1 S(0.5)S(0.5)PAFTKR 63.734 0.043756 130790000 56330 54738 50521 52903 83169 76680 60040 64893 60952 58806 TRUE FALSE 58553.9519 64138.8257 51837.61876 63367.0555 69031.96309 58872.2321 55333.90791 64023.21548 58758.34943 70327.90979 0.832584845 0.911996758 0.737084593 0.901022875 0.981572797 0.837110505 0.786798699 0.910352884 0.835491195 1 16.10180972 -2.459300003 2.118728689 2.298652663 0.861858697 0.28700109 0.066406378 2785428.392 188655.9862 17465823.44 0.017439243 0.003472962 2.459300003 -1.436793966 S(ph)SPAPHSGPCPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPAPHSGPCPSR 13 0 P85299;P85299-5;P85299-2;P85299-4;P85299-3 P85299 PRR5 Proline-rich protein 5 1 S(0.5)S(0.5)PAPHSGPCPSR;S(0.5)S(0.5)PAPHSGPCPSR;S(0.5)S(0.5)PAPHSGPCPSR;S(0.5)S(0.5)PAPHSGPCPSR 181.58 7.68E-06 944770000 495504 670460 602840 578070 715140 810810 644520 636970 641770 600620 TRUE FALSE 515066.8805 785606.2895 618550.5056 692410.5206 593580.7582 622511.6654 594000.8383 628432.459 618672.8231 718299.9894 0.717063745 1.093702215 0.861131163 0.963957303 0.826368881 0.866645795 0.826953706 0.874888582 0.861301451 1 19.45422697 5.018275119 16.47791477 0.896705367 0.357695984 0.318931747 0.082286931 14829820.4 304453105.3 0.018666129 197601961.6 104297.7931 -5.018275119 -0.539009383 S(ph)SPELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.756)S(0.244)PELTR 157.8 0.0015229 550110000 216410 263140 247440 245220 258030 275760 254600 268120 246040 211100 TRUE FALSE 224954.0339 308332.2481 253888.4897 293723.7841 214170.1528 211718.9192 234643.7867 264526.29 237185.0685 252461.0032 0.89104468 1.221306436 1.005654285 1.163442196 0.848329643 0.838620288 0.929425867 1.047790695 0.939491903 1 17.94570103 3.239569838 24.9999937 0.939236868 1.076521673 0.303216411 0.100946516 34.17564307 846569.5912 0.028435582 0.036406024 1736.080415 -3.239569838 0.137284805 S(ph)SPEQPRPSTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.959)S(0.041)PEQPRPSTSK;S(0.685)S(0.315)PEQPRPSTSK 225.92 4.35E-11 530980000 695940 504480 639940 487280 792610 774280 709290 629310 673190 417470 TRUE FALSE 723416.2486 591120.5157 656617.3621 583662.5296 657882.4353 594465.2043 653693.9964 620875.1288 648962.0234 499265.2536 1.448961736 1.183980883 1.315167353 1.16904296 1.317701223 1.190680105 1.309312018 1.243577686 1.299834144 1 18.92944698 -1.951073789 2.563428802 0.798508362 1.269007198 0.516803204 0.079664547 10649887.79 5137831.844 12782748.29 0.017112904 0.011192477 1.951073789 0.470498835 S(ph)SPGAGPSDHHSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 110.37 0.00059705 156816000 5233.7 34841 28126 39972 24993 39324 20112.2 31968 25310 31066 TRUE FALSE 5440.330517 40824.67072 28858.98667 47878.3423 20744.69879 30191.59696 18535.75321 31539.52125 24399.09804 37152.78791 0.146431286 1.098831959 0.776765037 1.28868774 0.558361834 0.812633416 0.498906119 0.848913985 0.656723208 1 15.18118285 S(ph)SPGAVAGLSNAPGTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 S(0.617)S(0.383)PGAVAGLSNAPGTPR;S(0.623)S(0.377)PGAVAGLSNAPGTPR 202.79 1.08E-11 877500000 591990 580640 637580 583670 679270 784490 636750 653030 646970 527730 TRUE FALSE 615362.2223 680360.4032 654195.8586 699118.1839 563807.928 602304.0866 586839.8712 644277.201 623685.6761 631128.5895 0.975018772 1.078005995 1.036549238 1.107727008 0.893332892 0.954328637 0.929826157 1.020833491 0.988206978 1 19.26757445 3.245168524 24.9999884 0.966397093 1.050461295 0.447640054 0.046165813 149.202318 564480.341 0.012994348 0.017192928 1758.605894 -3.245168524 0.084064202 S(ph)SPGGQDEGGFMAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.956)S(0.044)PGGQDEGGFMAQGK 306.07 1.65E-46 179290000 423430 294660 421780 329240 496760 541160 537430 463320 464570 285410 TRUE FALSE 440147.3434 345265.5629 432771.9333 394362.6893 412320.9126 415483.7914 495304.8323 457109.9532 447850.2164 341330.625 1.289504402 1.01152823 1.267896584 1.155368609 1.207981009 1.217247328 1.45109989 1.339199942 1.312071592 1 18.38081034 2.458833613 24.93507472 1.315563241 1.182842893 0.0629167 0.129563695 367.3485798 500874.2941 0.04162248 0.034829234 287.6296236 -2.458833613 -0.132720348 S(ph)SPGPDTLVVLEFNPASK ddPTM_MDA-MB-175_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 188.44 3.97E-14 111393000 188167 131859 178303 142337 203669 229773 232921 176373 182655 103465 TRUE FALSE 195595.9785 154504.7575 182949.7227 170490.8338 169049.4161 176411.703 214664.0434 174009.0084 176081.2822 123736.9858 1.580739802 1.248654608 1.478537088 1.377848609 1.366199565 1.425699049 1.734841382 1.406281293 1.423028702 1 16.91691727 0.57252628 2.535083144 1.000025304 1.450976606 0.54185883 0.124171767 3.988134912 22.7070438 0.117271516 0.03123427 3.73702738 -0.57252628 0.450951302 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQT(0.001)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.5)S(0.5)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 282.32 4.11E-61 17609808000 941055 1048879 1035710 986993 1287766 1453702 1095145 1104553 1041423 943609 TRUE FALSE 978208.5781 1229015.809 1062701.453 1182217.27 1068871.995 1116101.742 1009304.673 1089748.274 1003942.39 1128491.117 0.86682878 1.089078851 0.941701213 1.047608839 0.947169171 0.989021291 0.894384243 0.965668455 0.889632514 1 20.10596363 2.275302595 24.94757627 0.936458454 0.984990147 0.094343454 0.063946806 334.7046293 227261.257 0.020153772 0.016861406 188.4961979 -2.275302595 0.048531693 S(ph)SPIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPIMR 6 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8;K7ENU7;H0Y9S9 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 S(0.843)S(0.157)PIMR;S(0.712)S(0.288)PIMR;S(0.5)S(0.5)PIMR;S(0.5)S(0.5)PIMR 146.94 0.011491 2115340000 1074910 1245600 1268470 1169610 1388590 1598740 1317890 1295520 1149680 1034780 TRUE FALSE 1117348.277 1459522.111 1301527.37 1400955.367 1152557.968 1227456.864 1214590.338 1278155.673 1108303.241 1237525.329 0.902889218 1.179387667 1.051717763 1.132061974 0.931340911 0.991864033 0.981467053 1.03283193 0.895580248 1 20.23902662 3.234653577 24.99999737 0.979336227 1.073519664 0.267876352 0.075494511 128.8613314 824545.0549 0.020263648 0.025083457 1716.538613 -3.234653577 0.094183437 S(ph)SPKEELHPAAPSQLAPSFSSSSSSSSGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPKEELHPAAPSQLAPSFSSSSSSSSGPR 30 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR;S(0.492)S(0.492)PKEELHPAAPS(0.013)QLAPSFSSSSSSSSGPR;S(0.5)S(0.5)PKEELHPAAPSQLAPSFSSSSSSSSGPR 253.47 2.79E-58 1135890000 913968 598490.8 804340 586946.9 1132993 1279610 1087231 884673 992931 507579 TRUE FALSE 950052.1624 701276.9393 825301.7612 703043.245 940407.2546 982439.9702 1002010.993 872815.4055 957195.6073 607029.3869 1.565084299 1.15526028 1.359574642 1.158170033 1.549195599 1.618438895 1.650679547 1.437847037 1.576852172 1 19.21140683 3.219464304 24.99280602 1.508550741 1.302078732 0.11714501 0.204195769 370.4934007 484892.0664 0.054580223 0.065333294 1657.541092 -3.219464304 -0.206472009 S(ph)SPLKITLFLEEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPLKITLFLEEDK 14 1 Q9NQW6 Q9NQW6 ANLN Actin-binding protein anillin 1 S(0.5)S(0.5)PLKITLFLEEDK 132.79 2.93E-05 529060000 261370 104060 158450 77158 263270 288870 202910 154920 203920 91167 TRUE FALSE 271689.0894 121931.4955 162579.3372 92419.62211 218519.4594 221784.3204 187005.384 152843.5508 196580.959 109029.4282 2.491887686 1.118335642 1.491150967 0.847657588 2.004224576 2.034169344 1.715182654 1.401855934 1.803008255 1 16.73435806 -1.324161764 4.581313329 0.999503767 1.61931583 0.155756165 0.451079351 0.002204614 0.000325227 0.421155358 0.099190569 0.047406537 1.324161764 0.619812063 S(ph)SPLKLEFDFTEDTGNIEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPLKLEFDFTEDTGNIEAR 20 1 O75410-3;E7ET87;E7EVI4;O75410-2;O75410;O75410-9;O75410-7;H0YAY0;E5RFM9;R4GMT7 O75410-3 TACC1 Transforming acidic coiled-coil-containing protein 1 1 S(0.5)S(0.5)PLKLEFDFTEDTGNIEAR 77.445 0.0060658 40594000 18383 26481 27849 27329 28842 36748 30050 31837 27083 40089 TRUE FALSE 19108.77503 31028.90576 28574.76782 32734.59463 23939.44714 28213.83392 27694.60248 31410.27709 26108.28812 47943.672 0.398567199 0.64719502 0.596007077 0.682771954 0.499324439 0.588478787 0.577648756 0.655149591 0.544561712 1 15.54905279 -5 0.342827593 5.564280852 0.571178315 0.722348639 0.078678707 201.7334348 1.68637069 674.7241108 0.058307461 1.00E-05 5 -4.993102537 S(ph)SPLPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPLPAK 7 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 S(0.523)S(0.477)PLPAK 89.355 0.018812 350070000 916060 669680 873170 788670 970100 1033300 1238800 929190 919550 464790 TRUE FALSE 952226.7562 784692.3306 895925.5275 944666.5721 805202.7485 793331.7348 1141699.619 916735.7279 886455.5751 555856.7016 1.713079564 1.411680975 1.611792257 1.699478606 1.448579726 1.427223478 2.053945946 1.649230324 1.594755578 1 19.08435348 0.773278628 5.356424495 1.000000718 1.630803724 0.527504188 0.177173731 6.826712184 161.0243649 0.173007013 0.043630079 5.933058471 -0.773278628 0.630803007 S(ph)SPNPFITGLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.612)S(0.388)PNPFITGLTR;S(0.608)S(0.392)PNPFITGLTR;S(0.572)S(0.428)PNPFITGLTR;S(0.606)S(0.394)PNPFITGLTR 156.08 7.30E-05 1203080000 542799 603790 608126 554378 769910 839960 639251 636013 614617 589224 TRUE FALSE 564229.1237 707486.2357 623974.2631 664032.3137 639040.9732 644892.0197 589144.8362 627488.286 592497.0542 704671.1614 0.800698474 1.003994876 0.885482899 0.942329345 0.906864092 0.915167322 0.836056403 0.890469655 0.840813541 1 19.42659065 S(ph)SPNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_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(0.699)S(0.301)PNVANQPPS(1)PGGK 276.3 2.26E-33 316100000 700250 402130 502640 428040 609130 761340 736860 519100 585330 268180 TRUE FALSE 727896.4107 471192.6994 515739.2113 512705.0344 505590.3002 584530.3232 679102.9878 512142.3136 564264.0876 320724.7364 2.269536235 1.469149853 1.608043137 1.59858276 1.576399457 1.822529593 2.117401344 1.596828231 1.759340717 1 18.2909761 -0.054167004 1.581870607 0.999386811 1.743155194 0.466842808 0.242366323 33.01290206 47.54731323 0.305758313 0.064175215 0.882740385 0.054167004 0.743768383 S(ph)SPPFWALPPSAPSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPFWALPPSAPSER 16 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.5)S(0.5)PPFWALPPSAPSER 74.89 0.03254 104040000 42627 49076 48207 44030 51316 71108 47459 57140 57224 51102 TRUE FALSE 44309.94688 57504.42124 49463.31402 52739.00258 42593.32465 54594.24465 43739.03957 56374.13176 55164.51942 61114.45849 0.725032144 0.940929899 0.809355351 0.862954592 0.696943501 0.893311436 0.715690536 0.922435266 0.902642693 1 15.89922611 1.295414354 1.698814447 0.983731117 0.813969651 0.370233513 0.079147278 0.350778134 1.81341457 0.067011265 0.02023163 19.74305494 -1.295414354 -0.169761466 S(ph)SPPLPPPAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.619)S(0.381)PPLPPPAEER 155.86 7.63E-05 882620000 202400 299130 235350 189900 291020 267600 261700 255700 226880 209730 TRUE FALSE 210390.9083 350503.2506 241483.4143 227461.6532 241552.5243 205453.9555 241187.2702 252272.7597 218714.6331 250822.578 0.838803707 1.397415071 0.962765857 0.906862752 0.963041391 0.81912066 0.961585166 1.005781703 0.871989415 1 17.93630769 4.031871634 24.99973805 0.935491497 1.133604823 0.222572796 0.136176273 228.1019113 178917.6364 0.0306824 0.066280794 10761.47087 -4.031871634 0.198113326 S(ph)SPPSAGNSPSSLKFPSSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPSAGNSPSSLKFPSSHR 20 1 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.499)S(0.499)PPS(0.002)AGNSPSSLKFPSSHR 174.01 2.44E-12 102220000 78758 189380 216600 141810 238510 238480 148090 219350 204440 198540 TRUE FALSE 81867.42665 221904.5418 222244.7739 169859.5947 197968.1554 183096.6342 136482.3188 216409.972 197082.2443 237440.1117 0.344791897 0.934570575 0.936003493 0.715378684 0.83376037 0.771127645 0.574807339 0.911429709 0.830029277 1 17.85720415 -5 0.106459288 1.709195619 0.636741716 0.194083112 0.169095359 331.5724759 2.36819965 51.87668349 2.289364349 1.00E-05 5 -1.072453903 S(ph)SPPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_MDA-MB-175_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 186.01 4.24E-18 1726630000 276940 476010 524850 487440 518520 724630 468560 503820 524830 496660 TRUE FALSE 287873.805 557761.0147 538528.0222 583854.1771 430382.1556 556345.6644 431833.0428 497067.117 505941.4708 593971.0179 0.484659683 0.939037424 0.906657069 0.982967451 0.724584437 0.936654563 0.727027127 0.83685416 0.851794878 1 19.18003301 4.745344903 24.7510794 0.866184441 0.484659482 0.622105419 0.091618317 451.2639389 1646294.96 0.021088122 0.206279898 55634.59142 -4.745344903 -0.381524959 S(ph)SPQKEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPQKEVK 8 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 S(0.658)S(0.342)PQKEVK 83.862 0.026132 0 106180 49157 64214 42088 107720 89621 76693 63565 85796 39705 TRUE FALSE 110372.0684 57599.33236 65887.46959 50412.88078 89409.79288 68807.88097 70681.60226 62713.01515 82708.21872 47484.43455 2.324384178 1.213015021 1.387559317 1.061671709 1.882928453 1.449061816 1.488521511 1.32070679 1.741796433 1 15.53516705 -2.144582607 2.059121046 5.54E-05 1.503825612 0.172504529 0.346989938 2833493.105 611315.8235 13232527.71 0.079681197 0.00716832 2.144582607 1.503770232 S(ph)SPQLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.529)S(0.471)PQLAK;S(0.657)S(0.343)PQLAK;S(0.654)S(0.346)PQLAK 98.629 0.011667 3737510000 9609800 6725900 7935700 5985500 6285600 8296700 8281500 7712300 7506400 2991260 TRUE FALSE 9989202.324 7881021.005 8142510.861 7169414.035 5217175.957 6369917.163 7632374.39 7608929.233 7236246.13 3577340.126 2.792354647 2.203039333 2.276135501 2.004118642 1.458395281 1.780629445 2.13353333 2.126979534 2.022800705 1 21.77045586 4.897539764 0.883104015 1.86051217 3.472236441 0.448257352 0.341779736 2.899358021 1.464621081 0.11197186 4.821512177 78984.11631 -4.897539764 1.611724271 S(ph)SPQLDPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.5)S(0.5)PQLDPLR 65.056 0.070952 1011000000 730250 775390 798700 832630 901280 1018800 952530 907400 862310 695350 TRUE FALSE 759080.8339 908557.2008 819514.7781 997321.7288 748080.7475 782199.1401 877868.2096 895237.7872 831275.6315 831590.5192 0.912806022 1.092553582 0.985478741 1.199294251 0.899578254 0.94060613 1.055649613 1.076536789 0.999621343 1 19.66551378 S(ph)SPQLDPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.872)S(0.128)PQLDPLRK;S(0.983)S(0.017)PQLDPLRK;S(0.869)S(0.131)PQLDPLRK;S(0.5)S(0.5)PQLDPLRK 156.08 7.09E-06 22703291000 9939247 6250110 7835224 7576229 9418322 9926279 12253814 8717127 8856299 4497437 TRUE FALSE 10331656.15 7323517.773 8039416.374 9074784.483 7817398.991 7621051.136 11293328.04 8600288.171 8537562.529 5378623.672 1.920873587 1.361596985 1.494697689 1.687194539 1.453419958 1.416914735 2.09966875 1.598975629 1.587313605 1 22.35880562 0.662612068 3.404714099 1.000010802 1.625621642 0.425250724 0.218272569 5.682327173 56.29948104 0.205645617 0.053138624 4.598456349 -0.662612068 0.62561084 S(ph)SPRPTAEK ddPTM_MDA-MB-175_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(0.5)S(0.5)PRPT(0.001)AEK 75.819 0.022517 646880000 931740 702850 821770 697410 1114950 1099090 1099930 883000 937690 660150 TRUE FALSE 968525.8147 823559.0201 843186.0013 835355.6164 925431.1973 843843.0044 1013714.612 871164.8293 903942.7201 789493.7532 1.22676818 1.043148241 1.068008452 1.058090217 1.172183052 1.068840635 1.284005869 1.1034474 1.144965006 1 19.59056833 S(ph)SPSHSTTSGETDPTTIFPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSHSTTSGETDPTTIFPCK 21 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 S(0.313)S(0.313)PS(0.055)HS(0.07)T(0.07)T(0.09)S(0.09)GET(0.001)DPTTIFPCK 113.08 0.00013493 75771000 53937 97063 110320 102480 113160 130170 102540 111320 111180 82505 TRUE FALSE 56066.47441 113732.8152 113195.0298 122750.2381 93925.10362 99939.99025 94502.64686 109827.9375 107178.6535 98670.2751 0.568220514 1.152655297 1.147204968 1.244044754 0.951908805 1.012868264 0.957762069 1.113080281 1.086230411 1 16.59032791 4.743886645 24.9352811 1.075665743 0.568220292 0.74257898 0.089327546 286.470191 1341146.933 0.022291466 0.190310962 55448.09692 -4.743886645 -0.50744545 S(ph)SPSIICMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.663)S(0.337)PSIICMPK;S(0.567)S(0.433)PS(0.001)IICMPK;S(0.802)S(0.198)PSIICMPK 158.47 8.37E-06 459970000 961070 668490 838090 761590 1007530 1043330 1119270 849120 893810 511200 TRUE FALSE 999013.7857 783297.9574 859931.3139 912230.2289 836270.4105 801032.4193 1031538.693 837738.9353 861641.9527 611359.8525 1.634084707 1.28123879 1.406587807 1.49213303 1.367885718 1.310247011 1.687285628 1.37028778 1.409385895 1 19.22166229 0.496291759 1.89055266 1.000071582 1.439963229 0.531845115 0.124267267 3.03152684 10.50542786 0.111762475 0.031021573 3.135391372 -0.496291759 0.439891647 S(ph)SPSPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSPQKR 8 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 S(0.9)S(0.099)PSPQKR 68.016 0.061013 85045000 218840 157070 187470 171150 252260 229860 230470 206950 182710 134540 TRUE FALSE 227479.9722 184045.5507 192355.6222 205002.9592 209380.9353 176478.4986 212405.1592 204176.1738 176134.3028 160900.5371 1.413792498 1.143846714 1.195493972 1.27409742 1.301306628 1.096817337 1.320102239 1.268958932 1.094678153 1 17.29580962 1.073153781 3.786091699 1.002481627 1.247822938 0.490603437 0.085754391 0.160127578 4.394749489 0.077488864 0.020021487 11.83460539 -1.073153781 0.245341311 S(ph)SPSTDHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSTDHYK 9 0 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.474)S(0.474)PS(0.046)T(0.007)DHYK 64.374 0.045045 67485000 94867 121760 123520 127320 151290 156950 146140 122300 119480 108360 TRUE FALSE 98612.42241 142671.3328 126739.0327 152503.516 125573.7798 120500.7411 134685.1649 120660.7685 115179.9381 129591.0673 0.76095077 1.100934932 0.977992043 1.176805772 0.969000275 0.929853759 1.039309018 0.931088624 0.888795351 1 16.98360675 1.646775826 7.507555464 0.931993111 1.000562697 0.046105775 0.10633849 0.328155314 36.22847146 0.051466963 0.026253527 44.33797217 -1.646775826 0.068569586 S(ph)SPSTENMHFPSSISSQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPSTENMHFPSSISSQTR 19 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 S(0.367)S(0.367)PS(0.249)T(0.016)ENMHFPSSISSQTR;S(0.437)S(0.437)PS(0.118)T(0.007)ENMHFPSSISSQTR 110.94 0.00014549 432830000 104589 196149 186765 215314 234776 263847 186976 201422 191570 212468 TRUE FALSE 108718.2545 229836.0649 191632.2493 257902.4666 194868.8594 202572.5329 172320.3325 198722.2675 184675.4331 254097.0367 0.427861166 0.90452084 0.754169556 1.014976286 0.766907249 0.79722509 0.678167423 0.782072354 0.726790975 1 17.95502002 4.747368503 24.50484298 0.811182339 0.427860905 0.545213055 0.108149888 665.7050344 1852036.353 0.024842489 0.292730132 55894.42631 -4.747368503 -0.383321434 S(ph)SPSVLIHSLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSVLIHSLGK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 S(0.5)S(0.5)PSVLIHSLGK 178.67 6.94E-05 0 103110 132860 163410 176280 228430 239870 196810 199010 194990 126330 TRUE FALSE 107180.8624 155677.6715 167668.5988 211147.6579 189601.5502 184163.8278 181383.5179 196342.5965 187972.348 151081.9448 0.709422046 1.030418769 1.109785813 1.397570426 1.254958364 1.218966489 1.200563828 1.299576841 1.244174797 1 17.20497173 4.652118712 1.516977698 1.24305474 0.565368082 0.714655283 0.098969676 0.440859453 1.078496667 0.025062026 0.426040218 44886.80689 -4.652118712 -0.677686657 S(ph)SPVPEMLEESQELLEPVVDDVPK ddPTM_MDA-MB-175_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)PVPEMLEES(0.001)QELLEPVVDDVPK 128.12 0.00026722 33999000 65463 35731 48573 32635 66162 67813 62299 50003 54903 26697 TRUE FALSE 68047.52979 41867.5213 49838.85228 39090.10559 54915.80687 52064.45847 57415.84159 49332.79157 52927.05175 31927.76601 2.131296307 1.3113201 1.560987771 1.224329494 1.720001545 1.630695316 1.798304384 1.545137595 1.657712342 1 14.96252399 -1.523399657 6.286606046 0.999390607 1.604083038 0.376980637 0.238317401 0.001899007 0.000143968 0.215276511 0.050693989 0.029964038 1.523399657 0.60469243 S(ph)SPVPPVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.634)S(0.366)PVPPVPER;S(0.649)S(0.351)PVPPVPER 164.65 6.39E-06 2129210000 1401020 1443840 1506270 1356590 1724610 1904220 1616350 1545190 1496910 1257850 TRUE FALSE 1456333.351 1691808.288 1545524.634 1624919.453 1431461.408 1461993.764 1489656.263 1524479.255 1443036.502 1504301.625 0.968112596 1.124646986 1.02740342 1.080181944 0.951578716 0.971875414 0.990264345 1.013413288 0.959273378 1 20.52066244 3.241620643 24.99999833 0.984091843 1.053791806 0.403661759 0.040899139 76.12718936 621944.9157 0.010817118 0.014037994 1744.297839 -3.241620643 0.069699962 S(ph)SS(ph)PVTELASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.999)S(0.008)S(0.992)PVT(0.002)ELASR;S(0.996)S(0.044)S(0.96)PVTELASR;S(0.996)S(0.043)S(0.961)PVTELASR 137.88 0.00010117 193910000 439250 392541 413442 409595 493980 622590 517900 445560 417750 304655 TRUE FALSE 456591.9292 459956.8632 424216.6382 490611.6685 410013.456 478002.9079 477305.6447 439587.997 402715.2591 364346.3143 1.253181139 1.262416677 1.164322573 1.346553126 1.125339931 1.311946599 1.310032862 1.206511442 1.105308997 1 18.47495087 1.107465227 2.22305209 1.003065097 1.251458399 0.626026064 0.06354189 0.168288633 1.606349264 0.055900444 0.015613332 12.80752545 -1.107465227 0.248393302 S(ph)SSAPLIHGLSDLSQVFQPYTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.333)S(0.333)S(0.333)APLIHGLSDLSQVFQPYTLR;S(0.332)S(0.332)S(0.332)APLIHGLS(0.003)DLSQVFQPYTLR 118.85 0.00015643 24427000 11794.3 17765.3 15204.7 16160.3 17389.2 25269 18439.2 17822.7 17188 16465.4 TRUE FALSE 12259.94807 20816.35208 15600.94697 19356.75911 14433.39 19400.65771 16993.88732 17583.81586 16569.40724 19691.47988 0.62260166 1.057124818 0.792268893 0.983001746 0.732976398 0.985231066 0.863007119 0.892965687 0.841450584 1 14.26528392 -4.999914169 0.015969136 2.017382985 0.019079883 0.119005674 0.120522944 12830.09192 15.53745736 1234.35903 762.5144808 1.00E-05 4.999914169 -1.998303102 S(ph)SSAPNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;S(0.333)S(0.333)S(0.333)APNVHINTIEPVNIDDLIR 224.91 4.19E-26 1058928000 73027 86655 92570 87231 99911 109272 91308 89523 79023 86534 TRUE FALSE 75910.16235 101537.3222 94982.45025 104485.0314 82928.16391 83895.23403 84151.04037 88323.09062 76178.97767 103488.6805 0.733511742 0.981144234 0.917805211 1.009627632 0.801325937 0.810670632 0.813142461 0.853456534 0.736109276 1 16.65911345 3.203945989 24.9997208 0.827642712 0.916087055 0.129952519 0.092877151 298.8611556 215845.6544 0.025188641 0.030107496 1599.359111 -3.203945989 0.088444342 S(ph)SSDALSASFNGEMLGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSDALSASFNGEMLGNR 18 0 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.908)S(0.091)S(0.002)DALSASFNGEMLGNR;S(0.333)S(0.333)S(0.333)DALSASFNGEMLGNR;S(0.52)S(0.24)S(0.24)DALSASFNGEMLGNR;S(0.333)S(0.333)S(0.333)DALSASFNGEMLGNR 295.84 2.68E-49 311643000 171964 188127 194424 172764 216368 257660 203437 187285 195910 193481 TRUE FALSE 178753.2715 220436.3488 199490.8492 206936.2036 179589.8446 197822.3699 187491.0764 184774.7509 188859.2374 231389.8975 0.772519775 0.952661941 0.862141568 0.89431823 0.776135201 0.854930885 0.810282032 0.798542862 0.816194827 1 17.81996635 3.270693013 24.99848186 0.828862136 0.875694867 0.011336831 0.071604736 470.5225059 366055.7245 0.018167638 0.024597344 1865.060882 -3.270693013 0.046832731 S(ph)SSDPPAVHPPLPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSDPPAVHPPLPPLR 16 0 O43150 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 S(0.333)S(0.333)S(0.333)DPPAVHPPLPPLR;S(0.366)S(0.366)S(0.268)DPPAVHPPLPPLR;S(0.354)S(0.354)S(0.292)DPPAVHPPLPPLR 130.77 3.10E-05 549038000 662150 790190 794480 846570 986700 1092640 952460 965980 905310 867380 TRUE FALSE 688292.1933 925898.9857 815184.8015 1014019.019 818981.0864 838890.9191 877803.6964 953032.6181 872728.0699 1037326.504 0.66352512 0.892582019 0.785851705 0.977531197 0.789511387 0.808704796 0.846217361 0.918739292 0.841324372 1 19.98443863 -2.50613332 0.02393923 1.984735378 1.15E-06 0.363698557 0.075501053 1582.837463 4.631541531 238.9650708 152.850057 0.003117932 2.50613332 -1.98473423 S(ph)SSEAKPTSLGLAGGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSEAKPTSLGLAGGHK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.648)S(0.034)S(0.312)EAKPT(0.002)S(0.003)LGLAGGHK 108.14 0.00040458 120800000 122850 117740 127340 117640 212220 171650 191020 156310 184110 127340 TRUE FALSE 127700.2129 137960.9291 130658.585 140908.8409 176146.9202 131786.8889 176047.3533 154214.9201 177483.9171 152289.8349 0.838534055 0.905910294 0.857959988 0.92526754 1.156655796 0.865368913 1.156001997 1.01264093 1.165435087 1 17.21646012 3.418492811 6.826200776 1.054244727 0.874432879 0.505046702 0.087267497 0.164234337 15.13900973 0.022437986 0.030553511 2621.15565 -3.418492811 -0.179811848 S(ph)SSEDAESLAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.591)S(0.075)S(0.334)EDAESLAPR;S(0.65)S(0.082)S(0.267)EDAESLAPR;S(0.76)S(0.12)S(0.12)EDAESLAPR;S(0.94)S(0.008)S(0.052)EDAESLAPR;S(0.985)S(0.007)S(0.007)EDAESLAPR 296.28 2.90E-36 4209960000 1556130 1664730 1808950 1683430 2132650 2332830 2046930 1874480 1815200 1698090 TRUE FALSE 1617567.214 1950634.428 1856092.723 2016407.429 1770142.915 1791065.587 1886486.278 1849355.662 1749871.307 2030798.224 0.796517938 0.960525967 0.913972004 0.992913725 0.871648839 0.881951523 0.928938314 0.910654559 0.861666751 1 20.95361547 -1.662471399 3.043664927 1.008743859 0.906872911 0.238322138 0.05188148 4770302.677 5876761.546 252411.8255 0.011381081 0.021753473 1.662471399 -0.101870948 S(ph)SSETILSSLAGSDIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.33)S(0.33)S(0.33)ET(0.009)ILSSLAGSDIVK 99.344 0.0016827 82657000 119970 94652 111110 96640 132340 136700 126630 100790 126330 98106 TRUE FALSE 124706.5082 110907.7447 114005.6179 115755.1036 109844.8941 104953.4967 116704.4097 99439.07491 121783.408 117327.9923 1.062887941 0.945279489 0.97168302 0.986594088 0.936220691 0.894530748 0.994685133 0.847530695 1.037974021 1 16.84018773 7.566966435 1.187608971 0.945313562 129.4976419 0.226875046 0.053795216 2095.881333 3.531445497 0.013918027 733576.7368 36894908.27 -7.566966435 128.5523283 S(ph)SSFREMENQPHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSFREMENQPHKK 14 2 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 S(0.41)S(0.314)S(0.276)FREMENQPHKK 83.968 0.004341 76074000 103120 71711 100230 52505 144470 111750 74451 93494 112480 86694 TRUE FALSE 107191.2572 84026.80642 102842.0761 62890.33229 119913.041 85797.75609 68615.33608 92240.86586 108431.8668 103680.0294 1.033865999 0.810443505 0.991917891 0.606580965 1.156568354 0.827524419 0.661798964 0.889668592 1.045831751 1 16.66177851 1.28803481 6.600280645 1.022705416 0.863513096 0.128593658 0.156096673 0.335640968 32.70341387 0.104155924 0.036657108 19.41041453 -1.28803481 -0.15919232 S(ph)SSFSDTLEESSPIAAIFDTENLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.335)S(0.335)S(0.253)FS(0.028)DT(0.049)LEESSPIAAIFDTENLEK;S(0.288)S(0.288)S(0.288)FS(0.102)DT(0.035)LEESSPIAAIFDTENLEK 234.51 1.41E-38 275191000 336853 223223 278441 218149 426109 385432 343944 300221 359778 233186 TRUE FALSE 350152.2165 261559.8138 285697.4012 261298.2211 353679.1444 295921.2593 316984.7705 296197.0286 346829.6601 278874.3321 1.255591413 0.937912829 1.024466465 0.936974798 1.268238427 1.061127631 1.136658108 1.062116497 1.243677242 1 18.08925563 3.259340013 24.99870389 1.124402798 1.030515477 0.130745729 0.112448036 467.9381567 562950.7313 0.029283026 0.039606872 1816.937601 -3.259340013 -0.093887321 S(ph)SSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 44 0 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.32)S(0.32)S(0.32)IS(0.039)GVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR;S(0.333)S(0.333)S(0.333)ISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 341.18 7.98E-134 488931000 17264.2 32214.2 40935.2 33514.1 39583.5 39423 31882.1 39006 33296.2 42505 TRUE FALSE 17945.80395 37746.73826 42002.00494 40143.08895 32855.11081 30267.60571 29383.09769 38483.18837 32097.87627 50833.04094 0.353034239 0.742563057 0.826273702 0.789704653 0.646333766 0.595431734 0.578031476 0.757050683 0.631437263 1 15.63347892 -1.898109701 2.513690659 1.182896966 0.669987847 0.382334425 0.129662765 12726820.58 7089808.546 13779605.54 0.032677688 0.012644169 1.898109701 -0.512909119 S(ph)SSKDSRPSQAAGDNQGDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSKDSRPSQAAGDNQGDEAK 21 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.444)S(0.444)S(0.111)KDS(0.001)RPSQAAGDNQGDEAK;S(0.333)S(0.333)S(0.333)KDS(0.001)RPSQAAGDNQGDEAK;S(0.32)S(0.32)S(0.32)KDS(0.039)RPS(0.002)QAAGDNQGDEAK 290.1 5.54E-55 536680000 954090 247381 395255 243596 609320 739740 660770 437812 481983 179944 TRUE FALSE 991758.2099 289866.7624 405555.67 291778.5617 505748.004 567946.5959 608977.1208 431943.8463 464636.526 215200.5816 4.608529413 1.346960869 1.884547277 1.355844671 2.350123779 2.639149912 2.829811687 2.007168583 2.159085829 1 17.71532245 4.748094411 24.99314119 2.035599484 4.608530783 0.666794572 0.56049998 812.0905199 2128877.175 0.135449957 1.755928311 55987.92997 -4.748094411 2.572931299 S(ph)SSKDSRPSQAAGDNQGDEAKEQTFSGGTSQDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSKDSRPSQAAGDNQGDEAKEQTFSGGTSQDTK 34 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.333)S(0.333)S(0.333)KDS(0.002)RPSQAAGDNQGDEAKEQTFSGGTSQDTK 207.61 9.81E-27 52176000 62169 14679 28645 10718 54785 38346 26647 27794 38511 13584 TRUE FALSE 64623.48012 17200.00406 29391.51223 12837.98841 45472.66527 29440.72264 24558.33851 27421.46689 37124.99663 16245.52472 3.977925074 1.058753371 1.809206704 0.790247692 2.799088737 1.812235871 1.511698695 1.687939748 2.285244538 1 13.98775472 4.748177768 24.78917995 1.675335955 3.97792646 0.596753465 0.576024503 784.3035848 2021575.075 0.129625667 1.686403392 55998.67715 -4.748177768 2.302590505 S(ph)SSKESLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.547)S(0.265)S(0.187)KES(0.001)LVR 113.22 0.0011113 379230000 242880 142570 171420 120930 271100 262980 222870 179520 194430 121070 TRUE FALSE 252469.0899 167055.2885 175887.346 144849.5931 225018.5188 201906.8805 205400.867 177113.828 187432.5023 144791.3485 1.743675244 1.153765679 1.214764196 1.000402266 1.55408815 1.394467851 1.418599034 1.223234882 1.294500702 1 17.14361588 0.526720429 1.121436457 1.000506552 1.330093303 0.205781438 0.199022636 2.848551871 4.975960488 0.186759104 0.057610574 3.362950147 -0.526720429 0.329586752 S(ph)SSLESLQTAVAEVTLNGDIPFHRPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSLESLQTAVAEVTLNGDIPFHRPRPR 28 2 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 S(0.318)S(0.318)S(0.318)LES(0.046)LQTAVAEVTLNGDIPFHRPRPR 116.97 0.00013836 32274000 12284 12515 12977 9953.1 15034 13688 12326 11307 13344 14684 TRUE FALSE 12768.98181 14664.3539 13315.19128 11921.79347 12478.52605 10509.16944 11359.85591 11155.44816 12863.75205 17561.04866 0.72711955 0.835050012 0.758223016 0.678877082 0.710579778 0.598436326 0.646877993 0.635238156 0.732516167 1 14.10009138 0.961439508 22.23327874 1.000000001 0.695391185 0.666332624 0.063509595 1071.857913 618015.2113 0.069180234 0.017295058 9.150387956 -0.961439508 -0.304608817 S(ph)SSLKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.482)S(0.482)S(0.037)LKER;S(0.333)S(0.333)S(0.333)LKER 112.84 0.0037932 2971253000 1793744 1236160 1735752 940522 1789820 1769963 2098093 1536452 1806390 863019 TRUE FALSE 1864562.398 1448460.864 1780987.123 1126554.444 1485587.036 1358915.917 1933638.988 1515858.374 1741378.377 1032111.05 1.806552114 1.403396335 1.725577033 1.091505071 1.439367437 1.316637311 1.873479592 1.468696973 1.687200595 1 19.97716677 -1.776335218 2.765084346 0.873644166 1.524880067 0.328641867 0.228887348 48024540.35 35190554.32 40921524 0.053892797 0.016736505 1.776335218 0.651235901 S(ph)SSLSDLTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.333)S(0.333)S(0.333)LS(0.001)DLTHR 93.839 0.0054828 340280000 852290 519970 722120 491170 975620 747180 773960 558280 769400 503250 TRUE FALSE 885939.0673 609270.8027 740939.0404 588321.96 809784.4609 573658.7686 713294.9928 550797.1698 741709.4443 601852.2022 1.472020978 1.012326283 1.231097997 0.977518995 1.345487244 0.953155553 1.185166375 0.915170149 1.232378052 1 19.19904972 4.746113087 24.49458126 1.092054019 1.472021221 0.402077834 0.138004276 642.2585103 2082940.564 0.029872089 0.312132119 55733.08547 -4.746113087 0.379967203 S(ph)SSMSYVDGFIGTWPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.24)S(0.24)S(0.24)MS(0.155)Y(0.123)VDGFIGTWPK 71.344 0.042904 132480000 166350 145940 201570 157350 244680 232690 217030 212570 246040 170340 TRUE FALSE 172917.6265 171004.0597 206823.0798 188473.3604 203089.381 178651.274 200018.6215 209720.8468 237185.0685 203714.8616 0.848821854 0.839428495 1.01525769 0.925182183 0.996929627 0.876967309 0.981855815 1.029482312 1.164299288 1 17.63619171 1.745926272 2.324805664 1.082827517 0.922814862 0.496534676 0.066355051 0.224940851 2.493588746 0.042488296 0.018564695 55.70911657 -1.745926272 -0.160012655 S(ph)SSPAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.333)S(0.333)S(0.333)PAELDLKDDLQQTQGK 154.79 4.04E-10 0 859760 341470 537960 390570 798070 731320 753460 499440 611880 236240 TRUE FALSE 893703.9887 400114.8162 551979.6795 467823.5803 662414.3465 561482.0133 694401.8364 492745.8237 589858.5583 282526.7049 3.163254918 1.416201758 1.953725683 1.655856144 2.344607908 1.987359083 2.457827258 1.744068136 2.087797536 1 18.10802771 -0.204010608 0.823560692 0.964888312 2.06875481 0.331483127 0.463437962 10.60182041 6.004567397 1.647851351 0.140435529 0.625157422 0.204010608 1.103866498 S(ph)SSPAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.327)S(0.327)S(0.327)PAGET(0.018)EGDREPQARPGEGTAPLPPPGQK;S(0.319)S(0.319)S(0.304)PAGET(0.058)EGDREPQARPGEGT(0.001)APLPPPGQK;S(0.293)S(0.293)S(0.293)PAGET(0.111)EGDREPQARPGEGT(0.011)APLPPPGQK;S(0.333)S(0.333)S(0.333)PAGET(0.001)EGDREPQARPGEGTAPLPPPGQK;S(0.312)S(0.312)S(0.312)PAGET(0.064)EGDREPQARPGEGTAPLPPPGQK;S(0.333)S(0.333)S(0.333)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.331)S(0.331)S(0.331)PAGET(0.007)EGDREPQARPGEGTAPLPPPGQK;S(0.285)S(0.285)S(0.285)PAGET(0.143)EGDREPQARPGEGT(0.002)APLPPPGQK 210.21 1.59E-26 2493950000 735891 575458 714113 509172 889897 1014957 842622 727172 899626 607645 TRUE FALSE 764944.5449 674288.4351 732723.3714 609884.7019 738632.6258 779248.6186 776575.0859 717425.4488 867248.636 726701.4037 1.05262566 0.927875509 1.008286715 0.839250755 1.016418328 1.072309224 1.068630227 0.987235535 1.193404377 1 19.47100317 3.007608393 24.98868818 1.056225001 0.954746696 0.319902084 0.073252828 218.6816635 718221.6221 0.020258068 0.024169544 1017.67333 -3.007608393 -0.101478305 S(ph)SSPAPADIAQTVQEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR;S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR;S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR 105.31 0.00050502 1821843000 217491 264219 256417 237198 277240 316484 240439 250320 241702 259303 TRUE FALSE 226077.7126 309596.5579 263099.4377 284115.0564 230114.8438 242985.3874 221592.7629 246964.8698 233003.1922 310108.4582 0.729027882 0.998349286 0.848411034 0.916179643 0.742046332 0.783549693 0.714565363 0.796382244 0.751360326 1 18.24241335 3.240066561 24.99166969 0.78227569 0.880190279 0.111784476 0.096891762 62.24827106 1033014.879 0.02493201 0.03202271 1738.06719 -3.240066561 0.097914589 S(ph)SSPASALTPEGEATSVTLVEELSLQEAMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPASALTPEGEATSVTLVEELSLQEAMR 30 0 H0YFS7;E7EW59;F5H433;Q9Y467 H0YFS7 SALL2 Sal-like protein 2 1 S(0.214)S(0.214)S(0.214)PAS(0.214)ALT(0.045)PEGEAT(0.048)S(0.048)VT(0.003)LVEELSLQEAMR;S(0.231)S(0.231)S(0.231)PAS(0.231)ALT(0.061)PEGEAT(0.005)S(0.005)VT(0.005)LVEELSLQEAMR 49.445 0.038894 13335000 8913.1 12944.5 10397.9 11879.8 14130.4 17550 11421.8 11489.2 12738.9 11863.7 TRUE FALSE 9264.99607 15167.61718 10668.87782 14229.58898 11728.51966 13474.27847 10526.52947 11335.20607 12280.42948 14188.16487 0.653008769 1.069033051 0.751956149 1.002919624 0.82664106 0.949684374 0.741923256 0.798919816 0.86554037 1 13.79240038 2.250706754 24.99727944 0.827672229 0.882285386 0 0.128813884 811.9755864 1671080.086 0.040825206 0.033920184 178.1175668 -2.250706754 0.054613157 S(ph)SSPATEQSWMENDFDELREEGFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.46)S(0.46)S(0.08)PATEQSWMENDFDELREEGFRR;S(0.476)S(0.476)S(0.049)PATEQSWMENDFDELREEGFRR;S(0.333)S(0.333)S(0.333)PATEQSWMENDFDELREEGFRR 274.88 2.61E-53 1769440000 54562 91414 78787 73186 85056 89274 73211 76780 77549 77760 TRUE FALSE 56716.14989 107113.6434 80840.25394 87661.97236 70598.2115 68541.46646 67472.53052 75750.88969 74758.02664 92995.58319 0.609880039 1.151814309 0.869291327 0.942646622 0.759156608 0.73704002 0.725545539 0.814564381 0.803887927 1 16.50487458 3.238111026 24.9999871 0.790106935 0.910143046 0.06962626 0.142854335 22.89219555 1272970.084 0.037574145 0.047609119 1730.258638 -3.238111026 0.120036111 S(ph)SSPEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPEDAR 8 0 Q86TL0;K7EKP6;K7EQN3;K7EPJ0;K7ERK1 Q86TL0 ATG4D "Cysteine protease ATG4D;Cysteine protease ATG4D, mitochondrial" 1 S(0.438)S(0.438)S(0.124)PEDAR 84.615 0.018175 30079000 48157 62853 65097 56308 66698 71289 66532 68506 60218 67047 TRUE FALSE 50058.27555 73647.51382 66793.4813 67445.55434 55360.69778 54733.21015 61317.04799 67587.78912 58050.76594 80183.57596 0.624295873 0.918486273 0.833007015 0.841139267 0.690424406 0.682598768 0.764708324 0.842913132 0.723973273 1 16.29101914 -1.398150853 3.904902602 1.000994164 0.777351112 0.389217198 0.086228313 0.000739482 0.000113974 0.08272628 0.01941367 0.039980585 1.398150853 -0.223643052 S(ph)SSPEDPGAEV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPEDPGAEV 11 0 Q9Y5U2-2;Q9Y5U2 Q9Y5U2-2 TSSC4 Protein TSSC4 1 S(0.376)S(0.376)S(0.247)PEDPGAEV 81.296 0.014956 0 145570 163790 175070 161360 179090 227960 190350 168960 174760 159050 TRUE FALSE 151317.216 191919.6584 179632.468 193276.5264 148648.3458 175019.7448 175429.8696 166695.3676 168470.4217 190212.8023 0.795515413 1.008973403 0.944376329 1.016106824 0.781484443 0.920125999 0.922282136 0.876362503 0.885694442 1 17.53725482 3.27596277 24.99999002 0.893286048 0.946304562 0.070398624 0.075718926 387.7839211 259196.1837 0.019717781 0.026697397 1887.829508 -3.27596277 0.053018514 S(ph)SSPELVTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.572)S(0.143)S(0.285)PELVTHLK;S(0.39)S(0.39)S(0.221)PELVTHLK;S(0.609)S(0.223)S(0.168)PELVTHLK;S(0.333)S(0.333)S(0.333)PELVTHLK 231.66 5.82E-13 15007440000 11153320 9544410 12080000 10075910 14278090 15144500 14518240 12979220 13313920 8760920 TRUE FALSE 11593661.69 11183588.17 12394814.72 12068894.92 11851105.36 11627419.39 13380262.41 12805254.79 12834754.62 10477454.54 1.106534192 1.067395533 1.182998665 1.151891892 1.131105396 1.109756129 1.277052777 1.222172307 1.224987861 1 23.32078493 2.269383811 24.99730255 1.204756934 1.12647438 0.08651212 0.074762696 303.0552957 245773.7074 0.024444696 0.020449847 185.9447029 -2.269383811 -0.078282554 S(ph)SSPELVTHLKWDDPYYDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.36)S(0.36)S(0.279)PELVTHLKWDDPYYDIAR;S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR;S(0.361)S(0.361)S(0.277)PELVTHLKWDDPYYDIAR;S(0.333)S(0.333)S(0.333)PELVTHLKWDDPYYDIAR 237.97 4.28E-30 674077000 335094 424383 489327 273998 832099 639334 357143 416311 518346 743354 TRUE FALSE 348323.7699 497267.479 502079.2636 328193.9866 690659.1092 490858.3677 329149.1984 410731.032 499690.8287 888999.9839 0.391815271 0.559356004 0.564768586 0.369172095 0.7768944 0.552146655 0.370246574 0.462014668 0.562081932 1 19.76182387 0.860953545 6.458219603 0.9999992 0.506771657 0.61841451 0.115736547 2.511880858 116.5884365 0.110673076 0.027789626 7.260282926 -0.860953545 -0.493227542 S(ph)SSPGAGGGHSTSTSTSPATTLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPGAGGGHSTSTSTSPATTLQR 24 0 A0A1W2PR28;Q5JU85 A0A1W2PR28 IQSEC2 IQ motif and SEC7 domain-containing protein 2 1 S(0.333)S(0.333)S(0.333)PGAGGGHS(0.001)TSTSTSPATTLQR 59.667 0.0062797 0 28941 17875 18466 13826 20043 29622 16374 17250 13337 14414 TRUE FALSE 30083.61303 20944.8922 18947.23913 16560.74153 16636.09802 22742.73943 15090.56309 17018.79197 12857.00398 17238.14733 1.745176698 1.215031511 1.09914591 0.960703098 0.965074593 1.319326201 0.875416761 0.987275004 0.745846043 1 14.07331711 S(ph)SSPGKPQAVSSLNSSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSPGKPQAVSSLNSSHSR 19 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR;S(0.333)S(0.333)S(0.333)PGKPQAVSSLNSSHSR 251.51 1.25E-26 5715430000 980467 1918278 2265276 1937172 2770000 2909590 2382878 2550084 2342753 1697074 TRUE FALSE 1019176.594 2247727.324 2324310.954 2320338.84 2299156.389 2233881.818 2196101.796 2515904.295 2258437.777 2029583.158 0.50216055 1.107482251 1.145215925 1.143258817 1.132821969 1.100660404 1.082045733 1.239616266 1.11275942 1 20.95275202 4.738677779 5.365879276 1.13200663 0.4772081 0.911247345 0.05758341 0.037851489 3.997360337 0.013431143 0.091376884 54787.0326 -4.738677779 -0.654798531 S(ph)SSPHDKNLPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPHDKNLPQK 12 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.383)S(0.308)S(0.308)PHDKNLPQK;S(0.333)S(0.333)S(0.333)PHDKNLPQK 109.07 0.00098878 167480000 383468 360960 471056 306254 664590 603540 408661 463946 486690 361871 TRUE FALSE 398607.6127 422952.0721 483332.1063 366830.1271 551623.2292 463376.9817 376629.083 457727.5627 469174.122 432772.694 0.921055368 0.977307667 1.116826715 0.847627709 1.274625772 1.070716772 0.870269978 1.057662762 1.084112118 1 18.72324995 4.47065675 23.94991358 1.037568512 0.935118392 0.099659289 0.114813924 187.3942119 694270.0028 0.027129021 0.074777568 29556.75489 -4.47065675 -0.10245012 S(ph)SSPPPRK ddPTM_MDA-MB-175_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(0.333)S(0.333)S(0.333)PPPRK 77.677 0.019964 1823160000 1755730 1372800 1701700 1260090 2059960 2001740 1980950 1756930 1823470 1358670 TRUE FALSE 1825047.576 1608567.721 1746047.7 1509332.041 1709808.735 1536866.222 1825677.963 1733381.227 1757843.671 1624875.373 1.123192342 0.989963752 1.074573305 0.928890957 1.052270693 0.945836368 1.123580302 1.066777955 1.081832921 1 20.63189764 2.223701662 24.99957778 1.074664877 1.017721846 0.129206768 0.061204463 414.8269075 697923.9945 0.021286595 0.015787311 167.3792672 -2.223701662 -0.056943031 S(ph)SSPTLTPSQEGSPVFAGFEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.322)S(0.322)S(0.322)PT(0.033)LTPSQEGSPVFAGFEGR 126.26 2.09E-05 84497000 18043 19485 24195 22503 22838 29089 24348 19646 23041 21501 TRUE FALSE 18755.35157 22831.39718 24825.54158 26954.02624 18956.00492 22333.5206 22439.54014 19382.6775 22211.75891 25713.70929 0.729391134 0.887907572 0.96545937 1.048235629 0.737194494 0.868545271 0.872668345 0.753787689 0.863809988 1 14.65025012 3.217796847 24.99994359 0.834092519 0.910453567 0.062080474 0.101105451 532.6977527 641375.9477 0.029210756 0.034949941 1651.189229 -3.217796847 0.076361048 S(ph)SSPTSSLTQPIEMPTLSSS(ph)PTEERPTVGPGQQDNPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.162)S(0.162)S(0.162)PT(0.162)S(0.162)S(0.162)LT(0.026)QPIEMPTLS(0.004)S(0.021)S(0.821)PT(0.154)EERPTVGPGQQDNPLLK 179.54 2.81E-23 73546000 140120 106080 133080 110920 163180 167220 142360 137050 152750 111090 TRUE FALSE 145652.0458 124298.4148 136548.1741 132859.6449 135442.7219 128385.6892 131201.4512 135213.0689 147252.5573 132855.9586 1.096315494 0.935587806 1.027791118 1.000027747 1.019470435 0.966352512 0.987546608 1.017741849 1.108362462 1 17.01950341 1.43873664 9.550604184 1.057275246 1.002324373 0.147591524 0.046519051 0.383794322 83.21322863 0.025104631 0.010475001 27.46228312 -1.43873664 -0.054950873 S(ph)SSPVKR ddPTM_MDA-MB-175_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 60.91 0.057981 18160000 33464 38661 37389 36075 190420 52031 176230 45256 35884 46746 TRUE FALSE 34785.18456 45300.72601 38363.38806 43210.52733 158052.4764 39947.58879 162416.6321 44649.41734 34592.54185 55904.98369 0.622219743 0.810316416 0.686224832 0.772928002 2.827162553 0.714562212 2.905226357 0.798666137 0.618773847 1 15.77068928 3.431757527 24.99960435 1.510930687 0.718802881 0.187742782 0.767711445 200.0941854 110269.7329 0.204933484 0.277481373 2702.449127 -3.431757527 -0.792127806 S(ph)SSQIPEGFGLTSGGSNYSLAR ddPTM_MDA-MB-175_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 74.953 0.013138 50162000 26810 43586 38616 35061 40656 57644 40870 41007 42152 38858 TRUE FALSE 27868.4795 51071.55645 39622.36468 41995.96115 33745.30764 44257.0546 37666.50261 40457.36824 40634.95775 46471.48112 0.599689935 1.098987061 0.852616782 0.903693193 0.726150896 0.952348699 0.810529419 0.870584868 0.874406341 1 15.50405801 0.570547143 1.983926447 0.9999815 0.859359497 0.109339178 0.124795611 6.505434819 27.37949984 0.107416755 0.029616565 3.720036002 -0.570547143 -0.140622003 S(ph)SSQPSSCCSDPSKPGGNVEGATQSLAEQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.332)S(0.332)S(0.332)QPS(0.002)S(0.002)CCS(0.002)DPS(0.001)KPGGNVEGATQSLAEQMR 75.954 0.0018126 170160000 75354 64951 75556 64602 95438 106540 91381 83669 86556 57504 TRUE FALSE 78329.03411 76105.829 77525.05143 77380.08278 79215.48285 81797.69963 84218.31844 82547.55391 83440.86647 68770.80782 1.13898668 1.106658936 1.127295925 1.125187928 1.151876579 1.189424732 1.224623079 1.200328403 1.213318109 1 16.06950867 3.001451811 2.839657834 1.184272105 1.123351212 0.05003158 0.061062238 0.449703863 7.368102388 0.017871103 0.020724574 1003.348512 -3.001451811 -0.060920893 S(ph)SSQRSPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_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(0.253)S(0.253)S(0.253)QRS(0.253)PS(0.276)PGPNHT(0.276)S(0.276)NS(0.077)S(0.077)NAS(0.006)NATVVPQNSSAR 68.269 0.0058361 60650000 3097 10914 9425.1 9558.5 6818.4 15460 6697.8 11230 8044.6 10475 TRUE FALSE 3219.271951 12788.3946 9670.725849 11449.14277 5659.410803 11869.6493 6172.808935 11079.48022 7755.076417 12527.37569 0.256978958 1.020835881 0.771967416 0.913929865 0.451763477 0.947496873 0.492745575 0.884421485 0.619050359 1 13.6127966 -1.814458142 2.268224508 1.103975516 0.725937081 0.116965308 0.236543314 11526496.71 6588012.906 6552633.763 0.054273579 0.01532999 1.814458142 -0.378038434 S(ph)SSQRSPSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_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(0.179)S(0.179)S(0.179)QRS(0.052)PS(0.067)PGPNHT(0.085)S(0.085)NS(0.085)S(0.085)NAS(0.001)NATVVPQNSSAR 86.785 0.00022983 89777000 1809.6 33900 28320 31852 28984 53365 16570 39138 24558 49579 TRUE FALSE 1881.044405 39722.06129 29058.04247 38152.23053 24057.31003 40971.7875 15271.2001 38613.41913 23674.16238 59293.0558 0.031724531 0.669927713 0.490074969 0.643451919 0.405735709 0.691004823 0.257554614 0.65123004 0.399273778 1 15.85557553 -5 0.351153668 6.92075614 0.473436834 0.383449866 0.200226264 437.9453604 3.576724368 1953.441428 0.137261343 1.00E-05 5 -6.447319306 S(ph)SSSGSDDYAYTQALLLHQR ddPTM_MDA-MB-175_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(0.327)S(0.327)S(0.327)S(0.007)GS(0.011)DDYAYTQALLLHQR 153.1 3.66E-08 134030000 50211 73740 77422 62057 76425 86249 59725 67493 62033 65358 TRUE FALSE 52193.36905 86404.27138 79439.68092 74331.68938 63434.3058 66218.97687 55043.59844 66588.36673 59800.44445 78163.64875 0.667744788 1.105427814 1.016325136 0.950975173 0.811557633 0.847183799 0.704209685 0.851909651 0.765067207 1 16.25421019 3.240589018 23.60158086 0.816957094 0.953083739 0.131664557 0.126374321 40.08476054 466393.597 0.033705483 0.043418139 1740.159343 -3.240589018 0.136126645 S(ph)SSSPELQTLQDILGDPGDKADVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.32)S(0.32)S(0.32)S(0.03)PELQT(0.011)LQDILGDPGDKADVGR;S(0.25)S(0.25)S(0.25)S(0.25)PELQT(0.001)LQDILGDPGDKADVGR;S(0.326)S(0.326)S(0.326)S(0.023)PELQTLQDILGDPGDKADVGR;S(0.308)S(0.308)S(0.308)S(0.062)PELQT(0.014)LQDILGDPGDKADVGR 87.739 0.0095011 149204000 82469 67287 79326 61583 100118 105093 89921 78637 86154 63306 TRUE FALSE 85724.9398 78843.01883 81393.30073 73763.93359 83099.97812 80686.74345 82872.75706 77582.99964 83053.33437 75709.59863 1.13228628 1.041387357 1.075072411 0.974300946 1.097614829 1.065739945 1.09461361 1.024744564 1.096998741 1 16.2081886 0.529835394 0.005736272 1.79E-07 2.089958944 0.127591963 0.043810047 17321.19621 43.67896901 8063.572189 7847.745302 3.38715752 -0.529835394 2.089958765 S(ph)SSSQTLTQFDSNIAPADPDTAIVHPVPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSSQTLTQFDSNIAPADPDTAIVHPVPIR 30 0 Q96D71;Q96D71-3;H0YE73 Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.474)S(0.474)S(0.051)S(0.002)QTLTQFDSNIAPADPDTAIVHPVPIR;S(0.305)S(0.305)S(0.305)S(0.076)QT(0.007)LTQFDSNIAPADPDTAIVHPVPIR 211.6 2.69E-26 324300000 22395.2 18225.7 24699.9 18672.9 21288 23256.5 19410.6 21677.2 16142.2 16241.4 TRUE FALSE 23279.37979 21355.8222 25343.59969 22366.34389 17669.47336 17855.53033 17889.14645 21386.65259 15561.24538 19423.59137 1.198510582 1.099478556 1.304784435 1.151504038 0.909691366 0.919270283 0.921000968 1.101065822 0.80115181 1 14.24552236 3.321101822 5.344475589 0.955285297 1.19561207 0.665503263 0.085647094 0.13068244 6.287904604 0.024107287 0.032658122 2094.603486 -3.321101822 0.240326773 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.355)S(0.355)S(0.289)T(0.002)GNLLDKDDLAIPPPDYGAASR;S(0.352)S(0.352)S(0.284)T(0.011)GNLLDKDDLAIPPPDYGAASR;S(0.337)S(0.337)S(0.282)T(0.045)GNLLDKDDLAIPPPDYGAASR;S(0.345)S(0.345)S(0.303)T(0.007)GNLLDKDDLAIPPPDYGAASR 165.53 9.20E-12 1612060000 905970 595755 757370 595947 861600 935620 821970 686110 725420 450114 TRUE FALSE 941738.3952 698071.2869 777107.6844 713823.5379 715145.5398 718336.4345 757541.8436 676913.8177 699312.2759 538305.2203 1.749450608 1.29679457 1.443619075 1.326057246 1.328513105 1.334440773 1.407271962 1.257490717 1.299099933 1 19.03806489 7.999975594 0.035456263 8.28E-08 3.435399141 0.631569809 0.106704033 647.81511 1.754343253 49.85713937 142.0641815 99994380.53 -7.999975594 3.435399058 S(ph)SSVPHPFQVTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.5)S(0.5)SVPHPFQVTLLR;S(0.5)S(0.5)SVPHPFQVTLLR 200.58 1.23E-08 990117000 487230 641990 610570 592950 787820 822920 628880 717540 678910 642820 TRUE FALSE 506466.2166 752246.7885 626481.9558 710233.7402 653906.6378 631809.3015 579586.7423 707922.55 654476.1617 768768.2715 0.658802185 0.978509151 0.814916509 0.92385933 0.850590044 0.821846225 0.753916055 0.920852975 0.85133087 1 19.55218927 0.514339728 1.03425579 0.999710384 0.842735267 0.237711055 0.085877521 2.4222317 3.684137794 0.076425683 0.023993062 3.268434061 -0.514339728 -0.156975117 S(ph)SSVTSIDKESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSVTSIDKESR 12 1 H0Y332;Q5T5C0-2;Q5T5C0;Q5T5C0-3;Q5JRH0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 S(0.263)S(0.263)S(0.213)VT(0.213)S(0.047)IDKESR 68.044 0.032539 137230000 72731 70344 72509 54940 90505 89351 75416 65006 78105 54612 TRUE FALSE 75602.47604 82425.0348 74398.64411 65806.96802 75120.99243 68600.58438 69504.69686 64134.7009 75294.01631 65312.17579 1.157555618 1.262016367 1.13912365 1.007575804 1.150183584 1.05034909 1.064192029 0.981971587 1.152832767 1 15.99506435 3.983719877 5.21198727 1.057213457 1.209155434 0.51979942 0.059006171 0.122789924 10.14799097 0.014539568 0.029229987 9632.075467 -3.983719877 0.151941977 S(ph)STDSLPGPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.565)S(0.424)T(0.011)DSLPGPISR 152.32 7.31E-05 323740000 216140 253090 262610 271690 296830 350900 306910 252680 260490 209380 TRUE FALSE 224673.3741 296556.2387 269453.8323 325429.4711 246374.9426 269408.7929 282853.5922 249293.2379 251115.0158 250404.0022 0.897243543 1.184311098 1.076076381 1.299617691 0.983909764 1.075896514 1.129588943 0.995564111 1.002839466 1 17.9338981 1.685280183 6.586999533 0.999326069 1.098310209 0.146572026 0.101753326 0.23757416 21.55061307 0.049443992 0.025211963 48.44848301 -1.685280183 0.09898414 S(ph)STPGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTPGLK 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 1 S(0.54)S(0.287)T(0.173)PGLK 100.98 0.0098527 589130000 4108000 2613800 3295200 2705000 4327400 4570000 4070400 3627900 3529500 2198800 TRUE FALSE 4270187.012 3062699.817 3381075.619 3240040.926 3591830.094 3508686.759 3751351.412 3579273.935 3402473.984 2629612.761 1.623884351 1.164696134 1.285769399 1.232136143 1.365915981 1.33429789 1.426579406 1.361141073 1.293906857 1 21.32641893 0.812367364 4.169346315 1.000010715 1.341670431 0.446138038 0.115905995 1.635364703 35.44684059 0.104881067 0.026733767 6.491833365 -0.812367364 0.341659716 S(ph)STPLHS(ph)PSPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.982)S(0.008)T(0.01)PLHS(0.681)PS(0.318)PIR;S(0.994)S(0.003)T(0.004)PLHS(0.681)PS(0.318)PIR;S(0.991)S(0.299)T(0.222)PLHS(0.464)PS(0.024)PIR 97.797 0.0024927 408130000 63738 404040 343128 473170 250117 461220 268580 348112 269668 434350 TRUE FALSE 66254.42546 473430.727 352070.1976 566761.6137 207602.2017 354108.6449 247527.9978 343446.128 259962.7014 519452.5664 0.127546632 0.911403192 0.677771601 1.091074817 0.399655744 0.681695823 0.476517037 0.661169374 0.500455129 1 18.98663249 -1.209045156 4.362783627 1.000130743 0.630865784 0.169587278 0.253734994 0.000299194 5.42E-05 0.227800198 0.053674106 0.061795214 1.209045156 -0.36926496 S(ph)STPLHSPSPIR ddPTM_MDA-MB-175_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)PLHS(0.001)PSPIR 183.89 9.67E-06 244380000 74977 133140 125260 124780 122910 150670 116050 140960 118300 133470 TRUE FALSE 77937.14985 156005.7593 128524.3785 149461.1116 102017.8021 115679.1759 106953.6978 139070.6618 114042.4061 159620.8911 0.488264095 0.977351763 0.805185196 0.936350565 0.639125627 0.724712005 0.670048244 0.871256017 0.714457897 1 17.28428996 -1.47125118 2.665092284 1.008929243 0.770727546 0.208659223 0.139263259 11491624.94 11879884.08 759412.6997 0.033016359 0.033786937 1.47125118 -0.238201697 S(ph)STPPGESYFGVSSLQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK;S(0.333)S(0.333)T(0.333)PPGESYFGVSSLQLK;S(0.417)S(0.417)T(0.165)PPGESYFGVSSLQLK 239.55 6.71E-24 2496308000 1344279 979921 1309441 1002356 1562950 1525536 1498569 1341224 1385575 897336 TRUE FALSE 1397352.173 1148214.809 1343566.108 1200619.025 1297280.317 1171253.384 1381107.246 1323247.086 1335708.426 1073151.809 1.302101121 1.069946302 1.251981404 1.118778364 1.208850702 1.091414443 1.286963536 1.233047436 1.244659344 1 20.03342274 2.231256174 24.99359032 1.215722205 1.171762444 0 0.098578581 593.3896326 2030385.306 0.033206323 0.025027551 170.3162842 -2.231256174 -0.043959761 S(ph)STPSHGQTTATEPTPAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 S(0.333)S(0.333)T(0.333)PSHGQTTATEPTPAQK;S(0.371)S(0.371)T(0.256)PS(0.001)HGQTTATEPTPAQK;S(0.333)S(0.333)T(0.333)PSHGQTTATEPTPAQK 213.48 2.13E-17 552860000 381379 416476 524536 411709 617190 653935 548236 538293 530512 387381 TRUE FALSE 396436.1374 488002.5133 538205.8391 493143.8114 512280.2643 502068.5067 505263.8298 531078.0628 511418.9767 463280.8901 0.855714418 1.053362061 1.161726828 1.064459644 1.105766016 1.083723757 1.090620918 1.146341397 1.103906912 1 18.82152765 4.708844998 3.438209162 1.101203997 0.832403088 0.736789605 0.0423971 0.118580731 2.426526488 0.00952265 0.079578206 51149.92464 -4.708844998 -0.26880091 S(ph)STSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.24)S(0.24)T(0.24)S(0.24)PS(0.013)IINEDVIINGHS(0.026)HEDDNPFAEYMWMENEEEFNR;S(0.221)S(0.221)T(0.221)S(0.221)PS(0.04)IINEDVIINGHS(0.077)HEDDNPFAEYMWMENEEEFNR;S(0.291)S(0.291)T(0.232)S(0.185)PS(0.001)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.221)S(0.221)T(0.221)S(0.221)PS(0.106)IINEDVIINGHS(0.011)HEDDNPFAEYMWMENEEEFNR 295.11 2.67E-92 389742000 63416.4 82605.2 94523 91356.1 101497 105791 96856.3 94771.7 91226.6 97445.7 TRUE FALSE 65920.12844 96792.00052 96986.34703 109426.0639 84244.57619 81222.64353 89264.45012 93501.44038 87943.37249 116538.3192 0.565651958 0.830559435 0.832227097 0.938970672 0.722891636 0.696960829 0.765966514 0.802323571 0.754630521 1 16.83044488 -2.193635824 2.196619667 1.598673731 0.775192079 0.355326718 0.093353362 9323160.189 1787958.955 27754925.65 0.022358726 0.006402715 2.193635824 -0.823481651 S(ph)SVTVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVTVEER 8 0 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.984)S(0.016)VTVEER 110.38 0.0036049 178280000 191880 201220 203360 174840 234420 270070 239810 177170 195970 205500 TRUE FALSE 199455.5706 235777.9697 208659.7287 209422.8302 194573.3721 207350.3355 221013.0656 174795.3259 188917.078 245763.7905 0.811574277 0.959368218 0.849025515 0.852130535 0.791708867 0.843697662 0.899290596 0.711233032 0.768693702 1 17.90691285 3.71744065 2.363393339 0.819508316 0.885934007 0.013915126 0.08168135 0.707437092 7.733480126 0.022444024 0.043155421 5217.238015 -3.71744065 0.066425691 S(ph)TAALEEDAQILK ddPTM_MDA-MB-175_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(0.853)T(0.147)AALEEDAQILK;S(0.994)T(0.006)AALEEDAQILK;S(0.988)T(0.012)AALEEDAQILK;S(0.989)T(0.011)AALEEDAQILK;S(0.993)T(0.007)AALEEDAQILK;S(0.992)T(0.008)AALEEDAQILK 261.45 4.84E-24 1870460000 1952840 1454180 1890120 1526100 2780330 2556220 2237710 1968160 2123180 1600250 TRUE FALSE 2029939.631 1703924.103 1939378.08 1827958.025 2307730.5 1962576.645 2062312.443 1941780.034 2046767.167 1913788.349 1.060691812 0.890340932 1.013371244 0.955151611 1.205844158 1.025493047 1.077607377 1.014626323 1.0694846 1 20.86799986 S(ph)TCGDSEVEEESPGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STCGDSEVEEESPGKR 16 1 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 S(0.969)T(0.031)CGDSEVEEESPGKR 131.98 2.55E-05 364530000 77435 61115 104730 77810 115260 108700 125320 108250 113210 57545 TRUE FALSE 80492.19359 71611.02584 107459.3498 93200.58576 95668.14637 83456.07236 115497.0909 106799.0858 109135.5942 68819.84098 1.169607375 1.040557851 1.561458851 1.354269124 1.39012449 1.212674589 1.678252802 1.551864757 1.585815844 1 16.07053694 4.243883555 24.98659834 1.445249695 1.10508251 0.286597942 0.192588258 138.39434 649621.5369 0.045697689 0.117713593 17534.10308 -4.243883555 -0.340167185 S(ph)TDKEAQGQQFHHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STDKEAQGQQFHHHR 15 1 A6ND36 A6ND36 FAM83G Protein FAM83G 1 S(0.673)T(0.327)DKEAQGQQFHHHR 100.45 0.0012996 40321000 6978.8 8255.4 13005 7146.3 16117 11486 12785 10516 11321 7410.3 TRUE FALSE 7254.328413 9673.200732 13343.92098 8559.81681 13377.4381 8818.550572 11782.87829 10375.05022 10913.55942 8862.206406 0.81856911 1.091511559 1.505710923 0.965878746 1.509492951 0.995073932 1.329564868 1.170707355 1.231472042 1 13.11345021 4.637360758 3.858128922 1.220727938 0.813836309 0.287801925 0.186304125 0.245892115 5.87897437 0.039697324 0.2217444 43387.11352 -4.637360758 -0.40689163 S(ph)TELLLGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STELLLGVK 9 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 S(0.96)T(0.04)ELLLGVK 117.14 0.0012594 26382000 87260 54011 59849 61540 72531 84282 104100 66399 71831 41320 TRUE FALSE 90705.09218 63286.9691 61408.71411 73712.42832 60202.20653 64708.78281 95940.36999 65509.03001 69245.81634 49415.86288 1.835546055 1.280701488 1.242692337 1.491675426 1.218276946 1.309473902 1.941489319 1.325668038 1.401287204 1 15.59268661 0.650517146 2.095175035 1.000354582 1.448059297 0.250918996 0.234933465 2.776494342 14.79894067 0.219032395 0.059960446 4.472158077 -0.650517146 0.447704715 S(ph)TELVLSPDMPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STELVLSPDMPR 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 S(0.993)T(0.007)ELVLSPDMPR;S(0.961)T(0.039)ELVLSPDMPR;S(0.995)T(0.005)ELVLSPDMPR;S(0.989)T(0.011)ELVLSPDMPR 349.81 1.80E-71 844000000 498581 532943 533358 526938 688990 726340 596780 538760 565834 503061 TRUE FALSE 518265.3629 624471.8145 547257.7476 631164.7636 571875.7259 557658.5428 550002.8242 531538.8034 545469.7449 601626.1713 0.861440854 1.037973154 0.909630887 1.049097918 0.950549948 0.92691869 0.914193648 0.883503459 0.906658937 1 19.1985078 2.748520486 3.38976931 0.914186296 0.968885048 0.06574036 0.05902185 0.440383492 10.73555553 0.018113384 0.018236389 560.4288526 -2.748520486 0.054698752 S(ph)TENVNKLPELSSFGKPSSSVQGTGLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STENVNKLPELSSFGKPSSSVQGTGLIR 28 2 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 S(0.801)T(0.199)ENVNKLPELSSFGKPSSSVQGTGLIR;S(0.98)T(0.02)ENVNKLPELSSFGKPSSSVQGTGLIR 251.08 6.88E-47 3504600000 2273160 1374260 1942040 1256770 2882450 2243020 2216630 1883550 2465600 1125600 TRUE FALSE 2362906.112 1610278.465 1992651.158 1505355.355 2392492.179 1722112.598 2042884.749 1858304.093 2376863.538 1346139.769 1.755320039 1.196219369 1.480270625 1.118275672 1.77729849 1.279297022 1.517587397 1.380468905 1.765688521 1 20.36039678 -1.081458754 5.838018046 0.999998024 1.455283129 0.280265695 0.226236619 5.20E-06 8.18E-07 0.195698409 0.046126357 0.082897464 1.081458754 0.455285106 S(ph)TFSLPEEEEEPEPLVFAEQPSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STFSLPEEEEEPEPLVFAEQPSVK 24 0 H3BR17;Q6Q0C0;Q6Q0C0-2 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 S(0.333)T(0.333)FS(0.333)LPEEEEEPEPLVFAEQPSVK 62.848 0.032557 26310000 18076 17423 18822 11315 23425 28231 23544 21648 23226 12484 TRUE FALSE 18789.65444 20415.26472 19312.51678 13553.07323 19443.22687 21674.77809 21698.55976 21357.84397 22390.1008 14930.00078 1.258516641 1.367398771 1.29353756 0.907774449 1.302292421 1.451760011 1.453352889 1.430532006 1.499671777 1 13.86592662 2.998950216 24.99708836 1.40081811 1.209542862 0.145359168 0.173810617 61.35942854 1461132.332 0.04930505 0.058217387 997.5857013 -2.998950216 -0.191275248 S(ph)TGDIAGTVVPETNKEPR ddPTM_MDA-MB-175_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(0.992)T(0.008)GDIAGTVVPETNKEPR;S(0.916)T(0.084)GDIAGTVVPETNKEPR;S(0.968)T(0.032)GDIAGTVVPETNKEPR 208.98 3.47E-16 962410000 582870 444530 528240 481330 807870 719630 694080 581110 540350 378500 TRUE FALSE 605882.1577 520874.5695 542006.3684 576535.6374 670548.546 552506.8386 639676.196 573321.171 520902.9091 452659.8282 1.338493323 1.150697582 1.1973812 1.273662034 1.481352009 1.220578466 1.413149911 1.266560749 1.150760188 1 18.78806775 -0.644346685 8.054837213 0.999998934 1.280214012 0.394746225 0.102812809 0 0 0.098408842 0.023195186 0.226805361 0.644346685 0.280215077 S(ph)TGSIDQLSHFHNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STGSIDQLSHFHNKR 15 1 A0A2R8Y5P9;Q8TF72;Q8TF72-2 A0A2R8Y5P9;Q8TF72-2 SHROOM3 Protein Shroom3 1 S(0.365)T(0.365)GS(0.27)IDQLSHFHNKR 101.75 0.00077554 176370000 109680 145070 177400 169410 248980 214420 146870 182200 169240 187400 TRUE FALSE 114010.2511 169984.644 182023.1897 202918.7924 206658.4685 164624.2046 135357.9456 179757.907 163149.0855 224117.442 0.508707623 0.75846236 0.812177705 0.905412763 0.922098997 0.734544367 0.60395989 0.802070135 0.727962465 1 17.77389541 4.736560087 3.284393111 0.799568848 0.469194459 0.416126278 0.106869829 0.340129487 5.964138907 0.026693329 0.284697412 54520.53224 -4.736560087 -0.330374389 S(ph)TKPSLSPSKPQSSLVIPTSLFCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STKPSLSPSKPQSSLVIPTSLFCK 24 2 J3KPQ8;Q02108-2;Q02108 J3KPQ8 GUCY1A3 Guanylate cyclase soluble subunit alpha-3 1 S(0.299)T(0.299)KPS(0.208)LS(0.164)PS(0.028)KPQS(0.002)S(0.002)LVIPTSLFCK 99.871 0.0023996 544600000 1016100 461920 778760 489990 1155600 925980 893420 768220 878670 371120 TRUE FALSE 1056216.413 541251.1668 799055.1254 586908.5595 959171.5248 710935.1784 823391.4059 757923.2675 847046.8383 443833.8585 2.379756281 1.219490484 1.800347382 1.322360943 2.161104896 1.60180474 1.855179343 1.707673385 1.908477288 1 18.7596602 -0.625776795 7.672593133 0.999999893 1.750712365 0.328070967 0.330468228 0 0 0.284049595 0.066951132 0.236713597 0.625776795 0.750712473 S(ph)TMVGTPYWMAPEVVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.935)T(0.065)MVGTPYWMAPEVVTR;S(0.905)T(0.095)MVGTPYWMAPEVVTR;S(0.898)T(0.102)MVGTPYWMAPEVVTR 316.8 2.67E-58 109771000 51579 72218 76369 63340 92280 83467 62009 72084 71260 78403 TRUE FALSE 53615.37875 84620.87972 78359.23888 75868.46295 76594.27856 64083.0542 57148.57255 71117.83189 68695.36652 93764.56673 0.571808527 0.902482491 0.835702031 0.809137882 0.816878713 0.683446385 0.609490072 0.758472356 0.73263674 1 16.51675522 -0.984971525 4.494403134 1.000006441 0.750506364 0.377815774 0.097414743 12453893.11 2770978.714 837.4010332 0.022953232 0.103521004 0.984971525 -0.249500077 S(ph)TNTAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STNTAVSR 8 0 Q9NWB6;Q9NWB6-2 Q9NWB6 ARGLU1 Arginine and glutamate-rich protein 1 1 S(0.979)T(0.021)NTAVSR 139.98 0.00068903 616090000 619570 770670 792660 575970 1209700 1100100 654810 850010 899740 1465200 TRUE FALSE 644031.102 903026.5775 813317.3708 689895.1469 1004075.626 844618.4472 603484.2812 838617.0063 867358.5332 1752277.887 0.367539365 0.515344389 0.464148624 0.393713321 0.57301164 0.482011702 0.344399873 0.478586766 0.494989145 1 20.74080015 0.510826035 2.111431193 0.999980054 0.453889503 0.862873754 0.065137902 1.585661858 6.447906272 0.060443683 0.01649632 3.242097226 -0.510826035 -0.546090551 S(ph)TPDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STPDLLR 7 0 Q9P2M7;Q9P2M7-2;H0Y4A8 Q9P2M7 CGN Cingulin 1 S(0.995)T(0.005)PDLLR;S(0.994)T(0.006)PDLLR;S(0.992)T(0.008)PDLLR 185.47 0.00064306 481820000 656840 640060 775470 664380 866020 832340 671200 605870 634820 593740 TRUE FALSE 682772.5504 749985.326 795679.3853 795792.381 718814.2297 639041.6492 618589.5901 597749.3037 611972.9522 710071.9852 0.96155399 1.056210274 1.12056158 1.120720712 1.012311772 0.899967415 0.871164619 0.841815078 0.861846355 1 19.43760576 2.804928224 2.921960522 0.877096916 1.06809693 0.652431093 0.058412432 0.149249506 2.512349538 0.019407011 0.020203157 638.1580096 -2.804928224 0.191000014 S(ph)TPDSTYSESFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.558)T(0.442)PDSTYSESFK 231.83 2.63E-12 447030000 1180400 693850 905430 746870 1167400 1286200 1331100 1058700 1090700 532110 TRUE FALSE 1227003.103 813013.3401 929026.2496 894598.6568 968965.765 987499.5425 1226764.904 1044509.858 1051445.92 636366.7666 1.92813825 1.277586107 1.459891211 1.405790974 1.522652998 1.551777362 1.927763938 1.64136456 1.652264033 1 19.27949897 2.468218628 24.9766097 1.638188232 1.499993825 0 0.27113008 630.3193985 1768367.908 0.087631342 0.073419681 293.9128868 -2.468218628 -0.138194407 S(ph)TPDSTYSESFKDAATEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STPDSTYSESFKDAATEK 18 1 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.5)T(0.5)PDSTYSESFKDAATEK;S(0.944)T(0.055)PDS(0.001)TYSESFKDAATEK 134.83 5.88E-06 496900000 1468240 726820 1027550 496770 1673240 1448720 1034840 995170 1293320 657700 TRUE FALSE 1526207.249 851645.6811 1054328.797 595029.6233 1388823.262 1112276.736 953726.5367 981831.3739 1246773.666 786563.7226 1.940347877 1.082742131 1.34042388 0.756492584 1.765684359 1.414096155 1.212522914 1.248254078 1.585089205 1 19.58520412 -1.368555283 5.404413731 0.999867481 1.342661617 0.101195688 0.322033738 0.000479403 5.60E-05 0.290710482 0.068494817 0.042800093 1.368555283 0.342794136 S(ph)TPLEENVVDREQIDFLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.5)T(0.5)PLEENVVDREQIDFLAAR;S(0.602)T(0.398)PLEENVVDREQIDFLAAR;S(0.658)T(0.342)PLEENVVDREQIDFLAAR;S(0.952)T(0.048)PLEENVVDREQIDFLAAR 204.18 5.99E-22 442755000 92812 99639 109348 88844 121903 151559 114918 106718 107965 98762 TRUE FALSE 96476.28943 116751.2232 112197.6987 106417.078 101181.9716 116361.7191 105910.4269 105287.6198 104079.3607 118112.523 0.816816769 0.988474551 0.949922124 0.900980483 0.85665744 0.985176814 0.89669092 0.891417922 0.881188193 1 16.84980241 S(ph)TPLSQPSANGVQTEGLDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 S(0.487)T(0.487)PLS(0.025)QPSANGVQTEGLDYDR;S(0.391)T(0.391)PLS(0.218)QPSANGVQTEGLDYDR;S(0.467)T(0.467)PLS(0.067)QPSANGVQTEGLDYDR;S(0.496)T(0.496)PLS(0.009)QPSANGVQTEGLDYDR;S(0.498)T(0.498)PLS(0.004)QPSANGVQTEGLDYDR 346.44 1.21E-77 1572610000 300908 295031 334321 336320 436242 465058 413653 392282 396668 410380 TRUE FALSE 312788.0802 345700.2792 343033.6799 402843.0922 362089.7407 357055.3275 381229.797 387024.1014 382391.9962 490786.1038 0.637320572 0.704380741 0.698947418 0.820811936 0.737775047 0.727517191 0.776773821 0.788579991 0.779141857 1 18.90473488 -5 0.126232798 1.855023579 0.629071329 0.83328707 0.037793092 57.97973672 0.466886465 12.55401641 0.318838908 1.00E-05 5 -1.22595225 S(ph)TPVRDR ddPTM_MDA-MB-175_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(0.5)T(0.5)PVRDR 91.867 0.0097437 297650000 538750 488360 501550 454650 592250 675920 623520 516890 487790 394080 TRUE FALSE 560020.266 572232.0311 514620.805 544578.413 491579.5565 518947.8237 574646.8731 509961.935 470234.5332 471292.4309 1.188264927 1.214176154 1.091935222 1.155500019 1.043045728 1.101116398 1.219300026 1.082049915 0.997755326 1 18.84626299 7.999999999 0.049697317 0.747624085 1.792364744 0.456782184 0.057732948 489.5528184 1.836075484 9.124260308 39.31158766 99999999.86 -7.999999999 1.044740659 S(ph)TQKSPATAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STQKSPATAPK 11 1 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.45)T(0.272)QKS(0.252)PAT(0.026)APK 97.214 0.016924 63725000 210900 93936 123960 93772 184010 174170 174200 123030 130400 60968 TRUE FALSE 219226.4949 110068.7773 127190.4994 112319.8217 152732.0459 133721.6571 160545.7488 121380.9841 125706.9295 72913.5123 3.006664855 1.509579964 1.744402312 1.540452766 2.094701532 1.833976349 2.201865522 1.664725512 1.72405533 1 16.15389858 -2.017957268 0.238924347 4.27E-15 2.042928304 0.349794606 0.404315038 37.81297537 1.338135717 22.00591249 0.67906467 0.00959495 2.017957268 2.042928304 S(ph)TQLLQAAAAEASLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STQLLQAAAAEASLNK 16 0 Q2M2I8;Q2M2I8-2 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 S(0.801)T(0.199)QLLQAAAAEASLNK 116.43 0.00044952 22902000 45122 60890 60152 48788 76581 70701 63939 55246 65432 65441 TRUE FALSE 46903.4514 71347.38384 61719.61054 58438.12078 63563.78897 54281.76423 58927.29411 54505.51773 63077.1151 78262.91101 0.599306246 0.911637236 0.788618897 0.746689844 0.812182784 0.693582229 0.752940229 0.696441227 0.805964336 1 16.25604115 0.972441916 20.7315248 1.000000003 0.753923043 0.481520174 0.077702367 234.3509329 176299.9594 0.070312093 0.017578023 9.385165075 -0.972441916 -0.24607696 S(ph)TSATDTHHVEMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSATDTHHVEMAR 14 0 H3BTL2;H3BS02;O14874-2;O14874-3;O14874;H3BQP2;H3BNP3 H3BTL2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 S(0.983)T(0.014)S(0.003)ATDTHHVEMAR;S(0.971)T(0.027)S(0.002)ATDTHHVEMAR 220.64 1.58E-08 534730000 276810 333540 284250 331780 275890 459870 287680 258560 254390 341390 TRUE FALSE 287738.6725 390822.9004 291657.7885 397405.0937 228994.3163 353072.1619 265130.8899 255094.4261 245234.5536 408278.8342 0.704760199 0.957245068 0.714359315 0.973366877 0.560877266 0.864781939 0.64938681 0.624804435 0.600654585 1 18.63919525 2.226930062 24.96111683 0.679374411 0.796910027 0.031971328 0.156634402 462.9963617 993660.5853 0.054176779 0.040344623 168.6281448 -2.226930062 0.117535616 S(ph)TSDLDKDDASYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSDLDKDDASYLR 14 1 Q8TEP8;H0Y966 Q8TEP8 CEP192 Centrosomal protein of 192 kDa 1 S(0.974)T(0.02)S(0.006)DLDKDDASYLR 72.932 0.022557 120170000 42100 259330 126100 233060 95644 236460 87182 148140 87692 275980 TRUE FALSE 43762.14051 303867.9102 129386.2696 279158.5724 79386.46704 181545.7486 80348.44703 146154.4256 84535.98205 330052.997 0.132591253 0.920663993 0.392016648 0.845799235 0.240526424 0.550050296 0.243441047 0.442821083 0.256128509 1 18.33233817 -1.578974106 6.110224993 1.001449828 0.45814962 0.307358516 0.248496769 0.00451488 0.000311099 0.221338444 0.052052494 0.026364886 1.578974106 -0.543300207 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.316)T(0.316)S(0.316)FRGGMGS(0.011)GGLAT(0.04)GIAGGLAGMGGIQNEK;S(0.328)T(0.328)S(0.328)FRGGMGS(0.013)GGLAT(0.003)GIAGGLAGMGGIQNEK;S(0.321)T(0.321)S(0.321)FRGGMGS(0.013)GGLAT(0.025)GIAGGLAGMGGIQNEK;S(0.331)T(0.331)S(0.331)FRGGMGS(0.005)GGLAT(0.002)GIAGGLAGMGGIQNEK;S(0.299)T(0.299)S(0.299)FRGGMGS(0.042)GGLAT(0.06)GIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGS(0.001)GGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.332)T(0.332)S(0.332)FRGGMGS(0.003)GGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.333)T(0.333)S(0.333)FRGGMGS(0.001)GGLATGIAGGLAGMGGIQNEK;S(0.332)T(0.332)S(0.332)FRGGMGS(0.002)GGLAT(0.001)GIAGGLAGMGGIQNEK 163.43 2.53E-12 2823523000 1247300 1030209 1559151 812431 2053433 1630736 1399820 1603611 1921457 1273714 TRUE FALSE 1296544.367 1207139.382 1599783.756 973127.4269 1704391.192 1252022.278 1290098.451 1582117.218 1852304.138 1523273.872 0.851156441 0.792463788 1.050227268 0.63883944 1.118900038 0.821928546 0.846924821 1.038629525 1.216002042 1 20.53874392 1.597872633 4.147510464 1.113374624 0.876769133 0.344860227 0.134605073 0.171839085 6.713670256 0.073335602 0.032436892 39.61618332 -1.597872633 -0.236605491 S(ph)TSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.333)T(0.333)S(0.333)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 270.86 2.45E-77 4286260000 553260 708390 918480 322935 1448470 913090 422277 894500 904430 1127930 TRUE FALSE 575103.132 830050.472 942416.3433 386810.5791 1202259.587 701038.6855 389177.8253 882510.6906 871879.741 1348926.288 0.426341407 0.615341609 0.69864184 0.286754423 0.891271523 0.519701256 0.288509334 0.654231961 0.646350915 1 20.36338008 0.770233518 1.764118972 0.998723181 0.546860862 0.378968679 0.174723619 0.836288847 4.362380365 0.158688819 0.044852129 5.891603583 -0.770233518 -0.451862319 S(ph)TSGSPRPAGAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.28)T(0.28)S(0.247)GS(0.194)PRPAGAKPK 51.147 0.087052 347460000 722890 431860 595650 393880 776560 714840 720370 632570 660570 364230 TRUE FALSE 751430.2554 506028.5956 611173.1283 471788.2884 644560.6086 548829.2435 663905.5171 624091.4338 636796.2147 435593.8949 1.725070678 1.16169809 1.403080106 1.083092059 1.479728289 1.259956234 1.52413871 1.432736871 1.461903443 1 18.73262421 4.756524325 23.91092643 1.338614957 1.725071273 0.329226944 0.173200929 2494.352624 3320055.443 0.038967138 1.174577455 57085.3049 -4.756524325 0.386456316 S(ph)TSNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSNFK 6 0 A0A087X1U1;F5GXM9;E7EUN2;Q9UPQ3-2;Q9UPQ3;H7C211;H7C0A7 A0A087X1U1 AGAP1 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1" 1 S(0.981)T(0.018)SNFK 78.113 0.0741 176880000 377880 285060 375000 294000 533660 479440 459260 374910 456340 306410 TRUE FALSE 392798.9942 334016.8375 384772.8081 352152.3225 442948.6638 368097.326 423262.0011 369884.9447 439916.4125 366445.1729 1.071917501 0.911505628 1.050014672 0.960995937 1.208771998 1.004508595 1.155048647 1.009386866 1.200497223 1 18.48323783 3.285911716 24.99995682 1.090691193 0.996058628 0.246481863 0.083336418 164.8990248 87060.58743 0.020955259 0.028373491 1931.575623 -3.285911716 -0.094632565 S(ph)TSPFGIPEEASEMLEAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSPFGIPEEASEMLEAKPK 20 1 Q96D09 Q96D09 GPRASP2 G-protein coupled receptor-associated sorting protein 2 1 S(0.333)T(0.333)S(0.333)PFGIPEEASEMLEAKPK 66.853 0.013944 164680000 215230 121520 182510 102410 241650 189400 228490 190460 198510 127140 TRUE FALSE 223727.4466 142390.1147 187266.3605 122666.3923 200574.4193 145414.7204 210580.3568 187907.1952 191365.6639 152050.6488 1.471400802 0.936465026 1.23160514 0.806746918 1.319128994 0.956357119 1.384935602 1.235819753 1.258565257 1 17.21419245 2.234672723 24.99971618 1.24428418 1.111775375 0.048141324 0.203555722 243.8760291 1568136.58 0.068442406 0.052434985 171.6614288 -2.234672723 -0.132508805 S(ph)TSQSIVSLLTGTAGEDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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)QS(0.001)IVSLLTGTAGEDEK;S(0.333)T(0.333)S(0.333)QSIVSLLTGTAGEDEK;S(0.314)T(0.314)S(0.314)QS(0.057)IVSLLTGTAGEDEK 194.92 2.17E-15 91035000 178780 128682 148050 143027 224815 233832 202600 175854 177635 123964 TRUE FALSE 185838.3724 150782.1325 151908.3046 171317.3137 186601.0266 179528.0618 186719.6826 173496.9648 171241.951 148252.3724 1.253527141 1.017063876 1.024660194 1.155578902 1.258671437 1.210962488 1.259471802 1.170281204 1.155070562 1 17.17769567 5.075147243 20.21072435 1.152518202 4.590014753 0.107461737 0.091876042 1049.67487 292439.557 0.022415538 5849.029388 118890.5246 -5.075147243 3.437496551 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.331)T(0.331)S(0.331)T(0.007)PNVHMVSTTLPVDSR;S(0.32)T(0.32)S(0.32)T(0.041)PNVHMVSTTLPVDSR;S(0.329)T(0.329)S(0.329)T(0.014)PNVHMVSTTLPVDSR;S(0.352)T(0.352)S(0.29)T(0.005)PNVHMVSTTLPVDSR 171.52 6.52E-12 944660000 340630 426953 424063 355737 477260 528260 375284 420562 420589 434133 TRUE FALSE 354078.3354 500278.8565 435114.4302 426100.7168 396135.5157 405579.6209 345868.2595 414925.0543 405452.084 519193.0494 0.681978189 0.963570019 0.838059043 0.820698038 0.762983087 0.781173056 0.666165042 0.799172976 0.780927411 1 18.98591154 5.027617763 15.98535249 0.807886298 0.334021951 0.155684965 0.092648338 1140730.214 18034158.96 0.021556687 14210860.04 106565.7788 -5.027617763 -0.473864347 S(ph)TSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSTSSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPK 41 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 S(0.166)T(0.166)S(0.166)T(0.166)S(0.166)S(0.166)PVRPAAT(0.006)FPPATHCPLGGTLDGVYPTLMEPVLLPK 168.9 4.59E-20 153440000 182870 157740 177130 153080 238440 244250 208780 196900 205040 158210 TRUE FALSE 190089.8488 184830.618 181746.1533 183358.7671 197910.054 187526.6391 192415.2781 194260.8776 197660.6505 189208.2204 1.004659567 0.976863572 0.960561613 0.969084571 1.04599078 0.991112536 1.016949885 1.026704216 1.044672637 1 17.52961524 3.253216238 24.99967737 1.020890368 0.976495215 0.548243844 0.019157892 176.7547087 301507.9127 0.005284141 0.007125255 1791.497631 -3.253216238 -0.044395153 S(ph)TTELDDYSTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STTELDDYSTNK 12 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(1)TTELDDYSTNK;S(0.864)T(0.135)T(0.001)ELDDYSTNK;S(0.992)T(0.007)T(0.001)ELDDYSTNK;S(0.999)TTELDDYSTNK;S(0.989)T(0.011)TELDDYSTNK 333.58 3.15E-58 2613400000 5144140 3154120 4379490 3522620 5611980 5772100 6104620 4649220 4934470 2571870 TRUE FALSE 5347234.619 3695815.574 4493623.107 4219383.722 4658057.644 4431617.252 5626123.933 4586904.81 4756879.389 3075778.685 1.738497846 1.201586965 1.460970885 1.371809923 1.514431993 1.440811484 1.829170597 1.491298718 1.54656101 1 21.55252027 3.184860273 12.57352607 1.51729744 1.427243197 0 0.228967806 3.799449024 883.1055007 0.061899205 0.074019333 1530.59494 -3.184860273 -0.090054243 S(ph)TTISMY(ph)LASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STTISMYLASK 11 0 E9PQL0;Q86UB9-2;Q86UB9 E9PQL0 TMEM135 Transmembrane protein 135 2 S(0.471)T(0.528)T(0.359)IS(0.248)MY(0.394)LAS(0.001)K 56.951 0.04998 465810000 283760 424130 449080 417050 472980 587270 521980 464990 455680 410790 TRUE FALSE 294963.0639 496971.0282 460783.3937 499541.2452 392583.0285 450885.4427 481065.8437 458757.5696 439280.1658 491276.4355 0.600401409 1.011591423 0.937930991 1.016823135 0.799108201 0.917783574 0.979216199 0.933807397 0.894160872 1 18.90617551 4.746109083 24.80088601 0.939595709 0.600401227 0.732178811 0.062192475 413.4313191 1358314.344 0.014431041 0.151366721 55732.57171 -4.746109083 -0.339194482 S(ph)TTPAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STTPAPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.978)T(0.021)T(0.001)PAPK 66.692 0.070474 99540000 137530 101370 105100 87247 130030 153300 137320 130700 137150 105850 TRUE FALSE 142959.7906 118779.509 107838.9923 104504.1962 107927.547 117698.3983 126556.4996 128948.1803 132213.9983 126589.2809 1.129319873 0.938306215 0.851880914 0.825537482 0.852580458 0.929765913 0.999741042 1.018634274 1.04443281 1 16.94979572 2.224529236 3.278646656 1.020127527 0.909901961 0.250310279 0.079873753 0.339107559 7.621622655 0.033992147 0.025040279 167.6985224 -2.224529236 -0.110225566 S(ph)TTPPPAEPVSLPQEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.373)T(0.373)T(0.254)PPPAEPVSLPQEPPK;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK;S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK 179.81 8.58E-14 1418860000 584640 401961 491734 446732 618470 730140 651980 584280 620160 361444 TRUE FALSE 607722.0386 470994.6749 504548.992 535094.2562 513342.6903 560576.0504 600876.104 576448.6823 597840.5627 432262.0315 1.405911217 1.089604547 1.167229493 1.237893262 1.187572937 1.29684314 1.390073752 1.333563071 1.383051296 1 18.72154659 2.663213425 5.468732367 1.313982036 1.208969817 0.024666188 0.128736891 0.445190219 23.90423381 0.039232596 0.037045447 460.4828132 -2.663213425 -0.105012219 S(ph)TTPPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.348)T(0.348)T(0.304)PPPAEPVSLPQEPPKPR 89.946 0.0012152 274450000 124620 93234 111680 85677 128330 145210 146830 109120 129130 73569 TRUE FALSE 129540.0938 109246.2142 114590.4725 102623.6549 106516.5124 111487.1782 135321.0809 107657.4249 124482.6365 87983.43699 1.472323636 1.241667955 1.302409595 1.166397431 1.210642776 1.267138248 1.538029038 1.223610131 1.414841711 1 16.42494434 -2.205913704 2.431237883 0.02658584 1.30737518 0.398472062 0.115830837 5875307.452 1757208.698 31291233.16 0.027809712 0.00622424 2.205913704 1.28078934 S(ph)VAS(ph)SQPAKPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 S(1)VAS(0.538)S(0.462)QPAKPTK;S(0.999)VAS(0.981)S(0.019)QPAKPTK 138.02 0.00097863 204990000 509590 296600 415750 301010 570200 508090 525210 418770 485780 251100 TRUE FALSE 529709.0067 347538.7428 426584.7865 360548.8796 473277.6077 390093.7977 484042.6678 413157.0731 468296.8727 300298.2374 1.76394311 1.157311964 1.420537098 1.200636017 1.57602526 1.29902127 1.611873157 1.375822505 1.559439299 1 18.19603648 -1.105923633 4.737399388 0.999975129 1.427909073 0.344043736 0.181729338 4.28E-05 8.07E-06 0.157658179 0.037158232 0.078356741 1.105923633 0.427933945 S(ph)VASSQPAKPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVASSQPAKPTK 12 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 S(1)VASSQPAKPTK;S(0.978)VAS(0.011)S(0.011)QPAKPTK 136.34 6.76E-05 1345590000 1323360 748460 1049560 833810 1243460 1313550 1377740 1104640 1233690 638210 TRUE FALSE 1375607.275 877002.1828 1076912.396 998735.1293 1032097.113 1008497.92 1269749.139 1089834.108 1189289.738 763255.0302 1.80229048 1.149029024 1.410947001 1.308520861 1.352231001 1.321311855 1.663597472 1.427876744 1.55818133 1 19.54180567 -1.995136965 2.657101245 0.579690512 1.433030142 0.354489777 0.179125712 5838662.989 3029193.911 15021725.74 0.040858671 0.010112605 1.995136965 0.85333963 S(ph)VDEVFDEVVQIFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVDEVFDEVVQIFDK 15 0 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 1 S(1)VDEVFDEVVQIFDK 125.52 0.00051513 0 5144.4 4608.5 5088.3 4232.3 5633.7 5743.9 5835.1 5877 6253.2 5241 TRUE FALSE 5347.504884 5399.974026 5220.905278 5069.436308 4676.085686 4409.966275 5377.729615 5798.228428 6028.148553 6267.873605 0.853160932 0.861532055 0.832962757 0.808796831 0.746040201 0.703582515 0.857983098 0.925071052 0.961753369 1 12.61376037 1.701214742 2.35004199 0.973911906 0.802561717 0.704688156 0.047001158 0.164986454 1.960057638 0.035305052 0.014802023 50.25910398 -1.701214742 -0.171350189 S(ph)VDEVNYWDKQDHPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVDEVNYWDKQDHPISR 17 1 F5H5P2;P12694;P12694-2 F5H5P2 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 S(1)VDEVNYWDKQDHPISR;S(1)VDEVNYWDKQDHPISR 149.32 1.99E-07 388350000 151931 147748 147146 141628 153726 207417 147920 139231 151900 112744 TRUE FALSE 157929.3532 173122.5697 150980.7456 169641.5957 127595.7094 159247.5452 136325.6439 137364.8362 146433.1487 134834.0282 1.171287065 1.283967942 1.119752541 1.25815121 0.946316825 1.18106347 1.011062606 1.018769802 1.086025172 1 17.04082511 3.248909411 24.99972884 1.044286154 1.207371211 0.568525463 0.071546584 148.2996305 358247.2813 0.018621054 0.024941482 1773.819443 -3.248909411 0.163085056 S(ph)VDFDSLTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SVDFDSLTVR 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR 266.26 1.11E-17 13302160000 3272038 3102528 3465145 3080465 4438190 4675840 3809823 3667280 3580510 3254830 TRUE FALSE 3401220.587 3635363.05 3555449.525 3689771.783 3683788.049 3589947.023 3511199.118 3618126.11 3451648.145 3892551.621 0.873776617 0.933928026 0.91339817 0.947905678 0.946368451 0.922260608 0.9020302 0.92949984 0.886731502 1 21.89228474 S(ph)VDIHDSIQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SVDIHDSIQPR 11 0 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR;S(1)VDIHDSIQPR 196.5 3.88E-08 6285040000 661732 3607650 3498940 4476390 3703050 5266020 3205720 4144540 3322970 3652590 TRUE FALSE 687857.6903 4227235.824 3590125.251 5361806.581 3073606.884 4043066.662 2954447.29 4088989.22 3203376.959 4368245.077 0.157467742 0.967719473 0.821869009 1.227450953 0.703625101 0.925558569 0.676346505 0.936071385 0.7333327 1 22.05862237 4.742679098 24.86420124 0.882621269 0.157467436 0.661912817 0.156586832 219.4352874 1324726.123 0.034878206 0.270115044 55294.13873 -4.742679098 -0.725153833 S(ph)VEDDAEGHLIYHVGDWLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVEDDAEGHLIYHVGDWLQER 21 0 B1AVT0;P49760-3;P49760 B1AVT0 CLK2 Dual specificity protein kinase CLK2 1 S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER;S(1)VEDDAEGHLIYHVGDWLQER 326.86 9.32E-80 163899000 46039.3 47847.3 49130.1 46658.6 61629.7 58169.8 59418.2 47984.1 55166.5 42986.1 TRUE FALSE 47856.96711 56064.70157 50410.47077 55887.53182 51153.90561 44660.74552 54760.84622 47340.95163 53181.06844 51408.40328 0.930917205 1.090574653 0.980588144 1.087128334 0.995049493 0.868744071 1.065211964 0.920879635 1.034482012 1 15.64971658 3.004989585 24.98083221 0.971588181 1.026310355 0.082947271 0.067598555 273.2027916 1367799.832 0.018029163 0.021478297 1011.555194 -3.004989585 0.054722174 S(ph)VEDVRPHHTDANNQSACFEAPDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVEDVRPHHTDANNQSACFEAPDQK 25 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.5)VEDVRPHHT(0.5)DANNQSACFEAPDQK;S(0.684)VEDVRPHHT(0.311)DANNQS(0.005)ACFEAPDQK;S(0.941)VEDVRPHHT(0.059)DANNQSACFEAPDQK;S(0.992)VEDVRPHHT(0.008)DANNQSACFEAPDQK;S(0.993)VEDVRPHHT(0.007)DANNQSACFEAPDQK 171.88 3.98E-12 5725080000 2718160 2198600 2964060 2267590 3571610 3785010 3300040 2985000 3111470 1850230 TRUE FALSE 2825475.056 2576192.447 3041305.839 2716112.534 2964509.008 2905998.79 3041374.242 2944990.957 2999488.802 2212747.144 1.276908238 1.164250716 1.374447979 1.22748437 1.339741423 1.313299081 1.374478892 1.330920691 1.355549734 1 21.07740717 4.242943611 24.99994575 1.307243714 1.220579497 0.040544381 0.109603812 240.5876498 1372229.301 0.024043524 0.061281909 17496.19502 -4.242943611 -0.086664217 S(ph)VELCCASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVELCCASR 9 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(1)VELCCASR;S(1)VELCCASR 103.08 0.0036503 180046000 37583 72276 81925 71927 71211 88575 57160 76404 77366 85322 TRUE FALSE 39066.80586 84688.84077 84060.0328 86153.94592 59106.57966 68004.79862 52679.64984 75379.92935 74581.61277 102039.2123 0.382860716 0.829963686 0.823801271 0.844321942 0.579253586 0.666457503 0.516268684 0.73873492 0.730911295 1 16.63876414 0.68030793 1.849789186 0.999654792 0.679869066 0.325428873 0.140893149 1.658058983 7.86507564 0.133015174 0.037178535 4.789695782 -0.68030793 -0.319785726 S(ph)VENLPECGITHEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SVENLPECGITHEQR 15 0 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;F8W860;Q9UBF8-3 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR;S(1)VENLPECGITHEQR 277.28 1.50E-33 8986560000 1914613 2018699 2012157 1948075 2345061 2644632 2137229 2239498 2009944 1900279 TRUE FALSE 1990203.4 2365394.85 2064595.464 2333398.421 1946448.369 2030456.298 1969707.406 2209481.192 1937606.508 2272602.287 0.875737656 1.040830973 0.908471965 1.02675177 0.856484384 0.893449905 0.866718923 0.972225191 0.852593751 1 21.1159138 3.231334021 24.99842965 0.90675036 0.964620003 0.155253811 0.063986429 291.0034921 1006647.282 0.017110908 0.020855606 1703.468163 -3.231334021 0.057869643 S(ph)VEPQDAGPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVEPQDAGPLER 12 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 S(1)VEPQDAGPLER 64.675 0.065882 114370000 53687 65491 61092 58240 71334 77115 68858 74378 64769 61866 TRUE FALSE 55806.60422 76738.5698 62684.10771 69759.69817 59208.67216 59206.20994 63460.73003 73381.08457 62437.97634 73987.4582 0.754271137 1.037183486 0.847226128 0.942858423 0.800252821 0.800219542 0.857722803 0.991804373 0.843899464 1 16.17499312 0.728291127 0.748468123 0.996496935 0.873743217 0.149264485 0.085731673 2.052179784 2.240038862 0.083888679 0.030077129 5.349228217 -0.728291127 -0.122753718 S(ph)VGGSGGGSFGDNLVTR ddPTM_MDA-MB-175_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(0.536)VGGS(0.143)GGGS(0.32)FGDNLVTR 170.23 1.97E-09 174970000 189810 178640 199580 195560 216180 246590 211130 174920 194950 190080 TRUE FALSE 197303.8454 209320.0304 204781.2188 234241.1843 179433.8008 189323.2096 194581.0789 172575.4835 187933.7876 227322.5367 0.867946699 0.920806328 0.900839933 1.030435379 0.789335732 0.832839596 0.855969152 0.759165748 0.826727479 1 17.79438119 3.211543658 24.99543978 0.827582757 0.927266635 0.237809824 0.07183897 250.5820603 231831.8342 0.01975404 0.023616285 1627.584921 -3.211543658 0.099683878 S(ph)VHREESCSDSGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVHREESCSDSGTK 14 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK;S(1)VHREESCSDSGTK 307.57 1.07E-45 1316450000 446815 404042 477572 410046 649960 746920 524027 531301 572155 458955 TRUE FALSE 464455.6012 473433.0705 490017.9186 491151.8749 539480.0314 573459.1497 482952.3945 524179.7791 551563.2533 548878.445 0.846190273 0.862546297 0.892762183 0.894828134 0.982877058 1.044783512 0.879889525 0.955001574 1.004891444 1 19.06612716 3.367704448 3.616515537 0.970606569 0.869684018 0.598418033 0.041751121 0.18392494 4.62919521 0.012575378 0.017518635 2331.870604 -3.367704448 -0.10092255 S(ph)VHS(ph)EHS(ph)AR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVHSEHSAR 9 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 3 S(1)VHS(1)EHS(1)AR;S(1)VHS(1)EHS(1)AR 156.02 4.81E-05 358576000 605210 565200 570780 564810 648020 723740 623780 538260 487240 506070 TRUE FALSE 629104.1581 662268.7034 585654.9957 676527.7322 537869.7919 555662.3534 574886.4937 531045.5051 469704.3276 605224.7272 1.039455478 1.094252554 0.967665347 1.117812445 0.888710867 0.918109139 0.949872779 0.877435242 0.776082514 1 19.20711141 3.225048516 24.99729768 0.898506245 1.051391096 0.570586277 0.065002047 160.582123 297075.206 0.018161048 0.021818004 1678.991572 -3.225048516 0.152884851 S(ph)VIDPVPAPVGDSHVDGAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVIDPVPAPVGDSHVDGAAK 20 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 S(1)VIDPVPAPVGDSHVDGAAK 193.54 4.50E-18 52181000 103230 93384 131200 90928 221440 152200 119160 126860 134770 135800 TRUE FALSE 107305.6001 109421.9756 134619.1798 108913.287 183799.7079 116853.8566 109819.9278 125159.6492 129919.654 162407.41 0.660718622 0.673749896 0.828898015 0.67061772 1.131719962 0.719510622 0.676200229 0.770652332 0.799961369 1 17.30925793 -5 0.35951578 3.806311279 0.764380856 0.214114365 0.133021257 778.8678711 6.207505946 1691.566708 0.096631986 1.00E-05 5 -3.041930423 S(ph)VPGLNVDMEEEEEEEDIDHLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVPGLNVDMEEEEEEEDIDHLVK 23 0 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 S(1)VPGLNVDMEEEEEEEDIDHLVK 236.08 2.65E-37 22595000 11453 9776.2 16075 10322 18455 17876 12515 14031 15286 10568 TRUE FALSE 11905.17328 11455.1863 16493.92771 12363.66079 15318.02569 13724.56991 11534.0416 13842.9374 14735.85985 12638.59726 0.941969511 0.906365324 1.305044172 0.978246283 1.212003625 1.085925093 0.912604568 1.095290649 1.165941088 1 13.62554873 S(ph)VPNTPLRPNQQSVVNSSFSELFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 S(1)VPNTPLRPNQQSVVNSSFSELFVK 273.73 3.27E-53 604850000 149600 143790 206900 162850 258300 232010 190070 213120 214150 155850 TRUE FALSE 155506.3235 168484.814 212291.984 195061.2439 214394.2583 178129.1936 175171.8167 210263.475 206442.7833 186385.8236 0.834324846 0.903957236 1.138992118 1.046545495 1.150271271 0.955701406 0.939834443 1.128108731 1.1076099 1 17.50793261 4.388577268 5.397519627 1.059013714 0.850474089 0.53759902 0.071350366 0.139224535 6.376728907 0.017903428 0.051769746 24466.8054 -4.388577268 -0.208539625 S(ph)VS(ph)FY(ph)T(ph)RK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSFYTRK 8 1 H0YM52;G3V4P4;G3V3Z0;G3V499;G3V2G7;E7ES96;P49768-4;P49768-3;P49768-5;P49768-6;P49768-7;P49768-2;P49768 H0YM52 PSEN1 Presenilin;Presenilin-1;Presenilin-1 NTF subunit;Presenilin-1 CTF subunit;Presenilin-1 CTF12 4 S(1)VS(1)FY(1)T(1)RK 54.066 0.041189 1397800000 1466300 537410 838600 395780 891610 1091400 807040 690380 690060 453420 TRUE FALSE 1524190.656 629705.987 860454.6049 474064.1027 740054.4507 837938.8903 743782.096 681126.5853 665224.8754 542258.9677 2.810816873 1.161264312 1.58679645 0.874239304 1.364762032 1.54527438 1.371636322 1.256090956 1.226766019 1 19.04862248 4.741414406 24.98737799 1.2861542 2.810817427 0.829024145 0.210381049 98.29950062 860651.7264 0.047529167 0.332634229 55133.35313 -4.741414406 1.524663227 S(ph)VS(ph)PCSNVESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVSPCSNVESR 11 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(1)VS(1)PCSNVESR;S(1)VS(0.999)PCS(0.001)NVESR;S(1)VS(0.995)PCS(0.005)NVESR;S(1)VS(1)PCSNVESR;S(1)VS(0.999)PCS(0.001)NVESR 150.9 4.92E-05 3629110000 3705580 3723410 3797660 3405420 4289960 5032620 4026690 3756590 3787770 3306760 TRUE FALSE 3851879.16 4362876.703 3896630.139 4079001.912 3560754.132 3863870.275 3711067.516 3706239.056 3651448.898 3954656.31 0.974011104 1.103225252 0.985327127 1.031442834 0.900395345 0.977043255 0.93840456 0.937183605 0.92332901 1 21.91512089 3.255812696 24.99491969 0.943485293 1.026469411 0.457054139 0.041242398 192.6950675 279176.036 0.010532965 0.014227826 1802.240296 -3.255812696 0.082984118 S(ph)VS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPK 70.028 0.084995 736350000 3625400 2391400 3117200 2225700 3815800 4384700 3964900 3318800 3405600 2174900 TRUE FALSE 3768533.591 2802104.347 3198436.793 2665936.817 3167191.679 3366419.876 3654120.778 3274316.914 3283033.121 2601030.014 1.448862017 1.077305657 1.229680848 1.024954269 1.217668255 1.294264141 1.404874514 1.258853953 1.262205012 1 21.31065162 2.993479178 24.93373916 1.271348605 1.180751101 0.003738331 0.141941986 755.966781 2890618.63 0.039434328 0.045569063 985.0974119 -2.993479178 -0.090597504 S(ph)VS(ph)PPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 S(1)VS(1)PPPKR;S(1)VS(1)PPPKR 90.05 0.047143 4423880000 2023850 1331920 1651490 1336660 2091540 2212600 2091410 1659620 1841760 1146430 TRUE FALSE 2103753.161 1560666.899 1694529.186 1601047.358 1736020.778 1698757.182 1927479.819 1637375.508 1775475.417 1371051.009 1.534409112 1.138299661 1.235934459 1.167751855 1.266197076 1.239018221 1.405841072 1.194248425 1.294974006 1 20.38685082 -1.135234562 3.573178557 0.999787009 1.265877934 0.349864693 0.111892423 10615853.19 19346928.21 27108.25978 0.024556331 0.073242884 1.135234562 0.266090924 S(ph)VS(ph)PSPSVLSEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVSPSPSVLSEGR 13 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(1)VS(0.511)PS(0.48)PS(0.009)VLSEGR;S(1)VS(0.937)PS(0.062)PS(0.001)VLSEGR;S(1)VS(0.498)PS(0.498)PS(0.003)VLSEGR 164.93 5.29E-05 942410000 672350 648460 702000 715620 882710 1031080 928740 775410 797670 640530 TRUE FALSE 698894.8972 759827.9607 720294.6967 857167.5001 732667.2695 791627.2962 855942.932 765016.8973 768962.0125 766029.5898 0.912360184 0.991904191 0.94029618 1.118974399 0.956447739 1.03341608 1.117375808 0.998677998 1.00382808 1 19.5470406 3.794881 24.99837338 1.032645675 0.952558504 0.357792886 0.051771544 323.2957497 143496.7105 0.012792266 0.023061578 6235.639512 -3.794881 -0.080087171 S(ph)VS(ph)PSPSVLSEGRDEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(0.999)VS(0.556)PS(0.257)PS(0.185)VLS(0.003)EGRDEPQR 70.917 0.0060711 0 127940 116310 128140 92032 160660 188220 111890 145960 139000 133990 TRUE FALSE 132991.17 136285.3377 131479.4337 110235.6549 133351.0706 144508.7575 103119.7694 144003.6449 133997.4172 160242.7751 0.829935514 0.85049287 0.820501477 0.687929018 0.832181485 0.901811376 0.643522114 0.898659205 0.836215031 1 17.28989979 0.743823655 1.239201414 0.998676345 0.802503024 0.359017327 0.07773897 0.924583907 2.459383754 0.070846405 0.021569352 5.544005537 -0.743823655 -0.196173321 S(ph)VS(ph)PYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSPYSR 7 0 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 2 S(1)VS(0.986)PY(0.014)SR;S(1)VS(0.994)PY(0.006)SR 88.681 0.026943 170078000 478930 510160 529760 443240 586480 645710 532980 488860 513770 463470 TRUE FALSE 497838.5262 597776.0115 543565.9808 530911.5491 486790.3391 495753.6383 491203.6349 482307.6313 495279.5181 554278.0728 0.898174672 1.078476744 0.980673794 0.957843319 0.878242101 0.894413224 0.886204342 0.87015463 0.893557841 1 19.08025041 3.434643685 3.060214965 0.893962665 0.993724618 0.313855711 0.053638789 0.233781571 4.473086935 0.014326734 0.02113448 2720.468393 -3.434643685 0.099761953 S(ph)VSGS(ph)PEPAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 S(0.829)VS(0.174)GS(0.997)PEPAAK;S(0.999)VS(0.001)GS(1)PEPAAK;S(0.596)VS(0.405)GS(0.999)PEPAAK;S(0.653)VS(0.347)GS(1)PEPAAK 158.83 4.29E-05 1517940000 6175330 4353000 5284670 4278390 6602200 7016160 6394770 5355010 5619410 4084560 TRUE FALSE 6419136.797 5100593.888 5422392.842 5124642.772 5479960.402 5386763.171 5893531.218 5283234.85 5417168.532 4884851.328 1.314090515 1.044165635 1.110042553 1.049088791 1.121827469 1.102748642 1.20649142 1.081554892 1.108973061 1 22.21988322 -5 0.234910696 0.33143322 1.134324766 0.214968903 0.075159633 270.9045552 2.707586617 86.35745947 0.117318715 1.00E-05 5 0.802891546 NSQKHS(ph)PTSEPTPPGDALPPVSSPHTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 NSQKHSPTSEPTPPGDALPPVSSPHTHR 28 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2;A0A087WX39 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 NS(0.185)QKHS(0.57)PT(0.185)S(0.061)EPTPPGDALPPVSSPHTHR;NS(0.06)QKHS(0.903)PT(0.029)S(0.007)EPTPPGDALPPVSSPHTHR;NS(0.184)QKHS(0.719)PT(0.048)S(0.048)EPTPPGDALPPVSSPHTHR;NS(0.113)QKHS(0.542)PT(0.171)S(0.171)EPT(0.002)PPGDALPPVSSPHTHR 143.04 5.69E-08 8035020000 795830 2182620 3002130 2382800 3897540 3909850 3324120 3683130 3067980 1887370 TRUE FALSE 827249.9829 2557468.007 3080367.974 2854110.728 3235037.543 3001846.592 3063566.788 3633763.667 2957563.999 2257164.016 0.366499721 1.133044825 1.364707196 1.264467583 1.433231046 1.329919568 1.357263702 1.609880204 1.310300881 1 21.10607982 4.783921073 2.030270709 1.372667885 3.16E-13 0.79194962 0.147364456 0.333123091 1.354779731 0.036441545 0.88034583 60802.44909 -4.783921073 -1.372667885 down S(ph)VSKESVASMGADSGDDFASDGSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSKESVASMGADSGDDFASDGSSSR 26 1 Q92805;Q5T165 Q92805 GOLGA1 Golgin subfamily A member 1 1 S(0.488)VS(0.488)KES(0.024)VAS(0.001)MGADSGDDFASDGSSSR 140.34 1.92E-07 127340000 115340 74215 89338 62218 114320 128940 116900 90876 106860 61178 TRUE FALSE 119893.7123 86960.84894 91666.22167 74524.5347 94887.92723 98995.6391 107737.0725 89657.95586 103014.1295 73164.65778 1.638683429 1.188563599 1.252875698 1.018586527 1.296909329 1.353052719 1.472528893 1.22542712 1.407976646 1 16.1588593 -2.100604231 2.606569491 0.443835297 1.304060025 0.257030575 0.16038771 3291540.879 3611892.118 10727791.52 0.038751634 0.007932239 2.100604231 0.860224728 S(ph)VSPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPPPK 7 0 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.563)VS(0.437)PPPK 70.919 0.058451 713180000 201750 184370 218330 177180 259570 254300 223430 208820 222400 219680 TRUE FALSE 209715.2458 216034.1133 224019.8592 212225.6752 215448.3841 195242.679 205916.9728 206021.1095 214395.8674 262722.09 0.798239866 0.822291393 0.852687565 0.807795322 0.82006193 0.743152884 0.783782486 0.784178862 0.816055732 1 18.00317798 0.942288493 18.84413148 1 0.801021637 0.824425582 0.027326881 316.1295008 103224.4405 0.028599276 0.007149819 8.755652029 -0.942288493 -0.198978363 S(ph)VSPPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.97)VS(0.03)PPPKR 57.347 0.068509 332360000 659500 585770 656560 588090 752130 809350 747310 681740 657620 550620 TRUE FALSE 685537.5692 686371.4408 673670.493 704412.4467 624283.2113 621390.7283 688733.8895 672602.3904 633952.3847 658503.4467 1.041053882 1.042320195 1.0230326 1.069717175 0.948033324 0.943640814 1.045907797 1.021410584 0.962716881 1 19.32883147 3.25082818 24.99908628 0.992325321 1.042408878 0.430337808 0.03179244 272.3808781 555060.4953 0.009668838 0.012997272 1781.673744 -3.25082818 0.050083556 S(ph)VSPSPVPLLFQPDQNAPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.499)VS(0.409)PS(0.092)PVPLLFQPDQNAPPIR;S(0.333)VS(0.333)PS(0.333)PVPLLFQPDQNAPPIR 102.16 0.00030163 148271000 98058 119351 119555 113082 114956 138792 119897 120319 110552 121530 TRUE FALSE 101929.4056 139848.6058 122670.7015 135449.2821 95415.82018 106559.6614 110499.1598 118706.3206 106573.2551 145341.4767 0.701309825 0.962207135 0.844017168 0.931938255 0.656494088 0.733167599 0.76027272 0.816740846 0.733261128 1 17.14908694 5.037828073 20.9270249 0.814602577 0.000127986 0.102790247 0.105827632 2799.329013 342226.242 0.024031738 115483.0341 109100.8347 -5.037828073 -0.814474591 S(ph)VSPTFLNPSDENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 S(0.5)VS(0.5)PT(0.001)FLNPSDENLK 126.48 8.81E-05 493620000 204460 198060 216570 222900 305880 311150 244880 216660 277930 209400 TRUE FALSE 212532.2387 232075.2643 222213.9921 266988.9547 253886.6269 238890.128 225685.6657 213756.0271 267927.3536 250427.9208 0.84867629 0.926714815 0.887337128 1.06613094 1.013811184 0.95392769 0.901200094 0.853563079 1.069878122 1 17.9340359 4.45546707 1.696350147 0.960510652 0.849143367 0.22613737 0.068602748 1.047629205 4.447486232 0.019998282 0.159590117 28540.86098 -4.45546707 -0.111367285 S(ph)VSQDLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(1)VSQDLIK;S(0.998)VS(0.002)QDLIK;S(0.999)VS(0.001)QDLIK;S(0.998)VS(0.002)QDLIK;S(0.998)VS(0.002)QDLIK;S(0.998)VS(0.002)QDLIK 159.09 0.0003789 3316150000 4765350 3174200 4059370 3159810 5791880 5308210 5863680 4276930 5008110 3176950 TRUE FALSE 4953489.698 3719344.158 4165160.517 3784810.987 4807378.306 4075458.674 5404069.44 4219604.749 4827869.099 3799412.526 1.303751478 0.978926119 1.096264354 0.996156896 1.265295167 1.072654956 1.422343429 1.110593998 1.270688315 1 21.85734493 3.230973585 24.99993338 1.200335572 1.085749068 0.101548743 0.137847937 325.8432886 1073681.713 0.03671617 0.044675266 1702.054983 -3.230973585 -0.114586503 S(ph)VSQDLIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSQDLIKK 9 1 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(0.999)VS(0.001)QDLIKK 114.87 0.00096068 452070000 570110 314500 451760 300300 677900 537300 575640 490560 616710 326510 TRUE FALSE 592618.383 368512.9285 463533.2367 359698.4437 562670.8001 412520.2179 530519.8326 483984.8456 594514.7276 390483.3831 1.517653269 0.943735238 1.187075448 0.921161973 1.440959653 1.056434757 1.358623326 1.239450554 1.522509672 1 18.57490163 2.566034686 1.308584168 1.288709548 1.155725477 0.019146099 0.219314234 1.33163635 4.635309341 0.102348279 0.081895333 368.1583764 -2.566034686 -0.13298407 S(ph)VSSFPVPQDNVDTHPGSGK ddPTM_MDA-MB-175_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(0.97)VS(0.03)SFPVPQDNVDTHPGSGK;S(0.999)VSSFPVPQDNVDTHPGSGK 264.32 9.61E-37 2399500000 2353700 2135220 2596600 2155450 3715200 3410100 2840500 2851500 3167800 2478200 TRUE FALSE 2446625.893 2501927.425 2664269.529 2581791.577 3083691.631 2618155.956 2617854.188 2813280.307 3053791.497 2963755.842 0.825515334 0.844174608 0.89895041 0.871121548 1.0404675 0.883391242 0.883289423 0.949228093 1.030378904 1 21.49899517 8 0.192244475 1.00268651 0.169859729 0.498914123 0.052054888 48.41825438 0.56963789 0.104587416 12.01939941 100000000 -8 -0.832826781 S(ph)VSSSPWLPQDGFDPSDYAEPMDAVVKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVSSSPWLPQDGFDPSDYAEPMDAVVKPR 29 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 S(0.954)VS(0.021)S(0.021)S(0.004)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.25)VS(0.25)S(0.25)S(0.25)PWLPQDGFDPSDYAEPMDAVVKPR;S(0.865)VS(0.132)S(0.002)SPWLPQDGFDPSDYAEPMDAVVKPR;S(0.867)VS(0.133)SSPWLPQDGFDPSDYAEPMDAVVKPR;S(0.795)VS(0.164)S(0.021)S(0.021)PWLPQDGFDPSDYAEPMDAVVKPR 247.73 4.41E-46 636491000 307373 305913.5 361424 325781 506749 493825 410459 396885 409684 395993 TRUE FALSE 319508.3234 358451.7639 370843.0064 390219.5094 420611.986 379141.6277 378286.151 391565.4057 394939.5529 473580.2466 0.674665647 0.756897625 0.783062657 0.823977588 0.888153568 0.800585815 0.798779412 0.826819549 0.833944312 1 18.85324938 -5 0.042510785 1.81894167 0.334812993 0.729183328 0.041820278 447.1547975 1.416948447 46.11888841 12.8851525 1.00E-05 5 -1.484128677 S(ph)VSTTNIAGHFNDESPLGLRR ddPTM_MDA-MB-175_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(0.449)VS(0.449)T(0.096)T(0.006)NIAGHFNDESPLGLRR 104.83 0.0001904 365630000 103340 180080 194540 162460 241560 238140 212960 211550 237400 181640 TRUE FALSE 107419.943 211007.3392 199609.8722 194594.1031 200499.7175 182835.594 196267.6387 208714.5183 228856.0204 217228.8803 0.494501205 0.971359512 0.918891963 0.895802173 0.922988312 0.841672589 0.903506193 0.96080465 1.053524835 1 17.72885639 4.741563724 24.93601312 0.933596376 0.494501039 0.84798181 0.056631426 101.4184104 842074.9885 0.013755188 0.097030096 55152.31208 -4.741563724 -0.439095338 S(ph)VVDMDLDDTDDGDDNAPLFYQPGKR ddPTM_MDA-MB-175_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 282.28 3.93E-61 343540000 166435 144307 169969 137246 251438 219276 194423 197750 199195 153487 TRUE FALSE 173005.9823 169090.6047 174398.5318 164392.8492 208698.6586 168352.4722 179183.6172 195099.4847 192026.0109 183559.839 0.942504544 0.921174292 0.950090895 0.89558179 1.136951632 0.917153083 0.976159155 1.062865852 1.046122136 1 17.48589092 3.290192925 24.99999957 1.020742685 0.928522765 0.416285775 0.055562276 104.502286 50598.45676 0.015186306 0.020562338 1950.710966 -3.290192925 -0.09221992 S(ph)VVGTPAYLAPEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;S(1)VVGTPAYLAPEVLR;S(1)VVGTPAYLAPEVLR 181.26 6.24E-07 94920000 59582 61663 77300 59837 100883 88174 76780 68384 78191 86100 TRUE FALSE 61934.34337 72253.14058 79314.5015 71672.58 83734.94369 67696.92479 70761.78297 67467.42433 75376.92118 102969.6465 0.601481558 0.701693587 0.770270698 0.696055415 0.813200264 0.657445442 0.687210118 0.655216626 0.732030494 1 16.6518596 0.95741567 21.5393113 1.000000001 0.699625687 0.720702702 0.056075556 754.4635766 381611.6275 0.05379753 0.013449383 9.065999063 -0.95741567 -0.300374313 S(ph)VVSFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVVSFDK 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.999)VVS(0.001)FDK 101.65 0.0093424 206400000 129210 100250 94656 81306 153150 144610 104880 95690 109900 96234 TRUE FALSE 134311.3106 117467.1577 97122.81312 97388.08413 127117.6177 111026.5191 96659.23155 94407.43207 105944.7205 115089.2098 1.167019139 1.020661779 0.843891563 0.846196479 1.104513776 0.964699639 0.839863543 0.820297856 0.920544338 1 16.81239305 2.333940122 5.992286325 0.87276057 0.985803909 0.15517796 0.104983083 0.354518356 18.44326301 0.038513828 0.031956853 215.7446933 -2.333940122 0.113043339 S(ph)VWDLGWFVCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVWDLGWFVCK 11 0 Q8TDV0 Q8TDV0 GPR151 Probable G-protein coupled receptor 151 1 S(1)VWDLGWFVCK 62.2 0.08652 100720000 30232 183680 212410 135290 232650 236430 138330 198660 228800 212640 TRUE FALSE 31425.5827 215225.6112 217945.5791 162049.9582 193104.2361 181522.7156 127487.3331 195997.2876 220565.5327 254302.7368 0.12357548 0.846336197 0.857031984 0.637232459 0.759347849 0.713805592 0.501321121 0.770724256 0.867334483 1 17.95618746 -5 0.047322673 2.313185652 7.56E-12 0.294327055 0.196627356 925.8010339 3.250166752 158.483063 38.40506411 1.00E-05 5 -2.313185652 S(ph)WASPVYTEADGTFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.998)WAS(0.002)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.931)WAS(0.069)PVYTEADGTFSR;S(1)WASPVYTEADGTFSR;S(0.645)WAS(0.355)PVYTEADGTFSR;S(0.998)WAS(0.002)PVYTEADGTFSR;S(0.997)WAS(0.003)PVYTEADGTFSR 447.77 3.82E-182 15162800000 1273162 1417878 1484205 1345396 1742997 1832952 1470664 1483083 1472030 1487971 TRUE FALSE 1323427.419 1661387.517 1522884.602 1611511.313 1446722.993 1407276.677 1355389.513 1463204.698 1419051.928 1779510.429 0.743703098 0.933620557 0.855788523 0.905592509 0.812989331 0.790822382 0.761664271 0.822251263 0.797439512 1 20.76304896 3.201621175 24.58800686 0.815656649 0.86468025 0.008489807 0.076836172 344.3393213 229201.4915 0.020539806 0.024550442 1590.820484 -3.201621175 0.049023601 S(ph)WDNILAPGPR ddPTM_MDA-MB-175_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 204.01 3.64E-08 273752000 182532 217341 193447 178917 251706 269084 197764 209922 204321 207132 TRUE FALSE 189738.5043 254667.6261 198488.3877 214306.2486 208921.104 206593.319 182262.7409 207108.339 196967.5271 247715.5496 0.765953145 1.028064756 0.801275447 0.865130384 0.843391157 0.833994149 0.735774323 0.836073227 0.795135903 1 17.91832491 S(ph)WEDS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWEDSPER 8 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 2 S(1)WEDS(1)PER;S(1)WEDS(1)PER 139.31 0.00097676 177960000 396270 413700 385060 400420 484110 570090 436410 421460 408640 380570 TRUE FALSE 411915.0456 484749.7569 395094.9799 479621.8809 401821.1551 437695.2373 402203.0439 415811.0181 393933.1262 455135.405 0.905038459 1.065067124 0.86808228 1.05380042 0.882860684 0.961681364 0.88369975 0.913598488 0.865529515 1 18.79593629 3.191948007 24.99998618 0.913333489 0.97208059 0.138374631 0.066764977 210.9858247 113158.4052 0.017492523 0.020907618 1555.779366 -3.191948007 0.058747101 S(ph)WGEQCPETSGTDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWGEQCPETSGTDSGR 16 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 S(1)WGEQCPETSGTDSGR;S(1)WGEQCPETSGTDSGR 225.01 7.62E-15 382830000 90262 103213 80392 98372 108838 150230 112933 113075 110587 93834 TRUE FALSE 93825.61346 120939.0299 82487.08156 117829.688 90337.75564 115341.3593 104081.0164 111559.4146 106606.9955 112218.9757 0.83609401 1.077705701 0.735054664 1.049997892 0.80501319 1.027824024 0.927481432 0.994122552 0.949990808 1 16.77595712 2.700529953 24.96863747 0.976376931 0.909686236 0.130274778 0.100694153 1270.346276 834031.635 0.029510816 0.02782381 501.7991872 -2.700529953 -0.066690695 S(ph)WGQQAQEYQEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;S(1)WGQQAQEYQEQK 331.48 2.01E-62 2069190000 985540 761671 921288 754773 1209430 1290490 1090782 977189 1085258 742061 TRUE FALSE 1024449.88 892482.0693 945297.5221 904064.8466 1003851.521 990793.2551 1005283.657 964091.3798 1046199.777 887453.6453 1.154370018 1.005666126 1.065179604 1.018717824 1.131159386 1.116445079 1.132773145 1.086356887 1.178878223 1 19.75931224 3.225499936 24.92532557 1.112197056 1.057331883 0.135455668 0.056693608 353.5626376 674746.8301 0.015089623 0.018135363 1680.737677 -3.225499936 -0.054865173 S(ph)WHEESPFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SWHEESPFEK 10 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 S(1)WHEESPFEK;S(0.995)WHEES(0.005)PFEK;S(1)WHEESPFEK;S(1)WHEESPFEK 263.74 1.11E-17 634470000 1141290 1004308 1124033 960209 1479232 1480519 1392942 1161958 1402300 1147264 TRUE FALSE 1186349.01 1176790.087 1153326.223 1150135.474 1227792.673 1136690.9 1283759.566 1146383.854 1351831.497 1372048.415 0.864655356 0.857688456 0.840587118 0.838261581 0.894861041 0.828462675 0.935651798 0.835527261 0.985265157 1 20.38789996 1.228834229 24.2453862 0.992632798 0.862616104 0.74217113 0.030805242 69.43161438 173066.1725 0.026023852 0.006852459 16.93691193 -1.228834229 -0.130016693 S(ph)WITIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWITIPR 7 0 Q03188;H0Y8J2;Q03188-2 Q03188 CENPC Centromere protein C 1 S(1)WITIPR 100.98 0.0203 0 29421 29509 30854 27791 41821 38404 32324 34985 30829 30997 TRUE FALSE 30582.5638 34576.9412 31658.08059 33287.97685 34712.28136 29485.25302 29790.36042 34516.0833 29719.47031 37070.26868 0.824988998 0.932740507 0.854001919 0.897969668 0.936391415 0.795388166 0.803618681 0.931098817 0.801706364 1 15.17797495 -0.990301594 4.616980628 1.000001408 0.868982787 0.355742302 0.054481412 0.006507665 32307887.57 214.389352 0.012288659 0.102258262 0.990301594 -0.131018621 S(ph)WRT(ph)S(ph)QRDT(ph)SDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWRTSQRDTSDVK 13 2 Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9;Q8NFP9-3 Q5T321 NBEA Neurobeachin 4 S(0.996)WRT(0.997)S(0.997)QRDT(0.547)S(0.463)DVK;S(0.945)WRT(0.945)S(0.945)QRDT(0.583)S(0.583)DVK 58.071 0.023933 161390000 64638.3 354141 445933 322198 846548 470279 787397 483266 525116 287278 TRUE FALSE 67190.27 414961.9619 457554.3803 385927.8027 702652.0733 361063.8294 725678.7657 476788.6097 506217.1777 343564.6238 0.195568069 1.207813416 1.331785488 1.123304834 2.045181676 1.050934247 2.112204562 1.387769801 1.473426373 1 18.39022197 4.698667429 2.057005445 1.487402433 1.58E-25 0.512193246 0.36054007 0.484628985 2.409160817 0.084914887 1.30507643 49965.17685 -4.698667429 -1.487402433 S(ph)WSTAT(ph)SPLGGERPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWSTATSPLGGERPFR 16 1 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;D6RD46;H0Y8P3;D6RJ93;Q6NVB9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 2 S(0.999)WS(0.036)T(0.007)AT(0.566)S(0.392)PLGGERPFR;S(0.999)WS(0.265)T(0.176)AT(0.463)S(0.097)PLGGERPFR 86.539 0.015525 373680000 234230 235666 226080 250860 310400 336210 316500 295380 298370 274770 TRUE FALSE 243477.5813 276139.8023 231971.8305 300479.3593 257638.3189 258130.3228 291691.903 291420.9142 287631.722 328605.9207 0.740940945 0.84033727 0.705927118 0.914406407 0.784034318 0.785531564 0.887664782 0.88684012 0.875309006 1 18.32599895 0.523881288 0.157445809 1.119787106 0.701702748 0.587945315 0.053971344 6.316226896 0.502104247 0.777015201 0.397117644 3.341037024 -0.523881288 -0.418084357 S(ph)WTSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.799)WT(0.098)S(0.104)PK;S(0.998)WT(0.001)S(0.002)PK;S(0.756)WT(0.229)S(0.015)PK 94.114 0.047046 3362510000 3685250 1995740 2608380 2029160 3141310 3639200 3513020 2625380 2643490 1577810 TRUE FALSE 3830746.516 2338492.82 2676356.526 2430521.792 2607351.248 2794050.953 3237660.313 2590191.075 2548351.311 1886951.661 2.030124351 1.239296623 1.418349278 1.288067862 1.381779567 1.480722061 1.715815185 1.372685443 1.350512239 1 20.84762603 -3.018823451 0.301681695 6.05E-11 1.494985151 0.311912966 0.21912852 89.90582843 2.468563265 57.18984529 0.213403927 0.000957583 3.018823451 1.494985151 S(ph)YDNLTTACDNTVPLASR ddPTM_MDA-MB-175_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(0.996)YDNLT(0.004)TACDNTVPLASR;S(0.933)YDNLT(0.067)TACDNTVPLASR;S(1)YDNLTTACDNTVPLASR 266.99 3.43E-31 3127810000 951060 1004400 1024960 1037920 1148990 1315330 1192380 1083970 1018300 938730 TRUE FALSE 988608.5832 1176897.887 1051671.3 1243217.478 953685.0902 1009864.542 1098918.14 1069441.155 981651.5819 1122656.17 0.880597826 1.04831552 0.936770605 1.107389342 0.849489911 0.899531458 0.978855476 0.952599009 0.874400914 1 20.09848472 3.21714183 24.9994453 0.927906515 0.993164834 0.178433072 0.070824193 414.6877381 484011.4893 0.019558211 0.023397424 1648.70073 -3.21714183 0.065258318 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(0.999)Y(0.001)DVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK;S(1)YDVPPPPMEPDHPFYSNISK 304.49 1.26E-55 12753950000 7573070 6264846 8073930 6208693 10124470 9915170 9314950 8046648 8683130 5916612 TRUE FALSE 7872060.651 7340784.567 8284343.249 7436753.944 8403516.206 7612522.033 8584819.879 7938795.845 8370625.847 7075858.841 1.112523699 1.037440787 1.170789785 1.051003717 1.187631974 1.075844248 1.213254825 1.12195509 1.182983725 1 22.75447384 3.243067017 24.99786992 1.138437443 1.09453605 0.061707335 0.066820465 271.0050819 1503302.714 0.017030154 0.02228976 1750.116734 -3.243067017 -0.043901394 S(ph)YEDLTESEDGAASGDSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYEDLTESEDGAASGDSHK 19 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 S(1)YEDLTESEDGAASGDSHK 233.89 1.20E-26 0 87753 76766 108590 79555 137160 131680 130840 103910 107540 64522 TRUE FALSE 91217.5562 89949.96334 111419.9446 95290.74155 113845.5922 101099.3156 120584.4189 102517.2564 103669.6564 77163.85055 1.182128102 1.165700813 1.443939666 1.234914288 1.475374691 1.310190133 1.562706086 1.328565846 1.343500301 1 16.23563752 4.253768525 24.95571369 1.359450861 1.173914305 0.155962406 0.145042591 330.5524282 542416.5537 0.031780071 0.086302725 17937.77304 -4.253768525 -0.185536556 S(ph)YEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 SYEDMIGEEVPSDQYYWAPLAQHER 25 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(0.996)Y(0.004)EDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER;S(1)YEDMIGEEVPSDQYYWAPLAQHER 245.11 5.34E-39 3221443000 957523 989651 948267 913097 1040793 1345832 1112138 1004558 962208 750984 TRUE FALSE 995326.7474 1159615.861 972979.617 1093704.861 863879.3776 1033282.914 1024965.718 991093.5431 927578.322 898124.9363 1.108227494 1.291152059 1.08334551 1.21776472 0.961869939 1.150489061 1.141228437 1.103514114 1.032794308 1 19.77655662 7.999999094 0.055655037 0.795182356 1.750785082 0.270052525 0.080052905 497.6822108 2.077801899 7.708674577 39.39851154 99999791.28 -7.999999094 0.955602726 S(ph)YELPDGQVITIGNER ddPTM_MDA-MB-175_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(0.998)Y(0.002)ELPDGQVITIGNER;S(1)YELPDGQVITIGNER 215.48 1.69E-14 243671000 254124 231677 251051 254339 270689 334571 312014 257200 263018 187516 TRUE FALSE 264157.0117 271465.7226 257593.5953 304646.4951 224677.3805 256871.9557 287557.5274 253752.6547 253552.0336 224256.17 1.17792528 1.210516181 1.148657784 1.358475422 1.001878256 1.145439859 1.282272534 1.131530315 1.130635708 1 17.77478815 0.852615117 1.513417513 1.000979485 1.185612415 0.283729405 0.088689382 0.747637731 3.262473303 0.08080331 0.023613744 7.122215619 -0.852615117 0.18463293 S(ph)YENLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYENLLGR 8 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 S(0.989)Y(0.011)ENLLGR;S(0.997)Y(0.003)ENLLGR 92.611 0.012226 85974000 53813 121678 104960 117322 98049 134315 92167 105189 92142 119273 TRUE FALSE 55937.57879 142575.25 107695.3438 140527.9414 81382.666 103122.3768 84942.70971 103779.1135 88825.82742 142642.2607 0.392152918 0.999530218 0.755003063 0.985177469 0.570536849 0.722944072 0.595494696 0.727548154 0.622717468 1 17.12204195 -1.1269001 4.307984675 1.000046329 0.718294967 0.199515602 0.174410527 44930746203 93709255.69 21753465.86 0.039307459 0.074662048 1.1269001 -0.281751362 S(ph)YHDLSQASLYPHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYHDLSQASLYPHRK 15 1 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 S(1)YHDLSQASLYPHRK;S(1)YHDLSQASLYPHRK 207.53 1.57E-09 228240000 211875 289050 304000 277640 449100 384620 261870 305700 309400 325770 TRUE FALSE 220239.9886 338692.089 311922.4897 332556.3633 372762.1424 295297.834 241343.9451 301602.5915 298264.7544 389598.3943 0.565300042 0.86933646 0.800625707 0.853587613 0.956785623 0.757954443 0.619468531 0.774137152 0.765569773 1 18.57162821 -2.420913114 2.049045844 2.621013186 0.777531421 0.281350697 0.108370672 3477225.729 243240.2235 26235149.96 0.027656631 0.003793909 2.420913114 -1.843481765 S(ph)YPQLRRVFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYPQLRRVFQK 11 2 P04083 P04083 ANXA1 Annexin A1 1 S(0.571)Y(0.429)PQLRRVFQK 66.056 0.05021 326830000 16772 781420 384590 754450 253920 702680 211010 492850 236400 1262500 TRUE FALSE 17434.17151 915622.8064 394612.7313 903677.9582 210758.7691 539493.2192 194470.4848 486244.1519 227892.0102 1509862.703 0.011546859 0.606427859 0.261356699 0.598516644 0.139588036 0.357312766 0.128800112 0.322045277 0.150935585 1 20.52598594 -1.354973424 3.92570648 1.002036225 0.296975135 0.567876563 0.186568077 134376854.2 178358359.6 3004140.163 0.041049741 0.044159747 1.354973424 -0.70506109 S(ph)YS(ph)PAHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 S(0.999)Y(0.001)S(1)PAHNR;S(0.992)Y(0.048)S(0.96)PAHNR;S(0.999)Y(0.006)S(0.995)PAHNR 102.52 0.0072346 1249219000 1510330 1332980 1329220 1527780 1547350 1801810 1803360 1451770 1345620 960250 TRUE FALSE 1569958.995 1561908.946 1363860.565 1829970.324 1284332 1383366.934 1662007.931 1432311.398 1297191.399 1148392.602 1.36709257 1.36008273 1.187625697 1.593505845 1.118373627 1.204611499 1.447247159 1.247231474 1.129571365 1 20.13118451 1.132816931 2.233604141 1.005438454 1.320481396 0.400426085 0.129708773 0.273535465 2.55201628 0.116442573 0.032651774 13.57740993 -1.132816931 0.315042942 S(ph)YSHDVLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SYSHDVLPK 9 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.5)YS(0.5)HDVLPK;S(0.499)Y(0.002)S(0.499)HDVLPK;S(0.586)YS(0.414)HDVLPK;S(0.5)Y(0.001)S(0.5)HDVLPK 97.734 0.0041808 1342180000 3253370 3927450 4936290 4076170 6353750 6266570 5975260 5098630 5684840 4069040 TRUE FALSE 3381815.56 4601958.986 5064933.773 4882424.26 5273741.845 4811254.088 5506903.508 5030291.205 5480243.719 4866290.482 0.694947326 0.94568111 1.04082027 1.003315416 1.083729355 0.988690278 1.131642989 1.033701384 1.126164527 1 22.21439101 5.241868768 1.1376015 1.058648597 1.29E-16 0.840068613 0.047144023 1.47097418 0.719219549 0.012326273 2.449360032 174529.4694 -5.241868768 -1.058648597 S(ph)YSPAHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.785)Y(0.002)S(0.213)PAHNR;S(0.793)Y(0.001)S(0.206)PAHNR 71.349 0.031544 584800000 355840 575650 468930 519870 433930 604730 392370 413400 374500 542630 TRUE FALSE 369888.838 674513.4096 481150.701 622698.7343 360170.7336 464290.6223 361615.0141 407859.0492 361021.8182 648947.9592 0.569982281 1.039395224 0.741431873 0.95955111 0.555007113 0.71545124 0.557232686 0.628492691 0.556318597 1 19.30774326 3.232306601 24.99788088 0.643638137 0.8365649 0.162129333 0.170794839 203.7417109 814373.6811 0.044513261 0.054461016 1707.287265 -3.232306601 0.192926764 S(ph)YSPDGKES(ph)PSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.801)YS(0.199)PDGKES(0.981)PS(0.019)DKK 183.45 6.92E-06 1213000000 5183600 782170 1561800 726430 2654600 3251600 2790100 1612200 1845000 440400 TRUE FALSE 5388252.531 916501.6131 1602501.791 870115.6858 2203372.04 2496465.178 2571404.671 1590591.096 1778598.81 526687.948 10.23044585 1.740122622 3.042601975 1.652051635 4.183448754 4.739932227 4.882216654 3.019987645 3.376949894 1 19.00658892 4.746234571 24.81640659 3.247154774 10.23044958 0.744288765 1.25514783 435.2929854 1407634.757 0.301939728 3.216924652 55748.67771 -4.746234571 6.983294806 S(ph)YSPDGKESPSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 S(0.491)Y(0.018)S(0.491)PDGKESPSDKK;S(0.499)Y(0.003)S(0.499)PDGKESPSDKK 61.692 0.043291 34878000 91558 25835.6 42692 23849 82301 64446 46373 43375 56440 19927.9 TRUE FALSE 95172.78054 30272.66333 43804.58859 28566.26102 68311.50542 49479.39319 42738.16309 42793.62907 54408.73542 23832.39046 3.993421503 1.27023193 1.83802748 1.198631797 2.866330405 2.07614059 1.793280584 1.79560792 2.282974321 1 14.54063605 8 0.052936717 7.10E-13 5.796296347 0.190207509 0.757952528 911.7735977 3.630880133 89.49424671 423.1857507 100000000 -8 5.796296347 S(ph)YSPDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.539)Y(0.015)S(0.446)PDHR 65.246 0.091319 0 105080 173160 174120 154420 177810 186960 155490 170160 152650 170880 TRUE FALSE 109228.6395 202898.883 178657.7102 184963.8151 147585.9197 143541.3734 143302.2875 167879.2835 147156.1563 204360.6643 0.53448955 0.992847052 0.874227488 0.905085212 0.722183597 0.70239238 0.701222459 0.821485309 0.720080632 1 17.640758 4.76604606 24.40158858 0.812588466 0.534489003 0.382118597 0.110148411 8261.904107 7334752.399 0.02654001 2.404683189 58350.69866 -4.76604606 -0.278099464 S(ph)YSTLTTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSTLTTVR 9 0 Q96NY8-2;Q96NY8 Q96NY8-2 PVRL4 Nectin-4;Processed poliovirus receptor-related protein 4 1 S(0.984)YS(0.012)T(0.003)LTTVR;S(0.854)YS(0.112)T(0.034)LTTVR 188.91 4.07E-05 244740000 68548 90979 84744 90016 107706 128660 94333 80083 75484 109579 TRUE FALSE 71254.32797 106603.9355 86952.49826 107820.8961 89398.17259 98780.66486 86938.93297 79009.61837 72767.34558 131048.907 0.543723176 0.813466804 0.663511816 0.822753112 0.682174118 0.753769467 0.663408303 0.602901773 0.555268619 1 16.9997458 2.211407653 22.9161137 0.664549515 0.719095507 0 0.135769072 342.9957876 289470.4981 0.046951467 0.034690189 162.7075303 -2.211407653 0.054545992 S(ph)YTSDLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SYTSDLQK 8 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.737)YT(0.246)S(0.017)DLQK;S(0.999)YT(0.001)SDLQK;S(1)YTSDLQK;S(1)YTSDLQK;S(1)YTSDLQK 204.52 9.11E-05 1525042000 2326330 1583040 2001670 1709130 2989210 2592350 2547490 2147560 2324420 1624570 TRUE FALSE 2418175.305 1854914.806 2053835.165 2047190.813 2481105.152 1990316 2347811.077 2118775.471 2240764.578 1942873.387 1.244638647 0.954727579 1.057112202 1.053692344 1.277028739 1.024418788 1.208422068 1.09053708 1.153325066 1 20.88976046 5.080009251 15.05483844 1.100231954 3.557484362 0.190740184 0.093201892 1385910.202 4593911.142 0.021224123 109157185.6 120229.0044 -5.080009251 2.457252408 SAAAGALGS(ph)PGLPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 SAAAGALGS(1)PGLPLRK;SAAAGALGS(1)PGLPLRK;SAAAGALGS(1)PGLPLRK;SAAAGALGS(1)PGLPLRK 197.1 2.71E-11 3721310000 2873450 2346787 2530505 2044462 3234560 3411750 2416749 2539180 2452596 1954135 TRUE FALSE 2986896.025 2749829.412 2596452.039 2448850.481 2684750.647 2619422.768 2227317.898 2505146.445 2364327.549 2337010.339 1.278084215 1.176644093 1.111014357 1.047856075 1.148797077 1.120843466 0.95306292 1.071944956 1.011688956 1 21.15623269 8 0.331141595 1.017086211 3.652592674 0.713678424 0.048684281 32.26794657 0.460633213 0.044047264 52.09389607 100000000 -8 2.635506462 SAAAT(ph)SPAPHLVAGPLLGTVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAAATSPAPHLVAGPLLGTVGK 22 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.039)AAAT(0.48)S(0.48)PAPHLVAGPLLGTVGK 138.25 3.70E-08 0 197520 160220 191590 154280 232320 241410 208660 184560 190830 142550 TRUE FALSE 205318.2421 187736.5387 196582.9928 184796.1235 192830.3294 185346.1861 192304.684 182086.2751 183962.0656 170479.9432 1.204354238 1.101223611 1.153115077 1.083975745 1.131102731 1.087202298 1.128019404 1.068080336 1.079083334 1 17.37924249 -4.212001725 0.01973343 3.13E-09 1.915879196 0.696010296 0.028760944 1504.680547 2.557677224 160.8012462 95.27294108 6.14E-05 4.212001725 1.915879193 SAADS(ph)ISESVPVGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAADSISESVPVGPK 15 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 1 SAADS(0.84)IS(0.16)ESVPVGPK;SAADS(0.964)IS(0.036)ESVPVGPK 244.67 5.01E-18 191813000 365119 246122 368582 289926 484420 428210 401192 369293 374962 290671 TRUE FALSE 379534.1801 288391.5389 378187.5497 347272.4975 402078.4614 328764.7171 369745.5227 364343.2314 361467.1909 347622.4172 1.091800072 0.829611454 1.087926241 0.998993391 1.156652855 0.945752347 1.063641193 1.048100506 1.039827045 1 18.4071616 4.149164631 21.76404067 1.044659681 0.959996597 0.145028715 0.079403471 10.75428269 2610.401005 0.017724821 0.038290085 14098.23127 -4.149164631 -0.084663085 SAAEMYGSSFDLDYDFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 269.7 1.39E-31 281232000 184004 213183 166174 213970 209340 268172 192592 197286 153924 217629 FALSE TRUE 191268.62 249795.5219 170504.631 256292.6274 173756.4616 205893.1172 177496.1358 194641.7039 148384.3053 260269.2358 0.734887546 0.959758156 0.655108663 0.984721174 0.667602765 0.791077426 0.681971249 0.747847525 0.570118496 1 17.98964527 3.18229853 24.99996367 0.729977593 0.829884392 0.089425286 0.137523711 177.1831791 78730.08618 0.036087646 0.04313301 1521.5931 -3.18229853 0.0999068 SAAEMYGSVTEHPS(ph)PSPLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.85)PS(0.149)PLLSSSFDLDYDFQR;S(0.001)AAEMY(0.003)GS(0.004)VT(0.004)EHPS(0.938)PS(0.047)PLLS(0.001)S(0.001)S(0.001)FDLDYDFQR;SAAEMYGS(0.001)VTEHPS(0.987)PS(0.013)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.911)PS(0.089)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.987)PS(0.013)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.866)PS(0.134)PLLSSSFDLDYDFQR 295.16 1.63E-81 1069960000 195645 278143 235392 279006 283025 354823 256929 250011 237548 346261 TRUE FALSE 203369.2157 325911.8966 241526.5089 334192.5541 234916.5116 272420.7356 236790.2336 246660.0115 228998.6939 414104.2134 0.491106367 0.78702869 0.583250547 0.807025244 0.567288388 0.657855503 0.571813147 0.595647191 0.552997739 1 18.65963436 -1.461651142 4.332204909 1.001733189 0.627536792 0.579205 0.096153803 0.00149103 0.000185285 0.086241408 0.020239273 0.03454211 1.461651142 -0.374196396 SAAEMYGSVTEHPSPS(ph)PLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 SAAEMYGSVTEHPS(0.002)PS(0.998)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPSPS(1)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.008)PS(0.992)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.034)PS(0.965)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.999)PLLS(0.001)SSFDLDYDFQR;SAAEMYGSVTEHPS(0.009)PS(0.991)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.003)PS(0.996)PLLSSSFDLDYDFQR;SAAEMYGSVTEHPS(0.001)PS(0.999)PLLSSSFDLDYDFQR 280.65 4.47E-72 1246493000 210466 411200 343365 433871 415761 530710 378036 422685 334125 517073 TRUE FALSE 218775.3602 481820.4013 352313.374 519689.3888 345090.0937 407460.6455 348404.5505 417019.5989 322099.9065 618383.5544 0.353785864 0.779161085 0.569732768 0.840399757 0.558051862 0.658912487 0.563411734 0.674370455 0.520873985 1 19.23814243 -1.119950328 4.419673047 1.000048385 0.624816714 0.440576623 0.130169312 16314124.39 4134020.017 7627.784525 0.027223697 0.075866434 1.119950328 -0.375231671 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAAEMYGSVTEHPSPSPLLSSSFDLDYDFQR 31 0 P07910;G3V2Q1;G3V576;G3V555;G3V575 P07910 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 ; 149.84 8.98E-09 272110000 34744 87090 52767 85694 77497 98710 66600 76637 52167 82308 FALSE TRUE 36115.71995 102047.03 54142.15137 102644.0174 64324.08762 75786.09846 61379.71797 75609.80637 50289.51986 98434.67672 0.366900376 1.036697975 0.550031281 1.042762783 0.653469791 0.769912606 0.623557876 0.768121651 0.510892315 1 16.58687902 -2.332874022 2.27266274 2.605748559 0.71876543 0.155425959 0.20492119 7883714.32 1072131.762 65076508.56 0.044685727 0.0046465 2.332874022 -1.886983129 SAALPIFSSFVSNWDEATKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAALPIFSSFVSNWDEATKR 20 1 O76021;J3QSV6;O76021-2;I3L3U9 O76021 RSL1D1 Ribosomal L1 domain-containing protein 1 0 109.72 0.00030999 72769000 55879 55913 56968 58392 82813 85442 79464 75807 76335 48513 FALSE TRUE 58085.14607 65515.62281 58452.63288 69941.76332 68736.47584 65599.39039 73235.40404 74790.93116 73587.71826 58018.19351 1.001153992 1.129225487 1.007487985 1.205514324 1.184740022 1.130669302 1.262283425 1.289094448 1.268355904 1 15.82421776 3.620534141 1.04913134 1.222619498 1.035774873 0.293694231 0.090506487 0.61278676 1.312418853 0.032029911 0.083723375 4173.824088 -3.620534141 -0.186844625 SAAMLGNSEDHTALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAAMLGNSEDHTALSR 16 0 O60749;O60749-2 O60749 SNX2 Sorting nexin-2 0 ; 216.26 1.53E-14 642070000 226380 372150 341360 359850 372360 419780 355490 381420 342250 331940 FALSE TRUE 235317.6572 436063.8676 350256.122 431027.256 309066.3802 322292.4568 327625.7649 376307.6888 329932.4894 396977.2876 0.592773603 1.098460494 0.882307711 1.085773089 0.778549277 0.811866237 0.825301031 0.94793254 0.831111753 1 18.59869694 -0.865860105 3.774937451 1.000005906 0.884082415 0.063415126 0.14078049 23256692.33 45786371.16 1950.434349 0.032413968 0.13618833 0.865860105 -0.115923491 SAAS(ph)PVVSSMPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.998)PVVS(0.001)S(0.001)MPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER;SAAS(1)PVVSSMPER 284.26 1.23E-32 1748710000 1011080 975957 951944 988542 1212670 1336760 1110360 1017430 974541 945647 TRUE FALSE 1050998.219 1143570.023 976752.4427 1184072.657 1006540.787 1026317.749 1023327.082 1003793.015 939467.4598 1130928.424 0.929323374 1.011178071 0.863673086 1.046991686 0.890012812 0.90750018 0.904855745 0.887583152 0.830704614 1 20.10907619 SAAS(ph)REDLVGPEVGASPQSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SAASREDLVGPEVGASPQSGR 21 1 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 S(0.117)AAS(0.883)REDLVGPEVGASPQSGR;S(0.048)AAS(0.952)REDLVGPEVGASPQSGR;S(0.03)AAS(0.97)REDLVGPEVGASPQSGR 159.81 1.33E-11 1889790000 394207 481730 485598 497972 477445 569324 498375 506239 529750 527264 TRUE FALSE 409770.5968 564463.3802 498253.0828 596469.3753 396289.0694 437107.1292 459311.0652 499453.6942 510684.401 630571.2857 0.649840242 0.895161884 0.790161389 0.945919024 0.628460379 0.693192251 0.728404664 0.792065395 0.809875763 1 19.26629995 -1.529918107 3.466242039 1.005322164 0.772914122 0.341894385 0.095528188 226014672.7 515583710.2 12582083.47 0.022615808 0.029517658 1.529918107 -0.232408043 SAATWDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SAATWDER 8 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ;;; 121.85 0.0032934 1344950000 1848410 2265720 2003260 2063820 2487880 2733360 2225970 2187760 2090600 2366500 FALSE TRUE 1921386.654 2654839.785 2055466.601 2472037.436 2064991.046 2098578.564 2051492.655 2158436.656 2015359.714 2830170.366 0.678894344 0.938049461 0.726269565 0.873458879 0.729634891 0.741502558 0.724865429 0.762652553 0.712098374 1 21.43245747 -1.08512355 4.591431015 1.00001412 0.76847564 0.465060368 0.075454111 1.04E-05 2.08E-06 0.067732735 0.015963753 0.082200877 1.08512355 -0.23153848 SAAVETASLS(ph)PSLVPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 SAAVETAS(0.003)LS(0.877)PS(0.12)LVPAR;SAAVETAS(0.005)LS(0.991)PS(0.004)LVPAR 223.11 3.30E-15 239450000 214300 295340 289670 276080 298990 342760 310440 291350 248830 290590 TRUE FALSE 222760.7295 346062.3476 297219.0382 330687.8 248167.7866 263159.1846 286106.9016 287444.9298 239874.6569 347525.5468 0.640990947 0.995789664 0.855243711 0.951549614 0.714099406 0.757236948 0.82326869 0.827118848 0.690236039 1 18.40675951 4.781947658 23.11440969 0.836013478 0.64098917 0.253637642 0.104259198 17789.18794 9476593.069 0.02411946 10.14529565 60526.79221 -4.781947658 -0.195024308 SACGVCPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SACGVCPGR 9 0 P49207 P49207 RPL34 60S ribosomal protein L34 0 ;;; 125.25 0.001179 206824000 224811 199421 237879 228835 281305 294064 266694 256801 222638 222605 FALSE TRUE 233686.7119 233670.0055 244078.3222 274097.88 233488.8766 225772.0926 245789.8274 253359.0026 214625.3019 266220.1877 0.877794858 0.877732104 0.916828751 1.02959089 0.877051731 0.84806526 0.923257659 0.95168967 0.806194691 1 18.02226045 -1.760812105 4.482943406 1.007907334 0.906611006 0.202802671 0.057954123 0.004905999 0.00026176 0.060106106 0.013146277 0.017345543 1.760812105 -0.101296327 SACKEDIPSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SACKEDIPSEK 11 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 107.65 0.0019785 557720000 3538000 1333400 1983700 1338300 2959700 2918200 2754700 2042400 2540300 1077200 FALSE TRUE 3677682.972 1562401.078 2035396.852 1603011.746 2456611.251 2240492.276 2538779.416 2015024.969 2448875.099 1288256.716 2.854774927 1.212802587 1.579962151 1.244326326 1.906926796 1.739165997 1.970709242 1.564148624 1.900921664 1 20.29698868 -1.211303061 5.149697561 0.999936191 1.73530095 0.213996449 0.439661634 0.000295991 4.53E-05 0.391168341 0.092191316 0.061474774 1.211303061 0.735364759 SACMLS(ph)SPESSLTPPLSTNLHLESELDALASLENHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 S(0.001)ACMLS(0.445)S(0.445)PES(0.054)S(0.054)LTPPLSTNLHLESELDALASLENHVK 162.54 1.40E-17 58814000 15626 19145 21814 19252 29333 28333 27074 24687 26421 18878 TRUE FALSE 16242.92655 22433.00482 22382.49076 23059.98814 24346.98714 21753.09014 24951.86914 24356.11114 25470.11337 22576.78266 0.719452669 0.993631606 0.991394172 1.021402761 1.078408182 0.963515948 1.105200396 1.078812314 1.128155139 1 14.46255229 5.315048735 1.102322957 1.058070205 2.43E-17 0.796535423 0.049375449 2.185393494 0.897676006 0.01411076 3.656783229 206561.194 -5.315048735 -1.058070205 SACMLSS(ph)PES(ph)SLTPPLSTNLHLESELDALASLENHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 2 S(0.079)ACMLS(0.424)S(0.441)PES(0.355)S(0.357)LT(0.329)PPLS(0.007)T(0.007)NLHLES(0.001)ELDALASLENHVK 45.084 0.036665 39890000 12568 18161 18312 14404 25274 23246 22509 19522 20433 17219 TRUE FALSE 13064.19434 21280.01048 18789.22576 17253.06821 20977.93451 17847.4688 20744.68576 19260.33952 19697.62032 20592.73337 0.634407978 1.033374739 0.912420193 0.837823124 1.018705683 0.866687704 1.007378933 0.935297863 0.956532577 1 14.32984772 4.748557826 24.74291283 0.9467533 0.634407781 0.699625543 0.062348227 639.9622055 1583858.093 0.013812528 0.186888835 56047.70399 -4.748557826 -0.312345519 SACMLSS(ph)PESSLTPPLSTNLHLESELDALASLENHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 S(0.002)ACMLS(0.106)S(0.859)PES(0.015)S(0.015)LT(0.003)PPLSTNLHLESELDALASLENHVK 78.867 0.0035294 23828000 6446.9 8626.5 9763.2 9155.1 11209 9507.8 9872.1 9808.9 9960.7 6906.4 TRUE FALSE 6701.42859 10108.03427 10017.63701 10965.95145 9303.698184 7299.757542 9098.299006 9677.42774 9602.216353 8259.576849 0.811352532 1.223795656 1.212851118 1.327665043 1.126413417 0.883793162 1.101545415 1.171661444 1.162555483 1 13.01185216 2.995246414 24.99191158 1.077517242 1.163607383 0.053997032 0.14739603 637.2139841 3350166.931 0.044239056 0.051565871 989.1141488 -2.995246414 0.086090141 SACMLSSPESSLT(ph)PPLSTNLHLESELDALASLENHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SACMLSSPESSLTPPLSTNLHLESELDALASLENHVK 37 0 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 SACMLSSPES(0.01)S(0.015)LT(0.974)PPLS(0.001)TNLHLESELDALASLENHVK;SACMLSSPESSLT(1)PPLSTNLHLESELDALASLENHVK;SACMLSSPES(0.001)S(0.007)LT(0.977)PPLS(0.007)T(0.007)NLHLESELDALASLENHVK;SACMLSSPES(0.002)S(0.001)LT(0.996)PPLS(0.001)T(0.001)NLHLESELDALASLENHVK 233.36 2.36E-49 298428000 92228.9 111535.5 135221 118582 160788 169251 146233 141735 136985 110483.5 TRUE FALSE 95870.16819 130690.8545 138744.9703 142037.1657 133457.3132 129945.0203 134770.8754 139835.2742 132054.9366 132130.6265 0.725571132 0.98910342 1.050059127 1.074975344 1.010040721 0.983458746 1.019982111 1.058310839 0.999427159 1 17.01160538 4.735130596 3.529489125 1.027604149 0.690651115 0.912518765 0.027577966 0.075885316 1.676099063 0.007018001 0.067789647 54341.37155 -4.735130596 -0.336953034 SADEADELPPDLPKPPS(ph)PAPSSEDPGLAQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SADEADELPPDLPKPPSPAPSSEDPGLAQPR 31 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 SADEADELPPDLPKPPS(0.918)PAPS(0.041)S(0.041)EDPGLAQPR;SADEADELPPDLPKPPS(0.949)PAPS(0.025)S(0.025)EDPGLAQPR 93.737 0.00026684 165238000 475230 223953 269795 220025 361800 404210 366820 284965 314740 191637 TRUE FALSE 493992.4474 262415.1856 276826.0793 263545.2883 300301.3652 310338.3534 338067.6899 281145.5103 303412.5689 229184.601 2.155434724 1.14499484 1.207873819 1.149925811 1.310303414 1.354097753 1.475089026 1.22672077 1.323878513 1 17.80615059 4.743111059 24.94221008 1.261184937 2.155435095 0.824331648 0.126038512 179.3371743 982960.8577 0.029676415 0.238441247 55349.16311 -4.743111059 0.894250158 SADGVIVSGVKDVDDFFEHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SADGVIVSGVKDVDDFFEHER 21 1 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9;Q9UNH7-2 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 ;;;;; 210.74 1.13E-22 258465000 275994 271580 326060 184592 471189 400153 248138 307332 360178 357213 FALSE TRUE 286890.4562 318221.7524 334557.3915 221103.7466 391096.4621 307223.5301 228688.2952 303212.7172 347215.2641 427202.0481 0.671556837 0.744897535 0.783136207 0.517562469 0.915483584 0.719152756 0.535316477 0.709764194 0.812765916 1 18.70455904 0.943065496 2.884079223 0.999083874 0.698388578 0.423191196 0.108201648 0.281958472 5.582984719 0.100413691 0.026519289 8.771330918 -0.943065496 -0.300695296 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(ph)PHNIGTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGSPHNIGTSR 44 1 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(0.999)PHNIGTSR;SADLHPLSELPENRPCENGSTHSAGEFFTGPVQPGS(0.999)PHNIGT(0.001)S(0.001)R 196.9 6.23E-36 1056590000 78303 184174 151256 158555 176775 232542 161697 177803 136122 188202 TRUE FALSE 81394.4629 215804.4518 155197.8556 189916.7058 146726.8486 178537.6447 149022.7666 175419.8416 131222.9958 225076.5786 0.361630088 0.958804569 0.689533565 0.843787066 0.651897455 0.793230668 0.662098063 0.77937848 0.583014886 1 17.78005641 -2.191233468 2.466642388 1.835439887 0.718026976 0.246510148 0.15387303 16798432.09 4262763.438 78209621.09 0.032653966 0.006438231 2.191233468 -1.117412911 SADTLWDIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SADTLWDIQK 10 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 ;; 182.65 4.08E-06 266030000 863540 707320 903840 707400 1367180 1128890 930710 925010 959430 910510 FALSE TRUE 897633.226 828796.7078 927394.8129 847321.6086 1134787.232 866722.406 857758.5182 912611.754 924900.3017 1088907.002 0.824343332 0.761127173 0.851674947 0.778139554 1.042134204 0.795956316 0.787724312 0.838098894 0.849384107 1 20.05444932 SAEDWWWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEDWWWDR 9 0 Q8N531-2;Q8N531 Q8N531-2 FBXL6 F-box/LRR-repeat protein 6 0 108.98 0.0058716 47564000 48630 67899 67852 70284 65715 84577 62672 63255 54447 76866 FALSE TRUE 50549.94995 79560.12507 69620.27886 84185.96542 54544.78777 64935.27353 57759.60488 62407.17019 52487.46311 91926.42101 0.549895769 0.865476151 0.757347867 0.91579727 0.593352675 0.706383136 0.628324308 0.678881757 0.570972551 1 16.48819195 -1.048237363 4.645301676 1.000011292 0.7021484 0.382379574 0.115586556 1.32E-05 2.71E-06 0.109531333 0.025815805 0.089487554 1.048237363 -0.297862892 SAEFLLHMLK ddPTM_MDA-MB-175_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 ; 138.66 5.88E-05 257245000 574270 500470 562240 421310 1391910 905970 760880 539060 623320 1019890 FALSE TRUE 596942.623 586421.8294 576892.4363 504643.8605 1155313.635 695572.1976 701240.2374 531834.7824 600886.835 1219717.919 0.489410391 0.480784795 0.472972011 0.413738171 0.947197395 0.570273001 0.57492001 0.436030966 0.492644099 1 20.21811611 -2.175502895 2.312254321 2.168932904 0.540870422 0.476410289 0.144039514 8181799.738 1875460.069 50042512.56 0.038241057 0.006675705 2.175502895 -1.628062483 SAEHYTETALDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEHYTETALDEIR 14 0 H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3;D6RBM8 H3BLV9 SRPK1 SRSF protein kinase 1 0 120.53 0.00012423 75401000 20878 70471 63378 88022 59405 89025 56016 77208 65742 88722 FALSE TRUE 21702.27956 82573.84606 65029.68275 105432.4889 49307.35932 68350.29294 51625.31955 76173.15305 63375.95826 106105.3772 0.204535153 0.778224895 0.612878296 0.993658301 0.464701796 0.644173695 0.486547628 0.717900968 0.597292615 1 16.69513825 -4.366303098 0.566903023 9.259016871 0.623727558 0.255973498 0.197702456 3455.14429 26.15752816 36079.41335 0.076961884 4.30E-05 4.366303098 -8.635289313 SAEKEISLWFKPEELVDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAEKEISLWFKPEELVDYK 19 2 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 ; 184.26 1.42E-14 1212150000 534620 545070 602510 454910 740800 720970 343450 547880 659790 698210 FALSE TRUE 555727.2104 638681.5324 618211.9056 544889.8402 614879.0806 553535.6439 316529.4916 540536.5648 636044.2868 835010.8815 0.665532896 0.764878095 0.740363891 0.652554179 0.736372536 0.6629083 0.379072295 0.647340743 0.761719758 1 19.67143547 0.91023006 3.428579816 0.999562987 0.652444208 0.515122298 0.101277747 0.321457794 8.648366889 0.105031785 0.027185673 8.132612131 -0.91023006 -0.347118779 SAEPS(ph)PTVMSTSLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 S(0.001)AEPS(0.963)PT(0.036)VMSTSLGSNLSELDR;SAEPS(1)PTVMSTSLGSNLSELDR 233.31 2.17E-30 211945000 37526 37754 40585 41329 42842 47482 44936 44780 44574 34876 TRUE FALSE 39007.55546 44237.95581 41642.67844 49503.75285 35559.73214 36455.0251 41413.7989 44179.79735 42969.79045 41709.28446 0.935224758 1.060626103 0.998403089 1.186876099 0.852561548 0.874026624 0.992915593 1.059231725 1.030221233 1 15.34808094 -1.916419128 8.250448018 0.999544669 1.002227958 0 0.092176313 0.000941172 9.53E-06 0.108804934 0.021278316 0.012122184 1.916419128 0.002683289 SAEPSPTVMST(ph)SLGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.284)T(0.453)S(0.263)LGSNLSELDR 280.01 1.45E-44 388190000 294850 357750 410790 435200 530400 565930 477310 487270 457300 521240 TRUE FALSE 306490.9057 419190.7796 421495.5249 521281.2611 440242.7975 434501.3343 439897.195 480738.9427 440841.8623 623366.9983 0.491670086 0.672462259 0.676159511 0.836234935 0.706233725 0.697023319 0.705679313 0.771197295 0.70719474 1 19.24972225 -5 0.104319719 1.899158195 0.522058156 0.642318201 0.073619559 120.0050021 0.844068671 23.59209682 1.105778708 1.00E-05 5 -1.37710004 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SAEPSPTVMSTSLGSNLSELDR 22 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 SAEPSPTVMS(0.249)T(0.139)S(0.612)LGSNLSELDR;SAEPSPTVMS(0.225)T(0.18)S(0.576)LGS(0.019)NLSELDR;SAEPSPTVMS(0.029)T(0.026)S(0.944)LGSNLSELDR;SAEPSPTVMS(0.023)T(0.023)S(0.955)LGSNLSELDR;SAEPSPTVMS(0.01)T(0.004)S(0.986)LGSNLSELDR 283.83 7.82E-46 952661000 1203356 1007560 1171330 1196910 1469610 1800890 1344020 1397160 1285270 1372800 TRUE FALSE 1250865.424 1180600.592 1201855.822 1433655.226 1219806.217 1382660.59 1238672.2 1378433.355 1239013.384 1641773.876 0.761898726 0.719100608 0.73204711 0.873235496 0.742980647 0.842174803 0.754471866 0.839600006 0.75467968 1 20.64682401 -5 0.20808851 2.024025316 0.750871696 0.639100597 0.049779413 87.26468101 0.869011628 37.29565253 0.102791658 1.00E-05 5 -1.27315362 SAEVGPSS(ph)EPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 S(0.002)AEVGPS(0.209)S(0.78)EPEVQT(0.007)LPY(0.002)LPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 70.408 0.00019794 349590000 16684 14096 18284 14221 19001 29879 17892 18293 21247 18150 TRUE FALSE 17342.6972 16516.87835 18760.49606 17033.87135 15771.21681 22940.05507 16489.57829 18047.81226 20482.32462 21706.145 0.798976382 0.760930988 0.864294238 0.784748805 0.726578432 1.056846118 0.759673276 0.831460965 0.943618714 1 14.40581591 -5 0.096990909 1.582275788 0.701764344 0.320972557 0.087483411 235.0796232 1.562502544 27.39299983 1.579265652 1.00E-05 5 -0.880511444 SAEVGPSSEPEVQTLPY(ph)LPHYIPGVDPETSHGGHPHGNMPGLDRPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPS(0.002)S(0.002)EPEVQT(0.255)LPY(0.586)LPHY(0.035)IPGVDPET(0.04)S(0.04)HGGHPHGNMPGLDRPLS(0.04)R 40.602 0.022236 625540000 31768 41055 46371 27880 54645 53998 40285 44416 41351 46088 TRUE FALSE 33022.22517 48105.87689 47579.46635 33394.58079 45356.46242 41457.78285 37127.35643 43820.67617 39862.78559 55118.06119 0.599118047 0.872778829 0.863228229 0.605873648 0.82289655 0.752163301 0.673596923 0.795032975 0.723225468 1 15.75023752 -2.145698487 2.127589813 1.508277866 0.751073886 0.404682339 0.092430883 5697250.609 1311691.515 13962594.01 0.021622731 0.007149925 2.145698487 -0.75720398 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAEVGPSSEPEVQTLPYLPHYIPGVDPETSHGGHPHGNMPGLDRPLSR 48 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.146)S(0.146)HGGHPHGNMPGLDRPLS(0.708)R;SAEVGPSSEPEVQTLPYLPHYIPGVDPET(0.006)S(0.006)HGGHPHGNMPGLDRPLS(0.988)R 124 6.47E-11 244581000 0 9276 13734.4 11666 8578.7 12331.4 5304.1 13415 4996.6 14719 TRUE FALSE 0 10869.08084 14092.32975 13973.49998 7120.495638 9467.619234 4888.350782 13235.19387 4816.773342 17602.90624 0 0.617459452 0.800568358 0.793817782 0.404506821 0.537844098 0.277701348 0.751875497 0.273635119 1 14.10352602 -1.244873996 4.247110193 1.000272691 0.522851742 0.263483426 0.249351858 203.4932834 136443094.8 70260.61322 0.056417243 0.0569018 1.244873996 -0.47742095 SAFS(ph)PYQTPVAHFPPPPEEPTATAAFGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SAFSPYQTPVAHFPPPPEEPTATAAFGAR 29 0 A0A0A0MQV9;Q9UPS6-2;Q9UPS6 A0A0A0MQV9 SETD1B Histone-lysine N-methyltransferase;Histone-lysine N-methyltransferase SETD1B 1 S(0.086)AFS(0.89)PY(0.004)QT(0.02)PVAHFPPPPEEPTATAAFGAR;S(0.237)AFS(0.761)PYQT(0.002)PVAHFPPPPEEPTATAAFGAR;S(0.054)AFS(0.946)PYQTPVAHFPPPPEEPTATAAFGAR 139.73 5.74E-08 281909000 66284 72671 68211 66878 74057 83264 72761 68578 61481 66847 TRUE FALSE 68900.9435 85151.67895 69988.6347 80106.26879 61468.81759 63927.19788 67057.80269 67658.82408 59268.31082 79944.38979 0.861860897 1.065136393 0.875466495 1.002024895 0.7688947 0.799645829 0.838805611 0.846323604 0.741369232 1 16.28670917 3.240819821 24.99999943 0.825399097 0.953862071 0.319131424 0.084458146 61.93227003 685324.6921 0.021771252 0.028118908 1741.084386 -3.240819821 0.128462974 SAFS(ph)SLQNIPESLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAFSSLQNIPESLRR 15 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.021)AFS(0.49)S(0.49)LQNIPESLRR;S(0.002)AFS(0.499)S(0.499)LQNIPESLRR 91.622 0.0034038 369870000 74275 74052 80774 77073 103686 88595 78072 68119 73464 87377 TRUE FALSE 77207.43435 86769.85496 82879.0368 92317.80936 86061.49076 68020.15392 71952.51264 67205.97623 70820.04499 104496.8502 0.738849393 0.830358568 0.793124737 0.883450642 0.823579759 0.650930184 0.688561545 0.643138775 0.677724207 1 16.67309993 2.753061515 23.96700797 0.701208523 0.817501305 0.099903267 0.10354696 654.442015 1081656.439 0.029403774 0.031043426 566.3194987 -2.753061515 0.116292782 SAFSS(ph)LQNIPESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SAFSSLQNIPESLR 14 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.002)AFS(0.06)S(0.939)LQNIPESLR;SAFS(0.067)S(0.933)LQNIPESLR;SAFS(0.014)S(0.986)LQNIPESLR;SAFS(0.056)S(0.944)LQNIPESLR 209.93 6.24E-09 250621000 526669 580923 607229 578270 705440 790420 589715 570525 580129 568272 TRUE FALSE 547462.2988 680692.0063 623053.8866 692650.08 585529.5608 606856.9339 543491.5974 562878.0456 559250.2706 679614.0182 0.805548862 1.001586177 0.916776096 1.019181567 0.861561924 0.89294352 0.799706279 0.828231953 0.82289396 1 19.37435609 3.040453221 23.42842702 0.852798567 0.93927423 0.149518398 0.07500205 109.9878177 63698.01288 0.020435886 0.024425503 1097.623056 -3.040453221 0.086475664 SAGGRPGS(ph)GPQLGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 1 SAGGRPGS(1)GPQLGTGR;S(0.003)AGGRPGS(0.997)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR;SAGGRPGS(1)GPQLGTGR 208.89 8.28E-12 3426260000 659820 802045 889794 818621 906330 1122180 842730 934001 877016 888564 TRUE FALSE 685870.2031 939789.9897 912982.7626 980541.7905 752272.3503 861570.7018 776674.6205 921482.2443 845452.3655 1062661.103 0.645427033 0.884374131 0.859147625 0.922722952 0.707913697 0.810767138 0.730877058 0.867145924 0.795599239 1 20.01925014 -0.291287527 0.956214269 1.00444928 0.807274996 0.33901721 0.08229334 18.84388973 12.23070091 0.407962603 0.024433935 0.511343186 0.291287527 -0.197174283 SAGGRPGSGPQLGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAGGRPGSGPQLGTGR 16 1 O14908;O14908-2;K7EM11;K7ESN1 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 ; 189.45 9.27E-10 192250000 95944 90566 103837 100168 114164 133046 92587 102264 89361 100087 FALSE TRUE 99731.9432 106120.006 106543.0775 119980.9314 94758.44406 102148.0828 85329.78901 100893.3184 86144.91507 119697.1314 0.833202451 0.886571005 0.890105521 1.002370985 0.791651755 0.853387894 0.712880819 0.842905065 0.719690723 1 16.86902905 3.184625981 24.99999658 0.808705353 0.90096033 0.178567805 0.085062783 133.5858964 61919.6116 0.022920347 0.027395077 1529.76944 -3.184625981 0.092254977 SAGGSS(ph)PEGGEDS(ph)DREDGNYCPPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 2 S(0.001)AGGS(0.341)S(0.658)PEGGEDS(1)DREDGNYCPPVKR;S(0.006)AGGS(0.152)S(0.842)PEGGEDS(0.998)DREDGNY(0.002)CPPVKR;SAGGS(0.072)S(0.928)PEGGEDS(1)DREDGNYCPPVKR 249.46 4.60E-46 1655380000 1815750 1435900 1692550 1272730 2200480 2053160 1765520 1713050 1803460 1319110 TRUE FALSE 1887437.212 1682504.655 1736659.243 1524472.195 1826443.196 1576344.706 1627133.929 1690089.367 1738553.827 1577564.349 1.196424865 1.06652046 1.100848434 0.966345491 1.157761455 0.999226882 1.03142159 1.071328322 1.102049389 1 20.58926742 5.358700042 1.386655038 1.053514764 1.648165403 0.380214778 0.054436841 6.186547953 3.116989455 0.013611411 7.855552668 228402.0732 -5.358700042 0.59465064 SAGGSSPEGGEDS(ph)DREDGNYCPPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SAGGSSPEGGEDSDREDGNYCPPVKR 26 2 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7EID7;K7ENB9 Q9H6Z4 RANBP3 Ran-binding protein 3 1 SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGS(0.031)S(0.267)PEGGEDS(0.702)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR;SAGGSSPEGGEDS(1)DREDGNYCPPVKR 353.13 2.67E-110 6565230000 2033341 1720401 1907584 1630032 2450370 2494130 1995275 1988777 2119385 1637775 TRUE FALSE 2113618.873 2015866.489 1957297.206 1952447.464 2033856.983 1914906.106 1838880.132 1962120.697 2043108.748 1958665.654 1.079111623 1.029203981 0.999301337 0.996825293 1.038389058 0.97765849 0.938843303 1.001763978 1.043112562 1 20.90143972 5.792008679 0.861302582 0.994804927 1.493058656 0.433091085 0.027777975 11.31044993 1.643454665 0.009401149 8.145529117 619453.4541 -5.792008679 0.498253728 SAGVEQLMYIKEDLIIPHHHSFYDFIVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAGVEQLMYIKEDLIIPHHHSFYDFIVTK 29 1 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 71.528 0.0024879 176670000 18326 96020 94687 68311 122040 141670 61831 123370 100880 129780 FALSE TRUE 19049.52463 112510.6881 97154.62101 81822.71191 101295.6844 108769.2895 56984.52465 121716.4269 97249.34851 155207.9062 0.12273553 0.724903072 0.625964381 0.52718134 0.652645132 0.700797351 0.367149626 0.784215379 0.626574708 1 17.24384252 -5 0.091926118 2.301003946 0.260854977 0.419795145 0.171918283 210.5060831 1.340189008 53.85843379 3.585065842 1.00E-05 5 -2.040148969 SAHAGTYEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAHAGTYEVR 10 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 ; 162.36 6.79E-06 335470000 41778 130533 96869 150064 103614 159977 89167 80718 90158 142154 FALSE TRUE 43427.4277 152951.0273 99393.48572 179746.2113 86001.72929 122824.7662 82177.85755 79636.10724 86913.23119 170006.3546 0.255445908 0.899678296 0.584645709 1.057291133 0.505873616 0.722471619 0.483381093 0.46843018 0.511235191 1 17.37522915 SAIRHS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAIRHSPSK 9 1 O94964-2;H0YDM2;O94964 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 SAIRHS(0.99)PS(0.01)K;S(0.002)AIRHS(0.968)PS(0.031)K 64.64 0.041676 120854000 169547 168426 184898 133524 295810 263960 205274 187573 194489 180886 TRUE FALSE 176240.8465 197351.8553 189716.5938 159934.6487 245528.3219 202659.2904 189184.0875 185058.8907 187489.3789 216327.1484 0.814695926 0.912284273 0.876989297 0.739318434 1.134986171 0.936818572 0.874527718 0.855458467 0.86669371 1 17.72285521 6.460616233 0.679638078 0.911033073 1.56E-14 0.08166408 0.097764333 88.54901336 4.622292788 0.037793327 102.8587675 2888126.647 -6.460616233 -0.911033073 SAKGEEVDVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAKGEEVDVAR 11 1 O94760 O94760 DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1" 0 73.219 0.040273 202090000 410310 569500 587120 428410 745560 748160 492990 583520 658070 636660 FALSE TRUE 426509.3556 667307.1949 602420.8295 513148.2193 618829.9775 574411.1785 454348.1556 575698.8688 634386.1892 761401.3374 0.560163654 0.876419783 0.79120012 0.673952348 0.812751367 0.754413146 0.596726238 0.756104357 0.833182394 1 19.53829758 0.941405889 2.518126689 0.99894018 0.731005082 0.461730736 0.09104801 0.28807361 4.142917544 0.083193416 0.022382627 8.737876239 -0.941405889 -0.267935098 SAKSEES(ph)LTSLHAVDGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.203)AKS(0.137)EES(0.303)LT(0.303)S(0.055)LHAVDGDSK 172.02 5.54E-12 87056000 130070 110920 142260 98324 206410 209130 169990 146300 157440 105020 TRUE FALSE 135205.264 129969.6472 145967.4125 117772.1937 171324.5019 160562.7269 156665.7396 144339.0878 151773.7652 125596.6583 1.076503674 1.034817717 1.162191849 0.93770165 1.364084875 1.278399673 1.247371879 1.149227135 1.208422001 1 16.93843855 3.244326411 24.99986709 1.216592818 1.059332471 0.353850805 0.102131639 152.1336193 659630.9602 0.027561434 0.03632739 1755.199194 -3.244326411 -0.157260347 SAKSEESLT(ph)SLHAVDGDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAKSEESLTSLHAVDGDSK 19 1 A7KAX9;A7KAX9-2;G3V174 A7KAX9 ARHGAP32 Rho GTPase-activating protein 32 1 S(0.022)AKS(0.015)EES(0.033)LT(0.922)S(0.009)LHAVDGDSK 183.09 4.50E-14 356540000 119940 91567 124670 96876 176580 179240 160830 134590 151070 69710 TRUE FALSE 124675.3238 107292.92 127919.0026 116037.7837 146564.9947 137614.2264 148223.7243 132786.0412 145633.0202 83368.33982 1.49547567 1.28697441 1.534383471 1.391868711 1.758041422 1.650677304 1.77793782 1.59276341 1.746862424 1 16.34721199 3.255835948 24.84683356 1.630833632 1.424818844 0.094046429 0.220943882 380.6685094 547505.8622 0.055534846 0.075016959 1802.336793 -3.255835948 -0.206014788 SALSGHLETVILGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SALSGHLETVILGLLK 16 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YNP5;H0YKS4;H0YMM1;H0YMW4;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 ;; 115.82 0.00047616 460903700 340280 623823 678003 696925 741570 872811 793031 710484 644015 656184 FALSE TRUE 353714.5172 730959.7476 695672.3152 834774.6849 615518.1963 670113.8728 730871.158 700961.1241 620837.026 784750.6914 0.450734891 0.931454735 0.886488311 1.063745077 0.784348715 0.853919442 0.931341847 0.893227788 0.791126447 1 19.58187487 4.74093539 24.99380269 0.900751207 0.450734733 0.735893325 0.081434759 105.2381515 1107533.019 0.018568786 0.124931181 55072.5759 -4.74093539 -0.450016474 SALSPSKS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SALSPSKSPAK 11 1 P49792;Q7Z3J3 P49792 RANBP2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 4 1 SALSPSKS(1)PAK;SALSPS(0.003)KS(0.997)PAK;SALS(0.002)PS(0.047)KS(0.951)PAK 155.37 1.91E-05 1065010000 1983380 854790 1251720 834050 2012330 2068410 1847860 1323200 1421890 655370 TRUE FALSE 2061685.374 1001593.533 1284340.851 999022.6006 1670274.865 1588053.125 1703019.905 1305464.668 1370716.457 783777.2037 2.63044825 1.277905926 1.638655533 1.274625743 2.131058236 2.026153755 2.172836741 1.665606836 1.748859817 1 19.58008409 3.212544082 24.99546945 1.849225801 1.670104027 0 0.470521388 934.421996 897746.5502 0.129820994 0.155213847 1631.338486 -3.212544082 -0.179121774 SALSS(ph)SLRDLSEAGVHH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALS(0.001)S(0.813)S(0.187)LRDLSEAGVHH;SALS(0.008)S(0.765)S(0.227)LRDLSEAGVHH 257.22 2.43E-27 1725340000 348920 484060 508250 465290 549350 557140 406160 495690 442050 543720 TRUE FALSE 362695.631 567193.5395 521495.4125 557322.9732 455971.6832 427752.6785 374324.1179 489046.0863 426140.7068 650251.5239 0.557777441 0.872267913 0.801990297 0.8570883 0.701223552 0.657826492 0.575660501 0.752087567 0.655347494 1 19.31063835 -1.110268964 4.291225554 1.000042538 0.720219858 0.409518666 0.102616129 31545253378 6540571631 13828965.1 0.024283626 0.077576653 1.110268964 -0.27982268 SALSSS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SALSSSLR 8 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SALSS(0.007)S(0.993)LR;SALSS(0.002)S(0.998)LR;SALSS(0.011)S(0.989)LR;SALSS(0.002)S(0.998)LR;SALSS(0.003)S(0.996)LR;SALS(0.022)S(0.105)S(0.873)LR 134.23 0.00092897 1932000000 4270370 4284640 4485560 5436650 4744120 5528180 5440840 4694430 4231710 3525180 TRUE FALSE 4438967.505 5020493.59 4602457.379 6512003.143 3937716.177 4244343.975 5014372.744 4631508.844 4079411.584 4215871.527 1.052918116 1.190855451 1.091697731 1.544639845 0.934021863 1.006753633 1.189403593 1.098588706 0.967631854 1 22.00739947 SALSSS(ph)LRDLSEAGVHH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SALSSSLRDLSEAGVHH 17 1 A0A0C4DGT3 A0A0C4DGT3 IQSEC1 1 SALSS(0.206)S(0.794)LRDLSEAGVHH;SALS(0.008)S(0.461)S(0.532)LRDLSEAGVHH;SALS(0.001)S(0.191)S(0.808)LRDLSEAGVHH;SALS(0.001)S(0.387)S(0.612)LRDLSEAGVHH 228.85 7.84E-16 3009360000 715840 1169800 1153570 1073030 1240240 1412440 907520 1119600 984070 1315060 TRUE FALSE 744101.9159 1370704.05 1183632.982 1285272.131 1029424.448 1084422.216 836386.211 1104593.593 948653.5129 1572720.829 0.473130324 0.871549499 0.75260209 0.817228403 0.654550019 0.689519841 0.53180844 0.702345625 0.603192566 1 20.58483117 -0.972812133 4.453262123 1.000007751 0.684077972 0.412216403 0.115339826 14160907.06 3179894.803 1159.119539 0.026122207 0.106460344 0.972812133 -0.315929779 SALVQIYELEEHKIETWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SALVQIYELEEHKIETWR 18 1 F8VZX1;H0YIC9;F8VYY9;P54619-2;P54619;P54619-3;F8VSL2;F8VPF5;F8VVA3 F8VZX1 PRKAG1 5-AMP-activated protein kinase subunit gamma-1 0 91.589 0.0014974 80891000 113350 87899 124550 102700 103150 128320 146280 118690 120320 57889 FALSE TRUE 117825.1455 102994.9695 127795.8753 123013.7535 85616.59984 98519.62471 134814.1914 117099.1547 115989.7067 69231.2412 1.701907166 1.487694973 1.845927837 1.776853215 1.236675789 1.423051544 1.947302822 1.691420703 1.675395453 1 16.07913559 -1.852638204 2.420277649 0.715564024 1.646622171 0.484118319 0.199068001 16728423.96 9853228.62 27467820.9 0.049820534 0.014039828 1.852638204 0.931058146 SALWDSGLDYLHGTGHGVGSFLNVHEGPCGISYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SALWDSGLDYLHGTGHGVGSFLNVHEGPCGISYK 34 0 Q9NQW7-4;Q9NQW7-3;Q5T6H7;Q9NQW7-2;Q9NQW7 Q9NQW7-4 XPNPEP1 Xaa-Pro aminopeptidase 1 0 ; 221.72 9.66E-37 580180000 98270 170854 194035 177949 201854 264753 170190 195566 196920 169187 FALSE TRUE 102149.7755 200196.8454 199091.7115 213146.7811 167542.9292 203268.1281 156850.0631 192944.7577 189832.8877 202335.9534 0.50485232 0.98942794 0.983966063 1.053430088 0.828043293 1.004607064 0.775196205 0.953586125 0.938206406 1 17.62639317 4.742439275 24.93063611 0.941064583 0.504852145 0.730874356 0.080478374 187.5973548 1205759.225 0.018600827 0.14147862 55263.61301 -4.742439275 -0.436212437 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.693)S(0.307)PGAAR;SAMDSPVPASMFAPEPS(0.644)S(0.356)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR;SAMDSPVPASMFAPEPS(0.5)S(0.5)PGAAR 235.37 4.52E-37 930094000 628328 717924 673464 639901 791595 845980 682003 696773 690200 729738 TRUE FALSE 653134.8746 841221.8623 691015.0251 766471.5079 657039.9647 649513.966 628545.8228 687433.8976 665359.8368 872716.1894 0.748393215 0.963912292 0.791798105 0.878259756 0.752867854 0.744244204 0.720217902 0.787694678 0.762401162 1 19.73515303 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 SAMDSPVPASMFAPEPS(0.036)S(0.964)PGAAR;SAMDSPVPASMFAPEPS(0.001)S(0.999)PGAAR;SAMDSPVPASMFAPEPS(0.014)S(0.986)PGAAR;SAMDSPVPASMFAPEPS(0.007)S(0.993)PGAAR;SAMDSPVPASMFAPEPS(0.044)S(0.956)PGAAR;SAMDSPVPASMFAPEPS(0.097)S(0.903)PGAAR;SAMDSPVPASMFAPEPS(0.124)S(0.876)PGAAR;SAMDSPVPASMFAPEPS(0.056)S(0.944)PGAAR;SAMDSPVPASMFAPEPS(0.008)S(0.992)PGAAR;SAMDSPVPASMFAPEPS(0.016)S(0.984)PGAAR;SAMDSPVPASMFAPEPS(0.211)S(0.789)PGAAR 351.02 1.30E-101 4898955000 2321314 2796356 2714598 2692168 2860661 3307077 2725196 2792053 2748550 2781477 TRUE FALSE 2412961.269 3276608.39 2785342.654 3224670.795 2374406.865 2539058.486 2511588.017 2754630.096 2649630.222 3326454.164 0.725385396 0.985015343 0.837330838 0.969401842 0.713795155 0.763292792 0.755034608 0.828098017 0.796532912 1 21.66555372 5.033891488 15.84937468 0.837292764 0.339901053 0.11648206 0.097461984 6620387.518 87726178.57 0.022773921 90497504.88 108116.378 -5.033891488 -0.497391711 SAMPFTAS(ph)PASSTTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 SAMPFT(0.003)AS(0.826)PAS(0.07)S(0.07)T(0.016)T(0.016)AR;SAMPFT(0.003)AS(0.997)PASSTTAR 225.37 7.28E-15 465230000 319510 355160 324640 346830 376500 439850 393720 375570 378560 455830 TRUE FALSE 332124.5015 416155.9672 333100.3851 415431.9388 312502.6645 337701.5035 362859.1976 370536.0985 364935.6995 545141.1611 0.609244954 0.763391204 0.611035102 0.762063055 0.573250906 0.619475335 0.665624289 0.679706698 0.669433397 1 19.05627033 -0.257037972 1.048627562 1.005027335 0.661307083 0.743582771 0.05967516 8.758754097 6.573318198 0.245008781 0.016699091 0.55330173 0.257037972 -0.343720252 SANMDHWQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SANMDHWQQR 10 0 Q9NZL9;Q9NZL9-2;Q9NZL9-3;Q9NZL9-4;H7C0X7 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 0 ; 159.94 7.53E-06 479940000 204956 325010 304900 278710 387570 430660 321740 333770 317300 371290 FALSE TRUE 213047.8211 380827.9393 312845.9445 333838.0061 321690.9898 330645.7417 296521.1781 329296.3591 305880.435 444037.1667 0.479797272 0.857648791 0.704549006 0.751824467 0.724468612 0.744635284 0.667784592 0.741596388 0.688862235 1 18.76032091 -1.477593597 2.965441856 1.008032786 0.714508165 0.484808766 0.090361256 19342123.31 22428750.97 1281901.73 0.019043625 0.033297099 1.477593597 -0.293524621 SANPTRPSS(ph)PVTSHISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SANPTRPSSPVTSHISK 17 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 SANPTRPS(0.227)S(0.718)PVT(0.022)S(0.033)HISK;SANPTRPS(0.046)S(0.908)PVT(0.046)SHISK 186.88 3.02E-10 734170000 188388 497360 572660 492720 660970 742120 584450 653550 633560 521630 TRUE FALSE 195825.7037 582777.7111 587583.99 590178.5454 548618.5555 569773.8769 538639.2818 644790.2312 610758.2994 623833.4113 0.313907047 0.934188039 0.941892466 0.946051517 0.879431184 0.913342996 0.863434488 1.033593616 0.979040699 1 19.2508013 4.738598493 7.119361445 0.942659619 0.305246873 0.936901004 0.049016869 0.024445772 10.04141297 0.012356065 0.075010902 54777.03151 -4.738598493 -0.637412746 SANTS(ph)PESSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SANTSPESSSR 11 0 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 SANT(0.045)S(0.955)PESSSR;SANT(0.043)S(0.957)PESSSR;SANT(0.012)S(0.988)PESSSR;SANT(0.001)S(0.999)PESSSR;SANT(0.006)S(0.994)PESSSR;SANT(0.048)S(0.952)PESSSR 172.3 1.42E-05 1233978000 1312075 1478349 1474810 1523980 1577288 1888400 1685400 1590801 1533644 1330748 TRUE FALSE 1363876.734 1732243.941 1513244.76 1825418.695 1309181.149 1449847.719 1553293.944 1569478.915 1478448.452 1591482.592 0.856985016 1.088446678 0.950839656 1.146992562 0.822617323 0.911004447 0.976004357 0.986174101 0.928975573 1 20.60193995 4.809135067 21.3884216 0.976295858 0.856975243 0.154194181 0.085523104 46589.54503 14115038.58 0.019775471 83.8852865 64436.96351 -4.809135067 -0.119320615 SAPAS(ph)PTHPGLMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.073)APAS(0.893)PT(0.034)HPGLMS(1)PR 67.43 0.052342 164170000 71036 105520 105520 104920 105640 131340 100030 108940 117140 117180 TRUE FALSE 73840.55613 123642.2392 108269.9379 125672.8628 87683.35053 100838.2755 92189.38722 107479.8375 112924.1543 140139.1775 0.526908731 0.882281753 0.77258865 0.896771803 0.625687635 0.719558066 0.657841646 0.76695068 0.805800036 1 17.09650081 0.809104495 1.954995338 0.999554348 0.735860094 0.372834711 0.105571916 0.729215848 4.935738583 0.096106319 0.026724419 6.443242762 -0.809104495 -0.263694254 SAPAS(ph)PTHPGLMSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SAPASPTHPGLMSPR 15 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 S(0.006)APAS(0.984)PT(0.01)HPGLMSPR;SAPAS(0.992)PT(0.008)HPGLMSPR;S(0.008)APAS(0.976)PT(0.016)HPGLMSPR;S(0.006)APAS(0.972)PT(0.023)HPGLMSPR;S(0.001)APAS(0.977)PT(0.022)HPGLMSPR;SAPAS(0.859)PT(0.141)HPGLMSPR;SAPAS(0.962)PT(0.038)HPGLMSPR;SAPAS(0.925)PT(0.075)HPGLMSPR 226.39 9.14E-13 3243037000 1266443 1604122 1716967 1707569 1914753 2348410 1984172 1900154 1903494 1909847 TRUE FALSE 1316443.148 1879617.475 1761712.571 2045321.052 1589283.969 1803027.368 1828647.414 1874685.544 1834987.623 2284044.953 0.576364815 0.822933661 0.771312565 0.89548196 0.695819917 0.789400999 0.800617961 0.820774364 0.80339383 1 21.12315961 -5 0.125716116 1.71390333 0.683648742 0.490344185 0.075495111 129.8037959 1.042455986 23.50627445 0.605623812 1.00E-05 5 -1.030254588 HTTSIFDDFSHYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 HTTSIFDDFSHYEK 14 0 Q9Y5A9;Q9Y5A9-2 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 0 147.68 4.61E-06 92648000 21854 41323 45824 46147 56881 69996 51094 51961 51129 48590 FALSE TRUE 22716.81279 48419.9038 47018.21108 55274.73886 47212.38794 53740.4898 47089.11877 51264.54779 49288.87728 58110.28019 0.390925886 0.833241617 0.809120364 0.951204136 0.812461888 0.924801767 0.810340591 0.882194125 0.848195485 1 15.82650579 4.784299155 2.903963122 0.87339303 0.274962879 0.849019548 0.061365622 0.163619237 1.764026186 0.013428385 0.241188145 60855.40476 -4.784299155 -0.598430151 down SAPGTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAPGTSPR 8 0 Q03111 Q03111 MLLT1 Protein ENL 1 SAPGT(0.028)S(0.972)PR;SAPGT(0.028)S(0.972)PR 117.53 0.002163 1633730000 2109520 2540400 2406750 2241510 2520770 2851250 2336610 2532710 2347570 2501410 TRUE FALSE 2192805.479 2976693.938 2469471.882 2684873.988 2092290.416 2189090.399 2153460.403 2498763.165 2263081.414 2991513.397 0.733008744 0.995046167 0.825492503 0.897496896 0.699408673 0.731766871 0.719856513 0.835283963 0.756500511 1 21.51244409 SAPS(ph)SPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPSSPAPR 9 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 1 SAPS(0.807)S(0.193)PAPR 106.2 0.0031202 445000000 470840 578260 549950 610410 604880 745220 571760 571550 574690 607240 TRUE FALSE 489429.1268 677571.6568 564282.1488 731147.2761 502062.7137 572153.9489 526943.9572 563889.3071 554007.0192 726217.0517 0.673943314 0.93301535 0.777015835 1.006788913 0.691339748 0.787855294 0.72560119 0.776474892 0.762866994 1 19.47004128 SAPSS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAPSSPAPR 9 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 1 SAPS(0.176)S(0.824)PAPR 92.445 0.010564 342010000 423470 535040 522090 571500 573420 730720 562390 530260 512730 564660 TRUE FALSE 440188.9226 626928.958 535696.0943 684540.9942 475950.2732 561021.3542 518308.4023 523152.732 494276.9475 675294.3159 0.651847516 0.928378846 0.793277955 1.013692812 0.704804205 0.830780507 0.767529639 0.774703296 0.731943 1 19.36515689 SAPTAPT(ph)PPPPPPPATPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAPTAPTPPPPPPPATPR 18 0 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 SAPTAPT(1)PPPPPPPATPR;SAPTAPT(1)PPPPPPPATPR 114.52 0.002412 415280000 247510 340120 328730 348480 347130 407020 299610 320910 291280 309120 TRUE FALSE 257281.8859 398532.9642 337296.9739 417408.3039 288124.9666 312495.7734 276125.7853 316608.7264 280796.8897 369686.1455 0.695946789 1.078030565 0.91238738 1.129088306 0.779377237 0.845300202 0.746919485 0.856425728 0.759554809 1 18.49594145 3.183454383 24.99996792 0.8213397 0.959773477 0.181538554 0.126231432 125.2167308 56806.28126 0.033759507 0.040350359 1525.648137 -3.183454383 0.138433777 SAQGSSS(ph)PVPSMVQK ddPTM_MDA-MB-175_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(0.031)S(0.969)PVPSMVQK;SAQGSS(0.041)S(0.959)PVPSMVQK 275.04 1.78E-33 515800000 1254510 993730 1196000 1006910 1415610 1497350 1458760 1242550 1334200 889700 TRUE FALSE 1304039.023 1164395.397 1227168.743 1206073.793 1174985.118 1149613.155 1344418.579 1225895.65 1286182.403 1064019.681 1.225577917 1.094336335 1.153332748 1.133507034 1.104288895 1.080443507 1.263527925 1.152136255 1.208795689 1 20.02109341 SAQSLEYCAELLGLDQDDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 252.82 1.01E-35 95251000 91728 105364 107141 102643 117116 127799 113965 113991 114532 103103 FALSE TRUE 95349.49227 123459.4474 109933.1825 122945.479 97208.66415 98119.61906 105032.1255 112463.1371 110410.0157 123304.0588 0.77328754 1.001260206 0.89156175 0.997091906 0.788365485 0.79575336 0.851814016 0.912079766 0.895428883 1 16.91186076 -1.549558757 7.915802336 1.000032084 0.881996719 0.186186135 0.075882139 4.22E-05 2.40E-06 0.072100372 0.016989607 0.028212479 1.549558757 -0.118035365 SAS(ph)APTLAETEKETAEHLDLAGASSRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASAPTLAETEKETAEHLDLAGASSRPK 28 2 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.123)AS(0.877)APTLAETEKETAEHLDLAGASSRPK 238.65 1.57E-45 122860000 187400 99944 142080 91508 185470 165670 160930 135370 157830 72912 TRUE FALSE 194798.6967 117108.6045 145782.7215 109608.0093 153943.8756 127195.6533 148315.8861 133555.5866 152149.7291 87197.71042 2.233988665 1.343023848 1.671864099 1.257005588 1.765457773 1.458704049 1.700914914 1.531640979 1.744882158 1 16.41200263 -1.980298583 2.69370607 0.459222827 1.611082678 0.348299652 0.258508492 24564246.15 7461202.702 82560382.03 0.055718235 0.010464089 1.980298583 1.151859852 SAS(ph)ASPLTPCSVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASASPLTPCSVTR 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 SAS(0.996)AS(0.004)PLTPCSVTR;SAS(0.985)AS(0.015)PLTPCSVTR;SAS(0.992)AS(0.008)PLTPCSVTR;SAS(0.843)AS(0.157)PLTPCSVTR 253.83 3.23E-24 465471000 400556 413337 432675 368347 503112 468579 398398 416263 411790 393084 TRUE FALSE 416370.2602 484324.4144 443950.8659 441204.9372 417593.2019 359758.6286 367170.5237 410683.6754 396969.7583 470101.2838 0.885703304 1.03025546 0.944372801 0.938531658 0.888304747 0.765278975 0.781045567 0.873606794 0.844434534 1 18.84261209 3.147902316 3.109029993 0.840674861 0.957001021 0.296543961 0.068452545 0.256320762 4.968712855 0.01982289 0.024807576 1405.731302 -3.147902316 0.11632616 SAS(ph)DNTLVAMDFSGHAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASDNTLVAMDFSGHAGR 18 0 Q14451;Q14451-3;Q14451-4;Q14451-2 Q14451 GRB7 Growth factor receptor-bound protein 7 1 S(0.141)AS(0.859)DNTLVAMDFSGHAGR 263.83 4.10E-31 417900000 70522 114300 128010 102710 128540 152390 106100 126100 110580 118660 TRUE FALSE 73306.26301 133930.1359 131346.0458 123025.7314 106690.8167 116999.732 97783.60476 124409.8358 106600.2474 141909.1551 0.516571767 0.943773753 0.925564285 0.866933013 0.751824762 0.824469231 0.689057761 0.876686466 0.751186541 1 17.11460814 -1.403982442 2.991277998 1.003208224 0.804890849 0.203298136 0.120616356 23662459.51 28941975.68 651865.314 0.02738043 0.039447325 1.403982442 -0.198317375 SAS(ph)EPSLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SASEPSLHR 9 0 Q96II5;P10398;P04049;P04049-2;H7C155 Q96II5;P04049 ARAF;RAF1 Serine/threonine-protein kinase A-Raf;RAF proto-oncogene serine/threonine-protein kinase 1 S(0.096)AS(0.904)EPSLHR;S(0.038)AS(0.962)EPSLHR;S(0.101)AS(0.899)EPSLHR;S(0.082)AS(0.918)EPSLHR;S(0.099)AS(0.901)EPSLHR;S(0.101)AS(0.899)EPSLHR 128.01 0.00027647 5986860000 2641960 4526800 4305840 4521590 4856820 5508230 4334490 4636420 3991680 4537800 TRUE FALSE 2746266.621 5304242.686 4418053.728 5415947.006 4031259.471 4229027.061 3994741.348 4574276.374 3848020.217 5426895.029 0.506047492 0.977399168 0.814103406 0.997982636 0.742829823 0.779271948 0.736100722 0.842890152 0.709064796 1 22.37169557 -2.290063382 2.194304189 1.861257661 0.801112052 0.180623748 0.132433169 6717576.383 983762.2228 28686480.82 0.029672667 0.005127865 2.290063382 -1.060145609 SAS(ph)EPSLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASEPSLNR 9 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0 P15056 BRAF Serine/threonine-protein kinase B-raf 1 SAS(0.82)EPS(0.18)LNR 119.6 0.00083969 1389500000 258920 261590 359870 330830 386180 425370 341070 336750 346670 271850 TRUE FALSE 269142.3615 306516.0476 369248.5078 396267.1866 320537.2615 326584.264 314336.0422 332236.4171 334193.4144 325113.8026 0.827840465 0.942796169 1.135751558 1.218856854 0.985923264 1.004522913 0.966849268 1.021908065 1.027927488 1 18.31058528 4.489227455 4.7381898 1.043598434 0.847707009 0.467790568 0.072975713 0.169093574 10.0837888 0.019462776 0.072209597 30848.03147 -4.489227455 -0.195891425 SAS(ph)FSQGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASFSQGTR 9 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 S(0.001)AS(0.988)FS(0.011)QGTR;S(0.003)AS(0.995)FS(0.002)QGTR;S(0.006)AS(0.99)FS(0.004)QGTR;SAS(0.996)FS(0.004)QGTR 137.55 0.00016947 516520000 414683 575180 550250 553260 594430 768240 534310 580240 571830 810980 TRUE FALSE 431055.005 673962.6907 564589.967 662693.1767 493389.0009 589827.9028 492429.386 572462.8319 551249.95 969876.0038 0.444443417 0.694895727 0.582125926 0.683276186 0.508713484 0.608147743 0.507724064 0.590243319 0.568371573 1 19.88744079 -1.673465718 2.374637104 1.070448769 0.579949366 0.750706774 0.073199663 2222860.71 1656226.289 943993.3004 0.016792057 0.021209688 1.673465718 -0.490499403 SAS(ph)MKLPDNTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SASMKLPDNTVK 12 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 SAS(1)MKLPDNTVK;S(0.003)AS(0.997)MKLPDNTVK;S(0.099)AS(0.901)MKLPDNTVK;SAS(1)MKLPDNTVK;SAS(1)MKLPDNTVK;SAS(1)MKLPDNTVK;S(0.032)AS(0.968)MKLPDNTVK;S(0.005)AS(0.995)MKLPDNTVK;S(0.003)AS(0.997)MKLPDNTVK 226.39 9.34E-12 7780533000 12901420 6366040 10725410 5790670 16281070 12655970 13534850 10096050 13943670 5739960 TRUE FALSE 13410778.02 7459357.849 11004923 6936047.243 13513619.54 9716812.771 12473953.09 9960728.964 13441840.04 6864595.264 1.953615255 1.086642047 1.603142294 1.010408768 1.968596693 1.415496821 1.817143271 1.451029315 1.958140214 1 22.71074323 3.231529277 24.99997907 1.618181908 1.403657815 0.058934699 0.364212757 427.0106672 1518238.402 0.094939451 0.115803107 1704.234202 -3.231529277 -0.214524093 SAS(ph)PCIADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASPCIADK 9 0 Q05209;Q05209-2;Q05209-3 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 SAS(1)PCIADK;S(0.005)AS(0.995)PCIADK 155.26 7.73E-05 60982000 283250 200204 229038 191279 288900 321530 279890 272690 257029 178974 TRUE FALSE 294432.9287 234587.4796 235006.9184 229113.4153 239792.8812 246859.5303 257951.4904 269035.0366 247778.5765 214040.5286 1.375594289 1.095995609 1.097955233 1.070420713 1.12031531 1.153330782 1.205152557 1.256935022 1.157624577 1 17.70752447 2.401804511 6.148821673 1.185724856 1.140961031 0 0.102501277 0.817115604 51.67047584 0.035180344 0.029352442 252.2345136 -2.401804511 -0.044763825 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 S(0.131)AS(0.869)PDDDLGSSNWEAADLGNEER;S(0.108)AS(0.892)PDDDLGSSNWEAADLGNEER;S(0.327)AS(0.673)PDDDLGSSNWEAADLGNEER;S(0.025)AS(0.975)PDDDLGSSNWEAADLGNEER;S(0.026)AS(0.974)PDDDLGSSNWEAADLGNEER 348.12 9.79E-102 1938540000 846440 990820 967950 952830 1075910 1173910 935750 997230 1043910 1018620 TRUE FALSE 879858.1048 1160985.627 993175.5722 1141296.93 893027.2025 901287.1933 862403.4699 983863.763 1006339.883 1218199.086 0.72226134 0.953034394 0.815281823 0.936872259 0.73307164 0.739852134 0.707933112 0.807637909 0.826088194 1 20.2163185 7.980772412 8.912955076 0.815395572 0.73732708 0 0.100329736 0 0 0.021270366 0 95669259.32 -7.980772412 -0.078068492 SAS(ph)PDDDLGSSNWEAADLGNEERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 SAS(1)PDDDLGSSNWEAADLGNEERK;S(0.005)AS(0.995)PDDDLGSSNWEAADLGNEERK;S(0.004)AS(0.996)PDDDLGSSNWEAADLGNEERK;SAS(1)PDDDLGSSNWEAADLGNEERK 309.83 1.21E-73 9771700000 3575410 2416840 3172640 1863850 4487580 4043680 2542110 2782880 3438540 2660740 TRUE FALSE 3716569.948 2831913.47 3255321.605 2232513.967 3724782.755 3104596.603 2342852.776 2745580.045 3314787.617 3182061.06 1.167975685 0.889962014 1.023022985 0.701593692 1.170556656 0.975655886 0.736268956 0.862830723 1.041710877 1 21.60153009 2.427992996 24.9999648 0.884972904 0.981007117 0.050837353 0.148126245 286.7588101 145921.6495 0.049996764 0.041830302 267.9125114 -2.427992996 0.096034213 SAS(ph)PDGGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SASPDGGPR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.012)AS(0.988)PDGGPR;S(0.034)AS(0.966)PDGGPR;S(0.006)AS(0.994)PDGGPR 130.63 0.0011929 373420000 1262320 1448990 1359980 1337930 1611070 1787500 1436240 1474790 1349280 1409090 TRUE FALSE 1312157.368 1697842.761 1395422.196 1602568.561 1337220.897 1372380.215 1323663.756 1455022.852 1300719.676 1685174.207 0.778647907 1.007517652 0.828058126 0.950980946 0.793520867 0.814384774 0.785475917 0.863425779 0.771860661 1 20.68446631 3.227448777 24.99908685 0.828962143 0.895084984 0.08080156 0.084188821 419.010245 942675.78 0.022031385 0.026568093 1688.296723 -3.227448777 0.066122841 SAS(ph)PDYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.005)AS(0.995)PDYNR;S(0.001)AS(0.999)PDYNR 175.91 0.00027626 1458476000 1323960 1596220 1591900 1465900 1640100 1755260 1584820 1519560 1494050 1438320 TRUE FALSE 1376230.963 1870358.368 1633386.222 1755850.645 1361316.388 1347627.466 1460597.667 1499192.784 1440279.432 1720131.266 0.800073221 1.087334673 0.949570684 1.020765496 0.791402618 0.78344455 0.849119888 0.871557197 0.837307862 1 20.71408723 3.240508484 24.99997911 0.847023349 0.972152688 0.265496527 0.087743885 58.60913655 752212.0621 0.023178312 0.029866389 1739.836685 -3.240508484 0.125129339 SAS(ph)PHDVDLCLVS(ph)PCEFEHR ddPTM_MDA-MB-175_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(0.13)AS(0.87)PHDVDLCLVS(1)PCEFEHR;S(0.105)AS(0.895)PHDVDLCLVS(1)PCEFEHR 148.1 6.04E-08 93397000 52987 70537 67854 74672 75772 93181 75462 80270 72558 75466 TRUE FALSE 55078.96767 82651.18105 69622.33098 89441.89873 62892.30251 71541.12492 69547.09126 79194.11195 69946.65175 90252.11782 0.61027895 0.91578107 0.771420468 0.991022714 0.696851265 0.792680844 0.770586807 0.877476494 0.775013966 1 16.46167317 -4.999999944 0.334630636 2.99488326 0.801609888 0.252222068 0.102626442 516.9726393 4.417014251 735.0526842 0.077929005 1.00E-05 4.999999944 -2.193273372 SAS(ph)PHDVDLCLVS(ph)PCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 S(0.454)AS(0.546)PHDVDLCLVS(1)PCEFEHRK 188.17 2.67E-17 65833000 34069 40965 41640 35514 60662 51790 40191 46613 50790 43982 TRUE FALSE 35414.07043 48000.42009 42725.17261 42538.5632 50350.69491 39762.55739 37040.7244 45988.22898 48962.07782 52599.43081 0.673278586 0.91256539 0.812274429 0.808726683 0.957247904 0.755950336 0.704203902 0.874310392 0.930848054 1 15.68275957 1.216041567 2.46909746 0.990826132 0.811863402 0.385394074 0.081850393 0.285883716 2.980434314 0.073712541 0.020922108 16.44529117 -1.216041567 -0.17896273 SAS(ph)PHDVDLCLVSPCEFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SASPHDVDLCLVSPCEFEHR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.388)AS(0.612)PHDVDLCLVSPCEFEHR;S(0.122)AS(0.878)PHDVDLCLVSPCEFEHR;S(0.018)AS(0.982)PHDVDLCLVSPCEFEHR;S(0.074)AS(0.926)PHDVDLCLVSPCEFEHR;S(0.13)AS(0.87)PHDVDLCLVSPCEFEHR 267.25 4.92E-37 3890080000 372758 485134 472649 541091 474798 574351 506946 435775 403924 434503 TRUE FALSE 387474.7737 568451.9907 484966.6212 648117.1848 394092.0056 440966.6846 467210.2479 429934.1489 389386.8541 519635.5438 0.745666416 1.093943625 0.933282234 1.247253373 0.758400787 0.848607625 0.899111413 0.82737633 0.749346073 1 18.98714059 SAS(ph)PHDVDLCLVSPCEFEHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASPHDVDLCLVSPCEFEHRK 21 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 S(0.14)AS(0.86)PHDVDLCLVSPCEFEHRK;S(0.102)AS(0.898)PHDVDLCLVSPCEFEHRK 229.66 5.70E-26 1929580000 778390 912990 958940 719160 1317010 1198810 808620 947600 973500 962990 TRUE FALSE 809121.4382 1069788.93 983930.7642 861407.7015 1093145.111 920404.5456 745238.2515 934898.972 938463.9252 1151669.453 0.702563949 0.928902757 0.854351708 0.747964357 0.949183038 0.799191594 0.647093877 0.811777172 0.814872638 1 20.13529527 SAS(ph)PSPPESLVEEERPSGPGGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASPSPPESLVEEERPSGPGGGGK 24 1 K7EMK7;Q04725;Q04725-3 K7EMK7 TLE2 Transducin-like enhancer protein 2 1 S(0.007)AS(0.993)PSPPESLVEEERPSGPGGGGK;S(0.001)AS(0.863)PS(0.136)PPESLVEEERPSGPGGGGK 175 1.34E-12 294970000 371360 325940 366710 315854 465310 491930 443570 385610 442400 331830 TRUE FALSE 386021.5796 381917.6595 376266.7639 378328.9785 386216.7724 377686.7128 408801.8243 380441.5287 426478.1104 396845.7352 0.972724526 0.962383177 0.94814365 0.953340164 0.973216386 0.951721738 1.0301278 0.958663518 1.074669758 1 18.59821878 1.943786601 1.038199338 1.02132106 0.958982577 0.416144978 0.029792698 0.514745015 1.019632319 0.022628147 0.010230572 87.8590698 -1.943786601 -0.062338483 SAS(ph)PTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.005)AS(0.919)PT(0.076)VPR;S(0.022)AS(0.922)PT(0.056)VPR;S(0.021)AS(0.945)PT(0.034)VPR;S(0.005)AS(0.974)PT(0.021)VPR;S(0.032)AS(0.898)PT(0.071)VPR;S(0.04)AS(0.895)PT(0.065)VPR;S(0.019)AS(0.924)PT(0.057)VPR 128.36 0.0011925 18790550000 4240350 5341030 4928610 4974600 5555880 6189380 5327090 5232880 4809900 5186860 TRUE FALSE 4407762.292 6258310.355 5057053.625 5958561.032 4611493.502 4751990.296 4909538.766 5162741.803 4636792.639 6203125.909 0.710571147 1.008896232 0.815242782 0.96057393 0.743414461 0.766063815 0.791462053 0.832280673 0.74749291 1 22.56456398 5.023769019 16.81168107 0.840804156 0.38374919 0.150868306 0.097407186 22958910.97 410335674.2 0.022145337 283123445.5 105625.5586 -5.023769019 -0.457054966 SAS(ph)QS(ph)SLDKLDQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 S(0.37)AS(0.641)QS(0.863)S(0.126)LDKLDQELK;S(0.018)AS(0.951)QS(0.699)S(0.332)LDKLDQELK 114.64 0.0070569 231300000 3000700 726660 1247350 785220 1966250 2598600 2240440 1438590 1578120 439810 TRUE FALSE 3119169.953 851458.2024 1279856.966 940534.1724 1632027.527 1995114.532 2064828.458 1419308.054 1521323.769 525982.3488 5.930179901 1.618796152 2.433269802 1.788147786 3.102818053 3.793120694 3.925661124 2.698394836 2.892347572 1 19.00465486 SAS(ph)QS(ph)SLDKLDQELKEQQK ddPTM_MDA-MB-175_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 2 S(0.109)AS(0.693)QS(0.626)S(0.572)LDKLDQELKEQQK;S(0.214)AS(0.777)QS(0.533)S(0.476)LDKLDQELKEQQK 111.2 0.0010864 680120000 2168760 441820 849590 364013 1531680 1527010 1097420 833270 1043500 317011 TRUE FALSE 2254384.319 517699.1481 871731.0133 436013.6849 1271325.581 1172385.07 1011401.353 822101.3786 1005944.639 379123.2359 5.946310081 1.365516801 2.299334176 1.150057933 3.353330686 3.092358786 2.667737709 2.168427838 2.653344727 1 18.53230735 7.999999984 0.064234357 6.07E-08 8.102008778 0.193723378 1.220287547 636.9331426 3.039850833 72.85380635 474.8133883 99999996.39 -7.999999984 8.102008718 SAS(ph)QSS(ph)LDKLDQELK ddPTM_MDA-MB-175_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 S(0.015)AS(0.909)QS(0.08)S(0.996)LDKLDQELK 189.59 3.01E-06 111060000 920270 221950 373800 247290 618410 765820 720790 414500 491980 142700 TRUE FALSE 956602.9702 260068.186 383541.5351 296203.2239 513292.8891 587969.9111 664292.5964 408944.3055 474273.7359 170659.3328 5.605336399 1.523902512 2.247410257 1.735640348 3.007704768 3.445284247 3.892506699 2.396261011 2.779067092 1 17.38075979 SAS(ph)QSSLDKLDQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.758)QS(0.222)S(0.019)LDKLDQELK;SAS(1)QSSLDKLDQELK;S(0.134)AS(0.866)QS(0.001)SLDKLDQELK 272.31 1.23E-33 2186071000 2444880 975999 1618040 1065018 2350250 2258050 2645060 1737400 2066660 759938 TRUE FALSE 2541405.75 1143619.236 1660207.452 1275675.382 1950755.344 1733652.109 2437733.286 1714112.995 1992281.31 908833.3012 2.79633872 1.258337733 1.826745839 1.403640668 2.146439113 1.907557862 2.682266685 1.886058744 2.192130622 1 19.79365617 SAS(ph)QSSLDKLDQELKEQQK ddPTM_MDA-MB-175_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(0.009)AS(0.78)QS(0.173)S(0.039)LDKLDQELKEQQK;S(0.129)AS(0.836)QS(0.029)S(0.007)LDKLDQELKEQQK 124 1.57E-05 552200000 959940 280710 504760 240570 944140 672430 614660 486590 705770 260850 TRUE FALSE 997839.1724 328919.7589 517914.4603 288154.028 783655.42 516268.3233 566481.3431 480068.057 680369.4756 311958.5632 3.198627286 1.054370027 1.660202736 0.923693278 2.512049716 1.654925955 1.815886499 1.538884049 2.18096105 1 18.25099489 -1.086597678 5.345171737 0.999989803 1.777641205 0.128565824 0.637251204 7.05E-05 1.21E-05 0.562124838 0.13249236 0.081922335 1.086597678 0.777651402 SAS(ph)SDTSEELNSQDSPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASSDTSEELNSQDSPPK 18 0 O14745;O14745-2;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 S(0.006)AS(0.481)S(0.481)DT(0.032)SEELNSQDSPPK;SAS(0.947)S(0.047)DT(0.006)SEELNSQDSPPK;S(0.002)AS(0.591)S(0.401)DT(0.006)SEELNSQDSPPK;S(0.001)AS(0.991)S(0.008)DTSEELNSQDSPPK 520.6 2.30E-295 1474020000 1304270 751130 1074800 942760 1325790 1310350 1685400 1149200 1285480 582045 TRUE FALSE 1355763.587 880130.7345 1102810.171 1129235.114 1100432.689 1006041.071 1553293.944 1133796.854 1239215.826 696085.5738 1.947696717 1.264400194 1.584302581 1.622264786 1.580887079 1.44528361 2.231469811 1.628818203 1.780263623 1 19.40890515 SAS(ph)SGAEGDVSSEREP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.5)S(0.5)GAEGDVSSEREP;SAS(0.5)S(0.5)GAEGDVSSEREP 280.7 4.68E-35 977960000 757420 864960 893740 856250 1064860 1195910 996920 1010870 998180 1028530 TRUE FALSE 787323.5265 1013510.152 917031.5986 1025613.694 883855.4776 918178.0267 918778.8054 997320.9411 962255.6968 1230050.761 0.640074013 0.823957989 0.745523378 0.833797862 0.718552035 0.746455395 0.746943813 0.810796572 0.78228942 1 20.23028642 -4.999999998 0.251038034 2.449648326 0.743725074 0.665355148 0.051969637 104.5803888 1.035966005 77.70619533 0.069302945 1.00E-05 4.999999998 -1.705923252 SAS(ph)TDLGTADVVLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASTDLGTADVVLGR 15 0 A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5;H7C0E9;Q9Y2K5-3;Q9Y2K5-2 A0A0U1RRA6 R3HDM2 R3H domain-containing protein 2 1 S(0.002)AS(0.911)T(0.088)DLGTADVVLGR 143.64 4.59E-06 31955000 31276 42816 55224 41075 84582 52872 46403 46253 46574 57578 TRUE FALSE 32510.80063 50169.31494 56663.18281 49199.5124 70204.78185 40593.27928 42765.81161 45633.05419 44897.81084 68859.3067 0.47213372 0.728577114 0.822883435 0.714493287 1.019539481 0.589510427 0.621060735 0.662699879 0.652022406 1 16.07136404 4.736054884 5.764653779 0.740749504 0.46411068 0.257891786 0.142670307 0.195010345 28.43028563 0.033633973 0.212752148 54457.14686 -4.736054884 -0.276638824 SAS(ph)TLCLPSVGAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASTLCLPSVGAAR 14 0 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 S(0.004)AS(0.895)T(0.101)LCLPSVGAAR;S(0.002)AS(0.499)T(0.499)LCLPSVGAAR 154.13 6.51E-06 119870000 150005 157092 145229 170782 166942 207132 183424 138599 157071 138543 TRUE FALSE 155927.3132 184071.329 149013.787 204562.1699 138565.2585 159028.7321 169046.7476 136741.3071 151418.0454 165687.8483 0.941090821 1.110952498 0.89936461 1.234623854 0.836303084 0.959809266 1.020272454 0.825294725 0.91387538 1 17.33810827 SAS(ph)TLCLPSVGAARPQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.793)T(0.207)LCLPSVGAARPQVK;SAS(0.969)T(0.031)LCLPSVGAARPQVK;SAS(0.921)T(0.079)LCLPSVGAARPQVK 298.11 1.25E-49 2935210000 879940 810783 871190 870161 1244340 1027730 880930 903864 968128 809167 TRUE FALSE 914680.7107 950028.6732 893893.9271 1042276.249 1032827.531 789055.2829 811880.4047 891749.1815 933285.2624 967707.7812 0.945203427 0.981730944 0.923722992 1.077056803 1.067292783 0.815385903 0.838972695 0.921506677 0.964428808 1 19.88421194 2.743707558 24.99930113 0.899061555 0.998196196 0.309607076 0.067228309 525.3673831 2551775.945 0.021650197 0.022310328 554.2523691 -2.743707558 0.099134642 SAS(ph)VNKEPVSLPGIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 SASVNKEPVSLPGIMR 16 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.002)AS(0.998)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;SAS(1)VNKEPVSLPGIMR;S(0.002)AS(0.99)VNKEPVS(0.007)LPGIMR;SAS(1)VNKEPVSLPGIMR;S(0.022)AS(0.978)VNKEPVSLPGIMR;S(0.034)AS(0.966)VNKEPVSLPGIMR;S(0.031)AS(0.969)VNKEPVSLPGIMR;S(0.033)AS(0.967)VNKEPVSLPGIMR;S(0.003)AS(0.997)VNKEPVSLPGIMR;S(0.007)AS(0.993)VNKEPVSLPGIMR 205.68 1.33E-11 20529820000 9496850 6729610 9842740 7269450 13992100 12169910 12006740 10444870 11682640 7053500 TRUE FALSE 9871792.971 7885368.168 10099249.89 8707325.513 11613727.84 9343632.839 11065620.35 10304873.6 11262184.07 8435498.278 1.170267914 0.934783923 1.197232168 1.032224206 1.376768444 1.107656303 1.311792141 1.221608169 1.33509411 1 23.00804186 3.262373773 24.99970115 1.235823806 1.081110024 0.237445268 0.123680129 290.4396132 304909.3799 0.031019913 0.041977909 1829.674238 -3.262373773 -0.154713782 SAS(ph)VSSISLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASVSSISLTK 11 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 SAS(0.961)VS(0.038)S(0.001)ISLTK;SAS(0.995)VS(0.005)SISLTK 142.76 3.93E-05 200036000 311900 263140 317130 292810 428760 385150 352020 322460 337960 284680 TRUE FALSE 324214.0528 308332.2481 325394.6683 350726.944 355879.5283 295704.7495 324427.7526 318137.9511 325796.8856 340457.5955 0.952289087 0.905640679 0.955756819 1.03016337 1.045297661 0.868550896 0.952916771 0.934442219 0.956938221 1 18.37711559 4.123996782 0.00215043 1.9075758 5.44E-05 0.019652902 0.050395577 1039921.527 427.847166 187356.5218 192178.5492 13304.44558 -4.123996782 -1.907521446 SAS(ph)WGSADQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 SAS(0.989)WGS(0.011)ADQLK;S(0.004)AS(0.995)WGS(0.001)ADQLK;SAS(1)WGSADQLK;SAS(0.5)WGS(0.5)ADQLK 180.17 7.11E-06 1241540000 2553990 1716060 2187990 1768970 2953520 2676030 2534790 2195420 2298230 1445400 TRUE FALSE 2654823.497 2010779.956 2245010.817 2118866.986 2451481.725 2054562.588 2336106.536 2165993.986 2215517.151 1728598.456 1.53582429 1.163242943 1.298746281 1.225771653 1.418190394 1.188571343 1.35144546 1.25303478 1.281684097 1 20.72117135 -3.797946076 0.279768675 8.12E-11 1.317129595 0.440757771 0.103988979 95.73922841 1.710617326 55.09003108 0.108999239 0.000159241 3.797946076 1.317129595 SAS(ph)WGSTDHRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASWGSTDHRK 11 1 Q9C073;D6RJ87 Q9C073 FAM117A Protein FAM117A 1 S(0.02)AS(0.953)WGS(0.026)T(0.001)DHRK;S(0.026)AS(0.909)WGS(0.033)T(0.033)DHRK 99.941 0.0026948 641570000 178946 235590 245280 213618 300090 320320 257610 260720 269190 247480 TRUE FALSE 186010.9263 276050.7499 251672.1983 255871.0028 249080.809 245930.5345 237417.8551 257225.4749 259501.9045 295968.9677 0.628481181 0.932701668 0.850333061 0.864519699 0.84157745 0.830933514 0.802171447 0.869096098 0.876787545 1 18.17508639 -5 0.163496635 1.616383403 0.795320435 0.365410459 0.072322568 149.6291176 1.389479778 29.86452167 0.272630818 1.00E-05 5 -0.821062968 SASNKS(ph)PLVLEANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASNKSPLVLEANR 14 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 S(0.014)AS(0.227)NKS(0.759)PLVLEANR 82.709 0.0060306 294540000 133430 96992 114270 92734 127520 146910 140640 112430 113080 71534 TRUE FALSE 138697.9194 113649.6215 117247.9701 111076.5084 105844.1959 112792.3789 129616.2693 110923.0597 109010.2729 85549.7177 1.621255139 1.328462847 1.370524336 1.298385447 1.237224374 1.318442445 1.515098738 1.296591768 1.274232994 1 16.38447547 -3.942006609 0.200573203 2.36E-13 1.422179001 0.546183011 0.105108973 72.029513 1.04587483 29.54210465 0.261282465 0.000114286 3.942006609 1.422179001 SASPT(ph)VPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASPTVPR 8 0 Q92817;K7EKI0;K7EQ87 Q92817 EVPL Envoplakin 1 S(0.001)AS(0.427)PT(0.572)VPR 114.89 0.012754 0 337750 444960 387340 438510 474270 560000 500420 455020 425780 481280 TRUE FALSE 351084.6308 521378.4187 397434.3986 525245.9692 393653.7548 429948.4869 461195.7728 448921.2012 410456.261 575577.6013 0.609969238 0.905835143 0.690496638 0.912554568 0.683928203 0.746986133 0.801274705 0.779949046 0.713120629 1 19.13465092 -1.317782797 3.996716244 1.000436626 0.767331341 0.382856414 0.090862348 12698018.52 4186841.463 48151.14623 0.018761436 0.048107989 1.317782797 -0.233105285 SASQS(ph)S(ph)LDKLDQELK ddPTM_MDA-MB-175_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 S(0.002)AS(0.474)QS(0.532)S(0.992)LDKLDQELK 162.26 1.92E-05 118270000 1284500 319980 555210 329870 849380 1116200 1031500 580690 673380 193420 TRUE FALSE 1335213.052 374934.0759 569679.2287 395117.3014 705002.691 856979.4662 950648.3347 572906.8004 649145.1853 231316.9458 5.772223248 1.620867311 2.462764787 1.708120865 3.047777968 3.704784634 4.109721973 2.476717815 2.806301904 1 17.81951143 SASQS(ph)SLDKLDQELK ddPTM_MDA-MB-175_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 SAS(0.001)QS(0.713)S(0.287)LDKLDQELK 119.38 0.00013154 434700000 308710 100260 179110 109830 247240 300930 276220 178260 205680 68025 TRUE FALSE 320898.1092 117478.8751 183777.7537 131554.0462 205214.2331 231043.5681 254569.1546 175870.7163 198277.617 81353.19633 3.944505239 1.444059734 2.259010857 1.617072864 2.522509777 2.84000603 3.129184422 2.161816919 2.437244336 1 16.31191141 SASQS(ph)SLDKLDQELKEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.001)AS(0.009)QS(0.602)S(0.388)LDKLDQELKEQQK;SASQS(0.605)S(0.395)LDKLDQELKEQQK;SAS(0.001)QS(0.637)S(0.362)LDKLDQELKEQQK 228.62 5.19E-20 2027030000 3071250 716950 1437790 664740 2448610 2186790 1859470 1319120 1720260 514250 TRUE FALSE 3192505.322 840080.5854 1475259.989 796223.5879 2032396.147 1678941.164 1713719.883 1301439.354 1658348.179 615007.4416 5.191002752 1.365968163 2.398767704 1.294656835 3.304669195 2.729952599 2.786502677 2.116135946 2.696468476 1 19.23024434 -1.477885203 0.374598548 2.20E-15 2.65257871 0.187852602 1.035692471 43.10752998 3.359184663 42.9743945 0.691769812 0.03327475 1.477885203 2.65257871 SASQSS(ph)LDKLDQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-4;O60271-2;O60271-5;O60271-9 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 SAS(0.001)QS(0.25)S(0.749)LDKLDQELK;SASQS(0.398)S(0.602)LDKLDQELK;SASQS(0.02)S(0.98)LDKLDQELK;SAS(0.002)QS(0.19)S(0.808)LDKLDQELK 290.88 3.99E-44 1803317000 2845780 845805 1384527 978764 2082380 2398050 2469930 1485963 1600717 575690 TRUE FALSE 2958133.592 991065.4293 1420608.911 1172360.598 1728417.791 1841139.23 2276330.433 1466046.097 1543107.508 688485.4332 4.296581233 1.439486417 2.063382669 1.702811042 2.51046385 2.674187632 3.306286993 2.129378525 2.241307417 1 19.39306661 SASS(ph)GAEGDVSSEREP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SAS(0.032)S(0.968)GAEGDVSSEREP;SAS(0.011)S(0.989)GAEGDVSSEREP 309.33 3.40E-57 941780000 541060 617590 629810 609640 734970 815830 681150 660300 637870 692320 TRUE FALSE 562421.4666 723656.2783 646223.366 730224.9724 610040.0619 626365.8465 627759.6831 651449.7585 614913.1833 827966.8487 0.679280176 0.874016006 0.780494252 0.881949529 0.736792859 0.75651078 0.758194225 0.786806573 0.742678507 1 19.65921348 -0.62106163 13.569961 1 0.781228886 0.568235836 0.058121906 0 0 0.052490235 0.012372067 0.239297615 0.62106163 -0.218771113 SASSASSLFS(ph)PSSTLFSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SASSASSLFSPSSTLFSSSR 20 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 SASSASSLFS(0.969)PS(0.025)S(0.005)T(0.001)LFSSSR;SASSASSLFS(0.996)PS(0.004)STLFSSSR;SASSASSLFS(0.963)PS(0.032)S(0.003)T(0.001)LFSSSR 223.18 2.58E-26 47625000 91339 101916 110120 107903 127143 144116 108173 114581 116004 111864 TRUE FALSE 94945.13425 119419.2802 112989.8177 129245.8913 105531.2783 110647.2431 99694.1176 113045.2291 111829.0387 133781.609 0.709702439 0.892643474 0.844584084 0.966096104 0.788832479 0.827073646 0.745200468 0.844998277 0.835907413 1 17.02952028 0.459211443 2.473183074 0.999997649 0.830387645 0.364385481 0.068015189 12.435425 55.2618291 0.063404853 0.016929456 2.878799665 -0.459211443 -0.169610004 SASSGAEGDVSS(ph)EREP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 SASSGAEGDVS(0.008)S(0.992)EREP;SASSGAEGDVS(0.003)S(0.997)EREP 269.51 1.85E-27 515720000 865270 1063960 1054070 990360 1181660 1336080 1036210 1064210 1038010 1102210 TRUE FALSE 899431.5277 1246686.854 1081539.93 1186250.252 980801.8553 1025795.668 954989.1526 1049946.006 1000652.223 1318166.946 0.682335064 0.945773111 0.820487824 0.899924137 0.744064974 0.778198597 0.724482703 0.796519749 0.759124044 1 20.33010167 4.834172388 20.53864501 0.815483025 0.682285724 0.1881593 0.087455724 114369.9972 24541460.07 0.019997957 772.879766 68260.95941 -4.834172388 -0.133197301 SAST(ph)LCLPSVGAARPQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASTLCLPSVGAARPQVK 18 1 Q8IUC4;Q8IUC4-2;A8MT19 Q8IUC4 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 SAS(0.192)T(0.808)LCLPSVGAARPQVK 307.97 7.20E-61 3527200000 1233700 1056700 1248200 940560 1677100 1373000 1201500 1209700 1235900 1046300 TRUE FALSE 1282407.429 1238180.005 1280729.117 1126599.961 1392027.141 1054141.558 1107323.29 1193485.95 1191420.2 1251302.452 1.02485808 0.989512969 1.023516828 0.900341847 1.112462569 0.842435461 0.884936562 0.953794942 0.952144062 1 20.25499911 2.725802391 24.9926499 0.92287919 1.003636035 0.304041698 0.062632794 987.0320255 1933537.153 0.019439687 0.01843829 531.8661994 -2.725802391 0.080756845 SASTES(ph)GFHNHTDTAEGDVIAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SASTESGFHNHTDTAEGDVIAAAR 24 0 Q02410-2;Q02410 Q02410-2 APBA1 Amyloid beta A4 precursor protein-binding family A member 1 1 S(0.033)AS(0.191)T(0.191)ES(0.586)GFHNHTDTAEGDVIAAAR 170.18 5.33E-12 392110000 35721 44514 49271 42748 52919 73822 46078 61699 42273 48901 TRUE FALSE 37131.29266 52158.93323 50555.04274 51203.42681 43923.84728 56677.95928 42466.28596 60872.02582 40751.60299 58482.21468 0.63491598 0.891876847 0.864451577 0.875538437 0.751063336 0.969148648 0.726140181 1.040863896 0.696820447 1 15.83571033 7.999999998 0.035188818 1.406328249 0.000171673 0.160721238 0.119571631 1767.132925 4.750342238 55.90392171 158.0538048 99999999.65 -7.999999998 -1.406156576 SASYKPVFVTEITDDLHFYVQDVETGTQLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SASYKPVFVTEITDDLHFYVQDVETGTQLEK 31 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 397.12 5.61E-156 3262390000 1410825 905953 1320535 927093 1614657 1518483 1589474 1336011 1436103 864815 FALSE TRUE 1466525.46 1061543.38 1354949.227 1110469.228 1340198.18 1165838.336 1464886.875 1318103.958 1384417.934 1034258.941 1.417948061 1.026380665 1.310067695 1.073685886 1.295805263 1.12722094 1.416363752 1.274442893 1.338560276 1 19.980166 SAT(ph)FPNAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SATFPNAGPR 10 0 Q86X27;Q86X27-3 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SAT(1)FPNAGPR;S(0.003)AT(0.997)FPNAGPR 219.33 7.11E-08 1384950000 680270 780190 815060 657860 1223850 906730 793240 787040 777110 810680 TRUE FALSE 707127.5849 914181.5635 836301.1332 787982.7445 1015820.414 696155.6991 731063.7761 776491.0161 749141.9629 969517.2246 0.729360518 0.94292452 0.862595436 0.81275786 1.047759017 0.718043663 0.754049291 0.800904818 0.772695878 1 19.886907 SAT(ph)LSGSATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 S(0.073)AT(0.668)LS(0.073)GS(0.186)ATNLASLTAALAK 203.71 1.16E-20 163300000 295990 297960 318050 318420 414980 411660 395750 288820 383830 285620 TRUE FALSE 307675.9138 349132.3122 326338.6443 381402.5256 344441.8478 316058.2038 364730.0809 284948.8403 370016.0333 341581.7705 0.900738682 1.022104639 0.955374884 1.116577518 1.008373039 0.925278311 1.067767991 0.834203886 1.083242917 1 18.38187146 SATEYKNEEYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SATEYKNEEYQR 12 1 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 69.716 0.044894 183970000 70797 58290 62888 49468 93170 89689 75646 67330 74698 56725 FALSE TRUE 73592.12023 68300.85407 64526.91294 59252.62275 77332.99668 68860.089 69716.66886 66427.55148 72009.63357 67839.17768 1.084802657 1.006805454 0.951174751 0.873427786 1.139945962 1.015048993 1.027675618 0.979191578 1.061475626 1 16.04983106 4.735912158 6.631257016 1.003825119 1.086224367 0.114221988 0.065533505 0.247829661 71.31246615 0.015612836 0.092815284 54439.25306 -4.735912158 0.082399248 SATLSGS(ph)ATNLASLTAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SATLSGSATNLASLTAALAK 20 0 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SATLSGS(0.998)AT(0.002)NLASLTAALAK;SATLS(0.027)GS(0.973)AT(0.001)NLASLTAALAK;S(0.019)AT(0.019)LS(0.119)GS(0.824)AT(0.019)NLASLTAALAK;SATLSGS(0.969)AT(0.031)NLASLTAALAK;SATLS(0.002)GS(0.983)AT(0.014)NLASLTAALAK;SATLSGS(1)ATNLASLTAALAK;S(0.004)AT(0.022)LS(0.147)GS(0.825)AT(0.001)NLASLTAALAK;SATLSGS(1)ATNLASLTAALAK;SATLS(0.021)GS(0.976)AT(0.003)NLASLTAALAK 452.18 4.78E-198 2922740000 2505198.6 2123009.1 2497909 2109657.5 3063150.4 3056724.4 2708155.7 2444887.4 2470813.6 1963204.9 TRUE FALSE 2604105.775 2487619.398 2563006.561 2526941.457 2542477.189 2346846.483 2495883.38 2412117.683 2381889.501 2347857.312 1.109141412 1.059527504 1.091636424 1.076275566 1.082892549 0.999569467 1.063047301 1.027369794 1.014494999 1 21.1629133 2.597779685 0.386847123 0.999206434 1.103375879 0.661048803 0.021801801 0.910329116 0.28704452 0.022906409 0.035433134 396.077056 -2.597779685 0.104169445 SATREPPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SATREPPYR 9 1 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 91.584 0.0097167 201784000 114716 198622 194385 193198 178949 234059 176695 201789 192537 185364 FALSE TRUE 119245.0763 232733.7834 199450.8328 231411.9878 148531.3129 179702.3444 162845.1842 199084.3485 185607.631 221682.5268 0.537909225 1.049851726 0.899713819 1.043889165 0.670018134 0.810629268 0.734587369 0.898060625 0.837267753 1 17.75813553 0.292668202 1.375564523 1.000029677 0.838958097 0.100339486 0.149854296 13.39944948 23.47277018 0.137785702 0.040043906 1.961860855 -0.292668202 -0.16107158 SATRPS(ph)PS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.003)AT(0.016)RPS(0.981)PS(1)PER;S(0.005)AT(0.024)RPS(0.971)PS(1)PER;S(0.072)AT(0.048)RPS(0.881)PS(1)PER;SATRPS(0.999)PS(1)PER 124.39 0.0038904 9288510000 2769960 2719040 2828670 2593220 3300910 3784460 3138880 2967390 2838620 2432350 TRUE FALSE 2879320.16 3186013.969 2902387.464 3106151.176 2739822.497 2905576.519 2892846.384 2927616.991 2736458.621 2908922.412 0.989823636 1.09525574 0.997753481 1.067801315 0.941868537 0.998849783 0.994473545 1.006426634 0.940712138 1 21.47205339 3.247326803 24.99995108 0.984255389 1.038922264 0.376757582 0.035864379 201.7495216 575357.5467 0.009288228 0.012389988 1767.367251 -3.247326803 0.054666875 SATRPS(ph)PS(ph)PERSSTGPEPPAPTPLLAER ddPTM_MDA-MB-175_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(0.067)AT(0.021)RPS(0.909)PS(0.878)PERS(0.057)S(0.051)T(0.017)GPEPPAPTPLLAER 74.282 0.0050441 72048000 89874 111330 126980 100990 92319 126380 99746 118400 114650 113720 TRUE FALSE 93422.29492 130450.0615 130289.2031 120965.5206 76626.64936 97030.16031 91927.64788 116813.0417 110523.7689 136001.2567 0.686922292 0.959182765 0.957999994 0.889444138 0.563426039 0.713450468 0.675932341 0.858911487 0.812667262 1 17.05326046 SATRPSPS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SATRPSPSPER 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SATRPS(0.107)PS(0.893)PER 97.797 0.0036328 633800000 205680 301320 229450 237850 291240 303340 253100 257220 234830 252710 TRUE FALSE 213800.4052 353069.3661 235429.6555 284896.0201 241735.1288 232893.8822 233261.3606 253772.3866 226378.5142 302223.6861 0.707424385 1.168238567 0.77899141 0.942666089 0.799855008 0.770601025 0.77181694 0.839683977 0.749042926 1 18.20525721 3.230560311 24.93688206 0.810024351 0.90994224 0.071776199 0.130290463 351.678035 1096176.29 0.034393784 0.041794103 1700.43608 -3.230560311 0.099917889 SATTT(ph)PSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 2 SATTT(0.999)PS(0.001)GS(1)PR;SATT(0.001)T(0.999)PSGS(1)PR 200.42 2.49E-07 228500000 523570 588490 543460 521580 627920 698680 575610 589190 562910 556720 TRUE FALSE 544240.9479 689558.5797 557623.0141 624746.9672 521186.3827 536422.1586 530492.1841 581292.8718 542650.9791 665798.625 0.817425761 1.035686398 0.837525031 0.938342231 0.782798827 0.805682287 0.796775728 0.873076107 0.815037699 1 19.34472637 3.251598604 24.96493836 0.836529453 0.911439268 0.117462102 0.080250885 387.8076118 742563.8766 0.020532772 0.027632243 1784.837179 -3.251598604 0.074909815 SATTTGS(ph)PGTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 SATT(0.01)T(0.06)GS(0.931)PGTEK;SATTT(0.024)GS(0.976)PGTEK;SATTT(0.001)GS(0.999)PGTEK;SATTT(0.016)GS(0.984)PGTEK;SATTT(0.02)GS(0.98)PGTEK 335 2.76E-58 2699500000 5761000 3781970 4852500 3852240 6191430 6500470 5602270 4522820 4825330 3000740 TRUE FALSE 5988448.728 4431493.928 4978960.136 4614201.574 5139012.94 4990834.358 5163149.439 4462198.996 4651667.316 3588677.55 1.66870627 1.234854307 1.387408054 1.285766556 1.432007437 1.390716855 1.438733173 1.243410402 1.296206541 1 21.77502087 0.65122667 0.716114859 0.996368716 1.397101888 0.531932185 0.112808023 0.934979973 0.889955745 0.109220498 0.038689994 4.479470385 -0.65122667 0.400733171 SATTTPSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SATTTPSGSPR 11 0 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 1 SATTTPSGS(1)PR;SATTTPS(0.001)GS(0.999)PR 177.41 8.39E-06 328940000 187818 238720 252050 225966 258420 283770 271960 247170 249920 229080 TRUE FALSE 195233.1997 279718.303 258618.6301 270661.4004 214493.8607 217868.7181 250643.0646 243857.0904 240925.428 273963.84 0.712623971 1.021004462 0.943988192 0.98794571 0.782927633 0.795246256 0.914876447 0.890106849 0.879405939 1 18.06362596 -1.343498561 3.283638583 1.000787589 0.886474178 0.132372803 0.090465956 39247840.16 58534260.76 305086.6072 0.02127155 0.04534208 1.343498561 -0.114313411 LKGEMMDLQHGSLFLQTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 LKGEMMDLQHGSLFLQTPK 19 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ; 146.58 6.85E-08 508821000 198713 538933 700788 699875 775434 914390 721709 902770 754888 590474 FALSE TRUE 206558.3427 631490.5504 719051.111 838308.1861 643626.0057 702036.7802 665139.5627 890669.8448 727719.7283 706166.075 0.292506749 0.894252178 1.018246467 1.187126111 0.911437165 0.994152516 0.941902459 1.261275324 1.030522074 1 19.42964799 4.784461402 2.140675788 1.057188356 0.026527308 0.831160594 0.101115904 0.303258651 1.41363459 0.026891788 0.625414949 60878.14372 -4.784461402 -1.030661049 down SAVEDEGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAVEDEGLK 9 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 164.57 0.00014462 294150000 536680 372970 448690 390290 543730 599400 637710 442850 472480 312000 FALSE TRUE 557868.5408 437024.6962 460383.23 467488.1971 451306.9688 460198.434 587724.6239 436914.3201 455475.5371 373130.4264 1.495103324 1.171238434 1.233839959 1.25288147 1.209515325 1.233344701 1.575118463 1.170942623 1.220687204 1 18.50932048 0.861925955 1.74871139 1.002688487 1.291266172 0.327203229 0.127963897 0.638298683 3.772598744 0.117512559 0.033403713 7.276557324 -0.861925955 0.288577685 SAVGFDYQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SAVGFDYQGK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 112.36 0.0037955 74189000 151660 112410 140300 106690 158670 167100 138350 140940 140330 98862 FALSE TRUE 157647.6539 131715.5431 143956.3333 127792.9636 131699.3301 128293.5574 127505.7655 139050.9298 135279.5507 118232.1161 1.333374206 1.114042 1.217573854 1.080865063 1.113904872 1.085099055 1.078435959 1.176084252 1.144186159 1 16.85126245 7.898217023 1.024760573 1.112125399 199.9967931 0.577990907 0.056509056 1139.090817 1.702959067 0.015733681 531845.5484 79107383.95 -7.898217023 198.8846677 SAVGFEYQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAVGFEYQGK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 140.75 9.01E-05 306880000 178797 160027 188600 164527 227900 239600 192380 193864 200363 150241 FALSE TRUE 185856.0436 187510.3924 193515.0709 197069.9495 189161.6394 183956.5312 177300.7529 191265.5702 193151.9748 179677.8474 1.034384852 1.043592157 1.077011294 1.096796029 1.0527822 1.023813084 0.986770242 1.064491661 1.074990476 1 17.45505302 2.990278344 24.02712001 1.033408805 1.064095914 0.218308527 0.029356118 501.1609538 1238630.032 0.009263831 0.010466478 977.8637439 -2.990278344 0.03068711 SAVGHEYQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SAVGHEYQSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;; 184.36 1.57E-06 7082523700 7816324 9398112 10934602 9275148 13085919 13426098 12112663 11631824 11317954 9246021 FALSE TRUE 8124918.507 11012164.63 11219566.71 11109744.59 10861579.16 10308090.21 11163240.82 11475918.43 10910623.05 11057601.79 0.734781254 0.995890867 1.014647382 1.004715562 0.982272591 0.932217529 1.009553521 1.037830684 0.986707901 1 23.39853519 4.738483333 8.008658499 0.99819343 0.73266243 0.900836518 0.025990287 0.028248857 22.46864932 0.00686934 0.040659108 54762.50841 -4.738483333 -0.265531 SAVHYDEES(ph)GS(ph)EEETLQYFSTVDPNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAVHYDEESGSEEETLQYFSTVDPNYR 27 0 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 2 S(0.328)AVHY(0.492)DEES(0.596)GS(0.577)EEET(0.008)LQYFSTVDPNYR;S(0.045)AVHY(0.388)DEES(0.78)GS(0.778)EEET(0.01)LQYFSTVDPNYR 100.36 0.0016226 90800000 22521.6 35471 34847 39474 39969 44459 28273 41277 36368 38137 TRUE FALSE 23410.77016 41562.86832 35755.14145 47281.83938 33175.08366 34134.07103 26056.88838 40723.74933 35059.12278 45609.21497 0.513290355 0.911282256 0.783945557 1.036672949 0.727376774 0.74840295 0.571307539 0.892884242 0.768685074 1 15.47703772 0.280530113 1.295133477 1.000064522 0.77937437 0.176053077 0.14650246 8.982293657 14.37438664 0.137481395 0.040155758 1.907788001 -0.280530113 -0.220690151 SAVRPAS(ph)LNLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;S(0.016)AVRPAS(0.984)LNLNR 82.109 0.0095922 635700000 133835 496560 439750 577160 374640 661980 440950 518470 455570 703120 TRUE FALSE 139118.9091 581840.3173 451210.2463 691320.5253 310958.8266 508245.1774 406387.1868 511520.7577 439174.1247 840882.902 0.165443855 0.691939765 0.536591058 0.822136499 0.369800392 0.604418494 0.4832863 0.6083139 0.522277387 1 19.68154538 -5 0.383642152 7.551610469 0.536037458 0.407859674 0.168514417 594.4858187 4.391227107 3244.772024 0.102416591 1.00E-05 5 -7.015573012 SAVSDKQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SAVSDKQDR 9 1 O95757;E9PDE8;D6RJ96 O95757 HSPA4L Heat shock 70 kDa protein 4L 0 ; 98.033 0.0057348 136459000 305570 240370 287490 220380 399170 359590 298520 288440 308400 262760 FALSE TRUE 317634.1396 281651.6777 294982.2256 263970.5062 331319.226 276080.6721 275121.2224 284573.9336 297300.7442 314242.7912 1.010792128 0.896286838 0.938708011 0.840020881 1.054341532 0.87855849 0.875505278 0.905586195 0.946086124 1 18.26152012 4.748574347 23.73263558 0.920415658 1.010792231 0.145069097 0.060247647 1190.499834 2821378.093 0.013448868 0.17260605 56049.83611 -4.748574347 0.090376572 SAYQEYDS(ph)DSDVPEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SAYQEYDSDSDVPEELKR 18 1 Q96JG6;Q96JG6-3;H0Y7Q2 Q96JG6 CCDC132 Coiled-coil domain-containing protein 132 1 SAYQEYDS(0.992)DS(0.008)DVPEELKR;SAYQEYDS(0.994)DS(0.006)DVPEELKR;SAYQEYDS(0.998)DS(0.002)DVPEELKR 160.67 2.45E-11 1942510000 1670390 988310 1266260 991750 1539980 1847170 1761300 1118530 1221820 754460 TRUE FALSE 1736338.287 1158044.555 1299259.776 1187915.19 1278214.75 1418192.762 1623244.704 1103537.935 1177846.937 902281.992 1.924385394 1.283461894 1.43997086 1.316567548 1.416646637 1.571784402 1.799043667 1.223052155 1.305408894 1 19.78321887 1.166834916 1.616913953 1.030077714 1.504006061 0.384481974 0.204366152 0.370967142 1.838632779 0.186453178 0.055307251 14.68368017 -1.166834916 0.473928346 SCAHDWVYE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 110.12 0.0054405 23177700000 3598610 7125680 6637540 6532210 7694430 8733580 6310960 7057410 6224270 7771820 FALSE TRUE 3740685.902 8349460.11 6810519.745 7824261.641 6386533.537 6705338.404 5816290.465 6962816.963 6000259.739 9294559.329 0.402459737 0.898316942 0.732742619 0.841810931 0.687126018 0.721426177 0.625773666 0.74912825 0.645566888 1 23.14795504 -1.294201614 3.364410432 1.001215492 0.711276597 0.330269177 0.127121783 33505462.86 46075642.6 407311.428 0.027918064 0.050792359 1.294201614 -0.289938895 SCATFSSSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SCATFSSSHR 10 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-5;D6RCQ9;D6RE64;D6RBT0;D6RHE8 D6REX3 SEC31A Protein transport protein Sec31A 0 ;;; 136.96 0.00010389 697610000 178033 535110 453910 474260 651590 725130 470190 542840 429762 706160 FALSE TRUE 185061.8803 627010.9799 465739.2675 568067.2125 540832.9645 556729.547 433335.2792 535564.1177 414294.9496 844518.5318 0.219133001 0.742447864 0.551484959 0.672652158 0.640403904 0.659227153 0.513115181 0.634165027 0.4905694 1 19.68776956 -2.154945349 2.437938564 1.995019435 0.58308048 0.462563352 0.138572892 6869881.101 1931619.857 37720434.08 0.030099452 0.006999301 2.154945349 -1.411938955 SCDDFSHMGT(ph)LPHSKSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCDDFSHMGTLPHSKSPR 18 1 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 SCDDFSHMGT(0.445)LPHS(0.277)KS(0.277)PR 69.922 0.051949 84058000 26736 41054 30923 27816 32965 42929 39525 36688 32207 52197 TRUE FALSE 27791.55792 48104.70514 31728.87878 33317.92178 27361.62107 32959.39035 36426.92722 36196.25737 31047.87636 62424.00278 0.445206278 0.770612313 0.508280107 0.533735747 0.438318914 0.527992261 0.583540395 0.579845184 0.497370803 1 15.92981325 -1.352828799 3.26581175 1.003468143 0.548849135 0.703235099 0.089028763 23445233.88 33071807.23 783418.4438 0.021280551 0.044378355 1.352828799 -0.454619008 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVS(ph)PR ddPTM_MDA-MB-175_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 3 S(0.001)CDEPLT(0.998)PPPHS(0.72)PT(0.14)S(0.14)MLQLIHDPVS(1)PR;S(0.001)CDEPLT(0.944)PPPHS(0.687)PT(0.184)S(0.184)MLQLIHDPVS(0.999)PR 86.936 0.010738 143866000 65648 100649 94009 100174 103830 117894 86652 103797 95021 101526 TRUE FALSE 68239.83373 117934.6828 96458.95177 119988.1182 86181.01369 90514.9052 79859.98982 102405.771 91601.21277 121418.0759 0.562023679 0.971310754 0.794436504 0.98822286 0.709787345 0.745481301 0.657727354 0.843414543 0.754428137 1 16.88962369 -1.014457784 4.260796633 1.000012674 0.788468433 0.217230301 0.124078863 12869086.21 6128030.03 1502.406039 0.027328984 0.096725775 1.014457784 -0.211544241 SCDEPLT(ph)PPPHS(ph)PTSMLQLIHDPVSPR ddPTM_MDA-MB-175_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(1)PPPHS(0.763)PT(0.111)S(0.125)MLQLIHDPVS(0.001)PR;SCDEPLT(0.98)PPPHS(0.44)PT(0.314)S(0.266)MLQLIHDPVSPR 137.35 1.90E-05 309550000 117139 186243 168777 172084 183083 225670 167541 177510 175073 176812 TRUE FALSE 121763.7382 218228.7865 173175.4673 206121.7016 151962.6171 173261.5626 154408.6986 175130.7688 168772.1569 211454.9261 0.575837794 1.032034536 0.818971071 0.974778433 0.718652527 0.819378227 0.73022039 0.828217966 0.798147199 1 17.68999064 3.219347851 24.99711033 0.803141072 0.861133747 0.008172477 0.133199218 858.6674689 1117181.913 0.035454927 0.042439161 1657.096693 -3.219347851 0.057992675 SCDEPLT(ph)PPPHSPTSMLQLIHDPVSPR ddPTM_MDA-MB-175_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 1 SCDEPLT(1)PPPHSPTSMLQLIHDPVSPR 158.35 2.94E-11 66162000 93154 162490 147790 156080 167180 206060 144450 167990 164060 161050 TRUE FALSE 96831.79185 190396.3935 151641.5288 186952.1581 138762.8033 158205.6879 133127.6316 165738.3688 158155.5126 192604.664 0.502748946 0.988534699 0.787320128 0.97065229 0.720454014 0.821401126 0.691196302 0.860510672 0.821140617 1 17.55528311 0.54577716 1.36861302 0.999742992 0.800028999 0.178854818 0.132322799 3.183294179 7.689818761 0.115164292 0.033979551 3.513800982 -0.54577716 -0.199713993 SCDEPLTPPPHS(ph)PTSMLQLIHDPVSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SCDEPLTPPPHSPTSMLQLIHDPVSPR 27 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 SCDEPLTPPPHS(0.671)PT(0.165)S(0.165)MLQLIHDPVSPR;SCDEPLT(0.003)PPPHS(0.564)PT(0.216)S(0.216)MLQLIHDPVSPR;SCDEPLTPPPHS(0.884)PT(0.058)S(0.058)MLQLIHDPVSPR 123.31 0.00014271 855950000 162358 308050 275684 294268 301448 339087 263484 288563 272150 315819 TRUE FALSE 168768.0192 360955.1912 282868.5515 352473.3321 250207.9766 260339.1832 242831.4356 284695.285 262355.3747 377697.6863 0.446833606 0.955672233 0.748928473 0.933215492 0.662455677 0.689279264 0.642925399 0.753764969 0.694617373 1 18.52687242 -0.987651889 4.634303529 1.000004204 0.733928587 0.262569726 0.137425039 16301537.83 3517581.25 897.2838234 0.029960384 0.102884064 0.987651889 -0.266075617 SCDEPLTPPPHSPTS(ph)MLQLIHDPVS(ph)PR ddPTM_MDA-MB-175_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 2 S(0.001)CDEPLT(0.031)PPPHS(0.433)PT(0.475)S(0.48)MLQLIHDPVS(0.58)PR 47.784 0.058836 26251000 8159 14649 13357 11967 14405 16698 14303 15902 10475 16043 TRUE FALSE 8481.12362 17164.8518 13705.09439 14334.03688 11956.44325 12820.14256 13181.89349 15688.8597 10098.0068 19186.31869 0.442040172 0.89464019 0.714315999 0.747096778 0.623175474 0.668191891 0.68704652 0.817710784 0.526312888 1 14.22779031 -1.691867213 2.875878738 1.039369435 0.696773865 0.363531307 0.125256305 38450031.85 33246194.49 10959626.4 0.029098436 0.020329785 1.691867213 -0.342595569 SCFESS(ph)PDPELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SCFESSPDPELK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SCFESS(1)PDPELK;SCFESS(1)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.001)S(0.999)PDPELK;SCFES(0.039)S(0.961)PDPELK;SCFES(0.027)S(0.973)PDPELK 284.92 2.52E-28 24365000000 54314900 31521400 39775300 31055800 55013800 54596100 51284900 41651800 45339800 26088900 TRUE FALSE 56459294.19 36934955.25 40811876.99 37198544.55 45662573.93 41916983.19 47265055.53 41093525.75 43708029.45 31200520.45 1.809562577 1.183792921 1.308051161 1.192241155 1.463519623 1.34347064 1.514880356 1.317078214 1.400875012 1 24.89506676 -1.021994736 3.784461107 0.999930782 1.379347397 0.31772477 0.171610236 21595393.15 40011408.5 20980.7739 0.038209862 0.095061632 1.021994736 0.379416615 SCGYSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCGYSVR 7 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 111.73 0.015154 88283000 178127 222152 231035 219200 255980 273760 231280 217700 205200 209280 FALSE TRUE 185159.5915 260304.8779 237055.9619 262557.1058 212468.611 210183.3889 213151.6693 214782.0876 197814.8921 250284.4091 0.739796746 1.040036328 0.947146339 1.049035003 0.848908695 0.839778193 0.851637823 0.858152085 0.790360426 1 17.9332089 3.172962585 24.99990096 0.855869051 0.951089616 0.141005127 0.093573871 89.02451976 33926.925 0.025371265 0.030324473 1489.232771 -3.172962585 0.095220565 SCLLLQFTDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCLLLQFTDKR 11 1 P61019;E9PKL7;A0A3B3ITL1;Q8WUD1;E9PE37;H0YD31;H0YDL5 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 200.82 7.30E-08 1536840000 690560 550400 636600 640240 1147480 1023560 871160 714880 716990 683820 FALSE TRUE 717823.842 644926.9185 653190.319 766877.5611 952431.7595 785853.7022 802876.2028 705298.2029 691185.67 817801.4365 0.877748326 0.788610645 0.798715055 0.937730758 1.164624708 0.960934607 0.981749563 0.862432091 0.845175417 1 19.64139107 3.678123872 5.676422324 0.962935338 0.818498527 0.376461047 0.084563573 0.243636734 16.4054854 0.024754747 0.03910615 4765.668971 -3.678123872 -0.144436811 SCLLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCLLLR 6 0 Q9H0U4;E9PLD0;Q92928;P62820;E7END7;P62820-2;P62820-3 Q9H0U4;P62820 RAB1B;RAB1C;RAB1A Ras-related protein Rab-1B;Putative Ras-related protein Rab-1C;Ras-related protein Rab-1A 0 121.87 0.045283 238840000 200030 223610 218510 229760 273540 270960 215490 202880 196280 214110 FALSE TRUE 207927.3389 262013.2781 224204.5501 275205.8422 227043.7685 208033.6464 198599.3307 200160.7254 189215.9211 256060.7551 0.812023454 1.023246526 0.875591224 1.074767752 0.88667929 0.81243862 0.775594568 0.781692319 0.738949321 1 17.96612663 2.881822055 3.804337152 0.802654368 0.949819697 0.261275421 0.095138874 0.25618731 6.568163246 0.027683344 0.029808507 761.7668242 -2.881822055 0.147165329 SCPETLTHAVGMSES(ph)PIGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCPETLTHAVGMSESPIGPK 20 0 Q68CZ2;E9PCX8;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 SCPETLTHAVGMSES(1)PIGPK 202.17 7.64E-22 273310000 680640 542050 680140 547960 994470 871150 749230 705830 754510 598150 TRUE FALSE 707512.1928 635142.8709 697865.0071 656344.8525 825430.3446 668838.6149 690503.3949 696369.5034 727355.3325 715346.0402 0.98904887 0.887881997 0.97556283 0.917520774 1.153889584 0.934986115 0.965271849 0.973472228 1.016788088 1 19.44828177 SCS(ph)FSSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCSFSSESR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SCS(0.997)FS(0.003)SESR 214.71 6.99E-07 617470000 430940 468820 535470 469580 633670 625400 520180 556500 546880 523110 TRUE FALSE 447953.844 549336.1881 549424.7881 562461.5224 525958.9997 480160.328 479406.9324 549041.0278 527197.8956 625603.389 0.716034874 0.878090173 0.878231796 0.899070453 0.840722747 0.767515548 0.766311278 0.877618372 0.842703069 1 19.2548888 0.454392915 1.304891389 0.999904385 0.830089602 0.448412673 0.05706476 2.469939667 4.928587316 0.055811083 0.016575304 2.847035716 -0.454392915 -0.169814783 SCS(ph)PLAFSAFGDLTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCSPLAFSAFGDLTIK 16 0 E9PLZ8;Q96EY5;Q96EY5-2 E9PLZ8 MVB12A Multivesicular body subunit 12A 1 S(0.079)CS(0.921)PLAFSAFGDLTIK;SCS(1)PLAFSAFGDLTIK 281.68 1.65E-35 324140000 559580 481880 545200 483840 734500 741710 667930 604800 663030 482550 TRUE FALSE 581672.6505 564639.1415 559408.3599 579542.1079 609649.9524 569459.0932 615575.9013 596693.6453 639167.6798 577096.4335 1.007929727 0.978413847 0.969349882 1.004237895 1.056409149 0.98676592 1.066677708 1.033958296 1.107557841 1 19.13845289 3.097594253 0.938942967 1.050108588 0.98290926 0.346265001 0.033868374 0.582022076 1.126521659 0.015729286 0.02205366 1251.970955 -3.097594253 -0.067199328 SCS(ph)VTDAVAEQGHLPPPSAPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SCSVTDAVAEQGHLPPPSAPAGR 23 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-4 Q96PU5-7 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.215)CS(0.78)VT(0.004)DAVAEQGHLPPPSAPAGR;S(0.013)CS(0.983)VT(0.004)DAVAEQGHLPPPSAPAGR;S(0.158)CS(0.84)VT(0.002)DAVAEQGHLPPPSAPAGR 207.26 7.90E-25 707820000 575484 717944 712538 787022 892249 1024603 804349 778605 729978 796825 TRUE FALSE 598204.5527 841245.2972 731107.3256 942692.6026 740584.8337 786654.4813 741302.0236 768169.0735 703706.2344 952947.6026 0.627741285 0.882782322 0.767206217 0.989238653 0.777151684 0.825496049 0.777904285 0.806097913 0.73845218 1 19.86203736 -2.425851316 2.144548865 2.592402478 0.805560774 0.311992366 0.089030786 5242113.264 342555.5611 40734231.26 0.020270375 0.003751014 2.425851316 -1.786841704 SCSFS(ph)SESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCSFSSESR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 SCS(0.092)FS(0.908)SESR 206.84 1.33E-05 671930000 535060 572310 654600 574400 757610 727820 633340 637350 709660 608090 TRUE FALSE 556184.582 670599.7905 671659.4138 688014.6056 628831.7228 558794.8352 583697.1559 628807.3657 684119.4752 727233.5929 0.764794954 0.922124331 0.923581392 0.946070991 0.864690148 0.768384245 0.802626778 0.864656655 0.940714898 1 19.47205932 1.072417963 3.098090386 0.998401601 0.858973992 0.381073476 0.06007546 0.256028788 4.968413272 0.061282785 0.016215368 11.81457117 -1.072417963 -0.139427608 SCSSISTALPQVNEDLVSLPHQLPEASEPPQS(ph)PSEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCSSISTALPQVNEDLVSLPHQLPEASEPPQSPSEKR 37 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 SCSSISTALPQVNEDLVSLPHQLPEAS(0.005)EPPQS(0.96)PS(0.035)EKR 213.61 6.13E-32 52245000 33499 26096 27088 23061 32370 34475 29241 30972 27402 23428 TRUE FALSE 34821.56639 30577.785 27793.93553 27622.39697 26867.75896 26468.70372 26949.01401 30556.871 26415.80737 28018.26804 1.24281652 1.091351719 0.991993348 0.985870966 0.958937181 0.9446945 0.961837255 1.090605278 0.942806576 1 14.77408016 4.633292792 1.957449227 0.988669917 1.288349222 0.797267352 0.040473685 0.285135269 1.384612446 0.011572784 0.142484064 42982.61087 -4.633292792 0.299679305 SCT(ph)WPLPRPEIANQPSEPPEVEPDLGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCTWPLPRPEIANQPSEPPEVEPDLGEK 28 1 P98177-2;P98177 P98177-2 FOXO4 Forkhead box protein O4 1 S(0.028)CT(0.972)WPLPRPEIANQPSEPPEVEPDLGEK 184.81 1.71E-17 108860000 108900 72811 95704 68092 135130 134060 128020 102580 113010 62992 TRUE FALSE 113199.4561 85315.72286 98198.12486 81560.39437 112160.6509 102926.5967 117985.4579 101205.0829 108942.7922 75334.07635 1.502632827 1.132498426 1.303502075 1.082649424 1.488843513 1.366268782 1.566163197 1.343417054 1.446128996 1 16.20101498 3.21901885 24.97317697 1.395750925 1.249989092 0.078024896 0.175775588 444.8848801 568534.3499 0.046687872 0.055877772 1655.841831 -3.21901885 -0.145761834 SCTKPS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SCTKPSPSK 9 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 SCTKPS(0.993)PS(0.007)K;SCT(0.001)KPS(0.917)PS(0.082)K;SCTKPS(0.999)PS(0.001)K;SCTKPS(0.959)PS(0.04)K 117.09 0.0021282 2823430000 3322480 1386580 2146580 1267320 3039420 2878220 3108210 2234650 2350400 1018216 TRUE FALSE 3453654.076 1624714.329 2202521.638 1517992.113 2522780.474 2209797.025 2864580.378 2204698.172 2265809.563 1217715.93 2.836173848 1.334230988 1.808731892 1.246589681 2.071731519 1.814706509 2.352420878 1.810519282 1.860704543 1 20.21574619 SCTPSPDQISHRAS(ph)LEDAPVDDLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SCTPSPDQISHRASLEDAPVDDLTR 25 1 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 SCTPSPDQIS(0.002)HRAS(0.998)LEDAPVDDLTR;SCTPSPDQIS(0.067)HRAS(0.933)LEDAPVDDLTR;SCTPSPDQIS(0.006)HRAS(0.994)LEDAPVDDLTR 205.03 2.68E-25 399272000 88699 127159 135062 120563 158485 168181 130810 159169 161048 178566 TRUE FALSE 92200.90501 148997.5691 138581.8267 144410.0016 131545.7763 129123.5116 120556.7704 157035.5999 155251.9139 213552.5888 0.431748009 0.697709028 0.648935363 0.676226883 0.615987739 0.60464503 0.56452966 0.735348612 0.726996169 1 17.70423186 0.773857379 0.9648 0.999026925 0.614226879 0.71517339 0.074093879 0.44384478 0.779651529 0.067624804 0.022259475 5.940970272 -0.773857379 -0.384800046 SCTVNIMFGT(ph)PQEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCTVNIMFGTPQEHR 15 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 SCTVNIMFGT(1)PQEHR 86.539 0.027661 110870000 74495 89282 84360 88377 94680 105440 90927 80927 91493 86134 TRUE FALSE 77436.12012 104615.489 86558.4909 105857.7068 78586.32742 80953.15796 83799.90415 79842.30593 88200.1848 103010.3082 0.751731759 1.01558272 0.840289603 1.027641881 0.762897702 0.78587434 0.813509887 0.775090448 0.856226783 1 16.65242919 3.210787362 24.99919956 0.814757408 0.911543764 0.112637944 0.098006724 334.0195561 300656.066 0.02591879 0.030985248 1624.753054 -3.210787362 0.096786356 SCVEEPEPEPEAAEGDGDKKGNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SCVEEPEPEPEAAEGDGDKKGNAEGSSDEEGKLVIDEPAK 40 3 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 2 SCVEEPEPEPEAAEGDGDKKGNAEGS(1)S(1)DEEGKLVIDEPAK 164.15 6.95E-19 152890000 262630 28513 54594 20554 105680 139950 96071 59203 67101 18797 TRUE FALSE 272998.8352 33409.88595 56016.76449 24619.51985 87716.55135 107448.7335 88540.70399 58409.48062 64686.04812 22479.91226 12.1441237 1.486210692 2.49185868 1.095178645 3.901997051 4.779766585 3.938658788 2.598296646 2.877504475 1 14.45634878 4.743604137 24.99667121 2.828851274 12.14412756 0.846998891 1.204635989 201.8827941 1000538.647 0.297478787 2.49187085 55412.03974 -4.743604137 9.315276282 SCYDLSCHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SCYDLSCHAR 10 0 P41250 P41250 GARS Glycine--tRNA ligase 0 ;;;; 174.41 3.11E-06 2386250000 646940 1575185 1358012 1381084 1879666 2023870 1351890 1498258 1369961 2000050 FALSE TRUE 672481.6907 1845710.771 1393402.908 1654258.293 1560161.045 1553856.865 1245925.329 1478176.302 1320656.371 2391921.504 0.281147057 0.771643537 0.582545416 0.69160225 0.652262644 0.649627031 0.520888887 0.617986961 0.552131986 1 21.18973861 -2.107934585 2.375358332 1.720266454 0.600930246 0.49269686 0.124116457 7577758.279 2406296.998 29424439.74 0.028667692 0.007799476 2.107934585 -1.119336209 SCYLSSLDLLLEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SCYLSSLDLLLEHR 14 0 Q9BQ69 Q9BQ69 MACROD1 O-acetyl-ADP-ribose deacetylase MACROD1 0 ; 148.08 7.86E-06 395190000 258710 632610 605380 640300 604160 838630 472890 657550 585840 710240 FALSE TRUE 268924.0706 741255.8465 621156.7001 766949.4289 501465.099 643870.8921 435823.6461 648736.6178 564755.7328 849397.9296 0.316605517 0.872683839 0.731290575 0.90293301 0.590377115 0.758032095 0.513097137 0.763760536 0.664889462 1 19.69608107 -1.871110919 2.178818305 1.161852538 0.690982522 0.251411104 0.164911813 6274833.819 3050758.175 5241953.155 0.039250707 0.013455167 1.871110919 -0.470870016 SDALETLGFLNHYQMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDALETLGFLNHYQMK 16 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;; 304.89 2.69E-46 4087840000 3252320 2670750 3228170 2739280 4255620 4045170 3771710 3298710 3328930 2607880 FALSE TRUE 3380724.105 3129430.537 3312298.762 3281101.408 3532251.232 3105740.573 3476073.515 3254496.188 3209122.46 3118844.155 1.083966988 1.003394329 1.062027661 1.052024803 1.132551374 0.995798577 1.114539022 1.043494329 1.028946077 1 21.57258003 1.105362582 2.38889978 1.001651284 1.061512118 0.196458718 0.040437663 0.417940053 4.618249387 0.035388879 0.009778043 12.74566742 -1.105362582 0.059860834 SDANRAS(ph)SGGGGGGLMEEMNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDANRASSGGGGGGLMEEMNK 21 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3;G3V314;H0YJL6 H0YJN0 EVL Ena/VASP-like protein 1 S(0.237)DANRAS(0.677)S(0.085)GGGGGGLMEEMNK 52.674 0.097672 0 25318 24296 30990 23827 38969 36508 31273 32255 33912 28327 TRUE FALSE 26317.57419 28468.649 31797.62486 28539.90948 32345.0633 28029.57028 28821.74054 31822.67448 32691.51374 33877.1333 0.776853636 0.840350001 0.938616163 0.842453499 0.954775689 0.827389084 0.850772711 0.939355588 0.965002365 1 15.04802418 7.999999959 0.044900509 1.275389086 0.223958918 0.496995683 0.049939438 544.6479524 1.853743392 11.03397068 41.38964937 99999990.49 -7.999999959 -1.051430168 SDATADDLIDVVEGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDATADDLIDVVEGNR 16 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 200.13 3.60E-12 0 15423 14197 14782 13214 18028 18881 13610 14045 14763 15369 FALSE TRUE 16031.91195 16635.22431 15167.23106 15827.68976 14963.607 14496.17389 12543.21264 13856.74975 14231.68251 18380.26129 0.872235258 0.905059185 0.825191265 0.861124307 0.814112855 0.788681601 0.682428418 0.753892969 0.774291632 1 14.16586966 3.080645844 1.925203159 0.772687299 0.869249269 0.090517595 0.079726526 0.488420578 3.696256182 0.025151571 0.031306689 1204.053666 -3.080645844 0.096561971 SDDNRESLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDDNRESLEK 10 1 P30085;P30085-3;A0A494BXC7;P30085-2 P30085 CMPK1 UMP-CMP kinase 0 67.456 0.057381 268400000 186800 146150 193230 127290 249360 234450 161630 167250 200130 166320 FALSE TRUE 194175.0082 171250.1256 198265.7325 152467.5821 206973.8763 180002.5406 148961.0183 165008.2873 192927.3604 198907.2196 0.976208951 0.860954801 0.996774943 0.766526134 1.040554871 0.904957301 0.748896991 0.829574148 0.96993644 1 17.60173612 2.462471804 24.99603987 0.85921631 0.924641375 0.006271534 0.09771531 588.3781172 1003930.78 0.032391403 0.027110824 290.049288 -2.462471804 0.065425065 SDDS(ph)KS(ph)SSPELVTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDDSKSSSPELVTHLK 16 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 2 S(0.001)DDS(0.854)KS(0.496)S(0.347)S(0.301)PELVTHLK;S(0.001)DDS(0.98)KS(0.795)S(0.145)S(0.079)PELVTHLK 126.69 9.33E-05 430410000 920070 243250 356390 244250 488570 545640 550360 337190 325370 126897 TRUE FALSE 956395.074 285026.2953 365677.8162 292561.921 405523.0459 418923.3793 507221.3451 332670.5196 313659.9973 151760.0376 6.302021859 1.878138012 2.40957911 1.927792887 2.672133273 2.760432759 3.342258959 2.192082481 2.066815496 1 17.21143242 4.742782888 24.87339208 2.353271484 6.302023533 0.80330395 0.599573793 163.7955248 964880.6898 0.137418379 1.068753649 55307.35486 -4.742782888 3.948752049 SDEAVKPFGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 168.94 1.59E-05 27654360000 39217220 21513130 32163740 24843930 44754540 40299410 39131520 30384360 35756320 18043020 FALSE TRUE 40765546.13 25207842.73 33001953.49 29757985.2 37147179.28 30940482.77 36064289.21 29977107.35 34469457.03 21578204.31 1.889200118 1.168208548 1.529411484 1.37907607 1.721513928 1.433876625 1.67132949 1.389230861 1.597420088 1 24.36307148 -0.988881932 5.185788846 0.999997058 1.515276658 0.401383055 0.193693771 5.86E-06 1.14E-06 0.166753148 0.039303869 0.10259308 0.988881932 0.515279599 SDEGIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDEGIYR 7 0 H9KV31;O15394-2;O15394 H9KV31 NCAM2 Neural cell adhesion molecule 2 0 99.511 0.024369 224050000 152000 180570 183750 196870 219880 248680 200330 184940 185980 199710 FALSE TRUE 158001.0774 211581.4929 188538.676 235810.2984 182504.8761 190927.8388 184627.6111 182461.1818 179286.6161 238839.3508 0.661537041 0.885873673 0.789395363 0.987317616 0.764132357 0.799398584 0.773020068 0.763949413 0.750657777 1 17.86568103 SDEGQLS(ph)PATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(1)PATR;SDEGQLS(0.969)PAT(0.031)R;SDEGQLS(1)PATR;SDEGQLS(0.999)PAT(0.001)R 212.69 5.33E-09 7659659000 2847194 3002166 2988438 3058706 3263913 3877052 3288216 2994267 3017948 2445492 TRUE FALSE 2959603.418 3517764.657 3066319.149 3663708.917 2709114.234 2976665.43 3030477.038 2954133.748 2909332.641 2924639.336 1.011955006 1.202802894 1.048443516 1.252704521 0.926307118 1.017788892 1.036188292 1.010084803 0.994766297 1 21.47982729 3.224596984 24.99999742 1.00239499 1.128497476 0.461466951 0.069448485 199.8792957 357856.1091 0.018469019 0.022175287 1677.246845 -3.224596984 0.126102486 SDEMNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDEMNVK 7 0 F8VPF3;P60660;F8W1R7;J3KND3;G3V1V0;B7Z6Z4;P60660-2;G8JLA2 F8VPF3;P60660;P60660-2 MYL6 Myosin light polypeptide 6 0 ; 95.352 0.037373 237980000 527640 448070 521040 438610 757680 656790 682470 537120 571620 429090 FALSE TRUE 548471.6346 525022.537 534618.7304 525365.7489 628889.8242 504260.4762 628976.2181 529920.785 551047.5079 513161.9701 1.068808031 1.023112716 1.041812842 1.023781534 1.225519156 0.982653637 1.225687511 1.032657944 1.073827641 1 18.96905473 SDES(ph)PKPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SDESPKPGK 9 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK;SDES(1)PKPGK 114.86 0.0009504 2263950000 8398680 2125530 3288440 1960620 5413350 6396610 5266700 3442770 3860440 1484990 TRUE FALSE 8730266.372 2490573.243 3374139.448 2348424.784 4493190.701 4911094.269 4853882.292 3396625.299 3721503.518 1775945.359 4.915841768 1.402392946 1.899911746 1.322351937 2.530027559 2.765340862 2.73312592 1.912573088 2.095505642 1 20.76015576 4.746490317 24.72783285 2.040660076 4.915843409 0.703236826 0.573559224 485.8594474 1515054.14 0.138390741 1.516928287 55781.51656 -4.746490317 2.875183333 SDETAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDETAAK 7 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 ;;; 117.16 0.012315 937010000 987830 823050 954740 722540 1441670 1339480 1249490 966850 1155160 852510 FALSE TRUE 1026830.291 964402.4351 979621.3087 865456.2554 1196615.448 1028406.07 1151551.709 953890.9572 1113586.017 1019543.012 1.007147593 0.94591638 0.960843532 0.84886684 1.17367824 1.008693167 1.129478301 0.93560639 1.092240351 1 19.95949121 3.249348245 24.99990246 1.048228009 0.942505958 0.370125759 0.073582477 249.7051322 578678.3463 0.019877108 0.026644166 1775.61271 -3.249348245 -0.105722051 SDFFELLSNHHLDSQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDFFELLSNHHLDSQSR 17 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 135.28 8.19E-06 165800000 55227 161340 188110 196170 166330 247620 185260 199520 162770 162800 FALSE TRUE 57407.4046 189048.8899 193012.3011 234971.8405 138057.286 190114.0077 170738.8371 196845.7607 156911.9395 194697.543 0.294854284 0.970987548 0.991344308 1.206855705 0.709085918 0.976458176 0.876943974 1.011033615 0.805926655 1 17.57087515 4.739561376 24.89947812 0.952136828 0.294854063 0.707993923 0.126186631 41.04904198 1021174.878 0.028645051 0.175062834 54898.61345 -4.739561376 -0.657282765 SDGAHFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDGAHFQK 8 0 Q9BW83-2;Q9BW83;B1AH58;F5GZ09 Q9BW83-2 IFT27 Intraflagellar transport protein 27 homolog 0 ; 87.616 0.015198 327890000 267471 370380 371300 368500 456120 504830 416810 416750 401770 367550 FALSE TRUE 278030.9616 433989.8838 380976.383 441388.2001 378588.8853 387590.8833 384139.3431 411164.1479 387310.3762 439564.3853 0.63251476 0.987318123 0.866713491 1.004149141 0.861281983 0.881761344 0.873909161 0.93539004 0.881123196 1 18.74571497 4.747539289 24.94926252 0.915828948 0.632514609 0.714459726 0.054670492 579.5188054 1610287.97 0.011952984 0.146450067 55916.41108 -4.747539289 -0.283314339 SDGQFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDGQFKK 7 1 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 106.36 0.012379 1094670000 1141380 725780 965470 634280 1293470 1146100 1137030 966770 1056140 632440 FALSE TRUE 1186442.564 850427.0692 990630.9413 759738.6909 1073606.431 879935.6443 1047906.618 953812.0295 1018129.728 756354.5092 1.568632895 1.12437628 1.309744213 1.004474333 1.419448709 1.163390492 1.385470179 1.261064776 1.34610122 1 19.52870307 -1.658659227 2.517158551 0.961620715 1.277789184 0.239025132 0.152821348 10618576.71 8694235.447 2626308.375 0.036710046 0.021945262 1.658659227 0.316168469 SDGSLEDGDDVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 0 ; 175.74 1.42E-06 107930000 257190 440500 412970 478490 418130 589350 370450 448930 392210 526250 FALSE TRUE 267344.0598 516152.4484 423732.3375 573133.8938 347056.412 452482.3942 341413.161 442912.8277 378094.4387 629358.6118 0.424788117 0.82012455 0.673276459 0.910663464 0.551444606 0.718957977 0.542477936 0.703752708 0.600761524 1 19.26352278 -1.63564015 4.408956205 1.008190252 0.669064104 0.365092543 0.133826139 0.010042681 0.000829935 0.120781621 0.027973879 0.023139813 1.63564015 -0.339126147 SDIDEIVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDIDEIVLVGGSTR 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 181.49 3.80E-06 83366000 114825 129995 118022 138987 149270 179488 137872 114532 113813 107365 FALSE TRUE 119358.3797 152320.63 121097.7503 166478.2138 123897.1387 137804.6322 127065.2324 112996.8859 109716.8924 128401.1161 0.929574316 1.18628743 0.943120698 1.296548027 0.964922599 1.07323547 0.989596011 0.880030402 0.854485504 1 16.97029822 2.013484789 2.710548447 0.899997306 1.07227788 0.2737428 0.111675038 0.313350113 4.40848553 0.051824546 0.029927275 103.1536949 -2.013484789 0.172280574 SDKGS(ph)PGEDGFVPSALGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDKGSPGEDGFVPSALGTR 19 1 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 1 SDKGS(1)PGEDGFVPSALGTR;SDKGS(1)PGEDGFVPSALGTR 206.69 2.13E-16 913360000 790780 545900 707820 505460 979100 941830 871430 750930 738810 468460 TRUE FALSE 822000.605 639654.0785 726266.3707 605438.4794 812672.9317 723104.2561 803125.0395 740865.0116 712220.3724 560245.7678 1.467214305 1.14173835 1.296335309 1.080665869 1.450565053 1.290691153 1.433522725 1.322392875 1.271264173 1 19.09570032 0.804167321 4.450787042 1.000005229 1.307225724 0.376933433 0.118928965 2.607700435 58.42299123 0.109236578 0.027747579 6.370409071 -0.804167321 0.307220495 SDKLHELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 64.04 0.065773 134600000 18170 577920 422610 438000 313270 616460 188560 454140 317700 868350 FALSE TRUE 18887.36563 677173.2644 433623.5638 524635.0927 260020.4773 473296.5075 173780.1745 448052.9961 306266.0391 1038486.557 0.018187395 0.652077063 0.417553372 0.505191992 0.250384057 0.455756027 0.16733984 0.431448046 0.294915747 1 19.98605111 -1.433398741 3.53856449 1.006258679 0.366365361 0.558582992 0.171798264 267359034.5 402018605 16929342.44 0.037712302 0.036863898 1.433398741 -0.639893318 SDKNNEFIVIHNGIITNYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKNNEFIVIHNGIITNYK 19 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 130.56 1.04E-05 411290000 422330 265340 356010 286840 507790 467490 459900 392050 391760 221840 FALSE TRUE 439003.9145 310910.0809 365287.9131 343576.0959 421476.0372 358922.5324 423851.8363 386795.211 377660.6341 265305.3006 1.654712188 1.171895474 1.376858707 1.295021604 1.588645369 1.352866044 1.597600332 1.457924927 1.423494492 1 18.01729397 0.90657586 17.42513522 0.999999999 1.433428479 0.463177772 0.140661885 1820.930069 339637.1588 0.128778289 0.032198975 8.064470542 -0.90657586 0.43342848 SDKNQQGFS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKNQQGFSPK 11 1 D6RCT7;C9JKA9;Q9NS87-4;Q9NS87-2;Q9NS87 D6RCT7 KIF15 Kinesin-like protein;Kinesin-like protein KIF15 1 S(0.001)DKNQQGFS(0.999)PK 55.452 0.075847 137540000 265040 96625 139700 93474 207370 225570 194770 142820 160310 79610 TRUE FALSE 275503.9839 113219.5921 143340.6968 111962.8782 172121.3215 173184.786 179503.4185 140905.7315 154540.4744 95208.05527 2.893704562 1.189180808 1.505552197 1.175981149 1.807844105 1.819014006 1.88538058 1.479976995 1.623186966 1 16.53879602 -2.561630352 0.259521643 7.86E-22 1.750050996 0.190154351 0.455705182 83.2267488 2.524636378 48.29956477 0.615353023 0.002743909 2.561630352 1.750050996 SDKQYAENYTRPS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKQYAENYTRPSSR 15 2 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 SDKQYAENYT(0.073)RPS(0.463)S(0.463)R 78.552 0.01178 57804000 42724 57790 61403 45494 69280 77102 51139 58333 60058 62145 TRUE FALSE 44410.77651 67714.98296 63003.21262 54492.57741 57503.81035 59196.22899 47130.59155 57551.14155 57896.52431 74321.12291 0.59755255 0.911113561 0.847716102 0.733204441 0.773720957 0.796492661 0.634148001 0.774357804 0.779004973 1 16.18148468 -1.98590574 5.432143498 1.198152155 0.76364715 0.404713182 0.08696495 0.051598708 0.000133878 0.020818675 0.018956743 0.010329856 1.98590574 -0.434505006 SDKQYAENYTRPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDKQYAENYTRPSSR 15 2 C9JSU1;Q9Y608-4;Q9Y608;Q9Y608-2;Q9Y608-5 C9JSU1;Q9Y608-2 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 SDKQYAENYT(0.002)RPS(0.195)S(0.803)R;SDKQYAENYTRPS(0.029)S(0.971)R 161.04 1.32E-06 653650000 356270 314520 366010 269670 471290 469090 349710 343380 366590 308850 TRUE FALSE 370335.8147 368536.3634 375548.5213 323009.9211 391180.2941 360150.9566 322298.8164 338777.5528 353396.4975 369363.2442 1.0026331 0.997761334 1.016745784 0.874504776 1.059066651 0.975059003 0.872579558 0.917193462 0.956772237 1 18.49468078 2.454367653 24.32698267 0.926034195 0.988763628 0.173694028 0.053296573 243.9883438 260857.602 0.017865915 0.014948677 284.6870111 -2.454367653 0.062729432 SDKS(ph)PDLAPTPAPQSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;S(0.027)DKS(0.973)PDLAPTPAPQSTPR;S(0.06)DKS(0.94)PDLAPTPAPQSTPR;S(0.001)DKS(0.999)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR;SDKS(1)PDLAPTPAPQSTPR 210.26 2.62E-16 26676170000 9312200 4533939 6385410 4613260 8897690 9284430 8470290 6806200 7207670 3897677 TRUE FALSE 9679852.847 5312607.754 6551819.03 5525749.059 7385263.832 7128261.839 7806366.537 6714974.022 6948267.365 4661352.183 2.076619073 1.139713874 1.4055619 1.185439083 1.584360834 1.52922619 1.674700008 1.440563544 1.490611971 1 22.15231709 -0.009237843 2.099403379 0.999967997 1.487479736 0.268504965 0.247864852 150.7669205 307.6485187 0.233433777 0.060800954 0.97895371 0.009237843 0.487511739 SDKSPDLAPT(ph)PAPQSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-4;Q9BY44-3;Q9BY44;Q9BY44-2 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 SDKS(0.408)PDLAPT(0.592)PAPQSTPR 282.26 1.44E-38 538480000 751800 391260 540030 384880 767990 839340 717130 578660 583320 365780 TRUE FALSE 781481.6445 458455.8614 554103.6254 461008.1152 637447.3341 644416.0053 660919.4767 570904.0092 562326.4271 437447.5877 1.786457776 1.048024665 1.266674319 1.053859087 1.457197049 1.473127349 1.510854089 1.305079797 1.285471547 1 18.73875065 0.738250923 2.114453276 1.000334148 1.350925303 0.214373647 0.20743783 1.770316352 11.70933578 0.192366984 0.052690706 5.473321043 -0.738250923 0.350591155 SDLDYIRS(ph)PLPFQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDLDYIRSPLPFQNR 15 1 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 1 SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR;SDLDYIRS(1)PLPFQNR 229.22 2.98E-13 1822950000 1529010 1684410 1672730 1816780 1864700 2171710 1996140 1895820 1790990 1605290 TRUE FALSE 1589376.495 1973694.315 1716322.718 2176133.661 1547738.96 1667363.265 1839677.331 1870409.634 1726532.62 1919815.84 0.827879665 1.028064397 0.894003832 1.133511671 0.806191369 0.868501671 0.958257189 0.974265132 0.899321999 1 20.8725365 -1.07245143 4.312457544 1.000006185 0.938147565 0.04258939 0.092649413 1.80504E+11 38830377929 11598284.35 0.020370864 0.084634722 1.07245143 -0.06185862 SDLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDLESR 6 0 P61019;P61019-2;A0A3B3ITL1;Q8WUD1;H7C125;Q8WUD1-2 P61019 RAB2A;RAB2B Ras-related protein Rab-2A;Ras-related protein Rab-2B 0 ; 99.384 0.090404 462529000 405366 455736 440919 448698 470061 607730 443648 411701 411595 458345 FALSE TRUE 421370.1627 534005.1129 452409.7114 537449.1252 390160.1991 466593.9177 408873.7105 406182.8215 396781.7764 548148.9272 0.768714745 0.974197132 0.825340868 0.980480119 0.71177773 0.851217424 0.745917196 0.741008148 0.723857617 1 19.06420839 3.230833438 24.99998994 0.779270367 0.888981189 0.158447637 0.099120214 245.4230073 794024.2687 0.02617883 0.031841471 1701.505815 -3.230833438 0.109710822 SDLNGLPS(ph)PVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDLNGLPSPVEER 13 0 E7EWN3;Q9C0A6 E7EWN3 SETD5 SET domain-containing protein 5 1 SDLNGLPS(1)PVEER 201.04 4.70E-07 0 229210 187920 198660 154490 225170 273150 212090 195390 195180 151230 TRUE FALSE 238259.3878 220193.7982 203837.2428 185047.6609 186895.6838 209715.0521 195465.8316 192771.1166 188155.5099 180860.623 1.31736463 1.217477826 1.127040477 1.023150633 1.033368572 1.159539587 1.080753944 1.065854543 1.040334302 1 17.46451881 4.357100643 1.848950758 1.064974905 1.321946553 0.803233986 0.042162681 0.186627317 1.081375934 0.011447956 0.064403127 22756.2472 -4.357100643 0.256971648 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDLQPPNYYEVMEFDPLAPAVTTEAIYEEIDAHQHK 36 0 J3KQU4;I3L4I4;O75674;O75674-3 J3KQU4 TOM1L1 TOM1-like protein 1 0 62.663 0.0082843 21988000 13572 11844 16364 13154 18861 17684 17890 15235 15057 8764.5 FALSE TRUE 14107.83304 13878.11487 16790.45928 15755.82194 15655.01396 13577.159 16487.73505 15030.79974 14515.10151 10481.73597 1.345944325 1.324028282 1.601877717 1.50316913 1.493551641 1.295315876 1.572996601 1.433999081 1.384799384 1 13.35559005 0.695490381 2.386255393 1.000078552 1.451034015 0.653775647 0.096850166 1.054475352 7.464171458 0.092074534 0.024752712 4.960099413 -0.695490381 0.450955463 SDLYSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 242 1.90E-08 1322030000 362270 448970 463310 404130 502630 569940 470750 444410 422780 428620 FALSE TRUE 376572.6993 526077.105 475384.2392 484065.7078 417193.1321 437580.0725 433851.3849 438453.4109 407564.2304 512599.8826 0.734632824 1.026291895 0.92739826 0.94433441 0.813876761 0.853648406 0.846374335 0.855352148 0.795092321 1 18.96747362 3.245135182 24.99991346 0.852482826 0.917975882 0.059598204 0.085277733 324.4203159 1233607.002 0.022087399 0.029232457 1758.470883 -3.245135182 0.065493056 SDNKDDDIDIDAI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDNKDDDIDIDAI 13 1 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 90.653 0.04655 191910000 3505200 1922870 2645170 1849610 3736700 3854900 3551200 2700170 3005100 1642690 FALSE TRUE 3643588.003 2253107.965 2714105.303 2215457.337 3101537.069 2959657.897 3272847.665 2663978.638 2896947.038 1964543.654 1.854673982 1.146886179 1.381544919 1.127721103 1.578757012 1.506537098 1.665958228 1.35602924 1.474615762 1 20.9057628 -1.312920677 5.050231703 0.999850232 1.441906314 0.294961672 0.210075978 0.000335365 4.56E-05 0.192561542 0.045371954 0.048649606 1.312920677 0.442056083 SDNSDIRPS(ph)GSPPPPTLPASPSNHVSSLPPFIAPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDNSDIRPSGSPPPPTLPASPSNHVSSLPPFIAPPGR 37 1 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 S(0.043)DNS(0.032)DIRPS(0.462)GS(0.462)PPPPT(0.001)LPASPSNHVSSLPPFIAPPGR 114.72 5.11E-06 197840000 3575.8 30252 27410 28103 22470 43043 20714 40972 21341 31769 TRUE FALSE 3716.975345 35447.54567 28124.32712 33661.68952 18650.55743 33046.91557 19090.38255 40422.83736 20572.94158 37993.5273 0.097831805 0.932989069 0.74023996 0.885984848 0.490887758 0.86980383 0.502464075 1.063940103 0.541485433 1 15.21346604 4.746678115 24.62754752 0.778936707 0.097831388 0.517895189 0.197695243 622.1836643 1887579.624 0.042980337 0.478666159 55805.64278 -4.746678115 -0.681105319 SDPDGGDS(ph)PLPASGGPLTCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDPDGGDSPLPASGGPLTCK 20 0 Q8N1G0 Q8N1G0 ZNF687 Zinc finger protein 687 1 SDPDGGDS(1)PLPASGGPLTCK;SDPDGGDS(1)PLPASGGPLTCK 246.48 9.44E-30 109340000 278606 208329 277954 223265 305950 307200 309040 267042 300576 168144 TRUE FALSE 289605.58 244107.8852 285197.7096 267426.1506 253944.7283 235857.4557 284816.6373 263462.7388 289758.3285 201088.5975 1.44018897 1.213932009 1.418268928 1.329892167 1.262849965 1.172903181 1.416373881 1.310182388 1.440948577 1 17.61747175 -1.897074737 2.669008452 0.825686569 1.32818009 0.546874988 0.091057829 11420818.6 7508602.17 12541310.37 0.022092294 0.012674337 1.897074737 0.502493521 SDPDHLAELVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDPDHLAELVK 11 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0 Q9UM54-1 MYO6 Unconventional myosin-VI 0 100.93 0.0036614 157090000 420170 371170 476460 410620 646370 579190 589610 540160 525420 339200 FALSE TRUE 436758.636 434915.5602 488876.939 491839.4104 536500.2583 444681.9002 543394.8275 532920.0387 506510.2368 405659.7456 1.0766625 1.072119097 1.205140378 1.212443225 1.32253758 1.096194298 1.339533521 1.313711909 1.248608575 1 18.62991062 4.158698981 2.745046628 1.2419958 1.067837943 0.220043752 0.101090082 0.314831887 4.709302955 0.024993755 0.071820858 14411.16137 -4.158698981 -0.174157858 SDPEGENIHAGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDPEGENIHAGLLK 14 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 103.21 0.0011288 160760000 159660 139460 150100 135310 182100 196100 185240 158210 147070 118460 FALSE TRUE 165963.5001 163411.1702 154011.7293 162073.9141 151146.707 150558.7469 170720.4048 156089.4537 141776.9794 141669.9689 1.171479752 1.153463725 1.087116278 1.144024491 1.066893063 1.062742853 1.20505712 1.101782226 1.000755351 1 17.11217444 -5 0.091995813 0.601104934 1.210637069 0.419775996 0.05020523 223.8800124 1.426213006 17.12632117 1.137749886 1.00E-05 5 0.609532135 SDPES(ph)PIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDPESPIKK 9 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 S(0.001)DPES(0.999)PIKK;S(0.006)DPES(0.994)PIKK;SDPES(1)PIKK 89.403 0.00743 628800000 3002780 1233830 1813750 1208350 2952080 2779680 2610650 2036930 2388630 1071520 TRUE FALSE 3121332.073 1445730.705 1861017.815 1447358.023 2450286.496 2134141.446 2406020.431 2009628.285 2302663.673 1281463.829 2.435755113 1.1281869 1.452259341 1.129456791 1.912099617 1.665393434 1.877556259 1.568228646 1.79690103 1 20.28936133 SDPFLEFFR ddPTM_MDA-MB-175_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 ;;;; 147.29 0.00021579 953446000 454700 595496 625419 522734 1022873 891378 696233 572061 677380 968747 FALSE TRUE 472651.9071 697767.8057 641717.9329 626129.225 849005.4128 684368.9685 641660.4382 564393.458 653001.2261 1158554.427 0.407966942 0.602274515 0.55389537 0.540440061 0.732814439 0.590709381 0.553845744 0.487153167 0.563634484 1 20.14389439 -1.339474227 2.966120405 1.004815544 0.560194097 0.73984754 0.078415461 7598901.037 9398474.041 319760.0931 0.019320628 0.045764189 1.339474227 -0.444621446 SDPMVQCIIEESGEHIIAGAGELHLEICLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 SDPMVQCIIEESGEHIIAGAGELHLEICLK 30 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;;;;;; 335.34 9.89E-106 4459290000 1735736.6 1758209.5 2096049 1892468 2469932 2711245 2368726 2215907 2421379 1652076 FALSE TRUE 1804264.821 2060168.305 2150673.759 2266792.522 2050093.841 2081599.438 2183059.067 2186206.391 2334234.043 1975768.661 0.913196396 1.042717371 1.088525089 1.147296526 1.037618361 1.053564356 1.104916334 1.106509296 1.181430847 1 20.9139826 4.717746559 2.164922764 1.094089444 0.869803895 0.536546229 0.049457484 0.453359436 2.494941537 0.012148904 0.193464554 52209.14237 -4.717746559 -0.224285548 SDPNRETDDTLVLSFVGQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDPNRETDDTLVLSFVGQTR 20 1 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ; 150.98 7.40E-08 184953000 46803 84870 67714 50966 76065 85414 47615 61544 54266 92076 FALSE TRUE 48650.81858 99445.7623 69478.68247 61046.92268 63135.49847 65577.89296 43882.81188 60719.10335 52312.97726 110116.5293 0.441812132 0.903095684 0.630955978 0.554384733 0.573351693 0.595531782 0.398512486 0.551407711 0.475069252 1 16.74867152 -1.107732179 4.625471206 1.000031907 0.572388118 0.494048246 0.130710493 4.31E-05 8.32E-06 0.126909585 0.029910648 0.078031117 1.107732179 -0.42764379 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACK 41 0 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ; 387.74 1.56E-194 2030740000 300770 380420 403330 324040 496620 529820 456240 415070 467310 363890 FALSE TRUE 312644.6318 445754.1757 413841.1111 388134.1448 412204.7098 406777.3345 420478.7166 409506.6656 450491.6044 435187.2784 0.718413996 1.024281264 0.950949469 0.891878426 0.947189245 0.93471789 0.966201765 0.940989514 1.035167218 1 18.73127686 4.74826863 24.98169766 0.95884223 0.718413866 0.757973953 0.041759841 644.1688548 1657610.381 0.009707966 0.129204782 56010.39435 -4.74826863 -0.240428364 SDPYSTGHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDPYSTGHLR 10 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 0 123.96 0.0034278 0 40566 70313 57062 75323 75574 100400 72045 72921 59608 86383 FALSE TRUE 42167.577 82388.71079 58549.0826 90221.66458 62727.95847 77083.62158 66397.92465 71943.61327 57462.71972 103308.0949 0.408173019 0.797504889 0.566742448 0.873326186 0.607193062 0.746152774 0.64271754 0.696398606 0.55622669 1 16.65659378 -2.171996533 2.467913114 1.887532414 0.666091607 0.398557733 0.126499752 19013788.2 3576860.952 94670355.68 0.028255962 0.00672982 2.171996533 -1.221440807 SDQWKPLNLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDQWKPLNLEEK 12 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ; 178.84 1.96E-05 1377970000 1226060 569220 792940 513960 1283640 1140440 1023300 846290 1020040 532820 FALSE TRUE 1274465.796 666979.1071 813604.6678 615619.754 1065447.331 875590.0935 943091.0721 834946.8668 983328.9597 637215.8775 2.000053421 1.046708236 1.276811669 0.966108623 1.672035128 1.374087063 1.480018162 1.310304555 1.543164561 1 19.28142269 -1.076211795 4.607622389 0.999978707 1.384428155 0.152822713 0.283244676 5.74E-05 1.15E-05 0.254118192 0.059892917 0.08390507 1.076211795 0.384449448 SDRPELTGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDRPELTGAK 10 1 H0YL12;P13804-2;P13804;H0YK49;H0YNX6;H0YKF0;H0YLU7 H0YL12 ETFA "Electron transfer flavoprotein subunit alpha, mitochondrial" 0 86.114 0.012566 62433000 86606 70427 83034 77827 76236 102580 99814 96984 83925 84643 FALSE TRUE 90025.27175 82522.2894 85197.93425 93220.94831 63277.43195 78757.34961 91990.31786 95684.08811 80904.55564 101227.1753 0.88933897 0.815218731 0.841650812 0.920908324 0.625103208 0.778025757 0.908751209 0.945241116 0.799237511 1 16.62723712 -1.331439317 6.301605214 1.000009734 0.841043426 0.237147066 0.087845766 1.27E-05 1.34E-06 0.089657518 0.021131186 0.046618756 1.331439317 -0.158966307 SDS(ph)ASSEPVGIYQGFEK ddPTM_MDA-MB-175_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(0.389)DS(0.611)ASSEPVGIYQGFEK 257.15 4.24E-27 66772000 81537 71857 98216 76187 107530 118910 121670 89327 98927 66117 TRUE FALSE 84756.14372 84197.88078 100775.5896 91256.5612 89252.08901 91294.9546 112133.1875 88129.71767 95366.63659 79071.36026 1.071894342 1.0648341 1.274489136 1.154103849 1.128753682 1.154589402 1.418126451 1.114559271 1.206083167 1 16.27086762 4.266854669 24.56501983 1.190104988 1.068363961 0.15550129 0.103712676 285.7239387 248061.0668 0.02393045 0.065504127 18486.49887 -4.266854669 -0.121741027 SDS(ph)DAEAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSDAEAQGK 10 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.002)DS(0.998)DAEAQGK 142.51 3.74E-05 115850000 240460 162320 277330 174090 349760 310170 303090 237640 268400 187300 TRUE FALSE 249953.5465 190197.1973 284557.4476 208524.4824 290307.9201 238137.7182 279333.0138 234454.8245 258740.3364 223997.8489 1.115874763 0.849102785 1.270357948 0.930921807 1.296029946 1.063125022 1.247034358 1.046683375 1.15510188 1 17.77312535 3.258717659 24.99998363 1.135195943 1.044159557 0.104896787 0.133137931 562.5140029 697659.5938 0.033919687 0.045870815 1814.335752 -3.258717659 -0.091036386 SDS(ph)DSSTLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSDSSTLPR 10 0 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 SDS(1)DSSTLPR;S(0.001)DS(0.918)DS(0.07)S(0.006)T(0.006)LPR;SDS(1)DSSTLPR 223.96 4.40E-09 935050000 1036680 1051770 1074340 959610 1307560 1417470 1193940 1067970 1089100 962970 TRUE FALSE 1077608.927 1232403.316 1102338.183 1149417.994 1085301.418 1088284.074 1100355.863 1053655.609 1049903.504 1151645.534 0.935712331 1.070123818 0.957185306 0.998065776 0.942391896 0.944981804 0.955464012 0.91491312 0.911655082 1 20.13526531 3.229105122 12.35123509 0.939704076 0.993615999 0.229707347 0.039841765 0.555482163 716.4060625 0.010736952 0.013242309 1694.747967 -3.229105122 0.053911923 SDS(ph)DSSTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSDSSTLSK 10 0 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 S(0.005)DS(0.955)DS(0.011)S(0.011)T(0.017)LSK;SDS(0.982)DS(0.013)S(0.004)T(0.001)LSK 147.26 2.85E-05 312970000 618210 451080 528710 407880 701460 785620 751820 586370 653080 385540 TRUE FALSE 642617.4082 528549.4811 542488.6169 488557.4466 582226.0798 603171.6612 692890.3839 578510.6693 629575.7784 461079.1814 1.393724623 1.146331265 1.176562809 1.059595545 1.262746407 1.308173705 1.502757903 1.254688333 1.365439612 1 18.814655 3.007590762 24.6114055 1.312747837 1.185867408 0.071032725 0.141732909 278.830138 904036.3499 0.038977892 0.046498823 1017.632016 -3.007590762 -0.126880429 SDS(ph)ENVYEVIQDLHVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSENVYEVIQDLHVPPR 18 0 A0A0G2JRG8;A0A0G2JNY3;A0A0G2JP16 A0A0G2JRG8 1 S(0.078)DS(0.613)ENVY(0.309)EVIQDLHVPPR;S(0.017)DS(0.982)ENVY(0.001)EVIQDLHVPPR 151.42 3.08E-08 64976000 75215 85929 101538 96832 113210 115248 125533 100212 109929 69415 TRUE FALSE 78184.54628 100686.6373 104184.1637 115985.0806 93966.60464 88483.3986 115693.3954 98868.82205 105972.6768 83015.54022 0.941806149 1.212864929 1.254995913 1.397149019 1.131915836 1.06586548 1.393635398 1.19096764 1.276540229 1 16.34109381 -2.338342203 1.975019949 3.75E-05 1.214663492 0.179312376 0.132208647 3462343.781 399699.4697 15436773.55 0.031648449 0.004588363 2.338342203 1.21462595 SDS(ph)ENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SDSENVYEVIQDLHVPPREESAEQVDDPPEPVYANIER 38 1 A0A0G2JRG8;A0A0G2JNY3 A0A0G2JRG8 1 S(0.176)DS(0.812)ENVY(0.012)EVIQDLHVPPREESAEQVDDPPEPVYANIER;S(0.202)DS(0.795)ENVY(0.003)EVIQDLHVPPREESAEQVDDPPEPVYANIER;S(0.184)DS(0.805)ENVY(0.01)EVIQDLHVPPREES(0.001)AEQVDDPPEPVYANIER 82.994 0.00051245 182475000 36446.7 39629.4 45783.4 37902.2 61459 55012 43950.9 47820.1 47570.4 41897.7 TRUE FALSE 37885.64386 46435.44118 46976.55302 45399.14203 51012.22113 42236.29671 40505.91361 47179.14978 45858.3506 50106.75214 0.756098574 0.926730215 0.937529395 0.906048389 1.018070798 0.842926251 0.80839232 0.941572698 0.915212993 1 15.61271741 -5 0.26289611 1.667288496 0.890587936 0.175058922 0.070436047 385.6314295 3.777365936 139.1419642 0.091261642 1.00E-05 5 -0.776700561 SDS(ph)FENPVLQQHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 1 S(0.005)DS(0.995)FENPVLQQHFR;S(0.011)DS(0.989)FENPVLQQHFR;S(0.007)DS(0.993)FENPVLQQHFR;S(0.011)DS(0.989)FENPVLQQHFR 232.62 6.40E-14 919640000 916330 792590 937780 613150 1135340 1127600 1013630 1012750 1057780 768110 TRUE FALSE 952507.416 928711.167 962219.3172 734429.2399 942355.3123 865731.9889 934179.032 999175.7428 1019710.704 918606.4481 1.036904779 1.011000052 1.047477208 0.799503685 1.025853143 0.942440575 1.0169524 1.087708174 1.110062646 1 19.80908739 1.947548283 4.157717429 1.072919666 0.976025811 0.231289955 0.071982197 0.303439128 10.44473317 0.033120078 0.019622767 88.62337456 -1.947548283 -0.096893855 SDS(ph)LLSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 S(0.002)DS(0.995)LLS(0.003)FR;S(0.034)DS(0.966)LLSFR;SDS(0.978)LLS(0.022)FR;S(0.001)DS(0.783)LLS(0.216)FR;S(0.007)DS(0.993)LLSFR;S(0.002)DS(0.998)LLSFR 174.8 0.00028303 633057000 694158 837756 859860 807033 1025870 1181800 864930 880050 841904 859259 TRUE FALSE 721563.8938 981634.0762 882268.658 966661.7186 851492.9838 907344.8604 797134.5265 868254.3692 811604.0395 1027614.35 0.702173821 0.955255322 0.85856008 0.940685306 0.828611418 0.882962427 0.775713697 0.844922387 0.789794381 1 19.97086751 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 Q12888;Q12888-2;A6NNK5;Q12888-3 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 S(0.037)DS(0.963)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.106)DS(0.894)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.118)DS(0.882)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.129)DS(0.871)PEIPFQAAAGPSDGLDASSPGNSFVGLR 219.65 4.33E-35 1347510000 773340 688930 777450 730780 882450 1027480 906650 796510 830490 604650 TRUE FALSE 803872.0603 807248.3684 797710.9857 875326.1028 732451.4642 788863.3416 835584.4039 785834.0863 800600.8271 723119.5908 1.111672358 1.116341444 1.103152225 1.210485947 1.012905021 1.090916844 1.155527266 1.086727695 1.107148579 1 19.46387474 -5 0.27779295 0.200414117 1.117846048 0.332221133 0.047365504 258.0139919 2.479194342 118.7478336 0.053073359 1.00E-05 5 0.917431931 SDS(ph)PENKYSDSTGHSK ddPTM_MDA-MB-175_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 217.17 8.76E-15 298060000 384380 291460 427790 202480 642470 499260 490970 448650 490250 229910 TRUE FALSE 399555.6192 341515.9878 438938.5588 242529.9397 533263.1789 383314.4314 452486.4885 442636.5806 472605.9983 274956.4626 1.453159585 1.242072961 1.596392951 0.8820667 1.939445881 1.394091369 1.645665951 1.609842432 1.718839389 1 18.06884367 4.23599282 24.9997546 1.502258095 1.347616284 0.019163629 0.308207988 229.3872898 2233383.41 0.072024434 0.167896799 17218.40107 -4.23599282 -0.154641811 SDS(ph)VSASER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 SDS(0.998)VS(0.002)ASER;SDS(0.999)VS(0.001)ASER;SDS(0.982)VS(0.018)ASER;SDS(0.999)VS(0.001)ASER 224.13 3.37E-07 1080410000 867250 880080 1157920 900490 1386340 1477660 1219870 1170830 1204430 996400 TRUE FALSE 901489.6997 1031226.894 1188096.346 1078604.234 1150690.422 1134495.859 1124253.402 1155136.939 1161082.8 1191625.503 0.756520985 0.865395119 0.997038368 0.905153701 0.965647697 0.952057384 0.943462018 0.969379168 0.974368874 1 20.18449947 4.537215754 2.847845504 0.95938124 0.754277676 0.852644082 0.027049558 0.098184353 1.378508426 0.006288877 0.036863664 34452.10433 -4.537215754 -0.205103564 SDS(ph)YSQSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SDSYSQSLK 9 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 SDS(1)YSQSLK;SDS(0.962)YS(0.038)QSLK;SDS(0.999)YS(0.001)QSLK;SDS(0.991)YS(0.009)QSLK;SDS(0.599)YS(0.401)QSLK;SDS(1)YSQSLK;SDS(0.999)YS(0.001)QSLK;SDS(0.996)YS(0.003)QS(0.001)LK 266.57 1.56E-15 8103350000 4454320 3206120 4917470 4042280 7463080 6780940 6585170 5623280 5803230 3674530 TRUE FALSE 4630179.993 3756746.17 5045623.308 4841830.919 6194508.327 5206169.451 6069007.168 5547909.129 5594372.886 4394483.8 1.053634557 0.854877692 1.148172012 1.101797421 1.409610004 1.184705574 1.38105121 1.262471176 1.273044376 1 22.06726228 3.80705595 1.788426328 1.266505579 0.961437933 0.414771602 0.125263844 0.283026687 1.74563299 0.032919491 0.077954098 6412.921889 -3.80705595 -0.305067646 SDSAFFWEER ddPTM_MDA-MB-175_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 ; 152.97 3.97E-05 82912000 87584 104086 101266 116066 116721 140827 141918 117950 110298 100643 FALSE TRUE 91041.88395 121961.9608 103905.0752 139023.5084 96880.80611 108122.0635 130794.0963 116369.0732 106328.3965 120362.0689 0.756400125 1.013292326 0.86327093 1.15504419 0.804911439 0.898306788 1.086672051 0.966825132 0.883404527 1 16.87702129 4.747073421 24.55071048 0.964229012 0.756399989 0.275453213 0.100771627 1107.93412 3195161.26 0.022773303 0.262860421 55856.46169 -4.747073421 -0.207829023 ESWHGKPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 ESWHGKPLPK 10 1 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 0 ; 104.79 0.0015829 2586100000 1015580 2990900 3728500 3452000 5347900 4867700 4715300 4309800 3694300 3220800 FALSE TRUE 1055675.883 3504563.809 3825667.773 4134795.297 4438865.868 3737250.446 4345702.465 4252034.18 3561342.865 3851854.094 0.274069541 0.909838152 0.993201632 1.073455846 1.152397199 0.970247147 1.12821056 1.103892847 0.924578859 1 21.87712163 4.791570563 2.125269667 1.057621668 2.99E-18 0.915712363 0.069645908 0.198641987 0.894131468 0.017237227 0.420849362 61882.88651 -4.791570563 -1.057621668 down SDSDMWINQSSSLDSSTSS(ph)QEHLNHSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSDMWINQSSSLDSSTSSQEHLNHSSK 28 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 SDSDMWINQSSSLDSS(0.002)T(0.035)S(0.198)S(0.756)QEHLNHS(0.008)S(0.002)K 164.16 1.26E-11 118170000 10224 44714 39725 42994 43866 51354 32018 33404 40924 40792 TRUE FALSE 10627.65141 52393.28167 40760.26613 51498.08488 36409.67299 39427.81178 29508.3455 32956.27402 39451.15323 48784.41139 0.217849332 1.073975891 0.835518252 1.055625832 0.746338266 0.808205135 0.604872431 0.675549281 0.808683596 1 15.5741326 2.610498016 3.003305013 0.73261767 0.820406485 0 0.242378163 1.272613052 22.00243662 0.081337716 0.075396796 407.8476983 -2.610498016 0.087788816 SDSDYDLS(ph)PK ddPTM_MDA-MB-175_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 168.83 0.00084189 296170000 2453570 890080 1055320 883070 1648490 2044540 1521730 1205430 1195350 724710 TRUE FALSE 2550438.838 1042944.316 1082822.506 1057738.61 1368280.259 1569726.57 1402452.826 1189273.183 1152329.587 866703.0491 2.942690511 1.203346772 1.249358136 1.220416395 1.57871864 1.811146934 1.61814687 1.372180684 1.329555248 1 19.72517825 4.743234309 24.90655865 1.407821199 2.942691166 0.811264909 0.22624532 200.5875222 1068911.858 0.056380049 0.456766374 55364.87312 -4.743234309 1.534869968 SDSFENPVLQQHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDSFENPVLQQHFR 14 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;;; 242.8 1.68E-17 6374570000 2203030 2652930 2566410 2483850 2931040 3535580 2692130 2862830 2844940 2827170 FALSE TRUE 2290007.326 3108550.091 2633292.753 2975148.116 2432822.868 2714495.127 2481113.816 2824458.446 2742551.165 3381099.832 0.677296572 0.919390212 0.77882727 0.879935011 0.719535946 0.802843827 0.733818562 0.83536677 0.811141729 1 21.68906118 0.363598495 1.283962946 1.000089914 0.795659627 0.443874386 0.069110347 3.087792499 5.383307681 0.060723399 0.017974233 2.309928274 -0.363598495 -0.204430288 SDSILLTHDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDSILLTHDGR 11 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;;; 202.16 4.10E-08 1753762000 984610 1291220 1271830 1338800 1640960 1736590 1410920 1332560 1313040 1460540 FALSE TRUE 1023483.163 1512976.991 1304974.935 1603610.644 1362030.205 1333293.291 1300328.404 1314699.213 1265783.947 1746704.849 0.585950834 0.866189266 0.747106722 0.918077628 0.779771239 0.763319167 0.744446553 0.752673935 0.724669624 1 20.73620442 -1.534944112 3.149289355 1.007887924 0.769984266 0.419097201 0.082900048 24605847.58 32648277.2 1680788.476 0.018733258 0.029178025 1.534944112 -0.237903658 SDSKS(ph)SPQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.008)KS(0.862)S(0.13)PQAGR;SDS(0.081)KS(0.46)S(0.46)PQAGR 129.74 0.00062779 59481000 246372 167085 219701 170886 264397 282443 253022 217850 231614 137117 TRUE FALSE 256098.9568 195780.549 225426.5885 204686.7408 219454.8924 216849.8937 233189.4745 214930.0771 223278.2574 163982.4509 1.561746122 1.193911592 1.374699471 1.248223451 1.338282793 1.322396955 1.422039207 1.310689503 1.361598489 1 17.3231819 -1.109057911 4.418673077 0.999960518 1.341334988 0.551657699 0.093983277 3.24E-05 6.54E-06 0.080777712 0.019037291 0.077793281 1.109057911 0.34137447 SDSKSS(ph)PQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSKSSPQAGR 11 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SDS(0.002)KS(0.027)S(0.972)PQAGR;SDS(0.061)KS(0.21)S(0.729)PQAGR 141.34 2.31E-05 1228750000 823400 496690 639750 482740 837760 1102320 828060 618970 631510 384440 TRUE FALSE 855908.4678 581992.6438 656422.4106 578224.5312 695357.8544 846322.8858 763154.4935 610673.7196 608782.0785 459763.6575 1.861627064 1.265851779 1.427738796 1.257656019 1.512424575 1.84077813 1.659884336 1.328233995 1.324119618 1 18.81053291 1.024910359 1.530953702 1.011724886 1.52242095 0.402235567 0.20081442 0.42575451 2.033204038 0.194780868 0.057465618 10.59035112 -1.024910359 0.510696064 SDSLDSGVDSVSHT(ph)PTPSTPAGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSLDSGVDSVSHTPTPSTPAGFR 24 0 I3L2J0 I3L2J0 CIC 1 SDSLDSGVDSVS(0.001)HT(0.988)PT(0.011)PSTPAGFR 164.28 5.78E-11 203680000 62342 104500 92769 92128 99722 117720 87664 98651 92310 82724 TRUE FALSE 64803.3103 122447.0621 95186.63635 110350.6434 82771.29006 90381.31406 80792.66661 97328.74471 88987.78113 98932.18395 0.655027593 1.23768684 0.962140252 1.115417036 0.836646749 0.91356837 0.816646953 0.983792542 0.899482631 1 16.5941523 3.22507109 24.99942788 0.906746918 1.007903045 0.068413404 0.14789818 531.3127867 984652.1998 0.039688844 0.047693473 1679.078847 -3.22507109 0.101156127 SDSLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDSLSPPR 8 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 SDS(0.004)LS(0.996)PPR;SDS(0.013)LS(0.987)PPR 111.61 0.0033577 471380000 1107370 1168950 1172770 1009730 1314990 1582560 1317150 1263890 1244860 1200510 TRUE FALSE 1151089.823 1369708.069 1203333.35 1209451.58 1091468.47 1215034.424 1213908.341 1246949.622 1200057.732 1435726.949 0.801747034 0.954017106 0.838135239 0.842396655 0.760220089 0.846285169 0.84550084 0.868514464 0.835853734 1 20.45334997 -1.275670641 5.329822004 1.000021221 0.846072296 0.503213355 0.046553583 1.15E-05 1.57E-06 0.044346566 0.010451146 0.053006528 1.275670641 -0.153948925 SDSNLGGHSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDSNLGGHSIR 11 0 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6 Q14966 ZNF638 Zinc finger protein 638 0 71.558 0.048703 68538000 51955 158640 124610 112980 116480 165970 102070 123090 96875 176980 FALSE TRUE 54006.22352 185885.186 127857.439 135327.1068 96680.77121 127425.9828 94069.48669 121440.1799 93388.48767 211655.8425 0.255160561 0.87824264 0.604081784 0.639373358 0.456782908 0.602043304 0.4444455 0.573762474 0.441228017 1 17.69136079 -1.467025516 3.285903208 1.007893112 0.55463778 0.435613394 0.155313961 91738030.2 133585881.1 6773677.774 0.034568604 0.034117287 1.467025516 -0.453255332 SDSQASLTVPLS(ph)PQVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDSQASLTVPLSPQVVR 17 0 Q8TEV9;Q8TEV9-2 Q8TEV9 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 SDSQASLTVPLS(1)PQVVR;SDSQASLT(0.036)VPLS(0.964)PQVVR;SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR 334.98 3.96E-72 589000000 862353 985050 868384 908177 965776 1245810 914383 992981 824370 895157 TRUE FALSE 896399.3623 1154224.675 891014.8004 1087811.7 801613.7405 956489.5079 842711.2712 979671.7139 794701.0847 1070545.875 0.837329238 1.078164609 0.832299503 1.016128057 0.748789715 0.893459617 0.787179037 0.915114183 0.742332583 1 20.02991519 3.247606911 24.99999167 0.846483587 0.94301629 0.170205864 0.100713031 316.2960369 874098.13 0.025313606 0.033792599 1768.507522 -3.247606911 0.096532703 SDSVLPASHGHLPQAGS(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 118.44 0.00010963 493348000 193927 420070 351400 376200 412030 471550 386270 450520 360810 405460 TRUE FALSE 201583.3877 492213.7548 360557.7727 450611.2372 341993.2878 362039.6589 355993.1481 444481.5163 347824.5186 484902.124 0.415719746 1.01507857 0.743568145 0.929282869 0.70528313 0.746624197 0.734154648 0.916641719 0.717308713 1 18.88733405 -5 0.180157286 1.86267636 0.741317524 0.169300629 0.155168953 246.8308511 2.378209317 76.43592743 0.444611507 1.00E-05 5 -1.121358836 SDTALEEAVAEVLDHRPIEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDTALEEAVAEVLDHRPIEPK 21 1 A0A3B3ITN0;Q86TP1 A0A3B3ITN0 PRUNE Protein prune homolog 0 ;;; 270.77 7.26E-45 179522000 276957 187526 259973 197154 345165 326401 314021 257638 282007 162827 FALSE TRUE 287891.4762 219732.1318 266748.11 236150.4728 286493.9766 250599.3144 289407.2135 254184.784 271857.6232 194729.8331 1.478414846 1.128394803 1.369836895 1.212708238 1.471238238 1.286907663 1.486198642 1.305320196 1.39607588 1 17.5711144 -1.08798926 5.294086954 0.999994899 1.343526958 0.463092308 0.112416461 6.13E-06 1.06E-06 0.098515214 0.023219914 0.081660257 1.08798926 0.343532059 SDTS(ph)SPEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.091)S(0.454)S(0.454)PEVR 140.11 0.00011526 210140000 321330 371110 354540 344110 394260 467290 386010 355970 334500 331790 TRUE FALSE 334016.3565 434845.2557 363779.6037 412173.9309 327243.826 358768.9793 355753.5276 351198.8044 322461.4103 396797.898 0.841779551 1.095885986 0.916788132 1.038750288 0.824711592 0.904160484 0.896561018 0.885082321 0.812659069 1 18.59804486 3.237752715 24.99999811 0.883237787 0.978020424 0.219692609 0.079088657 28.19182414 872387.4469 0.020452315 0.025840112 1728.831691 -3.237752715 0.094782637 SDTSGHFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDTSGHFER 9 0 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;;;; 159.34 6.61E-05 3709080000 1338692 2869043 2701716 2623260 2557208 3223261 2639911 2686543 2488423 2603913 FALSE TRUE 1391544.594 3361778.817 2772124.938 3142132.998 2122534.698 2474707.482 2432987.878 2650534.285 2398865.142 3114099.897 0.446852908 1.079534674 0.890184975 1.009001992 0.681588506 0.794678258 0.781281256 0.851139775 0.77032376 1 21.57038379 -1.37373671 3.146976485 1.001877823 0.824125501 0.100666438 0.165153138 27955231.78 36007377.88 478042.9933 0.039465876 0.042292493 1.37373671 -0.177752322 SDTSGHFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDTSGHFQR 9 0 P50995;P50995-2 P50995 ANXA11 Annexin A11 0 111.46 0.002122 57778000 30820 88941 83591 72960 62873 103900 67163 71184 66871 101410 FALSE TRUE 32036.7974 104215.9249 85769.45013 87391.27024 52185.86992 79770.79962 61898.58856 70229.89491 64464.32577 121279.3479 0.264157072 0.859304793 0.707205733 0.720578332 0.430294777 0.657744299 0.510380288 0.579075466 0.531535887 1 16.88797438 -1.682339281 2.983219467 1.045833749 0.59358936 0.382242789 0.15809213 41695033.67 39457848.52 14443053.11 0.035416884 0.020780726 1.682339281 -0.452244389 SDTSS(ph)PEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SDT(0.001)S(0.012)S(0.987)PEVR 167.06 6.32E-05 206770000 410310 457420 443740 440910 493850 574740 486400 494640 474760 392320 TRUE FALSE 426509.3556 535978.3268 455304.2289 528120.682 409905.5534 441265.3453 448274.697 488010.1599 457673.4803 469187.5926 0.90903801 1.142354008 0.970409781 1.125606666 0.873649602 0.940488095 0.955427433 1.040117359 0.97545947 1 18.83980534 5.07909275 12.5313653 1.001822026 0.000113949 0.115061864 0.077824115 713186.3113 3077803.424 0.018082906 18195281.98 119975.5501 -5.07909275 -1.001708076 SDVKFEDRFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SDVKFEDRFDK 11 2 Q9HD45;Q5TB53 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 82.85 0.010017 42495000 93203 99633 99955 78952 161400 130540 108640 82756 95910 123240 FALSE TRUE 96882.72641 116744.1927 102559.9094 94568.46995 133965.2857 100224.0634 100124.5129 81646.79118 92458.21783 147386.5184 0.657337777 0.792095464 0.695856789 0.641635822 0.908938532 0.680008351 0.679332913 0.553963769 0.627318013 1 17.16924504 2.503355383 24.89872547 0.666610024 0.740306397 0 0.132385096 2055.040038 1950430.462 0.040884906 0.038424385 318.6804213 -2.503355383 0.073696373 SDVLELTDDNFESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 ;;;; 402.1 5.10E-132 7256680000 3390020 4190300 3800400 3778840 4539180 5010140 3928620 3915910 3465480 3663910 FALSE TRUE 3523860.607 4909951.429 3899441.546 4526283.273 3767611.805 3846610.914 3620684.499 3863423.632 3340758.052 4381783.015 0.804207008 1.120537328 0.889921188 1.032977502 0.859835321 0.877864308 0.826303924 0.881701266 0.762419782 1 22.06308661 3.214220051 24.41352157 0.861179361 0.968099101 0.18488599 0.095583102 239.5308851 240247.9908 0.025106557 0.030023353 1637.646085 -3.214220051 0.106919741 SDVS(ph)PIIQPVPSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDVSPIIQPVPSIK 14 0 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SDVS(1)PIIQPVPSIK;S(0.001)DVS(0.999)PIIQPVPSIK 155.26 6.18E-06 138256000 387410 304570 356060 323880 481000 491300 440610 402930 426800 341970 TRUE FALSE 402705.2459 356877.5283 365339.2161 387942.4973 399239.7918 377203.0207 406073.8369 397529.3824 411439.5514 408972.4741 0.984675672 0.872619922 0.893310037 0.948578503 0.976202109 0.922318847 0.99291239 0.972019898 1.00603238 1 18.64164422 2.486085114 0.64424131 1.00111601 0.915604035 0.424739091 0.033366248 0.717532125 0.607823942 0.02721823 0.022821864 306.2563579 -2.486085114 -0.085511975 SDYDGIGSR ddPTM_MDA-MB-175_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 ;;; 160.26 0.00015221 3503080000 1237610 2504920 2064160 2454640 2065690 2782860 1950600 2189630 1825570 2635370 FALSE TRUE 1286471.798 2935120.524 2117953.705 2940160.466 1714564.752 2136582.94 1797706.875 2160281.591 1759868.092 3151720.294 0.408180828 0.9312757 0.67199926 0.932874808 0.544009173 0.677910075 0.570389091 0.68542935 0.558383336 1 21.58770807 -1.059631024 4.614906946 1.000013578 0.674127247 0.290793543 0.156537111 19448007.62 4465466.44 2936.202146 0.033930292 0.087170387 1.059631024 -0.325886331 SDYDMVDYLNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SDYDMVDYLNELR 13 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 255.3 1.82E-23 573982000 687756 676682 781241 886703 799844 921556 924887 809793 772850 527763 FALSE TRUE 714909.1379 792896.8696 801600.7823 1062090.207 663886.8026 707538.5853 852391.9402 798939.0494 745035.2795 631168.0552 1.132676364 1.256237326 1.270027492 1.682737582 1.051838408 1.120998725 1.350499179 1.265810338 1.180407141 1 19.26766466 SDYLNTFEFMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SDYLNTFEFMDK 12 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ; 252.21 1.10E-20 328467000 247449 180305 216886 156869 292423 281333 240196 213734 234776 161788 FALSE TRUE 257218.4776 211270.9812 222538.2273 187897.22 242717.0429 215997.6744 221368.8099 210869.2453 226326.4576 193487.261 1.329381977 1.091911582 1.150144078 0.971108997 1.254434228 1.116340545 1.144100179 1.089835291 1.169722784 1 17.56187906 -4.99999997 0.018791619 3.70E-06 1.943342315 0.212400874 0.089975224 6472.113499 9.212802822 630.6113655 357.8312767 1.00E-05 4.99999997 1.943338611 SEAEEAITSFNGHKPPGSSEPITVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEAEEAITSFNGHKPPGSSEPITVK 25 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 0 184.59 1.12E-17 339900000 162690 207780 277850 212060 365090 340030 322790 280260 325220 221700 FALSE TRUE 169113.1268 243464.5987 285090.9993 254004.8351 303032.1322 261063.1857 297488.8763 276503.5731 313515.3957 265137.8703 0.637830901 0.918256598 1.075255673 0.958010392 1.142922857 0.984631827 1.122015788 1.042867142 1.182461771 1 18.01638322 4.941171894 1.344260612 1.068660077 0.270946476 0.783213033 0.068357088 0.824617075 0.933774529 0.01704756 1.016703431 87331.69592 -4.941171894 -0.797713601 SEAEEGEVRT(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.973)PT(0.027)K;SEAEEGEVRT(0.998)PT(0.002)K;SEAEEGEVRT(0.999)PT(0.001)K 153.95 7.43E-05 4421280000 1732990 1312510 1461530 1285980 1932880 2117850 2282730 1765450 1973590 1273240 TRUE FALSE 1801409.783 1537923.383 1499618.672 1540343.006 1604329.748 1626011.434 2103803.658 1741787.03 1902560.881 1522707 1.18303113 1.009992981 0.984837314 1.011582008 1.053603712 1.067842621 1.381620796 1.143875368 1.249459601 1 20.53820693 2.447192507 24.99834273 1.207801942 1.042849943 0.313566623 0.10217913 203.4063211 169896.5078 0.033125385 0.027715006 280.022228 -2.447192507 -0.164951999 SEAHLTELLEEICDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SEAHLTELLEEICDR 15 0 Q9Y2B0;F8VXJ7;F8W031;F8W1K5 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;;;;; 272.74 1.98E-33 1924975000 490494 1410514 1177024 1439309 1406754 1716089 1086132 1337463 1150357 1397026 FALSE TRUE 509859.0819 1652758.807 1207698.212 1724000.024 1167634.458 1317553.337 1000998.136 1319536.496 1108955.876 1670746.497 0.305168428 0.989233741 0.722849466 1.031874092 0.698869912 0.788601586 0.599132267 0.789788576 0.663748736 1 20.67206142 4.753717847 24.39877071 0.793166467 0.305167936 0.523040294 0.143690862 1588.355811 2556734.727 0.032390009 0.747271597 56717.60015 -4.753717847 -0.487998531 SEALKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEALKDR 7 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 86.095 0.018539 549380000 750330 567960 790860 686850 1040390 1024640 941030 762200 834700 613470 FALSE TRUE 779953.6078 665502.7119 811470.4613 822706.88 863544.8794 786682.8886 867269.6097 751983.9557 804659.31 733667.7009 1.06308838 0.907090105 1.106046321 1.121361727 1.177024528 1.07226049 1.182101391 1.024965328 1.09676262 1 19.48476725 4.212547823 24.8269957 1.101592683 0.985089243 0.324704765 0.06467344 181.8275329 173539.0134 0.015193384 0.032838823 16313.52537 -4.212547823 -0.11650344 SEALS(ph)SVLDQEEAMEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEALSSVLDQEEAMEIK 17 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SEALS(0.99)S(0.01)VLDQEEAMEIK;SEALS(0.993)S(0.007)VLDQEEAMEIK 312.1 3.96E-58 48850000 55475 37865 45766 35482 54022 54304 62232 47105 54959 31125 TRUE FALSE 57665.19584 44368.0192 46958.69956 42500.2337 44839.35974 41692.71899 57354.09323 46473.63452 52981.03633 37223.34783 1.54916737 1.191940591 1.261538854 1.141762796 1.204603088 1.120069027 1.540809642 1.24850765 1.423328084 1 15.1839202 4.745886452 24.1481302 1.251709898 1.549167598 0.288328104 0.145500968 724.9357852 2389506.573 0.033391293 0.339852463 55704.00895 -4.745886452 0.2974577 SEANDAVNS(ph)STKEEKGEEKPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEANDAVNSSTKEEKGEEKPDTK 23 3 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 SEANDAVNS(0.98)S(0.02)T(0.001)KEEKGEEKPDTK 180.71 3.19E-17 174320000 361250 40334 106380 36969 191590 234310 133550 96181 126630 32589 TRUE FALSE 375512.4289 47261.05075 109152.3502 44281.35786 159023.6002 179895.0535 123082.002 94891.85102 122072.611 38974.1906 9.634899999 1.212624304 2.800631611 1.136171327 4.080228423 4.615748288 3.158038696 2.434735643 3.132139736 1 15.25023144 4.746398554 24.96736704 2.740224423 9.634903404 0.763611469 1.169327703 461.7782405 1470937.241 0.279470444 3.057083776 55769.73161 -4.746398554 6.894678981 SEAS(ph)SSPPVVTSSSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEASSSPPVVTSSSHSR 17 0 P48431 P48431 SOX2 Transcription factor SOX-2 1 S(0.089)EAS(0.378)S(0.314)S(0.219)PPVVTSSSHSR 86.539 0.0022361 0 22693 114120 107670 95198 99031 143830 85900 118300 80707 112980 TRUE FALSE 23588.93716 133719.2223 110475.9687 114027.8803 82197.74599 110427.6623 79166.93354 116714.382 77802.37084 135116.2679 0.17458251 0.989660419 0.817636325 0.843924141 0.608348257 0.817278807 0.585917113 0.86380703 0.575817939 1 17.04384186 -2.761557204 1.949988847 9.532388502 0.720726634 0.139837039 0.218349116 4240709.947 108908.4626 161181169.1 0.048556877 0.001731581 2.761557204 -8.811661868 SEASLHPVLMSEAPWNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEASLHPVLMSEAPWNTR 18 0 O96019-2;O96019;H7C5S0 O96019-2 ACTL6A Actin-like protein 6A 0 72.421 0.021892 119430000 153910 184270 172080 191580 191060 265640 198840 209400 184210 183120 FALSE TRUE 159986.4856 215916.9391 176564.5462 229473.9522 158583.6894 203949.1358 183254.4012 206593.3355 177580.3181 218998.858 0.730535708 0.985927238 0.806235009 1.04783173 0.724130212 0.931279449 0.836782451 0.943353483 0.810873261 1 17.74056382 -2.226753473 2.228543791 1.394954688 0.876661296 0.125574419 0.10206176 6028514.443 1076048.418 12009066.41 0.022303852 0.00593262 2.226753473 -0.518293393 SEASS(ph)SPPVVTSSSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEASSSPPVVTSSSHSR 17 0 P48431 P48431 SOX2 Transcription factor SOX-2 1 S(0.008)EAS(0.342)S(0.417)S(0.233)PPVVTSSSHSR;S(0.145)EAS(0.106)S(0.429)S(0.32)PPVVTSSSHSR 75.912 0.01354 517000000 42995 302123 269725 296865 249687 365610 228454 296048 215557 283600 TRUE FALSE 44692.4758 354010.2751 276754.2551 355584.0109 207245.2929 280702.6184 210547.1785 292079.9608 207799.1457 339165.9902 0.13177169 1.043767021 0.815984689 1.048407037 0.611043852 0.827626078 0.62077916 0.861171135 0.612676836 1 18.37163199 -4.999999994 0.026332669 1.986034318 1.43E-08 0.085198493 0.252532302 6623.587089 13.16266445 733.8154343 332.0479767 1.00E-05 4.999999994 -1.986034304 SEASSS(ph)PPVVTSSSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEASSSPPVVTSSSHSR 17 0 P48431 P48431 SOX2 Transcription factor SOX-2 1 S(0.002)EAS(0.022)S(0.091)S(0.885)PPVVTSSSHSR 87.534 0.0029108 536350000 42714 234080 223230 245150 199140 294160 172430 240150 145740 264780 TRUE FALSE 44400.3817 274281.4191 229047.5572 293639.9383 165290.2539 225845.798 158914.486 236931.1821 140494.8459 316658.5715 0.140215316 0.866173992 0.723326566 0.927307721 0.521982567 0.713215489 0.501848048 0.74822286 0.443679276 1 18.27256861 -1.495639366 2.905018111 1.012193438 0.642590307 0.206840364 0.219093363 35679607.95 39379664.67 3481769.782 0.048459066 0.031941892 1.495639366 -0.369603131 SEAVVEYVFSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEAVVEYVFSGSR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 97.452 0.0087753 37106000 41319 60705 63336 59328 59558 66111 52962 56504 45392 52798 FALSE TRUE 42950.30603 71130.61153 64986.58819 71062.90132 49434.35243 50757.72217 48810.70005 55746.6563 43758.35079 63142.75722 0.680209543 1.12650468 1.029200989 1.125432345 0.782898223 0.803856601 0.77302136 0.882866995 0.693006652 1 15.94632964 3.220579835 24.99554122 0.817159316 1.002839187 0.258303127 0.138408153 287.7025476 399941.7341 0.037962505 0.045459896 1661.804135 -3.220579835 0.185679871 SECDS(ph)SPEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.704)S(0.296)PEPK;SECDS(0.827)S(0.173)PEPK;SECDS(0.811)S(0.189)PEPK 191.53 8.21E-07 744410000 2689860 1414130 1729350 1428690 2432220 2725950 2355160 1914120 2001880 1131610 TRUE FALSE 2796057.75 1656995.827 1774418.282 1711280.618 2018792.113 2092889.425 2170556.405 1888464.352 1929832.73 1353327.314 2.066061715 1.224386599 1.311152346 1.264498692 1.491724946 1.546476897 1.603866547 1.395423216 1.425991119 1 20.36807938 0.464049961 1.464803902 1.000099455 1.471944908 0.291572011 0.226159928 3.749425471 8.884285205 0.207041441 0.060102652 2.911051983 -0.464049961 0.471845452 SECDSS(ph)PEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SECDSSPEPK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SECDS(0.357)S(0.643)PEPK;SECDS(0.059)S(0.941)PEPK 217.22 7.71E-09 528399000 2420840 1282050 1645550 1257390 2195600 2551510 2211390 1776170 1968980 1081670 TRUE FALSE 2516416.632 1502232.115 1688434.385 1506097.989 1822392.696 1958960.471 2038055.473 1752363.346 1898116.794 1293602.527 1.945278075 1.161277969 1.305218837 1.164266425 1.408773297 1.514344963 1.575488167 1.35463816 1.467310673 1 20.30296297 -1.099888919 4.322443244 0.999946431 1.416486079 0.264609643 0.214958862 14090144.67 3585380.021 7114.271171 0.047906904 0.079453143 1.099888919 0.416539648 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 SEDDS(0.192)AKFDS(0.808)NEEDSASVFSPSFGLK;SEDDS(0.025)AKFDS(0.975)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDSAKFDS(1)NEEDSASVFSPSFGLK;SEDDS(0.004)AKFDS(0.996)NEEDSASVFSPSFGLK;SEDDS(0.048)AKFDS(0.952)NEEDSASVFSPSFGLK;SEDDS(0.002)AKFDS(0.998)NEEDSASVFSPSFGLK 319.4 2.62E-82 4190691000 3705880 1464170 2233560 1376409 3185630 2835760 3147000 2263850 2416160 1126418 TRUE FALSE 3852191.004 1715629.808 2291768.408 1648658.592 2644137.75 2177197.716 2900329.917 2233506.794 2329202.874 1347118.041 2.859579404 1.273555662 1.701238006 1.223841224 1.962810734 1.616189265 2.152988699 1.657988926 1.729026562 1 20.36144484 0.445966283 1.803879772 1.000081988 1.775689398 0.22631002 0.441901361 7.132959523 21.50257112 0.39035429 0.109117273 2.792327049 -0.445966283 0.77560741 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 SEDES(1)ET(1)EDEEEKSQEDQEQK;S(0.001)EDES(0.999)ET(1)EDEEEKSQEDQEQK 174.53 6.60E-12 567900000 1150310 249570 419880 253500 688530 954310 670760 404150 519480 164172 TRUE FALSE 1195725.127 292431.7061 430822.4177 303641.5434 571493.9165 732685.9652 618184.0785 398733.0303 500784.0163 196338.3601 6.090124855 1.489427262 2.194285505 1.546521745 2.910760364 3.731751476 3.148564947 2.03084629 2.550617291 1 17.58298255 4.747208491 24.66422859 2.38210608 6.090127136 0.672966928 0.792516788 574.1150213 1637365.034 0.192745216 2.263354025 55873.83631 -4.747208491 3.708021056 SEDES(ph)ETEDEEEKSQEDQEQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 SEDES(0.856)ET(0.144)EDEEEKSQEDQEQKR;S(0.006)EDES(0.855)ET(0.139)EDEEEKSQEDQEQKR 168.65 4.79E-12 382210000 576080 157212 228651 139934 418270 466300 377330 255850 292549 114889 TRUE FALSE 598824.0832 184211.9381 234609.8329 167612.5275 347172.6148 358008.8918 347753.8886 252420.7492 282020.2186 137399.2999 4.358276089 1.340705071 1.707503846 1.219893607 2.526742241 2.605609288 2.530972785 1.837132718 2.052559357 1 17.06801513 -1.736196966 0.352326353 1.52E-09 2.251453969 0.170792949 0.83986498 57.56768784 3.60061751 49.66025933 0.640769886 0.018357056 1.736196966 2.251453968 SEDFGVNEDLADSDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEDFGVNEDLADSDAR 16 0 P04083 P04083 ANXA1 Annexin A1 0 182.03 3.61E-12 0 141300 185060 168270 117370 204240 206700 140580 145320 169640 231010 FALSE TRUE 146878.6331 216842.6154 172655.2544 140585.4357 169523.3578 158697.0576 129560.9723 143372.2231 163534.6895 276271.9865 0.531645046 0.784888175 0.624946657 0.508866054 0.613610377 0.574423269 0.46896167 0.51895317 0.591933665 1 18.07572976 0.934742629 21.51341607 1 0.575834617 0.69850853 0.082848787 3912.504343 1289839.046 0.084689442 0.02117236 8.60483662 -0.934742629 -0.424165383 SEDHLTESHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEDHLTESHQR 11 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 0 124.42 0.00020208 72823000 33248 80517 73590 88335 67340 95776 72910 82022 69823 92690 FALSE TRUE 34560.65671 94345.16841 75507.81585 105807.3993 55893.57085 73533.4755 67195.12369 80922.62925 67310.08387 110850.8308 0.311776253 0.851100237 0.681165989 0.954502538 0.504223292 0.663355204 0.606176094 0.730013737 0.607213165 1 16.75826006 -1.033958421 4.050077627 1.000039175 0.669922924 0.270910381 0.167723821 53729905.32 129650483.4 31811.19894 0.037266964 0.092478671 1.033958421 -0.330116251 SEDIY(ph)ADPAAYVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SEDIYADPAAYVMR 14 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR;SEDIY(1)ADPAAYVMR 234.72 3.32E-16 381192000 664636 726798 748317 708512 868160 897300 699986 722384 690986 705755 TRUE FALSE 690876.3425 851619.9028 767818.7558 848653.5589 720590.4733 688915.6737 645119.2682 712701.6241 666117.5488 844034.1798 0.818540717 1.00898746 0.909701022 1.005472976 0.853745607 0.816217744 0.764328369 0.844399008 0.789206841 1 19.6869419 3.07353352 7.222836328 0.828459934 0.938742468 0.238964943 0.077576309 0.254989602 20.96713795 0.020705854 0.024791518 1184.495787 -3.07353352 0.110282534 SEDMPFS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;SEDMPFS(1)PK;SEDMPFS(1)PK 191.52 3.76E-05 4226260000 9513440 4480690 5927210 4279530 8346480 8798090 7650040 6473080 6615800 3702070 TRUE FALSE 9889037.957 5250213.653 6081677.962 5126008.261 6927748.311 6754866.934 7050409.875 6386318.95 6377698.65 4427419.736 2.233589437 1.185840504 1.373639349 1.15778683 1.564737189 1.525689304 1.592442166 1.442447143 1.440500118 1 22.07803472 -2.687721901 0.450151112 2.28E-07 1.490772378 0.223648379 0.280963679 193.5381852 8.361620064 187.7329751 0.141508373 0.002052476 2.687721901 1.49077215 SEDPPTT(ph)PIR ddPTM_MDA-MB-175_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(0.012)T(0.988)PIR;SEDPPT(0.051)T(0.949)PIR 169.21 5.26E-05 2053390000 1796490 1887300 1908100 1916760 2164940 2437870 2084180 2143300 1964190 1915880 TRUE FALSE 1867416.812 2211429.094 1957826.654 2295889.407 1796944.272 1871711.639 1920816.526 2114572.569 1893499.186 2291260.004 0.815017418 0.965158511 0.854475987 1.002020462 0.784260306 0.816891857 0.838323247 0.922886344 0.826400837 1 21.12770975 -1.414074399 2.857384041 1.002642638 0.873994798 0.24851413 0.067677 13236928.72 15553192.82 288231.8938 0.015569016 0.038541233 1.414074399 -0.128647839 SEDRRS(ph)S(ph)EER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEDRRSSEER 10 2 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 SEDRRS(1)S(1)EER;S(0.005)EDRRS(0.997)S(0.999)EER 101.45 0.016339 1016700000 1424350 1567250 1510680 1707390 1412120 1777530 1796580 1508650 1570990 975540 TRUE FALSE 1480584.438 1836412.996 1550049.562 2045106.646 1172088.347 1364725.596 1655759.365 1488429.014 1514450.377 1166678.385 1.269059628 1.574052472 1.328600565 1.752930946 1.004637063 1.169753047 1.419208058 1.275783484 1.298087284 1 20.15397548 -4.391120515 0.100486396 6.35E-12 1.599252519 0.258452064 0.190655085 215.051618 1.673985231 46.79926909 3.226369258 4.06E-05 4.391120515 1.599252519 SEDRRS(ph)S(ph)EEREAGEI ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEDRRSSEEREAGEI 15 3 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 2 S(0.002)EDRRS(0.999)S(0.999)EEREAGEI;S(0.044)EDRRS(0.968)S(0.987)EEREAGEI;S(0.219)EDRRS(0.809)S(0.972)EEREAGEI 109.83 0.001767 31900100000 3606730 4023750 4215740 3501150 4672660 4984440 4151930 4228210 3900260 3867510 TRUE FALSE 3749126.485 4714797.762 4325605.648 4193667.02 3878402.922 3826879.35 3826490.878 4171537.761 3759890.404 4625274.537 0.810573828 1.019355224 0.935210573 0.906684995 0.838523831 0.82738426 0.827300271 0.901900574 0.812901023 1 22.14110757 3.420567034 4.7857994 0.861430874 0.930183744 0.104641546 0.069540571 0.339346228 16.13538405 0.018227696 0.0253201 2633.704427 -3.420567034 0.06875287 SEDSGIGLSAS(ph)SPELSEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEDSGIGLSASSPELSEHLR 20 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SEDSGIGLSAS(0.631)S(0.368)PELSEHLR 185.5 2.33E-17 453190000 203240 286510 305470 356870 323080 385640 362890 330340 357910 270110 TRUE FALSE 211264.0721 335715.8638 313430.7991 427457.8208 268162.977 296080.9544 334445.7336 325912.3326 345028.889 323032.8829 0.654001754 1.039262197 0.970275213 1.323264112 0.830141423 0.916565991 1.035330306 1.008913797 1.068092158 1 18.30132151 4.740399309 24.44016691 1.020325368 0.654001583 0.456392787 0.120258725 107.8196407 1432996.301 0.027984889 0.181587622 55004.63772 -4.740399309 -0.366323784 SEDSGIGLSASS(ph)PELSEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEDSGIGLSASSPELSEHLR 20 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SEDSGIGLSAS(0.288)S(0.712)PELSEHLR;SEDSGIGLSAS(0.044)S(0.956)PELSEHLR;SEDSGIGLSAS(0.233)S(0.767)PELSEHLR 228.29 2.03E-25 2312860000 593850 945490 976000 1228800 1060370 1300170 1171730 1116070 1011890 844430 TRUE FALSE 617295.6566 1107870.553 1001435.362 1471852.972 880128.6862 998225.2218 1079886.741 1101110.907 975472.2766 1009879.891 0.611256509 1.097031996 0.991638086 1.457453491 0.871518182 0.988459351 1.069321957 1.090338482 0.965929003 1 19.94575229 4.741017303 24.40603363 1.065705004 0.611256285 0.45181998 0.14781809 141.8168157 1408762.988 0.033893674 0.228961314 55082.96416 -4.741017303 -0.454448718 SEDSKKPADDQDPIDALSGDLDSCPSTTETSQNTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEDSKKPADDQDPIDALSGDLDSCPSTTETSQNTAK 36 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;A0A0C4DGD1;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 110.59 9.43E-06 52872000 45721 15332 27490 14573 47866 25663 24603 24972 33354 17307 FALSE TRUE 47526.10038 17965.15173 28206.41198 17455.4959 39729.75442 19703.15718 22674.55257 24637.29119 32153.59606 20697.97529 2.296171472 0.867966624 1.362761893 0.843343161 1.919499558 0.951936453 1.095496166 1.190323732 1.553465767 1 14.33720203 4.749920684 24.65555812 1.207381612 2.296172251 0.515258617 0.319346927 1083.43259 2351396.608 0.070362738 1.088873062 56223.8633 -4.749920684 1.088790639 SEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEEAHAEDSVMDHHFR 16 0 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ; 157.38 2.51E-08 1191250000 607070 1004050 990800 1003220 971230 1184660 1095930 1032870 889430 929270 FALSE TRUE 631037.5924 1176487.777 1016621.062 1201653.922 806140.6715 909540.6687 1010028.143 1019026.067 857419.588 1111342.665 0.567815501 1.058618385 0.91476832 1.081263196 0.725375438 0.818416045 0.908835929 0.916932373 0.771516847 1 20.08387229 -2.512199947 2.215257027 2.68815262 0.876240348 0.067469202 0.145497633 7727740.237 712902.8099 65897721.14 0.032898398 0.003074681 2.512199947 -1.811912272 SEEEIDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEEEIDFLR 9 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 163.99 0.00014564 30049000 259744 234177 300991 281131 317344 282629 329052 293741 316456 259362 FALSE TRUE 269998.8937 274395.0781 308835.0727 336737.8727 263401.9802 216992.698 303260.0444 289803.8824 305066.8104 310179.0181 0.870461501 0.884634556 0.995667194 1.085624278 0.849193417 0.699572458 0.977693611 0.934311689 0.983518525 1 18.24274157 1.495989507 1.967179998 0.991252595 0.907873415 0.106672869 0.096286081 0.851369442 6.447554467 0.087542336 0.028870225 31.33210024 -1.495989507 -0.08337918 SEEEKDQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEEKDQEK 9 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 64.374 0.063779 160750000 133570 61280 84212 57392 128300 147800 138680 83300 100000 60005 FALSE TRUE 138843.4467 71804.36331 86406.6339 68743.9663 106491.6118 113475.6899 127809.8992 82183.49975 96401.01953 71761.83088 1.934781276 1.000592689 1.204075103 0.957946104 1.483958959 1.581281979 1.781028963 1.145225794 1.343346712 1 16.13092908 0.734617046 1.503393599 1.003365491 1.375024017 0.125731485 0.304463855 2.085777811 7.730327701 0.289735821 0.084334575 5.427715131 -0.734617046 0.371658525 SEEELEDYMVEIDILASCDHPNIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEEELEDYMVEIDILASCDHPNIVK 25 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 ; 270.58 6.51E-53 111808000 91024 104073 123275 107217 146174 146670 147309 130424 142225 84469 FALSE TRUE 94617.69781 121946.7282 126487.6478 128424.2026 121327.3957 112608.1153 135762.5357 128675.8796 137106.35 101019.0833 0.936631919 1.207165262 1.252116369 1.271286557 1.201034416 1.114721215 1.343929595 1.273777938 1.357232174 1 16.62426833 4.73965983 3.610336364 1.240701864 0.901697147 0.418940602 0.100893646 0.245215968 5.802959898 0.023072823 0.225159575 54911.06035 -4.73965983 -0.339004717 SEEHNDKEHSSDKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEEHNDKEHSSDKGR 15 2 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 0 ;; 117.2 0.00012496 94790000 8504.2 50388 47560 36181 44148 55535 29295.6 40501.6 44985.8 60895 FALSE TRUE 8839.952383 59041.74704 48799.45267 43337.49381 36643.73873 42637.83789 26999.33432 39958.7423 43366.76985 72826.20934 0.121384217 0.810721134 0.670080911 0.595081004 0.50316691 0.585473805 0.370736505 0.548686286 0.595483003 1 16.15217013 0.71329341 2.817694336 0.9999516 0.536937437 0.399111919 0.173202715 2.086506841 19.2650099 0.156388878 0.041181166 5.167653787 -0.71329341 -0.463014163 SEEHS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEHSPPR 8 0 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 SEEHS(1)PPR 79.201 0.018453 32237000 38292 47790 42253 44636 42776 52327 45471 44996 44271 40255 TRUE FALSE 39803.79773 55997.56075 43354.14789 53464.86757 35504.9508 40174.84727 41906.8642 44392.90222 42677.69536 48142.19652 0.826796461 1.163170042 0.900543619 1.11056145 0.73750168 0.834503828 0.870480934 0.922120415 0.886492484 1 15.55501435 3.246421694 24.99994305 0.872673827 1.004780571 0.241753713 0.108352074 234.8675246 746925.3958 0.028170395 0.037466658 1763.687732 -3.246421694 0.132106744 SEEIKDTILQTVDLVSQETGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEIKDTILQTVDLVSQETGEK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 143.95 9.47E-08 35529000 106780 47676 64400 60780 106980 85556 101200 77510 92372 56307 FALSE TRUE 110995.7569 55863.98213 66078.31691 72802.10259 88795.57781 65686.91561 93267.67956 76471.10523 89047.54976 67339.27859 1.648306296 0.829589852 0.9812745 1.081123887 1.318629776 0.975462122 1.385041264 1.135609214 1.322371603 1 16.03916065 SEEITTGSAWFSFLESHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEITTGSAWFSFLESHNK 19 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 217.65 3.55E-19 200270000 299580 228330 290110 306130 373890 369320 479130 358640 338670 186930 FALSE TRUE 311407.6497 267543.9013 297670.5049 366681.6003 310336.3114 283551.0271 441574.5386 353833.0174 326481.3329 223555.3545 1.392977817 1.196768031 1.331529301 1.640227321 1.388185544 1.268370546 1.975235796 1.582753489 1.46040489 1 17.77027258 3.887689256 6.218088767 1.519518545 1.287752278 0.068464223 0.244848368 0.441136949 21.22002616 0.061891098 0.113422913 7721.279188 -3.887689256 -0.231766267 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEISR 36 2 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 45.276 0.029669 2754000000 91904 91038 135470 85225 164840 148320 136290 125760 131130 96896 FALSE TRUE 95532.44089 106673.0683 139000.4595 102082.2506 136820.5557 113874.9278 125607.2337 124074.3929 126410.6569 115880.916 0.824401844 0.920540431 1.199511225 0.880923746 1.180699639 0.982689227 1.083933731 1.070706007 1.090866911 1 16.82228347 4.445504514 8.906985266 1.060649121 0.848012874 0.439349657 0.088245505 0.177602983 46.52825017 0.019077067 0.053118292 27893.59651 -4.445504514 -0.212636247 SEEKT(ph)PIKKPGDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEKTPIKKPGDGR 14 3 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 S(0.005)EEKT(0.995)PIKKPGDGR 87.287 0.0072023 103570000 496910 122540 231410 129950 330640 333130 393960 263180 299230 118900 TRUE FALSE 516528.3905 143585.2918 237440.7347 155653.7221 274437.9309 255765.6061 363080.3858 259652.5026 288460.7708 142196.1785 3.632505429 1.009768991 1.669810941 1.094640684 1.929995122 1.798681292 2.553376536 1.826016038 2.028611273 1 17.11752317 3.055913906 24.99998927 1.937207646 1.745275579 0 0.763515368 555.8382375 248519.476 0.210441686 0.251525899 1137.401785 -3.055913906 -0.191932066 SEENTKEEKPDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEENTKEEKPDSK 13 2 P50502;Q3KNR6;Q8NFI4;F6VDH7;Q8IZP2 P50502 ST13;ST13P5;ST13P4 Hsc70-interacting protein;Putative protein FAM10A5;Putative protein FAM10A4 0 ;; 152.88 2.44E-05 2463800000 5096900 1308240 2460940 1295880 3919400 3237410 3718200 2307610 2885380 782400 FALSE TRUE 5298129.548 1532920.043 2525074.118 1552201.196 3253181.788 2485570.591 3426757.768 2276680.262 2781535.737 935696.3 5.662232016 1.63826665 2.698604363 1.658872859 3.476749655 2.656386042 3.662254268 2.433140178 2.972690752 1 19.83568082 4.749608181 24.74727893 2.578168803 5.662234072 0.586591969 0.799945703 975.3162623 2184725.259 0.177544345 2.672960325 56183.42119 -4.749608181 3.084065269 SEEQLKEEGIEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEQLKEEGIEYK 13 1 E9PEX6;P09622-2;P09622;P09622-3 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 89.911 0.0065962 173060000 342760 157280 233500 151760 315510 337260 257650 211010 233700 141710 FALSE TRUE 356292.4295 184291.6165 239585.2018 181777.675 261879.7229 258936.4762 237454.7198 208181.7561 225289.1827 169475.3613 2.102325829 1.087424243 1.413687512 1.072590574 1.545237732 1.52787092 1.401116469 1.22838951 1.329332954 1 17.37071602 7.999999996 0.035438791 7.65E-08 3.477213098 0.249551034 0.263001464 1611.148669 4.361012083 125.5398522 357.5363227 99999999.06 -7.999999996 3.477213022 SEETLDEGPPKYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEETLDEGPPKYTK 14 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 103.76 0.0010005 936640000 268280 205360 244330 169920 400890 325750 262970 256710 315420 227490 FALSE TRUE 278871.9016 240628.9825 250697.4405 203529.6688 332746.861 250099.4993 242357.7243 253269.2223 304068.0958 272062.3099 1.02502953 0.884462764 0.921470676 0.748099466 1.22305387 0.919272866 0.890816976 0.93092359 1.117641381 1 18.05357758 1.254232674 24.94250426 1.058820685 0.939323723 0.134694176 0.117255583 381.0646135 606480.0207 0.076213699 0.027622116 17.95695415 -1.254232674 -0.119496961 SEETQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEETQER 7 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 136.11 0.0070063 126733000 106594 130980 134708 113390 145666 159718 138414 128241 133286 138010 FALSE TRUE 110802.4134 153474.7961 138218.6011 135818.2036 120905.7454 122625.915 127564.749 126522.1392 128489.0629 165050.4171 0.671324649 0.929866151 0.837432607 0.822889187 0.73253826 0.742960346 0.77288353 0.766566612 0.778483721 1 17.33254726 -1.27308283 3.782974404 1.000379899 0.786285099 0.492964693 0.065713309 9889965.584 3328319.72 30629.13531 0.015187498 0.053323319 1.27308283 -0.2140948 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK;SEEVPAFGVAS(1)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 259.78 5.28E-67 336026000 490624 419610 524672 429357 615858 613774 578380 493938 553256 405160 TRUE FALSE 509994.2144 491674.7534 538345.3833 514282.5331 511174.6771 471234.2903 533045.0643 487317.569 533344.4246 484543.3447 1.052525476 1.014717793 1.111036586 1.061375703 1.054961713 0.972532789 1.100097793 1.005725441 1.100715613 1 18.8862662 2.977479264 24.83236078 1.036458489 1.060066169 0.065641739 0.043877342 2143.376914 2363384.306 0.012655869 0.013529985 949.4656641 -2.977479264 0.02360768 SEEWADNHLPLTDAELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SEEWADNHLPLTDAELAR 18 0 O60664-4;O60664;O60664-3;O60664-2;K7ERZ3 O60664-4 PLIN3 Perilipin-3 0 ;;;;; 184.8 5.64E-14 4399760000 3774320 5204370 4954230 4760860 5270110 6055810 4922390 5005570 4914730 5108810 FALSE TRUE 3923333.068 6098180.063 5083341.304 5702543.898 4374298.585 4649439.904 4536560.21 4938478.522 4737849.827 6109783.505 0.642139458 0.998100842 0.832000234 0.933346311 0.71594985 0.760982758 0.742507522 0.808290264 0.77545298 1 22.54268983 4.804885527 22.57487831 0.825784056 0.642132233 0.255267988 0.098838021 61971.61519 21089751.23 0.022989353 91.82662162 63809.52724 -4.804885527 -0.183651824 SEEWPDWS(ph)EPEEPENQTVNIQIWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEEWPDWSEPEEPENQTVNIQIWPR 25 0 Q8IZE3;Q8IZE3-2;X6RHX1 Q8IZE3 SCYL3 Protein-associating with the carboxyl-terminal domain of ezrin 1 S(0.059)EEWPDWS(0.935)EPEEPENQT(0.006)VNIQIWPR 55.587 0.0673 15712000 4454.1 3788.5 5527.3 4643.9 7425 8247.3 5096.5 5949.9 6317.4 4771.7 TRUE FALSE 4629.951307 4439.145405 5671.345979 5562.449559 6162.901152 6331.989564 4697.023013 5870.151323 6090.038008 5706.623255 0.811329415 0.777893547 0.993818187 0.974735726 1.079955847 1.109586051 0.823082724 1.028655837 1.067187676 1 12.47842161 4.222004602 7.992172937 1.006994285 0.794219877 0.570871362 0.074547378 0.1011105 34.99149036 0.018816727 0.043191603 16672.64879 -4.222004602 -0.212774408 SEFGSVDGPLPHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEFGSVDGPLPHPR 14 0 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 0 77.894 0.023396 77335000 41279 45639 50433 50570 56162 70447 52890 49078 48990 50665 FALSE TRUE 42908.72679 53477.14323 51747.32541 60572.59506 46615.6033 54086.75188 48744.3436 48420.18969 47226.85947 60591.83671 0.708160193 0.88258 0.854031306 0.999682438 0.769338014 0.892640904 0.804470474 0.799120679 0.779426108 1 15.88683582 2.217723855 24.98483036 0.824934917 0.855678669 0 0.092655332 1183.873814 1419543.638 0.03307271 0.02445064 165.0911738 -2.217723855 0.030743752 SEFYANEACKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEFYANEACKR 11 1 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753;P49753-2 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 98.105 0.0092504 108540000 52055 61915 47137 51131 107040 99863 79116 87672 86779 82484 FALSE TRUE 54110.1716 72548.41962 48365.42894 61244.55919 88845.37903 76671.33169 72914.68119 86496.90024 83655.84074 98645.16055 0.548533464 0.73544834 0.490297027 0.62085721 0.900656236 0.777243721 0.73916126 0.876848897 0.848048098 1 16.58996065 3.10053489 0.235747558 1.026530337 0.414392731 0.654101426 0.090455203 3.099949143 0.313369234 0.185083391 0.578012137 1260.476896 -3.10053489 -0.612137606 SEGEGKPQGEGKPASQAKPESQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEGEGKPQGEGKPASQAKPESQPR 24 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 0 ; 141.53 1.21E-07 401510000 599340 277090 435420 247720 601000 531870 550710 431150 544200 199852 FALSE TRUE 623002.406 324678.052 446767.4029 296718.2766 498842.2347 408351.2531 507543.9112 425371.1395 524614.3483 239009.173 2.606604584 1.358433436 1.869247934 1.241451418 2.087125897 1.708517075 2.123533188 1.779727255 2.19495487 1 17.86670646 SEGEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEGEIAR 7 0 P50395;P50395-2;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;; 152.63 0.0041887 1542670000 1104160 1416450 1325170 1324280 1473190 1593680 1335800 1342590 1283520 1335030 FALSE TRUE 1147753.089 1659714.269 1359705.019 1586218.631 1222777.69 1223571.972 1231096.506 1324594.777 1237326.366 1596603.568 0.71887168 1.039528097 0.851623438 0.993495607 0.765861805 0.766359287 0.771072125 0.829632856 0.774974071 1 20.60657471 3.221374327 24.99926886 0.805488635 0.907264885 0.125607568 0.10351422 378.8983942 551146.6192 0.027385033 0.032805487 1664.846996 -3.221374327 0.101776249 SEGEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEGEVAR 7 0 P31150 P31150 GDI1 Rab GDP dissociation inhibitor alpha 0 ;; 151.17 0.0044183 386814000 334499 434813 407740 429417 457850 512170 407797 430000 394487 442660 FALSE TRUE 347705.2788 509488.7504 418366.0394 514354.4009 380024.8205 393226.2795 375832.8056 424236.5533 380289.4899 529390.7518 0.656802707 0.962405839 0.79027833 0.971596877 0.717853153 0.742790232 0.709934589 0.801367519 0.718353104 1 19.01397347 4.953206908 13.89516119 0.809838211 0.622560308 0.165919535 0.108335382 75131.60694 3820980.308 0.024813232 96415.46778 89785.64519 -4.953206908 -0.187277903 SEGFDTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SEGFDTYR 8 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ;;; 208.22 0.0001327 6299500000 6155200 6142600 6674100 6554400 7214600 8016700 7682200 7171500 6546300 5791500 FALSE TRUE 6398212.049 7197543.767 6848032.529 7850840.757 5988264.869 6154942.919 7080049.09 7075377.773 6310699.942 6926233.54 0.923764989 1.039171395 0.988709446 1.133493509 0.864577383 0.888642129 1.022207676 1.021533238 0.911130112 1 22.7236396 4.784519128 21.51642635 0.987381217 0.923763598 0.056054843 0.075641051 17630.79823 8253019.465 0.018210985 7.299853247 60886.23617 -4.784519128 -0.063617619 SEGGFIWACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEGGFIWACK 10 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;; 174.85 6.94E-06 638060000 442755 355544 431854 355534 522827 558610 486603 426876 449465 362240 FALSE TRUE 460235.3093 416605.9163 443108.47 425857.564 433957.0533 428881.2933 448461.7854 421154.4254 433288.8424 433213.9925 1.062374063 0.961663112 1.0228397 0.98301895 1.001715228 0.989998709 1.035196908 0.972162563 1.000172778 1 18.72472032 4.759439852 24.48651617 0.996502301 1.062374149 0.478899324 0.020673901 3299.879387 3869912.981 0.004491667 0.197929973 57469.82196 -4.759439852 0.065871848 SEGSMSTDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEGSMSTDKR 10 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;; 99.788 0.0071458 518650000 243828 204182 236511 186667 336987 333370 259522 233096 240384 206905 FALSE TRUE 253454.5177 239248.6702 242674.671 223589.1755 279706.0701 255949.8698 239179.9875 229971.7294 231732.6268 247444.0733 1.024290113 0.966879776 0.980725332 0.90359479 1.130380964 1.034374622 0.966602208 0.929388715 0.93650506 1 17.91674296 2.043075468 7.106061066 0.947534006 1.004503302 0.14581215 0.057007957 0.366409822 47.64820375 0.022381627 0.016359595 110.4270494 -2.043075468 0.056969296 SEGTYLNSVIESHTEFIFTTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEGTYLNSVIESHTEFIFTTIK 22 0 A0A0A0MSX9;P41252;J3KR24;Q5TCC6 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 260.34 2.96E-37 100720000 101539 79567 105605 91754 112498 128816 131328 107045 109457 59990 FALSE TRUE 105547.8381 93232.0133 108357.1531 109902.6673 93375.63014 98900.43623 121034.1682 105610.2369 105517.664 71743.89192 1.47117525 1.29951151 1.510332798 1.531874901 1.301513309 1.378520646 1.687030979 1.472044993 1.470754668 1 16.13056839 SEHPGLSIGDTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEHPGLSIGDTAK 13 0 P26583;D6R9A6 P26583 HMGB2 High mobility group protein B2 0 ; 177.42 1.55E-05 585660000 676830 863600 1101800 886340 1214020 1355460 1228360 1136580 1122800 869850 FALSE TRUE 703551.771 1011916.582 1130513.813 1061655.407 1007661.314 1040674.957 1132077.933 1121346.004 1082390.647 1040280.453 0.676309709 0.9727344 1.086739455 1.020547299 0.968643899 1.000379228 1.088243012 1.077926631 1.040479655 1 19.98854109 4.721447775 3.18468934 1.038798129 0.630222847 0.885918563 0.038433956 0.103971087 1.685760633 0.010336771 0.103378618 52655.98907 -4.721447775 -0.408575282 SEHPPLCGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEHPPLCGR 9 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 70.256 0.052925 171440000 127470 272980 255400 277380 303900 344400 243100 289900 238810 312940 FALSE TRUE 132502.614 319862.1915 262055.9338 332244.9361 252243.1866 264418.3194 224045.1868 286014.3647 230215.2747 374254.6014 0.354044048 0.854664686 0.700207647 0.887751105 0.673988204 0.706519889 0.598643773 0.764224043 0.615130112 1 18.51366053 -1.252647595 3.851456156 1.000400178 0.697143828 0.305939866 0.141570887 15211330.08 9894807.67 47233.36977 0.030348471 0.055892355 1.252647595 -0.303256349 SEIDLFNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SEIDLFNIR 9 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;;;; 209.84 1.81E-05 769424000 814045 865641 884514 898920 1157135 1152163 844443 949746 877051 904782 FALSE TRUE 846184.1252 1014308.108 907565.1615 1076723.693 960445.606 884590.6044 778253.3511 937016.2083 845486.1058 1082056.71 0.782014582 0.937389047 0.838740847 0.995071407 0.887611155 0.817508543 0.719235271 0.865958503 0.781369496 1 20.04534468 2.75871048 7.309813454 0.82195842 0.894258904 0.06731896 0.085786967 0.362962101 95.92876806 0.024985797 0.025857919 573.7338576 -2.75871048 0.072300484 SEIDLLDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 ; 83.948 0.036813 62355000 280110 301170 308910 315940 346910 389920 382320 338610 337600 301650 FALSE TRUE 291168.9591 352893.6047 316960.4484 378431.989 287942.3621 299366.9893 352352.7594 334071.4868 325449.8419 360752.5421 0.807115474 0.978215157 0.87860905 1.049007131 0.798171402 0.829840277 0.976715943 0.926040562 0.902141507 1 18.46065004 -0.214327083 0.497560551 1.012022375 0.903832303 0.122145157 0.076770661 13.26180474 3.473693161 0.378612623 0.037039618 0.610482075 0.214327083 -0.108190072 SEIPS(ph)PQSQLLEDAEANLVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SEIPSPQSQLLEDAEANLVGR 21 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 SEIPS(0.999)PQS(0.001)QLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;SEIPS(1)PQSQLLEDAEANLVGR;S(0.003)EIPS(0.915)PQS(0.082)QLLEDAEANLVGR;SEIPS(0.993)PQS(0.007)QLLEDAEANLVGR 227.95 1.95E-25 257958000 76602.6 85098 101454 84957.6 103020 109417.5 97679.8 95424.1 92533.7 94805.7 TRUE FALSE 79626.9298 99712.91953 104097.9746 101761.9597 85508.6972 84006.94386 90023.40204 94145.09602 89203.43021 113381.0618 0.702294797 0.879449513 0.918124888 0.897521668 0.754170898 0.740925712 0.79398976 0.830342339 0.78675776 1 16.79082016 -1.458024531 3.163311267 1.003537734 0.815771255 0.41407102 0.067094125 18081431.82 21587888.09 562575.9381 0.017839665 0.034831764 1.458024531 -0.18776648 SEISQVFEIALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEISQVFEIALKR 13 1 O95793-2;O95793-3;O95793;Q5JW30;A0A087X1A5;Q5JW28 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 147.39 6.86E-05 80716000 118730 125600 129660 109060 159990 171480 152140 132090 153830 121730 FALSE TRUE 123417.5521 147170.823 133039.0461 130631.7425 132794.9569 131656.3688 140214.8693 130319.5496 148293.6883 145580.6628 0.847760614 1.01092288 0.913851081 0.897315206 0.912174422 0.90435341 0.963142127 0.895170739 1.018635892 1 17.15145921 1.232165749 24.99894244 1.009318002 0.920629928 0.43804412 0.041252655 143.2757181 560069.8738 0.033454 0.009170881 17.06733642 -1.232165749 -0.088688075 SELISS(ph)TFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SELISSTFK 9 0 H0YHG7;Q92730 H0YHG7 RND1 Rho-related GTP-binding protein Rho6 1 SELIS(0.004)S(0.642)T(0.353)FK 72.547 0.048715 1100100000 21042 1375400 856900 1221000 573110 1295700 511990 908520 671010 1459900 TRUE FALSE 21872.75441 1611614.251 879231.518 1462510.156 475692.9669 994793.3115 471858.886 896342.7754 646860.4812 1745939.454 0.012527785 0.923064226 0.503586488 0.83766373 0.272456737 0.569775378 0.270260738 0.51338709 0.370494223 1 20.7355721 -1.056582363 4.831307426 1.000014133 0.489307072 0.273865103 0.255577165 62841881.91 13743197.89 9457.58043 0.054721686 0.087784459 1.056582363 -0.510707061 SELKELLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SELKELLTR 9 1 P26447 P26447 S100A4 Protein S100-A4 0 ; 129.89 0.00034347 2985700000 3749300 3746700 4180000 2463600 6363400 5299500 3166300 4787100 5341200 4506300 FALSE TRUE 3897325.259 4390166.58 4288934.234 2950892.727 5281751.541 4068771.44 2918117.132 4722936.755 5148971.255 5389223.207 0.723170132 0.814619549 0.795835331 0.547554372 0.980058041 0.754982914 0.54147268 0.876366885 0.955419929 1 22.36164591 1.507136954 6.505204777 0.959169973 0.742531331 0.397964438 0.120484206 0.134637909 12.7388945 0.06681981 0.030183746 32.14674117 -1.507136954 -0.216638642 SELNEIKENQRS(ph)PVR ddPTM_MDA-MB-175_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 227.64 3.67E-13 5470280000 3133300 2387421 3115050 2054420 3943180 3929320 3009550 2930970 3295260 2343660 TRUE FALSE 3257005.103 2797441.985 3196230.762 2460778.144 3272919.672 3016794.979 2773653.607 2891685.141 3176664.236 2802855.305 1.162031125 0.998068641 1.140348114 0.877954042 1.167709109 1.07632919 0.989581447 1.031692623 1.133367188 1 21.41846584 7.999222304 0.006543654 0.019907807 2.174986644 0.037486677 0.087969675 126306.5721 63.93663893 9551.395008 11597.44266 99821089.05 -7.999222304 2.155078838 SELNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 159.42 0.02122 426570000 372570 481390 459010 460340 541580 582240 488590 469480 438730 482540 FALSE TRUE 387279.3513 564064.9878 470972.1777 551393.878 449522.425 447023.5839 450293.0391 463187.3885 422940.193 577084.4742 0.671096466 0.977439202 0.81612346 0.955482087 0.778954287 0.774624174 0.780289644 0.802633599 0.732891304 1 19.13842299 SELPIAELTGHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SELPIAELTGHTR 13 0 A0A499FIZ0;Q9H7D7-2;Q9H7D7;H0Y9R3 A0A499FIZ0 WDR26 WD repeat-containing protein 26 0 ; 176.91 1.59E-05 138841000 160542 199423 200431 177611 212088 238060 199937 199268 201703 185632 FALSE TRUE 166880.3221 233672.349 205654.3965 212741.9257 176037.3575 182774.1728 184265.4155 196597.1384 194443.7484 222003.0363 0.751702882 1.052563753 0.926358486 0.958283856 0.792950225 0.823295825 0.830013042 0.885560584 0.875860762 1 17.76021988 5.02751278 15.11945356 0.894410461 0.379809696 0.247651445 0.078219571 1969333.849 30698623.26 0.019040375 24773864.15 106540.0214 -5.02751278 -0.514600765 SELTLTPDPAPPMAHS(ph)PLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SELTLTPDPAPPMAHSPLHR 20 0 M0R344;Q9NRA0-4;Q9NRA0-2;Q9NRA0;Q9NRA0-5;E9PCV4;Q9NRA0-3 M0R344 SPHK2 Sphingosine kinase 2 1 SELTLTPDPAPPMAHS(1)PLHR 140.2 1.32E-07 197550000 60743 64578 68068 86771 83517 96582 79967 69297 73908 77566 TRUE FALSE 63141.18054 75668.76915 69841.908 103934.0448 69320.81017 74152.29421 73698.97759 68368.18706 71248.06552 92763.57261 0.680667839 0.815716418 0.752902309 1.120418736 0.747284826 0.799368676 0.79448188 0.737015459 0.768060819 1 16.50127076 SELVAMLEEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SELVAMLEEEELR 13 0 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ; 167.18 7.53E-05 27031000 33872 39647 43085 44197 46844 55041 50467 46506 45435 41671 FALSE TRUE 35209.29271 46456.06384 44207.83049 52939.03469 38881.47361 42258.5619 46511.26467 45882.66314 43799.80323 49835.63461 0.706508365 0.932185658 0.887072691 1.062272711 0.780194211 0.847958739 0.933293316 0.920679821 0.878885231 1 15.60489008 7.99999422 0.019892835 1.598140134 4.72E-09 0.174334244 0.087984784 6486.582625 9.94300788 296.5190918 534.6068113 99998669.04 -7.99999422 -1.598140129 SELVAMLEEEELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SELVAMLEEEELRK 14 1 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 ;;;;; 291.51 2.78E-43 823401000 1017961 704679 1046561 755486 1363164 1243529 1267953 1092679 1213487 673104 FALSE TRUE 1058150.886 825702.1366 1073835.239 904918.8759 1131453.87 954738.2356 1168567.531 1078033.425 1169813.84 804985.8414 1.31449627 1.025734981 1.333980282 1.124142599 1.405557479 1.186031091 1.451662216 1.339195511 1.453210454 1 19.61860388 3.239835508 24.99981284 1.328112882 1.196769836 0.094303003 0.152346162 62.39531999 1223511.641 0.039452574 0.050602926 1737.142749 -3.239835508 -0.131343046 SENFEELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SENFEELLK 9 0 P29373;Q5SYZ4 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;;; 199.89 5.58E-05 889877000 1125416 804116 1001789 791410 1374506 1313051 1265759 1042688 1205054 801339 FALSE TRUE 1169848.293 942216.6678 1027896.444 947948.5359 1140867.961 1008114.805 1166545.502 1028712.473 1161684.342 958346.0345 1.220695084 0.98316958 1.072573379 0.98915058 1.190455138 1.051931942 1.217248739 1.073424876 1.212176291 1 19.87018715 3.234116694 24.9999919 1.127139908 1.060893491 0.088400372 0.089959294 237.691234 1337167.873 0.023604364 0.029158497 1714.417907 -3.234116694 -0.066246417 SENSEDGAAWMQEPGRYS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SENSEDGAAWMQEPGRYSPPPR 22 1 P35548 P35548 MSX2 Homeobox protein MSX-2 1 SENSEDGAAWMQEPGRYS(1)PPPR;SENSEDGAAWMQEPGRYS(1)PPPR 135.8 3.32E-06 349430000 229091 285086 295730 279954 279126 330020 322540 283850 298230 304691 TRUE FALSE 238135.6896 334047.3028 303436.9667 335328.0656 231680.2622 253377.8565 297258.472 280045.455 287496.7606 364389.3678 0.653519863 0.91673175 0.832727279 0.920246569 0.635804122 0.695349203 0.81577153 0.768533552 0.788982297 1 18.47512134 0.908956948 17.71555391 1 0.783849536 0.332556755 0.09308063 2736.463125 532478.0647 0.088849069 0.022211958 8.108806703 -0.908956948 -0.216150464 SEPFS(ph)PSLRPEPPKHPESIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPFSPSLRPEPPKHPESIK 20 2 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 S(0.003)EPFS(0.804)PS(0.194)LRPEPPKHPESIK;SEPFS(0.977)PS(0.023)LRPEPPKHPESIK 169.6 5.50E-12 490530000 553660 288170 428640 296430 610740 506290 647270 472200 508470 214585 TRUE FALSE 575518.9243 337660.9558 439810.7105 355062.9692 506926.633 388711.8204 596535.2861 465870.9314 490170.264 256628.8223 2.242612187 1.315756168 1.713800915 1.383566219 1.975330084 1.514684972 2.324506191 1.815349216 1.910035902 1 17.96932368 3.21462502 24.98926863 1.825433407 1.64262564 0 0.399463678 782.0044852 816426.9604 0.107367694 0.128391515 1639.173861 -3.21462502 -0.182807767 SEPHS(ph)PGIPEIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPHSPGIPEIFR 13 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 SEPHS(1)PGIPEIFR;SEPHS(1)PGIPEIFR 114.06 0.0004976 121196000 75672 187023 110014 167251 112185 194929 97273 126799 90300 210299 TRUE FALSE 78659.58899 219142.7454 112881.0552 200332.7486 93115.83377 149659.6939 89648.48808 125099.4668 87050.12064 251503.0626 0.312757977 0.871332313 0.448825768 0.796541984 0.370237375 0.595061119 0.35645088 0.49740733 0.346119525 1 17.94021644 -1.402809139 6.338306688 1.00007906 0.517899889 0.392371149 0.18252743 0.00018793 1.77E-05 0.162873307 0.038383363 0.039554041 1.402809139 -0.482179171 SEPIS(ph)PPRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPISPPRDR 10 1 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 S(0.005)EPIS(0.995)PPRDR;SEPIS(1)PPRDR 107.2 0.0014025 712960000 935940 538300 664070 537470 831620 817660 778450 607470 668530 544070 TRUE FALSE 972891.6339 630748.8376 681376.2097 643779.9618 690261.5294 627770.8568 717433.0549 599327.8583 644469.7359 650670.0997 1.495214909 0.969383468 1.047191519 0.989410705 1.060847163 0.964806677 1.10260646 0.921093283 0.990470803 1 19.31156673 4.741058695 24.9999219 1.004597912 1.495215082 0.896976712 0.049831383 62.1897099 622337.4715 0.011228462 0.076393862 55088.21435 -4.741058695 0.49061717 SEPQPEEGS(ph)PAGGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEPQPEEGSPAGGQK 15 0 F8WE91;Q9Y6K1;Q9Y6K1-3 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK;SEPQPEEGS(1)PAGGQK 216.72 2.27E-12 575960000 559540 373726 454843 373036 610110 647740 549580 481875 506808 322727 TRUE FALSE 581631.0713 437910.5333 466696.5822 446821.4074 506403.7201 497312.2016 506502.4835 475416.2538 488568.0791 385959.1767 1.506975624 1.134603242 1.209186387 1.15769085 1.3120655 1.288509852 1.312321391 1.231778599 1.265854289 1 18.55808873 -0.351924319 1.292779084 0.998062892 1.261849611 0.400564245 0.098295728 53.71832013 48.40267791 0.671062964 0.026372435 0.444708757 0.351924319 0.263786719 SEPRPPIS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 S(0.002)EPRPPIS(0.785)S(0.213)PR 73.834 0.025723 705320000 885650 1063000 990350 1116300 1184100 1407100 1027000 1002400 1020600 911040 TRUE FALSE 920616.1459 1245561.981 1016159.335 1337100.808 982827.1049 1080322.35 946501.0564 988964.4676 983868.8054 1089540.845 0.844957901 1.143198978 0.932649142 1.227214945 0.902056228 0.991539101 0.868715533 0.907689209 0.903012319 1 20.05528885 SEPRPPISS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-3;Q6WKZ4-2 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 SEPRPPIS(0.371)S(0.629)PR;SEPRPPIS(0.428)S(0.572)PR 81.904 0.012354 1514390000 1756510 2085120 2012980 2218790 2364300 2659200 2070960 2052540 2072360 1930530 TRUE FALSE 1825858.371 2443223.14 2065439.912 2657660.04 1962417.131 2041641.101 1908632.744 2025029.059 1997776.168 2308780.391 0.790832414 1.058231068 0.894602155 1.151109932 0.849979989 0.884294196 0.826684405 0.877099037 0.865295017 1 21.13869952 SEPSDHS(ph)RHSPQQPSNGSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEPSDHSRHSPQQPSNGSLR 20 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 SEPSDHS(0.5)RHS(0.5)PQQPSNGSLR 94.449 0.00082531 77672000 6104.7 33992 31384 31125 37494 47535 25041 35704 31413 52713 TRUE FALSE 6345.71827 39829.86158 32201.89282 37281.4321 31120.78327 36495.71665 23078.22099 35225.44628 30282.45227 63041.1031 0.100660013 0.631807815 0.510807889 0.591382927 0.493658609 0.578919385 0.366082125 0.55876951 0.480360444 1 15.94400516 -5 0.357489094 7.170260373 0.475927973 0.541432612 0.144223077 344.7055093 2.763853286 1635.13649 0.098209126 1.00E-05 5 -6.6943324 SEPSDHSRHS(ph)PQQPSNGSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEPSDHSRHSPQQPSNGSLR 20 1 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 SEPSDHS(0.002)RHS(0.998)PQQPSNGSLR 170.68 5.40E-12 66351000 6961.5 61606 53331 43290 58977 75880 31549 60230 45394 87382 TRUE FALSE 7236.345395 72186.35127 54720.84967 51852.63279 48952.11061 58258.01997 29076.10694 59422.71537 43760.27881 104502.8299 0.069245449 0.690759775 0.523630315 0.496184006 0.468428565 0.557477918 0.278232723 0.568623026 0.418747309 1 16.67318248 -1.276953553 2.890474621 1.004330432 0.466371504 0.499528331 0.16390571 6458672.754 8092253.326 244902.4858 0.037101166 0.052850177 1.276953553 -0.537958928 SEPTQALELTEDDIKEDGIVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEPTQALELTEDDIKEDGIVPLR 23 1 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 161.16 1.65E-11 72063000 105263 66085 86422 63879 103909 127986 110577 83306 94061 49180 FALSE TRUE 109418.8645 77434.58468 88674.22832 76514.07554 86246.5853 98263.19115 101909.6858 82189.41933 90675.76298 58815.87939 1.860362638 1.316559159 1.507657953 1.300908468 1.466382654 1.670691523 1.732689996 1.397401861 1.541688468 1 15.84391809 -0.148485673 1.272731767 0.997720145 1.522593885 0.465729871 0.170741358 21.62830954 22.40476281 0.398583897 0.047525605 0.710418606 0.148485673 0.52487374 SEPVKEES(ph)SELEQPFAQDTSSVGPDR ddPTM_MDA-MB-175_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(0.834)S(0.166)ELEQPFAQDTSSVGPDR 245.43 1.50E-45 255600000 147810 85431 99667 77448 128230 164910 119810 107170 107620 53071 TRUE FALSE 153645.6529 100103.1097 102264.4039 92766.98324 106433.5104 126612.1517 110418.9791 105733.5614 103746.7772 63469.24634 2.420788993 1.577190773 1.611243394 1.461605243 1.676930427 1.994858282 1.739724126 1.665902268 1.634599167 1 15.95377009 -2.352926236 0.305919664 2.63E-12 1.792807041 0.458016029 0.252795516 41.71877155 1.623848669 28.59086646 0.250527474 0.00443684 2.352926236 1.792807041 SEPVKEESSELEQPFAQDTSS(ph)VGPDR ddPTM_MDA-MB-175_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 SEPVKEESSELEQPFAQDT(0.002)S(0.205)S(0.793)VGPDR 174.93 1.24E-12 268590000 228930 169130 209070 165320 281650 265060 232630 212710 224590 149390 TRUE FALSE 237968.3332 198176.7619 214518.536 198019.8026 233775.2336 203503.832 214395.8527 209858.9704 216507.0498 178660.1103 1.331961191 1.109238999 1.200707509 1.108360463 1.308491488 1.139055784 1.200020824 1.174626894 1.211837659 1 17.44685803 -1.958304235 2.3661341 0.84609489 1.193204312 0.410259817 0.071077709 4739440.868 2042647.312 4004543.391 0.015396436 0.011007679 1.958304235 0.347109422 SEPVKEESSELEQPFAQDTSSVGPDRK ddPTM_MDA-MB-175_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 0 134.2 1.54E-05 184880000 167050 106290 148820 84426 181390 170520 163380 145070 177590 96479 FALSE TRUE 173645.263 124544.4807 152698.3715 101125.2108 150557.3926 130919.3143 150573.8487 143125.5739 171198.5706 115382.2128 1.504956949 1.079407975 1.323413442 0.876436743 1.304857906 1.134657683 1.305000528 1.240447469 1.48375184 1 16.81606131 2.22572967 24.55105112 1.274372747 1.193423091 0.013526418 0.190921642 704.0152835 1347068.492 0.066597478 0.049516537 168.1626993 -2.22572967 -0.080949656 SEPVS(ph)PSR ddPTM_MDA-MB-175_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(0.994)PS(0.006)R;SEPVS(0.999)PS(0.001)R;SEPVS(0.901)PS(0.099)R;SEPVS(0.993)PS(0.007)R 182.24 0.00024085 3029780000 2146830 2228400 2227450 2465220 2369570 2927920 2759260 2447980 2185140 1937110 TRUE FALSE 2231588.506 2611110.365 2285499.177 2952833.158 1966791.338 2247954.953 2542981.991 2415168.832 2106497.238 2316649.616 0.963282704 1.127106295 0.986553668 1.274613622 0.848980927 0.970347409 1.097698147 1.042526593 0.909286076 1 21.14360843 3.218296867 24.99999723 0.992260464 1.083452245 0.210119511 0.10191965 445.9130508 550134.9532 0.02911729 0.034838878 1653.0914 -3.218296867 0.091191781 SEPVS(ph)PSRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.512)PS(0.488)RER;SEPVS(1)PSRER;SEPVS(1)PSRER 130.56 0.00016549 1106580000 476779 588180 604172 522405 761290 756190 601434 636460 599190 658700 TRUE FALSE 495602.6031 689195.3396 619917.2187 625735.1498 631886.1977 580576.3327 554292.0315 627929.2947 577625.2689 787759.6534 0.629129203 0.874880221 0.786937 0.794322414 0.802130694 0.736996786 0.703630897 0.797107712 0.733250639 1 19.587396 -2.328774892 2.273707278 2.301881287 0.767184427 0.559082048 0.063247733 1868530.344 350046.1553 12450658.15 0.014313375 0.004690564 2.328774892 -1.534696861 SEPVSPS(ph)RER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEPVSPSRER 10 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 SEPVS(0.112)PS(0.888)RER 105.56 0.0066631 564700000 367590 498270 490670 410340 606460 604580 481140 504700 469250 500190 TRUE FALSE 382102.737 583843.9965 503457.2633 491504.0273 503374.1458 464175.4575 443426.9896 497935.322 452361.7842 598192.6538 0.638762002 0.976013317 0.841630635 0.821648384 0.841491688 0.775963153 0.741277892 0.832399594 0.756214208 1 19.19025067 2.779336125 23.91349007 0.806137737 0.833218357 0 0.102156097 1822.173889 1068640.718 0.028999444 0.030758252 601.6391995 -2.779336125 0.02708062 SEQAVAQLEEEKQHLLFMSQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEQAVAQLEEEKQHLLFMSQIR 22 1 Q9H0B6;A8MX29;E9PP09;C9JHT2;E9PM83 Q9H0B6 KLC2 Kinesin light chain 2 0 ; 212.94 9.00E-24 706520000 244923 254492 313713 229937 336700 340610 329037 299910 264045 255552 FALSE TRUE 254592.7492 298199.0213 321888.6185 275417.8523 279467.8543 261508.4895 303246.2202 295890.197 254542.072 305622.5216 0.833030066 0.975710232 1.053222835 0.901170015 0.914421663 0.855658438 0.992224718 0.968155735 0.832864249 1 18.22139134 -0.950077971 5.00411463 1.000000373 0.933007873 0.084861449 0.06955823 2.85E-07 5.98E-08 0.066225916 0.015609511 0.112181703 0.950077971 -0.0669925 SERPPTILMTEEPS(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SERPPTILMTEEPSSPK 17 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SERPPTILMTEEPS(0.592)S(0.408)PK 99.11 0.0010064 214800000 223370 82711 101420 121310 157560 198800 176640 149110 136650 56027 TRUE FALSE 232188.8201 96915.97085 104063.0885 145304.7559 130778.0075 152631.7128 162794.4952 147111.4243 131731.9932 67004.41795 3.465276279 1.446411652 1.553078016 2.168584705 1.95178186 2.27793506 2.429608378 2.195548127 1.966019514 1 16.0319686 SERPPTILMTEEPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SERPPTILMTEEPSSPK 17 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SERPPTILMTEEPS(0.093)S(0.907)PK;SERPPTILMTEEPS(0.206)S(0.794)PK;SERPPTILMTEEPS(0.012)S(0.988)PK 106.42 0.00045654 936840000 826410 445260 548490 494210 661160 800390 722700 568030 586350 370964 TRUE FALSE 859037.3049 521729.9414 562784.1 591963.2629 548776.2594 614511.5525 666052.8856 560416.487 565247.378 443647.2933 1.936306877 1.176001633 1.268539465 1.334310548 1.236965192 1.385135358 1.50131173 1.263202764 1.274091799 1 18.75905364 7.999821923 0.03128147 6.67E-08 3.307900945 0.320977466 0.193615888 1820.531426 4.362089939 144.1376769 363.4229297 99959004.64 -7.999821923 3.307900879 SES(ph)ELIDELSEDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SESELIDELSEDFDR 15 0 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;E9PDE4;H0Y7F0;E7EQ12;E7EQA0;D6RC54;P20810-5;E9PCH5;P20810-2;P20810-3;A0A0C4DGB5;E7EVY3;H0Y9H6;A0A0A0MR45;H0YD33 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 1 SES(1)ELIDELSEDFDR;SES(1)ELIDELSEDFDR;S(0.003)ES(0.997)ELIDELSEDFDR;S(0.01)ES(0.99)ELIDELSEDFDR;S(0.022)ES(0.978)ELIDELSEDFDR;S(0.001)ES(0.999)ELIDELSEDFDR 373.39 1.17E-97 638850000 510639 562638 588349 645874 764618 881284 861014 724322 683140 570904 TRUE FALSE 530799.422 659266.6998 603681.8583 773625.9495 634648.5055 676619.147 793525.4728 714613.6483 658553.9248 682761.7082 0.777429981 0.965588275 0.884176501 1.133083388 0.929531486 0.99100336 1.162229023 1.046651621 0.964544316 1 19.38102262 5.74500161 0.675174062 1.040206268 2.13E-17 0.472666351 0.077711733 8.818609419 1.098174766 0.029628998 9.605073628 555906.3175 -5.74500161 -1.040206268 SES(ph)ELIDELSEDFDRSECK ddPTM_MDA-MB-175_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 1 S(0.143)ES(0.857)ELIDELSEDFDRSECK;S(0.007)ES(0.993)ELIDELSEDFDRSECK;SES(1)ELIDELSEDFDRSECK;S(0.014)ES(0.986)ELIDELSEDFDRSECK;SES(1)ELIDELSEDFDRSECK;SES(1)ELIDELSEDFDRSECK 223.81 1.28E-19 620662000 390721 395758 525179 343738 837538 686045 591507 506043 666918 457814 TRUE FALSE 406146.9668 463726.3579 538865.5962 411728.3504 695173.5899 526721.4459 545143.1357 499260.3213 642915.7515 547513.8879 0.741802127 0.846967297 0.984204434 0.751996177 1.269691245 0.9620239 0.995669969 0.911867867 1.174245559 1 19.06253603 4.684257703 0.757388401 1.019064257 0.592836217 0.340967927 0.12863842 3.042677221 1.402321361 0.047312165 1.090323797 48334.55258 -4.684257703 -0.42622804 SES(ph)LDPDSSMDTTLILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESLDPDSSMDTTLILK 17 0 Q5SW79;H0Y2V6;Q5SW79-3;Q5SW79-2 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.046)ES(0.907)LDPDS(0.046)S(0.001)MDTTLILK;S(0.006)ES(0.994)LDPDSSMDTTLILK 242.41 2.20E-20 135127000 262930 201444 316450 188648 475610 321280 341350 312290 371700 197743 TRUE FALSE 273310.6794 236040.44 324696.947 225962.0113 394765.9821 246667.589 314594.095 308104.2634 358322.5896 236486.9548 1.155711441 0.998111884 1.373001514 0.955494613 1.669292847 1.043049454 1.330280967 1.302838305 1.515189664 1 17.85140108 3.908991109 1.217129902 1.299292462 1.088428806 0.074084623 0.22203319 1.257397626 3.340253649 0.06513273 0.231062242 8109.44455 -3.908991109 -0.210863655 SES(ph)LELPQAAPPQIYHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESLELPQAAPPQIYHEK 18 0 H0YGT9;Q15040;B0QY58;B0QY55;B0QY57;B0QY56 H0YGT9 JOSD1 Josephin-1 1 S(0.156)ES(0.844)LELPQAAPPQIYHEK 77.045 0.0091641 88914000 113790 97179 115190 107810 143520 156320 147090 129190 127010 86285 TRUE FALSE 118282.5171 113868.7373 118191.946 129134.4962 119124.5217 120017.0491 135560.7015 127458.4194 122438.9349 103190.8937 1.146249565 1.103476607 1.145371861 1.251413682 1.154409245 1.163058529 1.313688607 1.235171194 1.186528486 1 16.65495614 3.935533129 7.031983638 1.20328705 1.124643724 0.067994086 0.078775049 0.431836252 40.5020186 0.01938654 0.035536623 8620.513356 -3.935533129 -0.078643325 SES(ph)LESPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESLESPR 8 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SES(1)LESPR;SES(0.998)LES(0.002)PR 172.98 0.00029414 323090000 479740 521770 498720 471970 566420 707040 651860 579030 562120 472440 TRUE FALSE 498680.5056 611379.9387 511717.0529 565324.2573 470140.1307 542840.6753 600765.5099 571269.05 541889.411 565005.5726 0.882611659 1.082077715 0.905684966 1.000564038 0.832098219 0.96077048 1.0632913 1.011085691 0.959086843 1 19.10790557 2.456390545 23.83742865 1.011488376 0.944515263 0.182438742 0.067530691 236.4315802 271860.482 0.022712079 0.019004632 286.0161422 -2.456390545 -0.066973113 SES(ph)LESPRGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESLESPRGER 11 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 S(0.213)ES(0.703)LES(0.084)PRGER 81.904 0.015073 0 125430 157910 171900 120870 203130 182040 159440 160360 169380 168260 TRUE FALSE 130382.0733 185029.8141 176379.8552 144777.7252 168602.0352 139763.9688 146942.6762 158210.6365 163284.0469 201227.3255 0.647934235 0.919506403 0.876520397 0.719473486 0.837868489 0.694557603 0.730232218 0.786228392 0.811440725 1 17.6184667 0.705606182 2.533934234 0.999966671 0.780168823 0.413089527 0.079404943 1.797260184 14.16057956 0.07426825 0.019809294 5.076988522 -0.705606182 -0.219797849 SES(ph)LKGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SESLKGR 7 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.001)ES(0.999)LKGR;SES(1)LKGR;SES(1)LKGR;SES(1)LKGR;S(0.001)ES(0.999)LKGR 143.03 0.0014831 4002480000 6023240 3547570 4974080 3654530 6709220 6681950 6151690 4942930 5381160 2926540 TRUE FALSE 6261042.166 4156837.551 5103708.611 4377385.126 5568789.181 5130168.378 5669504.463 4876678.108 5187493.103 3499939.481 1.788900122 1.187688408 1.458227675 1.250703091 1.591110135 1.465787739 1.619886428 1.393360695 1.482166515 1 21.73889855 -0.994364686 5.110155787 0.999996658 1.460562246 0.420439961 0.165453695 5.75E-06 1.13E-06 0.14615469 0.034448741 0.101306034 0.994364686 0.460565588 SES(ph)LSNCSIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SESLSNCSIGK 11 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(0.998)LS(0.002)NCSIGK;SES(0.985)LS(0.015)NCSIGK;SES(1)LSNCSIGK;SES(1)LSNCSIGK;SES(0.922)LS(0.078)NCSIGK;SES(0.568)LS(0.432)NCSIGK 282.2 1.98E-27 3472010000 3773230 2595570 3407890 2778910 4365540 4248300 4155290 3385780 3592180 2187730 TRUE FALSE 3922200.034 3041338.957 3496702.413 3328570.104 3623487.07 3261696.709 3829587.512 3340399.157 3462898.143 2616373.807 1.49909773 1.162425242 1.336468972 1.272207394 1.384927131 1.246647822 1.463700448 1.276728558 1.323548697 1 21.31913725 0.115579814 1.560288621 0.999845813 1.325995626 0.518030311 0.095317168 12.09324536 20.22234763 0.085188452 0.023435448 1.304907761 -0.115579814 0.326149813 SES(ph)LSNCSIGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESLSNCSIGKK 12 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SES(0.89)LS(0.11)NCSIGKK;SES(0.998)LS(0.001)NCSIGKK 108.14 0.0010648 1376100000 907460 543900 859150 472630 1186140 872300 889190 779430 943850 527770 TRUE FALSE 943287.2215 637310.594 881540.1548 566114.8033 984520.3465 669721.5448 819492.9643 768983.0157 909881.0229 631176.4267 1.494490576 1.009718625 1.396662038 0.896920068 1.559817992 1.061068691 1.298358002 1.218332915 1.441563697 1 19.2676838 -1.14799333 4.729322323 0.999976514 1.251343181 0.123511744 0.20858605 4.50E-05 8.10E-06 0.175872462 0.041449666 0.071122444 1.14799333 0.251366667 SES(ph)PDHMVSQYQQALEEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESPDHMVSQYQQALEEIER 20 0 Q14149;H0YHQ4;H0YIR5 Q14149 MORC3 MORC family CW-type zinc finger protein 3 1 S(0.185)ES(0.815)PDHMVSQYQQALEEIER 154.92 2.31E-08 24480000 27485 20014 25596 24959 28798 31362 27840 22658 23995 18995 TRUE FALSE 28570.12902 23451.24881 26263.05279 29895.8157 23902.92625 24078.6508 25657.82805 22354.30657 23131.42464 22716.70657 1.257670382 1.032334892 1.156111812 1.316027727 1.052217943 1.059953419 1.129469537 0.984046983 1.018256082 1 14.47146607 2.342147888 0.900660753 0.999010194 1.17009121 0.408673227 0.082152524 0.619744229 0.979555003 0.060370072 0.037987253 219.8608428 -2.342147888 0.171081016 SES(ph)PKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 SES(1)PKEPEQLR;S(0.437)ES(0.563)PKEPEQLR;SES(1)PKEPEQLR;S(0.015)ES(0.985)PKEPEQLR;S(0.035)ES(0.965)PKEPEQLR;S(0.001)ES(0.999)PKEPEQLR;SES(1)PKEPEQLR;S(0.002)ES(0.998)PKEPEQLR;S(0.003)ES(0.997)PKEPEQLR;S(0.026)ES(0.974)PKEPEQLR;S(0.038)ES(0.962)PKEPEQLR 201.06 2.71E-08 66785610000 48521530 17276220 23382620 17468890 34084240 38678520 33440870 25420710 25760870 12531870 TRUE FALSE 50437197.47 20243276.39 23991990.29 20924184.3 28290613.06 29696019.91 30819687.23 25079986.96 24833741.32 14987249.99 3.365340373 1.350699855 1.600826723 1.396132334 1.887645371 1.981418868 2.056393751 1.67342154 1.656991198 1 23.83723235 8 0.049315209 3.10E-09 5.085736897 0.265843622 0.516778806 879.4679348 3.274297596 80.28437309 342.1173362 99999999.94 -8 5.085736894 SES(ph)PKEPEQLRK ddPTM_MDA-MB-175_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(0.008)ES(0.992)PKEPEQLRK;S(0.017)ES(0.983)PKEPEQLRK;SES(1)PKEPEQLRK;SES(1)PKEPEQLRK;S(0.017)ES(0.983)PKEPEQLRK;S(0.191)ES(0.809)PKEPEQLRK;S(0.178)ES(0.822)PKEPEQLRK;S(0.001)ES(0.999)PKEPEQLRK;S(0.004)ES(0.996)PKEPEQLRK;S(0.203)ES(0.797)PKEPEQLRK;S(0.384)ES(0.616)PKEPEQLRK 159.14 4.77E-05 40746417000 15300733 4423073 6897649 4068190 11294156 12558009 9517583 6911726 7875809 3115163 TRUE FALSE 15904817.75 5182701.381 7077407.399 4872865.84 9374379.397 9641601.728 8771569.975 6819085.618 7592360.173 3725519.546 4.26915429 1.3911352 1.899710178 1.307969473 2.516260962 2.587988496 2.354455497 1.83037172 2.037933254 1 21.8290102 -1.577083128 0.223541479 1.28E-26 2.425168944 0.211143524 0.776026483 44.36770411 1.76006468 27.90536827 1.615339947 0.026479932 1.577083128 2.425168944 SES(ph)PPAELPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 292.39 3.88E-36 624610000 804850 861770 906100 908080 911440 986630 977850 835290 800350 612770 TRUE FALSE 836626.0995 1009772.294 929713.7104 1087695.514 756513.7544 757500.135 901203.5619 824094.3038 771545.5598 732830.5493 1.141636495 1.377906932 1.268661236 1.484238771 1.032317437 1.033663424 1.229757087 1.124535958 1.052829417 1 19.48312012 3.221426442 24.99998813 1.095861293 1.31884993 0.569689561 0.101223843 181.5725278 264926.8278 0.028752853 0.034445013 1665.046789 -3.221426442 0.222988636 SES(ph)PPAELPSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESPPAELPSLRR 13 1 Q14669-3;Q14669;Q14669-2;G5E9G6;H7C1L9 Q14669-3;H7C1L9 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 S(0.214)ES(0.786)PPAELPSLRR 74.141 0.021387 68352000 137870 200990 173230 178570 210470 192080 165070 185920 202530 230100 TRUE FALSE 143313.2141 235508.469 177744.5161 213890.613 174694.3846 147472.331 152131.3821 183428.0465 195240.9849 275183.6895 0.520791092 0.855822776 0.64591225 0.777264864 0.634828267 0.535905058 0.552835753 0.666565838 0.709493303 1 18.07003544 0.7321088 2.468622374 0.999902376 0.651790931 0.528368524 0.099121286 1.1178277 9.1528144 0.094630796 0.025339149 5.396457982 -0.7321088 -0.348111445 SES(ph)PPPLSDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SESPPPLSDPK 11 0 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK 241.39 1.06E-15 5926080000 4004680 2320480 3112880 2345100 4115780 4104110 3908410 3226270 3584910 2108690 TRUE FALSE 4162787.859 2719004.389 3194004.21 2808953.781 3416181.186 3150992.651 3602058.611 3183027.128 3455889.789 2521847.432 1.65068981 1.078179574 1.266533482 1.113847628 1.354634361 1.249477907 1.42834121 1.262180688 1.3703802 1 21.26604957 -1.136005265 3.624764057 0.999799223 1.296761974 0.262496972 0.153924722 21541592.44 35398092.26 54675.33599 0.033963024 0.073113022 1.136005265 0.296962751 SES(ph)QERPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESQERPGSR 10 1 A0A3B3ISF0;Q659C4;Q659C4-9;H0Y9K3;D6R9W6;A0A3B3IT29;A0A3B3ISF8;G3V0E9;Q659C4-3 A0A3B3ISF0 LARP1B La-related protein 1B 1 SES(0.971)QERPGS(0.029)R 69.554 0.068454 0 23740 55724 42360 44882 47635 64118 33831 44938 40250 54437 TRUE FALSE 24677.27353 65294.16353 43463.9364 53759.52564 39538.01971 49227.56622 31179.23782 44335.67961 38801.41036 65102.88789 0.379050367 1.002938051 0.667619176 0.825762533 0.607315912 0.756150269 0.4789225 0.681009415 0.59600137 1 15.99043392 -0.937087702 4.412223912 1.000006221 0.674027834 0.267197116 0.165425411 16794094.04 7613319.176 1012.101895 0.035551032 0.11558788 0.937087702 -0.325978387 SES(ph)VEGFLSPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.121)ES(0.879)VEGFLSPSR 145 6.66E-05 48369000 47872 57366 56183 45989 67240 66640 56028 45933 55969 47674 TRUE FALSE 49762.02353 67218.16425 57647.17513 55085.48694 55810.56882 51163.86994 51636.37896 45317.34327 53954.68662 57014.80753 0.872791222 1.178959768 1.011091287 0.966161061 0.978878492 0.897378631 0.90566611 0.794834627 0.946327611 1 15.79904904 3.048081256 1.347454 0.884625366 1.030764398 0.204262372 0.086607984 0.473881676 1.797717355 0.032203996 0.040418394 1117.072231 -3.048081256 0.146139033 SES(ph)WER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SESWER 6 0 O43598;H0Y8X4;O43598-2 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 SES(1)WER;SES(1)WER;SES(1)WER 136.8 0.01365 991060000 822190 849270 939890 823520 1071460 1196150 1025530 977710 962700 835090 TRUE FALSE 854650.6961 995125.5161 964384.3055 986409.798 889333.6119 918362.2903 945146.2789 964605.3967 928052.6151 998709.8967 0.855754708 0.996410989 0.965630068 0.987684012 0.890482426 0.919548603 0.94636719 0.965851445 0.929251445 1 19.92970614 -3.648935005 0.437175363 1.301976666 0.942543882 0.15625547 0.041263574 602.7638522 12.14331444 169.4905337 0.0221111 0.000224422 3.648935005 -0.359432784 SESAPTLHPYSPLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 SESAPTLHPYSPLS(1)PK;SESAPTLHPYS(0.005)PLS(0.995)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYSPLS(1)PK;SESAPTLHPYS(0.007)PLS(0.993)PK;SESAPTLHPYSPLS(1)PK 246.48 2.16E-20 6296290000 3833470 2068787 2770919 2058862 4101537 4138108 3808655 3287058 3309700 2025001 TRUE FALSE 3984818.356 2424085.074 2843131.425 2466098.759 3404359.206 3177095.131 3510122.669 3243000.364 3190584.544 2421761.175 1.645421686 1.000959591 1.173993313 1.018307992 1.405736966 1.311894486 1.449409093 1.339108248 1.317464569 1 21.20762517 3.207261505 24.99262506 1.332028114 1.192213932 0.036770878 0.200667 447.5038198 357334.6624 0.054660587 0.065337694 1611.615757 -3.207261505 -0.139814183 SESELIDELS(ph)EDFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 SESELIDELS(1)EDFDR 65.092 0.058416 0 12564 14411 19070 11681 15906 23420 20237 19190 19524 12121 TRUE FALSE 13060.03642 16885.97715 19566.97987 13991.46694 13202.3038 17981.05993 18650.77106 18932.78944 18821.33505 14495.87788 0.900948292 1.164881305 1.349830623 0.965203146 0.910762626 1.240425732 1.286625841 1.306080915 1.29839222 1 13.82335509 2.541479407 15.59289258 1.256804023 1.075283819 0.224185855 0.149658595 6.566358363 1589.766919 0.049178948 0.046362593 347.92001 -2.541479407 -0.181520204 SESELIDELS(ph)EDFDRSECK ddPTM_MDA-MB-175_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 230.48 3.39E-20 107924000 146077 108274 145358 108090 186325 176812 161357 140053 161481 106902 TRUE FALSE 151844.2328 126869.2172 149146.1489 129469.8794 154653.5431 135750.0926 148709.4167 138175.8186 155669.3304 127847.4001 1.187699027 0.992348825 1.166595087 1.012690749 1.209672961 1.061813478 1.163179044 1.080787083 1.217618271 1 16.9640633 SESELIDELSEDFDR ddPTM_MDA-MB-175_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 0 ;;;; 396.65 1.69E-114 1216643000 673770 769563 754609 917298 852679 1025310 975422 870474 847885 727048 FALSE TRUE 700370.9599 901729.4589 774274.7305 1098736.807 707740.9281 787197.2912 898965.8748 858806.7198 817369.7845 869499.1354 0.805487816 1.037067689 0.890483612 1.263643357 0.813963924 0.905345686 1.033889326 0.987702788 0.94004669 1 19.72982507 4.749284635 23.81425157 0.985586962 0.805487614 0.184270848 0.11380802 1346.462732 2989902.18 0.025707154 0.361249755 56141.58049 -4.749284635 -0.180099348 SESELIDELSEDFDRSECK ddPTM_MDA-MB-175_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 ;;;;; 322.43 3.78E-62 1746227000 1211694 934331 1118789 864818 1537757 1383353 1207516 1163218 1287726 989460 FALSE TRUE 1259532.615 1094795.081 1147945.56 1035876.419 1276369.614 1062090.231 1112867.741 1147626.965 1241380.993 1183325.743 1.064400587 0.925184877 0.970101063 0.875394139 1.078629128 0.897546797 0.940457645 0.969831826 1.049061089 1 20.17441584 1.333168911 6.532907671 1.023848379 0.961276225 0.125039234 0.062359806 0.372323672 20.65176554 0.039903153 0.014335976 21.53619184 -1.333168911 -0.062572154 SESFS(ph)ISGVQPARTPPMLRPVDPQIPHLVAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESFSISGVQPARTPPMLRPVDPQIPHLVAVK 32 2 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 S(0.202)ES(0.202)FS(0.219)IS(0.219)GVQPART(0.158)PPMLRPVDPQIPHLVAVK 69.885 0.0016945 177080000 73538 61245 65875 52621 89911 89217 78031 73067 73225 53376 TRUE FALSE 76441.33702 71763.35233 67591.75662 63029.27674 74627.96034 68497.70385 71914.72632 72087.65638 70589.64655 63834.00525 1.197501813 1.124218229 1.058867548 0.98739342 1.169094122 1.073059783 1.126589598 1.129298657 1.105831387 1 15.96203755 -1.988936598 2.688317735 0.900369121 1.10670355 0.252612973 0.0556826 13112195.35 9939689.57 8109440.131 0.013426675 0.010258017 1.988936598 0.206334429 SESGGLGVSMVEYVLSS(ph)SPGDSCLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESGGLGVSMVEYVLSSSPGDSCLRK 26 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLS(0.02)S(0.565)S(0.412)PGDS(0.002)CLRK 117.03 0.00053347 261330000 60293 41452 58354 49470 75169 65623 56087 59884 67292 58379 TRUE FALSE 62673.4142 48571.05855 59874.75318 59255.01835 62391.80023 50383.05278 51690.75438 59081.35293 64870.17406 69817.24732 0.897678104 0.695688536 0.857592579 0.84871605 0.893644517 0.721641925 0.740372277 0.846228621 0.929142534 1 16.09129586 1.153993261 2.477239362 0.995926196 0.806562442 0.473109487 0.066859488 0.223813306 2.489373265 0.061803308 0.017180856 14.25585472 -1.153993261 -0.189363754 SESGGLGVSMVEYVLSSS(ph)PADKLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESGGLGVSMVEYVLSSSPADKLDSR 26 1 Q8TB72-3;Q8TB72;Q8TB72-4;Q8TB72-2;A0A0A0MR59;C9JW01 Q8TB72-3 PUM2 Pumilio homolog 2 1 SESGGLGVSMVEYVLS(0.019)S(0.244)S(0.737)PADKLDSR;SESGGLGVSMVEYVLS(0.014)S(0.2)S(0.786)PADKLDS(0.001)R 122.31 8.27E-05 99815000 69235 58260 61794 52305 76205 85546 76666 66770 68273 51835 TRUE FALSE 71968.45126 68265.7018 63404.4024 62650.77289 63251.70132 65679.23796 70656.71859 65875.05736 65815.86807 61991.07581 1.160948577 1.101218214 1.022798872 1.010641807 1.020335597 1.05949505 1.139788553 1.062653882 1.061699079 1 15.91977292 4.530238363 3.490943912 1.053071384 1.157220429 0.464630577 0.038091951 0.247347497 5.646242931 0.010193375 0.049836708 33903.01823 -4.530238363 0.104149046 SESGGLGVSMVEYVLSSS(ph)PGDSCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SESGGLGVSMVEYVLSSSPGDSCLR 25 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 SESGGLGVSMVEYVLSS(0.061)S(0.939)PGDSCLR;SESGGLGVSMVEYVLSS(0.026)S(0.974)PGDSCLR;SESGGLGVSMVEYVLS(0.002)S(0.192)S(0.805)PGDS(0.001)CLR;SESGGLGVSMVEYVLS(0.007)S(0.168)S(0.825)PGDSCLR 155.17 4.11E-08 94880000 125961 183544 167785 172209 174844 219467 170147 174735 171292 175146 TRUE FALSE 130934.0375 215066.2542 172157.6149 206271.4262 145124.0793 168499.1153 156810.4335 172392.9631 165127.2344 209462.5053 0.625095347 1.026752993 0.821901823 0.984765392 0.692840368 0.804435691 0.748632474 0.823025404 0.788337913 1 17.67633249 4.789051889 22.92505501 0.839897978 0.625092216 0.281478434 0.107709758 24891.59093 11300852.86 0.024568212 21.31734588 61525.03782 -4.789051889 -0.214805762 SESIRPDEFSLEIFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SESIRPDEFSLEIFER 16 1 Q01970;Q01970-2 Q01970 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 0 ;; 142.01 1.41E-06 126633000 48764 58853 66761 61169 71177 79053 65172 61881 59367 66396 FALSE TRUE 50689.24037 68960.54494 68500.8465 73268.04563 59078.35896 60694.13881 60063.64834 61051.58641 57230.39327 79405.02497 0.638363131 0.868465755 0.862676468 0.92271296 0.74401285 0.764361435 0.756421251 0.768863009 0.720740196 1 16.27694269 SESLIDASEDS(ph)QLEAAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESLIDASEDSQLEAAIR 18 0 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 SESLIDASEDS(1)QLEAAIR;SESLIDASEDS(1)QLEAAIR 204.23 1.15E-15 144558000 157716 190452 185656 191909 251532 274460 178389 201370 221147 308590 TRUE FALSE 163942.7495 223160.6495 190494.3479 229868.0274 208776.6805 210720.8245 164406.404 198670.9645 213187.9627 369052.3022 0.444226329 0.604685699 0.516171683 0.622860299 0.565710278 0.570978214 0.445482668 0.538327395 0.577663278 1 18.49346576 0.680295896 3.25065296 0.999993177 0.540509818 0.857866498 0.056012491 1.403238676 13.90122841 0.052112799 0.01352086 4.789563059 -0.680295896 -0.459483359 SESPKEPEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SESPKEPEQLR 11 1 F8W6I7;P09651-2;P09651;P09651-3;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ;;;;;;; 182.35 5.31E-06 13392580000 8250630 6423800 7843290 6104790 10091290 10154470 9366880 8097680 8533000 6014940 FALSE TRUE 8576371.243 7527037.68 8047692.581 7312299.241 8375976.13 7796248.235 8632679.47 7989143.845 8225898.997 7193452.33 1.1922469 1.046373471 1.118752473 1.01652154 1.164388912 1.083797859 1.200074606 1.110613302 1.143525893 1 22.77825289 SESPKEPEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 141.38 3.40E-05 4971400000 4474190 2601970 3561540 2367430 5203890 4566620 4282950 3682970 4188610 2240570 FALSE TRUE 4650834.476 3048838.107 3654356.658 2835700.588 4319334.637 3506091.713 3947241.188 3633605.811 4037862.744 2679566.793 1.735666559 1.13781008 1.363786366 1.058268297 1.611952592 1.308454681 1.473089306 1.35604226 1.506908786 1 21.35356835 -1.03365405 4.587149885 0.99998592 1.381554122 0.27107007 0.193081981 11556757.55 2604939.088 1637.754168 0.041257299 0.092543506 1.03365405 0.381568202 SESSEKPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SESSEKPAR 9 1 A0A087WVI0;E9PBL8;Q8WTW3 A0A087WVI0 COG1 Conserved oligomeric Golgi complex subunit 1 0 83.862 0.014485 76575000 124660 120560 142190 112480 156450 159750 153530 130110 122900 121520 FALSE TRUE 129581.6731 141265.2422 145895.5882 134728.2083 129856.6849 122650.4835 141495.9174 128366.0883 118476.853 145329.5174 0.891640428 0.972034069 1.003895085 0.927053297 0.893532761 0.843947505 0.973621326 0.883276093 0.815229109 1 17.14896823 3.468641282 5.484211739 0.898008062 0.958901053 0.150283767 0.05733235 0.272913814 27.09868388 0.015347238 0.021908481 2941.990609 -3.468641282 0.060892991 SESVVSGLDS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SESVVSGLDSPAK 13 0 O14578-4;H7BYJ3;O14578;O14578-2 O14578-4 CIT Citron Rho-interacting kinase 1 SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK 237.46 1.00E-16 317950000 923240 465690 583980 483360 743900 874020 817290 629760 581370 342830 TRUE FALSE 959690.2281 545668.6349 599198.9985 578967.1653 617452.1437 671042.1009 753228.6742 621319.0973 560446.6073 410000.9746 2.340702309 1.330895946 1.461457498 1.412111681 1.505977258 1.63668416 1.837138741 1.51540883 1.366939695 1 18.64526781 -2.745893198 0.249345011 5.24E-13 1.662374607 0.331748579 0.274590756 62.90617345 1.700501013 34.05511709 0.409522918 0.001795175 2.745893198 1.662374607 SETEDSILHQLFIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SETEDSILHQLFIVR 15 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 0 ; 212.87 6.56E-10 212258000 270490 389060 388140 376150 444920 479180 391520 405350 367400 396570 FALSE TRUE 281169.1541 455878.0285 398255.2473 450551.3473 369292.6573 367897.707 360831.6394 399916.9463 354177.3458 474270.2987 0.592845799 0.961219857 0.839722092 0.949988537 0.778654405 0.775713149 0.76081433 0.843225788 0.746783736 1 18.85535 -1.478303577 5.7588105 1.000184215 0.813930197 0.249282415 0.100320859 0.000221048 2.00E-05 0.090492846 0.0213084 0.03324271 1.478303577 -0.186254018 SETELKDTYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SETELKDTYAR 11 1 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 133.07 0.00015437 2422300000 3184500 2488800 3056200 2351200 3611200 3642300 3475900 3096100 3300900 2281900 FALSE TRUE 3310226.519 2916232.04 3135847.083 2816260.342 2997369.514 2796431.025 3203449.875 3054601.844 3182101.254 2728994.615 1.212983895 1.068610404 1.149085112 1.031977244 1.09834204 1.024711082 1.173857162 1.119313987 1.166034274 1 21.37993812 -2.46060805 2.056136689 1.97E-05 1.112959509 0.259291171 0.058653394 873831.243 111827.884 4066490.971 0.01416383 0.003462517 2.46060805 1.112939835 SETSWES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SETSWESPK 9 0 E5RJU9;Q86UE4 E5RJU9 MTDH Protein LYRIC 1 SETSWES(1)PK;SETSWES(1)PK 159.94 6.89E-05 413890000 1249600 602060 650590 734460 993130 1286830 982920 730300 740550 538080 TRUE FALSE 1298935.173 705459.1216 667544.9099 879733.9959 824318.1173 987983.2346 905876.162 720511.523 713897.7502 643506.4738 2.01852697 1.096273542 1.037355391 1.367094243 1.280978748 1.535312036 1.407718801 1.119664762 1.109387052 1 19.29559514 8 0.069357984 0.676726371 2.72149113 0.245843597 0.254283574 448.8227055 2.298685054 11.93333836 89.75526107 100000000 -8 2.044764759 SEVELAAALSDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SEVELAAALSDKR 13 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ;;; 213.18 1.28E-08 712490000 604836 569380 551140 503628 728660 769760 677700 609349 605200 541190 FALSE TRUE 628715.3923 667166.5858 565503.1612 603244.1152 604802.6335 590994.9058 624580.1032 601181.6733 583418.9702 647225.8188 0.971400358 1.030809598 0.873733935 0.932045814 0.934453812 0.913120102 0.965011106 0.928859226 0.901414859 1 19.30390963 4.252074503 24.99999857 0.929840029 1.001104981 0.391273774 0.034909488 208.516152 385737.2483 0.00779632 0.021100454 17867.94072 -4.252074503 0.071264952 SEVLSESSELLQQELEELRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SEVLSESSELLQQELEELRK 20 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 ; 243.95 1.16E-29 82572000 68904 54679 64334 47155 88469 84405 75089 65562 67277 52239 FALSE TRUE 71624.38313 64069.69291 66010.59689 56482.11826 73431.07098 64803.21792 69203.32797 64683.24863 64855.71391 62474.23187 1.146462805 1.025537906 1.056605178 0.904086638 1.175381734 1.037279147 1.107709945 1.035358846 1.038119429 1 15.93097364 SEVQQPVHPKPLS(ph)PDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(0.999)PDS(0.001)R;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(1)PDSR;SEVQQPVHPKPLS(0.999)PDS(0.001)R;SEVQQPVHPKPLS(0.775)PDS(0.225)R;SEVQQPVHPKPLS(0.997)PDS(0.003)R;SEVQQPVHPKPLS(0.912)PDS(0.088)R;SEVQQPVHPKPLS(0.994)PDS(0.006)R 213.82 1.98E-13 31164955000 16191552 10985051 13789742 10358624 17634149 18075295 17174499 14622733 15457769 10159973 TRUE FALSE 16830806.98 12871648.06 14149114 12407528.91 14636702.65 13877581.67 15828316.89 14426739.18 14901446.91 12150625.18 1.385180328 1.059340393 1.164476213 1.021143252 1.204604901 1.142129023 1.302675101 1.187324846 1.226393431 1 23.53452721 SEVQQPVHPKPLSPDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 144.66 3.03E-07 2275860000 1691220 1530520 1832690 1480240 2183210 2215670 1893260 1891740 1971750 1523500 FALSE TRUE 1757990.672 1793374.904 1880451.407 1773027.054 1812108.744 1701114.221 1744861.334 1866384.32 1900787.103 1822000.656 0.964868298 0.984288836 1.032080532 0.973120975 0.994570852 0.933651816 0.957662297 1.024359851 1.043241723 1 20.79709205 1.650601881 6.673492771 1.025894647 0.9785159 0.385188965 0.026089122 0.136879775 12.27693146 0.014104649 0.007069101 44.73030722 -1.650601881 -0.047378747 SEWLDPSQKS(ph)PLHVGETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 SEWLDPS(0.017)QKS(0.983)PLHVGETR;SEWLDPS(0.011)QKS(0.989)PLHVGETR;SEWLDPS(0.04)QKS(0.96)PLHVGETR;SEWLDPS(0.009)QKS(0.991)PLHVGETR 160.36 2.47E-11 1905190000 756580 439440 541180 373239 705390 728230 645820 540590 586280 375750 TRUE FALSE 786450.3626 514910.4016 555283.5954 447064.5602 585488.0598 559109.6189 595198.9409 533344.2753 565179.8973 449371.0183 1.750113671 1.14584693 1.235690716 0.994867363 1.302905697 1.244204891 1.324515638 1.186868431 1.25771328 1 18.77754756 4.742017176 24.95764925 1.200277996 1.750113883 0.705890081 0.108580503 172.1809997 1243155.137 0.024519495 0.179577433 55209.92737 -4.742017176 0.549835887 SEYSELDEDESQAPYDPNGKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SEYSELDEDESQAPYDPNGKPER 23 1 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 0 84.762 0.0066763 94421000 33302 43472 42790 42956 42678 57287 38274 39465 37868 53437 FALSE TRUE 34616.78867 50937.97783 43905.14255 51452.56859 35423.6088 43982.96244 35273.98387 38936.03623 36505.13808 63906.95704 0.541674808 0.797064673 0.687016635 0.80511686 0.554299726 0.688234341 0.551958433 0.609261308 0.571223225 1 15.96368537 -1.087079474 5.063024929 1.000008421 0.647232588 0.566499151 0.09312163 8.74E-06 1.58E-06 0.089015196 0.020980582 0.081831503 1.087079474 -0.352775832 SFAGAVSPQEEEEFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFAGAVSPQEEEEFRR 16 1 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 ;;; 211.78 9.96E-12 1329670000 511370 522141 539550 553237 607290 709970 554533 569250 543093 560860 FALSE TRUE 531559.2825 611814.6551 553611.1162 662665.6274 504063.0627 545090.2272 511067.2545 561620.1349 523547.189 670749.7787 0.792485215 0.912135456 0.825361609 0.98794759 0.751491955 0.81265808 0.761934287 0.837302005 0.780540234 1 19.35541515 3.204961209 24.99993541 0.812754328 0.877949484 0.090748294 0.08147085 357.0175105 265640.9742 0.021563457 0.025774706 1603.102196 -3.204961209 0.065195157 SFCPIELNINGS(ph)PGAESDLATFCTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFCPIELNINGSPGAESDLATFCTSK 26 0 Q9BYW2;C9JG86;H7C3H4;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 SFCPIELNINGS(1)PGAESDLATFCTSK 119.76 0.00020722 27045000 25688 24947 23385 19628 30767 28992 28104 22747 25407 22014 TRUE FALSE 26702.18208 29231.45319 23994.43231 23510.35982 25537.23633 22259.04738 25901.13504 22442.11367 24492.60703 26327.22182 1.014242303 1.110312869 0.911392492 0.893005725 0.969993587 0.845476501 0.983815734 0.852429999 0.930314911 1 14.68426767 4.227891164 24.99715382 0.91581869 1.062277583 0.512432342 0.053829463 120.4309152 282156.1874 0.012128466 0.026626159 16900.17352 -4.227891164 0.146458894 SFDFIHLDPFGTSVNYLDSAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFDFIHLDPFGTSVNYLDSAFR 22 0 Q7Z2T5-2;Q7Z2T5 Q7Z2T5-2 TRMT1L TRMT1-like protein 0 130.09 1.42E-05 164990000 111280 179130 183700 149890 158590 225020 191540 202990 198490 165000 FALSE TRUE 115673.4203 209894.1841 188487.3729 179537.7946 131632.9284 172762.5152 176526.5943 200269.2511 191346.3837 197328.5909 0.586196961 1.063678523 0.955195454 0.909841771 0.667074791 0.87550676 0.894581943 1.014902352 0.969684032 1 17.59024048 1.905197625 3.176411632 0.994994142 0.854088512 0.214244247 0.128745052 0.437059946 7.76409274 0.066032008 0.035814214 80.38918492 -1.905197625 -0.14090563 SFDVNKPGCEVDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFDVNKPGCEVDDLK 15 1 P41091;Q2VIR3;Q2VIR3-2 P41091 EIF2S3;EIF2S3L Eukaryotic translation initiation factor 2 subunit 3;Putative eukaryotic translation initiation factor 2 subunit 3-like protein 0 124.69 8.67E-05 341480000 417490 175980 243730 202050 342240 358110 401430 257180 288240 130030 FALSE TRUE 433972.8276 206203.1961 250081.804 242014.8869 284066.167 274944.3797 369964.8677 253732.9228 277866.2987 155506.8889 2.790698409 1.326006825 1.608171868 1.556296886 1.826711144 1.768052731 2.379089893 1.631650691 1.786842375 1 17.24661897 0.464331251 1.652422649 1.000272216 1.836281838 0.285699288 0.405085997 4.644975969 12.90387941 0.366068003 0.103907806 2.912938066 -0.464331251 0.836009621 SFDWGYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SFDWGYEER 9 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;A0A0G2JI50 P18615 NELFE Negative elongation factor E 0 ;; 108.81 0.0059357 332367000 359599 483897 454880 490220 473800 539040 437640 467080 455290 511330 FALSE TRUE 373796.2462 567002.5456 466734.5465 587184.0528 393263.6452 413856.1292 403336.6332 460819.5566 438904.2018 611515.3235 0.611262272 0.927209056 0.763242602 0.960211511 0.64309696 0.676771478 0.659569135 0.753569925 0.71773214 1 19.22202913 4.020128709 24.82638707 0.755337601 0.788233092 0 0.134842682 1658.080695 2045016.685 0.032295173 0.069750261 10474.38924 -4.020128709 0.032895491 SFEEKVENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFEEKVENLK 10 1 H0YC42;P55327-2;P55327-4;P55327-3 H0YC42;P55327-2 0 ; 156.71 9.54E-06 1105140000 2509080 1535100 1812250 1353240 2992600 2505500 2299730 2003370 2246720 1443590 FALSE TRUE 2608140.416 1798741.484 1859478.724 1620906.833 2483918.921 1923635.596 2119471.153 1976518.102 2165860.986 1726433.821 1.510709755 1.041882672 1.077063425 0.938875741 1.438757102 1.114224926 1.227658499 1.14485599 1.254528821 1 20.7193636 -1.996310935 2.970549143 0.822363851 1.182225066 0.105479831 0.166432336 22895.82205 30925662.96 18847.69439 0.036565046 0.010085306 1.996310935 0.359861215 SFEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFEELR 6 0 Q9NUU7;I3L0H8;F6QDS0;H3BQK0;Q9UMR2;Q9UMR2-2;Q9UMR2-4;H3BN59;H3BTB3;H3BMQ5 Q9NUU7 DDX19A;DDX19B ATP-dependent RNA helicase DDX19A;ATP-dependent RNA helicase DDX19B 0 ;;; 120.9 0.046264 799990000 1002310 1475510 1305710 1450730 1343650 1751880 1273190 1328930 1215830 1525600 FALSE TRUE 1041881.973 1728917.365 1339737.875 1737680.064 1115256.853 1345032.42 1173394.041 1311117.867 1172072.516 1824512.111 0.571046893 0.94760531 0.73429925 0.952408073 0.611263058 0.737201147 0.64312757 0.718612861 0.642403253 1 20.7990793 3.219651491 24.99924061 0.707102232 0.806998896 0.053630306 0.143584141 530.6910255 701610.61 0.037726576 0.045161852 1658.255671 -3.219651491 0.099896664 SFEHMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFEHMK 6 0 Q96EK6;G3V5E4;G3V4W4 Q96EK6 GNPNAT1 Glucosamine 6-phosphate N-acetyltransferase 0 ; 69.39 0.071022 361500000 222850 302880 248280 279430 485980 407730 348210 298160 293330 359520 FALSE TRUE 231648.2901 354897.2839 254750.3808 334700.42 403373.2932 313040.8867 320916.3903 294163.6529 282773.1106 429961.0606 0.538765743 0.825417268 0.592496401 0.778443563 0.938162383 0.728067994 0.746384777 0.684163474 0.657671442 1 18.71384648 4.750432151 24.00201588 0.756458178 0.53876551 0.250184361 0.118466891 1539.555152 3112589.611 0.027117873 0.430896496 56290.1169 -4.750432151 -0.217692668 SFELPPYTPPPILS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SFELPPYT(0.021)PPPILS(0.979)PVR;SFELPPYT(0.009)PPPILS(0.991)PVR;SFELPPYT(0.005)PPPILS(0.995)PVR;SFELPPYT(0.034)PPPILS(0.966)PVR 121.79 6.20E-05 151668300 161122 191718 194010 226111 202914 230696 245240 223282 185951 173951 TRUE FALSE 167483.221 224644.0751 199066.06 270835.0809 168422.7508 177120.3502 226017.448 220289.27 179258.6598 208033.368 0.80507864 1.07984636 0.956894857 1.301882883 0.809594886 0.851403561 1.086448055 1.058913155 0.861682246 1 17.66645543 1.24465477 24.97819766 0.930841126 1.002120354 0.025982936 0.14712369 527.9549568 2164005.192 0.101828702 0.035082858 17.56526757 -1.24465477 0.071279228 SFEVEEVETPNSTPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFEVEEVETPNSTPPRR 17 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;K7ENL0;K7EPY1;K7EJV0 Q9UHD8 9-Sep Septin-9 0 72.797 0.044303 192000000 172250 146070 182260 133810 207700 200090 168820 162480 216610 184290 FALSE TRUE 179050.563 171156.3862 187009.8453 160277.2186 172395.2282 153622.1299 155587.4473 160302.2214 208814.2484 220398.0971 0.812396139 0.77657833 0.848509347 0.72721689 0.782199259 0.697021127 0.705938252 0.727330333 0.947441249 1 17.74975224 1.158477894 4.906145838 0.99262823 0.756691167 0.778694463 0.045871516 0.094886147 3.806273114 0.046512587 0.011961515 14.40382693 -1.158477894 -0.235937063 SFFDNISCDDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFFDNISCDDNR 12 0 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 117.86 0.0016007 212510000 415190 308780 380050 324840 493330 494920 477920 414240 388750 331710 FALSE TRUE 431582.0218 361810.563 389954.4152 389092.3824 409473.9428 379982.3306 440459.3816 408687.7904 374758.9634 396702.2235 1.087924383 0.912045715 0.982990243 0.980817246 1.032194726 0.957852787 1.110302276 1.030213006 0.944685815 1 18.59769696 3.080522564 1.72089293 1.021499655 0.985063644 0.003248659 0.059000143 1.079784649 6.562084029 0.01994315 0.025078257 1203.711928 -3.080522564 -0.036436012 SFFDNISCDDNRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFFDNISCDDNRER 14 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;A0A0G2JQ95;A0A096LP11 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 222.07 3.67E-12 1359370000 683770 895130 808000 662913 975240 968580 626744 840190 783760 1059930 FALSE TRUE 710765.7676 1048861.614 829057.1438 794035.2128 809469.0531 743641.974 577618.1676 828928.6273 755552.6307 1267602.99 0.560716386 0.827436999 0.654035333 0.626406863 0.638582474 0.586652114 0.455677505 0.653933948 0.596048319 1 20.27367154 -1.379251377 5.509822951 1.000143029 0.623609298 0.62249662 0.088263882 0.000157323 1.77E-05 0.086699086 0.020427476 0.041758859 1.379251377 -0.376533731 SFFTDDDKQDHLSWEWNLSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFFTDDDKQDHLSWEWNLSIK 21 1 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;; 204.55 3.15E-22 888771000 392942.9 443774 654590 489914 768705 698351 747960 627893 682826 382165 FALSE TRUE 408456.5891 519988.7324 671649.1532 586817.527 638040.7987 536169.5639 689332.9408 619477.1214 658251.2256 457042.9148 0.893694172 1.137724086 1.469553802 1.283944041 1.39601945 1.173127395 1.508245547 1.355402526 1.440239427 1 18.80197011 4.523989542 3.384481182 1.345819882 0.907303148 0.462539803 0.1448056 0.189211503 4.069823757 0.032286897 0.158545049 33418.69929 -4.523989542 -0.438516734 SFFTDDDKQDHLSWEWNLSIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFFTDDDKQDHLSWEWNLSIKK 22 2 P52566;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 146.89 4.93E-08 92823000 118430 125920 190010 101490 308280 214750 207920 205570 241090 125090 FALSE TRUE 123105.7078 147545.7805 194961.8167 121564.4191 255878.6757 164877.5671 191622.6871 202814.6704 232413.218 149598.9905 0.82290467 0.986275241 1.303229494 0.812601868 1.710430497 1.102130212 1.280908958 1.355722186 1.553574775 1 17.19074091 5.00744311 0.622548271 1.324119847 0.323785128 0.273307889 0.243216312 5.580982252 1.293798093 0.101603713 4.292915166 101728.61 -5.00744311 -1.000334719 SFGEKS(ph)YLNVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.543)Y(0.456)LNVHR;S(0.002)FGEKS(0.558)Y(0.44)LNVHR;S(0.007)FGEKS(0.545)Y(0.448)LNVHR 70.488 0.028471 4250320000 4990600 1363580 2206200 1417160 2198900 4620600 3220070 1343100 2360640 1020250 TRUE FALSE 5187632.742 1597764.258 2263695.384 1697470.018 1825131.763 3547535.676 2967672.499 1325097.941 2275681.028 1220148.454 4.251640631 1.309483492 1.855262266 1.391199582 1.495827625 2.907462338 2.432222481 1.086013704 1.865085368 1 20.21862526 4.744560979 24.81644335 1.73649382 4.251641854 0.644809464 0.56664641 393.9978593 1629454.843 0.138262438 1.261226437 55534.25865 -4.744560979 2.515148033 SFGQTPSQLLIEPHPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFGQTPSQLLIEPHPPR 17 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 171.98 1.66E-09 746610000 332137 380297 375255 360926 371291 456580 353827 359736 342664 373691 FALSE TRUE 345250.0252 445610.0514 385034.4536 432316.0855 308179.0884 350546.2145 326093.1152 354914.3273 330331.5896 446908.5967 0.772529389 0.997094383 0.861550788 0.967347884 0.689579683 0.784380111 0.729664002 0.794154174 0.739147987 1 18.76962027 3.244908802 24.99994666 0.776138154 0.903872318 0.230690819 0.096586097 179.4723405 706780.1593 0.024433949 0.032298986 1757.554506 -3.244908802 0.127734164 SFGS(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SFGSPNR 7 0 D6RAD4;P50613;D6REC6;D6R9G1 D6RAD4 CDK7 Cyclin-dependent kinase 7 1 S(0.015)FGS(0.985)PNR;S(0.026)FGS(0.974)PNR;S(0.012)FGS(0.988)PNR;S(0.002)FGS(0.998)PNR;S(0.013)FGS(0.987)PNR 92.051 0.016735 4038710000 2368030 2744620 2536220 2575020 2899250 3247790 2720200 2595660 2458550 2620630 TRUE FALSE 2461521.653 3215987.135 2602315.977 3084351.27 2406436.521 2493539.993 2506983.616 2560869.423 2370067.266 3134092.274 0.785401781 1.026130329 0.830325258 0.984129056 0.767825677 0.795617926 0.799907405 0.817100838 0.756221278 1 21.57961623 3.227190799 24.99677704 0.811284114 0.909601071 0.16353131 0.090435924 304.4086161 669247.5384 0.023570097 0.028407523 1687.294144 -3.227190799 0.098316957 SFGTEDRPTDRPAPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFGTEDRPTDRPAPPR 16 2 Q9BX40;Q9BX40-2;Q5TBQ1;Q5TBQ0;A0A0C4DFV2 Q9BX40 LSM14B Protein LSM14 homolog B 0 ;;; 222.45 5.42E-15 654590000 192127 234743 210474 261374 226860 290842 267210 223789 207779 209522 FALSE TRUE 199712.3223 275058.2842 215959.1253 313072.9971 188298.4182 223298.3533 246265.382 220789.4745 200301.0744 250573.8244 0.797019892 1.097713558 0.86185828 1.249424188 0.751468828 0.891147963 0.982805697 0.88113543 0.799369507 1 17.93487619 SFGTEDRPTDRPIPPRDEVFEYIIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFGTEDRPTDRPIPPRDEVFEYIIFR 26 3 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9;I3L4Q1 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ; 276.75 5.12E-61 223530000 73866 83341 78286 77997 89597 106941 80154 80558 84927 88628 FALSE TRUE 76782.28672 97654.16845 80326.19747 93424.5738 74367.33394 82105.57346 73871.32004 79478.25178 81870.49386 105992.9597 0.724409309 0.921326933 0.75784465 0.881422446 0.701625223 0.774632331 0.696945535 0.749844631 0.772414452 1 16.69360892 5.04192359 17.8156415 0.790262801 0.356731997 0.040107417 0.094493255 2473.783699 57808.61886 0.02053528 39363.58976 110134.5522 -5.04192359 -0.433530804 SFGTRPLS(ph)SGFSPEEAQQQDEEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.776)S(0.159)GFS(0.066)PEEAQQQDEEFEK;SFGTRPLS(0.811)S(0.175)GFS(0.013)PEEAQQQDEEFEK;S(0.002)FGT(0.018)RPLS(0.788)S(0.15)GFS(0.042)PEEAQQQDEEFEK;SFGTRPLS(0.943)S(0.056)GFS(0.001)PEEAQQQDEEFEK;SFGTRPLS(0.762)S(0.236)GFS(0.002)PEEAQQQDEEFEK;SFGTRPLS(0.575)S(0.195)GFS(0.231)PEEAQQQDEEFEK 347.18 4.70E-103 10291220000 2024850 1467660 1839020 1553690 2433000 2442130 2358840 2117580 2175270 1519970 TRUE FALSE 2104792.642 1719719.188 1886946.372 1861005.245 2019439.529 1874982.318 2173947.957 2089197.304 2096982.458 1817779.02 1.157892471 0.946055142 1.038050473 1.023779692 1.110937857 1.031468786 1.195936323 1.149313135 1.153595918 1 20.7937454 2.25425481 24.99989577 1.140556229 1.047426187 0.189640354 0.071052134 290.4279482 462633.0113 0.023219823 0.019362891 179.5786945 -2.25425481 -0.093130042 SFGTRPLS(ph)SGFSPEEAQQQDEEFEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEKK 26 2 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGT(0.001)RPLS(0.804)S(0.175)GFS(0.02)PEEAQQQDEEFEKK 192.09 2.52E-18 130250000 112080 67113 83635 45677 277410 124790 103370 90538 110750 71596 TRUE FALSE 116505.0049 78639.13568 85814.59681 54711.77427 230255.9473 95809.41371 95267.58929 89324.4862 106764.1291 85623.86541 1.360660423 0.918425433 1.002227549 0.638978093 2.689156185 1.118956885 1.112628925 1.043219502 1.246896862 1 16.38572535 SFGTRPLSS(ph)GFSPEEAQQQDEEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 SFGTRPLS(0.33)S(0.659)GFS(0.01)PEEAQQQDEEFEK 300.2 2.12E-63 2427100000 634390 456350 589940 406440 771600 826420 727600 567470 693920 440840 TRUE FALSE 659436.2071 534724.5626 605314.321 486832.6189 640443.7076 634496.4795 670568.8108 559863.9928 668945.9547 527214.1576 1.250793814 1.014245454 1.148137455 0.923405815 1.214769555 1.203489076 1.271909718 1.06192898 1.268831546 1 19.00802959 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 329.71 7.36E-88 2654623000 3830900 3909069 4682700 3030205 6910150 5124060 3533504 4209712 5214420 5132400 FALSE TRUE 3982146.89 4580421.192 4804735.009 3629570.505 5735565.171 3934074.721 3256538.723 4153287.696 5026754.043 6137995.514 0.648769925 0.746240557 0.782785683 0.591328308 0.934436195 0.640938025 0.530554106 0.676652123 0.818956943 1 22.54933616 0.964079683 3.501182497 0.999249753 0.693334562 0.448854754 0.105394277 0.214756788 7.000126711 0.101084436 0.026150395 9.206184682 -0.964079683 -0.305915191 SFKLS(ph)GFSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFKLSGFSFK 10 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 SFKLS(0.983)GFS(0.017)FK;SFKLS(1)GFSFK 129.04 0.00018987 1368070000 2797600 1270950 1873610 1316210 2299800 2389000 2447200 1920960 2114330 1377150 TRUE FALSE 2908051.408 1489225.776 1922437.816 1576552.41 1908880.817 1834190.956 2255382.069 1895212.673 2038235.676 1646976.175 1.765691242 0.904218165 1.16725296 0.957240568 1.159021512 1.113671821 1.369407829 1.15072258 1.237562332 1 20.65138825 7.999999998 0.0145529 1.71E-07 2.583599521 0.071465303 0.225182376 25169.38801 28.27852669 2019.633472 3109.349428 99999999.49 -7.999999998 2.58359935 SFKPDFGAESIYGGFLLGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFKPDFGAESIYGGFLLGVR 20 1 P35606;P35606-2;H0Y938 P35606 COPB2 Coatomer subunit beta 0 ; 215.06 1.11E-24 1025680000 749710 684630 928930 777980 1011760 1108280 960130 824150 911040 669320 FALSE TRUE 779309.1297 802209.8768 953138.6789 931862.122 839781.3966 850898.7661 884872.5018 813103.6173 878251.8484 800460.4391 0.973576072 1.002185539 1.190738021 1.164157623 1.049122924 1.063011643 1.105454384 1.015794882 1.097183328 1 19.61047058 -0.8076978 8.691016202 1 1.073626603 0.102250862 0.065307294 0 0 0.065590083 0.015459731 0.155704871 0.8076978 0.073626603 SFLDDPIWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFLDDPIWR 9 0 Q7L576;Q7L576-2;Q7L576-3;H0YL50 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 ; 144.38 0.00023196 116432000 347290 345600 395880 412560 404110 488210 405890 367270 359820 324530 FALSE TRUE 361001.2774 404954.1116 406196.958 494163.1366 335419.5265 374830.6264 374075.2812 362347.3464 346870.1485 388115.44 0.930138923 1.04338573 1.046587989 1.273237511 0.864226186 0.965770974 0.963824787 0.933607141 0.893729321 1 18.5661263 SFLEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;;; 102.71 0.019865 684918000 1060140 1196090 1195540 1309680 1379130 1580260 1447790 1271950 1238480 1157630 FALSE TRUE 1101995.146 1401509.153 1226696.755 1568730.795 1144705.975 1213268.564 1334308.437 1254901.591 1193907.347 1384445.434 0.795983084 1.01232531 0.886056412 1.133111321 0.82683358 0.876357084 0.963785501 0.906429072 0.862372266 1 20.40087676 SFLEDIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFLEDIRK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 ;;; 114.89 0.0041182 4676890000 4301420 3183970 3895960 2964110 6095250 4871800 4634460 3948400 4291480 3610320 FALSE TRUE 4471243.383 3730792.08 3997491.918 3550402.111 5059181.582 3740398.283 4271198.915 3895478.156 4137030.473 4317693.08 1.035563043 0.864070699 0.925839758 0.822291452 1.171732564 0.866295546 0.989231711 0.902212845 0.958157608 1 22.04182926 SFLEEVLASGLHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFLEEVLASGLHSR 14 0 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ; 210.14 5.66E-09 432160000 204141 331986 309454 309032 353755 389612 318306 298805 271767 320471 FALSE TRUE 212200.6443 389002.013 317518.6255 370157.6072 293623.8515 299130.5176 293356.344 294800.0077 261986.1588 383261.1567 0.553671147 1.014978967 0.828465447 0.96581039 0.766119515 0.780487436 0.765421538 0.769188327 0.683570861 1 18.54796826 SFLIWVNEEDHTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SFLIWVNEEDHTR 13 0 P12532;P12532-2;F8WCN3 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ;; 205.61 6.85E-08 1772523000 1419531 1718850 1658892 1795670 1663911 2135217 1655490 1507446 1434743 1472512 FALSE TRUE 1475575.18 2014049.117 1702124.088 2150848.166 1381080.003 1639345.211 1525728.368 1487241.152 1383106.88 1761022.533 0.837908177 1.143681627 0.966554406 1.221363228 0.78424891 0.930905301 0.86638776 0.844532721 0.785399876 1 20.74798194 3.217355688 24.9930883 0.862556473 1.04419713 0.364744679 0.112185417 228.2017452 268968.2796 0.030001649 0.035892069 1649.512793 -3.217355688 0.181640657 SFLKPGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFLKPGEK 8 1 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 72.643 0.041609 616500000 1152500 785950 1032800 765190 1471900 1346700 1364300 1097700 1241500 867020 FALSE TRUE 1198001.59 920930.7987 1059715.616 916542.2981 1221706.964 1033949.334 1257362.601 1082987.127 1196818.658 1036895.969 1.155372984 0.88816123 1.022007654 0.883928885 1.178234847 0.997158216 1.212621747 1.044451092 1.154232144 1 19.98383973 3.232540639 24.99999942 1.099423296 0.982755796 0.234006915 0.097696765 188.3141701 782038.8132 0.025570642 0.031315014 1708.207556 -3.232540639 -0.116667501 SFLSEPSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SFLSEPSSPGR 11 0 Q69YN4-3;Q69YN4;H0YC41 Q69YN4-3 KIAA1429 Protein virilizer homolog 1 SFLSEPS(0.001)S(0.999)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPSS(1)PGR;SFLSEPS(0.012)S(0.988)PGR 244.71 7.14E-16 6095550000 4071370 4700760 4722750 4554740 5099230 5724240 4709150 4953960 4564250 4721540 TRUE FALSE 4232110.831 5508078.963 4845828.745 5455653.977 4232464.706 4394872.012 4340034.518 4887560.269 4399983.534 5646635.364 0.749492496 0.975462131 0.85817986 0.966177843 0.749555166 0.77831695 0.768605415 0.865570371 0.779222183 1 22.42896004 5.035531024 16.302721 0.850480563 0.366228099 0.114360411 0.088782947 844119.1432 10687229.98 0.020680101 11809471.11 108525.3072 -5.035531024 -0.484252465 SFLVASVLPGPDGNINS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFLVASVLPGPDGNINSPTR 20 0 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SFLVASVLPGPDGNINS(0.949)PT(0.051)R;SFLVASVLPGPDGNINS(0.97)PT(0.03)R 269.9 3.56E-34 132450000 309940 293000 302850 303780 363090 355040 302360 323080 280590 300320 TRUE FALSE 322176.6705 343320.4708 310742.5198 363866.7773 301372.0915 272587.3407 278660.2331 318749.6411 270491.6207 359161.954 0.897023382 0.955893203 0.865187741 1.013099448 0.83909804 0.75895383 0.775862337 0.887481643 0.753118802 1 18.45427501 3.080129321 10.30500346 0.825354373 0.929482499 0.27143654 0.077016595 0.461674074 56.04077887 0.020837777 0.024918595 1202.62249 -3.080129321 0.104128126 SFPIKPVPS(ph)PSWSGSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.954)PS(0.043)WS(0.003)GSCR 102.43 0.00057411 715740000 283960 239570 283500 284450 409690 387110 326270 333380 365730 231150 TRUE FALSE 295170.9601 280714.2839 290888.2429 340713.361 340051.0401 297209.5692 300696.1049 328911.5864 352567.4487 276439.4169 1.06776003 1.015464029 1.052267604 1.232506438 1.230110539 1.075134554 1.08774685 1.189814355 1.27538776 1 18.07660382 3.85375953 7.171725993 1.160744757 1.040095914 0.285948533 0.079911171 0.308993469 17.30874191 0.020418675 0.037106917 7141.008175 -3.85375953 -0.120648843 SFPIKPVPSPS(ph)WSGSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFPIKPVPSPSWSGSCR 17 1 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SFPIKPVPS(0.387)PS(0.577)WS(0.03)GS(0.007)CR 104.18 0.00052253 584040000 892450 745460 857120 795000 1030900 1116000 975180 889130 980190 723580 TRUE FALSE 927684.6151 873486.9561 879457.2513 952248.6272 855667.9862 856825.9131 898742.8434 877212.6667 944913.1534 865351.6472 1.072031952 1.00940116 1.01630043 1.100418114 0.988809565 0.990147665 1.038586852 1.013706589 1.091941243 1 19.72292698 -1.704412274 2.641260993 0.994659755 1.032257066 0.06646603 0.038225974 68350773.09 60031101.52 2439595.409 0.008816847 0.019750938 1.704412274 0.037597311 SFQSLACS(ph)PGLPAADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;SFQS(0.001)LACS(0.999)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR;SFQSLACS(1)PGLPAADR 245.25 4.36E-20 1358782000 1139268 1425988 1329371 1405003 1557859 1902878 1514060 1576279 1545275 1697949 TRUE FALSE 1184247.18 1670890.346 1364015.5 1682908.4 1293054.684 1460963.423 1395384.021 1555151.558 1489660.855 2030629.597 0.58319212 0.822843491 0.671720486 0.828761879 0.636775257 0.719463276 0.687168168 0.765846987 0.733595559 1 20.95349567 -0.144627677 0.732133992 1.01242595 0.714124133 0.581911725 0.072559125 4.435588165 2.221152389 0.222734776 0.022881996 0.716757628 0.144627677 -0.298301817 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFREPAPAEALPQQYPEPAPAALCGPPPRAPSR 33 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R;SFREPAPAEALPQQYPEPAPAALCGPPPRAPS(1)R 202.56 2.54E-27 781400000 163223 275403 213244 173591 269068 291706 142474 220583 206112 272087 TRUE FALSE 169667.1701 322701.3229 218801.3138 207926.7817 223331.9175 223961.7023 131306.5156 217626.4457 198694.0694 325397.2382 0.52141552 0.991715002 0.672412941 0.638993689 0.686336241 0.688271675 0.403526829 0.668802375 0.610620024 1 18.31184248 -1.085822009 3.791126574 1.000115692 0.655591906 0.351415808 0.14116921 44357190.24 84900677.09 66649.34383 0.033606124 0.082068783 1.085822009 -0.344523786 SFS(ph)ADNFIGIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SFSADNFIGIQR 12 0 Q8N7R7-3;Q8N7R7;Q8N7R7-2 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 1 S(0.001)FS(0.999)ADNFIGIQR;SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR;SFS(1)ADNFIGIQR;S(0.004)FS(0.996)ADNFIGIQR;SFS(1)ADNFIGIQR 181.58 1.89E-05 587380000 574879 740689 579726 759850 741848 956274 636159 660730 569778 677175 TRUE FALSE 597575.6668 867896.574 594834.1358 910146.0621 615748.9419 734193.856 586295.1953 651873.9951 549271.8011 809854.476 0.737880304 1.071669787 0.73449509 1.123839022 0.760320478 0.906575043 0.723951293 0.804927323 0.678235186 1 19.62730317 SFS(ph)ASQSTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SFSASQSTDR 10 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 SFS(0.85)AS(0.15)QSTDR;SFS(0.53)AS(0.47)QSTDR;SFS(0.998)AS(0.002)QSTDR 199.27 2.95E-07 1108650000 491444 567670 543423 652780 689000 790600 684920 673840 599970 594970 TRUE FALSE 510846.5886 665162.9066 557585.0498 781897.9356 571884.0261 606995.1317 631234.1807 664808.277 578377.1969 711542.9801 0.717941998 0.934817608 0.783628067 1.098876607 0.803723798 0.853068822 0.887134296 0.934319213 0.812849277 1 19.44059138 -1.482713939 0.01576712 1.912702555 3.24E-06 0.130192878 0.099947287 5558.80851 14.24803329 963.0131412 772.4734283 0.032906831 1.482713939 -1.912699319 SFS(ph)EDTLMDGPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 S(0.021)FS(0.978)EDTLMDGPAR;S(0.002)FS(0.997)EDTLMDGPAR;S(0.002)FS(0.998)EDTLMDGPAR;SFS(0.897)EDT(0.102)LMDGPAR;S(0.027)FS(0.972)EDTLMDGPAR;S(0.33)FS(0.665)EDT(0.005)LMDGPAR;S(0.392)FS(0.546)EDT(0.062)LMDGPAR;S(0.142)FS(0.858)EDTLMDGPAR;S(0.005)FS(0.995)EDTLMDGPAR 246.86 3.37E-17 2781672000 2436114 2477570 2636407 2327326 3010156 3112293 2750865 2699815 2707352 2400910 TRUE FALSE 2532293.662 2903073.375 2705113.932 2787664.136 2498490.758 2389510.118 2535245.013 2663628.396 2609914.93 2871322.346 0.881925941 1.011057981 0.942114331 0.970864222 0.87015335 0.832198489 0.882953813 0.927666098 0.908959224 1 21.45328387 5.110691349 12.13683864 0.921939792 5.24E-05 0.051604686 0.054122632 804580.544 1590768.544 0.013470392 19471738.74 129030.1937 -5.110691349 -0.921887405 SFS(ph)EGGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFSEGGER 8 0 Q07352;G3V2D5;G3V515;G3V2P5 Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 S(0.014)FS(0.986)EGGER;S(0.029)FS(0.971)EGGER 97.277 0.0089191 0 149349 336070 269670 288740 272581 398220 226476 295010 256487 466860 TRUE FALSE 155245.4138 393787.4082 276697.8217 345851.9102 226247.779 305739.4401 208724.2193 291055.8735 247256.083 558332.2784 0.278052013 0.705292213 0.495579125 0.619437427 0.405220668 0.547594062 0.373835129 0.521295087 0.442847552 1 19.09076444 -1.375064937 3.627408327 1.002730403 0.494571493 0.63482406 0.116463802 114201825.6 201322607.3 3397464.485 0.025419406 0.042163346 1.375064937 -0.50815891 SFS(ph)ENGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFSENGDR 8 0 P47974 P47974 ZFP36L2 "Zinc finger protein 36, C3H1 type-like 2" 1 S(0.015)FS(0.985)ENGDR;S(0.003)FS(0.997)ENGDR 115.91 0.0024882 432730000 405940 461280 512280 496400 644850 729250 531280 557900 545720 605880 TRUE FALSE 421966.8247 540501.2517 525630.4376 594586.4384 535238.6273 559892.7394 489636.8854 550422.263 526079.6438 724590.5857 0.582352066 0.745940207 0.72541715 0.820582616 0.738677314 0.7727022 0.675742819 0.759632093 0.726037095 1 19.46680654 -5 0.370000617 4.530802588 0.724943551 0.652883343 0.059739106 323.5642077 2.497409301 913.4421661 0.040293328 1.00E-05 5 -3.805859037 SFS(ph)KEVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.068)FS(0.932)KEVEER 106.79 0.0017438 5690800000 3369400 1755000 2595900 1762600 4156900 3883300 3539900 2816000 3245000 1903600 TRUE FALSE 3502426.514 2056407.598 2663551.287 2111237.019 3450311.623 2981462.427 3262433.388 2778256.126 3128213.084 2276573.973 1.538463742 0.90329048 1.169982315 0.927374662 1.515571935 1.309626861 1.433045193 1.220367165 1.374088047 1 21.11843291 3.238717723 25 1.321282262 1.120757629 0.142141083 0.206920382 6.945944288 1105120.022 0.054360636 0.069182529 1732.677451 -3.238717723 -0.200524633 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFSLEGLTGGAGVGNKPSSSLEVSSANAEELR 32 1 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.001)FS(0.997)LEGLT(0.002)GGAGVGNKPSSSLEVSSANAEELR 223.21 3.09E-36 126040000 52653 40471 54011 44194 60778 68757 71676 57354 48967 40023 TRUE FALSE 54731.7811 47421.57943 55418.57103 52935.44129 50446.97727 52789.22877 66057.84783 56585.26344 47204.68724 47864.74056 1.143467623 0.990741386 1.157816179 1.105938122 1.05394862 1.10288342 1.380094137 1.182190957 0.98621003 1 15.54667567 2.449690641 24.99990137 1.173374169 1.088353001 0 0.112598214 488.2348327 444968.2309 0.038680263 0.032362922 281.6376039 -2.449690641 -0.085021167 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELRHPFSGEER ddPTM_MDA-MB-175_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(0.109)FS(0.805)LEGLT(0.024)GGAGVGNKPS(0.028)S(0.016)S(0.016)LEVS(0.002)S(0.001)ANAEELRHPFSGEER 50.876 0.017939 266310000 20030 24088 25480 20610 32693 34426 25832 28898 32366 27821 TRUE FALSE 20820.79987 28224.92662 26144.02973 24686.59649 27135.85554 26431.08323 23807.22034 28510.66958 31201.15398 33271.99228 0.625775568 0.848308883 0.785766885 0.741963279 0.815576516 0.794394366 0.715533357 0.856896976 0.937760316 1 15.02202064 1.312197496 2.070928826 0.992351179 0.768026985 0.666273302 0.059024841 0.175080825 1.281757109 0.050076778 0.014895332 20.52095158 -1.312197496 -0.224324195 SFS(ph)LSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SFSLSWR 7 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7;A0A3B3IS41 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 SFS(0.997)LS(0.002)WR;S(0.001)FS(0.999)LSWR;SFS(0.978)LS(0.022)WR;SFS(0.977)LS(0.023)WR;SFS(0.997)LS(0.002)WR;S(0.002)FS(0.989)LS(0.009)WR 172.94 0.00092504 1105758000 1241344 1591701 1808110 1706865 2594620 2102620 1546769 1773565 1745735 2084510 TRUE FALSE 1290353.22 1865063.265 1855230.832 2044477.803 2153587.419 1614318.371 1425529.204 1749793.262 1682906.338 2492929.824 0.517605112 0.748141102 0.744196974 0.820110451 0.863878076 0.64755869 0.571828854 0.701902334 0.675071686 1 21.24941084 -2.321892521 2.170473386 2.484241881 0.702979557 0.451922508 0.099379124 4196077.692 477769.2121 30619450.65 0.02508802 0.004765489 2.321892521 -1.781262324 SFS(ph)MQDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFSMQDLR 8 0 Q9H6H4;E5RGS2 Q9H6H4 REEP4 Receptor expression-enhancing protein 4;Receptor expression-enhancing protein 1 S(0.005)FS(0.995)MQDLR;S(0.011)FS(0.989)MQDLR;S(0.005)FS(0.995)MQDLR;S(0.001)FS(0.999)MQDLR 141.08 0.00067049 766140000 1436190 1780420 1936720 1853500 2157800 2250210 1892990 1942770 1917280 1768580 TRUE FALSE 1492891.89 2086193.285 1987192.514 2220116.768 1791017.927 1727632.83 1744612.497 1916730.346 1848277.467 2115099.389 0.705825881 0.986333453 0.939526778 1.049651274 0.846777194 0.81680929 0.824837124 0.906212897 0.873848991 1 21.01229403 SFS(ph)PEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.001)FS(0.999)PEER;S(0.003)FS(0.997)PEER;SFS(1)PEER;SFS(1)PEER 191.85 0.00054533 4680700000 3349060 3639580 3618430 3518280 4298380 4578030 3992620 3623120 3756310 3711800 TRUE FALSE 3481283.475 4264649.553 3712729.258 4214185.283 3567742.903 3514851.913 3679668.012 3574558.003 3621121.137 4439056.143 0.784239569 0.960710884 0.836378081 0.949342641 0.803716553 0.791801635 0.828930271 0.805251812 0.815741234 1 22.08182152 3.207577856 24.97821282 0.826575045 0.884936009 0.05081845 0.074008935 382.2467039 308165.1212 0.019468127 0.023271259 1612.790126 -3.207577856 0.058360965 SFS(ph)PTMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SFSPTMK 7 0 A3KN83-3;A3KN83-2;A3KN83;A3KN83-4 A3KN83-3 SBNO1 Protein strawberry notch homolog 1 1 S(0.001)FS(0.995)PT(0.004)MK;SFS(0.977)PT(0.023)MK;SFS(0.996)PT(0.003)MK;SFS(0.995)PT(0.005)MK;SFS(0.926)PT(0.074)MK 126.82 0.0041061 1631920000 3649210 2609550 3243270 2689160 4141560 4115150 3908140 3419880 3472110 2415950 TRUE FALSE 3793283.629 3057719.913 3327792.281 3221067.822 3437579.111 3159468.778 3601809.775 3374042.102 3347149.439 2889309.146 1.31286873 1.058287555 1.151760546 1.114822838 1.189758152 1.093503193 1.246598959 1.167767771 1.158460127 1 21.46229314 -2.172129923 1.932082963 0.648779983 1.163303749 0.338004083 0.069595373 2792739.095 554272.1178 4286527.122 0.01577297 0.006727754 2.172129923 0.514523766 SFS(ph)SQRPGMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFSSQRPGMER 11 1 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 S(0.043)FS(0.864)S(0.093)QRPGMER;S(0.14)FS(0.72)S(0.14)QRPGMER 86.756 0.0086196 312020000 163740 202894 169393 177445 260490 246260 192896 203769 175178 231010 TRUE FALSE 170204.5816 237739.4662 173807.5207 212543.0914 216212.0028 189069.8471 177776.3075 201037.8099 168873.378 276271.9865 0.616076149 0.860526864 0.629117425 0.769325526 0.782605597 0.684361268 0.64348293 0.727680763 0.611257696 1 18.07572976 -1.204469436 5.076334942 1.000026741 0.707879602 0.562333026 0.078562102 2.18E-05 3.42E-06 0.069902918 0.016474769 0.06244973 1.204469436 -0.29214714 SFS(ph)SQRPVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 SFS(0.5)S(0.5)QRPVDR;S(0.264)FS(0.733)S(0.003)QRPVDR;S(0.304)FS(0.598)S(0.098)QRPVDR 125.03 0.00025424 3027410000 3182240 2914190 3170420 2766750 4254380 4098990 3703370 3603650 3465930 3197120 TRUE FALSE 3307877.292 3414679.463 3253043.75 3314004.892 3531222.007 3147061.693 3413090.182 3555348.966 3341191.856 3823534.451 0.865135998 0.893068836 0.850794936 0.866738599 0.923549154 0.823076589 0.892653179 0.929859273 0.873849026 1 21.86647544 -0.903451255 0.312004592 1.059840446 0.867258197 0.601819627 0.029752655 8.755820924 0.736121457 0.506273402 0.030447586 0.124896062 0.903451255 -0.192582249 SFS(ph)VER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFSVER 6 0 Q8NFH8-3;Q8NFH8-2;Q8NFH8-4;Q8NFH8 Q8NFH8-3 REPS2 RalBP1-associated Eps domain-containing protein 2 1 S(0.006)FS(0.994)VER 87.323 0.055145 108440000 134280 194930 175410 174220 223660 209080 172260 180660 196610 187400 TRUE FALSE 139581.4781 228407.7112 179981.3287 208680.196 185642.3531 160524.3386 158757.8111 178238.5482 189534.0445 224117.442 0.622805065 1.019142951 0.803067031 0.931119837 0.828326218 0.716250985 0.708368834 0.795290838 0.845690736 1 17.77389541 2.994690655 24.91273605 0.789608084 0.856878793 0 0.122045484 665.7965903 3124105.266 0.033351436 0.038800706 987.849205 -2.994690655 0.067270709 SFSERFPEDGPELEEILTQLATADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFSERFPEDGPELEEILTQLATADAR 26 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;; 210.5 1.30E-25 492804000 116855.6 151985 137337 138795 166178 172050 134482 146660 138461 159821 FALSE TRUE 121469.1493 178087.2415 140916.115 166248.2367 137931.1229 132093.9949 123940.9494 144694.2626 133477.8157 191134.865 0.635515396 0.931736036 0.737260128 0.869795454 0.721642924 0.691103609 0.648447626 0.757027048 0.698343631 1 17.54423144 -1.314391324 3.531069721 1.000956374 0.746927577 0.432248357 0.088132369 30356968.07 43547135.55 301613.3315 0.020664318 0.048485142 1.314391324 -0.254028797 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.011)FS(0.009)KEELMS(0.49)S(0.49)DLEETAGSTSIPK 178.63 3.09E-17 872560000 461820 422670 529940 394330 589930 577420 454210 448840 510640 469600 TRUE FALSE 480053.0102 495260.2846 543750.6718 472327.297 489653.9093 443322.9559 418607.8333 442824.034 492262.1661 561609.129 0.854781351 0.881859391 0.96820127 0.841024963 0.871876692 0.789379896 0.745372202 0.788491517 0.876520948 1 19.09920686 3.203137947 2.077909521 0.818050861 0.89708571 0.039812795 0.073194788 0.531982526 4.720490442 0.022517797 0.030230794 1596.386135 -3.203137947 0.079034848 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 S(0.002)FS(0.001)KEELMS(0.107)S(0.89)DLEETAGSTSIPK;S(0.001)FS(0.001)KEELMS(0.42)S(0.578)DLEETAGSTSIPK;SFSKEELMS(0.086)S(0.914)DLEETAGSTSIPK;SFSKEELMS(0.249)S(0.751)DLEETAGSTSIPK;S(0.006)FS(0.006)KEELMS(0.136)S(0.852)DLEETAGSTSIPK 233.87 2.85E-37 2822000000 2184794 1444365 2080012 1303996 2636970 2259670 1982106 1913494 2285418 1404873 TRUE FALSE 2271051.354 1692423.453 2134218.821 1561922.517 2188738.781 1734895.888 1826743.352 1887846.743 2203166.253 1680130.966 1.351710908 1.007316386 1.270269321 0.929643312 1.302719148 1.032595627 1.087262475 1.123630705 1.311306259 1 20.68014226 4.758646755 23.94872389 1.122630227 1.351711295 0.22872588 0.12836101 3822.490945 4557429.445 0.027454231 1.050005709 57364.96797 -4.758646755 0.229081068 SFSLASSSNS(ph)PISQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 SFSLASS(0.001)SNS(0.999)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR;SFSLASSSNS(1)PISQR 424.06 3.47E-153 3433440000 1831610 2052470 1922470 2165800 2183050 2471150 1857720 1907160 1752230 1810670 TRUE FALSE 1903923.377 2404965.756 1972571.148 2594188.776 1811975.941 1897262.863 1712107.052 1881597.64 1689167.585 2165436.119 0.879233222 1.110614964 0.910934814 1.197998294 0.836771828 0.876157392 0.790652302 0.86892318 0.780058839 1 21.04622618 3.178671773 24.99999793 0.849642018 1.022708636 0.387355198 0.101834336 65.38272387 27292.90264 0.026703597 0.031916917 1508.939312 -3.178671773 0.173066619 SFSQEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SFSQEGR 7 0 P10155-3;P10155-5;P10155-4;P10155;H0Y9N5;P10155-2 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 106.14 0.018074 135670000 152530 149070 135250 130290 164890 364650 142500 153570 153350 140560 FALSE TRUE 158552.0022 174671.6129 138774.7261 156060.9731 136862.0567 279965.5638 131330.4776 151511.6453 147830.9635 168100.0408 0.94320026 1.039093221 0.825548438 0.92838153 0.814170276 1.665469934 0.781263806 0.901318314 0.879422532 1 17.35896055 SFSS(ph)QRPVDR ddPTM_MDA-MB-175_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 1 SFS(0.098)S(0.902)QRPVDR 114.24 0.0036352 559410000 444700 519210 477100 483080 523570 645590 490020 504390 475270 536420 TRUE FALSE 462257.0994 608380.2786 489533.6179 578631.7822 434573.7584 495661.5065 451610.952 497629.4771 458165.1255 641521.2286 0.720563995 0.948340057 0.763082492 0.901968253 0.677411345 0.772634613 0.703968835 0.775702276 0.714185447 1 19.29113748 5.058467935 15.67693622 0.793085958 0.122154489 0.044597047 0.103894676 6513871.383 40978454 0.023199866 137407519 114411.0406 -5.058467935 -0.67093147 SFSSPPS(ph)PSNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SFSSPPSPSNKR 12 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SFSSPPS(0.868)PS(0.132)NKR;SFSSPPS(0.796)PS(0.204)NKR 126.71 0.00017318 430530000 540030 398090 458170 488280 572570 620670 711800 543370 559650 330140 TRUE FALSE 561350.8014 466458.8608 470110.2866 584860.3266 475244.7559 476528.7988 656007.2561 536087.0139 539508.3058 394824.6121 1.421772565 1.181433088 1.190681311 1.481316789 1.203685741 1.206937927 1.66151561 1.357785198 1.366450544 1 18.5908524 SFSSQRPVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SFSSQRPVDR 10 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 0 ;; 135.99 0.00011823 312824000 287150 348220 325151 302786 373591 401152 327439 319855 312833 331193 FALSE TRUE 298486.9037 408024.0762 333624.7022 362676.1671 310088.1353 307990.5275 301773.4756 315567.8669 301574.2014 396083.9273 0.753595092 1.030145502 0.842308105 0.915654845 0.782884924 0.777589057 0.761892758 0.796719698 0.761389647 1 18.59544663 3.235633745 24.98916911 0.797893433 0.892683166 0.112152722 0.092423633 116.1751879 991888.1267 0.024049619 0.029963034 1720.417078 -3.235633745 0.094789733 SFYGSTLFLCR ddPTM_MDA-MB-175_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 ; 166.34 4.78E-05 549150000 208735 286970 258050 227967 849380 489630 234820 303650 285950 967840 FALSE TRUE 216976.019 336254.8652 264774.995 273058.1922 705002.691 375920.8529 216414.1948 299580.0684 275658.7154 1157469.718 0.187457188 0.290508564 0.228753281 0.235909578 0.609089534 0.324778132 0.186971799 0.258823245 0.238156309 1 20.14254302 -1.070973702 4.559374268 1.000040277 0.286052716 0.774371361 0.115863486 32350673.41 7599010.079 13414.87148 0.027986794 0.08492319 1.070973702 -0.713987561 SGAGS(ph)SPETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)GAGS(0.652)S(0.346)PETK 69.01 0.05623 0 228480 152700 188770 131550 263730 282190 254930 203530 208780 134910 TRUE FALSE 237500.5668 178925.0372 193689.5013 157570.1974 218901.2688 216655.6491 234947.9205 200802.0133 201266.0486 161343.0315 1.472022464 1.108972823 1.200482596 0.97661607 1.356744489 1.342826195 1.456201227 1.244565764 1.247441843 1 17.29977174 SGAGSS(ph)PETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGAGSSPETK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGAGS(0.002)S(0.998)PETK;SGAGSS(1)PETK;SGAGS(0.028)S(0.972)PETK;SGAGS(0.34)S(0.66)PETK;SGAGS(0.401)S(0.599)PETK 303.79 1.01E-32 3771741000 7393580 3912065 5478330 3845621 7358220 7252180 7553070 5630400 6219410 3414780 TRUE FALSE 7685484.247 4583931.732 5621099.78 4606273.356 6107472.393 5567971.103 6961040.637 5554933.697 5995574.649 4083840.761 1.881925544 1.122456041 1.376424819 1.127926779 1.495521679 1.363415331 1.704532827 1.360222894 1.468121555 1 21.96149518 -1.076267761 5.419751364 0.999995855 1.42068732 0.256928508 0.220160166 1.02E-05 1.74E-06 0.197827905 0.046628025 0.083894258 1.076267761 0.420691465 SGAHSSAS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGAHSSASPPR 11 0 P18615;P18615-3;A0A0A0MT02;E9PD43;A0A0A0MSN9;P18615-4;A0A0G2JI50 P18615 NELFE Negative elongation factor E 1 SGAHS(0.003)S(0.009)AS(0.988)PPR;SGAHSS(0.03)AS(0.97)PPR;SGAHSS(0.001)AS(0.999)PPR;SGAHS(0.001)S(0.004)AS(0.995)PPR 117.21 0.00092866 1771347000 93438 334178 320263 332956 326127 432199 280264 387830 294983 353542 TRUE FALSE 97127.00439 391570.472 328609.3169 398813.703 270692.049 331827.3323 258296.1753 382631.7732 284366.6195 422811.7859 0.22971688 0.926110589 0.777199993 0.943241689 0.640218788 0.784810981 0.610901077 0.904969506 0.672560768 1 18.68965607 -3.317653038 0.037016035 2.010414901 4.24E-32 0.189573949 0.194106081 1370.854832 5.160778584 209.5518373 91.69409633 0.000481224 3.317653038 -2.010414901 SGAMS(ph)PMSWNSDASTSEAS ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGAMSPMSWNSDASTSEAS 19 0 Q13158 Q13158 FADD FAS-associated death domain protein 1 S(0.001)GAMS(0.999)PMSWNSDASTSEAS;S(0.015)GAMS(0.984)PMS(0.001)WNSDASTSEAS 269.57 3.28E-32 103955000 148456 168283 170353 183201 197303 246430 215039 191041 189559 186351 TRUE FALSE 154317.1575 197184.2962 174792.5391 219437.611 163765.5065 189200.3672 198183.6813 188480.4079 182736.8086 222862.9105 0.692430863 0.88477843 0.784305198 0.984630464 0.734826204 0.848954035 0.889262735 0.845723532 0.819951638 1 17.76579701 -5 0.186924122 1.675029827 0.806102383 0.310382247 0.077317071 166.5002238 1.622118938 41.97468849 0.203543414 1.00E-05 5 -0.868927444 SGAQASS(ph)TPLS(ph)PTR ddPTM_MDA-MB-175_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(0.149)S(0.496)T(0.355)PLS(0.99)PT(0.01)R 155.2 8.64E-06 625420000 831030 671090 605150 559590 622920 804180 617620 675900 671380 872400 TRUE FALSE 863839.7061 786344.4871 620920.7061 670275.2318 517036.2809 617421.3825 569209.3306 666840.666 647217.1649 1043330.077 0.827963964 0.753687164 0.595133525 0.64243833 0.495563477 0.59177953 0.545569751 0.639146403 0.620337877 1 19.99276422 -1.083549952 5.174357834 1.000006727 0.628602298 0.591265827 0.091012097 7.38E-06 1.31E-06 0.092081379 0.021703396 0.082499259 1.083549952 -0.371404428 SGAQASS(ph)TPLSPTR ddPTM_MDA-MB-175_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(0.024)S(0.837)T(0.139)PLSPTR 181.97 1.65E-06 366350000 362340 434030 406520 419210 442550 554620 411520 464050 417450 475940 TRUE FALSE 376645.463 508571.2762 417114.2452 502128.4868 367325.5091 425817.9103 379263.9871 457830.1688 402426.056 569191.3306 0.661720309 0.893497931 0.732819041 0.882178733 0.645346282 0.748110323 0.666320737 0.804351971 0.707013678 1 19.11855416 -1.184051884 4.956403368 1.00002224 0.753788621 0.449730715 0.083130122 1.88E-05 3.09E-06 0.074037949 0.017449337 0.065455797 1.184051884 -0.246233619 SGAQASST(ph)PLS(ph)PTR ddPTM_MDA-MB-175_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 2 SGAQAS(0.002)S(0.243)T(0.755)PLS(0.94)PT(0.06)R;SGAQAS(0.03)S(0.303)T(0.667)PLS(0.979)PT(0.021)R 158.45 5.55E-07 466140000 1258250 1075220 948150 833960 1028320 1208660 973090 983430 972730 1253440 TRUE FALSE 1307926.682 1259880.671 972859.5679 998914.7989 853526.5337 927967.0324 896816.6631 970248.7294 937721.6373 1499027.569 0.872516762 0.84046531 0.64899378 0.666375202 0.569386815 0.619046008 0.598265623 0.647252091 0.625553296 1 20.51559549 4.263642922 4.9103821 0.649242103 0.863195332 0.274646167 0.115759439 0.180921295 10.87327588 0.02566218 0.069691914 18350.28958 -4.263642922 0.213953229 SGAQASST(ph)PLSPTR ddPTM_MDA-MB-175_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(0.033)S(0.052)T(0.915)PLSPTR;S(0.002)GAQAS(0.051)S(0.183)T(0.749)PLS(0.015)PTR 175.26 2.70E-05 676290000 833040 909060 967530 871200 1000360 1178910 1000300 968850 934970 877630 TRUE FALSE 865929.0624 1065183.983 992744.6266 1043520.76 830319.1645 905126.0191 921893.8722 955864.1505 901320.6123 1049584.795 0.825020586 1.014862247 0.945845091 0.994222443 0.791092981 0.862365788 0.878341489 0.910706934 0.858740157 1 20.0013873 SGAQASSTPLS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SGAQASSTPLSPTR 14 0 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 SGAQASSTPLS(0.898)PT(0.102)R;SGAQASSTPLS(0.647)PT(0.353)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.997)PT(0.003)R;SGAQASSTPLS(1)PTR;SGAQASSTPLS(0.966)PT(0.034)R;SGAQASSTPLS(0.96)PT(0.04)R;SGAQASSTPLS(0.983)PT(0.017)R;SGAQASSTPLS(0.891)PT(0.109)R 251.38 4.31E-19 31221100000 5196744 5935080 5796250 5563580 6544872 7346523 6395748 6248013 5924389 5729776 TRUE FALSE 5401915.466 6954383.821 5947305.037 6664039.518 5432376.995 5640404.371 5894432.56 6164268.605 5711171.397 6852415.904 0.788322767 1.014880579 0.867913612 0.972509493 0.792768138 0.823126391 0.860197723 0.899575959 0.833453701 1 22.70818129 5.030512665 16.79130558 0.888667868 0.461856601 0.157477161 0.072976183 7724926.511 113512882.8 0.016649423 94902881.35 107278.4933 -5.030512665 -0.426811267 SGAVQGAGSLGPGS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGAVQGAGSLGPGSPVR 17 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR;SGAVQGAGSLGPGS(1)PVR 316.6 2.72E-58 1905940000 750343 754279 789683 711999 807281 999122 794543 764651 753075 688401 TRUE FALSE 779967.121 883820.5508 810262.7877 852830.2771 670059.664 767091.0573 732264.6435 754402.1041 725971.9779 823279.9957 0.947389861 1.073535802 0.984188602 1.035893355 0.813890374 0.931749904 0.889447876 0.916337222 0.881804467 1 19.65102365 3.262390919 24.99998679 0.90256608 1.012910556 0.480861917 0.05321916 175.825714 184454.6124 0.013397307 0.018130624 1829.746472 -3.262390919 0.110344476 SGCDVNS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGCDVNSPR 9 0 Q9P2R3;Q9P2R3-2;Q9P2R3-4 Q9P2R3 ANKFY1 Rabankyrin-5 1 S(0.013)GCDVNS(0.987)PR 58.676 0.069094 212430000 0 39138 28286 32336 14945 38796 13329 31536 26843 37939 TRUE FALSE 0 45859.64705 29023.1564 38731.96429 12404.65424 29786.21696 12284.23815 31113.3115 25876.92567 45372.42066 0 1.010738382 0.639665153 0.853645534 0.273396351 0.656482871 0.270742402 0.685731796 0.570322793 1 15.46952801 0.309134855 1.510995992 1.000033864 0.563804027 0.183569279 0.282999655 10.45123953 20.9832472 0.250917146 0.072023339 2.03767471 -0.309134855 -0.436229837 SGCRPFCEVYVGDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGCRPFCEVYVGDER 15 1 O14976-2;O14976 O14976-2 GAK Cyclin-G-associated kinase 0 139.49 4.66E-06 217090000 174270 261840 291550 278920 297000 366030 297890 334380 291780 255230 FALSE TRUE 181150.3142 306808.9832 299148.0325 334089.5435 246516.0461 281025.0797 274540.6034 329898.183 281278.8948 305237.4318 0.593473458 1.005148619 0.980050286 1.094523504 0.807620627 0.920676989 0.899432949 1.080792028 0.921508522 1 18.21957237 4.741820544 24.86884257 0.97009593 0.593473308 0.655775196 0.081334087 178.819124 1364080.315 0.019579057 0.141230398 55184.93609 -4.741820544 -0.376622622 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 P68104;A0A087WVQ9;Q5VTE0 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3 0 ;;;;;;;; 262.19 7.91E-54 7735528000 4205991 3971931 4738885 3921119 5552860 5724440 4969506 4908415 4894012 3970067 FALSE TRUE 4372046.772 4654079.252 4862384.236 4696704.635 4608986.841 4395025.565 4579983.134 4842625.725 4717877.464 4747925.617 0.920833038 0.980234239 1.024107079 0.989211924 0.970736952 0.925672793 0.964628241 1.019945575 0.993671309 1 22.1788659 1.74800841 25 1.005310344 0.96985521 0.254053232 0.028612737 3.591306485 9523.850272 0.014230052 0.007891391 55.97684414 -1.74800841 -0.035455134 SGDGEGTPVEHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGDGEGTPVEHVR 13 0 Q7L576;Q7L576-2;Q7L576-3 Q7L576 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 138.89 4.90E-06 0 143060 161500 185420 175870 167070 225100 173540 157750 154860 156580 FALSE TRUE 148708.1193 189236.3687 190252.1975 210656.5611 138671.5011 172823.9364 159937.4813 155635.6193 149286.6189 187258.8531 0.794131315 1.010560332 1.015985062 1.124948474 0.740533752 0.922914637 0.854098371 0.831125561 0.797220619 1 17.5146744 3.232427242 24.99999938 0.850888876 0.990244353 0.281787802 0.100280699 174.1794875 709965.2843 0.02788307 0.034138574 1707.76159 -3.232427242 0.139355477 SGDGVVTVDDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGDGVVTVDDLR 12 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;; 224.68 4.53E-11 2163340000 1747400 1787650 1922490 1744000 2228810 2360610 2016930 1899440 1947580 1691760 FALSE TRUE 1816388.701 2094664.982 1972591.669 2088957.995 1849957.672 1812394.103 1858837.756 1873981.114 1877486.976 2023227.981 0.897767685 1.035308428 0.974972513 1.032487695 0.914359474 0.895793316 0.918748541 0.926233292 0.927966099 1 20.94822746 3.217512772 24.99905943 0.924490965 0.987992146 0.2645688 0.043823007 258.1371513 306595.3215 0.011797252 0.014114372 1650.109526 -3.217512772 0.063501181 SGDIVMIQSEHTGAIDVLSADLESADLLGDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGDIVMIQSEHTGAIDVLSADLESADLLGDHR 32 0 Q6PL24 Q6PL24 TMED8 Protein TMED8 0 167.03 2.61E-14 12331000 14927 28865 28633 29645 28794 38217 28283 32208 26086 28468 FALSE TRUE 15516.32949 33822.33921 29379.1995 35508.69252 23899.60616 29341.68093 26066.10456 31776.30444 25147.16996 34045.75955 0.455749253 0.993437646 0.862932709 1.042969609 0.701984813 0.861830704 0.76561971 0.933341035 0.738628548 1 15.0551875 -5 0.0195813 2.03167839 1.23E-09 0.106978666 0.158796502 9621.191518 14.26651482 991.2055411 549.2572868 1.00E-05 5 -2.031678389 SGEDGEKDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGEDGEKDTK 10 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ; 83 0.014891 153796000 403570 128955 209033 151897 360120 347380 489740 252100 308050 104033 FALSE TRUE 419503.2552 151102.0181 214480.5717 181941.7732 298906.931 266706.2596 451352.8991 248721.0119 296963.3407 124416.2745 3.371771554 1.214487564 1.723894824 1.462363135 2.402474533 2.143660551 3.62776414 1.999103516 2.38685286 1 16.92481569 3.202293397 24.55555074 2.375574615 1.87542356 0.021358099 0.807838072 368.4063117 249436.6242 0.222737435 0.266231117 1593.284742 -3.202293397 -0.500151056 SGEISLPIKEEPS(ph)PISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGEISLPIKEEPSPISK 17 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5;I3L2A0 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 SGEISLPIKEEPS(0.999)PIS(0.001)K 129.85 1.95E-05 190670000 433460 165670 242440 159710 360230 367250 337450 258870 294460 158110 TRUE FALSE 450573.3355 194122.5338 248758.1856 191300.1613 298998.2333 281961.7532 310999.7872 255400.2711 283862.4421 189088.6273 2.38286851 1.026621942 1.315563972 1.011695754 1.581259738 1.491161881 1.64473026 1.350690809 1.501213723 1 17.52870307 -1.193044666 5.446037929 0.99998188 1.449654041 0.12996429 0.364579597 7.43E-05 1.10E-05 0.326828861 0.0770312 0.064114363 1.193044666 0.449672161 SGELTALEFSAS(ph)PGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGELTALEFSASPGLR 16 0 A0A2R8YF49;H0Y895;Q12774-2;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 SGELTALEFSAS(1)PGLR;SGELTALEFSAS(1)PGLR;SGELTALEFSAS(1)PGLR;SGELTALEFS(0.007)AS(0.993)PGLR 250.6 6.86E-21 365840000 434712 425884 478901 491155 516412 622630 553843 466742 453319 365779 TRUE FALSE 451874.7654 499026.2641 491381.5535 588303.993 428632.4727 478033.6185 510431.3385 460486.0869 437004.1377 437446.3918 1.032983181 1.140771243 1.123295477 1.344859631 0.97985143 1.092782173 1.166843179 1.052668614 0.99898901 1 18.7387467 1.522907081 3.646702203 1.00335034 1.12776733 0.245795616 0.090086055 0.284656545 8.209326 0.059457068 0.023422601 33.33550823 -1.522907081 0.12441699 SGELTALEFSAS(ph)PGLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGELTALEFSASPGLRR 17 1 A0A2R8YF49;H0Y895;Q12774-2;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 SGELTALEFS(0.008)AS(0.992)PGLRR;SGELTALEFSAS(1)PGLRR;SGELTALEFS(0.015)AS(0.985)PGLRR;SGELTALEFS(0.002)AS(0.998)PGLRR 208.17 3.32E-12 885030000 410175 462750 489010 417778 581590 620500 400250 475930 437821 478110 TRUE FALSE 426369.0257 542223.7128 501754.0023 500413.2415 482731.5395 476398.2788 368877.3591 469550.9368 422063.9077 571786.5005 0.74567872 0.948297507 0.877519847 0.875174984 0.844251375 0.833175107 0.645131284 0.82119976 0.738149479 1 19.12511703 2.466560073 24.9984996 0.779207068 0.862559324 0.053745049 0.095867206 400.3333309 947589.1544 0.03071846 0.025724796 292.7925846 -2.466560073 0.083352256 SGEQAEGS(ph)PGGPGDSQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGEQAEGSPGGPGDSQGR 18 0 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 SGEQAEGS(1)PGGPGDSQGR;SGEQAEGS(1)PGGPGDSQGR 253.37 1.75E-30 464580000 185832 189377 230600 185541 237680 275810 230430 204870 204360 164089 TRUE FALSE 193168.7909 221901.0266 236609.6254 222240.456 197279.2385 211757.3074 212368.2945 202124.0527 197005.1235 196239.0979 0.984354254 1.130768685 1.205721123 1.132498357 1.005300374 1.079078072 1.082191555 1.029988697 1.003903532 1 17.58225298 1.951781167 0.68588578 0.996660189 1.109187753 0.267937037 0.059541643 0.945062889 0.863234831 0.056019819 0.03111099 89.49137217 -1.951781167 0.112527563 SGERPVTAGEEDEQVPDSIDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGERPVTAGEEDEQVPDSIDAR 22 1 Q9Y3D0;H3BNV7 Q9Y3D0 FAM96B Mitotic spindle-associated MMXD complex subunit MIP18 0 146.06 8.05E-08 327200000 108280 151290 137050 139500 145700 184550 130040 143640 134750 142810 FALSE TRUE 112554.978 177272.8806 140621.6356 167092.6836 120933.966 141691.0594 119847.125 141714.7407 129900.3738 170790.8852 0.659022159 1.037952818 0.823355622 0.97834661 0.708082085 0.82961722 0.701718507 0.829755877 0.760581419 1 17.38187146 3.234368223 24.99897485 0.792993195 0.882667142 0.066135727 0.122040687 224.5013445 1338688.802 0.031740038 0.039239487 1715.411127 -3.234368223 0.089673947 SGES(ph)S(ph)SQLSQEQK ddPTM_MDA-MB-175_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(0.286)GES(0.57)S(0.611)S(0.511)QLS(0.022)QEQK 91.202 0.0097075 205100000 22269 371650 278010 389760 186130 376660 205740 310760 255900 508540 TRUE FALSE 23148.19732 435477.9965 285255.169 466853.3647 154491.6891 289186.4233 189613.5612 306594.7705 246690.209 608178.6764 0.038061508 0.716036279 0.469031849 0.767625342 0.254023522 0.475495828 0.311772787 0.504119566 0.405621273 1 19.21413571 -1.515931471 4.220609736 1.004971852 0.450987077 0.411131104 0.201246383 0.008652977 0.000992423 0.179083817 0.041930486 0.03048376 1.515931471 -0.553984775 SGEWTEDEVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGEWTEDEVLR 11 0 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;; 346.43 2.34E-70 2879770000 2464250 2511580 2826760 2667950 3106510 3428050 3013360 2684450 2796810 2211450 FALSE TRUE 2561540.493 2942924.328 2900427.688 3195662.547 2578466.54 2631937.34 2777164.969 2648469.339 2696153.354 2644741.287 0.968541046 1.112745637 1.096677283 1.208308186 0.974940934 0.995158715 1.050070562 1.001409609 1.019439356 1 21.33469517 3.193323889 24.9999977 1.008947526 1.09773233 0.373003015 0.05694616 136.5727014 75476.18311 0.016288765 0.019468879 1560.716023 -3.193323889 0.088784804 SGEWTEDEVLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGEWTEDEVLRR 12 1 Q13938-4;Q13938 Q13938-4 CAPS Calcyphosin 0 ;;;;; 287.13 1.78E-28 13722400000 2885730 3402390 3293270 2791330 4075230 4019910 3165640 3463570 3476640 3424330 FALSE TRUE 2999660.849 3986724.016 3379095.322 3343446.743 3382523.86 3086346.825 2917508.865 3417146.509 3351516.406 4095261.901 0.732471066 0.973496717 0.825123131 0.816418296 0.825960327 0.753638448 0.712410814 0.834414646 0.818388784 1 21.96552429 5.050389904 16.0271527 0.826703444 0.127477705 0.111543634 0.083796593 6822425.271 54974323.24 0.019337358 148465073.5 112302.6239 -5.050389904 -0.699225738 SGFEPASLKEEVGEEAIVELVENGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGK 25 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 240.3 1.32E-38 194375000 291292 143288 207680 152679 306870 273928 329570 226633 262316 106874 FALSE TRUE 302792.4331 167896.5994 213092.3114 182878.4505 254708.347 210312.3734 303737.4422 223595.3553 252875.2984 127813.9141 2.369009941 1.313601892 1.667207463 1.430818012 1.992806095 1.645457577 2.376403574 1.749381959 1.978464553 1 16.96368537 3.218784469 24.98857648 1.855048101 1.665908501 0 0.420233531 832.285167 1051649.441 0.112870516 0.135076764 1654.948444 -3.218784469 -0.1891396 SGFEPASLKEEVGEEAIVELVENGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 293 1.53E-70 1785840000 1834840 695370 1291710 712380 1994830 1621580 1702050 1371720 1624780 588260 FALSE TRUE 1907280.9 814794.3883 1325373.024 853286.6378 1655749.509 1244992.62 1568638.874 1353334.337 1566304.485 703518.2841 2.711060882 1.158170877 1.88392122 1.212884806 2.353527331 1.769666331 2.229705907 1.92366619 2.226387744 1 19.42422839 3.221899788 24.99907641 1.974193074 1.710014391 0.017430011 0.533875188 751.129685 1127045.174 0.141106518 0.16909241 1666.862545 -3.221899788 -0.264178683 SGFGEISS(ph)PVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGFGEISSPVIR 12 0 P57740;G3V1T4 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGFGEIS(0.017)S(0.983)PVIR;SGFGEIS(0.198)S(0.802)PVIR;SGFGEIS(0.003)S(0.997)PVIR;SGFGEIS(0.023)S(0.977)PVIR;SGFGEIS(0.008)S(0.992)PVIR;SGFGEIS(0.012)S(0.988)PVIR 246.3 1.64E-16 612530000 1603140 1599760 1581880 1482760 1706470 2024160 1650040 1618090 1590790 1579180 TRUE FALSE 1666433.205 1874506.336 1623105.092 1776045.502 1416404.839 1554079.516 1520705.553 1596402.15 1533537.779 1888590.086 0.882368926 0.992542717 0.859426884 0.940408147 0.749980025 0.82287815 0.805206786 0.845287796 0.812001392 1 20.84887817 3.265678078 24.99584368 0.829544065 0.919729291 0.235552218 0.068803794 263.677526 243046.1523 0.017450693 0.023622541 1843.648302 -3.265678078 0.090185226 SGFSLDNGELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGFSLDNGELR 11 0 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 82.261 0.045186 45064000 61582 113910 105770 114260 97180 134450 98062 113220 110120 124060 FALSE TRUE 64013.30491 133473.1564 108526.4531 136860.287 80661.37831 103226.0251 90375.6442 111702.4711 106156.8027 148367.1817 0.431451917 0.899613748 0.731472094 0.922443126 0.543660514 0.695747024 0.609135006 0.752878566 0.715500567 1 17.17881248 0.26150767 1.491720523 1.000090174 0.705852407 0.289512363 0.140811349 9.383952522 17.50869828 0.127227649 0.036447776 1.826028998 -0.26150767 -0.294237767 SGGASHSELIHNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 224.42 1.82E-12 1083576000 898379 1286610 1233106 1183950 1430480 1619940 1228226 1259960 1202472 1073500 FALSE TRUE 933847.6966 1507575.259 1265241.755 1418131.776 1187327.521 1243733.485 1131954.437 1243072.297 1159195.268 1283831.772 0.727391016 1.174277886 0.985519897 1.104608725 0.924831077 0.968766713 0.881699972 0.968251701 0.902918352 1 20.29202474 SGGGGYSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGGGGYSSR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 87.696 0.030909 22497000 16686 23208 21582 19201 23073 29094 23023 24447 19182 21721 FALSE TRUE 17344.77616 27193.79347 22144.44465 22998.90049 19151.0597 22337.35942 21218.3971 24119.32795 18491.64357 25976.81408 0.66770221 1.046848678 0.852469613 0.885362632 0.737236662 0.859896035 0.816820609 0.92849446 0.711851866 1 14.66493688 -1.303680022 3.883721684 1.000303998 0.845786916 0.174531683 0.105523124 4585335692 822113324.7 12893850.66 0.02263629 0.049695833 1.303680022 -0.154517082 SGGGLHSVAEGVRLS(ph)PEPGR ddPTM_MDA-MB-175_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 205.43 5.22E-22 760893000 344837 528863 559415 482214 614418 683209 482405 552626 510129 545325 TRUE FALSE 358451.431 619691.1063 573993.8145 577594.4899 509979.4478 524544.0639 444592.8356 545218.9524 491769.5569 652170.9929 0.549627989 0.950197284 0.88012779 0.88564885 0.781971988 0.804304499 0.681712067 0.836006137 0.75405003 1 19.31489075 -1.188828272 5.619486523 1.00000554 0.799604827 0.24823511 0.108021309 7.06E-06 1.02E-06 0.098506853 0.023217646 0.064739856 1.188828272 -0.200400714 SGGGPGPSGSET(ph)PPPPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGGGPGPSGSETPPPPRR 18 1 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 SGGGPGPSGSET(1)PPPPRR;SGGGPGPS(0.001)GS(0.027)ET(0.972)PPPPRR;S(0.005)GGGPGPS(0.006)GS(0.033)ET(0.956)PPPPRR;SGGGPGPS(0.002)GS(0.033)ET(0.965)PPPPRR 136.81 3.21E-06 1344510000 242264 262781 253490 222171 306889 331764 263037 280984 245550 272811 TRUE FALSE 251828.7698 307911.5926 260096.1576 266115.7607 254724.1174 254716.8389 242419.4726 277217.8691 236712.7035 326263.0922 0.771857975 0.94375245 0.797197611 0.815647761 0.780732248 0.780709939 0.743018375 0.849675847 0.725527064 1 18.31567627 6.172119058 14.22704814 0.8152925 0.522420621 0 0.083478674 0 0 0.016769393 0 1486343.055 -6.172119058 -0.292871879 SGGGYGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGGGYGGDR 9 0 Q92804-2;Q92804;A0A075B7F4;A0A075B7C1 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;;; 136.39 0.00045139 1084986000 1209379 1581877 1580687 1440604 1706732 1997474 1662527 1653793 1493549 1439356 FALSE TRUE 1257126.217 1853552.069 1621881.002 1725551.171 1416622.304 1533590.936 1532213.79 1631626.61 1439796.463 1721370.25 0.730305532 1.076788721 0.942203458 1.002428833 0.822962 0.890912885 0.890112856 0.947864999 0.836424623 1 20.71512601 3.254110632 24.99802955 0.898208013 0.948155099 0.036631112 0.094557625 737.3883651 1185409.578 0.024557923 0.033133369 1795.190875 -3.254110632 0.049947086 SGGIVIS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGGIVISPFR 10 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR;SGGIVIS(1)PFR 110.64 0.0019507 2005504000 1108411 1170142 1135745 1316971 1253058 1511386 1478326 1244392 1113942 914886 TRUE FALSE 1152171.922 1371104.786 1165343.448 1577463.933 1040063.649 1160389.507 1362450.945 1227712.961 1073851.445 1094140.395 1.053038465 1.253134234 1.065076706 1.441738135 0.950576044 1.060549004 1.245224974 1.122079914 0.981456721 1 20.06136644 1.299989663 4.742794128 0.989507494 1.154921295 0.192880708 0.130247829 0.300321682 12.21317387 0.093955463 0.031201271 19.95214826 -1.299989663 0.165413802 SGGIVIS(ph)PFRLEELTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR;SGGIVIS(1)PFRLEELTNR 301.03 1.34E-46 3703630000 1186030 1325020 1375760 1269890 1593730 1781450 1331250 1453330 1365330 1438960 TRUE FALSE 1232855.38 1552581.878 1411613.436 1521070.452 1322828.344 1367735.236 1226903.146 1433850.489 1316192.04 1720896.661 0.716402912 0.902193556 0.820277863 0.883882505 0.768685519 0.794780574 0.712944114 0.833199646 0.764829213 1 20.71472904 -1.320637524 3.198245115 1.001312897 0.80316175 0.500630895 0.059927399 91910011.14 116347080.5 1135616.457 0.014072933 0.0477928 1.320637524 -0.198151147 SGGLQT(ph)PECLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQT(0.997)PECLS(0.003)R;SGGLQT(1)PECLSR 143.64 0.00069724 429320000 373420 348380 333520 303370 381530 480600 368120 361480 322670 254250 TRUE FALSE 388162.9099 408211.555 342211.8052 363375.6805 316677.6669 368987.9336 339265.7925 356634.9519 311057.1697 304065.4196 1.276576963 1.342512264 1.125454534 1.195057567 1.041478729 1.213514954 1.115765788 1.172888888 1.02299423 1 18.21402223 8 0.176237333 1.019716267 2.213098561 0.570070272 0.069344889 43.84649506 0.485730479 0.161064544 13.94983862 100000000 -8 1.193382295 SGGLQTPECLS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGLQTPECLSR 12 0 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 1 SGGLQTPECLS(1)R;SGGLQTPECLS(1)R 120.75 0.00040756 1155120000 1703830 1066430 1199250 1273150 1630090 1836400 1642890 1443920 1364200 884050 TRUE FALSE 1771098.524 1249581.057 1230503.44 1524975.27 1353007.884 1409923.931 1514115.989 1424566.614 1315102.708 1057262.671 1.675173608 1.181902181 1.163857832 1.442380698 1.279727281 1.333560684 1.432109569 1.347410301 1.243875098 1 20.01190242 0.877346487 2.769801639 1.000334882 1.34787813 0.382437589 0.137669259 0.494971629 7.70196711 0.125067924 0.03311095 7.539568429 -0.877346487 0.347543248 SGGLQTPECLS(ph)REGS(ph)PIPHDPEFGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGLQTPECLSREGSPIPHDPEFGSK 26 1 P85037;P85037-2 P85037 FOXK1 Forkhead box protein K1 2 S(0.001)GGLQT(0.073)PECLS(0.926)REGS(1)PIPHDPEFGSK;S(0.001)GGLQT(0.023)PECLS(0.977)REGS(1)PIPHDPEFGSK 165.26 1.71E-11 474930000 463480 432960 552390 326450 809020 771080 433440 590030 665380 579890 TRUE FALSE 481778.5483 507317.512 566785.7372 391020.8356 671503.0694 592008.3558 399465.8402 582121.6129 641433.1038 693508.3428 0.694697552 0.731523301 0.817273135 0.563830039 0.968269634 0.853642731 0.57600726 0.839386604 0.924910436 1 19.40355371 1.27584699 2.844231956 0.983271702 0.750124173 0.360511111 0.115961497 0.281713706 3.791902869 0.100770304 0.029473206 18.87326294 -1.27584699 -0.233147529 SGGMERPFVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGMERPFVLAR 12 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 109.15 0.0014861 1197900000 910280 907250 952050 942140 1294750 1193950 1023140 969760 947690 870310 FALSE TRUE 946218.5573 1063063.13 976861.2051 1128492.48 1074668.857 916673.207 942943.6133 956761.9534 913582.822 1040830.581 0.909099496 1.021360391 0.938540068 1.084223024 1.03251084 0.880713176 0.905953025 0.919229287 0.877744023 1 19.98930383 2.737932878 24.9994855 0.911551182 1.000073609 0.342807372 0.0553683 59.74594278 2379311.989 0.01694865 0.0168675 546.9314254 -2.737932878 0.088522427 SGGPPPKR ddPTM_MDA-MB-175_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 ;; 83.206 0.029384 263541000 396127 353112 406296 308042 494820 462050 435244 423470 431380 320586 FALSE TRUE 411766.3998 413756.2392 416884.4075 368971.7882 410710.6731 354745.8899 401128.438 417794.0773 415854.7181 383398.6887 1.07399011 1.07918011 1.087339158 0.962371023 1.07123651 0.92526631 1.046243636 1.089711806 1.08465347 1 18.54848588 -0.748177775 9.155317213 1 1.046639288 0.062895745 0.054038405 0 0 0.052907829 0.012470495 0.178575644 0.748177775 0.046639288 SGGPS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGPSPKR 8 1 Q96E39 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 1 SGGPS(1)PKR;SGGPS(1)PKR 96.015 0.0056602 1018750000 1145770 738990 950680 609340 1258350 1255670 1045360 965200 1047560 638170 TRUE FALSE 1191005.884 865905.784 975455.5018 729865.6333 1044456.116 964059.6724 963421.9517 952263.0727 1009858.52 763207.193 1.560527594 1.134561875 1.278100509 0.956313882 1.368509267 1.263169007 1.262333427 1.247712393 1.323177414 1 19.54171524 -1.527763152 2.75580511 0.98724327 1.255462551 0.225591525 0.146702279 15412968.07 15424258.46 1461996.427 0.034206287 0.029664487 1.527763152 0.26821928 SGGTEGLLAEKLEALITQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGGTEGLLAEKLEALITQTR 20 1 Q9UHB9;Q9UHB9-4 Q9UHB9 SRP68 Signal recognition particle subunit SRP68 0 ; 220.63 7.65E-25 745330000 602920 532120 628640 458760 751360 821820 579920 549830 642790 516470 FALSE TRUE 626723.7472 623507.4707 645022.8748 549501.3587 623644.0956 630964.7598 534464.3551 542460.4282 619656.1135 617662.4081 1.014670375 1.0094632 1.044296798 0.889646758 1.009684396 1.021536606 0.865301738 0.878247439 1.003227824 1 19.236459 2.252153642 24.99576647 0.91918574 0.996408438 0.191105724 0.057598969 293.9440734 540523.4259 0.020169306 0.016789117 178.7119697 -2.252153642 0.077222699 SGILPILVHCLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGILPILVHCLER 13 0 O00629 O00629 KPNA4 Importin subunit alpha-3 0 ; 165.73 3.48E-05 653730000 439090 503980 464250 472820 583560 627720 504340 526230 484640 492560 FALSE TRUE 456425.6123 590534.6446 476348.7364 566342.3848 484366.6796 481941.5432 464808.513 519176.7476 467197.9011 589067.7014 0.774827089 1.002490279 0.80864854 0.961421554 0.822259782 0.818142876 0.789057882 0.881353275 0.793114102 1 19.16807393 SGITS(ph)PVEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGITSPVEKR 10 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 S(0.076)GIT(0.285)S(0.639)PVEKR;S(0.006)GIT(0.192)S(0.803)PVEKR;S(0.001)GIT(0.11)S(0.89)PVEKR 110.98 0.0011114 827538000 948340 694030 888190 634650 1213470 1194430 956680 931010 996740 686170 TRUE FALSE 985781.1955 813224.2537 911336.9611 760181.8758 1007204.803 917041.7343 881692.9218 918531.3338 960867.5221 820611.874 1.201275812 0.990997425 1.110557853 0.92635983 1.227382682 1.117509706 1.074433541 1.119324937 1.170915938 1 19.6463405 3.225351805 24.99999743 1.120735087 1.056366247 0.104939765 0.087026041 492.5282239 932194.6811 0.023532077 0.028285043 1680.164501 -3.225351805 -0.06436884 SGKNS(ph)QEDS(ph)EDS(ph)EDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 3 S(0.379)GKNS(0.621)QEDS(1)EDS(1)EDKDVK 78.837 0.0083199 240360000 726320 89314 171960 86505 266170 593490 268810 180100 179300 71165 TRUE FALSE 754995.6744 104652.9847 176441.4189 103615.4308 220926.5185 455660.9419 247739.9698 177686.0541 172847.028 85108.41921 8.87098693 1.22964315 2.07313707 1.217452184 2.595824485 5.353887972 2.910875 2.087761184 2.030903988 1 16.37701423 4.74489314 24.87424937 2.391896213 8.870990037 0.734825195 1.186434622 365.3474461 1435048.578 0.296397625 2.794178594 55576.74913 -4.74489314 6.479093824 SGKNS(ph)QEDSEDSEDKDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 S(0.023)GKNS(0.977)QEDSEDSEDKDVK;S(0.025)GKNS(0.975)QEDSEDSEDKDVK;S(0.016)GKNS(0.984)QEDSEDSEDKDVK 199.83 8.25E-16 1051250000 2164140 324387 665030 273521 1168140 1521750 1033860 622350 765860 218419 TRUE FALSE 2249581.918 380097.9439 682361.2281 327622.6374 969579.98 1168346.625 952823.3517 614008.4162 738296.8482 261214.0212 8.61202591 1.455120756 2.612268764 1.254230672 3.711822113 4.47275617 3.647673075 2.350595169 2.826405891 1 17.99487281 4.746122907 24.98259486 2.717402722 8.61202875 0.733853868 1.085206172 486.2994552 1606488.451 0.263828093 2.796076381 55734.34571 -4.746122907 5.894626028 SGKPAELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGKPAELLK 9 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 80.979 0.020202 0 1128800 710900 1066000 810070 2243300 1260000 1077500 951400 1097000 888330 FALSE TRUE 1173365.896 832991.545 1093780.836 970299.4282 1861984.667 967384.0955 993042.7345 938648.0392 1057519.184 1062381.255 1.104467807 0.784079671 1.029555849 0.913325064 1.752652033 0.910580915 0.934732921 0.883532192 0.995423422 1 20.01887017 SGKPAELLKMFGIDRDAIAQAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGKPAELLKMFGIDRDAIAQAVR 23 3 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 188.72 8.94E-18 1560950000 1853790 1267920 1702580 1684040 1431770 2057190 2011700 1888830 1429070 881940 FALSE TRUE 1926979.061 1485675.397 1746950.633 2017138.086 1188398.247 1579438.8 1854017.697 1863513.323 1377638.05 1054739.257 1.826971972 1.408571253 1.656286728 1.91245189 1.126722305 1.497468487 1.757797185 1.766800003 1.306140869 1 20.00845496 1.004221331 4.778844754 1.001137689 1.615401278 0.453215435 0.217812381 0.1381873 9.949846039 0.209214093 0.053023874 10.09767367 -1.004221331 0.61426359 SGKYDLDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 107.06 0.0025861 27237940000 49151000 26164100 39917700 28614900 62266800 50538400 52519700 39760100 44611400 22364900 FALSE TRUE 51091519.43 30657580.65 40957988.05 34274841.81 51682711.58 38801622.52 48403068.68 39227180.89 43005844.43 26746873.95 1.910186571 1.146211729 1.531318693 1.28145225 1.932289795 1.450697475 1.809671992 1.466608059 1.607883019 1 24.67286695 -1.116512182 4.616201862 0.999973482 1.559221023 0.328669918 0.24419583 15743999.78 3807973.663 7451.313001 0.05242355 0.076469424 1.116512182 0.559247541 SGKYDLDFKSPDDPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGKYDLDFKSPDDPSR 16 2 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 111.06 0.00047572 8523020000 15909030 9883510 13366440 6803499 24412290 16962970 10913810 12123420 16285710 11786540 FALSE TRUE 16537130.79 11580925.96 13714780.41 8149210.796 20262697.67 13023577.29 10058357.05 11960925.38 15699590.48 14095886.85 1.17318839 0.821581933 0.972963288 0.57812686 1.437490091 0.923927486 0.713566813 0.848540111 1.113771035 1 23.74877091 -2.072977626 9.187633925 1.302387576 0.935423838 0 0.232237386 0.189398949 0.001504401 0.029606996 0.050541078 0.008453224 2.072977626 -0.366963738 SGLEELVLSEMNS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGLEELVLSEMNSPSR 16 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SGLEELVLS(0.001)EMNS(0.959)PS(0.04)R 93.424 0.0046537 12625000 31038 30608 35459 32428 37754 41568 41637 35920 34039 39143 TRUE FALSE 32263.40421 35864.6859 36383.09067 38842.16161 31336.58857 31914.46197 38373.38314 35438.55115 32813.94304 46812.32141 0.689207526 0.766137735 0.777211844 0.829742265 0.669408985 0.681753457 0.819728268 0.757034688 0.70096808 1 15.51460069 -2.038781536 2.552336693 1.316837282 0.74777811 0.668356494 0.054135682 3561115.336 1604474.265 6590605.205 0.013884808 0.009145732 2.038781536 -0.569059173 SGLEPAS(ph)SPSKGSEPRPLVPPVSGHATIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGLEPASSPSKGSEPRPLVPPVSGHATIAR 30 2 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SGLEPAS(0.499)S(0.499)PS(0.002)KGSEPRPLVPPVSGHATIAR;SGLEPAS(0.499)S(0.499)PS(0.002)KGSEPRPLVPPVSGHATIAR 157.78 4.16E-10 797850000 177899 346410 384250 303200 541180 519430 398360 454350 437770 342460 TRUE FALSE 184922.5899 405903.2228 394263.8707 363172.055 449190.4169 398800.2545 367135.5023 448260.1814 422014.7432 409558.4802 0.451516935 0.991075127 0.962655859 0.886740411 1.096767467 0.973732138 0.896417777 1.094496154 1.030413881 1 18.64370994 4.738631365 8.359471009 0.994258753 0.447970242 0.855593795 0.066670057 0.030865017 31.54915927 0.016093025 0.094945365 54781.17773 -4.738631365 -0.546288511 SGLFTNTEPHS(ph)ITEDVTISAVMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGLFTNTEPHSITEDVTISAVMLR 24 0 P57740;P57740-2;F5GY77 P57740 NUP107 Nuclear pore complex protein Nup107 1 SGLFTNTEPHS(1)ITEDVTISAVMLR;SGLFTNTEPHS(0.999)IT(0.001)EDVTISAVMLR;SGLFT(0.002)NT(0.001)EPHS(0.989)IT(0.008)EDVTISAVMLR 153.01 5.44E-08 190715000 77640 107916 115202 111894 118607 144473 100008 104268 107195 102128 TRUE FALSE 80705.28715 126449.7335 118204.2588 134026.2992 98446.22451 110921.3353 92169.11164 102870.458 103337.0729 122138.0262 0.660771175 1.035301924 0.967792443 1.09733474 0.806024361 0.90816381 0.754630761 0.842247588 0.846067978 1 16.89815291 SGLIHVGDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGLIHVGDELR 11 0 S4R337;Q5T2T1-2;Q5T2T1 S4R337 MPP7 MAGUK p55 subfamily member 7 0 ; 132.76 0.0001757 246875000 196592 272040 252560 243294 277500 309050 282200 251290 231190 253580 FALSE TRUE 204353.604 318760.7538 259141.9211 291416.827 230330.6491 237277.8212 260080.4266 247921.8686 222869.5171 303264.1459 0.673846898 1.051099374 0.854508931 0.960933994 0.759505046 0.782413036 0.857603611 0.817511308 0.734902296 1 18.21021542 3.234569415 24.99869585 0.81674558 0.894769703 0.058163793 0.112093795 231.0982971 1447475.017 0.029573472 0.036599935 1716.205998 -3.234569415 0.078024123 SGLS(ph)LEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 S(0.001)GLS(0.999)LEELR;SGLS(1)LEELR 136.5 0.00020034 337130000 442040 496060 532330 468560 578330 627330 523250 513610 492830 476180 TRUE FALSE 459492.0805 581254.4462 546202.9571 561239.7695 480025.6732 481642.1148 482236.2977 506725.898 475093.1446 569478.354 0.806864874 1.020678735 0.959128566 0.985533103 0.842921719 0.845760179 0.84680356 0.889807127 0.834260234 1 19.11928148 3.234382023 24.99999758 0.869051897 0.949744512 0.175597839 0.068792495 144.2517001 863039.7719 0.018395215 0.022748001 1715.465635 -3.234382023 0.080692615 SGLSLEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 0 ; 76.221 0.036044 6521000000 41424 1726560 758440 1435610 313360 1257590 324280 827120 472620 2942400 FALSE TRUE 43059.45151 2023083.249 778205.5695 1719569.373 260095.1791 965533.7815 298862.0863 816033.8093 455610.4985 3518906.944 0.012236599 0.574918087 0.221149801 0.48866577 0.073913628 0.274384574 0.084930375 0.231899798 0.129475006 1 21.74669593 -1.388383461 3.468002144 1.00575058 0.239302717 0.645306495 0.17065761 87905584.24 126831926.5 5067296.465 0.03851635 0.040889946 1.388383461 -0.766447863 SGLTVPTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 SGLTVPT(0.147)S(0.853)PK;SGLTVPT(0.026)S(0.974)PK;SGLTVPT(0.028)S(0.972)PK;SGLTVPT(0.02)S(0.98)PK;SGLTVPT(0.008)S(0.992)PK;SGLTVPT(0.169)S(0.831)PK;SGLTVPT(0.017)S(0.983)PK;SGLTVPT(0.002)S(0.998)PK 202 2.43E-07 19464260000 38654800 15710160 21547240 15668960 30566100 36526500 28795980 23398310 22292430 11458170 TRUE FALSE 40180921.35 18408257.77 22108778.78 18768233.52 25370485.24 28043773.94 26538875.84 23084693.93 21490129.8 13703179.03 2.932233554 1.34335673 1.613405088 1.369626236 1.851430619 2.046515912 1.93669482 1.684623245 1.568258705 1 23.70800729 -2.232692666 0.280170804 9.26E-13 1.872437302 0.272810177 0.422683971 54.00817858 2.046988142 34.54013799 0.494346447 0.005852041 2.232692666 1.872437302 SGMNVAR ddPTM_MDA-MB-175_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 ; 148.98 0.0048655 307280000 632730 673860 669050 629030 831020 942100 717100 704570 707800 669610 FALSE TRUE 657710.669 789590.2131 686485.9926 753450.2565 689763.5172 723311.5527 660891.8282 695126.3916 682326.4163 800807.259 0.821309574 0.985992827 0.85724247 0.94086342 0.861335246 0.903228017 0.825282015 0.868032081 0.852048241 1 19.61109553 3.201553766 24.99961874 0.874591273 0.904247295 0 0.060676971 528.9663371 357336.8904 0.016041793 0.01917406 1590.573586 -3.201553766 0.029656022 SGMS(ph)PEQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SGMSPEQSR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.003)GMS(0.997)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(1)PEQSR;SGMS(0.999)PEQS(0.001)R;SGMS(0.999)PEQSR 167.11 6.32E-05 11925250000 4580950 5184140 5112730 4791260 5874960 6620320 5326470 5225620 4890600 4718440 TRUE FALSE 4761809.443 6074475.718 5245971.944 5738956.928 4876336.398 5082851.012 4908967.363 5155579.111 4714588.261 5642927.978 0.843854372 1.076475855 0.929654244 1.017017575 0.864150033 0.9007471 0.869932663 0.913635462 0.835486166 1 22.42801251 3.231241084 24.99934432 0.892799499 0.971938305 0.191801738 0.069116886 225.8706007 771444.4139 0.018036415 0.021978329 1703.103668 -3.231241084 0.079138806 SGMS(ph)PPPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGMSPPPCK 9 0 Q9H6T0-2;Q9H6T0 Q9H6T0-2 ESRP2 Epithelial splicing regulatory protein 2 1 SGMS(1)PPPCK;SGMS(1)PPPCK;S(0.003)GMS(0.997)PPPCK;SGMS(1)PPPCK;S(0.001)GMS(0.999)PPPCK 124.67 0.00054879 1267250000 3505500 2594080 3075200 2797650 3662120 3883440 4011100 3179710 3253650 1975010 TRUE FALSE 3643899.847 3039593.061 3155342.238 3351016.82 3039634.15 2981569.914 3696699.501 3137091.188 3136551.772 2361975.396 1.542734041 1.286885997 1.335891239 1.418734855 1.286903393 1.26232048 1.565088065 1.328164211 1.327935836 1 21.17156251 0.636334015 2.055644185 1.000133387 1.375118231 0.565874221 0.098906162 1.448549508 7.296152542 0.090161709 0.024748016 4.32846604 -0.636334015 0.374984844 SGNFGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGNFGGSR 8 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;; 157.2 0.00088571 2430690000 938280 1038710 1013970 967480 1319670 1369460 1068660 1115370 988420 1043110 FALSE TRUE 975324.0189 1217100.362 1040394.891 1158844.656 1095352.965 1051423.669 984895.6368 1100420.29 952846.9573 1247487.433 0.781830737 0.975641381 0.833992282 0.92894295 0.878047294 0.842833075 0.789503454 0.882109319 0.763812871 1 20.25059385 2.796781475 5.322843358 0.845801212 0.885651251 0.013715054 0.076447804 0.654225545 39.63017801 0.021638114 0.022792224 626.2986492 -2.796781475 0.039850039 SGNLTEDDKHNNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGNLTEDDKHNNAK 14 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 ;;; 267.11 3.59E-25 437310000 440100 237742 349644 244496 519932 442332 502178 374255 429555 214537 FALSE TRUE 457475.4878 278572.3391 358756.0099 292856.5791 431554.1444 339607.0966 462815.9762 369238.7239 414095.3995 256571.4176 1.783033715 1.085749698 1.398269586 1.141423241 1.682003975 1.323635734 1.803848537 1.439126491 1.613957639 1 17.96900094 3.233975017 24.97738603 1.509770056 1.336389155 0.039553443 0.270306544 277.4330281 1511155.11 0.070820112 0.087378514 1713.858714 -3.233975017 -0.173380901 SGNS(ph)DSIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.055)GNS(0.944)DS(0.001)IER 200.27 2.45E-05 321780000 247720 238540 252610 229800 306380 347790 326460 273580 264470 196200 TRUE FALSE 257500.1769 279507.3894 259193.2241 275253.7541 254301.637 267021.0433 300871.2122 269913.1076 254951.7764 234641.6335 1.097418958 1.191209698 1.104634417 1.173081477 1.083787362 1.13799516 1.282258428 1.150320612 1.086558138 1 17.84009949 0.989399398 3.1584192 1.000877369 1.156009053 0.438446048 0.053977766 0.210556238 5.196819449 0.051737031 0.013546444 9.758866963 -0.989399398 0.155131684 SGPFGQIFRPDNFVFGQS(ph)GAGNNWAK ddPTM_MDA-MB-175_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 157.75 3.09E-09 109450000 111370 122510 133030 81091 143420 147220 133860 112770 130130 101370 TRUE FALSE 115766.9736 143550.1395 136496.8711 97130.55777 119041.5196 113030.3861 123367.7034 111258.5026 125446.6467 121231.5107 0.95492478 1.184099239 1.125919081 0.801198939 0.981935464 0.932351544 1.017620772 0.917735843 1.034769311 1 16.88740521 3.783642144 24.99993703 0.953534252 1.097892921 0.354750899 0.082015309 425.1665215 235774.4316 0.019804125 0.035702177 6076.341083 -3.783642144 0.144358669 SGPFGQIFRPDNFVFGQSGAGNNWAK ddPTM_MDA-MB-175_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 0 251.09 1.88E-46 7130800000 295280 212970 296180 257900 326520 360430 326260 288630 326230 226290 FALSE TRUE 306937.8824 249545.9408 303898.6941 308911.8502 271018.247 276725.5949 300686.8887 284761.387 314489.046 270627.1929 1.134172361 0.92210224 1.122942195 1.14146641 1.001444992 1.022534328 1.111074188 1.052227546 1.162074818 1 18.04594728 2.232229886 24.99768071 1.083016821 1.055542883 0.023832068 0.074032307 690.7034585 2727294.112 0.026575444 0.020134185 170.6985713 -2.232229886 -0.027473938 SGPIS(ph)PGIHSCDLTVEGLATVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGPISPGIHSCDLTVEGLATVTR 23 0 Q9BUB4-2;Q9BUB4 Q9BUB4-2 ADAT1 tRNA-specific adenosine deaminase 1 1 S(0.002)GPIS(0.998)PGIHSCDLTVEGLATVTR 221.42 1.14E-32 165340000 62405 78533 67696 71583 84612 95143 83699 82877 75688 90457 TRUE FALSE 64868.79759 92020.43185 69460.21337 85741.90375 70229.68246 73047.48016 77138.45367 81766.16937 72964.00366 108180.3172 0.59963586 0.850620836 0.642078108 0.792583216 0.649190946 0.675238177 0.713054423 0.75583222 0.674466534 1 16.72307851 -1.877131544 2.643297776 1.136396831 0.7118604 0.599349685 0.07199753 15696896.64 9091263.876 13380716.6 0.016416138 0.013269925 1.877131544 -0.424536431 SGPKPFSAPKPQT(ph)SPSPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.461)S(0.461)PS(0.078)PKR 129.32 2.03E-05 10260000000 1193900 556380 739890 398900 1374800 916120 731350 787780 896590 469680 TRUE FALSE 1241036.094 651933.937 759172.1412 477801.2294 1141111.987 703365.0139 674024.876 777221.0976 864321.901 561704.8034 2.209409794 1.160634435 1.351550025 0.850626924 2.031515451 1.252196901 1.199962813 1.383682484 1.538747569 1 19.09945261 7.991252877 0.033709771 6.09E-06 3.491159194 0.135149295 0.378527869 2668.7832 6.889369679 215.037093 581.4172986 98006048.05 -7.991252877 3.491153102 SGPKPFSAPKPQTS(ph)PS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.469)S(0.535)PS(0.997)PK 89.365 0.0015579 2395200000 5053100 1690600 2012600 1385000 3189100 4251500 2782600 2222800 2459700 1286900 TRUE FALSE 5252600.29 1980947.399 2065050.009 1658948.866 2647017.921 3264153.557 2564492.541 2193007.002 2371175.877 1539043.416 3.412899361 1.287128991 1.34177502 1.077909076 1.719911143 2.120897646 1.666289927 1.424915619 1.540681603 1 20.5536025 4.74238163 24.85512716 1.495904214 3.412900162 0.779357546 0.31062125 165.9506053 1079436.815 0.077193813 0.581336715 55256.27824 -4.74238163 1.916995947 SGPKPFSAPKPQTS(ph)PS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGPKPFSAPKPQTSPSPKR 19 3 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 2 SGPKPFSAPKPQT(0.415)S(0.587)PS(0.997)PKR 78.202 0.015033 2004800000 1741200 519310 777380 364310 1400900 1273700 999670 805720 962340 322520 TRUE FALSE 1809943.92 608497.4528 797639.1614 436369.4306 1162775.518 977902.4781 921313.2532 794920.6413 927705.5714 385711.619 4.692479644 1.577596896 2.067967679 1.131335975 3.014624038 2.53532025 2.38860643 2.060919615 2.405179221 1 18.55716308 -1.551827681 0.258106296 1.68E-35 2.552012965 0.196982513 0.895932704 42.50013461 2.019056822 31.31523325 1.303123168 0.02806547 1.551827681 2.552012965 SGPKPFSAPKPQTS(ph)PSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 SGPKPFSAPKPQT(0.137)S(0.522)PS(0.341)PK;SGPKPFSAPKPQT(0.093)S(0.835)PS(0.071)PK 107.56 0.00032817 27408000000 6985300 2339650 3620660 2463030 5647340 4827010 4960190 3636030 4102490 1371610 TRUE FALSE 7261085.038 2741466.688 3715017.374 2950209.983 4687407.164 3706010.082 4571397.347 3587294.965 3954842.186 1640350.718 4.426544248 1.671268624 2.264770169 1.798523907 2.857564002 2.259279092 2.786841433 2.186907303 2.410973545 1 20.64557288 -1.51203315 0.34520569 1.56E-16 2.564684658 0.292710323 0.723017716 31.02006975 2.140621719 28.42238212 0.554616243 0.03075862 1.51203315 2.564684658 SGPKPFSAPKPQTSPSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ; 193.06 8.03E-15 993020000 1587190 774040 1087310 751520 1677860 1410750 1452960 1211390 1407430 690220 FALSE TRUE 1649853.487 906975.3488 1115646.192 900168.4129 1392657.957 1083124.693 1339073.199 1195153.298 1356776.869 825455.3939 1.99871913 1.098757553 1.351552367 1.090511274 1.687138962 1.312154116 1.622223573 1.44787145 1.643670729 1 19.65483073 3.21775585 24.99930044 1.477470089 1.362066194 0.005482193 0.299538246 974.746003 1171265.399 0.080779145 0.096646842 1651.033365 -3.21775585 -0.115403895 SGPLFNFDVHDDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGPLFNFDVHDDVR 14 0 Q14320;B0S8I6 Q14320 FAM50A Protein FAM50A 0 ;;;; 174.59 2.52E-06 1179200000 916240 1114410 1106280 1077900 1201850 1417900 1104830 1197230 1110970 1096350 FALSE TRUE 952413.8627 1305801.249 1135110.566 1291105.403 997559.9663 1088614.213 1018230.538 1181183.09 1070986.407 1311158.792 0.726390937 0.995913887 0.865730812 0.984705599 0.760823153 0.830268782 0.77658827 0.900869595 0.816824334 1 20.32241099 4.786851123 22.51868794 0.872169343 0.726388641 0.225660887 0.084578605 18581.56591 8664088.929 0.019331313 12.05692336 61214.0513 -4.786851123 -0.145780701 SGPPS(ph)PPSTATSFGGPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 SGPPS(1)PPSTATSFGGPRPR;SGPPS(0.93)PPS(0.035)T(0.035)ATSFGGPRPR;SGPPS(1)PPSTATSFGGPRPR 227.36 7.79E-20 1790250000 482104 452988 503106 401248 594453 608800 458459 470656 479843 380140 TRUE FALSE 501137.8382 530785.1652 516217.3557 480613.6568 493408.0914 467415.4265 422523.7856 464347.6262 462573.5442 454621.1548 1.102319663 1.167532922 1.135489078 1.057173983 1.085317052 1.028142711 0.929397546 1.021394674 1.017492343 1 18.79430529 3.137224094 1.129544629 0.993913803 1.138027974 0.74083282 0.033906829 0.237101725 0.647928935 0.014277028 0.020147139 1371.589318 -3.137224094 0.144114171 SGPS(ph)PLSS(ph)PNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGPSPLSSPNGK 12 0 O75179-6;O75179-2;O75179;O75179-4;H0YM23;O75179-7 O75179-6 ANKRD17 Ankyrin repeat domain-containing protein 17 2 SGPS(1)PLS(0.338)S(0.662)PNGK 184.8 2.03E-05 341470000 2411600 1491500 1819800 1411300 2481000 2595500 2400100 2024200 2040500 1253200 TRUE FALSE 2506811.83 1747653.523 1867225.483 1690450.928 2059280.506 1992734.46 2211973.891 1997068.91 1967062.804 1498740.546 1.672612272 1.166081432 1.24586306 1.127914323 1.374007337 1.329606025 1.475888469 1.332498087 1.312477205 1 20.51531922 0.694190502 3.908002768 1.000001695 1.331803496 0.32285073 0.146669528 8.211638286 103.8301019 0.136190809 0.034840685 4.945275626 -0.694190502 0.331801801 SGPS(ph)PLSSPNGK ddPTM_MDA-MB-175_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(1)PLSSPNGK;SGPS(1)PLSSPNGK 220.48 3.09E-11 258843000 534420 410960 486680 366580 646270 645460 588080 525910 548290 387440 TRUE FALSE 555519.3143 481539.1832 499363.2806 439088.4299 536417.2562 495561.697 541984.7529 518861.0367 528557.15 463351.45 1.19891567 1.039252566 1.077720336 0.947635817 1.157689819 1.069515801 1.169705529 1.119800179 1.140726224 1 18.82174736 SGQGAFGNMCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGQGAFGNMCR 11 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 ; 128.81 0.00060034 198905000 73604 85627 80403 76898 115584 125901 89125 93725 77349 97756 FALSE TRUE 76509.94275 100332.7712 82498.36823 92108.19488 95937.07297 96662.4008 82139.14962 92468.76968 74565.2246 116909.4165 0.654437812 0.858209494 0.705660593 0.787859504 0.820610314 0.8268145 0.70258797 0.790943727 0.637803411 1 16.83503161 -2.312121736 2.481100953 2.423544193 0.760699379 0.510264281 0.072057124 4441332.286 952567.5823 35978248.59 0.015858608 0.004873919 2.312121736 -1.662844814 SGQGFHGNSEVNAILS(ph)PR ddPTM_MDA-MB-175_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 237.71 4.75E-24 1419257000 319179 531972 527165 580666 575321 699409 569116 598142 536253 544100 TRUE FALSE 331780.4334 623334.0528 540903.353 695520.0017 477528.1419 536981.8594 524507.2008 590124.8849 516953.3593 650705.9776 0.509877648 0.957935034 0.831256161 1.068869852 0.733861619 0.82522964 0.806058679 0.906899437 0.794449993 1 19.31164628 7.999809318 0.030015606 1.433578129 4.19E-07 0.146724785 0.137015687 3280.068232 7.547163281 114.816666 278.9337279 99956103.55 -7.999809318 -1.433577711 SGQKPVLDVHAELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGQKPVLDVHAELDR 15 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 ; 110.37 0.00055694 659080000 1387330 1184760 1439490 1236890 1718710 1768650 1559550 1552000 1522470 1062580 FALSE TRUE 1442102.86 1388233.314 1477004.292 1481543.15 1426564.288 1357907.842 1437308.396 1531197.979 1467676.602 1270772.207 1.134824048 1.092432858 1.162288791 1.165860524 1.122596387 1.068569044 1.131051174 1.204935055 1.154948617 1 20.27727401 -1.140482936 5.448070376 0.999997097 1.139810597 0.559255726 0.036567956 1.42E-06 2.25E-07 0.039123167 0.009221228 0.072363083 1.140482936 0.1398135 SGS(ph)FGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGSFGK 6 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 SGS(1)FGK;SGS(1)FGK;SGS(1)FGK;SGS(1)FGK;SGS(1)FGK;SGS(1)FGK 111.74 0.028942 7751940000 11605760 6603870 9886650 6271700 14102430 12635110 13481960 9894410 11458330 5848020 TRUE FALSE 12063964.37 7738033.302 10144304.22 7512223.541 11705303.99 9700797.189 12425208.75 9761791.618 11045946.94 6993827.552 1.7249445 1.106408936 1.450465306 1.074121929 1.673662083 1.387051242 1.776596385 1.395772422 1.579385088 1 22.73765079 SGS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.989)FS(0.011)K;SGS(0.868)FS(0.132)K;SGS(0.97)FS(0.03)K;S(0.009)GS(0.988)FS(0.004)K;SGS(0.998)FS(0.002)K;SGS(0.975)FS(0.025)K 123.16 0.019836 13423320000 16345830 9944670 14632660 9716990 19920190 18249410 19344100 14974970 16708250 9387970 TRUE FALSE 16991175.99 11652589.71 15013999.14 11638981.62 16534163.22 14011261.1 17827858.9 14774255.02 16106923.35 11227362.98 1.513371931 1.037874142 1.337268526 1.036662094 1.472666667 1.247956544 1.587893696 1.31591497 1.434613219 1 23.42051578 3.215237457 24.99285699 1.368032683 1.22504785 0.064045725 0.195588926 484.3652174 519039.506 0.051490751 0.061577428 1641.487035 -3.215237457 -0.142984833 SGS(ph)GGGSAKEPQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSGGGSAKEPQEER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 S(0.005)GS(0.995)GGGSAKEPQEER;S(0.037)GS(0.963)GGGSAKEPQEER 181.64 3.51E-07 1503160000 779230 500440 692670 400840 920380 910170 717640 696640 713210 467220 TRUE FALSE 809994.6021 586386.6771 710721.5492 480124.9556 763934.1364 698796.8113 661389.5016 687302.6803 687541.7114 558762.8135 1.449621525 1.049437548 1.271955706 0.859264332 1.367188578 1.250614383 1.183667713 1.230043703 1.230471489 1 19.09187648 -1.806314145 2.609390856 0.936452651 1.203496287 0.141782986 0.154381003 21721972.46 14181784.24 8694106.075 0.036514769 0.015620174 1.806314145 0.267043637 SGS(ph)GSIDDDRDSLPEWCLEDAEEEMGTFDSSGAFLSLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSGSIDDDRDSLPEWCLEDAEEEMGTFDSSGAFLSLKK 39 2 Q6Y7W6;I1E4Y6;Q6Y7W6-3;C9JZC0;B8ZZD2;C9J7G1;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 S(0.137)GS(0.836)GS(0.027)IDDDRDSLPEWCLEDAEEEMGTFDSSGAFLSLKK 228.01 3.07E-40 58111000 11797 13306 10195 13728 16256 19090 13054 13501 16576 13802 TRUE FALSE 12262.75467 15591.20199 10460.69008 16443.35743 13492.81093 14656.63681 12030.79337 13320.04118 15979.433 16506.23764 0.742916401 0.944564251 0.633741638 0.996190518 0.817437094 0.887945341 0.728863453 0.806970157 0.968084511 1 14.0107237 1.194058985 5.697006434 0.991387227 0.820522537 0.301020881 0.10030752 0.225891074 16.67254681 0.084829177 0.022277324 15.63359961 -1.194058985 -0.17086469 SGS(ph)IKGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGSIKGSR 8 1 Q16629;Q16629-4;C9JAB2;H7BZZ6;H7C1N1 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 S(0.016)GS(0.984)IKGSR;S(0.196)GS(0.804)IKGSR;S(0.017)GS(0.983)IKGSR 100.09 0.0038478 424200000 1380570 914930 1204500 564060 1936520 1525290 1093230 1099880 1363540 1028970 TRUE FALSE 1435075.97 1072062.11 1235890.26 675629.3844 1607351.022 1171064.513 1007539.776 1085137.908 1314466.462 1230576.971 1.166181396 0.871186554 1.004317722 0.54903464 1.306176745 0.951638574 0.818753967 0.881812299 1.068170861 1 20.23090347 1.232299182 24.97335837 1.034085446 0.933765916 0.0323513 0.191882433 588.3188869 2346361.297 0.15966241 0.043847492 17.07258099 -1.232299182 -0.100319531 SGS(ph)IVELIAGGGS(ph)SCSPVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.406)GS(0.594)IVELIAGGGS(0.463)S(0.316)CS(0.218)PVLS(0.003)R;S(0.42)GS(0.58)IVELIAGGGS(0.399)S(0.339)CS(0.246)PVLS(0.017)R 108.17 0.00047639 161112000 165743 147050 173959 177711 224740 244000 187628 166186 172578 162745 TRUE FALSE 172286.6616 172304.6936 178492.5144 212861.7054 186538.7751 187334.6979 172921.2271 163958.5485 166366.9515 194631.7668 0.885192918 0.885285565 0.917078015 1.093663737 0.958418958 0.962508335 0.888453257 0.842403844 0.854777995 1 17.57038767 2.187650064 5.845743011 0.878140144 0.952776367 0.10739873 0.06862931 0.328842836 24.65984229 0.026957272 0.020015628 154.0458717 -2.187650064 0.074636223 SGS(ph)IVELIAGGGSS(ph)CSPVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.427)GS(0.573)IVELIAGGGS(0.086)S(0.587)CS(0.326)PVLS(0.001)R 101.94 0.00090111 0 20934 21167 22937 20160 29299 33239 23192 24877 22235 17944 TRUE FALSE 21760.49048 24802.26759 23534.75706 24147.58783 24318.76645 25519.74599 21374.15044 24543.56451 21434.76669 21459.78324 1.014012595 1.155755737 1.096691276 1.12524845 1.133225167 1.189189364 0.996009615 1.143700485 0.998834259 1 14.38934788 1.227087618 24.91119525 0.999417006 1.108474162 0.360824068 0.057093044 234.5318044 509219.1607 0.049091608 0.012704399 16.8689332 -1.227087618 0.109057156 SGS(ph)IVELIAGGGSSCS(ph)PVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 2 S(0.412)GS(0.588)IVELIAGGGS(0.123)S(0.219)CS(0.647)PVLS(0.012)R 89.663 0.0033285 31310000 51659 50166 50102 51415 68832 78898 51065 56240 50745 45649 TRUE FALSE 53698.53721 58781.62026 51407.69928 61584.73354 57131.96123 60575.13521 47062.39187 55486.19479 48918.69736 54593.04755 0.98361494 1.076723556 0.941652859 1.128069165 1.046506172 1.109575998 0.862058339 1.016360091 0.896060937 1 15.73642961 2.24792509 24.99996685 0.949669099 1.047789984 0.369974035 0.066343791 213.0524074 568777.8078 0.021867106 0.018066601 176.9803665 -2.24792509 0.098120885 SGS(ph)LER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSLER 6 0 Q8IXT5;B9ZVT1;O94964-2;H0YDM2;O94964;O94964-3 Q8IXT5;O94964-2;REV__P0CF75 RBM12B;SOGA1 RNA-binding protein 12B;Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 S(0.007)GS(0.993)LER 82.279 0.062583 201320000 324720 277060 340260 284170 400480 461400 391860 362630 333580 262920 TRUE FALSE 337540.1963 324642.8998 349127.4551 340377.9778 332406.5526 354246.8426 361144.9893 357769.538 321574.521 314434.1401 1.073484566 1.032467084 1.110335713 1.082509608 1.057157955 1.126616984 1.148555272 1.137820269 1.022708669 1 18.26239834 2.747272244 24.54476047 1.104138176 1.071843177 0 0.049449427 1255.462261 3537237.109 0.015009743 0.015690388 558.8203893 -2.747272244 -0.032294999 SGS(ph)MDPSGAHPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 S(0.081)GS(0.899)MDPS(0.019)GAHPSVR;S(0.044)GS(0.849)MDPS(0.107)GAHPSVR;S(0.002)GS(0.901)MDPS(0.097)GAHPSVR;S(0.01)GS(0.472)MDPS(0.472)GAHPS(0.047)VR;S(0.027)GS(0.957)MDPS(0.015)GAHPS(0.001)VR 188.81 8.30E-07 798683000 330973 921018 978972 980619 1215208 1425223 1022842 1160631 1035891 1017921 TRUE FALSE 344040.0696 1079195.677 1004484.815 1174582.511 1008647.378 1094236.558 942668.9713 1145074.64 998609.4853 1217363.131 0.282610883 0.886502679 0.825131622 0.964857964 0.82855095 0.898857974 0.774353147 0.940618794 0.820305347 1 20.21532815 4.739065027 24.93661913 0.877882676 0.282610697 0.875026649 0.067953836 11.48131284 567446.7055 0.014446289 0.085691676 54835.90641 -4.739065027 -0.595271979 SGS(ph)PAPETTNESVPFAQHSSLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSPAPETTNESVPFAQHSSLDSR 24 0 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 1 S(0.114)GS(0.473)PAPET(0.409)T(0.004)NESVPFAQHSSLDSR;S(0.031)GS(0.969)PAPETTNESVPFAQHSSLDSR 210.39 2.72E-25 420730000 17042.2 123851 111967 122381 130856 197485 104963 175955 119258 133132 TRUE FALSE 17715.03922 145121.4458 114884.952 146587.5965 108613.1439 151622.1017 96735.72579 173596.611 114965.9279 159216.6664 0.111263724 0.91147145 0.721563606 0.920679975 0.68217195 0.952300441 0.607572863 1.09031683 0.722072195 1 17.28063184 4.741715098 24.91277506 0.845244575 0.11126344 0.688823873 0.148018943 147.5029628 1164858.606 0.032059412 0.228550848 55171.53889 -4.741715098 -0.733981135 SGS(ph)PKLDPSEVYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.202)GS(0.798)PKLDPSEVYLK 139.9 6.11E-06 265910000 1294900 396520 651760 345790 1046200 1003100 791940 685740 713510 300900 TRUE FALSE 1346023.652 464619.2255 668745.401 414186.2299 868367.2977 770145.2271 729865.6734 676548.7769 687830.9145 359855.5939 3.74045499 1.291126867 1.858371559 1.150978995 2.413099344 2.140150772 2.028218224 1.880056301 1.911408148 1 18.45705856 -1.961614271 0.280620368 1.12E-24 2.104881032 0.195026516 0.662446414 55.54433537 2.396604453 38.28280036 0.765787363 0.010924102 1.961614271 2.104881032 SGS(ph)PLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGSPLEK 7 0 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SGS(1)PLEK;SGS(1)PLEK;S(0.014)GS(0.986)PLEK 145.46 0.0023969 853900000 3784800 1913070 2544230 1889650 3552350 3876200 3732040 2670540 2858810 1319320 TRUE FALSE 3934226.827 2241624.891 2610534.724 2263417.13 2948522.816 2976011.294 3439512.953 2634745.779 2755921.987 1577815.494 2.493464439 1.420714209 1.654524711 1.434525861 1.868737395 1.886159253 2.179920888 1.669869379 1.746669365 1 20.58949708 0.49147176 1.743856554 1.000198517 1.808333816 0.389707869 0.307969503 3.617767854 11.23490419 0.284340934 0.079986707 3.100785752 -0.49147176 0.808135299 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGSPRPTEPTDFLMLFEGSPSGK 23 1 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 S(0.158)GS(0.839)PRPT(0.002)EPT(0.002)DFLMLFEGSPSGK;S(0.157)GS(0.823)PRPT(0.01)EPT(0.011)DFLMLFEGSPSGK;S(0.143)GS(0.857)PRPT(0.001)EPTDFLMLFEGSPSGK;S(0.148)GS(0.852)PRPTEPTDFLMLFEGSPSGK;S(0.103)GS(0.897)PRPTEPTDFLMLFEGSPSGK 188.44 1.29E-17 887408000 867585 571007 813155 602263 1012210 976690 935794 768566 832819 546750 TRUE FALSE 901837.9257 669073.0104 834346.4873 721388.8238 840154.9058 749868.5494 862444.021 758264.6299 802846.0069 653875.1943 1.379220276 1.023242686 1.27600266 1.103251553 1.284885729 1.146806846 1.31897345 1.15964734 1.227827594 1 19.31865577 -1.443827614 4.368201674 0.99922799 1.207537289 0.281434813 0.101880665 7685479.963 2540495.337 57166.08881 0.020738281 0.035989216 1.443827614 0.208309299 SGS(ph)PSDNS(ph)GAEEMEVSLAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.085)GS(0.774)PS(0.141)DNS(1)GAEEMEVSLAKPK;S(0.021)GS(0.49)PS(0.49)DNS(1)GAEEMEVSLAKPK 105.55 0.00022072 297760000 728600 353100 548300 367060 782030 745890 695640 530650 621050 273650 TRUE FALSE 757365.6906 413742.1783 562589.1484 439663.3724 649100.8199 572668.3516 641113.9191 523537.5047 598698.5318 327266.4782 2.314217132 1.264236351 1.719055223 1.343441513 1.983401489 1.749853376 1.958996603 1.599728477 1.829391556 1 18.32010631 -1.185029239 5.239296925 0.999960785 1.730132478 0.371799901 0.291828229 0.000121835 1.90E-05 0.257489123 0.060687522 0.065308658 1.185029239 0.730171693 SGS(ph)PSDNSGAEEMEVSLAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.052)GS(0.479)PS(0.177)DNS(0.292)GAEEMEVSLAKPK;S(0.01)GS(0.945)PS(0.045)DNSGAEEMEVSLAKPK;S(0.032)GS(0.912)PS(0.056)DNSGAEEMEVSLAKPK;S(0.024)GS(0.465)PS(0.443)DNS(0.068)GAEEMEVSLAKPK;S(0.003)GS(0.992)PS(0.005)DNSGAEEMEVSLAKPK;S(0.004)GS(0.995)PS(0.001)DNSGAEEMEVSLAKPK;S(0.014)GS(0.985)PS(0.001)DNSGAEEMEVSLAKPK 213.54 2.13E-23 6246360000 5332840 2573188 4117720 2649251 5711930 5018530 5141550 3646460 4384240 1991158 TRUE FALSE 5543384.641 3015113.022 4225031.166 3173264.941 4741018.179 3853052.464 4738541.876 3597585.168 4226452.059 2381287.287 2.327894106 1.266169369 1.774263521 1.332583833 1.990947587 1.618054438 1.989907686 1.510773264 1.774860212 1 21.18331025 -1.215612997 0.787900129 0.828672235 1.711052573 0.337718266 0.305866688 97.08880454 24.78193434 37.82967902 0.092024152 0.060867716 1.215612997 0.882380337 SGS(ph)SPEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)GS(0.756)S(0.243)PEVK 85.676 0.018523 0 522940 295570 376820 334180 545400 559100 512580 423070 448080 272890 TRUE FALSE 543586.075 346331.8483 386640.2388 400279.8066 452693.1028 429257.4982 472402.6402 417399.4387 431953.6883 326357.5707 1.66561503 1.061203659 1.184713558 1.226506882 1.387107711 1.315298117 1.447500174 1.278963554 1.323559577 1 18.31609398 -0.924284735 4.604257359 0.999996747 1.31152483 0.279819257 0.153873677 5.17E-06 1.21E-06 0.14037911 0.033087305 0.119046125 0.924284735 0.311528082 SGS(ph)SPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.211)GS(0.395)S(0.395)PGLR 83.168 0.019284 165820000 133220 151800 156630 146040 159990 174950 155350 138190 131880 130420 TRUE FALSE 138479.6285 177870.4692 160711.9065 174926.2761 132794.9569 134320.5139 143173.2611 136337.7891 127133.6646 155973.302 0.887841872 1.140390483 1.030380869 1.12151422 0.851395433 0.861176318 0.917934411 0.874109783 0.815098885 1 17.25093958 3.22998144 24.9999843 0.881022568 1.050796696 0.49472915 0.078219308 135.9337489 396114.6288 0.020962589 0.025426514 1698.171076 -3.22998144 0.169774128 SGS(ph)TESLNPRPQTTISPADLHGMWYPTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSTESLNPRPQTTISPADLHGMWYPTVR 29 1 Q96JB2 Q96JB2 COG3 Conserved oligomeric Golgi complex subunit 3 1 S(0.143)GS(0.844)T(0.013)ESLNPRPQTTISPADLHGMWYPTVR 243.28 9.45E-46 193030000 79031 81433 89458 74487 110350 142080 107420 101030 111750 79384 TRUE FALSE 82151.20491 95418.48429 91789.34897 89220.30628 91592.74642 109084.0732 99000.13971 99675.8581 107728.1393 94937.7749 0.865316308 1.005063415 0.966836953 0.939776673 0.964766096 1.149006003 1.042789762 1.049907249 1.134723659 1 16.53469462 2.867860426 7.051571058 1.072989755 0.950559736 0.599253736 0.051975887 0.178776355 9.467993678 0.015147279 0.016099616 737.6671203 -2.867860426 -0.122430019 SGS(ph)TGSSLSVSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 S(0.099)GS(0.875)T(0.025)GS(0.001)S(0.001)LSVSVR;S(0.002)GS(0.972)T(0.023)GS(0.001)S(0.002)LSVSVR 135.04 9.29E-05 204348000 333277 296917 338290 317987 493750 546920 371510 381920 418840 336620 TRUE FALSE 346435.0333 347910.1851 347106.1153 380883.8795 409822.5514 419906.1187 342390.0754 376800.9871 403766.0302 402574.244 0.860549423 0.86421372 0.8622164 0.946120834 1.018004896 1.043052617 0.850501691 0.935978873 1.002960413 1 18.61889535 3.690211679 4.27683932 0.965183705 0.861744056 0.492272726 0.050591813 0.208895756 8.310409384 0.014803761 0.02434976 4900.176007 -3.690211679 -0.103439648 SGS(ph)VSNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGSVSNYR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 S(0.004)GS(0.977)VS(0.02)NYR;SGS(1)VSNYR;S(0.001)GS(0.995)VS(0.004)NYR 176.41 0.00027325 3328280000 1262240 1323350 1560380 1541420 1931500 2010000 1556000 1661370 1598560 1461060 TRUE FALSE 1312074.21 1550625.068 1601044.785 1846308.275 1603184.32 1543207.962 1434036.654 1639102.053 1541028.138 1747326.733 0.750903758 0.887427084 0.91628243 1.056647415 0.917506892 0.883182253 0.820703207 0.938062711 0.881934734 1 20.73671797 4.731527075 2.66743546 0.922102564 0.718461349 0.422050498 0.061558216 0.469401773 4.471531151 0.015727382 0.210881472 53892.34422 -4.731527075 -0.203641215 SGS(ph)YSGRSPS(ph)PYGR ddPTM_MDA-MB-175_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(0.065)GS(0.511)Y(0.007)S(0.356)GRS(0.063)PS(0.995)PY(0.002)GR 128.01 0.0041762 0 314700 352110 365690 308070 415010 554310 356790 404670 357490 318880 TRUE FALSE 327124.599 412582.1535 375220.1818 369005.3265 344466.7484 425579.9031 328823.8675 399246.0606 344624.0047 381358.4307 0.857787773 1.081875003 0.983904253 0.967607628 0.903262445 1.115957768 0.862243604 1.046905033 0.903674803 1 18.54078807 3.840020029 8.643808212 0.974199611 0.985356513 0 0.086151773 4.295599134 334.1573667 0.020374831 0.036855092 6918.628784 -3.840020029 0.011156902 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK 39 0 P28072;A0A087X2I4 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 170.19 1.36E-18 318450000 89193 85725 105720 89754 127690 140630 122370 100480 109880 83853 FALSE TRUE 92714.40851 100447.6019 108475.15 107507.0733 105985.2994 107970.8138 112778.3196 99133.22995 105925.4403 100282.3899 0.924533297 1.001647468 1.081696898 1.072043391 1.056868504 1.076667737 1.124607419 0.98854076 1.056271598 1 16.61370876 4.567057518 2.904105334 1.057634915 0.921788737 0.547025344 0.037376034 0.227585058 3.213672564 0.00935091 0.058543763 36902.64694 -4.567057518 -0.135846178 SGSAS(ph)PAPGDTLPWNLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGSASPAPGDTLPWNLPK 18 0 F6QMI7;E7ETB9;Q5T0V7;Q03001-11 F6QMI7 DST Dystonin 1 S(0.003)GS(0.003)AS(0.994)PAPGDTLPWNLPK;SGSAS(1)PAPGDTLPWNLPK;S(0.001)GS(0.011)AS(0.988)PAPGDTLPWNLPK;S(0.019)GS(0.019)AS(0.962)PAPGDTLPWNLPK 280.87 2.86E-39 276785000 406410 314196 370389 284419 460020 470822 388339 382121 364215 261797 TRUE FALSE 422455.3806 368156.7189 380041.6416 340676.2293 381825.9647 361480.7259 357899.9744 376999.293 351106.9733 313091.1097 1.349304939 1.175877268 1.213837218 1.088105726 1.219536272 1.154554424 1.143117653 1.204120083 1.121421089 1 18.25622302 -5 0.048376649 0.305720394 1.545514333 0.56547613 0.057678276 480.6330532 1.722988027 44.70239574 10.5009717 1.00E-05 5 1.239793939 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 SGSGSVGNGSSRY(0.001)S(0.997)PS(0.003)QNS(1)PIHHIPSR;S(0.001)GS(0.001)GS(0.001)VGNGS(0.031)S(0.034)RY(0.085)S(0.837)PS(0.041)QNS(0.968)PIHHIPSR;SGSGSVGNGS(0.006)S(0.01)RY(0.001)S(0.982)PS(0.001)QNS(0.999)PIHHIPSR;S(0.001)GS(0.002)GS(0.002)VGNGS(0.022)S(0.026)RY(0.007)S(0.934)PS(0.007)QNS(0.998)PIHHIPSR;S(0.001)GS(0.001)GS(0.002)VGNGS(0.092)S(0.099)RY(0.23)S(0.546)PS(0.134)QNS(0.894)PIHHIPS(0.001)R 226.28 1.96E-34 4520254000 243355 396056 438697 357119.8 443715 537942 361749 405702 397936.4 423889 TRUE FALSE 252962.8433 464075.5371 450129.8042 427757.0305 368292.4828 413013.1231 333394.1681 400264.2283 383614.7467 506941.9337 0.498997669 0.91544121 0.887931683 0.843798869 0.726498359 0.814714853 0.657657507 0.789566224 0.756723248 1 18.95146098 -0.963964882 4.131463919 1.000010346 0.772854882 0.271524342 0.114592963 36582603.49 59959311.29 5824.873893 0.02622517 0.108651348 0.963964882 -0.227155464 SGSGSVGNGSSRYS(ph)PSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_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(0.002)GS(0.013)GS(0.003)VGNGS(0.115)S(0.134)RY(0.075)S(0.616)PS(0.042)QNS(0.998)PIHHIPS(0.001)RR;SGSGSVGNGS(0.051)S(0.3)RY(0.242)S(0.388)PS(0.229)QNS(0.655)PIHHIPS(0.134)RR 120.69 2.73E-05 323110000 46025 75381 72186 49187 93071 98634 49055 76360 66987 94690 TRUE FALSE 47842.10254 88327.10037 74067.22646 58916.04179 77250.82466 75727.74831 45209.94092 75336.5191 64576.15096 113242.6926 0.422474082 0.779980574 0.654057448 0.52026352 0.682170504 0.668720838 0.399230537 0.665266053 0.570245634 1 16.78905843 -1.095401741 4.58338426 1.00001949 0.601511983 0.529750959 0.114127439 3.09E-05 6.10E-06 0.102929638 0.024259018 0.080278317 1.095401741 -0.398507507 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPS(ph)RR ddPTM_MDA-MB-175_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 2 S(0.004)GS(0.005)GS(0.005)VGNGS(0.031)S(0.035)RY(0.004)S(0.908)PS(0.012)QNS(0.487)PIHHIPS(0.509)RR 105.36 0.00050914 537370000 27702 47246 47307 33984 54841 66357 35112 49643 47457 65127 TRUE FALSE 28795.69635 55360.13298 48539.85928 40705.93377 45519.14641 50946.5924 32359.82969 48977.61678 45749.03184 77887.38872 0.369709356 0.71077146 0.623205632 0.522625478 0.584422551 0.654105796 0.415469439 0.628826022 0.587374061 1 16.24910213 0.269641837 1.474272323 1.000153438 0.568020024 0.631456092 0.099588575 4.183682195 7.769992315 0.088954233 0.02554534 1.860552104 -0.269641837 -0.432133414 SGSGSVGNGSSRYS(ph)PSQNSPIHHIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.018)S(0.012)RYS(0.918)PS(0.052)QNSPIHHIPSR;SGSGSVGNGS(0.005)S(0.005)RYS(0.979)PS(0.012)QNSPIHHIPSR 173.04 1.92E-12 627650000 27029 78874 66151 72827 74314 98545 62985 86074 64061 67001 TRUE FALSE 28096.12579 92419.99595 67874.9494 87231.96323 61682.13282 75659.41721 58048.07112 84920.31882 61755.45712 80128.56314 0.350638083 1.153396396 0.847075584 1.088650037 0.769789578 0.944225308 0.724436691 1.059800844 0.770704661 1 16.29002899 4.753199316 24.92062261 0.925298084 0.350637664 0.603759109 0.140459398 1614.023524 2747632.274 0.030375309 0.683520462 56649.92194 -4.753199316 -0.574660419 SGSIVELIAGGGSSCS(ph)PVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSIVELIAGGGSSCSPVLSR 21 0 P42858 P42858 HTT Huntingtin 1 SGSIVELIAGGGSSCS(1)PVLSR 289.97 1.41E-48 0 127120 143710 137400 144100 126410 194060 138710 136920 132400 116860 TRUE FALSE 132138.7958 168391.0746 140980.7569 172602.5499 104922.8734 148992.506 127837.5477 135084.8114 127634.9499 139756.4796 0.945493162 1.204889212 1.008760075 1.235023595 0.750754982 1.06608657 0.914716428 0.966572797 0.913266778 1 17.09255565 3.250905757 24.99999892 0.940399332 1.099724767 0.349501461 0.109005854 243.5539149 493215.2098 0.027455762 0.036914504 1781.992027 -3.250905757 0.159325435 SGSLDSELSVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;SGSLDSELSVS(1)PK 180.11 1.38E-05 351890000 1072420 474930 620210 473610 942840 1026240 791440 655110 705200 414280 TRUE FALSE 1114759.97 556495.5331 636373.1821 567288.6444 782576.3936 787911.3128 729404.8648 646329.322 679819.9898 495450.2341 2.24999383 1.123211767 1.284434113 1.144996218 1.579525732 1.590293552 1.472206116 1.304529249 1.372125681 1 18.91838063 -3.982636139 0.117550787 8.31E-33 1.659670658 0.212857712 0.296858844 218.040766 2.128244447 57.11424574 3.176511959 0.000104079 3.982636139 1.659670658 SGSMDPS(ph)GAHPSVR ddPTM_MDA-MB-175_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(0.136)GS(0.316)MDPS(0.546)GAHPS(0.002)VR;SGS(0.02)MDPS(0.98)GAHPSVR 205.8 1.23E-08 716110000 232387 756680 758030 711970 907330 1091860 792990 917120 782510 785400 TRUE FALSE 241561.8182 886633.9038 777784.8845 852795.541 753102.3707 838292.0623 730833.3717 904827.5065 754347.618 939284.0926 0.257176524 0.94394647 0.828061383 0.907920775 0.801783376 0.892479782 0.778074895 0.963316119 0.803109117 1 19.84120205 4.742432326 24.99972689 0.87534482 0.257176286 0.870977833 0.071878588 112.6796639 727546.7736 0.015339696 0.116131083 55262.72874 -4.742432326 -0.618168534 SGSMDPSGAHPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 ;;;;; 132.09 5.24E-05 962854000 411436 1643963 1458541 1609689 1515368 2195390 1295792 1861014 1441080 1795722 FALSE TRUE 427679.811 1926300.857 1496551.777 1928080.68 1257786.289 1685543.944 1194224.437 1836070.151 1389215.812 2147559.345 0.199146912 0.896972119 0.696861663 0.897800885 0.585681738 0.784864897 0.556084487 0.854956654 0.646881222 1 21.03426657 -4.999999917 0.040508839 2.171371524 9.16E-10 0.228251355 0.193503821 1382.944064 4.183619274 203.226475 60.25250008 1.00E-05 4.999999917 -2.171371523 SGSPS(ph)DNS(ph)GAEEMEVSLAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 2 S(0.047)GS(0.432)PS(0.521)DNS(1)GAEEMEVSLAKPK 139.73 9.78E-08 159540000 349450 153800 246460 168480 387740 333410 314630 229930 298450 141030 TRUE FALSE 363246.5558 180213.9536 252882.9501 201804.8411 321832.0933 255980.5804 289968.4785 226848.1644 287708.8428 168662.1283 2.153693656 1.068490926 1.499346371 1.196503585 1.908146758 1.517712263 1.719226962 1.344985781 1.705829552 1 17.36377654 -1.160455082 13.59656031 1.000003373 1.540925343 0.22973484 0.30851289 0 0 0.271607021 0.064018389 0.06911064 1.160455082 0.54092197 SGSPS(ph)DNSGAEEMEVSLAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 S(0.025)GS(0.143)PS(0.806)DNS(0.026)GAEEMEVSLAKPK 107.47 0.00051949 304760000 460060 212030 391750 242740 504780 438290 435630 326780 422020 189410 TRUE FALSE 478223.524 248444.5031 401959.3268 290753.2475 418977.6759 336503.7898 401484.1823 322400.0486 406831.5826 226521.263 2.111163948 1.096782261 1.774488282 1.283558301 1.849617428 1.48552849 1.77239071 1.423266162 1.795997326 1 17.78928695 -1.274935513 4.322909997 0.999562028 1.596808471 0.294074385 0.28656612 0.001048477 0.000175857 0.240502754 0.056646579 0.053096328 1.274935513 0.597246443 SGSPSDNS(ph)GAEEMEVSLAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749;P31749-2 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 SGS(0.001)PS(0.007)DNS(0.992)GAEEMEVSLAKPK 136.67 2.76E-06 2283400000 201860 134560 184880 137020 251330 233030 211490 179650 214590 128800 TRUE FALSE 209829.5887 157669.6333 189698.1247 164122.147 208609.0164 178912.3141 194912.8612 177242.0856 206866.9478 154035.894 1.362212295 1.023590211 1.231518965 1.065479888 1.354288348 1.161497554 1.265372999 1.150654442 1.34297885 1 17.23290705 4.807368645 21.68861553 1.187459562 1.362223394 0.17685388 0.11786932 47149.53963 14857872.99 0.025346637 103.781229 64175.40896 -4.807368645 0.174763833 SGSS(ph)PEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGSSPEVK 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SGS(0.002)S(0.998)PEVK;SGS(0.001)S(0.999)PEVK;S(0.003)GS(0.02)S(0.976)PEVK;S(0.045)GS(0.102)S(0.853)PEVK 177.58 0.00026659 2596950000 7556500 3956610 5614010 3711740 7468500 7671000 7497600 5951300 6212000 3307830 TRUE FALSE 7854836.455 4636126.989 5760315.713 4445911.094 6199007.038 5889526.505 6909918.521 5871532.558 5988431.333 3955935.956 1.98558231 1.171941872 1.456119557 1.123858208 1.567014003 1.488782066 1.746721534 1.484233472 1.513783691 1 21.91558764 SGSS(ph)PGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.004)GS(0.068)S(0.928)PGLR;S(0.014)GS(0.109)S(0.877)PGLR;S(0.004)GS(0.076)S(0.92)PGLR;S(0.003)GS(0.068)S(0.928)PGLR;S(0.056)GS(0.089)S(0.855)PGLR 125.98 0.0012994 4133260000 3146080 3404130 3392980 3146210 3850890 4529850 3724720 3586840 3470310 3064570 TRUE FALSE 3270289.668 3988762.847 3481403.846 3768520.947 3196317.093 3477860.988 3432766.714 3538764.277 3345414.221 3665013.817 0.89229941 1.088335009 0.94990197 1.028241948 0.872115974 0.948935301 0.936631316 0.965552779 0.912797165 1 21.80538721 3.263559495 24.99975025 0.939811849 0.993897985 0.158002616 0.056609968 377.37051 377381.0464 0.014368935 0.019447961 1834.676486 -3.263559495 0.054086136 SGSS(ph)QELDVKPSASPQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.007)GS(0.177)S(0.816)QELDVKPSASPQER;SGS(0.016)S(0.984)QELDVKPSASPQER 173.65 4.71E-12 666860000 553870 376350 485650 403930 630020 642860 622360 557550 546710 340410 TRUE FALSE 575737.2153 440985.1849 498306.438 483826.1484 522929.4254 493565.5076 573577.797 550076.9542 527034.0139 407106.822 1.414216575 1.08321738 1.224018884 1.188450113 1.28450175 1.212373463 1.408912271 1.351185793 1.294584088 1 18.63504787 3.188939736 9.124513297 1.289155355 1.216973414 0 0.128609745 0.937157975 161.8551395 0.035402128 0.042466415 1545.04003 -3.188939736 -0.072181941 SGSS(ph)S(ph)PDSEITELKFPSINHD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 2 S(0.164)GS(0.51)S(0.541)S(0.785)PDS(0.001)EITELKFPSINHD 113.6 0.00011214 67219000 57189 44355 55423 57044 77673 78614 67576 59465 64027 43125 TRUE FALSE 59446.86588 51972.62622 56867.36891 68327.13294 64470.1712 60357.08991 62279.21654 58667.96894 61722.68078 51574.51807 1.152640259 1.007719086 1.102625309 1.324823488 1.250039237 1.170288975 1.207557896 1.137537899 1.19676699 1 15.65437081 3.980162244 24.76494372 1.191571507 1.073927784 0.210921681 0.084916776 811.0781282 1012533.84 0.020790457 0.0381513 9553.494197 -3.980162244 -0.117643724 SGSS(ph)SPDSEITELKFPSINHD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.021)GS(0.093)S(0.428)S(0.428)PDS(0.029)EITELKFPSINHD 116.7 7.50E-05 710490000 127990 142720 166290 139020 227660 204930 186740 186160 188420 117200 TRUE FALSE 133043.144 167231.0498 170623.654 166517.7411 188962.4345 157338.1132 172102.8308 183664.8297 181638.801 140163.0961 0.949202378 1.19311755 1.21732224 1.188028416 1.348161105 1.122535943 1.227875494 1.310365102 1.295910308 1 17.09674702 4.788043654 2.57209146 1.230346154 0.867865052 0.396672071 0.09554992 0.549029846 4.157129974 0.022174747 0.454029271 61382.37021 -4.788043654 -0.362481102 SGSSHAPQDVSLSYPQHHVGNSS(ph)PTSTSPSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSHAPQDVSLSYPQHHVGNSSPTSTSPSSR 32 0 J3KPD3;I3L521;F5GXV8 J3KPD3 RBM7 1 SGSSHAPQDVSLSYPQHHVGNS(0.018)S(0.72)PT(0.095)S(0.135)T(0.026)S(0.005)PS(0.001)S(0.001)R 160.53 1.26E-13 144680000 18185 42942 38167 38154 39656 57866 35431 44199 38791 40462 TRUE FALSE 18902.95784 50316.95446 39161.66337 45700.74732 32915.28728 44427.49847 32653.82564 43606.5847 37394.91949 48389.75421 0.390639675 1.039826618 0.809296596 0.944430243 0.680211913 0.918117878 0.674808669 0.901153259 0.772785894 1 15.56241399 -4.615274598 0.023793433 2.033121206 1.90E-06 0.132765952 0.171528416 5378.467168 10.28301691 612.8530384 312.1056474 2.43E-05 4.615274598 -2.033119305 SGSSS(ph)PDSEITELKFPSINHD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SGSSSPDSEITELKFPSINHD 21 1 P17812;B4E1E0;P17812-2 P17812 CTPS1 CTP synthase 1;CTP synthase 1 S(0.017)GS(0.013)S(0.106)S(0.855)PDS(0.009)EITELKFPSINHD;S(0.024)GS(0.018)S(0.138)S(0.82)PDSEITELKFPSINHD;SGS(0.004)S(0.089)S(0.619)PDS(0.284)EIT(0.003)ELKFPSINHD;S(0.002)GS(0.014)S(0.162)S(0.742)PDS(0.079)EITELKFPSINHD;S(0.003)GS(0.015)S(0.109)S(0.82)PDS(0.053)EITELKFPSINHD;S(0.003)GS(0.017)S(0.118)S(0.861)PDS(0.001)EITELKFPSINHD;S(0.015)GS(0.012)S(0.095)S(0.604)PDS(0.274)EITELKFPSINHD 223.86 2.06E-25 3633920000 1203246 1358047 1809740 1359306 2250100 2289960 2005500 1902900 1913840 1336999 TRUE FALSE 1250751.081 1591281.008 1856903.311 1628172.67 1867628.806 1758151.495 1848303.67 1877394.738 1844961.272 1598958.356 0.782228678 0.995198532 1.161320621 1.018270841 1.168028422 1.099560529 1.155942344 1.174136106 1.153851985 1 20.60870093 4.65244873 2.145497245 1.125836091 0.72290442 0.740284106 0.060312496 0.241945585 1.449667905 0.014580294 0.174442419 44920.92907 -4.65244873 -0.402931671 SGSSSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGSSSER 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 76.592 0.093852 180810000 225180 248600 213170 237950 283540 283560 274350 240300 226770 234480 FALSE TRUE 234070.2803 291295.1162 218725.3853 285015.7998 235343.9721 217707.4874 252845.7301 237079.1716 218608.592 280421.8666 0.834707661 1.038774614 0.77998691 1.016382222 0.839249717 0.77635703 0.901661961 0.845437535 0.779570419 1 18.09723933 SGST(ph)GSSLSVSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGSTGSSLSVSVR 13 0 Q5TH69 Q5TH69 ARFGEF3 Brefeldin A-inhibited guanine nucleotide-exchange protein 3 1 SGS(0.463)T(0.517)GS(0.018)S(0.002)LSVSVR;SGS(0.058)T(0.826)GS(0.044)S(0.071)LSVSVR 234.52 1.29E-15 432190000 394550 423520 484360 442840 574670 687180 533360 478180 468690 441840 TRUE FALSE 410127.1387 496256.2655 496982.8195 530432.4303 476987.7987 527592.8593 491553.8495 471770.7792 451821.9385 528410.0885 0.77615312 0.939149869 0.940524851 1.00382722 0.902684883 0.998453419 0.93025069 0.892811832 0.855059259 1 19.01129849 4.739015043 24.40006477 0.937093593 0.776153059 0.522108199 0.047024371 21.98775529 1180093.341 0.01125444 0.066607896 54829.59569 -4.739015043 -0.160940534 SGT(ph)FDLLEMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGTFDLLEMDR 11 0 H0YA26;E9PHT6;Q9NVE7;H0YA31 H0YA26 PANK4 Pantothenate kinase 4 1 S(0.006)GT(0.994)FDLLEMDR;S(0.006)GT(0.994)FDLLEMDR;S(0.016)GT(0.984)FDLLEMDR;S(0.147)GT(0.853)FDLLEMDR 238.13 1.49E-14 235699000 264498 208322 266116 297460 404986 541836 429261 330725 312747 198706 TRUE FALSE 274940.5853 244099.683 273051.2016 356296.7002 336146.6244 416002.8006 395614.4012 326292.1723 301491.2966 237638.6362 1.15696921 1.027188537 1.149018551 1.499321431 1.414528503 1.750568877 1.664773066 1.37306028 1.26869646 1 17.85840989 3.800216522 4.686616211 1.462122828 1.093400873 0.332102061 0.199125049 0.214910456 9.664341745 0.051365701 0.094326098 6312.719933 -3.800216522 -0.368721955 SGT(ph)PPRQGSITSPQANEQSVTPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.312)GT(0.683)PPRQGS(0.004)IT(0.001)SPQANEQSVTPQR 78.583 0.032249 110510000 4937.3 10091 11194 12063 12639 14375 11977 11138 15341 9361.7 TRUE FALSE 5132.228416 11824.05075 11485.72484 14449.0254 10490.62729 11036.62411 11038.21144 10988.71333 14788.88041 11195.94587 0.45840061 1.0561011 1.02588249 1.290558704 0.937002323 0.985769691 0.985911469 0.981490394 1.320913889 1 13.4506888 4.738566855 11.67627711 1.056581109 0.45787064 0.675506778 0.125979093 0.035906211 379.7605336 0.029328504 0.169074264 54773.04119 -4.738566855 -0.59871047 SGT(ph)PTQDEMMDKPTSSSVDTMSLLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.201)GT(0.798)PT(0.001)QDEMMDKPTSSSVDTMSLLSK;S(0.072)GT(0.928)PTQDEMMDKPTSSSVDTMSLLSK;S(0.061)GT(0.919)PT(0.02)QDEMMDKPTSSSVDTMSLLSK;S(0.257)GT(0.626)PT(0.118)QDEMMDKPTSSSVDTMSLLSK;S(0.152)GT(0.824)PT(0.024)QDEMMDKPTSSSVDTMSLLSK 205.03 9.82E-25 1320930000 1676800 545923 924100 553931 1417810 1277240 1265590 961270 1123610 411895 TRUE FALSE 1743001.359 639681.0286 948182.8052 663496.8985 1176811.163 980620.3668 1166389.749 948385.748 1083171.496 492597.939 3.538385406 1.29858649 1.924861495 1.346933972 2.388989213 1.990711469 2.367833189 1.925273479 2.198895711 1 18.91005107 -1.62469879 6.006541063 0.994082489 2.062678539 0.235262288 0.594562342 0.042856845 0.002677784 0.523648954 0.123567012 0.02373019 1.62469879 1.06859605 SGTAT(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGTATPQR 8 0 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 1 SGT(0.005)AT(0.995)PQR;SGT(0.01)AT(0.989)PQR 127.94 0.012907 656570000 640950 743330 815990 715240 905420 1049720 850980 876900 790840 810520 TRUE FALSE 666255.2009 870991.1452 837255.3697 856712.3372 751517.0318 805938.4387 784277.964 865146.5898 762377.8229 969325.8757 0.687338714 0.898553487 0.863750149 0.883822829 0.775298639 0.8314422 0.809096284 0.892523981 0.786503117 1 19.88662224 -4.999999993 0.401185878 3.716699288 0.829515841 0.408924887 0.062256598 741.8310464 5.160768631 1766.183769 0.036345118 1.00E-05 4.999999993 -2.887183447 SGTHNMYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SGTHNMYR 8 0 Q02543;M0R3D6;M0R1A7;M0R117;M0R0P7 Q02543 RPL18A 60S ribosomal protein L18a 0 ;;;; 143.12 0.00060653 826286000 170757 920689 835118 832895 1259488 1277010 842548 931141 769533 1413820 FALSE TRUE 177498.6182 1078810.174 856881.8611 997639.1451 1045400.68 980443.7808 776506.8862 918660.5779 741837.6577 1690830.96 0.104977152 0.638035498 0.506781507 0.590028908 0.618276282 0.579859137 0.459245723 0.543318995 0.438741468 1 20.689301 -2.109795153 2.442084984 1.905691671 0.511609483 0.514541774 0.145807867 4703427.944 1315966.67 23676736.11 0.032638257 0.007766133 2.109795153 -1.394082187 SGTICSSELPGAFEAAGFHLNEHLYNMIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGTICSSELPGAFEAAGFHLNEHLYNMIIR 30 0 A0A0C4DGQ5;K7ELJ7;P04632;K7EKD8;U3KQE2;A0A075B7C0 A0A0C4DGQ5 CAPNS1 Calpain small subunit 1 0 ; 120.6 1.12E-05 534130000 395380 521100 444880 592660 742530 754730 634950 528330 455110 559460 FALSE TRUE 410989.9077 610594.8714 456473.9383 709886.3791 616315.0158 579455.3955 585180.9599 521248.6005 438730.68 669075.4755 0.61426539 0.912594907 0.682245808 1.060995964 0.921144233 0.866053856 0.874611283 0.779057998 0.655726739 1 19.35180944 4.747481834 24.10718515 0.85433218 0.614265184 0.270435651 0.121268347 985.5117689 2662982.781 0.028375625 0.334291321 55909.0141 -4.747481834 -0.240066997 SGTNS(ph)PPPPFSDWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SGTNSPPPPFSDWGR 15 0 D6RAU6;D6REP2;D6RAJ6;Q9UKT5-2;Q9UKT5 D6RAU6 FBXO4 F-box only protein 4 1 SGT(0.003)NS(0.997)PPPPFSDWGR;S(0.007)GT(0.007)NS(0.986)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;S(0.003)GT(0.005)NS(0.992)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;SGTNS(1)PPPPFSDWGR;S(0.015)GT(0.063)NS(0.922)PPPPFSDWGR;S(0.031)GT(0.031)NS(0.938)PPPPFSDWGR 258.13 8.63E-25 2048837000 1225791 1318278 1348306 1274403 1579438 1814881 1426783 1397835 1356633 1174058 TRUE FALSE 1274186.175 1544681.992 1383443.962 1526476.11 1310965.693 1393402.393 1314948.02 1379099.308 1307808.043 1404092.186 0.907480426 1.100128615 0.985294253 1.087162313 0.933674944 0.992386687 0.936511173 0.982199973 0.931426053 1 20.42120623 3.215787291 24.99996443 0.962784087 1.023258599 0.207249401 0.054770272 323.3208317 354932.2328 0.014381217 0.017199946 1643.56654 -3.215787291 0.060474512 SGTSSPQS(ph)PVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGTSSPQSPVFR 12 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 SGTSSPQS(1)PVFR;SGTSSPQS(1)PVFR;SGTSSPQS(1)PVFR;SGTSSPQS(1)PVFR 256.04 3.90E-21 1463110000 1170230 1338150 1341160 1232220 1464540 1747300 1400430 1460630 1373510 1209760 TRUE FALSE 1216431.584 1567966.853 1376111.731 1475949.438 1215598.014 1341516.056 1290660.637 1441052.644 1324077.643 1446789.31 0.840780047 1.083756178 0.951148673 1.020155062 0.840203895 0.927236638 0.892086103 0.996034899 0.915183458 1 20.46442341 7.200882989 8.530619039 0.948695982 0.094096361 0 0.075120836 0 0 0.015596038 0 15881188.09 -7.200882989 -0.854599621 SGVAFYHLGDYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGVAFYHLGDYDK 13 0 Q92623 Q92623 TTC9 Tetratricopeptide repeat protein 9A 0 105 0.0014872 771880000 1248200 1061100 1356800 1150600 1745400 1739900 1708800 1476500 1620900 1154900 FALSE TRUE 1297479.9 1243335.671 1392159.323 1378185.246 1448717.531 1335834.593 1574859.791 1456709.933 1562564.126 1381180.543 0.939399202 0.900197789 1.007948837 0.99783135 1.048898016 0.967168702 1.140227321 1.054684661 1.131325035 1 20.39747049 3.746601181 0.638810508 1.077741932 0.895171712 0.504417014 0.051514396 0.939070826 0.634783882 0.027201433 0.107745126 5579.575791 -3.746601181 -0.18257022 SGVGTGPPS(ph)PIALPPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGVGTGPPSPIALPPLR 17 0 Q92630 Q92630 DYRK2 Dual specificity tyrosine-phosphorylation-regulated kinase 2 1 SGVGTGPPS(1)PIALPPLR 153.92 1.65E-07 44840000 33097 40466 37590 38296 49976 50230 44304 45395 30947 44758 TRUE FALSE 34403.69512 47415.72072 38569.62628 45870.8345 41481.09737 38564.84374 40831.33671 44786.55428 29833.22352 53527.47316 0.642729669 0.88582027 0.720557576 0.856958713 0.774949665 0.720468228 0.762810839 0.836702195 0.55734414 1 15.70799193 -1.699781467 3.098042368 1.027830854 0.763048613 0.377555828 0.094798779 30465677.86 35755070.98 6704029.78 0.020855276 0.019962666 1.699781467 -0.264782241 SGVHSHMTNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGVHSHMTNTR 11 0 O14841 O14841 OPLAH 5-oxoprolinase 0 ;;; 113.22 0.00082137 24024400 11953.7 34459.3 31622.3 36628.9 32925.5 42679.1 28031.8 36417.2 29499.2 36457.5 FALSE TRUE 12425.64131 40377.41672 32446.40312 43873.98709 27328.83527 32767.52583 25834.59427 35929.087 28437.52955 43600.6491 0.28498753 0.926073752 0.744172479 1.006269127 0.626798817 0.751537569 0.592527744 0.82404936 0.652227206 1 15.41206199 -2.24257971 2.117630943 1.885944033 0.728602703 0.167940971 0.189071425 13581467.65 2326551.211 57518256.66 0.042115435 0.00572032 2.24257971 -1.157341331 SGVRGT(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SGVRGTPVR 9 1 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RFR3 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 1 S(0.001)GVRGT(0.999)PVR;S(0.001)GVRGT(0.999)PVR;SGVRGT(1)PVR 80.318 0.028048 1227780000 559420 587981 565481 510323 601660 753260 607488 620610 529835 568981 TRUE FALSE 581506.3336 688962.1629 580217.8994 611263.3662 499390.0481 578326.7808 559871.5032 612291.7381 510766.3418 680461.9332 0.854575848 1.012491852 0.852682378 0.898306483 0.733898582 0.849903209 0.822781519 0.899817768 0.750617069 1 19.37615493 4.083955638 12.77974241 0.845872539 0.933526342 0.143549746 0.080027968 1.076743402 159.5587812 0.018347224 0.039655371 12132.64914 -4.083955638 0.087653804 SGVSS(ph)DNEDDDDEEDGNYLHPSLFASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 S(0.006)GVS(0.157)S(0.837)DNEDDDDEEDGNYLHPSLFASK;S(0.001)GVS(0.141)S(0.858)DNEDDDDEEDGNYLHPSLFASK;SGVS(0.15)S(0.85)DNEDDDDEEDGNYLHPSLFASK;SGVS(0.118)S(0.882)DNEDDDDEEDGNYLHPSLFASK;SGVS(0.114)S(0.886)DNEDDDDEEDGNYLHPSLFASK;S(0.006)GVS(0.163)S(0.831)DNEDDDDEEDGNYLHPSLFASK 352.67 1.89E-110 2627670000 517140 1911620 2124500 1984960 2388170 2641980 2230570 2496210 2180690 1872080 TRUE FALSE 537557.0865 2239925.865 2179866.215 2377579.163 1982229.716 2028420.185 2055732.095 2462752.388 2102207.393 2238878.233 0.240101082 1.000467927 0.97364215 1.061951083 0.885367363 0.905998439 0.918197365 1.099993895 0.938955662 1 21.09434463 4.73953954 24.98876298 0.979645937 0.240100847 0.920857971 0.064719158 21.24986849 542364.1702 0.016215719 0.09902788 54895.85326 -4.73953954 -0.739545089 SGVYQHVTGEMMGGHAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGVYQHVTGEMMGGHAIR 18 0 P07858;R4GMQ5 P07858 CTSB Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain 0 ; 210.75 2.18E-16 1355500000 283260 615660 503800 538230 597270 841560 582780 571980 530340 645680 FALSE TRUE 294443.3235 721394.8158 516929.4419 644690.2875 495746.2587 646120.444 537100.1808 564313.5437 511253.167 772188.6337 0.381310098 0.934220972 0.66943415 0.834887046 0.642001497 0.836739128 0.695555668 0.730797527 0.662083259 1 19.55859379 -2.516924993 2.024651666 4.108295205 0.720797161 0.271771811 0.141524428 3664576.456 205699.2833 52382396.95 0.03021226 0.00304141 2.516924993 -3.387498045 SGWSSQSDYYASYYSSQYDYGDPGHWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGWSSQSDYYASYYSSQYDYGDPGHWDR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 214.61 3.78E-34 442830000 175730 227280 228880 235020 241870 311320 199210 244430 239870 229250 FALSE TRUE 182667.9561 266313.572 234844.8008 281506.2545 200757.0238 239020.6481 183595.3997 241153.8157 231237.1256 274167.1482 0.666264931 0.971354787 0.856575277 1.02676873 0.732243177 0.871806304 0.669647698 0.87958684 0.843416606 1 18.06469619 4.762277421 23.90908772 0.860147949 0.666264524 0.24586731 0.10636941 5634.413568 5679928.527 0.024396505 1.37589142 57846.54451 -4.762277421 -0.193883425 SGYFDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGYFDER 7 0 P12532;P12532-2;F8WCN3;C9JSQ1;C9J6W7;C9JT96 P12532 CKMT1A;CKMT1B "Creatine kinase U-type, mitochondrial" 0 ; 91.041 0.038841 1617890000 2815600 3529800 3238800 3402500 3537100 4334200 3168100 2916800 2874800 3019000 FALSE TRUE 2926762.062 4136015.692 3323205.789 4075504.345 2935865.005 3327647.735 2919776.044 2877705.067 2771336.51 3610515.248 0.810621715 1.145547216 0.92042425 1.128787462 0.813142946 0.92165453 0.808686806 0.797034459 0.767573689 1 21.7837733 3.215416848 24.99983275 0.838706694 1.005865278 0.303921141 0.110130933 239.2066531 258389.6784 0.029505178 0.035286651 1642.165213 -3.215416848 0.167158584 SGYFPSSSVKPCPVDGRPPIS(ph)RPPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGYFPSSSVKPCPVDGRPPISRPPSR 26 3 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 SGYFPSSSVKPCPVDGRPPIS(0.913)RPPS(0.087)R 111.58 0.01089 586660000 652730 559000 655860 690800 836990 1003000 934600 835420 812660 552640 TRUE FALSE 678500.2844 655003.9016 672952.2504 827438.1782 694718.7388 770068.4506 861343.6099 824222.5614 783412.5253 660919.2271 1.026600917 0.991049851 1.018206496 1.251950532 1.051140155 1.165147599 1.303250949 1.247085162 1.185337774 1 19.33411444 3.754813881 22.75331803 1.188485124 1.009862059 0.404732894 0.087339319 225.5462952 315744.2412 0.022654544 0.040631744 5686.091986 -3.754813881 -0.178623066 SGYHDDS(ph)DEDLLE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SGYHDDSDEDLLE 13 0 Q99523;Q99523-2 Q99523 SORT1 Sortilin 1 SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE;S(0.179)GYHDDS(0.821)DEDLLE;SGYHDDS(1)DEDLLE;SGYHDDS(1)DEDLLE 205.31 7.44E-08 10825860000 3195580 4366120 4472740 4524940 5198220 5802590 4443970 4307610 4203670 3750720 TRUE FALSE 3321743.966 5115967.146 4589303.279 5419959.626 4314628.421 4455026.412 4095640.019 4249873.534 4052380.738 4485601.772 0.740534745 1.140530838 1.02311875 1.208301562 0.961883966 0.993183666 0.913063671 0.947447801 0.90341964 1 22.09687011 3.030727087 24.99996252 0.948231186 1.0419558 0.085454331 0.116851879 410.8244802 334249.5576 0.032407325 0.038733779 1073.314723 -3.030727087 0.093724614 SGYHQSASEHGLVVIAPDTSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGYHQSASEHGLVVIAPDTSPR 22 0 P10768;X6RA14;U3KQT1;H7BZT7 P10768 ESD S-formylglutathione hydrolase 0 ; 88.935 0.0015073 339360000 31947 119336 88744 126633 106803 169232 90483 133220 87168 122296 FALSE TRUE 33208.29223 139831.0297 91056.74154 151680.6294 88648.66421 129930.4327 83390.70603 131434.4038 84030.84071 146257.5597 0.22705351 0.956060186 0.622578017 1.037078902 0.606113382 0.888367295 0.57016339 0.898650327 0.574540153 1 17.15815167 4.749602818 24.75883131 0.785784218 0.227053139 0.481752914 0.1764448 1121.786209 2515214.936 0.036812983 0.554334811 56182.72731 -4.749602818 -0.558731079 SGYIDEHELDALLKDLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGYIDEHELDALLKDLYEK 19 1 P22676 P22676 CALB2 Calretinin 0 ; 185.13 1.41E-14 139235000 279954 170493.5 266817 151611.3 414653 297401 307704 300510 306235 191649.1 FALSE TRUE 291006.8001 199774.4324 273770.4702 181599.5626 344170.4312 228334.1249 283585.3564 296482.155 295213.6622 229199.0718 1.269668318 0.871619727 1.194465877 0.792322417 1.501622273 0.99622622 1.237288416 1.293557398 1.288022939 1 17.80624168 3.24441801 24.99999654 1.228918362 1.032165407 0.19106148 0.18833671 216.5169525 924111.8264 0.048402545 0.063832707 1755.56943 -3.24441801 -0.196752955 SGYLSSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGYLSSER 8 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 136.27 0.001857 329010000 229820 280440 241590 232090 500770 414180 301640 264240 269390 442900 FALSE TRUE 238893.4711 328603.3885 247886.0339 277996.7093 415649.2943 317992.972 277996.6686 260698.295 259694.7065 529677.7752 0.451016603 0.620383569 0.467994025 0.524841181 0.784721039 0.600351736 0.524841105 0.492182809 0.490288093 1 19.01475545 -1.427070924 3.391888501 1.005075184 0.552385297 0.675381166 0.093434311 53324950.78 84068290.22 2687980.549 0.023218278 0.03740495 1.427070924 -0.452689887 SGYS(ph)SPGSPGTPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.073)GYS(0.509)S(0.417)PGSPGTPGSR 68.83 0.053984 71366000 74057 84270 93929 93960 103900 115260 97252 93136 80810 86898 TRUE FALSE 76980.82754 98742.71697 96376.8669 112545.0076 86239.11511 88492.61178 89629.13412 91887.66426 77901.66389 103923.9993 0.740741581 0.950143543 0.927378349 1.082954931 0.829828679 0.851512763 0.862448854 0.884181371 0.749602251 1 16.66516933 SGYSS(ph)PGS(ph)PGTPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 2 SGYS(0.03)S(0.969)PGS(0.987)PGT(0.013)PGSR 158.91 2.63E-06 405090000 257140 298090 282920 263820 303650 385800 306250 311660 289470 243630 TRUE FALSE 267292.0858 349284.6387 290293.1276 316002.8086 252035.6815 296203.7969 282245.3248 307482.7075 279052.0312 291364.6339 0.917379993 1.198788727 0.996322456 1.084561308 0.865018098 1.016608615 0.968701386 1.055319252 0.957741602 1 18.15246625 SGYSS(ph)PGSPGTPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SGYS(0.001)S(0.716)PGS(0.283)PGTPGSR;SGYSS(1)PGSPGTPGSR;SGYSS(1)PGSPGTPGSR;SGYS(0.024)S(0.975)PGS(0.001)PGTPGSR 314.16 3.09E-56 910674000 1244214 1490733 1424855 1358808 1578320 1862510 1457557 1474801 1463329 1303509 TRUE FALSE 1293336.529 1746754.796 1461987.892 1627576.167 1310037.73 1429970.279 1343309.874 1455033.705 1410664.075 1558906.631 0.829643356 1.120499946 0.937829029 1.044049806 0.840356763 0.917290523 0.861700019 0.93336809 0.904906071 1 20.57210309 3.242897625 24.99987385 0.905278418 0.989599663 0.164151887 0.080240562 164.8466519 950220.9961 0.020503128 0.026824997 1749.434249 -3.242897625 0.084321245 SGYSSPGS(ph)PGTPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SGYSSPGSPGTPGSR 15 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 S(0.025)GY(0.006)S(0.169)S(0.139)PGS(0.662)PGTPGSR;SGYS(0.001)S(0.005)PGS(0.978)PGT(0.016)PGSR 76.588 0.029803 1331309000 79140 92817 91479 103129 109698 126474 96398 101357 93464 105124 TRUE FALSE 82264.50831 108757.5977 93863.01789 123527.6084 91051.57314 97102.33023 88842.07287 99998.4752 90100.2489 125721.0351 0.65434164 0.865070811 0.746597559 0.982553224 0.724234994 0.772363433 0.706660368 0.795399713 0.716668049 1 16.93986653 -1.209747822 5.124156332 1.000019757 0.778638312 0.370717478 0.088220926 1.86E-05 2.87E-06 0.0798632 0.018822258 0.061695314 1.209747822 -0.221381445 SHDDGNIDLES(ph)DSFLKFDSEPSAVALELPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHDDGNIDLESDSFLKFDSEPSAVALELPTR 31 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 1 SHDDGNIDLES(0.996)DS(0.004)FLKFDSEPSAVALELPTR 213.22 4.43E-27 43959000 33701 27329 35752 23990 43224 40569 34891 31480 35543 24062 TRUE FALSE 35031.5415 32022.54316 36683.72649 28735.1504 35876.79992 31147.46458 32156.15225 31058.06209 34263.81437 28776.48821 1.217366805 1.112802331 1.274781211 0.998563487 1.246740035 1.082392833 1.117445326 1.079286043 1.190687833 1 14.81260292 -4.999999991 0.078894475 0.555594443 1.280307853 0.248534443 0.080077887 343.9463315 1.926150331 27.06875863 2.615120125 1.00E-05 4.999999991 0.72471341 SHDDGNIDLESDSFLKFDSEPSAVALELPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHDDGNIDLESDSFLKFDSEPSAVALELPTR 31 1 P18583-7;P18583;P18583-5;P18583-9;P18583-10;P18583-3;P18583-4;P18583-2;P18583-6;P18583-8 P18583-7 SON Protein SON 0 157.75 2.47E-10 63537000 62633 60540 74439 48879 104570 86125 71372 76123 78266 63157 FALSE TRUE 65105.7992 70937.27406 76378.94149 58547.12031 86795.22875 66123.77399 65777.67614 75102.6957 75449.22195 75531.40494 0.861969922 0.939175885 1.011220982 0.775136122 1.149127688 0.875447425 0.870865254 0.994324093 0.998911936 1 16.204789 7.999999945 0.09381223 1.036491005 0.670059057 0.075250969 0.096386873 444.8316467 2.98096964 1.443127365 20.97036613 99999987.25 -7.999999945 -0.366431948 SHEAEVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 ;; 101.43 0.0053999 1340010000 1569780 1621920 1871790 1542070 2626230 2632510 2178140 1680880 2007990 1641600 FALSE TRUE 1631756.127 1900472.143 1920570.385 1847086.843 2179824.363 2021149.449 2007411.695 1658350.553 1935722.832 1963240.09 0.831154648 0.96802839 0.978265672 0.940835944 1.11031981 1.02949683 1.02249934 0.84470084 0.985983753 1 20.90480518 4.747340533 3.587405759 0.981841639 0.812310731 0.345008351 0.064252268 0.394517947 9.027411077 0.017321634 0.182054616 55890.82664 -4.747340533 -0.169530907 SHEGETAYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 168.74 4.85E-06 2879400000 388020 463020 489350 472380 524490 491910 416420 478770 426550 501060 FALSE TRUE 403339.3292 542540.0832 502102.863 565815.3541 435337.3771 377671.3575 383779.9123 472352.8713 411198.5488 599233.1136 0.673092525 0.905390692 0.837909073 0.944232455 0.726490855 0.630257823 0.640451777 0.788262298 0.686207987 1 19.19275782 5.031357898 13.76649334 0.781288425 0.380759348 0.073204462 0.121544101 1638995.543 22575688.13 0.029590397 14711464.33 107487.4841 -5.031357898 -0.400529077 SHEGETSYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHEGETSYIR 10 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 ;; 185.08 1.49E-06 1363580000 284246 325899 326883 288378 485052 436203 439855 354800 327752 435479 FALSE TRUE 295468.2516 381869.6181 335401.8395 345418.3077 402603.0343 334901.464 405378.0158 350044.4863 315956.2695 520802.7723 0.567332332 0.733232691 0.644009321 0.663242068 0.773043186 0.643048543 0.778371463 0.672124852 0.606671635 1 18.9903776 -1.947686266 2.732647655 1.228859623 0.681879817 0.689777149 0.065131007 8453924.504 5612179.587 12321521.75 0.014695781 0.01128012 1.947686266 -0.546979807 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVK 48 0 P55735;P55735-4;P55735-3;P55735-2;A8MXL6 P55735 SEC13 Protein SEC13 homolog 0 ;; 145.69 1.18E-15 327816000 60324.1 95331 128257 124169 143227 211293 114594 138186 143382 114109 FALSE TRUE 62705.74205 111703.3577 131599.4828 148729.2576 118881.3257 162223.4029 105611.8228 136333.8427 138221.7098 136466.4738 0.459495584 0.818540661 0.964335629 1.089859315 0.871139426 1.188741809 0.773903069 0.999028105 1.012862031 1 17.05818704 4.708021796 2.017841706 0.984446636 0.32756087 0.698364475 0.105693285 0.349510189 1.624516877 0.025232488 0.413516437 51053.06214 -4.708021796 -0.656885766 SHELDIDENPAS(ph)DFDDSGSLLGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHELDIDENPASDFDDSGSLLGFK 24 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 SHELDIDENPAS(0.996)DFDDS(0.002)GS(0.002)LLGFK 118.43 0.00033888 30670000 17319 15056 18342 14780 19873 21883 20609 14787 16616 14056 TRUE FALSE 18002.76749 17641.75088 18820.00759 17703.43989 16494.99456 16801.00489 18993.61273 14588.80445 16017.99341 16810.00408 1.070955569 1.049479274 1.119571863 1.053149053 0.981260592 0.999464653 1.129899353 0.867864421 0.952884564 1 14.03703245 2.360827558 0.748338712 0.944987427 1.072783394 0.294570967 0.063114745 0.787189083 0.867436968 0.051327572 0.03517686 229.5237115 -2.360827558 0.127795967 SHES(ph)LLSPCSTVECLDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHESLLSPCSTVECLDLGR 19 0 Q9UJF2;Q9UJF2-2 Q9UJF2 RASAL2 Ras GTPase-activating protein nGAP 1 S(0.435)HES(0.563)LLS(0.002)PCSTVECLDLGR 117.18 6.70E-05 123610000 11418 18653 19305 18250 22787 25835 20800 16705 16437 18876 TRUE FALSE 11868.79146 21856.50765 19808.10416 21859.79553 18913.67388 19835.21278 19169.64165 16481.0968 15845.43558 22574.3908 0.525763533 0.968199224 0.877459079 0.96834487 0.837837621 0.878659936 0.849176477 0.730079361 0.70192085 1 14.46239943 -0.338898257 7.83427372 1.000000062 0.823382964 0.157700135 0.126836765 0 0 0.119002809 0.028049231 0.458249229 0.338898257 -0.176617098 SHESNAPGS(ph)AGGQASEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHESNAPGSAGGQASEKPR 19 1 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 SHESNAPGS(0.922)AGGQAS(0.078)EKPR;SHESNAPGS(0.999)AGGQAS(0.001)EKPR 113.24 0.00010929 133764000 53226 207370 214135 205710 247910 312630 208613 226130 213815 204339 TRUE FALSE 55327.40358 242984.1844 219715.534 246398.824 205770.3468 240026.4205 192261.368 223099.0972 206119.8399 244375.3147 0.226403406 0.994307402 0.899090541 1.008280334 0.84202591 0.982204036 0.786746272 0.912936306 0.843456059 1 17.89873903 4.742763549 24.99924303 0.911800052 0.226403136 0.888309923 0.073615547 119.8369794 712769.7446 0.016327739 0.127140363 55304.89202 -4.742763549 -0.685396916 SHFEQWGTLTDCVVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 243.9 3.85E-20 1825774000 876594 973255 1061861 1157177 982741 1278765 1106552 1026008 1015212 936964 FALSE TRUE 911202.608 1140403.975 1089533.97 1386063.157 815695.0358 981791.2086 1019817.563 1012256.041 978674.7184 1120544.157 0.813178671 1.01772337 0.972325779 1.23695541 0.727945464 0.876173601 0.910109215 0.903361135 0.873392372 1 20.09576807 3.214468727 24.99999499 0.880576703 1.007900249 0.231657111 0.114352745 338.9457951 351720.8669 0.032295346 0.03861963 1638.584063 -3.214468727 0.127323545 SHFEQWGTLTDCVVMRDPNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHFEQWGTLTDCVVMRDPNTK 21 1 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 249.34 7.06E-31 550953000 357460 306880 367980 334140 414730 487160 419930 337920 409210 276010 FALSE TRUE 371572.7968 359584.2528 377569.8611 400231.8947 344234.3427 374024.473 387014.7893 333390.7351 394482.612 330088.875 1.125675008 1.089355868 1.143843037 1.212497376 1.042853513 1.133102329 1.172456325 1.010002943 1.195079998 1 18.33249499 -5 0.237395991 0.328145592 1.131674613 0.252932131 0.061447965 232.6342019 2.32307352 75.31272943 0.095868654 1.00E-05 5 0.803529022 SHFEQWGTLTDCVVMRDPNTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHFEQWGTLTDCVVMRDPNTKR 22 2 F8W6I7;P09651-2;P09651;P09651-3;F8VZ49;Q32P51;F8W646 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 ; 165.1 7.93E-12 4214000000 1251670 1329470 1553330 1047940 1953190 1836540 1232190 1486740 1569570 1586990 FALSE TRUE 1301086.898 1557796.131 1593811.056 1255219.404 1621187.461 1410031.418 1135607.728 1466812.682 1513081.482 1897930.306 0.685529334 0.820786794 0.839762688 0.661362222 0.854187036 0.742931083 0.598340057 0.772848549 0.797227105 1 20.85599559 0.77699282 2.444120244 0.999800965 0.747326299 0.491999919 0.077024811 0.822893388 7.553238523 0.07287195 0.019558579 5.984017016 -0.77699282 -0.252474666 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHFGGPDYEEGPNSLINEEEFFDAVEAALDR 31 0 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2R8YFA1 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 ; 332.07 1.04E-105 81158000 46503 55944 55907 53203 60839 73141 60108 50515 56454 47982 FALSE TRUE 48338.97435 65551.94682 57363.98235 63726.3946 50497.60851 56155.11121 55396.5779 49837.92905 54422.23157 57383.15423 0.842389635 1.142355238 0.999665897 1.110541856 0.880007542 0.978599242 0.965380496 0.868511495 0.948400838 1 15.80833965 3.228590373 24.99959021 0.932756712 1.030491366 0.188274372 0.08372352 278.135494 697401.5648 0.022684294 0.027411963 1692.740451 -3.228590373 0.097734655 SHFTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHFTDK 6 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 127.66 0.016964 63228000 184520 191460 186440 177970 221360 248120 225150 185560 183870 147940 FALSE TRUE 191804.9921 224341.7656 191298.7796 213171.9348 183733.3063 190497.8903 207502.1547 183072.8717 177252.5546 176926.0105 1.084097197 1.26799765 1.081236043 1.204864871 1.038475381 1.076709353 1.172818819 1.034742552 1.001845653 1 17.43278663 1.984226223 0.433212569 0.986989943 1.170485107 0.375702577 0.067605097 1.059870634 0.479435467 0.069317871 0.063077392 96.43312104 -1.984226223 0.183495164 SHGLEPAAPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHGLEPAAPSPR 12 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 SHGLEPAAPS(1)PR;SHGLEPAAPS(1)PR 136.17 7.39E-05 290480000 223820 247000 233333 237280 261480 286850 215998 208031 221730 234250 TRUE FALSE 232656.5864 289420.3286 239413.8497 284213.2758 217033.723 220233.4348 199067.5124 205242.6847 213749.9806 280146.8025 0.830480963 1.033102381 0.8546014 1.014515508 0.774714261 0.786135814 0.710582846 0.732625477 0.762992755 1 18.0958235 3.218628355 24.35372527 0.772032982 0.934700298 0.321641825 0.095350295 162.0289106 197970.2502 0.025389492 0.030387783 1654.353652 -3.218628355 0.162667316 SHGRLSGSARPQELVGT(ph)FIQQEVGKPEDEASGSFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHGRLSGSARPQELVGTFIQQEVGKPEDEASGSFFK 36 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 S(0.106)HGRLS(0.106)GS(0.106)ARPQELVGT(0.682)FIQQEVGKPEDEASGSFFK 129.9 7.45E-09 188120000 98882 63253 79483 49732 127570 119940 100990 71190 87948 59678 TRUE FALSE 102785.9377 74116.21071 81554.39228 59568.84116 105885.697 92085.75271 93074.13991 70235.81449 84782.76866 71370.7615 1.440168713 1.038467422 1.142686313 0.834639282 1.483600493 1.290244783 1.304093413 0.984097872 1.187920191 1 16.12304555 -1.135989275 4.511299493 0.999977774 1.175660515 0.076870705 0.191694405 4.19E-05 8.03E-06 0.181659408 0.042812119 0.073115714 1.135989275 0.175682741 SHHCTLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHHCTLAR 8 0 Q9HCN6-3 Q9HCN6-3 0 ;; 92.692 0.02698 1733350000 1591210 2056320 1837550 1903290 2132470 2347740 1958020 2093550 1897130 2188870 FALSE TRUE 1654032.199 2409476.964 1885438.063 2279755.081 1769993.511 1802512.965 1804545.276 2065489.387 1828852.662 2617737.168 0.631855719 0.920442661 0.720254915 0.870887692 0.676154021 0.688576755 0.689353117 0.7890362 0.698638765 1 21.31988882 -1.402069253 5.486581041 1.000131917 0.74829266 0.440163817 0.086820636 0.000130895 1.43E-05 0.078542386 0.018502973 0.039621485 1.402069253 -0.251839257 SHHGEHERPEFIAYPHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHHGEHERPEFIAYPHLR 18 1 P12074;H0YIV9 P12074 COX6A1 "Cytochrome c oxidase subunit 6A1, mitochondrial" 0 ; 164.53 1.02E-11 953300000 105042 308960 261480 346560 198548 518090 245530 164242 213680 419340 FALSE TRUE 109189.1393 362021.4766 268294.3836 415108.5336 164798.8819 397771.4492 226284.717 162040.6046 205989.6985 501501.6443 0.217724389 0.721874954 0.534982062 0.827731152 0.328610851 0.793160808 0.451214307 0.323110814 0.410745809 1 18.93589491 -1.479635264 5.238731473 1.000912488 0.51440066 0.352609978 0.198296673 0.002047516 0.000203381 0.186019448 0.04376832 0.033140933 1.479635264 -0.486511828 SHIEIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHIEIIR 7 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 0 ;; 158.12 0.0014326 458400000 277332 349431 377719 448183 1301220 782870 740309 417939 388377 956030 FALSE TRUE 288281.2815 409443.0561 387562.6674 536832.2597 1080039.089 601060.307 682281.6461 412337.2113 374399.3876 1143345.774 0.252138319 0.358109563 0.338972406 0.46952748 0.944630324 0.525703003 0.596741302 0.360640867 0.327459458 1 20.12483034 3.606796952 4.222750908 0.580673984 0.32191374 0.291452976 0.208290546 0.346700688 10.21489076 0.057594947 0.091378872 4043.867824 -3.606796952 -0.258760244 SHILEDDENS(ph)VDISMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHILEDDENSVDISMLK 17 0 O75717;O75717-2 O75717 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 SHILEDDENS(1)VDISMLK 93.226 0.0032668 29201000 36396 41314 44653 34851 52579 49210 40557 44941 49013 47993 TRUE FALSE 37832.94218 48409.35812 45816.69386 41744.42378 43641.64036 37781.72328 37378.03636 44338.6394 47249.0317 57396.30947 0.659152871 0.843422836 0.798251565 0.727301532 0.76035621 0.658260499 0.651227173 0.772499832 0.823206791 1 15.80867036 0.89183519 1.983619833 0.999024003 0.733828639 0.650375603 0.059927288 0.295338089 2.359842946 0.059311672 0.016518483 7.795342291 -0.89183519 -0.265195364 SHISDQS(ph)PLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SHIS(0.001)DQS(0.999)PLSSK 111.22 0.00090513 108970000 108830 326660 345050 303740 364270 510400 346820 374510 349320 381140 TRUE FALSE 113126.6924 382761.3139 354042.2865 363818.8654 302351.5155 391867.3352 319635.3422 369490.306 336748.0414 455817.0856 0.248184406 0.839725684 0.776720087 0.798168557 0.663317644 0.859703042 0.701235983 0.810610918 0.738778892 1 18.79809548 4.742018855 24.91428182 0.786502153 0.248184193 0.77387548 0.089054892 131.4578755 947021.9395 0.018778912 0.137072358 55210.14084 -4.742018855 -0.53831796 SHKDEVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SHKDEVVK 8 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;;; 136.57 0.00047194 3768988000 8745330 4883983 7294180 4721459 10343180 8651070 9520260 6736630 8188760 4236990 FALSE TRUE 9090602.381 5722769.088 7484272.323 5655349.498 8585049.958 6641990.101 8774037.145 6646336.494 7894048.127 5067147.068 1.794027736 1.129386815 1.477018966 1.116081578 1.694257112 1.310794814 1.731553678 1.311652574 1.557888102 1 22.27274227 -1.036495574 4.734869191 0.999987839 1.44366626 0.263080636 0.228856476 2.61E-05 5.32E-06 0.197200692 0.046479376 0.091939984 1.036495574 0.443678421 SHKNPENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHKNPENR 8 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 114.5 0.0015892 20982000 59882 51475 63815 50211 69411 83287 66632 60985 64871 50854 FALSE TRUE 62246.1876 60315.43083 65478.07132 60142.58594 57612.54301 63944.85648 61409.20973 60167.59583 62536.30538 60817.86764 1.023485203 0.991738664 1.076625569 0.988896656 0.947296333 1.051415628 1.009723164 0.989307882 1.028255475 1 15.89220761 SHKNPENRKSWAS(ph) ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHKNPENRKSWAS 13 3 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SHKNPENRKS(0.268)WAS(0.732) 89.311 0.041487 460280000 287250 271150 304750 112920 529750 408510 130110 263260 319870 442660 TRUE FALSE 298590.8518 317717.9032 312692.0354 135255.239 439703.2842 313639.7435 119911.6382 259731.4303 308357.9412 529390.7518 0.564027329 0.600157638 0.590663955 0.255492259 0.830583615 0.592454142 0.226508751 0.490623286 0.582477008 1 19.01397347 0.81831119 4.246596231 0.999979031 0.513220773 0.4302251 0.165018778 1.673877285 38.18850712 0.15810927 0.040260891 6.581292449 -0.81831119 -0.486758258 SHLEPSGNPLPATPTTSAPS(ph)APPASSQGPDTAPRPSPPQEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPS(0.229)APPAS(0.229)S(0.229)QGPDT(0.177)APRPS(0.137)PPQEEAR 148.28 6.54E-14 371010000 22019 30982 31271 25214 21690 35197 26082 22075 28902 23150 TRUE FALSE 22888.32712 36302.91749 32085.94795 30201.25394 18003.14155 27023.03017 24037.62469 21779.12073 27861.82267 27685.79927 0.826717224 1.311246865 1.158931611 1.090857217 0.650266275 0.976061045 0.868229393 0.786653133 1.006357895 1 14.75685855 3.409638663 12.86711896 0.868570844 1.120977296 0.325512337 0.15047032 0.838495283 158.0326723 0.039268191 0.053170892 2568.258077 -3.409638663 0.252406452 SHLEPSGNPLPATPTTSAPSAPPAS(ph)SQGPDTAPRPSPPQEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPS(0.05)APPAS(0.267)S(0.267)QGPDT(0.226)APRPS(0.191)PPQEEAR 74.03 0.00079334 70699000 7803.3 8954.4 9350.4 8689.9 8151.3 10843 7573.8 7650.4 8799.5 8189.1 TRUE FALSE 8111.380309 10492.24854 9594.079105 10408.73628 6765.744938 8324.877577 6980.145766 7547.858902 8482.807714 9793.597355 0.828232979 1.071337545 0.979627685 1.062810314 0.690833479 0.850032657 0.712725418 0.770693202 0.866158512 1 13.25762317 3.244645933 24.99996156 0.796235615 0.991213637 0.388241481 0.103093242 124.6810736 512216.8741 0.02679109 0.035370318 1756.491017 -3.244645933 0.194978022 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPS(ph)PPQEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHLEPSGNPLPATPTTSAPSAPPASSQGPDTAPRPSPPQEEAR 43 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 SHLEPSGNPLPATPTTSAPS(0.008)APPAS(0.174)S(0.174)QGPDT(0.147)APRPS(0.495)PPQEEAR 84.198 0.00013068 695640000 16284 17300 17039 19027 17730 24265 19149 18973 17583 16376 TRUE FALSE 16926.90489 20271.14042 17483.05034 22790.48381 14716.26093 18629.82149 17648.05134 18718.69797 16950.19126 19584.56366 0.864298291 1.035057036 0.892695423 1.163696276 0.751421435 0.951250271 0.901120477 0.955788359 0.865487307 1 14.25742937 3.228383831 24.99994985 0.907618481 0.985356708 0.150686727 0.098229138 411.938743 1011953.66 0.02638353 0.03187134 1691.935609 -3.228383831 0.077738227 SHLGNVHDQDN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHLGNVHDQDN 11 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 ;; 193.22 1.05E-06 418190000 395750 401480 468630 364996 505692 581051 430042 336869 425423 432898 FALSE TRUE 411374.5156 470431.0669 480842.8828 437191.1194 419734.6545 446110.7112 396334.1843 332353.8221 410112.1093 517716.0748 0.794594828 0.908666139 0.928777193 0.844461165 0.810742944 0.861689897 0.765543516 0.641961566 0.792156414 1 18.98180159 2.221604311 6.076064121 0.755449808 0.861114545 0.002696186 0.093890256 0.24774248 31.48340006 0.033894526 0.025854213 166.5728862 -2.221604311 0.105664737 SHLLDCCPHDILAGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHLLDCCPHDILAGTR 16 0 Q9NQ29-3;Q9NQ29;Q9NQ29-2 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 ; 153.74 2.44E-07 196958000 121269 142963 148607 128452 167137 210698 137596 111470 144938 152061 FALSE TRUE 126056.7938 167515.7832 152479.8205 153859.4222 138727.1124 161766.5827 126810.866 109975.927 139721.7097 181854.4416 0.693174127 0.921153103 0.838471797 0.846058094 0.762846985 0.889538805 0.697320697 0.604746995 0.768316179 1 17.47242464 2.22546528 24.97864301 0.719405656 0.82828449 0 0.11405833 393.281886 750158.9417 0.040421619 0.030032423 168.0603562 -2.22546528 0.108878834 SHLLNCCPHDVLSGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHLLNCCPHDVLSGTR 16 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2 Q9Y383 LUC7L2 Putative RNA-binding protein Luc7-like 2 0 182.31 1.25E-09 700530000 356070 361300 368920 366880 505480 585510 465980 386570 381400 397750 FALSE TRUE 370127.9185 423350.4645 378534.3583 439447.769 419558.6902 449534.176 429455.27 381388.6615 367673.4885 475681.4971 0.778100306 0.889987244 0.795772719 0.923827754 0.882015997 0.945031873 0.902821053 0.801773169 0.772940488 1 18.85963638 5.723280446 1.288938636 0.874404977 4.81E-11 0.155231194 0.068208483 32.73687813 6.549141049 0.018792903 68.03297007 528786.6062 -5.723280446 -0.874404977 SHLVGVKPFEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHLVGVKPFEADR 13 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 109.83 0.00066457 874390000 919810 740190 889180 694230 1139100 1227800 1046000 840200 998650 803740 FALSE TRUE 956124.809 867311.8746 912352.7613 831546.6219 945476.1889 942662.0575 964011.7868 828938.4933 962708.7816 961217.4645 0.99470187 0.902305573 0.949163738 0.865097288 0.983623606 0.980695932 1.002907066 0.862383929 1.001551488 1 19.87450334 SHMAEESKNEYAAQLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHMAEESKNEYAAQLQR 17 1 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3;M0R2H7;Q15642-5 Q15642 TRIP10 Cdc42-interacting protein 4 0 144.68 3.02E-07 78879000 40068 32905 38867 32777 40090 59253 36674 35787 39346 34888 FALSE TRUE 41649.91558 38556.17778 39879.90595 39260.19277 33275.51612 45492.38874 33799.39605 35307.3338 37929.94515 41723.63563 0.998233135 0.924084807 0.955810905 0.940958097 0.797521971 1.090326575 0.810077922 0.846219014 0.909075745 1 15.34857725 5.739598857 0.53522805 0.896581601 1.216026803 0.055673434 0.084377924 26.55114318 2.577218405 0.041752996 6.691498069 549033.5162 -5.739598857 0.319445203 SHMMDVQGSTQDSAIKDFVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHMMDVQGSTQDSAIKDFVLK 21 1 P13667 P13667 PDIA4 Protein disulfide-isomerase A4 0 216.49 3.71E-25 407220000 179710 107220 165520 133470 232900 230680 188290 153680 188130 125310 FALSE TRUE 186805.0896 125634.2009 169833.5872 159869.9676 193311.7412 177108.066 173531.3378 151620.171 181359.238 149862.0953 1.246513264 0.838332073 1.133265799 1.066780545 1.289930858 1.181806952 1.157940155 1.01173129 1.210174178 1 17.193276 5.054249642 22.38416402 1.102576479 3.604314347 0.117184708 0.121179456 1700.268958 897909.7789 0.027687153 57831.33874 113305.1478 -5.054249642 2.501737868 SHNVAAGS(ph)YEAPLPPGS(ph)FHGDFAYGTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 SHNVAAGS(0.995)Y(0.005)EAPLPPGS(0.612)FHGDFAY(0.013)GT(0.358)Y(0.016)R;SHNVAAGS(0.998)Y(0.001)EAPLPPGS(0.521)FHGDFAY(0.004)GT(0.471)Y(0.004)R 111.27 0.00028432 182373000 48081 49092 57794 71441 88249 82286 73875 59660 69919 84495 TRUE FALSE 49979.27501 57523.16912 59300.15912 85571.81657 73248.4665 63176.32356 68084.48446 58860.35528 67402.62885 101050.1775 0.494598587 0.569253519 0.586838743 0.846825 0.72487222 0.625197552 0.673769073 0.582486412 0.66702138 1 16.62471233 -2.755612534 1.530396147 6.123742145 0.642566886 0.578646685 0.091844061 934756.1323 30170.73309 16608663.64 0.025814057 0.001755446 2.755612534 -5.481175258 SHNVAAGSYEAPLPPGS(ph)FHGDFAYGTYR ddPTM_MDA-MB-175_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(0.809)FHGDFAYGT(0.191)YR 173.6 3.16E-12 1241700000 205270 255700 273840 246930 337210 337480 257670 263920 230670 306760 TRUE FALSE 213374.2181 299614.4859 280976.4954 295772.017 279891.1646 259105.3846 237473.1521 260382.5841 222368.2318 366863.7487 0.581617069 0.816691447 0.765887871 0.806217616 0.762929468 0.70627143 0.647306126 0.709752831 0.606133019 1 18.48488483 -1.402675218 3.942926339 1.001243538 0.716993326 0.562646486 0.07618525 0.000834982 0.000126494 0.073631268 0.017281058 0.03956624 1.402675218 -0.284250212 SHNVAAGSYEAPLPPGSFHGDFAYGT(ph)YR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SHNVAAGSYEAPLPPGS(0.289)FHGDFAY(0.024)GT(0.657)Y(0.03)R;SHNVAAGSYEAPLPPGS(0.333)FHGDFAY(0.111)GT(0.409)Y(0.148)R 99.357 0.0029193 1302970000 194521 216590 222559 241764 272370 289818 212589 231109 213323 250057 TRUE FALSE 202200.8393 253787.6477 228359.0704 289584.1976 226072.6447 222512.1617 195925.7187 228011.3619 205645.5469 299050.8815 0.676141927 0.848643704 0.763612765 0.968344237 0.755967157 0.744061213 0.655158472 0.762450058 0.687660728 1 18.19003144 3.033618938 24.99955996 0.746843906 0.819174716 0.020957676 0.110866427 455.4587602 338683.253 0.029959454 0.035808227 1080.485487 -3.033618938 0.072330809 SHPDLLQLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHPDLLQLPR 10 0 Q27J81-2;Q27J81;A0A0A0MQU1 Q27J81-2 INF2 Inverted formin-2 0 ; 116.23 0.0011174 222250000 45174 52179 42517 49790 54774 55767 52909 43218 48736 51857 FALSE TRUE 46957.5044 61140.33735 43625.02795 59638.31339 45463.53504 42815.95941 48761.85433 42638.7334 46982.00088 62017.38629 0.757166776 0.985858015 0.703432224 0.961638614 0.733077251 0.69038639 0.786261035 0.687528707 0.757561769 1 15.9203851 3.181856926 24.9999992 0.752410991 0.85097183 0.074741666 0.114852985 147.9229511 65216.7026 0.030256221 0.036163121 1520.046684 -3.181856926 0.098560839 SHPFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHPFIK 6 0 O14579;M0QXB4;O14579-3;O14579-2 O14579 COPE Coatomer subunit epsilon 0 ; 106.84 0.03178 1057320000 3871000 3651500 3991200 3591300 4964100 5062900 4182000 4031300 4019700 3511800 FALSE TRUE 4023830.069 4278616.72 4095213.951 4301648.421 4120304.055 3887118.204 3854203.912 3977267.017 3875031.782 4199869.973 0.95808444 1.018749806 0.975081128 1.024233714 0.981055147 0.925532988 0.917696009 0.946997655 0.922655179 1 22.00191323 2.864267938 4.78909234 0.938129284 0.995258999 0.428767174 0.028180307 0.183074018 6.369823506 0.008033837 0.008573782 731.5902984 -2.864267938 0.057129715 SHPLDLS(ph)PNVQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.993)PNVQS(0.007)R;SHPLDLS(1)PNVQSR 115.34 0.00043279 364740000 173983 211889 209777 193330 233460 280219 216760 214632 228104 219298 TRUE FALSE 180851.9832 248279.2875 215243.961 231570.097 193776.5526 215142.384 199769.7848 211755.2091 219894.5816 262265.2444 0.689576629 0.946672473 0.820710962 0.882961437 0.738857156 0.820323656 0.761708953 0.807408582 0.83844347 1 18.00066711 0.775075113 3.413073004 0.999987457 0.811773736 0.413414039 0.067971917 1.647838053 23.85925482 0.060844598 0.015727343 5.957651748 -0.775075113 -0.188213721 SHPLDPIDTVDFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SHPLDPIDTVDFER 14 0 P47897;A0A1B0GVU9;P47897-2;A0A0U1RQT0;C9J165;A0A0U1RQE9;A0A0U1RQL2;A0A0U1RRI9;A0A0U1RQM8;A0A0U1RQU2 P47897 QARS Glutamine--tRNA ligase 0 ;;;;; 240.59 2.10E-17 3501650000 1793140 2003520 1975630 1965620 2209810 2500010 2064570 1986080 1839400 1891040 FALSE TRUE 1863934.552 2347608.975 2027116.541 2354413.769 1834187.286 1919420.566 1902743.609 1959459.846 1773200.353 2261553.082 0.824183419 1.038051679 0.896338254 1.041060583 0.811029951 0.848717893 0.841343776 0.866422222 0.784063115 1 21.10888243 3.220467885 24.99924153 0.851432724 0.952378014 0.23699396 0.079596509 291.5058878 402781.0277 0.020893601 0.025019234 1661.375818 -3.220467885 0.10094529 SHQGLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHQGLDR 7 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 117.39 0.012196 441370000 244570 251930 287410 300970 297350 361460 295020 254340 263410 225350 FALSE TRUE 254225.8124 295197.0178 294900.1407 360500.9677 246806.5532 277516.393 271895.5615 250930.9883 253929.9256 269503.0179 0.943313416 1.095338449 1.094236877 1.337650949 0.915784005 1.029733897 1.008877613 0.93108786 0.942215518 1 18.0399419 SHRPQQNVGVQGAATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHRPQQNVGVQGAATR 16 1 O75362 O75362 ZNF217 Zinc finger protein 217 0 ; 110.22 0.00054783 30592000 20723.6 25891.9 22844.9 21448.9 25318 32696.6 24899.5 23772.1 24888.5 24653.7 FALSE TRUE 21541.78373 30338.63241 23440.25686 25691.4284 21014.4554 25103.31017 22947.81213 23453.47388 23992.76775 29484.12049 0.730623243 1.028982107 0.795012925 0.871364924 0.712738079 0.851417975 0.778310892 0.795461201 0.813752194 1 14.84765054 SHRVPLDVACAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHRVPLDVACAR 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 61.038 0.052689 55820000 47254 62602 67150 61012 72535 84988 46147 69671 55415 74006 FALSE TRUE 49119.62441 73353.40652 68899.98416 73079.9915 60205.52661 65250.82501 42529.87756 68737.1742 53420.62497 88506.05877 0.55498601 0.828795311 0.778477599 0.825706087 0.680241866 0.737246985 0.480530691 0.776638065 0.603581559 1 16.4334886 -1.024748744 4.79159937 1.000004805 0.703096433 0.397955529 0.111798048 7.23E-06 1.47E-06 0.103969402 0.024505303 0.094460721 1.024748744 -0.296908372 SHS(ph)ANDSEEFFREDDGGADLHNATNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHSANDSEEFFREDDGGADLHNATNLR 27 1 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 S(0.183)HS(0.813)ANDS(0.004)EEFFREDDGGADLHNATNLR;S(0.015)HS(0.982)ANDS(0.003)EEFFREDDGGADLHNATNLR 179.08 1.19E-17 620110000 211481 216407 250605 233858 286455 311837 245611 218374 254156 252714 TRUE FALSE 219830.4332 253573.2188 257135.9722 280114.4144 237763.4814 239417.5827 226359.368 215447.0537 245008.9752 302228.4698 0.727365074 0.839011689 0.850799967 0.926830006 0.786701139 0.792174155 0.74896772 0.712861544 0.810674704 1 18.20528004 3.05118816 24.99967251 0.783925078 0.839710241 0 0.086069021 263.4728011 128674.9846 0.024133109 0.028844579 1125.09232 -3.05118816 0.055785163 SHS(ph)DNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.056)HS(0.9)DNDRPNCS(0.042)WNT(0.002)QYSSAYYTSR 101.74 0.0021763 677840000 9038.1 17089 9366.1 9689.7 15712 12316 12340 10360 9352.8 9985.4 TRUE FALSE 9394.931167 20023.90282 9610.18826 11606.29374 13041.27985 9455.795651 11372.75856 10221.14115 9016.194555 11941.84795 0.786723396 1.676784272 0.804748838 0.971900981 1.092065475 0.791820135 0.952344947 0.855909503 0.75500832 1 13.54373848 SHS(ph)DTSIASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSDTSIASR 10 0 E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622;H7C3H3 E9PEM3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 S(0.188)HS(0.698)DT(0.112)S(0.001)IASR 69.352 0.036867 484950000 90307 100430 103400 84957 113680 127610 106510 93563 96395 96256 TRUE FALSE 93872.39009 117678.0713 106094.6889 101761.241 94356.71421 97974.51145 98161.46789 92308.94102 92925.76278 115115.5203 0.815462501 1.022260691 0.921636706 0.883992365 0.819669789 0.851097326 0.852721402 0.801880935 0.80723922 1 16.81272283 3.539039593 3.183012311 0.842576981 0.92952351 0.121458223 0.070833828 0.357891395 7.126655816 0.018507839 0.029230331 3459.70917 -3.539039593 0.086946528 SHS(ph)FCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SHSFCK 6 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 S(0.003)HS(0.997)FCK;S(0.005)HS(0.995)FCK;S(0.003)HS(0.997)FCK;S(0.001)HS(0.999)FCK 96.253 0.027323 519880000 954640 981900 1004080 960020 1354380 1366240 1086230 1044760 1110850 947800 TRUE FALSE 992329.9243 1150533.687 1030247.15 1149909.091 1124162.971 1048951.466 1001088.454 1030756.701 1070870.725 1133503.263 0.875453963 1.015024592 0.908905323 1.01447356 0.991759801 0.925406657 0.883180919 0.90935486 0.944744281 1 20.11235711 2.618516052 7.670546277 0.921073461 0.96409957 0.051135345 0.050167038 0.523778249 30.92961418 0.015423855 0.014521418 415.447406 -2.618516052 0.043026109 SHS(ph)GPAGSFNKPAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHSGPAGSFNKPAIR 15 1 Q9UJM3 Q9UJM3 ERRFI1 ERBB receptor feedback inhibitor 1 1 S(0.008)HS(0.992)GPAGSFNKPAIR;S(0.008)HS(0.992)GPAGSFNKPAIR;S(0.002)HS(0.998)GPAGSFNKPAIR 180.78 3.73E-07 542460000 396070 385670 419670 360270 523390 602490 508570 468400 464190 389210 TRUE FALSE 411707.1494 451905.8224 430606.945 431530.3307 434424.3548 462570.8283 468706.9545 462121.8641 447483.8926 465468.2476 0.884501041 0.970862835 0.925104875 0.927088653 0.9333061 0.993775259 1.006957954 0.992810716 0.961362875 1 18.82832323 2.749361757 6.928586617 0.992139648 0.930172408 0.662325029 0.02239597 0.090566797 25.57874816 0.006691609 0.006820237 561.51551 -2.749361757 -0.061967239 SHS(ph)GTSPDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SHSGTSPDNTAPPPPPPRPQPSHSR 25 1 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.058)HS(0.314)GT(0.314)S(0.314)PDNTAPPPPPPRPQPSHSR;S(0.065)HS(0.341)GT(0.297)S(0.297)PDNTAPPPPPPRPQPSHSR;S(0.213)HS(0.531)GT(0.128)S(0.128)PDNTAPPPPPPRPQPSHSR;S(0.049)HS(0.362)GT(0.315)S(0.274)PDNTAPPPPPPRPQPSHSR;S(0.044)HS(0.319)GT(0.319)S(0.319)PDNTAPPPPPPRPQPSHSR 123.89 9.52E-05 3620560000 207660 249974 237565 212654 231379 296707 222070 216110 191178 193065 TRUE FALSE 215858.5771 292905.09 243756.1391 254716.3265 192049.2802 227801.2959 204663.5731 213213.3989 184297.5411 230892.3903 0.934888226 1.268578361 1.055713178 1.10318199 0.831769639 0.986612402 0.886402418 0.923431901 0.798196688 1 17.8168611 3.251666046 24.97884912 0.904728865 1.100812695 0.476746544 0.095317975 177.4986247 338308.9755 0.02444547 0.032903462 1785.114368 -3.251666046 0.19608383 SHS(ph)LSGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SHSLSGAR 8 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 S(0.111)HS(0.889)LSGAR;SHS(0.994)LS(0.006)GAR;S(0.002)HS(0.996)LS(0.002)GAR;S(0.025)HS(0.975)LSGAR 116.12 0.0024477 346750000 214060 348879 323135 347310 377702 468190 329093 315201 324981 383330 TRUE FALSE 222511.2541 408796.2543 331556.1636 416006.8814 313500.349 359459.968 303297.8307 310976.2462 313284.9973 458436.1742 0.485370192 0.891719016 0.723232987 0.907447764 0.68384732 0.784100357 0.661592273 0.678341422 0.683377567 1 18.80636136 -1.594710707 2.684048698 1.022245426 0.727102113 0.344567248 0.114792566 10947006.8 10514346.05 1726502.78 0.027763599 0.025426659 1.594710707 -0.295143313 SHS(ph)LSRPGPTEGDAEGEAEGPVGSTLGSYATLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR 34 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.002)HS(0.99)LS(0.008)RPGPTEGDAEGEAEGPVGSTLGSYATLTR;S(0.167)HS(0.792)LS(0.034)RPGPT(0.007)EGDAEGEAEGPVGSTLGSYATLTR 143.39 1.58E-10 154415000 27065 34329 30945 41977 47049 50950 41709 35338 42640 48103 TRUE FALSE 28133.5471 40224.73871 31751.45212 50279.92531 39051.62779 39117.63465 38439.73959 34864.35191 41105.39473 57527.86186 0.489042113 0.699221862 0.551931727 0.874009979 0.678829814 0.679977204 0.668193434 0.606042894 0.714530202 1 15.81197323 0.95103742 14.76603019 1.000000003 0.660517855 0.534024042 0.095922987 28.42529867 8573.294058 0.08810192 0.022026314 8.933824576 -0.95103742 -0.339482148 SHS(ph)PERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.024)HS(0.976)PERK;S(0.029)HS(0.971)PERK 62.823 0.050923 504570000 421010 248520 327440 250310 440760 432480 424240 326610 382430 262690 TRUE FALSE 437631.7999 291201.3768 335973.3554 299820.5709 365839.7726 332043.0743 390986.9603 322232.3272 368666.419 314159.076 1.393026124 0.92692333 1.06943705 0.954359093 1.164504866 1.056926569 1.244550898 1.025697972 1.173502366 1 18.26113573 SHS(ph)PSASQSGSQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 SHS(0.997)PS(0.003)ASQSGSQLR;SHS(0.997)PS(0.003)ASQSGSQLR;S(0.004)HS(0.996)PSASQSGSQLR;SHS(1)PSASQSGSQLR;S(0.001)HS(0.999)PSASQSGSQLR;SHS(1)PSASQSGSQLR;S(0.036)HS(0.95)PS(0.013)ASQSGSQLR;SHS(0.999)PSASQSGSQLR;S(0.157)HS(0.819)PS(0.023)ASQSGSQLR;S(0.011)HS(0.988)PS(0.001)ASQSGSQLR 300.2 5.19E-44 17164191000 2003334 3568484 3414269 3569791 3872818 4921909 3327242 3720216 3313114 3523915 TRUE FALSE 2082427.173 4181343.368 3503247.655 4275885.005 3214517.78 3778870.227 3066444.078 3670352.59 3193875.674 4214358.675 0.494126707 0.992165995 0.831264713 1.014599215 0.762753725 0.896665547 0.727618201 0.870916045 0.757855684 1 22.00688167 4.751565446 24.4735136 0.862809351 0.494126388 0.561299226 0.100052321 1129.564258 2125652.321 0.022135361 0.40212796 56437.1983 -4.751565446 -0.368682962 SHS(ph)QASLAGPGPVDPSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHSQASLAGPGPVDPSNR 18 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 SHS(1)QASLAGPGPVDPSNR;S(0.084)HS(0.906)QAS(0.01)LAGPGPVDPSNR;S(0.047)HS(0.949)QAS(0.004)LAGPGPVDPSNR 376.21 7.18E-108 3361170000 705760 934140 989850 908720 1081790 1225390 890630 894760 964300 1018450 TRUE FALSE 733623.9498 1094571.278 1015646.304 1088462.104 897907.7222 940811.7435 820820.0934 882767.2057 929595.0314 1217995.778 0.602320602 0.898665905 0.833866851 0.893650145 0.737201014 0.772426112 0.673910459 0.724770333 0.763216957 1 20.2160777 SHS(ph)SPASLQLGTGAGAAGSPAQQHAHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSSPASLQLGTGAGAAGSPAQQHAHLR 28 0 C9JR84;C9J038;Q9GZV5 C9JR84 WWTR1 WW domain-containing transcription regulator protein 1 1 S(0.161)HS(0.815)S(0.024)PASLQLGTGAGAAGSPAQQHAHLR 254.15 2.89E-53 162600000 13772 46202 30633 39616 41623 54676 38432 41682 43117 49488 TRUE FALSE 14315.72919 54136.8341 31431.32115 47451.92656 34547.93733 41978.32762 35419.59942 41123.32097 41565.22759 59184.2261 0.2418842 0.914717276 0.531075985 0.801766445 0.583735559 0.709282361 0.598463505 0.694835832 0.70230246 1 15.8529251 -5 0.196507857 2.549444559 0.592699254 0.32030648 0.165685845 162.3483373 1.601112877 98.61288231 0.369970427 1.00E-05 5 -1.956745305 SHS(ph)VGGPLQNIDFTQRPFHGISTVS(ph)LPNSLQEVVDPLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 2 S(0.154)HS(0.561)VGGPLQNIDFT(0.039)QRPFHGIS(0.136)T(0.15)VS(0.949)LPNS(0.011)LQEVVDPLGK 131.77 1.06E-08 181030000 37088 36663 49234 50698 89618 68472 59582 54156 71119 42739 TRUE FALSE 38552.26288 42959.58505 50517.07849 60725.91308 74384.76437 52570.4157 54911.80715 53430.1274 68559.44108 51112.88876 0.754257171 0.840484388 0.988343248 1.188074369 1.45530347 1.02851584 1.074324079 1.045335701 1.341333717 1 15.64139951 4.095377803 2.418860183 1.156580596 0.779768351 0.533135614 0.137044465 0.234394184 2.721179813 0.03748574 0.106395971 12455.97715 -4.095377803 -0.376812246 SHS(ph)VGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHSVGGPLQNIDFTQRPFHGISTVSLPNSLQEVVDPLGK 39 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.172)HS(0.812)VGGPLQNIDFT(0.005)QRPFHGIS(0.005)T(0.005)VSLPNSLQEVVDPLGK;S(0.221)HS(0.253)VGGPLQNIDFT(0.168)QRPFHGIS(0.168)T(0.168)VS(0.021)LPNSLQEVVDPLGK;S(0.163)HS(0.832)VGGPLQNIDFT(0.005)QRPFHGISTVSLPNSLQEVVDPLGK 175.49 2.74E-19 2086710000 562250 572490 779690 589900 1043470 963800 834790 725290 873750 569630 TRUE FALSE 584448.0642 670810.7041 800009.3619 706580.4593 866101.3421 739972.0565 769356.9785 715568.6739 842303.9082 681238.0923 0.857920411 0.984693475 1.174346196 1.037200455 1.271363642 1.0862165 1.129351085 1.050394395 1.236431018 1 19.37779958 4.48036765 3.222356467 1.122227349 0.86683688 0.515601462 0.082320671 0.183787581 3.710970468 0.018967616 0.08540393 30225.09326 -4.48036765 -0.255390469 SHSAHFFEFLTK ddPTM_MDA-MB-175_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 ; 117.25 0.00043594 914750000 365790 980480 965350 936680 1242520 1246020 1005380 1039060 1009750 1067120 FALSE TRUE 380231.6717 1148869.813 990507.814 1121952.508 1031316.894 956650.7386 926575.6885 1025133.1 973409.2947 1276201.733 0.2979401 0.900225868 0.776137337 0.879134136 0.808114319 0.749607773 0.72604171 0.803268852 0.762739361 1 20.28342497 4.744781884 24.99624076 0.809589306 0.297939872 0.795735055 0.079524702 288.5080954 1159156.191 0.017680065 0.164935556 55562.51355 -4.744781884 -0.511649434 SHSDASVGSHSSTESEHGSS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSDASVGSHSSTESEHGSSSPR 23 0 Q6XZF7;A0A1C7CYY6;A0A1B0GTX1;Q6XZF7-2 Q6XZF7 DNMBP Dynamin-binding protein 1 SHSDASVGSHSSTESEHGS(0.07)S(0.465)S(0.465)PR 210.56 3.32E-32 224040000 0 59250 50823 64118 34375 85434 31591 67222 33871 60066 TRUE FALSE 0 69425.7266 52147.48913 76800.34903 28531.94978 65593.24826 29114.81487 66320.99904 32651.98933 71834.78267 0 0.966463933 0.725936478 1.069124819 0.397188503 0.913112643 0.40530247 0.92324354 0.454542885 1 16.13239495 -5 0.037529785 2.048701057 4.37E-14 0.088685588 0.319460945 2956.66132 8.307927568 393.945168 127.6050407 1.00E-05 5 -2.048701057 SHSDNDRPNCS(ph)WNTQYSSAYYTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSDNDRPNCSWNTQYSSAYYTSR 24 1 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.127)HS(0.167)DNDRPNCS(0.706)WNTQYSSAYYTSR 226.51 3.12E-33 1081100000 115040 142030 162460 143470 173270 211760 146600 157720 141010 134110 TRUE FALSE 119581.868 166422.5477 166693.8411 171847.9378 143817.6273 162581.9493 135109.1089 155606.0214 135935.0776 160386.2868 0.745586611 1.037635767 1.039327267 1.071462787 0.896695286 1.013689839 0.842398135 0.970195298 0.847548006 1 17.29119127 2.262671117 24.98647165 0.916222175 0.975377887 0.059578092 0.098872968 624.9724055 647676.3377 0.033288495 0.027837848 183.0927371 -2.262671117 0.059155712 SHSESASPSALSSS(ph)PNNLS(ph)PTGWSQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSESASPSALSSSPNNLSPTGWSQPK 27 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 2 SHSESASPSALS(0.007)S(0.159)S(0.834)PNNLS(0.996)PT(0.004)GWSQPK 208.3 1.10E-25 143890000 79740 100600 134110 105190 151320 183330 138950 129500 145550 96790 TRUE FALSE 82888.19677 117877.2674 137605.0168 125996.268 125598.6805 140754.3859 128058.7359 127764.2643 140311.6839 115754.1473 0.716071075 1.018341633 1.188769646 1.088481674 1.085046915 1.215977044 1.106299332 1.103755392 1.212152542 1 16.82070436 4.689930622 2.812200272 1.126788057 0.663925998 0.789806362 0.063421403 0.14339225 1.674777321 0.014430797 0.14393243 48970.05838 -4.689930622 -0.46286206 SHSGTS(ph)PDNTAPPPPPPRPQPSHSR ddPTM_MDA-MB-175_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(0.243)HS(0.243)GT(0.243)S(0.272)PDNTAPPPPPPRPQPSHSR 58.418 0.052252 30241000 4795 5933.2 5235.1 4583.3 4931.7 7214.4 6875.3 4827.8 6243.7 6278.6 TRUE FALSE 4984.310303 6952.180946 5371.531007 5489.86306 4093.411396 5538.964935 6336.396021 4763.091238 6018.990457 7508.771459 0.663798376 0.925874623 0.715367492 0.731126668 0.545150617 0.737665937 0.843865878 0.634336957 0.801594574 1 12.87436117 0.981155515 22.38088634 1.000000006 0.726469999 0.411507181 0.099552621 314.6132182 373656.0926 0.09438924 0.02359731 9.575368921 -0.981155515 -0.273530007 SHSLSRPGPT(ph)EGDAEGEAEGPVGSTLGSYATLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHSLSRPGPTEGDAEGEAEGPVGSTLGSYATLTR 34 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.124)HS(0.124)LS(0.124)RPGPT(0.627)EGDAEGEAEGPVGSTLGSYATLTR;S(0.259)HS(0.214)LS(0.214)RPGPT(0.313)EGDAEGEAEGPVGSTLGSYATLTR;S(0.215)HS(0.215)LS(0.215)RPGPT(0.354)EGDAEGEAEGPVGSTLGSYATLTR 270.39 1.78E-73 579360000 196030 245716 231943 241111 308435 337414 229843 238328 247481 293625 TRUE FALSE 203769.4158 287915.8116 237987.6251 288802.0362 256007.3289 259054.7121 211827.3051 235133.603 238574.2072 351155.197 0.58028307 0.819910439 0.67772776 0.822434179 0.729043258 0.737721424 0.603229874 0.669600237 0.679398195 1 18.42174926 -1.112719582 4.456970604 1.000026524 0.703436883 0.582782449 0.075597357 2.41E-05 4.80E-06 0.071412461 0.016830212 0.077140139 1.112719582 -0.296589641 SHSPSASQSGSQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 0 ; 216.54 6.09E-12 158100000 18864 51342 43848 47512 48387 64323 39855 48184 38455 54888 FALSE TRUE 19608.76529 60159.58911 44990.7149 56909.73179 40162.19502 49384.95807 36731.06096 47538.17229 37071.01206 65642.25271 0.298721699 0.916476608 0.68539261 0.866967989 0.611834502 0.752334907 0.559564297 0.724200806 0.564743142 1 16.00233713 -1.464998348 3.595494711 1.003831642 0.678432354 0.265475687 0.165977662 17522849.68 14294457.01 488710.727 0.034968371 0.034276909 1.464998348 -0.325399287 SHSS(ph)PSQIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSSPSQIPK 10 0 Q9H792;H0YN99 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 S(0.001)HS(0.047)S(0.864)PS(0.088)QIPK 75.819 0.025856 0 101060 96653 103320 91343 129870 158600 122050 110320 113510 97326 TRUE FALSE 105049.9268 113252.4009 106012.6041 109410.3728 107794.7438 121767.5536 112483.4021 108841.3408 109424.7973 116395.1663 0.902528259 0.972999176 0.910799026 0.939990691 0.92611014 1.046156447 0.966392383 0.935101897 0.940114618 1 16.82867162 SHSS(ph)SPQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 S(0.003)HS(0.012)S(0.462)S(0.454)PQS(0.07)VLWNRPQPSEDRLPSQQGLAEAR 118.31 1.58E-05 164940000 5238.7 82237 74546 96028 58701 106680 55916 83090 59780 82543 TRUE FALSE 5445.527921 96360.56503 76488.73 115022.0518 48723.02499 81905.18675 51533.15781 81976.31446 57628.52948 98715.72047 0.055163736 0.976142043 0.774838391 1.165184747 0.493569056 0.829707633 0.522035979 0.830428164 0.583782696 1 16.59099223 -5 0.030244223 1.975701845 1.00E-13 0.083190956 0.290481949 5212.881743 11.86891491 606.5772368 244.1542806 1.00E-05 5 -1.975701845 SHSSS(ph)PQSVLWNRPQPSEDRLPSQQGLAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHSSSPQSVLWNRPQPSEDRLPSQQGLAEAR 31 2 Q8NCE2;Q8NCE2-2 Q8NCE2 MTMR14 Myotubularin-related protein 14 1 SHS(0.039)S(0.243)S(0.685)PQS(0.032)VLWNRPQPSEDRLPSQQGLAEAR 96.027 0.00019225 196320000 5496.7 33596 28504 34626 28480 42312 26002 35198 26904 36963 TRUE FALSE 5713.71396 39365.85166 29246.83766 41474.91945 23638.97977 32485.67924 23963.8953 34726.22838 25935.7303 44205.19215 0.129254363 0.890525518 0.66161544 0.93823638 0.534755729 0.734883792 0.542105896 0.785568995 0.586712308 1 15.43192821 -5 0.262958331 3.171649014 0.638833428 0.194458315 0.216157852 334.8569709 3.279787884 394.1290908 0.258088433 1.00E-05 5 -2.532815586 SHSVPRS(ph)PSQGSYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHSVPRSPSQGSYSR 15 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SHSVPRS(0.997)PS(0.003)QGSYSR;SHS(0.001)VPRS(0.964)PS(0.031)QGS(0.003)YS(0.001)R 91.441 0.0033983 737490000 44113 82565 75687 40149 86128 101818 36988 66418 61869 123967 TRUE FALSE 45854.6153 96744.89648 77659.4654 48090.35237 71487.99332 78172.31257 34088.78391 65527.77535 59642.34678 148255.9602 0.309293571 0.652553168 0.523820191 0.324373822 0.482193048 0.527279392 0.229931963 0.441990833 0.40229308 1 17.17773058 -1.482418342 3.542745119 1.008293722 0.434480051 0.678673083 0.117112409 380062152.7 524829384.3 30900028.39 0.027689001 0.032929236 1.482418342 -0.57381367 SHTCFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHTCFNR 7 0 O00308-2;O00308;O00308-3;A0A590UJQ1;Q96J02-3;Q96J02-2;Q96J02;A0A590UK44;A0A590UJW8;Q9H0M0-3;Q9H0M0;Q9H0M0-6 O00308-2;A0A590UJQ1;Q9H0M0-3 WWP2;ITCH;WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP2;E3 ubiquitin-protein ligase Itchy homolog;NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ; 84.244 0.021688 73932000 114035 171318 160487 167328 203880 209666 149264 174914 160027 218425 FALSE TRUE 118537.1899 200740.5338 164669.4231 200424.979 169224.5504 160974.249 137564.2977 172569.5639 154267.6595 261221.1968 0.4537809 0.768469544 0.630383082 0.767261545 0.647820899 0.616237315 0.526619966 0.66062619 0.590563329 1 17.99491244 -1.353853352 2.995379612 1.004232394 0.634915446 0.597934667 0.091133936 15292930.83 18983015.75 566382.2166 0.022419612 0.044273785 1.353853352 -0.369316948 SHTEEDCTEELFDFLHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SHTEEDCTEELFDFLHAR 18 0 P07919 P07919 UQCRH "Cytochrome b-c1 complex subunit 6, mitochondrial" 0 ;;;;; 374.11 5.26E-108 464284000 147880 197917 162085 218454 162374 277901 161154 145387 147477 231574 FALSE TRUE 153718.4166 231907.7052 166309.0683 261663.5492 134773.7255 213362.7044 148522.3284 143438.3251 142169.3316 276946.4915 0.555047351 0.837373689 0.600509749 0.944816263 0.486641751 0.770411292 0.536285286 0.517927937 0.513345848 1 18.07924774 -1.571678521 6.175618842 1.000815866 0.639613278 0.343213698 0.149289783 0.001638478 0.00011364 0.141229595 0.033217432 0.026811523 1.571678521 -0.361202587 SHTLEFQSLEDLIMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SHTLEFQSLEDLIMEK 16 0 Q96KN1 Q96KN1 FAM84B Protein FAM84B 0 ; 152.71 5.21E-07 151326000 167618 157602 181697 170086 225983 227124 218835 207458 202436 123161 FALSE TRUE 174235.6881 184668.9175 186432.1731 203728.5031 187570.4904 174377.8931 201682.1409 204677.3648 195150.3679 147292.0399 1.182926709 1.253760337 1.26573149 1.383160307 1.273459791 1.183892172 1.369267077 1.389602351 1.324921347 1 17.16831994 -1.954733802 2.77118433 0.775930806 1.299113204 0.596937197 0.071724706 20521507.04 15619832.98 29696880.94 0.018664594 0.011098549 1.954733802 0.523182397 SHTPSPTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SHTPSPTSPK 10 0 P40123;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;B7Z385 P40123 CAP2 Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 1 SHTPSPT(0.007)S(0.992)PK;SHTPS(0.001)PT(0.17)S(0.828)PK;SHTPSPT(0.004)S(0.996)PK 112.08 0.0010742 714090000 853700 469590 619690 484140 865780 1127600 859970 645090 711530 429140 TRUE FALSE 887404.7352 550238.4296 635839.6305 579901.447 718615.0248 865731.9889 792563.3043 636443.6237 685922.1743 513221.7666 1.729086319 1.072126058 1.238917894 1.129923719 1.400203716 1.686857505 1.544290121 1.24009476 1.3365025 1 18.96922283 0.605009565 1.439713283 1.001028374 1.372512252 0.227256845 0.209634297 2.493006898 7.07951167 0.204781412 0.059884454 4.027259037 -0.605009565 0.371483878 SHVAGQMLHGGGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHVAGQMLHGGGSR 14 0 P43155-2;P43155 P43155-2 CRAT Carnitine O-acetyltransferase 0 60.55 0.053232 123620000 125410 99959 126050 95386 167150 154170 130390 108070 126500 133690 FALSE TRUE 130361.2836 117126.1807 129334.9666 114253.0661 138737.9027 118366.354 120169.6911 106621.4984 121947.2897 159883.9959 0.815349172 0.732569761 0.808930036 0.714599766 0.867741027 0.740326468 0.751605503 0.666867862 0.762723555 1 17.28666601 0.930970435 22.74231728 1 0.7563364 0.633557836 0.054082998 12308.14334 4055015.67 0.052915167 0.013228792 8.530420404 -0.930970435 -0.2436636 SHVEDGDIAGAPAS(ph)SPEAPPAEQDPVQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.543)S(0.457)PEAPPAEQDPVQLK 90.907 0.0010013 729200000 45377 47103 54266 36313 69226 64398 59533 52416 46172 35897 TRUE FALSE 47168.519 55192.57384 55680.21654 43495.60302 57458.98925 49442.54046 54866.6479 51713.44926 44510.27874 42930.32986 1.098722492 1.285631255 1.296990187 1.013167221 1.338424127 1.151692536 1.278039281 1.204590075 1.036802626 1 15.38970964 1.207282342 4.433914965 1.005868285 1.213737592 0.394682026 0.094453517 0.183324562 7.58653941 0.078637918 0.021580017 16.11693084 -1.207282342 0.207869307 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 1 SHVEDGDIAGAPAS(0.026)S(0.974)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.03)S(0.97)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.142)S(0.858)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.151)S(0.849)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.031)S(0.969)PEAPPAEQDPVQLK 246.81 5.80E-46 3063590000 2312820 1929090 2329220 1919800 2743220 2893120 2577620 2192460 2441190 1851770 TRUE FALSE 2404131.919 2260396.201 2389921.387 2299530.71 2276928.444 2221236.726 2375579.409 2163073.66 2353332.049 2214588.877 1.085588366 1.020684347 1.079171584 1.038355576 1.028149499 1.003001843 1.072695449 0.976738248 1.062649629 1 21.07860747 3.417886105 3.21964977 1.021930195 1.057986763 0.221254 0.03129108 0.365175134 7.700247083 0.008363843 0.012119515 2617.496473 -3.417886105 0.036056568 SHVSSEPYEPIS(ph)PPQVPVVHEK ddPTM_MDA-MB-175_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 203.47 2.15E-22 1202690000 195665 698590 765550 697750 856440 1035480 727490 863360 812450 702590 TRUE FALSE 203390.0053 818567.3982 785500.8619 835762.8674 710862.6347 795005.4629 670467.4329 851788.0714 783210.0832 840249.0586 0.242059189 0.97419615 0.934842894 0.994660879 0.8460142 0.946154542 0.797938928 1.013732848 0.932116585 1 19.6804575 4.740556625 24.99654032 0.934467188 0.242058953 0.91130216 0.065104099 44.73483999 560186.1992 0.014749801 0.096520009 55024.56595 -4.740556625 -0.692408235 SICEVLDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SICEVLDLER 10 0 H0Y993;A0A494C028;P35659;B4DFG0;P35659-2;H0Y8X0;D6RDA2 H0Y993 DEK Protein DEK 0 ; 132.88 0.00049334 101477000 125162 190781 149717 142757 199302 218890 182315 181120 165334 193861 FALSE TRUE 130103.4924 223546.1527 153618.748 170993.9085 165424.7172 168056.1148 168024.6739 178692.3827 159383.6616 231844.3513 0.561167403 0.96420789 0.66259431 0.737537523 0.713516272 0.724866118 0.724730506 0.770742879 0.687459758 1 17.82279705 -2.032565991 2.6264892 1.322787683 0.73492064 0.418524418 0.096020635 17833811.35 6737575.602 34657747.45 0.021906689 0.009277565 2.032565991 -0.587867043 SIDQFANLVLHQTVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIDQFANLVLHQTVER 16 0 O15116 O15116 LSM1 U6 snRNA-associated Sm-like protein LSm1 0 ; 237.89 8.96E-20 397010000 153695 233640 219990 251810 265060 286640 235100 256500 238810 276950 FALSE TRUE 159762.9973 273765.8525 225723.1201 301617.2664 220005.1959 220072.2041 216672.2477 253062.037 230215.2747 331213.05 0.482357194 0.826555151 0.681504307 0.910644271 0.664240723 0.664443035 0.65417787 0.764046094 0.695067041 1 18.33739999 -1.357917894 0.896740178 1.076303481 0.71256286 0.398990257 0.108285071 212.5754282 58.13138214 40.04736969 0.03204036 0.043861361 1.357917894 -0.36374062 SIDRPFIDPQRYEEEQLSWL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIDRPFIDPQRYEEEQLSWL 20 2 Q9P253 Q9P253 VPS18 Vacuolar protein sorting-associated protein 18 homolog 0 ; 70.555 0.07341 68809000 50216 59849 49630 50190 70304 70778 44344 52983 57118 65047 FALSE TRUE 52198.56646 70127.60019 50923.39857 60117.4322 58353.75119 54340.88215 40868.20141 52272.84955 55062.33434 77791.71425 0.671004193 0.901479044 0.654612115 0.772799941 0.750128105 0.698543318 0.525354169 0.67195909 0.70781747 1 16.24732888 0.909960974 19.46859198 1 0.702674985 0.485421238 0.09077921 6572.636012 1421166.628 0.090506973 0.022626743 8.127574779 -0.909960974 -0.297325015 SIEAVHEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIEAVHEDIR 10 0 P23919-2;P23919;H7C312;H7BZ20 P23919-2 DTYMK Thymidylate kinase 0 ; 140.07 3.99E-05 726950000 734280 868310 842640 851060 948600 1090520 895610 853670 820350 909510 FALSE TRUE 763269.9414 1017435.488 864599.8906 1019397.128 787357.3108 837263.257 825409.748 842227.95 790825.7637 1087711.071 0.701721222 0.935391314 0.794880105 0.937194771 0.723866229 0.769747849 0.758850186 0.774312198 0.727054992 1 20.05286395 5.023851659 16.06567227 0.811132444 0.437328934 0.119918596 0.093676747 11672685.46 204436297.2 0.021187755 111197171.1 105645.6596 -5.023851659 -0.37380351 SIEIPRPVDGVEVPGCGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIEIPRPVDGVEVPGCGK 18 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 113.54 0.0002225 326130000 422190 361830 444390 367960 567380 540660 591030 479360 547460 454140 FALSE TRUE 438858.3872 423971.4879 455971.1685 440741.3897 470936.9503 415099.9088 544703.5242 472934.9633 527757.0215 543120.038 0.808032031 0.780622069 0.839540316 0.811499041 0.867095517 0.764287597 1.002915536 0.870774286 0.971713405 1 19.05091157 1.884869709 0.592937954 0.998623921 0.799900342 0.615101219 0.052733356 0.489514779 0.357414456 0.046200494 0.028246317 76.71313099 -1.884869709 -0.198723579 SIFDHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIFDHIK 7 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 0 81.784 0.026263 255040000 186680 192950 190570 176300 363370 303990 255040 241970 228780 270420 FALSE TRUE 194050.2705 226087.6616 195536.4108 211171.6138 301604.4972 233392.9295 235049.2984 238726.7879 220546.2525 323403.6215 0.600025039 0.699088218 0.60462035 0.652966138 0.932594681 0.72167692 0.726798597 0.738169804 0.681953565 1 18.30297631 -5 0.153737833 2.003163525 0.627718187 0.523820249 0.086068623 113.907743 1.027952624 35.19619752 0.419160347 1.00E-05 5 -1.375445338 SIFGEDALANVSIEKPIHQGPDAAVTGHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIFGEDALANVSIEKPIHQGPDAAVTGHIR 30 1 P53618 P53618 COPB1 Coatomer subunit beta 0 84.035 0.00092404 602470000 155380 144790 187750 164200 201380 242520 166990 194600 187900 138680 FALSE TRUE 161514.5224 169656.5562 192642.9192 196678.2699 167149.4995 186198.4054 153900.8875 191991.7053 181137.5157 165851.6908 0.973849115 1.022941372 1.161537264 1.185868344 1.007825116 1.122680176 0.927942831 1.157610781 1.092165626 1 17.33953419 -1.462420399 5.830409124 0.999944062 1.07622376 0.063133834 0.082656946 5.87E-05 5.41E-06 0.078090074 0.018392517 0.03448098 1.462420399 0.076279697 SIFQHIQSAQSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIFQHIQSAQSQR 13 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 105.14 0.0014764 809420000 474810 427630 469090 390720 718300 632940 499760 522750 524460 453940 FALSE TRUE 493555.8654 501072.126 481314.8708 468003.2498 596203.6226 485949.2773 460587.5053 515743.3913 505584.787 542880.8518 0.909142151 0.92298729 0.886593935 0.862073599 1.098221867 0.895130627 0.848413614 0.950012124 0.931299723 1 19.05027607 -4.999999948 0.306390319 1.669616214 0.918972716 0.113125999 0.065553343 675.7609785 6.169642302 291.4821703 0.06286254 1.00E-05 4.999999948 -0.750643497 SIGEAIQYLHSINIAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIGEAIQYLHSINIAHR 17 0 P49137-2;P49137 P49137-2 MAPKAPK2 MAP kinase-activated protein kinase 2 0 ; 246.95 6.12E-21 239000000 187720 239110 236660 224660 267270 292150 223050 240100 239610 270150 FALSE TRUE 195131.3306 280175.2825 242827.554 269097.0775 221839.5409 224302.5901 205566.7582 236881.8522 230986.4829 323080.7202 0.603970829 0.867199016 0.751600262 0.832909736 0.686638128 0.694261762 0.636270583 0.733197116 0.714949759 1 18.30153513 -1.785142786 8.364373746 1.004350411 0.727305532 0.541561713 0.075989857 0.006063946 0.000155766 0.072372878 0.016908421 0.016400505 1.785142786 -0.277044879 SIGS(ph)PESTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIGSPESTPK 10 0 Q8NEY1-5;Q8NEY1-3;Q8NEY1;Q8NEY1-2;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;H0Y6F6;Q8NEY1-6 Q8NEY1-5 NAV1 Neuron navigator 1 1 SIGS(1)PESTPK;SIGS(1)PESTPK;SIGS(1)PESTPK 160.62 0.00016404 383660000 1583090 1182060 1387160 1163360 1809300 1819960 1681270 1394100 1472160 999820 TRUE FALSE 1645591.616 1385069.61 1423310.529 1393469.136 1501755.832 1397301.872 1549487.664 1375414.37 1419177.249 1195715.586 1.376239998 1.158360421 1.190342039 1.165385106 1.255947359 1.168590497 1.29586641 1.150285558 1.186885297 1 20.18944284 -4.865837824 0.217350595 1.27E-16 1.240373808 0.508126601 0.066447735 114.619365 1.209181487 50.01409534 0.123220626 1.36E-05 4.865837824 1.240373808 SIGTANRPMGAGEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 92.307 0.0043921 271290000 315590 299790 334480 291220 397390 410620 385800 346240 347070 278980 FALSE TRUE 328049.7369 351276.6005 343196.8236 348822.4468 329841.7897 315259.728 355559.9879 341599.2191 334579.0185 333640.7896 0.983242299 1.052858677 1.028641684 1.045503001 0.988613503 0.944907631 1.065696998 1.023853287 1.002812093 1 18.34793615 1.193095037 8.660641354 1.001188173 1.018580899 0.028220483 0.034390352 1.349624503 229.559283 0.032748277 0.008311083 15.59893818 -1.193095037 0.017392727 SIGVSNFNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SIGVSNFNHR 10 0 S4R3P0;P52895;B4DK69 S4R3P0 AKR1C2 Aldo-keto reductase family 1 member C2 0 ;;; 150.04 2.23E-05 919450000 1029320 1276280 1156160 1152690 1872240 1848970 1424110 1476710 1384490 1537080 FALSE TRUE 1069958.348 1495471.162 1186290.479 1380688.642 1553997.314 1419574.739 1312484.537 1456917.118 1334662.475 1838241.397 0.582055409 0.813533611 0.645339878 0.751092127 0.845371732 0.772246094 0.713989218 0.792560281 0.726053976 1 20.8098948 -5 0.185814643 2.058720278 0.694824136 0.556587006 0.072010607 100.3082795 0.975612707 39.37614926 0.196715719 1.00E-05 5 -1.363896141 SIIDEFLHINDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIIDEFLHINDFK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 0 82.34 0.012616 71344000 109760 93092 130170 95280 149960 154010 131260 111820 130590 97076 FALSE TRUE 114093.4096 109079.8268 133562.3371 114126.0996 124469.8528 118243.5115 120971.4982 110321.2358 125890.0914 116096.1836 0.982749011 0.939564278 1.150445545 0.983030588 1.072126998 1.018496112 1.041993755 0.950257213 1.084360291 1 16.82496102 SIIECVDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SIIECVDDFR 10 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;;; 200.05 6.22E-07 310240000 419736 527680 465352 567065 532058 644323 491506 524984 475640 526166 FALSE TRUE 436307.5014 618304.9352 477479.4554 679228.7645 441618.9712 494688.7481 452980.4754 517947.4482 458521.8093 629258.1536 0.693368054 0.982593442 0.758797407 1.07941194 0.701808898 0.786145949 0.719864292 0.823108044 0.72867043 1 19.26329248 SIIPLPHPVRPEDIE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIIPLPHPVRPEDIE 15 1 P61599;A8MZB2 P61599 NAA20 N-alpha-acetyltransferase 20 0 106.19 0.0011455 99209000 112800 134410 131250 130810 142260 151020 117480 134420 135510 135740 FALSE TRUE 117253.4311 157493.8719 134670.4828 156683.8276 118078.696 115947.8937 108271.6106 132618.3198 130633.0216 162335.6541 0.722290071 0.970174253 0.829580437 0.965184318 0.727373766 0.714247861 0.666961372 0.816938956 0.804709368 1 17.30862037 5.038418474 16.9436456 0.81825436 0.292732478 0.070407347 0.109535028 18422889.72 211963159.9 0.026429516 300696207 109249.2523 -5.038418474 -0.525521881 SIITVEELTEIERLEDLDT(ph)CMMTPK ddPTM_MDA-MB-175_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 68.762 0.02238 25830000 58902 41523 48078 34459 78927 75312 36149 44959 48923 52328 TRUE FALSE 61227.49644 48654.25225 49330.95218 41274.88735 65511.01673 57821.92936 33315.54692 44356.39814 47162.27079 62580.66972 0.978377137 0.77746455 0.788277792 0.65954691 1.046825114 0.923958303 0.532361623 0.708787527 0.753623619 1 15.93342948 2.279031103 24.99997991 0.715889456 0.854339255 0.106329283 0.148787331 269.9155672 166734.8576 0.051006388 0.042674546 190.1214433 -2.279031103 0.138449799 SIITVEELTEIERLEDLDTCMMT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIITVEELTEIERLEDLDTCMMTPK 25 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SIITVEELTEIERLEDLDT(0.036)CMMT(0.964)PK 100.24 0.010205 21413000 18920 12166 15922 11276 29551 26644 12037 16259 14865 17917 TRUE FALSE 19666.97621 14255.41586 16336.9404 13506.35914 24527.93158 20456.33479 11093.50849 16041.0747 14330.01155 21427.49311 0.91783841 0.665286218 0.762428919 0.630328479 1.14469441 0.954676998 0.517723115 0.748621158 0.668767526 1 14.38717545 -1.318779074 3.353246733 1.001165651 0.77324023 0.126830554 0.173438896 71572219.47 101318301.7 837840.8619 0.042426301 0.047997755 1.318779074 -0.227925421 SIKDTICNQDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIKDTICNQDER 12 1 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0;H0YHL7 Q9ULV4 CORO1C Coronin-1C;Coronin 0 ;; 128.22 0.0002216 647820000 906070 897930 1000500 829670 1276470 1273650 1058070 975770 1131300 983270 FALSE TRUE 941842.3432 1052142.493 1026573.852 993776.2497 1059496.085 977864.0899 975135.7086 962691.3992 1090584.734 1175922.931 0.800938836 0.894737627 0.872994161 0.845103215 0.900991092 0.83157158 0.829251376 0.818668787 0.92742875 1 20.16536208 1.01062055 4.448599572 0.999615903 0.850410705 0.714149774 0.030663813 0.086696782 4.81644119 0.029917937 0.007611249 10.2475619 -1.01062055 -0.149205198 SILKPSTPIPPQEGEEVGES(ph)SEEQDNAPK ddPTM_MDA-MB-175_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(0.75)S(0.25)EEQDNAPK 242.83 9.99E-46 186740000 397180 179040 284390 186080 427850 380320 377760 307370 356490 187520 TRUE FALSE 412860.9731 209788.7273 291801.437 222886.0686 355124.2098 291996.4438 348150.1841 303250.2079 343659.9945 224260.9537 1.840984649 0.935467025 1.301169161 0.993869262 1.583531167 1.302038714 1.552433352 1.352220272 1.532411188 1 17.77481893 3.220483228 24.99734548 1.408142817 1.246507442 0.037300127 0.276577815 642.2806567 888141.2391 0.073708229 0.088259155 1661.434513 -3.220483228 -0.161635375 SILKPSTPIPPQEGEEVGESS(ph)EEQDNAPK ddPTM_MDA-MB-175_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(0.432)S(0.568)EEQDNAPK 154.08 1.17E-08 254080000 364030 185910 277440 199850 401700 337590 349620 276000 340830 184050 TRUE FALSE 378402.1855 217838.5963 284670.3143 239379.7335 333419.1775 259189.8387 322215.8708 272300.6714 328563.5949 220111.0736 1.719141973 0.98967577 1.293303011 1.08754062 1.514776935 1.177541113 1.463878511 1.237105735 1.492717242 1 17.7478722 -0.944316039 5.453605917 0.999999452 1.313290619 0.178444762 0.209881844 1.25E-06 2.41E-07 0.181203361 0.042709967 0.113679973 0.944316039 0.313291167 SILS(ph)PGGSCGPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SILSPGGSCGPIK 13 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;P78347-5 A0A494C1K3 GTF2I General transcription factor II-I 1 SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK;SILS(1)PGGSCGPIK 246.25 3.80E-17 1469750000 2024430 1457080 1728420 1440440 2280810 2344220 2093000 1775690 1981740 1919880 TRUE FALSE 2104356.06 1707322.155 1773464.045 1725354.733 1893118.731 1799810.432 1928945.191 1751889.78 1910417.565 2296043.728 0.91651393 0.743593049 0.772399943 0.751446809 0.824513361 0.783874632 0.840116923 0.763003665 0.832047553 1 21.13071869 0.913570916 7.716887813 0.99999968 0.795901256 0.600223628 0.048798817 1.447226761 129.2137222 0.043343553 0.010858195 8.195414346 -0.913570916 -0.204098424 SILYDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SILYDER 7 0 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 ;;;;; 138.9 0.0063773 3121740000 4280580 5033460 4839980 4890830 5722350 6311030 5106240 5265080 4816240 5286220 FALSE TRUE 4449580.604 5897917.6 4966113.855 5858221.576 4749666.991 4845388.927 4705999.566 5194510.215 4642904.463 6321953.598 0.70383 0.93292643 0.785534689 0.926647354 0.751297351 0.766438547 0.744390083 0.821662186 0.734409766 1 22.59193902 5.019246151 13.3967468 0.817428992 0.498144666 0.140617338 0.088789609 360624.0493 6404954.784 0.019661863 2229719.669 104531.2517 -5.019246151 -0.319284326 SINHQIES(ph)PSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.997)PS(0.003)ER;SINHQIES(0.968)PS(0.032)ER;SINHQIES(1)PSER;SINHQIES(0.984)PS(0.016)ER;SINHQIES(0.996)PS(0.004)ER 294.18 3.43E-36 6306320000 1062445 2772850 2485140 2741810 2643040 3100020 2145850 2681400 2455140 2690040 TRUE FALSE 1104391.149 3249065.418 2549904.79 3284131.835 2193777.005 2380087.336 1977652.67 2645460.219 2366779.991 3217101.834 0.343287594 1.009935521 0.792609287 1.020835523 0.681910961 0.739823437 0.614731137 0.822311619 0.735686998 1 21.61733017 -1.180903778 3.655884356 1.000225122 0.764066298 0.138193432 0.183871596 40478996.13 83133217 118515.8515 0.041091103 0.065931996 1.180903778 -0.236158824 SINKLDS(ph)PDPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SINKLDSPDPFK 12 1 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 SINKLDS(1)PDPFK 124.09 0.0001993 105140000 461650 154340 239260 174470 369630 399760 401040 267630 269770 97170 TRUE FALSE 479876.2985 180846.6944 245495.3122 208979.6453 306800.4246 306921.7984 369605.4369 264042.8576 260061.0304 116208.6011 4.129438734 1.556224692 2.112539949 1.798314783 2.640083624 2.641128071 3.180534259 2.272145566 2.237881086 1 16.82635733 -0.128122194 15.75057389 0.999999767 2.469564686 0.296434456 0.694554169 0 0 0.634070326 0.149451809 0.744522463 0.128122194 1.46956492 SINNAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SINNAEK 7 0 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 114.89 0.013499 58147000 72788 56374 64628 56040 73859 80861 74519 68391 65930 52788 FALSE TRUE 75661.72644 66055.79597 66312.25877 67124.54474 61304.47356 62082.25821 68678.00606 67474.33051 63557.19218 63130.79791 1.198491528 1.046332347 1.050394751 1.063261466 0.971070786 0.983390996 1.087868494 1.068802118 1.00675414 1 15.94605637 4.754960644 3.559721996 1.03430483 1.220813148 0.64881125 0.03701224 0.215857431 4.732588043 0.009660932 0.109880745 56880.13832 -4.754960644 0.186508318 SINNAEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SINNAEKR 8 1 P62244;I3L3P7;I3L246;H3BN98;H3BV27;H3BT37;I3L303 P62244 RPS15A 40S ribosomal protein S15a 0 ; 132.01 0.0015722 657350000 308240 349870 299260 257294 644220 494300 387200 410970 454640 555740 FALSE TRUE 320409.5532 409957.4509 307058.9614 308185.9853 534715.7145 379506.3162 356850.2522 405461.6194 438277.5952 664626.6127 0.482089563 0.616823707 0.462002206 0.463697931 0.804535516 0.571006801 0.536918392 0.61005926 0.659434315 1 19.34218454 -4.999999995 0.210915223 3.056073155 0.517463501 0.670077706 0.092229865 87.92153001 0.876935867 76.32853718 0.195170349 1.00E-05 4.999999995 -2.538609655 SINPLGGFVHYGEVTNDFVMLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SINPLGGFVHYGEVTNDFVMLK 22 0 P39023;G5E9G0 P39023 RPL3 60S ribosomal protein L3 0 ;; 241.71 1.12E-30 2173720000 1773039 1866993 2147270 1909152 2311060 2619090 2458670 2336620 2203171 1718149 FALSE TRUE 1843039.949 2187634.525 2203229.62 2286776.567 1918226.847 2010846.04 2265953.021 2305301.431 2123879.306 2054787.401 0.896949216 1.064652491 1.072242131 1.112901786 0.9335403 0.978615131 1.102767625 1.12191725 1.033624844 1 20.9705577 2.229876657 24.99938222 1.080793296 1.016365447 0.108766052 0.069458558 359.5806199 1035152.145 0.026431177 0.019824876 169.7761407 -2.229876657 -0.064427849 SIPLDEGEDEAQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIPLDEGEDEAQRR 14 1 Q14204;A0A2R8YFZ7;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 170.95 4.96E-06 1246130000 539023 690046 731643 728814 722052 831262 629392 653584 641818 709874 FALSE TRUE 560304.0443 808556.0327 750710.2176 872971.2339 599317.859 638213.9984 580058.6104 644823.7755 618719.0956 848960.2189 0.659988574 0.952407445 0.884270194 1.028282851 0.705943395 0.751759604 0.683257705 0.759545337 0.728796334 1 19.69533743 3.2077836 24.99821766 0.752882556 0.886537717 0.155813819 0.120209809 283.8426883 230546.5949 0.032646721 0.039024369 1613.554354 -3.2077836 0.133655161 SIPTDNQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIPTDNQIK 9 0 P15559-2;P15559;B4DLR8;P15559-3;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ; 134.26 0.0028239 103930000 492370 321290 409210 326110 510550 519690 511370 416720 419320 248960 FALSE TRUE 511809.1478 376469.0582 419874.3488 390613.5847 423766.8934 398999.8735 471287.4832 411134.55 404228.7551 297738.9454 1.718986232 1.264426653 1.4102097 1.311933124 1.423283383 1.340099707 1.582888267 1.380855801 1.357661674 1 18.18368842 0.672711048 2.065545018 1.000168324 1.421742361 0.507423602 0.126200936 1.268481734 6.962615332 0.111330292 0.03055733 4.706640717 -0.672711048 0.421574037 SIQEIQELDKDDESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SIQEIQELDKDDESLR 16 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;;;;; 293.2 1.25E-45 15389910000 11322681 6814016 9093888 6816650 11872293 11485491 11300648 9036448 10050517 6317742 FALSE TRUE 11769709.19 7984270.242 9330882.192 8164963.024 9854244.877 8818159.78 10414873.68 8915329.195 9688800.856 7555582.584 1.557750055 1.056737869 1.234965284 1.080653005 1.304233627 1.167105207 1.378434233 1.179965819 1.282336702 1 22.84911157 -1.331304847 3.175566438 0.99820696 1.238550175 0.220222081 0.139364372 131039390.7 197465195.9 2265760.844 0.030217808 0.046633193 1.331304847 0.240343215 SIQEIQELDKDDESLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SIQEIQELDKDDESLRK 17 2 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;; 302.18 1.03E-46 9459580000 7382950 3174820 5021200 3301892 7009770 6250300 6391050 4525030 5772360 2501496 FALSE TRUE 7674434.567 3720070.638 5152056.597 3954996.382 5818251.799 4798762.549 5890102.801 4464379.374 5564613.891 2991616.247 2.565313841 1.243498608 1.722164934 1.322026642 1.94485232 1.604070226 1.968869773 1.492296807 1.860069418 1 21.51249369 -1.504658376 3.15452107 0.980472832 1.713615198 0.274497303 0.360675915 121397733.3 155625039.8 20694530.71 0.076950932 0.031285394 1.504658376 0.733142366 SIQFVDWCPTGFK ddPTM_MDA-MB-175_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 0 229.97 1.14E-11 351680000 1064300 841500 1131100 919390 1270600 1285600 1240000 1071600 1155200 891180 FALSE TRUE 1106319.386 986021.079 1160577.395 1101242.598 1054623.866 987038.8835 1142805.56 1057236.955 1113624.578 1065789.658 1.038027886 0.92515542 1.088936627 1.033264481 0.989523456 0.926110397 1.072261821 0.991975243 1.044882139 1 20.02349131 SIRDS(ph)GYIDCWDSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIRDSGYIDCWDSER 15 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 SIRDS(1)GYIDCWDSER 208.87 1.62E-09 86948000 54586 63515 60244 61216 71451 81630 52259 57433 64976 94082 TRUE FALSE 56741.09743 74423.20717 61814.00813 73324.34209 59305.78454 62672.66961 48162.80303 56663.20458 62637.52645 112515.5666 0.504295531 0.661448095 0.549381832 0.651681757 0.527089596 0.557013323 0.428054575 0.503603246 0.556700982 1 16.77976509 0.923857458 21.04444096 1 0.545650283 0.811931458 0.065150801 4159.935514 1149734.353 0.066074309 0.016518577 8.391845087 -0.923857458 -0.454349717 SIRDT(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 1 S(0.001)IRDT(0.999)PAK;S(0.001)IRDT(0.999)PAK;S(0.001)IRDT(0.999)PAK;SIRDT(1)PAK 150.59 0.0030998 8463530000 13135200 8692500 10741100 7701100 12127600 13773200 12088200 10224000 10018800 7230910 TRUE FALSE 13653787.84 10185369.26 11021021.89 9224354.595 10066154.88 10574583.03 11140695.3 10086964 9658225.345 8647668.37 1.578898179 1.17781682 1.274450108 1.066686903 1.164031095 1.222824764 1.288288914 1.166437422 1.116858896 1 23.04387977 4.738758533 8.815011811 1.176609114 1.580903028 0.682749205 0.084431711 0.047384336 66.76434128 0.019194348 0.112856117 54797.2208 -4.738758533 0.404293914 SIRDTPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIRDTPAK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ; 94.309 0.0095309 204869000 341200 471000 455460 273940 765590 624640 274710 484980 556450 736430 FALSE TRUE 354670.8395 551890.5861 467329.6618 328124.5144 635455.2853 479576.8265 253177.5124 478479.6364 536423.4732 880719.3587 0.402705852 0.626636148 0.530622675 0.372564213 0.721518471 0.54452854 0.287466728 0.543282751 0.609074239 1 19.74832285 0.781864087 2.373681846 0.999630866 0.504325069 0.612262449 0.118460837 0.59851093 5.319543722 0.111184552 0.029968546 6.051514618 -0.781864087 -0.495305797 SIRNEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIRNEDK 7 1 P25685;P25685-2;M0R080;M0QZD0;M0QYT3;M0QXK0 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 78.149 0.032941 202340000 339170 282950 306400 210920 457180 399550 279980 310670 339220 315950 FALSE TRUE 352560.6935 331544.4615 314385.0357 252639.3465 379468.7069 306760.5677 258034.436 306505.9768 327011.5385 377854.3533 0.933059763 0.877439835 0.832027031 0.668615683 1.004272423 0.811848706 0.682893908 0.811174925 0.865443353 1 18.52747072 2.524605162 24.99769872 0.808916025 0.857022368 0 0.109360909 1518.077395 799182.7953 0.034846972 0.032853105 334.6610441 -2.524605162 0.048106342 SIRPDNMSEYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 106.58 0.0020011 998460000 343927 298499 318996 285174 392725 419686 395528 371988 380010 275268 FALSE TRUE 357505.5035 349763.8813 327309.2978 341580.566 325969.7448 322220.2869 364525.4818 367002.1093 366333.5143 329201.4943 1.085977767 1.062461402 0.994252163 1.037603328 0.990183066 0.978793513 1.107302027 1.114825162 1.112794203 1 18.32861136 2.220581459 24.99534152 1.096105599 1.024196072 0.282321698 0.044234 258.9211422 359960.3366 0.016531831 0.012235257 166.1810347 -2.220581459 -0.071909526 SIS(ph)ADDDLQESSR ddPTM_MDA-MB-175_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;S(0.048)IS(0.952)ADDDLQESSR 287.88 2.98E-33 445660000 227860 277610 317450 281340 376950 355520 326220 320130 350470 301300 TRUE FALSE 236856.0887 325287.358 325723.0078 336988.2123 312876.1736 272955.868 300650.024 315839.181 337856.6532 360333.9663 0.657323791 0.902738538 0.903947555 0.935210787 0.868294979 0.757508016 0.834364928 0.876517927 0.937620887 1 18.45897513 -5 0.14765019 1.528380365 0.807407988 0.299884097 0.078080816 194.7339032 1.721295861 29.97562791 0.421693389 1.00E-05 5 -0.720972377 SIS(ph)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 1 S(0.391)IS(0.609)EIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 285.81 5.89E-75 424800000 50577 51610 60762 34754 93872 48716 64637 66304 82838 55173 TRUE FALSE 52573.81901 60473.61603 62345.50764 41628.23747 77915.67097 37402.4473 59570.58304 65415.30333 79856.67656 65983.093 0.796777123 0.916501687 0.944870948 0.630892484 1.180842962 0.566848955 0.902815863 0.991394922 1.210259673 1 16.00980879 1.601984756 3.05895302 1.103547652 0.847792486 0.27846104 0.167286859 0.25680021 5.617482027 0.101985734 0.041468682 39.99307116 -1.601984756 -0.255755166 SIS(ph)ENSLVAMDFSGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISENSLVAMDFSGQK 16 0 Q14449-2;C9JD37;Q14449 Q14449-2 GRB14 Growth factor receptor-bound protein 14 1 S(0.028)IS(0.972)ENSLVAMDFSGQK 197.14 4.62E-11 101330000 104740 93070 117370 89465 107990 128280 105960 110630 120880 96455 TRUE FALSE 108875.2161 109054.0485 120428.7586 107160.91 89633.89837 98488.9141 97654.57833 109147.1858 116529.5524 115353.5105 0.943839642 0.945389941 1.043997344 0.928978316 0.777036589 0.853800753 0.846567893 0.946197349 1.010195112 1 16.81570238 5.057625058 0.001975922 1.835861404 2.47E-05 0.007906751 0.077909007 3079578.146 862.3450666 394271.9694 407012.5839 114189.2072 -5.057625058 -1.835836664 SIS(ph)ESSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SISESSR 7 0 Q9H307 Q9H307 PNN Pinin 1 S(0.053)IS(0.942)ES(0.005)SR;S(0.006)IS(0.993)ES(0.001)SR;S(0.008)IS(0.991)ESSR;S(0.429)IS(0.571)ESSR 181.69 0.00070089 2836090000 1417650 1549000 1543660 1574200 1782830 2037730 1806410 1752050 1711740 1782470 TRUE FALSE 1473619.917 1815028.7 1583889.048 1885572.061 1479785.193 1564498.09 1664818.864 1728566.636 1650134.812 2131710.869 0.691285079 0.851442251 0.743013075 0.884534619 0.694177252 0.733916645 0.7809778 0.810882311 0.774089411 1 21.02358034 -0.540286574 0.683177633 1.022717111 0.773658357 0.566112968 0.059447037 10.06615935 3.396512305 0.623226479 0.020406749 0.288212907 0.540286574 -0.249058754 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SISLGDSEGPIVATLAQPLR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 S(0.114)IS(0.886)LGDSEGPIVATLAQPLR;S(0.016)IS(0.984)LGDSEGPIVATLAQPLR;S(0.004)IS(0.996)LGDSEGPIVATLAQPLR;SIS(1)LGDSEGPIVATLAQPLR;SIS(0.998)LGDS(0.002)EGPIVATLAQPLR;S(0.009)IS(0.991)LGDSEGPIVATLAQPLR 332.61 7.30E-80 567460000 185193.2 196218.7 213901 214585 260837 272595 217034.2 221194 234439.5 238545.2 TRUE FALSE 192504.7705 229917.7354 219475.4358 257029.2725 216500.0199 209288.9425 200022.4923 218229.2562 226002.0682 285283.5647 0.67478395 0.805927028 0.769323799 0.900960673 0.75889412 0.733617244 0.701135702 0.764955585 0.792201501 1 18.12203711 0.726017921 3.203913801 0.999989569 0.765838006 0.597224044 0.057834141 1.786365517 20.0777748 0.056362422 0.014646605 5.32130217 -0.726017921 -0.234151562 SIS(ph)LLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.124)IS(0.759)LLEPS(0.117)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.112)IS(0.88)LLEPS(0.007)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.108)IS(0.889)LLEPS(0.002)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.119)IS(0.876)LLEPS(0.005)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.115)IS(0.876)LLEPS(0.009)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 269.62 5.79E-68 4678220000 69122.4 769486 663030 621631 679989 858039 469354 874661 623894 942782 TRUE FALSE 71851.40573 901639.2347 680309.1065 744587.7564 564404.7127 658772.446 432564.8071 862937.6 601440.1768 1127502.082 0.063726185 0.799678554 0.603377251 0.660387034 0.500579752 0.584276035 0.383648788 0.765353442 0.53342711 1 20.10469867 -5 0.20473353 3.041473758 0.495673203 0.342459594 0.195071956 163.8545409 1.62802535 136.9427234 0.412628648 1.00E-05 5 -2.545800555 SIS(ph)PEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SISPEWK 7 0 O00159-3;F5H6E2;O00159-2;O00159 O00159-3 MYO1C Unconventional myosin-Ic 1 S(0.01)IS(0.99)PEWK;S(0.001)IS(0.999)PEWK;SIS(1)PEWK 90.15 0.023357 248930000 878060 598710 707220 553490 874310 930560 857020 720390 777540 543050 TRUE FALSE 912726.4868 701533.7852 725650.7342 662968.67 725695.0985 714451.5428 789844.533 710734.3504 749556.4873 649450.2502 1.405383225 1.080196343 1.117330749 1.020815174 1.117399059 1.100086639 1.216174038 1.09436304 1.154139962 1 19.30885949 4.741655172 24.6541691 1.106391622 1.405383359 0.710219091 0.058383263 128.357067 1022553.187 0.013331801 0.095151742 55163.92657 -4.741655172 0.298991737 SIS(ph)PSALQDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 S(0.003)IS(0.996)PS(0.001)ALQDLLR;SIS(1)PSALQDLLR;SIS(1)PSALQDLLR 185.95 1.30E-05 247724000 152275 196627 172952 154172 195308 207345 164096 159343 148068 176577 TRUE FALSE 158286.9346 230396.1577 177459.2712 184666.7614 162109.6159 159192.2661 151233.7267 157207.2677 142739.0616 211173.8824 0.749557345 1.091025818 0.840346681 0.874477276 0.7676594 0.753844483 0.716157344 0.744444654 0.675931417 1 17.68807189 3.379438925 1.891889793 0.754860138 0.914823726 0.169916786 0.114719315 0.429021115 3.129071623 0.032834777 0.051064442 2395.735816 -3.379438925 0.159963589 SIS(ph)QDSLDELSMEDYWIELENIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISQDSLDELSMEDYWIELENIKK 24 1 Q8N392;Q8N392-2 Q8N392 ARHGAP18 Rho GTPase-activating protein 18 1 S(0.143)IS(0.851)QDS(0.007)LDELSMEDYWIELENIKK 138.16 5.25E-06 31132000 20521 17333 24625 12739 32773 24880 22257 18845 24521 12968 TRUE FALSE 21331.18493 20309.80792 25266.74773 15258.73618 27202.25717 19101.99706 20512.43818 18592.4136 23638.494 15508.83131 1.375421816 1.309564048 1.629184509 0.983874018 1.753984979 1.23168514 1.322629524 1.198827508 1.5241957 1 13.92080235 -3.55913504 0.269420612 9.59E-10 1.389060522 0.205626452 0.211855975 133.8751628 2.646776959 74.6956145 0.24394972 0.000275972 3.55913504 1.389060521 SIS(ph)QQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISQQK 6 0 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SIS(1)QQK;SIS(1)QQK 82.75 0.061279 177933000 269980 206276 260080 198552 355830 333030 313350 285190 324950 224725 TRUE FALSE 280639.0189 241702.2984 266857.8985 237824.993 295346.1437 255688.8296 288788.8082 281367.4945 313255.113 268755.5611 1.044216602 0.89933878 0.992939076 0.884911895 1.098939655 0.95138061 1.074540772 1.046927153 1.165576302 1 18.03593508 2.482282819 1.011904207 1.07940071 0.962280348 0.265430016 0.071804408 0.637292882 1.315484141 0.042175754 0.02994384 303.5867545 -2.482282819 -0.117120361 SIS(ph)REPS(ph)PALGPNLDGSGLLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SISREPSPALGPNLDGSGLLPR 22 1 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 2 S(0.458)IS(0.542)REPS(1)PALGPNLDGSGLLPR;S(0.458)IS(0.542)REPS(1)PALGPNLDGSGLLPR;S(0.457)IS(0.543)REPS(1)PALGPNLDGSGLLPR 138.88 4.58E-07 425358000 380055 375789 369251 401663 348735 422524 413084 360525 333247 276683 TRUE FALSE 395059.8649 440327.8375 378873.9844 481110.7426 289457.1493 324399.2044 380705.3967 355692.7521 321253.5056 330893.7364 1.193917628 1.330722794 1.145001983 1.453973556 0.874773734 0.980372756 1.150536728 1.074945558 0.970866082 1 18.33600846 3.234498141 24.99999519 1.024910297 1.274755186 0.626699347 0.102456717 72.12790429 443867.0901 0.029154104 0.036061832 1715.924365 -3.234498141 0.249844889 SIS(ph)SPNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SIS(0.5)S(0.5)PNVNR;SIS(0.931)S(0.069)PNVNR;SIS(0.996)S(0.004)PNVNR;S(0.001)IS(0.993)S(0.007)PNVNR;S(0.001)IS(0.977)S(0.022)PNVNR;SIS(0.995)S(0.005)PNVNR;S(0.001)IS(0.98)S(0.018)PNVNR;SIS(0.537)S(0.463)PNVNR 218.36 5.59E-07 28596920000 16719740 18724630 17673160 17316810 19206710 21333130 17877070 16944710 16004540 17564490 TRUE FALSE 17379848.25 21940439.55 18133737.07 20742023.33 15941960.29 16378833.86 16475818.54 16717593.88 15428539.73 21005915.52 0.827378756 1.044488612 0.863268114 0.987437244 0.758927183 0.779724828 0.784341845 0.795851714 0.73448547 1 24.32429233 3.234347415 24.99791332 0.795720902 0.933962497 0.304859988 0.088686114 105.8016713 627746.8038 0.022954481 0.02837736 1715.328942 -3.234347415 0.138241596 SIS(ph)SPSVSSETMDKPVDLSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 S(0.054)IS(0.467)S(0.467)PS(0.012)VSSETMDKPVDLSTR 115.11 2.92E-05 0 133770 115970 109970 110110 162240 167860 157080 133870 132180 95579 TRUE FALSE 139051.3429 135886.9454 112835.9085 131889.4294 134662.5028 128877.0589 144767.6591 132075.6916 127422.8676 114305.8751 1.216484654 1.188801059 0.987140061 1.153828963 1.178089076 1.127475371 1.266493599 1.155458471 1.114753441 1 16.80254003 0.877307507 3.110676588 1.000165301 1.158635023 0.331638748 0.068331487 0.6047289 11.74271831 0.066596509 0.017392595 7.538891752 -0.877307507 0.158469722 SIS(ph)TVNLSENSSVVIPPPDYLECLSMGAAADRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISTVNLSENSSVVIPPPDYLECLSMGAAADRR 33 1 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.195)IS(0.745)T(0.06)VNLSENSSVVIPPPDYLECLSMGAAADRR 88.149 0.00021279 91194000 14798 17057 25018 21752 23980 23782 14205 14693 19005 21092 TRUE FALSE 15382.23647 19986.40706 25669.98963 26054.48068 19903.88817 18258.99092 13091.57498 14496.06437 18321.01376 25224.57357 0.609811556 0.792338749 1.017658022 1.032900739 0.78906738 0.723857268 0.519000844 0.574680255 0.726316095 1 14.62254226 2.759230145 3.032421506 0.653651205 0.870710125 0.119852389 0.166329706 0.36754336 6.873231184 0.056338096 0.057054924 574.4207833 -2.759230145 0.21705892 SIS(ph)VSEHVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISVSEHVVR 10 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9 P49815 TSC2 Tuberin 1 S(0.274)IS(0.726)VSEHVVR;S(0.216)IS(0.769)VS(0.015)EHVVR 154.28 9.51E-06 216020000 103285 244930 259560 282480 310310 343290 215951 251590 240040 318650 TRUE FALSE 107362.7716 286994.8222 266324.3468 338353.7009 257563.617 263566.1001 199024.1963 248217.8476 231401.0073 381083.3666 0.281730406 0.753102464 0.698861116 0.887873181 0.675872105 0.691623207 0.522258943 0.651347892 0.60721886 1 18.53974711 -2.295108705 2.161948054 2.517577226 0.650798737 0.33749329 0.150302721 5416960.038 649800.0309 40268460.57 0.035380868 0.005068638 2.295108705 -1.866778489 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISEIKPPNLFPLAPQEITHCHDEDDDEEEEEEEE 35 1 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 258.86 3.83E-60 859980000 419580 415700 439450 418050 518740 616350 547870 498780 544790 421500 FALSE TRUE 436145.3424 487093.2413 450902.428 500739.0422 430564.7601 473212.0534 504926.5178 492094.6699 525183.1143 504084.8549 0.865222072 0.966292156 0.894497075 0.9933626 0.854151352 0.938754753 1.001669685 0.976213955 1.041854579 1 18.94330708 2.309182186 4.322725053 1.000388805 0.918802916 0.503238495 0.042241017 0.184365734 6.665484674 0.014427626 0.011669365 203.7896792 -2.309182186 -0.081585889 SISEPQHS(ph)DAEGDAASPLPSEWTSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISEPQHSDAEGDAASPLPSEWTSVR 26 0 A0A2R8YFA9 A0A2R8YFA9 1 S(0.005)IS(0.024)EPQHS(0.971)DAEGDAASPLPSEWTSVR 93.568 0.0056177 111670000 22219 34224 28074 32770 36317 40505 28992 30574 29874 39891 TRUE FALSE 23096.22328 40101.70577 28805.6315 39251.80819 30143.84931 31098.32761 26719.53128 30164.20554 28798.84058 47706.87769 0.484127748 0.840585419 0.603804585 0.822770428 0.631855422 0.651862564 0.560077133 0.632282115 0.603662238 1 15.54190965 -2.185167873 2.251020666 1.909311914 0.651799506 0.510646955 0.103342831 4920985.176 1052871.389 22788576.44 0.023344648 0.006528781 2.185167873 -1.257512408 SISLLEPS(ph)LELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.008)IS(0.008)LLEPS(0.943)LELES(0.034)T(0.006)S(0.001)ETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.071)IS(0.063)LLEPS(0.701)LELES(0.02)T(0.128)S(0.017)ETSDMPEVFSSHESSHEEPLQPFPQLAR;S(0.007)IS(0.05)LLEPS(0.923)LELES(0.01)T(0.008)S(0.001)ETSDMPEVFSSHESSHEEPLQPFPQLAR 184.54 8.55E-28 1000190000 16290.1 82010 68232 80175 69420 94418 55770.5 86845 65058 92626 TRUE FALSE 16933.24573 96094.57955 70010.18197 96033.3757 57620.0132 72490.85042 51399.06248 85680.98482 62716.57529 110774.2913 0.152862596 0.867480879 0.632007492 0.866928369 0.520156911 0.654401392 0.463998116 0.773473555 0.566165439 1 16.75726357 -4.99999983 0.38674833 6.467966647 0.621023958 0.248915109 0.201032111 895.32333 6.545359473 4115.967817 0.120413452 1.00E-05 4.99999983 -5.846942689 SISLLEPSLELES(ph)TSETSDMPEVFSSHESSHEEPLQPFPQLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISLLEPSLELESTSETSDMPEVFSSHESSHEEPLQPFPQLAR 43 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 S(0.038)IS(0.038)LLEPS(0.262)LELES(0.311)T(0.285)S(0.062)ET(0.003)S(0.001)DMPEVFSSHESSHEEPLQPFPQLAR 78.542 0.00088684 342870000 3450.8 20540 17938 18249 20830 27053 11625 23253 15821 23677 TRUE FALSE 3587.040249 24067.58522 18405.47902 21858.59773 17289.32404 20770.35074 10713.80212 22941.33157 15251.6053 28316.05483 0.126678673 0.849962517 0.650001532 0.771950678 0.610583789 0.733518524 0.378364931 0.810188132 0.538620418 1 14.78933265 -5 0.322321246 4.561071836 0.612396143 0.237542525 0.208747054 478.470111 4.215406696 1163.864636 0.16796401 1.00E-05 5 -3.948675693 SISPS(ph)ALQDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SISPSALQDLLR 12 0 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 1 S(0.003)IS(0.432)PS(0.566)ALQDLLR 95.264 0.0064454 26453000 30039 38355 31759 31243 37472 40484 31379 34870 34523 38590 TRUE FALSE 31224.96292 44942.17289 32586.66563 37422.77215 31102.52282 31082.20454 28919.43199 34402.62469 33280.52397 46150.97165 0.676583001 0.973807729 0.706088398 0.810877232 0.673929968 0.673489711 0.62662672 0.745436628 0.721122932 1 15.4940734 -1.426301652 2.770167589 1.006810838 0.735155876 0.423322485 0.093057324 12605772.79 13932067.77 673787.3075 0.023766735 0.037471264 1.426301652 -0.271654963 SISS(ph)PNVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISSPNVNR 9 0 Q9NQT8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 SIS(0.401)S(0.599)PNVNR;SIS(0.046)S(0.954)PNVNR 149.94 0.0014248 0 458460 599700 540680 589420 583510 707850 535930 566660 493380 588240 TRUE FALSE 476560.3548 702693.81 554770.565 706005.5168 484325.1786 543462.5651 493922.4062 559064.8496 475623.3502 703494.3655 0.677418865 0.99886203 0.788592762 1.00356954 0.688456372 0.772518718 0.702098596 0.794696983 0.676086936 1 19.42417934 3.216972271 24.99998185 0.759726466 0.870913276 0.118673822 0.123571562 401.7056185 465186.634 0.03235763 0.038707057 1648.057164 -3.216972271 0.11118681 SISSS(ph)NPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISSSNPDLAVAPGSVDDEVSR 22 0 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 1 SISS(0.005)S(0.995)NPDLAVAPGSVDDEVSR;SIS(0.003)S(0.02)S(0.977)NPDLAVAPGSVDDEVSR 415.81 1.00E-152 1557230000 363360 376260 409910 473270 393480 522260 366750 327450 388560 385990 TRUE FALSE 377705.7334 440879.7281 420592.5913 566881.3934 326596.4101 400973.0299 338003.1767 323061.0684 374575.8015 461617.3503 0.818222567 0.955076164 0.911128213 1.228033117 0.707504625 0.868626428 0.732215062 0.699846026 0.811442207 1 18.81633792 3.17225263 24.99999824 0.780702858 0.971708046 0.299298701 0.128149064 60.90458829 22962.03867 0.035877052 0.042881293 1486.800264 -3.17225263 0.191005188 SISVPPS(ph)PSDIPPPGPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SISVPPSPSDIPPPGPPR 18 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SIS(0.001)VPPS(0.918)PS(0.082)DIPPPGPPR;SISVPPS(0.981)PS(0.019)DIPPPGPPR 145.94 9.17E-08 139707000 89280 99349 99776 94871 113754 134828 110287 112048 108015 112867 TRUE FALSE 92804.84334 116411.4179 102376.2445 113636.2006 94418.13571 103516.2403 101642.4168 110546.1798 104127.5612 134981.1277 0.687539399 0.862427362 0.758448579 0.841867323 0.699491383 0.766894173 0.753012058 0.81897508 0.77142311 1 17.04239819 -0.533799856 0.699101503 1.021318118 0.773582884 0.621325091 0.053095439 9.083460206 3.185449121 0.544466904 0.017649119 0.292550028 0.533799856 -0.247735234 SITHDIEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 193.38 5.50E-05 5797990000 3494210 5755150 7050160 5890990 8721370 9044190 8437230 7953750 7700600 5247050 FALSE TRUE 3632164.109 6743552.244 7233892.961 7056210.239 7238914.643 6943813.939 7775897.866 7847142.991 7423456.91 6275108.987 0.578820881 1.074651015 1.152791605 1.124476125 1.153591859 1.106564675 1.239165389 1.250518996 1.183000475 1 22.58120909 4.778778118 2.514226076 1.166884279 0.413378303 0.861951183 0.068067826 0.201414103 1.466650358 0.017304607 0.337835464 60086.6675 -4.778778118 -0.753505976 SITS(ph)PTTLYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.003)S(0.921)PT(0.058)T(0.017)LYDR;SIT(0.075)S(0.874)PT(0.033)T(0.017)LYDR 244.94 6.90E-16 233710000 367950 449680 442560 415650 489030 526670 428220 441600 437380 430100 TRUE FALSE 382476.9501 526909.042 454093.4772 497864.3294 405904.8553 404358.8743 394654.9975 435681.0743 421638.7792 514369.8602 0.743583518 1.024377754 0.882815095 0.967911163 0.789130326 0.786124743 0.767259181 0.847019058 0.819719062 1 18.97244658 3.229262691 24.99856701 0.821923555 0.911661107 0.11263359 0.090907814 310.7279944 835427.8852 0.024242636 0.029344408 1695.362961 -3.229262691 0.089737552 SITSPT(ph)TLYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SITSPTTLYDR 11 0 Q08999;F5H837 Q08999 RBL2 Retinoblastoma-like protein 2 1 SIT(0.006)S(0.276)PT(0.635)T(0.083)LYDR;SIT(0.074)S(0.253)PT(0.52)T(0.153)LYDR 207.95 2.37E-07 578620000 1664640 1885320 1952860 1831770 2171060 2378070 2015860 1936730 1961910 1936760 TRUE FALSE 1730361.273 2209109.044 2003753.136 2194088.639 1802023.997 1825799.282 1857851.626 1910771.302 1891301.242 2316231.04 0.747059012 0.953751593 0.865092083 0.947266745 0.77799838 0.788263023 0.802101169 0.824948491 0.816542568 1 21.14334774 4.824371118 20.73456897 0.852118654 0.747036787 0.165888492 0.074496039 73182.05741 17670610.76 0.017484451 255.1407557 66737.68192 -4.824371118 -0.105081867 SITST(ph)PLSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 SIT(0.017)S(0.14)T(0.843)PLSGK;SITS(0.077)T(0.922)PLSGK;SITS(0.015)T(0.984)PLS(0.001)GK 153.74 0.00017577 635390000 1428030 1113670 1199090 1046130 1608140 1625090 1388000 1312020 1344610 1085440 TRUE FALSE 1484409.727 1304934.159 1230339.27 1253051.392 1334788.937 1247687.476 1279204.933 1294434.518 1296217.749 1298111.186 1.143515088 1.005256078 0.947791902 0.965288186 1.028254707 0.961156093 0.985435567 0.997167679 0.998541391 1 20.30798253 4.726589357 4.032035963 0.985419497 1.15572801 0.821962044 0.021916495 0.083045622 2.870747543 0.005245784 0.040515133 53283.08443 -4.726589357 0.170308514 SIVDKEGVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SIVDKEGVPR 10 1 Q99613-2;Q99613;B5ME19;H3BPE4;H3BPE3;H3BTY8 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 0 ;; 96.229 0.0062769 627740000 896160 764510 920040 672760 1168810 1146420 844700 878900 955670 851460 FALSE TRUE 931541.0888 895808.6454 944016.9982 805829.92 970136.0937 880181.3292 778490.2068 867119.7831 921275.6234 1018287.285 0.914811667 0.879720938 0.927063524 0.791358129 0.95271355 0.864374271 0.764509406 0.851547295 0.904730558 1 19.95771321 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ; 376.08 5.20E-128 1508160000 2672600 1590360 1782750 1800950 2738900 2755100 3255200 1973290 1977310 1791110 FALSE TRUE 2778116.312 1863491.959 1829209.93 2157172.535 2273342.756 2115269.779 3000048.918 1946841.275 1906146.999 2142043.712 1.296946601 0.869959819 0.853955463 1.007062798 1.061296156 0.987500753 1.400554481 0.908870937 0.889873063 1 21.03055649 3.393150127 5.754413397 1.04971152 0.983535302 0.002321072 0.174049688 0.956250979 50.80321917 0.048796029 0.066558667 2472.578718 -3.393150127 -0.066176217 SIVEGIIEEEEEDEEGSESISKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570;Q9Y570-4;Q9Y570-2 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 292.64 2.33E-61 134618000 90505 72102 91773 74445 122512 112644 99764 91869 98033 71652 FALSE TRUE 94078.20729 84484.95762 94164.67977 89169.9988 101687.454 86484.13814 91944.237 90637.64632 94504.81148 85690.83754 1.097879423 0.985927551 1.098888545 1.040601322 1.18667826 1.009257706 1.072976291 1.057728561 1.102857834 1 16.38685333 -1.058888896 4.359596514 0.999994447 1.070375714 0.143237596 0.052982013 2.63E-06 5.67E-07 0.047159512 0.011114727 0.087319473 1.058888896 0.070381267 SIVIRPLEPQPAPHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIVIRPLEPQPAPHLAR 17 1 Q15029;Q15029-3;Q15029-2;K7EP67 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ; 111.92 0.00029191 920600000 834410 987560 942970 969900 1083330 1115860 901500 949880 919840 936880 FALSE TRUE 867353.1511 1157165.748 967544.5729 1161743.325 899185.9536 856718.426 830838.0744 937148.4123 886735.1381 1120443.698 0.774115783 1.03277456 0.863536985 1.036860064 0.802526673 0.764624253 0.741525947 0.836408303 0.791414276 1 20.09563873 3.196898058 24.96584523 0.808064983 0.929869642 0.206173583 0.097447694 176.352109 105676.5476 0.025877882 0.030930265 1573.613448 -3.196898058 0.121804659 SIYDDISSPGLGST(ph)PLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SIYDDISSPGLGS(0.204)T(0.79)PLT(0.003)S(0.003)R 127.61 0.00025805 79897000 124230 117240 109230 117060 118200 146000 95109 112530 95598 115590 TRUE FALSE 129134.6963 137375.058 112076.6235 140214.1186 98108.40622 112093.7127 87654.10806 111021.7194 92157.44665 138237.6474 0.934149986 0.993760098 0.810753262 1.014297633 0.709708304 0.810876883 0.634082753 0.80312217 0.666659542 1 17.07679104 3.231705221 24.99998951 0.756507052 0.93309974 0.364864163 0.107196483 150.8898203 550258.502 0.028112858 0.034309682 1704.924772 -3.231705221 0.176592688 SIYGEK ddPTM_MDA-MB-175_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 ;;; 103.29 0.080996 3026640000 1840010 1794570 1886610 1621640 2249410 2353200 2042510 2033500 1810080 1494490 FALSE TRUE 1912655.016 2102773.438 1935776.606 1942395.552 1867056.092 1806704.963 1882412.729 2006244.259 1744935.574 1787306.702 1.070132515 1.176503974 1.08306907 1.086772377 1.044619868 1.010853348 1.053211923 1.122495796 0.976293309 1 20.76935579 7.999999999 0.117298046 0.978211625 1.43802509 0.349732693 0.045671933 119.5829241 0.967223565 0.345263444 8.966429273 99999999.79 -7.999999999 0.459813465 SIYGEKFEDENFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 ;;;;;;;;;; 250.17 8.96E-19 35219696000 13734249 8984816 12404416 7791256 17328189 14287982 13278360 11898407 13436722 8917664 FALSE TRUE 14276487.76 10527888.26 12727685.27 9332343.182 14382749.62 10969814.72 12237567.45 11738928.32 12953137 10664909.52 1.338641245 0.98715214 1.193417089 0.875051323 1.348604936 1.028589572 1.147460972 1.100705851 1.21455667 1 23.34636839 -1.755364112 2.551563744 0.96959125 1.128008626 0.074952671 0.141291754 19269231.55 15228678.81 3702820.27 0.030086104 0.017564504 1.755364112 0.158417377 SIYGERFPDENFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIYGERFPDENFK 13 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 211.82 1.72E-08 721670000 414060 503930 464420 285730 676980 600990 295170 387730 414830 583380 FALSE TRUE 430407.4085 590476.0575 476523.1667 342246.5412 561907.1814 461419.1806 272033.8041 382533.1135 399900.3493 697682.1415 0.616910457 0.846339647 0.683008978 0.490547946 0.805391378 0.661360171 0.389910803 0.548291393 0.573184156 1 19.41221038 -0.841874109 8.788873199 1 0.619085483 0.430147524 0.129766753 0 0 0.132668541 0.031270275 0.143921571 0.841874109 -0.380914517 SIYVGNVDYGATAEELEAHFHGCGSVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SIYVGNVDYGATAEELEAHFHGCGSVNR 28 0 Q92843-2;Q86U42-2;Q86U42;B4DEH8;G3V4T2 Q92843-2 PABPN1 Polyadenylate-binding protein 2 0 ; 216.71 1.94E-34 393800000 79290 108908 95402 101706 109571 129617 96002 99938 106261 95866 FALSE TRUE 82420.43043 127612.1018 97888.25449 121823.1432 90946.16056 99515.41611 88477.11239 98598.49458 102436.6874 114649.1072 0.718892911 1.113066686 0.853807385 1.06257385 0.793256596 0.867999922 0.771720901 0.860002288 0.893480026 1 16.8068656 3.211193591 24.99987667 0.85158939 0.943707087 0.078408139 0.116334741 419.3543647 383080.5426 0.030704369 0.03670711 1626.273522 -3.211193591 0.092117697 SIYYITGESK ddPTM_MDA-MB-175_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 0 172.59 0.0056885 0 459120 337200 422800 368380 544200 537040 523130 418900 467280 263910 FALSE TRUE 477246.4121 395111.4769 433818.5153 441244.4645 451697.0784 412320.5989 482125.7037 413285.3307 450462.6841 315618.1116 1.512100841 1.251865664 1.374504502 1.398032775 1.43115069 1.306390805 1.52756032 1.309447448 1.427239653 1 18.26782047 -1.107656513 4.306472371 0.999945323 1.387271712 0.664750135 0.083664774 5218431.849 1342219.919 2724.385513 0.017641658 0.078044713 1.107656513 0.387326389 SKAELMEISEDKTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKAELMEISEDKTK 14 2 P05455;E7ERC4;E9PGX9;E9PFL9 P05455 SSB Lupus La protein 0 ; 155.92 3.21E-06 1390200000 1429370 594590 958380 525130 1414130 1003130 1197530 835830 992470 339850 FALSE TRUE 1485802.631 696706.2072 983356.1701 628999.1466 1173756.688 770168.2601 1103664.469 824627.066 956751.1986 406437.1007 3.655676681 1.714179651 2.419454741 1.547592839 2.887917185 1.894926075 2.715461919 2.028916811 2.353995728 1 18.63267258 -1.686261902 0.399488354 6.03E-12 2.369470275 0.326035334 0.589090011 37.67356807 2.813805872 37.45856918 0.340041716 0.020593876 1.686261902 2.369470275 SKAEVACIAVYETDVFVVGTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 119.01 7.32E-05 35830000 45205 39465 45159 59417 89914 91114 79740 53184 53423 51479 FALSE TRUE 46989.72831 46242.80675 46335.88064 71169.50526 74630.4504 69954.15435 73489.77044 52471.15547 51500.31667 61565.32443 0.76324991 0.75111773 0.752629521 1.155999841 1.21221566 1.136259006 1.193687699 0.852284236 0.836514989 1 15.90983039 3.750852273 24.08246649 1.055023117 0.75521086 0.552483781 0.123570786 397.4045613 778612.4041 0.036256292 0.064714521 5634.459648 -3.750852273 -0.299812257 SKCEELSGLHGQLQEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKCEELSGLHGQLQEAR 17 1 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ;; 185.33 3.52E-10 426034000 502610 573390 641550 564250 791850 820270 603760 596190 682280 619400 FALSE TRUE 522453.4309 671865.2721 658269.32 675856.9659 657251.6198 629774.7238 556435.7136 588199.0482 657724.8761 740759.5709 0.705294203 0.906995061 0.888640992 0.912383711 0.887267132 0.850174265 0.751169118 0.79404853 0.887906012 1 19.49864584 2.473359141 24.9626111 0.828838774 0.867360229 0 0.084107447 405.8924015 2693162.349 0.028176596 0.023676201 297.4124474 -2.473359141 0.038521455 SKDAS(ph)PINRWS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKDASPINRWSPTR 14 2 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 S(0.068)KDAS(0.932)PINRWS(0.904)PT(0.096)R 88.565 0.03195 790220000 642670 462620 548110 379250 679230 695250 575910 535250 575820 385160 TRUE FALSE 668043.1078 542071.3863 562394.1969 454264.5181 563774.7272 533788.7241 530768.6693 528075.8492 555096.3507 460624.7277 1.450297971 1.176817817 1.22093792 0.98619221 1.223935003 1.15883645 1.152280018 1.146434 1.205094554 1 18.81323234 5.018414012 1.676501029 1.140311971 1.78567893 0.587365319 0.078406776 1.489441134 2.251127824 0.018885734 1.937155338 104331.1543 -5.018414012 0.64536696 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;; 200 3.31E-25 1176950000 1155811 671635 993788 759804 2332260 1395807 1540951 993465 1108059 812634 FALSE TRUE 1201443.311 786983.0867 1019686.932 910090.9634 1935823.278 1071651.978 1420167.234 980149.2267 1068180.173 971854.0735 1.236238386 0.809774953 1.049218149 0.936448165 1.991886777 1.102688158 1.461296786 1.00853539 1.099115806 1 19.89038018 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 294.68 7.96E-71 1058550000 1369610 794870 1229730 667960 2924390 1487870 1417120 1211470 1494200 948970 FALSE TRUE 1423683.26 931382.7393 1261777.774 800080.4943 2427303.232 1142334.741 1306042.431 1195232.226 1440424.034 1134902.502 1.254454244 0.820672029 1.111793984 0.704977293 2.138776879 1.006548791 1.150797032 1.053158508 1.269205091 1 20.11413693 5.073084106 20.32955717 1.143447331 4.651782102 0.008616653 0.367622383 3552.865801 1040906.484 0.082167973 30082.45597 118327.0687 -5.073084106 3.508334771 SKDEEEDEES(ph)DDADDTPILKPVSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKDEEEDEESDDADDTPILKPVSLLR 26 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 SKDEEEDEES(1)DDADDTPILKPVSLLR 221.23 1.46E-34 141650000 181370 80389 118610 73213 164940 159800 167180 113220 138680 67606 TRUE FALSE 188530.6276 94195.18541 121701.074 87694.31288 136903.5577 122688.8718 154075.9948 111702.4711 133688.9339 80852.1013 2.331796263 1.165030765 1.505230811 1.084626268 1.693259118 1.517448153 1.905652324 1.381565467 1.653499807 1 16.30299765 -1.320874699 3.569022074 0.997915836 1.555342061 0.204317495 0.340927576 55570309.64 79648675.86 1210905.265 0.075871062 0.047766707 1.320874699 0.557426225 SKDEYEKS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SKDEYEKSR 9 2 Q13247;Q13247-3;A0A590UJP7 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R;SKDEYEKS(1)R 143.31 8.05E-05 3093780000 4948630 1890840 2752980 2406120 3801370 3978110 4654070 2869940 3258340 1057367 TRUE FALSE 5144005.734 2215577.061 2824724.92 2882043.354 3155214.485 3054254.241 4289271.832 2831473.149 3141072.98 1264537.819 4.067893942 1.752084459 2.233800269 2.279127845 2.49515233 2.41531269 3.391968012 2.239136786 2.483969188 1 20.27017875 0.40647433 1.561946946 1.000193105 2.571337962 0.369868024 0.625915161 4.471345781 10.63060711 0.561004556 0.16068007 2.549613381 -0.40647433 1.571144857 SKDEYEKS(ph)RS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKDEYEKSRSR 11 3 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 SKDEYEKS(1)RS(1)R 72.898 0.064653 243850000 316690 107790 152590 106420 206410 242490 234450 159740 164220 55379 TRUE FALSE 329193.1657 126302.094 156566.6208 127469.5584 171324.5019 186175.3725 216073.1964 157598.9466 158309.7543 66229.45475 4.97049488 1.907038107 2.364002864 1.924665677 2.586832438 2.811066061 3.262493964 2.379589975 2.390322476 1 16.01518536 4.745227918 24.942897 2.39433286 4.970496085 0.653914937 0.58032644 460.9372474 1724356.24 0.133019477 1.294211191 55619.60725 -4.745227918 2.576163225 SKDGVCVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKDGVCVR 8 1 E9PLK3;P55786;P55786-2 E9PLK3 NPEPPS Puromycin-sensitive aminopeptidase 0 ;;; 111.06 0.0030151 1341870000 1117230 985940 1063770 1036980 1509090 1454170 1383460 1202010 1281960 1074370 FALSE TRUE 1161339.103 1155267.525 1091492.72 1242091.549 1252575.421 1116461.056 1275020.79 1185899.022 1235822.51 1284872.231 0.90385571 0.899130277 0.849495143 0.966704329 0.974863796 0.868927687 0.992332746 0.922970388 0.961825215 1 20.29319347 7.99999996 0.074089809 1.069105855 0.592586113 0.355072901 0.040068524 248.1859609 1.349729899 1.425784121 12.22359675 99999990.75 -7.99999996 -0.476519741 SKDILVDLGHLEGADAGEEDLEQQFHYHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKDILVDLGHLEGADAGEEDLEQQFHYHLR 30 1 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 0 180.88 2.33E-18 126890000 178670 175900 209610 179680 250320 249220 202720 216360 231690 204990 FALSE TRUE 185724.0296 206109.4567 215072.6088 215220.1677 207770.6958 191342.432 186830.2767 213460.0481 223351.5222 245153.8657 0.757581485 0.840735087 0.87729642 0.877898323 0.847511399 0.780499346 0.762093945 0.870718671 0.911066695 1 17.90332799 1.06634441 1.954001272 0.997186587 0.825628544 0.638657135 0.042210437 0.212603892 1.636293785 0.042598614 0.012067803 11.65049586 -1.06634441 -0.171558043 SKDKEEGKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKDKEEGKEER 11 3 Q3YEC7;Q3YEC7-2 Q3YEC7 RABL6 Rab-like protein 6 0 ; 95.018 0.0035357 251960000 663900 206268 333470 165417 566020 463870 498070 334470 438120 145218 FALSE TRUE 690111.2846 241692.9245 342160.5021 198135.9889 469808.1226 356143.2225 459029.9719 329986.9767 422352.1468 173670.6867 3.97367741 1.391673684 1.970168418 1.140871799 2.705166493 2.050681259 2.643105642 1.900072965 2.431913841 1 17.40599474 -0.498893457 7.121073007 1.000045691 2.183205474 0.195296025 0.748845152 0 0 0.666004764 0.156978828 0.317034513 0.498893457 1.183159783 SKDQDDQKPGPSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKDQDDQKPGPSER 14 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 ;;; 170.35 1.79E-06 1802250000 975717 518234 746100 502829 1038633 881732 914401 726402 829119 456596 FALSE TRUE 1014239.061 607236.6582 765543.9789 602287.0754 862086.5337 676963.1058 842727.8603 716665.7693 799279.1691 546057.2441 1.857385964 1.112038462 1.401948215 1.102974243 1.578747545 1.239729191 1.543295816 1.31243707 1.463727801 1 19.05869267 -1.399042931 5.235649174 0.999725007 1.385231305 0.231855241 0.217388442 0.000618389 7.10E-05 0.186532788 0.043935326 0.039898546 1.399042931 0.385506298 SKDVVDYSEENFAIVFAAMGVNMETAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SKDVVDYSEENFAIVFAAMGVNMETAR 27 1 P21281 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 ;;;; 155.22 3.26E-08 211604000 615170 536076 703374 641737 792176 830456 833773 677549 779650 493542 FALSE TRUE 639457.3866 628142.8829 721704.5043 768670.6632 657522.2065 637595.1797 768419.6936 668467.5639 751590.5488 590242.1055 1.083381515 1.064212256 1.22272623 1.302297237 1.113987295 1.080226527 1.301872039 1.132531139 1.273359765 1 19.17094731 4.247397865 24.96739155 1.185388256 1.073796829 0.15989337 0.094801265 296.3834249 837337.2223 0.021783386 0.057773051 17676.56459 -4.247397865 -0.111591427 SKEEVNDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKEEVNDKR 9 2 R4GMX3;P35226;Q5T8Z2 R4GMX3 COMMD3-BMI1;BMI1 Polycomb complex protein BMI-1 0 55.567 0.071792 66461000 139600 82941 118170 83094 161560 139360 148350 120970 146300 83605 FALSE TRUE 145111.5158 97185.47156 121249.6073 99529.74519 134098.0889 106995.752 136721.9394 119348.595 141034.6916 99985.79904 1.45132126 0.971992748 1.212668283 0.995438814 1.341171348 1.070109486 1.36741358 1.193655461 1.410547227 1 16.60943558 2.244696428 24.99908331 1.25590673 1.165880792 0.033999752 0.172022752 437.6627077 1783167.723 0.055347316 0.045212407 175.6695254 -2.244696428 -0.090025938 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.993)DEDDNS(0.007)FLK 434.56 4.67E-197 6129140000 2350394 1648146 2431002 1695208 3325216 2709581 2883119 2417477 2792080 1493461 TRUE FALSE 2443189.37 1931202.255 2494355.909 2030515.083 2759996.972 2080321.877 2657132.599 2385074.675 2691593.586 1786076.089 1.367908895 1.08125419 1.396556353 1.136858108 1.545285214 1.164744262 1.487692834 1.335371259 1.506987078 1 20.76836211 3.269780479 24.99998445 1.357043711 1.244681769 0.058397488 0.177904905 491.0801752 393239.8202 0.04443285 0.060156558 1861.146152 -3.269780479 -0.112361942 SKEGHSLEMENENLVENGADS(ph)DEDDNSFLKQQS(ph)PQEPK ddPTM_MDA-MB-175_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 SKEGHSLEMENENLVENGADS(0.998)DEDDNS(0.002)FLKQQS(1)PQEPK 194.36 4.43E-24 253450000 100970 53387 84574 32829 135000 97310 63942 76867 87273 54487 TRUE FALSE 104956.3736 62555.80196 86778.06792 39322.47822 112052.7482 74711.22725 58930.05896 75836.72359 84132.06178 65162.68443 1.610682164 0.959994244 1.331714135 0.603450864 1.719584593 1.146533908 0.904352844 1.163806007 1.291107979 1 15.99175842 4.751908503 24.10746627 1.130263578 1.610682684 0.211987178 0.281010659 2075.931453 3749206.384 0.062573503 1.160464478 56481.7966 -4.751908503 0.480419106 SKEGLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKEGLTER 8 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 0 ;;; 87.298 0.014066 654700000 1140490 1058140 1258780 1091970 1498980 1536080 1409390 1251850 1311490 970890 FALSE TRUE 1185517.426 1239867.314 1291584.841 1307958.407 1244183.915 1179348.7 1298918.329 1235070.998 1264289.731 1161117.307 1.021014345 1.067822611 1.112363784 1.126465344 1.071540238 1.015701594 1.118679673 1.063691835 1.088856159 1 20.1470823 -1.076402412 10.62456276 1 1.077487484 0.290084388 0.035730997 0 0 0.034334026 0.008092608 0.083868251 1.076402412 0.077487484 SKEIEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKEIEAK 7 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 124.23 0.0038 1327800000 2185830 1205750 1751020 1141910 2378400 2245740 2160120 1866300 2057870 1158470 FALSE TRUE 2272128.256 1412828.183 1796653.02 1367776.39 1974120.418 1724200.92 1990804.15 1841285.301 1983807.661 1385450.016 1.639992948 1.019761209 1.296801038 0.987243404 1.424894723 1.244506044 1.436936827 1.329016045 1.431886851 1 20.40192323 SKEIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKEIKR 6 2 Q15172;Q15172-2 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 0 76.847 0.041608 174940000 630420 520270 604080 486190 738700 712470 712740 621160 695570 537160 FALSE TRUE 655309.4684 609622.3254 619822.8211 582356.9309 613136.0379 547009.6401 656873.5764 612834.3662 670536.5716 642406.2175 1.020085813 0.948967038 0.964845614 0.906524431 0.95443665 0.851501161 1.022520577 0.953967053 1.043789044 1 19.29312633 SKEITVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKEITVR 7 1 P17844;P17844-2;J3KTA4;J3QRQ7;J3KRX8;J3QR02;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ; 119.27 0.0043945 308070000 665110 677470 740530 600860 946820 910500 759510 816110 771220 684070 FALSE TRUE 691369.0564 793820.2025 759828.8202 719708.3146 785879.8746 699050.1738 699977.6216 805171.3803 743463.9428 818100.4192 0.845090701 0.970321227 0.92877207 0.879731018 0.960615416 0.854479667 0.855613327 0.984196269 0.908768564 1 19.64191841 0.897578041 1.006452546 0.99676006 0.907023478 0.24432805 0.048057286 0.951609892 1.965981826 0.044450564 0.01458642 7.899107796 -0.897578041 -0.089736582 SKEQAELEAAR ddPTM_MDA-MB-175_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 ;;;;; 138.02 6.04E-05 2651740000 3472400 2750120 3253670 2580170 4070180 4431650 3676040 3132440 3325070 2641210 FALSE TRUE 3609493.033 3222431.717 3338463.313 3090519.925 3378332.257 3402466.45 3387902.379 3090454.765 3205401.38 3158704.53 1.142713096 1.020175102 1.056909021 0.978413744 1.06953095 1.077171485 1.072560712 0.978393115 1.014783545 1 21.59090156 4.741848717 24.64990735 1.030607707 1.142713146 0.471102976 0.03589104 240.7426975 1804671.15 0.008885343 0.063837713 55188.51604 -4.741848717 0.11210544 SKEQLLVLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKEQLLVLSLR 11 1 O15327;D6RJC3;E7EQN9;E9PHC0;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 183.79 0.00084965 0 400370 372510 435810 354350 637660 591680 485030 419490 463700 496970 FALSE TRUE 416176.9168 436485.6948 447167.5666 424439.3724 529270.781 454271.287 447012.0812 413867.4227 447011.5276 594341.7564 0.700231663 0.734401866 0.752374474 0.714133523 0.890515895 0.764326723 0.752112865 0.696345862 0.752111933 1 19.18093322 -1.235829954 3.369800989 1.00066491 0.749845856 0.675572987 0.05181904 14552269.78 21072375.88 99769.17976 0.013324424 0.058099186 1.235829954 -0.250819053 SKESSQVTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKESSQVTSR 10 1 A0A2R8YE10;Q9NRW7;A0A087WU65 A0A2R8YE10 VPS45 Vacuolar protein sorting-associated protein 45 0 ;;; 122.7 0.00043924 325060000 224387 232376 245253 205237 303842 310427 237248 262093 246561 239893 FALSE TRUE 233245.972 272284.7704 251644.4947 245832.266 252195.0454 238335.0338 218651.8818 258580.072 237687.3178 286895.4403 0.812999927 0.949073189 0.877129641 0.856870593 0.879048636 0.830738312 0.762130906 0.901304223 0.828480639 1 18.13016551 -1.572145801 2.7558105 1.00940684 0.857851263 0.441068744 0.048788647 8671448.511 8878448.5 599979.0142 0.012318151 0.02678269 1.572145801 -0.151555578 SKESVPEFPLS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKESVPEFPLSPPK 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK 142.26 5.72E-06 4130370000 6135350 1822000 2938960 2050890 4335370 4687390 4930280 3468620 3937580 1662860 TRUE FALSE 6377578.356 2134914.327 3015551.712 2456549.921 3598445.356 3598814.711 4543831.771 3422128.822 3795867.265 1988665.58 3.206963715 1.073541147 1.51636944 1.235275526 1.809477367 1.809663096 2.284864694 1.720816641 1.908750925 1 20.92336926 3.036943252 24.97712749 1.826039494 1.670694773 0 0.619771246 1089.200581 736395.4594 0.171146392 0.204558658 1088.787815 -3.036943252 -0.155344721 SKESVPEFPLS(ph)PPKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKESVPEFPLSPPKKK 16 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 SKESVPEFPLS(1)PPKKK;SKESVPEFPLS(1)PPKKK;SKESVPEFPLS(1)PPKKK 106.03 0.0068403 3077370000 5024800 1457010 2501350 1119370 4989800 3543100 3056870 2820190 3517920 1622350 TRUE FALSE 5223182.984 1707240.134 2566537.236 1340778.045 4141635.578 2720268.721 2817264.542 2782389.966 3391310.746 1940218.421 2.692059269 0.879921619 1.322808406 0.6910449 2.134623367 1.402042519 1.452034736 1.434060174 1.74790153 1 20.88778764 -2.100677194 2.414684942 0.150514906 1.485087017 0.072895368 0.546022525 13553123.45 4429207.624 63190401.17 0.1214689 0.007930906 2.100677194 1.334572111 SKETQEELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKETQEELNK 10 1 Q8TBA6-2;Q8TBA6 Q8TBA6-2 GOLGA5 Golgin subfamily A member 5 0 76.533 0.02602 0 62657 31619 47055 38424 74452 67636 52810 44011 53507 31676 FALSE TRUE 65130.74674 37049.31729 48281.29196 46024.15252 61796.67563 51928.56403 48670.61421 43421.10453 51581.29352 37882.30573 1.719292041 0.978011147 1.274507743 1.214924795 1.631280738 1.370786784 1.284784896 1.14621071 1.361619694 1 15.20923652 -1.624923797 4.322524795 0.992554581 1.31129086 0.183104972 0.206058256 0.014356296 0.001245731 0.193730943 0.044842234 0.023717898 1.624923797 0.31873628 SKEYFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKEYFSK 7 1 Q06830;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 ;;; 108.98 0.0065041 20640120000 12733940 9923680 12963850 9357720 15116090 13724250 14718050 12311670 13213270 8094000 FALSE TRUE 13236685.78 11627994.84 13301698.58 11208649.09 12546662.42 10537000.93 13564410.78 12146652.2 12737726.99 9679864.331 1.367445383 1.201255973 1.374161675 1.157934523 1.296160978 1.08854841 1.401301745 1.254837029 1.315899331 1 23.2065554 -2.250351801 2.269368957 9.20E-05 1.270270612 0.424715077 0.095289724 819629.9412 249405.7233 4221395.789 0.022840747 0.00561886 2.250351801 1.27017859 SKFDNLYGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKFDNLYGCR 10 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;; 160.67 6.66E-06 7813800000 4432260 4218580 4565300 3712620 7693830 6105120 5272780 4754240 4701160 6308320 FALSE TRUE 4607249.047 4943088.299 4684275.468 4446965.155 6386035.525 4687298.404 4859485.726 4690517.189 4531966.17 7544314.524 0.610691539 0.655207081 0.620901402 0.589445885 0.846469948 0.621302093 0.644125548 0.621728743 0.600712783 1 22.84695839 -1.207931182 4.883834 1.000047825 0.646821991 0.699225158 0.069723157 3.55E-05 5.76E-06 0.065987262 0.015551246 0.061953924 1.207931182 -0.353225834 SKFDS(ph)DEEEEDTENVEAASSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 S(0.01)KFDS(0.99)DEEEEDTENVEAASSGK;S(0.006)KFDS(0.994)DEEEEDTENVEAASSGK;S(0.161)KFDS(0.839)DEEEEDTENVEAASSGK;S(0.319)KFDS(0.681)DEEEEDTENVEAASSGK 333.13 4.82E-81 1628140000 1607420 672866 1147832 739065 1849550 1616920 1700970 1324140 1525750 633650 TRUE FALSE 1670882.183 788425.5013 1177745.445 885249.8511 1535164.152 1241414.835 1567643.527 1306392.069 1470838.556 757801.5855 2.204907214 1.040411522 1.554160703 1.168181577 2.0258128 1.638179252 2.068672799 1.723923642 1.940928316 1 19.53146063 3.232644789 24.99983303 1.783797603 1.464111093 0.069081352 0.403426249 280.4867469 1185315.565 0.105941933 0.129826043 1708.61726 -3.232644789 -0.31968651 SKFGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKFGGR 6 1 P25391 P25391 LAMA1 Laminin subunit alpha-1 0 ; 68.398 0.087774 1089350000 1096530 1219650 1180440 1114790 1516350 1527170 1401880 1302770 1287120 1412350 FALSE TRUE 1139821.851 1429115.4 1211203.236 1335292.135 1258601.369 1172507.912 1291996.982 1285308.499 1240796.803 1689072.941 0.674820976 0.846094544 0.717081664 0.790547348 0.74514329 0.694172456 0.764914854 0.760954999 0.734602262 1 20.6878002 -2.027997296 2.658760432 1.295825992 0.750772118 0.728155388 0.04623033 5015044.361 3158464.388 9026312.532 0.010397919 0.009375678 2.027997296 -0.545053874 SKFVLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKFVLVK 7 1 P30040;F8W1G0 P30040 ERP29 Endoplasmic reticulum resident protein 29 0 92.439 0.026257 0 275440 394250 247670 333290 425820 340250 286980 249200 290690 273380 FALSE TRUE 286314.5839 461959.3707 254124.4837 399213.7672 353439.2685 261232.094 264485.7577 245859.8816 280228.1237 326943.5768 0.875730873 1.412963592 0.777273211 1.221047898 1.081040563 0.799012773 0.808964532 0.751994837 0.857114632 1 18.31868215 2.741827636 23.40718253 0.819149668 1.084191867 0.298109908 0.174256302 123.0878617 881887.1574 0.049983492 0.050979872 551.8583726 -2.741827636 0.265042199 SKGGVVGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKGGVVGIK 9 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 123.79 0.0015734 0 1215500 852990 1209100 978300 1740700 1542800 1459500 1280800 1145700 859930 FALSE TRUE 1263488.879 999484.3972 1240610.139 1171804.82 1444816.436 1184508.081 1345100.576 1263632.971 1104466.481 1028416.819 1.228576638 0.971867028 1.206330076 1.139425959 1.404893822 1.151778208 1.307933273 1.228716749 1.073948287 1 19.97199368 5.058771988 21.67651826 1.183090109 2.083403894 0.004285015 0.126625707 5977.468293 1942338.827 0.02855291 30342.28872 114491.1686 -5.058771988 0.900313785 SKGGVVGIKVDK ddPTM_MDA-MB-175_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 ; 109.81 0.00087623 2719100000 8057700 4520200 7014300 3205200 9556500 7578800 5873400 7068500 8620200 4586300 FALSE TRUE 8375824.218 5296509.188 7197098.42 3839178.993 7932089.543 5818738.558 5413027.561 6973758.319 8309960.686 5484897.675 1.527070278 0.965653236 1.312166397 0.699954534 1.446169102 1.060865471 0.986896727 1.271447296 1.515062118 1 22.38703328 1.579495557 8.438971179 1.300673813 1.133262722 0.037222463 0.25767789 0.297829231 43.85812752 0.127559998 0.060229864 37.9748054 -1.579495557 -0.167411091 SKGHYEVTGS(ph)DDETGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVTGS(1)DDETGK;SKGHYEVTGS(1)DDETGK 217.42 8.62E-15 366000000 402490 351220 464730 362820 608780 672560 736630 539430 581820 276000 TRUE FALSE 418380.616 411539.3029 476841.2456 434584.7131 505299.7931 516368.1327 678891.0158 532199.8232 560880.4119 330076.9157 1.267524617 1.246798196 1.444636759 1.316616499 1.530854686 1.564387294 2.056766116 1.612350934 1.699241556 1 18.33244272 3.050748852 2.076242877 1.662050722 1.315650698 0.17643209 0.251078319 0.406503434 3.556586103 0.078331361 0.095021734 1123.954814 -3.050748852 -0.346400024 SKGHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 SKGHYEVT(0.002)GS(0.998)DDETGKLQGSGVSLASK 143.75 9.43E-08 514460000 170180 127850 212020 116800 286050 268170 234640 190560 246540 127110 TRUE FALSE 176898.8378 149807.243 217545.4154 139902.6914 237427.3232 205891.5817 216248.3037 188005.8549 237667.0736 152014.7708 1.16369506 0.985478202 1.431080771 0.92032301 1.561870086 1.354418262 1.42254797 1.23676044 1.563447238 1 17.21385199 4.242026942 24.99905605 1.31778926 1.074586609 0.173166572 0.206516383 135.1070997 974346.364 0.047081087 0.118739549 17459.30462 -4.242026942 -0.243202651 SKGQENDHVHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKGQENDHVHEK 12 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 ; 220.53 1.89E-11 261400000 275510 199975 280360 179167 373860 324180 328250 278890 298990 175449 FALSE TRUE 286387.3475 234319.1507 287666.4119 214605.6978 310311.4107 248894.108 302520.9073 275151.9357 288229.4083 209824.8724 1.36488751 1.116736772 1.370983376 1.022784837 1.478906706 1.186199258 1.441778107 1.311340894 1.373666549 1 17.67882618 SKGQESFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKGQESFK 8 1 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 ;; 110.53 0.0031076 8245980000 7957840 5235490 7499320 4874030 9377260 8741860 8636580 7459020 7776230 5215310 FALSE TRUE 8272021.668 6134644.681 7694758.44 5838098.586 7783316.695 6711695.499 7959622.292 7359044.037 7496365.001 6237150.141 1.326250207 0.983565337 1.233697805 0.93602021 1.247896318 1.076083684 1.27616333 1.179872838 1.201889458 1 22.57245556 SKGYAFIEFASFEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKGYAFIEFASFEDAK 16 1 P19338;H7BY16 P19338 NCL Nucleolin 0 152.37 5.05E-07 37371000 125620 77957 113360 56266 157770 125300 107590 102540 111520 76623 FALSE TRUE 130579.5746 91345.50833 116314.2547 67395.24686 130952.3118 96200.97394 99156.81467 101165.619 107506.417 91635.80981 1.424984129 0.996832008 1.269310054 0.735468448 1.429051721 1.04981856 1.082074954 1.103996562 1.173192196 1 16.48362387 4.750278725 24.23546644 1.099587829 1.42498443 0.248320993 0.172809793 1574.291922 3255866.43 0.037179506 0.585075179 56270.23446 -4.750278725 0.325396601 SKHEEEEWT(ph)DDDLVESL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 S(0.012)KHEEEEWT(0.988)DDDLVESL;S(0.005)KHEEEEWT(0.995)DDDLVESL;S(0.003)KHEEEEWT(0.997)DDDLVESL 171.85 2.71E-09 1494420000 1474960 1616850 1981120 1648150 2389430 2355080 2130730 1941590 2075510 1516750 TRUE FALSE 1533192.56 1894531.41 2032749.615 1974149.151 1983275.542 1808148.362 1963717.815 1915566.162 2000812.801 1813928.123 0.845233359 1.044435767 1.120634048 1.088328212 1.093359498 0.996813677 1.082577524 1.05603201 1.103027609 1 20.79068586 4.729249289 4.175008695 1.069530818 0.828913054 0.742905729 0.03896438 0.095903337 3.755516949 0.008969982 0.068163371 53610.42981 -4.729249289 -0.240617764 SKIETEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKIETEIK 8 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ;; 121.83 0.0012918 1176570000 2092790 1145540 1618140 1122220 2426240 2079870 2153020 1622140 2016390 1090030 FALSE TRUE 2175414.965 1342277.584 1660310.058 1344191.767 2013828.591 1596851.713 1984260.667 1600397.867 1943820.518 1303600.509 1.668774253 1.029669423 1.273634098 1.031137805 1.544820348 1.22495481 1.52213861 1.227675086 1.491116722 1 20.31407039 3.23647002 24.99999107 1.345884835 1.236639338 0.02943577 0.226526751 180.9397178 2163739.861 0.059278494 0.074263378 1723.733095 -3.23647002 -0.109245497 SKLEVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKLEVGR 7 1 P41223;C9JCD9 P41223 BUD31 Protein BUD31 homolog 0 ; 89.355 0.030569 0 229204 420100 385430 406320 369460 486550 371990 417700 364350 428110 FALSE TRUE 238253.1509 492248.9071 395474.6224 486688.8833 306659.3212 373556.1362 342832.4518 412101.4147 351237.1147 511989.9578 0.465347312 0.961442504 0.772426522 0.950582869 0.598955734 0.729616139 0.669607766 0.804901363 0.686023445 1 18.96575599 -1.9510579 3.858913144 1.162800411 0.748511105 0.230749608 0.142464239 0.098242982 0.001246004 0.067914942 0.029926154 0.011192887 1.9510579 -0.414289306 SKLS(ph)PS(ph)PSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 SKLS(1)PS(0.955)PS(0.045)LR;S(0.064)KLS(0.936)PS(0.99)PS(0.01)LR 106.55 0.0013666 598180000 1101800 760640 924810 699970 1289940 1307410 1133120 976100 1046660 680950 TRUE FALSE 1145299.915 891274.003 948911.3083 838421.9768 1070676.46 1003783.841 1044303.094 963016.9761 1008990.911 814369.1149 1.406364625 1.094434927 1.165210334 1.029535577 1.31473117 1.232590754 1.282346143 1.18253131 1.238984746 1 19.63532332 -1.081404244 4.712836882 0.999990164 1.209903861 0.284823555 0.102375014 1.01E-05 1.96E-06 0.094446974 0.022260323 0.08290787 1.081404244 0.209913698 SKLS(ph)PSPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKLSPSPSLR 10 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 S(0.001)KLS(0.999)PSPSLR;SKLS(0.81)PS(0.19)PSLR 187.97 7.10E-07 1276820000 2422900 1807140 2297700 1849290 2761900 2748800 2711500 2258030 2251100 1709640 TRUE FALSE 2518557.963 2117502.237 2357579.95 2215074.042 2292433.225 2110432.858 2498965.545 2227764.801 2170083.351 2044611.225 1.231802864 1.035650304 1.153070041 1.083371751 1.121207395 1.032192738 1.222220398 1.089578681 1.061367229 1 20.96339512 1.056875739 2.406992346 1.002192406 1.119633405 0.271922128 0.063909949 0.338083248 4.078521013 0.05506407 0.015080171 11.39923584 -1.056875739 0.117440999 SKLTFSCLGGSDNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKLTFSCLGGSDNFK 15 1 A0A087WYT3;Q15185-4;Q15185;Q15185-3;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 ; 199.65 6.67E-09 1755060000 2407000 1762220 2261150 1526170 3114600 2803800 2190950 2249860 2509800 2145260 FALSE TRUE 2502030.219 2064867.577 2320077.427 1828041.871 2585181.405 2152659.942 2019217.614 2219704.307 2419472.788 2565582.624 0.975228861 0.804833786 0.904308209 0.712525044 1.007639115 0.839053057 0.787040571 0.865185275 0.943050037 1 21.29085506 1.089338658 3.142937658 0.99795296 0.856957729 0.233187124 0.082337458 0.296390506 5.68604194 0.072387579 0.019171371 12.28396748 -1.089338658 -0.140995231 SKPAGS(ph)DGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.001)KPAGS(0.999)DGER 84.58 0.0089779 305050000 634160 499600 636720 449890 757200 741090 735500 610680 676520 457900 TRUE FALSE 659197.1265 585402.4137 653313.4463 538876.8992 628491.4145 568983.0788 677849.5881 602494.8335 652172.1774 547616.738 1.203756351 1.069000221 1.193012194 0.984040227 1.147684815 1.039016961 1.237817512 1.100212597 1.190928129 1 19.06280702 2.29415833 24.9999995 1.139742905 1.10469432 0.018896783 0.085402525 326.3108375 146726.9568 0.027158673 0.022722558 196.8603849 -2.29415833 -0.035048585 SKPAGS(ph)DGERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.001)KPAGS(0.999)DGERR;S(0.129)KPAGS(0.871)DGERR;S(0.001)KPAGS(0.999)DGERR 98.676 0.0042079 1408000000 2329740 1722360 1993400 1741150 2592350 2537940 2311990 2028770 2129230 1480220 TRUE FALSE 2421719.934 2018161.932 2045349.642 2085544.273 2151703.273 1948541.898 2130770.183 2001577.657 2052599.428 1770240.768 1.368017265 1.140049403 1.155407602 1.178113345 1.215486227 1.1007214 1.203661231 1.130681031 1.15950297 1 20.75551416 -4.999999999 0.047109077 0.298235561 1.549092478 0.520763745 0.061417381 522.5416556 1.826595954 48.23722941 11.76327133 1.00E-05 4.999999999 1.250856917 SKPAGSDGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKPAGSDGER 10 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 103.08 0.0026097 565560000 606410 498460 623060 506890 688860 698010 766440 600960 611490 443480 FALSE TRUE 630351.5351 584066.6275 639297.4554 607151.3291 571767.8233 535907.7559 706364.4301 592905.1142 589482.5943 530371.4151 1.188509631 1.101240774 1.205376906 1.144766313 1.078051733 1.010438611 1.331829752 1.117905485 1.111452423 1 19.0166435 0.848436396 2.538586481 1.000381501 1.147964205 0.231236724 0.080958959 0.863706135 10.4382584 0.075719106 0.020259147 7.054015281 -0.848436396 0.147582704 SKPAGSDGERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKPAGSDGERR 11 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;; 144.57 2.06E-05 477360000 576520 492400 579011 452384 715920 660770 562500 549970 578480 476799 FALSE TRUE 599281.4548 576965.8697 594100.5023 541864.205 594228.1741 507316.1816 518409.7802 542598.5517 557660.6178 570218.6352 1.050967853 1.011832715 1.041881948 0.950274459 1.042105848 0.889687131 0.909142122 0.951562292 0.977976838 1 19.12115566 3.401593446 1.175913867 0.945251136 1.035174633 0.377399507 0.042451535 0.471143125 1.349552956 0.015264195 0.028620184 2521.119584 -3.401593446 0.089923497 SKPCGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPCGSPR 8 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 S(0.003)KPCGS(0.997)PR;SKPCGS(1)PR 84.17 0.010684 440270000 828870 575890 761680 624510 937510 879930 858430 751420 783530 574420 TRUE FALSE 861594.4276 674794.6277 781530.0065 748036.214 778152.3851 675579.593 791144.0135 741348.444 755330.9084 686966.6011 1.254201334 0.982281565 1.137653571 1.088897499 1.132736852 0.983424219 1.151648439 1.079162281 1.099516202 1 19.38988043 -5 0.156141302 0.663574077 1.123615887 0.159731077 0.074538604 262.0569335 2.382856844 27.62233965 0.308070486 1.00E-05 5 0.460041809 SKPDLESS(ph)LESLVFDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPDLESSLESLVFDLR 17 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 SKPDLES(0.033)S(0.967)LESLVFDLR;SKPDLES(0.04)S(0.96)LESLVFDLR 215.79 3.33E-15 116234000 148263 125974 141474 115990 164538 162218 172203 145258 144969 103693 TRUE FALSE 154116.5377 147609.0546 145160.9287 138932.4758 136569.8895 124545.3279 158705.2789 143311.0541 139751.594 124009.658 1.242778508 1.190302892 1.170561479 1.120335932 1.101284301 1.004319582 1.279781603 1.155644297 1.12694121 1 16.92009296 -4.999999963 0.262947771 1.08E-10 1.166897321 0.305560572 0.071622914 271.1377057 2.65571504 147.0191141 0.096299313 1.00E-05 4.999999963 1.16689732 SKPGAAMVEMADGYAVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SKPGAAMVEMADGYAVDR 18 1 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ;;;;;;; 207.43 6.78E-16 3838230000 3240826 3387163 3890571 3512201 4398117 4705288 4221052 3920854 4020382 3319545 FALSE TRUE 3368776.313 3968881.897 3991962.476 4206903.875 3650526.643 3612556.171 3890194.915 3868301.365 3875689.237 3969946.286 0.848569746 0.999731888 1.005545715 1.059687858 0.919540563 0.909976083 0.979911221 0.974396399 0.976257349 1 21.92068806 7.999874547 0.010667085 1.360054758 0.523053714 0.057496823 0.054980677 51549.5358 42.49762661 1422.063414 1951.298705 99971117.55 -7.999874547 -0.837001044 SKPIPIMPAS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 94.01 0.0024064 362560000 1102210 528930 688050 584320 902810 969450 1116280 752210 840700 370620 TRUE FALSE 1145726.102 619769.613 705981.1482 699896.752 749350.6787 744309.9297 1028783.057 742127.8553 810443.3712 443235.8931 2.584912729 1.3982839 1.592788759 1.57906154 1.690636274 1.679263664 2.321073435 1.674340609 1.828469634 1 18.75771519 -0.649285966 9.840370822 1.000000002 1.795944096 0.334691674 0.344271037 0 0 0.314339116 0.07409044 0.22424049 0.649285966 0.795944093 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPIPIMPASPQKGHAVNLLDVPVPVAR 28 2 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 1 S(0.11)KPIPIMPAS(0.89)PQKGHAVNLLDVPVPVAR;SKPIPIMPAS(1)PQKGHAVNLLDVPVPVAR 256.15 7.90E-54 4977000000 3313000 2192580 2976500 2019260 4058100 3821100 3162400 3144800 3374600 2106380 TRUE FALSE 3443799.798 2569138.559 3054070.035 2418663.601 3368305.612 2933707.434 2914522.825 3102649.1 3253148.805 2519084.832 1.367083694 1.019869806 1.212372841 0.960135828 1.3371148 1.164592552 1.156976846 1.231657251 1.291401053 1 21.26446828 3.211710031 24.99987661 1.205655737 1.136473097 0.040098042 0.132398339 650.6164997 605770.3638 0.035478004 0.042415744 1628.208551 -3.211710031 -0.06918264 SKPLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPLTR 6 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 94.407 0.0406 972000000 1330840 1366890 1497280 1277900 1742970 1856240 1574250 1515990 1442910 1102060 FALSE TRUE 1383382.591 1601642.725 1536300.347 1530664.806 1446700.582 1425156.392 1450856.171 1495670.634 1390979.951 1317987.557 1.049617338 1.215218396 1.16564101 1.161365142 1.097658756 1.081312478 1.100811737 1.134813926 1.055381702 1 20.32990532 0.392993554 0.298037344 0.970605399 1.155429573 0.443236651 0.045426792 3.430023565 0.609380508 0.19391781 0.06140072 2.471687459 -0.392993554 0.184824173 SKPNLPSES(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPNLPSESR 10 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 SKPNLPS(0.012)ES(0.988)R;SKPNLPS(0.005)ES(0.995)R 93.228 0.0054072 404350000 542370 452820 541800 590480 576970 635420 816620 606220 572680 345160 TRUE FALSE 563783.1864 530588.3125 555919.7531 707275.1816 478896.8455 487853.3349 752611.1906 598094.6125 552069.3587 412787.4935 1.365795222 1.285378847 1.34674563 1.713412331 1.160153476 1.181851055 1.823241262 1.448916505 1.337417842 1 18.65503974 3.980144813 24.76647544 1.419796166 1.323205726 0 0.236668194 2840.61994 3543277.484 0.059889701 0.109915538 9553.110768 -3.980144813 -0.09659044 SKPYEGSQRNS(ph)TELAPPLPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKPYEGSQRNSTELAPPLPVR 21 2 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SKPYEGS(0.001)QRNS(0.796)T(0.204)ELAPPLPVR 201.16 3.70E-22 524510000 159810 142710 196260 148320 244210 255070 170280 194180 231570 156540 TRUE FALSE 166119.4222 167219.3324 201374.6968 177657.2533 202699.2714 195833.8581 156933.0087 191577.3347 223235.8409 187211.0159 0.88733786 0.893213103 1.075656237 0.948967947 1.08273154 1.046059481 0.838268026 1.02332298 1.192428981 1 17.5143058 4.257353669 24.40012189 1.017192459 0.890275284 0.27431832 0.087334697 253.7398114 329437.6334 0.021250075 0.057956558 18086.46402 -4.257353669 -0.126917175 SKPYEGSQRNS(ph)TELAPPLPVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKPYEGSQRNSTELAPPLPVRR 22 3 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SKPYEGS(0.016)QRNS(0.963)T(0.021)ELAPPLPVRR;S(0.005)KPYEGS(0.2)QRNS(0.74)T(0.055)ELAPPLPVRR 124.45 1.62E-05 135063000 110096 110914 143182 90684 173270 158313 113438 119374 159385 153601 TRUE FALSE 114442.6751 129962.6167 146913.4405 108621.0245 143817.6273 121547.205 104546.4331 117773.9868 153648.765 183696.1751 0.622999771 0.707486787 0.799763199 0.591308036 0.782910299 0.661675209 0.569126892 0.641134671 0.836428766 1 17.48696206 1.010710507 3.668123037 0.998652507 0.672173508 0.683261849 0.071359763 0.110141249 3.709782367 0.069243906 0.017868123 10.24968472 -1.010710507 -0.326478999 SKQEALKNDLVEALKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKQEALKNDLVEALKR 16 3 P47756-2;B1AK88 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ; 118.24 0.00012603 1013960000 1999170 930990 1461260 922950 2179490 1815200 1705250 1507000 1903180 865990 FALSE TRUE 2078098.775 1090880.29 1499341.636 1105506.755 1809021.068 1393647.31 1571588.049 1486801.13 1834684.924 1035664.16 2.006537307 1.053314706 1.447710265 1.067437494 1.746725568 1.345655632 1.517468799 1.435601604 1.771505662 1 19.98212482 -0.974727422 5.530758595 0.999999009 1.463942277 0.204648166 0.285083414 3.15E-06 5.84E-07 0.249797501 0.05887771 0.105991876 0.974727422 0.463943268 SKRPNPCAYT(ph)PPSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKRPNPCAYTPPSLK 15 2 Q9UD71;J3KSJ8;Q9UD71-2 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 1 SKRPNPCAYT(1)PPSLK 158.15 8.76E-05 910010000 993660 518040 725570 556180 998110 916390 765770 752350 784110 518910 TRUE FALSE 1032890.464 607009.3402 744478.9503 666190.744 828451.6187 703572.3105 705746.9464 742265.9788 755890.0343 620580.4794 1.664394061 0.97813154 1.19964932 1.073496132 1.33496242 1.133732584 1.137236781 1.19608335 1.218037079 1 19.24325879 SKS(ph)AT(ph)TTPSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 S(0.01)KS(0.972)AT(0.657)T(0.179)T(0.18)PS(0.035)GS(0.967)PR 136.66 0.00050162 239680000 573610 378490 440990 346530 585110 608180 499070 443550 464890 339210 TRUE FALSE 596256.5657 443492.7133 452482.5617 415072.5997 485653.2112 466939.4121 459951.5893 437604.9378 448158.6997 405671.7049 1.469800724 1.09323058 1.115390983 1.023173652 1.197158208 1.151027805 1.13380249 1.078716934 1.104732458 1 18.62995315 4.739699834 24.98509603 1.105174878 1.469800842 0.803326418 0.054878207 39.40151734 864040.7656 0.012568096 0.077910327 54916.11859 -4.739699834 0.364625963 SKS(ph)ATT(ph)TPSGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSATTTPSGSPR 13 1 A0A096LNZ0;A0A096LP60;A0A096LP25;Q2M2I8;Q2M2I8-2 A0A096LNZ0;A0A096LP25;Q2M2I8 AAK1 AP2-associated protein kinase 1 3 S(0.008)KS(0.953)AT(0.098)T(0.435)T(0.336)PS(0.182)GS(0.988)PR 119.08 0.0027135 273900000 419290 303400 368660 299000 475840 504430 434350 367620 379220 283640 TRUE FALSE 435843.893 355506.5899 378267.5825 358141.3076 394956.8868 387283.7772 400304.512 362692.6552 365571.9463 339213.8274 1.28486476 1.04803095 1.115130198 1.05579808 1.164330151 1.141709877 1.180094913 1.069215421 1.077703551 1 18.37183545 1.130002319 1.433394497 1.004923184 1.133085491 0.30797769 0.06493081 0.478634943 1.945745194 0.057793943 0.017492763 13.48970086 -1.130002319 0.128162307 SKS(ph)DLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SKSDLSER 8 1 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 S(0.368)KS(0.632)DLSER;S(0.033)KS(0.967)DLSER;S(0.01)KS(0.99)DLSER;S(0.066)KS(0.934)DLSER;S(0.019)KS(0.981)DLSER;S(0.004)KS(0.996)DLSER 141.38 0.00038422 7075650000 5965650 4431580 5294380 4280890 6807970 6541540 6510040 5488030 5871600 3951280 TRUE FALSE 6201178.468 5192669.392 5432355.892 5127637.265 5650753.691 5022366.473 5999766.054 5414471.934 5660282.263 4725457.664 1.312291615 1.098871212 1.149593601 1.085109132 1.195810881 1.062831757 1.269668777 1.145809003 1.197827314 1 22.17202263 4.748166663 24.48782475 1.14349812 1.312291736 0.33927493 0.073586294 1136.359982 2896739.906 0.016068642 0.209600991 55997.24531 -4.748166663 0.168793616 SKS(ph)DSYTLDPDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.021)KS(0.978)DSYT(0.001)LDPDTLR;S(0.025)KS(0.487)DS(0.487)YT(0.001)LDPDTLR 239.33 6.16E-17 822030000 937460 682580 915790 723320 1249800 1154670 1030970 972730 954750 717230 TRUE FALSE 974471.6447 799807.8053 939656.2397 866390.5371 1037359.442 886515.3917 950159.8775 959692.1454 920388.734 857757.4863 1.136068948 0.932440484 1.09548008 1.010064676 1.209385472 1.033526849 1.107725543 1.118838554 1.073017431 1 19.71021029 SKS(ph)EDMDNVQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSEDMDNVQSK 12 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 S(0.155)KS(0.845)EDMDNVQSK;S(0.345)KS(0.655)EDMDNVQSK;S(0.001)KS(0.999)EDMDNVQSK 180.78 1.15E-05 1214584000 2159110 980394 1552030 1028565 2320790 2031700 2277950 1550640 1876710 755683 TRUE FALSE 2244353.33 1148769.043 1592477.177 1232012.087 1926302.945 1559868.466 2099398.327 1529856.207 1809167.574 903744.6154 2.483393308 1.271121314 1.762087596 1.363230348 2.13146824 1.72600582 2.322999541 1.692797037 2.001857099 1 19.78555562 3.225548342 24.99786689 1.866721765 1.690907515 0 0.448830977 908.9910242 1746258.638 0.119346648 0.143478438 1680.925022 -3.225548342 -0.17581425 SKS(ph)EEAHAEDSVMDHHFR ddPTM_MDA-MB-175_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(0.231)KS(0.769)EEAHAEDSVMDHHFR 158.8 2.24E-11 510520000 116820 92307 133500 83670 136830 152200 175800 120750 166160 76731 TRUE FALSE 121432.1438 108160.0092 136979.1197 100219.6763 113571.6855 116853.8566 162020.3366 119131.5438 160179.9341 91764.97035 1.323295189 1.17866337 1.492716874 1.09213435 1.237636595 1.273403742 1.765601144 1.29822462 1.745545533 1 16.48565591 2.426668784 24.99995564 1.474717854 1.262393079 0.137687893 0.225352462 176.1785 87298.05356 0.071371396 0.059713603 267.0968608 -2.426668784 -0.212324775 SKS(ph)ERECPHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSERECPHSK 11 2 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 S(0.169)KS(0.831)ERECPHSK 88.561 0.0067239 27631000 30182 24413 27824 19629 50486 37199 26707 30058 37941 31485 TRUE FALSE 31373.60867 28605.74284 28549.1163 23511.55761 41904.40775 28560.09601 24613.63555 29655.12167 36575.51082 37653.88293 0.833210448 0.759702337 0.758198466 0.624412565 1.112884104 0.758490062 0.653681205 0.78757141 0.971360932 1 15.20051103 1.223668605 5.78591683 0.99152303 0.782067734 0.291727428 0.124577477 0.203917584 21.83930521 0.106239357 0.03022531 16.73665274 -1.223668605 -0.209455296 SKS(ph)HESQLGNR ddPTM_MDA-MB-175_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(0.001)KS(0.869)HES(0.13)QLGNR;S(0.268)KS(0.723)HES(0.008)QLGNR 116.96 0.00055637 118526000 39418 100014 121329 101563 137788 145560 117213 120512 119304 92777 TRUE FALSE 40974.25308 117190.6265 124490.9334 121651.8583 114366.845 111755.896 108025.5388 118896.7338 115010.2723 110954.8768 0.369287536 1.056200771 1.121996049 1.096408394 1.030750953 1.007219324 0.973598835 1.071577358 1.036549953 1 16.75961355 4.739062007 24.99967193 1.046430048 0.36928733 0.957266755 0.042751584 7.857771275 391688.6568 0.010964095 0.064897339 54835.52516 -4.739062007 -0.677142718 SKS(ph)ISSS(ph)NPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.384)KS(0.499)IS(0.328)S(0.371)S(0.418)NPDLAVAPGSVDDEVSR 135.39 1.61E-05 206340000 211840 132260 210030 142620 304010 253860 197060 193250 232400 151340 TRUE FALSE 220203.6068 154974.6262 215503.5543 170829.8103 252334.4888 194904.8623 181613.9223 190659.7998 224035.9694 180992.1754 1.216647108 0.85625042 1.190678845 0.943851909 1.394173467 1.076868996 1.003435214 1.053414599 1.237821297 1 17.4655678 SKS(ph)LDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SKSLDSR 7 1 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 S(0.047)KS(0.953)LDSR;S(0.407)KS(0.593)LDSR;SKS(1)LDSR;S(0.001)KS(0.999)LDSR;S(0.034)KS(0.966)LDSR 158.79 0.00085243 12289800000 33173600 23207700 31337300 22190300 38517600 35933300 37046600 31760700 33106100 20280100 TRUE FALSE 34483319.34 27193441.94 32153975.78 26579475.11 31970392.11 27588335.65 34142790.69 31334999.77 31914617.93 24253597.31 1.421781639 1.121212726 1.325740482 1.095898261 1.318171144 1.137494587 1.407741303 1.291973284 1.315871519 1 24.53169541 2.259814694 24.99985264 1.284326014 1.232814561 0 0.137492809 980.5484837 1153354.157 0.04342857 0.036304085 181.8924591 -2.259814694 -0.051511453 SKS(ph)MSDVSAEDVQNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SKSMSDVSAEDVQNLR 16 1 E9PMS6;E9PJ10 E9PMS6 LMO7 1 S(0.033)KS(0.965)MS(0.002)DVSAEDVQNLR;S(0.063)KS(0.934)MS(0.003)DVSAEDVQNLR;S(0.248)KS(0.751)MS(0.001)DVSAEDVQNLR;S(0.203)KS(0.796)MSDVSAEDVQNLR;S(0.001)KS(0.999)MSDVSAEDVQNLR;SKS(0.995)MS(0.005)DVSAEDVQNLR;S(0.062)KS(0.937)MS(0.001)DVSAEDVQNLR;S(0.016)KS(0.983)MS(0.001)DVSAEDVQNLR;S(0.002)KS(0.996)MS(0.002)DVSAEDVQNLR 245.09 2.58E-20 14648750000 5650960 4510360 5830440 4035276 7483480 6687570 5568790 5476830 6008240 4558260 TRUE FALSE 5874064.264 5284979.244 5982386.056 4833441.549 6211440.743 5134483.219 5132293.688 5403422.052 5792004.616 5451363.774 1.07754032 0.969478366 1.097410906 0.88664814 1.139428774 0.941871325 0.941469676 0.991205554 1.06248727 1 22.37818577 SKS(ph)NPDFLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSNPDFLKK 10 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;H7C3G6;J3QL44;J3QRL2;K7EL39;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 SKS(1)NPDFLKK 156.24 5.89E-06 1295900000 1746500 773650 1164700 695400 1745700 1328300 1488200 1070900 1288300 528580 TRUE FALSE 1815453.169 906518.3693 1195053.039 832948.0444 1448966.538 1019822.456 1371550.995 1056546.337 1241934.335 632145.1307 2.871892988 1.434035201 1.890472584 1.317653184 2.292142211 1.613272658 2.169677387 1.671366725 1.964634819 1 19.26989629 -2.106975782 0.476789249 2.86E-13 1.895172431 0.284919103 0.432513856 95.58105366 6.609028542 103.8158071 0.195725855 0.007816714 2.106975782 1.895172431 SKS(ph)PASVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKSPASVDR 9 1 Q13243;Q13243-3 Q13243 SRSF5 Serine/arginine-rich splicing factor 5 1 S(0.409)KS(0.588)PAS(0.003)VDR;S(0.055)KS(0.944)PASVDR;S(0.002)KS(0.826)PAS(0.172)VDR;S(0.008)KS(0.974)PAS(0.018)VDR 155.66 4.41E-05 1655333000 1777370 1249760 1486860 1168530 1916990 1865680 1773460 1515900 1571250 1177540 TRUE FALSE 1847541.94 1464396.558 1525608.793 1399661.746 1591140.725 1432404.095 1634451.571 1495581.84 1514701.019 1408256.418 1.31193575 1.039864999 1.083331682 0.993896941 1.129865772 1.017147216 1.160620716 1.062009604 1.075586094 1 20.42547862 4.742564533 24.98992453 1.067857815 1.311935846 0.68016216 0.051198995 216.3442618 1350233.924 0.011154314 0.085365261 55279.55431 -4.742564533 0.244078031 SKS(ph)PIPGQGYLGTERPSSVSSVHSEGDYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPIPGQGYLGTERPSSVSSVHSEGDYHR 30 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KRE4 O75376 NCOR1 Nuclear receptor corepressor 1 1 S(0.247)KS(0.752)PIPGQGY(0.001)LGTERPSSVSSVHSEGDYHR 65.058 0.0039295 152700000 17693 29549 36385 28521 35547 40737 32760 32591 32305 29073 TRUE FALSE 18391.5333 34623.81089 37333.22299 34162.36867 29504.73364 31276.44913 30192.1856 32154.17095 31142.34936 34769.29771 0.52895901 0.995815653 1.073741072 0.98254411 0.848585838 0.899542159 0.868357648 0.924786322 0.895685315 1 15.08552631 4.743523974 24.98882384 0.937826173 0.528958841 0.77838022 0.066258733 262.2788625 1320442.524 0.017335285 0.144534268 55401.81256 -4.743523974 -0.408867333 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 S(0.44)KS(0.56)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK;S(0.194)KS(0.806)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 334.67 2.14E-129 5593240000 1443820 382275 806344 457804 1176070 1243610 1138911 715398 822203 293757 TRUE FALSE 1500823.128 447927.7576 827357.9871 548356.2648 976162.0415 954800.4246 1049640.18 705809.26 792612.0746 351313.0598 4.272039101 1.275010265 2.355044778 1.560876402 2.778610172 2.717805097 2.987763052 2.009060694 2.256141787 1 18.42239768 4.755397722 24.69079407 2.198163828 4.272041048 0.509917123 0.63151325 2423.648431 3554093.15 0.144654763 4.094318419 56937.41182 -4.755397722 2.073877221 SKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPPKVPIVIQDDSLPAGPPPQIR 25 2 Q7Z422-5;Q7Z422;Q7Z422-4;Q7Z422-2;Q7Z422-3 Q7Z422-5 SZRD1 SUZ domain-containing protein 1 1 S(0.118)KS(0.882)PPKVPIVIQDDSLPAGPPPQIR 237.5 1.42E-38 429240000 283080 121320 192340 135930 253390 274140 274700 200440 194100 101040 TRUE FALSE 294256.217 142155.7663 197352.5384 162816.5483 210318.8583 210475.1396 253168.2962 197753.4297 187114.3789 120836.8535 2.435152923 1.176427242 1.633214808 1.347408043 1.740519157 1.741812482 2.095124864 1.636532432 1.54848768 1 16.882701 SKS(ph)PSGQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.236)KS(0.61)PS(0.153)GQKR 59.57 0.052916 335200000 183530 93889 150080 86075 209360 162240 174770 148800 166830 102570 TRUE FALSE 190775.9061 110013.7054 153991.2081 103100.3781 173773.062 124562.2188 161071.0707 146805.5794 160825.8209 122666.6277 1.555238859 0.896851144 1.255363508 0.84049248 1.416628673 1.015453193 1.313079798 1.196784995 1.311080478 1 16.90438328 3.166229947 24.80630276 1.215275858 1.128155046 0.024010985 0.219257442 155.9129441 53467.60307 0.058037259 0.069367817 1466.324012 -3.166229947 -0.087120812 SKS(ph)PSPPR ddPTM_MDA-MB-175_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(0.007)KS(0.677)PS(0.316)PPR;S(0.007)KS(0.496)PS(0.496)PPR 82.008 0.012951 420150000 320770 225342 284910 225600 344680 382870 346930 296230 302350 205145 TRUE FALSE 333434.2473 264042.7356 292334.9887 270223.0067 286091.4167 293954.245 319736.7201 292259.5214 291468.4826 245339.235 1.359074293 1.076235261 1.19155417 1.101425977 1.166105441 1.198154241 1.303243324 1.191246567 1.188022301 1 17.90441844 0.629683684 3.856523954 1.000000392 1.194657825 0.359349208 0.078986105 15.09415879 156.0171673 0.072720711 0.018617933 4.262689353 -0.629683684 0.194657433 SKS(ph)PTISDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSPTISDK 9 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 S(0.001)KS(0.69)PT(0.308)ISDK;S(0.001)KS(0.855)PT(0.144)ISDK;S(0.004)KS(0.913)PT(0.083)ISDK 131.06 0.00020817 677660000 2278210 1122905 1661327 1120005 2328752 2274474 2307325 1775967 2012870 1079535 TRUE FALSE 2368155.49 1315755.199 1704622.546 1341538.646 1932911.567 1746261.883 2126470.837 1752163.067 1940427.202 1291049.214 1.834287542 1.019136361 1.320338936 1.039107287 1.49716335 1.35259126 1.647087356 1.357162103 1.502984689 1 20.30011257 SKS(ph)PVGNPQLIQFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 S(0.009)KS(0.991)PVGNPQLIQFSR;S(0.027)KS(0.973)PVGNPQLIQFSR 166.27 8.34E-07 1491580000 193297 133825 202569 98065 201474 220700 195191 152112 176794 146361 TRUE FALSE 200928.5148 156808.4027 207848.1146 117461.9643 167227.5214 169445.7697 179891.4194 150073.1874 170431.2185 175037.6357 1.14791607 0.895855352 1.187448138 0.671066904 0.955380372 0.968053351 1.027729943 0.857376683 0.973683276 1 17.41730563 3.788278709 24.99999276 0.921858429 1.058951273 0.259693906 0.118886211 551.7212343 277422.8224 0.028923551 0.052142598 6141.560142 -3.788278709 0.137092844 SKS(ph)QSSSNCSNPISVPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSQSSSNCSNPISVPLRR 19 2 P35568 P35568 IRS1 Insulin receptor substrate 1 1 S(0.045)KS(0.916)QS(0.034)S(0.003)S(0.001)NCSNPISVPLRR;S(0.004)KS(0.989)QS(0.006)S(0.001)SNCSNPISVPLRR;S(0.041)KS(0.866)QS(0.041)S(0.041)S(0.009)NCS(0.001)NPISVPLRR 138.99 4.40E-07 1176290000 592046 519084 646838 472787 855190 818014 533137 647820 693743 629372 TRUE FALSE 615420.4332 608232.6391 663695.1297 566302.8575 709825.1093 628042.6456 491348.3288 639137.0325 668775.3249 752685.3933 0.817633023 0.808083489 0.881769642 0.752376574 0.943056841 0.834402595 0.652793761 0.849142335 0.888519069 1 19.52168745 0.970979471 2.512261067 0.998485584 0.81507043 0.38058415 0.072389737 0.306688129 4.43368836 0.068368376 0.018437979 9.353614591 -0.970979471 -0.183415154 SKS(ph)TAALSGEAASCSPIIMPYK ddPTM_MDA-MB-175_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(0.193)KS(0.616)T(0.151)AALS(0.04)GEAASCSPIIMPYK;S(0.309)KS(0.478)T(0.134)AALS(0.079)GEAASCSPIIMPYK 181.31 3.03E-17 1068690000 1141620 1321880 1615830 1036110 2700600 1710990 1020570 1383990 1454660 1622760 TRUE FALSE 1186692.039 1548902.607 1657939.857 1241049.466 2241552.977 1313638.503 940575.0566 1365439.878 1402307.071 1940708.752 0.611473534 0.798111827 0.854296068 0.639482593 1.155017709 0.676885958 0.484655441 0.703577946 0.722574714 1 20.88815219 SKS(ph)VIEQVSWDT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSVIEQVSWDT 12 1 Q6WCQ1 Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.177)KS(0.823)VIEQVSWDT 129.01 0.00063635 276260000 1003200 855070 1027000 777820 1588000 1280700 1196300 1089400 1248000 1005600 TRUE FALSE 1042807.111 1001921.621 1053764.464 931670.4744 1318072.327 983276.8342 1102530.88 1074798.375 1203084.724 1202628.067 0.867106913 0.833110127 0.876218087 0.774695436 1.09599332 0.817606758 0.916767961 0.893708042 1.000379716 1 20.1977591 3.420357014 0.111886444 1.079713913 0.685712814 0.236973055 0.08140597 40.06932868 1.251214083 1.27937676 3.181546116 2632.431108 -3.420357014 -0.394001099 SKS(ph)YDEGLDDYREDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSYDEGLDDYREDAK 16 2 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 S(0.127)KS(0.873)YDEGLDDYREDAK 155.01 1.57E-07 142160000 377820 153330 253620 141470 362780 320410 327950 230330 279420 106490 TRUE FALSE 392736.6253 179663.2348 260229.5456 169452.3438 301114.7852 245999.6334 302244.4221 227242.8031 269363.7288 127354.6766 3.083802148 1.410731349 2.04334503 1.330554545 2.364379489 1.931610522 2.373249496 1.784330259 2.115067432 1 16.95849241 -1.225422335 3.859762309 0.998973268 2.011459212 0.29820768 0.479539798 12605222.43 8004754.148 101246.8306 0.101392867 0.059508317 1.225422335 1.012485944 SKSDGEAKPEPSPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKSDGEAKPEPSPSPR 16 2 P26358;K7EJL0;K7ENQ6;K7ERQ1 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 SKSDGEAKPEPS(0.223)PS(0.777)PR;SKSDGEAKPEPS(0.209)PS(0.791)PR;SKSDGEAKPEPS(0.158)PS(0.842)PR 108.18 0.00055843 562790000 963060 497970 716130 470020 950280 911980 901880 676830 761000 405130 TRUE FALSE 1001082.352 583492.4738 734792.9361 562988.5531 788751.745 700186.4662 831188.289 667758.2009 733611.7587 484507.4668 2.066185603 1.204300271 1.516577115 1.16198117 1.627945489 1.445151033 1.715532465 1.37822066 1.514139222 1 18.88615937 -0.217069096 1.102216723 0.994620495 1.499205793 0.280827146 0.24574327 24.45355978 20.15024567 0.811535132 0.06642805 0.606639805 0.217069096 0.504585298 SKSDS(ph)YTLDPDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.008)KS(0.194)DS(0.798)YT(0.001)LDPDTLR 242.1 4.77E-17 146840000 271670 228460 293380 246400 382810 366360 328740 298430 307770 208630 TRUE FALSE 282395.7414 267696.2278 301025.7238 295137.1846 317740.0929 281278.4422 302972.4998 294430.034 296693.4178 249507.054 1.131814659 1.072900439 1.206481817 1.182881124 1.273471382 1.127336633 1.214284305 1.180046933 1.189118356 1 17.92872108 4.236168469 24.99998259 1.182536489 1.102357542 0.123362441 0.069283577 88.47181582 924648.782 0.015421644 0.036040103 17225.36642 -4.236168469 -0.080178947 SKSEEAHAEDSVMDHHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SKSEEAHAEDSVMDHHFR 18 1 Q8NC51;Q8NC51-2;Q8NC51-3;Q8NC51-4 Q8NC51;Q8NC51-3 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 ;;;; 139.9 4.40E-08 3202690000 2561980 3522840 4232670 3213070 4772550 4828800 4034860 4175270 4102680 3773880 FALSE TRUE 2663128.949 4127860.366 4342976.857 3848605.656 3961313.656 3707384.381 3718597.13 4119307.335 3955025.348 4513299.531 0.590062532 0.91459925 0.96226205 0.852725513 0.87769793 0.821435483 0.823919863 0.912704177 0.876304646 1 22.1057511 7.999990368 0.030470329 1.458965442 3.49E-08 0.279056569 0.089859789 2102.432874 4.909295012 74.35961796 183.0806884 99997782.15 -7.999990368 -1.458965407 SKSERPPTILMTEEPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSERPPTILMTEEPSSPK 19 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 SKSERPPTILMTEEPS(0.031)S(0.969)PK 96.903 0.0010656 200580000 426320 123670 172410 150030 279510 265230 268300 214290 219270 89366 TRUE FALSE 443151.4428 144909.3605 176903.1462 179705.4862 231998.99 203634.3521 247269.9449 211417.7931 211378.5155 106875.5567 4.146424651 1.355869995 1.655225495 1.681446083 2.170739477 1.905340738 2.313624861 1.978167877 1.97780037 1 16.70557241 8 0.052791298 4.56E-15 5.863341046 0.235321479 0.698277348 846.4939437 3.362160702 84.24494755 396.7061746 100000000 -8 5.863341046 SKSIS(ph)S(ph)SNPDLAVAPGSVDDEVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSISSSNPDLAVAPGSVDDEVSR 24 1 K7ESB7;K7EKT0;K7EP20;Q96HP0 K7ESB7;Q96HP0 DOCK6 Dedicator of cytokinesis protein 6 2 S(0.345)KS(0.406)IS(0.432)S(0.424)S(0.392)NPDLAVAPGSVDDEVSR 92.632 0.004834 114190000 53602 39694 51343 37471 85187 63727 53099 54048 61560 40889 TRUE FALSE 55718.24835 46511.13572 52681.04076 44882.65196 70706.94417 48927.37004 48936.96163 53323.57496 59344.46763 48900.41668 1.139422772 0.951139865 1.077312717 0.917837822 1.445937457 1.000551189 1.000747334 1.090452364 1.213577954 1 15.57755914 SKSPS(ph)GQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKSPSGQKR 9 2 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 1 S(0.38)KS(0.13)PS(0.489)GQKR 73.386 0.034705 1054300000 1267500 694190 1097100 610240 1433700 1179600 1234600 1035700 1261500 744580 TRUE FALSE 1317541.879 813411.7325 1125691.327 730943.6506 1190000.186 905655.777 1137828.826 1021818.136 1216098.861 890466.1952 1.479609092 0.913467279 1.264159531 0.820855025 1.336378846 1.017058011 1.27779003 1.147509182 1.365687848 1 19.76420132 2.218856623 24.93988647 1.205759175 1.128611033 0.017870422 0.203637113 983.0109961 1244216.2 0.069576251 0.051457704 165.5223423 -2.218856623 -0.077148141 SKT(ph)FDWAEFRPIQQALAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKTFDWAEFRPIQQALAQER 20 2 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 S(0.058)KT(0.942)FDWAEFRPIQQALAQER;S(0.189)KT(0.811)FDWAEFRPIQQALAQER 162.26 1.02E-09 1573880000 242500 183170 261862 183087 347688 306602 265544 246941 267783 201629 TRUE FALSE 252074.0873 214628.0226 268686.3388 219301.0621 288588.118 235398.3321 244729.9674 243631.1598 258145.5421 241134.3421 1.045367844 0.890076547 1.114259945 0.90945595 1.196793934 0.976212389 1.014911295 1.010354467 1.070546567 1 17.87947761 4.240145555 24.99933908 1.033610629 0.967722236 0.100449683 0.082026955 90.09427327 1420937.895 0.01836757 0.045265222 17383.83354 -4.240145555 -0.065888393 SKTDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKTDLLVNDNPDPAPLSPELQDFK 24 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK;SKTDLLVNDNPDPAPLS(1)PELQDFK 249.13 2.04E-38 590380000 966360 466120 638260 518570 790230 813880 909680 679660 716680 341167 TRUE FALSE 1004512.639 546172.4841 654893.5799 621141.5982 655906.9869 624868.7045 838376.9046 670550.2694 690886.8268 408012.1416 2.461967517 1.338618213 1.605083558 1.522360574 1.607567325 1.531495367 2.054784206 1.643456655 1.693299675 1 18.63825256 4.749627304 24.75459779 1.601391811 2.461968088 0.522896912 0.256454 1138.572573 2546768.143 0.057801653 0.870004812 56185.89512 -4.749627304 0.860576276 SKVDDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SKVDDLR 7 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ;;; 96.711 0.011429 2533720000 9430700 7681200 9399100 7388400 12167200 11813900 10764400 9809700 10280800 7647700 FALSE TRUE 9803031.318 9000386.349 9644048.267 8849803.468 10099023.69 9070300.766 9920658.2 9678217.017 9910796.016 9146120.391 1.071823997 0.984066026 1.05444143 0.9676019 1.104186612 0.991710187 1.084684847 1.058177304 1.083606556 1 23.12472848 3.235096355 24.99987316 1.055967139 1.019450543 0.127300148 0.043689378 168.3604876 1214981.143 0.011435349 0.014186931 1718.289573 -3.235096355 -0.036516596 SKVDEAVAVLQAHQAK ddPTM_MDA-MB-175_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 0 108.96 0.00060665 1022100000 697840 435520 514570 415830 718950 711260 644800 536830 623030 352740 FALSE TRUE 725391.262 510317.1721 527980.1169 498079.9329 596743.1358 546080.6442 594258.8911 529634.6719 600607.272 421852.6494 1.719537054 1.209704794 1.251574733 1.180696467 1.414577191 1.29448196 1.408688299 1.255496849 1.42373711 1 18.68637964 -2.084953763 2.574508047 0.444834487 1.335508142 0.328905029 0.148927068 10775717.51 3108494.542 35192479.4 0.035312123 0.008223302 2.084953763 0.890673654 SKVGS(ph)TENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.965)T(0.035)ENIK;SKVGS(0.554)T(0.446)ENIK;SKVGS(0.5)T(0.5)ENIK;SKVGS(0.5)T(0.5)ENIK;SKVGS(0.5)T(0.5)ENIK 174.44 1.88E-06 10762770000 9729680 4757870 7025610 4666330 9866140 8953350 8976610 6827870 8205880 3636290 TRUE FALSE 10113815.28 5574997.161 7208703.168 5589316.146 8189097.047 6874070.152 8272999.852 6736353.571 7910551.982 4348751.405 2.325682555 1.281976513 1.657648943 1.285269179 1.883091556 1.580699726 1.902385095 1.549031652 1.819039822 1 22.05216981 -1.367883812 5.903556779 0.999874968 1.674147717 0.332392859 0.295114339 0.000436867 4.68E-05 0.257036853 0.06057311 0.042866319 1.367883812 0.674272749 SKVGS(ph)TENIKHQPGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.972)T(0.028)ENIKHQPGGGR 142.04 3.14E-07 90904000 123010 95897 119440 50038 199680 139810 68024 116320 138010 116050 TRUE FALSE 127866.5298 112366.5638 122552.7045 59935.36705 165738.4649 107341.2463 62692.10113 114760.9207 133043.0471 138787.7756 0.921309742 0.809628682 0.883022327 0.431849036 1.194186334 0.773420036 0.451711982 0.826880611 0.95860782 1 17.08252098 2.511963426 24.97003024 0.764361628 0.840604681 0 0.222775378 2930.165319 2099931.639 0.07119362 0.067091699 325.0599213 -2.511963426 0.076243053 SKVGST(ph)ENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.273)T(0.727)ENIK;SKVGS(0.232)T(0.768)ENIK;SKVGS(0.308)T(0.692)ENIK 165.72 1.19E-05 5693370000 3005100 1535370 2188860 1384950 2962110 2701290 2661680 2209270 2415680 1143530 TRUE FALSE 3123743.668 1799057.854 2245903.49 1658888.976 2458611.6 2073956.336 2453050.567 2179658.349 2328740.149 1367582.809 2.284134933 1.315501951 1.642243142 1.213008064 1.79777896 1.516512435 1.793712637 1.593803559 1.702814727 1 20.38319676 -1.177391185 3.731577435 0.999468415 1.631629268 0.327983277 0.278331326 59499090.36 127015962 404225.3747 0.060873731 0.066467419 1.177391185 0.632160852 SKVGST(ph)ENIKHQPGGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.368)T(0.632)ENIKHQPGGGR 153.65 7.98E-06 207990000 185650 140000 157010 82231 292730 204070 104270 154950 196790 175600 TRUE FALSE 192979.6054 164043.911 161101.8096 98496.04636 242971.8592 156677.8352 96097.04494 152873.1487 189707.5663 210005.4579 0.918926619 0.781141179 0.767131536 0.469016602 1.156978783 0.746065539 0.457593083 0.727948455 0.903345885 1 17.6800673 2.492688647 24.96050585 0.719936779 0.809995872 0 0.2078852 2733.649525 4383092.162 0.067875644 0.062187686 310.9486296 -2.492688647 0.090059093 SKVSS(ph)PIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SKVSSPIEK 9 1 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 S(0.018)KVS(0.103)S(0.878)PIEK 73.848 0.025896 207470000 238200 121170 183100 118270 271920 259610 221870 182860 208590 128420 TRUE FALSE 247604.3199 141980.0049 187871.7364 141663.453 225699.1355 199319.5119 204479.2497 180409.0608 201082.8866 153581.4403 1.612202096 0.924460695 1.223271094 0.922399561 1.469572985 1.297809889 1.331405991 1.174680095 1.309291581 1 17.22864436 -1.053547335 4.406350597 0.999983927 1.237961261 0.118066859 0.2032693 2.97E-05 6.38E-06 0.182220726 0.042946937 0.088400081 1.053547335 0.237977334 SKYDEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SKYDEER 7 1 Q15075 Q15075 EEA1 Early endosome antigen 1 0 ;; 114.5 0.0053731 562670000 1101090 1028560 1133120 913490 1461610 1367160 1285730 1181240 1206340 925030 FALSE TRUE 1144561.883 1205207.179 1162650.038 1094175.596 1213166.054 1049657.81 1184951.123 1165407.41 1162924.059 1106271.918 1.034611713 1.089431233 1.050962263 0.989065688 1.096625554 0.948824419 1.071121036 1.053454753 1.051209961 1 20.07727461 3.995660352 24.83350487 1.034167878 1.064065295 0.083589059 0.042337944 423.3894647 2422907.623 0.010008619 0.020740654 9900.573495 -3.995660352 0.029897416 SKYTTPSGEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SKYTTPSGEVR 11 1 E9PLK3;P55786;P55786-2;A6NEC2;E9PP11 E9PLK3 NPEPPS;NPEPPSL1 Puromycin-sensitive aminopeptidase;Puromycin-sensitive aminopeptidase-like protein 0 ; 80.312 0.022576 268720000 244000 298860 292480 262640 456700 427950 315980 311070 308000 364200 FALSE TRUE 253633.3084 350186.8802 300102.2691 314589.4081 379070.2971 328565.0981 291212.6619 306900.6155 296915.1402 435558.017 0.582318081 0.803995947 0.689006418 0.722267519 0.870309539 0.754354381 0.668596721 0.704614778 0.681689071 1 18.73250538 -2.196796264 2.326213681 1.794261408 0.723217309 0.561194135 0.074302605 3062694.295 826935.9877 12746605.06 0.017773177 0.00635629 2.196796264 -1.071044098 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLAALDALNTDDENDEEEYEAWK 23 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK 216.71 9.23E-32 569571000 298512 200751 270210 208461 314181 307079 272666 260226 291916 191801 TRUE FALSE 310297.4843 235228.4226 277251.8946 249693.9636 260776.6258 235764.5561 251293.7264 256738.0961 281410.0002 229380.7337 1.352761757 1.025493374 1.208697392 1.088556827 1.136872403 1.027830683 1.095531095 1.119266174 1.22682492 1 17.8073847 4.751082726 24.568568 1.108548177 1.352761952 0.523867844 0.071205068 1189.762193 2334277.219 0.015740775 0.270615787 56374.50304 -4.751082726 0.244213775 SLADELALVDVLEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;;;; 323.45 1.67E-56 355795200 750767 385950.8 555230 478758.4 706274 686556 857093 607098 632619 308789 FALSE TRUE 780407.8609 452234.8476 569699.7499 573455.3826 586221.7978 527113.7739 789911.8111 598960.8443 609851.1658 369290.2924 2.113263947 1.224605295 1.542688128 1.552857994 1.587428128 1.4273697 2.138999663 1.621924152 1.651414018 1 18.49439581 SLADELALVDVLEDKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLADELALVDVLEDKLK 17 1 A0A5F9ZHM4;P07195;A0A3B3IS95;A8MW50;C9J7H8;F5H793 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 ;; 208.2 4.92E-12 1510660000 3076860 1459920 2256430 1548390 3310670 2539330 2947670 2265860 2552650 1101690 FALSE TRUE 3198336.809 1710649.903 2315234.419 1854656.921 2747923.496 1949609.091 2716623.923 2235489.853 2460780.625 1317545.062 2.427497093 1.298361591 1.757233574 1.407661091 2.085639098 1.479728585 2.061883119 1.696708459 1.867701299 1 20.32942087 -1.732498781 7.378014736 0.99185027 1.766957264 0.340777399 0.327292988 0.038597766 0.001399421 0.278781314 0.066266263 0.018514041 1.732498781 0.775106994 SLAEDFAEQPIKDAVITVPVFFNQAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLAEDFAEQPIKDAVITVPVFFNQAER 27 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2;J3QL06;J3KTF1 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 131.7 3.72E-05 264120000 108470 126730 123070 127630 176040 158470 139280 137870 140760 112210 FALSE TRUE 112752.4794 148494.8917 126277.3053 152874.8331 146116.7837 121667.7441 128362.8697 136022.0782 135694.0751 134195.4011 0.840211203 1.106557233 0.940995774 1.139195768 1.088835999 0.906646153 0.956537024 1.013612069 1.011167849 1 17.03397571 4.759050301 24.27951041 1.015739791 0.840210951 0.362195028 0.070780276 3835.477592 4544789.689 0.01696071 0.681335818 57418.29612 -4.759050301 -0.175528841 SLAES(ph)IDDALNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLAESIDDALNCR 13 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLAES(1)IDDALNCR 179.33 4.81E-07 0 46776 45335 43409 44282 50236 55719 39993 40923 44708 43619 TRUE FALSE 48622.7526 53120.93359 44540.2742 53040.84743 41696.90266 42779.10668 36858.24416 40374.49412 43098.96781 52165.30791 0.932089823 1.01831918 0.853829412 1.016783942 0.799322468 0.820068133 0.706566215 0.773972123 0.826199816 1 15.67080305 3.222975377 24.82367595 0.799692414 0.952515395 0.369132888 0.083181622 190.1034059 302790.0135 0.022636058 0.027145513 1670.995874 -3.222975377 0.152822981 SLAGSSGPGASSGTSGDHGELVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLAGSSGPGASSGTSGDHGELVVR 24 0 P29692;P29692-2;E9PRY8;E9PK01;E9PQ49;A0A087X1X7;E9PI39;E9PPR1;E9PL12;E9PMW7;H0YCK7;E9PIZ1 P29692 EEF1D Elongation factor 1-delta 0 ;; 399.55 3.80E-138 2762410000 138159 873230 703180 744590 761760 1026700 525040 824920 752480 1107290 FALSE TRUE 143613.624 1023200.46 721505.4485 891867.6796 632276.3073 788264.4848 483885.9929 813863.2967 725398.3918 1324242.275 0.10844966 0.772668626 0.544843993 0.673492832 0.477462711 0.595257001 0.36540594 0.614587913 0.547783744 1 20.33673566 0.180718776 1.243195971 1.000837762 0.529534546 0.408410622 0.172654272 6.277235238 8.561891567 0.160525882 0.045037505 1.51606833 -0.180718776 -0.471303216 SLALDIDRDAEDQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLALDIDRDAEDQNR 15 1 H7BXT7;A0A0C4DH16;B8ZZS0;Q9NYM9;E9PQJ6 H7BXT7 BET1L BET1-like protein 0 ; 176.33 7.06E-09 319340000 419960 526910 500740 586980 554480 702440 511040 512170 496880 550050 FALSE TRUE 436540.3451 617402.6937 513789.6958 703082.892 460229.6877 539308.9556 470983.3494 505305.1989 478997.3859 657821.7662 0.66361493 0.938556195 0.781046968 1.068804543 0.699626725 0.819840545 0.715974104 0.768149102 0.72815679 1 19.32733722 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;S(0.001)LAPDRS(0.999)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR;SLAPDRS(1)DDEHDPLDNTSRPR 181.92 2.54E-17 24765310000 1813190 2174287 2090557 2111598 2542450 2597510 2062241 2089862 2140238 2335466 TRUE FALSE 1884776.141 2547703.879 2145038.633 2529265.782 2110285.257 1994277.668 1900597.162 2061850.818 2063211.252 2793055.848 0.674807897 0.91215644 0.767989883 0.905555034 0.755547104 0.714012815 0.680472309 0.738206084 0.738693161 1 21.41341299 3.036196314 24.98982026 0.747496761 0.820173569 0.011279647 0.104470243 388.0049547 267874.9709 0.027739279 0.033154696 1086.916831 -3.036196314 0.072676808 SLAQAEAEKQKEEAER ddPTM_MDA-MB-175_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 0 106.28 0.00068528 166680000 191780 117280 147390 73307 240480 217320 139220 138390 168610 109840 FALSE TRUE 199351.6225 137421.9277 151231.1045 87806.9058 199603.2955 166850.7235 128307.5726 136535.1084 162541.759 131361.045 1.517585541 1.046139118 1.151262952 0.668439459 1.519501428 1.270168972 0.976755115 1.039388111 1.23736652 1 17.00317798 4.743245731 24.03936165 1.100001196 1.517585832 0.260027073 0.210818636 392.0774387 2011629.867 0.049322858 0.393334075 55366.32918 -4.743245731 0.417584636 SLASEAPSQPSLNGGS(ph)PEGVESQDGVDHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLASEAPSQPSLNGGSPEGVESQDGVDHFR 30 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 1 SLASEAPSQPSLNGGS(1)PEGVESQDGVDHFR;SLASEAPSQPSLNGGS(1)PEGVESQDGVDHFR;SLASEAPSQPSLNGGS(0.999)PEGVESQDGVDHFR 209.08 5.31E-26 645772000 195157 255733 240698 260177 256199 318903 238674 274991 220138 277098 TRUE FALSE 202861.9491 299653.1534 246970.7876 311639.234 212650.3855 244842.6113 219966.1082 271305.1954 212215.2764 331390.0477 0.612154621 0.904230997 0.745257105 0.9404001 0.64169213 0.738835137 0.663767997 0.818688423 0.640379148 1 18.33817075 -1.028701815 4.326881524 1.000014393 0.753583486 0.3336542 0.107482305 12904980.36 3068116.664 1880.643173 0.023275599 0.093604814 1.028701815 -0.246430907 SLDADEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLDADEFR 8 0 Q13938-4;Q13938;K7ES72;A0A499FJ41;Q13938-3 Q13938-4 CAPS Calcyphosin 0 ;;;;;;; 236.21 3.05E-08 17567340000 7042930 8329250 8137620 8067490 9048060 9596800 8115860 8451880 7974210 9079810 FALSE TRUE 7320990.315 9759733.895 8349693.062 9663215.443 7510073.993 7368088.641 7479717.686 8338596.373 7687219.74 10858824.93 0.674197288 0.898783613 0.768931548 0.889895132 0.691610192 0.67853462 0.68881465 0.767909643 0.70792372 1 23.37236466 -1.373949386 3.061472417 1.002945677 0.755015344 0.470692702 0.078881572 16901434.29 20995544.27 443352.5033 0.020468298 0.042271788 1.373949386 -0.247930333 SLDAFPEDFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDAFPEDFCR 11 0 E9PS17;Q96KG9-2;Q96KG9;Q96KG9-3;E9PK59;Q96KG9-4;E9PPN3;Q96KG9-5;Q96KG9-6 E9PS17 SCYL1 N-terminal kinase-like protein 0 120.68 0.00099418 72245000 62787 101500 62336 89030 83351 109110 57091 86011 79810 119350 FALSE TRUE 65265.87924 118931.8354 63960.52737 106639.8683 69183.02679 83770.85608 52616.05824 84858.16323 76937.65369 142734.3474 0.457254196 0.833239074 0.448108872 0.74712128 0.484697818 0.586900474 0.36862927 0.594518172 0.539026906 1 17.12297302 -1.253768612 6.020546646 1.000014008 0.564383195 0.492974629 0.13319177 2.29E-05 2.84E-06 0.118154977 0.027848501 0.055748269 1.253768612 -0.435630813 SLDFLIELLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLDFLIELLHK 11 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;; 156.51 3.10E-05 355755000 881977 719886 874081 896094 1082149 1134602 1246389 992886 992981 630604 FALSE TRUE 916798.133 843520.8206 896860.2689 1073338.719 898205.6995 871107.8806 1148693.773 979577.9872 957243.8078 754158.7802 1.215656646 1.118492342 1.189219422 1.423226444 1.191003437 1.155072252 1.523145793 1.298901522 1.269286831 1 19.52450877 3.97571689 24.30913394 1.288300113 1.163769804 0.070310713 0.137443464 970.5679581 971612.3621 0.033930131 0.061619658 9456.205254 -3.97571689 -0.12453031 SLDFYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLDFYTR 7 0 Q04760;Q04760-2 Q04760 GLO1 Lactoylglutathione lyase 0 ;;; 136.11 0.0070063 1520390000 626680 852870 694920 597190 834040 906590 627140 694640 657620 1064040 FALSE TRUE 651421.8103 999343.7881 713030.1861 715312.3996 692270.1787 696048.212 577983.1281 685329.487 633952.3847 1272518.266 0.511915489 0.785327657 0.560330021 0.562123483 0.544015907 0.546984849 0.45420419 0.538561611 0.498187257 1 20.27925493 -1.449734242 6.076526954 1.000201029 0.556428989 0.720727052 0.082962778 0.000230586 2.09E-05 0.08197921 0.019314086 0.035503058 1.449734242 -0.443772039 SLDGAAAVDSADRS(ph)PRPTSAPAITQGQVAEGGVLDASAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDGAAAVDSADRSPRPTSAPAITQGQVAEGGVLDASAK 39 2 A0A2R8Y4N6;A0A2R8YD30;A0A2U3TZH6;A0A3B3IU06;A0A2R8Y5Z6;A0A2R8Y5G2;A0A2R8Y570;A0A2R8YCW8;A0A2R8Y6G5;A0A3B3ITP0;A0A2R8YFR9;Q4VB86;A0A3B3IUD6;A0A2R8Y7Y3;A0A2R8Y7N0;A0A2R8Y420;P11171-3;P11171-7;P11171-5;P11171-4;P11171-6;P11171-2;P11171 A0A2R8Y4N6 EPB41 Protein 4.1 1 SLDGAAAVDS(0.002)ADRS(0.998)PRPTSAPAITQGQVAEGGVLDASAK 291.18 1.09E-92 131720000 95869 62523 79151 77534 82655 102360 96346 81636 71797 65576 TRUE FALSE 99653.98215 73260.83889 81213.74008 92869.99378 68605.33262 78588.44128 88794.14877 80541.80295 69213.03999 78424.36167 1.270701859 0.934159199 1.035567754 1.184198275 0.874796188 1.002092202 1.132226605 1.02699979 0.882545149 1 16.25901426 4.750491919 24.70217194 1.017066157 1.270702041 0.412547433 0.093467507 1607.204671 3327431.486 0.021886545 0.359923384 56297.86419 -4.750491919 0.253635884 SLDGAEFSRPAS(ph)VSENHDAGPDGDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDGAEFSRPASVSENHDAGPDGDKR 26 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.013)RPAS(0.891)VS(0.096)ENHDAGPDGDKR;SLDGAEFS(0.004)RPAS(0.498)VS(0.498)ENHDAGPDGDKR 175.38 7.96E-13 1241730000 286545 276773 313472 342866 393033 412490 511300 431610 365412 262557 TRUE FALSE 297858.0179 324306.6098 321641.3378 410683.8714 326225.391 316695.4488 471222.97 425824.9739 352260.8935 314000.0172 0.948592362 1.032823541 1.024335415 1.307910347 1.03893431 1.008584177 1.500710013 1.356130416 1.121849918 1 18.26040511 2.266923444 24.99756661 1.29119678 1.067615591 0.231802585 0.155204815 247.3023147 217958.9948 0.053717809 0.044935578 184.8942665 -2.266923444 -0.223581189 SLDGAEFSRPAS(ph)VSENHDAGPDGDKRDEDGESGGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLDGAEFSRPASVSENHDAGPDGDKRDEDGESGGQR 36 3 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0;Q9H4G0-4;H7C2K6 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLDGAEFS(0.038)RPAS(0.789)VS(0.173)ENHDAGPDGDKRDEDGESGGQR;SLDGAEFS(0.015)RPAS(0.533)VS(0.055)ENHDAGPDGDKRDEDGES(0.397)GGQR;SLDGAEFS(0.066)RPAS(0.717)VS(0.217)ENHDAGPDGDKRDEDGESGGQR 256.92 3.66E-62 2292240000 317418 282397 336153 295563 497003 490120 483748 356939 430001 354244 TRUE FALSE 329949.9077 330896.488 344913.4233 354024.4792 412522.6076 376297.0578 445830.5677 352154.8165 414525.348 423651.3294 0.7788242 0.781058538 0.814144556 0.83565058 0.973731413 0.888223479 1.052352576 0.831237369 0.978458745 1 18.69251787 3.39696887 3.523301197 0.941668673 0.793278849 0.617101153 0.058564054 0.16330122 4.026429894 0.016198041 0.022934403 2494.415922 -3.39696887 -0.148389824 SLDGAEFSRPASVSENHDAGPDGDKRDEDGES(ph)GGQR ddPTM_MDA-MB-175_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 SLDGAEFSRPASVSENHDAGPDGDKRDEDGES(1)GGQR 121.01 1.95E-08 387240000 27427 24274 20709 20070 36330 37435 33170 27940 26531 20690 TRUE FALSE 28509.83914 28442.87067 21248.69355 24039.7861 30154.63958 28741.28858 30570.04873 27565.51 25576.15449 24743.80937 1.152200889 1.149494415 0.858747869 0.971547499 1.218674099 1.161554721 1.235462506 1.11403663 1.03363852 1 14.59478 4.418561833 24.99999744 1.086853001 1.151562334 0.062666277 0.110219705 243.6333727 104010.0502 0.029228305 0.080045045 26215.7226 -4.418561833 0.064709333 SLDGIPFTVDAGGLIHCIEDFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDGIPFTVDAGGLIHCIEDFHK 23 0 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 215.79 1.53E-32 167840000 110200 115280 141490 135750 156000 184920 140300 152760 132730 113080 FALSE TRUE 114550.7811 135078.4432 145177.3456 162600.9448 129483.1757 141975.1325 129302.9194 150712.5021 127953.0732 135235.861 0.847044418 0.998835977 1.073512193 1.202350794 0.957461836 1.049833465 0.956128933 1.114441843 0.946147511 1 17.04511824 4.697006312 3.130703921 1.044049005 0.826330729 0.356240367 0.076048173 0.316932593 4.948528078 0.017987681 0.160221401 49774.43187 -4.697006312 -0.217718276 SLDGIPFTVDAGGLIHCIEDFHKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDGIPFTVDAGGLIHCIEDFHKK 24 1 Q93052;A0A087WZF1 Q93052 LPP Lipoma-preferred partner 0 ; 123.99 4.44E-05 594030000 1205100 769120 1058090 715280 1477410 1282110 1253450 1130580 1276540 818620 FALSE TRUE 1252678.279 901210.3771 1085664.695 856760.2491 1226280.376 984359.3831 1155201.314 1115426.424 1230597.575 979012.9156 1.279531923 0.92052961 1.108938072 0.875126605 1.252568129 1.00546108 1.179965346 1.139337803 1.256977876 1 19.90096837 3.216740049 24.99996099 1.142121962 1.041560275 0.108662373 0.130086093 477.2487796 546785.3165 0.034816675 0.041646297 1647.176163 -3.216740049 -0.100561687 SLDLFNCEITNLEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLDLFNCEITNLEDYR 16 0 Q9BTT0;Q9BTT0-3;Q9BTT0-2;E9PPH5 Q9BTT0 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 ;; 144.68 3.01E-06 105084000 55402 59355.6 67526.6 75098.8 61841.9 83670.4 86560.2 74431.9 60721.6 62365.2 FALSE TRUE 57589.31374 69549.46258 69286.39867 89953.11849 51330.03593 64239.21764 79775.38534 73434.26213 58536.24148 74584.46689 0.772135488 0.932492588 0.928965528 1.206057002 0.688213486 0.861294856 1.069597849 0.984578495 0.784831533 1 16.18658758 4.746928067 3.788305366 0.945772657 0.752901786 0.118037583 0.136816984 0.592642872 16.28892686 0.032643203 0.322748639 55837.77024 -4.746928067 -0.192870871 SLDLFNCEVTNLNDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 316.61 1.73E-57 924516000 160822 198281 192893 210210 197588 252006 204461 209913 174152 190403 FALSE TRUE 167171.3767 232334.2193 197919.95 251788.9106 164002.0623 193481.4257 188434.8126 207099.4596 167884.3035 227708.8224 0.734145366 1.02031277 0.869179982 1.105749474 0.720227089 0.849687876 0.827525304 0.909492471 0.737276236 1 17.79683066 3.21721755 24.9999974 0.840787967 0.934118432 0.128464233 0.116904445 467.4772588 547573.8742 0.031547294 0.037740047 1648.98821 -3.21721755 0.093330466 SLDLFNCEVTNLNDYRENVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDLFNCEVTNLNDYRENVFK 21 1 P39687;H0YN26 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 ; 375.17 1.23E-112 1597030000 289361 253863 271347 225814 463998 374699 261092 311781 334317 340834 FALSE TRUE 300785.1957 297461.9955 278418.5257 270479.3352 385127.7857 287680.8359 240626.9268 307602.0857 322284.9965 407613.8966 0.737916931 0.729764117 0.683044734 0.663567502 0.944834778 0.705767979 0.590330528 0.754640821 0.790662436 1 18.63684371 0.810067454 2.262340062 0.999621992 0.724103331 0.480888476 0.085579646 0.63017541 5.573184755 0.082573627 0.022434102 6.457545186 -0.810067454 -0.27551866 SLDLLAALPT(ph)PPHNQTEDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLDLLAALPTPPHNQTEDVR 20 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 SLDLLAALPT(0.999)PPHNQT(0.001)EDVR;SLDLLAALPT(0.997)PPHNQT(0.003)EDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(1)PPHNQTEDVR;SLDLLAALPT(0.999)PPHNQT(0.001)EDVR 188.3 9.57E-17 636755000 591845 648065 620666 696953 673528 774727 707672 673936 632860 575091 TRUE FALSE 615211.4976 759365.1225 636841.0658 834808.2232 559041.9511 594808.3954 652202.8195 664902.9903 610083.4922 687769.0707 0.894503001 1.10409897 0.925951883 1.213791458 0.812833806 0.864837372 0.94828751 0.966753259 0.887047002 1 19.39156471 3.209636864 24.99999881 0.915610448 1.031792324 0.274475249 0.096521721 278.0446222 240324.8573 0.026578709 0.031772725 1620.454586 -3.209636864 0.116181875 SLDNEWDRDYGRPLDEQESQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLDNEWDRDYGRPLDEQESQFR 22 2 P49750;P49750-1;H0YIQ2;P49750-3 P49750 YLPM1 YLP motif-containing protein 1 0 ;; 180.63 2.95E-17 499514000 74696 96423 95739 84224 102804 118556 86737 100893 91944 105973 FALSE TRUE 77645.05576 112982.9002 98234.03699 100883.2558 85329.4128 91023.16573 79938.3273 99540.69436 88634.9534 126736.3804 0.612650097 0.89147962 0.775105275 0.796008656 0.673282703 0.718208659 0.630744914 0.785415317 0.699364722 1 16.95147119 -1.155317073 4.968303007 1.000016761 0.736403346 0.504103832 0.079791697 1.42E-05 2.41E-06 0.07401015 0.017443251 0.069933124 1.155317073 -0.263613415 SLDQEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SLDQEIAR 8 0 P48681 P48681 NES Nestin 0 ;;;;;; 139.31 0.0015537 9184863000 4854080 5427320 5420040 5345540 5785280 6324360 5950180 5283910 5010480 5167280 FALSE TRUE 5045722.827 6359419.991 5561290.695 6402871.857 4801900.172 4855623.237 5483789.344 5213087.829 4830153.804 6179709.582 0.816498374 1.029080721 0.899927516 1.036112097 0.777043016 0.785736477 0.887386255 0.843581362 0.781615016 1 22.55910761 3.23004192 24.99909106 0.838720717 0.948133174 0.244934863 0.084982255 227.7740235 668428.3591 0.022749406 0.027602202 1698.407581 -3.23004192 0.109412458 SLDRALEEAGS(ph)SGILSLSGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 50.358 0.07116 65798000 978.71 169320 50890 67990 27031 100710 9242.9 56799 17964 312590 TRUE FALSE 1017.350227 198399.3929 52216.23521 81438.21907 22436.28028 77321.62877 8518.417346 56037.70231 17317.47915 373836.0256 0.002721381 0.530712343 0.139676841 0.217844759 0.060016367 0.206833006 0.022786507 0.14989915 0.04632373 1 18.51204608 -1.493396576 4.117555886 1.006906252 0.158179256 0.754724359 0.144832634 0.008762061 0.001078039 0.133813327 0.031419554 0.032107273 1.493396576 -0.848726996 SLDS(ph)DES(ph)EDEEDDYQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 S(0.095)LDS(0.924)DES(0.98)EDEEDDYQQK;S(0.042)LDS(0.964)DES(0.994)EDEEDDYQQK 191.64 1.22E-10 804810000 453383 265616 376965 278073 453732 462479 471451 346826 330436 211545 TRUE FALSE 471282.9109 311233.4818 386789.0176 333075.0094 376606.7967 355075.2612 434497.4387 342177.3648 318543.6729 252993.1925 1.862828428 1.230204966 1.528851483 1.316537438 1.488604468 1.403497295 1.717427392 1.352516095 1.25909978 1 17.94873904 1.046609464 1.927068634 1.007169175 1.485061303 0.444432674 0.175563461 0.28177473 2.143003694 0.152035559 0.043073895 11.13292962 -1.046609464 0.477892127 SLDS(ph)DES(ph)EDEEDDYQQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 SLDS(1)DES(1)EDEEDDYQQKR;S(0.001)LDS(0.999)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR;SLDS(1)DES(1)EDEEDDYQQKR 243.23 1.55E-23 13455700000 9060000 6064340 7819730 5243770 9777730 9720780 8442010 7466810 8004600 5298040 TRUE FALSE 9417695.796 7105843.221 8023518.588 6280972.055 8115714.947 7463276.165 7780303.197 7366729.625 7716516.01 6336089.501 1.48635776 1.121487192 1.266320273 0.991301031 1.280871261 1.177899423 1.227934548 1.162661863 1.217867268 1 22.59516128 -4.999987915 0.029534019 4.06E-09 1.905070391 0.269913895 0.116276922 2291.617144 5.09751813 254.6135649 104.6840188 1.00E-05 4.999987915 1.905070387 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLDSEPSVPSAAKPPSPEK 19 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK;SLDSEPSVPSAAKPPS(1)PEK 280.85 7.09E-40 3769370000 9658140 1930180 3090370 2090840 5270660 6418030 5948920 3614050 3821480 1218240 TRUE FALSE 10039450.82 2261673.4 3170907.581 2504401.911 4374755.096 4927539.799 5482628.106 3565609.571 3683945.681 1456930.803 6.890821995 1.552354714 2.176429775 1.718957349 3.002719886 3.382137152 3.763135554 2.447343115 2.528565991 1 20.47450093 0.789122653 1.420523243 1.010159383 3.028371723 0.167937602 1.429910377 1.392221496 5.007783173 1.297992351 0.383313327 6.153506348 -0.789122653 2.01821234 SLDTITLS(ph)GDERDFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLDTITLSGDERDFGR 16 1 Q8N9U0;Q8N9U0-2;H0YJ73 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 SLDTITLS(1)GDERDFGR;SLDTITLS(1)GDERDFGR;SLDT(0.093)IT(0.43)LS(0.477)GDERDFGR;SLDTIT(0.001)LS(0.999)GDERDFGR 207.43 1.06E-11 345554000 192675 275092 250178 298734 264668 347874 233869 268093 239056 316318 TRUE FALSE 200281.9578 322336.9111 256697.8442 357822.6936 219679.8279 267085.5356 215537.7367 264499.6518 230452.4213 378294.4558 0.529434029 0.852079395 0.678566234 0.945884054 0.580711201 0.706025509 0.569761817 0.699189871 0.609187943 1 18.52915011 -1.000311546 4.532899895 1.000008396 0.691066777 0.369929784 0.122892414 1.06E-05 2.33E-06 0.111564465 0.026295223 0.09992829 1.000311546 -0.30894162 SLDVNQDSELKFNEYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLDVNQDSELKFNEYWR 17 1 Q99584 Q99584 S100A13 Protein S100-A13 0 85.203 0.0046463 654160000 217280 149880 165960 167580 253250 260980 201210 180920 211280 198830 FALSE TRUE 225858.3822 175620.7241 170285.0539 200726.8238 210202.6555 200371.3502 185438.6344 178495.0633 203676.0741 237786.9317 0.949835134 0.738563397 0.716124527 0.844145733 0.883995828 0.842650808 0.779852085 0.750651275 0.856548645 1 17.8593099 0.978710053 21.78063335 1.000000003 0.807232084 0.40496628 0.067684883 285.9424813 292534.5399 0.065773607 0.016443402 9.521602638 -0.978710053 -0.192767919 SLEAQVAHADQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLEAQVAHADQQLR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 174.68 1.44E-07 888530000 724810 1649810 1346560 1619500 1184650 1733940 1101110 1462090 1176670 1641320 FALSE TRUE 753426.0585 1933152.034 1381652.46 1939832.266 983283.6161 1331258.713 1014802.121 1442493.075 1134321.877 1962905.229 0.383832111 0.984842266 0.703881389 0.988245503 0.500932802 0.678208348 0.516989871 0.734876577 0.577879084 1 20.90455909 -1.125815232 4.303600792 1.000054386 0.685495845 0.212661345 0.186851648 35969951.22 100219950.3 28070.35998 0.042081183 0.074848787 1.125815232 -0.314558541 SLEDQVEMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLEDQVEMLR 10 0 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;; 218.94 1.52E-08 607830000 256965 416650 327711 385788 350553 448662 283682 299832 273580 418420 FALSE TRUE 267110.1766 488206.3964 336251.4179 462095.7149 290966.1263 344467.05 261446.2636 295813.2425 263733.9092 500401.3879 0.533791838 0.975629581 0.6719634 0.923450107 0.581465466 0.688381484 0.522473098 0.591151923 0.52704472 1 18.93272627 3.213321778 24.99407476 0.621887289 0.783007074 0.095365395 0.173238062 370.8973745 367299.4491 0.045725766 0.054672734 1634.262358 -3.213321778 0.161119785 SLEEFNDVYLVTHLMGADLNNIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLEEFNDVYLVTHLMGADLNNIVK 24 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 180.63 3.49E-17 88699000 60418 56406 64796 57573 73148 82766 80467 56209 74176 57781 FALSE TRUE 62803.34929 66093.29172 66484.63699 68960.76756 60714.32909 63544.85083 74159.78628 55455.61029 71506.42025 69102.08067 0.90884889 0.956458779 0.962122071 0.997955009 0.878617959 0.919579414 1.073191799 0.802517229 1.034794026 1 16.07644153 SLEEIYLFSLPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLEEIYLFSLPIK 13 0 P15880;H0YEN5;E9PQD7;E9PPT0;E9PMM9;H3BNG3;H0YE27 P15880 RPS2 40S ribosomal protein S2 0 183 2.50E-05 28781000 208730 168830 187800 178600 257650 260450 227080 188010 190890 177820 FALSE TRUE 216970.8216 197825.2392 192694.2223 213926.5469 213854.745 199964.4347 209280.8762 185490.0335 184019.9062 212660.4244 1.02026892 0.930240028 0.906112281 1.005953729 1.005616092 0.940299236 0.984108241 0.872235791 0.865322764 1 17.69819205 1.745367146 25 0.901303776 0.967923751 0.217671438 0.048737366 1.825560917 6725.815417 0.021980826 0.012189511 55.63744085 -1.745367146 0.066619975 SLEELRLEDYQANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 89.624 0.0055408 100210000 31442 181970 149940 182860 120510 187120 117080 151340 133520 264380 FALSE TRUE 32683.35444 213221.932 153847.5596 219029.1622 100025.7532 143664.2158 107902.9637 149311.5348 128714.6413 316180.1991 0.10336939 0.67436839 0.486581892 0.692735228 0.316356791 0.454374487 0.341270465 0.472235565 0.407092669 1 18.2703875 -1.261205064 3.463646864 1.001518594 0.448946278 0.518354888 0.162044944 67339884.2 101505546.6 1079731.883 0.035628194 0.054801814 1.261205064 -0.552572316 SLELYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLELYR 6 0 D6RHI9;O00584;H0YAE9;D6REQ6;A0A087WZM2;Q07343-4;Q07343-2 D6RHI9 RNASET2 Ribonuclease T2 0 106.85 0.073919 169290000 86698 126210 106270 108370 143460 142480 109350 97427 99267 120550 FALSE TRUE 90120.90399 147885.5857 109039.4835 129805.2625 119074.7204 109391.1793 100778.8613 96121.15042 95694.40006 144169.4644 0.625103966 1.025776064 0.756328561 0.900365851 0.82593579 0.758768022 0.699030559 0.666723365 0.663763304 1 17.1374061 2.645121669 3.146483277 0.722467825 0.838736814 0.034542008 0.13249245 0.491896297 9.387939299 0.04207547 0.039709255 441.6941721 -2.645121669 0.11626899 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SLENETLNKEEDCHS(0.945)PT(0.027)S(0.027)KPPKPDQPLK;SLENETLNKEEDCHS(0.976)PT(0.021)S(0.004)KPPKPDQPLK;SLENETLNKEEDCHS(0.998)PT(0.002)SKPPKPDQPLK 227.58 7.84E-35 2867980000 4161670 1342966 2258970 1335499 3934370 3038050 3324360 2401950 2938590 832807 TRUE FALSE 4325975.945 1573609.964 2317840.614 1599656.716 3265607.193 2332508.93 3063787.977 2369755.789 2832830.72 995979.5866 4.343438363 1.579962064 2.327196908 1.606113958 3.278789281 2.341924434 3.076155393 2.379321646 2.844265844 1 19.92575665 4.753341439 24.68309118 2.365227965 4.343440027 0.449992674 0.680325062 2071.679157 3459510.902 0.151474869 3.410507457 56668.46373 -4.753341439 1.978212062 SLENPTPPFT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLENPTPPFTPK 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLENPTPPFT(1)PK;SLENPTPPFT(1)PK;SLENPTPPFT(1)PK;SLENPT(0.001)PPFT(0.999)PK 168.45 0.00043508 424970000 1339040 891500 904460 804790 1441960 1279710 1021950 1024300 999260 842900 TRUE FALSE 1391906.333 1044608.19 928030.9706 963975.0599 1196856.154 982516.7467 941846.8886 1010570.934 963296.8278 1008050.117 1.380790806 1.036266127 0.920619873 0.956276919 1.187298265 0.974670535 0.93432546 1.002500686 0.955604103 1 19.94313594 4.730532346 4.084772291 0.993161751 1.411095358 0.730030173 0.070558091 0.111619183 4.048051117 0.017285483 0.135929517 53769.04779 -4.730532346 0.417933607 SLENYHFVDEHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLENYHFVDEHGK 13 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 160.78 2.50E-05 467890000 485240 314290 417370 350810 462660 525350 493390 404040 427160 286990 FALSE TRUE 504397.6499 368266.8627 428247.0051 420199.1709 384017.2185 403345.4243 454716.8026 398624.5047 411786.595 343220.1957 1.469603643 1.072975504 1.247732536 1.224284515 1.118865449 1.175179751 1.324854447 1.161424967 1.19977379 1 18.38877492 -4.915987765 0.214502134 1.40E-13 1.24398426 0.3058161 0.104051178 180.6918711 1.865836506 78.0375495 0.197019987 1.21E-05 4.915987765 1.24398426 SLENYHFVDEHGKDQGINIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLENYHFVDEHGKDQGINIR 20 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ;; 204.31 6.29E-22 1508270000 791960 824210 884600 708770 1047390 1125720 864770 847360 863000 842030 FALSE TRUE 823227.1923 965761.656 907653.4027 848962.5905 869355.0219 864288.5905 796987.0677 836002.5252 831940.7986 1007009.657 0.81749682 0.959039121 0.901335351 0.843053078 0.86330356 0.858272395 0.791439349 0.830183226 0.826149772 1 19.94164609 3.739847499 23.93768982 0.846976813 0.899265305 0.032095044 0.061554142 124.6800722 2319159.814 0.014962765 0.025227101 5493.479381 -3.739847499 0.052288492 SLEPEPQQSLEDGS(ph)PAKGEPSQAWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLEPEPQQSLEDGSPAKGEPSQAWR 25 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 SLEPEPQQS(0.31)LEDGS(0.69)PAKGEPSQAWR;SLEPEPQQS(0.063)LEDGS(0.937)PAKGEPSQAWR;SLEPEPQQS(0.002)LEDGS(0.998)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR;SLEPEPQQSLEDGS(1)PAKGEPSQAWR 214.16 2.67E-28 6295020000 2220390 1546360 1957090 1619210 2429920 2793540 2226600 1915360 2128310 1587550 TRUE FALSE 2308052.712 1811935.301 2008093.373 1939484.905 2016883.066 2144782.672 2052073.274 1889687.732 2051712.539 1898600.027 1.215660318 0.954353353 1.05767057 1.021534224 1.062300136 1.129665354 1.080834955 0.99530586 1.080644954 1 20.85650458 -5 0.142219172 0.792948182 1.080356123 0.083929922 0.067935093 400.7663752 3.470496918 23.47516 0.383344015 1.00E-05 5 0.287407941 SLEPSPS(ph)PGPQEEDGEVALVLLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLEPSPSPGPQEEDGEVALVLLGR 24 0 A0A0G2JNZ2;A0A669KB89;Q14160;A0A0G2JMS7;Q14160-2;A0A0G2JPP5;Q14160-3;H0YCG0 A0A0G2JNZ2 SCRIB Protein scribble homolog 1 S(0.002)LEPS(0.034)PS(0.964)PGPQEEDGEVALVLLGR;SLEPS(0.04)PS(0.96)PGPQEEDGEVALVLLGR 76.417 0.014779 35991000 23979.2 23335.2 26898.8 31887 26343.8 36020 35660 28607 29807 24959.2 TRUE FALSE 24925.91733 27342.83908 27599.80483 38194.15343 21865.89029 27654.90089 32864.87602 28223.56996 28734.25189 29849.47737 0.835053727 0.916024048 0.924632766 1.279558532 0.732538463 0.926478563 1.101020149 0.945529786 0.962638358 1 14.86541805 4.373823331 2.562170613 0.986379588 0.848245124 0.115412269 0.131480018 0.662855409 8.133797629 0.032804966 0.139891575 23649.57445 -4.373823331 -0.138134464 SLEQYDQVLDGAHGAS(ph)LTDLANLSEGVSLAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(0.995)LT(0.005)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.994)LT(0.006)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.999)LT(0.001)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.993)LT(0.007)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.997)LT(0.003)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.99)LT(0.01)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.982)LT(0.018)DLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(1)LTDLANLSEGVSLAER;SLEQYDQVLDGAHGAS(0.994)LT(0.006)DLANLSEGVSLAER 443.77 3.47E-231 2724546000 695802 785278 845530 813006 865796 938627 780590 787982 733019 845039 TRUE FALSE 723272.8002 920143.3879 867565.2064 973816.1602 718628.3052 720645.1043 719405.3161 777420.3902 706637.7894 1010608.213 0.715680707 0.910484772 0.858458496 0.963594148 0.711084965 0.713080594 0.711853819 0.769259917 0.699220312 1 19.94679238 3.218906323 24.999485 0.750795899 0.865257014 0.160230343 0.101860005 335.2116247 426375.0846 0.027349752 0.032731741 1655.412854 -3.218906323 0.114461116 SLESINSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLESINSR 8 0 E5RI99;P62888;E5RJH3;A0A0C4DH44 E5RI99 RPL30 60S ribosomal protein L30 0 ; 153.08 0.0010393 409870000 292520 342140 381710 347710 420510 463810 371940 355230 358920 341280 FALSE TRUE 304068.9155 400899.8835 391657.6762 416486.0002 349031.8604 356097.1566 342786.3709 350468.7229 346002.5393 408147.2818 0.744998017 0.982243179 0.959598884 1.02043066 0.855161546 0.872472199 0.839859497 0.858681997 0.847739418 1 18.63873032 SLETENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SLETENR 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;; 171.08 0.0022125 24191250000 16072800 19384660 17922770 17934960 20820630 23169020 19045830 18607250 18266160 18864670 FALSE TRUE 16707366.55 22713824.56 18389852.11 21482441.56 17281546.75 17788366.23 17552968.08 18357850.25 17608764.47 22560840.9 0.740547156 1.006780938 0.815122636 0.952200392 0.765997457 0.788462022 0.778028095 0.813704167 0.780501248 1 24.42731751 3.225464193 24.99763422 0.807720166 0.88327551 0.073327333 0.092607742 430.2099909 821156.4356 0.024229075 0.029123662 1680.599356 -3.225464193 0.075555344 SLETENRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLETENRR 8 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 160.69 0.00056423 25623250000 5342802 6028450 6040962 5587010 6839269 7391660 5972831 5869805 5587349 6513490 FALSE TRUE 5553739.949 7063789.393 6198394.432 6692103.902 5676732.498 5675058.987 5504664.899 5791129.865 5386261.401 7789683.657 0.71296091 0.906813383 0.795718376 0.859098289 0.728750068 0.728535232 0.706660905 0.743435821 0.691460865 1 22.89313331 5.046045764 16.38754122 0.781441124 0.323837095 0.045807388 0.09509415 12211946.3 111127871.4 0.021865997 174727365.7 111184.8884 -5.046045764 -0.457604029 SLFDYHDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLFDYHDTR 9 0 A0A087X142;A6NMH6;A6NFQ9;F8W8I8;Q92599-2;Q92599-4;Q92599;Q92599-3;C9J4G8;C9JV02 A0A087X142 8-Sep Septin-8 0 ;;;;; 178.32 5.11E-05 2128500000 1543614 2305665 2367009 2553439 2587090 2991500 2722300 2598020 2410070 2254998 FALSE TRUE 1604557.073 2701645.028 2428695.199 3058501.613 2147337.366 2296769.462 2508919.013 2563197.791 2323332.051 2696821.684 0.594980781 1.001788529 0.900576858 1.134113402 0.796247442 0.851657889 0.930324399 0.950451343 0.86150748 1 21.3628287 4.745731523 24.83762984 0.933359195 0.594980608 0.562644289 0.090243709 575.0177494 1991615.688 0.020869887 0.213551842 55684.14076 -4.745731523 -0.338378586 SLFNYHDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLFNYHDTR 9 0 D6RGI3;Q9NVA2;D6RER5;D6RDU5;Q9NVA2-2 D6RGI3 11-Sep Septin-11 0 99.283 0.0054422 190370000 352470 411570 447950 352810 554820 565120 496780 496290 465910 495050 FALSE TRUE 366385.7878 482253.9459 459623.945 422594.765 460511.8946 433879.4445 457841.0855 489638.0443 449141.9901 592045.5692 0.618847276 0.814555452 0.776332041 0.713787565 0.77783184 0.732848056 0.773320686 0.827027631 0.758627399 1 19.1753487 -5 0.182481857 2.004655826 0.711541184 0.688221051 0.051448482 73.62304074 0.712234729 26.74453392 0.146131558 1.00E-05 5 -1.293114642 SLFPVRDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLFPVRDEK 9 1 Q9NQT8;H0YBA8;Q9NQT8-2 Q9NQT8 KIF13B Kinesin-like protein KIF13B 0 110.38 0.0020941 426100000 325410 238230 259760 239320 353150 346440 324320 288210 282600 215610 FALSE TRUE 338257.4381 279144.1493 266529.559 286656.7817 293121.6891 265984.5603 298898.9509 284347.0164 272429.2812 257854.6514 1.311814374 1.082563948 1.033642626 1.111699092 1.136770997 1.031529037 1.159176107 1.102741466 1.056522656 1 17.97619854 4.739227447 24.87027792 1.086858742 1.311814448 0.676885187 0.047923725 29.15258371 1087041.313 0.010871982 0.064524918 54856.4181 -4.739227447 0.224955706 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 SLFS(1)PQNTLAAPTGHPPTSGVEK;SLFS(0.955)PQNT(0.045)LAAPTGHPPTSGVEK 271.25 8.40E-52 305580000 419730 373130 427520 370030 551840 593770 499230 442700 505060 407890 TRUE FALSE 436301.2645 437212.175 438661.5224 443220.8296 458038.4339 455875.9162 460099.0481 436766.3306 486882.9893 487808.236 0.894411435 0.896278789 0.899249931 0.908596446 0.938972326 0.934539195 0.943196556 0.895364814 0.998103257 1 18.89595459 -4.999999998 0.056763757 1.337675099 0.771985803 0.652540216 0.022686567 284.2275398 1.183937213 13.41514452 2.462865694 1.00E-05 4.999999998 -0.565689295 SLGADERLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGADERLR 9 1 A6NGE7 A6NGE7 URAD Putative 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 0 74.173 0.031522 0 49816 75115 53997 58568 69638 77740 64214 60792 58040 68740 FALSE TRUE 51782.77415 88015.41694 55404.20618 70152.57559 57800.95763 59686.06316 59180.73889 59977.18268 55951.15174 82208.28689 0.629897254 1.070639229 0.673949163 0.85335163 0.703103785 0.72603463 0.719887752 0.729575873 0.680602332 1 16.32699621 SLGDDISSETSGDFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGDDISSETSGDFRK 16 1 P12429;D6RA82;D6RFG5 P12429 ANXA3 Annexin A3;Annexin 0 ; 202.63 4.79E-11 641570000 252860 252630 267730 223158 366320 355780 298820 271280 294610 231934 FALSE TRUE 262843.1081 296017.2373 274707.2637 267297.9863 304053.0572 273155.4869 275397.7076 267643.9353 284007.0436 277377.0267 0.947602299 1.067201711 0.990374967 0.963663031 1.096172459 0.9847805 0.992864156 0.964910247 1.023902545 1 18.08148878 -3.075681861 10.15855953 0.999998721 1.002583691 0 0.044624041 0 0 0 0.009406763 0.000840075 3.075681861 0.002584971 SLGELGLEHFQAPLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGELGLEHFQAPLVR 16 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 105.39 0.0012873 198140000 168930 249290 284210 201420 309340 310810 258990 243780 264560 231280 FALSE TRUE 175599.4868 292103.6183 291616.7461 241260.2748 256758.4973 238629.0879 238689.6871 240512.5278 255038.5373 276594.8879 0.63486165 1.056070199 1.054309963 0.872251388 0.928283597 0.862738606 0.862957696 0.869547987 0.92206526 1 18.07741497 2.769191115 22.96915943 0.890013049 0.923331227 0 0.116465711 1469.375788 1101848.008 0.034755649 0.036857823 587.7479392 -2.769191115 0.033318178 SLGEYQCLLELHGFHQVQVVHLGGVLDAILATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGEYQCLLELHGFHQVQVVHLGGVLDAILATK 33 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 33.798 0.081683 30604000 9992.8 6373.5 9427.3 6495 16484 12744 11057 10529 11630 9121.5 FALSE TRUE 10387.32346 7468.099046 9672.983183 7779.691614 13682.05557 9784.399137 10190.32345 10387.87598 11211.43857 10908.68328 0.952206897 0.684601326 0.886723258 0.713165046 1.254235292 0.896936769 0.934147888 0.952257546 1.027753605 1 13.41318935 3.287481356 24.99999954 0.994311427 0.805815303 0.415775396 0.116118601 113.5762719 58040.10121 0.030455655 0.041237077 1938.569411 -3.287481356 -0.188496123 SLGGES(ph)SGGT(ph)TPVGSFHTEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(0.016)LGGES(0.493)S(0.493)GGT(0.499)T(0.499)PVGSFHTEAAR 86.131 0.005383 167020000 81902 171610 147190 178650 175530 235110 157610 170600 173020 157100 TRUE FALSE 85135.5542 201082.6826 151025.8923 213986.4368 145693.4733 180509.2656 145256.1164 168313.386 166793.044 187880.7371 0.453136152 1.07026769 0.803839151 1.13894825 0.775457216 0.960765155 0.773129372 0.895852276 0.887760217 1 17.51945763 4.751256344 24.6840417 0.911658601 0.453135805 0.590004684 0.11714106 1152.310654 2240365.956 0.025488007 0.459568175 56397.0443 -4.751256344 -0.458522796 SLGGES(ph)SGGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 S(0.008)LGGES(0.413)S(0.405)GGT(0.291)T(0.883)PVGSFHTEAAR 81.315 0.0098223 149450000 53996 97289 96538 96246 112490 143240 104770 122810 95543 107940 TRUE FALSE 56127.80377 113997.6289 99053.85959 115283.1715 93368.98998 109974.6808 96557.85363 121163.9328 92104.42609 129088.7764 0.43480003 0.883094814 0.767331308 0.893053407 0.723292858 0.851930616 0.747995731 0.938609353 0.713496779 1 16.97800405 4.743143729 24.95859386 0.831192349 0.434799866 0.633487142 0.09136719 269.7009277 1468678.223 0.019436388 0.156745826 55353.32698 -4.743143729 -0.396392483 SLGGESS(ph)GGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 SLGGES(0.063)S(0.878)GGT(0.066)T(0.993)PVGSFHTEAAR;SLGGES(0.1)S(0.9)GGTT(1)PVGSFHTEAAR 199.87 3.04E-22 977950000 142703 338050 308970 350650 396290 408800 311630 383540 325970 387040 TRUE FALSE 148337.0246 396107.4578 317022.012 420007.5234 328928.7674 313862.3954 287203.6263 378399.2736 314238.4034 462873.0777 0.320470193 0.855758256 0.684900521 0.907392423 0.710624107 0.678074424 0.6204803 0.817501151 0.678886759 1 18.82025713 -5 0.194861474 2.24621979 0.662149737 0.275545866 0.151111852 191.6763883 1.886915709 93.18191011 0.365316713 1.00E-05 5 -1.584070053 SLGGESS(ph)GGTTPVGSFHTEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SLGGES(0.147)S(0.852)GGTTPVGSFHTEAAR;SLGGES(0.152)S(0.848)GGTTPVGSFHTEAAR;SLGGES(0.036)S(0.964)GGTTPVGSFHTEAAR;SLGGES(0.127)S(0.873)GGTTPVGSFHTEAAR 311.27 2.15E-67 1772930000 333036 905140 794000 869890 857930 1104220 751080 853240 710670 849030 TRUE FALSE 346184.5184 1060590.754 814692.2923 1041951.646 712099.365 847781.6396 692208.387 841803.7134 685093.1255 1015381.173 0.340940454 1.044524738 0.80235119 1.026167979 0.701312358 0.834939294 0.681722692 0.829051923 0.674715214 1 19.95358998 -2.541713167 1.996600167 3.578193409 0.78643576 0.111977446 0.189119517 5880068.101 383140.2333 68503486.48 0.042918325 0.002872677 2.541713167 -2.791757649 SLGGESSGGTT(ph)PVGSFHTEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGGESSGGTTPVGSFHTEAAR 22 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 S(0.001)LGGES(0.008)S(0.007)GGT(0.205)T(0.778)PVGS(0.001)FHTEAAR 76.55 0.0069974 0 18963 34007 34788 29505 28132 37352 35016 28200 20009 38918 TRUE FALSE 19711.67388 39847.43771 35694.60386 35341.00094 23350.13269 28677.56408 32271.35442 27822.02513 19288.88 46543.23697 0.423513171 0.856138084 0.766912793 0.759315493 0.501686909 0.616148896 0.693362914 0.597767301 0.414429276 1 15.50628393 -1.099708474 4.820386309 1.000016614 0.636735814 0.386732805 0.140847603 2.47E-05 4.61E-06 0.133847652 0.031546752 0.079486162 1.099708474 -0.3632808 SLGGQQGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SLGGQQGSPK 10 0 A0A0C4DGT3;A0A3B3IU98;Q6DN90-2;A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A0C4DGT3;A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK;SLGGQQGS(1)PK 154.74 1.46E-05 1927548000 4394430 1787731 2423310 1776865 3212220 3784040 3012620 2402470 2507240 1395113 TRUE FALSE 4567925.49 2094759.893 2486463.449 2128323.594 2666207.992 2905254.058 2776482.972 2370268.819 2417004.922 1668458.681 2.737811575 1.255506005 1.490275712 1.275622596 1.598006604 1.741280195 1.664100528 1.420633814 1.448645357 1 20.67008453 4.744397854 24.81987451 1.465739194 2.737812186 0.778673379 0.208074242 260.9684169 1109599.82 0.048048186 0.429692979 55513.40345 -4.744397854 1.272072992 SLGGSSLTETEAAPSLTLPSVDYIPQDS(ph)PTPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGGSSLTETEAAPSLTLPSVDYIPQDSPTPSVR 34 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SLGGSSLTETEAAPSLTLPS(0.001)VDY(0.003)IPQDS(0.745)PT(0.197)PS(0.053)VR;SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.712)PT(0.219)PS(0.069)VR 98.002 0.00010562 339420000 167894 210927 190287 217196 208999 276138 207482 227778 192910 231007 TRUE FALSE 174522.5848 247152.0715 195246.0355 260156.7205 173473.4246 212009.1344 191219.0187 224725.0085 185967.2068 276268.3988 0.63171389 0.894608549 0.70672591 0.941681067 0.627916278 0.76740277 0.692149444 0.813430018 0.673139627 1 18.07571102 -1.262076583 5.318306572 1.000028899 0.757123235 0.35269971 0.101230726 3.10E-05 4.30E-06 0.087510576 0.020623989 0.054691951 1.262076583 -0.242905664 SLGGSSLTETEAAPSLTLPSVDYIPQDSPT(ph)PSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGGSSLTETEAAPSLTLPSVDYIPQDSPTPSVR 34 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 SLGGSSLTETEAAPSLTLPSVDYIPQDS(0.398)PT(0.52)PS(0.082)VR 126.64 2.51E-07 68909000 56370 77262 76982 74290 79843 103890 76344 87434 76893 84017 TRUE FALSE 58595.53113 90531.14749 78988.21416 88984.34027 66271.31538 79763.12197 70359.95779 86262.09024 74125.63595 100478.5225 0.583164737 0.900999987 0.786120378 0.88560558 0.659557025 0.793832552 0.70024873 0.858512725 0.737726173 1 16.61652763 -4.999994501 0.458957229 6.394074668 0.773460131 0.3410223 0.096347012 1631.825425 9.103646299 8965.696684 0.045994158 1.00E-05 4.999994501 -5.620614537 SLGLSLS(ph)GGDQEDAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SLGLSLSGGDQEDAGR 16 0 C9JEV6;Q9UJ70;Q9UJ70-2;H7C3G9;H0YEB7;H0YE82;H7C1L7 C9JEV6 NAGK N-acetyl-D-glucosamine kinase 1 SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLS(0.001)LS(0.999)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLSLS(1)GGDQEDAGR;SLGLS(0.004)LS(0.996)GGDQEDAGR 270.32 4.19E-35 1957040000 1866992 2069167 2134568 1972662 2322023 2658284 2086187 2149615 2093347 2112715 TRUE FALSE 1940702.286 2424530.336 2190196.596 2362848.656 1927326.36 2040937.828 1922666.212 2120802.927 2018007.85 2526661.054 0.768089682 0.959578782 0.866834351 0.935166453 0.762795768 0.807760829 0.760951378 0.839369778 0.79868562 1 21.26880071 3.241048892 24.99994593 0.816195568 0.886815775 0.088469618 0.079202094 116.0527653 1165982.696 0.020432142 0.026428189 1742.002972 -3.241048892 0.070620207 SLGNILQAKPTSS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGNILQAKPTSSPAK 16 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 SLGNILQAKPTS(0.029)S(0.971)PAK;SLGNILQAKPT(0.003)S(0.092)S(0.906)PAK 151.96 3.59E-07 997310000 1227170 504590 731340 604780 1002510 1076660 1195590 794540 904360 377150 TRUE FALSE 1275619.619 591249.4073 750399.3212 724403.6789 832103.7083 826622.0319 1101876.532 783890.4909 871812.2603 451045.3215 2.828140673 1.310842568 1.663689402 1.606055189 1.844833919 1.832680648 2.442939721 1.73794174 1.932870642 1 18.78291288 2.809838216 4.087916983 1.880475813 1.794236343 0 0.497319973 2.228645745 72.5120449 0.149333856 0.157045801 645.4137543 -2.809838216 -0.08623947 SLGNILQAKPTSS(ph)PAKGPPQK ddPTM_MDA-MB-175_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(0.003)S(0.141)S(0.857)PAKGPPQK;SLGNILQAKPT(0.003)S(0.099)S(0.898)PAKGPPQK 173.47 3.35E-12 862180000 1041690 356530 553960 296690 924080 750560 740910 588380 810190 305170 TRUE FALSE 1082816.726 417761.2541 568396.6527 355374.3965 767005.2117 576253.8148 682835.5382 580493.7285 781031.4202 364962.2187 2.966928274 1.144669866 1.557412312 0.973729275 2.101601679 1.578941012 1.870975962 1.590558416 2.140033626 1 18.4773876 SLGREEEEDEEEELEEGTIDVTDFLSMTQQDSHAPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGREEEEDEEEELEEGTIDVTDFLSMTQQDSHAPLR 37 1 H7BXY3;Q7L2E3-3;Q7L2E3;Q7L2E3-2 H7BXY3 DHX30 Putative ATP-dependent RNA helicase DHX30 0 ; 140.3 3.27E-13 20079900 8746.9 11558.7 10948.5 8487.8 10973.3 13035.1 6631 9335.4 12308.6 14016.9 FALSE TRUE 9092.234366 13543.81681 11233.8269 10166.66151 9108.062386 10007.89557 6111.244893 9210.274233 11865.61589 16763.24319 0.542391127 0.807947284 0.67014639 0.606485356 0.543335337 0.597014281 0.364562205 0.549432716 0.707835337 1 14.03301367 0.908317464 3.875124719 0.999760329 0.583599294 0.586970055 0.105448678 0.306185182 10.40214023 0.109798593 0.028136189 8.096875555 -0.908317464 -0.416161034 SLGS(ph)PLLHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGSPLLHER 10 0 E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82;H7C3L4;E7EQA9;Q92844 E7EV32 TANK TRAF family member-associated NF-kappa-B activator 1 SLGS(1)PLLHER;S(0.096)LGS(0.904)PLLHER 117.7 0.00059411 332530000 194375 221710 230320 215574 294830 290340 225880 224480 206556 227030 TRUE FALSE 202049.0751 259786.9678 236322.3284 258213.8938 244714.9019 222912.9351 208174.9354 221471.2128 199122.0899 271512.1817 0.744162099 0.956815146 0.870393096 0.951021395 0.901303582 0.821005281 0.766724108 0.815695308 0.73338179 1 18.0506574 2.692303333 5.793112003 0.810502159 0.891642498 0.082127489 0.085985534 0.356342897 30.1362976 0.025940907 0.02470264 492.3833205 -2.692303333 0.081140339 SLGS(ph)VQAPSYGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(1)VQAPSYGAR;SLGS(0.999)VQAPS(0.001)YGAR;SLGS(1)VQAPSYGAR 197.73 1.38E-07 2830780000 741498 853637 932196 774825 1019746 981734 790819 831406 852203 870658 TRUE FALSE 770772.9136 1000242.514 956489.7936 928083.0724 846409.9392 753741.1568 728832.5404 820262.3625 821532.3805 1041246.765 0.740240392 0.960620045 0.918600495 0.891319045 0.812881218 0.723883312 0.699961397 0.787769422 0.788989131 1 19.98988058 3.120256343 4.109898294 0.778118666 0.886448821 0.112022543 0.09304659 0.321189807 9.849884617 0.026106197 0.031794031 1319.035071 -3.120256343 0.108330154 SLGSVQAPSYGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ; 125.46 0.00025007 0 224525 132163 233558 142336 162590 160768 119346 101151 104339 103129 FALSE TRUE 233389.4204 154860.9672 239644.7134 170489.636 134953.0099 123432.0685 109991.3487 99795.23629 100583.8598 123335.153 1.892318732 1.255610938 1.943036575 1.382328005 1.09419745 1.000785789 0.891808588 0.809138626 0.815532776 1 16.91222453 3.217106367 1.725203915 0.878635243 1.662906458 0.775092492 0.186919367 0.153150251 0.942629202 0.058260313 0.081368268 1648.566106 -3.217106367 0.784271215 SLGSVQAPSYGARPVSS(ph)AASVYAGAGGSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 SLGSVQAPSYGARPVS(0.186)S(0.771)AAS(0.014)VYAGAGGS(0.014)GS(0.014)R 99.143 3.74E-11 0 20549 31107 25200 20970 36657 31658 14337 21409 25109 42242 TRUE FALSE 21360.29039 36449.38527 25856.7327 25117.80341 30426.05623 24305.90928 13213.22848 21122.04737 24205.33199 50518.51113 0.422821059 0.721505532 0.511826895 0.497199994 0.602275395 0.481128773 0.261552215 0.418105104 0.479137874 1 15.6245245 -1.175378912 5.981416092 1.000006024 0.484394061 0.646162458 0.113541468 9.77E-06 1.35E-06 0.117800535 0.027765528 0.066776106 1.175378912 -0.515611963 ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 352.53 1.70E-145 1343676000 225199 436814 526477 588315 571351 715765 639416 618350 538125 466086 FALSE TRUE 234090.0304 511833.4066 540197.4231 704681.9511 474232.9611 549539.4263 589296.9031 610062.0297 518757.9864 557406.6279 0.419962768 0.918240618 0.9691263 1.264215235 0.850784575 0.985886064 1.057211869 1.094464972 0.93066347 1 19.08837063 4.794917901 2.211377297 1.029319343 0.203998096 0.747871536 0.10380812 0.361578707 1.791455669 0.025489258 0.616938872 62361.69361 -4.794917901 -0.825321247 down SLGTADVHFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLGTADVHFER 11 0 E9PB61;Q86V81 E9PB61 ALYREF THO complex subunit 4 0 ;;;;;;; 208.74 1.85E-08 8314530000 4519750 6071970 6169090 5642480 6558090 6904570 5782730 6196370 5669400 6340040 FALSE TRUE 4698193.22 7114783.614 6329861.553 6758545.703 5443348.204 5301088.257 5329464.512 6113317.795 5465359.401 7582249.451 0.619630527 0.938347341 0.834826339 0.891364198 0.717906769 0.699144534 0.702886992 0.806267037 0.720809759 1 22.85419449 -1.549517756 3.191354644 1.008163034 0.776253826 0.353927145 0.092840753 69407306.6 105466701.3 5056266.635 0.022137686 0.028215142 1.549517756 -0.231909207 SLGTIQQCCDAIDHLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLGTIQQCCDAIDHLCR 17 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 246.21 1.23E-20 591660000 303380 401670 443720 449300 458870 507580 412080 438120 469230 417100 FALSE TRUE 315357.6767 470653.6979 455283.7077 538170.199 380871.4413 389702.2374 379780.0928 432247.718 452342.504 498822.7591 0.632203866 0.943528917 0.912716389 1.078880603 0.763540625 0.781243899 0.761352777 0.866535678 0.906820099 1 18.92816777 0.95224399 2.503650295 0.99919361 0.847949111 0.152734579 0.115117563 0.6476346 9.25518418 0.110426564 0.029755686 8.958679298 -0.95224399 -0.151244498 SLGYAYVNFQQPADAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGYAYVNFQQPADAER 17 0 P11940-2;E7EQV3;P11940;A0A087WTT1;E7ERJ7;H0YBN4;E5RGH3;B1ANR1;E5RJB9;E5RHG7;E5RH24;B1ANR0;Q13310-2;Q13310;Q13310-3 P11940-2;B1ANR0 PABPC1;PABPC4 Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 4 0 228.25 3.47E-15 62068000 28987 34946 32181 27844 34867 44341 34427 34210 26261 33439 FALSE TRUE 30131.42914 40947.70366 33019.6633 33351.46009 28940.31979 34043.47474 31728.52178 33751.47091 25315.87174 39990.73182 0.753460309 1.023929841 0.825682897 0.833979739 0.723675674 0.851284115 0.793396878 0.843982327 0.633043472 1 15.28737806 4.022846085 24.82812517 0.806169972 0.897722928 0.0720426 0.107466114 434.9434129 472670.3294 0.024260075 0.052403024 10540.13285 -4.022846085 0.091552956 SLGYHGSSYS(ph)PEGVEPVS(ph)PVSSPSLTHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGYHGSSYSPEGVEPVSPVSSPSLTHDK 29 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 2 SLGYHGS(0.006)S(0.106)YS(0.888)PEGVEPVS(0.996)PVS(0.001)S(0.002)PSLTHDK 166.51 2.03E-12 237370000 24216 144740 107690 115680 103660 150220 92148 158140 99247 177990 TRUE FALSE 25172.06638 169597.9691 110496.4899 138561.1587 86039.91023 115333.6816 84925.19898 156020.392 95675.11986 212863.7327 0.118254369 0.796744316 0.519094956 0.650938312 0.40420183 0.541819314 0.398965093 0.732959016 0.449466514 1 17.69957064 -4.99999999 0.281956723 4.476386353 0.501996046 0.389686708 0.182777205 231.0242873 2.205851095 470.2491826 0.188898718 1.00E-05 4.99999999 -3.974390308 SLGYTGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLGYTGAR 8 0 Q8NFU3;Q8NFU3-4;R4GNF9;Q8NFU3-2 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 76.774 0.081265 163110000 279380 302550 315200 263030 331480 385310 331080 301040 319810 303260 FALSE TRUE 290410.1381 354510.609 323414.3709 315056.5489 275135.148 295827.5919 305129.0845 297005.0512 308300.1006 362677.9907 0.800738246 0.977480349 0.891739723 0.868694977 0.758621022 0.815675612 0.841322309 0.818922181 0.850065646 1 18.46832967 5.087774104 13.04820767 0.858050605 0.000130776 0.059287585 0.070155447 1179222.67 3835939.222 0.016691677 27744759.76 122397.9386 -5.087774104 -0.857919829 SLHDAIMIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLHDAIMIVR 10 0 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;; 183.67 1.64E-06 1523830000 134357.5 258765 223145 240398 335657 333236 241435 235955 211108 328601 FALSE TRUE 139662.0378 303205.8758 228960.342 287948.0069 278602.143 255846.9892 222510.6938 232792.4092 203510.2643 392984.0745 0.355388543 0.771547489 0.5826199 0.732721821 0.708940034 0.651036533 0.566207916 0.592371102 0.517858808 1 18.58411132 -1.896202917 2.867692801 1.192970946 0.617032829 0.514294493 0.113811577 62070453.51 27883935.84 80352282.93 0.025714592 0.012699806 1.896202917 -0.575938118 SLHDALCVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLHDALCVIR 10 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;; 188.87 1.07E-06 1301150000 357574 454080 451408 461940 618080 632300 573300 548770 525042 581030 FALSE TRUE 371691.2976 532064.7077 463172.0633 553310.3532 513018.9824 485457.9076 528363.248 541414.6358 506145.841 694871.704 0.534906365 0.765702078 0.666557669 0.796276996 0.738293097 0.698629552 0.760375253 0.779157696 0.728401859 1 19.40638711 -5 0.139449923 1.933609089 0.625937806 0.661155931 0.064352232 81.66848694 0.699317433 21.24702766 0.374432878 1.00E-05 5 -1.307671284 SLHDALCVLAQTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLHDALCVLAQTVK 14 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 142.1 9.49E-06 386900000 570500 711730 836010 780330 1121230 1131690 896780 866990 876080 950620 FALSE TRUE 593023.7805 833964.091 857797.1074 934676.9449 930643.7251 868872.1484 826488.0403 855369.4172 844550.0519 1136875.788 0.521625833 0.73355779 0.754521396 0.822145176 0.818597541 0.764263042 0.726981829 0.752385991 0.742869239 1 20.11664321 -5 0.180376477 2.007715006 0.69154105 0.5375346 0.075656821 115.5155324 1.113426676 42.05434346 0.24318144 1.00E-05 5 -1.316173956 RHQYS(ph)DYDYHSSSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RHQYSDYDYHSSSEK 15 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 RHQYS(1)DYDYHSSSEK 152.04 1.36E-06 169000000 54689 155790 188740 163130 222470 269760 189380 220910 216980 220590 TRUE FALSE 56848.16395 182545.7206 193658.7195 195396.6271 184654.6289 207112.3283 174535.9007 217949.0628 209170.9322 263810.387 0.215488725 0.691958049 0.734082997 0.740670712 0.699952079 0.785080264 0.661596015 0.826158004 0.792883611 1 18.00914184 4.808367277 2.385491998 0.767413007 0.019810964 0.787056882 0.08739741 0.303745443 1.776321252 0.019941775 0.501782302 64323.14596 -4.808367277 -0.747602043 down SLHINNIS(ph)PGNTISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLHINNISPGNTISR 15 0 Q8IZ41 Q8IZ41 RASEF Ras and EF-hand domain-containing protein 1 SLHINNIS(1)PGNTISR 162.44 1.03E-06 300680000 62802 158880 166050 160630 172460 197310 144230 166640 143910 163570 TRUE FALSE 65281.47145 186166.4041 170377.3994 192402.1346 143145.3108 151487.7428 132924.8757 164406.4634 138730.7072 195618.4098 0.333718445 0.95168141 0.870968124 0.983558423 0.73175787 0.774404326 0.679511074 0.840444739 0.709190446 1 17.57768262 4.747656054 24.76687674 0.826635778 0.333718152 0.655521048 0.1093807 661.4005859 1800949.938 0.025906445 0.318199462 55931.44687 -4.747656054 -0.492917626 SLHLS(ph)PQEQSASYQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLHLSPQEQSASYQDR 16 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 S(0.001)LHLS(0.999)PQEQSASYQDR;SLHLS(1)PQEQSASYQDR 197.68 2.75E-11 406290000 112596 188965 185412 220370 187581 232810 178531 205546 184899 182378 TRUE FALSE 117041.377 221418.2688 190243.989 263958.5283 155696.0486 178743.4058 164537.2737 202790.9921 178244.5211 218111.4773 0.536612646 1.015161016 0.872232821 1.210200085 0.713837028 0.819504815 0.754372378 0.929758464 0.817217523 1 17.73470616 -2.654880328 1.949110041 3.576939783 0.863710576 0.059319652 0.171158675 5739451.602 209875.5549 65680417.08 0.039405377 0.002213705 2.654880328 -2.713229206 SLHLS(ph)PQEQSASYQDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLHLSPQEQSASYQDRR 17 1 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 S(0.003)LHLS(0.996)PQEQSASYQDRR;SLHLS(1)PQEQSASYQDRR;SLHLS(1)PQEQSASYQDRR 161.51 1.39E-09 403323000 58220 156578 149988 112424 150023 165711 129604 133564 138108 164166 TRUE FALSE 60518.57056 183469.0535 153896.8105 134661.1316 124522.144 127227.1316 119445.2998 131773.793 133137.5201 196331.1846 0.308247366 0.93448758 0.783863301 0.685887634 0.634245366 0.648023043 0.608386793 0.671181164 0.678127218 1 17.58292982 -1.771137674 2.062962889 1.111108945 0.670399606 0.318024158 0.148231014 1404253.998 761713.2888 785862.1216 0.036138576 0.016938008 1.771137674 -0.440709339 SLHPWYGITPTSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SLHPWYGITPTS(0.039)S(0.961)PK;SLHPWYGITPTS(0.306)S(0.694)PK 224.86 6.93E-13 1808060000 774270 817100 1065620 837110 1315880 1463030 1245240 1139050 1176140 755510 TRUE FALSE 804838.7775 957430.5688 1093390.933 1002687.859 1092207.188 1123263.455 1147634.835 1123782.898 1133810.951 903537.7194 0.890763894 1.059646485 1.210122067 1.109735474 1.208811945 1.243183799 1.270157084 1.243758698 1.254857353 1 19.7852253 5.528729553 0.80372101 1.219059293 5.22E-10 0.572383441 0.079944853 4.768222007 0.938052504 0.025238917 6.987247891 337854.3798 -5.528729553 -1.219059293 SLIEEGGDWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLIEEGGDWDR 11 0 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;; 185.6 1.02E-05 923010000 812560 923430 898830 939150 1021160 1095990 1032950 941640 925780 837410 FALSE TRUE 844640.4962 1082021.919 922254.2482 1124911.067 847583.5879 841462.9324 951984.6799 929018.856 892461.3586 1001484.456 0.843388523 1.080418086 0.920887231 1.123243661 0.846327252 0.840215669 0.950573595 0.927641812 0.891138502 1 19.9337086 3.199978136 24.99997932 0.906948723 0.993223478 0.186096303 0.08459279 248.0433043 160721.8675 0.023000468 0.0274913 1584.813405 -3.199978136 0.086274755 SLIEEGGDWDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLIEEGGDWDRR 12 1 Q15008;Q15008-4;Q15008-3;Q15008-2;C9J0E9;H7C531 Q15008 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 ;;;;; 233.46 8.59E-16 6569530000 2488870 2835620 2879210 2662680 3250550 3521600 2981440 3106820 2976970 2991540 FALSE TRUE 2587132.509 3322615.677 2954244.578 3189350.157 2698022.672 2703761.77 2747746.942 3065178.16 2869829.431 3577674.987 0.723132347 0.928708083 0.825744258 0.891458886 0.754127382 0.755731524 0.768025869 0.85675143 0.802149285 1 21.7705909 -1.312303868 3.011509406 1.001555431 0.815754852 0.450572836 0.062219677 8192974.399 10547568.4 114984.0104 0.015645275 0.048718749 1.312303868 -0.185800579 SLIGS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLIGSPGR 8 0 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 SLIGS(1)PGR;S(0.001)LIGS(0.999)PGR;SLIGS(1)PGR;SLIGS(1)PGR;SLIGS(1)PGR;SLIGS(1)PGR 115.13 0.0026459 4351410000 3463990 3982520 3692260 3722370 4054400 4663950 3780940 3928590 3575770 4001150 TRUE FALSE 3600751 4666486.83 3788483.329 4458643.676 3365234.536 3580818.295 3484580.043 3875933.677 3447078.736 4785098.736 0.752492519 0.975212234 0.791725216 0.931776735 0.703273793 0.74832694 0.728214868 0.810000773 0.720377766 1 22.19011726 3.239776285 24.99986745 0.772556076 0.865754104 0.121598448 0.098922803 54.07679932 1112057.171 0.025399602 0.03256117 1736.905878 -3.239776285 0.093198028 SLIIDEGEDDLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLIIDEGEDDLGR 13 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 ; 155.48 0.00010867 364000000 364760 374410 392280 354190 484400 491520 386680 363500 341050 430850 FALSE TRUE 379161.0065 438712.005 402503.1391 424247.7248 402061.861 377371.9291 356371.0112 358627.8771 328775.6771 515266.8084 0.735853737 0.851426868 0.781154797 0.823355431 0.78029839 0.732381599 0.691624233 0.696004228 0.638068806 1 18.97496014 2.804996236 3.368685581 0.724496428 0.80055367 0.011797228 0.096442378 0.523329248 11.75238931 0.028820865 0.03008979 638.2579544 -2.804996236 0.076057242 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_MDA-MB-175_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(0.634)RIS(0.366)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.546)RIS(0.447)EDET(0.007)ER;SLIPDIKPLAGQEAVVDLHADDS(0.615)RIS(0.385)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.686)RIS(0.314)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.587)RIS(0.408)EDET(0.005)ER;SLIPDIKPLAGQEAVVDLHADDS(0.578)RIS(0.421)EDET(0.001)ER 164.8 2.89E-14 3509394000 432691 335435 423450 402600 493654 549488 563017 463862 445797 320706 TRUE FALSE 449773.9748 393043.3519 434485.4549 482233.0784 409742.8694 421877.7396 518886.2564 457644.6886 429752.8531 383542.2004 1.172684451 1.024772115 1.132823075 1.257314261 1.06831235 1.099951294 1.352879177 1.193205567 1.12048388 1 18.5490258 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLIPDIKPLAGQEAVVDLHADDSRISEDETERNGDDGTHDK 41 3 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.483)RIS(0.483)EDET(0.034)ERNGDDGTHDK;SLIPDIKPLAGQEAVVDLHADDS(0.491)RIS(0.369)EDET(0.14)ERNGDDGTHDK 181.79 6.65E-28 624470000 598080 291510 439450 269780 615410 503970 503930 419600 510280 321180 TRUE FALSE 621692.6602 341574.5749 450902.428 323141.6788 510802.828 386930.6052 464430.6498 413975.9483 491915.1225 384109.0716 1.618531574 0.889264535 1.17389164 0.841275832 1.32983797 1.007345657 1.20911138 1.077756239 1.280665204 1 18.55115651 4.753479702 24.49308946 1.096701596 1.618532067 0.518940907 0.152563607 1560.69733 2562184.05 0.032885506 0.748937429 56686.5077 -4.753479702 0.521830471 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;Q9UKV3;E7EQT4;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 SLIPDIKPLAGQEAVVDLHADDS(0.13)RIS(0.707)EDET(0.163)ER;SLIPDIKPLAGQEAVVDLHADDS(0.066)RIS(0.934)EDETER;SLIPDIKPLAGQEAVVDLHADDS(0.012)RIS(0.987)EDET(0.001)ER 263.7 8.71E-60 2195730000 752657 672610 778614 729530 839400 969000 973550 838150 888530 586260 TRUE FALSE 782372.4795 788125.5353 798905.3205 873828.8566 696719.0878 743964.4353 897240.6071 826915.9702 856551.9789 701126.4224 1.115879326 1.124084773 1.139459725 1.246321389 0.993713923 1.061098843 1.279713014 1.179410651 1.221679788 1 19.41931508 2.25835366 24.9999129 1.187913884 1.115693368 0.074174013 0.089727196 490.9842215 620143.9974 0.030376073 0.025382801 181.2815726 -2.25835366 -0.072220516 SLIPDIKPLAGQEAVVDLHADDSRIS(ph)EDETERNGDDGTHDK ddPTM_MDA-MB-175_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(0.218)RIS(0.782)EDET(0.001)ERNGDDGTHDK 220.06 2.02E-44 1966700000 1137100 639030 856180 543670 1178000 1130100 919190 842710 996490 602240 TRUE FALSE 1181993.586 748778.4315 878492.7542 651206.3033 977763.9808 867651.4018 847141.4859 831414.8508 960626.5196 720237.3974 1.641116652 1.039627259 1.219726659 0.904155082 1.357557917 1.204674188 1.176197583 1.154362234 1.333763733 1 19.45811299 7.999998717 0.017937161 7.82E-10 2.688376682 0.115176535 0.186597163 10736.37966 14.85074682 850.9516676 1448.059042 99999704.57 -7.999998717 2.688376681 SLKDMEESIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLKDMEESIR 10 1 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 143.97 3.01E-05 4011810000 3994000 5028100 4777980 4341780 6528600 6299740 4209320 4447350 4821590 5080930 FALSE TRUE 4151686.204 5891637.062 4902498.084 5200571.125 5418870.904 4836720.858 3879382.499 4387740.548 4648061.918 6076440.953 0.683243075 0.96958682 0.8068042 0.855858086 0.891783685 0.795979241 0.63843005 0.722090543 0.764931636 1 22.53479514 2.477493713 24.9999966 0.745950458 0.847091988 0.02518183 0.110715914 24.15983363 1621852.748 0.035369001 0.029903213 300.2573953 -2.477493713 0.10114153 SLKEEGVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLKEEGVQR 9 1 P40222 P40222 TXLNA Alpha-taxilin 0 76.143 0.033075 78462000 110490 99110 114400 88563 153330 137750 127890 98531 109750 111390 FALSE TRUE 114852.2305 116131.3715 117381.358 106080.4971 127267.0214 105759.6501 117865.6476 97210.35311 105800.1189 133214.7378 0.86215859 0.871760688 0.881143933 0.796312021 0.955352414 0.793903526 0.884779339 0.729726716 0.794207313 1 17.02339417 SLKELQEMDKDDESLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLKELQEMDKDDESLIK 17 2 P52566;F5H3P3;H0YGX7;F5H2R5;F5H6Q0 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ; 109.54 0.00033845 706250000 661370 249620 327040 171688 770770 456870 364250 308730 466210 211202 FALSE TRUE 687481.3983 292490.2932 335562.9311 205647.374 639754.7907 350768.8664 335699.1332 304591.9793 449431.1932 252582.9882 2.721804042 1.157996805 1.328525462 0.814177453 2.532849878 1.388727202 1.329064699 1.205908527 1.779340709 1 17.94639795 4.745126234 24.79467573 1.402424129 2.721804714 0.438102264 0.45136474 632.9955754 2390400.362 0.104347334 1.001756312 55606.58621 -4.745126234 1.319380585 SLKES(ph)EQES(ph)EEEILAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLKESEQESEEEILAQK 17 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 S(0.243)LKES(0.757)EQES(1)EEEILAQK 169.6 1.11E-09 78004000 283000 101530 158780 122110 217870 244010 246440 173710 197850 87715 TRUE FALSE 294173.0585 118966.9877 162917.9372 146262.9935 180836.5352 187342.3755 227123.3888 171381.7016 190729.4171 104901.0748 2.804290223 1.134087405 1.553062611 1.394294518 1.723876857 1.785895672 2.165119749 1.633745906 1.818183631 1 16.67866993 3.015748398 24.60089335 1.752532696 1.653907946 0 0.492669124 1631.277045 2548228.563 0.135088352 0.161416869 1036.927514 -3.015748398 -0.09862475 SLKQPLEQNQTIS(ph)PLSTYEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLKQPLEQNQTISPLSTYEESK 22 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 SLKQPLEQNQTIS(1)PLSTYEESK 244.14 5.10E-31 168070000 257350 153590 204380 151350 306690 239980 222030 206470 244160 131870 TRUE FALSE 267510.3767 179967.8877 209706.3107 181286.5783 254558.9433 184248.2819 204626.7084 203702.6074 235372.7293 157707.4017 1.696244906 1.141150547 1.329717619 1.149512175 1.614121725 1.168291912 1.29750859 1.291648998 1.492464696 1 17.26689085 -1.425635708 3.379336345 0.996181616 1.336671191 0.246576253 0.18323786 6056488.065 7671269.078 142616.4653 0.038839823 0.037528767 1.425635708 0.340489574 SLKS(ph)PIQSDLDAFHSGFQTCAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLKSPIQSDLDAFHSGFQTCAK 22 1 Q9C0J9 Q9C0J9 BHLHE41 Class E basic helix-loop-helix protein 41 1 S(0.027)LKS(0.967)PIQS(0.006)DLDAFHSGFQTCAK;S(0.01)LKS(0.989)PIQSDLDAFHSGFQTCAK 290.05 1.40E-55 1070210000 1044930 658720 902000 606290 1233880 1098680 1118040 914380 1071340 578100 TRUE FALSE 1086184.643 771850.0359 925506.861 726212.3524 1024145.518 843528.2207 1030405.103 902124.2317 1032782.683 691367.6266 1.571066682 1.116410439 1.338660975 1.050399707 1.481332766 1.220086374 1.490386682 1.304840141 1.493825633 1 19.39909353 3.17973858 25 1.34950772 1.263173905 0.019731565 0.191379851 259.148878 110139.3587 0.050568043 0.060440404 1512.650448 -3.17973858 -0.086333815 SLLENDQLLSHGGQDLSADAFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLENDQLLSHGGQDLSADAFHR 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 0 172.2 3.06E-12 171090000 27533 30837 36716 35685 33323 40793 35737 36940 40764 37624 FALSE TRUE 28620.0241 36133.01487 37672.84912 42743.38649 27658.76836 31319.44397 32935.84056 36444.87972 39296.9116 44995.70245 0.63606128 0.803032577 0.837254384 0.949943754 0.614698001 0.696054118 0.731977473 0.809963569 0.873348108 1 15.4574996 1.032158419 1.70835391 0.997722554 0.759007898 0.41010783 0.09273218 0.380614559 2.268653848 0.090488712 0.026145489 10.7685795 -1.032158419 -0.238714656 SLLEPLGLHCTFIDDFTPYHMLHGEVHCGTNVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLLEPLGLHCTFIDDFTPYHMLHGEVHCGTNVCR 34 0 Q9ULW8 Q9ULW8 PADI3 Protein-arginine deiminase type-3 0 ; 179.01 2.77E-20 233660000 50534 65139 63712 92008 81546 101176 64582 72068 75915 79997 FALSE TRUE 52529.12134 76326.11654 65372.38706 110206.9078 67684.84005 77679.40734 59519.89409 71102.04634 73182.83398 95670.88051 0.549060707 0.79779883 0.683304959 1.151937843 0.707475876 0.811944104 0.622131768 0.74319423 0.764943665 1 16.54579226 4.921463299 2.277159845 0.796574787 0.383240736 0.207550335 0.149600755 2.316894024 8.603565834 0.036742067 2.306458009 83457.10176 -4.921463299 -0.413334052 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_MDA-MB-175_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 2 SLLGDSAPTLHLNKGT(0.973)PS(0.606)QS(0.42)PVVGR 146.94 5.66E-07 1977000000 949780 943090 1012000 775910 1235800 1348100 963940 998310 1008500 928800 TRUE FALSE 987278.0478 1105058.371 1038373.551 929382.6821 1025739.157 1035024.206 888383.864 984929.2874 972204.282 1110780.577 0.888814648 0.994848482 0.934814285 0.836693314 0.923439947 0.931798977 0.799783398 0.886700135 0.875244222 1 20.08314243 3.97477353 23.13635776 0.885862554 0.947581511 0.111460408 0.056725628 433.8950553 397947.7035 0.013751717 0.024960641 9435.68708 -3.97477353 0.061718957 SLLGDSAPTLHLNKGT(ph)PSQS(ph)PVVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 SLLGDSAPTLHLNKGT(0.999)PS(0.014)QS(0.987)PVVGR;SLLGDSAPTLHLNKGT(0.997)PS(0.378)QS(0.624)PVVGR;SLLGDSAPTLHLNKGT(1)PS(0.227)QS(0.773)PVVGR;SLLGDSAPTLHLNKGT(0.993)PS(0.036)QS(0.971)PVVGR 247.62 7.75E-38 6189880000 3272750 3152820 3523500 2661270 4400700 4359890 3051820 3378570 3531900 3067590 TRUE FALSE 3401960.697 3694292.309 3615325.305 3187661.263 3652670.586 3347371.622 2812610.374 3333285.795 3404787.609 3668625.528 0.92731206 1.006996294 0.985471337 0.868897967 0.995650976 0.91243208 0.766665977 0.908592542 0.928082625 1 21.80680822 2.484584975 24.98915583 0.883995998 0.956121733 0.125145176 0.065743476 548.2541936 1835607.492 0.021747308 0.018916857 305.2003131 -2.484584975 0.072125736 SLLGLDSGELQSGPESSS(ph)SPGVHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLGLDSGELQSGPESSSSPGVHVR 25 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 SLLGLDSGELQSGPES(0.229)S(0.152)S(0.405)S(0.214)PGVHVR 107.3 0.0023578 78123000 40854 62064 57572 55362 59552 71299 46972 56370 53601 60757 TRUE FALSE 42466.94747 72723.00921 59072.37362 66312.43836 49429.37231 54740.8878 43290.2119 55614.45235 51671.91048 72661.17089 0.584451736 1.00085105 0.812984059 0.912625513 0.680272169 0.753371947 0.59578192 0.765394387 0.71113512 1 16.14889699 5.014937331 16.24859256 0.784694377 0.234311284 0.196486689 0.12790753 7389380.634 163654882.9 0.03016472 94832488.8 103499.2806 -5.014937331 -0.550383093 SLLLEPPRGT(ph)PDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLLEPPRGTPDR 13 1 Q53GT1-3;Q53GT1 Q53GT1-3 KLHL22 Kelch-like protein 22 1 SLLLEPPRGT(1)PDR 95.428 0.0075993 366280000 448100 459820 439860 457460 488470 586750 528410 470360 450230 395760 TRUE FALSE 465791.334 538790.5081 451323.1129 547944.2226 405440.0439 450486.2048 486991.8435 464055.5936 434026.3102 473301.5947 0.984132188 1.138366137 0.953563474 1.157706267 0.856620912 0.95179524 1.028925 0.980464885 0.917018483 1 18.85240026 3.239922893 24.99999372 0.961400851 1.056659538 0.324430889 0.072269778 45.31477801 831585.343 0.019401015 0.024885054 1737.492319 -3.239922893 0.095258687 SLLLTTIPQIGSTEWSETLHNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLLLTTIPQIGSTEWSETLHNLK 23 0 B4DUC8;Q13126-4;Q13126;Q13126-3;Q13126-2 B4DUC8 MTAP S-methyl-5-thioadenosine phosphorylase 0 ; 197.72 2.92E-24 301920000 190940 173432 212161 186199 257770 278150 236260 223208 232970 196249 FALSE TRUE 198478.4586 203217.5969 217690.09 223028.6065 213954.3475 213553.8779 217741.3238 220216.2619 224585.4552 234700.2341 0.845667919 0.865860222 0.927523957 0.950270064 0.911606877 0.909900575 0.927742252 0.938287355 0.956903414 1 17.84045976 8 0.121677024 1.013455697 0.532586153 0.747360835 0.021112913 53.64049787 0.447029356 0.152502537 4.384142873 100000000 -8 -0.480869544 SLLNEIESVYDEHQEQHSEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLLNEIESVYDEHQEQHSEGR 21 0 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 0 ; 94.463 0.00090764 42053000 27744 30457 30728 30451 29407 37363 28105 25772 28300 27619 FALSE TRUE 28839.35454 35687.75283 31528.79692 36474.11691 24408.40864 28686.00949 25902.05666 25426.56849 27281.48853 33030.41425 0.873115133 1.080451264 0.954538344 1.104258537 0.738967682 0.868472592 0.784188066 0.769792601 0.825950541 1 15.01150744 3.234333067 24.99999526 0.815061389 1.005148534 0.459699116 0.0902518 80.00423844 473112.4563 0.023757448 0.029364242 1715.272272 -3.234333067 0.190087145 SLLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLLSPK 6 0 Q9P0U3-2;Q9P0U3 Q9P0U3-2 SENP1 Sentrin-specific protease 1 1 SLLS(1)PK;SLLS(1)PK 89.698 0.052312 260911000 988070 477560 615990 458470 881500 1053880 852550 671420 695920 429980 TRUE FALSE 1027079.767 559577.2151 632043.2054 549153.9976 731662.9449 809132.3417 785724.9033 662420.7131 670873.9751 514226.3485 1.997330105 1.088192421 1.22911478 1.067922714 1.422842192 1.57349452 1.527974802 1.288188976 1.304627772 1 18.97204401 0.745314204 1.59263341 1.001300146 1.384075604 0.180803784 0.255530236 1.61167314 6.721303128 0.2377688 0.068439026 5.563065898 -0.745314204 0.382775458 SLLS(ph)PLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLLSPLHR 8 0 Q9BY84 Q9BY84 DUSP16 Dual specificity protein phosphatase 16 1 SLLS(1)PLHR;SLLS(1)PLHR;S(0.001)LLS(0.999)PLHR 117.52 0.001329 551810000 246511 298956 288483 313050 380339 416263 365107 359720 391873 400124 TRUE FALSE 256243.4446 350299.3674 296001.104 374970.3556 315689.1126 319592.2268 336488.9593 354898.5418 377769.5673 478520.637 0.535490896 0.732046521 0.61857542 0.783603311 0.659718909 0.667875536 0.703185889 0.741657756 0.789453031 1 18.86822162 -5 0.148043674 2.128382887 0.592395948 0.750527632 0.058833364 62.98576769 0.55753149 20.72444883 0.288421814 1.00E-05 5 -1.535986939 SLLSHEFQDET(ph)DTEEETLYSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSK 22 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 S(0.002)LLS(0.002)HEFQDET(0.658)DT(0.335)EEET(0.002)LYSSK 99.614 0.0036092 94961000 23526 20279 22668 24116 35524 35461 28832 24519 21835 19852 TRUE FALSE 24454.82465 23761.7605 23258.7467 28886.07282 29485.64317 27225.72017 26572.0725 24190.36291 21049.16262 23741.61931 1.030040299 1.000848349 0.979661345 1.216685031 1.241939009 1.146750768 1.119219045 1.018901137 0.886593384 1 14.53513072 1.53736988 3.666128652 0.943891591 1.106880353 0.369916453 0.085022933 0.225429653 6.699446139 0.062226195 0.024991163 34.46433319 -1.53736988 0.162988763 SLLSHEFQDET(ph)DTEEETLYSSKH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLLSHEFQDETDTEEETLYSSKH 23 1 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 SLLSHEFQDET(0.998)DT(0.002)EEETLYSSKH 204.05 1.37E-24 111120000 87486 157020 157990 192540 223460 236220 146930 181290 153300 176810 TRUE FALSE 90940.01483 183986.9636 162107.3492 230623.8373 185476.349 181361.4849 135413.2427 178860.1041 147782.7629 211452.5343 0.430072948 0.870109995 0.76663706 1.090664806 0.877153587 0.857693598 0.640395459 0.845864083 0.698893316 1 17.68997433 4.74103763 24.46020532 0.841459952 0.430072749 0.50304005 0.124886526 143.2246703 1414209.791 0.029598337 0.200824058 55085.54235 -4.74103763 -0.411387203 SLLSNVS(ph)IEDEEEELVAIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLLSNVSIEDEEEELVAIVR 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 SLLSNVS(1)IEDEEEELVAIVR;SLLS(0.003)NVS(0.997)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR;SLLSNVS(1)IEDEEEELVAIVR 250.28 1.31E-30 93228000 38649 49283.9 57375.4 48353 63847.3 61392 53137.2 54606.4 56098.8 53098.5 TRUE FALSE 40174.89236 57748.02645 58870.65006 57917.07908 52994.55875 47134.6384 48972.16742 53874.49053 54079.81515 63502.13444 0.632654205 0.909387172 0.92706569 0.912049329 0.834531929 0.742252821 0.771189313 0.848388657 0.851622006 1 15.95451746 0.64404302 1.947849256 0.999914025 0.827609472 0.278538219 0.085201065 2.516608787 11.95921852 0.082310524 0.022790235 4.405985062 -0.64404302 -0.172304553 SLLTEADAGHTEFTDEVYQNESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLLTEADAGHTEFTDEVYQNESR 23 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 ;; 369.66 2.05E-118 284846000 137272 201414 173477 222996 176174 220673 165497 157221 156721 184478 FALSE TRUE 142691.6046 236005.2877 177997.9531 267103.9432 146228.0064 169425.0401 152524.9127 155113.7097 151080.6418 220622.9321 0.646766876 1.069722379 0.806797151 1.210680779 0.662796043 0.767939391 0.691337529 0.703071563 0.684791197 1 17.75122323 SLLVNPEGPTLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 162.93 9.22E-05 733679000 556412 587826 582298 604097 715640 773980 579071 604950 575926 549014 FALSE TRUE 578379.5754 688780.5428 597473.1642 723585.5836 593995.7684 594234.8748 533681.9019 596841.6347 555198.5358 656582.7818 0.880893608 1.049038388 0.909973854 1.102047759 0.904677651 0.905041818 0.812817388 0.909012011 0.845588022 1 19.32461739 3.025710103 24.99859023 0.885942629 0.986974943 0.254707457 0.074268362 258.3138979 251163.382 0.019684207 0.02352645 1060.987099 -3.025710103 0.101032314 SLNFQEDDDT(ph)SRETFASDTNEALASLDESQEGHAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAK 37 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 SLNFQEDDDT(0.494)S(0.494)RET(0.012)FASDTNEALASLDESQEGHAEAK 151.67 2.86E-13 77820000 39340 29393 41247 27100 54606 53876 44843 41754 50348 45126 TRUE FALSE 40893.17358 34441.0191 42321.9307 32460.29911 45324.09162 41364.1155 41328.08848 41194.35593 48535.98531 53967.57571 0.757735975 0.638179845 0.784210336 0.601477808 0.839839311 0.766462361 0.765794793 0.763316776 0.89935456 1 15.71980526 0.775004854 0.427922479 1.022179713 0.702352764 0.632591284 0.066222108 0.952988074 0.408225148 0.10110617 0.043470985 5.956688015 -0.775004854 -0.31982695 SLNFQEDDDTS(ph)RETFAS(ph)DTNEALASLDESQEGHAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLNFQEDDDTSRETFASDTNEALASLDESQEGHAEAK 37 1 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 2 S(0.001)LNFQEDDDT(0.471)S(0.522)RET(0.017)FAS(0.953)DT(0.035)NEALASLDESQEGHAEAK 128.21 1.98E-08 28718000 27001 27228 39176 30327 45140 39783 38745 42344 43133 26348 TRUE FALSE 28067.02033 31904.1972 40196.95874 36325.59008 37467.11892 30544.00117 35708.06566 41776.44794 41580.65176 31510.38614 0.89072283 1.012497818 1.275673315 1.152813232 1.189040298 0.969331224 1.133215744 1.325799302 1.319585599 1 14.94353981 4.433559157 4.777388178 1.180293162 0.914780304 0.386568769 0.114359023 0.175299779 8.883862903 0.029499268 0.092500272 27136.83271 -4.433559157 -0.265512857 SLNS(ph)TPPPPPAPAPAPPPALARPR ddPTM_MDA-MB-175_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(0.01)LNS(0.942)T(0.049)PPPPPAPAPAPPPALARPR;S(0.002)LNS(0.499)T(0.499)PPPPPAPAPAPPPALARPR;SLNS(0.5)T(0.5)PPPPPAPAPAPPPALARPR 106.28 0.0016462 4388200000 2016910 2700590 2452070 2151740 2813050 3021160 2054510 2443140 2259910 2755040 TRUE FALSE 2096539.164 3164395.325 2515972.959 2577347.75 2334888.766 2319541.376 1893472.138 2410393.704 2178576.281 3294837.34 0.636310369 0.960410181 0.763610673 0.782238236 0.708650694 0.703992682 0.574678487 0.731566829 0.661209054 1 21.65177581 5.03903088 16.73847873 0.747367315 0.136450841 0.073895297 0.123111751 13275898.39 150042784.1 0.028564978 249027379.8 109403.4153 -5.03903088 -0.610916474 SLNST(ph)PPPPPAPAPAPPPALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLNSTPPPPPAPAPAPPPALAR 22 0 Q8TE68;B4DKV7;Q8TE68-2;K7ELW3;Q8TE68-4 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.003)LNS(0.125)T(0.872)PPPPPAPAPAPPPALAR;S(0.003)LNS(0.156)T(0.84)PPPPPAPAPAPPPALAR 170.06 8.48E-11 689790000 360510 355680 387380 433970 369860 461830 438420 392640 366420 328330 TRUE FALSE 374743.2132 416765.2732 397475.441 519807.9707 306991.3293 354576.9816 404055.4948 387377.303 353232.6158 392659.9772 0.954370791 1.061389745 1.012263699 1.323811951 0.781824854 0.90301279 1.029021337 0.986546441 0.89958905 1 18.58292103 3.214484773 24.99999356 0.941495282 1.080654775 0.317614828 0.110438512 308.2810242 320113.5634 0.032112213 0.038400284 1638.644609 -3.214484773 0.139159493 SLNST(ph)PPPPPAPAPAPPPALARPR ddPTM_MDA-MB-175_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(0.022)LNS(0.442)T(0.536)PPPPPAPAPAPPPALARPR 80.733 0.02744 1267200000 400630 506730 460830 433190 508410 546660 409050 464750 416690 533870 TRUE FALSE 416447.1818 593756.9357 472839.6084 518873.6891 421990.6498 419706.4997 376987.5921 458520.7864 401693.4083 638471.6049 0.652256386 0.92996608 0.740580481 0.812680916 0.66093879 0.657361262 0.590453184 0.718153764 0.629148431 1 19.28426293 5.046644554 16.44115586 0.732019399 0.186127774 0.035501188 0.126102355 13561383.03 121956494.6 0.029135203 233217089.8 111338.2919 -5.046644554 -0.545891625 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_MDA-MB-175_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 214 1.90E-26 3370690000 2533260 2024500 2298500 1980130 2647750 2909100 2713110 2314230 2620410 1826060 TRUE FALSE 2633275.061 2372192.127 2358400.798 2371793.804 2197686.401 2233505.613 2500449.349 2283211.532 2526101.956 2183841.495 1.205799536 1.086247391 1.079932222 1.086064996 1.006339703 1.022741631 1.144977488 1.045502404 1.15672404 1 21.05843672 4.854661685 2.163686404 1.068758875 1.273315961 0.40062431 0.050284804 1.01428505 4.080032164 0.012144824 0.44665789 71558.57525 -4.854661685 0.204557086 SLPAT(ph)PQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPATPQGK 9 0 Q13111;Q13111-2;Q13111-3;K7EPA1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 SLPAT(1)PQGK 82.912 0.048799 0 330200 268700 343040 249030 451400 399420 441340 372990 378430 270220 TRUE FALSE 343236.551 314847.1348 351979.9042 298287.3907 374671.1892 306660.7583 406746.6176 367990.6791 364810.3782 323164.4353 1.062111153 0.974262946 1.089166584 0.923020475 1.159382495 0.948931023 1.258636697 1.138710325 1.128869202 1 18.30190891 2.248406687 24.99987348 1.146767357 1.028020763 0.250951349 0.087617201 232.72762 590912.3176 0.028074776 0.023224112 177.176732 -2.248406687 -0.118746594 SLPDCTPHPNS(ph)ISIDAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPDCTPHPNSISIDAGPR 19 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 SLPDCTPHPNS(0.617)IS(0.383)IDAGPR 118.51 5.01E-05 171800000 67842 76993 120530 86073 109620 104090 95369 92332 127120 83215 TRUE FALSE 70520.45455 90215.94883 123671.1108 103097.9825 90986.83156 79916.675 87893.72858 91094.44056 122544.976 99519.386 0.708610225 0.906516333 1.24268362 1.035958788 0.914262389 0.803026206 0.883181982 0.915343675 1.231367887 1 16.60268996 1.259566663 24.90709282 1.115683977 0.932155761 0.218652107 0.142924416 319.6842931 379055.041 0.100196214 0.03650486 18.17886076 -1.259566663 -0.183528215 SLPDCTPHPNSIS(ph)IDAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPDCTPHPNSISIDAGPR 19 0 Q9Y2H0-3;Q9Y2H0;Q9Y2H0-1;A0A0B4J2C2;F8WF49;A0A087X246;A0A087WWE6 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 SLPDCTPHPNS(0.032)IS(0.968)IDAGPR 128.52 1.37E-05 221940000 40657 54202 90827 69068 66606 53541 65422 57972 77062 68586 TRUE FALSE 42262.16975 63510.77187 93194.02624 82729.44425 55284.33591 41106.91417 60294.05269 57194.98016 74288.55367 82024.11354 0.515240798 0.774293913 1.136178402 1.008599065 0.674001017 0.501156457 0.735077163 0.697294706 0.905691637 1 16.32376048 4.72284011 5.316627847 0.808694096 0.505977351 0.207566833 0.18005564 0.256665988 24.77296846 0.0469249 0.27170234 52825.07355 -4.72284011 -0.302716744 SLPEEDVAEIQHAEEFLIKPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 ; 235.25 2.61E-37 94993000 172314 101417 143028 96144 188063 167759 194893 135428 152817 87548 FALSE TRUE 179117.0898 118834.5808 146755.4272 115160.9962 156096.1184 128799.5147 179616.7774 133612.8092 147317.146 104701.3544 1.710742815 1.13498609 1.40165739 1.099899776 1.490870098 1.230160922 1.715515319 1.276132577 1.407022353 1 16.67592058 -1.406762746 5.0720816 0.999632045 1.37561502 0.245563915 0.201932177 0.000760539 8.90E-05 0.176980127 0.041674571 0.039195594 1.406762746 0.375982975 SLPELDRDKS(ph)DSDTEGLLFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPELDRDKSDSDTEGLLFSR 21 2 Q9H4G0-2;A0A1B0GTW6;Q9H4G0-3;A0A0C4DH22;Q9H4G0 Q9H4G0-2 EPB41L1 Band 4.1-like protein 1 1 SLPELDRDKS(0.892)DS(0.108)DTEGLLFSR;SLPELDRDKS(0.972)DS(0.028)DTEGLLFSR 200.09 4.00E-22 566150000 211311 125463 151447 112319 227508 225420 160161 146796 173868 140110 TRUE FALSE 219653.7214 147010.2943 155393.8332 134535.363 188836.2714 173069.6213 147607.1623 144828.4397 167610.5246 167561.8719 1.310881282 0.877349319 0.927381817 0.802899618 1.126964442 1.032869944 0.880911395 0.864328132 1.000290357 1 17.35433438 2.239339151 24.99667488 0.916990406 0.998619748 0.056073521 0.138255173 60.63897828 1947052.651 0.049504333 0.039158399 173.5158494 -2.239339151 0.081629342 SLPLSPELESS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLPLSPELESSP 12 0 Q6DT37 Q6DT37 CDC42BPG Serine/threonine-protein kinase MRCK gamma 1 SLPLSPELES(0.081)S(0.919)P;SLPLSPELES(0.008)S(0.992)P;SLPLSPELES(0.064)S(0.936)P;SLPLSPELES(0.073)S(0.927)P 183.33 7.71E-05 47686000 113211 124541 125019 125150 118868 141426 113104 119496 111755 123245 TRUE FALSE 117680.6577 145929.948 128277.0978 149904.2965 98662.85982 108581.9548 104238.6129 117894.3516 107732.9594 147392.4981 0.798416875 0.990077174 0.870309544 1.017041562 0.669388613 0.736685762 0.7072179 0.799866704 0.730925663 1 17.16930357 3.23738089 24.99999989 0.760428789 0.920565867 0.32353841 0.101532809 31.52626518 668090.8979 0.026499703 0.033408276 1727.352172 -3.23738089 0.160137078 SLPS(ph)LEDIDPDVLDSMHSLGCFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSLEDIDPDVLDSMHSLGCFR 23 0 Q8IWQ3-6;Q8IWQ3-3;Q8IWQ3-2;Q8IWQ3-4;Q8IWQ3;Q8IWQ3-5 Q8IWQ3-6 BRSK2 Serine/threonine-protein kinase BRSK2 1 S(0.001)LPS(0.999)LEDIDPDVLDSMHSLGCFR;S(0.002)LPS(0.998)LEDIDPDVLDSMHSLGCFR 190.19 1.03E-17 78551000 30123 47897 39695 47322 49137 57609 43947 46066 45830 54617 TRUE FALSE 31312.2793 56122.93716 40729.48431 56682.15036 40784.71029 44230.18282 40502.31931 45448.56062 44180.58725 65318.15544 0.479380948 0.859224159 0.623555335 0.867785533 0.624400827 0.677149906 0.620077512 0.695802879 0.676390614 1 15.99519643 -1.415311956 2.727743513 1.007975302 0.685917838 0.437060822 0.108647209 10599119.25 11568125.93 655734.7359 0.023760821 0.038431563 1.415311956 -0.322057464 SLPS(ph)SPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.088)LPS(0.637)S(0.274)PERR;S(0.074)LPS(0.53)S(0.397)PERR 72.2 0.029047 611070000 133757 135348 100306 153807 118219 169510 113974 111339 103416 108077 TRUE FALSE 139037.8296 158592.9661 102920.0568 184229.5655 98124.17661 130143.8714 105040.4201 109846.6828 99694.07836 129252.6189 1.075706093 1.227000021 0.796270572 1.425344934 0.759165868 1.006895431 0.812675371 0.849860403 0.771311864 1 16.97983399 3.197546829 24.99999967 0.86137661 1.114018547 0.378318448 0.16540147 150.2777826 91601.50536 0.044136421 0.052752656 1575.965945 -3.197546829 0.252641937 SLPSRS(ph)PPITPNWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLPSRSPPITPNWR 14 1 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.005)LPS(0.042)RS(0.941)PPIT(0.012)PNWR;S(0.004)LPS(0.055)RS(0.932)PPIT(0.009)PNWR 59.372 0.06142 694330000 173154 194476 187443 207557 207087 266240 224230 213460 187146 264950 TRUE FALSE 179990.2536 227875.7402 192327.9186 248611.1551 171886.4257 204409.7949 206654.2667 210598.9179 180410.652 316861.8797 0.568040099 0.719164263 0.606977143 0.784604179 0.54246483 0.645106931 0.65219037 0.664639489 0.569366855 1 18.27349458 -1.423105128 4.039474631 1.001661346 0.644329559 0.704864168 0.069973714 0.0009501 0.000135688 0.061451722 0.014420439 0.03774808 1.423105128 -0.357331787 SLPSS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLPSSPERR 9 1 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.022)LPS(0.152)S(0.826)PERR 77.062 0.02062 246790000 53789 62765 58935 61749 39516 71343 48724 53710 58337 33729 TRUE FALSE 55912.63125 73544.40051 60470.89452 73962.7679 32799.08443 54774.66946 44904.88556 52990.1053 56237.46277 40337.55177 1.386118612 1.823224199 1.499121584 1.833595859 0.813115397 1.357907633 1.113227838 1.313666868 1.394171443 1 15.2998359 3.254190402 24.99996376 1.194917394 1.639180468 0.552083315 0.206430379 181.2417107 289895.7721 0.053588945 0.072310911 1795.520642 -3.254190402 0.444263074 SLPTTVPES(ph)PNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SLPTTVPESPNYR 13 0 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR 317.77 8.09E-51 29573507000 5574840 6291320 5665340 5191050 5520922 6397700 5055668 5184331 4738998 5093178 TRUE FALSE 5794938.988 7371805.27 5812983.415 6217824.196 4582477.65 4911931.133 4659391.532 5114843.523 4568442.388 6091088.714 0.951379837 1.210260697 0.954342267 1.020806704 0.752324891 0.806412673 0.76495217 0.839725665 0.750020662 1 22.53826869 3.289120804 6.904386108 0.808912617 1.042928701 0.549092124 0.09523138 0.138380147 14.69893409 0.024642464 0.033191664 1945.901283 -3.289120804 0.234016085 SLQALGEVIEAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLQALGEVIEAELR 14 0 K7ER00;Q9Y285;Q9Y285-2;K7ER16;K7EK06 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ;;; 172.57 6.60E-06 51175500 52774.3 69768.6 68891.4 64566.2 75193 82669 68661.5 68852.9 63881.2 68282.6 FALSE TRUE 54857.87011 81750.81433 70686.76648 77337.20165 62411.72072 63470.37761 63279.63222 67930.0395 61582.12809 81661.26812 0.671773429 1.001096557 0.865609463 0.947048747 0.764275674 0.777239676 0.774903864 0.831851391 0.754116725 1 16.31736435 3.226248477 24.99841415 0.805744821 0.880235056 0.052941637 0.103589205 486.564813 987913.9611 0.027638617 0.03326162 1683.637062 -3.226248477 0.074490235 SLQEEHVAVAQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 130.61 0.00014003 2501610000 1382600 1913180 1635610 1747930 2010500 2166010 1508870 1701350 1573240 1945110 FALSE TRUE 1437186.116 2241753.783 1678235.34 2093665.337 1668755.928 1662987.004 1390600.827 1678546.186 1516619.4 2326217.063 0.617821156 0.963690714 0.721443999 0.900030083 0.717368966 0.714889006 0.597794956 0.721577626 0.651968135 1 21.14955429 3.044184005 24.0027019 0.709579129 0.806968473 0.038435413 0.132907726 188.8553677 102592.8016 0.035065428 0.041911171 1107.092747 -3.044184005 0.097389343 SLQELFLAHILSPWGAEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLQELFLAHILSPWGAEVK 19 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ; 189.51 1.39E-14 749640000 1405530 1250880 1553600 1221890 1923720 1920610 1761000 1558130 1710040 1261520 FALSE TRUE 1461021.41 1465708.91 1594088.092 1463576.195 1596726.762 1474577.435 1622968.218 1537245.816 1648495.994 1508690.691 0.968403543 0.971510541 1.056603651 0.970096922 1.058352631 0.977388834 1.075746161 1.01892709 1.092666644 1 20.52486563 6.936571801 0.400707243 1.040638171 0.506689053 0.243835854 0.039762412 39.42143004 1.185656615 0.025722542 14.52789036 8641155.106 -6.936571801 -0.533949118 SLQLPAS(ph)PAPDPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLQLPASPAPDPSPR 15 0 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 S(0.001)LQLPAS(0.999)PAPDPSPR;SLQLPAS(1)PAPDPSPR 145.8 4.19E-06 309970000 287350 277230 281430 316060 304850 351730 331990 317340 291630 221550 TRUE FALSE 298694.7999 324842.0959 288764.297 378575.7247 253031.7059 270046.038 305967.7563 313086.5764 281134.2933 264958.4807 1.127326814 1.226011317 1.089847346 1.428811502 0.95498625 1.019201338 1.154776233 1.181643915 1.061050367 1 18.01540678 3.206788516 24.99997988 1.082747809 1.209418557 0.331386101 0.105873898 278.2908641 218973.2947 0.031065283 0.037133108 1609.861505 -3.206788516 0.126670748 SLQLPAS(ph)PAPDPSPRPAYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLQLPASPAPDPSPRPAYK 19 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 SLQLPAS(0.992)PAPDPS(0.008)PRPAYK;S(0.011)LQLPAS(0.989)PAPDPSPRPAYK 125.62 1.63E-05 615840000 702400 614150 731990 574940 881040 897560 660250 717210 792290 728940 TRUE FALSE 730131.2944 719625.4851 751066.2607 688661.416 731281.1355 689115.2927 608497.8798 707596.9731 763775.6377 871761.8366 0.837535281 0.825484043 0.861549828 0.789965088 0.838854266 0.790485731 0.698009312 0.811686109 0.876128784 1 19.73357452 0.934737347 2.884880498 0.999460576 0.804346011 0.664553507 0.042169423 0.195752843 3.8343541 0.042970402 0.011343558 8.60473197 -0.934737347 -0.195114565 SLQSVAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLQSVAEER 9 0 P61313;A0A2R8YEM3;E7EQV9;E7EX53;A0A2R8Y738;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ;;; 179.81 0.00011487 1577470000 1285620 1614040 1483640 1489940 1746930 1940480 1576550 1586980 1463820 1756170 FALSE TRUE 1336377.27 1891238.815 1522304.877 1784645.685 1449987.463 1489832.928 1452975.891 1565709.129 1411137.404 2100257.888 0.63629199 0.90047933 0.724818074 0.849726929 0.690385438 0.70935714 0.691808325 0.745484227 0.671887682 1 21.00213505 -1.102880371 4.585387601 1.000020021 0.739914094 0.514727342 0.076918842 1.48E-05 2.89E-06 0.069794052 0.01644935 0.078907744 1.102880371 -0.260105927 SLQYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLQYER 6 0 P22059 P22059 OSBP Oxysterol-binding protein 1 0 111.73 0.064213 177400000 164620 179480 196580 198480 227370 241320 181980 194460 186690 197550 FALSE TRUE 171119.3247 210304.2938 201703.0363 237738.7516 188721.7286 185277.0872 167715.9321 191853.5818 179971.0634 236256.1402 0.724295777 0.89015377 0.853747277 1.006275441 0.798801371 0.784221257 0.709890257 0.812057547 0.76176248 1 17.8499923 3.047915636 24.99985353 0.79408903 0.873274705 0.062771758 0.0956578 228.1744746 119047.8164 0.026251132 0.031376098 1116.646312 -3.047915636 0.079185675 SLRDDYEVSCPELDQLVEAALAVPGVYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLRDDYEVSCPELDQLVEAALAVPGVYGSR 30 1 P51570;P51570-2;K7EII7 P51570 GALK1 Galactokinase 0 ; 197.01 2.53E-25 617640000 422110 560000 535030 541490 621580 692070 559240 565370 571090 659480 FALSE TRUE 438775.2287 656175.6438 548973.3213 648595.1058 515924.0536 531347.2309 515405.3075 557792.1399 550536.5825 788692.4795 0.556332462 0.83197908 0.696054971 0.822367555 0.654151101 0.673706476 0.653493371 0.707236539 0.698037064 1 19.58910336 -1.943807153 2.349578559 1.219128485 0.702962953 0.582810151 0.076275257 6154805.106 2755535.291 7375369.28 0.019013826 0.011381326 1.943807153 -0.516165532 SLRQS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 122.96 0.002598 247430000 99418 137486 161425 137617 160321 168275 169607 149069 149893 136327 TRUE FALSE 103343.0994 161098.151 165631.8681 164837.2319 133069.6937 129195.6815 156312.7602 147070.9739 144498.3802 163037.6655 0.633860274 0.988103887 1.015911677 1.011037734 0.816189886 0.792428431 0.958752443 0.902067467 0.886288329 1 17.31484577 -2.970852405 1.587822184 4.546634484 0.898080103 0.075630703 0.112367479 2916248.115 43532.21465 37475510 0.027691957 0.001069418 2.970852405 -3.648554381 SLRVDIAEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLRVDIAEGR 10 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ;;; 164.9 5.49E-06 2221420000 661810 903440 861970 647040 1099850 1030090 598230 786000 846590 1163450 FALSE TRUE 687938.7698 1058598.792 884433.6463 775022.5808 912897.8899 790867.2087 551339.1694 775464.9556 816121.3913 1391405.752 0.494419955 0.760812431 0.635640355 0.557006883 0.656097539 0.568394379 0.396246148 0.557324817 0.5865445 1 20.40811176 0.909332614 18.22846765 1 0.577353077 0.655417155 0.091557857 2030.104983 408150.9291 0.091726192 0.022931548 8.115823886 -0.909332614 -0.422646923 SLS(ph)APGNLLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSAPGNLLTK 11 0 Q96RR4-6;Q96RR4-5;Q96RR4-2;Q96RR4-3;Q96RR4-4;Q96RR4-7;Q96RR4;F5GZ00 Q96RR4-6 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2 1 S(0.002)LS(0.998)APGNLLTK 66.004 0.065136 0 359990 246870 332130 284050 442150 451450 373800 365130 383390 276140 TRUE FALSE 374202.6832 289268.0021 340785.5806 340234.2422 366993.5009 346607.5793 344500.5793 360236.0296 369591.8688 330244.346 1.133108523 0.875921134 1.031919501 1.030250014 1.11127868 1.049548867 1.043168743 1.090816645 1.119146696 1 18.33317434 3.609156286 2.755782299 1.071634153 0.998745784 0.109904185 0.067147206 0.448198461 6.566707211 0.017601267 0.029742235 4065.896189 -3.609156286 -0.07288837 SLS(ph)APLHPEFEEVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSAPLHPEFEEVYR 15 0 Q53HC0-2;Q53HC0 Q53HC0-2 CCDC92 Coiled-coil domain-containing protein 92 1 S(0.014)LS(0.986)APLHPEFEEVYR;S(0.129)LS(0.871)APLHPEFEEVYR 203.89 3.33E-09 136056000 135997 177698 196073 167741 201142 201410 187159 175959 197527 197511 TRUE FALSE 141366.2666 208216.2492 201182.8235 200919.6691 166951.9547 154635.5799 172488.9885 173600.5574 190418.0419 236209.4989 0.598478331 0.881489738 0.851713519 0.850599447 0.706796109 0.654654367 0.730237308 0.734943168 0.806140493 1 17.84970746 0.856106754 4.007851173 0.999974316 0.755685799 0.433812251 0.085135442 0.884713658 23.12434402 0.083818004 0.021420056 7.179707542 -0.856106754 -0.244288518 SLS(ph)CLSDLDGGVALEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSCLSDLDGGVALEPR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 1 S(0.022)LS(0.978)CLSDLDGGVALEPR;S(0.001)LS(0.999)CLSDLDGGVALEPR 295.43 4.25E-46 151374000 99821 168758 142793 171881 454230 170925 183695 153764 152785 216369 TRUE FALSE 103762.0102 197740.8737 146514.3029 205878.5488 377020.1468 131230.2591 169296.5059 151703.0451 147286.2977 258762.3629 0.40099344 0.764179425 0.566211798 0.795627874 1.457013078 0.507145853 0.654254753 0.58626395 0.569195211 1 17.98126827 5.048323827 1.661913189 0.756452026 1.21E-09 0.138195039 0.269683112 5.762446913 7.967445994 0.072679266 8.94266581 111769.6335 -5.048323827 -0.756452025 SLS(ph)DPIPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSDPIPQR 9 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.007)LS(0.993)DPIPQR;SLS(1)DPIPQR;S(0.146)LS(0.854)DPIPQR 130.79 0.00036856 322700000 430920 513320 509180 474040 549220 603860 536020 494650 496400 502450 TRUE FALSE 447933.0543 601478.7169 522449.6491 567803.6971 455863.7806 463622.6666 494005.3518 488020.0258 478534.661 600895.4575 0.74544257 1.00097065 0.86945182 0.944929255 0.75864075 0.771552956 0.822115304 0.812154626 0.796369244 1 19.19675449 3.241738761 24.99381926 0.81443687 0.896628949 0.10054161 0.087517178 139.0735524 1093703.693 0.022611823 0.029371846 1744.772314 -3.241738761 0.082192079 SLS(ph)DS(ph)ESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 SLS(1)DS(1)ESDDSK 162.93 3.59E-05 149090000 486240 223370 326380 239960 416500 529370 472780 323140 365140 187270 TRUE FALSE 505437.1307 261732.0599 334885.7309 287423.3718 345703.4788 406431.8402 435722.2682 318808.8369 351998.6827 223961.971 2.256798904 1.1686451 1.495279442 1.283357931 1.543581159 1.81473595 1.945518993 1.423495406 1.57168952 1 17.77289426 0.438627041 1.501729987 1.000273272 1.599670655 0.266578858 0.304549059 4.70304934 11.11580385 0.282092996 0.0814462 2.74553536 -0.438627041 0.599397383 SLS(ph)DSES(ph)DDSKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 2 S(0.079)LS(0.762)DS(0.445)ES(0.714)DDSKSK 75.376 0.017957 192460000 545700 145650 207680 139660 367420 419990 323680 210630 245130 120800 TRUE FALSE 567244.6574 170664.2545 213092.3114 167284.3312 304966.0796 322453.6875 298309.1158 207806.8494 236307.8192 144468.4471 3.926425933 1.181325458 1.475009358 1.157929876 2.110952846 2.232000786 2.06487383 1.438423777 1.6357054 1 17.14039491 4.745586797 24.73977409 1.634056669 3.926427169 0.746088841 0.408391008 372.7518533 1312452.557 0.10083873 1.004160446 55665.58744 -4.745586797 2.2923705 SLS(ph)DSESDDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLSDSESDDSK 11 0 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.403)LS(0.583)DS(0.014)ESDDSK;SLS(0.909)DS(0.091)ESDDSK;SLS(0.992)DS(0.008)ESDDSK;SLS(0.991)DS(0.009)ESDDSK;SLS(0.85)DS(0.149)ESDDSK;S(0.16)LS(0.84)DSESDDSK;S(0.005)LS(0.992)DS(0.003)ESDDSK;S(0.058)LS(0.942)DSESDDSK 364.15 1.20E-85 1563942000 4274270 2160825 2905981 2245096 3830100 4357340 4087820 2973707 3231919 1774718 TRUE FALSE 4443021.48 2531929.885 2981713.252 2689169.288 3179060.97 3345413.821 3767405.987 2933849.322 3115602.867 2122440.013 2.093355502 1.192933543 1.404851602 1.267017806 1.497833131 1.576211248 1.77503532 1.382300232 1.467934475 1 21.01729235 0.497782833 1.532861502 1.000299479 1.508838569 0.288079562 0.245168295 3.461551033 9.1582728 0.223251641 0.064295038 3.146174688 -0.497782833 0.508539091 SLS(ph)DSESDDSKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 S(0.003)LS(0.906)DS(0.09)ESDDSKSK 174.94 5.03E-05 92085000 224150 93488 146400 59055 256550 184170 107830 119120 167240 92963 TRUE FALSE 232999.6151 109543.8368 150215.3043 70735.90274 212941.7226 141399.3086 99378.00284 117523.3912 161221.0651 111177.32 2.095747722 0.985307406 1.351132626 0.636244 1.915334195 1.271835916 0.893869387 1.057080628 1.450125485 1 16.76250298 4.74573308 24.78200902 1.171789447 2.095748211 0.407311135 0.333765914 744.6782524 2572910.666 0.07669701 0.778775371 55684.34043 -4.74573308 0.923958764 SLS(ph)ELESLKLPAESNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSELESLKLPAESNEK 17 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 S(0.002)LS(0.998)ELESLKLPAESNEK 147.67 2.37E-07 193020000 610250 310070 493920 321350 747910 630710 672560 472630 626420 333740 TRUE FALSE 634343.1412 363322.1105 506791.961 384912.0709 620780.5253 484237.161 619842.9898 466295.1679 603875.2666 399129.9632 1.589314759 0.91028523 1.269741708 0.964377788 1.555334309 1.213231793 1.552985361 1.168279034 1.512979035 1 18.60649906 3.240611865 24.99992357 1.339628891 1.170084719 0.084466265 0.240474839 120.9722383 1474353.308 0.061681198 0.079559179 1740.250893 -3.240611865 -0.169544172 SLS(ph)ESSVIMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSESSVIMDR 11 0 H3BSS6;Q9H2Y7;A0A0C4DGM5;Q9H2Y7-2;H3BNX5 H3BSS6 ZNF106 Zinc finger protein 106 1 S(0.006)LS(0.903)ES(0.046)S(0.046)VIMDR;SLS(1)ESSVIMDR;SLS(0.984)ES(0.013)S(0.002)VIMDR;S(0.003)LS(0.972)ES(0.013)S(0.013)VIMDR 237.67 1.44E-15 396705000 407088 529721 534968 558725 662872 702950 572610 516069 508822 689329 TRUE FALSE 423160.1486 620696.4611 548909.7056 669239.1374 550197.2542 539700.5158 527727.332 509151.9392 490509.5956 824389.8195 0.513301036 0.752916213 0.66583756 0.811799371 0.66739938 0.654666643 0.640142951 0.617610658 0.594997153 1 19.65296716 -1.12841342 4.467424632 1.000043237 0.661468698 0.637883114 0.077338816 3.26E-05 6.37E-06 0.073387064 0.017295292 0.074402337 1.12841342 -0.338574538 SLS(ph)ESYELSSDLQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSESYELSSDLQDK 15 0 A0A3B3IRZ4;Q6DN90-3;A0A2R8Y7T6;Q6DN90;A0A2R8Y695 A0A3B3IRZ4 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 S(0.015)LS(0.983)ES(0.001)YELSSDLQDK;SLS(1)ESYELSSDLQDK 371.89 1.35E-97 78255000 228009 158234 244254 199045 354778 312377 309707 267630 303068 209106 TRUE FALSE 237010.9714 185409.4586 250619.4599 238415.5069 294472.9623 239832.1759 285431.3561 264042.8576 292160.6419 250076.3171 0.947754566 0.741411505 1.002171908 0.953370994 1.177532386 0.95903594 1.141376998 1.055849113 1.168285927 1 17.93200891 3.792436585 1.721803633 1.080354278 0.850913952 0.474695545 0.090014038 0.278967493 1.59305133 0.02386822 0.056778344 6200.640966 -3.792436585 -0.229440326 SLS(ph)FEMQQDELIEKPMSPMQYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 SLSFEMQQDELIEKPMSPMQYAR 23 1 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 SLS(1)FEMQQDELIEKPMSPMQYAR;S(0.022)LS(0.978)FEMQQDELIEKPMSPMQYAR;SLS(1)FEMQQDELIEKPMSPMQYAR;S(0.009)LS(0.991)FEMQQDELIEKPMSPMQYAR;S(0.001)LS(0.999)FEMQQDELIEKPMSPMQYAR;S(0.002)LS(0.998)FEMQQDELIEKPMSPMQYAR;S(0.126)LS(0.874)FEMQQDELIEKPMSPMQYAR;S(0.004)LS(0.996)FEMQQDELIEKPMSPMQYAR;S(0.022)LS(0.978)FEMQQDELIEKPMSPMQYAR;S(0.141)LS(0.859)FEMQQDELIEKPMSPMQYAR;S(0.024)LS(0.976)FEMQQDELIEKPMSPMQYAR;S(0.056)LS(0.944)FEMQQDELIEKPMSPMQYAR;S(0.204)LS(0.796)FEMQQDELIEKPMSPMQYAR;S(0.207)LS(0.793)FEMQQDELIEKPMSPMQYAR 258.25 7.41E-44 5325155000 2865669 2650337 3288132 2368029 4522339 3784282 3581861 3490062 3837395 2611648 TRUE FALSE 2978807.825 3105511.763 3373823.421 2836418.068 3753633.432 2905439.857 3301105.375 3443283.427 3699287.904 3123350.423 0.95372194 0.994288614 1.080193691 0.908133153 1.201797085 0.930231791 1.056911627 1.102432632 1.184397331 1 21.57466301 4.367140567 0.422484197 1.087904207 0.906399749 0.138520729 0.089693479 7.541110914 1.336120762 0.068800076 0.671878422 23288.44909 -4.367140567 -0.181504458 SLS(ph)FSDEMSSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSFSDEMSSCR 12 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 SLS(0.5)FS(0.5)DEMSSCR;SLS(0.994)FS(0.006)DEMSSCR 302.87 1.23E-36 243590000 186482 243640 230351 245422 282140 299120 237708 250513 240573 267530 TRUE FALSE 193844.4534 285483.2747 236354.1363 293965.7391 234181.9436 229653.9132 219075.8258 247155.283 231914.8247 319947.3813 0.605863541 0.892281954 0.738728147 0.918794015 0.731938929 0.717786507 0.684724547 0.772487282 0.724853017 1 18.28747513 -0.938156652 4.756651388 1.000002145 0.758894678 0.414820191 0.087433676 0.006429864 52175651.82 273.6188458 0.019262844 0.115303728 0.938156652 -0.241107467 SLS(ph)FSEPQQPAPAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSFSEPQQPAPAMK 15 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 S(0.167)LS(0.832)FSEPQQPAPAMK;S(0.197)LS(0.803)FSEPQQPAPAMK;S(0.082)LS(0.917)FSEPQQPAPAMK 189.86 9.36E-10 177388000 396414 336945 394691 363798 522725 504504 438991 448244 468790 368433 TRUE FALSE 412064.7308 394812.6827 404976.9717 435756.1586 433872.3912 387340.5918 404581.7383 442236.0224 451918.3395 440620.3923 0.935192147 0.896038153 0.919106285 0.988960489 0.984685228 0.879080039 0.918209292 1.003666717 1.025640999 1 18.74917674 1.663023923 5.066871351 1.013060868 0.932082588 0.541701003 0.032951996 0.12483601 7.158160765 0.019267216 0.009285264 46.02819269 -1.663023923 -0.08097828 SLS(ph)GSSPCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.011)LS(0.987)GS(0.002)SPCPK;SLS(0.985)GS(0.015)SPCPK;SLS(1)GSSPCPK 160.18 7.82E-06 427610000 746410 535580 700040 558530 835370 887280 758810 697450 730480 539540 TRUE FALSE 775878.8432 627561.6988 718283.6175 669005.567 693374.1058 681222.6669 699332.4894 688101.8235 704190.1675 645252.5329 1.20244215 0.972583085 1.113182174 1.036811997 1.074577891 1.055745824 1.083812079 1.066407009 1.091340416 1 19.29950437 -2.421763506 2.100904762 0.436759767 1.073204015 0.146323358 0.055266659 1042106.044 198027.883 2778143.693 0.01179004 0.003786487 2.421763506 0.636444248 SLS(ph)LDPGQSLEPHPEGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSLDPGQSLEPHPEGPQR 19 0 P98174 P98174 FGD1 "FYVE, RhoGEF and PH domain-containing protein 1" 1 S(0.035)LS(0.964)LDPGQSLEPHPEGPQR;S(0.135)LS(0.865)LDPGQSLEPHPEGPQR 174.99 2.21E-12 376120000 370080 524120 618620 474850 720200 653410 586670 680140 663500 558210 TRUE FALSE 384691.0442 614133.5329 634741.7454 568773.9127 597780.6612 501665.43 540685.2724 671023.8358 639620.7646 667580.5619 0.576246623 0.919939207 0.950809208 0.851992921 0.89544348 0.751468 0.809917639 1.00515784 0.958117718 1 19.34858242 4.740702129 24.77199671 0.900177143 0.576246496 0.61807436 0.077396462 120.4897906 1393660.374 0.019562971 0.12911286 55043.00415 -4.740702129 -0.323930646 SLS(ph)LESTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLSLESTDR 9 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 SLS(0.995)LES(0.004)TDR;SLS(0.897)LES(0.095)T(0.007)DR;SLS(0.995)LES(0.005)TDR;SLS(0.998)LES(0.002)TDR;S(0.003)LS(0.994)LES(0.002)T(0.001)DR;S(0.002)LS(0.972)LES(0.025)T(0.001)DR 181.87 4.93E-05 3293530000 2660610 2575980 2728190 3041370 3173800 3687010 3321320 2829270 2811170 2613370 TRUE FALSE 2765652.937 3018384.527 2799288.873 3642943.908 2634318.61 2830757.805 3060986.26 2791348.263 2709996.541 3125409.816 0.884892894 0.965756398 0.895654982 1.165589194 0.84287142 0.90572372 0.979387165 0.89311432 0.867085183 1 21.57561394 SLS(ph)LESTDRGSWDP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSLESTDRGSWDP 14 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 S(0.179)LS(0.82)LESTDRGSWDP;S(0.013)LS(0.986)LES(0.001)T(0.001)DRGSWDP 96.489 0.0088155 298290000 348480 572150 519300 435300 624420 690060 390130 505250 544870 748740 TRUE FALSE 362238.2595 670412.3118 532833.3846 521401.0408 518281.3114 529804.023 359550.5912 498477.9502 525260.2351 895441.2675 0.404536035 0.748694902 0.595051182 0.582283908 0.578799895 0.591668088 0.401534533 0.556684138 0.586593732 1 19.77223928 0.700003273 3.943215948 0.999997939 0.560173604 0.664681252 0.093803138 3.842616946 49.98012073 0.087588004 0.022394483 5.01191011 -0.700003273 -0.439824335 SLS(ph)LGDKEISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.004)LS(0.996)LGDKEISR;S(0.003)LS(0.997)LGDKEISR;SLS(1)LGDKEISR;SLS(0.884)LGDKEIS(0.116)R;S(0.017)LS(0.957)LGDKEIS(0.026)R 185.27 2.75E-06 1843748000 2808790 2093350 2692470 2165140 4126370 3795800 3386790 3012990 3347750 2231640 TRUE FALSE 2919683.198 2452866.578 2762637.98 2593398.23 3424971.101 2914282.976 3121324.55 2972605.797 3227265.131 2668887.131 1.093970279 0.91905969 1.035127319 0.971715214 1.283295596 1.09194688 1.169522875 1.113799742 1.20921754 1 21.34780686 3.271046121 24.99947261 1.147003673 1.000985953 0.414173199 0.081288051 168.6406608 129777.6734 0.020481126 0.02772966 1866.577905 -3.271046121 -0.14601772 SLS(ph)LSLADSGHLPDVHGFNS(ph)YGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 2 S(0.465)LS(0.525)LS(0.01)LADSGHLPDVHGFNS(0.697)YGS(0.303)HR 97.609 0.0039186 19259000 7749.3 15008 15283 15504 20918 22819 12518 19668 16054 17812 TRUE FALSE 8055.248348 17585.50725 15681.28754 18570.64493 17362.36583 17519.63308 11536.80645 19404.38263 15476.21968 21301.92037 0.378146581 0.82553624 0.736144313 0.871782666 0.815061062 0.822443835 0.541585277 0.910921752 0.726517582 1 14.37869587 6.998352187 0.078038187 1.12031804 9.95E-62 0.280799285 0.146698349 259.6310869 1.804052118 4.781326006 32.16357039 9962129.594 -6.998352187 -1.12031804 SLS(ph)MDSQVPVYSPSIDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 S(0.096)LS(0.848)MDS(0.056)QVPVYSPSIDLK;S(0.134)LS(0.866)MDSQVPVYSPSIDLK;S(0.092)LS(0.908)MDSQVPVYSPSIDLK;S(0.126)LS(0.874)MDSQVPVYSPSIDLK;S(0.144)LS(0.856)MDSQVPVYSPSIDLK 243.95 4.26E-24 398170000 1327050 1094290 1397950 1077880 1834660 1749490 1702790 1531140 1677910 1140270 TRUE FALSE 1379442.959 1282225.795 1434381.725 1291081.447 1522805.149 1343197.461 1569320.87 1510617.573 1617522.347 1363684.075 1.011556111 0.940266018 1.05184313 0.946759936 1.116684705 0.984977009 1.150795041 1.107747462 1.186141553 1 20.37907802 2.769761567 1.04520685 1.117165769 0.988431553 0.31634173 0.067873197 0.513004967 1.183697223 0.032830905 0.03142826 588.520462 -2.769761567 -0.128734216 SLS(ph)MVDLQDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSMVDLQDAR 11 0 Q5VWQ8;A0A3B3ITG3;Q5VWQ8-2;Q5VWQ8-5;H0Y3A3;Q5VWQ8-3;Q5VWQ8-4 Q5VWQ8 DAB2IP Disabled homolog 2-interacting protein 1 SLS(1)MVDLQDAR;S(0.001)LS(0.999)MVDLQDAR;SLS(1)MVDLQDAR;SLS(1)MVDLQDAR 263.33 8.99E-21 803870000 938200 1199740 1230570 1135510 1281300 1425670 1102130 1152880 1112400 1316690 TRUE FALSE 975240.8604 1405786.012 1262639.665 1360110.489 1063505.084 1094579.749 1015742.171 1137427.529 1072364.941 1574670.196 0.619330234 0.892749489 0.801843883 0.863743082 0.675382748 0.695116826 0.645050737 0.722327464 0.681009232 1 20.58661827 3.229441023 24.99938593 0.714780574 0.801970964 0.035787782 0.116087419 403.4682661 1106019.226 0.03084104 0.037352461 1696.059263 -3.229441023 0.08719039 SLS(ph)PFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSPFR 6 0 Q12802-2;Q12802;Q12802-4;A8MYJ1;A0A087WTD7;H0YMW2;A0A087WY36;H0YLH1 Q12802-2 AKAP13 A-kinase anchor protein 13 1 S(0.005)LS(0.995)PFR 75.213 0.082117 81839000 55248 57509 52147 61055 73002 69822 52970 58119 51063 69687 TRUE FALSE 57429.2337 67385.72339 53505.99366 73131.49677 60593.14612 53606.89866 48818.07299 57340.00987 49225.2526 83340.83341 0.689088786 0.80855591 0.642014142 0.877498985 0.727052318 0.643224893 0.585764157 0.688018196 0.590649872 1 16.34673591 -1.297935436 5.387100785 1.000050224 0.69590666 0.525903599 0.086968111 5.32E-05 6.93E-06 0.085350675 0.020114033 0.050357547 1.297935436 -0.304143565 SLS(ph)PFRR ddPTM_MDA-MB-175_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 SLS(1)PFRR 93.598 0.0090761 238060000 76540 87017 77366 86097 80964 109860 75257 82706 76101 84134 TRUE FALSE 79561.8583 101961.4929 79382.22152 103126.7296 67201.7682 84346.67994 69358.15969 81597.46135 73362.13988 100618.4465 0.790728352 1.013347914 0.788943025 1.024928661 0.667887158 0.838282471 0.689318531 0.810959265 0.72911223 1 16.61853529 3.235462627 24.9994648 0.777560805 0.904009618 0.193854848 0.113619256 111.1134592 896639.7622 0.029092945 0.036202274 1719.739346 -3.235462627 0.126448814 SLS(ph)PGGAALGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLSPGGAALGYR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 S(0.002)LS(0.998)PGGAALGYR;SLS(1)PGGAALGYR;SLS(1)PGGAALGYR;S(0.021)LS(0.979)PGGAALGYR;SLS(1)PGGAALGYR;S(0.001)LS(0.999)PGGAALGYR;S(0.01)LS(0.99)PGGAALGYR;SLS(1)PGGAALGYR 229.56 8.30E-12 10065140000 3422560 4007490 3997630 3721380 4685400 4914280 4063700 4039800 3815040 4494550 TRUE FALSE 3557685.312 4695745.234 4101811.522 4457457.857 3888977.382 3773012.947 3745176.575 3985653.089 3677737.456 5375171.019 0.661873883 0.873599224 0.763103445 0.8292681 0.723507655 0.701933563 0.696754868 0.741493261 0.684208454 1 22.35787923 -1.007396992 4.362828816 1.000011004 0.744930689 0.6044213 0.062629616 6866201.11 3170874.074 735.4841568 0.014521997 0.098311203 1.007396992 -0.255080315 SLS(ph)PGVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSPGVSR 8 0 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 S(0.004)LS(0.996)PGVSR;SLS(1)PGVSR 153.7 0.00045825 1069040000 1284900 1356360 1346800 1442810 1451900 1582090 1454480 1374690 1248030 1238270 TRUE FALSE 1335628.844 1589304.279 1381898.714 1728193.512 1205106.557 1214673.574 1340474.057 1356264.529 1203113.644 1480885.298 0.901912421 1.073212274 0.933157157 1.167000249 0.813774408 0.820234744 0.905184256 0.915847116 0.81242865 1 20.49802847 3.212944859 24.99967907 0.875910746 1.016586994 0.388989284 0.086476686 217.983766 212740.4823 0.023562208 0.028171186 1632.844617 -3.212944859 0.140676248 SLS(ph)PIIGK ddPTM_MDA-MB-175_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;S(0.014)LS(0.986)PIIGK;S(0.002)LS(0.998)PIIGK;S(0.001)LS(0.999)PIIGK;SLS(1)PIIGK;S(0.001)LS(0.999)PIIGK 151.22 0.00050003 7465840000 10184490 8391430 9586530 8020220 11083170 11898460 12209040 9923690 9853910 7182750 TRUE FALSE 10586581.53 9832592.826 9836362.847 9606595.578 9199256.722 9135222.988 11252063.54 9790679.167 9499269.704 8590072.34 1.232420533 1.144646103 1.145084984 1.118336982 1.070917259 1.06346287 1.309891593 1.139766789 1.105842806 1 23.03423885 4.879618952 1.997419196 1.130662363 1.29162742 0.152455238 0.076380407 2.59768163 8.078005924 0.019544511 0.865986528 75791.22952 -4.879618952 0.160965057 SLS(ph)PILPGR ddPTM_MDA-MB-175_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(0.002)LS(0.998)PILPGR;S(0.002)LS(0.998)PILPGR 183.22 4.76E-05 829670000 581070 653770 617460 657180 732040 797820 633370 631280 579940 570360 TRUE FALSE 604011.0923 766049.9119 633551.5148 787168.2425 607608.1023 612538.3961 583724.8044 622818.7242 559068.0727 682111.1218 0.885502483 1.123057354 0.92880983 1.154017604 0.890775832 0.898003824 0.855762039 0.913075164 0.819614363 1 19.37964726 3.145488019 23.307818 0.890723765 1.023287729 0.34194019 0.085864938 10.08339581 2517.963058 0.022409551 0.026784558 1397.938351 -3.145488019 0.132563965 SLS(ph)PNHNTLQTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSPNHNTLQTLK 13 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 S(0.138)LS(0.862)PNHNTLQTLK;S(0.152)LS(0.848)PNHNTLQTLK;S(0.129)LS(0.871)PNHNTLQTLK;SLS(1)PNHNTLQTLK 209.6 3.84E-08 2484160000 2009220 2684910 2989440 2595300 3703250 3725610 3101480 2930050 2790580 2604980 TRUE FALSE 2088545.557 3146022.407 3067347.262 3108642.594 3073772.888 2860393.54 2858377.893 2890777.472 2690147.571 3115375.956 0.670399203 1.00983716 0.98458334 0.997838668 0.986645892 0.918153565 0.917506566 0.927906459 0.863506559 1 21.57097484 4.745664774 24.94292089 0.952975944 0.670399067 0.780141692 0.045490381 394.1878173 1383970.319 0.011520159 0.116189855 55675.58309 -4.745664774 -0.282576878 SLS(ph)PSHLTEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLSPSHLTEDR 11 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 SLS(1)PSHLTEDR;S(0.018)LS(0.981)PS(0.001)HLTEDR;S(0.11)LS(0.889)PS(0.002)HLTEDR;S(0.027)LS(0.973)PSHLTEDR;S(0.16)LS(0.838)PS(0.001)HLTEDR 252.22 2.33E-20 3042592000 930412 1609590 1352240 1453350 1393390 1636240 1365150 1391860 1296600 1563210 TRUE FALSE 967145.3842 1886024.562 1387480.485 1740818.292 1156542.066 1256248.057 1258145.976 1373204.393 1249935.619 1869491.07 0.517330839 1.008843846 0.742170159 0.931172296 0.618640059 0.671973286 0.672988492 0.734533807 0.668596732 1 20.83421415 4.974029006 12.86649904 0.763427097 0.403339886 0.238285535 0.138607485 41677.51745 1503161.596 0.031749156 151015.3778 94195.25065 -4.974029006 -0.360087211 SLS(ph)PSLLGYQQPALMAAPLSLADAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.17)LS(0.782)PS(0.048)LLGYQQPALMAAPLSLADAHR;S(0.194)LS(0.755)PS(0.051)LLGYQQPALMAAPLSLADAHR 197.13 4.27E-25 864660000 169564 232527 214040 205501 283420 254530 266760 208383 234970 236270 TRUE FALSE 176258.5177 272461.7034 219618.0582 246148.4844 235244.3696 195419.2649 245850.6542 205589.9667 226513.4756 282562.5828 0.623785768 0.964252594 0.777236873 0.871129086 0.832538998 0.6915964 0.870075053 0.72759091 0.801640024 1 18.10821091 -0.691996744 4.215232728 1.000000605 0.798343914 0.302801856 0.092987079 13242489.67 33831902.28 142.4216561 0.020233046 0.203237225 0.691996744 -0.201656691 SLS(ph)PSSNSAFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSPSSNSAFSR 12 0 Q9P266 Q9P266 KIAA1462 Junctional protein associated with coronary artery disease 1 S(0.002)LS(0.981)PS(0.011)S(0.005)NS(0.001)AFSR 98.339 0.0046305 56056000 59869 73663 71405 72266 88589 98161 81969 76032 70249 78177 TRUE FALSE 62232.67435 86314.04723 73265.87296 86559.99911 73530.67342 75364.59539 75544.05559 75012.9154 67720.75221 93494.28636 0.665630776 0.923201306 0.783640111 0.925831968 0.786472375 0.806087712 0.80800719 0.802326199 0.724330383 1 16.51259058 -1.85734949 2.703404566 1.078610149 0.808878995 0.383956434 0.074569872 17174485.87 9692114.913 8651836.362 0.016255351 0.013888345 1.85734949 -0.269731154 SLS(ph)PVAAPPLREPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 S(0.003)LS(0.997)PVAAPPLREPR;S(0.015)LS(0.985)PVAAPPLREPR;S(0.031)LS(0.969)PVAAPPLREPR;S(0.053)LS(0.947)PVAAPPLREPR 119.08 0.00012621 6007600000 3967400 4813010 4581100 4308730 4479330 5297470 4195120 4583900 4410640 4552330 TRUE FALSE 4124036.015 5639607.027 4700487.229 5160983.934 3717935.087 4067212.876 3866295.532 4522460.318 4251901.928 5444271.904 0.757500009 1.035879017 0.863382159 0.947965867 0.682907678 0.747062775 0.71015842 0.830682302 0.780986329 1 22.37630769 3.254915124 24.99961896 0.779290835 0.908103039 0.201208942 0.104432351 315.3240989 482003.6908 0.026871509 0.036279467 1798.519387 -3.254915124 0.128812204 SLS(ph)PVFNHTMVYDGFGPADLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSPVFNHTMVYDGFGPADLR 21 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 S(0.13)LS(0.87)PVFNHTMVYDGFGPADLR 157.11 5.62E-09 224200000 281980 307350 335490 280820 465840 377570 354020 398770 377240 258660 TRUE FALSE 293112.7881 360134.9716 344233.145 336365.3578 386656.6832 289885.0896 326270.9873 393425.1404 363663.2061 309339.4747 0.947544081 1.164206321 1.112800574 1.087366422 1.24994291 0.937109918 1.054734407 1.271823264 1.175612025 1 18.23883142 1.76792291 25 1.177736804 1.085097634 0.061284038 0.107886597 45.51455112 38774.27554 0.048145663 0.026702984 58.60341302 -1.76792291 -0.09263917 SLS(ph)SPNCFGPQPGGPEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSSPNCFGPQPGGPEMR 18 0 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 S(0.001)LS(0.968)S(0.031)PNCFGPQPGGPEMR;SLS(0.5)S(0.5)PNCFGPQPGGPEMR 249.33 1.26E-24 126533000 65893 81462 85678 78475 88390 105043 75186 90499 82776 94676 TRUE FALSE 68494.50652 95452.46481 87910.83907 93997.12078 73365.49937 80648.35519 69292.72486 89286.00893 79796.90793 113225.9495 0.604936473 0.843026402 0.776419535 0.830172952 0.647956583 0.71227802 0.611986255 0.788564894 0.704758125 1 16.78884511 -1.524206487 4.055711448 1.003181234 0.729431746 0.509418693 0.080988193 0.002273225 0.000266682 0.076518054 0.017841771 0.029908423 1.524206487 -0.273749489 SLS(ph)SPTVTLSAPLEGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 S(0.004)LS(0.875)S(0.121)PTVTLSAPLEGAK;S(0.194)LS(0.784)S(0.021)PT(0.001)VTLSAPLEGAK;SLS(0.928)S(0.072)PTVTLSAPLEGAK;SLS(0.892)S(0.108)PTVTLSAPLEGAK;SLS(0.499)S(0.499)PT(0.002)VTLSAPLEGAK;SLS(0.887)S(0.113)PTVTLSAPLEGAK 409.89 2.04E-140 3119987000 2055697 1705750 1843563 1643847 2486913 2575914 2162024 1850080 1968666 1512865 TRUE FALSE 2136857.505 1998699.294 1891607.766 1968995.03 2064188.417 1977697.012 1992558.909 1825282.704 1897814.095 1809281.931 1.181052808 1.10469201 1.045501938 1.088274302 1.140888206 1.093083934 1.101298186 1.008843714 1.04893221 1 20.7869858 1.766924229 6.528038445 1.022090512 1.105465656 0.568800652 0.035255091 0.135253105 15.05226968 0.017283846 0.009438526 58.46880652 -1.766924229 0.083375144 SLS(ph)SSATPLSSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSSATPLSSPAR 14 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 S(0.002)LS(0.953)S(0.043)S(0.002)ATPLSSPAR 107.46 0.0019277 0 56506 88265 74681 72833 109010 112690 72392 97321 83144 120270 TRUE FALSE 58736.90051 103423.8271 76627.24821 87239.15002 90480.51914 86519.45533 66717.72588 96016.57118 80151.66368 143834.6038 0.408364183 0.719046908 0.532745572 0.606524075 0.629059467 0.601520448 0.463850312 0.66754848 0.557248823 1 17.13405128 -4.649994141 0.50238522 10 0.580243067 0.67802293 0.087498395 894.6967684 6.074338499 8983.618492 0.037063597 2.24E-05 4.649994141 -9.419756933 SLS(ph)TSGESLYHVLGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 SLS(0.46)T(0.46)S(0.046)GES(0.033)LYHVLGLDK;SLS(0.917)T(0.08)S(0.003)GESLYHVLGLDK;S(0.002)LS(0.612)T(0.367)S(0.015)GES(0.004)LYHVLGLDK;S(0.112)LS(0.858)T(0.022)S(0.007)GES(0.001)LYHVLGLDK 311.97 2.46E-58 7238730000 3516560 4684330 4995090 6169570 6631020 7378940 7101810 5430890 5064790 4359920 TRUE FALSE 3655396.504 5488827.238 5125266.149 7389892.532 5503881.589 5665293.014 6545151.575 5358097.803 4882509.197 5214162.848 0.701051465 1.052676604 0.982950916 1.417273059 1.055563807 1.086520153 1.255264127 1.027604614 0.936393691 1 22.31400421 4.921642141 1.775573741 1.110378456 0.403461569 0.428086243 0.135396153 1.438565824 3.086567786 0.034405176 1.983283929 83491.4764 -4.921642141 -0.706916887 SLS(ph)TSGESLYHVLGLDKNATSDDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSTSGESLYHVLGLDKNATSDDIKK 26 2 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.111)LS(0.649)T(0.111)S(0.111)GES(0.019)LYHVLGLDKNATSDDIKK 118.43 0.00030751 386280000 135370 105580 150940 85498 212640 172380 121540 136920 178880 116670 TRUE FALSE 140714.5121 123712.5437 154873.6204 102409.2492 176495.5288 132347.3574 112013.3772 135084.8114 172442.1437 139529.2527 1.008494702 0.886642344 1.109972406 0.733962572 1.26493567 0.948527673 0.802794934 0.968146885 1.235885238 1 17.09020809 1.326781075 11.1387297 1.117586665 0.961374317 0.140548295 0.150634258 0.694534718 81.94931285 0.094555793 0.034576218 21.22174416 -1.326781075 -0.156212348 SLS(ph)VEHLETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSVEHLETK 10 0 J3KN34;P26045-2;P26045 J3KN34 PTPN3 Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 3 1 S(0.129)LS(0.871)VEHLETK;S(0.234)LS(0.766)VEHLETK;S(0.029)LS(0.971)VEHLETK;S(0.269)LS(0.731)VEHLETK 168.98 3.07E-06 1121660000 2849580 2458400 2708770 2354540 3395470 3586110 3235960 2720880 2788970 2085430 TRUE FALSE 2962083.619 2880611.076 2779362.771 2820260.984 2818309.222 2753290.301 2982317 2684411.054 2688595.514 2494030.081 1.187669564 1.155002539 1.114406275 1.130804719 1.130022145 1.103952323 1.195782289 1.076334674 1.078012465 1 21.25004743 1.11411566 1.312278162 1.002942343 1.141547643 0.674846011 0.031255514 0.237781839 0.828708268 0.028487364 0.008794892 13.0051588 -1.11411566 0.1386053 SLS(ph)VPDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSVPDSGR 9 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 S(0.003)LS(0.997)VPDSGR 119.53 0.0017177 0 187260 161250 208520 173960 220190 244240 191550 188050 215350 200100 TRUE FALSE 194653.1694 188943.4331 213954.2025 208368.7688 182762.1824 187518.9615 176535.8105 185529.4973 207599.5956 239305.7639 0.813407777 0.789548192 0.894062053 0.870721897 0.763718264 0.783595675 0.737699785 0.775282193 0.867507712 1 17.86849562 0.930404612 4.253455071 0.999896439 0.802207339 0.639818154 0.044926747 0.21870926 10.25670269 0.047947174 0.012215935 8.519313741 -0.930404612 -0.1976891 SLS(ph)VPVDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 S(0.001)LS(0.999)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR;SLS(1)VPVDLSR 227.81 2.50E-09 388599000 500280 621240 598000 593550 833030 782410 626730 635790 652400 721660 TRUE FALSE 520031.4407 727933.1374 613584.3713 710952.4184 691431.8582 600707.135 577605.2649 627268.275 628920.2514 863055.46 0.602546956 0.843437266 0.710944313 0.823762147 0.801144179 0.696023793 0.669256255 0.726799498 0.7287136 1 19.71909374 -0.969101351 4.652710514 1.000003706 0.736224412 0.570011827 0.069373509 8479002.395 1822379.004 364.6068662 0.015577973 0.107373881 0.969101351 -0.263779294 SLS(ph)YEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSYEEPR 8 0 Q8IZD4;Q8IZD4-2;F5GZK9 Q8IZD4 DCP1B mRNA-decapping enzyme 1B 1 SLS(1)YEEPR;S(0.004)LS(0.996)YEEPR;S(0.002)LS(0.998)YEEPR;S(0.005)LS(0.995)YEEPR 137.95 0.00076162 583731000 1236130 1296850 1450320 1247170 1927020 1778110 1539420 1594340 1642790 1511020 TRUE FALSE 1284933.367 1519573.899 1488116.531 1493856.504 1599465.829 1365170.9 1418756.238 1572970.48 1583666.309 1807075.439 0.711056849 0.840902304 0.823494415 0.826670803 0.885112926 0.755458721 0.785111793 0.870450921 0.876369782 1 20.7852253 0.919116055 1.179856647 0.998384442 0.809365643 0.611562701 0.047078087 0.382901495 1.074374756 0.043657646 0.013624302 8.300725559 -0.919116055 -0.189018799 SLS(ph)YS(ph)PVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 SLS(0.952)Y(0.171)S(0.877)PVER;SLS(0.967)Y(0.123)S(0.909)PVER;S(0.006)LS(0.968)Y(0.063)S(0.963)PVER;SLS(0.99)Y(0.132)S(0.878)PVER;S(0.001)LS(0.981)Y(0.035)S(0.982)PVER 142.71 0.00015159 3089070000 3093000 3336980 3056380 3051160 3651370 3986270 3335090 3354180 3116170 3070890 TRUE FALSE 3215114.028 3910080.357 3136031.774 3654670.341 3030711.432 3060519.205 3073676.931 3309222.703 3004019.65 3672572.1 0.875439322 1.064670822 0.853906115 0.995125553 0.825228573 0.833344893 0.836927594 0.901064054 0.817960701 1 21.80835938 3.235157688 24.99860136 0.862953357 0.94900017 0.207340429 0.074294718 119.3814173 877000.9121 0.019524167 0.024248675 1718.532257 -3.235157688 0.086046813 SLSDS(ph)ESDDSKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSDSESDDSKSK 13 1 Q13185;S4R2Y4 Q13185 CBX3 Chromobox protein homolog 3 1 SLS(0.018)DS(0.887)ES(0.095)DDSKSK 242.07 1.70E-16 89902000 266420 114650 144410 76710 290920 236180 135490 127060 180290 108000 TRUE FALSE 276938.4673 134340.2456 148173.4432 91883.00904 241469.5223 181330.7743 124869.9398 125356.9685 173801.3981 129160.5322 2.144141578 1.040102912 1.147203722 0.711386114 1.869530252 1.403917832 0.966780932 0.970551657 1.345623118 1 16.97880577 4.742797081 24.64204795 1.158055228 2.144142058 0.487785219 0.302009207 307.1974021 1786778.927 0.073239163 0.568859113 55309.16237 -4.742797081 0.98608683 SLSEINKPNFYNNDFDDDFSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSEINKPNFYNNDFDDDFSHR 22 1 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 0 123.99 1.41E-05 64699000 33710 38458 44510 35243 47648 58139 44675 43042 48087 41881 FALSE TRUE 35040.89683 45062.86234 45669.96717 42213.96021 39548.80998 44637.09836 41173.25676 42465.09239 46356.35826 50086.78009 0.699603703 0.899695733 0.911816792 0.842816411 0.789605758 0.891195207 0.822038404 0.847830352 0.92552083 1 15.61214225 1.037789057 2.589892932 0.999286867 0.841475501 0.447142211 0.058358922 0.231711471 3.364830732 0.053028599 0.014327549 10.90910338 -1.037789057 -0.157811366 SLSFPILNPALSQPSQPS(ph)SPLPGSHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 SLSFPILNPALSQPSQPS(0.498)S(0.498)PLPGS(0.005)HGR 172.83 2.16E-12 360960000 151040 158250 207190 187360 189310 230940 203340 212760 214690 207590 TRUE FALSE 157003.1758 185428.2065 212589.5416 224419.2488 157131.1538 177307.6849 187401.6795 209908.3002 206963.3488 248263.2859 0.632405936 0.746901443 0.856306807 0.903956652 0.632921429 0.71419213 0.754850556 0.845506815 0.833644605 1 17.9215114 0.932165553 1.009142076 0.996723921 0.75394043 0.457724367 0.082257231 0.607714213 1.283582605 0.081728049 0.026887214 8.553927255 -0.932165553 -0.242783491 SLSFPILNPALSQPSQPSS(ph)PLPGSHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 SLSFPILNPALSQPS(0.001)QPS(0.225)S(0.768)PLPGS(0.006)HGR 162.28 7.96E-12 307570000 137140 177240 191690 153500 187440 247010 175530 174430 194280 186310 TRUE FALSE 142554.3931 207679.5913 196685.5989 183861.8418 155579.0158 189645.671 161771.4999 172092.0512 187287.9008 222813.8774 0.639791358 0.932076555 0.882734959 0.825181286 0.698246526 0.851139405 0.726038709 0.772357867 0.840557612 1 17.76547956 0.88150856 4.517310705 0.999978079 0.794727751 0.362210549 0.083229519 0.844376774 30.50865984 0.077616396 0.019705857 7.612171434 -0.88150856 -0.205250328 SLSFPKLDSDDS(ph)NQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSFPKLDSDDSNQK 15 1 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 1 S(0.012)LS(0.079)FPKLDS(0.079)DDS(0.83)NQK 64.507 0.038837 91794000 5182.2 43856 45675 35756 51208 59442 26673 46595 45109 69356 TRUE FALSE 5386.797258 51387.92685 46865.32802 42828.43008 42503.68245 45637.49635 24582.30056 45970.47024 43485.5359 82944.9803 0.064944223 0.619542336 0.565017049 0.516347462 0.512432245 0.550214084 0.296368755 0.554228479 0.524269651 1 16.33986705 -5 0.311870557 5.705723704 0.452691334 0.523265998 0.154637305 234.734797 2.118130699 726.0510893 0.136327708 1.00E-05 5 -5.25303237 SLSGSS(ph)PCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SLSGSSPCPK 10 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SLSGS(0.064)S(0.936)PCPK;SLSGS(0.004)S(0.996)PCPK;SLSGS(0.046)S(0.954)PCPK;SLSGS(0.003)S(0.997)PCPK;SLSGS(0.132)S(0.868)PCPK;SLSGS(0.182)S(0.818)PCPK;SLSGS(0.01)S(0.99)PCPK;SLSGS(0.064)S(0.936)PCPK 221.6 5.56E-09 5487240000 9309600 6199830 7532510 5828230 9516160 9692650 8758610 7504380 7626050 5135040 TRUE FALSE 9677150.197 7264602.575 7728813.399 6981036.498 7898606.522 7441678.931 8072087.262 7403796.061 7351589.95 6141152.772 1.575787243 1.182937934 1.258528111 1.136763204 1.286176524 1.211772318 1.314425412 1.205603628 1.1971026 1 22.55007806 -4.999999983 0.044604999 7.00E-12 1.809640809 0.437341374 0.10501649 723.9504196 2.402219529 93.58291717 24.57424817 1.00E-05 4.999999983 1.809640809 SLSKS(ph)DSDLLTCSPTEDATMGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLSKSDSDLLTCSPTEDATMGSR 23 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 S(0.002)LS(0.052)KS(0.941)DS(0.006)DLLTCSPTEDATMGSR;SLS(0.09)KS(0.908)DS(0.002)DLLTCSPTEDATMGSR;SLS(0.241)KS(0.758)DS(0.001)DLLTCSPTEDATMGSR;SLS(0.008)KS(0.991)DSDLLTCSPTEDATMGSR;S(0.025)LS(0.088)KS(0.76)DS(0.127)DLLTCSPTEDATMGSR;SLS(0.03)KS(0.97)DSDLLTCSPTEDATMGSR 294.57 7.67E-62 4531430000 2077410 1528220 1956960 1529100 2555480 2463340 2139900 1815230 2105430 1547220 TRUE FALSE 2159427.751 1790679.897 2007959.985 1831551.416 2121100.422 1891266.617 1972169.046 1790899.811 2029655.986 1850368.136 1.167026015 0.967742506 1.085167836 0.989830824 1.146312662 1.022102889 1.065825231 0.967861355 1.09689307 1 20.8193809 1.864196568 0.008659087 3.10E-08 2.076069271 0.083735711 0.0656663 3719.663344 27.87017078 3318.587625 3359.587288 73.14700827 -1.864196568 2.07606924 SLSLESTDRGS(ph)WDP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSLESTDRGSWDP 14 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 SLSLES(0.001)T(0.001)DRGS(0.999)WDP 82.908 0.024734 44590000 155300 180840 195140 175500 224970 267230 182870 193300 212480 211060 TRUE FALSE 161431.3639 211897.8633 200225.5087 210213.3762 186729.6798 205169.8824 168536.1716 190709.1297 204832.8863 252413.166 0.639552074 0.839488156 0.793245106 0.832814625 0.739777892 0.812833521 0.667699606 0.755543511 0.811498424 1 17.94542764 0.834559839 3.44963181 0.999946099 0.762858284 0.569189748 0.062499952 0.632022327 11.99738849 0.057671579 0.014901481 6.832188489 -0.834559839 -0.237087815 SLSLS(ph)LADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 1 S(0.204)LS(0.313)LS(0.483)LADSGHLPDVHGFNSYGSHR 196.15 1.46E-24 423930000 19065 52672 54297 53110 52630 58319 40583 55186 40769 52836 TRUE FALSE 19817.70092 61718.00627 55712.02443 63614.99948 43683.9714 44775.29608 37401.99842 54446.32194 39301.73165 63188.20259 0.313629762 0.976733057 0.881683956 1.006754376 0.691331128 0.708602148 0.591914264 0.861653279 0.621978946 1 15.94736761 -2.090209707 2.338306952 1.394154284 0.757498666 0.13096904 0.196477661 14480878.57 4364972.245 30377881.79 0.048604727 0.008124381 2.090209707 -0.636655618 SLSLS(ph)TNLQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSLSTNLQER 11 0 A0A087WWS6;P01562 A0A087WWS6 IFNA13;IFNA1 Interferon alpha-1/13 1 SLS(0.022)LS(0.489)T(0.489)NLQER;SLS(0.004)LS(0.498)T(0.498)NLQER;SLS(0.024)LS(0.488)T(0.488)NLQER 79.889 0.027179 693630000 841920 1019870 964720 973140 1100270 1223900 942060 1015320 899870 1047910 TRUE FALSE 875159.6517 1195024.739 989861.3957 1165624.187 913246.4984 939667.7734 868218.8756 1001711.296 867483.8545 1253227.901 0.698324424 0.9535574 0.789849472 0.93009754 0.728715422 0.749798 0.692786104 0.799304975 0.692199602 1 20.25721736 5.034673608 16.3304272 0.802686661 0.313938493 0.089559546 0.105194473 11123877.14 144142906.8 0.023975487 156358905.5 108311.2599 -5.034673608 -0.488748168 SLSLSLADSGHLPDVHGFNSYGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSLSLADSGHLPDVHGFNSYGSHR 25 0 Q9Y446;Q9Y446-2;E9PKC4;E9PRW6 Q9Y446 PKP3 Plakophilin-3 0 135.3 1.44E-05 245280000 41267 70811 75397 72233 77366 103870 48585 71711 76724 92565 FALSE TRUE 42896.25303 82972.23842 77361.90776 86520.47181 64215.35495 79747.76667 44776.78075 70749.83134 73962.71823 110701.3395 0.387495339 0.749514313 0.698834433 0.781566621 0.580077488 0.720386646 0.404482737 0.639105468 0.668128485 1 16.75631315 0.721186678 3.062905977 0.999965746 0.625192743 0.441808316 0.127207626 2.190650545 22.96736905 0.118009062 0.030799942 5.26243419 -0.721186678 -0.374773004 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(1)NPDISGTPTSPDDEVR;SLSNS(1)NPDISGTPTSPDDEVR;SLS(0.001)NS(0.999)NPDISGTPTSPDDEVR 415.88 4.53E-152 1010690000 487310 531670 511500 530470 547110 569150 476540 530670 450260 479160 TRUE FALSE 506549.3751 622980.1867 524830.1102 635395.3827 454112.4376 436973.5381 439187.5496 523557.2367 434055.2306 573042.2279 0.883965178 1.087145338 0.915866379 1.10881075 0.792458942 0.762550327 0.766413936 0.913645123 0.75745767 1 19.12828193 3.222238402 24.9973296 0.826084613 0.99931249 0.421737276 0.095563448 209.522731 320881.5732 0.025885048 0.031024319 1668.162683 -3.222238402 0.173227877 SLSNVIAHEISHSWTGNLVTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSNVIAHEISHSWTGNLVTNK 22 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 129.2 8.97E-06 449530000 369810 464640 517660 509900 625790 702360 637020 598720 584690 463240 FALSE TRUE 384410.3844 544438.3056 531150.6449 610756.6981 519418.4393 539247.5344 587088.7079 590695.1377 563647.1211 554003.0087 0.693877792 0.982735287 0.95875047 1.102442926 0.937573318 0.973365714 1.059721154 1.06623092 1.017408051 1 19.07953429 5.213988856 1.464488328 1.023013542 0.010033551 0.791686146 0.048890798 1.790864023 1.354819369 0.013291642 3.725439365 163677.4521 -5.213988856 -1.012979991 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 S(0.014)LS(0.095)QS(0.891)FENLLDEPAYGLIQK;S(0.031)LS(0.198)QS(0.771)FENLLDEPAYGLIQK;S(0.002)LS(0.052)QS(0.946)FENLLDEPAYGLIQK 294.38 9.44E-55 380177000 313797 276314 329971 262408 382574 389324 356502 320160 332042 255577 TRUE FALSE 326185.9479 323768.7801 338570.3153 314311.5192 317544.2081 298909.4013 328558.4417 315868.7789 320091.8733 305652.4198 1.067179341 1.059271117 1.107697153 1.02832989 1.038906246 0.977938933 1.074941405 1.033424761 1.047241417 1 18.22153246 3.711918586 24.49602071 1.031352577 1.076171397 0.405340555 0.027238359 574.8793445 528573.2504 0.007051827 0.010927862 5151.320673 -3.711918586 0.04481882 SLSS(ph)PGGPSKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLSSPGGPSKPK 12 1 Q9BZE9;Q9BZE9-2;J3KRY8;Q9BZE9-3;J3QL04;J3QR12;Q9BZE9-4 Q9BZE9 ASPSCR1 Tether containing UBX domain for GLUT4 1 SLS(0.047)S(0.953)PGGPSKPK;SLS(0.038)S(0.961)PGGPSKPK;SLS(0.106)S(0.894)PGGPSKPK;S(0.013)LS(0.185)S(0.802)PGGPSKPK 120.92 0.00023341 391540000 1312720 771100 1019500 750800 1347340 1328510 1274610 1006660 1113210 655315 TRUE FALSE 1364547.199 903530.4267 1046069.008 899305.9991 1118319.628 1019983.686 1174702.738 993167.3693 1073145.79 783711.4275 1.741134749 1.15288663 1.334762989 1.147496346 1.426953326 1.301478644 1.498897038 1.267261564 1.369312418 1 19.57996301 -0.948323114 1.05370878 0.972914985 1.347691965 0.298109257 0.164704882 186.7418981 86.75965276 17.95791817 0.045156805 0.112635914 0.948323114 0.37477698 SLSS(ph)PTVTLSAPLEGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-7;Q96PU5;A0A1B0GVY1;Q96PU5-2;Q96PU5-4;Q96PU5-5;Q96PU5-6;Q96PU5-9 Q96PU5-7;Q96PU5-5 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 SLS(0.36)S(0.64)PTVTLSAPLEGAK 351.42 1.14E-87 105620000 226540 181180 203560 196990 292450 308860 266460 232090 239250 191510 TRUE FALSE 235483.9741 212296.2556 208864.9408 235954.034 242739.4535 237131.9458 245574.1689 228979.2132 230639.4392 229032.7178 1.028167401 0.926925453 0.911943686 1.030219771 1.05984619 1.035362755 1.072223092 0.999766389 1.007015248 1 17.80519418 3.716635441 23.64747213 1.031394625 0.952803514 0.463126949 0.036184001 313.5874759 338220.6853 0.009645912 0.014960665 5207.573897 -3.716635441 -0.078591111 SLSS(ph)SPQAQPPRPAELSDEEVAELFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 S(0.038)LS(0.121)S(0.442)S(0.399)PQAQPPRPAELSDEEVAELFQR;S(0.042)LS(0.129)S(0.415)S(0.415)PQAQPPRPAELSDEEVAELFQR 57.088 0.042261 1943920000 32409 270864 109648 236206 85445 215631 69840 151352 77227 324473 TRUE FALSE 33688.53235 317382.785 112505.517 282926.8418 70921.08942 165553.9682 64365.75831 149323.374 74447.61536 388047.2719 0.086815537 0.81789722 0.289927349 0.729104061 0.182764046 0.426633506 0.165870921 0.384807174 0.191851923 1 18.56587289 -1.386710405 5.410538357 1.000300579 0.374560159 0.40711875 0.229944491 0.000762943 8.65E-05 0.203740295 0.047999662 0.041047773 1.386710405 -0.62574042 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 SLS(0.001)S(0.121)S(0.878)PQAQPPRPAELSDEEVAELFQR;S(0.002)LS(0.058)S(0.344)S(0.596)PQAQPPRPAELSDEEVAELFQR 146.03 9.20E-08 354920000 76712 65949 84078 67653 102064 108265 83650 90841 94481 97308 TRUE FALSE 79740.64899 77275.22774 86269.14175 81034.56148 84715.19774 83122.09452 77093.29442 89623.42498 91080.64727 116373.6395 0.685212298 0.664026906 0.74131171 0.696330903 0.727958652 0.714269098 0.66246355 0.770135104 0.782657032 1 16.82840478 0.667477516 0.97032774 1.000291215 0.700047679 0.91218713 0.027740288 0.281110977 0.452790054 0.026041418 0.008463355 4.650263005 -0.667477516 -0.300243536 SLSSS(ph)PVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 SLS(0.038)S(0.153)S(0.808)PVKK;S(0.041)LS(0.165)S(0.132)S(0.663)PVKK;S(0.006)LS(0.171)S(0.14)S(0.683)PVKK;SLSS(0.015)S(0.985)PVKK;SLSS(0.01)S(0.99)PVKK 145.41 5.96E-05 3806200000 7549300 3621950 5617880 3688830 8170700 7715340 8318370 6271960 7451650 3711900 TRUE FALSE 7847352.193 4243991.738 5764286.568 4418469.564 6781847.333 5923569.212 7666354.423 6187894.635 7183466.572 4439175.736 1.767749839 0.956031477 1.298503801 0.995335582 1.527726708 1.334384932 1.726977006 1.393928739 1.618198287 1 22.08186039 3.202392126 24.98966826 1.464241859 1.236242067 0.084678554 0.275140171 321.37225 222042.7867 0.073454501 0.087797537 1593.646988 -3.202392126 -0.227999792 SLSTSGES(ph)LYHVLGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 S(0.163)LS(0.163)T(0.206)S(0.206)GES(0.261)LYHVLGLDK;S(0.165)LS(0.144)T(0.219)S(0.219)GES(0.252)LYHVLGLDK 164.68 1.65E-09 465109000 237949 309685 355900 370084 490729 487309 506190 362698 366992 300170 TRUE FALSE 247343.4103 362870.9897 365175.0464 443285.5106 407315.0599 374138.87 466513.5051 357836.6266 353784.0296 358982.5644 0.689012322 1.010831794 1.017250091 1.234838554 1.134637446 1.042220172 1.299543631 0.996807818 0.985518698 1 18.45355425 4.895559032 1.624258508 1.101493808 0.410021319 0.584881865 0.10090377 1.05325545 1.964378053 0.026235381 1.287731861 78624.70546 -4.895559032 -0.691472489 SLSYS(ph)PVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;S(0.001)LS(0.006)YS(0.993)PVER;SLSYS(1)PVER 219.35 5.20E-07 1619350000 1825480 1917010 1849070 1900950 2044660 2204280 1823340 1840270 1811380 1841930 TRUE FALSE 1897551.36 2246241.555 1897258.283 2276952.236 1697109.424 1692369.376 1680421.846 1815604.191 1746188.788 2202820.918 0.861418804 1.019711379 0.861285758 1.033652903 0.770425508 0.7682737 0.762849959 0.824217791 0.792705741 1 21.07092078 3.223945742 24.99996938 0.805841405 0.94351456 0.338528059 0.083757914 221.1102503 378226.9648 0.022075575 0.026492186 1674.733633 -3.223945742 0.137673155 SLTEISTDFDRS(ph)SPPLQPPPVNSLTTENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTEISTDFDRSSPPLQPPPVNSLTTENR 29 1 J3KRR7;Q9NQC7-2;Q9NQC7 J3KRR7 CYLD Ubiquitin carboxyl-terminal hydrolase CYLD 1 SLTEIS(0.003)T(0.003)DFDRS(0.497)S(0.497)PPLQPPPVNSLTTENR 63.033 0.011156 491940000 14447 17778 15375 16434 14326 18301 17184 15935 15980 18925 TRUE FALSE 15017.37872 20831.23321 15775.68513 19684.59615 11890.87164 14050.8701 15837.07318 15721.41739 15404.88292 22632.99141 0.663517184 0.920392397 0.697021655 0.8697302 0.525377818 0.620813654 0.699733981 0.694623928 0.680638394 1 14.46613966 -1.020032165 4.898035801 1.000004608 0.709306782 0.399511698 0.107392002 5.36E-06 1.07E-06 0.103093887 0.024299077 0.095492186 1.020032165 -0.290697826 SLTELQELEAVYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTELQELEAVYER 14 0 A0A6I8PIQ6;A0A0A0MS45;J3KNI1;Q9H9E3;Q9H9E3-2;E9PRT5;H3BSD2;H3BMV9;J3QLW1 A0A6I8PIQ6 COG4 Conserved oligomeric Golgi complex subunit 4 0 159.08 1.16E-05 16053000 32085 44326 41646 38421 51465 49792 38996 40111 37718 43163 FALSE TRUE 33351.74058 51938.64569 42731.32897 46020.55912 42716.99768 38228.56261 35939.39162 39573.37765 36360.53655 51619.96344 0.646101592 1.006173624 0.827806262 0.89152638 0.827528631 0.740577096 0.696230474 0.766629323 0.704389041 1 15.6556415 2.884817493 4.586901231 0.760663148 0.854112908 0.042253241 0.115592284 0.461513396 15.40951182 0.033033356 0.035405108 767.0390832 -2.884817493 0.09344976 SLTES(ph)LESILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTESLESILSR 12 0 C9JIE2;Q86TI0-2;Q86TI0;H0Y8P0 C9JIE2 TBC1D1 TBC1 domain family member 1 1 SLT(0.001)ES(0.991)LES(0.008)ILSR 94.122 0.0071199 7491700 9536.6 12859 15174 12517 13063 18340 16565 14239 13790 14165 TRUE FALSE 9913.112332 15067.43322 15569.44691 14992.82524 10842.55593 14080.81295 15266.59202 14048.1495 13293.70059 16940.36054 0.585177175 0.889439937 0.919074117 0.885035782 0.640042808 0.83119913 0.901196405 0.829270986 0.784735399 1 14.04817696 -5 0.221444194 1.931926549 0.792905099 0.234776191 0.105849669 246.2065865 2.46384774 102.5754197 0.198539605 1.00E-05 5 -1.139021451 SLTNDWEDHLAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 SLTNDWEDHLAVK 13 0 P08238;P07900;P07900-2 P08238;P07900 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 ;;;;;;;;;;; 240.11 7.79E-17 50548546800 24684404 19808130 25994512 21140357 30892565 29442705 31395693 26651750 28296906 17303800 FALSE TRUE 25658963.33 23210022.24 26671950.34 25321856.52 25641457.84 22605082.97 28934816.55 26294526.88 27278505.88 20694148.31 1.239913958 1.121574171 1.288864366 1.223623999 1.239068042 1.092341788 1.398212486 1.270626193 1.318174852 1 24.30271954 4.230540129 24.9986089 1.244055103 1.180744058 0.015006731 0.11045199 513.221769 1599651.323 0.025968149 0.057680127 17003.57058 -4.230540129 -0.063311045 SLTPAVPVESKPDKPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;H0YA91;E7EQK6;P20810-5;E9PCH5;P20810-2;P20810-3;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 ; 133.16 7.45E-06 2218500000 1430750 710660 1043490 643730 1583370 1246200 1357980 978290 1309510 548230 FALSE TRUE 1487237.115 832710.3268 1070684.207 771057.8727 1314229.333 956788.9363 1251537.979 965177.6227 1262380.991 655645.172 2.268356694 1.27006247 1.633023856 1.176029208 2.004482591 1.459309055 1.908864783 1.472103607 1.92540271 1 19.32255573 -1.749978825 8.586263972 0.995355964 1.651093564 0.273020096 0.32978859 0.02617442 0.000762166 0.285076525 0.067280123 0.017783661 1.749978825 0.6557376 SLTSS(ph)LENIFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 SLTS(0.011)S(0.989)LENIFSR;SLTS(0.042)S(0.958)LENIFSR;SLTS(0.011)S(0.989)LENIFSR;SLTS(0.225)S(0.774)LENIFSR;SLTS(0.013)S(0.987)LENIFSR;SLTS(0.026)S(0.974)LENIFSR 299.76 2.02E-36 2548290000 2412180 2758670 2794820 2966840 3175250 3495340 2762130 3033810 2816700 2824260 TRUE FALSE 2507414.729 3232450.113 2867655.305 3553672.097 2635522.139 2683600.257 2545627.033 2993146.739 2715327.517 3377619.673 0.742361477 0.957020158 0.84901664 1.052123223 0.780289788 0.794524108 0.75367486 0.886170448 0.803917486 1 21.68757546 SLTTECHLLDS(ph)PGLNCSNPFTQLER ddPTM_MDA-MB-175_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 216.69 1.03E-33 281340000 48188 77202 61512 77800 68894 78530 63898 70798 69703 72179 TRUE FALSE 50090.49945 90460.84295 63115.05325 93188.60779 57183.42249 60292.59763 58889.50779 69849.06861 67194.40265 86321.0931 0.580281107 1.04795757 0.731166057 1.079557782 0.662450166 0.698468885 0.682214574 0.809177295 0.778423908 1 16.39742551 4.971352723 12.9480125 0.81430664 0.480764172 0.196615122 0.148857765 46840.83012 1761920.258 0.034064293 150649.4879 93616.56956 -4.971352723 -0.333542468 SLTVSDDAES(ph)SEPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVS(0.016)DDAES(0.492)S(0.492)EPER 143.05 4.70E-06 90739000 92646 101890 101590 98919 118170 142580 102040 110890 117170 105750 TRUE FALSE 96303.73562 119388.8149 104237.5189 118484.883 98083.50561 109467.9558 94041.83817 109403.7009 112953.0746 126469.6878 0.761476819 0.944011304 0.824209506 0.936863884 0.77554952 0.865566744 0.743591922 0.865058678 0.893123693 1 16.94843212 0.902921489 2.281564976 0.999364139 0.840568743 0.370011417 0.064179016 0.424788625 4.666376366 0.056896107 0.015501441 7.99689675 -0.902921489 -0.158795396 SLTVSDDAESS(ph)EPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTVSDDAESSEPER 15 0 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 SLTVSDDAES(0.015)S(0.985)EPER 219.52 1.88E-12 64747000 80946 99670 98385 102280 111230 130130 96092 99782 97739 101930 TRUE FALSE 84141.81058 116787.5472 100948.9939 122510.6787 92323.16433 99909.27964 88560.05795 98444.5855 94221.39248 121901.2319 0.690245777 0.95805059 0.828121196 1.004999513 0.757360388 0.819592042 0.726490262 0.807576625 0.772932242 1 16.89535318 SLTWPPS(ph)GSPSHAGTTPPENGLSEHPCETEQINAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLTWPPSGSPSHAGTTPPENGLSEHPCETEQINAK 35 0 P23497;P23497-2;P23497-3;P23497-4;E9PHV6;P23497-7;P23497-6;P23497-5 P23497 SP100 Nuclear autoantigen Sp-100 1 S(0.017)LT(0.014)WPPS(0.339)GS(0.339)PS(0.29)HAGTTPPENGLSEHPCETEQINAK 131.99 4.07E-08 102670000 32987 48339 49390 47318 66862 66710 52226 57127 57903 49223 TRUE FALSE 34289.35223 56640.84722 50677.14397 56677.35917 55496.82112 51217.6135 48132.38965 56361.30601 55819.08234 58867.30442 0.582485517 0.962178374 0.860870809 0.962798615 0.942744392 0.870051958 0.817642155 0.957429707 0.948218759 1 15.84517895 4.743129848 24.97909255 0.918303167 0.58248538 0.781490362 0.054186488 207.4876387 1134254.645 0.01266209 0.101367593 55351.55779 -4.743129848 -0.335817787 SLVDTVYALKDEVQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLVDTVYALKDEVQELR 17 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 0 ; 200.67 1.11E-11 456310000 666380 540900 658240 532700 763020 792370 752250 662130 727050 543970 FALSE TRUE 692689.197 633795.3674 675394.2752 638066.47 633322.1329 608354.076 693286.6794 653255.2304 700883.6125 650550.5066 1.064773895 0.974244676 1.038188839 0.980810043 0.973517239 0.935137349 1.065692321 1.004157592 1.07737002 1 19.31130154 2.209630374 24.99987099 1.034635688 0.993944326 0.207901315 0.040410166 349.5052918 302020.5307 0.014715232 0.01086987 162.0430369 -2.209630374 -0.040691361 SLVEIIEHGLVDEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLVEIIEHGLVDEQQK 16 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ;;; 249.6 1.30E-20 246980000 566824 406252 530775 424579 618898 655234 633947 512048 555745 383322 FALSE TRUE 589202.6492 476022.6208 544607.4325 508559.459 513697.939 503065.8337 584256.5776 505184.8341 535743.846 458426.6068 1.285271493 1.038383492 1.187992635 1.109358513 1.120567462 1.097374861 1.27448226 1.101997194 1.168657836 1 18.80633125 -2.406019311 1.98944192 0.041288122 1.149240307 0.2747601 0.074627528 1339724.906 134253.5735 5771943.55 0.016981913 0.003926275 2.406019311 1.107952185 SLVESVS(ph)SSPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_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(0.147)LVES(0.116)VS(0.262)S(0.235)S(0.235)PNKES(0.005)NEEEQVWHFLGK 68.269 0.020167 1761000000 90650 74880 101280 66562 106440 105880 91854 90267 97179 70525 TRUE FALSE 94228.932 87740.05751 103919.44 79727.76493 88347.36682 81290.97463 84654.24346 89057.11851 93681.54677 84343.02347 1.117210744 1.040276408 1.232104752 0.945279902 1.047476877 0.963813855 1.003689932 1.055891938 1.110720756 1 16.36398112 3.725571151 24.99545661 1.020660591 1.120905222 0.401991761 0.062112688 801.9324699 1543148.417 0.016177556 0.025242276 5315.830818 -3.725571151 0.100244632 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-2;Q9H2U2;Q9H2U2-3;Q9H2U2-6;Q9H2U2-4 Q9H2U2-2 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 S(0.001)LVES(0.005)VS(0.052)S(0.471)S(0.471)PNKESNEEEQVWHFLGK;S(0.001)LVES(0.017)VS(0.079)S(0.451)S(0.451)PNKESNEEEQVWHFLGK;S(0.003)LVES(0.064)VS(0.074)S(0.43)S(0.43)PNKESNEEEQVWHFLGK;S(0.009)LVES(0.054)VS(0.054)S(0.442)S(0.442)PNKESNEEEQVWHFLGK 172 3.21E-12 2749694000 592576 297821 422659 291049 555492 562015 524297 409253 461587 270588 TRUE FALSE 615971.358 348969.44 433673.8408 348617.6235 461069.6683 431495.5337 483201.2311 403767.6329 444974.574 323604.5379 1.90346947 1.078382406 1.340135227 1.077295225 1.424793581 1.333403841 1.493184349 1.247719317 1.375056657 1 18.30387231 -2.911212452 0.502277053 1.52E-11 1.348988399 0.191537801 0.22196276 387.3730581 14.72279971 417.6080316 0.095727413 0.001226839 2.911212452 1.348988399 SLVESVSSS(ph)PNKESNEEEQVWHFLGK ddPTM_MDA-MB-175_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(0.001)VS(0.021)S(0.121)S(0.857)PNKESNEEEQVWHFLGK 134.67 2.28E-05 60448000 65747 39264 51879 39897 69680 69145 54316 54937 60978 40916 TRUE FALSE 68342.74233 46007.28657 53231.00936 47788.50752 57835.81849 53087.12165 50058.56999 54200.65937 58783.41369 48932.70682 1.39666793 0.940215442 1.087841095 0.976616881 1.181946029 1.084900573 1.023008398 1.107657085 1.201311301 1 15.57851147 4.753673274 24.73188473 1.071925011 1.3966682 0.601863291 0.080337419 1621.663117 2653802.071 0.018337084 0.425564352 56711.77946 -4.753673274 0.324743189 SLVGS(ph)WLK ddPTM_MDA-MB-175_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 143.5 0.00062981 700290000 1677180 1245220 1516380 1096220 1691860 1791830 1686320 1476400 1667290 1043540 TRUE FALSE 1743396.361 1459076.849 1555898.109 1313049.044 1404278.242 1375704.638 1554141.832 1456611.273 1607284.559 1248001.683 1.396950329 1.169130513 1.246711546 1.052121212 1.125221432 1.102325948 1.245304276 1.167154894 1.287886531 1 20.25118845 5.428717298 1.405674 1.156462787 2.364103408 0.419499673 0.085349402 7.362084505 3.180804321 0.022033465 20.21888917 268359.7001 -5.428717298 1.207640621 SLVLQRPQTWADCVTWACHHWHTQYSNNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SLVLQRPQTWADCVTWACHHWHTQYSNNIR 30 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;; 193.34 3.39E-19 1420872000 23805.8 37206 16410.8 26000.1 51212.3 59437.7 15182.45 37501.3 51285.4 31238.3 FALSE TRUE 24745.67137 43595.84108 16838.47893 31142.84218 42507.25154 45634.19496 13992.4099 36998.65641 49439.64847 37358.84679 0.662377817 1.166948255 0.450722663 0.833613584 1.13780952 1.221509733 0.374540734 0.990358632 1.323371911 1 15.1891623 2.387855605 0.33823191 1.063638441 0.773877839 0.083097894 0.29742998 5.692694691 1.537561833 0.385169633 0.591849908 244.2618292 -2.387855605 -0.289760602 SLVPAAELLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLVPAAELLESR 12 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 113.93 0.0025893 44791000 60177 83514 65899 74407 76359 88904 71470 71694 67320 85108 FALSE TRUE 62552.83443 97856.87985 67616.38208 89124.48252 63379.52445 68257.39335 65867.99465 70733.0592 64897.16635 101783.2831 0.614568842 0.961423889 0.664317165 0.875629866 0.622690903 0.67061497 0.647139615 0.694937882 0.637601425 1 16.63514111 -1.162934433 3.453894551 1.000363609 0.713041794 0.385664094 0.109783868 32458500.95 52380818.97 132376.8036 0.02508021 0.068717218 1.162934433 -0.287321815 SLYGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLYGER 6 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 0 97.071 0.096521 562480000 340160 426890 287600 327950 398540 402570 277740 306790 292960 363590 FALSE TRUE 353589.7795 500205.0368 295095.0923 392817.5312 330796.3132 309079.2185 255970.0131 302677.9819 282416.4268 434828.4991 0.813170664 1.150350167 0.678647082 0.903384971 0.760751224 0.710807178 0.588668897 0.696085888 0.649489229 1 18.73008697 4.221226317 24.99981763 0.732055469 0.981760486 0.30798846 0.138127219 216.7470263 312597.2307 0.032831799 0.07118695 16642.79704 -4.221226317 0.249705016 SLYQSAGVAPES(ph)FEYIEAHGTGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLYQSAGVAPESFEYIEAHGTGTK 24 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 SLYQSAGVAPES(1)FEYIEAHGTGTK 212.78 1.00E-25 185310000 141590 137880 187700 170600 222820 214730 188830 186710 210860 118590 TRUE FALSE 147180.0825 161559.8174 192591.6162 204344.1708 184945.136 164862.2118 174029.0112 184207.4578 203271.1898 141825.44 1.037755163 1.13914554 1.357948308 1.440814644 1.304033578 1.162430463 1.227064843 1.298832268 1.43324914 1 17.11375681 -2.156061473 2.56658716 0.322620532 1.269329786 0.299110166 0.122471687 13751829.12 3392670.167 55660105.45 0.030759636 0.006981336 2.156061473 0.946709254 SLYQSAGVAPESFEYIEAHGTGTK ddPTM_MDA-MB-175_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 ;;;;;; 356.49 3.66E-102 11398104400 6568389.9 6584256.2 7982354.1 7753192.4 9709689 9909148 8070411.2 8181718.3 8360023.9 6796030 FALSE TRUE 6827715.005 7715050.984 8190380.805 9286750.716 8059239.532 7607898.552 7437831.282 8072055.749 8059148.273 8127581.961 0.840067198 0.949243086 1.007726633 1.142621601 0.991591296 0.936059284 0.915134577 0.993168176 0.991580068 1 22.95439477 4.66241741 2.830171977 0.994856784 0.825194064 0.414154608 0.056564575 0.377858136 4.589060836 0.015356583 0.134574855 45963.95702 -4.66241741 -0.169662719 SLYSTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLYSTSPR 8 0 F5H4N6;Q9Y3R0-3;Q9Y3R0-2;Q9Y3R0;F5H4P8;H0YFK8;H0YGM4 F5H4N6 GRIP1 Glutamate receptor-interacting protein 1 1 SLYS(0.002)T(0.01)S(0.988)PR 69.375 0.05673 129820000 272000 301860 273120 255230 333820 358250 283730 307720 262910 282600 TRUE FALSE 282738.77 353702.1069 280237.7316 305713.7322 277077.3956 275051.8668 261490.5012 303595.5167 253447.9205 337970.0593 0.836579343 1.046548643 0.829179165 0.904558625 0.81982823 0.813835011 0.773709073 0.89829116 0.749912347 1 18.36653592 4.182411277 24.99997565 0.843748349 0.941567346 0.16576368 0.082777386 110.1313178 49034.53155 0.01872245 0.040445161 15219.88171 -4.182411277 0.097818997 SLYVAEYHSEPVEDEKP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SLYVAEYHSEPVEDEKP 17 1 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 226.25 3.42E-15 489640000 847540 507180 623810 518300 901950 897490 820720 626740 670110 464660 FALSE TRUE 881001.5336 594284.2197 640067.0011 620818.193 748636.8612 689061.5491 756389.8218 618339.5754 645992.872 555701.2305 1.585387048 1.069431175 1.151818578 1.117179806 1.347193096 1.239985646 1.361144767 1.112719464 1.162482349 1 19.08394991 1.096031453 1.351149501 1.009640497 1.248148497 0.235403958 0.143903542 0.622611839 2.298669295 0.12958845 0.039623062 12.47473856 -1.096031453 0.238508 SMAHS(ph)PGPVSQASPGTSSAVLFLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMAHSPGPVSQASPGTSSAVLFLSK 25 0 Q8TDZ2-2;Q8TDZ2;Q8TDZ2-4;H0Y6Z4 Q8TDZ2-2 MICAL1 Protein-methionine sulfoxide oxidase MICAL1 1 S(0.012)MAHS(0.988)PGPVSQASPGTSSAVLFLSK;S(0.001)MAHS(0.999)PGPVSQASPGTSSAVLFLSK 200.79 4.18E-25 919770000 376150 635420 700800 621280 754140 845550 692450 803580 782360 613070 TRUE FALSE 391000.6925 744548.4421 719063.4237 744167.3297 625951.5522 649183.8269 638173.9596 792809.3245 754203.0164 733189.3286 0.533287484 1.015492743 0.980733619 1.014972942 0.853737947 0.885424544 0.87040814 1.081315962 1.028660657 1 19.48382626 4.742339069 24.79675716 0.968706205 0.533287296 0.769103805 0.071794917 169.1892594 1110283.263 0.018662542 0.140316759 55250.86338 -4.742339069 -0.435418909 SMDELNHDFQALALEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;Q14671-4;E9PR38 Q5T1Z4 PUM1 Pumilio homolog 1 0 ;; 197.21 1.53E-11 176025000 129013 169791 164628 177640 182601 207495 149100 166518 160236 183939 FALSE TRUE 134106.5329 198951.2835 168918.3409 212776.6618 151562.5472 159307.4309 137413.1524 164286.0986 154469.1377 219978.3253 0.609635211 0.90441312 0.767886294 0.96726194 0.688988549 0.724196034 0.624666781 0.746828572 0.702201626 1 17.74700186 SMDFEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMDFEEAER 9 0 O43396;K7ER96 O43396 TXNL1 Thioredoxin-like protein 1 0 ; 136.21 0.0004634 599990000 515250 587150 542270 603240 658220 693320 542700 577810 588990 599800 FALSE TRUE 535592.4679 687988.4451 556402.0017 722559.0715 546335.9995 532306.9374 500161.7559 570065.4021 567792.365 717319.3261 0.746658355 0.959110427 0.775668494 1.00730462 0.761635689 0.742078065 0.697265134 0.794716358 0.791547564 1 19.45225598 SMEAEMIQLQEELAAAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;; 288.12 7.04E-40 575845700 389847.7 550526 545823 508164 584662 654321 544588 541963 532969 558337 FALSE TRUE 405239.1882 645074.558 560047.5958 608677.3225 485281.3621 502364.8641 501901.7695 534698.8725 513787.5498 667732.4451 0.606888569 0.966067416 0.838730542 0.911558704 0.726760195 0.752344547 0.751651014 0.800768147 0.769451228 1 19.34891062 -1.378381632 2.865912969 1.003330309 0.797153315 0.302821427 0.094532459 13622692.31 16356022.75 380044.3704 0.02182894 0.041842572 1.378381632 -0.206176994 SMEMLVEHQAHDILT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SMEMLVEHQAHDILT 15 0 Q9UNM6;J3KNQ3;A0A087WUL9;Q9UNM6-2;H0YD73 Q9UNM6 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 ;;; 132.65 4.62E-05 1842980000 857350 1105770 1099240 1076380 1199890 1310780 1102310 1104420 1075230 1052600 FALSE TRUE 891198.84 1295677.396 1127887.097 1289284.751 995933.1264 1006371.21 1015908.062 1089617.056 1036532.682 1258836.817 0.707954223 1.029265572 0.89597562 1.024187356 0.791153478 0.799445327 0.80702125 0.865574506 0.823405122 1 20.26365985 3.210115981 24.99547171 0.837896034 0.921242282 0.089564045 0.100133572 397.7473858 349515.899 0.027015688 0.032295403 1622.243271 -3.210115981 0.083346249 SMESS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMESSPR 7 0 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 SMES(0.091)S(0.909)PR;SMES(0.187)S(0.813)PR 85.161 0.08215 126896000 232130 296030 277000 279940 292820 362640 282770 292770 262490 322550 TRUE FALSE 241294.6716 346870.8497 284218.8476 335311.2965 243046.561 278422.3559 260605.7485 288845.897 253043.0362 385747.4969 0.625524919 0.89921737 0.736800238 0.869250738 0.630066463 0.72177359 0.675586363 0.748795259 0.655981019 1 18.55729727 -1.094010349 4.419838058 1.000021091 0.734207333 0.457282352 0.088347114 0.72172596 49090561.07 2694.857426 0.019504981 0.080535925 1.094010349 -0.265813759 SMFQDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMFQDVR 7 0 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 79.116 0.077928 123350000 261180 320870 246950 235300 519160 426980 299490 263050 267220 493180 FALSE TRUE 271491.5881 375976.9265 253385.7199 281841.6377 430913.3686 327820.3659 276015.1912 259524.245 257602.8044 589809.1785 0.460304108 0.637455198 0.429606268 0.477852241 0.730597936 0.555807502 0.467973713 0.440013914 0.436756181 1 19.16988875 -1.011614883 4.612677309 1.000013384 0.515067102 0.704451196 0.094214129 18055756.41 60007152.02 4045.352912 0.023507997 0.09736102 1.011614883 -0.484946282 SMGFIGHYLDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMGFIGHYLDQK 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 179.67 2.04E-05 4874200000 6820800 6450600 8080000 6360800 10403300 10201800 9645700 8226300 8955200 6264500 FALSE TRUE 7090090.451 7558440.371 8290571.438 7618947.255 8634950.782 7832586.56 8889644.83 8116039.904 8632904.101 7491908.834 0.946366354 1.008880452 1.106603353 1.016956749 1.152570189 1.045472754 1.186566071 1.08330735 1.152297004 1 22.83690191 5.29531487 0.737033107 1.10630897 0.673000051 0.394551617 0.058244274 4.997184298 1.154291532 0.019309886 2.162994727 197385.329 -5.29531487 -0.43330892 SMGTGDTPGLEVPS(ph)SPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.5)S(0.5)PLR;SMGTGDTPGLEVPS(0.5)S(0.5)PLR 118.21 0.00042709 182375000 254881 280910 272434 253268 286353 360190 287452 276461 275684 277189 TRUE FALSE 264943.8987 329154.1073 279533.8538 303363.6545 237678.8193 276541.3312 264920.7611 272755.4925 265762.1867 331498.8774 0.799230153 0.992926763 0.843242234 0.915127245 0.716982275 0.834214985 0.799160357 0.822794619 0.801698602 1 18.33864446 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDTPGLEVPS(0.5)S(0.5)PLRK 101.6 0.00019328 710570000 679320 534070 685390 522720 851630 837980 762720 703260 791880 592740 TRUE FALSE 706140.0781 625792.368 703251.8265 626112.4558 706870.2368 643371.8447 702936.0134 693833.95 763380.3935 708876.0543 0.996140403 0.882795186 0.992065993 0.883246728 0.997170426 0.90759427 0.99162048 0.978780346 1.076888391 1 19.43517387 1.65119191 1.830570891 1.034236089 0.943667454 0.351459157 0.04681914 0.313480975 2.166585975 0.03220974 0.012051412 44.7911188 -1.65119191 -0.090568635 SMGTGDTPGLEVPSS(ph)PLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SMGTGDT(0.041)PGLEVPS(0.078)S(0.881)PLRK 257.2 5.83E-31 72035000 100280 81843 86819 72615 126200 120180 102710 100330 103380 77692 TRUE FALSE 104239.1318 95898.8986 89081.57446 86978.03027 104748.5691 92270.01635 94659.32182 98985.24046 99659.37399 92914.2599 1.121885187 1.032122504 0.958750299 0.936110672 1.127368062 0.993066258 1.018781422 1.0653396 1.072595037 1 16.50361241 3.245805521 24.99998264 1.04618357 1.009819946 0.073840609 0.058700844 477.0440247 1646125.54 0.016731806 0.022227507 1761.187202 -3.245805521 -0.036363624 SMIEISR ddPTM_MDA-MB-175_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 ; 107.59 0.017314 263397000 123099 155244 145270 163448 167574 175583 152470 139895 144402 176733 FALSE TRUE 127959.0436 181905.9494 149055.8555 195777.5266 139089.8313 134806.5092 140519.003 138019.9363 139205.0002 211360.4476 0.605406759 0.860643282 0.705221139 0.92627324 0.658069345 0.63780386 0.66483112 0.6530074 0.658614238 1 17.6893459 -1.065183812 4.315475819 1.000025508 0.709094089 0.443978741 0.098101461 0.876991542 56708988.78 3282.338452 0.023076885 0.086062942 1.065183812 -0.290931419 SMIIDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 107.59 0.011934 375541000 495477 546898 531641 505994 631269 681000 631578 549496 525513 515519 FALSE TRUE 515038.8146 640823.4772 545496.0012 606078.103 523966.1209 522848.0707 582073.266 542130.9049 506599.8898 616525.0778 0.835389886 1.039411859 0.884791261 0.983055069 0.849869924 0.848056453 0.944119367 0.879333095 0.821702 1 19.23380005 3.233656593 24.99981841 0.885991402 0.939439095 0.087720931 0.070005458 252.7486007 1288464.403 0.01860111 0.022914145 1712.602575 -3.233656593 0.053447693 SMMQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMMQDR 6 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 97.602 0.095116 264330000 140770 162470 175360 179990 216810 219440 194080 185770 163270 161550 FALSE TRUE 146327.7083 190372.9587 179930.0257 215591.4848 179956.7136 168478.3856 178867.5025 183280.057 157393.9446 193202.6294 0.757379487 0.98535387 0.931302158 1.115882767 0.931440292 0.872029465 0.92580263 0.948641628 0.814657363 1 17.5597552 SMMQDREDQSILCTGESGAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMMQDREDQSILCTGESGAGK 21 1 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 271.66 1.05E-44 416310000 536430 481170 597140 401794 744510 696590 511500 583740 626030 507810 FALSE TRUE 557608.6706 563807.2045 612701.959 481267.654 617958.4561 534817.5294 471407.2934 575915.9201 603499.3026 607305.6469 0.918168098 0.928374711 1.008885661 0.792463657 1.0175411 0.88063981 0.776227417 0.948313132 0.993732408 1 19.21206326 1.479783489 15.76790729 0.988259462 0.904277927 0.205680359 0.073600839 0.105495085 294.7242203 0.039035079 0.018084081 30.18446546 -1.479783489 -0.083981535 SMNLRPEEDDIPWEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SMNLRPEEDDIPWEDLR 17 1 Q14CX7;Q14CX7-2 Q14CX7 NAA25 "N-alpha-acetyltransferase 25, NatB auxiliary subunit" 0 ;; 134.37 1.57E-05 163598000 135496 175131 165893 191665 195658 228340 194759 181406 178559 160872 FALSE TRUE 140845.4867 205208.3869 170216.3079 229575.7649 162400.123 175311.4955 179493.2807 178974.5493 172132.6965 192391.7883 0.732076394 1.066617181 0.884737906 1.193272161 0.844111511 0.9112213 0.932957078 0.930260854 0.894698771 1 17.5536877 SMQGFPFYDKPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMQGFPFYDKPMR 13 1 P09012;M0R221;M0R2B8;M0QZG7 P09012 SNRPA U1 small nuclear ribonucleoprotein A 0 114.69 0.00065943 313910000 199420 213370 242820 217660 256780 329080 264790 232800 254990 220930 FALSE TRUE 207293.2556 250014.6377 249148.0887 260712.4983 213132.6273 252656.1573 244035.0679 229679.6968 245812.9597 264217.0035 0.784556833 0.946247344 0.942967657 0.986736262 0.806657499 0.956244882 0.92361606 0.869284314 0.930344968 1 18.01136379 0.980027598 22.15224995 1.000000004 0.905198994 0.185671767 0.06185423 534.3396438 592661.9188 0.056214778 0.014053694 9.550532737 -0.980027598 -0.09480101 SMQHS(ph)PNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SMQHSPNLR 9 0 O76041-2;O76041 O76041-2 NEBL Nebulette 1 SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;SMQHS(1)PNLR;S(0.024)MQHS(0.976)PNLR;SMQHS(1)PNLR;S(0.002)MQHS(0.998)PNLR 165.35 3.97E-05 5860370000 1168639 2542218 2228109 2468309 2302773 2954650 2072869 2501771 2151749 2736608 TRUE FALSE 1214777.77 2978824.166 2286175.351 2956533.153 1911348.468 2268477.316 1910392.111 2468238.852 2074307.974 3272793.942 0.371174535 0.910177731 0.698539349 0.903366727 0.584011246 0.693131727 0.583719032 0.75416873 0.633803414 1 21.64209134 -2.214647252 2.274446901 1.945183852 0.692958461 0.28512993 0.150359801 8773893.566 1492698.351 42746440.54 0.033329366 0.006100322 2.214647252 -1.25222539 SMQNWHQLENLSNFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMQNWHQLENLSNFIK 16 0 B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;Q99439-2;A0A087X271;K7ES69;H3BQH0;A0A087WV51 B4DDF4 CNN2 Calponin;Calponin-2 0 ; 254.59 1.38E-26 1420890000 1313880 1355630 1634940 1356640 1750240 1973740 1713720 1690830 1722250 1398150 FALSE TRUE 1365752.997 1588448.907 1677547.88 1624979.343 1452734.83 1515368.797 1579394.148 1668167.189 1660266.559 1672090.723 0.816793597 0.949977705 1.003263672 0.971824866 0.868813402 0.906271876 0.944562473 0.997653516 0.992928515 1 20.6732217 1.831442047 3.401972444 0.997018805 0.924786111 0.32643129 0.049225257 0.323965674 6.515551864 0.027169984 0.01421196 67.8331597 -1.831442047 -0.072232694 SMS(ph)AAFCSLLAPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SMSAAFCSLLAPER 14 0 E9PNR2;Q13671-2;Q13671 E9PNR2 RIN1 Ras and Rab interactor 1 1 S(0.008)MS(0.992)AAFCSLLAPER;SMS(1)AAFCSLLAPER;S(0.027)MS(0.973)AAFCSLLAPER;SMS(1)AAFCSLLAPER;S(0.006)MS(0.994)AAFCSLLAPER 249.82 3.56E-18 223137000 262317 273699 328274 236379 457874 381263 378198 334997 328756 305558 TRUE FALSE 272673.4777 320704.6742 336829.0901 283134.0607 380044.741 292720.4463 348553.8525 330506.9132 316924.1358 365426.2398 0.74617925 0.877618078 0.921743032 0.774804953 1.040003972 0.801038389 0.9538282 0.904442202 0.86727252 1 18.47922071 5.566636119 1.183556022 0.906434031 5.69E-14 0.281408246 0.076955225 11.66939676 3.20483411 0.019635767 20.8877752 368668.574 -5.566636119 -0.906434031 SMS(ph)AEDLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SMSAEDLLER 10 0 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 SMS(1)AEDLLER;S(0.001)MS(0.999)AEDLLER;SMS(1)AEDLLER;SMS(1)AEDLLER;S(0.007)MS(0.993)AEDLLER;S(0.018)MS(0.982)AEDLLER 205.09 1.84E-07 1540304000 2236772 1628913 1857877 1502141 2078140 2300560 1683496 1750744 1804167 1625370 TRUE FALSE 2325081.486 1908666.137 1906294.801 1799260.006 1724898.505 1766289.805 1551539.185 1727278.14 1739235.382 1943830.132 1.19613409 0.981909944 0.980690015 0.925626153 0.887371009 0.908664691 0.798186611 0.888595208 0.89474659 1 20.89047072 7.999991685 0.673342781 0.884383873 33.15978615 0.757111303 0.049527832 106.076985 0.621738368 0.017865222 5129.353249 99998085.45 -7.999991685 32.27540228 SMS(ph)APSDLEMIGNEDLEFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSAPSDLEMIGNEDLEFTR 20 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.125)MS(0.872)APS(0.004)DLEMIGNEDLEFTR 150.7 8.85E-08 45353000 15100 21277 25533 23713 27877 29340 25099 21476 24718 24044 TRUE FALSE 15696.15966 24931.15924 26198.41096 28403.36062 23138.4775 22526.22965 23131.6748 21188.14935 23828.40401 28754.96145 0.545859179 0.867021132 0.911091848 0.987772516 0.804677744 0.783385841 0.804441169 0.736851948 0.828671047 1 14.81152328 -2.572225135 1.799058416 3.017959818 0.811445991 0.214460992 0.110176451 3745985.757 198659.6283 30788044.04 0.028925585 0.00267778 2.572225135 -2.206513826 SMS(ph)ASSGLSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMSASSGLSAR 11 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-6;H0Y7V8 Q5VT25-2;Q5VT25-3 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 S(0.003)MS(0.987)AS(0.008)S(0.001)GLSAR;S(0.002)MS(0.765)AS(0.171)S(0.061)GLSAR 114.23 0.0013485 252744000 243000 300180 312140 331630 391250 429900 320870 335790 346530 329140 TRUE FALSE 252593.8276 351733.5799 320274.6248 397225.4242 324745.4648 330062.2402 295719.371 331289.2843 334058.453 393628.6812 0.64170585 0.893566949 0.813646566 1.009137401 0.82500458 0.838511663 0.751264796 0.841628926 0.848663903 1 18.58647582 4.744335941 24.72362578 0.858280709 0.64170574 0.43359869 0.07707121 528.2634355 2261368.449 0.017790055 0.15773283 55505.49003 -4.744335941 -0.216574969 SMS(ph)DVSAEDVQNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSDVSAEDVQNLR 14 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 SMS(1)DVSAEDVQNLR 168.89 3.59E-06 66482000 74205 82509 76716 79189 92415 97249 79917 90700 77894 80094 TRUE FALSE 77134.6707 96679.27892 78715.28198 94852.34784 76706.33131 74664.39357 73652.89672 89484.31486 75090.61016 95786.88581 0.805273812 1.009316444 0.821775145 0.990243571 0.800802017 0.779484508 0.76892464 0.934202152 0.783934142 1 16.54754053 5.052433965 15.825787 0.871162223 0.36007402 0.046845609 0.093646072 7898013.284 60111070.82 0.021384043 124902081.4 112832.4363 -5.052433965 -0.511088203 SMS(ph)FQGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SMSFQGIR 8 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.001)MS(0.999)FQGIR;S(0.005)MS(0.995)FQGIR;SMS(1)FQGIR;S(0.001)MS(0.999)FQGIR;SMS(1)FQGIR;S(0.016)MS(0.984)FQGIR 150.06 0.0005194 2128210000 992701 1497586 1522347 1359826 2052346 1750381 1339598 1494407 1452680 1635134 TRUE FALSE 1031893.602 1754784.746 1562020.613 1628795.524 1703488.96 1343881.54 1234596.808 1474376.919 1400398.331 1955507.201 0.527685913 0.897355297 0.798780292 0.832927398 0.871123849 0.687229144 0.631343525 0.753961386 0.71613049 1 20.89911142 -1.085737101 4.308226732 1.000022488 0.751915184 0.335061029 0.106961748 1.024399141 60142369.84 3615.882618 0.024515223 0.082084829 1.085737101 -0.248107304 SMS(ph)GGHGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMSGGHGLR 9 0 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.013)MS(0.987)GGHGLR;S(0.158)MS(0.842)GGHGLR 83.397 0.028639 186653000 100619 122642 124067 166719 177820 188829 126295 132260 132985 148010 TRUE FALSE 104591.5158 143704.8095 127300.2879 199695.5206 147594.2199 144976.3265 116395.6679 130487.271 128198.8958 177009.7257 0.590880051 0.81184697 0.71917115 1.128161291 0.833819833 0.819030287 0.657566512 0.737175715 0.724247752 1 17.4334691 -2.44415701 2.051037991 2.763590447 0.783528257 0.188987536 0.136435993 5531755.481 400455.6046 45380191.55 0.034366034 0.003596193 2.44415701 -1.980062191 SMS(ph)PTSTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMSPTSTPK 9 0 E9PQ01;E9PKN0;O94913 E9PQ01 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 SMS(0.514)PT(0.47)S(0.016)T(0.001)PK;SMS(0.73)PT(0.256)S(0.011)T(0.003)PK 104.82 0.0033541 175658000 393740 326540 367770 284690 444380 461780 399450 351620 372720 277620 TRUE FALSE 409285.1592 382620.7049 377354.3883 341000.8323 368844.4463 354538.5933 368140.0652 346907.109 359305.88 332014.3236 1.23273344 1.152422283 1.136560568 1.027066629 1.110929319 1.067841259 1.10880778 1.044855852 1.082199937 1 18.34088596 7.999999963 0.50268401 1.05991634 6.834052521 0.715165119 0.03437177 54.93521816 0.578805808 0.016776573 335.3900231 99999991.38 -7.999999963 5.774136181 SMS(ph)VDLSHIPLKDPLLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSVDLSHIPLKDPLLFK 18 1 A0A0C4DGH6;A0JNW5 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 S(0.189)MS(0.802)VDLS(0.009)HIPLKDPLLFK 80.98 0.0046664 125200000 157770 133890 177350 121330 219230 185160 185530 131990 194690 127390 TRUE FALSE 163998.8814 156884.566 181971.8867 145328.7119 181965.3629 142159.3961 170987.6738 130220.8899 187683.1449 152349.6315 1.076463919 1.029766626 1.194436015 0.953915743 1.194393194 0.933112832 1.122337298 0.854750279 1.231923853 1 17.21702648 2.723423883 24.95277114 1.01370859 1.084724726 0.0570393 0.116461503 2070.06856 3412484.79 0.035041072 0.03314221 528.9612805 -2.723423883 0.071016136 SMSSIPPYPASSLAS(ph)SSPPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPAS(0.011)S(0.011)LAS(0.368)S(0.313)S(0.267)PPGS(0.028)GR 94.384 0.0044756 417500000 82882 92181 96006 92250 108240 118310 105960 101530 97142 105700 TRUE FALSE 86154.24536 108012.3697 98507.99523 110496.7747 89841.40346 90834.29551 97654.57833 100169.1564 93645.8784 126409.8913 0.681546709 0.854461376 0.779274424 0.874114941 0.710714981 0.718569525 0.772523237 0.792415494 0.74081132 1 16.94774983 -1.877849033 2.763734632 1.104048522 0.77361819 0.587012554 0.057933036 10395066.62 6853024.866 7073129.463 0.013350057 0.01324802 1.877849033 -0.330430332 SMSSIPPYPASSLASS(ph)SPPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPAS(0.027)S(0.027)LAS(0.032)S(0.446)S(0.446)PPGS(0.022)GR 87.654 0.006716 478340000 66530 82180 89540 95553 103040 122910 84734 90965 78197 86588 TRUE FALSE 69156.65577 96293.77573 91873.48596 114453.0982 85525.2976 94366.01522 78092.32767 89745.76296 75382.70524 103553.2608 0.667836582 0.929896123 0.887209976 1.105258273 0.825906369 0.911279998 0.754127172 0.866662839 0.72796071 1 16.66001346 2.283418354 24.99291402 0.827854801 0.896837899 0.034653211 0.122008488 372.5629926 207575.4253 0.040865904 0.034190706 192.0517875 -2.283418354 0.068983098 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SMSSIPPYPASSLASSSPPGSGR 23 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 SMSSIPPYPAS(0.001)S(0.001)LAS(0.048)S(0.274)S(0.633)PPGS(0.043)GR;SMSSIPPYPASSLAS(0.054)S(0.055)S(0.889)PPGS(0.002)GR;SMSSIPPYPASSLASS(0.031)S(0.969)PPGSGR;SMSSIPPYPASSLAS(0.004)S(0.291)S(0.706)PPGSGR;SMSSIPPYPASSLAS(0.002)S(0.187)S(0.811)PPGSGR;SMSSIPPYPASSLASS(0.013)S(0.987)PPGSGR;SMSSIPPYPASSLASS(0.015)S(0.985)PPGSGR 386.14 6.71E-137 1363155000 468891 524681 526768 498964 542240 635588 540432 531667 528965 519007 TRUE FALSE 487403.1787 614790.8803 540496.0068 597657.5899 450070.2385 487982.3194 498071.5277 524540.8735 509927.653 620696.4847 0.785252037 0.99048552 0.870789541 0.962882189 0.725105184 0.786185086 0.802439743 0.845084331 0.821541068 1 19.24352845 5.077913531 13.34145501 0.856962041 5.92E-05 0.062548638 0.087442937 2887503.269 12029673.41 0.020776543 67955910.59 119650.2282 -5.077913531 -0.856902807 SMVEGLGGPLGHAGEESEVDNDVDS(ph)PGSLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMVEGLGGPLGHAGEESEVDNDVDSPGSLRR 31 1 Q96DR7;Q96DR7-4;Q96DR7-3 Q96DR7 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 SMVEGLGGPLGHAGEESEVDNDVDS(0.944)PGS(0.056)LRR 152 4.10E-09 31044000 11208 22054 19023 19150 16637 24474 14254 17025 17529 23367 TRUE FALSE 11650.50049 25841.60294 19518.75501 22937.81284 13809.04868 18790.28441 13136.73423 16796.80772 16898.13471 27945.31626 0.416903512 0.924720361 0.698462484 0.820810637 0.494145371 0.672394767 0.470087156 0.601059854 0.604685757 1 14.77031888 -1.057376923 4.349284793 1.000027952 0.636892325 0.353547391 0.148539286 19208598.09 4669901.49 5259.136229 0.033787707 0.087624 1.057376923 -0.363135627 SMVNTKPEKTEEDSEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SMVNTKPEKTEEDSEEVR 18 2 Q16543 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ;; 160.67 2.25E-11 870260000 1486080 699062 1116310 707674 1563030 1472960 1388960 1071610 1347550 637565 FALSE TRUE 1544751.586 819120.4606 1145401.956 847649.805 1297346.719 1130887.363 1280089.686 1057246.821 1299051.939 762483.6548 2.025947148 1.07427937 1.502198701 1.111695706 1.701474793 1.483162761 1.678842133 1.386582931 1.703711195 1 19.54034689 -0.716615703 8.87200448 1 1.496144891 0.243674189 0.2715315 0 0 0.237875086 0.056067695 0.192036728 0.716615703 0.496144891 SMYEEEINETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SMYEEEINETR 11 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 ; 235.01 3.81E-15 619810000 180679 264070 220490 236370 260310 297290 222750 243350 227100 259250 FALSE TRUE 187812.3464 309421.9683 226236.1505 283123.2805 216062.5992 228248.903 205290.273 240088.2913 218926.7154 310045.0739 0.605758202 0.997990274 0.729687938 0.913168131 0.696874801 0.736179744 0.662130413 0.774365767 0.706112542 1 18.24211844 SMYEEEINETRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SMYEEEINETRR 12 1 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 94.688 0.0032485 0 30550 147890 79706 116850 66280 102510 62890 55531 56743 184190 FALSE TRUE 31756.13759 173288.9571 81783.20384 139962.5812 55013.74927 78703.60605 57960.51747 54786.69778 54700.83051 220278.504 0.144163579 0.786681197 0.371271833 0.635389195 0.249746336 0.357291359 0.263123802 0.248715589 0.248325776 1 17.74896919 -1.304343964 5.207634308 1.000150109 0.370305016 0.506809447 0.187252267 0.000320736 4.28E-05 0.17819003 0.041989922 0.049619917 1.304343964 -0.629845093 SNAAAYLQHLCYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNAAAYLQHLCYR 13 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;E9PKY0 O60716-13 CTNND1 Catenin delta-1 0 ; 114.56 0.00073315 1228750000 596840 817000 663930 650820 825930 1025730 673760 683280 636520 972320 FALSE TRUE 620403.7041 957313.3946 681232.5612 779550.2535 685538.7136 787519.7526 620948.9307 674121.7492 613611.7695 1162827.488 0.533530305 0.823263472 0.585841467 0.670392007 0.589544641 0.67724556 0.533999185 0.579726362 0.527689426 1 20.14920565 -1.934317036 4.229218278 1.202785366 0.615563864 0.645269818 0.08596444 0.04941837 0.000767505 0.02502511 0.018861486 0.011632765 1.934317036 -0.587221502 SNAHYNLQNAFNLAEQHLGLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNAHYNLQNAFNLAEQHLGLTK 22 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 249.99 1.05E-31 276200000 200855 265410 299130 255560 344050 379420 307020 293860 287750 252400 FALSE TRUE 208784.9105 310992.1029 306925.5735 306109.0052 285568.5039 291305.4552 282954.9702 289921.2874 277393.9337 301852.9475 0.691677561 1.030276847 1.016804958 1.014099772 0.946051732 0.965057514 0.937393431 0.960471944 0.918970432 1 18.20348636 4.745578976 24.99385603 0.974019527 0.69167743 0.851840402 0.035629794 316.0565046 1125515.818 0.009114994 0.091059282 55664.58507 -4.745578976 -0.282342097 SNATNSSYS(ph)PTTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNATNSSYSPTTGR 14 0 Q13009;Q13009-2 Q13009 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 SNATNS(0.029)S(0.024)YS(0.941)PT(0.005)TGR 125.41 9.59E-05 99045000 106120 118260 111040 108850 141580 154830 127710 108650 110960 111940 TRUE FALSE 110309.6995 138570.2351 113933.7936 130380.2051 117514.2822 118873.079 117699.7565 107193.7245 106966.5713 133872.4998 0.823990735 1.035091115 0.851061972 0.973913278 0.877807484 0.887957416 0.879192939 0.800715043 0.799018256 1 17.03050011 2.582891523 1.539912742 0.847946253 0.922369736 0.042181572 0.077373288 0.728474133 3.488350664 0.032154363 0.027088442 382.7291345 -2.582891523 0.074423483 SNDRNS(ph)MDIQCEVDALLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNDRNSMDIQCEVDALLER 19 1 Q02241;H7BYN4;A0A2U3TZL8;A0A2R8Y531;H0YME6;Q02241-2 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 SNDRNS(1)MDIQCEVDALLER;SNDRNS(1)MDIQCEVDALLER;S(0.214)NDRNS(0.786)MDIQCEVDALLER 260.32 2.54E-31 251070000 125050 176203 176295 176103 190151 219843 175912 185583 182112 183296 TRUE FALSE 129987.0706 206464.4946 180889.3925 210935.6478 157829.2009 168787.795 162123.5578 183095.5634 175557.8247 219209.3418 0.592981437 0.941859927 0.825190163 0.962256654 0.719993043 0.769984498 0.739583252 0.835254383 0.800868354 1 17.74194976 -0.139452383 1.516640165 1.000292838 0.804643863 0.260785486 0.101222023 62.41931983 79.63654285 0.188346143 0.026328505 0.725350003 0.139452383 -0.195648975 SNDS(ph)GEEAEKEFIFV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SNDSGEEAEKEFIFV 15 1 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.011)NDS(0.989)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;S(0.001)NDS(0.999)GEEAEKEFIFV;SNDS(1)GEEAEKEFIFV;S(0.006)NDS(0.994)GEEAEKEFIFV 250.26 2.42E-18 1495196000 3348260 2045930 2779960 2076030 3663310 3623220 3234330 2684400 2884920 1759700 TRUE FALSE 3480451.89 2397302.562 2852408.041 2486662.538 3040621.875 2781782.065 2980814.763 2648420.009 2781092.293 2104479.524 1.653830247 1.139142736 1.355398335 1.18160453 1.444833195 1.321838504 1.416414239 1.258467939 1.32151074 1 21.00503204 0.026218653 0.802746736 0.992100995 1.342139172 0.365904609 0.136649808 5.291113128 3.476827881 0.243948135 0.04151811 1.062230221 -0.026218653 0.350038177 SNEDQSMGNWQIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 258.42 3.56E-24 3473950000 1250221 1444277 1354856 1110639 1971036 2071233 1527634 1759714 1930392 1537378 FALSE TRUE 1299580.69 1692320.34 1390164.66 1330320.079 1636000.005 1590220.526 1407894.055 1736127.912 1860917.569 1838597.784 0.706832512 0.920440759 0.756100476 0.723551443 0.889808537 0.86490941 0.765743366 0.94426738 1.012139569 1 20.81017448 1.585833911 3.90601397 0.999883081 0.80932179 0.611696833 0.067156089 0.119367406 4.164795848 0.039963268 0.017219117 38.53309656 -1.585833911 -0.190561291 SNEEGSEEKGPEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 268.61 2.90E-25 4974720000 5415080 3439400 4644420 3354570 6551240 6054550 5792310 4853710 5310480 3014450 FALSE TRUE 5628871.54 4030090.195 4765457.401 4018093.934 5437662.565 4648472.52 5338293.607 4788653.957 5119356.862 3605073.762 1.56137486 1.117893963 1.321875145 1.114566358 1.508336007 1.289425079 1.480772367 1.328309564 1.420042196 1 21.78159735 -1.077007441 4.505294795 0.999976231 1.342272656 0.346207272 0.143670781 3.17E-05 6.50E-06 0.128656923 0.030322624 0.083751493 1.077007441 0.342296425 SNEHDHSKS(ph)KEKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNEHDHSKSKEKDR 14 3 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 SNEHDHS(0.028)KS(0.972)KEKDR 108.49 0.00033478 143940000 262900 83271 162460 52720 295140 242340 180870 162830 185330 62450 TRUE FALSE 273279.495 97572.14649 166693.8411 63147.85865 244972.2082 186060.2077 166692.9368 160647.5302 178660.0095 74685.88182 3.659051595 1.306433614 2.231932421 0.845512661 3.280033686 2.491236672 2.231920314 2.150975877 2.392152374 1 16.18854793 SNFAEALAAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNFAEALAAHK 11 0 P07237;H7BZ94;I3L312;I3L3U6;I3L0S0;I3NI03;I3L514;I3L3P5;I3L1Y5 P07237 P4HB Protein disulfide-isomerase 0 143.31 3.72E-05 1340500000 1423900 1489800 1709100 1256400 2370900 2094500 1697200 1615400 1577600 1406000 FALSE TRUE 1480116.671 1745661.561 1753640.55 1504912.17 1967895.265 1608084.117 1564169.029 1593748.205 1520822.484 1681478.781 0.880247012 1.038170437 1.042915659 0.894993257 1.170336068 0.956351121 0.930234177 0.947825345 0.904455353 1 20.68129914 -0.497032646 5.358992481 0.999999995 0.97678518 0.007603697 0.083825829 10426127.37 1945538.538 0.110168694 0.018947062 0.318395818 0.497032646 -0.023214815 SNFSSGPGFPEYGYPADTVWPAMEQVS(ph)S(ph)RPTSPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNFSSGPGFPEYGYPADTVWPAMEQVSSRPTSPEK 35 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 2 SNFSSGPGFPEYGYPADT(0.008)VWPAMEQVS(0.483)S(0.514)RPT(0.513)S(0.482)PEK 149.54 9.35E-11 35421000 73154 45291 52923 43379 68772 86339 74504 57545 60361 31863 TRUE FALSE 76042.17641 53069.37693 54302.21686 51959.23673 57082.16 66288.07573 68664.1818 56773.7034 58188.6194 38105.9448 1.995546281 1.392679731 1.425032686 1.363546738 1.49798569 1.739573079 1.801928339 1.489890979 1.527022088 1 15.21772847 0.517595091 1.772422031 1.000158624 1.577587351 0.455353173 0.191777901 2.951192857 9.768654938 0.184604026 0.051806346 3.293025478 -0.517595091 0.577428727 SNFSSGPGFPEYGYPADTVWPAMEQVS(ph)SRPTSPEKFSVPHVCAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNFSSGPGFPEYGYPADTVWPAMEQVSSRPTSPEKFSVPHVCAR 44 2 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 1 SNFSSGPGFPEYGYPADT(0.067)VWPAMEQVS(0.217)S(0.217)RPT(0.217)S(0.217)PEKFS(0.067)VPHVCAR;SNFSSGPGFPEYGYPADT(0.015)VWPAMEQVS(0.232)S(0.232)RPT(0.232)S(0.232)PEKFS(0.058)VPHVCAR 95.603 2.62E-05 1415650000 679550 478980 670540 446310 875840 1017700 712620 675560 826840 529440 TRUE FALSE 706379.1587 561241.0891 688014.8233 534588.7859 726965.0296 781354.5984 656762.9823 666505.2232 797082.1899 633173.6313 1.115616829 0.886393655 1.086613196 0.844300456 1.148129034 1.234028961 1.037255738 1.052642104 1.258868264 1 19.27224165 3.198923372 24.9998793 1.118831441 0.983698105 0.284507444 0.107605613 198.8725507 125431.6692 0.0298505 0.035678682 1580.969066 -3.198923372 -0.135133336 SNIHCNTIAPNAGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNIHCNTIAPNAGSR 15 0 P51659-3;P51659;P51659-2;A0A2R8YD50;A0A2R8Y7L2;E7ET17;E7ER27;A0A2R8Y7W2 P51659-3 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 ; 108 0.0011133 266750000 183944 285300 261080 294610 315700 386620 292070 254660 266970 241870 FALSE TRUE 191206.2512 334298.0557 267883.9593 352882.9787 262037.4268 296833.3643 269176.7902 251246.6992 257361.8018 289259.7956 0.661019105 1.155701763 0.926101599 1.219951697 0.905889552 1.026182583 0.930571045 0.86858493 0.88972545 1 18.14200629 2.079649757 5.499858746 0.903544887 0.994739128 0.032346432 0.145724748 0.538127615 27.72000454 0.052379107 0.038087452 120.1295241 -2.079649757 0.091194242 SNLDEEVNVIPPHT(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNLDEEVNVIPPHTPVR 17 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 SNLDEEVNVIPPHT(1)PVR;SNLDEEVNVIPPHT(1)PVR 110.26 0.0020867 252170000 185111 188011 187591 200949 196873 241585 198753 197826 187807 162984 TRUE FALSE 192419.3252 220300.4267 192479.7756 240696.1124 163408.5978 185480.545 183174.2205 195174.466 181047.8628 194917.5943 0.987182947 1.130223403 0.98749308 1.234860882 0.838347089 0.951584415 0.93975211 1.001317848 0.928843101 1 17.5725048 3.226533988 24.99997502 0.947456428 1.081214132 0.437779944 0.078501209 207.8520741 432065.1327 0.021331643 0.025683103 1684.744268 -3.226533988 0.133757704 SNMGHPEPASGLAALAK ddPTM_MDA-MB-175_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 ;; 150.45 2.87E-07 2107060000 1996470 2066940 2682810 2329590 3230560 3406320 2767060 2584780 2737970 2162610 FALSE TRUE 2075292.177 2421920.866 2752726.233 2790375.949 2681430.565 2615253.803 2550170.607 2550135.252 2639430.995 2586332.024 0.802407486 0.936430761 1.064335981 1.078893167 1.036769657 1.011182547 0.986018262 0.986004592 1.020530609 1 21.30247606 4.594307264 2.968613747 1.020416198 0.795362521 0.835160162 0.030147739 0.130039202 1.865718771 0.008690383 0.057410101 39292.2831 -4.594307264 -0.225053677 SNMS(ph)PHGLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SNMSPHGLPAR 11 0 E7ESY4;Q13330-3;Q13330;H0Y4T7 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SNMS(1)PHGLPAR;SNMS(1)PHGLPAR;S(0.004)NMS(0.996)PHGLPAR;S(0.003)NMS(0.997)PHGLPAR 140.27 2.49E-05 1081970000 713430 949910 940540 913600 1140770 1184170 976300 956420 967640 902990 TRUE FALSE 741596.7673 1113049.653 965051.2451 1094307.353 946862.3229 909164.4638 899775.0549 943600.7543 932814.8254 1079913.602 0.68671861 1.030683984 0.893637457 1.013328614 0.876794515 0.841886298 0.833191705 0.873774303 0.863786532 1 20.04248446 3.03017405 24.98859867 0.869540934 0.917971901 0.000657678 0.097480159 650.3904502 538615.6799 0.026319411 0.031457468 1071.948818 -3.03017405 0.048430967 SNNIAELS(ph)PGAINSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNNIAELSPGAINSCR 16 0 Q9Y2I9;F8VZ81;Q9Y2I9-2;Q9Y2I9-3 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 SNNIAELS(1)PGAINSCR;SNNIAELS(1)PGAINSCR;SNNIAELS(1)PGAINSCR 403.07 9.78E-140 560123000 571590 663728 678945 610575 754546 874830 696954 738694 641573 648271 TRUE FALSE 594156.8146 777718.1209 696638.8645 731344.9126 626288.5404 671663.9907 642324.9243 728793.0152 618482.9131 775287.2906 0.766369863 1.003135393 0.898555765 0.943321168 0.807814791 0.866342063 0.828499231 0.940029617 0.797746746 1 19.56437149 -1.394385509 3.60244513 1.000788533 0.879651 0.218196353 0.071274293 941844926.5 2435252293 8877177.992 0.016028939 0.040328725 1.394385509 -0.121137533 SNNWS(ph)LEDVTASDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNNWSLEDVTASDK 14 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 SNNWS(1)LEDVTASDK;SNNWS(1)LEDVTASDK;S(0.001)NNWS(0.999)LEDVTASDK 192.16 4.25E-07 253412000 261488 171133 214709 176688 254416 276781 294833 216311 222301 116236 TRUE FALSE 271811.7482 200523.7615 220304.4929 211636.359 211170.4592 212502.8074 271723.2191 213411.7049 214300.4304 139010.2187 1.955336454 1.442510942 1.584807901 1.522451809 1.519100258 1.528684793 1.954699601 1.535223143 1.541616382 1 17.08483141 0.64715482 2.02820126 1.000292291 1.623491464 0.548974691 0.170572956 1.379773877 6.982441307 0.156347487 0.043013821 4.437668129 -0.64715482 0.623199173 SNPKS(ph)PQKPIVR ddPTM_MDA-MB-175_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(0.055)NPKS(0.945)PQKPIVR;SNPKS(1)PQKPIVR 143.93 3.27E-05 5121900000 6139600 2868020 4595700 3088500 6349900 5511200 5520000 4551400 5071200 2491520 TRUE FALSE 6381996.149 3360580.125 4715467.717 3699396.082 5270546.266 4231307.323 5087327.976 4490395.928 4888688.503 2979685.641 2.141835387 1.127830426 1.582538659 1.241539051 1.768826279 1.420051587 1.707337145 1.507003244 1.640672571 1 21.5067287 -1.608664149 6.685702193 0.998664016 1.552283413 0.286266094 0.268977689 0.004748622 0.000277952 0.230886143 0.054312092 0.02462271 1.608664149 0.553619398 SNPVIPIS(ph)SSNHSARSPFEGAVTESQSLFSDNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNPVIPISSSNHSARSPFEGAVTESQSLFSDNFR 34 1 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(0.01)NPVIPIS(0.198)S(0.198)S(0.198)NHS(0.198)ARS(0.198)PFEGAVTESQSLFSDNFR 76.476 0.0015418 24476000 3822.8 9335.1 9726 5852.7 9762 12310 5799.9 9447.8 9943.9 17300 TRUE FALSE 3973.727096 10938.33081 9979.46755 7010.346591 8102.658727 9451.18906 5345.288683 9321.167694 9586.020981 20689.60377 0.192063953 0.528687303 0.48234213 0.33883426 0.391629478 0.456808606 0.258356262 0.450524225 0.463325499 1 14.3366184 0.500792216 1.564102511 0.999931954 0.390732844 0.780390339 0.097017167 1.150514072 3.142404139 0.08726985 0.025038777 3.16805138 -0.500792216 -0.60919911 SNRDELELELAENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNRDELELELAENR 14 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 168.1 7.93E-07 508710000 298041 330369 335617 338124 380193 415317 334789 354684 319452 350147 FALSE TRUE 309807.8888 387107.3058 344363.4547 405003.918 315567.9297 318865.9209 308547.3634 349930.0411 307954.9849 418751.6007 0.739836906 0.924431824 0.822357345 0.967169838 0.753592175 0.761467945 0.736826708 0.835650635 0.735412078 1 18.67573518 3.191305994 24.99999676 0.792031065 0.864871138 0.082715012 0.092342949 233.6551735 123614.0867 0.024599838 0.029402514 1553.481172 -3.191305994 0.072840072 SNRDELELELAENRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNRDELELELAENRK 15 2 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ;; 238.83 4.94E-18 972630000 702960 542530 675250 577800 855280 860810 775450 705530 732290 539630 FALSE TRUE 730713.4036 635705.3072 692847.5697 692087.1154 709899.8111 660899.9232 714668.2027 696073.5244 705935.0259 645360.1667 1.132256748 0.98503958 1.073582792 1.072404451 1.100005621 1.0240792 1.107394351 1.078581481 1.093862098 1 19.29974501 SNRNS(ph)IER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SNRNSIER 8 1 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 SNRNS(1)IER;SNRNS(1)IER;S(0.111)NRNS(0.889)IER;S(0.001)NRNS(0.999)IER;SNRNS(1)IER;S(0.002)NRNS(0.998)IER 128.85 0.00067586 2026675000 1198600 1184881 1335547 1238605 1593793 1591781 1352307 1371341 1277252 1267747 TRUE FALSE 1245921.654 1388375.095 1370352.452 1483597.372 1322880.635 1222113.986 1246309.644 1352960.417 1231283.95 1516137.752 0.821773386 0.915731498 0.903844291 0.97853732 0.872533273 0.806070546 0.822029292 0.892373015 0.812118786 1 20.53196941 3.014450558 24.96843739 0.857017751 0.908144119 0.067669183 0.063262002 477.9599852 825838.7921 0.017413488 0.020805301 1033.833398 -3.014450558 0.051126368 SNS(ph)APLIHGLSDTSPVFQAEAPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.004)NS(0.996)APLIHGLSDTSPVFQAEAPSAR;S(0.165)NS(0.835)APLIHGLSDTSPVFQAEAPSAR 278.63 2.36E-53 411030000 97563 120554 140682 126719 165194 166858 143118 149509 137704 133729 TRUE FALSE 101414.8626 141258.2117 144348.2885 151783.64 137114.3829 128107.7583 131900.0372 147505.0764 132748.0599 159930.6372 0.634117792 0.883246726 0.902568082 0.949059184 0.857336564 0.801020746 0.824732769 0.922306564 0.83003521 1 17.28708681 -1.733350795 0.020339624 1.919956372 3.84E-06 0.283767776 0.080472096 2431.637542 7.444473776 408.4320744 300.2725555 0.018477755 1.733350795 -1.919952533 SNS(ph)AWQIYLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SNSAWQIYLQR 11 0 Q8N4C8;Q8N4C8-4 Q8N4C8 MINK1 Misshapen-like kinase 1 1 S(0.007)NS(0.993)AWQIYLQR;S(0.019)NS(0.98)AWQIY(0.001)LQR;S(0.015)NS(0.985)AWQIYLQR;S(0.032)NS(0.968)AWQIYLQR 147.73 3.69E-05 547819000 276149 380606 321408 317616 497454 451916 313077 336358 330139 415200 TRUE FALSE 287051.5758 445972.1198 329784.1565 380439.4968 412896.9468 346965.3579 288537.2067 331849.6712 318257.3619 496550.4905 0.578091415 0.898140528 0.664150299 0.766164779 0.831530639 0.698751415 0.581083318 0.668310026 0.640936557 1 18.9215809 -1.111367054 5.107783638 1.000008526 0.705072629 0.453331522 0.097814207 9.40E-06 1.64E-06 0.093718521 0.022089029 0.077380752 1.111367054 -0.294935898 SNS(ph)DNNLNASAPDWAVCSTATSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SNSDNNLNASAPDWAVCSTATSHR 24 0 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.261)NS(0.739)DNNLNASAPDWAVCSTATSHR;S(0.215)NS(0.785)DNNLNASAPDWAVCSTATSHR;S(0.239)NS(0.761)DNNLNASAPDWAVCSTATSHR;S(0.272)NS(0.728)DNNLNASAPDWAVCSTATSHR 274.76 3.47E-52 2370040000 224188 281437 275097 275028 312594 396497 285840 291099 287049 247477 TRUE FALSE 233039.1154 329771.6155 282266.2538 329427.7175 259459.3835 304416.5807 263435.1139 287197.294 276718.1626 295965.3799 0.787386401 1.114223615 0.953713755 1.113061662 0.876654505 1.028554694 0.890087597 0.970374623 0.934968011 1 18.1750689 3.192766763 24.99985182 0.94961564 0.998080318 0.042820374 0.095578639 382.0732192 208580.7794 0.025378574 0.030333297 1558.715172 -3.192766763 0.048464678 SNS(ph)DVTISDIDAEDVLDQNAVNPNTGAALHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSDVTISDIDAEDVLDQNAVNPNTGAALHR 31 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.242)NS(0.758)DVTISDIDAEDVLDQNAVNPNTGAALHR 232.5 1.27E-36 622030000 71185 103210 115560 102210 127400 149090 132730 118730 102870 103750 TRUE FALSE 73995.43877 120935.5146 118571.5885 122426.8329 105744.5935 114466.107 122326.2758 117138.6186 99167.72879 124077.8261 0.596363114 0.974674674 0.955622711 0.98669389 0.852244086 0.922534756 0.985883454 0.94407375 0.799238123 1 16.92088579 4.742552141 24.99368458 0.935852983 0.596362982 0.73686536 0.060827363 194.4990697 1217845.543 0.01405002 0.107321888 55277.97705 -4.742552141 -0.339490001 SNS(ph)EDKLNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNSEDKLNSK 10 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 SNS(1)EDKLNSK;S(0.023)NS(0.977)EDKLNSK;SNS(0.977)EDKLNS(0.023)K 204.31 1.15E-07 1509460000 2608440 900760 1451530 876290 2168800 2000330 1979190 1310290 1634120 636410 TRUE FALSE 2711423.225 1055458.523 1489358.064 1049617.547 1800148.151 1535783.673 1824055.916 1292727.706 1575308.34 761102.3547 3.562494858 1.38674978 1.956843327 1.379075416 2.365185365 2.017841179 2.396597389 1.698493899 2.069771997 1 19.53773096 -1.895882284 0.314373362 1.29E-14 2.126664067 0.242523536 0.589570304 46.64145525 2.353932929 35.61528524 0.533355246 0.012709185 1.895882284 2.126664067 SNS(ph)FIGVPNGEVEMPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-2;Q9H7E2;Q9H7E2-3 Q9H7E2-2 TDRD3 Tudor domain-containing protein 3 1 S(0.156)NS(0.844)FIGVPNGEVEMPLK;S(0.206)NS(0.794)FIGVPNGEVEMPLK 160.55 3.23E-09 77586000 339020 227641 325710 276474 464200 428440 433670 351890 389870 221083 TRUE FALSE 352404.7714 266736.5709 334198.2702 331159.732 385295.4498 328941.3031 399677.8122 347173.4901 375838.6549 264399.981 1.332847189 1.00883733 1.263987497 1.252495294 1.45724462 1.244104867 1.511640851 1.313061706 1.421477617 1 18.01236255 3.70792356 2.414024488 1.345942453 1.172315803 0.096811837 0.154182093 0.466198364 5.321929116 0.039296635 0.074413562 5104.151537 -3.70792356 -0.173626651 SNS(ph)FNNPLGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 S(0.003)NS(0.997)FNNPLGNR;SNS(1)FNNPLGNR;SNS(1)FNNPLGNR;SNS(1)FNNPLGNR;SNS(1)FNNPLGNR 237.26 1.48E-15 1473680000 905700 917710 1029190 962150 1213030 1340770 1071060 1042700 1021130 928150 TRUE FALSE 941457.7354 1075319.554 1056011.537 1152460.398 1006839.594 1029396.487 987107.5185 1028724.312 984379.7308 1110003.222 0.84815766 0.968753543 0.951358983 1.038249597 0.907060064 0.927381531 0.889283471 0.926775969 0.886826012 1 20.08213243 SNS(ph)FSDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.109)NS(0.674)FS(0.217)DER;S(0.085)NS(0.864)FS(0.051)DER;S(0.01)NS(0.986)FS(0.005)DER 184.44 0.00022866 2177680000 3596030 3511160 3212680 3747790 3308480 4530400 4009160 3236650 3110490 2396450 TRUE FALSE 3738004.041 4114174.417 3296405.08 4489091.676 2746105.751 3478283.259 3694911.563 3193268.001 2998544.073 2865988.495 1.30426345 1.435516725 1.150180849 1.566332762 0.958170543 1.213641738 1.289227633 1.114194285 1.04625126 1 21.45060139 2.496546376 0.280950013 0.971052162 1.436134322 0.348968532 0.148788685 2.696485804 0.511872467 0.229573962 0.438504274 313.7230121 -2.496546376 0.46508216 SNS(ph)GRELTDEEILASVMIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.194)NS(0.76)GRELT(0.046)DEEILASVMIK;S(0.48)NS(0.52)GRELT(0.001)DEEILASVMIK 234.18 6.00E-24 623670000 521360 415630 552580 374100 675570 663180 584530 529790 560040 423520 TRUE FALSE 541943.6954 487011.2193 566980.6887 448095.8634 560736.8527 509166.4956 538713.0112 522689.0316 539884.2698 506500.6352 1.069976339 0.961521438 1.119407656 0.884689638 1.107080256 1.005263291 1.063597899 1.031961256 1.065910351 1 18.95020455 SNS(ph)ISQIPSLEEMQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SNSISQIPSLEEMQQLR 17 0 A0A1B0GV57;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 S(0.05)NS(0.95)ISQIPSLEEMQQLR;S(0.001)NS(0.999)IS(0.001)QIPSLEEMQQLR;S(0.028)NS(0.958)IS(0.013)QIPSLEEMQQLR;SNS(0.773)IS(0.227)QIPSLEEMQQLR;S(0.042)NS(0.957)IS(0.001)QIPSLEEMQQLR;S(0.17)NS(0.825)IS(0.004)QIPSLEEMQQLR;S(0.048)NS(0.95)IS(0.001)QIPSLEEMQQLR 365.02 1.39E-104 854111000 761861 900514 882427 806790 1038137 1119051 871119 919447 966277 868883 TRUE FALSE 791939.8606 1055170.274 905423.7725 966370.654 861674.8436 859168.3646 802838.4165 907123.3169 931500.8795 1039123.988 0.762122586 1.015442129 0.871333722 0.929985897 0.829231981 0.826819874 0.772610801 0.872969277 0.896429002 1 19.98693638 5.036134856 15.24044557 0.878354753 0.349047403 0.203343361 0.072740594 895242.3841 11113035.46 0.017141929 12595359.89 108676.3029 -5.036134856 -0.52930735 SNS(ph)LDKHQQSSTLGNSVVR ddPTM_MDA-MB-175_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(0.175)NS(0.825)LDKHQQSSTLGNSVVR;S(0.003)NS(0.97)LDKHQQS(0.006)S(0.01)T(0.01)LGNS(0.001)VVR 279.69 8.06E-40 670550000 882920 533510 805780 564510 1032610 1019280 948790 799690 836190 507380 TRUE FALSE 917778.3634 625136.1924 826779.2888 676168.3931 857087.321 782567.6673 874421.3606 788971.4636 806095.6852 606791.3966 1.512510508 1.030232459 1.362542866 1.11433418 1.412490892 1.289681547 1.441057611 1.300235086 1.328456022 1 19.2108411 -0.915827245 4.687879921 0.999998359 1.305446652 0.31362334 0.137497701 7985676.857 1703472.94 207.0212922 0.029323863 0.121387161 0.915827245 0.305448293 SNS(ph)LNNGQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSLNNGQPK 10 0 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 S(0.002)NS(0.998)LNNGQPK;SNS(1)LNNGQPK 159.77 7.95E-06 122357000 247720 178186 219282 173451 305000 323540 288820 241380 283500 151706 TRUE FALSE 257500.1769 208788.0594 224996.6691 207759.0901 253156.2089 248402.7383 266181.5337 238144.6959 273296.8904 181429.8861 1.419282029 1.150791988 1.240130134 1.145120545 1.395339072 1.36913903 1.467131681 1.312599049 1.506349898 1 17.4690526 3.222719996 24.99157232 1.363773212 1.23263543 0.09373447 0.147049782 414.5485887 654027.3516 0.038961384 0.046709402 1670.013556 -3.222719996 -0.131137783 SNS(ph)LPHSAVSNAGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.18)NS(0.798)LPHS(0.022)AVSNAGSK;S(0.152)NS(0.848)LPHSAVSNAGSK;S(0.169)NS(0.831)LPHSAVSNAGSK;SNS(0.999)LPHS(0.001)AVSNAGSK;S(0.011)NS(0.843)LPHS(0.143)AVS(0.002)NAGSK 255.98 6.23E-25 4021183000 2395371 2336195 3396820 2630219 4164960 4111390 3895540 3466080 3758960 2472478 TRUE FALSE 2489942.097 2737418.318 3485343.92 3150468.468 3457001.587 3156581.981 3590197.396 3419622.867 3623675.764 2956912.726 0.842074937 0.925769061 1.178710447 1.065458727 1.169125337 1.067526259 1.214170904 1.156484206 1.225492972 1 21.49566023 4.342961111 4.161665306 1.141568395 0.860233342 0.684585536 0.068707838 0.10323436 3.14367369 0.015886875 0.048290051 22027.29209 -4.342961111 -0.281335053 SNS(ph)LRRDS(ph)PPPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSLRRDSPPPPAR 14 2 O96013;O96013-4;O96013-2;M0R2X4 O96013 PAK4 Serine/threonine-protein kinase PAK 4 2 S(0.293)NS(0.707)LRRDS(0.999)PPPPAR 83.167 0.042691 1207400000 479590 525160 601550 533830 678480 769370 593480 572870 560620 542440 TRUE FALSE 498524.5835 615352.1448 617226.8872 639419.9807 563152.2119 590695.4774 546961.4868 565191.6147 540443.3957 648720.7324 0.768473333 0.948562477 0.951452384 0.985662934 0.868096523 0.910554339 0.843138595 0.871240253 0.833090988 1 19.30723802 SNS(ph)LSEQLAINTSPDAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.034)NS(0.71)LS(0.257)EQLAINTSPDAVK;S(0.005)NS(0.992)LS(0.004)EQLAINTSPDAVK 435.45 2.31E-169 579290000 710260 467210 643030 595110 1050850 995340 982660 774740 910490 606470 TRUE FALSE 738301.6132 547449.6831 659787.8901 712820.9818 872226.8924 764187.3695 905636.5415 764355.8775 877721.6428 725296.1849 1.017931196 0.754794654 0.909680629 0.98279985 1.202580284 1.053621107 1.248643741 1.053853437 1.210156156 1 19.46821073 3.474886081 3.245172046 1.130148185 0.882920693 0.551373124 0.095399107 0.16066628 3.512939054 0.02484539 0.037426765 2984.599631 -3.474886081 -0.247227493 SNS(ph)LSTPRPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SNS(0.473)LS(0.258)T(0.258)PRPT(0.01)R;SNS(0.475)LS(0.26)T(0.26)PRPT(0.005)R 89.43 0.032195 425250000 449800 529540 574130 496430 685260 696850 581460 594010 610440 522630 TRUE FALSE 467558.4513 620484.3758 589092.2995 594622.3723 568779.75 535017.1484 535883.6458 586048.2676 588470.3836 625029.3421 0.748058403 0.992728395 0.942503431 0.951351132 0.910004878 0.855987251 0.857373582 0.937633209 0.941508412 1 19.25356439 1.03587313 1.734671435 0.997823729 0.902048466 0.199805172 0.064033257 0.604156477 3.710760892 0.05871264 0.016922655 10.86108293 -1.03587313 -0.095775263 SNS(ph)LVSTFTMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SNSLVSTFTMEK 12 0 Q9HB21 Q9HB21 PLEKHA1 Pleckstrin homology domain-containing family A member 1 1 S(0.002)NS(0.945)LVS(0.032)T(0.02)FT(0.001)MEK;S(0.026)NS(0.966)LVS(0.008)T(0.001)FTMEK;SNS(1)LVSTFTMEK;S(0.001)NS(0.998)LVS(0.001)TFTMEK;SNS(0.957)LVS(0.043)TFTMEK;SNS(0.745)LVS(0.253)T(0.001)FTMEK;S(0.001)NS(0.999)LVSTFTMEK;S(0.206)NS(0.79)LVS(0.003)T(0.001)FTMEK 238.01 4.21E-16 1511228000 3342004 2533802 3019382 2471719 4490608 3923912 3473893 3066813 3067900 2266389 TRUE FALSE 3473948.899 2968962.783 3098069.575 2960617.641 3727296.056 3012642.905 3201600.189 3025707.388 2957486.878 2710444.532 1.281689722 1.095378543 1.143011613 1.09229966 1.375160426 1.111494026 1.181208526 1.116314078 1.091144587 1 21.37009805 1.123950434 1.068587747 1.0025221 1.181601368 0.329575155 0.083477451 0.575147714 1.389289921 0.075497099 0.024887428 13.30302583 -1.123950434 0.179079267 SNS(ph)MLELAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SNSMLELAPK 10 0 Q9P2M7;Q9P2M7-2;A6PVU7;A2A3M4 Q9P2M7 CGN Cingulin 1 SNS(1)MLELAPK;S(0.004)NS(0.996)MLELAPK;SNS(1)MLELAPK;S(0.001)NS(0.999)MLELAPK;S(0.001)NS(0.999)MLELAPK;S(0.044)NS(0.956)MLELAPK 169.55 4.82E-06 1438620000 3064170 2140190 2822410 2132490 3840860 3442430 3067160 2740890 2890870 1905050 TRUE FALSE 3185145.798 2507750.984 2895964.323 2554290.157 3187991.989 2642977.803 2826747.985 2704152.853 2786828.153 2278308.073 1.398031212 1.100707588 1.271103042 1.121134664 1.399280469 1.160061641 1.240722455 1.186912729 1.223200754 1 21.11953141 -4.320469419 0.262263981 1.49E-07 1.247237697 0.356985484 0.09589218 140.9477462 1.925689123 75.38224459 0.113583325 4.78E-05 4.320469419 1.247237548 SNS(ph)PDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SNSPDKFK 8 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 S(0.001)NS(0.999)PDKFK;S(0.004)NS(0.996)PDKFK;S(0.019)NS(0.981)PDKFK;S(0.098)NS(0.902)PDKFK;SNS(1)PDKFK;SNS(1)PDKFK 117.86 0.0012099 5920560000 15482610 4662820 7236820 5054400 10529480 11391970 12199880 7356370 7937390 3020377 TRUE FALSE 16093875.4 5463623.063 7425417.474 6054145.234 8739682.751 8746357.614 11243621.53 7257769.893 7651724.884 3612162.045 4.45546883 1.512563112 2.055671197 1.676044751 2.419515693 2.421363579 3.112712383 2.00925922 2.118322708 1 21.78443118 4.747922321 24.95409034 2.124740288 4.45547009 0.633226758 0.548656921 804.8040005 2145199.888 0.127784699 1.623725962 55965.74907 -4.747922321 2.330729802 SNS(ph)PGTASSGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSPGTASSGSSR 13 0 Q96GY0;H0YAP0 Q96GY0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 SNS(0.86)PGT(0.139)ASSGSSR 124.5 0.00012678 0 111430 123940 156500 113770 148550 161350 143280 134820 145940 127370 TRUE FALSE 115829.3424 145225.7309 160578.5186 136273.3664 123299.5241 123878.9078 132049.3392 133012.9584 140687.6479 152325.7129 0.760405714 0.953389472 1.054178678 0.894618275 0.809446559 0.813250143 0.866888044 0.873214088 0.923597502 1 17.21679997 4.752860161 24.05143976 0.900606152 0.760405549 0.261317311 0.073920617 2328.468192 3916304.648 0.018984927 0.383618616 56605.69947 -4.752860161 -0.140200603 SNS(ph)PLPVPPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 S(0.013)NS(0.987)PLPVPPSK;SNS(1)PLPVPPSK;S(0.063)NS(0.937)PLPVPPSK;S(0.039)NS(0.961)PLPVPPSK;SNS(1)PLPVPPSK;SNS(1)PLPVPPSK;S(0.005)NS(0.995)PLPVPPSK;S(0.055)NS(0.945)PLPVPPSK 150.26 3.56E-05 13972740000 13345460 8213680 11245570 8825840 15166050 14612960 15604680 11546950 12534960 7182360 TRUE FALSE 13872349.07 9624315.646 11538638.79 10571564.81 12588130.24 11219321.5 14381544.41 11392182.02 12083829.24 8589605.927 1.615015774 1.120460674 1.343325746 1.23073921 1.465507306 1.306150899 1.674296182 1.326275282 1.406796696 1 23.03416051 -0.754734285 6.419469289 0.999999997 1.382194989 0.351548464 0.157778025 8.55E-09 1.67E-09 0.143479564 0.033818457 0.17589995 0.754734285 0.382194993 SNS(ph)QSYIGRPIHLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSQSYIGRPIHLDK 15 1 F8WBA3;Q15139 F8WBA3 PRKD1 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 1 S(0.292)NS(0.562)QS(0.147)YIGRPIHLDK;S(0.197)NS(0.802)QS(0.002)YIGRPIHLDK 122.53 6.54E-05 600200000 782590 558380 675880 561350 912810 912720 779590 674930 736640 539890 TRUE FALSE 813487.2575 654277.4214 693493.988 672383.3545 757650.8822 700754.6124 718483.6987 665883.6673 710128.4703 645671.1087 1.259909645 1.013329252 1.074066934 1.041371289 1.1734316 1.085312016 1.112770401 1.031304728 1.099830023 1 19.30043995 0.486209272 0.012717645 6.37E-07 2.1073189 0.211237421 0.066758177 2484.646029 13.43873601 1147.346577 1077.676984 3.063439248 -0.486209272 2.107318263 SNS(ph)SEALLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSSEALLVDR 11 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 SNS(0.907)S(0.093)EALLVDR;S(0.008)NS(0.966)S(0.025)EALLVDR 186.08 0.0008329 0 183436 203402 219420 167001 225130 263940 244740 192687 205050 182492 TRUE FALSE 190678.1949 238334.7113 225138.2655 200033.2994 186862.483 202643.935 225556.6393 190104.3459 197670.2906 218247.8134 0.873677459 1.092037109 1.031571689 0.916542055 0.856194067 0.92850385 1.033488656 0.871048113 0.905714873 1 17.73560767 3.732199756 24.52143159 0.924885614 1.008389589 0.156630575 0.071544181 567.0113751 2185860.605 0.018531883 0.029508778 5397.588304 -3.732199756 0.083503975 SNS(ph)TTQVSQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSTTQVSQPR 11 0 I3L2J8;Q9UPN4-3;Q9UPN4-2;Q9UPN4 I3L2J8 CEP131 Centrosomal protein of 131 kDa 1 SNS(0.82)T(0.165)T(0.015)QVSQPR;SNS(0.966)T(0.031)T(0.002)QVSQPR 240.75 2.91E-06 0 323700 393740 443920 341160 442660 470300 453460 420600 373770 311160 TRUE FALSE 336479.926 461361.7821 455488.9199 408640.4297 367416.8113 361079.9525 417916.6203 414962.545 360318.0907 372125.8445 0.904210043 1.23980043 1.224018505 1.098124293 0.98734559 0.970316783 1.123051856 1.115113479 0.968269461 1 18.50543106 3.471342517 23.41774475 1.042518291 1.138835845 0.148272367 0.099916312 125.9851382 510536.9899 0.027925209 0.037952878 2960.346298 -3.471342517 0.096317554 SNS(ph)VEKPVSSILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSVEKPVSSILSR 14 1 H0YJN0;Q9UI08-5;Q9UI08;Q9UI08-2;Q9UI08-4;Q9UI08-3 H0YJN0 EVL Ena/VASP-like protein 1 S(0.001)NS(0.999)VEKPVSSILSR;S(0.015)NS(0.985)VEKPVSSILSR 96.562 0.0020119 160600000 327320 207425 288540 177996 466000 366070 347410 311210 327290 193929 TRUE FALSE 340242.8463 243048.6302 296059.5894 213203.0775 386789.4865 281055.7903 320179.0964 307038.739 315510.8968 231925.6746 1.467033984 1.047959139 1.276527879 0.919273288 1.66773035 1.211835606 1.380524588 1.323866965 1.36039659 1 17.82330301 3.255692095 24.99994658 1.337516141 1.175490887 0.107320324 0.204556019 485.7702268 708879.6525 0.051912071 0.070117135 1801.739894 -3.255692095 -0.162025254 SNS(ph)WVNTGGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSWVNTGGPK 11 0 Q96N67-2;Q96N67-6;Q96N67;A0A1B0GWE0;A0A0U1RRC1 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 S(0.005)NS(0.995)WVNTGGPK;S(0.001)NS(0.999)WVNTGGPK 108.58 0.0013386 0 272930 169295 232507 164303 307430 316880 257365 217297 252948 157433 TRUE FALSE 283705.4871 198370.0993 238566.3234 196801.643 255173.1584 243289.4224 237192.0588 214384.4891 243844.4509 188278.9821 1.506835675 1.053596621 1.267089511 1.04526613 1.355292851 1.292175152 1.259790425 1.138653326 1.295123057 1 17.52251243 -3.497323004 0.417363428 5.23E-09 1.237778167 0.231490919 0.132501999 328.5901277 7.511548998 290.4187408 0.072072015 0.000318183 3.497323004 1.237778162 SNSFFEGVDWEHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SNSFFEGVDWEHIR 14 0 Q15208 Q15208 STK38 Serine/threonine-protein kinase 38 0 ;; 138.19 1.69E-05 237423000 156344 177876 194537 196621 207319 248949 213138 202186 195825 209650 FALSE TRUE 162516.5818 208424.8193 199606.794 235512.0469 172078.9904 191134.3676 196431.6866 199476.0274 188777.2965 250726.9035 0.648181665 0.831282229 0.796112389 0.939317016 0.686320407 0.762320935 0.78344878 0.795590838 0.752919985 1 17.93575728 -1.980097084 2.261863689 1.196162888 0.782388494 0.442759096 0.074761343 7924387.837 3136592.827 8124529.239 0.017567204 0.010468945 1.980097084 -0.413774394 SNSFS(ph)DER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.003)NS(0.202)FS(0.795)DER 150.22 0.0005168 887130000 1531000 1445800 1357800 1480200 1338200 1817000 1683300 1294000 1263500 941420 TRUE FALSE 1591445.062 1694104.903 1393185.383 1772979.142 1110733.242 1395029.287 1551358.548 1276656.047 1218026.882 1125873.224 1.413520659 1.504703075 1.237426518 1.574759132 0.986552676 1.239064272 1.377915838 1.133925223 1.08185083 1 20.10261296 7.897861841 0.105614535 0.842209942 2.719304105 0.448600782 0.146103056 100.6284359 0.762515662 1.466303207 27.40545313 79042713.6 -7.897861841 1.877094163 SNSGRELT(ph)DEEILASVMIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 S(0.064)NS(0.064)GRELT(0.871)DEEILASVMIK 119.06 0.00010837 40558000 29462 22413 33479 20144 40273 39937 30915 29178 37239 26488 TRUE FALSE 30625.18251 26262.2584 34351.49024 24128.42308 33427.40985 30662.237 28491.80152 28786.91664 35898.77566 31677.81646 0.966770628 0.829042571 1.084402086 0.761682015 1.055230871 0.967940358 0.899424414 0.908740559 1.133246533 1 14.95118527 1.250131728 24.98939107 1.066623278 0.932195172 0.235601575 0.095391031 245.7691237 530778.9662 0.05908141 0.021182649 17.78818871 -1.250131728 -0.134428106 SNSIS(ph)QIPSLEEMQQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSISQIPSLEEMQQLR 17 0 A0A1B0GV57;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 S(0.001)NS(0.326)IS(0.674)QIPSLEEMQQLR 195.77 1.74E-11 370700000 215410 254360 248400 208790 310370 296710 243710 265730 262140 242440 TRUE FALSE 223914.5531 298044.3514 254873.5081 250088.0388 257613.4183 227803.5992 224607.3734 262168.324 252705.6326 289941.4762 0.772274999 1.027946589 0.879051564 0.862546615 0.888501437 0.785688209 0.774664516 0.904211179 0.871574622 1 18.1454022 5.042050549 15.55084061 0.878364033 0.294109881 0.16314607 0.075881651 3081550.314 32347868.27 0.017883532 51264050.92 110166.7528 -5.042050549 -0.584254152 SNSLS(ph)TPRPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 SNS(0.162)LS(0.279)T(0.279)PRPT(0.279)R 100.73 0.010032 134110000 103250 102210 120130 95241 141560 145070 119120 116620 124520 90923 TRUE FALSE 107326.3897 119763.7724 123260.6865 114079.3855 117497.6818 111379.6911 109783.0631 115056.8997 120038.5495 108737.621 0.987021683 1.10140144 1.133560633 1.049125266 1.080561453 1.024297663 1.009614355 1.058114924 1.103928414 1 16.73049164 2.751256082 23.97555655 1.041531939 1.074394378 0.104915035 0.044440462 1035.424815 1955410.803 0.013694871 0.014426864 563.9701036 -2.751256082 0.032862439 SNSLSEQLAINTS(ph)PDAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 SNSLSEQLAINT(0.032)S(0.968)PDAVK;S(0.001)NS(0.001)LS(0.001)EQLAINT(0.171)S(0.827)PDAVK 258.81 1.19E-30 85247000 235021 171605 195599 150804 243907 244695 227816 191847 200066 140470 TRUE FALSE 244299.8106 201076.8238 200696.4706 180632.5811 202447.7753 187868.2946 209959.1866 189275.6048 192865.6637 167992.407 1.454231265 1.196939953 1.194675844 1.075242532 1.205100747 1.118314202 1.24981355 1.126691427 1.148061791 1 17.3580365 4.957837537 1.702455544 1.146716512 1.71764492 0.667445531 0.066293734 1.007207166 1.813084329 0.015698352 1.115034439 90748.09923 -4.957837537 0.570928408 SNSS(ph)EALLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNSSEALLVDR 11 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 S(0.002)NS(0.344)S(0.653)EALLVDR 105.17 0.0018492 0 60625 54013 63469 55127 63036 76978 60705 50846 69476 48296 TRUE FALSE 63018.52181 63289.31259 65123.05428 66030.95606 52321.16324 59101.02611 55946.78348 50164.49254 66975.57233 57758.67652 1.09106589 1.095754204 1.127502537 1.143221418 0.90585807 1.023240657 0.968629942 0.868518733 1.159575952 1 15.81775006 3.248432109 24.99816025 0.973861473 1.113992084 0.403757476 0.074334019 184.0330485 466034.6704 0.020376163 0.027260518 1771.871038 -3.248432109 0.140130611 SNT(ph)LDIMDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNTLDIMDGR 10 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 S(0.003)NT(0.997)LDIMDGR;S(0.002)NT(0.998)LDIMDGR 139.74 0.0090455 0 841060 725880 901820 806650 1211300 1233170 1014340 937040 959780 653290 TRUE FALSE 874265.6982 850544.2434 925322.1701 966202.9624 1005403.659 946784.9564 934833.3803 924480.5115 925237.7053 781289.6675 1.119003277 1.088641356 1.184352243 1.236677 1.286851344 1.211823215 1.196525974 1.183274975 1.184244133 1 19.57549801 4.174867464 5.566727183 1.19869587 1.103934278 0.15832485 0.070618441 0.253586565 14.94391529 0.016568009 0.037719179 14957.79111 -4.174867464 -0.094761592 SNT(ph)LNEKPALPVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNTLNEKPALPVIR 14 1 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WZS7;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.189)NT(0.811)LNEKPALPVIR 114.52 0.00076435 452890000 246300 169760 238990 209650 374210 321860 244930 239320 219200 167490 TRUE FALSE 256024.1142 198914.9595 245218.2757 251118.1443 310601.9179 247112.8928 225731.7466 236112.3068 211311.0348 200306.4587 1.278162051 0.993053148 1.224215521 1.253669731 1.550633564 1.233674113 1.126931942 1.178755335 1.054938698 1 17.61184941 1.396815046 1.233808009 1.005047359 1.247292819 0.305181733 0.129722335 0.580015534 1.708277083 0.126754476 0.042149217 24.93532572 -1.396815046 0.242245461 SNT(ph)PTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNTPTPR 7 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9;Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4E4;H7C4W5;H0Y5S0;H7C4P7;Q5JSY7 H0YKT5;Q04727-4 TLE3;TLE4 Transducin-like enhancer protein 3;Transducin-like enhancer protein 4 1 S(0.01)NT(0.982)PT(0.008)PR 111.61 0.073118 127180000 151310 151820 147430 129380 205470 236280 177280 183260 155180 113620 TRUE FALSE 157283.8356 177893.904 151272.1469 154970.9778 170544.2828 181407.5509 163384.3304 180803.6995 149595.1021 135881.6636 1.157505961 1.309182558 1.113263872 1.140484843 1.255094162 1.335040697 1.202401605 1.330596746 1.100921921 1 17.05199126 1.019934597 6.226522835 1.000203368 1.233410346 0.504194993 0.074728772 0.107014067 14.7926604 0.072760278 0.018285819 10.46970868 -1.019934597 0.233206979 SNTENLSQHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SNTENLSQHFR 11 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;;; 252.21 2.22E-20 2798230000 707840 1841630 1744180 1730050 2030410 2294010 1685870 1855800 1630320 2126380 FALSE TRUE 735786.0698 2157915.627 1789634.764 2072248.726 1685281.633 1761260.944 1553727.104 1830926.036 1571645.102 2543003.449 0.289337425 0.848569681 0.703748461 0.814882389 0.662713074 0.692590859 0.610981123 0.719985668 0.618027122 1 21.27810199 -2.245041637 2.270251705 2.168139557 0.67559577 0.325660176 0.144645529 9720260.886 1348581.032 58484242.81 0.032403523 0.005687984 2.245041637 -1.492543787 SNTEPQS(ph)PPIASPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNTEPQSPPIASPK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SNTEPQS(1)PPIASPK;SNTEPQS(1)PPIASPK 159.18 2.43E-07 0 139450 102917 122549 105532 165846 171798 150000 134947 148394 92143 TRUE FALSE 144955.5937 120592.1942 125742.7276 126405.9146 137655.5562 131900.5181 138242.608 133138.2562 143053.3289 110196.6567 1.315426421 1.094336233 1.141075704 1.147093918 1.249180876 1.196955716 1.254508188 1.2081878 1.298163967 1 16.74972093 3.250040245 24.97282136 1.214553509 1.166372054 0.004358201 0.091971449 659.6905779 1435084.631 0.023561498 0.031620007 1778.444207 -3.250040245 -0.048181455 SNTEPQSPPIAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SNTEPQSPPIASPK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK 274.89 4.96E-33 1282780000 1752590 767360 991060 793350 1502020 1847610 1407730 1226890 1255440 682160 TRUE FALSE 1821783.606 899148.1108 1016887.838 950272.2621 1246707.177 1418530.578 1297388.444 1210445.546 1210256.96 815816.1913 2.233080964 1.102145459 1.24646685 1.164811721 1.528171652 1.738786988 1.590295042 1.483723367 1.483492204 1 19.63788461 0.472687591 3.627851537 1.00000005 1.488939164 0.195615415 0.306833915 95.13831725 650.9485715 0.286060597 0.073537322 2.969529138 -0.472687591 0.488939114 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETR 38 1 P13639 P13639 EEF2 Elongation factor 2 0 165.49 4.13E-18 435230000 181490 217800 220970 195040 234060 275520 181190 209020 211720 186240 FALSE TRUE 188655.3653 255205.4558 226728.6597 233618.3299 194274.5648 211534.6555 166987.8543 206218.4288 204100.2386 222730.1622 0.847013101 1.145805549 1.017952205 1.048885016 0.872241832 0.949735112 0.74973166 0.925866648 0.91635653 1 17.76493742 3.237419959 24.99913547 0.892308834 1.024480395 0.25921323 0.091751385 34.28082877 751321.1404 0.024602134 0.031025267 1727.50757 -3.237419959 0.132171561 SNVSDAVAQSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVSDAVAQSTR 12 0 P60174;P60174-3;P60174-4 P60174 TPI1 Triosephosphate isomerase 0 81.92 0.025892 0 106280 56741 62610 54578 73200 105510 85047 60182 67870 66128 FALSE TRUE 110476.0165 66485.82537 64241.66803 65373.3655 60757.49015 81006.90152 78380.79391 59375.35873 65427.37196 79084.5155 1.396936123 0.840693339 0.812316642 0.826626617 0.768260256 1.024307995 0.991101651 0.750783619 0.827309512 1 16.27110763 4.739985368 24.69078303 0.862332989 1.396936333 0.736906461 0.094092467 52.55516006 910667.3601 0.022935157 0.144063765 54952.23588 -4.739985368 0.534603344 SNVSSPATPTASSSSS(ph)TTPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTAS(0.004)S(0.021)S(0.016)S(0.061)S(0.4)T(0.287)T(0.208)PT(0.004)RK 102.39 0.00015249 0 23118 16547 20901 17696 27918 29707 26245 24584 20089 16851 TRUE FALSE 24030.71649 19388.81853 21445.69723 21196.21598 23172.50833 22807.99946 24187.84832 24254.49169 19366.00081 20152.63082 1.192435703 0.962098632 1.064163653 1.051784066 1.149850287 1.131762878 1.20023279 1.203539722 0.960966386 1 14.29868057 3.243947755 24.89457839 1.130909891 1.059836305 0.004670341 0.091475264 273.0078729 1261591.791 0.024910414 0.03278302 1753.669526 -3.243947755 -0.071073586 SNVSSPATPTASSSSST(ph)TPTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.006)T(0.775)T(0.218)PT(0.001)RK 200.97 9.28E-23 97409000 38815 33306 39986 31780 50644 50012 41538 44080 41350 33027 TRUE FALSE 40347.44617 39026.04642 41028.06801 38065.98915 42035.55097 38397.47094 38282.14302 43489.1797 39861.82158 39498.00831 1.02150584 0.988050995 1.038737642 0.963744522 1.064244826 0.972136889 0.969217048 1.101047409 1.009210927 1 15.26949229 1.756323926 25 1.046693198 1.003070201 0.120595416 0.039710104 10.73556769 15125.04748 0.017232673 0.009556456 57.05896971 -1.756323926 -0.043622997 SNVSSPATPTASSSSSTT(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSS(0.002)S(0.025)T(0.102)T(0.859)PT(0.013)R 213.48 4.29E-22 277380000 83002 98162 93569 88652 106390 131800 96566 109290 102240 92578 TRUE FALSE 86278.98305 115020.5599 96007.48501 106187.101 88305.8658 101191.4474 88996.90459 107825.1463 98560.40237 110716.8866 0.779275734 1.038870975 0.86714401 0.959086769 0.797582632 0.913965797 0.803824126 0.973881669 0.890202077 1 16.75651575 0.682547894 1.015153484 0.998579466 0.891299233 0.144179809 0.079506407 2.026524728 3.575485683 0.069931428 0.022445358 4.814463446 -0.682547894 -0.107280232 SNVSSPATPTASSSSSTT(ph)PTRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNVSSPATPTASSSSSTTPTRK 22 1 Q12888;Q12888-2;A6NNK5;Q12888-3;H7BZY0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 SNVSSPATPTASSSSS(0.006)T(0.241)T(0.729)PT(0.023)RK;SNVSSPATPTASSSS(0.006)S(0.015)T(0.275)T(0.68)PT(0.023)RK 205.59 6.04E-23 503180000 214010 163279 171195 158059 245940 235950 204333 194878 201230 165110 TRUE FALSE 222459.2801 191320.8981 175656.4823 189322.5984 204135.2066 181154.1884 188316.8455 192265.9792 193987.7716 197460.1433 1.126603457 0.96890894 0.889579433 0.958788925 1.033804611 0.917421538 0.953695477 0.973695126 0.982414822 1 17.59120195 4.735580018 5.981431446 0.961450822 1.130890403 0.620543628 0.038066362 0.080386679 13.91882088 0.009022338 0.055696433 54397.63486 -4.735580018 0.169439581 SNVVS(ph)PTKNEDNGAPENSVEKPHEKPEAR ddPTM_MDA-MB-175_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 SNVVS(0.5)PT(0.5)KNEDNGAPENSVEKPHEKPEAR;S(0.001)NVVS(0.856)PT(0.143)KNEDNGAPENSVEKPHEKPEAR 269.13 3.49E-59 1467110000 2407200 708650 1259430 697500 1892200 1686020 1888950 1241520 1503840 467220 TRUE FALSE 2502238.115 830355.125 1292251.78 835463.4182 1570564.52 1294467.407 1740889.163 1224879.455 1449717.092 558762.8135 4.478175809 1.486060104 2.312701828 1.495202254 2.810789268 2.316667064 3.115613854 2.192127725 2.594512478 1 19.09187648 -1.445059101 2.675391917 0.951920625 2.471686462 0.239180365 0.813827991 11836336.82 12442036.95 4281117.628 0.190798904 0.035887309 1.445059101 1.519765837 SNVVSPT(ph)KNEDNGAPENSVEKPHEKPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SNVVSPTKNEDNGAPENSVEKPHEKPEAR 29 3 Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4;X6RLN4;Q71RC2-2;Q71RC2-6 Q71RC2-5 LARP4 La-related protein 4 1 SNVVS(0.188)PT(0.812)KNEDNGAPENSVEKPHEKPEAR 174.06 5.96E-13 441930000 591970 177060 285710 172010 491350 432330 442650 323200 358640 113140 TRUE FALSE 615341.4327 207468.6777 293155.8373 206033.0646 407830.5025 331927.9095 407953.9363 318868.0326 345732.6165 135307.6168 4.547722052 1.533311151 2.166587841 1.522701157 3.014098631 2.453135436 3.015010877 2.356615542 2.555160047 1 17.04588353 -0.467053214 6.720467471 0.999999969 2.516581044 0.246345463 0.82034777 0 0 0.734323064 0.173081606 0.341151108 0.467053214 1.516581074 SNYNFEKPFLWLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 192.32 3.54E-07 9833700000 5783300 5426500 5737800 4663900 8084200 7983400 6793600 6743200 6114100 6720000 FALSE TRUE 6011629.15 6358459.163 5887331.782 5586405.5 6710050.572 6129376.34 6261099.88 6652818.434 5894054.735 8036655.338 0.748026249 0.791182264 0.732559944 0.695115725 0.834930738 0.762677517 0.779067861 0.82780935 0.73339648 1 22.93816378 -5 0.256066399 2.445252037 0.751440263 0.737760958 0.041502149 93.40013162 0.921243292 70.84101185 0.055448505 1.00E-05 5 -1.693811774 SNYNLPMHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SNYNLPMHK 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 ; 132.01 0.00031705 2650800000 3397700 3202200 3930400 3105600 4521400 4911000 4260300 3981400 3701900 3025500 FALSE TRUE 3531843.82 3752152.94 4032829.453 3719878.411 3752854.043 3770494.677 3926366.554 3928035.845 3568669.342 3618288.798 0.976108878 1.036996533 1.11456815 1.028076701 1.0371903 1.042065708 1.085144601 1.085605949 0.986286485 1 21.78687613 2.408122561 24.99998882 1.053431726 1.041882994 0 0.043875049 329.8234547 119498.1345 0.015449559 0.012926028 255.9308042 -2.408122561 -0.011548731 SPAAET(ph)PPLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPAAETPPLQR 11 0 Q8TE68;B4DKV7;Q8TE68-2;K7EN83;Q8TE68-3;K7EKX9 Q8TE68 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein 1 1 S(0.002)PAAET(0.998)PPLQR;S(0.001)PAAET(0.999)PPLQR;S(0.062)PAAET(0.938)PPLQR 121.66 0.0045505 2111820000 805420 935890 904970 948130 956770 1158600 939090 941530 865030 932690 TRUE FALSE 837218.6035 1096621.827 928554.2616 1135667.284 794138.5771 889532.7088 865481.6719 928910.3304 833897.7393 1115432.748 0.750577392 0.983135764 0.832461001 1.018140525 0.711955587 0.79747767 0.775915602 0.832780221 0.747600194 1 20.0891721 3.227114779 24.99996892 0.801840451 0.897752937 0.144869029 0.099821855 349.8448885 764128.8613 0.026297427 0.031686635 1686.99882 -3.227114779 0.095912486 SPAAPYFLGSS(ph)FSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGS(0.142)S(0.461)FS(0.397)PVR 68.257 0.036264 0 11692 16375 20197 14136 19011 22572 16383 18489 17343 19367 TRUE FALSE 12153.60919 19187.27887 20723.35041 16932.05861 15779.51701 17329.99508 15098.85765 18241.1852 16718.82882 23161.59285 0.524731147 0.828409298 0.894729069 0.731040336 0.68127944 0.748221212 0.651892024 0.787561776 0.721834156 1 14.49944685 -1.195084162 1.085783754 1.035148152 0.737044105 0.415622864 0.095714368 368.5128649 149.3104664 42.0863743 0.027756119 0.063813981 1.195084162 -0.298104047 SPAAPYFLGSSFS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPAAPYFLGSSFSPVR 16 0 P30291 P30291 WEE1 Wee1-like protein kinase 1 SPAAPYFLGSS(0.026)FS(0.974)PVR;SPAAPYFLGSS(0.008)FS(0.992)PVR 137.61 1.16E-05 101628000 84156 95728 84702 89161 111976 117405 109890 95689 104943 95137 TRUE FALSE 87478.54386 112168.5393 86909.4037 106796.7797 92942.35952 90139.46804 101276.5347 94406.44547 101166.1219 113777.2736 0.768857796 0.985860671 0.763855566 0.93864773 0.816879826 0.792244929 0.890129737 0.829747826 0.889159308 1 16.79585289 0.898069591 4.536729388 0.999984272 0.851328622 0.308444369 0.068440142 0.664363019 27.33773689 0.058420015 0.014830135 7.908053362 -0.898069591 -0.14865565 SPADPIDLGGQT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPADPIDLGGQTSPR 15 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.64)S(0.36)PR 155.22 2.62E-05 126460000 241490 223350 237930 219720 282920 268690 237480 215440 219280 234280 TRUE FALSE 251024.2117 261708.6251 244130.6513 263179.9602 234829.3595 206290.8195 218865.6971 212552.3792 211388.1556 280182.6804 0.89593051 0.934064249 0.871326703 0.939315591 0.838129463 0.736272561 0.781153556 0.758620693 0.754465463 1 18.09600825 3.035059825 4.969438025 0.786427354 0.908190356 0.294668956 0.072921902 0.185684863 11.25409759 0.019793744 0.023371523 1084.076237 -3.035059825 0.121763003 SPADPIDLGGQT(ph)SPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPADPIDLGGQTSPRR 16 1 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.5)S(0.5)PRR 58.366 0.064822 265280000 216690 254030 237410 229630 247120 273540 218190 241280 227150 250320 TRUE FALSE 225245.0885 297657.6764 243597.0996 275050.1286 205114.6307 210014.4805 201087.6977 238046.0363 218974.9159 299365.4113 0.752408528 0.994295484 0.813711573 0.918777248 0.685164762 0.701532216 0.671713197 0.795168805 0.731463648 1 18.19154802 3.243682713 24.99949784 0.747825085 0.874684689 0.181765694 0.10624678 169.9230536 829340.9268 0.027438331 0.0360555 1752.599617 -3.243682713 0.126859604 SPADPIDLGGQTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPADPIDLGGQTSPR 15 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.194)S(0.806)PR;SPADPIDLGGQT(0.155)S(0.845)PR;SPADPIDLGGQT(0.001)S(0.999)PR;SPADPIDLGGQT(0.011)S(0.989)PR 210.91 1.72E-09 4146430000 3170650 3802650 3617150 3470090 3543620 4191570 3508300 3490060 3349030 3701890 TRUE FALSE 3295829.71 4455725.557 3711415.901 4156463.445 2941276.738 3218141.391 3233310.279 3443281.454 3228499.064 4427204.469 0.7444494 1.006442234 0.838320418 0.938846054 0.664364332 0.72690146 0.73032775 0.777755236 0.729241011 1 22.07796457 3.249974941 24.9998663 0.756934109 0.887781217 0.202431492 0.104947107 277.6858451 608189.1328 0.026626948 0.03573931 1778.176804 -3.249974941 0.130847108 SPADPIDLGGQTS(ph)PRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPADPIDLGGQTSPRR 16 1 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 SPADPIDLGGQT(0.2)S(0.8)PRR;SPADPIDLGGQT(0.222)S(0.778)PRR 72.864 0.022458 883870000 573030 718370 671520 618400 722540 800770 621140 638540 582920 762270 TRUE FALSE 595653.6669 841744.4594 689020.3629 740717.6743 599722.9089 614803.3033 572453.4238 629981.4157 561940.8231 911622.212 0.653399686 0.923347905 0.755817875 0.812527015 0.657863423 0.674405796 0.627950281 0.69105536 0.616418529 1 19.79807655 3.242537461 24.9791509 0.68850226 0.793888814 0.065288185 0.120553331 181.1362561 1137734.696 0.03076362 0.040172036 1747.984033 -3.242537461 0.105386555 SPAGLQVLNDYLADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPAGLQVLNDYLADK 15 0 P24534;C9JZW3;F2Z2G2;F8WF65 P24534 EEF1B2 Elongation factor 1-beta 0 ; 164.81 3.40E-06 133357000 161536 115799 124752 121929 157977 174701 165810 139989 142984 116875 FALSE TRUE 167913.566 135686.5775 128003.1396 146046.1923 131124.126 134129.3404 152813.3789 138112.6764 137838.0338 139774.4185 1.201318294 0.970754011 0.915783739 1.044870684 0.938112477 0.959612938 1.093285742 0.988111257 0.986146358 1 17.09274082 4.741751752 24.80120112 0.989959357 1.201318382 0.636240662 0.048259961 175.7801943 1366073.243 0.011504687 0.082222684 55176.19555 -4.741751752 0.211359025 SPAGPAATPAQAQAAS(ph)TPR ddPTM_MDA-MB-175_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(0.667)T(0.333)PR 163.96 2.59E-11 182650000 211580 256280 216490 249700 222300 299780 243250 232950 198510 208850 TRUE FALSE 219933.3418 300294.0964 222131.9072 299089.9147 184513.5254 230160.6382 224183.4294 229827.6863 191365.6639 249770.1588 0.880542907 1.202281721 0.889345262 1.197460562 0.738733267 0.921489738 0.897558902 0.920156705 0.766167042 1 17.9302416 3.235192737 24.99999948 0.877297145 1.042894156 0.311832587 0.122489498 100.6567234 747183.0343 0.031892149 0.039608583 1718.670952 -3.235192737 0.165597012 SPAGPAATPAQAQAAST(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.198)T(0.802)PR;SPAGPAATPAQAQAAS(0.015)T(0.985)PR;SPAGPAATPAQAQAAS(0.248)T(0.752)PR 201.25 2.61E-21 241919000 222378 278146 226432 271127 254854 322105 266476 267977 219006 229054 TRUE FALSE 231157.6552 325915.4118 232333.0039 324755.1114 211534.0081 247300.9953 245588.9148 264385.2066 211124.0168 273932.7458 0.843848203 1.189764338 0.84813885 1.185528625 0.772211469 0.902779967 0.896529964 0.965146412 0.770714783 1 18.06346221 3.223941401 24.99996027 0.890117703 1.017124575 0.204270758 0.127596707 366.6271882 626958.9349 0.033732807 0.040481178 1674.716894 -3.223941401 0.127006872 SPAGS(ph)PELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPAGSPELR 9 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 S(0.006)PAGS(0.994)PELR;SPAGS(1)PELR 134.57 0.0012466 238540000 248480 303380 291660 350810 387890 420860 333910 345920 351430 363400 TRUE FALSE 258290.1823 355483.155 299260.8992 420199.1709 321956.5964 323121.6432 307737.2617 341283.5082 338782.1029 434601.2723 0.594315293 0.817952403 0.68858726 0.966861346 0.740809144 0.743489869 0.708091028 0.785279588 0.779523956 1 18.72933287 0.406256444 1.550841398 1.000007146 0.759983294 0.3910838 0.090867007 4.222653886 9.945862996 0.08206838 0.023535762 2.548334558 -0.406256444 -0.240023852 SPAGSQQQFGYSPGQQQTHPQGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPAGSQQQFGYSPGQQQTHPQGSPR 25 0 Q8TAP9 Q8TAP9 MPLKIP M-phase-specific PLK1-interacting protein 1 SPAGSQQQFGY(0.002)S(0.005)PGQQQT(0.127)HPQGS(0.867)PR;SPAGSQQQFGYSPGQQQTHPQGS(1)PR;SPAGSQQQFGYSPGQQQTHPQGS(1)PR 267.05 1.03E-45 347680000 94832.6 124293.7 107225.9 107504.6 112174.4 127467.8 92444 115068.8 113028.7 109841.4 TRUE FALSE 98576.66427 145640.1761 110020.295 128768.689 93107.03556 97865.33524 85197.99772 113526.491 108960.8192 131362.7193 0.750415832 1.108687281 0.837530584 0.980252919 0.708778229 0.745000833 0.6485706 0.864221535 0.829465314 1 17.00319637 3.244168679 24.99352515 0.784841821 0.926919842 0.174987996 0.12472218 195.5802145 871638.3968 0.032880515 0.043306755 1754.561839 -3.244168679 0.14207802 SPALKS(ph)PLQSVVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPALKS(0.998)PLQS(0.001)VVVR;SPALKS(0.999)PLQSVVVR 101.5 0.00082435 1194760000 785490 513190 661600 614690 774010 878340 767760 701470 769370 553120 TRUE FALSE 816501.7517 601326.3904 678841.8395 736273.8473 642444.0567 674358.8464 707580.965 692067.942 741680.524 661493.2739 1.234331147 0.909043847 1.026226367 1.113048124 0.971202705 1.019449287 1.069672199 1.046220679 1.121221565 1 19.33536696 2.221010503 24.139414 1.061552225 1.038155698 0.001409232 0.085667143 973.5498989 1339062.254 0.030305982 0.022442394 166.345288 -2.221010503 -0.023396527 SPAPEQFQS(ph)REDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPAPEQFQSREDFR 14 1 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 S(0.001)PAPEQFQS(0.999)REDFR 64.275 0.037805 226110000 131000 179470 144800 114600 144030 197820 124030 128700 141190 180550 TRUE FALSE 136171.9812 210292.5764 148573.607 137267.538 119547.832 151879.303 114308.2045 126974.987 136108.5995 215925.3157 0.630643891 0.973913484 0.688078684 0.635717667 0.553653617 0.703388125 0.529387692 0.588050487 0.630350355 1 17.72017287 4.014433182 24.61997828 0.634524617 0.809458126 0.10133257 0.147345552 287.2107845 489912.5314 0.033132214 0.071523438 10337.92035 -4.014433182 0.17493351 SPAPPPPAVFPAARPEPGDGLS(ph)SPAGGSYETGDRDDGR ddPTM_MDA-MB-175_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 SPAPPPPAVFPAARPEPGDGLS(0.806)S(0.194)PAGGSYETGDRDDGR 118.42 1.38E-06 542240000 79936 93520 101990 96052 112110 133170 118540 107660 102600 103640 TRUE FALSE 83091.935 109581.3325 104647.9432 115050.7989 93053.58224 102243.2857 109248.5251 106216.9938 98907.44604 123946.2737 0.670386713 0.884103485 0.844300842 0.928231204 0.750757401 0.824900037 0.88141839 0.85695996 0.797986443 1 16.91935537 -5 0.236987018 1.921907846 0.816130492 0.357960827 0.069818969 189.1420299 1.889056599 84.06313613 0.108158264 1.00E-05 5 -1.105777354 SPAPPPPAVFPAARPEPGDGLSS(ph)PAGGSYETGDRDDGR ddPTM_MDA-MB-175_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 SPAPPPPAVFPAARPEPGDGLS(0.244)S(0.756)PAGGSYETGDRDDGR 117.15 2.18E-06 227230000 109480 105880 117620 119610 116340 129030 121840 119080 124330 117890 TRUE FALSE 113802.3549 124064.0664 120685.2738 143268.501 96564.56836 99064.73797 112289.8624 117483.9274 119855.3876 140988.2884 0.807175945 0.879960086 0.855995028 1.016173064 0.684911984 0.702645157 0.796448157 0.833288557 0.850108821 1 17.1052158 SPARPSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPARPSESR 9 1 Q8IY33;Q8IY33-5;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 0 63.283 0.087664 0 19199 24365 18605 19963 26203 27594 19101 19695 20216 28034 FALSE TRUE 19956.99134 28549.49922 19089.86158 23911.62182 21749.02342 21185.71169 17603.81371 19431.02074 19488.43011 33526.72556 0.595256203 0.851544514 0.569392366 0.713210772 0.648707056 0.631905184 0.525068089 0.579568103 0.58128045 1 15.03302397 -1.103616451 5.224929571 1.000007634 0.631641125 0.611340007 0.08781048 7.88E-06 1.35E-06 0.085791402 0.020220808 0.078774118 1.103616451 -0.368366509 SPAVATSTAAPPPPS(ph)SPLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.5)S(0.5)PLPSK 158.64 2.47E-11 76535000 171560 152720 150530 166070 193020 208100 174900 174480 170580 147910 TRUE FALSE 178333.3213 178948.472 154452.9355 198918.1503 160210.5293 159771.9288 161190.881 172141.381 164440.8591 176890.1326 1.008158673 1.011636259 0.873157441 1.124529375 0.905706424 0.903226915 0.911248573 0.973154231 0.929621436 1 17.43249405 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPAVATSTAAPPPPSSPLPSK 21 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 SPAVATSTAAPPPPS(0.063)S(0.937)PLPSK;SPAVATSTAAPPPPS(0.186)S(0.814)PLPSK;SPAVATSTAAPPPPS(0.001)S(0.999)PLPSK;SPAVATSTAAPPPPS(0.001)S(0.999)PLPSK;SPAVATSTAAPPPPS(0.031)S(0.969)PLPSK;SPAVATSTAAPPPPS(0.02)S(0.98)PLPSK 383.15 5.97E-131 13088100000 4674630 3788650 4337820 3752020 5065390 5368300 4954940 4509260 4599860 3613670 TRUE FALSE 4859188.002 4439321.166 4450867.153 4494158.357 4204376.817 4121593.682 4566558.855 4448820.745 4434311.937 4321699.449 1.124369721 1.027216543 1.029888174 1.039905345 0.972852663 0.953697436 1.056658129 1.029414655 1.026057455 1 22.04316731 SPDDPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPDDPSR 7 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ; 117.93 0.01191 1413170000 3750000 4371000 4309300 4879700 5150000 5231200 4734500 4565600 4381300 4639600 FALSE TRUE 3898052.896 5121685.248 4421603.898 5844890.096 4274604.84 4016333.08 4363397.519 4504405.6 4223617.869 5548640.789 0.702523923 0.923052229 0.796880545 1.053391329 0.77038774 0.723840889 0.78639034 0.811803426 0.761198648 1 22.40370298 SPDEALPGGLSGCSSGSGHS(ph)PYALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPDEALPGGLSGCSSGSGHSPYALER 26 0 Q5JSZ5;A0A494C0D3;H0Y412;A0A494C065;Q5JSZ5-5 Q5JSZ5;Q5JSZ5-5 PRRC2B Protein PRRC2B 1 SPDEALPGGLSGCS(0.002)S(0.005)GS(0.094)GHS(0.89)PY(0.009)ALER;SPDEALPGGLSGCSS(0.001)GS(0.014)GHS(0.978)PY(0.007)ALER 128.22 5.75E-05 453120000 98665 175217 163576 167480 162680 193313 151474 169191 181427 161320 TRUE FALSE 102560.3704 205309.1568 167838.9249 200607.0441 135027.7117 148418.9854 139601.0721 166923.2714 174897.4777 192927.5653 0.531600397 1.06417741 0.869958239 1.039804985 0.699888124 0.769299012 0.723593188 0.865212139 0.906544782 1 17.55769976 1.027836226 2.290206902 0.997631704 0.827343356 0.128598262 0.148931328 0.621768062 6.993809677 0.135778988 0.03733908 10.6619398 -1.027836226 -0.170288348 SPDEATAADQES(ph)EDDLSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPDEATAADQESEDDLSASR 20 0 C9JME2;Q9Y4F1;Q9Y4F1-2;M0QXT1 C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 SPDEATAADQES(1)EDDLSASR 219.61 9.54E-25 71509000 59540 87885 61823 104570 57936 98223 80329 62291 55424 73734 TRUE FALSE 61890.68517 102978.5651 63434.15817 125253.6339 48088.05941 75412.19683 74032.60308 61456.09103 53429.30107 88180.76558 0.701861509 1.167812101 0.71936502 1.420418989 0.545335018 0.855200069 0.839555005 0.696933063 0.605906523 1 16.42817638 3.185818395 24.99999664 0.749348278 0.993981516 0.216486351 0.228019521 139.8822949 66304.06968 0.060771446 0.072635843 1533.975399 -3.185818395 0.244633238 SPDKPGGS(ph)PSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 SPDKPGGS(0.796)PS(0.203)AS(0.001)R;SPDKPGGS(0.999)PS(0.001)ASR;SPDKPGGS(0.954)PS(0.045)AS(0.001)R 140.3 2.38E-05 654320000 866220 655116 767099 616935 881560 853120 850110 702285 717620 530027 TRUE FALSE 900419.0345 767627.0769 787090.2301 738962.9016 731712.7461 654995.8092 783476.1569 692872.0183 691792.9964 633875.6427 1.420497924 1.211005796 1.241710798 1.165785293 1.154347473 1.033319101 1.236009249 1.093072476 1.091370215 1 19.27384031 8 0.382100954 1.087835489 5.490762925 0.711762861 0.062054185 37.26400263 0.508490059 0.043852085 121.6686941 100000000 -8 4.402927436 SPDLEAS(ph)LDTLENNCHVGSDIDFRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPDLEASLDTLENNCHVGSDIDFRPK 26 1 Q13111;Q13111-2;Q13111-3;K7EJF1 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 S(0.157)PDLEAS(0.667)LDT(0.176)LENNCHVGSDIDFRPK 85.191 0.008205 71651000 24746 21614 27592 15539 24474 32321 31480 28976 30890 12322 TRUE FALSE 25722.99119 25326.03637 28311.07019 18612.56782 20313.91822 24814.93758 29012.51534 28587.62412 29778.27493 14736.25998 1.74555764 1.718620355 1.921184223 1.263045565 1.378498903 1.683937282 1.968784168 1.939951124 2.020748478 1 13.8470828 2.465738245 22.09845831 1.829715434 1.602300348 0 0.325166751 132.9668878 258127.3434 0.109385258 0.091637505 292.2390485 -2.465738245 -0.227415086 SPDTNYLFMGDYVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 73.927 0.084493 156140000 39015 51062 45645 47513 47801 57814 44032 51166 49060 46145 FALSE TRUE 40555.34233 59831.50129 46834.5462 56910.92959 39675.80309 44387.57468 40580.65678 50480.20346 47294.34018 55186.22925 0.734881562 1.084174478 0.84866364 1.031252368 0.718943904 0.804323384 0.735340271 0.914724636 0.85699532 1 15.75202069 5.039495687 16.18520421 0.877648071 0.112826558 0.130202299 0.116049028 6558936.204 73812330.8 0.027037006 147880352.5 109520.5678 -5.039495687 -0.764821513 SPDVGLYGVIPECGETYHSDLAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPDVGLYGVIPECGETYHSDLAEAK 25 0 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;; 301.19 3.03E-63 1839370000 1207005 1002918 1091838 870955 1382071 1320122 1109668 1107480 1173545 870947 FALSE TRUE 1254658.489 1175161.365 1120292.195 1043227.299 1147147.065 1013543.672 1022689.323 1092636.042 1131309.345 1041592.389 1.204558042 1.12823536 1.075557201 1.001569626 1.101339715 0.973071311 0.981851762 1.049005401 1.086134419 1 19.99035938 4.523835599 1.223305989 1.027026543 1.248307493 0.668693822 0.040285544 0.611265696 1.033560365 0.011769133 0.155838223 33406.8555 -4.523835599 0.22128095 SPEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPEDKR 6 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 92.692 0.074506 169460000 369490 275100 336860 264620 393170 368210 382880 380070 341900 290200 FALSE TRUE 384077.7505 322346.285 345638.8483 316961.0462 326339.1038 282698.8078 352868.8651 374975.7833 329595.0858 347059.1338 1.106663716 0.92879355 0.995907656 0.913276774 0.940298272 0.814555159 1.016739889 1.080437732 0.949679907 1 18.40482197 2.034580285 24.99751586 1.026380056 0.946169019 0.128327706 0.075149193 281.2853605 203335.4297 0.02789591 0.020602394 108.287988 -2.034580285 -0.080211037 SPEDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPEDLER 7 0 P06744;A0A2U3TZU2;P06744-2;Q8N196 P06744 GPI;SIX5 Glucose-6-phosphate isomerase;Homeobox protein SIX5 0 ;;; 166.05 0.002647 4604700000 2568670 2789680 2759810 2733050 2952080 3370430 2843620 2730550 2664540 3091510 FALSE TRUE 2670083.075 3268785.839 2831732.916 3273639.133 2450286.496 2587698.712 2620729.634 2693951.444 2568643.726 3697232.194 0.722184308 0.884117001 0.765906161 0.885429684 0.662735356 0.699901596 0.708835555 0.728640048 0.694747744 1 21.81801422 5.06168176 14.57281093 0.766557451 0.370690757 0.011151863 0.103727969 1766339.271 10729255.66 0.023644034 20297711.17 115260.8346 -5.06168176 -0.395866694 SPEEGAETPVYLALLPPDAEGPHGQFVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPEEGAETPVYLALLPPDAEGPHGQFVSEK 30 0 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 0 115.63 0.00011944 36171000 40032 34761 39873 35301 52069 54524 46357 41994 40099 35998 FALSE TRUE 41612.49427 40730.93135 40912.12314 42283.43244 43218.32998 41861.62732 42723.41721 41431.13912 38655.84482 43051.11888 0.96658334 0.94610622 0.950314979 0.982168026 1.003884013 0.972370252 0.99238808 0.962370786 0.897905695 1 15.39376311 3.749398932 24.01798353 0.973231689 0.953511981 0.08240095 0.028515901 1138.821939 2523642.575 0.007452133 0.013267706 5615.635774 -3.749398932 -0.019719707 SPFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPFNSPSPQDSPR 13 0 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 SPFNS(0.009)PS(0.991)PQDSPR 150.76 4.66E-05 139520000 84042 88699 88480 96387 94222 114270 120310 91356 86104 74096 TRUE FALSE 87360.04305 103932.3633 90785.86149 115452.0609 78206.1781 87732.52428 110879.7878 90131.52225 83005.13386 88613.69255 0.985852644 1.172870245 1.024512791 1.302869315 0.882551848 0.990056071 1.251271498 1.017128614 0.936707765 1 16.43524202 3.222752914 24.99982121 1.029224255 1.118264239 0.155043358 0.120538244 546.4974688 864281.7786 0.034810832 0.041734355 1670.140141 -3.222752914 0.089039984 SPFSVAVSPS(ph)LDLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPFSVAVSPSLDLSK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 SPFSVAVS(0.248)PS(0.752)LDLSK;SPFSVAVS(0.083)PS(0.917)LDLSK 145.62 4.23E-06 154901000 515190 398470 489500 361470 647580 620600 580770 464670 533590 390090 TRUE FALSE 535530.099 466904.1228 502256.7721 432967.6871 537504.5829 476475.0553 535247.7298 458441.8587 514386.2001 466520.6668 1.147923634 1.000821949 1.076601334 0.928078257 1.152155995 1.021337508 1.147318368 0.982682851 1.1026011 1 18.83158147 SPGET(ph)SKPRPFAGGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 S(0.312)PGET(0.562)S(0.127)KPRPFAGGGYR 99.407 0.0025544 1150000000 481620 330460 462760 373750 456740 520810 529390 446050 488630 315590 TRUE FALSE 500634.7295 387213.9344 474819.9058 447676.6345 379103.4979 399859.7705 487895.0285 440071.4293 471044.3017 377423.8182 1.3264524 1.025939317 1.258054958 1.186137739 1.004450381 1.059444983 1.292698036 1.165987434 1.248051339 1 18.52582594 -2.198345132 2.418014682 0.489610063 1.169158133 0.191733968 0.106820404 7487508.112 2623622.331 20726480.06 0.02532072 0.006333662 2.198345132 0.679548069 SPGETSKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGETSKPR 9 1 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 99.688 0.0047132 56285000 67687 73085 86526 65166 86299 94729 97337 85344 87984 49333 FALSE TRUE 70359.33503 85636.78023 88780.93864 78055.6403 71629.92681 72729.62538 89707.4716 84200.10327 84817.47303 58998.85681 1.192554209 1.451498976 1.504790829 1.323002589 1.21409008 1.2327294 1.520495081 1.427148047 1.437612144 1 15.84839938 2.258327955 24.99630199 1.391706083 1.329517357 0 0.161392944 1030.604793 1303222.214 0.054955147 0.045918732 181.270843 -2.258327955 -0.062188726 SPGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGETSKPRPFAGGGYR 17 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 0 ; 158.17 1.90E-09 3117500000 1834150 1831810 2058060 1752950 2459700 2486800 1875560 2045260 2121600 1933370 FALSE TRUE 1906563.658 2146409.118 2111694.734 2099678.278 2041601.073 1909278.388 1728548.706 2017846.635 2045244.03 2312176.835 0.824575192 0.928306644 0.913292921 0.908095889 0.882977911 0.825749293 0.747584994 0.872704287 0.884553465 1 21.14082031 2.938095352 6.002734094 0.849879117 0.897304964 0.00745345 0.064755897 0.514570171 37.61765626 0.019247814 0.020681677 867.1522443 -2.938095352 0.047425847 SPGGPGSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPGGPGSHVR 10 0 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 ;; 156.48 1.09E-05 88970000 119497 168933 157659 165528 164205 201654 166778 159292 158018 160000 FALSE TRUE 124214.8338 197945.9286 161767.7231 198268.9443 136293.4928 154822.9146 153705.5046 157156.9513 152330.963 191348.9366 0.64915351 1.034476241 0.845406961 1.036164339 0.712277242 0.809113013 0.803273367 0.821310816 0.796089938 1 17.54584636 3.222411287 24.99944328 0.813340639 0.898249094 0.064141807 0.121636865 534.217466 826976.2468 0.032375084 0.038808119 1668.826882 -3.222411287 0.084908454 SPGKAEAES(ph)DALPDDTVIESEALPSDIAAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7;Q9GZR7-2;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 S(0.487)PGKAEAES(0.513)DALPDDTVIESEALPSDIAAEAR 206.06 2.82E-27 100280000 74853 51304 71540 46304 95743 86603 74480 68504 74438 42961 TRUE FALSE 77808.25424 60115.06291 73404.39117 55462.793 79468.63906 66490.76573 68642.06298 67585.81593 71758.99092 51378.38541 1.514416103 1.170045778 1.428701789 1.079496612 1.5467329 1.294138872 1.336010512 1.315452313 1.396676644 1 15.64887393 -1.347552975 3.475415717 0.998195656 1.334910474 0.36314727 0.13570617 16754548.74 27824423.92 315061.3584 0.028934438 0.044920753 1.347552975 0.336714818 SPGQLQRPTGVAVDTNGDIIVADYDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGQLQRPTGVAVDTNGDIIVADYDNR 27 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 0 176.71 3.28E-14 180370000 31167 35307 34920 34634 44825 39285 32080 40708 39578 41140 FALSE TRUE 32397.49723 41370.7026 35830.04389 41484.50183 37205.66251 30161.65412 29565.48577 40162.37584 38153.59551 49200.59533 0.658477748 0.840857765 0.728244113 0.843170729 0.756203502 0.613034333 0.600917236 0.816298575 0.7754702 1 15.58638815 0.699110938 1.496008584 0.999030958 0.731370992 0.48990611 0.082240519 0.939357621 3.272654241 0.081076734 0.023592444 5.001622824 -0.699110938 -0.267659965 SPGS(ph)NSKVPEIEVTVEGPNNNNPQTSAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 S(0.025)PGS(0.488)NS(0.488)KVPEIEVTVEGPNNNNPQTSAVR 100.59 0.00044074 173260000 52620 59300 48374 40340 76423 66172 42895 55704 61898 66661 TRUE FALSE 54697.47823 69484.31371 49634.66618 48319.1316 63432.64576 50804.55585 39532.77781 54957.37899 59670.30307 79721.94665 0.686103144 0.871583254 0.622597268 0.606095732 0.795673568 0.637271893 0.495883248 0.689363234 0.748480256 1 16.28268932 0.826054586 2.770291952 0.999754658 0.673261511 0.500634152 0.097230631 0.628771156 8.237903808 0.09558146 0.025266716 6.699688124 -0.826054586 -0.326493148 SPGS(ph)PPGPELPIETALDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGSPPGPELPIETALDDR 19 0 Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q5VWV2;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;Q8TEW0-5;Q8TEW0-3;F5GZI3;B1AP52 Q8TEW0-4 PARD3 Partitioning defective 3 homolog 1 SPGS(1)PPGPELPIETALDDR 166.52 6.03E-11 0 7531.2 5477.2 5730.6 7563.1 7874.1 8143.6 7149.5 8845.7 6732.4 4584.5 TRUE FALSE 7828.537591 6417.866493 5879.944144 9059.058606 6535.663295 6252.372317 6589.103508 8727.13786 6490.102239 5482.744999 1.427850026 1.170557174 1.072445307 1.652285234 1.192042179 1.140372627 1.20178916 1.59174608 1.18373228 1 12.42068266 5.437312764 4.94369639 1.27876799 23.12372444 0.04581278 0.202775358 7292.299253 886.0432581 0.048458144 1781619.59 273723.9284 -5.437312764 21.84495645 SPGS(ph)PPGPELPIETALDDRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 SPGS(1)PPGPELPIETALDDRER;S(0.064)PGS(0.936)PPGPELPIETALDDRER 127.14 1.23E-05 65605000 33010 36666 40531 29830 40683 43116 35846 42727 39888 41485 TRUE FALSE 34313.26029 42963.10028 41587.27116 35730.28497 33767.71819 33102.96243 33036.29685 42154.31445 38452.43867 49613.19147 0.691615663 0.865961229 0.838230114 0.720177112 0.680619754 0.667220984 0.665877277 0.849659399 0.775044651 1 15.59843614 0.650451416 1.111995644 0.998518629 0.743397518 0.524514038 0.072603056 0.997169058 1.982171937 0.074664042 0.023281277 4.471481267 -0.650451416 -0.25512111 SPGS(ph)PVGEGTGSPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPGSPVGEGTGSPPK 15 0 P35611;P35611-3;E7EV99;E7ENY0;P35611-2;P35611-6;P35611-4;H0Y9H2;P35611-5;A0A0A0MSR2 P35611 ADD1 Alpha-adducin 1 SPGS(1)PVGEGTGSPPK;SPGS(1)PVGEGTGSPPK 186.85 3.82E-07 322570000 246912 183714 251299 211623 286566 298685 292170 237739 250885 154759 TRUE FALSE 256660.2764 215265.4504 257848.0584 253481.3978 237855.6137 229319.9354 269268.952 234552.4976 241855.6979 185081.063 1.386745204 1.163087389 1.393162835 1.369569602 1.285142898 1.239024304 1.454870356 1.267296036 1.306755504 1 17.49779776 0.273224742 1.491181206 0.99990399 1.319226841 0.583022195 0.080916673 4.730941332 8.946885446 0.073323109 0.02103139 1.875965047 -0.273224742 0.319322851 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_MDA-MB-175_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(1)TPT(0.036)T(0.557)PT(0.387)S(0.019)S(0.001)QAPQK;SPGS(1)TPT(0.079)T(0.914)PT(0.007)SSQAPQK;SPGS(0.967)T(0.032)PT(0.032)T(0.966)PT(0.001)S(0.001)SQAPQK 317.83 1.20E-57 1317420000 1490930 1110650 1280720 1217150 1507230 1679520 1723050 1454450 1388400 884160 TRUE FALSE 1549793.068 1301395.498 1314096.615 1457898.637 1251031.583 1289476.933 1587992.839 1434955.477 1338431.755 1057394.224 1.465671963 1.230757147 1.242768861 1.378765464 1.183126931 1.219485509 1.501798292 1.357067633 1.265783116 1 20.01208192 4.751211849 23.20751361 1.288475653 1.465672273 0.160531465 0.127818367 1431.010132 2624922.23 0.029635495 0.487454202 56391.26652 -4.751211849 0.17719662 SPGS(ph)TPTTPT(ph)SSQAPQK ddPTM_MDA-MB-175_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(1)TPT(0.001)T(0.171)PT(0.828)S(0.001)SQAPQK 325.67 1.09E-58 187010000 341390 250850 311870 298830 364110 413890 394190 330890 348840 226090 TRUE FALSE 354868.3408 293931.5362 319997.5884 357937.6821 302218.7123 317770.3201 363292.3578 326454.9608 336285.3165 270388.0067 1.312441129 1.087073128 1.183475526 1.323792747 1.117722328 1.175238221 1.34359642 1.2073574 1.243713878 1 18.04467164 -1.111420278 4.958543714 0.99999138 1.219564511 0.397980602 0.081730498 7.45E-06 1.34E-06 0.075733641 0.01784989 0.077371269 1.111420278 0.219573131 SPGS(ph)TPTTPTSSQAPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658;P35658-5;P35658-4;P35658-3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 SPGS(0.989)T(0.011)PTTPTSSQAPQK;S(0.234)PGS(0.765)T(0.001)PTTPTSSQAPQK;S(0.192)PGS(0.807)T(0.001)PTTPTSSQAPQK;S(0.008)PGS(0.958)T(0.034)PTTPTSSQAPQK 299.65 2.79E-46 668370000 517126 404132 474457 401803 520800 581148 559978 456192 478596 292206 TRUE FALSE 537542.5338 473538.5273 486821.7392 481278.4341 432274.602 446185.1844 516085.4611 450077.4924 461371.4234 349458.1711 1.538217098 1.355064973 1.393075851 1.37721328 1.236985247 1.276791391 1.476816122 1.287929514 1.32024792 1 18.41476025 -4.001232421 0.192746809 2.04E-13 1.428362452 0.667015207 0.080342737 55.6501238 0.773641683 21.93516667 0.218517664 9.97E-05 4.001232421 1.428362452 SPGSGSQSS(ph)GWHEVEPGMPS(ph)PTTLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGSGSQSSGWHEVEPGMPSPTTLKK 26 1 Q12857-3;A0A590UK09;B1AKN8;Q12857-2;Q12857;Q12857-4;B1AKN5;A0A590UJU2;A0A590UK38;A0A590UJA3;S4R3W2 Q12857-3 NFIA Nuclear factor 1 A-type;Nuclear factor 1 2 S(0.335)PGS(0.143)GS(0.062)QS(0.078)S(0.382)GWHEVEPGMPS(0.694)PT(0.162)T(0.144)LKK 83.917 0.014564 50164000 38518 44627 70210 45646 75909 78768 60666 65244 69395 43931 TRUE FALSE 40038.72038 52291.3401 72039.73028 54674.64256 63006.01529 60475.32574 55910.8404 64369.5109 66897.48751 52538.43834 0.762084326 0.99529681 1.371181416 1.040659835 1.199236545 1.151068202 1.064189233 1.225188889 1.273305595 1 15.6810857 4.532664696 4.15136217 1.168813101 0.787994471 0.575352498 0.107271116 0.14156435 4.792919947 0.024258652 0.108529895 34092.95899 -4.532664696 -0.38081863 SPGTGPSPFSSSLGHLNHLGGS(ph)LDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGTGPSPFSSSLGHLNHLGGSLDR 25 0 O15049 O15049 N4BP3 NEDD4-binding protein 3 1 SPGTGPSPFSS(0.014)S(0.059)LGHLNHLGGS(0.927)LDR 139.19 3.03E-06 52658000 7322.5 30673 23458 26884 27811 39739 24079 31350 25989 30943 TRUE FALSE 7611.597954 35940.84915 24069.33475 32201.57496 23083.69615 30510.2195 22191.62506 30929.80453 25053.66097 37005.68841 0.205687241 0.971224984 0.650422564 0.870179055 0.623787778 0.824473772 0.599681455 0.835812164 0.677021886 1 15.17545943 -4.999997679 0.039093659 2.176314411 2.15E-11 0.220244229 0.194066375 1489.230477 4.353186117 215.2470781 66.5550023 1.00E-05 4.999997679 -2.176314411 SPGVVISDDEPGYDLDLFCIPNHYAEDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPGVVISDDEPGYDLDLFCIPNHYAEDLER 30 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 266.36 1.08E-58 234270000 86129 132850 91055 113860 102670 108060 100700 104850 105740 114120 FALSE TRUE 89529.43943 155665.9541 93427.9681 136381.1682 85218.19007 82964.70267 92806.87087 103444.6573 101934.4381 136479.629 0.655991228 1.140580138 0.68455614 0.999278567 0.624402269 0.60789074 0.680005298 0.757949432 0.746883903 1 17.0583261 3.23181826 24.99973033 0.717007607 0.876168181 0.128969543 0.16576125 258.9599414 960187.0671 0.044009315 0.053733252 1705.368589 -3.23181826 0.159160574 SPHSKS(ph)PAEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPHSKSPAEQR 11 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 S(0.006)PHS(0.007)KS(0.987)PAEQR;S(0.09)PHS(0.143)KS(0.767)PAEQR 84.046 0.0098434 37830200 40392 46678 56292 39131 70539 70755 42417 52501 54259 47111 TRUE FALSE 41986.70735 54694.5834 57759.01576 46870.99501 58548.80598 54323.22355 39092.2447 51797.30997 52306.22919 56341.49846 0.745218152 0.970769058 1.025159382 0.831908918 1.039177295 0.964177827 0.693844604 0.919345622 0.928378382 1 15.78191031 SPIIFIGTGEHIDDFEPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPIIFIGTGEHIDDFEPFK 19 0 G3V4F7;P61011-2;P61011 G3V4F7 SRP54 Signal recognition particle 54 kDa protein 0 ; 221.24 2.71E-19 823600000 1002770 743370 948700 833880 1169720 1266210 1115810 930400 1063330 711710 FALSE TRUE 1042360.134 871038.0149 973423.9014 998818.9751 970891.4122 972151.9171 1028349.897 917929.5098 1025060.961 851155.948 1.224640604 1.0233589 1.143649297 1.173485279 1.140673944 1.142154877 1.208180356 1.078450444 1.204316275 1 19.69906396 -1.07438735 4.615640796 0.99999236 1.143012469 0.365311196 0.05838544 4.22E-06 8.46E-07 0.051966047 0.01224786 0.084258292 1.07438735 0.143020108 SPITS(ph)SPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPITSSPPK 9 0 Q52LA3;G3V5T8 Q52LA3;G3V5T8 LIN52 Protein lin-52 homolog 1 SPIT(0.033)S(0.626)S(0.341)PPK 105.86 0.0031772 106010000 379790 185810 229150 187940 291540 368080 310380 252140 238010 121810 TRUE FALSE 394784.4025 217721.4221 235121.8372 225113.9711 241984.1349 282598.9983 286051.6046 248760.4757 229444.0666 145676.3373 2.710010491 1.49455585 1.614001571 1.545302245 1.661108039 1.939910102 1.963610631 1.707624452 1.575026328 1 17.15240703 -2.262735537 0.288534949 7.74E-13 1.856137351 0.368902227 0.32979618 44.84672089 1.725079752 29.44268468 0.364344361 0.005460903 2.262735537 1.856137351 SPLAQMEEERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SPLAQMEEERR 11 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRM2 E7EPK1 7-Sep Septin-7 0 ;;;;;; 195.77 1.01E-07 6402860000 1440630 1654010 1562650 1589510 1867250 2026210 1716280 1582280 1636730 1732270 FALSE TRUE 1497507.185 1938073.351 1603373.943 1903910.334 1549855.512 1555653.435 1581753.489 1561072.125 1577824.407 2071675.14 0.72284846 0.935510261 0.773950467 0.919019733 0.748117058 0.750915723 0.763514249 0.75353133 0.761617677 1 20.98236636 5.037968511 16.41675425 0.808277741 0.364051596 0.080907905 0.089708138 12858825.6 150692723.2 0.020310796 169681349.7 109136.1204 -5.037968511 -0.444226145 SPLDPMT(ph)SPGSGLILQANFVHSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.486)S(0.431)PGS(0.083)GLILQANFVHSQR 74.65 0.071987 131290000 36481 66004 53221 69244 51432 75535 54725 62613 54064 90431 TRUE FALSE 37921.29805 77339.67356 54607.98298 82940.25653 42689.60701 57993.14099 50435.5115 61773.77515 52118.2472 108149.223 0.350638654 0.715120011 0.50493181 0.766905709 0.394728744 0.536232618 0.466351122 0.571190189 0.48191051 1 16.72266378 -1.316684955 3.226733786 1.00287012 0.539151364 0.567276664 0.122480332 25980507.49 36862353.03 721692.9219 0.02830776 0.048229754 1.316684955 -0.463718755 SPLELGEKLS(ph)PLPGGPGAGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPLELGEKLSPLPGGPGAGDPR 22 1 Q15742;Q15742-2;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 1 S(0.002)PLELGEKLS(0.998)PLPGGPGAGDPR;SPLELGEKLS(1)PLPGGPGAGDPR 92.463 0.0012533 227770000 590980 377500 465590 362360 589990 671650 565490 483050 502760 346850 TRUE FALSE 614312.3467 442332.6885 477723.6579 434033.7265 489703.7105 515669.4665 521165.4162 476575.5049 484665.7658 414808.6167 1.480953679 1.066353665 1.151672455 1.046346939 1.180553371 1.243150325 1.256399687 1.148904545 1.168408144 1 18.66208634 0.528319829 1.475126947 1.00013263 1.188936011 0.20693022 0.1144455 3.588260731 9.419514953 0.104394444 0.030313053 3.375357898 -0.528319829 0.188803382 SPLLAGGS(ph)PPQPVVPAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 SPLLAGGS(1)PPQPVVPAHK;S(0.001)PLLAGGS(0.999)PPQPVVPAHK;S(0.001)PLLAGGS(0.999)PPQPVVPAHK 191.65 1.38E-14 944800000 1103950 926160 1077710 969130 1193420 1460790 1320820 1126040 1133160 946740 TRUE FALSE 1147534.798 1085220.775 1105796.008 1160821.021 990562.8947 1121543.661 1217290.677 1110947.276 1092377.793 1132235.577 1.013512402 0.958476132 0.97664835 1.025246906 0.874873494 0.99055681 1.075121381 0.981197993 0.96479727 1 20.11074273 2.481649601 24.99101711 1.007473984 0.968603678 0.116140998 0.046175362 414.1320605 2285528.453 0.015702071 0.013460462 303.1444357 -2.481649601 -0.038870307 SPLNDMS(ph)DDDDDDDSS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPLNDMSDDDDDDDSSD 17 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 2 SPLNDMS(1)DDDDDDDS(0.14)S(0.86)D;SPLNDMS(1)DDDDDDDS(0.304)S(0.696)D 405.05 9.12E-109 159220000 143319 158864 169982 142153 164933 209453 165823 165431 158697 141750 TRUE FALSE 148977.3448 186147.6562 174411.8706 170270.4391 136897.7476 160810.715 152825.36 163213.668 152985.526 169523.1985 0.878802111 1.098065975 1.028837776 1.004407896 0.807545804 0.948605951 0.901501159 0.962780725 0.902445962 1 17.37112319 3.436182831 24.99995878 0.920350025 1.012369393 0.248817307 0.069136704 177.1260748 108165.5035 0.018097292 0.024503875 2730.12688 -3.436182831 0.092019369 SPLNDMS(ph)DDDDDDDSSD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPLNDMSDDDDDDDSSD 17 0 Q9H8W4 Q9H8W4 PLEKHF2 Pleckstrin homology domain-containing family F member 2 1 SPLNDMS(1)DDDDDDDSSD 278.27 3.13E-35 163010000 53346 56924 69275 61052 66848 74552 61801 57771 61160 67128 TRUE FALSE 55452.14127 66700.25419 71080.36341 73127.90338 55485.20084 57238.42785 56956.87613 56996.67424 58958.86355 80280.44636 0.690730356 0.8308406 0.8854007 0.91090554 0.691142157 0.712980937 0.709473835 0.709969573 0.734411257 1 16.29276102 4.761505951 22.42775994 0.782204048 0.690729942 0.072794379 0.101434698 4576.282045 4472760.369 0.024833047 1.107214903 57743.8785 -4.761505951 -0.091474106 SPLS(ph)PTETFSWPDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPLSPTETFSWPDVR 15 0 A1L390-3;A1L390;A1L390-2;G3V311 A1L390-3 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 SPLS(0.999)PT(0.001)ETFSWPDVR 181.26 6.24E-07 22822000 19100 13420 13802 14439 13146 16867 14005 13533 13581 17396 TRUE FALSE 19854.08275 15724.78061 14161.69146 17294.9911 10911.44762 12949.89487 12907.2515 13351.61227 13092.22246 20804.41313 0.954320731 0.755838701 0.680706126 0.831313577 0.524477549 0.622459033 0.620409306 0.641768272 0.629300254 1 14.34460197 6.287131029 0.837362164 0.662618572 4.451208678 0.253960081 0.128161198 30.33566749 1.990732727 0.03842666 185.4224696 1937006.283 -6.287131029 3.788590106 SPMFPALGEASS(ph)DDDLFQSAKPKPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPMFPALGEASSDDDLFQSAKPKPAKK 27 3 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;Q5SRD0 Q641Q2;A0A0A0MR88 FAM21A;FAM21C;FAM21D WASH complex subunit FAM21A;WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 SPMFPALGEAS(0.177)S(0.823)DDDLFQSAKPKPAKK 191.12 3.75E-18 607690000 805390 286900 572410 250740 884890 610060 646060 505360 718750 268720 TRUE FALSE 837187.4191 336172.8432 587327.4748 300335.6236 734476.7139 468382.8105 595420.129 498586.4758 692882.3279 321370.539 2.605053412 1.046059929 1.827570992 0.934546224 2.285451293 1.457454102 1.852752685 1.551438029 2.156023169 1 18.29387815 -1.655651067 8.211786663 0.998952673 1.704384893 0.162577646 0.500041777 0.008502251 0.000356529 0.429329277 0.10108333 0.022097795 1.655651067 0.70543222 SPMVERRMMGQRS(ph)PAS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPMVERRMMGQRSPASER 18 3 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 2 S(0.001)PMVERRMMGQRS(1)PAS(1)ER 44.567 0.048668 0 57604 77578 69021 93922 93779 117830 84511 67050 60521 73542 TRUE FALSE 59878.2504 90901.41803 70819.74396 112499.4913 77838.47908 90465.76823 77886.80699 66151.30442 58342.86103 87951.14685 0.680812616 1.033544431 0.805216833 1.279113409 0.885019489 1.028591115 0.885568975 0.752136917 0.663355318 1 16.42441477 1.95283706 4.429850884 0.78321331 0.961096412 0.127485041 0.167980276 0.355539323 14.67231133 0.072615173 0.043686032 89.70921583 -1.95283706 0.177883102 SPPHCELMAGHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPHCELMAGHLR 13 0 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 0 116.24 0.00034759 75337000 17994 17142 22486 21513 28896 23904 20631 20118 16695 18036 FALSE TRUE 18704.41701 20086.00515 23072.00363 25768.20719 23984.26824 18352.65827 19013.88831 19848.35112 16094.15021 21569.80888 0.86715729 0.931209232 1.069643397 1.194642351 1.111936984 0.850849369 0.881504719 0.92019133 0.746142458 1 14.39672577 2.728778813 24.88075282 0.878822162 1.039959042 0.360709031 0.103181849 752.6255352 1914356.597 0.035507395 0.03385738 535.5238453 -2.728778813 0.16113688 SPPHHS(ph)GFQQYQQADASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPHHSGFQQYQQADASK 18 0 E9PD50;B1ALB4;Q92540-2;Q92540;Q92540-5;Q92540-4 E9PD50 SMG7 Protein SMG7 1 S(0.434)PPHHS(0.552)GFQQY(0.014)QQADASK 128.26 3.96E-05 134830000 36355 139520 147230 190080 169240 196330 161900 192230 150790 132590 TRUE FALSE 37790.32347 163481.4747 151066.9348 227677.2567 140472.6453 150735.3329 149209.855 189653.4713 145363.0974 158568.4719 0.238321799 1.030983478 0.952692127 1.435829291 0.885880046 0.950600905 0.940980594 1.196035183 0.91672131 1 17.27474642 4.739435343 6.113233236 1.046977467 0.217623313 0.696548333 0.157472543 0.068897163 13.08119673 0.036693465 0.236754361 54882.68409 -4.739435343 -0.829354155 SPPLLES(ph)PDATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPLLESPDATR 12 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 SPPLLES(1)PDATR;S(0.048)PPLLES(0.952)PDATR 110.14 0.001596 585480000 174202 193077 205920 194674 227181 262992 231420 207881 220177 220437 TRUE FALSE 181079.6295 226236.4728 211286.4444 233179.9362 188564.8548 201916.0937 213280.6957 205094.6952 212252.8728 263627.4096 0.686877096 0.858167492 0.801458561 0.884505661 0.715270294 0.765914644 0.80902322 0.777971818 0.805124448 1 18.00814085 0.844315542 7.273033396 0.999999975 0.790761241 0.563696683 0.055723789 7.167012109 335.0358448 0.050517444 0.012663132 6.987398971 -0.844315542 -0.209238734 SPPMELQPPVS(ph)PQQSECNPVGALQELVVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPMELQPPVSPQQSECNPVGALQELVVQK 30 0 H3BV98;F8VSA1;Q15633-2;Q15633;F8VW32;F8VZ57 H3BV98 TARBP2 RISC-loading complex subunit TARBP2 1 SPPMELQPPVS(0.78)PQQS(0.22)ECNPVGALQELVVQK 98.795 0.00037102 16698000 36740 30935 36450 28514 36050 44618 34443 31688 37117 32648 TRUE FALSE 38190.52357 36247.84561 37399.91694 34153.98409 29922.23388 34256.14569 31743.26766 31263.27419 35781.16642 39044.75052 0.978121849 0.928366685 0.957873119 0.874739463 0.76635741 0.877355989 0.812997067 0.800703648 0.916414267 1 15.25284097 3.640529074 4.198672822 0.844759333 0.952225181 0.272716113 0.063937252 0.233171453 7.17566901 0.016241103 0.026053194 4370.479362 -3.640529074 0.107465849 SPPS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPPSPGR 7 0 Q03252 Q03252 LMNB2 Lamin-B2 1 SPPS(1)PGR;S(0.002)PPS(0.998)PGR 80.455 0.031329 734050000 632630 717810 663810 655560 711800 853020 707780 686470 621500 804680 TRUE FALSE 657606.7209 841088.2837 681109.4339 785227.8113 590808.4902 654919.0326 652302.3542 677268.9925 599132.3364 962341.6395 0.683340192 0.874001757 0.707762614 0.815955352 0.613928013 0.680547329 0.677828255 0.703771888 0.622577588 1 19.87618963 -1.169201509 4.266937167 1.000081159 0.711319615 0.569207645 0.075957529 5.88E-05 1.14E-05 0.072686154 0.017127419 0.067732716 1.169201509 -0.288761544 SPPS(ph)TGSTYGSSQKEESAASGGAAYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.037)PPS(0.525)T(0.434)GS(0.002)T(0.002)YGSSQKEESAASGGAAYTK 161.61 7.84E-12 472270000 228040 122200 182190 152230 216580 201240 274920 193130 205420 84946 TRUE FALSE 237043.1953 143186.8994 186938.0211 182340.6396 179765.809 154505.0598 253371.052 190541.4082 198026.9743 101589.5423 2.333342487 1.409464952 1.840130557 1.794876082 1.769530651 1.520875636 2.494066282 1.875600617 1.949285033 1 16.63239237 -0.593150889 8.917802337 0.999999993 1.881291548 0.424967885 0.309624087 0 0 0.28581939 0.067368276 0.255181456 0.593150889 0.881291556 SPPVLGSAAAS(ph)PVHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPPVLGSAAASPVHLK 16 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 SPPVLGSAAAS(1)PVHLK 186.89 9.20E-10 189610000 170850 159200 190050 148190 200060 239770 202460 174960 187940 193340 TRUE FALSE 177595.2899 186541.3616 195002.8591 177501.5397 166053.8727 184087.0512 186590.6562 172614.9474 181176.0761 231221.2713 0.768075052 0.806765574 0.84336038 0.767669595 0.718160019 0.796151021 0.806978766 0.74653576 0.783561457 1 17.8189146 0.910515567 21.49188821 1 0.780987188 0.796457453 0.033073675 13566.69838 3258381.152 0.033277863 0.008319466 8.13796031 -0.910515567 -0.219012812 SPQDPGDPVQYNRT(ph)TDEELSELEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPQDPGDPVQYNRTTDEELSELEDR 25 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C2D8;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 SPQDPGDPVQYNRT(0.58)T(0.42)DEELSELEDR 127.59 0.00019402 592770000 86632 117830 111700 87982 126000 147870 79641 115360 100880 142190 TRUE FALSE 90052.29825 138066.3859 114610.9938 105384.577 104582.565 113529.4335 73398.53032 113813.7879 97249.34851 170049.4081 0.529565491 0.811919238 0.673986432 0.619729161 0.615012814 0.667626161 0.431630613 0.669298348 0.57188878 1 17.37559446 -1.535234116 5.164266907 1.001494407 0.624470464 0.58771597 0.095148174 0.001587592 0.000142878 0.089339867 0.02098081 0.029158547 1.535234116 -0.377023943 SPQEEDFRCPS(ph)DEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQEEDFRCPSDEDFR 16 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 SPQEEDFRCPS(1)DEDFR;SPQEEDFRCPS(1)DEDFR 118.32 0.00017044 1152270000 291850 329230 274040 351360 314280 367270 342300 291850 328940 273490 TRUE FALSE 303372.4634 385772.6914 281181.7075 420857.9593 260858.7979 281977.1085 315469.6316 287938.2281 317101.5137 327075.1292 0.927531433 1.179462016 0.859685382 1.286731768 0.797550087 0.862117243 0.964517334 0.880342779 0.969506653 1 18.31926254 3.200211333 24.99999976 0.905993364 1.057099865 0.260672904 0.124138369 204.0779347 133038.3938 0.032892329 0.039314539 1585.664609 -3.200211333 0.151106502 SPQESALLFIPVHSPSTEGPQLPPVPAAT(ph)QEKSPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPQESALLFIPVHSPSTEGPQLPPVPAATQEKSPEER 37 1 Q7RTP6;J3QR21;J3QLA3 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 SPQESALLFIPVHSPSTEGPQLPPVPAAT(0.5)QEKS(0.5)PEER;SPQESALLFIPVHS(0.001)PS(0.003)T(0.003)EGPQLPPVPAAT(0.497)QEKS(0.497)PEER 90.82 0.00085527 132465000 44505 32317 41114 31646 42407 52188 44223 35992 41636 34299 TRUE FALSE 46262.09177 37867.19336 42185.46462 37905.48435 35198.67329 40068.12792 40756.6857 35509.58611 40137.52849 41019.23236 1.127814664 0.923157046 1.028431353 0.924090534 0.858101707 0.976813207 0.993599426 0.865681391 0.978505111 1 15.32401287 7.102082303 1.3953996 0.940431803 159.7575613 0.460444845 0.055720999 1037.72322 3.071676066 0.014976151 526660.8672 12649760.51 -7.102082303 158.8171295 SPQPVPS(ph)PRPQSQPPHSSPSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.867)PRPQS(0.03)QPPHS(0.036)S(0.061)PS(0.006)PR;SPQPVPS(0.995)PRPQS(0.005)QPPHSSPSPR;SPQPVPS(0.942)PRPQS(0.056)QPPHS(0.001)S(0.001)PSPR;SPQPVPS(0.893)PRPQS(0.016)QPPHS(0.062)S(0.028)PS(0.001)PR;SPQPVPS(0.77)PRPQS(0.013)QPPHS(0.106)S(0.109)PS(0.002)PR 183.31 2.60E-17 945639000 86237.8 524730 426856 518090 438034 704916 334583 564853 402617 651551 TRUE FALSE 89642.53493 614848.2957 437980.218 620566.6557 363577.1371 541209.9421 308357.5102 557282.0694 388126.8928 779209.9438 0.115042853 0.789066285 0.562082429 0.796404949 0.466597148 0.694562417 0.395730974 0.715188601 0.498103105 1 19.57165256 -2.255160627 2.13041171 2.477495005 0.577461585 0.305309142 0.197756523 5740757.297 869654.5385 40857715.76 0.04299815 0.005556987 2.255160627 -1.900033421 SPQPVPSPRPQSQPPHSS(ph)PSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPQPVPSPRPQSQPPHSSPSPR 22 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 SPQPVPS(0.033)PRPQS(0.005)QPPHS(0.246)S(0.612)PS(0.104)PR 139.31 9.82E-08 70226000 7650.3 42061 37638 39196 30115 52774 25333 42593 32886 47040 TRUE FALSE 7952.339751 49284.64956 38618.8772 46948.85181 24996.06306 40518.0383 23347.33326 42022.1105 31702.43928 56256.58736 0.141358375 0.876068952 0.686477424 0.834548522 0.44432242 0.720236335 0.415015101 0.746972265 0.563532926 1 15.77973442 -2.277840371 2.02654716 2.387979716 0.620477862 0.237036518 0.211543262 11068974.05 1582879.826 70283282.99 0.046758555 0.005274237 2.277840371 -1.767501855 SPQT(ph)PELVEALAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPQTPELVEALAFR 14 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 SPQT(1)PELVEALAFR;SPQT(1)PELVEALAFR;S(0.022)PQT(0.978)PELVEALAFR;SPQT(1)PELVEALAFR 172.93 3.11E-05 178065000 134485 148937 141305 152805 166253 183392 149494 144648 155303 145122 TRUE FALSE 139794.5716 174515.7712 144987.5244 183029.3729 137993.3744 140801.9873 137776.2697 142709.2302 149713.6754 173555.8774 0.805472991 1.005530748 0.835393918 1.0545847 0.795094793 0.811277552 0.793843872 0.822266767 0.862625211 1 17.4050407 SPQYCQVIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPQYCQVIHR 10 0 Q13228;Q13228-4;A6PVX1;F2Z2W8;F8WCR4;C9JVL0 Q13228 SELENBP1 Selenium-binding protein 1 0 ;; 169.65 4.57E-06 919600000 452248 582730 527947 555136 776193 724275 517761 541564 505859 782616 FALSE TRUE 470103.1003 682809.3445 541705.7325 664940.2439 644255.9911 556073.1077 477177.5399 534305.2204 487653.2334 935954.6211 0.502271253 0.729532532 0.578773501 0.710440687 0.688341055 0.594124005 0.509829781 0.570866587 0.521022304 1 19.83607906 -1.172251156 6.005695928 1.000004242 0.603020223 0.698057853 0.078793108 4.53E-06 6.24E-07 0.077193146 0.018194405 0.067258758 1.172251156 -0.396984019 SPS(ph)AGDVHILTGFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSAGDVHILTGFAK 15 0 A0A3B3ITL0;A0A3B3IRJ9;Q9Y2H2-4;Q9Y2H2 A0A3B3ITL0 INPP5F Phosphatidylinositide phosphatase SAC2 1 S(0.117)PS(0.883)AGDVHILTGFAK;S(0.078)PS(0.922)AGDVHILTGFAK 265.77 1.98E-25 323160000 896100 656720 858360 864750 957010 1077130 1164750 877200 910200 566480 TRUE FALSE 931478.7199 769506.5514 880729.5668 1035794.969 794337.782 826982.8816 1073453.851 865442.5688 877442.0798 677470.9101 1.374935375 1.135851798 1.30002566 1.52891431 1.172504635 1.220691353 1.584501763 1.277460856 1.295173072 1 19.36979947 0.628059697 2.365725187 1.000069586 1.3252283 0.337306694 0.135674849 3.306756492 19.6218217 0.127713224 0.034341033 4.246779355 -0.628059697 0.325158714 SPS(ph)FASEWDEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 SPS(1)FASEWDEIEK;S(0.001)PS(0.999)FASEWDEIEK;S(0.022)PS(0.978)FASEWDEIEK;SPS(1)FASEWDEIEK;S(0.002)PS(0.998)FASEWDEIEK;S(0.038)PS(0.962)FASEWDEIEK 338.48 9.81E-63 1893415000 1685568 1121204 1513944 1057059 1802512 1835822 1653421 1488175 1534893 1022353 TRUE FALSE 1752115.526 1313762.065 1553398.624 1266142.115 1496121.654 1409480.163 1523821.542 1468228.448 1479652.501 1222663.496 1.433031682 1.074508292 1.270503805 1.035560577 1.223657743 1.152794834 1.246313108 1.200844266 1.210187844 1 20.22159597 -2.401824711 1.743866634 2.74E-05 1.199189346 0.259640157 0.103529354 1553234.546 139937.8606 6107496.445 0.022738958 0.00396438 2.401824711 1.199161959 SPS(ph)FGAGEGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 S(0.032)PS(0.968)FGAGEGLLR;S(0.004)PS(0.996)FGAGEGLLR;S(0.023)PS(0.977)FGAGEGLLR;S(0.001)PS(0.999)FGAGEGLLR;S(0.051)PS(0.949)FGAGEGLLR;S(0.003)PS(0.997)FGAGEGLLR 233.7 5.55E-16 627092000 407843 560759 550522 511371 631697 689586 512805 554075 521821 597493 TRUE FALSE 423944.9566 657064.9962 564869.0556 612518.6575 524321.3696 529440.1023 472610.0041 546648.5309 503040.7641 714560.3137 0.593294853 0.919537488 0.790512774 0.857196581 0.733767828 0.7409313 0.661399738 0.765013842 0.70398643 1 19.44669626 -1.040386118 4.694770741 1.000007601 0.756763964 0.417202323 0.087846698 11126660.32 2465726.677 872.890519 0.019703561 0.091120036 1.040386118 -0.243243637 SPS(ph)FNMQLISQV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSFNMQLISQV 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 S(0.235)PS(0.765)FNMQLISQV;S(0.149)PS(0.851)FNMQLISQV;S(0.147)PS(0.853)FNMQLISQV 102.4 0.0024736 68649000 114372 114668 110072 116951 144167 154382 127954 113226 112107 141760 TRUE FALSE 118887.4949 134361.337 112940.5667 140083.5587 119661.5448 118529.1202 117924.6311 111708.3907 108072.291 169535.1578 0.701255695 0.792527867 0.666177849 0.826280286 0.705821414 0.699141828 0.695576261 0.658909881 0.637462414 1 17.37122496 -1.138373186 5.073548767 1.000012363 0.709168023 0.71358961 0.05526205 7.79E-06 1.32E-06 0.053909182 0.012705976 0.07271547 1.138373186 -0.290844341 SPS(ph)IDSIQKDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSIDSIQKDPR 12 1 A0A0D9SF60;Q99569-2;Q99569;B4DRK2;E9PHB5;E7EPC8;Q9UQB3-2;Q9UQB3 A0A0D9SF60;E7EPC8 PKP4;CTNND2 Plakophilin-4;Catenin delta-2 1 S(0.129)PS(0.871)IDSIQKDPR 67.115 0.034054 223440000 919050 746500 732650 647450 867450 1062900 961050 788080 809000 569420 TRUE FALSE 955334.8037 874705.568 751743.4609 775513.6776 720001.1588 816057.5834 885720.3898 777517.0766 779884.248 680986.9468 1.402868011 1.284467451 1.103902893 1.138808433 1.05729069 1.198345412 1.300642243 1.141750338 1.145226427 1 19.37726762 4.463293572 3.391756659 1.148866442 1.390841209 0.555414102 0.076901984 0.180586323 4.168327025 0.019289518 0.079726268 29059.86366 -4.463293572 0.241974767 SPS(ph)LDNPTPFPNLGPSENPLKR ddPTM_MDA-MB-175_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(0.488)PS(0.512)LDNPTPFPNLGPSENPLKR 97.057 0.00083922 325080000 39774 206620 204490 215720 198850 263700 212750 230940 231920 174940 TRUE FALSE 41344.30823 242105.3777 209819.1774 258388.7721 165049.548 202459.6714 196074.0991 227844.627 223573.2445 209216.1436 0.197615287 1.157202181 1.002882348 1.235032669 0.788894897 0.96770578 0.937184367 1.089039417 1.068623294 1 17.67463465 4.744163506 24.90213983 1.025370171 0.197614912 0.820635566 0.116376337 225.7660528 1003389.9 0.027231922 0.239087013 55483.4561 -4.744163506 -0.827755259 SPS(ph)LDVTVPEAELNLETPEISVGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSLDVTVPEAELNLETPEISVGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 S(0.303)PS(0.349)LDVT(0.349)VPEAELNLETPEISVGGK 80.061 0.015426 19752000 33972 33870 34937 31912 47012 48294 47632 44438 44067 35251 TRUE FALSE 35313.24079 39686.90903 35847.48692 38224.09835 39020.91703 37078.4504 43898.47938 43842.3813 42481.03728 42157.75853 0.837645122 0.941390397 0.850317668 0.906691904 0.925592783 0.879516646 1.04129064 1.03995997 1.00766831 1 15.36351054 2.238580414 25 1.027664446 0.893066185 0.803934915 0.031880115 0.203918851 257345.4661 0.010814171 0.008508631 173.2129724 -2.238580414 -0.13459826 SPS(ph)LGSDLTFATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 S(0.431)PS(0.566)LGS(0.003)DLTFATR;S(0.195)PS(0.798)LGS(0.007)DLTFATR;S(0.004)PS(0.995)LGS(0.002)DLTFATR 139.64 4.09E-05 341162000 344585 304626 345505 340931 415890 446080 387388 374754 342102 338558 TRUE FALSE 358189.4819 356943.1458 354509.1441 408366.1342 345197.1664 342484.6804 357023.5163 369731.0356 329789.8158 404891.958 0.884654473 0.881576279 0.875564795 1.008580502 0.852566122 0.845866838 0.881774778 0.913159741 0.81451313 1 18.62717746 -1.122254357 4.814310665 1.000006695 0.887346834 0.334584479 0.048794833 3.42E-06 6.23E-07 0.04601222 0.010844539 0.075465012 1.122254357 -0.112659861 SPS(ph)MPSLNQTWPELNQSSEDTAIVHPVPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSMPSLNQTWPELNQSSEDTAIVHPVPIR 30 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71-2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 S(0.222)PS(0.759)MPS(0.013)LNQT(0.006)WPELNQSSEDTAIVHPVPIR 88.634 0.0007507 118790000 17733 18728 21613 25488 29708 26173 23271 28039 25415 17497 TRUE FALSE 18433.11253 21944.38832 22176.25254 30529.45033 24658.24477 20094.71741 21446.95821 27663.18307 24500.31911 20925.20215 0.880904873 1.048706156 1.059786777 1.458979947 1.178399358 0.960311746 1.024934338 1.322003146 1.170852207 1 14.35295394 4.489039101 2.006936526 1.167234058 0.873341079 0.241401555 0.144596908 0.641594843 4.023638941 0.039224283 0.287298747 30834.6555 -4.489039101 -0.29389298 SPS(ph)PAHLPDDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SPSPAHLPDDPK 12 0 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.008)PS(0.992)PAHLPDDPK;S(0.124)PS(0.876)PAHLPDDPK;S(0.074)PS(0.926)PAHLPDDPK;S(0.006)PS(0.994)PAHLPDDPK;S(0.041)PS(0.959)PAHLPDDPK;S(0.124)PS(0.876)PAHLPDDPK;S(0.022)PS(0.978)PAHLPDDPK 198.37 1.93E-07 8978500000 8806030 6936300 7799090 6948430 9596900 11190470 9725770 8321310 8262520 5641650 TRUE FALSE 9153698.864 8127555.568 8002340.692 8322808.715 7965622.366 8591652.936 8963438.734 8209776.45 7965153.519 6747023.302 1.356701831 1.204613532 1.186054996 1.233552686 1.180612844 1.273399031 1.328502709 1.216799777 1.180543354 1 22.68581971 0.815978457 2.025588001 1.000420357 1.245647184 0.650581895 0.054897132 0.415639992 3.047666109 0.052494219 0.014515599 6.546037025 -0.815978457 0.245226827 SPS(ph)PAHLPDDPKVAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSPAHLPDDPKVAEK 16 1 Q92615;H0Y4V9;A0A087X183;H0Y641 Q92615 LARP4B La-related protein 4B 1 S(0.016)PS(0.984)PAHLPDDPKVAEK;S(0.003)PS(0.997)PAHLPDDPKVAEK;S(0.003)PS(0.997)PAHLPDDPKVAEK;S(0.172)PS(0.828)PAHLPDDPKVAEK 194.51 1.22E-10 1244430000 1842340 1173210 1599280 683260 2711450 1964260 1156490 1359790 1801960 1257760 TRUE FALSE 1915077.006 1374699.691 1640958.551 818406.7887 2250558.698 1508090.384 1065841.292 1341564.239 1737107.812 1504193.991 1.273158261 0.913911171 1.090922155 0.544083272 1.496189129 1.002590353 0.708579677 0.891882462 1.154842941 1 20.52055921 2.465546542 24.98881723 0.910067577 1.050124416 0.045803379 0.251782616 680.2382191 1468565.907 0.085312647 0.071428283 292.1100791 -2.465546542 0.140056839 SPS(ph)PAVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSPAVPLR 9 0 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 S(0.49)PS(0.51)PAVPLR;S(0.489)PS(0.511)PAVPLR;S(0.108)PS(0.892)PAVPLR;S(0.108)PS(0.892)PAVPLR 140.17 0.00011511 1025860000 853420 1045840 985250 945840 1035590 1206210 1008940 1004260 907550 925810 TRUE FALSE 887113.6806 1225454.884 1010926.424 1132924.329 859560.7817 926086.0078 929856.6464 990799.5373 874887.4528 1107204.744 0.801219183 1.106800609 0.913043798 1.023229295 0.776334085 0.836418027 0.839823575 0.89486569 0.790176756 1 20.0784906 3.244795222 24.99994972 0.852098727 0.968051645 0.230857317 0.093182504 190.487786 763826.2248 0.023878563 0.031550696 1757.094916 -3.244795222 0.115952919 SPS(ph)PFDCSTDQEEKIEDVASHCLPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPFDCSTDQEEKIEDVASHCLPQK 26 1 Q8TD26;A0A075B6P4;Q8TD26-2;Q8TD26-3 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 1 S(0.031)PS(0.901)PFDCS(0.034)T(0.034)DQEEKIEDVASHCLPQK 83.559 0.0087501 39205000 54905 32957 40130 21281 53939 51025 40226 30760 39882 27841 TRUE FALSE 57072.6918 38617.10838 41175.82077 25490.31828 44770.46805 39175.21704 37072.98101 30347.71251 38446.65461 33295.9109 1.714105133 1.159815345 1.236662991 0.765569032 1.344623614 1.176577423 1.113439459 0.911454641 1.154695984 1 15.02305739 5.066695478 1.569113724 1.074916554 2.533478551 0.588807227 0.156069134 1.82205277 2.170305328 0.040500857 5.226392923 116599.1752 -5.066695478 1.458561997 SPS(ph)PFTHTHLAQGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPFTHTHLAQGYR 15 0 P38398-7;P38398;P38398-4;P38398-8;Q5YLB2 P38398-7 BRCA1 Breast cancer type 1 susceptibility protein 1 S(0.115)PS(0.885)PFTHTHLAQGYR 162.59 1.02E-06 111740000 64512 69195 75499 64269 88789 85939 68936 69407 72447 79952 TRUE FALSE 67058.98357 81078.70299 77466.56596 76981.21638 73696.67749 65980.96967 63532.61619 68476.71269 69839.64662 95617.06363 0.701328623 0.847952237 0.81017512 0.805099147 0.770748177 0.690054339 0.664448518 0.716155779 0.730409866 1 16.54498048 2.976956613 7.440698928 0.732468498 0.795610872 0 0.094974518 0.475422346 117.3880726 0.026628662 0.029273177 948.3237185 -2.976956613 0.063142373 SPS(ph)PGLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSPGLFR 8 0 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 S(0.005)PS(0.995)PGLFR;S(0.061)PS(0.939)PGLFR;S(0.003)PS(0.997)PGLFR 121.73 0.0014902 147685000 556180 577060 581890 560490 646600 725320 620430 642210 606990 653650 TRUE FALSE 578138.4159 676165.5661 597054.5314 671353.2491 536691.163 556875.4223 571799.0754 633602.2254 585144.5485 781720.2026 0.739572054 0.864971334 0.763770118 0.858815273 0.686551481 0.712371793 0.731462579 0.810523028 0.74853451 1 19.5762928 -1.734272868 4.311593736 1.016365647 0.771102721 0.602454712 0.056378735 0.00921327 0.000567822 0.05670574 0.012802774 0.018438566 1.734272868 -0.245262927 SPS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSPGPNHTSNSSNASNATVVPQNSSAR 28 0 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.009)PS(0.991)PGPNHTSNSSNASNATVVPQNSSAR;S(0.006)PS(0.994)PGPNHTSNSSNASNATVVPQNSSAR 199.61 3.04E-25 368020000 4412.5 81379 63605 70243 49920 105233 45573 73234 53233 84215 TRUE FALSE 4586.708907 95355.21021 65262.59855 84136.85575 41434.61623 80794.23057 42000.86918 72252.41802 51317.15473 100715.3169 0.045541324 0.946779628 0.647990798 0.835392852 0.411403325 0.802204005 0.417025637 0.71739255 0.509526816 1 16.61992358 -1.768686007 2.684399503 1.092573776 0.612848923 0.190152871 0.249097501 51496746.79 38234975.58 31376164.95 0.055199012 0.017033896 1.768686007 -0.479724853 SPS(ph)PLTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SPSPLTGK 8 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 S(0.001)PS(0.999)PLTGK;S(0.007)PS(0.993)PLTGK;S(0.006)PS(0.994)PLTGK;S(0.037)PS(0.963)PLTGK;S(0.433)PS(0.567)PLTGK 105.4 0.004611 1754750000 2881820 2189290 2648860 2300450 3251450 3373980 3342480 2743630 2795370 1839320 TRUE FALSE 2995596.479 2565283.527 2717891.468 2755472.144 2698769.69 2590424.278 3080487.684 2706856.128 2694765.18 2199699.538 1.361820752 1.166197239 1.235573959 1.252658418 1.226881055 1.177626414 1.400412934 1.23055721 1.225060574 1 21.06887505 0.66582926 2.432160784 1.000052465 1.254540973 0.548540502 0.069390855 1.667598389 11.2210648 0.063159438 0.016927873 4.632647545 -0.66582926 0.254488508 SPS(ph)PLVSLQAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSPLVSLQAVK 12 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 S(0.164)PS(0.836)PLVSLQAVK;S(0.001)PS(0.999)PLVSLQAVK 182.02 1.83E-05 306990000 518380 345330 438440 399800 623180 599230 498380 415550 447730 415190 TRUE FALSE 538846.0427 404637.7412 449866.1066 478879.2467 517252.0862 460067.9139 459315.6733 409980.232 431616.2848 496538.5312 1.085204891 0.814917103 0.906004425 0.964435218 1.041715907 0.926550278 0.925035308 0.825676571 0.869250335 1 18.92154615 1.968988848 6.624649953 0.877796428 0.950046359 0.076000972 0.080847511 0.395164866 58.4897703 0.033479765 0.021419464 93.10839669 -1.968988848 0.072249931 SPS(ph)PPLPTHIPPEPPRT(ph)PPFPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSPPLPTHIPPEPPRTPPFPAK 23 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 S(0.414)PS(0.586)PPLPTHIPPEPPRT(1)PPFPAK;S(0.426)PS(0.574)PPLPTHIPPEPPRT(1)PPFPAK 138.4 5.78E-05 299070000 159664 155069 155565 132624 202152 189848 171693 147842 152186 129502 TRUE FALSE 165967.658 181700.8945 159619.1517 158856.6314 167790.2752 145758.6792 158235.254 145860.4198 146708.8556 154875.4374 1.07162027 1.173206659 1.030629223 1.02570578 1.083388548 0.941134899 1.02169367 0.941791818 0.94727 1 17.24074883 3.386349485 0.667959264 0.960842366 1.125676152 0.557268171 0.046193222 0.617564633 0.563139316 0.026482079 0.060851944 2434.16204 -3.386349485 0.164833786 SPS(ph)PPTQHTGQPPGQPSAPSQLSAPR ddPTM_MDA-MB-175_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 S(0.002)PS(0.978)PPT(0.02)QHTGQPPGQPSAPSQLSAPR;S(0.005)PS(0.994)PPT(0.001)QHTGQPPGQPSAPSQLSAPR;S(0.009)PS(0.988)PPT(0.004)QHTGQPPGQPSAPSQLSAPR;SPS(0.997)PPT(0.003)QHTGQPPGQPSAPSQLSAPR;S(0.078)PS(0.913)PPT(0.004)QHT(0.005)GQPPGQPSAPSQLSAPR;S(0.008)PS(0.737)PPT(0.254)QHT(0.001)GQPPGQPSAPSQLSAPR 220.01 1.99E-34 9132710000 234201 266969 274364 261380 290311 327622 264204 283070 268967 257187 TRUE FALSE 243447.4363 312818.849 281514.1512 313080.1839 240964.0399 251536.7557 243495.0001 279275.9097 259286.9302 307577.8685 0.791498548 1.017039524 0.915261402 1.017889178 0.783424507 0.817798618 0.791653188 0.907984411 0.842996056 1 18.23059217 5.041323593 15.60430334 0.891180845 0.351516286 0.117905338 0.085920404 4421076.954 47322843.42 0.020733861 67910365.81 109982.5013 -5.041323593 -0.539664559 SPS(ph)PRPNMPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPRPNMPVR 11 1 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 S(0.206)PS(0.794)PRPNMPVR 63.292 0.045762 298490000 132080 101450 107150 108200 134040 157720 143010 105900 131460 99429 TRUE FALSE 137294.6204 118873.2483 109942.417 129601.6371 111255.9287 121091.9203 131800.5025 104480.5837 126728.7803 118910.2089 1.154607512 0.999689173 0.924583499 1.089911777 0.935629747 1.018347553 1.108403591 0.878651082 1.065751894 1 16.85951306 4.73758873 7.456111581 0.99667356 1.156345627 0.294666752 0.070202406 0.114642983 61.42655939 0.015839554 0.093510811 54649.81929 -4.73758873 0.159672067 SPS(ph)PSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSPSFR 7 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 S(0.171)PS(0.829)PSFR;S(0.033)PS(0.967)PSFR 141.2 0.0026991 1054860000 1090720 1395680 1335050 1369080 1491670 1654250 1302650 1364630 1216320 1219520 TRUE FALSE 1133782.468 1635377.183 1369842.5 1639879.938 1238116.466 1270075.508 1200544.889 1346339.367 1172544.881 1458461.595 0.777382464 1.121302878 0.939237965 1.124390209 0.848919485 0.870832329 0.823158384 0.923122948 0.803960066 1 20.47601597 3.195746718 24.999784 0.873788869 0.996249186 0.21475463 0.104709783 183.6999101 107264.9736 0.027793626 0.033219967 1569.447232 -3.195746718 0.122460317 SPS(ph)PSLSSLLLPSSPGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPSLSSLLLPSSPGPR 18 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 S(0.003)PS(0.997)PSLSSLLLPSSPGPR 117.4 0.00013912 53526000 29760 39277 43477 35562 46121 53484 41898 33561 46574 38540 TRUE FALSE 30934.94778 46022.51922 44610.04634 42596.05746 38281.36889 41063.15156 38613.92528 33111.16969 44897.81084 46091.17511 0.671168563 0.998510433 0.967865242 0.924169483 0.830557451 0.890911361 0.837772636 0.718384151 0.974108617 1 15.49220293 3.237846381 24.99429447 0.849942425 0.903679774 0 0.111820552 67.47313282 2361224.494 0.031359486 0.039659575 1729.204595 -3.237846381 0.053737349 SPS(ph)PVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 S(0.34)PS(0.66)PVLR 66.299 0.071592 230370000 253260 192860 229350 179660 337490 348200 233380 242610 251940 290050 TRUE FALSE 263258.9004 225982.2048 235327.0494 215196.2118 280123.5703 267335.827 215087.0658 239358.2098 242872.7286 346879.7442 0.758934198 0.65147132 0.678411044 0.620376991 0.807552401 0.770687339 0.62006234 0.690032248 0.700164056 1 18.40407607 -1.750791904 2.166442435 1.087498052 0.696576329 0.693753345 0.059814295 1256621.767 748505.1113 586217.321 0.015693341 0.017750398 1.750791904 -0.390921723 SPS(ph)PVQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSPVQGK 8 0 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.41)PS(0.59)PVQGK 75.474 0.04017 257110000 620700 536000 595060 487870 660360 783700 694600 635910 635310 420910 TRUE FALSE 645205.7153 628053.8305 610567.7524 584369.2299 548112.2431 601697.5521 640155.437 627386.6666 612445.3172 503379.2557 1.281748717 1.247675234 1.212937851 1.160892554 1.088865377 1.195316544 1.271715967 1.246349863 1.216667771 1 18.94128624 4.273689888 2.372443209 1.186655155 1.276230733 0.184049176 0.075569533 0.609149606 6.58345303 0.020009221 0.075231045 18779.75351 -4.273689888 0.089575578 SPS(ph)QESIGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSQESIGAR 10 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 S(0.071)PS(0.929)QESIGAR 94.402 0.0085262 184360000 139450 140160 128890 142820 125420 183910 157210 161560 122870 137770 TRUE FALSE 144955.5937 164231.3897 132248.9793 171069.3697 104101.1532 141199.6897 144887.4694 159394.5525 118447.9327 164763.3937 0.879780335 0.996771103 0.802659962 1.038272919 0.631822099 0.856984592 0.879366867 0.967414842 0.718897141 1 17.33003622 4.92898657 0.002573693 1.74507894 2.62E-07 0.006304165 0.123988442 1998477.916 756.0608268 251243.0339 261475.1862 84915.42148 -4.92898657 -1.745078678 SPS(ph)SLLIANLHLQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSSLLIANLHLQ 13 0 Q658Y4 Q658Y4 FAM91A1 Protein FAM91A1 1 S(0.066)PS(0.892)S(0.042)LLIANLHLQ 122.33 0.00024789 52610000 41538 48960 50914 47791 60733 57684 45847 47980 51893 65010 TRUE FALSE 43177.95231 57368.49914 52240.86067 57243.91716 50409.62635 44287.76521 42253.39234 47336.90658 50025.38107 77747.46481 0.555361547 0.73788257 0.671930085 0.736280177 0.648376464 0.569636133 0.543469712 0.608854664 0.643434242 1 16.24650801 -1.482603502 4.172577082 1.002534203 0.634642318 0.739944542 0.064910552 0.001642305 0.000203645 0.067451594 0.01579846 0.0329152 1.482603502 -0.367891886 SPS(ph)VAAMASPQLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSVAAMASPQLCR 14 0 P25325-2 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase 1 S(0.072)PS(0.928)VAAMASPQLCR 130.72 5.70E-05 0 49305 46443 53639 57281 66502 65658 53434 51710 49433 55718 TRUE FALSE 51251.59947 54419.22397 55036.8764 68611.01083 55198.01379 50409.92456 49245.70346 51016.91203 47653.91599 66634.87531 0.769140772 0.816677809 0.825947016 1.029656175 0.82836523 0.756509625 0.739037977 0.765618781 0.715149773 1 16.02398983 2.993612893 24.99001608 0.776821353 0.864056957 0.074247177 0.097829992 560.755526 2194008.611 0.028024421 0.03239198 985.4007604 -2.993612893 0.087235604 SPS(ph)WTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSWTR 6 0 D3DX86;H3BLZ2;Q9H9R9;Q9H9R9-2;Q9H9R9-3 D3DX86 MGC3101;DBNDD1 Dysbindin domain-containing protein 1 1 S(0.005)PS(0.992)WT(0.003)R 79.713 0.069677 262790000 140560 185710 187370 194950 210880 248200 226130 192550 218480 250280 TRUE FALSE 146109.4173 217604.2479 192253.0161 233510.5281 175034.6929 190559.3115 208405.3397 189969.1822 210616.9475 299317.5741 0.488141793 0.727001241 0.642304471 0.78014306 0.584779205 0.636645917 0.696268304 0.634674335 0.703657138 1 18.19131746 -5 0.346626373 4.875530514 0.646189639 0.65996989 0.075088508 239.3091784 1.979611343 688.1127871 0.054103368 1.00E-05 5 -4.229340875 SPSDLHIS(ph)PLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSDLHISPLAK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 SPSDLHIS(1)PLAK;SPSDLHIS(1)PLAK 119.65 0.00031864 328490000 363530 440120 440860 385680 524640 592690 523350 476840 473950 443700 TRUE FALSE 377882.4451 515707.1863 452349.1738 461966.3529 435461.8802 455046.7298 482328.4595 470448.7398 456892.6321 530634.5199 0.712133174 0.971868899 0.852468426 0.870592349 0.820643708 0.857552068 0.908965477 0.886577714 0.861030738 1 19.01735901 -5 0.174874258 1.538523372 0.835273746 0.343089399 0.061082089 151.8413289 1.44818837 28.34647048 0.190135631 1.00E-05 5 -0.703249627 SPSFGDPQLS(ph)PEARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 1 SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR 146.13 6.99E-07 1291670000 1497550 1707600 1658830 1547510 1645470 1958390 1511350 1625740 1547930 1838670 TRUE FALSE 1556674.43 2000867.017 1702060.473 1853602.859 1365773.597 1503583.602 1392886.438 1603949.614 1492220.302 2198922.183 0.707926111 0.909930798 0.774043068 0.842959734 0.621110473 0.683782088 0.633440532 0.729425364 0.67861442 1 21.06836512 5.08392029 14.84229616 0.748149663 7.79E-05 0.004499354 0.117425389 726426.2293 2156140.051 0.027362479 17278435.54 121316.6167 -5.08392029 -0.748071798 SPSGS(ph)AFGSQENLR ddPTM_MDA-MB-175_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(0.026)PS(0.039)GS(0.613)AFGS(0.322)QENLR 144.15 9.37E-06 358080000 134700 130920 113320 135760 130600 151120 128250 119570 119110 124660 TRUE FALSE 140018.06 153404.4916 116273.2123 162612.9228 108400.6586 116024.6702 118197.4299 117967.3597 114823.2544 149084.7402 0.939184385 1.028975141 0.779913572 1.090741564 0.727107674 0.778246453 0.792820444 0.791277226 0.770187842 1 17.18577307 3.221829893 24.99998025 0.796572232 0.951809524 0.339300583 0.101117061 243.2143487 363423.6976 0.02682711 0.032145696 1666.594304 -3.221829893 0.155237291 SPSGSAFGS(ph)QENLR ddPTM_MDA-MB-175_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;SPSGSAFGS(1)QENLR;SPSGSAFGS(1)QENLR 235.92 3.14E-17 1133820000 597370 586640 646600 627500 651060 780870 569320 618780 568040 570680 TRUE FALSE 620954.6289 687390.8566 663450.9272 751617.6271 540393.0538 599524.7767 524695.2108 610486.2662 547596.3514 682493.8197 0.909831871 1.007175211 0.972098073 1.101281221 0.791791864 0.878432536 0.768791153 0.894493472 0.802346242 1 19.38045646 3.226905195 24.99999181 0.848882667 0.996459471 0.456995185 0.075385633 175.7267717 376919.8609 0.020153323 0.024277005 1686.184895 -3.226905195 0.147576804 SPSPGGPQLS(ph)PQLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SPSPGGPQLSPQLPR 15 0 H7C1V4;Q9HCH0-2;Q9HCH0 H7C1V4 NCKAP5L Nck-associated protein 5-like 1 SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR;SPSPGGPQLS(1)PQLPR 231.37 2.13E-13 1062690000 521222 675647 686995 655155 727472 816414 659723 678332 704078 766763 TRUE FALSE 541800.247 791684.1164 704898.6541 784742.7036 603816.5693 626814.2214 608012.1874 669240.0691 678738.3703 916995.5293 0.590842845 0.863345667 0.76870457 0.855775932 0.658472752 0.683552102 0.663048148 0.729818246 0.740176313 1 19.80655517 0.633416496 3.82361618 0.999999653 0.730181398 0.501224451 0.081381725 10.66354779 110.3302898 0.077136054 0.019759516 4.299485571 -0.633416496 -0.269818254 SPSSDLDT(ph)DAEGDDFELLDQSELSQLDPASSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 S(0.236)PS(0.236)S(0.236)DLDT(0.293)DAEGDDFELLDQSELSQLDPASSR 124.18 5.41E-07 30170000 16698 14202 18599 15441 21297 21987 19418 17218 14875 12101 TRUE FALSE 17357.24993 16641.08302 19083.70522 18495.18371 17676.94355 16880.85247 17895.96642 16987.22087 14339.65166 14471.95926 1.199371116 1.149884596 1.318667699 1.278001366 1.221461671 1.166452459 1.236595964 1.173802425 0.990857658 1 13.82097263 1.314889063 3.243905297 0.988540681 1.223901643 0.786788447 0.046865265 0.110421578 1.915778086 0.041656571 0.012784381 20.6485264 -1.314889063 0.235360962 SPSSESS(ph)PQHPTPPARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPSSESSPQHPTPPARPR 18 1 O14733;O14733-4;O14733-2;O14733-3 O14733 MAP2K7 Dual specificity mitogen-activated protein kinase kinase 7 1 S(0.005)PS(0.002)S(0.007)ES(0.173)S(0.813)PQHPTPPARPR;SPSS(0.001)ES(0.435)S(0.563)PQHPTPPARPR 111.45 0.00018387 241830000 71503 72786 89449 67911 102245 106245 91802 85394 82511 86163 TRUE FALSE 74325.99365 85286.4293 91780.11442 81343.59311 84865.43142 81571.20891 84606.31936 84249.43311 79541.44523 103044.9902 0.721296528 0.827662065 0.890680025 0.789398815 0.823576491 0.791607712 0.821061938 0.817598536 0.771909873 1 16.65291484 -1.536605719 3.252978933 1.005890507 0.810080286 0.661119969 0.04156104 19083950.41 29461709.72 1026886.953 0.009949186 0.029066603 1.536605719 -0.195810221 SPSSQETHDS(ph)PFCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPSSQETHDSPFCLR 15 0 Q8TB45;Q8TB45-2 Q8TB45 DEPTOR DEP domain-containing mTOR-interacting protein 1 SPSSQETHDS(1)PFCLR;SPSSQETHDS(1)PFCLR;SPSSQETHDS(1)PFCLR 193.85 4.90E-08 570480000 427860 530330 479110 554640 523580 625280 482260 501100 449320 403036 TRUE FALSE 444752.2432 621410.0521 491596.0002 664346.1366 434582.0586 480068.1962 444459.201 494383.5741 433149.061 482003.1876 0.922716394 1.289223947 1.019901969 1.378302372 0.901616566 0.995985522 0.922108427 1.025685279 0.898643561 1 18.87868316 3.192999717 24.99999954 0.962521705 1.152827467 0.369140202 0.124900261 127.0184976 69696.66658 0.032869359 0.039286535 1559.551488 -3.192999717 0.190305762 SPSVPKS(ph)PTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSVPKSPTPK 11 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 SPSVPKS(0.953)PT(0.047)PK 103.83 0.0016237 423390000 1121300 478170 657320 496930 982950 1081100 1042100 678850 816080 343710 TRUE FALSE 1165569.79 560291.9779 674450.2992 595221.2708 815868.5101 830030.9092 960417.479 669751.1261 786709.4402 411053.3938 2.835567854 1.363063744 1.640785137 1.448038819 1.984823681 2.019277597 2.336478651 1.629353111 1.913886255 1 18.64896628 SPSVPKS(ph)PTPKS(ph)PPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPSVPKSPTPKSPPSR 16 2 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 2 S(0.011)PS(0.077)VPKS(0.908)PT(0.082)PKS(0.92)PPS(0.002)R 74.029 0.017924 145330000 358000 135550 196860 102680 329370 309750 248940 181140 237040 113920 TRUE FALSE 372134.1164 158829.6581 201990.3333 122989.7975 273383.805 237815.2568 229427.4323 178712.1146 228508.9767 136240.4429 2.731451165 1.165804035 1.482601855 0.902740735 2.006627396 1.745555518 1.683989185 1.311740558 1.677247753 1 17.0557955 8 0.039692095 2.29E-12 4.092656914 0.165031798 0.466178929 1787.430269 5.401480147 153.196005 493.9693138 100000000 -8 4.092656914 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 S(0.128)PT(0.872)GPSNSFLANMGGTVAHK;S(0.247)PT(0.753)GPSNSFLANMGGTVAHK 272.3 7.41E-44 4127800000 1183320 918440 1179800 1150480 1384130 1446260 1738050 1265940 1376730 826380 TRUE FALSE 1230038.387 1076174.926 1210546.557 1378041.51 1148856.077 1110388.033 1601817.099 1248972.145 1327181.756 988293.339 1.244608598 1.088922573 1.224885881 1.394364867 1.162464657 1.123540946 1.620791152 1.263766633 1.342902662 1 19.91457979 SPT(ph)PPPSSKPSSIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPTPPPSSKPSSIPR 15 1 B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3;H7C5F9 B4E2D5 SUPT20H Transcription factor SPT20 homolog 1 S(0.205)PT(0.795)PPPSSKPSSIPR 100.77 0.0032777 250870000 322290 277630 333600 302760 390550 419050 385700 348330 382630 276220 TRUE FALSE 335014.2581 325310.7928 342293.8901 362645.0244 324164.4505 321731.9883 355467.8262 343661.2061 368859.221 330340.0204 1.014149777 0.984775603 1.036186562 1.097793189 0.981305414 0.973941903 1.07606649 1.040325679 1.116604705 1 18.33359224 2.21392091 24.99920475 1.05984558 1.016568983 0.196363539 0.043019441 398.5132217 404325.315 0.016286144 0.012033895 163.6518465 -2.21392091 -0.043276598 SPTDWALFTYEGNSNDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SPTDWALFTYEGNSNDIR 18 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;F8WC20;F8WBB2;F8WFE1;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 162.32 8.35E-11 66152000 37573 47519 49395 44226 48455 57546 51012 41261 41536 46071 FALSE TRUE 39056.41105 55680.0186 50682.27428 52973.7708 40218.63641 44181.81362 47013.54614 40707.96378 40041.12747 55097.73037 0.708856985 1.01056828 0.91986138 0.961451052 0.729950873 0.801880827 0.853275549 0.738831954 0.726729163 1 15.74970527 3.242404283 24.9986837 0.794585415 0.909474482 0.144341503 0.105290202 147.129791 956903.6863 0.02781782 0.03627987 1747.448088 -3.242404283 0.114889067 SPTLYGISHDDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPTLYGISHDDLK 13 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 166.48 3.36E-05 96218000 136240 108280 142690 123250 172400 172280 185760 132290 144540 88166 FALSE TRUE 141618.8604 126876.2477 146408.6186 147628.4821 143095.5096 132270.5809 171199.6458 130516.8689 139338.0336 105440.4397 1.343117127 1.203297787 1.388543324 1.400112543 1.357121708 1.25445779 1.623662101 1.237825538 1.321485704 1 16.68606877 -0.394018861 8.270469112 1.000000002 1.347846139 0.469463154 0.110899007 0 0 0.102031071 0.024048954 0.403627864 0.394018861 0.347846137 SPTPKS(ph)PPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPTPKSPPSR 10 1 Q9NVD7;Q9NVD7-2 Q9NVD7 PARVA Alpha-parvin 1 S(0.001)PT(0.008)PKS(0.991)PPSR;S(0.005)PT(0.014)PKS(0.981)PPSR;SPT(0.006)PKS(0.994)PPSR 90.376 0.0065849 1223430000 253179 244455 272666 198478 341978 365385 237874 260216 290376 264941 TRUE FALSE 263174.7024 286438.2447 279771.9 237736.356 283848.7017 280529.8712 219228.8143 256728.2301 279925.4245 316851.1163 0.830594209 0.904015261 0.882975901 0.750309353 0.895842517 0.885368101 0.691898507 0.810248779 0.883460433 1 18.27344557 SPTVEYISAHPHILFMLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPTVEYISAHPHILFMLLK 19 0 Q9H9S4;B7ZBJ5;Q5TAW7 Q9H9S4 CAB39L Calcium-binding protein 39-like 0 105.6 0.00019107 121740000 34384 44552 56781 56172 83208 89871 66134 58936 63065 67231 FALSE TRUE 35741.50687 52203.45943 58260.75951 67282.65394 69064.33388 68999.82226 60950.24427 58146.05932 60795.30297 80403.62723 0.444526051 0.649267468 0.724603622 0.836811177 0.858970376 0.858168028 0.758053416 0.723177067 0.756126372 1 16.29497297 4.65166059 1.371474707 0.80812617 0.332291943 0.709176596 0.075756096 0.621816963 1.182223633 0.021420673 0.392440796 44839.48228 -4.65166059 -0.475834227 SPVDIVTGGIS(ph)PVRDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPVDIVTGGISPVRDLDR 18 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6;H0Y9N9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR;SPVDIVTGGIS(1)PVRDLDR 250.75 2.73E-25 1509231000 789377 956027 949287 900614 1028693 1105884 900531 939294 883840 1055046 TRUE FALSE 820542.2135 1120217.2 974026.1991 1078752.761 853836.1313 849059.2008 829945.0271 926704.3003 852030.771 1261762.064 0.650314538 0.887819687 0.771957112 0.854957359 0.676701381 0.672915461 0.657766667 0.734452499 0.675270557 1 20.26700845 -1.294633057 3.530785451 1.000857603 0.734266612 0.507251105 0.079387567 1168988760 1905695228 10821297.51 0.01953771 0.050741925 1.294633057 -0.266590991 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 SPVGKS(0.933)PPS(0.051)T(0.016)GSTYGSSQK;S(0.001)PVGKS(0.998)PPS(0.001)TGSTYGSSQK;SPVGKS(0.999)PPS(0.001)TGSTYGSSQK 198.56 4.45E-16 696490000 692610 352475 510030 380382 642130 668880 745210 516140 559310 260600 TRUE FALSE 719954.7776 413009.8394 523321.8008 455620.4243 532980.972 513542.757 686798.493 509221.9875 539180.5424 311659.5805 2.310067852 1.32519539 1.67914556 1.461916953 1.710138258 1.647768235 2.203681632 1.633904489 1.73003038 1 18.24961154 SPVKAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVKAEAK 8 1 P12036-2;P12036 P12036-2 NEFH Neurofilament heavy polypeptide 0 49.813 0.095847 119380000 15336 269830 267380 282600 188750 366010 180690 271190 209810 365540 FALSE TRUE 15941.47712 316171.2035 274348.1425 338497.4365 156666.3424 281009.7244 166527.0457 267555.1416 202258.9791 437160.5643 0.036465954 0.723238163 0.627568369 0.774309176 0.358372541 0.642806665 0.380928792 0.612029454 0.462665198 1 18.73780374 -1.512405448 2.649237816 1.023977433 0.530080956 0.331062067 0.206352704 12108887.82 11986715.68 2095845.136 0.047168097 0.030732264 1.512405448 -0.493896477 SPVPSPGSS(ph)SPQLQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.028)S(0.525)S(0.447)PQLQVK 229.02 3.75E-15 207530000 199980 158050 201450 176140 228440 264970 236320 221610 224850 154870 TRUE FALSE 207875.3648 185193.858 206699.9525 210979.9663 189609.8504 203434.7332 217796.6209 218639.6804 216757.6924 185213.8113 1.122353475 0.999892269 1.11600723 1.139115732 1.023734942 1.09837777 1.175919978 1.180471796 1.170310631 1 17.49883216 2.384180282 5.805447711 1.150891836 1.079174557 0.096988568 0.063916515 0.310184454 15.77864243 0.021339913 0.017764225 242.2034258 -2.384180282 -0.071717279 SPVPSPGSSS(ph)PQLQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 SPVPSPGS(0.005)S(0.141)S(0.854)PQLQVK;SPVPSPGS(0.012)S(0.354)S(0.635)PQLQVK;SPVPSPGS(0.204)S(0.101)S(0.694)PQLQVK 347.33 3.59E-59 588790000 850620 697990 858440 782950 1025420 1104770 1038070 935300 967020 664200 TRUE FALSE 884203.1344 817864.3529 880811.6516 937815.1731 851119.4747 848203.9105 956703.3609 922763.8333 932217.1391 794337.2731 1.113133129 1.029618502 1.108863554 1.180625919 1.071483743 1.067813307 1.204404468 1.161677621 1.173578492 1 19.59939218 2.254983388 24.99912387 1.151812734 1.095691192 0.06201119 0.063090799 440.6278879 670732.4977 0.021136206 0.01763763 179.8802108 -2.254983388 -0.056121542 SPVQEASSATDTDTNS(ph)QEDPADTASVSSLSLSTGHTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVQEASSATDTDTNSQEDPADTASVSSLSLSTGHTKR 38 1 Q658Y4;E7ER68 Q658Y4 FAM91A1 Protein FAM91A1 1 SPVQEASSATDTDT(0.002)NS(0.998)QEDPADTASVSSLSLSTGHTKR 159.78 4.87E-18 200800000 30307 51263 54082 30558 70032 75408 33926 57879 55414 66374 TRUE FALSE 31503.54376 60067.02148 55491.42135 36602.28119 58127.98565 57895.63482 31266.79147 57103.22668 53419.66096 79378.71449 0.396876467 0.756714465 0.699071807 0.461109523 0.73228681 0.729359693 0.393893901 0.719377065 0.67297211 1 16.27646458 0.6248711 1.420479877 0.999387453 0.61327067 0.427174947 0.135319402 1.296194108 3.712613609 0.121605447 0.035684317 4.215713613 -0.6248711 -0.386116783 SPVS(ph)PLAAQGIPLPAQLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 S(0.379)PVS(0.621)PLAAQGIPLPAQLTK 305.85 1.82E-50 404590000 505400 401340 486770 434600 510360 572600 582760 492660 462860 308950 TRUE FALSE 525353.5823 470267.023 499455.6261 520562.5828 423609.1895 439622.3278 537081.7484 486056.6985 446201.759 369482.8373 1.421861936 1.272770953 1.351769489 1.408895165 1.146492196 1.189831525 1.453604049 1.315505484 1.207638661 1 18.49514783 0.919907555 2.926694273 1.000586055 1.31853534 0.526554898 0.093038042 0.277667076 5.461342989 0.090115419 0.023731494 8.315867377 -0.919907555 0.317949285 SPVVSGDTS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPVVSGDTSPR 11 0 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 SPVVSGDT(0.162)S(0.837)PR 69.815 0.056088 152950000 240290 237270 229830 244370 239990 287510 245270 230170 235420 239340 TRUE FALSE 249776.8347 278019.2768 235819.5586 292705.6566 199196.5855 220740.1598 226045.0965 227084.9476 226947.2802 286234.0906 0.872631329 0.971300366 0.823869575 1.022609348 0.695921947 0.771187525 0.789721085 0.793353954 0.792872993 1 18.12683598 3.237034524 24.99985426 0.794014852 0.919028689 0.285583912 0.087899187 45.06159824 738187.2312 0.02289732 0.028787278 1725.975091 -3.237034524 0.125013837 SPWSNKYDPPLEDGAMPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SPWSNKYDPPLEDGAMPSAR 20 1 P47756-2;B1AK88;B1AK87;P47756;B1AK85;A0A6I8PRV6 P47756-2 CAPZB F-actin-capping protein subunit beta 0 ;; 88.036 0.0020777 1179800000 1680320 1585720 1825620 1540730 2049870 2192540 1840120 1839820 1886410 1757860 FALSE TRUE 1746660.331 1858055.075 1873197.157 1845481.795 1701433.83 1683355.813 1695886.586 1815160.222 1818518.473 2102279.011 0.83084135 0.883828961 0.89103166 0.877848176 0.809328268 0.800729021 0.806689587 0.863424984 0.865022418 1 21.00352272 0.585492834 1.760619038 0.999937995 0.845314415 0.68308545 0.031432959 1.371583811 5.060973857 0.033587473 0.009447861 3.850284617 -0.585492834 -0.15462358 SPWWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SPWWVR 6 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9;A0A1B0GV31;C9JYZ0;A0A1B0GVA5 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 104.94 0.077699 552900000 329920 332120 329900 363080 430840 458720 371870 341860 351140 423990 FALSE TRUE 342945.4964 389159.0265 338497.465 434896.1403 357605.9707 352189.232 342721.8577 337277.9259 338502.54 507062.7227 0.676337425 0.767477097 0.667565273 0.857677208 0.705249971 0.69456739 0.675896378 0.665160168 0.667575282 1 18.95180469 -1.150552474 7.077473123 1.000000284 0.708383347 0.696721098 0.057674455 2.60E-07 3.12E-08 0.05613195 0.013230415 0.070704577 1.150552474 -0.291616936 SPYLYPLYGLGELPQGFAR ddPTM_MDA-MB-175_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 ; 201.95 1.34E-15 345590000 135815 171298 164890 152729 175487 198158 165218 168289 153826 164506 FALSE TRUE 141177.0811 200717.099 169187.1689 182938.3403 145657.7824 152138.8076 152267.7814 166033.3612 148289.8323 196737.801 0.717590012 1.020226402 0.859962691 0.929858621 0.740365002 0.773307452 0.773963014 0.843932179 0.753743467 1 17.58591466 3.248802854 24.9934667 0.804546167 0.890221589 0.094317016 0.098769636 380.5245833 928564.159 0.02525291 0.033819241 1773.384279 -3.248802854 0.085675422 SPYQEFTDHLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SPYQEFTDHLVK 12 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 0 ;;;;; 194.3 1.71E-06 5124230000 4835450 4157150 5075640 4119850 6067360 5968830 5491660 5066070 5250090 4332620 FALSE TRUE 5026357.3 4871108.174 5207915.348 4934744.033 5036032.314 4582659.691 5061209.339 4998167.618 5061140.286 5181513.936 0.970055733 0.940093616 1.005095309 0.952374942 0.971922951 0.884424851 0.97678196 0.9646153 0.976768633 1 22.30494226 1.051356209 1.446246503 0.999203637 0.956680866 0.170506074 0.029441081 0.723755548 3.071203328 0.027184903 0.008140033 11.25527756 -1.051356209 -0.042522771 SQAEEEIDEIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQAEEEIDEIRK 12 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 0 157.2 0.00011837 82890000 95442 65099 84224 64675 103420 97522 87892 87918 82849 65796 FALSE TRUE 99210.12386 76279.24685 86418.94663 77467.52196 85840.70534 74873.99346 81002.79538 86739.60301 79867.28067 78687.46646 1.260812278 0.969395131 1.098255548 0.98449633 1.090906967 0.951536462 1.029424367 1.102330611 1.014993674 1 16.26384624 4.74874698 24.8736377 1.033799284 1.260812412 0.644213078 0.051935995 820.4252431 2003318.36 0.01177189 0.160677594 56072.12043 -4.74874698 0.227013127 SQAFIEMETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQAFIEMETR 10 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 139.86 9.38E-05 409115000 273837 341784 291540 335940 365920 403210 336981 330835 297946 333040 FALSE TRUE 284648.2962 400482.7433 299137.7719 402387.9293 303721.0491 309570.5882 310567.5487 326400.698 287222.9817 398292.8116 0.714670935 1.005498296 0.751049889 1.010281676 0.762557195 0.777243724 0.779746809 0.819499344 0.721135239 1 18.60346992 SQAIHQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQAIHQLK 8 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 77.677 0.032593 546110000 855140 794840 916050 743330 1122480 1235720 1033200 900920 934550 777860 FALSE TRUE 888901.5875 931347.587 939923.0155 890358.4554 931681.2505 948742.7575 952215.0842 888844.641 900915.7281 930266.774 0.95553406 1.001161831 1.010380078 0.957100135 1.001520506 1.019860952 1.023593566 0.955472845 0.968448786 1 19.82728497 4.747982674 23.91067861 0.991927948 0.955534024 0.187021041 0.023364733 1277.080694 3240760.783 0.005915415 0.071092746 55973.52702 -4.747982674 -0.036393924 SQANGAGALSYVS(ph)PNTSK ddPTM_MDA-MB-175_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 167.63 2.38E-11 50785000 121710 86794 107700 76201 130600 143430 118540 109490 114430 83594 TRUE FALSE 126515.2048 101700.1943 110506.7505 91273.33036 108400.6586 110120.5562 109248.5251 108022.4656 110311.6867 99972.6438 1.26549824 1.017280233 1.105369892 0.912983061 1.084303211 1.101506892 1.092784195 1.080520246 1.10341872 1 16.60924575 7.999960215 0.007424208 0.001602863 2.251254838 0.09035431 0.082234811 80991.26639 46.49590665 6307.086149 7861.217991 99990839.48 -7.999960215 2.249651974 SQATS(ph)PGQTNGDSSLEVLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQATSPGQTNGDSSLEVLATR 21 0 Q96JY6;Q96JY6-5;Q96JY6-3;A0A087WVI1;Q96JY6-4;C9JS55;C9JSR2;C9K0F0;C9J0X3;Q96JY6-2;C9J760 Q96JY6 PDLIM2 PDZ and LIM domain protein 2 1 SQAT(0.001)S(0.999)PGQTNGDSSLEVLATR;SQAT(0.028)S(0.972)PGQTNGDSSLEVLATR 306.4 8.46E-56 316110000 288900 341950 340500 330330 350510 431440 350690 349190 349410 378300 TRUE FALSE 300305.9951 400677.2525 349373.7097 395668.2881 290930.4354 331244.5985 323202.0014 344509.6792 336834.8024 452420.642 0.663776069 0.88562991 0.772232028 0.874558434 0.643052965 0.732160666 0.714383853 0.761480903 0.744516875 1 18.78730523 -1.990996321 6.229595055 1.213405085 0.757174643 0.496482755 0.074087111 0.038431285 5.55E-05 0.012554651 0.016235029 0.010209481 1.990996321 -0.456230442 SQDADS(ph)PGSSGAPENLTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQDADSPGSSGAPENLTFK 19 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;H0Y8L4;H0Y8U8 P55196-5 MLLT4 Afadin 1 SQDADS(1)PGSSGAPENLTFK;SQDADS(1)PGSSGAPENLTFK;SQDADS(0.991)PGS(0.009)SGAPENLTFK;SQDADS(1)PGSSGAPENLTFK 300.74 6.73E-50 660820000 1239070 903120 1129740 892190 1302560 1419680 1343920 1148770 1214020 845460 TRUE FALSE 1287989.44 1058223.835 1159181.952 1068662.519 1081151.316 1089980.835 1238580.039 1133372.617 1170327.657 1011111.7 1.273834969 1.046594392 1.146443022 1.05691836 1.06926991 1.078002397 1.224968556 1.120917321 1.15746624 1 19.94751095 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR;SQDATFSPGSEQAEKS(1)PGPIVSR 247.41 6.73E-38 2170460000 1474950 911770 1200470 887970 1662540 1731260 1354470 1261090 1437160 876008 TRUE FALSE 1533182.165 1068359.405 1231755.234 1063607.816 1379942.045 1329201.102 1248303.102 1244187.151 1385436.892 1047644.995 1.463455819 1.019772356 1.175737239 1.01523686 1.317184782 1.268751446 1.19153254 1.187603775 1.322429734 1 19.9987185 -0.997062918 5.191271062 0.999998716 1.206614016 0.19795331 0.129824953 1.80E-06 3.48E-07 0.117352375 0.027660048 0.10067858 0.997062918 0.2066153 SQDDQHMLPFWTDLCSIFGSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQDDQHMLPFWTDLCSIFGSNK 22 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;K7EMK2 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 0 178.58 5.98E-17 57884000 73656 60329 86840 75699 92903 88316 89153 81653 82310 60215 FALSE TRUE 76563.99575 70690.03646 89103.12174 90672.03626 77111.38124 67805.94744 82164.9549 80558.57509 79347.67918 72012.97636 1.063197213 0.981629146 1.237320359 1.259106912 1.070798419 0.941579572 1.140974295 1.118667484 1.101852516 1 16.13596928 SQDIYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQDIYLR 7 0 J3QQ67;Q07020;F8VYV2;G3V203;A0A075B7A0;F8VXR6 J3QQ67 RPL18 60S ribosomal protein L18 0 ;;;; 195.6 0.0010794 3787340000 1577760 1622260 1706050 1623080 1830900 2118160 1877140 1770870 1666360 1487760 FALSE TRUE 1640051.183 1900870.536 1750511.065 1944120.38 1519684.272 1626249.441 1730004.862 1747134.384 1606388.029 1779258.087 0.921761264 1.068350089 0.983843253 1.092657886 0.854111207 0.914004243 0.972318111 0.981945451 0.902841494 1 20.76284436 3.244151782 24.99994442 0.941045754 1.018002181 0.30274067 0.058662026 175.788599 786003.3064 0.016029758 0.021108765 1754.493574 -3.244151782 0.076956427 SQDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQDLAK 6 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 114.02 0.059648 1400340000 1415840 1102320 1252040 984690 1670100 1614000 1583730 1281260 1459230 1082090 FALSE TRUE 1471738.456 1291634.885 1284669.191 1179458.743 1386216.999 1239172.96 1459593.104 1264086.805 1406712.597 1294104.818 1.137263718 0.998091397 0.992708762 0.911408973 1.0711783 0.957552235 1.12787858 0.976804033 1.087015965 1 20.30352304 SQDLHCGACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQDLHCGACR 10 0 Q9Y2B0;F8VXJ7;F8W031;F8W1U5;F8VP03;Q9Y2B0-2 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ; 77.062 0.034125 581840000 788480 1189490 917530 1038040 1713970 1519450 1042860 1041560 1006180 1513930 FALSE TRUE 819609.7992 1393775.655 941441.5856 1243361.214 1422629.992 1166580.765 961117.9082 1027599.592 969967.7783 1810555.598 0.452684138 0.769805499 0.519973862 0.686729099 0.785742229 0.644321979 0.530841422 0.567560363 0.535729353 1 20.78800105 -1.090133618 4.017878388 1.000078567 0.613941654 0.553688125 0.104898962 5779359.818 3136122.451 4000.058814 0.024103076 0.081258047 1.090133618 -0.386136913 SQDPQEDKKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQDPQEDKKEEK 12 2 Q8IWE2;Q8IWE2-2 Q8IWE2 FAM114A1 Protein NOXP20 0 103.85 0.0012381 136750000 286950 78432 126380 64738 208440 247440 182180 124250 151030 48869 FALSE TRUE 298279.0076 91902.08588 129673.5666 77542.98318 173009.4433 189975.81 167900.2556 122584.632 145594.4598 58443.9449 5.103676833 1.572482591 2.218768203 1.326792422 2.960262925 3.250564457 2.872842616 2.097473608 2.491181252 1 15.83476594 4.747584958 24.85667264 2.284718827 5.10367841 0.606078366 0.699467717 772.9368548 2128930.489 0.166377052 2.036377771 55922.29134 -4.747584958 2.818959584 SQDS(ph)PGESEETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQDSPGESEETLR 13 0 Q8IWU2 Q8IWU2 LMTK2 Serine/threonine-protein kinase LMTK2 1 SQDS(1)PGESEETLR 216.98 2.79E-11 75991000 88285 98699 88813 111210 101780 122900 88658 86211 91454 90783 TRUE FALSE 91770.55997 115649.7855 91127.53974 133207.0061 84479.47195 94358.33757 81708.7543 85055.48256 88162.5884 108570.1907 0.845264795 1.065207537 0.839342173 1.226920623 0.778109271 0.86909986 0.752589212 0.783414692 0.812033099 1 16.72826852 SQDSYPGS(ph)PSLSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 SQDSYPGS(0.995)PS(0.005)LSPR;SQDSYPGS(0.999)PS(0.001)LSPR 196.97 2.53E-08 304920000 391470 454430 456460 449790 502010 565960 406810 456670 396590 415800 TRUE FALSE 406925.5379 532474.8175 468355.7226 538757.1195 416678.5195 434524.3672 374923.1692 450549.0856 382316.8034 497268.049 0.818322309 1.070800383 0.941857663 1.083434016 0.837935436 0.873823219 0.753965934 0.906048733 0.768834443 1 18.92366421 3.210282097 24.9487496 0.849623456 0.982564399 0.284221178 0.094228009 226.8402451 200129.4272 0.025017149 0.02990664 1622.863889 -3.210282097 0.132940943 SQDSYPGSPSLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;Q6VN20;R4GMX8;Q6VN20-2;Q6VN20-3 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 SQDS(0.004)Y(0.003)PGS(0.087)PS(0.097)LS(0.809)PR 63.257 0.073976 161280000 8370.1 29424 36191 38112 18202 40019 27917 32214 23318 40970 TRUE FALSE 8700.558011 34477.34311 37134.16719 45650.43985 15108.03054 30725.19374 25728.79259 31782.22402 22478.78973 48997.28708 0.17757224 0.703658206 0.757882107 0.931693213 0.308344226 0.627079489 0.525106473 0.64865273 0.458776211 1 15.58041425 -1.339801999 3.180897821 1.00326943 0.587617873 0.273797726 0.208029956 60781371.34 83862651.55 1875594.998 0.049726619 0.045729663 1.339801999 -0.415651557 SQDVAVS(ph)PQQQQCSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 430.86 1.86E-153 7909000000 5494575 4410413 5416227 4693793 6411335 7193015 6324023 5888492 6406945 4729362 TRUE FALSE 5711505.064 5167867.124 5557378.325 5622211.246 5321538.567 5522546.277 5828329.553 5809566.396 6176360.301 5655989.935 1.009815281 0.913698077 0.982565102 0.994027802 0.940867758 0.976406666 1.030470284 1.027152888 1.092003411 1 22.43134812 2.228076071 3.268773025 1.040094349 0.966455483 0.507478802 0.032886406 0.188108158 4.204202273 0.012563595 0.009276355 169.0737054 -2.228076071 -0.073638865 SQDVELWEGEVVK ddPTM_MDA-MB-175_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 ; 136.24 0.00017354 30410000 61026 57109 68083 60051 80304 86855 73459 68943 72377 69196 FALSE TRUE 63435.3536 66917.0265 69857.29891 71928.90857 66653.95476 66684.24255 67701.09163 68018.93185 69772.16591 82753.63136 0.766556737 0.808629487 0.844159921 0.86919338 0.805450512 0.805816512 0.818104179 0.82194498 0.843131168 1 16.336535 0.545037908 1.730309616 0.999997482 0.818699041 0.823165582 0.025229619 1.053185591 3.537298223 0.025050961 0.00706267 3.507824908 -0.545037908 -0.181298442 SQEADVQDWEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 ; 217.45 8.53E-11 962890000 1086050 1201760 1155500 1171670 1246330 1472470 1268670 1241730 1172180 1096580 FALSE TRUE 1128928.093 1408152.932 1185613.279 1403422.829 1034479.272 1130511.158 1169228.33 1225086.64 1129993.471 1311433.856 0.860834946 1.073750632 0.904058771 1.070143815 0.788815438 0.862042072 0.891564851 0.934158162 0.861647323 1 20.32271361 3.241850973 24.99999658 0.888612201 0.978869543 0.226310083 0.079211826 121.1614711 920571.8506 0.020799024 0.027033939 1745.223182 -3.241850973 0.090257342 SQECLIPVHVDGDGHCLVHAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQECLIPVHVDGDGHCLVHAVSR 23 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 0 88.836 0.0020953 55947000 23526 30667 27027 20919 30300 39842 29269 25620 23535 32161 FALSE TRUE 24454.82465 35933.81869 27731.34582 25056.71576 25149.61682 30589.29931 26974.8193 25276.60581 22687.97995 38462.33219 0.63581232 0.934260006 0.721000112 0.651461166 0.653876543 0.795305369 0.701330828 0.657178189 0.589875305 1 15.23115862 -1.110658643 4.928768991 1.000012098 0.70753179 0.474764301 0.093206625 1.24E-05 2.24E-06 0.090235154 0.02126775 0.077507077 1.110658643 -0.292480309 SQEEPKDTFEHDPSESIDEFNK ddPTM_MDA-MB-175_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 0 ; 150.83 3.19E-08 380750000 883340 393770 601360 403080 874140 776560 801440 585950 721810 355300 FALSE TRUE 918214.9453 461396.9344 617031.9356 482808.0209 725553.995 596215.7089 738621.0386 578096.2987 695832.1991 424914.2324 2.160941845 1.085858979 1.452132898 1.136248175 1.707530461 1.403143655 1.738282652 1.360501143 1.637582707 1 18.69681214 -1.371359412 6.288084042 0.999944783 1.495562737 0.210624508 0.298726547 0.000208521 2.08E-05 0.260772561 0.061457873 0.042524634 1.371359412 0.495617955 SQEPIPDDQKVS(ph)DDDKEKGEGALPTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQEPIPDDQKVSDDDKEKGEGALPTGK 27 3 E5RJU9;Q86UE4;H0YBJ8 E5RJU9 MTDH Protein LYRIC 1 SQEPIPDDQKVS(1)DDDKEKGEGALPTGK 151.5 5.90E-08 1077100000 494250 35646 79123 48458 167060 307680 161140 83929 100940 29890 TRUE FALSE 513763.3716 41767.92321 81185.01038 58042.84777 138663.2009 236225.9829 148509.4257 82804.06904 97307.18912 35746.37322 14.37246147 1.168452054 2.271139785 1.623740887 3.87908446 6.608390213 4.154531281 2.316432734 2.722155574 1 15.12550925 4.744304972 24.86366247 3.018735671 14.37246675 0.823584061 1.596897097 247.4659754 1071089.302 0.404637946 3.598059576 55501.53212 -4.744304972 11.35373108 SQEPLDLVLVPDDCRPGT(ph)PPSDLIEIQVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQEPLDLVLVPDDCRPGTPPSDLIEIQVVK 30 1 Q8NCA9 Q8NCA9 ZNF784 Zinc finger protein 784 1 SQEPLDLVLVPDDCRPGT(0.933)PPS(0.067)DLIEIQVVK 101.25 0.00070127 40400000 98124 85129 102580 86549 122700 134340 105160 106650 106390 85204 TRUE FALSE 101998.0113 99749.24354 105253.3191 103668.1339 101843.4978 103141.5709 96917.28442 105220.5312 102561.0447 101898.0925 1.000980576 0.978911785 1.032927276 1.017370702 0.999464223 1.012203158 0.951119713 1.032605505 1.006506032 1 16.63676752 SQESGYYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQESGYYDR 9 0 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;; 132.13 0.00072948 3217490000 2007360 2196580 2249460 2061300 2459990 2833130 2399510 2238470 2181760 2078760 FALSE TRUE 2086612.123 2573825.528 2308082.776 2469018.988 2041841.778 2175178.494 2211430.136 2208466.971 2103238.884 2486053.222 0.839327213 1.035305884 0.928412455 0.993148081 0.821318611 0.874952505 0.889534511 0.888342595 0.846015228 1 21.24542575 3.248766139 24.99993723 0.881390956 0.953735655 0.181145102 0.064048376 290.9374425 712690.2239 0.016320555 0.021853029 1773.234364 -3.248766139 0.072344699 SQESGYYDRMDYEDDRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQESGYYDRMDYEDDRLR 18 2 P43243;A0A0R4J2E8;D6REM6;D6R991;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 95.666 0.00097638 71071000 13811 36121 27515 15447 42076 39169 11383 26483 28074 71586 FALSE TRUE 14356.26894 42324.50077 28232.0635 18502.3705 34923.93655 30072.59336 10490.77072 26128.0387 27063.62222 85611.9061 0.167690098 0.49437634 0.329767959 0.216119128 0.407933174 0.351266485 0.122538689 0.305191648 0.316119842 1 16.38552383 0.571443482 3.833417683 0.999999737 0.301211833 0.80129737 0.104417943 10.5744769 94.04162791 0.097584331 0.024992137 3.727721701 -0.571443482 -0.698787904 SQET(ph)PEKPR ddPTM_MDA-MB-175_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(0.011)QET(0.989)PEKPR 73.466 0.070876 234950000 274680 204650 229620 180890 309640 263830 295580 235650 255490 164050 TRUE FALSE 285524.5785 239797.0455 235604.0858 216669.5021 257007.5034 202559.4809 272411.6672 232491.4972 246294.9648 196192.4566 1.455329035 1.222254157 1.20088249 1.104372237 1.309976479 1.032452952 1.388492055 1.185017514 1.255374285 1 17.58191005 -2.354816295 1.784513421 2.08E-05 1.232713272 0.267248377 0.118440311 1179546.863 131242.6547 4739862.383 0.029282509 0.004417573 2.354816295 1.232692451 SQFFEQGS(ph)SDSVVPDLPVPTISAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQFFEQGSSDSVVPDLPVPTISAPSR 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.114)QFFEQGS(0.391)S(0.391)DS(0.104)VVPDLPVPTISAPSR 61.522 0.036145 101190000 7887.4 8259.8 8053.7 8990 11283 8698 8036.9 8498.4 8419.6 7715.3 TRUE FALSE 8198.800642 9678.356398 8263.586038 10768.19517 9365.11969 6678.021319 7406.946777 8384.492849 8116.580241 9226.965317 0.888569574 1.04892086 0.895590885 1.167035401 1.014972894 0.72375056 0.80275004 0.908694523 0.879658692 1 13.17164052 2.780717661 24.6996135 0.856690132 1.008712059 0.331161314 0.0991489 459.9480723 269480.5206 0.029727603 0.031530637 603.5561238 -2.780717661 0.152021927 SQGDEAGGHGEDRPEPLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 202.87 6.75E-22 13485120000 9264950 4515447 5777370 4557093 8437360 9940680 8167500 6535970 6581850 4149097 TRUE FALSE 9630737.38 5290939.897 5927933.008 5458472.394 7003180.561 7632107.722 7527310.008 6448366.013 6344970.504 4962033.118 1.940885349 1.06628468 1.19465809 1.100047554 1.411353047 1.538100924 1.516981009 1.299541107 1.27870378 1 22.24249993 0.798050074 1.861685164 1.001014533 1.368503971 0.187847911 0.240308418 1.280214096 7.747889878 0.224194607 0.062835948 6.281307781 -0.798050074 0.367489438 SQGKDDDSFDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQGKDDDSFDRK 12 2 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 88.087 0.0057276 295420000 145910 72728 106190 67444 175490 139630 128010 104230 131340 67137 FALSE TRUE 151670.6395 85218.46825 108957.3986 80784.2219 145660.2725 107203.0486 117976.2417 102832.9673 126613.0991 80291.20973 1.889006779 1.061367347 1.357027737 1.006140301 1.81414968 1.335177898 1.469354393 1.280750006 1.576923545 1 16.29295443 -1.182878525 4.452358794 0.999908291 1.398596184 0.173725615 0.271546879 0.000225675 4.14E-05 0.240030357 0.056562735 0.065632882 1.182878525 0.398687893 SQGRLS(ph)VGS(ph)NRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQGRLSVGSNRDR 13 2 H3BLT5;H0Y781;Q2LD37-4;Q2LD37 H3BLT5 KIAA1109 Uncharacterized protein KIAA1109 2 S(0.53)QGRLS(0.536)VGS(0.933)NRDR;S(0.35)QGRLS(0.67)VGS(0.98)NRDR 51.265 0.086558 1880740000 34477 73044 36994 70394 50631 63766 37017 47633 33152 105516 TRUE FALSE 35838.17858 85588.7388 37958.09403 84317.72309 42024.7607 48957.31288 34115.51081 46994.55755 31958.866 126189.84 0.284002092 0.678253802 0.300801507 0.668181552 0.333028085 0.387965568 0.270350694 0.372411579 0.253260215 1 16.94523623 -1.517721386 5.901552283 1.000856983 0.398598633 0.604171506 0.147053636 0.001568383 0.000128169 0.134678404 0.03170316 0.030358381 1.517721386 -0.60225835 SQGS(ph)SQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQGSSQFR 8 0 Q15172 Q15172 PPP2R5A Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform 1 SQGS(0.761)S(0.238)QFR;SQGS(0.812)S(0.188)QFR;SQGS(0.708)S(0.292)QFR;S(0.001)QGS(0.888)S(0.111)QFR 102.53 0.0051894 2232750000 1020110 1214240 1150080 1161180 1319100 1605820 1181480 1205200 1143020 1143880 TRUE FALSE 1060384.73 1422776.275 1180052.03 1390857.938 1094879.853 1232892.641 1088872.51 1189046.265 1101882.933 1368001.385 0.775134252 1.040040083 0.862610259 1.01670799 0.80034996 0.901236398 0.795958632 0.869184986 0.805469165 1 20.38363826 3.220245979 24.99931408 0.85385157 0.927580627 0.096980925 0.089692008 446.7457078 609802.5769 0.023412686 0.028033912 1660.527142 -3.220245979 0.073729057 SQHSGNAQVTQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQHSGNAQVTQTK 13 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 140.31 3.93E-05 179656000 147585 362317 398755 345765 437470 520170 371506 437800 404910 372901 FALSE TRUE 153411.7698 424542.1263 409146.8829 414156.285 363109.0057 399368.4008 342386.389 431932.0071 390337.3682 445963.8113 0.34400049 0.951965419 0.917444134 0.928676889 0.814211818 0.895517507 0.767744782 0.968536003 0.875266912 1 18.76656712 4.742053815 24.95990851 0.896673474 0.344000278 0.863615625 0.066509816 107.758807 769933.3708 0.015126295 0.111292176 55214.58539 -4.742053815 -0.552673196 SQIDVALS(ph)QDSTYQGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 SQIDVALS(0.999)QDS(0.001)TYQGER;SQIDVALS(0.996)QDS(0.004)TYQGER;SQIDVALS(0.999)QDST(0.001)YQGER;SQIDVALS(1)QDSTYQGER 363.55 3.00E-89 1041050000 520587 615690 567052 593580 622045 743689 519339 554884 536206 628144 TRUE FALSE 541140.1767 721429.9681 581829.841 710988.3523 516310.0131 570978.5005 478631.8521 547446.6876 516908.0508 751216.7903 0.720351547 0.960348567 0.774516556 0.946448963 0.687298287 0.760071537 0.637142112 0.728746608 0.688094379 1 19.51886978 3.223076202 24.99486568 0.72916863 0.852847308 0.141183601 0.1141151 336.8584427 543754.1608 0.0299343 0.035897185 1671.383852 -3.223076202 0.123678678 SQIHDIVLVGGSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;E9PNE6;P11142-2;A8K7Q2;E9PN89 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;;; 149 7.60E-06 16692100000 4658450 6731670 6684740 7092420 7475210 8843530 7301090 7485640 6585810 6676640 FALSE TRUE 4842369.203 7887781.957 6858949.816 8495279.507 6204576.474 6789754.182 6728811.488 7385307.24 6348787.985 7984799.776 0.606448419 0.987849687 0.859000853 1.063931438 0.777048473 0.850334933 0.842702595 0.92492078 0.795109228 1 22.9288248 -3.782514441 0.014021697 1.951173195 1.15E-06 0.101484534 0.118532962 16271.52257 21.25811334 1754.330118 1243.096108 0.000165001 3.782514441 -1.951172044 SQIYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQIYGSR 7 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;; 136.27 0.0069713 546640000 324303 451030 418050 433920 484510 600470 394570 440700 398110 522790 FALSE TRUE 337106.7329 528490.894 428944.7264 519748.0809 402153.1633 461019.9427 363642.5724 434793.1373 383782.0989 625220.6911 0.539180385 0.845286955 0.686069307 0.831303391 0.643217937 0.737371538 0.581622741 0.695423462 0.61383461 1 19.254006 -1.038991617 4.273095607 1.000022845 0.690949247 0.498938168 0.094302329 26485502.5 68465417.3 9833.191575 0.02110298 0.091413089 1.038991617 -0.309073598 SQKPVMVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQKPVMVK 8 1 P46779 P46779 RPL28 60S ribosomal protein L28 0 87.913 0.013668 468290000 511530 356920 498260 350030 636490 651930 594580 466840 497530 367510 FALSE TRUE 531725.5994 418218.2335 511245.0649 419264.8893 528299.6571 500529.1376 547975.266 460582.7734 479623.9925 439516.5481 1.209796541 0.951541496 1.163198672 0.953922875 1.202001744 1.138817502 1.246768224 1.047930449 1.091253548 1 18.74555796 3.21087088 24.99999208 1.127686784 1.06786538 0.057714812 0.099782987 566.5106763 511479.2129 0.027158593 0.032467891 1625.065535 -3.21087088 -0.059821404 SQLDDHPES(ph)DDEENFIDANDDEDMEKFTDADKETEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQLDDHPESDDEENFIDANDDEDMEKFTDADKETEIVK 38 2 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 S(0.003)QLDDHPES(0.996)DDEENFIDANDDEDMEKFT(0.001)DADKETEIVK;SQLDDHPES(1)DDEENFIDANDDEDMEKFTDADKETEIVK 156.56 1.97E-14 196944000 237873 76566 130815 61984 204223 159660 170516 118372 138393 56699 TRUE FALSE 247264.4097 89715.6149 134224.1464 74244.2502 169509.2474 122581.3847 157150.5104 116785.417 133412.263 67808.08348 3.646532936 1.323081413 1.97947117 1.094917396 2.499838348 1.807769493 2.317577821 1.722293434 1.967497916 1 16.04916965 -1.97818134 0.238604297 1.77E-37 2.147210357 0.19689357 0.659371821 55.4263471 1.992229445 33.71767065 1.08969569 0.010515227 1.97818134 2.147210357 SQLDIIIHSLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQLDIIIHSLKK 12 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 176.08 1.68E-05 958820000 2719700 1701790 2567000 1979700 3377500 3009700 3113600 2621800 2907200 1660770 FALSE TRUE 2827075.856 1994059.194 2633898.129 2371278.751 2803393.756 2310742.787 2869547.896 2586659.059 2802570.44 1986166.084 1.423383411 1.003974043 1.326121793 1.193897514 1.411459887 1.163418712 1.444767343 1.302337745 1.411045361 1 20.92155484 SQLEEKENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQLEEKENK 9 1 P04080;A0A1W2PS52 P04080 CSTB Cystatin-B 0 108.7 0.0023433 242120000 246140 116790 148570 101700 195950 201720 171150 159400 166100 92836 FALSE TRUE 255857.7973 136847.774 152441.8563 121815.9565 162642.489 154873.5871 157734.8158 157263.5037 160122.0934 111025.4367 2.304497102 1.232580371 1.373035412 1.097189617 1.46491195 1.394937878 1.420708807 1.416463725 1.442210886 1 16.76053072 4.742409301 24.99582572 1.339070971 2.304497474 0.793118688 0.151069147 159.7234644 1037304.916 0.033992318 0.258343275 55259.79898 -4.742409301 0.965426503 SQLLGSAHEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQLLGSAHEVQR 12 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ;;; 186.16 1.21E-05 1177610000 784240 1385470 1368900 1318920 1602660 1777740 1345470 1459810 1351810 1455930 FALSE TRUE 815202.4008 1623413.695 1404574.659 1579798.439 1330240.426 1364886.827 1240008.546 1440243.635 1303158.622 1741191.608 0.468186498 0.932357868 0.806674379 0.907308783 0.763982792 0.78388089 0.712160879 0.827159761 0.748429188 1 20.73164354 -2.270026152 2.187504683 1.846414726 0.782799122 0.238435174 0.120795594 8143666.627 1334680.685 34024435.49 0.027544185 0.005369995 2.270026152 -1.063615604 SQLPTLEQDGGTQNPVS(ph)SPGMSQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQLPTLEQDGGTQNPVSSPGMSQELR 26 0 P46937-6;P46937-7;P46937-5;P46937-3;P46937;P46937-9;P46937-2;P46937-8;P46937-4;H0YCI3 P46937-6 YAP1 Transcriptional coactivator YAP1 1 SQLPTLEQDGGTQNPVS(0.5)S(0.5)PGMSQELR 136.71 1.37E-05 59838000 8148.3 11684 15531 11755 12443 19065 10879 12150 10684 13003 TRUE FALSE 8470.001176 13690.63611 15935.75062 14080.10391 10327.9433 14637.44268 10026.27555 11987.14912 10299.48493 15550.68889 0.54467048 0.880387757 1.024761715 0.905432808 0.664146995 0.941272942 0.644747999 0.770843607 0.662316956 1 13.92469087 2.237414524 24.99999252 0.748800644 0.834397597 0.022789714 0.15800077 95.68508379 2087118.669 0.056022549 0.043718251 172.7485952 -2.237414524 0.085596953 SQLQALHIGLDSS(ph)SIGS(ph)GPGDAEADDGFPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.068)S(0.495)S(0.445)IGS(0.991)GPGDAEADDGFPESR;SQLQALHIGLDS(0.07)S(0.485)S(0.445)IGS(0.999)GPGDAEADDGFPESR 118.58 4.73E-07 176462000 40878 70301 70784 64519 71669 96526 76117 64368 63399 66650 TRUE FALSE 42491.895 82374.64988 72628.68919 77280.66563 59486.72898 74109.29937 70150.75065 63505.25224 61117.28237 79708.79141 0.533089189 1.033444974 0.911175391 0.969537541 0.746300727 0.929750634 0.880087998 0.796715784 0.766757108 1 16.28245123 1.767492155 24.99902417 0.832555143 0.869244972 0 0.14294213 142.8285295 123485.0972 0.062268184 0.034537193 58.54531611 -1.767492155 0.036689828 SQLQALHIGLDSS(ph)SIGSGPGDAEADDGFPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.06)S(0.47)S(0.47)IGSGPGDAEADDGFPESR;SQLQALHIGLDS(0.066)S(0.501)S(0.391)IGS(0.041)GPGDAEADDGFPESR;SQLQALHIGLDS(0.081)S(0.559)S(0.294)IGS(0.066)GPGDAEADDGFPESR 171.8 1.48E-14 301727000 45331 60587 61492 72581 73197 85214 60936 71459 61133 68815 TRUE FALSE 47120.70288 70992.34595 63094.53204 86937.30517 60755.00009 65424.33993 56159.67709 70501.20899 58932.83527 82297.98171 0.572562071 0.862625601 0.766659531 1.056372263 0.738231957 0.794968948 0.682394342 0.856657813 0.716090894 1 16.32856943 -2.35617769 2.186843155 2.24842594 0.79232735 0.218765434 0.121895917 3891278.345 448990.8405 24072803.08 0.028742608 0.004403746 2.35617769 -1.45609859 SQLQALHIGLDSSS(ph)IGS(ph)GPGDAEADDGFPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 2 SQLQALHIGLDS(0.079)S(0.438)S(0.483)IGS(1)GPGDAEADDGFPESR 94.406 4.80E-05 34555000 12089 13383 18428 17850 16825 22513 17501 16241 17769 18191 TRUE FALSE 12566.28305 15681.42614 18908.24882 21380.67672 13965.09251 17284.69694 16129.22589 16023.31596 17129.49716 21755.17816 0.577622622 0.720813501 0.869137852 0.982785641 0.641920393 0.794509556 0.741397095 0.736528832 0.787375632 1 14.40907121 -2.613899799 1.163664399 2.220544831 0.764401112 0.311374681 0.106389413 42592.34888 2535.759917 134925.1422 0.03137199 0.002432765 2.613899799 -1.45614372 SQLQALHIGLDSSS(ph)IGSGPGDAEADDGFPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQLQALHIGLDSSSIGSGPGDAEADDGFPESR 32 0 O75116;E9PF63;Q14DU5 O75116 ROCK2 Rho-associated protein kinase 2 1 SQLQALHIGLDS(0.035)S(0.183)S(0.782)IGSGPGDAEADDGFPESR;SQLQALHIGLDS(0.027)S(0.175)S(0.798)IGSGPGDAEADDGFPESR 259.77 1.72E-59 449090000 60624 97355 103993 78543 96174 115226 79725 97219 88602 104385 TRUE FALSE 63017.48233 114074.9639 106703.143 94078.57097 79826.37783 88466.50777 73475.94618 95915.93832 85413.23133 124837.2422 0.504797136 0.913789523 0.854738067 0.753609815 0.639443618 0.708654775 0.58857393 0.768327918 0.684196718 1 16.92968887 -1.930121257 7.706672138 1.081007623 0.720064194 0.360689497 0.114309743 0.065258942 0.000591723 0.045397455 0.025413379 0.011745696 1.930121257 -0.360943429 SQNKEDYAGLKEEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQNKEDYAGLKEEFR 15 2 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 126.63 4.67E-05 838410000 1376300 722570 1098200 938050 1532000 1474500 1579200 1168300 1300700 700320 FALSE TRUE 1430637.387 846665.7767 1126819.994 1123593.49 1271591.187 1132069.721 1455418.178 1152640.849 1253888.061 837534.2956 1.708153797 1.010902815 1.345401615 1.341549231 1.518255663 1.35166969 1.737741589 1.376231225 1.497118468 1 19.67578874 3.363142393 7.125084106 1.447132652 1.324309837 0 0.234974281 0.686911896 40.25335022 0.060419687 0.081926595 2307.503629 -3.363142393 -0.122822816 SQNKEDYAGLKEEFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQNKEDYAGLKEEFRK 16 3 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 ; 193.27 1.76E-10 2545300000 5179300 2510940 4456000 2352430 6130600 4689900 4464700 4076200 4957200 2394450 FALSE TRUE 5383782.763 2942174.413 4572127.021 2817733.633 5088522.802 3600741.801 4114745.148 4021565.206 4778791.34 2863596.633 1.880077208 1.02744024 1.596637937 0.983984127 1.776969124 1.257419344 1.436915067 1.404375588 1.668807431 1 21.44939686 -1.201269774 4.867795203 0.999986935 1.427962237 0.181223 0.282829887 0.000148791 2.44E-05 0.239727484 0.056497021 0.062911527 1.201269774 0.427975303 SQPCLTSFNS(ph)VDIASSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQPCLTSFNSVDIASSK 17 0 Q93073;Q93073-2;J3KPI1 Q93073 SECISBP2L Selenocysteine insertion sequence-binding protein 2-like 1 SQPCLTSFNS(1)VDIASSK 210.12 3.84E-12 64413000 81732 89774 113450 67553 147920 108220 114030 107330 119820 75847 TRUE FALSE 84958.84247 105191.9862 116406.6002 80914.78177 122776.6112 83087.54509 105092.0306 105891.4169 115507.7016 90707.76747 0.93662147 1.159680026 1.283314577 0.892038069 1.353540217 0.915991512 1.158578075 1.16739084 1.273404746 1 16.46893848 2.038830089 24.99998727 1.164895233 1.099445893 0.028485306 0.156254938 596.5989203 384105.8554 0.054829383 0.040494139 109.3528457 -2.038830089 -0.06544934 DKPSVEPVEEYDYEDLKES(ph)SNSVSNHQLSGFDQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 DKPSVEPVEEYDYEDLKESSNSVSNHQLSGFDQAR 35 2 Q9Y450;E9PN23;G5E991;E9PLR4;E9PMN1;Q9Y450-2 Q9Y450;Q9Y450-2 HBS1L HBS1-like protein 1 DKPSVEPVEEYDYEDLKES(0.445)S(0.105)NS(0.445)VS(0.005)NHQLSGFDQAR 116.3 3.18E-06 142560000 15212 18811 33330 22602 52008 39190 38339 38384 43305 29579 TRUE FALSE 15812.58151 22041.64292 34198.60718 27072.60814 43167.69874 30088.71643 35333.889 37869.52526 41746.46151 35374.43873 0.447005863 0.623095199 0.966760418 0.765315553 1.220307665 0.850577918 0.9988537 1.070533601 1.180130711 1 15.11041964 4.810161921 0.73528974 1.048421489 4.71E-14 0.710808422 0.12442509 1.561892472 0.598139691 0.045117636 1.391331426 64589.49969 -4.810161921 -1.048421489 down SQPPGEDS(ph)DT(ph)DVDDDSRPPGRPAEVHLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQPPGEDSDTDVDDDSRPPGRPAEVHLER 29 2 Q14676;Q14676-3;Q14676-2;Q14676-4 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 2 S(0.024)QPPGEDS(0.977)DT(0.999)DVDDDS(0.001)RPPGRPAEVHLER;SQPPGEDS(1)DT(1)DVDDDSRPPGRPAEVHLER 128.99 3.12E-05 734010000 88527 136638 133581 147530 136545 151656 137491 138865 119403 143178 TRUE FALSE 92022.11432 160104.5136 137062.2306 176710.9937 113335.1297 116436.1924 126714.0962 137003.7418 115105.7094 171230.9878 0.537415076 0.935020674 0.800452257 1.032003587 0.661884459 0.679994865 0.740018485 0.800110678 0.672224758 1 17.38558429 -1.148927398 3.713277189 1.000155517 0.772139855 0.215224584 0.135055826 39904069.48 66446927.95 74072.83837 0.031275313 0.07096964 1.148927398 -0.228015662 SQPWDLTPMLSSS(ph)EPWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQPWDLTPMLSSSEPWGR 18 0 Q9H201 Q9H201 EPN3 Epsin-3 1 SQPWDLTPMLS(0.004)S(0.256)S(0.74)EPWGR;SQPWDLTPMLS(0.001)S(0.033)S(0.966)EPWGR;SQPWDLTPMLS(0.125)S(0.183)S(0.692)EPWGR;SQPWDLTPMLSS(0.082)S(0.918)EPWGR 248.94 5.53E-24 662802000 455249 636458 693544 736849 923790 982400 807936 859860 873130 916010 TRUE FALSE 473222.582 745764.7105 711618.3264 882595.5329 766764.5058 754252.4884 744607.8652 848334.9831 841706.2219 1095484.621 0.431975559 0.680762373 0.649592256 0.805666748 0.699931784 0.688510339 0.679706361 0.774392416 0.768341431 1 20.0631378 -5 0.046206529 2.307430026 1.44E-13 0.695298546 0.074767154 381.3910953 1.308865064 64.18969585 16.076307 1.00E-05 5 -2.307430026 SQQLSNDHICYFLYQILR ddPTM_MDA-MB-175_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 0 155.03 2.17E-08 209600000 109650 137650 170300 161620 213930 202490 205130 215680 184690 151670 FALSE TRUE 113979.0667 161290.3167 174738.1579 193587.9536 177566.255 155464.7663 189051.3746 212789.1624 178043.043 181386.8326 0.628375638 0.889206313 0.963345329 1.067265748 0.978936853 0.857089592 1.042255228 1.173123536 0.981565422 1 17.4687102 5.184509411 1.059130748 1.027603478 2.65E-12 0.695891057 0.076346926 2.43947567 1.16981629 0.025512754 3.53219535 152935.8888 -5.184509411 -1.027603478 SQQQPTPVT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQQQPTPVTPK 11 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SQQQPTPVT(1)PK;SQQQPT(0.013)PVT(0.987)PK;SQQQPT(0.003)PVT(0.997)PK;SQQQPT(0.001)PVT(0.999)PK 189.61 2.94E-05 2228160000 2889190 1475760 1896740 1425650 2631780 2792290 2527300 2122720 2119570 1273590 TRUE FALSE 3003257.452 1729210.3 1946170.603 1707639.315 2184430.976 2143822.965 2329203.622 2094268.41 2043287.09 1523125.576 1.971772715 1.13530383 1.277747963 1.121141514 1.434176545 1.407515571 1.529226256 1.374980792 1.341509277 1 20.53860346 0.695395041 2.666772639 1.000046733 1.389690902 0.221328624 0.225861199 3.378882779 27.63889132 0.205163312 0.054364895 4.959010647 -0.695395041 0.38964417 SQRPEESEPLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQRPEESEPLEK 12 1 Q5TFE4;Q5TFE4-2 Q5TFE4 NT5DC1 5-nucleotidase domain-containing protein 1 0 91.307 0.007635 215080000 68789 130680 157230 135000 186140 173620 155910 172110 158360 124750 FALSE TRUE 71504.84284 153123.2735 161327.543 161702.5971 154499.9893 133299.3862 143689.3668 169803.147 152660.6545 149192.374 0.479279476 1.026347858 1.08133907 1.083852966 1.035575647 0.893473189 0.963114688 1.138148971 1.023247036 1 17.18681427 4.738397546 7.456824373 1.033302973 0.473077529 0.866609907 0.064459498 0.035441646 18.78583441 0.016760258 0.100342252 54751.69218 -4.738397546 -0.560225444 SQRPFS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQRPFSPR 8 1 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.003)QRPFS(0.997)PR 52.167 0.087586 159200000 525400 444420 600680 475910 726100 707420 655810 591760 623160 496550 TRUE FALSE 546143.1977 520745.6779 616334.2143 570043.5776 602677.7814 543132.4261 604405.8986 583828.4251 600732.5933 593839.4655 0.919681546 0.87691322 1.037880185 0.959928753 1.014883342 0.914611537 1.017793417 0.983141841 1.011607729 1 19.17971345 4.249009125 24.99992994 0.989783627 0.898297354 0.544813721 0.034364715 143.761611 343968.4866 0.007706644 0.02062409 17742.26759 -4.249009125 -0.091486274 SQS(ph)CSDTAQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSCSDTAQER 11 0 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.024)QS(0.873)CS(0.092)DT(0.01)AQER 82.651 0.013723 0 38186 49065 46012 44977 56700 63847 45982 53236 47810 54794 TRUE FALSE 39693.61277 57491.53208 47211.11052 53873.31636 47062.15425 49019.50186 42377.81069 52522.4585 46089.32744 65529.83521 0.605733444 0.877333689 0.720452148 0.822118905 0.718179042 0.748048606 0.646694907 0.801504511 0.703333486 1 15.99986428 -2.102375577 2.442352329 1.455070513 0.74417034 0.511235819 0.076604628 4165267.492 1367344.445 10523098.85 0.016826671 0.007899951 2.102375577 -0.710900174 SQS(ph)DLSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQSDLSSR 8 0 Q1W6H9 Q1W6H9 FAM110C Protein FAM110C 1 SQS(1)DLSSR;S(0.001)QS(0.997)DLS(0.001)SR;S(0.004)QS(0.992)DLS(0.004)SR;SQS(1)DLSSR;SQS(1)DLSSR 190.57 0.00019483 2787050000 4659350 4785450 4753720 4290320 5595520 7585600 4996390 4855400 5042710 4517020 TRUE FALSE 4843304.736 5607313.812 4877605.848 5138932.491 4644395.509 5823959.361 4604759.896 4790321.305 4861223.852 5402043.585 0.896568985 1.037998625 0.90291864 0.951294156 0.859747878 1.078102994 0.852410726 0.886760951 0.899886085 1 22.36507385 SQS(ph)DLSSSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSDLSSSSSR 11 0 J3KP75 J3KP75 PHACTR2 Phosphatase and actin regulator 1 SQS(0.998)DLS(0.002)SSSSR;SQS(0.985)DLS(0.015)SSSSR;S(0.069)QS(0.93)DLS(0.002)SSSSR;S(0.003)QS(0.917)DLS(0.079)SSSSR 272.67 4.75E-27 1750310000 1224771 1560899 1477848 1489091 1656648 1884092 1563431 1542298 1468611 1535163 TRUE FALSE 1273125.905 1828971.261 1516361.933 1783628.755 1375051.565 1446540.187 1440885.193 1521626.018 1415755.977 1835948.797 0.693443034 0.996199493 0.825928226 0.97150245 0.748959648 0.787897892 0.784817744 0.828795455 0.771130425 1 20.80809439 4.959818107 14.39871674 0.844974709 0.653462782 0.211287827 0.092241033 133682.7334 6630484.045 0.021024704 201758.4645 91162.89468 -4.959818107 -0.191511927 SQS(ph)DRTEYNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSDRTEYNQK 11 1 Q9NXL2-1;Q9NXL2 Q9NXL2-1 ARHGEF38 Rho guanine nucleotide exchange factor 38 1 S(0.001)QS(0.999)DRTEYNQK;SQS(0.999)DRTEYNQK;S(0.011)QS(0.989)DRTEYNQK 157.58 1.85E-05 1235230000 543140 474400 552470 441340 664060 656200 585090 530160 558870 425170 TRUE FALSE 564583.5866 555874.5097 566867.8221 528635.7347 551183.3184 503807.4948 539229.117 523054.0724 538756.3779 508473.9211 1.110349151 1.093221278 1.114841486 1.039651618 1.083995256 0.990822683 1.060485296 1.028674334 1.059555575 1 18.95581426 3.544974154 1.317631853 1.034207242 1.108158255 0.562311036 0.027253165 0.320726847 1.112411053 0.008345036 0.017459496 3507.310004 -3.544974154 0.073951013 SQS(ph)ES(ph)SDEVTELDLSHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 2 S(0.112)QS(0.888)ES(0.561)S(0.439)DEVTELDLSHGK 171.72 9.48E-15 0 204310 160940 180390 184220 283090 281660 292610 236810 235270 136900 TRUE FALSE 212376.3166 188580.1931 185091.1116 220658.1662 234970.4629 216248.7336 269674.4636 233635.9493 226802.6787 163722.9339 1.297169013 1.151825151 1.130514261 1.347753555 1.435171343 1.320821271 1.647139208 1.427020294 1.385283499 1 17.3208969 3.578295433 4.394690098 1.408397946 1.19047269 0.176608755 0.15809536 0.285495604 9.26742308 0.040549671 0.06367548 3787.001113 -3.578295433 -0.217925256 SQS(ph)ES(ph)SDEVTELDLSHGKK ddPTM_MDA-MB-175_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(0.108)QS(0.888)ES(0.534)S(0.47)DEVTELDLSHGKK 120 4.97E-05 220470000 256290 163760 239130 151560 359650 299400 287390 241440 302620 149640 TRUE FALSE 266408.5271 191884.5061 245361.9242 181538.1156 298516.8215 229868.8875 264863.6208 238203.8917 291728.7653 178959.093 1.488655998 1.072225518 1.371050334 1.014411241 1.668072946 1.284477272 1.480023264 1.331052185 1.630142176 1 17.44927032 3.246284313 24.99992918 1.409702104 1.234450449 0.117918311 0.216340387 338.2639208 1094880.709 0.054568676 0.072535123 1763.129912 -3.246284313 -0.175251654 SQS(ph)ESSDEVTELDLSHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.016)QS(0.982)ES(0.001)S(0.001)DEVTELDLSHGK 227.25 1.98E-19 153940000 164210 165760 197090 155100 230470 239670 216500 194890 193680 154590 TRUE FALSE 170693.1376 194227.9906 202226.3273 185778.3171 191294.7917 184010.2747 199530.1643 192277.8183 186709.4946 184878.9507 0.923269723 1.050568439 1.093830999 1.004864623 1.034702929 0.99530138 1.079247602 1.040020065 1.009901311 1 17.49622145 4.74262193 24.70367668 1.037439223 0.92326967 0.521021689 0.031798164 263.2679706 1601301.341 0.007381924 0.056422229 55286.86069 -4.74262193 -0.114169553 SQS(ph)ESSDEVTELDLSHGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-5;Q86YS7-3;Q86YS7-2;Q86YS7-4 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 S(0.199)QS(0.788)ES(0.013)SDEVTELDLSHGKK;S(0.169)QS(0.761)ES(0.07)SDEVTELDLSHGKK 246.21 5.75E-25 865510000 2710120 1715030 2386780 1365040 3609400 2670470 2394930 2271700 2775100 1540160 TRUE FALSE 2817117.63 2009573.061 2448981.448 1635040.838 2995875.477 2050293.814 2207209.129 2241251.577 2675224.693 1841924.864 1.529442208 1.091017935 1.329577278 0.887680529 1.626491686 1.113125651 1.198316594 1.21679859 1.452407069 1 20.81278278 -1.255101046 3.972274781 0.999720946 1.256164919 0.126392059 0.210744724 0.000472754 8.87E-05 0.183572752 0.043221301 0.055577493 1.255101046 0.256443973 SQS(ph)FSHQQPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 SQS(0.838)FS(0.162)HQQPSR;SQS(0.925)FS(0.075)HQQPSR;S(0.051)QS(0.719)FS(0.23)HQQPSR;S(0.006)QS(0.886)FS(0.108)HQQPSR;S(0.287)QS(0.692)FS(0.021)HQQPSR;SQS(0.897)FS(0.102)HQQPS(0.002)R 226.85 4.65E-12 2838720000 1235408 1824849 1738921 1676203 2101666 2348089 1573120 1657696 1724218 1758910 TRUE FALSE 1284182.862 2138252.62 1784238.71 2007750.95 1744425.564 1802780.915 1449814.744 1635477.297 1662163.731 2103534.738 0.61048807 1.016504544 0.848209767 0.954465317 0.829282984 0.857024551 0.689227859 0.777490035 0.790176507 1 21.00438421 2.437497177 24.96303666 0.787829604 0.86411712 0.000148716 0.123300396 394.0774962 248265.4474 0.039772375 0.033276008 273.8401832 -2.437497177 0.076287516 SQS(ph)FSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSFSK 6 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75;REV__E7ESW5 COBLL1 Cordon-bleu protein-like 1 1 SQS(0.999)FS(0.001)K;SQS(0.999)FS(0.001)K;SQS(0.999)FS(0.001)K 102.62 0.037115 1136390000 2978220 2075360 2841030 2171290 3599070 3430430 3404120 2908370 2970480 1922930 TRUE FALSE 3095802.425 2431786.936 2915069.576 2600764.681 2987301.367 2633764.621 3137296.179 2869388.057 2863573.005 2299691.317 1.346181726 1.057440587 1.267591678 1.130919034 1.29900102 1.145268759 1.36422491 1.247727483 1.24519886 1 21.13300879 SQS(ph)GEDESMNQPGPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 S(0.023)QS(0.977)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK;SQS(1)GEDESMNQPGPIK 388.46 2.36E-121 1028800000 1062640 856070 1061510 896970 1299740 1335310 1276620 1066050 1087580 732350 TRUE FALSE 1104593.848 1003093.363 1089173.823 1074387.989 1078810.659 1025204.489 1176555.189 1051761.343 1048438.208 875839.9608 1.26118229 1.145292985 1.243576305 1.226694416 1.231744048 1.170538609 1.34334495 1.200860192 1.197065965 1 19.74030775 0.662371443 2.121887697 1.00009104 1.228086538 0.645407948 0.050436243 1.072319739 5.971181643 0.045623707 0.012468218 4.595909238 -0.662371443 0.227995498 SQS(ph)IEQESQEK ddPTM_MDA-MB-175_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 301.59 7.35E-36 1226737000 2213200 1421200 1851560 1346450 2337860 2471200 2118310 1770920 1966830 1260350 TRUE FALSE 2300578.845 1665280.045 1899813.175 1612773.791 1940471.392 1897301.251 1952271.327 1747183.714 1896044.172 1507291.452 1.526299935 1.10481622 1.260415278 1.069981382 1.287389635 1.258748764 1.295218204 1.15915453 1.257914765 1 20.52352697 -4.332333708 0.256572052 2.03E-12 1.257078337 0.284601193 0.118542513 171.4697597 2.323609923 89.82127 0.151907244 4.65E-05 4.332333708 1.257078337 SQS(ph)IVSSVFSEAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSIVSSVFSEAWK 14 0 C9K0J5;Q70E73;C9J164;Q70E73-5;Q70E73-2;Q70E73-8;Q70E73-7;Q70E73-4;Q70E73-3;Q70E73-9;Q70E73-6 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 S(0.117)QS(0.839)IVS(0.041)S(0.003)VFSEAWK;SQS(0.935)IVS(0.062)S(0.003)VFSEAWK 173.03 2.90E-06 142734000 168082 134870 165108 180251 248990 222890 196827 162110 173897 139956 TRUE FALSE 174718.0071 158032.8734 169410.8501 215904.1098 206666.7687 171127.1754 181399.1854 159937.1806 167638.4809 167377.6986 1.043854759 0.944169233 1.012147087 1.289921606 1.234733005 1.022401293 1.083771536 0.955546539 1.001558047 1 17.35274779 1.92715471 2.434072984 0.982449161 1.096793377 0.182806072 0.0987184 0.54500243 5.890072228 0.061862651 0.031930467 84.55800154 -1.92715471 0.114344216 SQS(ph)LNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSLNIR 7 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 SQS(1)LNIR;SQS(1)LNIR;SQS(1)LNIR;SQS(1)LNIR 153.24 0.0018453 1821550000 1489580 1618340 1717830 1559360 2094730 2018910 1820840 1707090 1783030 1776030 TRUE FALSE 1548389.769 1896277.306 1762598.061 1867796.754 1738668.543 1550048.749 1678117.803 1684209.251 1718859.099 2124009.074 0.728993952 0.892782111 0.829844883 0.879373246 0.818578679 0.729775013 0.79007092 0.792938821 0.809252239 1 21.0183585 -1.234208723 3.587508994 1.000339448 0.809239915 0.562575393 0.050790768 2109535.209 1211509.072 5219.12775 0.011960846 0.058316477 1.234208723 -0.191099532 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7;F8WDP1 A0A0A0MRY0 TBC1D22A TBC1 domain family member 22A 1 S(0.217)QS(0.767)LPHS(0.014)AT(0.002)VTLGGTSDPSTLSSSALSER;S(0.15)QS(0.85)LPHSATVTLGGTSDPSTLSSSALSER;S(0.248)QS(0.752)LPHSATVTLGGTSDPSTLSSSALSER;S(0.25)QS(0.732)LPHS(0.016)AT(0.002)VTLGGTSDPSTLSSSALSER 276.99 2.18E-71 1454790000 288831 329173 432533 353497 465670 450421 440179 423577 486646 415299 TRUE FALSE 300234.2709 385705.9021 443805.1653 423417.6515 386515.5797 345817.5489 405676.6198 417899.6431 469131.7055 496668.8877 0.604495829 0.776585592 0.893563451 0.852514949 0.778215808 0.696273831 0.816794911 0.841404915 0.944556257 1 18.92192485 -5 0.065606001 1.762509712 0.511260919 0.501925059 0.077384626 331.548927 1.577166492 38.57044359 5.470938974 1.00E-05 5 -1.251248793 SQS(ph)LPNSLDYTQTSDPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQSLPNSLDYTQTSDPGR 18 0 Q96TC7;H0YLG5;H0YNE5 Q96TC7 RMDN3 Regulator of microtubule dynamics protein 3 1 S(0.226)QS(0.774)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR;S(0.002)QS(0.998)LPNSLDYTQTSDPGR;S(0.008)QS(0.99)LPNS(0.002)LDYTQTSDPGR;S(0.003)QS(0.997)LPNSLDYTQTSDPGR;SQS(1)LPNSLDYTQTSDPGR 368.97 1.53E-107 9550750000 2294280 3163420 2150430 3100270 2374540 3449370 2345290 2151000 1912720 2586860 TRUE FALSE 2384859.946 3706712.777 2206471.972 3713494.153 1970916.539 2648306.093 2161460.042 2122169.363 1843881.581 3093705.689 0.770874862 1.198146543 0.713213277 1.200338535 0.637073057 0.856030392 0.698663758 0.685963559 0.596010664 1 21.56090453 3.215335598 24.99907088 0.729098134 0.968505841 0.266931326 0.18143349 270.2124197 290851.9834 0.047815376 0.057183097 1641.858017 -3.215335598 0.239407707 SQS(ph)LPTTLLSPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 S(0.001)QS(0.908)LPT(0.033)T(0.058)LLSPVR;S(0.007)QS(0.7)LPT(0.11)T(0.184)LLSPVR;SQS(1)LPTTLLSPVR;SQS(1)LPTTLLSPVR;S(0.005)QS(0.954)LPT(0.015)T(0.027)LLSPVR;S(0.003)QS(0.51)LPT(0.17)T(0.317)LLSPVR 203.96 8.57E-08 1958967000 1548898 1876303 1842188 1485061 2499820 2318190 1899660 1853869 1765400 2136210 TRUE FALSE 1610049.689 2198543.445 1890196.933 1778801.633 2074901.489 1779825.505 1750759.685 1829020.918 1701863.599 2554759.449 0.630215768 0.860567693 0.739872763 0.696269715 0.812170981 0.696670485 0.685293359 0.715926863 0.666154146 1 21.28475603 -1.740338724 2.741826156 1.053182466 0.725909282 0.622313591 0.064791656 68512205.39 56216659.59 24799301.19 0.015072918 0.018182822 1.740338724 -0.327273184 SQS(ph)MDAMGLSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSMDAMGLSNK 12 0 J3KPC5;P47736-3;P47736;P47736-4;F2Z357;X6R8W7;P47736-2;A0A0A0MQY8 J3KPC5 RAP1GAP Rap1 GTPase-activating protein 1 1 S(0.207)QS(0.793)MDAMGLSNK 86.378 0.0078505 0 158910 121510 147040 136880 188780 186200 189360 156070 156110 103240 TRUE FALSE 165183.8895 142378.3973 150871.9832 163954.4555 156691.243 142957.8719 174517.4684 153978.1369 150491.6316 123467.9014 1.337869096 1.153161232 1.221953087 1.327911576 1.26908485 1.157854554 1.413464281 1.247110668 1.218872516 1 16.9137765 0.760975535 2.610950863 1.0001114 1.265334273 0.524097793 0.075782611 0.931979313 8.996468496 0.069969934 0.01860841 5.767339733 -0.760975535 0.265222873 SQS(ph)MDIDGVSCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSMDIDGVSCEK 13 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 SQS(1)MDIDGVSCEK 260.56 5.33E-24 102260000 223300 187570 274930 181030 386580 298160 297440 267650 324800 182170 TRUE FALSE 232116.0564 219783.6884 282094.9017 216837.1937 320869.2697 228916.8587 274125.8756 264062.5895 313110.5114 217862.7236 1.065423458 1.008817317 1.294828674 0.99529277 1.472804821 1.050738992 1.258250475 1.212059526 1.437191761 1 17.73305985 4.247604693 24.98473947 1.219995407 1.037120312 0.169604854 0.157274427 296.6865853 819594.2206 0.03484709 0.09258892 17684.98488 -4.247604693 -0.182875095 SQS(ph)NPILGSPFFSHFDGQDSYAAAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSNPILGSPFFSHFDGQDSYAAAVR 26 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 S(0.151)QS(0.849)NPILGSPFFSHFDGQDSYAAAVR;S(0.124)QS(0.876)NPILGSPFFSHFDGQDSYAAAVR 202.56 2.91E-25 167639000 28324.1 34255.8 38578 28833.3 41701.6 45870 29571.4 41048 36332.3 37030 TRUE FALSE 29442.35734 40138.96718 39583.37437 34536.44068 34613.17693 35217.38767 27253.5164 40497.8187 35024.70762 44285.31952 0.66483335 0.906371854 0.893826099 0.779862064 0.781594833 0.795238423 0.615407469 0.914475026 0.790887545 1 15.43454091 0.44247597 1.147481702 0.999668295 0.794552818 0.307390298 0.092817809 2.874635535 4.708010857 0.087356314 0.026604727 2.769975768 -0.44247597 -0.205115476 SQS(ph)PAASDCSSSSSSASLPSSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQSPAASDCSSSSSSASLPSSGR 23 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 S(0.001)QS(0.999)PAASDCSSSSSSASLPSSGR;SQS(1)PAASDCSSSSSSASLPSSGR;SQS(1)PAASDCSSSSSSASLPSSGR;S(0.012)QS(0.988)PAASDCSSSSSSASLPSSGR;S(0.161)QS(0.839)PAASDCSSSSSSASLPSSGR;SQS(1)PAASDCSSSSSSASLPSSGR 418.19 3.95E-158 6692930000 1059483 1208190 1193389 1114723 1299428 1453537 1229716 1228858 1144151 1185056 TRUE FALSE 1101312.207 1415687.234 1224489.698 1335211.882 1078551.693 1115975.06 1133327.647 1212387.169 1102973.229 1417245.034 0.777079602 0.998900825 0.863992936 0.942117877 0.761019913 0.787425628 0.799669513 0.85545346 0.77825161 1 20.43465778 3.247022466 24.99933061 0.821410176 0.900654816 0.123753098 0.082569323 307.3793776 908103.1242 0.021135507 0.028166001 1766.129178 -3.247022466 0.07924464 SQS(ph)PHYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 SQS(1)PHYFR;S(0.001)QS(0.999)PHYFR 136.81 0.00049931 1477520000 682640 1017800 966000 942260 953200 1146210 906500 942070 809700 942690 TRUE FALSE 709591.1543 1192599.233 991174.7536 1128636.216 791175.4045 880020.0985 835446.1613 929443.0926 780559.0552 1127392.057 0.629409397 1.057838953 0.87917486 1.001103573 0.701774862 0.780580361 0.74104315 0.824418699 0.692358129 1 20.10455788 3.232990018 24.99857051 0.780623528 0.902828154 0.120333161 0.132144732 230.6218056 1034935.566 0.03495615 0.042901459 1709.976011 -3.232990018 0.122204626 SQS(ph)PINCIRPSVLGPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSPINCIRPSVLGPLK 17 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 S(0.005)QS(0.995)PINCIRPSVLGPLK;SQS(1)PINCIRPSVLGPLK 227.2 1.11E-15 1479900000 752600 575170 702740 708330 931830 879130 808960 744420 763560 542650 TRUE FALSE 782313.2291 673950.9733 721053.9817 848435.5598 773437.8694 674965.3808 745551.6014 734442.2675 736079.6248 648971.8778 1.205465531 1.038490259 1.111071229 1.307353352 1.191789499 1.040053358 1.148819582 1.131701223 1.134224224 1 19.30779644 2.768428755 24.77796971 1.106493174 1.167745804 0.195793324 0.077692458 1407.902573 1167963.592 0.024703608 0.026196975 586.717112 -2.768428755 0.06125263 SQS(ph)PINCIRPSVLGPLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSPINCIRPSVLGPLKR 18 2 Q96E09 Q96E09 FAM122A Protein FAM122A 1 SQS(1)PINCIRPSVLGPLKR;S(0.001)QS(0.999)PINCIRPSVLGPLKR 119.52 5.62E-05 922400000 640730 563470 659210 543480 815150 774460 635820 655940 704260 563960 TRUE FALSE 666026.5152 660241.5893 676389.5541 650978.7219 676591.0942 594603.4021 585982.767 647148.1972 678913.8202 674457.1643 0.987500097 0.978922939 1.002865104 0.965189127 1.003163922 0.881602915 0.868821325 0.959509709 1.006607767 1 19.36336729 2.772790656 24.97961702 0.936201719 0.986661156 0.203342089 0.042600688 917.030654 669208.135 0.013497111 0.014315411 592.6395849 -2.772790656 0.050459437 SQS(ph)SDLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSSDLLER 9 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 S(0.004)QS(0.879)S(0.117)DLLER;SQS(0.96)S(0.04)DLLER 129.37 0.00041038 766930000 823800 939450 932490 871320 1048990 1183010 998250 972170 971620 892410 TRUE FALSE 856324.2601 1100793.23 956791.4554 1043664.495 870683.0545 908273.8562 920004.5566 959139.6513 936651.586 1067260.653 0.802357191 1.031419294 0.896492766 0.977890914 0.815811069 0.851032832 0.862024243 0.898692975 0.877622147 1 20.02548113 5.023450503 16.36232945 0.904104015 0.556206501 0.189250541 0.06634842 4291862.894 76502921.24 0.015438653 38786053.38 105548.1201 -5.023450503 -0.347897514 SQS(ph)SDTEQQSPTSGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.075)QS(0.462)S(0.462)DTEQQSPTSGGGK 107.34 0.00074385 29199000 49354 39517 52346 38565 56057 62094 60094 48330 57330 38851 TRUE FALSE 51302.53403 46303.73735 53710.17976 46193.04189 46528.45116 47673.60954 55383.67525 47682.2154 55266.7045 46463.1096 1.104156275 0.996569919 1.155974712 0.994187481 1.001406311 1.026052926 1.191992437 1.026238145 1.18947494 1 15.50379809 SQS(ph)SSQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSSSQFR 8 0 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 S(0.004)QS(0.783)S(0.209)S(0.004)QFR;SQS(0.838)S(0.158)S(0.004)QFR;S(0.043)QS(0.813)S(0.127)S(0.017)QFR;S(0.01)QS(0.794)S(0.185)S(0.012)QFR 123.79 0.0013977 2663520000 4039550 4619660 4603430 4214410 5010430 5388070 4094890 4573700 4309520 4612500 TRUE FALSE 4199034.553 5413050.669 4723399.168 5048007.719 4158758.898 4136772.399 3773921.822 4512397.033 4154421.217 5516231.063 0.761214406 0.981295128 0.8562729 0.915118975 0.753913107 0.749927324 0.684148611 0.818021758 0.753126758 1 22.39525146 3.236091809 24.98772441 0.777209871 0.884233738 0.15197657 0.093871674 89.62234266 907102.9352 0.024705977 0.030866127 1722.232614 -3.236091809 0.107023867 SQS(ph)TSEQEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSTSEQEKR 10 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 SQS(0.868)T(0.122)S(0.01)EQEKR;SQS(0.972)T(0.028)SEQEKR;S(0.04)QS(0.452)T(0.452)S(0.056)EQEKR 143.98 2.02E-05 1144944000 864860 644683 918450 537192 1299080 974810 1002750 875957 1025720 654646 TRUE FALSE 899005.3406 755402.2903 942385.5615 643446.9742 1078262.846 748425.1509 924151.8348 864216.2292 988804.5376 782911.3497 1.148284976 0.964863123 1.20369383 0.82186441 1.377247687 0.955951336 1.180404186 1.103849407 1.262984038 1 19.57848943 3.243857905 24.9999994 1.142158676 1.041762656 0.119571444 0.14816065 303.249236 1431143.398 0.03782006 0.04974227 1753.30675 -3.243857905 -0.10039602 SQS(ph)TTFNPDDMSEPEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSTTFNPDDMSEPEFK 17 0 F5GZP6;Q86W92-3;Q86W92-4;Q86W92;Q86W92-2 F5GZP6;Q86W92-2 PPFIBP1 Liprin-beta-1 1 S(0.048)QS(0.901)T(0.048)T(0.003)FNPDDMSEPEFK;S(0.002)QS(0.932)T(0.062)T(0.004)FNPDDMSEPEFK;SQS(0.999)T(0.001)TFNPDDMSEPEFK;S(0.183)QS(0.577)T(0.183)T(0.058)FNPDDMSEPEFK 384.31 1.09E-121 516259000 664320 491687 607890 397495 791010 742830 702250 624290 619680 350086 TRUE FALSE 690547.8666 576130.4175 623732.1128 476118.3246 656554.4027 570318.9902 647205.81 615922.4137 597377.8378 418678.6489 1.649350566 1.376068302 1.489763365 1.137192751 1.568158311 1.362187902 1.545829508 1.471110159 1.426817057 1 18.67548382 0.919432592 16.79099285 0.999999999 1.445755679 0.506163656 0.132694598 549.6468792 114553.5718 0.119223894 0.029805849 8.306777763 -0.919432592 0.44575568 SQS(ph)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSVPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 36 0 A0A494C1V1;Q6ZNJ1-2;Q6ZNJ1-3;Q6ZNJ1;H0Y764 A0A494C1V1 NBEAL2 Neurobeachin-like protein 2 1 S(0.144)QS(0.855)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR;S(0.232)QS(0.768)VPASTGLGWGSGLVAPLQEGSIDSTLAGTQDTR 177.49 4.95E-23 190768000 33925 30200 40857 29016 62172 42594 32538 36368 50788 47270 TRUE FALSE 35264.3852 35386.61508 41921.76698 34755.2782 51604.02565 32702.18902 29987.58654 35880.54645 48960.1498 56531.65146 0.623798957 0.625961106 0.741562751 0.614793258 0.912834214 0.578475742 0.530456581 0.63469836 0.866066151 1 15.78677122 1.07185868 3.698803667 0.996402061 0.65683775 0.564436919 0.099931794 0.14665729 3.890663299 0.096864917 0.025084104 11.79936619 -1.07185868 -0.339564312 SQS(ph)WEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 S(0.012)QS(0.988)WEER;S(0.009)QS(0.991)WEER;S(0.003)QS(0.997)WEER 101.93 0.0091417 1016520000 1082670 1304390 1356880 1298490 1734410 1740900 1567610 1474880 1575260 1636640 TRUE FALSE 1125414.648 1528408.836 1392241.407 1555327.446 1439595.608 1336602.359 1444736.632 1455111.646 1518566.7 1957308.273 0.574980785 0.780872823 0.711304104 0.794625695 0.735497636 0.682877796 0.738124215 0.743424869 0.775844419 1 20.90043957 -5 0.241149297 2.569017288 0.70206906 0.697089631 0.055856908 92.85584719 0.925708868 71.38900267 0.082380295 1.00E-05 5 -1.866948229 SQS(ph)WEERGDR ddPTM_MDA-MB-175_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(0.258)QS(0.742)WEERGDR;S(0.221)QS(0.779)WEERGDR;S(0.108)QS(0.892)WEERGDR 97.631 0.0035896 1118610000 527440 1602520 1448920 1524430 1452570 1903100 1126440 1522970 1420790 1938770 TRUE FALSE 548263.7385 1877740.344 1486680.046 1825957.704 1205662.67 1461133.867 1038146.689 1502557.078 1369656.045 2318634.862 0.236459715 0.80984737 0.641187653 0.787514125 0.519988158 0.630169886 0.447740482 0.648035231 0.590716576 1 21.14484421 -1.203453747 2.850220225 1.002138964 0.600427307 0.379096383 0.156850634 4401043.926 5629399.628 84064.84038 0.037414018 0.062595953 1.203453747 -0.401711657 SQSASVES(ph)IPEVLEECTSPADHSDSASVHDMDYVNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 S(0.001)QS(0.004)AS(0.004)VES(0.992)IPEVLEECTSPADHSDSASVHDMDYVNPR;S(0.001)QS(0.001)AS(0.001)VES(0.977)IPEVLEECT(0.001)S(0.018)PADHS(0.001)DSASVHDMDYVNPR;S(0.01)QS(0.01)AS(0.009)VES(0.815)IPEVLEECT(0.076)S(0.076)PADHS(0.002)DSASVHDMDYVNPR 197.72 6.32E-30 338888000 58263 140853 125870 148574 136521 181059 110067 142401 120931 140215 TRUE FALSE 60563.26823 165043.4071 129150.2756 177961.4938 113315.2092 139010.7912 101439.6609 140492.3475 116578.7169 167687.4447 0.361167578 0.984232346 0.770184529 1.061269042 0.675752495 0.828987474 0.604932952 0.837822699 0.695214345 1 17.35541515 -2.431510206 2.132008647 2.899549086 0.77169646 0.127946583 0.186568973 7072603.375 556092.7672 64994739.38 0.045256572 0.003702455 2.431510206 -2.127852626 SQSASVESIPEVLEECT(ph)SPADHSDSASVHDMDYVNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSASVES(0.013)IPEVLEECT(0.445)S(0.445)PADHS(0.083)DS(0.007)AS(0.008)VHDMDYVNPR 100.19 0.00021027 68514000 7079 16731 14967 14949 18989 20606 11548 16122 15164 15690 TRUE FALSE 7358.484386 19604.4191 15357.05232 17905.86758 15761.25656 15820.56879 10642.83758 15905.91096 14618.2506 18764.1551 0.392156447 1.044780274 0.81842493 0.954259197 0.839966227 0.843127159 0.567189811 0.847675308 0.779051896 1 14.19569171 SQSASVESIPEVLEECTS(ph)PADHSDSASVHDMDYVNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SQSASVESIPEVLEECTSPADHSDSASVHDMDYVNPR 37 0 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 SQSASVESIPEVLEECT(0.068)S(0.333)PADHS(0.243)DS(0.178)AS(0.178)VHDMDYVNPR;SQSASVESIPEVLEECT(0.13)S(0.848)PADHS(0.02)DS(0.001)AS(0.001)VHDMDYVNPR;SQSAS(0.001)VES(0.007)IPEVLEECT(0.157)S(0.749)PADHS(0.066)DS(0.008)AS(0.011)VHDMDYVNPR 193.51 1.06E-23 278147000 54504 113793 87698 120562 110730 138420 92098 108869 109359 116904 TRUE FALSE 56655.86001 133336.0626 89983.48192 144408.8038 91908.15415 106274.0528 84879.11811 107409.7891 105423.191 139809.1005 0.405237283 0.953700882 0.643616772 1.032899884 0.657383202 0.760136875 0.607107247 0.768260354 0.754050992 1 17.09309875 0.510569667 2.139758356 0.999978325 0.737791048 0.189211418 0.166757389 8.196508676 33.84773274 0.144581026 0.039382094 3.240183955 -0.510569667 -0.262187277 SQSDLDDQHDYDS(ph)VAS(ph)DEDTDQEPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 SQSDLDDQHDYDS(1)VAS(1)DEDTDQEPLR 158.64 1.07E-11 623650000 111570 147620 119950 128510 136140 154470 119830 126170 115980 123130 TRUE FALSE 115974.8698 172972.5867 123075.9955 153928.8944 112998.9714 118596.6835 110437.4115 124478.8975 111805.9025 147254.966 0.787578666 1.174646882 0.835802003 1.045322264 0.767369512 0.805383253 0.749974106 0.845329029 0.759267449 1 17.16795676 3.230619016 24.99990664 0.810256219 0.967178456 0.241715313 0.119997961 208.733322 657085.1209 0.031258197 0.037992377 1700.665948 -3.230619016 0.156922238 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;Q9Y2X7;Q9Y2X7-3;A0A0C4DGN6;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 SQSDLDDQHDYDSVAS(0.99)DEDT(0.01)DQEPLR 148.14 1.14E-07 341970000 54063 63143 55745 54072 53304 70900 55326 55593 55848 47171 TRUE FALSE 56197.44899 73987.31907 57197.7605 64767.28021 44243.40512 54434.5495 50989.40355 54847.86677 53838.04139 56413.25431 0.996174564 1.311523683 1.013906416 1.148086226 0.784273229 0.964924824 0.903855028 0.972251423 0.954350924 1 15.78374654 3.264810786 24.99988619 0.931377341 1.123893153 0.470771516 0.097277838 181.0072563 172384.7277 0.025077099 0.033944298 1839.970185 -3.264810786 0.192515812 SQSES(ph)SDEVTELDLSHGKK ddPTM_MDA-MB-175_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(0.007)QS(0.054)ES(0.45)S(0.361)DEVT(0.128)ELDLSHGKK 83.453 0.0015773 117330000 190660 118280 165590 130680 190400 209830 172200 122690 148900 106780 TRUE FALSE 198187.404 138593.6699 169905.4114 156528.114 158035.876 161100.1625 158702.514 121045.5412 143541.1181 127701.4966 1.551958351 1.085294015 1.330488804 1.225734374 1.237541299 1.261536997 1.242761583 0.947878799 1.124036303 1 16.96241591 1.802837903 7.12501711 1.024928502 1.268029292 0.49281063 0.117254964 0.193055471 17.52546634 0.047906972 0.028401364 63.50938442 -1.802837903 0.24310079 SQSFNTDTTTSGISSMSS(ph)SPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMS(0.089)S(0.411)S(0.411)PS(0.089)R;SQSFNTDTTTSGISSMS(0.063)S(0.312)S(0.312)PS(0.312)R 216.38 1.41E-25 156061000 289203 327916 319166 387087 303013 407298 406755 365994 326080 250519 TRUE FALSE 300620.9578 384233.0222 327483.7282 463651.6533 251506.9585 312709.2122 374872.4802 361088.4491 314344.4445 299603.4016 1.003396344 1.282472162 1.093057443 1.547551366 0.839466298 1.043743864 1.251229052 1.20522146 1.049201854 1 18.19269448 3.219028004 24.99888186 1.09546508 1.225354699 0.173944909 0.170180677 533.5239189 682831.118 0.049411063 0.059133806 1655.876735 -3.219028004 0.12988962 SQSFNTDTTTSGISSMSSS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSFNTDTTTSGISSMSSSPSR 22 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 SQSFNTDTTTSGISSMS(0.001)S(0.173)S(0.654)PS(0.173)R 331.01 9.82E-81 100750000 63988 70941 64081 76654 59957 84472 83093 69678 66660 52040 TRUE FALSE 66514.29565 83124.56491 65751.0035 91815.93241 49765.53056 64854.65819 76579.95354 68744.08038 64260.91962 62236.24163 1.068738952 1.335629574 1.05647452 1.475280801 0.799623005 1.042072215 1.230472013 1.104566705 1.032532138 1 15.92546732 3.012534303 0.202872947 0.98450376 1.285034854 0.086681481 0.171567992 16.26089926 1.367784814 0.486904368 1.401636598 1029.281822 -3.012534303 0.300531094 SQSFT(ph)HSPSGDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 S(0.001)QS(0.403)FT(0.596)HSPSGDPK 184.22 0.00010832 245350000 236260 191560 259110 220790 361220 317360 336650 261270 301880 205100 TRUE FALSE 245587.7272 224458.9399 265862.6195 264461.603 299819.9534 243657.9496 310262.4933 257768.103 291015.3978 245285.4181 1.001232479 0.915092881 1.083890846 1.078179066 1.222330931 0.993365001 1.264903946 1.050890448 1.186435786 1 17.90410194 4.113532766 4.594641785 1.117977004 0.959119623 0.326854169 0.087579416 0.202666836 7.159653886 0.019902217 0.045811655 12987.71548 -4.113532766 -0.158857381 SQSGGYSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQSGGYSDR 9 0 Q14011;K7EMY9;K7EPM4;K7EQR7;D6W5Y5;Q14011-2;Q14011-3;F6WMK9 Q14011 CIRBP Cold-inducible RNA-binding protein 0 ;;; 128.6 0.0009602 1923660000 882530 1026140 1019730 949560 1066730 1202640 984640 1040260 904990 983770 FALSE TRUE 917372.9659 1202371.563 1046305.002 1137380.134 885407.6156 923345.0862 907461.3439 1026317.016 872419.5867 1176520.896 0.779733678 1.021972127 0.889321222 0.966731775 0.752564292 0.784809763 0.77130916 0.872332161 0.74152494 1 20.16609551 3.243200642 24.99788666 0.813192038 0.920326412 0.20012745 0.091093011 158.1896374 852232.4485 0.023552878 0.03086326 1750.655298 -3.243200642 0.107134373 SQSQNLFSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSQNLFSVK 10 0 Q86W26 Q86W26 NLRP10 "NACHT, LRR and PYD domains-containing protein 10" 0 60.518 0.097569 338550000 767780 482280 630370 447100 953180 825020 725840 653800 783360 490420 FALSE TRUE 798092.5473 565107.8384 646797.9601 535535.0455 791158.8041 633421.6083 668946.7642 645036.8804 755167.0266 586508.4093 1.360752096 0.963511911 1.102794009 0.91309014 1.348930026 1.079987257 1.140557839 1.099791359 1.287563852 1 19.16179227 4.762798689 23.7039679 1.109229294 1.360752702 0.266176262 0.127617355 4669.551891 4566506.531 0.028701713 1.652459426 57916.01721 -4.762798689 0.251523409 SQSRPNDIMAEVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQSRPNDIMAEVCR 14 1 Q13131-2;Q13131 Q13131-2 PRKAA1 5-AMP-activated protein kinase catalytic subunit alpha-1 0 138.01 1.63E-05 169210000 78644 99673 78565 75024 104150 125810 90453 97314 82723 88648 FALSE TRUE 81748.92585 116791.0624 80612.46844 89863.52328 86446.6202 96592.53417 83363.05751 96009.665 79745.81539 106016.8783 0.771093501 1.101627064 0.760373911 0.847634119 0.815404316 0.911105247 0.786318734 0.905607357 0.752199241 1 16.69393444 4.190485444 24.99997562 0.845119062 0.936368008 0.105856333 0.103339347 196.866771 102373.9348 0.02290887 0.049488988 15505.48818 -4.190485444 0.091248946 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.019)QS(0.147)S(0.834)DTEQQS(1)PTSGGGK;SQS(0.002)S(0.998)DTEQQS(0.727)PT(0.256)S(0.017)GGGK;SQS(0.005)S(0.995)DTEQQS(0.595)PT(0.403)S(0.001)GGGK;SQS(0.017)S(0.983)DTEQQS(0.996)PT(0.004)SGGGK;S(0.004)QS(0.144)S(0.851)DTEQQS(0.999)PTSGGGK;S(0.264)QS(0.343)S(0.392)DT(0.367)EQQS(0.63)PT(0.002)SGGGK;SQS(0.157)S(0.843)DTEQQS(0.957)PT(0.043)SGGGK;SQS(0.004)S(0.996)DTEQQS(0.995)PT(0.005)SGGGK 298.91 4.25E-46 2274080000 5184903 3562862 4533378 3412441 5586349 6053568 5372805 4655548 5098530 3150295 TRUE FALSE 5389606.974 4174755.833 4651521.555 4087411.645 4636783.392 4647718.575 4951670.505 4593147.994 4915034.901 3767534.989 1.430539329 1.108086811 1.234632609 1.084903433 1.230720725 1.233623201 1.314299806 1.219138776 1.304575781 1 21.84518948 -2.318554665 1.985177989 3.48E-05 1.233134042 0.36762501 0.094060616 2208252.219 285505.3879 9886156.628 0.022141234 0.004802256 2.318554665 1.233099257 SQSS(ph)DTEQQSPTSGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQS(0.002)S(0.998)DTEQQSPTSGGGK;SQS(0.001)S(0.999)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQSS(1)DTEQQSPTSGGGK;SQS(0.005)S(0.995)DTEQQSPTSGGGK;SQS(0.037)S(0.963)DTEQQSPTSGGGK 409.3 2.15E-140 3157240000 3474575 2660554 3249498 2513155 3892752 4120281 3679702 3313496 3523961 2235746 TRUE FALSE 3611753.904 3117483.453 3334182.587 3010249.558 3231063.405 3163408.181 3391277.342 3269084.006 3397134.332 2673797.623 1.35079554 1.165938449 1.2469839 1.125832985 1.208417338 1.183114292 1.268337332 1.222637038 1.270527845 1 21.35045884 -2.015058156 2.979866118 0.753053767 1.222698325 0.563764365 0.059786864 2702134.868 7103039.054 4639232.305 0.013081849 0.009659215 2.015058156 0.469644558 SQSSDTEQQS(ph)PTSGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SQSSDTEQQS(0.941)PT(0.059)SGGGK;SQSSDTEQQS(0.975)PT(0.024)S(0.001)GGGK;SQSSDTEQQS(0.738)PT(0.24)S(0.022)GGGK;SQSSDTEQQS(0.9)PT(0.099)S(0.001)GGGK;SQSSDTEQQS(0.998)PT(0.002)SGGGK;SQSSDTEQQS(0.98)PT(0.02)SGGGK;SQSSDT(0.017)EQQS(0.983)PTSGGGK;SQSSDTEQQS(0.994)PT(0.006)SGGGK;SQSSDT(0.001)EQQS(0.994)PT(0.003)S(0.003)GGGK;SQSSDTEQQS(0.717)PT(0.256)S(0.028)GGGK;SQSSDTEQQS(0.499)PT(0.499)S(0.003)GGGK 443.39 1.93E-182 10995187000 10187392.5 7365395 9084431.1 6796446 10301424.3 11524216.2 10331782.5 9326865.4 9803660.4 6690312 TRUE FALSE 10589598.62 8630344.296 9321178.837 8140762.733 8550391.877 8847891.639 9521950.391 9201854.025 9450828.577 8001150.543 1.323509484 1.07863791 1.16497981 1.017449014 1.068645294 1.105827417 1.190072645 1.150066353 1.181183697 1 22.93177604 SQSSHS(ph)YDDSTLPLIDR ddPTM_MDA-MB-175_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 1 SQSSHS(1)YDDSTLPLIDR;SQSS(0.003)HS(0.997)YDDSTLPLIDR;SQSS(0.001)HS(0.999)YDDSTLPLIDR;S(0.003)QS(0.002)S(0.014)HS(0.981)YDDSTLPLIDR;S(0.003)QS(0.01)S(0.058)HS(0.929)YDDSTLPLIDR 228.19 1.59E-15 3265790000 759904 1509060 1364220 1439890 1546150 1908120 1388920 1538140 1353420 1588160 TRUE FALSE 789905.5967 1768229.316 1399772.694 1724695.944 1283335.975 1464988.048 1280052.821 1517523.749 1304710.679 1899329.545 0.415886542 0.930975523 0.73698253 0.908055134 0.675678414 0.771318517 0.673949829 0.798978647 0.686932229 1 20.85705881 -2.059885182 2.28839726 1.349253683 0.745212596 0.251874385 0.136539826 15977244.82 5024663.497 29163507.27 0.029625513 0.008711939 2.059885182 -0.604041087 SQSSHSYDDSTLPLIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 220.34 4.04E-15 1080500000 129733 534021 425281 495062 426892 624158 415277 502770 400601 510065 FALSE TRUE 134854.959 625734.9526 436364.1722 592983.786 354329.0503 479206.7637 382726.5036 496031.1905 386183.4483 610002.471 0.221072808 1.025790849 0.715348204 0.972100629 0.580864943 0.785581676 0.627417956 0.813162592 0.633085056 1 19.21845556 -2.289388967 2.106630342 2.110756878 0.727138713 0.138517857 0.213645315 8787004.556 1272238.408 46409050.54 0.046883004 0.005135835 2.289388967 -1.383618165 SQSSSLLDMGNMSAS(ph)DLDVADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQSSSLLDMGNMSASDLDVADR 22 0 Q9NV70;Q9NV70-2 Q9NV70;Q9NV70-2 EXOC1 Exocyst complex component 1 1 SQSSSLLDMGNMS(0.144)AS(0.856)DLDVADR;SQSSSLLDMGNMS(0.089)AS(0.911)DLDVADR 135.54 3.79E-06 45494000 43559 53717 48691 49162 54960 59215 46817 53130 51661 44702 TRUE FALSE 45278.74295 62942.47689 49959.92746 58886.09687 45617.91883 45463.21366 43147.36121 52417.87925 49801.7307 53460.50103 0.846956951 1.177364141 0.934520375 1.101487935 0.853301371 0.850407549 0.807088605 0.980497344 0.931561241 1 15.70618574 3.228357258 24.97485078 0.89912964 1.020919487 0.22839606 0.099743158 268.4239834 657022.8184 0.027305906 0.032989056 1691.832088 -3.228357258 0.121789847 SQT(ph)PERPAKK ddPTM_MDA-MB-175_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(0.001)QT(0.999)PERPAKK 97.86 0.0092789 103850000 152380 91628 118050 79800 164320 158640 146410 119510 147590 86338 TRUE FALSE 158396.0801 107364.3962 121126.48 95584.20182 136388.9451 121798.2642 134934.0016 117908.1639 142278.2647 103254.2781 1.534038909 1.039805791 1.173089215 0.925716625 1.320903576 1.17959533 1.306812697 1.141920375 1.377940628 1 16.65584203 SQT(ph)PPGVATPPIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 S(0.001)QT(0.999)PPGVATPPIPK;S(0.079)QT(0.921)PPGVATPPIPK 200.46 2.15E-07 1619470000 1057150 734060 891930 689100 1195100 1191400 1100170 904150 998740 598070 TRUE FALSE 1098887.098 860129.0948 915174.4285 825401.9232 991957.3289 914715.4058 1013935.801 892031.3481 962795.5425 715250.3658 1.536367055 1.202556665 1.279516198 1.154004196 1.386867279 1.278874433 1.417595641 1.247159583 1.346095841 1 19.4480888 -1.191594953 3.995540233 0.999818979 1.308145052 0.444298073 0.105832927 7123860.664 2124567.206 11174.25022 0.022865225 0.06432874 1.191594953 0.308326073 SQT(ph)PPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SQTPPRR 7 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.029)QT(0.971)PPRR;S(0.004)QT(0.996)PPRR;S(0.008)QT(0.992)PPRR;S(0.003)QT(0.997)PPRR;S(0.023)QT(0.977)PPRR 93.649 0.0086612 3526380000 1378268 1412653 1458222 1405554 1624610 1909121 1598112 1525008 1488493 1178338 TRUE FALSE 1432683.085 1655265.164 1496224.463 1683568.386 1348459.372 1465756.581 1472847.806 1504567.762 1434922.428 1409210.77 1.016656355 1.174604395 1.061746401 1.194688844 0.956889772 1.040125872 1.045157926 1.067666948 1.018245431 1 20.42645598 3.234893472 24.99999999 1.030058554 1.11281705 0.386577536 0.05524152 101.3532393 690955.1743 0.014883076 0.018450715 1717.487054 -3.234893472 0.082758496 SQTGDVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;SQTGDVS(1)PK 104.24 0.0034527 349940000 481800 212565 274370 210193 394190 532500 370510 286140 318170 185284 TRUE FALSE 500821.836 249071.3852 281520.3076 251768.548 327185.7246 408834.9451 341468.4581 282304.7613 306719.1239 221586.8523 2.260160433 1.124035035 1.270473878 1.136207069 1.476557482 1.845032505 1.541014074 1.274014042 1.384193695 1 17.75751276 0.827098573 1.139884845 1.006789004 1.480580464 0.174669892 0.326622827 1.340740388 3.319304833 0.30551817 0.095665982 6.715812665 -0.827098573 0.47379146 SQVDHVIWPDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SQVDHVIWPDGK 12 0 O43865-2;O43865;H0Y8B3;Q96HN2-4;Q96HN2-3;Q96HN2-2;Q96HN2 O43865-2 AHCYL1;AHCYL2 Putative adenosylhomocysteinase 2;Adenosylhomocysteinase;Putative adenosylhomocysteinase 3 0 75.462 0.033745 228520000 330400 311450 402900 359790 459960 510170 540550 446870 444130 301330 FALSE TRUE 343444.4471 364939.1148 413399.905 430955.3881 381776.1635 391690.7492 498180.2785 440880.4386 428145.8481 360369.8442 0.953033259 1.012679392 1.147154546 1.19586973 1.059400973 1.086913224 1.382413891 1.22341102 1.188073461 1 18.45911877 5.127869307 0.635024638 1.196554717 0.637232261 0.306425252 0.101659439 5.639144209 1.212166588 0.044685472 2.555581866 134236.0942 -5.127869307 -0.559322456 SQVEEELFSVR ddPTM_MDA-MB-175_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 ;;; 236.42 3.49E-15 393650000 329106 417942 412656 412975 440970 502423 383220 424538 377591 396891 FALSE TRUE 342099.359 489720.2874 423410.1544 494660.2224 366014.0769 385742.8725 353182.215 418847.7625 364001.5737 474654.1925 0.720733882 1.031741203 0.892039217 1.042148643 0.771117337 0.812681903 0.74408321 0.882427184 0.766877401 1 18.8565173 3.214002342 24.99996581 0.821201628 0.927412199 0.146808193 0.107337338 359.1439706 365602.321 0.02875587 0.034384394 1636.825347 -3.214002342 0.10621057 SQVIAEKAPEPDLMS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SQVIAEKAPEPDLMSPTR 18 1 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 SQVIAEKAPEPDLMS(0.956)PT(0.044)R;SQVIAEKAPEPDLMS(0.972)PT(0.028)R;SQVIAEKAPEPDLMS(0.992)PT(0.008)R;SQVIAEKAPEPDLMS(0.984)PT(0.016)R 169.33 1.12E-11 731490000 950840 809780 1029560 734000 1329090 1340190 1059610 1098960 1246290 1028940 TRUE FALSE 988379.8974 948853.4158 1056391.179 879183.0092 1103171.757 1028951.183 976554.9994 1084230.239 1201436.266 1230541.093 0.803207551 0.771086331 0.858476962 0.71446863 0.896493228 0.836177832 0.79359804 0.881100392 0.976347944 1 20.23086141 1.361027317 2.171418334 1.000379124 0.811077748 0.696663806 0.046644683 0.160291616 1.303943925 0.039566437 0.012017315 22.96293079 -1.361027317 -0.189301376 SQWLDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SQWLDVK 7 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ; 138.54 0.0064565 854030000 1122290 804730 1004050 788940 1300150 1328480 1287990 1076470 1097450 816150 FALSE TRUE 1166598.876 942936.1176 1030216.368 944989.9772 1079150.967 1019960.653 1187033.978 1062041.68 1057952.989 976058.9664 1.195213523 0.966064705 1.055485789 0.968168942 1.105620669 1.044978519 1.216149863 1.088091721 1.083902741 1 19.89660878 3.122989687 18.20512387 1.100282621 1.040583541 0.057268714 0.078688622 3.114505347 478.6605804 0.021615129 0.025835255 1327.362938 -3.122989687 -0.05969908 SRAARPT(ph)MDPS(ph)AHRSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRAARPTMDPSAHRSR 16 3 Q96AX9-14;Q96AX9-12;Q96AX9-4;Q96AX9-6;Q96AX9-5;Q96AX9-9;Q96AX9-3;Q96AX9;Q96AX9-13;D6RHY5 Q96AX9-14 MIB2 E3 ubiquitin-protein ligase MIB2 2 S(0.164)RAARPT(0.905)MDPS(0.883)AHRS(0.048)R 52.298 0.085257 59691000 1388 11142 5862.9 11943 2581.6 8860.3 2818.6 5020.2 4145 10939 TRUE FALSE 1442.799312 13055.55183 6015.69199 14305.28975 2142.780554 6802.629604 2597.670767 4952.91243 3995.82226 13082.28761 0.110286469 0.997956337 0.459834868 1.093485343 0.163792497 0.519987773 0.198563955 0.378596816 0.305437579 1 13.67532722 3.209515966 24.99851213 0.384702902 0.674463771 0.09887165 0.336340721 370.1879952 318617.043 0.088512405 0.105808778 1620.003547 -3.209515966 0.289760869 SRADLT(ph)AEMISAPLGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRADLTAEMISAPLGDFR 18 1 Q9H3Q1;Q9H3Q1-2;J3KRZ9;J3QQS6;J3QR93 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 S(0.404)RADLT(0.596)AEMISAPLGDFR;S(0.436)RADLT(0.564)AEMISAPLGDFR 88.79 0.00832 66398000 25008 28135 31681 28756 39259 39452 29771 31235 29228 31631 TRUE FALSE 25995.33515 32966.96739 32506.63289 34443.85097 32585.7692 30289.8709 27437.47123 30816.34592 28176.08999 37828.48884 0.687189363 0.87148518 0.85931619 0.910526749 0.861408166 0.800715858 0.725312379 0.814633279 0.744837842 1 15.20718552 2.720914187 20.43417951 0.798947153 0.84506138 0 0.089106258 240.5145611 278506.6214 0.027323863 0.025867153 525.9133403 -2.720914187 0.046114227 SRAEDLNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRAEDLNTR 9 1 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ; 114.45 0.0020316 102360000 63930 107148 82347 119867 141792 157941 125221 93315 82860 172920 FALSE TRUE 66454.00576 125549.8355 84493.03047 143576.3348 117690.2465 121261.5964 115405.8508 92064.26506 79877.88479 206800.3632 0.321343757 0.607106455 0.408572931 0.694275061 0.569100773 0.586370326 0.558054391 0.445184252 0.386256018 1 17.65787919 -1.522023853 4.196699202 1.004783146 0.515118324 0.642453886 0.109904587 0.004769943 0.000543265 0.103199104 0.024138719 0.030059112 1.522023853 -0.489664822 SRAS(ph)PVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SRASPVSR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.197)RAS(0.786)PVS(0.017)R;S(0.038)RAS(0.92)PVS(0.042)R;S(0.035)RAS(0.965)PVSR;S(0.134)RAS(0.864)PVS(0.002)R;S(0.115)RAS(0.885)PVSR;S(0.278)RAS(0.721)PVS(0.001)R;S(0.028)RAS(0.97)PVS(0.001)R 78.903 0.017818 5728446000 950595.5 1098479 992281 996903 1110742.2 1294738 1100348 1096009.1 1028127 979444 TRUE FALSE 988125.7444 1287134.223 1018140.658 1194087.438 921938.6376 994054.7214 1014099.849 1081318.891 991124.9101 1171347.299 0.843580503 1.098849354 0.869204768 1.01941366 0.787075394 0.848642177 0.865755058 0.923141148 0.846140945 1 20.15973746 3.251633729 24.99999253 0.875790524 0.961514197 0.172559126 0.084793868 365.1879616 698352.5534 0.02179767 0.02933839 1784.981539 -3.251633729 0.085723674 SRDAT(ph)PPVS(ph)PINMEDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRDATPPVSPINMEDQER 18 1 P17275 P17275 JUNB Transcription factor jun-B 2 S(0.004)RDAT(0.996)PPVS(1)PINMEDQER 133.15 3.04E-05 385090000 229410 268840 308370 307300 397610 430570 382280 396810 394000 401210 TRUE FALSE 238467.2839 315011.1787 316406.3755 368083.0228 330024.3942 330576.6429 352315.8947 391491.411 379820.017 479819.4179 0.496993817 0.65652028 0.659428034 0.767128234 0.687809584 0.688960535 0.734267688 0.815914064 0.791589508 1 18.87213202 1.551924044 0.064166546 1.5741496 8.05E-19 0.849810186 0.04803143 8.48501164 0.558115875 6.630041207 6.628357507 35.6388797 -1.551924044 -1.5741496 SRDAT(ph)PPVSPINMEDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRDATPPVSPINMEDQER 18 1 P17275 P17275 JUNB Transcription factor jun-B 1 S(0.012)RDAT(0.988)PPVSPINMEDQER;S(0.014)RDAT(0.986)PPVSPINMEDQER 120.49 0.00012685 0 16070.1 32903 27992 25163 35134 38487 24539.2 26086 32504 36820 TRUE FALSE 16704.55996 38553.8343 28721.49452 30140.1663 29161.93523 29548.97753 22615.75338 25736.35984 31334.18739 44034.17404 0.379354452 0.875543487 0.652254644 0.684472162 0.662256892 0.671046481 0.513595494 0.584463326 0.711587944 1 15.42633598 0.891313885 5.201532446 0.999982511 0.633669477 0.46145026 0.120495449 0.794262211 37.0276119 0.109391402 0.027615616 7.785990785 -0.891313885 -0.366313034 SRDEIVEMIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRDEIVEMIR 10 1 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 166.14 5.14E-06 227790000 86704 132404 103906 111625 120680 142843 102346 111139 112169 136188 FALSE TRUE 90127.14087 155143.357 106613.8757 133704.0918 100166.8567 109669.8781 94323.85309 109649.3635 108132.0596 162871.4311 0.553363719 0.952551076 0.654589175 0.820918014 0.615005689 0.673352455 0.579130744 0.6732265 0.663910539 1 17.31337404 -1.08925372 4.512701546 1.000020739 0.68962007 0.412704729 0.11186348 2.57E-05 5.18E-06 0.102442906 0.024144152 0.081422846 1.08925372 -0.310400669 SRDPFWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRDPFWNR 8 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 140.35 0.00059364 313190000 40139 50530 51265 51414 65594 63432 50194 51621 49450 73145 FALSE TRUE 41723.71871 59208.13443 52601.00801 61583.53574 54444.35531 48700.87932 46259.66312 50929.10493 47670.30416 87476.3623 0.476971351 0.67684724 0.60131682 0.70400202 0.622389339 0.556731876 0.528824724 0.582204193 0.544950692 1 16.41660561 -1.669746222 2.603510453 1.056388941 0.591465264 0.78608821 0.064417727 13437680.62 11292861.71 5028855.203 0.01610902 0.021392118 1.669746222 -0.464923677 SRDPQLCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRDPQLCR 8 1 Q8TAT6;Q8TAT6-2;I3L4S2 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 ;;; 93.162 0.010273 543500000 209200 305057 273199 290881 315626 350521 260051 278367 258375 430118 FALSE TRUE 217459.3775 357448.1667 280318.7904 348416.3936 261976.0053 269117.8099 239667.5231 274635.9457 249076.1342 514391.387 0.422750814 0.694895319 0.544952341 0.677337145 0.509293141 0.523177131 0.465924448 0.533904635 0.484215211 1 18.97250696 -1.487512474 3.319160512 1.009085207 0.543129275 0.741117198 0.081607904 28138050.87 34609017.55 2323994.933 0.019452378 0.032545244 1.487512474 -0.465955932 SRDSFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRDSFLK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 91.069 0.015208 60372000 59212 45493 59657 39169 89764 82489 68208 66386 63276 68185 FALSE TRUE 61549.73548 53306.06886 61211.71043 46916.51129 74505.94734 63332.17988 62861.67873 65496.20426 60998.70912 81544.54527 0.75479893 0.653704901 0.750653649 0.575348248 0.913684013 0.776657466 0.770887599 0.803195407 0.748041563 1 16.31530075 -5 0.131091802 1.842226081 0.646852773 0.487260545 0.080687055 116.9605876 0.964861583 25.81811687 0.573082551 1.00E-05 5 -1.195373308 SRDYNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRDYNGR 7 1 P98179 P98179 RBM3 RNA-binding protein 3 0 105.12 0.0072951 31694000 26229 16287 26019 16284 33594 35830 29725 31080 24131 34300 FALSE TRUE 27264.54117 19084.16555 26697.07651 19504.9266 27883.70388 27509.02551 27395.07683 30663.42344 23262.53002 41020.42829 0.664657643 0.465235648 0.650823934 0.475493002 0.679751652 0.670617706 0.667839854 0.747515926 0.567096225 1 15.32405493 -4.999999999 0.157316874 2.397205433 0.517971921 0.647906289 0.084859724 74.96387851 0.684077483 32.58817505 0.35198665 1.00E-05 4.999999999 -1.879233513 SREDVSNFDPDFIKEEPVLT(ph)PIDEGHLPMINQDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFR 36 2 P24723-2;P24723 P24723-2 PRKCH Protein kinase C eta type 1 SREDVSNFDPDFIKEEPVLT(1)PIDEGHLPMINQDEFR;SREDVSNFDPDFIKEEPVLT(0.999)PIDEGHLPMINQDEFR 103.96 2.53E-05 105669000 82575 66440 72820 63669 92707 92109 92324 77409 83877 68647 TRUE FALSE 85835.12476 77850.55317 74717.74902 76262.53817 76948.69725 70718.08068 85087.40364 76371.45897 80858.28315 82097.06532 1.045532193 0.948274495 0.910114737 0.928931355 0.937289256 0.861395963 1.036424424 0.930258087 0.984910762 1 16.32504303 2.222418126 24.99945395 0.978474052 0.937237422 0.181917293 0.049592311 501.4620758 776595.9276 0.0185002 0.013705549 166.8853164 -2.222418126 -0.04123663 SREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SREEAAAGTIPGALNIPVSELESALQMEPAAFQALYSAEKPK 42 2 Q8NFU3;Q8NFU3-4;Q8NFU3-3 Q8NFU3 TSTD1 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1 0 56.347 0.010005 244650000 242020 32623 56414 36746 61839 127910 68169 50562 62573 34029 FALSE TRUE 251575.1365 38225.74648 57884.19518 44014.24912 51327.62887 98204.84099 62825.73565 49884.29909 60321.00995 40696.33103 6.181764551 0.939292204 1.422344318 1.081528679 1.261234799 2.413112891 1.543769034 1.225768954 1.482222314 1 15.31261111 4.741934233 24.99927691 1.401944548 6.181766332 0.929439968 0.397309369 77.62017691 575157.9234 0.096540553 0.700860906 55199.38418 -4.741934233 4.779821784 SRENLS(ph)AVMLYNPGLEFER ddPTM_MDA-MB-175_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(0.098)RENLS(0.902)AVMLYNPGLEFER;S(0.234)RENLS(0.766)AVMLYNPGLEFER;S(0.265)RENLS(0.735)AVMLYNPGLEFER;S(0.317)RENLS(0.683)AVMLYNPGLEFER 218 2.10E-19 1445510000 314062 328835 363872 315212 452787 499827 377697 394795 367498 329172 TRUE FALSE 326461.4103 385309.8533 373354.8032 377559.9928 375822.4275 383749.7542 348092.1222 389503.4188 354271.8188 393666.951 0.829283254 0.978771147 0.94840271 0.95908481 0.954671014 0.974808155 0.884229985 0.989423719 0.899927763 1 18.58661608 4.745972071 24.67590897 0.953083203 0.829283184 0.533902996 0.035043371 536.7896649 1787150.632 0.007509017 0.077685954 55714.99182 -4.745972071 -0.123800019 SRES(ph)MIQLF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRESMIQLF 9 1 P30520;G3V5D8;G3V232;Q8N142;Q8N142-2 P30520;Q8N142 ADSS;ADSSL1 Adenylosuccinate synthetase isozyme 2;Adenylosuccinate synthetase isozyme 1 1 S(0.175)RES(0.825)MIQLF;S(0.119)RES(0.881)MIQLF 93.345 0.024891 107930000 160142 198505 229770 193399 277900 260760 203129 200827 213186 222668 TRUE FALSE 166464.5298 232596.6896 235757.995 231652.745 230662.6573 200202.4419 187207.2182 198135.2426 205513.4775 266295.5314 0.625111991 0.873453221 0.885324638 0.869908495 0.866190492 0.751805488 0.703005481 0.744042686 0.771749629 1 18.02266869 2.728566825 23.65880796 0.768134708 0.832702937 0 0.104351699 895.0328062 2118851.264 0.032252011 0.030769941 535.2625087 -2.728566825 0.064568229 SRES(ph)S(ph)PSHGLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRESSPSHGLLK 12 1 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 2 S(0.398)RES(0.805)S(0.779)PS(0.019)HGLLK 63.709 0.039125 385670000 466680 408010 446660 340570 622840 552120 524570 408170 443770 295590 TRUE FALSE 485104.8868 478082.5436 458300.3265 407933.7295 516969.8793 423898.4975 483452.8327 402699.1488 427798.8044 353505.2011 1.372270861 1.352405968 1.296445781 1.153968112 1.462410957 1.19912945 1.36759751 1.139160464 1.210162688 1 18.43137192 0.939818195 0.574122884 0.994463919 1.32480048 0.533068111 0.090249897 0.710312606 0.555415836 0.091947798 0.039904506 8.705990617 -0.939818195 0.330336561 SRFS(ph)GGFGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRFSGGFGAR 10 1 A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;A0A0J9YVQ7 A0A2R8YFS5 1 S(0.004)RFS(0.996)GGFGAR;S(0.211)RFS(0.789)GGFGAR 108.97 0.00126 454360000 125570 153785 104967 114171 170846 172805 137383 125988 129260 167346 TRUE FALSE 130527.6006 180196.3775 107702.5263 136753.683 141805.6579 132673.6576 126614.5615 124299.3369 124607.9578 200134.2447 0.652200231 0.900377533 0.538151411 0.683309762 0.708552693 0.662923319 0.632648159 0.621079801 0.622621871 1 17.61060852 -1.897474974 6.572398099 1.070282211 0.668349467 0.556544505 0.088610905 0.05025597 0.00078396 0.04725009 0.019571392 0.012662662 1.897474974 -0.401932744 SRGPATVEDLPSAFEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRGPATVEDLPSAFEEK 17 1 O14908;O14908-2;K7EM11 O14908 GIPC1 PDZ domain-containing protein GIPC1 0 180.88 7.62E-10 282780000 198450 121770 137890 112860 267670 224970 226790 177200 173410 128240 FALSE TRUE 206284.9592 142683.0503 141483.5267 135183.3711 222171.549 172724.127 209013.6072 174824.9238 167169.008 153366.1727 1.345048622 0.930342381 0.922521076 0.881441903 1.448634631 1.126220495 1.362840342 1.139918411 1.089999216 1 17.22662078 3.262242122 24.9997757 1.205596355 1.006494721 0.196881115 0.171215623 333.9176591 352503.3202 0.045824 0.062011996 1829.11968 -3.262242122 -0.199101634 SRGSPS(ph)SYNSSSSSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 S(0.147)RGS(0.202)PS(0.651)S(0.001)YNSSSSSPR;SRGS(0.166)PS(0.396)S(0.396)YNS(0.029)S(0.004)S(0.004)S(0.004)SPR 230.32 6.24E-15 439360000 200390 257266 239638 214918 260912 280465 228734 248478 239068 193088 TRUE FALSE 208301.5519 301449.4342 245883.1631 257428.1389 216562.2714 215331.2542 210805.2314 245147.5588 230463.9894 230919.8967 0.902051122 1.305428586 1.064798515 1.114794102 0.937824218 0.93249329 0.912893321 1.061612976 0.998025691 1 17.81703296 3.247480368 24.97230921 0.976564281 1.109388896 0.264154988 0.099588243 236.6494331 662534.7026 0.026581397 0.035463573 1767.992296 -3.247480368 0.132824615 SRGSPSSYNSSSS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRGSPSSYNSSSSSPR 16 1 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SRGS(0.011)PS(0.282)S(0.032)YNS(0.093)S(0.031)S(0.01)S(0.524)S(0.018)PR 134.14 7.86E-05 37748000 65541 71187 70445 63815 75227 90326 67076 71792 62891 68301 TRUE FALSE 68128.60929 83412.81349 72280.85457 76437.41653 62439.94141 69349.1554 61818.40785 70829.74567 60627.5652 81683.27325 0.834058267 1.021173738 0.88489175 0.935778079 0.76441527 0.849000691 0.756806203 0.867126682 0.74222742 1 16.31775306 3.255526981 24.98143196 0.822307066 0.923840816 0.215795204 0.08218567 305.0425742 449144.8894 0.020608242 0.027832539 1801.055025 -3.255526981 0.101533751 SRIPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 Q96GY3;K7EMY4 Q96GY3 LIN37 Protein lin-37 homolog 1 SRIPS(0.999)PLQPEMQGT(0.001)PDDEPSEPEPSPSTLIYR;S(0.002)RIPS(0.998)PLQPEMQGTPDDEPSEPEPSPSTLIYR;SRIPS(1)PLQPEMQGTPDDEPSEPEPSPSTLIYR;S(0.039)RIPS(0.961)PLQPEMQGTPDDEPSEPEPSPSTLIYR 211.47 9.40E-28 1044560000 235266 279174 256442 272060 329908 368107 289165 316058 270846 314686 TRUE FALSE 244554.4833 327119.9628 263125.0892 325872.656 273830.356 282619.728 266499.4917 311821.7595 261098.3054 376342.6967 0.649818598 0.869207682 0.699163532 0.865893397 0.727609061 0.750963764 0.708129835 0.82855802 0.693778058 1 18.52168745 -1.765787158 2.689097323 1.055831822 0.761827585 0.507469587 0.07217274 11956729.59 8628565.362 4393426.726 0.016369258 0.017147975 1.765787158 -0.294004238 SRKS(ph)PHKDLGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRKSPHKDLGHR 12 3 O94888;C9JAT7 O94888 UBXN7 UBX domain-containing protein 7 1 S(0.056)RKS(0.944)PHKDLGHR;S(0.439)RKS(0.561)PHKDLGHR 95.662 0.0042254 1173380000 1422800 732440 1201860 613960 1663880 1459380 1258670 1090780 1391290 855160 TRUE FALSE 1478973.243 858230.8724 1233181.459 735399.4555 1381054.272 1120461.112 1160012.156 1076159.878 1341217.745 1022712.229 1.446128442 0.839171419 1.205795163 0.719067822 1.35038404 1.095578092 1.134250793 1.052260692 1.311432196 1 19.96396883 SRLDS(ph)YVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRLDSYVR 8 1 Q9Y5R8 Q9Y5R8 TRAPPC1 Trafficking protein particle complex subunit 1 1 S(0.006)RLDS(0.994)YVR;S(0.003)RLDS(0.997)YVR 73.951 0.025579 375550000 108828 129428 124014 107311 144611 139667 124607 122422 111313 128401 TRUE FALSE 113124.6135 151656.2522 127245.9067 128536.7955 120030.0739 107231.4559 114839.9777 120781.1333 107306.8669 153558.7176 0.736686365 0.987610828 0.828646584 0.837053067 0.781655876 0.698309139 0.747857104 0.7865469 0.698800228 1 17.22843089 3.350551158 2.574909615 0.76868685 0.862428959 0.071352918 0.098347723 0.502477883 6.758624343 0.027004479 0.038728083 2241.564078 -3.350551158 0.093742109 SRLEVTDDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRLEVTDDLEK 11 1 P35813;P35813-3;P35813-2 P35813 PPM1A Protein phosphatase 1A 0 152.4 3.01E-05 173560000 326360 199270 260780 208460 385600 388040 337390 273460 311290 214500 FALSE TRUE 339244.9448 233493.0724 267576.141 249692.7658 320055.8497 297923.5908 310944.4902 269794.716 300086.7337 256527.1681 1.322452305 0.910207968 1.043071356 0.973357978 1.247648941 1.16137247 1.212130834 1.051719855 1.169804882 1 17.9687521 4.779186262 23.54861326 1.093555581 1.322453751 0.313607399 0.10456256 17327.47088 10043386.93 0.025276866 8.736469692 60143.16263 -4.779186262 0.228898169 SRLNS(ph)HGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 SRLNS(1)HGGR;SRLNS(1)HGGR;SRLNS(1)HGGR;SRLNS(1)HGGR 113.93 0.0010418 798457000 200150 243226 289159 216464 507018 426301 334004 390272 375544 488862 TRUE FALSE 208052.0765 284998.1735 296694.7211 259279.9331 420835.2615 327299.0534 307823.8937 385041.0422 362028.2448 584645.1491 0.355860434 0.487472057 0.507478291 0.44348257 0.719813142 0.559825142 0.526514064 0.658589305 0.619227313 1 19.15720172 -5 0.108256968 2.476778641 0.273274165 0.806293875 0.074822365 70.64918109 0.510946497 23.12482431 0.970225913 1.00E-05 5 -2.203504476 SRLT(ph)PVS(ph)PESSSTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 2 S(0.005)RLT(0.995)PVS(0.988)PES(0.01)S(0.001)STEEK 146.72 2.51E-06 431640000 259220 159090 189360 154420 269160 279090 266530 206180 225370 171930 TRUE FALSE 269454.2058 186412.47 194294.8772 184963.8151 223408.2793 214275.5771 245638.6822 203416.4943 217258.9777 205616.3917 1.310470452 0.906603158 0.944938658 0.899557733 1.08652952 1.042113303 1.194645427 0.989300963 1.05662285 1 17.64959575 SRLT(ph)PVSPESSSTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.25)RLT(0.75)PVSPESSSTEEK 180.63 3.94E-09 495690000 374200 223470 320340 217140 378690 420380 384770 327320 367400 236270 TRUE FALSE 388973.7049 261849.2341 328688.3236 260089.6439 314320.4091 322753.1159 354610.722 322932.8108 354177.3458 282562.5828 1.376593111 0.926694651 1.163240795 0.920467393 1.112392186 1.142235864 1.254981174 1.142871811 1.253447439 1 18.10821091 2.705023267 3.57779555 1.17548114 1.082818253 0.034513181 0.13739786 0.586389874 15.9208288 0.042507053 0.041443802 507.0178705 -2.705023267 -0.092662887 SRLTPVS(ph)PESSSTEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.004)RLT(0.003)PVS(0.993)PESSSTEEK 96.718 0.0020093 118430000 61507 32412 44219 28976 102410 76644 81707 64595 59150 52680 TRUE FALSE 63935.34385 37978.50887 45371.38347 34707.36632 85002.38478 58844.59255 75302.59184 63729.20968 57021.20305 63001.63738 1.014820352 0.602817807 0.720161973 0.550896259 1.349209137 0.934016876 1.195248171 1.011548467 0.905074938 1 15.9431017 3.251021621 24.99964316 1.065502441 0.713504932 0.505434888 0.16645701 175.6075062 352307.005 0.04373017 0.058799337 1782.467505 -3.251021621 -0.351997509 SRNS(ph)FSSYAQLPKPTSTYSLSSFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRNSFSSYAQLPKPTSTYSLSSFFR 25 2 G3V4K3;Q9H9C1 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 1 S(0.387)RNS(0.596)FS(0.007)S(0.009)YAQLPKPTSTYSLSSFFR 72.163 0.018885 406160000 151970 100690 134340 148470 184780 199440 140910 162570 142210 142500 TRUE FALSE 157969.8929 117982.7242 137841.0108 177836.9229 153371.1616 153123.0825 129865.106 160391.0151 137091.8899 170420.1467 0.926943768 0.692305027 0.80883049 1.043520536 0.899959099 0.898503408 0.762029071 0.941150552 0.804434761 1 17.37873637 -2.749595483 1.958748371 4.942465156 0.865890794 0.153904068 0.095456835 2708292.913 96495.65106 47714436.2 0.023533289 0.001779937 2.749595483 -4.076574361 SRNS(ph)PLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 SRNS(1)PLLER;S(0.001)RNS(0.999)PLLER;S(0.277)RNS(0.723)PLLER;SRNS(1)PLLER;S(0.361)RNS(0.639)PLLER 152 4.94E-05 16075430000 1375344 1807440 1607230 1611390 1926930 2068960 1664370 1653950 1472700 1689370 TRUE FALSE 1429643.643 2117853.76 1649115.734 1930118.132 1599391.127 1588475.395 1533912.33 1631781.506 1419697.815 2020369.707 0.707614868 1.048250601 0.816244536 0.955329179 0.791632899 0.78623006 0.759223584 0.807664805 0.702692091 1 20.94618788 3.209652386 24.32173855 0.794843472 0.889058051 0.090142148 0.109570213 275.4215067 231722.975 0.028782829 0.03440847 1620.512504 -3.209652386 0.094214578 SRNTDEMVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SRNTDEMVELR 11 1 P61978;P61978-2;S4R457;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ;;;; 192.68 1.17E-06 2108360000 1186130 666514 994555 581379 2347190 1539960 1675580 1410610 1214136 1629140 FALSE TRUE 1232959.328 780982.5947 1020473.92 696374.031 1948215.482 1182327.628 1544243.661 1391703.08 1170439.483 1948338.791 0.632825941 0.400845376 0.523766157 0.357419374 0.999936711 0.606838828 0.79259504 0.714302403 0.600737145 1 20.89381313 3.254346857 24.99983321 0.760214485 0.476370144 0.509912251 0.146169658 199.727325 316295.6869 0.037676069 0.050845533 1796.167595 -3.254346857 -0.283844342 SRPDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRPDSPR 7 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 S(0.028)RPDS(0.972)PR 80.688 0.076903 105460000 85413 111990 117330 108720 115370 133800 111030 117490 109590 106400 TRUE FALSE 88785.17119 131223.4113 120387.7162 130224.4915 95759.44861 102726.9778 102327.1785 115915.2387 105645.8773 127247.0428 0.697738582 1.031249202 0.946094412 1.023398961 0.752547536 0.807303458 0.804161544 0.910946425 0.830242298 1 16.9572726 4.771682798 23.59025461 0.892081884 0.697737781 0.288546616 0.094732573 10203.68024 7266977.81 0.023222328 3.496602995 59112.97246 -4.771682798 -0.194344103 SRPELLEYYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRPELLEYYIK 11 1 Q14258 Q14258 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 85.973 0.013513 429300000 218050 277490 270120 258820 349220 381560 301000 302730 278590 280080 FALSE TRUE 226658.7824 325146.7489 277159.5491 310013.8235 289859.7091 292948.4726 277406.8335 298672.3995 268563.6003 334956.3135 0.676681624 0.970713898 0.827449843 0.925535095 0.865365713 0.874587105 0.828188102 0.891675683 0.801786948 1 18.35361342 -2.591441447 2.202846404 3.834036632 0.858918752 0.254655981 0.075302757 3608969.246 329222.2665 51072652.23 0.01679686 0.002561879 2.591441447 -2.97511788 SRPFTVAASFQSTSVKS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRPFTVAASFQSTSVKSPK 19 2 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 SRPFTVAASFQSTS(0.005)VKS(0.995)PK;SRPFTVAASFQSTS(0.001)VKS(0.999)PK;SRPFTVAASFQS(0.004)T(0.124)S(0.072)VKS(0.8)PK;SRPFTVAASFQSTS(0.009)VKS(0.99)PK 208.89 1.30E-16 10341999000 5986015 1764007 3054529 1816149 4602761 4790526 4392039 3280488 3651961 1464747 TRUE FALSE 6222347.494 2066961.48 3134132.535 2175377.852 3820385.329 3677998.938 4047779.507 3236518.424 3520527.637 1751736.13 3.552103189 1.179950247 1.789157899 1.241841059 2.180913702 2.099630689 2.31072445 1.847606137 2.00973627 1 20.74035404 4.751728708 24.69996227 1.805156677 3.552104527 0.607613588 0.434039513 1284.828429 2409958.188 0.101387807 1.911410838 56458.4184 -4.751728708 1.74694785 SRPTS(ph)EGS(ph)DIESTEPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 SRPT(0.1)S(0.9)EGS(0.459)DIES(0.461)T(0.08)EPQK;S(0.003)RPT(0.364)S(0.812)EGS(0.821)DIESTEPQK 206.64 8.12E-11 725050000 2135270 1441770 1860550 1466630 2487460 2437750 2320970 1990030 2021520 1255630 TRUE FALSE 2219572.108 1689382.782 1909037.461 1756725.037 2064642.438 1871619.507 2139046.307 1963356.903 1948765.89 1501646.658 1.478092131 1.125020172 1.271296048 1.169865778 1.374918944 1.246378099 1.424467131 1.307469299 1.297752624 1 20.51811395 -0.400155487 7.54119252 1.000000091 1.296628954 0.436266785 0.102080832 0 0 0.092537874 0.021811386 0.397964665 0.400155487 0.296628863 SRPTS(ph)EGSDIES(ph)TEPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 2 SRPT(0.154)S(0.846)EGS(0.026)DIES(0.972)T(0.002)EPQK 267.22 1.13E-26 546160000 3268600 2202700 2849500 2227800 3590200 3798800 3414400 2990800 3090800 1946800 TRUE FALSE 3397646.852 2580996.59 2923760.311 2668452.191 2979939.086 2916586.271 3146770.406 2950713.218 2979562.712 2328238.186 1.459320989 1.10856209 1.255782303 1.146125086 1.27991161 1.252700986 1.351567217 1.267358828 1.279749954 1 21.15080723 -1.185691675 5.615515065 0.999992985 1.262279643 0.429932826 0.092029556 7.49E-06 1.09E-06 0.082629569 0.019475455 0.065209118 1.185691675 0.262286658 SRPTSEGS(ph)DIESTEPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;H0YA82;D6RFF0 Q4G0J3 LARP7 La-related protein 7 1 S(0.056)RPT(0.236)S(0.152)EGS(0.556)DIESTEPQK;SRPT(0.08)S(0.08)EGS(0.84)DIESTEPQK;S(0.007)RPT(0.239)S(0.239)EGS(0.516)DIESTEPQK;S(0.002)RPT(0.081)S(0.081)EGS(0.836)DIESTEPQK 212.65 8.37E-13 4345890000 3477800 2515500 3181490 2503530 3730640 3891070 3741620 3012740 3252520 2045330 TRUE FALSE 3615106.229 2947517.557 3264402.243 2998720.762 3096507.145 2987427.962 3448342.047 2972359.148 3135462.441 2446073.253 1.477922309 1.204999708 1.334548031 1.225932526 1.265909409 1.22131582 1.409746026 1.21515541 1.281835054 1 21.22203618 -3.833454967 0.281794423 1.03E-15 1.307907063 0.526226383 0.084619469 84.48462565 1.486030516 48.99002705 0.088921067 0.000146739 3.833454967 1.307907063 SRQELASGLPS(ph)PAATQELPVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRQELASGLPSPAATQELPVER 22 1 O95359-3;E9PBC6;E7EMZ9;O95359 O95359-3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 SRQELASGLPS(1)PAATQELPVER;SRQELASGLPS(1)PAATQELPVER 157.16 3.90E-09 667000000 198881 220560 218654 209499 262830 261130 200795 225560 202700 235848 TRUE FALSE 206732.9754 258439.4643 224352.3029 250937.2769 218154.2505 200486.515 185056.1632 222536.7371 195404.8666 282057.9 0.73294517 0.916263874 0.795412229 0.889665834 0.773437831 0.710799148 0.656092821 0.788975374 0.692782817 1 18.10563182 5.088957667 12.45272903 0.79015033 0.000110297 0.027802467 0.101932176 624135.2232 2098594.079 0.023782015 12800288.89 122731.9592 -5.088957667 -0.790040033 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 S(0.054)RQPS(0.946)PLLLLPPPAGLTSDPGPSVR;S(0.048)RQPS(0.952)PLLLLPPPAGLTSDPGPSVR;S(0.036)RQPS(0.964)PLLLLPPPAGLTSDPGPSVR;S(0.11)RQPS(0.89)PLLLLPPPAGLTSDPGPSVR 104.9 0.0025957 1663400000 404398 493632 456616 467481 514575 577640 498989 481755 514164 499743 TRUE FALSE 420363.9453 578409.4561 468515.7881 559947.3465 427107.7253 443491.8642 459876.9383 475297.8622 495659.3381 597658.0727 0.703351907 0.967793263 0.783919451 0.936902507 0.714635583 0.742049484 0.769464949 0.7952672 0.829335971 1 19.18896081 0.79001202 3.938971458 0.999994734 0.804374237 0.338868952 0.082546929 2.392674632 43.73179555 0.076034403 0.019446197 6.16612068 -0.79001202 -0.195620497 SRQT(ph)PS(ph)PDVVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRQTPSPDVVLR 12 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 S(0.098)RQT(0.904)PS(0.998)PDVVLR 78.597 0.057977 1047400000 498330 477860 469390 505400 586740 636590 504150 521790 519880 465880 TRUE FALSE 518004.4532 559928.7378 481622.689 605366.6115 487006.1444 488751.6201 464633.4056 514796.2585 501169.6204 557160.2662 0.929722532 1.004968896 0.86442397 1.086521506 0.87408628 0.877219087 0.833931337 0.923964413 0.899507109 1 19.08773285 SRS(ph)APPNLWAAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSAPPNLWAAQR 13 1 Q92934;F5H1R6;F5H3B1 Q92934;F5H1R6 BAD Bcl2-associated agonist of cell death 1 SRS(1)APPNLWAAQR;S(0.014)RS(0.986)APPNLWAAQR 240.53 4.54E-17 416620000 149975 143776 197759 142319 255241 234718 187707 173639 178349 250457 TRUE FALSE 155896.1288 168468.4096 202912.762 170469.2734 211855.226 180208.3017 172994.0349 171311.6532 171930.2543 299529.2539 0.520470461 0.562443926 0.677438879 0.569123954 0.70729394 0.601638402 0.577553052 0.5719363 0.574001544 1 18.19233739 -1.161695476 3.824556593 1.000235883 0.597216967 0.839920411 0.052938823 2171679.424 1100753.597 4259.475733 0.012368374 0.068913534 1.161695476 -0.403018916 SRS(ph)AVTLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSAVTLPR 9 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 S(0.164)RS(0.836)AVTLPR 73.082 0.037457 0 35941 39357 35661 30763 50371 50008 36300 37540 35867 46549 TRUE FALSE 37359.97843 46116.2586 36590.35496 36847.82958 41808.95541 38394.39988 33454.71115 37036.8377 34576.15368 55669.38532 0.671104562 0.828395326 0.657279665 0.661904732 0.751022401 0.689686075 0.600953486 0.665299922 0.621098176 1 15.76459653 -1.513458964 6.059043711 1.000357181 0.68314448 0.704526569 0.06159271 0.000302351 2.43E-05 0.060674104 0.014285277 0.030657804 1.513458964 -0.317212701 SRS(ph)DIDVNAAAGAK ddPTM_MDA-MB-175_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(0.018)RS(0.982)DIDVNAAAGAK;S(0.004)RS(0.996)DIDVNAAAGAK;S(0.005)RS(0.995)DIDVNAAAGAK 204.81 3.45E-08 730510000 1193410 881520 1083560 816490 1355030 1264330 1224840 997040 1089150 761770 TRUE FALSE 1240526.748 1032914.203 1111798.464 977989.285 1124702.485 970708.5186 1128833.84 983676.3096 1049951.704 911024.2465 1.36168357 1.133794415 1.220382957 1.073505221 1.234547257 1.065513374 1.239082104 1.079747672 1.152495895 1 19.79712993 8 0.062062342 0.816510804 1.880780775 0.40939358 0.07881329 319.0699663 1.475022313 4.964524061 30.43514029 100000000 -8 1.064269971 SRS(ph)DIDVNAAASAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSDIDVNAAASAK 14 1 Q7Z460;Q7Z460-4;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;H0Y5T1 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 S(0.011)RS(0.934)DIDVNAAAS(0.055)AK;S(0.046)RS(0.954)DIDVNAAASAK 176.87 5.69E-06 567560000 691000 512390 632970 454160 828140 789320 671800 591350 671590 478380 TRUE FALSE 718281.2136 600388.9967 649465.7182 543991.4925 687373.0586 606012.3923 619142.5606 583423.9205 647419.6071 572109.4019 1.255496259 1.049430397 1.135212454 0.950852216 1.201471356 1.059259628 1.082210078 1.019776844 1.131636021 1 19.12593153 4.742668796 24.64163342 1.070855877 1.255496347 0.393898139 0.069028504 321.0636437 1925711.414 0.01501805 0.114114501 55292.82716 -4.742668796 0.184640471 SRS(ph)FDYNYR ddPTM_MDA-MB-175_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(0.026)RS(0.974)FDYNYR;S(0.001)RS(0.999)FDYNYR;S(0.113)RS(0.887)FDYNYR;S(0.066)RS(0.934)FDYNYR 182.23 2.82E-05 933260000 612095 669550 682160 636050 661340 788770 709630 685400 635010 587460 TRUE FALSE 636260.9832 784540.0041 699937.65 761858.7916 548925.663 605590.1214 654007.3463 676213.3341 612156.1141 702561.5394 0.905630251 1.116685102 0.996265253 1.084401506 0.7813204 0.861974485 0.930889765 0.962496943 0.871320276 1 19.42226508 3.259682708 24.99996897 0.904025277 1.030135481 0.388298471 0.076374472 246.2240688 291427.2992 0.020733969 0.028046564 1818.371884 -3.259682708 0.126110203 SRS(ph)FTLDDESLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 S(0.484)RS(0.506)FT(0.009)LDDESLK 186.94 6.73E-06 118600000 326140 460390 463200 519020 536050 719890 555040 563510 555210 524480 TRUE FALSE 339016.259 539458.4012 475271.3725 621680.6069 444932.4125 552706.4575 511534.5145 555957.0702 535228.1006 627241.8142 0.540487339 0.860048531 0.757716341 0.99113387 0.709347499 0.881169662 0.815529996 0.886352054 0.853304242 1 19.25866221 5.125518865 1.814239773 0.858386141 3.99E-08 0.548264478 0.086572325 2.332259913 3.056499729 0.020021297 4.843542029 133511.5583 -5.125518865 -0.858386101 SRS(ph)GEGEVSGLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSGEGEVSGLMR 13 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 S(0.247)RS(0.753)GEGEVSGLMR;S(0.019)RS(0.981)GEGEVSGLMR;S(0.015)RS(0.985)GEGEVSGLMR;S(0.187)RS(0.813)GEGEVSGLMR 227.31 5.64E-12 3320410000 883770 1035408 1121069 1057973 1246994 1398572 1014573 1183421 1080839 1154328 TRUE FALSE 918661.922 1213231.27 1150284.979 1267236.902 1035030.405 1073774.849 935048.1172 1167559.177 1041939.816 1380496.471 0.665457639 0.878836922 0.833240072 0.917957364 0.749752301 0.777817888 0.677327423 0.845753105 0.754757319 1 20.39675577 -1.021439185 4.900287178 1.000001531 0.794185515 0.39622708 0.077905891 0.013646833 49350353.47 366.697677 0.017685715 0.095183313 1.021439185 -0.205816016 SRS(ph)HSDNDRPNCSWNTQYSSAYYTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSHSDNDRPNCSWNTQYSSAYYTSR 26 2 O75494-6;O75494-3 O75494-6 SRSF10 Serine/arginine-rich splicing factor 10 1 S(0.179)RS(0.667)HS(0.153)DNDRPNCSWNTQYSSAYYTSR 244.57 1.47E-45 543270000 169320 419780 324610 412520 376180 469860 286700 329180 349620 552460 TRUE FALSE 176004.8843 491873.9496 333069.6033 494115.2248 312237.058 360742.1358 264227.7048 324767.8805 337037.2445 660703.9595 0.266389934 0.744469505 0.504113224 0.747861758 0.472582393 0.545996631 0.399918452 0.491548258 0.510118397 1 19.33364447 -1.319969098 3.043099463 1.00404733 0.524799094 0.527518165 0.136127689 22732054.13 29579373.18 832686.8521 0.032623343 0.047866415 1.319969098 -0.479248236 SRS(ph)MLEVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSMLEVPR 9 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 S(0.053)RS(0.947)MLEVPR;S(0.014)RS(0.986)MLEVPR;S(0.103)RS(0.897)MLEVPR;S(0.229)RS(0.771)MLEVPR 120.53 0.00039383 736730000 301128 335181 325580 307848 381984 385311 303829 346089 325714 348032 TRUE FALSE 313016.766 392745.7294 334064.8823 368739.4156 317054.4961 295828.3597 280014.0891 341450.243 313991.6168 416222.2069 0.752042445 0.943596288 0.802611866 0.885919611 0.761743345 0.710746219 0.67275144 0.820355659 0.754384585 1 18.66699441 6.184936542 8.8944511 0.802028652 0.721974907 0 0.099017436 0 0 0.021157627 0 1530863.761 -6.184936542 -0.080053745 SRS(ph)PIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPIQR 7 1 Q9Y252 Q9Y252 RNF6 E3 ubiquitin-protein ligase RNF6 1 S(0.207)RS(0.793)PIQR 77.192 0.047969 0 19684 26959 16360 16666 25867 26227 17528 20021 21545 21400 TRUE FALSE 20461.13952 31588.99854 16786.35504 19962.48506 21470.13658 20136.17672 16154.10956 19752.65124 20769.59966 25592.92027 0.799484361 1.2342866 0.655898384 0.780000283 0.838909212 0.786786991 0.631194463 0.771801382 0.811536919 1 14.64345715 4.223107925 24.99998879 0.770345821 1.01688562 0.312543524 0.136562196 205.552318 332552.1664 0.031045189 0.067443777 16715.05943 -4.223107925 0.246539799 SRS(ph)PITTNHRPS(ph)PDPEQRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 2 S(0.444)RS(0.556)PIT(0.02)T(0.01)NHRPS(0.97)PDPEQRPLR;S(0.143)RS(0.857)PIT(0.002)T(0.001)NHRPS(0.997)PDPEQRPLR;S(0.16)RS(0.84)PIT(0.003)T(0.01)NHRPS(0.987)PDPEQRPLR 128.71 2.54E-05 860310000 187547 172416 194221 189319 188716 215917 175150 168462 164483 168763 TRUE FALSE 194951.5004 202027.1068 199282.5588 226765.7331 156638.1217 165773.549 161421.2853 166204.0424 158563.289 201828.8787 0.965924706 1.000982159 0.987383768 1.123554442 0.776093702 0.821356934 0.799792807 0.823489897 0.785632314 1 17.62277309 3.227176876 24.99999608 0.822675794 1.015850091 0.616274634 0.071159144 126.0016088 276713.4598 0.019079084 0.022992 1687.240051 -3.227176876 0.193174297 SRS(ph)PITTNHRPSPDPEQRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPITTNHRPSPDPEQRPLR 21 3 P41212 P41212 ETV6 Transcription factor ETV6 1 S(0.467)RS(0.532)PIT(0.001)TNHRPSPDPEQRPLR;S(0.408)RS(0.587)PIT(0.002)T(0.003)NHRPSPDPEQRPLR 110.03 0.00020116 998990000 389600 506960 483810 447310 434170 580760 469800 525780 401670 437930 TRUE FALSE 404981.7088 594026.4364 496418.4861 535786.5829 360369.9385 445887.2915 432975.8484 518732.7791 387213.9752 523733.9988 0.77325839 1.134214005 0.947844683 1.023012797 0.688078183 0.851362128 0.826709454 0.99045084 0.73933328 1 18.99847474 SRS(ph)PLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPLAR 7 1 Q8N3Y1 Q8N3Y1 FBXW8 F-box/WD repeat-containing protein 8 1 S(0.112)RS(0.888)PLAR;S(0.153)RS(0.847)PLAR 103.7 0.0050369 248637000 68048 90315 84205 84642 88184 102263 99990 96121 77616 101137 TRUE FALSE 70734.58758 105825.8987 86399.45148 101383.935 73194.51518 78513.96806 92152.52252 94832.65522 74822.61532 120952.8588 0.584811209 0.874935076 0.714323352 0.838210324 0.605149113 0.649128668 0.761887924 0.784046414 0.61860973 1 16.88408534 -1.734826216 2.807742016 1.049595675 0.724388886 0.442629144 0.095519303 21743853.87 18085614.93 7520891.349 0.021853074 0.018415087 1.734826216 -0.32520679 SRS(ph)PLHPMSEIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPLHPMSEIPR 13 1 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 S(0.176)RS(0.824)PLHPMSEIPR 97.095 0.0023834 232270000 83175 95231 93784 102530 110500 126240 103370 105060 91486 96601 TRUE FALSE 86458.81323 111586.1835 96228.08808 122810.128 91717.24947 96922.67319 95267.58929 103651.8425 88193.43673 115528.1164 0.748378974 0.965879016 0.832940855 1.063032375 0.79389548 0.838953115 0.824626872 0.897200143 0.763393704 1 16.81788448 SRS(ph)PLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPLLK 7 1 A0A0U1RQD2;Q6ZUS6-6;Q6ZUS6;Q6ZUS6-5;Q6ZUS6-4 A0A0U1RQD2 CCDC149 Coiled-coil domain-containing protein 149 1 S(0.099)RS(0.901)PLLK;S(0.187)RS(0.813)PLLK 87.149 0.011842 975010000 916890 771050 910810 760650 1171690 1186640 1109080 1010130 894950 726080 TRUE FALSE 953089.5252 903471.8396 934546.4568 911104.2997 972526.5523 911060.8437 1022147.412 996590.8596 862740.9243 868341.4744 1.097597608 1.040456855 1.076243027 1.049246554 1.11998169 1.049196509 1.177126098 1.147694644 0.993550291 1 19.72790297 3.24591967 24.99613724 1.097580454 1.06480943 0 0.058366967 525.526373 1785023.388 0.016232769 0.021543469 1761.650169 -3.24591967 -0.032771023 SRS(ph)PPRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSPPRPK 8 2 Q8WUQ7-2;Q8WUQ7 Q8WUQ7-2 CACTIN Cactin 1 S(0.165)RS(0.835)PPRPK 55.314 0.065073 176560000 61930 47194 56398 51896 72148 81769 67418 61249 58709 50623 TRUE FALSE 64375.04422 55299.20238 57867.77821 62160.87391 59884.30873 62779.38897 62133.601 60428.05734 56596.07456 60541.60761 1.063319042 0.913408226 0.955834846 1.026746338 0.989143022 1.036962701 1.026295856 0.998124426 0.934829397 1 15.88563936 5.086729855 18.34871498 0.990672255 3.89931721 0.252968158 0.038935673 256.758437 55215.07024 0.009297559 506.7460834 122103.9898 -5.086729855 2.908644955 SRS(ph)PSLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSPSLNR 8 1 Q9UPX8;Q9UPX8-3;A0A2R8Y2H5;A0A087X158 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 S(0.332)RS(0.652)PS(0.016)LNR;S(0.171)RS(0.829)PS(0.001)LNR 87.568 0.0092245 323820000 105042 118358 116837 124082 150429 166328 140532 130156 130899 130405 TRUE FALSE 109189.1393 138685.0658 119881.8682 148625.0493 124859.1323 127700.8427 129516.7346 128411.4717 126187.9706 155955.363 0.700130712 0.889261281 0.768693464 0.95299736 0.800608135 0.818829441 0.830473106 0.823386059 0.809128767 1 17.25077364 -2.172360836 2.256352348 1.427524308 0.825419149 0.415039579 0.06342009 6582268.639 1226567.423 14414267.87 0.013804453 0.006724177 2.172360836 -0.602105159 SRS(ph)RDDLYDQDDSRDFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSRDDLYDQDDSRDFPR 18 3 S4R3V8;Q86X29-6;Q86X29-5;Q86X29-2;Q86X29-3;Q86X29-4;Q86X29 S4R3V8 LSR Lipolysis-stimulated lipoprotein receptor 1 S(0.12)RS(0.88)RDDLYDQDDSRDFPR 177.22 5.25E-13 316170000 96082 117700 117840 106350 163840 201550 108770 125830 116870 179970 TRUE FALSE 99875.39155 137914.0594 120911.0072 127385.7126 135990.5353 154743.067 100244.3232 124143.4547 112663.8715 215231.6758 0.464036677 0.640770272 0.561771434 0.591853927 0.631833278 0.718960471 0.465750791 0.57678989 0.523453953 1 17.71553089 -1.330183362 5.400719866 1.000101794 0.578095899 0.744569638 0.074654377 8.81E-05 1.09E-05 0.069585736 0.016397586 0.04675377 1.330183362 -0.422005895 SRS(ph)SDIVSSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SRSSDIVSSVR 11 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 S(0.001)RS(0.496)S(0.496)DIVS(0.004)S(0.004)VR;S(0.059)RS(0.929)S(0.012)DIVSSVR;S(0.003)RS(0.979)S(0.018)DIVSSVR;S(0.091)RS(0.905)S(0.004)DIVSSVR;S(0.002)RS(0.703)S(0.295)DIVSSVR 172.82 7.82E-06 2530330000 797480 757970 1103360 791200 1722770 1186670 1010550 1013240 1251730 1165750 TRUE FALSE 828965.1262 888145.4513 1132114.468 947696.9985 1429934.171 911083.8767 931340.4504 999659.1751 1206680.482 1394156.393 0.59459981 0.637048652 0.812042662 0.679763765 1.025662672 0.653501918 0.668031546 0.717035176 0.865527345 1 20.41096098 -5 0.168666612 2.013789478 0.673069398 0.345292833 0.117894766 164.4154216 1.546733288 55.80090015 0.442728052 1.00E-05 5 -1.34072008 SRS(ph)SHKDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSSHKDSPR 10 2 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.064)RS(0.929)S(0.007)HKDSPR;S(0.015)RS(0.933)S(0.052)HKDSPR;S(0.156)RS(0.826)S(0.018)HKDSPR;S(0.126)RS(0.858)S(0.016)HKDSPR 142.1 1.90E-05 196306000 129116 126161 166582 87411.6 240984 195976 128370 157733 174255 205852 TRUE FALSE 134213.5994 147828.1704 170923.2638 104701.3536 200021.6258 150463.544 118308.024 155618.8471 167983.5966 246184.7581 0.545174285 0.600476534 0.69428857 0.42529584 0.812485823 0.611181396 0.480565998 0.632122185 0.682347672 1 17.90938192 0.746379271 2.09649817 0.99973803 0.600090086 0.583189042 0.101332035 0.695921322 4.630211357 0.091645999 0.025141706 5.576725533 -0.746379271 -0.399647945 SRS(ph)SPSTDHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.008)RS(0.613)S(0.319)PS(0.008)T(0.051)DHYK 102.63 0.0017216 327270000 323640 324340 389740 322890 461530 512550 483240 410450 406560 278170 TRUE FALSE 336417.5571 380042.872 399896.9446 386756.6783 383079.2955 393518.0303 445362.3861 404948.5891 391927.985 332672.0856 1.011258749 1.142394834 1.202075443 1.162576288 1.151522211 1.182900662 1.33874288 1.2172605 1.178121045 1 18.34374129 5.712940342 1.019317156 1.198560175 3.47E-15 0.259001271 0.079803461 13.25304096 2.463458365 0.022975504 27.66744597 516345.4354 -5.712940342 -1.198560175 SRS(ph)SPSTDHYKQEASVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSPSTDHYKQEASVELR 19 2 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.116)RS(0.437)S(0.437)PS(0.007)T(0.002)DHYKQEASVELR 73.574 0.0088936 254010000 87113 122500 130810 101340 172830 156630 125690 117520 139270 116890 TRUE FALSE 90552.28851 143538.4221 134219.0161 121384.7495 143452.4183 120255.0563 115838.0894 115944.8366 134257.6999 139792.3575 0.647762797 1.026797349 0.960131287 0.868321786 1.026182124 0.860240562 0.828643936 0.829407549 0.96040801 1 17.09292596 -3.377110579 0.937116651 3.125645958 0.891134595 0.087093377 0.107054788 66962.69208 968.3183253 300625.5524 0.031763193 0.000419652 3.377110579 -2.234511363 SRS(ph)SSS(ph)PPPKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.263)RS(0.41)S(0.327)S(0.026)S(0.974)PPPKQK 80.632 0.010629 306670000 205320 145090 187300 108650 263220 229110 183270 182020 214030 152000 TRUE FALSE 213426.1921 170008.0789 192181.1919 130140.6457 218477.9584 175902.6747 168904.8185 179580.3196 206327.1021 181781.4898 1.174080994 0.93523317 1.057209907 0.715918028 1.201871316 0.967659991 0.929164013 0.98789112 1.135028117 1 17.47184578 1.282623605 24.40793486 1.067514182 0.989392441 0.042666957 0.132210492 282.3018569 156375.7747 0.082179214 0.030008923 19.17006585 -1.282623605 -0.078121742 SRS(ph)TTELDDYSTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.144)RS(0.514)T(0.301)T(0.041)ELDDYSTNK;SRS(0.991)T(0.008)TELDDYSTNK;S(0.184)RS(0.706)T(0.089)T(0.022)ELDDYSTNK;S(0.407)RS(0.578)T(0.015)TELDDYSTNK 292.76 4.21E-43 5234050000 5072770 3584015 4951310 3802915 5966720 6205400 5697430 5100280 5402290 3507607 TRUE FALSE 5273046.877 4199541.696 5080345.206 4555120.236 4952499.066 4764289.894 5250850.549 5031919.089 5207862.638 4194855.434 1.25702708 1.001117145 1.211089461 1.085882531 1.180612572 1.135745908 1.251735759 1.199545292 1.241487989 1 22.00018966 2.340638209 18.74003373 1.193233493 1.14058592 0.001584932 0.092590667 5.814419068 1045.349083 0.02922005 0.024447067 219.0978972 -2.340638209 -0.052647573 SRS(ph)TTELDDYSTNKNGNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSTTELDDYSTNKNGNNK 19 2 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(0.285)RS(0.681)T(0.033)T(0.002)ELDDYSTNKNGNNK 235.23 1.94E-24 134630000 137890 107380 132460 65766 213730 161140 88460 111110 160390 137390 TRUE FALSE 143334.0037 125821.6797 135912.0164 78774.31851 177400.2509 123717.6771 81526.27405 109620.7522 154617.5952 164308.94 0.872344522 0.765762835 0.827173594 0.479428073 1.079674976 0.752957673 0.496176739 0.667162433 0.941017544 1 17.32605145 1.132497708 5.487058126 0.992890255 0.734027001 0.233145167 0.16587168 0.288682766 12.06914366 0.157989396 0.039997339 13.56743369 -1.132497708 -0.258863254 SRS(ph)WEDS(ph)PER ddPTM_MDA-MB-175_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(0.237)RS(0.763)WEDS(0.999)PER;S(0.029)RS(0.971)WEDS(1)PER;S(0.126)RS(0.874)WEDS(1)PER;S(0.013)RS(0.987)WEDS(1)PER;S(0.029)RS(0.971)WEDS(1)PER;S(0.009)RS(0.991)WEDS(1)PER 116.79 0.012483 9957310000 3609490 3871390 3922530 3607660 4725500 5001830 4260360 4081650 3987200 3751810 TRUE FALSE 3751995.452 4536271.117 4024754.354 4321244.38 3922261.198 3840230.786 3926421.851 4026942.158 3843701.451 4486905.337 0.836210076 1.011002189 0.89700006 0.963079017 0.874157332 0.855875152 0.87508462 0.897487657 0.856648661 1 22.09728932 3.221265852 24.9986246 0.885908245 0.930705455 0.066510164 0.057206122 475.4878913 687290.2403 0.015106602 0.018097163 1664.431216 -3.221265852 0.044797211 SRS(ph)WEDSPER ddPTM_MDA-MB-175_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 S(0.011)RS(0.969)WEDS(0.02)PER;S(0.038)RS(0.924)WEDS(0.038)PER 131.06 0.00068437 1235230000 502660 457040 465870 395630 521120 737390 507850 455360 477170 429910 TRUE FALSE 522505.4049 535533.0647 478010.9549 473884.4332 432540.2085 566142.3478 468043.39 449256.644 459996.7449 514142.6334 1.01626547 1.04160408 0.929724407 0.921698382 0.841284462 1.101138694 0.910337637 0.873797687 0.894687029 1 18.97180912 4.233422239 24.65497955 0.927737557 1.028934792 0.228813568 0.068869442 128.9562987 618772.963 0.017177277 0.038984382 17116.78669 -4.233422239 0.101197235 SRS(ph)WPASPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRSWPASPR 9 1 Q86YD1 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 SRS(1)WPASPR;SRS(1)WPASPR;S(0.019)RS(0.962)WPAS(0.019)PR;SRS(1)WPASPR 145.83 5.83E-05 1900570000 297890 326338 359060 315578 451853 419858 345012 372007 352238 415132 TRUE FALSE 309650.9272 382384.0129 368417.3986 377998.3865 375047.1885 322352.3425 317969.0579 367020.8546 339561.0232 496469.1672 0.623706259 0.77020697 0.742075083 0.761373337 0.755428964 0.649289752 0.640460836 0.739262131 0.683951886 1 18.9213446 -2.050521567 2.478259846 1.386030278 0.710680175 0.741121686 0.051861993 4741052.405 1272195.027 10389183.53 0.012670126 0.008901812 2.050521567 -0.675350103 SRSES(ph)ETSTMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 S(0.329)RS(0.329)ES(0.342)ETSTMAAK;S(0.209)RS(0.209)ES(0.581)ET(0.001)STMAAK 137.61 8.90E-05 716350000 510720 416850 561830 498470 746530 776410 733940 700620 676910 464210 TRUE FALSE 530883.62 488440.7449 576471.7513 597065.8782 619635.0973 596100.5441 676411.865 691229.3349 652548.1413 555163.0617 0.956266107 0.87981492 1.038382758 1.075478394 1.11613171 1.073739565 1.218402145 1.245092447 1.175417074 1 19.08255205 3.717960745 0.852242315 1.175588299 0.894679352 0.559697626 0.072794832 0.510630233 0.670933481 0.030211196 0.102431222 5223.489726 -3.717960745 -0.280908946 SRSESET(ph)STMAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSESETSTMAAK 13 1 Q96B23-2;Q96B23;A0A087WVF1 Q96B23-2 C18orf25 Uncharacterized protein C18orf25 1 SRS(0.16)ES(0.252)ET(0.47)S(0.058)T(0.058)MAAK 140.77 0.00025171 471820000 476620 435200 579300 496500 761680 695070 773840 646510 688560 384460 TRUE FALSE 495437.3256 509942.2146 594397.0339 594706.2181 632209.9057 533650.5264 713184.3987 637844.5909 663778.8601 459787.5761 1.077535261 1.109082196 1.292764452 1.293436902 1.375004325 1.160645816 1.551117159 1.3872593 1.443664193 1 18.81060796 4.260673581 1.29338925 1.350777772 1.033001082 0.244182388 0.146204369 0.771267758 1.96580482 0.040696355 0.261503748 18225.25362 -4.260673581 -0.31777669 SRSS(ph)KEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSKEENR 9 2 Q14696 Q14696 MESDC2 LDLR chaperone MESD 1 S(0.002)RS(0.011)S(0.988)KEENR 100.55 0.0036082 106460000 86861 63003 70421 59626 98133 103600 88087 73178 71478 57720 TRUE FALSE 90290.33935 73823.27515 72256.22911 71419.84483 81452.38771 79540.47007 81182.51077 72197.16861 68905.52074 69029.12888 1.308003459 1.069451061 1.046749833 1.034633436 1.179971253 1.152273994 1.176061644 1.045894245 0.998209334 1 16.07491766 7.603270797 0.016345846 1.31E-06 2.430533248 0.278500441 0.080356513 6899.971367 9.275262606 548.1847573 863.7920769 40111674.89 -7.603270797 2.430531936 SRSS(ph)PSTDHYKQEASVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSPSTDHYKQEASVELR 19 2 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.015)RS(0.047)S(0.908)PS(0.025)T(0.005)DHYKQEASVELR 156.2 9.56E-09 509730000 109300 125450 164450 116240 213830 208120 143130 170050 165960 147960 TRUE FALSE 113615.2484 146995.0616 168735.7021 139231.9251 177483.253 159787.2841 131911.0966 167770.7579 159987.132 176949.9291 0.642075693 0.830715572 0.953578806 0.786843633 1.003013982 0.903008466 0.745471316 0.948125601 0.90413787 1 17.43298166 4.686253914 2.992065068 0.897231524 0.614770246 0.497362672 0.079525688 0.264019352 3.655545121 0.018479005 0.166329194 48557.23111 -4.686253914 -0.282461278 SRSS(ph)SS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSSSSPPPK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.182)RS(0.362)S(0.461)S(0.256)S(0.74)PPPK;S(0.311)RS(0.412)S(0.459)S(0.314)S(0.503)PPPK 65.895 0.038464 805880000 846490 491050 620940 525210 742730 797570 785130 615330 624370 384470 TRUE FALSE 879910.0788 575384.0177 637122.2065 629094.9704 616481.0199 612346.4548 723589.459 607082.5078 601899.0457 459799.5354 1.913681966 1.251380163 1.385652132 1.368194011 1.340760424 1.33176832 1.573706373 1.320319968 1.309046659 1 18.81064548 -4.091447456 0.120793961 9.12E-20 1.616334683 0.41170558 0.17080466 128.3693735 1.247752567 33.75319084 1.640231352 8.10E-05 4.091447456 1.616334683 SRSS(ph)SS(ph)PPPKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRSSSSPPPKQK 12 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.062)RS(0.382)S(0.442)S(0.17)S(0.943)PPPKQK;S(0.233)RS(0.345)S(0.422)S(0.037)S(0.964)PPPKQK 79.81 0.011816 478580000 555040 383490 537690 262380 764780 624300 462640 487780 610150 408980 TRUE FALSE 576953.4078 449351.4244 551702.6431 314277.9809 634782.9688 479315.7864 426377.0679 481242.1069 588190.8207 489111.8006 1.179594128 0.918709023 1.127968375 0.642548351 1.297827957 0.97997183 0.871737438 0.983910236 1.202569269 1 18.89980475 1.282516362 24.9771759 1.10128535 0.992415518 0.048598782 0.176021139 340.3960876 193424.4114 0.109146984 0.039856493 19.16533266 -1.282516362 -0.108869832 SRSSPS(ph)TDHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSSPSTDHYK 11 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.017)RS(0.057)S(0.193)PS(0.366)T(0.366)DHYK 97.223 0.0038921 457570000 294220 353460 387350 393150 470340 506700 511260 401510 422580 286970 TRUE FALSE 305836.0328 414164.0055 397444.6592 470913.8966 390391.7748 389026.6041 471186.1053 396128.4152 407371.4283 343196.2771 0.891140298 1.206784668 1.158068096 1.372141623 1.137517511 1.133539697 1.37293478 1.154232845 1.186992562 1 18.38867438 4.738979972 22.96291309 1.203320207 0.891140024 0.414969301 0.106086811 9.649689097 527784.5394 0.02338726 0.137435608 54825.16805 -4.738979972 -0.312180183 SRST(ph)TELDDYSTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRSTTELDDYSTNK 14 1 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.002)RS(0.073)T(0.923)T(0.002)ELDDYSTNK 279.19 2.10E-32 483620000 764440 536670 698220 540010 914830 881120 855230 729370 723770 457490 TRUE FALSE 794620.6815 628838.8978 716416.1868 646822.3662 759327.5234 676493.2335 788194.8379 719593.9882 697721.6591 547126.4063 1.452353007 1.14934847 1.309416213 1.182217416 1.387846601 1.236447786 1.440608292 1.315224379 1.275247641 1 19.06151466 0.772298557 4.112967599 1.000005206 1.306453675 0.482620199 0.095404454 2.473495214 43.96445658 0.085235141 0.021740668 5.919684441 -0.772298557 0.306448468 SRSWEDS(ph)PER ddPTM_MDA-MB-175_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 S(0.014)RS(0.149)WEDS(0.837)PER;SRSWEDS(1)PER 107.17 0.0021147 936670000 548980 267850 420550 262820 789890 558570 575660 506040 541080 562590 TRUE FALSE 570654.1543 313851.1539 431509.8785 314805.0116 655624.7799 428850.5827 530538.265 499257.3615 521606.6365 672818.7391 0.848154371 0.466472076 0.641346403 0.46788978 0.974444887 0.637393934 0.78853075 0.742038431 0.77525581 1 19.35985836 0.187376313 0.223110529 1.12832527 0.584111211 0.312552934 0.145190114 7.752351228 0.771837446 1.193203383 0.372434479 1.539488018 -0.187376313 -0.544214059 SRT(ph)GS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.422)RT(0.591)GS(0.915)ES(0.062)S(0.01)QTGTSTTSSR 76.807 0.033507 817120000 102770 130930 132470 116480 155800 178700 113950 133250 135490 135960 TRUE FALSE 106827.439 153416.209 135922.277 139519.3963 129317.1717 137199.6332 105018.3012 131464.0017 130613.7414 162598.7589 0.657000334 0.943526322 0.835936744 0.858059418 0.795314629 0.843792623 0.645873941 0.808517867 0.803288674 1 17.31095672 3.209466662 23.14074127 0.796557297 0.833073678 0 0.105047413 419.460615 333627.7681 0.028721032 0.034336774 1619.819647 -3.209466662 0.036516381 SRT(ph)PSASNDDQQE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SRTPSASNDDQQE 13 1 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 S(0.005)RT(0.995)PSASNDDQQE;S(0.004)RT(0.995)PS(0.001)ASNDDQQE;S(0.048)RT(0.899)PS(0.053)ASNDDQQE;S(0.001)RT(0.944)PS(0.055)ASNDDQQE 225.7 7.65E-11 1416940000 1214380 1324410 1310270 1187710 1397930 1540710 1290240 1262250 1189650 1254380 TRUE FALSE 1262324.66 1551867.115 1344416.713 1422635.493 1160310.358 1182903.452 1189107.617 1245331.603 1146834.729 1500151.744 0.841464648 1.034473426 0.896187147 0.948327726 0.773461993 0.788522532 0.792658224 0.83013709 0.764479149 1 20.51667701 3.246420009 24.99892026 0.813664978 0.935144268 0.298565537 0.077739725 178.7586961 568586.8775 0.019753415 0.026268008 1763.680888 -3.246420009 0.12147929 SRT(ph)S(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 3 S(0.542)RT(0.607)S(0.851)VQT(1)EDDQLIAGQSAR;S(0.239)RT(0.803)S(0.958)VQT(1)EDDQLIAGQSAR 169.26 2.13E-11 318060000 226980 160592 161955 141560 181702 237960 199167 145738 148840 146191 TRUE FALSE 235941.3457 188172.4268 166175.6803 169560.1455 150816.3589 182697.3963 183555.7701 143784.6205 143483.2775 174834.3275 1.349513846 1.076289934 0.950475131 0.969833258 0.862624412 1.044974399 1.04988404 0.822404974 0.820681382 1 17.41562895 4.814183504 1.518584752 0.931950158 1.569372509 0.716064814 0.078699893 0.735363719 1.376138817 0.022304277 0.739383551 65190.37873 -4.814183504 0.637422352 SRT(ph)S(ph)VQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 S(0.328)RT(0.898)S(0.774)VQTEDDQLIAGQSAR;S(0.438)RT(0.655)S(0.859)VQT(0.048)EDDQLIAGQSAR 182.03 6.91E-14 730720000 490547 588902 452697 513492 469466 713641 555276 509976 436914 438583 TRUE FALSE 509914.1743 690041.3375 464494.6557 615059.185 389666.337 547908.6931 511752.0162 503140.6059 421189.5505 524514.9417 0.972163296 1.315579944 0.885569921 1.172624717 0.742907982 1.044600734 0.975667184 0.959249329 0.803007726 1 19.00062435 3.726491734 1.508754628 0.938046899 1.117186528 0.166533543 0.1445651 0.653019727 2.866521363 0.040730218 0.097033046 5327.110846 -3.726491734 0.179139629 SRT(ph)SPITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.111)RT(0.444)S(0.444)PITR;S(0.104)RT(0.578)S(0.318)PITR 87.001 0.025275 3338600000 296030 311270 278620 273000 306420 359630 237160 293500 292670 250910 TRUE FALSE 307717.493 364728.2012 285881.0661 326998.5852 254334.8379 276111.3827 218570.7795 289566.1126 282136.8639 300071.0105 1.025482243 1.215472966 0.952711378 1.089737341 0.847582169 0.920153474 0.728396852 0.96499196 0.940233658 1 18.19494442 3.243928 24.99914435 0.89224104 1.072742613 0.446483497 0.092805309 113.6321611 529249.6587 0.025128116 0.033057782 1753.589756 -3.243928 0.180501573 SRT(ph)SVQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.265)RT(0.599)S(0.135)VQTEDDQLIAGQSAR;S(0.111)RT(0.445)S(0.445)VQTEDDQLIAGQSAR;S(0.076)RT(0.447)S(0.447)VQT(0.03)EDDQLIAGQSAR;S(0.286)RT(0.508)S(0.206)VQTEDDQLIAGQSAR;S(0.118)RT(0.441)S(0.441)VQTEDDQLIAGQSAR 322.88 5.95E-62 8803040000 1329060 1505420 1340630 1324830 1301280 1887310 1402140 1485690 1299870 1440450 TRUE FALSE 1381532.315 1763964.174 1375567.919 1586877.42 1080088.89 1449010.855 1292236.603 1465776.756 1253087.933 1722678.598 0.801967538 1.023965919 0.798505258 0.921168592 0.626982242 0.841138246 0.750132151 0.850870706 0.727406687 1 20.71622213 SRTGS(ph)ESS(ph)QTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 S(0.263)RT(0.323)GS(0.511)ES(0.153)S(0.74)QT(0.005)GT(0.003)S(0.001)T(0.001)TSSR 56.453 0.05682 187120000 47196 61434 59025 51317 79348 81270 59625 75469 71930 83291 TRUE FALSE 49059.33452 71984.81161 60563.23999 61467.34943 65860.4553 62396.27416 54951.4367 74457.4615 69341.25335 99610.27675 0.492512782 0.722664508 0.608001925 0.617078392 0.66118133 0.626403984 0.551664331 0.747487749 0.696125496 1 16.60400697 0.519747823 0.763306619 1.003615982 0.617880692 0.750078244 0.065646954 0.722542245 0.68231692 0.064471608 0.0213335 3.309389031 -0.519747823 -0.38573529 SRTGS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 S(0.001)RT(0.07)GS(0.915)ES(0.004)S(0.004)QT(0.005)GTSTTSSR;S(0.058)RT(0.058)GS(0.883)ESSQTGTSTTSSR 181.83 4.33E-14 456830000 131120 124425 156756 90098 273300 237674 163342 185184 190571 273940 TRUE FALSE 136296.7188 145794.0259 160841.1901 107919.1155 226844.5636 182477.8155 150538.8272 182701.9114 183712.3869 327613.2981 0.416029263 0.445018645 0.490948295 0.329410058 0.692415616 0.556991479 0.459501577 0.557675505 0.560759859 1 18.32163439 -5 0.201526443 3.298375583 0.421473903 0.767657878 0.085183013 65.44337864 0.648559249 60.48770584 0.198500993 1.00E-05 5 -2.876901679 SRTGSESSQTGTSTTSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 SRT(0.006)GS(0.071)ES(0.141)S(0.04)QT(0.011)GT(0.003)S(0.003)T(0.005)T(0.01)S(0.078)S(0.632)R 166.52 6.71E-11 680530000 38519 42411 51833 32598 78176 71517 47901 61727 56250 76076 TRUE FALSE 40039.75986 49694.75934 53183.81056 39045.7871 64887.67144 54908.2606 44146.39445 60899.65053 54225.57349 90981.63564 0.440086173 0.546206484 0.584555446 0.429161191 0.713195262 0.603509271 0.485223135 0.66936201 0.596005701 1 16.47328775 -5 0.195842501 2.939734906 0.492384137 0.740188526 0.080313014 67.26753328 0.662927716 50.86880717 0.194269095 1.00E-05 5 -2.447350769 SRTS(ph)PAPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRTSPAPWK 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.127)RT(0.127)S(0.745)PAPWK 64.224 0.042947 675230000 1405900 1337100 1400300 1475200 1570700 1763600 1563000 1384300 1348000 1241500 TRUE FALSE 1461406.018 1566736.524 1436792.968 1766990.157 1303712.975 1354030.628 1440487.976 1365745.723 1299485.743 1484748.155 0.984278723 1.055220388 0.967701467 1.190094193 0.878070109 0.911959798 0.97019011 0.919850089 0.875223006 1 20.50178681 3.196648185 24.99999913 0.924215862 1.043915594 0.456294093 0.065891681 125.5246694 74872.79382 0.018004997 0.021520276 1572.708321 -3.196648185 0.119699732 SRTS(ph)PAPWKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSPAPWKR 10 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.018)RT(0.095)S(0.887)PAPWKR;S(0.075)RT(0.075)S(0.851)PAPWKR 94.191 0.0043161 428890000 360100 487110 484620 400170 557640 586330 405400 455360 452810 639190 TRUE FALSE 374317.0261 570767.3533 497249.5953 479322.4316 462852.552 450163.7434 373623.6887 449256.644 436513.4566 764427.0425 0.489670047 0.746660337 0.650486662 0.627034897 0.605489506 0.588890396 0.488763045 0.587703756 0.571033509 1 19.54401929 -1.461648686 3.329432381 1.006500915 0.596893395 0.745779803 0.070916168 31706641.03 40995851.23 1909080.287 0.017257997 0.034542305 1.461648686 -0.409607521 SRTS(ph)PITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.062)RT(0.04)S(0.897)PITR;S(0.057)RT(0.042)S(0.9)PITR;S(0.136)RT(0.098)S(0.764)PIT(0.003)R 67.93 0.035017 1654140000 176548 388340 354130 416350 457475 559630 454442 454658 413500 473330 TRUE FALSE 183518.2514 455034.3741 363358.9187 498702.7873 379713.5629 429664.4138 418821.6486 448564.0532 398618.2158 566069.951 0.324197126 0.803848311 0.641897557 0.880991451 0.670789117 0.759030599 0.739876137 0.792418061 0.704185437 1 19.11062082 6.156489322 0.108656689 1.046773297 5.53E-49 0.42132515 0.127873197 78.77368509 0.920239198 1.385307207 12.21992421 1433802.463 -6.156489322 -1.046773297 RLREEFSFIPSAALDLLDHMLTLDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 RLREEFSFIPSAALDLLDHMLTLDPSK 27 2 Q9NYV4-3;J3QSD7;Q9NYV4;Q9NYV4-2 Q9NYV4-3;Q9NYV4;Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 0 56.303 0.041839 244890000 76361 148270 207140 167240 308190 282850 254970 219160 199520 211010 FALSE TRUE 79375.79124 173734.2191 212538.2386 200319.5728 255803.9739 217162.3741 234984.7852 216222.5187 192339.3142 252353.3695 0.314542229 0.68845611 0.842224691 0.793805818 1.013673701 0.86054874 0.931173559 0.856824377 0.762182469 1 17.94508582 4.823923603 1.402576409 0.887070199 7.34E-22 0.845139054 0.074740356 0.523665945 0.800267025 0.019516886 0.691245577 66668.94812 -4.823923603 -0.887070199 down SRTS(ph)PVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SRTSPVTR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.288)RT(0.139)S(0.573)PVTR;S(0.302)RT(0.133)S(0.565)PVTR;S(0.336)RT(0.166)S(0.497)PVTR;S(0.066)RT(0.033)S(0.901)PVTR;S(0.295)RT(0.172)S(0.533)PVTR;S(0.018)RT(0.02)S(0.961)PVTR;S(0.145)RT(0.087)S(0.768)PVTR 98.898 0.0043579 17597502000 1229434.1 1587764.9 1559388.5 1530429 1732149.1 1942905 1644372.9 1707876.2 1506436.8 1634788 TRUE FALSE 1277973.108 1860451.17 1600027.445 1833143.288 1437719.015 1491694.759 1515482.655 1684984.913 1452220.434 1955093.409 0.653663453 0.951591961 0.818389259 0.937624402 0.73537101 0.762978767 0.775145908 0.861843688 0.742788261 1 20.89880611 -1.903251814 7.329396873 1.036681211 0.812263156 0.30467769 0.087933717 0.042465242 0.000560542 0.068597129 0.018696209 0.012495343 1.903251814 -0.224418055 SRTS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 SRT(0.08)S(0.92)VQT(1)EDDQLIAGQSAR;S(0.005)RT(0.398)S(0.596)VQT(0.999)EDDQLIAGQSAR 213.82 4.31E-16 735760000 732750 855390 742530 735790 786530 1074300 761830 766200 743660 836320 TRUE FALSE 761679.5358 1002296.578 761880.9418 881327.0659 652835.9115 824810.1062 702115.7739 755930.3423 716895.8219 1000180.892 0.761541779 1.002115304 0.761743149 0.88116767 0.65271784 0.824660932 0.70198879 0.755793625 0.716766165 1 19.93182952 3.28319874 24.99995014 0.76013187 0.855968814 0.095701448 0.108769162 234.0025604 131053.432 0.02732221 0.036994263 1919.546955 -3.28319874 0.095836944 SRWDETPASQMGGS(ph)TPVLTPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.644)T(0.356)PVLTPGK 123.79 7.04E-06 0 173350 129530 138740 114080 189250 187580 169890 147160 143900 96916 TRUE FALSE 180193.9919 151775.7699 142355.6784 136644.6835 157081.3526 144017.3878 156573.5779 145187.5609 138721.0671 115904.8346 1.554671921 1.3094861 1.228211738 1.1789386 1.355261436 1.242548581 1.350880473 1.252644563 1.196853156 1 16.82258122 -5 0.11692489 0.062070098 1.442403777 0.551129163 0.091289067 132.3755662 1.012097308 29.55441531 0.972680188 1.00E-05 5 1.380333679 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 SRWDETPASQMGGS(0.009)T(0.991)PVLTPGK 178.41 9.76E-17 232550000 346340 235650 321610 286530 387960 408080 359490 333270 333870 225970 TRUE FALSE 360013.7706 276121.0544 329991.4208 343204.7788 322014.6978 313309.6045 331312.2344 328803.0608 321854.0839 270244.495 1.332177999 1.021745343 1.22108471 1.269978797 1.19156802 1.159356103 1.225972186 1.216687358 1.190973692 1 18.0439057 0.927135826 17.26839767 1 1.201502826 0.39468526 0.075607889 634.178077 150298.9733 0.06754672 0.01688668 8.45543249 -0.927135826 0.201502827 SRWS(ph)GSQQVEQPTGSVLWMAPEVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SRWSGSQQVEQPTGSVLWMAPEVIR 25 1 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.119)RWS(0.441)GS(0.441)QQVEQPTGSVLWMAPEVIR;S(0.003)RWS(0.964)GS(0.033)QQVEQPTGSVLWMAPEVIR;S(0.039)RWS(0.95)GS(0.011)QQVEQPTGSVLWMAPEVIR 275.5 2.89E-53 913201000 113833 136896 143512 134787 158970 184470 128752 157479 126844 137324 TRUE FALSE 118327.2147 160406.8231 147252.0406 161447.4663 131948.3362 141629.6382 118660.0818 155368.2516 122278.9092 164230.0086 0.720496916 0.976720543 0.896620794 0.983057041 0.803436213 0.862385866 0.722523751 0.946040574 0.744558868 1 17.32535824 3.204462629 24.99933856 0.843095872 0.900287959 0.04702192 0.103169594 519.6201032 380964.0976 0.027923779 0.03337681 1601.262854 -3.204462629 0.057192087 SS(ph)CELEVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSCELEVLLR 10 0 Q9H2D6-3;Q9H2D6-2;Q9H2D6;Q9H2D6-5;Q9H2D6-7 Q9H2D6-3 TRIOBP TRIO and F-actin-binding protein 1 S(0.146)S(0.854)CELEVLLR 97.734 0.0061437 11060000 12017 10068 15045 14567 14902 17317 17187 13992 13426 11056 TRUE FALSE 12491.44044 11797.10068 15437.08506 17448.30912 12368.96336 13295.38919 15839.83803 13804.46013 12942.80088 13222.21152 0.944731554 0.892218421 1.16751158 1.319621086 0.935468575 1.00553445 1.197971913 1.044035645 0.978868086 1 13.69067588 4.250114961 24.99090589 1.087156838 0.918474907 0.251652776 0.111807464 294.1197071 636139.2703 0.027721433 0.074558356 17787.50196 -4.250114961 -0.168681931 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 2 S(0.37)S(0.63)DEENGPPS(0.002)S(0.998)PDLDR 244.6 6.69E-20 525750000 352000 346500 411080 364480 410330 492840 468560 417590 379030 310720 TRUE FALSE 365897.2318 406008.6796 421793.0825 436573.0561 340582.2532 378385.3791 431833.0428 411992.8891 365388.7843 371599.6349 0.984654444 1.09259709 1.135073996 1.174847915 0.916530107 1.018260901 1.162092215 1.108701006 0.983286177 1 18.50338956 SS(ph)DGSLS(ph)HEEDLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDGSLSHEEDLAK 14 0 Q13136-2;A0A2R8Y7R9;Q13136;E9PJZ7;H0YEF9 Q13136-2 PPFIA1 Liprin-alpha-1 2 S(0.173)S(0.827)DGS(0.328)LS(0.672)HEEDLAK 257.54 3.49E-24 353060000 1014900 655700 929890 660700 1261600 1266700 1172700 917650 1029300 578080 TRUE FALSE 1054969.036 768311.3744 954123.6973 791384.488 1047153.683 972528.122 1080780.71 905350.4027 992255.6941 691343.708 1.525968955 1.111330537 1.380100356 1.144704839 1.514664371 1.406721593 1.563304471 1.309551808 1.435256707 1 19.39904361 3.23201515 24.99991362 1.396093371 1.28412464 0.035604249 0.180288802 387.6123976 1480454.956 0.047441232 0.057969307 1706.141907 -3.23201515 -0.111968731 SS(ph)DKLNLVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDKLNLVTK 10 1 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 S(0.351)S(0.649)DKLNLVTK 85.522 0.037309 90281000 291750 164940 247730 179480 358610 309210 310380 270770 283840 161610 TRUE FALSE 303268.5153 193267.1619 254186.0473 214980.6083 297653.6003 237400.6636 286051.6046 267140.771 273624.6538 193274.3853 1.569108678 0.999962626 1.315156413 1.11230781 1.540057157 1.228308983 1.480028531 1.382184042 1.415731595 1 17.56029092 3.252939802 24.99390474 1.365579257 1.23605189 0.039656131 0.196738064 563.2126203 978969.9123 0.049551087 0.066792818 1790.357675 -3.252939802 -0.129527367 SS(ph)DTEEESR ddPTM_MDA-MB-175_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(0.121)S(0.879)DTEEESR;S(0.243)S(0.757)DTEEESR 255.11 2.96E-10 96711000 347830 334710 349240 307650 432960 453060 408020 388020 386850 317030 TRUE FALSE 361562.597 392193.8388 358341.4813 368502.2518 359365.6138 347843.6812 376038.3262 382819.2266 372927.3441 379145.9586 0.953623766 1.034413871 0.945128052 0.971927152 0.947829209 0.917440034 0.991803599 1.009688269 0.983598363 1 18.53239382 2.023154536 24.99989777 0.99931552 0.963317835 0.257905428 0.028728682 321.1756091 346771.0614 0.011051585 0.00816171 105.4762149 -2.023154536 -0.035997685 SS(ph)FSQHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSFSQHAR 8 0 P02545;P02545-6;P02545-3;P02545-5;P02545-4;A0A0C4DGC5;P02545-2;Q3BDU5;Q5TCI8 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.367)S(0.566)FS(0.067)QHAR;S(0.072)S(0.928)FSQHAR;S(0.474)S(0.526)FS(0.001)QHAR 118.6 0.0015701 2875540000 964508 2498500 2448559 2224106 2621130 3246250 2079820 2471130 2357676 2305398 TRUE FALSE 1002587.521 2927597.939 2512370.459 2664027.529 2175591.259 2492357.635 1916798.274 2438008.544 2272823.701 2757096.599 0.363638881 1.061840902 0.911237735 0.966243812 0.789087789 0.903979076 0.695223473 0.88426664 0.824354033 1 21.39471838 7.999996923 0.026430748 1.454737088 2.79E-10 0.097608686 0.178375776 6072.181183 12.32812346 228.1844778 498.8987311 99999291.46 -7.999996923 -1.454737087 SS(ph)GDESKKPLPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGDESKKPLPSSSR 15 2 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 S(0.154)S(0.844)GDES(0.002)KKPLPSSSR 85.636 0.006195 98601000 108610 47478 71521 44205 110440 93588 107140 72613 82927 30735 TRUE FALSE 112898.0067 55631.97717 73384.89602 52948.61706 91667.44825 71853.60534 98742.08684 71639.74151 79942.47347 36756.93479 3.07147501 1.513509695 1.996491177 1.440506869 2.493881733 1.954831265 2.686352586 1.949012939 2.174894994 1 15.16572884 4.755291621 23.94575356 1.982829898 3.071476554 0.33855258 0.477016965 2145.897868 3071161.383 0.106280572 2.813207787 56923.5034 -4.755291621 1.088646656 SS(ph)GFISELPSEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.085)S(0.915)GFISELPSEEGK;S(0.092)S(0.908)GFISELPSEEGK;S(0.208)S(0.792)GFISELPSEEGK 337.22 1.18E-68 437930000 1322700 822840 1113700 927850 1666630 1597190 1428780 1140230 1186620 758550 TRUE FALSE 1374921.217 964156.3692 1142723.937 1111375.961 1383336.828 1226266.828 1316788.49 1124947.082 1143913.778 907173.3492 1.51561024 1.062813816 1.259653337 1.225097675 1.524886979 1.351744768 1.451529073 1.240057463 1.260964929 1 19.79101873 0.725194207 1.466285806 1.001124754 1.32706894 0.352394911 0.134695683 1.073288309 3.755419051 0.126568886 0.037020388 5.311218978 -0.725194207 0.325944186 SS(ph)GSETEQVVDFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 S(0.008)S(0.855)GS(0.137)ETEQVVDFSDR;S(0.245)S(0.723)GS(0.032)ETEQVVDFSDR;S(0.009)S(0.851)GS(0.141)ETEQVVDFSDR;S(0.008)S(0.496)GS(0.496)ETEQVVDFSDR 383.89 2.86E-114 974110000 652301 730138 723460 718161 854120 981110 819890 814000 774000 657891 TRUE FALSE 678054.3472 855533.5218 742313.9619 860211.1023 708936.9875 753262.0714 755624.8794 803089.6614 746143.8912 786792.1454 0.86179603 1.08736917 0.943468953 1.093314298 0.901047363 0.957383822 0.960386913 1.020713877 0.948336731 1 19.58562303 -1.177758203 4.26554659 1.000006077 0.980455559 0.005773524 0.070362473 3.66E-06 7.05E-07 0.061298595 0.014443726 0.066411272 1.177758203 -0.019550518 SS(ph)GSLGHRPSQEMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGSLGHRPSQEMDK 15 1 Q5SW79;H0Y2V6;H0YB66 Q5SW79 CEP170 Centrosomal protein of 170 kDa 1 S(0.305)S(0.347)GS(0.347)LGHRPS(0.001)QEMDK 67.995 0.06799 20947000 28864 27976 31867 32040 41781 46145 26393 31193 30675 32399 TRUE FALSE 30003.57301 32780.66038 32697.4802 38377.41637 34679.08054 35428.52308 24324.24769 30774.90886 29571.01274 38746.96373 0.774346429 0.846018816 0.843872062 0.990462547 0.895014143 0.914356111 0.62777171 0.79425343 0.763182709 1 15.24179564 SS(ph)IDSQASLSGPLSGGAPGAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSIDSQASLSGPLSGGAPGAGAR 23 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 S(0.206)S(0.794)IDSQASLSGPLSGGAPGAGAR;S(0.205)S(0.793)IDS(0.002)QASLSGPLSGGAPGAGAR;S(0.005)S(0.993)IDS(0.003)QASLSGPLSGGAPGAGAR;S(0.186)S(0.814)IDSQASLSGPLSGGAPGAGAR 375.52 1.17E-118 1156150000 801120 750470 793910 894180 901670 1111030 985740 903340 920100 697953 TRUE FALSE 832748.8362 879357.3847 814599.9468 1071046.135 748404.4555 853010.1203 908475.123 891232.2049 886985.7807 834703.5272 0.997658221 1.053496668 0.975915304 1.283145572 0.896611109 1.021931851 1.088380597 1.067723061 1.062635717 1 19.67090434 2.251262578 24.95461336 1.062122583 1.040702043 0.004358025 0.095229988 1636.761332 3215628.921 0.032333276 0.026887597 178.3456736 -2.251262578 -0.02142054 SS(ph)LETLEDIEENAPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 S(0.145)S(0.855)LETLEDIEENAPLRR;S(0.193)S(0.807)LETLEDIEENAPLRR;S(0.265)S(0.734)LETLEDIEENAPLRR;S(0.019)S(0.981)LETLEDIEENAPLRR 260.11 1.92E-27 735270000 141620 125031 128611 127240 190855 165747 153991 164609 153165 146250 TRUE FALSE 147211.267 146504.1016 131962.7083 152407.6922 158413.5353 127254.7712 141920.783 162402.6856 147652.6216 174904.8874 0.841664685 0.837621543 0.754482681 0.871374691 0.905712457 0.727565553 0.811416909 0.928519998 0.844188083 1 17.41621108 0.761496809 0.735056112 0.998966804 0.823228693 0.443365864 0.056836446 0.942780824 1.022551607 0.05793966 0.021101642 5.774266306 -0.761496809 -0.175738112 SS(ph)LGSLQTPEAVTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSLGSLQTPEAVTTR 15 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 S(0.029)S(0.971)LGSLQTPEAVTTR;S(0.069)S(0.931)LGSLQTPEAVTTR;S(0.158)S(0.842)LGSLQTPEAVTTR 297.96 4.01E-44 474507000 434521 483879 475240 466479 599270 667760 516400 512110 500410 492740 TRUE FALSE 451676.2246 566981.4542 487625.1448 558747.1539 497406.2995 512682.86 475923.2186 505246.0031 482400.3418 589282.9689 0.766484437 0.962154829 0.827488949 0.948181406 0.84408735 0.870011331 0.807631043 0.857391151 0.818622576 1 19.16860105 SS(ph)LPNGEGLQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLPNGEGLQLK 12 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 S(0.185)S(0.815)LPNGEGLQLK;S(0.391)S(0.609)LPNGEGLQLK;S(0.081)S(0.919)LPNGEGLQLK;S(0.128)S(0.872)LPNGEGLQLK 174.44 3.19E-05 818350000 3760130 2592230 3233430 3081730 3885210 4440890 5044900 3575310 3793490 1991960 TRUE FALSE 3908582.836 3037425.338 3317695.842 3691286.996 3224803.392 3409560.6 4649467.556 3527388.817 3656963.036 2382246.424 1.640713067 1.275025668 1.392675338 1.549498389 1.353681701 1.431237577 1.95171562 1.480698547 1.535090157 1 21.18389123 SS(ph)LPSLDDQEQASSGWGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLPSLDDQEQASSGWGSR 19 0 R4GMM2;Q9NPB6-2;Q9NPB6 R4GMM2 PARD6A Partitioning defective 6 homolog alpha 1 S(0.033)S(0.484)LPS(0.484)LDDQEQASSGWGSR 79.393 0.0092116 81457000 24062 30312 24592 26404 36021 38879 32029 36082 30981 31401 TRUE FALSE 25011.98634 35517.85021 25232.88772 31626.63239 29898.16329 29849.94147 29518.48329 35598.37981 29865.99986 37553.42474 0.666037426 0.945795236 0.671919749 0.842177048 0.796150111 0.794866025 0.786039715 0.947939637 0.79529364 1 15.19665686 0.079788713 0.239187378 1.07743344 0.751829272 0.360950761 0.085153643 7.178813311 0.735227563 0.656130187 0.174845522 1.201679667 -0.079788713 -0.325604168 SS(ph)LQVDWHEEEWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLQVDWHEEEWEK 14 0 Q96PE3-2;Q96PE3-4;Q96PE3-3;Q96PE3 Q96PE3-2 INPP4A "Type I inositol 3,4-bisphosphate 4-phosphatase" 1 S(0.169)S(0.831)LQVDWHEEEWEK 245.61 7.37E-18 141720000 208150 146140 208300 164410 249920 253660 271540 189070 219730 118490 TRUE FALSE 216367.9227 171238.4082 213728.4691 196929.8073 207438.6877 194751.3093 250255.9853 186535.8259 211821.9602 141705.8469 1.5268807 1.2084075 1.508254415 1.389708411 1.463868233 1.37433503 1.766024415 1.316359417 1.494800426 1 17.11253976 -1.308454867 5.090725933 0.999865669 1.445289566 0.479940729 0.140409732 0.000198578 2.70E-05 0.126113264 0.029716292 0.049152446 1.308454867 0.445423897 SS(ph)LS(ph)GDEEDELFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 S(0.403)S(0.597)LS(1)GDEEDELFK;S(0.111)S(0.889)LS(1)GDEEDELFK;S(0.408)S(0.592)LS(1)GDEEDELFK;S(0.419)S(0.581)LS(1)GDEEDELFK;S(0.387)S(0.613)LS(1)GDEEDELFK;S(0.132)S(0.868)LS(1)GDEEDELFK 254.45 1.21E-23 1394547000 4426864 2047951 2928546 2031266 4359398 4901672 4148964 3008299 3344117 1618944 TRUE FALSE 4601640.009 2399670.653 3004866.315 2433044.352 3618389.085 3763332.964 3823757.36 2967977.672 3223762.882 1936145.08 2.376702064 1.239406426 1.551984066 1.256643615 1.868862578 1.943724673 1.974933283 1.532931443 1.665042003 1 20.88475563 0.392937727 1.428161583 1.000102018 1.700778663 0.298179076 0.328371539 4.890779863 10.17733067 0.30745365 0.089474562 2.471369755 -0.392937727 0.700676645 SS(ph)LSGDEEDELFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 S(0.158)S(0.842)LSGDEEDELFK;S(0.167)S(0.832)LSGDEEDELFK;S(0.182)S(0.818)LSGDEEDELFK;S(0.14)S(0.86)LSGDEEDELFK 291.51 1.57E-40 379911000 1458730 842400 1103390 794970 1548010 1606250 1382740 1105910 1278070 679603 TRUE FALSE 1516321.787 987075.647 1132145.25 952212.6933 1284879.813 1233222.78 1274357.226 1091087.085 1232072.51 812758.1961 1.865649334 1.214476399 1.392966882 1.171581779 1.580888165 1.517330476 1.567941402 1.342449809 1.515915209 1 19.63246667 -1.014073161 4.771921058 0.999991178 1.447024408 0.345563306 0.190074043 1.67E-05 3.45E-06 0.172223873 0.040592756 0.096811475 1.014073161 0.44703323 SS(ph)LSLEEADSEVEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLSLEEADSEVEGR 15 0 Q5JTZ5 Q5JTZ5 C9orf152 Uncharacterized protein C9orf152 1 S(0.231)S(0.769)LSLEEADSEVEGR 148.18 3.09E-06 0 27599 34040 28031 28702 46180 40147 33664 38334 32274 29700 TRUE FALSE 28688.62983 39886.10521 28761.51089 34379.16993 38330.3401 30823.46768 31025.32772 37820.19543 31112.46504 35519.14636 0.8076948 1.122946616 0.809746681 0.967905298 1.07914587 0.867798662 0.873481795 1.064783344 0.875935044 1 15.11630929 3.926721702 0.006890618 1.887683604 1.05E-07 0.019191401 0.108719042 57499.11794 81.85236526 10793.78028 11637.02344 8447.373592 -3.926721702 -1.887683498 SS(ph)LVTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.137)S(0.863)LVTSK;S(0.023)S(0.977)LVTSK;S(0.12)S(0.88)LVTSK;S(0.038)S(0.962)LVTSK;S(0.008)S(0.992)LVTSK 240.46 4.41E-08 10827970000 35775540 24990260 33561260 24269340 43593050 36521480 37219940 31611210 36828050 20137770 TRUE FALSE 37187985.94 29282142.76 34435894.01 29069743.02 36183118.93 28039919.76 34302543.85 31187513.44 35502615.67 24083380.47 1.544134802 1.21586514 1.429861312 1.20704579 1.502410302 1.164285047 1.424324292 1.294980722 1.474154167 1 24.52153457 -1.127483546 4.532692474 0.999962087 1.351794182 0.416534858 0.12799353 4.36E-05 8.40E-06 0.107080847 0.025236402 0.074561812 1.127483546 0.351832095 SS(ph)LYGIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSLYGIAK 8 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.034)S(0.966)LYGIAK;S(0.03)S(0.97)LYGIAK;S(0.066)S(0.934)LYGIAK;S(0.37)S(0.63)LYGIAK;S(0.005)S(0.995)LYGIAK 189.18 0.00020252 1447160000 5294710 4072850 4943540 4228880 7224150 6961310 6180250 5467770 5688050 4006280 TRUE FALSE 5503749.239 4772330.305 5072372.714 5065339.842 5996191.563 5344651.252 5695825.856 5394483.487 5483338.192 4791233.861 1.148712294 0.996054554 1.058677756 1.057209894 1.251492149 1.115506236 1.18880147 1.125906947 1.144452212 1 22.1919658 SS(ph)PELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.328)S(0.672)PELTR;S(0.273)S(0.727)PELTR;S(0.065)S(0.935)PELTR;S(0.477)S(0.523)PELTR;S(0.104)S(0.896)PELTR 225.4 1.79E-05 4321240000 3980200 3957040 3915770 4091600 4283640 5175450 4900490 4228300 3872950 3138070 TRUE FALSE 4137341.369 4636630.839 4017818.183 4900906.268 3555508.403 3973530.172 4516376.789 4171626.555 3733563.286 3752914.735 1.102434151 1.235474602 1.070586056 1.305893316 0.947399196 1.058785092 1.203431761 1.111569766 0.994843622 1 21.83958008 0.99053652 0.187504048 0.941765564 1.20102921 0.184148093 0.098283511 7.798346154 1.140543877 0.758957841 0.502967967 9.784452291 -0.99053652 0.259263645 SS(ph)PEQPIGQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPEQPIGQGR 11 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 S(0.383)S(0.617)PEQPIGQGR 60.47 0.098019 733990000 1376300 1062800 1179100 1080700 1624900 1822300 1469800 1216100 1382000 1001200 TRUE FALSE 1430637.387 1245327.633 1209828.315 1294459.234 1348700.078 1399098.442 1354593.235 1199800.169 1332262.09 1197365.971 1.194820482 1.040055975 1.010408133 1.081089045 1.126389184 1.168480211 1.131310951 1.002032961 1.112660726 1 20.19143274 -1.301135837 4.462127612 0.999931691 1.089728177 0.175620522 0.06113053 4.29E-05 6.72E-06 0.06116076 0.014404769 0.049987816 1.301135837 0.089796486 SS(ph)PEQPRPSTSK ddPTM_MDA-MB-175_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(0.136)S(0.864)PEQPRPSTSK;S(0.102)S(0.898)PEQPRPSTSK;S(0.126)S(0.874)PEQPRPSTSK;S(0.027)S(0.973)PEQPRPSTSK;S(0.164)S(0.834)PEQPRPS(0.002)TSK;S(0.122)S(0.878)PEQPRPSTSK 157.56 4.30E-05 7149190000 5318270 3927320 4919500 3878100 6176800 5984600 5524890 4862290 5247210 3335900 TRUE FALSE 5528239.406 4601806.66 5047706.211 4645176.605 5126869.742 4594767.347 5091834.685 4797118.956 5058363.937 3989505.735 1.385695315 1.15347789 1.265246009 1.164348898 1.285088951 1.151713433 1.276307148 1.202434405 1.26791745 1 21.92777859 -1.438237797 2.794508119 0.993744939 1.233253069 0.512222534 0.069795979 7629708.892 8465805.666 377024.5235 0.014845649 0.036455428 1.438237797 0.23950813 SS(ph)PGAGPSDHHSASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPGAGPSDHHSASR 15 0 I3VM54;Q9Y2K7;Q9Y2K7-3;Q9Y2K7-2;Q9Y2K7-4;Q9Y2K7-5 I3VM54;Q9Y2K7-5 KDM2A Lysine-specific demethylase 2A 1 S(0.226)S(0.774)PGAGPSDHHSASR;S(0.053)S(0.947)PGAGPSDHHSASR 249.89 7.60E-19 857860000 29837 462560 328740 448220 328630 589760 288040 482250 308840 484290 TRUE FALSE 31014.9878 542001.0818 337307.2345 536876.5782 272769.59 452797.1779 265462.6721 475786.2276 297724.9087 579177.3532 0.05355007 0.935811939 0.582390234 0.926964038 0.470960386 0.781793652 0.458344358 0.821486242 0.514047911 1 19.14364567 -5 0.235333553 2.95201368 0.60274234 0.167987246 0.25394133 300.1466914 2.999447039 280.6603581 0.377082835 1.00E-05 5 -2.34927134 SS(ph)PGAVAGLSNAPGTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 S(0.002)S(0.998)PGAVAGLSNAPGTPR;S(0.004)S(0.996)PGAVAGLSNAPGTPR 338.8 2.48E-72 781480000 555920 547720 554560 546060 571950 706770 614240 578240 532520 553600 TRUE FALSE 577868.1509 641786.6493 569012.2892 654069.0382 474730.1433 542633.3787 566094.2638 570489.6386 513354.7092 662067.3207 0.872823855 0.96936766 0.85944778 0.987919231 0.717042102 0.819604535 0.855040335 0.861679199 0.775381435 1 19.3366184 3.261156908 24.99996625 0.833754738 0.921249323 0.222810337 0.076827475 333.6605283 369151.1595 0.019838077 0.02684218 1824.554784 -3.261156908 0.087494585 SS(ph)PGGQDEGGFMAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSPGGQDEGGFMAQGK 16 0 F5GZ78;A0A1B0GTU4;P49023;A0A1B0GV30 F5GZ78 PXN Paxillin 1 S(0.122)S(0.878)PGGQDEGGFMAQGK;S(0.079)S(0.921)PGGQDEGGFMAQGK;S(0.145)S(0.855)PGGQDEGGFMAQGK;S(0.033)S(0.967)PGGQDEGGFMAQGK;S(0.411)S(0.589)PGGQDEGGFMAQGK 392.88 1.55E-121 1261620000 2235800 1670410 2094410 1650880 2517930 2611200 2559470 2037640 2364770 1335680 TRUE FALSE 2324071.11 1957289.924 2148992.045 1977419.137 2089933.158 2004788.373 2358852.053 2010328.769 2279662.39 1597380.923 1.454926046 1.225311944 1.345322217 1.237913329 1.308349892 1.255047149 1.476699778 1.258515574 1.427125088 1 20.60727696 -1.529604859 4.354584848 0.997092352 1.32502545 0.55938018 0.088230078 0.00226739 0.00024493 0.077771755 0.018184028 0.029538956 1.529604859 0.327933097 SS(ph)PGQTPEEGAQALAEFAALHGPALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 S(0.16)S(0.84)PGQTPEEGAQALAEFAALHGPALR;S(0.073)S(0.927)PGQTPEEGAQALAEFAALHGPALR 330.38 3.85E-95 7878600000 1220040 1328040 1430790 1286410 1616400 1831000 1420210 1443980 1361280 1292040 TRUE FALSE 1268208.121 1556120.539 1468077.563 1540858.058 1341644.905 1405777.999 1308890.229 1424625.81 1312287.799 1545190.5 0.820745482 1.007073587 0.950094867 0.997196176 0.868271521 0.909776496 0.847073697 0.921974222 0.8492725 1 20.55935328 3.223347472 24.99376452 0.894292179 0.948749927 0.102293962 0.062649245 427.7060634 702679.5279 0.016811576 0.020166712 1672.428163 -3.223347472 0.054457748 SS(ph)PKT(ph)PPRRPVPVADCEPPPVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPKTPPRRPVPVADCEPPPVDR 23 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 2 S(0.461)S(0.539)PKT(1)PPRRPVPVADCEPPPVDR 98.151 0.0058172 121290000 23106 12923 17127 14621 21302 28985 23000 17760 21192 11495 TRUE FALSE 24018.24272 15142.42472 17573.34369 17512.99016 17681.09365 22253.67302 21197.1999 17521.95625 20429.30406 13747.22516 1.747133871 1.10148954 1.278319332 1.273929098 1.286157274 1.618775626 1.541925708 1.274581309 1.486067466 1 13.74685282 -1.406093461 5.051379007 0.999614399 1.385643066 0.291503372 0.18614765 0.000781325 9.19E-05 0.174207998 0.041021038 0.039256045 1.406093461 0.386028667 SS(ph)PLLNYNTGVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPLLNYNTGVYR 13 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 S(0.239)S(0.761)PLLNYNTGVYR;S(0.322)S(0.678)PLLNYNTGVYR 148.85 4.56E-05 121976000 172025 180390 189787 179631 220920 228320 176773 191879 169790 206029 TRUE FALSE 178816.6798 211370.5793 194733.0051 215161.4757 183368.0973 175296.1402 162917.0703 189307.1759 163679.2911 246396.4379 0.725727536 0.857847545 0.790323946 0.873232899 0.744199465 0.711439426 0.661198968 0.768303217 0.664292441 1 17.91062187 3.116680464 10.05578066 0.739221117 0.813465235 0.047302207 0.097520546 0.637943404 53.28937781 0.025843717 0.030910383 1308.219036 -3.116680464 0.074244118 SS(ph)PNPFITGLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 S(0.136)S(0.864)PNPFITGLTR;S(0.149)S(0.851)PNPFITGLTR;S(0.056)S(0.944)PNPFITGLTR 236.75 4.60E-16 883157000 359945 354003 383685 356921 491854 542388 404919 404577 373684 366173 TRUE FALSE 374155.9065 414800.2615 393684.1463 427518.9085 408248.8328 416426.607 373180.3907 399154.3071 360235.1858 437917.5885 0.854397988 0.947210782 0.898991401 0.976254253 0.932250367 0.950924598 0.852170364 0.911482702 0.822609539 1 18.74029987 -0.065615271 7.997408144 0.999999999 0.908374158 0.266568457 0.046927781 5974634.747 747071.2797 0.043936696 0.010656214 0.859774834 0.065615271 -0.091625841 SS(ph)PNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_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(0.401)S(0.599)PNVANQPPS(1)PGGK;S(0.264)S(0.736)PNVANQPPS(1)PGGK;S(0.424)S(0.576)PNVANQPPS(1)PGGK;S(0.427)S(0.573)PNVANQPPS(1)PGGK 251.21 3.93E-19 410740000 1314660 797059 1040460 815840 1239110 1432610 1340900 1056300 1094770 540882 TRUE FALSE 1366563.792 933947.683 1067575.242 977210.717 1028486.525 1099908.039 1235796.754 1042142.026 1055369.442 646857.4721 2.112619628 1.44382298 1.650402582 1.510704845 1.589973942 1.700387004 1.910462208 1.611084468 1.6315332 1 19.30308834 0.481000979 1.919099023 1.000057497 1.679885139 0.556365669 0.183954595 3.316844295 11.41074787 0.166887788 0.046203475 3.026920251 -0.481000979 0.679827642 SS(ph)PPAPPLPPGS(ph)GSPGTPQALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 2 S(0.43)S(0.57)PPAPPLPPGS(0.792)GS(0.197)PGT(0.011)PQALPR;S(0.452)S(0.548)PPAPPLPPGS(0.639)GS(0.358)PGT(0.003)PQALPR;S(0.445)S(0.555)PPAPPLPPGS(0.607)GS(0.391)PGT(0.002)PQALPR 167.53 1.57E-11 293562000 201479 217465 227875 208700 251204 289610 228879 230929 217156 195306 TRUE FALSE 209433.5465 254812.9221 233813.6097 249980.2371 208504.4338 222352.4666 210938.8659 227833.7745 209340.598 233572.4713 0.896653383 1.090937304 1.001032392 1.070247002 0.892675548 0.951963497 0.903098146 0.975430765 0.89625544 1 17.83351072 3.235519403 24.99992108 0.936520811 1.01918428 0.302933545 0.057915522 87.7029733 720951.9686 0.015246635 0.018971192 1719.964181 -3.235519403 0.082663469 SS(ph)PPLPPPAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 S(0.491)S(0.509)PPLPPPAEER 140.16 6.24E-05 554600000 252010 268190 289260 224260 294380 321940 269580 204970 303280 208100 TRUE FALSE 261959.5494 314249.5463 296798.3532 268617.9587 244341.3927 247174.314 248449.6152 202222.7124 292365.012 248873.2107 1.052582352 1.262689324 1.192568507 1.079336574 0.981790656 0.993173646 0.998297947 0.812553155 1.174754853 1 17.92505142 3.438242527 2.540298466 0.971540818 1.178010711 0.391102332 0.095951149 0.244888146 3.19116182 0.027902912 0.042500057 2743.105602 -3.438242527 0.206469892 SS(ph)PPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPLR 6 0 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 S(0.072)S(0.928)PPLR 77.923 0.074626 150760000 50940 150820 111010 141670 111960 169840 98444 145020 108080 265600 TRUE FALSE 52951.15053 176722.1618 113903.0118 169691.9032 92929.07919 130397.234 90727.70204 143076.2441 104190.2219 317639.2348 0.166702173 0.55636125 0.358592388 0.534228409 0.292561715 0.410519922 0.285631283 0.450436308 0.328014334 1 18.2770296 -1.300819563 4.079974702 1.000861828 0.384887353 0.734325286 0.112501677 31547695.72 10059323.58 241964.3016 0.02345973 0.050024233 1.300819563 -0.615974475 SS(ph)PPSAGNSPSSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 S(0.004)S(0.996)PPSAGNSPSSLK;S(0.04)S(0.96)PPSAGNSPSSLK;S(0.135)S(0.865)PPSAGNSPSSLK 313.32 8.99E-56 362620000 530792 367292 478907 398271 573763 586231 603386 481703 497683 275321 TRUE FALSE 551748.078 430371.5439 491387.7098 477047.8151 476234.9702 450087.7347 556091.0287 475246.5592 479771.486 329264.8786 1.675696723 1.307067871 1.492378148 1.448826905 1.44635824 1.366947294 1.688886562 1.443356368 1.457098881 1 18.32888911 0.494898291 2.398559973 1.00001141 1.479492617 0.619349393 0.113215397 4.860155367 22.25652157 0.100722821 0.027003748 3.125347348 -0.494898291 0.479481206 SS(ph)PPVLQGPAPAGFSQHPGLLVPHTHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPVLQGPAPAGFSQHPGLLVPHTHAR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 S(0.122)S(0.878)PPVLQGPAPAGFSQHPGLLVPHTHAR 122.78 7.55E-05 2132600000 412520 130280 130380 135140 223490 325490 231730 180940 170180 111470 TRUE FALSE 428806.6081 152654.5766 133777.8099 161870.2886 185501.2496 249899.8803 213566.3971 178514.7953 164055.255 133310.4123 3.21660252 1.145106177 1.003506085 1.214235902 1.391498582 1.874571356 1.602023379 1.339091165 1.230625967 1 17.02442994 4.742229959 24.99022917 1.342251476 3.216603237 0.833097645 0.255515236 150.0386026 1021802.539 0.066010469 0.493149035 55236.98416 -4.742229959 1.874351761 SS(ph)PQKEVK ddPTM_MDA-MB-175_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(0.141)S(0.859)PQKEVK;S(0.047)S(0.953)PQKEVK 65.278 0.039175 247880000 507600 422110 450560 384380 698550 697620 507110 497700 545240 445950 TRUE FALSE 527640.44 494604.1089 462301.9637 460409.2167 579810.7205 535608.3275 467361.3931 491029.1456 525616.9189 533325.3643 0.989340608 0.927396561 0.866829134 0.863280181 1.087161345 1.00428062 0.876315706 0.920693405 0.985546449 1 19.02465642 SS(ph)PQLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPQLAK 7 0 Q13370-2;Q13370 Q13370-2 PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase B" 1 S(0.014)S(0.986)PQLAK;S(0.218)S(0.782)PQLAK;S(0.471)S(0.529)PQLAK 90.709 0.017769 3573760000 8701800 5822700 6873400 5501000 5975100 7589000 7347200 6765600 6720100 2688710 TRUE FALSE 9045353.783 6822703.431 7052526.451 6589081.381 4959454.636 5826569.762 6771307.266 6674918.198 6478244.914 3215511.246 2.813037521 2.121809849 2.193283093 2.049155135 1.542353379 1.812019712 2.105826025 2.075849744 2.014685821 1 21.6166167 -1.593845468 0.139427024 4.73E-33 2.558680147 0.595362181 0.282349671 34.60804424 0.800850853 16.35382639 2.444685857 0.025477366 1.593845468 2.558680147 SS(ph)PQLDPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPQLDPLR 9 0 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.138)S(0.862)PQLDPLR;S(0.027)S(0.973)PQLDPLR 168.85 6.18E-05 1789140000 1159010 1007380 1053340 1174770 1290080 1499390 1524020 1178080 1043230 932860 TRUE FALSE 1204768.61 1180389.679 1080790.906 1407136 1070792.662 1151179.396 1404563.33 1162289.765 1005684.356 1115636.056 1.079893934 1.058041887 0.968766561 1.261285875 0.959804639 1.03185926 1.258979864 1.041818036 0.901444831 1 20.08943504 1.466554381 25 0.957691522 1.087624204 0.230222043 0.099490912 3.437009305 8135.784014 0.05208931 0.024113662 29.27887471 -1.466554381 0.129932682 SS(ph)PQLDPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SSPQLDPLRK 10 1 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 S(0.145)S(0.855)PQLDPLRK;S(0.207)S(0.793)PQLDPLRK;S(0.391)S(0.609)PQLDPLRK;S(0.057)S(0.943)PQLDPLRK;S(0.17)S(0.83)PQLDPLRK;S(0.272)S(0.728)PQLDPLRK;S(0.119)S(0.881)PQLDPLRK;S(0.258)S(0.742)PQLDPLRK 147.73 1.62E-05 12980810000 6646020 4545990 5589890 5245530 6739060 7016650 8503020 6101160 6065310 3203480 TRUE FALSE 6908410.001 5326728.42 5735567.126 6283080.178 5593556.988 5387139.376 7836531.074 6019383.93 5847020.678 3831140.572 1.803225403 1.390376657 1.497091276 1.640002516 1.460023949 1.406145057 2.045482521 1.571172818 1.526182756 1 21.86934253 3.791670633 24.96798379 1.569591081 1.546245778 0 0.262530125 6282.856 2953656.892 0.064751154 0.116731798 6189.714721 -3.791670633 -0.023345303 SS(ph)PQLDPLRKS(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.199)S(0.801)PQLDPLRKS(0.936)PT(0.064)MEQAVQTASAHLPAPAAVGR;S(0.471)S(0.529)PQLDPLRKS(0.823)PT(0.158)MEQAVQT(0.014)AS(0.004)AHLPAPAAVGR;S(0.43)S(0.57)PQLDPLRKS(0.982)PT(0.018)MEQAVQTASAHLPAPAAVGR;S(0.483)S(0.517)PQLDPLRKS(0.984)PT(0.014)MEQAVQT(0.001)ASAHLPAPAAVGR;S(0.466)S(0.534)PQLDPLRKS(1)PTMEQAVQTASAHLPAPAAVGR;S(0.448)S(0.552)PQLDPLRKS(0.831)PT(0.169)MEQAVQTASAHLPAPAAVGR;S(0.449)S(0.551)PQLDPLRKS(0.599)PT(0.399)MEQAVQT(0.001)ASAHLPAPAAVGR 217.28 3.23E-36 10196460000 1538682 1872502 2069380 1427331 2732460 2728777 2187204 2219291 2258204 1841700 TRUE FALSE 1599430.353 2194089.652 2123309.743 1709652.812 2267997.425 2095059.897 2015765.235 2189545.034 2176931.679 2202545.854 0.726173465 0.996160715 0.964025216 0.776216672 1.029716326 0.951199219 0.915197853 0.994097367 0.988370651 1 21.07074062 4.745154696 24.9080689 0.953651462 0.726173356 0.512138342 0.067570554 595.1077606 2247861.24 0.015747895 0.151663982 55610.23062 -4.745154696 -0.227478106 SS(ph)PQLDPLRKSPT(ph)MEQAVQTASAHLPAPAAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGR 33 2 Q8ND56-2;Q8ND56;Q8ND56-3 Q8ND56-2 LSM14A Protein LSM14 homolog A 2 S(0.464)S(0.536)PQLDPLRKS(0.264)PT(0.734)MEQAVQT(0.001)ASAHLPAPAAVGR 131.79 2.30E-07 743580000 91630 100080 129530 86464 168570 158910 118240 139950 141580 103240 TRUE FALSE 95247.62315 117267.9615 132905.6582 103566.3211 139916.5316 122005.5608 108972.0398 138074.1992 136484.5635 123467.9014 0.771436318 0.949785006 1.076438951 0.838811707 1.133221915 0.988156108 0.882594088 1.118300365 1.105425475 1 16.9137765 4.681164336 2.93511353 1.017175089 0.745026004 0.388664503 0.093015568 0.338545149 4.464728576 0.022369294 0.201994583 47991.50129 -4.681164336 -0.272149084 SS(ph)PRPTAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPRPTAEK 9 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 S(0.144)S(0.856)PRPTAEK 59.57 0.061418 400570000 705230 464840 592380 474700 784930 769760 702070 608560 628090 424120 TRUE FALSE 733073.025 544672.654 607817.9094 568594.2432 651507.879 590994.9058 647039.9189 600403.2486 605485.1636 507218.1937 1.445281408 1.073842896 1.198336174 1.121005221 1.284472614 1.165168981 1.27566386 1.183717887 1.193737076 1 18.95224697 0.401600995 1.447447585 0.999977295 1.212282824 0.309795529 0.097011506 4.365137225 9.349399088 0.084181378 0.024445853 2.521163408 -0.401600995 0.212305529 SS(ph)PSARPPDVPGQQPQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 S(0.132)S(0.868)PSARPPDVPGQQPQAAK;S(0.016)S(0.966)PS(0.018)ARPPDVPGQQPQAAK;S(0.157)S(0.842)PS(0.001)ARPPDVPGQQPQAAK 193.14 3.59E-15 860370000 674840 487226 595203 498987 684380 746280 724120 597409 635680 391970 TRUE FALSE 701483.2043 570903.2754 610714.4791 597685.1393 568049.3321 572967.78 667361.5823 589401.7095 612802.001 468769.0168 1.496436793 1.217877579 1.302804702 1.275009904 1.211789414 1.222281677 1.423646953 1.257339304 1.307257901 1 18.83851769 -2.295409376 1.79030331 9.16E-06 1.295886657 0.513719911 0.087873451 1009283.055 131288.6778 4071377.806 0.022490251 0.00506513 2.295409376 1.295877498 SS(ph)PSIICMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPSIICMPK 10 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 S(0.187)S(0.813)PSIICMPK;S(0.062)S(0.938)PSIICMPK;S(0.478)S(0.521)PS(0.001)IICMPK 173.28 3.63E-06 566850000 1411550 913230 1171530 1054050 1302720 1511470 1558760 1163980 1139350 691000 TRUE FALSE 1467279.084 1070070.149 1202061.034 1262537.944 1081284.12 1160453.999 1436580.318 1148378.752 1098345.016 826388.22 1.775532429 1.29487585 1.454596042 1.527778244 1.308445708 1.404247993 1.738384313 1.389635917 1.329090843 1 19.65646016 0.885237644 1.982618903 1.00209545 1.482638438 0.489968 0.152247718 0.389901116 3.086198598 0.137747635 0.038352226 7.677815018 -0.885237644 0.480542988 SS(ph)PSPQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPSPQKR 8 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 S(0.022)S(0.978)PSPQKR;S(0.108)S(0.892)PSPQKR;S(0.069)S(0.931)PSPQKR 131.44 0.00061557 676780000 666740 443780 576760 538580 757680 687300 685750 521740 504560 335200 TRUE FALSE 693063.41 519995.7629 591790.8394 645109.5165 628889.8242 527684.9911 631999.1231 514746.9287 486400.9842 400876.0222 1.728872199 1.29714858 1.476244042 1.609249446 1.568788826 1.316329643 1.576545087 1.28405517 1.213345167 1 18.6127966 1.2143124 1.052775667 1.001590779 1.509654555 0.641795669 0.125938403 0.286504891 0.664713364 0.111388501 0.037466191 16.37994351 -1.2143124 0.508063777 SS(ph)PVESLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SSPVESLKK 9 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.113)S(0.887)PVESLKK;S(0.042)S(0.958)PVESLKK;S(0.096)S(0.904)PVESLKK;S(0.23)S(0.77)PVESLKK;S(0.008)S(0.992)PVESLKK;S(0.01)S(0.99)PVESLKK;S(0.196)S(0.804)PVESLKK 150.06 5.28E-05 7571890000 20918190 10013970 15352400 10415410 21348050 20015870 22311770 15337290 17604240 7660630 TRUE FALSE 21744056.29 11733791.45 15752496.16 12475547.01 17719316.09 15367487.54 20562915.17 15131718.71 16970666.84 9161583.777 2.373394909 1.280760154 1.719407533 1.361723837 1.934088747 1.67738329 2.244471662 1.651648785 1.852372609 1 23.12716559 SS(ph)PVKVGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPVKVGEK 9 1 P49916-3;P49916;P49916-4;P49916-2 P49916-3 LIG3 DNA ligase 3 1 S(0.395)S(0.605)PVKVGEK;S(0.205)S(0.795)PVKVGEK 131.69 0.00019743 871200000 3049820 1329760 1878440 1270110 3104100 2997980 2940480 2040070 2279310 982700 TRUE FALSE 3170229.249 1558135.936 1927393.69 1521333.967 2576466.191 2301744.58 2709997.494 2012726.199 2197278.078 1175241.25 2.697513594 1.325800925 1.639998332 1.294486529 2.192287065 1.958529434 2.305907399 1.712606836 1.869640023 1 20.16452551 3.215024116 24.99631127 1.900718904 1.702799202 0 0.49014554 914.0747562 970766.2304 0.134415516 0.160742642 1640.680877 -3.215024116 -0.197919702 SS(ph)PVPPVPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPVPPVPER 10 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 S(0.148)S(0.852)PVPPVPER;S(0.073)S(0.927)PVPPVPER;S(0.167)S(0.833)PVPPVPER 141.95 3.84E-05 2520339000 1691330 1809720 1985320 1776470 2160670 2399080 2026230 2014360 1936380 1737940 TRUE FALSE 1758105.014 2120525.332 2037059.07 2127850.464 1793400.085 1841930.028 1867408.798 1987360.799 1866690.062 2078456.068 0.845870664 1.020240632 0.980082813 1.023764946 0.862852053 0.886201088 0.898459595 0.956171665 0.898113793 1 20.98708082 4.779339787 22.91294038 0.943196442 0.845869808 0.227574494 0.055605953 15026.2828 8442407.164 0.013758199 4.346249139 60164.42733 -4.779339787 -0.097326634 SS(ph)REKEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSREKEQR 8 2 H7C1L9 H7C1L9 TRIP12 1 S(0.446)S(0.554)REKEQR;S(0.455)S(0.545)REKEQR;S(0.242)S(0.758)REKEQR 74.944 0.020698 264141000 10548.5 211418 247735 173682 259707 247010 178168 230478 255513 254359 TRUE FALSE 10964.96293 247727.3969 254191.1776 208035.7812 215562.0969 189645.671 164202.7266 227388.8194 246317.137 304195.7761 0.036045744 0.8143683 0.835617052 0.683887804 0.708629488 0.623432953 0.539792921 0.747508142 0.809732273 1 18.21464059 -4.664689768 0.052305943 2.301147687 5.12E-17 0.31003844 0.204213791 698.8251259 2.855959845 129.0672817 29.26019304 2.16E-05 4.664689768 -2.301147687 SS(ph)RSS(ph)PELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.432)S(0.525)RS(0.276)S(0.767)PELTR;S(0.412)S(0.559)RS(0.237)S(0.79)PELT(0.001)R;S(0.435)S(0.558)RS(0.148)S(0.859)PELTR;S(0.425)S(0.574)RS(0.004)S(0.996)PELTR 116.86 0.00058836 1851370000 864153 993489 979580 1023211 1053680 1268830 998810 1001277 953377 1051877 TRUE FALSE 898270.4277 1164113.007 1005108.66 1225599.082 874575.85 974163.4618 920520.6623 987856.5196 919065.148 1257972.159 0.714062248 0.925388531 0.79899118 0.974265665 0.695226714 0.774391909 0.73174963 0.785276934 0.730592598 1 20.26266856 5.0348483 16.22347459 0.810855696 0.358266027 0.082423244 0.10187777 10775296 139061906.5 0.023183811 139245617.3 108354.8363 -5.0348483 -0.452589669 SS(ph)SESLIFSGNQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 S(0.239)S(0.76)S(0.001)ESLIFSGNQGR;S(0.202)S(0.797)S(0.001)ESLIFSGNQGR;S(0.026)S(0.974)SESLIFSGNQGR;S(0.225)S(0.77)S(0.005)ESLIFSGNQGR;S(0.007)S(0.993)SESLIFSGNQGR;S(0.02)S(0.968)S(0.012)ESLIFSGNQGR 401.7 2.35E-132 1476270000 1368010 1356450 1533580 1591510 1644260 2037030 1775740 1704180 1660430 1498800 TRUE FALSE 1422020.091 1589409.736 1573546.355 1906305.928 1364769.273 1563960.654 1636552.859 1681338.255 1600671.449 1792461.164 0.793333836 0.886719204 0.877869148 1.063513099 0.761394054 0.872521361 0.913019982 0.938005402 0.893002025 1 20.77351043 -5 0.088785974 1.339509658 0.803974538 0.194597103 0.075304941 387.2288919 2.396060213 25.1384825 1.829829889 1.00E-05 5 -0.53553512 SS(ph)SKESLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.009)S(0.676)S(0.315)KESLVR 122.7 0.00035032 252530000 467090 216060 276520 203440 464900 433950 364880 320360 310130 172870 TRUE FALSE 485531.0739 253166.6243 283726.3384 243679.8248 385876.4641 333171.6891 336279.7522 316066.0982 298968.4819 206740.5667 2.348504126 1.224561915 1.372378643 1.178674455 1.866476765 1.611544819 1.626578458 1.528805417 1.446104587 1 17.65746198 0.70498876 1.672774797 1.000358841 1.573849483 0.239586511 0.317744614 1.615953466 6.848100297 0.288997112 0.082294062 5.069775864 -0.70498876 0.573490642 SS(ph)SLKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.336)S(0.595)S(0.069)LKER 111.46 0.0039819 2704200000 2131300 1510000 2402600 1277400 2350700 2431900 2730700 2128200 2573000 1208300 TRUE FALSE 2215445.37 1769330.754 2465213.73 1530065.907 1951128.854 1867128.081 2516660.599 2099674.96 2480398.233 1445043.251 1.533134298 1.2244137 1.705979201 1.058837448 1.350221769 1.292091486 1.741581505 1.453018765 1.716487193 1 20.46268124 SS(ph)SPAPADIAQTVQEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 S(0.277)S(0.609)S(0.114)PAPADIAQTVQEDLR 371.6 1.24E-107 21173000000 630620 777470 715990 651720 777030 903380 690460 722050 669920 708650 TRUE FALSE 655517.3645 910994.4246 734649.2876 780628.2708 644950.7181 693583.6859 636339.941 712372.1008 645809.7101 847496.3996 0.773475103 1.074924242 0.8668465 0.921099218 0.76100703 0.818391307 0.750846778 0.840560622 0.762020594 1 19.69284771 3.255245734 24.54188905 0.811115551 0.917914761 0.154940296 0.096583485 278.9415925 410287.9314 0.024430241 0.032984063 1799.889045 -3.255245734 0.106799211 SS(ph)SPELVTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.395)S(0.53)S(0.075)PELVTHLK 97.911 0.006203 823840000 490680 371280 479420 389780 613140 600140 637930 569970 608140 356750 TRUE FALSE 510052.4253 435044.4518 491914.079 466877.3206 508918.6818 460766.5802 587927.3797 562330.4844 586253.1602 426648.3321 1.195486744 1.019679251 1.152973168 1.094290744 1.192829418 1.07996808 1.378014012 1.31801871 1.374089891 1 18.70268788 2.245918391 24.99204797 1.299601549 1.121157023 0.268549466 0.11233322 164.6747769 559349.3674 0.036151476 0.029681947 176.1644982 -2.245918391 -0.178444526 SS(ph)SPVTELAS(ph)RSPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.079)S(0.461)S(0.461)PVTELAS(0.566)RS(0.434)PIR 149.36 1.92E-06 474540000 206160 231480 190620 196760 222230 261350 216630 206880 201340 160600 TRUE FALSE 214299.356 271234.8893 195587.7138 235678.5407 184455.424 200655.4233 199649.9745 204107.112 194093.8127 192066.4951 1.115756061 1.412192632 1.018333331 1.227067431 0.960372728 1.044718514 1.039483614 1.062689835 1.01055529 1 17.55124635 3.735843138 1.305250528 1.031353189 1.244685263 0.369718361 0.101963243 0.45527456 1.480152634 0.029743627 0.078615433 5443.060203 -3.735843138 0.213332074 SS(ph)SPVTELASRS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.281)S(0.359)S(0.359)PVTELAS(0.023)RS(0.977)PIR;S(0.274)S(0.363)S(0.363)PVTELAS(0.006)RS(0.994)PIR 126.25 4.86E-05 852320000 409390 484370 456100 437300 504020 586040 502000 476630 467470 411650 TRUE FALSE 425553.0333 567556.7796 467986.3407 523796.6348 418346.8604 449941.0915 462651.9283 470241.5545 450645.846 492304.936 0.864409439 1.152856163 0.950602577 1.063967871 0.849771818 0.913947959 0.939766991 0.955183505 0.9153795 1 18.90919268 3.25097269 24.99994706 0.928804833 1.014211911 0.196015393 0.077920971 331.0273595 666739.436 0.019952323 0.026826766 1782.26669 -3.25097269 0.085407078 SS(ph)SPVTELASRS(ph)PIRQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.268)S(0.366)S(0.366)PVTELAS(0.014)RS(0.986)PIRQDR;S(0.275)S(0.363)S(0.363)PVTELAS(0.141)RS(0.859)PIRQDR;S(0.276)S(0.362)S(0.362)PVTELAS(0.365)RS(0.635)PIRQDR;S(0.275)S(0.362)S(0.362)PVTELAS(0.06)RS(0.94)PIRQDR 220.69 3.56E-19 2950200000 715490 821340 760670 718630 996460 1042950 730116 794870 800140 861900 TRUE FALSE 743738.0977 962398.7559 780493.6851 860772.8691 827082.0851 800740.6686 672887.6001 784216.0678 771343.1177 1030772.803 0.72153446 0.933667199 0.757192742 0.835075263 0.802390287 0.77683527 0.652799141 0.760803996 0.748315357 1 19.97529495 2.741710655 3.815519963 0.760315077 0.816188981 0 0.097968418 0.656394696 21.80074304 0.029686635 0.029759049 551.7097445 -2.741710655 0.055873904 SS(ph)SVPHPFQVTLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 S(0.13)S(0.857)S(0.012)VPHPFQVTLLR;S(0.02)S(0.879)S(0.101)VPHPFQVTLLR;S(0.168)S(0.832)SVPHPFQVTLLR 220.52 4.83E-12 2663440000 1117280 1356630 1538440 1489830 1844340 1965020 1621780 1574520 1402030 1494250 TRUE FALSE 1161391.077 1589620.649 1578533.01 1784513.927 1530839.746 1508673.885 1494660.646 1553416.135 1351571.214 1787019.678 0.649903911 0.889537294 0.883332752 0.998597804 0.856644034 0.844240219 0.836398538 0.869277576 0.75632699 1 20.76912409 4.740527998 24.65374174 0.876872714 0.649903818 0.501205005 0.069195844 120.4013558 1508641.827 0.01602379 0.104621057 55020.93902 -4.740527998 -0.226968896 SS(ph)TDFSELEQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTDFSELEQPR 12 0 Q86V48;Q86V48-2;Q86V48-3 Q86V48 LUZP1 Leucine zipper protein 1 1 S(0.017)S(0.983)TDFSELEQPR 228.61 1.07E-11 139210000 192470 226130 221570 230620 268800 306500 273520 241440 270390 253410 TRUE FALSE 200068.8642 264966.0685 227344.2962 276235.9477 223109.472 235320.0201 252080.7877 238203.8917 260658.7167 303060.8377 0.660160731 0.874299928 0.750160588 0.911486782 0.736187076 0.776477825 0.831782785 0.785993643 0.860087099 1 18.20924791 0.86069762 2.349374018 0.99999505 0.794916642 0.471466919 0.067398931 0.428132712 4.605242278 0.057941175 0.015683573 7.256005787 -0.86069762 -0.205078408 SS(ph)TDS(ph)LPGPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 2 S(0.009)S(0.991)TDS(1)LPGPISR 191.57 0.00015644 0 133370 134140 166010 160650 209340 206620 179110 163520 159160 132430 TRUE FALSE 138635.5506 157177.5015 170336.357 192426.0905 173756.4616 158635.6364 165070.8902 161328.2819 153431.8627 158377.123 0.875350859 0.992425538 1.07551112 1.214986653 1.097105809 1.001632265 1.042264735 1.018633745 0.968775413 1 17.27300443 1.628796249 1.548186294 0.984930641 1.051977153 0.066627908 0.081884906 1.06405869 5.029964339 0.073401298 0.026481729 42.53987885 -1.628796249 0.067046512 SS(ph)TDSLPGPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 S(0.002)S(0.986)T(0.012)DSLPGPISR;S(0.001)S(0.988)T(0.011)DSLPGPISR;S(0.004)S(0.986)T(0.011)DSLPGPISR 247.69 1.21E-16 1461850000 1228100 1352040 1556100 1431800 1563650 1862220 1703670 1529450 1438210 1100870 TRUE FALSE 1276586.336 1584242.353 1596653.244 1715005.767 1297861.332 1429747.627 1570131.894 1508950.224 1386449.103 1316564.399 0.969634556 1.203315503 1.212742229 1.302637203 0.985794035 1.085968623 1.192597867 1.146127167 1.053081113 1 20.32834666 3.23228715 24.99998852 1.09685865 1.177217584 0.166281515 0.098035369 316.6089638 1261697.757 0.028777334 0.035185847 1707.210801 -3.23228715 0.080358933 SS(ph)TETCYSAIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTETCYSAIPK 12 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 S(0.041)S(0.794)T(0.06)ET(0.104)CYS(0.001)AIPK 99.498 0.0039467 113650000 76299 103330 100450 97401 121310 140640 129590 113220 114740 86744 TRUE FALSE 79311.34344 121076.1237 103067.8095 116666.6271 100689.7695 107978.4914 119432.3972 111702.4711 110610.5298 103739.826 0.764521655 1.167113233 0.993522098 1.124607893 0.970598982 1.040858613 1.151268532 1.076755913 1.066230146 1 16.66261033 4.750294322 24.99676697 1.068271952 0.764521473 0.668468312 0.063598762 1027.968808 2189881.562 0.01423416 0.236565874 56272.25538 -4.750294322 -0.303750479 SS(ph)TPLHS(ph)PSPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.279)S(0.361)T(0.361)PLHS(0.976)PS(0.024)PIR 107.5 0.00095479 1274900000 619420 777190 788270 684660 961640 1031400 780860 786630 775590 725500 TRUE FALSE 643875.1799 910666.3368 808812.9638 820083.7045 798180.7763 791872.981 719654.1528 776086.5115 747676.6674 867647.8345 0.742092764 1.049580602 0.932190379 0.945180374 0.919936344 0.912666349 0.829431163 0.89447179 0.86172827 1 19.72675007 2.46414662 24.38032986 0.884367888 0.926324784 0.001354371 0.081589003 540.9661473 1016507.057 0.026307068 0.022023792 291.1699958 -2.46414662 0.041956895 SS(ph)TPPRQS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSTPPRQSPSR 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.09)S(0.682)T(0.228)PPRQS(0.948)PS(0.052)R;S(0.287)S(0.357)T(0.357)PPRQS(1)PSR;S(0.263)S(0.368)T(0.368)PPRQS(0.998)PS(0.001)R;S(0.264)S(0.369)T(0.369)PPRQS(0.996)PS(0.003)R 104.24 0.0048292 1227660000 506320 561820 560400 497250 631040 761450 598340 571440 568820 510822 TRUE FALSE 526309.9046 658308.2146 575004.4844 595604.5659 523776.0462 584614.7774 551440.5473 563780.7815 548348.2793 610907.7906 0.861521023 1.077590145 0.941229582 0.974950025 0.857373329 0.95696075 0.902657579 0.92285741 0.89759582 1 19.22059511 SS(ph)TSSIDSNISSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTSSIDSNISSK 13 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 S(0.188)S(0.812)TSSIDSNISSK 213.99 1.56E-09 95348000 214450 166810 178480 180990 257900 281850 322350 232550 249700 147320 TRUE FALSE 222916.6516 195458.3199 183131.3354 216789.2818 214062.2501 216394.609 297083.3647 229433.0476 240713.3458 176184.5334 1.265245293 1.109395451 1.039429125 1.230467156 1.214988887 1.228227046 1.686205701 1.302231491 1.366256964 1 17.42672776 2.460482744 24.99988736 1.379824808 1.170054208 0.165013663 0.167276279 317.0478626 476371.6125 0.054975349 0.046005958 288.7239057 -2.460482744 -0.2097706 SS(ph)VDLEESSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVDLEESSTK 11 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 S(0.022)S(0.978)VDLEESSTK 196.02 0.00087386 0 212640 135490 182480 141900 252730 243660 238030 185240 204860 112160 TRUE FALSE 221035.1914 158759.3535 187235.5787 169967.3965 209771.0449 187073.6577 219372.5866 182757.1608 197487.1286 134135.6046 1.647848773 1.183573549 1.395867856 1.267131102 1.563872959 1.394660712 1.635453818 1.362480613 1.472294617 1 17.03333271 -1.534033824 6.113026167 0.999392266 1.428723345 0.455644422 0.142742999 0.001101297 8.39E-05 0.128741536 0.030303946 0.029239246 1.534033824 0.42933108 SS(ph)VEKENQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSVEKENQK 9 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 S(0.073)S(0.927)VEKENQK;S(0.013)S(0.987)VEKENQK 179.6 3.00E-05 760220000 1065050 398610 664380 412840 966450 906960 1034520 718060 853720 311220 TRUE FALSE 1107098.996 467068.1667 681694.2886 494498.5198 802173.1742 696332.2851 953431.6192 708435.5802 822994.784 372197.6003 2.974492569 1.254893009 1.831538645 1.32859137 2.155234675 1.870867207 2.561627529 1.903385674 2.211177029 1 18.50570923 SS(ph)WPNSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSWPNSEK 8 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.19)S(0.809)WPNSEK 88.056 0.015982 0 243620 172850 242360 183120 299350 316360 307030 227460 269730 176150 TRUE FALSE 253238.3057 202535.6429 248676.1007 219340.5894 248466.5939 242890.1845 282964.1863 224411.2707 260022.47 210663.2199 1.202100233 0.961419098 1.180443842 1.041190719 1.179449332 1.152978601 1.343206405 1.065260803 1.234304071 1 17.68457893 3.217074414 24.87254546 1.170751742 1.092666037 0.081188064 0.106776308 480.9531694 556752.8501 0.028719121 0.034354877 1648.444819 -3.217074414 -0.078085705 SSAIPDFRDPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSAIPDFRDPQK 12 1 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 0 ; 104.87 0.0019077 407510000 743900 587020 714010 551310 934230 949650 837200 727200 797050 561000 FALSE TRUE 773269.7464 687836.1186 732617.6872 660357.4725 775429.9183 729108.1796 771578.0764 717453.0735 768364.3262 670917.209 1.152556137 1.025217582 1.09196437 0.984260746 1.155775866 1.08673346 1.150034708 1.06936156 1.145244623 1 19.35577522 3.211229624 24.9999937 1.104847243 1.062798293 0.086063719 0.059443652 474.2321596 433785.0028 0.015780471 0.0188658 1626.408458 -3.211229624 -0.04204895 SSALREEVQSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSALREEVQSLR 12 1 Q14980;Q14980-2;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 160.69 6.15E-05 142560000 85268 92462 88569 81688 106680 141880 88330 100800 89868 100890 FALSE TRUE 88634.44648 108341.6292 90877.1809 97845.64259 88546.57171 108930.5202 81406.46379 99448.94088 86633.66823 120657.4638 0.734595637 0.897927288 0.753183251 0.810937338 0.733867337 0.902807972 0.674690659 0.824225354 0.718013337 1 16.88055764 -1.162400696 5.232323489 1.000008838 0.786724086 0.448841085 0.071932678 6.56E-06 1.05E-06 0.061639169 0.014527889 0.068801721 1.162400696 -0.213284752 SSAQLLEDWGMEDIDHVFSEEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 274.85 5.35E-52 802522000 288154.6 424377 399533 411665 427182 466568 406862 417906.3 385720 381609.7 FALSE TRUE 299531.1661 497260.4486 409945.1582 493091.1083 354569.7562 358214.6529 374971.0933 412304.9496 371838.0125 456378.8144 0.656321364 1.089578291 0.898256329 1.08044259 0.776919842 0.784906402 0.82162248 0.903427014 0.814757392 1 18.7998723 4.778551479 23.31062458 0.898272267 0.656319697 0.317476456 0.109812243 13662.92267 7963693.558 0.026204454 7.987944765 60055.31913 -4.778551479 -0.24195257 SSAS(ph)SSPKRPSVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSASSSPKRPSVER 14 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 S(0.015)S(0.055)AS(0.325)S(0.285)S(0.285)PKRPS(0.036)VER 63.337 0.055038 40486000 42629 29073 42944 27240 53933 55585 37025 41999 46101 33398 TRUE FALSE 44312.02584 34066.06159 44063.15592 32627.9907 44765.48792 42676.22615 34122.88375 41436.0721 44441.83402 39941.69866 1.109417659 0.852894662 1.10318683 0.816890413 1.120770759 1.068462974 0.85431729 1.037413868 1.112667601 1 15.28560807 SSASSS(ph)PKRPSVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSASSSPKRPSVER 14 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 S(0.078)S(0.078)AS(0.078)S(0.333)S(0.432)PKRPSVER 64.275 0.032573 132070000 151020 113630 135740 77551 188610 190090 131700 126400 168000 100400 TRUE FALSE 156982.3862 133145.0686 139277.4959 92890.35633 156550.1396 145944.4783 121377.0099 124705.8147 161953.7128 120071.4577 1.307408015 1.10888192 1.159955068 0.773625623 1.303808103 1.215480191 1.010873126 1.038596658 1.348811082 1 16.87353372 4.137623938 0.010115613 1.37E-07 2.274898721 0.027773655 0.166328187 26162.02072 50.39377505 5331.663399 6012.599599 13728.52685 -4.137623938 2.274898583 SSASSSPKRPS(ph)VER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSASSSPKRPSVER 14 2 S4R3M9;O75764;S4R419;O75764-2 S4R3M9 TCEA3 Transcription elongation factor A protein 3 1 SSAS(0.013)S(0.057)S(0.023)PKRPS(0.908)VER;SS(0.001)AS(0.007)S(0.037)S(0.089)PKRPS(0.866)VER 100.24 0.001468 554820000 550700 392330 540580 337580 670270 679630 521230 491700 575280 433680 TRUE FALSE 572442.0612 459709.6256 554667.9589 404352.3164 556337.7448 521796.2324 480374.6306 485109.5658 554575.7852 518651.2927 1.103712782 0.886355885 1.069442932 0.779622691 1.072662409 1.006063688 0.926199621 0.935328944 1.069265213 1 18.98440536 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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;SSATSGDIWPGLS(0.002)AYDNS(0.998)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLS(0.016)AY(0.245)DNS(0.739)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLS(0.009)AY(0.073)DNS(0.918)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR 327.23 1.04E-79 6835633000 2809706 2873482 2767944 3614665 2893035 3561061 3783029 3227373 2961342 2110013 TRUE FALSE 2920635.362 3366980.181 2840078.895 4329634.948 2401277.944 2734058.551 3486505.302 3184115.344 2854763.88 2523429.649 1.157407088 1.334287319 1.125483683 1.715773987 0.951592982 1.083469298 1.381653459 1.261820533 1.131303138 1 21.26695444 SSAWAEGGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSAWAEGGSPR 11 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 SSAWAEGGS(1)PR 153.49 3.40E-05 233840000 154820 185340 185510 170240 205100 240640 187440 174460 174130 189680 TRUE FALSE 160932.4131 217170.7033 190344.543 203912.9639 170237.1753 184755.0069 172747.963 172121.6491 167863.0953 226844.1644 0.709440393 0.957356359 0.839098257 0.898912099 0.750458694 0.814457835 0.761527031 0.758766043 0.739993007 1 17.79134202 3.236700092 24.99911456 0.787694152 0.857919709 0.039428731 0.092163924 102.0225766 1370839.17 0.024117002 0.030240693 1724.646502 -3.236700092 0.070225557 SSCS(ph)TPLSQANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSCSTPLSQANR 12 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SSCS(0.5)T(0.5)PLSQANR 310.01 3.06E-46 504920000 497540 555420 476400 508470 576370 720190 492320 519330 464870 518480 TRUE FALSE 517183.2634 650809.0644 488815.3754 609043.8484 478398.8333 552936.7871 453730.672 512369.2308 448139.4195 620066.2291 0.834077457 1.049579922 0.788327686 0.982223865 0.771528606 0.891738271 0.731745499 0.826313717 0.722728313 1 19.24206279 3.229300121 24.99958475 0.813059273 0.914323891 0.152376644 0.10150294 303.4953588 819313.093 0.026679762 0.032298994 1695.509083 -3.229300121 0.101264618 SSCST(ph)PLSQANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSCSTPLSQANR 12 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 SSCS(0.151)T(0.849)PLSQANR;S(0.001)S(0.004)CS(0.147)T(0.846)PLS(0.002)QANR;SSCS(0.015)T(0.985)PLSQANR 211.38 3.64E-07 1027700000 1172290 1352030 1186550 1268820 1402790 1758990 1183400 1240130 1161570 1296910 TRUE FALSE 1218572.914 1584230.635 1217472.468 1519788.809 1164344.257 1350491.23 1090642.016 1223508.086 1119765.323 1551014.684 0.785661752 1.021415627 0.784952251 0.979867454 0.75069841 0.870714665 0.703179684 0.788843651 0.721956623 1 20.56478091 3.222314866 24.9770578 0.791080562 0.894432819 0.131557358 0.105532084 372.835604 573215.6048 0.02777388 0.033290318 1668.456413 -3.222314866 0.103352257 SSDEENGPPSS(ph)PDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36;Q96B36-3;Q96B36-2 Q96B36 AKT1S1 Proline-rich AKT1 substrate 1 1 SSDEENGPPS(0.006)S(0.994)PDLDR;SSDEENGPPS(0.002)S(0.998)PDLDR 324.29 1.71E-58 1260890000 1155170 1275980 1294180 1278530 1473960 1596880 1261710 1360510 1269280 1297700 TRUE FALSE 1200777.004 1495119.639 1327907.394 1531419.418 1223416.806 1226028.821 1162813.873 1342274.589 1223598.861 1551959.469 0.773716729 0.963375442 0.855632779 0.986765085 0.788304611 0.789987655 0.74925531 0.864890234 0.788421918 1 20.56565945 3.204113036 24.99963053 0.819030691 0.896962976 0.114616226 0.084746077 306.7906277 222646.2038 0.022685052 0.02711495 1599.974409 -3.204113036 0.077932285 SSDKPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSDKPIR 7 1 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 0 ;; 101.41 0.0082796 1184590000 2217620 1873390 2219800 1819860 2623870 2761770 2533050 2310970 2361810 1803930 FALSE TRUE 2305173.35 2195130.16 2277649.812 2179822.876 2177865.515 2120390.773 2334502.922 2279995.227 2276808.919 2157375.545 1.068508149 1.017500251 1.055750269 1.010404925 1.009497637 0.98285659 1.082103173 1.05683743 1.055360493 1 21.0408459 2.22193316 24.99961731 1.054717733 1.023941194 0.126840577 0.029779545 395.2629397 594278.5872 0.010902092 0.008074885 166.6990635 -2.22193316 -0.030776539 SSDQPLTVPVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSDQPLTVPVSPK 13 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK;SSDQPLTVPVS(1)PK 251.28 2.29E-18 3646880000 8645240 3505400 4483340 3303060 6442700 7723710 6158780 4999500 5306660 3075090 TRUE FALSE 8986560.751 4107425.182 4600179.524 3956395.409 5347572.155 5929995.406 5676038.731 4932489.88 5115674.343 3677595.009 2.443597168 1.116878061 1.250866262 1.075810523 1.454094902 1.61246559 1.543410494 1.341227043 1.391037983 1 21.81033118 7.99999798 0.034522709 3.91E-06 3.581703865 0.181834376 0.353054565 2336.73993 6.165532745 190.2960104 527.6279196 99999534.91 -7.99999798 3.581699953 SSDTSST(ph)SPLNSSASQEELHQDEGLVAAPIVSNSEKPIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDTSSTSPLNSSASQEELHQDEGLVAAPIVSNSEKPIAK 40 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 S(0.002)S(0.002)DT(0.013)S(0.012)S(0.071)T(0.445)S(0.445)PLNS(0.005)S(0.005)AS(0.001)QEELHQDEGLVAAPIVSNSEKPIAK 145.37 4.34E-13 106410000 89349 49804 82300 71783 111560 126850 90776 77287 102720 56635 TRUE FALSE 92876.56751 58357.44958 84444.80561 85981.46315 92597.07105 97391.00993 83660.73992 76251.09418 99023.12727 67731.54391 1.371245393 0.861599282 1.24675743 1.269444902 1.367118859 1.437897386 1.235181351 1.125784085 1.461994243 1 16.04754026 5.062435782 22.40494917 1.228850779 4.938781339 0.057920165 0.178059572 3694.38233 1399386.732 0.040734076 37782.57452 115461.1244 -5.062435782 3.70993056 SSDTSSTS(ph)PLNSSASQEELHQDEGLVAAPIVSNSEKPIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSDTSSTSPLNSSASQEELHQDEGLVAAPIVSNSEKPIAK 40 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 SSDTS(0.001)S(0.008)T(0.048)S(0.293)PLNS(0.293)S(0.293)AS(0.064)QEELHQDEGLVAAPIVSNSEKPIAK 160.19 1.15E-18 169520000 75282 55812 71760 51820 88577 89837 83139 74387 79955 48333 TRUE FALSE 78254.19149 65397.27684 73630.12455 62069.84133 73520.71318 68973.71824 76622.34794 73389.96394 77077.43517 57802.92596 1.353810213 1.131383503 1.273813104 1.073818328 1.27192027 1.193256519 1.325579054 1.269658287 1.333452137 1 15.8188549 2.329265065 23.34835044 1.258908521 1.211133324 0 0.114309675 42.49379903 10916.76557 0.036381133 0.030438618 213.4347184 -2.329265065 -0.047775197 SSDYQFPS(ph)SPFTDTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 SSDYQFPS(0.76)S(0.24)PFTDTLK;SSDYQFPS(0.607)S(0.392)PFTDTLK;SSDYQFPS(0.868)S(0.132)PFTDTLK;SSDYQFPS(0.88)S(0.119)PFTDTLK 210.08 1.11E-11 356896000 985429 683826 852317 763243 1035225 1092637 1120390 886487 941224 547936 TRUE FALSE 1024334.498 801267.7961 874529.0812 914210.1873 859257.8243 838888.6158 1032570.904 874605.0918 907349.5321 655293.5683 1.563168856 1.222761576 1.334560758 1.395115459 1.311256307 1.28017221 1.575737889 1.334676753 1.384645869 1 19.32178185 -1.137249794 4.792870246 0.999972624 1.373623668 0.525886342 0.107603871 2.94E-05 5.29E-06 0.097303874 0.022933065 0.072903807 1.137249794 0.373651044 SSEEIESAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSEEIESAFR 10 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFH4 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 165.15 1.38E-05 285320000 350520 449830 396360 439160 490520 540790 455030 463790 412100 419870 FALSE TRUE 364358.8003 527084.8033 406689.4672 526024.5372 407141.5856 415199.7183 419363.5596 457573.6537 397268.6015 502135.4876 0.725618502 1.049686422 0.809919787 1.047574908 0.810820178 0.826867904 0.835160171 0.911255358 0.791158186 1 18.93771716 SSEIEQAVQSLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSEIEQAVQSLDR 13 0 Q9BPX5 Q9BPX5 ARPC5L Actin-related protein 2/3 complex subunit 5-like protein 0 ; 121.02 0.00058509 71884000 83551 97538 87172 87947 118730 123891 101401 101809 98916 98507 FALSE TRUE 86849.658 114289.3928 89443.77393 105342.6541 98548.31701 95119.19284 93452.92466 100444.4169 95356.03248 117807.5606 0.737216334 0.970136315 0.759236279 0.894192644 0.83651946 0.807411615 0.793267632 0.852614351 0.80942201 1 16.84607261 -1.48281985 5.959850334 1.000138603 0.832471766 0.394207729 0.063495199 0.000103314 8.97E-06 0.054317038 0.012792112 0.032898807 1.48281985 -0.167666837 SSELEGDTITLKPRPSADLTNSSAPS(ph)PSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSELEGDTITLKPRPSADLTNSSAPSPSHK 30 2 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 SSELEGDTITLKPRPSADLTNSS(0.001)APS(0.998)PS(0.001)HK 171.93 6.17E-13 293460000 121410 65033 91787 70972 133220 117010 93992 99934 102140 54846 TRUE FALSE 126203.3605 76201.91186 94179.04462 85010.04977 110575.312 89836.2008 86624.66144 98594.54819 98464.00135 65592.02361 1.924065665 1.16175577 1.435830753 1.296042493 1.685804247 1.369620815 1.320658468 1.503148443 1.501158158 1 16.00123276 -1.726181942 2.753752322 0.92038226 1.452282427 0.31839628 0.203797247 18777994.27 16226265.2 10297464.63 0.044485261 0.018785297 1.726181942 0.531900166 SSEMS(ph)PVPMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSEMSPVPMR 10 0 E9PCH4;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;Q8TEU7;Q8TEU7-4;D6RE77;B7Z7Y1;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 SSEMS(1)PVPMR;SSEMS(1)PVPMR;S(0.001)S(0.006)EMS(0.993)PVPMR 136.81 0.00011319 866630000 591457 822260 788040 782810 941360 991250 699680 788150 695380 677180 TRUE FALSE 614808.1791 963476.7587 808576.9698 937647.4815 781347.9634 761047.21 644837.2533 777586.1384 670353.4096 809860.4556 0.759153228 1.189682435 0.998415177 1.157788944 0.964793327 0.93972635 0.796232547 0.960148298 0.827739403 1 19.62731382 2.844115609 3.056861598 0.896697051 1.037096431 0.171887061 0.122101222 0.384866045 6.904741819 0.03695651 0.039302281 698.4182978 -2.844115609 0.140399379 SSENFDELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSENFDELLK 10 0 P29762 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 125.74 0.00093304 39912000 97848 73522 89147 78648 117570 107990 98054 92060 100390 71856 FALSE TRUE 101711.1146 86148.83158 91470.24406 94204.33966 97585.49339 82910.9591 90368.27126 90826.08628 96776.98351 85934.80743 1.183584599 1.002490541 1.064414372 1.096230299 1.135575866 0.964812299 1.051591014 1.056918483 1.126167456 1 16.39095499 2.775280119 24.99567281 1.045452702 1.089445665 0.180577654 0.058716925 1293.072806 880217.4632 0.017659689 0.018730319 596.0464678 -2.775280119 0.043992963 SSEPVKETVQTT(ph)QSPTPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKET(0.002)VQT(0.09)T(0.499)QS(0.409)PTPVEK 263.57 2.72E-36 1395300000 1097900 581630 973680 585030 1140900 1108700 1098600 886930 1082300 493120 TRUE FALSE 1141245.94 681520.428 999054.9007 700747.1879 946970.2255 851221.2275 1012488.861 875042.1541 1043348.234 589737.4226 1.935176395 1.15563368 1.694067329 1.188235918 1.605748913 1.443390219 1.716846892 1.483782647 1.769174203 1 19.16971322 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 SSEPVKETVQTT(0.002)QS(0.998)PTPVEK;SSEPVKETVQTTQS(1)PTPVEK;SSEPVKETVQTTQS(0.991)PT(0.009)PVEK;SSEPVKETVQTTQS(1)PTPVEK 333.71 3.85E-80 2238960000 2705090 1444050 2176230 1491320 2767520 2702640 2779210 2237360 2372380 1224941 TRUE FALSE 2811889.042 1692054.354 2232944.342 1786298.645 2297097.939 2074992.819 2561368.258 2207371.849 2286998.507 1464944.736 1.919450593 1.155029478 1.524251589 1.219362479 1.568044092 1.416430783 1.748440194 1.506795304 1.561150022 1 20.48241481 SSEPVQADESQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;SSEPVQADES(0.01)QS(0.99)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR;SSEPVQADESQS(1)PR 392.56 4.01E-114 6350640000 3235276 3725570 3391480 3553907 3742856 4335329 3478167 3556761 3331465 3067098 TRUE FALSE 3363007.195 4365407.667 3479864.755 4256859.197 3106646.674 3328514.542 3205539.182 3509088.436 3211566.225 3668037.13 0.916841099 1.190120904 0.948699436 1.160527837 0.846950716 0.907437527 0.873911323 0.956666553 0.875554448 1 21.80657681 3.228253014 24.99999373 0.908706026 1.056242022 0.393681811 0.087496853 188.9150256 458192.6749 0.022850531 0.027596022 1691.426046 -3.228253014 0.147535996 SSEPVQHEESIRKPS(ph)PEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSEPVQHEESIRKPSPEPR 19 2 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 SSEPVQHEES(0.003)IRKPS(0.997)PEPR;SSEPVQHEES(0.001)IRKPS(0.999)PEPR;SSEPVQHEES(0.003)IRKPS(0.997)PEPR;SSEPVQHEESIRKPS(1)PEPR;SSEPVQHEESIRKPS(1)PEPR;SSEPVQHEES(0.015)IRKPS(0.985)PEPR 244.26 8.69E-25 11820050000 5900700 5760780 6545800 4773923 8609550 8464580 6825870 6815800 7523340 6018990 TRUE FALSE 6133664.192 6750149.152 6716388.925 5718190.721 7146101.766 6498809.577 6290840.473 6724445.349 7252576.463 7198295.85 0.852099486 0.937742668 0.933052637 0.794381176 0.992749106 0.902826129 0.873934693 0.93417185 1.007540759 1 22.77922397 1.366165763 3.393940104 1.004706553 0.900949513 0.405455823 0.050425735 0.234135888 4.40064486 0.03845094 0.01245273 23.23623517 -1.366165763 -0.103757041 SSESPS(ph)SSPSS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.467)S(0.467)S(0.066)PS(0.011)S(0.989)PAR 165.89 5.69E-06 185750000 248260 270870 283220 298620 318500 369000 303680 294230 268050 249210 TRUE FALSE 258061.4965 317389.8154 290600.9459 357686.1447 264361.4838 283305.3422 279876.7681 290286.3281 258402.9329 298037.9281 0.865867972 1.064930955 0.97504686 1.200136328 0.887006179 0.950568084 0.939064266 0.97399123 0.867013586 1 18.18513641 SSESPSS(ph)SPSS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.035)S(0.965)SPS(0.001)S(0.999)PAR 236.67 4.16E-17 140870000 169650 180940 191820 211780 206630 256930 198080 206440 183630 174390 TRUE FALSE 176347.913 212015.0375 196818.9868 253669.4519 171507.1064 197261.9013 182553.972 203673.0095 177021.1922 208558.3816 0.845556585 1.016574044 0.943711709 1.216299484 0.822345787 0.945835405 0.875313524 0.976575518 0.848784838 1 17.67009177 SSESPSS(ph)SPSS(ph)PARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 2 SSESPS(0.003)S(0.976)S(0.022)PS(0.271)S(0.728)PARK;SSESPS(0.023)S(0.976)S(0.002)PS(0.2)S(0.798)PARK 152.89 9.62E-06 1188150000 1560050 1189860 1555320 1077370 1935520 1962910 1558010 1442220 1570030 1089490 TRUE FALSE 1621641.979 1394209.199 1595852.917 1290470.57 1606521.002 1507053.901 1435889.105 1422889.4 1513524.927 1302954.706 1.244588144 1.070036581 1.22479539 0.990418596 1.232983 1.156643354 1.102025342 1.092048245 1.161609778 1 20.3133555 -4.999999982 0.173566785 0.461260569 1.167188344 0.247143757 0.075925538 185.4487599 1.763899505 34.40967202 0.239103397 1.00E-05 4.999999982 0.705927775 SSESPSSSPS(ph)SPARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSS(0.002)S(0.016)PS(0.49)S(0.49)PARK 56.215 0.080941 59866000 32964 27763 37057 29008 50528 47903 44325 41981 44644 28654 TRUE FALSE 34265.44417 32531.07928 38022.73586 34745.69582 41939.26861 36778.25423 40850.69068 41418.31336 43037.27116 34268.20269 0.999919502 0.94930801 1.109563178 1.013934 1.223853757 1.073247248 1.192087343 1.208651464 1.255895197 1 15.06458291 3.697083059 0.895950826 1.176290393 0.965023192 0.376186016 0.083136456 0.654929771 0.970692073 0.031241827 0.099885718 4978.322867 -3.697083059 -0.211267201 SSESPSSSPSS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSESPSSSPSSPAR 14 0 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSSPS(0.002)S(0.998)PAR;SSESPSSSPSS(1)PAR 244 1.52E-17 378460000 393610 451830 556790 504180 558040 677990 605260 559510 533390 466860 TRUE FALSE 409150.0267 529428.2878 571300.4048 603905.2992 463184.5601 520537.0975 557818.1396 552010.6836 514193.3981 558332.2784 0.732807403 0.948231561 1.023226539 1.081623475 0.829585854 0.932307011 0.999079153 0.988677719 0.92094514 1 19.09076444 4.731240121 4.328357765 0.972088547 0.716616175 0.553662621 0.063988013 0.15008779 6.708486184 0.015681506 0.116848178 53856.74732 -4.731240121 -0.255472372 SSESPSSSPSS(ph)PARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSESPSSSPSSPARK 15 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 SSESPSSSPS(0.026)S(0.974)PARK;SSESPSSS(0.001)PS(0.141)S(0.858)PARK 193.19 6.32E-08 406070000 170824 144614 217162 163267 266540 248080 225090 197951 236040 149911 TRUE FALSE 177568.2634 169450.3296 222821.4201 195560.7253 221233.626 190467.1797 207446.8576 195297.7906 227544.9665 179283.1902 0.990434537 0.945154587 1.242846135 1.09079231 1.233989789 1.062381696 1.157090396 1.089325722 1.26919298 1 17.4518807 4.255082183 24.9956135 1.142765696 0.967794444 0.420098211 0.082433521 205.4361596 310800.7351 0.01804179 0.049111338 17992.11354 -4.255082183 -0.174971252 SSETGAFRVPS(ph)PGMEEAGCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSETGAFRVPSPGMEEAGCSR 21 1 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 SSETGAFRVPS(1)PGMEEAGCSR 83.879 0.0018948 159050000 74255 103710 93892 74533 117190 111720 75191 93192 90532 113610 TRUE FALSE 77186.64474 121521.3857 96338.90265 89275.40494 97270.08566 85774.72313 69297.33294 91942.91367 87273.771 135869.7043 0.568093124 0.894396484 0.709053598 0.657066308 0.715907098 0.631301316 0.510027848 0.676699152 0.642334297 1 17.05186428 -0.962026111 4.402110642 1.000008377 0.668865337 0.51889696 0.096120885 10700646.7 4862267.075 864.5561901 0.022669462 0.109137472 0.962026111 -0.33114304 SSFASSSASDASKPSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 SSFASSSASDAS(0.002)KPS(0.129)S(0.87)PR 106.73 0.00026674 129280000 201750 133530 176320 134110 221750 243400 199940 175540 192760 105500 TRUE FALSE 209715.2458 156462.7388 180915.044 160636.5577 184057.0142 186874.0388 184268.1804 173187.1734 185822.6053 126170.7051 1.662154822 1.240087695 1.433891044 1.273168424 1.458793577 1.481120666 1.460467232 1.372641718 1.472787246 1 16.94501745 -1.286091654 4.028755698 0.999451312 1.418741773 0.56817947 0.111745563 7939895.526 2534736.26 38697.84084 0.02389313 0.051749761 1.286091654 0.41929046 SSFATCVLVSEEDKHAIIVEPEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSFATCVLVSEEDKHAIIVEPEKR 24 2 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;; 258.48 3.70E-44 2167679000 2828580 1437631 2426550 1502630 3465830 2967750 3231560 2371670 2769980 1468833 FALSE TRUE 2940254.523 1684532.941 2489787.886 1799845.729 2876709.455 2278535.039 2978261.883 2339881.643 2670288.961 1756622.704 1.673811067 0.958961157 1.417372029 1.024605754 1.637636499 1.297111232 1.695447677 1.332034271 1.520126636 1 20.74437292 3.232297247 24.99998292 1.437156204 1.257184518 0.064408723 0.260351232 332.364534 1326618.215 0.067649054 0.082760505 1707.250493 -3.232297247 -0.179971686 SSFDWLTGSSTDPLVDHTS(ph)PSSDSLLFAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 1 SSFDWLTGSSTDPLVDHT(0.02)S(0.782)PS(0.02)S(0.02)DS(0.157)LLFAHK;SSFDWLTGSSTDPLVDHT(0.186)S(0.72)PS(0.039)S(0.039)DS(0.016)LLFAHK;SSFDWLTGSSTDPLVDHT(0.047)S(0.932)PS(0.018)S(0.004)DSLLFAHK;SSFDWLTGSSTDPLVDHT(0.013)S(0.971)PS(0.013)S(0.003)DS(0.001)LLFAHK 259.78 4.83E-58 950490000 284832 316661 485335 412706 517868 456390 477355 456489 472429 320188 TRUE FALSE 296077.3873 371045.0635 497983.2288 494338.015 429840.9823 350400.3392 439938.6678 450370.5116 455426.3726 382922.7082 0.773204046 0.968981613 1.300479752 1.290960302 1.122526748 0.915068058 1.148896783 1.176139471 1.189342817 1 18.54669369 4.485085556 4.656629137 1.147720518 0.806698468 0.519542999 0.111807525 0.143105237 8.132762838 0.028704739 0.105575032 30555.22991 -4.485085556 -0.34102205 SSFFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SSFFSDR 7 0 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 0 ;;;;;; 130.04 0.0083798 2983280000 2339070 3001680 2767050 2677460 3330640 3579700 2810460 2799710 2606410 3149960 FALSE TRUE 2431418.29 3517195.19 2839161.596 3207053.597 2764499.002 2748368.926 2590168.801 2762184.467 2512605.813 3767134.352 0.645429141 0.933652708 0.753666137 0.851324454 0.733846671 0.729564881 0.687570062 0.733232268 0.666980675 1 21.84503606 3.20926035 24.6615961 0.738526527 0.802824027 0.006353985 0.110847678 472.1338725 397386.3759 0.029233879 0.034946445 1619.050331 -3.20926035 0.064297501 SSFFSDRGS(ph)GSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSFFSDRGSGSR 12 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;A0A087WX09;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6 A0A0D9SFB3;A0A2R8YFS5 DDX3X ATP-dependent RNA helicase DDX3X 1 SSFFSDRGS(0.954)GS(0.046)R;SSFFSDRGS(0.943)GS(0.057)R;SSFFSDRGS(0.945)GS(0.055)R;SSFFSDRGS(0.934)GS(0.066)R;SSFFSDRGS(0.999)GS(0.001)R 174.21 1.88E-05 1507520000 794547 825250 1214240 791577 1593690 1174300 1003570 979730 1151540 1469990 TRUE FALSE 825916.3291 966980.2679 1245884.092 948148.568 1322795.143 901586.6217 924907.5611 966598.3219 1110096.3 1758006.396 0.469802801 0.550043658 0.708691444 0.539331694 0.752440461 0.512846042 0.526111602 0.549826397 0.631451798 1 20.74550889 0.818034956 4.617406291 0.999994563 0.578661939 0.69745161 0.083228616 1.247852035 31.2372679 0.078521099 0.01991177 6.577107738 -0.818034956 -0.421332623 SSFLSS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSFLSSPER 9 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 SSFLS(0.031)S(0.969)PER 114.89 0.0016408 76296000 137330 173330 148270 152370 238290 239400 163030 167320 157630 257560 TRUE FALSE 142751.8944 203098.0792 152134.038 182508.3312 197785.5509 183802.9781 150251.2826 165077.3491 151956.9271 308023.9507 0.463444138 0.659358075 0.493903275 0.592513442 0.642110948 0.596716514 0.487790908 0.535923745 0.493328284 1 18.23268301 -1.421474212 3.355388703 1.005089644 0.55420461 0.810124584 0.065103161 26028173.9 37852457.02 1282979.942 0.015182243 0.037890103 1.421474212 -0.450885034 SSFREEDNTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSFREEDNTYR 11 1 O43747;O43747-2;H3BNR4;H3BR36;H3BUN9;H3BN71;B4DGE1;H3BRM7;H3BN75;H3BS13;H3BV30 O43747 AP1G1 AP-1 complex subunit gamma-1 0 162.93 0.0010756 0 111900 125490 104180 97133 128390 154960 91505 106690 103970 116070 FALSE TRUE 116317.8984 147041.9313 106895.0164 116345.6175 106566.3137 118972.8884 84332.599 105259.9951 100228.14 138811.6942 0.837954605 1.059290661 0.770072125 0.838154294 0.76770415 0.857081164 0.60753238 0.758293425 0.722043921 1 17.08276959 4.213623032 24.70997975 0.774420479 0.948622611 0.245983477 0.108256544 196.1651003 194374.9926 0.025310066 0.05471385 16353.96381 -4.213623032 0.174202132 SSFSQHAR ddPTM_MDA-MB-175_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 0 ;;; 159.28 0.00036011 1695720000 180864 1556010 1251430 1262020 2148240 2122040 1143050 1389500 1136910 2965520 FALSE TRUE 188004.6504 1823242.613 1284043.294 1511643.789 1783082.932 1629228.37 1053454.754 1370876.025 1095992.831 3546556.866 0.053010471 0.514088081 0.362053491 0.42622855 0.502764512 0.459383123 0.297035912 0.386537162 0.309030102 1 21.75798765 -1.312003859 5.177420579 1.000170514 0.37796691 0.691205788 0.126604377 0.000231008 3.07E-05 0.113639511 0.026777862 0.048752416 1.312003859 -0.622203604 SSFTPS(ph)SPENVIGDFLLQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 S(0.009)S(0.009)FT(0.067)PS(0.457)S(0.457)PENVIGDFLLQDR;S(0.001)S(0.001)FT(0.009)PS(0.494)S(0.494)PENVIGDFLLQDR 92.31 0.0010761 14014900 20365.1 24845 22362 23835 27519 26408 23886 24964 22551 21966 TRUE FALSE 21169.12987 29111.93548 22944.77209 28549.49186 22841.33021 20275.14222 22013.75291 24629.39841 21739.39392 26269.81714 0.805834687 1.108189499 0.873427172 1.086779238 0.869489502 0.771803706 0.83798653 0.937555 0.827542643 1 14.68111854 3.077364251 24.9999931 0.868336714 0.972537159 0.170370661 0.101536013 53.66754033 17339.94956 0.027398642 0.032747639 1194.989946 -3.077364251 0.104200446 SSFTPSS(ph)PENVIGDFLLQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSFTPSSPENVIGDFLLQDR 20 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 SSFTPS(0.124)S(0.876)PENVIGDFLLQDR;SSFTPS(0.101)S(0.899)PENVIGDFLLQDR;SSFTPS(0.136)S(0.864)PENVIGDFLLQDR;SSFTPS(0.108)S(0.892)PENVIGDFLLQDR 152.32 6.90E-08 161762000 137653 177007 167633 172293 188856 225169 176312 171421 169317 175196 TRUE FALSE 143087.6467 207406.5753 172001.6537 206372.0412 156754.3246 172876.9122 162492.2047 169123.3819 163223.3142 209522.3019 0.682923228 0.989902142 0.820922891 0.984964557 0.748151023 0.825100291 0.775536558 0.807185585 0.779025969 1 17.67674429 3.204957212 24.99961015 0.809607654 0.874783547 0.037957597 0.103668554 452.4577354 336609.3943 0.027324921 0.032661173 1603.087443 -3.204957212 0.065175893 SSFVCVLLSHGEEGIIFGTNGPVDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSFVCVLLSHGEEGIIFGTNGPVDLK 26 0 P42574;A8MVM1 P42574 CASP3 Caspase-3;Caspase-3 subunit p17;Caspase-3 subunit p12 0 ; 108.44 0.002602 90946000 85977 69077 80225 78741 104013 107230 112875 89581 79822 69898 FALSE TRUE 89371.43835 80940.43741 82315.72941 94315.73478 86332.90741 82327.45759 104027.5626 88380.31322 76949.22181 83593.17482 1.069123628 0.9682661 0.984718305 1.128270759 1.032774597 0.984858606 1.244450432 1.057267096 0.920520389 1 16.35109753 3.775826704 24.87996589 1.062765503 1.003459011 0.045240991 0.08624054 1421.584325 949087.8935 0.02220833 0.040035877 5967.971001 -3.775826704 -0.059306492 SSFVSDNS(ph)LNRSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSFVSDNSLNRSPR 14 1 Q6UB98-2;Q6UB98 Q6UB98-2 ANKRD12 Ankyrin repeat domain-containing protein 12 1 SSFVSDNS(0.629)LNRS(0.37)PR 64.507 0.071552 0 106330 129710 118280 98597 144070 174250 115160 128200 123240 131210 TRUE FALSE 110527.9905 151986.6835 121362.474 118099.1923 119581.0329 133783.0783 106133.4583 126481.6887 118804.6165 156918.0873 0.704367434 0.968573388 0.773412906 0.752616823 0.762060224 0.852566333 0.676362171 0.80603639 0.757112316 1 17.25965213 -1.092552548 4.010958828 1.000046613 0.786060774 0.414030199 0.077157605 23150246.45 38909512.31 14148.7602 0.017529651 0.080806715 1.092552548 -0.213985839 SSGEIVYCGQVFEKS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 265.95 2.59E-31 3244330000 3051360 1930620 2672400 2072500 3288470 3283170 3205690 3012560 3076330 1796510 TRUE FALSE 3171830.049 2262188.967 2742044.939 2482434.314 2729497.044 2520703.524 2954419.641 2972181.561 2965613.484 2148501.738 1.476298572 1.052914655 1.276259121 1.155425788 1.27041882 1.173237833 1.375106936 1.383374055 1.380317005 1 21.03489951 2.237383172 24.99999651 1.32588447 1.225849216 0 0.148249041 73.89984233 1569003.04 0.04938058 0.038518123 172.7361245 -2.237383172 -0.100035254 SSGFFSSFEES(ph)DIENHLISGHNIVQPTDIEENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGFFSSFEESDIENHLISGHNIVQPTDIEENR 33 0 C9JIE2;Q86TI0-2;Q86TI0 C9JIE2 TBC1D1 TBC1 domain family member 1 1 S(0.01)S(0.01)GFFS(0.294)S(0.294)FEES(0.392)DIENHLIS(0.001)GHNIVQPTDIEENR 93.983 0.00034381 45096000 8533.5 17029 20551 14064 27577 21550 16065 21051 20879 21934 TRUE FALSE 8870.409169 19953.59828 21086.57594 16845.81722 22889.47139 16545.33909 14805.78332 20768.84578 20127.56887 26231.54735 0.33815806 0.760671798 0.803863213 0.642196856 0.872593259 0.630742017 0.564426609 0.791750692 0.767303911 1 14.67901529 -5 0.132430351 2.016274445 0.571575847 0.364635747 0.138452942 170.3483693 1.414198939 45.99991466 0.983934364 1.00E-05 5 -1.444698598 SSGFGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;SSGFGS(1)PR;SSGFGS(1)PR;SSGFGS(1)PR 123.29 0.0014203 1632010000 1863330 2168710 2099430 2033000 2442990 2811360 2214240 2218710 2085080 2006730 TRUE FALSE 1936895.707 2541169.072 2154142.871 2435121.332 2027731.432 2158464.247 2040682.083 2188971.822 2010038.378 2399910.322 0.807070035 1.058860012 0.897593069 1.014671802 0.844919668 0.899393709 0.850315974 0.912105674 0.837547286 1 21.19454907 3.224489668 24.99969279 0.885817225 0.949359863 0.103249948 0.076392533 430.5810676 765007.4444 0.019979556 0.023990103 1676.832444 -3.224489668 0.063542638 SSGGGYGGGPAGGHGGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-2;Q9H2U1;Q9H2U1-3 Q9H2U1-2 DHX36 ATP-dependent RNA helicase DHX36 0 ; 176.25 1.33E-12 49708000 19367.4 27959 31150 30859 28852 32656 31104 26456.2 24987.8 26625.9 FALSE TRUE 20132.03991 32760.74076 31961.79459 36962.8181 23947.74735 25072.13891 28665.9872 26101.59791 24088.49396 31842.73532 0.632233371 1.028829352 1.003738977 1.160792806 0.752063135 0.787373907 0.900236331 0.819703384 0.756483189 1 14.95867665 3.191608694 24.99985414 0.828843975 0.964956334 0.144830926 0.142114969 206.8320547 110128.295 0.040241132 0.048097487 1554.564315 -3.191608694 0.136112359 SSGGGYSGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSGGGYSGDR 10 0 Q92804-2;Q92804;A0A075B7F4 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 ;;; 179.37 4.92E-06 1240790000 501734 607085 598362 548171 668796 759415 633172 634037 570954 596533 FALSE TRUE 521542.8457 711347.1263 613955.8053 656597.5877 555114.2948 583052.3753 583542.3242 625538.7711 550405.4771 713412.22 0.731053984 0.997105329 0.860590537 0.920362126 0.778111559 0.817272762 0.81795953 0.876826544 0.771511143 1 19.4443764 5.033035806 13.36725417 0.862300914 0.368241578 0.220182413 0.077487173 465406.0553 6113625.346 0.01747455 5028518.373 107903.5682 -5.033035806 -0.494059336 SSGGSGGGPLSHFYSGS(ph)PTSYFTSGLQAGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGGSGGGPLSHFYSGSPTSYFTSGLQAGLK 31 0 A0A087WZ13;Q8IY67-2;E9PAU2;K7EQG2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 SSGGSGGGPLSHFYS(0.058)GS(0.923)PT(0.019)SYFTSGLQAGLK 187.68 1.12E-18 262180000 67384 84017 104410 81365 124950 127410 103590 117160 114560 90185 TRUE FALSE 70044.37235 98446.26619 107131.0104 97458.75415 103711.0436 97820.95842 95470.34512 115589.6618 110437.008 107855.0241 0.64943078 0.91276477 0.993287159 0.903608849 0.961578235 0.9069671 0.885172906 1.071713282 1.023939394 1 16.71873386 4.733432445 3.027464066 0.967170765 0.600116006 0.748491336 0.055178278 0.192893509 2.64881341 0.01466992 0.169593717 54129.3042 -4.733432445 -0.367054759 SSGNS(ph)PTPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSGNSPTPVSR 11 0 H0YBT1;O95429-2;O95429 H0YBT1 BAG4 BAG family molecular chaperone regulator 4 1 SSGNS(1)PTPVSR;SSGNS(1)PTPVSR;SSGNS(0.992)PT(0.008)PVSR;SSGNS(0.999)PT(0.001)PVSR 202.8 4.07E-08 1592420000 1137750 1146880 1219920 1090760 1394640 1685220 1246060 1243980 1150980 1109070 TRUE FALSE 1182669.249 1343847.719 1251712.117 1306509.072 1157579.591 1293853.195 1148390.561 1227306.483 1109556.455 1326371.032 0.89165793 1.013176318 0.943711893 0.985025337 0.872741912 0.975483604 0.865813964 0.925311586 0.8365355 1 20.33905297 3.247723913 24.99695648 0.909779235 0.96125733 0.142283505 0.054570947 325.9339334 889124.3497 0.013901383 0.018559741 1768.984034 -3.247723913 0.051478095 SSGNSSSSGSGSGSTSAGS(ph)SSPGAR ddPTM_MDA-MB-175_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 SSGNSSSSGSGSGSTS(0.002)AGS(0.333)S(0.333)S(0.333)PGAR 79.311 0.026341 24174000 18930 25424 16722 33765 21641 41981 25076 19077 18882 27270 TRUE FALSE 19677.37102 29790.37423 17157.78906 40443.61622 17962.47055 32231.54898 23110.4776 18821.30402 18202.44051 32613.03438 0.603359098 0.913449938 0.526102198 1.240105896 0.550775814 0.988302671 0.708627027 0.57710987 0.558133913 1 14.99316106 2.012197941 24.9520393 0.65928718 0.808068774 0.021779419 0.23471828 549.0769193 1123183.883 0.08091418 0.059718298 102.8484951 -2.012197941 0.148781594 SSGNSSSSGSGSGSTSAGSSS(ph)PGAR ddPTM_MDA-MB-175_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 SSGNSSSSGSGSGSTSAGS(0.004)S(0.151)S(0.845)PGAR;SSGNSSSSGSGSGSTSAGS(0.022)S(0.108)S(0.87)PGAR 241.54 1.35E-38 187178000 97609 145993 120123 202090 137967 217830 144872 128174 118253 150158 TRUE FALSE 101462.6787 171066.1621 123253.5041 242062.7988 114515.4186 167242.2837 133516.5541 126456.0372 113997.0976 179578.5852 0.565004333 0.952597783 0.686348564 1.347949137 0.637689725 0.931304162 0.74349931 0.704182167 0.634803407 1 17.45425579 2.212457927 21.95443237 0.741403871 0.863057499 0.024498611 0.223220254 171.6057984 144329.7572 0.07913365 0.058482376 163.1014893 -2.212457927 0.121653629 SSGNSSSSGSGSGSTSAGSSS(ph)PGARR ddPTM_MDA-MB-175_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(0.192)S(0.192)S(0.616)PGARR 77.439 0.013417 100860000 3143.6 7909.5 5387.9 5327.6 5403.3 6996 3122.6 3445.4 2849 9100.7 TRUE FALSE 3267.711755 9267.895098 5528.3131 6381.383379 4484.848996 5371.285025 2877.842453 3399.220049 2746.465047 10883.80792 0.300236074 0.851530564 0.507939238 0.586319 0.412066165 0.49351156 0.264415035 0.312319004 0.252344131 1 13.40989578 -1.086958009 4.723975502 1.000020351 0.443634136 0.481952555 0.173457755 50087069.78 11524730.97 14081.42045 0.042603147 0.081854393 1.086958009 -0.556386214 SSGPTS(ph)LFAVTVAPPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGPTSLFAVTVAPPGAR 18 0 Q00839;A0A1X7SBS1;A0A1W2PP22;Q00839-2;A0A1W2PPS1;A0A1W2PP35 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 S(0.002)S(0.004)GPT(0.158)S(0.836)LFAVTVAPPGAR 97.183 0.0015257 28619000 18035 21143 23658 21253 29485 27465 18484 21272 20264 28074 TRUE FALSE 18747.03573 24774.14578 24274.54692 25456.77997 24473.15023 21086.66999 17035.17578 20986.88363 19534.7026 33574.56279 0.558370211 0.73788439 0.723004111 0.758216276 0.728919402 0.628054939 0.507383399 0.625082857 0.581830439 1 15.03508099 -0.977399757 4.403685557 1.000010579 0.65128054 0.627475858 0.08092918 9742771.115 4425568.175 967.2544368 0.020637454 0.105341681 0.977399757 -0.34873004 SSGPYGGGGQYFAKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-2;P09651;P09651-3;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 ; 316.1 7.13E-58 12013200000 1881470 1877450 1890670 1662660 3055250 2811530 2535520 2542130 2427440 2318570 FALSE TRUE 1955751.888 2199887.433 1939942.413 1991529.185 2535919.696 2158594.767 2336779.317 2508056.905 2340076.909 2772849.4 0.705322074 0.79336708 0.699620547 0.718224793 0.914553707 0.778475299 0.842735749 0.904505274 0.843924992 1 21.40293783 2.389259085 0.164071135 1.074406082 0.584533105 0.679193914 0.053734631 3.707917277 0.359495405 0.341484416 0.595793319 245.0524703 -2.389259085 -0.489872977 SSGRNS(ph)PSAASTSSNDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSGRNSPSAASTSSNDSK 18 1 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 S(0.009)S(0.271)GRNS(0.698)PS(0.022)AASTSSNDSK;S(0.014)S(0.046)GRNS(0.927)PS(0.014)AASTSSNDSK 138.93 5.89E-07 414010000 266680 177495 243419 181417 311350 374710 310920 242060 277860 156474 TRUE FALSE 277208.7323 207978.3855 249762.6991 217300.7411 258426.8382 287689.2813 286549.278 238815.5816 267859.8729 187132.0844 1.481353308 1.111398861 1.334686673 1.161215843 1.380986264 1.537359465 1.531267494 1.276187258 1.431394695 1 17.51369741 3.119451393 11.25067012 1.386677893 1.265222025 0.044728363 0.171277013 0.844318201 78.94593997 0.046703178 0.055841596 1316.59255 -3.119451393 -0.121455868 SSGS(ph)ETEQVVDFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 SS(0.149)GS(0.851)ETEQVVDFSDR 386.49 2.43E-114 532880000 274500 306650 315280 313130 402230 402360 349340 358160 371660 292750 TRUE FALSE 285337.472 359314.7521 323496.4558 375066.1794 333859.0883 308917.9878 321957.818 353359.451 358284.0292 350108.7575 0.814996671 1.026294671 0.923988472 1.071284769 0.953586796 0.882348645 0.919593729 1.009284811 1.023350663 1 18.41744362 4.750245609 24.43934155 0.975382616 0.814996539 0.439103334 0.055434382 1316.754251 2753941.134 0.013441027 0.215973868 56265.94392 -4.750245609 -0.160386077 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 29 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;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.016)S(0.016)GS(0.969)PYGGGYGSGGGSGGYGSR;S(0.024)S(0.024)GS(0.952)PYGGGYGSGGGSGGYGSR;S(0.003)S(0.02)GS(0.977)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.002)GS(0.997)PYGGGYGSGGGSGGYGSR;S(0.004)S(0.004)GS(0.992)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.166)S(0.166)GS(0.666)PY(0.001)GGGYGSGGGSGGYGSR;S(0.134)S(0.134)GS(0.729)PY(0.003)GGGYGSGGGSGGYGSR;S(0.001)S(0.002)GS(0.997)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.004)GS(0.995)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.002)S(0.006)GS(0.991)PYGGGYGSGGGSGGYGSR;S(0.045)S(0.202)GS(0.753)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR 595.73 0 40799844300 3090048.6 3463012.2 3325809.5 3193538.6 3796127.9 4369585.1 3583390.5 3566276.5 3443633.7 3156021.5 TRUE FALSE 3212046.105 4057757.607 3412482.828 3825211.003 3150863.436 3354815.182 3302514.989 3518476.397 3319697.996 3774383.487 0.851012123 1.075078253 0.904116616 1.013466442 0.834802146 0.888837924 0.874981305 0.932198969 0.879533838 1 21.84780958 3.24654259 24.99724058 0.898312264 0.965015358 0.147852045 0.069047611 293.9200784 920468.1081 0.017601475 0.023417204 1764.178763 -3.24654259 0.066703094 SSGSPYGGGYGSGGGSGGYGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;H7C1J8;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 444.65 3.07E-198 83422000 7371.7 9034.1 10926 9830.9 10382 12995 11053 9999.7 7836.8 9090.7 FALSE TRUE 7662.740408 10585.6364 11210.74054 11775.42268 8617.271348 9977.108191 10186.63698 9865.670378 7554.755099 10871.84861 0.704824053 0.973674007 1.031171509 1.083111355 0.792622456 0.91770117 0.93697377 0.907451044 0.694891492 1 13.40830965 3.218077371 24.98773697 0.879123186 0.955942136 0.078626681 0.121193461 633.6852523 773037.8753 0.035105751 0.04200523 1652.256126 -3.218077371 0.07681895 SSHKDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSHKDSPR 8 1 O15042-2;O15042;E7ET15;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 S(0.002)S(0.002)HKDS(0.996)PR;S(0.001)S(0.001)HKDS(0.999)PR;S(0.001)S(0.001)HKDS(0.998)PR;S(0.002)S(0.002)HKDS(0.995)PR;SSHKDS(1)PR;S(0.011)S(0.011)HKDS(0.978)PR 84.817 0.010406 1480645000 1961854 2744135 3419478 2424591 4170846 3994616 4023300 3518454 3693487 2537008 TRUE FALSE 2039309.511 3215418.84 3508592.406 2904167.863 3461887.087 3066926.973 3707943.233 3471294.879 3560559.124 3034086.144 0.672133029 1.059765177 1.156391823 0.957180425 1.140998285 1.010823961 1.222095569 1.144098986 1.173519457 1 21.53283062 4.734535894 3.861138231 1.107508724 0.631267077 0.711771936 0.081193401 0.123419472 3.678914296 0.019126857 0.165578243 54267.01001 -4.734535894 -0.476241648 SSHPEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSHPEDLR 8 0 B0QYR6;Q9UJY5-4;Q9UJY5-3;Q9UJY5;Q9UJY5-6;Q9UJY5-2 B0QYR6 GGA1 ADP-ribosylation factor-binding protein GGA1 0 79.474 0.027943 478360000 199040 445160 394450 405570 437220 552540 407060 416100 387400 478240 FALSE TRUE 206898.2529 521612.7671 404729.691 485790.5355 362901.5006 424220.9588 375153.5735 410522.8601 373457.5497 571941.9715 0.361746931 0.912002953 0.707641179 0.84937032 0.634507553 0.741720279 0.655929434 0.717770124 0.652964056 1 19.12550925 -1.776205119 2.333259845 1.089041678 0.703458888 0.303405825 0.138851414 8649748.175 5519491.829 4393519.573 0.033344682 0.01674152 1.776205119 -0.38558279 SSHYDELLAAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;; 198.74 1.23E-07 3004900000 1098260 2480480 2323430 2351260 2587380 3108830 2273270 2332430 2244190 2495500 FALSE TRUE 1141620.153 2906483.145 2383980.495 2816332.21 2147578.072 2386851.347 2095085.157 2301167.591 2163422.04 2984445.446 0.382523378 0.973877123 0.798801834 0.943670193 0.719590326 0.799763772 0.702001493 0.771053662 0.724899175 1 21.50903145 -2.41587154 1.995965224 2.566010767 0.768468949 0.182454889 0.152464259 5582164.155 484323.4107 39455943.92 0.033916338 0.003838208 2.41587154 -1.797541818 SSHYGGS(ph)LPNVNQIGS(ph)GLAEFQSPLHSPLDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 2 S(0.041)S(0.045)HYGGS(0.914)LPNVNQIGS(0.687)GLAEFQS(0.289)PLHS(0.02)PLDS(0.002)S(0.002)R 77.788 0.00089369 37434000 10091 18927 20320 16435 19475 23693 17708 19474 21644 18187 TRUE FALSE 10489.40047 22177.56502 20849.55589 19685.79395 16164.64646 18190.65982 16320.00069 19212.98288 20865.03667 21750.39444 0.48226254 1.01963967 0.958582887 0.905077561 0.743188658 0.836337009 0.750331252 0.883339515 0.959294634 1 14.40875394 1.285600304 2.793068914 0.992494116 0.828391205 0.179825717 0.139059461 0.479883894 6.197645693 0.119163581 0.03504492 19.3019108 -1.285600304 -0.164102911 SSHYGGS(ph)LPNVNQIGSGLAEFQS(ph)PLHSPLDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 2 S(0.015)S(0.02)HYGGS(0.965)LPNVNQIGS(0.142)GLAEFQS(0.854)PLHS(0.004)PLDSSR 154.9 4.09E-11 40570000 7899.6 16807 17484 18783 17136 20055 13494 17848 17178 14828 TRUE FALSE 8211.482308 19693.47151 17939.6474 22498.22134 14223.22884 15397.53019 12436.30502 17608.77675 16559.76714 17733.2627 0.463055358 1.110538531 1.011638281 1.268701745 0.802064971 0.868285236 0.701298189 0.992980088 0.933825174 1 14.11417038 SSHYGGS(ph)LPNVNQIGSGLAEFQSPLHSPLDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSHYGGSLPNVNQIGSGLAEFQSPLHSPLDSSR 33 0 Q53ET0 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 SSHYGGS(0.999)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(0.915)LPNVNQIGS(0.084)GLAEFQSPLHSPLDSSR;SSHYGGS(0.999)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR;SSHYGGS(1)LPNVNQIGSGLAEFQSPLHSPLDSSR 340.57 2.21E-117 4013680000 177876 814967 798607 758866 743835 998593 602133 847722 703499 843171 TRUE FALSE 184898.6818 954931.2427 819419.3545 908967.4298 617398.1924 766684.9096 554936.2421 836359.6732 678180.2084 1008374.214 0.183363159 0.947000855 0.812614348 0.901418756 0.612270905 0.760317845 0.55032768 0.829413983 0.672548146 1 19.9435997 -4.999999988 0.393562321 5.40153583 0.708887663 0.1567411 0.208426159 1321.388031 9.439524788 4987.714577 0.12356093 1.00E-05 4.999999988 -4.692648167 SSILLDVKPWDDETDMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSILLDVKPWDDETDMAK 18 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 ; 225.87 3.49E-19 2146360000 3309210 1327220 2164540 1383800 3159970 2838330 3319810 2152470 2655840 965500 FALSE TRUE 3439860.166 1555159.711 2220949.691 1657511.51 2622839.428 2179170.873 3059594.617 2123619.66 2560256.837 1154671.239 2.97908188 1.346841991 1.923447658 1.435483498 2.271503211 1.887265222 2.649753898 1.83915524 2.217303722 1 20.13905071 SSILLDVKPWDDETDMAQLEACVR ddPTM_MDA-MB-175_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 ; 68.762 0.035195 140392000 133654 89436 116319 99180 155141 170553 142538 137733 138033 90463 FALSE TRUE 138930.7631 104795.9373 119350.3687 118797.508 128770.1882 130944.6505 131365.4991 135886.9144 133065.2193 108187.4928 1.284166584 0.968651131 1.103180835 1.098070626 1.19025023 1.210349247 1.21423924 1.256031643 1.229950115 1 16.7231742 3.194660349 4.746197011 1.204537948 1.102010752 0.082747624 0.098137962 0.314158189 15.57016245 0.026768229 0.033209353 1565.526232 -3.194660349 -0.102527196 SSKAS(ph)LGS(ph)LEGEAEAEASSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 S(0.465)S(0.497)KAS(0.483)LGS(0.555)LEGEAEAEASSPK;S(0.087)S(0.32)KAS(0.816)LGS(0.778)LEGEAEAEASSPK;S(0.154)S(0.179)KAS(0.728)LGS(0.939)LEGEAEAEASSPK 146.03 6.41E-08 227163000 564396 263917 366415 224583 503568 494355 419971 341765 402620 213055 TRUE FALSE 586678.7899 309242.6918 375964.0759 269004.8471 417971.6912 379548.5433 387052.5756 337184.1992 388129.7848 254799.0481 2.302515627 1.213672869 1.475531713 1.055752952 1.640397381 1.489599534 1.519050321 1.323333826 1.523278002 1 17.95900036 8 0.037300197 7.47E-14 3.73906701 0.248985492 0.300831499 1479.078594 4.208077805 120.3151895 361.808914 99999999.92 -8 3.73906701 SSLDVLPSQVYSLVGSS(ph)PLR ddPTM_MDA-MB-175_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(0.173)S(0.827)PLR 211.43 1.17E-25 0 84539 91247 79397 92858 99993 103400 90801 88455 93269 101140 TRUE FALSE 87876.665 106917.9624 81466.15105 111225.0352 82996.22558 79386.91704 83683.78036 87269.40541 89912.26691 120956.4466 0.726514936 0.883937694 0.673516405 0.919546154 0.686166202 0.656326465 0.691850519 0.721494454 0.74334415 1 16.88412814 -1.149097365 3.640201141 1.000203987 0.743585994 0.456015777 0.083628738 25135733.24 39805625.51 59083.0965 0.019759897 0.070941871 1.149097365 -0.256617993 SSLFPFEDAFLDDSHGDQALSSGLS(ph)SPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALS(0.001)S(0.001)GLS(0.496)S(0.496)PT(0.007)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.698)S(0.293)PT(0.009)R 245.17 7.78E-46 144576000 55580 73518 66960 65939 76026 89048 75214 76733 72352 77446 TRUE FALSE 57774.34132 86144.14461 68705.03261 78981.53739 63103.12768 68367.95154 69318.53014 75704.51964 69748.06565 92620.06091 0.623777838 0.930080846 0.741794293 0.85274763 0.681311662 0.738154897 0.748418102 0.817366334 0.753055709 1 16.49903709 -1.448994168 2.938793217 1.005462253 0.771395951 0.425010634 0.081648103 11758367.99 14029619.68 534589.6308 0.018457356 0.035563609 1.448994168 -0.234066302 SSLFPFEDAFLDDSHGDQALSSGLSS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLFPFEDAFLDDSHGDQALSSGLSSPTR 29 0 Q8NE35-2 Q8NE35-2 1 SSLFPFEDAFLDDSHGDQALSSGLS(0.121)S(0.709)PT(0.171)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.29)S(0.706)PT(0.005)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.148)S(0.703)PT(0.148)R;SSLFPFEDAFLDDSHGDQALSSGLS(0.188)S(0.706)PT(0.106)R 299.14 3.84E-81 541459000 152070.1 220579.7 202447.2 207183.7 243795.3 295858.3 209705.5 238862.7 229344.2 236391.1 TRUE FALSE 158073.945 258462.5476 207723.1403 248164.0175 202355.062 227149.6936 193268.2349 235661.1362 221090.147 282707.4101 0.559143267 0.914240442 0.734763692 0.877812214 0.715775586 0.803479801 0.683633425 0.833586697 0.782045815 1 18.10895017 0.190907424 0.943980281 1.001820944 0.768681353 0.346421771 0.096526207 4.275549109 4.089237934 0.102637228 0.026932 1.552056133 -0.190907424 -0.233139591 SSLFPIDDGLLDDGHSDQVGVLNS(ph)PTCYSAHQNGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLFPIDDGLLDDGHSDQVGVLNSPTCYSAHQNGER 36 0 A0A5K1VW61;A0A5K1VW79;A0A5K1VW71;A0A5K1VW93;Q7Z5Q1-7;Q7Z5Q1-5;Q7Z5Q1-4;Q7Z5Q1-6;Q7Z5Q1-3;Q7Z5Q1;Q7Z5Q1-8;Q7Z5Q1-9 A0A5K1VW61 CPEB2 Cytoplasmic polyadenylation element-binding protein 2 1 SSLFPIDDGLLDDGHSDQVGVLNS(0.808)PT(0.186)CY(0.003)S(0.003)AHQNGER 126.83 3.12E-08 40292000 10780 18647 16089 19142 18999 26955 17003 20577 17449 21902 TRUE FALSE 11205.60272 21849.4772 16508.29256 22928.23047 15769.55677 20695.10976 15670.26043 20301.19897 16821.0139 26193.27756 0.427804527 0.834163542 0.630249213 0.875347898 0.602045954 0.790092409 0.598255044 0.775053787 0.642188205 1 14.67690897 -2.285877253 2.20777376 2.296152307 0.69701438 0.348054399 0.128092258 4730768.185 525331.7824 30748169.85 0.027894944 0.005177531 2.285877253 -1.599137927 SSLFS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 S(0.042)S(0.103)LFS(0.856)PR;S(0.002)S(0.007)LFS(0.991)PR;SS(0.002)LFS(0.998)PR 91.265 0.01734 269621000 436300 440860 432770 417680 547210 593910 495570 481530 437700 465430 TRUE FALSE 453525.4609 516574.2756 444048.3417 500295.8573 454195.4397 455983.4033 456725.9285 475075.878 421947.2625 556622.0973 0.814781632 0.928052045 0.797755504 0.898807036 0.815985283 0.819197451 0.820531435 0.853498056 0.758049787 1 19.08633866 4.221116681 24.99710707 0.839666871 0.871416923 0.017385215 0.067508937 784.4263324 1124084.611 0.01511684 0.032773399 16638.59617 -4.221116681 0.031750052 SSLGQSAS(ph)ETEEDTVSVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLGQSASETEEDTVSVSK 19 0 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(0.999)ET(0.001)EEDTVSVSK 310.92 1.68E-61 94390000 97984 68062 91594 77261 103700 118250 119720 87871 95778 57694 TRUE FALSE 101852.484 79751.11905 93981.01489 92542.9952 86073.11104 90788.2296 110336.0336 86693.23297 92330.96849 68998.03468 1.476165002 1.155846241 1.36208249 1.341241031 1.247471923 1.315808921 1.599118498 1.256459454 1.338168093 1 16.07426765 0.319503837 1.736448106 1.000005175 1.342018812 0.438597268 0.116643021 7.851403837 18.86656329 0.107153285 0.030087574 2.086910562 -0.319503837 0.342013637 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSLGQSASETEEDTVSVSKK 20 1 Q13435;E9PPJ0;H0YCG1;E9PJ04 Q13435 SF3B2 Splicing factor 3B subunit 2 1 SSLGQSAS(0.796)ET(0.204)EEDTVSVSKK;SSLGQSAS(0.97)ET(0.03)EEDTVSVSKK;SSLGQS(0.001)AS(0.992)ET(0.007)EEDTVSVSKK;SSLGQSAS(0.801)ET(0.199)EEDTVSVSKK 308.65 2.01E-66 1931550000 1956870 1018710 1551250 1025560 2042860 1901580 1591090 1460970 1929860 902480 TRUE FALSE 2034128.739 1193665.518 1591676.849 1228412.707 1695615.387 1459966.864 1466376.208 1441388.087 1860404.716 1079303.677 1.884667663 1.10595891 1.47472568 1.13815299 1.571027157 1.35269331 1.358631717 1.335479641 1.723708309 1 20.04166941 -1.861767106 2.853330603 0.83361232 1.412620579 0.239437688 0.230300749 64680519.97 61077365.29 73917090.51 0.049814572 0.01374779 1.861767106 0.579008259 SSLLDDLLTESEDMAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLLDDLLTESEDMAQR 17 0 O00429-3;O00429-5;O00429-2;O00429;O00429-8;O00429-6;O00429-7;O00429-4;O00429-9 O00429-3;O00429-4 DNM1L Dynamin-1-like protein 0 166.48 5.45E-09 9654000 17205 11190 16856 12084 21058 20112 19227 17677 17757 13843 FALSE TRUE 17884.26669 13111.79545 17295.28121 14474.17913 17478.56868 15441.2928 17719.9375 17440.06873 17117.92904 16555.27081 1.080276299 0.792001267 1.044699383 0.874294314 1.055770629 0.93271158 1.070350205 1.053445089 1.033986652 1 14.01500299 2.616356316 1.239895168 1.04369234 0.948557237 0.120586924 0.085802774 0.745611635 2.343121405 0.039475892 0.032853904 413.3865249 -2.616356316 -0.095135102 SSLS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSLSPGR 7 0 Q9BUQ8;F8VVA2;F8W1J5 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 1 SSLS(1)PGR 133.05 0.0034712 1401200000 2243900 2092800 2174500 2012100 2448900 2573700 2284600 2111200 2111400 1984100 TRUE FALSE 2332490.905 2452222.12 2231169.256 2410087.374 2032636.853 1975997.18 2105527.082 2082902.817 2035411.126 2372846.407 0.982992788 1.033451686 0.940292321 1.015694639 0.856623862 0.832753934 0.88734234 0.877807687 0.857793037 1 21.17818729 3.237641831 24.99988922 0.877056776 0.992217032 0.543859861 0.047964047 16.33435067 444458.994 0.012641332 0.015964637 1728.390344 -3.237641831 0.115160256 SSMIT(ph)SLEGLGTDNVFSLHEDNHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.015)S(0.015)MIT(0.485)S(0.485)LEGLGTDNVFSLHEDNHYR;S(0.025)S(0.025)MIT(0.475)S(0.475)LEGLGTDNVFSLHEDNHYR 114.2 0.0034739 45884000 6900.5 12075 11029.2 12587.3 7676.9 13786.3 9171.9 10250.1 8042 11221.5 TRUE FALSE 7172.937068 14148.78732 11316.63001 15077.03037 6371.98328 10584.64076 8452.982512 10112.71418 7752.569991 13420.13808 0.534490556 1.054295212 0.843257346 1.123463133 0.47480758 0.788713253 0.629872991 0.7535477 0.577681835 1 13.71211189 3.237568139 24.99995709 0.695057394 0.897433631 0.175191679 0.195467739 40.59528204 1022584.765 0.051165487 0.064561861 1728.097092 -3.237568139 0.202376237 SSMITS(ph)LEGLGTDNVFSLHEDNHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSMITSLEGLGTDNVFSLHEDNHYR 25 0 Q8IZQ1-2;Q8IZQ1 Q8IZQ1-2 WDFY3 WD repeat and FYVE domain-containing protein 3 1 S(0.001)S(0.001)MIT(0.131)S(0.867)LEGLGTDNVFSLHEDNHYR;S(0.003)S(0.003)MIT(0.128)S(0.866)LEGLGTDNVFSLHEDNHYR 153.84 1.56E-07 123403000 16170.9 30474 32253 33216 28520.4 35221 23993.2 25071.9 20409.9 31771 TRUE FALSE 16809.33962 35707.67245 33093.53968 39786.02566 23672.5126 27041.45653 22112.55029 24735.85219 19675.35169 37995.91916 0.442398552 0.939776514 0.870976158 1.047113125 0.623027765 0.711693706 0.581971716 0.651013391 0.517828023 1 15.21355686 3.159490369 24.99999999 0.65767119 0.836587981 0.11400841 0.189255463 54.00577817 17072.09759 0.052084485 0.062252886 1443.744588 -3.159490369 0.178916791 SSNADAEEKLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSNADAEEKLDR 12 1 O60828-2;O60828;A0A5H1ZRR1;O60828-3;O60828-6 O60828-2 PQBP1 Polyglutamine-binding protein 1 0 71.279 0.041053 206440000 208730 154450 157620 128570 261440 248900 211510 191450 197370 123840 FALSE TRUE 216970.8216 180975.586 161727.7067 154000.7623 217000.5222 191096.7471 194931.2935 188883.9259 190266.6923 148104.0769 1.464988851 1.221948712 1.091986865 1.03981447 1.46518939 1.290286878 1.316177769 1.275345891 1.284682341 1 17.17625183 -1.11816719 5.710961112 0.999997541 1.267308922 0.285928266 0.128866486 4.09E-06 6.31E-07 0.126390695 0.029790298 0.076178569 1.11816719 0.267311381 SSNKQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSNKQPK 7 1 O94933 O94933 SLITRK3 SLIT and NTRK-like protein 3 0 59.205 0.063049 401440000 5536.5 340100 266220 373430 166640 353940 224340 284340 202190 350090 FALSE TRUE 5755.085295 398509.5294 273157.9119 447293.3394 138314.5923 271742.799 206755.6446 280528.8874 194913.2214 418683.4326 0.013745672 0.951815855 0.652421115 1.068333028 0.33035602 0.649041204 0.493823324 0.670026243 0.465538414 1 18.67550031 -1.362869626 3.642334379 1.001864682 0.609807512 0.156141966 0.283168785 146951740.7 276007460.9 3047195.475 0.062731916 0.043364104 1.362869626 -0.39205717 SSPAAKPGSTPSRPS(ph)SAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPAAKPGSTPSRPSSAKR 19 3 Q15555-4;Q15555-5;Q15555-3;Q15555;K7EL66;K7ERD8;Q15555-2 Q15555-4 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 SSPAAKPGS(0.01)T(0.01)PS(0.15)RPS(0.691)S(0.138)AKR 95.835 0.0075864 492560000 576540 258400 430520 266130 572650 563530 508260 454690 426520 302020 TRUE FALSE 599302.2444 302778.1899 441739.7049 318769.7197 475311.1575 432658.6979 468421.2531 448595.6243 411169.6285 361195.0365 1.659220598 0.838267859 1.222994948 0.882541806 1.315940446 1.197853387 1.296865144 1.24197616 1.138359022 1 18.46241854 SSPAFGDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 0 ;;; 107.15 0.0045211 325164000 207857 261690 235948 233042 342783 331035 240262 224976 224395 338373 FALSE TRUE 216063.3549 306633.2218 242096.9987 279137.012 284516.8681 254157.1381 221429.6366 221960.5647 216319.0678 404670.7108 0.533923877 0.75773515 0.598256786 0.689788029 0.703082433 0.628059139 0.547184737 0.548496738 0.534555781 1 18.62638891 -1.158188596 4.378167158 1.00007911 0.616449681 0.702687147 0.074995631 6.05E-05 1.16E-05 0.075857281 0.017876057 0.069472256 1.158188596 -0.383629429 SSPCIHYFTGTPDPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPCIHYFTGTPDPSR 16 0 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 ;;; 147.12 1.06E-06 2146080000 641542 1307770 1225440 1159810 1394370 1690430 1244010 1305050 1218300 1196730 FALSE TRUE 666870.5735 1532369.324 1257375.973 1389216.956 1157355.485 1297853.251 1146501.246 1287557.939 1174453.621 1431206.331 0.465949989 1.070683724 0.878542769 0.970661551 0.808657327 0.9068247 0.801073347 0.899631249 0.820603987 1 20.44880024 4.75359048 24.76835961 0.896629716 0.465949638 0.714046595 0.083397305 1263.541386 2082204.681 0.018679365 0.432157981 56700.96883 -4.75359048 -0.430680078 SSPDLTGVVTIYEDLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPDLTGVVTIYEDLRR 17 1 O60784;O60784-4;O60784-2;V9GYF4;B0QY02;V9GZ68;Q6UW50;B0QY01 O60784 TOM1 Target of Myb protein 1 0 234.63 6.20E-20 47572000 22567 28800 27980 26392 30469 32212 25002 25300 28195 28481 FALSE TRUE 23457.96259 33746.17597 28709.18179 31612.25883 25289.89026 24731.25118 23042.27791 24960.89488 27180.26746 34061.30665 0.688698259 0.990748133 0.842867894 0.928098829 0.742481506 0.726080518 0.676494245 0.732822588 0.797980763 1 15.05584616 3.223938211 24.77217103 0.754566214 0.870346813 0.095076865 0.110105012 316.3329695 535906.3127 0.029587192 0.03551128 1674.70459 -3.223938211 0.115780599 SSPGAVAGLSNAPGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;Q9BWG4-2;Q9BWG4;U3KPY3 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 SSPGAVAGLS(0.001)NAPGT(0.999)PR;SSPGAVAGLSNAPGT(1)PR;SSPGAVAGLSNAPGT(1)PR 171.3 1.95E-08 228450000 220184 160719 184211 153949 203643 245291 179374 185964 180485 146556 TRUE FALSE 228877.0343 188321.238 189011.69 184399.6527 169027.8356 188325.8827 165314.1972 183471.4568 173989.3801 175270.8422 1.305847747 1.074458453 1.078397796 1.052084023 0.964380803 1.074484953 0.943192804 1.046788242 0.992688675 1 17.41922649 7.999999799 0.838802704 1.009950726 96.6387737 0.825685522 0.040023371 222.2106501 0.643378994 0.011851696 40518.0122 99999953.68 -7.999999799 95.62882297 SSPLIQFHLLHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPLIQFHLLHSK 13 0 O94973-3;O94973;O94973-2;A0A0G2JQM1;A0A0G2JS82 O94973-3 AP2A2 AP-2 complex subunit alpha-2 0 ; 171.76 1.42E-05 387160000 290845 300370 323750 255064 490790 453000 409930 367880 373800 306687 FALSE TRUE 302327.7852 351956.2109 332187.191 305514.8979 407365.6911 347797.6153 377798.6154 362949.1703 360347.011 366776.4458 0.824283535 0.959593275 0.905693904 0.832973059 1.110664809 0.948255046 1.030051465 0.9895651 0.982470426 1 18.48454147 3.253713358 24.99781712 1.006830269 0.88806561 0.58621813 0.053122862 175.1332987 288919.5681 0.013924382 0.018781667 1793.549461 -3.253713358 -0.118764659 SSPNVANQPPS(ph)PGGK ddPTM_MDA-MB-175_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 1 SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK 219.24 1.92E-12 2216210000 1878600 1231590 1637990 1222200 2000030 2249720 2123910 1752530 1933170 1077560 TRUE FALSE 1952768.579 1443106.002 1680677.365 1463947.512 1660065.615 1727256.625 1957432.384 1729040.202 1863595.589 1288687.251 1.515316131 1.119826398 1.304177848 1.135999065 1.28818347 1.340322583 1.518935167 1.341706609 1.446119365 1 20.29747075 2.759800902 3.970274285 1.366247357 1.2566363 0.003020619 0.163616471 0.544836924 19.77241955 0.048868328 0.049759347 575.176193 -2.759800902 -0.109611057 SSPPAPPLPPGS(ph)GSPGTPQALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 SSPPAPPLPPGS(0.966)GS(0.034)PGTPQALPR;SSPPAPPLPPGS(0.961)GS(0.039)PGTPQALPR 282.97 4.66E-52 806800000 186178 195129 202083 187323 206966 259680 200684 204246 173414 182605 TRUE FALSE 193528.4512 228640.8879 207349.449 224374.9303 171785.9932 199373.2555 184953.8637 201508.4164 167172.864 218382.9536 0.88618845 1.04697223 0.949476347 1.027437932 0.786627301 0.912952464 0.846924454 0.922729605 0.765503265 1 17.73650072 3.251655422 24.99954178 0.872471555 0.980476675 0.319418745 0.075080308 253.1179603 483229.6511 0.019028839 0.025609362 1785.070701 -3.251655422 0.10800512 SSPPAPPLPPGSGS(ph)PGTPQALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 SSPPAPPLPPGS(0.081)GS(0.756)PGT(0.163)PQALPR 245.75 1.63E-37 567100000 102860 120930 108020 102920 115330 152830 108450 113180 103890 104070 TRUE FALSE 106920.9922 141698.7868 110835.0899 123277.2688 95726.24779 117337.5487 99949.40562 111663.0072 100151.0192 124460.524 0.859075543 1.138503859 0.890524051 0.990492928 0.769129397 0.9427692 0.803061103 0.897176098 0.804681003 1 16.9253287 3.271661553 24.99444026 0.86548865 0.976058444 0.210160854 0.094629584 253.818802 191656.2754 0.023801309 0.032225037 1869.224881 -3.271661553 0.110569794 SSPPAPPLPPGSGSPGT(ph)PQALPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPPAPPLPPGSGSPGTPQALPR 23 0 Q9Y3L3;A0A2R8Y5V0 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 SSPPAPPLPPGS(0.106)GS(0.411)PGT(0.483)PQALPR 154.07 4.90E-07 516940000 45816 48698 46505 47647 50812 66380 41542 47586 41224 41777 TRUE FALSE 47624.85106 57061.50268 47716.9585 57071.43439 42174.99439 50964.251 38285.82949 46948.1875 39740.35629 49962.40328 0.953213775 1.142088829 0.955057311 1.142287613 0.844134622 1.020052032 0.766292792 0.939670321 0.795405218 1 15.60855525 3.227901374 24.99945051 0.89160599 1.048220631 0.378848455 0.096506442 199.958756 468968.6934 0.025325562 0.030563965 1690.057086 -3.227901374 0.156614641 SSPS(ph)PALEQPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSPSPALEQPFR 12 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 S(0.002)S(0.01)PS(0.988)PALEQPFR;SSPS(1)PALEQPFR;SSPS(1)PALEQPFR;S(0.001)S(0.01)PS(0.989)PALEQPFR 242.35 2.87E-16 567240000 634850 676670 678890 696500 778780 917660 777490 731050 672760 696910 TRUE FALSE 659914.3682 792882.8087 696582.4311 834265.6212 646403.2538 704547.3723 716548.3022 721251.4705 648547.499 833456.1714 0.791780529 0.951319141 0.835775719 1.000971197 0.775569581 0.84533224 0.859731233 0.865374204 0.778142296 1 19.66874681 4.883410487 15.74911403 0.871979847 0.790614149 0.097009606 0.077225371 34039.73602 3605660.801 0.016999984 2575.512754 76455.80889 -4.883410487 -0.081365698 SSPS(ph)TENMHFPSSISSQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSTENMHFPSSISSQTR 19 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 S(0.129)S(0.129)PS(0.712)T(0.029)ENMHFPSSISSQTR 127.16 1.54E-05 430330000 143920 262330 257580 273250 298030 324490 272580 286350 251560 289470 TRUE FALSE 149602.0727 307383.1369 264292.7464 327298.0344 247370.9671 249132.1152 251214.4673 282511.9466 242506.4047 346186.1043 0.432143494 0.887912984 0.763441233 0.945439549 0.714560648 0.719647935 0.725663059 0.816069574 0.700508778 1 18.40118829 -2.511270697 2.06476215 3.755122555 0.757662012 0.252190325 0.130086936 4601419.699 294733.1372 59371048.97 0.029558593 0.003081267 2.511270697 -2.997460543 SSPSGASS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSPSGASSPR 10 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 SSPSGAS(0.001)S(0.999)PR;SSPSGASS(1)PR 167.84 5.37E-06 954740000 1570020 1785550 1873900 1635120 2004350 2283700 1784760 1880560 1650260 1562870 TRUE FALSE 1632005.602 2092204.323 1922735.373 1958541.856 1663651.303 1753345.285 1644865.848 1855354.169 1590867.465 1869084.454 0.873157764 1.119373883 1.028704385 1.047861616 0.890088888 0.938077079 0.880038269 0.992654005 0.851147984 1 20.83390033 3.243728413 24.99945519 0.927081279 1.025383669 0.279355042 0.07183896 151.2938164 731885.6942 0.01880948 0.024726388 1752.784051 -3.243728413 0.09830239 SSPSGNTQSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSPSGNTQSSPK 12 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 SSPSGNTQS(0.011)S(0.989)PK;SSPSGNT(0.001)QS(0.06)S(0.939)PK;SSPSGNTQS(0.004)S(0.996)PK 110.44 0.00040051 103314000 470950 204273 294338 203937 388446 499460 378457 321565 310015 181349 TRUE FALSE 489543.4697 239355.2987 302008.6901 244275.1299 322418.0877 383467.9844 348792.5514 317254.9471 298857.6207 216880.8644 2.257199919 1.103625713 1.39250962 1.126310201 1.486613808 1.768104279 1.60822188 1.462807463 1.377980586 1 17.72654324 0.798208846 2.075694319 1.00059249 1.504367191 0.205710128 0.310571121 1.22688408 9.053562226 0.284217296 0.078226442 6.283604555 -0.798208846 0.503774701 SSPSTGS(ph)LDSGNESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSPSTGSLDSGNESK 15 0 Q15057;A0A0U1RQT1;A0A087X1H5 Q15057 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 SSPST(0.012)GS(0.988)LDSGNESK 300.33 8.47E-36 0 249360 161070 196810 151460 269910 288300 257720 222140 238020 131140 TRUE FALSE 259204.9253 188732.5195 201939.0303 181418.3359 224030.7946 221346.6942 237519.233 219162.5766 229453.7067 156834.3722 1.652730341 1.203387478 1.287594215 1.156751122 1.428454691 1.411340455 1.514459042 1.397414187 1.46303201 1 17.25888225 SSQKS(ph)PELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSQKSPELGK 10 1 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 S(0.001)S(0.004)QKS(0.995)PELGK 82.543 0.023592 0 60744 32822 40851 28695 53504 57701 57827 42371 46338 24596 TRUE FALSE 63142.22002 38458.92318 41915.61062 34370.78535 44409.40919 44300.81722 53294.36864 41803.08605 44670.30443 29415.11528 2.146590942 1.307454443 1.424968429 1.16847359 1.509747923 1.506056216 1.811802134 1.42114303 1.51861735 1 14.84427007 4.745135915 24.56836027 1.43778224 2.146591355 0.524662643 0.209254025 481.7708573 1800057.345 0.048561713 0.463727302 55607.82585 -4.745135915 0.708809115 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 SSQQPS(0.032)T(0.968)PQQAPPGQPQQGTFVAHK;SSQQPS(0.119)T(0.881)PQQAPPGQPQQGTFVAHK;SSQQPS(0.172)T(0.828)PQQAPPGQPQQGTFVAHK;SSQQPS(0.027)T(0.973)PQQAPPGQPQQGTFVAHK 218.55 5.22E-33 1870550000 1138460 1054020 1216130 978640 1418350 1580090 1223620 1256360 1322200 1045960 TRUE FALSE 1183407.28 1235039.736 1247823.347 1172212.071 1177259.374 1213138.044 1127709.467 1239520.549 1274614.28 1250895.836 0.946047821 0.987324204 0.997543769 0.937098068 0.941133018 0.969815399 0.901521481 0.990906288 1.018961167 1 20.25453023 1.522388508 7.711933096 1.007961014 0.95605751 0.437311073 0.025944637 0.113053687 12.95548512 0.014515738 0.006703986 33.29572747 -1.522388508 -0.051903504 SSQRHS(ph)PPFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSQRHSPPFSK 11 1 Q8WV28-3;Q8WV28;Q8WV28-2 Q8WV28-3 BLNK B-cell linker protein 1 SS(0.007)QRHS(0.992)PPFSK;S(0.005)S(0.005)QRHS(0.991)PPFSK 95.428 0.0046895 273633000 202792 358880 387050 348780 467190 508970 417700 450040 390690 344040 TRUE FALSE 210798.3847 420514.8483 397136.841 417767.643 387777.2107 390769.431 384959.5825 444007.9499 376629.1432 411448.051 0.512332928 1.022036311 0.965217456 1.015359392 0.942469431 0.949741845 0.935621354 1.079134897 0.915374717 1 18.65035076 4.741387166 24.98282864 0.983791876 0.512332757 0.899535534 0.046931241 73.13353411 646366.3737 0.011100309 0.077506321 55129.89504 -4.741387166 -0.471459119 SSQS(ph)ASSLEVAGPGREPLELEVAVEALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSQSASSLEVAGPGREPLELEVAVEALAR 29 1 A0A2R8Y5E4;A0A2R8YFK2;A0A2R8Y6M6;A0A2R8Y4C2;A0A2R8YFS8;A0A2R8Y8C4;A0A2R8Y5C9;A0A2R8Y596;P56945-4;P56945-5;P56945-8;P56945;P56945-7;P56945-3;P56945-2;P56945-6 A0A2R8Y5E4 BCAR1 Breast cancer anti-estrogen resistance protein 1 1 S(0.17)S(0.15)QS(0.601)AS(0.04)S(0.04)LEVAGPGREPLELEVAVEALAR 50.942 0.051271 39907000 0 0 734.25 1082.2 1174 1394.9 894.68 1804.9 0 1336.5 TRUE FALSE 0 0 753.3851582 1296.25593 974.4438993 1070.955615 824.5526438 1780.708268 0 1598.361586 0 0 0.471348389 0.810990417 0.609651726 0.670033379 0.515873661 1.114083498 0 1 10.6423781 4.12137302 3.270711083 0.691102003 1.47E-14 0.465754178 0.284227401 0.190471819 3.976115287 0.068867681 0.175409364 13224.30995 -4.12137302 -0.691102003 SSRFS(ph)GGFGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSRFSGGFGAR 11 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8Y7T2;A0A087WVZ1 A0A0D9SFB3 DDX3X ATP-dependent RNA helicase DDX3X 1 SSRFS(1)GGFGAR;SSRFS(1)GGFGAR 133.48 9.74E-05 561310000 199784 226060 244890 196378 330230 340260 241730 239440 264030 314980 TRUE FALSE 207671.6266 264884.0465 251272.0346 235220.9823 274097.6226 261239.7717 222782.571 236230.6984 254527.6119 376694.3003 0.551300156 0.703180394 0.66704496 0.624434673 0.727639421 0.693506038 0.591414765 0.627115139 0.675687452 1 18.52303468 0.853665432 7.532590594 0.999999956 0.650070451 0.812591393 0.050391387 3.957112498 203.8355103 0.047774362 0.011970962 7.139461098 -0.853665432 -0.349929504 SSRPAS(ph)ASSSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSRPASASSSTK 12 1 Q14686;A0A0D9SFT8;F6M2K2 Q14686 NCOA6 Nuclear receptor coactivator 6 1 S(0.001)S(0.001)RPAS(0.998)AS(0.001)S(0.001)STK 98.281 0.0026934 67755000 71817 59706 73532 64045 97274 105030 90547 74616 80922 54211 TRUE FALSE 74652.39061 69960.04105 75448.30433 76712.90984 80739.40023 80638.37425 83449.68954 73615.89457 78009.63303 64832.60752 1.151463646 1.079087264 1.163740087 1.183245789 1.245351735 1.243793476 1.287156151 1.135476381 1.203246885 1 15.98443198 3.969861995 3.249884306 1.197930993 1.115288813 0.098504616 0.076468676 0.419883816 9.040850502 0.019012698 0.041551171 9329.577894 -3.969861995 -0.082642179 SSRSS(ph)PELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSRSSPELTR 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.001)S(0.001)RS(0.01)S(0.989)PELTR;S(0.005)S(0.005)RS(0.081)S(0.91)PELTR;S(0.004)S(0.004)RS(0.044)S(0.947)PELTR;S(0.001)SRS(0.028)S(0.971)PELTR 121.48 0.00031129 2110090000 431963 460892 514926 362531 592443 653582 458014 506664 467839 479063 TRUE FALSE 449017.2328 540046.6158 528345.3946 434238.5498 491739.7505 501797.4856 422113.6659 499872.9978 451001.5658 572926.2226 0.783726098 0.942611098 0.922187489 0.757931009 0.858295067 0.875850093 0.736767928 0.872491043 0.787189603 1 19.12798985 5.056119856 14.2048038 0.852415994 0.353193068 0.070144033 0.078947676 2349601.368 17040415.29 0.017828108 32139094.86 113794.1289 -5.056119856 -0.499222926 SSS(ph)ADFGTFNTSQSHQTASAVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSADFGTFNTSQSHQTASAVSK 23 0 B8ZZY2;P52594-2;P52594-3;P52594;P52594-4;C9J2I0 B8ZZY2 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 S(0.176)S(0.176)S(0.647)ADFGT(0.001)FNTSQSHQTASAVSK;S(0.129)S(0.129)S(0.742)ADFGTFNTSQSHQTASAVSK;S(0.166)S(0.166)S(0.667)ADFGT(0.002)FNTSQSHQTASAVSK 172.67 1.02E-14 563190000 115215 355860 396900 341450 485300 520500 405450 467970 485660 439900 TRUE FALSE 119763.7772 416976.1868 407243.5401 408987.7909 402808.8793 399621.7633 373669.7696 461697.6276 468181.1915 526089.9826 0.227648845 0.792594804 0.774094838 0.777410337 0.765665367 0.759607247 0.710277295 0.877602013 0.889926071 1 19.00495005 4.73910476 6.014883307 0.806162855 0.212027569 0.82819087 0.080343718 0.049187141 8.668379807 0.018480221 0.119447674 54840.9235 -4.73910476 -0.594135286 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309;Q7Z309-2;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 S(0.101)S(0.101)S(0.799)APLIHGLSDLSQVFQPYTLR;S(0.113)S(0.113)S(0.774)APLIHGLSDLSQVFQPYTLR 242.45 1.56E-37 2972900000 229263 244560 257010 267798 344740 368430 275160 271150 278390 278790 TRUE FALSE 238314.4803 286561.2776 263707.8917 320767.6451 286141.2179 282867.7161 253592.2402 267515.6778 268370.7983 333413.5627 0.714771404 0.859476967 0.790933307 0.962071376 0.858217091 0.848398949 0.760593655 0.802353916 0.80491866 1 18.34695327 4.743135116 24.2693389 0.843155524 0.714771324 0.239931778 0.072064108 479.7620526 2545169.432 0.016763526 0.133384887 55352.22917 -4.743135116 -0.128384199 SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSSAPNVHINTIEPVNIDDLIR 22 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8YDP5;A0A2R8Y492;A0A2R8Y679 P15056 BRAF Serine/threonine-protein kinase B-raf 1 S(0.237)S(0.237)S(0.525)APNVHINTIEPVNIDDLIR;S(0.124)S(0.124)S(0.752)APNVHINTIEPVNIDDLIR;S(0.108)S(0.108)S(0.784)APNVHINTIEPVNIDDLIR;S(0.002)S(0.008)S(0.99)APNVHINTIEPVNIDDLIR;S(0.154)S(0.154)S(0.692)APNVHINTIEPVNIDDLIR;S(0.175)S(0.175)S(0.649)APNVHINTIEPVNIDDLIR 303.25 3.78E-56 5503229000 933724 1058348 1081473 1101673 1284005 1539415 1135246 1089026 1096370 948176 TRUE FALSE 970588.1445 1240111.036 1109657.075 1319580.631 1065750.289 1181909.196 1046262.452 1074429.388 1056911.858 1133952.933 0.85593336 1.093617733 0.978574191 1.16369965 0.939854078 1.042291229 0.922668324 0.947507922 0.932059724 1 20.11292933 2.237891535 24.99915822 0.945486559 1.018075292 0.119673842 0.080712569 32.33896203 1208213.588 0.027337485 0.021409379 172.9384391 -2.237891535 0.072588733 SSS(ph)ASSPEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.001)S(0.998)ASSPEMK;S(0.011)S(0.037)S(0.951)ASSPEMK;SSS(0.999)ASSPEMK;SSS(1)ASSPEMK;SSS(1)ASSPEMK;S(0.001)S(0.047)S(0.952)ASSPEMK;SSS(1)ASSPEMK 249.29 6.11E-13 2489240000 4454620 3331780 4305290 3354430 5921440 5793270 5491930 4639600 5074120 3272380 TRUE FALSE 4630491.837 3903987.297 4417489.394 4017926.242 4914915.744 4447870.84 5061458.176 4577413.751 4891503.412 3913540.208 1.183197717 0.997559011 1.128770668 1.026673045 1.2558746 1.13653383 1.29331958 1.169635038 1.249892208 1 21.90004284 3.240155911 24.99968095 1.19619848 1.0810665 0.221901893 0.090152507 51.90512663 813388.9102 0.022959536 0.029535394 1738.424809 -3.240155911 -0.115131981 SSS(ph)EDAESLAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSEDAESLAPR 12 0 Q4G0J3;Q4G0J3-3;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 S(0.027)S(0.019)S(0.953)EDAESLAPR 124.12 0.00034476 224900000 166330 220360 210400 215540 279050 313920 267730 237950 243460 234630 TRUE FALSE 172896.8368 258205.1158 215883.1968 258173.1687 231617.1807 241016.8375 246744.623 234760.6695 234697.9222 280601.2562 0.616165584 0.920185174 0.769359338 0.920071322 0.825431731 0.858930002 0.879342546 0.836634421 0.836410803 1 18.09816194 -5 0.022555623 2.100484138 3.26E-11 0.371221364 0.077403454 2935.988968 5.007856845 326.2234195 165.3187085 1.00E-05 5 -2.100484138 SSS(ph)EITLSECDAEDAGEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 SS(0.002)S(0.998)EITLSECDAEDAGEPR;S(0.107)S(0.107)S(0.785)EITLSECDAEDAGEPR;SSS(1)EITLSECDAEDAGEPR 440.29 6.41E-191 728340000 1253024 287294 309306 282402 468754 1140943 413280 354489 335648 270931 TRUE FALSE 1302494.355 336634.5097 317366.7685 338260.2727 389075.3625 875976.2794 380886.0337 349737.6548 323568.094 324014.7422 4.0198614 1.038948128 0.979482496 1.043965686 1.200795248 2.703507481 1.175520691 1.079388093 0.998621519 1 18.30569993 4.741453574 24.83273547 1.266182033 4.019862499 0.739343918 0.493856776 129.9553397 1115454.854 0.122673019 0.858041683 55138.32562 -4.741453574 2.753680466 SSS(ph)ENDVELLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 S(0.001)S(0.049)S(0.95)ENDVELLTK;S(0.001)S(0.057)S(0.942)ENDVELLTK 213.83 4.23E-09 171362000 626650 469210 598270 468220 762510 763050 710950 616670 677480 434600 TRUE FALSE 651390.6259 549793.1676 613861.4077 560832.5185 632898.8226 585843.2016 655223.8813 608404.5473 653097.6271 519751.5491 1.253273082 1.057799959 1.181067009 1.079039629 1.217694923 1.127160088 1.260648251 1.170568031 1.256557346 1 18.98746263 3.214606981 24.99998255 1.18374719 1.139457501 0.015900895 0.086319167 684.5919564 714494.3723 0.022723774 0.027172566 1639.105776 -3.214606981 -0.044289689 SSS(ph)ESYTQSFQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSESYTQSFQSR 13 0 Q9BTU6;E9PAM4 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 SS(0.001)S(0.999)ESYTQSFQSR;S(0.001)S(0.011)S(0.988)ESYTQSFQSR;SSS(0.999)ESYTQSFQSR 242.92 6.17E-17 599790000 678090 1033120 975150 1138650 1180870 1367520 1009820 1067080 1014640 1258190 TRUE FALSE 704861.5168 1210550.323 1000563.21 1363871.571 980146.1392 1049934.205 930667.6697 1052777.538 978123.3046 1504708.241 0.468437334 0.804508336 0.664954961 0.906402673 0.651386171 0.69776597 0.618503737 0.699655594 0.650041834 1 20.52105235 -1.153551805 4.607459021 1.000037207 0.691302292 0.429942081 0.108698511 4.02E-05 7.38E-06 0.097465369 0.02296992 0.070217958 1.153551805 -0.308734915 SSS(ph)ETILSSLAGSDIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 S(0.107)S(0.107)S(0.786)ETILSSLAGSDIVK;S(0.105)S(0.105)S(0.79)ETILSSLAGSDIVK;S(0.133)S(0.133)S(0.734)ETILSSLAGSDIVK;S(0.074)S(0.074)S(0.852)ETILSSLAGSDIVK 276.34 9.92E-36 348678000 700326 549938 674076 550549 891291 840640 758153 683326 738233 526872 TRUE FALSE 727975.4112 644385.5736 691642.9743 659445.949 739789.6742 645414.1 698726.9868 674167.1327 711664.1385 630102.4808 1.155328591 1.022667888 1.097667436 1.046569358 1.174078339 1.024300205 1.108910071 1.069932516 1.129441893 1 19.26522696 -0.999629404 4.771597362 0.999998507 1.088615792 0.234840541 0.049515243 6.94E-07 1.46E-07 0.042324729 0.009975866 0.100085369 0.999629404 0.088617285 SSS(ph)FGSVSTSSNSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSFGSVSTSSNSSK 15 0 A0A0C4DGW2;P57768-2;P57768;E5RGS8;E5RH07;E5RGQ6;E5RG30;E5RJ65;E5RHF1 A0A0C4DGW2 SNX16 Sorting nexin-16 1 SSS(1)FGSVSTSSNSSK;SSS(1)FGSVSTSSNSSK;SSS(1)FGSVSTSSNSSK 370.98 1.47E-97 1820980000 3070470 2367470 3060710 2582370 4034750 4107980 3605330 3293200 3261070 2401030 TRUE FALSE 3191694.527 2774064.556 3140474.617 3093155.078 3348924.636 3153963.902 3322734.814 3249060.041 3143704.728 2871465.858 1.111520974 0.966079589 1.093683426 1.077204199 1.166277017 1.098381126 1.157156302 1.131498754 1.094808325 1 21.45335598 3.833070814 2.42700595 1.117086643 1.039726884 0.12539485 0.056298331 0.392607382 4.496849419 0.014160291 0.030053828 6808.803709 -3.833070814 -0.077359758 SSS(ph)FSLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 S(0.002)S(0.102)S(0.896)FSLPSR;SS(0.014)S(0.986)FSLPSR;SS(0.001)S(0.999)FSLPSR;SS(0.027)S(0.973)FS(0.001)LPSR 210.64 6.77E-06 2105050000 1787890 2105500 2184750 2010730 2518280 2610290 2173360 2290510 2196120 2061730 TRUE FALSE 1858477.278 2467103.246 2241686.38 2408446.393 2090223.665 2004089.707 2003006.364 2259809.46 2117082.07 2465686.519 0.753736237 1.000574577 0.909153034 0.976785319 0.847724822 0.812791769 0.812352401 0.916503149 0.858617693 1 21.23355796 3.197178795 24.99974881 0.86666125 0.916462844 0.037118551 0.079865566 375.5489647 226877.0491 0.022025156 0.026325348 1574.630992 -3.197178795 0.049801594 SSS(ph)FTLLQSLAIEDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSFTLLQSLAIEDSR 16 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 S(0.026)S(0.026)S(0.948)FTLLQSLAIEDSR 151.95 6.24E-07 43222000 28815 30515 35325 34493 45342 45659 39436 37660 35423 32907 TRUE FALSE 29952.63845 35755.71388 36245.59852 41315.61245 37634.78304 35055.38922 36344.90327 37155.2293 34148.13315 39354.49661 0.761098249 0.908554726 0.921002723 1.049832065 0.95630198 0.890759436 0.923526062 0.944116492 0.867706008 1 15.26424087 4.776878938 2.266699988 0.943181 0.704247823 0.555576243 0.049028213 0.534485204 2.949206176 0.012487658 0.26424827 59824.48077 -4.776878938 -0.238933177 SSS(ph)FVLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSFVLPK 8 0 Q8WYP3-2;Q8WYP3 Q8WYP3-2 RIN2 Ras and Rab interactor 2 1 S(0.008)S(0.033)S(0.96)FVLPK;S(0.052)S(0.026)S(0.922)FVLPK;S(0.013)S(0.013)S(0.974)FVLPK;S(0.002)S(0.001)S(0.998)FVLPK 129.38 0.0011466 247600000 944840 789760 1002900 837990 1391130 1281290 1159100 982630 1129690 855540 TRUE FALSE 982143.0128 925395.1365 1029036.398 1003741.921 1154666.219 983729.8156 1068246.713 969459.4521 1089032.678 1023166.683 0.959905194 0.904442211 1.005736812 0.981015056 1.128522106 0.961456068 1.044059322 0.947508816 1.064374648 1 19.96460976 4.168731425 6.828697564 1.013861567 0.932520758 0.299223242 0.051587188 0.233276611 18.23314838 0.012368073 0.027313962 14747.94212 -4.168731425 -0.081340809 SSS(ph)ISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSISGVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 44 0 A0A2R8Y7M0;P82094;P82094-2 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 S(0.14)S(0.14)S(0.71)IS(0.009)GVDMAGLQTSFLSQDESHDHSFGPMPISANGSNLYDAVR 324.11 8.00E-115 362130000 5809.2 35022 21765 27223 21851 28585 21136 17690 14242 28203 TRUE FALSE 6038.551702 41036.75607 22332.21378 32607.62815 18136.77482 21946.56696 19479.30509 17452.89449 13729.4332 33728.83787 0.179032308 1.216666765 0.662110384 0.966758128 0.537723087 0.650676642 0.57752672 0.517447252 0.407053254 1 15.04169499 3.208811859 24.99706339 0.585539301 0.782320191 0.046495937 0.28564769 460.7550459 387158.5622 0.076116579 0.090988419 1617.379219 -3.208811859 0.196780891 SSS(ph)KESLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSKESLVR 9 1 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 S(0.015)S(0.137)S(0.846)KES(0.002)LVR;S(0.006)S(0.06)S(0.915)KES(0.02)LVR;S(0.011)S(0.081)S(0.908)KESLVR;S(0.036)S(0.382)S(0.58)KES(0.003)LVR 146.36 5.75E-05 8503700000 5675120 2790410 3643900 2594930 5343590 5388590 4735330 3784190 3962340 2114860 TRUE FALSE 5899178.12 3269641.211 3738863.027 3108199.409 4435288.48 4137171.637 4364162.461 3733469.123 3819736.157 2529226.326 2.332404206 1.292743626 1.478263527 1.228913118 1.753614706 1.635745918 1.725493056 1.476130896 1.510238969 1 21.27026471 0.51363158 1.179662552 1.000104751 1.599758618 0.289277136 0.289015929 2.381227475 4.421817034 0.26228628 0.079885047 3.263108995 -0.51363158 0.599653867 SSS(ph)LDALGPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSLDALGPTR 11 0 Q9H425;Q9H425-3;Q9H425-2;E5RI90 Q9H425 C1orf198 Uncharacterized protein C1orf198 1 SSS(1)LDALGPTR;SS(0.006)S(0.994)LDALGPTR;S(0.005)S(0.01)S(0.984)LDALGPTR;SSS(1)LDALGPTR 238.01 1.41E-15 614380000 897790 785010 867410 827610 1046950 1107230 925310 875660 897280 823520 TRUE FALSE 933235.4424 919829.361 890015.4172 991308.7878 868989.813 850092.6127 852781.7844 863923.21 864987.0681 984872.9768 0.947569346 0.933957356 0.903685489 1.006534661 0.882336944 0.863149495 0.865879971 0.877192522 0.87827272 1 19.90957814 3.1288742 24.18893637 0.884334595 0.943875802 0.236773436 0.044624219 7.816371835 1688.506434 0.011975331 0.01431326 1345.470561 -3.1288742 0.059541207 SSS(ph)LDGEHHDGYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSLDGEHHDGYHR 14 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 S(0.303)S(0.303)S(0.395)LDGEHHDGYHR 87.138 0.011803 457370000 231180 232040 309740 316900 304010 366800 313310 289660 269990 285930 TRUE FALSE 240307.1649 271891.065 317812.0789 379581.8741 252334.4888 281616.2589 288751.9435 285777.5815 260273.1126 341952.509 0.702750115 0.795113525 0.929404144 1.110042664 0.737922612 0.823553714 0.844421187 0.835723014 0.761138187 1 18.38343645 SSS(ph)LDMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 SSSLDMNR 8 0 E9PMG1;H0YDT0;Q96D71-4;Q96D71;Q96D71-3 E9PMG1;Q96D71 REPS1 RalBP1-associated Eps domain-containing protein 1 1 SS(0.002)S(0.998)LDMNR;SS(0.026)S(0.974)LDMNR;SS(0.011)S(0.989)LDMNR;SS(0.01)S(0.99)LDMNR;S(0.054)S(0.281)S(0.665)LDMNR;S(0.006)S(0.029)S(0.965)LDMNR;S(0.002)S(0.005)S(0.993)LDMNR;SS(0.027)S(0.973)LDMNR;S(0.001)S(0.033)S(0.966)LDMNR;SS(0.003)S(0.997)LDMNR 182.16 0.0002413 5401360000 8375690 9201260 10045510 9359910 12090440 12983610 10799460 10172580 9955220 9413370 TRUE FALSE 8706368.709 10781504.83 10307304.24 11211272.26 10035311.33 9968363.346 9952970.106 10036233.2 9596933.577 11257739.62 0.77336739 0.957697121 0.915574937 0.995872408 0.89141441 0.88546757 0.884100223 0.891496299 0.852474289 1 23.42441385 SSS(ph)LEGFHNHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSLEGFHNHFK 12 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 S(0.112)S(0.112)S(0.777)LEGFHNHFK;S(0.288)S(0.288)S(0.424)LEGFHNHFK 215.09 7.06E-11 904300000 477300 550050 730610 589990 945340 924590 809470 792810 890250 631110 TRUE FALSE 496144.1726 644516.8087 749650.2968 706688.2611 784651.4445 709867.9848 746021.6262 782183.6787 858210.0764 754763.9212 0.657350144 0.853931661 0.993224869 0.936303712 1.039598506 0.940516584 0.98841718 1.036328919 1.137057631 1 19.52566594 5.309561876 0.845564706 1.020124325 8.94E-16 0.818940188 0.052249865 2.195628715 0.615519217 0.017394552 2.616577841 203967.9243 -5.309561876 -1.020124325 SSS(ph)LESLQTAVAEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 SS(0.002)S(0.998)LESLQTAVAEVR;SS(0.003)S(0.997)LESLQTAVAEVR;S(0.001)S(0.049)S(0.95)LESLQTAVAEVR;SSS(1)LESLQTAVAEVR 288.41 7.88E-35 371308000 526870 549680 569540 562990 610480 716440 598120 579030 546933 487385 TRUE FALSE 547671.2344 644083.2641 584382.6803 674347.7416 506710.8277 550057.6678 551237.7915 571269.05 527248.9882 582878.7592 0.939597173 1.105003835 1.002580161 1.156926258 0.869324572 0.943691392 0.945716039 0.98008212 0.904560305 1 19.1528363 3.228013911 24.99999455 0.942845195 1.05142189 0.419833426 0.063581252 194.6922866 461499.6379 0.017188574 0.02074809 1690.495081 -3.228013911 0.108576696 SSS(ph)LESQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSLESQGK 9 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SS(0.001)S(0.998)LES(0.001)QGK;SS(0.009)S(0.991)LESQGK;SS(0.001)S(0.999)LESQGK;SSS(1)LESQGK 209.97 7.92E-06 1074760000 3109420 2126710 2737700 2188270 3472340 3638820 3441850 2905700 3117580 1832000 TRUE FALSE 3232182.303 2491955.899 2809046.711 2621103.275 2882112.887 2793759.202 3172068.803 2866753.844 3005378.905 2190945.324 1.475245533 1.137388447 1.282116299 1.196334407 1.315465455 1.275138713 1.44780829 1.308455219 1.371727022 1 21.06312205 -1.005787702 5.545163641 0.999999056 1.307731443 0.479599508 0.097459081 1.09E-06 1.95E-07 0.090286829 0.021280744 0.098676173 1.005787702 0.307732387 SSS(ph)LGNLKK ddPTM_MDA-MB-175_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(0.304)S(0.061)S(0.635)LGNLKK;S(0.008)S(0.035)S(0.956)LGNLKK;S(0.001)S(0.012)S(0.987)LGNLKK;SS(0.002)S(0.998)LGNLKK 146.36 5.82E-05 2672580000 4577000 2528310 3500720 2344840 4731620 4215140 3868000 3400960 3463950 1869900 TRUE FALSE 4757703.494 2962527.575 3591951.639 2808642.353 3927340.922 3236237.616 3564816.053 3355375.694 3339283.116 2236271.104 2.127516421 1.324762266 1.606223697 1.255948954 1.75620072 1.447157999 1.594089396 1.500433328 1.493237162 1 21.09266367 -2.952106584 0.229560045 3.75E-15 1.63405778 0.386879728 0.224433908 57.54581222 1.333818596 28.64454485 0.379740314 0.001116589 2.952106584 1.63405778 SSS(ph)LKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSLKER 7 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 S(0.283)S(0.283)S(0.433)LKER;SS(0.003)S(0.997)LKER 91.658 0.042727 795570000 1651350 1157330 1557660 962980 1688810 1793710 1989100 1586530 1747980 974970 TRUE FALSE 1716546.573 1356092.425 1598253.899 1153454.57 1401746.679 1377148.036 1833189.144 1565265.16 1685070.541 1165996.705 1.472171033 1.163032811 1.370719053 0.989243422 1.202187514 1.181090848 1.572207826 1.342426745 1.445176075 1 20.15313228 SSS(ph)LPAYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSLPAYGR 9 0 Q08495;Q08495-2;Q08495-3;Q08495-4 Q08495 DMTN Dematin 1 SS(0.002)S(0.998)LPAYGR;S(0.001)S(0.004)S(0.995)LPAYGR;S(0.005)S(0.224)S(0.771)LPAYGR 187.41 4.25E-05 485990000 578320 627450 637160 601820 735980 781550 664980 636790 621810 615790 TRUE FALSE 601152.5202 735209.6566 653764.913 720858.1997 610878.3825 600046.857 612857.13 628254.8716 599431.1796 736442.2605 0.816292807 0.998326272 0.887734108 0.97883872 0.829499358 0.81479145 0.832186259 0.85309454 0.813955434 1 19.49021289 3.219654411 24.99183702 0.846654003 0.923545449 0.156418929 0.068977969 331.2448779 437866.7002 0.018182285 0.021766534 1658.266819 -3.219654411 0.076891446 SSS(ph)LSDLTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSLSDLTHR 10 0 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.304)S(0.304)S(0.392)LSDLTHR;S(0.207)S(0.207)S(0.585)LSDLTHR;S(0.147)S(0.147)S(0.706)LSDLTHR 157.47 5.87E-06 1491610000 466353 814380 769520 782580 885990 1044250 880840 850890 831310 728390 TRUE FALSE 484764.9765 954243.43 789574.3234 937371.9882 735389.7363 801738.7633 811797.4592 839485.2113 801391.3155 871104.0746 0.556494902 1.095441357 0.906406417 1.076073474 0.84420422 0.920370811 0.931917876 0.963702542 0.919971951 1 19.73248557 4.75112856 24.98980181 0.956719235 0.55649465 0.732740286 0.073409097 982.1668858 1952882.421 0.016307342 0.29121224 56380.45289 -4.75112856 -0.400224585 SSS(ph)LSDLTHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSLSDLTHRR 11 1 Q5T9C2-3;Q5T9C2;Q5T9C2-2 Q5T9C2-3 FAM102A Protein FAM102A 1 S(0.159)S(0.159)S(0.673)LS(0.009)DLTHRR;S(0.13)S(0.13)S(0.737)LS(0.002)DLTHRR 80.746 0.014434 375133000 130502 238885 245805 184900 288135 317573 200342 220091 216386 295417 TRUE FALSE 135654.3197 279911.6405 252210.8802 221472.6681 239157.9156 243821.4836 184638.6705 217141.0401 208598.3101 353298.305 0.383965385 0.7922813 0.713875149 0.626871584 0.676929134 0.69012922 0.522614085 0.614611044 0.590431109 1 18.4305273 -1.133857107 5.148262002 1.000012878 0.629323865 0.529694269 0.106296983 1.48E-05 2.49E-06 0.097125062 0.022891802 0.073475558 1.133857107 -0.370689013 SSS(ph)MAAGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSMAAGLER 10 0 Q9UQB8;Q9UQB8-2;Q9UQB8-4;Q9UQB8-5;Q9UQB8-3;I3L4C2;Q9UQB8-6;B4DWA1;I3L3C6;I3L0Y9 Q9UQB8 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 S(0.005)S(0.074)S(0.921)MAAGLER;S(0.004)S(0.076)S(0.92)MAAGLER;SS(0.004)S(0.996)MAAGLER;SS(0.019)S(0.98)MAAGLER 173.04 3.71E-06 1697390000 918970 1089580 1214630 1083400 1602460 1457120 1100920 1134600 1104880 1325170 TRUE FALSE 955251.6452 1276706.889 1246284.256 1297693.286 1330074.422 1118725.963 1014627.014 1119392.543 1065115.585 1584811.69 0.602754038 0.805589016 0.786392645 0.818831218 0.839263384 0.705904664 0.640219289 0.706325269 0.672077062 1 20.59588 -1.172929358 4.261540817 1.000079567 0.733727577 0.530956249 0.07585629 6.01E-05 1.17E-05 0.076999256 0.018143488 0.067153808 1.172929358 -0.266351989 SSS(ph)MADGDNSYCLEAIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSMADGDNSYCLEAIIR 18 0 Q9ULV0;A0A0A0MR36;Q9ULV0-2;Q9ULV0-3 Q9ULV0 MYO5B Unconventional myosin-Vb 1 S(0.26)S(0.26)S(0.481)MADGDNSYCLEAIIR;S(0.002)S(0.079)S(0.919)MADGDNSYCLEAIIR;SS(0.004)S(0.995)MADGDNSYCLEAIIR;SS(0.001)S(0.999)MADGDNSYCLEAIIR;S(0.001)S(0.031)S(0.968)MADGDNSYCLEAIIR 310.19 4.11E-61 332453000 395923 401447 461494 472061 506888 586054 511290 464289 463027 436052 TRUE FALSE 411554.3458 470392.3994 473520.9128 565433.2568 420727.3588 449951.8402 471213.7538 458065.9654 446362.7487 521488.0407 0.789192299 0.902019534 0.908018738 1.084268886 0.806782373 0.862822932 0.903594554 0.878382493 0.855940528 1 18.99227464 SSS(ph)MSSLTGAYASGIPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSMSSLTGAYASGIPSSSR 20 0 Q96HA1-2;Q96HA1-3;Q96HA1 Q96HA1-2 POM121 Nuclear envelope pore membrane protein POM 121 1 S(0.007)S(0.007)S(0.987)MSSLTGAYASGIPSSSR;S(0.039)S(0.039)S(0.92)MS(0.001)SLTGAYASGIPSSSR 242.85 8.69E-30 168889000 98897 116322 119051 124063 152468 169426 134407 138442 137033 144957 TRUE FALSE 102801.5299 136299.3986 122153.5669 148602.2911 126551.5438 130079.3792 123871.8281 136586.4114 132101.2091 173358.5488 0.592999484 0.786228309 0.704629611 0.857196211 0.729998865 0.750348801 0.714541215 0.787883911 0.762011508 1 17.40339946 -5 0.231714283 2.374957898 0.719110606 0.614351962 0.062655298 105.2736077 1.053044182 67.90241868 0.100311328 1.00E-05 5 -1.655847292 SSS(ph)MSSLTGAYTSGIPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSMSSLTGAYTSGIPSSSR 20 0 A8CG34-2;A8CG34 A8CG34-2 POM121C Nuclear envelope pore membrane protein POM 121C 1 S(0.021)S(0.132)S(0.846)MSSLTGAYTSGIPSSSR;S(0.137)S(0.137)S(0.726)MS(0.001)SLTGAYTSGIPSSSR 150.7 8.85E-08 134799000 83762 106827 102513 117639 115997 148571 115592 118260 106253 124671 TRUE FALSE 87068.98844 125173.7063 105184.573 140907.6431 96279.87137 114067.6369 106531.597 116674.9181 102428.9753 149097.8955 0.583971948 0.839540396 0.705473224 0.945067954 0.645749365 0.765051958 0.714507718 0.782539001 0.686991422 1 17.18590037 -1.50035799 2.894051734 1.008988397 0.748213081 0.39246322 0.096301163 20630385.64 22520374.17 1472843.896 0.020759123 0.031596721 1.50035799 -0.260775316 SSS(ph)MSYVDGFIGTWPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSMSYVDGFIGTWPK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 S(0.095)S(0.095)S(0.808)MS(0.002)YVDGFIGTWPK 225.85 6.82E-15 182000000 553120 492380 638970 447050 728340 722270 677040 633680 730310 527420 TRUE FALSE 574957.6047 576942.4348 655622.0831 535475.1557 604537.027 554533.7386 623971.8357 625186.5561 704026.2858 630757.8509 0.911534599 0.914681338 1.039419616 0.848939343 0.958429651 0.879154715 0.989241489 0.9911673 1.11615937 1 19.26672673 1.689496853 2.069220299 1.05393037 0.929641581 0.434002965 0.05687808 0.258114 2.33171323 0.038029583 0.01518563 48.92117196 -1.689496853 -0.124288789 SSS(ph)NASSVSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSNASSVSTR 11 0 P98177-2;P98177 P98177-2 FOXO4 Forkhead box protein O4 1 S(0.001)S(0.028)S(0.971)NASSVSTR;S(0.003)S(0.121)S(0.876)NASSVSTR 200.05 5.05E-08 162686000 143011 177305 180267 175692 215077 249457 187837 195127 174598 190914 TRUE FALSE 148657.1847 207755.7545 184964.9061 210443.3532 178518.2884 191524.3923 173113.8451 192511.6417 168314.2521 228319.943 0.651091546 0.909932579 0.81011279 0.921703774 0.781877772 0.838842152 0.758207289 0.843166125 0.737185941 1 17.80069735 -1.449364256 3.098753828 1.003666254 0.812890423 0.363215149 0.076627297 33777024.09 45020532.22 1096511.115 0.017218418 0.035533316 1.449364256 -0.190775832 SSS(ph)PAELDLKDDLQQTQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 S(0.024)S(0.095)S(0.881)PAELDLKDDLQQTQGK;S(0.082)S(0.082)S(0.836)PAELDLKDDLQQTQGK;S(0.097)S(0.097)S(0.806)PAELDLKDDLQQTQGK 221.14 1.66E-19 2172270000 3595410 1458920 2263610 1649340 3361080 3379060 3003260 2174480 2693740 1086830 TRUE FALSE 3737359.563 1709478.161 2322601.536 1975574.529 2789764.822 2594324.525 2767856.634 2145334.652 2596792.824 1299773.53 2.875392887 1.315212321 1.786927863 1.5199375 2.14634685 1.995981966 2.129491461 1.650544963 1.997880988 1 20.30982884 -2.036331058 0.610084429 0.048935687 1.903791553 0.320464806 0.405610889 180.7589701 16.95060076 240.2669147 0.148151481 0.009197482 2.036331058 1.854855866 SSS(ph)PAGETEGDREPQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSPAGETEGDREPQAR 17 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 SS(0.004)S(0.996)PAGETEGDREPQAR;SS(0.002)S(0.998)PAGETEGDREPQAR;S(0.114)S(0.114)S(0.773)PAGETEGDREPQAR;S(0.015)S(0.015)S(0.969)PAGETEGDREPQAR;S(0.005)S(0.021)S(0.974)PAGETEGDREPQAR 250.64 1.32E-21 1678370000 728738 735475 738284 846284 764728 965178 965228 809379 727092 535851 TRUE FALSE 757509.1389 861787.11 757524.2875 1013676.449 634739.8077 741030.0369 889570.9072 798530.5984 700924.1009 640840.744 1.182055208 1.344775778 1.182078847 1.581791512 0.990479793 1.156340392 1.388131007 1.246067148 1.09375708 1 19.28960635 1.117819111 3.20904649 1.004645877 1.264180506 0.254657157 0.149343432 0.299389151 5.679737545 0.135469472 0.036010207 13.11653465 -1.117819111 0.259534629 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 S(0.028)S(0.15)S(0.823)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.319)S(0.319)S(0.362)PAGETEGDREPQARPGEGTAPLPPPGQK;S(0.162)S(0.162)S(0.677)PAGETEGDREPQARPGEGTAPLPPPGQK 271.16 7.72E-72 2760100000 802150 660920 830970 607700 1023730 1052890 873830 845720 1015250 752940 TRUE FALSE 833819.5014 774427.8688 852625.7608 727901.2462 849716.7403 808372.2542 805336.9213 834384.5067 978711.3508 900464.1771 0.925988532 0.860031846 0.946873604 0.808362248 0.943643025 0.897728388 0.894357534 0.926615992 1.086896487 1 19.78030936 1.367580588 4.762439402 1.041657482 0.897076177 0.639159783 0.043320825 0.115980449 3.862094082 0.028502721 0.009954541 23.31205653 -1.367580588 -0.144581305 SSS(ph)PALKPKPNPPSPENTASSAPVDWRDPSQMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPALKPKPNPPSPENTASSAPVDWRDPSQMEK 34 3 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 S(0.091)S(0.091)S(0.696)PALKPKPNPPS(0.121)PENTASSAPVDWRDPSQMEK 190.89 1.78E-20 692660000 262330 113880 185610 101410 250820 229300 213960 201010 224570 94443 TRUE FALSE 272686.991 133438.0041 190447.1491 121468.5953 208185.706 176048.5501 197189.2561 198315.7897 216487.7696 112947.2976 2.414285217 1.181418298 1.686159413 1.075444901 1.843211041 1.558678727 1.745851917 1.755825893 1.916714911 1 16.78529023 SSS(ph)PAPADIAQTVQEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 SS(0.001)S(0.999)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;S(0.001)S(0.004)S(0.995)PAPADIAQTVQEDLR;S(0.168)S(0.168)S(0.664)PAPADIAQTVQEDLR;SS(0.016)S(0.984)PAPADIAQTVQEDLR;S(0.182)S(0.182)S(0.636)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.02)S(0.02)S(0.959)PAPADIAQTVQEDLR;SS(0.002)S(0.998)PAPADIAQTVQEDLR;S(0.001)S(0.004)S(0.995)PAPADIAQTVQEDLR;S(0.064)S(0.064)S(0.871)PAPADIAQTVQEDLR;S(0.018)S(0.018)S(0.964)PAPADIAQTVQEDLR;S(0.002)S(0.002)S(0.995)PAPADIAQTVQEDLR;S(0.003)S(0.013)S(0.984)PAPADIAQTVQEDLR 438.28 3.16E-170 1.2016E+11 6023788 6467824 6586059 6477869 7444144 8669064 6790219 6767811 6886501 6530800 TRUE FALSE 6261611.802 7578622.459 6757697.108 7759172.154 6178791.062 6655805.267 6257983.892 6677099.563 6638657.174 7810385.22 0.801703325 0.970326334 0.865219438 0.993442953 0.7910994 0.852173751 0.801238827 0.854900159 0.8499782 1 22.89696228 3.221482486 24.99979709 0.8472479 0.909115895 0.088297145 0.072811484 438.2469317 641525.8492 0.019225877 0.023033928 1665.261671 -3.221482486 0.061867995 SSS(ph)PAPPSQQSLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPAPPSQQSLYK 14 0 I3L3F1;A0A494BZY0;A0A494C199;A0A494C0J4;A0A494C1N2;Q9BXL6-3;Q9BXL6-2;Q9BXL6 I3L3F1 CARD14 Caspase recruitment domain-containing protein 14 1 SSS(1)PAPPSQQSLYK;S(0.028)S(0.028)S(0.945)PAPPSQQSLYK 231.58 5.12E-13 268030000 418320 342060 381120 322620 475910 521640 462490 407350 425360 274450 TRUE FALSE 434835.5966 400806.1441 391052.3003 386433.2731 395014.9882 400497.0155 426238.8253 401890.1395 410051.3767 328223.2228 1.324816669 1.221138897 1.191421792 1.177348969 1.203494941 1.220197072 1.298624825 1.224441513 1.249306411 1 18.32431779 -1.122880214 5.355961703 0.999995346 1.232083777 0.721271614 0.043714786 2.46E-06 4.03E-07 0.042914921 0.010114941 0.075356338 1.122880214 0.232088431 SSS(ph)PATEQSWMENDFDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPATEQSWMENDFDELR 19 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.091)S(0.091)S(0.819)PATEQSWMENDFDELR;S(0.048)S(0.048)S(0.903)PATEQSWMENDFDELR 422.15 4.99E-169 143925000 80192 92545 88041 102846 84719 113169 113876 93915 91184 70637 TRUE FALSE 83358.04208 108438.8838 90335.42079 123188.6318 70318.49464 86887.21484 104950.1016 92656.22304 87902.30565 84476.96772 0.986754666 1.283650287 1.069349708 1.458251109 0.832398422 1.028531411 1.242351666 1.096822312 1.040547596 1 16.36627043 3.229920789 24.99997918 1.061639562 1.196215541 0.203169658 0.151017573 351.2416865 1016341.915 0.042687466 0.051778986 1697.933939 -3.229920789 0.134575979 SSS(ph)PATEQSWMENDFDELREEGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.01)S(0.021)S(0.969)PATEQSWMENDFDELREEGFR;S(0.001)S(0.019)S(0.981)PATEQSWMENDFDELREEGFR;S(0.001)S(0.002)S(0.996)PATEQSWMENDFDELREEGFR;SS(0.001)S(0.999)PATEQSWMENDFDELREEGFR 393.96 9.65E-138 1231680000 19580.2 23778 26986 21078.9 29141.9 18685.1 30022.6 27828.6 23899.8 18799.3 TRUE FALSE 20353.24142 27861.68653 27689.27733 25248.24351 24188.37025 14345.7687 27669.35016 27455.60314 23039.65087 22482.6629 0.905286064 1.23925207 1.23158353 1.123009477 1.075867674 0.638081386 1.230697195 1.221190001 1.02477411 1 14.4565253 -2.771214167 1.349756934 0.000163802 1.091002005 0.010491617 0.179853119 1129231.159 40723.84007 3436899.812 0.048228464 0.001693502 2.771214167 1.090838203 SSS(ph)PATEQSWMENDFDELREEGFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.305)S(0.305)S(0.389)PATEQSWMENDFDELREEGFRR;S(0.3)S(0.3)S(0.401)PATEQSWMENDFDELREEGFRR 233.44 1.21E-38 758070000 28339 53472 49516 30668 51333 49953 44441 47625 36565 42318 TRUE FALSE 29457.8456 62655.40005 50806.42764 36734.03887 42607.435 38352.1728 40957.5983 46986.66477 35249.03279 50609.40187 0.58206271 1.238018979 1.003893066 0.725834282 0.841887741 0.757807272 0.809288329 0.928417706 0.696491788 1 15.6271178 3.755360729 24.42295625 0.823609732 0.970994337 0.083069502 0.172144913 1203.069707 1748940.981 0.041435005 0.074433839 5693.256222 -3.755360729 0.147384604 SSS(ph)PCRT(ph)PEPDNDAHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPCRTPEPDNDAHLR 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 2 S(0.256)S(0.327)S(0.417)PCRT(1)PEPDNDAHLR 118.54 0.00037516 160930000 52140 69239 53888 69469 64820 84708 57359 55285 50181 61693 TRUE FALSE 54198.52746 81130.25965 55292.36555 83209.76086 53801.91955 65035.85076 52863.0517 54543.995 48374.99561 73780.56217 0.734590871 1.099615634 0.749416431 1.127800581 0.729215365 0.881476758 0.716490227 0.739273237 0.655660437 1 16.17095316 3.147816109 23.54254873 0.771395298 0.927658015 0.171882149 0.14908855 17.79739777 4608.618388 0.039431112 0.047129226 1405.452293 -3.147816109 0.156262718 SSS(ph)PELVTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.056)S(0.298)S(0.646)PELVTHLK;S(0.364)S(0.125)S(0.511)PELVTHLK;S(0.031)S(0.204)S(0.765)PELVTHLK;S(0.006)S(0.034)S(0.959)PELVTHLK;S(0.171)S(0.171)S(0.658)PELVTHLK 251.24 2.29E-17 24821450000 14934040 12533730 15806360 13494690 18558720 20009530 19706380 16758160 17574380 11369930 TRUE FALSE 15523647.43 14686300.63 16218286.73 16163899.4 15404115.4 15362619.9 18161742.44 16533544.28 16941881.5 13597650.09 1.141641925 1.080061667 1.192727171 1.188727412 1.132851287 1.12979962 1.335653022 1.215911879 1.245941864 1 23.69685401 SSS(ph)PELVTHLKWDDPYYDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPELVTHLKWDDPYYDIAR 21 1 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 S(0.303)S(0.303)S(0.395)PELVTHLKWDDPYYDIAR;S(0.211)S(0.211)S(0.578)PELVTHLKWDDPYYDIAR 237.97 4.28E-30 542260000 268060 336080 368920 189841 710660 525220 275340 349100 386720 594760 TRUE FALSE 278643.2158 393799.1257 378534.3583 227390.9832 589862.267 403245.6148 253758.1313 344420.8855 372802.0227 711291.8346 0.391742464 0.553639317 0.532178692 0.319687324 0.829283057 0.566920067 0.356756705 0.48421881 0.524119643 1 19.44008208 0.905869066 14.86203675 1 0.505140559 0.547172102 0.134787156 269.7141562 42586.18916 0.127619304 0.031905877 8.05135666 -0.905869066 -0.494859442 RS(ph)SLPLDHGSPAQENPESEKSS(ph)PAVSR ddPTM_MDA-MB-175_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(0.789)S(0.211)LPLDHGSPAQENPES(0.034)EKS(0.38)S(0.587)PAVSR 247.36 7.43E-46 311280000 43248 119350 126430 125780 206230 200220 148320 161030 136610 135020 TRUE FALSE 44955.46443 139847.4341 129724.8697 150658.9086 171175.0983 153721.9394 136694.2908 158871.6562 131693.4328 161474.5839 0.278405823 0.866064682 0.803376399 0.933019333 1.060074559 0.951988453 0.846537502 0.983880264 0.815567562 1 17.30094758 4.839493605 2.187866268 0.929852374 5.31E-17 0.855451027 0.079026545 0.32539504 1.401371362 0.019674803 0.647221573 69102.47536 -4.839493605 -0.929852374 down SSS(ph)PIPLTPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 SSS(1)PIPLTPSK;S(0.001)S(0.007)S(0.992)PIPLTPSK;S(0.001)S(0.03)S(0.969)PIPLTPSK;SS(0.001)S(0.999)PIPLTPSK 220.45 9.59E-12 1680130000 4576270 4276840 4710870 3947690 5875690 6012610 5374640 4919850 5265140 3933860 TRUE FALSE 4756944.673 5011354.001 4833639.142 4728531.299 4876942.313 4616272.449 4953361.673 4853907.458 5075648.64 4704624.549 1.011120999 1.065197435 1.027422931 1.005081543 1.036627315 0.981220159 1.05287077 1.031731099 1.078863698 1 22.16564816 SSS(ph)PPILTKPTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPPILTKPTLK 13 1 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 S(0.323)S(0.323)S(0.353)PPILTKPTLK 64.52 0.036994 421250000 818590 971590 828640 958050 857070 1048000 1073800 909600 688350 861420 TRUE FALSE 850908.5653 1138453.025 850235.0391 1147549.431 711385.5475 804617.8826 989632.7501 897408.2998 663576.418 1030198.756 0.825965437 1.105080954 0.825311654 1.113910713 0.69053233 0.781031697 0.960623127 0.8711021 0.644124655 1 19.97449127 3.236536322 24.99997641 0.829180171 0.967228474 0.209570924 0.135873418 86.30296834 1065844.107 0.036938397 0.046294965 1723.996271 -3.236536322 0.138048304 SSS(ph)PPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSPPPR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.009)S(0.009)S(0.983)PPPR;S(0.017)S(0.017)S(0.967)PPPR;S(0.002)S(0.002)S(0.997)PPPR;S(0.008)S(0.023)S(0.969)PPPR;SS(0.002)S(0.998)PPPR 137.84 0.0029827 1452800000 1213566 1444478 1447946 1338645 1539205 1770002 1620379 1503160 1402092 1397128 TRUE FALSE 1261478.523 1692555.86 1485680.662 1603424.986 1277571.484 1358945.86 1493369.46 1483012.599 1351630.983 1670868.482 0.754983732 1.012979704 0.889166729 0.959635664 0.764615227 0.813317071 0.893768406 0.887569916 0.808939182 1 20.67216675 7.763616693 17.86486502 0.877742369 0.059735477 0 0.08785126 0 0 0.018223623 0 58025206.27 -7.763616693 -0.818006893 SSS(ph)PPPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.32)S(0.32)S(0.36)PPPRK 78.934 0.017971 4204800000 867950 666800 839950 610330 990290 912880 933370 854420 871090 657620 TRUE FALSE 902217.3362 781317.713 861839.787 731051.4523 821960.8595 700877.4548 860210.0205 842967.8974 839739.6411 786468.0481 1.147176085 0.99345131 1.095835729 0.929537384 1.045129375 0.891170921 1.093763469 1.071839981 1.067735229 1 19.58502863 -0.200071464 6.996956566 1.000000437 1.03561912 0.021513938 0.074687578 0 0 0.069027425 0.01626992 0.630853527 0.200071464 0.035618683 SSS(ph)PQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPQPK 7 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.004)S(0.996)PQPK;SS(0.012)S(0.988)PQPK;S(0.002)S(0.08)S(0.918)PQPK 87.476 0.020259 279123000 1652270 1114140 1332940 1036550 1921730 1985460 1714550 1328240 1637320 1059800 TRUE FALSE 1717502.895 1305484.878 1367677.511 1241576.496 1595075.021 1524367.005 1580159.091 1310437.115 1578393.173 1267447.519 1.355087978 1.030010994 1.079080192 0.979588092 1.258493939 1.202706212 1.24672546 1.033918246 1.245332173 1 20.27349458 -1.083854421 4.160931576 0.999977314 1.147155364 0.135139463 0.117272974 0.326964212 31433981.13 1504.301251 0.026533388 0.082441442 1.083854421 0.147178049 SSS(ph)PTLTPSQEGSPVFAGFEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 S(0.106)S(0.106)S(0.773)PT(0.015)LTPSQEGSPVFAGFEGR 233.49 2.15E-30 87908000 76934 97542 97812 96857 106860 133550 93566 100380 100330 94572 TRUE FALSE 79971.41373 114294.0797 100361.0611 116015.0255 88695.97537 102535.0365 86232.05243 99034.57029 96719.1429 113101.5727 0.707076054 1.010543682 0.887353364 1.025759614 0.784215226 0.906574807 0.76243018 0.87562505 0.855152944 1 16.78725946 3.207683206 24.99995366 0.854149023 0.913578587 0.036073289 0.101540242 531.7763957 430552.5251 0.02721075 0.03252608 1613.1814 -3.207683206 0.059429564 SSS(ph)PTQYGLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPTQYGLTK 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 SS(0.001)S(0.999)PTQYGLTK;S(0.003)S(0.094)S(0.903)PTQYGLTK 248.22 3.50E-16 1626480000 1629930 1296660 1577470 1256500 1986730 1948920 1816630 1589630 1720500 1198590 TRUE FALSE 1694280.895 1519351.268 1618580.164 1505031.95 1649026.344 1496312.866 1674237.794 1568323.61 1658579.541 1433430.762 1.181976095 1.059940465 1.129165222 1.049950922 1.150405299 1.043868254 1.167993487 1.094104893 1.157069867 1 20.45104079 4.758719357 23.57760528 1.100533454 1.181976265 0.186192614 0.053497507 3568.499612 4173558.602 0.01127697 0.419841244 57374.55851 -4.758719357 0.081442811 SSS(ph)PTSSLTQPIEMPTLSSS(ph)PTEERPTVGPGQQDNPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPTSSLTQPIEMPTLSSSPTEERPTVGPGQQDNPLLK 39 1 Q7LBC6;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 2 S(0.035)S(0.037)S(0.241)PT(0.226)S(0.226)S(0.226)LT(0.008)QPIEMPT(0.005)LS(0.018)S(0.097)S(0.444)PT(0.435)EERPT(0.001)VGPGQQDNPLLK 152.46 1.90E-13 101050000 39495 31879 39227 29732 40675 52683 48398 40550 46848 29672 TRUE FALSE 41054.2931 37353.97027 40249.28785 35612.90086 33761.07803 40448.17167 44604.4383 40006.49358 45161.94963 35485.6603 1.156926284 1.052649717 1.134240916 1.00358569 0.951400587 1.139845541 1.256970786 1.127398877 1.272681676 1 15.11494853 2.491357524 24.64002007 1.175934563 1.058906594 0.238063738 0.088980767 689.4564855 1193307.57 0.028121175 0.02556831 309.9970236 -2.491357524 -0.117027968 SSS(ph)PTSYWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 SS(0.001)S(0.99)PT(0.009)SYWK;S(0.001)S(0.035)S(0.963)PT(0.001)SYWK;SS(0.004)S(0.977)PT(0.018)S(0.001)YWK;SS(0.014)S(0.985)PTSYWK;S(0.001)S(0.019)S(0.979)PT(0.002)SYWK 197.21 2.98E-05 2845160000 4735710 3582210 4246880 3850680 5179020 5448600 5909440 4452040 4798280 3041050 TRUE FALSE 4922679.488 4197426.702 4357557.182 4612333.011 4298692.03 4183245.224 5446242.651 4392367.686 4625590.84 3636885.523 1.3535426 1.154126704 1.198156267 1.268209566 1.181970673 1.150227357 1.497501809 1.207727782 1.271854946 1 21.79427208 SSS(ph)PVGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 S(0.031)S(0.014)S(0.955)PVGLAK;SS(0.015)S(0.984)PVGLAK;S(0.003)S(0.06)S(0.937)PVGLAK 112.36 0.0020724 13159300000 1983320 1444440 1846380 1481310 2332930 2291310 2153990 1942220 2030210 1389710 TRUE FALSE 2061623.005 1692511.334 1894498.18 1774308.697 1936379.392 1759187.978 1985154.635 1916187.718 1957143.139 1661997.067 1.240449244 1.01836 1.139892613 1.06757631 1.165091943 1.058478389 1.194439313 1.1529429 1.177585194 1 20.66448641 2.232866501 24.99687383 1.146748492 1.111839382 0 0.076489961 481.5062275 2113766.37 0.025673111 0.019495399 170.9489749 -2.232866501 -0.03490911 SSS(ph)PVTELASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SS(0.006)S(0.993)PVTELASR;SS(0.002)S(0.998)PVTELASR;SSS(1)PVTELASR;S(0.001)S(0.001)S(0.998)PVTELASR;S(0.001)S(0.002)S(0.998)PVTELASR;S(0.03)S(0.17)S(0.8)PVTELASR 310.68 1.39E-45 5268970000 3791290 3983490 3986600 4428910 4194440 4990730 4987780 4267390 3939850 3334200 TRUE FALSE 3940973.057 4667623.42 4090494.071 5304935.179 3481470.587 3831708.593 4596824.77 4210192.617 3798055.568 3987472.653 0.988338579 1.170571895 1.02583627 1.330400392 0.87310206 0.960936645 1.152816626 1.05585492 0.952496957 1 21.92704319 3.215116237 24.99999868 1.014337374 1.124418108 0.243769459 0.109783465 387.5798664 413296.2715 0.031608831 0.037799922 1641.028928 -3.215116237 0.110080734 SSS(ph)PVTELASRS(ph)PIRQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPVTELASRSPIRQDR 18 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 S(0.189)S(0.237)S(0.574)PVTELAS(0.467)RS(0.533)PIRQDR 135.66 4.26E-06 165130000 112610 136870 166860 110690 162810 184920 127830 138890 136100 192310 TRUE FALSE 117055.9298 160376.3578 171208.5087 132584.1516 135135.6144 141975.1325 117810.3506 137028.4067 131201.7876 229989.4625 0.508962143 0.69732046 0.744418926 0.576479245 0.587573069 0.617311467 0.512242384 0.595802978 0.570468691 1 17.81120824 -1.564554447 3.15594289 1.016763852 0.603130896 0.747924324 0.069452444 32493197.26 39225275.39 4615482.809 0.017167028 0.02725496 1.564554447 -0.413632955 SSS(ph)QGPLSSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSQGPLSSIR 11 0 A0A0U1RQE4 A0A0U1RQE4 1 SS(0.015)S(0.985)QGPLSSIR;S(0.001)S(0.035)S(0.964)QGPLSSIR 170.66 1.62E-05 213980000 192768 230280 223100 219710 298600 309490 244000 237650 245520 250690 TRUE FALSE 200378.6295 269828.7987 228914.1693 263167.9822 247844.0787 237615.6379 224874.6424 234464.6905 236683.7832 299807.9058 0.668356723 0.900005615 0.763536134 0.877788668 0.826676261 0.792559613 0.750062417 0.782049726 0.789451441 1 18.1936789 -1.198451941 3.556695769 1.00028475 0.797006778 0.498430111 0.061798236 21314825.37 36605457.82 69208.44528 0.013784589 0.063321043 1.198451941 -0.203277972 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 S(0.151)S(0.151)S(0.698)QIPEGFGLTSGGSNYSLAR;S(0.119)S(0.119)S(0.763)QIPEGFGLTSGGSNYSLAR;S(0.095)S(0.095)S(0.81)QIPEGFGLTSGGSNYSLAR 294.63 1.80E-55 322913000 228492 229291 237363 245384 287920 353318 243182 259559 240656 277771 TRUE FALSE 237513.0406 268669.9456 243548.8748 293920.2228 238979.4612 271265.2491 224120.7594 256080.0362 231994.8376 332194.9092 0.714980977 0.808772014 0.733150533 0.884782441 0.719395315 0.816584606 0.674666448 0.770872849 0.698369635 1 18.34167044 -1.18998427 4.211199786 1.000093055 0.760183088 0.589060542 0.060624183 4.9056978 31324825.26 5436.725234 0.013062812 0.064567761 1.18998427 -0.239909968 SSS(ph)QPPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSQPPGR 8 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 S(0.001)S(0.069)S(0.929)QPPGR;SS(0.001)S(0.999)QPPGR 167.12 0.00032988 145590000 347280 399980 394870 361490 473280 472360 397650 402000 383540 448330 TRUE FALSE 360990.8826 468673.4536 405160.6366 432991.6431 392832.0347 362661.5487 366481.1539 396611.8475 369736.4703 536171.6797 0.673274804 0.874110796 0.755654675 0.807561569 0.732660917 0.67639072 0.683514568 0.739710549 0.689585975 1 19.03233549 -1.041989827 4.298347811 1.00001925 0.739397795 0.626798002 0.060868675 8077247.502 1958056.969 1502.346876 0.014412975 0.09078418 1.041989827 -0.260621455 SSS(ph)SESLSDKGSELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSSESLSDKGSELKK 16 2 Q86X27;Q86X27-3;Q86X27-2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SS(0.005)S(0.99)S(0.005)ESLSDKGSELKK;S(0.045)S(0.045)S(0.863)S(0.045)ES(0.004)LSDKGSELKK 125.23 4.08E-05 168131000 519830 199021 346420 155507 483220 426920 489910 295900 385680 122593 TRUE FALSE 540353.2898 233201.3086 355447.9898 186265.8205 401082.437 327774.3 451509.5741 291933.9445 371799.4521 146612.7512 3.685581817 1.590593633 2.424400245 1.270461259 2.735658623 2.235646609 3.079606449 1.991190685 2.535928486 1 17.16165106 3.976228019 24.72592639 2.207465396 2.48044077 0.056481535 0.759948507 2981.487901 3101142.95 0.183569575 0.333482343 9467.340971 -3.976228019 0.272975375 SSS(ph)SPELQTLQDILGDPGDKADVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.04)S(0.029)S(0.928)S(0.004)PELQTLQDILGDPGDKADVGR;S(0.141)S(0.141)S(0.712)S(0.006)PELQTLQDILGDPGDKADVGR 172.05 3.85E-12 298490000 98324 73690 100759 76302 134474 136434 115724 89597 94010 74714 TRUE FALSE 102205.9074 86345.68427 103384.8623 91394.30786 111616.1575 104749.2712 106653.2505 88396.09877 90626.59846 89352.77781 1.143847007 0.96634583 1.157041391 1.022847975 1.249162704 1.172311301 1.193619864 0.989293237 1.014256083 1 16.44722496 1.669395914 7.687749871 1.001540767 1.126022358 0.364178904 0.07731342 0.141828935 15.26707151 0.03931043 0.020412135 46.70849931 -1.669395914 0.12448159 SSS(ph)SPELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_MDA-MB-175_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 2 S(0.292)S(0.322)S(0.355)S(0.03)PELQT(0.001)LQDILGDPGDKADVGRLS(1)PEVK 82.363 0.00054984 147900000 96619 31838 62891 43028 89690 93156 75185 53675 70675 22641 TRUE FALSE 100433.5927 37305.92883 64529.99113 51538.80997 74444.52584 71521.93079 69291.80324 52955.57442 68131.42056 27077.07046 3.709174996 1.377768281 2.383196927 1.903411599 2.749356728 2.641420566 2.559058349 1.955735001 2.51620354 1 14.72478404 -1.69882646 0.480466598 5.02E-05 2.396218988 0.344062906 0.586110042 51.93502529 4.807080404 60.94763961 0.269591105 0.020006612 1.69882646 2.396168791 SSS(ph)TSDILEPFTVER ddPTM_MDA-MB-175_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 SSS(0.999)T(0.001)SDILEPFTVER;SSS(1)TSDILEPFTVER;SSS(0.993)T(0.006)SDILEPFTVER;SSS(0.997)T(0.003)SDILEPFTVER;SSS(0.935)T(0.065)SDILEPFTVER;SSS(0.958)T(0.041)SDILEPFTVER;S(0.001)S(0.034)S(0.95)T(0.015)SDILEPFTVER;S(0.02)S(0.02)S(0.95)T(0.01)SDILEPFTVER 337.74 3.95E-69 6457470000 4824680 5218020 5367260 5483240 6233710 6857240 5483880 5480230 5519110 5172070 TRUE FALSE 5015162.092 6114174.344 5507135.205 6567808.506 5174106.201 5264749.932 5054039.156 5406776.481 5320478.309 6185438.091 0.810801437 0.988478787 0.890338748 1.061817839 0.836497937 0.851152312 0.817086693 0.874113749 0.860161921 1 22.56044435 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 S(0.07)S(0.095)S(0.835)VGS(0.997)S(0.003)SSYPISPAVSR;S(0.012)S(0.018)S(0.97)VGS(0.952)S(0.048)SSYPISPAVSR;SS(0.003)S(0.997)VGS(0.99)S(0.01)SSYPISPAVSR;S(0.018)S(0.028)S(0.954)VGS(0.988)S(0.012)SSYPISPAVSR;S(0.001)S(0.002)S(0.997)VGS(0.984)S(0.016)SSYPISPAVSR 255.23 2.17E-30 1381980000 900880 973700 1039480 973700 1356470 1339040 994780 1057100 1070100 1032650 TRUE FALSE 936447.438 1140925.401 1066569.703 1166294.954 1125897.714 1028068.253 916806.5442 1042931.304 1031587.31 1234977.996 0.758270545 0.923842695 0.86363458 0.94438521 0.911674311 0.832458762 0.742366704 0.844493835 0.835308251 1 20.23605391 2.717531013 22.34745933 0.832703714 0.88540469 0.006425852 0.076536252 491.2554303 522037.8547 0.023543483 0.022231058 521.8323671 -2.717531013 0.052700976 SSS(ph)VGSS(ph)SSYPISPAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 SS(0.001)S(0.999)VGS(0.025)S(0.974)S(0.001)SYPISPAVSR 308.24 6.42E-61 584440000 318130 373340 440790 379220 507650 506960 402340 443590 377430 361010 TRUE FALSE 330690.018 437458.2408 452277.3495 454228.5841 421359.8343 389226.2231 370803.5395 437644.4016 363846.368 431742.9975 0.765941822 1.013237605 1.047561517 1.052080953 0.975950593 0.901522955 0.858852469 1.013668789 0.842738319 1 18.71981325 2.826575918 7.011235228 0.926368292 0.982469679 0.057125729 0.090635167 0.732960866 50.34423287 0.027772396 0.029484579 670.773533 -2.826575918 0.056101387 SSS(ph)VGSSSSYPIS(ph)PAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 2 SSS(1)VGSSSSYPIS(1)PAVSR;SSS(1)VGSSSSYPIS(1)PAVSR;S(0.005)S(0.009)S(0.985)VGSSS(0.002)S(0.001)YPIS(0.997)PAVSR;S(0.01)S(0.378)S(0.611)VGSSSSYPIS(1)PAVSR 501.48 1.17E-266 2408050000 1850570 2206140 2123420 2100210 2440300 2792740 2110210 2307850 2057900 2220830 TRUE FALSE 1923631.933 2585027.384 2178758.07 2515625.269 2025498.678 2144168.459 1944806.226 2276917.046 1983836.581 2655959.118 0.724270159 0.973293364 0.820328165 0.947162647 0.762624192 0.807304768 0.732242531 0.85728618 0.746937921 1 21.34080151 3.219442528 24.97992288 0.807639594 0.870627515 0.051625786 0.095504787 556.5341959 727172.7836 0.025156723 0.030112781 1657.457982 -3.219442528 0.062987921 SSS(ph)VGSSSSYPISPAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 17 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 SS(0.001)S(0.999)VGSSSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;S(0.001)S(0.026)S(0.974)VGSSSSYPISPAVSR;SS(0.001)S(0.998)VGS(0.001)SSSYPISPAVSR;S(0.015)S(0.015)S(0.97)VGSSSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;S(0.023)S(0.023)S(0.954)VGSSSSYPISPAVSR;S(0.002)S(0.136)S(0.862)VGSSSSYPISPAVSR;S(0.14)S(0.14)S(0.72)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;SSS(1)VGSSSSYPISPAVSR;S(0.001)S(0.036)S(0.963)VGSSSSYPISPAVSR 497.25 1.14E-266 1.14804E+11 7633748 9321897 9063296 9164836 10954600 11802120 9501994 9886749 9123439 8821561 TRUE FALSE 7935134.266 10922860.3 9299492.939 10977613.21 9092541.005 9061256.493 8757202.881 9754233.301 8795088.213 10549976.98 0.752147069 1.035344467 0.881470449 1.040534328 0.861854109 0.858888746 0.830068435 0.924573894 0.83365947 1 23.33073652 SSS(ph)VTSIDKESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSVTSIDKESR 12 1 H0Y332;Q5T5C0-2;Q5T5C0;Q5T5C0-3;Q5JRH0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 S(0.058)S(0.177)S(0.753)VT(0.006)S(0.006)IDKESR;S(0.117)S(0.117)S(0.762)VT(0.004)S(0.001)IDKESR;S(0.005)S(0.192)S(0.801)VTSIDKESR 145.86 3.89E-05 428880000 313517 258144 266731 224660 362480 351820 286603 279889 288869 216742 TRUE FALSE 325894.8932 302478.2239 273682.229 269097.0775 300865.7791 270115.1369 264138.308 276137.5458 278472.6611 259208.4451 1.257269581 1.166930436 1.055838396 1.038149345 1.160709787 1.042076915 1.019018913 1.06531076 1.0743194 1 17.9837532 4.466437735 2.474680484 1.059424543 1.259099981 0.715157634 0.040995325 0.174422315 1.875580435 0.010370867 0.056982081 29271.01181 -4.466437735 0.199675438 SSS(ph)WGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSWGR 6 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7;E9PF00 H7C1F9 RALGAPA2;IST1 Ral GTPase-activating protein subunit alpha-2 1 S(0.001)S(0.009)S(0.99)WGR;SS(0.009)S(0.99)WGR 111.82 0.028873 1715320000 1893370 2274700 2398500 2310100 2683000 3041700 2383900 2286300 2271600 2313100 TRUE FALSE 1968121.71 2665362.03 2461006.88 2767030.885 2226944.618 2335311.272 2197043.689 2255655.888 2189845.56 2766307.658 0.711461613 0.963508893 0.889636 1.000261441 0.805024203 0.844197957 0.794215236 0.815403117 0.791613165 1 21.39953019 SSSASS(ph)PEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 SSSAS(0.008)S(0.992)PEMK 216.91 7.86E-09 309240000 764950 446430 580320 459440 746440 787870 796440 640640 629400 377880 TRUE FALSE 795150.8167 523100.8798 595443.6159 550315.8607 619560.3954 604899.1328 734012.9517 632053.2687 606748.0169 451918.3511 1.759501058 1.157511923 1.317591141 1.217732937 1.370956488 1.338514206 1.624215857 1.398600582 1.342605397 1 18.78570262 0.786509271 3.983546914 1.000014381 1.389645132 0.331182408 0.16837722 2.66425255 48.56967407 0.155838719 0.039827637 6.116588605 -0.786509271 0.389630751 SSSFS(ph)DTLEESSPIAAIFDTENLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSFSDTLEESSPIAAIFDTENLEK 25 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 1 S(0.223)S(0.223)S(0.223)FS(0.286)DT(0.044)LEESSPIAAIFDTENLEK 189.78 6.25E-18 165430000 191150 115520 186620 116800 228770 228520 195520 200510 199690 148180 TRUE FALSE 198696.7496 135359.6614 191483.4705 139902.6914 189883.7571 175449.6933 180194.6315 197822.4914 192503.1959 177213.0339 1.121231013 0.763824525 1.080527015 0.789460506 1.071499951 0.990049599 1.016824934 1.116297639 1.086281249 1 17.43512519 2.578289038 1.276417964 1.072636194 0.943021335 0.129915308 0.113332843 0.709386178 2.353179522 0.052520557 0.042320042 378.694535 -2.578289038 -0.129614858 SSSGLLEWESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSGLLEWESK 11 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2;M0QYT0;M0R076 A0A3B3ITJ4;P14866;M0QYT0 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 164.33 5.33E-05 160420000 412820 381010 446790 355900 559020 576880 457990 445530 499830 401800 FALSE TRUE 429118.4524 446445.5037 458433.7144 426295.9577 463997.9801 442908.3627 422091.5471 439558.3991 481841.2159 480525.0171 0.893020003 0.929078587 0.954026738 0.887146231 0.965606292 0.921717594 0.878396612 0.914746129 1.002739085 1 18.87425202 1.237741794 24.99999578 1.001369589 0.918078249 0.618676273 0.026190941 13.7208141 418792.8236 0.020569372 0.006292405 17.28788218 -1.237741794 -0.083291341 SSSHSSPGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSHSSPGSPK 11 0 Q6NZY4;Q6NZY4-2;F5GX80 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 SSSHSSPGS(1)PK 73.834 0.027359 108830000 6027.8 162680 170030 134670 170240 253750 142130 239880 174390 179810 TRUE FALSE 6265.782198 190619.0245 174461.1215 161307.3241 141302.6656 194820.4081 130989.4792 236664.801 168113.738 215040.3268 0.029137708 0.886433849 0.811294905 0.750125925 0.657098451 0.905971503 0.609139137 1.100560088 0.781777727 1 17.71424771 4.740937042 24.69249447 0.832258966 0.029137371 0.745635261 0.140956865 88.22062755 916597.6421 0.032904606 0.221117073 55072.78539 -4.740937042 -0.803121595 SSSISEEKGDS(ph)DDEKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR;SSSISEEKGDS(1)DDEKPR 252.91 4.21E-27 5068665000 10388030 2035852 3571769 2051728 6033608 8514820 5757698 3746614 4159544 1364931 TRUE FALSE 10798157.45 2385493.744 3664852.234 2457553.675 5008017.467 6537382.098 5306394.586 3696396.768 4009842.824 1632363.096 6.615046291 1.461374464 2.245120735 1.505519011 3.067955578 4.004857812 3.250744027 2.264445194 2.456465007 1 20.63853057 4.74724314 24.98209791 2.474415516 6.615048412 0.682145134 0.867936084 684.1245568 1968378.328 0.212776873 2.527800445 55878.29426 -4.74724314 4.140632896 SSSLEMTPYNTPQLS(ph)PATTPANKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSLEMTPYNTPQLSPATTPANKK 24 1 Q14C86-2;Q14C86-6;Q14C86-3;Q14C86-4;Q14C86-5;Q14C86;F8W9S7;C9IZ08;H0Y7I9;H0Y4E7;B4DGD8;B0QZ65;A0A0A0MQV8 Q14C86-2 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 SSSLEMTPYNTPQLS(0.996)PAT(0.003)TPANKK;SSSLEMTPYNTPQLS(0.775)PAT(0.196)T(0.029)PANKK 185.02 1.51E-17 1061490000 914470 622930 900250 602310 1276580 1155320 866360 868690 952980 550250 TRUE FALSE 950573.9817 729913.3818 923711.2546 721445.1203 1059587.388 887014.439 798452.4394 857046.6314 918682.436 658060.9523 1.444507501 1.109188107 1.403686469 1.0963196 1.610166025 1.347921398 1.21334116 1.302381836 1.396044595 1 19.32786169 -1.138823777 5.823595353 0.999996938 1.317053278 0.300535004 0.148243105 5.45E-06 8.06E-07 0.132748086 0.031288722 0.072640065 1.138823777 0.31705634 SSSMKSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSMKSLR 8 1 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 0 60.973 0.081085 611100000 921140 755930 930580 745330 1045300 1065000 990150 945210 1050500 709770 FALSE TRUE 957507.3185 885755.0972 954831.6793 892754.0494 867620.2794 817669.8902 912539.4557 932541.006 1012692.71 848835.8421 1.128024137 1.043493987 1.124872009 1.051739341 1.022129647 0.963283888 1.075048214 1.098611722 1.193037169 1 19.69512605 -0.809187675 7.57453494 1.000000019 1.074037246 0.126750152 0.060543752 0 0 0.059870764 0.014111674 0.155171631 0.809187675 0.074037227 SSSPATEQS(ph)WMENDFDELREEGFRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSPATEQSWMENDFDELREEGFRR 25 2 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 S(0.025)S(0.113)S(0.113)PAT(0.131)EQS(0.618)WMENDFDELREEGFRR 115.27 0.0012458 236820000 65154 77581 96452 78107 112460 113010 78604 94657 92894 91604 TRUE FALSE 67726.33023 90904.93325 98965.61836 93556.33147 93344.08937 86765.14018 72442.81309 93388.27774 89550.76309 109552.0499 0.618211437 0.829787606 0.903366194 0.853989784 0.852052421 0.791999239 0.661263875 0.852455776 0.817426631 1 16.74125695 0.557388179 1.692305227 0.999849716 0.799599031 0.340731522 0.084906574 2.805078014 9.335052296 0.081567005 0.023092192 3.609010778 -0.557388179 -0.200250685 SSSPELVTHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSPELVTHLK 11 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 188.28 3.22E-06 1114700000 1625890 1550200 1842770 1672780 2251280 2198100 1959980 1864010 1860560 1462770 FALSE TRUE 1690081.393 1816434.791 1890794.1 2003650.891 1868608.23 1687624.588 1806351.646 1839025.995 1793598.809 1749371.775 0.966107615 1.038335485 1.080841778 1.145354532 1.068159585 0.964703222 1.032571619 1.051249381 1.025281667 1 20.73840549 SSSQPSSCCSDPS(ph)KPGGNVEGATQSLAEQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSQPSSCCSDPSKPGGNVEGATQSLAEQMR 31 1 Q13501;Q13501-2;E7EMC7 Q13501 SQSTM1 Sequestosome-1 1 S(0.037)S(0.037)S(0.026)QPS(0.097)S(0.25)CCS(0.092)DPS(0.46)KPGGNVEGATQSLAEQMR 108 7.66E-05 180600000 82291 63533 81384 72765 111600 120600 96283 93973 97501 54797 TRUE FALSE 85539.91222 74444.29853 83504.9339 87157.69982 92630.27186 92592.47771 88736.08687 92713.44564 93991.95806 65533.423 1.305286803 1.135974517 1.274234277 1.329973254 1.41348136 1.412904644 1.354058476 1.414750541 1.434259859 1 15.99994327 3.790679862 2.824444804 1.366249829 1.219132943 0.091768743 0.127031278 0.412714467 6.502935161 0.031452737 0.061454721 6175.610008 -3.790679862 -0.147116886 SSSQRS(ph)PS(ph)PGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_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(0.269)S(0.287)S(0.299)QRS(0.336)PS(0.656)PGPNHT(0.06)S(0.061)NS(0.014)S(0.014)NAS(0.003)NATVVPQNSSAR 83.436 0.00061314 71415000 3125.8 13044 12464 10385 10237 16493 10380 16239 10100 13951 TRUE FALSE 3249.208998 15284.20553 12788.82208 12439.122 8496.918397 12662.7507 9566.388477 16021.34277 9736.502973 16684.43134 0.194744965 0.916075904 0.766512314 0.74555265 0.50927228 0.758956086 0.573372162 0.960257047 0.583568164 1 14.0262149 -5 0.044499432 2.256745963 0.000591241 0.223939875 0.203884691 1111.40941 3.679540946 178.8703266 47.11700656 1.00E-05 5 -2.256154722 SSSQRS(ph)PSPGPNHTSNSSNASNATVVPQNSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSQRSPSPGPNHTSNSSNASNATVVPQNSSAR 33 1 Q9BTA9-2;Q9BTA9;A0A0A0MRT2;Q9BTA9-5 Q9BTA9-2 WAC WW domain-containing adapter protein with coiled-coil 1 S(0.113)S(0.113)S(0.113)QRS(0.542)PS(0.113)PGPNHT(0.002)S(0.002)NSSNASNATVVPQNSSAR;S(0.056)S(0.056)S(0.056)QRS(0.295)PS(0.295)PGPNHT(0.056)S(0.056)NS(0.056)S(0.056)NAS(0.013)NATVVPQNSSAR 125.02 6.49E-08 138465000 3426.4 55795 47704 39521 38613 70579 22276.3 61586 39493 63450 TRUE FALSE 3561.676918 65377.35723 48947.20543 47338.13584 32049.57605 54188.09689 20530.2254 60760.5404 38071.65464 75881.81268 0.046937162 0.861568206 0.645045284 0.62384034 0.422361761 0.714111787 0.270555284 0.800726001 0.501723052 1 16.21146652 -5 0.271121045 4.025802058 0.532614058 0.256450664 0.234358812 291.9839718 2.831769568 494.6280555 0.262413315 1.00E-05 5 -3.493188 VFIDQNLS(ph)PGKGVVSLVAVHPSTVNPLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFIDQNLSPGKGVVSLVAVHPSTVNPLGK 29 1 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGKGVVSLVAVHPSTVNPLGK 165.37 2.88E-12 151250000 171750 397820 497540 389050 677710 683210 517610 581630 593310 424160 TRUE FALSE 178530.8226 466142.4904 510506.3011 466002.9288 562513.0963 524544.8316 477038.3757 573834.2012 571956.889 507266.031 0.351947128 0.918931018 1.006387714 0.918655893 1.108911423 1.034062602 0.940410646 1.131229308 1.127528465 1 18.95238303 4.851955756 1.968488326 1.039496658 1.83E-10 0.895471252 0.069486736 0.32636646 1.05032603 0.018274114 0.677058687 71114.10618 -4.851955756 -1.039496658 down SSSRPCSPVHHHEGHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSRPCSPVHHHEGHAK 17 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 0 49.463 0.056332 3127100 2583 6498.2 4599.3 5675.5 5477.1 4264.4 4720.8 4461.7 3899.3 4399.7 FALSE TRUE 2684.978835 7614.215301 4719.161536 6798.09696 4546.104498 3274.057728 4350.77136 4401.898209 3758.964955 5261.736978 0.510283742 1.447091585 0.896882827 1.291987226 0.863993111 0.622238957 0.826869792 0.836586517 0.71439621 1 12.36132342 3.01749711 24.31894883 0.790913851 1.058668296 0.167539113 0.247712039 257.4632293 357840.5184 0.06557943 0.078365105 1041.111179 -3.01749711 0.267754446 SSSS(ph)PELQTLQDILGDPGDKADVGR ddPTM_MDA-MB-175_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(0.022)S(0.022)S(0.122)S(0.833)PELQTLQDILGDPGDKADVGR 154.88 4.26E-08 45510000 34527 23863 34621 23229 43190 44315 38579 31070 41779 21969 TRUE FALSE 35890.15262 27961.28462 35523.2517 27823.62687 35848.57923 34023.51285 35555.07717 30653.55747 40275.38195 26273.40493 1.366025938 1.064242899 1.352061212 1.059003465 1.364443601 1.294979198 1.353272531 1.166714309 1.532933476 1 14.68131556 SSSS(ph)PELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSSPELQTLQDILGDPGDKADVGRLSPEVK 31 2 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 2 S(0.208)S(0.234)S(0.263)S(0.296)PELQTLQDILGDPGDKADVGRLS(1)PEVK;S(0.215)S(0.236)S(0.261)S(0.288)PELQT(0.001)LQDILGDPGDKADVGRLS(1)PEVK 140.73 1.34E-08 117575000 228907 89317 148253 90994 220846 224563 171855 137696 153653 69183 TRUE FALSE 237944.4251 104656.5 152116.595 108992.3416 183306.6758 172411.6465 158384.556 135850.4103 148123.0585 82738.08426 2.875875448 1.264913261 1.838531751 1.317317685 2.21550544 2.083824494 1.914288413 1.641933235 1.790264542 1 16.33626393 0.321252566 0.82588108 0.99117052 1.883196984 0.277590293 0.43416435 3.355727785 2.984785733 0.465862483 0.135382594 2.095330653 -0.321252566 0.892026464 SSSS(ph)PPPKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSSPPPKQK 10 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.004)S(0.004)S(0.019)S(0.973)PPPKQK 89.301 0.0070289 81779000 89925 55621 79919 39527 107260 93194 75298 76850 93175 66801 TRUE FALSE 93475.30844 65173.47408 82001.75479 47345.32262 89027.98351 71551.10587 69395.94601 75819.95145 89821.64995 79889.37697 1.170059299 0.8157965 1.026441286 0.592636023 1.11439076 0.895627286 0.868650484 0.949061744 1.124325328 1 16.28571606 1.380216534 6.055802747 1.059908346 0.918639249 0.105085469 0.155199482 0.423091323 20.61306391 0.098569242 0.035697073 24.00029249 -1.380216534 -0.141269097 SSSSESSHSSSSHSHGKT(ph)TPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSSESSHSSSSHSHGKTTPTK 22 1 O75582-3;O75582 O75582-3 RPS6KA5 Ribosomal protein S6 kinase alpha-5 1 SSSSESSHSS(0.001)S(0.001)SHS(0.004)HGKT(0.484)T(0.484)PT(0.026)K 112.86 0.00015461 39471000 0 27472 24205 20487 24594 43545 12197 42569 19285 33309 TRUE FALSE 0 32190.1023 24835.80218 24539.26745 20413.52066 33432.33368 11240.96727 41998.43218 18590.93662 39835.26081 0 0.808080621 0.623462773 0.616018747 0.512448525 0.839264837 0.282186361 1.05430293 0.466695491 1 15.2817584 3.148229426 0.114894875 1.195625206 4.57E-15 0.239974938 0.268717071 33.88397736 1.264543572 4.023743997 8.931728594 1406.790496 -3.148229426 -1.195625206 SSSSSASPSS(ph)PSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(0.003)S(0.997)PSSR;SSSSSASPSS(1)PSSR;SSSSSASPS(0.048)S(0.827)PS(0.063)S(0.063)R;SSSSSASPS(0.304)S(0.691)PS(0.005)SR;SSSSSAS(0.013)PS(0.179)S(0.796)PS(0.006)S(0.006)R;SSSSSASPS(0.199)S(0.801)PSSR 343.53 2.43E-69 4172835000 1097401 1350584 1302755 1284967 1431400 1662685 1393114 1378501 1264058 1135688 TRUE FALSE 1140727.239 1582536.296 1336705.866 1539129.637 1188091.139 1276551.607 1283918.084 1360024.449 1218564.8 1358204.32 0.839878966 1.165168063 0.984171414 1.133209205 0.874751407 0.939881864 0.945305552 1.0013401 0.897188134 1 20.3732691 3.229066667 24.99923105 0.947117814 1.036901611 0.183178315 0.089915495 311.9127466 821320.1202 0.024091386 0.029160142 1694.597911 -3.229066667 0.089783796 SSSSSASPSS(ph)PSSREEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSSSASPSSPSSREEK 17 1 E9PK91;Q9NYF8-3;H0YF63;Q9NYF8;Q9NYF8-2;Q9NYF8-4 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 SSSSSASPS(0.001)S(0.998)PS(0.001)SREEK 229.37 6.86E-16 461470000 90161 74215 91746 32294 133150 119600 45994 79750 87440 95296 TRUE FALSE 93720.6259 86960.84894 94136.97613 38681.65681 110517.2106 91824.71256 42388.8701 78681.08169 84293.05148 113967.4266 0.822345723 0.763032487 0.825998962 0.339409759 0.969726296 0.805710151 0.371938468 0.690382191 0.739624066 1 16.79826202 0.81444099 3.789575185 0.999957786 0.690341656 0.183551976 0.188950297 2.315294584 45.22754005 0.177486867 0.045516683 6.522904045 -0.81444099 -0.30961613 SSSSSGVPYS(ph)PAIPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;SSSSSGVPYS(1)PAIPNK;S(0.001)S(0.001)SSSGVPY(0.007)S(0.989)PAIPNK 255.72 1.35E-26 3732710000 3415260 2661590 3116740 2649170 3753660 3883160 3033310 2966260 2968430 2035570 TRUE FALSE 3550097.102 3118697.378 3197964.805 3173167.919 3115614.214 2981354.94 2795551.236 2926502.137 2861596.784 2434400.968 1.458304178 1.281094371 1.31365574 1.303469708 1.279827873 1.224677027 1.148352828 1.202144665 1.175482931 1 21.21513538 8 0.066060954 0.689608974 2.480944751 0.882153244 0.039470359 86.4381248 0.423351204 2.122749409 14.56229485 100000000 -8 1.791335777 SSSSSGVPYS(ph)PAIPNKR ddPTM_MDA-MB-175_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;SSSSSGVPYS(1)PAIPNKR 220.36 2.47E-15 1311560000 1197410 970350 1150240 936730 1299580 1403490 1110770 1057940 1055950 780890 TRUE FALSE 1244684.671 1137000.064 1180216.199 1122012.398 1078677.856 1077550.718 1023704.945 1043760.045 1017946.566 933890.4445 1.332795168 1.21748763 1.26376301 1.201438996 1.155036827 1.153829899 1.096172416 1.117647205 1.090006405 1 19.83289379 7.999999999 0.131983887 0.951512414 2.178393779 0.931940829 0.023623406 17.59718075 0.156552385 0.111361362 4.032101875 99999999.68 -7.999999999 1.226881366 SSSSSSQPEHSAMLVSTAAS(ph)PSLIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSSSSQPEHSAMLVSTAASPSLIK 25 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 SSSSSSQPEHSAMLVSTAAS(1)PSLIK;SSSSSSQPEHSAMLVSTAAS(0.999)PSLIK 299.52 2.45E-63 488090000 260390 352260 424160 359430 503000 567880 454890 482320 461110 403820 TRUE FALSE 270670.3983 412757.9148 435213.9581 430524.1812 417500.2397 435998.4763 419234.5332 475855.2893 444514.7412 482940.7974 0.560462897 0.854676012 0.901174555 0.891463682 0.864495694 0.902799015 0.868086804 0.985328413 0.920433195 1 18.88148682 4.821898496 2.15735338 0.91496854 0.411901061 0.863239951 0.042342153 0.305301414 1.328123882 0.010897514 0.319736253 66358.79573 -4.821898496 -0.503067479 SSSSTPTS(ph)PKPLLQSPKPSLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSSTPTSPKPLLQSPKPSLAAR 23 2 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 S(0.008)S(0.008)S(0.007)S(0.021)T(0.023)PT(0.228)S(0.705)PKPLLQS(0.001)PKPSLAAR 48.634 0.076314 349570000 328290 166070 245760 170260 267270 300160 359590 235030 263140 110270 TRUE FALSE 341251.1427 194591.2307 252164.7075 203936.9198 221839.5409 230452.389 331404.3962 231879.8073 253669.6428 131875.2953 2.587680597 1.475570009 1.91214516 1.546437636 1.682191804 1.747502355 2.513013492 1.758326355 1.923556966 1 17.0088148 -1.183035357 8.695189124 0.99999993 1.888012673 0.370619862 0.353229865 4.51E-07 4.29E-08 0.322679988 0.076056396 0.065609185 1.183035357 0.888012742 SSSTGSSSSTGGGGQESQPS(ph)PLALLAATCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSSTGSSSSTGGGGQESQPSPLALLAATCSR 31 0 P08047;H3BVI2;P08047-2 P08047 SP1 Transcription factor Sp1 1 SSSTGSSSSTGGGGQESQPS(1)PLALLAATCSR 164.01 1.03E-12 72796000 8492.3 10203 9084.1 8849.8 10625 14162 10135 12021 9747.4 9325.6 TRUE FALSE 8827.582561 11955.28588 9320.839109 10600.26403 8818.966295 10873.09013 9340.592217 11859.87816 9396.592978 11152.77277 0.791514607 1.071956376 0.835741864 0.950459966 0.79074204 0.974922591 0.837513003 1.063401757 0.842534244 1 13.44511481 1.752705701 25 0.973163381 0.899321813 0.108599677 0.097639709 9.816802837 17374.20111 0.041260318 0.02288114 56.58557082 -1.752705701 -0.073841568 SSSVGSSSSYPIS(ph)PAVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSVGSSSSYPISPAVSR 18 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR 464.76 2.65E-214 3015370000 1395626 1603865 1340284 1274549 1425620 1874260 1404577 1362299 1279396 1343385 TRUE FALSE 1450726.392 1879316.337 1375212.902 1526650.988 1183293.622 1438991.52 1294482.585 1344039.61 1233350.788 1606595.57 0.902981696 1.169750728 0.855979518 0.950239759 0.736522398 0.89567751 0.805730209 0.836576196 0.767679689 1 20.61557537 4.146719667 9.70562985 0.847119634 1.035936323 0.357685419 0.096098574 0.257727724 24.69920764 0.021777447 0.047198839 14019.08493 -4.146719667 0.188816689 SSSVS(ph)PSASFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSSVSPSASFR 11 0 Q04727-4;Q04727;Q04727-3;Q04727-2;H7C4W5;H7C4P7;Q5JSY7 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 SSSVS(0.68)PS(0.32)ASFR;SS(0.001)S(0.017)VS(0.933)PS(0.049)ASFR 182.23 6.16E-06 283320000 299602 543030 444490 516200 487060 631780 393580 488770 414770 603370 TRUE FALSE 311430.5183 636291.1783 456073.7746 618302.8193 404269.7152 485058.6697 362730.1712 482218.8376 399842.5087 721588.7993 0.431590012 0.881791928 0.632041095 0.856863105 0.560249432 0.672209256 0.502682652 0.668273729 0.554114073 1 19.46081742 -1.881089012 6.832158323 1.054304086 0.647425249 0.387085994 0.135616887 0.068935291 0.001199791 0.080692918 0.028498728 0.013149553 1.881089012 -0.406878837 SSSVS(ph)PSSWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSSVSPSSWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 SSSVS(0.952)PS(0.047)S(0.001)WK;SSSVS(0.998)PS(0.002)SWK;SSSVS(0.995)PS(0.005)SWK 167.18 5.58E-06 431580000 1021920 717910 923970 857040 1148230 1188950 1179680 1008190 1043590 724670 TRUE FALSE 1062266.191 841205.4579 948049.4172 1026559.954 953054.2747 912834.3812 1087213.599 994676.8621 1006031.4 866655.2119 1.225707959 0.970634511 1.093917632 1.18450791 1.099692544 1.053284361 1.25449381 1.147719241 1.160820804 1 19.72509862 SST(ph)PKGDMSAVNDESF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSTPKGDMSAVNDESF 16 1 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 SS(0.013)T(0.987)PKGDMSAVNDESF;SS(0.053)T(0.946)PKGDMSAVNDESF 147.64 6.43E-06 298790000 398980 288220 355220 219600 578680 514790 345840 365510 402450 283590 TRUE FALSE 414732.0385 337719.543 364477.325 263036.2246 480316.1803 395237.8242 318732.1571 360610.9363 387965.9031 339154.0308 1.222842723 0.995770394 1.074666057 0.775565674 1.416218404 1.165363782 0.939785844 1.06326596 1.14392243 1 18.37158111 -1.149546693 3.220785724 0.999855527 1.080211993 0.023736618 0.162644051 17830828830 24910410581 26474047.66 0.037960341 0.070868511 1.149546693 0.080356466 SST(ph)PLHS(ph)PSPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.246)S(0.324)T(0.429)PLHS(0.997)PS(0.003)PIR;S(0.003)S(0.245)T(0.752)PLHS(0.755)PS(0.245)PIR;S(0.264)S(0.328)T(0.409)PLHS(0.931)PS(0.069)PIR;S(0.27)S(0.329)T(0.402)PLHS(0.997)PS(0.003)PIR 176.86 0.00012739 1813235000 1032308 1273060 1395385 1234645 1646974 1816128 1354590 1394328 1319459 1236518 TRUE FALSE 1073064.317 1491698.152 1431749.879 1478854.096 1367021.948 1394359.796 1248413.696 1375639.314 1271971.928 1478790.028 0.725636701 1.008728842 0.96819011 1.000043325 0.924419236 0.942905869 0.844212953 0.930246545 0.860143702 1 20.49598579 SST(ph)PLPTISSSAENTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.001)S(0.082)T(0.917)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;SST(1)PLPTISSSAENTR;SS(0.002)T(0.998)PLPTISSSAENTR;SS(0.019)T(0.981)PLPTISSSAENTR;SS(0.072)T(0.928)PLPTISSSAENTR;S(0.028)S(0.028)T(0.944)PLPTISSSAENTR;S(0.218)S(0.218)T(0.564)PLPTISSSAENTR 414.86 3.17E-139 16464470000 3053120 3161730 3245480 3119520 3962770 4836900 3632320 3314990 3285070 3382960 TRUE FALSE 3173659.535 3704732.533 3330059.875 3736551.745 3289179.771 3713603.279 3347609.267 3270557.981 3166840.972 4045786.241 0.784435792 0.915701501 0.823093381 0.923566279 0.812989015 0.91789409 0.827431077 0.808386253 0.782750443 1 21.94798867 SST(ph)PPGESYFGVSSLQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 S(0.122)S(0.122)T(0.757)PPGESYFGVSSLQLK;S(0.114)S(0.114)T(0.77)PPGES(0.001)Y(0.001)FGVSSLQLK;S(0.015)S(0.015)T(0.97)PPGESYFGVSSLQLK;S(0.108)S(0.108)T(0.785)PPGESYFGVSSLQLK;S(0.074)S(0.074)T(0.851)PPGESYFGVSSLQLK 180.64 8.67E-13 4313100000 3303504 2358949 3046789 2392430 3898070 3857770 3607573 3226960 3382669 2134400 TRUE FALSE 3433928.889 2764080.141 3126190.824 2865645.513 3235477.454 2961861.383 3324802.002 3183707.879 3260927.403 2552594.814 1.345269868 1.082851115 1.224710952 1.122640184 1.267524887 1.160333542 1.302518513 1.247243731 1.277495114 1 21.28353312 3.211972215 24.99906703 1.227162158 1.188141193 0 0.103786456 902.3745249 848432.3549 0.027642689 0.033047267 1629.191799 -3.211972215 -0.039020965 SST(ph)PSHGQTTATEPTPAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 S(0.156)S(0.156)T(0.681)PS(0.006)HGQTTATEPTPAQK 201.24 2.24E-15 538240000 397300 440510 495140 338730 633710 625060 574030 565660 544920 396890 TRUE FALSE 412985.7108 516164.1658 508043.7552 405729.783 525992.2006 479899.2879 529036.0287 558078.2529 525308.4356 474652.9966 0.870079224 1.087455825 1.070347725 0.854792419 1.10816155 1.011052898 1.114574294 1.175760518 1.106720993 1 18.85651367 2.543069243 1.588191166 1.119476915 0.993367723 0.214886103 0.089433796 0.506631686 2.58285487 0.038998893 0.031910961 349.1959859 -2.543069243 -0.126109192 SST(ph)SPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.069)S(0.069)T(0.43)S(0.43)PS(0.002)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 237.47 7.43E-50 190690000 27198 28443 28952 37826 39555 47103 39453 31242 37363 32688 TRUE FALSE 28271.79804 33327.86399 29706.5129 45307.8699 32831.45523 36164.0421 36360.57077 30823.25209 36018.31293 39092.58775 0.723200987 0.852536655 0.759901419 1.158988763 0.839838371 0.925086933 0.930114195 0.788467939 0.921359137 1 15.25460747 SSTAISSIAADGEFLHELEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSTAISSIAADGEFLHELEEK 21 0 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 201.31 7.00E-22 125728000 76452 55033 76989 64704 96284 108589 105705 80251 82275 47639 FALSE TRUE 79470.38399 64484.48965 78995.39659 77502.25808 79917.68007 83370.85043 97419.56589 79175.36661 79313.93882 56972.94995 1.39487922 1.131843967 1.386542151 1.360334302 1.402730246 1.463340945 1.709926658 1.389701019 1.392133265 1 15.79798949 4.024901293 22.02036732 1.421663948 1.262318756 0.053391718 0.174138536 116.1264791 102685.1728 0.041071387 0.088710766 10590.13005 -4.024901293 -0.159345193 SSTEESS(ph)PQDQPPVMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSTEESSPQDQPPVMR 16 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 1 SSTEES(0.001)S(0.999)PQDQPPVMR;SSTEES(0.005)S(0.995)PQDQPPVMR 316.96 6.50E-38 360830000 426330 479200 483960 476450 557040 621740 492460 501410 505430 498470 TRUE FALSE 443161.8376 561498.8723 496572.3952 570690.3879 462354.5398 477350.3076 453859.6984 494689.4191 487239.673 596135.6527 0.743390931 0.941897821 0.832985568 0.957316318 0.775586123 0.800741082 0.761336277 0.829826931 0.817330201 1 19.18528113 3.199066777 24.99999597 0.816898879 0.871547397 0.032201315 0.083045166 365.4448969 231329.0538 0.022096418 0.026410632 1581.491189 -3.199066777 0.054648518 SSTFPQTDVLSSS(ph)LEAEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-3;Q86WP2;Q86WP2-2;Q86WP2-4 D4PHA4 GPBP1 Vasculin 1 SSTFPQTDVLSS(0.041)S(0.959)LEAEHR;SSTFPQTDVLSS(0.05)S(0.95)LEAEHR;SSTFPQTDVLSS(0.053)S(0.947)LEAEHR;SSTFPQTDVLSS(0.054)S(0.945)LEAEHR 192.12 5.25E-15 1764690000 1283090 1707710 1830300 1847820 2072410 2470040 1992320 2058350 1945050 1997250 TRUE FALSE 1333747.384 2000995.908 1877999.122 2213313.281 1720142.488 1896410.644 1836156.752 2030761.185 1875048.03 2388572.898 0.558386719 0.837737006 0.786243168 0.926625804 0.720154905 0.793951336 0.76872544 0.850198538 0.785007664 1 21.18771748 -5 0.134919645 1.691671456 0.708434697 0.392380648 0.087528423 153.0707944 1.285331002 28.76708527 0.574419032 1.00E-05 5 -0.983236759 SSTLSSSSMSLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SSTLSSSSMSLSPK 14 0 O15119;O15119-2;O15119-3 O15119 TBX3 T-box transcription factor TBX3 1 SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMSLS(1)PK;SSTLSSSSMS(0.077)LS(0.923)PK;SSTLSSSSMS(0.001)LS(0.999)PK;SSTLSSSSMS(0.006)LS(0.994)PK 237.05 1.09E-16 2068490000 3719870 1637640 2114870 1650684 3113960 3481460 2862090 2363210 2481680 1339713 TRUE FALSE 3866733.34 1918891.931 2169985.25 1977184.368 2584650.191 2672943.677 2637751.907 2331535.035 2392364.822 1602204.112 2.413383732 1.1976576 1.354375035 1.234040253 1.613184096 1.66829161 1.646327011 1.455204751 1.493171066 1 20.61162652 0.4025832 1.226093379 0.999721933 1.550087726 0.217420743 0.322818786 4.511160569 7.740781545 0.295831252 0.088612814 2.526871752 -0.4025832 0.550365793 SSTPLHS(ph)PSPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSTPLHS(0.985)PS(0.014)PIR 78.191 0.017001 467070000 88332 1733000 1514000 1777100 1297300 2025500 1038800 1597600 1227500 2007200 TRUE FALSE 91819.41557 2030629.269 1553456.084 2128605.076 1076785.409 1555108.322 957376.1416 1576186.785 1183322.515 2400472.41 0.038250561 0.845929018 0.647145986 0.886744237 0.448572291 0.647834283 0.398828221 0.656615247 0.492954016 1 21.19488692 -1.088540225 4.066312951 1.00007353 0.580684109 0.241661121 0.230472417 11948840 6397344.614 8118.418869 0.049604902 0.081556724 1.088540225 -0.419389421 SSTPLHSPS(ph)PIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SS(0.002)T(0.092)PLHS(0.321)PS(0.585)PIR 74.537 0.038011 195820000 54732 86711 91124 95506 121860 125060 113730 102370 94985 109780 TRUE FALSE 56892.86162 101602.9397 93498.7663 114396.8017 101146.2807 96016.7103 104815.5454 100997.8976 91566.5084 131289.2891 0.433339703 0.773885977 0.712158371 0.87133385 0.770407711 0.731336965 0.798355647 0.769277511 0.697440812 1 17.0023897 -4.999999988 0.035328209 2.155933889 3.45E-13 0.435072969 0.102342506 1123.509257 2.97704524 152.9225415 52.88887681 1.00E-05 4.999999988 -2.155933889 SSTS(ph)PCGTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SSTSPCGTSK 10 0 H0Y459;O75376;O75376-2;A0A088AWL3;O75376-3 H0Y459;O75376 NCOR1 Nuclear receptor corepressor 1 1 SS(0.001)T(0.124)S(0.874)PCGT(0.001)SK;SST(0.103)S(0.897)PCGTSK;SST(0.002)S(0.998)PCGTSK;SST(0.049)S(0.949)PCGT(0.002)SK 155.99 1.23E-05 288488000 1386540 926970 1156420 1040210 1472670 1573700 1648860 1295420 1356330 779030 TRUE FALSE 1441281.67 1086169.887 1186557.255 1245960.433 1222346.079 1208232.025 1519618.045 1278057.014 1307515.948 931666.0131 1.546993933 1.165836117 1.273586498 1.337346663 1.31200029 1.296851026 1.631075969 1.371797399 1.403417029 1 19.82945334 SSTS(ph)PSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.116)S(0.116)T(0.116)S(0.629)PS(0.022)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR;S(0.023)S(0.023)T(0.135)S(0.816)PS(0.004)IINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 315.47 5.58E-110 191006000 36441 55544 56176 57987 60719 74184 59623 61754 62216 53684 TRUE FALSE 37879.71882 65083.24993 57639.99271 69456.65553 50398.00607 56955.89027 54949.59346 60926.28864 59976.85831 64202.35196 0.590005158 1.01372065 0.897786311 1.081839737 0.784986913 0.8871309 0.855881316 0.948972846 0.934184753 1 15.97033853 4.74774587 24.85515432 0.927103183 0.590004967 0.619802413 0.080632019 742.5808707 2009366.615 0.018485233 0.231253692 55943.01521 -4.74774587 -0.337098216 SSTSPSIINEDVIINGHSHEDDNPFAEY(ph)MWMENEEEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNR 39 0 Q9BPZ3;D6RA77;D6R9Y1 Q9BPZ3 PAIP2 Polyadenylate-binding protein-interacting protein 2 1 S(0.134)S(0.134)T(0.134)S(0.134)PS(0.125)IINEDVIINGHS(0.165)HEDDNPFAEY(0.173)MWMENEEEFNR 43.271 0.064512 19162000 3018.4 4183.5 5283.2 3142.2 4501.5 6725.3 4681.2 4386.9 3724.6 4325.1 TRUE FALSE 3137.568763 4901.983582 5420.884532 3763.717781 3736.336638 5163.450998 4314.275312 4328.100781 3590.552374 5172.520536 0.606584109 0.947697268 1.048016048 0.727637088 0.72234351 0.998246592 0.834076014 0.836748883 0.694159134 1 12.33665175 -2.452461504 2.310552708 2.840741484 0.83426258 0.129661501 0.134467948 4433386.833 883370.9762 43134280.09 0.031972696 0.003528081 2.452461504 -2.006478904 SSTVATLQGTPDHGDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSTVATLQGTPDHGDPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;; 128.26 3.75E-05 766440000 812580 1063760 1004640 1079120 1054230 1341220 1102580 1097650 1001290 925910 FALSE TRUE 844661.2858 1246452.505 1030821.744 1292566.715 875032.3612 1029741.981 1016156.899 1082937.797 965253.7685 1107324.337 0.762794836 1.125643557 0.930912208 1.167288275 0.790222279 0.929937099 0.917668712 0.977977058 0.871699227 1 20.07864642 3.221479292 24.99946649 0.918813509 1.001176703 0.106665739 0.115680688 533.0779601 780187.3572 0.031214517 0.037395052 1665.249424 -3.221479292 0.082363194 SSVASGPIS(ph)PTNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVASGPISPTNYR 14 0 Q9BYK8 Q9BYK8 HELZ2 Helicase with zinc finger domain 2 1 SSVASGPIS(0.979)PT(0.021)NYR 118.19 0.00027245 213450000 96010 74343 78169 76709 103860 128730 96593 85921 77766 75381 TRUE FALSE 99800.54894 87110.83194 80206.14836 91881.81125 86205.9143 98834.40842 89021.78826 84769.36953 74967.21685 90150.46369 1.107044211 0.966282683 0.889692022 1.019205088 0.956244824 1.096327233 0.987480093 0.940309856 0.831578827 1 16.46004729 1.636243004 3.76696678 0.908469271 0.999862834 0.206071039 0.071378986 0.268685315 8.949351131 0.041442485 0.018479 43.27559059 -1.636243004 0.091393563 SSVQGAS(ph)SREGS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 SSVQGAS(0.547)S(0.453)REGS(1)PAR;SSVQGAS(0.55)S(0.45)REGS(1)PAR 105.67 0.00073784 4974700000 1786650 2089140 2102480 1628040 2423230 2689200 1558240 1966950 2077920 2230590 TRUE FALSE 1857188.322 2447933.544 2157272.356 1950061.453 2011330.23 2064674.055 1436101.077 1940586.253 2003136.065 2667631.403 0.696193754 0.917643097 0.808684571 0.731008583 0.753976066 0.773972766 0.538343144 0.727456668 0.750904365 1 21.34712791 2.448792001 24.99985655 0.715640148 0.785390335 0 0.119838067 597.0352204 526865.3937 0.039624109 0.033152433 281.0554432 -2.448792001 0.069750187 SSVQGASS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SSVQGASSR 9 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 SSVQGAS(0.061)S(0.939)R;SSVQGAS(0.015)S(0.985)R 83.455 0.016949 745260000 1588700 1634560 1685540 1729580 1800320 2206860 2019710 1929830 1715240 1443080 TRUE FALSE 1651423.103 1915282.965 1729466.557 2071685.762 1494302.249 1694350.21 1861399.853 1903963.785 1653508.847 1725823.897 0.956889695 1.109778911 1.002110679 1.200403915 0.865848626 0.981763095 1.078557237 1.103220201 0.958098246 1 20.71885383 SSVQGASS(ph)REGS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SSVQGASSREGSPAR 15 1 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 2 S(0.001)S(0.001)VQGAS(0.092)S(0.906)REGS(1)PAR;SSVQGAS(0.424)S(0.576)REGS(1)PAR;S(0.002)S(0.003)VQGAS(0.322)S(0.674)REGS(0.999)PAR 142.97 5.37E-05 1666090000 2145470 2365860 2503560 1712620 3004200 3518090 1977190 2357580 2341080 2634750 TRUE FALSE 2230174.812 2772178.051 2568804.83 2051371.124 2493547.157 2701066.915 1822212.681 2325980.496 2256824.988 3150978.817 0.707772074 0.879783144 0.815240273 0.651026631 0.791356369 0.857215193 0.578300518 0.738177129 0.716229819 1 21.58736863 SSVS(ph)HSVLSEMQVIEQETPVSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVSHSVLSEMQVIEQETPVSAK 23 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 S(0.204)S(0.204)VS(0.276)HS(0.276)VLS(0.04)EMQVIEQETPVSAK 136.67 6.74E-06 45462000 48621 56934 82202 63356 121170 88479 80259 77991 85524 69393 TRUE FALSE 50540.59462 66711.97161 84344.25165 75887.6277 100573.5667 67931.09316 73968.08986 76945.65821 82446.00795 82989.22974 0.609001852 0.803863005 1.016327684 0.914427426 1.211886976 0.818553123 0.891297462 0.927176435 0.99345431 1 16.3406365 4.548388949 2.726934053 0.963853516 0.600056074 0.567979972 0.099173084 0.234274852 2.926878049 0.024593108 0.155258706 35349.96178 -4.548388949 -0.363797442 SSVSHS(ph)VLSEMQVIEQETPVSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVSHSVLSEMQVIEQETPVSAK 23 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 S(0.043)S(0.043)VS(0.146)HS(0.622)VLS(0.146)EMQVIEQETPVSAK 102.9 1.56E-05 0 22727 22267 26014 27530 41806 32240 25086 28364 28814 23177 TRUE FALSE 23624.27951 26091.18404 26691.94621 32975.35183 34699.83105 24752.7486 23119.69377 27983.82697 27776.98977 27718.0894 0.852305481 0.941305285 0.962979296 1.189669005 1.251883943 0.89301785 0.834101277 1.009587153 1.002124979 1 14.7585402 -0.738566746 9.413764956 0.999992102 0.995136055 1.80E-05 0.128340537 0 0 0.132508504 0.031232554 0.182571613 0.738566746 -0.004856047 SSVSHSVLS(ph)EMQVIEQETPVSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSVSHSVLSEMQVIEQETPVSAK 23 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 S(0.186)S(0.186)VS(0.186)HS(0.208)VLS(0.234)EMQVIEQETPVSAK 65.775 0.0046843 0 17149 24537 26846 25493 36433 31439 24470 25994 22852 33767 TRUE FALSE 17826.05576 28751.03888 27545.62881 30535.43931 30240.13167 24137.76871 22551.97746 25645.59295 22029.56098 40382.99714 0.441424783 0.711959015 0.68210957 0.756145939 0.748833267 0.597721081 0.558452296 0.635059177 0.54551575 1 15.30146037 -1.54350085 3.108927041 1.013801869 0.637604386 0.579369827 0.09421372 69097142.95 76835709.72 7941157.507 0.022825634 0.028608768 1.54350085 -0.376197483 KEELGAS(ph)SPSYGPPNLGFVDSPSSGTHLGGLELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KEELGASSPSYGPPNLGFVDSPSSGTHLGGLELK 34 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 KEELGAS(0.538)S(0.454)PS(0.008)YGPPNLGFVDSPSSGTHLGGLELK 127.17 3.08E-08 211850000 38694 78603 96009 81395 140290 137930 104560 122300 133350 82467 TRUE FALSE 40221.669 92102.4538 98511.07341 97494.68806 116443.5559 105897.8478 96364.31398 120660.7685 128550.7595 98624.82972 0.407824978 0.933866797 0.998846575 0.988541003 1.180671807 1.073744291 0.977079649 1.223431958 1.303432005 1 16.58966328 4.868643457 1.303656387 1.113630278 3.37E-20 0.798330474 0.103872778 0.796561933 0.956888269 0.029554125 1.275449603 73899.83307 -4.868643457 -1.113630278 down SSWYWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SSWYWGR 7 0 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 0 107.43 0.0174 489230000 390370 422990 401800 379300 725080 587210 508790 445370 468790 671210 FALSE TRUE 405782.109 495635.2421 412271.2381 454324.4079 601831.1606 450839.3768 468909.7103 439400.5436 451918.3395 802720.7484 0.505508435 0.617444165 0.513592353 0.565980646 0.749739136 0.561639123 0.58415048 0.547389045 0.562983255 1 19.61453866 -1.34564094 5.476050585 1.000109646 0.579954824 0.791494869 0.064865489 8.56E-05 1.02E-05 0.061905464 0.014587478 0.045118958 1.34564094 -0.420154822 SSYSS(ph)PTSLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.019)S(0.981)PTS(0.058)LS(0.942)PR;SSYS(0.016)S(0.983)PT(0.001)S(0.006)LS(0.994)PR 240.73 4.25E-16 1080850000 1051950 1121010 1052540 1021130 1230850 1351180 1083940 1143730 995960 989540 TRUE FALSE 1093481.798 1313534.747 1079970.057 1223106.466 1021630.557 1037388.922 998977.9504 1128400.17 960115.5942 1183421.417 0.924000345 1.109946743 0.912582823 1.033534165 0.863285506 0.876601443 0.844143883 0.953506632 0.8113049 1 20.17453248 3.235390382 24.99977913 0.889686855 0.997337276 0.331178431 0.072028363 87.27435626 688227.3203 0.019005245 0.023639071 1719.453289 -3.235390382 0.107650421 SSYSSPTSLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 222.81 3.79E-11 877720000 1103293 1089866 1062039 991467 1314937 1549640 1146077 1117884 1062915 1020538 TRUE FALSE 1146851.86 1277042.008 1089716.609 1187576.213 1091424.478 1189759.595 1056244.49 1102900.593 1024660.897 1220492.882 0.939662883 1.046333024 0.892849623 0.97303002 0.89424895 0.974818955 0.865424539 0.903651803 0.839546803 1 20.21903245 3.592642773 0.772686247 0.901454242 0.987354996 0.137279673 0.057259729 1.301807267 1.479491925 0.025379173 0.074488393 3914.197837 -3.592642773 0.085900753 ST(ph)DEEEEAQTPQAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STDEEEEAQTPQAPR 15 0 Q9P2K3;Q9P2K3-3 Q9P2K3 RCOR3 REST corepressor 3 1 S(0.205)T(0.795)DEEEEAQTPQAPR 268.13 1.65E-24 72805000 47501 43916 38278 53954 51677 64430 64680 54354 48615 40745 TRUE FALSE 49376.37616 51458.23138 39275.55613 64625.94016 42892.962 49467.10895 59610.21259 53625.47354 46865.35565 48728.20264 1.013301815 1.05602564 0.806012822 1.326253313 0.880249212 1.015163833 1.223320569 1.100501776 0.961770661 1 15.57246939 ST(ph)FSTNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.175)T(0.687)FS(0.094)T(0.044)NYR;S(0.011)T(0.692)FS(0.296)T(0.001)NYR 150.18 0.005515 584490000 569630 562670 572360 504700 602040 686570 535590 516410 616060 508950 TRUE FALSE 592119.4323 659304.1955 587276.1718 604528.1536 499705.4558 527124.5226 493609.0563 509488.3686 593888.1209 608669.0081 0.972810221 1.083190021 0.964853088 0.99319687 0.820980614 0.866028195 0.810964662 0.837053245 0.975716051 1 19.21529838 3.311432587 6.677666836 0.868693304 1.008057812 0.420125527 0.066482951 0.173928306 12.76717116 0.01789877 0.0242116 2048.484053 -3.311432587 0.139364508 ST(ph)PDSTYSESFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STPDSTYSESFK 12 0 Q6ISB3;Q6ISB3-2 Q6ISB3 GRHL2 Grainyhead-like protein 2 homolog 1 S(0.247)T(0.752)PDS(0.001)TYSESFK;S(0.124)T(0.876)PDSTYSESFK;S(0.232)T(0.768)PDSTYSESFK;S(0.059)T(0.941)PDSTYSESFK 381.9 1.00E-86 1557680000 2797350 1611600 2089220 1739870 2647400 2800620 2959420 2158470 2366860 1212810 TRUE FALSE 2907791.538 1888379.763 2143666.79 2084011.093 2197395.894 2150218.449 2727452.927 2129539.24 2281677.171 1450436.899 2.004769418 1.301938585 1.47794557 1.436816103 1.514988963 1.482462595 1.880435426 1.468205368 1.573096474 1 20.4680561 -0.467675245 1.873417186 0.999246996 1.559181043 0.418707795 0.201450278 622.0080445 778.8331853 4.092038467 0.050315555 0.340662834 0.467675245 0.559934046 ST(ph)PVRDR ddPTM_MDA-MB-175_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(0.399)T(0.601)PVRDR 93.649 0.023895 363290000 604220 546430 608340 535240 679420 702940 636010 616700 595860 465910 TRUE FALSE 628075.0722 640275.1019 624193.8402 641108.8745 563932.4311 539692.8382 586157.8743 608434.1452 574415.115 557196.1441 1.127206422 1.149101817 1.120240775 1.150598189 1.012089615 0.968586814 1.051977621 1.091956848 1.03090289 1 19.08782575 3.241125554 24.99993043 1.033772119 1.1364846 0.738900835 0.032083155 42.1222867 410552.9979 0.010420813 0.013490962 1742.310502 -3.241125554 0.10271248 ST(ph)SFRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.067)T(0.466)S(0.466)FRGGMGSGGLATGIAGGLAGMGGIQNEK 221.67 1.57E-34 2553600000 1347700 974250 1664700 734940 2441200 1669300 1483800 1725100 2254700 1360300 TRUE FALSE 1400908.237 1141569.859 1708083.45 880308.9384 2026245.696 1281630.373 1367495.879 1701977.856 2173553.787 1626824.74 0.861130398 0.701716559 1.049949271 0.541120943 1.24552181 0.787810968 0.84059201 1.046196197 1.336071264 1 20.63362741 1.565380784 3.94001958 1.175263233 0.862823706 0.294468244 0.193795875 0.20059693 7.032679669 0.110648165 0.046887946 36.76044703 -1.565380784 -0.312439527 ST(ph)SFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.115)T(0.483)S(0.402)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.066)T(0.462)S(0.462)FRGGMGS(0.011)GGLATGIAGGLAGMGGIQNEKETMQSLNDR 237.12 1.64E-50 807928000 233576 298188 415230 118175 598028 354938 200447 394571 473901 543448 TRUE FALSE 242797.7608 349399.4694 426051.2349 141549.6623 496375.4142 272509.0286 184735.4404 389282.4211 456845.3956 649926.2307 0.373577414 0.537598658 0.655537836 0.217793429 0.763741161 0.419292245 0.284240629 0.59896401 0.702918845 1 19.30991645 1.003041348 1.855676259 0.9947254 0.475831903 0.525572675 0.156184551 0.264508465 1.902332942 0.140005491 0.039754378 10.0702754 -1.003041348 -0.518893497 ST(ph)SPSTSSEAEPVKTVDSTPLSVHT(ph)PTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSPSTSSEAEPVKTVDSTPLSVHTPTLR 29 1 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;H0Y6V3 Q5VT25-2 CDC42BPA Serine/threonine-protein kinase MRCK alpha 2 S(0.294)T(0.324)S(0.324)PS(0.015)T(0.017)S(0.02)S(0.005)EAEPVKTVDSTPLS(0.003)VHT(0.97)PT(0.027)LR 103.57 0.00062767 61465000 16295 34589 32733 34664 49056 53327 34164 35698 28088 40041 TRUE FALSE 16938.33918 40529.39168 33586.04887 41520.43574 40717.47864 40942.61243 31486.13641 35219.5267 27077.11837 47886.26732 0.353720182 0.846367737 0.701371202 0.867063525 0.850295521 0.854996948 0.657519121 0.735482815 0.565446419 1 15.54732436 4.744692313 24.41758325 0.774539496 0.353719921 0.542527897 0.118767644 381.5156811 1519208.496 0.027354042 0.249771293 55551.05524 -4.744692313 -0.420819575 ST(ph)TPTSSPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;H7C5N8;A0A2R8YET2;A0A2R8Y7F4;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.018)T(0.486)T(0.486)PT(0.01)SSPFR;S(0.011)T(0.494)T(0.494)PT(0.001)SSPFR 123.96 0.0050114 2002060000 2212100 2375600 2261500 2090600 2801800 2946800 2436900 2277000 2169200 2588900 TRUE FALSE 2299435.416 2783590.82 2320436.548 2504114.44 2325551.037 2262450.359 2245889.41 2246480.539 2091130.916 3096145.388 0.742676822 0.899050423 0.749459815 0.808784513 0.751111704 0.730731305 0.725382412 0.725573337 0.675398166 1 21.56204179 3.226235758 10.96902057 0.748040625 0.80346583 5.98E-05 0.092662987 0.844934869 725.115519 0.024389059 0.029978276 1683.587753 -3.226235758 0.055425204 STAGDTHLGGEDFDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 STAGDTHLGGEDFDNR 16 0 P11142;E9PKE3;P11142-2;E9PN89;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 ;;;;;;;;;;; 228.73 3.83E-15 90991340000 16784820 21806540 21697330 20265450 22722890 25635360 20415000 22433740 20200620 21020240 FALSE TRUE 17447497.65 25551643.61 22262780.24 24273895.52 18860461.27 19681936.15 18814818.96 22133052.41 19473603.63 25138753.57 0.694047842 1.016424444 0.885596025 0.965596622 0.750254432 0.782932061 0.748438816 0.880435553 0.774644756 1 24.58340978 4.846831405 19.43951134 0.856502674 0.693882874 0.215304519 0.097245562 85820.46651 15369271.91 0.023030473 1584.505293 70279.94371 -4.846831405 -0.1626198 STAPETAIECTQAPAPAS(ph)EDEKVVVEPPEGEEKVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STAPETAIECTQAPAPASEDEKVVVEPPEGEEKVEK 36 2 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y4X2;A0A2R8Y445;A0A2R8YER1;A0A2R8YDW2;A0A2R8Y7I0;A0A2R8Y7M9;A0A2R8Y5M9;A0A2R8YE38;A0A2R8Y6G9 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 STAPETAIECTQAPAPAS(1)EDEKVVVEPPEGEEKVEK 86.8 0.0004812 88053000 80837 30905 41853 26496 70764 69886 58212 45675 54438 19939 TRUE FALSE 84028.50718 36212.69334 42943.72356 31736.82972 58735.56056 53656.03563 53649.19133 45062.80133 52478.78701 23845.66529 3.523848303 1.518627931 1.800902723 1.330926578 2.463154617 2.250137917 2.249850892 1.889769095 2.200768415 1 14.54143941 -1.129853383 3.902633454 0.999632089 2.087414117 0.25762055 0.573339471 8557675.851 3716383.926 30353.25016 0.126476527 0.074156055 1.129853383 1.087782028 STAPSAAASASASAAAS(ph)SPAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASAS(0.001)AAAS(0.5)S(0.5)PAGGGAEALELLEHCGVCR 85.864 0.00053621 38570000 5054.6 6955.8 6706.7 8932.1 8468.9 8894.8 6730.7 6096.1 6766.6 6700.4 TRUE FALSE 5254.159511 8150.404541 6881.482112 10698.84272 7029.359403 6829.117502 6203.130147 6014.391751 6523.071388 8013.215093 0.655686819 1.0171204 0.858766679 1.335149824 0.877220856 0.852231897 0.774112522 0.75055913 0.814039223 1 12.96816549 3.009374737 24.99369096 0.816992336 0.980526767 0.105364537 0.169834484 363.298352 968570.2801 0.048367381 0.057741429 1021.820795 -3.009374737 0.16353443 STAPSAAASASASAAASS(ph)PAGGGAEALELLEHCGVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 STAPSAAASASASAAASSPAGGGAEALELLEHCGVCR 37 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 1 STAPSAAASASASAAAS(0.019)S(0.981)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.087)S(0.913)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.008)S(0.992)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.005)S(0.995)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.015)S(0.985)PAGGGAEALELLEHCGVCR;STAPSAAASASAS(0.001)AAAS(0.205)S(0.794)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.008)S(0.992)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.058)S(0.942)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.273)S(0.727)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.061)S(0.939)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.034)S(0.966)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.004)S(0.996)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.002)S(0.998)PAGGGAEALELLEHCGVCR;STAPSAAASASASAAAS(0.003)S(0.997)PAGGGAEALELLEHCGVCR 337.78 1.56E-129 31110010000 1008510.1 1258177.6 1154925.7 1251758.5 1303394.6 1580402 1222142.4 1311460.2 1175377.6 1316674.1 TRUE FALSE 1048326.857 1474259.816 1185024.013 1499352.595 1081844.051 1213377.587 1126347.685 1293882.221 1133075.99 1574651.181 0.6657518 0.936245331 0.75256287 0.952180784 0.687037272 0.770569128 0.715299807 0.821694504 0.719572692 1 20.58660085 -1.137316245 3.785617693 1.000109617 0.785792331 0.333317876 0.092985299 4745216.398 2853487.271 4146.02102 0.019941645 0.072892653 1.137316245 -0.214317286 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 STAQQELDGKPASPTPVIVASHTANK 26 1 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.995)PT(0.005)PVIVASHTANK;STAQQELDGKPAS(0.989)PT(0.011)PVIVASHTANK;STAQQELDGKPAS(0.922)PT(0.078)PVIVASHTANK;STAQQELDGKPAS(0.998)PT(0.002)PVIVASHTANK;STAQQELDGKPAS(0.944)PT(0.056)PVIVASHTANK;STAQQELDGKPAS(0.998)PT(0.002)PVIVASHTANK 339.74 1.32E-95 6775960000 6199160 2511081 3596910 3206153 4848240 5091300 6147110 3853100 4258620 1503120 TRUE FALSE 6443907.624 2942339.628 3690648.429 3840320.494 4024137.897 3908922.734 5665283.456 3801455.497 4105353.098 1797627.585 3.584673309 1.63679043 2.053066197 2.136327082 2.238582635 2.174489737 3.151533445 2.114706922 2.283761738 1 20.77766274 4.753084841 24.11921316 2.176009064 3.584674922 0.422448076 0.515885468 1535.961851 2550576.774 0.116627878 2.440978506 56634.99162 -4.753084841 1.408665858 STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 P35606;P35606-2;H0YAC7 P35606 COPB2 Coatomer subunit beta 1 STAQQELDGKPAS(0.993)PT(0.007)PVIVASHTANKEEK;STAQQELDGKPAS(0.991)PT(0.009)PVIVASHTANKEEK;STAQQELDGKPAS(1)PTPVIVASHTANKEEK;STAQQELDGKPAS(0.996)PT(0.004)PVIVASHTANKEEK;STAQQELDGKPAS(0.994)PT(0.006)PVIVASHTANKEEK;STAQQELDGKPAS(0.974)PT(0.026)PVIVASHTANKEEK;STAQQELDGKPAS(0.996)PT(0.004)PVIVASHTANKEEK;STAQQELDGKPAS(0.997)PT(0.003)PVIVASHTANKEEK;STAQQELDGKPAS(0.981)PT(0.019)PVIVASHTANKEEK;S(0.023)T(0.023)AQQELDGKPAS(0.857)PT(0.096)PVIVAS(0.001)HTANKEEK;STAQQELDGKPAS(0.978)PT(0.022)PVIVASHTANKEEK;STAQQELDGKPAS(0.944)PT(0.056)PVIVASHTANKEEK;STAQQELDGKPAS(0.841)PT(0.159)PVIVASHTANKEEK 273.01 2.14E-71 45504885000 7841713 1993790 3674723 2009219 6099586 5277859 5432366 3824985 4726286 1498040 TRUE FALSE 8151309.884 2336207.923 3770489.3 2406636.521 5062780.55 4052156.234 5006562.958 3773717.332 4556187.89 1791552.256 4.549858848 1.304013274 2.104593537 1.343324769 2.825918436 2.261813028 2.794539172 2.106395345 2.543150988 1 20.77277869 -0.625830142 6.287053135 0.999999997 2.355507843 0.191690276 0.867661804 3.43E-08 7.27E-09 0.76735026 0.180866191 0.236684522 0.625830142 1.355507846 STAS(ph)PASTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.977)PAS(0.023)TK;STAS(0.998)PAS(0.002)TK;STAS(0.999)PAS(0.001)TK;STAS(0.978)PAS(0.022)TK;STAS(1)PASTK;STAS(0.996)PAS(0.004)TK;STAS(0.999)PAS(0.001)TK 211.84 4.71E-06 3168063000 7383090 5334816 6662509 5269624 7903460 8059960 8116200 6923768 7183620 4636507 TRUE FALSE 7674580.094 6251029.149 6836139.458 6311939.899 6560032.692 6188156.44 7480031.036 6830966.215 6925082.919 5544941.775 1.384068653 1.127339006 1.232860458 1.138323927 1.183066109 1.116000256 1.348982792 1.231927492 1.248900926 1 22.40274088 4.752173053 24.29149384 1.195757254 1.384068839 0.300653684 0.090448905 2044.741169 3648761.437 0.0206274 0.402898034 56516.21301 -4.752173053 0.188311585 STASDKEEVKPDDLEWASQQSTETGS(ph)LDGSCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STASDKEEVKPDDLEWASQQSTETGSLDGSCR 32 2 Q93073;Q93073-2 Q93073 SECISBP2L Selenocysteine insertion sequence-binding protein 2-like 1 STASDKEEVKPDDLEWASQQSTET(0.005)GS(0.995)LDGSCR 173.7 7.37E-15 152730000 45487 21083 30851 20595 44758 45231 33891 30549 38366 16966 TRUE FALSE 47282.86188 24703.84125 31655.0024 24668.62953 37150.05115 34726.78573 31234.53486 30139.54062 36985.21515 20290.16287 2.330334271 1.217527992 1.560115738 1.215792583 1.830939031 1.711508476 1.539393009 1.485426254 1.822815095 1 14.30849283 -1.142779137 4.698609605 0.999943455 1.602780453 0.269240884 0.309744612 0.000168483 3.07E-05 0.27539485 0.064905125 0.071981495 1.142779137 0.602836998 STAYEDYYYHPPPR ddPTM_MDA-MB-175_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 ;;;;; 161.1 4.65E-06 2998130000 1023431 1295260 1225970 1184310 1393970 1536350 1277170 1351360 1349940 1305250 FALSE TRUE 1063836.846 1517710.829 1257919.785 1418562.983 1157023.477 1179555.996 1177062.078 1333247.23 1301355.923 1560988.747 0.681514744 0.972275317 0.80584808 0.908759263 0.741211927 0.7556467 0.754049048 0.854104318 0.833674122 1 20.57402871 0.545212893 1.421891835 0.999809199 0.81183135 0.333247651 0.080729515 2.262240264 5.774625656 0.073769873 0.021591134 3.509238564 -0.545212893 -0.187977849 STDEPSEKDALQPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 STDEPSEKDALQPGR 15 1 P09467;A0A3B3IUC7;Q5VZC3 P09467 FBP1 "Fructose-1,6-bisphosphatase 1" 0 ;;;;;; 242.41 5.77E-18 5758530000 3953810 2950224 3768910 2698343 4681670 4514970 4065820 3775750 4032680 2767176 FALSE TRUE 4109909.472 3456902.022 3867130.891 3232067.192 3885881.406 3466436.643 3747130.404 3725142.247 3887544.635 3309351.156 1.241907938 1.044586041 1.168546554 0.976646792 1.174212473 1.047467156 1.132285523 1.125641273 1.174715058 1 21.65811695 4.75345517 24.28145097 1.100344326 1.241908089 0.284966021 0.069695248 2256.953353 3679245.573 0.015035042 0.328794168 56683.30573 -4.75345517 0.141563763 STDEVDSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STDEVDSKR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 112.75 0.0030661 199590000 251920 238210 254520 199600 326070 340530 297920 263020 289660 230260 FALSE TRUE 261865.9961 279120.7145 261153.0003 239080.2843 270644.7379 261447.0683 274568.2519 259494.6471 279235.1932 275375.0384 0.950943112 1.01360209 0.948353931 0.868198823 0.982822334 0.949421813 0.997070227 0.942331769 1.014017809 1 18.07103827 1.233047191 24.98930347 1.007008931 0.957179196 0.226920822 0.037209627 218.7232943 991298.8989 0.032281009 0.008984353 17.10201138 -1.233047191 -0.049829736 STDSEVSQS(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STDSEVSQSPAK 12 0 O75175;H7C3F5;A0A2H2FJL5;B7Z6J7;A0A0G2JNJ7;H7C148 O75175 CNOT3 CCR4-NOT transcription complex subunit 3 1 STDSEVSQS(1)PAK;STDSEVSQS(1)PAK;STDSEVS(0.001)QS(0.999)PAK;STDSEVSQS(1)PAK 183.7 1.60E-05 1639720000 4374000 2894570 3444620 2629500 4559840 4889190 4022460 3600370 3912070 2910430 TRUE FALSE 4546688.897 3391689.881 3534389.627 3149607.252 3784760.026 3753749.719 3707169.074 3552112.929 3771275.365 3480673.035 1.306267165 0.974435072 1.015432818 0.90488455 1.087364423 1.078455138 1.065072484 1.020524736 1.08349027 1 21.73093487 4.745220691 24.94628202 1.027177527 1.306267296 0.706093849 0.054329706 423.6918935 1586958.29 0.013226758 0.128176235 55618.68171 -4.745220691 0.279089768 STEDGAELEEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STEDGAELEEQK 12 0 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 0 ; 81.017 0.018781 1535900000 39606 1671030 1738520 1825940 1487990 2037690 1675850 1748100 1662630 1407090 FALSE TRUE 41169.67546 1958016.404 1783827.259 2187105.482 1235061.991 1564467.379 1544492.498 1724669.579 1602792.271 1682782.345 0.024465241 1.163558917 1.060046336 1.299696 0.733940426 0.929690868 0.917820717 1.024891653 0.952465585 1 20.68241716 4.744184337 24.98364195 1.006137222 0.024464819 0.809845652 0.143132662 253.6196712 1126683.826 0.034465308 0.303587167 55486.11753 -4.744184337 -0.981672403 STEESLSEDVFTESELS(ph)PIREELVSSDELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STEESLSEDVFTESELSPIREELVSSDELR 30 1 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573;H0YC07 Q8N573-2 OXR1 Oxidation resistance protein 1 1 S(0.001)T(0.001)EES(0.001)LS(0.009)EDVFT(0.034)ES(0.134)ELS(0.76)PIREELVS(0.031)S(0.031)DELR 45.187 0.06922 13979000 2097.7 3212.8 3892.1 3161.5 5554 3962.1 4463.4 4227.7 3323.4 4143.9 TRUE FALSE 2180.518816 3764.573408 3993.531323 3786.835264 4609.933064 3041.962321 4113.547045 4171.034597 3203.791483 4955.817865 0.439991718 0.759627071 0.805826895 0.764119136 0.930206313 0.613816408 0.830044032 0.841644045 0.646470789 1 12.27490745 4.742249608 3.557791567 0.798077211 0.39650396 0.496154859 0.109234516 0.227512376 5.111377973 0.024233767 0.245827174 55239.48337 -4.742249608 -0.401573251 STELDSNWNWFQLR ddPTM_MDA-MB-175_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 0 158.3 1.18E-05 152850000 174170 187040 168310 157030 252070 269780 205410 180640 197800 178010 FALSE TRUE 181046.3661 219162.665 172696.2969 188090.0653 209223.2314 207127.6836 189309.4275 178218.8163 190681.2166 212887.6513 0.850431507 1.029475706 0.811208616 0.883517969 0.982787072 0.972943627 0.889245695 0.837149619 0.895689419 1 17.69973274 -0.810171836 5.368738789 1.000000039 0.904556202 0.155268357 0.065836412 3.09E-08 6.73E-09 0.063841603 0.015047604 0.154820392 0.810171836 -0.095443837 STELKTEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STELKTEIKEEEDQPSTSATQSSPAPGQSK 30 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 STELKTEIKEEEDQPSTSATQSS(1)PAPGQSK;STELKTEIKEEEDQPS(0.021)T(0.021)S(0.021)AT(0.02)QS(0.225)S(0.692)PAPGQSK;STELKTEIKEEEDQPSTSATQS(0.013)S(0.987)PAPGQSK 347.66 2.46E-120 1160740000 2057310 607090 1084390 461408 1834800 1550320 1294160 1037450 1266500 454736 TRUE FALSE 2138534.187 711352.985 1112650.094 552673.1252 1522921.351 1190281.675 1192720.358 1023544.68 1220918.912 543832.8128 3.932337544 1.308036162 2.045941451 1.01625557 2.800348408 2.188690435 2.193174685 1.882094378 2.245026199 1 19.05280368 -1.883769226 0.449558617 5.63E-13 2.144793623 0.17765386 0.755048423 90.13554073 6.823128906 96.15748966 0.378676988 0.013068651 1.883769226 2.144793623 STEQTTTNSVTSLNS(ph)PHSGLHTINGEGMEESQSPMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STEQTTTNSVTSLNSPHSGLHTINGEGMEESQSPMK 36 0 H0Y6I7;F5H5V6;F5H6S1;F8W8R6;A0A087X0R0;O15550 H0Y6I7 KDM6A Lysine-specific demethylase 6A 1 STEQTTTNSVTSLNS(0.998)PHS(0.002)GLHTINGEGMEESQSPMK 252.99 1.11E-61 137120000 13007 18541 20277 16717 21851 24707 22677 23403 22394 19188 TRUE FALSE 13520.5264 21725.27252 20805.43528 20023.5727 18136.77482 18969.17369 20899.51748 23089.32106 21588.04431 22947.52122 0.589193328 0.946737223 0.90665284 0.872581074 0.790358778 0.826632799 0.910752725 1.00617931 0.940757135 1 14.4860507 2.03030563 3.321546734 0.98046041 0.832604236 0.380549296 0.091656736 0.273475128 6.119922003 0.0407805 0.02553431 107.227364 -2.03030563 -0.147856174 STETHVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STETHVER 8 0 Q9H3S7 Q9H3S7 PTPN23 Tyrosine-protein phosphatase non-receptor type 23 0 ; 126.24 0.0012275 190919000 123464 148761 144855 157341 150259 194694 160823 163530 157008 151344 FALSE TRUE 128338.4541 174309.5446 148630.0403 188462.5802 124718.0289 149479.2691 148217.273 161338.1478 151357.3127 180996.9591 0.709064145 0.963052337 0.82117424 1.041247218 0.68906146 0.82586619 0.818893719 0.891385958 0.836242296 1 17.46560593 -1.35948962 3.014903581 1.001760952 0.849588044 0.1787174 0.099679748 16678793.07 20906971.12 258361.3684 0.021893896 0.043702912 1.35948962 -0.152172908 STETSDFENIES(ph)PLNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STETSDFENIESPLNER 17 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 STETSDFENIES(1)PLNER;STETSDFENIES(1)PLNER;STETSDFENIES(1)PLNER 401.92 3.64E-140 880980000 549636 628192 571427 552626 645421 692183 566045 637460 578445 540382 TRUE FALSE 571336.0537 736079.0893 586318.8571 661933.7734 535712.569 531433.9884 521676.9138 628915.8914 557626.8774 646259.5067 0.884065995 1.13898377 0.907249876 1.024253828 0.828943425 0.822322895 0.807225129 0.973163079 0.862852881 1 19.30175407 3.244685046 24.99619645 0.87952684 0.993563871 0.261272124 0.087262128 187.87223 766775.4276 0.023532261 0.031072436 1756.649215 -3.244685046 0.114037031 STFDAHIYEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 107.34 0.0022098 1399650000 1533410 1809990 1887870 1900000 2441190 2471440 2053900 1841740 1897150 1977200 FALSE TRUE 1593950.211 2120841.703 1937069.443 2275814.329 2026237.396 1897485.515 1892909.951 1817054.488 1828871.942 2364594.484 0.674090302 0.896915609 0.819197311 0.962454385 0.856906928 0.80245705 0.800522019 0.768442327 0.773439993 1 21.17316136 2.738332084 24.34382205 0.808692945 0.850403384 0 0.092945228 52.61547418 5604660.203 0.027925205 0.027876123 547.4343995 -2.738332084 0.041710439 STFREES(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 S(0.001)T(0.001)FREES(0.998)PLR;STFREES(1)PLR;STFREES(1)PLR;STFREES(1)PLR;S(0.001)T(0.001)FREES(0.998)PLR;STFREES(1)PLR;S(0.003)T(0.003)FREES(0.993)PLR;STFREES(1)PLR 200.05 1.62E-07 24271077000 5239320 6179960 6213470 5182560 7515300 7615050 5490360 6039620 5909520 6652810 TRUE FALSE 5446172.399 7241320.057 6375398.133 6207654.9 6237851.99 5846570.045 5060011.237 5958668.773 5696837.53 7956300.744 0.684510626 0.910136543 0.801301803 0.780218735 0.784014103 0.734835225 0.635975361 0.748924527 0.716015861 1 22.92366638 3.037114561 2.324378224 0.741632432 0.804328128 0 0.10241403 0.84112899 9.195370411 0.031020501 0.037066214 1089.217377 -3.037114561 0.062695696 STFS(ph)PAPRPEMPGTVEVESTFLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STFSPAPRPEMPGTVEVESTFLAR 24 1 Q92576-2;Q92576;E7EVH3;E7ER40 Q92576-2 PHF3 PHD finger protein 3 1 S(0.041)T(0.041)FS(0.917)PAPRPEMPGTVEVESTFLAR;ST(0.003)FS(0.997)PAPRPEMPGTVEVESTFLAR 171.15 4.27E-12 170171000 51035 58082 55727 53170 55892 63255 61989 57597 55761 48502 TRUE FALSE 53049.90121 68057.13168 57179.2914 63686.8673 46391.4978 48564.98489 57130.1402 56825.00642 53754.1725 58005.03827 0.914574023 1.173296902 0.985764222 1.097954061 0.799783936 0.837254596 0.984916861 0.97965639 0.926715577 1 15.8238906 3.263277259 24.99884329 0.924943245 1.048130632 0.31840413 0.08686607 278.3083356 281483.9316 0.024029983 0.032522491 1833.48457 -3.263277259 0.123187387 STFS(ph)PISDIGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STFSPISDIGLAK 13 0 Q8TEK3;Q8TEK3-1;H7C2S2 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 ST(0.001)FS(0.999)PISDIGLAK;S(0.028)T(0.037)FS(0.905)PIS(0.03)DIGLAK 151.74 4.71E-05 44646000 170174 142972 169153 137392 201623 218830 196445 173046 179084 143616 TRUE FALSE 176892.6009 167526.3288 173561.2661 164567.7275 167351.1945 168010.0489 181047.1276 170726.6014 172638.8018 171754.8055 1.029913547 0.975380737 1.010517672 0.958155011 0.974361061 0.978197078 1.054102254 0.994013535 1.005146851 1 17.38999094 STFS(ph)TNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.007)T(0.363)FS(0.607)T(0.024)NYR;STFS(0.862)T(0.137)NYR;S(0.001)T(0.052)FS(0.874)T(0.072)NYR 191.79 0.0001881 1425800000 808460 860490 858490 710320 910460 1055280 750160 799290 808210 883510 TRUE FALSE 840378.6251 1008272.464 880862.9547 850819.1759 755700.3344 810207.2129 691360.499 788576.8249 779122.68 1056616.869 0.795348484 0.954246041 0.833663536 0.805229598 0.715207524 0.766793752 0.65431522 0.746322388 0.737374826 1 20.01102092 3.650047252 2.389600317 0.749379847 0.875157931 0.134943069 0.093604804 0.395106573 4.398527307 0.024430532 0.044154508 4467.321947 -3.650047252 0.125778084 STFST(ph)NYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 ST(0.001)FS(0.256)T(0.743)NYR 183.72 0.0024793 628390000 260830 342860 319320 258210 329770 371740 308060 307000 292110 297350 TRUE FALSE 271127.7698 401743.5379 327641.7415 309283.1673 273715.8132 285409.0188 283913.4522 302885.1672 281597.0182 355610.0394 0.762430021 1.129730585 0.921351214 0.869725635 0.769707778 0.80258988 0.798384243 0.851734016 0.791870271 1 18.43993653 3.701101503 3.245331874 0.826378824 0.960114106 0.152105042 0.102841588 0.331706715 7.125985146 0.025851884 0.045141949 5024.600106 -3.701101503 0.133735282 STFSTNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 186.09 0.000487 22261680000 7824410 8770700 8194690 7165800 12178200 11784440 9402610 8534680 8360160 10896450 FALSE TRUE 8133323.749 10276999.5 8408250.353 8583173.852 10108153.91 9047682.405 8665608.859 8420286.575 8059279.475 13031400.75 0.624132732 0.788633524 0.645229973 0.658653204 0.775676699 0.694298531 0.664979078 0.646153605 0.618450743 1 23.63548883 -1.309196999 3.412457891 1.001395987 0.681221356 0.747966494 0.055792221 50241853.08 77769379.12 725833.2691 0.013236901 0.049068525 1.309196999 -0.320174631 STFVLDEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;; 156.48 1.74E-05 6829690000 5585610 4036849 4888320 3940873 7133710 6798960 5553480 5073960 5453370 4540713 FALSE TRUE 5806134.196 4730146.413 5015713.635 4720365.917 5921124.522 5220004.579 5118183.726 5005951.866 5257104.279 5430378.775 1.069195067 0.871052759 0.923639739 0.869251688 1.090370445 0.961259757 0.942509526 0.921842117 0.968091637 1 22.3726214 4.765356751 23.76667565 0.947263068 1.069195392 0.256626674 0.060836924 6366.199711 5646281.929 0.014430824 1.098259544 58258.15826 -4.765356751 0.121932324 STGEAFVQFASQEIAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STGEAFVQFASQEIAEK 17 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;D6RIU0;E7EN40;E5RGV0;E5RGH4;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 206.06 1.70E-11 14668000 25281 18827 25513 17947 29151 32326 27686 22674 26492 22570 FALSE TRUE 26279.1134 22060.3908 26177.88974 21496.86303 24195.92343 24818.77641 25515.89898 22370.09212 25538.55809 26992.15937 0.973583219 0.817288846 0.969833105 0.796411385 0.896405623 0.919480952 0.945307807 0.828762598 0.946147277 1 14.72025278 2.996234058 24.94856417 0.911242539 0.884455554 0.043301875 0.066800967 643.3376596 4262039.554 0.018571064 0.021735796 991.3660861 -2.996234058 -0.026786985 STGEPLGHVPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STGEPLGHVPAR 12 0 Q93052;C9JUT4;C9JE51;C9J2R5;C9JIY7;C9JT42;C9J3U9;C9J1K7;C9J5C8;C9J4E3 Q93052 LPP Lipoma-preferred partner 0 ; 112.13 0.0013075 628550000 424930 554010 592390 584700 659350 728770 549500 606670 564780 603820 FALSE TRUE 441706.5645 649156.9079 607828.1701 700351.9148 547273.9225 559524.2121 506428.7541 598538.581 544453.6781 722126.9682 0.611674379 0.898951205 0.84171925 0.969845949 0.757863848 0.774828024 0.701301539 0.828855045 0.753958379 1 19.461893 -1.323592007 6.063528312 1.000015869 0.79956364 0.295461211 0.095340135 1.98E-05 2.21E-06 0.08923637 0.02103155 0.047468772 1.323592007 -0.200452229 STGS(ph)PTQETQAPFIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 STGSPTQETQAPFIAK 16 0 O15231-3;H0Y704;O15231-2 O15231-3 ZNF185 Zinc finger protein 185 1 ST(0.001)GS(0.998)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;S(0.001)T(0.003)GS(0.996)PTQETQAPFIAK;S(0.003)T(0.004)GS(0.992)PTQETQAPFIAK;STGS(1)PTQETQAPFIAK;S(0.013)T(0.013)GS(0.974)PT(0.001)QETQAPFIAK 340.52 5.18E-72 2169000000 1784320 1425500 1744170 1472767 2049180 2278300 2136060 1869860 2024270 1470270 TRUE FALSE 1854766.331 1670318.536 1789624.503 1764075.917 1700861.116 1749199.353 1968630.036 1844797.585 1951416.918 1758341.256 1.054838658 0.949939911 1.01779134 1.003261404 0.96731002 0.994800837 1.119594975 1.049169254 1.109805569 1 20.74578366 2.262522184 24.9675854 1.072744995 0.995551296 0.428066467 0.040452005 183.3609567 191058.654 0.012841306 0.010738453 183.0299596 -2.262522184 -0.077193699 STGSVDYLALDFQPS(ph)SPSPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STGSVDYLALDFQPSSPSPHR 21 0 Q9UQC2;Q9UQC2-2 Q9UQC2 GAB2 GRB2-associated-binding protein 2 1 STGSVDYLALDFQPS(0.613)S(0.322)PS(0.065)PHR 101.5 0.00034377 42834000 52765 59265 57426 63017 71242 86608 71337 61905 59735 51479 TRUE FALSE 54848.20294 69443.30273 58922.56874 75481.57451 59132.31029 66494.60456 65745.41954 61075.26473 57585.14902 61565.32443 0.890894403 1.12796129 0.957073958 1.226040392 0.960480771 1.080065852 1.067896907 0.992040005 0.935350371 1 15.90983039 1.586010233 4.486139069 0.96653826 1.049115012 0.108430355 0.090756725 0.312085847 13.94020435 0.048427877 0.02162019 38.54874403 -1.586010233 0.082576753 STGVFQDEELLFSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STGVFQDEELLFSHK 15 0 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 0 75.376 0.032013 105310000 37704 42082 43550 29785 66917 61237 36644 47459 44237 45971 FALSE TRUE 39192.58303 49309.25615 44684.94878 35676.3841 55542.47224 47015.63481 33771.74753 46822.88973 42644.91901 54978.13728 0.71287579 0.896888447 0.812776696 0.648919477 1.010264716 0.855169657 0.61427595 0.851663808 0.775670496 1 15.74657041 -1.737030355 2.253124487 1.051017285 0.800280753 0.227460902 0.111798386 5358903.703 3436003.804 1525048.014 0.028067908 0.018321864 1.737030355 -0.250736532 STHALSEVEVESDSFMNAVLWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STHALSEVEVESDSFMNAVLWLR 23 0 C9JIF9;P13798 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;; 234.04 4.66E-37 222529000 43554 131214 102942 169200 228767 246799 188152 131030 116163 253125 FALSE TRUE 45273.54555 153748.9838 105624.7531 202667.255 189881.2671 189483.6725 173404.1546 129273.7572 111982.3163 302719.9974 0.149555847 0.507891732 0.348918981 0.669487502 0.627250491 0.625937084 0.572820283 0.427040692 0.369920446 1 18.20762446 -2.559531532 2.150721862 9.163063224 0.488966304 0.514453608 0.151881708 7946346.972 376036.9638 317454178.6 0.037050413 0.002757201 2.559531532 -8.67409692 STHDHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STHDHWK 7 0 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 107.43 0.0074794 250910000 152252 468860 478730 443090 539530 626430 477290 520020 504770 498730 FALSE TRUE 158263.0265 549383.0578 491206.0971 530731.8795 447820.8833 480951.1261 439878.7626 513049.9825 486603.4263 596446.5947 0.265343164 0.92109346 0.823554198 0.889822969 0.75081472 0.806360754 0.737498992 0.86017757 0.815837379 1 19.18603344 4.743952743 24.9976838 0.833609568 0.265342924 0.842169943 0.075137688 202.3355906 937991.3965 0.016676055 0.143982215 55456.53651 -4.743952743 -0.568266644 STIGGQIMYLTGMVDKR ddPTM_MDA-MB-175_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 ; 216.35 8.53E-15 826720000 406490 426270 523640 415330 612280 633880 495370 521850 548050 478310 FALSE TRUE 422538.5391 499478.5566 537286.4886 497481.0344 508204.8643 486670.9765 456541.605 514855.4543 528325.7876 572025.6867 0.738670568 0.873175048 0.939269863 0.869683033 0.888430146 0.85078518 0.798113818 0.900056529 0.923605006 1 19.12572041 1.054154278 1.827309682 0.997641146 0.857976681 0.442593311 0.051693596 0.322399183 2.181629844 0.048954054 0.014006046 11.32802707 -1.054154278 -0.139664465 STIGVMVT(ph)ASHNPEEDNGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.815)AS(0.185)HNPEEDNGVK 227.87 1.26E-24 2156200000 1147400 746780 1054500 799040 1399400 1351400 1319300 1066500 1202700 649560 TRUE FALSE 1192700.238 875033.6559 1081981.136 957087.7271 1161530.488 1037557.831 1215889.819 1052205.312 1159415.062 776828.8454 1.535344941 1.126417564 1.392817919 1.232044527 1.495220594 1.335632471 1.565196537 1.354487952 1.492497438 1 19.56723725 3.24440959 24.98770608 1.399943277 1.31279362 0.006869707 0.175584406 444.9938018 1901070.418 0.044399937 0.058563097 1755.535396 -3.24440959 -0.087149657 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 21 STIGVMVTASHNPEEDNGVK 20 0 O95394-4;O95394;A0A494C0G1;O95394-3;H0Y987;A0A494C099;A0A494C163;D6RCQ8;D6RF77;D6RC77 O95394-4 PGM3 Phosphoacetylglucosamine mutase 1 STIGVMVT(0.023)AS(0.977)HNPEEDNGVK;STIGVMVT(0.043)AS(0.957)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.047)AS(0.953)HNPEEDNGVK;STIGVMVT(0.01)AS(0.99)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.031)AS(0.969)HNPEEDNGVK;STIGVMVT(0.039)AS(0.961)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.006)AS(0.994)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.003)AS(0.997)HNPEEDNGVK;STIGVMVT(0.007)AS(0.993)HNPEEDNGVK;STIGVMVTAS(1)HNPEEDNGVK 318.18 9.83E-67 37722880000 29754690 22268320 29131930 20676090 36698110 36861890 32123310 28468520 31169380 21964620 TRUE FALSE 30929428.14 26092730.74 29891132.03 24765758.89 30460178.37 28301274.69 29605401.02 28086946.05 30047600.1 26268166.75 1.177449056 0.993321345 1.137922273 0.942804998 1.159585237 1.077398167 1.127044811 1.069238913 1.14387884 1 24.64681218 4.785580853 22.69688281 1.077498798 1.177450414 0.166546319 0.069679884 23427.12599 11307439.84 0.015050667 9.243425631 61035.26766 -4.785580853 0.099951616 STKPGAAPTEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STKPGAAPTEHK 12 1 Q8N163-2;Q8N163;H0YB24;G3V119 Q8N163-2 CCAR2 Cell cycle and apoptosis regulator protein 2 0 ;; 149.26 3.79E-05 778350000 954120 569290 826130 575300 1052730 985380 969600 841880 897570 526220 FALSE TRUE 991789.3943 667061.129 847659.6265 689092.6229 873787.3306 756540.4286 893600.2184 830595.9756 865266.631 629322.7339 1.57596308 1.05996668 1.346939465 1.09497494 1.388456643 1.202150165 1.419939516 1.319825156 1.374917168 1 19.26344053 -1.132951511 4.099621695 0.9999207 1.301982181 0.284263783 0.146801319 4.829291618 36128790.62 6074.567473 0.030952341 0.07362893 1.132951511 0.302061481 STLDIVLANKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STLDIVLANKDR 12 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 ; 139.48 5.37E-05 1113260000 1518630 1039270 1219230 917360 1804000 1623930 1364190 1142880 1289190 1293280 FALSE TRUE 1578586.685 1217756.538 1251004.135 1098811.07 1497356.724 1246796.868 1257261.223 1127561.563 1242792.304 1546673.455 1.020633464 0.787339134 0.808835331 0.710435074 0.968114323 0.806115127 0.812880844 0.729023673 0.80352598 1 20.56073721 2.544400292 24.99977332 0.805264666 0.848345498 0 0.105889281 735.5469794 273315.0249 0.033288282 0.03138448 350.267862 -2.544400292 0.043080832 STLEPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STLEPVEK 8 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 ;; 147.29 0.0012555 385980000 652399 525580 611858 511754 800340 837630 751752 631797 698596 529357 FALSE TRUE 678156.2163 615844.2766 627803.5221 612977.4138 664298.4927 643103.1269 692827.7139 623328.7946 673453.6664 633074.369 1.071210982 0.972783462 0.991674206 0.968254985 1.049321415 1.015841358 1.09438598 0.984605957 1.063782866 1 19.27201546 3.223480843 24.99022682 1.03376127 0.998302033 0.146911507 0.039509025 422.3603643 699935.6995 0.010885047 0.013057878 1672.941841 -3.223480843 -0.035459237 STLESEKPGS(ph)PEAAETS(ph)PPSNIIDHCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STLESEKPGSPEAAETSPPSNIIDHCEK 28 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 STLES(0.001)EKPGS(0.998)PEAAET(0.258)S(0.736)PPS(0.005)NIIDHCEK;S(0.001)T(0.001)LES(0.005)EKPGS(0.993)PEAAET(0.261)S(0.737)PPS(0.003)NIIDHCEK;STLES(0.005)EKPGS(0.995)PEAAET(0.165)S(0.832)PPS(0.003)NIIDHCEK 117.36 0.00032224 1139370000 1088010 522000 736860 518760 1065900 965530 925280 723570 837320 414521 TRUE FALSE 1130965.475 611649.4394 756063.1769 621369.1797 884718.6987 741300.2902 852754.1358 713871.7277 807185.0168 495738.4535 2.281375324 1.233814797 1.525125137 1.253421386 1.784648119 1.49534555 1.720169436 1.440016853 1.628247741 1 18.91921964 -2.506597923 0.469664336 2.13E-10 1.580288316 0.279679466 0.285209852 150.0969507 7.640774434 153.841139 0.132571336 0.003114599 2.506597923 1.580288315 STLESEKPGS(ph)PEAAETSPPSNIIDHCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STLESEKPGSPEAAETSPPSNIIDHCEK 28 1 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 STLESEKPGS(1)PEAAETSPPSNIIDHCEK;STLESEKPGS(1)PEAAETSPPSNIIDHCEK;STLESEKPGS(1)PEAAETSPPSNIIDHCEK 300.42 9.70E-72 2469400000 2503890 1182930 1923980 1285970 2699820 2567500 2332970 1913470 2131390 1125140 TRUE FALSE 2602745.511 1386089.026 1974120.499 1540331.028 2240905.561 1971237.036 2150105.715 1887823.064 2054681.69 1345589.641 1.934278796 1.030097872 1.467104412 1.144725688 1.665370699 1.464961513 1.597891103 1.402970867 1.526974962 1 20.35980707 -1.501971492 6.166094591 0.999613537 1.454990326 0.253816263 0.240692688 0.001158471 9.36E-05 0.211129356 0.049722939 0.031479549 1.501971492 0.455376789 STLINSLFLTDLYPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STLINSLFLTDLYPER 16 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;C9IZU3;C9JQJ4;A0A1B0GXJ2;C9JZI2;B5MD47;F8WB65;C9JFT1 Q15019-2 2-Sep Septin-2 0 223.72 4.29E-13 0 59271 58944 73441 54901 71077 84983 63551 61361 59065 53378 FALSE TRUE 61611.06485 69067.17348 75354.93279 65760.25394 58995.35693 65246.98618 58569.70656 60538.55616 56939.26219 63836.39712 0.965140071 1.081940344 1.180438374 1.030137303 0.92416489 1.02209694 0.917497058 0.948339175 0.891956075 1 15.96209161 3.415662774 5.101248979 0.949927544 1.080951945 0.471898637 0.060205897 0.161544274 8.406689249 0.016737439 0.023089614 2604.130679 -3.415662774 0.131024401 STLINSLFLTDLYS(ph)PEYPGPSHR ddPTM_MDA-MB-175_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;STLINSLFLTDLYS(1)PEYPGPSHR 200 1.62E-24 290270000 121277 134912 146895 132480 172744 193091 163631 156719 148544 126977 TRUE FALSE 126065.1096 158082.0865 150723.2044 158684.1486 143381.0366 148248.5416 150805.1746 154618.4381 143197.9305 151855.712 0.830163765 1.041001912 0.992542212 1.04496661 0.94419258 0.976246067 0.993082003 1.0181931 0.94298679 1 17.21234165 4.748327411 24.99881283 0.995667266 0.830163676 0.692481619 0.0329095 732.2660486 1874250.178 0.007576918 0.09988434 56017.97574 -4.748327411 -0.16550359 STLINSLFLTDLYSPEYPGPSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STLINSLFLTDLYSPEYPGPSHR 23 0 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 E7EPK1 7-Sep Septin-7 0 ; 216.38 2.56E-32 2121300000 497020 607290 656050 611100 663100 767310 700960 677300 637520 560720 FALSE TRUE 516642.7334 711587.3334 673147.202 731973.756 550386.4989 589113.8812 646016.9236 668221.9013 614575.7797 670582.3484 0.77043891 1.061148322 1.003824815 1.091549394 0.820759002 0.878510868 0.963367027 0.996480004 0.9164807 1 19.35505498 -1.416095877 3.24397253 1.000594829 0.952770002 0.022742326 0.096507978 2320134518 2617986574 12562780.12 0.022688014 0.038362255 1.416095877 -0.047824827 STLLGVLTHGELDNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STLLGVLTHGELDNGR 16 0 O00178;F5H716 O00178 GTPBP1 GTP-binding protein 1 0 112.67 0.00072112 289060000 103690 251380 197970 273340 175080 251020 174240 197060 169180 268030 FALSE TRUE 107783.7613 294552.5595 203129.2608 327405.8362 145319.9641 192724.4092 160582.6135 194418.733 163091.2448 320545.3468 0.336251212 0.918910733 0.633698985 1.021402555 0.453352281 0.601239142 0.500966915 0.606524896 0.508793051 1 18.29016894 -1.134436105 4.396766077 1.000048908 0.628882934 0.250410244 0.19664777 0.000106146 2.09E-05 0.180609238 0.042563363 0.073377666 1.134436105 -0.371165974 STLPDADRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STLPDADRER 10 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 152.69 1.60E-05 4334110000 1906646 2359680 1904330 2033040 2417220 2618040 2286750 1922750 1681973 3117970 FALSE TRUE 1981921.856 2764936.684 1953958.404 2435169.244 2006341.808 2010039.887 2107508.56 1896978.681 1621439.12 3728876.524 0.531506432 0.741493226 0.524007269 0.653057088 0.538055308 0.539047049 0.565185934 0.508726601 0.434833149 1 21.83030959 -1.838429361 3.958250757 1.100504395 0.561749764 0.73482489 0.07936739 0.046462949 0.001896557 0.050722738 0.01788179 0.014506767 1.838429361 -0.538754631 STLS(ph)PPEASPGPPAAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STLSPPEASPGPPAAPR 17 0 Q6NUJ5-2;Q6NUJ5 Q6NUJ5-2 PWWP2B PWWP domain-containing protein 2B 1 STLS(1)PPEASPGPPAAPR 308.98 4.83E-58 105260000 50783 57329 52523 52137 69517 70356 63604 57655 49623 55560 TRUE FALSE 52787.95205 67174.80979 53891.79253 62449.54299 57700.52517 54016.88526 58618.55228 56882.22903 47837.07792 66445.91824 0.794449884 1.010969696 0.811062499 0.939855218 0.868383291 0.812945124 0.882199446 0.856068071 0.719940053 1 16.01989296 3.003709615 24.89401085 0.84791279 0.893705164 0.031398758 0.086333412 317.8347253 2132851.878 0.023090939 0.027483506 1008.578289 -3.003709615 0.045792375 STLTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 143.37 0.02654 5652570000 2054598 2409708 2389155 2251990 2535352 2923385 2462378 2519458 2107909 2175855 FALSE TRUE 2135715.116 2823556.604 2451418.342 2697426.9 2104393.773 2244473.138 2269370.378 2485688.787 2032045.767 2602172.128 0.820743214 1.085076799 0.942066175 1.036605869 0.808706599 0.862538306 0.872106174 0.955236112 0.780903671 1 21.31128497 3.243530767 24.99986604 0.881693657 0.977187074 0.206182345 0.087308897 183.8225437 924621.445 0.022930394 0.030100296 1751.986547 -3.243530767 0.095493417 STMDNPTTTQYASLMHSFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STMDNPTTTQYASLMHSFILK 21 0 Q9NP97;B1AKR6 Q9NP97 DYNLRB1 Dynein light chain roadblock-type 1 0 174.71 2.66E-12 143740000 93529 121850 140300 117250 144610 192330 135130 134820 126890 144630 FALSE TRUE 97221.59714 142776.7896 143956.3333 140441.7 120029.2439 147664.2723 124538.1575 133012.9584 122323.2537 172967.4794 0.56208021 0.825454531 0.832273984 0.811954366 0.693941105 0.853711188 0.72000909 0.769005589 0.707203771 1 17.40014129 -1.992356225 3.708659782 1.225178995 0.759632341 0.441764078 0.083034084 62066.87643 38254048.06 32260.80182 0.018113997 0.010177562 1.992356225 -0.465546654 STMGKPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STMGKPQR 8 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 68.016 0.05253 1150900000 1714900 1783500 1900600 1534300 2329700 2134200 2025500 1910700 1898800 1364000 FALSE TRUE 1782605.576 2089802.251 1950131.197 1837779.961 1933698.426 1638564.394 1866736.017 1885090.192 1830462.559 1631249.685 1.092785239 1.281105076 1.195482957 1.126608623 1.185409226 1.004484114 1.144359466 1.155611069 1.122122858 1 20.63754619 3.361678314 1.706873509 1.107480322 1.195837884 0.23933144 0.070402229 0.546121233 3.259308194 0.021954884 0.034597426 2299.737749 -3.361678314 0.088357562 STNGDTFLGGEDFDQALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STNGDTFLGGEDFDQALLR 19 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 96.591 0.0029123 79453000 82543 82798 90297 78036 82259 113692 90185 83067 79906 80992 FALSE TRUE 85801.86138 97017.91242 92650.214 93471.28789 68276.64456 87288.75602 83116.06405 81953.62274 77030.19867 96860.83171 0.885826189 1.001621715 0.956529201 0.965006042 0.704894263 0.901177024 0.858097774 0.846096624 0.795266748 1 16.56362577 STNLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STNLKR 6 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 0 86.866 0.085126 254890000 412640 379780 401120 364930 634380 690400 616080 593680 598380 486920 FALSE TRUE 428931.3458 445004.2607 411573.5167 437112.0648 526548.3142 530065.0631 567790.0398 585722.6907 576844.4207 582322.6514 0.736587088 0.764188478 0.706779164 0.750635518 0.904220904 0.91026008 0.975043712 1.005838755 0.990592448 1 19.15145921 2.974653615 1.265876665 0.994342322 0.729640902 0.949411249 0.025978919 0.087810195 0.294712313 0.010940991 0.012880637 943.3082121 -2.974653615 -0.26470142 STPDGTEHGEFLALDLGGTNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STPDGTEHGEFLALDLGGTNFR 22 0 E9PB90;P52789 E9PB90 HK2 Hexokinase;Hexokinase-2 0 ; 208.44 6.88E-23 351805000 119723 169564 168208 187153 178711 213400 167337 171984 175768 169534 FALSE TRUE 124449.7565 198685.298 172591.6387 224171.3048 148333.7681 163841.0841 154220.6887 169678.8358 169442.144 202750.9414 0.61380606 0.979947598 0.851249506 1.105648651 0.731605817 0.808090374 0.760641049 0.836883097 0.835715696 1 17.62934909 STPESGDS(ph)DKESVGSSSTSNEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STPESGDSDKESVGSSSTSNEGGR 24 1 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 STPES(0.06)GDS(0.94)DKESVGSSSTSNEGGR;STPES(0.029)GDS(0.969)DKES(0.001)VGSSSTSNEGGR;STPESGDS(1)DKESVGSSSTSNEGGR 187.55 1.13E-17 511140000 543650 283007 361987 273008 503190 636500 486310 382073 397270 229259 TRUE FALSE 565113.7218 331611.2508 371420.6786 327008.1676 417657.9435 488682.5213 448191.7515 376951.9364 382972.3303 274177.9116 2.061120527 1.209474712 1.354670318 1.19268604 1.52330996 1.782355546 1.634674904 1.374844291 1.396802274 1 18.06475282 0.744937554 1.446571867 1.002090673 1.505538105 0.281380433 0.249672672 1.194316733 4.195175583 0.235813717 0.069227717 5.558243311 -0.744937554 0.503447432 STPFIVPS(ph)SPTEQEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.564)S(0.427)PT(0.009)EQEGR;STPFIVPS(0.639)S(0.36)PT(0.001)EQEGR;STPFIVPS(0.497)S(0.497)PT(0.005)EQEGR;ST(0.001)PFIVPS(0.568)S(0.428)PT(0.002)EQEGR 124.09 8.85E-05 1268729000 922386 1146789 1004092 1021986 1203404 1339382 1092100 1065221 1050376 1049425 TRUE FALSE 958802.5115 1343741.09 1030259.462 1224131.78 998849.8179 1028330.829 1006498.348 1050943.455 1012573.173 1255039.736 0.763961876 1.070676132 0.820897883 0.975372927 0.79587107 0.819361172 0.801965324 0.83737863 0.806805668 1 20.25930161 3.226925735 24.99756668 0.831813697 0.913164327 0.089637176 0.095255042 393.1975999 844784.2485 0.024875509 0.029962279 1686.264645 -3.226925735 0.08135063 STPFIVPSS(ph)PTEQEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 STPFIVPSSPTEQEGR 16 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 STPFIVPS(0.353)S(0.645)PT(0.003)EQEGR;STPFIVPS(0.015)S(0.985)PTEQEGR;STPFIVPS(0.29)S(0.706)PT(0.003)EQEGR;STPFIVPS(0.05)S(0.948)PT(0.002)EQEGR;STPFIVPS(0.012)S(0.988)PTEQEGR;STPFIVPS(0.008)S(0.992)PTEQEGR 388.3 2.39E-121 23240100000 6659490 8014470 7856730 7867490 8345490 9718280 7587010 8053180 7868400 7812390 TRUE FALSE 6922411.807 9390892.879 8061482.838 9423656.04 6926926.591 7461356.752 6992320.331 7945240.294 7585217.821 9343078.243 0.740913394 1.005117653 0.862829426 1.008624331 0.741396616 0.798597267 0.74839578 0.850387858 0.811854254 1 23.15546652 3.228077425 24.99958258 0.813593464 0.90860012 0.129749767 0.097635326 335.6585047 800453.447 0.025998982 0.031388108 1690.742328 -3.228077425 0.095006656 STPLASPSPSPGRS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STPLASPSPSPGRSPQR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 STPLASPSPS(0.002)PGRS(0.998)PQR 123.6 3.21E-05 200430000 102990 135150 163470 133440 169130 180450 150800 150530 142760 138710 TRUE FALSE 107056.1247 158360.9612 167730.1625 159834.0337 140381.343 138543.2222 138979.902 148512.3916 137622.0955 165887.5687 0.64535351 0.95462826 1.011107485 0.963508206 0.846243899 0.835163378 0.837795761 0.895259317 0.829610661 1 17.33984625 3.182632697 24.99544402 0.866464749 0.906396849 0 0.10340481 369.3747944 165079.9177 0.029712997 0.035513847 1522.764336 -3.182632697 0.0399321 STPLEENVVDREQIDFLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STPLEENVVDREQIDFLAAR 20 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ;;; 214.55 1.15E-24 777766000 348290 469290 389699 420991 448097 563146 403579 427374 411791 452220 FALSE TRUE 362040.7581 549886.9069 399854.8761 504261.7633 371929.632 432363.8761 371945.4234 421645.7506 396970.7223 540823.8507 0.669424541 1.016757871 0.739344013 0.932395571 0.687709374 0.799454158 0.687738573 0.779636013 0.734011124 1 19.04479925 5.031861574 16.63795247 0.804359272 0.212127246 0.117456297 0.116961739 9034107.285 127338128.8 0.025954469 154001043.2 107612.2159 -5.031861574 -0.592232026 STPS(ph)PTPVESSDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STPSPTPVESSDPK 14 0 Q9NW07 Q9NW07 ZNF358 Zinc finger protein 358 1 S(0.046)T(0.046)PS(0.873)PT(0.023)PVES(0.005)S(0.005)DPK 62.891 0.076721 0 39516 36089 43599 32613 45979 57170 43808 43947 47855 35637 TRUE FALSE 41076.12219 42287.00502 44735.22576 39063.75406 38163.506 43893.13392 40374.21449 43357.96235 46132.7079 42619.38784 0.963789587 0.992201136 1.049644963 0.916572387 0.895449417 1.029886541 0.947320375 1.017329543 1.082434785 1 15.37922225 1.551638268 4.964814418 1.043904464 0.972074677 0.271321337 0.047819463 0.197262893 10.51559507 0.028050107 0.012470221 35.61543622 -1.551638268 -0.071829787 STPSHGSVSSLNSTGSLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STPSHGSVSSLNSTGSLSPK 20 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK;STPSHGSVSSLNSTGSLS(1)PK 309.96 1.96E-66 4329530000 371218 1691300 1853980 1679400 2109470 2552420 1834050 2402840 1861460 1446390 TRUE FALSE 385873.9733 1981767.619 1902296.242 2011580.307 1750903.043 1959659.137 1690292.369 2370633.86 1794466.418 1729782.428 0.223076595 1.1456745 1.09973151 1.162909436 1.012209984 1.132893424 0.977170505 1.370480947 1.037394293 1 20.72215916 4.739514641 24.99189022 1.121032257 0.223076311 0.853667183 0.109253199 27.13220856 710659.8149 0.025803432 0.157302309 54892.70613 -4.739514641 -0.897955946 STPST(ph)KQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STPSTKQR 8 1 Q9NQ75-2;Q9NQ75 Q9NQ75-2 CASS4 Cas scaffolding protein family member 4 1 S(0.011)T(0.011)PS(0.011)T(0.966)KQR 72.643 0.073758 104040000 8643.4 134930 152320 128270 114450 168880 112700 120950 127260 170340 TRUE FALSE 8984.648106 158103.1779 156289.5843 153641.4232 94995.82988 129660.1794 103866.2795 119328.8631 122679.9375 203714.8616 0.044104039 0.776100362 0.767197754 0.754198402 0.466317622 0.636478745 0.509861081 0.585764152 0.602213979 1 17.63619171 0.583453215 3.138828089 0.999998548 0.58355013 0.28473382 0.203200718 12.58626429 93.19029487 0.184973358 0.048130858 3.832244545 -0.583453215 -0.416448418 STPTAEAEEAGIGDTPS(ph)LEDEAAGHVTQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STPTAEAEEAGIGDTPSLEDEAAGHVTQAR 30 0 P10636-7;P10636-4 P10636-7 MAPT Microtubule-associated protein tau 1 STPTAEAEEAGIGDT(0.001)PS(0.999)LEDEAAGHVTQAR;STPTAEAEEAGIGDT(0.005)PS(0.995)LEDEAAGHVTQAR 269.7 1.08E-59 250310000 68481 94684 104530 91261 103401 110817 91068 104798 107897 95200 TRUE FALSE 71184.68276 110945.2405 107254.1377 109312.1534 85824.93495 85081.4312 83929.8522 103393.3542 104013.808 113852.6173 0.625235365 0.97446368 0.942043672 0.960119811 0.753824875 0.747294469 0.737179822 0.90813331 0.913582933 1 16.79680793 1.184376172 1.972305057 0.989793181 0.832239068 0.209885643 0.108383554 0.532086077 3.726184135 0.103961445 0.0299549 15.28889762 -1.184376172 -0.157554113 STPTDLILCVPHLYSCLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STPTDLILCVPHLYSCLEDR 20 0 Q14008;Q14008-3;Q14008-2 Q14008 CKAP5 Cytoskeleton-associated protein 5 0 118.52 6.43E-05 124040000 128700 140040 124590 117730 146720 162750 116540 117200 138810 117220 FALSE TRUE 133781.1754 164090.7806 127836.9178 141016.6426 121780.5868 124953.779 107405.2903 115629.1257 133814.2552 140187.0147 0.954305045 1.17051341 0.911902704 1.005918008 0.868700907 0.891336329 0.766157197 0.824820515 0.954541014 1 17.0969932 3.508537731 1.318949618 0.861360818 1.045799852 0.300736511 0.088874907 0.429190057 1.504007463 0.028529056 0.057279431 3225.0595 -3.508537731 0.184439033 STQIENQHQGAQDTSDLMS(ph)PSKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STQIENQHQGAQDTSDLMSPSKR 23 1 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 STQIENQHQGAQDT(0.001)S(0.001)DLMS(0.862)PS(0.136)KR;STQIENQHQGAQDT(0.011)S(0.011)DLMS(0.791)PS(0.187)KR;STQIENQHQGAQDTSDLMS(0.962)PS(0.038)KR;STQIENQHQGAQDT(0.001)S(0.003)DLMS(0.833)PS(0.164)KR;STQIENQHQGAQDT(0.045)S(0.035)DLMS(0.791)PS(0.129)KR 220.96 8.69E-33 1285810000 783149 471235 570843 454180 736962 816308 733581 593847 666741 354355 TRUE FALSE 814068.3272 552165.9456 585719.6375 544015.4484 611693.4625 626732.8383 676081.0044 585887.4523 642745.1217 423784.0777 1.920950715 1.302941697 1.382118084 1.283709033 1.443408317 1.478896616 1.5953431 1.382514075 1.516680676 1 18.69296986 -1.365750098 3.053713978 0.994654074 1.462779461 0.403301045 0.173665622 20158645.48 25807039.52 960267.6702 0.038954488 0.043077442 1.365750098 0.468125387 STQKS(ph)PATAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STQKSPATAPK 11 1 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 1 STQKS(1)PATAPK 139.7 2.36E-05 1161200000 3153300 1391300 1804100 1253700 2643700 2445100 2249500 1723900 1731500 861150 TRUE FALSE 3277794.719 1630244.952 1851116.328 1501678.118 2194324.818 1877262.581 2073178.312 1700793.94 1669183.653 1029875.855 3.18270858 1.582952882 1.79741696 1.458115666 2.130669253 1.822804731 2.013037108 1.651455301 1.620762003 1 19.97403901 8 0.057181724 5.84E-11 5.514814711 0.411400159 0.414471712 431.3224812 1.847139392 37.61868455 200.8191391 100000000 -8 5.514814711 STRHPSGGS(ph)SPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STRHPSGGSSPPPR 14 1 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 STRHPS(0.001)GGS(0.499)S(0.499)PPPR 75.463 0.01828 65873000 11630 57626 55799 38411 56073 75515 31308 49786 45581 99734 TRUE FALSE 12089.16138 67522.81723 57253.16778 46008.58115 46541.73149 57977.78569 28853.99715 49118.7001 43940.54871 119274.9678 0.101355394 0.566110547 0.48000992 0.385735431 0.390205358 0.486085109 0.24191159 0.411810634 0.368397071 1 16.86393177 -1.297756048 3.171375014 1.003621846 0.388761206 0.690254397 0.124247811 25385815.57 34835917.19 875794.7469 0.029473709 0.050378351 1.297756048 -0.61486064 STS(ph)EGAWPQLPSGLSMMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSEGAWPQLPSGLSMMR 18 0 G3V1A6;P57764 G3V1A6 GSDMD Gasdermin-D 1 S(0.044)T(0.044)S(0.911)EGAWPQLPSGLSMMR 144.3 1.06E-06 0 35125 60486 57149 50658 67792 78250 56106 59138 56487 61350 TRUE FALSE 36511.76212 70873.99998 58638.34989 60678.0012 56268.74005 60077.62339 51708.26511 58345.35184 54454.0439 73370.35788 0.497636419 0.965975934 0.799210357 0.827009748 0.766913801 0.818826909 0.704756888 0.795216945 0.742180432 1 16.1629097 -1.060032286 4.421486078 1.00001556 0.777119354 0.274872361 0.111974477 0.316494434 59321919.75 1997.789758 0.023561389 0.087089884 1.060032286 -0.222896206 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 STSFRGGMGSGGLATGIAGGLAGMGGIQNEK 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.001)T(0.001)S(0.996)FRGGMGS(0.002)GGLATGIAGGLAGMGGIQNEK;S(0.044)T(0.044)S(0.904)FRGGMGS(0.007)GGLAT(0.001)GIAGGLAGMGGIQNEK;S(0.121)T(0.121)S(0.758)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.117)T(0.117)S(0.766)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.047)T(0.031)S(0.922)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.032)T(0.145)S(0.823)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.122)T(0.122)S(0.755)FRGGMGSGGLATGIAGGLAGMGGIQNEK;S(0.271)T(0.271)S(0.457)FRGGMGSGGLATGIAGGLAGMGGIQNEK 265.42 4.13E-59 25350850000 9992190 8443410 13150590 6230920 18162180 13291610 11921210 14135510 16452030 10562820 TRUE FALSE 10386689.38 9893499.987 13493305.18 7463377.379 15074979.13 10204835.01 10986794.41 13946046.61 15859924.65 12632402.34 0.822225979 0.783184363 1.068150366 0.590812197 1.193358058 0.807830113 0.869731197 1.103990059 1.255495528 1 23.59062569 1.678844618 4.44124533 1.142448716 0.878534759 0.315582765 0.163909961 0.181370825 8.330464702 0.083881928 0.039988564 47.73584539 -1.678844618 -0.263913956 STS(ph)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 40 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 S(0.009)T(0.202)S(0.789)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR;S(0.165)T(0.165)S(0.669)FRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDR 294.23 2.66E-93 4088890000 576079 697538 919310 305143 1317380 943760 386673 846069 1107870 1197880 TRUE FALSE 598823.0437 817334.7254 943267.9738 365499.3746 1093452.218 724586.0428 356364.5599 834728.8289 1067997.975 1432581.651 0.418002732 0.570532733 0.65843924 0.255133363 0.763273924 0.505790398 0.248756893 0.582674522 0.745505832 1 20.45018594 1.041421506 2.36267513 0.994281105 0.496477406 0.525267712 0.152576388 0.20855885 2.470780277 0.139423357 0.038216347 11.00073002 -1.041421506 -0.4978037 STS(ph)GSPRPAGAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.011)T(0.067)S(0.504)GS(0.418)PRPAGAKPK 66.826 0.028328 574810000 1334700 766900 1095200 733550 1503200 1280700 1284900 1108800 1195000 658210 TRUE FALSE 1387394.987 898609.1093 1123741.812 878644.0006 1247686.601 983276.8342 1184186.181 1093938.35 1151992.183 787173.6473 1.762501821 1.141564015 1.427565335 1.116200985 1.585020796 1.249123161 1.504351911 1.389703979 1.463453696 1 19.5863224 -1.484281838 4.622614066 0.998374227 1.393575533 0.29311611 0.187721998 0.00280008 0.000312389 0.161809856 0.03799355 0.032788244 1.484281838 0.395201307 STS(ph)LNERPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STSLNERPK 9 1 P49815;P49815-4;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y6C9;X5D2U8;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;A0A2R8YGU4;A0A2R8Y5F1;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7 P49815 TSC2 Tuberin 1 S(0.004)T(0.134)S(0.863)LNERPK;S(0.003)T(0.091)S(0.906)LNERPK;S(0.001)T(0.033)S(0.966)LNERPK;ST(0.02)S(0.979)LNERPK;S(0.031)T(0.111)S(0.858)LNERPK 142.97 6.24E-05 3740080000 2578200 1653460 2257360 2031300 3182950 3154480 2797650 2340880 2513810 1637150 TRUE FALSE 2679989.327 1937428.893 2316188.656 2433085.077 2641913.296 2421899.827 2578362.883 2309504.333 2423338.469 1957918.197 1.368795351 0.989535158 1.182985407 1.242689853 1.349348149 1.236977025 1.316889994 1.179571412 1.237711807 1 20.90088906 -0.185147187 1.294999645 0.998980518 1.22964225 0.320284787 0.101972665 36.15671346 37.1003992 0.285968325 0.028579724 0.652909237 0.185147187 0.230661732 STS(ph)LSALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STSLSALVR 9 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 S(0.006)T(0.001)S(0.993)LSALVR;S(0.001)T(0.002)S(0.997)LSALVR;S(0.001)T(0.044)S(0.956)LSALVR;S(0.006)T(0.013)S(0.981)LSALVR;S(0.168)T(0.168)S(0.633)LS(0.03)ALVR 234.28 3.78E-10 1805080000 1712680 1831670 2011300 1919970 2718640 2695300 2142040 2203010 2132420 2452210 TRUE FALSE 1780297.929 2146245.074 2063716.13 2299734.335 2256526.544 2069357.423 1974141.308 2173482.254 2055674.621 2932673.599 0.607056281 0.731839055 0.703697858 0.78417671 0.769443468 0.705621459 0.673154117 0.741126546 0.700955818 1 21.48378508 -1.849995189 2.709020807 1.111060163 0.716903889 0.765767779 0.047573532 5522544.759 3512151.454 3956092.047 0.011512084 0.014125532 1.849995189 -0.394156274 STS(ph)MFDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STSMFDMR 8 0 Q9UPQ0-4;Q9UPQ0-5;E7EPK0;Q9UPQ0-9;E9PDJ9 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 S(0.183)T(0.13)S(0.688)MFDMR;S(0.008)T(0.026)S(0.966)MFDMR;S(0.051)T(0.051)S(0.899)MFDMR 112.3 0.0032187 219574000 598520 879500 936880 791860 1361000 978810 630650 837460 839910 1126570 TRUE FALSE 622150.0318 1030547.283 961295.8625 948487.5445 1129657.706 751496.2115 581218.0051 826235.2185 809681.8032 1347299.822 0.461775487 0.764898255 0.713498099 0.703991442 0.838460518 0.557779493 0.431394702 0.613252674 0.60096631 1 20.36163951 -1.506083686 6.053450082 1.000374815 0.633802847 0.451513485 0.12173377 0.000640827 5.23E-05 0.122660578 0.028882607 0.031182886 1.506083686 -0.366571968 STS(ph)PAGQHHS(ph)PISSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSPAGQHHSPISSR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.28)T(0.33)S(0.39)PAGQHHS(0.999)PIS(0.001)SR 119.79 9.77E-05 721460000 296250 410180 412070 374720 429370 527350 415920 415340 395670 414570 TRUE FALSE 307946.1788 480625.2242 422808.8827 448838.4976 356385.8408 404880.9546 383319.1036 409773.0467 381429.914 495797.0541 0.621113369 0.969399113 0.852786194 0.905286738 0.718813954 0.816626382 0.773137114 0.826493508 0.769326705 1 18.91939017 -1.160298535 4.181251206 1.000052605 0.812438918 0.28556636 0.091583068 4.57E-05 9.18E-06 0.082088969 0.019342598 0.069135557 1.160298535 -0.187613687 STS(ph)PAGQHHSPIS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSPAGQHHSPISSR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 2 S(0.126)T(0.159)S(0.715)PAGQHHS(0.34)PIS(0.642)S(0.018)R 145.04 2.18E-06 472850000 298160 463310 387980 409320 463750 521150 446230 417890 423610 484720 TRUE FALSE 309931.587 542879.8884 398091.0775 490282.2743 384921.9406 400120.8106 411253.3266 412288.8681 408364.3588 579691.6035 0.534649088 0.936497761 0.686729073 0.845763974 0.664011585 0.690230475 0.709434679 0.711221045 0.70445105 1 19.14492606 -1.373300486 6.433656294 1.000025511 0.725400102 0.405574826 0.101405787 3.33E-05 3.25E-06 0.088189684 0.02078458 0.042334995 1.373300486 -0.274625409 STS(ph)PIIGS(ph)PPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STSPIIGSPPVR 12 0 Q86TB9-4;Q86TB9;Q86TB9-2 Q86TB9-4 PATL1 Protein PAT1 homolog 1 2 ST(0.001)S(0.999)PIIGS(1)PPVR;S(0.002)T(0.007)S(0.991)PIIGS(1)PPVR;ST(0.006)S(0.994)PIIGS(1)PPVR;STS(1)PIIGS(1)PPVR 191.19 8.31E-06 552720000 1067510 1071210 1098540 1176120 1296640 1525100 1283020 1194670 1181260 1231010 TRUE FALSE 1109656.119 1255181.985 1127168.855 1408753.026 1076237.596 1170918.638 1182453.54 1178657.403 1138746.683 1472202.84 0.753738608 0.852587667 0.765634207 0.956901445 0.731038935 0.795351433 0.803186563 0.800608021 0.773498496 1 20.48954503 -1.094755281 6.421985068 1.000000299 0.805706937 0.48978779 0.060096918 2.36E-07 3.33E-08 0.053489366 0.012607545 0.080397903 1.094755281 -0.194293362 STS(ph)PPPS(ph)PEVWADSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSPPPSPEVWADSR 15 0 Q08495;Q08495-2;Q08495-3;E5RGQ0;E5RFK4;E5RJ61;E5RGQ7;E5RJC0 Q08495 DMTN Dematin 2 S(0.01)T(0.015)S(0.975)PPPS(1)PEVWADSR 125.33 0.0001332 166220000 254460 253230 254220 309760 289560 343610 326450 280940 319530 287450 TRUE FALSE 264506.2773 296720.2826 260845.182 371029.6035 240340.6946 263811.785 300861.996 277174.4588 308030.1777 343770.3239 0.769427315 0.863135245 0.758777486 1.079295034 0.699131594 0.767407093 0.875183153 0.806278028 0.896034812 1 18.39108548 0.950447524 3.687303385 0.999862425 0.829805303 0.229842713 0.097837504 0.364209073 13.33083887 0.088454464 0.02276982 8.921698117 -0.950447524 -0.170057122 STS(ph)PPPSPEVWADSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSPPPSPEVWADSR 15 0 Q08495;Q08495-2;Q08495-3;E5RGQ0;E5RFK4;E5RJ61;E5RGQ7;E5RJC0 Q08495 DMTN Dematin 1 S(0.004)T(0.025)S(0.971)PPPSPEVWADSR;S(0.004)T(0.008)S(0.989)PPPSPEVWADSR 266.63 2.61E-25 355090000 289700 308890 285310 257908 285800 319120 255137 248934 256481 235858 TRUE FALSE 301137.5797 361939.4547 292745.413 308921.4326 237219.8181 245009.2163 235138.6953 245597.4469 247250.2989 282069.8593 1.067599283 1.28315537 1.037847197 1.095194763 0.84099669 0.868611829 0.83361865 0.870697236 0.876556962 1 18.10569299 3.306058382 4.525389934 0.870944635 1.132789931 0.711180859 0.074531133 0.101608415 4.030431667 0.02015191 0.027205964 2023.291152 -3.306058382 0.261845296 STS(ph)PSTSSEAEPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSPSTSSEAEPVK 14 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;H0Y6V3 Q5VT25-2 CDC42BPA Serine/threonine-protein kinase MRCK alpha 1 ST(0.032)S(0.758)PS(0.209)TSSEAEPVK;ST(0.001)S(0.995)PS(0.004)TSSEAEPVK 223.46 3.68E-12 976080000 1530290 1180150 1483800 1431270 1692790 1922510 1924180 1399920 1526490 989270 TRUE FALSE 1590707.031 1382831.582 1522469.047 1714370.934 1405050.16 1476036.188 1773357.744 1381156.362 1471551.923 1183098.516 1.344526267 1.168822007 1.28684892 1.449051716 1.187601997 1.247602096 1.498909617 1.167406048 1.243811824 1 20.17413878 0.754358423 1.283904851 1.002011803 1.29890607 0.417192944 0.105458199 0.804263083 2.306869789 0.096817453 0.029228837 5.680131935 -0.754358423 0.296894267 STS(ph)PTFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STSPTFNK 8 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 S(0.001)T(0.02)S(0.979)PTFNK;S(0.004)T(0.025)S(0.971)PTFNK;S(0.003)T(0.016)S(0.961)PT(0.02)FNK;ST(0.002)S(0.998)PTFNK 156.16 0.00041684 856360000 2994600 2458680 2922920 2362250 3505450 3684500 3489920 3142490 3113160 2384340 TRUE FALSE 3112829.12 2880939.164 2999093.696 2829495.999 2909594.861 2828830.714 3216370.951 3100370.062 3001117.98 2851505.772 1.091643984 1.010322052 1.051757891 0.992281351 1.020371373 0.992048041 1.127955266 1.087274693 1.052467791 1 21.44329252 2.250586094 24.99888112 1.07751841 1.025000311 0.171366595 0.041019894 282.2176722 586681.2775 0.013730887 0.011404157 178.0680872 -2.250586094 -0.052518098 STS(ph)PVTDPSIPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STSPVTDPSIPIR 13 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 S(0.089)T(0.089)S(0.823)PVTDPSIPIR;S(0.071)T(0.071)S(0.859)PVTDPSIPIR;S(0.063)T(0.063)S(0.873)PVTDPSIPIR;S(0.269)T(0.124)S(0.608)PVTDPSIPIR 140.24 4.12E-05 903310000 1059450 1258520 1234400 1225610 1291280 1615700 1379430 1341110 1275290 1364930 TRUE FALSE 1101277.904 1474661.02 1266569.478 1468032 1071788.687 1240478.161 1271306.672 1323134.614 1229392.562 1632361.9 0.674653031 0.903390982 0.775912178 0.899329983 0.656587664 0.759928396 0.778814227 0.810564504 0.753137256 1 20.63852951 -1.586668054 3.297864443 1.009355147 0.784076013 0.429234473 0.076211873 32855552.83 31285092.81 2585677.033 0.017142349 0.025901919 1.586668054 -0.225279134 STS(ph)QGSINSPVYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 S(0.001)T(0.003)S(0.996)QGSINSPVYSR;STS(1)QGSINSPVYSR;ST(0.001)S(0.999)QGSINSPVYSR;S(0.002)T(0.002)S(0.996)QGSINSPVYSR 314.17 8.40E-56 2666230000 2162880 2427680 2515140 2298620 2753150 3001110 2404840 2450190 2465690 2479340 TRUE FALSE 2248272.173 2844615.155 2580686.615 2753280.175 2285170.546 2304147.685 2216342.357 2417349.211 2376950.299 2965119.203 0.758240063 0.959359459 0.870348353 0.92855632 0.770684209 0.777084335 0.747471587 0.815262067 0.801637349 1 21.49965867 3.233501872 24.99770272 0.803312068 0.884230029 0.097063746 0.082083992 200.439006 990465.6709 0.021721704 0.026731554 1711.992555 -3.233501872 0.080917961 STS(ph)S(ph)S(ph)RS(ph)RK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSSSRSRK 9 2 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 4 S(0.237)T(0.237)S(0.881)S(0.881)S(0.881)RS(0.881)RK 49.65 0.076231 1524700000 1120300 863200 1004200 723720 1361200 1391600 1129800 1016300 1233700 898840 TRUE FALSE 1164530.309 1011447.885 1030370.277 866869.6559 1129823.71 1068421.99 1041243.324 1002678.161 1189299.378 1074950.489 1.083333904 0.94092509 0.958528126 0.806427519 1.051047208 0.993926698 0.968643054 0.932766831 1.106375959 1 20.03583878 STS(ph)TPNVHMVSTTLPVDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 STSTPNVHMVSTTLPVDSR 19 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 S(0.127)T(0.127)S(0.729)T(0.017)PNVHMVSTTLPVDSR;S(0.154)T(0.154)S(0.673)T(0.019)PNVHMVSTTLPVDSR;S(0.107)T(0.107)S(0.765)T(0.02)PNVHMVSTTLPVDSR;S(0.117)T(0.117)S(0.762)T(0.003)PNVHMVSTTLPVDSR;S(0.17)T(0.17)S(0.623)T(0.037)PNVHMVSTTLPVDSR 247.64 5.79E-25 4337840000 769660 1058180 1060040 1019310 1079960 1290570 1025460 1073970 990020 1095690 TRUE FALSE 800046.7711 1239914.184 1087665.513 1220926.476 896388.785 990854.6763 945081.7657 1059575.189 954389.3736 1310369.477 0.610550524 0.946232498 0.830044909 0.931742151 0.684073309 0.756164344 0.721233043 0.808607959 0.728336084 1 20.32154223 -1.425647783 2.85783936 1.004879919 0.786182808 0.304403848 0.099483201 19256584.67 21790847.48 759328.0425 0.023106771 0.037527723 1.425647783 -0.218697111 STS(ph)TPTS(ph)PGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSTPTSPGPR 11 0 Q8WWM7;Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7 ATXN2L Ataxin-2-like protein 2 ST(0.015)S(0.982)T(0.004)PT(0.03)S(0.969)PGPR;ST(0.008)S(0.991)T(0.005)PT(0.261)S(0.735)PGPR 147.02 5.19E-05 80909000 530630 589370 540040 480810 534410 661800 503910 507580 487500 503720 TRUE FALSE 551579.6821 690589.7128 554113.886 575912.7829 443571.1791 508106.9797 464412.2175 500776.7203 469954.9702 602414.2897 0.915615203 1.146370072 0.919821949 0.956007838 0.736322472 0.843451074 0.770918329 0.831282938 0.780119227 1 19.20039647 3.583136179 2.100538611 0.817867583 1.018725993 0.400902937 0.09132496 0.258608765 2.240266442 0.024241427 0.043138223 3829.448022 -3.583136179 0.200858411 STS(ph)YGYS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 S(0.061)T(0.119)S(0.819)YGYS(1)R 108.68 0.0055016 276110000 640780 643420 625220 671020 696490 802740 806250 704030 636080 546480 TRUE FALSE 666078.4892 753922.3799 641513.7468 803745.7532 578100.8786 616315.8006 743054.0183 694593.6294 613187.6051 653552.293 1.019166326 1.153576214 0.981579827 1.22981093 0.884551833 0.943024464 1.13694654 1.062797326 0.938238013 1 19.31794315 3.232969893 24.99999995 1.009186942 1.091968275 0.21725613 0.091928255 260.1020688 1163095.766 0.026685073 0.032755601 1709.896775 -3.232969893 0.082781332 STS(ph)YGYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 S(0.008)T(0.284)S(0.708)YGYSR;S(0.011)T(0.064)S(0.925)YGYSR 136.84 0.0008116 921260000 1105970 1295620 1193300 1191140 1382100 1541100 1154520 1285770 1134510 1245030 TRUE FALSE 1149634.55 1518132.656 1224398.378 1426743.937 1147171.136 1183202.881 1064025.706 1268536.356 1093679.207 1488969.791 0.772100654 1.019585935 0.822312438 0.958208787 0.770446212 0.794645323 0.714605301 0.851955737 0.734520749 1 20.50588305 3.226750058 24.99960044 0.799771021 0.897037279 0.138682334 0.097552556 340.9321418 721655.02 0.02559058 0.030815329 1685.58267 -3.226750058 0.097266258 STSAPQMS(ph)PGSSDNQSS(ph)SPQPAQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 2 STSAPQMS(0.92)PGS(0.059)S(0.021)DNQS(0.004)S(0.614)S(0.382)PQPAQQK 103.78 0.0024173 206010000 65932 57887 75823 52820 64887 77684 76445 56949 81601 41357 TRUE FALSE 68535.04627 67828.64195 77799.00967 63267.63835 53857.53092 59643.06831 70453.04115 56185.6918 78664.19595 49460.11232 1.385662973 1.37138067 1.572964678 1.279164874 1.088908383 1.205882185 1.424441592 1.135979867 1.590457285 1 15.5939779 3.551974564 9.141962537 1.245380564 1.43511165 0.230559153 0.165795411 0.631627779 73.34292807 0.041845327 0.064814291 3564.302569 -3.551974564 0.189731086 STSAPQMS(ph)PGSSDNQSSSPQPAQQK ddPTM_MDA-MB-175_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(0.96)PGS(0.037)S(0.003)DNQSSSPQPAQQK;STSAPQMS(0.991)PGS(0.006)S(0.002)DNQSSSPQPAQQK;STSAPQMS(0.998)PGS(0.002)S(0.001)DNQSSSPQPAQQK 295.78 1.86E-62 1614730000 738970 766620 938790 760340 1052200 1265660 995490 969200 1036010 805110 TRUE FALSE 768145.1062 898281.0215 963255.6386 910732.9826 873347.4198 971729.6463 917460.8926 956209.4593 998724.2025 962855.8897 0.797777855 0.932934026 1.00041517 0.945866346 0.90703856 1.00921608 0.952853799 0.99309717 1.037252005 1 19.87696036 4.704438773 2.761231573 0.977007597 0.771244633 0.70579412 0.035471866 0.215651085 2.358105064 0.008815852 0.096960491 50633.59607 -4.704438773 -0.205762964 STSAPQMSPGS(ph)SDNQSSSPQPAQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 STSAPQMS(0.309)PGS(0.545)S(0.146)DNQSSSPQPAQQK 170.44 5.51E-12 1080200000 792500 717640 943500 665000 969820 1120000 907210 832780 919020 784460 TRUE FALSE 823788.5119 840889.0875 968088.3851 796535.0152 804970.3428 859896.9738 836100.5096 821617.9463 885944.6497 938159.9176 0.878089648 0.896317431 1.031901243 0.8490397 0.858031054 0.916578248 0.891213208 0.875776007 0.944342892 1 19.83947434 0.981756927 4.89843538 0.999910479 0.900031243 0.300111218 0.048174118 0.204476097 17.71748248 0.046309494 0.011721416 9.588638083 -0.981756927 -0.099879235 STSESFIQHIVSLVHHVK ddPTM_MDA-MB-175_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 ; 229.16 7.07E-20 294730000 152198 345870 394730 346810 431420 478930 382530 431780 391190 358490 FALSE TRUE 158206.8946 405270.482 405016.9881 415407.9829 358087.3825 367705.7658 352546.299 425992.6953 377111.1483 428729.2518 0.36901353 0.94528302 0.944691752 0.968928481 0.835229649 0.857664282 0.822305214 0.993617052 0.879602096 1 18.70970733 4.740577596 24.99400905 0.913705279 0.369013344 0.877435107 0.06136417 57.77852955 715929.398 0.014792818 0.097106886 55027.22299 -4.740577596 -0.544691935 STSGPRPGCQPSS(ph)PCVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STSGPRPGCQPSSPCVPK 18 1 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 STSGPRPGCQPS(0.053)S(0.947)PCVPK;STSGPRPGCQPS(0.017)S(0.983)PCVPK;STSGPRPGCQPS(0.038)S(0.962)PCVPK 224.8 2.67E-19 1183900000 667040 446465 558440 457259 712240 789260 645420 601963 673630 414697 TRUE FALSE 693375.2543 523141.8907 572993.4052 547703.4654 591173.6992 605966.3264 594830.2939 593894.6706 649386.1879 495948.9373 1.398077911 1.054830148 1.155347581 1.10435455 1.192005174 1.22183209 1.1993781 1.197491568 1.309381146 1 18.91983206 3.022207955 24.74525779 1.199544135 1.16527301 0 0.110719621 1094.271563 1219282.576 0.029954557 0.035800849 1052.46571 -3.022207955 -0.034271126 STSGS(ph)PRPAGAKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSGSPRPAGAKPK 14 2 H7BXF5;A0A2R8YDB8;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 S(0.128)T(0.128)S(0.128)GS(0.615)PRPAGAKPK 58.98 0.054545 335070000 499280 313040 401890 276090 542450 490690 496310 418740 462810 260180 TRUE FALSE 518991.9599 366802.1849 412363.5836 330699.778 450244.5428 376734.684 457407.9253 413127.4752 446153.5585 311157.2896 1.667940869 1.178832048 1.325257667 1.062805819 1.446999823 1.2107532 1.470021564 1.327712668 1.433852182 1 18.24728452 -2.172486292 2.485349326 0.09646339 1.336708059 0.288449813 0.162822864 9182725.437 2169673.843 46854801.95 0.03682841 0.006722235 2.172486292 1.240244669 STSHTSDFNPNSGSDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSHTSDFNPNSGSDQR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4;F8W0B5;F8WB06;F8VRK6 Q99700;F8WB06 ATXN2 Ataxin-2 0 136.36 1.06E-05 74904000 7092.9 48378 36372 44955 33068 58832 26782 51877 33183 54748 FALSE TRUE 7372.933169 56686.54517 37319.8842 53846.96482 27447.11317 45169.15961 24682.75686 51181.67367 31988.75031 65474.82239 0.11260715 0.865776234 0.569988323 0.822407192 0.419201033 0.68987067 0.376980891 0.781700077 0.488565668 1 15.99865262 -4.999999968 0.406876105 7.91520801 0.583018272 0.249091775 0.221415574 1096.15331 7.473067859 6749.17806 0.120969542 1.00E-05 4.999999968 -7.332189738 STSLSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSLSSPR 8 0 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 STSLS(0.198)S(0.801)PR 73.573 0.037549 0 206220 249890 225590 218030 263150 296010 250510 250640 232770 241840 TRUE FALSE 214361.7248 292806.6636 231469.0607 261155.6832 218419.857 227266.1636 230874.3716 247280.5808 224392.6532 289223.9177 0.741161819 1.012387447 0.800310924 0.902953273 0.755192927 0.785779286 0.798254769 0.854979708 0.775844041 1 18.14182734 5.060635929 14.13493206 0.844159809 6.92E-05 0.122013938 0.087281659 1240006.726 7966318.855 0.01943893 29085304.19 114983.6072 -5.060635929 -0.844090638 STSMDSGSSES(ph)PASLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STSMDSGSSESPASLKR 17 1 F8W7U0;Q15811-6;Q15811-12;Q15811-11;Q15811-3;Q15811-10;Q15811-7;Q15811-2;Q15811-4;Q15811-9;Q15811-8;Q15811;H0Y7J7 F8W7U0 ITSN1 Intersectin-1 1 STSMDSGSSES(0.999)PASLKR 172.3 9.91E-10 210980000 71992 66264 63398 64299 91366 87162 72609 73975 68219 47590 TRUE FALSE 74834.29975 77644.32654 65050.20396 77017.15029 75835.63996 66919.94645 66917.71685 72983.48612 65763.81152 56914.34933 1.314858215 1.36423112 1.142949093 1.353211469 1.332452024 1.175800958 1.175761783 1.282338935 1.155487365 1 15.79650481 -5 0.12978632 0.097701938 1.371228621 0.595669445 0.071247011 101.050162 0.82837092 23.48374218 0.540454644 1.00E-05 5 1.273526683 STSQGSINS(ph)PVYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.004)INS(0.996)PVYSR;STSQGS(0.004)INS(0.996)PVYSR;STSQGS(0.009)INS(0.991)PVYSR;STSQGS(0.003)INS(0.997)PVYSR 317.31 6.25E-56 967320000 882060 933610 917170 853200 915590 1117460 777067 845000 775120 757385 TRUE FALSE 916884.4099 1093950.255 941072.2037 1021960.413 759958.3388 857946.8503 716158.4581 833674.1571 747223.5826 905780.0897 1.0122594 1.207743764 1.038963226 1.128265486 0.839009763 0.947191112 0.790653787 0.920393555 0.824950329 1 19.7888013 3.240975113 24.99997847 0.881852322 1.100600217 0.649193748 0.075466755 34.39047228 356079.1245 0.019256836 0.024892776 1741.707065 -3.240975113 0.218747895 STSSFPCPAGHFNGFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSSFPCPAGHFNGFR 16 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 174.83 3.73E-09 1232080000 760510 1149810 1051460 1092240 1661700 1728950 1266970 1084450 909020 1462640 FALSE TRUE 790535.522 1347280.923 1078861.911 1308281.812 1379244.828 1327427.565 1167661.581 1069914.722 876304.5478 1749216.304 0.451936973 0.770219738 0.616768726 0.747924547 0.788493009 0.758869879 0.667534128 0.611653755 0.500969803 1 20.73827727 4.748914621 24.00162418 0.700876249 0.451936727 0.271796834 0.12792422 1151.411012 2668992.325 0.029192109 0.394223127 56093.76887 -4.748914621 -0.248939522 STST(ph)PTSPGPR ddPTM_MDA-MB-175_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(0.001)T(0.477)PT(0.261)S(0.261)PGPR 129.22 0.0027892 111730000 290090 354230 329260 316770 351160 430950 331200 318260 320780 318630 TRUE FALSE 301542.9772 415066.247 337840.7861 379426.1605 291469.9486 330868.3936 305239.6786 313994.2453 309235.1905 381059.448 0.791327912 1.089242766 0.886582889 0.995713825 0.764893641 0.868285501 0.801029026 0.824003307 0.811514298 1 18.53965656 3.244866806 24.99914147 0.833591573 0.947459132 0.197082663 0.092611294 191.9872767 761075.2728 0.023417921 0.030945971 1757.384557 -3.244866806 0.113867559 STSTLEIQPSRAS(ph)PTSDIESVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 STSTLEIQPSRAS(0.97)PT(0.015)S(0.015)DIESVER;STSTLEIQPS(0.001)RAS(0.842)PT(0.079)S(0.079)DIESVER 251.16 7.05E-39 2813200000 897990 978340 987910 1004410 1120550 1200890 1073640 1059440 1023660 949830 TRUE FALSE 933443.3386 1146362.285 1013655.746 1203079.3 930079.3113 922001.4972 989485.2914 1045239.94 986818.6766 1135931.003 0.82174299 1.009183024 0.892356792 1.059113007 0.818781518 0.811670335 0.871078691 0.920161468 0.868731176 1 20.11544378 5.046561057 14.36255805 0.910364797 0.408439998 0.111621987 0.078581585 1090151.442 10246460.72 0.018572786 14446577.94 111316.888 -5.046561057 -0.501924799 STSTPTS(ph)PGPR ddPTM_MDA-MB-175_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 STS(0.001)T(0.45)PT(0.018)S(0.531)PGPR;STST(0.009)PT(0.067)S(0.924)PGPR;STST(0.015)PT(0.003)S(0.982)PGPR;ST(0.001)S(0.04)T(0.136)PT(0.086)S(0.736)PGPR;STSTPTS(0.999)PGPR;STSTPT(0.001)S(0.999)PGPR;STSTPT(0.004)S(0.996)PGPR 202.05 4.34E-08 20458450000 7996850 9345990 9139040 8763830 9722320 11791480 9412220 9505720 8703210 8953030 TRUE FALSE 8312571.813 10951091.08 9377210.89 10497289.42 8069723.519 9053087.472 8674465.602 9378311.372 8389983.172 10707204.81 0.776353115 1.022777772 0.875785142 0.98039494 0.753672285 0.845513617 0.810152206 0.875887922 0.783582954 1 23.35207857 3.249214875 24.99987131 0.838949478 0.918892541 0.128800641 0.086753785 362.9311998 851601.2304 0.021951055 0.029417622 1775.067511 -3.249214875 0.079943062 STSYGYS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R;STSYGYS(1)R 143.39 0.00063163 24040900000 11084200 12755600 12708600 13895400 14134100 16385800 15149300 13249400 12153800 10334700 TRUE FALSE 11521812.77 14946275.08 13039796.56 16643868.65 11731590.73 12580446.28 13961858.28 13071813.46 11716387.11 12359586.6 0.932216679 1.209286003 1.055035009 1.346636355 0.949189574 1.017869504 1.129637968 1.057625461 0.947959466 1 23.55912715 STT(ph)PPPAEPVSLPQEPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.011)T(0.011)T(0.977)PPPAEPVSLPQEPPK;S(0.07)T(0.07)T(0.86)PPPAEPVSLPQEPPK;S(0.095)T(0.095)T(0.811)PPPAEPVSLPQEPPK 223.32 5.83E-18 1501120000 919700 662348 758999 639636 951420 1109560 993710 772785 891990 584908 TRUE FALSE 956010.4662 776101.1166 778779.1375 766154.0917 789697.9682 851881.5055 915820.4136 762427.0811 859887.4541 699509.5239 1.366686848 1.109493281 1.113321707 1.095273282 1.128930974 1.217826887 1.30923223 1.089945247 1.229271975 1 19.41598417 -2.256553058 2.322659513 0.306204706 1.175930692 0.264791514 0.091213869 3369036.606 759439.1732 12274976.81 0.02177393 0.005539199 2.256553058 0.869725986 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 S(0.179)T(0.179)T(0.643)PPPAEPVSLPQEPPKPR;S(0.143)T(0.143)T(0.715)PPPAEPVSLPQEPPKPR;ST(0.034)T(0.966)PPPAEPVSLPQEPPKPR;S(0.001)T(0.001)T(0.998)PPPAEPVSLPQEPPKPR;S(0.097)T(0.125)T(0.778)PPPAEPVSLPQEPPKPR;ST(0.016)T(0.984)PPPAEPVSLPQEPPKPR;S(0.02)T(0.025)T(0.955)PPPAEPVSLPQEPPKPR;S(0.009)T(0.035)T(0.955)PPPAEPVSLPQEPPKPR 199.94 2.27E-21 45240670000 14811510 10889950 13161480 11031980 16833750 17565410 16305370 15255450 15358140 9100990 TRUE FALSE 15396279.85 12760214.2 13504478.98 13214072.72 13972355.19 13486109.73 15027312.49 15050975.65 14805403.54 10884154.74 1.414559074 1.172366114 1.240746691 1.214065128 1.283733604 1.239058986 1.380659578 1.38283367 1.36027132 1 23.37572604 2.264092372 24.69168661 1.322764875 1.254749999 0 0.121576158 547.5831118 529563.9495 0.039271526 0.032844506 183.6929004 -2.264092372 -0.068014876 STT(ph)PTSSPFR ddPTM_MDA-MB-175_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(0.001)T(0.986)PT(0.012)S(0.001)SPFR;S(0.072)T(0.028)T(0.873)PT(0.026)SSPFR;S(0.013)T(0.028)T(0.937)PT(0.022)SSPFR 217.61 8.01E-08 3479860000 3101140 3409780 3147900 2907160 4042840 4191680 3411230 3219250 3007170 3608170 TRUE FALSE 3223575.402 3995383.191 3229936.86 3482187.571 3355639.501 3218225.846 3143848.879 3176101.219 2898942.539 4315121.829 0.747041574 0.925902755 0.748515798 0.806973177 0.777646526 0.745801851 0.728565497 0.736039756 0.671810126 1 22.04096986 3.567839935 1.291370595 0.75612003 0.826313477 0 0.094528393 1.213466062 4.021867724 0.029105303 0.063175171 3696.918995 -3.567839935 0.070193446 STTNY(ph)VDFYSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STTNYVDFYSTK 12 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 STT(0.024)NY(0.976)VDFYSTK 119.45 0.00031622 0 95581 73646 75490 68915 91859 112270 85742 64213 77921 72574 TRUE FALSE 99354.61168 86294.12761 77457.33142 82546.18131 76244.83999 86196.99397 79021.31799 63352.32977 75116.63843 86793.48579 1.144724293 0.994246594 0.892432545 0.951064248 0.878462701 0.993127459 0.910452176 0.72992033 0.865464012 1 16.40529915 8 0.593495452 0.872504276 17.1548297 0.48449092 0.074564002 137.3543824 1.084504952 0.034475912 2894.56914 100000000 -8 16.28232542 STTS(ph)VSEEDVSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 STT(0.014)S(0.985)VSEEDVSSR 200.79 4.67E-07 0 204690 255830 245430 272700 291540 332080 265210 277370 276780 277960 TRUE FALSE 212771.3193 299766.8124 251826.1074 326639.2461 241984.1349 254959.4527 244422.1472 273652.3088 266818.7419 332420.9401 0.640065933 0.90176874 0.757551878 0.982607311 0.727944921 0.766977714 0.735279032 0.823210201 0.802653232 1 18.34265174 0.268488911 1.608864782 1.000031831 0.796260458 0.320363376 0.090381545 10.26533596 21.13696522 0.080854146 0.022932237 1.85561943 -0.268488911 -0.203771373 STTTGHLIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 STTTGHLIYK 10 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5;P68104;A0A087WVQ9;Q5VTE0;A0A087WV01;A6PW80;Q5JR01 A0A2U3TZH3;P68104 EEF1A2;EEF1A1;EEF1A1P5 Elongation factor 1-alpha 2;Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 111.61 0.001731 48853580000 52993610 72929760 87424370 76557080 100768100 106273690 99737150 94769290 89926590 67025760 FALSE TRUE 55085838.64 85454878.97 89702720.9 91699841.92 83639574.36 81593236.09 91919491.57 93499062.68 86690149.59 80158174.39 0.687214237 1.066078159 1.119071406 1.143986158 1.043431627 1.017902874 1.14672636 1.166432038 1.081488573 1 26.25634632 4.738459671 4.165527134 1.099746767 0.653656236 0.831371539 0.05399258 0.084204532 3.270126537 0.01358034 0.11245159 54759.52478 -4.738459671 -0.446090531 STTTIGLVQALGAHLYQNVFACVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 STTTIGLVQALGAHLYQNVFACVR 24 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 ; 256.11 7.41E-44 282820000 199413 230810 269650 246240 280860 307220 295440 266440 276220 238880 FALSE TRUE 207285.9792 270449.822 276677.3005 294945.537 233119.5175 235872.811 272282.6408 262868.8076 266278.8962 285683.9624 0.725577934 0.946674849 0.968473338 1.032418952 0.816004915 0.825642465 0.953090396 0.920138483 0.932075059 1 18.12406052 -5 0.012567225 2.051368144 4.06E-10 0.153032502 0.082427904 19862.99073 18.94989615 1867.157453 1277.86694 1.00E-05 5 -2.051368143 STVDGLQVTQLNVDHTTENEDELFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 STVDGLQVTQLNVDHTTENEDELFR 25 0 Q15750;Q15750-2 Q15750 TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 0 ;; 262.24 3.94E-45 249731000 65681 85718 84879 85096 97262 104351 84134 96375 98366 89176 FALSE TRUE 68274.1366 100439.3997 87091.01647 101927.7348 80729.43998 80117.0617 77539.35724 95083.25076 94825.82687 106648.3298 0.640180083 0.941781272 0.816618663 0.955736813 0.756968629 0.751226595 0.727056461 0.891558742 0.889144978 1 16.70250185 1.09587389 1.64398024 0.993488124 0.809658933 0.307171821 0.092067571 0.44423804 2.368366173 0.08430086 0.024695809 12.47021354 -1.09587389 -0.18382919 STVLSLDWHPNNVLLAAGSCDFK ddPTM_MDA-MB-175_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 ; 268.36 1.98E-44 614440000 1148590 930910 1199630 957690 1450000 1446320 1473020 1217640 1350850 751200 FALSE TRUE 1193937.22 1090786.551 1230893.343 1147118.224 1203529.518 1110434.099 1357560.843 1201319.527 1302233.172 898383.2574 1.328984273 1.214166161 1.370120528 1.276869548 1.339661562 1.236036057 1.511115476 1.337201598 1.449529654 1 19.77697152 STVPGHAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STVPGHAGR 9 0 P00491;G3V5M2;G3V2H3 P00491 PNP Purine nucleoside phosphorylase 0 ;;; 134.05 0.00025974 1146110000 1201730 1809400 1907340 1967510 2186780 2470340 2035470 2070690 1869990 1805360 FALSE TRUE 1249175.228 2120150.375 1957046.847 2356677.606 1815071.917 1896640.973 1875924.543 2042935.788 1802689.425 2159085.726 0.578566758 0.981966741 0.906423874 1.091516459 0.840666906 0.878446349 0.868851348 0.94620411 0.834931843 1 21.0419891 4.744425998 24.83272235 0.924495995 0.578566592 0.654067791 0.076133685 357.239454 1512425.31 0.017544616 0.158427305 55517.001 -4.744425998 -0.345929403 STVTGERQS(ph)GDGQESTEPVENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK;STVTGERQS(1)GDGQESTEPVENK 319.55 9.20E-68 2151730000 1443650 1014340 1291470 923880 1568690 1765170 1377880 1254610 1385270 895740 TRUE FALSE 1500646.417 1188545.005 1325126.769 1106620.706 1302044.634 1355236.019 1269878.165 1237794.005 1335414.403 1071243.103 1.400845814 1.10950073 1.236999114 1.033024813 1.215452058 1.265105946 1.185424822 1.155474422 1.246602568 1 20.03085449 -1.588477888 2.715829232 0.985017415 1.196449913 0.299578803 0.093316886 12480312.74 12189680.58 1342215.834 0.020695147 0.025794203 1.588477888 0.211432497 STYNHLSSWLTDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 STYNHLSSWLTDAR 14 0 P61106;X6RFL8 P61106 RAB14 Ras-related protein Rab-14 0 131.96 5.32E-05 441850000 82073 503340 462710 709830 408650 712550 342210 500160 396600 551660 FALSE TRUE 85313.30541 589784.7296 474768.6027 850232.2554 339187.819 547071.0613 315386.686 493456.1733 382326.4435 659747.2148 0.129312112 0.893955619 0.719621989 1.288724281 0.514117849 0.829213143 0.478041709 0.747947338 0.579504445 1 19.33155383 4.745624517 24.7126272 0.767411393 0.129311762 0.418652162 0.230556209 700.8229536 2451714.096 0.052891198 0.531109216 55670.42251 -4.745624517 -0.638099631 SVAAEGALLPQT(ph)PPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 SVAAEGALLPQT(1)PPS(1)PR 227.66 8.92E-15 235530000 268300 242370 233490 232510 291220 337540 265820 260510 254610 223260 TRUE FALSE 278892.6912 283995.1621 239574.9412 278499.784 241718.5284 259151.4505 244984.3338 257018.2896 245446.6358 267003.5224 1.044528134 1.06363826 0.897272587 1.043056592 0.905300897 0.970591879 0.917532217 0.962602617 0.919263662 1 18.02649925 4.254845874 24.9995136 0.951620519 1.054083274 0.471942451 0.04321162 183.6974172 281989.0527 0.009442899 0.025692695 17982.32631 -4.254845874 0.102462755 SVAAEGALLPQTPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SVAAEGALLPQTPPSPR 17 0 Q86X27;Q86X27-3;H7C2H2 Q86X27 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQT(0.324)PPS(0.676)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQTPPS(1)PR;SVAAEGALLPQT(0.03)PPS(0.97)PR;SVAAEGALLPQTPPS(1)PR 350.63 1.21E-87 3705300000 2059130 2401910 2264300 2218500 2313950 2890460 2347700 2394910 2258370 2347310 TRUE FALSE 2140426.042 2814419.358 2323309.518 2657312.678 1920625.606 2219194.47 2163681.139 2362810.149 2177091.705 2807220.453 0.762471661 1.002564425 0.82761919 0.946599216 0.684173416 0.790530886 0.770755691 0.841690273 0.77553286 1 21.42071093 5.071852545 13.91976634 0.838686864 0.000161511 0.054981172 0.099725047 1444580.328 6803452.506 0.022904899 34438121.63 117991.9952 -5.071852545 -0.838525353 SVAHVTEADLFHTIETLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVAHVTEADLFHTIETLMR 19 0 A5YKK6-3;A5YKK6-2;A5YKK6;H3BMZ2 A5YKK6-3 CNOT1 CCR4-NOT transcription complex subunit 1 0 ; 250.95 8.55E-26 158254000 51163 107464 114959 121536 109776 137577 105891 117135 100374 108728 FALSE TRUE 53182.95475 125920.106 117954.926 145575.4581 91116.31473 105626.8267 97590.98673 115564.9969 96761.55935 130031.1699 0.409001586 0.968384013 0.907128084 1.119542785 0.700726717 0.812319284 0.750519947 0.888748421 0.744141266 1 16.98849797 -1.738956451 0.018164172 1.839797691 7.65E-06 0.078999592 0.179345548 7685.781906 20.97285309 1215.670508 923.1189807 0.018240786 1.738956451 -1.839790038 SVAPLPPQRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVAPLPPQRSPR 12 1 Q9BST9;Q9BST9-3;Q9BST9-2 Q9BST9 RTKN Rhotekin 1 SVAPLPPQRS(1)PR 63.682 0.041755 119190000 76013 188660 160330 169080 146740 195910 124560 161200 126190 183590 TRUE FALSE 79014.05193 221060.8874 164508.3315 202523.5193 121797.1872 150412.8715 114796.6617 159039.3777 121648.4465 219560.9455 0.359872981 1.006831552 0.749260444 0.922402292 0.554730656 0.685062051 0.522846454 0.724351853 0.55405321 1 17.74426193 -1.191869438 4.350857723 1.000095219 0.687546411 0.219565717 0.182270714 0.000158009 2.93E-05 0.165640167 0.039029904 0.064288096 1.191869438 -0.312548808 SVASGGWQEPENPHTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVASGGWQEPENPHTQR 17 0 E5RGG1;H9KVE0;Q9UJW0-2;Q9UJW0;Q9UJW0-3 E5RGG1 DCTN4 Dynactin subunit 4 0 ; 198.07 1.45E-11 328780000 115459 154119 173792 136787 215254 214853 162878 172787 181215 148580 FALSE TRUE 120017.4105 180587.7394 178321.1623 163843.0603 178665.202 164956.6469 150111.1968 170471.0729 174693.1075 177691.4063 0.675426083 1.016299793 1.0035441 0.92206519 1.005480263 0.928332159 0.844785912 0.959365883 0.983126372 1 17.43901438 4.746139861 24.86673582 0.956294539 0.675425938 0.744974067 0.050278881 454.4977443 1491123.313 0.012424226 0.132103616 55736.52148 -4.746139861 -0.280868601 SVASLNRS(ph)PERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVASLNRSPERR 12 2 Q12923-3;Q12923;Q12923-4 Q12923-3 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 SVASLNRS(0.999)PERR;SVASLNRS(1)PERR 105.19 0.0010732 597590000 306790 342350 381510 338760 432970 464510 329560 405980 337060 350880 TRUE FALSE 318902.3061 401145.9494 391452.464 405765.7169 359373.9141 356634.5922 303728.2261 400538.5021 324929.2764 419628.218 0.759963921 0.955955611 0.932855435 0.966964802 0.856410267 0.849882293 0.72380315 0.954508026 0.774326565 1 18.67875217 3.056161773 24.96945173 0.854291244 0.90996302 0.049696783 0.091161225 224.6397237 99872.6861 0.025203839 0.030124345 1138.051126 -3.056161773 0.055671776 SVAVS(ph)DEEEVEEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVAVSDEEEVEEEAER 16 0 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER;SVAVS(1)DEEEVEEEAER 432.86 2.01E-160 2159260000 752161.6 842845.5 870702.2 789112.6 941446 908072 778226.5 815660.2 778587 714824 TRUE FALSE 781857.5208 987597.6582 893393.4146 945196.717 781419.3452 697186.04 717227.0734 804727.6092 750565.806 854880.0767 0.914581521 1.155247017 1.045051159 1.105648316 0.914068963 0.815536657 0.83897975 0.941333915 0.87797789 1 19.70536253 3.162584226 6.004514128 0.888786186 1.06120444 0.5131532 0.074800488 0.148365988 8.941252588 0.020768514 0.025087161 1454.066356 -3.162584226 0.172418254 SVAVS(ph)DEEEVEEEAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVAVSDEEEVEEEAERR 17 1 Q9Y6X9;Q9Y6X9-2 Q9Y6X9 MORC2 MORC family CW-type zinc finger protein 2 1 SVAVS(1)DEEEVEEEAERR 196.89 9.55E-12 313960000 38231 45760 44048 42009 54972 55723 53468 45512 43614 53629 TRUE FALSE 39740.3894 53618.92404 45195.92707 50318.25482 45627.87908 42782.17774 49277.03845 44901.98608 42044.34066 64136.57576 0.619621315 0.836011642 0.70468257 0.784548508 0.711417448 0.667048049 0.768314146 0.700099523 0.655543895 1 15.96885971 -1.380280724 3.686992617 1.001448115 0.72078582 0.656718705 0.061445203 9118030.548 3414172.092 105097.8146 0.013226962 0.041660001 1.380280724 -0.280662295 SVDDVLSHFAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVDDVLSHFAQR 12 0 Q86Y56;H0Y650;Q86Y56-2 Q86Y56 DNAAF5 "Dynein assembly factor 5, axonemal" 0 84.821 0.012021 230450000 187860 163300 205530 184550 232010 243600 192470 176680 180570 185570 FALSE TRUE 195276.8579 191345.5047 210886.2806 221053.4392 192573.0231 187027.5918 177383.6985 174311.8936 174071.321 221928.8885 0.879907339 0.862192867 0.950242585 0.996055271 0.867724001 0.842736577 0.799281696 0.785440304 0.784356296 1 17.75973795 2.89929598 3.31120319 0.821961727 0.920626053 0.196391164 0.068950989 0.310816542 6.436829124 0.02146457 0.023373711 793.0416199 -2.89929598 0.098664326 SVDEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVDEALR 7 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ; 191.91 0.0012072 2523500000 3034800 3675000 3323800 3510800 3924100 4228600 3398700 3501800 3258500 3712400 FALSE TRUE 3154616.247 4306152.662 3410420.959 4205225.761 3257082.884 3246571.735 3132301.013 3454864.099 3141227.222 4439773.702 0.710535369 0.969903637 0.76815198 0.947171195 0.733614617 0.73124712 0.70550916 0.778162206 0.707519669 1 22.08205471 5.048730896 16.12207711 0.802448304 0.149575391 0.066260929 0.10862553 7743906.108 65592434.97 0.024945147 157136431.5 111874.4455 -5.048730896 -0.652872913 SVDETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SVDETLR 7 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5;Q13162;H7C3T4 Q06830;Q13162 PRDX1;PRDX4 Peroxiredoxin-1;Peroxiredoxin-4 0 ;;;;;;; 179.97 0.0016129 7505060000 4484522 5188886 4846290 5025605 5492360 5944991 5193396 5184860 4840489 5262852 FALSE TRUE 4661574.391 6080036.807 4972588.299 6019654.669 4558770.609 4564356.937 4786324.051 5115365.432 4666280.746 6294007.086 0.740636979 0.966004125 0.790051271 0.956410533 0.72430338 0.725190944 0.760457366 0.812735887 0.74138473 1 22.58554737 SVDFEMPPPS(ph)PPLNLHELSGPAEGASLTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SVDFEMPPPSPPLNLHELSGPAEGASLTPK 30 0 A0A087X165;Q9C0H9;A0A590UJ70;Q9C0H9-2;A0A087WVV7;Q9C0H9-4 A0A087X165 SRCIN1 SRC kinase signaling inhibitor 1 1 SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;S(0.001)VDFEMPPPS(0.999)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK;SVDFEMPPPS(1)PPLNLHELSGPAEGASLTPK 305.27 3.67E-81 1473125000 1043914 933679 1091857 940393 1389716 1400579 1306985 1191590 1348552 1002839 TRUE FALSE 1085128.531 1094031.105 1120311.69 1126399.929 1153492.571 1075315.753 1204540.101 1175618.685 1300017.877 1199326.102 0.904781885 0.912204866 0.934117659 0.939194042 0.96178393 0.896599975 1.004347441 0.980232719 1.083956962 1 20.19379256 1.870993089 1.518647687 1.033616002 0.926816513 0.657278871 0.031942199 0.228966416 0.990746485 0.021797981 0.009441698 74.30073138 -1.870993089 -0.10679949 SVDISLGDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVDISLGDSPR 11 0 E9PKC0;Q6IQ23;Q6IQ23-2;A0A1B0GTN9;H0YDE2;Q6IQ23-3 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR;SVDISLGDS(1)PR 229.63 2.51E-12 2320083000 1303355 1523539 1440846 1533697 1478546 1742560 1490367 1431407 1348231 1319964 TRUE FALSE 1354812.462 1785194.972 1478395.63 1837057.689 1227223.279 1337876.849 1373548.14 1412221.33 1299708.43 1578585.674 0.858244493 1.130882537 0.936531767 1.163736451 0.777419496 0.847516148 0.870113142 0.894611774 0.823337277 1 20.59020113 3.226704019 24.99986827 0.864918591 1.023971454 0.372964924 0.097426403 210.0250736 442841.2653 0.025782714 0.031049309 1685.403994 -3.226704019 0.159052864 SVDISLGDS(ph)PRR ddPTM_MDA-MB-175_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 201.4 9.11E-08 1110550000 913270 1041780 950060 956140 1076710 1203740 961690 1061340 977740 1044030 TRUE FALSE 949326.6048 1220697.611 974819.3441 1145261.638 893691.2188 924189.6279 886310.2249 1047114.473 942551.3284 1248587.689 0.760320331 0.9776627 0.78073759 0.917245659 0.715761677 0.740188003 0.709850203 0.838639114 0.754893979 1 20.25186572 6.263546702 14.05878168 0.81260175 0.743911004 0 0.103077642 0 0 0.021504549 0 1834622.444 -6.263546702 -0.068690746 SVDISPT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVDISPTR 8 0 Q9P2Q2 Q9P2Q2 FRMD4A FERM domain-containing protein 4A 1 SVDIS(0.444)PT(0.556)R 105.2 0.049572 195790000 328720 414910 384250 385560 387400 439840 410340 403640 366240 389560 TRUE FALSE 341698.1194 486167.5649 394263.8707 461822.6172 321549.8864 337693.8258 378176.4786 398229.866 353059.0939 465886.8234 0.733435895 1.043531477 0.846265339 0.991276409 0.69018884 0.724840903 0.811734652 0.854778126 0.757821591 1 18.82962 3.247615755 24.99801392 0.799885473 0.909523133 0.153686408 0.11058209 318.1554274 878308.3129 0.028951535 0.038644266 1768.543537 -3.247615755 0.10963766 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVDLHPTEPWMLASLYNGSVCVWNHETQTLVK 32 0 P35606;D6R997 P35606 COPB2 Coatomer subunit beta 0 111.38 1.98E-06 244320000 134230 159480 180070 179810 218750 232420 200330 208100 193760 146130 FALSE TRUE 139529.504 186869.4494 184762.7721 215375.8813 181566.9531 178443.9774 184627.6111 205310.7599 186786.6154 174761.3757 0.798400124 1.069283466 1.057228872 1.232399782 1.038942114 1.021072172 1.056455469 1.17480627 1.068809482 1 17.41502684 4.754752052 3.542467415 1.091159318 0.758315578 0.606566425 0.06767168 0.207573784 4.48179204 0.016475381 0.187927598 56852.82537 -4.754752052 -0.33284374 SVDYNMPRS(ph)PVEMDEDFDVIFDPYAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVDYNMPRSPVEMDEDFDVIFDPYAPK 27 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 SVDYNMPRS(1)PVEMDEDFDVIFDPYAPK 182.73 9.31E-18 28277000 18799 21525 29259 15188 34649 32255 16635 26255 28430 35328 TRUE FALSE 19541.19904 25221.75131 30021.51358 18192.14107 28759.37536 24764.26508 15331.10523 25903.09467 27406.80985 42249.8452 0.462515281 0.596966715 0.710570972 0.430584798 0.680697769 0.586138599 0.362867726 0.613093244 0.648684267 1 15.36665844 0.754230993 2.019452869 0.99950299 0.555580533 0.626401332 0.103090613 0.600193815 3.826809318 0.095211486 0.026282471 5.678465518 -0.754230993 -0.443922457 SVEDRFDQQKNDYDQLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVEDRFDQQKNDYDQLQK 18 2 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 147.56 4.26E-08 79752000 144800 86180 116660 65729 163350 140440 99345 104590 123120 86205 FALSE TRUE 150516.8158 100980.7446 119700.2554 78730.00002 135583.8253 107824.9384 91558.07931 103188.1421 118688.9353 103095.2193 1.459978619 0.979490081 1.161065046 0.763662957 1.315132034 1.045877192 0.888092387 1.000901331 1.151255471 1 16.65361791 4.742756793 24.6924028 1.030487015 1.459978821 0.438816813 0.144489468 320.1065332 1883582.462 0.032559281 0.253231152 55304.03177 -4.742756793 0.429491806 SVEEEEQVWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVEEEEQVWR 10 0 Q9P2E9;A0A087WVV2;Q9P2E9-3;F8W7S5;A0A087WU26 Q9P2E9 RRBP1 Ribosome-binding protein 1 0 ; 204.86 2.37E-06 414860000 343880 442520 402180 436280 410270 467540 393530 364130 371300 358620 FALSE TRUE 357456.6479 518519.3677 412661.1412 522574.8818 340532.4519 358960.9206 362684.0903 359249.4329 357936.9855 428884.7228 0.833456239 1.208994725 0.962172629 1.218450679 0.793995295 0.836963644 0.845644694 0.837636348 0.834576208 1 18.7102304 3.219772979 24.99997347 0.847544069 1.060027911 0.408434055 0.116056678 201.6764136 268362.3122 0.030430928 0.0364299 1658.71961 -3.219772979 0.212483842 SVEEGKIDGIIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVEEGKIDGIIDK 13 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 0 ; 156.17 4.29E-05 420350000 493377 253258 372753 248929 497020 478119 436038 363933 443952 243757 FALSE TRUE 512855.9049 296753.0914 382467.2494 298166.4132 412536.7179 367083.1082 401860.2022 359055.0734 427974.2542 291516.5171 1.759268771 1.017963216 1.311991695 1.022811387 1.415140116 1.259218901 1.378516065 1.231680033 1.468096074 1 18.1532181 -1.994418725 2.652688753 0.71093339 1.299115507 0.17242118 0.205367299 29782433.05 11878331.39 52629040.87 0.04598427 0.010129343 1.994418725 0.588182117 SVEGWILFVTGVHEEATEEDIHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVEGWILFVTGVHEEATEEDIHDK 24 0 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 253.9 4.95E-44 93014000 101760 69927 106950 80690 120170 144250 144420 104590 127790 68569 FALSE TRUE 105777.5634 81936.41829 109737.2049 96650.24116 99743.54632 110750.1236 133099.983 103188.1421 123190.8629 82003.78272 1.289910781 0.999178521 1.338196864 1.178607108 1.216328601 1.350548962 1.62309565 1.258333929 1.502258296 1 16.32340284 2.73033246 4.625044923 1.378284119 1.197738208 0.13314013 0.17354858 0.310264449 18.36719783 0.052131947 0.051670262 537.443061 -2.73033246 -0.180545911 SVEMHHEALSEALPGDNVGFNVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 144.01 8.97E-08 58832000 58655 65099 78962 61367 86910 89958 89085 84216 79780 64225 FALSE TRUE 60970.74469 76279.24685 81019.81459 73505.20944 72137.06924 69066.61783 82102.28492 83087.22227 76908.73338 76808.65909 0.793800405 0.993107389 1.054826572 0.956991182 0.939178865 0.899203536 1.068919649 1.081742908 1.001302904 1 16.22898134 2.228187392 24.99557891 1.049622408 0.947973992 0.326706264 0.067795645 246.0572379 592901.2613 0.025750688 0.019227889 169.1170489 -2.228187392 -0.101648417 SVESTS(ph)PEPSK ddPTM_MDA-MB-175_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 SVEST(0.023)S(0.977)PEPSK;SVEST(0.016)S(0.984)PEPSK;SVEST(0.012)S(0.987)PEPSK;SVESTS(1)PEPSK;SVES(0.001)T(0.102)S(0.897)PEPSK;SVES(0.013)T(0.119)S(0.868)PEPSK 301.35 7.64E-36 5400560000 11836440 8749750 10288670 8299550 13049270 13868330 12555250 10691580 10961190 7655710 TRUE FALSE 12303751.79 10252451.5 10556801.19 9941176.218 10831159.75 10647620.53 11571136.7 10548276.86 10566698.91 9155699.797 1.343835213 1.119788954 1.153030508 1.085790976 1.182996383 1.16294994 1.263817835 1.152099467 1.154111553 1 23.12623873 0.641129507 1.898131153 1.000103927 1.178896177 0.382525126 0.069375883 1.8354716 8.359726754 0.063573196 0.017675899 4.376525939 -0.641129507 0.17879225 SVETLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVETLK 6 0 P14618;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34;H3BU13 P14618;P14618-2;H3BU13 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ; 107.22 0.07317 359440000 687350 691080 803420 638420 957980 1075150 850780 774400 814780 619720 FALSE TRUE 714487.1087 809767.6141 824357.7852 764697.5705 795142.9018 825462.7066 784093.6405 764020.4347 785456.227 741142.2687 0.964035029 1.092594025 1.112280084 1.031782429 1.072861359 1.11377092 1.057952938 1.030868791 1.059791433 1 19.49939098 0.814730739 0.887117672 1.001461889 1.065969062 0.146450768 0.042236721 1.478683759 2.312167506 0.039583729 0.013506963 6.527257399 -0.814730739 0.064507173 SVFALTNGIYPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVFALTNGIYPHK 13 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 ; 194.3 1.14E-06 6238700000 3100600 3022500 3403600 2887770 4444500 4378100 3670200 3821300 3796600 2974690 FALSE TRUE 3223014.082 3541590.863 3492300.612 3458962.287 3689025.478 3361352.626 3382520.134 3770081.724 3659961.108 3557523.552 0.905971257 0.99552141 0.981666196 0.972294979 1.036964457 0.944857448 0.950807517 1.059748915 1.028794625 1 21.76244188 5.843581611 1.177299333 1.000447701 1.22E-22 0.367218763 0.035279225 20.95701121 3.130578167 0.010574391 46.41582969 697560.0667 -5.843581611 -1.000447701 SVFEPEDSSIVDNELWSEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVFEPEDSSIVDNELWSEMR 20 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 0 67.93 0.036851 0 13948 11915 14444 11766 14405 15973 14793 12751 13887 15687 FALSE TRUE 14498.67781 13961.30856 14820.42251 14093.27968 11956.44325 12263.51282 13633.48601 12580.0937 13387.20958 18760.5673 0.772827259 0.744183709 0.789977311 0.751218204 0.637317787 0.653685607 0.726709688 0.67056041 0.713582344 1 14.19541583 -1.868573524 8.108212887 1.024543049 0.714528754 0.756332913 0.048023578 0.020789879 0.000336984 0.045371435 0.011913587 0.013534009 1.868573524 -0.310014296 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVFKPIVQIAVIENSESLDCQLLAVTHAGVR 31 1 O75694;O75694-2;E9PF10 O75694 NUP155 Nuclear pore complex protein Nup155 0 ; 284.67 2.17E-72 395510000 219120 210099 289910 252996 295967 338218 288487 259565 277829 221485 FALSE TRUE 227771.0268 246181.8689 297465.2928 303037.8537 245658.6351 259671.9952 265874.6351 256085.9557 267829.9886 264880.7452 0.859900279 0.929406434 1.123015916 1.144053916 0.927431078 0.980335491 1.003752217 0.966797173 1.011134231 1 18.01498345 4.468216826 24.47613859 1.015513271 0.877276771 0.401619164 0.063363101 132.6727814 364686.8815 0.016654029 0.04576385 29391.16667 -4.468216826 -0.1382365 SVFPEQANNNEWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVFPEQANNNEWAR 14 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 140.24 2.33E-05 85707000 17679 19854 20401 23212 26404 30252 25305 22362 21131 21254 FALSE TRUE 18376.98057 23263.77006 20932.66682 27803.26432 21915.85751 23226.43147 23321.52798 22062.27397 20370.49944 25418.31437 0.722981875 0.915236539 0.823526947 1.093828014 0.862207352 0.913767575 0.917508834 0.867967626 0.801410319 1 14.63358074 5.0554494 1.992936516 0.908704583 0.481272476 0.319003955 0.081271074 3.113373663 5.850114776 0.019832238 3.306303307 113618.5913 -5.0554494 -0.427432107 SVFWASS(ph)PYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVFWASSPYR 10 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SVFWAS(0.036)S(0.964)PYR;SVFWAS(0.005)S(0.995)PYR 150.09 2.33E-05 199260000 225110 248000 154248 142170 735430 400180 187322 149899 160768 999980 TRUE FALSE 233997.5166 290592.0708 158267.8296 170290.8017 610421.8713 307244.2598 172639.2122 147889.8491 154981.9911 1195906.935 0.195665323 0.242988867 0.132341259 0.142394694 0.510425898 0.256913185 0.1443584 0.123663343 0.129593689 1 20.18967369 -1.493097819 4.209537124 1.005828145 0.206827606 0.821313609 0.110723219 0.006407145 0.000771533 0.113415004 0.026623055 0.032129368 1.493097819 -0.799000538 SVFWASS(ph)PYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVFWASSPYRR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3 O15027 SEC16A Protein transport protein Sec16A 1 SVFWAS(0.137)S(0.863)PYRR;SVFWAS(0.02)S(0.98)PYRR;SVFWAS(0.05)S(0.95)PYRR 103.97 0.0016306 861323000 424782 434844 430082 420444 484854 570536 377545 432718 434950 483911 TRUE FALSE 441552.7214 509525.0744 441290.2902 503606.5683 402438.6903 438037.6606 347952.0364 426918.123 419296.2345 578724.0954 0.762976218 0.880428305 0.762522753 0.870201487 0.695389553 0.756902407 0.601239933 0.737688523 0.724518363 1 19.14251619 3.232041042 24.99120847 0.729554541 0.819381241 0.066151767 0.102144963 273.1795234 1047167.015 0.027013901 0.033007092 1706.243626 -3.232041042 0.089826699 SVGGDS(ph)DTEDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVGGDSDTEDMR 12 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 SVGGDS(0.988)DT(0.012)EDMR 93.348 0.028236 55609000 110870 122070 132380 113350 144740 157850 143580 144500 136040 129030 TRUE FALSE 115247.2332 143034.5729 135829.9316 135770.2917 120137.1465 121191.7297 132325.8244 142563.2139 131143.947 154310.9581 0.74685061 0.926924275 0.880235164 0.879848673 0.778539308 0.785373451 0.857527074 0.92386967 0.849868011 1 17.23548099 0.629999595 0.722587225 0.99958479 0.841557537 0.402602798 0.056794161 1.364810895 1.295979047 0.060754043 0.021294441 4.265791214 -0.629999595 -0.158027253 SVGGS(ph)GGGSFGDNLVTR ddPTM_MDA-MB-175_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(0.243)VGGS(0.744)GGGS(0.013)FGDNLVTR;S(0.093)VGGS(0.558)GGGS(0.348)FGDNLVTR;SVGGS(1)GGGSFGDNLVTR 279.93 7.11E-36 687960000 472551 546662 544818 501497 588495 649470 540940 549839 527720 510197 TRUE FALSE 491207.6784 640546.9461 559016.4047 600691.6098 488462.8301 498640.4353 498539.7093 542469.3076 508727.4603 610160.3338 0.805046889 1.049801029 0.916179525 0.98448158 0.80054832 0.817228534 0.817063453 0.889060264 0.833760296 1 19.21882887 3.243008961 24.99958459 0.851748044 0.945179117 0.190873685 0.078535913 151.6496337 852260.8979 0.02042132 0.026728981 1749.882796 -3.243008961 0.093431074 SVGGSGGGS(ph)FGDNLVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 S(0.015)VGGS(0.039)GGGS(0.946)FGDNLVTR;S(0.352)VGGS(0.021)GGGS(0.627)FGDNLVTR 233.79 4.26E-20 474330000 557240 616650 572110 562050 649530 693340 554780 579620 583410 512430 TRUE FALSE 579240.2655 722554.8406 587019.6566 673221.8124 539123.1226 532322.2927 511294.894 571851.142 562413.1881 612830.8474 0.945187841 1.179044501 0.957882031 1.098544264 0.879725825 0.868628423 0.83431651 0.933130479 0.917729893 1 19.22512939 3.231090625 24.99901171 0.897887381 1.048493035 0.454124119 0.074646581 133.0501048 445263.9063 0.019952286 0.024290154 1702.513739 -3.231090625 0.150605654 SVGKPALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVGKPALER 9 1 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ; 71.451 0.045185 665680000 1409210 1169120 1326750 1120380 1699700 1662110 1455850 1326970 1311200 1150810 FALSE TRUE 1464846.699 1369907.266 1361326.195 1341987.82 1410785.601 1276110.142 1341736.673 1309184.138 1264010.168 1376289.186 1.064345135 0.995362951 0.989128018 0.97507692 1.025064801 0.92721076 0.974894438 0.951242043 0.918419022 1 20.39235221 7.999999997 0.450171146 0.956941843 3.222118185 0.499469458 0.029407333 69.45469081 0.836748027 0.016932459 144.6033445 99999999.42 -7.999999997 2.265176342 SVGRPS(ph)PLASGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVGRPSPLASGR 12 1 Q92738;X6RAB3;Q92738-2 Q92738 USP6NL USP6 N-terminal-like protein 1 SVGRPS(1)PLASGR;SVGRPS(1)PLASGR;SVGRPS(1)PLASGR;SVGRPS(1)PLASGR 123.42 0.0002066 2262170000 535328 612340 517750 609320 589295 777320 614560 582198 499077 527180 TRUE FALSE 556463.1628 717504.6317 531242.9903 729841.6774 489126.8464 596799.2104 566389.1813 574394.5881 481115.3163 630470.8275 0.882615243 1.138045728 0.842613119 1.157613716 0.77581202 0.946592902 0.898359062 0.911056568 0.763104802 1 19.26607009 3.22437542 24.99998806 0.88438862 1.003094497 0.221401801 0.112693384 342.5518707 603712.2739 0.029663686 0.035615564 1676.391384 -3.22437542 0.118705877 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVGYKPDFVGFEIPDKFVVGYALDYNEYFR 30 2 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 159.59 2.60E-12 550980000 210772 183880 224842 170928 296091 255231 254355 229936 253026 161449 FALSE TRUE 219093.4413 215459.9596 230701.5672 204737.0482 245761.5576 195957.4683 234417.9905 226854.084 243919.6437 193081.8404 1.134718008 1.115899658 1.194838244 1.060364081 1.272836208 1.014893311 1.214086161 1.174911548 1.263296658 1 17.55885296 SVHELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SVHELEK 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 137.18 0.002908 15453140000 6721180 14803740 16728760 14062790 19195950 20435350 17516490 17717190 16434240 14173780 FALSE TRUE 6986537.376 17346167.19 17164725.23 16844367.89 15933029.28 15689549.66 16143501.74 17479720.05 15842774.91 16950860.82 0.412164164 1.023320725 1.012616729 0.99371755 0.939953991 0.925590142 0.952370615 1.03119955 0.93462952 1 24.0148552 4.741219102 24.99991274 0.979959703 0.412163962 0.955324571 0.036790726 47.64046543 447977.8543 0.009296043 0.063869253 55108.56495 -4.741219102 -0.567795741 SVHELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVHELER 7 0 Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-4;A1L2Z2 Q7Z406 MYH14 Myosin-14 0 66.351 0.068109 100810000 56044 107270 99104 103980 120400 141620 99253 111440 109380 127550 FALSE TRUE 58256.6604 125692.7881 101686.7317 124546.9337 99934.45101 108730.9013 91473.29051 109946.3291 105443.4352 152540.9804 0.38190826 0.823993577 0.666619104 0.816481796 0.655131826 0.712797971 0.599663712 0.720765848 0.691246607 1 17.21883735 -4.99999985 0.380257962 5.485340726 0.675074925 0.411806995 0.117198601 565.2251785 4.221806474 2090.841886 0.071695172 1.00E-05 4.99999985 -4.810265801 SVHPYEVAEVIALPVEQGNFPYLQWVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVHPYEVAEVIALPVEQGNFPYLQWVR 27 0 O60888-3;O60888;O60888-2 O60888-3 CUTA Protein CutA 0 55.846 0.016244 0 191850 91947 139370 67599 227870 211030 159180 148090 173670 102540 FALSE TRUE 199424.3861 107738.182 143002.0967 80969.88044 189136.7388 162021.4807 146703.0557 146105.0958 167419.6506 122630.7498 1.626218437 0.878557639 1.166119403 0.660273876 1.542327183 1.321214141 1.196299101 1.191423 1.36523385 1 16.90396126 3.206817962 24.99999849 1.270168493 1.074154525 0.107266725 0.263277453 420.8081041 331420.3929 0.072645661 0.086835372 1609.97066 -3.206817962 -0.196013967 SVIDLRPEDVVHES(ph)GSLGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVIDLRPEDVVHESGSLGDR 20 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 SVIDLRPEDVVHES(0.656)GS(0.344)LGDR 110.68 0.00010822 137220000 63127 252210 194130 261580 182730 265540 166480 226240 168490 300900 TRUE FALSE 65619.3027 295525.1056 199189.1873 313319.7433 151669.6199 203872.3593 153430.8626 223207.6229 162426.0778 359855.5939 0.182348986 0.82123249 0.553525333 0.870681875 0.421473564 0.566539364 0.426367869 0.620269982 0.451364604 1 18.45705856 -1.535838324 3.459409436 1.010903211 0.560141433 0.337898262 0.189733426 19793231.39 17709093.61 1512799.528 0.040611631 0.029118009 1.535838324 -0.450761778 SVIDYQTHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVIDYQTHFR 10 0 Q9Y3B3;A0A0A6YYA0;Q86XR7-2;Q9Y3B3-2 Q9Y3B3 TMED7;TMED7-TICAM2 Transmembrane emp24 domain-containing protein 7 0 ; 179.57 2.09E-06 365960000 300100 418080 318480 560020 800090 721350 572970 373720 307070 768000 FALSE TRUE 311948.1797 489881.9878 326779.8504 670790.2845 664090.9876 553827.3947 528059.1142 368710.8947 296018.6107 918474.8958 0.339637132 0.533364592 0.355785283 0.73033056 0.723036624 0.602985882 0.574930373 0.401438185 0.322293633 1 19.80888076 3.756438442 24.72775512 0.586809982 0.421972561 0.202126299 0.183897885 1464.253177 2025278.321 0.047797772 0.085928433 5707.401725 -3.756438442 -0.164837421 SVISHSVTSDMQTIEQES(ph)PIMAKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVISHSVTSDMQTIEQESPIMAKPR 25 1 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61;H0Y6A0 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 SVISHSVTSDMQTIEQES(1)PIMAKPR;SVISHSVTSDMQTIEQES(1)PIMAKPR;SVISHSVTSDMQTIEQES(1)PIMAKPR;SVISHSVTSDMQTIEQES(1)PIMAKPR 317.65 5.92E-75 909500000 259938 461716 450598 441177 479285 552500 377971 465505 397561 475659 TRUE FALSE 270200.553 541012.1313 462340.9541 528440.4938 397816.3069 424190.2482 348344.6454 459265.6669 383252.8573 568855.274 0.474989976 0.951054084 0.812756733 0.928954196 0.699327799 0.745690983 0.612360756 0.807350635 0.673726473 1 19.11770213 -1.086161673 4.488571155 1.000017834 0.755370456 0.23876055 0.135419245 2.46E-05 5.01E-06 0.123078638 0.02900762 0.082004621 1.086161673 -0.244647377 SVKEDSNLTLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVKEDSNLTLQEK 13 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 193.96 1.30E-06 456400000 388860 240470 330030 193960 483830 399840 364290 321280 390070 235990 FALSE TRUE 404212.4931 281768.8519 338630.8529 232324.7091 401588.7494 306983.2196 335735.9979 316973.7671 376031.4569 282227.7222 1.43222108 0.998374113 1.199849718 0.823181746 1.422924532 1.08771462 1.189592558 1.123113508 1.332368961 1 18.10650018 3.208655076 24.99938484 1.18850111 1.111363462 0.043036596 0.182267541 759.4072017 634820.5526 0.049329065 0.058967336 1616.795442 -3.208655076 -0.077137648 SVKEDSVPTGAEENVVCES(ph)PVEIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVKEDSVPTGAEENVVCESPVEIIK 25 1 O75363 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 SVKEDSVPTGAEENVVCES(1)PVEIIK 67.11 0.0050431 0 56938 54559 59493 51601 84754 85058 57015 75927 71419 54438 TRUE FALSE 59185.95621 63929.08384 61043.43645 61807.52379 70347.54535 65304.56857 52546.01532 74909.32276 68848.64414 65104.08382 0.909097444 0.981951977 0.937628377 0.949364773 1.080539672 1.00307945 0.807107822 1.150608662 1.05751652 1 15.99046042 3.533030778 0.378668497 1.043509599 0.903710084 0.122577492 0.085452392 5.309847022 1.147196777 0.087267084 0.312963995 3412.170923 -3.533030778 -0.139799515 SVKHDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVKHDSIPAADTFEDLSDVEGGGSEPTQR 29 1 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 S(0.007)VKHDS(0.006)IPAADT(0.032)FEDLS(0.955)DVEGGGSEPTQR 103.5 0.00034158 80721000 7550.9 26834 29671 21828 34464 39480 17599 30382 26597 44470 TRUE FALSE 7849.015363 31442.53076 30444.25063 26145.51325 28605.82159 30311.36833 16219.54439 29974.77898 25639.77917 53183.04507 0.147584918 0.591213435 0.572442789 0.491613694 0.537874835 0.569944205 0.30497585 0.56361532 0.482104384 1 15.69867876 -4.839270213 0.435074408 10 0.476068579 0.581584327 0.134091898 649.3716228 4.622345577 5585.623604 0.069956555 1.45E-05 4.839270213 -9.523931421 SVLIMDGASAFGTIAIQLAHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVLIMDGASAFGTIAIQLAHHR 22 0 H7C3S0;H7C338;C9K0F7;C9JAL0;F8WF64;C9JZK8;H7C3I5;A6NND8;A6NHJ8;A6NMA8;O95825-2;O95825 H7C3S0 CRYZL1 Quinone oxidoreductase-like protein 1 0 78.987 0.00468 9362400 5205.3 3781 4894.7 5815.2 5607.1 6936 5837.8 4879.5 5977.5 5513.1 FALSE TRUE 5410.809263 4430.357338 5022.259903 6965.429203 4654.007145 5325.219116 5380.217982 4814.098284 5762.370943 6593.28639 0.820654366 0.67194978 0.761723305 1.056442689 0.705870619 0.807672957 0.816014604 0.730151551 0.873975526 1 12.68678203 0.969832416 6.696970804 0.999981975 0.795049071 0.287655298 0.099005238 0.288362746 55.75447805 0.093475019 0.02345844 9.32894249 -0.969832416 -0.204932904 SVLLLAYKPMEGNFEEIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVLLLAYKPMEGNFEEIAR 19 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 218.69 3.01E-19 858760000 867380 842280 1023840 915510 1228100 1218520 1163880 1049370 1094060 814670 FALSE TRUE 901624.8322 986935.038 1050522.111 1096595.145 1019348.001 935537.1968 1072652.044 1035304.912 1054684.994 974288.9887 0.925418272 1.012979772 1.078244878 1.125533757 1.046248097 0.960225567 1.100958809 1.062626103 1.082517617 1 19.89399024 4.624964625 2.80947722 1.060026596 0.916448624 0.434723388 0.045531053 0.306503424 3.765351793 0.011371287 0.08781143 42166.21564 -4.624964625 -0.143577972 SVLNSITEEVLDHMGTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVLNSITEEVLDHMGTFR 18 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 0 145.75 8.88E-08 37292000 40440 44050 52982 52637 57904 71373 61336 51452 59476 44145 FALSE TRUE 42036.60243 51615.24484 54362.75445 63048.44149 48061.49876 54797.70242 56528.32405 50762.3701 57335.47038 52794.36754 0.796232712 0.977665748 1.029707466 1.194226665 0.910352771 1.037945996 1.070726418 0.961511094 1.086014911 1 15.6880964 4.717272488 2.558242496 1.033586185 0.752496935 0.502545765 0.071778586 0.37898423 3.288756176 0.017312781 0.225471189 52152.18255 -4.717272488 -0.28108925 SVLSGGPLPQGHEFELYEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVLSGGPLPQGHEFELYEVR 20 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 ;; 261.69 2.15E-36 1005650000 498757 641126 675248 693497 718715 764053 589599 637807 635219 578774 FALSE TRUE 518448.3115 751234.4032 692845.5176 830668.6367 596548.081 586613.2701 543384.6897 629258.2404 612357.5923 692173.684 0.749014768 1.085326444 1.000970614 1.200086995 0.861847387 0.847494326 0.785040955 0.909104543 0.884687769 1 19.40077457 SVMEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVMEELKR 8 1 P61326;Q96A72;F5H6N1;F5H6P7;F5H3U9 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 112.84 0.0047514 1186200000 485520 570430 614530 594190 744690 748760 624330 650740 601350 541190 FALSE TRUE 504688.7045 668396.9152 630545.1566 711719.0085 618107.8598 574871.8376 575393.3832 642017.8947 579707.531 647225.8188 0.779772206 1.032710525 0.974227446 1.099645576 0.955011129 0.888209062 0.889014879 0.991953467 0.895680478 1 19.30390963 3.003542637 24.99915734 0.932559984 0.982541358 0.03880371 0.084091506 306.3205304 2161566.13 0.023897128 0.028438635 1008.190583 -3.003542637 0.049981374 SVNEILGLAES(ph)SPNEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.5)S(0.5)PNEPK;SVNEILGLAES(0.818)S(0.182)PNEPK 123.14 5.73E-05 115088000 145630 90311 115335 88310 158209 162972 134827 114352 134190 89312 TRUE FALSE 151379.5849 105821.2117 118340.7248 105777.4544 131316.6907 125124.2229 124258.9074 112819.2985 129360.5281 106810.9764 1.417266183 0.990733493 1.107945352 0.990323822 1.229430674 1.171454724 1.163353352 1.056251916 1.211116427 1 16.70470039 -2.122436231 2.496405836 0.7254687 1.135810436 0.112625093 0.120416736 7159737.921 3149782.808 11131681.66 0.026922469 0.007543341 2.122436231 0.410341736 SVNEILGLAESS(ph)PNEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 SVNEILGLAES(0.025)S(0.975)PNEPK;SVNEILGLAES(0.002)S(0.998)PNEPK;SVNEILGLAES(0.015)S(0.985)PNEPK;SVNEILGLAES(0.005)S(0.995)PNEPK 313.93 3.46E-58 305447000 883076 511511 657669 482519 827233 853195 759781 645116 720908 443739 TRUE FALSE 917940.5224 599359.0352 674808.3944 577959.818 686620.2301 655053.3915 700227.3799 636469.2752 694962.6619 530681.1612 1.729740171 1.12941457 1.271589127 1.089090513 1.293847003 1.23436338 1.319487917 1.199344016 1.309567237 1 19.01748581 7.999998315 0.025093019 3.66E-08 2.965148871 0.270264667 0.15891606 3092.397024 5.964867365 241.8787385 508.4081816 99999611.93 -7.999998315 2.965148834 SVNELIYKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVNELIYKR 9 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 130.94 0.00055655 1067180000 2096730 2160840 2246840 1675760 3178270 2803570 1985830 2333900 2381180 2766970 FALSE TRUE 2179510.519 2531947.461 2305394.496 2007220.326 2638028.801 2152483.356 1830175.456 2302617.888 2295481.797 3309104.795 0.658640525 0.765145747 0.696682227 0.606575026 0.79720316 0.65047301 0.55307268 0.695843145 0.693686643 1 21.65800955 -1.90246654 2.315930588 1.190907212 0.67881284 0.674572354 0.066737673 4493635.58 2240277.516 4671018.371 0.016499356 0.012517957 1.90246654 -0.512094372 SVNESLNNLFITEEDYQALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVNESLNNLFITEEDYQALR 20 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 240.24 2.50E-29 117708000 83333 76956 98613 96957 96046 122438 88478 98295 81946 89094 FALSE TRUE 86623.05119 90172.59437 101182.9358 116134.8052 79720.13523 94003.63007 81542.86317 96977.5163 78996.77947 106550.2635 0.812978292 0.846291613 0.949626331 1.089953243 0.748192755 0.88224681 0.765299498 0.910157452 0.741403887 1 16.70117464 3.174440229 24.99999995 0.838522711 0.920912933 0.139371723 0.101335787 123.8627826 48291.88523 0.028694109 0.034296032 1494.308371 -3.174440229 0.082390222 SVNVKPLVTHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVNVKPLVTHR 11 1 Q00796 Q00796 SORD Sorbitol dehydrogenase 0 ; 88.163 0.0079215 1236770000 1171420 1049950 1215070 1097280 1442420 1544760 1359210 1353360 1290580 1053290 FALSE TRUE 1217668.566 1230270.745 1246735.722 1314318.709 1197237.964 1186012.901 1252671.569 1335220.423 1244132.278 1259662.009 0.966662928 0.976667341 0.98973829 1.043389972 0.950443814 0.941532643 0.994450543 1.059983085 0.987671509 1 20.26460525 1.988449864 24.58328378 1.023716448 0.979230315 0.214452264 0.031333913 580.7378072 1236041.393 0.012745539 0.008759492 97.37553669 -1.988449864 -0.044486133 SVPAFLQDES(ph)DDRETDTASESSYQLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVPAFLQDESDDRETDTASESSYQLSR 27 1 A0A0U1RR07;Q9HCH5-7;Q9HCH5-13;Q9HCH5-8;A0A0U1RQP0;Q9HCH5;Q9HCH5-14;E9PRW5;E9PS29;Q9HCH5-2;E9PK22;E9PS39;Q9HCH5-12 A0A0U1RR07;Q9HCH5-12 SYTL2 Synaptotagmin-like protein 2 1 S(0.003)VPAFLQDES(0.997)DDRETDTASESSYQLSR;SVPAFLQDES(1)DDRETDTASESSYQLSR 234.17 3.45E-45 444330000 60522 65729 67812 67140 69915 89432 59036 65733 61784 67195 TRUE FALSE 62911.45529 77017.44445 69579.23643 80420.09161 58030.87327 68662.77336 54408.60406 64851.95665 59560.40591 80360.57372 0.782864686 0.95839839 0.865837975 1.000740635 0.722131147 0.854433588 0.677055943 0.807012116 0.741164518 1 16.29420024 3.228386079 24.99667632 0.78604272 0.90341154 0.195023202 0.098646576 267.2745658 656635.7645 0.025975719 0.031381143 1691.944367 -3.228386079 0.11736882 SVPGYKVEEKS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVPGYKVEEKSP 12 2 S5FZ81 S5FZ81 PHF10 1 SVPGYKVEEKS(1)P;SVPGYKVEEKS(1)P;SVPGYKVEEKS(1)P 93.51 0.0056167 534430000 1709930 672150 1006590 504770 1705680 1578480 1091100 960170 1107790 629900 TRUE FALSE 1777439.357 787586.5339 1032822.562 604611.9994 1415749.123 1211901.942 1005576.731 947300.4917 1067920.854 753316.8448 2.359484417 1.045491733 1.37103341 0.802599867 1.879354129 1.608754604 1.334865585 1.257506052 1.417625082 1 19.52289726 7.999999961 0.036276923 2.42E-12 3.575567981 0.144263147 0.399133354 2260.120762 6.258544995 178.694669 521.5417988 99999991.06 -7.999999961 3.575567981 SVPHEEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVPHEEYR 8 0 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0;H0YN19 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ; 158.07 0.00036709 770660000 194746 229630 215950 204527 225682 291670 273920 233570 215935 196674 FALSE TRUE 202434.7225 269067.1662 221577.8344 244981.8301 187320.6543 223934.0628 252449.4346 230439.3762 208163.5415 235208.5047 0.860660726 1.143951689 0.942048565 1.041551752 0.796402555 0.952066181 1.073300623 0.979723826 0.885017069 1 17.8435807 SVPHLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVPHLQK 7 0 P07355-2;P07355;H0YN42;H0YMU9;H0YMD0;H0YM50;A6NMY6;H0YL33;H0YNP5;H0YN28 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 102.72 0.0085375 282890000 636420 780550 750170 778620 722330 1045800 891930 756580 748890 826350 FALSE TRUE 661546.353 914603.3907 769720.0465 932628.7121 599548.6046 802928.7993 822018.196 746439.2826 721937.5952 988257.4611 0.669406889 0.925470767 0.77886591 0.943710267 0.60667248 0.812469251 0.831785469 0.755308522 0.730515704 1 19.91452742 -1.107254347 4.199237144 1.000037301 0.78793761 0.301604908 0.098516868 1.451499305 51080994.36 3970.275273 0.021362045 0.078117017 1.107254347 -0.212099691 SVPIWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVPIWER 7 0 O00204;O00204-2 O00204 SULT2B1 Sulfotransferase family cytosolic 2B member 1 0 95.531 0.03117 323640000 944830 862680 1113500 864950 1418200 1326500 1088300 1205700 1228700 923200 FALSE TRUE 982132.618 1010838.579 1142518.725 1036034.528 1177134.871 1018440.478 1002996.202 1189539.564 1184479.327 1104083.364 0.889545708 0.915545521 1.034812009 0.938366216 1.066164846 0.922430779 0.908442455 1.077400133 1.072816932 1 20.07441768 6.794013179 0.477239888 1.012770981 2.30E-16 0.27643414 0.06096673 41.34134394 1.465065039 0.03566822 35.60248819 6223191.697 -6.794013179 -1.012770981 SVPNT(ph)PLRPNQQSVVNSSFSELFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 1 S(0.343)VPNT(0.657)PLRPNQQSVVNSSFSELFVK 243.34 1.71E-38 784540000 209160 179530 184740 153540 285300 232690 203650 199190 218630 166940 TRUE FALSE 217417.7983 210362.881 189554.4762 183909.7537 236804.8079 178651.274 187687.3809 196520.1839 210761.549 199648.6967 1.089001841 1.053665185 0.949440088 0.921166813 1.186107457 0.89482815 0.940088185 0.984329911 1.055662033 1 17.60710413 SVQNHNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVQNHNNK 8 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;; 111.17 0.0032855 1238914000 976057 985699 1319310 1040034 1535390 1438200 1441020 1261660 1350140 1029201 FALSE TRUE 1014592.484 1154985.136 1353692.302 1245749.621 1274404.956 1104199.846 1328069.087 1244749.511 1301548.725 1230853.231 0.824300135 0.93836138 1.099799934 1.012102491 1.035383362 0.897101148 1.078982493 1.011289957 1.057436169 1 20.23122731 4.547780643 3.665540345 1.022433046 0.831308286 0.580863832 0.052626021 0.162306945 3.945816267 0.012381204 0.061225338 35300.48263 -4.547780643 -0.19112476 SVRPTDSNVS(ph)PAISIHEIGAVGATK ddPTM_MDA-MB-175_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(0.045)VRPT(0.045)DS(0.065)NVS(0.841)PAIS(0.003)IHEIGAVGATK 133.79 3.43E-05 201960000 107980 197580 219380 208000 250030 300970 216630 232900 224310 207370 TRUE FALSE 112243.1338 231512.828 225097.223 249141.7792 207529.9899 231074.2787 199649.9745 229778.3564 216237.1269 248000.1812 0.452592951 0.933518786 0.90764943 1.004603214 0.836813864 0.931750443 0.805039632 0.926524954 0.871923262 1 17.91998165 4.740546286 24.9519287 0.907592934 0.452592792 0.839769473 0.06030208 60.06736479 754751.3585 0.013399095 0.087668338 55023.25595 -4.740546286 -0.455000142 SVS(ph)ANPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.051)VS(0.949)ANPK;SVS(1)ANPK;S(0.083)VS(0.917)ANPK;S(0.005)VS(0.995)ANPK 105.35 0.0083367 1476030000 3155550 2153690 2786940 1992460 4412470 3736290 3235660 2900150 3251980 2533750 TRUE FALSE 3280133.551 2523569.504 2859569.946 2386562.641 3662439.925 2868593.272 2982040.514 2861278.233 3134941.875 3030189.801 1.082484519 0.832809055 0.943693344 0.787595101 1.208650337 0.946671153 0.984110142 0.9442571 1.034569476 1 21.53097673 3.280178446 24.99999986 1.006285674 0.908303724 0.209431192 0.10076994 248.1900259 149087.0906 0.02671263 0.036168778 1906.243806 -3.280178446 -0.09798195 SVS(ph)EAALAQPQGPLGTDSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSEAALAQPQGPLGTDSLK 20 0 M0R201;M0QY29;Q05469-2;Q05469 M0R201 LIPE Hormone-sensitive lipase 1 S(0.115)VS(0.885)EAALAQPQGPLGTDSLK;S(0.134)VS(0.866)EAALAQPQGPLGTDSLK;SVS(1)EAALAQPQGPLGTDSLK;S(0.001)VS(0.999)EAALAQPQGPLGTDSLK 354.86 3.02E-95 551254000 1271970 942380 1175220 953000 1480200 1467350 1205380 1052620 1176140 930530 TRUE FALSE 1322188.358 1104226.434 1205847.199 1141500.556 1228596.133 1126580.2 1110899.166 1038511.351 1133810.951 1112849.537 1.188110624 0.992251331 1.083567147 1.025745635 1.104009205 1.012338292 0.998247408 0.933200146 1.018835802 1 20.08582712 2.469555163 2.799353482 0.977007034 1.071214526 0.392685417 0.052962181 0.259009273 4.143355875 0.018561731 0.015763732 294.8187926 -2.469555163 0.094207492 SVS(ph)EESANSLVSVGVEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSEESANSLVSVGVEAK 18 0 Q8NEZ4;Q8NEZ4-3;H0YMU7;C9J4Z5 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 S(0.063)VS(0.937)EESANSLVSVGVEAK;S(0.124)VS(0.876)EESANSLVSVGVEAK 217.61 8.73E-19 108117000 172904 111224 166059 120801 230310 212336 191025 157964 187234 122691 TRUE FALSE 179730.3834 130325.8568 170386.634 144695.0772 191161.9885 163024.182 176051.9613 155846.751 180495.4849 146729.9524 1.224905893 0.888202134 1.161225988 0.986131835 1.302815038 1.111049103 1.19983656 1.06213318 1.230120245 1 17.16280388 3.288404048 24.9999691 1.149274927 1.059344858 0.113953009 0.11680983 223.3934232 112045.786 0.029577214 0.040047679 1942.692431 -3.288404048 -0.089930069 SVS(ph)HGSNHTQKPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 S(0.344)VS(0.655)HGSNHTQKPDEQR;S(0.091)VS(0.909)HGSNHTQKPDEQR 228.85 2.25E-15 1814610000 36681.5 349036 354239 388430 393712 569340 326331 499100 375990 411600 TRUE FALSE 38129.71394 408980.2179 363470.7594 465260.2947 326788.9749 437119.4134 300752.3235 492410.3809 362458.1933 492245.1394 0.077460824 0.830846635 0.738393801 0.945180069 0.663874457 0.88801164 0.610980789 1.000335689 0.736336765 1 18.90901744 4.73905501 24.63140587 0.820430894 0.077460544 0.750035025 0.129240078 14.54289821 724298.3045 0.02779108 0.164373783 54834.64165 -4.73905501 -0.74297035 SVS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSPER 6 0 Q14966;Q14966-3;Q14966-4;A0A096LPI0;Q14966-2;Q14966-6;A0A096LPB4;A0A096LNR2;A0A096LNX0;A0A096LNQ0 Q14966 ZNF638 Zinc finger protein 638 1 S(0.011)VS(0.989)PER;S(0.004)VS(0.996)PER 82.529 0.06189 961320000 484310 539530 481720 471240 491140 529690 505740 496810 480480 494490 TRUE FALSE 503430.9328 632190.0805 494274.0189 564449.8655 407656.1982 406677.525 466098.7773 490151.0746 463187.6187 591375.8479 0.851287611 1.069015725 0.835803526 0.954468918 0.689335217 0.687680308 0.788159981 0.828831743 0.783237294 1 19.1737158 3.257504967 24.99351476 0.785169684 0.931181943 0.285554784 0.10088615 277.0982908 365576.8397 0.02676565 0.036181506 1809.276601 -3.257504967 0.146012258 SVS(ph)PESNDSISEELNHFKPIVCSPCTPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPESNDSISEELNHFKPIVCSPCTPPK 29 1 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 S(0.051)VS(0.949)PESNDSISEELNHFKPIVCSPCTPPK 259.81 2.63E-58 106830000 45656 44901 52395 28895 59841 52191 54244 54769 49821 29309 TRUE FALSE 47458.53413 52612.39747 53760.45674 34610.34476 49669.24819 40070.43121 49992.21354 54034.91114 48027.95194 35051.5374 1.35396441 1.501001137 1.533754601 0.98741303 1.417034797 1.143186125 1.426248811 1.541584625 1.370209569 1 15.0971901 -2.169890566 2.26072011 0.098742406 1.372192111 0.299501255 0.166479994 1809639.145 531875.5959 8328554.871 0.042843735 0.006762534 2.169890566 1.273449704 SVS(ph)PLVWCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPLVWCR 9 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 SVS(1)PLVWCR 133.81 0.00027965 69051000 65406 76911 66175 77028 73513 78854 63446 82284 66009 96609 TRUE FALSE 67988.27938 90119.86597 67899.57486 92263.90849 61017.28652 60541.35354 58472.93673 81181.11757 63633.34898 115537.6839 0.588451119 0.78000409 0.587683365 0.798561174 0.528115888 0.5239966 0.506094071 0.702637571 0.550758392 1 16.81800395 -1.278306869 4.543939729 1.000198085 0.623138971 0.561973655 0.10097378 0.000199098 3.16E-05 0.096065281 0.022631008 0.052685746 1.278306869 -0.377059114 SVS(ph)PSPSVLS(ph)EGRDEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 2 S(0.125)VS(0.874)PS(0.003)PS(0.021)VLS(0.978)EGRDEPQR;S(0.095)VS(0.905)PSPS(0.028)VLS(0.972)EGRDEPQR;S(0.275)VS(0.725)PS(0.028)PS(0.044)VLS(0.928)EGRDEPQR 148.29 1.26E-07 758540000 562190 614460 603980 534300 604060 745270 574520 512570 615390 610880 TRUE FALSE 584385.6953 719988.7252 619720.215 639982.9453 501382.097 572192.3372 529487.6212 505699.8375 593242.2341 730570.24 0.799903505 0.985516088 0.848269175 0.876004674 0.686288695 0.783213312 0.724759362 0.692198792 0.81202628 1 19.47866346 3.319647895 8.736794937 0.759033314 0.883825242 0.163116276 0.095433905 0.349279704 33.92404071 0.024588881 0.033290149 2087.602918 -3.319647895 0.124791928 SVS(ph)PSPSVLSEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSPSPSVLSEGR 13 0 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 1 SVS(1)PSPSVLSEGR;S(0.001)VS(0.797)PS(0.194)PS(0.008)VLSEGR;SVS(1)PSPSVLSEGR;SVS(1)PSPSVLSEGR 346.18 8.46E-76 3706440000 1804910 2216700 1890230 2042300 1888930 2252660 1887820 1952700 1699490 1863040 TRUE FALSE 1876169.24 2597400.981 1939490.947 2446260.844 1567850.353 1729513.854 1739847.736 1926527.25 1638325.687 2228067.018 0.842061404 1.165764297 0.870481422 1.097929651 0.703681864 0.776239602 0.780877649 0.864663062 0.735312571 1 21.0873612 3.238568923 25 0.804160818 0.997496859 0.371592199 0.116989389 0.215767742 638893.5827 0.030313282 0.038533873 1732.083891 -3.238568923 0.193336041 SVS(ph)PSPSVLSEGRDEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVSPSPSVLSEGRDEPQR 18 1 C9IYE1;A0A087X1P3;Q86UW7-3;Q86UW7-2;Q86UW7 C9IYE1 CADPS2 Calcium-dependent secretion activator 2 1 S(0.007)VS(0.992)PS(0.001)PSVLSEGRDEPQR;S(0.001)VS(0.995)PS(0.003)PSVLSEGRDEPQR;SVS(0.998)PS(0.002)PSVLSEGRDEPQR 257.73 7.49E-31 1551510000 871210 1014360 936260 772940 960970 1123490 742620 884690 803710 942940 TRUE FALSE 905606.0435 1188568.439 960659.7047 925825.225 797624.6626 862576.4742 684411.5039 872832.1776 774784.6341 1127691.039 0.803062197 1.053984113 0.851882006 0.820991914 0.707307795 0.764904964 0.606914022 0.773999391 0.687053995 1 20.10494043 3.671420717 2.155435265 0.738728567 0.928018936 0.2433382 0.112645368 0.341214644 3.090476636 0.029609456 0.056352594 4692.677591 -3.671420717 0.18929037 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.178)VS(0.817)PS(0.004)PVPLLFQPDQNAPPIR;S(0.12)VS(0.863)PS(0.017)PVPLLFQPDQNAPPIR;S(0.011)VS(0.988)PS(0.002)PVPLLFQPDQNAPPIR;S(0.147)VS(0.853)PSPVPLLFQPDQNAPPIR 270.72 1.27E-44 691710000 86242 114947 102359 96059 99279 119329 103953 108359 93980 104973 TRUE FALSE 89646.90075 134688.2531 105026.5596 115059.1835 82403.59104 91616.6482 95804.89223 106906.6248 90597.67816 125540.4495 0.714087779 1.072867379 0.836595376 0.916510845 0.65639076 0.729777921 0.76313963 0.851571149 0.721661253 1 16.93779275 3.288975475 24.99999244 0.780501006 0.894974977 0.135034553 0.119669732 180.2708489 89392.27943 0.031050057 0.04204192 1945.250228 -3.288975475 0.114473971 SVS(ph)PSPVPLSSNYIAQISNGQQLMSQPQLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPSPVPLSSNYIAQISNGQQLMSQPQLHR 31 0 Q02241;H7BYN4 Q02241 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 S(0.028)VS(0.485)PS(0.485)PVPLS(0.001)S(0.001)NYIAQISNGQQLMSQPQLHR 134.05 1.61E-06 241380000 32819 55389 65194 56292 52765 61533 51065 65671 46066 55816 TRUE FALSE 34114.71946 64901.62988 66893.0092 67426.38959 43796.02415 47242.89329 47062.39187 64790.78766 44408.09366 66752.07654 0.511066041 0.972278815 1.002111285 1.010101754 0.656099801 0.707736684 0.705032627 0.970618309 0.665269097 1 16.0265251 4.752161942 23.88371487 0.850820272 0.511065616 0.33147357 0.146181453 1522.053248 2672613.647 0.035951765 0.673412128 56514.76705 -4.752161942 -0.339754656 SVS(ph)PTFLNPSDENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 SVS(1)PTFLNPSDENLK 361.38 4.70E-83 345770000 535520 436610 456280 423310 609020 607970 619040 446610 542770 384240 TRUE FALSE 556662.7431 511594.3711 468171.0316 507039.4545 505498.9979 466778.1814 570518.0272 440623.9235 523235.8137 459524.4713 1.211388681 1.113312572 1.018816322 1.103400333 1.100048049 1.015785253 1.241540033 0.958869333 1.138646245 1 18.80978217 8 0.06422269 0.914121632 1.4647849 0.143733037 0.081072185 605.629872 2.889967563 4.709131808 30.68095313 100000000 -8 0.550663268 SVS(ph)SDSLGPPRPAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.001)VS(0.956)S(0.042)DSLGPPRPAPAR;S(0.025)VS(0.955)S(0.02)DSLGPPRPAPAR 160.45 5.32E-09 961010000 333799 343528 369325 313437 438686 441497 366771 336300 338917 302496 TRUE FALSE 346977.6423 402526.2617 378949.9129 375433.9031 364118.3104 338966.0127 338022.5306 331792.4486 326719.4434 361764.2996 0.959126267 1.112675469 1.047505001 1.037785938 1.006507029 0.936980274 0.934372272 0.917150888 0.903127931 1 18.46469052 2.885049677 2.114693923 0.92965284 1.045937399 0.558785131 0.042284565 0.203197884 1.797209574 0.013747986 0.014975829 767.4492702 -2.885049677 0.11628456 SVS(ph)SDSLGPPRPAPART(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 2 S(0.409)VS(0.474)S(0.118)DS(0.352)LGPPRPAPART(0.615)PT(0.033)QPPPEPGDLPTIEEALQIIHSAEPR 87.029 0.0024198 12987000 1351.8 3126.8 1553.8 2156.6 1947.8 2884.2 2855.3 1346.8 2564.3 2572.9 TRUE FALSE 1405.170108 3663.803577 1594.293304 2583.169043 1616.713652 2214.38826 2631.494125 1328.748349 2472.011344 3077.010494 0.456667311 1.190702334 0.518130604 0.839506088 0.525417009 0.719655739 0.855211294 0.431830945 0.803380862 1 11.58731365 0.989812097 24.70516616 1.000000036 0.693251499 0.15756802 0.21884342 686.1040921 1663773.945 0.19468028 0.04867007 9.768144991 -0.989812097 -0.306748537 SVS(ph)TMNLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 S(0.002)VS(0.991)T(0.007)MNLSK;SVS(0.995)T(0.005)MNLSK;SVS(0.982)T(0.018)MNLSK;SVS(0.918)T(0.082)MNLSK 150.51 8.92E-05 1049650000 1017692 916970 1170840 803497 1758740 1188300 1054720 1061821 1122710 945170 TRUE FALSE 1057871.266 1074452.464 1201353.052 962426.3084 1459790.003 912335.3339 972048.2904 1047589.026 1082303.886 1130357.965 0.935872793 0.950541773 1.062807614 0.851434977 1.291440453 0.807120719 0.859947309 0.926776347 0.957487734 1 20.10834829 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SVS(0.848)T(0.145)T(0.007)NIAGHFNDESPLGLR;S(0.015)VS(0.959)T(0.022)T(0.004)NIAGHFNDESPLGLR;SVS(0.915)T(0.082)T(0.002)NIAGHFNDESPLGLR;SVS(0.961)T(0.037)T(0.001)NIAGHFNDESPLGLR;S(0.005)VS(0.948)T(0.043)T(0.005)NIAGHFNDESPLGLR 351.07 2.64E-95 11773580000 1986870 2753310 2556270 2458220 2842720 3009020 2478270 2630860 2374080 2645910 TRUE FALSE 2065313.162 3226169.575 2622888.496 2944448.579 2359515.47 2310220.707 2284016.722 2595597.625 2288637.325 3164325.405 0.652686717 1.019544188 0.828893416 0.930513838 0.74566145 0.730083165 0.7218021 0.82026887 0.723262317 1 21.59346654 5.024958876 16.04086024 0.82224648 0.226422959 0.19651574 0.107953182 1017508.425 17291074.28 0.025244956 15596367.34 105915.3428 -5.024958876 -0.595823521 SVS(ph)VATGLNMMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSVATGLNMMK 12 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 S(0.001)VS(0.998)VAT(0.001)GLNMMK;S(0.006)VS(0.941)VAT(0.054)GLNMMK 145.58 0.00022685 0 328390 483760 558020 417750 944290 580960 402330 536010 478710 591660 TRUE FALSE 341355.0908 566842.0169 572562.4596 500379.7031 783779.9231 446040.8445 370794.3233 528825.6627 461481.3206 707584.449 0.48242311 0.801094509 0.809178976 0.707166055 1.10768393 0.630371181 0.524028367 0.747367559 0.65219257 1 19.43254282 SVS(ph)VDESRPELIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 S(0.178)VS(0.822)VDESRPELIFR;S(0.041)VS(0.959)VDESRPELIFR;S(0.004)VS(0.996)VDESRPELIFR;S(0.002)VS(0.998)VDESRPELIFR 225.68 1.63E-12 485634000 423065 377649 439864 450145 672934 666897 613092 486605 493406 615323 TRUE FALSE 439767.9329 442507.278 451327.2172 539182.3375 558548.919 512020.2787 565036.247 480082.8559 475648.4144 735883.7608 0.59760516 0.601327685 0.613313191 0.732700416 0.759017862 0.695789615 0.767833559 0.652389523 0.646363515 1 19.48911837 -5 0.236757651 2.775874034 0.643366724 0.730760138 0.059527153 95.22354216 0.951126421 81.50773605 0.105501923 1.00E-05 5 -2.132507309 SVS(ph)VDSGEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSVDSGEQR 10 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 SVS(0.999)VDS(0.001)GEQR 140.78 4.06E-05 61765000 174900 186660 189100 202270 271590 302010 227690 240080 287070 326770 TRUE FALSE 181805.1871 218717.403 194028.1013 242278.4023 225425.2288 231872.7545 209843.0628 236862.1203 276738.4068 390794.3251 0.465219619 0.559673949 0.496496722 0.619963973 0.576838542 0.593337056 0.536965481 0.606104299 0.708143361 1 18.57604999 -5 0.187853844 2.873357333 0.488607715 0.910553277 0.042773302 36.14997318 0.352668509 25.17902755 0.119089607 1.00E-05 5 -2.384749618 SVSDNDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSDNDIR 8 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 ;;; 147.29 0.0012555 1987100000 3057300 3723020 3484350 3709570 4086080 4424900 3692570 3707350 3509750 3753840 FALSE TRUE 3178004.565 4362419.724 3575155.023 4443311.874 3391529.581 3397284.035 3403136.715 3657659.037 3383434.783 4489333.076 0.707901265 0.971730021 0.796366623 0.989748766 0.755464013 0.756745819 0.758049505 0.814744412 0.753660895 1 22.09806971 SVSDQFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVSDQFYR 8 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54;H0YK11;H0YK29 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;; 152.63 0.0010562 1379260000 1216321 1198800 1110150 1058250 1331980 1329410 1224053 1093390 1174542 1367450 FALSE TRUE 1264342.292 1404684.575 1139081.421 1267568.691 1105570.515 1020674.675 1128108.527 1078734.895 1132270.463 1635375.646 0.773120411 0.858936953 0.696525856 0.775093291 0.676034597 0.624122462 0.689816147 0.659625144 0.692361089 1 20.64119063 -1.169007309 4.83405712 1.000027638 0.712539114 0.631993785 0.064919434 2.10E-05 3.60E-06 0.068138711 0.016058906 0.06776301 1.169007309 -0.287488525 SVSDYDGKLSNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSDYDGKLSNFK 13 1 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 121.56 0.00022367 810340000 1120100 1036800 1044580 706340 1634550 1427100 965890 1004080 1208040 1063410 FALSE TRUE 1164322.413 1214862.335 1071802.613 846051.9438 1356709.775 1095677.653 890181.0179 990621.9499 1164562.876 1271764.829 0.915517072 0.955257062 0.84276793 0.665258171 1.066792966 0.861541087 0.699957254 0.778934853 0.915706151 1 20.27840049 2.466301037 24.99732695 0.815163058 0.886419851 0 0.121571427 646.4699119 1493491.481 0.042005239 0.035173263 292.6179993 -2.466301037 0.071256793 SVSEINS(ph)DDELSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SVSEINSDDELSGK 14 0 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 SVS(0.007)EINS(0.993)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK;SVSEINS(1)DDELSGK 355.87 4.21E-82 5972710000 8363330 4826500 6326450 4634670 7790540 8562340 7566450 5914030 6707250 4183360 TRUE FALSE 8693520.726 5655413.83 6491322.484 5551393.893 6466306.794 6573866.299 6973371.878 5834762.101 6465857.383 5003009.297 1.737658319 1.130402423 1.297483594 1.109610949 1.292483465 1.313982427 1.393835483 1.166250501 1.292393637 1 22.2543647 -5 0.049088692 8.37E-14 1.811647498 0.281700822 0.162250997 864.4698858 3.142174832 118.5692867 27.27427697 1.00E-05 5 1.811647498 SVSGS(ph)PEPAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 SVSGS(1)PEPAAK;SVSGS(1)PEPAAK;SVSGS(1)PEPAAK;SVSGS(1)PEPAAK 198.33 5.67E-08 742350000 1942700 1386650 1616150 1289750 2041850 2124130 1969730 1605030 1775980 1215270 TRUE FALSE 2019399.296 1624796.351 1658268.197 1544858.7 1694777.066 1630832.999 1815337.416 1583517.198 1712062.827 1453378.889 1.389451375 1.117944098 1.140974463 1.062942852 1.166094457 1.122097625 1.249046226 1.089541902 1.177987956 1 20.47097942 8 0.016567247 7.21E-16 2.563124338 0.295492782 0.085508778 6693.629905 8.555814145 516.6072042 844.2031798 99999999.92 -8 2.563124338 SVSHGSNHTQKPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSHGSNHTQKPDEQR 16 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 0 ; 127.75 4.16E-05 82482000 20234.2 68681 62631 67042 54676 91847 48011 73255 52911 67195 FALSE TRUE 21033.06184 80476.42749 64263.21531 80302.7075 45382.19305 70516.9262 44247.77237 72273.13655 51006.74345 80360.57372 0.261733595 1.001441674 0.79968587 0.999279918 0.564732069 0.877506505 0.550615436 0.899360634 0.634723485 1 16.29420024 -2.503300954 2.110941571 3.860538476 0.752339125 0.109960278 0.222029696 12302383.25 617384.9869 169139406.6 0.04919456 0.003138333 2.503300954 -3.108199351 SVSPS(ph)PVPLLFQPDQNAPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-2;Q02241-3 Q02241-2 KIF23 Kinesin-like protein KIF23 1 S(0.33)VS(0.276)PS(0.394)PVPLLFQPDQNAPPIR 116.65 8.05E-05 124270000 64726 77504 73353 73599 74725 86165 75355 75687 75966 86450 TRUE FALSE 67281.43246 90814.7091 75264.63944 88156.66253 62023.27119 66154.48459 69448.4782 74672.53956 73231.9985 103388.2223 0.650764961 0.87838544 0.727980787 0.852676065 0.599906545 0.639864804 0.671725238 0.72225383 0.708320511 1 16.65771232 -1.935795145 8.09698403 1.085023919 0.718546406 0.504614947 0.084142356 0.047929778 0.000380058 0.030236064 0.01919883 0.011593241 1.935795145 -0.366477513 SVSSDS(ph)LGPPRPAPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 SVS(0.007)S(0.059)DS(0.934)LGPPRPAPAR 184.44 4.79E-09 208540000 252710 284230 309070 265000 347410 324970 311790 286770 336990 285520 TRUE FALSE 262687.1859 333044.2915 317124.6181 317416.2091 288357.3723 249500.6425 287351.0851 282926.3172 324861.7957 341462.1774 0.769300975 0.975347531 0.928725461 0.929579409 0.844478222 0.7306831 0.841531227 0.828572931 0.95138442 1 18.38136626 4.795631305 21.8162504 0.878179463 0.76929729 0.161171707 0.078442685 27536.51544 10524525.98 0.019418473 23.99882546 62464.21769 -4.795631305 -0.108882174 SVSSDSLGPPRPAPART(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSSDSLGPPRPAPARTPTQPPPEPGDLPTIEEALQIIHSAEPR 44 2 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 S(0.042)VS(0.042)S(0.042)DS(0.173)LGPPRPAPART(0.659)PT(0.042)QPPPEPGDLPTIEEALQIIHSAEPR 66.555 0.083464 43158000 7574.5 8971.7 7479.4 9703.6 9472.2 8975 8169.4 9258.2 7991.4 11161 TRUE FALSE 7873.547109 10512.51968 7674.319308 11622.94312 7862.118827 6890.692267 7529.061081 9134.108972 7703.791075 13347.78426 0.589876713 0.787585376 0.574950805 0.870776969 0.58902052 0.516242406 0.564068233 0.684316497 0.577158795 1 13.70431265 -1.318020357 4.69988297 1.000222394 0.643262739 0.511867267 0.105599068 0.000239495 3.48E-05 0.09951059 0.023440396 0.048081681 1.318020357 -0.356959655 SVSSNVASVS(ph)PIPAGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSSNVASVSPIPAGSK 17 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 SVSSNVAS(0.039)VS(0.961)PIPAGSK;SVSSNVASVS(1)PIPAGSK 321.84 1.27E-58 249370000 502930 352460 387020 337170 450180 508150 479650 410240 395520 361690 TRUE FALSE 522786.0647 412992.2632 397106.0591 403861.2196 373658.5644 390139.8636 442053.7797 404741.4038 381285.3125 432556.2305 1.208596774 0.954771274 0.918044941 0.933661779 0.863838128 0.901940224 1.021956797 0.935696622 0.881469935 1 18.72252816 4.73849421 4.116640808 0.931512822 1.231819569 0.763741511 0.045869645 0.1047959 3.900307175 0.011143708 0.093393898 54763.87997 -4.73849421 0.300306746 SVSSVLSSLT(ph)PAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSSVLSSLTPAK 13 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 SVSSVLSS(0.002)LT(0.998)PAK;SVSSVLSSLT(1)PAK 204.28 1.42E-06 226070000 975560 627780 678430 606270 971630 994340 820900 731110 791510 635560 TRUE FALSE 1014075.862 735596.3315 696110.4431 726188.3965 806472.6797 763419.6044 756555.713 721310.6663 763023.7097 760085.8135 1.334159702 0.967780635 0.915831385 0.955403171 1.061028459 1.004386072 0.995355655 0.94898583 1.003865217 1 19.53580278 4.73988025 24.99476858 0.981178125 1.334159816 0.88661802 0.037596593 36.24671598 686463.7065 0.00957966 0.059921388 54938.93673 -4.73988025 0.352981691 SVST(ph)MNLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVSTMNLSK 9 0 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3 Q14244-6 MAP7 Ensconsin 1 SVS(0.308)T(0.691)MNLSK 119.74 0.0047822 0 204050 191630 237650 173780 372990 252680 216750 240200 241210 190230 TRUE FALSE 212106.0516 224540.9618 243843.3542 208153.1653 309589.293 193998.8994 199760.5686 236980.5119 232528.8992 227501.9263 0.932326398 0.986984882 1.071829844 0.914951221 1.360820535 0.852735195 0.878060999 1.04166376 1.022096397 1 17.79551924 -0.362462358 11.11749475 0.999999536 1.00813834 0.000143081 0.136275137 0 0 0.12612617 0.029728223 0.434047883 0.362462358 0.008138804 SVST(ph)PSEAGSQDSGDGAVGSR ddPTM_MDA-MB-175_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 SVS(0.018)T(0.981)PS(0.001)EAGSQDSGDGAVGSR 214.5 7.73E-24 173520000 42113 55024 52494 54946 60741 61963 47301 47387 50863 57739 TRUE FALSE 43775.65376 64473.94397 53862.03676 65814.1548 50416.26652 47573.03231 43593.42402 46751.85477 49032.45057 69051.85157 0.633953366 0.933703333 0.780023063 0.953112093 0.730121863 0.688946512 0.631314339 0.677054325 0.710081619 1 16.07539248 3.027349271 24.89335 0.709043273 0.831208562 0.071756469 0.126103557 337.9614406 307610.6007 0.033745427 0.040332746 1064.999174 -3.027349271 0.122165288 SVST(ph)TNIAGHFNDESPLGLR ddPTM_MDA-MB-175_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 SVS(0.383)T(0.589)T(0.028)NIAGHFNDESPLGLR 311.26 1.03E-65 4927500000 568210 834590 700480 717530 785830 798940 679000 715880 722390 731500 TRUE FALSE 590643.3696 977924.3403 718735.0843 859455.2924 652254.8973 613398.2931 625778.2058 706284.7995 696391.325 874823.4196 0.675157245 1.117853407 0.821577324 0.982432881 0.745584632 0.701168121 0.715319448 0.807345555 0.796036445 1 19.73863232 3.227179471 24.99811149 0.776766978 0.909320956 0.122867855 0.131516319 337.3708721 741016.6401 0.035042938 0.042234735 1687.250131 -3.227179471 0.132553977 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GZ14;V9GYF5;V9GYG5 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 SVSTTNIAGHFNDES(1)PLGLR;SVSTTNIAGHFNDES(1)PLGLR 278.43 8.22E-45 746470000 430020 474730 465910 481240 458760 564220 495420 466890 419970 403420 TRUE FALSE 446997.5216 556261.1846 478051.9973 576427.8356 380780.1391 433188.4558 456587.6859 460632.1032 404855.3617 482462.4251 0.926491885 1.152962709 0.990858505 1.194762132 0.789243098 0.897869831 0.946369421 0.954752286 0.839143819 1 18.88005706 3.236706515 24.99990662 0.908474558 1.067074768 0.438181663 0.089634402 44.97460428 606421.8033 0.024071508 0.030197745 1724.672011 -3.236706515 0.15860021 SVT(ph)PASTLTK ddPTM_MDA-MB-175_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 SVT(0.999)PASTLTK;SVT(0.998)PAS(0.002)T(0.001)LTK 133.49 0.0021891 250450000 832640 711510 752520 667550 961500 981910 800820 728920 674840 630850 TRUE FALSE 865513.2701 833706.3077 772131.2894 799589.3976 798064.5734 753876.2835 738049.6358 719150.0197 650552.6402 754452.9791 1.147206379 1.105047406 1.023431958 1.059826682 1.057805583 0.999235611 0.978257965 0.95320721 0.862283877 1 19.52507146 3.047999337 0.557726263 0.929347231 1.127429773 0.703673188 0.0415757 0.550074367 0.360690381 0.03276432 0.053573481 1116.861544 -3.047999337 0.198082542 SVT(ph)PDS(ph)LGHTPPARGEEELSNYICMGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVTPDSLGHTPPARGEEELSNYICMGGK 28 1 P35568 P35568 IRS1 Insulin receptor substrate 1 2 S(0.457)VT(0.543)PDS(0.765)LGHT(0.234)PPARGEEELSNYICMGGK 131.84 4.79E-05 164520000 48874 103410 98544 98509 112720 128880 88796 106530 96257 135970 TRUE FALSE 50803.58326 121169.8631 101112.1376 117993.7862 93559.89466 98949.5732 81835.93749 105102.1396 92792.72937 162610.7182 0.312424567 0.745152991 0.621804877 0.725621211 0.57536118 0.608505849 0.503262875 0.646342017 0.570643377 1 17.31106283 -2.184820739 2.221989683 2.031627841 0.599293111 0.531074837 0.115303107 7674737.368 1517493.114 39843613.5 0.025531679 0.006534002 2.184820739 -1.43233473 SVT(ph)PTKEFLKDEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVTPTKEFLKDEIK 14 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 S(0.001)VT(0.997)PT(0.002)KEFLKDEIK 156.13 0.00026952 462240000 1893200 610910 977830 681710 1669200 1454400 1795600 1143100 1319400 400970 TRUE FALSE 1967944.998 715829.0403 1003313.053 816550.2033 1385469.98 1116637.642 1654856.18 1127778.614 1271915.052 479532.3945 4.103883326 1.492764719 2.092273775 1.702805092 2.889210398 2.328596888 3.45097891 2.351829881 2.652406941 1 18.87126875 SVTDSIRDEYAFLQK ddPTM_MDA-MB-175_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 ; 174.62 8.23E-07 179124000 148859 148647 167566 147818 199352 193257 159561 157809 167323 155058 FALSE TRUE 154736.0683 174175.9659 171932.9076 177055.9592 165466.2182 148375.9906 147054.1919 155693.8285 161301.0779 185438.6463 0.834432689 0.939264654 0.927168694 0.954795361 0.892296301 0.800135212 0.793007255 0.839597525 0.869835286 1 17.50058241 2.987655279 22.51775617 0.844433082 0.917531837 0.116391149 0.06191596 222.8166435 406438.4597 0.017599831 0.019595885 971.9754131 -2.987655279 0.073098755 SVTDYDFAPFLNNS(ph)PQQNPAAQIPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVTDYDFAPFLNNSPQQNPAAQIPAR 26 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2 Q9UM54-1 MYO6 Unconventional myosin-VI 1 SVTDYDFAPFLNNS(1)PQQNPAAQIPAR;S(0.001)VT(0.001)DY(0.001)DFAPFLNNS(0.996)PQQNPAAQIPAR;SVTDYDFAPFLNNS(1)PQQNPAAQIPAR;SVTDYDFAPFLNNS(1)PQQNPAAQIPAR 208.19 1.50E-25 393312000 220321 271306 217007 249880 263223 334650 243147 256625 262025 295684 TRUE FALSE 229019.4432 317900.695 222662.3807 299305.5182 218480.4485 256932.6092 224088.5028 253185.3616 252594.7714 353617.6186 0.647647151 0.898995633 0.629669929 0.846410084 0.617843787 0.726583167 0.633702879 0.715986275 0.714316137 1 18.43183063 -1.871248151 5.380087183 1.057753378 0.715374659 0.480934442 0.088954447 0.044321166 0.001060658 0.061948206 0.018340734 0.013450916 1.871248151 -0.342378719 SVTEQGAELSNEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;;; 392.86 8.59E-114 6695780000 1545369 1791273 1776541 1712729 1989655 2244540 1846698 1868060 1700148 1718633 FALSE TRUE 1606381.361 2098910.204 1822839.118 2051501.684 1651454.154 1723279.601 1701948.985 1843021.711 1638960.006 2055366.231 0.781554809 1.021185505 0.886868282 0.998119777 0.803484133 0.838429461 0.828051449 0.896687745 0.797405339 1 20.97096405 3.228609088 24.99997985 0.855200026 0.926517073 0.116337971 0.081484038 361.6507028 908528.3657 0.021579044 0.026081765 1692.813398 -3.228609088 0.071317047 SVTLGYLFSQGHLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVTLGYLFSQGHLTR 15 0 A0A3B3IRQ9;P55265-3;P55265-2;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 78.902 0.010502 0 69171 101490 101830 104050 107020 134020 97464 105110 99435 102140 FALSE TRUE 71901.92449 118920.118 104483.7735 124630.7794 88828.77863 102895.8861 89824.51701 103701.1724 95856.35377 122152.3774 0.588624847 0.97353912 0.855356037 1.020289429 0.727196478 0.842356803 0.735348087 0.848949276 0.784727697 1 16.89832242 SVTLLEVCGS(ph)WPEGFGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;SVTLLEVCGS(1)WPEGFGLR;SVTLLEVCGS(1)WPEGFGLR 277.44 4.07E-39 540935000 172780 211894 212793 235211 249265 277767 219758 232969 230129 254729 TRUE FALSE 179601.4878 248285.1462 218338.5604 281735.0338 206895.0243 213259.8238 202532.7937 229846.4316 221846.7022 304638.2705 0.58955655 0.815016268 0.716714154 0.924818255 0.679149813 0.700042787 0.664830435 0.754489681 0.728229916 1 18.21673767 -1.989996499 2.260297133 1.25213774 0.734382068 0.470273758 0.085769333 15167761.87 5710009.296 19937367.68 0.019696076 0.010233012 1.989996499 -0.517755672 SVTQATQTS(ph)PGVPWPSQSANFPEFSFDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVTQATQTSPGVPWPSQSANFPEFSFDFTR 30 0 A0A0C4DGH6;A0JNW5;H0YHT7 A0A0C4DGH6 UHRF1BP1L UHRF1-binding protein 1-like 1 SVTQAT(0.001)QT(0.044)S(0.954)PGVPWPSQSANFPEFSFDFTR;S(0.003)VT(0.003)QAT(0.011)QT(0.054)S(0.928)PGVPWPSQSANFPEFSFDFTR 135.11 2.80E-06 409840000 159806 198848 166945 170502 197582 226950 179090 176130 187557 224490 TRUE FALSE 166115.2643 232998.5972 171295.7238 204226.7867 163997.0822 174244.302 165052.4578 173769.2654 180806.8602 268474.5174 0.618737547 0.867861127 0.638033455 0.760693375 0.610847852 0.649016166 0.61477886 0.647246775 0.673460044 1 18.03442563 -0.674165753 11.1497475 0.99999999 0.675243408 0.619104271 0.07632718 0 0 0.071663437 0.016891234 0.211755279 0.674165753 -0.324756582 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SVTVVEDDEDEDGDDLLHHHHGSHCSSSGDPAEYNLR 37 0 P02545;P02545-6;P02545-5;P02545-4 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;; 241.51 2.43E-50 9157350000 80572.3 1342867 1078268 1271972 906110 1782957 840141 1495963 843439 1623335 FALSE TRUE 83753.35662 1573493.961 1106368.55 1523564.265 752089.7459 1368892.258 774288.5531 1475912.063 813083.7951 1941396.413 0.043140781 0.810495966 0.569882865 0.784777522 0.387396279 0.70510703 0.398830732 0.760232198 0.418813896 1 20.8886633 -4.999999996 0.317704187 5.022154453 0.547095139 0.260118329 0.228097239 424.4933238 3.780540648 1147.341124 0.185967429 1.00E-05 4.999999996 -4.475059314 SVTVVEDDEDEDGDDLLHHHHVSGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 SVTVVEDDEDEDGDDLLHHHHVSGSR 26 0 P02545-2;Q3BDU5;Q5TCI8 P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;;;;;;;; 272.78 8.94E-61 5662422000 324310.3 1552672.6 1335547.3 1480761.5 1318997 2014730 1152332 1556253.9 1285879.1 1707149.1 FALSE TRUE 337114.3211 1819332.041 1370352.76 1773651.705 1094794.361 1546839.491 1062009.207 1535394.862 1239600.562 2041632.281 0.165119999 0.891116416 0.671204493 0.868741997 0.536234841 0.757648429 0.520176536 0.752042802 0.607161522 1 20.96129161 SVVLFGVETHVCIQQTALELVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVVLFGVETHVCIQQTALELVGR 23 0 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 ;; 238.96 3.35E-37 109670000 54420 71465 80155 71960 79870 92331 76343 84466 78278 68867 FALSE TRUE 56568.54362 83738.55783 82243.90515 86193.47322 66293.72593 70888.52454 70359.03617 83333.87143 75460.79007 82360.17011 0.686843453 1.016736096 0.998588335 1.046543166 0.804924587 0.860713673 0.854284736 1.011822478 0.916229167 1 16.32965919 1.730954688 20.37852081 0.972945291 0.90513119 0.106154744 0.104353527 0.673369895 1742.29874 0.049051114 0.027179164 53.82136256 -1.730954688 -0.067814102 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVVLMSHLGRPDGVPMPDKYSLEPVAVELK 30 2 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ; 164.6 1.97E-12 6504600000 4891200 3134200 4656900 3140900 6153600 5445700 5416700 4710600 5433700 3016100 FALSE TRUE 5084308.353 3672474.469 4778262.64 3762160.645 5107613.27 4181018.705 4992124.9 4647462.112 5238142.198 3607047.048 1.409548665 1.018138777 1.324702056 1.043002931 1.416009606 1.159125082 1.383992178 1.28843956 1.452196805 1 21.78238681 3.226691928 24.99952969 1.297977326 1.194929833 0.055050476 0.164473167 539.2166979 1135773.966 0.043033612 0.051819517 1685.357073 -3.226691928 -0.103047494 SVVLYVILAPFDNEQSDLVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVVLYVILAPFDNEQSDLVHR 21 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 125.09 2.37E-05 523870000 403330 381470 485150 325440 647740 556490 442110 407110 562850 384600 FALSE TRUE 419253.7798 446984.5051 497793.4076 389811.0607 537637.3862 427253.6312 407456.263 401653.3563 542593.1384 459955.0064 0.911510417 0.9718005 1.08226544 0.847498245 1.168891258 0.9289031 0.885861133 0.873244884 1.179665687 1 18.81113322 3.163013451 0.002551497 1.947582745 4.12E-05 0.004280036 0.114359253 836742.935 635.076445 240083.4163 244663.2208 1455.50416 -3.163013451 -1.947541535 SVVS(ph)DLEADDVK ddPTM_MDA-MB-175_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;S(0.023)VVS(0.977)DLEADDVK 319.12 1.36E-46 368491000 1769680 887841 1204580 1055970 1586980 1791970 2003600 1332430 1367860 628575 TRUE FALSE 1839548.333 1040320.785 1235972.344 1264837.714 1317225.706 1375812.125 1846552.597 1314570.955 1318630.986 751732.2365 2.447079217 1.383898062 1.644165681 1.682564154 1.752253851 1.830189073 2.456396716 1.74872234 1.754123239 1 19.51985935 2.705969626 6.059342279 1.857556402 1.746538829 0 0.418801299 1.214042308 141.7897719 0.129379502 0.124142256 508.1239035 -2.705969626 -0.111017573 SVVS(ph)FDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVVSFDK 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 SVVS(1)FDK;SVVS(1)FDK;SVVS(1)FDK 117.7 0.0054259 1288050000 2643300 1539870 1977030 1889560 2961680 3074210 3199640 2443490 2433000 1414330 TRUE FALSE 2747659.525 1804330.694 2028553.026 2263309.328 2458254.691 2360271.318 2948843.856 2410739.013 2345436.805 1691440.885 1.624449042 1.0667418 1.199304714 1.338095436 1.453349457 1.395420519 1.743391615 1.425257622 1.386650179 1 20.68982133 3.386605256 3.860178391 1.444679599 1.272793414 0.018038199 0.215664677 0.486966329 13.90161058 0.058411558 0.081538044 2435.59602 -3.386605256 -0.171886185 SVVS(ph)FDKVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SVVSFDKVK 9 1 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.034)VVS(0.966)FDKVK;SVVS(1)FDKVK 151.1 5.07E-05 508770000 1538860 613337 1091200 720697 2018640 1663260 1693480 1211910 1401340 702946 TRUE FALSE 1599615.381 718672.8587 1119637.568 863248.7155 1675512.294 1276993.072 1560740.613 1195666.329 1350906.047 840674.81 1.90277544 0.854876166 1.331831946 1.026852126 1.99305638 1.519009558 1.856533102 1.422269723 1.606930565 1 19.68118832 3.258146248 24.99994256 1.593312955 1.252551166 0.132032268 0.354150428 401.7434077 512799.2808 0.09045466 0.122306448 1811.95016 -3.258146248 -0.340761789 SVVS(ph)FDKVKEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVVSFDKVKEPR 12 2 Q15424;Q15424-3;Q15424-4;Q15424-2 Q15424 SAFB Scaffold attachment factor B1 1 S(0.022)VVS(0.978)FDKVKEPR;S(0.2)VVS(0.8)FDKVKEPR;S(0.126)VVS(0.874)FDKVKEPR;S(0.21)VVS(0.79)FDKVKEPR 110.97 0.00074726 3024640000 7115310 3951140 6084930 3322070 11481400 8707770 6142640 6112540 7771550 4873110 TRUE FALSE 7396227.933 4629717.559 6243508.275 3979165.531 9529795.729 6685522.385 5661163.826 6030611.399 7491853.434 5827902.603 1.269106304 0.794405445 1.071313078 0.682778317 1.635201612 1.147157535 0.971389574 1.034782461 1.285514523 1 22.47454534 3.319868269 20.98186305 1.155777486 0.951347777 0.181263487 0.230615816 15.50987924 3997.964955 0.062813108 0.085049298 2088.662498 -3.319868269 -0.204429709 SVVSDLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 S(0.001)VVS(0.001)DLEADDVKGS(0.018)VPLS(0.301)S(0.301)S(0.301)PPAT(0.076)HFPDET(0.001)EIT(0.001)NPVPK 62.895 0.0062603 661360000 88813 48372 67541 40945 111090 78544 70833 75570 68452 51060 TRUE FALSE 92319.40582 56679.51472 69301.17395 49043.79879 92206.96148 60303.34635 65280.92437 74557.10776 65988.42589 61064.2294 1.511841003 0.928195038 1.134889847 0.803151031 1.509999592 0.987539627 1.069053438 1.220962067 1.080639624 1 15.8980399 0.992647231 23.03863036 0.999999966 1.135214565 0.041177532 0.216557726 389.2684916 1219718.218 0.190076451 0.047519113 9.832121365 -0.992647231 0.135214598 SVWVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SVWVAR 6 0 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;; 135.25 0.031826 2910510000 1858980 1981510 1878190 1725870 2461520 2359840 1981800 1836910 1843570 2129440 FALSE TRUE 1932373.966 2321818.928 1927137.174 2067241.935 2043111.71 1811802.924 1826461.338 1812289.226 1777220.276 2546662.997 0.758786682 0.911710317 0.756730347 0.811745385 0.802270152 0.711441964 0.717197894 0.71163292 0.69786237 1 21.28017663 2.858856564 5.883121544 0.742928867 0.812415235 0.012147809 0.093065888 0.504071735 22.3533507 0.026381351 0.028073393 722.5311313 -2.858856564 0.069486368 SVYAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVYAAEK 7 0 P50461 P50461 CSRP3 Cysteine and glycine-rich protein 3 0 ;; 96.964 0.012345 620140000 1047770 1025740 1172460 1029370 1417190 1650410 1462910 1291380 1248790 913260 FALSE TRUE 1089136.769 1201902.866 1203015.271 1232976.314 1176296.55 1267127.29 1348243.292 1274071.163 1203846.292 1092195.812 0.997199181 1.100446324 1.101464827 1.128896761 1.077001521 1.160164941 1.234433677 1.16652266 1.102225699 1 20.0588001 6.23589285 0.695802946 1.14247097 7.19E-09 0.248650278 0.059796626 24.01760208 1.685036287 0.022140831 34.27844824 1721443.803 -6.23589285 -1.142470963 SVYAHFPINVVIQENGSLVEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SVYAHFPINVVIQENGSLVEIR 22 0 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9V9 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ;; 301.48 8.18E-56 1716213000 891747 1225463 1264887 1301034 1351435 1572463 1419073 1352578 1247372 1081501 FALSE TRUE 926953.8601 1435926.737 1297850.994 1558374.642 1121718.561 1207282.299 1307842.35 1334448.904 1202479.325 1293400.414 0.71667973 1.11019505 1.003440992 1.204866354 0.867263184 0.933417282 1.011165866 1.031736877 0.929703835 1 20.30273755 4.751032865 24.35850867 1.01118962 0.716679466 0.488057411 0.090179539 1197.524183 2338723.499 0.021187472 0.366771052 56368.03102 -4.751032865 -0.294510154 SVYATMGDHENRS(ph)PVKEPVEQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SVYATMGDHENRSPVKEPVEQPR 23 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 SVYATMGDHENRS(1)PVKEPVEQPR 120.93 3.39E-05 300230000 263220 79472 125570 60938 163880 222670 156490 133630 145970 60782 TRUE FALSE 273612.1289 93120.69779 128842.4574 72991.35452 136023.7361 170958.2671 144223.9049 131838.9084 140716.5682 72691.06916 3.764040508 1.281047299 1.772466121 1.00413098 1.871257882 2.35184692 1.984066359 1.813687843 1.935816461 1 16.1494905 -0.436981057 1.030783533 0.977393978 1.924447336 0.145975802 0.697857537 62.39624203 40.09746088 6.638430127 0.199638733 0.365610738 0.436981057 0.947053359 SVYRGS(ph)LTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SVYRGSLTQR 10 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36-3;Q9BV36 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 1 SVYRGS(0.999)LT(0.001)QR;SVYRGS(0.999)LT(0.001)QR;SVYRGS(0.989)LT(0.011)QR;SVYRGS(1)LTQR;SVYRGS(0.738)LT(0.262)QR;SVYRGS(1)LTQR;SVYRGS(1)LTQR 170.95 2.53E-06 10728670000 2374690 2669110 2686690 2394150 3288950 3362480 2402680 2742180 2578570 3075800 TRUE FALSE 2468444.595 3127508.88 2756707.349 2867705.724 2729895.454 2581594.979 2214351.663 2705425.562 2485767.769 3678444.12 0.671056706 0.850226013 0.749422108 0.779597469 0.742133186 0.701817098 0.601980509 0.735480946 0.675766082 1 21.81066424 -0.979448186 4.348978812 1.000009319 0.724647482 0.629262155 0.063762167 7197940.313 3310175.112 645.2553435 0.015313736 0.104845987 0.979448186 -0.275361837 SWAQASVTHGAHGDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWAQASVTHGAHGDGGR 17 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 0 ; 123.59 3.07E-05 127484000 53624 63636 68724 68812 77137 92411 82579 77584 81310 74344 FALSE TRUE 55741.11693 74564.98798 70515.0039 82422.80822 64025.28029 70949.94575 76106.2422 76544.11338 78383.66898 88910.2834 0.626936669 0.838654261 0.793102903 0.927033466 0.720111081 0.797994822 0.855989198 0.860914064 0.881604084 1 16.44006267 -4.748356507 0.028609661 2.171582118 1.16E-07 0.521240614 0.068629679 1281.120553 2.875154129 164.0079279 71.65211215 1.79E-05 4.748356507 -2.171582002 SWAS(ph)PVYTEADGTFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWASPVYTEADGTFSR 16 0 E9PMS6;E9PJ10;E9PK58;E9PLU6;Q8WWI1-3;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.439)WAS(0.561)PVYTEADGTFSR 349.86 3.67E-87 464730000 102180 105560 100460 109000 119560 131450 103900 112080 102730 102740 TRUE FALSE 106214.1453 123689.1089 103078.0701 130559.8747 99237.23391 100922.7296 95756.04651 110577.7509 99032.76737 122869.9359 0.864443727 1.006666992 0.838920191 1.062586008 0.807660826 0.821378549 0.77932853 0.899957749 0.805996736 1 16.90677243 3.188741031 24.99978011 0.844692371 0.940247333 0.216251161 0.083815995 146.5709893 73549.65946 0.022254443 0.026599189 1544.333282 -3.188741031 0.095554963 SWDSSSPVDRPEPEAAS(ph)PTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0;Q86WB0-2 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 SWDSSSPVDRPEPEAAS(0.996)PT(0.004)TR;SWDSSSPVDRPEPEAAS(0.999)PT(0.001)TR 209.2 1.64E-22 797700000 513650 514820 529020 526690 629420 697600 544190 559380 556160 592400 TRUE FALSE 533929.2986 603236.3303 542806.6958 630867.71 522431.4132 535592.9722 501534.9658 551882.4261 536143.9102 708469.4378 0.75363773 0.851464154 0.766168118 0.890465666 0.737408539 0.755985994 0.70791334 0.778978452 0.75676364 1 19.43434609 -1.004257381 4.483501448 1.000007301 0.77797682 0.628737463 0.051259381 3.87E-06 8.60E-07 0.049215461 0.011599797 0.099024491 1.004257381 -0.222030482 SWEDS(ph)PER ddPTM_MDA-MB-175_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 211.84 2.92E-05 5782320000 5377500 6090060 5697830 5444780 6100880 7096180 5933060 5855840 5851690 5762090 TRUE FALSE 5589807.852 7135980.431 5846320.131 6521741.233 5063854.597 5448199.739 5468011.254 5777352.043 5641088.82 6891061.214 0.811167929 1.035541582 0.848391844 0.946405935 0.734843943 0.790618392 0.793493351 0.838383503 0.818609594 1 22.71629474 3.25952069 24.99065597 0.818393772 0.914889677 0.171161014 0.085136879 335.2934247 399767.0776 0.02169144 0.029340502 1817.69365 -3.25952069 0.096495905 SWEQKLEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWEQKLEEMR 10 1 Q16543;K7EKQ2;K7EQA9 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 67.08 0.058412 144380000 107480 125800 116620 112040 185150 150270 118920 120000 126530 178440 FALSE TRUE 111723.3934 147405.1714 119659.213 134201.1776 153678.2691 115372.0699 109598.7397 118391.5963 121976.21 213401.9016 0.523535135 0.690739728 0.560722337 0.628865894 0.720135425 0.540632811 0.513579021 0.554782293 0.571579771 1 17.70321351 -1.386123244 3.264683684 1.004045569 0.589226047 0.776305398 0.066123299 43146201.1 62733256.48 1680340.019 0.016322583 0.041103306 1.386123244 -0.414819522 SWHDIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SWHDIEK 7 0 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;; 124.08 0.0041813 753240000 262196 965390 1020850 1173460 1071060 1326330 1132890 1122910 1026070 889030 FALSE TRUE 272547.7005 1131188.223 1047454.19 1405566.886 889001.6038 1018309.958 1044091.122 1107859.228 989141.9411 1063218.407 0.256342158 1.063928366 0.985173115 1.321992618 0.836142036 0.957761784 0.982010013 1.041986501 0.930328082 1 20.02000656 4.740767148 24.9825511 1.015794667 0.256341893 0.784010954 0.119178876 84.43686968 955939.302 0.027564404 0.182888398 55051.24531 -4.740767148 -0.759452774 SWHDIEKDNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWHDIEKDNAR 11 1 A0A2R8YFH5;Q15437;Q5QPE2 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 134.99 7.77E-05 192090000 37415 131900 134450 128240 169030 188290 111830 132320 134190 141770 FALSE TRUE 38892.17309 154552.799 137953.8775 153605.4892 140298.341 144562.5011 103064.4724 130546.4668 129360.5281 169547.1171 0.229388584 0.911562529 0.813661003 0.905975235 0.827488803 0.852639098 0.607881007 0.76997161 0.762976866 1 17.37132673 4.744621713 24.86338916 0.81155833 0.229388307 0.758438955 0.100968102 311.7473959 1278789.005 0.024252173 0.22270143 55542.02545 -4.744621713 -0.582170023 SWHDVQVSSAYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWHDVQVSSAYVK 13 0 O43399;O43399-7;O43399-5;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ; 140.82 3.95E-05 866180000 652620 1238480 1462820 1214780 2004820 2001960 1384000 1622830 1525490 1952650 FALSE TRUE 678385.9415 1451179.306 1500942.291 1455059.858 1664041.413 1537035.13 1275518.464 1601078.618 1470587.913 2335234.382 0.290500151 0.621427689 0.642737321 0.623089429 0.712580041 0.658193088 0.546205757 0.685617954 0.629738892 1 21.15513593 -5 0.133506041 2.264814961 0.459452147 0.61192421 0.102165158 101.1135993 0.843618807 34.4525684 0.715344201 1.00E-05 5 -1.805362814 SWLKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWLKPR 6 1 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ; 100.27 0.034518 4940400000 5545000 5586000 5976600 5294500 8109600 7721300 6623800 6094100 6229400 6002900 FALSE TRUE 5763920.882 6545352.047 6132355.106 6341736.297 6731133.089 5928145.092 6104609.248 6012418.557 6005205.111 7179053.323 0.802880355 0.911729131 0.854201081 0.883366652 0.93760734 0.825755824 0.850336245 0.837494623 0.836489832 1 22.77536218 -2.445617237 2.290633701 2.456585122 0.861152339 0.542340304 0.038572825 1636213.644 292135.8009 12369919.3 0.009176563 0.003584122 2.445617237 -1.595432784 SWLSYSYQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWLSYSYQSR 10 0 Q15393 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 147.4 6.27E-05 78635000 136502 189403 139746 171416 201071 213600 140991 141433 149859 284520 FALSE TRUE 141891.2044 221931.4919 143387.8956 205321.5732 166893.0232 163994.6371 129939.757 139537.322 144465.6039 340266.2465 0.417000528 0.652228936 0.421399116 0.603414459 0.490477751 0.481959756 0.381876717 0.410082761 0.424566366 1 18.37630452 -1.696646458 4.164855092 1.028629627 0.474903366 0.779680757 0.083580343 0.022035036 0.001604955 0.08025691 0.019296651 0.02010729 1.696646458 -0.553726261 SWMEGLTLQDYSEHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWMEGLTLQDYSEHCK 16 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 176.04 3.31E-09 102690000 35349 121130 63735 110770 49515 101640 53894 67748 59870 163550 FALSE TRUE 36744.60582 141933.1352 65395.98646 132679.9754 41098.45799 78035.65037 49669.64745 66839.94887 57715.29039 195594.4911 0.187861149 0.725649963 0.334344726 0.678342087 0.210120734 0.398966504 0.253941955 0.341727154 0.295076257 1 17.57750621 -1.172363275 4.946497339 1.00004954 0.385020734 0.5337259 0.173619161 8.89E-05 1.49E-05 0.157498655 0.037119811 0.067241397 1.172363275 -0.615028806 SWPEGHFATITLTFIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SWPEGHFATITLTFIDK 17 0 O95433;G3V438 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 133.71 1.94E-05 201720000 390630 326400 406610 404050 491460 495810 541860 408930 452550 313830 FALSE TRUE 406052.374 382456.661 417206.5906 483969.884 407921.8047 380665.6416 499387.5973 403448.9622 436262.8139 375318.9799 1.081886064 1.01901764 1.111605362 1.289489501 1.086866976 1.014245647 1.330568461 1.074949533 1.162378769 1 18.51775772 4.020437879 11.790712 1.145025166 1.054082433 0.097048708 0.10199443 1.351537549 766.3993094 0.024233301 0.052011381 10481.84852 -4.020437879 -0.090942734 SWPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SWPSPK 6 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 SWPS(1)PK;S(0.001)WPS(0.999)PK;SWPS(1)PK;S(0.024)WPS(0.976)PK 101.64 0.038067 913980000 5005180 2431070 3127560 2359800 4203130 4866560 3979230 3197870 3430910 2098870 TRUE FALSE 5202788.371 2848587.361 3209066.783 2826561.397 3488683.464 3736375.193 3667327.555 3155007.783 3307432.219 2510103.391 2.072738673 1.134848617 1.278460001 1.126073693 1.38985648 1.488534379 1.461026493 1.256923438 1.317647803 1 21.25931536 7.999999817 0.031497755 2.63E-10 3.338566833 0.240479438 0.244821683 2249.490927 5.426258179 179.1304577 454.5392669 99999957.8 -7.999999817 3.338566833 SWQGDGS(ph)PMANGAGAVVHHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 SWQGDGSPMANGAGAVVHHQR 21 0 Q9H201;I6L9I8 Q9H201 EPN3 Epsin-3 1 SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR;S(0.014)WQGDGS(0.986)PMANGAGAVVHHQR;SWQGDGS(1)PMANGAGAVVHHQR 235.42 1.41E-29 6971750000 1278151 1347694 1318215 1391328 1504541 1743505 1418094 1378072 1434418 1287900 TRUE FALSE 1328613.388 1579149.961 1352568.766 1666528.526 1248799.658 1338602.387 1306940.087 1359601.199 1382793.576 1540239.347 0.862601901 1.025262706 0.878154924 1.081993217 0.810782857 0.869087256 0.848530515 0.882720729 0.897778374 1 20.55472313 3.210725938 24.99999154 0.876153849 0.960532789 0.197444733 0.075002799 292.5077007 262717.9309 0.019817047 0.023690637 1624.523277 -3.210725938 0.08437894 SWS(ph)LATFR ddPTM_MDA-MB-175_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(0.005)WS(0.995)LATFR;SWS(1)LATFR;S(0.133)WS(0.867)LATFR 150.62 0.00051008 120786000 157096 150216 197336 152288 214244 195418 206302 170483 199676 141111 TRUE FALSE 163298.2714 176014.4295 202478.7383 182410.1119 177826.8814 150035.1311 190131.5102 168197.9542 192489.6998 168758.9987 0.96764186 1.042992853 1.199810024 1.080891172 1.053732736 0.889049664 1.126645166 0.996675469 1.140618878 1 17.36460491 2.999942153 24.4260697 1.029170332 1.07821468 0.05101169 0.084688998 4.69923262 1985991.175 0.024517936 0.028998686 999.8668108 -2.999942153 0.049044348 SWS(ph)PPPEVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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;SWS(1)PPPEVSR;SWS(1)PPPEVSR;S(0.014)WS(0.986)PPPEVSR;S(0.002)WS(0.998)PPPEVSR;S(0.001)WS(0.999)PPPEVSR;SWS(0.999)PPPEVSR 155.33 1.35E-05 38866578000 3642100 4143233 4090192 3902787 4499920 4871770 4163110 4020330 3994365 4264994 TRUE FALSE 3785892.92 4854801.038 4196785.764 4674746.62 3735025.206 3740375.25 3836794.56 3966444.052 3850608.584 5100637.916 0.742239105 0.951802719 0.822796253 0.916502347 0.73226629 0.733315188 0.75221857 0.77763686 0.754926864 1 22.28224626 5.071824512 14.14594305 0.813770856 0.000129501 0.053934683 0.092759032 969827.9102 4504259.064 0.02177881 22890268.92 117984.3793 -5.071824512 -0.813641354 SWS(ph)TATSPLGGERPFR ddPTM_MDA-MB-175_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(0.386)WS(0.525)T(0.086)AT(0.002)SPLGGERPFR 137.73 6.33E-06 2023700000 43911 35961 38249 49464 55820 38386 50033 50901 52713 44856 TRUE FALSE 45644.64019 42137.02201 39245.80036 59247.83156 46331.73634 29471.43325 46111.28272 50218.75535 50815.86943 53644.67438 0.850869927 0.785483788 0.731588006 1.104449458 0.86367821 0.549382275 0.859568694 0.936136829 0.947267739 1 15.71114733 1.738678981 3.660032433 0.960595034 0.81683212 0.201921959 0.129862174 0.369201361 10.63541763 0.074926761 0.036628708 54.78718433 -1.738678981 -0.143762914 SWSHYTVPAGMTVIQWVSDFSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SWSHYTVPAGMTVIQWVSDFSER 23 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 257.86 1.26E-43 1039640000 113111 276210 267280 302980 295050 394290 259620 298710 276116 302420 FALSE TRUE 117576.7096 323646.9189 274245.5364 362908.5397 244897.5064 302722.123 239270.306 294706.281 266178.6391 361673.4088 0.325090833 0.894859592 0.758268453 1.003415045 0.67712334 0.837004092 0.66156455 0.814840886 0.735964084 1 18.46432801 -5 0.030452204 2.089491334 1.74E-14 0.201726649 0.166934061 2786.107018 6.386233875 343.8501442 137.5454985 1.00E-05 5 -2.089491334 SWST(ph)ATSPLGGERPFR ddPTM_MDA-MB-175_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(0.224)WS(0.246)T(0.515)AT(0.015)S(0.001)PLGGERPFR 135.24 3.87E-05 2219400000 86106 115010 103430 96377 89022 160570 118670 108300 109570 110760 TRUE FALSE 89505.53137 134762.0728 106125.4708 115440.0829 73890.07224 123280.051 109368.3353 106848.4156 105626.5971 132461.3014 0.675710796 1.017369386 0.801180946 0.871500444 0.557823843 0.9306873 0.825662546 0.806638728 0.797414762 1 17.01521141 -0.841516282 8.224899823 1 0.813489415 0.184825624 0.119841774 0 9.74E-11 0.107485558 0.025334589 0.144040201 0.841516282 -0.186510585 SWSTATS(ph)PLGGERPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 SWS(0.005)T(0.001)AT(0.259)S(0.735)PLGGERPFR;SWSTAT(0.021)S(0.979)PLGGERPFR;SWSTAT(0.116)S(0.884)PLGGERPFR;SWSTAT(0.004)S(0.996)PLGGERPFR 169.67 3.36E-09 3309300000 541460 702010 711391 667397 737350 804680 724860 701910 749140 752190 TRUE FALSE 562837.2589 822574.7566 729930.4339 799406.1346 612015.5104 617805.265 668043.5791 692502.0445 722178.5977 899567.229 0.625675592 0.914411653 0.811423994 0.888656355 0.680344382 0.686780538 0.742627741 0.769816888 0.802806699 1 19.77887158 0.715072549 2.613972099 0.999975901 0.769177808 0.401528282 0.085523619 1.838847061 15.50137752 0.081361726 0.021618395 5.188867121 -0.715072549 -0.230798093 SWTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SWTSPK 6 0 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 SWT(0.001)S(0.999)PK;SWT(0.006)S(0.994)PK;SWT(0.028)S(0.972)PK;SWT(0.018)S(0.982)PK 118.07 0.023268 1068880000 7781800 4037550 4987580 3843250 6596300 7897900 6558000 5232920 5564220 3287620 TRUE FALSE 8089031.473 4730967.805 5117560.432 4603433.379 5475063.282 6063732.419 6043966.824 5162781.267 5363964.809 3931766.194 2.057353127 1.203267837 1.301593274 1.170830907 1.392520056 1.542241354 1.5372142 1.313094679 1.364263424 1 21.9067461 -3.45531732 0.239413483 4.57E-15 1.463454302 0.245709165 0.236190503 116.0542348 2.255150037 57.88021952 0.377197293 0.000350496 3.45531732 1.463454302 SWVIGS(ph)PEILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SWVIGSPEILR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR;SWVIGS(1)PEILR 173.06 1.32E-05 130683000 264688 294227 289700 303050 287511 348706 279699 286518 257630 282791 TRUE FALSE 275138.0866 344758.1985 297249.82 362992.3855 238639.9829 267724.3162 257775.4615 282677.6949 248357.9466 338198.4821 0.813540276 1.019396055 0.878921213 1.073311693 0.705621094 0.791618917 0.76220171 0.835833718 0.734355592 1 18.36751066 3.230052976 24.99999153 0.796063595 0.946701792 0.322018643 0.099983308 191.0241268 561330.1791 0.026309774 0.031925013 1698.450819 -3.230052976 0.150638198 SWWDAVCTLIHR ddPTM_MDA-MB-175_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 62.338 0.078474 63606000 63924 70715 77123 81383 104980 109660 93562 89524 89565 102780 FALSE TRUE 66447.76888 82859.75116 79132.88874 97480.3145 87135.5371 84193.12691 86228.36596 88324.07721 86341.57315 122917.7732 0.540587152 0.674107162 0.643787198 0.793053047 0.708892903 0.684954867 0.701512595 0.718562295 0.702433594 1 16.90733401 -5 0.196635595 2.373407916 0.637137485 0.754384145 0.055573386 69.42458271 0.684772881 37.45120768 0.140028781 1.00E-05 5 -1.73627043 SYCAEIAHNVSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SYCAEIAHNVSSK 13 0 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 ;;;;; 179.67 1.35E-05 3812390000 3822040 3874700 4343060 3640720 4994310 5141560 4955500 4349500 4560910 3632430 FALSE TRUE 3972937.09 4540149.584 4456243.711 4360843.55 4145378.97 3947510.611 4567074.961 4291202.067 4396763.74 4344135.111 0.914551916 1.045121634 1.025806886 1.003846206 0.954247247 0.908698857 1.051319732 0.987815056 1.012114869 1 22.05063754 SYDLTPVDKFWQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYDLTPVDKFWQK 13 1 Q8WVM8;Q8WVM8-2;Q8WVM8-3 Q8WVM8 SCFD1 Sec1 family domain-containing protein 1 0 85.536 0.0084274 213830000 208580 160580 217590 167010 276720 235500 190320 196590 255170 208510 FALSE TRUE 216814.8995 188158.3659 223260.5742 200044.0795 229683.2332 180808.694 175402.2211 193955.0326 245986.4815 249363.5423 0.869473129 0.754554431 0.895321634 0.802218631 0.921077841 0.725080709 0.703399621 0.777800278 0.986457279 1 17.92789103 1.232701997 24.30702827 0.993228882 0.802088491 0.548511846 0.067825065 79.5806898 330151.0898 0.060578295 0.016784585 17.08842344 -1.232701997 -0.191140391 SYDPPCPGHWT(ph)PEAPGSGTTCPGLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYDPPCPGHWTPEAPGSGTTCPGLPR 26 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3;J3QLT7 H3BM67 NOL3 Nucleolar protein 3 1 SYDPPCPGHWT(1)PEAPGSGTTCPGLPR 107.95 5.22E-08 0 39002 40431 35461 32469 41842 41672 33804 28958 36431 41882 TRUE FALSE 40541.82908 47374.70974 36385.14279 38891.27129 34729.71179 31994.30955 31154.35415 28569.86538 35119.85543 50087.97602 0.809412404 0.945829988 0.726424697 0.77645923 0.69337423 0.638762276 0.621992674 0.570393688 0.701163397 1 15.6121767 3.75933868 1.250673565 0.666392422 0.874645637 0.153486525 0.120741585 0.610391357 1.803347087 0.036770372 0.103195477 5745.643558 -3.75933868 0.208253216 SYDQVHSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SYDQVHSGK 9 0 Q15067-2;Q15067;Q15067-3 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ;;; 117.52 0.0011383 1034590000 2247160 2137570 2170820 2349680 2790540 3022620 2617130 2174420 2437660 1702920 FALSE TRUE 2335879.612 2504681.02 2227393.353 2814439.691 2316205.008 2320662.313 2411992.512 2145275.457 2349929.093 2036574.57 1.146964932 1.229849894 1.093695947 1.381947773 1.137304296 1.139492925 1.184337931 1.053374371 1.153863516 1 20.95771321 1.383582077 0.587588767 1.009561569 1.204512724 0.338395646 0.079950074 0.784971237 0.657207572 0.075892645 0.038150145 24.18700403 -1.383582077 0.194951155 SYDS(ph)LHRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SYDSLHRPK 9 1 Q8N8S7 Q8N8S7 ENAH Protein enabled homolog 1 S(0.036)YDS(0.964)LHRPK;SYDS(1)LHRPK;SYDS(1)LHRPK 105.03 0.0019107 850250000 1048800 708890 1005340 675130 1553220 1256430 900880 908250 891710 791930 TRUE FALSE 1090207.434 830636.3431 1031539.986 808668.6989 1289204.219 964643.1739 830266.6716 896076.3943 859617.5313 947093.5211 1.151108533 0.877037298 1.089163808 0.853842499 1.361221664 1.01853001 0.876646976 0.946132958 0.907637432 1 19.85314737 2.448760948 11.83625738 0.930558947 1.059819464 0.177200854 0.135783178 1.354165956 559.7873919 0.045749395 0.038341564 281.0353477 -2.448760948 0.129260517 SYDSLHRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYDSLHRPK 9 1 Q8N8S7 Q8N8S7 ENAH Protein enabled homolog 0 ; 119.68 0.00047338 166126000 283880 302290 361440 341620 378420 463430 408300 329990 351220 350230 FALSE TRUE 295087.8016 354205.956 370859.4233 409191.4164 314096.3036 355805.4058 376296.3791 325567.0238 338579.6608 418850.8629 0.704517593 0.845661278 0.885421175 0.97693822 0.749900099 0.84947994 0.898401824 0.777286267 0.808353738 1 18.67607712 -2.371174635 2.254353304 2.128319112 0.835724987 0.31158359 0.07441288 5035084.425 659225.5426 28931339.05 0.019254187 0.004254273 2.371174635 -1.292594124 SYDVPPPPMEPDHPFYSNISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 0 ;;;;; 255.98 1.49E-36 2232070000 1851550 1894900 2131940 1765640 2538740 2607730 2311930 2168100 2266610 1921650 FALSE TRUE 1924650.624 2220334.335 2187500.108 2114878.322 2107205.882 2002124.228 2130714.885 2139040.166 2185035.149 2298160.525 0.837474407 0.966135442 0.951848265 0.920248302 0.916909789 0.871185544 0.927139276 0.93076186 0.950775686 1 21.13204814 0.947456158 1.347861609 0.999501596 0.915717512 0.373046656 0.034816275 0.54536362 2.004815702 0.032131188 0.009696462 8.860457733 -0.947456158 -0.083784084 SYEALVQHVIEDHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SYEALVQHVIEDHER 15 0 A0A669KBJ7;Q9H2P0;A0A2R8Y6X0 A0A669KBJ7 ADNP Activity-dependent neuroprotector homeobox protein 0 ;;;; 214.22 1.45E-12 856461000 423241 549514 520868 522681 553709 670618 524557 532005 515126 555068 FALSE TRUE 439950.8815 643888.7549 534442.248 626065.7418 459589.742 514877.1328 483440.8517 524874.3432 496586.7159 663822.9472 0.662753349 0.969970619 0.805097579 0.943121572 0.692337835 0.775624186 0.728267761 0.790684241 0.74807103 1 19.34043898 5.016942537 14.60315165 0.813266986 0.396690551 0.1781506 0.102166728 1224099.333 24136535.9 0.023269442 10700759.44 103978.258 -5.016942537 -0.416576435 SYEDMIGEEVPSDQYYWAPLAQHER ddPTM_MDA-MB-175_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 ; 145.89 2.71E-07 184659000 60227 80315 76044 81888 76123 93775 66261 76296 79335 83774 FALSE TRUE 62604.80847 94108.47649 78025.76911 98085.20199 63183.63965 71997.17742 61067.28968 75273.37692 76479.74885 100187.9113 0.624873876 0.939319677 0.778794248 0.979012345 0.630651331 0.718621403 0.609527525 0.75132195 0.763363043 1 16.61234892 5.01735392 14.39174271 0.777105058 0.354324183 0.119341544 0.130602457 1657549.213 32078424.46 0.030632623 14514129.09 104076.7975 -5.01735392 -0.422780874 SYEFFNELYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYEFFNELYHR 11 0 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 106.26 0.0023557 209450000 158430 98360 143390 98733 188120 182020 149650 133840 145550 137430 FALSE TRUE 164684.9387 115252.5649 147126.8612 118262.0927 156143.4296 139748.6135 137920.042 132046.0937 140311.6839 164356.7772 1.001996641 0.701234028 0.895167596 0.719544972 0.950027326 0.850275942 0.839150318 0.80341131 0.853701845 1 17.32647142 0.952382595 20.82521338 1.000000002 0.838812644 0.215546453 0.087584835 1818.443168 795289.1657 0.075029017 0.018757254 8.961538906 -0.952382595 -0.161187358 SYELPDGQVITIGNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 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 ;;;;;;;;;;;;;; 279.77 4.60E-35 33901054000 2292375 2339272 2169003 2184743 2358815 2676176 2185178 2201209 2113478 2244167 FALSE TRUE 2382879.735 2741023.769 2225529 2616878.645 1957864.469 2054674.682 2013898.038 2171705.394 2037414.34 2683868.556 0.887852622 1.021295831 0.829224291 0.975039794 0.729493426 0.765564572 0.750371338 0.809169804 0.759133429 1 21.35588259 3.241630394 24.99998922 0.788874716 0.927911274 0.334578773 0.085853336 78.24552875 637218.6751 0.022096413 0.028689469 1744.337003 -3.241630394 0.139036559 SYETLVDFDNHLDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ;;;; 259.29 9.71E-27 1199565000 1325727 1614950 1582834 1838949 1749165 1989019 1790972 1665535 1581553 1491585 FALSE TRUE 1378067.726 1892305.1 1624083.954 2202687.623 1451842.558 1527099.481 1650590.935 1643211.228 1524633.216 1783832.523 0.772532011 1.060808723 0.910446431 1.234806292 0.813889499 0.856077833 0.925305999 0.921169004 0.854695268 1 20.76654874 SYETLVDFDNHLDDIRNDWTNPEINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYETLVDFDNHLDDIRNDWTNPEINK 26 1 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 ; 131.43 3.82E-05 113070000 43116 49172 56178 33266 71706 66229 39813 49721 52138 60527 FALSE TRUE 44818.25297 57616.90849 57642.04483 39845.91551 59517.43973 50848.31846 36692.35303 49054.57132 50261.56356 72386.10679 0.619155456 0.795966395 0.796313649 0.55046358 0.822221865 0.702459639 0.506897727 0.677679371 0.694353734 1 16.1434252 -1.841916339 6.929617205 1.025376842 0.683847344 0.476276078 0.099070248 0.035607006 0.000812294 0.087937248 0.022330926 0.014390758 1.841916339 -0.341529498 SYIEGYVPSQADVAVFEAVSS(ph)PPPADLCHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 1 SYIEGYVPSQADVAVFEAVS(0.255)S(0.745)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.232)S(0.768)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.078)S(0.922)PPPADLCHALR;SYIEGYVPSQADVAVFEAVS(0.039)S(0.961)PPPADLCHALR 171.1 1.69E-14 2019100000 753689 869500 887770 928670 898110 1066560 919360 886780 875760 859080 TRUE FALSE 783445.2237 1018829.861 910906.0155 1112358.154 745449.583 818867.6039 847298.1609 874894.1646 844241.5687 1027400.278 0.762551111 0.991658152 0.886612584 1.08269209 0.725568796 0.797028793 0.824701121 0.851561152 0.821726047 1 19.97056694 3.22123152 24.99980249 0.828397358 0.932058122 0.174368099 0.099318 367.4620448 530117.5693 0.027024586 0.032371693 1664.299642 -3.22123152 0.103660764 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYIEGYVPSQADVAVFEAVSSPPPADLCHALR 32 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 116.57 1.60E-06 196416000 98177 117888 112731 134674 130882 146246 123206 115188 113462 107333 FALSE TRUE 102053.1038 138134.347 115668.8625 161312.1152 108634.7244 112282.5829 113548.7918 113644.0933 109378.5248 128362.8463 0.795036155 1.076124057 0.901108582 1.256688519 0.846309719 0.874728055 0.884592349 0.885334787 0.852104233 1 16.96986816 SYLLGNSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SYLLGNSSPR 10 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 SYLLGNS(0.094)S(0.906)PR;SYLLGNS(0.049)S(0.951)PR;SYLLGNS(0.128)S(0.872)PR 86.803 0.013961 353880000 694790 791640 775260 729600 827660 964850 794270 847160 777340 807800 TRUE FALSE 722220.8457 927598.0119 795463.9125 873912.7024 686974.6488 740778.2099 732013.042 835805.2059 749363.6852 966072.9437 0.747584176 0.960173885 0.823399431 0.904603227 0.711100185 0.766793248 0.75772026 0.865157451 0.775680232 1 19.8817726 5.041618983 16.26252019 0.830750546 0.352453866 0.080611051 0.088803591 11933857.9 125721628.5 0.020249219 171815009.2 110057.3328 -5.041618983 -0.47829668 SYLTPVRDEESESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYLTPVRDEESESQR 15 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;F8VZN8;H0YHI8;H0YIS4;A0A3B3ISH4 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 155.57 2.08E-06 113530000 167880 150610 186090 150110 217590 251130 211510 182310 200790 189310 FALSE TRUE 174508.032 176476.0959 190939.6583 179801.31 180604.1295 192808.8634 194931.2935 179866.4326 193563.6071 226401.6699 0.770789509 0.779482307 0.843366828 0.79416954 0.797715536 0.851622974 0.860997596 0.794457182 0.854956623 1 17.78852507 -5 0.195414819 1.821468275 0.783662921 0.822858283 0.026801647 57.05586893 0.562024569 18.24217256 0.070467947 1.00E-05 5 -1.037805354 SYMNPGDQS(ph)PADSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYMNPGDQSPADSNK 15 0 Q92754;Q92754-2 Q92754 TFAP2C Transcription factor AP-2 gamma 1 SYMNPGDQS(1)PADSNK 282.2 8.70E-34 92622000 213250 138680 157410 135370 197320 208590 213320 156950 173760 97241 TRUE FALSE 221669.2747 162497.2112 161512.2339 162145.782 163779.6169 160148.1337 196599.421 154846.342 167506.4115 116293.5122 1.906119013 1.397302465 1.388832712 1.394280549 1.408329784 1.377102907 1.690545047 1.331513161 1.440376238 1 16.82741109 -3.312320933 0.218263548 1.76E-17 1.54241435 0.455026637 0.164487882 62.87761455 1.21737665 29.03848237 0.326618967 0.000487168 3.312320933 1.54241435 SYNPFDDDGEDEGARPAPWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 ;;; 220.36 7.83E-25 1558570000 359205 436516 406060 428657 435840 510490 422171 417980 407587 454474 FALSE TRUE 373386.6908 511484.2274 416642.2572 513444.0752 361756.0725 391936.4341 389080.1339 412377.6618 392918.0235 543519.4789 0.68697941 0.941059607 0.766563616 0.944665454 0.665580695 0.721108349 0.715853155 0.758717356 0.722914337 1 19.05197221 5.041426238 15.00898636 0.789053869 0.259752306 0.077437869 0.110833252 2556977.705 27471794.17 0.025263551 36633944.92 110008.4987 -5.041426238 -0.529301563 SYNQEHSQSFTFDDAQQEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYNQEHSQSFTFDDAQQEDR 20 0 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;E9PI04 Q9NPQ8-4 RIC8A Synembryn-A 0 208.28 5.83E-22 193690000 27090 44669 29010 32706 31503 31809 33593 33559 38536 40755 FALSE TRUE 28159.53412 52340.55327 29766.02443 39175.14918 26148.13131 24421.84182 30959.89288 33109.1965 37149.09689 48740.16195 0.577748062 1.073869088 0.610708361 0.803755006 0.536480189 0.501061975 0.635202914 0.679300092 0.762186571 1 15.57282342 -0.800294967 6.833334057 1.000000002 0.686607389 0.263686913 0.157060342 4.46E-09 6.52E-10 0.149568011 0.035253518 0.158381712 0.800294967 -0.313392613 SYQFGIIGNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYQFGIIGNDR 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 0 81.525 0.033616 0 94567 89883 108400 85339 155470 123510 115510 105010 118620 107760 FALSE TRUE 98300.57818 105319.7061 111224.9931 102218.7995 129043.2649 94826.67431 106456.0244 103602.5127 114350.8894 128873.5088 0.762767919 0.817233169 0.863055519 0.79317154 1.001317231 0.735812 0.826050484 0.803908528 0.887311057 1 16.97559621 0.934384448 3.998809013 0.999894808 0.827405852 0.383782868 0.067801103 0.295723176 12.41246274 0.061549092 0.015743057 8.597742771 -0.934384448 -0.172488957 SYQSELEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SYQSELEALRR 11 1 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ;; 187.93 5.41E-06 670870000 405744 538643 460826 428701 587040 623477 484918 476797 513262 617096 FALSE TRUE 421763.0864 631150.7452 472835.5041 513496.7783 487255.1505 478683.9156 446908.8601 470406.3161 494789.8009 738004.1462 0.571491486 0.855213007 0.640694916 0.695791183 0.660233622 0.648619548 0.605564159 0.637403351 0.670443118 1 19.4932694 -1.855557674 3.875018683 1.09218317 0.665521391 0.664055845 0.071470621 0.041322296 0.001540299 0.050239265 0.01555185 0.013945764 1.855557674 -0.426661779 SYS(ph)EPEKMNEVGIVEEAEPAPLGPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 SYSEPEKMNEVGIVEEAEPAPLGPQR 26 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 S(0.136)YS(0.864)EPEKMNEVGIVEEAEPAPLGPQR;S(0.186)YS(0.814)EPEKMNEVGIVEEAEPAPLGPQR;S(0.02)YS(0.98)EPEKMNEVGIVEEAEPAPLGPQR 167.32 6.39E-12 511691000 587500 420875 577470 340523 769390 772760 568100 550260 616900 456390 TRUE FALSE 610694.9536 493157.0073 592519.3426 407877.433 638609.3626 593298.2013 523570.8375 542884.6647 594697.8895 545810.8824 1.118876471 0.903530917 1.085576271 0.747287103 1.170019476 1.087003247 0.959253204 0.99463877 1.089567667 1 19.05804163 SYS(ph)EPEKMNEVGLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSEPEKMNEVGLTR 15 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 S(0.162)YS(0.838)EPEKMNEVGLTR;S(0.003)YS(0.997)EPEKMNEVGLTR 129.38 0.00024339 127460000 169997 144770 168740 135814 232183 268092 201103 172323 198239 148495 TRUE FALSE 176708.6128 169633.1213 173137.503 162677.6038 192716.6166 205831.696 185340.0214 170013.292 191104.4171 177589.7521 0.995038344 0.955196566 0.974929583 0.916030356 1.085178701 1.15902913 1.043641422 0.95733729 1.076100478 1 17.43818881 3.235027128 24.99997728 1.049167981 0.960979334 0.422363641 0.053273825 105.7715579 748352.2291 0.017133562 0.021256542 1718.0157 -3.235027128 -0.088188647 SYS(ph)LSELSVLQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 SYS(0.999)LS(0.001)ELSVLQAK;SYS(1)LSELSVLQAK;S(0.001)YS(0.998)LS(0.001)ELSVLQAK;SYS(0.991)LS(0.009)ELSVLQAK;SYS(0.996)LS(0.004)ELSVLQAK;SYS(0.904)LS(0.096)ELSVLQAK 414.01 1.17E-126 1778971000 2267810 1924067 2161130 1972350 2733470 2871530 2506960 2272600 2306050 1935802 TRUE FALSE 2357344.89 2254510.54 2217450.823 2362474.943 2268835.746 2204660.676 2310457.924 2242139.514 2223055.711 2315085.339 1.018253993 0.973834745 0.957826818 1.020469917 0.980022511 0.95230212 0.998001191 0.968491086 0.960247846 1 21.14263394 3.01027657 24.98439909 0.974384039 0.990206898 0.108458626 0.022260108 508.3899709 1235988.525 0.006292438 0.007514585 1023.944859 -3.01027657 0.015822858 SYS(ph)PAHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPAHNR 8 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 S(0.437)Y(0.004)S(0.56)PAHNR;S(0.442)Y(0.001)S(0.557)PAHNR 82.417 0.013093 239320000 171067 308010 249200 287970 204077 289830 230670 221320 200147 307650 TRUE FALSE 177820.8573 360908.3215 255694.3567 344929.6065 169388.0644 222521.3749 212589.4827 218353.5674 192943.7486 367928.1272 0.483303244 0.980920715 0.694957351 0.937491812 0.460383569 0.60479577 0.57780166 0.593467994 0.524406085 1 18.48906445 3.236091486 24.99999129 0.601715172 0.783278376 0.121881253 0.185973536 103.6116203 1049072.888 0.048186205 0.060202635 1722.231333 -3.236091486 0.181563204 SYS(ph)PDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SYSPDGK 7 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(1)PDGK;SYS(1)PDGK;S(0.001)YS(0.999)PDGK;S(0.001)YS(0.999)PDGK;SYS(1)PDGK;S(0.001)YS(0.999)PDGK;SYS(1)PDGK 146.27 0.0023392 26872233000 37086039 20987042 27694502 22553441 33705815 34539887 39033149 28617214 28969940 16239915 TRUE FALSE 38550224.46 24591403.21 28416243.47 27014444.31 27976512.61 26518521.7 35973628.79 28233647.05 27927317.52 19421815.41 1.984892948 1.266174283 1.463109543 1.390933017 1.440468464 1.36539871 1.852227921 1.453707929 1.437935483 1 24.21117472 4.750752795 24.24628089 1.443599635 1.984893459 0.415969637 0.201159482 1255.368423 2496449.647 0.04549591 0.757671185 56331.69184 -4.750752795 0.541293824 SYS(ph)PDGKES(ph)PSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 2 S(0.072)Y(0.001)S(0.927)PDGKES(0.999)PS(0.001)DKK;S(0.011)Y(0.001)S(0.988)PDGKES(0.999)PS(0.001)DKK;S(0.096)YS(0.904)PDGKES(0.641)PS(0.359)DKK;S(0.099)Y(0.003)S(0.898)PDGKES(0.88)PS(0.12)DKK;S(0.057)YS(0.943)PDGKES(0.999)PS(0.001)DKK;S(0.016)Y(0.002)S(0.982)PDGKES(0.986)PS(0.014)DKK;S(0.073)Y(0.01)S(0.918)PDGKES(0.605)PS(0.395)DKK 164.59 2.20E-06 7837309000 25605900 4040590 7470340 3848180 13130310 15942140 13439920 8046360 9149940 2399190 TRUE FALSE 26616840.7 4734529.901 7665023.197 4609338.518 10898424.6 12239819.59 12386463.95 7938511.705 8820635.447 2869265.345 9.276535106 1.650084371 2.671423614 1.606452511 3.798332773 4.265837459 4.316946138 2.766740176 3.074179062 1 21.45224996 0.736904602 1.085330588 1.012294525 3.6892785 0.147413293 2.05104882 1.858069459 3.881888754 1.864784475 0.588904968 5.456379914 -0.736904602 2.676983975 SYS(ph)PDGKESPSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPDGKESPSDK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(0.997)PDGKES(0.003)PSDK;SYS(0.801)PDGKES(0.197)PS(0.003)DK 203.52 2.24E-07 217290000 446490 184161 281230 152573 446050 371430 317420 269130 303120 152812 TRUE FALSE 464117.77 215789.2192 288559.0848 182751.484 370230.5803 285171.0116 292539.791 265522.7526 292210.7704 182752.5856 2.539596189 1.180772455 1.57896034 0.999993972 2.025856866 1.560421214 1.600742282 1.452908322 1.598941921 1 17.47953229 -2.979852152 0.195241591 4.74E-27 1.707939921 0.192093013 0.39816267 101.662519 2.038635841 44.35407204 1.03007199 0.001047485 2.979852152 1.707939921 SYS(ph)PDGKESPSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SYSPDGKESPSDKK 14 2 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 1 SYS(0.997)PDGKES(0.001)PS(0.002)DKK;SYS(0.998)PDGKES(0.001)PSDKK;S(0.001)YS(0.999)PDGKES(0.001)PSDKK;S(0.002)YS(0.994)PDGKES(0.004)PSDKK;S(0.001)YS(0.999)PDGKES(0.001)PSDKK;S(0.002)YS(0.95)PDGKES(0.046)PS(0.002)DKK;S(0.002)YS(0.998)PDGKESPSDKK 173.77 2.09E-06 14464580000 12958750 3750920 6551820 2934980 11154850 8548760 7710670 6137500 7548840 2853570 TRUE FALSE 13470371.46 4395111.332 6722565.812 3515510.284 9258752.581 6563440.048 7106287.537 6055236.851 7277158.723 3412672.407 3.94716218 1.287879646 1.969883133 1.030134119 2.713050501 1.923255228 2.082323379 1.774338738 2.132392992 1 21.7024705 7.999999999 0.052875762 4.59E-10 5.739272049 0.197167723 0.740372114 892.0110691 3.54830956 86.7781615 409.6262736 99999999.87 -7.999999999 5.739272049 SYS(ph)PDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPDHR 7 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 S(0.028)Y(0.001)S(0.972)PDHR;S(0.342)Y(0.001)S(0.657)PDHR 99.7 0.010842 1071260000 1117750 1669340 1706680 1506450 1768320 1717630 1645130 1736040 1553090 1637540 TRUE FALSE 1161879.633 1956036.159 1751157.483 1804421.314 1467741.598 1318736.463 1516180.412 1712771.223 1497194.594 1958384.61 0.593284704 0.998800822 0.894184663 0.921382503 0.749465447 0.673379711 0.774199513 0.874583682 0.764504881 1 20.9012327 -1.616524135 2.900440094 1.014332492 0.814342483 0.201588505 0.115120606 33512960.09 37369000.45 3679955.098 0.028228592 0.02418109 1.616524135 -0.199990008 SYS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPER 6 0 F8W0Q9;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8;F8W6A0;F8VWU8;Q8NEY8-6;F8WF16;B7Z8L1;Q8NEY8-3;Q8NEY8-5 F8W0Q9;Q8NEY8-6 PPHLN1 Periphilin-1 1 S(0.02)YS(0.98)PER;S(0.082)YS(0.918)PER 98.503 0.041812 1129850000 738040 817820 754490 780680 787920 914050 786230 765970 693510 759830 TRUE FALSE 767178.3891 958274.2232 774152.6292 935096.1739 653989.6398 701775.7401 724603.2382 755703.425 668550.7106 908704.1407 0.844255412 1.054550299 0.851930342 1.029043593 0.719694795 0.772281878 0.797402813 0.83162758 0.73571879 1 19.79345113 3.238128627 24.99999493 0.800801484 0.946129967 0.325997082 0.094947855 11.88454385 687802.3102 0.024567442 0.031124398 1730.328763 -3.238128627 0.145328483 SYS(ph)PGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSPGRR 7 1 Q8IWX8;J3QK89 Q8IWX8 CHERP Calcium homeostasis endoplasmic reticulum protein 1 SYS(1)PGRR 62.104 0.053575 127290000 91845 112500 98177 101460 95961 115950 96576 101980 96211 100980 TRUE FALSE 95471.11152 131820.9999 100735.5733 121528.4852 79649.5835 89022.36974 89006.12077 100613.1249 92748.3849 120765.0976 0.790552183 1.091548821 0.834144759 1.00632126 0.659541416 0.73715313 0.73701858 0.833130821 0.768006541 1 16.88184404 3.249577871 24.97725487 0.77863906 0.935242473 0.266266159 0.114175579 248.4973419 563365.7519 0.029345936 0.039362782 1776.551783 -3.249577871 0.156603412 SYS(ph)PYDYQPCLAGPNQDFHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSPYDYQPCLAGPNQDFHSK 21 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7 E9PGF5 TNS1 Tensin-1 1 S(0.165)YS(0.835)PYDYQPCLAGPNQDFHSK;S(0.13)YS(0.869)PYDYQPCLAGPNQDFHSK 152.14 4.42E-13 0 178402 159870 171404 155366 229450 235900 195262 180725 198712 149949 TRUE FALSE 185445.4487 187326.4289 175870.929 186096.9311 190448.171 181115.8001 179956.8542 178302.677 191560.3939 179328.6356 1.034109517 1.044598529 0.980718603 1.037742413 1.062006468 1.009965862 1.00350317 0.994278891 1.068208618 1 17.45224635 1.262692581 24.9999525 1.034104507 1.019764866 0.033583387 0.027912085 783.3217769 811502.7479 0.018860738 0.006878997 18.31017862 -1.262692581 -0.014339642 SYS(ph)SER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSSER 6 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.027)YS(0.896)S(0.077)ER 71.342 0.092816 272360000 283200 350110 350360 368940 377960 533180 351760 348690 311260 341070 TRUE FALSE 294380.9547 410238.669 359490.6694 441915.2308 313714.4942 409357.0254 324188.132 344016.3809 300057.8134 407896.1363 0.721705671 1.005742964 0.88132894 1.083401365 0.769103863 1.003581522 0.794781081 0.843392105 0.735623083 1 18.63784232 2.21324102 24.97445488 0.83051854 0.915189606 0.065835002 0.119751367 503.9642119 497091.1751 0.041374793 0.030568724 163.3958493 -2.21324102 0.084671066 SYS(ph)SERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSSERR 7 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 S(0.002)YS(0.592)S(0.407)ERR;SYS(0.993)S(0.007)ERR 117.81 0.0031527 699670000 535930 612680 636230 517680 681660 769540 574410 609100 596590 602600 TRUE FALSE 557088.9302 717903.024 652810.6765 620075.5589 565791.6767 590825.9975 529386.2433 600936.0108 575118.8424 720667.9325 0.773017509 0.996163408 0.905841161 0.860417858 0.785093454 0.819831119 0.734577216 0.83385979 0.798035845 1 19.45897513 3.482805866 4.120102523 0.814657938 0.900637026 0.088591148 0.082356269 0.340375923 13.52516659 0.021220802 0.031437289 3039.526021 -3.482805866 0.085979088 SYS(ph)SPDITQAIQEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 SYSSPDITQAIQEEEK 16 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.932)S(0.068)PDITQAIQEEEK;S(0.009)YS(0.976)S(0.014)PDITQAIQEEEK;SYS(0.871)S(0.129)PDITQAIQEEEK;SYS(0.5)S(0.5)PDITQAIQEEEK 427.08 4.00E-160 631720000 925410 607729 797050 604660 1076630 1187910 1021730 840200 950210 600190 TRUE FALSE 961945.9014 712101.7283 817821.7778 724259.9433 893624.8172 912035.9055 941644.1328 828938.4933 916012.1277 717785.7392 1.340157444 0.992081187 1.139367548 1.009019689 1.244974326 1.270624165 1.31187356 1.154855061 1.276163732 1 19.45319373 3.20585609 24.96203957 1.2227748 1.112380319 0.11006092 0.120656173 320.5283847 244645.4845 0.032557346 0.03891588 1606.408856 -3.20585609 -0.11039448 SYS(ph)SPDITQAIQEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.916)S(0.084)PDITQAIQEEEKR;SYS(0.985)S(0.015)PDITQAIQEEEKR;SYS(0.849)S(0.151)PDITQAIQEEEKR;SYS(0.774)S(0.226)PDITQAIQEEEKR;S(0.063)YS(0.673)S(0.264)PDITQAIQEEEKR;SYS(0.903)S(0.097)PDITQAIQEEEKR;SYS(0.79)S(0.21)PDITQAIQEEEKR 328.2 3.86E-72 13617197000 2910950 1920740 2422490 1881320 3212350 3213520 2927640 2549760 2768370 1808170 TRUE FALSE 3025876.554 2250612.154 2485622.079 2253439.481 2666315.894 2467228.681 2698163.927 2515584.638 2668736.904 2162446.292 1.399284026 1.040771353 1.149449163 1.04207882 1.233009071 1.140943334 1.247736851 1.163305025 1.234128641 1 21.04423287 -2.406115888 1.857410289 5.54E-05 1.176062212 0.229629899 0.099969722 1070710.093 89439.32574 4498140.804 0.022783602 0.003925402 2.406115888 1.176006778 SYSFDEIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SYSFDEIRK 9 1 P43490 P43490 NAMPT Nicotinamide phosphoribosyltransferase 0 ;;;; 173.39 8.89E-05 2685640000 2278820 1912040 2203190 1715059 2927980 2761720 2554500 2212580 2346380 2237150 FALSE TRUE 2368789.573 2240417.996 2260606.941 2054292.551 2430283.005 2120352.384 2354271.615 2182923.984 2261934.242 2675476.71 0.885371031 0.837390207 0.844936132 0.767822999 0.908355134 0.792513864 0.879944724 0.815900948 0.84543223 1 21.35136454 -2.346192921 1.864354507 1.706796751 0.840102445 0.577400858 0.040532592 1300019.547 144881.5585 3862988.753 0.009141015 0.004506165 2.346192921 -0.866694306 SYSPYDMLESIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSPYDMLESIRK 13 1 P07355-2;P07355;H0YN42;H0YM50;A6NMY6;H0YL33;H0YN28 P07355-2 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 116.84 0.00088791 367750000 318360 350260 403030 328410 445090 468850 383810 369310 357990 410460 FALSE TRUE 330929.0986 410414.4304 413533.2929 393368.5178 369433.7608 359966.693 353725.9693 364360.0035 345106.0098 490881.7783 0.674152338 0.836075912 0.842429504 0.801350825 0.752592125 0.733306285 0.720592992 0.742256119 0.703032838 1 18.90501609 -1.021682986 4.596304733 1.000006168 0.758879201 0.660390297 0.052418454 4.31E-06 9.17E-07 0.052963572 0.012483236 0.095129894 1.021682986 -0.241126966 SYSS(ph)PDITQAIQEEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 SYS(0.246)S(0.754)PDITQAIQEEEKR 311.16 2.47E-58 1092600000 564540 361780 490110 368600 568330 564980 512580 448410 477750 336830 TRUE FALSE 586828.4751 423912.9007 502882.6692 441507.9798 471725.4696 433771.9574 472402.6402 442399.7974 460555.8708 402825.3895 1.456781252 1.052349012 1.248388712 1.096028183 1.171042049 1.076823777 1.172723102 1.098242089 1.143313909 1 18.61979509 4.746389566 24.99337601 1.125697208 1.456781412 0.696571577 0.066957856 492.3739343 1571833.403 0.014122815 0.15375337 55768.57736 -4.746389566 0.331084204 SYSSGGEDGYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 ; 118.4 0.0014641 230765000 254470 356550 315100 352030 346200 466900 307820 350050 327610 432270 FALSE TRUE 264516.6721 417784.6889 323311.7649 421660.4833 287353.0477 358469.5509 283692.2641 345358.1523 315819.3801 516965.0302 0.511672273 0.808148839 0.62540355 0.815646047 0.5558462 0.693411604 0.548764902 0.66804935 0.610910529 1 18.97970717 -1.978165212 2.716979904 1.302707374 0.652924635 0.538200857 0.097564882 13139429.45 4206653.396 24937528.49 0.022558907 0.010515618 1.978165212 -0.649782739 SYT(ph)MDDAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SYTMDDAWK 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 S(0.002)YT(0.998)MDDAWK 122.51 0.0065256 70100000 137390 148560 220500 117930 350030 222380 175910 189330 256820 207330 TRUE FALSE 142814.2633 174074.0244 226246.4111 141256.202 290532.0256 170735.6152 162121.7145 186792.341 247577.0984 247952.3439 0.575974645 0.702046295 0.912459256 0.569690932 1.171725264 0.68858238 0.653842234 0.753339686 0.998486622 1 17.91970334 -4.759505913 0.032868026 2.169433042 3.39E-06 0.196674485 0.174472515 2234.190962 5.735402939 302.060388 116.5716504 1.74E-05 4.759505913 -2.169429655 SYVAWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYVAWDR 7 0 P78527;P78527-2 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 0 ; 93.195 0.03516 1021130000 377590 511970 550840 561120 602060 594060 495080 461490 483380 583410 FALSE TRUE 392497.5448 599896.8649 565195.3429 672107.8612 499722.0563 456098.5681 456274.3359 455304.4814 465983.2482 697718.0194 0.562544658 0.85979844 0.8100627 0.9632944 0.716223521 0.653700428 0.653952346 0.652562308 0.667867584 1 19.41228457 3.024219424 24.99679038 0.693325255 0.808530003 0.04084769 0.136591022 441.569255 455738.9476 0.037399011 0.044698459 1057.351594 -3.024219424 0.115204747 SYVS(ph)EPELATLSGDMAQPSLGLVGPESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.04)YVS(0.96)EPELATLSGDMAQPSLGLVGPESR;S(0.028)YVS(0.972)EPELATLSGDMAQPSLGLVGPESR;S(0.032)YVS(0.968)EPELATLSGDMAQPSLGLVGPESR 244.44 1.18E-45 328218000 114897 130761 128932 122311 143164 161759 117518 128093 124488 140943 TRUE FALSE 119433.2223 153218.1846 132292.0738 146503.7507 118829.0344 124192.9237 108306.6321 126376.1229 120007.7012 168558.0823 0.708558264 0.908993401 0.784845627 0.86915886 0.704973815 0.736796017 0.642547842 0.749748224 0.71196646 1 17.36288628 5.044777692 15.81186008 0.774405933 0.372410332 0.034496916 0.103064128 1276250.383 12288583.39 0.023831154 15193670.94 110860.7192 -5.044777692 -0.4019956 SYYVDHNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 SYYVDHNSR 9 0 P46934-4;H0Y8X6;P46934-3;P46934-2;P46934 P46934-4 NEDD4 E3 ubiquitin-protein ligase NEDD4 0 ; 97.456 0.0066786 168932000 49703 172745 142536 157019 159445 195022 129994 158543 141884 205407 FALSE TRUE 51665.31282 202412.61 146250.6053 188076.8895 132342.5959 149731.0961 119804.7306 156417.9904 136777.6226 245652.5689 0.210318634 0.823979211 0.595355489 0.765621505 0.538738904 0.609523836 0.487699889 0.636744778 0.556792966 1 17.9062598 -1.628065765 2.675886706 1.041141997 0.592526563 0.388685793 0.157170572 21847696.16 19946542.33 6248157.633 0.034730184 0.023546927 1.628065765 -0.448615434 T(ph)AMRVSPHHPAPTPNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TAMRVSPHHPAPTPNPR 17 1 A8MZI9;Q01196-7;Q01196-3;Q01196-4;Q01196;Q01196-9;Q01196-10;Q01196-2;Q01196-8;Q01196-11 A8MZI9 RUNX1 Runt-related transcription factor 1 1 T(0.5)AMRVS(0.5)PHHPAPTPNPR;T(0.585)AMRVS(0.415)PHHPAPTPNPR;T(0.5)AMRVS(0.5)PHHPAPTPNPR 104.06 0.001734 234610000 107201 120490 130160 117473 157615 168893 132638 146526 138238 121093 TRUE FALSE 111433.3783 141183.2202 133552.0765 140708.8088 130823.6586 129670.1603 122241.487 144562.0586 133262.8414 144818.8549 0.769467335 0.974895295 0.922200888 0.971619399 0.903360676 0.895395565 0.844099251 0.998226776 0.920203667 1 17.14388992 -5 0.012165621 2.063859446 1.46E-11 0.210994793 0.061222676 15347.13875 14.17562691 1442.986511 999.6024721 1.00E-05 5 -2.063859446 T(ph)AS(ph)PPPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK;T(1)AS(1)PPPPPK 123.67 0.0029241 3333440000 5398500 3755840 4782000 3481490 6125600 6086300 5798500 4873600 5095700 3329350 TRUE FALSE 5611636.949 4400876.304 4906622.848 4170118.331 5084372.7 4672849.064 5343998.418 4808277.364 4912306.752 3981672.388 1.409366819 1.105283377 1.232302 1.047328339 1.276944009 1.173589539 1.342149202 1.207602458 1.233729517 1 21.92494309 -1.070434393 4.253765319 0.999976223 1.220904528 0.313801169 0.099782618 6174791.733 1553849.235 1403.17173 0.02154329 0.085028713 1.070434393 0.220928304 T(ph)AS(ph)PPPPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR 106.26 0.0021124 2814390000 3902340 2895350 3742830 2774470 4291230 4536380 4028930 3525190 3834960 2585690 TRUE FALSE 4056407.396 3392603.84 3840371.225 3323251.885 3561808.257 3482874.495 3713131.939 3477940.594 3696940.539 3092306.449 1.311774063 1.097111135 1.241911592 1.074683877 1.151829004 1.12630315 1.200764542 1.124707609 1.195528515 1 21.56025187 -5 0.230394332 0.136640711 1.18174132 0.36458562 0.067347826 171.1330169 1.712257421 69.117297 0.10570547 1.00E-05 5 1.045100609 T(ph)ASFGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_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 203.06 1.49E-21 49241000 101360 103350 100720 99242 133170 140190 120590 113500 104420 92449 TRUE FALSE 105361.7711 121099.5585 103344.8459 118871.7714 110533.811 107632.9971 111137.8407 111978.7181 100661.9446 110562.6115 0.952960224 1.095302986 0.934717845 1.075153434 0.999739509 0.973502666 1.005202746 1.012808187 0.910451944 1 16.75450407 1.272945383 24.9829321 0.955225855 1.007924884 0.137818113 0.050820835 266.3528996 193523.9793 0.030460544 0.011123404 18.74758722 -1.272945383 0.05269903 T(ph)CNSPQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.554)CNS(0.306)PQNS(0.119)T(0.021)DSVSDIVPDSPFPGALGSDTR 186.17 1.63E-17 222120000 56159 70228 57718 60336 73139 85224 65943 63390 61533 53299 TRUE FALSE 58376.20068 82289.1127 59222.1785 72270.28072 60706.8589 65432.01758 60774.21535 62540.36074 59318.43935 63741.91858 0.915821205 1.290973264 0.929093128 1.13379519 0.952385185 1.026514718 0.95344189 0.981149644 0.930603293 1 15.95995482 3.224463113 24.99080569 0.974628892 1.073508203 0.168060468 0.101442975 369.1284696 654357.2443 0.0267599 0.032131772 1676.729917 -3.224463113 0.098879311 T(ph)ES(ph)KIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TESKIRR 7 2 Q6P6B7-2;Q6P6B7 Q6P6B7-2 ANKRD16 Ankyrin repeat domain-containing protein 16 2 T(1)ES(1)KIRR;T(1)ES(1)KIRR;T(1)ES(1)KIRR 68.915 0.067494 2801800000 1731530 2018400 2123350 1725790 2681440 2609290 1936000 2108430 2106240 2129820 TRUE FALSE 1799892.141 2365044.499 2178686.245 2067146.111 2225649.787 2003321.942 1784251.261 2080169.945 2030436.834 2547117.451 0.706638848 0.928518038 0.855353664 0.811562934 0.873791582 0.786505522 0.700498228 0.816676099 0.797150847 1 21.28043406 2.718141649 23.62635583 0.799718314 0.84016833 0 0.088454111 1405.543936 1626320.824 0.026836593 0.02533548 522.5666011 -2.718141649 0.040450017 T(ph)FSLTEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.602)FS(0.397)LTEVR 197.86 0.0015717 272840000 290170 319740 388660 381160 495020 566350 476100 479330 460530 449170 TRUE FALSE 301626.1357 374652.8578 398788.7989 456552.3104 410876.6772 434823.7956 438782.0379 472905.3654 443955.6153 537176.2616 0.561503099 0.697448649 0.742379787 0.849911552 0.764882417 0.809462046 0.816830656 0.880354176 0.826461717 1 19.03503603 6.459062385 0.186459048 0.971027926 3.44E-31 0.816621984 0.047243728 13.51732896 0.256267056 0.106827744 3.363707566 2877811.772 -6.459062385 -0.971027926 T(ph)GGPSPAGPAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGGPSPAGPAAAR 13 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 T(0.585)GGPS(0.415)PAGPAAAR 99.259 0.0038256 0 261420 407810 323250 348120 374790 458310 348720 353360 316040 374990 TRUE FALSE 271741.0635 477848.1952 331674.1606 416977.097 311083.3297 351874.4483 321386.4152 348623.7872 304665.7821 448462.1109 0.605939848 1.065526348 0.739581232 0.929793369 0.693666917 0.784624698 0.716641177 0.777376235 0.679356795 1 18.77462658 3.231394746 24.99968972 0.761728398 0.844830714 0.035353051 0.139665421 427.8180093 1492533.87 0.036305309 0.044265433 1703.706365 -3.231394746 0.083102316 T(ph)GSQEGTSMEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.89)GS(0.11)QEGTSMEGSRPAAPAEPGTLK 152.16 1.59E-07 153960000 75295 65831 81910 75002 103820 105460 89173 76040 93462 55050 TRUE FALSE 78267.70474 77136.96216 84044.64189 89837.17174 86172.71348 80968.51326 82183.38725 75020.80818 90098.32088 65835.9935 1.18882849 1.171653347 1.276575888 1.364560128 1.30889972 1.229851772 1.248304808 1.139510535 1.36852679 1 16.00658892 -1.637216147 2.898389985 0.977909992 1.24896969 0.519208138 0.073451199 130822909.1 122958757.8 21576129.66 0.018535866 0.023055994 1.637216147 0.271059698 T(ph)HAVSVSETDDYAEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 1 T(0.238)HAVS(0.217)VS(0.198)ET(0.181)DDY(0.166)AEIIDEEDTYTMPSTR 82.476 0.013032 69788000 8651.7 14329 16017 9328 16114 17457 11912 11627 14427 14189 TRUE FALSE 8993.275797 16789.89429 16434.41618 11173.05056 13374.94804 13402.87631 10978.30631 11471.15908 13907.77509 16969.06289 0.529980698 0.989441456 0.968492856 0.658436511 0.788196032 0.789841867 0.646960082 0.676004277 0.819595942 1 14.05061927 4.776125459 23.24170821 0.790480139 0.529979072 0.288302052 0.129292042 12083.9046 7476045.497 0.032029311 7.342463987 59720.77836 -4.776125459 -0.260501068 T(ph)HSAGTSPTITHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 T(0.327)HS(0.268)AGT(0.221)S(0.182)PT(0.001)ITHQK 83.966 0.030614 256070000 199610 155130 173500 134570 224180 237860 197480 151020 167290 121460 TRUE FALSE 207490.7569 181772.3708 178021.5525 161187.5443 186073.9637 182620.6198 182001.0016 148995.8239 161269.2656 145257.7615 1.428431464 1.251378025 1.225556216 1.109665623 1.28099154 1.257217638 1.252951992 1.025733994 1.110228217 1 17.14825573 8 0.093664049 0.852266437 2.245978432 0.605344108 0.078051806 105.8843986 0.708599278 1.309495372 18.95559002 100000000 -8 1.393711994 T(ph)HT(ph)GQY(ph)S(ph)ALSVACGPSGEAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THTGQYSALSVACGPSGEAGPR 22 0 Q8N9L1-2 Q8N9L1-2 4 T(0.652)HT(0.69)GQY(0.692)S(0.711)ALS(0.689)VACGPS(0.566)GEAGPR 46.307 0.060061 780660000 5100.2 46197 48418 32893 53902 61041 46872 58017 51661 30850 TRUE FALSE 5301.559834 54130.97539 49679.81286 39399.13722 44739.75729 46865.15284 43198.05016 57239.37701 49801.7307 36894.46684 0.143695255 1.467184107 1.346538305 1.067887426 1.212641383 1.270248816 1.170854436 1.551435267 1.349842807 1 15.17111685 4.743993658 24.99810624 1.289473048 0.14369477 0.814090953 0.161351897 238.8259159 1098834.912 0.039218956 0.340251523 55461.7614 -4.743993658 -1.145778278 T(ph)HTDSSEKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 T(0.273)HT(0.273)DS(0.227)S(0.227)EKELEPEAAEEALENGPK;T(0.268)HT(0.268)DS(0.232)S(0.232)EKELEPEAAEEALENGPK;T(0.326)HT(0.26)DS(0.207)S(0.207)EKELEPEAAEEALENGPK;T(0.27)HT(0.27)DS(0.23)S(0.23)EKELEPEAAEEALENGPK 176.85 6.43E-17 530740000 1014550 332731 556903 323252 956650 916780 814880 506844 644195 225631 TRUE FALSE 1054605.217 389874.961 571416.3497 387190.2808 794038.9747 703871.7389 751007.5763 500050.5852 621010.5478 269839.0745 3.908274661 1.444842493 2.117618995 1.434893303 2.942638964 2.608487078 2.783168367 1.853143716 2.301410754 1 18.04173975 0.362864766 0.982943076 0.996679923 2.361508864 0.257663017 0.704932737 3.600534855 4.319101956 0.679774088 0.207227862 2.306029009 -0.362864766 1.364828941 T(ph)IGT(ph)GLVT(ph)NT(ph)LAMTEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIGTGLVTNTLAMTEEEK 18 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 4 T(0.91)IGT(0.924)GLVT(0.764)NT(0.764)LAMT(0.638)EEEK 49.577 0.049001 21321000 25119 14422 18754 15975 24928 20854 22845 19202 18435 14093 TRUE FALSE 26110.71752 16898.86631 19242.74465 19134.80732 20690.74746 16010.97455 21054.34921 18944.6286 17771.52795 16854.25352 1.549206405 1.002646975 1.141714441 1.135310282 1.227627639 0.9499664 1.249200932 1.124026559 1.054423913 1 14.04082511 4.74744099 24.86491017 1.111565823 1.549206648 0.674004213 0.093665156 613.8752273 1718801.556 0.020776899 0.251882428 55903.75623 -4.74744099 0.437640825 T(ph)IS(ph)IFEERAHILY(ph)MS(ph)LEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TISIFEERAHILYMSLEK 18 1 Q9NUC0 Q9NUC0 SERTAD4 SERTA domain-containing protein 4 4 T(1)IS(1)IFEERAHILY(1)MS(1)LEK 49.593 0.062857 746480000 965560 177740 236500 187100 455130 739070 638150 275310 327150 95161 TRUE FALSE 1003681.054 208265.4624 242663.3843 224107.8216 377767.1652 567432.1932 588130.1355 271619.9198 315375.9354 113805.976 8.819229796 1.830004625 2.132255202 1.96920961 3.31939656 4.985961311 5.167831745 2.386692943 2.771172012 1 16.79621679 4.745631723 24.89305982 2.994496294 8.81923267 0.661650893 1.278393927 518.1404154 1824008.579 0.321804768 3.246616554 55671.34621 -4.745631723 5.824736376 T(ph)KFASDDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.62)KFAS(0.38)DDEHDEHDENGATGPVK 176.28 7.86E-13 760720000 720220 338780 442200 301470 732170 601000 660560 486810 529570 216340 TRUE FALSE 748654.8417 396962.8297 453724.0953 361099.8662 607716.0049 461426.8582 608783.5811 480285.1082 510510.8791 258727.6809 2.89360164 1.534288207 1.753674341 1.395675426 2.348863495 1.783446041 2.35298975 1.856334454 1.973159104 1 17.98107489 -0.093505066 1.902504722 0.999773325 1.963552775 0.331577427 0.419526339 121.6087814 206.6876473 0.499052022 0.104196146 0.806296796 0.093505066 0.96377945 T(ph)KSPTDDEVTPSAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.431)KS(0.427)PT(0.142)DDEVTPSAVVR;T(0.605)KS(0.265)PT(0.129)DDEVTPSAVVR 177.08 4.86E-09 4523900000 573670 323720 502690 326100 639810 600880 577130 497380 487560 294950 TRUE FALSE 596318.9346 379316.3918 515790.5144 390601.6067 531055.3247 461334.7264 531893.0426 490713.4346 470012.8108 352739.8053 1.690534852 1.075343316 1.462240741 1.107336345 1.505515728 1.30786126 1.507890617 1.391148453 1.332463203 1 18.42824486 0.798431926 4.505118771 1.000004614 1.373044489 0.294244875 0.175585915 3.367932546 74.36829545 0.150995285 0.038332142 6.286833026 -0.798431926 0.373039875 T(ph)KSSDDLLAGMAGGVTVTNGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKSSDDLLAGMAGGVTVTNGVK 22 1 Q69YQ0-2;Q69YQ0;F8WAN1;C9J8U1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 T(0.333)KS(0.333)S(0.333)DDLLAGMAGGVTVTNGVK 126.36 3.20E-05 23769000 40658 18340 31885 19147 41435 42719 34400 26993 36318 17746 TRUE FALSE 42263.20923 21489.75233 32715.94929 22934.21945 34391.8935 32798.15966 31703.63811 26631.20299 35010.92227 21222.98893 1.991388177 1.012569549 1.541533542 1.080630986 1.620501882 1.545407189 1.493834738 1.254828105 1.649669723 1 14.37334023 -1.161063834 4.230828897 0.999876531 1.4374877 0.199942345 0.274269021 0.000286902 5.69E-05 0.238518461 0.056203562 0.069013836 1.161063834 0.437611169 T(ph)LPWLLCLPFMVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLPWLLCLPFMVHR 14 0 A0A087WWZ6 A0A087WWZ6 PRDM11 1 T(1)LPWLLCLPFMVHR 62.378 0.052693 296970000 18134 273380 167370 235210 134970 269470 98686 199720 129640 331610 TRUE FALSE 18849.94432 320330.8884 171731.7997 281733.836 112027.8476 206889.6764 90950.73345 197043.0801 124974.2817 396582.6304 0.047530938 0.807727984 0.43302905 0.710403871 0.282482991 0.521681134 0.22933615 0.496852522 0.315127976 1 18.59726197 -1.294922766 4.368368721 1.000464963 0.440943845 0.391014085 0.213854448 0.00087407 0.00014108 0.18689295 0.044015471 0.050708088 1.294922766 -0.559521118 T(ph)LTEPSVDFNHSDDFTPISTVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.49)LT(0.49)EPS(0.019)VDFNHSDDFTPISTVQK 114.74 0.0023577 249450000 91016 72371 87238 70451 159910 140600 101280 96072 111970 82978 TRUE FALSE 94609.38196 84800.15628 89511.49395 84385.99752 132728.5553 107947.7808 93341.40895 94784.31198 107940.2216 99235.95039 0.953378101 0.854530601 0.902006718 0.850357126 1.337504753 1.087789056 0.940600746 0.95514087 1.087712882 1 16.59857524 T(ph)LTPPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.948)LT(0.052)PPLRR 114.39 0.0015615 680090000 251200 249520 248830 214050 327250 369810 278050 259850 242460 211220 TRUE FALSE 261117.57 292373.119 255314.7142 256388.4511 271624.1619 283927.232 256255.7145 256367.1358 233733.912 252604.5149 1.03370112 1.157434257 1.010729021 1.014979685 1.075294169 1.123999039 1.014454213 1.014895303 0.92529586 1 17.9465209 1.707110025 2.099963131 0.966952921 1.067335898 0.40642512 0.048463748 0.28396215 2.622612017 0.033520151 0.013677926 50.94599225 -1.707110025 0.100382977 T(ph)NSDSALHQSTMTPTQPESFSSGSQDVHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNSDSALHQSTMTPTQPESFSSGSQDVHQK 30 0 M0QXN6;M0QX46;Q6UUV9;Q6UUV9-2;Q6UUV9-3 M0QXN6 CRTC1 CREB-regulated transcription coactivator 1 1 T(0.606)NS(0.392)DS(0.002)ALHQSTMTPTQPESFSSGSQDVHQK 266.72 1.84E-58 283290000 21003 88760 98639 77360 114930 148330 98446 121510 98622 82778 TRUE FALSE 21832.21466 104003.8395 101209.6134 92661.5771 95394.23965 113882.6055 90729.54528 119881.3572 95072.61348 98996.76422 0.220534629 1.050578172 1.022352742 0.936006119 0.963609674 1.150366947 0.916490008 1.21096238 0.960360818 1 16.59509375 4.739332413 24.99272009 1.032548749 0.220534376 0.878738351 0.08941745 19.4851308 630866.0643 0.020920251 0.126049308 54869.67821 -4.739332413 -0.812014373 T(ph)NSIGHNPPHWGAERPFYNHLGGNQVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TNSIGHNPPHWGAERPFYNHLGGNQVSK 28 1 O95622;C9JRT8;B3KWA8;O95622-2 O95622 ADCY5 Adenylate cyclase type 5 1 T(0.5)NS(0.5)IGHNPPHWGAERPFYNHLGGNQVSK;T(0.5)NS(0.5)IGHNPPHWGAERPFYNHLGGNQVSK;T(0.573)NS(0.427)IGHNPPHWGAERPFYNHLGGNQVSK 103.1 0.00059973 1236410000 297842 274661 256483 283055 400470 459360 367290 293970 300719 248359 TRUE FALSE 309601.0321 321831.8902 263167.1577 339042.4342 332398.2524 352680.6017 338500.8501 290029.813 289896.1819 297020.1909 1.042356855 1.083535396 0.886024471 1.141479416 1.119109955 1.187396051 1.139656025 0.976464974 0.976015068 1 18.18020148 1.660375055 7.435762549 0.981928787 1.085004637 0.264817043 0.077283689 0.180656605 18.76983297 0.041501423 0.021333673 45.74830992 -1.660375055 0.10307585 T(ph)NSSDSERSPDLGHSTQIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 T(0.413)NS(0.286)S(0.286)DS(0.01)ERS(0.004)PDLGHSTQIPR 124 4.06E-05 182630000 48422 94448 88476 86653 119720 123800 76298 109980 98375 102900 TRUE FALSE 50333.73795 110668.7093 90781.75724 103792.7048 99370.03716 95049.32621 70317.56339 108505.898 94834.50297 123061.2849 0.40901359 0.899297528 0.73769551 0.843422892 0.807484151 0.772373914 0.571402805 0.881722453 0.770628253 1 16.90901744 -5 0.148960473 1.856788659 0.677599183 0.264848138 0.138171435 195.9909823 1.740501697 49.89191738 0.677122241 1.00E-05 5 -1.179189476 T(ph)PDRER ddPTM_MDA-MB-175_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 89.355 0.081256 231370000 256920 286530 285420 257650 306980 297210 297060 278630 278120 297150 TRUE FALSE 267063.4 335739.2986 292858.2797 308612.401 254799.6493 228187.4818 273775.661 274895.4206 268110.5155 355370.8532 0.751506201 0.944757556 0.824092007 0.868423502 0.716996475 0.642110853 0.770394247 0.773545208 0.754452745 1 18.43896583 5.088666343 13.64982586 0.797823664 0.000128785 0.016203711 0.101065113 1010835.593 3006162.71 0.024096983 23410943.25 122649.6585 -5.088666343 -0.797694879 T(ph)PDSTFSETFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPDSTFSETFK 11 0 Q9NZI5-3;Q9NZI5;B7Z1S6 Q9NZI5-3 GRHL1 Grainyhead-like protein 1 homolog 1 T(0.951)PDS(0.049)T(0.001)FSETFK;T(0.928)PDS(0.072)TFSETFK;T(0.997)PDS(0.003)TFSETFK 184.87 5.27E-05 1028750000 1474770 1203840 1486960 1352930 1759390 1963890 2017000 1555970 1697040 1074610 TRUE FALSE 1532995.058 1410590.155 1525711.399 1620535.516 1460329.516 1507806.311 1858902.27 1535114.767 1635963.862 1285159.255 1.19284443 1.0975995 1.187176915 1.260960857 1.136302377 1.17324472 1.44643729 1.194493804 1.272965865 1 20.29351572 4.001183894 21.68479176 1.227385372 1.144513438 0.043103929 0.109425191 17.88081371 327301.2579 0.026135131 0.055465538 10027.29736 -4.001183894 -0.082871934 T(ph)PDTIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 T(0.998)PDT(0.002)IRR 56.258 0.071897 310060000 282720 278110 268120 278640 345400 388320 274690 288800 281560 313050 TRUE FALSE 293882.0039 325873.2291 275107.4275 333754.1603 286689.0314 298138.565 253159.08 284929.1084 271426.7106 374386.1538 0.78497028 0.870420088 0.734822655 0.891470363 0.76575757 0.79633972 0.676197764 0.761056747 0.724991317 1 18.51416755 4.240932085 24.99982097 0.780747155 0.827695165 0.005718937 0.08999231 212.5287759 2240327.172 0.020685122 0.051383984 17415.3451 -4.240932085 0.04694801 T(ph)PDVDNPEQPFDALNIEECSLTQQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPDVDNPEQPFDALNIEECSLTQQNK 26 0 Q9Y485;F5H269 Q9Y485 DMXL1 DmX-like protein 1 1 T(1)PDVDNPEQPFDALNIEECSLTQQNK 147.41 7.02E-07 17568000 24318 17418 23303 23941 26602 30429 31354 23528 24331 11512 TRUE FALSE 25278.09342 20409.40601 23910.29532 28676.45834 22080.20154 23362.32591 28896.39155 23212.64564 23455.33206 13767.55599 1.836062511 1.482427674 1.736713135 2.08290116 1.603785128 1.696911632 2.098875906 1.686039676 1.703667091 1 13.74898486 0.553269559 1.913978106 1.000162067 1.779577998 0.618409145 0.18239914 1.940450594 7.550153471 0.17210083 0.047711065 3.574946603 -0.553269559 0.779415931 T(ph)PELPEPSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPELPEPSVK 10 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(1)PELPEPSVK;T(1)PELPEPSVK 150.46 0.00024078 414630000 773260 644670 716760 606600 967470 933300 798570 756070 807320 618580 TRUE FALSE 803788.9019 755387.0577 735439.3544 726583.6695 803019.795 716555.2193 735975.9967 745936.1183 778264.7109 739778.9076 1.086525844 1.021098398 0.994133986 0.982163268 1.0854862 0.968607258 0.994859395 1.008323042 1.052023386 1 19.49673464 4.723549534 3.776664161 1.010074703 1.093257484 0.326007106 0.032474059 0.272374852 7.535023606 0.007569087 0.061672239 52911.43427 -4.723549534 0.083182782 T(ph)PESFLGPNAALVDLDSLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPESFLGPNAALVDLDSLVSR 21 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.989)PES(0.011)FLGPNAALVDLDSLVSR;T(0.995)PES(0.005)FLGPNAALVDLDSLVSR;T(0.877)PES(0.123)FLGPNAALVDLDSLVSR 112.56 0.0024798 1598980000 76957 75757 82569 96872 81063 106107 113728 87366 80896 63013 TRUE FALSE 79995.32178 88767.67544 84720.81597 116032.9925 67283.94021 81465.25732 104813.7022 86195.00167 77984.56876 75359.19089 1.061520444 1.177927661 1.12422672 1.539732461 0.892843188 1.081026167 1.39085493 1.143788842 1.034838191 1 16.20149585 1.254411329 4.333557942 1.009931058 1.18446794 0.127134982 0.168578509 0.393882407 15.64047593 0.137041711 0.041344863 17.96434259 -1.254411329 0.174536882 T(ph)PESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.921)PES(0.079)FLGPNAALVDLDSLVSRPGPTPPGAK;T(1)PESFLGPNAALVDLDSLVSRPGPTPPGAK 166.01 4.68E-12 1593055000 103242 71454 85344 79678 107239 120643 96308 99274 98175 76857 TRUE FALSE 107318.0739 83725.66867 87568.13475 95438.07058 89010.55308 92625.49161 88759.12731 97943.39441 94641.70093 91915.65763 1.167571191 0.910896694 0.952700954 1.03832223 0.968393801 1.007722667 0.965658405 1.065578999 1.029658095 1 16.48802302 1.736784987 24.99999314 1.03669432 0.996608807 0.036051503 0.066596135 0.659957849 9027.058209 0.029082685 0.016127809 54.54877306 -1.736784987 -0.040085513 T(ph)PHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSR 33 1 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 T(0.297)PHY(0.226)GS(0.201)QT(0.201)PLHDGS(0.034)RT(0.034)PAQS(0.008)GAWDPNNPNTPSR 103.07 7.00E-06 122910000 16068 28906 25297 20212 26359 35393 17382 28007 21363 26728 TRUE FALSE 16702.37705 33870.38064 25956.2606 24209.87327 21878.5066 27173.51214 16019.55342 27631.61198 20594.1498 31964.83986 0.522523408 1.05961365 0.81202536 0.757390726 0.684455379 0.850106312 0.501161698 0.864437679 0.644275081 1 14.96419825 5.002596904 20.61143451 0.781093139 0.230054663 0.210948475 0.156569881 2848.139176 14925.08201 0.03398727 39560.55674 100599.7505 -5.002596904 -0.551038475 T(ph)PNGPNIDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPNGPNIDKK 10 1 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 1 T(1)PNGPNIDKK;T(1)PNGPNIDKK 69.602 0.033102 490460000 643470 293610 424560 342510 606190 610550 637330 468490 516160 252320 TRUE FALSE 668874.6925 344035.2335 435624.3824 410257.4557 503150.0403 468759.0155 587374.4092 462210.6578 497583.5024 301757.273 2.216598413 1.140105854 1.44362513 1.359561119 1.667399878 1.553430712 1.946512849 1.531729967 1.648952807 1 18.20302902 3.197881719 24.99884093 1.606663769 1.50452774 0 0.34088663 787.9723466 484238.521 0.092637434 0.110723979 1577.181662 -3.197881719 -0.102136029 T(ph)PPFSESEEQLHLHDAGMKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPFSESEEQLHLHDAGMKPR 21 1 Q8IVM0-2 Q8IVM0-2 CCDC50 Coiled-coil domain-containing protein 50 1 T(1)PPFSESEEQLHLHDAGMKPR 165.01 2.24E-11 557720000 241780 201930 264990 272080 294540 290130 348130 257670 270360 179280 TRUE FALSE 251325.6611 236609.9067 271895.8571 325896.6119 244474.196 222751.7045 320842.6609 254216.3551 260629.7964 214406.4835 1.17219245 1.103557611 1.268132627 1.519994203 1.140236956 1.038922428 1.496422383 1.185674757 1.215587291 1 17.70998901 0.666477259 2.081164263 1.000198195 1.245357745 0.188828862 0.148802197 2.924440676 15.99941958 0.141736165 0.038852528 4.63956495 -0.666477259 0.24515955 T(ph)PPKSYSTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPKSYSTAR 10 1 Q05519-2;Q05519;Q5T757;Q5T760 Q05519-2;Q5T760 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.992)PPKS(0.008)YSTAR 76.01 0.060271 295900000 397610 350740 435950 356130 453990 479900 490900 401400 419340 332430 TRUE FALSE 413307.9498 410976.8666 447311.2151 426571.4511 376820.942 368450.498 452421.9753 396019.8896 404248.0353 397563.2937 1.039602892 1.033739465 1.125132079 1.072964878 0.947826291 0.926771922 1.13798729 0.99611784 1.016814283 1 18.60082504 3.305053016 24.9998326 1.009117478 1.069513915 0.225972412 0.057215364 94.32966891 35464.64792 0.016395248 0.022199265 2018.61277 -3.305053016 0.060396437 T(ph)PPRDLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(1)PPRDLPTIPGVTSPSSDEPPMEAS(0.528)QS(0.31)HLRNS(0.162)PEDKR 161.98 7.94E-18 681880000 70774 87440 100590 82588 116950 134000 118210 119030 105730 84164 TRUE FALSE 73568.21217 102457.1398 103211.458 98923.6599 97070.88077 102880.5308 108944.3913 117434.5975 101924.798 100654.3244 0.730899667 1.017910959 1.025405105 0.982805861 0.964398513 1.022117345 1.082361756 1.166711895 1.012622146 1 16.61904963 5.232866396 1.552566994 1.045776342 6.10E-11 0.714037527 0.056127936 2.720165474 2.134721934 0.017608862 6.343751329 170948.9335 -5.232866396 -1.045776342 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 TPPRDLPTIPGVTSPSSDEPPMEASQSHLR 30 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.996)PPRDLPT(0.004)IPGVTSPSSDEPPMEASQSHLR;T(0.969)PPRDLPT(0.031)IPGVTSPSSDEPPMEASQSHLR;T(1)PPRDLPTIPGVTSPSSDEPPMEASQSHLR;T(0.995)PPRDLPT(0.005)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.951)PPRDLPT(0.049)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.999)PPRDLPT(0.001)IPGVTSPSSDEPPMEASQSHLR;T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEASQSHLR 162.8 5.51E-12 11845120000 309696.2 544518.2 507524.3 564845.9 500842.7 616981.3 571497 499769.3 458372.8 508067.4 TRUE FALSE 321923.2451 638034.9651 520750.8002 676570.7331 415709.6368 473696.7435 526701.5718 493070.71 441876.0525 607613.4795 0.529815838 1.050067167 0.85704287 1.113488683 0.684167897 0.779602098 0.866836549 0.811487445 0.727232142 1 19.21279435 T(ph)PPRDLPTIPGVTSPSSDEPPMEASQSHLRNS(ph)PEDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKR 37 3 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 T(0.998)PPRDLPT(0.002)IPGVTSPSSDEPPMEAS(0.123)QS(0.323)HLRNS(0.554)PEDKR 184.13 2.29E-23 147650000 15189 17237 18143 14840 28066 30243 27990 21646 22730 15488 TRUE FALSE 15788.67345 20197.32066 18615.82148 17775.30771 23295.35134 23219.52159 25796.07066 21355.87078 21911.95174 18522.57706 0.852401553 1.090416339 1.005034095 0.959656296 1.257673339 1.253579429 1.392682593 1.152964337 1.182986129 1 14.17699722 3.239375246 24.99999587 1.224757818 0.986998204 0.514305772 0.108357083 16.54331157 507683.3861 0.029554009 0.037780156 1735.302716 -3.239375246 -0.237759614 T(ph)PPRWAEDQNSLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPPRWAEDQNSLLK 14 1 P49792;J3KNE0;A6NKT7;Q7Z3J3 P49792 RANBP2;RGPD3;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4 1 T(1)PPRWAEDQNSLLK;T(1)PPRWAEDQNSLLK 107.98 0.0013781 373970000 228505 224473 203414 208825 262380 282358 239640 232992 238896 195706 TRUE FALSE 237526.5538 263024.4916 208715.1359 250129.9617 217780.7413 216784.6337 220856.3906 229869.1233 230298.1796 234050.8437 1.014850236 1.123792111 0.891751265 1.068699253 0.930484752 0.926228807 0.943625697 0.982133282 0.983966458 1 17.83646244 3.228471406 24.99961142 0.958923525 1.022344431 0.219150476 0.058750319 312.2390299 773681.9635 0.016469846 0.019898749 1692.27682 -3.228471406 0.063420905 T(ph)PPVPDSGSANGSFFAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPPVPDSGSANGSFFAPSR 19 0 Q9NPA3 Q9NPA3 MID1IP1 Mid1-interacting protein 1 1 T(1)PPVPDSGSANGSFFAPSR;T(0.998)PPVPDS(0.002)GSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR;T(1)PPVPDSGSANGSFFAPSR 173.49 7.06E-11 1840572000 20864.2 21996.6 27096.9 27402.5 36498.5 28629.9 30268.5 19531.9 22963.5 25923.3 TRUE FALSE 21687.93473 25774.34494 27803.06747 32822.63271 30294.49801 21981.03962 27895.97588 19270.10683 22137.04812 31002.4743 0.699554962 0.831364126 0.896801565 1.058710101 0.977163878 0.709009204 0.899798371 0.621566738 0.714041334 1 14.92009574 2.732263308 24.9398985 0.763158963 0.898758872 0.117564584 0.132709055 843.2293391 3339520.329 0.043457425 0.041901806 539.8378206 -2.732263308 0.135599909 T(ph)PRPSVDNVHHNPPTIELLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPRPSVDNVHHNPPTIELLHR 21 1 P41212 P41212 ETV6 Transcription factor ETV6 1 T(1)PRPSVDNVHHNPPTIELLHR 117.37 5.98E-05 86758000 37308 35420 32783 30157 34407 41826 27131 36720 28658 27618 TRUE FALSE 38780.94865 41503.10947 33637.35191 36121.96459 28558.51043 32112.54538 25004.40133 36227.82846 27626.60418 33029.21832 1.174140674 1.256557423 1.018411989 1.093636678 0.864643848 0.972246605 0.757038846 1.096841836 0.836429246 1 15.01145521 3.882376273 1.299976773 0.931479377 1.223556142 0.525160329 0.101980007 0.380021445 1.179829212 0.030076989 0.097306505 7627.395619 -3.882376273 0.292076765 T(ph)PRT(ph)PQLK ddPTM_MDA-MB-175_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 111.63 0.015739 603620000 1299860 1089110 1396610 1007480 1779710 1910790 1479370 1559710 1694690 1356270 TRUE FALSE 1351179.477 1276156.17 1433006.804 1206756.537 1477195.53 1467037.981 1363413.114 1538804.639 1633698.438 1622005.139 0.83303033 0.786776897 0.883478584 0.743990576 0.910721855 0.904459515 0.840572623 0.948705156 1.007209163 1 20.62934696 1.80921046 0.66217375 1.015660675 0.818976004 0.652473512 0.048418823 0.418596341 0.369876895 0.043393032 0.023150357 64.44815071 -1.80921046 -0.196684671 T(ph)PRTPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.946)PRT(0.054)PQLK;T(0.647)PRT(0.353)PQLK 74.841 0.064561 3219900000 566490 616690 619000 455660 795680 752050 553580 587790 585370 744770 TRUE FALSE 588855.4626 722601.7103 635131.6485 545788.188 660430.5978 577397.7849 510188.9531 579911.6365 564302.648 890693.422 0.661120255 0.811279945 0.71307549 0.612767732 0.741479146 0.648256483 0.572799732 0.651078836 0.633554301 1 19.76456941 -1.031424172 5.275769029 1.000002555 0.67083309 0.698486555 0.06470449 2.04E-06 3.74E-07 0.065639913 0.015471356 0.093019891 1.031424172 -0.329169465 T(ph)PRTPRT(ph)PQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPRTPRTPQLK 11 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 T(0.834)PRT(0.166)PRT(1)PQLK;T(0.758)PRT(0.242)PRT(0.999)PQLK;T(0.993)PRT(0.008)PRT(0.999)PQLK;T(0.933)PRT(0.069)PRT(0.998)PQLK;T(0.817)PRT(0.185)PRT(0.998)PQLK 108.14 0.0033323 2594460000 1931220 1614240 2217980 1358140 2963440 2869800 2070090 2280260 2681140 2269540 TRUE FALSE 2007466.057 1891473.163 2275782.381 1626776.038 2459715.527 2203332.442 1907830.937 2249696.844 2584646.295 2714212.91 0.739612596 0.696877226 0.83846863 0.599354617 0.906235291 0.811775832 0.702903936 0.828857912 0.952263651 1 21.37210246 1.283531563 2.489028659 0.996408464 0.75906879 0.542249932 0.080140459 0.204605442 2.102829332 0.069094567 0.020210808 19.21018569 -1.283531563 -0.237339673 T(ph)PS(ph)PESHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPSPESHR 8 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(0.999)PS(0.94)PES(0.06)HR;T(0.97)PS(0.659)PES(0.371)HR;T(1)PS(1)PESHR;T(1)PS(1)PESHR 114.4 0.014129 1314700000 928320 1016609 902490 1027017 966155 1120551 1044941 931816 886982 851927 TRUE FALSE 964970.7904 1191203.688 926009.6308 1230157.897 801928.3182 860320.0124 963035.794 919326.5307 855059.6911 1018845.785 0.947121542 1.169169766 0.908881054 1.207403432 0.787094897 0.844406509 0.945222337 0.902321573 0.839243489 1 19.95850427 3.227160066 24.99997383 0.8851323 1.055412751 0.415092344 0.099858413 200.0799285 438749.4312 0.026677859 0.032151613 1687.174747 -3.227160066 0.170280451 T(ph)PS(ph)PESHRS(ph)PAEGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 3 T(0.998)PS(0.904)PES(0.106)HRS(0.972)PAEGS(0.02)ER 118.22 0.00024198 405720000 102510 120700 120210 109440 126530 144940 110800 111790 124120 117340 TRUE FALSE 106557.174 141429.2861 123342.7714 131086.9054 105022.4758 111279.8816 102115.2065 110291.6379 119652.9454 140330.5264 0.759329967 1.007829798 0.878944692 0.934129649 0.748393657 0.792984139 0.727676359 0.785941881 0.85265087 1 17.09846935 3.24474431 24.99986608 0.798740639 0.901962637 0.123417778 0.091820496 211.9736455 856976.0002 0.023798826 0.031428231 1756.888944 -3.24474431 0.103221997 T(ph)PSPAAEDAREPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.796)PS(0.204)PAAEDAREPEAK 129.11 0.00010976 1053200000 999520 566930 862630 683150 1026700 1217800 1262700 830580 1019100 524790 TRUE FALSE 1038981.821 664295.8174 885110.8465 818275.031 852181.9007 934984.4059 1163726.275 819447.4337 982422.7901 627612.5528 1.655450989 1.058448902 1.410282255 1.303790097 1.357815259 1.489747778 1.85421128 1.305658133 1.565333239 1 19.25951468 2.771653431 5.89779139 1.482888078 1.339670672 0.015025196 0.243840513 0.537604606 57.71412647 0.071124181 0.074089362 591.0897541 -2.771653431 -0.143217406 T(ph)PSPEPVDKDFYSEFGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPEPVDKDFYSEFGNK 18 1 Q9Y2I1;Q9Y2I1-2 Q9Y2I1 NISCH Nischarin 1 T(0.5)PS(0.5)PEPVDKDFYSEFGNK 59.469 0.055171 0 152870 90704 126810 85587 167820 157510 165810 127070 139200 68530 TRUE FALSE 158905.4256 106281.7064 130114.7728 102515.8531 139294.0163 120930.6896 152813.3789 125366.8345 134190.2192 81957.14141 1.938884433 1.296796162 1.587595303 1.250847106 1.699595837 1.475535719 1.864552329 1.529663338 1.63732186 1 16.32258204 -1.062968811 4.733796179 0.999978841 1.577048145 0.418224467 0.207326949 4.25E-05 8.41E-06 0.184308485 0.043440336 0.086503004 1.062968811 0.577069304 T(ph)PSPES(ph)HRS(ph)PAEGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 3 T(0.991)PS(0.616)PES(0.707)HRS(0.618)PAEGS(0.069)ER 62.589 0.06331 322990000 96887 105790 99689 96850 112590 128460 111170 99559 102810 99166 TRUE FALSE 100712.1736 123958.6096 102286.9772 116006.6409 93451.99202 98627.11183 102456.2049 98224.57445 99109.88818 118595.6791 0.849206096 1.045220286 0.862484857 0.978169204 0.787988169 0.831624833 0.863911786 0.828230634 0.835695609 1 16.85569192 3.245565395 24.99994347 0.847291916 0.936639032 0.193779013 0.073833733 212.2379097 757468.746 0.018736662 0.02483628 1760.213691 -3.245565395 0.089347116 T(ph)PSPES(ph)HRSPAEGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPESHRSPAEGSER 16 1 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 2 T(0.995)PS(0.012)PES(0.973)HRS(0.02)PAEGSER 79.942 0.038833 294340000 58367 274490 221720 239340 272170 305770 175550 254680 199410 323150 TRUE FALSE 60671.37423 321631.5223 227498.2053 286680.7376 225906.6406 234759.5515 161789.9323 251266.4312 192233.2731 386465.0554 0.156990583 0.832239598 0.588664362 0.741802483 0.584546099 0.607453502 0.418640521 0.650165979 0.497414373 1 18.55997844 -1.099807782 4.301751709 1.000047981 0.578939842 0.354937609 0.175237167 21867013.59 5590635.167 11579.78312 0.03719845 0.079467988 1.099807782 -0.421108139 T(ph)PTDPGLDSALEPSGDPHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPTDPGLDSALEPSGDPHGK 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.973)PT(0.027)DPGLDSALEPSGDPHGK;T(0.979)PT(0.021)DPGLDSALEPSGDPHGK 217.39 3.90E-24 335490000 447270 334590 435710 411900 509560 564100 643710 498760 499270 352250 TRUE FALSE 464928.565 392053.2298 447064.9605 493372.5906 422945.1732 433096.324 593254.3282 492074.938 481301.3702 421266.6433 1.103644384 0.93065339 1.061239877 1.171164626 1.003984483 1.028081219 1.408263241 1.168084267 1.142510042 1 18.68437416 T(ph)PTPEPAEVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.932)PT(0.068)PEPAEVETR 146.36 0.00072291 333520000 129830 143650 150790 140030 148930 174320 160550 128530 139100 130160 TRUE FALSE 134955.7887 168320.7701 154719.7113 167727.5161 123614.9318 133836.8218 147965.6715 126807.2656 134093.8182 155662.3599 0.866977661 1.08131966 0.993944274 1.077508501 0.794122175 0.859789238 0.950555237 0.81463024 0.861440224 1 17.24806061 3.240836112 24.99999261 0.871082229 1.009608157 0.370412538 0.07912508 56.0215447 615480.5363 0.021018873 0.027137421 1741.149698 -3.240836112 0.138525928 T(ph)PTQPPPEPGDLPTIEEALQIIHSAEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPTQPPPEPGDLPTIEEALQIIHSAEPR 28 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 T(0.952)PT(0.048)QPPPEPGDLPTIEEALQIIHSAEPR;T(0.935)PT(0.065)QPPPEPGDLPTIEEALQIIHSAEPR 78.694 0.025078 85566000 16090.9 13555.1 17113.3 17794.3 17130.9 17689 19471.4 20255 17211.1 15112.4 TRUE FALSE 16726.18116 15883.08298 17559.28666 21313.95943 14218.99574 13580.99783 17945.18079 19983.51486 16591.67587 18073.38544 0.925459218 0.878810616 0.971554926 1.179300884 0.786736707 0.751436297 0.99290644 1.105687417 0.918017044 1 14.14157915 2.013620149 24.89022641 1.027057676 0.918360077 0.115691918 0.116844866 430.5504062 786808.5916 0.046368279 0.034229194 103.1858507 -2.013620149 -0.108697599 T(ph)PVDRDT(ph)EDGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPVDRDTEDGLK 12 1 Q9NVR0 Q9NVR0 KLHL11 Kelch-like protein 11 2 T(1)PVDRDT(1)EDGLK 91.087 0.027448 296230000 47475 662670 522340 622430 512120 731930 443370 535270 530400 741240 TRUE FALSE 49349.34966 776478.4176 535952.6095 745544.7962 425070.0253 561950.35 408617.5009 528095.5812 511311.0076 886471.7861 0.055669397 0.875920057 0.604590713 0.841024845 0.479507675 0.633917919 0.460948117 0.595727455 0.576793323 1 19.75771519 -2.184488726 1.925361429 1.944978929 0.582999932 0.264568384 0.214318261 3566478.567 683129.2747 14666513.03 0.050590735 0.006538999 2.184488726 -1.361978997 T(ph)PVS(ph)PVKFSPGDFWGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPVSPVKFSPGDFWGR 16 1 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 2 T(1)PVS(1)PVKFSPGDFWGR;T(1)PVS(1)PVKFSPGDFWGR 116.21 0.0010201 161375000 238560 177882 205350 179591 280160 290280 271320 225240 237720 172608 TRUE FALSE 247978.533 208431.8498 210701.5897 215113.5638 232538.5033 222866.8692 250053.2294 222221.0262 229164.5036 206427.2328 1.201287881 1.00971101 1.020706361 1.042079385 1.126491404 1.079638894 1.211338378 1.076510222 1.110146663 1 17.65527378 3.237570888 24.99965897 1.109104488 1.060840804 0.036238465 0.069922787 63.11525633 1594237.112 0.019051464 0.02404745 1728.108028 -3.237570888 -0.048263683 T(ph)QTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 T(0.501)QT(0.501)PPVS(0.999)PAPQPTEERLPS(0.549)S(0.445)PVY(0.006)EDAASFK 228.42 4.62E-35 166210000 118040 87850 95743 77012 151200 161510 144310 144440 129820 73550 TRUE FALSE 122700.3103 102937.5541 98238.14123 92244.74374 125499.078 124001.7502 132998.6051 142504.0181 125147.8036 87960.7143 1.394944451 1.170267374 1.116841104 1.048703896 1.426762834 1.409740146 1.512022795 1.620087094 1.422769296 1 16.4245717 3.156922712 7.513294254 1.451777073 1.177674437 0.236622569 0.175101577 0.250857325 19.72164362 0.049570856 0.059477922 1435.233993 -3.156922712 -0.274102636 T(ph)QTPPVS(ph)PAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 3 T(0.499)QT(0.503)PPVS(0.998)PAPQPT(0.001)EERLPS(0.256)S(0.716)PVY(0.027)EDAASFK 127.09 1.23E-05 139440000 66415 46167 47639 45461 84643 100480 91689 69749 70224 46783 TRUE FALSE 69037.11548 54095.82312 48880.51148 54453.05011 70255.41309 77145.04279 84502.1766 68814.12874 67696.65196 55949.23314 1.233924249 0.966873362 0.873658292 0.973258203 1.255699304 1.378840039 1.510336637 1.22993873 1.209965681 1 15.77183074 3.191841366 5.441931921 1.296924429 0.998434605 0.393276981 0.150292878 0.168212449 11.24445351 0.043576945 0.05343528 1555.397391 -3.191841366 -0.298489824 T(ph)RSDGDAGSLGAFPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRSDGDAGSLGAFPSR 16 1 E7ESL9 E7ESL9 AGAP3 1 T(0.5)RS(0.5)DGDAGSLGAFPSR 97.69 0.0048303 54146000 21093 23266 23424 24293 32142 36018 25856 23455 26707 25805 TRUE FALSE 21925.76793 27261.75452 24034.44868 29098.08289 26678.51432 27653.36536 23829.33916 23140.62409 25745.82029 30860.99568 0.710468585 0.883372487 0.77879693 0.9428757 0.864473544 0.896061995 0.772150692 0.749834008 0.834251122 1 14.91349699 -2.502032276 2.027321012 2.824699429 0.82486796 0.36403607 0.069059977 5253608.169 311522.343 44104725.29 0.017287894 0.003147514 2.502032276 -1.99983147 T(ph)RSLDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRSLDFR 7 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 T(0.579)RS(0.421)LDFR 107.79 0.011962 189520000 127560 130860 158970 138330 207200 230960 175990 181550 182490 151510 TRUE FALSE 132596.1673 153334.1871 163112.8888 165691.2611 171980.218 177323.0402 162195.4439 179116.6192 175922.2205 181195.4837 0.731785167 0.846236252 0.900203943 0.914433725 0.949141858 0.978628367 0.895140655 0.988526952 0.970897381 1 17.46718747 5.916448479 0.554581815 0.967983728 1.85E-14 0.883647595 0.026381588 3.927396685 0.337638958 0.012265108 3.271216984 824989.6103 -5.916448479 -0.967983728 T(ph)RSNPEGAEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.514)RS(0.486)NPEGAEDR 190.44 3.67E-06 204440000 109480 111450 119660 111790 161300 181080 151710 134420 129580 117400 TRUE FALSE 113802.3549 130590.6705 122778.4379 133901.7283 133882.2836 139026.9143 139818.5738 132618.3198 124916.4411 140402.2822 0.810544908 0.930117862 0.874476084 0.953700511 0.953562018 0.990204091 0.9958426 0.944559573 0.889703779 1 17.09920686 6.241493112 0.617487811 0.962542358 2.21E-15 0.589750357 0.036784555 13.70410261 0.913887751 0.015498613 14.10642997 1743785.699 -6.241493112 -0.962542358 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.474)RS(0.474)PDVIS(0.013)S(0.013)AS(0.013)T(0.013)ALSQDIPEIASEALSR;T(0.5)RS(0.5)PDVISSASTALSQDIPEIASEALSR;T(0.489)RS(0.489)PDVIS(0.005)S(0.005)AS(0.005)T(0.005)ALSQDIPEIASEALSR;T(0.487)RS(0.487)PDVIS(0.007)S(0.007)AS(0.007)T(0.007)ALSQDIPEIASEALSR;T(0.481)RS(0.481)PDVIS(0.008)S(0.008)AS(0.01)T(0.01)ALSQDIPEIASEALSR;T(0.597)RS(0.402)PDVISSASTALSQDIPEIASEALSR;T(0.341)RS(0.341)PDVIS(0.073)S(0.073)AS(0.087)T(0.087)ALSQDIPEIASEALSR;T(0.297)RS(0.297)PDVIS(0.112)S(0.112)AS(0.151)T(0.031)ALSQDIPEIASEALSR 170.44 6.12E-12 19382998000 210444.1 230445.7 234046.9 217693.7 291391.4 306975.4 279513 242398.6 233071.5 206445.7 TRUE FALSE 218752.5956 270022.9564 240146.3545 260752.8641 241860.7939 235685.0156 257604.0407 239149.6433 224683.3022 246894.7823 0.886015466 1.093676237 0.972666787 1.056129505 0.979610795 0.954596988 1.043375799 0.968629799 0.910036657 1 17.91353682 1.522183237 7.262534561 0.950023276 1.000873151 0.083550742 0.05844465 0.24011089 25.20511144 0.029435147 0.013546612 33.27999385 -1.522183237 0.050849875 T(ph)RSYDNLTTACDNTVPLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.5)RS(0.5)YDNLTTACDNTVPLASR;T(0.662)RS(0.338)YDNLTTACDNTVPLASR;T(0.643)RS(0.357)YDNLTTACDNTVPLASR 219.94 1.43E-24 1186000000 285412 321579 331874 322533 434445 497534 325789 387109 386579 352023 TRUE FALSE 296680.2861 376807.6917 340522.9091 386329.0647 360598.1941 381989.2687 300252.8069 381920.437 372666.0973 420995.167 0.704711858 0.895040422 0.8088523 0.917656769 0.85653761 0.907348347 0.713197752 0.907184849 0.885202792 1 18.68344415 -5 0.172919752 1.609061269 0.811448386 0.330027959 0.072079417 160.6545853 1.525959648 33.51532384 0.236998071 1.00E-05 5 -0.797612884 T(ph)RTPASINATPANINLADLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.643)RT(0.356)PAS(0.001)INATPANINLADLTR;T(0.5)RT(0.5)PASINATPANINLADLTR 196.68 1.54E-21 1284420000 329220 354620 415970 361380 452430 537010 450480 444220 398490 381250 TRUE FALSE 342217.8598 415523.2264 426810.5199 432859.8854 375526.1102 412297.566 415170.2005 438265.9575 384148.4227 455948.638 0.750562303 0.911337795 0.93609342 0.949361067 0.82361494 0.904263181 0.910563528 0.961217824 0.84252565 1 18.79851179 7.999999921 0.019192095 1.613786872 1.57E-06 0.272179715 0.059842756 4877.498718 7.215189825 227.60259 401.9459371 99999981.86 -7.999999921 -1.613785297 T(ph)SNRYSPESQAQSVHHQRPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.299)S(0.299)NRY(0.103)S(0.299)PES(0.001)QAQSVHHQRPGSR 91.767 0.0021861 58123000 7857.4 18213 17896 19455 21522 26428 15991 20798 18651 17511 TRUE FALSE 8167.616219 21340.94107 18362.38446 23303.14093 17863.69813 20290.49752 14737.58364 20519.23683 17979.75415 20941.94518 0.390012301 1.019052475 0.876823251 1.112749591 0.853010452 0.968892686 0.703735184 0.97981523 0.85855225 1 14.35410783 4.744804691 24.85593288 0.92454442 0.390012042 0.694239223 0.10750547 348.1254796 1385749.962 0.024108816 0.224151203 55565.43152 -4.744804691 -0.534532377 T(ph)SPADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPADHGGSVGSESGGSAVDSVAGEHSVSGR 31 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR;T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR;T(0.5)S(0.5)PADHGGSVGSESGGSAVDSVAGEHSVSGR 270.46 2.87E-71 817790000 55126.9 71820 80915 77510 85469 112383 84527.1 71550 67775 49240 TRUE FALSE 57303.35258 84154.52632 83023.71137 92841.24666 70941.00991 86283.75143 77901.64503 70590.98928 65335.79099 58887.63524 0.973096514 1.429069549 1.409866622 1.576583034 1.204684305 1.465226971 1.322886285 1.198740432 1.109499315 1 15.84567712 1.383463185 1.506123658 1.013770776 1.357565641 0.35893821 0.155236831 0.38042417 1.606048399 0.136154954 0.043078405 24.1803835 -1.383463185 0.343794865 T(ph)SPDPSPVSAAPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPDPSPVSAAPSK 14 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 T(0.648)S(0.352)PDPSPVSAAPSK;T(0.5)S(0.5)PDPSPVSAAPSK 209.11 7.93E-08 516400000 630340 412885 512042 376453 702408 723993 679099 539306 552811 347222 TRUE FALSE 655226.3099 483794.787 525386.2352 450914.2798 583012.9391 555856.598 625869.4459 532077.4852 532915.4401 415253.5029 1.57789472 1.165058894 1.265218069 1.085877125 1.403992826 1.338595807 1.507198474 1.28133172 1.283349656 1 18.66363281 0.655072223 2.239045599 1.000106702 1.321906795 0.332629314 0.138520943 2.492090775 14.67238914 0.129635929 0.035141706 4.519310939 -0.655072223 0.321800093 T(ph)SPDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.872)S(0.128)PDTLRR;T(0.961)S(0.039)PDTLRR;T(0.983)S(0.017)PDTLRR;T(0.766)S(0.234)PDTLRR 153.1 0.00026162 17105550000 5280000 4884470 5403340 4627560 6449720 7391140 6079750 5393640 5273270 3907870 TRUE FALSE 5488458.477 5723339.727 5544155.479 5542877.556 5353398.898 5674659.749 5603203.309 5321347.078 5083486.043 4673542.306 1.174367989 1.224625638 1.186285502 1.186012064 1.145469228 1.21420956 1.198919993 1.138611086 1.08771585 1 22.15608502 1.104824004 1.426633901 1.001560012 1.190559787 0.889575551 0.021408549 0.115410233 0.469544753 0.020089729 0.006068737 12.72987104 -1.104824004 0.188999775 T(ph)SPENVQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.839)S(0.161)PENVQDR 123.2 0.0063097 200180000 233390 222190 243270 219500 277940 358310 302810 283800 239840 180450 TRUE FALSE 242604.4174 260349.4041 249609.816 262916.4449 230695.8581 275097.9327 279074.961 279996.1252 231208.2053 215805.7226 1.124179723 1.206406396 1.156641321 1.218301543 1.068997871 1.27474809 1.293176833 1.297445322 1.071371984 1 17.7193736 2.711409924 24.97842064 1.221866948 1.161384952 0 0.100337343 1995.911536 1836220.196 0.031394466 0.029605146 514.5290791 -2.711409924 -0.060481996 T(ph)SPGGRT(ph)SPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPGGRTSPEAR 12 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 2 T(0.833)S(0.168)PGGRT(0.766)S(0.233)PEAR;T(0.882)S(0.118)PGGRT(0.628)S(0.372)PEAR 112.96 0.003932 251081000 384370 371420 397490 328060 509440 582130 440450 425380 420130 334160 TRUE FALSE 399545.2244 435208.4958 407848.9159 392949.2888 422845.5708 446939.1298 405926.3781 419678.4769 405009.6034 399632.2541 0.999782225 1.089022448 1.020560557 0.983277212 1.058086694 1.11837602 1.01574979 1.050161674 1.013455744 1 18.6083135 5.082671475 16.79265817 1.040672432 3.42E-05 0.079248893 0.03934934 13059610.2 30779987.44 0.009286112 498984181.6 120968.2713 -5.082671475 -1.040638212 T(ph)SPINEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPINEDIR 9 0 Q9P2R6;A0A590UJ84;B1AKN3;Q9P2R6-2;D6RA28 Q9P2R6 RERE Arginine-glutamic acid dipeptide repeats protein 1 T(0.872)S(0.128)PINEDIR 117.25 0.013212 219200000 144130 161480 202840 198300 221540 279560 238950 194760 184470 130060 TRUE FALSE 149820.3637 189212.9339 208126.177 237523.1481 183882.7099 214636.4268 220220.4746 192149.5608 177830.9607 155542.7669 0.963210098 1.21646887 1.338064002 1.527060068 1.182200328 1.379919048 1.41581945 1.235348738 1.143293027 1 17.24695178 -1.70069557 2.592352654 0.953206419 1.279443454 0.216006069 0.150781613 15513944.83 12700071.04 4744168.497 0.038791483 0.019920692 1.70069557 0.326237035 T(ph)SPINLGLNVNDLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.5)S(0.5)PINLGLNVNDLLK;T(0.5)S(0.5)PINLGLNVNDLLK 207.53 3.74E-08 759663000 2136950 1211313 1746234 1109874 2371190 2389190 2172850 1638820 1925100 1044065 TRUE FALSE 2221318.436 1419346.585 1791742.293 1329403.765 1968135.971 1834336.831 2002536.339 1616854.298 1855816.027 1248629.547 1.779005183 1.136723529 1.434967078 1.064690298 1.576236904 1.469080109 1.603787404 1.294903122 1.486282326 1 20.25191408 -1.391188042 5.123703741 0.999686388 1.412824019 0.280027433 0.20436353 0.000677177 8.05E-05 0.183024738 0.043107195 0.040626738 1.391188042 0.413137631 T(ph)SPKPAVVETVTTAKPQQIQALMDEVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPKPAVVETVTTAKPQQIQALMDEVTK 28 2 P56192;H0YIP0;H0YI94 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK;T(0.5)S(0.5)PKPAVVETVTTAKPQQIQALMDEVTK 135.01 0.00056607 3499400000 665710 201038 344690 192617 580920 506030 495810 277530 393130 118129 TRUE FALSE 691992.7448 235564.7126 353672.9046 230716.0677 482175.4259 388512.2015 456947.1166 273810.1643 378981.3281 141274.1158 4.898227398 1.667430097 2.503451552 1.633109267 3.413048619 2.750059338 3.234471608 1.938148136 2.682595646 1 17.10813763 -1.233525803 0.319046461 9.27E-10 2.836383083 0.260030142 0.909508683 25.35229429 1.837945716 23.0039649 0.836540382 0.05840825 1.233525803 2.836383083 T(ph)SPPCS(ph)PANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.733)S(0.267)PPCS(1)PANLSR 106.14 0.010367 467090000 401520 358170 379750 421820 464130 637660 455680 442780 446750 265150 TRUE FALSE 417372.3196 419682.9113 389646.597 505254.737 385237.3484 489573.1288 419962.6109 436845.2583 430671.5548 317101.0659 1.316212289 1.323498898 1.228777317 1.59335553 1.214872449 1.543902501 1.32438095 1.377621539 1.35815234 1 18.2745832 -0.562685934 8.447741548 1.000000136 1.366037594 0.476772845 0.114553218 0 0 0.099988462 0.023567506 0.273724749 0.562685934 0.366037458 T(ph)SPPCSPANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.608)S(0.392)PPCSPANLSR 136.93 0.0011309 1278000000 501110 469540 541280 482430 652830 820180 709340 561340 519870 353710 TRUE FALSE 520894.2097 550179.8425 555386.2015 577853.2141 541862.1898 629705.6249 653740.0773 553816.1555 501159.9803 423012.7023 1.231391414 1.30062251 1.312930317 1.366042227 1.280959619 1.488621078 1.545438408 1.309218736 1.18473979 1 18.69034146 1.033884058 2.498135203 1.00389646 1.362447717 0.611228173 0.090086 0.183020739 2.472615957 0.091720423 0.02490489 10.81145283 -1.033884058 0.358551257 T(ph)SPPLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.828)S(0.172)PPLLDR;T(0.545)S(0.455)PPLLDR;T(0.956)S(0.044)PPLLDR;T(0.638)S(0.362)PPLLDR;T(0.97)S(0.03)PPLLDR;T(0.841)S(0.159)PPLLDR 170.85 0.0032731 19426690000 6696810 5926440 6782440 6443440 8144540 9781780 8275780 7188310 6820070 4717210 TRUE FALSE 6961205.23 6944259.969 6959195.958 7717933.2 6760134 7510109.839 7627102.739 7091962.462 6574617.013 5641456.983 1.233937483 1.23093378 1.233581321 1.368074457 1.198295763 1.33123586 1.351973925 1.257115402 1.165411175 1 22.42763638 -1.026860242 5.392295083 0.999998485 1.267904113 0.607176992 0.063464836 1.13E-06 2.04E-07 0.06015762 0.014179207 0.094002577 1.026860242 0.267905628 T(ph)SPQVLGSILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.632)S(0.368)PQVLGSILK 207.97 2.36E-07 109010000 640150 412220 555150 453860 821570 729970 716810 560780 612030 379570 TRUE FALSE 665423.6163 483015.5784 569617.6651 543632.1534 681919.8249 560445.5303 660624.5592 553263.6614 590003.1599 453939.4742 1.465886212 1.064052822 1.254831751 1.197587309 1.502226318 1.234626117 1.455314192 1.218804913 1.299739708 1 18.79214042 0.081383695 1.352905664 0.999578775 1.295246633 0.31871396 0.131075484 14.30472979 19.56985173 0.133991475 0.034809963 1.20610105 -0.081383695 0.295667858 T(ph)SPSGGTWSSVVSGVPR ddPTM_MDA-MB-175_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(0.574)S(0.425)PSGGTWSSVVSGVPR 84.842 0.057944 609000000 127490 121330 129010 110050 140920 179570 151870 136550 135700 108060 TRUE FALSE 132523.4036 142167.4837 132372.1066 131817.5615 116966.4687 137867.5889 139966.0326 134719.7706 130816.1835 129232.2881 1.025466666 1.100092599 1.024295929 1.020004857 0.905087037 1.066819995 1.083057761 1.042462163 1.01225619 1 16.97960704 2.582739106 0.002858658 6.99E-05 2.06185073 0.024274655 0.050530309 179654.968 226.2586695 81040.2427 82139.83697 382.5948375 -2.582739106 2.061780871 T(ph)SPTPPESATTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.611)S(0.389)PTPPESATTVK 166.6 0.00037269 275820000 333950 231720 281110 237390 409240 410540 376060 303610 335860 199740 TRUE FALSE 347134.6039 271516.1075 288435.9575 284345.0335 339677.531 315198.3068 346583.4346 299540.6046 323772.4642 238875.2287 1.453204695 1.13664405 1.20747538 1.190349602 1.421987256 1.319510225 1.450897342 1.253962607 1.355404099 1 17.86589773 -1.079371375 4.423538877 0.999976615 1.304320134 0.431874953 0.106469099 2.67E-05 5.56E-06 0.101767422 0.023984783 0.083296859 1.079371375 0.304343519 T(ph)SPYILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.635)S(0.365)PYILR;T(0.844)S(0.156)PYILR;T(0.741)S(0.259)PYILR 176.09 0.0085506 501186000 947130 869200 901230 844030 1051310 1314030 1103550 957360 932470 700170 TRUE FALSE 984523.4237 1018478.339 924716.7942 1010976.615 872608.7017 1008866.447 1017050.867 944528.1551 898910.5868 837354.9059 1.175754052 1.216304259 1.104330777 1.207345425 1.042101378 1.204825385 1.214599521 1.127990233 1.073512056 1 19.6754797 1.101441014 2.109471935 1.002494488 1.164250706 0.50451738 0.05282309 0.231553917 2.005361696 0.047881443 0.013465054 12.63109537 -1.101441014 0.161756218 T(ph)SSDSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.333)S(0.333)S(0.333)DS(0.002)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.332)S(0.332)S(0.332)DS(0.003)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.333)S(0.333)S(0.333)DSALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.327)S(0.327)S(0.327)DS(0.02)ALHTSVMNPSPQDTYPGPTPPSILPSR;T(0.328)S(0.328)S(0.328)DS(0.014)ALHT(0.001)S(0.001)VMNPSPQDTYPGPTPPSILPSR 217.35 3.01E-35 2079599000 60563 280727 258837 258871 297112 410873 217773 299485 228911 270611 TRUE FALSE 62954.074 328939.6785 265582.5049 310074.9111 246609.0084 315453.9726 200703.3832 295470.8934 220672.5378 323632.0443 0.194523611 1.016400212 0.820631052 0.958109423 0.762004297 0.97473034 0.62015918 0.912984047 0.681862448 1 18.30399494 4.74745848 24.93308663 0.85202403 0.19452326 0.700204186 0.130670912 578.2297924 1620246.64 0.028159412 0.342942825 55906.00764 -4.74745848 -0.657500769 T(ph)SSEEEDSRREEPSLLLVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK;T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK;T(0.333)S(0.333)S(0.333)EEEDSRREEPSLLLVLK 214.44 6.02E-23 254438000 438189 285421 380511 242067 506320 479636 407252 359337 401070 250296 TRUE FALSE 455489.0401 334439.8365 390427.4293 289947.1301 420255.9073 368247.808 375330.5241 354520.6753 386635.569 299336.709 1.521661147 1.117269705 1.304308551 0.96863205 1.403957131 1.230212656 1.253874025 1.184354156 1.29164101 1 18.19140969 -3.70957256 0.354862695 1.75E-19 1.25000463 0.216761611 0.143022681 252.3768908 4.951794805 187.5833258 0.098306368 0.000195176 3.70957256 1.25000463 T(ph)SSESIYSRPGSSIPGSPGHTIYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.466)S(0.466)S(0.015)ES(0.015)IY(0.001)S(0.012)RPGS(0.012)S(0.012)IPGSPGHTIYAK 109.41 0.0045587 689350000 49196 62690 78047 66151 101470 96227 89309 79476 86845 57476 TRUE FALSE 51138.29607 73456.51984 80080.96894 79235.47036 84222.16564 73879.73758 82308.72721 78410.75422 83719.46541 68737.32176 0.743966957 1.068655542 1.165028938 1.152728508 1.225275636 1.074812572 1.197438671 1.140730424 1.217962284 1 16.06880602 4.742618526 2.535866099 1.153993482 0.65279949 0.776844075 0.064448414 0.201281267 1.627797481 0.014294495 0.217915961 55286.42728 -4.742618526 -0.501193991 T(ph)SSGTSLSAMHSSGSSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.324)S(0.324)S(0.324)GT(0.012)S(0.012)LS(0.003)AMHSSGSSGK;T(0.345)S(0.345)S(0.287)GT(0.006)S(0.006)LS(0.01)AMHSSGSSGK;T(0.289)S(0.289)S(0.289)GT(0.048)S(0.048)LS(0.035)AMHSSGSSGK 120.23 0.00014434 308127000 85149 278018 327222 306765 329899 447867 290434 413902 299619 294709 TRUE FALSE 88510.74827 325765.4288 335749.6741 367442.2014 273822.8858 343856.6767 267669.0242 408354.3207 288835.7707 352451.586 0.251128813 0.92428419 0.952612181 1.04253241 0.776909217 0.975613929 0.759449056 1.158611103 0.819504812 1 18.42706557 4.738614249 6.005797531 0.942663341 0.232506112 0.753595643 0.117170805 0.058704004 10.29493511 0.026535114 0.170420597 54779.01883 -4.738614249 -0.710157229 T(ph)SSISGPLSPAYTGQVPYNYNQLEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 T(0.303)S(0.303)S(0.303)IS(0.091)GPLSPAYTGQVPYNYNQLEGR;T(0.31)S(0.31)S(0.31)IS(0.07)GPLSPAYTGQVPYNYNQLEGR 160.12 6.85E-11 170065000 220743 217011 246139 222701 339657 376335 242070 224453 269322 259734 TRUE FALSE 229458.1041 254280.9511 252553.5845 266750.5931 281922.2245 288936.8997 223095.9209 221444.5747 259629.1538 310623.9044 0.738700727 0.818613595 0.813052637 0.858757453 0.9075999 0.930182435 0.718218777 0.712902554 0.83583121 1 18.24480933 -2.423665171 1.970604038 2.293693965 0.810815771 0.380548957 0.070687573 3473812.375 286763.2832 20033130.3 0.019965982 0.003769943 2.423665171 -1.482878194 T(ph)SSLDTLAAPYLAGHWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.326)S(0.326)S(0.326)LDT(0.021)LAAPYLAGHWPR 162.37 1.32E-10 69537000 39058 38702 42285 37112 53560 57612 42100 41666 38521 32576 TRUE FALSE 40600.04 45348.76744 43386.98184 44452.64283 44455.89033 44232.48612 38800.09199 41107.53542 37134.63673 38958.64349 1.042131767 1.164023266 1.113667673 1.14102132 1.141104678 1.135370284 0.995930261 1.055158284 0.953180948 1 15.24965582 2.240160395 24.99975424 1.010619226 1.125989733 0.70417884 0.038450448 23.26740007 363606.9524 0.013135895 0.010454131 173.8442758 -2.240160395 0.115370508 T(ph)SSPHKEESPK ddPTM_MDA-MB-175_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 95.981 0.010779 132960000 259960 110970 176800 121890 261520 278870 249100 174600 196810 86340 TRUE FALSE 270223.4215 130028.2343 181407.5532 145999.4782 217066.9238 214106.6688 229574.8911 172259.7726 189726.8465 103256.6699 2.617006938 1.25927201 1.756860389 1.413947189 2.102207286 2.073538387 2.223342001 1.668267752 1.837429453 1 16.65587545 3.216054665 24.9960879 1.876980566 1.725527586 0 0.46192452 1137.330943 1263165.886 0.126171855 0.150909238 1644.578716 -3.216054665 -0.15145298 T(ph)SSPHKEESPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.333)S(0.333)S(0.333)PHKEESPKK 71.692 0.044118 124480000 272280 86161 150240 96796 271140 216480 219170 158320 170600 53761 TRUE FALSE 283029.8246 100958.4815 154155.3778 115941.9599 225051.7196 166205.8008 201990.8827 156197.9794 164460.1393 64294.43863 4.402088745 1.570252166 2.397647154 1.803296869 3.500329491 2.585072742 3.141654037 2.429416644 2.557921693 1 15.97240633 0.366278782 1.398500518 0.999632108 2.683555532 0.306551303 0.774093438 4.922787863 9.633548497 0.691382856 0.201704415 2.324228287 -0.366278782 1.683923424 T(ph)SSPPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.373)S(0.373)S(0.254)PPRK;T(0.333)S(0.333)S(0.333)PPRK 72.485 0.030166 2555820000 1472550 968580 1300600 943720 1726510 1635150 1612850 1401290 1411400 968590 TRUE FALSE 1530687.411 1134926.08 1334494.704 1130384.999 1433038.447 1255411.193 1486430.603 1382508 1360603.99 1158366.666 1.321418732 0.979764106 1.152048608 0.975843861 1.237119894 1.083777038 1.283212515 1.193497742 1.174588349 1 20.14366056 3.192896901 24.999978 1.177678426 1.10135815 0.039237941 0.116984142 301.002222 164791.7115 0.03135269 0.037473788 1559.182317 -3.192896901 -0.076320275 T(ph)SSPRSPPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.276)S(0.276)S(0.276)PRS(0.17)PPS(0.001)S(0.001)S(0.001)EIFTPAHEENVR 104.12 0.0024442 382630000 65649 89134 90163 79904 88192 108470 73853 72257 78101 85783 TRUE FALSE 68240.87321 104442.0711 92512.72185 95708.77271 73201.15534 83279.48638 68064.20888 71288.5131 75290.16027 102590.5364 0.665177078 1.018047812 0.901766626 0.932920092 0.713527367 0.811765776 0.663455044 0.69488391 0.733889917 1 16.64653813 3.236129945 24.99995828 0.745305634 0.890967812 0.143536308 0.121932617 86.31449125 887764.6795 0.032695603 0.040866271 1722.383853 -3.236129945 0.145662178 T(ph)SSSETEEKKPEKPLILQSLGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSSETEEKKPEKPLILQSLGPK 23 3 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 T(0.332)S(0.332)S(0.264)S(0.07)ET(0.003)EEKKPEKPLILQSLGPK 172.06 2.88E-12 1490500000 2203400 357130 903100 449650 1729800 1370700 1780000 1118900 1288400 299280 TRUE FALSE 2290391.933 418464.2994 926635.5279 538589.4279 1435769.214 1052375.698 1640478.949 1103902.976 1242030.736 357918.1859 6.399205247 1.169161881 2.588959054 1.504783632 4.01144527 2.940268865 4.583390879 3.084232707 3.470152634 1 18.44927032 T(ph)SWPPATAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSWPPATAR 9 0 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 T(0.604)S(0.396)WPPATAR 97.452 0.014402 0 217510 232800 229220 254950 345470 348990 291740 251070 236750 236730 TRUE FALSE 226097.4628 272781.5891 235193.6615 305378.3491 286747.1328 267942.3615 268872.6565 247704.8173 228229.4137 283112.711 0.798612898 0.963508802 0.830742147 1.078645844 1.012837367 0.946415866 0.949701818 0.874933578 0.806143295 1 18.111017 -0.877181369 4.561491895 1.000000489 0.923018377 0.071968459 0.086689008 1.78538E+12 4.39626E+11 11569191.02 0.020347778 0.132684023 0.877181369 -0.076982112 T(ph)T(ph)GQSKGFAFISFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTGQSKGFAFISFHR 15 1 O75821;K7ENA8;K7EP16 O75821 EIF3G Eukaryotic translation initiation factor 3 subunit G 2 T(0.667)T(0.667)GQS(0.667)KGFAFISFHR 81.311 0.070798 27371000 7829.5 4487.6 4270.6 6259.2 5979.9 6850.1 6140 5386.4 6236.4 4652.5 TRUE FALSE 8138.614706 5258.310391 4381.895344 7497.251078 4963.438734 5259.268089 5658.730756 5314.204118 6011.953182 5564.068298 1.462709347 0.94504778 0.787534428 1.34744052 0.892052086 0.945219902 1.017013173 0.955093258 1.080495936 1 12.44192441 4.742232263 24.78380534 0.993976204 1.462709549 0.50405173 0.138664873 252.8350347 1706568.589 0.031412861 0.233401396 55237.27718 -4.742232263 0.468733346 T(ph)TGTPPDSSLVTYELHSRPEQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.351)T(0.351)GT(0.298)PPDS(0.001)SLVTYELHSRPEQDK 141.5 2.68E-07 255840000 199980 116540 175610 145280 234540 236830 250140 166890 205600 96073 TRUE FALSE 207875.3648 136554.8384 180186.5409 174015.9504 194672.9746 181829.8217 230533.3732 164653.1125 198200.4962 114896.6649 1.809237587 1.188501325 1.568248661 1.514543094 1.694330943 1.582550911 2.006440947 1.433053889 1.725032631 1 16.8099774 -1.225067761 6.167457186 0.999989979 1.602952529 0.435029855 0.209447405 2.74E-05 3.44E-06 0.192635478 0.045403864 0.059556921 1.225067761 0.60296255 T(ph)THSPYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 T(0.745)T(0.103)HS(0.151)PY(0.001)EER 122.57 0.0065069 230880000 105630 126670 129230 117270 127180 156810 125310 126840 117730 142050 TRUE FALSE 109800.354 148424.5871 132597.84 140465.656 105561.989 120393.254 115487.8748 125139.9173 113492.9203 169881.9778 0.646333151 0.873692366 0.780529175 0.826842599 0.621384272 0.708687617 0.679812398 0.736628564 0.668069219 1 17.37417328 -1.092589934 4.621367026 1.00001348 0.730510114 0.534938174 0.07632824 1.35E-05 2.65E-06 0.073405256 0.017300677 0.080799759 1.092589934 -0.269503366 T(ph)TPDGSIGEMEHPENDLRPLPDVAMTGTCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPDGSIGEMEHPENDLRPLPDVAMTGTCTR 31 1 Q08174-2 Q08174-2 PCDH1 Protocadherin-1 1 T(0.498)T(0.498)PDGS(0.003)IGEMEHPENDLRPLPDVAMTGTCTR 111.56 0.00013667 53384000 3643.6 4703.7 3659.5 4199.1 4416.8 3614.8 4824.1 4341.3 3438.2 3358.4 TRUE FALSE 3787.452141 5511.523885 3754.869576 5029.669447 3666.033914 2775.317483 4445.974437 4283.111974 3314.459854 4016.41418 0.94299342 1.372249882 0.934881068 1.25227858 0.912762915 0.690993846 1.106951185 1.066401965 0.825228601 1 11.97169233 3.220121559 24.9794092 0.946565473 1.129595722 0.243810419 0.164556408 359.2237723 486639.8153 0.04710029 0.056392374 1660.051491 -3.220121559 0.183030249 T(ph)TPDQELAPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_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 200.06 2.62E-23 377850000 47631 58807 57344 40730 74462 86488 58117 56399 56553 45502 TRUE FALSE 49511.50866 68906.6448 58838.43175 48786.27243 61804.97584 66402.47274 53561.63768 55643.06366 54517.66858 54417.24571 0.909849589 1.266264837 1.081246046 0.896522266 1.135760824 1.220246851 0.984276896 1.022526277 1.001845424 1 15.73177632 T(ph)TPDQELVPASEPVWERPWSVEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTPDQELVPASEPVWERPWSVEEIR 25 1 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIR;T(0.5)T(0.5)PDQELVPASEPVWERPWSVEEIR 84.035 0.029855 208290000 13789.8 12779.7 11589.1 15503.7 18972.5 21752 16882.6 17781.1 17805.1 14402.2 TRUE FALSE 14334.23195 14974.51406 11891.12147 18570.28559 15747.56123 16700.42765 15559.2977 17542.77344 17164.29793 17224.03534 0.832222628 0.869396385 0.690379532 1.07816114 0.914278269 0.969600173 0.903347989 1.018505425 0.996531741 1 14.07213556 3.735761784 24.99977329 0.97793993 0.804539203 0.641627728 0.06341431 152.74792 1364380.327 0.01606548 0.026172643 5442.040681 -3.735761784 -0.173400726 T(ph)TPDQELVPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTPDQELVPASEPVWERPWSVEEIRR 26 2 A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5;A0A0A0MT65 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 T(0.616)T(0.384)PDQELVPASEPVWERPWSVEEIRR;T(0.595)T(0.405)PDQELVPASEPVWERPWSVEEIRR 200.06 2.62E-23 858660000 160821 136395 145095 118376 205813 235310 149412 148907 175011 129644 TRUE FALSE 167170.3373 159819.7802 148876.2949 141790.4195 170828.9798 180662.8187 137700.697 146911.1452 168712.3883 155045.2596 1.078203472 1.030794367 0.960211846 0.914509865 1.101800727 1.165226329 0.888132261 0.947537162 1.088149284 1 17.24232989 1.040350819 0.004748215 2.51E-08 2.003240684 0 0.085923444 42968.11739 144.4771655 30642.33082 30301.6359 10.97364278 -1.040350819 2.003240658 T(ph)TPPEAAQNGQSPMAALILVADNAGGSHASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTPPEAAQNGQSPMAALILVADNAGGSHASK 31 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK;T(0.5)T(0.5)PPEAAQNGQSPMAALILVADNAGGSHASK 232.53 6.61E-36 499794000 107386 189676 216529 239152 245586 286499 295003 268857 238796 135586 TRUE FALSE 111625.6822 222251.3775 222171.9236 286455.5518 203841.3794 219963.9492 271879.894 265253.4117 230201.7786 162151.4807 0.688403718 1.370640444 1.370150446 1.766592266 1.257104644 1.356533706 1.676703122 1.635837122 1.419671147 1 17.30698267 4.843447496 2.137464384 1.481764454 0.316783961 0.511570485 0.213858923 0.719299657 2.892926807 0.051838591 1.767987054 69734.46861 -4.843447496 -1.164980493 T(ph)TPPESAPQNGPSPMAALMSVADTLGTAHSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 T(0.439)T(0.439)PPES(0.122)APQNGPS(0.001)PMAALMSVADTLGTAHSPK 82.726 0.0012221 38624000 42040 30518 37251 19527 38239 33865 39115 28224 39008 18022 TRUE FALSE 43699.77166 35759.2291 38221.79166 23389.38232 31739.14844 26000.36698 36049.06409 27845.70345 37604.1097 21553.06585 2.02754318 1.659124941 1.773380731 1.08519978 1.47260481 1.206341927 1.672572447 1.291960208 1.744722072 1 14.39560548 3.863858392 7.539334231 1.378788726 1.811607668 0.444897857 0.237940209 0.245319789 13.9436579 0.056567107 0.102664318 7309.007238 -3.863858392 0.432818942 T(ph)TPPPGAQCEVPASPQRPSRPGALPEQTRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 T(0.499)T(0.499)PPPGAQCEVPAS(0.002)PQRPSRPGALPEQTRPLR 65.758 0.0024408 254210000 15888 15249 16169 17655 21729 22550 16937 22693 17650 14503 TRUE FALSE 16515.27051 17867.89713 16590.37742 21147.10631 18035.51234 17313.10425 15609.43368 22388.83745 17014.77995 17344.58517 0.952185961 1.030171489 0.956516242 1.219233905 1.039835324 0.998184971 0.899960047 1.290825767 0.980985119 1 14.08219772 T(ph)TPPPGRPPAPSSEEEDGEAVAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.816)T(0.184)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH;T(0.811)T(0.189)PPPGRPPAPSSEEEDGEAVAH;T(0.759)T(0.241)PPPGRPPAPSSEEEDGEAVAH;T(0.5)T(0.5)PPPGRPPAPSSEEEDGEAVAH 130.48 5.57E-05 14287200000 3184380 2644920 3710680 2383480 4369730 4739770 3655830 2998830 3329130 2399590 TRUE FALSE 3310101.781 3099164.435 3807383.369 2854925.23 3626964.855 3639030.249 3369276.492 2958635.589 3209315.262 2869743.718 1.153448568 1.079944671 1.326732888 0.994836303 1.26386368 1.268068025 1.174068775 1.030975544 1.118328178 1 21.45249047 1.770330184 7.576767849 1.056620644 1.181588524 0.28517026 0.094367758 0.240258574 38.80686951 0.042859148 0.0237406 58.92915094 -1.770330184 0.124967879 T(ph)TPTMSEEPPLDLTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.5)T(0.5)PTMSEEPPLDLTGK 135.99 0.00022231 111090000 196030 125520 149650 123910 217330 218490 214630 173920 169940 110640 TRUE FALSE 203769.4158 147077.0836 153550.0019 148419.0282 180388.3242 167749.0087 197806.7398 171588.8869 163823.8926 132317.7897 1.540000149 1.11154429 1.160463777 1.12168612 1.363296082 1.267773662 1.494936851 1.296793782 1.23810935 1 17.01364751 3.22086356 24.9912212 1.306131467 1.219506456 0 0.163169909 731.4698873 1032955.913 0.045249477 0.054194321 1662.890148 -3.22086356 -0.08662501 T(ph)TPVDLCLLEESVGSLEGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTPVDLCLLEESVGSLEGSR 20 0 Q9UKK3 Q9UKK3 PARP4 Poly [ADP-ribose] polymerase 4 1 T(0.5)T(0.5)PVDLCLLEESVGSLEGSR;T(0.5)T(0.5)PVDLCLLEESVGSLEGSR;T(0.5)T(0.5)PVDLCLLEESVGSLEGSR 168.32 1.39E-10 105014000 35536 35402.2 39595.1 36004.4 49633 56888 38855.1 39683.8 40871.2 35557.2 TRUE FALSE 36938.98872 41482.25246 40626.98083 43125.96286 41196.40039 43676.62415 35809.53573 39151.90357 39400.2535 42523.95256 0.868663106 0.975503216 0.955390513 1.01415697 0.968781073 1.027106408 0.842102711 0.920702362 0.926542598 1 15.37598808 -0.347115349 7.894312492 1.000002386 0.944519306 0.083859324 0.055200166 0 0 0.054466421 0.012837859 0.449660409 0.347115349 -0.05548308 T(ph)TSFAESCKPVQQPSAFGSMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 T(0.345)T(0.345)S(0.306)FAES(0.004)CKPVQQPSAFGSMK 71.506 0.027158 156020000 43381 42356 55014 39045 81167 60912 58826 57030 44020 46692 TRUE FALSE 45093.71538 49630.31352 56447.71003 46767.98446 67370.26233 46766.11113 54215.06441 56265.60613 42435.7288 55840.40343 0.807546375 0.888788592 1.010875756 0.837529487 1.206478789 0.837495939 0.970893136 1.007614607 0.759946673 1 15.76902174 4.520763053 3.607962529 0.958377624 0.813852787 0.130362242 0.117301643 0.444517562 11.22758343 0.02674985 0.124889283 33171.34288 -4.520763053 -0.144524837 T(ph)TSPPLSIPTTHLIHQPAGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSPPLSIPTTHLIHQPAGSR 21 0 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 T(0.333)T(0.333)S(0.333)PPLSIPTTHLIHQPAGSR 69.704 0.035264 107300000 94667 60489 94136 48821 114360 105780 81529 90751 92253 63073 TRUE FALSE 98404.52626 70877.51521 96589.26149 58477.64808 94921.12805 81214.19811 75138.54394 89534.63128 88932.83255 75430.94674 1.30456438 0.939634437 1.280499128 0.775247436 1.258384418 1.076669479 0.99612357 1.186974778 1.178996637 1 16.20286891 1.703422058 24.99990968 1.137683067 1.08552663 0.004659079 0.162663399 3.438674373 2428.053607 0.069032336 0.038281821 50.51519785 -1.703422058 -0.052156437 T(ph)VDIDDAQILPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVDIDDAQILPR 12 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 T(1)VDIDDAQILPR 91.62 0.010431 0 13450 19182 16676 16335 19020 21174 17038 13529 16361 14895 TRUE FALSE 13981.01639 22476.35928 17110.59026 19566.01424 15786.98719 16256.6594 15702.51704 13347.66588 15772.17081 17813.39007 0.784859947 1.261767648 0.960546544 1.09838802 0.886242716 0.912608961 0.881500769 0.749305204 0.88541096 1 14.12067448 3.152745347 6.179450601 0.864281193 1.038058364 0.21829507 0.125994238 0.2497253 14.41564115 0.034637048 0.041740467 1421.495034 -3.152745347 0.173777171 T(ph)VHRDSEEEDDYLFDDPLPIPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVHRDSEEEDDYLFDDPLPIPLR 23 1 B3KSJ7;Q96SD1-2;Q96SD1-3;Q96SD1 B3KSJ7 DCLRE1C Protein artemis 1 T(0.346)VHRDS(0.346)EEEDDY(0.309)LFDDPLPIPLR;T(0.35)VHRDS(0.35)EEEDDY(0.3)LFDDPLPIPLR 103.27 0.0025652 104424000 45352 56470 50625 50331 59054 65037 59128 57313 53506 57667 TRUE FALSE 47142.53198 66168.28322 51944.32909 60286.32158 49016.02217 49933.1424 54493.39286 56544.81298 51580.32951 68965.74455 0.683564461 0.959436944 0.753190289 0.874148782 0.710729979 0.724028178 0.790151592 0.819897086 0.747912313 1 16.07359233 -1.169199685 4.826518336 1.000020513 0.790157865 0.401354435 0.078606405 1.61E-05 2.77E-06 0.070648911 0.016650481 0.067733001 1.169199685 -0.209862647 T(ph)VLSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 1 T(0.998)VLS(0.002)SAR;T(0.998)VLS(0.002)SAR 122.18 0.041552 344110000 354590 428310 388890 289260 422270 490520 349600 399150 468920 479030 TRUE FALSE 368589.487 501868.9107 399024.7929 346474.7646 350492.6962 376604.1639 322197.4385 393800.0471 452043.6608 572886.7569 0.643389784 0.876035106 0.696516001 0.604787526 0.61180101 0.657379769 0.562410345 0.687395969 0.789062856 1 19.12789046 0.924902988 2.448224613 0.999103402 0.666257561 0.623468887 0.079588779 0.247527103 3.27982611 0.080458913 0.021715264 8.41207214 -0.924902988 -0.332845841 T(ph)VQEEEQLK ddPTM_MDA-MB-175_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 92.062 0.038009 268190000 15032 457970 213820 375990 73017 241290 103080 144720 129960 1036500 TRUE FALSE 15625.47497 536622.785 219392.3249 450359.6998 60605.59642 185254.0543 95000.32025 142780.2651 125282.765 1239582.33 0.012605435 0.432906127 0.17698891 0.363315682 0.048891949 0.14944877 0.076638976 0.115184173 0.101068531 1 20.24142266 -1.748404817 5.400566525 1.036473792 0.166822666 0.794503201 0.127526062 0.047184079 0.002198155 0.104030213 0.028333543 0.017848231 1.748404817 -0.869651125 T(ph)VQSPNSSVPSPGLAGPVTMTSVHPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVQSPNSSVPSPGLAGPVTMTSVHPPIR 28 0 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 T(0.341)VQS(0.341)PNS(0.155)S(0.155)VPS(0.008)PGLAGPVTMTSVHPPIR 69.181 0.0060002 0 17796 31030 33233 32994 33498 47065 30188 28742 31307 35077 TRUE FALSE 18498.59982 36359.16112 34099.07928 39520.11472 27804.02193 36134.86703 27821.78568 28356.7605 30180.26719 41949.66656 0.44097132 0.866733018 0.81285698 0.94208412 0.662794825 0.861386275 0.663218279 0.675971058 0.719439978 1 15.35637172 -2.404022095 2.116549415 2.837583324 0.743527158 0.251154726 0.135260207 5594810.781 427232.1377 49412209.42 0.032889978 0.003944372 2.404022095 -2.094056165 T(ph)WTLCGTPEYLAPEIILSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.335)WT(0.335)LCGT(0.299)PEY(0.031)LAPEIILSK 78.012 0.039527 11147000 9629 6285.8 10366 8129.3 23331 12900 13380 10975 14381 8894.3 TRUE FALSE 10009.16036 7365.337253 10636.14648 9737.251276 19365.20495 9904.170501 12331.24064 10827.89808 13863.43062 10636.96779 0.940978722 0.692428274 0.999922786 0.915416072 1.820556885 0.931108441 1.159281562 1.017949691 1.30332543 1 13.37679933 3.443333455 24.99968901 1.193647629 0.875644812 0.28952498 0.244295577 233.9084285 173068.885 0.066301426 0.089772976 2775.450304 -3.443333455 -0.318002817 LYFAQTLHIGSSHLAPPNPDKQFLIS(ph)PPAS(ph)PPVGWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 LYFAQTLHIGSSHLAPPNPDKQFLISPPASPPVGWK 36 1 V9GYW9;E9PD55;E9PDJ2;P53805-4;P53805-3;P53805-2;P53805 V9GYW9 RCAN1 Calcipressin-1 2 LYFAQTLHIGSSHLAPPNPDKQFLIS(1)PPAS(1)PPVGWK 110.58 8.43E-06 390070000 110810 240840 245930 206900 370360 353160 273790 320240 346150 263380 TRUE FALSE 115184.8644 282202.3965 252339.1378 247824.2025 307406.3395 271143.9422 252329.6244 315947.7066 333692.1291 314984.2683 0.365684499 0.895925368 0.801116637 0.786782793 0.975941882 0.860817411 0.801086434 1.003058687 1.059393001 1 18.26492025 4.92116369 2.223519656 0.908610545 1.87E-15 0.748703644 0.093911089 0.703732875 2.482792801 0.024405416 1.509250774 83399.5466 -4.92116369 -0.908610545 down T(ph)YSFTSAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYSFTSAMSR 10 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 T(0.604)YS(0.393)FT(0.003)SAMSR 103.21 0.031794 521700000 209330 177300 212110 256700 417940 298840 193380 255130 243200 285610 TRUE FALSE 217594.51 207749.8958 217637.7609 307474.4938 346898.7081 229438.939 178222.3703 251710.3997 234447.2795 341569.8112 0.637042569 0.608220894 0.637169193 0.900180531 1.015601194 0.67171902 0.521774362 0.736922267 0.686381735 1 18.38182095 -2.482189268 1.918136611 3.406175051 0.713969223 0.282363402 0.137356124 5637172.201 369384.8958 58925623.84 0.037539659 0.003294661 2.482189268 -2.692205828 TAAAAAEHSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TAAAAAEHSQR 11 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;;;;;; 192.68 1.28E-06 1618343000 1474666 1617539 1689701 1549843 1965599 2238778 1720794 1760739 1680511 1488623 FALSE TRUE 1532886.952 1895338.741 1733735.996 1856397.32 1631487.184 1718855.739 1585913.67 1737139.174 1620029.737 1780290.175 0.86103208 1.06462349 0.97385023 1.042749853 0.91641644 0.965491897 0.890817515 0.975761815 0.909980721 1 20.76368098 3.216727422 24.99882219 0.941660361 0.990374373 0.108825825 0.058837764 442.8972008 507112.1803 0.015691153 0.018768994 1647.128272 -3.216727422 0.048714012 TAAAVAIQSAVGTALVFEGPAEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAAAVAIQSAVGTALVFEGPAEQEK 25 0 Q499Z4 Q499Z4 ZNF672 Zinc finger protein 672 0 60.278 0.043212 339670000 14127 590200 549500 434420 427180 714490 269110 544610 469480 744770 FALSE TRUE 14684.74487 691562.2589 563820.4214 520346.9794 354568.0962 548560.5257 248016.455 537310.3938 452583.5065 890693.422 0.016486868 0.776431308 0.633012895 0.584204359 0.398080964 0.615880293 0.278453224 0.603249536 0.508124901 1 19.76456941 0.130332208 1.305885475 1.000767137 0.500807151 0.357682865 0.204561196 9.712451499 13.37052015 0.197721376 0.053730594 1.34999515 -0.130332208 -0.499959986 TAADKDRGEEDADGSK ddPTM_MDA-MB-175_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 ;; 202.33 1.72E-11 994250000 1955460 713170 1228200 728810 1753660 1814900 1823480 1171930 1402690 489622 FALSE TRUE 2032663.071 835651.3998 1260207.901 872966.4427 1455573.5 1393416.98 1680550.873 1156222.195 1352207.461 585554.0565 3.471349994 1.427112306 2.152163215 1.490838349 2.485805509 2.379655584 2.870018326 1.974578064 2.309278615 1 19.15944284 TAADKDRGEEDADGSKTQDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 177.08 2.85E-17 353120000 414920 208473 323870 146465 528470 406330 279780 312870 367840 205082 FALSE TRUE 431301.362 244276.6161 332310.3183 175435.3398 438640.8582 311966.0155 257850.1125 308676.4894 354601.5103 245263.8914 1.758519608 0.995974641 1.354909263 0.715292165 1.788444502 1.271960637 1.051317057 1.258548446 1.445795825 1 17.90397533 -1.83303299 2.370560357 0.890914985 1.271450399 0.069735165 0.312362824 23247621.38 13500551.62 14410902.29 0.075757391 0.014688147 1.83303299 0.380535413 TAAKGEAAAERPGEAAVASS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAAKGEAAAERPGEAAVASSPSK 23 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 TAAKGEAAAERPGEAAVAS(0.132)S(0.841)PS(0.027)K 93.529 0.002368 129830000 230270 107150 157690 76047 217850 194110 147810 146580 173000 86237 TRUE FALSE 239361.2374 125552.179 161799.5309 91088.86962 180819.9348 149030.8943 136224.266 144615.3349 166773.7638 103133.489 2.320887615 1.217375463 1.568836005 0.883213304 1.753261104 1.445029114 1.320853849 1.402215092 1.61706702 1 16.65415335 4.744463143 24.81209438 1.37531502 2.320888072 0.559996839 0.255980032 412.9697586 1735920.927 0.055885085 0.504451618 55521.74953 -4.744463143 0.945573052 TAAKGEAAAERPGEAAVASS(ph)PSKANGQENGHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAAKGEAAAERPGEAAVASSPSKANGQENGHVK 33 3 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 TAAKGEAAAERPGEAAVAS(0.207)S(0.755)PS(0.037)KANGQENGHVK 112.74 4.10E-06 143340000 102930 42780 74291 35803 118780 86524 58819 63692 80336 41623 TRUE FALSE 106993.7559 50127.13222 76227.08449 42884.72654 98589.81803 66430.11228 54208.61309 62838.31292 77444.72305 49778.22993 2.149408608 1.007009134 1.53133377 0.861515699 1.980581032 1.334521384 1.089002425 1.262365355 1.555795037 1 15.60322731 4.751591141 24.55670439 1.3048159 2.149409301 0.398355662 0.315964566 1678.910887 3163923.019 0.070499785 1.307812082 56440.53752 -4.751591141 0.844593401 TAALESNLPGS(ph)PNTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAALESNLPGSPNTSR 16 0 A0A2U3TZV8;Q4KWH8-2;Q4KWH8 A0A2U3TZV8 PLCH1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1" 1 TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR;TAALESNLPGS(1)PNTSR 455.54 7.49E-183 1268080000 783880 836907 841800 775581 982690 1125160 853140 860610 837000 739771 TRUE FALSE 814828.1877 980639.267 863737.9995 928988.6069 815652.7048 863858.642 786268.6575 849074.9306 806876.5335 884714.9637 0.92100645 1.108423964 0.976289579 1.050042833 0.921938408 0.976425942 0.888725397 0.959715802 0.912018635 1 19.7548532 3.232354691 24.99527253 0.940239817 1.018000147 0.288425654 0.054217985 159.5026735 642419.8424 0.014125625 0.01728669 1707.476327 -3.232354691 0.07776033 TAAPS(ph)PSLLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 TAAPS(0.994)PS(0.006)LLYK;TAAPS(0.994)PS(0.006)LLYK;TAAPS(0.997)PS(0.003)LLYK;TAAPS(0.991)PS(0.009)LLYK 189.24 2.93E-06 388078000 1263715 924089 1114191 859738 1473770 1467300 1223516 1245003 1212863 864402 TRUE FALSE 1313607.444 1082794.097 1143227.733 1029791.61 1223259.102 1126541.812 1127613.619 1228315.771 1169212.298 1033765.022 1.270702158 1.047427679 1.10588742 0.996156369 1.18330479 1.089746498 1.090783297 1.188196297 1.131023272 1 19.97947686 TADEDRGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TADEDRGPR 9 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ;; 115.78 0.0012953 821533000 1242225 1885253 1671845 1779496 1982339 2253020 1552302 1739709 1577403 2095800 FALSE TRUE 1291269.002 2209030.538 1715414.654 2131474.998 1645381.725 1729790.25 1430628.513 1716391.046 1520632.574 2506431.883 0.515182164 0.881344732 0.684405056 0.850402124 0.656463771 0.690140539 0.570782922 0.684794611 0.60669216 1 21.2572036 -1.092570365 4.815159768 1.000012835 0.687542816 0.440818795 0.107214871 1.45E-05 2.74E-06 0.098197231 0.023144321 0.0808034 1.092570365 -0.312470019 TADGIVSHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TADGIVSHLK 10 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 123.79 0.00045266 3831380000 4450668 3882190 4406790 4214050 5733880 5837270 5141240 4680500 4304860 3291568 FALSE TRUE 4626383.809 4548925.933 4521634.568 5047576.512 4759237.126 4481652.507 4738256.175 4617765.553 4149928.93 3936487.729 1.175256759 1.155579859 1.148646936 1.282253842 1.20900596 1.138490151 1.203676094 1.173067433 1.054221229 1 21.90847755 1.156250953 2.90130545 1.001507675 1.187992425 0.738212847 0.0385275 0.123327264 1.865000174 0.037244539 0.010163978 14.33015715 -1.156250953 0.186484749 TADGRVS(ph)PAGGTLDDKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TADGRVSPAGGTLDDKPK 18 2 C9JA69;Q8WY36-2;Q8WY36 C9JA69 BBX HMG box transcription factor BBX 1 T(0.006)ADGRVS(0.987)PAGGT(0.007)LDDKPK;TADGRVS(1)PAGGTLDDKPK;T(0.001)ADGRVS(0.999)PAGGTLDDKPK 159.73 2.21E-11 795020000 2003100 652885 1041223 649881 1780970 1622900 1507440 1038718 1285770 484215 TRUE FALSE 2082183.935 765012.92 1068358.127 778425.5221 1478241.356 1246006.07 1389282.914 1024795.684 1239495.389 579087.6584 3.595628234 1.321065833 1.844898801 1.344227443 2.552707408 2.151670912 2.399089143 1.769672811 2.140427914 1 19.14342222 -0.445779535 0.802226064 0.938732648 2.085102063 0.22315114 0.62449361 24.47257204 11.15071451 5.257456922 0.195010243 0.358278267 0.445779535 1.146369415 TADSVS(ph)PLEPPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TADSVSPLEPPTK 13 0 Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;Q9UMZ2-9;Q9UMZ2-6 Q9UMZ2-4;Q9UMZ2-9 SYNRG Synergin gamma 1 TADS(0.001)VS(0.999)PLEPPTK;TADS(0.04)VS(0.96)PLEPPTK 150.69 4.65E-05 173535000 764950 493120 704210 577290 839140 943660 984980 750550 794730 467460 TRUE FALSE 795150.8167 577809.5241 722562.2911 691476.239 696503.2825 724509.2663 907774.6938 740490.1049 766127.8225 559049.8369 1.42232546 1.033556377 1.292482787 1.236877633 1.245869753 1.295965437 1.623781341 1.324551151 1.3704106 1 19.09261737 2.471165424 24.99851862 1.374952767 1.239904377 0.024842835 0.168443574 318.2936207 1335966.564 0.054240133 0.045499809 295.9139399 -2.471165424 -0.13504839 TAEALDKDGWLHTGDIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAEALDKDGWLHTGDIGK 18 1 E7EPM6;P33121-2;P33121;P33121-3;B7Z3Z9;H0Y9U7 E7EPM6 ACSL1 Long-chain-fatty-acid--CoA ligase 1 0 ; 198.42 1.04E-15 1200080000 2653900 1499350 2163090 1628320 3324900 2758800 2631000 2026260 2624500 1304120 FALSE TRUE 2758678.021 1756851.699 2219461.902 1950396.836 2759734.686 2118110.51 2424775.345 1999101.299 2530044.758 1559637.345 1.768794541 1.126448853 1.42306281 1.250545098 1.769472047 1.358078862 1.554704594 1.281773167 1.622200677 1 20.57277917 -1.419884501 5.761093582 0.999798722 1.442481651 0.305605719 0.206963825 0.000485919 4.89E-05 0.181990162 0.042876297 0.038029052 1.419884501 0.442682928 TAELSLGRNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAELSLGRNER 11 1 Q9H611-2;Q9H611;Q9H611-3 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 0 ; 85.958 0.0089094 172364000 7634.1 288470 149621 215110 108796 261440 81354 150884 107725 381310 FALSE TRUE 7935.500163 338012.4785 153520.2462 257658.116 90302.89478 200724.5222 74977.2609 148861.6468 103847.9983 456020.3939 0.017401634 0.741222285 0.33665215 0.565014459 0.198023808 0.44016567 0.164416464 0.32643638 0.227726654 1 18.79873882 -1.654073763 5.160466931 1.010753779 0.344304793 0.504415234 0.197493665 0.022425162 0.001503246 0.175497018 0.041364775 0.022178197 1.654073763 -0.666448986 TAENATSGETLEENEAGD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 320.99 3.06E-61 570420000 900580 994900 954670 965300 1139290 1287490 1053600 1049980 1060940 928060 FALSE TRUE 936135.5938 1165766.336 979549.4845 1156233.459 945633.8927 988489.9596 971016.0789 1035906.736 1022756.977 1109895.588 0.843444738 1.050338742 0.882560031 1.041749757 0.852002569 0.890615271 0.874871555 0.933337105 0.921489361 1 20.08199253 5.046920682 15.56401475 0.931868576 0.368292217 0.147800037 0.06679913 2788068.842 25294316.42 0.01503189 46177619.69 111409.1042 -5.046920682 -0.563576359 TAENFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TAENFR 6 0 C9JQD4;O43447;A6NM32;R4GN99;H0Y548;P30405-2;P30405;P49792;P62937;F8WE65;C9J5S7;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;Q08752 C9JQD4;P30405;P49792;P62937;Q08752 PPIH;PPIF;RANBP2;PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D;PPID "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase H;Peptidyl-prolyl cis-trans isomerase F, mitochondrial;E3 SUMO-protein ligase RanBP2;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D;Peptidyl-prolyl cis-trans isomerase D" 0 ;;;;;; 155.73 0.02372 14579413000 8899710 8765730 8283260 7443750 10068040 10797420 8314540 9019850 8212500 7993030 FALSE TRUE 9251077.423 10271175.94 8499128.56 8916101.533 8356678.157 8289882.841 7662824.629 8898953.664 7916933.729 9559111.193 0.967775898 1.074490686 0.889112846 0.932733321 0.874210791 0.867223184 0.801625222 0.930939445 0.828208143 1 23.18844505 4.222965725 24.83008414 0.885870391 1.021133267 0.444797079 0.058192191 150.6786957 239910.6687 0.013489492 0.029301682 16709.58735 -4.222965725 0.135262876 TAESQT(ph)PTPSATSFFSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TAESQTPTPSATSFFSGK 18 0 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQT(0.987)PT(0.013)PSATSFFSGK;TAES(0.001)QT(0.996)PT(0.003)PSATSFFSGK;TAESQT(0.981)PT(0.019)PSATSFFSGK 293.63 3.38E-48 557826000 981795 702984 854995 765772 1059980 1137420 1090220 934977 950269 572733 TRUE FALSE 1020557.025 823716.0335 877276.8721 917239.416 879804.9782 873271.4428 1004765.708 922445.1626 916069.0043 684949.0657 1.489975059 1.202594579 1.280791399 1.339135217 1.284482339 1.274943622 1.466920327 1.346735413 1.33742646 1 19.38563718 -1.221659846 3.618722827 0.999492086 1.333838318 0.597976344 0.082607665 2593006.115 1313105.756 9804.584344 0.018733036 0.060026104 1.221659846 0.334346232 TAESQTPTPSATSFFSGKS(ph)PVTTLLECMHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAESQTPTPSATSFFSGKSPVTTLLECMHK 30 1 A0A3B3IRQ9;P55265-3;P55265-2;A0A3B3ISX1;A0A3B3ITG9;P55265-5;P55265;P55265-4 A0A3B3IRQ9;P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 1 TAESQTPTPSATSFFS(0.001)GKS(0.998)PVTT(0.001)LLECMHK;TAESQTPTPSATSFFS(0.002)GKS(0.997)PVTTLLECMHK 258.83 1.90E-58 696690000 1887290 1007800 1603580 1008560 2165240 1943550 1978650 1493130 1733600 789570 TRUE FALSE 1961801.667 1180881.81 1645370.612 1208050.158 1797193.278 1492189.967 1823558.243 1473117.035 1671208.075 944271.1243 2.077583033 1.250574946 1.74247689 1.279346712 1.903259807 1.580255849 1.931180776 1.560057272 1.769839225 1 19.84884163 -1.410762863 5.924371951 0.999786164 1.662126447 0.385648398 0.255776038 0.000644457 6.41E-05 0.220929686 0.052057262 0.038836236 1.410762863 0.662340283 TAFDDAIAELDTLNEDSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAFDDAIAELDTLNEDSYK 19 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;;; 182.17 6.94E-14 47442900 148579.7 83075.7 119359.2 103705.7 158202.5 164260 177249.5 127821.8 137025.2 66245 FALSE TRUE 154445.7413 97343.30524 122469.7988 124218.3779 131311.2956 126113.1044 163356.221 126108.5578 132093.6898 79224.43941 1.949470926 1.228702986 1.545858825 1.567930033 1.657459447 1.591845967 2.061942277 1.591788579 1.667335115 1 16.27365793 3.323574278 3.385747626 1.654083866 1.541923161 0 0.294354732 1.074145368 24.38838766 0.080075981 0.109946837 2106.562156 -3.323574278 -0.112160704 TAFDEAIAELDTLNEESYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TAFDEAIAELDTLNEESYK 19 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 ;; 248.54 6.95E-25 35979100 104698 61082 83864 71867 103950 111849 127032 86387 93301 51329 FALSE TRUE 108831.5579 71572.35835 86049.56474 86082.0781 86280.61613 85873.76484 117074.8999 85229.12357 89943.11524 61385.9348 1.772907071 1.165940677 1.401779822 1.402309477 1.405543736 1.398915975 1.907194218 1.388414526 1.465207226 1 15.90562051 TAFDEAIAELDTLS(ph)EESYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 1 TAFDEAIAELDT(0.024)LS(0.976)EESYK;TAFDEAIAELDT(0.027)LS(0.952)EES(0.019)Y(0.002)K 137.42 2.51E-06 22910000 62654 33900 45200 38583 56667 54760 73536 46958 48975 25028 TRUE FALSE 65127.6283 39722.06129 46377.94913 46214.60224 47034.76358 42042.8199 67772.05617 46328.60482 47212.39932 29931.75741 2.175870511 1.327087506 1.549456268 1.543998958 1.5714 1.404622499 2.264219078 1.547807707 1.577334691 1 14.86938937 0.693604665 2.347456599 1.000350284 1.662781768 0.321271055 0.29186486 2.047286024 14.1056189 0.266362038 0.071767837 4.938609239 -0.693604665 0.662431484 TAFDEAIAELDTLSEESYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAFDEAIAELDTLSEESYK 19 0 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 281.51 2.50E-39 337070000 335160 220230 272370 271520 376870 342620 372370 288280 307380 175500 FALSE TRUE 348392.3756 258052.7893 279468.186 325225.8456 312809.772 263051.6975 343182.6664 284416.0781 296317.4538 209885.8648 1.659913477 1.229491036 1.33152457 1.549536677 1.490380366 1.253308305 1.635091847 1.355098774 1.41180281 1 17.67924548 0.304448744 1.428444911 0.999851523 1.433460102 0.462835656 0.140995386 4.762847331 8.870548354 0.127153853 0.036803864 2.015806051 -0.304448744 0.433608579 TAFQEALDAAGDKLVVVDFSATWCGPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAFQEALDAAGDKLVVVDFSATWCGPCK 28 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ;;; 188.41 6.37E-18 948210000 1125331 706053 943641 764851 1266797 1243406 1120328 1027695 1115320 613532 FALSE TRUE 1169759.937 827312.1104 968233.0597 916136.2449 1051467.298 954643.8005 1032513.764 1013920.429 1075179.851 733741.8486 1.59423909 1.127524772 1.319582714 1.248581155 1.433020756 1.301062223 1.407189417 1.381848986 1.465338052 1 19.48491305 -0.551809124 12.60217898 1 1.356398325 0.448840483 0.120813774 0 0 0.108381295 0.025545716 0.280666692 0.551809124 0.356398325 TAFYNEDDS(ph)EEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR 319.15 5.00E-56 600290000 591790 640380 554460 599780 575740 757050 660080 561990 491670 453940 TRUE FALSE 615154.3262 750360.2835 568909.6831 718414.6938 477875.9204 581236.6107 608341.2048 554457.4433 473974.8927 542880.8518 1.133129533 1.382182262 1.047945753 1.323337693 0.880259303 1.07065226 1.120579595 1.021324369 0.873073514 1 19.05027607 3.242905964 24.99993178 1.009204531 1.220708121 0.493972984 0.112113356 96.88823465 557419.4634 0.030155778 0.039453757 1749.467842 -3.242905964 0.21150359 TAGAMQVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAGAMQVEK 9 0 Q5M9N0 Q5M9N0 CCDC158 Coiled-coil domain-containing protein 158 0 ; 78.934 0.021518 392018000 40696 1269950 830230 1038860 490480 1210550 413380 974780 598910 1986520 FALSE TRUE 42302.7095 1488054.034 851866.4758 1244343.407 407108.3848 929418.1086 380978.1954 961714.6685 577355.3461 2375740.56 0.017806115 0.626353761 0.358568814 0.523770747 0.171360624 0.391211955 0.160361869 0.404806267 0.24302121 1 21.17994587 -1.219931335 4.022981448 1.000483635 0.333766902 0.582920259 0.171808409 18576256.77 11266415.11 73588.52272 0.036577011 0.060265486 1.219931335 -0.666716733 TAGAPDPAWDWQHVGPGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAGAPDPAWDWQHVGPGYR 19 0 H3BM67;H3BUP2;H3BUN4;O60936;O60936-3 H3BM67 NOL3 Nucleolar protein 3 0 ;;; 231.21 3.91E-20 983410000 291714 359048 360828 359772 413248 499420 351163 375883 341158 372070 FALSE TRUE 303231.094 420711.701 370231.4741 430933.8278 343004.2526 383437.2738 323637.9265 370844.9032 328879.7902 444969.9928 0.681464141 0.945483309 0.832036947 0.968455929 0.770848053 0.861714902 0.727325284 0.833415532 0.739105548 1 18.76334852 TAGTICLETFKDFPQMGR ddPTM_MDA-MB-175_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 ; 151.95 4.01E-08 921070000 1081370 446449 603880 425115 799280 1274480 763000 571800 660220 410188 FALSE TRUE 1124063.323 523123.1429 619617.6089 509201.4782 663418.6711 978501.3349 703194.0663 564135.9563 636458.8112 490556.4851 2.29140447 1.066387172 1.26309126 1.038007841 1.352379779 1.994676178 1.433461972 1.149991843 1.297422072 1 18.90405974 7.999989963 0.035850287 5.47E-07 3.518482501 0.154165706 0.372952525 2309.059732 6.320816254 180.8708935 521.3523268 99997689.02 -7.999989963 3.518481954 TAGYPNVNIHNFTTSWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAGYPNVNIHNFTTSWR 17 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 89.468 0.0040417 719070000 222870 276520 276710 302080 328030 388280 285240 307510 272970 253560 FALSE TRUE 231669.0797 324010.159 283921.2899 361830.5224 272271.5778 298107.8544 262882.1435 303388.3314 263145.863 303240.2273 0.763978717 1.068493326 0.936291641 1.193214125 0.897874204 0.983074894 0.866910521 1.000488405 0.867780193 1 18.21010163 TAHETDKSEGGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAHETDKSEGGKR 13 2 P83916;J3KS05;K7ELA4;B5MD17;C9JWS9 P83916 CBX1 Chromobox protein homolog 1 0 ;;; 203.82 4.97E-08 1298395000 1016488 749855 1084703 684293 1505904 1398176 1264108 1132276 1261579 676811 FALSE TRUE 1056619.731 878636.7632 1112971.251 819644.113 1249930.976 1073470.814 1165023.912 1117099.692 1216175.018 809419.1571 1.305404897 1.085515157 1.375024598 1.012632461 1.544232015 1.326223631 1.439333257 1.380125096 1.502528088 1 19.62652747 3.232979675 24.99995083 1.386948273 1.199733653 0.190968043 0.168597227 188.258176 843306.3841 0.043640674 0.053551154 1709.93529 -3.232979675 -0.18721462 TAHNSEAADLEESFNEHELEPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAHNSEAADLEESFNEHELEPSSPK 25 0 A0A0D9SGE8;Q5JRC6;Q8IWS0-2 A0A0D9SGE8 PHF6 PHD finger protein 6 1 TAHNSEAADLEESFNEHELEPS(0.084)S(0.916)PK 106.6 0.0064238 197750000 8036.4 21107 20988 18699 33154 31188 23730 34025 29128 18487 TRUE FALSE 8353.683277 24731.96306 21534.96452 22397.60639 27518.49492 23945.05966 21869.98059 33568.95053 28079.68897 22109.1737 0.377837878 1.118629009 0.974028465 1.013045838 1.244664106 1.083037294 0.989181274 1.518326781 1.270046966 1 14.43235749 4.863716197 2.122795688 1.16612422 7.70E-32 0.649328169 0.1649393 0.717241457 2.687899437 0.045440371 1.790117825 73066.14543 -4.863716197 -1.16612422 TAHNSEADLEESFNEHELEPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 TAHNSEADLEESFNEHELEPS(0.182)S(0.818)PK;TAHNSEADLEESFNEHELEPS(0.226)S(0.774)PK 180.23 2.31E-17 371270000 75717 169369 184142 147833 232750 238970 192441 213090 197441 133961 TRUE FALSE 78706.36563 198456.8082 188940.8918 177073.9262 193187.2381 183472.8391 177356.9716 210233.8771 190335.137 160208.0931 0.491275841 1.238743963 1.179346737 1.105274538 1.205851929 1.145215798 1.107041274 1.312255037 1.18804945 1 17.2895875 4.741690801 24.99839162 1.177124262 0.491275589 0.861331956 0.080914816 96.00114519 766651.5075 0.018729311 0.133443083 55168.45235 -4.741690801 -0.685848673 TAHSLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAHSLFK 7 0 P55060-3;P55060;P55060-4;P55060-2 P55060-3 CSE1L Exportin-2 0 105.12 0.0079989 312060000 539120 354700 523340 418830 890460 719340 651460 444120 512710 467860 FALSE TRUE 560404.8739 415616.9658 536978.6703 501673.3239 739099.9273 552284.1867 600396.8629 438167.2978 494257.6673 559528.2093 1.001566793 0.742798949 0.959699013 0.896600592 1.320934164 0.987053338 1.073041275 0.783101353 0.883347183 1 19.09385134 5.049813371 21.83628136 0.955991554 1.559364294 0.005520642 0.152952825 17736.3391 2531269.631 0.036871684 659379.7849 112153.6395 -5.049813371 0.603372739 TAITT(ph)PNFK ddPTM_MDA-MB-175_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(0.073)T(0.927)PNFK 99.215 0.01339 0 316260 220720 255180 195230 292870 291210 272550 254160 236480 207880 TRUE FALSE 328746.189 258626.943 261830.2004 233845.9113 243088.062 223580.8908 251186.8188 250753.4009 227969.131 248610.1059 1.322336386 1.040291351 1.053176014 0.940613055 0.977788337 0.899323421 1.010364474 1.00862111 0.916974514 1 17.92352542 5.966185632 1.030583569 0.969682496 4.828198597 0.863595599 0.041573809 6.462467265 0.742490236 0.012162409 48.35563606 925093.5052 -5.966185632 3.858516102 TALAEAELEYNPEHVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TALAEAELEYNPEHVSR 17 0 Q9NSE4 Q9NSE4 IARS2 "Isoleucine--tRNA ligase, mitochondrial" 0 192.55 1.80E-10 104560000 41120 105160 91177 95579 94256 152080 91870 101070 83989 97392 FALSE TRUE 42743.44935 123220.412 93553.14752 114484.2409 78234.39879 116761.7248 84668.98934 99715.32197 80966.2523 116474.0977 0.366978154 1.057921155 0.803209893 0.982915886 0.671689245 1.002469451 0.726934065 0.856115857 0.695143846 1 16.82964963 4.754158181 24.58929192 0.855299214 0.366977701 0.555733862 0.133601284 1652.828735 2605601.482 0.028736852 0.699669443 56775.13573 -4.754158181 -0.488321513 TALIHDGLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 ;;;;;;; 181.87 1.84E-06 10657710000 4909170 5580250 5605010 5216590 6600160 7431620 5719880 5660620 5380070 5081980 FALSE TRUE 5102987.822 6538614.529 5751081.165 6248415.932 5478267.161 5705738.882 5271540.859 5584748.648 5186442.332 6077696.681 0.839625287 1.075837587 0.946259984 1.028089466 0.901372255 0.938799546 0.867358333 0.918892294 0.85335656 1 22.53509325 3.212991991 24.71444119 0.90801837 0.977966765 0.148654311 0.068151552 295.5694088 285694.2479 0.018055053 0.02158773 1633.021832 -3.212991991 0.069948395 TALPTSGS(ph)SAGELELLAGEVPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPT(0.005)S(0.015)GS(0.532)S(0.448)AGELELLAGEVPAR;TALPT(0.02)S(0.018)GS(0.944)S(0.018)AGELELLAGEVPAR;TALPT(0.01)S(0.062)GS(0.492)S(0.436)AGELELLAGEVPAR;TALPT(0.017)S(0.156)GS(0.788)S(0.038)AGELELLAGEVPAR;TALPTS(0.001)GS(0.916)S(0.083)AGELELLAGEVPAR 276.79 9.41E-52 163325000 89631 90496 103609 92511 114407 131282 116428 101869 103936 97185 TRUE FALSE 93169.70109 106037.984 106309.1357 110809.3997 94960.13901 100793.7451 107302.0691 100503.6127 100195.3637 116226.54 0.801621567 0.912338817 0.914671775 0.953391537 0.817026292 0.867217979 0.923214862 0.864721712 0.862069572 1 16.82658002 -2.314256852 2.180046781 1.570438893 0.882224868 0.389097569 0.045155374 4159061.222 603950.9256 11667359.11 0.010723247 0.004850016 2.314256852 -0.688214025 TALPTSGSS(ph)AGELELLAGEVPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 TALPTSGS(0.001)S(0.999)AGELELLAGEVPAR;TALPTSGS(0.119)S(0.881)AGELELLAGEVPAR 298.11 9.72E-62 141385000 95126 105803 100349 95856 118656 136566 111427 107112 108271 95559 TRUE FALSE 98881.64793 123973.8422 102964.1774 114816.0307 98486.8955 104850.6162 102693.0606 105676.3388 104374.3479 114281.9565 0.865242869 1.084806789 0.900966177 1.004673303 0.861788672 0.917473059 0.898593827 0.92469837 0.913305574 1 16.80223811 3.249579713 24.99390009 0.914758551 0.968060018 0.101708144 0.063627661 401.51317 910721.1735 0.016035712 0.021505879 1776.559318 -3.249579713 0.053301467 TALPTSGSSAGELELLAGEVPARS(ph)PGAFDMSGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.01)S(0.031)GS(0.024)S(0.024)AGELELLAGEVPARS(0.911)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(1)PGAFDMSGVR;TALPTSGSSAGELELLAGEVPARS(0.998)PGAFDMS(0.002)GVR 324.89 1.47E-105 3620183000 761803 996754 1032956 787567 1194160 1371396 875074 1033215 1093583 1206138 TRUE FALSE 791879.5707 1167938.746 1059875.682 943345.4019 991177.1097 1052910.063 806483.4133 1019366.443 1054225.161 1442457.648 0.548979425 0.809686681 0.734770746 0.653984818 0.687144687 0.729941752 0.559103704 0.70668726 0.730853459 1 20.46009753 0.697259465 2.240987978 0.999889374 0.681570896 0.623936427 0.074472202 0.980860794 6.397291579 0.06790296 0.018418802 4.980345416 -0.697259465 -0.318318477 TAMPS(ph)PGVSQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAMPSPGVSQNK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;TAMPS(1)PGVSQNK;TAMPS(0.999)PGVS(0.001)QNK 231.69 2.97E-12 736090000 1830690 1106740 1414440 1195090 1621510 1818550 1838070 1469650 1553500 853780 TRUE FALSE 1902967.055 1296813.986 1451301.468 1431475.235 1345886.309 1396219.323 1693997.27 1449951.746 1497589.838 1021061.844 1.863713805 1.270064093 1.421364902 1.401947632 1.318124183 1.367418958 1.659054522 1.42004302 1.466698464 1 19.96163882 -1.998638709 2.560151101 0.548596043 1.455080489 0.413973644 0.165705062 12882449.32 7566075.416 34292407.06 0.037265269 0.010031394 1.998638709 0.906484445 TANKDHLVTAYNHLFETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TANKDHLVTAYNHLFETK 18 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 211.16 2.14E-16 1250700000 1226300 747420 1085300 722850 1598300 1490000 1380300 1206900 1319600 657080 FALSE TRUE 1274715.271 875783.5709 1113583.81 865827.5725 1326621.537 1143970.081 1272108.479 1190723.48 1272107.854 785822.2454 1.622142003 1.114480502 1.417093772 1.101810973 1.688195447 1.455761895 1.618824724 1.515258045 1.618823928 1 19.58384348 3.232957607 24.99989638 1.516487985 1.307011148 0.107325597 0.226158991 227.4645256 1014916.875 0.058792905 0.072153979 1709.848402 -3.232957607 -0.209476836 TANKDHLVTAYNHLFETKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TANKDHLVTAYNHLFETKR 19 2 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 172.66 2.55E-12 789720000 430620 354330 474110 244250 750270 541470 343810 484180 511330 430320 FALSE TRUE 447621.2101 415183.4212 486465.6961 292561.921 622739.3734 415721.7986 316861.2738 477690.3591 492927.3332 514632.965 0.869787286 0.806756367 0.945267266 0.568486554 1.210065067 0.807802505 0.615703415 0.928215625 0.957823083 1 18.97318435 1.51293791 11.06006745 0.966895522 0.83435608 0.117960272 0.166088913 0.242937779 54.68751939 0.086741301 0.040260726 32.57901202 -1.51293791 -0.132539442 TANQASDTFS(ph)GIGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TANQASDTFSGIGKK 15 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 1 TANQASDTFS(1)GIGKK;TANQASDT(0.047)FS(0.953)GIGKK 176.67 4.81E-07 619420000 739490 317190 511160 327490 630040 672750 682560 490070 550370 203370 TRUE FALSE 768685.6362 371664.9151 524481.2495 392266.5445 522946.0258 516514.0081 629059.1637 483501.4132 530562.2912 243216.4577 3.160500088 1.528124036 2.156438155 1.612828952 2.150125985 2.123680334 2.586416929 1.987946941 2.181440747 1 17.89188133 4.753737572 24.39025478 1.996281552 3.160501272 0.423588733 0.425081914 1914.08642 3075975.779 0.093923653 2.155844896 56720.17631 -4.753737572 1.16421972 TANQASDTFSGIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TANQASDTFSGIGK 14 0 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 259.51 4.69E-24 157892000 227090 170124 188888 184809 246840 286760 310470 224170 232790 105844 FALSE TRUE 236055.6886 199341.4736 193810.5765 221363.6686 204882.225 220164.3359 286134.5501 221165.3678 224411.9334 126582.1053 1.864842491 1.574799796 1.531105649 1.748775375 1.618571792 1.739300633 2.260466039 1.747208796 1.772856699 1 16.94971394 2.480777218 24.97908874 1.802475954 1.661341905 0 0.305449134 540.578016 3693504.475 0.098278574 0.083887339 302.5361098 -2.480777218 -0.141134049 TANQASDTFSGIGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TANQASDTFSGIGKK 15 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 ; 214.28 4.00E-12 2419100000 2173450 1396680 1776180 1198240 2713810 2375710 2242530 1980180 2297990 1213780 FALSE TRUE 2259259.484 1636548.925 1822468.71 1435248.296 2252517.546 1823987.357 2066754.639 1953638.926 2215285.789 1451596.952 1.556395859 1.12741276 1.255492241 0.988737469 1.551751361 1.256538431 1.423779952 1.345854938 1.526102536 1 20.4692095 3.224924578 24.99844972 1.366769361 1.226215634 0.076785245 0.196468264 509.1774661 933454.4398 0.052735336 0.063350552 1678.512495 -3.224924578 -0.140553726 TAPAAPAEDAVAAAAAAPS(ph)EPSEPSRPSPQPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.51)EPS(0.067)EPS(0.067)RPS(0.356)PQPKPR 198.52 2.21E-27 1332900000 1444300 1121100 1399000 1128500 1830100 1883200 1550000 1473600 1610000 1047300 TRUE FALSE 1501322.079 1313640.204 1435459.089 1351713.932 1519020.256 1445855.34 1428506.95 1453848.802 1552056.414 1252498.383 1.19866189 1.048815888 1.146076601 1.079214113 1.212792189 1.154377011 1.140525983 1.160759025 1.239168398 1 20.25637731 3.254034078 24.99552018 1.158633257 1.115228442 0.04458091 0.069681085 611.4297217 987685.9765 0.017689009 0.023866071 1794.87446 -3.254034078 -0.043404815 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.051)EPS(0.155)EPS(0.408)RPS(0.386)PQPKPR 138.57 2.26E-09 1193300000 830030 605350 709760 559760 944440 939090 785930 756310 870040 511180 TRUE FALSE 862800.2253 709314.1535 728256.9287 670478.8573 783904.4261 721000.5795 724326.753 746172.9015 838727.4304 611335.9339 1.411335695 1.160269034 1.191254903 1.096743738 1.282280957 1.179385244 1.184826072 1.220561168 1.371958336 1 19.22160584 -1.723385722 2.694049473 0.959890851 1.223178371 0.36001654 0.092406586 13211091.89 11228072.16 3573962.234 0.022615702 0.018906637 1.723385722 0.26328752 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPK 32 1 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPSEPS(0.002)EPS(0.04)RPS(0.957)PQPK 163.43 3.74E-14 207370000 148970 91014 125050 81915 145420 155040 166930 121620 150210 82075 TRUE FALSE 154851.4506 106644.9465 128308.9057 98117.54251 120701.5603 119034.3097 153845.5904 119989.8828 144803.9714 98156.02483 1.577605154 1.08648396 1.307193379 0.999607947 1.229690796 1.212705077 1.567357589 1.222440324 1.475242826 1 16.5827892 TAPAAPAEDAVAAAAAAPSEPSEPSRPS(ph)PQPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 TAPAAPAEDAVAAAAAAPS(0.005)EPS(0.004)EPS(0.048)RPS(0.943)PQPKPR;TAPAAPAEDAVAAAAAAPSEPS(0.001)EPS(0.063)RPS(0.936)PQPKPR;TAPAAPAEDAVAAAAAAPS(0.009)EPS(0.06)EPS(0.027)RPS(0.903)PQPKPR;TAPAAPAEDAVAAAAAAPSEPSEPS(0.035)RPS(0.965)PQPKPR;TAPAAPAEDAVAAAAAAPSEPSEPS(0.035)RPS(0.965)PQPKPR 324.12 2.87E-105 7916450000 2592880 1902417 2387570 1699441 2959930 3279770 2901410 2545860 2732780 1694164 TRUE FALSE 2695248.905 2229142.321 2449792.036 2035585.357 2456802.156 2518093.123 2673989.903 2511736.911 2634427.782 2026102.999 1.330262531 1.100211747 1.209115251 1.004680097 1.212575154 1.242825821 1.319769974 1.239688659 1.30024376 1 20.95027609 3.012011488 24.9549739 1.242093134 1.153711953 0.042209513 0.112846351 457.7911602 951095.9471 0.030516446 0.036450068 1028.043492 -3.012011488 -0.088381181 TAPFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAPFDSR 7 0 P14854;A0A494C160;K7EQD3 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 ; 86.866 0.045975 354870000 577040 740100 613220 684760 712460 857430 631040 592810 551290 570530 FALSE TRUE 599821.9848 867206.4178 629201.017 820203.4842 591356.3037 658304.877 581577.4359 584864.3516 531449.1806 682314.43 0.879099076 1.27097769 0.922156984 1.202090192 0.866691774 0.9648116 0.852359866 0.857177169 0.778891897 1 19.3800772 3.214146862 24.92296626 0.879367714 1.072579046 0.345834954 0.122281319 214.989953 219473.5404 0.032378956 0.038717761 1637.370126 -3.214146862 0.193211331 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TAPPALPTGYDSEEEEESRPMSYDEK 26 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPTGYDS(1)EEEEESRPMSYDEK;TAPPALPT(0.058)GY(0.148)DS(0.794)EEEEESRPMSYDEK;TAPPALPT(0.001)GYDS(0.998)EEEEESRPMSYDEK 272.09 9.75E-61 705480000 458733 337147 437072 343420 527264 617206 608028 442690 472982 285076 TRUE FALSE 476844.1331 395049.3746 448462.4554 411347.451 437639.8536 473869.2603 560369.1766 436756.4646 455959.4702 340931.1841 1.398652148 1.158736405 1.315404622 1.206540998 1.283660381 1.389926421 1.643643066 1.281069274 1.337394441 1 18.37912104 2.833715831 5.302931972 1.367700413 1.263346785 0.004867483 0.159871141 0.581026762 25.48499795 0.047121112 0.050054843 681.8923703 -2.833715831 -0.104353628 TAPPALPTGYDS(ph)EEEEESRPMSYDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAPPALPTGYDSEEEEESRPMSYDEKR 27 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 TAPPALPTGYDS(1)EEEEESRPMSYDEKR;TAPPALPTGYDS(1)EEEEESRPMSYDEKR 338.26 8.02E-96 1298420000 1036870 845260 1085650 706710 1386960 1288510 1062160 1076490 1138280 879880 TRUE FALSE 1077806.428 990426.8298 1113942.931 846495.1287 1151205.035 989273.0801 978905.1238 1062061.412 1097313.525 1052275.64 1.024262453 0.941223756 1.058603743 0.804442388 1.094014716 0.940127323 0.930274433 1.009299629 1.042800464 1 20.00508123 1.561517306 6.809219988 1.022665421 0.969767235 0.075330495 0.076034951 0.316430158 28.60029556 0.038603476 0.01794968 36.43487683 -1.561517306 -0.052898186 TAPPAS(ph)PEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPPAS(1)PEAR;TAPPAS(1)PEAR 131.54 0.0002594 949730000 609820 650420 635760 675740 665120 834870 657290 660070 672610 618150 TRUE FALSE 633896.1645 762124.5754 652328.4279 809399.3551 552063.14 640984.0951 605769.8923 651222.8413 648402.8975 739264.6573 0.85746851 1.030922509 0.882401751 1.094870892 0.746773344 0.867056322 0.819422228 0.880906229 0.877091703 1 19.49573142 3.232405548 24.99919078 0.857827508 0.965022516 0.245291064 0.086375599 185.1207705 751878.8551 0.022762173 0.027854161 1707.676288 -3.232405548 0.107195008 TAPS(ph)PLVEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAPSPLVEAK 10 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6;A0A0A0MS48;Q8TEH3-4;Q8TEH3-3;Q8TEH3-5;Q8TEH3-2 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 TAPS(1)PLVEAK;T(0.001)APS(0.999)PLVEAK;TAPS(1)PLVEAK;T(0.011)APS(0.989)PLVEAK 184.03 1.68E-06 808400000 2457990 1605790 2158080 1837020 2865200 2823530 2606980 2168090 2116280 1218730 TRUE FALSE 2555033.343 1881571.941 2214321.338 2200377.073 2378174.327 2167807.949 2402638.096 2139030.3 2040115.496 1457516.81 1.753004375 1.290943562 1.519242401 1.509675263 1.631661681 1.487329638 1.648446234 1.467585338 1.399720046 1 20.47508109 0.756285119 1.624502306 1.000709967 1.536511045 0.663218338 0.116104778 0.475126981 2.088641172 0.102498544 0.029402153 5.705387145 -0.756285119 0.535801078 TAPTALGITLSSS(ph)PTSTPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 TAPTALGITLS(0.001)S(0.007)S(0.93)PT(0.028)S(0.028)T(0.007)PELR;TAPTALGITLS(0.001)S(0.006)S(0.945)PT(0.036)S(0.01)T(0.003)PELR;TAPTALGITLSS(0.039)S(0.925)PT(0.027)S(0.007)T(0.002)PELR;TAPTALGIT(0.001)LS(0.004)S(0.195)S(0.78)PT(0.016)S(0.003)T(0.001)PELR 193.85 6.08E-18 407888000 514402 542405 522014 533298 570847 722350 576466 570079 533652 559939 TRUE FALSE 534710.9882 635558.8394 535618.1137 638782.7527 473814.6308 554595.1598 531281.0886 562438.0235 514445.9688 669648.3264 0.798495221 0.949093449 0.79984985 0.953907786 0.707557403 0.828188675 0.793373279 0.839900589 0.768233039 1 19.35304412 5.06818466 14.78689609 0.840200492 0.373558193 0.020407683 0.08778482 3462909.145 17236162.37 0.019246231 48953477.55 116999.6761 -5.06818466 -0.466642299 TAPTLS(ph)PEHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 TAPT(0.001)LS(0.999)PEHWK;TAPTLS(1)PEHWK;TAPTLS(1)PEHWK;TAPT(0.002)LS(0.998)PEHWK;TAPTLS(1)PEHWK 214.48 8.71E-12 3654760000 1774280 1327310 1626800 1306780 2128780 2130050 1894400 1708170 1734360 1225200 TRUE FALSE 1844329.944 1555265.167 1669195.744 1565257.184 1766930.736 1635378.169 1745911.978 1685274.775 1671940.722 1465254.482 1.258709642 1.06143007 1.139184875 1.068249374 1.205886593 1.116105215 1.19154181 1.150158417 1.141058255 1 20.48271982 -2.130681526 1.934215201 0.738989717 1.1458483 0.376805267 0.057051536 2347965.64 533575.8303 2687561.429 0.013384782 0.007401478 2.130681526 0.406858583 TAQEHDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAQEHDKR 8 1 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 87.308 0.010008 23414000 23279 14054 17949 17892 22978 23102 33405 21868 24459 11187 FALSE TRUE 24198.0729 16467.66518 18416.76569 21430.9842 19072.20777 17736.91061 30786.62881 21574.89523 23578.72537 13378.87846 1.808677234 1.230870377 1.376555272 1.601852073 1.425546082 1.325739722 2.301136743 1.612608657 1.762384301 1 13.70766956 TAQEHDKRDPVVAYYCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAQEHDKRDPVVAYYCR 17 2 A0A087WY55;Q9NP79 A0A087WY55 VTA1 Vacuolar protein sorting-associated protein VTA1 homolog 0 ; 100.04 0.00086003 229526000 268610 184405 252940 185693 349550 352510 271570 255280 285980 195633 FALSE TRUE 279214.9302 216075.1243 259531.8242 222422.5212 290133.6159 270644.8948 250283.6338 251858.3892 275687.6357 233963.5407 1.193412142 0.923541863 1.109283196 0.950671718 1.240080463 1.156782352 1.069754856 1.076485628 1.178335884 1 17.8359242 3.253314122 24.99983809 1.118952132 1.040253748 0.135678101 0.093740184 463.7572238 785832.947 0.024580478 0.033142331 1791.901457 -3.253314122 -0.078698384 TAQVPS(ph)PPR ddPTM_MDA-MB-175_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 112.64 0.0020235 12997562000 1729233 1725878 1868034 1731362 2020707 2573128 2141930 1944646 1732744 1422919 TRUE FALSE 1797504.454 2022284.121 1916716.501 2073820.236 1677227.946 1975558.018 1974039.93 1918581.201 1670382.882 1701712.735 1.056291357 1.188381611 1.126345512 1.218666461 0.985611679 1.160923332 1.160031238 1.12744129 0.981589224 1 20.69855609 1.241691918 24.76782715 0.990794558 1.130694228 0.431237579 0.062948481 57.61550285 455759.8252 0.043642432 0.014412477 17.44584131 -1.241691918 0.13989967 TAQVPS(ph)PPRGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 97.797 0.0036328 7437840000 3606120 4200030 4749570 3489050 6227790 6148070 3775160 4920410 4897580 4478710 TRUE FALSE 3748492.402 4921352.481 4873347.696 4179173.676 5169192.48 4720273.917 3479253.095 4854459.952 4721317.052 5356227.474 0.699838164 0.918809461 0.909847037 0.780245741 0.965080834 0.881268382 0.649571571 0.906320722 0.881463133 1 22.3527858 0.883430601 1.943513083 0.998464577 0.84061665 0.208202269 0.095809074 0.772160742 5.844874831 0.088252282 0.024652023 7.645934988 -0.883430601 -0.157847928 TAS(ph)EGDGGAAAGAAAAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASEGDGGAAAGAAAAGAR 19 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 TAS(1)EGDGGAAAGAAAAGAR 257.56 5.62E-31 135860000 131510 112920 133870 145350 183560 233790 201240 158260 170280 128860 TRUE FALSE 136702.1163 132313.1316 137358.7622 174099.7962 152358.5368 179495.8156 185466.283 156138.7836 164151.6561 154107.6498 0.887056006 0.858576013 0.891316961 1.129728449 0.988650057 1.16474306 1.203485247 1.013179967 1.065175261 1 17.23357895 3.765740185 9.769305726 1.084088152 0.876685768 0.654518657 0.067124662 0.300731681 104.9891457 0.017458548 0.031115717 5830.961643 -3.765740185 -0.207402384 TAS(ph)EINFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASEINFDK 9 0 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 TAS(1)EINFDK;T(0.001)AS(0.999)EINFDK 155.88 7.58E-05 111070000 357250 236510 293390 264320 477640 446870 438700 347970 360310 213785 TRUE FALSE 371354.5059 277128.7527 301035.9844 316601.7071 396450.9234 343091.2149 404313.5477 343306.0313 347342.5135 255672.0776 1.452464068 1.083922638 1.17743004 1.23831163 1.550622685 1.341918985 1.581375454 1.342759188 1.35854692 1 17.96393508 5.067950914 21.16088348 1.322174817 5.02532597 0.049317068 0.176083696 2273.82945 731713.4421 0.041045334 13198.96376 116936.7215 -5.067950914 3.703151153 TAS(ph)EINFDKLQFEPPLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASEINFDKLQFEPPLRK 18 2 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 T(0.02)AS(0.98)EINFDKLQFEPPLRK;T(0.132)AS(0.868)EINFDKLQFEPPLRK 135.86 5.91E-06 1251150000 773760 489670 648560 424760 1230060 919070 712090 680670 816000 503460 TRUE FALSE 804308.6423 573767.0134 665462.0064 508776.2602 1020974.841 705629.9211 656274.5251 671546.732 786632.3194 602103.3477 1.33583154 0.952937757 1.105228876 0.844998225 1.695680392 1.171941534 1.089969899 1.115334659 1.306473918 1 19.19965161 6.303034837 10.20156173 1.159198475 1.3542071 0 0.227399057 0 0 0.048307983 0 2009253.977 -6.303034837 0.195008625 TAS(ph)FGNILDVPEIVISGNGQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TASFGNILDVPEIVISGNGQPR 22 0 O43318;O43318-3 O43318 MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 T(0.152)AS(0.848)FGNILDVPEIVISGNGQPR;T(0.128)AS(0.872)FGNILDVPEIVISGNGQPR;T(0.126)AS(0.874)FGNILDVPEIVISGNGQPR;T(0.144)AS(0.856)FGNILDVPEIVISGNGQPR 331.02 9.81E-81 556982000 422590 427964 452177 430380 545373 620296 485192 497424 443740 386834 TRUE FALSE 439274.1795 501463.4879 463961.1041 515507.8794 452670.6923 476241.6547 447161.3832 490756.8449 427769.8841 462626.7159 0.949521859 1.083948399 1.002884373 1.114306333 0.978479359 1.029429642 0.966570602 1.060805241 0.92465452 1 18.81948906 TAS(ph)FSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 TAS(1)FSESR;TAS(1)FSESR;TAS(0.979)FS(0.021)ESR;TAS(0.994)FS(0.006)ESR;T(0.002)AS(0.995)FS(0.003)ESR;TAS(0.795)FS(0.205)ESR;T(0.038)AS(0.951)FS(0.011)ESR;T(0.002)AS(0.996)FS(0.001)ESR;TAS(0.994)FS(0.006)ESR;TAS(0.999)FSESR;TAS(1)FSESR 216.26 8.37E-06 55667130000 9098227 9318541 10864569 10907695 12823969 14402090 13401065 11914186 10990620 8661390 TRUE FALSE 9457432.027 10918927.93 11147708.59 13065204.51 10644155.33 11057422.86 12350654.51 11754495.82 10595069.73 10358423.54 0.913018472 1.054110974 1.076197411 1.261312058 1.027584486 1.067481246 1.192329553 1.134776521 1.022845773 1 23.30430112 4.714361216 2.009407595 1.110907601 0.862578119 0.332751731 0.077224878 0.726331661 3.301041563 0.019197407 0.325600384 51803.75207 -4.714361216 -0.248329482 TAS(ph)FSESRADEVAPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.009)AS(0.971)FS(0.019)ESRADEVAPAK;T(0.16)AS(0.677)FS(0.16)ES(0.003)RADEVAPAK;T(0.001)AS(0.94)FS(0.058)ESRADEVAPAK;T(0.003)AS(0.992)FS(0.005)ESRADEVAPAK;T(0.001)AS(0.997)FS(0.002)ESRADEVAPAK;T(0.009)AS(0.986)FS(0.005)ESRADEVAPAK 233.2 3.16E-19 3128370000 1622802 1281876 1711150 1143729 2628615 2241735 1808317 1770674 2055996 1443925 TRUE FALSE 1686871.476 1502028.231 1755743.975 1369955.183 2181803.961 1721126.02 1666576.388 1746941.011 1982001.106 1726834.458 0.976857665 0.869815994 1.016741336 0.793333244 1.263470248 0.996694276 0.965104895 1.01164359 1.147765552 1 20.71969836 3.265867494 24.99999953 1.05125009 0.918343109 0.34583578 0.100016952 275.3022233 252042.8441 0.026904317 0.036419773 1844.452579 -3.265867494 -0.132906981 TAS(ph)FSESRADEVAPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 T(0.127)AS(0.839)FS(0.034)ESRADEVAPAKK;T(0.031)AS(0.938)FS(0.031)ESRADEVAPAKK;T(0.015)AS(0.973)FS(0.012)ESRADEVAPAKK;T(0.077)AS(0.919)FS(0.004)ESRADEVAPAKK;T(0.023)AS(0.969)FS(0.008)ESRADEVAPAKK;TAS(0.998)FS(0.002)ESRADEVAPAKK 218.07 2.49E-15 8997880000 4580720 2862980 4380020 2219870 7231320 5121590 3654700 4358010 5307770 3234530 TRUE FALSE 4761570.363 3354674.544 4494166.919 2658953.66 6002142.809 3932178.341 3368235.064 4299598.004 5116744.395 3868274.225 1.230928855 0.867227696 1.161801532 0.687374655 1.551633225 1.016520058 0.87073327 1.111502896 1.322746035 1 21.88325864 TAS(ph)LNQRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TASLNQRPR 9 1 A0A0A0MRT6;Q8IZP0-2;Q8IZP0-4;Q8IZP0-3;Q8IZP0-5;Q8IZP0-6;Q8IZP0-9;Q8IZP0;Q8IZP0-12;B6VEX4;Q8IZP0-10;Q8IZP0-8;Q8IZP0-7;Q8IZP0-11 A0A0A0MRT6 ABI1 Abl interactor 1 1 T(0.017)AS(0.983)LNQRPR;T(0.013)AS(0.987)LNQRPR;T(0.015)AS(0.985)LNQRPR 112.13 0.0012192 1927320000 461860 447830 624450 549080 907770 885830 655270 626070 616210 632000 TRUE FALSE 480094.5894 524741.3189 640723.68 657686.3852 753467.5796 680109.4074 603908.2252 617678.5557 594032.7225 755828.2996 0.635190016 0.694259952 0.847710625 0.870153162 0.996876645 0.899819983 0.79900187 0.817220731 0.785936069 1 19.52769901 4.28960672 2.853615148 0.87088353 0.64248081 0.602629507 0.069848531 0.190870688 3.043779353 0.018883408 0.064140457 19480.79698 -4.28960672 -0.228402719 TAS(ph)LPGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;TAS(1)LPGYGR;TAS(1)LPGYGR;TAS(1)LPGYGR 205.59 1.54E-05 4739460000 2144360 2091640 2479840 2158710 2984170 3207830 2516910 2311120 2292430 1886090 TRUE FALSE 2229020.989 2450862.899 2544466.668 2585696.395 2476921.849 2462860.098 2319628.017 2280143.217 2209925.892 2255633.224 0.988201878 1.086552048 1.128049827 1.146328387 1.098104879 1.09187082 1.028371099 1.010866125 0.979736363 1 21.10510107 2.065483078 2.037553562 0.996035947 1.095453525 0.530389575 0.039777105 0.267771636 2.119955141 0.022948542 0.012735969 116.2741243 -2.065483078 0.099417578 TAS(ph)LTSAASVDGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TAS(0.999)LT(0.001)SAASVDGNR;TAS(0.866)LT(0.126)S(0.008)AASVDGNR;TAS(0.984)LT(0.014)S(0.001)AASVDGNR;TAS(0.999)LTSAASVDGNR;TAS(0.996)LT(0.004)SAASVDGNR 324.7 1.20E-56 6195950000 1148880 1068630 1283330 1222690 1547020 1797920 1483280 1334110 1399160 1063410 TRUE FALSE 1194238.67 1252158.89 1316774.634 1464534.433 1284058.093 1380380.328 1367016.638 1316228.438 1348804.505 1271764.829 0.939040491 0.984583675 1.03539161 1.151576454 1.009666303 1.085405333 1.074897344 1.034962131 1.060576982 1 20.27840049 4.315170294 2.751959038 1.06111936 0.947082268 0.485666173 0.040522118 0.209210806 3.057835363 0.009780837 0.035429013 20661.90186 -4.315170294 -0.114037092 TAS(ph)NPKVENEDEPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 T(0.11)AS(0.89)NPKVENEDEPVR;T(0.031)AS(0.969)NPKVENEDEPVR;T(0.153)AS(0.847)NPKVENEDEPVR 211.16 9.19E-10 3847530000 4250710 2095880 3208790 1997010 4653610 4582170 3722530 3066880 3356450 1527650 TRUE FALSE 4418531.313 2455831.086 3292413.703 2392012.618 3862591.034 3518030.461 3430748.372 3025773.49 3235652.02 1826963.769 2.41851064 1.344214444 1.802123151 1.309283007 2.114213265 1.925615888 1.877841493 1.656175969 1.77105429 1 20.80101659 0.008565034 1.007633526 0.992712118 1.791550604 0.373445377 0.311855862 7.966063308 7.056192504 0.475987173 0.088722117 1.019917477 -0.008565034 0.798838486 TAS(ph)PLPLRPDAPVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TASPLPLRPDAPVEK 15 1 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 T(0.036)AS(0.964)PLPLRPDAPVEK;T(0.204)AS(0.796)PLPLRPDAPVEK;T(0.121)AS(0.879)PLPLRPDAPVEK;T(0.014)AS(0.986)PLPLRPDAPVEK;T(0.048)AS(0.952)PLPLRPDAPVEK 164.59 4.45E-09 1828350000 3168140 2163856 2677800 1992792 3595780 3566530 3363840 2804100 3018400 1799138 TRUE FALSE 3293220.614 2535481.436 2747585.668 2386960.31 2984570.6 2738257.459 3100173.431 2766515.626 2909768.374 2151644.645 1.530559715 1.178392279 1.276970003 1.109365487 1.3871113 1.272634617 1.44083896 1.285767905 1.35234616 1 21.0370084 -1.221267586 5.237357293 0.999974261 1.308391977 0.398153513 0.115895924 3.27E-05 4.86E-06 0.105219667 0.024798446 0.060080344 1.221267586 0.308417716 TAS(ph)PLPLRPDAPVEKS(ph)PEETATQVPSLESLTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASPLPLRPDAPVEKSPEETATQVPSLESLTLK 33 2 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 2 T(0.448)AS(0.552)PLPLRPDAPVEKS(1)PEETATQVPSLESLTLK 244.02 2.56E-47 122610000 101010 33944 58326 30653 79320 91158 74895 60470 71539 28408 TRUE FALSE 104997.9528 39773.61795 59846.02348 36716.07191 65837.21473 69987.93601 69024.5342 59659.49856 68964.32536 33974.0037 3.090538099 1.170707412 1.761524017 1.080710776 1.937870359 2.06004381 2.031686781 1.756033793 2.029914578 1 15.05214362 TAS(ph)PPGPPPYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TASPPGPPPYGK 12 0 P54259 P54259 ATN1 Atrophin-1 1 TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK;TAS(1)PPGPPPYGK 187.78 1.05E-05 1191980000 1871690 1381140 1612390 1283080 2098390 2134290 1835700 1683150 1774820 1213140 TRUE FALSE 1945585.766 1618340.051 1654410.208 1536869.394 1741706.417 1638633.493 1691813.037 1660590.127 1710944.575 1450831.556 1.341014233 1.115456887 1.140318599 1.059302431 1.200488375 1.129444343 1.166098869 1.14457817 1.179285471 1 20.4684486 TAS(ph)PPPPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TASPPPPPK 9 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TAS(1)PPPPPK;T(0.042)AS(0.958)PPPPPK;TAS(1)PPPPPK;T(0.002)AS(0.998)PPPPPK;T(0.002)AS(0.998)PPPPPK;TAS(1)PPPPPK 117.71 0.0011624 5073810000 2969400 2100920 2598800 1993030 3310340 3458110 3190580 2676540 2788500 1782490 TRUE FALSE 3086634.205 2461736.667 2666526.863 2387245.385 2747649.589 2655016.361 2940494.003 2640665.359 2688142.43 2131734.788 1.447944755 1.154804379 1.250871768 1.119860406 1.288926561 1.245472174 1.379390166 1.238740098 1.261011663 1 21.02359653 0.162142751 2.396952148 0.999998462 1.260945443 0.435683306 0.090436043 72.22195464 203.3130333 0.082092006 0.021982446 1.452588999 -0.162142751 0.260946982 TAS(ph)PPPPPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.06)AS(0.94)PPPPPKR;T(0.054)AS(0.946)PPPPPKR;T(0.003)AS(0.997)PPPPPKR;T(0.006)AS(0.994)PPPPPKR;T(0.002)AS(0.998)PPPPPKR 117.09 0.00061473 6192408000 2162799 1569667 2048787 1631337 2563658 2523019 2360009 2025482 2156896 1396884 TRUE FALSE 2248187.975 1839245.097 2102180.072 1954010.59 2127888.329 1937086.074 2175025.328 1998333.727 2079269.734 1670576.675 1.345755635 1.100964191 1.258355934 1.16966232 1.273744786 1.159531378 1.30196079 1.196193959 1.244641905 1 20.67191477 -1.315297056 3.249915147 0.998668113 1.223836595 0.492444272 0.06929262 8089130.157 12318006.98 106378.8792 0.014967695 0.048384131 1.315297056 0.225168482 TAS(ph)PWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TASPWK 6 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A1B0GTD1 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK;TAS(1)PWK 102.41 0.037308 3674540000 8691410 4997030 6200720 4797970 8609360 9138520 8084160 6420570 6834580 4103090 TRUE FALSE 9034553.578 5855231.031 6362315.857 5746994.145 7145944.062 7016237.226 7450502.415 6334512.761 6588604.801 4907011.927 1.841151746 1.193237579 1.2965764 1.171179983 1.456271998 1.429839041 1.518337947 1.290910406 1.342691825 1 22.22641335 0.516580856 1.249478262 1.000302771 1.389886051 0.302549067 0.181538559 2.410436813 4.894718913 0.165926117 0.049889953 3.285344047 -0.516580856 0.38958328 TAS(ph)QEGCQELTQEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASQEGCQELTQEQR 15 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 TAS(1)QEGCQELTQEQR 155.28 2.44E-06 84566000 25948 28851 28629 28310 40118 41267 32639 28917 33113 24167 TRUE FALSE 26972.44708 33805.93482 29375.09526 33909.6335 33298.75669 31683.36466 30080.66989 28529.41491 31921.2696 28902.06094 0.933236115 1.169672117 1.016366802 1.173260051 1.152123952 1.09623202 1.040779408 0.987106593 1.104463438 1 14.81888475 2.186231656 4.673843847 1.025993557 1.097166696 0.118210268 0.074741528 0.365223196 16.70829855 0.027431582 0.020300919 153.5435777 -2.186231656 0.071173139 TAS(ph)QGPQTDSVIQNSENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASQGPQTDSVIQNSENIK 19 0 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TAS(1)QGPQTDSVIQNSENIK 399.26 1.04E-127 232320000 261830 164530 233070 208190 356180 354400 317380 283860 303600 180830 TRUE FALSE 272167.2506 192786.7476 239143.9957 249369.3606 295636.6508 272095.971 292502.9263 280055.321 292673.4953 216260.1763 1.258517658 0.891457461 1.105816151 1.15309885 1.367041569 1.258188057 1.35255104 1.294992568 1.353339761 1 17.7224085 3.467179132 3.441816943 1.290809573 1.069696751 0.285614817 0.130027687 0.23430456 5.874205368 0.033724236 0.050156607 2932.102392 -3.467179132 -0.221112822 TASDTDSSYCIPTAGMS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASDTDSSYCIPTAGMSPSR 20 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 TASDTDSSYCIPTAGMS(0.998)PS(0.002)R;TASDTDSSYCIPTAGMS(0.965)PS(0.035)R 284.07 6.26E-45 413550000 176582 204718 188380 202363 249660 282570 207847 216166 213523 218018 TRUE FALSE 183553.5937 239876.724 193289.3376 242389.7974 207222.8824 216947.3999 191555.409 213268.6483 205838.3489 260734.4529 0.703986725 0.92000394 0.741326416 0.92964238 0.794766016 0.83206265 0.734676246 0.817953462 0.789455888 1 17.9922217 -1.740893689 6.427228707 1.004108201 0.809897794 0.404292467 0.070173083 0.003751136 0.000151223 0.061698076 0.014287282 0.018159601 1.740893689 -0.194210406 TASESISNLSEAGS(ph)IK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;TASESISNLS(0.041)EAGS(0.959)IK;TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK 369.33 3.01E-104 2230800000 3605510 1545424 2040620 1581246 2911580 3721580 3122760 2399910 2407550 1132495 TRUE FALSE 3747858.319 1810838.55 2093800.234 1894011.739 2416670.672 2857299.446 2877989.911 2367743.132 2320902.746 1354385.712 2.767201606 1.33701835 1.545940875 1.398428618 1.784329715 2.109664492 2.124941134 1.748204452 1.713620223 1 20.36920723 3.011767632 24.7643703 1.827060454 1.700717936 0 0.475048784 1264.851485 2661790.137 0.132498464 0.158257194 1027.466408 -3.011767632 -0.126342518 TASFSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 121.31 0.0033468 201839000 548420 290070 257080 229675 491720 1048410 404630 284320 302130 308540 FALSE TRUE 570072.0451 339887.2661 263779.716 275104.0295 408137.61 804932.6663 372914.0433 280509.1555 291256.4003 368992.5056 1.544942069 0.92112241 0.714864698 0.745554517 1.106086448 2.181433644 1.010627689 0.760202853 0.789328769 1 18.49323199 1.999752157 25 0.838753531 1.180070783 0.131753484 0.405982894 20.01461172 2019019.856 0.166034575 0.121309261 99.94294842 -1.999752157 0.341317252 TASLT(ph)SAASVDGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TAS(0.216)LT(0.728)S(0.057)AASVDGNR 243.29 1.77E-16 1230500000 443600 418120 459570 466160 621550 695400 545600 468670 547380 434340 TRUE FALSE 461113.6705 489928.8575 471546.7717 558365.0567 515899.153 533903.8889 502834.4463 462388.2452 527679.9007 519440.6071 0.88771202 0.943185517 0.907797283 1.074935323 0.993182177 1.027843957 0.968030684 0.890165765 1.015861859 1 18.98659927 TASLTSAAS(ph)VDGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASLTSAASVDGNR 14 0 Q9UN36;Q9UN36-5;G3V578;H0YJT9;A0A0A0MS87;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36-4 Q9UN36 NDRG2 Protein NDRG2 1 TASLTSAAS(1)VDGNR;TASLT(0.001)S(0.003)AAS(0.996)VDGNR 321.82 3.17E-56 1017750000 671970 795630 824990 591480 876510 946100 779930 831510 837940 574370 TRUE FALSE 698499.8945 932273.2634 846489.9171 708472.9786 727521.1433 726382.6133 718797.0486 820364.9685 807782.7031 686906.8045 1.016877238 1.357204874 1.232321345 1.03139607 1.059126418 1.057468944 1.046425867 1.194288604 1.175971322 1 19.38975485 3.751674997 24.56136675 1.090999513 1.21764154 0.239251006 0.096875725 855.01048 1601306.812 0.024813299 0.044401853 5645.143634 -3.751674997 0.126642027 TASRPDDIPDSPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 TASRPDDIPDSPS(0.201)S(0.799)PK;TASRPDDIPDSPS(0.101)S(0.899)PK 204.94 1.45E-11 933720000 1228270 471400 600610 513450 1018980 1206050 912370 710730 766950 373570 TRUE FALSE 1276763.048 552359.283 616262.39 615008.8775 845774.1436 925963.1654 840856.0554 701203.8269 739347.6193 446763.8891 2.857802699 1.236356153 1.379391677 1.376585916 1.893112143 2.072600736 1.882103894 1.569517689 1.654895656 1 18.76915306 0.550258834 1.197452343 1.001052143 1.758455984 0.221494619 0.439449871 2.621452356 5.209016439 0.409210233 0.124468976 3.550249166 -0.550258834 0.75740384 TAST(ph)PT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;C9JF13;C9J6B6;C9K073;C9J2Z7;C9JWW9;C9JSU8;C9J556;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 2 T(0.081)AS(0.434)T(0.485)PT(0.88)PPQT(0.12)GGGLEPQANGETPQVAVIVRPDDR 90.515 0.00217 85185000 31199 27590 29168 25511 36327 53278 31856 37219 33197 22767 TRUE FALSE 32430.76061 32328.36788 29928.14204 30556.99966 30152.14952 40904.99194 29359.04348 36720.14018 32002.24645 27227.75775 1.19109186 1.187331259 1.099177623 1.122273818 1.107404796 1.502326865 1.078276212 1.348628871 1.175353724 1 14.73279056 TAST(ph)PTPPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.037)AS(0.151)T(0.762)PT(0.05)PPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.015)T(0.985)PTPPQTGGGLEPQANGETPQVAVIVRPDDR;TAS(0.014)T(0.986)PTPPQTGGGLEPQANGETPQVAVIVRPDDR 225.02 3.16E-36 1310370000 160356 144897 168291 149074 174011 211230 167769 153718 159253.6 142335 TRUE FALSE 166686.9787 169781.9326 172676.8017 178560.3923 144432.6724 162175.0337 154618.8274 151657.6616 153522.094 170222.8181 0.97922817 0.997409951 1.014416302 1.048980356 0.848491841 0.952722059 0.908331968 0.890936147 0.90188904 1 17.37706492 3.24697555 24.99999519 0.911348795 1.009423616 0.55177175 0.04084461 126.5398942 375936.3451 0.010727419 0.014291345 1765.938398 -3.24697555 0.098074821 TASTAETPRRLTPVPGSLQEAFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TASTAETPRRLTPVPGSLQEAFIK 24 2 E9PJY3;Q9C0D2-4;Q9C0D2-3 E9PJY3 CEP295 0 52.853 0.071282 31944000 60800 40611 64413 56125 70559 71883 87858 63778 73466 38078 FALSE TRUE 63200.43095 47585.62334 66091.6557 67226.35748 58565.40638 55189.26265 80971.46039 62923.16023 70821.97301 45538.65505 1.387841404 1.044950126 1.451330866 1.476248198 1.286059202 1.211921226 1.778081946 1.381752714 1.555205636 1 15.47480406 TAT(ph)PPGYKPGS(ph)PPSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 2 T(0.115)AT(0.885)PPGY(0.001)KPGS(0.972)PPS(0.027)FR;T(0.116)AT(0.884)PPGY(0.001)KPGS(0.995)PPS(0.004)FR 81.665 0.027833 871540000 860440 473880 621770 504780 843510 992270 739960 622710 652240 421630 TRUE FALSE 894410.8356 555265.2037 637973.837 604623.9774 700130.4715 761830.3305 681960.0017 614363.591 628766.0098 504240.3259 1.77377887 1.101191585 1.265217802 1.199078983 1.388485679 1.510847688 1.352450343 1.218394403 1.246957011 1 18.94375197 0.917273585 1.077342774 1.005283627 1.351290385 0.283155673 0.175482446 0.820747675 1.940844514 0.160364445 0.051483337 8.265584793 -0.917273585 0.346006758 TATADDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TATADDKK 8 1 P20290-2;Q96K17-3;Q96K17;E9PL10;P20290 P20290-2;Q96K17;P20290 BTF3;BTF3L4 Transcription factor BTF3;Transcription factor BTF3 homolog 4 0 75.378 0.061803 82045000 274520 127300 175510 118590 372040 325100 347980 248550 287050 126730 FALSE TRUE 285358.2616 149162.7847 180083.9348 142046.748 308800.7737 249600.4519 320704.4183 245218.5938 276719.1266 151560.3171 1.882803276 0.984181002 1.188199776 0.937229156 2.037477749 1.646872062 2.116018391 1.617960417 1.825801977 1 17.20953254 3.238250301 24.99999956 1.75446329 1.224972892 0.260898471 0.372854284 9.377254523 755486.8167 0.098405409 0.124787441 1730.813609 -3.238250301 -0.529490397 TATAVAHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TATAVAHCK 9 0 P62249;M0R210;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 74.92 0.039727 263950000 515490 402130 463340 370140 629350 532280 498840 477220 474150 383450 FALSE TRUE 535841.9432 471192.6994 475415.021 443352.5872 522373.3118 408666.0368 459739.6173 470823.6465 457085.4341 458579.6859 1.16848164 1.027504519 1.036711908 0.966795087 1.139111321 0.891155996 1.0025294 1.026699745 0.996741566 1 18.80681292 TATESFASDPILYRPVAVALDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;H3BUW1;H3BTJ2;H3BT25;P14618-2;H3BTN5;H3BQ34 P14618;P14618-2 PKM Pyruvate kinase PKM;Pyruvate kinase 0 ;;; 308.37 3.81E-73 5089021000 5696881 3910936 5126166 4090460 6385320 6727785 6684475 5218046 5661610 3348016 FALSE TRUE 5921798.261 4582608.835 5259758.097 4899540.779 5299945.587 5165358.894 6160528.383 5148106.628 5457849.762 4003995.634 1.478972207 1.144508949 1.313627331 1.223662868 1.323664178 1.290051081 1.53859518 1.285742318 1.363100828 1 21.93300897 -1.005799635 4.530495015 0.999990445 1.325098272 0.455151966 0.107942018 1.06E-05 2.32E-06 0.099398681 0.023427761 0.098673462 1.005799635 0.325107827 TATESFASDPILYRPVAVALDTKGPEIR ddPTM_MDA-MB-175_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 ; 271.44 1.12E-61 2921600000 2202120 2109990 2500250 1412490 3939400 3204300 1974210 2429960 2781500 2639600 FALSE TRUE 2289061.398 2472364.369 2565408.569 1691876.306 3269782.195 2460149.887 1819466.262 2397390.361 2681394.358 3156779.082 0.725125623 0.783192078 0.812666488 0.535950177 1.035796966 0.779322792 0.576367942 0.759441918 0.849408302 1 21.59002187 0.958732608 3.018008351 0.999048186 0.749615597 0.266161361 0.128170492 0.357653523 8.005070702 0.119048758 0.031288399 9.093532188 -0.958732608 -0.249432589 TATNDEESPLSVS(ph)SPEGTGTWLHYTSGVGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 32 0 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 TATNDEESPLS(0.016)VS(0.538)S(0.446)PEGTGTWLHYTSGVGTGR;TATNDEESPLS(0.018)VS(0.954)S(0.028)PEGTGTWLHYTSGVGTGR 270.94 1.60E-73 775820000 123165 241390 239400 300950 305440 384340 312920 341500 297570 285130 TRUE FALSE 128027.6493 282846.8547 245638.9607 360477.0118 253521.4179 295082.8597 288392.5127 336922.7511 286860.5138 340995.7644 0.375452316 0.82947322 0.720357806 1.057130467 0.743473803 0.865356379 0.845736349 0.988055531 0.841243628 1 18.37939429 4.936558025 1.568870152 0.890877886 2.18E-19 0.687665225 0.101999719 0.976765809 1.549280937 0.025263899 1.540792707 86408.81025 -4.936558025 -0.890877886 TATPPGYKPGS(ph)PPSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 TATPPGYKPGS(0.965)PPS(0.035)FR;TATPPGYKPGS(0.795)PPS(0.205)FR 116.65 0.00024921 653050000 734110 511070 636870 489920 868100 889570 749120 672790 703650 437540 TRUE FALSE 763093.2297 598842.2969 653467.3554 586824.7137 720540.6721 682980.8491 690402.0169 663772.3505 678325.774 523267.5858 1.458323142 1.144428421 1.248820629 1.121462001 1.377002306 1.305222925 1.319405283 1.268514176 1.29632676 1 18.99718937 -1.1654372 5.288766308 0.999989324 1.276829071 0.446539534 0.094072498 1.12E-05 1.76E-06 0.085807584 0.020224262 0.068322351 1.1654372 0.276839747 TATPQQAQEVHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TATPQQAQEVHEK 13 0 P60174;P60174-3;P60174-4;U3KPZ0 P60174 TPI1 Triosephosphate isomerase 0 ;;; 246.64 3.36E-17 3031920000 3243020 2791070 2900360 2128570 3890310 3765390 2809820 2766940 2864680 2820010 FALSE TRUE 3371056.934 3270414.561 2975945.764 2549594.793 3229036.496 2890935.238 2589578.966 2729853.695 2761580.726 3372536.967 0.999561151 0.969719411 0.882405677 0.755987204 0.95745029 0.857198977 0.767843019 0.809436256 0.818843723 1 21.68540283 4.197226792 3.270913593 0.840718851 0.991403961 0.329043935 0.073224084 0.232205255 5.01236072 0.018036415 0.049918729 15748.05025 -4.197226792 0.15068511 TATYNGPPAS(ph)PSLSHEATPLSQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TATYNGPPASPSLSHEATPLSQTR 24 0 H0YIY6;P27448-6;P27448-7;A2SY06;J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 H0YIY6;J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 TATYNGPPAS(1)PSLSHEATPLSQTR;TATYNGPPAS(0.992)PS(0.008)LSHEATPLSQTR;TATYNGPPAS(1)PSLSHEATPLSQTR;TATYNGPPAS(1)PSLSHEATPLSQTR 336.73 3.03E-87 1342210000 278077 453195 438512 461933 478902 564391 423513 463319 384270 361648 TRUE FALSE 289055.6947 531027.7159 449939.983 553301.9687 397498.4091 433319.7437 390316.9444 457108.9666 370440.1978 432506.0014 0.668327593 1.227792711 1.040309225 1.279293159 0.919058713 1.001881459 0.902454401 1.056884679 0.856497243 1 18.72236063 TAVAHRPGAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAVAHRPGAFK 11 1 Q969H8 Q969H8 MYDGF Myeloid-derived growth factor 0 ; 111.63 0.00098203 2953800000 3415800 2969800 3157200 2960200 4806400 4778900 3936300 3563000 3242200 2592900 FALSE TRUE 3550658.422 3479840.048 3239479.226 3545718.725 3989409.845 3669072.9 3627762.52 3515243.813 3125513.855 3100929.111 1.145030504 1.122192712 1.044680194 1.14343753 1.286520814 1.183217277 1.169895341 1.133609859 1.007928187 1 21.56426911 1.26356089 3.719351523 0.997237227 1.155904313 0.532638464 0.056407787 0.18665006 4.736357488 0.05309319 0.015823241 18.34682381 -1.26356089 0.158667086 TAVAPSAVNLADPRT(ph)PTAPAVNLAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAVAPSAVNLADPRTPTAPAVNLAGAR 27 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 TAVAPSAVNLADPRT(0.864)PT(0.136)APAVNLAGAR 80.486 0.019094 145870000 94986 116610 135630 109340 162970 183400 126070 120130 150110 131350 TRUE FALSE 98736.12063 136636.8604 139164.6292 130967.1257 135268.4176 140808.1295 116188.304 118519.8538 144707.5704 157085.5177 0.628550118 0.869824682 0.885916355 0.833731382 0.861113231 0.89637881 0.739650005 0.754492557 0.921202493 1 17.26119065 1.0301036 5.206965007 0.999483378 0.81294242 0.393996017 0.078211142 0.158643067 11.18159961 0.075514214 0.019076025 10.71774945 -1.0301036 -0.186540959 TAVEHATDEDILAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAVEHATDEDILAK 14 0 A0A494C1L5;P50851-2;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 204.13 1.41E-08 774440000 1083770 808690 1152490 807310 1396580 1459460 1212110 1074990 1179370 720510 FALSE TRUE 1126558.076 947576.2168 1182524.836 966993.5084 1159189.83 1120522.533 1117101.651 1060581.517 1136924.704 861680.1395 1.307397055 1.099684411 1.372347791 1.122218633 1.34526697 1.300392665 1.296422651 1.230829711 1.319427769 1 19.71679291 -1.214093299 4.817951517 0.99995711 1.262321714 0.462171944 0.086001351 3.57E-05 5.83E-06 0.075071962 0.017691742 0.061081079 1.214093299 0.262364604 TAVIKENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAVIKENER 9 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 0 62.408 0.092178 0 44739 50867 45148 32751 83914 72567 45117 51584 55078 59320 FALSE TRUE 46505.33027 59603.01156 46324.59397 39229.05005 69650.32825 55714.41401 41580.61165 50892.60085 53095.75354 70942.61825 0.65553445 0.840158046 0.65298681 0.552968737 0.98178401 0.785344767 0.586116113 0.717376975 0.748432393 1 16.11436496 0.754658671 3.927885381 0.999994799 0.721815939 0.327271417 0.119039288 3.933026361 61.86454296 0.1134394 0.029014682 5.684060232 -0.754658671 -0.27817886 TAVIPINGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TAVIPINGSPR 11 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR;TAVIPINGS(1)PR 212.78 5.01E-09 4203340000 2381940 2570360 2762350 2761080 3298960 3606400 3099780 2908390 2651690 2405810 TRUE FALSE 2475980.83 3011799.335 2834339.11 3307213.383 2738203.958 2768868.256 2856811.144 2869407.789 2556256.195 2877182.407 0.860557476 1.046787763 0.985109287 1.149462535 0.951696337 0.962354089 0.992919718 0.997297836 0.888458162 1 21.45622526 TAVPS(ph)PVEAAAASDPAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;Q147X3-2;J3KNC2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 TAVPS(1)PVEAAAASDPAAAR;TAVPS(1)PVEAAAASDPAAAR 194.05 4.15E-15 474260000 107101 97159 97654 86046 98140 116801 104076 95674 87182 74368 TRUE FALSE 111329.4302 113845.3025 100198.9435 103065.642 81458.19785 89675.73789 95918.25117 94391.64652 84044.33685 88938.98574 1.251750616 1.280038236 1.126603172 1.158835365 0.915888541 1.008283793 1.07847251 1.061307881 0.944966216 1 16.44052833 3.825127238 1.49097221 1.016817514 1.268334262 0.735495511 0.059732732 0.223720819 0.94457303 0.018244802 0.049365508 6685.397552 -3.825127238 0.251516748 TAWLDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TAWLDGK 7 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 86.953 0.045825 279970000 1295000 892340 956260 909310 1297100 1535000 986910 1021300 991990 877490 FALSE TRUE 1346127.6 1045592.454 981180.9212 1089168.804 1076619.405 1178519.513 909553.4154 1007611.144 956288.4737 1049417.365 1.282738065 0.996355205 0.93497683 1.037879532 1.025921088 1.123022691 0.866722284 0.960162446 0.911256575 1 20.00115714 2.237628124 24.99997014 0.932013657 1.054446039 0.323967957 0.092554804 32.4842488 870858.5593 0.033282912 0.026008215 172.8335792 -2.237628124 0.122432382 TAWVFDDKYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TAWVFDDKYK 10 1 P05198;G3V4T5;H0YJS4 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 147.72 2.41E-05 1998010000 2147440 1057550 1550200 930230 3000300 2071730 2044170 1433490 1800950 1069160 FALSE TRUE 2232222.589 1239175.986 1590599.486 1114226.718 2490310.078 1590602.105 1883942.614 1414276.411 1736134.161 1278641.432 1.745776833 0.969134861 1.243976181 0.871414526 1.947621918 1.24397823 1.473394 1.106077416 1.357795953 1 20.28618032 0.37388602 0.849200311 0.999256711 1.322286752 0.087889805 0.31362865 6.008129692 5.858343249 0.320733239 0.097754671 2.365298849 -0.37388602 0.323030041 TCAYTNHTVLPEALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TCAYTNHTVLPEALER 16 0 P11216;P11217;P11217-2 P11216 PYGB;PYGM "Glycogen phosphorylase, brain form;Glycogen phosphorylase, muscle form" 0 ;;; 141 1.65E-06 1368670000 396223 537577 599127 567037 591159 702300 577687 573632 537447 522267 FALSE TRUE 411866.19 629901.668 614740.7418 679195.2262 490674.0043 539201.4685 532406.3834 565943.4013 518104.3875 624595.2192 0.659412972 1.00849582 0.984222618 1.087416626 0.785587192 0.863281453 0.852402271 0.906096275 0.829504248 1 19.252562 3.199626579 24.99999194 0.868988269 0.943669874 0.061671644 0.116049835 403.3700123 259007.2894 0.032736948 0.039128721 1583.531034 -3.199626579 0.074681604 TCDISFSDPDDLLNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCDISFSDPDDLLNFK 16 0 P61081 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 250.69 1.39E-20 63372000 76263 59489 74704 61225 87905 97348 88635 68659 78932 50988 FALSE TRUE 79273.92213 69705.77299 76650.84761 73335.12226 72962.9395 74740.40232 81687.5571 67738.73841 76091.25274 60978.12238 1.300038752 1.143127572 1.257022103 1.202646448 1.196542902 1.225692091 1.339620735 1.110869534 1.247845125 1 15.89600411 -0.482036652 0.620164184 0.974428825 1.224876476 0.518686403 0.064652801 8.480696968 2.581265415 0.548131805 0.023819516 0.329581896 0.482036652 0.25044765 TCEEHQLCVVAVLPHILDTGAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCEEHQLCVVAVLPHILDTGAAGR 24 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 186.28 1.25E-17 558290000 135650 118560 124070 135900 144620 192800 139880 103870 148170 102900 FALSE TRUE 141005.5667 138921.7577 127303.3661 162780.6144 120037.5441 148025.1219 128915.8401 102477.7925 142837.3906 123061.2849 1.145815818 1.128882718 1.03447129 1.322760562 0.975428984 1.202856951 1.047574306 0.832737873 1.160701278 1 16.90901744 2.001222631 23.10531974 0.969460304 1.130942707 0.21776736 0.114839566 18.15280979 343037.4332 0.04072586 0.02978498 100.2819179 -2.001222631 0.161482404 TCEERPAEDGS(ph)DEEDPDSMEAPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 303.25 1.34E-62 6107690000 1336732 1621900 1585310 1528440 1810700 2033420 1665290 1710550 1611400 1584840 TRUE FALSE 1389507.212 1900448.708 1626624.481 1830760.87 1502917.861 1561189.022 1534760.218 1687622.875 1553406.029 1895359.054 0.733110282 1.002685324 0.858214425 0.965917706 0.792946253 0.823690381 0.809746425 0.890397453 0.819584039 1 20.85403975 -1.464952258 3.120542697 1.002985234 0.860359562 0.241290324 0.07655842 129531050 152330273.4 3341451.311 0.01725589 0.034280547 1.464952258 -0.142625673 TCEESSFCKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TCEESSFCKR 10 1 Q14697;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;;; 150.15 3.54E-05 1048990000 694740 674720 672500 589200 1017910 917330 646640 668760 736260 635250 FALSE TRUE 722168.8717 790597.9114 690025.9025 705742.0014 844886.0218 704294.0098 595954.6671 659796.3661 709762.1464 759715.0749 0.950578573 1.040650551 0.908269331 0.928956164 1.112109065 0.927050197 0.784444967 0.868478707 0.934247812 1 19.53509892 2.480334707 24.99780705 0.877276799 0.98693632 0.23546471 0.07511814 156.1008541 1214340.462 0.025202354 0.021483186 302.2280065 -2.480334707 0.109659522 TCFETFPDKVAIQLNDTHPALSIPELMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCFETFPDKVAIQLNDTHPALSIPELMR 28 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 202.17 2.33E-25 306500000 464110 403750 487620 400350 584610 642260 483920 558270 574340 433320 FALSE TRUE 482433.4212 473090.9218 500327.7778 479538.0351 485238.201 493104.8485 445989.0859 550787.3038 553669.6156 518220.7576 0.930941909 0.912913879 0.965472283 0.925354741 0.936354235 0.951534344 0.86061602 1.062842998 1.068404936 1 18.98320728 1.670478419 7.879923958 1.048864847 0.928751376 0.742912146 0.031545427 0.054911858 6.098517472 0.014761024 0.00769803 46.8250682 -1.670478419 -0.120113471 TCFS(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TCFSPNR 7 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 1 TCFS(1)PNR;TCFS(1)PNR;TCFS(1)PNR 116.73 0.005654 650980000 737240 746570 782740 823420 839850 1076990 994620 768130 796040 641650 TRUE FALSE 766346.8045 874787.59 803138.8474 986290.0183 697092.597 826875.3944 916659.0854 757834.4738 767390.6759 767369.0324 0.99866788 1.13998292 1.046613576 1.285287752 0.908418984 1.077545952 1.194547925 0.987575002 1.000028205 1 19.54956102 1.611194779 25 0.995343475 1.092618055 0.172636843 0.097446861 0.53859675 4010.973137 0.045280018 0.023808537 40.85025567 -1.611194779 0.09727458 TCFS(ph)PNRVIGLSSDLQQVGGASAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCFSPNRVIGLSSDLQQVGGASAR 24 1 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 1 T(0.068)CFS(0.932)PNRVIGLSSDLQQVGGASAR;T(0.066)CFS(0.934)PNRVIGLSSDLQQVGGASAR 203.73 7.05E-25 237362000 88512 85748 84134 71254 97548 109360 78359 94304 86987 92205 TRUE FALSE 92006.52211 100474.552 86326.60116 85347.82853 80966.8258 83962.79737 72217.01683 93040.00913 83856.35486 110270.8044 0.834368831 0.911161867 0.782859993 0.773983912 0.734254423 0.761423641 0.654906049 0.843741094 0.760458358 1 16.75069134 4.188864348 9.265991488 0.776414558 0.872621023 0.118126779 0.086335102 0.478096931 84.39870325 0.019802876 0.043123236 15447.71856 -4.188864348 0.096206466 TCFVDCLIEQTHPEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCFVDCLIEQTHPEIR 16 0 Q15029;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 72.797 0.036853 158310000 42477 37938 50791 47904 49019 60816 53467 43334 49929 51040 FALSE TRUE 44154.02476 44453.55638 52114.65519 57379.26822 40686.76789 46692.40568 49276.11683 42753.17861 48132.06504 61040.31078 0.723358453 0.728265564 0.853774408 0.940022544 0.666555713 0.764943774 0.807271723 0.700408928 0.788529161 1 15.89747469 0.949702947 22.16046476 1.000000001 0.772288958 0.446986894 0.075319779 3485.198335 1535552.352 0.074059415 0.018514854 8.906415402 -0.949702947 -0.227711043 TCHSFIINEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCHSFIINEK 10 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 ; 136.02 0.00012868 820800000 1074080 887580 1042250 897740 1469350 1425040 1282260 1155840 1122710 798820 FALSE TRUE 1116485.508 1040014.961 1069411.891 1075310.293 1219590.412 1094096.057 1181753.111 1140347.855 1082303.886 955333.4847 1.168686669 1.088640749 1.11941213 1.125586311 1.276612232 1.145250401 1.237005851 1.193664698 1.132906889 1 19.86564491 3.429661293 24.99991899 1.180976677 1.121987289 0.03461068 0.072170283 223.7832196 117878.9547 0.018407021 0.024923229 2689.436491 -3.429661293 -0.058989388 TCNS(ph)PQNSTDSVSDIVPDSPFPGALGSDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCNSPQNSTDSVSDIVPDSPFPGALGSDTR 30 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 T(0.154)CNS(0.721)PQNS(0.049)T(0.074)DS(0.002)VSDIVPDSPFPGALGSDTR;T(0.176)CNS(0.68)PQNS(0.117)T(0.02)DS(0.006)VSDIVPDSPFPGALGSDTR 198.7 1.61E-25 396320000 98981 118402 117414 104008 130807 160925 130563 123207 127891 104512 TRUE FALSE 102888.8463 138736.6225 120473.9053 124580.472 108572.4729 123552.6076 120329.1309 121555.6117 123288.2279 124989.1254 0.823182385 1.109989545 0.963875096 0.996730488 0.868655353 0.988506858 0.9627168 0.972529501 0.986391636 1 16.93144305 1.156718797 1.573727707 0.999847705 0.963960327 0.032911036 0.072044661 1.696192959 8.054284391 0.062895388 0.018726948 14.34560264 -1.156718797 -0.035887378 TCNTNPHLNALSTDSACRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCNTNPHLNALSTDSACRR 19 1 Q9NZB2;Q9NZB2-4;Q9NZB2-6;A0A0C4DG79 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ; 159.95 2.10E-11 160271000 31096.1 64251 44794 52098 51816 66523 33255 48972 41702 78722 FALSE TRUE 32323.79804 75285.60945 45961.36844 62402.8289 43008.33483 51074.04142 30648.3862 48315.61044 40201.15317 94146.06868 0.343336673 0.799668117 0.488192116 0.662829896 0.456825605 0.542497867 0.325540797 0.513198385 0.427008305 1 16.52261323 -1.43736567 5.802973435 1.000265639 0.511072612 0.548261493 0.134313129 0.00043629 4.23E-05 0.122918424 0.028956786 0.03652871 1.43736567 -0.489193027 TCNVLVALEQQS(ph)PDIAQGVHLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 TCNVLVALEQQS(1)PDIAQGVHLDR;TCNVLVALEQQS(1)PDIAQGVHLDR 220.38 1.25E-32 95743000 50266 58904 63608 60226 63366 76848 60342 60825 58768 45270 TRUE FALSE 52250.54049 69020.30379 65265.67673 72138.52304 52595.06995 59001.21664 55612.23637 60009.74036 56652.95116 54139.78975 0.965104237 1.274853562 1.205502959 1.332449265 0.971467939 1.089793974 1.027197125 1.108422117 1.046419859 1 15.72440166 3.226094666 24.99990386 1.051434007 1.201006208 0.37634406 0.096318468 237.2593034 475811.8634 0.026803039 0.032247127 1683.040883 -3.226094666 0.149572201 TCNVLVALEQQSPDIAQGVHLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCNVLVALEQQSPDIAQGVHLDR 23 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ; 203.33 1.92E-24 457620000 285020 312130 323240 337190 357090 427160 379010 349170 337060 268810 FALSE TRUE 296272.8097 365735.8995 331663.8999 403885.1756 296391.9693 327958.5637 349302.2058 344489.9473 324929.2764 321478.1728 0.921595414 1.137669461 1.031684039 1.256337785 0.921966075 1.020158105 1.086550302 1.071581141 1.01073511 1 18.29436126 TCPSLSPTS(ph)PLNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCPSLSPTSPLNNK 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 TCPSLSPT(0.021)S(0.978)PLNNK 203.7 1.12E-07 0 154480 111640 142560 117210 175300 180120 158070 146530 150610 91077 TRUE FALSE 160578.9897 130813.3016 146275.2307 140393.7882 145502.5686 138289.8597 145680.0604 144566.005 145189.5755 108921.7944 1.474259496 1.200983718 1.342938129 1.288941198 1.335844396 1.269625244 1.33747393 1.3272459 1.332970838 1 16.73293313 -1.022469094 4.835988635 0.999995997 1.319264079 0.686956325 0.065433833 3.70E-06 7.49E-07 0.055600231 0.013104854 0.094957857 1.022469094 0.319268082 TCS(ph)FGGFDLTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TCSFGGFDLTNR 12 0 O94885;A0A1B0GWB9 O94885 SASH1 SAM and SH3 domain-containing protein 1 1 T(0.003)CS(0.997)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR;TCS(1)FGGFDLTNR 277.24 7.22E-28 983111000 1365420 1256640 1470660 1291140 1976530 1901530 1492750 1537800 1507310 1275910 TRUE FALSE 1419327.836 1472458.145 1508986.608 1546523.638 1640560.137 1459928.475 1375744.354 1517188.306 1453062.208 1525900.136 0.930157749 0.964976744 0.988915705 1.013515631 1.075142533 0.956765414 0.901595276 0.994290695 0.9522656 1 20.54122912 4.618931563 2.727592376 0.98423297 0.926476811 0.136051309 0.042569495 0.785831272 9.048865021 0.01132732 0.088862635 41584.50758 -4.618931563 -0.057756158 TCS(ph)LPDLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCSLPDLSK 9 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 T(0.028)CS(0.972)LPDLSK 73.781 0.032318 0 153290 120880 136490 94094 178900 187250 162250 126310 152460 93140 TRUE FALSE 159342.0076 141640.1997 140047.0415 112705.5124 148490.6419 143764.0253 149532.421 124617.0211 146972.9944 111388.9997 1.43050039 1.271581575 1.257278922 1.011819054 1.333081743 1.290648319 1.342434364 1.118755185 1.319456991 1 16.76524724 -4.26783542 0.249707777 7.36E-14 1.277809563 0.324392076 0.11327737 152.0955373 2.113543369 77.44239837 0.164920185 5.40E-05 4.26783542 1.277809563 TCSDGGPSSELAHS(ph)PTNSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCSDGGPSSELAHSPTNSGK 20 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 TCSDGGPSSELAHS(1)PTNSGK 171.78 1.37E-15 0 47708 43970 51348 38328 58895 59540 58792 51552 44628 28111 TRUE FALSE 49591.54868 51521.50546 52686.17106 45909.164 48884.04894 45712.73734 54183.72942 50861.02976 43021.847 33618.81223 1.475113051 1.532520099 1.56716337 1.365579595 1.454068294 1.359736835 1.611708618 1.512874084 1.279695627 1 15.03698113 0.970102196 3.285898498 1.001197128 1.486861954 0.798749231 0.0759198 0.102120374 2.829068046 0.075140669 0.019567788 9.334739357 -0.970102196 0.485664826 TCTDIKPEWLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCTDIKPEWLVK 12 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 78.705 0.022809 447810000 442840 232000 337430 241580 482290 435830 400020 309060 424620 168020 FALSE TRUE 460323.6651 271844.1953 346223.703 289363.803 400310.5181 334615.0876 368665.3871 304917.5562 409338.0091 200940.3021 2.290847881 1.352860489 1.723017729 1.440048611 1.992186306 1.665246265 1.83470107 1.517453458 2.03711254 1 17.61640743 -1.457895825 4.377694569 0.996908655 1.729985214 0.401604996 0.276460606 0.007506756 0.000929586 0.24090372 0.056597822 0.034842088 1.457895825 0.733076559 TCVQEITAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TCVQEITAHR 10 0 F5GYK2;Q9NRL3;Q9NRL3-3;M0R317;Q13033-2;Q13033 F5GYK2;Q13033-2 STRN4;STRN3 Striatin-4;Striatin-3 0 ; 93.442 0.0087829 274930000 56184 681210 419940 566630 282310 675550 218140 455890 306350 866900 FALSE TRUE 58402.1877 798202.5184 430883.9814 678707.7228 234323.047 518663.7506 201041.6168 449779.5402 295324.5233 1036752.457 0.056331854 0.769906561 0.415609318 0.654647807 0.226016389 0.500277329 0.193914772 0.433835037 0.284855388 1 19.98364004 -1.303564152 3.930212698 1.001088683 0.404113903 0.441714771 0.204428899 202078436.9 428177860.3 2739555.471 0.045094736 0.049709094 1.303564152 -0.59697478 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TCVQTLEGHAQNVSCASFHPELPIIITGSEDGTVR 35 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 75.384 0.001835 49831000 10931 33706 30218 27495 33942 42013 28225 35333 26901 30361 FALSE TRUE 11362.56432 39494.7433 31005.5059 32933.42894 28172.55096 32256.11746 26012.65075 34859.41893 25932.83826 36309.65665 0.312935053 1.087720098 0.853919006 0.907015708 0.775896926 0.888361952 0.716411367 0.960059173 0.71421326 1 15.14806567 4.752809947 24.99993236 0.87090444 0.312934671 0.686711401 0.114440922 1372.888317 2408641.547 0.025092523 0.544200815 56599.15489 -4.752809947 -0.557969768 TDALTSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDALTSSPGR 10 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 TDALT(0.001)S(0.049)S(0.951)PGR 85.821 0.014663 231090000 259980 239200 289750 341480 338130 408530 412830 316490 305630 187210 TRUE FALSE 270244.2111 280280.7393 297301.123 409023.7248 280654.7834 313655.0988 380471.3059 312247.9692 294630.436 223890.2151 1.207038954 1.251866854 1.327887969 1.826894152 1.253537513 1.400932589 1.699365493 1.39464768 1.315959413 1 17.77243195 0.852957446 2.624704513 1.000628705 1.430272521 0.309946313 0.188408345 0.693872945 9.040548488 0.18096606 0.048207242 7.127831856 -0.852957446 0.429643816 TDCDIEDDRLAAMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDCDIEDDRLAAMFR 15 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ;; 266.15 2.56E-25 892997000 771275 718015 844070 910685 1015008 1153705 853813 794546 840474 796735 FALSE TRUE 801725.5326 841328.4909 866067.1576 1090815.775 842477.3027 885774.4983 786888.906 783896.4105 810225.5049 952839.9688 0.841406279 0.882969353 0.90893244 1.144804805 0.884175024 0.929615179 0.825835326 0.822694719 0.85032695 1 19.86187441 2.300142451 7.427785066 0.854846607 0.936596288 0.070191915 0.090445908 0.443936621 45.09444103 0.032079591 0.026678222 199.5916879 -2.300142451 0.08174968 TDCSSGDASRPSSDNADS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDCSSGDASRPSSDNADSPK 20 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 TDCSSGDASRPSSDNADS(1)PK;TDCSSGDASRPSSDNADS(1)PK;TDCSSGDASRPSSDNADS(1)PK 144.76 9.25E-08 463384000 901356 226527 311108 233705 523792 616979 424524 347514 375287 163860 TRUE FALSE 936942.2309 265431.2501 319215.7301 279931.1515 434758.0229 473694.9777 391248.6996 342856.1432 361780.4942 195965.2297 4.781165681 1.354481356 1.628940657 1.428473571 2.218546747 2.417239927 1.996521016 1.749576411 1.846146353 1 17.58023817 4.743704398 24.99956282 1.793579439 4.78116692 0.838648191 0.399802288 209.2531605 1016970.374 0.096024464 0.813618898 55424.83364 -4.743704398 2.987587482 TDDEVVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDDEVVQR 8 0 P14625;Q96GW1;A0A1W2PRR1;F8VPC7 P14625 HSP90B1 Endoplasmin 0 ; 147.06 0.0012641 191618000 255540 294740 255850 332120 321600 360940 335820 292790 269490 217760 FALSE TRUE 265628.9165 345359.3022 262517.6612 397812.3447 266934.5469 277117.1551 309497.5509 288865.629 259791.1075 260425.9027 1.019978864 1.326132687 1.008032068 1.527545227 1.024992307 1.064092136 1.188428446 1.109204676 0.997562473 1 17.99051342 TDDEVVQREEEAIQLDGLNASQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 ;;;;; 357.61 2.83E-102 3106540000 771460 882852 860250 767291 1196074 1267060 759810 922312 916608 849285 FALSE TRUE 801917.8365 1034474.963 882668.8217 919058.8697 992765.7687 972804.5175 700254.1068 909949.9162 883619.4571 1015686.135 0.789533113 1.018498656 0.86903699 0.904865034 0.977433613 0.957780641 0.689439466 0.895896759 0.869972944 1 19.95402322 TDDIPVWDQEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2;E5RGM3 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 179.6 3.17E-05 40011000 107117 72424 87829 78000 112693 118082 121276 89775 98572 57515 FALSE TRUE 111346.0619 84862.25862 90117.89589 93428.16719 93537.48411 90659.24505 111770.0702 88571.71297 95024.41297 68783.96306 1.618779392 1.233750643 1.310158529 1.358284156 1.359873435 1.318028811 1.624943741 1.287679701 1.381490812 1 16.06978462 0.224513542 1.50177169 0.999872413 1.383622703 0.464635636 0.124922716 7.707203279 13.88600109 0.114029955 0.032480927 1.676924624 -0.224513542 0.38375029 TDDVHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDDVHAK 7 0 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 ;; 94.887 0.013871 276330000 1945790 1321740 1751010 1254340 2356520 2193380 2197560 1908740 1934250 1197220 FALSE TRUE 2022611.292 1548738.563 1796642.759 1502444.708 1955959.572 1684000.736 2025309.505 1883156.462 1864636.72 1431792.337 1.412642909 1.081678204 1.254820768 1.049345404 1.366091661 1.176148728 1.414527409 1.315244127 1.302309471 1 20.44939083 TDDYLDQPCYETINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDDYLDQPCYETINR 15 0 P50395;P50395-2;Q5SX87;Q5SX91 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;;; 305.84 1.72E-44 1368670000 907141 895065 981751 869346 1184932 1303298 1055270 1003323 1007423 792478 FALSE TRUE 942955.6271 1048785.451 1007336.238 1041300.044 983517.6819 1000626.791 972555.18 989875.0963 971166.043 947748.8912 0.994942475 1.106606888 1.062872504 1.098708797 1.037740789 1.055793154 1.026173904 1.044448699 1.024708182 1 19.85414534 1.510739926 0.582878035 1.002242293 1.06620681 0.279505368 0.02996886 0.875250082 0.697173172 0.027690745 0.014681532 32.41454468 -1.510739926 0.063964517 TDEAAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDEAAFQK 8 0 P26447 P26447 S100A4 Protein S100-A4 0 ;; 119.27 0.0040145 747060000 624420 1168250 798220 935320 730700 1151330 647530 756210 690890 1394310 FALSE TRUE 649072.5838 1368887.85 819022.2689 1120323.504 606495.875 883951.0561 596774.9066 746074.2419 666025.0039 1667498.349 0.389249311 0.820923062 0.491168264 0.671858839 0.363716027 0.530106106 0.357886355 0.447421278 0.39941569 1 20.6692539 -1.058449617 4.739413202 1.000017291 0.498566384 0.535799689 0.140487004 2.52E-05 5.00E-06 0.133336496 0.031426631 0.087407839 1.058449617 -0.501450907 TDEFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDEFPR 6 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 ;;; 170.96 0.012978 1097720000 1211780 1242530 1336120 1155970 1668040 1786180 1403150 1384970 1369500 1157370 FALSE TRUE 1259622.01 1455924.862 1370940.385 1384617.416 1384507.157 1371366.765 1293167.437 1366406.743 1320211.963 1384134.492 0.910043075 1.051866614 0.990467612 1.000348899 1.00026924 0.99077566 0.934278745 0.987192177 0.953817689 1 20.4005527 2.446024116 24.86250597 0.967877491 0.994635741 0.073858143 0.036393005 404.5863836 323469.2197 0.01166706 0.009761435 279.2698915 -2.446024116 0.02675825 TDEGIAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDEGIAYR 8 0 P32119 P32119 PRDX2 Peroxiredoxin-2 0 ;;;;; 143.85 0.0013837 11018010000 7563160 9335150 9575660 10288680 11098260 12589200 9934140 9830800 9492120 8500190 FALSE TRUE 7861759.397 10938389.4 9825209.566 12323750.2 9211781.729 9665549.091 9155476.149 9699034.206 9150500.455 10165639.48 0.773365946 1.076015868 0.966511707 1.212294634 0.906168446 0.950805811 0.900629632 0.954099761 0.90014017 1 23.27719764 TDENIDTPGT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDENIDTPGTPK 12 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9;A0A0U1RR74 Q6ULP2-7 AFTPH Aftiphilin 1 TDENIDTPGT(1)PK;TDENIDTPGT(1)PK 221.24 3.09E-10 305650000 506120 266410 348680 277910 521180 556790 441840 377690 386880 230920 TRUE FALSE 526102.0084 312163.8451 357766.8872 332879.7685 432590.0098 427483.9607 407207.4263 372627.6833 372956.2644 276164.3528 1.905032287 1.130355319 1.295485401 1.205368344 1.566422333 1.547933165 1.474511182 1.349296821 1.350486624 1 18.07516758 0.598436389 1.324660523 1.000497812 1.423338099 0.285623362 0.205935988 1.950825785 4.8246488 0.189330959 0.056367052 3.966764236 -0.598436389 0.422840288 TDEQGLIVEDLVEEVGREEDPHEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDEQGLIVEDLVEEVGREEDPHEGK 25 1 E9PGC0;P20936-2;P20936-4;P20936;P20936-3 E9PGC0 RASA1 Ras GTPase-activating protein 1 0 93.966 0.0066196 16574000 31117 18514 27840 24095 38272 36144 36659 26806 31678 19346 FALSE TRUE 32345.52319 21693.63548 28565.53327 28860.91908 31766.53911 27750.10377 33785.57179 26446.70942 30537.91497 23136.4783 1.398031402 0.937637751 1.234653472 1.247420576 1.373006674 1.19940915 1.46027288 1.143074113 1.319903339 1 14.49788166 5.060086537 22.064724 1.227344086 5.012099345 0.112754758 0.150994703 2072.345517 769359.2294 0.033021954 4181.306046 114838.2423 -5.060086537 3.784755258 TDEVPAGGS(ph)RSEAEDEDDEDYVPYVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 TDEVPAGGS(0.5)RS(0.5)EAEDEDDEDYVPYVPLR 103.15 0.00065368 66760000 83029 54301 66451 41213 87159 87333 71641 60081 72218 50303 TRUE FALSE 86307.04903 63626.77435 68182.76765 49364.80839 72343.74431 67051.23429 66025.59122 59275.71247 69618.88829 60158.90974 1.43465115 1.057645071 1.133377715 0.820573521 1.202544139 1.114568641 1.097519744 0.985318928 1.157249834 1 15.8764908 4.738916878 24.41181244 1.061383337 1.434651302 0.539448381 0.102952181 15.3831277 1053509.343 0.023363302 0.137203692 54817.20366 -4.738916878 0.373267965 TDEVPAGGSRS(ph)EAEDEDDEDYVPYVPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 Q9UJV9;D6RGI7;A0A499FJW5;D6RD33 Q9UJV9 DDX41 Probable ATP-dependent RNA helicase DDX41 1 T(0.003)DEVPAGGS(0.463)RS(0.534)EAEDEDDEDYVPYVPLR 144.45 6.22E-08 58209000 26045 29853 30527 19410 31504 38483 26966 28626 25532 28586 TRUE FALSE 27073.27671 34980.02053 31322.5587 23249.24007 26148.96133 29545.90647 24852.33446 28242.31529 24613.10831 34186.87939 0.791920093 1.023200162 0.91621579 0.680063243 0.764882955 0.864246957 0.726955338 0.826115627 0.719957737 1 15.06115512 3.863061039 9.80180243 0.789732509 0.922896526 0.20650712 0.099882014 0.461735231 34.64959281 0.023539755 0.042516182 7295.600402 -3.863061039 0.133164017 TDFEMVHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDFEMVHLR 9 0 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 ; 141.88 0.00010566 180748000 130176 153412 159085 168687 219300 227500 173564 162733 147660 188430 FALSE TRUE 135315.449 179759.3176 163230.8858 202052.7851 182023.4643 174666.5728 159959.6002 160551.8303 142345.7454 225349.2508 0.600469931 0.797692102 0.724346255 0.896620621 0.807739381 0.77509276 0.70982974 0.712457795 0.631667267 1 17.78180313 -2.252155361 2.418772961 2.039274445 0.744864661 0.475550035 0.081883897 3668359.038 820709.8717 20934531.41 0.019976277 0.005595574 2.252155361 -1.294409784 TDFKEEPEPGFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDFKEEPEPGFKR 13 2 P47897;A0A1B0GVU9;P47897-2;B4DDN1;H7C0R3;A0A0U1RQX5;A0A0U1RRC8 P47897 QARS Glutamine--tRNA ligase 0 ;; 132.47 6.66E-05 697000000 2539180 1202620 1828910 1180490 2826140 2377020 2238210 1858240 2083300 927740 FALSE TRUE 2639428.787 1409160.63 1876572.897 1413987.399 2345753.732 1824993.129 2062773.252 1833333.332 2008322.44 1109512.89 2.378907726 1.270071436 1.691348441 1.274421785 2.11421945 1.64485978 1.859170154 1.652376776 1.810093833 1 20.081495 -0.977424098 5.635691014 0.999998753 1.722250728 0.324484018 0.320646969 4.54E-06 8.24E-07 0.280734764 0.066169705 0.105335777 0.977424098 0.722251975 TDGALLVNAMFFKPHWDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDGALLVNAMFFKPHWDEK 19 1 P50454;E9PR70;E9PPV6;E9PK86;E9PMI5 P50454 SERPINH1 Serpin H1 0 ;; 217.42 2.16E-19 6456580000 8974660 5250850 7555360 5945300 11582720 9941110 9238380 7174310 8365180 4080082 FALSE TRUE 9328986.507 6152642.642 7752258.888 7121262.595 9613893.392 7632437.861 8514251.636 7078150.109 8064118.806 4879495.95 1.911875038 1.260917665 1.588741741 1.459425864 1.970263628 1.564185715 1.744903925 1.450590426 1.652654063 1 22.21830069 -0.527322678 0.76769065 0.954547805 1.61583757 0.456198129 0.203413504 15.50548593 6.257570914 2.2229169 0.065263755 0.296945892 0.527322678 0.661289765 TDGCHAYLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDGCHAYLSK 10 0 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 ;;;;; 136.02 0.00012868 4314150000 11284080 9251710 11370830 9453480 16100100 15348400 14084300 12148590 12246600 8167850 FALSE TRUE 11729584.19 10840619.22 11667163.17 11323350.13 13363410.75 11783966.71 12980335.76 11985758.02 11805847.26 9768183.825 1.200794785 1.109788618 1.194404546 1.159207313 1.368054798 1.206362095 1.328838195 1.227020113 1.208602077 1 23.21965892 TDGEPGPQGWS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDGEPGPQGWSPR 13 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 TDGEPGPQGWS(1)PR 82.651 0.0093025 0 69979 52684 81242 66339 89558 94972 95827 78324 77240 58593 TRUE FALSE 72741.82496 61732.06718 83359.23326 79460.6562 74334.96315 72916.19231 88315.82934 77274.19489 74460.14749 70073.17652 1.038083737 0.880965731 1.189602604 1.133966806 1.060819087 1.040572098 1.260337175 1.102764263 1.062605567 1 16.09657468 4.237787249 24.99991953 1.114492574 0.959524734 0.34690842 0.079948696 18.87184549 610143.7905 0.019041206 0.045380142 17289.69169 -4.237787249 -0.15496784 TDGFAEAIHS(ph)PQVAGVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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;TDGFAEAIHS(1)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR 272.27 3.61E-39 13303790000 4123980 3605930 3981990 3903650 5598860 6764760 5584990 5505570 5462870 5220570 TRUE FALSE 4286797.915 4225220.427 4085763.931 4675780.319 4647167.777 5193747.011 5147223.89 5431776.839 5266262.376 6243440.738 0.686608249 0.676745501 0.654409019 0.748910819 0.744328003 0.831872557 0.824421037 0.869997341 0.843487205 1 22.57390988 2.357090118 0.256064692 1.023355198 0.580278898 0.929681024 0.026773348 0.613484574 0.110399593 0.053329428 0.095792474 227.5569575 -2.357090118 -0.4430763 TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.012)DGS(0.988)IS(0.999)GDRQPVT(0.001)VADYISR;T(0.014)DGS(0.983)IS(0.583)GDRQPVT(0.061)VADY(0.027)IS(0.332)R 123.19 0.00035061 65703000 153341 156939 169332 147379 210120 249720 187509 168668 169548 147857 TRUE FALSE 159395.0211 183892.0524 173744.931 176530.1263 174403.8775 191726.3145 172811.5546 166407.2813 163446.0006 176826.7483 0.901419172 1.039956083 0.982571544 0.998322528 0.986298053 1.084260817 0.977293064 0.941075278 0.924328487 1 17.431977 1.999052067 24.99912587 0.951236582 1.001966108 0.144772114 0.047080171 54.02107948 1424671.563 0.01707508 0.012461359 99.78196834 -1.999052067 0.050729526 TDGS(ph)ISGDRQPVT(ph)VADYISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 T(0.005)DGS(0.983)IS(0.213)GDRQPVT(0.741)VADY(0.003)IS(0.055)R 89.859 0.050635 177490000 314190 250390 294940 265370 357340 503030 351090 326800 293860 239100 TRUE FALSE 326594.4638 293392.5347 302626.3787 317859.3939 296599.4744 386208.906 323570.6484 322419.7805 283284.036 285947.0672 1.142150074 1.026037923 1.058330067 1.111602218 1.037253074 1.350630765 1.131575335 1.127550577 0.990686979 1 18.12538858 TDGS(ph)ISGDRQPVTVADYISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 TDGS(0.993)IS(0.007)GDRQPVTVADYISR;TDGS(1)ISGDRQPVTVADYISR 272.38 1.21E-44 593130000 444860 379020 437430 397060 581660 667910 437480 413050 472990 363100 TRUE FALSE 462423.4163 444113.7366 448829.7852 475597.2829 482789.641 512798.0248 403189.1745 407513.7404 455967.1823 434242.493 1.064896743 1.0227321 1.033592503 1.095234323 1.111797322 1.180902452 0.928488531 0.938447404 1.050028935 1 18.72814138 2.21823772 24.99922253 0.968661231 1.081401055 0.491641722 0.052101342 206.5050098 254020.5211 0.020894691 0.015451089 165.2866282 -2.21823772 0.112739824 TDHGAEIVYKS(ph)PVVS(ph)GDT(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDHGAEIVYKSPVVSGDTSPR 21 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 3 TDHGAEIVY(0.022)KS(0.977)PVVS(0.832)GDT(0.613)S(0.555)PR 70.051 0.018201 65019000 57361 39202 51481 39932 62334 69570 62161 50006 54030 34656 TRUE FALSE 59625.65657 45934.63855 52822.63715 47830.43041 51738.48895 53413.42184 57288.65839 49335.75136 52085.47085 41446.17967 1.438628531 1.108296082 1.274487482 1.154037134 1.248329505 1.288741743 1.382242196 1.190357031 1.256701372 1 15.33895151 0.15966086 1.351119426 0.999732447 1.256157217 0.410470698 0.093427161 8.50432882 12.57425612 0.088246459 0.024640889 1.44431147 -0.15966086 0.25642477 TDIELEIYGMEGIPEKDMDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDIELEIYGMEGIPEKDMDER 21 1 J3QRS9;O43670-2;O43670;O43670-4;X6R4W8;J3QS27;J3KTL1;J3KRB6;J3KRW6;H0Y3M2 J3QRS9 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 105.96 0.000345 42301000 39865 34233 46034 32416 56374 54905 55919 52542 48096 27240 FALSE TRUE 41438.90098 40112.25145 47233.68386 38827.78805 46791.56762 42154.14584 51535.92266 51837.76043 46365.03436 32577.15646 1.272023267 1.23129996 1.449901986 1.191871614 1.436330629 1.293978678 1.581965041 1.591230361 1.423237612 1 14.99157306 2.262864102 24.88724939 1.46845414 1.315255527 0 0.175167146 395.6426808 405144.6145 0.057256157 0.04788234 183.1741152 -2.262864102 -0.153198613 TDIIDRLEQELLCASNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 183.7 6.17E-10 31466000 19923.7 22292 24235 22728 29406 32597 23414 25239 25768 21989 FALSE TRUE 20710.30306 26120.47759 24866.58401 27223.53056 24407.57862 25026.84076 21578.7495 24900.71249 24840.61471 26297.32355 0.78754414 0.993275135 0.94559372 1.035220581 0.928139268 0.951687753 0.820568278 0.946891513 0.944606194 1 14.68262835 TDKVFEVMLATDR ddPTM_MDA-MB-175_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 ; 184 9.01E-06 658170000 911080 765790 934310 684790 1372490 1235040 903400 1036900 969950 799210 FALSE TRUE 947050.1419 897308.4755 958658.8861 820239.4181 1139194.64 948220.6772 832589.1474 1023002.052 935041.689 955799.8977 0.99084562 0.938803695 1.0029912 0.858170649 1.191875666 0.992070285 0.87109148 1.070309857 0.978281847 1 19.86634909 TDLADKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 91.065 0.026742 513420000 863440 579310 703460 775120 1101040 1141740 1008510 786710 757110 509720 FALSE TRUE 897529.2779 678801.9861 721792.7455 928436.4225 913885.6141 876588.1882 929460.3509 776165.4392 729861.759 609589.8748 1.472349386 1.113538814 1.184062884 1.523050925 1.499181092 1.437996634 1.524730625 1.273258417 1.197299675 1 19.21747941 1.076159118 1.871677259 1.007156444 1.383994176 0.452449465 0.135044227 0.319902968 2.234561669 0.136868994 0.039095149 11.91678538 -1.076159118 0.376837732 TDLCDHALHISHDEL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDLCDHALHISHDEL 15 0 Q9Y2B0;H0YI18 Q9Y2B0 CNPY2 Protein canopy homolog 2 0 ;;; 247.14 1.78E-18 766340000 112151 645280 582470 649610 613160 779660 493980 616110 533210 568830 FALSE TRUE 116578.8081 756101.8204 597649.6467 778100.9191 508935.2822 598595.7809 455260.5568 607852.0532 514019.8763 680281.3476 0.171368521 1.111454581 0.878533049 1.143792817 0.748124705 0.879923848 0.66922393 0.893530383 0.755598956 1 19.37577201 4.749911202 24.97344789 0.886134795 0.171368096 0.689411993 0.146085512 963.6193311 2120105.666 0.034110827 0.535893204 56222.63578 -4.749911202 -0.714766699 TDLEKDIISDTSGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 160.25 8.07E-09 361430000 1048700 922350 1083730 889010 1205240 1343810 1343660 1040900 1061230 747380 FALSE TRUE 1090103.486 1080756.438 1111972.894 1064853.525 1000373.735 1031730.493 1238340.418 1026948.438 1023036.54 893814.8015 1.21960778 1.209150302 1.244075274 1.191358123 1.119218135 1.154300076 1.38545526 1.148949913 1.144573281 1 19.76961641 0.913436056 1.963567057 1.00174546 1.211823393 0.468757935 0.068300099 0.375657909 3.003624399 0.065044942 0.018169622 8.192869862 -0.913436056 0.210077933 TDLEKDIISDTSGDFRK ddPTM_MDA-MB-175_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 ; 246.21 6.91E-21 1250260000 1263250 884180 1245260 781110 1532110 1500700 1521450 1150000 1221440 647570 FALSE TRUE 1313124.085 1036031.037 1277712.499 935611.2266 1271682.489 1152185.168 1402194.773 1134586.131 1177480.613 774448.943 1.695559271 1.337765448 1.649834389 1.208099301 1.642048196 1.48774839 1.810570969 1.465023797 1.520410898 1 19.5628106 0.365079085 2.055591797 1.000008363 1.534252453 0.48041274 0.167084335 9.139588829 28.40911563 0.148474209 0.040638004 2.317816684 -0.365079085 0.53424409 TDLFYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDLFYER 7 0 Q7RTV0 Q7RTV0 PHF5A PHD finger-like domain-containing protein 5A 0 ;;; 139.68 0.0062246 732210000 655510 745240 716730 635720 1154170 1046060 841970 723770 720290 911200 FALSE TRUE 681390.041 873229.1728 735408.5726 761463.5186 957984.5957 803128.4182 775974.1913 714069.047 694366.9036 1089732.194 0.625282106 0.801324562 0.674852571 0.698762065 0.87910094 0.736996138 0.712077881 0.655270213 0.63719041 1 20.0555422 -2.224338983 2.469073192 2.018441545 0.715552758 0.575722355 0.073782499 10293056.02 1710465.201 58785672.9 0.018049463 0.005965695 2.224338983 -1.302888788 TDLLVNDNPDPAPLS(ph)PELQDFK ddPTM_MDA-MB-175_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 138.02 1.36E-06 30890000 63449 36536 48731 50147 55674 72985 83526 55918 58524 25811 TRUE FALSE 65954.01551 42810.77379 50000.96989 60065.92693 46210.55337 56035.33985 76979.01387 55168.51067 56417.73267 30868.17127 2.136635013 1.38689051 1.619822874 1.945885501 1.497029188 1.815311291 2.493798975 1.787229642 1.827699224 1 14.9138324 2.482965074 24.9474826 1.896891634 1.701186412 0 0.396749488 864.7401735 3691629.744 0.127537838 0.109978934 304.0640486 -2.482965074 -0.195705222 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.998)PS(0.002)KVEGVHTPR;TDLQGSAS(0.999)PS(0.001)KVEGVHTPR 184.53 1.49E-14 902650000 396150 259220 331330 247010 465220 454180 412110 320410 353460 211600 TRUE FALSE 411790.3079 303739.0185 339964.732 295867.8407 386142.0706 348703.5782 379807.7414 316115.428 340739.0436 253058.9687 1.6272504 1.200269724 1.343420997 1.169165599 1.525897591 1.377953842 1.50086655 1.24917694 1.346480804 1 17.94911408 0.383932579 1.037903696 0.999417889 1.371876305 0.398191503 0.13804367 2.513860656 3.336126999 0.128927701 0.039457635 2.420653227 -0.383932579 0.372458416 TDLQGSASPS(ph)KVEGVHTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSAS(0.004)PS(0.725)KVEGVHT(0.271)PR 82.477 0.0026579 234860000 185090 170330 207330 167910 249050 258410 211200 205060 209050 158650 TRUE FALSE 192397.4961 199582.8525 212733.1901 201122.0968 206716.57 198398.1937 194645.5921 202311.5061 201526.3313 189734.43 1.014035756 1.051906354 1.121215534 1.06001898 1.089504788 1.045662581 1.025884402 1.066287791 1.062149507 1 17.53362197 -0.287814975 8.324757015 1 1.060634761 0.279703718 0.02866626 0 0 0.027885694 0.006572721 0.515448197 0.287814975 0.060634761 TDLQGSASPSKVEGVHT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDLQGSASPSKVEGVHTPR 19 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 TDLQGSASPS(0.015)KVEGVHT(0.984)PR;TDLQGSASPSKVEGVHT(1)PR;TDLQGSASPSKVEGVHT(1)PR 185.84 3.20E-14 993610000 753580 615920 697780 490272 880100 911160 639430 692210 644800 474310 TRUE FALSE 783331.9203 721699.4688 715964.72 587246.3383 730500.9164 699556.8988 589309.8058 682932.0572 621593.774 567241.9633 1.380948468 1.272295626 1.262185745 1.035266035 1.28781184 1.233260132 1.038903755 1.203951931 1.095817683 1 19.11360474 8 0.141586025 0.993465428 2.197626366 0.535096147 0.083790951 61.86052003 0.581616827 0.340538295 15.1267429 100000000 -8 1.204160938 TDMDNQIVVSDYAQMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDMDNQIVVSDYAQMDR 17 0 P50991;P50991-2 P50991 CCT4 T-complex protein 1 subunit delta 0 169.04 4.71E-09 96923000 38868 47848 46874 41172 51442 59616 47125 40422 48396 36399 FALSE TRUE 40402.53865 56065.52179 48095.57495 49315.69871 42697.90721 45771.08749 43431.21936 39880.20921 46654.23741 43530.68715 0.928139235 1.287953981 1.104865972 1.132895021 0.98086913 1.051467149 0.997714996 0.916140126 1.071755133 1 15.40974517 3.240338065 24.97875424 0.995101335 1.125313061 0.258520703 0.090181111 53.25234351 748351.4314 0.024214504 0.031173436 1739.154102 -3.240338065 0.130211726 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDNAGDQHGGGGGGGGGAGAAGGGGGGENYDDPHKTPASPVVHIR 45 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 117.28 8.88E-08 949400000 340708 329971 414903 315164 467250 590550 497090 440690 437785 243199 FALSE TRUE 354159.4149 386640.9524 425715.713 377502.4985 387827.0119 453403.7124 458126.7869 434783.2714 422029.2034 290849.1877 1.217673729 1.32935201 1.463699164 1.297932105 1.33342993 1.558896265 1.575135177 1.494875316 1.451024177 1 18.14991175 6.090094068 0.678763508 1.439377522 1.21E-08 0.062100875 0.161164705 31.45227144 2.623908695 0.058960969 52.7274935 1230535.274 -6.090094068 -1.43937751 TDPVPEEGEDVAATISATETLSEEEQEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-8;H0YC44;P55327-2;P55327-4;P55327-3;E5RFR7 H0YC42;P55327-2 TPD52 0 ;; 241.54 9.85E-46 190574000 10612.9 14661 17036.1 11682.4 16203.8 19140.4 15482.1 14066.3 13671.2 15836 FALSE TRUE 11031.90549 17178.9127 17480.07476 13993.14385 13449.48386 14695.33218 14268.57255 13877.76426 13179.17618 18938.761 0.582504076 0.907076904 0.922978793 0.738862688 0.710156481 0.77593947 0.753405809 0.732770441 0.695883758 1 14.20905433 -1.249685406 5.098752147 1.000035374 0.763216234 0.373895752 0.093810457 3.74E-05 5.50E-06 0.089945243 0.021197134 0.056274882 1.249685406 -0.23681914 TDQAQKAEGAGDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDQAQKAEGAGDAK 14 1 P05204 P05204 HMGN2 Non-histone chromosomal protein HMG-17 0 ;;; 166.35 3.48E-06 676902000 745860 399545 639060 233493 1012570 741780 446711 546040 691600 396648 FALSE TRUE 775307.1287 468163.7457 655714.4286 279677.2185 840453.7131 569512.8368 411696.6246 538721.2269 666709.4511 474363.5813 1.634415371 0.986930203 1.382303479 0.589584086 1.77175008 1.200582969 0.867892563 1.135671557 1.40548195 1 18.85563373 4.75152371 23.50360386 1.150171448 1.634416094 0.182327784 0.308434609 1524.142737 2763333.027 0.069218545 1.195699208 56431.77484 -4.75152371 0.484244646 TDQDEEHCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TDQDEEHCR 9 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;;;; 204.28 1.68E-05 984250000 777072 780839 757430 809828 906686 1089667 935600 853831 812608 690430 FALSE TRUE 807751.4026 914942.0242 777169.248 970009.5613 752567.8376 836608.3533 862265.2273 842386.792 783362.3968 825706.5394 0.978254821 1.10807167 0.941217262 1.174763085 0.911422887 1.013203013 1.044275643 1.020201187 0.948717685 1 19.65526961 3.195362582 24.99995774 0.99743564 1.046874014 0.148465466 0.069793909 305.8010279 176974.9834 0.018932304 0.02262858 1568.05966 -3.195362582 0.049438374 TDQVIQSLIALVNDPQPEHPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDQVIQSLIALVNDPQPEHPLR 22 0 P68036-2;P68036;P68036-3;A0A1B0GUS4 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 ; 212.39 2.16E-23 3248600000 347420 318210 354230 369490 392140 498730 440570 378660 391920 275666 FALSE TRUE 361136.4099 372860.0922 363461.5248 442574.0192 325484.1829 382907.5158 406036.9722 373584.6821 377814.8758 329677.4748 1.095423368 1.130984434 1.102476064 1.342445429 0.987280624 1.161460959 1.231618789 1.133182309 1.146013618 1 18.33069579 -1.235157429 3.608847736 0.999740647 1.149935785 0.204943373 0.087293099 4581052.517 3146828.151 8470.743844 0.019121893 0.058189225 1.235157429 0.150195137 TDQVIQSLIALVNDPQPEHPLRADLAEEYSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDQVIQSLIALVNDPQPEHPLRADLAEEYSK 31 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 191.51 5.31E-19 859210000 191670 119800 137630 104370 191440 200020 142410 141960 159190 97816 FALSE TRUE 199237.2796 140374.7181 141216.7509 125014.0745 158899.0972 153568.3863 131247.5321 140057.2584 153460.783 116981.1724 1.703156803 1.199977015 1.207175035 1.068668333 1.358330524 1.31276156 1.121954323 1.197263248 1.311841725 1 16.83591683 4.738883932 24.99999999 1.204615884 1.703156952 0.668074972 0.106810823 15.08968739 1166306.783 0.024249002 0.141999465 54813.04545 -4.738883932 0.498541068 TDRDKYNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDRDKYNR 8 2 P61077-3;P61077-2;P61077;A0A087WY85;H9KV45;D6RAH7 P61077-3 UBE2D3 Ubiquitin-conjugating enzyme E2 D3 0 ; 152.34 0.00025797 383460000 510630 441630 535190 343740 801000 700650 470750 496700 570920 505790 FALSE TRUE 530790.0667 517476.5171 549137.4911 411730.746 664846.3061 537934.656 433851.3849 490042.5489 550372.7007 604889.8666 0.877498692 0.855488818 0.907830535 0.680670596 1.099119597 0.889310081 0.717240293 0.81013516 0.909872575 1 19.20631297 5.8522555 1.616160756 0.8611111 1.261808302 0 0.117129228 776.8700893 97.26000733 0.03026271 1041.272382 711632.0511 -5.8522555 0.400697201 TDS(ph)IGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDSIGEK 7 0 A0A286YFF8;Q7Z3U7-2;Q7Z3U7-6;Q7Z3U7-5;Q7Z3U7;Q7Z3U7-3 A0A286YFF8 MON2 Protein MON2 homolog 1 TDS(1)IGEK;T(0.002)DS(0.998)IGEK;TDS(1)IGEK;TDS(1)IGEK 127.94 0.0039919 1965330000 4344230 1871470 3090500 1991230 5718900 4971470 4084130 3377430 3730720 1751860 TRUE FALSE 4515743.555 2192880.414 3171040.969 2385089.351 4746803.421 3816921.436 3764005.219 3332161.075 3596452.116 2095103.426 2.155379777 1.04666929 1.513548654 1.13841127 2.265665438 1.8218296 1.796572509 1.590451829 1.716598843 1 20.99859003 3.277412324 24.99999894 1.730283098 1.437303696 0.0711421 0.401975501 355.1544511 228529.6791 0.104426415 0.141391698 1894.141086 -3.277412324 -0.292979402 TDS(ph)PDMHEDT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 TDSPDMHEDT 10 0 Q9BW61 Q9BW61 DDA1 DET1- and DDB1-associated protein 1 1 TDS(1)PDMHEDT;T(0.006)DS(0.994)PDMHEDT;T(0.001)DS(0.999)PDMHEDT;T(0.002)DS(0.998)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT;TDS(1)PDMHEDT 244.28 7.22E-12 5517644400 4415742 4014873 4462002 3805854 5740378 6860117 5309580 4766176 4645346 3491951 TRUE FALSE 4590078.904 4704396.206 4578285.438 4558640.562 4764630.598 5266958.793 4893401.246 4702293.207 4478160.905 4176131.941 1.099122099 1.126496067 1.096298082 1.091593998 1.140919556 1.261205074 1.171754464 1.125992491 1.072322658 1 21.99373586 1.024579205 2.348455132 1.001055209 1.141755036 0.473161114 0.046809654 0.266290474 3.177681906 0.048889583 0.013387323 10.58227895 -1.024579205 0.140699827 TDS(ph)REDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 2 T(0.042)DS(0.958)REDEIS(1)PPPPNPVVK;T(0.047)DS(0.953)REDEIS(1)PPPPNPVVK 138.24 1.39E-06 135642000 240680 127872 189609 115922 240810 250680 204978 170418 187444 101840 TRUE FALSE 250182.2322 149833.0213 194550.3663 138851.0256 199877.2022 192463.3691 188911.2887 168133.8255 180697.9271 121793.5982 2.054149282 1.230220829 1.597377606 1.140051922 1.64111419 1.580242082 1.551077328 1.380481635 1.4836406 1 16.89407878 -3.05047652 0.252871595 1.94E-13 1.556045072 0.319278638 0.233470873 73.55422784 1.762240168 39.50593257 0.317570095 0.000890274 3.05047652 1.556045072 TDS(ph)SPNQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.7)S(0.3)PNQAR 84.658 0.016094 35297000 39366 42965 42756 39068 53338 54899 49857 49966 46189 38406 TRUE FALSE 40920.20008 50343.90453 43870.25648 46795.53379 44271.62581 42149.53925 45949.07806 49296.2875 44526.66691 45930.92037 0.89090747 1.096078723 0.955135585 1.018824213 0.963874128 0.917672429 1.000395326 1.073270187 0.969426838 1 15.48717807 1.99743835 24.99699797 1.025988298 0.978310753 0.079122564 0.058036753 206.992709 2019883.382 0.021109807 0.015327806 99.4118945 -1.99743835 -0.047677545 TDS(ph)TSDGRPAWMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.013)DS(0.937)T(0.047)S(0.002)DGRPAWMR;T(0.003)DS(0.952)T(0.044)S(0.001)DGRPAWMR;TDS(0.988)T(0.012)SDGRPAWMR;TDS(0.987)T(0.013)SDGRPAWMR;T(0.001)DS(0.948)T(0.049)S(0.003)DGRPAWMR;T(0.005)DS(0.949)T(0.037)S(0.009)DGRPAWMR;T(0.006)DS(0.851)T(0.122)S(0.022)DGRPAWMR;T(0.002)DS(0.765)T(0.204)S(0.03)DGRPAWMR;T(0.004)DS(0.851)T(0.12)S(0.026)DGRPAWMR 218.12 1.49E-11 12520142000 3725020 3419706 4049680 3716760 5341830 5766860 4473080 4012010 4152320 3263980 TRUE FALSE 3872086.666 4007013.904 4155217.988 4451924.035 4433827.645 4427594.163 4122468.301 3958235.568 4002878.814 3903494.388 0.991953947 1.026519704 1.064486733 1.140497101 1.135861155 1.134264257 1.056096895 1.014023635 1.025460374 1 21.89633476 1.892032365 3.860327467 1.015798629 1.084681302 0.307790014 0.045896616 0.331290043 8.168920578 0.025396155 0.01423143 77.98882282 -1.892032365 0.068882673 TDSAINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDSAINR 7 0 A0A3B3IT47;Q9Y2I8;Q9Y2I8-2 A0A3B3IT47 WDR37 WD repeat-containing protein 37 0 76.847 0.092244 115690000 105890 52547 47323 61834 53102 88252 52684 58397 42728 57348 FALSE TRUE 110070.619 61571.53849 48556.27626 74064.58064 44075.74101 67756.81047 48554.49042 57614.28373 41190.22763 68584.24261 1.604896617 0.897750506 0.707980061 1.079906664 0.64265113 0.987935536 0.707954022 0.840051323 0.600578589 1 16.06558953 4.733734092 4.08147756 0.818070421 1.668825507 0.700414518 0.152838043 0.107474728 3.888451017 0.033086903 0.267751302 54166.91381 -4.733734092 0.850755085 TDSEKPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDSEKPFR 8 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ; 88.819 0.013082 862700000 960700 1090820 1133300 1055420 1391010 1544380 1286340 1269150 1182940 977900 FALSE TRUE 998629.1778 1278159.85 1162834.729 1264178.926 1154566.617 1185721.15 1185513.31 1252139.12 1140366.22 1169500.782 0.853893553 1.092910641 0.994300087 1.080956033 0.987230308 1.013869481 1.013691763 1.070661208 0.975088036 1 20.1574614 4.752184947 24.84039035 1.028225565 0.853893427 0.628102194 0.039540619 1271.951993 2319026.857 0.008657054 0.173715688 56517.76074 -4.752184947 -0.174332138 TDSEKPFRGS(ph)QS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDSEKPFRGSQSPKR 15 3 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 TDS(0.001)EKPFRGS(0.999)QS(1)PKR 64.2 0.095675 766010000 590530 185590 289090 207570 511250 473240 483150 335040 380010 161260 TRUE FALSE 613844.5804 217463.6388 296623.9229 248626.7265 424347.9076 363337.182 445279.4405 330549.3368 366333.5143 192855.8095 3.18291983 1.127597034 1.538060604 1.289184532 2.200337697 1.883983599 2.308872321 1.713971374 1.899520244 1 17.55716308 4.753823425 24.56927947 1.721893705 3.182921175 0.542674901 0.415534692 1804.014914 2903948.061 0.098474087 2.319317323 56731.39006 -4.753823425 1.461027471 TDSHFDWWEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDSHFDWWEGK 11 0 H7C499;Q96HL8-4;Q96HL8-3;Q96HL8-2;Q96HL8 H7C499 SH3YL1 SH3 domain-containing YSC84-like protein 1 0 ; 142.08 3.78E-05 211422000 661180 542730 658120 504800 847110 821230 776390 676110 707920 463570 FALSE TRUE 687283.8969 635939.6556 675271.1479 604647.9333 703118.5448 630511.7784 715534.5231 667047.8513 682442.0975 554397.6659 1.239694788 1.14708213 1.218026679 1.090639392 1.268256683 1.137291546 1.29065212 1.203193831 1.230961347 1 19.08056166 -1.016123825 5.077606633 0.999997957 1.202295965 0.518688095 0.058623883 1.24E-06 2.41E-07 0.051977372 0.01225106 0.096355426 1.016123825 0.202298008 TDSREDEIS(ph)PPPPNPVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TDSREDEISPPPPNPVVK 18 1 P10644;P10644-2;K7EPB2;K7EIE5;K7EID3;K7EJ40;K7EK41;K7EMU2;K7EMZ6 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK 232.11 2.55E-20 27028020000 5496460 3989220 5025940 3785940 6445500 6367510 5914140 5044230 5494650 3747550 TRUE FALSE 5713464.485 4674337.503 5156920.125 4534787.632 5349896.212 4888752.303 5450574.253 4976620.348 5296898.62 4481810.671 1.274811656 1.042957377 1.150633193 1.011820437 1.19369081 1.090798488 1.216154508 1.110403967 1.18186577 1 22.09565027 TDSS(ph)PNQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDSSPNQAR 9 0 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 TDS(0.025)S(0.975)PNQAR;TDS(0.017)S(0.983)PNQAR;TDS(0.002)S(0.998)PNQAR;TDS(0.001)S(0.999)PNQAR;TDS(0.001)S(0.999)PNQAR;TDS(0.01)S(0.99)PNQAR 240 2.53E-10 7264900000 4431710 4421570 4623490 4183830 5352010 6213450 5566130 4899430 4836020 3958660 TRUE FALSE 4606677.333 5180940.252 4743981.948 5011379.087 4442277.252 4770470.403 5129842.186 4833761.155 4661972.585 4734283.634 0.973046334 1.094345133 1.002048528 1.058529542 0.938320894 1.007643558 1.083551934 1.021012159 0.984726084 1 22.17471471 1.276969197 8.859649704 0.99240304 1.024831032 0.063273585 0.04530478 0.680144312 146.8098696 0.03005641 0.010804251 18.92209404 -1.276969197 0.032427992 TDSTSDGRPAWMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDSTSDGRPAWMR 13 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 174.72 1.78E-05 964800000 890390 936760 1036750 970300 1177060 1324060 1068920 991330 1039760 920880 FALSE TRUE 925543.2847 1097641.243 1063768.557 1162222.444 976983.7616 1016567.131 985135.2573 978042.8428 1002339.241 1101308.805 0.840403056 0.996669815 0.965913059 1.055310226 0.887111551 0.923053668 0.894513195 0.888073208 0.910134593 1 20.07078762 TDTGEPMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDTGEPMGR 9 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;; 150.35 0.00019879 2033654000 1529770 1639370 1744980 1662300 2076860 2362740 2004250 1809050 1722640 1549000 FALSE TRUE 1590166.501 1920919.045 1790455.612 1991097.979 1723836.079 1814029.443 1847151.648 1784802.644 1660642.523 1852496.893 0.858390914 1.036935097 0.966509374 1.074818525 0.930547353 0.97923481 0.997114573 0.963457834 0.896434714 1 20.82103969 -0.073815066 8.050835511 0.999999999 0.972296978 0.019890894 0.059947588 0 0 0.053594241 0.012632284 0.843693948 0.073815066 -0.027703021 TDTS(ph)PVLETAGTVAAMAATPSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 T(0.014)DT(0.088)S(0.898)PVLETAGTVAAMAATPSAR 176.39 4.39E-13 34802000 44177 46141 42060 48057 57582 63396 57762 50226 50889 39964 TRUE FALSE 45921.14207 54065.35782 43156.11815 57562.53116 47794.23221 48673.23978 53234.46351 49552.80262 49057.51483 47794.18064 0.960810322 1.13121215 0.90295759 1.20438368 1.000001079 1.018392598 1.113827307 1.036795734 1.026432804 1 15.54454735 5.137360299 7.111460454 1.049591187 0.118926225 0.098374046 0.079275029 2577.652349 6289.924507 0.017068123 33859.1535 137201.9548 -5.137360299 -0.930664962 TDVAVQIISNIYHNFPEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDVAVQIISNIYHNFPEQR 19 0 O60306 O60306 AQR Intron-binding protein aquarius 0 ; 213.51 3.16E-17 200181000 140361 142342 169855 144988 187133 214250 188157 164769 172673 141827 FALSE TRUE 145902.5607 166788.1312 174281.5608 173666.1937 155324.1995 164493.6845 173408.7627 162560.5411 166458.5325 169615.2852 0.860197007 0.983331962 1.027510938 1.023882921 0.915744117 0.969804604 1.022365186 0.95840738 0.981388748 1 17.37190666 4.737716311 7.197315649 0.985801692 0.85857585 0.575411543 0.032654102 0.076265627 33.561845 0.007992394 0.047680561 54665.87592 -4.737716311 -0.127225842 TDVSNFDEEFTGEAPTLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDVSNFDEEFTGEAPTLSPPR 21 0 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPTLS(1)PPR;TDVSNFDEEFTGEAPTLS(1)PPR 200.09 4.93E-22 127059000 109370 108325 117859 113422 127634 153219 133351 122344 114444 88092 TRUE FALSE 113688.0121 126928.9761 120930.5024 135856.5331 105938.8183 117636.2093 122898.6002 120704.1788 110325.1828 105351.9408 1.079125939 1.204809092 1.147871615 1.28954941 1.005570638 1.116602204 1.166552787 1.145723353 1.047205984 1 16.68485737 1.124251753 3.31510482 1.001798463 1.147456897 0.328749036 0.070488123 0.250029292 4.983258755 0.064634461 0.01713796 13.31225882 -1.124251753 0.145658434 TDVSNFDEEFTGEAPTLS(ph)PPRDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 TDVSNFDEEFTGEAPT(0.007)LS(0.993)PPRDAR;TDVSNFDEEFTGEAPT(0.254)LS(0.746)PPRDAR;TDVSNFDEEFTGEAPT(0.209)LS(0.791)PPRDAR;TDVSNFDEEFTGEAPT(0.01)LS(0.99)PPRDAR 185.44 1.43E-17 913410000 241526 267434 289527 245792 373927 394166 243587 291764 305051 312979 TRUE FALSE 251061.633 313363.7092 297072.3115 294408.924 310367.0221 302626.9201 224494.0144 287853.3808 294072.2741 374301.2427 0.670747527 0.83719655 0.793671721 0.786556095 0.829190467 0.808511663 0.599768285 0.769042012 0.785656687 1 18.51384031 0.722052867 3.397213354 0.999989247 0.762773534 0.508998372 0.069741445 2.587682101 30.72762635 0.067544728 0.017460665 5.27294046 -0.722052867 -0.237215713 TDWDAGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDWDAGFK 8 0 P52298-2;P52298;C9JQX9;B3KSB0;P52298-3 P52298-2 NCBP2 Nuclear cap-binding protein subunit 2 0 82.452 0.047074 42898000 157400 122460 148080 124000 214880 190360 188980 147470 173470 102760 FALSE TRUE 163614.2735 143491.5524 151939.0864 148526.8299 178354.7744 146151.7749 174167.2538 145493.4059 167226.8486 122893.8545 1.331346259 1.167605597 1.236344055 1.208578171 1.451291238 1.189252103 1.417216951 1.183894886 1.360742156 1 16.90705325 -1.281002166 5.073975851 0.999937698 1.277151335 0.431132088 0.097292559 6.27E-05 8.88E-06 0.086113679 0.020292638 0.052359782 1.281002166 0.277213637 TDWHMAFTGMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TDWHMAFTGMSR 12 0 Q96M27;Q96M27-3;Q96M27-2 Q96M27 PRRC1 Protein PRRC1 0 97.716 0.0047648 281560000 355030 387570 459930 399790 548510 537870 524760 385830 366710 424020 FALSE TRUE 369046.8585 454132.1326 471916.1536 478867.2687 455274.4661 412957.844 483627.94 380658.5799 353512.1787 507098.6006 0.72776154 0.895549962 0.930620106 0.944327727 0.897802647 0.814354138 0.953715785 0.75065989 0.697127104 1 18.95190677 1.715423647 12.1645566 0.793700158 0.883636377 0.071323101 0.096950613 0.205377707 79.65262281 0.04339587 0.023754583 51.93063667 -1.715423647 0.089936219 TDYNASVSVPDSSGPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TDYNASVSVPDSSGPER 17 0 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 261.79 6.09E-27 333740000 243330 198076 220763 194922 288380 329970 250760 231530 254830 195521 FALSE TRUE 252936.8563 232094.0122 226516.2651 233476.9898 239361.2706 253339.4682 231104.776 228426.7191 245658.7181 233829.5965 1.081714463 0.992577568 0.968723671 0.998492036 1.02365686 1.08343628 0.988346982 0.976893954 1.050588641 1 17.83509802 4.74567935 24.40291635 1.007270946 1.081714512 0.298273348 0.033254596 804.0206766 2756071.894 0.008343866 0.083135921 55677.45173 -4.74567935 0.074443566 TDYYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TDYYAR 6 0 P46777;A0A2R8Y4A2;R4GNJ2 P46777 RPL5 60S ribosomal protein L5 0 ;;;;; 185.69 0.0026655 4715200000 2124350 2362170 2328660 2197010 2912720 3017990 2557880 2431480 2318760 2216930 FALSE TRUE 2208220.978 2767854.322 2389346.793 2631572.021 2417616.895 2317107.561 2357386.682 2398889.988 2235308.281 2651294.988 0.832883926 1.043963171 0.901199906 0.992561006 0.911862658 0.873953133 0.889145377 0.904799352 0.843100557 1 21.33826577 3.014449623 23.8858813 0.895726369 0.947588194 0.076642046 0.063923236 271.6192071 448993.3932 0.016797405 0.020067032 1033.831173 -3.014449623 0.051861826 TEADVEEEALRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEADVEEEALRR 12 1 Q9BV36-2;Q9BV36-5;H7C3K9;H7C2D8;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ; 105.65 0.0032178 198021000 398280 335640 388470 303600 477480 444840 401000 349940 353050 295200 FALSE TRUE 414004.4019 393283.5591 398593.8473 363651.1738 396318.1202 341532.6516 369568.5722 345249.6267 340343.7995 353038.7881 1.172688146 1.113995324 1.129036981 1.030060113 1.12259087 0.967408294 1.046821439 0.977936811 0.964040811 1 18.42946717 3.592793203 0.483846783 0.974975702 1.194167018 0.719422986 0.038531395 0.854915241 0.327889131 0.028131987 0.096475402 3915.553866 -3.592793203 0.219191316 TEAEIAHIALETLEGHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEAEIAHIALETLEGHQR 18 0 O75955;A0A140T9R1;A0A140T9X0;A2AB09;A0A140T9C3;A0A140T959;A2AB13;A2AB11;A0A0G2JJQ6;A0A140T910;A2AB12;A0A140T957;A2AB10;A0A140T9B1 O75955 FLOT1 Flotillin-1 0 ; 165.16 1.67E-11 36431000 30952 35479 30938 34434 40591 42793 37547 36605 35053 31036 FALSE TRUE 32174.00886 41572.24226 31744.2697 41244.94242 33691.35632 32854.97428 34603.96803 36114.36985 33791.44938 37116.90998 0.866828863 1.120035108 0.855250874 1.111217029 0.907709083 0.885175364 0.932296574 0.972989666 0.91040578 1 15.17978899 TEAPQASPLAKPLQSS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEAPQASPLAKPLQSSSPR 19 1 Q8IY33;Q8IY33-5;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 TEAPQASPLAKPLQS(0.074)S(0.463)S(0.463)PR 89.365 0.0014584 177650000 82595 73994 74410 72530 95522 99660 80594 77015 76079 79675 TRUE FALSE 85855.91438 86701.89391 76349.18573 86876.21752 79285.20456 76515.47536 74276.83169 75982.7399 73340.93165 95285.79078 0.901035859 0.909914198 0.801265174 0.91174368 0.832077941 0.803010341 0.779516348 0.797419419 0.769694317 1 16.53997347 3.054354834 6.52052236 0.812271469 0.87717904 0.088175202 0.068586077 0.349116959 31.55856113 0.018573248 0.022190553 1133.325952 -3.054354834 0.06490757 TEAPQASPLAKPLQSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEAPQASPLAKPLQSSSPR 19 1 Q8IY33;Q8IY33-5;Q8IY33-4;Q8IY33-2 Q8IY33 MICALL2 MICAL-like protein 2 1 TEAPQASPLAKPLQS(0.001)S(0.03)S(0.97)PR 171.45 6.21E-12 210550000 236790 198000 240630 192440 308820 285470 218510 199600 200120 184730 TRUE FALSE 246138.652 232004.9598 246901.0155 230504.0576 256326.8867 219173.9188 201382.6152 196924.6885 192917.7203 220924.3066 1.114131151 1.050155881 1.117581941 1.043362141 1.160247555 0.99207698 0.911545761 0.891367236 0.873229946 1 17.75319263 2.468138888 3.594567582 0.909077931 1.09253132 0.776240995 0.044956165 0.094856337 2.653135443 0.014959304 0.012888411 293.8589269 -2.468138888 0.183453389 TEAQDLCRAS(ph)PEPPGPESSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 242.56 2.85E-30 7205469000 2393502 3413334 3057451 2157159 4182040 4324680 1956516 3071116 3284824 4033590 TRUE FALSE 2487999.307 3999547.562 3137130.685 2583838.612 3471178.335 3320338.611 1803159.164 3029952.713 3166603.826 4823894.733 0.515765672 0.8291117 0.650331497 0.535633291 0.719580034 0.688310752 0.37379737 0.628113357 0.65644132 1 22.20176699 0.722021381 3.317596148 0.999979837 0.617930028 0.485386484 0.117405975 2.492215082 28.79388036 0.112017957 0.029016589 5.272558183 -0.722021381 -0.38204981 TEAQGEEDDAEGQDQDKKS(ph)PKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEAQGEEDDAEGQDQDKKSPKPK 23 3 O14617-5;O14617-2;A0A2R8Y611 O14617-5 AP3D1 AP-3 complex subunit delta-1 1 TEAQGEEDDAEGQDQDKKS(1)PKPK 184.4 2.39E-17 277500000 486220 36121 78608 42909 153400 248980 200680 80168 89116 12885 TRUE FALSE 505416.341 42324.50077 80656.58906 51396.27213 127325.1228 191158.1683 184950.1772 79093.47909 85908.73257 15409.56905 32.79886279 2.746637536 5.234188496 3.335347793 8.262730928 12.40515992 12.00229394 5.132750879 5.575024991 1 13.9115389 4.743788622 24.99970682 6.651621854 32.79887369 0.832334361 3.577585238 226.7443011 1084230.934 0.892519026 7.619409914 55435.58337 -4.743788622 26.14725184 TEAVSPT(ph)VSQLSAVFENTDSPSAIISEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEAVSPTVSQLSAVFENTDSPSAIISEK 28 0 Q9ULJ8;Q9ULJ8-4;Q9ULJ8-5;Q9ULJ8-3 Q9ULJ8 PPP1R9A Neurabin-1 1 TEAVS(0.403)PT(0.596)VS(0.001)QLSAVFENTDSPSAIISEK;T(0.001)EAVS(0.419)PT(0.58)VSQLSAVFENTDSPSAIISEK 226.9 4.56E-34 135450000 164389 123075 149308 121478 185583 196203 193722 173840 173837 112206 TRUE FALSE 170879.2047 144212.1739 153199.0891 145505.9858 154037.6679 150637.8267 178537.5634 171509.9591 167580.6403 134190.6174 1.273406502 1.074681499 1.141652763 1.084323097 1.147901925 1.122566016 1.330477249 1.278106938 1.248825317 1 17.03392428 2.266078152 24.98947465 1.245195354 1.135552447 0.087508216 0.097047391 298.4168165 270999.941 0.031361402 0.026233314 184.5347464 -2.266078152 -0.109642907 TEDEEFLIQHLLQAPS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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 234.3 2.53E-24 2550063000 597025 547591 650144 622198 685164 804194 751695 637087 658677 437454 TRUE FALSE 620596.008 641635.4946 667087.2867 745266.9073 568700.068 617432.1312 692775.1817 628547.8908 634971.3434 523164.7357 1.186234403 1.2264502 1.27509987 1.424535823 1.087038229 1.18018683 1.324200838 1.20143398 1.213712049 1 18.99690577 -0.728439654 0.521568893 0.946595673 1.245710822 0.407364316 0.08582835 13.56098212 2.679370236 1.296227312 0.039525158 0.186878933 0.728439654 0.29911515 TEDGDWEWS(ph)DDEMDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 TEDGDWEWSDDEMDEK 16 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK 344.16 1.11E-72 2389407000 3978851 1987532 2593908 2308048 3717056 4190217 4477901 2872865 3173680 1357757 TRUE FALSE 4135939.11 2328875.16 2661507.373 2764573.006 3085232.149 3217102.605 4126911.419 2834358.944 3059459.877 1623783.488 2.547100115 1.43422764 1.639077742 1.702550263 1.900026802 1.981238649 2.541540451 1.74552763 1.884155061 1 20.63092785 3.085664959 7.676816621 1.92569282 1.789171671 0 0.447654193 1.294934363 100.3044599 0.124026645 0.148515864 1218.049559 -3.085664959 -0.13652115 TEDGDWEWS(ph)DDEMDEKSEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TEDGDWEWSDDEMDEKSEEGK 21 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK;TEDGDWEWS(1)DDEMDEKSEEGK 273.88 6.07E-45 4946070000 5010330 1623675 2639223 1366422 4553840 4628770 3418645 2529882 3085401 1355242 TRUE FALSE 5208141.697 1902528.551 2708003.32 1636696.193 3779779.903 3553808.317 3150682.672 2495973.07 2974358.021 1620775.722 3.213363592 1.173838258 1.670806937 1.009822748 2.332080776 2.192658903 1.943935011 1.539986709 1.835144727 1 20.62825304 0.281605006 0.824746912 0.991157678 1.862334501 0.167034848 0.591253006 5.276086613 4.514385535 0.676112917 0.188450001 1.912515686 -0.281605006 0.871176822 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 O95747;C9JIG9 O95747 OXSR1 Serine/threonine-protein kinase OSR1 1 TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR;TEDGGWEWS(1)DDEFDEESEEGKAAISQLR 189.39 3.64E-18 201332000 105886 68909 97091 55611 110857 132103 94429 84587 95139 59671 TRUE FALSE 110066.461 80743.58471 99621.27122 66610.68982 92013.56674 101424.0803 87027.40824 83453.24962 91714.96597 71362.38998 1.542359513 1.131458528 1.395991239 0.933414504 1.289384601 1.421253973 1.219513644 1.169429018 1.285200314 1 16.12287631 -5 0.17620505 0.001457106 1.308221881 0.208050072 0.159652694 222.2354881 2.125281005 77.86936552 0.503879745 1.00E-05 5 1.306764775 TEDGKVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEDGKVEK 8 1 O75436;S4R3Q6;O75436-2;S4R2Y3 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 92.062 0.010984 523420000 1043330 666580 726890 582230 995310 954510 940920 708110 800960 771290 FALSE TRUE 1084521.474 781059.9297 745833.3505 697393.3562 826127.5617 732839.5182 867168.2318 698618.9437 772133.6061 922409.5083 1.175748368 0.846760493 0.808570753 0.756056123 0.895619087 0.794483916 0.940111983 0.757384803 0.837083312 1 19.81504786 4.738125127 5.994290739 0.836685158 1.184867833 0.628936471 0.07496973 0.073174561 12.74112368 0.016307064 0.104097445 54717.35899 -4.738125127 0.348182675 TEDPDLPAFYFDPLINPISHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEDPDLPAFYFDPLINPISHR 21 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 ;;; 261.28 1.24E-36 368692000 180479 197211 227484 209669 229177 266168 237503 218332 215559 197392 FALSE TRUE 187604.4503 231080.4552 233412.4199 251140.9024 190221.5754 204354.5158 218886.8943 215405.6167 207801.0737 236067.1831 0.794707879 0.97887581 0.988754205 1.063853514 0.805794236 0.865662534 0.927222884 0.912475905 0.880262436 1 17.84883797 3.231338466 24.99983866 0.895997322 0.960443162 0.116074558 0.077891406 341.2965325 1181414.026 0.022294198 0.027164514 1703.485595 -3.231338466 0.064445839 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH 31 1 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 0 320.67 4.75E-93 212120000 61431 86533 89047 54775 114670 113610 62824 89588 103620 126770 FALSE TRUE 63856.34332 101394.3696 91367.63797 65609.33151 95178.43436 87225.79928 57899.69072 88387.2194 99890.73644 151608.1543 0.42119333 0.668792322 0.602656489 0.432755954 0.627792316 0.575337123 0.381903539 0.582997793 0.658874431 1 17.20998783 0.815091424 2.101773209 0.999360453 0.53756125 0.707214453 0.090081837 0.355115441 2.783237751 0.083145107 0.022853373 6.53268059 -0.815091424 -0.461799203 TEDSLMPEEEFLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEDSLMPEEEFLRR 14 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 137.62 3.23E-05 72455000 26765 27240 35492 30812 32656 40044 40251 32139 35761 27881 FALSE TRUE 27821.70287 31918.2581 36416.95068 36906.52164 27105.14478 30744.38787 37096.02144 31708.22927 34473.9686 33343.74814 0.834390386 0.957248656 1.092167279 1.10684982 0.812900358 0.922043549 1.112533039 0.95094976 1.033896023 1 15.02512866 4.673567083 3.77585667 1.000447471 0.827076598 0.249425777 0.088068191 0.328263735 8.166963856 0.021775772 0.137006898 47159.27102 -4.673567083 -0.173370873 TEDTEHVIIPVCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEDTEHVIIPVCLR 14 0 Q9Y4E8;Q9Y4E8-2;Q9Y4E8-3 Q9Y4E8;Q9Y4E8-2 USP15 Ubiquitin carboxyl-terminal hydrolase 15 0 ; 118.76 0.00022687 291050000 288240 287010 316140 291370 313310 363500 327400 319490 322330 204210 FALSE TRUE 299619.9378 336301.7349 324378.8681 349002.1163 260053.6781 279082.6339 301737.5325 315207.7591 310729.4063 244221.0397 1.226839171 1.377038339 1.328218357 1.429041973 1.064829134 1.142746072 1.235509983 1.290665864 1.27232857 1 17.89782797 -5 0.170685023 1.95E-07 1.326211348 0.390123456 0.099930592 148.0211385 1.399036936 50.47378061 0.379158507 1.00E-05 5 1.326211153 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 TEEARPSPAPGPGT(0.959)PT(0.041)GTPTR;TEEARPSPAPGPGT(0.999)PT(0.001)GTPTR;TEEARPSPAPGPGT(0.999)PT(0.001)GTPTR;TEEARPSPAPGPGT(0.998)PT(0.002)GTPTR 294.57 1.28E-54 3501130000 572741 660890 595320 668190 728100 829380 645630 687870 598802 524676 TRUE FALSE 595353.2569 774392.7165 610834.5283 800355.9877 604337.8221 636769.0644 595023.8336 678650.2278 577251.233 627476.2167 0.948806092 1.234138754 0.973478376 1.275516054 0.963124667 1.01480988 0.948281095 1.0815553 0.919957152 1 19.25920125 TEEDSEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEEDSEEVR 9 0 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 ; 208.37 2.36E-05 361130000 544910 533860 531470 633140 602360 718880 808550 588350 555440 381170 FALSE TRUE 566423.4676 625546.3021 545320.5448 758373.2023 499971.0624 551931.0147 745173.7382 580464.1306 535449.8229 455852.9636 1.242557388 1.372254547 1.196264121 1.663635564 1.096781424 1.210765442 1.634680035 1.273358247 1.174610819 1 18.79820903 1.049755252 2.564354188 1.005544407 1.344552549 0.276760533 0.173745089 0.319412092 4.453416054 0.15760451 0.042710122 11.21386316 -1.049755252 0.339008142 TEEDSEEVREQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEEDSEEVREQK 12 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 93.959 0.0062736 244930000 153130 102700 115750 74722 174040 163360 142530 117150 142830 83165 FALSE TRUE 159175.6906 120337.9261 118766.5401 89501.78858 144456.743 125422.1157 131358.1262 115579.7959 137689.5762 99459.58946 1.600405667 1.209917784 1.194118543 0.899880937 1.452416441 1.261035929 1.320718564 1.16207795 1.384377082 1 16.60182286 -2.301157057 1.942803712 4.79E-05 1.259958054 0.172357491 0.178379631 2372149.695 313380.5298 10396600.58 0.046040672 0.004998537 2.301157057 1.259910106 TEEEEIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEEEEIDR 8 0 Q13435;E9PPJ0;H0YEX5 Q13435 SF3B2 Splicing factor 3B subunit 2 0 106.93 0.01462 0 48483 48391 53528 62509 62896 61853 72520 60148 53518 44701 FALSE TRUE 50397.14628 56701.77782 54922.98365 74873.09363 52204.96039 47488.57814 66835.6929 59341.81444 51591.89763 53459.3051 0.942719816 1.060653103 1.027379304 1.400562418 0.976536457 0.888312672 1.250216268 1.110037146 0.965068617 1 15.70615346 4.743076093 2.112332916 1.091420627 0.902498426 0.06756159 0.142735568 1.862021195 9.14508393 0.036124451 0.672757174 55344.70708 -4.743076093 -0.188922201 TEEEFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TEEEFKK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 110.78 0.010786 5236760000 7331920 3377910 4154700 4033060 9499190 10052250 12389950 8242750 8363990 3431660 FALSE TRUE 7621389.863 3958039.766 4262974.895 4830787.231 7884521.077 7717767.281 11418793.34 8132269.419 8062971.634 4104028.074 1.857051103 0.964428044 1.038729467 1.177084353 1.921166458 1.880534719 2.78233802 1.981533574 1.964648265 1 21.96860917 3.186539245 4.547921609 2.038063615 1.219551358 0.309331318 0.466434627 0.198878208 8.575974687 0.13125396 0.162625034 1536.523634 -3.186539245 -0.818512256 TEEGSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEEGSVR 7 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 0 ;;; 97.071 0.050165 0 1780750 1705110 1771560 1733030 2099680 2401850 2060900 1849980 1975920 1433560 FALSE TRUE 1851055.385 1997949.379 1817728.309 2075818.161 1742777.144 1844056.738 1899361.273 1825184.044 1904807.025 1714438.635 1.079685996 1.165366516 1.060246936 1.210785921 1.016529322 1.075603816 1.107861917 1.064595727 1.111038323 1 20.70930484 3.217325424 24.99997336 1.069353354 1.126705045 0.283009559 0.051063015 331.5394307 390316.875 0.01367501 0.016358972 1649.397851 -3.217325424 0.057351691 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR;TEELIES(1)PKLESSEGEIIQTVDR 234.48 2.75E-37 884840000 421741 147253 216794 149370 302647 345566 290444 223523 237022 113524 TRUE FALSE 438391.6603 172542.5573 222443.8297 178914.9402 251203.171 265313.5336 267678.2403 220527.0398 228491.6245 135766.8543 3.229003594 1.270873942 1.638425159 1.317810162 1.850254043 1.954184879 1.971602287 1.624306912 1.682970603 1 17.05077178 7.999994181 0.046466559 1.35E-08 4.849744925 0.246996822 0.498468865 1037.931624 3.650749434 94.58356737 371.2414418 99998660.2 -7.999994181 4.849744912 TEEPASDKGS(ph)EAEAHMPPPFTPYVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEEPASDKGSEAEAHMPPPFTPYVPR 26 1 O94886 O94886 TMEM63A CSC1-like protein 1 1 T(0.006)EEPAS(0.195)DKGS(0.798)EAEAHMPPPFTPYVPR 105.49 0.001931 149010000 194580 134170 184140 124310 225020 247170 215590 162540 177560 111940 TRUE FALSE 202262.1686 157212.6538 188938.8397 148898.147 186771.1808 189768.5134 198691.4925 160361.4172 171169.6503 133872.4998 1.51085674 1.174346143 1.411334217 1.11223849 1.395142252 1.417531709 1.484184525 1.197866757 1.278602032 1 17.03050011 0.754272618 1.22663661 1.002694501 1.340168692 0.397449163 0.12649304 0.844727236 2.231855401 0.114865747 0.035083082 5.679009794 -0.754272618 0.337474191 TEEPDRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEEPDRDER 9 1 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 ;; 157.66 6.20E-05 739080000 872170 872010 937180 944760 1046260 1189630 1117210 968850 929000 740230 FALSE TRUE 906603.9451 1021770.934 961603.6807 1131630.708 868417.0989 913356.4615 1029640.161 955864.1505 895565.4715 885263.8959 1.024105862 1.154199261 1.08623393 1.278297594 0.980969746 1.031733549 1.163088392 1.079750518 1.011636728 1 19.75574806 3.188009004 24.99999965 1.058058297 1.133499945 0.241181768 0.076980149 180.1805274 89106.46158 0.022207937 0.026543599 1541.732418 -3.188009004 0.075441648 TEERAELAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEERAELAESR 11 1 P06753-2;A0A087WWU8;P06753-6;P06753-3;J3KN67;A0A2R2Y2Q3;A0A494C0P6 P06753-2;P06753-3;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 92.856 0.0046061 0 45140 85938 77331 30520 99257 83887 35283 67200 78263 114920 FALSE TRUE 46922.16206 100697.183 79346.30939 36556.76491 82385.33059 64405.51557 32517.42627 66299.29392 75446.32992 137436.3737 0.341410071 0.732682188 0.577331221 0.265990465 0.599443425 0.468620597 0.236599856 0.482399907 0.548954603 1 17.06840435 0.752100752 2.795136276 0.999883844 0.464542808 0.550642163 0.144795204 1.099988525 11.34758691 0.137975138 0.03638371 5.650680493 -0.752100752 -0.535341036 TEES(ph)PAS(ph)DEAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 2 TEES(1)PAS(1)DEAGEK;TEES(1)PAS(1)DEAGEK 300.84 9.32E-41 293860000 1558190 655450 909170 869160 1173980 1534610 1895530 1038420 1112620 367020 TRUE FALSE 1619708.544 768018.4388 932863.7171 1041077.254 974427.2989 1178220.085 1746953.406 1024501.678 1072577.024 438930.542 3.69012495 1.749749369 2.125310563 2.371849653 2.220003408 2.684297337 3.980022437 2.334086103 2.44361447 1 18.74363313 2.717723901 21.51778748 2.673961847 2.373223568 0 0.829729679 616.8771888 637035.261 0.257472886 0.243201696 522.0641856 -2.717723901 -0.300738279 TEES(ph)PASDEAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEES(1)PASDEAGEK;TEES(1)PASDEAGEK 278.93 2.61E-32 317240000 928550 528160 720900 676530 855750 1031370 1278860 794120 818590 349710 TRUE FALSE 965209.871 618867.3715 739687.2462 810345.6148 710289.9207 791849.9481 1178619.612 783476.1203 789129.1058 418228.9789 2.307850292 1.479733358 1.768617871 1.937564482 1.698327846 1.893340701 2.818120386 1.873318588 1.886835073 1 18.6739335 2.466385671 24.99233139 2.03366483 1.817693161 0 0.460065195 761.9793125 1773867.113 0.150862922 0.126333594 292.6750299 -2.466385671 -0.215971669 TEESPAS(ph)DEAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEESPASDEAGEK 13 0 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPAS(1)DEAGEK;TEESPAS(1)DEAGEK 241.42 7.24E-17 271130000 636260 297775 405587 376080 519490 689330 793090 506460 526150 189721 TRUE FALSE 661380.0361 348915.5399 416156.9304 450467.5015 431187.2754 529243.5544 730925.5334 499671.7321 507213.9643 226893.1975 2.914939907 1.537796389 1.834153403 1.985372441 1.900397544 2.332566865 3.221451949 2.202233199 2.235474531 1 17.79165383 2.724874249 20.31426873 2.350719342 1.993072407 0 0.609039916 182.6222091 271056.693 0.186521049 0.177347282 530.7307482 -2.724874249 -0.357646935 TEESPAS(ph)DEAGEKEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEESPASDEAGEKEAK 16 1 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPAS(1)DEAGEKEAK 150.13 4.66E-07 374160000 474830 155330 258410 147190 426240 392720 384970 264300 281580 85518 TRUE FALSE 493576.655 182006.7192 265144.3769 176303.7427 353787.877 301516.7317 354795.0455 260757.4908 271445.9908 102273.6148 4.826040971 1.779605812 2.592500299 1.723843858 3.459229224 2.948138016 3.469077008 2.549606674 2.654115545 1 16.64207447 4.751793384 24.61108918 2.583226274 4.826042785 0.467109337 0.747158945 1600.579469 2976787.905 0.169772588 3.201521536 56466.8269 -4.751793384 2.242816511 TEESPASDEAGEKEAKS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEESPASDEAGEKEAKSD 18 2 P05114;A6NL93;A6NEL0 P05114 HMGN1 Non-histone chromosomal protein HMG-14 1 TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D;TEESPASDEAGEKEAKS(1)D 221.6 4.85E-19 1916120000 3793010 842017 1428300 794767 2443060 2850340 2348370 1572510 1679290 476024 TRUE FALSE 3942760.964 986626.8698 1465522.671 951969.5405 2027789.534 2188391.732 2164298.623 1551433.076 1618852.681 569291.7888 6.925729549 1.73307764 2.5742909 1.672199668 3.561951136 3.844059892 3.801738697 2.725198406 2.843625559 1 19.11880877 0.654535008 1.295483596 1.005170586 3.27050681 0.202868002 1.402760572 1.965784314 5.058623327 1.276422691 0.382801221 4.513724084 -0.654535008 2.265336224 TEFLDLDNSPLSPPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 TEFLDLDNSPLS(0.01)PPS(0.99)PR;TEFLDLDNSPLS(0.002)PPS(0.998)PR 167.92 2.27E-09 90389000 172561 106747 119429 104001 139302 166745 130375 131653 118117 101985 TRUE FALSE 179373.8415 125079.9669 122541.4179 124572.0874 115623.4958 128021.0008 120155.8668 129888.4069 113865.9922 121967.0081 1.470675097 1.025522957 1.00470955 1.021358885 0.947989932 1.049636314 0.985150564 1.064947061 0.933580269 1 16.89613143 4.738984542 5.222099277 1.006477456 1.490814515 0.930256595 0.038390835 0.034146065 3.209052512 0.008573863 0.059523082 54825.745 -4.738984542 0.484337059 TEFLHSQNSLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEFLHSQNSLSPR 13 0 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 TEFLHSQNS(0.082)LS(0.918)PR 118.13 0.00047418 47898000 36780 34450 37637 36647 46822 53363 38671 43944 39859 36020 TRUE FALSE 38232.1028 40366.51952 38617.85114 43895.66722 38863.21316 40970.25197 35639.86597 43355.00256 38424.48238 43077.42936 0.887520527 0.937068904 0.896475294 1.018994584 0.902171131 0.951083957 0.827344308 1.006443588 0.891986429 1 15.39464454 -4.999956973 0.428546781 2.403005758 0.927223532 0.141726969 0.054657661 2042.686561 12.85304964 2704.746625 0.02872728 1.00E-05 4.999956973 -1.475782226 TEGAQVDEPVVIT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEGAQVDEPVVITPR 15 0 A0A0J9YWL0;A0A494C1M5 A0A0J9YWL0 1 TEGAQVDEPVVIT(1)PR;TEGAQVDEPVVIT(1)PR 235.72 9.66E-13 306340000 358180 377880 383690 375990 507820 562210 414680 414700 406970 425480 TRUE FALSE 372321.223 442777.9505 393689.2766 450359.6998 421500.9378 431645.2479 382176.298 409141.6248 392323.2292 508844.6597 0.731699185 0.870163304 0.77369246 0.885063233 0.828348946 0.848284913 0.751066737 0.804059976 0.771007854 1 18.95686577 -1.107631756 4.194512733 1.000032928 0.809235076 0.587481611 0.048475909 6302809.967 1664363.517 1980.482367 0.010689746 0.078049162 1.107631756 -0.190797852 TEGT(ph)PPPPGQPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TEGTPPPPGQPAK 13 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;A0A494C150;Q9Y4D8-2 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 1 TEGT(1)PPPPGQPAK;TEGT(1)PPPPGQPAK;TEGT(1)PPPPGQPAK;TEGT(1)PPPPGQPAK;T(0.028)EGT(0.972)PPPPGQPAK 179.5 0.00015308 1215690000 3056910 2050860 2640590 2204520 3438210 3413220 2969390 2500590 2783880 1688790 TRUE FALSE 3177599.167 2403079.252 2709405.945 2640567.476 2853784.292 2620551.383 2736641.453 2467073.681 2683688.703 2019676.067 1.573321197 1.189833999 1.341505199 1.307421284 1.412991093 1.297510738 1.354990287 1.221519491 1.32877185 1 20.94569249 -4.111770003 0.198164958 9.08E-12 1.386991778 0.547782615 0.095416342 68.99137144 0.936757209 27.6308459 0.221059518 7.73E-05 4.111770003 1.386991778 TEHAEFLHCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEHAEFLHCK 10 0 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 ; 118.4 0.00047974 99177000 152118 134754 171498 147779 224530 214572 200834 175735 191761 122678 FALSE TRUE 158123.7361 157896.9513 175967.3788 177009.2451 186364.4708 164740.9049 185092.1063 173379.5598 184859.5591 146714.4053 1.07776558 1.076219823 1.199387193 1.206488516 1.270253391 1.122867959 1.261581001 1.181748714 1.259995968 1 17.162651 4.238609355 24.99999992 1.198444055 1.076992658 0.242972058 0.076399486 1.356725756 693764.6074 0.016815648 0.040499405 17322.45155 -4.238609355 -0.121451397 TEIKEEEDQPSTSATQS(ph)SPAPGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSAT(0.003)QS(0.585)S(0.412)PAPGQSK 158.2 1.52E-11 486880000 318480 112410 185720 116320 270050 289380 283410 191280 245810 70894 TRUE FALSE 331053.8363 131715.5431 190560.0158 139327.7488 224146.9975 222175.8806 261195.5836 188716.2045 236963.3461 84784.32195 3.904658653 1.553536551 2.247585537 1.643319727 2.643731675 2.620483074 3.080706169 2.225838458 2.794895809 1 16.37150989 TEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 TEIKEEEDQPSTSAT(0.002)QS(0.148)S(0.849)PAPGQSK 120.18 0.00018425 637730000 241760 88565 132550 100150 195040 201420 214060 154760 180710 53629 TRUE FALSE 251304.8715 103775.3498 136004.3619 119959.3711 161887.1705 154643.2575 197281.4179 152685.6953 174206.2824 64136.57576 3.918277028 1.618036956 2.120542924 1.870373802 2.524100617 2.411155502 3.075958071 2.380633726 2.716176851 1 15.96885971 TEIMS(ph)PLYQDEAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEIMSPLYQDEAPK 14 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 TEIMS(0.998)PLY(0.002)QDEAPK 150.59 7.52E-06 47083000 146680 90581 115420 96027 146090 163400 163100 116660 127500 79673 TRUE FALSE 152471.0397 106137.5821 118427.94 115020.854 121257.674 125452.8264 150315.7958 115096.3635 122911.2999 95283.39892 1.600184727 1.113914736 1.242902136 1.207144742 1.272600215 1.316628372 1.577565426 1.207937215 1.289955032 1 16.53993726 0.54074254 1.667350199 1.000277155 1.310913156 0.288975373 0.148545437 3.226271255 10.23370264 0.136830085 0.038828681 3.473301947 -0.54074254 0.310636 TEKHESQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEKHESQR 8 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ; 111.46 0.0019408 125349000 87097 247068 251209 205860 321456 348900 221991 275189 261804 319170 FALSE TRUE 90535.65681 289500.0071 257755.7129 246578.4936 266815.0239 267873.2626 204590.7654 271500.5416 252381.7252 381705.2506 0.23718735 0.758438629 0.675274214 0.645991883 0.699008 0.701780398 0.535991488 0.711283225 0.66119532 1 18.54209951 -5 0.161989396 2.336447902 0.540958582 0.440698526 0.134968032 128.4396957 1.187880347 55.39152917 0.526813022 1.00E-05 5 -1.79548932 TELADKVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TELADKVTK 9 1 P35579 P35579 MYH9 Myosin-9 0 80.706 0.021299 334340000 906820 618160 759830 500560 1148100 963330 837170 763580 834880 563040 FALSE TRUE 942621.9538 724324.1714 779631.794 599569.274 952946.3721 739611.2069 771550.4279 753345.4591 804832.8319 673356.9079 1.399884582 1.075691306 1.157828463 0.890418242 1.41521734 1.098394029 1.145826855 1.118790719 1.195254437 1 19.36101187 -5 0.218954683 0.224925436 1.177059133 0.107989021 0.144459717 371.1230332 3.712320594 127.2420884 0.263008306 1.00E-05 5 0.952133697 TELDAHFENLLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TELDAHFENLLAR 13 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9 B7ZC38 SH3GLB2 Endophilin-B2 0 ;;;; 210.38 3.04E-08 1866199000 2384723 2672183 2852813 2808490 3138930 3716180 3213492 3063424 2833971 2452176 FALSE TRUE 2478873.705 3131109.644 2927159.65 3364000.939 2605375.8 2853153.514 2961610.1 3022363.812 2731976.937 2932632.937 0.845272408 1.067678673 0.998133661 1.147092395 0.888408422 0.972898271 1.009880937 1.030597377 0.931578208 1 21.48376508 1.242665233 24.99363048 0.965789112 1.000462976 0.016580939 0.081707568 434.6942469 2647055.208 0.056384987 0.018896064 17.48498374 -1.242665233 0.034673864 TELESTIFGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TELESTIFGSPR 12 0 Q9UQK1 Q9UQK1 PPP1R3C Protein phosphatase 1 regulatory subunit 3C 1 TELES(0.001)T(0.001)IFGS(0.999)PR;TELESTIFGS(1)PR 202.92 1.38E-07 38384000 25584.6 33580 34876.6 33730.3 50045 51211 44746 43423 38070 40131 TRUE FALSE 26594.69976 39347.10378 35785.51285 40402.05267 41538.36878 39318.02136 41238.6916 42840.98571 36699.86814 47993.9011 0.554126653 0.819835498 0.745626257 0.841816392 0.865492653 0.819229537 0.859248585 0.892633954 0.764677747 1 15.55056346 5.341281219 0.942941178 0.858036455 3.28E-31 0.646616992 0.065364608 3.359402079 1.059118894 0.018544878 3.86067271 219422.5304 -5.341281219 -0.858036455 TELFVHAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TELFVHAFK 9 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 105.52 0.0030845 866580000 1763610 1191700 1652400 1386270 2459320 2220760 2122430 1705130 1781710 1247480 FALSE TRUE 1833238.685 1396365.205 1695462.901 1660470.068 2041285.665 1705022.146 1956068.391 1682275.521 1717586.605 1491899.822 1.228794761 0.935964456 1.136445542 1.112990326 1.3682458 1.142852973 1.311125829 1.127606222 1.151274757 1 20.50871923 5.073606181 21.43774953 1.154736553 4.031276435 0.035831672 0.120339105 3498.593083 1035509.079 0.027477137 7859.694253 118469.3977 -5.073606181 2.876539883 TELLVPLPGPREPS(ph)PHPGVGLTSGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TELLVPLPGPREPSPHPGVGLTSGSSR 27 1 E9PIR9;E7ET48;Q8N1P7 E9PIR9 AIM1L Absent in melanoma 1-like protein 1 TELLVPLPGPREPS(1)PHPGVGLTSGSSR 56.957 0.042606 64525000 68733 53828 57282 43949 72665 87092 42849 52854 55457 81519 TRUE FALSE 71446.63191 63072.54028 58774.81598 52641.98103 60313.42926 66866.20289 39490.38341 52145.57858 53461.1134 97491.08727 0.73285296 0.646956989 0.602873736 0.539967114 0.618655827 0.685869906 0.405066602 0.534875341 0.54836924 1 16.57298271 -1.745790749 6.753160971 1.008007376 0.582932638 0.664671925 0.087081336 0.011005453 0.000414278 0.088388312 0.020758023 0.017955986 1.745790749 -0.425074738 TEMDKS(ph)PFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 2 TEMDKS(1)PFNS(0.081)PS(0.919)PQDSPR 221.21 3.62E-19 111760000 243570 138710 158150 121230 219600 237070 196130 200450 203730 106670 TRUE FALSE 253186.3317 162532.3635 162271.5189 145208.9322 182272.4704 182014.0853 180756.8181 197763.2956 196397.7971 127569.9442 1.984686388 1.274064706 1.272019988 1.138269152 1.428804187 1.426778749 1.416923236 1.550234241 1.539530321 1 16.96092894 -1.714815162 2.514923785 0.916726228 1.434301119 0.276777454 0.216211061 16235633.27 12406988.69 8508362.377 0.050844851 0.019283455 1.714815162 0.517574891 TEMDKS(ph)PFNSPSPQDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TEMDKS(1)PFNSPSPQDSPR;TEMDKS(1)PFNSPSPQDSPR;TEMDKS(1)PFNSPSPQDSPR 218.44 4.77E-19 926470000 1348610 897000 1152340 868190 1505640 1545940 1350260 1206200 1153050 808080 TRUE FALSE 1401854.164 1051052.772 1182370.927 1039915.391 1249711.851 1186918.864 1244423.093 1190032.862 1111551.956 966407.8044 1.450582412 1.087587215 1.22346997 1.076062699 1.293151654 1.228175992 1.28767906 1.231398232 1.150189341 1 19.88227258 0.914228876 2.928687993 1.000322432 1.228588158 0.340254213 0.100102721 0.398746243 7.747268451 0.088996245 0.023429621 8.207839881 -0.914228876 0.228265725 TEMDKSPFNSPS(ph)PQDSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 P08651-3;P08651-2;P08651-6;A0A286YEX4;P08651;P08651-5;P08651-4 P08651-3 NFIC Nuclear factor 1 C-type 1 TEMDKSPFNS(0.003)PS(0.994)PQDS(0.003)PR 245.38 2.00E-24 371460000 509310 343200 450400 309700 572870 596360 497430 449100 516710 318340 TRUE FALSE 529417.9521 402141.9303 462137.794 370957.7356 475493.762 457864.4279 458440.1368 443080.5491 498113.708 380712.628 1.390597299 1.056287343 1.213875664 0.974377282 1.248957158 1.202651013 1.204163201 1.163818892 1.308371909 1 18.5383429 -1.229350457 3.525470684 0.999661591 1.186145549 0.213261329 0.111471323 4009774.471 4194722.241 8968.025595 0.023992801 0.058972501 1.229350457 0.186483958 TEMEDLMSSKDDVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TEMEDLMSSKDDVGK 15 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;; 235.35 1.02E-17 1611120000 1616616 780649 1174116 670951 1932900 1524964 1433674 1100989 1394569 665286 FALSE TRUE 1680441.248 914719.3931 1204714.428 803663.1052 1604346.348 1170814.222 1321298.886 1086232.043 1344378.734 795636.054 2.112072774 1.149670617 1.514152635 1.010088848 2.016432438 1.471544956 1.660682518 1.365237332 1.689690566 1 19.60174913 -1.539790718 6.394636223 0.999396922 1.528742351 0.202763089 0.326242803 0.002556707 0.000184001 0.287922757 0.067792098 0.028854216 1.539790718 0.529345429 TENDHINLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TENDHINLK 9 0 A8MUA9;A8MU27;P55854;P55854-2 A8MUA9 SUMO3 Small ubiquitin-related modifier 3 0 ;; 127.76 0.00043624 1764350000 3196520 2431760 3056900 2418360 4113050 3913160 3692320 3223430 3424170 2139730 FALSE TRUE 3322721.078 2849395.864 3136565.325 2896704.39 3413915.23 3004387.895 3402906.31 3180225.193 3300934.791 2558969.126 1.298460792 1.113493647 1.225714407 1.131980984 1.334097858 1.174061799 1.329795767 1.242775914 1.289947095 1 21.28713131 3.261291568 24.99980184 1.244896908 1.189154152 0.013690309 0.10220991 674.2369136 741529.8852 0.025583817 0.0346155 1825.120605 -3.261291568 -0.055742756 TENNDHINLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TENNDHINLK 10 0 P61956;P61956-2 P61956 SUMO2 Small ubiquitin-related modifier 2 0 ;;;;; 184.36 1.57E-06 9544070000 12548060 9756040 12344530 9465130 15462960 15399120 15247430 12397280 12940090 8010490 FALSE TRUE 13043467.1 11431563.98 12666238.59 11337304.46 12834571.58 11822907.76 14052296.59 12231114.74 12474378.69 9579992.145 1.361532129 1.19327488 1.322155426 1.183435674 1.339726733 1.234124995 1.466838008 1.276735362 1.302128279 1 23.19159304 -0.710794946 5.097430874 0.99999993 1.297351877 0.556835056 0.079693107 4795126.029 940694.6816 4.279402178 0.017489779 0.194627881 0.710794946 0.297351947 TENSWGEPSSPS(ph)TLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TENSWGEPSSPSTLVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 45 1 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0;K7ELY5 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 TENSWGEPS(0.042)S(0.162)PS(0.634)T(0.162)LVDNGTAAWGKPPSSGSGWGDHPAEPPVAFGR 194.6 1.06E-29 206030000 74354 92860 95210 84593 125010 128930 95286 86495 104370 92218 TRUE FALSE 77289.55333 108807.9826 97691.25082 101325.2429 103760.8449 98987.96145 87817.23434 85335.676 100613.7441 110286.3515 0.700807963 0.986595179 0.885796379 0.918746894 0.94083124 0.89755405 0.796265659 0.773764612 0.912295517 1 16.75089474 2.278222678 24.04381796 0.841394398 0.896498478 0 0.09261821 281.095475 170403.2949 0.030679545 0.02566787 189.7678676 -2.278222678 0.05510408 TEPAAEAEAASGPSES(ph)PSPPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 TEPAAEAEAAS(0.016)GPS(0.451)ES(0.511)PS(0.023)PPAAEELPGSHAEPPVPAQGEAPGEQAR 146.32 9.96E-15 256460000 37857 48758 51975 45192 60176 62381 52312 41990 48901 46855 TRUE FALSE 39351.62359 57131.80722 53329.5112 54130.84272 49947.30501 47893.95814 48211.64875 41427.19273 47141.06256 56035.34016 0.702264383 1.01956742 0.951712099 0.966012566 0.891353651 0.854709867 0.860379336 0.739304743 0.841273782 1 15.77404937 2.696735495 2.244224944 0.830376012 0.920750185 0.015476369 0.099415226 0.610561603 6.065688271 0.03485589 0.033651496 497.4340332 -2.696735495 0.090374173 TEPSS(ph)PLSDPSDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEPSSPLSDPSDIIR 15 0 Q9ULJ3;Q9ULJ3-2 Q9ULJ3;Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 TEPSS(1)PLSDPSDIIR;TEPS(0.114)S(0.886)PLSDPSDIIR;TEPS(0.001)S(0.999)PLSDPSDIIR 267.84 1.75E-25 536830000 501660 542870 540260 553540 609080 694230 710040 590710 557570 432630 TRUE FALSE 521465.9242 636103.6996 554339.6194 663028.5598 505548.7992 533005.6037 654385.2095 582792.4987 537503.1646 517395.5653 1.007867015 1.229434 1.071403886 1.281473218 0.977103078 1.030170414 1.26476772 1.126396393 1.038863107 1 18.98090816 3.227215684 24.99970396 1.093418911 1.147955189 0.090034888 0.104705204 703.6481042 1550556.907 0.030176189 0.036372651 1687.390829 -3.227215684 0.054536279 TEPTS(ph)PTPSAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 TEPT(0.002)S(0.874)PT(0.124)PSAFK;TEPT(0.035)S(0.866)PT(0.099)PSAFK;TEPT(0.001)S(0.499)PT(0.499)PS(0.001)AFK;TEPTS(0.995)PT(0.004)PS(0.001)AFK 256.25 3.84E-21 739700000 2679960 1670880 2260370 1906080 2842980 3057370 3118220 2504560 2557300 1419180 TRUE FALSE 2785766.89 1957840.642 2319277.099 2283096.935 2359731.275 2347342.152 2873805.768 2470990.47 2465263.273 1697241.149 1.641350077 1.153542997 1.366498273 1.345181229 1.390333528 1.383033963 1.693221832 1.455886496 1.45251208 1 20.69476013 -0.40280607 12.86607214 0.999999985 1.429522789 0.447585878 0.143728557 0 0 0.138612254 0.032671222 0.395543207 0.40280607 0.429522804 TEQELPRPQS(ph)PSDLDSLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 1 TEQELPRPQS(0.962)PS(0.038)DLDSLDGR 201.21 7.76E-22 191090000 138290 147590 162670 158670 187320 204070 168500 159130 161050 147120 TRUE FALSE 143749.796 172937.4344 166909.3138 190054.4524 155479.4133 156677.8352 155292.5297 156997.1226 155253.842 175945.3472 0.817013909 0.982904278 0.948642953 1.080190272 0.883680164 0.890491495 0.882617996 0.892306191 0.882398111 1 17.42476784 TES(ph)PATAAETASEELDNR ddPTM_MDA-MB-175_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;TES(1)PATAAETASEELDNR;TES(1)PATAAETASEELDNR;T(0.007)ES(0.993)PATAAETASEELDNR;TES(1)PATAAETASEELDNR 514.96 3.42E-295 3035420000 969355 1030209 999650 962847 1209895 1428990 1151969 1083678 1088933 905005 TRUE FALSE 1007625.884 1207139.382 1025701.7 1153295.263 1004237.48 1097128.729 1061674.66 1069153.069 1049742.514 1082323.402 0.930984105 1.115322259 0.947685043 1.065573617 0.927853429 1.013679208 0.980921837 0.987831425 0.969897271 1 20.04570022 3.243898485 24.99995481 0.981599549 1.017264439 0.0912726 0.053541829 306.6834456 1436345.774 0.013503829 0.017782152 1753.470587 -3.243898485 0.03566489 TESALSYYEFLLHIQQQVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TESALSYYEFLLHIQQQVNK 20 0 O95486 O95486 SEC24A Protein transport protein Sec24A 0 198.85 1.52E-21 66158000 140070 108430 169100 127630 198430 185130 184590 168450 189330 101550 FALSE TRUE 145600.0718 127052.009 173506.8849 152874.8331 164700.9395 142136.3632 170121.3535 166192.2033 182516.0503 121446.7782 1.198879657 1.046153804 1.428666017 1.258780474 1.356157338 1.170359274 1.40078935 1.368436493 1.502848021 1 16.88996469 4.243170797 24.99999203 1.325522777 1.122516713 0.218367161 0.140244746 142.0948375 770521.6652 0.031709327 0.080989006 17505.34993 -4.243170797 -0.203006064 TESDDLHTFLLEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TESDDLHTFLLEIK 14 0 A0A494C1F2;P35658-2;P35658;P35658-5;A0A0A0MSW3;P35658-4;P35658-3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 0 ; 180.84 1.71E-06 96317000 249577 186955 242778 186412 341760 349900 312790 260540 289000 174063 FALSE TRUE 259430.4927 219063.0669 249104.9941 223283.7372 283667.7573 268641.0278 288272.7025 257047.8875 278598.9465 208167.3122 1.246259511 1.052341334 1.19665759 1.072616708 1.362691165 1.290505339 1.384812531 1.234813885 1.338341469 1 17.66738402 3.240939421 24.99993997 1.285829637 1.139473167 0.220414387 0.113807302 76.75028078 806595.1335 0.029140624 0.037657284 1741.563928 -3.240939421 -0.14635647 TESEVPPRPAS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TESEVPPRPASPK 13 1 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 TESEVPPRPAS(1)PK;TESEVPPRPAS(1)PK;TESEVPPRPAS(1)PK;TESEVPPRPAS(1)PK 136.81 4.12E-05 921170000 1640720 744986 1009569 729277 1446190 1590540 1309310 1024740 1144560 643335 TRUE FALSE 1705496.893 872931.5503 1035879.198 873525.8139 1200367.14 1221161.19 1206682.861 1011005.036 1103367.509 769384.1759 2.216703886 1.134584747 1.346374451 1.135357135 1.560166141 1.587193015 1.56837494 1.314044489 1.434091763 1 19.55334463 -3.216135335 0.255533112 1.43E-14 1.501697062 0.2056972 0.290048284 116.3118947 2.610067642 62.48744827 0.396415771 0.000607946 3.216135335 1.501697062 TESSTEGKEQEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TESSTEGKEQEEK 13 1 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 ;;; 204.35 7.17E-08 1350040000 2319490 855740 1298000 774450 2216550 2133350 1955300 1480050 1696690 611126 FALSE TRUE 2411065.256 1002706.688 1331826.946 927633.8985 1839781.623 1637911.794 1802038.477 1460212.351 1635626.458 730864.439 3.298922656 1.371946198 1.822262618 1.269228395 2.517267943 2.241061004 2.465626155 1.997925022 2.237934111 1 19.47924431 TET(ph)PPPLASLNVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 TET(1)PPPLASLNVSK;TET(1)PPPLASLNVSK 129.53 0.00075297 425220000 762080 317020 414260 364880 592570 708440 745990 493210 513690 219360 TRUE FALSE 792167.5069 371465.7189 425055.9559 437052.1749 491845.1631 543915.5465 687517.3545 486599.3267 495202.3972 262339.3921 3.019628507 1.41597385 1.620252119 1.665979979 1.874842962 2.073327769 2.62071719 1.854846589 1.887640256 1 18.00107493 2.856536382 7.55112784 1.992893426 1.859466562 0 0.552628671 1.869959273 109.5691836 0.162759985 0.172883725 718.6813623 -2.856536382 -0.133426864 TET(ph)QEKNPLPSKETIEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 T(0.008)ET(0.992)QEKNPLPSKETIEQEK 150.06 3.78E-06 199960000 324510 69864 165780 76040 288480 209450 210830 128650 206470 56689 TRUE FALSE 337321.9054 81862.59853 170100.363 91080.48504 239444.2726 160808.4117 194304.5937 126925.6572 199039.185 67796.12417 4.975533771 1.207481984 2.50899834 1.343446785 3.531828339 2.371941076 2.866013302 1.872166864 2.935849025 1 16.04891518 -1.554056603 0.402882075 1.25E-18 2.58894359 0.174463848 1.042734752 51.62974585 4.216827789 54.16578685 0.605836692 0.027921799 1.554056603 2.58894359 TETGQELECLQDHLDDLVVECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TETGQELECLQDHLDDLVVECR 22 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ;; 247.84 4.25E-31 160414000 79079 85280 70439 115576 148061 163811 122844 85807 84887 135145 FALSE TRUE 82201.09998 99926.17661 72274.69821 138436.5878 122893.6441 125768.3778 113215.1663 84656.89752 81831.93345 161624.0752 0.508594403 0.618262944 0.447177799 0.856534447 0.760367191 0.778153735 0.700484542 0.523788906 0.506310296 1 17.30228259 3.753105886 24.96961776 0.702909135 0.534036843 0.289255181 0.143824132 1269.079098 2178600.453 0.038380918 0.068812172 5663.773613 -3.753105886 -0.168872291 TETQEKNPLPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 182.89 1.49E-05 2325330000 3460050 1930750 2835910 2027230 3640720 3545400 3899360 2990540 3330850 1485210 FALSE TRUE 3596655.446 2262341.293 2909816.144 2428210.043 3021871.715 2722034.581 3593717.974 2950456.703 3210973.359 1776208.463 2.024906153 1.273691315 1.6382177 1.36707492 1.701304648 1.532497247 2.023252365 1.661098212 1.807768303 1 20.76036948 2.791985772 2.470571675 1.686152895 1.563235653 0 0.3119692 1.266786123 15.23383993 0.099066888 0.102029152 619.4207821 -2.791985772 -0.122917242 TETQEKNPLPSKETIEQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 ;;; 185.27 1.30E-14 5399669000 953320 440383 715650 347079 1105270 893520 722670 602240 830020 337637 FALSE TRUE 990957.8097 516015.3545 734300.4269 415730.1903 917396.6002 686013.5214 666025.2371 594167.9579 800147.7423 403790.5057 2.45413846 1.277928399 1.818518307 1.029569008 2.27196179 1.698934254 1.649432633 1.471475801 1.981591273 1 18.62324746 -1.952493431 2.772849412 0.482994357 1.700288889 0.222459697 0.408828262 111876838.3 96418895.27 374764764.6 0.092636691 0.01115595 1.952493431 1.217294531 TEVLS(ph)PNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEVLSPNSK 9 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TEVLS(0.999)PNS(0.001)K;TEVLS(0.996)PNS(0.004)K 124.21 0.00056239 186080000 1105710 722600 903200 813890 1152930 1304530 1310850 961530 937310 530450 TRUE FALSE 1149364.285 846700.929 926738.134 974875.0128 956955.3704 1001572.678 1208102.152 948642.2631 903576.3962 634381.5214 1.811787144 1.334687251 1.460852977 1.536732991 1.508485569 1.578817548 1.904377903 1.495381298 1.424342238 1 19.27499122 0.836207678 2.23966109 1.001221078 1.57579807 0.554767747 0.156864338 0.45858967 4.245928361 0.14959261 0.040744401 6.858161033 -0.836207678 0.574576992 TEVS(ph)PVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TEVSPVPR 8 0 O43159;E9PPY3 O43159 RRP8 Ribosomal RNA-processing protein 8 1 TEVS(1)PVPR 118.03 0.0020606 233910000 296490 277970 274830 286040 311470 400520 349030 304980 274840 250890 TRUE FALSE 308195.6541 325709.1852 281992.2956 342617.8583 258526.4407 307505.2999 321672.1166 300892.2419 264948.5621 300047.0919 1.027157611 1.085526885 0.939826791 1.141880283 0.861619551 1.024856792 1.072072102 1.002816725 0.883023263 1 18.19482942 4.870139684 0.30532014 0.978375266 1.109518727 0.069495452 0.080882498 25.89698418 1.856726684 0.086722398 1.295148588 74154.87101 -4.870139684 0.131143462 TEVSLTLTNKFDVPGDENAEMDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEVSLTLTNKFDVPGDENAEMDAR 24 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ; 166.59 1.34E-11 503093000 389290 309766 391640 275316 523540 487260 449330 426000 451860 294791 FALSE TRUE 404659.4698 362965.9009 401846.4601 329772.6831 434548.8578 374101.2495 414110.3405 420290.1668 435597.6469 352549.6523 1.147808449 1.029545479 1.139829404 0.935393585 1.232589098 1.061130672 1.174615654 1.192144607 1.235563967 1 18.42746693 3.213613518 24.99969572 1.158706682 1.066221653 0.181286379 0.088307096 341.3859406 342104.7886 0.023933539 0.028617873 1635.360553 -3.213613518 -0.092485028 TEWLDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 TEWLDGK 7 0 P62937;P0DN26;A0A0H2UH34;A0A0B4J2A2;A0A075B767;A0A075B759;Q9Y536;F5H284;P0DN37;P62937-2 P62937;P62937-2 PPIA;PPIAL4C;PPIAL4E;PPIAL4A;PPIAL4D "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A-like 4A/B/C;Peptidyl-prolyl cis-trans isomerase A-like 4D" 0 ;;;;;;;;;; 170.06 0.0023005 34389698000 23935430 18583570 22161730 16342940 29188200 28118430 23545150 22934740 22276150 15032650 FALSE TRUE 24880419.26 21775153.59 22739282.89 19575524.75 24226800.19 21588350.77 21699619.62 22627337.32 21474435.71 17978009.95 1.383936227 1.211210454 1.264838709 1.088859379 1.347579641 1.200819826 1.207008989 1.258611903 1.19448347 1 24.09973 -4.400894042 0.245165523 3.73E-12 1.26187199 0.487963715 0.076178154 107.2656964 1.39954217 53.43363749 0.108670328 3.97E-05 4.400894042 1.26187199 TEWLDGKHVVFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEWLDGKHVVFGK 13 1 P62937;P62937-2 P62937;P62937-2 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 ; 135.58 4.94E-05 3979500000 7835900 1932770 6347100 4942200 7206000 6159900 10388400 5485400 7903900 805270 FALSE TRUE 8145267.383 2264708.213 6512510.64 5919752.409 5981126.694 4729356.579 9574130.063 5411877.185 7619440.183 963047.2387 8.457806695 2.351606569 6.762399993 6.146897235 6.210626492 4.910825128 9.941495784 5.619534503 7.911803157 1 19.87724704 TEYGDLELCIEVVDNVQDAIDHIHK ddPTM_MDA-MB-175_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 0 178.35 1.69E-17 24833000 37321 25946 35676 40155 35812 52225 38432 33063 40096 25848 FALSE TRUE 38794.4619 30402.02367 36605.74587 48097.53915 29724.68903 40096.53523 35419.59942 32619.84457 38652.95279 30912.42071 1.254979746 0.983488933 1.184175973 1.555929236 0.961577526 1.29710111 1.14580478 1.055234233 1.250402004 1 14.91589901 2.005978971 24.86611114 1.106141778 1.201659803 0.073975892 0.166634712 431.0907182 1792865.729 0.061457359 0.045262823 101.3862293 -2.005978971 0.095518025 TEYLSNADER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TEYLSNADER 10 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 200.09 6.20E-07 360910000 308300 314530 328080 331760 454240 457540 362850 362400 380020 316750 FALSE TRUE 320471.9221 368548.0808 336630.0343 397381.1378 377028.4471 351283.2691 334408.8689 357542.6208 366343.1544 378811.098 0.845994016 0.972907295 0.888648818 1.0490219 0.99529409 0.927330986 0.8827853 0.943854662 0.967086647 1 18.53111907 7.999989284 0.007243599 1.810699719 1.64E-07 0.111314346 0.055572182 76912.8334 43.0901567 4835.038433 5994.002317 99997532.65 -7.999989284 -1.810699555 TEYNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TEYNLR 6 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;; 144.66 0.02616 625440000 596720 562990 710850 661420 779230 874560 788470 693470 702050 492440 FALSE TRUE 620278.9664 659679.153 729375.335 792246.9019 646776.7629 671456.6941 726667.6611 684175.1689 676783.3576 588924.1897 1.053240769 1.120142736 1.238487649 1.345244287 1.09823433 1.140141135 1.233889988 1.161737251 1.149185871 1 19.16772241 0.662630839 1.888949335 1.000075262 1.178689172 0.302801016 0.078548293 1.950061787 9.210146018 0.077020634 0.021442423 4.598655103 -0.662630839 0.17861391 TFCPAHK ddPTM_MDA-MB-175_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 ;;;;;;; 110.63 0.0067597 25585160000 17512580 14087950 17068090 15442770 20969190 21359400 18197520 16599130 16691660 12323800 FALSE TRUE 18203990.18 16507445.82 17512898.45 18497303.81 17404854.57 16399003.05 16771150.83 16376645.81 16090930.42 14738412.66 1.23513913 1.120028744 1.188248616 1.255040434 1.180917849 1.112670912 1.137921106 1.111153975 1.091768211 1 23.81307782 1.28176597 0.478340868 0.99749176 1.199125903 0.715564797 0.03774501 0.515417546 0.31975972 0.044058518 0.025308409 19.13224659 -1.28176597 0.201634143 TFDAQIVIIEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFDAQIVIIEHK 12 0 P15170-2;P15170-3;P15170 P15170-2 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 107.37 0.0018211 138380000 102330 81618 106450 77547 129210 122880 127750 110460 123930 67431 FALSE TRUE 106370.0674 95635.2566 109224.1744 92885.56515 107246.9304 94342.98226 117736.6212 108979.4644 119469.7835 80642.81341 1.319027238 1.185911708 1.354419195 1.151814541 1.329900655 1.16988704 1.459976608 1.351384702 1.481468447 1 16.29925835 2.245748839 24.99984618 1.356209954 1.252496706 0.038680954 0.139845186 345.005408 1199893.418 0.044486615 0.036492256 176.0957356 -2.245748839 -0.103713249 TFDGDVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFDGDVFR 8 0 P98088;A0A0G2JM87;A0A0G2JR65;Q02817;Q9HC84 P98088;Q9HC84 MUC5AC;MUC2;MUC5B Mucin-5AC;Mucin-2;Mucin-5B 0 142.64 0.0014291 224380000 144220 177040 159100 166900 204140 226450 164990 160510 140200 203560 FALSE TRUE 149913.917 207445.2428 163246.2767 199912.3219 169440.3557 173860.4194 152057.6527 158358.626 135154.2294 243443.6846 0.615805324 0.852128258 0.670571007 0.821185081 0.696014587 0.714170999 0.624611203 0.650493876 0.555176568 1 17.89322855 -1.059172615 4.855607921 1.000008318 0.692158115 0.540068185 0.086079053 7.67E-06 1.49E-06 0.082421787 0.019426477 0.087262447 1.059172615 -0.307850204 TFDHMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFDHMAR 7 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 0 133.81 0.0032352 153090000 98803 199490 178030 192320 165470 241850 159330 174590 167090 239160 FALSE TRUE 102703.8187 233750.8557 182669.6081 230360.322 137343.4685 185684.0028 146841.2983 172249.9066 161076.4635 286018.823 0.359080629 0.817256897 0.63866289 0.805402664 0.480190314 0.649202038 0.513397324 0.602232765 0.563167353 1 18.12575057 -1.820685944 2.656321663 1.130306899 0.609782536 0.446967074 0.132237095 29890081.16 21947690.47 25003137.95 0.030377331 0.015111725 1.820685944 -0.520524363 TFDHYCEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TFDHYCEYR 9 0 Q14204;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8YGC7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;;; 192.92 3.42E-05 2490610000 2416105 2650670 2860850 2948720 3746250 3838620 2890140 2882560 2821940 3116800 FALSE TRUE 2511494.691 3105901.953 2935406.101 3531968.015 3109463.763 2947158.68 2663603.275 2843923.998 2720378.931 3727477.285 0.673778671 0.833245038 0.787504759 0.947549172 0.834200593 0.790657717 0.714586051 0.762962127 0.729817708 1 21.82976813 2.54729687 6.147212226 0.77472135 0.821494065 0 0.097826969 0.805844906 55.55752923 0.030796363 0.028758183 352.6118234 -2.54729687 0.046772715 TFDQLTPDESKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TFDQLTPDESKER 13 1 Q15293 Q15293 RCN1 Reticulocalbin-1 0 ;; 157.86 3.65E-05 1247370000 1151790 920620 1109170 814460 1598420 1444240 1118500 986390 1026630 837360 FALSE TRUE 1197263.559 1078729.324 1138075.881 975557.7571 1326721.139 1108837.148 1030829.047 973169.0555 989681.7868 1001424.66 1.195560292 1.077194688 1.136456817 0.974169896 1.324833702 1.107259679 1.029362556 0.971784593 0.988273833 1 19.93362246 2.180282577 3.341411907 0.987571163 1.135651504 0.406382792 0.083524326 0.243717037 5.534443533 0.033488404 0.023923707 151.4546378 -2.180282577 0.148080342 TFDQLTPEESKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TFDQLTPEESKER 13 1 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-9;O43852-13;O43852-14;O43852-11;O43852-12;O43852-2;O43852-4;O43852-8;O43852-7 O43852;O43852-2 CALU Calumenin 0 ;;;;; 203.32 7.92E-08 2075262000 2384414 1858619 2251700 1696182 3242905 3003313 2314340 2178953 2332822 1840636 FALSE TRUE 2478552.506 2177822.355 2310381.152 2031681.737 2691677.166 2305839.071 2132935.983 2149747.699 2248864.192 2201273.383 1.125963056 0.989346608 1.049565751 0.922957481 1.222781862 1.047502363 0.968955514 0.976592783 1.021619672 1 21.0699069 2.304207755 6.864638611 0.987803031 1.057683705 0.162906043 0.075257385 0.396696624 33.33990929 0.026090862 0.021662783 201.4687793 -2.304207755 0.069880675 TFEGIDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFEGIDPK 8 0 P50395;P50395-2;Q5SX87;Q5SX86 P50395;Q5SX86 GDI2 Rab GDP dissociation inhibitor beta 0 79.906 0.062405 153950000 475060 327230 397490 310710 505760 513820 510580 427630 471250 259090 FALSE TRUE 493815.7356 383429.207 407848.9159 372167.5106 419791.0959 394493.092 470559.4054 421898.3193 454289.8046 309853.7249 1.593705984 1.237452308 1.31626275 1.201107105 1.354804097 1.273159108 1.518650149 1.361604801 1.466142789 1 18.24122779 -1.98425305 2.886117612 0.673964951 1.362039996 0.465208822 0.11853382 33014116.99 21998778.94 71766156.45 0.027547377 0.010369241 1.98425305 0.688075045 TFEHVTSEIGAEEAEEVGVEHLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TFEHVTSEIGAEEAEEVGVEHLLR 24 0 P51665;H3BNT7;H3BTM8 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ;;;;;; 352.68 3.21E-102 1150637000 110097.8 164011.6 174959.2 173058.9 192109.3 212401.7 165606.9 170707.5 154841.5 186892.6 FALSE TRUE 114444.5462 192179.3165 179518.7805 207289.4339 159454.6298 163074.6242 152626.1984 168419.4452 149268.7847 223510.6267 0.512031789 0.859821832 0.803177832 0.927425407 0.713409614 0.729605686 0.682858801 0.753518737 0.667837529 1 17.7699839 -1.049248335 4.3930363 1.000013585 0.746960754 0.344821445 0.107469308 19938823.84 60846486.52 5200.037309 0.025028589 0.089279483 1.049248335 -0.253052831 TFEINPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TFEINPR 7 0 P14625;H0YIV0;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 ;;; 169.37 0.0023599 1393410000 1278800 1664790 1481170 1702940 1892390 2058180 1544830 1525060 1466280 1449360 FALSE TRUE 1329288.011 1950704.732 1519770.507 2039776.449 1570722.224 1580198.887 1423742.188 1504619.065 1413508.869 1733334.342 0.766896483 1.125405921 0.876790167 1.17679342 0.906185371 0.911652673 0.821389246 0.868048955 0.815485411 1 20.72511853 3.017400252 24.98995895 0.873488617 0.995177057 0.143187143 0.118169991 372.5501906 535046.8127 0.031483443 0.037622843 1040.879014 -3.017400252 0.12168844 TFEQLHSTIGHQALEDILPFLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFEQLHSTIGHQALEDILPFLLK 23 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 61.89 0.02853 511990000 107330 165370 208180 197660 229960 240400 225990 212810 190180 184180 FALSE TRUE 111567.4713 193771.0111 213605.3418 236756.558 190871.4813 184570.7433 208276.3133 209957.63 183335.4589 220266.5447 0.506511197 0.879711494 0.969758445 1.074863904 0.866547762 0.837942701 0.9455649 0.953198001 0.832334566 1 17.74889086 4.73372512 3.594987171 0.933852738 0.459688284 0.764759885 0.070845426 0.128640061 3.020649981 0.017485628 0.16338558 54165.79474 -4.73372512 -0.474164454 TFGETHPFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFGETHPFTK 10 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 125.75 0.00040089 1546940000 2561900 2329800 2638700 2230300 3285300 3375700 2869600 2735900 2903400 2093140 FALSE TRUE 2663045.79 2729925.027 2707466.69 2671446.683 2726865.879 2591744.834 2644673.254 2699229.736 2798907.201 2503250.707 1.06383503 1.090551985 1.081580315 1.067191023 1.089329915 1.035351684 1.056495558 1.078289812 1.118109022 1 21.25537136 TFGLHGVVLDVDSVNELVQVETYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFGLHGVVLDVDSVNELVQVETYLR 25 0 F8VWT9;J3KPF0;Q9Y4D8-4;Q9Y4D8;A0A494C150 F8VWT9 HECTD4 Probable E3 ubiquitin-protein ligase HECTD4 0 149.32 1.94E-07 9665400 13958 18148 17848 20113 20991 24851 22673 18184 21511 17555 FALSE TRUE 14509.07262 21264.77783 18313.13354 24091.29137 17422.95732 19079.73187 20895.83102 17940.27322 20736.82331 20994.56614 0.691087042 1.012870554 0.872279685 1.147501273 0.82987937 0.908793816 0.995297111 0.854519836 0.987723355 1 14.35772835 4.747822883 24.45608649 0.947479247 0.691086859 0.437550366 0.089761978 853.1482609 2252587.332 0.020089154 0.249511286 55952.93644 -4.747822883 -0.256392388 TFHIFYYLLSGAGEHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TFHIFYYLLSGAGEHLK 17 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;; 246.27 7.03E-21 1113146000 1011855 749124 1104898 697362 1504990 1478948 1515910 1254626 1389379 773895 FALSE TRUE 1051803.817 877780.2196 1133692.55 835298.1222 1249172.337 1135484.741 1397089.013 1237809.791 1339375.521 925524.9081 1.136440313 0.948413394 1.224918465 0.90251285 1.349690674 1.22685487 1.509509902 1.337413807 1.447152323 1 19.81991229 3.21877586 24.9243609 1.338478218 1.057870504 0.395906697 0.154405692 198.7932562 250434.3595 0.041195559 0.049301834 1654.915637 -3.21877586 -0.280607714 TFIAIKPDGVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 174.51 2.75E-05 26417770000 9291050 7669160 9529180 8330530 11755990 11831340 10694920 10380350 9916180 6917230 FALSE TRUE 9657867.828 8986278.572 9777518.259 9978283.97 9757711.019 9083690.591 9856624.224 10241218.39 9559298.619 8272528.78 1.167462584 1.086279518 1.18192617 1.206195135 1.179531831 1.098054879 1.191488659 1.237979179 1.155547339 1 22.97989698 4.210205603 24.79354353 1.170604419 1.12687095 0 0.066589384 474.4551963 414863.014 0.015856854 0.03426585 16225.78073 -4.210205603 -0.04373347 TFIGPGGNMPGYLRPETAQGIFLNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFIGPGGNMPGYLRPETAQGIFLNFK 26 1 P41250 P41250 GARS Glycine--tRNA ligase 0 118.01 0.00061446 355250000 57063 41263 68977 60941 77910 82520 78434 65566 85000 49778 FALSE TRUE 59315.8913 48349.59927 70774.59729 72994.94791 64666.88603 63355.9806 72286.13813 64687.19501 81940.8666 59531.04604 0.99638584 0.812174529 1.188868699 1.226166056 1.086271623 1.064251089 1.214259499 1.086612773 1.37643922 1 15.86135462 4.230365419 24.99870361 1.154773916 0.904280171 0.462138968 0.108345813 127.1618389 387899.6262 0.02517412 0.055880101 16996.73172 -4.230365419 -0.250493744 TFIGPGGNMPGYLRPETAQGIFLNFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFIGPGGNMPGYLRPETAQGIFLNFKR 27 2 P41250 P41250 GARS Glycine--tRNA ligase 0 102.95 0.0013366 114660000 35155 44384 47062 31962 57091 52487 32277 51348 53014 52436 FALSE TRUE 36542.94655 52006.60674 48288.47438 38283.9882 47386.69221 40297.6897 29747.0444 50659.76405 51106.0365 62709.83025 0.582730752 0.82932144 0.770030379 0.610494209 0.755650143 0.642605626 0.474360149 0.807844063 0.81496053 1 15.93640399 1.069151763 1.828051849 0.990990384 0.679210121 0.493242821 0.102481436 0.279969927 1.874965608 0.096463032 0.027641604 11.72605058 -1.069151763 -0.311780262 TFLDKDAQRLS(ph)PIPEEVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TFLDKDAQRLSPIPEEVPK 19 2 Q96T23-2;Q96T23;Q96T23-3;H0YCN2;H0YER1 Q96T23-2 RSF1 Remodeling and spacing factor 1 1 T(0.066)FLDKDAQRLS(0.934)PIPEEVPK;T(0.001)FLDKDAQRLS(0.999)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK;TFLDKDAQRLS(1)PIPEEVPK 189.24 7.53E-15 6196300000 4179490 2090761 3244040 1860401 4674160 3970370 3488000 2971350 3488060 1931597 TRUE FALSE 4344499.492 2449832.938 3328582.347 2228382.765 3879647.953 3048311.739 3214601.446 2931523.913 3362525.402 2310056.449 1.880689753 1.060507824 1.440909528 0.964644291 1.679460237 1.319583225 1.391568352 1.26902696 1.455603132 1 21.13949668 -1.999023678 2.842377896 0.63815859 1.364194579 0.167298921 0.253783935 2236220.79 11425372.73 5305326.059 0.053129515 0.010022506 1.999023678 0.726035989 TFLEGDWTS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TFLEGDWT(0.002)S(0.998)PSK;TFLEGDWT(0.002)S(0.998)PSK;TFLEGDWT(0.009)S(0.969)PS(0.021)K;TFLEGDWTS(0.998)PS(0.001)K;TFLEGDWT(0.04)S(0.959)PS(0.001)K;TFLEGDWTS(0.795)PS(0.205)K 290.26 4.42E-36 1849517000 5959540 3544670 4603010 3561450 6296380 6471160 6168830 4971440 5362320 3166270 TRUE FALSE 6194827.241 4153439.499 4722968.222 4265894.18 5226123.577 4968331.161 5685300.985 4904805.978 5169331.151 3786639.985 1.635969426 1.096866751 1.247271523 1.1265645 1.380147993 1.312068531 1.501410488 1.295292396 1.365149888 1 21.85248683 -1.428141284 6.497545719 0.999938334 1.320430292 0.294727473 0.152152378 0.000128954 1.13E-05 0.139770958 0.03293802 0.037312875 1.428141284 0.320491958 TFLVGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TFLVGER 7 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ;;;; 126.67 0.0091423 1306928000 879820 988854 955124 1053901 1029946 1249250 1166249 1052533 982253 857895 FALSE TRUE 914555.973 1158681.982 980015.3161 1262359.472 854876.1468 959130.6201 1074835.356 1038425.517 946901.9064 1025983.1 0.891394774 1.129338273 0.955196354 1.230390123 0.833226344 0.934840564 1.047615069 1.012127312 0.922921544 1 19.96857554 3.216911387 24.99999431 0.967671619 1.050249726 0.163892121 0.101756602 474.8742508 548371.8121 0.028425373 0.03400302 1647.826137 -3.216911387 0.082578108 TFLVIPELAQELHVWTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFLVIPELAQELHVWTDK 18 0 P49902-2;P49902;Q5JUV6 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ; 202.07 1.33E-15 775600000 1010410 746130 1072480 973800 1258230 1288060 1541310 1158420 1221410 599560 FALSE TRUE 1050301.767 874272.0234 1100429.71 1166414.733 1044356.514 988927.5857 1420498.095 1142893.275 1177451.693 717032.3027 1.464790028 1.219292381 1.534700328 1.626725503 1.456498557 1.379195305 1.981079638 1.593921599 1.642118058 1 19.45167859 4.110491169 6.959141235 1.571022076 1.343925828 0.064324956 0.241478949 0.410804642 23.50739544 0.05718116 0.125297316 12897.07331 -4.110491169 -0.227096248 TFNIKNDFTEEEEAQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFNIKNDFTEEEEAQVR 17 1 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ; 178.71 8.73E-10 245660000 236890 219890 229260 186647 296930 295630 247690 218520 264030 234590 FALSE TRUE 246242.6001 257654.397 235234.7039 223565.2195 246457.9447 226974.4128 228275.4106 215591.0968 254527.6119 280553.419 0.877703081 0.918379102 0.838466716 0.796872197 0.878470651 0.80902387 0.813661125 0.768449366 0.90723404 1 18.09791597 4.222834815 21.67439561 0.835417119 0.898041018 0.031921375 0.064865778 82.30303719 113438.849 0.015121818 0.03294515 16704.55131 -4.222834815 0.062623899 TFNQVEIKPEMIGHYLGEFSITYKPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFNQVEIKPEMIGHYLGEFSITYKPVK 27 2 K7EM56;A0A0B4J2B4;S4R417;K7ELC2;P62841 K7EM56 RPS15 40S ribosomal protein S15 0 ; 208.88 1.13E-25 3020330000 1490950 838610 1303050 875750 1746880 1556320 1613120 1314380 1585260 796240 FALSE TRUE 1549813.857 982634.744 1337008.553 1048970.736 1449945.962 1194888.266 1486679.439 1296762.886 1528206.802 952247.9831 1.627531783 1.031910554 1.404055012 1.101573072 1.522655849 1.254807873 1.561231387 1.361791161 1.604841207 1 19.8609778 3.219610276 24.99460104 1.405323379 1.280798223 0.034304385 0.222755881 659.901385 870376.6377 0.058443161 0.069958399 1658.098307 -3.219610276 -0.124525157 TFNVDMYEEIHR ddPTM_MDA-MB-175_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 0 126.95 0.00023647 0 83665 99053 107330 114180 113190 147580 125040 112780 111800 88491 FALSE TRUE 86968.1588 116064.5822 110127.108 136764.4632 93950.00423 113306.7816 115239.0381 111268.3686 107776.3398 105829.1172 0.82177912 1.096716908 1.040612554 1.292314127 0.887751941 1.070657912 1.08891618 1.051396549 1.018399687 1 16.69137709 4.743266451 24.62999286 1.064514701 0.821778998 0.358254622 0.095833162 419.9159566 2197716.111 0.021538321 0.175582065 55368.97084 -4.743266451 -0.242735703 TFQARPLS(ph)ADLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFQARPLSADLTK 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 TFQARPLS(0.999)ADLT(0.001)K;TFQARPLS(1)ADLTK 133.93 6.14E-05 758040000 340670 282610 327100 276850 461220 486060 440870 385710 413830 304490 TRUE FALSE 354119.9147 331146.0691 335624.4947 331610.1037 382821.9891 373179.9313 406313.4574 380540.1883 398936.3391 364148.9857 0.97245888 0.909369742 0.921668075 0.910644041 1.051278472 1.024800139 1.115789068 1.045012353 1.095530552 1 18.4741693 3.222711519 10.38729047 1.059535649 0.92665864 0.759909839 0.034882284 0.131200862 82.16896945 0.009502115 0.01162118 1669.980957 -3.222711519 -0.132877009 TFS(ph)ATVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TFS(0.893)AT(0.107)VR;T(0.001)FS(0.989)AT(0.011)VR;TFS(0.998)AT(0.002)VR;TFS(0.999)AT(0.001)VR;TFS(0.905)AT(0.095)VR;TFS(0.998)AT(0.002)VR;TFS(0.759)AT(0.241)VR;TFS(0.991)AT(0.009)VR;T(0.006)FS(0.953)AT(0.041)VR;T(0.005)FS(0.912)AT(0.082)VR;T(0.003)FS(0.875)AT(0.122)VR;T(0.007)FS(0.926)AT(0.067)VR 186.54 0.00062667 1.23826E+11 13605380 13156390 15011780 13907670 17743380 18613970 17121730 15671820 14557140 12616620 TRUE FALSE 14142530.91 15415897.64 15402999.32 16658565.62 14727366.61 14291157.56 15779684.06 15461764.89 14033231.37 15088605.13 0.937298762 1.02169137 1.020836531 1.104049412 0.976058852 0.94714902 1.04580138 1.02473123 0.930054916 1 23.84695611 TFS(ph)LTEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 T(0.002)FS(0.998)LTEVR;T(0.427)FS(0.573)LTEVR;TFS(1)LTEVR;T(0.427)FS(0.57)LT(0.003)EVR 197.79 0.00014809 757489000 751779 871390 1008790 1037780 1310380 1508680 1296380 1235800 1164940 1164370 TRUE FALSE 781459.8154 1021044.454 1035079.896 1243049.787 1087642.076 1158311.934 1194766.348 1219236.122 1123014.037 1392506.008 0.561189547 0.733242405 0.743321673 0.89267104 0.781068138 0.831818267 0.857997266 0.875569739 0.806469796 1 20.40925212 5.492971524 0.614094258 0.867571027 2.00E-26 0.730640921 0.057578353 3.975129936 0.574389353 0.023147454 2.992232926 311151.2316 -5.492971524 -0.867571027 TFSATVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFSATVR 7 0 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 0 ; 138.33 0.0065044 273560000 167744 171216 187628 170083 218860 228920 198278 187820 186327 173137 FALSE TRUE 174366.6626 200621.0161 192517.7398 203724.9098 181658.2554 175756.7993 182736.4523 185302.5801 179621.1277 207059.8802 0.842107425 0.968903372 0.92976843 0.983893691 0.877322324 0.848821119 0.882529498 0.894922666 0.867483974 1 17.65968852 3.193123063 24.99998008 0.887416365 0.933763896 0.091795876 0.051873644 223.9763301 123232.1109 0.014049172 0.016792035 1559.994485 -3.193123063 0.046347531 TFSHELSDFGLESTAGEIPVVAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TFSHELSDFGLESTAGEIPVVAIR 24 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;;; 257.5 6.68E-44 4163750000 1379075 1815300 1762411 2114240 2005126 2451470 1998393 1786936 1701602 1650925 FALSE TRUE 1433521.946 2127063.654 1808340.878 2532430.362 1664295.399 1882153.245 1841753.735 1762985.046 1640361.676 1974392.145 0.726057359 1.077325829 0.915897525 1.282637985 0.84294065 0.953282381 0.932820635 0.892925476 0.830818579 1 20.91297713 TFTAWCNSHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 129.34 0.00024697 519110000 232140 430420 354650 432850 625480 554130 482160 396630 393300 604810 FALSE TRUE 241305.0665 504341.2868 363892.4703 518466.4381 519161.133 425441.7054 444367.0393 391313.8236 379145.2098 723310.9397 0.333611803 0.697267605 0.503092723 0.716796069 0.717756506 0.588186466 0.614351332 0.541003602 0.524180113 1 19.46425645 -2.111964213 2.500287664 1.783066592 0.589052056 0.557826497 0.111530504 13378145.85 3953605.039 59524366.96 0.026498983 0.007727443 2.111964213 -1.194014536 TFTEMDSHEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TFTEMDSHEEK 11 0 B0YIW6;P48444;P48444-2;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;;;; 194.5 4.85E-07 1815160000 2945170 2658910 3014420 2397090 3939050 4017460 3473170 3124250 3318240 2431680 FALSE TRUE 3061447.586 3115557.109 3092978.262 2871227.247 3269491.688 3084465.8 3200933.86 3082374.539 3198817.191 2908121.139 1.052723542 1.071329893 1.063565826 0.987313496 1.12426255 1.060638692 1.100687938 1.059919581 1.09996009 1 21.47165594 4.756846286 20.95688894 1.065871928 1.052723446 0.001586993 0.04048714 3053.364747 3498860.808 0.009009345 0.22493993 57127.64033 -4.756846286 -0.013148482 TFVEKYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFVEKYEK 8 1 Q16543;K7EKQ2 Q16543 CDC37 "Hsp90 co-chaperone Cdc37;Hsp90 co-chaperone Cdc37, N-terminally processed" 0 90.108 0.012248 434010000 293230 193150 316190 144060 390800 326750 241950 247160 306690 210580 FALSE TRUE 304806.9468 226322.01 324430.1712 172554.638 324371.9556 250867.2644 222985.3268 243847.2245 295652.2868 251839.1192 1.210324066 0.898676944 1.288243749 0.685178056 1.288012588 0.99614097 0.885427679 0.968265872 1.173972843 1 17.94214287 2.51668693 24.99416488 0.989246374 1.063377898 0.029511939 0.183912509 2065.103351 1304550.953 0.055673183 0.052481026 328.6146567 -2.51668693 0.074131525 TFVNITPAEVGVLVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFVNITPAEVGVLVGK 16 0 P07737;I3L3D5 P07737 PFN1 Profilin-1 0 147.18 2.45E-06 116940000 146390 132770 148210 145200 200500 213010 173750 165040 167820 130920 FALSE TRUE 152169.5902 155572.2147 152072.4744 173920.1266 166419.0816 163541.6557 160131.021 162827.9088 161780.191 156571.2674 0.97188707 0.993619182 0.971266803 1.110804872 1.062896688 1.044518949 1.022735676 1.039960342 1.033268707 1 17.25645996 3.783748447 24.99209919 1.045537563 0.980393798 0.54343077 0.027691166 337.1407355 186461.7095 0.007151063 0.012891665 6077.828581 -3.783748447 -0.065143765 TFVNITPAEVGVLVGKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TFVNITPAEVGVLVGKDR 18 1 P07737;I3L3D5 P07737 PFN1 Profilin-1 0 139.02 7.20E-07 165890000 207990 157330 240330 147710 279410 255210 221890 185430 300400 173560 FALSE TRUE 216201.6058 184350.2036 246593.1972 176926.5971 231915.988 195941.3452 204497.682 182944.6142 289588.6627 207565.759 1.041605354 0.888153251 1.188024453 0.852388168 1.117313323 0.943996477 0.985218771 0.881381472 1.39516587 1 17.66320894 1.255189143 24.98761041 1.197583169 0.983875624 0.28259699 0.133956039 233.1195113 350310.3318 0.081086824 0.02943343 17.99654528 -1.255189143 -0.213707545 TFYEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TFYEKR 6 1 P62753;A2A3R7 P62753 RPS6 40S ribosomal protein S6 0 ; 113.25 0.042167 836940000 992280 922140 1023290 617790 1589500 1278760 901880 1035890 1098100 1374390 FALSE TRUE 1031455.981 1080510.372 1049957.778 739987.0181 1319317.358 981787.3698 831188.289 1022005.589 1058579.596 1643675.406 0.627530215 0.657374545 0.638786572 0.450202647 0.802662954 0.597312198 0.505688828 0.621780666 0.644032022 1 20.64849399 0.627574293 2.68068683 0.999985445 0.611113177 0.633675075 0.087841832 2.400312795 16.54329198 0.081019659 0.021441522 4.242035447 -0.627574293 -0.388872268 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGADTTAAGPLFQQRPYPSPGAVLR 25 1 O60828-2;O60828;O60828-5;O60828-4;H7C053 O60828-2 PQBP1 Polyglutamine-binding protein 1 1 TGADTTAAGPLFQQRPYPS(1)PGAVLR;TGADTTAAGPLFQQRPY(0.003)PS(0.997)PGAVLR 160.41 1.34E-11 296420000 234696 228007 232419 197668 236625 304849 227821 223109 250201 217049 TRUE FALSE 243961.9793 267165.4286 238476.0301 236766.1404 196403.567 234052.4398 209963.7947 220118.5888 241196.3149 259575.5959 0.939849443 1.029239392 0.918715141 0.912127889 0.756633405 0.901673514 0.8088734 0.847994158 0.929194881 1 17.98579523 3.846490105 2.402992166 0.862282783 0.982276312 0.248610773 0.067706726 0.313512812 3.516979008 0.017355785 0.037438202 7022.47344 -3.846490105 0.119993529 TGCTFPEKPDFH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGCTFPEKPDFH 12 1 P55263-3;P55263-2;P55263;P55263-4;A0A5F9ZHJ1 P55263-3 ADK Adenosine kinase 0 112.43 0.0011625 201830000 634780 492430 620620 518570 778060 756530 774140 656590 700410 410520 FALSE TRUE 659841.6046 577001.0219 636793.867 621141.5982 645805.6391 580837.3728 713460.884 647789.485 675202.3809 490953.5341 1.344000111 1.175266052 1.297055267 1.265173902 1.315410918 1.183080134 1.453214682 1.31945172 1.375287749 1 18.90522696 3.256918606 22.07392372 1.300039399 1.265486175 0 0.121959842 355.7806564 427783.7727 0.031686934 0.042777943 1806.835465 -3.256918606 -0.034553224 TGDDKGESNDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGDDKGESNDGK 12 1 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 72.937 0.036981 72785000 169680 57265 91894 53644 156150 155170 153380 96555 118720 45565 FALSE TRUE 176379.0974 67099.81829 94288.83313 64254.62309 129607.6788 119134.1191 141357.6748 95260.83816 114447.2904 54492.58936 3.236753832 1.23135676 1.730305611 1.179144244 2.378445956 2.186244415 2.594071533 1.748142991 2.100235862 1 15.73377243 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-2;Q15637-4;Q15637-3;Q15637;Q15637-7;Q15637-5 Q15637-6;Q15637-5 SF1 Splicing factor 1 2 TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(0.999)PEPIY(0.001)NSEGK;TGDLGIPPNPEDRS(1)PS(1)PEPIYNSEGK;TGDLGIPPNPEDRS(1)PS(0.999)PEPIY(0.001)NS(0.001)EGK 235.67 3.63E-45 6673660000 3699550 2320690 3161620 2376580 4078200 4143980 3938410 3299830 3384300 1866160 TRUE FALSE 3845611.091 2719250.455 3244014.414 2846660.431 3384989.021 3181603.448 3629707.133 3255601.176 3262499.704 2231798.322 1.723099732 1.218412268 1.453542814 1.275500749 1.516709188 1.425578385 1.626359827 1.458734485 1.461825503 1 21.08977523 -0.28650459 8.818795973 1 1.457094672 0.497523695 0.139262299 0 0 0.125229113 0.029516785 0.517005794 0.28650459 0.457094672 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.899)PS(0.851)PEPIY(0.11)NS(0.141)EGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(1)PS(0.999)PEPIYNS(0.001)EGKR;TGDLGIPPNPEDRS(0.999)PS(0.999)PEPIY(0.001)NSEGKR 163.22 5.69E-11 2186770000 1400696 1116929 1365340 916715 1921910 1855600 1268565 1436519 1571680 1201719 TRUE FALSE 1455996.56 1308752.867 1400921.882 1098038.491 1595224.425 1424665.022 1169131.561 1417264.812 1515115.544 1437172.83 1.01309775 0.910644037 0.974776209 0.764026753 1.109973965 0.991296935 0.81349406 0.986147792 1.054233362 1 20.45480214 1.484343815 12.38733485 1.024830069 0.938769492 0.125614922 0.093483893 0.15827502 122.0999096 0.049132278 0.0227704 30.50308852 -1.484343815 -0.086060577 TGDPQETLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGDPQETLRR 10 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 104.43 0.0043009 533880000 1071030 1180800 1223700 1010520 1539800 1689980 1098430 1234050 1164780 1175410 FALSE TRUE 1113315.091 1383593.215 1255590.627 1210397.84 1278065.346 1297507.757 1012332.186 1217509.578 1122859.795 1405709.085 0.791995373 0.984267107 0.893208019 0.86105856 0.909196191 0.923027226 0.720157675 0.866117742 0.79878533 1 20.42286663 TGENFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGENFR 6 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 ;;; 123.99 0.043155 1886620000 1227020 1445740 1534870 1306360 1691370 2050810 1639540 1544480 1439450 1259110 FALSE TRUE 1275463.697 1694034.599 1574869.973 1564754.109 1403871.532 1574540.458 1511028.571 1523778.772 1387644.476 1505808.497 0.847029154 1.125000026 1.045863386 1.03914549 0.932304163 1.045644556 1.003466625 1.011933971 0.921527856 1 20.52210687 1.275210372 23.82532842 0.960763941 1.01131944 0.056078279 0.072418754 235.4180004 153040.948 0.045057877 0.016452892 18.8456175 -1.275210372 0.050555499 TGEPSPPHDILHEPPDVVS(ph)DDEKDHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGEPSPPHDILHEPPDVVSDDEKDHGK 27 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 TGEPSPPHDILHEPPDVVS(1)DDEKDHGK;TGEPSPPHDILHEPPDVVS(1)DDEKDHGK 297.02 5.45E-71 721130000 1141660 366263 578750 372247 945670 1065400 854090 573500 636610 246176 TRUE FALSE 1186733.618 429165.8211 593832.7004 445876.3456 784925.3512 817976.9963 787144.1941 565813.1706 613698.5305 294409.4739 4.030894804 1.457717428 2.017029862 1.514476894 2.666100859 2.778365063 2.673637447 1.921857891 2.084506733 1 18.16746457 0.719067999 1.207550358 1.006977808 2.356543634 0.262401931 0.703578454 1.326006496 3.277246255 0.645607036 0.197633953 5.236824251 -0.719067999 1.349565826 TGFLEIDEHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGFLEIDEHMR 11 0 P35813;P35813-3;P35813-2;E9PL75;E9PJN3;E9PKB5 P35813 PPM1A Protein phosphatase 1A 0 ;; 174.4 0.00014364 205370000 517570 546640 597870 500940 735680 746910 595710 610460 585250 525710 FALSE TRUE 538004.0633 640521.1677 613450.9834 600024.4368 610629.3764 573451.472 549016.6936 602277.7822 564186.9668 628712.8092 0.855723083 1.018781801 0.975725283 0.954369671 0.971237372 0.912104006 0.873239237 0.957953732 0.897368335 1 19.26204163 2.738720141 24.99977616 0.923707728 0.959799355 0.060712104 0.050093436 32.40640476 5078761.972 0.014891836 0.014933668 547.92377 -2.738720141 0.036091626 TGFSTSPESPYTHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGFSTSPESPYTHWK 15 0 E9PKG1;Q99873-2;Q99873-3;Q99873;Q99873-5 E9PKG1 PRMT1 Protein arginine N-methyltransferase 1 0 ; 195.2 2.03E-08 1572720000 919640 985100 1349940 1129140 1627110 1604360 1517840 1489620 1395710 846900 FALSE TRUE 955948.0973 1154283.262 1385120.545 1352480.522 1350534.423 1231771.704 1398867.735 1469654.08 1345478.67 1012833.84 0.943835069 1.139657085 1.367569379 1.335342944 1.333421505 1.216163654 1.381142374 1.451031771 1.328429814 1 19.94996608 4.512016283 2.712053101 1.327459422 0.940715502 0.459111717 0.118903293 0.238297038 3.067142404 0.028421121 0.162233333 32509.94858 -4.512016283 -0.38674392 TGGIGDSRPPSFHPHAGGGS(ph)QENLDNDTETDSLVSAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQR 38 1 Q92997-2;Q92997 Q92997-2 DVL3 Segment polarity protein dishevelled homolog DVL-3 1 TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;TGGIGDSRPPSFHPHAGGGS(1)QENLDNDTETDSLVSAQR;T(0.001)GGIGDS(0.129)RPPS(0.129)FHPHAGGGS(0.74)QENLDNDTETDSLVSAQR;TGGIGDSRPPS(0.001)FHPHAGGGS(0.999)QENLDNDTETDSLVSAQR 384.16 1.60E-179 2395530000 143060.5 504092 505366 470738 549333 665182 431024 573978 451110 459236 TRUE FALSE 148708.639 590665.8797 518536.2531 563848.5714 455957.5729 510703.5614 397239.2126 566284.7637 434874.6392 549214.5016 0.270766046 1.075473932 0.944141591 1.026645454 0.830199442 0.929879965 0.723286096 1.03108123 0.791812011 1 19.06701019 4.746723974 24.91154048 0.925031114 0.270765707 0.767663657 0.108469196 436.5175476 1332058.093 0.02445531 0.275200835 55811.53587 -4.746723974 -0.654265407 TGGMAFHSYFMEAIAPPLLQELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 158.89 2.07E-11 2346737000 2887010 1870050 2606670 2339150 3447130 3659140 3511400 2697950 2865000 1478517 FALSE TRUE 3000991.384 2191216.541 2674601.962 2801826.888 2861188.074 2809360.19 3236167.293 2661788.393 2761889.21 1768204.098 1.697197392 1.239232814 1.512609299 1.584560793 1.618132249 1.588821218 1.830200086 1.505362642 1.561974216 1 20.75385338 0.291011722 2.089328116 0.99999717 1.570052775 0.590400076 0.142683397 13.20263028 37.67146561 0.137759688 0.037599932 1.954392206 -0.291011722 0.570055604 TGGMAFHSYFMEAIAPPLLQELKK ddPTM_MDA-MB-175_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 ;;; 171.58 4.22E-12 2299568000 3948580 2056840 3400750 2255670 5132830 4252950 3639420 3302000 3789330 1897460 FALSE TRUE 4104472.987 2410086.27 3489376.339 2701834.793 4260353.39 3265266.817 3354152.751 3257742.091 3652952.754 2269230.958 1.808750658 1.062071827 1.53769114 1.190638963 1.877443711 1.43893102 1.478101089 1.435615039 1.609775656 1 21.11377202 -1.289739026 5.019592598 0.999869755 1.478611756 0.283454099 0.234224325 0.000309746 4.38E-05 0.205758784 0.048484729 0.051316966 1.289739026 0.478742001 TGGPS(ph)PAGPAAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGGPSPAGPAAAR 13 0 P78411-3;P78411-2;P78411 P78411-3 IRX5 Iroquois-class homeodomain protein IRX-5 1 T(0.1)GGPS(0.9)PAGPAAAR 109.55 0.0005708 0 229030 461850 391210 472870 388220 544730 301630 388410 333060 512700 TRUE FALSE 238072.2812 541169.1448 401405.254 566402.2746 322230.5031 418224.713 277987.4524 383203.9993 321073.2357 613153.7488 0.388275015 0.882599423 0.654656772 0.923752445 0.525529696 0.682087835 0.45337316 0.624972122 0.523642294 1 19.22588935 -0.970748116 4.469192315 1.000008143 0.635771736 0.317457826 0.163010871 28427971.98 92602866.8 4309.731302 0.037442182 0.106967509 0.970748116 -0.364236407 TGGQVPDTNYIFMGDFVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGGQVPDTNYIFMGDFVDR 19 0 O00743;O00743-3;Q5T1S7 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed;Serine/threonine-protein phosphatase" 0 113.59 0.00040519 21872000 7994.2 9036 11107 11004 10984 12373 10792 9502.6 6373.3 7443.8 FALSE TRUE 8309.817189 10587.86271 11396.45754 13180.55836 9116.943603 9499.558265 9946.09484 9375.23319 6143.926178 8902.27009 0.933449233 1.189344134 1.280174318 1.480583966 1.024114469 1.067093917 1.117253772 1.05312837 0.690152749 1 13.11995756 1.478009908 3.517225734 0.845304867 1.164244181 0.369461247 0.158341068 0.223863057 5.504645742 0.115168667 0.042318796 30.06144883 -1.478009908 0.318939314 TGHSGTLDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGHSGTLDPK 10 0 O60832;O60832-2;C9IYT0;H7C0M1;H7C2Q9 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 107.83 0.0022318 50483000 136250 77127 117540 82781 140240 146650 124540 105720 123890 68681 FALSE TRUE 141629.2552 90372.96229 120603.189 99154.83472 116402.0549 112592.76 114778.2294 104302.9963 119431.2231 82137.72697 1.724289927 1.1002613 1.468304437 1.207177729 1.417157002 1.370780081 1.397387456 1.269854915 1.454036135 1 16.3257574 -1.458843302 2.938677677 0.990701161 1.362837389 0.331227888 0.160036789 21251008.15 24760931.01 1627458.498 0.03458226 0.034766158 1.458843302 0.372136228 TGIIVTTSEAVLLQLVADKDHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGIIVTTSEAVLLQLVADKDHPK 23 1 Q96CN7 Q96CN7 ISOC1 Isochorismatase domain-containing protein 1 0 186.63 1.61E-17 431780000 215770 98153 164400 106500 230120 210880 223630 163490 172130 86004 FALSE TRUE 224288.7662 115010.0142 168684.3991 127565.3821 191004.2846 161906.3159 206101.2963 161298.684 165935.0749 102854.8372 2.180634109 1.118177982 1.640023977 1.240246795 1.857027728 1.574124469 2.003807521 1.568216804 1.613293837 1 16.65025012 0.460392271 2.429548027 1.00001223 1.634036679 0.28969169 0.302365195 13.11798218 57.27507708 0.268510579 0.07185619 2.886637643 -0.460392271 0.634024448 TGKPEEASLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGKPEEASLDSR 12 1 Q9BY42;A2A2L5;A0A0A0MQR2 Q9BY42 RTFDC1 Protein RTF2 homolog 0 ; 78.964 0.022172 427710000 830770 601270 723670 579620 1030000 1066950 1027140 804050 840270 547300 FALSE TRUE 863569.4411 704533.4453 742529.4347 694267.106 854920.9679 819167.0323 946630.0829 793273.0249 810028.8468 654532.9563 1.319367394 1.076391095 1.134441631 1.06070611 1.306154197 1.251529086 1.44626802 1.211968041 1.237567702 1 19.32010631 3.227106452 24.99922699 1.264150567 1.141682235 0.108878866 0.12277626 350.1555251 764228.6851 0.033603335 0.040495566 1686.966475 -3.227106452 -0.122468332 TGKPMINLYTDKDTGKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGKPMINLYTDKDTGKPK 18 3 Q92804-2;Q92804;A0A075B7D9 Q92804-2 TAF15 TATA-binding protein-associated factor 2N 0 83.253 0.0017693 854030000 507980 265100 386810 233550 542340 444150 485040 352990 405360 188170 FALSE TRUE 528035.4426 310628.8628 396890.5864 279745.4929 450153.2405 341002.8937 447021.2974 348258.7464 390771.1728 225038.3088 2.346424684 1.380337706 1.763657879 1.24310165 2.000340489 1.515310418 1.986423111 1.547553163 1.736465115 1 17.77981109 -2.26586109 0.563119492 2.31E-07 1.708638479 0.328211742 0.310020864 176.7670989 12.60628668 221.6673164 0.117229469 0.005421743 2.26586109 1.708638248 TGLFEWDNDFEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGLFEWDNDFEDIR 14 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 ;;; 139.89 2.35E-05 78266000 72929 84901 86102 95098 91962 116425 108590 81629 88242 63726 FALSE TRUE 75808.29323 99482.08631 88345.88885 113908.1006 76330.33209 89387.05819 100078.4321 80534.89677 85066.18766 76211.88959 0.994704286 1.305335517 1.159213993 1.494623755 1.001554121 1.172875501 1.313160356 1.056723527 1.11618001 1 16.21772847 1.638137067 8.543681133 1.064112246 1.209557165 0.18524874 0.141950281 0.189538167 28.31703508 0.067459511 0.034890924 43.46473805 -1.638137067 0.145444919 TGLYNYYDDEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TGLYNYYDDEKEK 13 1 P50454;E9PKH2;E9PR70;E9PPV6 P50454 SERPINH1 Serpin H1 0 ;;;; 207.31 5.00E-08 4774760000 3704310 1377180 1966470 1455480 3558090 3194720 3106630 2028350 2278330 824250 FALSE TRUE 3850559.019 1613699.952 2017717.824 1743369.6 2953287.133 2452794.696 2863124.223 2001163.286 2196333.348 985746.0063 3.906238518 1.637034228 2.046894241 1.768578913 2.995991984 2.488262373 2.904525308 2.030100323 2.228092566 1 19.91085643 0.591820547 1.187940107 1.002736028 2.448967842 0.326308745 0.63680102 1.682347663 3.475465901 0.58069169 0.177362633 3.906794318 -0.591820547 1.446231815 TGMGSGS(ph)AGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGMGSGSAGK 10 0 Q86YS7;H0YFE9;Q86YS7-3 Q86YS7;Q86YS7-3 C2CD5 C2 domain-containing protein 5 1 TGMGS(0.001)GS(0.999)AGK;TGMGS(0.001)GS(0.999)AGK;TGMGS(0.353)GS(0.647)AGK 167.18 5.58E-06 558220000 1111260 578350 859950 702400 1146950 1174090 1316710 959610 993240 503820 TRUE FALSE 1155133.403 677677.1136 882361.0035 841332.6235 951991.8487 901425.391 1213502.83 946747.9976 957493.4864 602533.8828 1.91712605 1.124712042 1.464417236 1.39632417 1.579980605 1.496057594 2.013999319 1.571277607 1.58911144 1 19.20068285 3.133212764 5.425101148 1.602202573 1.450211044 0 0.295280065 0.670864026 29.76637683 0.08128868 0.098161051 1358.979057 -3.133212764 -0.151991529 TGNAWHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGNAWHSK 8 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 61.161 0.087716 153850000 459220 385210 449020 343710 644020 652900 557610 464370 495590 352090 FALSE TRUE 477350.3602 451366.821 460721.8301 411694.8121 534549.7104 501273.8698 513903.0712 458145.8797 477753.8127 421075.2943 1.133646088 1.071938504 1.094155455 0.977722554 1.269487233 1.190461365 1.220454104 1.088037902 1.134604236 1 18.68371871 3.246434044 24.99989753 1.156835085 1.071320158 0.203466002 0.078012837 275.9282893 876128.6798 0.021376594 0.028430192 1763.737886 -3.246434044 -0.085514927 TGPFAEHSNQLWNISAVPSWSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGPFAEHSNQLWNISAVPSWSK 22 0 Q15257;Q15257-2;A6PVN5;F6WIT2;Q15257-3;Q15257-4;A6PVN9;H0Y6E5;Q68CR8;B7ZBQ0;B4DDQ6;B7ZBP7;B7ZBP9 Q15257 PPP2R4;DKFZp781M17165 Serine/threonine-protein phosphatase 2A activator 0 ; 197.68 1.98E-22 889230000 892940 754650 875390 737260 1234540 1234440 1087060 977650 982950 702030 FALSE TRUE 928193.9607 884255.2671 898203.3825 883087.8275 1024693.332 947760.0181 1001853.397 964546.2009 947573.8215 839579.3373 1.105546456 1.053212279 1.069825498 1.051821773 1.220484219 1.128851052 1.193280197 1.148844615 1.128629278 1 19.67930714 3.269056088 24.99989857 1.147779638 1.068875376 0.237281541 0.056394227 229.4636519 188110.5591 0.014292812 0.019350455 1858.044401 -3.269056088 -0.078904262 TGPPPIS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.984)PS(0.016)K 217.22 7.71E-09 1103303000 1350250 717470 986960 725660 1369510 1487550 1257540 1029540 1061530 556078 TRUE FALSE 1403558.913 840689.8914 1012680.988 869193.3821 1136721.179 1142089.057 1158970.729 1015740.7 1023325.743 665030.8373 2.110517037 1.264136705 1.522757941 1.306997109 1.709275895 1.717347516 1.742732312 1.527358798 1.538764348 1 19.34306171 0.499968058 1.647326185 1.000126722 1.598918213 0.392239284 0.227152136 3.046010594 8.90427837 0.206859465 0.058785289 3.162045085 -0.499968058 0.598791491 TGPPPIS(ph)PSKR ddPTM_MDA-MB-175_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(0.976)PS(0.024)KR 59.57 0.043341 0 107160 42886 61676 40291 96970 98673 86284 69970 74998 41767 TRUE FALSE 111390.7595 50251.33689 63283.32723 48260.43954 80487.07404 75757.69115 79520.83462 69032.1666 72298.83663 49950.44397 2.230025415 1.006023829 1.266922217 0.966166378 1.611338511 1.516657013 1.591994551 1.382013074 1.447411292 1 15.60820988 -1.371639959 5.693395108 0.99988782 1.424049703 0.133734952 0.336579885 0.000450486 4.97E-05 0.306323039 0.072182096 0.042497173 1.371639959 0.424161883 TGQAGS(ph)LSGS(ph)PKPFSPQLSAPITTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-19;Q9ULU4-22;A0A087WVZ6;Q9ULU4-11;Q9ULU4-10;Q9ULU4-13;Q9ULU4;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-16;Q9ULU4-9;Q9ULU4-14;Q9ULU4-21;Q9ULU4-23;Q9ULU4-6;H7C4X9;Q9ULU4-3;Q9ULU4-17;Q9ULU4-8;Q9ULU4-4;A0A087WYS3;A0A087WV57 Q9ULU4-19 ZMYND8 Protein kinase C-binding protein 1 2 T(0.001)GQAGS(0.998)LS(0.033)GS(0.968)PKPFSPQLSAPITTK 186.85 8.37E-18 774600000 1455500 428820 688870 437150 1137700 1182300 982970 748770 799470 252430 TRUE FALSE 1512964.264 502466.4992 706822.5181 523616.9652 944314.1604 907728.7429 905922.2429 738733.9629 770697.2309 301888.8254 5.011660374 1.66440907 2.341333824 1.734469517 3.128019591 3.006831212 3.000847221 2.447039773 2.552917385 1 18.20365783 4.749100468 24.9787021 2.425209626 5.01166184 0.600389338 0.653801777 1045.696705 2478178.605 0.150979538 2.168629446 56117.77812 -4.749100468 2.586452213 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_MDA-MB-175_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 TGQAGS(0.002)LS(0.055)GS(0.939)PKPFS(0.003)PQLSAPITTK;TGQAGSLS(0.018)GS(0.981)PKPFS(0.001)PQLSAPITTK 168.57 6.71E-12 3328000000 2047680 1343260 1760480 1358190 2516130 2340780 1981240 1889490 2135360 1317520 TRUE FALSE 2128523.988 1573954.456 1806359.555 1626835.928 2088439.121 1797169.32 1825945.232 1864164.477 2058508.811 1575662.819 1.350875303 0.998915782 1.146412503 1.032477196 1.3254353 1.140579887 1.158842622 1.183098602 1.306439923 1 20.58752741 3.266549993 24.99993095 1.189990178 1.123669435 0.042135918 0.121441572 630.3888425 563055.32 0.031228252 0.042274378 1847.353437 -3.266549993 -0.066320744 TGQIWPNDGEGAFHGDADGS(ph)FGTPPGYGCAADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 33 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.877)FGT(0.123)PPGYGCAADR 109.89 5.01E-06 229890000 97230 111920 125950 146710 152310 191870 156140 161420 141580 120040 TRUE FALSE 101068.7155 131141.3894 129232.3605 175728.8001 126420.4006 147311.1003 143901.3388 159256.4289 136484.5635 143559.5397 0.704019501 0.913498258 0.900200438 1.224083056 0.880613026 1.026132437 1.002380887 1.109340621 0.950717478 1 17.13128968 4.706303225 1.376914811 1.027670863 0.588435082 0.515934801 0.092362527 0.895281055 1.58442973 0.024183053 0.538517211 50851.43644 -4.706303225 -0.439235781 TGQIWPNDGEGAFHGDADGS(ph)FGTPPGYGCAADRAEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADRAEEQR 38 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.526)FGT(0.473)PPGY(0.001)GCAADRAEEQR 64.705 0.0031552 80669000 17053 25038 23805 18771 37958 40049 20369 26487 31076 40056 TRUE FALSE 17726.26561 29338.08173 24425.37786 22483.84777 31505.91272 30748.2267 18772.42456 26131.98509 29957.58083 47904.20628 0.370035681 0.612432269 0.509879607 0.469350179 0.657685727 0.641869036 0.391874243 0.545505022 0.625364308 1 15.54786472 0.776299359 2.454399023 0.999795718 0.528095755 0.706032017 0.091875139 0.521790843 4.810974764 0.085468816 0.022925822 5.974469648 -0.776299359 -0.471699963 TGQIWPNDGEGAFHGDADGSFGT(ph)PPGYGCAADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGQIWPNDGEGAFHGDADGSFGTPPGYGCAADR 33 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 TGQIWPNDGEGAFHGDADGS(0.276)FGT(0.724)PPGYGCAADR;TGQIWPNDGEGAFHGDADGS(0.206)FGT(0.792)PPGY(0.002)GCAADR 134.43 1.37E-07 319840000 129424 155795 159606 200984 212982 250202 213462 203741 189649 172759 TRUE FALSE 134533.7595 182551.5793 163765.4635 240738.0353 176779.3957 192096.3773 196730.2907 201010.1851 182823.5695 206607.8184 0.65115522 0.883565689 0.792639237 1.16519325 0.855627813 0.92976335 0.952191898 0.972906963 0.884882145 1 17.65653532 5.021538858 1.157807551 0.954104168 0.343745883 0.493948678 0.091210436 2.230915551 1.629952822 0.024560881 1.920525354 105084.5474 -5.021538858 -0.610358285 TGQLEGAPAPGPAAS(ph)PQTLDHSGATATGGASELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 TGQLEGAPAPGPAAS(0.998)PQT(0.002)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.984)PQT(0.016)LDHSGATATGGASELK;TGQLEGAPAPGPAAS(0.998)PQT(0.002)LDHSGATATGGASELK 353.53 3.02E-132 10143300000 2257080 1305055 1760998 1414564 2199890 2510960 2400970 2009501 2021504 961757 TRUE FALSE 2346191.261 1529188.044 1806891.055 1694360.537 1825953.484 1927827.594 2212775.698 1982566.926 1948750.466 1150194.87 2.039820662 1.329503447 1.570943413 1.473107367 1.587516629 1.676087804 1.923826784 1.723679158 1.694278523 1 20.13344688 2.750419344 6.114540815 1.68068799 1.576044988 0 0.284790728 0.714909783 118.1159643 0.08367891 0.085205764 562.8845701 -2.750419344 -0.104643001 TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGQPAQPAPSAQQPPRPPASPDEPSVAASSVGSSR 35 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPS(0.001)AQQPPRPPAS(0.998)PDEPS(0.001)VAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR;TGQPAQPAPSAQQPPRPPAS(1)PDEPSVAASSVGSSR 289.01 2.94E-77 2876060000 389910 418912 435414 396357 441376 593364 397712 437302 388784 336481 TRUE FALSE 405303.9479 490856.8773 446761.2465 474755.2316 366351.0652 455564.2035 366538.2942 431440.682 374791.7398 402408.0096 1.007196522 1.219798974 1.110219568 1.17978574 0.910397051 1.132095268 0.910862322 1.072147352 0.931372465 1 18.6182995 3.251312328 24.9982053 1.00224456 1.134358649 0.387262652 0.083473821 227.1522947 445302.2735 0.021075531 0.028346193 1783.661049 -3.251312328 0.132114089 TGQPMIHIYLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGQPMIHIYLDK 12 0 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 65.043 0.061815 316480000 556680 360700 545940 515440 704160 750160 805110 603460 648190 367200 FALSE TRUE 578658.1563 422647.4191 560167.6449 617392.4936 584467.1347 575946.7088 742003.3744 595371.6058 624861.7685 439145.8095 1.317690261 0.962430723 1.27558463 1.405894079 1.330918164 1.311515894 1.689651497 1.355749259 1.422902724 1 18.74434051 4.004450811 24.03681998 1.385630659 1.134797173 0.184139148 0.177617262 99.45828705 537101.0163 0.04130338 0.08861574 10103.01065 -4.004450811 -0.250833486 TGQPMIHIYLDKETGKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGQPMIHIYLDKETGKPK 18 2 B0QYK0;Q01844-6;Q01844-3;Q01844;Q01844-5;A0A0D9SFL3;C9JGE3;Q01844-2;H7BY36 B0QYK0 EWSR1 RNA-binding protein EWS 0 ; 147.1 4.74E-08 1867500000 3708000 1701740 2801000 1576780 4110400 3492500 3283300 2717900 3412600 1367110 FALSE TRUE 3854394.703 1994000.607 2873996.361 1888662.378 3411715.676 2681419.804 3025946.367 2681470.996 3289781.193 1634969.03 2.357472609 1.219595339 1.757829237 1.155167067 2.086715781 1.640043179 1.85076678 1.640074489 2.012136703 1 20.64083188 -1.678757258 8.948093512 0.999039716 1.719308071 0.287410834 0.350326284 0.00604649 0.000217073 0.305599407 0.071962629 0.020952833 1.678757258 0.720268355 TGS(ph)EPALSPAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 TGS(1)EPALSPAVVR;TGS(0.999)EPALSPAVVR 166.62 3.49E-05 168085000 157229 140043 166371 134038 228862 285730 183448 158761 157775 121383 TRUE FALSE 163436.5223 164094.2959 170706.7649 160550.3163 189960.119 219373.5378 169068.8664 156633.0685 152096.7086 145165.6748 1.125862037 1.130393229 1.175944418 1.105979885 1.308574628 1.511194282 1.164661457 1.078995215 1.047745679 1 17.14734084 1.729200771 3.304235994 1.039286404 1.224947493 0.344123167 0.113139577 0.278011766 6.557240876 0.071387894 0.033821815 53.60444092 -1.729200771 0.185661089 TGS(ph)ESS(ph)QTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 T(0.009)GS(0.989)ES(0.09)S(0.912)QTGTSTTSSR;TGS(1)ESS(1)QTGTSTTSSR 199.84 5.42E-11 362560000 735940 490270 662340 681610 1105650 1537050 963350 797390 806490 514540 TRUE FALSE 764995.4795 574470.0587 679601.1245 816430.4236 917712.0079 1180093.432 887840.1098 786702.2913 777464.5824 615354.2615 1.243178974 0.933559893 1.104406302 1.326764881 1.491355574 1.917746419 1.442811345 1.278454283 1.263442266 1 19.23105769 3.653588582 3.237595686 1.428480509 1.073272803 0.25502965 0.229482461 0.316030917 6.380306404 0.065348191 0.110020098 4503.898372 -3.653588582 -0.355207706 TGS(ph)ESSQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 T(0.003)GS(0.722)ES(0.275)SQTGTSTTSSR;T(0.013)GS(0.987)ES(0.001)SQTGTSTTSSR;T(0.001)GS(0.979)ES(0.02)SQTGTSTTSSR;T(0.001)GS(0.701)ES(0.295)S(0.004)QTGTSTTSSR;T(0.01)GS(0.963)ES(0.027)SQTGTSTTSSR 396.06 9.64E-122 2571802000 1138707 897758 1102660 979213 1590334 2292267 1547757 1257680 1318683 824974 TRUE FALSE 1183664.032 1051940.953 1131396.225 1172898.409 1320009.595 1759922.729 1426439.762 1240822.857 1271223.856 986611.8602 1.199726133 1.066215596 1.146749062 1.188814422 1.33792188 1.783804554 1.445796285 1.257660593 1.288474128 1 19.9121231 3.26078497 3.835506294 1.385567006 1.137876231 0.213632276 0.186250316 0.303799327 9.642178012 0.055228495 0.072889878 1822.992871 -3.26078497 -0.247690775 TGS(ph)IVLPYIMSSTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSIVLPYIMSSTLR 15 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 T(0.002)GS(0.998)IVLPYIMSSTLR 155.98 2.32E-06 253190000 136260 110560 126790 117160 251410 260870 154480 136980 120000 116620 TRUE FALSE 141639.65 129547.82 130094.2516 140333.8983 208675.418 200286.896 142371.4539 135144.0072 115681.2234 139469.4562 1.015560352 0.928861584 0.932779514 1.006198075 1.496208731 1.436062788 1.020807407 0.968986406 0.829437689 1 17.08958968 1.829217814 3.408818526 0.9243382 1.132430858 0.182568974 0.188874281 0.466245654 9.43892787 0.113016422 0.059048722 67.48664114 -1.829217814 0.208092659 TGS(ph)NAAQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGSNAAQYK 9 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 T(0.001)GS(0.999)NAAQYK;T(0.012)GS(0.988)NAAQYK;T(0.035)GS(0.965)NAAQYK 115.33 0.0015672 233804000 635803 244793 354499 252960 611023 597319 481245 371129 408102 225671 TRUE FALSE 660904.9934 286834.2935 363737.5352 302994.733 507161.5287 458600.7147 443523.7594 366154.6228 393414.4887 269886.9117 2.44882195 1.062794382 1.347740551 1.122672941 1.879163111 1.699232882 1.643368908 1.356696479 1.457701251 1 18.04199549 0.691146272 1.061754386 1.003171078 1.556201248 0.172859588 0.378637325 1.90119081 3.651988275 0.347214969 0.110016469 4.910732441 -0.691146272 0.55303017 TGS(ph)PGDAPERPPLCDFSEGLSAPMDFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGSPGDAPERPPLCDFSEGLSAPMDFYR 28 1 A0A2R8Y575;Q5VVD7;Q8IWE5 A0A2R8Y575 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 T(0.219)GS(0.781)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.027)GS(0.973)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.13)GS(0.87)PGDAPERPPLCDFSEGLSAPMDFYR;T(0.177)GS(0.823)PGDAPERPPLCDFSEGLSAPMDFYR 184.36 6.66E-18 305419000 80700 62861.3 81526 69968 111671 129261 94894 90588 85342 66443 TRUE FALSE 83886.09831 73657.23928 83650.63453 83807.46157 92689.20331 99242.09172 87455.96032 89373.81603 82270.55809 79461.23372 1.055685828 0.926958164 1.052722574 1.054696204 1.16647073 1.248937212 1.10061166 1.1247474 1.035354653 1 16.27796357 3.671544035 2.255916295 1.123040242 0.996039655 0.270338457 0.072542004 0.342082956 3.395817522 0.020483684 0.038387003 4694.010263 -3.671544035 -0.127000587 TGS(ph)PGPELLFHEGQQK ddPTM_MDA-MB-175_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(0.159)GS(0.841)PGPELLFHEGQQK;T(0.019)GS(0.981)PGPELLFHEGQQK;T(0.011)GS(0.989)PGPELLFHEGQQK 256.13 8.05E-27 634000000 1998600 804770 1182340 883530 1664430 1772740 1581370 1211640 1258920 581610 TRUE FALSE 2077506.271 942982.9873 1213152.752 1058289.597 1381510.783 1361048.001 1457418.087 1195399.948 1213611.715 695565.3439 2.98678807 1.355707261 1.744124779 1.521481204 1.986169661 1.95675074 2.095300032 1.718601937 1.744784621 1 19.40782653 -2.107505913 0.336497512 1.36E-09 1.92644193 0.310381024 0.413673978 49.539522 2.406191099 38.25871292 0.328653582 0.007807178 2.107505913 1.926441928 TGS(ph)QEGTSMEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.043)GS(0.955)QEGT(0.001)S(0.001)MEGSRPAAPAEPGTLK;T(0.169)GS(0.809)QEGT(0.011)S(0.011)MEGSRPAAPAEPGTLK 136.66 2.91E-05 601890000 1220600 425950 736910 426250 1095700 1181290 879070 651010 758450 315400 TRUE FALSE 1268790.231 499103.5991 756114.48 510560.9778 909453.3054 906953.3001 810166.1964 642284.2758 731153.5327 377196.5913 3.363737265 1.323192231 2.004563396 1.353567316 2.411085695 2.404457837 2.147861924 1.702783881 1.938388494 1 18.52495711 0.511010255 0.852650107 0.997097373 2.081003576 0.261542988 0.554923186 2.249191403 2.518033778 0.531133204 0.172978295 3.243472764 -0.511010255 1.083906203 TGS(ph)TSSKEDDYESDAATIVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.022)GS(0.91)T(0.066)S(0.002)SKEDDYESDAATIVQK;T(0.024)GS(0.973)T(0.002)SSKEDDYESDAATIVQK;T(0.003)GS(0.977)T(0.016)S(0.003)SKEDDYESDAATIVQK;T(0.194)GS(0.777)T(0.02)S(0.004)S(0.004)KEDDYESDAATIVQK 307.43 1.13E-56 1296334000 1552820 329747 636095 406261 1231680 1297790 968420 661382 768245 235939 TRUE FALSE 1614126.533 386378.4822 652672.1583 486618.2132 1022319.474 996397.9407 892512.7099 652517.2561 740596.0125 282166.7297 5.720470781 1.369326861 2.313072696 1.724576862 3.623104235 3.531238221 3.163068554 2.312523722 2.624675181 1 18.10618836 0.60305655 1.035362133 1.004975338 2.924183581 0.210842847 1.150872471 2.130615646 3.57569216 1.058716316 0.335484766 4.009189184 -0.60305655 1.919208244 TGS(ph)YGALAEITASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.002)GS(0.998)YGALAEITASK 165.49 4.15E-06 314810000 399180 219940 263760 202690 422680 418970 300700 276250 263780 165440 TRUE FALSE 414939.9346 257712.9841 270633.8023 242781.477 350833.0046 321670.5671 277130.3483 272547.3206 254286.6093 197854.8005 2.097194173 1.302535918 1.367840465 1.227068924 1.773184192 1.625791066 1.400675382 1.377511791 1.285218295 1 17.59408254 -3.045217374 0.119768118 4.27E-12 1.774181317 0.363391681 0.235280589 105.8339881 1.336248384 29.8529548 2.617202782 0.00090112 3.045217374 1.774181317 TGSDHTNPTS(ph)PLLVKPSDLLEENKINSSVK ddPTM_MDA-MB-175_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(0.126)S(0.874)PLLVKPSDLLEENKINSSVK 192.94 5.69E-19 1026000000 399000 331950 533330 305600 865240 604740 706240 636460 677760 286940 TRUE FALSE 414752.8281 388959.8303 547229.0179 366046.7679 718166.8139 464298.2999 650883.0634 627929.2947 653367.55 343160.3992 1.208626721 1.133463626 1.59467415 1.066692919 2.092802128 1.353006644 1.89673128 1.829841952 1.903971296 1 18.38852355 3.25160203 24.99999082 1.727353147 1.267036429 0.290160485 0.322777899 258.716136 495947.9898 0.082859539 0.111514791 1784.851259 -3.25160203 -0.460316718 TGSEPALS(ph)PAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSEPALSPAVVR 13 0 O75815;O75815-3;O75815-2 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 TGSEPALS(1)PAVVR;TGSEPALS(1)PAVVR 150.29 4.63E-05 225040000 349580 354150 379470 374140 414420 512220 402260 375390 356290 322690 TRUE FALSE 363381.6883 414972.5076 389359.2999 448143.7753 343977.0364 393264.6678 370729.8101 370358.5111 343467.1925 385914.9272 0.941610865 1.0752953 1.008925212 1.161250171 0.891328664 1.019044976 0.960651646 0.959689519 0.890007533 1 18.55792332 3.216447863 24.9998612 0.955518804 1.046104758 0.337984533 0.063938948 265.6103977 300288.5434 0.017506367 0.020939989 1646.068343 -3.216447863 0.090585954 TGSES(ph)SQTGTSTTSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 TGS(0.018)ES(0.491)S(0.491)QT(0.001)GTSTTSSR;TGS(0.04)ES(0.942)S(0.017)QTGTSTTSSR;T(0.004)GS(0.047)ES(0.902)S(0.047)QTGTSTTSSR;TGS(0.033)ES(0.966)S(0.001)QTGTSTTSSR 344.41 8.41E-73 11678849000 686640 561512 705581 612544 937909 1306492 905661 789612 763844 517749 TRUE FALSE 713749.0774 657947.318 723969.0205 733703.3749 778483.5632 1003079.033 834672.9243 779028.5427 736353.4036 619192.0036 1.152710425 1.06259014 1.169215714 1.184936773 1.257257133 1.619980599 1.348003397 1.258137279 1.189216591 1 19.24002731 3.323364744 2.815340421 1.310681629 1.127677929 0.161884875 0.148042067 0.396913709 6.367336766 0.04403211 0.061428655 2105.546051 -3.323364744 -0.183003701 TGSET(ph)PQAPMSGVGPVSGGPGGFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSETPQAPMSGVGPVSGGPGGFGR 25 0 Q8WXF1 Q8WXF1 PSPC1 Paraspeckle component 1 1 T(0.131)GS(0.131)ET(0.739)PQAPMSGVGPVSGGPGGFGR 91.128 5.44E-05 0 21378 25157 23571 23795 25226 31636 18845 20906 20188 25288 TRUE FALSE 22222.01995 29477.51906 24185.27962 28501.57998 20938.09353 24289.01845 17367.87966 20625.78927 19461.43782 30242.69943 0.734789565 0.974698675 0.799706378 0.942428438 0.69233547 0.803136588 0.57428338 0.68200887 0.643508622 1 14.8842993 3.224456522 24.99242302 0.707063727 0.86637673 0.190220839 0.125233319 288.370105 510990.1854 0.033641811 0.04039171 1676.70447 -3.224456522 0.159313003 TGSGS(ph)PFAGNS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 TGS(0.001)GS(0.999)PFAGNS(1)PAR;TGS(0.002)GS(0.998)PFAGNS(1)PAR;TGS(0.016)GS(0.984)PFAGNS(1)PAR;T(0.001)GS(0.005)GS(0.994)PFAGNS(1)PAR 181.15 2.44E-06 1111868000 1582930 1415010 1448760 1336820 1518920 1843380 1686790 1389900 1254260 896330 TRUE FALSE 1645425.299 1658026.96 1486515.876 1601239.006 1260734.521 1415282.932 1554574.992 1371270.664 1209119.428 1071948.702 1.534985112 1.546740956 1.386741616 1.493764583 1.176114602 1.320289794 1.450232636 1.27923161 1.12796389 1 20.03180444 8 0.040132611 5.13E-09 3.552321489 0.720912108 0.092944874 416.0169118 1.270678088 30.73146486 100.3707498 100000000 -8 3.552321484 TGSGS(ph)PFAGNS(ph)PAREGEQDAASLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSGSPFAGNSPAREGEQDAASLK 24 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 T(0.279)GS(0.354)GS(0.367)PFAGNS(1)PAREGEQDAASLK 103.07 4.52E-06 0 213560 142410 166010 106960 204150 219650 165760 174020 176910 98976 TRUE FALSE 221991.5137 166867.8097 170336.357 128116.3688 169448.6559 168639.6163 152767.2981 171687.5465 170543.0437 118368.4522 1.875428035 1.409732126 1.439035096 1.082352319 1.431535623 1.424700697 1.290608226 1.450450212 1.440781226 1 16.8529251 8 0.031773058 6.60E-11 3.446478021 0.377084499 0.177171349 1589.707683 3.867553266 130.1156904 332.8422982 100000000 -8 3.446478021 TGSGS(ph)PFAGNS(ph)PAREGEQDAASLKDVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSGSPFAGNSPAREGEQDAASLKDVFK 28 2 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 T(0.073)GS(0.092)GS(0.835)PFAGNS(1)PAREGEQDAASLKDVFK;T(0.02)GS(0.137)GS(0.843)PFAGNS(1)PAREGEQDAASLKDVFK 124.79 2.13E-05 272800000 397370 208388 261070 131941 420550 347420 220378 216100 278440 161104 TRUE FALSE 413058.4744 244177.018 267873.6987 158038.536 349065.0612 266736.9702 203104.1965 213203.533 268418.9988 192669.2443 2.143873434 1.267337809 1.390329316 0.820258244 1.811732135 1.38442942 1.054159927 1.106577927 1.393159556 1 17.55576677 4.74037814 5.646164145 1.246402319 2.17470933 0.51555289 0.2607251 0.115899775 15.22178797 0.061139442 0.41399914 55001.9567 -4.74037814 0.928307011 TGSGS(ph)PFAGNSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 T(0.038)GS(0.347)GS(0.615)PFAGNSPAR;TGS(0.004)GS(0.996)PFAGNSPAR;TGS(0.002)GS(0.998)PFAGNSPAR;T(0.019)GS(0.042)GS(0.939)PFAGNSPAR 211.06 4.58E-09 1120160000 586144 1109600 1160870 1009860 1288960 1389750 1160530 1082460 1110640 922090 TRUE FALSE 609285.4177 1300165.169 1191123.226 1209607.294 1069863.04 1067001.624 1069564.626 1067951.394 1070668.283 1102755.881 0.552511601 1.179014495 1.080133188 1.096894893 0.970172146 0.96757736 0.969901539 0.96843863 0.970902356 1 20.07268202 4.751237337 24.80104716 1.017642065 0.552511272 0.804781267 0.069414035 860.3044156 1683086.994 0.018003799 0.327363366 56394.57611 -4.751237337 -0.465130794 TGSGSPFAGNS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TGSGSPFAGNSPAR 14 0 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR;TGSGSPFAGNS(1)PAR 335.85 1.38E-68 3118610000 1249221 1377190 1584750 1675460 1802090 2246320 2080890 1822260 1689300 1234990 TRUE FALSE 1298541.21 1613711.669 1626049.887 2006860.987 1495771.385 1724646.223 1917784.404 1797835.585 1628502.423 1476962.645 0.879197056 1.092588005 1.100941782 1.358775724 1.012734743 1.16769793 1.29846507 1.217251899 1.102602309 1 20.49420191 4.797138707 1.589280593 1.178475269 0.740277332 0.364835547 0.108638232 1.176518169 2.531813723 0.027709807 0.833432872 62681.4028 -4.797138707 -0.438197937 TGSGSPFAGNS(ph)PAREGEQDAASLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSGSPFAGNSPAREGEQDAASLK 24 1 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAREGEQDAASLK 166.2 8.05E-12 76218000 96364 87296 105060 83008 152400 160160 119700 125760 142450 87503 TRUE FALSE 100168.5251 102288.4089 107797.9499 99426.73465 126495.1024 122965.2672 110317.6012 124074.3929 137323.2523 104647.5375 0.957199066 0.977456435 1.030104984 0.9501106 1.208772853 1.175042148 1.054182486 1.185640827 1.312245425 1 16.67517884 3.241733878 24.99992856 1.160366786 0.982298169 0.528124816 0.081995117 64.10649684 505045.4435 0.022470797 0.029200241 1744.752695 -3.241733878 -0.178068617 TGSGSPFAGNS(ph)PAREGEQDAASLKDVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSGSPFAGNSPAREGEQDAASLKDVFK 28 2 Q9UPT8;M0QY97 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 TGSGSPFAGNS(1)PAREGEQDAASLKDVFK 188.4 3.65E-18 182750000 206640 139080 214940 89181 321730 276990 187480 203590 253140 153550 TRUE FALSE 214798.3068 162965.9081 220541.513 106820.7356 267042.4495 212663.2703 172784.8277 200861.2091 244029.5408 183635.1826 1.169701272 0.887443821 1.200976359 0.581700816 1.454200909 1.158074762 0.940913529 1.093805698 1.328882284 1 17.48648297 3.220642162 24.99997855 1.146890345 0.971991646 0.178089431 0.211070103 476.8285187 665273.7577 0.059094812 0.07076801 1662.042643 -3.220642162 -0.174898699 TGSNISGASS(ph)DISLDEQYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 TGSNISGAS(0.317)S(0.671)DIS(0.011)LDEQYK 129.51 5.75E-06 0 101970 146750 156000 160940 159090 184410 161080 176880 156770 194940 TRUE FALSE 105995.8543 171953.1709 160065.4882 192773.4516 132047.9386 141583.5723 148454.1287 174509.2129 151127.8783 233134.7606 0.45465487 0.737569852 0.686579246 0.826875628 0.566401759 0.607303569 0.636773891 0.748533648 0.648242578 1 17.8308046 -5 0.312469465 4.022035241 0.650356052 0.526151209 0.097980065 241.0619129 2.172362175 479.8431054 0.088746352 1.00E-05 5 -3.371679189 TGSQEGTS(ph)MEGSRPAAPAEPGTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGSQEGTSMEGSRPAAPAEPGTLK 24 1 Q8IV36-2;Q8IV36;Q8IV36-3 Q8IV36-2 HID1 Protein HID1 1 T(0.211)GS(0.211)QEGT(0.105)S(0.414)MEGS(0.06)RPAAPAEPGTLK 68.234 0.020753 659870000 364240 146110 230930 148350 365840 343120 283800 240670 273480 161230 TRUE FALSE 378620.4765 171203.2559 236948.2255 177693.1872 303654.6475 263435.58 261555.0144 237444.2123 263637.5082 192819.9316 1.963596156 0.887891903 1.228857533 0.921549893 1.574809435 1.366225877 1.356472914 1.231429813 1.367273114 1 17.55689466 -2.01492004 2.323850126 0.675588327 1.299637179 0.094509783 0.291709865 14275473.02 5648402.985 24722648.74 0.065930021 0.009662288 2.01492004 0.624048852 TGSQGQCTQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSQGQCTQVR 11 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ; 101.93 0.0068324 42861000 23324 22193 21741 21034 39085 36195 22028 26331 23121 28213 FALSE TRUE 24244.84953 26004.47511 22307.58832 25194.46242 32441.34566 27789.25979 20301.3878 25978.07601 22288.87973 33740.79718 0.718561847 0.770713121 0.661145859 0.746706199 0.961487231 0.823610054 0.601686667 0.769930713 0.660591379 1 15.04220644 -2.271328879 2.382664385 2.115880385 0.748175512 0.392543915 0.094740038 4782721.538 676458.6379 29112768.12 0.024039016 0.005353911 2.271328879 -1.367704873 TGSS(ph)PTQGIVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TGSSPTQGIVNK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 TGS(0.028)S(0.971)PTQGIVNK;TGS(0.003)S(0.997)PTQGIVNK;TGSS(1)PTQGIVNK;TGS(0.003)S(0.996)PTQGIVNK;TGS(0.002)S(0.998)PTQGIVNK;TGS(0.02)S(0.979)PTQGIVNK 250.53 3.32E-17 2415650000 5522140 3838000 5091020 3802590 6324490 6575080 6029040 5192110 5217250 3129900 TRUE FALSE 5740158.351 4497146.645 5223696.164 4554730.952 5249455.449 5048117.316 5556468.091 5122518.258 5029482.192 3743143.979 1.533512572 1.201435657 1.395537065 1.216819598 1.40241879 1.348630281 1.484438782 1.368506872 1.343651812 1 21.83581911 0.696631284 3.926331518 1.000001577 1.365225026 0.563029165 0.096940806 4.691267644 60.08165036 0.086639221 0.022157759 4.973146858 -0.696631284 0.365223448 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 F5GZ78;A0A1B0GTU4;P49023;P49023-2;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 T(0.001)GS(0.003)S(0.117)S(0.879)PPGGPPKPGSQLDSMLGSLQSDLNK;TGSS(0.03)S(0.97)PPGGPPKPGSQLDSMLGSLQSDLNK 373.71 4.74E-137 7782000000 2490200 1117040 1800540 1131430 2641300 2445400 2468900 1749800 2183540 803970 TRUE FALSE 2588515.019 1308882.931 1847463.552 1355223.477 2192332.769 1877492.91 2275381.167 1726346.793 2104954.822 961492.5286 2.692184226 1.361303278 1.921453882 1.409499748 2.280135003 1.952685907 2.366509462 1.795486436 2.189257596 1 19.87491612 3.210151349 24.99984653 1.988335644 1.816861781 0 0.493397188 942.4055586 829304.0787 0.131369826 0.157043768 1622.375387 -3.210151349 -0.171473863 TGTITTFEHAHNMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 TGTITTFEHAHNMR 14 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;;;;; 174.73 1.44E-06 11682880000 4149130 4230550 4813470 4248060 5780750 6413960 5304110 5047340 5078000 3698340 FALSE TRUE 4312940.856 4957114.053 4938912.983 5088313.589 4798140.18 4924414.995 4888359.998 4979688.663 4895243.772 4422958.914 0.975125689 1.120768732 1.116653597 1.150432027 1.084825854 1.113375704 1.105223922 1.125872693 1.106780295 1 22.07658041 4.741629809 24.69511787 1.10910598 0.97512563 0.49223507 0.038359225 174.3070424 1402417.705 0.008115008 0.057198228 55160.70509 -4.741629809 -0.13398035 TGTLQDLIQHGS(ph)PINNECHPSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGTLQDLIQHGSPINNECHPSLER 24 0 A0A2R8YH03;Q5VWN6 A0A2R8YH03 FAM208B Protein FAM208B 1 TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER;TGTLQDLIQHGS(1)PINNECHPSLER 233.87 4.04E-37 403320000 96738 237269 183445 218598 199698 281771 187128 211811 165157 193303 TRUE FALSE 100557.2909 278018.1051 188225.7274 261836.032 165753.4053 216333.9555 172460.4184 208972.02 159213.0318 231177.0218 0.434979611 1.202619979 0.81420604 1.132621356 0.716997753 0.935793505 0.746010209 0.903948058 0.688706129 1 17.81863848 TGTRFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TGTRFER 7 1 Q16401-2;Q16401;Q4VXH0 Q16401-2 PSMD5 26S proteasome non-ATPase regulatory subunit 5 0 ;;; 95.909 0.011965 463937000 215846 240696 249946 210139 353569 370946 232530 265438 271127 299697 FALSE TRUE 224367.7667 282033.6656 256459.7981 251703.867 293469.4677 284799.4132 214303.691 261880.2378 261369.1922 358416.8891 0.625996636 0.786887209 0.715534914 0.702265643 0.818793636 0.794603775 0.59791739 0.730658196 0.729232355 1 18.4512791 0.539500566 3.472945128 0.999999688 0.723087947 0.611984763 0.066321535 14.96311609 111.8556163 0.062460468 0.016110352 3.463383356 -0.539500566 -0.276911741 TGTRPEDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGTRPEDSK 9 1 Q5JRG1;H7BYF2;Q9BVL2-2;Q9BVL2-3;Q9BVL2 Q5JRG1 NUPL1 Nucleoporin p58/p45 0 91.658 0.0096707 363920000 210240 234260 180560 213520 249210 314970 263560 217100 204960 205070 FALSE TRUE 218540.4375 274492.3327 185265.5419 255753.6187 206849.3732 241822.9909 242901.4785 214190.1296 197583.5296 245249.5402 0.891094178 1.11923689 0.75541647 1.042830166 0.843424102 0.986028315 0.990425826 0.873355887 0.805642814 1 17.90389091 1.656048252 8.202970613 0.879636986 0.947227893 0.046693797 0.106235534 0.309900299 37.55832419 0.048260629 0.025150615 45.2947902 -1.656048252 0.067590907 TGVELGKPTHFTVNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGVELGKPTHFTVNAK 16 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 139.34 1.08E-06 1299350000 1746410 1700400 2172160 1571810 2990500 3040000 2595800 2320400 2721600 1686850 FALSE TRUE 1815359.615 1992430.473 2228768.274 1882709.327 2482175.878 2334006.072 2392334.413 2289298.833 2623650.148 2017355.961 0.899870747 0.987644477 1.104796733 0.933255887 1.230410461 1.156962934 1.185876196 1.13480163 1.300539022 1 20.94403424 3.238627763 25 1.172661463 0.990653185 0.522832919 0.087136551 1.405501771 523051.3671 0.02330435 0.029640634 1732.31858 -3.238627763 -0.182008277 TGVIHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TGVIHEK 7 0 Q96M27;Q96M27-3;Q96M27-2;Q96M27-5 Q96M27 PRRC1 Protein PRRC1 0 ;; 74.127 0.047024 765360000 2127810 1906390 2174780 1749950 2856320 2973060 2359110 2335470 2254450 1649790 FALSE TRUE 2211817.582 2233797.653 2231456.553 2096084.887 2370803.747 2282611.872 2174196.794 2304166.845 2173312.785 1973034.763 1.121023118 1.132163353 1.130976805 1.062365918 1.201602623 1.156904032 1.101955644 1.167828812 1.101507599 1 20.91198494 0.961196223 12.48141153 1.000000003 1.134781754 0.564916762 0.03546657 4.146681091 1334.357401 0.033063178 0.008266911 9.145263488 -0.961196223 0.134781751 TGVKVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TGVKVDK 7 1 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ; 77.732 0.033972 2240900000 4104500 2557400 3430100 2165630 5816100 4963700 4807900 4061300 4598900 2326450 FALSE TRUE 4266548.829 2996613.556 3519491.224 2593985.15 4827481.399 3810955.901 4431044.235 4006864.916 4433386.487 2782273.335 1.5334758 1.077037802 1.264969613 0.932325778 1.735085241 1.369727357 1.592598462 1.440140645 1.593440311 1 21.40783273 3.237358853 24.99997258 1.479634188 1.19753106 0.218605828 0.231714441 41.56118651 864594.7125 0.060311147 0.075988594 1727.264524 -3.237358853 -0.282103128 TGVTST(ph)SDS(ph)EEEGDDQEGEKKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TGVTSTSDSEEEGDDQEGEKKR 22 2 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 2 TGVT(0.007)S(0.057)T(0.468)S(0.468)DS(1)EEEGDDQEGEKKR 163.61 2.82E-11 147480000 287750 97958 160580 64150 265770 258870 155830 133570 172580 81780 TRUE FALSE 299110.5922 114781.5245 164764.8467 76838.67853 220594.5103 198751.3657 143615.6374 131779.7126 166368.8795 97803.22523 3.058289658 1.173596517 1.684656578 0.785645651 2.255493209 2.032155537 1.468414125 1.34739639 1.70105719 1 16.57759442 4.746590937 24.76622729 1.519832607 3.05829052 0.54606846 0.427222985 678.1014188 2091270.672 0.099785251 1.100476312 55794.44182 -4.746590937 1.538457912 THAPSALS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THAPSALSPPR 11 0 H9KVB4;O15417;O15417-2 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 THAPSALS(1)PPR;THAPSALS(1)PPR 95.538 0.004949 397050000 141312 230350 216171 209100 246400 285040 223980 241360 214740 245690 TRUE FALSE 146891.1069 269910.8206 221804.5938 250459.3559 204517.016 218843.7798 206423.8623 238124.964 207011.5493 293828.2515 0.499921659 0.918600643 0.754878378 0.852400525 0.696042722 0.744801695 0.702532385 0.810422288 0.704532489 1 18.16461359 -1.861785918 2.589917706 1.108425247 0.75274935 0.342164775 0.10621439 40937830.68 24368929.71 27312257.22 0.023947261 0.013747195 1.861785918 -0.355675898 THAVS(ph)VSETDDYAEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 1 T(0.017)HAVS(0.983)VSETDDYAEIIDEEDTYTMPSTR;T(0.023)HAVS(0.943)VS(0.015)ET(0.019)DDYAEIIDEEDTYTMPSTR;T(0.04)HAVS(0.955)VS(0.002)ET(0.003)DDY(0.001)AEIIDEEDTYTMPSTR 230.45 3.25E-35 236370000 76047 97747 103447 109167 151169 147075 133821 120565 134332 138629 TRUE FALSE 79049.39428 114534.2869 106142.9138 130759.9068 125473.3474 112919.0602 123331.7603 118949.0234 129497.4176 165790.6983 0.476802348 0.690836627 0.64022237 0.788704723 0.756817775 0.681094062 0.743900361 0.717465 0.781089765 1 17.33900354 -5 0.061061322 2.031318102 0.265262493 0.717244342 0.066429612 226.1004147 1.007448949 35.13345489 5.688609902 1.00E-05 5 -1.766055609 THAVSVSETDDY(ph)AEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 1 THAVSVSET(0.005)DDY(0.995)AEIIDEEDTYTMPSTR;THAVS(0.001)VS(0.011)ET(0.018)DDY(0.969)AEIIDEEDTYTMPSTR 257.34 8.05E-53 334940000 81611 120392 123740 108464 144111 165945 117371 118977 105622 133928 TRUE FALSE 84833.0653 141068.3895 126964.7661 129917.8555 119615.0637 127406.7887 108171.1543 117382.3079 101820.6849 160168.6274 0.52964845 0.880749194 0.79269435 0.811131728 0.746807072 0.795454083 0.67535794 0.73286704 0.635709293 1 17.28923207 -1.870010264 2.799404327 1.112038698 0.740924955 0.412902557 0.094994719 20223467.77 16760859.68 15158241.06 0.021399984 0.01348931 1.870010264 -0.371113742 THAVSVSETDDYAEIIDEEDTYTMPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;Q05397-2;Q05397-4;Q05397-3;H0YB99;H0YB33 E7ESA6 PTK2 Focal adhesion kinase 1 0 163.62 7.87E-12 58528000 20343 20971 23695 24266 23239 29765 23432 23902 22925 24757 FALSE TRUE 21146.15735 24572.60612 24312.51117 29065.74237 19288.84308 22852.52984 21595.33861 23581.63279 22099.93373 29607.66015 0.714212378 0.829940833 0.821156114 0.981696704 0.651481508 0.771845182 0.729383494 0.796470666 0.746426216 1 14.85368286 -1.094186347 3.756500054 1.000079536 0.785255876 0.378627466 0.083517912 20949913.99 41001470.87 22611.24917 0.019723394 0.080503294 1.094186347 -0.21482366 THEAQIQEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 THEAQIQEMR 10 0 P35579 P35579 MYH9 Myosin-9 0 ;;;;;; 176.6 2.97E-06 9017106000 3281734 3735452 3951972 3812198 4397064 5063878 4037733 3683728 3718134 3545964 FALSE TRUE 3411299.392 4376986.823 4054963.637 4566239.386 3649652.632 3887869.078 3721244.937 3634353.652 3584319.084 4240727.754 0.804413674 1.032131058 0.956195227 1.076758436 0.860619413 0.916792896 0.877501493 0.857011782 0.845213202 1 22.01588044 3.17768043 24.99995929 0.883954003 0.97120553 0.17512515 0.077624902 99.03480592 40667.12074 0.021239087 0.025385576 1505.498856 -3.17768043 0.087251526 THEDIEAQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THEDIEAQIR 10 0 O75533;B4DGZ4;A0A494C1M2;O75533-2;F8WC19 O75533 SF3B1 Splicing factor 3B subunit 1 0 166.69 5.47E-06 365680000 108490 160710 131510 158020 169630 198760 162600 158020 122820 168870 FALSE TRUE 112773.269 188310.6923 134937.2586 189275.8844 140796.3532 152601.0022 149854.9871 155902.0004 118399.7322 201956.8433 0.558402811 0.932430361 0.668148979 0.937209561 0.697160596 0.75561194 0.742014901 0.771957007 0.586262541 1 17.62368751 -1.049310746 4.194203166 1.000024181 0.749474234 0.298616624 0.119085324 13982059.14 3499791.57 3284.976025 0.02485987 0.089266654 1.049310746 -0.250549948 THETLSHAGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 THETLSHAGQK 11 0 Q16890-5;E9PPQ1;J3KNE7;Q16890;E9PNK6;E9PNQ9;Q16890-4;Q16890-3;Q16890-2 Q16890-5 TPD52L1 Tumor protein D53 0 ;; 244.16 4.24E-16 377446000 190759 299232 348510 268756 462540 458470 385454 333805 375720 293469 FALSE TRUE 198290.3126 350622.7683 357592.4569 321915.1346 383917.616 351997.2907 355241.1083 329330.89 362197.9106 350968.6317 0.564980157 0.999014546 1.018872983 0.917219106 1.09388014 1.002930914 1.012173386 0.938348502 1.031995107 1 18.42098257 4.738624239 24.21267286 0.99824526 0.56498 0.890510448 0.045916298 0.949727429 360182.7782 0.0106423 0.06123043 54780.27895 -4.738624239 -0.433265259 THFELEPS(ph)PPSGLGFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THFELEPSPPSGLGFTR 17 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 THFELEPS(0.998)PPS(0.002)GLGFTR;THFELEPS(1)PPSGLGFTR;THFELEPS(0.995)PPS(0.005)GLGFTR;THFELEPS(0.992)PPS(0.008)GLGFTR 92.913 0.0020557 609380000 323233 352192 348171 336553 392061 494755 357823 342778 400155 340705 TRUE FALSE 335994.4884 412678.2363 357244.6223 403122.1789 325418.6113 379855.6493 329775.8983 338183.6216 385753.4997 407459.6216 0.824608061 1.012807686 0.876760796 0.989354914 0.798652416 0.932253478 0.809346205 0.829980699 0.946728165 1 18.63629757 3.245991676 24.99981403 0.871459427 0.928583041 0.038752586 0.078132418 374.7165447 1260624.995 0.020252943 0.026889328 1761.942276 -3.245991676 0.057123614 THFEYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THFEYEK 7 0 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 0 ; 112.17 0.0064142 174140000 337000 259108 311140 251374 417590 436250 398230 311640 353370 228013 FALSE TRUE 350305.0202 303607.7834 319248.564 301095.0269 346608.201 334937.5489 367015.692 307462.9755 340652.2827 272687.7818 1.284637757 1.113389758 1.170747592 1.104174983 1.27108079 1.228282202 1.345919093 1.12752751 1.24923926 1 18.05689053 -1.13786104 3.554840299 0.999824773 1.205843599 0.403369333 0.076630013 12547016.48 26682648.44 27566.46231 0.018641504 0.072801271 1.13786104 0.206018827 THFGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 4757860000 18384530 13159020 17007130 13477520 21833560 21882950 19843500 17128040 17829520 11861940 FALSE TRUE 19110365.44 15418979.32 17450349.78 16143333.23 18122299.27 16800966.5 18288114.62 16898466.64 17187839.06 14186060.03 1.347122837 1.086910621 1.230105451 1.137971586 1.277472338 1.184329297 1.289160949 1.191202251 1.211600615 1 23.75797062 0.182782826 1.779210584 0.999974812 1.214467507 0.454493708 0.071380498 15.75558606 32.89575403 0.061791677 0.017185789 1.523290823 -0.182782826 0.214492695 THILLFLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 ; 117.89 0.0010783 1429330000 1477620 1283190 1332020 1192430 2582200 2277300 1790260 1319520 1287300 1483840 FALSE TRUE 1535957.579 1503567.901 1366733.535 1428289.095 2143278.566 1748431.588 1649934.743 1301833.993 1240970.324 1774570.038 0.865537874 0.847285747 0.770177286 0.804864877 1.207773444 0.985270545 0.929765919 0.733605304 0.699307606 1 20.75903808 -2.658426637 2.118553815 4.190511838 0.871522237 0.071343285 0.139072673 9903600.261 455425.4755 152758901.1 0.039024516 0.002195702 2.658426637 -3.318989601 THINIVVIGHVDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 197.75 4.78E-09 6511737300 6127040 4684003 6138006 4817703 7851505 8410112 7496265 5806266 6802359 4280213 FALSE TRUE 6368940.27 5488444.079 6297967.479 5770630.274 6516908.985 6456990.944 6908688.161 5728442.501 6557543.428 5118838.788 1.244215834 1.072204909 1.230350816 1.127331903 1.273122529 1.261417132 1.349659258 1.119090235 1.281060744 1 22.28738514 3.244574836 24.99965837 1.224394605 1.166061872 0.039562762 0.102293486 412.2770677 1713722.509 0.026839064 0.035442996 1756.20349 -3.244574836 -0.058332733 THKHS(ph)PEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THKHSPEKR 9 2 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 THKHS(1)PEKR;THKHS(1)PEKR;THKHS(1)PEKR;THKHS(1)PEKR 131.32 0.00015973 515262000 675960 328559 425061 322957 658990 644940 608240 426525 503940 270784 TRUE FALSE 702647.4228 384986.4524 436138.4389 386836.9307 546975.1152 495162.4592 560564.5595 420808.13 485803.2978 323838.9403 2.16974346 1.188820752 1.346775772 1.194534945 1.689034415 1.529039277 1.730998004 1.299436472 1.50013861 1 18.30491695 0.266391573 0.957367035 0.997423978 1.506097742 0.233237978 0.281025485 4.970547361 5.212199225 0.290229935 0.083166115 1.846679691 -0.266391573 0.508673764 THKNPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THKNPALK 8 1 Q01518-2;Q01518;Q5T0S3 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 0 ; 76.221 0.021848 2335500000 4965400 2961990 3990400 3072100 6353800 5794800 5137800 3987300 4712000 2787050 FALSE TRUE 5161437.826 3470688.741 4094393.102 3679752.211 5273783.346 4449045.521 4735085.811 3933856.765 4542416.04 3333119.086 1.548530878 1.041273549 1.228396885 1.103996622 1.582236701 1.334799449 1.420617052 1.180232888 1.362812406 1 21.66844143 -1.191907935 3.900614552 0.999809092 1.299469453 0.231146366 0.169135925 11799777.72 3605669.766 20945.33721 0.038017483 0.064282397 1.191907935 0.299660361 ENDPMDSHQSQES(ph)PNLENIANPLEENVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 ENDPMDSHQSQESPNLENIANPLEENVTK 29 0 Q96JQ2 Q96JQ2 CLMN Calmin 1 ENDPMDS(0.188)HQS(0.114)QES(0.698)PNLENIANPLEENVTK 143.16 4.67E-08 47954000 16390 29293 34562 35199 39787 51517 44585 40051 38437 32078 TRUE FALSE 17037.08986 34323.84488 35462.71411 42161.25714 33024.01995 39552.9575 41090.3112 39514.18186 37053.65988 38363.06993 0.444101316 0.894710589 0.924397192 1.099006342 0.860828396 1.031016485 1.071090277 1.03000573 0.965867954 1 15.22743055 4.937109279 1.600819558 1.007666514 8.38E-20 0.867382694 0.064835601 0.561884916 0.929529894 0.016598931 1.021167029 86518.55932 -4.937109279 -1.007666514 down THLENNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THLENNR 7 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 168.45 0.0010486 276880000 462340 528440 511550 504050 658930 783410 550580 511380 534930 539730 FALSE TRUE 480593.5402 619195.4593 524881.4132 603749.5856 546925.314 601474.9002 507424.1009 504525.7875 515677.9738 645479.7597 0.744552456 0.959279435 0.81316479 0.935350143 0.847315978 0.93182612 0.786119306 0.781629137 0.798906497 1 19.30001233 2.222072599 24.97802081 0.817649815 0.874980791 0 0.08454277 560.019663 848379.3571 0.028958015 0.021447386 166.752594 -2.222072599 0.057330976 THLMSESEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THLMSESEWR 10 0 P61024;Q5T179;Q9BZU3 P61024 CKS1B Cyclin-dependent kinases regulatory subunit 1;Cyclin-dependent kinases regulatory subunit 0 ;;; 175.15 2.89E-06 888467000 396413 518694 532394 502850 634076 730163 540843 496924 515373 556420 FALSE TRUE 412063.6913 607775.6596 546268.625 602312.2291 526295.988 560593.709 498450.3124 490263.5466 496824.8264 665439.8457 0.619235073 0.913344254 0.820913609 0.905134 0.79089942 0.84244085 0.749053901 0.736751112 0.746611177 1 19.34394873 2.247620691 24.94469379 0.779546662 0.823008767 0 0.105017842 721.0101652 1985126.329 0.03440198 0.028387202 176.8563635 -2.247620691 0.043462105 THLPGCGARARLCGTGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THLPGCGARARLCGTGAR 18 2 Q9NYQ6;Q9NYQ6-2 Q9NYQ6 CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1 0 50.178 0.084681 418250000 19142 541930 166710 481390 72178 290120 62691 190620 56548 517580 FALSE TRUE 19897.74094 635002.2619 171054.5996 576607.5052 59909.20934 222744.0268 57777.11561 188065.0507 54512.84853 618989.8913 0.032145502 1.025868549 0.276344738 0.93152976 0.096785441 0.359850831 0.093340968 0.303825722 0.088067429 1 19.23955632 -1.802296356 4.697930265 1.074573113 0.36703422 0.252100014 0.332100092 0.166677608 0.007014316 0.206620146 0.071947348 0.015765351 1.802296356 -0.707538894 THLPGFVEQAEALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THLPGFVEQAEALK 14 0 P30044-2;P30044 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 156.5 5.55E-06 634570000 384000 261340 354230 248470 468240 465190 368510 292130 355350 224870 FALSE TRUE 399160.6165 306223.1121 363461.5248 297616.6244 388648.7321 357156.6725 339625.2233 288214.4752 342561.0229 268928.9711 1.484260379 1.138676546 1.35151495 1.106673718 1.44517242 1.328070647 1.262880759 1.071712259 1.273797395 1 18.03686566 1.131861691 0.636442601 1.010429769 1.304166968 0.329292943 0.126127816 0.846859217 0.831503171 0.12054852 0.052516078 13.54757895 -1.131861691 0.293737199 THLSLSHNPEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THLSLSHNPEQK 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" 0 164.64 3.28E-05 96822000 18854 105600 105760 105640 120280 171640 111380 124970 101550 116590 FALSE TRUE 19598.37048 123735.9785 108516.1925 126535.2767 99834.84856 131779.2112 102649.7446 123294.9816 97895.23534 139433.5782 0.140557036 0.887418799 0.778264417 0.907495011 0.716002916 0.945103847 0.736190994 0.884256024 0.702092255 1 17.08921851 4.741282257 24.98233517 0.833301935 0.140556786 0.822642495 0.097340742 86.25540372 791707.662 0.020177061 0.139329288 55116.57947 -4.741282257 -0.692745149 THMQDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 136.8 0.0029452 1608568000 3904440 2696570 3339530 2567150 5041640 4849630 4315200 3206900 3708540 2623380 FALSE TRUE 4058590.306 3159684.921 3426560.895 3074924.608 4184663.834 3723376.929 3976963.348 3163916.751 3575070.37 3137381.083 1.29362363 1.007109062 1.092172358 0.980092799 1.333807951 1.186778664 1.267606084 1.008457904 1.139507849 1 21.58112935 1.679274932 11.6763382 1.056252515 1.156960108 0.172330184 0.115518271 0.245455205 43.2263132 0.055032018 0.030010836 47.78316708 -1.679274932 0.100707594 THNDIIHNENMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 THNDIIHNENMR 12 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;;;;;;;;;; 213.18 6.70E-09 13190390000 2562573 3212226 3398947 3072374 3892577 4741307 3399417 2940014 3015560 3273554 FALSE TRUE 2663745.361 3763900.828 3487526.351 3680080.407 3230918.152 3640210.304 3132961.813 2900607.921 2907030.585 3914944.23 0.680404421 0.96141876 0.890824018 0.940008386 0.825278206 0.929824307 0.800257074 0.740906575 0.742547125 1 21.90056033 2.133529458 8.147029442 0.792149224 0.877185363 0.024596628 0.101843593 0.48019602 33.69832131 0.035874448 0.026476745 135.9970407 -2.133529458 0.08503614 THPQYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THPQYSR 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;; 116.73 0.0053911 744960000 1560950 1857300 1749820 1640410 2394210 2505980 1746050 1697690 1491270 1813400 FALSE TRUE 1622577.511 2176276.827 1795421.747 1964878.202 1987243.039 1924004.123 1609190.039 1674935.242 1437599.484 2168701.01 0.748179442 1.003493251 0.827878872 0.906016179 0.916328729 0.887168916 0.742006404 0.77232188 0.662885053 1 21.04839974 2.248730682 24.7112599 0.773817712 0.887314261 0.138238441 0.101024219 247.3470784 601004.614 0.032255381 0.026692119 177.3089599 -2.248730682 0.113496549 THPVEIFYTPEPERDYLEAAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 THPVEIFYTPEPERDYLEAAIR 22 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;; 140.97 7.56E-08 422427000 27641.5 38330.6 41725.6 32428.4 40126.4 46421 34792.2 35840.3 32039.6 35194.9 FALSE TRUE 28732.80776 44913.58238 42813.00341 38842.64073 33305.72886 35640.42627 32065.09645 35359.9194 30886.50105 42090.66681 0.682640831 1.067067495 1.017161444 0.92283263 0.79128537 0.846753662 0.761810132 0.840089314 0.733808785 1 15.36121274 3.309997609 5.926541277 0.818808103 0.941405524 0.124803721 0.115731472 0.322588341 19.87601748 0.030588306 0.041350811 2041.726703 -3.309997609 0.122597421 THPYS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 THPYSPK 7 0 M0QZ39;M0R1C6;H0YD59;E9PME6;M0QXT0;B1AQP1;B4DLJ1;Q15853-4;P22415-2;Q15853-3;P22415;Q15853-2;Q15853 M0QZ39 USF2;USF1 Upstream stimulatory factor 2;Upstream stimulatory factor 1 1 THPYS(1)PK;THPYS(1)PK;THPYS(1)PK 113.74 0.0053572 1066640000 4569420 2634790 3488470 2636360 4972760 5633850 4465730 3707990 3672420 2183920 TRUE FALSE 4749824.23 3087294.687 3579382.394 3157824.139 4127492.031 4325473.719 4115694.414 3658290.459 3540250.322 2611817.31 1.818589766 1.182048482 1.370456647 1.209052458 1.580314218 1.656116491 1.575797203 1.400668586 1.355473948 1 21.31662256 0.766940081 1.783006812 1.000836785 1.466265502 0.372886641 0.185523023 0.919765544 4.860723839 0.176158179 0.049688725 5.847094071 -0.766940081 0.465428717 THQPERPRS(ph)PAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 THQPERPRSPAAR 13 2 Q9P2Y4;G3V2Q8 Q9P2Y4 ZNF219 Zinc finger protein 219 1 THQPERPRS(1)PAAR;THQPERPRS(1)PAAR;THQPERPRS(1)PAAR;THQPERPRS(1)PAAR;THQPERPRS(1)PAAR 118.55 0.0002186 767484000 187034 278843 258219 206855 266428 292937 213552 221736 216452 255358 TRUE FALSE 194418.2467 326732.1162 264948.3993 247770.3016 221140.6637 224906.8213 196813.2362 218763.9916 208661.9348 305390.511 0.636621767 1.069883 0.867572468 0.811322856 0.724124214 0.736456482 0.64446415 0.716341811 0.683262666 1 18.22029571 3.448090936 2.765202795 0.727337227 0.877593523 0.096056363 0.133657724 0.414812947 6.42844693 0.03594839 0.054339967 2806.021121 -3.448090936 0.150256296 THS(ph)AGTS(ph)PTITHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 2 THS(0.999)AGT(0.034)S(0.903)PT(0.062)IT(0.002)HQK 120.11 7.85E-05 536910000 392080 228930 336960 284850 534950 545880 481240 376770 452060 271810 TRUE FALSE 407559.6212 268246.9467 345741.4544 341192.4798 444019.3901 419107.6429 443519.1513 371720.0144 435790.4489 325065.9654 1.253775124 0.825207728 1.06360398 1.049609975 1.365936263 1.289300288 1.364397379 1.143521789 1.340621582 1 18.31037299 3.311573025 7.979278305 1.259130644 1.031623592 0.3227213 0.142741665 0.25901766 24.78010962 0.037069694 0.050167463 2049.146576 -3.311573025 -0.227507052 THS(ph)AGTSPTITHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 THS(0.79)AGT(0.055)S(0.155)PTITHQK 194.05 1.21E-07 316750000 291740 199300 253620 221380 358250 372970 322230 241890 290140 188430 TRUE FALSE 303258.1205 233528.2247 260229.5456 265168.3032 297354.793 286353.3699 296972.7706 238647.8602 279697.9181 225349.2508 1.345725 1.036294657 1.154783274 1.176699289 1.319528651 1.270709217 1.317833406 1.059013329 1.241175274 1 17.78180313 -1.355618769 7.031548526 0.99999399 1.204099578 0.277952542 0.10223495 9.60E-06 8.79E-07 0.098634928 0.023247791 0.044094176 1.355618769 0.204105588 THS(ph)EGSLLQEPR ddPTM_MDA-MB-175_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 T(0.128)HS(0.872)EGSLLQEPR 188.39 5.96E-06 536840000 72431 95077 95104 78973 110410 137680 99509 92991 105660 84081 TRUE FALSE 75290.63181 111405.7352 97582.48837 94593.62369 91642.54764 105705.9066 91709.22456 91744.60775 101857.3172 100555.0621 0.748750289 1.107907775 0.970438348 0.940714686 0.911366824 1.051224119 0.912029913 0.912381792 1.012950667 1 16.61762619 4.764402974 24.55186224 0.969993693 0.748749922 0.545434842 0.062719901 5439.825479 5168067.66 0.014895305 1.132772432 58130.35481 -4.764402974 -0.221243771 THS(ph)FENVSCHLPDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THSFENVSCHLPDSR 15 0 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 T(0.187)HS(0.813)FENVSCHLPDSR;T(0.035)HS(0.965)FENVSCHLPDSR;T(0.182)HS(0.818)FENVSCHLPDSR;T(0.137)HS(0.863)FENVSCHLPDSR 211.75 7.86E-10 3061480000 389042 950080 1002230 857064 1425710 1308670 961931 1024378 1073700 869330 TRUE FALSE 404401.6786 1113248.849 1028348.937 1026588.701 1183368.323 1004751.226 886532.3347 1010647.888 1035057.747 1039658.569 0.388975468 1.070783123 0.989121783 0.987428692 1.138227836 0.966424224 0.852714883 0.972095954 0.995574679 1 19.98767838 4.743166327 24.99618403 0.991400836 0.388975226 0.873343347 0.069427933 164.3368479 891860.6692 0.017550135 0.141614073 55356.20732 -4.743166327 -0.60242561 THS(ph)TSSSLGSGESPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.17)HS(0.768)T(0.061)SSSLGSGESPFSR;T(0.073)HS(0.457)T(0.457)S(0.012)S(0.001)SLGSGESPFSR 211.16 1.76E-12 1811560000 136794 354330 324570 326690 451910 516800 399990 412550 356210 398950 TRUE FALSE 142194.7327 415183.4212 333028.5608 391308.3069 375094.4996 396781.0322 368637.7386 407020.442 343390.0717 477116.6141 0.298029305 0.870192756 0.69800244 0.820152339 0.786169436 0.831622753 0.772636558 0.853083774 0.719719376 1 18.8639824 4.742797118 24.98951343 0.808304402 0.298029103 0.7878836 0.080649041 168.603667 994492.3538 0.016983553 0.132901208 55309.16707 -4.742797118 -0.5102753 THSAGT(ph)SPTITHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 THS(0.007)AGT(0.579)S(0.413)PTITHQK 146.2 3.08E-05 272280000 199470 148970 188830 131810 226410 233130 189920 147470 165360 119640 TRUE FALSE 207345.2296 174554.4387 193751.0649 157881.6246 187924.9091 178989.0906 175033.5741 145493.4059 159408.7259 143081.1674 1.449144101 1.219967952 1.35413394 1.103440987 1.313414704 1.250961912 1.223316649 1.016859231 1.11411396 1 17.12647427 6.774983098 0.116946315 0.874544655 2.158787832 0.612627138 0.086301307 48.42488185 0.520968451 0.709921518 9.835701264 5956389.617 -6.774983098 1.284243177 THSAGTS(ph)PTITHQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSAGTSPTITHQK 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 T(0.001)HS(0.056)AGT(0.061)S(0.878)PT(0.004)ITHQK 134.08 2.63E-05 316930000 316680 225970 300400 208820 362540 370730 314680 228410 271220 168340 TRUE FALSE 329182.7709 264778.5897 308228.6708 250123.9727 300915.5803 284633.576 290014.5593 225348.5376 261458.8452 201322.9999 1.635097684 1.315192948 1.531015686 1.242401379 1.494690524 1.413815491 1.440543601 1.119338265 1.298703304 1 17.61915248 1.275687637 0.595514146 1.002045852 1.456719194 0.566912742 0.121055248 0.511949828 0.447420182 0.114247926 0.054730536 18.86633915 -1.275687637 0.454673342 THSLCNGDS(ph)PGPVQK ddPTM_MDA-MB-175_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 205.24 2.90E-09 413480000 313630 196730 252150 192616 288700 339710 308220 222020 274970 163767 TRUE FALSE 326012.3546 230516.8472 258721.2361 230714.8699 239626.8771 260817.5009 284060.911 219044.1851 265073.8834 195854.0081 1.664568204 1.176983046 1.320990255 1.17799412 1.223497438 1.331693455 1.45037068 1.118405424 1.35342588 1 17.57941913 -5 0.138527677 0.025003204 1.403313419 0.30251492 0.148308594 182.7806991 1.559096286 49.71725838 0.898705089 1.00E-05 5 1.378310214 THSQGGYGSQGYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THSQGGYGSQGYK 13 0 K7ER00;Q9Y285;Q9Y285-2;K7EPH2;K7ERS0 K7ER00 FARSA Phenylalanine--tRNA ligase alpha subunit 0 ; 168 3.10E-05 194324000 188742 158561 202590 165878 253620 273270 227490 195875 212144 139315 FALSE TRUE 196193.6799 185792.6183 207869.6618 198688.1733 210509.763 209807.1839 209658.7394 193249.616 204508.9789 166611.1069 1.177554627 1.115127447 1.24763388 1.192526579 1.26347977 1.25926289 1.258371925 1.159884353 1.227463059 1 17.34612505 -0.872658624 8.156054156 1.000000046 1.210255915 0.643849979 0.047130918 0 0 0.047225628 0.011131187 0.134073015 0.872658624 0.210255868 THSTSS(ph)SLGSGESPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.008)HS(0.048)T(0.048)S(0.212)S(0.52)S(0.165)LGSGESPFSR 151.96 1.48E-07 155490000 40857 88598 113020 89418 107860 119700 106760 85969 103140 90224 TRUE FALSE 42470.06591 103814.0173 115965.394 107104.6135 89525.99573 91901.48907 98391.87223 84816.72617 99428.01155 107901.6654 0.393599726 0.962116914 1.074732199 0.992613165 0.829699852 0.851715205 0.911866114 0.786055766 0.921468739 1 16.71935761 4.741796997 24.94428931 0.913897148 0.393599527 0.785633443 0.083164678 151.1176509 1164677.974 0.022169289 0.1592406 55181.94413 -4.741796997 -0.520297621 THSTSSS(ph)LGSGESPFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THSTSSSLGSGESPFSR 17 0 Q5TH30;Q9UGV2;Q9UGV2-2;F8WBF9;Q9UGV2-3 Q5TH30 NDRG3 Protein NDRG3 1 T(0.002)HS(0.007)T(0.024)S(0.107)S(0.107)S(0.753)LGSGESPFSR;T(0.003)HS(0.018)T(0.024)S(0.172)S(0.172)S(0.612)LGSGESPFSR 164.69 1.65E-09 539520000 111606 152071 190622 161961 204536 228895 182428 184656 166533 142710 TRUE FALSE 116012.2911 178188.0113 195589.7659 193996.4024 169769.0438 175737.6052 168128.8167 182180.9884 160539.5099 170671.2922 0.679741095 1.044042083 1.146002725 1.136666864 0.994713532 1.029684623 0.985103086 1.067437798 0.940635697 1 17.38086088 4.738592871 24.74390734 1.043710896 0.679743903 0.751147759 0.061834455 1.10479818 843370.1124 0.015149449 0.087403479 54776.32239 -4.738592871 -0.363966993 THT(ph)GEKPYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.03)HT(0.97)GEKPYK 75.695 0.05502 40691000 259840 84004 105440 65418 185780 184590 145680 103980 139490 66392 TRUE FALSE 270098.6838 98431.03354 108187.853 78357.48515 154201.182 141721.77 134261.2209 102586.3182 134469.7821 79400.24125 3.401736312 1.239681794 1.362563278 0.986867092 1.942074477 1.784903519 1.690942229 1.292015195 1.693568937 1 16.27685577 4.742632274 24.97035829 1.465314962 3.401737079 0.78048182 0.31134798 182.5223812 1119316.163 0.074175837 0.571579672 55288.17748 -4.742632274 1.936422117 THTDSSEKELEPEAAEEALENGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 0 ; 143.47 1.47E-07 404310000 453280 200764 341230 187471 507540 448320 425740 302125 392492 182813 FALSE TRUE 471175.8444 235243.6553 350122.7341 224552.2043 421268.5321 344204.4744 392369.3863 298075.5086 378366.2896 218631.7072 2.155112131 1.075981422 1.601427069 1.027079773 1.926840976 1.574357529 1.794659116 1.363368161 1.730610324 1 17.73814312 -1.559670034 4.790761186 0.995670961 1.557066815 0.209342666 0.336611641 0.014196022 0.001304788 0.297272522 0.069687278 0.027563221 1.559670034 0.561395855 THTGEKPYQCSECGKAFSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THTGEKPYQCSECGKAFSQK 20 2 Q86T29;Q86T29-2 Q86T29 ZNF605 Zinc finger protein 605 0 62.203 0.024894 465660000 523260 162950 281740 152030 481400 400600 430460 311260 471160 125980 FALSE TRUE 543918.7088 190935.3949 289082.3759 182101.0802 399571.8 307566.7212 396719.4204 307088.0688 454203.0436 150663.369 3.610158943 1.267298058 1.918730331 1.208661943 2.652083268 2.041416724 2.633151131 2.038239759 3.014687955 1 17.20096917 THTGEKPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THTGEKPYR 9 1 Q9HCG1;Q8N8E2-2;M0QZI7;Q8N8E2;Q9UJW8-3;G5E9B8;Q9NX65-3;Q8WXB4;Q9NX65;Q9UJW8;Q9UJW8-4;A0A0A0MP75;A0A1W2PQ54;Q9BSK1-2;O94892;Q86UD4;Q86TJ5;Q9BSK1;Q9NX65-2;Q9UJW8-2;E7EN86;P52747-2;P52747-3;P52747;Q99612;Q499Z4 Q9HCG1;E7EN86;Q99612;Q499Z4 ZNF160;ZNF513;ZNF180;ZSCAN32;ZNF606;ZNF577;ZNF432;ZNF329;ZNF554;ZNF143;KLF6;ZNF672 Zinc finger protein 160;Zinc finger protein 513;Zinc finger protein 180;Zinc finger and SCAN domain-containing protein 32;Zinc finger protein 606;Zinc finger protein 577;Zinc finger protein 432;Zinc finger protein 329;Zinc finger protein 554;Zinc finger protein 143;Krueppel-like factor 6;Zinc finger protein 672 0 65.347 0.040147 21826000 35648 28248 30899 27898 37820 39717 32940 28379 36817 25183 FALSE TRUE 37055.41057 33099.37426 31704.25332 33416.14113 31391.36991 30493.32867 30358.07673 27998.62592 35491.96336 30117.12669 1.230376687 1.09902165 1.052698474 1.109539481 1.042309588 1.012491297 1.008000432 0.929657939 1.178464457 1 14.87829652 8 0.530069271 1.0159315 9.087023633 0.453797719 0.062955975 103.88161 1.010074029 0.030580617 946.779459 100000000 -8 8.071092133 THTMEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 THTMEGK 7 0 P33176;O60282;Q12840 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A 0 ;;;;; 101.64 0.0089085 688977000 1592854 1364826 1517941 1181301 2094980 2162870 1848579 1576019 1760615 1254129 FALSE TRUE 1655741.106 1599224.249 1557499.789 1414958.812 1738876.048 1660576.221 1703682.548 1554895.043 1697250.81 1499851.566 1.103936645 1.066255012 1.038435953 0.94339923 1.159365425 1.107160374 1.135900769 1.036699283 1.13161252 1 20.5163883 4.743937519 21.14748287 1.070601354 1.103936762 0.026004851 0.063694415 347.3018233 1365521.399 0.015090726 0.121220667 55454.59253 -4.743937519 0.033335408 THTRVS(ph)VQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 THTRVSVQR 9 1 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 THTRVS(1)VQR;THTRVS(1)VQR;THTRVS(1)VQR;T(0.003)HT(0.003)RVS(0.994)VQR;T(0.001)HT(0.005)RVS(0.994)VQR;THTRVS(1)VQR 141.08 6.51E-05 4669540000 1021658 1103670 1180254 1055348 1505643 1625003 1161985 1158504 1068317 1153556 TRUE FALSE 1061993.847 1293216.737 1211012.389 1264092.685 1249714.341 1247620.68 1070905.579 1142976.149 1029868.48 1379573.212 0.769798832 0.937403485 0.877816689 0.91629257 0.905870257 0.904352643 0.776258607 0.828499813 0.746512379 1 20.39579059 2.256140988 24.99425825 0.822370793 0.889635756 0.070114843 0.075791561 423.1129891 601544.4788 0.024231212 0.020230547 180.3603161 -2.256140988 0.067264963 THTTALAGRS(ph)PS(ph)PASGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 THTTALAGRSPSPASGR 17 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 T(0.001)HT(0.001)T(0.001)ALAGRS(0.994)PS(0.917)PAS(0.086)GR;THTTALAGRS(0.989)PS(0.933)PAS(0.078)GR;THTTALAGRS(0.986)PS(0.994)PAS(0.02)GR;THTTALAGRS(0.999)PS(1)PASGR;THTTALAGRS(0.999)PS(0.994)PAS(0.006)GR;T(0.002)HT(0.002)T(0.002)ALAGRS(0.995)PS(0.999)PASGR 94.707 0.001564 12939100000 1351104 4170073 4111885 3532906 4552840 5724164 3446653 3992040 3464397 4002925 TRUE FALSE 1404446.629 4886250.599 4219044.101 4231704.262 3778949.883 4394813.662 3176495.332 3938533.233 3339714.029 4787221.513 0.293374064 1.02068613 0.881313741 0.883958315 0.789382708 0.918030145 0.663536317 0.822717984 0.697630979 1 22.19075713 4.750579686 24.8399257 0.839898625 0.293373701 0.696309534 0.110575036 959.5138605 1982996.623 0.025659525 0.4283213 56309.24258 -4.750579686 -0.546524924 THTTALAGRS(ph)PS(ph)PASGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 THTTALAGRSPSPASGRR 18 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;I3L1I8;Q9UQ35-3;A0A087X1W1 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 THTTALAGRS(0.994)PS(0.858)PAS(0.147)GRR;THTTALAGRS(1)PS(0.997)PAS(0.004)GRR 112.85 0.00014156 244800000 29246 75268 67696 58428 79186 103815 60116 69520 70953 89103 TRUE FALSE 30400.65466 88194.6935 69460.21337 69984.88401 65725.992 79705.53958 55403.95084 68588.19811 68399.41539 106561.0269 0.28528868 0.827644929 0.65183506 0.656758724 0.616792029 0.747980213 0.519926961 0.643651813 0.64188022 1 16.70132036 0.466046119 2.540067697 0.999997641 0.628401537 0.410218843 0.136086579 11.05819612 51.22412592 0.118043411 0.031415149 2.92446292 -0.466046119 -0.371596104 THVADFAPEVAWVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;;; 170.45 1.14E-06 2126100000 1271210 1427610 1419120 1442320 1680760 1965760 1514120 1438420 1417620 1312050 FALSE TRUE 1321398.352 1672790.912 1456103.433 1727606.591 1395065.016 1509242.031 1395439.318 1419140.333 1366600.133 1569121.077 0.842126444 1.066068729 0.927973918 1.101002731 0.889074168 0.961839117 0.889312711 0.904417354 0.870933514 1 20.58152525 THVEKEDGEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 THVEKEDGEAR 11 1 Q13573;G3V4X8;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 ;;; 146.16 2.16E-05 693470000 613601 588030 604984 500970 772404 845890 598452 560454 670369 534010 FALSE TRUE 637826.4413 689019.5783 620750.38 600060.3708 641111.044 649444.8671 551543.7685 552942.0308 646242.5506 638639.0353 0.998727616 1.078887353 0.971989411 0.939592379 1.003870745 1.016920093 0.86362364 0.865813081 1.011905811 1 19.28464121 2.254338084 24.99883888 0.91574086 1.00110468 0.217259654 0.057009942 277.5976022 439842.7022 0.02032603 0.016952102 179.613131 -2.254338084 0.08536382 THVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 THVSEK 6 0 A0A0C4DGB5;H0Y944;E7EN75;D6RGF7;D6RBR1 A0A0C4DGB5 CAST 0 ;; 122.15 0.019343 341465000 144420 554859 584761 534378 682362 731010 613993 681142 596285 580624 FALSE TRUE 150121.8131 650151.717 600000.352 640076.3734 566374.351 561244.0061 565866.6243 672012.4056 574824.8193 694386.1561 0.216193557 0.936297061 0.864073033 0.921787348 0.815647527 0.80825921 0.814916339 0.967779095 0.827817223 1 19.40537866 4.741519247 24.93959598 0.880038827 0.216193307 0.902165781 0.065968537 74.03464797 624038.1299 0.015334582 0.108284962 55146.66416 -4.741519247 -0.66384552 THYDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THYDAK 6 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 122.98 0.018986 75726000 220820 171180 220880 179000 273140 267560 296780 222740 222160 142510 FALSE TRUE 229538.1441 200578.8334 226636.3143 214405.6657 226711.7604 205423.2449 273517.6081 219754.5346 214164.505 170432.106 1.346801078 1.176884087 1.329774768 1.258012183 1.330217444 1.205308376 1.604847904 1.289396346 1.256597187 1 17.37883761 0.802908471 2.801889561 1.000229814 1.319828712 0.428815067 0.109708375 0.865495779 10.64284293 0.103021467 0.027182226 6.351970482 -0.802908471 0.319598898 THYDPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 THYDPPR 7 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;H0YBD7;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 ;;;;; 101.64 0.0089085 2945530000 1575610 1789350 1767040 1634010 1986800 2428280 1864070 1777090 1758220 1654470 FALSE TRUE 1637816.299 2096656.943 1813090.514 1957212.301 1649084.446 1864348.771 1717959.323 1753271.015 1694942.006 1978631.72 0.827751968 1.05964992 0.916335514 0.989174631 0.833446886 0.942241425 0.868256233 0.886102754 0.856623286 1 20.91607168 3.252136825 24.99990631 0.891813374 0.953908674 0.104836812 0.070165549 415.0371051 764264.9657 0.017694264 0.023829442 1787.050497 -3.252136825 0.062095301 THYDPPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 76.827 0.022587 1051310000 723190 770450 818400 762110 903320 1016310 844610 840730 814010 767750 FALSE TRUE 751742.0996 902768.7942 839728.1763 912853.0833 749773.9891 780287.4048 778407.2612 829461.3895 784713.9391 918175.913 0.818734285 0.983219862 0.914561321 0.994202821 0.816590784 0.849823431 0.847775737 0.9033796 0.85464444 1 19.80841106 5.041251025 12.86149058 0.899998031 0.543055209 0.140313454 0.063468664 389811.0349 4212845.384 0.014984819 3072227.495 109964.1255 -5.041251025 -0.356942822 THYPAQQGEYQTHQPVYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 THYPAQQGEYQTHQPVYHK 19 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 0 254.72 2.28E-31 119110000 133230 110260 138750 112600 146750 168070 155160 136080 151250 116440 FALSE TRUE 138490.0233 129196.2973 142365.939 134871.9439 121805.4874 129038.2896 142998.1538 134256.0702 145806.542 139254.1886 0.994512443 0.92777315 1.02234583 0.968530608 0.874698913 0.92663848 1.026885835 0.964107949 1.047053187 1 17.0873612 2.237978869 24.99999988 1.002703836 0.951674853 0.294552824 0.042761621 23.37547903 1004463.034 0.016063962 0.012581627 172.9732195 -2.237978869 -0.051028983 TIADHCPDSACK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIADHCPDSACK 12 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ; 140.24 5.95E-05 418440000 553620 416018 436476 443540 544160 675360 631750 511860 468160 330789 FALSE TRUE 575477.3451 487465.8553 447850.9231 531270.8882 451663.8776 518517.8752 582231.7842 504999.3539 451311.0131 395600.7712 1.454692172 1.232216646 1.132077983 1.342947049 1.141716373 1.310709971 1.47176605 1.27653784 1.140824401 1 18.59368571 1.037635864 3.038819405 1.002776028 1.292981444 0.444055624 0.106618888 0.211315881 4.306531601 0.102355931 0.027033678 10.90525597 -1.037635864 0.290205417 TIADHCPDSACKQDLLAYLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIADHCPDSACKQDLLAYLQR 21 1 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 0 ; 137.12 2.29E-06 471090000 391400 436190 361195 296564 491980 518170 278538 356100 394920 498170 FALSE TRUE 406852.7742 511102.2394 370608.0384 355223.474 408353.4153 397832.8704 256705.4637 351327.062 380706.9063 595776.8735 0.68289454 0.857875259 0.62205845 0.596235755 0.685413338 0.667754806 0.430875174 0.589695703 0.639009205 1 19.1844126 -0.9325532 5.680416205 1.000000315 0.635147953 0.533449754 0.10048417 4.30E-07 8.07E-08 0.10434379 0.024594046 0.116801064 0.9325532 -0.364852362 TIADLELHYQEFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIADLELHYQEFIR 14 0 P15924;P15924-3;P15924-2 P15924 DSP Desmoplakin 0 ; 146 8.43E-06 198498000 167084 189717 188038 181688 216200 253775 193032 202061 183472 189311 FALSE TRUE 173680.6053 222299.419 192938.4248 217625.3441 179450.4012 194839.6022 177901.6474 199352.7028 176868.8786 226402.8659 0.767130772 0.981875464 0.852190735 0.961230518 0.792615414 0.860588056 0.785774715 0.880521994 0.781213073 1 17.78853269 3.22694414 24.99702818 0.84284978 0.894382061 0.051103035 0.08130621 529.949568 1140374.516 0.021272873 0.025622119 1686.336112 -3.22694414 0.051532281 TIAPTGHLHTVEFHQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIAPTGHLHTVEFHQQR 17 0 Q96FX7;H0Y2Q1 Q96FX7 TRMT61A tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 0 ; 71.781 0.010354 105764000 23078.4 66932 51025 54496 50493 72622 51892 58265 45362 65700 FALSE TRUE 23989.55305 78427.05034 52354.75342 65275.14615 41910.2179 55756.6411 47824.56945 57484.05298 43729.43048 78572.6571 0.30531681 0.998146852 0.666322807 0.830761598 0.533394433 0.709618882 0.608666821 0.731603781 0.556547686 1 16.26173973 -2.193256635 2.334518621 1.918530689 0.675038703 0.248566786 0.175591172 11748414.86 2475671.607 57013692.26 0.038372072 0.006408308 2.193256635 -1.243491986 TIDDLEDKLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIDDLEDKLK 10 1 P06753-2;A0A087WWU8;P06753-5;P06753-7;J3KN67 P06753-2;J3KN67 TPM3 Tropomyosin alpha-3 chain 0 ; 169.58 4.19E-06 2124100000 5029600 1799900 2936600 1679700 4785100 3858100 4071500 2879700 3349400 1535210 FALSE TRUE 5228172.492 2109018.824 3013130.208 2011939.647 3971730.411 2962114.745 3752365.191 2841102.332 3228855.748 1836005.006 2.847580739 1.148699931 1.641133983 1.095824706 2.16324596 1.613347859 2.043766318 1.547437138 1.758631233 1 20.80813856 -0.2568981 1.076752701 0.990332464 1.731406581 0.180543195 0.482789328 34.94185974 27.11503903 1.94331242 0.13220729 0.553479959 0.2568981 0.741074118 TIDDLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TIDDLEEK 8 0 P67936;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 164.77 0.00076339 984320000 1722030 1301480 1404510 1115230 1911100 2106300 1829410 1509680 1536970 1114940 FALSE TRUE 1790017.074 1524999.066 1441112.684 1335819.165 1586251.905 1617143.746 1686016.064 1489445.209 1481654.75 1333391.146 1.342454597 1.143699709 1.080787651 1.001820935 1.189637346 1.212805223 1.264457222 1.117035472 1.111192882 1 20.34666862 0.926749309 1.849964094 1.001620301 1.165983862 0.254565639 0.089477803 0.644438846 4.564170015 0.088365421 0.02496034 8.447910596 -0.926749309 0.164363561 TIDLGAAAHYTGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIDLGAAAHYTGDK 14 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 197.19 2.38E-08 486850000 776080 716290 787100 709380 1025070 997480 947540 864970 887500 613210 FALSE TRUE 806720.2377 839307.2355 807612.4726 849693.2467 850828.9675 765830.387 873269.3389 853376.492 855559.0484 733356.7589 1.100037912 1.144473308 1.101254557 1.158635598 1.160184259 1.044280806 1.190783787 1.163658044 1.166634163 1 19.48415568 TIDLGAAAHYTGDKAS(ph)PDQNASTHTPQSSVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TIDLGAAAHYTGDKASPDQNASTHTPQSSVK 31 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 1 TIDLGAAAHYTGDKAS(0.999)PDQNAS(0.001)THTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK;TIDLGAAAHYTGDKAS(1)PDQNASTHTPQSSVK 328.78 7.84E-106 7137860000 1404120 1605043 2076880 1535690 3046190 2733040 2767170 2507680 2702410 1412280 TRUE FALSE 1459555.742 1880696.65 2131005.199 1839444.898 2528399.712 2098332.88 2550271.985 2474068.651 2605150.792 1688989.226 0.864159297 1.113504231 1.261704436 1.089080303 1.49698984 1.242360133 1.509939759 1.464822044 1.542431859 1 20.68772869 5.072100798 0.579435765 1.410307931 0.320751463 0.429037528 0.1715791 4.337765005 0.83841002 0.077674108 3.443369848 118059.4614 -5.072100798 -1.089556468 TIDQIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TIDQIHK 7 0 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7;H7C044 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 ;;; 114.93 0.0057939 1479410000 2377840 2008620 2283390 1903320 2877840 2855220 2566130 2348390 2452530 1897400 FALSE TRUE 2471718.959 2353584.86 2342897.019 2279791.015 2388665.785 2192138.426 2364990.025 2316913.673 2364263.924 2269159.202 1.089266437 1.037205701 1.032495656 1.004685354 1.052665579 0.966057571 1.042231864 1.021045007 1.041911877 1 21.1137264 5.082749645 1.306998021 1.020007459 1.178644746 0.435846513 0.023835015 2.66924126 2.202254083 0.006093872 0.699684988 120990.047 -5.082749645 0.158637286 TIEAEAAHGTVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIEAEAAHGTVTR 13 0 P48735;P48735-2;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 209.25 3.94E-08 215480000 145230 338490 262010 327080 230370 406790 260760 258530 246540 308990 FALSE TRUE 150963.7925 396623.0244 268838.1958 391775.4478 191211.7897 312319.1875 240320.9498 255064.8282 237667.0736 369530.6745 0.408528447 1.073315564 0.72751253 1.060197366 0.517444972 0.845177976 0.650341004 0.690239934 0.643159256 1 18.4953346 TIEDAIAVLSVAEEAADRHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 ;;;;; 184.35 2.37E-17 794494000 237465 289137 289737 269578 339862 339996 302932 305544 299408 302024 FALSE TRUE 246840.3016 338794.0306 297287.7842 322899.7238 282092.3786 261037.0817 279187.3983 301448.6824 288632.3646 361199.8202 0.683389879 0.937968436 0.823056291 0.893964243 0.780987041 0.722694384 0.772944455 0.834575948 0.799093323 1 18.46243765 -1.975793627 6.26595124 1.134176763 0.809737471 0.40333283 0.070827604 0.046229078 0.00017859 0.023880049 0.015597314 0.010573198 1.975793627 -0.324439293 TIEDAIAVLSVAEEAADRHPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIEDAIAVLSVAEEAADRHPERR 23 2 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 52.509 0.070823 10404000 5126.2 9799.2 6656.9 3684 8759.2 10591 2798.7 7338.6 7800.7 13495 FALSE TRUE 5328.586334 11482.13637 6830.384283 4412.684204 7270.314313 8131.400758 2579.330581 7240.238071 7519.954331 16139.08687 0.330166531 0.711448948 0.423219996 0.273415977 0.450478665 0.503832765 0.159818867 0.4486151 0.465946704 1 13.97827133 0.627320448 2.537556677 0.999954259 0.412741714 0.617153872 0.13798836 2.232517058 14.4081529 0.131063202 0.034918771 4.239556706 -0.627320448 -0.587212545 TIEDLDENQLKDEFFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIEDLDENQLKDEFFK 16 1 Q9H993;F5GZY1 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 107.46 0.0010268 32402000 43753 18470 28674 27459 44631 44725 50269 34963 39972 15055 FALSE TRUE 45480.40222 21642.07882 29421.268 32890.30824 37044.63856 34338.29656 46328.78443 34494.37817 38533.41553 18004.739 2.526023966 1.202021247 1.63408467 1.826758401 2.057493783 1.907181024 2.573143905 1.915849942 2.140181844 1 14.13608907 3.390617859 4.238089661 2.014710732 1.728497888 0 0.479936703 0.608994154 20.40190122 0.126610651 0.17559262 2458.203651 -3.390617859 -0.286212844 TIEELSNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIEELSNAR 9 0 Q15643-2;Q15643;H0YJ97 Q15643-2 TRIP11 Thyroid receptor-interacting protein 11 0 64.485 0.069257 877570000 55473 1420700 909850 1327900 590160 1397000 588680 977540 690140 1602500 FALSE TRUE 57663.11687 1664694.173 933561.4385 1590554.657 489844.814 1072567.922 542537.7234 964437.6752 665301.9962 1916479.193 0.030088047 0.868621052 0.48712318 0.829935781 0.255596208 0.559655396 0.28309085 0.503234096 0.34714804 1 20.8700269 -1.531584392 3.436456923 1.01284244 0.47714253 0.304617878 0.242652503 209434980.8 273506391.4 25039148.36 0.053448044 0.029404622 1.531584392 -0.53569991 TIEGQS(ph)PEPVFGDADVDVSAVQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TIEGQSPEPVFGDADVDVSAVQAK 24 0 Q9Y2I9;F8VZ81;Q9Y2I9-2 Q9Y2I9 TBC1D30 TBC1 domain family member 30 1 T(0.015)IEGQS(0.985)PEPVFGDADVDVSAVQAK;T(0.001)IEGQS(0.999)PEPVFGDADVDVSAVQAK;T(0.166)IEGQS(0.834)PEPVFGDADVDVSAVQAK;T(0.119)IEGQS(0.881)PEPVFGDADVDVSAVQAK 213.47 5.07E-26 618300000 298432 233769 303894 240027 355752 357143 308662 309548 308487 227235 TRUE FALSE 310214.3258 273917.0073 311813.7273 287503.6242 295281.4021 274201.9508 284468.2659 305399.0154 297384.6131 271757.3476 1.141512193 1.007947015 1.147397596 1.057942414 1.086562718 1.008995537 1.046773044 1.123793039 1.094302015 1 18.05195952 TIEGSS(ph)PADNRYSEYAEEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TIEGSSPADNRYSEYAEEFSK 21 1 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 T(0.008)IEGS(0.233)S(0.757)PADNRYS(0.001)EYAEEFSK;TIEGS(0.255)S(0.745)PADNRYSEYAEEFSK;TIEGS(0.168)S(0.832)PADNRYSEYAEEFSK 151.42 3.76E-08 474440000 632570 532550 637510 486410 774080 771240 735070 672570 733450 547970 TRUE FALSE 657544.3521 624011.3198 654124.0343 582620.4462 642502.1581 592131.1983 677453.2927 663555.2993 707053.2778 655334.23 1.003372511 0.952203153 0.998153315 0.889043208 0.980419042 0.903556035 1.033752338 1.012544849 1.078920107 1 19.32187136 2.212899745 24.95405313 1.030277918 0.954548204 0.478199798 0.039319813 187.0903086 181935.8084 0.013957564 0.010312107 163.267501 -2.212899745 -0.075729713 TIEKFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 114.28 0.0054175 38384980000 16877210 11272830 15682740 8526050 21181120 17242040 14638400 14180130 17574460 10772380 FALSE TRUE 17543535.28 13208850.86 16091445.09 10212477.24 17580760.79 13237837.52 13491003.96 13990068.55 16941958.62 12883021.61 1.361756257 1.025291369 1.249042777 0.792708229 1.364645758 1.027541358 1.047192527 1.08593069 1.315060948 1 23.61896767 4.749682607 23.44162741 1.101229255 1.361756626 0.192678853 0.160232384 1061.711628 2237645.442 0.034746613 0.4953093 56193.05029 -4.749682607 0.260527371 TIELDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIELDGK 7 0 Q9H0U4;E9PLD0;H0YMN7;H0YNE9;Q92930;P61006-2;P61006;P62820;P62820-3 Q9H0U4;P62820 RAB1B;RAB8B;RAB8A;RAB1A Ras-related protein Rab-1B;Ras-related protein Rab-8B;Ras-related protein Rab-8A;Ras-related protein Rab-1A 0 87.616 0.044693 70108000 217430 213920 209740 201850 266220 303010 213500 219370 203380 230670 FALSE TRUE 226014.3043 250659.0959 215205.9967 241775.3275 220968.0195 232640.5197 196765.3121 216429.704 196060.3935 275865.3701 0.819292049 0.90862835 0.780112403 0.876425075 0.800999486 0.843311792 0.713265721 0.784548289 0.710710422 1 18.07360484 TIET(ph)SPSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIETSPSLSR 10 0 F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1;H3BP78 F8W7R3 FANCI Fanconi anemia group I protein 1 TIET(0.571)S(0.181)PS(0.248)LSR 135.16 0.0016936 196150000 373610 519320 541030 460590 524190 631800 477070 474990 489010 699430 TRUE FALSE 388360.4113 608509.1703 555129.6863 551693.3273 435088.371 485074.025 439676.0068 468623.536 471410.6256 836469.9171 0.464284971 0.727472869 0.663657682 0.659549514 0.520148259 0.579906121 0.525632779 0.560239557 0.563571524 1 19.67395413 -1.386642982 3.542882745 1.002769358 0.587032565 0.73641081 0.074486968 3647187.581 1904468.253 75031.09874 0.017632969 0.041054146 1.386642982 -0.415736793 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TIFTGHTAVVEDVSWHLLHESLFGSVADDQK 31 0 Q09028-3;Q09028;Q09028-2;Q09028-4 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 ;; 148.02 5.03E-09 853990000 145309.8 470050 525620 449710 583647 564760 466864 467886 553660 478540 FALSE TRUE 151046.7431 550777.431 539318.089 538661.2957 484438.8914 433603.049 430269.9798 461614.7535 533733.8848 572300.7508 0.263928962 0.962391593 0.942368306 0.941220669 0.846476072 0.757648926 0.751824944 0.806594702 0.932610841 1 19.12641397 4.744153493 24.97741431 0.866333718 0.263928702 0.826513053 0.084713344 261.3749229 1167248.173 0.021908609 0.19322187 55482.17692 -4.744153493 -0.602405016 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_MDA-MB-175_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 1 TIGGGDDS(0.49)FNT(0.49)FFS(0.021)ETGAGK;TIGGGDDS(1)FNTFFSETGAGK;TIGGGDDS(1)FNTFFSETGAGK;T(0.146)IGGGDDS(0.842)FNT(0.012)FFSETGAGK 395.16 3.68E-131 662010000 1023304 818547 1054691 890144 1302324 1338296 1211639 1046245 1131148 775553 TRUE FALSE 1063704.832 959126.0798 1082177.114 1066211.826 1080955.432 1027497.036 1116667.569 1032221.797 1090438.204 927507.7615 1.146841974 1.034089546 1.166758014 1.14954491 1.165440848 1.107804246 1.203944178 1.112898285 1.175664776 1 19.82299983 4.213775512 24.99999155 1.141903924 1.090465629 0.07602623 0.058920533 390.0054283 393386.9053 0.013048972 0.028208881 16359.70665 -4.213775512 -0.051438295 TIGGGDDSFNTFFSETGAGK ddPTM_MDA-MB-175_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 ;;; 344.38 1.01E-80 505229000 837388 641197 849453 641628 1125490 1110672 954838 870734 954126 631373 FALSE TRUE 870448.7248 751317.5969 871590.443 768540.1033 934179.6118 852735.2604 879995.3026 859063.235 919787.1916 755078.451 1.152792433 0.995019254 1.154304486 1.017828151 1.237195434 1.129333329 1.165435593 1.137713881 1.218134606 1 19.52626702 3.249074699 24.99954346 1.153873187 1.079225499 0.158755632 0.075931154 334.1119613 794420.2249 0.019044642 0.025513553 1774.494669 -3.249074699 -0.074647688 TIISYIDEQFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TIISYIDEQFER 12 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310;C9IZU3;C9JQJ4 Q15019-2 2-Sep Septin-2 0 ;;;;; 236.35 1.05E-15 764295800 524714 644515 709208 632619 824325 819568 752105 714793 720392 620278 FALSE TRUE 545430.1139 755205.4376 727690.5431 757749.15 684206.5309 629235.7527 693153.0448 705212.369 694465.2326 741809.5982 0.735269691 1.018058326 0.98096674 1.02148739 0.922347908 0.848244286 0.934408299 0.950664929 0.9361772 1 19.50068941 0.437521228 1.158195099 0.999951616 0.931977274 0.066979165 0.079969489 7.63572376 12.60114994 0.074891691 0.022755157 2.738553489 -0.437521228 -0.067974342 TIPWLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIPWLEDR 8 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 153.71 0.0010159 247090000 195168 251010 193171 291070 196863 282190 296260 221740 184561 233790 FALSE TRUE 202873.3833 294119.0149 198205.195 348642.7772 163400.2976 216655.6491 273038.3671 218767.938 177918.6857 279596.6743 0.725592977 1.051940319 0.708896826 1.246948942 0.58441431 0.77488636 0.976543686 0.782441131 0.636340493 1 18.09298768 3.195353418 24.99999954 0.793622299 0.925788523 0.118943332 0.187406744 309.2235384 178917.9907 0.051182703 0.061175407 1568.026571 -3.195353418 0.132166223 TIPWLEDRVPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ; 158.34 6.72E-05 2593600000 970950 853400 880480 932130 1166090 1301420 1182420 940120 966000 893400 FALSE TRUE 1009283.856 999964.8115 903426.0321 1116502.532 967878.4383 999184.9282 1089738.831 927519.2291 931233.8487 1068444.625 0.944629073 0.935907007 0.845552508 1.044979315 0.905876089 0.935177084 1.019930098 0.868102293 0.871578954 1 20.02708071 5.965948419 2.957970567 0.932981074 9.781220855 0 0.064005721 23766.33805 309.8495788 0.015500602 1424278.332 924588.3546 -5.965948419 8.848239782 TIQEVLEEQS(ph)EDEDR ddPTM_MDA-MB-175_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 375.7 8.73E-98 431990000 265517 253546 248359 328538 271472 356180 328354 287514 248601 226687 TRUE FALSE 275999.8162 297090.5532 254831.4396 393521.8358 225327.2864 273462.593 302616.7555 283660.3451 239653.8986 271101.9775 1.018066407 1.09586273 0.939983699 1.451563871 0.831153238 1.008707482 1.11624695 1.046323408 0.88399908 1 18.04847611 TIQEVLEEQS(ph)EDEDREAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 264.97 3.18E-31 1814390000 613906 392484 463973 385777 647104 671067 608548 530408 465939 365196 TRUE FALSE 638143.4829 459890.0739 476064.5175 462082.5392 537109.4932 515221.8594 560848.4176 523298.7483 449169.9464 436749.1641 1.461121246 1.05298444 1.090018154 1.058004404 1.229789402 1.179674517 1.284143082 1.198167716 1.028439167 1 18.73644542 1.210309193 6.399234073 1.009639241 1.187487922 0.28278621 0.114385854 0.241092867 30.51059362 0.100522506 0.0271421 16.22965146 -1.210309193 0.177848681 TIQEVLEEQS(ph)EDEDREAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIQEVLEEQSEDEDREAKR 19 2 P18858;P18858-3;P18858-2;M0R0Q7 P18858 LIG1 DNA ligase 1;DNA ligase 1 TIQEVLEEQS(1)EDEDREAKR 145.65 6.43E-08 431710000 218530 153440 183820 129580 232560 262430 192110 173700 177410 152670 TRUE FALSE 227157.7331 179792.1264 188610.5002 155210.5372 193029.5343 201484.6097 177051.9162 171371.8356 171025.0488 182582.7635 1.244135694 0.984715769 1.033013723 0.850083186 1.057216632 1.103524812 0.969707725 0.938598104 0.936698763 1 17.47819105 4.738636232 9.841503318 0.98424058 1.244831875 0.572744548 0.066883726 0.055561321 162.8854101 0.016414305 0.095428018 54781.79172 -4.738636232 0.260591295 TIQGDEEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIQGDEEDLR 10 0 P54920;M0R0Y2;M0R213 P54920 NAPA Alpha-soluble NSF attachment protein 0 ; 182.46 4.13E-06 613790000 762460 884210 842430 840690 962470 1131830 885910 925610 816770 799000 FALSE TRUE 792562.5095 1036066.189 864384.4179 1006975.973 798869.6932 868979.6355 816470.0593 913203.7119 787374.6072 955548.7522 0.829431787 1.084263034 0.904594785 1.053819568 0.836032375 0.909403768 0.854451494 0.955685107 0.824002549 1 19.86596996 3.228265646 24.99996576 0.896319087 0.971798963 0.149715082 0.08320019 352.9764107 857155.1163 0.021836567 0.026372481 1691.475245 -3.228265646 0.075479876 TIS(ph)AQDTLAYATALLNEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 T(0.231)IS(0.769)AQDTLAYATALLNEK;T(0.003)IS(0.997)AQDTLAYATALLNEK;T(0.145)IS(0.855)AQDTLAYATALLNEK;T(0.123)IS(0.877)AQDTLAYATALLNEK;T(0.112)IS(0.888)AQDTLAYATALLNEK 245.66 3.31E-24 2662650000 741848 505973 772712 639805 951165 1029673 989854 813153 851328 507583 TRUE FALSE 771136.7319 592869.9268 792849.5095 766356.5194 789486.313 790547.0506 912266.657 802254.0141 820688.8716 607034.1706 1.270334965 0.97666648 1.30610359 1.262460264 1.300563216 1.302310626 1.502825872 1.321596136 1.351964867 1 19.2114182 4.132907015 9.87238171 1.31617329 1.123931089 0.187681237 0.135122533 0.356632802 30.3969779 0.031234238 0.067664843 13580.22655 -4.132907015 -0.1922422 TIS(ph)DGTISASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.997)DGT(0.003)ISASK;T(0.007)IS(0.94)DGT(0.048)IS(0.004)ASK 142.76 3.93E-05 411540000 1129800 897610 1119830 913890 1399600 1330500 1264920 1131160 1278960 783210 TRUE FALSE 1174405.376 1051767.535 1149013.69 1094654.714 1161696.492 1021511.539 1165772.265 1115998.65 1232930.479 936665.004 1.253815795 1.122885483 1.226707184 1.168672588 1.240247567 1.09058365 1.244598934 1.191459749 1.316298222 1 19.83717364 7.432703398 4.825029924 1.19106445 1.229179769 0 0.088277116 0 0 0.017218168 0 27083413.38 -7.432703398 0.03811532 TIS(ph)EPDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TISEPDEQR 9 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 T(0.017)IS(0.983)EPDEQR;T(0.352)IS(0.648)EPDEQR;T(0.001)IS(0.999)EPDEQR;T(0.001)IS(0.999)EPDEQR 157.25 7.24E-05 7844600000 1956995 3058510 2942720 3018360 2916960 3602920 3185976 3022760 2808250 2728360 TRUE FALSE 2034258.674 3583785.301 3019409.701 3615382.599 2421136.181 2766196.433 2936250.876 2982244.846 2707181.631 3262929.904 0.623445411 1.098333524 0.925367626 1.108017244 0.742012931 0.84776459 0.89988169 0.913977601 0.829678145 1 21.63773656 4.763218859 23.86195608 0.922147904 0.623444735 0.41369857 0.108974674 4065.035831 3933645.242 0.025591249 1.58721465 57972.07679 -4.763218859 -0.298703169 TIS(ph)EPDEQRSELPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TISEPDEQRSELPR 14 1 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 TIS(1)EPDEQRSELPR;T(0.003)IS(0.997)EPDEQRSELPR;T(0.032)IS(0.968)EPDEQRSELPR;T(0.002)IS(0.998)EPDEQRSELPR 216.19 3.77E-12 4011920000 1661910 1984980 1947030 1358570 2403760 2375910 1389660 1759060 2061350 2213660 TRUE FALSE 1727523.49 2325884.874 1997771.201 1627291.091 1995169.734 1824140.91 1280734.818 1735482.678 1987162.416 2647384.294 0.652539752 0.878559595 0.75462078 0.614678834 0.753638124 0.689035179 0.483773671 0.655546186 0.75061351 1 21.3361362 0.873260242 4.428075396 0.99996175 0.68336129 0.484514217 0.097194331 0.769043738 25.5485101 0.099310306 0.02523771 7.468961858 -0.873260242 -0.31660046 TIS(ph)NPEVVMK ddPTM_MDA-MB-175_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(0.009)IS(0.991)NPEVVMK;T(0.034)IS(0.966)NPEVVMK;T(0.005)IS(0.995)NPEVVMK;T(0.003)IS(0.997)NPEVVMK;T(0.001)IS(0.999)NPEVVMK;TIS(1)NPEVVMK;TIS(1)NPEVVMK 171.95 4.05E-06 1466850000 3580130 2660870 3862070 2720120 5020400 4331800 4465040 3761830 4262280 2535990 TRUE FALSE 3721476.297 3117853.724 3962718.717 3258151.617 4167034.201 3325805.099 4115058.498 3711408.822 4108881.375 3032868.686 1.227048277 1.028021338 1.30659093 1.074280477 1.373958002 1.096587239 1.35682053 1.223728821 1.354783804 1 21.5322516 3.25730597 24.99988833 1.245853477 1.160174003 0.06838604 0.132119749 586.1556692 781726.1476 0.033148851 0.044805125 1808.447768 -3.25730597 -0.085679474 TIS(ph)PSTSNNIPLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TISPSTSNNIPLMR 14 0 F8WBA3;Q15139;O94806;O94806-2 F8WBA3;O94806 PRKD1;PRKD3 Serine/threonine-protein kinase;Serine/threonine-protein kinase D1;Serine/threonine-protein kinase D3 1 TIS(0.999)PS(0.001)TSNNIPLMR;TIS(1)PSTSNNIPLMR;T(0.131)IS(0.418)PS(0.304)T(0.074)S(0.074)NNIPLMR;T(0.008)IS(0.64)PS(0.217)T(0.047)S(0.088)NNIPLMR 294.18 1.52E-43 817111000 358086 408705 383717 397863 433622 496308 415328 405883 390029 377395 TRUE FALSE 372223.5118 478896.9045 393716.9802 476559.1139 359915.0873 381047.9886 382773.5061 400442.8023 375991.9325 451338.3246 0.824710625 1.061059694 0.872332259 1.055880008 0.797439676 0.844262425 0.848085539 0.887234211 0.833060062 1 18.78384976 3.224472854 24.99999977 0.862032831 0.955381436 0.195791114 0.083923765 322.8855359 572988.2023 0.022026834 0.02644744 1676.767526 -3.224472854 0.093348605 TIS(ph)QSSSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TISQSSSLK 9 0 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 T(0.001)IS(0.999)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(1)QSSSLK;TIS(0.999)QS(0.001)SSLK 232.56 1.31E-08 3987200000 2952970 2488760 3238790 2568530 4808920 4357150 4192380 3770380 3981680 3024280 TRUE FALSE 3069555.536 2916185.17 3323195.528 3076577.568 3991501.496 3345267.946 3863770.301 3719844.223 3838380.115 3616829.763 0.848686761 0.80628212 0.918814472 0.850628249 1.103591199 0.924917169 1.068275411 1.028481977 1.061255399 1 21.78629426 3.252833762 24.99999421 1.029913574 0.857023614 0.736357239 0.051290038 115.2246939 201819.5475 0.013503012 0.018197865 1789.920581 -3.252833762 -0.172889961 TISINS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.01)INS(0.99)PK;TISINS(1)PK;TIS(0.006)INS(0.994)PK;TIS(0.014)INS(0.986)PK 133.85 0.0009457 2002210000 5092580 2526220 3125570 2396600 4482030 5001430 4033490 3357830 3509110 2030600 TRUE FALSE 5293638.991 2960078.634 3207024.922 2870640.327 3720176.142 3839923.68 3717334.514 3312823.781 3382817.817 2428457.192 2.179836239 1.218913244 1.320601793 1.182083974 1.531909294 1.581219423 1.530739157 1.364168079 1.392990508 1 21.21160862 -3.408887653 0.206355712 4.86E-17 1.539521995 0.253880089 0.261177619 106.4219052 1.909192782 46.37842555 0.595612197 0.000390043 3.408887653 1.539521995 TITGFQTHTTPVLLAHGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TITGFQTHTTPVLLAHGER 19 0 Q13200;Q13200-3;Q13200-2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 185.61 1.29E-14 2132050000 760840 1023460 913610 962640 1213540 1518110 969760 978710 1148760 1046890 FALSE TRUE 790878.5507 1199231.294 937419.4271 1153047.319 1007262.904 1165551.96 893747.6772 965591.9933 1107416.352 1252008.052 0.631688071 0.957846311 0.748732747 0.920958389 0.804517913 0.930946058 0.713851381 0.771234651 0.884512165 1 20.25581241 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_MDA-MB-175_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(0.96)PIS(0.04)VPGGSALISNLGK;TIT(0.001)LVKS(0.987)PIS(0.011)VPGGSALISNLGK 232.47 3.93E-34 1289690000 1540290 752850 1094720 715100 1714780 1428680 1352430 1182130 1347860 754710 TRUE FALSE 1601101.839 882146.1311 1123249.303 856544.6456 1423302.308 1096890.722 1246423.003 1166285.481 1299350.782 902580.9747 1.773914899 0.977359545 1.244485907 0.948994793 1.576924783 1.215282343 1.380954216 1.292167145 1.439594694 1 19.78369684 3.231839822 24.99527185 1.328722705 1.218293638 0.021180413 0.252756978 568.3325356 2113681.176 0.067644232 0.082614282 1705.453262 -3.231839822 -0.110429067 TITVALADGGRPDNTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TITVALADGGRPDNTGR 17 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 170.09 1.73E-09 1642760000 965610 756760 905770 771060 1153600 1216890 902540 907780 973420 755670 FALSE TRUE 1003733.028 886727.6432 929375.1103 923573.3666 957511.4841 934285.7396 831796.5565 895612.6939 938386.8043 903729.0683 1.110657014 0.981187476 1.02837802 1.021958238 1.059511659 1.033811761 0.920404782 0.991019018 1.038349697 1 19.7855308 2.426343613 24.99976175 0.983830338 1.036496473 0.275831296 0.040833976 135.3483688 66636.35049 0.013772194 0.011522646 266.896951 -2.426343613 0.052666135 TIVAVGS(ph)MEEAVILPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TIVAVGSMEEAVILPFR 17 0 Q9UPX8;Q9UPX8-3;H7C1X5;E7EUA2;A6NHU9;A0A0A0MSQ6;A0A590UJ45;Q9UPX8-4;A0A590UJF3 Q9UPX8 SHANK2 SH3 and multiple ankyrin repeat domains protein 2 1 TIVAVGS(1)MEEAVILPFR;TIVAVGS(1)MEEAVILPFR 105.46 0.00083979 17663100 10957.5 11387 14262.5 10847.3 19824.2 14390 12632.8 13405.4 16227.3 13698.9 TRUE FALSE 11390.11056 13342.62867 14634.19247 12992.86356 16454.48957 11048.14058 11642.60813 13225.72254 15643.28264 16382.93717 0.695242278 0.814422257 0.893258169 0.793072904 1.004367495 0.674368733 0.710654506 0.80728641 0.954852141 1 13.99990641 1.183368877 4.165547137 0.993647294 0.800438633 0.376684954 0.092548508 0.225963468 7.341612236 0.086363621 0.023041794 15.25347791 -1.183368877 -0.193208661 TIVCPMIDVIDHDDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TIVCPMIDVIDHDDFR 16 0 Q86SR1-3;Q86SR1-2;Q86SR1 Q86SR1-3 GALNT10 Polypeptide N-acetylgalactosaminyltransferase 10 0 99.927 0.002228 15176000 9416 15610 12525 17998 19916 21068 16392 14366 12938 17282 FALSE TRUE 9787.750951 18290.89607 12851.41179 21557.95068 16530.68543 16175.27629 15107.15221 14173.44727 12472.36391 20668.07702 0.473568535 0.884982965 0.621800073 1.043055465 0.799817294 0.782621251 0.730941354 0.685765166 0.603460298 1 14.33511654 -2.476969917 2.268826905 4.08140372 0.745031649 0.21547606 0.150150182 4343741.079 484295.9964 70352627.99 0.034677401 0.003334495 2.476969917 -3.33637207 TIVLVPS(ph)PLGQQQDMIFEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TIVLVPSPLGQQQDMIFEAR 20 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR;TIVLVPS(1)PLGQQQDMIFEAR 167.14 1.49E-11 125571000 162840 181977 170147 158400 190427 218249 176882 184410 176061 204651 TRUE FALSE 169269.0489 213230.1342 174581.1706 189731.0472 158058.2866 167563.9773 163017.5266 181938.2856 169724.599 244748.4452 0.691604185 0.871221609 0.713308599 0.775208386 0.64579894 0.684637556 0.666061541 0.743368504 0.693465484 1 17.90094017 -1.897067536 6.324520431 1.062033261 0.722269808 0.650783503 0.061406847 0.036033756 0.000586454 0.039887936 0.013945628 0.012674548 1.897067536 -0.339763453 TIVMGAS(ph)FR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TIVMGASFR 9 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 1 TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR;TIVMGAS(1)FR 125.74 0.001424 0 964600 1179270 1114270 1052820 1420240 1453160 1117620 1140790 1093810 1204910 TRUE FALSE 1002683.153 1381800.449 1143308.792 1261064.654 1178828.112 1115685.613 1030018.024 1125499.576 1054443.992 1440989.045 0.695829823 0.95892502 0.793419489 0.875138266 0.818068754 0.774249892 0.714799344 0.781060467 0.731750179 1 20.45862794 2.88786252 4.333264726 0.779767993 0.838220437 0 0.096609165 0.620731856 19.32101627 0.027559041 0.029606977 772.4360246 -2.88786252 0.058452444 TKADVT(ph)PPPDGSTTHNLEVSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKADVTPPPDGSTTHNLEVSPK 22 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 T(0.003)KADVT(0.996)PPPDGSTTHNLEVSPK;T(0.003)KADVT(0.996)PPPDGSTTHNLEVSPK 178.95 8.57E-17 573300000 455090 317570 474410 335560 664420 603190 565340 527880 578520 275150 TRUE FALSE 473057.3046 372110.1771 486773.5143 401932.7665 551482.1257 463108.2639 521027.1736 520804.632 557699.1782 329060.3744 1.437600335 1.130826456 1.479283293 1.221455993 1.675929916 1.407365638 1.583378656 1.582702363 1.694823265 1 18.32799278 3.248008003 24.99854656 1.525990419 1.315543429 0.129992743 0.208066179 310.3662289 821249.0905 0.052828273 0.070604115 1770.141578 -3.248008003 -0.210446989 TKDEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TKDEPQR 7 1 A6NNI4;A0A2R8Y478;G8JLH6;P21926;A0A087WU13 A6NNI4 CD9 Tetraspanin;CD9 antigen 0 ;;; 101.64 0.0081244 891380000 983880 840704 858152 758478 1100590 1102400 1021080 978058 937040 703485 FALSE TRUE 1022724.342 985088.3722 880516.1461 908502.6846 913512.1049 846384.307 941045.0815 964948.7323 903316.1134 841319.4167 1.215619564 1.170885103 1.046589593 1.07985465 1.085808893 1.006020175 1.118534843 1.146946942 1.073689844 1 19.68229411 4.384058137 4.633883411 1.079876724 1.20596656 0.558626483 0.043873034 0.154716017 5.625763626 0.01140162 0.034303929 24213.53161 -4.384058137 0.126089837 TKDGVVEITGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;; 177.42 7.29E-06 60754814000 24628149 13837194 21026869 14502395 26823918 24475956 28618054 21237507 23118973 10716186 FALSE TRUE 25600487.34 16213624.43 21574846.48 17370925.45 22264398 18791786.16 26374896.15 20952852.96 22286925.68 12815817.47 1.997569597 1.265126042 1.683454569 1.355428593 1.737259293 1.466296332 2.057995614 1.634921299 1.739017095 1 23.61142217 TKDGVVEITGKHEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TKDGVVEITGKHEER 15 2 P04792 P04792 HSPB1 Heat shock protein beta-1 0 ;;;; 189.81 1.46E-07 11178210000 6117610 4724280 6562840 2634510 10895120 7806880 4554210 6002860 7602500 6026130 FALSE TRUE 6359137.967 5535638.34 6733873.002 3155608.215 9043171.394 5993850.434 4197239.12 5922401.48 7328887.51 7206834.796 0.882375987 0.768109509 0.93437316 0.437863265 1.254804869 0.831689723 0.582397022 0.821775668 1.016935689 1 22.78093434 1.249282481 9.070044934 1.00889273 0.808411209 0.127557818 0.202844104 0.271506521 185.7434619 0.142972974 0.047590283 17.75343854 -1.249282481 -0.200481521 TKDIEDVFYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKDIEDVFYK 10 1 J3KTL2;Q07955;Q07955-3;Q07955-2;J3QQV5;J3KSW7 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ; 129.34 0.00027873 4887200000 15609400 8909100 13322000 8550600 19011600 16591000 16287200 13055200 14712300 8667400 FALSE TRUE 16225671.17 10439168.62 13669182.26 10241883.16 15780015.02 12737991.69 15010566.71 12880216.4 14182807.2 10365611.08 1.565336673 1.007096305 1.318704913 0.988063615 1.522342957 1.228870309 1.448112088 1.242591131 1.368255772 1 23.30530183 3.232940294 24.99998784 1.315365087 1.211671851 0.035143629 0.200967247 411.7625461 1831578.395 0.052468844 0.064386136 1709.78024 -3.232940294 -0.103693236 TKDIVNGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKDIVNGLR 9 1 P47756-2;B1AK88;B1AK87;P47756 P47756-2 CAPZB F-actin-capping protein subunit beta 0 125.68 0.00045119 1039300000 1114200 1025700 1094100 831100 1725200 1495800 1210200 1084600 1121600 1107500 FALSE TRUE 1158189.476 1201855.996 1122613.145 995489.0994 1431951.12 1148423.119 1115341.362 1070062.711 1081233.835 1324493.421 0.874439584 0.907408053 0.847579254 0.751599883 1.081131169 0.86706593 0.842089016 0.80790338 0.816337641 1 20.33700925 -1.226366409 8.672910264 1.000000026 0.864564944 0.191551901 0.082420517 4.19E-08 3.75E-09 0.079341889 0.018701059 0.059379097 1.226366409 -0.135435082 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKDQILLLIDIEQSYINTNHEDFIGFANAQQR 32 1 P50570-2;P50570-5;P50570;P50570-3;P50570-4 P50570-2 DNM2 Dynamin-2 0 382.24 8.11E-150 320070000 254500 212580 305450 257750 362700 366700 322890 321200 326800 201470 FALSE TRUE 264547.8565 249088.9614 313410.2779 308732.1807 301048.3836 281539.4824 297581.0381 316894.8394 315038.5318 240944.1891 1.097963215 1.033803564 1.300758815 1.281343127 1.249452766 1.168484218 1.235062108 1.315220925 1.30751662 1 17.87833948 4.242714372 24.99997627 1.247114715 1.065883335 0.341939366 0.090439788 94.66486081 569732.802 0.020781276 0.052823597 17486.96223 -4.242714372 -0.18123138 TKDQPDGSSLS(ph)PAQS(ph)PSQSQPPAASSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 2 TKDQPDGS(0.005)S(0.029)LS(0.966)PAQS(1)PSQSQPPAASSLR 141.13 7.27E-08 262930000 157360 111780 128700 123100 152080 192040 198260 147240 166360 84418 TRUE FALSE 163572.6943 130977.3455 132054.0277 147448.8126 126229.4959 147441.6204 182719.8631 145266.4886 160372.7361 100958.0908 1.620203918 1.297343724 1.308008369 1.460495255 1.250315798 1.460424016 1.809858543 1.438879118 1.588508012 1 16.62339701 2.483155896 24.9915733 1.51775914 1.379284408 0 0.213936652 690.5157441 2859683.775 0.067591213 0.058380201 304.1976789 -2.483155896 -0.138474732 TKDSGS(ph)ISLQETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKDSGSISLQETR 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 T(0.007)KDS(0.104)GS(0.886)IS(0.004)LQETR;TKDS(0.066)GS(0.93)IS(0.003)LQETR 108.71 0.00072341 614020000 371590 255440 373510 310680 582400 489150 423930 368040 365460 304370 TRUE FALSE 386260.6601 299309.833 383243.9774 372131.5767 483403.856 375552.3256 390701.2589 363107.0258 352307.166 364005.474 1.061139702 0.822267395 1.052852237 1.022324122 1.3280126 1.031721643 1.073338965 0.997531773 0.967862275 1 18.47360062 5.088081427 21.45437686 1.036385808 2.983960783 0.004316393 0.118439049 11115.86354 3178584.941 0.028173027 183695.314 122484.5827 -5.088081427 1.947574975 TKEAEQTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKEAEQTCR 9 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;Q14980-5;H0YFY6;K4DIE0 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 62.466 0.07518 27595000 18086 41603 38989 42165 34636 43176 30441 34088 38516 64227 FALSE TRUE 18800.04925 48747.99162 40005.08537 50505.11115 28748.58509 33149.02834 28054.95488 33631.10612 37129.81668 76811.05095 0.244757089 0.634648153 0.520824606 0.657524022 0.374276679 0.431565874 0.365246335 0.437842025 0.483391598 1 16.22902627 0.916831053 16.89332979 1.000000001 0.463081076 0.655865182 0.117188342 517.8614855 105190.0999 0.110511021 0.027628048 8.257166707 -0.916831053 -0.536918925 TKECS(ph)VEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TKECSVEK 8 1 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 TKECS(1)VEK;TKECS(1)VEK;TKECS(1)VEK;TKECS(1)VEK 94.122 0.0064096 1642900000 5199130 1767800 2655570 1974810 4449450 4638300 4608270 3044150 3516340 1276810 TRUE FALSE 5404395.667 2071405.898 2724776.336 2365421.524 3693134.078 3561125.119 4247061.756 3003348.148 3389787.61 1526976.473 3.539278935 1.356540808 1.784425879 1.549088388 2.418592652 2.332141445 2.78135376 1.966859477 2.219934406 1 20.5422464 TKECS(ph)VEKGTGDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKECSVEKGTGDSLR 15 2 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 T(0.004)KECS(0.996)VEKGTGDSLR;T(0.005)KECS(0.99)VEKGT(0.005)GDSLR 68.952 0.026665 689420000 1194040 585890 823370 433890 1412090 1261820 837940 833000 990920 571760 TRUE FALSE 1241181.621 686512.0499 844827.6986 519712.147 1172063.446 968781.4281 772260.0733 821834.9975 955256.9828 683785.425 1.815162441 1.003987545 1.235515803 0.760051513 1.714080768 1.416791573 1.129389491 1.201890195 1.397012788 1 19.38318415 -1.153339809 4.483913554 0.999956268 1.273635647 0.077482317 0.297799422 0.000122964 2.32E-05 0.272316669 0.064175411 0.070252242 1.153339809 0.273679378 TKEGVMYVGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKEGVMYVGAK 11 1 O76070;F8W754 O76070 SNCG Gamma-synuclein 0 ; 144.47 3.35E-05 2196840000 3150300 2169690 3008100 1949270 4477400 3787400 3376100 3111800 3498400 2285010 FALSE TRUE 3274676.277 2542317.38 3086493.557 2334829.788 3716333.147 2907833.749 3111472.46 3070091.411 3372493.267 2732713.96 1.198323836 0.930326926 1.129460896 0.854399627 1.359942241 1.064082736 1.13860159 1.12345875 1.234118651 1 21.38190303 3.248405314 24.99999612 1.151874739 1.028380198 0.189643772 0.126805011 332.1341149 843429.2651 0.032384752 0.043324892 1771.76172 -3.248405314 -0.123494542 TKENILEEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKENILEEFSK 11 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 143.98 9.42E-05 491040000 2744800 1513470 2290100 1694200 2971800 2680500 2788800 2271200 2534700 1258560 FALSE TRUE 2853166.823 1773396.699 2349781.887 2029307.703 2466654.498 2057994.498 2570206.569 2240758.279 2443476.642 1505150.735 1.895602053 1.178218671 1.561160508 1.348242176 1.638808951 1.367301261 1.707607423 1.488726827 1.623409925 1 20.52147654 -1.236695063 4.391522864 0.999767796 1.522338699 0.406794743 0.193088693 13105435.88 3708030.274 29259.26094 0.040082516 0.057983568 1.236695063 0.522570903 TKENVVQSVTSVAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKENVVQSVTSVAEK 15 1 O76070 O76070 SNCG Gamma-synuclein 0 ; 234.57 1.07E-17 4583400000 4401800 2470900 3704700 2451210 4909200 4385400 4524300 3882800 4172100 2061690 FALSE TRUE 4575586.463 2895257.854 3801247.525 2936052.022 4074735.938 3366957.311 4169673.544 3830757.417 4021946.936 2465638.682 1.855740866 1.17424255 1.541688794 1.190787622 1.6526087 1.365551788 1.691112966 1.553657251 1.631198831 1 21.23352997 TKEPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKEPSR 6 1 Q9NYU2-2;Q9NYU2;H7BZG0 Q9NYU2-2 UGGT1 UDP-glucose:glycoprotein glucosyltransferase 1 0 68.915 0.086532 41655000 60689 71980 76141 69891 89239 98311 73169 77803 70627 69520 FALSE TRUE 63085.04858 84342.00507 78125.29701 83715.2312 74070.18666 75479.76017 67433.82259 76760.17805 68085.14807 83141.11296 0.758770797 1.014444023 0.939671051 1.006905347 0.890897223 0.907851212 0.811076737 0.92325175 0.818910713 1 16.34327444 3.037237086 24.97073829 0.88533812 0.938205741 0.041704924 0.082310352 412.3880296 276539.9355 0.022325554 0.026684092 1089.524713 -3.037237086 0.052867621 TKEPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TKEPSTR 7 1 Q641Q2;F8W7U3;A0A0A0MR88;A0A096LPC5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A 0 ;; 71.379 0.049681 121893000 179767 171125 182425 139091 264657 242385 211322 213804 225901 201792 FALSE TRUE 186864.34 200514.3876 187179.1454 166602.7847 219670.6977 186094.7571 194758.0295 210938.3071 217770.8671 241329.2789 0.77431276 0.830874681 0.775617224 0.690354629 0.91025299 0.771123827 0.807021968 0.874068443 0.902380632 1 17.88064343 1.146831773 0.798045928 1.000580419 0.78725098 0.621860786 0.052159143 0.384200012 0.556564932 0.047975889 0.018169852 14.0227042 -1.146831773 -0.21332944 TKEQILEEFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKEQILEEFSK 11 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 174.39 1.01E-05 1265380000 3056600 1804350 2673100 1773760 3596800 3047300 3057100 2494700 2923700 1485880 FALSE TRUE 3177276.928 2114233.077 2742763.182 2124604.434 2985417.221 2339610.757 2817476.514 2461262.627 2818476.608 1777009.737 1.787990725 1.189770113 1.543471105 1.195606523 1.680022995 1.316599852 1.585515518 1.385058605 1.586078314 1 20.76102016 -1.145585714 4.248017089 0.999896015 1.460464767 0.355821331 0.190681478 10.56384889 47020347.48 9995.408695 0.038876165 0.071517823 1.145585714 0.460568753 TKEQLGYIVFSGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKEQLGYIVFSGPR 14 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 75.445 0.027573 374620000 583710 379790 441220 368880 611540 511980 557070 426260 510580 359190 FALSE TRUE 606755.3215 445015.9781 452718.5557 441843.363 507590.6492 393080.4041 513405.3978 420546.6819 492204.3255 429566.4034 1.412483185 1.03596551 1.053896562 1.028579888 1.181634889 0.915063192 1.195171209 0.979002731 1.145816623 1 18.71252164 4.740901411 24.83779067 1.059553818 1.41248332 0.605107846 0.085555604 117.3944387 1245567.711 0.017962486 0.120926437 55068.26722 -4.740901411 0.352929502 TKETNCESDRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKETNCESDRER 12 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 132.06 0.00010557 87315000 105840 103470 121440 90522 154000 130470 121340 116880 127170 94195 FALSE TRUE 110018.6449 121240.1676 124604.8262 108426.9814 127823.135 100170.3198 111829.0537 115313.4148 122593.1765 112650.7068 0.976635195 1.076248619 1.106116683 0.962506002 1.134685602 0.889211641 0.992706188 1.023636851 1.088259275 1 16.78149684 2.761592608 24.99814961 1.001644038 1.050747072 0.132608144 0.066895726 1791.068069 1943962.703 0.020032762 0.021229957 577.5540165 -2.761592608 0.049103035 TKEVYELLDSPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 67.358 0.048669 668480000 1434300 566280 843210 502330 1376200 1072100 1065600 751610 1027100 466440 FALSE TRUE 1490927.272 663534.185 865184.7453 601689.3747 1142274.016 823121.0228 982075.4876 741535.8973 990134.8716 557829.9875 2.672727005 1.18949178 1.550982853 1.078625008 2.04770995 1.475576863 1.760528314 1.329322399 1.774976057 1 19.08946597 7.999991991 0.039855504 3.75E-07 4.147101865 0.188080623 0.431913316 1564.446012 4.746484894 135.5145279 439.0413318 99998155.89 -7.999991991 4.14710149 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 320.16 1.02E-92 4177530000 1498050 551946 812320 493638 1293840 1294540 1043450 884730 1005960 416970 TRUE FALSE 1557194.171 646738.432 833489.7265 591278.123 1073913.539 993902.7039 961661.6625 872871.6415 969755.6961 498667.2881 3.122711691 1.296933742 1.671434534 1.185716683 2.153567247 1.993117912 1.928463497 1.750408864 1.944694828 1 18.92771804 -0.953196949 4.689098466 0.99998947 1.853073181 0.217489477 0.503404183 0.423063662 146609813.1 3720.965625 0.109813973 0.111378933 0.953196949 0.853083711 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 T(0.295)KFAS(0.705)DDEHDEHDENGATGPVK;T(0.151)KFAS(0.849)DDEHDEHDENGATGPVK;T(0.252)KFAS(0.748)DDEHDEHDENGATGPVK 325.62 1.10E-68 2846770000 3675860 1590670 2620220 1665960 3749180 3469300 3686490 2776040 3069840 1205440 TRUE FALSE 3820985.791 1863855.199 2688505.086 1995481.916 3111895.723 2663607.653 3397533.281 2738831.724 2959357.058 1441622.888 2.650475254 1.292886797 1.86491565 1.384191339 2.158605935 1.84764523 2.35674205 1.899825361 2.052795555 1 20.45926239 TKFAS(ph)DDEHDEHDENGATGPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TKFASDDEHDEHDENGATGPVKR 23 2 P05455 P05455 SSB Lupus La protein 1 T(0.058)KFAS(0.942)DDEHDEHDENGATGPVKR;T(0.014)KFAS(0.986)DDEHDEHDENGATGPVKR;T(0.048)KFAS(0.952)DDEHDEHDENGATGPVKR;T(0.001)KFAS(0.999)DDEHDEHDENGATGPVKR;T(0.002)KFAS(0.998)DDEHDEHDENGATGPVKR 221.3 8.53E-33 9339640000 3110485 1581287 2478919 1207975 3818440 3074950 2246455 2191241 2746989 1593336 TRUE FALSE 3233289.35 1852860.742 2543521.666 1446908.85 3169382.933 2360839.464 2070371.987 2161870.999 2648125.402 1905519.683 1.696801864 0.97236505 1.334817839 0.759325061 1.663264337 1.238947824 1.086513042 1.13453092 1.389712962 1 20.86175308 5.61744481 0.021883125 3.78E-07 2.630602175 0.071415008 0.274703217 5536.280413 14.81301788 723.0994061 1087.980454 414423.9159 -5.61744481 2.630601796 TKFEECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TKFEECR 7 1 P43487;F6WQW2;P43487-2;C9JXG8;C9JGV6 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;;;; 110.87 0.006116 5083639000 6645790 5405980 6447491 5352328 8525539 8300111 7755290 6658207 6805651 4788671 FALSE TRUE 6908170.921 6334415.012 6615517.912 6411002.503 7076370.926 6372536.01 7147410.105 6568964.626 6560716.95 5726919.398 1.206262991 1.106077207 1.155161694 1.119450451 1.235633058 1.112733665 1.248037489 1.147032841 1.145592682 1 22.44932787 -1.274730562 6.149097396 0.999994318 1.163795573 0.516566319 0.047595065 3.39E-06 4.00E-07 0.042113655 0.009925939 0.053121391 1.274730562 0.163801256 TKFENLCK ddPTM_MDA-MB-175_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 ; 109.66 0.0032602 4953900000 5535400 3875000 4457300 3705700 10026200 7277100 7134200 5956400 6463500 5051000 FALSE TRUE 5753941.866 4540501.107 4573460.9 4438676.4 8321950.105 5587103.811 6575002.762 5876564.201 6230879.898 6040646.743 0.952537387 0.751658109 0.757114444 0.734801519 1.377658794 0.92491815 1.088460068 0.972836925 1.031492183 1 22.52627159 3.333327265 24.43438269 1.053779214 0.792644151 0.508014879 0.12826129 10.75754579 2766.52851 0.033874443 0.045866203 2154.404588 -3.333327265 -0.261135063 TKFICVTPTTCSNTIDLPMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKFICVTPTTCSNTIDLPMSPR 22 1 P40763;P40763-2;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 1 TKFICVTPTTCSNTIDLPMS(1)PR 211.04 2.28E-23 229800000 254400 267300 271810 179140 419900 395600 228770 311080 298190 366950 TRUE FALSE 264443.9084 313206.6957 278893.5919 214573.3573 348525.548 303727.8954 210838.4096 306910.4814 287458.2001 438846.8268 0.602588175 0.713703909 0.63551466 0.48894818 0.794184956 0.692104572 0.480437357 0.699356729 0.655030828 1 18.74335795 0.323139574 1.507999715 1.000059762 0.637691488 0.579563641 0.092127038 4.016515859 8.186563141 0.085696624 0.024625254 2.104454665 -0.323139574 -0.362368274 TKFPAEQYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKFPAEQYYR 10 1 E9PGT1;Q15631;H7C1D4;Q15631-2 E9PGT1 TSN Translin 0 82.543 0.01614 409670000 232410 185540 197900 159280 428800 323180 264300 236260 228690 300570 FALSE TRUE 241585.7263 217405.0517 203057.4366 190785.1086 355912.7292 248126.3428 243583.4754 233093.3211 220459.4916 359460.9367 0.67207783 0.60480856 0.564894307 0.530753384 0.990129087 0.690273455 0.677635455 0.648452439 0.613305839 1 18.45547547 TKGDFILVGDLMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKGDFILVGDLMR 13 1 Q16531;F5GY55;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 129.93 0.00013495 416150000 679830 595980 740590 574500 1083360 982180 857390 763760 801960 729980 FALSE TRUE 706670.2133 698334.9289 759890.3838 688134.3853 899210.8542 754083.5801 790185.5314 753523.0465 773097.6163 873005.6047 0.809468129 0.799920327 0.870430132 0.788235931 1.030017275 0.863778624 0.905132255 0.863136551 0.885558594 1 19.73563139 8 0.055526127 1.161402812 0.316925937 0.376971494 0.060107946 448.228296 1.867252308 6.14806638 31.30696012 100000000 -8 -0.844476874 TKGGQQVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TKGGQQVDR 9 1 Q8TE77;Q8TE77-3;C9JUG3;Q8TE77-4 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 0 ;;; 118.28 0.00092591 795110000 1101840 911420 1076690 869700 1288560 1328130 1208650 1113540 1167460 719520 FALSE TRUE 1145341.494 1067949.295 1104749.426 1041724.064 1069531.031 1019691.936 1113912.855 1098614.818 1125443.343 860496.168 1.331024514 1.241085475 1.283851651 1.210608603 1.242923643 1.185004621 1.294500657 1.276722499 1.30790047 1 19.71480924 -1.696405115 2.945503797 0.966642941 1.261608268 0.776505872 0.042433579 10003295.71 11831282.53 2536711.558 0.010472014 0.020118467 1.696405115 0.294965326 TKGS(ph)PRT(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKGSPRTSPK 10 2 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.211)KGS(0.788)PRT(0.58)S(0.42)PK;T(0.355)KGS(0.645)PRT(0.645)S(0.355)PK 75.589 0.042535 525110000 1625480 559770 939740 387840 1605850 1515960 878750 816360 1038490 536930 TRUE FALSE 1689655.206 655906.1431 964230.3964 464553.5944 1332888.191 1163901.265 809871.2788 805418.0295 1001114.948 642131.1534 2.631324141 1.021451988 1.501609743 0.723455936 2.075725782 1.812560033 1.261224089 1.25428898 1.559050581 1 19.29250847 4.748796361 24.59461786 1.375559164 2.631325016 0.501544316 0.380816918 972.7708934 2337331.771 0.089242837 1.223523961 56078.49646 -4.748796361 1.255765852 TKGTSSFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKGTSSFGK 9 1 P61927;D6RG19;D6R9X9 P61927 RPL37 60S ribosomal protein L37;Ribosomal protein L37 0 68.069 0.053913 553960000 202520 151050 180450 118110 314740 248010 197970 212910 231790 194130 FALSE TRUE 210515.646 176991.6625 185152.6752 141471.8055 261240.6072 190413.4361 182452.5941 210056.2897 223447.9232 232166.0567 0.906746012 0.762349437 0.797501056 0.609356111 1.125231703 0.82016053 0.785871099 0.904767444 0.962448716 1 17.82479754 1.343068571 0.440753486 1.011361668 0.800535798 0.183956522 0.123671815 1.689682634 0.927423126 0.145935867 0.092420768 22.03274313 -1.343068571 -0.21082587 TKHQERPPESHRVT(ph)PNLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKHQERPPESHRVTPNLNR 19 3 Q5TC79;Q5TC79-2;Q5TC79-3 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 TKHQERPPES(0.11)HRVT(0.89)PNLNR 65.833 0.014851 18744000 2900 3923.4 4880.9 2318.4 5549.2 5975.5 4113 3797.7 4009.4 3107 TRUE FALSE 3014.494239 4597.21343 5008.100264 2776.9726 4605.948966 4587.780685 3790.612313 3746.798043 3865.102477 3715.757163 0.81127321 1.237221172 1.347800743 0.7473504 1.239572115 1.234682592 1.020145329 1.008353851 1.040192431 1 11.8594405 2.055441925 24.99985732 1.016393429 1.111686515 0.050069559 0.180798333 273.8516376 123483.5428 0.066782103 0.049321899 113.6166356 -2.055441925 0.095293087 TKIDCDNLEQYFIQQGGGPDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKIDCDNLEQYFIQQGGGPDKK 22 2 F1T0B3;A0A087X2G1;Q92499;Q92499-3;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 212.05 1.44E-23 249260000 419750 153010 266040 150290 378710 313900 339120 274860 310290 116230 FALSE TRUE 436322.0541 179288.2772 272973.221 180016.9134 314337.0095 241001.4822 312538.8883 271175.9513 299122.7235 139003.0431 3.138938862 1.289815483 1.963793128 1.295057355 2.261367826 1.733785655 2.248431985 1.950863414 2.151914928 1 17.08475694 -0.961685546 5.937829221 0.999999338 1.96932033 0.261041781 0.503661448 3.98E-06 6.97E-07 0.439264223 0.103535499 0.109223089 0.961685546 0.969320992 TKIDWNK ddPTM_MDA-MB-175_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 ; 67.169 0.060092 3551900000 13356500 7779500 10440200 7519900 16785400 13780700 13624100 10523700 12212200 7751700 FALSE TRUE 13883824.93 9115568.609 10712280.19 9007313.775 13932223.7 10580341.27 12556207.44 10382647.01 11772685.31 9270497.2 1.497635416 0.983287996 1.155523804 0.971610646 1.502856147 1.141291675 1.35442654 1.119966577 1.269908728 1 23.14421529 -1.156331429 4.5665954 0.99997046 1.210434697 0.1197779 0.178010776 4.92E-05 9.08E-06 0.15830301 0.037307144 0.069769976 1.156331429 0.210464237 TKKDDSHS(ph)AEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 TKKDDS(0.021)HS(0.979)AEDS(1)EDEKEDHK;TKKDDS(0.013)HS(0.987)AEDS(1)EDEKEDHK;TKKDDS(0.131)HS(0.869)AEDS(1)EDEKEDHK 170.82 4.19E-12 692520000 1400270 101362.9 220254 89085.5 499091 881149 436893 219631 277110 57882.9 TRUE FALSE 1455553.741 118771.1896 225994.0002 106706.346 414255.6901 676515.4987 402648.1851 216687.2057 267136.8652 69223.94602 21.02673749 1.71575295 3.264679539 1.54146581 5.984283097 9.772853725 5.816602609 3.130234812 3.859023945 1 16.07898356 4.743842352 24.98859237 4.24613115 21.02674458 0.80591237 2.502917365 251.8090508 1191305.247 0.632325574 5.407498756 55442.44215 -4.743842352 16.78061343 TKKDDSHS(ph)AEDSEDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TKKDDS(0.147)HS(0.618)AEDS(0.235)EDEKEDHK 64.152 0.011609 201280000 117570 33190 56178 34821 76790 102220 59123 62181 64721 30135 TRUE FALSE 122211.7544 38890.12432 57642.04483 41708.48987 63737.26323 78480.95416 54488.78477 61347.5654 62391.70385 36039.37628 3.391061861 1.079100926 1.599418491 1.157303321 1.768545125 2.177644628 1.511923634 1.702237157 1.731209313 1 15.13728642 7.999999951 0.04619917 5.31E-09 4.693664398 0.178068682 0.595027661 1286.4731 4.500003807 113.9472334 443.7996772 99999988.62 -7.999999951 4.693664393 TKKDDSHSAEDS(ph)EDEKEDHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKKDDSHSAEDSEDEKEDHK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TKKDDSHSAEDS(1)EDEKEDHK 220.98 3.32E-25 124690000 415710 38333 84650 38068 180630 220200 135980 75676 96348 22797 TRUE FALSE 432122.5518 44916.39456 86856.04854 45597.73678 149926.5771 169061.8872 125321.5323 74661.687 92880.4543 27263.63568 15.84977723 1.64748367 3.185783788 1.672474549 5.499141014 6.20100302 4.596655185 2.738508095 3.406752328 1 14.73469034 4.743828606 24.98703919 3.504207582 15.84978243 0.843071097 1.619161168 214.8983308 1019270.682 0.397693439 3.402280506 55440.68737 -4.743828606 12.34557485 TKLDDLALLEDLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKLDDLALLEDLEK 14 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 113.69 0.00047531 105760000 530980 239630 434400 255000 586310 470010 562360 401090 489220 223800 FALSE TRUE 551943.5004 280784.5884 445720.8209 305438.2389 486649.2356 360857.3006 518280.7537 395714.0446 471613.0678 267649.3251 2.062189024 1.049076393 1.665316439 1.141188153 1.818234496 1.34824663 1.936417189 1.478479516 1.762055883 1 18.02998449 TKMIMVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TKMIMVEER 9 1 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 ;;; 87.308 0.018223 1229186000 3493.82 317530 242698 267289 157188 300848 136982 228834 166163 398032 FALSE TRUE 3631.758711 372063.3075 249022.9093 320157.9664 130469.2399 230980.6114 126244.9929 225766.8545 160182.8261 476018.7496 0.007629445 0.781614816 0.523136766 0.672574277 0.274084246 0.485234272 0.265210127 0.474281433 0.336505287 1 18.86065887 -1.488858126 4.511811969 1.002775119 0.438360421 0.404548937 0.208860131 0.005411082 0.00061302 0.187687621 0.044057914 0.032444559 1.488858126 -0.564414699 TKNETDEDGWTTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKNETDEDGWTTVR 14 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 119.46 0.00016982 482360000 154440 118700 189540 142730 211040 190970 198770 162180 181010 98091 FALSE TRUE 160537.4105 139085.8016 194479.5681 170961.568 175167.4962 146620.1117 183189.888 160006.2424 174495.4855 117310.0534 1.368488086 1.185625593 1.657825246 1.457347969 1.493201061 1.249851206 1.561587287 1.363960187 1.48747256 1 16.83996713 -0.762775543 7.397507892 1 1.424228057 0.478262119 0.133179149 0 1.23E-10 0.122242586 0.028812854 0.172673009 0.762775543 0.424228058 TKPIVKPQT(ph)SPEYGQGINPISR ddPTM_MDA-MB-175_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(0.84)S(0.16)PEYGQGINPISR 138.99 1.04E-06 1633300000 835660 448790 658470 474480 912370 823460 771250 637200 725020 343250 TRUE FALSE 868652.5021 525866.1914 675630.2691 568330.7278 757285.6733 632223.8947 710797.4097 628659.3762 698926.6718 410503.2656 2.116067215 1.281028034 1.645858452 1.384473098 1.84477381 1.540119038 1.731526809 1.53143575 1.702609286 1 18.64703417 -0.991858786 5.359921874 0.999997537 1.623772403 0.424039787 0.223555735 5.82E-06 1.09E-06 0.191434701 0.045121414 0.101892264 0.991858786 0.623774866 TKPIVKPQTS(ph)PEYGQGINPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 TKPIVKPQT(0.036)S(0.964)PEYGQGINPISR;TKPIVKPQT(0.12)S(0.88)PEYGQGINPISR 190.31 9.53E-18 12676000000 3742800 2153110 3076400 2351740 3884000 4061600 3850600 3139800 3362200 1848350 TRUE FALSE 3890568.634 2522889.894 3156573.511 2816907.153 3223799.067 3118354.954 3548779.91 3097716.117 3241195.079 2210498.794 1.760041057 1.141321543 1.42799151 1.274331007 1.45840345 1.410701948 1.605420424 1.401365215 1.466273172 1 21.07594052 -0.896962969 4.21774168 0.999990953 1.429495586 0.407332563 0.158324104 19460530.24 42315005.67 2827.02151 0.035024703 0.126775996 0.896962969 0.429504633 TKPIVKPQTSPEYGQGINPISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKPIVKPQTSPEYGQGINPISR 22 2 O95793-2;O95793-3;O95793;A0A087X1A5 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 131.43 6.82E-06 902760000 237740 193520 191890 184170 258670 245040 229490 203000 203660 150370 FALSE TRUE 247126.1588 226755.5546 196890.811 220598.2763 214701.3658 188133.1736 211501.9741 200279.117 196330.3164 179832.1225 1.37420476 1.26092909 1.094858962 1.226690055 1.193898859 1.046160002 1.176107868 1.113700457 1.091742196 1 17.45629122 8 0.376646393 1.09019639 4.840340108 0.660435097 0.061527569 42.41096895 0.58281359 0.045676888 115.7130254 100000000 -8 3.750143718 TKPIWTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 66.621 0.061448 170030000 77508 86127 86870 78851 102920 122360 93275 86902 82341 88481 FALSE TRUE 80568.07569 100918.6423 89133.90356 94447.49245 85425.69516 93943.74438 85963.86177 85737.22083 79377.56349 105817.1579 0.761389526 0.953707738 0.842338855 0.892553668 0.807295309 0.887793117 0.812381125 0.810239309 0.750138872 1 16.69121405 3.239737275 24.99677114 0.833432105 0.867572564 0 0.07697846 114.6269747 2435073.545 0.020227809 0.025913679 1736.749868 -3.239737275 0.034140459 TKPPRPDS(ph)PATTPNISVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 TKPPRPDS(1)PATTPNISVK;T(0.041)KPPRPDS(0.959)PATTPNISVK;T(0.009)KPPRPDS(0.988)PAT(0.002)TPNISVK 186.55 3.74E-14 875270000 944790 534310 797960 536590 1071910 988340 1014120 810920 903740 465360 TRUE FALSE 982091.0387 626073.5861 818755.4931 642725.9004 889707.1211 758813.0134 934630.6245 800050.9438 871214.5739 556538.3821 1.764642063 1.124942333 1.471157281 1.154863566 1.598644675 1.363451359 1.679364181 1.437548549 1.565416873 1 19.08612166 3.198164171 24.99998887 1.473165564 1.367349093 0.004031248 0.240102872 525.3779473 325136.9538 0.063315322 0.075677131 1578.207747 -3.198164171 -0.105816471 TKPQDMISAGGESVAGITAISGKPGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKPQDMISAGGESVAGITAISGKPGDK 27 2 P20810-6;P20810-10;P20810-7;P20810-9;P20810;P20810-8;B7Z574;E7ES10;P20810-4;P20810-5;E9PCH5;P20810-2;F8W7E0;E9PSG1;A0A0C4DGB5;H0Y944;E7EVY3 P20810-6;P20810-5;A0A0C4DGB5;E7EVY3 CAST Calpastatin 0 86.732 0.0045275 772530000 207170 81293 132000 68844 212710 190020 171380 145550 153820 99673 FALSE TRUE 215349.2316 95254.44038 135440.0284 82461.13772 176553.6302 145890.7348 157946.7878 143599.1403 148284.0482 119202.016 1.806590516 0.799100918 1.136222633 0.691776368 1.481129566 1.223894861 1.325034535 1.2046704 1.243972654 1 16.86304911 TKPQMQEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKPQMQEER 9 1 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 ; 94.692 0.0077976 172269000 251600 224730 197940 163697 558300 389810 303600 233480 266290 388260 FALSE TRUE 261533.3623 263325.6293 203098.479 196075.778 463400.3654 299282.5351 279803.0387 230350.5825 256706.2749 464332.1133 0.563246338 0.567106219 0.437399166 0.42227486 0.997993359 0.644544124 0.602592478 0.496090139 0.552850573 1 18.82479754 TKPSDEEMLFIYGHYK ddPTM_MDA-MB-175_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 ; 212.69 2.32E-12 7483400000 5196100 3235700 4379800 3446200 5104600 5120200 5395700 4279800 4415800 2529700 FALSE TRUE 5401246.04 3791406.305 4493941.186 4127848.074 4236921.915 3931111.147 4972770.935 4222436.281 4256876.221 3025346.281 1.785331509 1.253213997 1.48543035 1.364421686 1.400475027 1.29939213 1.643703058 1.395686936 1.407070737 1 21.52866885 0.539709385 2.011880244 1.000059348 1.444785553 0.447101914 0.15020359 3.127502912 12.64263058 0.131073249 0.036045411 3.465049037 -0.539709385 0.444726205 TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 2 TKPTQAAGPS(0.185)S(0.815)PQKPPT(0.998)PEET(0.002)K;TKPT(0.015)QAAGPS(0.085)S(0.9)PQKPPT(1)PEETK;T(0.001)KPT(0.004)QAAGPS(0.142)S(0.854)PQKPPT(1)PEETK 185.65 3.83E-17 695120000 1367040 194354 379129 236745 623110 888260 728940 420610 466190 102464 TRUE FALSE 1421011.795 227732.7876 389009.4132 283572.4544 517193.9848 681975.0767 671803.7781 414972.4109 449411.913 122539.859 11.59632308 1.858438466 3.174554111 2.31412421 4.220618409 5.565332637 5.482328636 3.38642801 3.667475355 1 16.90289157 4.746371244 24.91447572 3.616826212 11.59632713 0.754298242 1.397474142 466.3588931 1487563.521 0.339431491 3.685534272 55766.22461 -4.746371244 7.97950092 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKPTQAAGPSSPQKPPTPEETK 22 2 F5H8D7;P18887 F5H8D7 XRCC1 DNA repair protein XRCC1 1 TKPTQAAGPS(0.163)S(0.837)PQKPPTPEETK 136.67 2.17E-06 256200000 574640 208790 324090 198310 561070 504910 523540 381270 454380 158890 TRUE FALSE 597327.2309 244648.0583 332536.0516 237535.1261 465699.5218 387652.3045 482503.5668 376159.6993 438026.9526 190021.4534 3.143472594 1.287475988 1.74999215 1.250043729 2.450773392 2.04004494 2.539205749 1.979564373 2.305144734 1 17.53580278 3.205594971 24.99773189 2.124634464 1.809313616 0.012515032 0.63027148 594.1328776 450527.1566 0.170833353 0.20419753 1605.443298 -3.205594971 -0.315320848 TKQGVTEAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TKQGVTEAAEK 11 1 O76070;F8W754;G4Y816;Q16143 O76070 SNCG;SNCB Gamma-synuclein;Beta-synuclein 0 ;;; 151.74 3.03E-05 2439930000 4311400 2507260 3680030 2241530 5828090 4635050 3979710 3640640 4285370 2606440 FALSE TRUE 4481617.401 2937862.401 3775934.605 2684897.944 4837433.344 3558629.882 3667769.931 3591843.176 4131140.371 3117122.015 1.437742052 0.942491948 1.21135284 0.861338738 1.551890918 1.141639585 1.176652667 1.1522947 1.325305956 1 21.5717832 4.779036752 23.24591823 1.161789426 1.437743899 0.173584782 0.186179556 18448.55537 10594653.07 0.041420035 12.85743318 60122.46141 -4.779036752 0.275954473 TKS(ph)DES(ph)GEEKNGDEDCQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKSDESGEEKNGDEDCQR 18 2 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YBM7;E5RHK4 Q6PKG0 LARP1 La-related protein 1 2 T(0.116)KS(0.889)DES(0.995)GEEKNGDEDCQR;T(0.432)KS(0.568)DES(1)GEEKNGDEDCQR 96.303 0.00086761 350155000 1528320 273892 373436 265260 778270 1446240 703710 396051 500466 164590 TRUE FALSE 1588659.254 320930.8204 383168.0489 317727.6363 645979.9434 1110372.678 648551.3714 390742.5842 482454.3264 196838.2592 8.070886523 1.630429072 1.946613684 1.614155894 3.281780412 5.641040935 3.294844071 1.985094695 2.451019067 1 17.58665114 4.745206191 24.72468366 2.644809602 8.070889412 0.638153956 1.247499541 455.8535621 1695939.268 0.316215644 3.051672748 55616.82479 -4.745206191 5.426079811 TKS(ph)PTDDEVTPSAVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TKSPTDDEVTPSAVVR 16 1 A0A1B0GUN5;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 T(0.473)KS(0.513)PT(0.014)DDEVTPSAVVR;T(0.024)KS(0.957)PT(0.019)DDEVTPSAVVR;T(0.113)KS(0.876)PT(0.011)DDEVTPSAVVR;TKS(0.999)PT(0.001)DDEVTPSAVVR;T(0.084)KS(0.912)PT(0.003)DDEVTPSAVVR;T(0.014)KS(0.957)PT(0.029)DDEVTPSAVVR 271.62 2.25E-35 7895890000 1736780 1131690 1434570 1050950 1935130 1903450 1883110 1565790 1627060 889390 TRUE FALSE 1805349.415 1326048.954 1471956.073 1258824.773 1606197.294 1461402.585 1735506.918 1544803.146 1568502.428 1063648.942 1.697316985 1.246697949 1.383873959 1.183496475 1.510082162 1.373951994 1.631653875 1.452361851 1.474642964 1 20.02059064 TKVEAFQTTISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TKVEAFQTTISK 12 1 A0A087X1Z3;Q9UL46;H0YM70 A0A087X1Z3 PSME2 Proteasome activator complex subunit 2 0 ; 157.33 6.74E-05 993590000 1813230 1041560 1772920 1204180 2220350 2090160 1902330 1641560 1893610 922960 FALSE TRUE 1884817.721 1220439.828 1819123.752 1442363.21 1842935.7 1604752.017 1753220.404 1619557.573 1825459.346 1103796.341 1.707577431 1.105674827 1.648061046 1.306729472 1.669633819 1.453847922 1.58835497 1.467261227 1.653800867 1 20.07404258 -0.993588783 5.269098209 0.999997505 1.501040482 0.421836639 0.179191175 4.65E-06 8.89E-07 0.153733653 0.036235189 0.101487188 0.993588783 0.501042977 TKVQDHSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TKVQDHSK 8 1 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 56.916 0.068845 15523000 27174 26383 26952 20781 38451 38169 31002 27702 29678 32563 FALSE TRUE 28246.8505 30914.07502 27654.39126 24891.41977 31915.11275 29304.82821 28571.98223 27330.7 28609.89458 38943.09639 0.725336532 0.793826837 0.710123072 0.63917413 0.819531976 0.752503805 0.733685425 0.701811169 0.734658957 1 15.24907998 0.885153583 19.99778003 1 0.733319242 0.743152677 0.046818621 21127.70315 3678897.415 0.044953576 0.011238394 7.676329051 -0.885153583 -0.266680758 TLAEEQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLAEEQHK 8 0 O60437;K7EKI8;K7EQ71 O60437 PPL Periplakin 0 ; 99.802 0.0065549 249040000 384530 335250 364540 280090 513220 483480 372270 365150 398100 337340 FALSE TRUE 399711.5413 392826.5796 374040.2119 335490.966 425983.0477 371199.0972 343090.5047 360255.7615 383772.4588 403435.3142 0.990769839 0.973704001 0.927138004 0.831585521 1.05588934 0.920095698 0.85042259 0.89297032 0.951261442 1 18.62197785 2.492838715 24.86433403 0.907007397 0.952283631 0.035438832 0.064714314 1631.032225 2580223.448 0.021162546 0.019395507 311.0560946 -2.492838715 0.045276234 TLAGDVHIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 ;;; 166.97 5.38E-06 2041404000 1920788 2382580 2311940 2235840 2542200 2880180 2579910 2364990 2331930 2284550 FALSE TRUE 1996622.193 2791769.581 2372191.056 2678082.479 2110077.752 2211301.845 2377689.913 2333291.177 2248004.295 2732163.832 0.730784212 1.021816316 0.86824627 0.98020567 0.772310111 0.809359167 0.870258908 0.854008515 0.822792641 1 21.38161257 4.824854436 21.18840698 0.878456545 0.730756874 0.246940404 0.080985716 78060.29594 19155289.33 0.01866106 331.2808731 66811.99439 -4.824854436 -0.147699671 TLAGHEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLAGHEGK 8 0 O43172-2;O43172 O43172-2 PRPF4 U4/U6 small nuclear ribonucleoprotein Prp4 0 ; 78.516 0.030423 109356000 331320 299220 345560 294350 439360 454700 405860 382900 369550 272730 FALSE TRUE 344400.7694 350608.7074 354565.5775 352571.5515 364677.7441 349102.816 374047.6327 377767.8518 356249.9677 326166.2218 1.05590569 1.07493874 1.087070192 1.080956665 1.118073301 1.070321795 1.146800642 1.158206542 1.0922344 1 18.31524786 3.777785846 0.901239503 1.112572828 1.059775026 0.006672579 0.043000236 1.518884396 2.184315332 0.016524244 0.059541357 5994.953875 -3.777785846 -0.052797802 TLALLAFDSPEESPFGDLLHTMQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLALLAFDSPEESPFGDLLHTMQR 24 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 ; 196.43 1.98E-24 246370000 271000 276162 329195 292892 373090 408350 335200 306470 326080 317480 FALSE TRUE 281699.2893 323590.6753 337774.0921 350825.1634 309672.2951 313516.9011 308926.1481 302362.2709 314344.4445 379684.1275 0.741930644 0.852262847 0.88961868 0.923992177 0.815605059 0.82573086 0.813639881 0.796352149 0.827910417 1 18.53444016 TLAYIITELDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLAYIITELDER 12 0 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 138.25 0.00018094 12934000 10907 13618 12582 13223 14323 17876 14305 14303 13280 9620 FALSE TRUE 11337.61678 15956.78557 12909.89726 15838.46993 11888.38158 13724.56991 13183.73672 14111.29168 12802.05539 11504.85481 0.985463699 1.386961055 1.122126047 1.37667708 1.03333608 1.192937254 1.145928126 1.226551044 1.112752451 1 13.48995516 -0.297290223 0.470791909 0.968449332 1.197622382 0.160807912 0.122875519 10.7442015 2.431837317 0.68227445 0.05914379 0.504324163 0.297290223 0.229173051 TLAYLLPAIVHINHQPYLER ddPTM_MDA-MB-175_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 ; 161.02 1.34E-11 4306000000 716990 806490 789430 764100 926640 1069350 832100 821650 738380 839870 FALSE TRUE 745297.3188 944998.3839 810003.1943 915236.6994 769130.0638 821009.6687 766877.8277 810637.1257 711805.848 1004426.446 0.742012839 0.940833834 0.80643356 0.911203307 0.765740554 0.817391529 0.763498244 0.807064697 0.708668963 1 19.93794049 3.221546322 24.99173067 0.798517852 0.853479883 0.036251743 0.087748986 587.5704981 863061.0966 0.02300563 0.027564011 1665.506461 -3.221546322 0.054962031 TLCGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLCGCR 6 0 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 163.53 0.018286 394980000 244220 272950 269550 245710 353130 372050 292240 258960 255570 320010 FALSE TRUE 253861.9942 319827.0392 276574.6944 294310.7046 293105.0887 285647.026 269333.4652 255489.0648 246372.0856 382709.8325 0.663327599 0.835690678 0.72267465 0.769017881 0.765867673 0.74638016 0.703753712 0.667579046 0.643756874 1 18.54589144 -1.079608914 5.470538704 1.000002532 0.725509835 0.691810614 0.055212874 1.76E-06 2.97E-07 0.055321425 0.013039264 0.083251312 1.079608914 -0.274492698 TLDDSANRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLDDSANRR 9 1 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 ;;; 122.94 0.00091673 864470000 722280 821510 789400 784110 938710 1013270 799050 802210 805540 820110 FALSE TRUE 750796.1721 962597.952 809972.4125 939204.6177 779148.4095 777953.3988 736418.3731 791457.6871 776548.7728 980794.8525 0.765497668 0.981446782 0.82583265 0.957595378 0.794405076 0.793186666 0.750838334 0.806955384 0.791754535 1 19.90359188 3.204232651 24.99989388 0.806738718 0.885599863 0.086714666 0.085674842 302.5613381 220344.4174 0.02255411 0.026958532 1600.415141 -3.204232651 0.078861146 TLDGFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 114.78 0.0093439 5898100000 5529500 4067400 4889500 4017200 7600700 5847600 5509000 4812500 5182700 2941400 FALSE TRUE 5747808.93 4765944.31 5016924.387 4811790.17 6308735.729 4489583.521 5077190.185 4747996.309 4996175.639 3517711.013 1.633962798 1.354842479 1.426190033 1.367875346 1.793420695 1.276279804 1.443322139 1.349740297 1.420291667 1 21.74620554 -1.72801178 0.281034033 0.58297741 1.498525297 0.500183228 0.140146033 21.27685822 1.027828489 6.159631626 0.164274905 0.018706314 1.72801178 0.915547887 TLDRS(ph)GDLGDMEPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLDRSGDLGDMEPLK 15 1 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20;O60716-27;O60716-29;O60716-32;O60716-31;O60716-25;O60716-26;O60716-28;O60716-30;H0YC95 O60716-13 CTNND1 Catenin delta-1 1 T(0.002)LDRS(0.998)GDLGDMEPLK;T(0.091)LDRS(0.909)GDLGDMEPLK;T(0.004)LDRS(0.996)GDLGDMEPLK 141.78 2.85E-06 426920000 553820 433080 466511 378744 619170 666910 604680 473430 512120 319131 TRUE FALSE 575685.2412 507458.1211 478668.6599 453658.4328 513923.7046 512030.2596 557283.6016 467084.4452 493688.9012 381658.6093 1.508377454 1.329612666 1.254180171 1.188649808 1.346553417 1.341592321 1.460162533 1.223827876 1.293535346 1 18.54192321 0.499997244 1.09910498 1.000124553 1.331435835 0.540892932 0.091886494 1.461176969 2.400040866 0.089684885 0.027727498 3.162257592 -0.499997244 0.331311282 TLDS(ph)DEERPRPAPPDWSHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TLDSDEERPRPAPPDWSHMR 20 2 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 T(0.003)LDS(0.997)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.002)LDS(0.998)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.001)LDS(0.999)DEERPRPAPPDWSHMR;TLDS(1)DEERPRPAPPDWSHMR;T(0.06)LDS(0.94)DEERPRPAPPDWSHMR;T(0.088)LDS(0.912)DEERPRPAPPDWSHMR 266.38 5.11E-37 5880180000 1363070 1608620 1712440 1574410 1834960 2079270 1719850 1646470 1623360 1580560 TRUE FALSE 1416885.056 1884887.972 1757067.593 1885823.599 1523054.155 1596391.054 1585043.663 1624401.763 1564935.591 1890240.47 0.749579262 0.99716835 0.929547124 0.997663328 0.805746242 0.844543898 0.838540751 0.859362493 0.827902912 1 20.85013835 3.225886377 24.99997862 0.853593196 0.924899277 0.09358408 0.081241727 408.2334948 805240.0972 0.021967581 0.026422088 1682.233886 -3.225886377 0.071306081 TLDSGTSEIVKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLDSGTSEIVKSPR 14 1 Q9H501 Q9H501 ESF1 ESF1 homolog 1 TLDSGTSEIVKS(1)PR;TLDSGTSEIVKS(1)PR 148.52 4.69E-06 467950000 712190 523290 610290 476830 780420 760890 691460 629860 679430 473380 TRUE FALSE 740307.8111 613160.9869 626194.6588 571145.5508 647764.4872 584184.8289 637261.5584 621417.7569 654977.447 566129.7476 1.307664567 1.083075019 1.10609743 1.008859812 1.144197933 1.031892126 1.125645775 1.097659608 1.156938758 1 19.11077321 4.739321956 24.76520521 1.087846007 1.307664645 0.625463441 0.05188153 33.55224477 1091185.575 0.011273299 0.067364797 54868.35701 -4.739321956 0.219818638 TLEAEFNSPS(ph)PPTPEPGEGPR ddPTM_MDA-MB-175_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 TLEAEFNS(0.009)PS(0.991)PPTPEPGEGPR 206.8 4.21E-22 63877000 43172 50320 51679 49318 49726 63202 54246 54232 48341 50662 TRUE FALSE 44876.4639 58962.06856 53025.79719 59072.9532 41273.59228 48524.29334 49994.05677 53505.10875 46601.21685 60588.24892 0.740679335 0.973160136 0.875182864 0.97499027 0.681214477 0.800886215 0.825144441 0.883093829 0.769146125 1 15.88675039 7.179329895 9.400449133 0.850562586 0.173281424 0 0.102471442 0 0 0.021427915 0 15112276.64 -7.179329895 -0.677281162 TLEAEFNSPSPPT(ph)PEPGEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 TLEAEFNSPS(0.009)PPT(0.99)PEPGEGPR;TLEAEFNS(0.028)PS(0.167)PPT(0.804)PEPGEGPR 208.28 3.59E-21 80715000 131073 151650 154448 150762 164141 197777 154368 164057 164060 160561 TRUE FALSE 136247.8633 177694.7078 158473.0418 180582.2736 136240.3714 151846.2891 142268.2328 161858.0843 158155.5126 192019.8538 0.709550916 0.925397579 0.825295086 0.940435429 0.709511901 0.790784318 0.740903766 0.842923693 0.823641459 1 17.55089596 -1.995831298 6.146209128 1.17452131 0.814872823 0.356736067 0.075630258 0.047468748 3.22E-05 0.019219243 0.016449001 0.01009645 1.995831298 -0.359648487 TLEDEEEQERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEDEEEQERER 12 1 O00515;E9PDI4;A0A0J9YYF6;A0A0J9YW63;A0A0J9YVY2 O00515 LAD1 Ladinin-1 0 ; 215.14 3.84E-11 848850000 683810 656180 691690 694240 859520 895350 711980 663810 689640 714100 FALSE TRUE 710807.3468 768873.8106 709716.0096 831558.5999 713419.0974 687418.5317 656173.1472 654912.7127 664819.9911 854014.2227 0.832313242 0.900305627 0.831035351 0.973705798 0.835371447 0.804926327 0.768339835 0.766863941 0.778464777 1 19.70390057 3.00743299 24.93083787 0.803287592 0.884531147 0.10153949 0.074600348 260.6591378 874262.8827 0.020206161 0.024103991 1017.262395 -3.00743299 0.081243555 TLEDPDLNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEDPDLNVR 10 0 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 156.92 2.35E-05 201659000 151317 159169 157896 172769 188178 213700 167513 159896 171574 148474 FALSE TRUE 157291.112 186505.0376 162010.8995 206942.1925 156191.5708 164071.4137 154382.8933 157752.8557 165399.0853 177564.6376 0.885824532 1.050350115 0.912405204 1.165447103 0.879632189 0.924009509 0.869446166 0.888424958 0.931486626 1 17.43798477 TLEDPDLNVRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEDPDLNVRR 11 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 128.01 0.0017766 0 623210 810570 759890 574950 1008030 910610 460720 674540 732500 961620 FALSE TRUE 647814.812 949779.0921 779693.3577 688673.3939 836685.4207 699134.6279 424607.5625 665498.8946 706137.4681 1150031.028 0.56330203 0.82587258 0.677975932 0.598830273 0.72753291 0.607926753 0.369214006 0.578679078 0.614016014 1 20.13324135 -0.327905114 9.94169658 1 0.614686287 0.510293578 0.11217426 0 0 0.115653522 0.027259797 0.469996783 0.327905114 -0.385313713 TLEEDEEELFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLEEDEEELFK 11 0 P43487;F6WQW2;P43487-2;C9JJ34;C9JDM3 P43487 RANBP1 Ran-specific GTPase-activating protein 0 ;;; 269.14 3.36E-21 972110000 1651230 970174 1360180 1006222 1841380 1779640 1680270 1391450 1484260 918729 FALSE TRUE 1716421.835 1136793.838 1395627.408 1205249.708 1528382.885 1366345.581 1548566.047 1372799.889 1430841.773 1098736.357 1.562178064 1.0346375 1.270211365 1.096941682 1.391036963 1.243560907 1.409406393 1.249435207 1.302261241 1 20.06741382 -1.162529398 5.415183561 0.999991935 1.276474833 0.259932046 0.143407707 1.27E-05 1.96E-06 0.126059645 0.029711677 0.068781335 1.162529398 0.276482898 TLEEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLEEEAK 7 0 P35579 P35579 MYH9 Myosin-9 0 89.296 0.067322 0 151820 102280 137150 111250 183830 175810 185280 148470 175430 100520 FALSE TRUE 157813.9708 119845.7944 140724.2417 133254.918 152582.6423 134980.7919 170757.2695 146480.0025 169116.3086 120214.9694 1.312764721 0.996929043 1.170604978 1.10847192 1.269248272 1.122828484 1.420432666 1.218483881 1.406782445 1 16.87525703 3.233870687 24.75686102 1.255137032 1.138131852 0.091140887 0.136686179 192.029452 1013670.76 0.03624254 0.044679313 1713.447045 -3.233870687 -0.117005181 TLEFVPINLHLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEFVPINLHLQR 13 0 O15327;D6RJC3;E7EQN9;E9PHC0;E9PCZ3;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ; 190.1 4.70E-06 896530000 1366880 1588300 1548700 1486530 2176810 2123690 1665300 1574410 1590740 1994400 FALSE TRUE 1420845.478 1861078.17 1589060.394 1780561.197 1806796.614 1630495.182 1534769.435 1553307.609 1533489.578 2385164.495 0.595701253 0.780272461 0.666226752 0.746515052 0.757514468 0.683598631 0.643464817 0.6512371 0.642928226 1 21.18565734 -1.446002297 3.214593602 1.005165733 0.686938711 0.741267845 0.055773999 45048500.89 58445305.42 2115099.12 0.013430428 0.035809454 1.446002297 -0.318227021 TLEGELHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 238.01 3.43E-12 27975000000 6872660 8029870 7817310 7655070 8226990 9259780 8163440 7907360 7323310 7291780 FALSE TRUE 7143997.924 9408937.709 8021035.521 9169219.998 6828569.178 7109336.428 7523568.242 7801374.773 7059745.504 8720464.681 0.819222161 1.078949122 0.919794508 1.051460023 0.783051068 0.815247431 0.862748548 0.894605398 0.809560701 1 23.05597358 3.236709436 24.99999438 0.856432876 0.971930072 0.264276674 0.086719451 58.78726912 793919.9534 0.02292529 0.0287661 1724.683609 -3.236709436 0.115497196 TLEGELHDLRGQVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEGELHDLRGQVAK 15 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 ; 221.59 9.10E-13 388960000 539910 501850 641260 313460 1042070 775520 395810 606140 805830 731240 FALSE TRUE 561226.0637 588038.8336 657971.7624 375461.4524 864939.3136 595417.2331 364785.3779 598015.6847 776828.3357 874512.4776 0.641758783 0.672419032 0.752386935 0.429338016 0.989053142 0.680856189 0.417129986 0.683827504 0.888298744 1 19.73811944 1.142060512 3.478050939 0.99066231 0.654337294 0.372692326 0.151813742 0.229509589 4.92498213 0.139964897 0.03711241 13.86949066 -1.142060512 -0.336325016 TLEGGRKPLHYAADCGQLEILEFLLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLEGGRKPLHYAADCGQLEILEFLLLK 27 2 P58546 P58546 MTPN Myotrophin 0 ; 74.074 0.010612 661060000 288320 242980 406830 172674 608550 435800 289190 365600 498420 395610 FALSE TRUE 299703.0962 284709.9249 417432.324 206828.4018 505108.8884 334592.0546 266522.5321 360699.73 480481.9616 473122.2051 0.633458107 0.601768257 0.882292819 0.437156404 1.067607656 0.707200066 0.563327042 0.76238174 1.01555572 1 18.85185335 1.290620081 4.496591084 1.012393172 0.704195843 0.352021458 0.164721976 0.208260115 7.890524596 0.121822553 0.039423646 19.52630557 -1.290620081 -0.308197329 TLEPVKPPTVPNDYMT(ph)SPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.001)MT(0.633)S(0.366)PAR;TLEPVKPPTVPNDYMT(0.565)S(0.434)PAR 102.67 0.00047933 170330000 256760 207404 240110 201208 294000 287600 279060 245600 236090 202175 TRUE FALSE 266897.0831 243024.0236 246367.4639 241006.3419 244025.985 220809.2586 257186.548 242308.1337 227593.167 241787.3204 1.103850618 1.005114839 1.01894286 0.996769977 1.009258817 0.913237544 1.063689145 1.002154014 0.941294881 1 17.88337906 TLEPVKPPTVPNDYMTS(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.001)MT(0.169)S(0.829)PAR;TLEPVKPPTVPNDYMT(0.191)S(0.808)PAR;TLEPVKPPTVPNDYMT(0.479)S(0.52)PAR 102.27 0.00018318 677140000 562400 424720 492300 429870 615160 600860 557400 511920 505540 408700 TRUE FALSE 584603.9863 497662.3561 505129.7424 514897.003 510595.3229 461319.3711 513709.5315 505058.5497 487345.7142 488776.94 1.196054761 1.018178878 1.033456575 1.053439639 1.044638732 0.943823927 1.051010163 1.03331092 0.997071822 1 18.8988167 4.739411019 24.53876063 1.022351273 1.196054833 0.739737803 0.031385625 27.70365041 799232.7793 0.007391637 0.044754785 54879.61039 -4.739411019 0.17370356 TLEQHDNIVTHYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLEQHDNIVTHYK 13 0 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;; 198.23 7.37E-08 1962350000 2081010 1843050 2311760 1917750 2739420 2720300 2399230 2117100 2367170 1753950 FALSE TRUE 2163169.882 2159579.501 2372006.365 2297075.226 2273774.367 2088551.552 2211172.083 2088723.737 2281976.014 2097602.921 1.031258042 1.029546383 1.13081763 1.09509536 1.083987033 0.995684898 1.054142355 0.995766985 1.087897042 1 21.00031017 2.755697658 24.64939159 1.02617249 1.075976265 0.275849729 0.038371817 891.3583924 1282101.161 0.011835776 0.012526707 569.7674799 -2.755697658 0.049803775 TLETVPLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLETVPLER 9 0 P22626;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 117.04 0.0028307 153830000 104240 135340 114130 127940 145470 160920 119040 126870 125080 145350 FALSE TRUE 108355.4757 158583.5922 117104.3216 153246.1501 120743.0614 123548.7688 109709.3337 125169.5152 120578.3952 173828.5496 0.623346832 0.912298886 0.673677148 0.881593677 0.694610072 0.710750731 0.6311353 0.720074553 0.693662782 1 17.40730552 -0.980073736 4.75856234 1.000002705 0.728979716 0.445596129 0.091393274 3.45E-06 7.41E-07 0.083012544 0.01956597 0.104695078 0.980073736 -0.271022989 TLFGLHLSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLFGLHLSQK 10 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 159.83 7.56E-06 349100000 97549 619880 533640 548960 923970 1043400 551820 751690 548810 1131000 FALSE TRUE 101400.3098 726339.568 547547.0968 657542.6495 766913.9094 801086.1629 508566.9065 741614.8251 529058.4353 1352597.796 0.074967082 0.536995972 0.404811466 0.486133167 0.566993316 0.592257481 0.375992707 0.548289246 0.391142465 1 20.36730148 -5 0.213673146 3.61109663 0.382163191 0.594569322 0.140050267 102.328701 1.021914564 115.033708 0.273410936 1.00E-05 5 -3.228933439 TLFLGIPDENFEDHS(ph)APPS(ph)PEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 2 T(0.019)LFLGIPDENFEDHS(0.982)APPS(1)PEEK 42.709 0.08298 0 58028 26165 32592 28094 41139 60099 42199 33000 34257 24356 TRUE FALSE 60318.99025 30658.63521 33441.37429 33650.90935 34146.20747 46141.91806 38891.33211 32557.68898 33024.09726 29128.09188 2.070818456 1.052545266 1.148079814 1.155273387 1.172277526 1.584103698 1.335182966 1.117741908 1.133754226 1 14.83012358 4.744742965 24.90513163 1.204521761 2.070818859 0.739970741 0.156611121 355.0219193 1430138.555 0.038921313 0.36132193 55557.53451 -4.744742965 0.866297099 TLFLGIPDENFEDHSAPPS(ph)PEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 1 TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHS(0.003)APPS(0.997)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK;TLFLGIPDENFEDHSAPPS(1)PEEK 171.15 4.19E-12 362475000 466281 238560 359096 291395 533851 517129 454009 368503 426595 227782 TRUE FALSE 484690.1339 279530.8243 368454.3368 349032.0613 443107.1977 397033.6269 418422.5882 363563.82 411241.9293 272411.5218 1.779257099 1.026134366 1.352565172 1.281267617 1.626609605 1.457477365 1.53599446 1.334612493 1.509634859 1 18.0554282 -1.043249232 4.463386031 0.999980967 1.419312115 0.305279112 0.195201537 4.09E-05 8.76E-06 0.176716449 0.041650234 0.090521297 1.043249232 0.419331148 TLFYSSPLLGPSSTSEAVGSSS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLFYSSPLLGPSSTSEAVGSSSPR 24 0 Q5SXH7-4;Q5SXH7-3;Q5SXH7-2;Q5SXH7-1;Q5SXH7 Q5SXH7-4 PLEKHS1 Pleckstrin homology domain-containing family S member 1 1 TLFYSSPLLGPSSTSEAVGS(0.017)S(0.121)S(0.862)PR;TLFYSSPLLGPSSTSEAVGSS(0.006)S(0.994)PR 215.37 9.13E-33 176259000 73380 84028 81700 70783 95737 107653 77515 83628 77840 83459 TRUE FALSE 76277.09906 98459.15535 83829.16912 84783.66613 79463.65894 82652.22225 71439.17175 82507.10345 75038.55361 99811.19313 0.764213879 0.986454047 0.839877437 0.849440463 0.796139756 0.828085705 0.71574309 0.826631772 0.751804996 1 16.60691399 3.537552167 2.140783438 0.80567734 0.87709808 0.029818548 0.087086112 0.686162836 6.218342536 0.023556865 0.040164796 3447.880198 -3.537552167 0.07142074 TLGECGFTSQTARPQAPATVGLAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLGECGFTSQTARPQAPATVGLAFR 25 1 B8ZZU8;Q15370;Q15370-2;I3L0M9 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 273.66 4.95E-53 501120000 24814 13530 25717 22677 27822 33802 19116 22598 24741 20215 FALSE TRUE 25793.67588 15853.67225 26387.20615 27162.44292 23092.82638 25951.99777 17617.63797 22295.11077 23850.57624 24175.74221 1.066923847 0.655767757 1.0914745 1.123541221 0.955206511 1.073472638 0.728732041 0.922209981 0.986549908 1 14.56127256 1.09205082 6.174093045 0.999317459 0.944794974 0.010761452 0.146897631 1.147922075 57.81298798 0.138857007 0.034922742 12.36092071 -1.09205082 -0.054522485 TLGEDDPWLDDTAAWIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLGEDDPWLDDTAAWIER 18 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ;; 151.99 1.02E-07 100440000 121964 140722 150995 134329 158148 174238 152447 156724 161885 144618 FALSE TRUE 126779.2329 164889.9088 154930.0537 160898.8753 131266.0594 133773.8651 140497.8058 154623.3711 156058.7905 172953.1282 0.733026538 0.953379164 0.895792145 0.930303354 0.758968981 0.773468896 0.812346138 0.894018933 0.902318403 1 17.40002158 0.990496959 1.509942314 0.997428468 0.843663732 0.3311989 0.07001267 0.528678028 2.463305844 0.068019162 0.020067848 9.783561047 -0.990496959 -0.153764736 TLGT(ph)PTQPGSTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLGTPTQPGSTPR 13 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 TLGT(0.771)PT(0.229)QPGSTPR;T(0.001)LGT(0.999)PTQPGSTPR;TLGT(0.998)PT(0.002)QPGSTPR;TLGT(0.995)PT(0.005)QPGSTPR 196.97 1.54E-06 706246000 757020 857550 827850 796770 903270 1085480 899880 853260 851800 766170 TRUE FALSE 786907.7341 1004827.542 849424.4511 954368.7279 749732.488 833393.7206 829345.0542 841823.4454 821143.8844 916286.3423 0.858801117 1.096630491 0.92702948 1.041561665 0.81822947 0.909534151 0.905115591 0.918734032 0.896165147 1 19.80543899 3.252408302 24.99998528 0.904880794 0.985409142 0.19650413 0.07197694 329.9088375 595598.9581 0.018198436 0.024515849 1788.167933 -3.252408302 0.080528348 TLGTMIAGDTSGDYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLGTMIAGDTSGDYRR 16 1 P20073-2;P20073 P20073-2 ANXA7 Annexin A7 0 ;; 226.09 1.01E-14 891090000 391150 418660 450640 382500 470970 525500 448790 439240 439380 402050 FALSE TRUE 406592.904 490561.5983 462384.0486 458157.3584 390914.6876 403460.589 413612.6671 433352.7063 423566.7996 480823.9998 0.845616908 1.020251898 0.96164927 0.952858756 0.813009933 0.839102435 0.860216352 0.901270957 0.880918589 1 18.87514938 3.278520694 24.51624288 0.875734501 0.95164526 0.192552807 0.061390904 167.7162564 102895.676 0.016191584 0.021923154 1898.981325 -3.278520694 0.075910759 TLHCEGTEINS(ph)DDEQESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLHCEGTEINSDDEQESK 18 0 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGT(0.001)EINS(0.999)DDEQESK 92.95 0.0014426 315760000 49957 55139 131050 51080 173030 94362 197750 129140 136740 45979 TRUE FALSE 51929.34094 64608.69433 134465.2707 61183.47154 143618.4224 72447.85557 182249.8383 127409.0895 131818.7541 54987.70473 0.944380952 1.174966197 2.445369766 1.112675494 2.611827919 1.317528272 3.314374353 2.317046877 2.397240524 1 15.74682145 4.776659611 0.670115031 2.260902852 9.39E-12 0.201852365 0.715856647 4.365735809 1.433178277 0.284039404 7.654588794 59794.27593 -4.776659611 -2.260902852 TLHCEGTEINS(ph)DDEQESKEVEETATAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLHCEGTEINSDDEQESKEVEETATAK 27 1 Q9BPX3;H0Y9Z8 Q9BPX3 NCAPG Condensin complex subunit 3 1 TLHCEGTEINS(1)DDEQESKEVEETATAK 190 3.98E-18 495720000 713160 322850 475330 286770 702380 688780 564310 507530 544410 295560 TRUE FALSE 741316.1075 378296.9761 487717.4903 343492.2501 582989.6985 528821.2836 520077.9077 500727.3905 524816.7904 353469.3232 2.097257269 1.070239908 1.379801466 0.971773864 1.649336053 1.4960882 1.471352317 1.416607772 1.48475909 1 18.43122549 -1.478671316 6.072322277 0.999707372 1.428539867 0.173579842 0.29069263 0.001063929 9.13E-05 0.260031777 0.061249287 0.033214574 1.478671316 0.428832495 TLHEWCDGCEAVLLGIEQQVLR ddPTM_MDA-MB-175_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 ; 157.97 4.65E-10 81949000 54650 63609 60974 67595 66880 80974 59933 64582 64174 69714 FALSE TRUE 56807.6242 74533.35094 62563.03253 80965.08925 55511.76149 62169.01567 55235.29485 63716.38392 61864.39028 83373.12354 0.68136615 0.893973355 0.750398088 0.971117379 0.665823219 0.745672143 0.662507203 0.7642317 0.742018382 1 16.34729477 3.193459718 24.99991674 0.74503512 0.823926221 0.049873328 0.114355704 287.0606563 159119.8604 0.030306555 0.036223409 1561.204226 -3.193459718 0.078891101 TLHGQETYTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLHGQETYTPR 11 0 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-4 Q9BUK6-2 MSTO1 Protein misato homolog 1 0 ;; 161.99 2.57E-05 149220000 198181 220806 221246 221656 265220 281309 258899 247707 237746 244878 FALSE TRUE 206005.3389 258727.7129 227011.8525 265498.8952 220137.9991 215979.248 238605.8199 244386.8928 229189.5679 292857.1556 0.703432834 0.883460444 0.775162389 0.906581554 0.751690696 0.737490083 0.814751545 0.834491793 0.78259849 1 18.15983762 -1.807637437 2.506407136 1.064671708 0.803658928 0.498566656 0.060344792 8179760.566 5466846.486 3210135.213 0.013713929 0.015572651 1.807637437 -0.26101278 TLHNLVIQYASQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLHNLVIQYASQGR 14 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;G5E9S8;E9PQ02;Q9H0B6;Q9H0B6-2;A8MZ87;A8MX29 Q07866-6;Q9H0B6 KLC1;KLC2 Kinesin light chain 1;Kinesin light chain 2 0 ; 146.78 8.21E-06 1607930000 929600 1090020 1020400 915710 1145820 1357890 959390 1026600 1043770 1113150 FALSE TRUE 966301.3258 1277222.456 1046992.462 1096834.705 951053.9257 1042540.627 884190.5049 1012840.106 1006204.922 1331250.43 0.725859916 0.959415619 0.786472957 0.823913127 0.714406474 0.783128856 0.664180446 0.760818613 0.755834439 1 20.34435056 TLHPDLGTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLHPDLGTDK 10 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 143.96 3.31E-05 833610000 2069330 1370710 1703400 1591480 2354000 2303800 2559700 1806620 1846270 1044210 FALSE TRUE 2151028.746 1606118.78 1747792.003 1906269.994 1953867.921 1768777.364 2359064.025 1782405.214 1779823.103 1248802.957 1.722472496 1.286126663 1.399573883 1.526477803 1.564592645 1.416378264 1.88906025 1.427290994 1.425223326 1 20.25211443 0.753726289 2.057088692 1.000800339 1.527123724 0.486844875 0.16298804 0.819194631 5.377654987 0.151367631 0.041659468 5.671870267 -0.753726289 0.526323385 TLHPDLGTDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLHPDLGTDKDK 12 1 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 162.32 3.79E-05 679220000 2884700 1199390 1839820 1354930 2617500 2587500 2902700 1928230 2236900 909180 FALSE TRUE 2998590.183 1405375.903 1887767.221 1622931.11 2172578.285 1986592.339 2675178.789 1902385.231 2156394.406 1087316.414 2.757789863 1.292517877 1.736170996 1.49260242 1.998110447 1.827060011 2.460349863 1.749615114 1.983226206 1 20.0523404 TLHPDLGTDKDKEQWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 252.36 8.90E-27 3156700000 8335600 2492970 4944900 2608320 7338600 5678100 6631300 4263100 5418500 1732090 FALSE TRUE 8664695.924 2921118.205 5073768.156 3124237.911 6091187.393 4359447.327 6111521.378 4205960.118 5223489.243 2071459.873 4.182893446 1.410173686 2.449368305 1.508229994 2.94052879 2.104528977 2.950345048 2.030432823 2.521646358 1 20.98221644 -1.389800459 2.762103266 0.971375228 2.394690896 0.244260251 0.761277299 11698738.26 13140091.46 2671968.368 0.173297505 0.04075675 1.389800459 1.423315667 TLHS(ph)PPLQLQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLHSPPLQLQQR 12 0 B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;A0A2R8YGT1;F8W9A8;Q6PFW1 B7WPL9 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR;TLHS(1)PPLQLQQR 190.86 3.93E-06 3004610000 802740 913630 885810 906730 1067710 1151940 926660 921460 936820 1001460 TRUE FALSE 834432.7951 1070538.845 908894.9363 1086078.488 886221.0356 884419.3928 854025.9678 909109.3359 903104.0312 1197676.913 0.696709426 0.893846107 0.75888157 0.906820926 0.739950003 0.738445722 0.713068741 0.759060583 0.754046456 1 20.19180735 -1.310361548 3.491262393 1.000880754 0.774657986 0.50665662 0.067063437 28731403.1 46987950.29 268903.4434 0.015815948 0.048937125 1.310361548 -0.226222768 TLHSCSVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLHSCSVR 8 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ; 79.474 0.027994 43922000 229010 219240 253960 212430 330900 328270 272110 233740 247100 281560 FALSE TRUE 238051.4916 256892.7645 260578.4062 254448.02 274653.7362 252034.2675 250781.3072 230607.0976 238206.9193 336726.2912 0.706958434 0.762912702 0.773858214 0.75565237 0.815658722 0.748484078 0.744763072 0.684850288 0.707420019 1 18.36121684 -1.701090257 2.747064747 1.038619069 0.744097502 0.82168766 0.035705324 7050437.883 6115565.95 1884785.748 0.009616522 0.019902597 1.701090257 -0.294521567 TLHSDDEGTVLDDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLHSDDEGTVLDDSR 15 0 O00170;E9PMH2 O00170 AIP AH receptor-interacting protein 0 ;;; 228.03 7.60E-13 1644400000 865934 1001685 1030658 977666 1084670 1223120 974642 999050 1012442 1103869 FALSE TRUE 900121.743 1173716.607 1057517.794 1171045.417 900298.1808 939068.9166 898247.0133 985659.3689 976004.4102 1320150.996 0.681832416 0.889077545 0.80105821 0.887054148 0.681966066 0.711334476 0.680412329 0.746626236 0.73931271 1 20.33227152 3.234128491 24.99990007 0.739885189 0.819085906 0.043395991 0.102026627 226.6427145 1278404.956 0.026904294 0.033211525 1714.464475 -3.234128491 0.079200717 TLIPS(ph)PPPRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLIPSPPPRPK 11 1 J3KSG3;J3KSS7;Q9NZ52-3;Q9NZ52-4;Q9NZ52-2;Q9NZ52 J3KSG3 GGA3 ADP-ribosylation factor-binding protein GGA3 1 TLIPS(1)PPPRPK;TLIPS(1)PPPRPK 106.32 0.0014213 603680000 1755170 1263200 1616060 1333310 2051390 2018740 1669540 1621560 1611490 1264030 TRUE FALSE 1824465.467 1480144.774 1658175.851 1597034.738 1702695.461 1549918.229 1538677.092 1599825.641 1553492.79 1511692.477 1.206902524 0.979130872 1.096900247 1.056454777 1.126350423 1.025286725 1.017850598 1.058300987 1.027651333 1 20.52773325 2.710127474 24.20685843 1.03109984 1.084983473 0.261541277 0.055375518 796.8536739 678408.2092 0.01673571 0.015782414 513.0119412 -2.710127474 0.053883633 TLKPEEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLKPEEQR 8 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 78.934 0.026759 226790000 563620 375090 529860 436360 635970 630210 707850 561560 596960 342130 FALSE TRUE 585872.1528 439508.7897 543668.5869 522670.7056 527868.0466 483853.2784 652366.8674 554033.2067 575475.5262 409163.823 1.43187672 1.074163367 1.328730832 1.277411824 1.290114172 1.182541689 1.59439039 1.354062054 1.406467273 1 18.64231907 TLKPTYRT(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLKPTYRTPER 11 2 H0Y9P1;Q9NSY1;Q5H9B9 H0Y9P1 BMP2K;BMP2KL BMP-2-inducible protein kinase;Putative BMP-2-inducible kinase-like protein 1 TLKPT(0.004)YRT(0.996)PER 85.909 0.0239 203470000 242190 219100 255440 207590 271740 283910 255550 241440 235080 214150 TRUE FALSE 251751.8482 256728.7206 262096.9762 248650.6824 225549.7319 217976.2052 235519.3232 238203.8917 226619.5167 256108.5924 0.982988684 1.002421349 1.023382206 0.970879892 0.880680065 0.851108521 0.919607269 0.930089418 0.884857141 1 17.96639613 3.407394236 4.822690019 0.907377879 1.002252157 0.546721078 0.038093809 0.143832236 6.390364467 0.01050162 0.014503358 2555.019597 -3.407394236 0.094874278 TLLEGSGLESIISIIHSSLAEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 333.01 1.32E-86 3128600000 90415 496960 397030 684180 481860 647820 368150 633160 468150 696560 FALSE TRUE 93984.65402 582309.0142 407376.928 819508.7619 399953.6093 497373.6228 339293.441 624673.5258 451301.3729 833037.5956 0.112821624 0.699018889 0.489025862 0.983759636 0.480114717 0.597060235 0.407296673 0.74987435 0.541753908 1 19.66802208 -5 0.183663742 2.712170106 0.49733249 0.284213824 0.21465726 182.031697 1.764446142 114.2415671 0.60468495 1.00E-05 5 -2.214837615 TLLEQLDDDQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLLEQLDDDQ 10 0 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 102.52 0.0068296 19374000 32138 33694 33593 29596 34630 41190 35604 35806 31954 33066 FALSE TRUE 33406.83306 39480.6824 34468.46118 35450.00046 28743.60497 31624.24674 32813.26545 35326.07914 30803.98178 39544.64961 0.844787686 0.998382405 0.871634001 0.89645504 0.726864576 0.799709874 0.829777625 0.893321334 0.778967119 1 15.27119489 3.449234469 24.999836 0.832788355 0.909240408 0.140635579 0.077690726 351.0071492 314668.5063 0.020632897 0.027937584 2813.419341 -3.449234469 0.076452053 TLLISSLS(ph)PALPAEHLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 TLLIS(0.003)S(0.003)LS(0.994)PALPAEHLEDR;TLLIS(0.012)S(0.003)LS(0.984)PALPAEHLEDR 180.45 2.16E-14 96004000 52486 63281 62264 59893 65788 75914 62342 51278 52804 67085 TRUE FALSE 54558.18781 74149.01949 63886.65099 71739.65664 54605.37926 58284.12399 57455.47114 50590.70228 50903.59435 80229.02133 0.680030579 0.924216926 0.796303506 0.894185863 0.680618788 0.726471831 0.716143238 0.630578579 0.634478565 1 16.29183658 3.226948793 24.98113573 0.706454812 0.828909365 0.109672179 0.116121151 324.3174672 697720.443 0.03117044 0.0375541 1686.354177 -3.226948793 0.122454553 TLLIVSHDQGFLDDVCTDIIHLDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLLIVSHDQGFLDDVCTDIIHLDAQR 26 0 Q8NE71;Q8NE71-2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 ;; 279.96 4.99E-61 414528000 112116 129874 146010 149514 162436 184309 163610 144189 174752 122485 FALSE TRUE 116542.4263 152178.8492 149815.1405 179087.4229 134825.1867 141506.028 150785.8207 142256.3823 168462.7097 146483.5906 0.795600557 1.03887984 1.022743503 1.222576687 0.920411537 0.966019657 1.029370048 0.971142103 1.150044923 1 17.16037953 4.739691156 24.41624019 1.031389023 0.79560045 0.418097843 0.084835723 68.60114052 1481313.341 0.019867241 0.122034919 54915.02122 -4.739691156 -0.235788572 TLLLS(ph)SDDEF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLLLSSDDEF 10 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 TLLLS(0.688)S(0.312)DDEF 100.15 0.0044164 21235000 46932 76090 79068 90423 76312 106930 75718 79826 82503 82989 TRUE FALSE 48784.9116 89157.8656 81128.57704 108308.3995 63340.5135 82097.12804 69783.02531 78756.06304 79533.73315 99249.10563 0.491540063 0.898324121 0.817423759 1.091278343 0.638197323 0.827182548 0.703109865 0.793519121 0.801354658 1 16.59876648 -1.806646767 1.438117562 1.109799495 0.791570664 0.155323813 0.14987453 42020.94775 13572.55546 15948.12447 0.039428256 0.015608215 1.806646767 -0.318228831 TLLSESSSQSSKS(ph)PSLSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 TLLSESSSQSSKS(0.803)PS(0.196)LSSK;TLLSESSSQSS(0.002)KS(0.804)PS(0.193)LSSK 273.45 1.35E-39 829980000 816330 428490 648840 475140 909310 847550 746160 613790 760960 371380 TRUE FALSE 848559.3387 502079.8243 665749.3034 569121.2738 754745.811 650719.3572 687674.0295 605563.149 733573.1982 444144.8005 1.910546601 1.130441747 1.498946521 1.281386776 1.699323757 1.465106327 1.548310435 1.363436312 1.651653239 1 18.76067058 -1.223571907 5.060543256 0.999942926 1.484825464 0.338731642 0.21009725 0.00012114 1.86E-05 0.182154084 0.042929095 0.059762409 1.223571907 0.484882538 TLLTGDGGGEATGS(ph)PLAQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLLTGDGGGEATGSPLAQGK 20 0 A0A494BZV2;Q6WCQ1-2;J3KSW8;H0Y2S9;Q6WCQ1-3;Q6WCQ1 A0A494BZV2;Q6WCQ1 MPRIP Myosin phosphatase Rho-interacting protein 1 TLLTGDGGGEAT(0.003)GS(0.997)PLAQGK 307.82 1.16E-48 0 49982 42901 50356 37668 63726 76356 53718 50222 54398 39783 TRUE FALSE 51955.32795 50268.91303 51668.31873 45118.61797 52893.87728 58623.47619 49507.44279 49548.85624 52440.22661 47577.71716 1.092009686 1.056564208 1.085977256 0.948314057 1.111736343 1.232162443 1.040559441 1.041429879 1.102201403 1 15.53799843 -1.458193279 3.022593469 0.998258668 1.075889787 0.107630004 0.067708782 1731676.16 1725230.97 17302.53893 0.016178434 0.034818233 1.458193279 0.077631119 TLMELLNQMDGFDTLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLMELLNQMDGFDTLHR 17 0 A0A087X2I1;P62333 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 ;; 218.12 4.75E-15 3046128000 559480 650474 636789 675756 777438 848760 706471 710135 661762 691703 FALSE TRUE 581568.7024 762187.8495 653384.2445 809418.5199 645289.3665 651648.3531 651095.957 700616.8019 637945.3149 827228.9594 0.70303233 0.921374718 0.789846918 0.978469758 0.780061383 0.787748477 0.78708071 0.846944239 0.771183489 1 19.65792717 -1.050347974 4.466776196 1.000010102 0.823686361 0.340332732 0.075521879 7.00E-06 1.49E-06 0.06741197 0.015888244 0.089053712 1.050347974 -0.176323741 TLMLPLTEGS(ph)LR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLMLPLTEGSLR 12 0 Q7L4E1;Q7L4E1-3 Q7L4E1 FAM73B Protein FAM73B 1 TLMLPLT(0.01)EGS(0.99)LR 102.73 0.0024361 8770900 24615 41610 26245 36136 29931 45519 27177 27502 25933 36713 TRUE FALSE 25586.81921 48756.19382 26928.96626 43283.59294 24843.33931 34947.9021 25046.79573 27133.38067 24999.6764 43906.20944 0.582760833 1.11046238 0.613329336 0.985819398 0.565827468 0.795967189 0.570461355 0.617985042 0.569388173 1 15.42213737 3.225159014 24.9935442 0.66161408 0.828636289 0.099068743 0.192715644 409.198143 763139.7024 0.050680957 0.060899376 1679.418815 -3.225159014 0.167022208 TLNAET(ph)PKSS(ph)PLPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 2 T(0.001)LNAET(0.999)PKS(0.209)S(0.791)PLPAK 111.57 0.0019068 519210000 1084800 313470 446590 254970 748950 774880 533980 474670 436410 212250 TRUE FALSE 1127628.742 367306.034 458228.5023 305402.305 621643.7465 594925.8634 492125.2523 468307.8251 420703.6893 253836.3237 4.442345859 1.4470192 1.805212491 1.203146581 2.448994444 2.343738101 1.938750314 1.844920452 1.657381746 1 17.95353901 4.743314952 24.99701528 1.805559046 4.442346931 0.775749267 0.434196853 227.1659223 1194337.327 0.101751474 0.834075793 55375.15461 -4.743314952 2.636787885 TLNAETPKSS(ph)PLPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 TLNAETPKS(0.041)S(0.959)PLPAK;TLNAETPKS(0.083)S(0.917)PLPAK 205.21 2.73E-09 1809660000 2314900 1279360 1860400 1205240 2536400 2196500 2152800 1751050 2092000 1119730 TRUE FALSE 2406294.039 1499080.128 1908883.552 1443632.875 2105263.634 1686396.163 1984057.911 1727580.039 2016709.329 1339119.655 1.796922352 1.119451964 1.425476465 1.078046214 1.572125109 1.259331948 1.481613613 1.290086388 1.505996362 1 20.35285345 -1.127756545 4.778918222 0.999974573 1.374700537 0.243200677 0.205455592 4.90E-05 8.95E-06 0.175290232 0.041313504 0.074514957 1.127756545 0.374725964 TLNDELEIIEGMKFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLNDELEIIEGMKFDR 16 1 P10809;E7EXB4;E7ESH4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 ; 243.09 5.08E-20 179959000 260250 265540 280870 206131 350450 401240 212289 235700 300660 357170 FALSE TRUE 270524.871 311144.4294 288189.7029 246903.0966 290880.6342 308058.0909 195649.2335 232540.827 289839.3053 427150.6231 0.633324304 0.728418531 0.674679346 0.578023496 0.68097907 0.721193121 0.458033356 0.544400065 0.678541221 1 18.70438536 -1.829922403 5.438670202 1.044489614 0.625670036 0.650034834 0.080606403 0.040190234 0.001256825 0.072136227 0.019912058 0.014793727 1.829922403 -0.418819578 TLNMT(ph)TSPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 T(0.018)LNMT(0.327)T(0.327)S(0.327)PEEK 67.997 0.052951 0 340650 211750 258060 203730 364140 362510 313540 264710 266370 180930 TRUE FALSE 354099.125 248116.4153 264785.2556 244027.1859 302243.6129 278322.5464 288963.9155 261161.9954 256783.3957 216379.7694 1.636470572 1.146671041 1.223706155 1.12777265 1.396820108 1.2862688 1.335447932 1.206961243 1.186725526 1 17.72320609 -5 0.146847444 0.009838681 1.366670312 0.332621371 0.135220644 170.3340221 1.501244092 49.00949074 0.704801243 1.00E-05 5 1.356831631 TLNMTT(ph)SPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.004)T(0.498)S(0.498)PEEK;TLNMT(0.001)T(0.917)S(0.082)PEEK;TLNMT(0.028)T(0.546)S(0.427)PEEK 215.61 1.42E-10 1294840000 3412020 1884000 2451010 1841370 3388940 3841740 3139110 2659170 2706700 1577770 TRUE FALSE 3546729.184 2207562.345 2514885.334 2205587.49 2812889.189 2949554.107 2893058.356 2623528.176 2609286.396 1886903.823 1.879655518 1.169938985 1.332810556 1.168892374 1.490743277 1.563171409 1.533230428 1.390387864 1.382840166 1 20.84758946 0.565126589 1.928907162 1.000080966 1.428203852 0.310850718 0.195242225 3.508338472 14.09390557 0.180540384 0.049996994 3.673893726 -0.565126589 0.428122886 TLNMTTS(ph)PEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLNMTTSPEEK 11 0 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 TLNMT(0.019)T(0.257)S(0.724)PEEK;TLNMT(0.014)T(0.275)S(0.711)PEEK;TLNMT(0.002)T(0.174)S(0.823)PEEK 215.96 5.49E-06 472800000 3106530 1763750 2182310 1683720 2963620 3347380 2773650 2347420 2412490 1422110 TRUE FALSE 3229178.203 2066660.342 2239182.791 2016754.791 2459864.931 2570001.725 2556244.065 2315956.675 2325664.956 1700745.227 1.898684267 1.215149871 1.316589197 1.185806527 1.446345339 1.5111033 1.503014106 1.361730516 1.367438767 1 20.69773561 0.512508871 1.517797097 1.000127082 1.416811337 0.315043704 0.188645159 3.014675575 8.043854386 0.173147707 0.04997682 3.254684313 -0.512508871 0.416684255 TLNPS(ph)PAGWFVQQHPELELMSSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLNPSPAGWFVQQHPELELMSSFR 24 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 TLNPS(1)PAGWFVQQHPELELMSSFR;TLNPS(1)PAGWFVQQHPELELMSSFR;T(0.009)LNPS(0.991)PAGWFVQQHPELELMSSFR 251.66 6.26E-44 2434785000 281895 265914 312374 274575 410089 391153 323820 335171 362960 321502 TRUE FALSE 293024.4323 311582.661 320514.7231 328885.1155 340382.2183 300313.6437 298438.1423 330678.581 349897.1405 384494.1614 0.762103724 0.810370331 0.833601015 0.855370896 0.885272788 0.781061649 0.776183808 0.860035377 0.910019386 1 18.55260217 1.063050355 1.856338419 0.997904081 0.818759121 0.721262505 0.036262185 0.181140861 1.257795434 0.036121816 0.010316717 11.56246297 -1.063050355 -0.17914496 TLPAHSDPVSAVHFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLPAHSDPVSAVHFNR 16 0 P61964 P61964 WDR5 WD repeat-containing protein 5 0 ; 182.02 1.28E-09 280370000 91876 244315 210215 234674 228887 299662 172658 223153 175714 311349 FALSE TRUE 95503.33542 286274.2007 215693.3756 281091.8168 189980.8695 230070.0419 159124.6148 220161.999 169390.0875 372351.8754 0.256486785 0.768827068 0.579272967 0.754909094 0.510218645 0.617883398 0.42735011 0.591274044 0.454919388 1 18.5063071 -1.156753287 4.718281188 1.000045999 0.562048498 0.461933757 0.144877719 6.41E-05 1.15E-05 0.128305086 0.03023863 0.069702236 1.156753287 -0.437997501 TLPGWNTDISNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLPGWNTDISNAR 13 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 127.78 0.00040246 56525000 50247 66080 55457 42589 53364 71729 57678 47420 48222 60435 FALSE TRUE 52230.79036 77428.72597 56902.25498 51012.97708 44293.20634 55071.02681 53157.04765 46784.41246 46486.49964 72276.08115 0.722656646 1.071291148 0.787290264 0.705807181 0.612833535 0.761953691 0.735472189 0.647301455 0.643179582 1 16.14123066 4.007586568 24.87759353 0.711035329 0.905053154 0.200018985 0.128814329 199.331834 653627.1334 0.02921234 0.062915259 10176.22189 -4.007586568 0.194017825 TLPLTGSTFHDQIAMLSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLPLTGSTFHDQIAMLSHR 19 0 P55265-5;P55265;P55265-4 P55265-5 ADAR Double-stranded RNA-specific adenosine deaminase 0 ; 249.5 2.75E-25 1904380000 302190 386510 415480 357810 453590 548510 423840 399990 408800 382720 FALSE TRUE 314120.6945 452890.0859 426307.7501 428583.75 376488.9338 421126.8652 390618.3133 394628.7883 394087.3679 457706.6564 0.686292607 0.98947673 0.931399498 0.936372115 0.822555077 0.920080273 0.853425022 0.86218713 0.861004231 1 18.80406375 -1.6978347 2.342680978 1.023801986 0.878440748 0.187271925 0.078397468 7498521.394 5268398.402 1050571.574 0.017964022 0.020052351 1.6978347 -0.145361238 TLPQQES(ph)LEIELAEEKPVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 269.25 1.38E-37 1095400000 1179160 735910 1300120 666680 1622830 1165040 1355650 1100510 1449600 635690 TRUE FALSE 1225714.147 862296.8179 1334002.195 798547.3142 1346981.936 894477.1164 1249390.611 1085759.464 1397429.179 760241.2845 1.61226991 1.134240978 1.754708962 1.050386674 1.771782148 1.176570037 1.643413264 1.428177456 1.838139033 1 19.53609785 TLPSGS(ph)PRPGQLERPTSLALDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLPSGSPRPGQLERPTSLALDSR 23 2 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 T(0.006)LPS(0.143)GS(0.851)PRPGQLERPTSLALDSR;T(0.003)LPS(0.146)GS(0.851)PRPGQLERPTSLALDSR;T(0.003)LPS(0.219)GS(0.779)PRPGQLERPTSLALDSR 139.22 3.19E-07 1896420000 1134060 1365820 1257280 1345580 1467680 1621460 1251990 1274330 1275240 1274710 TRUE FALSE 1178833.564 1600388.96 1290045.75 1611731.708 1218204.278 1244900.488 1153855.752 1257249.691 1229344.362 1524465.019 0.773276887 1.049803663 0.846228502 1.05724414 0.799102808 0.816614664 0.756892246 0.824715343 0.806410345 1 20.53987162 3.187666532 24.99996256 0.819315665 0.933979064 0.17862306 0.099644435 137.7306708 67654.84523 0.026135293 0.031237692 1540.517129 -3.187666532 0.114663399 TLQALEFHTVPFQLLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLQALEFHTVPFQLLAR 17 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 212.69 1.35E-12 1179480000 581030 707640 756840 802840 1203060 1083020 858210 711390 640280 992640 FALSE TRUE 603969.5131 829171.6653 776563.8722 961639.3558 998564.2909 831505.0183 790941.2577 701854.9806 617236.4479 1187128.803 0.508764939 0.698468156 0.654153004 0.810054775 0.841159181 0.700433699 0.666264062 0.591220581 0.519940588 1 20.17904504 4.749387749 4.373368503 0.70456879 0.492856114 0.184560392 0.129637719 0.418641793 19.01219471 0.031092495 0.277290048 56154.91173 -4.749387749 -0.211712676 TLQLEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLQLEYR 7 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57 Q99829 CPNE1 Copine-1 0 ; 101.6 0.045658 112340000 370469 408760 409708 341218 547290 521470 393125 371117 397210 429160 FALSE TRUE 385095.4022 478961.3503 420385.3271 408709.902 454261.8413 400366.4955 362310.8353 366142.7836 382914.4897 513245.6852 0.750313959 0.933200929 0.819072306 0.796324088 0.885076786 0.780067923 0.70592086 0.713386969 0.746064703 1 18.96929007 2.532343503 7.852292935 0.757430883 0.838499904 0.013689908 0.091997614 0.561200423 72.93615106 0.027946031 0.026174483 340.6775404 -2.532343503 0.081069021 TLQRLS(ph)SGFDDIDLPSAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 T(0.113)LQRLS(0.837)S(0.05)GFDDIDLPSAVK;T(0.003)LQRLS(0.958)S(0.039)GFDDIDLPSAVK;T(0.001)LQRLS(0.874)S(0.125)GFDDIDLPSAVK;T(0.002)LQRLS(0.874)S(0.124)GFDDIDLPSAVK 210.96 9.18E-17 5064970000 4152230 3476850 4246070 2936050 6053310 5814170 4491760 4570320 5135330 4356450 TRUE FALSE 4316163.247 4073971.941 4356726.072 3516791.927 5024370.528 4463917.132 4139684.114 4509062.336 4950510.476 5210012.968 0.828436181 0.781950442 0.836221733 0.675006367 0.964368142 0.856795781 0.794563111 0.865460866 0.950191584 1 22.31285553 1.033208664 0.504021779 1.010382115 0.801235895 0.43823243 0.068940564 0.953057772 0.61865766 0.078804945 0.038463377 10.79465245 -1.033208664 -0.20914622 TLQRLSS(ph)GFDDIDLPSAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLQRLSSGFDDIDLPSAVK 19 1 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 T(0.01)LQRLS(0.36)S(0.63)GFDDIDLPSAVK;T(0.019)LQRLS(0.364)S(0.617)GFDDIDLPSAVK 228.46 6.25E-20 1547840000 1163160 946110 1132450 820850 1671250 1621080 1270270 1239130 1534540 1224340 TRUE FALSE 1209082.455 1108597.033 1161962.577 983211.68 1387171.522 1244608.738 1170702.918 1222521.489 1479312.205 1464225.982 0.825748532 0.757121542 0.793567791 0.671489027 0.947375295 0.850011373 0.799537047 0.834926784 1.010303207 1 20.4817068 1.280751215 4.082073892 1.010000202 0.807108187 0.586569243 0.065794838 0.144583137 4.481124093 0.054216914 0.016874071 19.08759515 -1.280751215 -0.202892015 TLQTDSIDSFETQRT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TLQTDSIDSFET(0.001)QRT(0.999)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR;TLQTDSIDSFETQRT(1)PR 286.92 2.53E-36 7749610000 5021200 5814120 5871910 5647900 6519010 7518580 5749280 6119360 5876970 6212050 TRUE FALSE 5219440.853 6812649.882 6024936.798 6765037.763 5410911.009 5772503.74 5298636.411 6037339.988 5665458.998 7429182.261 0.702559268 0.917012081 0.810982499 0.910603284 0.728331978 0.77700392 0.713219332 0.812652022 0.762595236 1 22.82477199 3.228805946 24.99438234 0.78453958 0.839390435 0.020911387 0.093071961 530.7556124 1359952.678 0.02461334 0.02975994 1693.580895 -3.228805946 0.054850855 TLQVVPPSDPDPLLASWHGGTGT(ph)SPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.049)GT(0.551)S(0.4)PPR 131.58 0.00015233 133680000 53212 136770 132610 144230 135190 176810 123990 143900 135980 140030 TRUE FALSE 55312.85085 160259.1836 136065.9255 172758.2635 112210.4521 135748.5571 114271.3398 141971.2559 131086.1064 167466.1975 0.33029263 0.956964367 0.812497851 1.031600801 0.670048367 0.810602731 0.682354657 0.847760671 0.782761586 1 17.3535104 -4.999999983 0.026991855 2.07212484 5.34E-12 0.158709801 0.176885869 4210.61793 8.57365233 491.2072915 217.9235781 1.00E-05 4.999999983 -2.07212484 TLQVVPPSDPDPLLASWHGGTGTS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLQVVPPSDPDPLLASWHGGTGTSPPR 27 0 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 TLQVVPPSDPDPLLASWHGGT(0.006)GT(0.198)S(0.796)PPR;TLQVVPPSDPDPLLAS(0.002)WHGGT(0.038)GT(0.264)S(0.696)PPR;TLQVVPPSDPDPLLASWHGGT(0.041)GT(0.206)S(0.752)PPR 150.07 6.49E-08 451950000 144180 341830 335110 326040 357100 440300 295397 374370 329721 354720 TRUE FALSE 149872.3377 400536.6434 343843.2419 390529.7389 296400.2696 338046.9978 272243.0113 369352.1825 317854.4056 424220.5925 0.353288691 0.944170676 0.810529352 0.920581758 0.698693733 0.796866073 0.641748694 0.870660663 0.7492668 1 18.69445513 -5 0.197205387 2.017074136 0.729478774 0.185769862 0.159713424 251.8366765 2.485496223 101.144562 0.372465998 1.00E-05 5 -1.287595363 TLRDS(ph)PNVEAAHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 T(0.002)LRDS(0.998)PNVEAAHLAR;T(0.003)LRDS(0.997)PNVEAAHLAR;T(0.277)LRDS(0.723)PNVEAAHLAR;T(0.005)LRDS(0.995)PNVEAAHLAR 228.08 3.89E-13 4077970000 1060250 1171180 1181630 1189070 1438710 1497830 1223340 1239580 1214090 1147360 TRUE FALSE 1102109.489 1372321.054 1212424.249 1424264.497 1194158.588 1149981.682 1127451.414 1222965.458 1170395.138 1372163.224 0.803191245 1.000115023 0.883586025 1.037970171 0.870274445 0.838079364 0.821659839 0.891268208 0.852956206 1 20.38802068 3.068137025 24.99997281 0.869040061 0.935408512 0.094832132 0.074819477 92.19976474 33827.1984 0.020016752 0.023924594 1169.86844 -3.068137025 0.066368451 TLS(ph)DESICSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLSDESICSNR 11 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 TLS(1)DESICSNR;TLS(1)DESICSNR;TLS(0.997)DES(0.003)ICSNR 352.34 6.98E-71 1816130000 736970 826340 861820 782900 994580 1229780 1028850 881860 913350 786700 TRUE FALSE 766066.1447 968257.467 884279.7372 937755.2833 825521.6469 944182.2325 948206.0486 870040.1091 880478.7119 940838.8027 0.814237404 1.029142786 0.939884425 0.996722585 0.877431548 1.003553669 1.007830508 0.92474939 0.935844386 1 19.84358804 4.754763856 24.78273477 0.964314392 0.814237275 0.508966857 0.045256196 2394.877799 3662879.83 0.010295823 0.278990672 56854.37061 -4.754763856 -0.150077116 TLS(ph)DESICSNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TLSDESICSNRR 12 1 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 T(0.06)LS(0.94)DESICSNRR;T(0.314)LS(0.686)DESICSNRR;T(0.243)LS(0.756)DESICSNRR 129.38 0.00014411 1050280000 722280 772900 772440 659560 932870 1088990 780550 784550 860160 813370 TRUE FALSE 750796.1721 905639.5627 792570.421 790018.9994 774301.0906 836088.5763 719368.4514 774034.3905 829203.0096 972734.2786 0.771840973 0.931024621 0.814786153 0.812163215 0.796004734 0.859524122 0.739532334 0.795730558 0.852445553 1 19.89168623 0.874456702 4.72621808 0.999987762 0.815239962 0.563316723 0.048737152 0.707550209 25.74414563 0.046437946 0.011765475 7.489566855 -0.874456702 -0.1847478 TLS(ph)DESIYNSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(1)DESIYNSQR;TLS(1)DESIYNSQR 338.79 1.73E-58 3015500000 1190260 1200610 1275820 1164140 1583600 1704270 1432160 1322430 1344810 1098250 TRUE FALSE 1237252.384 1406805.428 1309068.917 1394403.417 1314420.238 1308479.121 1319903.557 1304704.989 1296410.551 1313431.06 0.942000248 1.071091944 0.996678819 1.061649492 1.000753125 0.996229768 1.00492793 0.993356278 0.987041186 1 20.32490905 3.028069998 24.98582835 0.996621521 1.021527183 0.082080072 0.033453622 448.4878099 399206.961 0.008864804 0.010595191 1066.768044 -3.028069998 0.024905662 TLS(ph)DESLCSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TLSDESLCSGR 11 0 O60292;M0R2Q7 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.001)LS(0.999)DESLCSGR;TLS(0.998)DES(0.001)LCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR;TLS(1)DESLCSGR 295.26 1.49E-35 3955730000 1146622 1129557 1264185 1100543 1404410 1614220 1392360 1278560 1213446 971887 TRUE FALSE 1191891.522 1323549.628 1297130.7 1318227.121 1165688.89 1239341.869 1283223.185 1261422.995 1169774.315 1162309.65 1.025450939 1.138723772 1.11599409 1.134144521 1.002907349 1.066275126 1.104028677 1.085272754 1.006422269 1 20.14856304 3.257931273 24.99991515 1.055919007 1.106975554 0.273898341 0.044882335 367.9055697 474818.8406 0.012457619 0.016843471 1811.053471 -3.257931273 0.051056547 TLS(ph)DPPS(ph)PLPHGPPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSDPPSPLPHGPPNK 16 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 2 T(0.276)LS(0.725)DPPS(0.999)PLPHGPPNK;T(0.457)LS(0.544)DPPS(0.998)PLPHGPPNK 61.096 0.023659 193150000 322530 245540 304580 228150 430280 415010 387090 338570 377690 237060 TRUE FALSE 335263.7334 287709.585 312517.605 273277.389 357141.1593 318630.217 356748.8743 334032.0229 364097.0107 283507.3682 1.18255739 1.014822249 1.102326218 0.963916355 1.259724435 1.123886899 1.25834075 1.178212845 1.284259429 1 18.11302671 3.228818987 24.99997448 1.194100142 1.064858213 0.273572789 0.093471452 225.6562901 579101.5138 0.024602595 0.029753411 1693.631753 -3.228818987 -0.12924193 TLS(ph)FGSDLNYATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSFGSDLNYATR 13 0 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 TLS(1)FGSDLNYATR 155.28 4.89E-05 38855000 62751 58035 65242 57040 81280 79402 61591 65849 60814 57535 TRUE FALSE 65228.45793 68002.0598 66942.26012 68322.34175 67464.05463 60962.08885 56763.33648 64966.40186 58625.31602 68807.88168 0.947979452 0.988288814 0.972886514 0.992943542 0.980469868 0.885975376 0.824953989 0.944170933 0.852014545 1 16.07028621 2.741608222 24.08768215 0.895511267 0.977879085 0.392782353 0.046376517 147.6507196 1167003.053 0.01355631 0.013814613 551.5796338 -2.741608222 0.082367818 TLS(ph)INEEEPEGGFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLSINEEEPEGGFSK 15 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 TLS(1)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK;T(0.002)LS(0.998)INEEEPEGGFSK;TLS(1)INEEEPEGGFSK 304.24 1.43E-44 893700000 886410 627910 1054220 689392 1519170 1163040 1220980 1072020 1326300 776420 TRUE FALSE 921406.1513 735748.658 1081693.839 825751.68 1260942.026 892941.586 1125276.397 1057651.325 1278566.722 928544.6335 0.992312182 0.792367573 1.164934673 0.889296702 1.357976753 0.96165715 1.21187109 1.139041988 1.376957742 1 19.82461173 3.759210355 1.038142517 1.170363748 0.898471346 0.244312081 0.160289782 0.797127853 1.579456702 0.052409071 0.167581868 5743.946085 -3.759210355 -0.271892402 TLS(ph)MDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSMDK 6 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 1 TLS(1)MDK 91.069 0.050678 130370000 218970 119550 200000 126090 261060 210940 280070 184250 240800 102450 TRUE FALSE 227615.1047 140081.7825 205212.1643 151030.2257 216685.1144 161952.3818 258117.3816 181780.4301 232133.655 122523.116 1.85773193 1.143309011 1.674885287 1.232667195 1.768524353 1.321810832 2.106683131 1.483641913 1.894611096 1 16.90269444 3.214571183 24.99977639 1.632579686 1.467426467 0.020938663 0.344437812 734.7395117 765681.9965 0.09072375 0.10848863 1638.970676 -3.214571183 -0.165153218 TLS(ph)MDKGF ddPTM_MDA-MB-175_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 135.86 0.002146 1648110000 3762540 2227540 4048150 2106150 5603240 4039080 4637860 3616340 4851860 2196600 TRUE FALSE 3911087.985 2610102.667 4153648.115 2522740.184 4650803.266 3101064.883 4274332.414 3567868.877 4677242.506 2626981.714 1.488814317 0.993574738 1.581148469 0.960318898 1.770398036 1.180466871 1.627088758 1.358162814 1.780462529 1 21.32497473 3.239968192 24.99999328 1.46210197 1.260449535 0.09866971 0.290444412 84.24542269 1496261.075 0.07383917 0.094785475 1737.673556 -3.239968192 -0.201652434 TLS(ph)MIEEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLSMIEEEIR 10 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 T(0.003)LS(0.997)MIEEEIR;T(0.003)LS(0.997)MIEEEIR;T(0.001)LS(0.999)MIEEEIR;T(0.001)LS(0.999)MIEEEIR 142.07 3.82E-05 91518000 87889 122023 122726 127920 156187 180040 127729 138001 146893 159516 TRUE FALSE 91358.92559 142979.501 125924.3404 153222.1942 129638.3895 138228.4385 117717.2672 136151.3223 141606.3496 190770.1061 0.478895396 0.749485881 0.660084239 0.803177171 0.679552956 0.724581232 0.617063489 0.713693173 0.742287943 1 17.54147559 -5 0.25413815 2.941048214 0.662138994 0.587813358 0.081361996 129.1639068 1.276204175 130.4237196 0.107321089 1.00E-05 5 -2.27890922 TLS(ph)NAEDYLDDEDS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 2 T(0.117)LS(0.883)NAEDYLDDEDS(1)D 145.43 1.09E-05 0 60651 79509 85420 70583 87308 116600 87647 86562 92306 89891 TRUE FALSE 63045.54831 93164.05226 87646.11537 84544.10673 72467.41735 89521.41709 80776.99912 85401.77798 88983.92509 107503.4204 0.586451557 0.866614773 0.815286761 0.786431784 0.674094062 0.832730873 0.751390038 0.794409868 0.827731106 1 16.71402304 0.521660233 0.895271181 1.001352 0.76334904 0.472076026 0.076247821 1.361013705 1.663819112 0.070896002 0.022974397 3.323994017 -0.521660233 -0.23800296 TLS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSPGR 6 0 Q13523 Q13523;REV__F5H6U2 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.002)LS(0.998)PGR;T(0.005)LS(0.995)PGR 102.41 0.037308 1210710000 1038240 1177150 1145630 1203980 1291440 1395630 1263630 1188160 1173590 1061140 TRUE FALSE 1079230.517 1379316.356 1175486.059 1442123.65 1071921.49 1071516.083 1164583.379 1172234.659 1131352.725 1269050.066 0.850423908 1.086888841 0.926272407 1.136380423 0.844664461 0.844345004 0.917681193 0.923710332 0.891495738 1 20.27531756 3.200962727 24.99926441 0.899810596 1.000933342 0.237871813 0.084307088 215.627828 143372.7774 0.022727903 0.027165578 1588.410418 -3.200962727 0.101122746 TLS(ph)PGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSPGRR 7 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 T(0.002)LS(0.998)PGRR;T(0.002)LS(0.998)PGRR 73.233 0.030287 2373700000 1340360 1565920 1655770 1505260 1756540 1935400 1642910 1619200 1518940 1458170 TRUE FALSE 1393278.448 1834854.579 1698920.726 1802995.935 1457963.958 1485932.681 1514134.421 1597497.272 1464273.646 1743870.493 0.798957522 1.052173648 0.974224137 1.033904721 0.836050592 0.852088895 0.868260818 0.916064168 0.839668801 1 20.73386147 3.231867824 24.99896582 0.880956382 0.971726992 0.197526984 0.077661396 215.8597863 806279.9756 0.021078171 0.025738894 1705.563227 -3.231867824 0.090770611 TLS(ph)PTPSAEGYQDVR ddPTM_MDA-MB-175_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;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(0.997)PT(0.003)PSAEGYQDVR;TLS(1)PTPSAEGYQDVR;TLS(1)PTPSAEGYQDVR 370.86 1.49E-97 17857840000 1559752 1400853 1471990 1438277 1608480 1962430 1577532 1532442 1519216 1459103 TRUE FALSE 1621332.213 1641438.606 1510351.269 1722763.898 1335071.144 1506685.373 1453880.92 1511902.122 1464539.713 1744986.297 0.929137505 0.940659883 0.86553761 0.987265001 0.765089758 0.863436794 0.833176124 0.866426358 0.839284363 1 20.73478428 3.25263829 24.99996629 0.85370485 0.926714083 0.228201841 0.061441185 313.4884082 556707.7584 0.015600032 0.021020474 1789.115138 -3.25263829 0.073009233 TLS(ph)SSAQEDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.797)S(0.2)S(0.003)AQEDIIR;TLS(0.987)S(0.013)SAQEDIIR 200.55 1.66E-07 1269910000 274960 319020 365320 311610 570880 513870 362680 365700 380240 513100 TRUE FALSE 285815.6331 373809.2034 374840.5393 373245.5279 473842.0215 394531.4803 334252.1939 360798.3897 366555.2367 613632.1211 0.465776845 0.609174765 0.610855473 0.608256177 0.772192337 0.642944635 0.544711045 0.587971811 0.597353405 1 19.22701448 -1.932355401 2.48216297 1.267050332 0.606892469 0.727017234 0.072715689 16048241.91 7860920.841 24821566.91 0.018545356 0.011685427 1.932355401 -0.660157864 TLSALRS(ph)PDVGLYGVIPECGETYHSDLAEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSALRSPDVGLYGVIPECGETYHSDLAEAK 31 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 TLSALRS(1)PDVGLYGVIPECGETYHSDLAEAK;T(0.002)LS(0.014)ALRS(0.984)PDVGLYGVIPECGETYHSDLAEAK 220.64 3.76E-35 502220000 152828 128627 145897 135250 202203 194824 151591 159969 173088 124661 TRUE FALSE 158861.7674 150717.6867 149699.1957 162002.0463 167832.6063 149579.0786 139708.9013 157824.8772 166858.5967 149085.9362 1.065571787 1.010945033 1.004113463 1.086635336 1.125744055 1.003307773 0.937103156 1.058616804 1.119210846 1 17.18578464 2.326464381 0.002265402 7.11E-05 2.077980171 0.013340398 0.056588209 320593.1761 391.3499234 178743.2281 180205.5116 212.0627462 -2.326464381 2.077909047 TLSASTQDLS(ph)PH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 TLSASTQDLS(1)PH;TLSASTQDLS(1)PH 172.3 3.79E-05 858280000 637530 606050 643610 621230 714870 883750 673840 694360 658210 691620 TRUE FALSE 662700.1767 710134.3731 660383.0053 744107.4398 593356.6527 678512.4559 621022.66 685053.2399 634521.1507 827129.6971 0.801204671 0.858552625 0.79840321 0.899626071 0.717368334 0.82032172 0.750816543 0.82822953 0.767136222 1 19.65775404 -0.937637563 8.170355938 1 0.806001316 0.581425843 0.049718006 3.32E-10 8.13E-11 0.044570215 0.0105053 0.115441626 0.937637563 -0.193998684 TLSDPPS(ph)PLPHGPPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSDPPSPLPHGPPNK 16 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 T(0.001)LS(0.001)DPPS(0.997)PLPHGPPNK;T(0.012)LS(0.01)DPPS(0.979)PLPHGPPNK 87.676 0.0041152 737500000 1309810 1033410 1152570 901200 1395620 1430550 1285590 1173250 1217380 937990 TRUE FALSE 1361522.31 1210890.129 1182606.921 1079454.67 1158393.011 1098326.443 1184822.097 1157524.503 1173566.732 1121771.182 1.21372552 1.079444853 1.054231862 0.962277056 1.032646434 0.979100249 1.056206574 1.031872205 1.046173008 1 20.09734699 4.779052345 1.618894415 1.019673142 1.297238474 0.806410761 0.028985654 0.46467685 1.08119849 0.007625176 0.208901712 60124.62006 -4.779052345 0.277565332 TLSDVEDQKELAS(ph)PVSPELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 TLSDVEDQKELAS(0.996)PVS(0.004)PELR;TLSDVEDQKELAS(1)PVSPELR 153.87 2.91E-08 400560000 415010 240140 359040 276580 470970 441890 389110 347970 391380 255480 TRUE FALSE 431394.9153 281382.177 368396.8774 331286.6985 390914.6876 339267.7444 358610.5415 343306.0313 377294.3103 305536.4145 1.411926352 0.920944816 1.205738039 1.084278936 1.279437308 1.110400359 1.173708024 1.123617399 1.234858735 1 18.22098481 -2.06105703 2.423545475 0.773252604 1.161253747 0.143855253 0.123301189 12825318.54 3727492.926 16113365.08 0.026076437 0.008688463 2.06105703 0.388001144 TLSKEEETKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLSKEEETKK 10 2 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 ;;; 122.33 0.00027645 3280540000 5491840 1999001 3060759 1627332 5367730 4312870 4241330 3247873 3847800 1651468 FALSE TRUE 5708662.084 2342313.872 3140524.894 1949213.412 4455325.172 3311271.305 3908883.472 3204340.575 3709318.43 1975041.535 2.890401028 1.185956766 1.590105746 0.986922744 2.255813406 1.676557807 1.979139882 1.622416804 1.878096416 1 20.91345156 -1.253551496 5.489901367 0.99994034 1.747676114 0.173941472 0.50739128 0.000341472 4.64E-05 0.452678549 0.106688904 0.055776146 1.253551496 0.747735774 TLSNAEDYLDDEDS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 410.08 4.57E-133 836760000 1283230 1504360 1395140 1275830 1382250 1567870 1261715 1244600 1177060 1045130 TRUE FALSE 1333892.911 1762722.128 1431498.495 1528185.366 1147295.639 1203755.954 1162818.481 1227918.173 1134697.841 1249903.213 1.067196961 1.4102869 1.145287475 1.222642961 0.917907584 0.963079334 0.93032682 0.982410606 0.907828565 1 20.25338495 3.242604486 24.90965391 0.950875205 1.220844148 0.693564114 0.084927533 49.57851509 305393.9123 0.022001194 0.02873501 1748.253822 -3.242604486 0.269968943 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.102)S(0.895)PS(0.003)NRPSGETSVPPPPAVGR;T(0.021)LS(0.139)S(0.823)PS(0.017)NRPSGETSVPPPPAVGR;T(0.002)LS(0.068)S(0.893)PS(0.037)NRPSGETSVPPPPAVGR 170.82 4.17E-12 1092030000 355918 328545 359303 310959 419482 456980 376333 364838 340187 350605 TRUE FALSE 369969.9175 384970.048 368666.7314 372465.7621 348178.5995 350853.3206 346835.0361 359947.9434 327943.7363 419299.337 0.882352737 0.918127013 0.879244728 0.888305154 0.830381946 0.836760972 0.82717764 0.85845102 0.782123193 1 18.67762102 3.316494488 6.543613303 0.84681073 0.893567753 0.082727032 0.054307004 0.396360271 26.68656302 0.013760672 0.018623994 2072.499755 -3.316494488 0.046757023 TLSS(ph)SAQEDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.283)S(0.627)S(0.089)AQEDIIR 244.68 2.15E-16 201870000 101970 133900 147810 118500 230370 194500 148470 151330 146900 211650 TRUE FALSE 105995.8543 156896.2834 151662.05 141938.9463 191211.7897 149330.3227 136832.5334 149301.6689 141613.0977 253118.7652 0.418759369 0.619852437 0.599173475 0.560760267 0.755423208 0.589961485 0.540586287 0.589848282 0.559472932 1 17.94945494 -1.038923193 4.641449202 1.000011105 0.586449562 0.719143289 0.078399456 1.12E-05 2.32E-06 0.073139429 0.017238532 0.091427492 1.038923193 -0.413561543 TLSS(ph)SSMDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLS(0.001)S(0.75)S(0.243)S(0.005)MDLSR;TLS(0.001)S(0.821)S(0.153)S(0.025)MDLSR 236.7 5.75E-15 570370000 621630 793290 814950 653040 1084640 949390 720070 799520 792270 959770 TRUE FALSE 646172.4324 929531.3866 836188.2665 782209.3629 900273.2802 728908.5606 663629.0318 788803.7422 763756.3575 1147818.556 0.562956949 0.809824325 0.728502133 0.68147475 0.78433414 0.63503814 0.57816545 0.687219891 0.665398162 1 20.13046317 -1.981279354 2.378890468 1.285213046 0.683978141 0.617707055 0.075160193 7900592.583 3276506.159 12383352.73 0.017945767 0.010440484 1.981279354 -0.601234905 TLSSFFT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 169.58 0.00065238 262751000 333542 419010 397980 356629 406810 449310 369650 384330 335309 406050 TRUE FALSE 346710.4957 490971.7081 408351.6857 427169.1518 337660.5815 344964.5619 340675.8671 379178.685 323241.2946 485607.7232 0.713972367 1.011045922 0.840908549 0.879658892 0.695336102 0.710377009 0.701545406 0.780833308 0.665642821 1 18.88943184 3.250051059 24.794946 0.744362833 0.870622298 0.160259038 0.111126892 277.4717933 598745.7314 0.028240058 0.037908396 1778.488491 -3.250051059 0.126259465 TLSSS(ph)AQEDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSSSAQEDIIR 12 0 Q9H788-2;Q9H788 Q9H788-2 SH2D4A SH2 domain-containing protein 4A 1 TLS(0.024)S(0.314)S(0.662)AQEDIIR 268.21 5.73E-22 278560000 113280 145240 175300 132560 239430 218460 159020 162000 156000 228020 TRUE FALSE 117752.3819 170183.8402 179868.462 158779.9723 198731.7741 167725.9758 146555.5969 159828.655 150385.5905 272696.1533 0.431808005 0.624078624 0.659592957 0.58225967 0.728766327 0.615065426 0.537431845 0.586105279 0.551476758 1 18.05693482 -1.135055436 3.715685862 1.000229359 0.595303574 0.730949849 0.074444238 22149227.83 36403282.54 64752.10597 0.017851018 0.0732731 1.135055436 -0.404925785 TLSSS(ph)SMDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLSS(0.019)S(0.947)S(0.034)MDLSR;TLSS(0.2)S(0.774)S(0.026)MDLSR;TLSS(0.259)S(0.739)S(0.002)MDLSR;TLSS(0.279)S(0.718)S(0.003)MDLSR;TLS(0.004)S(0.12)S(0.849)S(0.027)MDLSR;TLSS(0.285)S(0.713)S(0.002)MDLSR;TLSS(0.059)S(0.938)S(0.003)MDLSR;TLSS(0.007)S(0.989)S(0.003)MDLSR;TLS(0.001)S(0.378)S(0.581)S(0.04)MDLSR 289.48 2.18E-35 10513550000 4770520 6090700 6389730 5330480 8299450 7096570 5425770 6058330 6194540 7210750 TRUE FALSE 4958863.813 7136730.346 6556251.613 6384833.034 6888712.453 5448499.167 5000483.97 5977127.996 5971599.715 8623558.404 0.575036845 0.827585321 0.760272188 0.740394247 0.798824816 0.631815651 0.579863177 0.693116196 0.692475129 1 23.03985187 -1.05982087 5.086790635 1.000004923 0.701656338 0.550537484 0.081324834 4.63E-06 8.56E-07 0.080288161 0.018923789 0.08713229 1.05982087 -0.298348585 TLSSSS(ph)MDLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 TLS(0.007)S(0.232)S(0.232)S(0.53)MDLSR 81.92 0.079576 147270000 95738 129800 138000 108610 166760 155330 119010 132310 131000 141360 TRUE FALSE 99517.81017 152092.1403 141596.3934 130092.7338 138414.1948 119256.9615 109681.6852 130536.6009 126285.3356 169056.7855 0.588664985 0.899651202 0.837567052 0.769520924 0.818743799 0.705425465 0.648786057 0.772146474 0.746999508 1 17.3671484 -1.154970299 5.528321792 1.00000515 0.75824917 0.42321116 0.085978786 5.32E-06 8.13E-07 0.081164773 0.019130313 0.069988986 1.154970299 -0.24175598 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.997)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;T(0.025)LS(0.023)VAAAFNEDEDS(0.953)EPEEMPPEAK 152.15 3.31E-07 987377000 961154 772843 987313 776420 1190836 1282579 1108533 991539 1078473 747280 TRUE FALSE 999101.1021 905572.7734 1013043.188 929993.5586 988418.1221 984719.4649 1021643.287 978249.0415 1039658.967 893695.2085 1.117943895 1.013290398 1.133544388 1.040616029 1.105990177 1.101851566 1.143167466 1.094611488 1.163326107 1 19.76942336 3.044203622 24.90053575 1.10839962 1.075601519 0.044560742 0.051445216 311.4363237 175434.1132 0.013530858 0.01617246 1107.142755 -3.044203622 -0.032798101 TLT(ph)EPSVDFNHSDDFTPISTVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.133)LT(0.866)EPS(0.001)VDFNHSDDFTPISTVQK;T(0.003)LT(0.801)EPS(0.196)VDFNHSDDFTPISTVQK 277.82 3.02E-51 305400000 244500 184373 235140 213040 417140 364300 314510 298090 290110 212070 TRUE FALSE 254153.0488 216037.6285 241267.9416 255178.6761 346234.6918 279696.846 289857.8844 294094.5911 279668.9978 253621.0562 1.002097589 0.851812668 0.951293024 1.006141525 1.365165405 1.102813979 1.142877838 1.159582708 1.102704176 1 17.952315 3.464254441 24.98836244 1.154451141 0.935404721 0.519595143 0.092438132 156.9963878 304898.3692 0.024291386 0.032909668 2912.422927 -3.464254441 -0.219046421 TLT(ph)PPLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 T(0.428)LT(0.572)PPLRR;T(0.261)LT(0.739)PPLRR;T(0.006)LT(0.994)PPLRR;T(0.21)LT(0.79)PPLRR;T(0.01)LT(0.99)PPLRR 120.45 0.0008784 2065020000 1081200 1052740 1138300 964930 1427270 1571560 1220050 1178530 1126270 930520 TRUE FALSE 1123886.611 1233539.906 1167965.033 1155790.274 1184663.155 1206589.007 1124419.293 1162733.733 1085735.763 1112837.578 1.009928702 1.108463562 1.049537737 1.038597453 1.064542732 1.084245384 1.010407372 1.044836871 0.975646208 1 20.08581161 1.559408684 1.371808893 0.990458231 1.058642362 0.411899488 0.029568041 0.366926949 1.328664759 0.024100052 0.008374977 36.25840401 -1.559408684 0.068184131 TLTAEEAEEEWERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTAEEAEEEWERR 14 1 P35269;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 122.64 0.00017246 255090000 116100 156780 134420 130040 164660 168200 123780 162050 123100 201250 FALSE TRUE 120683.7176 183705.7454 137923.0956 155761.5239 136671.152 129138.0991 114077.8002 159877.9848 118669.655 240681.0843 0.501425851 0.763274546 0.573053325 0.647169778 0.567851655 0.536552756 0.473979085 0.664273162 0.493057672 1 17.87676324 -1.288257083 3.960467269 1.000625606 0.586707419 0.685424257 0.085238755 12563024 4086684.077 67657.67065 0.018937674 0.051492374 1.288257083 -0.413918187 TLTAVHDAILEDLVFPSEIVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTAVHDAILEDLVFPSEIVGK 22 0 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ; 179.95 5.49E-17 4840900000 2707080 2374260 2799300 2406470 3677700 3434100 3338400 2996400 2940400 2288280 FALSE TRUE 2813957.609 2782020.686 2872252.058 2882462.583 3052565.868 2636582.319 3076727.485 2956238.159 2834575.578 2736624.654 1.028258517 1.01658833 1.049560104 1.05329117 1.115449232 0.963443165 1.124278216 1.080249772 1.035792605 1 21.38396614 4.08464131 3.247468477 1.06058914 1.022299798 0.04809811 0.046176825 0.567310161 11.88329153 0.011434734 0.028234339 12151.8195 -4.08464131 -0.038289342 TLTDEELADWKR ddPTM_MDA-MB-175_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 ; 83.226 0.020714 194268000 139847 159365 177297 153289 225230 225919 182106 198722 198761 150455 FALSE TRUE 145368.2675 186734.6991 181917.5055 183609.1067 186945.4851 173452.7361 167832.0559 196058.4566 191607.6304 179933.7766 0.807898719 1.037796808 1.011024772 1.020426015 1.038968272 0.963980968 0.932743474 1.089614526 1.064878613 1 17.4571065 4.741727214 24.91531835 1.018701529 0.807898637 0.678947491 0.043279475 176.0962434 1385485.558 0.010921418 0.077973057 55173.07808 -4.741727214 -0.210802892 TLTDEVNS(ph)PDSDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNS(0.998)PDS(0.002)DRR;TLTDEVNS(1)PDSDRR;T(0.005)LT(0.007)DEVNS(0.985)PDS(0.004)DRR;TLTDEVNS(1)PDSDRR;TLTDEVNS(1)PDSDRR 224.15 2.00E-12 2126670000 1373380 1412300 1414080 1312710 1591730 1773450 1530830 1460310 1392150 1419740 TRUE FALSE 1427602.103 1654851.539 1450932.086 1572360.12 1321168.303 1361593.114 1410839.545 1440736.933 1342046.793 1697910.87 0.840799201 0.974639816 0.854539606 0.926055747 0.77811405 0.801922609 0.83092674 0.848535078 0.790410626 1 20.6953293 3.25472592 24.99339895 0.832698978 0.901234471 0.139025799 0.067672627 376.6269568 582304.5938 0.017179753 0.023191063 1797.73602 -3.25472592 0.068535493 TLTDEVNSPDS(ph)DRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 TLTDEVNSPDS(1)DRR;TLTDEVNSPDS(1)DRR 264.64 1.12E-24 1034000000 1036410 1185800 1170790 1136480 1327170 1504550 1218720 1205810 1153420 1124260 TRUE FALSE 1077328.267 1389451.926 1201301.749 1361272.352 1101578.117 1155141.064 1123193.542 1189648.089 1111908.64 1344537.222 0.801263252 1.033405326 0.89346857 1.012446759 0.819299086 0.859136546 0.835375565 0.884801157 0.826982416 1 20.35867826 3.224562072 24.99996849 0.863681238 0.939187562 0.139848405 0.076501346 364.6224218 651176.8358 0.020099848 0.024134766 1677.112022 -3.224562072 0.075506325 TLTEPS(ph)VDFNHSDDFTPISTVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 T(0.004)LT(0.35)EPS(0.646)VDFNHSDDFTPISTVQK 279.57 4.47E-52 312000000 252540 208660 301200 248200 493640 428090 403840 355770 367750 283190 TRUE FALSE 262510.4742 244495.7319 309049.5194 297293.2192 409731.2491 328672.5853 372185.9656 351001.4851 354514.7493 338675.6585 0.775108773 0.721917049 0.912523565 0.877811002 1.209804244 0.970464151 1.09894513 1.036394191 1.046767727 1 18.36954477 3.7808906 1.610051331 1.056092443 0.751697559 0.696988533 0.077146033 0.195278518 0.972525121 0.021142826 0.051603841 6037.965123 -3.7808906 -0.304394884 TLTGDVKTS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTGDVKTSPPR 12 1 Q9H8T0;Q9H8T0-2;H3BSX7;H3BNB8;H3BVH0;H3BRV2;H3BM79 Q9H8T0 AKTIP AKT-interacting protein 1 TLTGDVKT(0.076)S(0.923)PPR 63.727 0.041564 640720000 1082100 706070 922710 599540 1336200 1188100 966830 900290 1022800 625620 TRUE FALSE 1124822.144 827332.03 946756.5806 718127.2226 1109073.201 912181.7808 891047.3383 888223.0851 985989.6278 748198.2608 1.503374443 1.105765775 1.265381959 0.95980873 1.482325287 1.219171213 1.190924097 1.187149358 1.317818658 1 19.51306109 -2.083527684 2.529561264 0.616716974 1.235607529 0.184988962 0.154192339 7899024.085 2137044.822 17685750.04 0.034932953 0.008250349 2.083527684 0.618890555 TLTLVDTGIGMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTLVDTGIGMTK 13 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 195.25 9.16E-07 0 130290 105690 123760 112140 152950 164130 134730 120890 147720 116020 FALSE TRUE 135433.9498 123841.4353 126985.2873 134320.9573 126951.6136 126013.2949 124169.5105 119269.6673 142403.5861 138751.8977 0.976087189 0.892538678 0.915196761 0.968065731 0.914954071 0.908191506 0.894903152 0.859589449 1.026318115 1 17.08214798 1.223701714 24.99506724 1.01315915 0.913102038 0.576759362 0.033142193 192.9018908 324482.9212 0.032736731 0.008322334 16.73792872 -1.223701714 -0.100057111 TLTPDQWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TLTPDQWAR 9 0 Q9H3K6;A0A087WZT3 Q9H3K6 BOLA2 BolA-like protein 2 0 ;;; 157.68 0.00021538 1193430000 1350540 1558040 1593470 1409310 1848290 1926530 1625640 1585550 1411390 1640660 FALSE TRUE 1403860.362 1825621.25 1634997.137 1688067.312 1534118.326 1479122.604 1498218.089 1564298.296 1360594.35 1962115.915 0.715482888 0.930434964 0.833282644 0.860330065 0.781869366 0.753840583 0.763572671 0.797250705 0.693432197 1 20.90397884 5.023763611 16.39055154 0.812660503 0.477220804 0.114626507 0.08540194 15062283.96 266510434.7 0.019378368 131968778.5 105624.2435 -5.023763611 -0.335439698 TLTPGGHAEHDGKPFCHKPCYATLFGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTPGGHAEHDGKPFCHKPCYATLFGPK 28 2 P52943;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 68.689 0.0040817 668240000 244540 422250 594520 470720 733830 690440 654520 688150 578810 380730 FALSE TRUE 254194.628 494768.1529 610013.6796 563827.011 609093.8387 530095.7737 603217.0121 678926.4748 557978.7412 455326.754 0.558268597 1.086622186 1.339727293 1.238290977 1.337707116 1.16420959 1.324800282 1.491075297 1.22544686 1 18.79654271 4.707482752 2.34674614 1.294256269 0.409682486 0.738847894 0.125320945 0.242982859 1.691891722 0.030988483 0.426814022 50989.73464 -4.707482752 -0.884573783 TLTPGGHAEHDGQPYCHKPCYGILFGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTPGGHAEHDGQPYCHKPCYGILFGPK 28 1 P52943;H0YFA4;H0YHD8;P52943-2 P52943;P52943-2 CRIP2 Cysteine-rich protein 2 0 ; 91.583 0.00094873 2505200000 888350 1704020 1800700 1807170 2374500 2455800 2021950 2267340 2047550 1695140 FALSE TRUE 923422.744 1996672.18 1847627.721 2164622.832 1970883.338 1885477.668 1863464.276 2236950.016 1973859.075 2027270.228 0.45550057 0.984906774 0.911386995 1.067752489 0.972185805 0.930057396 0.919198758 1.10342962 0.973653659 1 20.95110698 4.738822469 7.755872146 0.988721816 0.450469014 0.880208897 0.058556179 0.030916206 20.26169001 0.014478147 0.086696862 54805.28864 -4.738822469 -0.538252802 TLTPIIQEYFEHGDTNEVAEMLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTPIIQEYFEHGDTNEVAEMLR 23 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 ; 306.24 1.44E-62 186337000 88823 106479 107677 103279 114247 119129 103195 110467 96271 95904 FALSE TRUE 92329.80063 124765.94 110483.1511 123707.2779 94827.33575 91463.09517 95106.30625 108986.3706 92806.22552 114694.5526 0.805005979 1.087810512 0.963281591 1.078580239 0.826781513 0.797449339 0.829213804 0.950231446 0.809159837 1 16.80743735 3.223788966 24.99999781 0.866152559 0.989651949 0.263030175 0.09391494 291.2508281 492920.8823 0.026000325 0.031197895 1674.12918 -3.223788966 0.12349939 TLTSGGHAEHEGKPYCNHPCYAAMFGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTSGGHAEHEGKPYCNHPCYAAMFGPK 28 1 P50238;K4DIB9;H3BRQ4 P50238 CRIP1 Cysteine-rich protein 1 0 38.146 0.066798 1319000000 420690 656570 792160 706980 989460 937420 901670 920960 937600 595910 FALSE TRUE 437299.166 769330.7901 812804.3404 846818.5339 821271.9426 719718.4117 830994.7493 908616.0376 903855.9592 712667.1551 0.613609261 1.079509256 1.140510454 1.188238475 1.15239202 1.009894179 1.166034864 1.274951471 1.268272226 1 19.44286891 4.778106563 2.543449502 1.162882806 0.462062744 0.772388598 0.086592818 0.275934055 2.07816036 0.022550723 0.433559554 59993.82656 -4.778106563 -0.700820062 TLTTGSSAYLWKPPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TLTTGSSAYLWKPPSR 16 1 Q9BQS8;Q9BQS8-4;Q9BQS8-3;Q9BQS8-2 Q9BQS8 FYCO1 FYVE and coiled-coil domain-containing protein 1 1 TLTTGSSAYLWKPPS(1)R;TLTTGSSAYLWKPPS(1)R 161.59 5.07E-09 3879200000 2185750 1260740 1502890 1346970 2171340 2233000 1917310 1653760 1605260 1101130 TRUE FALSE 2272045.098 1477262.288 1542056.548 1613396.646 1802256.402 1714419.591 1767026.232 1631594.052 1547487.006 1316875.341 1.725330429 1.121793568 1.170996601 1.225170368 1.368585428 1.301884497 1.341832577 1.238988993 1.175120346 1 20.32868735 -4.999999999 0.139172263 1.09E-12 1.394464683 0.306365031 0.153517537 190.2534493 1.627234664 52.65362249 0.935030064 1.00E-05 4.999999999 1.394464683 TLTTVQGIADDYDKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLTTVQGIADDYDKKK 16 2 K7EM18;P41567;O60739 K7EM18 EIF1;EIF1B Eukaryotic translation initiation factor 1;Eukaryotic translation initiation factor 1b 0 61.477 0.047722 559990000 688120 177320 329450 177580 471480 540510 383470 270160 338000 155860 FALSE TRUE 715287.5089 207773.3306 338035.7376 212704.794 391337.998 414984.744 353412.6194 266538.9471 325835.446 186397.7829 3.837424984 1.114677049 1.813518017 1.141133712 2.099477751 2.226339485 1.896012999 1.429946982 1.748065031 1 17.50802517 4.747295156 24.85268999 1.650202028 3.837426194 0.730154214 0.405914809 540.9062224 1539022.924 0.09485781 1.127384341 55884.98723 -4.747295156 2.187224166 TLVS(ph)PNKAETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TLVSPNKAETK 11 1 O75363;G3XAF7;O75363-2;H0Y542;H7C1E7 O75363 BCAS1 Breast carcinoma-amplified sequence 1 1 TLVS(1)PNKAETK 78.285 0.018349 220250000 188020 63646 97233 65430 130550 148060 125100 87997 108450 61745 TRUE FALSE 195443.1748 74576.7054 99766.97186 78371.85871 108359.1576 113675.3089 115294.3351 86817.54415 104546.9057 73842.75057 2.646748303 1.00993943 1.351073343 1.061334499 1.467431221 1.539424087 1.561349411 1.175708427 1.415804597 1 16.17216867 4.746415172 24.96117517 1.307257449 2.646748967 0.798740188 0.204550865 405.6617005 1289131.323 0.047838367 0.523371542 55771.86558 -4.746415172 1.339491518 TLVVHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TLVVHEK 7 0 P00441;H7BYH4 P00441 SOD1 Superoxide dismutase [Cu-Zn] 0 ;;;;;;; 100.45 0.0097841 18472170000 18193870 15458340 18156330 14444850 21681300 21380500 19736730 18301920 18208420 14718580 FALSE TRUE 18912178.04 18113189.65 18629498.88 17301998.22 17995920.37 16415202.9 18189713.53 18056612.7 17553102.52 17602403.95 1.074408819 1.029017951 1.058349697 0.982933824 1.022355834 0.932554607 1.033365305 1.025803791 0.997199165 1 24.06926913 3.747434092 24.57341885 1.002004056 1.051434739 0.429695459 0.028733763 533.8955381 1478519.497 0.007482717 0.013224061 5590.286835 -3.747434092 0.049430684 TMDILASLATSVDKGECLGGSTLSLLHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMDILASLATSVDKGECLGGSTLSLLHDR 29 1 F2Z2B9;Q9BSJ2-3;Q9BSJ2;Q9BSJ2-4 F2Z2B9 TUBGCP2 Gamma-tubulin complex component 2 0 ; 216.76 1.56E-34 213611000 97345 111002 183415 154866 218570 190924 173900 185806 168980 118056 FALSE TRUE 101188.2558 130065.73 188194.9456 185498.0326 181417.5495 146584.7945 160269.2636 183315.5745 162898.4428 141186.8129 0.716697641 0.921231434 1.332949882 1.313848148 1.284946843 1.038232902 1.135157458 1.298390202 1.153779446 1 17.10724582 4.428556088 4.289260717 1.207716878 0.753728992 0.660680179 0.111527998 0.105651935 4.048690921 0.027751896 0.090829448 26826.01034 -4.428556088 -0.453987886 TMELS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TMELSPR 7 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TMELS(1)PR 85.666 0.021654 129570000 319590 314400 365520 361000 369070 454340 351640 336020 347540 370550 TRUE FALSE 332207.66 368395.7543 375045.7515 432404.7225 306335.6132 348826.4206 324077.538 331516.2015 335032.1033 443152.1779 0.749646908 0.831307557 0.846313682 0.975747709 0.691265052 0.787148158 0.73130079 0.74808659 0.756020437 1 18.75744268 4.759858704 21.10016613 0.804976822 0.749646445 0.02705736 0.096906344 2638.475783 2613589.5 0.02276033 0.752017251 57525.27502 -4.759858704 -0.055330377 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK;TMFAQVES(1)DDEEAKNEPEWK 283.17 4.27E-45 829060000 869310 253622 470803 252814 639640 765700 621740 427941 524405 203515 TRUE FALSE 903631.0301 297179.6056 483072.5129 302819.8546 530914.2213 587877.7793 573006.3942 422205.1509 505531.7665 243389.8677 3.712689598 1.221002371 1.984768378 1.244176093 2.18133247 2.415374908 2.354273822 1.734686636 2.077045241 1 17.89290958 0.017190681 0.92580753 0.986150494 2.06577358 0.195978255 0.666098134 10.64680292 8.482845934 1.085844843 0.196207202 1.040376854 -0.017190681 1.079623086 TMGYSVTAPEDTRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMGYSVTAPEDTRR 14 1 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ; 224.42 5.06E-12 541610000 283890 354710 346680 317100 397290 425150 340470 348650 322720 323240 FALSE TRUE 295098.1964 415628.6832 355714.7656 379821.4336 329758.7877 326415.3557 313783.0717 343976.917 311105.3702 386572.6892 0.763370524 1.07516308 0.920175624 0.982535611 0.853031776 0.844382867 0.811705225 0.88981174 0.804778452 1 18.56038019 3.224640431 24.94183771 0.858981812 0.944219515 0.117189786 0.088406469 366.0973641 655962.7641 0.023494583 0.028216983 1677.414646 -3.224640431 0.085237703 TMHHLLLEVEVIEGTLQCPESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TMHHLLLEVEVIEGTLQCPESGR 23 0 F5GYQ2;Q9UI30;Q9UI30-2 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 ;;; 247.31 6.58E-38 483254000 116982.7 158189.4 128550.2 135649.8 148794.4 184238 153551.6 143050.8 136152.7 113001.6 FALSE TRUE 121601.2673 185357.1989 131900.3238 162480.9256 123502.381 141451.5167 141515.8244 141133.438 131252.5909 135142.1 0.899803003 1.371572581 0.976012093 1.202296883 0.913870519 1.046687277 1.04716313 1.044333617 0.971219116 1 17.04411765 3.244615192 24.99999088 1.013549409 1.121188437 0.150708957 0.124276109 266.10903 1098784.865 0.031729575 0.041885666 1756.366691 -3.244615192 0.107639028 TMIIS(ph)PER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PER;TMIIS(1)PER;TMIIS(1)PER 141.29 0.00066697 823680000 885990 984080 951690 1184290 985370 1194630 1209680 930550 876260 752270 TRUE FALSE 920969.5693 1153088.085 976491.8232 1418539.027 817877.1594 917195.2873 1114862.121 918077.4993 844723.5738 899662.9034 1.023682944 1.281689042 1.085397452 1.576745047 0.909092902 1.019487726 1.239199834 1.020468329 0.938933428 1 19.77902501 TMIIS(ph)PERLDPFADGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TMIISPERLDPFADGGK 17 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 TMIIS(1)PERLDPFADGGK;TMIIS(1)PERLDPFADGGK;T(0.001)MIIS(0.999)PERLDPFADGGK;T(0.004)MIIS(0.996)PERLDPFADGGK;T(0.175)MIIS(0.825)PERLDPFADGGK;T(0.014)MIIS(0.986)PERLDPFADGGK;T(0.007)MIIS(0.993)PERLDPFADGGK;T(0.001)MIIS(0.999)PERLDPFADGGK 187.07 2.95E-10 1032919000 2916279 1873482 2684275 2256556 2975645 3427835 3793711 2751192 2948227 1513687 TRUE FALSE 3031415.947 2195237.96 2754229.412 2702896.042 2469845.926 2631772.271 3496350.019 2714316.771 2842120.886 1810264.986 1.674570281 1.212661117 1.521450966 1.493094139 1.364356017 1.45380499 1.931402333 1.499403011 1.570002683 1 20.78776946 2.437315871 24.99998234 1.568864827 1.442186924 0 0.241139581 467.3821844 293539.5054 0.07758741 0.064914348 273.7258866 -2.437315871 -0.126677903 TMIIS(ph)PERLDPFADGGKT(ph)PDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 2 T(0.468)MIIS(0.532)PERLDPFADGGKT(1)PDPK;T(0.408)MIIS(0.592)PERLDPFADGGKT(1)PDPK 113.47 0.0010488 202903000 471830 148145 203936 135435 361010 368520 231055 200618 218097 118123 TRUE FALSE 490458.2127 173587.7513 209250.7397 162223.6388 299645.6491 282936.815 212944.3054 197929.0439 210247.7316 141266.9402 3.47185415 1.228792462 1.481243519 1.148348216 2.121130737 2.002852291 1.507389521 1.401099532 1.488301022 1 17.10806436 4.743802358 24.83498222 1.519261156 3.471855049 0.762118418 0.332294334 250.163484 1185215.665 0.080484819 0.685506946 55437.3367 -4.743802358 1.952593893 TMIIS(ph)PERLDPFADGGKTPDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TMIISPERLDPFADGGKTPDPK 22 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 T(0.43)MIIS(0.57)PERLDPFADGGKTPDPK;T(0.321)MIIS(0.679)PERLDPFADGGKTPDPK;T(0.179)MIIS(0.821)PERLDPFADGGKTPDPK;T(0.066)MIIS(0.934)PERLDPFADGGKTPDPK 92.819 0.0010516 446203000 2014940 913700 1513980 839607 2051760 1842470 1699850 1365890 1705610 798268 TRUE FALSE 2094491.387 1070620.867 1553435.563 1005678.759 1703002.568 1414584.265 1566611.315 1347582.479 1644225.429 954673.3308 2.19393516 1.121452577 1.627190697 1.0534271 1.783858953 1.481746918 1.640992018 1.411563972 1.72229115 1 19.86464763 -1.09699755 4.66250695 0.99996719 1.532429162 0.220449898 0.311952265 9.45E-05 1.83E-05 0.268327587 0.063241529 0.079983877 1.09699755 0.532461972 TMLELINQLDGFDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMLELINQLDGFDPR 15 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 99.522 0.005839 171911000 196150 242970 248447 247086 271610 309050 260330 266690 259823 257150 FALSE TRUE 203894.1535 284698.2075 254921.7329 295958.8733 225441.8292 237277.8212 239924.6544 263115.4568 250472.021 307533.6191 0.662997932 0.925746617 0.828923139 0.962362665 0.733064014 0.771550837 0.780157484 0.855566483 0.814454113 1 18.23038461 -1.518786971 2.599107993 1.01007754 0.82042415 0.306805841 0.083070473 10287145.71 9948988.63 731759.0422 0.019961149 0.030283985 1.518786971 -0.18965339 TMLELLNQLDGFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMLELLNQLDGFDSR 15 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 211.77 2.82E-09 289700000 288970 352670 320420 324540 417550 460690 386550 365100 347730 347190 FALSE TRUE 300378.7587 413238.3291 328770.4084 388733.0433 346575.0001 353701.7293 356251.2009 360206.4317 335215.2652 415215.2331 0.723429043 0.995238845 0.791807193 0.936220573 0.834687585 0.851851524 0.857991645 0.867517381 0.807328919 1 18.66349985 -1.632039243 3.738765627 1.006006479 0.85732791 0.278066967 0.071142174 0.003208179 0.000315742 0.062043259 0.014070198 0.023332472 1.632039243 -0.148678569 TMLITHMQDLQEVTQDLHYENFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TMLITHMQDLQEVTQDLHYENFR 23 0 Q15019-2;Q15019-3;Q15019;B5MCX3 Q15019-2 2-Sep Septin-2 0 ;;; 308.81 2.36E-73 3235613000 650994.4 937307 801453 804062 950812 1075582 887628 821982 790451 840674 FALSE TRUE 676696.1616 1098282.186 822339.5236 963103.0637 789193.3159 825794.3811 818053.398 810964.6758 762002.8229 1005387.975 0.673069679 1.092396382 0.817932524 0.957941698 0.78496395 0.821368866 0.813669368 0.806618635 0.757919174 1 19.93932091 3.224783397 24.99544031 0.818729068 0.895310709 0.041458358 0.116627693 544.2944172 987489.1217 0.030668887 0.036833299 1677.96693 -3.224783397 0.076581642 TMPGGNDHEIFTDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TMPGGNDHEIFTDPR 15 0 O15305;H3BRM0;H3BV55 O15305 PMM2 Phosphomannomutase 2;Phosphomannomutase 0 ;; 77.754 0.024947 1123630000 1203000 1532960 1406130 1371240 1651260 1676280 1447610 1459750 1411190 1402410 FALSE TRUE 1250495.369 1796233.955 1442774.903 1642467.179 1370579.415 1286989.374 1334142.546 1440184.439 1360401.548 1677185.389 0.745591619 1.070981161 0.860235793 0.979299719 0.817190171 0.767350695 0.795465161 0.858691263 0.81112175 1 20.67761074 3.219736297 24.99119042 0.829851514 0.921395852 0.107437546 0.097856242 398.9236791 529610.3419 0.026042783 0.031177312 1658.579513 -3.219736297 0.091544338 TMS(ph)EVGGSVEDLIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.093)MS(0.907)EVGGSVEDLIAK 77.912 0.0097959 0 18418 14313 14357 8726.9 18254 18316 15637 17411 15951 12062 TRUE FALSE 19145.15686 16771.14641 14731.15521 10453.05477 15151.1916 14062.38658 14411.33108 17177.63402 15376.92663 14425.31796 1.327191325 1.162618838 1.021201422 0.724632539 1.050319421 0.974840667 0.999030394 1.190797601 1.065967951 1 13.8163155 4.493178619 2.714094554 1.010606026 1.324145813 0.4670047 0.109997771 0.305114336 4.009405487 0.030649588 0.165696857 31129.96401 -4.493178619 0.313539787 TMSS(ph)DDEDCSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TMSSDDEDCSAK 12 0 Q9NVR2;H0YBW3 Q9NVR2 INTS10 Integrator complex subunit 10 1 T(0.001)MS(0.057)S(0.942)DDEDCSAK 86.699 0.042861 35624000 104200 94098 94442 93921 124820 147810 108770 97519 101300 93426 TRUE FALSE 108313.8965 110258.5995 96903.2361 112498.2935 103603.141 113483.3676 100244.3232 96211.91731 97654.23279 111731.036 0.96941638 0.986821599 0.867290232 1.006867004 0.927254814 1.015683481 0.897193178 0.861102884 0.874011701 1 16.76967046 2.104408601 10.48485326 0.892013027 0.959427293 0.172346933 0.053601733 0.436736216 40.5691445 0.018891787 0.013950757 127.1770073 -2.104408601 0.067414265 TMVGFGPEDDHFVAELTYNYGVGDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TMVGFGPEDDHFVAELTYNYGVGDYK 26 0 Q9HC38-2;F6TLX2;Q9HC38;I3L3Q4;Q9HC38-3 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ; 277.91 1.06E-60 416780000 476940 406900 481430 373620 569600 585500 492030 468610 464250 434040 FALSE TRUE 495769.9595 476781.9098 493976.4613 447520.9209 472779.5955 449526.4983 453463.4029 462329.0494 447541.7332 519081.8278 0.955090186 0.918510116 0.95163505 0.862139449 0.910799743 0.866003151 0.873587513 0.890666991 0.862179543 1 18.98560246 3.748869815 24.8365769 0.888845415 0.93942162 0.213078181 0.0398139 819.902209 1975275.319 0.009222863 0.016394233 5608.798201 -3.748869815 0.050576204 TMYLEDR ddPTM_MDA-MB-175_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 96.285 0.029881 208860000 236990 293190 282970 285040 301140 329230 259960 257980 247060 240810 FALSE TRUE 246346.5482 343543.1018 290344.4307 341420.0612 249952.3304 252771.322 239583.6559 254522.2001 238168.3589 287992.1089 0.855393396 1.192890677 1.008168008 1.185518806 0.867913816 0.87770225 0.831910488 0.883781854 0.826996128 1 18.13566976 3.214791331 24.86170386 0.872724298 1.066212229 0.437553329 0.099106685 170.6032552 178443.5854 0.026193539 0.031323886 1639.801694 -3.214791331 0.193487931 TNAVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TNAVSPK 7 0 Q6XZF7 Q6XZF7 DNMBP Dynamin-binding protein 1 TNAVS(1)PK;TNAVS(1)PK;TNAVS(1)PK 110.54 0.0071124 597979000 1953030 844740 1208360 904600 1702530 2060430 1565170 1256050 1265790 635600 TRUE FALSE 2030137.132 989817.5238 1239850.854 1083527.18 1413134.559 1581926.359 1442487.886 1239214.704 1220234.465 760133.6507 2.670763399 1.302162485 1.631095865 1.425442985 1.85906065 2.081116074 1.897676658 1.630258972 1.605289365 1 19.53589358 0.731892114 1.341539039 1.002398254 1.795889412 0.32073245 0.358605719 1.095966635 3.309437366 0.327034439 0.097590715 5.393766155 -0.731892114 0.793491158 TNDAS(ph)SESIASFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNDASSESIASFSK 14 0 A0A1W2PPI1;J3KSA2;A0A1W2PR65;J3QQS3;A0A1W2PRQ6;J3QS66;A0A1W2PS04;A0A1W2PP78;A0A1W2PNV7;A0A1W2PPG2;A0A1W2PPJ9;A0A1W2PQF1;Q7RTN6-6;Q7RTN6 A0A1W2PPI1 STRADA STE20-related kinase adapter protein alpha 1 TNDAS(0.972)S(0.028)ESIASFSK;TNDAS(0.828)S(0.107)ES(0.065)IASFSK 206.81 1.08E-08 124818000 305800 212741 238519 191230 307010 338880 305520 239535 261820 150756 TRUE FALSE 317873.2201 249277.6119 244735.0011 229054.7232 254824.5499 260180.2558 281572.5441 236324.4251 252397.1493 180293.7518 1.76308506 1.38261925 1.357423641 1.270452919 1.413385363 1.443090807 1.561743218 1.310774349 1.399921777 1 17.45998987 -3.292456179 0.264682471 3.43E-10 1.463221296 0.512269873 0.129893467 62.5398203 1.386407847 34.57067085 0.170342503 0.000509969 3.292456179 1.463221296 TNEGVIEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TNEGVIEFR 9 0 Q13247;Q13247-3;A0A590UJP7;A0A590UJK4;A0A590UK01;A0A590UK80 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 ;;; 150.35 0.00019879 985880000 1112930 1417170 1412050 1388020 1608400 1836130 1510340 1508690 1383410 1298790 FALSE TRUE 1156869.336 1660557.923 1448849.183 1662566.213 1335004.743 1409716.634 1391955.604 1488468.478 1333621.344 1553263.034 0.744799374 1.06907709 0.932777741 1.070370039 0.859484011 0.907583972 0.896149315 0.958284879 0.858593371 1 20.56687073 TNGHS(ph)PSQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNGHSPSQPR 10 0 Q9Y2D5;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5-6;Q9Y2D5-4;C9JVY5 Q9Y2D5 AKAP2 A-kinase anchor protein 2 1 TNGHS(0.885)PS(0.115)QPR 81.565 0.019545 0 33438 33753 36061 30448 51395 57422 37126 37288 39311 33416 TRUE FALSE 34758.15806 39549.81519 37000.77928 36470.52352 42658.89626 44086.61074 34215.96711 36788.21535 37896.20479 39963.22541 0.869753572 0.989655234 0.925870695 0.912602102 1.067453786 1.103179493 0.856186325 0.920551707 0.948276932 1 15.28638541 6.402037157 9.451158633 0.956974002 0.539847645 0 0.076554027 0 0 0.017454394 0 2523696.685 -6.402037157 -0.417126358 TNHIGHTGYLNTVTVSPDGSLCASGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNHIGHTGYLNTVTVSPDGSLCASGGK 27 0 P63244;J3KPE3;D6RHH4;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" 0 114.74 0.00049549 569400000 340600 129360 208170 126010 270420 266750 242470 233310 206930 95273 FALSE TRUE 354047.151 151576.5737 213595.0812 150934.4019 224454.105 204801.3551 223464.5678 230182.8611 199482.6297 113939.9202 3.107314366 1.330320167 1.874629022 1.324684111 1.969933843 1.797450399 1.961249116 2.020212587 1.750770312 1 16.79791378 4.749195472 24.96312641 1.736672096 3.107315153 0.626275477 0.329500821 983.204659 2307824.317 0.074481374 1.084355893 56130.05559 -4.749195472 1.370643057 TNHRLS(ph)LPMPASGTSLSAAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNHRLSLPMPASGTSLSAAIHR 22 1 Q14451;Q14451-3;Q14451-4 Q14451 GRB7 Growth factor receptor-bound protein 7 1 T(0.166)NHRLS(0.834)LPMPASGTSLSAAIHR;T(0.141)NHRLS(0.859)LPMPASGTSLSAAIHR 261.23 1.63E-37 3012600000 446310 737740 845670 840730 971690 1177710 970450 879120 908190 700240 TRUE FALSE 463930.6634 864441.1062 867708.8549 1007023.885 806522.4809 904204.7009 894383.5932 867336.8344 875504.4193 837438.6211 0.553987662 1.032244136 1.036146212 1.202504708 0.9630825 1.079726535 1.06799898 1.035701976 1.045455031 1 19.67562393 4.740354208 4.788470371 1.056487046 0.52519923 0.86476529 0.059061002 0.056227682 3.695759334 0.013348486 0.099943367 54998.92591 -4.740354208 -0.531287816 TNHSNIMDDPFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNHSNIMDDPFIR 13 0 P61201;P61201-2;B4DIH5;H0YMC2 P61201 COPS2 COP9 signalosome complex subunit 2 0 ; 146 4.21E-05 190795000 147446 177368 193888 185181 195684 234699 196190 184620 169854 144527 FALSE TRUE 153267.2819 207829.5743 198940.8806 221809.2491 162421.7036 180193.7141 180812.1152 182145.4709 163740.9877 172844.2985 0.886736116 1.202409198 1.150983181 1.283289359 0.939699516 1.04252044 1.046098232 1.053812434 0.947332305 1 17.39911349 3.21575261 24.99464542 1.015208547 1.137403415 0.267066298 0.101122461 318.2654329 348777.1086 0.028625867 0.034235959 1643.435295 -3.21575261 0.122194868 TNIIPVLEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNIIPVLEDAR 11 0 A6NHQ2 A6NHQ2 FBLL1 rRNA/tRNA 2-O-methyltransferase fibrillarin-like protein 1 0 85.288 0.035658 26917000 18055 37629 33430 38309 33892 45805 30177 34496 29903 57890 FALSE TRUE 18767.82534 44091.48804 34301.21326 45886.40586 28131.04995 35167.48293 27811.64789 34033.63754 28826.79687 69232.43713 0.27108428 0.636861706 0.495450033 0.662787672 0.406327599 0.507962516 0.401714125 0.491585144 0.416377035 1 16.07916051 -1.351725441 3.250726198 1.004017474 0.483649274 0.674450643 0.108976799 38635278.13 53363583.28 1487235.022 0.024065505 0.044491245 1.351725441 -0.5203682 TNILQYASTRPPTLS(ph)PIPHIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNILQYASTRPPTLSPIPHIPR 22 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 TNILQYASTRPPT(0.001)LS(0.999)PIPHIPR;TNILQYASTRPPTLS(1)PIPHIPR 239.87 8.00E-31 1865360000 820810 751790 851850 897290 896180 1171520 1140350 981760 914760 602310 TRUE FALSE 853216.2126 880904.0844 874049.9108 1074771.284 743847.6437 899452.2346 1050966.387 968601.113 881837.9663 720321.1126 1.184494245 1.22293248 1.213417038 1.492072445 1.032661171 1.248682315 1.459024828 1.34467961 1.22422896 1 19.45828066 2.455582355 24.98733675 1.305169905 1.232324818 0 0.153290687 826.2072904 958480.2674 0.051321909 0.042942399 285.4843824 -2.455582355 -0.072845086 TNIVTASVDAINFHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNIVTASVDAINFHDK 16 0 O00154-6;O00154-4;O00154-7;O00154;O00154-5;K7EKP8;O00154-2;O00154-3 O00154-6 ACOT7 Cytosolic acyl coenzyme A thioester hydrolase 0 150.91 6.94E-07 474950000 403740 218750 324380 260740 407560 456660 390060 260020 350550 183700 FALSE TRUE 419679.967 256318.6109 332833.6093 312313.5938 338283.0968 350607.6357 359486.078 256534.8572 337933.774 219692.4979 1.910306319 1.166715356 1.51499761 1.421594259 1.539802679 1.595901723 1.636314765 1.16769967 1.538212626 1 17.74512608 0.270276154 0.550673454 0.974576853 1.51537814 0.350219937 0.205702333 2.951914234 1.319266234 0.375037559 0.088919937 1.863271557 -0.270276154 0.540801287 TNKLPGS(ph)PGLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNKLPGSPGLSK 12 1 Q8N9U0;Q8N9U0-2 Q8N9U0 TC2N Tandem C2 domains nuclear protein 1 TNKLPGS(1)PGLSK;T(0.001)NKLPGS(0.997)PGLS(0.002)K 100.35 0.0019872 3259700000 4660800 2269370 3128100 2501070 4807500 4862300 3641900 3161800 3069370 1854960 TRUE FALSE 4844811.983 2659116.644 3209620.856 2995774.181 3990322.867 3733104.514 3356438.362 3119421.243 2958903.973 2218403.897 2.183917902 1.198662087 1.446815371 1.350418734 1.798735962 1.682788477 1.512996965 1.406155681 1.333798583 1 21.08109062 1.008356929 1.069439508 1.00655374 1.578973358 0.347464562 0.254458532 0.619874071 1.492301645 0.230400428 0.074832779 10.19428871 -1.008356929 0.572419618 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNLDESDVQPVKEQLAQAMFDHIPVGVGSK 30 1 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 97.352 0.0003964 219570000 182510 149780 206390 114440 211670 258550 234510 177720 233200 115550 FALSE TRUE 189715.6357 175503.5499 211768.693 137075.8904 175690.409 198505.6809 216128.4934 175337.9541 224807.1776 138189.8102 1.372862699 1.270018026 1.532447962 0.991939205 1.271370218 1.436471189 1.563997325 1.268819704 1.626799959 1 17.07629171 2.746288178 23.06676147 1.400350542 1.283906629 0.043217381 0.203033555 582.5456472 1738894.87 0.05939939 0.061811353 557.5555946 -2.746288178 -0.116443913 TNLEFLQEQFNSIAAHVLHCTDSGFGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNLEFLQEQFNSIAAHVLHCTDSGFGAR 28 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ; 233.87 2.62E-45 584430000 160376 229668 293253 265506 309380 360330 299070 307330 273740 223403 FALSE TRUE 166707.7683 269111.6924 300895.4141 318022.2943 256791.6981 276648.8184 275628.1119 303210.744 263888.1509 267174.5405 0.623965772 1.007250511 1.1262129 1.190316614 0.961138354 1.035461005 1.031640632 1.134878883 0.987699465 1 18.02742301 4.729354434 3.688693714 1.065987297 0.580203396 0.778333936 0.068994032 0.111208964 2.848509024 0.016702521 0.146243378 53623.41076 -4.729354434 -0.485783901 TNLSGRQS(ph)PSFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.948)PS(0.052)FK 138.91 4.01E-05 531650000 839550 741930 858770 426690 1437670 1104940 540040 828520 899170 912150 TRUE FALSE 872696.0823 869350.7061 881150.2517 511088.0085 1193295.367 848334.4305 497710.2537 817415.0446 866809.0473 1090868.328 0.800001301 0.796934592 0.807751246 0.468514847 1.09389496 0.777668953 0.456251447 0.749325123 0.794604651 1 20.05704554 0.840886886 3.323288134 0.999854907 0.738565901 0.166869173 0.171024954 1.403892423 25.98482894 0.160978292 0.041736897 6.932452241 -0.840886886 -0.261289006 TNNVSEHEDTDKYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TNNVSEHEDTDKYR 14 1 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;;;; 229.68 7.19E-13 3164819000 3390710 3074570 4284870 3526390 5400630 5535700 5013720 4365410 4399890 2593940 FALSE TRUE 3524577.849 3602603.481 4396537.232 4223899.417 4482632.842 4250117.569 4620731.525 4306898.819 4241538.818 3102172.879 1.136164226 1.161316155 1.41724443 1.361593819 1.444997754 1.370045363 1.489514513 1.388349066 1.367279963 1 21.56484766 4.246782421 23.14398421 1.379961875 1.148739761 0.278647362 0.127661927 70.41646325 198206.2623 0.02779718 0.073105298 17651.53269 -4.246782421 -0.231222115 TNPPTQKPPS(ph)PPMSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 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 TNPPT(0.001)QKPPS(0.725)PPMS(0.274)GR;TNPPTQKPPS(1)PPMSGR;TNPPTQKPPS(0.992)PPMS(0.008)GR;TNPPTQKPPS(0.869)PPMS(0.131)GR;TNPPTQKPPS(0.794)PPMS(0.206)GR;TNPPTQKPPS(0.987)PPMS(0.013)GR;TNPPTQKPPS(0.985)PPMS(0.015)GR;TNPPTQKPPS(0.995)PPMS(0.005)GR;TNPPTQKPPS(0.984)PPMS(0.016)GR;TNPPT(0.001)QKPPS(0.976)PPMS(0.023)GR;TNPPTQKPPS(0.952)PPMS(0.048)GR 129.02 3.49E-05 13990380000 4226643 2168015 2887938 1960035 3964925 4548123 3510860 2833956 3032772 1777476 TRUE FALSE 4393514.129 2540354.711 2963200.037 2347724.073 3290968.465 3491890.361 3235669.619 2795971.455 2923623.128 2125738.39 2.066817887 1.195045789 1.393962705 1.104427564 1.548153093 1.642671731 1.522139147 1.315294237 1.375344747 1 21.01953263 -3.306700016 0.231964043 8.72E-11 1.505494422 0.255186725 0.249369131 101.1718208 2.048113876 49.01860257 0.430337484 0.000493515 3.306700016 1.505494422 TNPS(ph)PTNPFSSDLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.999)PT(0.001)NPFSSDLQK;TNPS(0.994)PT(0.006)NPFSSDLQK;TNPS(0.999)PT(0.001)NPFSSDLQK;TNPS(0.999)PT(0.001)NPFSSDLQK 265.77 3.22E-25 761300000 575130 427645 580588 429606 741680 766820 739710 626390 599800 412664 TRUE FALSE 597836.5765 501089.7021 595718.6002 514580.7846 615609.4985 588737.6763 681729.5973 617994.2666 578213.3152 493517.6099 1.211378408 1.015343105 1.207086816 1.042679682 1.247391149 1.192941578 1.381368332 1.252223334 1.171616379 1 18.91274204 3.217996771 24.977463 1.233280697 1.117992415 0.11396915 0.107333664 350.3051174 425490.2604 0.029252704 0.034999091 1651.949515 -3.217996771 -0.115288282 TNQELQEINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNQELQEINR 10 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 0 121.61 0.0011877 79393000 39526 55861 62720 57579 61085 83173 56244 61962 52026 62139 FALSE TRUE 41086.517 65454.69221 64354.53473 68967.95434 50701.79352 63857.33125 51835.44831 61131.50074 50153.59442 74313.94733 0.552877602 0.880786105 0.865981919 0.928062051 0.682264842 0.859291338 0.697519782 0.822611407 0.674888042 1 16.18134538 -2.159212948 2.416247735 1.524694516 0.783667882 0.262219339 0.112735981 6834917.449 2212327.818 19558434.18 0.025324397 0.006930859 2.159212948 -0.741026634 TNRGS(ph)QLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TNRGSQLHK 9 1 P42356;P42356-2 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 T(0.039)NRGS(0.961)QLHK;T(0.001)NRGS(0.999)QLHK;TNRGS(1)QLHK;T(0.011)NRGS(0.989)QLHK 125.82 0.0002973 538346000 354749 247623 345756 289919 440759 483041 401095 332339 366812 219034 TRUE FALSE 368754.7644 290150.324 354766.6854 347264.1129 365838.9426 370862.0483 369656.1258 327884.5393 353610.5078 261949.5186 1.407732171 1.107657405 1.354332267 1.325690975 1.396600935 1.415776789 1.411173144 1.251708883 1.349918525 1 17.99892929 -0.300813534 1.030234876 0.994117209 1.332875123 0.554888857 0.090028151 15.71461431 11.15382296 0.485577498 0.02726949 0.500249273 0.300813534 0.338757914 TNRT(ph)SQDYDQLPSCSDGSQAPARPPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNRTSQDYDQLPSCSDGSQAPARPPKPR 28 3 Q13191 Q13191 CBLB E3 ubiquitin-protein ligase CBL-B 1 T(0.146)NRT(0.427)S(0.427)QDYDQLPSCSDGSQAPARPPKPR 141.13 1.31E-07 189040000 46994 31219 48108 42128 59952 67425 63431 59507 57135 34006 TRUE FALSE 48849.35941 36580.6204 49361.734 50460.79266 49761.38045 51766.56559 58459.11247 58709.406 55078.72251 40668.82462 1.201150018 0.899475722 1.213748724 1.240773323 1.223575575 1.27288079 1.437442882 1.443597314 1.35432295 1 15.31163568 3.540786662 1.034564553 1.346613452 1.055080305 0.232129872 0.143810235 0.605101248 1.295400973 0.052498024 0.124331434 3473.654832 -3.540786662 -0.291533147 SSSQSTFHIPLS(ph)PVEVKPGNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 SSSQSTFHIPLSPVEVKPGNVR 22 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR;SSSQSTFHIPLS(1)PVEVKPGNVR 180.71 3.16E-17 2814350000 1251348 2336290 2697260 2502700 3337480 3665850 3109780 3319570 3206290 2500210 TRUE FALSE 1300752.185 2737529.634 2767552.811 2997726.59 2770176.342 2814511.894 2866027.318 3275076.594 3090896.249 2990078.28 0.435022787 0.915537781 0.925578715 1.002557896 0.926456127 0.941283682 0.95851247 1.095314666 1.033717502 1 21.51175182 4.939456008 1.804627355 0.992743116 1.18E-15 0.913986193 0.050287153 0.479959006 1.022000808 0.014771679 0.957618939 86987.33147 -4.939456008 -0.992743116 down TNS(ph)MGSATGPLPGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TNSMGSATGPLPGTK 15 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 T(0.018)NS(0.977)MGS(0.005)AT(0.001)GPLPGTK;T(0.003)NS(0.985)MGS(0.012)ATGPLPGTK;T(0.011)NS(0.989)MGSATGPLPGTK;T(0.047)NS(0.952)MGS(0.001)ATGPLPGTK;T(0.006)NS(0.992)MGS(0.002)ATGPLPGTK;TNS(0.998)MGS(0.001)ATGPLPGTK;TNS(0.968)MGS(0.031)ATGPLPGTK;TNS(1)MGSATGPLPGTK 248.18 2.47E-18 2169922000 3257040 1870030 2608520 1989190 3732020 3764410 3461910 2921160 2986690 1663720 TRUE FALSE 3385630.454 2191193.106 2676500.174 2382645.845 3097652.573 2890182.828 3190556.448 2882006.628 2879199.61 1989694.08 1.701583418 1.10127136 1.345181755 1.197493559 1.556848665 1.452576482 1.603541208 1.448467208 1.447056429 1 20.9241152 3.233191034 24.99716172 1.454751181 1.320217388 0.015163975 0.211784388 327.3620404 1523977.623 0.056068902 0.068883799 1710.76767 -3.233191034 -0.134533793 TNS(ph)MQQLEQWIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.003)NS(0.997)MQQLEQWIK;T(0.008)NS(0.992)MQQLEQWIK;T(0.006)NS(0.994)MQQLEQWIK;T(0.034)NS(0.966)MQQLEQWIK 219.52 3.33E-11 239354000 566110 375890 459040 358649 655720 653200 534140 457084 485910 340105 TRUE FALSE 588460.4599 440446.1835 471002.9595 429588.7017 544260.9486 501504.1993 492272.7111 450957.5366 468422.194 406742.063 1.446765686 1.082863622 1.157989306 1.056169845 1.33809851 1.232978452 1.210282279 1.10870642 1.151644338 1 18.63375467 -4.999999999 0.14227055 0.310188916 1.259571674 0.270543612 0.109176443 199.5153584 1.728085295 38.62151853 0.62979101 1.00E-05 4.999999999 0.949382758 TNS(ph)MSSSGLGSPNRS(ph)SPSIICMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 T(0.173)NS(0.191)MS(0.171)S(0.161)S(0.169)GLGS(0.182)PNRS(0.464)S(0.441)PS(0.049)IICMPK 42.355 0.052626 0 149080 123480 147470 116860 184330 196650 160230 156010 148600 96988 TRUE FALSE 154965.7935 144686.7295 151313.1893 139974.5592 152997.6524 150981.0178 147670.7539 153918.9411 143251.915 115990.9417 1.336016342 1.2473968 1.304525915 1.20677147 1.319048283 1.301662144 1.273123158 1.326991047 1.235026744 1 16.82365262 0.885826119 5.649287731 1.000004435 1.288076325 0.845102796 0.037048879 0.44857034 21.94862466 0.033543688 0.008447193 7.688225601 -0.885826119 0.288071891 TNS(ph)PGFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TNSPGFQK 8 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 T(0.001)NS(0.999)PGFQK;TNS(1)PGFQK;T(0.023)NS(0.977)PGFQK;T(0.005)NS(0.995)PGFQK 74.841 0.041889 623570000 2045560 1177080 1569210 1204850 2103460 2222850 1989640 1575350 1761670 966830 TRUE FALSE 2126320.288 1379234.334 1610104.902 1443165.734 1745914.621 1706626.775 1833686.818 1554235.01 1698267.841 1156261.827 1.838960898 1.192839114 1.392508914 1.24813057 1.509964767 1.475986437 1.58587508 1.344189502 1.468757163 1 20.14103669 -1.376131279 2.767412277 0.991846614 1.43695427 0.378507632 0.172475941 6813868.502 7781650.461 447741.2722 0.040851794 0.042059947 1.376131279 0.445107657 TNS(ph)SSSSPVVLK ddPTM_MDA-MB-175_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(0.005)NS(0.892)S(0.082)S(0.021)S(0.001)SPVVLK;TNS(0.486)S(0.486)S(0.012)S(0.012)S(0.003)PVVLK;T(0.005)NS(0.979)S(0.013)S(0.002)SSPVVLK 148.21 6.95E-05 609204000 1062410 727470 873880 675100 1358930 1315610 1118010 920310 1037650 644360 TRUE FALSE 1104354.767 852407.3136 896654.0307 808632.765 1127939.564 1010079.516 1030377.455 907974.7498 1000305.179 770610.005 1.433091655 1.10614618 1.163563962 1.049341119 1.463697015 1.310753182 1.337093274 1.178254557 1.298069286 1 19.55564139 -1.163565605 3.441159847 0.999671421 1.251800235 0.266182925 0.128863263 21019307.96 33933748.72 77229.52688 0.030771989 0.068617422 1.163565605 0.252128814 TNS(ph)TGGSSGSSVGGGSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.736)T(0.263)GGSSGSSVGGGSGK;TNS(0.5)T(0.5)GGSSGSSVGGGSGK;TNS(0.995)T(0.005)GGSSGSSVGGGSGK;TNS(0.969)T(0.031)GGSSGSSVGGGSGK;T(0.005)NS(0.965)T(0.029)GGSSGSSVGGGSGK 278.57 3.67E-39 920580000 1466261 876386.6 1225484 887286 1672190 1622693 1461312 1259036 1313834 686763 TRUE FALSE 1524150.116 1026899.181 1257421.12 1062788.523 1387951.741 1245847.143 1346770.547 1242160.682 1266549.371 821321.061 1.855729981 1.250301776 1.530973914 1.293998867 1.689901559 1.516882011 1.639761369 1.512393558 1.542088023 1 19.64758677 -1.190768116 4.821463607 0.999933754 1.528299368 0.481623531 0.166886149 0.000108027 1.81E-05 0.146870711 0.034613437 0.06445133 1.190768116 0.528365614 TNSAEVT(ph)PPVLSVMGEATPVSIEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNSAEVTPPVLSVMGEATPVSIEPR 25 0 A0A1C7CYX1;A0A0A0MSU2;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 T(0.034)NS(0.034)AEVT(0.899)PPVLS(0.034)VMGEATPVSIEPR 132.93 0.00024132 32629000 20797 22915 25312 26388 26654 34111 26908 26756 26509 23122 TRUE FALSE 21618.08162 26850.473 25971.65151 31607.46764 22123.3626 26189.23721 24798.88065 26397.37958 25554.94627 27652.3132 0.781782032 0.97100278 0.93922166 1.143031594 0.80005468 0.947090286 0.896810349 0.954617409 0.924152207 1 14.75511255 -4.999999998 0.007042209 1.997764267 8.65E-11 0.050921083 0.093748498 123229.4775 65.96344467 10401.53303 8409.620454 1.00E-05 4.999999998 -1.997764267 TNSGISSASGGSTEPT(ph)TPDSERPAQALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSASGGSTEPT(0.642)T(0.357)PDSERPAQALLR 128.6 2.77E-05 307070000 32986 41649 49888 51147 58188 83738 51866 43267 60318 45281 TRUE FALSE 34288.31275 48801.89177 51188.12226 61263.72394 48297.22454 64291.11856 47800.60739 42687.07664 58147.16696 54152.94499 0.633175403 0.901186293 0.945250942 1.131309183 0.891866999 1.187213707 0.882696359 0.788268794 1.073758167 1 15.72475218 4.762782833 2.261184501 0.973269656 0.534477714 0.460703553 0.11456677 0.657994551 3.721968075 0.030257198 0.588773325 57913.90285 -4.762782833 -0.438791942 TNSGISSASGGSTEPTT(ph)PDSERPAQALLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-2;Q86X10-3;Q86X10;Q86X10-4;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 TNSGISSAS(0.001)GGST(0.001)EPT(0.159)T(0.838)PDS(0.001)ERPAQALLR;TNSGISSASGGST(0.001)EPT(0.287)T(0.712)PDSERPAQALLR;TNSGISSASGGSTEPT(0.03)T(0.97)PDSERPAQALLR 206.39 3.15E-25 2659100000 210312 236092 277256 273882 304656 405938 277550 289611 299316 239222 TRUE FALSE 218615.2802 276638.9645 284481.5191 328055.0421 252870.6819 311665.0515 255794.9058 285729.2383 288543.6756 286092.9707 0.76414069 0.966954776 0.994367385 1.14667285 0.8838759 1.089383814 0.894097136 0.998728621 1.008566114 1 18.12612453 4.746060568 3.069663105 0.99968025 0.724924915 0.480724329 0.073706337 0.310576393 4.351960432 0.016837317 0.209336497 55726.3461 -4.746060568 -0.274755334 TNSMSSSGLGS(ph)PNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 TNSMSSSGLGSPNR 14 0 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 1 TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR;TNSMSSSGLGS(1)PNR 285.91 1.09E-33 5007860000 2846426 2896746 3244409 2885262 3738120 4432650 3731211 3573335 3361114 2778135 TRUE FALSE 2958805.096 3394239.592 3328960.964 3455958.212 3102715.698 3403234.215 3438748.932 3525440.289 3240148.164 3322457.363 0.890547198 1.021605162 1.001957467 1.040181358 0.933861705 1.024312382 1.035001674 1.061094216 0.975226409 1 21.66381925 2.520005023 24.93914245 1.027719863 0.984318826 0.151517741 0.045663859 799.4239695 464905.834 0.014439838 0.013612757 331.1349512 -2.520005023 -0.043401037 TNSMSSSGLGS(ph)PNRS(ph)SPSIICMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 T(0.025)NS(0.03)MS(0.138)S(0.125)S(0.138)GLGS(0.546)PNRS(0.576)S(0.418)PS(0.004)IICMPK;TNS(0.001)MS(0.008)S(0.033)S(0.151)GLGS(0.807)PNRS(0.588)S(0.409)PS(0.003)IICMPK;T(0.004)NS(0.004)MS(0.015)S(0.085)S(0.1)GLGS(0.792)PNRS(0.692)S(0.255)PS(0.053)IICMPK 93.807 0.0040748 664490000 617980 459600 579080 458000 725660 779830 617460 582420 593400 358150 TRUE FALSE 642378.3276 538532.7248 594171.3005 548591.033 602312.5724 598726.3009 569061.8718 574613.6125 572043.6499 428322.6353 1.499753398 1.257306246 1.387204998 1.280789264 1.406212333 1.397839506 1.3285823 1.341543886 1.335543823 1 18.70833839 -3.139565052 0.383377445 1.57E-09 1.365767583 0.740602757 0.06419047 57.43973033 1.667159229 46.45020223 0.038920536 0.000725162 3.139565052 1.365767581 TNSMSSSGLGS(ph)PNRSS(ph)PSIICMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNSMSSSGLGSPNRSSPSIICMPK 24 1 Q9NZN8;Q9NZN8-5;F8VP97;F8VV52;F8VUB4;Q9NZN8-4;F8VX63;F8VVY1;F8VQD8;A0A087X050 Q9NZN8 CNOT2 CCR4-NOT transcription complex subunit 2 2 T(0.012)NS(0.047)MS(0.038)S(0.042)S(0.152)GLGS(0.71)PNRS(0.1)S(0.883)PS(0.017)IICMPK;T(0.003)NS(0.003)MS(0.003)S(0.003)S(0.004)GLGS(0.985)PNRS(0.115)S(0.626)PS(0.258)IICMPK 100.55 4.70E-06 422330000 396296 333629 374056 311550 507320 509240 411940 393816 406128 256283 TRUE FALSE 411942.0721 390927.1855 383804.2067 373173.6601 421085.9276 390976.7276 379651.0664 388537.5407 391511.5326 306496.747 1.344034076 1.275469281 1.252229299 1.217545255 1.373867526 1.275630921 1.238678942 1.267672641 1.277375817 1 18.22551224 -3.484780355 0.366065466 8.93E-16 1.286730826 0.788914182 0.043632062 65.09219793 1.484159159 49.94111093 0.030932685 0.000327506 3.484780355 1.286730826 TNSS(ph)DSERS(ph)PDLGHSTQIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNSSDSERSPDLGHSTQIPR 20 1 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 2 T(0.048)NS(0.309)S(0.643)DS(0.001)ERS(0.999)PDLGHSTQIPR;T(0.06)NS(0.419)S(0.521)DS(0.001)ERS(1)PDLGHSTQIPR 160.43 1.37E-11 926030000 1558010 800340 898590 769720 1204880 2002580 1160310 1012740 932380 704650 TRUE FALSE 1619521.438 937792.1692 922007.9936 921968.3186 1000074.928 1537511.144 1069361.87 999165.8768 898823.8259 842712.6762 1.921795511 1.112825517 1.094095318 1.094048238 1.186732983 1.824478482 1.268951922 1.185654263 1.066583963 1 19.6846813 1.50005371 2.31276885 1.031910666 1.338390078 0.181255612 0.278438233 0.551641258 5.910238783 0.228215789 0.076963554 31.62668772 -1.50005371 0.306479412 TNSTFNQVVLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNSTFNQVVLKR 12 1 J3QQ67;Q07020;F8VYV2;G3V203;H0YHA7;Q07020-2;A0A075B7A0 J3QQ67 RPL18 60S ribosomal protein L18 0 ; 142.39 0.00048335 0 297110 249720 289850 215450 403250 355370 273270 240580 324780 222949 FALSE TRUE 308840.1322 292607.4674 297403.7291 258065.3669 334705.709 272840.7032 251850.3833 237355.4186 313091.2312 266631.5879 1.158302865 1.097422364 1.115410711 0.967872445 1.255311539 1.023287246 0.94456319 0.890199921 1.174246584 1 18.02448818 2.490095533 24.67861423 0.980791291 1.112113208 0.24716142 0.095385814 647.2364574 1231123.077 0.030989881 0.027969197 309.0975285 -2.490095533 0.131321917 TNT(ph)PVKEDWNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 T(0.025)NT(0.975)PVKEDWNVR;T(0.003)NT(0.997)PVKEDWNVR;T(0.003)NT(0.997)PVKEDWNVR;T(0.016)NT(0.984)PVKEDWNVR 140.22 9.62E-05 2413810000 6323900 2530000 3212510 2460650 4344730 6297800 4033750 3158750 3492660 2596130 TRUE FALSE 6573572.455 2964507.819 3296230.65 2947359.226 3606214.346 4835231.394 3717574.135 3116412.123 3366959.849 3104791.968 2.117234431 0.954816893 1.061659101 0.949293626 1.161499509 1.557344725 1.197366578 1.003742652 1.084439758 1 21.56606518 4.744249811 24.80266578 1.116049758 2.117234914 0.761355082 0.16948777 285.9898416 1246763.185 0.043387885 0.383061252 55494.48313 -4.744249811 1.001185156 TNTMNGSKS(ph)PVISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 TNTMNGSKSPVISR 14 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6;Q8N8S7 ENAH Protein enabled homolog 1 T(0.008)NT(0.006)MNGS(0.255)KS(0.732)PVISR;TNTMNGS(0.054)KS(0.946)PVISR;TNTMNGS(0.001)KS(0.999)PVISR;TNTMNGS(0.004)KS(0.996)PVISR;TNTMNGS(0.054)KS(0.946)PVISR;TNTMNGSKS(1)PVISR;TNTMNGS(0.012)KS(0.988)PVISR;TNTMNGS(0.023)KS(0.977)PVISR;T(0.004)NT(0.012)MNGS(0.344)KS(0.64)PVISR;TNTMNGS(0.024)KS(0.976)PVISR;TNT(0.001)MNGS(0.014)KS(0.984)PVISR;TNT(0.002)MNGS(0.07)KS(0.928)PVISR 213.69 4.18E-10 18898370000 14029270 9540490 12096730 8982707 16257820 17120390 14827240 12852600 12919940 7471090 TRUE FALSE 14583156.41 11178994.94 12411980.72 10759459.63 13494321.56 13144438.88 13665042.19 12680331.92 12454953.88 8934907.043 1.632155359 1.251159625 1.389156111 1.204204989 1.510292329 1.471133255 1.52939948 1.419190134 1.393965692 1 23.09102129 0.653770593 3.330851715 1.000003588 1.420469043 0.528593716 0.119888644 4.685649055 44.21257818 0.112120378 0.029024752 4.505786326 -0.653770593 0.420465456 TNTNVNCPIECFMPLDVQADREDS(ph)RE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TNTNVNCPIECFMPLDVQADREDSRE 26 2 H0Y7Z1;P02751-12;P02751-10;P02751-6;P02751-5;P02751-9;P02751-14;P02751-13;P02751-8;P02751-17;P02751-3;P02751-11;P02751-1;P02751-7;P02751 H0Y7Z1 FN1 Fibronectin;Anastellin;Ugl-Y1;Ugl-Y2;Ugl-Y3 1 TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE;TNTNVNCPIECFMPLDVQADREDS(1)RE 222.56 1.96E-34 675280000 140624 164524 174478 130013 228485 234442 158101 190635 203852 161876 TRUE FALSE 146175.9441 192779.7172 179025.04 155729.1833 189647.2013 179996.3985 145708.6305 188079.8496 196515.4063 193592.5029 0.755070273 0.995801564 0.924751927 0.804417428 0.979620587 0.929769468 0.75265637 0.971524449 1.015098226 1 17.56266356 1.538043887 8.241775267 1.002488924 0.885363604 0.310241652 0.08119286 0.146376145 16.97415545 0.04257549 0.019767561 34.51786188 -1.538043887 -0.117125321 TNTPVKEDWNVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 0 ; 133.16 0.00015337 774580000 1223700 1174800 1385100 1245610 1648130 1785440 1487370 1359530 1433770 1066310 FALSE TRUE 1272012.621 1376562.761 1421196.844 1491987.94 1367981.451 1370798.619 1370786.053 1341307.724 1382168.898 1275233.029 0.997474651 1.079459777 1.114460504 1.169972787 1.072730568 1.074939707 1.074929854 1.051813821 1.083855944 1 20.28232947 0.427092555 0.564485339 0.99750382 1.088671134 0.247633805 0.041381915 2.890111985 1.529940952 0.065089246 0.019294656 2.673576128 -0.427092555 0.091167314 TNVLGHLQQGGAPTPFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TNVLGHLQQGGAPTPFDR 18 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 204.94 1.02E-15 1589180000 788750 786710 897420 794590 1032920 1305690 977820 995200 899750 751800 FALSE TRUE 819890.459 921821.3227 920807.5024 951757.5304 857344.6273 1002463.285 901175.9133 981860.9718 867368.1733 899100.8159 0.911900473 1.025270255 1.024142661 1.058565973 0.953557835 1.114962046 1.00230797 1.092047693 0.964706246 1 19.77812337 4.743872592 4.193814193 1.032700282 0.901646572 0.32326139 0.048900729 0.235935087 9.321671987 0.010769967 0.09357434 55446.3028 -4.743872592 -0.13105371 TNYNDRYDEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;; 204.48 3.01E-08 9597190000 4734670 4924250 5585520 5067190 6307140 7159140 6449970 6064190 5753420 4298180 FALSE TRUE 4921598.428 5769951.632 5731083.24 6069465.058 5235054.596 5496538.233 5944404.498 5982909.452 5546355.538 5140326.077 0.957448682 1.122487474 1.114926009 1.180754872 1.018428504 1.06929758 1.156425567 1.163916328 1.078989048 1 22.29342845 2.262477216 24.9099796 1.120428345 1.083028462 0 0.071877745 710.9779112 740506.6137 0.024718322 0.020670356 183.0110091 -2.262477216 -0.037399883 TNYNDRYDEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;;;; 152.16 3.54E-05 13906330000 2657090 2939830 3322840 2257478 3960510 3876480 2836090 3003000 3117260 3225350 FALSE TRUE 2761993.965 3444722.934 3409435.94 2704000.411 3287303.925 2976226.269 2613789.855 2962749.697 3005070.422 3857295.579 0.716044158 0.893040957 0.883892839 0.701009387 0.852230237 0.771583667 0.677622391 0.76808988 0.779061485 1 21.87915827 3.757399663 24.93075701 0.777279351 0.83719747 0.013664591 0.095429496 2152.287626 2848232.692 0.022967967 0.041307764 5720.047867 -3.757399663 0.059918119 TPAAAAAMNLAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 177.07 2.24E-06 1648246000 469991 457881 448371 461514 529204 632138 491834 496096 473586 524683 TRUE FALSE 488546.6076 536518.4999 460055.9166 552800.0917 439250.0931 485333.5296 453282.7659 489446.6446 456541.7324 627484.5882 0.778579453 0.855030562 0.733174846 0.880977959 0.700017341 0.773458885 0.722380716 0.78001381 0.727574415 1 19.2592205 -1.153189618 4.445162652 1.000039058 0.773052477 0.608472967 0.054779309 1.98E-05 3.77E-06 0.049459799 0.011655782 0.070276542 1.153189618 -0.226986582 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 337.65 4.39E-87 3881410000 806668 961661 977378 865646 960047 1155720 912515 947758 885002 957268 TRUE FALSE 838515.8755 1126818.796 1002849.274 1036868.195 796858.5539 887321.5451 840989.6899 935054.8542 853150.9509 1144826.337 0.732439365 0.984270505 0.875983755 0.905699111 0.696051906 0.77507087 0.73460023 0.816765674 0.74522303 1 20.12669734 3.26478601 24.98848438 0.782819077 0.882530925 0.132858533 0.096490982 339.8836779 323850.9556 0.024532018 0.033205988 1839.865222 -3.26478601 0.099711847 TPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.499)S(0.499)PGS(0.001)R 160.92 1.11E-11 46198000 65773 48302 62634 54921 61626 70242 64833 54370 61973 36437 TRUE FALSE 68369.76883 56597.49276 64266.29349 65784.20988 51150.83453 53929.36003 59751.22005 53641.25908 59742.60384 43576.13252 1.56897285 1.29881863 1.474804894 1.509638558 1.173826854 1.237589407 1.371191443 1.230977968 1.370993716 1 15.41125054 -3.253115267 0.062762746 1.27E-10 1.902223885 0.55699199 0.108540293 197.0298421 1.266989855 36.91433711 9.374536057 0.000558322 3.253115267 1.902223885 TPADTGFAFPDWAYKPESS(ph)PGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 TPADTGFAFPDWAYKPES(0.024)S(0.976)PGSR;TPADTGFAFPDWAYKPES(0.04)S(0.959)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.139)S(0.846)PGS(0.015)R;TPADTGFAFPDWAYKPES(0.163)S(0.835)PGS(0.002)R;TPADTGFAFPDWAYKPES(0.086)S(0.913)PGS(0.001)R 261.78 5.24E-44 1799564000 2217949 1590369 2125691 1764614 2485157 2426630 2712678 2164341 2283170 1339505 TRUE FALSE 2305515.339 1863502.504 2181088.254 2113649.382 2062730.901 1863081.958 2500051.21 2135331.549 2200999.158 1601955.358 1.439188256 1.163267437 1.361516251 1.319418404 1.287633198 1.163004917 1.560624768 1.332953217 1.373945376 1 20.61140251 TPAEGRDS(ph)PTREPGALPCACGQLPDLEDELSLLDPLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPAEGRDSPTREPGALPCACGQLPDLEDELSLLDPLPR 38 2 Q96RY5 Q96RY5 CRAMP1L Protein cramped-like 1 T(0.12)PAEGRDS(0.44)PT(0.44)REPGALPCACGQLPDLEDELSLLDPLPR;T(0.013)PAEGRDS(0.939)PT(0.048)REPGALPCACGQLPDLEDELSLLDPLPR;T(0.003)PAEGRDS(0.915)PT(0.082)REPGALPCACGQLPDLEDELSLLDPLPR 154.2 5.64E-14 391992000 18678.5 20379.7 21079.3 24603.4 26120.2 28193.6 24370.4 25286.5 20179.1 23918 TRUE FALSE 19415.9416 23879.75494 21628.64387 29469.87909 21680.29773 21646.06368 22460.18437 24947.57583 19452.85813 28604.27416 0.678777636 0.834831704 0.756133288 1.030261384 0.757939097 0.756742281 0.785203786 0.87216252 0.680068231 1 14.80394312 -1.157323861 4.388660329 1.000038968 0.804179987 0.281299415 0.097396389 1.63614521 54215432.16 4127.021642 0.021694255 0.069610722 1.157323861 -0.195858982 TPALVFEHVNNTDFK ddPTM_MDA-MB-175_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 ; 154.72 2.43E-06 2458200000 1775700 1182850 1551320 1290870 2070510 1989950 2018930 1582660 1797300 1083000 FALSE TRUE 1845806.007 1385995.286 1591748.674 1546200.233 1718565.45 1527814.27 1860680.991 1561447.031 1732615.524 1295193.115 1.425120305 1.070107052 1.228966287 1.193798991 1.326879699 1.179603453 1.436605067 1.205570825 1.337727559 1 20.30473579 -0.990905302 4.519483437 0.999992832 1.260592441 0.347798435 0.109419626 7.22E-06 1.61E-06 0.096870582 0.022831987 0.102116212 0.990905302 0.260599608 TPAPPEPGS(ph)PAPGEGPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPAPPEPGSPAPGEGPSGR 19 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(1)PAPGEGPSGR 151.39 6.93E-08 645140000 393510 343390 376640 338270 426900 495820 476480 416910 434970 322490 TRUE FALSE 409046.0787 402364.5613 386455.5478 405178.7964 354335.6905 380673.3192 439132.2526 411322.0034 419315.5147 385675.7411 1.06059582 1.043271636 1.002021923 1.05056853 0.918739897 0.987029462 1.138604807 1.066496955 1.087222944 1 18.55702888 2.258894232 24.99933859 1.079465661 1.009149257 0.276209617 0.049275942 284.649748 349964.4639 0.01717156 0.014351807 181.5073566 -2.258894232 -0.070316404 TPAQFDADELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPAQFDADELR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 135.16 0.00029266 169050000 60168 86588 80121 75228 88177 109570 77568 77856 76065 86185 FALSE TRUE 62543.4791 101458.8154 82209.01908 90107.87387 73188.70504 84124.02805 71488.01747 76812.46767 73327.43551 103071.3006 0.606798194 0.984355634 0.797593691 0.874228552 0.710078408 0.816173149 0.6935783 0.745236232 0.711424374 1 16.65328316 3.240432405 24.99657534 0.761322847 0.826491245 0.005044887 0.120929495 145.6759968 1945381.264 0.031281525 0.040303728 1739.53193 -3.240432405 0.065168398 TPARPFGS(ph)VGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;TPARPFGS(1)VGR;TPARPFGS(1)VGR 125.97 0.00019205 2176120000 464364 493571 492974 535920 677740 587010 506283 572606 535730 565289 TRUE FALSE 482697.4493 578337.9798 505821.3074 641923.3764 562537.9969 450685.8237 466599.2155 564931.1532 516449.1819 676046.5564 0.714000308 0.855470639 0.748204843 0.949525399 0.832099493 0.666649093 0.690187992 0.835639421 0.763925468 1 19.36676308 -1.110042958 4.703257493 1.00001059 0.787317722 0.385675323 0.081697065 1.20E-05 2.27E-06 0.079860708 0.018822122 0.077617034 1.110042958 -0.212692868 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 TPASTPVS(0.005)GT(0.995)PQAS(1)PMIER;TPASTPVSGT(1)PQAS(1)PMIER;TPASTPVS(0.011)GT(0.989)PQAS(1)PMIER;TPASTPVS(0.029)GT(0.971)PQAS(1)PMIER;TPASTPVS(0.025)GT(0.975)PQAS(1)PMIER 283.64 4.09E-39 1685330000 730770 836960 833510 857380 895450 1047300 929540 923770 830880 812129 TRUE FALSE 759621.3639 980701.3694 855231.9553 1026967.205 743241.7288 804080.447 856680.2259 911388.3741 800976.7911 971250.1284 0.782106835 1.009731006 0.880547585 1.057366352 0.765242348 0.827881947 0.882038726 0.938366284 0.82468642 1 19.88948336 -1.646417148 2.674530311 1.01221962 0.892045709 0.124482918 0.089654112 20941787.85 19352041.85 1769910.485 0.021853786 0.022572666 1.646417148 -0.120173911 TPASTPVSGT(ph)PQASPMIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVS(0.072)GT(0.815)PQAS(0.113)PMIER 152.89 5.34E-07 121340000 91714 96686 95509 106370 95763 121790 121610 104520 103950 87921 TRUE FALSE 95334.93954 113291.0684 97998.043 127409.6685 79485.23947 93506.11825 112077.8904 103119.0804 100208.8598 105147.4366 0.906678685 1.077449646 0.932006011 1.211723962 0.75594082 0.889285762 1.065911772 0.980709409 0.953031886 1 16.68205415 3.242636418 24.99969204 0.948843918 1.028073545 0.141522346 0.108740415 244.5903607 1500229.216 0.030329505 0.039622344 1748.382369 -3.242636418 0.079229627 TPASTPVSGTPQAS(ph)PMIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER;TPASTPVSGTPQAS(1)PMIER 329.78 3.26E-75 1099290000 244007 305037 270966 318216 285410 359647 357858 312718 296500 229481 TRUE FALSE 253640.5848 357424.7319 278027.5966 381158.175 236896.1101 276124.4348 329808.1549 308526.5267 285829.0229 274443.4083 0.924199952 1.30236224 1.013059845 1.388840699 0.863187466 1.006125221 1.201734656 1.124189969 1.041486202 1 18.06614916 -4.999894592 0.232178124 0.416815032 1.117252449 0.032103725 0.155641562 621.8075291 6.21955417 170.1274551 0.24831502 1.00E-05 4.999894592 0.700437417 TPAVEGLTEAEEEELRAELTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPAVEGLTEAEEEELRAELTK 21 1 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 ;; 183.09 4.05E-17 113490000 81519 109247 100036 110446 108481 139870 117712 102959 92514 125322 FALSE TRUE 84737.43307 128009.3224 102643.0203 132291.8892 90041.43837 107387.3123 108485.4259 101579.003 89184.43921 149876.4465 0.56538192 0.854098996 0.684850907 0.882672977 0.600771105 0.716505594 0.723832386 0.677751611 0.595053067 1 17.19341415 -1.136506345 4.954271859 1.000015493 0.706160635 0.45134928 0.098991587 1.56E-05 2.72E-06 0.088298221 0.020810994 0.073028714 1.136506345 -0.293854857 TPAVEGLTEAEEEELRAELTKVEEEIVTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPAVEGLTEAEEEELRAELTKVEEEIVTLR 30 2 O43399;O43399-7;O43399-2;O43399-3;O43399-5;O43399-4;O43399-6;A0A087WZ51;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 77.522 0.0020268 10851000 5096.5 5472.4 6779.8 4264.2 8995.8 8731.3 4902.6 5423.6 7083.7 7261.7 FALSE TRUE 5297.713755 6412.242131 6956.487158 5107.646033 7466.697129 6703.587899 4518.321401 5350.905513 6828.759021 8684.491081 0.610020058 0.738355543 0.801024158 0.588134179 0.859773711 0.771903366 0.520274747 0.616144972 0.786316545 1 13.08422559 0.943309 5.856027854 0.999966383 0.687367806 0.470606847 0.10062002 0.349307857 33.55519616 0.100375631 0.025256207 8.776250278 -0.943309 -0.312598578 TPDGTENGDFLALDLGGTNFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPDGTENGDFLALDLGGTNFR 21 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 58.487 0.056329 0 9409.3 13080 10004 14748 16230 13507 15245 11442 11069 10782 FALSE TRUE 9780.78643 15326.38825 10264.71246 17665.11038 13471.2304 10370.20395 14050.05706 11288.63871 10670.62885 12894.52647 0.758522343 1.18859644 0.796051913 1.369969687 1.044724708 0.804233019 1.089614039 0.875459734 0.827531657 1 13.65447117 2.868256424 14.89646747 0.922984661 1.046159623 0.08431202 0.181548586 2.534531358 288.3262296 0.052662121 0.055858779 738.3400455 -2.868256424 0.123174962 TPDS(ph)PPTPAPLLLDLGIPVGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPDSPPTPAPLLLDLGIPVGQR 22 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 T(0.031)PDS(0.969)PPTPAPLLLDLGIPVGQR;T(0.05)PDS(0.95)PPTPAPLLLDLGIPVGQR;T(0.04)PDS(0.954)PPT(0.005)PAPLLLDLGIPVGQR;T(0.001)PDS(0.999)PPTPAPLLLDLGIPVGQR;T(0.185)PDS(0.815)PPTPAPLLLDLGIPVGQR 203.56 1.34E-22 348642000 51380.9 50053.9 58181.8 51916.4 62418.3 64754.8 55092.1 51139.7 57052 57029.8 TRUE FALSE 53409.45761 58650.26796 59698.0655 62185.30897 51808.45966 49716.47907 50773.83725 50454.25597 54998.70966 68203.69741 0.783087422 0.859927983 0.875290751 0.911758619 0.759613652 0.728941113 0.744444058 0.739758369 0.806388975 1 16.05756233 3.221654464 24.95686307 0.774201878 0.858958082 0.083407346 0.08072546 356.9235851 526889.6703 0.021932612 0.026277975 1665.921234 -3.221654464 0.084756204 TPDSEDKLFS(ph)PVIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPDSEDKLFSPVIAR 15 1 Q5VZ89-7;Q5VZ89-3;Q5VZ89;Q5VZ89-5;X6RAE7;X6R5W5 Q5VZ89-7 DENND4C DENN domain-containing protein 4C 1 TPDS(0.001)EDKLFS(0.999)PVIAR;TPDSEDKLFS(1)PVIAR 114.88 0.00034582 253610000 226120 154722 188890 171850 238860 286510 271370 233150 241360 171650 TRUE FALSE 235047.3922 181294.2999 193812.6286 205841.4171 198258.6625 219972.3946 250099.3103 230025.0056 232673.5007 205281.5311 1.145000191 0.88314959 0.944130861 1.002727406 0.965789087 1.071564468 1.218323485 1.120534343 1.133436114 1 17.64724431 2.556775187 4.235598661 1.13219515 0.981590498 0.365098753 0.079923149 0.203203054 6.735677078 0.025566057 0.023536836 360.3920371 -2.556775187 -0.150604653 TPDTIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPDTIRR 7 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 108.7 0.011536 889110000 1005580 1212330 1194590 1014790 1610980 1479950 957310 1146010 1122090 1580970 FALSE TRUE 1045281.075 1420538.247 1225721.997 1215512.433 1337146.195 1136254.041 882273.5407 1130649.61 1081706.2 1890730.802 0.552845002 0.751317028 0.648279488 0.642879691 0.707211303 0.600960243 0.466630966 0.597996081 0.572110106 1 20.85051254 -1.845708849 5.046583256 1.06397253 0.615729837 0.699375475 0.075610597 0.042935676 0.001312689 0.057757928 0.018115827 0.014265636 1.845708849 -0.448242693 TPEEIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPEEIRK 7 1 E5RJR5;P63208;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 ;;; 94.662 0.022505 1501920000 1666390 1390360 1701700 1264620 2034350 1905900 1813380 1584450 1785620 1432240 FALSE TRUE 1732180.364 1629143.515 1746047.7 1514758.061 1688551.914 1463283.609 1671242.537 1563213.039 1721355.885 1712860.006 1.01127959 0.951124732 1.019375602 0.884344346 0.985808477 0.854292589 0.975702936 0.912633276 1.004960054 1 20.70797581 3.758634203 24.96216811 0.939940906 0.989646446 0.156603807 0.050224895 1344.775844 1672268.314 0.011742717 0.021136331 5736.330999 -3.758634203 0.04970554 TPEELDDS(ph)DFETEDFDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 TPEELDDSDFETEDFDVR 18 0 P35221-2;P35221;G3XAM7;P35221-3 P35221-2 CTNNA1 Catenin alpha-1 1 TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR 419.08 2.35E-148 29265620000 5717673 6945488 5578471 5982651 5836618 7074914 5672898 5790764 5114415 6009118 TRUE FALSE 5943411.145 8138321.536 5723850.537 7166001.511 4844511.757 5431872.445 5228241.431 5713148.28 4930348.203 7186489.621 0.827025635 1.132447407 0.796473778 0.99714908 0.67411379 0.755845027 0.727509773 0.794984559 0.686057931 1 22.7768558 3.244804667 24.99994046 0.761368376 0.942014934 0.306417009 0.120932279 157.7254839 631497.2668 0.030804589 0.040694094 1757.133128 -3.244804667 0.180646558 TPEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPEELR 6 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 99.919 0.088987 1524080000 2231600 2386300 2319000 2248200 2575800 2827800 2156840 2373600 2181000 2258100 FALSE TRUE 2319705.291 2796128.462 2379435.045 2692887.25 2137966.436 2171086.306 1987781.245 2341785.774 2102506.236 2700531.461 0.858981028 1.035399329 0.881098806 0.997169368 0.791683588 0.803947792 0.73607039 0.867157376 0.778552765 1 21.36481193 3.231622589 24.99912476 0.818553742 0.945317413 0.310836807 0.081856812 162.3847705 585104.7206 0.021529726 0.026266288 1704.600412 -3.231622589 0.126763671 TPEEREWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPEEREWR 8 1 Q6P4R8-3;Q6P4R8;E9PQ59;Q6P4R8-2;E9PJG2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 0 ;;; 69.954 0.047957 2800390000 1869530 2267610 2142500 2257040 2565110 2737030 1973290 1958360 1938840 1980040 FALSE TRUE 1943340.488 2657054.378 2198335.31 2703475.775 2129093.518 2101396.263 1818618.374 1932111.387 1869061.527 2367990.928 0.82067058 1.122071181 0.928354617 1.141674887 0.899113883 0.887417362 0.768000566 0.815928543 0.789302655 1 21.17523212 2.893680868 2.880387137 0.830285524 1.006708658 0.291492423 0.10605369 0.271737339 4.360179869 0.03170381 0.034573726 782.8541681 -2.893680868 0.176423134 TPEEVIEYSAVFWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPEEVIEYSAVFWER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 112.51 0.003676 0 3225.2 5758 5091 4799.6 4794.9 8862.7 3781.5 6868.5 5223.8 6646.6 FALSE TRUE 3352.533386 6746.891709 5223.675642 5748.946555 3979.864611 6804.472241 3485.096149 6776.438992 5035.796458 7948.874013 0.421762048 0.84878584 0.657159194 0.723240367 0.500682814 0.8560297 0.438438972 0.852503006 0.633523245 1 12.9565348 -4.999999999 0.258113596 3.119231923 0.643138567 0.302431445 0.156616422 227.8224234 2.242731372 255.4255568 0.189595958 1.00E-05 4.999999999 -2.476093356 TPEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPEFLR 6 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 107.55 0.072514 396550000 220900 264700 245660 263670 267240 322080 234560 274020 258350 271570 FALSE TRUE 229621.3026 310160.1659 252062.1014 315823.139 221814.6403 247281.8012 216174.5743 270347.2101 249052.034 324778.942 0.707007976 0.954988535 0.776103586 0.972424927 0.682971128 0.761384958 0.665605267 0.832403753 0.766835536 1 18.30909857 5.03563464 14.86279488 0.810346603 0.35716884 0.077791534 0.112375801 2310100.441 29030132.52 0.025459248 26824679.32 108551.2027 -5.03563464 -0.453177763 TPEKLDNT(ph)PASPPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_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 2 TPEKLDNT(0.95)PAS(0.05)PPRS(1)PAEPNDIPIAK 197.63 7.10E-25 199500000 264710 156190 219220 156760 317090 278200 268340 230680 294220 154420 TRUE FALSE 275160.9552 183014.4175 224933.0533 187766.6601 263191.1551 213592.2662 247306.8096 227588.1119 283631.0797 184675.6425 1.489968853 0.991004634 1.217989824 1.016737549 1.425153591 1.156580604 1.339141461 1.232366699 1.535833724 1 17.49463407 3.234628086 24.99846553 1.28697442 1.168292659 0.066369291 0.186126344 247.938147 1576106.368 0.049048571 0.060704825 1716.437862 -3.234628086 -0.118681761 TPEKLDNTPAS(ph)PPRS(ph)PAEPNDIPIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 T(0.001)PEKLDNT(0.007)PAS(0.993)PPRS(1)PAEPNDIPIAK;T(0.004)PEKLDNT(0.19)PAS(0.806)PPRS(1)PAEPNDIPIAK;TPEKLDNT(0.02)PAS(0.98)PPRS(1)PAEPNDIPIAK;TPEKLDNTPAS(1)PPRS(1)PAEPNDIPIAK 150.45 7.30E-08 3852360000 3680340 2012090 2904940 1835420 4130230 3505590 3295860 2953500 3355900 1958620 TRUE FALSE 3825642.665 2357650.806 2980645.123 2198460.598 3428174.98 2691469.85 3037521.881 2913913.163 3235121.815 2342374.089 1.633233002 1.006521894 1.272488941 0.938560842 1.463547175 1.149035017 1.296770612 1.243999913 1.38112944 1 21.15954007 -2.080051737 2.933637405 0.568716759 1.251143613 0.13971599 0.194567805 608491.2838 24926582.36 208865.5508 0.042204151 0.008316647 2.080051737 0.682426854 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPELRDDDFLGGAECSLGQIVSSQVLTLPLMLKPGKPAGR 40 3 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58;Q5JX56;Q5JX54;Q5JX55;E7EV27;Q5JX57 Q99829 CPNE1 Copine-1 0 193.58 3.27E-25 238480000 179000 122070 182450 140550 174840 201800 208800 180940 197880 107840 FALSE TRUE 186067.0582 143034.5729 187204.7969 168350.3705 145120.7593 154935.0083 192433.7104 178514.7953 190758.3375 128969.1833 1.442724948 1.109060082 1.451546735 1.305353467 1.125235933 1.201333562 1.492090634 1.384166285 1.479100143 1 16.97666685 2.255372172 24.99188534 1.376609491 1.268043666 0.016497513 0.167759086 591.5789234 879433.5367 0.054914476 0.045827615 180.0413133 -2.255372172 -0.108565825 TPELTWER ddPTM_MDA-MB-175_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 ;; 141.39 0.0014757 490310000 276278 290794 289071 280440 399796 406843 343551 311386 307879 364043 FALSE TRUE 287185.6688 340735.6074 296604.4277 335910.195 331838.8187 312359.879 316622.5749 307212.38 296798.4949 435370.2558 0.659635483 0.782634098 0.681269388 0.77155063 0.762199104 0.717458014 0.727248981 0.705634746 0.68171514 1 18.73188332 -1.761338866 2.770997993 1.060349374 0.723280786 0.820887937 0.039079213 10367518.97 7867500.027 4252128.939 0.0086926 0.017324517 1.761338866 -0.337068588 TPEPVVPTAPELRPS(ph)TSTDRPVTPKPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPT(0.02)APELRPS(0.194)T(0.194)S(0.194)T(0.194)DRPVT(0.194)PKPT(0.005)S(0.005)R 48.693 0.06921 220390000 106820 78003 94482 81111 138660 136870 116360 107770 106860 78863 TRUE FALSE 111037.3361 91399.40847 96944.27854 97154.51371 115090.6227 105084.0168 107239.3991 106325.5194 103014.1295 94314.69493 1.177306847 0.969089796 1.027880953 1.030110035 1.220283041 1.114184983 1.137038075 1.127348389 1.092238379 1 16.52519495 3.339083098 19.26392823 1.123478908 1.04356457 0.156249438 0.070529767 3.681059926 694.6247124 0.018273404 0.024742272 2183.147595 -3.339083098 -0.079914338 TPEPVVPTAPELRPSTSTDRPVT(ph)PKPTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPEPVVPTAPELRPSTSTDRPVTPKPTSR 29 3 Q14676;Q14676-2 Q14676 MDC1 Mediator of DNA damage checkpoint protein 1 1 TPEPVVPTAPELRPS(0.03)T(0.03)S(0.03)T(0.03)DRPVT(0.781)PKPT(0.05)S(0.05)R;TPEPVVPTAPELRPS(0.144)T(0.144)S(0.144)T(0.144)DRPVT(0.365)PKPT(0.029)S(0.029)R 114.52 0.00022666 613630000 66704 65400 63509 49745 90206 103174 73844 74842 70231 60861 TRUE FALSE 69337.52543 76631.94126 65164.09671 59584.41253 74872.81634 79213.40212 68055.91432 73838.86541 67703.40003 72785.5477 0.952627652 1.052845567 0.895288952 0.81862972 1.028676966 1.088312235 0.935019609 1.014471523 0.930176418 1 16.1513644 TPES(ph)FLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPESFLGPNAALVDLDSLVSRPGPTPPGAK 30 1 Q9Y6I3;Q9Y6I3-3;Q9Y6I3-1 Q9Y6I3 EPN1 Epsin-1 1 T(0.487)PES(0.513)FLGPNAALVDLDSLVSRPGPTPPGAK;T(0.156)PES(0.844)FLGPNAALVDLDSLVSRPGPTPPGAK 196.38 1.75E-25 1143064000 55402 48781 61594 49095 59814 75959 75945 61435 59627 44783 TRUE FALSE 57589.31374 57158.75729 63199.19024 58805.84447 49646.83765 58318.67342 69992.23245 60611.56431 57481.03592 53557.37143 1.075282677 1.067243514 1.180027857 1.097997211 0.92698421 1.088900965 1.306864594 1.131712829 1.073260961 1 15.70879754 2.456304226 24.98122357 1.150874679 1.070187953 0.059839722 0.093202567 477.4808174 572992.0261 0.032585786 0.027265735 285.9593003 -2.456304226 -0.080686726 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TPESQPDTPPGTPLVSQDEKR 21 1 A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60;A0A0D9SEV0;M0R000;M0QYI1 A0A0D9SFD6 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 1 TPESQPDT(0.999)PPGT(0.001)PLVSQDEKR;TPESQPDT(0.996)PPGT(0.004)PLVSQDEKR;TPESQPDT(0.997)PPGT(0.002)PLVS(0.001)QDEKR;TPESQPDT(0.998)PPGT(0.002)PLVSQDEKR;TPESQPDT(0.961)PPGT(0.039)PLVSQDEKR;TPESQPDT(0.977)PPGT(0.018)PLVS(0.005)QDEKR;TPESQPDT(1)PPGTPLVSQDEKR 186.28 1.93E-17 8414040000 3137440 2449490 3012580 2293560 3507480 3656040 3345420 2996640 3254200 2119650 TRUE FALSE 3261308.554 2870170.853 3091090.31 2747219.322 2911279.802 2806980.118 3083197.239 2956474.942 3137081.978 2534954.834 1.286535172 1.132237472 1.219386739 1.083735018 1.148454309 1.107309716 1.216273046 1.166283084 1.237529732 1 21.27352861 -1.445811856 3.080309215 0.996608084 1.172902039 0.441210507 0.059732169 7362524.587 10321231.63 221330.4018 0.013480076 0.03582516 1.445811856 0.176293956 TPEYLHIDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPEYLHIDQR 10 0 O00178;B0QY59 O00178 GTPBP1 GTP-binding protein 1 0 112.83 0.0025012 0 139510 196280 169110 157870 156370 209370 158490 144080 134140 207880 FALSE TRUE 145017.9625 229989.5632 173517.1455 189096.2148 129790.2833 160746.9905 146067.1397 142148.8433 129312.3276 248610.1059 0.583314833 0.925101425 0.697948882 0.760613548 0.522063585 0.646582688 0.587535004 0.571774195 0.520141074 1 17.92352542 3.262804852 24.80939287 0.613709556 0.751713393 0.076682194 0.15208222 367.2772991 375836.0645 0.038419258 0.051993705 1831.491267 -3.262804852 0.138003837 TPGHPPPPEIPSELGACDFEKPES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPGHPPPPEIPSELGACDFEKPESPR 26 1 A0A669KBG8;A0A669KB10;Q92538;Q92538-3;Q92538-2 A0A669KBG8;Q92538-3 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR;TPGHPPPPEIPSELGACDFEKPES(1)PR 201.8 2.91E-25 5039400000 3401360 1897630 2742900 2346950 3751180 3888340 3335490 2645690 2875830 1861860 TRUE FALSE 3535648.319 2223533.191 2814382.227 2811169.705 3113555.763 2985331.963 3074045.578 2610228.853 2772329.44 2226655.82 1.587873747 0.998597615 1.263950271 1.262507515 1.398310298 1.340724479 1.380566117 1.172264178 1.245064197 1 21.08644714 0.75783103 1.065837687 1.002727548 1.300668839 0.290453871 0.143769601 1.105350247 2.281869484 0.129810999 0.041284742 5.725732178 -0.75783103 0.297941291 TPGRQS(ph)PGPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPGRQSPGPGHR 12 1 O15169-2;O15169 O15169-2 AXIN1 Axin-1 1 T(0.014)PGRQS(0.986)PGPGHR;T(0.023)PGRQS(0.977)PGPGHR;T(0.161)PGRQS(0.839)PGPGHR 61.127 0.052725 139440000 62671 71934 71292 71446 79134 99351 80200 70701 74255 63099 TRUE FALSE 65145.29947 84288.10493 73149.92809 85577.80555 65682.83095 76278.23593 73913.71444 69753.36874 71582.57705 75462.04095 0.863285682 1.116960314 0.969360584 1.134051034 0.870408885 1.010815967 0.979482048 0.924350413 0.948590525 1 16.2034635 3.22487966 24.99928697 0.954175419 1.024092446 0.13828408 0.079659138 413.5736943 755724.074 0.021280512 0.025564968 1678.338898 -3.22487966 0.069917027 TPHDILEDINAS(ph)PEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 204.47 1.62E-11 296564000 115717 164133 142798 135802 158482 186610 157081 161469 155768 158464 TRUE FALSE 120285.5965 192321.566 146519.4332 162663.2303 131543.2862 143272.6556 144768.5808 159304.7722 150161.9401 189511.9868 0.634712339 1.014825337 0.773140716 0.858326869 0.694115916 0.756008409 0.763901974 0.840605256 0.792361173 1 17.53192958 -1.396417677 2.923975468 1.003470889 0.797993813 0.29228492 0.096694163 16025511.9 18948902.18 465899.9754 0.021373981 0.040140458 1.396417677 -0.205477077 TPHS(ph)PPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPHSPPLAK 9 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 TPHS(1)PPLAK;T(0.01)PHS(0.99)PPLAK;T(0.149)PHS(0.851)PPLAK 112.15 0.0012945 1237150000 1259430 1049520 1239970 1069950 1561930 1620800 1395430 1322620 1335850 993420 TRUE FALSE 1309153.269 1229766.896 1272284.637 1281582.917 1296433.697 1244393.763 1286052.55 1304892.442 1287773.019 1188061.629 1.101923703 1.035103623 1.07089111 1.078717539 1.091217547 1.047415162 1.082479662 1.098337334 1.083927793 1 20.18017824 TPHYGSQT(ph)PLHDGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 1 TPHYGS(0.004)QT(0.996)PLHDGSR 100.39 0.0080048 144470000 47333 60882 50283 63614 61260 81588 51605 56031 50599 57151 TRUE FALSE 49201.74339 71338.0099 51593.41629 76196.65933 50847.04708 62640.42348 47560.06526 55279.99609 48777.95187 68348.64423 0.719864219 1.043737015 0.75485647 1.114823274 0.74393644 0.916483775 0.695845043 0.808794333 0.713663781 1 16.0606251 TPHYGSQTPLHDGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPHYGSQTPLHDGSR 15 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 147.64 2.12E-06 267540000 67225 119228 108431 101646 97722 143925 110824 123779 129971 134990 FALSE TRUE 69879.09491 139704.4815 111256.8009 121751.2754 81111.24935 110500.6 102137.3253 122119.945 125293.3691 161438.706 0.432852174 0.865371664 0.689158156 0.754164094 0.502427524 0.684474019 0.632669376 0.756447744 0.77610489 1 17.30062699 0.867304895 1.10347689 0.998003839 0.661082402 0.453147199 0.115436395 0.587926342 1.411908391 0.102760584 0.032595795 7.367241305 -0.867304895 -0.336921437 TPIS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPISPLK 7 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 TPIS(1)PLK;TPIS(1)PLK;TPIS(1)PLK;T(0.001)PIS(0.999)PLK;T(0.001)PIS(0.999)PLK 110.76 0.0070616 5256920000 7731000 5030140 6503010 5445900 8167800 9959500 9420000 7017980 7208900 4036810 TRUE FALSE 8036225.85 5894027.416 6672483.783 6523082.766 6779440.273 7646557.063 8681635.785 6923915.457 6949453.097 4827745.63 1.664591813 1.220865362 1.382111713 1.351165381 1.404266254 1.583877372 1.798279456 1.434192269 1.439482034 1 22.20291823 2.89525569 7.82714638 1.502588038 1.388463606 0 0.214726499 0.886656873 59.23362955 0.062520205 0.066432952 785.6980767 -2.89525569 -0.114124432 TPIS(ph)PLKTGVSKPIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPISPLKTGVSKPIVK 16 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 T(0.018)PIS(0.982)PLKTGVSKPIVK;T(0.002)PIS(0.998)PLKTGVSKPIVK 131.71 2.25E-05 2070540000 2026370 1099580 1583480 808390 2959800 1952050 1415150 1559620 2009340 1395450 TRUE FALSE 2106372.652 1288424.311 1624746.79 968287.1292 2456694.253 1498715.971 1304226.845 1538715.845 1937024.246 1668861.71 1.262161292 0.772037793 0.973565862 0.580208128 1.472077787 0.898046832 0.781506842 0.922015189 1.160685894 1 20.67043298 4.761356491 22.93617463 0.94357736 1.262162376 0.142511481 0.228210321 3661.123277 3683472.856 0.052069844 2.381887007 57724.00963 -4.761356491 0.318585017 TPITSVPLGPLAS(ph)SPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPITSVPLGPLASSPTK 17 0 Q15911 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TPITSVPLGPLAS(0.536)S(0.461)PT(0.003)K 93.424 0.0032154 76865000 260020 175400 215800 153220 270370 312150 268370 234680 234930 153110 TRUE FALSE 270285.7904 205523.5856 221423.9253 183526.4587 224412.604 239657.8932 247334.4581 231534.4985 226474.9152 183108.973 1.476092547 1.122411328 1.209246721 1.002279985 1.22556858 1.308826592 1.35075007 1.264462875 1.236831333 1 17.48234296 3.001930434 24.99934 1.260214515 1.186849919 0 0.14185117 206.2774953 2671247.221 0.039617565 0.047062162 1004.454883 -3.001930434 -0.073364597 TPITSVPLGPLASS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPITSVPLGPLASSPTK 17 0 Q15911 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 TPITSVPLGPLAS(0.392)S(0.606)PT(0.002)K 115.58 0.00032278 99157000 579340 362010 460410 369460 609710 605470 568580 521880 546400 361860 TRUE FALSE 602212.7905 424182.4015 472408.6628 442538.0853 506071.712 464858.7685 524013.2139 514885.0522 526735.1707 432759.5388 1.391564452 0.980180362 1.091619295 1.022595797 1.169406256 1.074173362 1.210864619 1.1897717 1.217154386 1 18.72320609 2.23842792 24.99999998 1.173802403 1.11147365 0.003349 0.119350349 11.04466724 2080162.823 0.040487091 0.031821139 173.1521627 -2.23842792 -0.062328753 TPKDS(ph)PGIPPSANAHQLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPKDSPGIPPSANAHQLFR 19 1 B4DG22;B1AXG1;B7ZB17;P51812 B4DG22 RPS6KA3 Ribosomal protein S6 kinase alpha-3 1 TPKDS(1)PGIPPSANAHQLFR 109.08 0.00015847 356500000 93056 77438 106820 78909 102940 118990 114860 100520 103860 61244 TRUE FALSE 96729.92273 90737.37412 109603.817 94516.96468 85442.29557 91356.37581 105856.9731 99172.69382 100122.0989 73243.58921 1.320660604 1.238843906 1.496428809 1.290446928 1.166549817 1.24729518 1.445272879 1.354011933 1.366974229 1 16.16041487 -1.583975515 2.872063725 0.97915219 1.326998796 0.52442631 0.092880069 11137199.25 12311786.34 1782831.88 0.023803841 0.026063005 1.583975515 0.347846606 TPLALAGS(ph)PTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPLALAGSPTPK 12 0 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785 M0QXA7 WIZ Protein Wiz 1 TPLALAGS(0.997)PT(0.003)PK;TPLALAGS(1)PTPK 142.1 6.41E-05 291020000 655070 364870 464240 397760 598790 687150 694070 525850 550690 334240 TRUE FALSE 680932.6694 427533.5842 476338.4758 476435.7408 497007.8897 527569.8264 639666.9798 518801.8409 530870.7745 399727.9286 1.703490351 1.069561453 1.191656729 1.191900057 1.243365435 1.319822281 1.600255909 1.297887397 1.328080268 1 18.60865885 2.583719752 5.929463137 1.351415137 1.259500976 0 0.20777116 0.880450182 41.56673744 0.064999077 0.060952864 383.4597211 -2.583719752 -0.091914161 TPLAVELEVLDGHDPDPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPLAVELEVLDGHDPDPGR 19 0 Q86TX2;G3V4F2;A0A087X0W7;A0A087WT95;P49753 Q86TX2 ACOT1;ACOT2 "Acyl-coenzyme A thioesterase 1;Acyl-coenzyme A thioesterase 2, mitochondrial" 0 ;;; 168.89 1.52E-11 662160000 581570 698040 679050 692470 726130 872280 726150 714120 647400 719950 FALSE TRUE 604530.8327 817922.94 696746.6008 829438.4992 602702.682 669706.1895 669232.4656 704548.3895 624100.2005 861010.4182 0.702117907 0.949957077 0.80921971 0.963331548 0.699994645 0.77781427 0.777264074 0.818280911 0.724846282 1 19.71567117 5.018884339 14.38710122 0.824339523 0.473644941 0.134368982 0.097960055 2230178.105 41708593.82 0.021999389 16465334.46 104444.2027 -5.018884339 -0.350694582 TPLCATAPCLPS(ph)PTATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPLCATAPCLPSPTATR 17 0 Q6PI47-3;Q6PI47 Q6PI47-3 KCTD18 BTB/POZ domain-containing protein KCTD18 1 TPLCATAPCLPS(0.959)PT(0.02)AT(0.02)R 75.574 0.022802 47187000 49352 47580 43658 42171 51311 59339 56990 44937 46963 47881 TRUE FALSE 51300.45507 55751.49488 44795.76335 50512.29793 42589.17455 45558.41654 52522.97488 44334.69302 45272.8108 57262.36521 0.895884319 0.973614951 0.782289785 0.882120355 0.743755072 0.795608361 0.917233766 0.774237893 0.790620692 1 15.80529964 4.240227291 24.99914387 0.826350897 0.934749645 0.204599952 0.076319036 54.17704979 812556.8977 0.017309688 0.042648928 17387.10555 -4.240227291 0.108398749 TPLDLFAHFGPEPGDHSDPLPPS(ph)APSPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.845)APS(0.152)PT(0.003)R 240.26 3.56E-45 199220000 84495 98403 97904 112520 102870 121030 113750 106700 99366 78580 TRUE FALSE 87830.92784 115302.9498 100455.4587 134776.1202 85384.19414 92922.61673 104833.9778 105269.861 95789.83707 93976.2465 0.934607745 1.226937169 1.068945211 1.434150918 0.908572084 0.98878834 1.115536975 1.120175203 1.019298393 1 16.52000853 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 Q8N1G0;F8WCX2;Q8N1G0-2 Q8N1G0 ZNF687 Zinc finger protein 687 1 TPLDLFAHFGPEPGDHSDPLPPS(0.073)APS(0.89)PT(0.037)R;TPLDLFAHFGPEPGDHSDPLPPS(0.092)APS(0.772)PT(0.135)R;TPLDLFAHFGPEPGDHS(0.011)DPLPPS(0.123)APS(0.836)PT(0.03)R 149.72 6.76E-08 359966000 100769 111492 105806 116025 111049 121087 119316 112345 101708 92674 TRUE FALSE 104747.4379 130639.8837 108563.3913 138974.3987 92172.93065 92966.37934 109963.7001 110839.199 98047.54895 110831.6959 0.945103628 1.178723131 0.979533791 1.253922874 0.831647751 0.838806792 0.992168343 1.000067698 0.884652609 1 16.758011 3.222695144 24.99996518 0.930420841 1.087864858 0.389705403 0.100844272 252.6332251 398085.0712 0.02844102 0.034099669 1669.91799 -3.222695144 0.157444017 TPLGAS(ph)LDEQSSSTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK;TPLGAS(1)LDEQSSSTLK 355.72 2.14E-87 965008000 1506551 1304151 1752211 1136672 2326600 1918940 1774383 1718182 1896090 1111392 TRUE FALSE 1566030.797 1528128.789 1797875.058 1361502.329 1931125.363 1473295.267 1635302.224 1695152.581 1827850.091 1329147.984 1.17822155 1.149705532 1.352652286 1.024342169 1.452904708 1.108450891 1.230338716 1.275367831 1.375204352 1 20.34207031 TPLHNDNSWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPLHNDNSWIR 11 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ; 180.47 6.65E-06 489710000 382840 463970 417710 430530 486600 560440 458360 460380 426410 493950 FALSE TRUE 397954.8188 543653.2383 428595.8658 515687.549 403887.9058 430286.3036 422432.5455 454209.3591 411063.5874 590730.0453 0.673666122 0.920307411 0.725535918 0.872966515 0.683709774 0.728397526 0.715102523 0.768894968 0.695856916 1 19.17213947 -1.112393908 4.33338703 1.000032724 0.757753371 0.47584735 0.077411327 2.40E-05 4.91E-06 0.069639286 0.016411801 0.077198008 1.112393908 -0.242279353 TPLNPPEPPSNPPEVLDVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPLNPPEPPSNPPEVLDVTK 20 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 A0A0A0MTS7 TTN Titin 0 57.745 0.080239 164540000 489950 222180 313100 287440 586810 470080 453330 408030 426990 349490 FALSE TRUE 509293.6043 260337.6867 321259.6432 344294.7741 487064.2458 360911.0441 417796.81 402561.0253 411622.7133 417965.8741 1.218505232 0.622868284 0.768626491 0.823738959 1.165320606 0.863494047 0.999595507 0.963143286 0.984823735 1 18.67302563 TPLRPLDPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 115.57 0.0010988 972160000 1267580 1486650 1314250 1304070 1789490 1879760 1456350 1354740 1276780 1724880 FALSE TRUE 1317625.037 1741970.573 1348500.435 1562011.154 1485313.129 1443214.228 1342197.482 1336581.926 1230828.937 2062837.211 0.638744071 0.844453728 0.653711513 0.757214939 0.720034097 0.699625846 0.650656035 0.647933787 0.596667992 1 20.97619854 -1.134318706 5.017970404 1.000013968 0.691610685 0.656021911 0.067355284 1.04E-05 1.80E-06 0.064613416 0.015228839 0.073397504 1.134318706 -0.308403283 TPLS(ph)PSPMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TPLSPSPMK 9 0 Q69YQ0-2;Q69YQ0;A0A494C1J1;F8WAN1 Q69YQ0-2 SPECC1L;SPECC1L-ADORA2A Cytospin-A 1 TPLS(0.973)PS(0.027)PMK;T(0.029)PLS(0.9)PS(0.071)PMK;TPLS(0.995)PS(0.005)PMK;TPLS(1)PSPMK;TPLS(0.907)PS(0.093)PMK;TPLS(0.918)PS(0.082)PMK 159.83 6.90E-05 3224080000 7171350 5902170 7278050 5929390 9980200 9905100 9487800 8185740 8715830 6838840 TRUE FALSE 7454480.435 6915821.785 7467721.962 7102205.645 8283769.169 7604790.638 8744121.444 8076023.544 8402148.981 8178779.76 0.91144164 0.845581124 0.91306065 0.868369837 1.012836806 0.929819712 1.069122987 0.987436241 1.027310825 1 22.96345418 3.236714354 24.99998458 1.003712489 0.88385724 0.711356771 0.037384722 24.90545068 337242.7671 0.010074976 0.012640409 1724.703138 -3.236714354 -0.119855249 TPLSFTNPLHS(ph)DDS(ph)DSDERNSDGAVTQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPLSFTNPLHSDDSDSDERNSDGAVTQNK 29 1 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 T(0.005)PLS(0.026)FT(0.131)NPLHS(0.839)DDS(0.611)DS(0.309)DERNS(0.08)DGAVTQNK 122.96 1.48E-05 116810000 110650 101130 114570 82319 137670 141850 125600 116640 117590 94221 TRUE FALSE 115018.5474 118498.2908 117555.7883 98601.4525 114268.9026 108907.4873 115755.1438 115076.6316 113357.9589 112681.801 1.020737568 1.051618716 1.043254432 0.875043278 1.014084809 0.966504673 1.027274527 1.021253038 1.006000595 1 16.781895 0.100224928 7.867130998 1 1.003385144 0.00021378 0.048021074 3220366.715 2.14E-07 0.046635179 0.011310692 1.259577598 -0.100224928 0.003385144 TPLYLQPDAYGS(ph)LDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPLYLQPDAYGSLDR 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR 255.2 1.07E-24 1404330000 935718 1196838 1244909 1128968 1434831 1471893 995387 1133917 1119413 1243569 TRUE FALSE 972660.8692 1402385.616 1277352.351 1352274.501 1190938.939 1130068.158 917365.966 1118718.697 1079125.545 1487222.536 0.654011653 0.942956136 0.858884478 0.909261706 0.80078059 0.759851421 0.616831674 0.752220108 0.725597897 1 20.50418911 2.892829259 3.422912467 0.74290304 0.850136124 0.046029984 0.115605426 0.453896387 9.904340854 0.034495002 0.037416457 781.3205716 -2.892829259 0.107233084 TPMAGVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPMAGVSPK 9 0 A0A087WWD1;B7Z6K7;Q9H707 A0A087WWD1 ZNF814;ZNF552 Putative uncharacterized zinc finger protein 814;Zinc finger protein 552 1 TPMAGVS(1)PK;TPMAGVS(1)PK 124.12 0.00056484 141627000 323800 187308 231410 177319 310780 384660 293080 232750 238510 171714 TRUE FALSE 336583.874 219476.6919 237440.7347 212392.169 257953.7266 295328.5446 270107.6238 229630.367 229926.0717 205358.0706 1.639009721 1.068751237 1.156227919 1.034252846 1.25611682 1.438115111 1.315300747 1.118194996 1.119634943 1 17.64778212 1.593847948 4.368876249 1.076401361 1.256460483 0.214622025 0.168966838 0.299733453 12.81225872 0.099939592 0.044615524 39.25074893 -1.593847948 0.180059122 TPNNVVST(ph)PAPS(ph)PDASQLASSLSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPNNVVSTPAPSPDASQLASSLSSQK 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 2 TPNNVVS(0.009)T(0.991)PAPS(0.998)PDAS(0.002)QLASSLSSQK 159.36 3.45E-11 202480000 151120 128610 164890 124080 180620 185990 140540 164600 167520 126330 TRUE FALSE 157086.3343 150697.7671 169187.1689 148622.6537 149918.2769 142796.6412 129524.1076 162393.8062 161490.9879 151081.9448 1.039742601 0.997457157 1.119837113 0.983722138 0.99229777 0.9451602 0.857310301 1.074872358 1.068896672 1 17.20497173 TPNNVVSTPAPS(ph)PDASQLASSLSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPNNVVSTPAPSPDASQLASSLSSQK 26 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 TPNNVVSTPAPS(1)PDASQLASSLSSQK;TPNNVVSTPAPS(1)PDASQLASSLSSQK 178.46 1.57E-17 239550000 365020 333550 386520 325280 397020 462870 449980 407990 429520 273910 TRUE FALSE 379431.2715 390834.6178 396593.0287 389619.4131 329534.6822 355375.4574 414709.3918 402521.5614 414061.6591 327577.4202 1.15829495 1.193106099 1.210684877 1.189396427 1.00597496 1.084859442 1.265988943 1.228782989 1.2640116 1 18.32147639 2.236499817 24.9997496 1.212950174 1.142096032 0.042358253 0.090901053 122.0118611 1480104.636 0.033171949 0.025712648 172.3851367 -2.236499817 -0.070854142 TPPGPCCS(ph)PGVGWAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPGPCCSPGVGWAQR 16 0 H3BSW6;Q2VPK5-3;Q2VPK5;Q2VPK5-5 H3BSW6 CTU2 Cytoplasmic tRNA 2-thiolation protein 2 1 TPPGPCCS(1)PGVGWAQR 120.92 0.00098361 0 29576 34773 29430 29344 33953 43453 28923 26968 22084 29173 TRUE FALSE 30743.68332 40744.99225 30196.96998 35148.15562 28181.68119 33361.69929 26655.93968 26606.53807 21289.20115 34888.8908 0.881188327 1.167850032 0.8655182 1.007431157 0.807755149 0.956226997 0.764023707 0.762607737 0.6102 1 15.09048011 2.850342379 0.924992485 0.765279841 0.998335872 0.264727003 0.128538844 0.618689551 1.147487801 0.066788926 0.070307664 708.5041191 -2.850342379 0.23305603 TPPKS(ph)PSSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPPKSPSSAK 10 1 A0A0G2JQJ7;A0A0G2JPD5;P10636;A0A0G2JS76;A0A0G2JMX7;P10636-9;P10636-6;P10636-2;I3L170;P10636-3;P10636-7;P10636-4;P10636-8;P10636-5 A0A0G2JQJ7;P10636-7;P10636-8 MAPT Microtubule-associated protein tau;Microtubule-associated protein 1 T(0.013)PPKS(0.944)PS(0.034)S(0.009)AK;TPPKS(0.998)PS(0.001)SAK 86.288 0.0082728 493770000 1243620 606060 934430 576020 1303650 1147930 1167160 871100 1037170 526430 TRUE FALSE 1292719.078 710146.0905 958782.0134 689955.0368 1082056.039 881340.6545 1075674.949 859424.3293 999842.4543 629573.8794 2.053323875 1.127978961 1.522906278 1.095907977 1.718711773 1.399900287 1.708576205 1.365088924 1.588125694 1 19.26401616 -1.481520809 6.149931427 0.99968365 1.488404217 0.236879816 0.271806095 0.001052951 8.88E-05 0.235046022 0.055366136 0.03299736 1.481520809 0.488720567 TPPSTTVGSHS(ph)PPETPVLTR ddPTM_MDA-MB-175_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 219.64 5.85E-25 1522930000 400289 531840 476898 492880 542610 589550 517050 512313 525940 523070 TRUE FALSE 416092.7188 623179.3829 489326.3537 590370.1929 450377.346 452635.9472 476522.2699 505446.2822 507011.5221 625555.5517 0.665157103 0.996201506 0.782226858 0.943753423 0.71996379 0.723574343 0.761758518 0.807995838 0.810497998 1 19.25477848 0.513426551 2.926043032 0.999999434 0.803988747 0.279590293 0.095683184 18.13675057 107.1342238 0.087463359 0.02291207 3.26156885 -0.513426551 -0.196010687 TPPT(ph)PPSSIVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPPTPPSSIVAK 12 0 Q96QT6;Q96QT6-4 Q96QT6 PHF12 PHD finger protein 12 1 T(0.012)PPT(0.988)PPSSIVAK 102.33 0.026444 91784000 140340 108110 134840 114770 167020 184320 159930 147460 148250 109880 TRUE FALSE 145880.7316 126677.0515 138354.0412 137471.1634 138630.0001 141514.4734 147394.2687 145483.5399 142914.5115 131408.8822 1.110128395 0.963991546 1.052851518 1.046132964 1.05495152 1.076901888 1.121646164 1.107105832 1.087555948 1 17.00370327 2.839925386 2.117442367 1.091581861 1.038221036 0.090344329 0.045359577 0.47604487 4.208644074 0.014966432 0.015839005 691.712121 -2.839925386 -0.053360825 TPQEAIMDGTEIAVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR;TPQEAIMDGTEIAVS(1)PR 264.69 1.81E-27 453162000 242985 292447 263662 250517 272497 317136 260693 269792 274310 275504 TRUE FALSE 252578.2354 342672.4973 270533.2483 300068.5149 226178.0573 243485.9702 240259.2015 266175.8795 264437.6367 329483.734 0.766587875 1.040028572 0.821082258 0.910723304 0.686461983 0.738992385 0.729198976 0.807857421 0.802581765 1 18.32984772 3.265932365 24.99993483 0.77944142 0.891169828 0.146447747 0.102843987 321.7308156 293849.9786 0.026457046 0.035814415 1844.728109 -3.265932365 0.111728408 TPQEAITDGLEIVVS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPQEAITDGLEIVVSPR 17 0 X6RFN3;Q99496-2;Q99496 X6RFN3 RNF2 E3 ubiquitin-protein ligase RING2 1 TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR;TPQEAITDGLEIVVS(1)PR 179.7 9.45E-10 172535000 76359 92419 83554 80839 91566 105365 86682 85775 82652 95002 TRUE FALSE 79373.71228 108291.2443 85731.48588 96828.71292 76001.64403 80895.57557 79887.63834 84625.32642 79677.37067 113615.823 0.698614948 0.953135237 0.754573471 0.852246724 0.668935383 0.712009766 0.703138315 0.744837508 0.701287625 1 16.79380424 5.056862155 15.86983787 0.772966984 0.104837786 0.042747086 0.107690197 8679492.706 57376499.43 0.024482295 183866259.8 113988.793 -5.056862155 -0.668129199 TPQS(ph)PAPCVLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPQSPAPCVLLR 12 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 T(0.016)PQS(0.984)PAPCVLLR;T(0.026)PQS(0.974)PAPCVLLR;TPQS(1)PAPCVLLR;T(0.009)PQS(0.991)PAPCVLLR 145.92 6.75E-05 1363640000 1003140 1042300 1006220 1101200 1230130 1324280 999130 1098410 1069300 1177240 TRUE FALSE 1042744.742 1221306.917 1032442.92 1319014.073 1021032.942 1016736.04 920815.5799 1083687.611 1030816.102 1407897.638 0.740639599 0.867468546 0.733322432 0.936867878 0.725218165 0.722166166 0.654035886 0.769720455 0.732166937 1 20.42511102 4.201995959 24.99965813 0.770336725 0.804054959 0 0.104513158 856.0017287 585257.2843 0.024948684 0.053898077 15921.93911 -4.201995959 0.033718234 TPRPAS(ph)PGPS(ph)LPARSPS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.456)PRPAS(0.793)PGPS(0.503)LPARS(0.29)PS(0.958)PPR 61.488 0.033035 909740000 107630 128530 143780 128150 144940 150900 113660 131500 124810 169690 TRUE FALSE 111879.3155 150604.0277 147527.0249 153497.6875 120303.1506 115855.7619 104751.0322 129737.4576 120318.1125 202937.5066 0.55129935 0.742120223 0.726957906 0.756379095 0.592808853 0.570893788 0.516173841 0.639297584 0.59288258 1 17.630676 -1.892209908 5.540955394 1.092488065 0.634114007 0.657525684 0.079644238 0.050994431 0.000992012 0.043215215 0.019434338 0.012817109 1.892209908 -0.458374058 TPRPAS(ph)PGPSLPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPRPASPGPSLPAR 14 1 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 1 T(0.001)PRPAS(0.995)PGPS(0.004)LPAR;T(0.006)PRPAS(0.991)PGPS(0.003)LPAR;T(0.004)PRPAS(0.995)PGPS(0.001)LPAR;T(0.011)PRPAS(0.989)PGPSLPAR 120.4 7.97E-05 1663570000 795090 858120 870450 792920 941250 1005440 872210 889490 922870 835840 TRUE FALSE 826480.7671 1005495.435 893134.6421 949757.2094 781256.6612 771941.7976 803843.9011 877567.8415 889656.089 999606.8449 0.82680583 1.005890906 0.893485921 0.950130758 0.781563937 0.77224541 0.804160061 0.877912997 0.890005999 1 19.93100125 5.094445555 12.92226486 0.876592726 6.02E-05 0.035924962 0.079364717 683778.9436 1873822.993 0.019518664 16484123.03 124292.6808 -5.094445555 -0.876532557 TPRPAS(ph)PGPSLPARS(ph)PS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPRPASPGPSLPARSPSPPR 20 2 Q8IY33;Q8IY33-5;Q8IY33-3 Q8IY33 MICALL2 MICAL-like protein 2 3 T(0.075)PRPAS(0.903)PGPS(0.118)LPARS(0.912)PS(0.993)PPR 54.441 0.070597 189280000 77309 88116 87101 80797 93835 102600 67437 83297 85850 97567 TRUE FALSE 80361.21902 103249.2376 89370.92361 96778.40545 77884.96022 78772.70492 62151.11173 82180.53996 82760.27527 116683.3856 0.688711753 0.884866659 0.765926727 0.829410331 0.667489718 0.675097868 0.532647484 0.704303698 0.709272146 1 16.83223963 3.234288395 24.97480696 0.686420949 0.796967133 0.061369378 0.120319702 185.254984 1082975.122 0.032109333 0.039667738 1715.095846 -3.234288395 0.110546184 TPRT(ph)PQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPRTPQLK 8 1 Q6PKG0;Q6PKG0-3;A0A0B4J210;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 T(0.098)PRT(0.902)PQLK;T(0.018)PRT(0.982)PQLK;T(0.211)PRT(0.789)PQLK;T(0.355)PRT(0.645)PQLK 93.561 0.017753 1464000000 2066420 1916580 2356680 1559350 2914840 2897440 2030330 2235240 2348980 2301620 TRUE FALSE 2148003.857 2245737.706 2418097.017 1867784.776 2419376.538 2224553.471 1871187.429 2205280.264 2264440.669 2752578.372 0.780360654 0.815866945 0.878484348 0.678558255 0.878949193 0.808170802 0.679794424 0.801168928 0.822661651 1 21.39235221 0.747243985 2.697067977 0.999939714 0.789322789 0.485874529 0.06442678 1.183275277 11.45265615 0.059520407 0.015761433 5.587840297 -0.747243985 -0.210616925 TPS(ph)ASNDDQQE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSASNDDQQE 11 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 T(0.001)PS(0.971)AS(0.028)NDDQQE;T(0.004)PS(0.873)AS(0.123)NDDQQE 153.49 3.40E-05 293120000 221360 290710 280370 307020 342930 418620 306840 330120 312860 287690 TRUE FALSE 230099.4637 340637.1811 287676.6725 367747.6396 284638.8811 321401.8492 282789.079 325695.2814 301600.2297 344057.3473 0.668782299 0.990059313 0.836130008 1.06885565 0.827300691 0.934151971 0.821924255 0.946630798 0.876598718 1 18.39228953 TPS(ph)FELPDASERPPTYCELVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPSFELPDASERPPTYCELVPR 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 T(0.048)PS(0.952)FELPDASERPPTYCELVPR;T(0.001)PS(0.999)FELPDASERPPTYCELVPR;T(0.001)PS(0.999)FELPDASERPPTYCELVPR;T(0.001)PS(0.999)FELPDASERPPTYCELVPR 212.76 1.03E-23 2975430000 324153 327164 310933 325601 440186 398876 391428 375409 384708 353511 TRUE FALSE 336950.8107 383351.872 319036.1694 390003.906 365363.341 306243.094 360746.8506 370377.2564 370862.4342 422774.7121 0.796998499 0.906752133 0.754624532 0.922486362 0.864203394 0.724364739 0.853283889 0.876062938 0.877210542 1 18.68952956 0.756666425 1.063058581 0.99910124 0.834219627 0.415660144 0.059073366 0.836521562 1.717107707 0.054165218 0.0172391 5.710398614 -0.756666425 -0.164881614 TPS(ph)FLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSFLKK 7 1 P35611;P35611-3;P35612;Q9UEY8-2;Q9UEY8 P35611;Q9UEY8-2 ADD1;ADD2;ADD3 Alpha-adducin;Beta-adducin;Gamma-adducin 1 T(0.151)PS(0.849)FLKK 60.064 0.061104 347190000 1077000 572840 873450 560310 1331700 1046300 1090500 856420 1040600 530930 TRUE FALSE 1119520.792 671220.8139 896212.8245 671137.6456 1105338.11 803312.6818 1005023.761 844941.0907 1003149.009 634955.5682 1.763148238 1.05711462 1.41145754 1.056983637 1.740811743 1.265147865 1.582825336 1.330709002 1.579872765 1 19.27629612 -1.162176625 4.469744403 0.999932456 1.405464949 0.216164457 0.238824208 15577812.18 4050385.089 11127.28565 0.050260733 0.068837228 1.162176625 0.405532493 TPS(ph)IDLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSIDLQR 8 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 T(0.064)PS(0.936)IDLQR 82.008 0.022432 135240000 107720 157650 153870 143650 168360 178790 143950 172370 143090 145460 TRUE FALSE 111972.8688 184725.1612 157879.9786 172063.5412 139742.2273 137268.7321 132666.8229 170059.6621 137940.2189 173960.102 0.643669827 1.061882346 0.907564302 0.989097726 0.803300445 0.789081695 0.762627875 0.977578537 0.792941699 1 17.40839693 -1.595720581 3.062664054 1.007502793 0.870056889 0.104744299 0.1198698 244475542 341087574.6 15328244.94 0.027492337 0.025367602 1.595720581 -0.137445903 TPS(ph)PAAEDAREPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 T(0.106)PS(0.894)PAAEDAREPEAK;T(0.041)PS(0.959)PAAEDAREPEAK 98.062 0.0018611 1530090000 590880 373790 477320 439780 621990 690800 650380 474750 569330 301423 TRUE FALSE 614208.3987 437985.5248 489759.3513 526767.1714 516264.362 530372.1692 599401.5161 468386.7528 548839.9245 360481.0658 1.703857586 1.215002857 1.358627118 1.461289431 1.432153894 1.47128995 1.662782246 1.299338016 1.522520811 1 18.45956396 -1.636945177 5.796449332 0.996492046 1.446151872 0.480775621 0.142434174 0.0060784 0.000380715 0.129824796 0.030428042 0.023070384 1.636945177 0.449659825 TPS(ph)PAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSPAPK 7 0 Q96P11-2;Q63ZY6;Q63ZY6-6;Q3KNT7-3 Q96P11-2 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 1 T(0.432)PS(0.568)PAPK;T(0.016)PS(0.984)PAPK 109.71 0.0073072 1408000000 2503900 1765380 2256500 1818370 2721000 3090100 2729100 2320500 2369500 1537180 TRUE FALSE 2602755.905 2068570.282 2315306.244 2178038.159 2258485.392 2372471.106 2515186.011 2289397.493 2284222.158 1838360.99 1.415802402 1.125225292 1.259440478 1.184771745 1.228532048 1.290536037 1.368167637 1.245347081 1.242531891 1 20.80998866 0.588159372 2.571101415 1.000011356 1.260905702 0.501572661 0.078647205 3.912656391 23.43160548 0.072247991 0.019211124 3.87399782 -0.588159372 0.260894346 TPS(ph)PGPVESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSPGPVESK 10 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 T(0.001)PS(0.999)PGPVESK;T(0.023)PS(0.977)PGPVESK 150.33 2.28E-05 549860000 628850 427270 520250 415850 711450 747820 649340 541930 570990 407960 TRUE FALSE 653677.4836 500650.2988 533808.1424 498103.8888 590517.9831 574150.1383 598443.0341 534666.3148 550440.1814 487891.9511 1.339799687 1.026149945 1.094111393 1.020930736 1.210345819 1.176797725 1.226589274 1.095870333 1.128200988 1 18.89620216 0.607512385 1.458769436 1.000325741 1.14418365 0.189806319 0.091790034 2.668252192 7.760472587 0.084822145 0.024738709 4.050534959 -0.607512385 0.14385791 TPS(ph)PNSNEQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSPNSNEQQK 11 0 Q9H4E7 Q9H4E7 DEF6 Differentially expressed in FDCP 6 homolog 1 T(0.025)PS(0.975)PNSNEQQK 94.747 0.0034108 0 186900 132220 156530 117990 184410 195630 153500 126050 148540 87074 TRUE FALSE 194278.9563 154927.7565 160609.3004 141328.0698 153064.0541 150197.8973 141468.2689 124360.5059 143194.0744 104134.4832 1.865654396 1.487766125 1.542325803 1.357168783 1.469869052 1.442345443 1.35851511 1.194229828 1.375087964 1 16.66808836 8 0.108828017 0.850988334 3.451602696 0.779339438 0.10043342 49.33677674 0.375062512 0.908437061 19.26413951 100000000 -8 2.600614362 TPS(ph)PSQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.048)PS(0.952)PSQPK;T(0.225)PS(0.773)PS(0.002)QPK;T(0.005)PS(0.995)PSQPK;T(0.006)PS(0.994)PSQPK;T(0.092)PS(0.905)PS(0.003)QPK 154.85 0.0004389 2677150000 4337730 3396850 4525560 3462300 5226260 5396560 5002560 4144540 4542890 2677050 TRUE FALSE 4508986.93 3980232.564 4643499.811 4147132.606 4337902.192 4143290.726 4610446.275 4088989.22 4379392.276 3201566.692 1.40836889 1.243214009 1.450383596 1.29534475 1.354931072 1.29414475 1.44005942 1.277183833 1.367890379 1 21.61034663 -2.836267795 0.550633744 2.03E-10 1.346440212 0.707682259 0.067023523 150.1661355 6.292660785 178.3981421 0.02548799 0.001457915 2.836267795 1.346440212 TPS(ph)PSQPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSPSQPKK 9 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 T(0.24)PS(0.754)PS(0.006)QPKK;T(0.029)PS(0.971)PS(0.001)QPKK 84.718 0.0093731 357010000 513630 285435 389180 265129 559880 502330 449160 382990 434120 244563 TRUE FALSE 533908.509 334456.2409 399322.3505 317570.7249 464711.7976 385671.4704 413953.6655 377856.6455 418496.106 292480.4374 1.825450323 1.143516619 1.365295929 1.085784498 1.588864547 1.318623132 1.415320865 1.291903995 1.430851614 1 18.15798061 -2.03321387 2.275454985 0.561914987 1.368101689 0.245360277 0.200617738 8212005.762 3003046.757 18748613.47 0.045870506 0.009263735 2.03321387 0.806186702 TPS(ph)SEEISPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSSEEISPTK 11 0 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.057)PS(0.908)S(0.036)EEISPTK;T(0.01)PS(0.932)S(0.058)EEISPTK 198.33 5.67E-08 529530000 989600 770680 963380 878540 1118730 1250270 1284640 995190 1039190 603970 TRUE FALSE 1028670.172 903038.2949 988486.4742 1052312.59 928568.6742 959913.7405 1183946.56 981851.1059 1001789.755 722306.3578 1.424146639 1.250215072 1.368514154 1.456878482 1.28556071 1.328956516 1.639119672 1.359327791 1.386931936 1 19.46225134 0.37976123 2.850511532 1.000000531 1.390636448 0.56849973 0.101628039 27.65487144 125.4298984 0.097587572 0.025628184 2.39751443 -0.37976123 0.390635918 TPS(ph)SEEISPTKFPGLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TPSSEEISPTKFPGLYR 17 1 Q15311;J3QLT3;E7ENF8;A0A1W2PRI7 Q15311 RALBP1 RalA-binding protein 1 1 T(0.348)PS(0.652)S(0.001)EEISPTKFPGLYR;T(0.006)PS(0.981)S(0.013)EEISPTKFPGLYR;TPS(0.989)S(0.011)EEISPTKFPGLYR;TPS(0.912)S(0.087)EEISPTKFPGLYR;T(0.017)PS(0.976)S(0.007)EEISPTKFPGLYR;T(0.002)PS(0.89)S(0.109)EEISPTKFPGLYR 335.96 2.07E-72 8357690000 4289490 3477930 4248150 3233140 5728590 5001040 4798890 4024070 4839410 3159570 TRUE FALSE 4458842.377 4075237.423 4358860.279 3872645.442 4754846.318 3839624.251 4422740.462 3970133.924 4665240.579 3778627.248 1.180016468 1.078496807 1.153556568 1.024881574 1.258352837 1.016142636 1.170462227 1.050681547 1.234639003 1 21.84943078 -1.257690404 4.698902453 0.999960132 1.12265324 0.183166067 0.080944406 2.96E-05 4.67E-06 0.068565149 0.016155712 0.055247114 1.257690404 0.122693107 TPS(ph)SPSKSPASFEIPASAMEANGVDGDGLNKPAKK ddPTM_MDA-MB-175_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(0.07)PS(0.434)S(0.434)PS(0.059)KS(0.003)PASFEIPASAMEANGVDGDGLNKPAKK 218.53 1.19E-36 919170000 705090 240570 399870 194690 699030 517900 593960 447680 582290 165630 TRUE FALSE 732927.4976 281886.0261 410290.9407 233199.1009 580209.1303 397625.5739 547403.8632 441679.5819 561333.4966 198082.0273 3.700121145 1.423077247 2.071318364 1.177285512 2.929135662 2.007378353 2.763521106 2.229781206 2.833843657 1 17.59573846 3.179421476 24.99999949 2.364456318 2.043478304 0.00862803 0.811557941 297.6679889 125831.8059 0.218706851 0.261404816 1511.546376 -3.179421476 -0.320978014 TPS(ph)SQNLLALLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSSQNLLALLAR 13 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 T(0.075)PS(0.914)S(0.011)QNLLALLAR;T(0.096)PS(0.901)S(0.003)QNLLALLAR 175.08 1.98E-05 103598000 42639 42327 52905 60330 87675 76337 62534 69692 68201 67928 TRUE FALSE 44322.42064 49596.33299 54283.74776 72263.09393 72772.03482 58608.88865 57632.42168 68757.89273 65746.45933 81237.19104 0.545592728 0.610512653 0.668213008 0.889532159 0.895797034 0.721453904 0.709433954 0.846384419 0.809314779 1 16.30985274 3.966289731 3.261735043 0.82315972 0.581584568 0.62729334 0.082489888 0.16396159 3.546128106 0.021756264 0.047312959 9253.152734 -3.966289731 -0.241575151 TPS(ph)SSSTLAYSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSSSSTLAYSPR 13 0 H3BR17;Q6Q0C0;A0A087WUB0 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 T(0.015)PS(0.95)S(0.031)S(0.002)S(0.001)T(0.002)LAYSPR 72.321 0.041818 170150000 123310 106280 114810 105560 138080 158050 162980 130180 121260 72326 TRUE FALSE 128178.374 124532.7633 117802.0429 126439.4529 114609.2109 121345.2828 150205.2017 128435.15 116895.8763 86496.89494 1.481884108 1.439736806 1.361922217 1.461780253 1.325009539 1.402885998 1.736538657 1.484852724 1.351445926 1 16.40036072 0.870460662 3.658309172 1.00017664 1.464660475 0.637900268 0.104535509 0.417445732 10.36392815 0.106956554 0.027513802 7.420969767 -0.870460662 0.464483835 TPSKQPGSIGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSKQPGSIGSR 12 1 Q66K14-2;Q66K14 Q66K14-2 TBC1D9B TBC1 domain family member 9B 1 TPSKQPGS(0.008)IGS(0.992)R 61.641 0.050518 112820000 51670 43571 48969 37399 64033 60064 47445 46752 57189 54312 TRUE FALSE 53709.9715 51053.98031 50245.17237 44796.41058 53148.69353 46115.04628 43726.13693 46125.36591 55130.77906 64953.39653 0.826900122 0.786009401 0.773557274 0.689670024 0.81825888 0.709971283 0.673192462 0.710130161 0.848774383 1 15.98711735 0.9639269 4.013867725 0.9996527 0.744903656 0.704912156 0.050402817 0.11872401 5.581943345 0.05097953 0.013042292 9.202946563 -0.9639269 -0.254749045 TPSNELYKPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPSNELYKPLR 11 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 ;; 125.54 0.00029744 1675620000 859005 721635 810267 714524 1015870 1082650 990060 874201 881809 775227 FALSE TRUE 892919.1807 845570.1977 831383.2237 855854.7146 843192.7803 831220.9452 912456.5102 862483.7655 850072.8663 927117.888 0.963112882 0.912041725 0.896739492 0.923134723 0.909477415 0.896564456 0.984186069 0.930284893 0.916898355 1 19.82239327 2.253482121 24.97769376 0.950850954 0.915663885 0.318788666 0.028607934 314.2210593 525985.8293 0.009693606 0.00807981 179.2594755 -2.253482121 -0.035187068 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;TPSNTPSAEADWS(1)PGLELHPDYK;TPSNTPSAEADWS(1)PGLELHPDYK 283.7 2.52E-52 4213920000 3520840 2768020 3369720 2731150 4121860 4522020 3914670 3313790 3499310 2485050 TRUE FALSE 3659845.482 3243405.903 3457537.671 3271363.318 3421227.709 3471849.387 3607827.936 3269374.065 3373370.517 2971947.968 1.231463512 1.09134007 1.163391051 1.100747171 1.151173488 1.168206652 1.213960666 1.100077828 1.135070517 1 21.50297743 0.538786834 1.137066562 1.000220197 1.152545704 0.523478355 0.043784836 1.269953225 2.298440654 0.03966392 0.01220619 3.457696212 -0.538786834 0.152325508 TPSPKEEDEEPES(ph)PPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPSPKEEDEEPESPPEK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TPSPKEEDEEPES(1)PPEK;TPSPKEEDEEPES(1)PPEK;TPSPKEEDEEPES(1)PPEK 188.32 2.53E-10 1123570000 2275670 782910 1240390 732510 1974970 1933000 1695640 1262090 1434370 618561 TRUE FALSE 2365515.209 917368.7023 1272715.582 877398.2917 1639265.305 1484090.045 1562731.306 1245173.748 1382747.304 739756.1849 3.19769575 1.240096022 1.720452777 1.186064151 2.215953497 2.006188086 2.112495087 1.683221815 1.869193299 1 19.49669033 0.095194993 1.069822994 0.995214195 1.885506026 0.206507327 0.535696138 10.54978055 10.92447782 0.628998888 0.150321372 1.245073509 -0.095194993 0.890291831 TPSPKEEDEEPES(ph)PPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 TPSPKEEDEEPESPPEKK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK 184.3 3.07E-14 41455500000 13699710 2876930 5027317 2555329 9201180 8980220 7840110 5127467 6052967 2010571 TRUE FALSE 14240585.13 3371020.348 5158333.011 3060765.449 7637166.71 6894700.002 7225581.692 5058741.692 5835121.9 2404503.893 5.922462913 1.401960861 2.145279543 1.272930129 3.176192284 2.867410622 3.005019752 2.103860887 2.426746705 1 21.19730783 8 0.065090416 1.09E-13 8.059090215 0.20367744 1.19055792 606.9352815 2.93232429 68.1110024 454.7061247 100000000 -8 8.059090215 TPSS(ph)PCPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPSSPCPASK 10 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 TPS(0.002)S(0.998)PCPASK;T(0.001)PS(0.049)S(0.949)PCPASK 121.61 0.0029032 171690000 564620 501320 543060 467690 598230 659020 606030 508350 519530 406100 TRUE FALSE 586911.6336 587417.8103 557212.5897 560197.6861 496543.0783 505972.5925 558527.785 501536.3997 500832.2168 485667.5197 1.208463835 1.209506064 1.147312857 1.153459236 1.022393012 1.041808587 1.150020873 1.03267437 1.031224441 1 18.88960948 8 0.214759934 1.001884943 2.225068333 0.71394961 0.041437042 27.47859772 0.3466956 0.068569645 11.57178275 100000000 -8 1.22318339 TPSS(ph)PSK ddPTM_MDA-MB-175_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 TPS(0.077)S(0.923)PSK 128.57 0.0039279 176110000 607710 353050 515510 427530 597700 705300 802110 508320 595800 310660 TRUE FALSE 631702.8601 413683.5912 528944.6141 512094.158 496103.1675 541504.7639 739238.5223 501506.8018 574357.2744 371527.8791 1.70028387 1.113465811 1.423701003 1.378346517 1.335305358 1.457507752 1.989725574 1.349849716 1.545933177 1 18.50311095 2.478810334 24.99311196 1.529577795 1.378081679 0.001744252 0.265048131 188.3449136 2786995.037 0.085617002 0.072621605 301.1690468 -2.478810334 -0.151496116 TPSSS(ph)PPITPPASETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPSSSPPITPPASETK 16 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 TPS(0.001)S(0.007)S(0.992)PPITPPASETK 162.29 7.61E-09 0 65825 55002 65158 60026 89849 90817 81841 73214 72623 52837 TRUE FALSE 68423.82183 64448.16564 66856.07101 71898.96364 74576.49907 69726.12809 75426.08857 72232.68608 70009.31242 63189.39852 1.082837049 1.019920543 1.058026703 1.137832695 1.18020587 1.103446618 1.193650997 1.143114 1.107928134 1 15.94739491 3.762356487 5.600701159 1.135907498 1.049296295 0.251042033 0.052616544 0.186585841 19.35300659 0.012677195 0.022379358 5785.70768 -3.762356487 -0.086611203 TPT(ph)PEPAEVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 T(0.137)PT(0.863)PEPAEVETR;TPT(1)PEPAEVETR;T(0.062)PT(0.938)PEPAEVETR;T(0.005)PT(0.995)PEPAEVETR;T(0.177)PT(0.823)PEPAEVETR 323.44 5.96E-46 6377420000 2322200 2299720 2333910 2288390 2646090 3042670 2733720 2493430 2477930 1908610 TRUE FALSE 2413882.249 2694679.021 2394733.612 2741026.712 2196308.567 2336056.005 2519443.883 2460009.649 2388749.783 2282565.587 1.057530291 1.180548343 1.049141206 1.200853429 0.962210497 1.02343434 1.103777213 1.077738867 1.046519669 1 21.12222488 7.999956631 0.038793842 0.790893673 1.533279424 0.161955226 0.064972866 1453.438685 4.295845821 22.92269388 72.00229546 99990014.31 -7.999956631 0.742385751 TPTHQPPKPGS(ph)PGRPACPLSNLLLQSYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPTHQPPKPGSPGRPACPLSNLLLQSYEER 30 2 Q96F63 Q96F63 CCDC97 Coiled-coil domain-containing protein 97 1 T(0.007)PT(0.007)HQPPKPGS(0.985)PGRPACPLS(0.002)NLLLQSYEER;TPTHQPPKPGS(1)PGRPACPLSNLLLQSYEER;TPTHQPPKPGS(0.999)PGRPACPLS(0.001)NLLLQSYEER 178.77 3.77E-18 1798370000 783339 634670 807135 638661 970630 950420 862880 820160 883030 659297 TRUE FALSE 814265.8286 743669.6355 828169.6012 764986.2396 805642.6593 729699.3588 795245.2109 809167.0967 851249.9228 788473.6241 1.032711563 0.9431763 1.050345345 0.970211579 1.021775028 0.925458172 1.008588222 1.026244978 1.0796175 1 19.58870297 1.713151114 3.248438562 1.042033272 0.990512373 0.187341876 0.040831197 0.302181779 7.07366946 0.022030113 0.010227431 51.65960892 -1.713151114 -0.051520898 TPTS(ph)PLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TPTSPLK 7 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 T(0.032)PT(0.017)S(0.951)PLK;TPT(0.001)S(0.999)PLK;TPT(0.002)S(0.998)PLK;TPT(0.003)S(0.996)PLK;T(0.006)PT(0.021)S(0.973)PLK;T(0.005)PT(0.075)S(0.921)PLK 138.26 0.0029403 15605200000 20586700 13770820 17756800 14098730 22681900 24847400 22713300 17385050 18485500 11609010 TRUE FALSE 21399478.81 16135851.21 18219556.8 16887416.71 18826438.74 19076967.92 20932972.2 17152031.84 17820210.47 13883573.24 1.541352391 1.162226102 1.312310345 1.216359537 1.356022575 1.374067582 1.507751055 1.23541912 1.283546401 1 23.72687559 0.662967997 1.467545958 1.000875123 1.335536157 0.448075415 0.112814316 1.107771828 3.538452589 0.103508119 0.030202802 4.602226585 -0.662967997 0.334661033 TPTSS(ph)PASSPLVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 TPT(0.004)S(0.18)S(0.723)PAS(0.069)S(0.023)PLVAK;TPT(0.017)S(0.114)S(0.834)PAS(0.012)S(0.024)PLVAK 81.703 0.01339 140123000 461040 361880 445690 360970 547020 581000 518190 474910 479100 384150 TRUE FALSE 479242.2152 424030.075 457305.0475 432368.7886 454037.7358 446071.5551 477572.9138 468544.6082 461857.2846 459416.8375 1.043153355 0.922974607 0.995403325 0.941125256 0.988291457 0.970951691 1.039519832 1.019868168 1.005312054 1 18.80944421 2.252891838 24.98139857 1.018823606 0.974249706 0.263577071 0.031774074 258.4885035 450582.6074 0.010146276 0.008452034 179.0159957 -2.252891838 -0.044573901 TPTVPDS(ph)PGYMGPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPTVPDSPGYMGPTR 15 0 A0A087WXN9;Q765P7 A0A087WXN9 MTSS1L MTSS1-like protein 1 TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR;TPTVPDS(1)PGYMGPTR 230.67 5.08E-13 990850000 502255 598720 654140 641670 779490 818740 742150 779510 767080 804450 TRUE FALSE 522084.4152 701545.5026 671187.4258 768590.4108 646992.5682 628600.0431 683978.3438 769061.9435 739472.9406 962066.5754 0.542669737 0.729206814 0.697651746 0.798895243 0.672502907 0.653385181 0.710946998 0.799385368 0.768629697 1 19.87577721 -4.999999996 0.144245526 2.042262314 0.612227839 0.709395057 0.061249937 76.12994139 0.664480098 22.57913476 0.348742562 1.00E-05 4.999999996 -1.430034475 TPVCHQCHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPVCHQCHK 9 0 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 0 73.233 0.025734 18616000 25274 38259 35886 39773 49232 53189 36867 39426 35280 55984 FALSE TRUE 26271.83704 44829.68564 36821.21864 47639.98069 40863.56223 40836.66084 33977.26821 38897.55896 34010.27969 66952.99292 0.392392272 0.669569554 0.549956276 0.711543706 0.610332122 0.609930327 0.507479453 0.580968188 0.507972507 1 16.03086093 -1.102556797 4.31680241 1.000054196 0.577372357 0.692553113 0.085634223 3.028632245 46228596.04 5395.199189 0.01880626 0.078966557 1.102556797 -0.422681839 TPVEPEVAIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RJX2;E5RIP1 P60866 RPS20 40S ribosomal protein S20 0 ;;; 202.56 3.96E-08 6890340000 1764120 1979930 2012350 2002710 2105240 2284230 2127210 2014290 1893230 1755720 FALSE TRUE 1833768.82 2319967.576 2064793.494 2398840.061 1747392.057 1753752.2 1960473.722 1987291.737 1825093.022 2099719.719 0.87333981 1.104893932 0.983366244 1.142457271 0.832202527 0.835231571 0.933683531 0.94645572 0.869207926 1 21.00176533 3.226019658 24.99998801 0.902374552 1.028602303 0.348981119 0.082415176 239.5678525 477569.9193 0.022905018 0.027554277 1682.750229 -3.226019658 0.12622775 TPVLLHDHDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPVLLHDHDER 11 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 ; 90.005 0.0068293 1810200000 548370 583670 679940 591930 626840 733940 544370 659890 711490 660730 FALSE TRUE 570020.071 683910.7822 697659.795 709011.9873 520289.9607 563493.558 501700.857 651045.2539 685883.6139 790187.3931 0.721373279 0.865504548 0.882904234 0.89727069 0.658438701 0.71311383 0.63491377 0.823912479 0.868001211 1 19.5918353 0.993680693 2.205863467 0.997501117 0.773379713 0.396680582 0.087332878 0.344951266 3.663901943 0.089778153 0.024751268 9.855546079 -0.993680693 -0.224121404 TPVLPAGPPTTDPWALNS(ph)PHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TPVLPAGPPTTDPWALNSPHHK 22 0 Q9H201 Q9H201 EPN3 Epsin-3 1 TPVLPAGPPTTDPWALNS(1)PHHK;TPVLPAGPPTT(0.001)DPWALNS(0.999)PHHK;TPVLPAGPPTTDPWALNS(1)PHHK 162.47 1.04E-11 852040000 899370 609150 794430 787380 937260 1006970 1219710 882320 988180 576710 TRUE FALSE 934877.8221 713766.774 815133.4984 943121.4139 777944.88 773116.4783 1124105.943 870493.9436 952615.5948 689705.2827 1.355474353 1.034886627 1.181857699 1.367426693 1.12793812 1.120937446 1.629835194 1.262124512 1.381192255 1 19.39562049 TPVS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPVSPVK 7 0 P23443-5;P23443;P23443-3;P23443-2 P23443-5 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 T(0.007)PVS(0.993)PVK;T(0.02)PVS(0.98)PVK 81.547 0.028222 369100000 1328950 1260230 1125150 1316580 1302860 1794680 1501390 1248440 1155220 1149900 TRUE FALSE 1381417.972 1476664.699 1154472.333 1576995.594 1081400.323 1377892.769 1383707.129 1231706.704 1113643.858 1375200.889 1.004520855 1.073781083 0.839493592 1.146738347 0.786358074 1.001957445 1.006185453 0.895655838 0.809804492 1 20.39121095 4.275742334 0.477601503 0.918106507 1.072658265 0.081320971 0.107818741 7.748216646 1.886215143 0.07198688 0.645593657 18868.7154 -4.275742334 0.154551758 TPVS(ph)PVKFSPGDFWGR ddPTM_MDA-MB-175_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(0.149)PVS(0.851)PVKFSPGDFWGR;T(0.001)PVS(0.999)PVKFSPGDFWGR 177.4 1.79E-09 2189000000 1554820 1031300 1324440 1097640 1703090 1622780 1477940 1285810 1358130 1047650 TRUE FALSE 1616205.494 1208417.753 1358955.994 1314749.916 1413599.37 1245913.938 1362095.201 1268575.82 1309251.167 1252916.959 1.289954201 0.964483515 1.08463373 1.049351201 1.128246657 0.994410627 1.087139248 1.012497924 1.044962443 1 20.25685937 4.750339487 24.98598625 1.044581528 1.289954348 0.713679164 0.047315721 933.528312 1980215.568 0.01040832 0.173305674 56278.10779 -4.750339487 0.24537282 TPVSGSLKS(ph)PVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPVSGSLKSPVPR 13 1 Q8NI27;A0A0C4DG98;Q8NI27-2;H0Y7U4;H7C477 Q8NI27 THOC2 THO complex subunit 2 1 TPVS(0.002)GS(0.005)LKS(0.992)PVPR 67.645 0.031846 327190000 274970 196250 264240 214230 367430 351840 317950 301510 300310 211900 TRUE FALSE 285826.0279 229954.4109 271126.3115 256604.0546 304974.3798 270130.4922 293028.2482 297468.7516 289501.9018 253417.7479 1.127884808 0.907412416 1.06987894 1.012573337 1.20344523 1.065949384 1.156305155 1.173827619 1.142390003 1 17.95115804 3.258640805 24.99766094 1.134578564 1.023609946 0.266551479 0.075016849 261.2400786 325213.5497 0.019252015 0.02603473 1814.014714 -3.258640805 -0.110968617 TPVSHPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPVSHPQR 8 0 A0A1B0GVJ7;Q9BY89-2;Q9BY89 A0A1B0GVJ7;Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 0 84.498 0.017409 11243000 10813 11361 11221 9015.9 21869 15128 10714 8460.3 8499.7 22717 FALSE TRUE 11239.90559 13312.16337 11513.42848 10799.21811 18151.71519 11614.75127 9874.208684 8346.903517 8193.797457 27167.96121 0.413719142 0.489994935 0.423786989 0.39749829 0.668129458 0.427516485 0.363450485 0.307233342 0.301597805 1 14.72961868 -1.284227468 4.047258889 1.000733513 0.419415723 0.756351932 0.098506629 26069085.32 16544740.23 158761.3045 0.025002921 0.051972371 1.284227468 -0.58131779 TPVSITEHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TPVSITEHPK 10 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 82.831 0.016836 129500000 105160 91319 106540 114320 118980 118810 127000 106920 114440 84238 FALSE TRUE 109311.798 107002.3279 109316.5199 136932.1548 98755.8221 91218.17808 117045.4081 105486.9123 110321.3268 100742.8233 1.085057917 1.062133504 1.085104788 1.359224909 0.980276499 0.905455844 1.161823784 1.047091087 1.095078768 1 16.62031754 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TPYHVNLLLAGYDEHEGPALYYMDYLAALAK 31 0 P49721 P49721 PSMB2 Proteasome subunit beta type-2 0 ; 119.75 9.71E-06 1699350000 487300 405470 556440 504300 644350 632420 705230 591310 605670 405660 FALSE TRUE 506538.9803 475106.3184 570941.2835 604049.0348 534823.6172 485550.0394 649952.2298 583384.4566 583872.055 485141.3102 1.044106057 0.979315322 1.176855633 1.245099154 1.102407909 1.000842495 1.339717349 1.202504187 1.203509251 1 18.88804551 4.232422569 24.9820595 1.172566483 1.011710674 0.246427093 0.100678693 159.9613536 651058.5011 0.024969245 0.056183425 17077.43218 -4.232422569 -0.160855809 TQAPT(ph)KASE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQAPTKASE 9 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 TQAPT(0.802)KAS(0.198)E 88.496 0.081174 309020000 378040 265160 295340 243030 412060 436750 379960 347440 318470 224000 TRUE FALSE 392965.3111 310699.1673 303036.803 291100.6086 342018.1884 335321.4315 350177.7424 342783.1351 307008.3269 267888.5113 1.466898708 1.159807734 1.131204924 1.08664835 1.276718388 1.25172009 1.307177156 1.279573855 1.14603021 1 18.03127319 0.958131953 4.395704727 1.000203829 1.238926438 0.362997936 0.100514573 0.249213355 14.80155577 0.097703562 0.024853668 9.080963982 -0.958131953 0.238722609 TQAPTKAS(ph)E ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQAPTKASE 9 1 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 1 TQAPT(0.332)KAS(0.668)E;TQAPT(0.472)KAS(0.528)E 91.313 0.010918 291550000 572830 365090 468300 372110 645920 679000 601550 517980 536990 313310 TRUE FALSE 595445.7707 427791.3675 480504.2827 445712.2474 536126.7491 521312.5403 554398.9391 511037.3253 517663.8348 374697.0958 1.589139007 1.141699181 1.28238059 1.189526827 1.430827074 1.391290582 1.479592304 1.363867858 1.381552834 1 18.51536527 -1.075964912 4.822625756 0.999987551 1.355955864 0.428417916 0.125000105 1.63E-05 3.13E-06 0.118005965 0.027813301 0.083952781 1.075964912 0.355968313 TQATGLTKPTLPPS(ph)PLMAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQATGLTKPTLPPSPLMAAR 20 1 B1AHC3;B1AHC4;H0Y9T8;P85298-4;P85298-3;P85298 B1AHC3 PRR5-ARHGAP8;ARHGAP8 Rho GTPase-activating protein 8 1 TQATGLTKPT(0.001)LPPS(0.999)PLMAAR;TQATGLTKPTLPPS(1)PLMAAR;TQATGLTKPT(0.001)LPPS(0.999)PLMAAR;TQATGLTKPT(0.001)LPPS(0.999)PLMAAR 134.03 5.88E-06 4409220000 4136030 3636990 4428540 3527480 5525310 5636840 4575140 4676060 4570170 3649030 TRUE FALSE 4299323.658 4261614.741 4543951.39 4225205.016 4586119.78 4327769.337 4216528.572 4613385.064 4405690.474 4363987.564 0.985182381 0.976541449 1.041238391 0.968198226 1.050901203 0.991700658 0.966210034 1.057148994 1.009556148 1 22.05721556 4.277156246 24.99965049 1.011928311 0.980861842 0.134615957 0.030032922 302.3142805 195813.9681 0.007060788 0.019335968 18930.24548 -4.277156246 -0.031066469 TQDECILHFLR ddPTM_MDA-MB-175_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 ;;; 159.44 2.87E-05 606570000 595791 662290 625240 640730 838840 848850 706090 665380 658640 672010 FALSE TRUE 619313.2887 776033.1556 641534.268 767464.4816 696254.2764 651717.4519 650744.8208 656461.6694 634935.6751 803677.4931 0.770599269 0.965602698 0.798248394 0.954940866 0.866335417 0.810919128 0.809708902 0.816822264 0.790037895 1 19.61625715 2.8906461 6.286095777 0.830260352 0.87801395 0.005774727 0.079319055 0.631652348 31.49070439 0.022198476 0.023643487 777.402799 -2.8906461 0.047753598 TQDHDENVALEACEFWLTLAEQPICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQDHDENVALEACEFWLTLAEQPICK 26 0 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 121.35 0.00014431 60789000 53259 41508 58103 49483 67925 70866 62352 57876 61436 41784 FALSE TRUE 55361.70644 48636.67611 59617.21191 59270.58971 56379.13276 54408.44548 57464.68731 57100.26689 59224.93036 49970.7748 1.10788169 0.973302421 1.193041576 1.186105077 1.128242117 1.088805321 1.149965906 1.142673235 1.185191356 1 15.60879697 4.233476604 24.99972633 1.140228606 1.040592056 0.26303794 0.062067873 129.0940272 634809.0711 0.014271938 0.032409573 17118.92954 -4.233476604 -0.09963655 TQEDEEEISTS(ph)PGVSEFVSDAFDACNLNQEDLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TQEDEEEISTSPGVSEFVSDAFDACNLNQEDLRK 34 1 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 TQEDEEEIST(0.004)S(0.996)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.003)S(0.997)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.004)S(0.996)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.006)S(0.994)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIST(0.004)S(0.996)PGVSEFVSDAFDACNLNQEDLRK;TQEDEEEIS(0.007)T(0.154)S(0.813)PGVS(0.025)EFVS(0.001)DAFDACNLNQEDLRK 273.25 4.82E-74 1346958000 942961 685029 885124 637926 1199824 1140942 953723 911095 1059943 689628 TRUE FALSE 980189.8284 802677.402 908191.0586 764105.8588 995878.345 875975.5116 878967.6992 898883.2618 1021795.858 824747.4029 1.188472768 0.973240291 1.101174803 0.926472586 1.207494976 1.062113695 1.0657417 1.089889169 1.238919765 1 19.6535928 3.226969935 24.99935934 1.108087561 1.045892576 0.100426713 0.092652323 518.0269086 1117304.56 0.025165766 0.030307963 1686.436273 -3.226969935 -0.062194985 TQEHFTHNTVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQEHFTHNTVR 11 0 Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5 Q08209-3 PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform;Serine/threonine-protein phosphatase 0 132.14 0.00010909 182120000 100940 278240 283400 299760 202540 314530 206250 279820 247140 284780 FALSE TRUE 104925.1891 326025.5556 290785.6368 359051.6333 168112.3231 241485.1742 190083.5861 276069.4706 238245.4797 340577.1886 0.308080496 0.957273612 0.853802447 1.054244516 0.49361005 0.709046825 0.558121896 0.810592958 0.69953446 1 18.37762228 -1.833479701 4.293108758 1.052139052 0.729571235 0.137921235 0.210549159 0.094284775 0.0036571 0.182932479 0.045732027 0.014673047 1.833479701 -0.322567817 TQGLVPEHVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQGLVPEHVETR 12 0 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14;Q9NZM1-5 Q9NZM1-6 MYOF Myoferlin 0 69.92 0.048676 147460000 78853 89396 89463 92495 109730 127130 94645 83929 89324 98888 FALSE TRUE 81966.17733 104749.0676 91794.47927 110790.2349 91078.13379 97605.98417 87226.47759 82804.06904 86109.24669 118263.2103 0.693082634 0.885728261 0.776187954 0.93681065 0.770130741 0.825328384 0.737562234 0.700167608 0.728115248 1 16.85164182 2.247389961 24.63383087 0.758338243 0.819575623 0 0.100801976 414.1649198 1155518.741 0.032891392 0.027130774 176.7624292 -2.247389961 0.061237379 TQHIQQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQHIQQPR 8 0 P51397 P51397 DAP Death-associated protein 1 0 ;; 128.69 0.0024512 0 192928 263832 244722 230681 414491 389494 265034 238756 233093 392116 FALSE TRUE 200544.9464 309143.0937 251099.6564 276309.0133 344035.9679 299039.9213 244259.9425 235555.8663 224704.0285 468943.6227 0.427652572 0.659232963 0.53545809 0.589215846 0.733640359 0.637688428 0.520872725 0.502311696 0.479170667 1 18.83905496 -1.192503297 4.274661309 1.000152654 0.568001501 0.690609279 0.087321138 0.000130645 2.47E-05 0.086949868 0.020487089 0.064194335 1.192503297 -0.432151152 TQIAICPNNHEVHIYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQIAICPNNHEVHIYEK 17 0 A0A1W2PNV4;C9JEY1;C9K057;O15143;F8VXW2;C9JBJ7;C9JTT6 A0A1W2PNV4;C9JEY1 ARPC1B Actin-related protein 2/3 complex subunit 1B 0 ; 190.23 1.79E-10 2168100000 2126700 1757190 2204700 1772450 2707300 2785200 2420000 2339100 2357100 1586550 FALSE TRUE 2210663.758 2058973.713 2262156.293 2123035.32 2247114.113 2138379.51 2230314.077 2307748.19 2272268.431 1897404.096 1.165099075 1.085152982 1.192237488 1.118915746 1.18430972 1.127002685 1.175455498 1.216266053 1.197566947 1 20.85559554 2.216579207 24.28562436 1.171161325 1.145398588 0 0.063884024 683.2737252 754892.6706 0.022253869 0.016451416 164.6566242 -2.216579207 -0.025762737 TQILAASYELHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQILAASYELHK 12 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 140.1 0.00029952 0 182410 129450 140040 108370 205740 208930 186450 141110 136840 144430 FALSE TRUE 189611.6877 151682.0305 143689.5574 129805.2625 170768.3883 160409.1739 171835.5618 139218.6513 131915.1551 172728.2932 1.09774539 0.878153936 0.831881997 0.751499712 0.988653249 0.928679204 0.994831585 0.805997956 0.763714807 1 17.39814489 1.677681824 11.27720501 0.839235987 0.915037548 0.067087964 0.106328814 0.29527983 49.66856959 0.050361122 0.0273955 47.60820678 -1.677681824 0.075801561 TQLAS(ph)WSDPTEETGPVAGILDTETLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQLASWSDPTEETGPVAGILDTETLEK 27 0 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 1 T(0.151)QLAS(0.819)WS(0.028)DPT(0.001)EETGPVAGILDTETLEK;T(0.011)QLAS(0.953)WS(0.027)DPT(0.009)EETGPVAGILDTETLEK 177.99 1.36E-17 76944000 62364 49269 62515 51096 89099 78839 68989 69324 76171 50566 TRUE FALSE 64826.17888 57730.56749 64144.19226 61202.63629 73953.98381 60529.83707 63581.46191 68394.82517 73429.62059 60473.43956 1.071977704 0.954643359 1.060700247 1.012058132 1.222916777 1.0009326 1.051394833 1.1309895 1.21424581 1 15.88401402 TQLEELEDELQATEDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TQLEELEDELQATEDAK 17 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4;P35749;P35749-2;P35749-4;P35749-3 P35579;P35580;P35749 MYH9;MYH10;MYH11 Myosin-9;Myosin-10;Myosin-11 0 ;;;; 264.3 4.29E-27 182477000 388391 218769 274347 250550 384703 396607 409917 308085 336880 190377 FALSE TRUE 403724.9766 256340.874 281496.7082 300108.0422 319311.3215 304501.0349 377786.6344 303955.6245 324755.7546 227677.7282 1.773229994 1.125893499 1.236382278 1.318126479 1.402470606 1.337421264 1.659304305 1.335025727 1.426383499 1 17.79663365 -1.463892167 6.180811844 0.999809887 1.391375774 0.307400952 0.180250569 0.0004477 3.88E-05 0.16546745 0.038982403 0.034364326 1.463892167 0.391565887 TQLS(ph)PSIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQLSPSIKR 9 1 H0Y9Y2;Q8NFC6 H0Y9Y2;Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 T(0.001)QLS(0.9)PS(0.099)IKR;TQLS(0.925)PS(0.075)IKR 84.169 0.0096005 527470000 600700 487460 644080 511730 712220 792480 714040 629260 633570 486050 TRUE FALSE 624416.0998 571177.4631 660865.2539 612948.6666 591157.0988 608438.5302 658071.679 620825.799 610767.9395 581282.1915 1.074204765 0.982616484 1.136909514 1.05447694 1.016988147 1.046717995 1.13210363 1.068028245 1.050725359 1 19.14887918 TQLS(ph)QGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQLSQGR 7 0 Q8ND56-2;Q8ND56 Q8ND56-2 LSM14A Protein LSM14 homolog A 1 T(0.001)QLS(0.999)QGR 65.719 0.07324 122250000 100390 99383 136490 114620 156340 149500 163280 135270 125970 131400 TRUE FALSE 104353.4747 116451.2572 140047.0415 137291.4939 129765.3826 114780.8907 150481.6869 133456.9269 121436.3643 157145.3142 0.664057183 0.741041868 0.891194512 0.873659483 0.825766796 0.730412429 0.957595762 0.849258074 0.772764781 1 17.26173973 8 0.045042881 1.308630987 7.47E-12 0.392918292 0.077861358 683.5648726 2.333636351 17.19651894 64.77266616 99999999.98 -8 -1.308630987 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQLWASEPGTPPLPTSLPSQNPILK 25 0 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 1 TQLWASEPGT(1)PPLPTSLPSQNPILK 174.89 9.25E-12 1013600000 949570 765900 809110 786880 1028000 1095700 971520 898230 947020 652730 TRUE FALSE 987059.7568 897437.3671 830196.0713 942522.5154 853260.9272 841240.2805 895369.7238 886190.6961 912936.9352 780619.9462 1.264456233 1.149646984 1.063508658 1.207402552 1.093055502 1.077656656 1.146998265 1.135239626 1.169502444 1 19.5742608 -5 0.229192854 0.269300401 1.1567952 0.369185225 0.057137011 182.6739831 1.828055364 62.19860882 0.098174708 1.00E-05 5 0.887494799 TQMAEVLPS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TQMAEVLPSPR 11 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR;TQMAEVLPS(1)PR 211.94 8.01E-09 3499410000 1883060 2248960 2180090 2051910 2391020 2690250 2183210 2157620 2073800 2223210 TRUE FALSE 1957404.663 2635201.386 2236904.936 2457771.674 1984595.274 2065480.209 2012084.295 2128700.633 1999164.343 2658805.434 0.73619703 0.991122311 0.841319529 0.924389443 0.746423657 0.776845189 0.756762518 0.800622944 0.751903211 1 21.34234678 3.238560908 25 0.79141904 0.87939477 0.102508911 0.092224283 0.063909297 1102245 0.023755675 0.030192944 1732.051926 -3.238560908 0.087975729 TQNKEESYDFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQNKEESYDFSK 12 1 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;A0A3B3ISZ5;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 0 93.494 0.0065126 192160000 338050 191790 256630 177530 374500 343090 339380 265840 295420 166680 FALSE TRUE 351396.475 224728.4406 263317.9886 212644.9041 310842.6238 263412.5471 312778.5088 262276.8496 284787.8919 199337.7547 1.76281947 1.127375197 1.320963954 1.066756794 1.559376568 1.321438317 1.56908815 1.315740964 1.42867011 1 17.60485546 -1.078926234 5.169224911 0.999993523 1.373766223 0.253405954 0.197695541 1.36E-05 2.43E-06 0.17676075 0.041662187 0.08338228 1.078926234 0.3737727 TQPDGTSVPGEPAS(ph)PISQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 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(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR;TQPDGTSVPGEPAS(1)PISQR 410.88 9.82E-148 28771295000 4168271 4226518 4350362 4361987 4870475 5674645 4519698 4525200 4134828 3710873 TRUE FALSE 4332837.558 4952389.589 4463736.008 5224775.009 4042593.399 4356794.699 4165432.261 4464547.096 3986016.348 4437947.515 0.976315638 1.115918918 1.005810905 1.177295358 0.910915099 0.981713885 0.938594304 1.005993667 0.898166626 1 22.08146118 3.216390621 24.9984078 0.959579103 1.067696667 0.449555983 0.061135747 206.0773018 232367.7684 0.016269622 0.019460099 1645.851398 -3.216390621 0.108117564 TQPNLDNCPFHDQPHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQPNLDNCPFHDQPHLK 17 0 P01034 P01034 CST3 Cystatin-C 0 ;;; 215.45 3.24E-15 1229800000 1097820 941710 1040240 951190 1280210 1374480 1102510 1051920 1037780 880770 FALSE TRUE 1141162.781 1103441.367 1067349.509 1139332.543 1062600.361 1055277.85 1016092.385 1037820.733 1000430.501 1053340.018 1.083375512 1.04756427 1.013300065 1.081637955 1.008791409 1.001839703 0.964638548 0.985266595 0.949769764 1 20.00653978 2.845431574 1.809422222 0.975379482 1.052875122 0.692547851 0.023701914 0.193824752 1.262978102 0.00832844 0.008814442 700.5378005 -2.845431574 0.07749564 TQQHYYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQQHYYDK 8 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 83.31 0.018252 244090000 622040 396330 547630 465340 764040 732390 727770 559090 593410 374210 FALSE TRUE 646598.6195 464396.5945 561901.6877 557382.8631 634168.7537 562303.522 670725.4857 551596.313 572053.29 447529.2848 1.444818566 1.037689846 1.255564064 1.245466793 1.417044147 1.256461959 1.498729823 1.232536801 1.278247725 1 18.77162257 0.490696929 1.855191214 1.000071283 1.295627964 0.34006037 0.124194393 4.576881043 15.34831316 0.11464005 0.03191574 3.095258528 -0.490696929 0.295556681 TQQHYYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQQHYYER 8 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 123.63 0.0013396 1137910000 577946 539142 600430 616900 755110 813040 712860 592518 565772 466262 FALSE TRUE 600763.7544 631735.4446 616077.6991 738920.9787 626756.6719 624223.7817 656984.1705 584576.2654 545409.9762 557617.1118 1.077376827 1.13291976 1.104840017 1.325140429 1.123991102 1.119448755 1.178199443 1.04834707 0.978108391 1 19.08891531 1.569799773 3.39347895 0.992601701 1.153514883 0.520375438 0.064269461 0.160497203 4.231335748 0.042428893 0.017221069 37.13639758 -1.569799773 0.160913181 TQQHYYERDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQQHYYERDPK 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;; 123.84 0.00021729 497040000 540940 361034 460920 353054 682170 659420 543460 496185 532590 291232 FALSE TRUE 562296.7289 423038.781 472931.9538 422887.0274 566214.9871 506279.6986 500862.1851 489534.4517 513422.1899 348293.3344 1.614434367 1.214604872 1.357855311 1.214169166 1.625684247 1.453601458 1.438047001 1.405523458 1.474108572 1 18.40994334 -1.213928855 5.232164957 0.999968017 1.414746654 0.479373727 0.131740671 4.71E-05 7.07E-06 0.122188524 0.028797895 0.061104212 1.213928855 0.414778637 TQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 TQQLHPVLQKPSVFGNDS(1)DDDDETSVSESLQR 260.03 1.57E-59 604080000 375240 408640 408940 418360 505700 587150 462580 505430 461800 497910 TRUE FALSE 390054.7649 478820.7412 419597.3123 501110.3593 419741.2946 450793.3108 426321.7709 498655.5376 445179.9082 595465.9314 0.655041278 0.80411106 0.704653768 0.84154329 0.704895566 0.757042993 0.715946536 0.837420768 0.747616085 1 19.18365944 -5 0.233635364 2.347631292 0.730473439 0.643238064 0.056214487 96.02595908 0.960097578 61.18940837 0.085952465 1.00E-05 5 -1.617157852 TQQYHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQQYHK 6 0 Q8WXF1;Q8WXF1-2 Q8WXF1 PSPC1 Paraspeckle component 1 0 ; 100.07 0.038083 468380000 816130 704270 835790 617660 1089670 1028140 977600 852030 835590 751370 FALSE TRUE 848351.4426 825222.894 857571.374 739831.3045 904448.2826 789370.0666 900973.1575 840609.9315 805517.2791 898586.5657 0.944095399 0.91835659 0.954355882 0.823327805 1.006523264 0.878457454 1.00265594 0.93548019 0.896427022 1 19.77729797 TQS(ph)APLPQNAQALQHLVIQQQHQQFLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQSAPLPQNAQALQHLVIQQQHQQFLEK 28 0 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 T(0.125)QS(0.875)APLPQNAQALQHLVIQQQHQQFLEK;T(0.024)QS(0.976)APLPQNAQALQHLVIQQQHQQFLEK 295.81 4.38E-71 725760000 367322 248142 349228 236638 458280 442110 364599 318853 353820 233302 TRUE FALSE 381824.1562 290758.4582 358329.1686 283444.2901 380381.7293 339436.6527 336020.7777 314579.2971 341086.0873 279013.0601 1.368481304 1.042096231 1.28427382 1.015881802 1.363311557 1.216561879 1.204319173 1.127471585 1.222473555 1 18.08997313 -1.457472223 0.403574177 0.875719554 1.206164996 0.229256475 0.112649035 37.75406208 3.27386733 4.908928616 0.064986372 0.034876089 1.457472223 0.330445442 TQS(ph)GNFYTDTLGMAEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TQSGNFYTDTLGMAEFR 17 0 E9PP16;Q8ND30-3;Q8ND30-2;Q8ND30;H0YDJ2 E9PP16 PPFIBP2 Liprin-beta-2 1 T(0.047)QS(0.953)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;TQS(1)GNFYTDTLGMAEFR;T(0.029)QS(0.971)GNFYTDTLGMAEFR;T(0.002)QS(0.998)GNFYTDTLGMAEFR;T(0.003)QS(0.997)GNFYTDTLGMAEFR;T(0.205)QS(0.79)GNFYT(0.005)DTLGMAEFR 260.11 3.29E-27 1244655000 611280 570941 682102 601958 876051 868403 692973 664612 743675 605601 TRUE FALSE 635413.8064 668995.6754 699878.1385 721023.4957 727140.1639 666729.564 638655.9655 655703.9632 716910.282 724256.921 0.877332046 0.923699389 0.966339593 0.995535527 1.003980967 0.920570511 0.881808578 0.905347183 0.989856308 1 19.46614204 3.838284282 0.004729276 1.871584979 1.22E-05 0.104567399 0.045083818 86072.00472 87.24162537 16835.99767 17693.66367 6891.032242 -3.838284282 -1.87157276 TQS(ph)LSALPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQSLSALPK 9 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 T(0.009)QS(0.874)LS(0.118)ALPK;T(0.01)QS(0.984)LS(0.005)ALPK;TQS(0.998)LS(0.002)ALPK 174.23 5.75E-05 581535000 872040 592498 784880 560080 1145630 1088300 966620 831510 882820 553587 TRUE FALSE 906468.8126 694254.9225 805334.6176 670862.1523 950896.2218 835558.8183 890853.7986 820364.9685 851047.4806 662051.7736 1.369181156 1.048641436 1.216422415 1.013307688 1.436286798 1.262074737 1.345595366 1.239125098 1.285469679 1 19.33658452 3.243075251 24.99999381 1.276542518 1.157694466 0.105509228 0.137610736 208.4692026 1154397.153 0.035380577 0.046331879 1750.149914 -3.243075251 -0.118848052 TQS(ph)PEFEAQSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQSPEFEAQSSK 12 0 Q9H5H4;H3BS42 Q9H5H4 ZNF768 Zinc finger protein 768 1 TQS(1)PEFEAQSSK;TQS(1)PEFEAQSSK;T(0.003)QS(0.997)PEFEAQSSK 281.14 4.83E-28 473977000 818445 573360 748902 558949 879340 917670 912090 708137 802782 415094 TRUE FALSE 850757.8406 671830.1199 768419.0013 669507.4439 729870.1009 704555.0499 840598.0025 698645.5818 773890.0326 496423.7218 1.713773543 1.353340081 1.547909513 1.348661263 1.470256293 1.419261447 1.693307482 1.407357366 1.558930403 1 18.92121253 -1.372095123 3.351567436 0.996135808 1.492671539 0.6007836 0.122435516 13828570 19571830.51 521534.3359 0.026468975 0.042452657 1.372095123 0.496535732 TQS(ph)PGGCSAEAVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQSPGGCSAEAVLAR 15 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7 Q96MH2 HEXIM2 Protein HEXIM2 1 TQS(1)PGGCSAEAVLAR;TQS(1)PGGCSAEAVLAR;T(0.002)QS(0.998)PGGCSAEAVLAR;T(0.022)QS(0.977)PGGCSAEAVLAR 282.46 8.36E-34 1844920000 645743 642490 647519 604739 749159 843170 649406 667348 652751 529002 TRUE FALSE 671237.4323 752832.6596 664393.8771 724354.5692 621817.2208 647356.5459 598503.8608 658403.2916 629258.619 632649.8135 1.060993646 1.189967409 1.050176358 1.144953422 0.982877427 1.023246245 0.946027088 1.040707319 0.994639697 1 19.27104763 3.233964408 24.99973172 1.000297649 1.112744025 0.619084867 0.043628157 70.49880462 383457.6443 0.011520545 0.014208634 1713.816846 -3.233964408 0.112446376 TQS(ph)VEITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQSVEITK 8 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 T(0.003)QS(0.997)VEITK;TQS(1)VEITK;T(0.001)QS(0.999)VEITK 125.97 0.0012998 426110000 726218 461605 843463 521626 816185 867480 1048310 683172 970820 375799 TRUE FALSE 754889.6474 540882.068 865444.3387 624802.0659 677450.1652 666020.9168 966140.723 674015.1968 935880.3778 449429.6189 1.679661543 1.203485585 1.925650429 1.390211147 1.507355405 1.481924841 2.149704163 1.499712454 2.08237361 1 18.77773568 TQSAS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQSASPPPK 9 0 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQS(0.002)AS(0.998)PPPK;TQS(0.002)AS(0.998)PPPK;TQS(0.001)AS(0.999)PPPK;TQS(0.02)AS(0.98)PPPK 136.27 0.00020698 932510000 1051970 710900 940420 835380 1060600 1216920 1307670 941580 961350 518367 TRUE FALSE 1093502.588 832991.545 964928.1178 1000615.671 880319.5908 934308.7726 1205171.408 928959.6602 926751.2013 619931.0889 1.763909905 1.343684096 1.556508675 1.614075642 1.42002814 1.507117145 1.944040926 1.498488585 1.494926159 1 19.24174833 0.694734111 2.220117376 1.000315746 1.578861903 0.536013615 0.161466033 1.203212075 7.697291182 0.150864409 0.040976446 4.951469532 -0.694734111 0.578546156 TQSAS(ph)PPPKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 TQS(0.042)AS(0.958)PPPKER;TQS(0.02)AS(0.98)PPPKER;TQS(0.153)AS(0.847)PPPKER 86.497 0.0087367 3277800000 1773000 1325820 1662450 1313330 2083520 2132410 1753920 1644620 1673930 1223120 TRUE FALSE 1842999.409 1553519.272 1705774.813 1573102.754 1729364.015 1637190.094 1616443.167 1622576.559 1613685.586 1462766.946 1.259940563 1.062041548 1.166128902 1.07542952 1.182255327 1.119241926 1.105058582 1.109251589 1.103173401 1 20.4802685 -5 0.115055948 0.580747084 1.196953333 0.436821324 0.050856424 148.8541846 1.125231834 14.57006902 0.505235453 1.00E-05 5 0.616206249 TQSEESRPQSLQQPATSTTETPAS(ph)PAHTTPQTQSTSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQSEESRPQSLQQPATSTTETPASPAHTTPQTQSTSGR 38 1 B8ZZU6;E9PBF9;P15336-5;P15336;P15336-4;F5H629;P15336-2 B8ZZU6 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 TQSEESRPQSLQQPATSTTETPAS(1)PAHTTPQTQSTSGR;TQSEESRPQSLQQPATSTTETPAS(0.978)PAHT(0.012)T(0.009)PQTQSTSGR 276.61 1.12E-76 874270000 54708 156317 144298 174996 173257 210946 152435 158082 140222 153622 TRUE FALSE 56867.91408 183163.2288 148058.5244 209609.6865 143806.837 161956.9884 140486.7464 155963.1694 135175.4376 183721.2896 0.30953361 0.99696246 0.805886594 1.140911252 0.782744544 0.881536314 0.7646732 0.848911793 0.735763601 1 17.48715929 4.746249741 24.73427565 0.875074627 0.309533293 0.668844535 0.12114712 472.4295079 1519663.387 0.027608603 0.295217362 55750.62504 -4.746249741 -0.565541334 TQSGS(ph)SLSLASAATTEPESVHSGGTPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQSGSSLSLASAATTEPESVHSGGTPSQR 29 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.047)QS(0.1)GS(0.752)S(0.1)LS(0.001)LASAATTEPESVHSGGTPSQR 135.35 6.14E-14 0 214230 46735 41912 40377 40466 190050 34114 43465 51472 44009 TRUE FALSE 222687.9658 54761.3727 43004.26115 48363.45009 33587.60377 145913.7677 31440.05554 42882.42277 49619.53277 52631.72095 4.231059935 1.040463274 0.817078757 0.918903072 0.63816275 2.772354107 0.597359444 0.814763834 0.942768579 1 15.68364495 4.738672255 23.65592418 1.050147229 4.231061559 0.722115873 0.59007072 2.189288456 462602.9366 0.139452222 0.80690647 54786.33574 -4.738672255 3.18091433 TQSPCFGDDDPAKKEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQSPCFGDDDPAKKEPR 17 2 Q12765;Q12765-2;Q12765-3 Q12765 SCRN1 Secernin-1 0 224.19 1.57E-15 571720000 977060 441770 655360 379810 1053000 905900 862910 657500 778830 311220 FALSE TRUE 1015635.083 517640.561 672439.22 454935.2844 874011.4361 695518.454 795272.8594 648687.288 750800.0604 372197.6003 2.728752368 1.390768131 1.806672637 1.22229505 2.348245758 1.868680651 2.13669529 1.742857255 2.017208224 1 18.50570923 -1.110198177 5.502255888 0.999988709 1.888482622 0.304384562 0.414177804 5.28E-05 8.54E-06 0.369294094 0.087042347 0.077589298 1.110198177 0.888493913 TQSRPGGPPNPPGPS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQSRPGGPPNPPGPSPK 17 1 M0QXA7;A0A669KBH9;A0A669KAV7;O95785-3;B9EGQ5;A0A669KBG4;A0A2R8YFV2;O95785-4;O95785;O95785-2 M0QXA7 WIZ Protein Wiz 1 TQSRPGGPPNPPGPS(1)PK 79.568 0.008033 116490000 156430 45144 72570 42345 97026 125220 90154 72410 89321 49847 TRUE FALSE 162605.9772 52897.13083 74461.23382 50720.71461 80533.55518 96139.55273 83087.49391 71439.46239 86106.35466 59613.56527 2.727667377 0.88733379 1.249065267 0.850825049 1.350926669 1.612712682 1.393768239 1.198375941 1.444408739 1 15.86335304 4.746927335 24.95966031 1.238599145 2.727668135 0.787266583 0.234824772 474.5293742 1415587.477 0.05680538 0.653628523 55837.67609 -4.746927335 1.48906899 TQSSS(ph)CEDLPSTTQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQSSSCEDLPSTTQPK 16 0 A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 1 TQSS(0.048)S(0.952)CEDLPSTTQPK;TQSSS(1)CEDLPSTTQPK;TQSS(0.001)S(0.999)CEDLPSTTQPK;T(0.008)QS(0.043)S(0.238)S(0.711)CEDLPSTTQPK 365.61 3.86E-104 5343760000 5887300 4567210 4895580 4161090 6277300 6867400 5724450 5219650 5425850 3878290 TRUE FALSE 6119735.15 5351592.79 5023162.837 4984141.182 5210286.788 5272550.426 5275752.651 5149689.129 5230574.718 4638166.671 1.319429763 1.153816404 1.083006108 1.074592945 1.123350487 1.136774679 1.137465086 1.110285484 1.127724614 1 22.14512323 4.710329134 2.917232378 1.106733985 1.348879441 0.734199538 0.039619686 0.175298569 2.222581067 0.009157031 0.096509542 51325.02084 -4.710329134 0.242145456 TQSSSCERDS(ph)PSTSR ddPTM_MDA-MB-175_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(0.772)PS(0.223)T(0.004)S(0.001)R;TQSSSCERDS(0.983)PS(0.016)T(0.001)SR;TQSSSCERDS(0.964)PS(0.035)TSR 153.36 1.61E-06 2746492000 736089 904092 857807 739464 862033 1057537 838749 800540 751543 720076 TRUE FALSE 765150.3621 1059362.768 880162.1551 885727.7721 715504.9386 811940.0589 773005.6617 789810.0707 724495.1142 861161.1055 0.888510126 1.23015631 1.022064454 1.028527376 0.830860723 0.942843393 0.89763188 0.917145544 0.841300321 1 19.71592364 3.374738907 5.951136395 0.903604843 1.058881569 0.359578262 0.089483043 0.196663133 9.809175848 0.023141374 0.031477384 2369.94849 -3.374738907 0.155276725 TQT(ph)PPLGQTPQLGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQTPPLGQTPQLGLK 15 0 D3DQV9;P78344;H0Y3P2;P78344-2;E9PKF8 D3DQV9 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 T(0.025)QT(0.975)PPLGQTPQLGLK;TQT(1)PPLGQTPQLGLK;T(0.002)QT(0.998)PPLGQTPQLGLK;T(0.048)QT(0.952)PPLGQTPQLGLK 209.12 2.85E-08 2168740000 1649830 1111400 1377220 1104400 1871530 1843050 1599780 1355010 1424890 900920 TRUE FALSE 1714966.562 1302274.305 1413111.485 1322847.024 1553407.999 1415029.569 1474385.063 1336848.307 1373608.487 1077438.025 1.59170785 1.208676763 1.311547813 1.227770872 1.441760884 1.31332804 1.368417514 1.240765851 1.274883989 1 20.03917346 -4.087983403 0.202488811 4.58E-17 1.380340123 0.506433348 0.103689574 76.99520925 1.066100885 31.4707412 0.233441761 8.17E-05 4.087983403 1.380340123 TQT(ph)PPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER;TQT(1)PPVS(1)PAPQPTEER 277.03 1.36E-34 11800450000 1694280 1424290 1698890 1817440 1857230 2579330 2551970 2010800 1779740 1062424 TRUE FALSE 1761171.483 1668900.728 1743164.469 2176924.207 1541538.708 1980319.698 2351939.923 1983848.515 1715687.505 1270585.641 1.386110015 1.313489366 1.3719378 1.713323476 1.213250534 1.558588129 1.851067607 1.561365445 1.350312367 1 20.27706219 TQT(ph)PPVS(ph)PAPQPTEERLPSSPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.024)QT(0.976)PPVS(0.571)PAPQPT(0.42)EERLPS(0.004)S(0.005)PVYEDAASFK;T(0.013)QT(0.987)PPVS(1)PAPQPTEERLPSSPVYEDAASFK;T(0.006)QT(0.994)PPVS(0.994)PAPQPT(0.006)EERLPSSPVYEDAASFK;T(0.004)QT(0.996)PPVS(0.764)PAPQPT(0.228)EERLPS(0.006)S(0.001)PVYEDAASFK;T(0.058)QT(0.941)PPVS(0.916)PAPQPT(0.063)EERLPS(0.017)S(0.005)PVYEDAASFK;T(0.132)QT(0.868)PPVS(0.955)PAPQPT(0.017)EERLPS(0.022)S(0.006)PVYEDAASFK 224.5 2.02E-34 13506660000 2505890 1441430 2047660 1414390 2685240 2662130 2374230 2148890 2224820 1276920 TRUE FALSE 2604824.472 1688984.39 2101023.702 1694152.12 2228803.864 2043890.652 2188131.649 2120087.644 2144749.163 1527108.026 1.705723779 1.106001908 1.375818649 1.109385906 1.459493255 1.338406071 1.432859766 1.388302339 1.404451503 1 20.54237069 -1.016776381 4.664605755 0.999990661 1.360291134 0.314537713 0.162942397 1.44E-05 3.03E-06 0.143515774 0.033826116 0.096210754 1.016776381 0.360300473 TQT(ph)PPVSPAPQPTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQT(1)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER;T(0.028)QT(0.972)PPVSPAPQPTEER;T(0.001)QT(0.999)PPVSPAPQPTEER;TQT(1)PPVSPAPQPTEER 281.02 1.91E-34 3955030000 361006 338391 357967 375720 412854 554433 514042 387486 336455 214166 TRUE FALSE 375258.7956 396507.0219 367295.9141 450036.2946 342677.2245 425674.3383 473750.0448 382292.384 324346.0503 256127.7272 1.46512367 1.548083162 1.434034175 1.757077609 1.337915376 1.661961174 1.849663252 1.492584923 1.266344936 1 17.96650392 1.069683547 2.545302467 1.00761536 1.578760168 0.62043389 0.144470109 0.160951667 2.137088544 0.134890269 0.036699684 11.74041766 -1.069683547 0.571144808 TQT(ph)PPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.182)QT(0.791)PPVS(0.095)PAPQPT(0.201)EERLPS(0.349)S(0.311)PVY(0.072)EDAASFK 79.019 0.0069728 540390000 273700 151830 217990 140820 288630 287650 254090 223640 239550 133920 TRUE FALSE 284505.8873 177905.6214 223670.9985 168673.7757 239568.7757 220847.6469 234173.7619 220642.4716 230928.6423 160159.0599 1.776395837 1.110805854 1.39655539 1.053164122 1.495817819 1.378926968 1.46213247 1.377645896 1.441870615 1 17.28914589 -1.044379266 4.678939443 0.999987282 1.376459125 0.271067058 0.190083438 11541886.21 2576247.736 1509.370734 0.040749108 0.090286067 1.044379266 0.376471843 TQT(ph)PPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.143)QT(0.822)PPVS(0.035)PAPQPT(0.366)EERLPS(0.156)S(0.477)PVYEDAASFK 194.99 3.45E-18 419890000 24604 19745 29300 18312 34503 33407 35345 32382 25563 19027 TRUE FALSE 25575.38492 23136.05016 30063.58207 21934.05894 28638.19238 25648.73054 32574.56654 31947.97226 24642.99262 22754.97636 1.12394689 1.016746833 1.321187137 0.96392361 1.258546348 1.127170169 1.431535943 1.403999361 1.082971577 1 14.47389447 3.093673437 24.99999996 1.259020211 1.114859497 0.072407789 0.155341914 30.09806365 8017.116008 0.044743418 0.053478611 1240.719011 -3.093673437 -0.144160714 TQTGDSSS(ph)ISSFSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WT45;A0A087WXA6;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 TQTGDS(0.002)S(0.282)S(0.716)ISSFSYR;TQTGDS(0.003)S(0.059)S(0.935)IS(0.003)SFSYR;TQTGDSS(0.205)S(0.795)ISSFSYR;TQTGDS(0.004)S(0.202)S(0.793)IS(0.001)SFSYR 322.37 1.03E-56 962520000 1142760 1182160 1328250 1356840 1628200 1883660 1361630 1316810 1331250 1224480 TRUE FALSE 1187877.047 1385186.784 1362865.286 1625218.902 1351439.146 1446208.512 1254901.883 1299160.316 1283338.573 1464393.412 0.811173444 0.945911647 0.930668818 1.109823965 0.922866174 0.987581957 0.856943136 0.887166184 0.876361886 1 20.48187176 -0.26517115 11.19967964 1 0.927379844 0.076596053 0.077440298 0 0 0.07626192 0.017975107 0.543036286 0.26517115 -0.072620156 TQTPPVS(ph)PAPQPTEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVS(1)PAPQPTEER;TQTPPVS(1)PAPQPTEER 340.49 5.22E-72 681190000 351680 360010 423470 512470 381170 601780 681150 516870 498530 313830 TRUE FALSE 365564.598 421838.917 434505.9761 613835.0364 316378.8596 462025.7151 627759.6831 509942.2031 480588.0027 375318.9799 0.974010422 1.123947734 1.15769785 1.635502251 0.842959926 1.231021451 1.672603084 1.358690155 1.280478815 1 18.51775772 2.464319206 24.86101767 1.379497988 1.159674155 0.092537291 0.245486999 409.5158161 795256.0164 0.082981165 0.0694657 291.2857275 -2.464319206 -0.219823834 TQTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 2 T(0.009)QT(0.046)PPVS(0.944)PAPQPTEERLPS(0.539)S(0.46)PVY(0.001)EDAASFK 141.76 2.90E-08 102790000 124010 110680 163500 124030 186650 208540 195180 187790 223640 145490 TRUE FALSE 128906.0106 129688.429 167760.9443 148562.7638 154923.2997 160109.7455 179881.2816 185272.9822 215591.2401 173995.9799 0.740856258 0.74535302 0.964165634 0.853828714 0.890384363 0.920192211 1.033824354 1.064811855 1.239058742 1 17.40869445 2.47119622 0.788462266 1.124045176 0.806096299 0.684740701 0.080499601 0.37101048 0.464900455 0.060142338 0.044240095 295.934924 -2.47119622 -0.317948877 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.5)S(0.5)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.87)S(0.13)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.634)S(0.366)PVYEDAASFK 291.89 4.25E-81 17767200000 1299865 980389 1318697 948552 1659474 1714376 1429705 1313290 1537379 971050 TRUE FALSE 1351184.674 1148763.184 1353063.327 1136172.754 1377397.202 1316238.156 1317640.986 1295687.496 1482049.03 1161308.656 1.163501768 0.989197126 1.165119472 0.978355538 1.186073311 1.133409408 1.134617382 1.115713286 1.27618874 1 20.14732004 3.202522008 24.99999829 1.143755669 1.074488051 0.127027429 0.085805287 330.8445012 229506.1769 0.022745789 0.027187448 1594.123663 -3.202522008 -0.069267618 TQTPPVSPAPQPTEERLPSS(ph)PVYEDAASFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YCD9;H0YEV2 Q14247 CTTN Src substrate cortactin 1 TQTPPVSPAPQPTEERLPS(0.014)S(0.986)PVYEDAASFK;TQTPPVSPAPQPTEERLPS(0.026)S(0.974)PVYEDAASFK;TQTPPVSPAPQPT(0.002)EERLPS(0.237)S(0.757)PVY(0.005)EDAASFK;TQTPPVSPAPQPTEERLPS(0.214)S(0.781)PVY(0.004)EDAASFK;TQTPPVSPAPQPTEERLPS(0.25)S(0.75)PVYEDAASFK 271.08 1.95E-71 3298650000 2166550 1683283 2273560 1714692 2742450 2798090 2437010 2304120 2461760 1605175 TRUE FALSE 2252087.067 1972373.761 2332810.841 2053852.96 2276289.329 2148276.003 2245990.788 2273237.04 2373161.738 1919678.308 1.173158574 1.027450148 1.215209252 1.069894342 1.185766031 1.119081251 1.169982897 1.184176031 1.236228866 1 20.87243314 3.210536436 24.98577072 1.160009122 1.12141393 0.019670047 0.075758126 649.069515 578695.1491 0.020299301 0.024267373 1623.814577 -3.210536436 -0.038595192 TQTVCNFTDGALVQHQEWDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TQTVCNFTDGALVQHQEWDGK 21 0 Q01469;I6L8B7;A8MUU1 Q01469 FABP5;FABP5P3 "Fatty acid-binding protein, epidermal;Putative fatty acid-binding protein 5-like protein 3" 0 ; 356.38 1.32E-95 911480000 1169300 789230 1037360 907680 1218430 1411050 1418960 1115700 1149310 631020 FALSE TRUE 1215464.867 924774.1131 1064394.454 1087216.395 1011321.704 1083355.022 1307738.207 1100745.866 1107946.558 754656.2874 1.610620473 1.225424248 1.410436077 1.440677581 1.340109028 1.435560851 1.732892483 1.458605573 1.468147256 1 19.52546018 2.475278161 24.99933519 1.478771806 1.396700485 0 0.193582508 234.0574108 3174608.096 0.062247801 0.052427764 298.7295337 -2.475278161 -0.082071321 TQVLS(ph)PDSLFTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TQVLSPDSLFTAK 13 0 P55196-5;P55196;J3KN01;A8MQ02;H0Y8L4;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TQVLS(0.999)PDS(0.001)LFTAK;T(0.005)QVLS(0.986)PDS(0.009)LFTAK;TQVLS(1)PDSLFTAK;TQVLS(0.988)PDS(0.012)LFTAK 233.14 1.31E-16 114499000 476116 361504 403692 330767 526386 586164 538568 452651 474246 363871 TRUE FALSE 494913.4273 423589.4999 414212.5452 396191.7254 436911.0957 450036.2944 496353.6329 446583.9537 457177.9791 435164.5557 1.137301788 0.973400738 0.951852672 0.910441166 1.004013516 1.034174977 1.140611353 1.026241563 1.050586435 1 18.73120153 2.70214795 3.704191929 1.058789966 0.986307211 0.14842762 0.06451373 0.374478239 10.99391637 0.02162932 0.021030423 503.6721642 -2.70214795 -0.072482755 TRAEQSHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRAEQSHEK 9 1 D3DX86;H3BLZ2;Q9H9R9;Q9H9R9-2;Q9H9R9-3 D3DX86 MGC3101;DBNDD1 Dysbindin domain-containing protein 1 0 69.276 0.033467 14521000 20578 11492 16626 11853 25600 21181 21839 15763 20508 15765 FALSE TRUE 21390.43533 13465.6616 17059.28722 14197.48802 21248.52114 16262.03375 20127.20211 15551.72277 19769.92109 18853.84991 1.134539387 0.714212835 0.904817175 0.75302859 1.127012321 0.862531198 1.067538047 0.824856612 1.048588017 1 14.20257153 3.254611744 24.99997138 0.968979974 0.867058919 0.129746415 0.135435184 517.1881199 805526.6827 0.034920281 0.047132916 1797.263455 -3.254611744 -0.101921055 TRAS(ph)LPVVR ddPTM_MDA-MB-175_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(0.005)RAS(0.995)LPVVR;TRAS(1)LPVVR;T(0.003)RAS(0.997)LPVVR;T(0.044)RAS(0.956)LPVVR 155.86 6.67E-05 758330000 358798 352721 382912 341865 426993 501343 363015 370635 350052 371550 TRUE FALSE 372963.6221 413298.088 392891.0013 409484.8766 354412.8824 384913.6862 334560.9357 365667.2441 337453.6969 444348.1087 0.839350083 0.930122307 0.884196407 0.921540721 0.79760187 0.866243557 0.752925306 0.822929674 0.75943543 1 18.76133082 3.237192603 24.99992544 0.820471052 0.895710523 0.139526399 0.069500386 53.03975562 969292.1072 0.018093956 0.022775001 1726.603445 -3.237192603 0.075239471 TRDDGDEEGLLT(ph)HS(ph)EEELEHS(ph)QDTDADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 3 T(0.001)RDDGDEEGLLT(0.998)HS(0.997)EEELEHS(0.579)QDT(0.425)DADDGALQ 89.915 0.00013905 78782000 19442 19268 19141 19357 20735 26339 17043 18940 17618 21505 TRUE FALSE 20209.58517 22577.12912 19639.83018 23185.75683 17210.47211 20222.16642 15707.12513 18686.14028 16983.93162 25718.49301 0.785799742 0.877855833 0.763646228 0.901520817 0.669186647 0.786288933 0.610732717 0.726564355 0.660378181 1 14.65051849 3.232629756 24.99970348 0.721738701 0.830569282 0.129055717 0.106874555 217.7560383 917882.9471 0.027927748 0.034220469 1708.558116 -3.232629756 0.10883058 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 2 TRDDGDEEGLLT(1)HS(1)EEELEHSQDTDADDGALQ;T(0.003)RDDGDEEGLLT(0.622)HS(0.662)EEELEHS(0.544)QDT(0.169)DADDGALQ 198.52 1.37E-25 2381200000 586570 633430 628630 585730 799040 888950 631420 599970 488110 545640 TRUE FALSE 609728.2365 742216.6751 645012.6142 701585.6458 663219.4662 682504.8347 581927.6505 591928.3835 470543.0164 652547.7111 0.934381082 1.137413652 0.988452803 1.075148428 1.016353984 1.045907944 0.891777935 0.907103609 0.721085996 1 19.31572386 2.200538861 4.910228318 0.874137737 1.037243638 0.461226963 0.080909659 0.159849514 8.939074895 0.028628196 0.021399057 158.6860906 -2.200538861 0.163105901 TRDDGDEEGLLTHS(ph)EEELEHS(ph)QDT(ph)DADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 3 TRDDGDEEGLLT(0.04)HS(0.962)EEELEHS(0.999)QDT(1)DADDGALQ 135.67 3.55E-08 217570000 27476 20178 25639 27141 29221 34156 20970 24305 22353 24426 TRUE FALSE 28560.7737 23643.41454 26307.1734 32509.40879 24254.02486 26223.78664 19326.31661 23979.23123 21548.5199 29211.80704 0.977713349 0.809378705 0.900566451 1.112885922 0.830281565 0.897711895 0.661592642 0.820874628 0.737664735 1 14.83426399 2.687620716 2.37612071 0.791710872 0.933739487 0.18753005 0.113147453 0.422788254 4.707881516 0.038915211 0.037444687 487.1029004 -2.687620716 0.142028616 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLT(0.002)HS(0.998)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.122)HS(0.878)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.371)HS(0.629)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.004)HS(0.996)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.003)HS(0.991)EEELEHS(0.005)QDTDADDGALQ;TRDDGDEEGLLT(0.064)HS(0.936)EEELEHSQDTDADDGALQ;TRDDGDEEGLLT(0.043)HS(0.957)EEELEHSQDTDADDGALQ 314.57 2.37E-104 38418270000 4420701 4359593 3841636 4158768 5211077 6191277 4622595 4294498 3661062 4148103 TRUE FALSE 4595233.689 5108319.185 3941752.19 4981359.898 4325299.993 4753446.746 4260263.925 4236937.279 3529301.094 4960844.363 0.926300717 1.029727766 0.794572839 1.004135493 0.871887864 0.958193081 0.858777985 0.854075832 0.71143153 1 22.24215427 2.126834691 5.354266552 0.84318161 0.929588427 0.138768255 0.089502729 0.358383794 15.47286891 0.031962627 0.023383863 133.9166852 -2.126834691 0.086406816 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 1 TRDDGDEEGLLTHSEEELEHS(0.04)QDT(0.96)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.03)QDT(0.97)DADDGALQ;TRDDGDEEGLLTHSEEELEHS(0.018)QDT(0.982)DADDGALQ 164.11 8.59E-14 1193276000 331877 334491 344878 345171 414846 462229 314673 353378 278524 353139 TRUE FALSE 344979.7602 391937.2273 353865.804 413444.7936 344330.6251 354883.3199 290008.108 348641.5459 268499.9756 422329.8258 0.816849152 0.92803587 0.837889683 0.978961864 0.815312119 0.840298975 0.686686306 0.825519593 0.635758971 1 18.68801061 2.794802614 2.342468998 0.777198558 0.888017801 0.139093973 0.101267341 0.466228833 5.035890126 0.032125284 0.033106053 623.4514134 -2.794802614 0.110819243 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9;Q9UKM9-2 Q9UKM9 RALY RNA-binding protein Raly 0 ; 100.1 1.62E-05 121052000 84436 84426 74714 81281 107049 115760 87466 87128 74754 76197 FALSE TRUE 87769.59848 98925.50876 76661.10822 97358.1392 88852.84922 88876.49436 80610.18637 85960.19167 72063.61814 91126.34327 0.963163837 1.085586288 0.841261763 1.068386327 0.975051187 0.975310664 0.884598059 0.943307814 0.790809941 1 16.47558056 2.316967493 5.474063931 0.904174273 0.987206103 0.198634779 0.078935576 0.3191214 16.36444541 0.026172578 0.021582328 207.4758216 -2.316967493 0.083031829 TRDELDQFLDKMDDPDYWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRDELDQFLDKMDDPDYWR 19 2 Q14137;Q14137-2;A0A075B729 Q14137 BOP1 Ribosome biogenesis protein BOP1 0 56.817 0.051721 42019000 21795 20487 21490 17007 30364 26381 20457 20266 24594 19252 FALSE TRUE 22655.48343 24005.48288 22050.04705 20370.93384 25202.73813 20254.41256 18853.52689 19994.36742 23708.86674 23024.0608 0.983991644 1.042625934 0.957695832 0.884767201 1.094626111 0.879706353 0.818861931 0.868411858 1.029743057 1 14.49085469 TRDELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRDELER 7 1 A0A5K1VW66;P35240-4;P35240-6;P35240-5;P35240-3;P35240;P35240-2;F8VVF8;F8VW54;F8VWE0;Q12999 A0A5K1VW66 NF2;TSPAN31 Merlin;Tetraspanin-31 0 ; 104.44 0.0074343 240420000 197955 163455 168168 164277 194327 221840 164375 139253 177802 157581 FALSE TRUE 205770.4163 191527.1247 172550.5962 196770.5003 161295.366 170321.022 151490.858 137386.5413 171402.9408 188455.9799 1.091875229 1.016296351 0.915601597 1.044119165 0.855878206 0.903770855 0.803852752 0.729011313 0.909511817 1 17.52386805 3.184067618 1.170900852 0.829456242 1.026832929 0.382504343 0.084122673 0.406793002 1.187855228 0.033110924 0.048769953 1527.803912 -3.184067618 0.197376686 TRDELEVIHLIEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;;;;;; 195.23 1.22E-08 1711059000 483255 550249 560477 562210 647874 726413 611163 604433 593290 476020 FALSE TRUE 502334.2806 644749.9854 575083.4911 673413.46 537748.6089 557714.5896 563258.4471 596331.5643 571937.6088 569287.005 0.882391968 1.132557005 1.01018201 1.182906783 0.944600183 0.979672089 0.989410336 1.047506019 1.004656006 1 19.11879664 TREFEDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TREFEDRDR 9 2 Q13951-2;A0A494C0A9;Q13951;J3KS23 Q13951-2 CBFB Core-binding factor subunit beta 0 139.15 6.55E-05 76936000 60775 58747 59451 53701 78899 90857 57633 67357 65648 75170 FALSE TRUE 63174.44393 68836.34026 61000.3419 64322.89752 65487.77616 69756.8387 53115.57486 66454.18959 63285.3413 89898.12228 0.702733743 0.765714995 0.678549678 0.715508799 0.728466563 0.775954346 0.590841872 0.739216659 0.703967332 1 16.45600336 -1.137294506 3.413127965 1.000325121 0.71114891 0.75815055 0.048931374 6803866.944 11100041.31 24778.06694 0.011085076 0.072896301 1.137294506 -0.289176211 TRGTS(ph)KTDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRGTSKTDSK 10 2 O75494-2;O75494 O75494-2 SRSF10 Serine/arginine-rich splicing factor 10 1 T(0.014)RGT(0.177)S(0.799)KT(0.01)DS(0.001)K 57.434 0.092635 54736000 100550 33618 61713 26556 110800 86014 76681 58855 78805 36107 TRUE FALSE 104519.7916 39391.62999 63321.29148 31808.69754 91966.25558 66038.55205 70670.54285 58066.14499 75968.82344 43181.47534 2.42047755 0.912234463 1.466399445 0.736628318 2.129761775 1.529325979 1.636593986 1.34470035 1.759291984 1 15.39812491 -0.768138405 5.431608479 0.99999991 1.511034261 0.101866724 0.477029094 5.56E-07 1.26E-07 0.423823298 0.099896089 0.170553877 0.768138405 0.511034351 TRHS(ph)PT(ph)PQQSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 2 TRHS(1)PT(1)PQQSNR;TRHS(1)PT(1)PQQSNR 126.07 0.00067392 6676800000 3089900 3275500 3053800 2899700 3318600 3652300 2800800 3001200 2890600 2625900 TRUE FALSE 3211891.638 3838041.645 3133384.537 3473252.005 2754505.557 2804108.676 2581265.977 2960973.823 2786567.871 3140394.829 1.022766822 1.222152581 0.997767704 1.105992142 0.877120779 0.892915964 0.821955874 0.942866736 0.887330423 1 21.58251452 3.239466098 24.9988471 0.897708438 1.0904256 0.619066531 0.07039413 14.30668632 394975.3873 0.018672436 0.023888864 1735.665766 -3.239466098 0.192717162 TRHS(ph)PTPQQSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TRHSPTPQQSNR 12 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 TRHS(0.983)PT(0.017)PQQSNR;TRHS(0.988)PT(0.012)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;TRHS(0.999)PT(0.001)PQQSNR;T(0.06)RHS(0.923)PT(0.017)PQQSNR;T(0.068)RHS(0.928)PT(0.003)PQQSNR;T(0.005)RHS(0.993)PT(0.002)PQQSNR 163.41 3.64E-05 83236390000 12302183.6 13133047.6 14701149 13596119.6 16604929.8 19546656 15103106 16258819.9 14556440.5 13428437.9 TRUE FALSE 12787883.31 15388546.36 15084273.02 16285391.48 13782429.76 15007241.38 13919285.09 16040897.01 14032557.05 16059483.2 0.796282368 0.958221767 0.93927512 1.01406697 0.858211288 0.934478475 0.866733064 0.998842666 0.87378634 1 23.93692213 -4.999722514 0.009391491 2.01953193 0.000839964 0.125999119 0.064394583 34875.09665 24.88600812 3079.658763 2319.56793 1.00E-05 4.999722514 -2.018691966 TRIEGLLAAFPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRIEGLLAAFPK 12 1 B0YIW6;P48444;Q6P1Q5;E9PK34 B0YIW6 ARCN1 Coatomer subunit delta 0 ; 100.55 0.0028905 415790000 1149240 1005560 1255990 914180 1995850 1659080 1368950 1359160 1372430 1297380 FALSE TRUE 1194612.883 1178257.108 1288722.131 1095002.075 1656596.13 1273783.814 1261648.122 1340942.683 1323036.512 1551576.771 0.769934756 0.759393367 0.830588699 0.705735028 1.06768557 0.820960869 0.813139347 0.86424514 0.852704511 1 20.56530365 -2.562056983 0.025353535 1.984359579 3.06E-06 0.306821308 0.086557236 1600.22528 4.892225276 242.092336 149.85609 0.002741214 2.562056983 -1.984356522 TRLQQELDDLLVDLDHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 266.7 2.13E-31 834553000 650735 655893 761558 432742 1170696 1024586 588996 831634 867662 1088608 FALSE TRUE 676426.5203 768537.5206 781404.8271 518337.076 971701.5121 786641.4293 542828.9545 820487.3065 836435.0141 1301899.895 0.519568765 0.590319981 0.600203464 0.398138964 0.746371911 0.604225741 0.416951377 0.630223038 0.642472603 1 20.31218709 0.656157576 1.567377549 0.999600359 0.560964205 0.653365635 0.095439073 0.770885338 2.706698598 0.087519988 0.025195378 4.530619356 -0.656157576 -0.438636153 TRLS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 T(0.005)RLS(0.995)PPR;T(0.002)RLS(0.998)PPR;T(0.011)RLS(0.989)PPR;T(0.005)RLS(0.995)PPR;T(0.012)RLS(0.988)PPR;T(0.002)RLS(0.998)PPR;T(0.003)RLS(0.997)PPR;T(0.002)RLS(0.998)PPR;T(0.002)RLS(0.998)PPR;T(0.02)RLS(0.98)PPR;T(0.035)RLS(0.965)PPR;T(0.008)RLS(0.992)PPR;T(0.005)RLS(0.995)PPR;T(0.003)RLS(0.997)PPR 93.111 0.0091904 20126026300 837361.9 905867.2 897944.3 812850.9 1213443 1330737.7 1117150.27 1002557.2 1061038.4 914072.1 TRUE FALSE 870421.5944 1061442.845 921345.4661 973630.3819 1007182.392 1021694.037 1029585.113 989119.5606 1022851.835 1093167.027 0.796238427 0.970979566 0.842822225 0.89065107 0.921343553 0.934618417 0.941836963 0.904820157 0.935677541 1 20.06008242 7.999999996 0.035016973 1.28139621 0.344398296 0.445959079 0.042060064 960.5701862 2.569871445 20.30445001 57.11774158 99999999.18 -7.999999996 -0.936997914 TRNEELAQTWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRNEELAQTWK 11 1 Q8TAT6;Q8TAT6-2;I3L283;I3L281;I3L3I1 Q8TAT6 NPLOC4 Nuclear protein localization protein 4 homolog 0 80.318 0.016444 0 42766 33251 41898 34472 58249 55493 49937 43748 46074 27906 FALSE TRUE 44454.4347 38961.60059 42989.8963 41290.45871 48347.85579 42605.59175 46022.80745 43161.62962 44415.80574 33373.64641 1.332022104 1.16743613 1.288139024 1.23721748 1.448683647 1.276623814 1.379016452 1.2932848 1.330864635 1 15.0264217 -1.005280227 5.09634893 0.999997401 1.304991695 0.617054603 0.072296454 2.08E-06 4.05E-07 0.068057025 0.016041058 0.098791544 1.005280227 0.304994294 TRNS(ph)GIWESPELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 T(0.001)RNS(0.999)GIWESPELDR;TRNS(1)GIWESPELDR;T(0.001)RNS(0.999)GIWESPELDR;T(0.001)RNS(0.775)GIWES(0.224)PELDR;TRNS(1)GIWESPELDR;TRNS(1)GIWESPELDR;T(0.082)RNS(0.918)GIWESPELDR 267.32 3.38E-25 6273690000 1584596 1719530 1664050 1726332 2092610 2161390 1827600 1749199 1660713 1469720 TRUE FALSE 1647157.074 2014845.901 1707416.51 2067795.317 1736908.9 1659439.929 1684347.936 1725753.849 1600944.264 1757683.495 0.937118132 1.146307573 0.971401572 1.176432118 0.988180696 0.944106225 0.958277154 0.981834246 0.910826249 1 20.74524388 3.016794285 24.98724269 0.960470976 1.061006277 0.309456796 0.069808926 262.516855 390580.9393 0.018328488 0.021901954 1039.427698 -3.016794285 0.1005353 TRPAS(ph)QPTPFALHHAASCEVDPSSGDSISLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TRPASQPTPFALHHAASCEVDPSSGDSISLAR 32 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 T(0.031)RPAS(0.924)QPT(0.046)PFALHHAASCEVDPSSGDSISLAR;T(0.031)RPAS(0.939)QPT(0.031)PFALHHAASCEVDPSSGDSISLAR;T(0.053)RPAS(0.829)QPT(0.118)PFALHHAASCEVDPSSGDSISLAR;T(0.038)RPAS(0.789)QPT(0.173)PFALHHAASCEVDPSSGDSISLAR 278.02 9.14E-74 2050310000 372938 579404 606686 592923 649728 861370 597821 681140 622371 677870 TRUE FALSE 387661.8802 678912.1299 622496.7356 710201.3997 539287.4666 661329.8717 550962.2279 672010.4324 599971.9893 810685.6479 0.478190136 0.837454236 0.767864507 0.876050293 0.665223898 0.815766103 0.679624993 0.828940828 0.740079698 1 19.62878308 -5 0.188391047 2.040671219 0.706612281 0.355203142 0.107568645 153.0154049 1.493921315 59.85058746 0.279026555 1.00E-05 5 -1.334058938 TRPDGNCFYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRPDGNCFYR 10 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5GYJ8 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ;; 180.19 1.85E-06 1096320000 264985 259249 267533 266373 331848 372405 306642 282127 267829 273881 FALSE TRUE 275446.8124 303772.9991 274505.1298 319060.7844 275440.5955 285919.5826 282606.5988 278345.549 258189.8866 327542.7382 0.840949227 0.927430114 0.838074235 0.974104284 0.840930246 0.872922979 0.862808317 0.849799176 0.788263199 1 18.32132364 TRPEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRPEDYR 7 1 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 0 63.565 0.071744 116330000 83267 84165 84807 97730 111980 120000 95536 88987 85657 85753 FALSE TRUE 86554.44546 98619.68404 87017.14009 117060.7023 92945.6796 92131.81862 88047.63868 87794.27482 82574.2213 102554.6585 0.843983557 0.961630466 0.848495245 1.141446951 0.906303828 0.898367953 0.858543531 0.856073006 0.805172798 1 16.6460335 2.765867378 3.365203079 0.869604243 0.949409908 0.086975308 0.090208647 0.484872457 11.46983909 0.02871318 0.029262439 583.2669624 -2.765867378 0.079805665 TRPGS(ph)FQSLSDALSDTPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRPGSFQSLSDALSDTPAK 19 1 G3V4K3;Q9H9C1;Q9H9C1-2 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 1 T(0.008)RPGS(0.97)FQS(0.021)LS(0.002)DALSDTPAK;T(0.007)RPGS(0.94)FQS(0.048)LS(0.005)DALSDTPAK 195.97 5.19E-16 846800000 507610 362290 547170 400180 793760 718050 682590 553850 640410 408550 TRUE FALSE 527650.8348 424510.4893 561429.6997 479334.4096 658836.9587 551293.7697 629086.8122 546426.5467 617361.7692 488597.5503 1.07992935 0.868834666 1.149063681 0.981041369 1.348424605 1.128318734 1.287535747 1.118357115 1.263538405 1 18.8982871 3.265857404 24.99861496 1.195183657 1.018178895 0.351427523 0.113921414 221.5205922 202868.7575 0.028847212 0.039049983 1844.409727 -3.265857404 -0.177004761 TRPKS(ph)PR ddPTM_MDA-MB-175_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 58.37 0.086604 740540000 979250 688560 994560 660770 1175400 1258100 1151800 1017400 1001500 663560 TRUE FALSE 1017911.546 806814.8237 1020479.051 791468.3338 975605.9278 965925.3417 1061518.906 1003763.417 965456.2106 793571.8774 1.282696092 1.016687772 1.28593147 0.997349272 1.229385712 1.217186961 1.33764683 1.264867677 1.216595797 1 19.59800137 3.044223408 24.99992144 1.23620571 1.142334195 0.0423462 0.120324769 268.3614188 151705.6047 0.032048707 0.038305506 1107.193195 -3.044223408 -0.093871515 TRPWLQELSMGS(ph)PGPVTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRPWLQELSMGSPGPVTNK 19 1 A0A1B0GV70;Q96N21-2;Q96N21 A0A1B0GV70 ENTHD2 AP-4 complex accessory subunit tepsin 1 TRPWLQELS(0.002)MGS(0.998)PGPVTNK;TRPWLQELSMGS(1)PGPVTNK 152.99 3.04E-08 399490000 503430 396000 500650 385130 583970 606390 522920 504100 498320 355080 TRUE FALSE 523305.8051 464009.9195 513697.3503 461307.5645 484706.988 465565.1124 481932.164 497343.364 480385.5605 424651.1276 1.232319359 1.092685005 1.209692656 1.086321299 1.141423998 1.096347289 1.134889637 1.171181075 1.13124758 1 18.69591856 -1.898736929 1.596216596 0.90150442 1.142919494 0.466333275 0.046204334 75481.19587 23992.33176 27877.10711 0.011508211 0.012625921 1.898736929 0.241415074 TRQPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRQPDAK 7 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 0 70.69 0.051386 38159000 47071 36918 42101 28887 58033 57958 46724 42874 47732 32542 FALSE TRUE 48929.39943 43258.37932 43198.18665 34600.76238 48168.57139 44498.13286 43061.65079 42299.34416 46014.13464 38917.98185 1.257244007 1.111526787 1.109980133 0.889068773 1.237694482 1.143382333 1.106471835 1.086884318 1.182336094 1 15.24814928 0.110011936 0.01014733 4.70E-05 2.159111103 0.093288687 0.097912794 9428.346368 31.34948804 3446.899243 3221.713143 1.288284959 -0.110011936 2.159064102 TRS(ph)EITFGQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRSEITFGQVK 11 1 F5H5A3;Q8IVH8-3;Q8IVH8-2;Q8IVH8;H7C1A4 F5H5A3 MAP4K3 Mitogen-activated protein kinase kinase kinase kinase;Mitogen-activated protein kinase kinase kinase kinase 3 1 T(0.036)RS(0.942)EIT(0.022)FGQVK 90.731 0.0081385 0 100590 87927 80178 68939 157050 123360 95432 89950 89630 86735 TRUE FALSE 104561.3709 103027.7783 82267.50455 82574.92844 130354.6971 94711.50954 87951.79047 88744.36738 86404.23381 103729.0626 1.008023868 0.993239269 0.793099855 0.796063575 1.256684422 0.913066282 0.847899212 0.85554005 0.832979993 1 16.66246064 2.480601296 24.95891077 0.870813915 0.964674307 0.086832624 0.128339879 350.3638087 2512846.752 0.045277157 0.038623931 302.4135843 -2.480601296 0.093860393 TRS(ph)EREWDRDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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(0.023)RS(0.977)EREWDRDK;T(0.169)RS(0.831)EREWDRDK;T(0.087)RS(0.913)EREWDRDK;T(0.019)RS(0.981)EREWDRDK 107.61 0.012015 2145780000 499536 402554 566231 389947 884370 753830 655840 616872 754760 593430 TRUE FALSE 519258.067 471689.5181 580987.445 467077.3527 734045.1033 578764.4069 604433.5471 608603.8398 727596.335 709701.2466 0.731657256 0.664631097 0.818636642 0.658132355 1.034301555 0.815504284 0.851673222 0.857549346 1.02521496 1 19.43685231 4.699227046 0.197107971 1.031748523 0.391457011 0.509217202 0.092515763 11.92829841 0.445363471 0.206060628 1.917635036 50029.60175 -4.699227046 -0.640291512 TRS(ph)LDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRSLDFR 7 1 Q9H1K0 Q9H1K0 RBSN Rabenosyn-5 1 T(0.028)RS(0.972)LDFR;T(0.165)RS(0.835)LDFR;T(0.414)RS(0.586)LDFR 116.75 0.0032622 630870000 405480 408680 487010 406360 660460 641690 531260 518220 528300 457250 TRUE FALSE 421488.6635 478867.6109 499701.8807 486736.7951 548195.2451 492667.2224 489618.453 511274.1085 509286.5862 546839.3829 0.770772327 0.875700664 0.913800096 0.890090967 1.002479452 0.900935883 0.895360627 0.93496212 0.931327556 1 19.06075762 5.583615795 0.906278776 0.933825686 0.21492173 0.658276203 0.036494625 5.067037047 1.057601529 0.010994872 5.179672162 383367.943 -5.583615795 -0.718903956 TRS(ph)LSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TRSLSSLR 8 1 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 T(0.002)RS(0.998)LSSLR;T(0.007)RS(0.992)LS(0.001)SLR;T(0.205)RS(0.791)LS(0.004)SLR;T(0.007)RS(0.989)LS(0.003)SLR;T(0.162)RS(0.838)LSSLR;T(0.172)RS(0.828)LSSLR 127.83 0.00070221 1405367000 310429 330118 407939 299376 542118 525900 396253 440523 438662 434672 TRUE FALSE 322684.9766 386813.1985 418570.2255 358591.6793 449968.976 403767.6951 365193.6544 434618.5097 422874.6403 519837.6561 0.620741827 0.744103845 0.805194123 0.689814743 0.865595192 0.776718828 0.702514814 0.836065846 0.813474429 1 18.98770162 -5 0.115993069 1.770709715 0.640430968 0.629709552 0.061194636 104.3166443 0.793096618 18.89995049 0.638431626 1.00E-05 5 -1.130278746 TRS(ph)NPEGAEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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(0.021)RS(0.979)NPEGAEDR;T(0.339)RS(0.661)NPEGAEDR;T(0.249)RS(0.751)NPEGAEDR;T(0.153)RS(0.847)NPEGAEDR;T(0.173)RS(0.827)NPEGAEDR;T(0.003)RS(0.997)NPEGAEDR;T(0.003)RS(0.997)NPEGAEDR 187.56 2.14E-06 4890170000 1426990 1419942 1589094 1449961 2040329 2297637 1838517 1645721 1675361 1370817 TRUE FALSE 1483328.667 1663805.993 1630507.095 1736758.958 1693514.605 1764045.628 1694409.233 1623662.802 1615065.085 1639402.345 0.904798429 1.014885698 0.99457409 1.05938543 1.033007309 1.076029709 1.033553013 0.990399219 0.985154797 1 20.64473854 5.081594128 1.686950409 1.024280983 0.73922696 0.592597069 0.028762948 2.056153546 2.688684576 0.008062396 1.257961474 120668.5595 -5.081594128 -0.285054024 TRS(ph)PDVIS(ph)SASTALSQDIPEIASEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 2 T(0.378)RS(0.423)PDVIS(0.271)S(0.264)AS(0.246)T(0.236)ALS(0.181)QDIPEIASEALSR 61.014 0.019757 37071000 8714.4 9123.2 9914.4 8176.7 11041 12625 10626 11486 8893.7 10065 TRUE FALSE 9058.451241 10690.03863 10172.77741 9794.026855 9164.254764 9693.035084 9793.106354 11332.04896 8573.617474 12037.04404 0.752547819 0.888095 0.845122554 0.813657142 0.761337645 0.805267061 0.81358067 0.941431212 0.712269345 1 13.55519353 -4.999999996 0.418454044 4.198234279 0.821683247 0.414889742 0.064240931 936.1743602 6.118400994 2751.611439 0.037269319 1.00E-05 4.999999996 -3.376551031 TRS(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9;Q6P2E9-2 Q6P2E9 EDC4 Enhancer of mRNA-decapping protein 4 1 T(0.171)RS(0.828)PDVISSASTALSQDIPEIASEALSR;T(0.204)RS(0.796)PDVISSASTALSQDIPEIASEALSR;T(0.19)RS(0.804)PDVIS(0.002)S(0.002)AS(0.001)T(0.001)ALSQDIPEIASEALSR;T(0.179)RS(0.821)PDVISSASTALSQDIPEIASEALSR 257.5 8.29E-54 5430490000 370690 389415 397298 389824 430946 503288 408904 433127 387131 360909 TRUE FALSE 385325.1274 456293.997 407651.9123 466930.0237 357693.9529 386406.9894 376853.036 427321.641 373198.2309 431622.2085 0.892737027 1.057160609 0.944464636 1.081802591 0.828719991 0.89524353 0.873108539 0.990036269 0.864640937 1 18.71940957 3.236571904 24.99990772 0.910692956 0.99500855 0.262263112 0.070123466 71.56809828 899678.7445 0.019031246 0.023852415 1724.137526 -3.236571904 0.084315594 TRS(ph)YDNLTTACDNTVPLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 T(0.235)RS(0.765)YDNLTTACDNTVPLASR;T(0.282)RS(0.718)YDNLTTACDNTVPLASR 286.78 1.64E-45 2406000000 534960 550720 574090 462240 723000 781000 585490 558220 595660 589200 TRUE FALSE 556080.6339 645301.876 589051.257 553669.6924 600104.7182 599624.5862 539597.7639 550737.974 574222.313 704642.4591 0.789167083 0.915786251 0.835957654 0.785745572 0.851644278 0.850962894 0.765775262 0.781584997 0.814913018 1 19.42653188 4.006633277 24.92288609 0.82067192 0.858325482 0 0.069220272 529.5635501 1989652.225 0.016050842 0.034547932 10153.90925 -4.006633277 0.037653563 TRSDIVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TRSDIVSR 8 1 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 ;;; 123.35 0.0012323 933530000 83762 127380 103726 112981 142597 160757 124363 120140 99483 167029 FALSE TRUE 87068.98844 149256.5241 106429.1848 135328.3046 118358.4129 123423.623 114615.1031 118529.7198 95902.62626 199755.1346 0.4358786 0.747197435 0.532798243 0.677470969 0.5925175 0.617874596 0.573778007 0.593375084 0.480100932 1 17.60787306 -1.457499102 3.479454655 1.005297909 0.59069271 0.681961536 0.08521115 5280356.713 3324549.581 202280.9325 0.017758254 0.03487393 1.457499102 -0.414605199 TRSYDNLT(ph)TACDNTVPLASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRSYDNLTTACDNTVPLASR 20 1 Q13615-3;Q13615-2;Q13615;G5E953 Q13615-3 MTMR3 Myotubularin-related protein 3 1 TRS(0.001)YDNLT(0.805)T(0.142)ACDNT(0.051)VPLAS(0.001)R 212.2 1.25E-21 145700000 125450 133460 161040 117410 190760 196080 160390 162900 151160 166040 TRUE FALSE 130402.8629 156380.7168 165236.8347 140633.3476 158334.6833 150543.3916 147818.2127 160716.592 145719.7811 198572.359 0.656701988 0.7875251 0.832124046 0.708222173 0.797365173 0.758128636 0.744404778 0.80936034 0.733837186 1 17.59930529 -4.999999999 0.376499619 4.250976286 0.758092259 0.681507081 0.049357846 317.0482482 2.397145141 840.5523766 0.031605199 1.00E-05 4.999999999 -3.492884027 TRT(ph)PAS(ph)INATPANINLADLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 2 T(0.146)RT(0.854)PAS(1)INATPANINLADLTR 150.24 1.68E-07 107260000 72000 101770 118150 94168 96187 140840 107380 105930 108390 95257 TRUE FALSE 74842.6156 119248.2058 121229.0861 112794.1493 79837.1681 108132.0445 98963.27501 104510.1816 104489.0651 113920.7853 0.656970678 1.046764254 1.064152478 0.990110356 0.700813007 0.949186262 0.868702535 0.917393444 0.917208082 1 16.79767147 0.591860838 1.948532942 0.999974764 0.906640036 0.051415343 0.12627746 9.155189532 39.21533529 0.118262608 0.03271113 3.907156779 -0.591860838 -0.093334728 TRT(ph)PASINATPANINLADLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 1 T(0.374)RT(0.626)PASINATPANINLADLTR 191.19 2.48E-17 201790000 78977 78720 72864 76216 99095 103300 81013 94869 92049 86199 TRUE FALSE 82095.07294 92239.54764 74762.8957 91291.29732 82250.8673 79310.14053 74662.98937 93597.43623 88736.17447 103088.0437 0.796358821 0.89476475 0.725233432 0.885566299 0.797870096 0.769343735 0.724264296 0.907936875 0.860780468 1 16.65351749 1.001028472 1.265814401 0.994667527 0.805594472 0.484628717 0.060412838 0.394252042 1.297922367 0.05487979 0.016905707 10.02370951 -1.001028472 -0.189073055 TRTDS(ph)TSDGRPAWMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRTDSTSDGRPAWMR 15 2 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 1 T(0.001)RT(0.002)DS(0.688)T(0.155)S(0.155)DGRPAWMR;TRTDS(0.956)T(0.037)S(0.006)DGRPAWMR;TRTDS(0.873)T(0.106)S(0.021)DGRPAWMR 136.49 1.78E-05 2655070000 346382 373550 420760 354893 497520 566200 362196 411860 423070 406049 TRUE FALSE 360057.4288 437704.3067 431725.3513 425089.7762 412951.7281 434708.6308 333806.1311 406339.6904 407843.7933 485606.5273 0.741459203 0.901355896 0.889043551 0.875379041 0.850383397 0.89518696 0.687400421 0.836767357 0.839864727 1 18.88942829 TRTFS(ph)ATVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TRTFSATVR 9 1 Q9Y2V2;H3BSW7;H3BUY4;H3BPY5;H3BNU9;H3BTK3;I3L3X8 Q9Y2V2 CARHSP1 Calcium-regulated heat stable protein 1 1 TRTFS(0.994)AT(0.006)VR;TRT(0.002)FS(0.981)AT(0.017)VR;TRT(0.001)FS(0.999)ATVR;TRTFS(1)ATVR;TRTFS(0.992)AT(0.008)VR;TRTFS(1)ATVR 140.63 6.58E-05 7721790000 1733823 985247 1489147 946526 3660420 2377830 2047490 2162370 1821460 2500640 TRUE FALSE 1802275.671 1154455.508 1527955.394 1133746.018 3038223.116 1825615.019 1887002.384 2133386.967 1755906.01 2990592.53 0.602648356 0.386029021 0.510920621 0.379104143 1.015926805 0.610452611 0.630979435 0.713365979 0.587143181 1 21.51199993 3.273780935 24.99998696 0.727906864 0.466646773 0.454580377 0.153240458 170.9588344 121348.3985 0.040116037 0.05431526 1878.369097 -3.273780935 -0.261260091 TRVEDTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRVEDTNR 8 1 O60437;K7EKI8 O60437 PPL Periplakin 0 65.347 0.058831 62134000 76288 59430 59861 53393 81620 95927 79087 59820 63405 72676 FALSE TRUE 79299.90915 69636.6402 61421.02684 63953.97604 67746.26155 73649.40804 72887.95428 59018.21075 61123.06644 86915.47073 0.912379677 0.801199598 0.706675421 0.735818094 0.779449976 0.847368224 0.83860737 0.679029985 0.703247258 1 16.40732538 4.698148289 3.837515129 0.772126832 0.921058857 0.132265021 0.09012667 0.370764592 10.3246735 0.020906915 0.142970172 49905.48602 -4.698148289 0.148932026 TRVEDTNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TRVEDTNRK 9 2 O60437;K7EKI8 O60437 PPL Periplakin 0 65.5 0.037336 25641000 27611 19068 21291 18693 30874 33031 24565 20065 25702 22700 FALSE TRUE 28701.1036 22342.78067 21845.86095 22390.41961 25626.04851 25360.05084 22639.53111 19796.06149 24776.99004 27147.63038 1.057223161 0.823010346 0.804705996 0.824765156 0.943951577 0.934153386 0.833941335 0.729200347 0.912675975 1 14.72853866 2.173428608 15.43054477 0.833370428 0.889082755 0 0.09687177 6.339535396 1497.435872 0.03637408 0.026864635 149.0831663 -2.173428608 0.055712327 TRWS(ph)GAQPLEQPSGSVLWMAAEVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TRWSGAQPLEQPSGSVLWMAAEVIR 25 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 T(0.205)RWS(0.795)GAQPLEQPSGSVLWMAAEVIR;T(0.206)RWS(0.794)GAQPLEQPSGSVLWMAAEVIR;T(0.183)RWS(0.817)GAQPLEQPSGSVLWMAAEVIR 274.53 3.10E-53 2102519000 271196 308334 322611 303113 366589 368864 333665 304735 335250 305676 TRUE FALSE 281903.0275 361287.966 331018.5077 363067.8467 304276.3327 283200.9262 307511.4654 300650.5258 323184.418 365567.3597 0.771138396 0.98829383 0.905492514 0.993162647 0.832339991 0.774688764 0.841189612 0.82242169 0.884062566 1 18.47977774 3.197177108 24.99918185 0.843483366 0.919146517 0.08353043 0.079876436 243.0880856 146845.2283 0.021663802 0.025893419 1574.624876 -3.197177108 0.075663151 TS(ph)FS(ph)VGSDDELGPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 T(0.447)S(0.553)FS(0.971)VGS(0.029)DDELGPIR 103.21 0.0021787 25176000 83550 92649 94980 96856 131580 141320 117510 118870 120990 100620 TRUE FALSE 86848.61851 108560.745 97455.25683 116013.8277 109214.0786 108500.5717 108299.2591 117276.7421 116635.5935 120334.5625 0.7217263 0.902157641 0.809869208 0.964093983 0.90758695 0.901657591 0.89998465 0.974589009 0.96926096 1 16.87669155 6.76784674 0.334732554 0.969368368 9.99E-31 0.680440512 0.045286988 15.46857627 0.468499262 0.03896695 7.992371444 5859313.566 -6.76784674 -0.969368368 TS(ph)FSFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFSFQK 7 0 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 T(0.051)S(0.949)FSFQK 118.67 0.005197 131820000 681150 471210 591050 466120 843160 748750 733840 604980 643620 387040 TRUE FALSE 708042.328 552136.652 606453.2486 558317.1448 699839.9644 574864.1599 676319.7033 596871.2326 620456.2419 462873.0777 1.529668417 1.192846762 1.310193394 1.206199219 1.511947871 1.241947712 1.461134242 1.28949222 1.340445733 1 18.82025713 -1.620874466 4.357775264 0.992493797 1.336949822 0.441961045 0.115348909 0.007692205 0.00066922 0.10212896 0.023681741 0.023940077 1.620874466 0.344456024 TS(ph)FSVGS(ph)DDELGPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 T(0.437)S(0.562)FS(0.042)VGS(0.959)DDELGPIR 87.647 0.010366 33411000 88427 91633 101860 92016 164260 154130 143210 118630 126870 106660 TRUE FALSE 91918.16624 107370.2549 104514.5553 110216.4902 136339.1439 118335.6434 131984.826 117039.9589 122303.9735 127557.9849 0.720599078 0.841736839 0.819349376 0.864050105 1.068840528 0.92770079 1.034704539 0.917543179 0.9588108 1 16.96079369 3.436208687 5.682757422 0.977160982 0.804789615 0.732304837 0.052308188 0.096340331 7.760350967 0.014148889 0.019549539 2730.289424 -3.436208687 -0.172371367 TS(ph)PADGKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.189)S(0.811)PADGKPR 100.69 0.0027201 189790000 195220 111430 139610 106250 199620 214590 165980 141220 162560 96034 TRUE FALSE 202927.4363 130567.2357 143248.3513 127265.9329 165688.6637 164754.7246 152970.0539 139327.1769 156709.4974 114850.0236 1.76689068 1.136849881 1.247264448 1.108105413 1.442652413 1.434520599 1.331911384 1.213122753 1.364470746 1 16.80939163 -3.692777336 0.276255365 1.16E-12 1.346210151 0.244301941 0.179247998 149.6911515 2.804924311 85.27298479 0.206683695 0.000202872 3.692777336 1.346210151 TS(ph)PADHGGSVGSESGGSAVDSVAGEHSVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPADHGGSVGSESGGSAVDSVAGEHSVSGR 31 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;A0A0A0MSW0;X6RE05 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 T(0.259)S(0.72)PADHGGS(0.008)VGS(0.013)ESGGSAVDSVAGEHSVSGR 171.22 4.47E-13 264740000 41163 28785 34972 32739 41645 50938 40387 41596 37092 32472 TRUE FALSE 42788.14702 33728.59983 35883.39905 39214.67648 34566.19778 39108.42147 37221.36141 41038.47366 35757.06617 38834.26669 1.101814214 0.86852676 0.924013819 1.009795725 0.890095288 1.00705961 0.958466957 1.05675933 0.920760689 1 15.2450426 TS(ph)PAKQQAPPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPAKQQAPPVR 12 1 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 T(0.44)S(0.56)PAKQQAPPVR 83.692 0.0076649 157000000 394610 247260 297940 139120 504660 417650 219680 260660 346210 246910 TRUE FALSE 410189.5075 289724.9816 305704.5612 166637.5208 418878.0735 320657.117 202460.9076 257166.2791 333749.9697 295287.2871 1.389120106 0.981163071 1.035278437 0.564323383 1.418544217 1.085915754 0.685640447 0.870901967 1.130255125 1 18.17175972 TS(ph)PAPWKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPAPWKR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.295)S(0.705)PAPWKR 57.108 0.069438 157750000 349940 272600 346490 302670 433570 488140 359560 290380 333090 279960 TRUE FALSE 363755.9014 319416.9295 355519.814 362537.2226 359871.9263 374776.8828 331376.7477 286487.9311 321102.156 334812.8018 1.086445618 0.954016476 1.061846537 1.082805737 1.07484518 1.119362464 0.989737387 0.855666 0.959049816 1 18.35299517 2.001668003 8.883424916 0.922224861 1.059287797 0.527141313 0.052978084 0.07272786 74.64950565 0.020595526 0.014535768 100.3848104 -2.001668003 0.137062935 TS(ph)PDPSPVSAAPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPDPSPVSAAPSK 14 0 Q13469-3;Q13469-4;Q13469-2;Q13469;Q13469-5 Q13469-3 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 T(0.211)S(0.789)PDPSPVSAAPSK;T(0.094)S(0.906)PDPSPVSAAPSK 132.06 5.52E-05 547577000 1029130 687410 869150 665200 1149090 1219770 1184110 882950 1001460 586890 TRUE FALSE 1069760.847 805467.3202 891800.763 796774.5746 953768.0922 936496.9033 1091296.364 871115.4995 965417.6502 701879.8588 1.524136693 1.147585744 1.270588908 1.135200796 1.358876566 1.334269521 1.554819319 1.241117676 1.375474218 1 19.42086458 -1.371081611 5.068128847 0.99979239 1.319659806 0.354599743 0.131980631 0.000299002 3.71E-05 0.123412898 0.029069992 0.042551844 1.371081611 0.319867417 TS(ph)PDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TSPDTLR 7 0 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.104)S(0.896)PDTLR;T(0.163)S(0.837)PDTLR;T(0.095)S(0.905)PDTLR;T(0.243)S(0.757)PDTLR;T(0.191)S(0.809)PDTLR;T(0.446)S(0.553)PDT(0.001)LR;T(0.345)S(0.655)PDTLR;T(0.012)S(0.988)PDTLR 214.81 4.31E-05 17061380000 24308220 20801220 23737570 23156870 26791990 33773610 30518740 24375520 23583110 14679270 TRUE FALSE 25267927.3 24373667.72 24356190.57 27737229.77 22237897.11 25930200.92 28126601.41 24048806.02 22734358.48 17555391.9 1.439325732 1.38838642 1.387390877 1.579983513 1.266727466 1.47705053 1.602163117 1.369881467 1.295007175 1 24.06541087 0.890484687 1.910933096 1.001747067 1.443477674 0.679062593 0.09256324 0.26158112 1.926270017 0.085661984 0.024007286 7.771139176 -0.890484687 0.441730607 TS(ph)PDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 T(0.352)S(0.648)PDTLRR 144.65 0.00035648 6086900000 955040 881080 1007700 866550 1273700 1432900 1212100 988010 1050900 669430 TRUE FALSE 992745.7167 1032398.636 1033961.49 1037951.004 1057196.929 1100130.691 1117092.435 974767.342 1013078.314 800591.9915 1.240014548 1.289544046 1.291496169 1.296479374 1.320518991 1.37414651 1.395333012 1.217558197 1.265411502 1 19.61070766 0.586494493 1.168938178 1.000654236 1.310190053 0.773772774 0.049248982 0.673526926 1.347540856 0.049255016 0.015100375 3.859175182 -0.586494493 0.309535817 TS(ph)PENVQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 T(0.288)S(0.712)PENVQDR 92.112 0.010801 243050000 135330 129140 151270 146320 167010 213010 180880 157380 156650 123600 TRUE FALSE 140672.9329 151318.7904 155212.2205 175261.6593 138621.6999 163541.6557 166702.153 155270.5785 151012.1971 147817.0535 0.951669172 1.023689668 1.050029186 1.185666032 0.937792335 1.106378809 1.12775995 1.050423986 1.021615527 1 17.1734532 4.606407278 2.251949703 1.066027221 0.940009332 0.199500332 0.065555662 0.674870378 4.897851672 0.015911224 0.150333425 40402.41058 -4.606407278 -0.126017888 TS(ph)PINLGLNVNDLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 T(0.21)S(0.79)PINLGLNVNDLLK;T(0.185)S(0.815)PINLGLNVNDLLK 288.92 1.33E-35 724067000 1659712 1042942 1291103 946515 1990610 2001440 1690033 1430329 1443045 856202 TRUE FALSE 1725238.711 1222059.176 1324750.205 1133732.842 1652246.823 1536635.892 1557563.797 1411157.779 1391110.092 1023958.389 1.684871895 1.193465661 1.293753945 1.107205971 1.613587858 1.50068197 1.521120208 1.378139771 1.358561156 1 19.96572566 0.627771597 2.250792744 1.000059557 1.40397761 0.340561573 0.170589002 3.058735447 17.0346475 0.163077794 0.044155789 4.243963078 -0.627771597 0.403918053 TS(ph)PITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPITR 6 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.247)S(0.753)PITR;T(0.156)S(0.844)PITR 122.13 0.020302 1342540000 1127080 1323850 1320990 1458870 1501080 1958410 1597600 1425600 1369890 1107570 TRUE FALSE 1171577.989 1551210.939 1355416.085 1747430.132 1245926.958 1503598.957 1472375.937 1406492.164 1320587.926 1324577.136 0.884492082 1.171098985 1.023282109 1.319236218 0.940622425 1.135153942 1.111581876 1.061842399 0.996988315 1 20.33710043 1.3519259 3.312016416 0.996969896 1.090034566 0.077117079 0.114329608 0.583489894 10.43259989 0.085827356 0.027309929 22.48670903 -1.3519259 0.09306467 TS(ph)PLKDNPS(ph)PEPQLDDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 T(0.41)S(0.59)PLKDNPS(1)PEPQLDDIKR;T(0.439)S(0.561)PLKDNPS(1)PEPQLDDIKR 204.31 2.49E-16 650190000 1468830 386095 645645 356246 1069910 1224870 979140 636888 765530 267940 TRUE FALSE 1526820.543 452403.8128 662471.0391 426710.3955 888047.0804 940412.5056 902392.4483 628351.5581 737978.7248 320437.713 4.764796654 1.411830738 2.067394106 1.331648487 2.771356318 2.934774739 2.816124357 1.960916374 2.303033304 1 18.28968443 4.74866499 24.84104956 2.147731955 4.764798225 0.616159622 0.636034354 890.2987054 2188703.169 0.151494436 2.062940263 56061.53561 -4.74866499 2.61706627 TS(ph)PLKDNPSPEPQLDDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.126)S(0.874)PLKDNPSPEPQLDDIKR;T(0.013)S(0.987)PLKDNPSPEPQLDDIKR;T(0.136)S(0.849)PLKDNPS(0.014)PEPQLDDIKR 209.56 1.14E-16 1322130000 1162530 409700 635750 363860 965260 970750 934830 662340 748320 311206 TRUE FALSE 1208427.582 480062.788 652318.1673 435830.422 801185.45 745308.0244 861555.5819 653462.4157 721388.1094 372180.8573 3.246882687 1.289864265 1.752691345 1.171017836 2.152677749 2.002542607 2.314884189 1.755765787 1.938273007 1 18.50564433 4.750400479 24.51848284 1.766877083 3.24688386 0.551781993 0.412926586 1071.290755 2218419.84 0.096060005 1.548209188 56286.01196 -4.750400479 1.480006776 TS(ph)PLNSSGSSQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPLNSSGSSQGR 13 0 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.053)S(0.947)PLNSSGSSQGR 116.41 0.00061627 90426000 117640 84995 108590 101510 117630 158630 160580 110810 97115 65164 TRUE FALSE 122284.518 99592.23008 111419.9446 121588.375 97635.29462 121790.5866 147993.32 109324.7732 93619.85012 77931.63816 1.569125466 1.277943496 1.429713878 1.560192727 1.252832571 1.562787456 1.899014617 1.402829143 1.201307355 1 16.24992152 1.123103642 2.876042012 1.013730997 1.500139208 0.481265256 0.171088252 0.210999498 3.256295486 0.166392844 0.044967982 13.27711272 -1.123103642 0.486408211 TS(ph)PPCS(ph)PANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 T(0.175)S(0.825)PPCS(1)PANLSR;T(0.101)S(0.899)PPCS(1)PANLSR 126.71 0.00041336 1409810000 736930 760730 819250 779760 937050 1154850 884720 829460 821350 620730 TRUE FALSE 766024.5654 891379.4598 840600.328 933994.2006 777770.5757 886653.5894 815373.3346 818342.4454 791789.7739 742350.1589 1.031891158 1.200753376 1.132350169 1.258158552 1.047713894 1.194387283 1.098367563 1.102367172 1.06659878 1 19.50174033 1.156511267 0.842113169 1.000944582 1.148167682 0.317622109 0.064970403 0.623293266 0.990638686 0.056500665 0.020818301 14.33874915 -1.156511267 0.1472231 TS(ph)PPCSPANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 T(0.291)S(0.709)PPCSPANLSR;T(0.021)S(0.979)PPCSPANLSR;T(0.132)S(0.868)PPCSPANLSR 116.19 0.00091117 2576290000 1406570 1353410 1554010 1423670 1836600 2241360 1709680 1528710 1524160 1131780 TRUE FALSE 1462102.47 1585847.639 1594508.777 1705267.677 1524415.388 1720838.108 1575670.814 1508220.143 1469305.779 1353530.622 1.08021381 1.1716378 1.178036722 1.259866345 1.126251127 1.271369912 1.164119074 1.114285941 1.085535677 1 20.3682961 1.210552773 1.327904729 1.005892514 1.183017547 0.529862582 0.053720111 0.298802979 1.033898541 0.048809318 0.015231821 16.23875663 -1.210552773 0.177125033 TS(ph)PPLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 T(0.146)S(0.854)PPLLDR;T(0.143)S(0.857)PPLLDR 204.28 9.31E-05 15032200000 9208000 8472600 8676800 8549700 10786700 12818600 11218900 9954700 8920400 6545000 TRUE FALSE 9571538.95 9927703.142 8902924.536 10240805.14 8953180.587 9841674.418 10339533.3 9821273.529 8599356.547 7827367.438 1.222829901 1.268332325 1.137409813 1.308333258 1.143830369 1.257341564 1.320946459 1.25473521 1.098626916 1 22.90009574 1.062816656 3.584440201 1.002197311 1.241080787 0.653555876 0.057421171 0.116620263 3.026284168 0.053295888 0.01383445 11.55624275 -1.062816656 0.238883476 TS(ph)PQVLGSILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 T(0.026)S(0.974)PQVLGSILK 159 3.06E-05 131660000 583300 342380 440390 346750 649820 648060 587390 479750 500070 324500 TRUE FALSE 606329.1344 401181.1017 451866.9252 415336.1151 539363.8285 497557.8864 541348.8369 473319.736 482072.5784 388079.5621 1.562383577 1.033759932 1.164366716 1.070234446 1.389827966 1.282102783 1.394942919 1.21964613 1.242200377 1 18.56599293 0.486712275 2.06109547 1.000024402 1.256235594 0.215270454 0.150095986 8.470924646 32.06782415 0.13855613 0.037942079 3.066989399 -0.486712275 0.256211192 TS(ph)PSGGTWSSVVSGVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSPSGGTWSSVVSGVPR 17 0 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4 Q99700 ATXN2 Ataxin-2 1 T(0.108)S(0.889)PS(0.003)GGTWSSVVSGVPR;T(0.165)S(0.834)PS(0.001)GGTWSSVVSGVPR;T(0.177)S(0.823)PSGGTWSSVVSGVPR;T(0.018)S(0.82)PS(0.162)GGTWSSVVSGVPR 216.98 5.37E-15 1235760000 1137040 1138830 1222610 1087060 1362520 1760170 1393300 1233970 1266830 986970 TRUE FALSE 1181931.217 1334415.194 1254472.221 1302077.223 1130919.337 1351397.193 1284089.505 1217430.651 1221237.036 1180347.875 1.00134142 1.130527044 1.062798729 1.103130061 0.958123754 1.144914327 1.087890725 1.031416819 1.034641619 1 20.17078069 1.613925513 4.867094655 1.022210312 1.071651974 0.144400925 0.053541937 0.299204863 15.54319825 0.028657539 0.01326636 41.10792099 -1.613925513 0.049441661 TS(ph)PTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 1 T(0.25)S(0.75)PTFR;T(0.182)S(0.818)PTFR;T(0.083)S(0.916)PT(0.001)FR 132.57 0.015568 1784540000 2085120 1993260 2224730 1874320 2643300 2910820 2404650 2083740 2135010 1644510 TRUE FALSE 2167442.148 2335586.9 2282708.291 2245054.902 2193992.81 2234826.169 2216167.25 2055810.874 2058171.407 1966720.248 1.102059202 1.187554204 1.160667509 1.141522239 1.115559171 1.13632133 1.126834003 1.045299084 1.046499322 1 20.90736033 1.610667304 1.012858936 1.00325688 1.147528943 0.816558501 0.023778288 0.189737238 0.372520661 0.020857751 0.007978969 40.80067089 -1.610667304 0.144272062 TS(ph)PTGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPTGPK 7 0 C9JB30;Q9UPY8;Q9UPY8-2 C9JB30;Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 T(0.16)S(0.84)PTGPK;T(0.019)S(0.981)PTGPK 97.635 0.012433 794610000 2621000 1236050 1793700 1336170 2508790 2707700 3002400 1965980 2205660 868950 TRUE FALSE 2724479.104 1448331.972 1840445.296 1600460.438 2082346.772 2078877.711 2767064.043 1939629.254 2126278.727 1039204.115 2.621697762 1.393693453 1.771014248 1.540082852 2.003789959 2.000451769 2.662676178 1.866456479 2.046064576 1 19.98704762 3.045190875 24.90720803 2.019567685 1.793002503 0 0.488697527 430.0920772 237044.8017 0.133212772 0.159219656 1109.662411 -3.045190875 -0.226565182 TS(ph)PTPPESATTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 T(0.022)S(0.978)PTPPESATTVK;T(0.054)S(0.946)PTPPESATTVK;T(0.129)S(0.871)PTPPESATTVK 277.24 3.05E-32 1199720000 1766060 1172230 1510850 1129350 2038710 2085210 1951270 1527050 1676260 952160 TRUE FALSE 1835785.412 1373551.384 1550223.992 1352732.059 1692170.802 1600951.579 1798324.359 1506582.393 1615931.73 1138717.522 1.612151721 1.206226617 1.36137713 1.187943483 1.486032111 1.405925129 1.579254138 1.32305191 1.419080412 1 20.11897848 -1.399719513 5.593763134 0.999828574 1.390753984 0.447591713 0.13239666 0.000268066 2.88E-05 0.121407536 0.028603623 0.039836437 1.399719513 0.39092541 TS(ph)PTVATQTGASATSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 T(0.028)S(0.967)PT(0.004)VATQTGASATSTR;T(0.246)S(0.747)PT(0.007)VATQTGASATSTR 128.45 3.87E-05 220210000 201535 195265 224540 190151 270050 328710 250710 235300 237940 167059 TRUE FALSE 209491.7574 228800.2448 230391.6969 227762.3003 224146.9975 252372.0841 231058.6951 232146.1884 229376.5859 199791.0125 1.048554461 1.145197884 1.153163468 1.140002733 1.12190731 1.263180365 1.156501948 1.161945102 1.148082604 1 17.60813216 4.741244303 4.093239144 1.153155011 1.039394752 0.165029164 0.060684596 0.345970165 12.57755476 0.013481157 0.116697055 55111.76282 -4.741244303 -0.113760259 TS(ph)PYILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 T(0.356)S(0.644)PYILR 127.56 0.0040307 273170000 1152900 688270 753400 627750 1072800 1236500 985590 749770 744930 562510 TRUE FALSE 1198417.382 806475.0185 773034.2229 751917.0764 890445.8392 949341.6143 908336.8804 739720.5595 718120.1148 672723.0646 1.781442387 1.198821716 1.149112114 1.117721565 1.323643987 1.411192308 1.350238944 1.099591494 1.067482524 1 19.3596532 4.73886082 24.97054831 1.203806493 1.781442563 0.660990152 0.126578585 15.51030252 1289535.038 0.031692132 0.185622258 54810.12841 -4.73886082 0.57763607 TS(ph)SESIYSRPGSSIPGS(ph)PGHTIYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 2 T(0.46)S(0.535)S(0.003)ES(0.003)IY(0.002)S(0.006)RPGS(0.014)S(0.012)IPGS(0.965)PGHTIYAK 122.11 0.00023336 58221000 68598 75243 82437 71310 112430 121310 114160 96805 91294 52633 TRUE FALSE 71306.30201 88165.39994 84585.37594 85414.90516 93319.18876 93137.59097 105211.8409 95507.48732 88008.34677 62945.42863 1.132827333 1.400664065 1.343789021 1.356967567 1.48254116 1.479656156 1.671477074 1.517306171 1.398168996 1 15.94181399 5.765090766 0.7559613 1.462821203 9.88E-17 0.147809331 0.168286363 15.71010621 2.130796211 0.056171889 27.87969138 582224.8885 -5.765090766 -1.462821203 TS(ph)SKSEAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.017)S(0.558)S(0.391)KS(0.034)EAGAR 105.95 0.0015026 282580000 168840 81102 112200 76790 185480 178840 175740 126310 131470 62927 TRUE FALSE 175505.9336 95030.63761 115124.0242 91978.8328 153952.1759 137307.1203 161965.0396 124617.0211 126738.4204 75256.34084 2.332108253 1.262759211 1.529758461 1.222207083 2.045703713 1.824525599 2.15217798 1.655900615 1.684089593 1 16.19952552 3.226220619 24.9974611 1.785442493 1.55950111 0.014284598 0.405877014 645.3397103 1307279.176 0.110950856 0.133502383 1683.529066 -3.226220619 -0.225941382 TS(ph)SPHKEESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.005)S(0.497)S(0.497)PHKEESPK 193.06 6.77E-07 406390000 975470 375270 587470 409240 974120 944950 932030 685280 713070 255050 TRUE FALSE 1013982.309 439719.7033 602779.9508 490186.4505 808539.4303 725499.6834 858975.0532 676094.9425 687406.75 305022.1643 3.324290585 1.441599185 1.976184099 1.607051906 2.650756322 2.37851464 2.816107004 2.216543654 2.253628852 1 18.21855455 3.226335125 24.99902893 2.322303797 2.033225658 0 0.657344658 805.5742628 1647257.456 0.177834703 0.214003928 1683.973003 -3.226335125 -0.289078139 TS(ph)SPHKEESPKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSPHKEESPKK 12 2 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 T(0.283)S(0.599)S(0.118)PHKEESPKK;T(0.018)S(0.827)S(0.156)PHKEESPKK 113.4 0.00061066 1146960000 2068900 664330 1273760 629420 2013140 1593100 1767390 1270380 1565520 427350 TRUE FALSE 2150581.77 778423.5097 1306955.232 753917.3974 1670947.182 1223126.669 1628857.354 1253352.634 1509177.241 511081.0504 4.20790747 1.523092099 2.557236726 1.475142537 3.269436776 2.393214673 3.187082269 2.452355909 2.952911754 1 18.96319258 TS(ph)SPLFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSPLFNK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 T(0.002)S(0.74)S(0.258)PLFNK 135.55 0.00086962 476870000 1231300 889430 1068300 854140 1487400 1502700 1306400 1120700 1165700 711710 TRUE FALSE 1279912.675 1042182.684 1096140.776 1023086.343 1234572.279 1153720.699 1204000.954 1105678.85 1123746.685 851155.948 1.50373463 1.224432122 1.287826018 1.20199635 1.450465431 1.355475106 1.414548012 1.299032042 1.320259451 1 19.69906396 0.302617668 1.50541211 0.999920077 1.338058545 0.561288065 0.090305619 4.607677908 9.135197819 0.084049417 0.024129909 2.007324883 -0.302617668 0.338138468 TS(ph)SPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSPPR 6 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.111)S(0.445)S(0.445)PPR 77.741 0.075128 123180000 158550 180150 205140 163200 223900 247050 220010 201970 188740 167140 TRUE FALSE 164809.6764 211089.3611 210486.1169 195480.4729 185841.558 189676.3816 202765.0413 199262.9225 181947.2843 199887.8829 0.824510591 1.056038806 1.053020893 0.977950589 0.929728982 0.948913855 1.014393861 0.996873445 0.910246692 1 17.60883149 TS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSVQTEDDQLIAGQSAR 17 0 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 T(0.412)S(0.588)VQT(1)EDDQLIAGQSAR;T(0.024)S(0.976)VQT(1)EDDQLIAGQSAR 218.72 1.68E-17 180240000 249100 236620 211902 234660 256310 373830 254280 224290 206830 185716 TRUE FALSE 258934.6603 277257.6444 217424.3402 281075.0476 212742.5178 287013.6479 234348.8692 221283.7594 199386.2287 222103.4945 1.165828845 1.248326349 0.97893255 1.265513847 0.957853087 1.292251834 1.055133643 0.99630922 0.897717657 1 17.76087257 1.815948785 2.765727801 0.95494451 1.145250438 0.366403516 0.108912403 0.264144145 3.759235448 0.057255949 0.028022292 65.45589792 -1.815948785 0.190305928 TS(ph)VQTEDDQLIAGQSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSVQTEDDQLIAGQSAR 17 0 P35221-2;P35221;G3XAM7;P35221-3;P26232;P26232-5;P26232-2;P26232-3;P26232-6;P26232-4;A0A0A0MRI5;A0A0A0MTJ6 P35221-2 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 T(0.006)S(0.994)VQTEDDQLIAGQSAR;T(0.069)S(0.931)VQTEDDQLIAGQSAR;T(0.173)S(0.827)VQTEDDQLIAGQSAR 418.07 3.91E-141 879830000 575966 569630 489126 575503 544793 813530 674640 544673 522366 385101 TRUE FALSE 598705.5824 667459.5214 501873.0254 689335.7757 452189.2805 624599.9867 621759.954 537372.5493 503566.1497 460554.1677 1.299967787 1.449253026 1.089715522 1.496752877 0.981837343 1.356192236 1.350025681 1.166795541 1.093391798 1 18.81301132 1.312899004 1.977833275 1.014399333 1.285611746 0.309321747 0.146619864 0.368721851 2.487262622 0.124042075 0.037015399 20.5541255 -1.312899004 0.271212413 TSAAEASLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSAAEASLR 9 0 Q96QP1-2 Q96QP1-2 0 76.035 0.056279 0 157730 190430 168890 181640 219640 212650 172190 167230 144040 219910 FALSE TRUE 163957.3022 223134.8712 173291.4121 217567.8499 182305.6713 163265.2602 158693.2979 164988.5554 138856.0285 262997.1541 0.623418541 0.848430744 0.658909838 0.827263134 0.693184958 0.620787175 0.603403099 0.627339699 0.527975403 1 18.00468766 -1.110762216 4.395185503 1.000037583 0.672615764 0.525776446 0.093970942 3.81E-05 7.72E-06 0.093232804 0.021972473 0.077488595 1.110762216 -0.327421819 TSADAQEPAS(ph)PVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_MDA-MB-175_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 3 T(0.003)S(0.003)ADAQEPAS(0.994)PVVS(0.012)PQQS(0.97)PPT(0.586)S(0.378)PHT(0.055)WR 83.185 0.027591 367100000 117460 77044 91312 75788 118010 142950 86255 75667 99553 76974 TRUE FALSE 122097.4115 90275.70768 93691.66573 90778.6402 97950.70235 109752.0289 79494.10771 74652.80763 95970.10698 92055.58154 1.32634447 0.980665226 1.017772786 0.986128583 1.064038711 1.19223655 0.86354468 0.810953626 1.042523499 1 16.49021758 2.222913567 24.99993897 0.900730093 1.079552931 0.310172237 0.11643476 269.7714859 431022.3142 0.043298843 0.03208922 167.0758067 -2.222913567 0.178822838 TSADAQEPAS(ph)PVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_MDA-MB-175_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(1)PVVSPQQS(1)PPT(0.104)S(0.887)PHT(0.01)WR;TSADAQEPAS(1)PVVSPQQS(0.973)PPT(0.305)S(0.706)PHT(0.016)WR 171.57 2.09E-12 537800000 169814 179190 189106 152672 209787 255240 180500 190124 188146 167453 TRUE FALSE 176518.3878 209964.4886 194034.2577 182870.0659 174127.4807 195964.3782 166351.9384 187575.6988 181374.6622 200262.2093 0.881436335 1.048447879 0.968901014 0.913153144 0.869497452 0.978538981 0.830670644 0.936650502 0.905685915 1 17.61153068 3.75382119 6.190721878 0.912931974 0.974905312 0.105768593 0.059428649 0.264271216 43.80371037 0.014274491 0.024822319 5673.109816 -3.75382119 0.061973338 TSADAQEPASPVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.999)PPT(0.736)S(0.265)PHTWR;TSADAQEPASPVVSPQQS(0.996)PPT(0.683)S(0.311)PHT(0.009)WR;TSADAQEPASPVVSPQQS(0.998)PPT(0.683)S(0.306)PHT(0.013)WR 175.04 2.59E-12 1700100000 477650 475898 547170 531660 626810 749120 524466 574470 589670 485720 TRUE FALSE 496507.9908 557629.7795 561429.6997 636820.7612 520265.0601 575148.233 483356.9845 566770.1693 568447.8919 580887.5343 0.854740309 0.959961691 0.966503267 1.096289253 0.89563819 0.990119772 0.832100804 0.975696905 0.97858511 1 19.14789934 -3.465687981 0.004306718 1.967293099 6.02E-08 0.040850761 0.071327282 322688.7032 137.9397924 33105.8683 29972.99578 0.000342225 3.465687981 -1.967293039 TSADAQEPASPVVSPQQS(ph)PPTS(ph)PHTWR ddPTM_MDA-MB-175_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(0.997)PPT(0.373)S(0.607)PHT(0.023)WR 139.6 1.23E-07 307410000 86314 89791 107460 91260 111280 139920 109730 118250 98200 89785 TRUE FALSE 89721.74337 105211.9058 110260.4959 109310.9556 92364.66535 107425.7005 101129.0759 116665.0522 94665.80118 107376.6517 0.835579634 0.979839696 1.026857274 1.018014195 0.860193197 1.000456792 0.941816254 1.086502981 0.881623702 1 16.7123208 TSAEAPSHHLQQQQQQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSAEAPSHHLQQQQQQQR 18 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 0 ;; 171.56 7.50E-12 111685000 65928 115064 113430 112230 121543 153112 106272 125406 111784 110371.5 FALSE TRUE 68530.88835 134825.3469 116386.079 134428.759 100883.1643 117554.0584 97942.12295 123725.1377 107760.9157 131996.6822 0.519186446 1.021429817 0.881734882 1.018425287 0.764285606 0.890583433 0.74200443 0.937335209 0.816391093 1 17.01014214 -5 0.016160668 2.010886329 5.69E-15 0.103939819 0.140173892 15045.88144 18.43824856 1460.693985 897.1473173 1.00E-05 5 -2.010886329 TSALS(ph)PNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSALSPNAK 9 0 P50616 P50616 TOB1 Protein Tob1 1 TSALS(1)PNAK;TSALS(1)PNAK 146.5 9.93E-05 310960000 468960 313360 380090 274960 558590 540500 489680 420610 452600 279120 TRUE FALSE 487474.9029 367177.1424 389995.4576 329346.2673 463641.0713 414977.0664 451297.6021 414972.4109 436311.0144 333808.2199 1.460344215 1.099964352 1.168321912 0.986633185 1.388944441 1.243160119 1.351966714 1.243146172 1.307070912 1 18.34865996 3.209022696 24.99954178 1.271901764 1.172433575 0.053677865 0.148193438 486.784033 411990.4887 0.040410886 0.048306463 1618.164602 -3.209022696 -0.099468189 TSASEGNPYVSSTLSVPAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSASEGNPYVSSTLSVPASPR 21 0 E9PDY7;G5E9V3;A0A1W2PQ63;E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0 E9PDY7 PHLDB2 Pleckstrin homology-like domain family B member 2 1 TSASEGNPYVSSTLSVPAS(1)PR;TSASEGNPYVSSTLS(0.001)VPAS(0.999)PR;TSASEGNPYVSSTLSVPAS(1)PR 392.2 2.99E-131 583640000 270711 293034 274603 259657 365587 438650 302085 300312 313573 290683 TRUE FALSE 281398.8793 343360.31 281759.3798 311016.3796 303444.6523 336780.1853 278406.7883 296286.8089 302287.569 347636.7684 0.809462361 0.987698487 0.810499364 0.894659046 0.872878475 0.968770326 0.800855415 0.852288468 0.869550049 1 18.40722115 TSAVSS(ph)PLLDQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 TSAVS(0.002)S(0.998)PLLDQQR;TSAVS(0.003)S(0.997)PLLDQQR;TSAVS(0.013)S(0.987)PLLDQQR;TSAVS(0.001)S(0.999)PLLDQQR;TSAVS(0.002)S(0.998)PLLDQQR;TSAVS(0.001)S(0.999)PLLDQQR 326.24 1.99E-52 2833760000 3011360 3300160 3303980 3283230 4049520 4626010 3518510 3553500 3475580 3035810 TRUE FALSE 3130250.818 3866936.808 3390084.433 3932643.095 3361184.037 3551689.285 3242719.992 3505871.145 3350494.555 3630618.845 0.862181064 1.065090271 0.933748371 1.083188091 0.925788187 0.978260026 0.893159026 0.9656401 0.922843928 1 21.79178405 TSCSGSGERES(ph)PERK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSCSGSGERESPERK 15 2 Q9H8Y5;C9JQZ3;C9K022 Q9H8Y5 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 TSCSGSGERES(1)PERK;TSCSGSGERES(1)PERK 177.22 3.98E-07 767260000 805170 415570 542110 414030 780290 790880 652130 579230 630310 338140 TRUE FALSE 836958.7333 486940.9148 556237.8319 495923.8982 647656.5845 607210.1059 601014.3466 571466.3693 607625.2662 404392.0589 2.069671535 1.204130754 1.375491481 1.226344305 1.601556139 1.501538155 1.486216985 1.413149335 1.502564783 1 18.62539514 -1.806583888 2.381054966 0.838266171 1.467034733 0.286456618 0.228565559 10651380.09 6678515.601 9925766.806 0.052885892 0.015610475 1.806583888 0.628768562 TSDANETEDHLESLICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSDANETEDHLESLICK 17 0 Q09161;F2Z2T1 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 0 120.9 6.20E-05 103130000 88624 68055 97161 79345 106440 113960 104680 85786 95801 62266 FALSE TRUE 92122.94395 79742.91686 99693.09548 95039.20418 88347.36682 87494.51708 96474.90807 84636.17899 92353.14072 74465.83055 1.237116987 1.070865876 1.338776386 1.276279382 1.186414845 1.174961945 1.295559418 1.136577385 1.240208295 1 16.18429096 -1.44394127 0.479554715 0.881268579 1.219632735 0.429051915 0.075002137 31.68858141 3.466936459 4.698572102 0.03635132 0.035979799 1.44394127 0.338364156 TSDDEVGS(ph)PKEESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSDDEVGSPKEESR 14 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 TSDDEVGS(1)PKEESR;TSDDEVGS(1)PKEESR 159.26 2.99E-06 674960000 1038200 442610 587010 406340 912440 1059490 761520 607940 662180 355700 TRUE FALSE 1079188.938 518624.8245 602307.9628 486712.8392 757343.7747 813439.5042 701830.0725 599791.5587 638348.2711 425392.6047 2.536924539 1.219167467 1.415887244 1.144149743 1.780340717 1.912208852 1.649840794 1.409971758 1.500609705 1 18.69843543 0.704904521 1.017396497 1.003524404 1.622189856 0.209322051 0.375624007 1.66085595 3.006816504 0.350221197 0.11254758 5.068792589 -0.704904521 0.618665451 TSDIFGS(ph)PVTATSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.998)PVT(0.002)ATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(1)PVTATSR;TSDIFGS(0.739)PVT(0.26)AT(0.001)SR;TSDIFGS(1)PVTATSR;TSDIFGS(0.868)PVT(0.114)AT(0.013)S(0.005)R 383.73 8.06E-114 6998136000 3641550 3777460 4041250 3839070 5014770 5728490 4394030 4500140 4264110 3894680 TRUE FALSE 3785321.206 4426209.37 4146568.295 4598426.588 4162361.187 4398135.014 4049614.447 4439822.984 4110645.514 4657767.978 0.812689946 0.9502855 0.890247929 0.987259694 0.893638585 0.944258073 0.869432412 0.953208276 0.882535483 1 22.15120734 TSEEFVHINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSEEFVHINR 10 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6;A0A3B3IS13;A0A3B3ISK3;A0A3B3IU76 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ;;;;; 183.67 1.64E-06 3466740000 2685610 3111240 3207430 3277840 3786840 4150640 3273890 3381260 3204130 2661760 FALSE TRUE 2791639.957 3645571.268 3291018.261 3926186.969 3143154.289 3186716.764 3017273.947 3335939.74 3088813.987 3183280.91 0.876969402 1.145224494 1.033844751 1.233377474 0.987394571 1.001079344 0.947850357 1.047956443 0.970324038 1 21.60208304 TSES(ph)PSKPGEK ddPTM_MDA-MB-175_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;T(0.002)S(0.015)ES(0.966)PS(0.017)KPGEK;TSES(1)PSKPGEK;TS(0.001)ES(0.996)PS(0.003)KPGEK;TSES(1)PSKPGEK;T(0.002)S(0.004)ES(0.8)PS(0.195)KPGEK;T(0.042)S(0.042)ES(0.899)PS(0.018)KPGEK 191.46 1.10E-06 4499940000 9563700 2874319 4396943 2646217 7242620 7401990 6600510 4531768 5149176 1924127 TRUE FALSE 9941282.261 3367960.929 4511530.947 3169630.824 6011522.039 5682990.001 6083144.779 4471027.062 4963858.162 2301122.846 4.320187546 1.46361631 1.960578052 1.377427907 2.612429862 2.469659545 2.643554989 1.942976261 2.157146095 1 21.13390657 0.447360959 1.058238333 0.998826395 2.305476668 0.210793948 0.780483949 3.392953941 4.962838543 0.720277394 0.222883953 2.801308629 -0.447360959 1.306650273 TSESPSKPGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 112.51 0.0013833 228840000 231990 99152 160930 103210 258050 215680 201570 155280 176710 85828 FALSE TRUE 241149.1443 116180.5847 165123.968 123624.6299 214186.7532 165591.5887 185770.4167 153198.7256 170350.2416 102644.3533 2.349365908 1.131875071 1.608699969 1.204397767 2.086688125 1.613255706 1.809845458 1.49251976 1.659616297 1 16.64729474 -0.206644765 0.951676709 0.987452214 1.644426572 0.245351474 0.346749162 17.76047765 12.22490614 1.172710135 0.099070435 0.621377087 0.206644765 0.656974357 TSEVNCYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 142.19 0.0014458 702760000 532570 551770 663740 553270 606620 832500 638900 599160 623630 468090 FALSE TRUE 553596.2748 646532.2053 681037.6097 662705.1547 503506.9491 639164.4917 588821.3485 591129.2402 601185.6781 559803.2734 0.988912179 1.154927518 1.216565965 1.183817934 0.899435521 1.141766263 1.051836201 1.055958885 1.07392312 1 19.0945604 TSFDDRLEDDDFDLIEENLGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFDDRLEDDDFDLIEENLGVK 22 1 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 150.83 6.72E-08 29196000 40304 25750 36794 26503 45305 46511 43299 35912 34729 25746 FALSE TRUE 41895.23304 30172.36219 37752.88187 31745.2143 37604.07228 35709.52513 39905.11124 35430.65838 33479.11007 30790.43576 1.36065736 0.979926443 1.226123662 1.031008932 1.221290682 1.159760304 1.296022945 1.150703376 1.087321736 1 14.91019466 1.0382757 2.721654874 1.002067015 1.174388746 0.224694277 0.10645423 0.354918237 5.727091947 0.09271932 0.024870019 10.92133428 -1.0382757 0.172321731 TSFGS(ph)LTDSSEEALEGMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSFGSLTDSSEEALEGMVR 19 0 G3V160;Q969H4-2;Q969H4 G3V160 CNKSR1 Connector enhancer of kinase suppressor of ras 1 1 TSFGS(0.999)LTDSSEEALEGMVR;T(0.002)S(0.002)FGS(0.996)LTDSSEEALEGMVR;T(0.03)S(0.03)FGS(0.937)LT(0.002)DSSEEALEGMVR;T(0.102)S(0.102)FGS(0.794)LT(0.002)DSSEEALEGMVR 137.14 4.68E-06 92713000 78500 89453 98814 99629 132070 152903 120193 112803 116177 117997 TRUE FALSE 81599.24062 104815.8569 101389.174 119335.3188 109620.7886 117393.5955 110771.9586 111291.0603 111995.8125 141116.253 0.578241265 0.742762472 0.718479777 0.845652548 0.776811928 0.831892805 0.784969529 0.788648068 0.793642193 1 17.10652463 -4.999990246 0.033695888 2.190123356 1.31E-06 0.693699345 0.055676477 711.268472 1.799860444 96.19060423 34.92644013 1.00E-05 4.999990246 -2.190122042 TSFLDDAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFLDDAFR 9 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 182.73 0.00010699 86592000 193770 202900 203290 239440 279180 293270 248070 235300 193350 214220 FALSE TRUE 201420.1892 237746.4967 208587.9044 286800.5173 231725.0833 225162.487 228625.6252 232146.1884 186391.3713 256192.3075 0.786207014 0.928000138 0.814184885 1.119473571 0.904496648 0.878880749 0.892398478 0.906140355 0.727544762 1 17.96686763 -0.049843016 7.825785987 0.999999998 0.892249011 0.105030803 0.098943041 6211619.955 793737.3934 0.091421273 0.022172916 0.891573157 0.049843016 -0.107750987 TSFLDDAFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFLDDAFRK 10 1 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2;A0A2R8Y5T0;A0A2R8Y542;H0YJ21 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 125.17 0.00066725 728540000 869130 648220 863810 665950 1238100 1156800 804120 704330 922540 651980 FALSE TRUE 903443.9235 759546.7425 886321.5982 797672.9223 1027648.204 888150.7315 741090.9732 694889.6084 889337.9656 779722.9981 1.158672921 0.974123816 1.136713423 1.023020899 1.317965748 1.139059299 0.950454168 0.891200606 1.140581935 1 19.57260216 2.240498411 24.99856322 0.97499561 1.122749659 0.263310343 0.103713166 62.65748955 808326.6406 0.037628065 0.030020429 173.9796331 -2.240498411 0.147754048 TSFNYAMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSFNYAMK 8 0 P15559-2;P15559;B4DLR8;P15559-3;H3BRK3 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 106.91 0.0095488 175730000 96468 81853 103620 71559 178800 138100 118610 95601 96444 134610 FALSE TRUE 100276.6311 95910.61602 106320.4223 85713.15662 148407.6399 106028.3679 109313.0383 94319.62497 92972.99928 160984.2522 0.622897145 0.595776386 0.660439893 0.532431933 0.921876754 0.658625713 0.679029388 0.585893487 0.577528535 1 17.29656004 -2.086333178 2.518128426 1.579410031 0.648775727 0.522424991 0.100884776 5698684.68 1764388.31 18969079.9 0.024780789 0.008197224 2.086333178 -0.930634304 TSFSQEQSCDS(ph)AGEGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSFSQEQSCDSAGEGSER 18 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 TSFSQEQSCDS(1)AGEGSER;TSFSQEQSCDS(1)AGEGSER 445.56 1.04E-190 369190000 224725 246982 234108 240154 292769 340350 251647 253621 246349 253637 TRUE FALSE 233597.3165 289399.2372 240209.0468 287655.7444 243004.23 261308.8706 231922.2506 250221.6253 237482.9476 303332.314 0.770103631 0.954066626 0.791900618 0.948318828 0.801115538 0.86146071 0.764581417 0.824909229 0.782913447 1 18.21053967 TSFSVGS(ph)DDELGPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;TSFSVGS(1)DDELGPIR;TSFSVGS(1)DDELGPIR 418.72 5.97E-134 5514340000 2851570 2786930 3155850 2871900 3684410 4128130 3378300 3161640 3021290 2667640 TRUE FALSE 2964152.185 3265563.548 3238094.044 3439953.248 3058135.304 3169434.37 3113500.018 3119263.387 2912554.363 3190312.983 0.929110154 1.023587205 1.014976919 1.078249459 0.958569056 0.993455622 0.975923063 0.977729584 0.912936874 1 21.60526653 2.478505609 1.322529508 0.96363559 1.00858066 0.137705878 0.042053314 0.800124193 2.829444224 0.021854526 0.016066003 300.9578041 -2.478505609 0.04494507 TSFSVGS(ph)DDELGPIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSFSVGSDDELGPIRK 16 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 TSFS(0.002)VGS(0.998)DDELGPIRK;TSFSVGS(1)DDELGPIRK;TSFS(0.07)VGS(0.93)DDELGPIRK 212.76 2.24E-12 414790000 287889 235051 280332 221176 348790 344230 296746 277742 307597 204018 TRUE FALSE 299255.08 275419.1808 287637.6822 264923.9527 289502.8004 264287.7994 273486.2731 274019.3228 296526.6441 243991.4209 1.22649837 1.128806823 1.17888441 1.085792081 1.186528605 1.083184804 1.120884792 1.123069499 1.215315862 1 17.8964709 -1.921557304 2.752810036 0.912163023 1.144419261 0.462721622 0.048129605 8560652.623 5163111.399 4837146.382 0.010812174 0.01197961 1.921557304 0.232256238 TSGAPGS(ph)PQTPPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSGAPGSPQTPPER 14 0 Q96MH2;K7ESM2;K7ELS4;K7EJA3;K7ERG7;K7EIM4 Q96MH2 HEXIM2 Protein HEXIM2 1 TSGAPGS(0.945)PQT(0.054)PPER 100.23 0.0019591 57047000 77177 90785 81184 84417 112290 133560 100340 94106 88755 64618 TRUE FALSE 80224.00755 106376.6175 83299.72173 101114.4306 93202.98591 102542.7141 92475.08861 92844.663 85560.72489 77278.65991 1.038113337 1.376532896 1.077913642 1.308439235 1.206063692 1.326921484 1.196644568 1.201426928 1.107171436 1 16.23778246 1.035256286 1.728665466 1.000383039 1.226157569 0.32905881 0.099050276 0.364081087 2.220824946 0.083081924 0.023960316 10.84566749 -1.035256286 0.22577453 TSGHDHPDVATMLNILALVYR ddPTM_MDA-MB-175_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 ; 198.38 4.97E-22 1083110000 323620 711130 743860 758260 871960 1054100 782260 831810 734880 683410 FALSE TRUE 336396.7675 833261.0457 763245.6027 908241.5648 723744.5507 809301.25 720944.4171 820660.9475 708431.8124 817311.1048 0.411589621 1.01951514 0.933849544 1.111255628 0.885519047 0.990199748 0.882093016 1.004098614 0.86678354 1 19.64052581 4.741945016 24.99901607 0.965710383 0.411589414 0.842882421 0.071799509 109.4646074 808529.4282 0.015693743 0.114246866 55200.75472 -4.741945016 -0.55412097 TSGHVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSGHVDK 7 0 P41250 P41250 GARS Glycine--tRNA ligase 0 66.258 0.068362 152120000 109580 127380 156610 121860 218020 219170 236190 176720 168620 120670 FALSE TRUE 113906.303 149256.5241 160691.3853 145963.5443 180961.0383 168271.0891 217676.8106 174351.3575 162551.3991 144312.9761 0.789300492 1.034255741 1.113492283 1.01143742 1.253948488 1.16601496 1.508366167 1.208147473 1.126381033 1 17.1388415 5.443927941 0.611558749 1.232987092 0.019195764 0.445905554 0.133496197 6.385271001 0.961516497 0.058072954 6.599997761 277925.2092 -5.443927941 -1.213791328 TSGNVEDDLIIFPDDCEFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSGNVEDDLIIFPDDCEFKR 20 1 Q16186 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 ;;; 181.29 8.26E-17 202471000 410483 268457 367518 302388 469560 472440 439070 385048 398656 249740 FALSE TRUE 426689.1858 314562.4014 377095.821 362199.4439 389744.3589 362722.9699 404654.5461 379887.0614 384308.4484 298671.7714 1.42862241 1.053204325 1.262576035 1.212700625 1.304925327 1.214453472 1.354846975 1.271921546 1.286725045 1 18.18820136 -0.974333817 5.178831735 0.999998722 1.261940594 0.420711807 0.093395307 1.27E-06 2.51E-07 0.083070055 0.019579704 0.106087981 0.974333817 0.261941872 TSHLDLPEDFQEMGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSHLDLPEDFQEMGLLR 17 0 E9PMS5;E9PRT1;E9PJJ5;Q4G0X4 E9PMS5 KCTD21 BTB/POZ domain-containing protein KCTD21 0 ;; 155.11 1.13E-07 96210000 46148 55225 61232 53041 67549 72663 66541 59131 59214 48106 FALSE TRUE 47969.95867 64709.46416 62827.75622 63532.35149 56067.04511 55788.11947 61325.34255 58338.44566 57082.89971 57531.44965 0.833804101 1.124766794 1.092059328 1.10430646 0.974546017 0.969697788 1.065944677 1.014027041 0.992203396 1 15.8120632 3.216765825 24.99629866 1.006951792 1.04868835 0.039633392 0.079480598 747.6089453 857424.7578 0.022627606 0.027066771 1647.273929 -3.216765825 0.041736558 TSIDAYDNFDNISLAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 422.83 4.22E-160 300140000 182395 162870 183840 184371 216924 248659 186060 207419 188535 156328 FALSE TRUE 189596.0954 190841.6555 188631.0214 220839.0335 180051.336 190911.7157 171476.131 204638.8876 181749.6622 186957.4785 1.01411346 1.020775724 1.008951463 1.181225995 0.963060357 1.021150463 0.917193216 1.094574495 0.972144381 1 17.51235066 TSIFWNDVKDPVSIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSIFWNDVKDPVSIEER 17 1 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;; 220.34 3.68E-15 1752780000 1039790 696020 983840 791380 1250450 1150320 1242750 988900 1149060 581404 FALSE TRUE 1080841.712 815556.0207 1009479.679 947912.602 1037898.956 883175.6133 1145340.008 975645.413 1107705.555 695318.9821 1.554454488 1.172923567 1.451822407 1.363277325 1.492694695 1.27017331 1.647215216 1.403162344 1.593089767 1 19.40731545 -0.948860845 5.511561183 0.999999304 1.432668315 0.476309337 0.137885824 1.09E-06 2.08E-07 0.123057566 0.0290049 0.112496537 0.948860845 0.432669011 TSKEPPSS(ph)PLQPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSKEPPSSPLQPQK 14 1 Q92615;H0Y4V9;A0A087X183 Q92615 LARP4B La-related protein 4B 1 TSKEPPS(0.167)S(0.833)PLQPQK;TSKEPPS(0.247)S(0.753)PLQPQK;TSKEPPS(0.051)S(0.949)PLQPQK 119.8 0.00010076 1256270000 2164570 1126460 1624540 1080490 2271150 2125860 2013050 1634290 1830240 922640 TRUE FALSE 2250028.895 1319920.742 1666876.847 1294207.697 1885100.734 1632161.233 1855261.881 1612385.016 1764370.02 1103413.643 2.039152687 1.196215717 1.510654556 1.172912539 1.708426161 1.479192543 1.681383852 1.461269784 1.599010517 1 20.07354229 -1.376746369 6.105406466 0.999918277 1.521869634 0.313161432 0.23816414 0.000240102 2.45E-05 0.208987011 0.049251064 0.04200042 1.376746369 0.521951357 TSKEPVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSKEPVSR 8 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 ;; 89.047 0.012935 505187000 397365 456620 461145 383021 590908 612176 469734 497041 452871 419590 FALSE TRUE 413053.277 535040.933 473162.8175 458781.4106 490465.6692 470007.4016 432915.0217 490378.9784 436572.2612 501800.627 0.82314221 1.066242058 0.942929905 0.914270302 0.977411432 0.936641719 0.862723158 0.977238672 0.87001139 1 18.93675475 2.480482488 24.89224252 0.925233935 0.950474159 0.010207456 0.068527708 583.9753009 4324802.964 0.021962534 0.018730602 302.3308659 -2.480482488 0.025240225 TSLAEDSCLGRHS(ph)PVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;TSLAEDSCLGRHS(1)PVPR 247.55 5.58E-21 639450000 187790 280820 248737 255947 291510 379940 280920 291630 267390 283423 TRUE FALSE 195204.0942 329048.6505 255219.2906 306572.5527 241959.2343 291704.693 258900.7564 287721.1769 257766.6861 338954.3104 0.575900905 0.970775826 0.752960746 0.904465715 0.713840264 0.86060181 0.763821991 0.848849441 0.760476201 1 18.37073129 -2.091452299 1.991613365 1.298882654 0.803488298 0.254173382 0.104551638 3531735.98 917243.7805 4783143.41 0.025055964 0.008101169 2.091452299 -0.495394355 TSLDIEEYS(ph)DTEVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 TSLDIEEYS(1)DTEVQK;TSLDIEEYS(1)DTEVQK 233.4 1.31E-17 218831000 516400 326490 438990 321570 580320 585560 546470 444680 475950 287820 TRUE FALSE 536787.8707 382562.1178 450430.44 385175.5862 481677.4137 449572.5642 503636.2535 438719.7919 458820.6525 344212.8184 1.559465081 1.111411596 1.30858125 1.119004191 1.399359315 1.306088967 1.463153685 1.274559716 1.332956322 1 18.3929413 -0.942410176 4.732566261 0.999997287 1.312480986 0.348245136 0.130777195 3.93E-06 8.79E-07 0.116848706 0.027541232 0.114179944 0.942410176 0.312483699 TSLGSDSSTQAKDAHLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSLGSDSSTQAKDAHLSPK 19 1 O60503 O60503 ADCY9 Adenylate cyclase type 9 1 TSLGS(0.016)DS(0.016)S(0.016)T(0.016)QAKDAHLS(0.936)PK 64.295 0.019017 585960000 849780 320240 485140 274960 812010 736720 707430 413290 551960 226990 TRUE FALSE 883329.9706 375238.7289 497783.1469 329346.2673 673984.8302 565627.9451 651979.7881 407750.5236 532095.0674 271464.3445 3.25394472 1.382276297 1.833696237 1.213221088 2.482774787 2.083617818 2.401714263 1.502040809 1.960091917 1 18.05040319 0.477084595 0.875822347 0.998426485 2.010305071 0.22660937 0.568099992 2.70382479 3.055713981 0.546542428 0.175327812 2.999746774 -0.477084595 1.011878585 TSLS(ph)PTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSLSPTSK 8 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 TSLS(0.994)PT(0.004)S(0.002)K 100.79 0.0061429 177040000 308310 195420 250130 209160 375360 373580 325980 301930 300500 208310 TRUE FALSE 320482.3169 228981.8648 256648.5933 250531.2237 311556.4413 286821.7067 300428.8358 297883.1222 289685.0637 249124.3562 1.286435103 0.91914684 1.030202736 1.00564725 1.250606107 1.15131941 1.205939236 1.19572059 1.162813095 1 17.92650655 3.247870621 24.99994102 1.174942051 1.048117518 0.165388431 0.106761832 268.6115024 721291.6806 0.027697892 0.037001853 1769.58171 -3.247870621 -0.126824534 TSMTEEYRVPDGMVGLIIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSMTEEYRVPDGMVGLIIGR 20 1 A0A087WTP3;Q92945 A0A087WTP3 KHSRP Far upstream element-binding protein 2 0 170.38 8.56E-12 561690000 192020 223660 241640 200360 284560 271420 243080 213930 201450 221320 FALSE TRUE 199601.0979 262071.8652 247937.3369 239990.61 236190.5928 208386.8184 224026.7544 211062.6183 194199.8539 264683.4166 0.754112594 0.990133302 0.936731663 0.906708146 0.892351307 0.787305911 0.846395129 0.797415346 0.733706163 1 18.01390828 2.852151655 5.515655491 0.820089554 0.905497487 0.107057096 0.085568456 0.379183377 15.95525399 0.024777321 0.026367935 711.4619116 -2.852151655 0.085407934 TSNKPLMIIHHLDECPHSQALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSNKPLMIIHHLDECPHSQALK 22 1 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 229.97 8.02E-27 6549400000 5959600 4152700 5491100 4514600 6989400 6700700 6590700 5230400 5260900 2887900 FALSE TRUE 6194889.61 4865893.921 5634202.577 5407574.405 5801344.285 5144563.975 6074103.712 5160295.043 5071561.237 3453728.713 1.79368159 1.408881336 1.631339067 1.565720662 1.679733635 1.489568059 1.758708983 1.494122866 1.46843069 1 21.71972333 0.674725081 1.330531946 1.000710802 1.604726278 0.724204495 0.11239877 0.519691756 1.435920293 0.096018177 0.02863957 4.728518379 -0.674725081 0.604015476 TSNKPLMIIHHLDECPHSQALKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSNKPLMIIHHLDECPHSQALKK 23 2 O95994;B5MC07;C9J3E2 O95994 AGR2 Anterior gradient protein 2 homolog 0 ; 228.62 2.13E-33 1982540000 3716900 2147730 3419700 2219750 4993700 4018800 3858500 3279900 3558200 1622850 FALSE TRUE 3863646.082 2516585.92 3508820.191 2658809.925 4144872.658 3085494.606 3556060.688 3235938.305 3430141.077 1940816.386 1.99073241 1.296663578 1.807909402 1.369944083 2.135633586 1.589792124 1.83224993 1.667307803 1.767370217 1 20.88823221 -1.31673004 5.600017137 0.999894384 1.708038794 0.439090886 0.243075017 0.000285972 3.49E-05 0.209984147 0.04948645 0.048224747 1.31673004 0.70814441 TSNRYS(ph)PESQAQSVHHQRPGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TSNRYSPESQAQSVHHQRPGSR 22 2 O75376;O75376-2;A0A088AWL3;E7EVK1;J3KS29;J3QKP0 O75376 NCOR1 Nuclear receptor corepressor 1 1 T(0.002)S(0.002)NRYS(0.989)PES(0.006)QAQSVHHQRPGSR;T(0.066)S(0.066)NRY(0.001)S(0.851)PES(0.016)QAQSVHHQRPGSR;T(0.007)S(0.007)NRYS(0.984)PES(0.001)QAQSVHHQRPGSR;T(0.039)S(0.039)NRYS(0.83)PES(0.092)QAQSVHHQRPGSR;T(0.005)S(0.005)NRYS(0.984)PES(0.005)QAQSVHHQRPGSR 212.75 8.19E-24 1208947000 86335.9 363325 354227 347278 371132 516208 333426 430680 363137 331472 TRUE FALSE 89744.508 425723.2425 363458.4466 415968.5519 308047.1152 396326.5152 307291.1989 424907.4391 350067.7703 396417.592 0.226388813 1.073926211 0.916857511 1.049319103 0.777077308 0.99977025 0.775170439 1.071868271 0.883078293 1 18.59666146 4.744695748 24.9990497 0.947842729 0.226388496 0.809038377 0.105415741 261.168761 1064164.729 0.022999852 0.212560998 55551.49463 -4.744695748 -0.721454233 TSPDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSPDTLRR 8 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 172.21 0.00045678 2104090000 2060700 2364780 2405520 2017860 3318260 3344250 2321230 2510470 2416880 2615200 FALSE TRUE 2142058.027 2770912.57 2468209.827 2416986.685 2754223.35 2567598.62 2139285.927 2476821.256 2329896.961 3127598.369 0.684889098 0.88595537 0.789170966 0.772793179 0.880619257 0.820948957 0.684002763 0.791924334 0.74494762 1 21.57662383 -2.004644922 2.460698665 1.21896949 0.786696036 0.495428301 0.065366269 9097612.715 3224092.362 11280294.41 0.015358727 0.009893617 2.004644922 -0.432273453 TSPENVQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 66.435 0.063739 278840000 184580 155910 122690 152330 119090 149400 153830 135590 130620 138440 FALSE TRUE 191867.3609 182686.3297 125887.4022 182460.4193 98847.12434 114704.1142 141772.4026 133772.6378 125919.0117 165564.6674 1.158866586 1.103413745 0.760351856 1.102049261 0.597030308 0.692805512 0.856296243 0.807978175 0.760542776 1 17.3370353 4.457804756 1.107000183 0.798296589 1.272586079 0.410070285 0.141766399 0.986655092 1.39855468 0.041339673 0.49002301 28694.90264 -4.457804756 0.47428949 TSPGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPGSPR 7 0 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 TSPGS(1)PR 81.547 0.028222 625100000 658220 689820 690660 608940 822980 863380 696220 758800 652560 644810 TRUE FALSE 684207.0339 808291.2189 708659.167 729386.5145 683090.1536 662873.0797 641648.4572 748629.5271 629074.4931 771148.1739 0.887257543 1.048165899 0.918966278 0.945844831 0.885809209 0.859592361 0.832068958 0.970798548 0.815763448 1 19.55664857 3.479670531 2.124003469 0.892417698 0.962439902 0.139087135 0.065894364 0.542858701 4.899265349 0.018634005 0.03042123 3017.661565 -3.479670531 0.070022203 TSPLKDNPS(ph)PEPQLDDIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 T(0.002)S(0.057)PLKDNPS(0.942)PEPQLDDIKR 174.99 1.79E-12 200800000 585930 220040 376120 208920 550720 556800 494690 354660 395140 192850 TRUE FALSE 609062.9688 257830.1583 385921.9962 250243.7524 457108.8111 427491.6384 455914.9052 349906.3628 380918.9886 230635.2652 2.640805899 1.117912988 1.67330003 1.085019467 1.981955408 1.853539779 1.976778811 1.517141633 1.651607738 1 17.8152536 0.458833227 1.314577508 1.000385008 1.707586361 0.20745584 0.425379019 4.029190524 8.170299524 0.382063973 0.113321292 2.876293682 -0.458833227 0.707201353 TSPPCS(ph)PANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPPCSPANLSR 12 0 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 TS(0.004)PPCS(0.995)PANLSR 118.73 0.0002051 0 37997 46489 41616 53594 64766 75595 62003 53588 55567 61565 TRUE FALSE 39497.1509 54473.12412 42700.54715 64194.73324 53757.09845 58039.2069 57143.04285 52869.74051 53567.15452 73627.48302 0.536445758 0.739847702 0.579953917 0.871885478 0.730122724 0.788281828 0.776110231 0.71807073 0.727542927 1 16.16795676 -5 0.092802135 1.7975098 0.52412518 0.533812505 0.08526424 169.9875572 1.090589525 27.40194888 1.779138898 1.00E-05 5 -1.27338462 TSPSGGTWSSVVSGVPRLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSPSGGTWSSVVSGVPRLSPK 21 1 Q99700;A0A2R8Y5A6;Q99700-4;Q99700-2;Q99700-5;H0YH87;A0A5F9ZHW5;A0A2R8Y7P6;A0A2R8YDM9;F8VQP2;V9GY86;A0A5F9ZI57;A0A2R8Y7E6;A0A5F9ZHX3;A0A5F9ZHH4 Q99700 ATXN2 Ataxin-2 1 TSPSGGTWSSVVSGVPRLS(1)PK;TSPSGGTWSSVVSGVPRLS(1)PK 201.97 4.02E-22 2046370000 1420210 766640 1071520 671700 1474680 1536200 1099420 1141920 1168900 758140 TRUE FALSE 1476280.987 898304.4564 1099444.691 804560.2552 1224014.42 1179440.831 1013244.588 1126614.43 1126831.517 906683.0175 1.628221726 0.990759107 1.212600953 0.887366632 1.349991559 1.300830399 1.117529024 1.242567037 1.242806467 1 19.79023874 -1.155276105 6.173514327 0.99999874 1.206729958 0.102531106 0.191375944 3.06E-06 4.18E-07 0.170545655 0.040197751 0.069939721 1.155276105 0.206731218 TSPTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPTFR 6 0 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3 P62750 RPL23A 60S ribosomal protein L23a 0 97.64 0.095015 111670000 68620 81592 74195 69970 87901 107430 82642 84944 90102 71284 FALSE TRUE 71329.17059 95604.7913 76128.58265 83809.85716 72959.61942 82481.01062 76164.3041 83805.46462 86859.24662 85250.73499 0.8366986 1.121454159 0.892996203 0.983098353 0.855823934 0.967510845 0.893415219 0.983046828 1.018868009 1 16.37942465 1.523610978 5.993368325 1.006997942 0.941047414 0.13528072 0.076122186 0.279164962 21.35574595 0.040174301 0.018119748 33.38958166 -1.523610978 -0.065950528 TSPVVAPTS(ph)EPS(ph)SPLHTQLLKDPEPAFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPVVAPTSEPSSPLHTQLLKDPEPAFQR 29 1 B7ZM87;O75044 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 2 T(0.001)S(0.001)PVVAPT(0.479)S(0.52)EPS(0.518)S(0.477)PLHT(0.005)QLLKDPEPAFQR 90.014 0.0021647 82144000 57309 48812 71625 59880 86146 89295 74715 70028 74677 59449 TRUE FALSE 59571.60357 57195.0813 73491.60634 71724.08528 71502.93369 68557.58953 68858.64307 69089.3892 71989.38936 71096.89333 0.837893202 0.804466674 1.033682386 1.008821651 1.005711084 0.964283899 0.968518311 0.971763828 1.012553235 1 16.1174989 4.243699616 24.99999998 0.991900232 0.821179869 0.906910003 0.022334978 34.8093573 169333.7918 0.005910944 0.015194777 17526.67834 -4.243699616 -0.170720364 TSPVVAPTSEPS(ph)SPLHTQLLKDPEPAFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSPVVAPTSEPSSPLHTQLLKDPEPAFQR 29 1 B7ZM87;O75044 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 TSPVVAPT(0.003)S(0.003)EPS(0.468)S(0.411)PLHT(0.114)QLLKDPEPAFQR 42.582 0.088775 125240000 50234 49304 53954 43499 63428 74627 60177 51261 62461 37277 TRUE FALSE 52217.27711 57771.57847 55360.08556 52102.97237 52646.53122 57296.01023 55460.1695 50573.93014 60213.04081 44580.71444 1.171297449 1.295887228 1.24179449 1.168733454 1.180926144 1.285219651 1.244039495 1.134435165 1.350652217 1 15.44413212 -1.471577782 3.272808682 0.995814326 1.224824 0.534799968 0.06426196 21325034.99 32204419.04 836710.8432 0.014915423 0.033761538 1.471577782 0.229009674 TSPYDHMLPGAEHFAEYAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSPYDHMLPGAEHFAEYAGR 20 0 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;; 165.17 9.87E-12 576960000 484789 659350 704204 655358 861634 920533 742299 785844 713782 724848 FALSE TRUE 503928.8441 772588.2335 722556.1348 784985.8564 715173.7604 706753.1616 684115.6647 775311.0466 688093.1252 866868.0875 0.581321254 0.89124083 0.833524899 0.905542455 0.825008754 0.815294936 0.789180816 0.894381807 0.793769127 1 19.72545295 -4.576887037 0.023006166 2.055560056 2.55E-06 0.334028387 0.08460811 2997.419809 5.578016897 343.1735673 179.4232665 2.65E-05 4.576887037 -2.055557506 TSQEELLAEVVQGQSRT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.024)RT(0.976)PR;TSQEELLAEVVQGQS(0.014)RT(0.986)PR 189.18 2.36E-14 148626000 191022 185777 184799 139204 193110 217872 139243 162861 153408 169756 TRUE FALSE 198563.6961 217682.7546 189615.0138 166738.1357 160285.2312 167274.5299 128328.7698 160678.1147 147886.876 203016.438 0.978067087 1.072242015 0.933988477 0.821303621 0.789518488 0.823945743 0.632110242 0.791453718 0.728447792 1 17.63123702 3.812174629 2.004513525 0.775033743 1.027407151 0.506655457 0.090408814 0.229195747 1.784308029 0.023931178 0.05379051 6488.953006 -3.812174629 0.252373407 TSQLGDS(ph)PFYPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSQLGDSPFYPGK 13 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 TSQLGDS(1)PFYPGK 179.79 1.41E-05 99173000 131000 92016 98069 86629 123650 154440 113230 105850 108390 95550 TRUE FALSE 136171.9812 107819.0322 100624.7587 103763.9576 102632.0172 118573.6506 104354.7367 104431.2539 104489.0651 114271.1931 1.191656248 0.943536418 0.880578525 0.908050007 0.898144269 1.037651287 0.913219981 0.913889591 0.914395503 1 16.80210223 4.736167205 5.176815466 0.928869582 1.202908379 0.736450014 0.046144126 0.074936457 6.806025687 0.010855001 0.073268168 54471.23291 -4.736167205 0.274038797 TSQLLETLNQLSTHTHVVDITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSQLLETLNQLSTHTHVVDITR 22 0 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;E7EWF7 E7EX90 DCTN1 Dynactin subunit 1 0 99.366 0.00058908 136690000 39556 71799 67206 69117 82301 105190 61227 76984 69379 77837 FALSE TRUE 41117.70142 84129.91973 68957.44357 82788.13631 68311.50542 80761.21667 56427.86775 75952.1554 66882.06334 93087.66987 0.441709428 0.90377082 0.740779565 0.889356629 0.733840535 0.867582321 0.606179828 0.815920685 0.718484665 1 16.50630246 -2.605948635 1.890999912 4.405626464 0.75659093 0.241228407 0.133836214 4471489.336 180919.826 65458519.28 0.030709986 0.002477715 2.605948635 -3.649035534 TSQTWHGGIATIFQSPGDEVWGVVWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSQTWHGGIATIFQSPGDEVWGVVWK 26 0 O75223;B8ZZK2;H7BZK5;O75223-2;O75223-4 O75223 GGCT Gamma-glutamylcyclotransferase 0 ; 261.46 7.93E-53 801820000 404920 505950 563410 516760 643540 736360 628680 599860 564940 408900 FALSE TRUE 420906.5543 592842.9768 578092.9274 618973.5856 534151.3007 565351.5496 579402.4189 591819.8579 544607.9198 489016.1261 0.860721215 1.212317846 1.182155141 1.265752912 1.092297927 1.156100013 1.184832949 1.210225647 1.113680901 1 18.89952252 4.743496209 24.79140933 1.169153224 0.860721072 0.6044645 0.071458837 279.827598 1405517.573 0.015684166 0.130572981 55398.27086 -4.743496209 -0.308432152 TSQVGAASAPAKES(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;TSQVGAAS(0.003)APAKES(0.997)PR 272.51 2.14E-35 20716892000 10592393 6414961 8402401 6035330 11218716 11766417 10604355 8927181 9179671 5136842 TRUE FALSE 11010588.85 7516680.65 8621374.473 7229100.26 9311762.662 9033844.974 9773157.946 8807526.741 8849296.434 6143307.839 1.792289943 1.223555916 1.403376601 1.176743938 1.51575713 1.470518035 1.59086248 1.433678235 1.440477454 1 22.55058425 0.37503574 3.834247481 1.000000007 1.441840575 0.40123533 0.16455354 211.8584075 1295.830194 0.150615871 0.038571337 2.371568867 -0.37503574 0.441840568 TSQVGAASAPAKES(ph)PRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 186.55 2.70E-10 1194766000 2597741 916235 1430226 916758 2215454 2444039 2168945 1627173 1762678 701890 TRUE FALSE 2700301.821 1073591.234 1467498.865 1098089.996 1838871.92 1876447.982 1998937.423 1605363.407 1699239.563 839411.907 3.216897209 1.27898023 1.748246424 1.308165856 2.190666948 2.235431695 2.381354621 1.912485865 2.024321491 1 19.6790194 TSRPENAIIYNNNEDFQVGQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ;;; 257.29 3.53E-37 1941740000 788360 620720 821820 587320 1761700 1124140 981710 827190 842860 843010 FALSE TRUE 819485.0615 727323.8315 843237.3043 703490.143 1462246.863 863075.5215 904761.005 816102.8711 812525.6332 1008181.669 0.812834717 0.7214214 0.836394204 0.697781129 1.450380331 0.856071428 0.897418623 0.809479974 0.805931766 1 19.9433242 TSS(ph)ASRPASLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSASRPASLPR 12 1 Q69YQ0-2;Q69YQ0;A0A494C1J1 Q69YQ0-2 SPECC1L Cytospin-A 1 T(0.186)S(0.186)S(0.624)AS(0.003)RPASLPR 130.47 0.00013077 319790000 155370 156980 168620 189630 239510 278600 196870 193970 188540 201390 TRUE FALSE 161504.1276 183940.0939 173014.3757 227138.248 198798.1758 213899.3722 181438.815 191370.1494 181754.4822 240848.5147 0.670563104 0.763716953 0.718353509 0.943075146 0.825407522 0.8881075 0.753331675 0.794566451 0.754642321 1 17.8777665 -2.662331869 2.141739952 6.396043539 0.794176853 0.408494697 0.075602799 2150338.973 139532.1956 57552974.48 0.018536122 0.002176046 2.662331869 -5.601866685 TSS(ph)DPVLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TSSDPVLLK 9 0 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 TSS(1)DPVLLK;TSS(1)DPVLLK;TS(0.004)S(0.996)DPVLLK;TSS(1)DPVLLK;TS(0.002)S(0.998)DPVLLK;TSS(1)DPVLLK;TS(0.036)S(0.964)DPVLLK;T(0.001)S(0.006)S(0.993)DPVLLK 236.35 3.33E-10 7981190000 12773300 8106180 10924560 8192310 14250200 14130700 13721470 11153510 11708770 6485350 TRUE FALSE 13277599.75 9498353.358 11209263.01 9812724.466 11827956.09 10849059.08 12645945.33 11004015.44 11287373.65 7756030.163 1.711906667 1.224641106 1.445232003 1.265173582 1.525001302 1.398790212 1.630466239 1.418769037 1.45530296 1 22.88688698 -1.059670819 5.160599192 0.99999373 1.44659193 0.484893028 0.139878996 9.25E-06 1.69E-06 0.124172486 0.029267325 0.0871624 1.059670819 0.4465982 TSS(ph)DSALHTSVMNPSPQDTYPGPTPPSILPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSDSALHTSVMNPSPQDTYPGPTPPSILPSR 32 0 Q53ET0;H0YDQ8 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 T(0.15)S(0.15)S(0.665)DS(0.034)ALHTSVMNPSPQDTYPGPTPPSILPSR 220.03 2.27E-35 338960000 7254.1 40767 33921 34265 41528 55996 29561 46303 26064 33998 TRUE FALSE 7540.497469 47768.41513 34805.00913 41042.51473 34469.08539 42991.77763 27243.93158 45682.38402 25125.96173 40659.25717 0.185455859 1.174847217 0.856016847 1.009426084 0.847754922 1.057367513 0.670054828 1.123542022 0.617964112 1 15.31129624 4.750426533 24.84891516 0.931041859 0.18545537 0.621947892 0.173796513 998.8496411 2091691.389 0.036813015 0.608228747 56289.38876 -4.750426533 -0.745586489 TSS(ph)EDNLYLAVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 TS(0.001)S(0.999)EDNLYLAVLR;TSS(1)EDNLYLAVLR;TS(0.002)S(0.998)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;TS(0.001)S(0.999)EDNLYLAVLR;T(0.001)S(0.05)S(0.949)EDNLYLAVLR 380.66 5.00E-92 1471067000 1605750 1442898 1568000 1383772 2030730 2306650 1995850 1718530 1649480 1276761 TRUE FALSE 1669146.25 1690704.507 1608863.368 1657477.971 1685547.24 1770965.495 1839410.062 1695495.916 1590115.537 1526917.873 1.093147365 1.107266172 1.053667258 1.085505646 1.103888605 1.159830222 1.204655532 1.110404133 1.041389039 1 20.54219104 3.076069885 4.591003395 1.11957029 1.084614601 0 0.055611601 0.596311768 23.66118743 0.016518685 0.019829287 1191.433713 -3.076069885 -0.03495569 TSS(ph)EEEDSRREEPSLLLVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSEEEDSRREEPSLLLVLK 20 2 A0A087WZV0;O43314-2;O43314;D6RBU4 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 T(0.301)S(0.301)S(0.398)EEEDSRREEPSLLLVLK 200.95 6.82E-22 105440000 179060 106960 182150 100670 223070 209220 182040 140360 159560 105630 TRUE FALSE 186129.4271 125329.548 186896.9786 120582.2255 185152.6411 160631.8258 167771.2291 138478.7038 153817.4668 126326.1761 1.473403477 0.992110676 1.479479427 0.954530797 1.465671224 1.271564063 1.328079693 1.096199601 1.21762149 1 16.94679409 1.003393083 0.938722034 1.00887377 1.267750334 0.16790071 0.180549641 1.023456774 1.944743949 0.154328155 0.052687896 10.07843462 -1.003393083 0.258876564 TSS(ph)FAEPGGGGGGGGGGPGGSASGPGGTGGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSFAEPGGGGGGGGGGPGGSASGPGGTGGGK 32 0 P49840 P49840 GSK3A Glycogen synthase kinase-3 alpha 1 T(0.119)S(0.119)S(0.763)FAEPGGGGGGGGGGPGGSASGPGGTGGGK;T(0.142)S(0.142)S(0.715)FAEPGGGGGGGGGGPGGSASGPGGTGGGK 305.64 1.88E-90 945220000 2315400 1543240 2057070 1786830 3014870 3002260 2466070 2334770 2305970 1491050 TRUE FALSE 2406813.78 1808279.465 2110678.934 2140259.641 2502403.474 2305030.615 2272772.99 2303476.227 2222978.59 1783192.7 1.349721643 1.014068455 1.183651624 1.200240244 1.403327568 1.292642469 1.274552655 1.291770781 1.24662836 1 20.76603118 5.070788101 20.75704796 1.23070983 4.856892884 0.088733328 0.119515668 1416.510418 422004.2972 0.027522963 3798.198203 117703.1542 -5.070788101 3.626183053 TSS(ph)FTEQLDEGTPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TSSFTEQLDEGTPNR 15 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71;C9JHJ5;C9J0Y3 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 TSS(0.892)FT(0.108)EQLDEGTPNR;TSS(0.957)FT(0.043)EQLDEGTPNR;TS(0.001)S(0.975)FT(0.024)EQLDEGTPNR;TSS(1)FTEQLDEGTPNR;TS(0.001)S(0.99)FT(0.008)EQLDEGTPNR;TSS(0.833)FT(0.166)EQLDEGTPNR;TSS(0.982)FT(0.018)EQLDEGTPNR;TS(0.023)S(0.88)FT(0.097)EQLDEGTPNR 380.2 3.02E-98 6899090000 3558840 3393070 3776840 3874910 4350830 5177850 4773780 4214310 3941720 2838070 TRUE FALSE 3699345.751 3975803.378 3875267.553 4641355.633 3611277.471 3975372.809 4399598.65 4157824.068 3799858.267 3394135.478 1.089922832 1.171374391 1.141753939 1.36746328 1.063975641 1.171247534 1.296235427 1.225002388 1.119536415 1 21.69461272 0.957812439 4.289486209 1.000203509 1.195644893 0.319712245 0.085543538 0.252835214 14.04279992 0.08040603 0.020481809 9.074285502 -0.957812439 0.195441384 TSS(ph)FTEQLDEGTPNRENASTHASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSFTEQLDEGTPNRENASTHASK 24 1 Q13439-5;E7EVX2;C9JHJ5 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 T(0.098)S(0.098)S(0.8)FT(0.003)EQLDEGTPNRENASTHASK;T(0.008)S(0.139)S(0.852)FT(0.001)EQLDEGTPNRENASTHASK 233.67 1.48E-37 1221150000 103438 631430 712350 492140 917440 1012650 471460 817890 716860 739650 TRUE FALSE 107521.8121 739873.1907 730914.4262 589483.8231 761493.8765 777477.3844 434505.7333 806927.5223 691060.3486 884570.256 0.121552597 0.836421059 0.826293244 0.666407014 0.860863082 0.878932317 0.491205453 0.912225475 0.78123851 1 19.75461721 4.74073907 24.91377895 0.794430184 0.121552354 0.701380591 0.133782029 97.82136029 1118651.508 0.029773026 0.197389543 55047.68628 -4.74073907 -0.672877831 TSS(ph)GTSLSAMHSSGSSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSSGTSLSAMHSSGSSGK 18 0 Q12888;Q12888-2;A6NNK5;Q12888-3;M0R142 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.003)S(0.106)S(0.886)GT(0.002)S(0.002)LSAMHSSGSSGK;T(0.016)S(0.086)S(0.865)GT(0.016)S(0.016)LS(0.001)AMHSSGSSGK;T(0.177)S(0.177)S(0.583)GT(0.03)S(0.03)LS(0.002)AMHSSGSSGK 198.35 1.12E-15 999960000 114070 945010 950140 982200 1020330 1486270 807780 1278310 948120 943210 TRUE FALSE 118573.5717 1107308.116 974901.4289 1176476.228 846894.6711 1141106.317 744464.0929 1261176.345 913997.3464 1128013.941 0.105117115 0.981644 0.864263635 1.04296249 0.750783869 1.011606573 0.659977741 1.118050318 0.810271322 1 20.10535347 4.741346168 24.93731571 0.916864386 0.105116814 0.762433046 0.135706653 106.45865 953005.9997 0.029177549 0.202235865 55124.69097 -4.741346168 -0.811747573 TSS(ph)IADEGTYTLDSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSSIADEGTYTLDSILR 17 0 A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3;E7ERV5 A0A087WY00 MYO5A Unconventional myosin-Va 1 T(0.018)S(0.018)S(0.964)IADEGTYTLDSILR;TS(0.023)S(0.976)IADEGTYTLDSILR;T(0.001)S(0.001)S(0.997)IADEGTYTLDSILR;T(0.054)S(0.054)S(0.892)IADEGTYTLDSILR 246.96 1.11E-20 424205000 532160 461146 599760 618460 849700 854330 845110 715570 717010 527584 TRUE FALSE 553170.0877 540344.2383 615390.2383 740789.5421 705268.2975 655924.805 778868.0699 705978.9546 691204.9502 630953.9836 0.876720176 0.856392467 0.975332995 1.174078556 1.117780878 1.039576296 1.234429277 1.118907199 1.095491855 1 19.26717527 3.971414473 3.433088128 1.12057766 0.869509102 0.717874895 0.062057044 0.109442164 2.672624204 0.015623815 0.033661359 9362.988138 -3.971414473 -0.251068558 TSS(ph)KES(ph)SPIPS(ph)PTSDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.106)S(0.12)S(0.759)KES(0.611)S(0.404)PIPS(0.913)PT(0.04)S(0.047)DRK 88.79 0.0027794 349820000 1405000 296890 464180 263390 849350 1179800 875340 554900 567060 168760 TRUE FALSE 1460470.485 347878.548 476276.9121 315487.7559 704977.7904 905809.33 806728.5635 547462.4731 546651.6214 201825.2909 7.236310566 1.723661819 2.35984752 1.563172556 3.493010154 4.488086335 3.997162892 2.712556344 2.708538751 1 17.62274745 TSS(ph)KES(ph)SPIPSPTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDR 16 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 T(0.293)S(0.332)S(0.376)KES(0.818)S(0.18)PIPSPTSDR 54.117 0.082968 158970000 358280 127700 170780 105190 270390 403140 248930 178150 198550 79800 TRUE FALSE 372425.1711 149631.4816 175230.6671 125996.268 224429.2044 309516.8446 229418.2161 175762.1906 191404.2243 95435.28214 3.902384555 1.567884312 1.836120386 1.320227333 2.351637669 3.24321192 2.403914056 1.841689852 2.005591852 1 16.5422351 4.747231876 24.52182577 2.019768385 3.902385818 0.487602806 0.596124449 793.3172195 2243390.587 0.146565114 1.713638823 55876.84501 -4.747231876 1.882617433 TSS(ph)KESS(ph)PIPS(ph)PTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDR 16 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.289)S(0.33)S(0.378)KES(0.185)S(0.817)PIPS(0.861)PT(0.115)S(0.024)DR 70.917 0.0099662 0 347340 128290 156990 126510 285330 390890 236120 171230 204360 86607 TRUE FALSE 361053.2514 150322.8095 161081.2884 151533.3004 236829.7085 300111.7215 217612.2974 168934.9419 197005.1235 103575.9835 3.48587809 1.451328817 1.555199217 1.463015801 2.286531111 2.897502987 2.100991853 1.631024261 1.902034786 1 16.66032999 0.804358066 1.031859624 1.015599743 2.103284862 0.229624027 0.622710492 1.259587897 2.555285461 0.597014197 0.192571048 6.373207608 -0.804358066 1.08768512 TSS(ph)KESS(ph)PIPSPTSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDR 16 1 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 T(0.121)S(0.144)S(0.733)KES(0.253)S(0.748)PIPSPTSDR 77.631 0.013307 154750000 383060 133510 193490 104940 277000 438470 279870 194240 213470 103590 TRUE FALSE 398183.5046 156439.3039 198532.5084 125696.8188 229915.6389 336641.9876 257933.0581 191636.5305 205787.2564 123886.4771 3.214099825 1.262763358 1.602535748 1.014612908 1.855857429 2.717342484 2.082011403 1.546872063 1.661095393 1 16.91865919 0.888751271 1.377478545 1.013332826 1.890268874 0.17111788 0.616911261 1.073073951 3.99794874 0.585194332 0.174978757 7.740183761 -0.888751271 0.876936048 TSS(ph)KESS(ph)PIPSPTSDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 T(0.262)S(0.302)S(0.436)KES(0.169)S(0.827)PIPS(0.003)PTSDRK 99.923 0.00078366 432060000 499490 122040 197600 89819 290810 436310 278460 173780 212260 65520 TRUE FALSE 519210.2509 142999.4207 202749.6183 107584.9301 241378.2201 334983.6148 256633.5776 171450.7633 204620.8041 78357.38954 6.626181065 1.824964072 2.587498378 1.37300299 3.08047807 4.275073695 3.275167525 2.188061194 2.611378522 1 16.25778171 4.745033726 24.88911115 2.568995004 6.626183011 0.651769195 0.909064019 446.5068757 1716770.898 0.219947701 2.083556576 55594.74291 -4.745033726 4.057188007 TSS(ph)KSEAGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSKSEAGAR 10 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 T(0.001)S(0.004)S(0.618)KS(0.378)EAGAR;T(0.005)S(0.241)S(0.649)KS(0.105)EAGAR 155.86 7.25E-06 996980000 1498030 629500 1075560 710960 1598970 1656820 1574010 1120100 1201590 575630 TRUE FALSE 1557173.381 737611.7282 1103589.977 851585.766 1327177.651 1272048.664 1450634.983 1105086.892 1158345.011 688413.6774 2.261973334 1.071465824 1.6030913 1.237026215 1.927878097 1.847796908 2.107214065 1.60526574 1.68262928 1 19.39291624 3.22286453 24.99912062 1.751551532 1.513944691 0.020051111 0.399724308 635.8301237 1012683.049 0.108005625 0.129506624 1670.569429 -3.22286453 -0.237606841 TSS(ph)LDTITGPYLTGQWPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C2L5;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 TS(0.005)S(0.995)LDTITGPYLTGQWPR;TS(0.025)S(0.975)LDTITGPYLTGQWPR 244.97 3.70E-24 468590000 232406 239260 234638 212080 293270 325350 238650 246160 221936 171084 TRUE FALSE 241581.5683 280351.0438 240752.859 254028.791 243420.0702 249792.3932 219943.9894 242860.6278 213948.5667 204604.6342 1.180723835 1.370208671 1.176673539 1.241559322 1.189709466 1.220854035 1.074970712 1.186975206 1.045668235 1 17.6424793 1.669456328 0.374081392 0.98709925 1.276675904 0.615131412 0.062654922 0.714299358 0.297813287 0.075267807 0.06626709 46.71499733 -1.669456328 0.289576654 TSS(ph)LTQFPPSQSEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 TSSLTQFPPSQSEER 15 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3 Q9H6Z4 RANBP3 Ran-binding protein 3 1 TS(0.005)S(0.994)LTQFPPSQSEER;T(0.001)S(0.028)S(0.958)LT(0.014)QFPPSQSEER;T(0.01)S(0.03)S(0.956)LT(0.003)QFPPSQSEER;TS(0.025)S(0.974)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;TSS(1)LTQFPPSQSEER;T(0.011)S(0.021)S(0.968)LTQFPPSQSEER;TS(0.008)S(0.992)LTQFPPSQSEER;TS(0.019)S(0.98)LTQFPPSQSEER;TS(0.001)S(0.999)LTQFPPSQSEER;T(0.001)S(0.058)S(0.941)LTQFPPSQSEER;TSS(0.999)LT(0.001)QFPPSQSEER 407.59 2.49E-114 2944670000 3008007 3137425 3414200 3339531 4393220 5019150 3919050 3946270 3741850 3249683 TRUE FALSE 3126765.439 3676253.338 3503176.857 4000080.264 3646462.034 3853528.478 3611864.62 3893376.705 3607181.549 3886396.165 0.804541098 0.945928614 0.901394688 1.029251804 0.938263079 0.991542888 0.929360896 1.001796147 0.928155905 1 21.89000154 5.666611039 1.041695964 0.970391205 4.24E-11 0.621224166 0.037778233 6.236910874 1.281081262 0.009981042 10.63045545 464099.434 -5.666611039 -0.970391205 TSS(ph)PHKEESPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSPHKEESPK 11 1 G3XAH6;P51003;H0YJL4 G3XAH6 PAPOLA Poly(A) polymerase alpha 1 TS(0.017)S(0.983)PHKEESPK;T(0.106)S(0.132)S(0.761)PHKEES(0.001)PK 173.06 7.65E-06 467630000 973200 394230 659090 380610 1075070 978780 981240 681400 775090 261570 TRUE FALSE 1011622.687 461935.9358 676266.4268 455893.522 892329.9854 751473.1786 904327.8448 672266.9475 747194.6623 312819.6334 3.233884895 1.476684602 2.161841376 1.457368634 2.8525383 2.402257078 2.890892221 2.14905612 2.388579815 1 18.25497154 3.226854729 24.99965338 2.370963763 2.044847332 0.00864732 0.672885785 711.9740402 1520523.781 0.180351416 0.21724729 1685.988971 -3.226854729 -0.326116431 TSS(ph)PLFNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSSPLFNK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 T(0.001)S(0.043)S(0.956)PLFNK;T(0.004)S(0.04)S(0.956)PLFNK;T(0.003)S(0.039)S(0.958)PLFNK;TS(0.035)S(0.965)PLFNK 135.87 0.000855 1294331000 4260020 3022420 3770310 3014340 5173360 4985070 4464410 4044300 3956920 2494190 TRUE FALSE 4428208.879 3541497.124 3868567.376 3610567.455 4293994.115 3827363.042 4114477.879 3990092.774 3814511.222 2982878.776 1.484542018 1.187274908 1.296924101 1.210430502 1.439546974 1.283110488 1.379364764 1.337665079 1.278801959 1 21.50827392 0.791589119 3.795104843 1.000011949 1.323013639 0.554616678 0.087441555 1.31667921 23.20451095 0.078102264 0.020024977 6.188553069 -0.791589119 0.32300169 TSS(ph)PPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSPPRK 7 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 T(0.031)S(0.019)S(0.95)PPRK;T(0.001)S(0.041)S(0.957)PPRK 76.605 0.042696 743740000 1685930 1198130 1607950 1157890 1965940 1900990 1927700 1656720 1754510 1073360 TRUE FALSE 1752491.818 1403899.507 1649854.498 1386917.186 1631770.221 1459513.882 1776601.837 1634514.378 1691365.528 1283664.341 1.36522591 1.093665581 1.2852694 1.080436015 1.27118139 1.136990283 1.384008093 1.273319142 1.317607316 1 20.29183658 2.267890195 24.99839687 1.271436387 1.201311772 0.002166881 0.125546746 568.6202529 484648.493 0.039557541 0.033091915 185.3063043 -2.267890195 -0.070124616 TSS(ph)TLDSEGTFNSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSTLDSEGTFNSYR 15 0 Q92609;Q92609-2;C9J397;C9JWX0;C9JW04;C9JDR8;C9JNM0;C9JED7;F2Z3C3;C9K0P2 Q92609 TBC1D5 TBC1 domain family member 5 1 TSS(0.999)T(0.001)LDSEGTFNSYR;TSS(1)TLDSEGTFNSYR 332.29 6.85E-69 356890000 324340 296720 329810 364450 479760 542180 446370 403270 379700 318960 TRUE FALSE 337145.1936 347679.3518 338405.1195 436537.1222 398210.5666 416266.9118 411382.353 397864.8253 366034.6712 381454.1051 0.88384209 0.911457885 0.887145046 1.144402738 1.043927857 1.091263421 1.078458319 1.04302148 0.959577224 1 18.54114996 3.757770419 24.98632921 1.055476368 0.895879269 0.695268254 0.047690069 434.3030698 564899.3729 0.012041407 0.021664972 5724.93314 -3.757770419 -0.159597098 TSS(ph)VPEYVYNLHLVENDFVGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 T(0.041)S(0.041)S(0.917)VPEYVYNLHLVENDFVGGR;T(0.117)S(0.117)S(0.766)VPEYVYNLHLVENDFVGGR;T(0.003)S(0.016)S(0.98)VPEYVYNLHLVENDFVGGR;T(0.006)S(0.023)S(0.971)VPEYVYNLHLVENDFVGGR;T(0.001)S(0.028)S(0.971)VPEYVYNLHLVENDFVGGR;T(0.004)S(0.021)S(0.976)VPEYVYNLHLVENDFVGGR 400.36 4.14E-133 2596840000 236642 276574 240184 215494 351034 359592 225770 271837 225205 243026 TRUE FALSE 245984.8089 324073.4331 246443.3924 258118.07 291365.3661 276082.2077 208073.5575 268193.4697 217099.916 290642.2917 0.846348986 1.11502504 0.847926814 0.888095358 1.00248785 0.949903767 0.71590943 0.922761337 0.746966021 1 18.14888512 TSS(ph)VPEYVYNLHLVENDFVGGRS(ph)PVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSSVPEYVYNLHLVENDFVGGRSPVPK 27 1 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 2 T(0.311)S(0.329)S(0.349)VPEY(0.005)VY(0.006)NLHLVENDFVGGRS(1)PVPK;T(0.091)S(0.108)S(0.8)VPEYVYNLHLVENDFVGGRS(1)PVPK;T(0.278)S(0.33)S(0.392)VPEYVYNLHLVENDFVGGRS(1)PVPK 198.06 7.61E-25 118201000 167176 119737 152648 110902 240318 230038 152913 153176 147448 111688 TRUE FALSE 173776.2376 140300.8983 156626.1323 132838.0846 199468.8322 176615.1608 140927.2795 151122.9263 142141.3753 133571.1252 1.301001525 1.050383443 1.172604723 0.994511983 1.493352938 1.322255544 1.055072938 1.131404157 1.064162446 1 17.02724864 2.213260047 24.96925644 1.079140337 1.214235649 0.245282007 0.135558312 404.0694699 398775.5199 0.052995429 0.03915422 163.4030079 -2.213260047 0.135095311 TSS(ph)VSSISQVSPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 TS(0.001)S(0.999)VSSISQVSPER;TS(0.001)S(0.988)VS(0.01)S(0.001)ISQVSPER;T(0.005)S(0.166)S(0.829)VSSISQVSPER 308.03 1.26E-55 296580000 500751 525309 554248 559985 682047 754030 600618 534194 570437 440735 TRUE FALSE 520521.0361 615526.7344 568692.1582 670748.3616 566112.8946 578917.9599 553539.9917 527034.0032 549907.0838 527088.5849 0.987539953 1.167786122 1.078930894 1.272553383 1.074037478 1.098331431 1.050183987 0.999896447 1.043291582 1 19.00768592 2.249077425 1.757354569 1.013739203 1.124910492 0.295711162 0.069550233 0.420865984 2.601958484 0.034787898 0.022050192 177.4505806 -2.249077425 0.111171289 TSS(ph)VVTLEVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSSVVTLEVAK 11 0 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 TSS(1)VVTLEVAK;TSS(0.999)VVTLEVAK;T(0.001)S(0.002)S(0.997)VVTLEVAK;TSS(1)VVTLEVAK 251.81 2.38E-20 1212390000 3173630 2080690 2769340 2067960 4128850 3529900 3391910 2756370 3069160 1826680 TRUE FALSE 3298927.363 2438032.322 2841511.275 2476996.316 3427029.552 2710134.221 3126043.231 2719425.369 2958701.531 2184582.972 1.510094789 1.116017269 1.300711079 1.133853164 1.568733985 1.240572803 1.430956513 1.244825856 1.354355302 1 21.05892647 -0.273096744 8.970818053 0.999995103 1.314409722 0.316533581 0.141631202 0 0 0.124509157 0.02934709 0.533216103 0.273096744 0.314414619 TSSAFVGKT(ph)PEAS(ph)PEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSAFVGKTPEASPEPK 17 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 2 TS(0.001)S(0.001)AFVGKT(0.998)PEAS(1)PEPK;TSSAFVGKT(1)PEAS(1)PEPK 147.56 9.06E-07 861740000 3715700 923700 1536590 961710 2639500 3172400 2521980 1656050 1799680 669210 TRUE FALSE 3862398.705 1082338.29 1576634.798 1151933.368 2190838.733 2435658.178 2324300.618 1633853.359 1734909.868 800328.8867 4.826014367 1.352366893 1.96998362 1.439324991 2.737423038 3.043321588 2.904181839 2.04147743 2.167746157 1 19.61023346 0.752082183 1.333009152 1.007896608 2.490746508 0.197925477 0.93880493 1.437820452 4.400933648 0.860399723 0.2573727 5.650438897 -0.752082183 1.4828499 TSSAQVEGGVHSLHSYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSAQVEGGVHSLHSYEK 18 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ; 266.78 2.01E-31 904030000 328830 717660 763640 722700 1057260 1146030 864600 943010 757040 742560 FALSE TRUE 341812.4623 840912.5224 783541.0857 865647.903 877547.3228 879881.9008 796830.3928 930370.4934 729794.2783 888050.4148 0.384902092 0.946919801 0.882315995 0.974773378 0.988172865 0.990801745 0.897280582 1.047655041 0.821793747 1 19.76028206 4.739144944 6.644028249 0.955041784 0.374341954 0.87842545 0.063046516 0.033955943 9.693774712 0.014161139 0.088385687 54845.99811 -4.739144944 -0.58069983 TSSESIYSRPGSSIPGS(ph)PGHTIYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 TSSESIYSRPGSSIPGS(0.999)PGHTIYAK 126.88 7.68E-05 120750000 59624 76866 111110 83063 128490 129870 103360 97497 115110 83639 TRUE FALSE 61978.00156 90067.13757 114005.6179 99492.61348 106649.3157 99709.6607 95258.37312 96190.21219 110967.2136 100026.4607 0.619616061 0.900433115 1.139754592 0.99466294 1.06621103 0.996832838 0.952331738 0.961647663 1.109378587 1 16.61002217 4.657959739 3.201753884 1.018651282 0.59388152 0.808462988 0.059935796 0.115715359 1.907325341 0.014759125 0.108055808 45494.58824 -4.657959739 -0.424769762 TSSGDPPS(ph)PLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSGDPPSPLVK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 TSSGDPPS(1)PLVK;T(0.001)S(0.001)S(0.004)GDPPS(0.994)PLVK 160.46 7.13E-05 286860000 1029380 617610 829290 620560 1160060 1221710 1103830 922630 930330 562530 TRUE FALSE 1070020.717 723679.7132 850901.9787 743304.9158 962873.4156 937986.3677 1017308.92 910263.654 896847.605 672746.9832 1.590524735 1.075708597 1.264817234 1.10488034 1.431256386 1.394263209 1.512171657 1.353054977 1.333112786 1 19.35970449 3.211899131 24.98248129 1.3689425 1.246308282 0.023849419 0.181831584 507.2207457 475277.2533 0.049123668 0.058729792 1628.917658 -3.211899131 -0.122634218 TSSISGPLS(ph)PAYTGQVPYNYNQLEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 TSSISGPLS(1)PAYTGQVPYNYNQLEGR;TSSISGPLS(1)PAYTGQVPYNYNQLEGR 250.25 3.49E-46 467290000 215670 238660 228470 249810 303210 394040 306270 327850 284390 316080 TRUE FALSE 224184.8181 279647.9985 234424.1159 299221.6724 251670.4725 302530.1817 282263.7571 323455.707 274154.8595 378009.8243 0.593066116 0.739790293 0.620153501 0.791571153 0.665777597 0.800323596 0.746710109 0.855680689 0.725258556 1 18.5280642 -5 0.06335444 1.989315532 0.338400726 0.687952038 0.062975003 185.4027346 0.854429344 27.69466561 4.194219817 1.00E-05 5 -1.650914807 TSSKDDKGSTSS(ph)TSGSSGSSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 TSSKDDKGS(0.098)T(0.02)S(0.137)S(0.712)T(0.027)S(0.005)GSSGSSTK 127.73 9.25E-06 124500000 159000 56284 96678 48575 182960 126140 135690 97797 122800 44238 TRUE FALSE 165277.4428 65950.33917 99197.5081 58182.99002 151860.5246 96845.89667 125054.2632 96486.19118 118380.452 52905.58911 3.124007228 1.246566578 1.874991088 1.099751293 2.870406078 1.830541882 2.363724993 1.823742875 2.237579318 1 15.69113252 -1.258662848 6.065324053 0.999967727 2.012253766 0.211905724 0.604405412 0.000241175 2.95E-05 0.535087564 0.126117354 0.055123547 1.258662848 1.012286039 TSSKDDKGSTSSTS(ph)GSSGSSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKDDKGSTSSTSGSSGSSTK 22 2 Q9NWH9;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 T(0.007)S(0.007)S(0.007)KDDKGS(0.144)T(0.144)S(0.144)S(0.144)T(0.175)S(0.215)GS(0.009)S(0.003)GSSTK 45.042 0.090853 23513000 50144 20821 31204 18526 46518 46750 42739 31121 34332 15175 TRUE FALSE 52123.72384 24396.84479 32017.20187 22190.38751 38610.88698 35893.021 39389.0055 30703.8739 33096.39803 18148.25071 2.872107328 1.34430834 1.764203195 1.222728728 2.127526647 1.977767532 2.170402324 1.691836552 1.823668769 1 14.14754287 0.339393182 1.369770411 0.999772931 1.86971948 0.271520534 0.436870619 5.870471957 10.81771311 0.397114325 0.116045768 2.184706909 -0.339393182 0.869946549 TSSKES(ph)S(ph)PIPS(ph)PTSDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSSKESSPIPSPTSDRK 17 2 Q01082;A0A087WUZ3 Q01082 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 T(0.352)S(0.381)S(0.401)KES(0.433)S(0.433)PIPS(0.956)PT(0.023)S(0.021)DRK 63.184 0.036837 397470000 1647500 316800 548800 303470 987170 1539800 873870 593610 677870 218520 TRUE FALSE 1712544.572 371207.9356 563102.1788 363495.4602 819371.196 1182204.786 805373.786 585653.6289 653473.5911 261334.8102 6.553067197 1.420430502 2.154715548 1.390918646 3.135331246 4.523717239 3.081770031 2.241008875 2.50052257 1 17.99553978 4.748145742 24.53222193 2.493385409 6.553070031 0.616767998 0.982641721 713.1535589 1825199.906 0.243849197 3.112222781 55994.54779 -4.748145742 4.059684622 TSSPRS(ph)PPSSSEIFTPAHEENVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 T(0.288)S(0.288)S(0.069)PRS(0.333)PPS(0.007)S(0.007)S(0.007)EIFTPAHEENVR;T(0.063)S(0.063)S(0.054)PRS(0.773)PPS(0.016)S(0.016)S(0.016)EIFTPAHEENVR;T(0.029)S(0.029)S(0.029)PRS(0.897)PPS(0.012)S(0.002)S(0.002)EIFTPAHEENVR 135.02 1.02E-05 1720270000 179136 235721 253044 200530 321440 369550 210058 248703 258145 247518 TRUE FALSE 186208.4276 276204.2481 259638.5345 240194.2355 266801.7436 283727.6131 193593.1051 245369.5431 248854.4119 296014.4131 0.629051895 0.933077026 0.877114502 0.811427501 0.901313354 0.958492562 0.653998915 0.828910797 0.840683429 1 18.1753079 4.751857474 24.24142396 0.853431691 0.62905167 0.369986363 0.091661632 1656.89495 3020593.603 0.021640877 0.403561872 56475.16052 -4.751857474 -0.224380021 TSSVSNPQDSVGS(ph)PCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSSVSNPQDSVGSPCSR 17 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR;TSSVSNPQDSVGS(1)PCSR 407.7 2.48E-140 4039390000 1860598 2192230 2286590 2212510 2745220 3361950 2619040 2623040 2668800 2410870 TRUE FALSE 1934055.846 2568728.449 2346180.414 2650137.874 2278588.485 2581188.063 2413752.801 2587882.439 2572750.409 2883233.818 0.670793965 0.890919229 0.813732275 0.919154686 0.790289178 0.895240631 0.837168594 0.89756246 0.892314176 1 21.45925641 8 0.037917562 1.398458562 1.79E-11 0.506482434 0.059222584 713.1301357 2.06151971 21.48401193 65.78097634 100000000 -8 -1.398458562 TSTDRHS(ph)LSLDDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSTDRHSLSLDDIR 14 1 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 TSTDRHS(1)LSLDDIR;TSTDRHS(0.998)LS(0.001)LDDIR 137.45 1.28E-05 280380000 319950 442560 474580 468120 585420 649610 454040 519470 444070 467090 TRUE FALSE 332581.8731 518566.2374 486947.9447 560712.7388 485910.5175 498747.9224 418451.1584 512507.3543 428088.0074 558607.3425 0.595376838 0.928319766 0.871717766 1.003769009 0.869860599 0.892841688 0.749097132 0.917473358 0.766348694 1 19.09147501 4.743968673 24.90114331 0.88393536 0.595376709 0.549503879 0.079599338 410.1656558 1888527.361 0.01799153 0.15605699 55458.57073 -4.743968673 -0.288558651 TSTS(ph)PPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 TST(0.002)S(0.998)PPPEK;TST(0.003)S(0.997)PPPEK;TST(0.001)S(0.999)PPPEK;TST(0.004)S(0.996)PPPEK;TST(0.004)S(0.996)PPPEK;TST(0.001)S(0.998)PPPEK;TS(0.002)T(0.033)S(0.965)PPPEK;TST(0.012)S(0.988)PPPEK 169.65 6.12E-05 21035670000 17609670 12486880 16984110 15953580 17239290 21339660 20704660 17036640 17094010 7426490 TRUE FALSE 18304913.37 14631404.51 17426729.86 19109150.51 14308961.64 16383847.37 19081774.65 16808291.71 16478799.92 8881568.527 2.061000072 1.647389699 1.962122997 2.151551322 1.611084979 1.844702016 2.148469 1.892491361 1.855392983 1 23.08238306 0.594161366 2.811420724 1.000013571 1.912612838 0.710747208 0.174190433 3.131437106 21.05166852 0.162446816 0.042748696 3.927908529 -0.594161366 0.912599267 TSTTGVATTQS(ph)PTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TSTTGVATTQSPTPR 15 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 TSTTGVATTQS(0.999)PT(0.001)PR;TSTTGVATTQS(0.997)PT(0.003)PR;TSTTGVATTQS(0.997)PT(0.003)PR;TSTTGVATTQS(0.976)PT(0.024)PR;TSTTGVATTQS(0.998)PT(0.002)PR 279.32 1.24E-33 3748270000 3543590 3591700 3999780 3530130 4913230 5357940 4356480 4279750 4239870 3409880 TRUE FALSE 3683493.669 4208546.535 4104017.553 4228379.178 4078080.92 4113639.635 4015007.714 4222386.952 4087277.907 4077980.7 0.903264125 1.032017276 1.006384742 1.036880625 1.000024576 1.008744263 0.984557802 1.035411215 1.002279856 1 21.95942352 4.744714539 24.97106164 1.012832354 0.903264076 0.793690606 0.016595134 272.3508193 1105100.172 0.003751876 0.034198121 55553.89828 -4.744714539 -0.109568278 TSVDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TSVDFK 6 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 97.071 0.096521 53373000 233630 158150 195610 160930 273210 281970 235680 214000 220370 144560 FALSE TRUE 242853.8928 185311.0323 200707.7573 192761.4737 226769.8618 216486.7408 217206.7858 211131.68 212438.9267 172883.7642 1.404723537 1.071882216 1.160940463 1.114977306 1.311689752 1.252209782 1.25637469 1.221234862 1.228796282 1 17.39944286 -1.001245688 4.667135389 0.999995203 1.219939872 0.357225746 0.090239204 4.31E-06 9.22E-07 0.083571988 0.019697677 0.099713581 1.001245688 0.219944669 TSVDTGQVSRPENPSQPAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSVDTGQVSRPENPSQPASPR 21 1 O15018;O15018-2 O15018 PDZD2 PDZ domain-containing protein 2;Processed PDZ domain-containing protein 2 1 TSVDTGQVSRPENPS(0.011)QPAS(0.989)PR;TSVDTGQVSRPENPSQPAS(1)PR;TSVDTGQVSRPENPSQPAS(1)PR 210.43 1.24E-22 887880000 648370 750860 771820 710140 905670 1022150 774700 801930 816350 883100 TRUE FALSE 673968.1483 879814.3641 791934.2633 850603.5724 751724.5369 784771.1533 713976.9897 791181.44 786969.723 1056126.537 0.638150946 0.833057719 0.749847897 0.805399299 0.711775067 0.743065462 0.676033567 0.749135082 0.745147192 1 20.01035127 -1.942352862 1.445425184 1.213579295 0.741243543 0.682782063 0.053337906 20433.80276 5375.729936 14677.49136 0.013967405 0.011419501 1.942352862 -0.472335752 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR;TSVLGGGEDGIEPVS(1)PPEGMTEPGHSR 218.98 2.00E-34 1361810000 510029 582025 576738 611460 635617 805043 710309 625399 607953 469952 TRUE FALSE 530165.3387 681983.2662 591768.2661 732404.963 527575.0494 618083.9638 654633.1245 617016.5494 586072.8903 562030.0966 0.943304179 1.213428374 1.052912059 1.303141891 0.93869537 1.099734636 1.164765247 1.097835424 1.042778481 1 19.10028786 1.098920908 3.005992102 1.001744942 1.108039808 0.08960739 0.105535411 0.514989117 8.953902564 0.091792616 0.024508446 12.55801242 -1.098920908 0.106294866 TSVLPEHKDPPPEVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSVLPEHKDPPPEVGR 16 1 O15327;D6RJC3;E7EQN9;E9PG59 O15327 INPP4B "Type II inositol 3,4-bisphosphate 4-phosphatase" 0 ;; 91.457 0.0030671 1063880000 1650390 1285650 1642700 1220640 2143110 2065930 1821910 1690090 1738270 1082800 FALSE TRUE 1715548.672 1506450.387 1685510.111 1462078.949 1778824.928 1586149.067 1679103.934 1667437.108 1675710.002 1294953.929 1.32479514 1.163323539 1.301598516 1.129058661 1.373658853 1.224869111 1.296651484 1.287642032 1.294030595 1 20.30446934 -0.842360502 5.483240373 0.999999881 1.265096522 0.562911072 0.070360202 9.18E-08 1.96E-08 0.061576105 0.01451362 0.143760475 0.842360502 0.265096641 TSVPENHAQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSVPENHAQSR 11 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 ;;; 168.98 1.74E-05 401395000 224523 396015 372029 381131 466028 533210 380275 426923 366733 361055 FALSE TRUE 233387.3414 464027.4957 381724.3814 456517.5742 386812.727 409380.0584 350468.0518 421200.7955 353534.351 431796.8144 0.540502694 1.074643166 0.884037048 1.057250908 0.895821169 0.948084943 0.811650388 0.975460637 0.818751642 1 18.71999307 4.751247103 24.95080717 0.936424144 0.540502439 0.662840246 0.085564975 1142.467245 2246875.586 0.018778394 0.341205754 56395.84437 -4.751247103 -0.395921705 TSVPS(ph)PEQPQPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TSVPSPEQPQPYR 13 0 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 TSVPS(1)PEQPQPYR;TSVPS(1)PEQPQPYR 149.69 4.60E-05 295678000 155814 185958 192617 188583 224876 272564 198549 196738 191746 159299 TRUE FALSE 161965.657 217894.8399 197636.7573 225884.1545 186651.6578 209265.1417 182986.2106 194101.0489 184845.0989 190510.5891 0.850166166 1.143741358 1.037405628 1.185677687 0.979744269 1.098443623 0.960504145 1.018846511 0.970261547 1 17.53951166 2.232166772 24.96580739 0.991157499 1.056004779 0.102795534 0.087787303 329.3820465 1286113.712 0.030479856 0.023054713 170.6737662 -2.232166772 0.06484728 TSVS(ph)PAPDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 TSVS(1)PAPDK;TSVS(1)PAPDK;TSVS(1)PAPDK 202.03 2.15E-05 1459070000 2295200 1364660 1894140 1444360 2476930 2643830 2745210 2082840 2198770 1228000 TRUE FALSE 2385816.268 1599029.739 1943502.844 1730050.097 2055902.323 2029840.55 2530033.267 2054922.937 2119636.697 1468603.089 1.62454804 1.088810007 1.323368349 1.178024281 1.399903309 1.382157348 1.722748159 1.399236426 1.443301266 1 20.48601311 3.048260272 10.10452099 1.43536811 1.289442077 0.015887411 0.210344542 1.017698445 205.9216691 0.057152086 0.068304789 1117.532784 -3.048260272 -0.145926033 TSVS(ph)PAPDKTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TSVSPAPDKTK 11 1 O75362 O75362 ZNF217 Zinc finger protein 217 1 TSVS(1)PAPDKTK;TS(0.001)VS(0.999)PAPDKTK;TSVS(1)PAPDKTK;T(0.011)S(0.001)VS(0.988)PAPDKTK 182.37 3.52E-06 1558610000 2255170 1096280 1671550 1028180 2369010 2186540 2151530 1667690 1847700 879210 TRUE FALSE 2344205.853 1284557.562 1715111.966 1231550.935 1966326.526 1678749.222 1982887.457 1645337.343 1781201.638 1051474.366 2.229446507 1.221672733 1.631149576 1.171261017 1.870066061 1.596566951 1.88581626 1.564790732 1.694003863 1 20.00398225 -1.304038716 5.795450591 0.999941293 1.634048296 0.304238064 0.294554024 0.000203917 2.45E-05 0.260278197 0.061342517 0.049654805 1.304038716 0.634107003 TSYAQHQQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TSYAQHQQVR 10 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6 P61247 RPS3A 40S ribosomal protein S3a 0 ;;;;; 210.08 8.38E-08 1088456000 575929 923106 803161 664690 1797070 1439400 952975 821164 709881 1620860 FALSE TRUE 598667.1216 1081642.275 824092.0355 796163.6981 1491604.683 1105121.164 878278.3294 810157.6397 684332.5215 1938436.484 0.308840205 0.557997275 0.425132339 0.410724677 0.769488552 0.570109557 0.453085947 0.417943867 0.353033245 1 20.88646203 -1.505300094 2.882271369 1.019524852 0.479361331 0.614934817 0.124797107 32289688.71 35411585.28 4972543.09 0.032840367 0.0312392 1.505300094 -0.540163522 TT(ph)PDQELAPASEPVWERPWSVEEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPDQELAPASEPVWERPWSVEEIRR 26 2 Q641Q2;Q641Q2-2;E7ESD2;A0A087WYF6;Q5T1D7 Q641Q2 FAM21A WASH complex subunit FAM21A 1 T(0.435)T(0.565)PDQELAPASEPVWERPWSVEEIRR 200.94 2.45E-23 161890000 32214 28552 29369 24250 34437 52610 37087 38962 41685 25488 TRUE FALSE 33485.83359 33455.5839 30134.38027 29046.57762 28583.41104 40392.12481 34180.02403 38439.77812 40184.76499 30481.8856 1.098548628 1.097556245 0.988599612 0.952912756 0.937717942 1.325118969 1.121322495 1.261069562 1.318316246 1 14.89566453 2.743878558 24.99725417 1.217341082 1.014726341 0.461618222 0.102226103 372.406561 1750517.234 0.030859402 0.031871098 554.4706445 -2.743878558 -0.202614741 TT(ph)PPPGRPPAPS(ph)SEEEDGEAVAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 2 T(0.41)T(0.59)PPPGRPPAPS(0.545)S(0.455)EEEDGEAVAH 109.53 0.0026233 254710000 26925 34157 28321 26459 43191 58513 30354 34605 30398 30156 TRUE FALSE 27988.01979 40023.19905 29059.06853 31692.51123 35849.40925 44924.24252 27974.77416 34141.17658 29303.98192 36064.49083 0.77605476 1.109767478 0.805752913 0.878773289 0.994036195 1.245664128 0.775687484 0.94667014 0.812543897 1 15.13829144 4.822017068 20.85822354 0.945915221 0.776029865 0.124989402 0.138873049 82443.6937 20592365.38 0.032379218 408.3604464 66376.91561 -4.822017068 -0.169885357 TT(ph)PPPGRPPAPSSEEEDGEAVAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 T(0.462)T(0.538)PPPGRPPAPSSEEEDGEAVAH;T(0.461)T(0.539)PPPGRPPAPSSEEEDGEAVAH;T(0.45)T(0.55)PPPGRPPAPSSEEEDGEAVAH 111.43 0.0015535 1782250000 415245 298906 446853 336280 597562 447459 464524 368092 442438 267654 TRUE FALSE 431639.1932 350240.7803 458498.3563 402795.1803 495988.6247 343543.4286 428113.3951 363158.3288 426514.7428 320095.6768 1.3484693 1.094175291 1.432379097 1.258358702 1.549501167 1.073252323 1.337454474 1.134530564 1.332460179 1 18.28814367 -0.386460835 0.371369087 0.925704729 1.307337351 0.264122928 0.143071588 9.662588604 1.423220198 1.079522694 0.103315416 0.410713676 0.386460835 0.381632622 TT(ph)PTMSEEPPLDLTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPTMSEEPPLDLTGK 16 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 T(0.166)T(0.833)PT(0.001)MSEEPPLDLTGK 176.4 3.56E-08 120580000 188200 125040 177700 129440 223630 226850 218050 168520 171370 90342 TRUE FALSE 195630.2813 146514.6473 182331.008 155042.8457 185617.4525 174167.5254 200958.6712 166261.265 165202.4272 108042.7852 1.810674178 1.356079881 1.687581523 1.43501341 1.717999514 1.612023655 1.859991584 1.53884653 1.529046358 1 16.72124321 0.648595603 1.820488395 1.000403459 1.624888392 0.618735789 0.147251368 0.982324417 4.274702602 0.131174513 0.036735492 4.452414652 -0.648595603 0.624484933 TT(ph)SPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.027)T(0.664)S(0.31)PEPR 110.22 0.076605 1213700000 1307600 1285700 1364300 1266000 1615600 1837700 1484500 1470800 1319300 1242500 TRUE FALSE 1359225.058 1506508.974 1399854.779 1516411.021 1340980.889 1410922.026 1368141.011 1451086.332 1271818.651 1485944.086 0.914721537 1.013839611 0.942064235 1.02050342 0.902443707 0.949512192 0.920721731 0.976541678 0.855899399 1 20.5029484 3.225407024 24.99793723 0.935786604 0.973520745 0.139343979 0.046875625 443.0299455 841960.6275 0.012492897 0.015013321 1680.378141 -3.225407024 0.03773414 TT(ph)SPLEEEEREIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTSPLEEEEREIK 13 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 T(0.005)T(0.498)S(0.498)PLEEEEREIK 212.39 2.31E-08 182110000 159770 108090 135460 80899 222350 205950 127150 110480 158280 101050 TRUE FALSE 166077.843 126653.6167 138990.1989 96900.58074 184555.0264 158121.2337 117183.6508 108999.1963 152583.5337 120848.8128 1.37426127 1.048033603 1.150116378 0.801833121 1.527156305 1.308421904 0.96967151 0.90194677 1.262598533 1 16.88284377 2.2220655 24.98665296 1.010168046 1.188936702 0.135802961 0.202830152 480.7155695 728178.8745 0.077139521 0.057134711 166.7498684 -2.2220655 0.178768656 TTAAHGLELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTAAHGLELR 10 0 P08243-2;P08243;P08243-3 P08243-2 ASNS Asparagine synthetase [glutamine-hydrolyzing] 0 ; 128.17 0.00033681 96334000 103295 125645 124184 130358 173320 175580 161717 134698 123920 137347 FALSE TRUE 107373.1664 147223.5514 127420.3371 156142.4233 143859.1283 134804.2059 149041.199 132892.5936 119460.1434 164257.515 0.653687999 0.896297204 0.775735205 0.95059531 0.875814591 0.82068821 0.907363045 0.809050311 0.727273534 1 17.32559985 TTAGS(ph)VDWTDQLGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR;TTAGS(1)VDWTDQLGLR 288.41 7.88E-35 1050663000 927739 935940 1039760 944887 1132570 1202940 1013130 985540 998490 866977 TRUE FALSE 964366.8521 1096680.414 1066857 1131782.828 940056.1559 923575.4157 933718.2233 972330.4483 962554.5399 1036844.544 0.930097822 1.057709587 1.028945955 1.091564628 0.906651013 0.89075592 0.9005383 0.93777843 0.928349911 1 19.98376817 3.222271083 24.9995521 0.921737716 1.029400685 0.511591368 0.047528871 172.7792801 265163.8612 0.01325033 0.015881245 1668.288218 -3.222271083 0.107662969 TTAPTEGKS(ph)PLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTAPTEGKSPLKK 13 2 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPT(0.001)EGKS(0.999)PLKK 104.44 0.00079923 312280000 818120 186210 352540 266780 541970 573380 704830 393990 405360 110090 TRUE FALSE 850420.0093 218190.119 361727.482 319548.2877 449846.133 440221.1847 649583.5829 388709.2085 390771.1728 131660.0277 6.459211837 1.657223706 2.747435864 2.4270714 3.416725189 3.343620629 4.933794973 2.952370703 2.968031981 1 17.00645788 0.73694967 1.988273271 1.003557721 3.415366424 0.254712209 1.275604486 1.468984792 8.787057128 1.154110278 0.31922258 5.456946168 -0.73694967 2.411808703 TTAPTEGKS(ph)PLKKEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTAPTEGKSPLKKEDR 16 3 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 TTAPTEGKS(1)PLKKEDR 93.269 0.024807 244600000 695340 160770 296320 164810 532800 475170 429270 309130 361780 143340 TRUE FALSE 722792.5601 188380.9969 304042.3426 197408.9261 442234.8463 364818.9688 395622.6957 304986.618 348759.6085 171424.7286 4.216384451 1.098913782 1.77362009 1.151577883 2.5797611 2.128158357 2.307850792 1.779128487 2.034476655 1 17.38721571 -1.89249769 0.305384053 2.25E-21 2.145557921 0.148084262 0.825146731 64.22208511 3.144147007 48.15831239 0.798788111 0.012808619 1.89249769 2.145557921 TTCGQGLEGPWERPPPLDESER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTCGQGLEGPWERPPPLDESER 22 1 Q9UD71;Q9UD71-2;J3KT77 Q9UD71 PPP1R1B Protein phosphatase 1 regulatory subunit 1B 0 ; 151.45 4.43E-08 527990000 410980 381500 413540 452050 498990 575770 509630 443750 411640 312120 FALSE TRUE 427205.8077 447019.6573 424317.1921 541464.1408 414171.858 442056.1434 469683.8689 437802.2571 396825.1568 373273.9381 1.144483352 1.197564608 1.136744757 1.450581156 1.109565431 1.184267366 1.258281977 1.172871214 1.063093659 1 18.50987526 1.18746665 2.48353472 1.002705058 1.21285708 0.39162663 0.090019273 0.264116877 2.850716095 0.080729032 0.022666118 15.39808277 -1.18746665 0.210152022 TTDEELS(ph)ELEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;TTDEELS(1)ELEDR;TTDEELS(1)ELEDR 245.72 1.82E-16 2242540000 1557660 1693630 1590810 1562610 2080040 2170560 1782900 1720800 1668940 1522170 TRUE FALSE 1619157.62 1984497.778 1632267.815 1871689.594 1726475.544 1666480.335 1643151.639 1697735.491 1608875.175 1820410.068 0.889446641 1.090137773 0.896648422 1.028169217 0.94839925 0.915442276 0.902627198 0.93261157 0.883798219 1 20.79583204 3.003441629 24.91570983 0.922637448 0.979785056 0.122116322 0.061348669 169.7451764 1228851.465 0.016118898 0.019178431 1007.956127 -3.003441629 0.057147609 TTDGVYEGVAIGGDRYPGSTFMDHVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TTDGVYEGVAIGGDRYPGSTFMDHVLR 27 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ;;;;; 245.2 1.26E-45 3072776000 723683 986525 1048166 833230 1179574 1225224 1014288 1080237 957979 947078 FALSE TRUE 752254.5636 1155952.995 1075482.067 998040.4071 979070.4328 940684.2944 934785.4562 1065758.19 923501.5229 1132639.801 0.664160453 1.02058306 0.949535824 0.881163108 0.864414646 0.830523785 0.82531574 0.940950679 0.815353232 1 20.1112577 -1.24493438 3.869289434 1.000149322 0.875349231 0.155205428 0.091523944 8285586528 1616869666 11442728.26 0.020091738 0.056893889 1.24493438 -0.124800092 TTDGYLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTDGYLLR 8 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;H0Y9Y4;D6RB09;D6RAS7;D6R9B6;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 85.064 0.039567 123910000 77144 148730 116490 111150 136760 148070 107280 114600 104050 200960 FALSE TRUE 80189.70469 174273.2205 119525.8251 133135.1383 113513.584 113682.9865 98871.11328 113063.9744 100305.2608 240334.2644 0.33365906 0.725128483 0.497331604 0.553958207 0.472315441 0.473020303 0.411390001 0.470444673 0.417357305 1 17.87468282 -1.626218297 4.116456043 1.014803359 0.488299054 0.713622979 0.098056028 0.012799063 0.001162178 0.091217607 0.021310006 0.023647308 1.626218297 -0.526504305 TTEINFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTEINFK 7 0 P29373;Q5SYZ4;P29762;B5MCB5 P29373;P29762 CRABP2;CRABP1 Cellular retinoic acid-binding protein 2;Cellular retinoic acid-binding protein 1 0 101.99 0.045273 0 199730 166920 214890 171430 275590 277170 250110 245100 251570 156890 FALSE TRUE 207615.4946 195587.2115 220490.2099 205338.3423 228745.3102 212801.4681 230505.7247 241814.8354 242516.0448 187629.5917 1.106517862 1.042411327 1.175135585 1.094381438 1.219132378 1.134157284 1.22851477 1.288788369 1.29252557 1 17.51752785 3.266997562 0.930350505 1.225094379 1.085354546 0.151573731 0.087284454 0.767749784 1.435066598 0.037971917 0.065912794 1849.258239 -3.266997562 -0.139739832 TTEYHDRDEQFYWIIEALGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTEYHDRDEQFYWIIEALGIR 21 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ;; 240.44 5.29E-30 2769930000 2019140 2102100 2473430 2282370 2884540 3291090 2732710 2410030 2613070 2057470 FALSE TRUE 2098857.206 2463119.323 2537889.618 2733815.974 2394226.921 2526784.224 2518513.05 2377727.49 2519026.121 2460591.854 0.852988765 1.001027179 1.031414297 1.11104 0.973028874 1.026900996 1.023539538 0.966323401 1.023748054 1 21.23057394 4.735473237 3.965431127 1.017653038 0.838355787 0.637184191 0.03743417 0.153711301 5.021665733 0.009349652 0.079240657 54384.26171 -4.735473237 -0.179297251 TTFDEAMADLHTLSEDSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 TTFDEAMADLHTLSEDSYK 19 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;;;;;;;;; 312.21 1.47E-61 2199194000 2154216 1496633 2101081 1730105 2738476 2734594 2975865 2297966 2492187 1249807 FALSE TRUE 2239266.111 1753668.076 2155836.897 2072314.605 2272990.828 2099525.987 2742608.925 2267165.524 2402493.677 1494682.753 1.49815478 1.173271099 1.442337441 1.38645783 1.520717907 1.404663286 1.834910399 1.516820556 1.607360273 1 20.51140787 3.323388721 1.548847103 1.534353316 1.347331468 0.019915703 0.21430624 0.81108293 4.018932985 0.066563716 0.10430957 2105.662296 -3.323388721 -0.187021848 TTFVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTFVKR 6 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 87.989 0.083079 986380000 1363800 1314200 1524700 1090400 2367900 1935300 1535500 1479000 1577600 1685600 FALSE TRUE 1417643.877 1539903.627 1564434.935 1306077.865 1965405.204 1485855.905 1415143.498 1459176.424 1520822.484 2015861.047 0.703244839 0.763893736 0.776062882 0.647900741 0.974970575 0.737082502 0.702004486 0.723847721 0.754428231 1 20.94296477 -2.230153843 2.007695018 1.715452397 0.75313452 0.448414192 0.081943379 3795200.15 647032.5245 12307185.45 0.020510076 0.005886351 2.230153843 -0.962317877 TTGIVMDS(ph)GDGVTHTVPIYEGYALPHAILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 1 T(0.306)T(0.306)GIVMDS(0.384)GDGVT(0.003)HT(0.003)VPIYEGYALPHAILR 67.778 0.012127 35829000 12737 17404 15921 16125 14542 20796 17014 15353 17346 14244 TRUE FALSE 13239.8666 20393.00162 16335.91434 19314.47687 12070.15603 15966.44417 15680.39822 15147.21815 16721.72085 17034.83908 0.777222874 1.197134972 0.958970863 1.133822091 0.708557092 0.937281772 0.920489953 0.889190563 0.98161895 1 14.0562007 3.268321783 24.99995124 0.90238188 1.025539777 0.151383954 0.127420022 340.4708693 285999.8149 0.032584116 0.044113104 1854.905476 -3.268321783 0.123157897 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 375.28 3.72E-137 93087290000 8520006 9719531 10912667 10125307 12481884 14364620 11634221 11434915 11451080 8501221.9 FALSE TRUE 8856382.416 11388784.84 11197060.07 12128062.5 10360217.82 11028654.7 10722300.36 11281648.67 11038957.87 10166873.57 0.871101854 1.120185549 1.101327758 1.192899904 1.01901708 1.084763633 1.054631032 1.109647779 1.085777038 1 23.27737277 4.743406346 24.90870784 1.089965404 0.87110176 0.608623619 0.051425507 299.3959586 1538944.495 0.01162195 0.094332642 55386.80912 -4.743406346 -0.218863644 TTGT(ph)PPDSSLVTYELHSRPEQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTGTPPDSSLVTYELHSRPEQDK 23 1 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.147)T(0.147)GT(0.7)PPDS(0.005)SLVTYELHSRPEQDK;T(0.12)T(0.12)GT(0.761)PPDSSLVTYELHSRPEQDK;T(0.03)T(0.03)GT(0.941)PPDSSLVTYELHSRPEQDK 216.14 3.81E-32 481950000 594800 366926 533000 399957 660810 708910 723390 536650 567900 262901 TRUE FALSE 618283.1633 429942.6862 546890.4179 479067.3008 548485.7522 544276.3961 666688.8016 529457.0845 547461.3899 314411.4174 1.966478089 1.367452524 1.739410173 1.523695624 1.744484207 1.731096156 2.120434452 1.683962653 1.741226176 1 18.26229408 TTGT(ph)PPDSSLVTYELHSRPEQDKFSQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.034)T(0.034)GT(0.924)PPDS(0.007)S(0.002)LVTYELHSRPEQDKFSQAAK;T(0.006)T(0.006)GT(0.986)PPDS(0.001)SLVTYELHSRPEQDKFSQAAK;T(0.027)T(0.027)GT(0.946)PPDSSLVTYELHSRPEQDKFSQAAK 234.25 3.28E-45 3527710000 2081650 1237720 1789710 1170570 2581740 2195940 2053940 1767830 2039090 1084590 TRUE FALSE 2163835.149 1450288.782 1836351.313 1402105.252 2142896.757 1685966.215 1892946.816 1744135.13 1965703.549 1297094.645 1.668216855 1.118105597 1.415741959 1.080958323 1.652074323 1.299802001 1.459374475 1.344647546 1.515466552 1 20.30685232 -1.61401209 6.074608627 0.998269236 1.38279238 0.28546872 0.186557805 0.003925362 0.000249422 0.162146568 0.038068655 0.024321363 1.61401209 0.384523143 TTGTPPDS(ph)SLVTYELHSRPEQDKFSQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 1 T(0.002)T(0.002)GT(0.061)PPDS(0.455)S(0.455)LVT(0.023)Y(0.001)ELHSRPEQDKFSQAAK 118.93 4.30E-05 510030000 373230 166050 255620 146230 395130 338300 303890 238750 301900 144120 TRUE FALSE 387965.4086 194567.7958 262281.6672 175153.8575 327965.9437 259734.952 280070.3077 235549.9468 291034.678 172357.5547 2.250933586 1.128861431 1.521730032 1.016223849 1.902823142 1.506954264 1.624937812 1.366635464 1.688551909 1 17.39504501 -1.192018336 4.403142287 0.999854218 1.526487294 0.190891843 0.338650326 22821674.32 6178303.404 32057.26717 0.072171432 0.064266058 1.192018336 0.526633076 TTGTPPDSSLVTYELHSRPEQDKFSQAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTGTPPDSSLVTYELHSRPEQDKFSQAAK 29 2 Q13561;Q13561-3;Q13561-2;H0YI98;F8W1I6;F8VW18 Q13561 DCTN2 Dynactin subunit 2 0 182.33 5.81E-18 418530000 288200 172560 223470 151190 344210 349820 279800 264840 290770 150050 FALSE TRUE 299578.3585 202195.8377 229293.8118 181094.9307 285701.3071 268579.6066 257868.5449 261290.253 280305.2445 179449.4246 1.669430588 1.126756679 1.27776287 1.009169749 1.592099321 1.49668692 1.436998449 1.456066262 1.562029219 1 17.45321777 3.215390756 24.99773805 1.451090441 1.260991105 0.095781792 0.220570423 424.8506465 458366.0898 0.059704039 0.071401438 1642.066556 -3.215390756 -0.190099336 TTHFVEGGDAGNREDQINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TTHFVEGGDAGNREDQINR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ;;;;;;; 238.3 1.81E-24 20394080000 1510468 1658413 1927139 1824746 2225011 2562956 2025173 1946449 1809760 1711705 FALSE TRUE 1570102.443 1943232.532 1977361.826 2185675.312 1846804.425 1967748.311 1866434.648 1920360.035 1744627.091 2047080.822 0.766995824 0.949270059 0.965942235 1.067703477 0.90216488 0.961246029 0.911754254 0.938096832 0.852251202 1 20.96513663 4.738673002 24.98348869 0.948682856 0.766995771 0.498988315 0.054949243 7.552723957 1676960.326 0.012972753 0.075277563 54786.43006 -4.738673002 -0.181687085 TTHLAGALS(ph)PGEAWPFESV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTHLAGALSPGEAWPFESV 19 0 Q9Y3X0 Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV;TTHLAGALS(1)PGEAWPFESV 218.63 3.48E-19 219093000 223845 241694 267337 249043 294275 357588 268829 266872 280081 268747 TRUE FALSE 232682.5734 283203.0644 274304.0218 298302.9621 244254.2406 274543.6063 247757.4805 263295.0174 270000.9395 321402.8292 0.723959319 0.881146769 0.853458641 0.928127991 0.759962945 0.854204075 0.770862787 0.819205662 0.840070202 1 18.2940231 0.778448736 4.778181933 0.999999361 0.826219005 0.455747784 0.057349136 4.234373976 90.79421922 0.052613018 0.013321736 6.004111327 -0.778448736 -0.173780356 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR;TTHLAGALS(1)PGGGQSAPAFPESGPSLR 280.49 2.88E-61 3312320000 620759 736786 760873 710212 976034 1094630 783186 853868 836934 811426 TRUE FALSE 645267.0447 863323.2641 780701.9754 850689.8138 810128.0893 840418.7718 721797.8348 842423.2961 806812.9088 970409.389 0.664943118 0.889648507 0.804507854 0.876629826 0.834831256 0.86604559 0.743807555 0.868111238 0.831414986 1 19.88823398 -5 0.245960349 2.036414684 0.80794988 0.423349884 0.064476736 168.3304326 1.673529209 87.53536222 0.089098007 1.00E-05 5 -1.228464804 TTHLIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTHLIAK 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ; 81.297 0.027584 724460000 2254200 1794880 2037230 1994950 3192300 3164000 2894500 2559200 2671400 1887840 FALSE TRUE 2343197.557 2103136.678 2090321.887 2389545.156 2649673.986 2429208.951 2667621.527 2524898.11 2575256.836 2257726.103 1.037857317 0.931528707 0.925852735 1.058385759 1.173602937 1.075953787 1.181552325 1.118336767 1.140641831 1 21.10643904 3.52600867 4.439917551 1.123319718 0.963441384 0.58218705 0.05644073 0.127896134 5.399888353 0.014311314 0.021949826 3357.443165 -3.52600867 -0.159878334 TTHS(ph)PYEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 T(0.001)THS(0.999)PYEER;TTHS(1)PYEER;T(0.001)T(0.001)HS(0.998)PYEER;T(0.004)T(0.004)HS(0.992)PYEER;T(0.203)T(0.081)HS(0.716)PYEER;TTHS(1)PYEER 195.8 3.22E-05 3121270000 1053514 1120575 1095970 987258 1334119 1443681 1148840 1117759 1115811 1026300 TRUE FALSE 1095107.546 1313025.039 1124531.879 1182534.686 1107345.929 1108407.967 1058790.919 1102777.269 1075653.18 1227383.835 0.892229077 1.069775405 0.916202288 0.963459557 0.90220019 0.903065476 0.86264043 0.898477915 0.876378806 1 20.22715506 3.364574336 1.661145506 0.89723384 0.972505231 0.153431182 0.056007795 0.492609942 2.786039728 0.016594239 0.026421644 2315.124422 -3.364574336 0.07527139 TTIENIQLPHTLLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTIENIQLPHTLLSR 15 0 A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;A0A3B3ITP6;E5RG31 A0A3B3IS57 MCM4 DNA replication licensing factor MCM4 0 64.476 0.068293 0 148490 165750 169130 118460 218870 229800 156420 155900 197660 186360 FALSE TRUE 154352.4999 194216.2731 173537.6667 141891.0344 181666.5556 176432.4327 144159.3917 153810.4155 190546.2552 222873.6739 0.692555999 0.871418637 0.778636901 0.636643314 0.815109979 0.791625272 0.646821085 0.690123749 0.854951829 1 17.76586669 0.980592638 4.496257942 0.999645142 0.74034511 0.563901335 0.071646539 0.129980923 8.568350765 0.070769892 0.017985117 9.562966573 -0.980592638 -0.259300032 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR 296 1.91E-80 1211056000 345241 388684 383927 390470 426388 503529 423571 388502 364845 388706 TRUE FALSE 358871.3813 455437.4535 393932.453 467703.8006 353910.7201 386592.0208 390370.3982 383294.7662 351714.2997 464865.4985 0.77198971 0.979718768 0.84741168 1.006105642 0.761318535 0.831621237 0.839749131 0.824528315 0.756593683 1 18.82645383 3.219877985 24.9999324 0.82699995 0.903057768 0.114939953 0.087270412 426.724313 571014.6121 0.023071206 0.027621741 1659.120711 -3.219877985 0.076057819 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 ;;; 355.71 2.37E-120 1450350000 150614 183193 180555 170290 197531 236102 187714 179407 152640 166811 FALSE TRUE 156560.357 214654.9727 185260.4116 203972.8537 163954.7512 181270.8887 173000.4862 177002.3426 147146.5162 199494.4217 0.784785638 1.075994862 0.928649584 1.022448909 0.821851307 0.908651416 0.867194605 0.887254597 0.737597147 1 17.60598888 3.232337086 24.99921309 0.867964867 0.960020103 0.155365677 0.09360679 237.2047202 952823.301 0.024866442 0.030420875 1707.407112 -3.232337086 0.092055236 TTIPHALLTWRPNSGETAPPPPS(ph)PVSEKPLDTISQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTIPHALLTWRPNSGETAPPPPSPVSEKPLDTISQK 36 2 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 1 TTIPHALLTWRPNSGETAPPPPS(0.997)PVS(0.003)EKPLDTISQK;TTIPHALLTWRPNSGETAPPPPS(0.716)PVS(0.205)EKPLDT(0.061)IS(0.019)QK 189.18 1.40E-23 2726290000 956560 472650 755200 531800 1065840 999170 1030800 823490 927910 431310 TRUE FALSE 994325.7274 553823.9608 774881.1324 636988.4527 884668.8975 767127.9101 950003.2025 812452.4635 894514.7004 515816.9366 1.927671732 1.073683165 1.502240577 1.23491186 1.715083075 1.48720962 1.841744881 1.575079075 1.73417086 1 18.97649962 2.445342318 24.99430647 1.602531816 1.468694706 0 0.303567286 704.4756194 554070.4847 0.097693268 0.081736607 278.8318104 -2.445342318 -0.13383711 TTLIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTLIHK 6 0 Q5TDF0;Q9BSD7 Q5TDF0 NTPCR Cancer-related nucleoside-triphosphatase 0 68.033 0.097205 233620000 538760 473030 512180 437450 692680 733910 608000 580790 582960 471160 FALSE TRUE 560030.6608 554269.2228 525527.8316 523976.3043 574938.501 563470.525 560343.3713 573005.46 561979.3835 563474.7811 0.993887712 0.983662874 0.932655461 0.929901962 1.02034469 0.999992447 0.99444268 1.016914118 0.997346114 1 19.10399152 3.226716748 24.99999852 1.005502816 0.959760165 0.548670494 0.019905309 175.0833367 369564.5475 0.006172463 0.007431461 1685.453395 -3.226716748 -0.045742651 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTLIPGGSESLVYTTLSGGIGILVPFTSHEDHDFFQHVEMHLR 43 0 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 ; 152.28 1.96E-14 576470000 291705 358992 363143 355339 452272 504768 441268 423600 424256 329089 FALSE TRUE 303221.7386 420646.0834 372606.8049 425623.9936 375394.967 387543.2818 406680.2611 417922.3349 408987.1094 393567.6888 0.77044368 1.068802383 0.94674135 1.08145055 0.953825677 0.984692832 1.033317197 1.061881722 1.039178574 1 18.58625226 4.745440831 24.99044827 1.020031217 0.770443566 0.736683309 0.044553562 395.9438242 1438118.648 0.010335164 0.102504922 55646.88152 -4.745440831 -0.249587652 TTLLHMLKDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTLLHMLKDDR 11 1 Q9Y6B6;D6RD69;D6RDB2;D6RAA2;Q9NR31;Q5SQT8;X1WI22 Q9Y6B6;Q9NR31 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 74.611 0.024244 1081200000 76796 70809 83820 46902 186830 127570 81703 74791 90660 116640 FALSE TRUE 79827.96538 82969.89493 86004.41806 56179.07561 155072.7033 97943.80084 75298.90537 73788.54898 87397.16431 139493.3748 0.572270658 0.59479452 0.616548407 0.402736515 1.111685079 0.702139446 0.539802736 0.528975294 0.626532726 1 17.08983708 TTMRPQSFYDGSHSCAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 61.097 0.097883 33846000 63099 52615 69092 62028 82010 81707 77179 68615 66610 57350 FALSE TRUE 65590.19724 61651.21696 70892.59428 74296.95326 68069.96949 62731.78753 71129.50831 67695.32816 64212.71911 68586.63447 0.956311645 0.898880918 1.033621125 1.08325702 0.992466973 0.914635745 1.037075355 0.987004665 0.936227876 1 16.06563984 4.241505455 24.99999487 0.998878358 0.927596277 0.259478798 0.047581753 100.859692 856198.3011 0.012073802 0.030244159 17438.35262 -4.241505455 -0.07128208 TTNESLLTS(ph)FPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTNESLLTSFPK 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 TTNESLLT(0.021)S(0.979)FPK 73.881 0.039865 36272000 211120 155450 180320 120620 245890 247550 191080 167620 192310 122370 TRUE FALSE 219455.1806 182147.3283 185019.2873 144478.276 204093.7056 190060.2642 176102.6503 165373.3281 185388.8007 146346.0586 1.499563314 1.244634328 1.264258765 0.98723722 1.394596531 1.298704359 1.203330325 1.130015592 1.266783694 1 17.15902437 7.823888833 0.025688082 4.11E-06 2.895422171 0.328574243 0.12420084 2340.834488 4.752949108 184.0977023 385.702784 66663610.69 -7.823888833 2.895418063 TTNSS(ph)LEEIMDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTNSSLEEIMDK 12 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 1 TTNS(0.003)S(0.997)LEEIMDK;T(0.001)T(0.003)NS(0.033)S(0.963)LEEIMDK 153.95 7.46E-05 78335000 253820 173344 239980 206843 395340 383600 351880 225530 251210 178374 TRUE FALSE 263841.0096 203114.4836 246234.0759 247755.928 328140.248 294514.7135 324298.7261 222507.1392 242169.0012 213322.9701 1.236814814 0.952145395 1.154278303 1.161412331 1.538232136 1.380604786 1.520224128 1.043052884 1.135222339 1 17.70267979 5.10359372 20.18117129 1.221304848 3.149704031 0 0.195923044 20271.33365 4084191.844 0.047795144 61653.60158 126938.6048 -5.10359372 1.928399183 TTPATGEQS(ph)PGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 184.66 9.77E-06 590200000 340050 379120 384300 378720 461210 536030 424410 405130 375400 360260 TRUE FALSE 353475.4366 444230.9109 394315.1737 453629.6856 382813.6889 411545.1561 391143.6352 399699.895 361889.4273 430846.0494 0.820421673 1.03106646 0.915211302 1.052881154 0.888516187 0.955202344 0.907850114 0.927709319 0.839950669 1 18.71681293 TTPDVIFVFGFR ddPTM_MDA-MB-175_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 ; 173.37 7.73E-05 324750000 272610 237050 261090 244120 299890 321760 267220 266680 281790 228050 FALSE TRUE 283372.8533 277761.4935 267894.2199 292406.2074 248914.8049 247036.1163 246274.5982 263105.5908 271648.4329 272732.0312 1.039015667 1.01844104 0.982261668 1.072137387 0.912671694 0.905783289 0.902991105 0.964703668 0.996026876 1 18.05712462 3.230372467 24.99999992 0.941752679 1.024019288 0.511041248 0.038499635 147.1958766 449416.7411 0.01133096 0.013760685 1699.700755 -3.230372467 0.082266609 TTPES(ph)PPYSSGSYDSIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTPESPPYSSGSYDSIK 17 0 A0A087WTU5;A0A087X0N3;Q96MY1-2;Q96MY1 A0A087WTU5 NOL4L Nucleolar protein 4-like 1 TTPES(1)PPYSSGSYDSIK;TTPES(1)PPYSSGSYDSIK 379.99 2.06E-105 1132620000 766960 547820 668390 551690 879250 896160 856490 746790 814230 492350 TRUE FALSE 797240.173 641903.8236 685808.7925 660812.6354 729795.3991 688040.4214 789356.0758 736780.5016 784926.0214 588816.5559 1.353970375 1.090159265 1.164724031 1.122272512 1.239427444 1.168514055 1.340580641 1.251290396 1.333056983 1 19.16745871 2.315998306 24.99969043 1.255252298 1.183353561 0.012371889 0.111239313 82.88808429 26755.37262 0.035689388 0.02985987 207.0133275 -2.315998306 -0.071898737 TTPPPGAQCEVPAS(ph)PQRPSRPGALPEQTRPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TTPPPGAQCEVPASPQRPSRPGALPEQTRPLR 32 3 Q9H074;D6R9H8 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 1 TTPPPGAQCEVPAS(0.996)PQRPS(0.002)RPGALPEQT(0.001)RPLR;TTPPPGAQCEVPAS(0.861)PQRPS(0.137)RPGALPEQT(0.002)RPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR;TTPPPGAQCEVPAS(0.994)PQRPS(0.005)RPGALPEQT(0.001)RPLR;TTPPPGAQCEVPAS(1)PQRPSRPGALPEQTRPLR 253.87 2.97E-59 5642910000 111593.1 91450.3 109197.1 103635.5 117735 140366.9 104955.8 110876.3 101982.1 96819.2 TRUE FALSE 115998.8818 107156.1776 112042.8661 124134.2926 97722.44675 107768.8148 96729.09015 109390.1846 98311.78414 115789.0685 1.00181203 0.925442954 0.967646321 1.072072642 0.843969539 0.93073393 0.83539052 0.944736718 0.849059289 1 16.82113953 3.224870871 24.99999587 0.89806053 0.985286529 0.362973481 0.058813045 249.3524033 455362.5103 0.015999622 0.01921882 1678.304931 -3.224870871 0.087225999 TTPPPGRPPAPSS(ph)EEEDGEAVAH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTPPPGRPPAPSSEEEDGEAVAH 23 1 Q96KN1 Q96KN1 FAM84B Protein FAM84B 1 TTPPPGRPPAPS(0.185)S(0.815)EEEDGEAVAH 136.16 7.54E-06 368850000 46753 54649 59499 58503 72737 86515 71223 59815 70021 60031 TRUE FALSE 48598.84454 64034.54064 61049.59282 70074.71879 60373.19072 66423.2024 65640.35515 59013.27776 67500.95789 71792.92509 0.676930832 0.891933858 0.850356672 0.976067192 0.840935101 0.925205406 0.914301166 0.821992943 0.940217407 1 16.13155406 4.742448692 5.153626651 0.897700526 0.666461532 0.604383387 0.055364697 0.11042684 9.730110768 0.012398722 0.090679998 55264.81137 -4.742448692 -0.231238994 TTPQQGASGPGRS(ph)PVGQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTPQQGASGPGRSPVGQAR 19 1 A0A2R8YF49;H0Y895;A0A2R8YFR7;Q12774 A0A2R8YF49;A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR;TTPQQGASGPGRS(1)PVGQAR 240.49 1.53E-24 1286460000 183135 164010 163179 145112 189415 239876 155663 159929 161836 160145 TRUE FALSE 190365.3112 192177.4417 167431.5788 173814.7205 157218.306 184168.4344 143461.7273 157785.4133 156011.554 191522.3466 0.993958745 1.003420463 0.874214324 0.907542768 0.82088753 0.96160285 0.749059992 0.82384858 0.814586688 1 17.54715321 4.235162621 0.973592021 0.846068795 1.039235686 0.300542252 0.072870743 1.040467319 1.319725953 0.023229374 0.179237392 17185.51777 -4.235162621 0.193166891 TTPS(ph)YVAFTDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 1 T(0.048)T(0.191)PS(0.761)YVAFTDTER 110.55 0.0011012 108390000 47026 79650 73541 79397 75585 104920 76144 76412 71685 82581 TRUE FALSE 48882.62279 93329.26791 75457.53887 95101.48962 62737.0887 80553.92008 70175.63431 75387.82212 69105.07085 98761.16584 0.494957936 0.944999658 0.764040584 0.962944178 0.635240463 0.815643673 0.710558991 0.763334672 0.699719067 1 16.59165625 -1.094242702 4.490031405 1.000016234 0.763093372 0.238671991 0.130695016 2.40E-05 4.84E-06 0.114223314 0.026920387 0.080492849 1.094242702 -0.236922862 TTPSYVAFTDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 234.39 2.71E-16 8857210000 1009681 1087387 1198702 1046074 1440308 1681350 1247555 1272763 1261019 1145714 FALSE TRUE 1049543.986 1274137.259 1229941.159 1252984.315 1195484.961 1290881.944 1149768.379 1255703.694 1215635.173 1370194.722 0.765981629 0.929895027 0.897639685 0.914457117 0.87249275 0.942115688 0.839127724 0.916441783 0.887198843 1 20.3859495 -5 0.205039967 1.511269624 0.871860154 0.356953703 0.047858934 159.5413303 1.585527098 33.55816675 0.100294971 1.00E-05 5 -0.63940947 TTQAAAIIDHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTQAAAIIDHER 12 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;Q5VT25-4;H0Y6V3;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 0 ; 68.944 0.051306 227510000 183042 179920 230100 183072 282040 275920 232560 184125 215610 190422 FALSE TRUE 190268.6395 210819.8604 236096.595 219283.0952 234098.9415 211841.7616 214331.3395 181657.1055 207850.2382 227731.5451 0.835495317 0.925738507 1.036732065 0.962901715 1.027960099 0.930225813 0.941157886 0.797680908 0.912698494 1 17.79697462 1.975555189 23.8879355 0.878089761 0.957578213 0.054631112 0.071020343 680.5724326 665066.6685 0.02901301 0.018849492 94.52685062 -1.975555189 0.079488452 TTQETIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTQETIDK 8 0 Q15847;Q5TBU2 Q15847 ADIRF Adipogenesis regulatory factor 0 ;; 209.58 0.00010706 1275640000 1225900 830340 1092150 946970 1233230 1337360 1372830 1095120 1065650 689400 FALSE TRUE 1274299.479 972944.4359 1120612.326 1134277.84 1023606.005 1026778.408 1265223.997 1080441.708 1027297.465 824474.7306 1.54558949 1.180077933 1.35918335 1.375758161 1.241525018 1.245372805 1.534581898 1.31046067 1.246002365 1 19.65311575 0.862877553 2.418175346 1.000676661 1.345234815 0.471032721 0.112260594 0.440769117 5.045577421 0.10138649 0.027329392 7.292518724 -0.862877553 0.344558154 TTQETIDKTANQASDTFSGIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTQETIDKTANQASDTFSGIGK 22 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 270 8.34E-39 567540000 574440 375720 462980 298270 673020 597050 492920 498060 555500 342720 FALSE TRUE 597119.3348 440246.9873 475045.6391 357266.9158 558620.3008 458394.1859 454283.6424 491384.3204 535507.6635 409869.4222 1.456852603 1.074115227 1.159017027 0.87166033 1.362922605 1.118390787 1.108361878 1.198880165 1.30653236 1 18.64480484 TTQETIDKTANQASDTFSGIGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTQETIDKTANQASDTFSGIGKK 23 2 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 214.92 1.57E-32 3257500000 1730000 1005900 1280800 647360 2195500 1504900 1087900 1280700 1668600 827880 FALSE TRUE 1798301.736 1178655.5 1314178.7 775405.8758 1822309.694 1155409.782 1002627.555 1263534.311 1608547.412 990087.2353 1.816306353 1.190456213 1.327336272 0.783169248 1.84055468 1.166977758 1.012665874 1.276184831 1.624652207 1 19.91719612 4.742406133 23.74674171 1.249808523 1.816306804 0.257102417 0.290339781 255.0877767 1575075.208 0.06543947 0.486667039 55259.3959 -4.742406133 0.566498281 TTQFSCTLGEKFEETTADGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTQFSCTLGEKFEETTADGRK 21 2 Q01469;I6L8B7 Q01469 FABP5 "Fatty acid-binding protein, epidermal" 0 211.06 9.55E-23 302530000 210190 99795 148480 88961 275900 222010 192900 168190 205570 116080 FALSE TRUE 218488.4635 116934.015 152349.5108 106557.2203 229002.6165 170451.5421 177779.9939 165935.6882 198171.5759 138823.6535 1.573856169 0.842320541 1.097431936 0.767572511 1.649593645 1.227827807 1.280617456 1.19529838 1.427505838 1 17.08289388 3.24853811 24.99999859 1.294524088 1.055949832 0.15963467 0.253719839 355.8273008 891569.8175 0.066444423 0.088917209 1772.303561 -3.24853811 -0.238574257 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 TTQSMQDFPVVDS(1)EEEAEEEFQK 219.43 1.34E-32 102490000 230420 169310 216170 158510 254740 279600 257940 235090 246750 137630 TRUE FALSE 239517.1595 198387.6755 221803.5678 189862.8049 211439.3858 214667.1374 237721.9888 231939.0031 237869.5157 164595.9634 1.455182463 1.205300977 1.347563836 1.153508269 1.284596423 1.304206573 1.444275934 1.409141502 1.445172231 1 17.32856943 2.457884888 23.52477786 1.36807776 1.28168158 0 0.143398433 323.7150561 395876.4787 0.04603075 0.038519378 287.0019765 -2.457884888 -0.086396179 TTQVPQFILDDFIQNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTQVPQFILDDFIQNDR 17 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 246.96 2.46E-20 196052000 76177.7 95333 100294 99288 110761.1 129478.9 96375 98577.8 96023.6 92830.6 FALSE TRUE 79185.25442 111705.7012 102907.744 118926.8701 91933.96778 99409.38775 88820.87567 97256.52583 92567.72939 111018.9787 0.713258718 1.006185631 0.926938306 1.071230085 0.828092357 0.89542697 0.800051277 0.876035133 0.833800945 1 16.7604468 TTS(ph)FAESCKPVQQPSAFGSMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TTSFAESCKPVQQPSAFGSMK 21 1 A0A3B3ITW1;P49841;P49841-2 A0A3B3ITW1 GSK3B Glycogen synthase kinase-3 beta 1 T(0.001)T(0.099)S(0.901)FAESCKPVQQPSAFGSMK;TT(0.002)S(0.998)FAESCKPVQQPSAFGSMK;T(0.141)T(0.141)S(0.713)FAES(0.005)CKPVQQPSAFGSMK;T(0.012)T(0.012)S(0.975)FAESCKPVQQPSAFGSMK;T(0.209)T(0.132)S(0.659)FAESCKPVQQPSAFGSMK 297.5 3.73E-55 4958190000 4140840 2474210 3236170 2752700 5934030 4600330 4082830 3825120 3885960 2326530 TRUE FALSE 4304323.561 2899136.321 3320507.249 3297175.844 4925365.7 3531973.076 3762807.116 3773850.523 3746105.059 2782369.009 1.546999534 1.041966867 1.19341009 1.185024644 1.770205779 1.269412168 1.352375297 1.356344363 1.346372478 1 21.40788234 5.067222972 18.43896489 1.304771407 5.752203397 0.124297418 0.203280212 296.6510427 84165.16966 0.046236112 1819.231315 116740.8825 -5.067222972 4.44743199 TTS(ph)PEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTSPEPR 7 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 T(0.023)T(0.36)S(0.617)PEPR;T(0.002)T(0.154)S(0.843)PEPR;T(0.009)T(0.088)S(0.903)PEPR;T(0.018)T(0.218)S(0.764)PEPR 121.58 0.0046408 5920620000 4477750 4724620 4693740 4377370 5305710 6002010 5154750 5095160 4592180 4283750 TRUE FALSE 4654535.028 5536036.733 4816062.72 5243200.721 4403847.309 4608134.139 4750707.226 5026867.714 4426908.339 5123068.795 0.908544315 1.080609485 0.940073794 1.023449212 0.859611199 0.89948707 0.927316695 0.981221981 0.864112608 1 22.28857683 3.257191891 24.99984501 0.924489332 0.991336689 0.225379028 0.059909438 359.1133879 481863.1953 0.015824653 0.021388476 1807.972794 -3.257191891 0.066847357 TTS(ph)PGGRPSAR ddPTM_MDA-MB-175_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(0.388)T(0.035)S(0.561)PGGRPS(0.017)AR 87.573 0.03584 113210000 172700 194780 192230 197420 210710 259450 220270 212580 195980 167470 TRUE FALSE 179518.3294 228231.9498 197239.6717 236469.0868 174893.5895 199196.6695 203004.6618 209730.7128 188926.7181 200282.5401 0.896325407 1.139549906 0.984807121 1.18067749 0.873234329 0.994578306 1.013591408 1.047174221 0.943300989 1 17.61167713 3.231164059 24.99996925 0.988569974 1.052031203 0.139212477 0.085177266 366.8040007 1239775.806 0.023265438 0.028341257 1702.801636 -3.231164059 0.063461229 TTS(ph)PLEEEER ddPTM_MDA-MB-175_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(0.004)T(0.268)S(0.728)PLEEEER;TT(0.004)S(0.996)PLEEEER;T(0.001)T(0.012)S(0.987)PLEEEER;T(0.001)T(0.017)S(0.982)PLEEEER 342.24 9.19E-54 1880680000 1398620 1482250 1498280 1590120 1562170 1915520 1742150 1465770 1463530 1092340 TRUE FALSE 1453838.598 1736814.907 1537326.408 1904640.99 1296632.901 1470669.51 1605595.731 1446123.751 1410857.841 1306363.109 1.11289012 1.329503945 1.1767987 1.457972119 0.992551682 1.125773914 1.229057771 1.106984529 1.079989041 1 20.31712452 3.220369007 24.99995296 1.106358787 1.266985623 0.403303855 0.10613935 258.1959113 354826.8336 0.02938662 0.035185985 1660.997609 -3.220369007 0.160626836 TTS(ph)PLEEEEREIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTSPLEEEEREIK 13 1 S4R3H4;Q9UKV3;E7EQT4;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 TT(0.012)S(0.988)PLEEEEREIK;T(0.002)T(0.147)S(0.851)PLEEEEREIK 210.9 1.58E-08 727410000 585410 415520 542750 341470 804140 728720 537800 484430 639480 465470 TRUE FALSE 608522.4388 486882.3277 556894.5109 409011.7468 667452.57 559485.8239 495645.8307 477937.0082 616465.2397 556669.9345 1.093147664 0.874633778 1.000403428 0.734747328 1.199009554 1.005058454 0.890376505 0.858564436 1.107416085 1 19.08646264 4.762979812 22.97738026 0.953877162 1.093148166 0.083278448 0.125694025 5572.198249 5242936.991 0.02905796 1.575941755 57940.17625 -4.762979812 0.139271003 TTS(ph)PSSDTDLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTSPSSDTDLLDR 13 0 K7ENU0;K7ERZ4;K7EJ43;Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3 K7ENU0;Q96QT6 PHF12 PHD finger protein 12 1 TT(0.009)S(0.99)PS(0.001)SDTDLLDR;TT(0.005)S(0.995)PSSDTDLLDR;TT(0.001)S(0.999)PS(0.001)SDTDLLDR 266.89 1.87E-24 785590000 788790 771590 818420 772270 940060 1059200 821280 811760 825910 717530 TRUE FALSE 819932.0383 904104.5804 839748.6975 925022.701 780268.937 813216.8523 756905.9276 800879.685 796185.6604 858116.2656 0.955502268 1.053592172 0.978595479 1.077968963 0.909281141 0.947676772 0.882055216 0.933299737 0.927829587 1 19.71081361 3.220013871 24.99982114 0.927474363 1.016368891 0.470381572 0.042904302 179.5234154 241985.5054 0.01133637 0.013572244 1659.639914 -3.220013871 0.088894528 TTSIS(ph)PALAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TTSISPALAR 10 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 TTS(0.003)IS(0.997)PALAR;TTS(0.005)IS(0.995)PALAR;TT(0.006)S(0.249)IS(0.744)PALAR;TTS(0.001)IS(0.999)PALAR;TTSIS(1)PALAR 236.42 4.02E-12 2668190000 2735250 3019700 2935090 2762090 3397760 3759710 2779120 2976290 2739120 2520180 TRUE FALSE 2843239.782 3538309.985 3011580.857 3308423.158 2820209.969 2886574.331 2561285.313 2936397.701 2640539.606 3013961.019 0.943356521 1.173973373 0.999210288 1.097699385 0.935715476 0.957734461 0.849807047 0.974265321 0.876102773 1 21.52322933 3.225005639 23.7377133 0.929499191 1.058278725 0.419610227 0.0697479 105.6424312 185002.3965 0.018402438 0.022127942 1678.825817 -3.225005639 0.128779534 TTSRS(ph)PVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTSRSPVLSR 10 1 O95819-3;O95819-6;E7EN19;O95819;H7C360;O95819-2;A0A0D9SEY1;H7C0P6;A0A0D9SG62;G5E948;E7ENQ1;G3XAA2;C9J840;E7EX83;O95819-4;O95819-5;H7C3Z6 O95819-3 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 T(0.17)T(0.17)S(0.135)RS(0.526)PVLSR;T(0.148)T(0.148)S(0.12)RS(0.584)PVLSR 70.622 0.032358 482100000 304670 385300 352950 333540 474570 506300 400590 360010 364150 383650 TRUE FALSE 316698.6069 451472.2778 362148.167 399513.2165 393902.7609 388719.4981 369190.7091 355184.6548 351044.3126 458818.8721 0.69024756 0.983988029 0.789305299 0.870742772 0.858514732 0.847217762 0.804654585 0.774128259 0.765104345 1 18.80756521 2.245853363 23.51511521 0.812093535 0.846481797 0 0.092915933 339.6253095 1095108.087 0.029982941 0.02457157 176.1381224 -2.245853363 0.034388263 TTSSANNPNLMYQDECDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TTSSANNPNLMYQDECDRR 19 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 ;;;;;;; 294.59 1.93E-49 4387740000 744802 981943 1033567 928818 1263679 1320482 1062565 1092718 1079123 960053 FALSE TRUE 774207.3581 1150584.072 1060502.605 1112535.428 1048879.295 1013820.068 979278.3788 1078071.903 1040285.574 1148157.004 0.674304433 1.002113881 0.923656435 0.968974996 0.913532985 0.882997764 0.8529133 0.938958608 0.906048189 1 20.13088851 7.999937451 0.015299498 1.660476623 1.22E-06 0.161900328 0.082150253 12429.63976 14.67820303 633.7143404 997.4394871 99985598.63 -7.999937451 -1.660475402 TTSSYQNLVWSDHSQELHS(ph)PTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTSSYQNLVWSDHSQELHSPTLK 23 0 Q8WVV4-1;Q8WVV4;Q8WVV4-3 Q8WVV4-1 POF1B Protein POF1B 1 TTSSYQNLVWS(0.002)DHS(0.021)QELHS(0.952)PT(0.025)LK;TTSSYQNLVWSDHSQELHS(0.994)PT(0.006)LK;TTSSYQNLVWSDHSQELHS(0.994)PT(0.006)LK;TTSSYQNLVWSDHSQELHS(1)PTLK 280.17 1.09E-51 2110750000 502499 815146 995040 902680 1268860 1426480 1212120 1255090 1080030 843570 TRUE FALSE 522338.0485 955140.9845 1020971.56 1081227.41 1053179.63 1095201.639 1117110.867 1238267.571 1041159.931 1008851.39 0.517755195 0.946760835 1.01201383 1.071741012 1.043939316 1.085592634 1.107309637 1.227403345 1.032025074 1 19.94428224 4.978453539 1.285728351 1.098199153 1.61E-17 0.880814402 0.061175111 0.754717823 0.729699666 0.018154566 1.259126238 95159.80402 -4.978453539 -1.098199153 TTTAAAVASTGPSSRS(ph)PSTLLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTTAAAVASTGPSSRSPSTLLPK 23 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 TTTAAAVAS(0.108)T(0.108)GPS(0.074)S(0.074)RS(0.491)PS(0.06)T(0.084)LLPK 70.488 0.01404 338620000 189180 142050 153100 88957 240300 223480 130940 172280 211570 147680 TRUE FALSE 196648.9725 166445.9825 157089.9118 106552.4291 199453.8918 171580.1569 120676.5807 169970.8684 203955.637 176615.0685 1.113432586 0.942422319 0.889447957 0.603303161 1.129314127 0.971492174 0.683274545 0.962380333 1.154803148 1 17.43024891 1.467785588 25 1.071132144 0.898826973 0.155423205 0.158841569 3.494269995 9362.635134 0.085327101 0.039500835 29.36199688 -1.467785588 -0.17230517 TTTELFHSNEESGFFNELEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TTTELFHSNEESGFFNELEALR 22 0 A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6;A0A0A0MRE9;H7BYL6 A0A0A0MRF6 AKAP9 A-kinase anchor protein 9 0 ;; 254.24 4.78E-37 244653000 87541.8 102553.5 103343.5 109584.7 119511 132254 108244.1 116811.7 111446 90364.8 FALSE TRUE 90998.01786 120166.2659 106036.7165 131260.2266 99196.56291 101540.0128 99759.6446 115246.0302 107435.0802 108070.0524 0.842028072 1.111929375 0.98118502 1.214584648 0.917891319 0.939575864 0.923101658 1.066401169 0.994124439 1 16.72160726 TTTS(ph)PFFSEDTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTTSPFFSEDTFR 13 0 A0A494C0H4;H0Y9M2;Q17R98-2;Q17R98;H0Y9K9;G5E9Z1;A0A590UJE4;Q17R98-3;A0A5F9ZGT0;A0A5F9ZHK5 A0A494C0H4 ZNF827 Zinc finger protein 827 1 TTT(0.039)S(0.96)PFFSEDTFR;TTT(0.003)S(0.997)PFFSEDTFR 138.31 5.31E-05 192596000 502450 516660 554260 499400 662010 697910 566710 579080 584300 513810 TRUE FALSE 522287.114 605392.3359 568704.4709 598179.8294 549481.7767 535830.9794 522289.7894 571318.3798 563271.1571 614481.232 0.849964306 0.98520883 0.925503402 0.973471277 0.894220601 0.872005444 0.84996866 0.929757249 0.916661287 1 19.22900942 0.517989526 1.994075335 0.99997947 0.91144774 0.272640238 0.043840672 5.697969066 21.89965577 0.042464347 0.011690833 3.296017627 -0.517989526 -0.08853173 TTVSHNTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTVSHNTK 8 0 Q9UHQ9 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 ; 91.853 0.012192 44666000 135849 146362 155713 155627 202461 226081 188859 163075 151688 146361 FALSE TRUE 141212.4234 171498.535 159771.0087 186409.5561 168046.7515 173577.114 174055.7381 160889.2464 146228.7785 175037.6357 0.806754632 0.979780916 0.912780889 1.06496843 0.96006068 0.991655956 0.994390363 0.919169444 0.835413355 1 17.41730563 4.742741321 24.53663891 0.961577508 0.806754553 0.385542785 0.058803045 346.3622071 2032704.918 0.01399832 0.107878898 55302.06147 -4.742741321 -0.154822954 TTWDIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TTWDIDR 7 0 Q2M2H8 Q2M2H8 Probable maltase-glucoamylase-like protein LOC93432;Glucoamylase 0 ; 98.133 0.026723 150282000 1826630 179900 141962 192759 267700 358510 239180 236186 189025 172963 FALSE TRUE 1898746.763 210796.4256 145661.6463 230886.1549 222196.4496 275251.4858 220432.4466 233020.313 182222.0272 206851.7883 9.179262015 1.019069873 0.704183645 1.116191244 1.074181913 1.330670081 1.065654053 1.126508574 0.880930393 1 17.6582379 4.738679226 24.999999 1.046827767 9.179264407 0.995983432 0.155151495 0.529506417 111481.3893 0.038274314 0.221120841 54787.21521 -4.738679226 8.13243664 TTWGDGGENS(ph)PCNVVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TTWGDGGENSPCNVVSK 17 0 H3BV99;H3BP15;H3BQY9;H3BM38;O00161 H3BV99;H3BM38 SNAP23 Synaptosomal-associated protein;Synaptosomal-associated protein 23 1 TTWGDGGENS(1)PCNVVSK 192.98 1.64E-10 255470000 204760 202260 182230 201820 251880 302800 239120 178310 173490 153280 TRUE FALSE 212844.0829 236996.5816 186979.0635 241739.3936 209065.5276 232479.289 220377.1496 175920.0461 167246.1288 183312.2813 1.161101053 1.292857085 1.020002927 1.31872994 1.140488385 1.268214477 1.202195227 0.959674087 0.912356377 1 17.48394392 1.717546705 4.829026023 0.949327752 1.202571787 0.642499391 0.08303331 0.093243274 5.178471083 0.040368617 0.020123676 52.1851222 -1.717546705 0.253244034 TTYLVLDEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TTYLVLDEADR 11 0 P17844;P17844-2;J3KTA4;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 ;;; 192.64 3.03E-06 342362000 417262 465433 483167 486923 570150 659406 519018 508558 489563 444413 FALSE TRUE 433735.826 545367.4972 495758.7289 583234.9161 473236.1067 506268.9499 478336.013 501741.6118 471943.7233 531487.2185 0.816079504 1.026115922 0.93277639 1.097363955 0.890399788 0.952551505 0.899995327 0.944033261 0.887968152 1 19.01967547 TVAEGHGDTLYVGTTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVAEGHGDTLYVGTTR 16 0 O95834;O95834-2;O95834-3;K7EIK7;A0A0C4DGQ7;C9JRL6;K7ELI8;K7EKG3;K7EII6 O95834 EML2 Echinoderm microtubule-associated protein-like 2 0 ;; 149.3 8.49E-07 607220000 321364 354599 418770 376045 472780 488340 393130 410980 416690 392050 FALSE TRUE 334051.6989 415498.6199 429683.4902 450425.5786 392417.0245 374930.4359 362315.4433 405471.4853 401693.4083 468864.6912 0.712469301 0.88618023 0.916433884 0.960672849 0.836951538 0.799655941 0.77275054 0.864794242 0.856736316 1 18.83881211 0.522454463 2.204064537 0.999987558 0.847326923 0.322044178 0.067489522 6.526294933 28.5340133 0.066974719 0.018167464 3.330078435 -0.522454463 -0.152660635 TVAISDAAQLPHDYCT(ph)TPGGTLFS(ph)TTPGGTRIIYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.047)CT(0.463)T(0.466)PGGT(0.092)LFS(0.291)T(0.291)T(0.291)PGGT(0.046)RIIY(0.012)DR 83.054 0.017901 68736000 13138 15654 18191 11116 22210 26832 15018 20682 25285 28222 TRUE FALSE 13656.69838 18342.45273 18665.0724 13314.71162 18434.75213 20600.67464 13840.84992 20404.79162 24374.99779 33751.56056 0.404624206 0.543454952 0.553013612 0.394491733 0.546189623 0.610362137 0.410080295 0.604558464 0.722188764 1 15.04266659 0.975823295 1.483929048 0.99827831 0.500056806 0.82871032 0.071130556 0.161061802 0.723512167 0.064385158 0.01904482 9.45852236 -0.975823295 -0.498221504 TVAISDAAQLPHDYCT(ph)TPGGTLFS(ph)TTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.012)CT(0.329)T(0.329)PGGT(0.327)LFS(0.325)T(0.325)T(0.325)PGGT(0.013)RIIY(0.013)DRK 89.129 0.0012634 330140000 80151 65441 91302 62771 146700 126070 64799 110590 103180 134560 TRUE FALSE 83315.42337 76679.98269 93681.40513 75186.91645 121763.9864 96792.15311 59719.88506 109107.7219 99466.57196 160924.4557 0.517730031 0.476496766 0.582145235 0.467218709 0.756653088 0.601475722 0.371105093 0.678005847 0.618094817 1 17.29602406 -4.999999928 0.239501017 3.509667938 0.518904316 0.633820885 0.101770039 108.3671168 1.08119353 132.1953912 0.159262195 1.00E-05 4.999999928 -2.990763622 TVAISDAAQLPHDYCT(ph)TPGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.002)CT(0.827)T(0.171)PGGT(0.04)LFS(0.128)T(0.141)T(0.689)PGGT(0.002)R;TVAISDAAQLPHDY(0.002)CT(0.775)T(0.223)PGGT(0.012)LFS(0.035)T(0.141)T(0.809)PGGT(0.003)R 140.01 4.42E-08 316900000 99992 135099 128191 157184 155306 191587 155251 176280 154007 154508 TRUE FALSE 103939.7614 158301.2023 131531.7628 188274.5261 128907.1416 147093.8228 143082.0209 173917.2549 148464.3182 184780.8844 0.562502781 0.856696854 0.711825594 1.018906943 0.697621629 0.796044587 0.774333457 0.941208045 0.803461455 1 17.49545599 7.999987609 0.07081894 1.165122351 6.09E-09 0.318960432 0.111874958 308.5766985 1.6107618 4.566889573 35.77135628 99997147.02 -7.999987609 -1.165122345 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTRIIYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDR 36 1 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.15)CT(0.393)T(0.425)PGGT(0.308)LFS(0.256)T(0.241)T(0.226)PGGT(0.001)RIIYDR 76.716 0.0033658 620960000 81498 147400 126160 103770 175500 186080 86386 169180 124870 228180 TRUE FALSE 84715.60397 172714.8034 129447.8332 124295.3963 145668.5727 142865.7401 79614.83959 166912.4188 120375.9531 272887.5022 0.310441494 0.632915769 0.474363363 0.455482187 0.533804485 0.523533467 0.291749673 0.611652851 0.441119333 1 18.0579468 -1.875243528 0.674256974 1.427139471 0.481542119 0.687461505 0.106023954 93.15288206 11.22110055 63.16539252 0.035698843 0.013327739 1.875243528 -0.945597352 TVAISDAAQLPHDYCTT(ph)PGGT(ph)LFSTTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.038)CT(0.451)T(0.499)PGGT(0.327)LFS(0.245)T(0.223)T(0.203)PGGT(0.007)RIIY(0.006)DRK 89.462 0.00075493 743560000 35947 37680 41277 27361 64727 56623 31619 39238 47397 55966 TRUE FALSE 37366.21532 44151.24689 42352.71253 32772.92414 53724.72766 43473.16638 29140.62016 38712.07879 45691.19123 66931.46617 0.558275763 0.659648584 0.632777301 0.48964898 0.802682665 0.649517617 0.435379976 0.578383846 0.682656362 1 16.030397 0.848891614 3.780765395 0.999930047 0.600007938 0.614164257 0.094728472 0.585925513 13.58793738 0.09207352 0.023621804 7.061413019 -0.848891614 -0.399922109 TVAISDAAQLPHDYCTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.034)CT(0.174)T(0.397)PGGT(0.39)LFS(0.312)T(0.312)T(0.312)PGGT(0.036)RIIY(0.032)DRK;TVAISDAAQLPHDYCT(0.029)T(0.971)PGGT(0.028)LFS(0.403)T(0.347)T(0.222)PGGTRIIYDRK;TVAISDAAQLPHDYCT(0.465)T(0.528)PGGT(0.109)LFS(0.337)T(0.298)T(0.262)PGGTRIIYDRK 162.96 2.26E-17 1679990000 338275 328759 403237 276319 650427 558180 291323 441471 468799 586695 TRUE FALSE 351630.3582 385220.8009 413745.6875 330974.0735 539867.6509 428551.1543 268488.342 435553.8033 451927.0156 701646.6523 0.501150197 0.549023928 0.589678132 0.471710472 0.769429526 0.610779162 0.382654633 0.620759469 0.644094879 1 19.42038515 0.710674945 1.88043398 0.999597647 0.560992077 0.64966819 0.096430866 0.709200089 3.670145013 0.091233022 0.025450151 5.136590513 -0.710674945 -0.43860557 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDYCT(0.47)T(0.53)PGGT(0.305)LFS(0.13)T(0.091)T(0.474)PGGT(0.001)R;TVAISDAAQLPHDYCT(0.076)T(0.924)PGGTLFS(0.017)T(0.094)T(0.881)PGGT(0.009)R;TVAISDAAQLPHDY(0.003)CT(0.223)T(0.774)PGGT(0.001)LFS(0.141)T(0.124)T(0.733)PGGT(0.002)R;TVAISDAAQLPHDYCT(0.054)T(0.775)PGGT(0.171)LFS(0.004)T(0.02)T(0.974)PGGT(0.002)R;TVAISDAAQLPHDYCT(0.026)T(0.974)PGGT(0.005)LFS(0.05)T(0.032)T(0.898)PGGT(0.015)R;TVAISDAAQLPHDYCT(0.026)T(0.974)PGGT(0.004)LFS(0.062)T(0.065)T(0.67)PGGT(0.199)R;TVAISDAAQLPHDYCT(0.126)T(0.873)PGGT(0.384)LFS(0.127)T(0.089)T(0.397)PGGT(0.002)R;TVAISDAAQLPHDYCT(0.173)T(0.824)PGGT(0.003)LFS(0.252)T(0.174)T(0.512)PGGT(0.06)R 210.7 4.54E-26 37997930000 4375317 5107482 5081442 6351240 6363410 7697450 5669397 6287290 6111520 5995920 TRUE FALSE 4548057.894 5984652.303 5213868.553 7607496.315 5281759.841 5909833.893 5225014.849 6203019.161 5891567.589 7170705.725 0.63425527 0.834597393 0.727106753 1.060913194 0.73657462 0.824163495 0.728661174 0.865050024 0.821616144 1 22.77368368 -5 0.188493403 1.805716033 0.773237053 0.250391284 0.106400395 200.6551079 1.959321721 60.78654677 0.28261315 1.00E-05 5 -1.03247898 TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 2 TVAISDAAQLPHDY(0.001)CT(0.129)T(0.772)PGGT(0.098)LFS(0.062)T(0.053)T(0.885)PGGTRIIYDRK 158.67 7.93E-18 926800000 294830 316290 302250 209260 564010 497060 253480 355510 402960 454260 TRUE FALSE 306470.1161 370610.3471 310126.8833 250651.0034 468139.7817 381625.348 233611.5753 350744.9699 388457.5483 543263.5497 0.564127883 0.682192552 0.570858994 0.461380123 0.861717636 0.702468163 0.430015184 0.645625811 0.71504438 1 19.05129273 0.836681774 2.423644642 0.999494596 0.614058951 0.498227074 0.116651801 0.521564754 5.599742217 0.111504874 0.030016788 6.865651802 -0.836681774 -0.385435645 TVAISDAAQLPHDYCTT(ph)PGGTLFSTTPGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDY(0.002)CT(0.203)T(0.795)PGGTLFSTTPGGTR 154.02 2.14E-08 277290000 115320 170890 152850 137050 144080 165440 135890 151260 134310 132030 TRUE FALSE 119872.9226 200239.0282 156833.3966 164158.0809 119589.3331 127019.0673 125238.5867 149232.6071 129476.2093 157898.7506 0.759175878 1.268148274 0.993252929 1.039641418 0.757379856 0.804433643 0.793157553 0.94511582 0.819995148 1 17.26864023 3.256438713 24.90616927 0.850782076 1.031575554 0.257171562 0.133419398 280.9117446 391338.728 0.034888478 0.047139224 1804.840022 -3.256438713 0.180793477 TVAISDAAQLPHDYCTTPGGTLFST(ph)TPGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGT(0.003)LFS(0.079)T(0.524)T(0.394)PGGTR;TVAISDAAQLPHDYCTTPGGTLFS(0.047)T(0.87)T(0.083)PGGTR 307 5.45E-82 2906510000 1254770 1263380 1343930 1225910 1321610 1625200 1449880 1378510 1313520 1241670 TRUE FALSE 1304309.288 1480355.687 1378953.92 1468391.339 1096963.204 1247771.93 1336234.617 1360033.328 1266246.672 1484951.463 0.878351462 0.9969051 0.92861885 0.988848037 0.738719905 0.840277922 0.899850702 0.915877294 0.852719232 1 20.50198435 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 TVAISDAAQLPHDYCTTPGGTLFS(0.001)T(0.133)T(0.867)PGGTR;TVAISDAAQLPHDYCTTPGGTLFST(0.025)T(0.961)PGGT(0.014)R;TVAISDAAQLPHDYCTTPGGTLFS(0.009)T(0.033)T(0.958)PGGTR 340.9 1.24E-105 9230300000 2215640 2499520 2798480 2412700 2395140 3002970 2543780 2737190 2699970 2005800 TRUE FALSE 2303115.178 2928793.116 2871410.688 2889924.859 1988014.958 2305575.728 2344391.877 2700502.445 2602798.607 2398798.107 0.960112138 1.220941899 1.197020575 1.204738678 0.828754597 0.96113788 0.977319379 1.125773127 1.085042797 1 21.19388031 3.286414807 24.99993553 1.007982121 1.154743131 0.34008747 0.100838766 146.6942063 76634.70831 0.029445004 0.039868635 1933.814475 -3.286414807 0.14676101 TVALWDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVALWDLR 8 0 Q09028-3;Q09028;Q09028-2;Q09028-4;H0YF10;H0YCT5;H0YDK2;H0YEU5;Q16576;E9PC52;Q16576-2;Q5JP02 Q09028-3;Q16576 RBBP4;RBBP7 Histone-binding protein RBBP4;Histone-binding protein RBBP7 0 128.69 0.0026123 210450000 466360 564580 401470 310320 1204000 844810 533050 419240 460610 1353600 FALSE TRUE 484772.2529 661542.2232 411932.638 371700.3698 999344.5101 648615.6807 491268.1481 413620.7735 444032.7361 1618812.004 0.299461736 0.408659079 0.254466014 0.229613055 0.617332036 0.400673876 0.303474491 0.255508838 0.274295431 1 20.62650402 -1.672203314 3.928680504 1.034170173 0.337088377 0.767793348 0.109189387 0.032410151 0.0027042 0.10485072 0.025761603 0.02127143 1.672203314 -0.697081797 TVANLLSGKS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVANLLSGKSPR 12 1 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 TVANLLS(0.002)GKS(0.998)PR;TVANLLSGKS(1)PR 123.92 0.00020118 5238000000 13051100 9144300 11475700 8153900 13518600 13922600 12424300 11669400 12426500 8321200 TRUE FALSE 13566367.51 10714762.39 11774766.17 9766717.083 11220713.2 10689287.15 11450450.9 11512990.78 11979272.69 9951579.821 1.363237571 1.076689589 1.18320572 0.98142378 1.127530845 1.07412967 1.150616395 1.156900812 1.203755877 1 23.24649414 4.74369947 24.82129834 1.113153666 1.363237687 0.543386215 0.070462078 377.1120381 1821433.232 0.01612678 0.13566288 55424.20472 -4.74369947 0.250084021 TVAS(ph)DLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVASDLQK 8 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK;TVAS(1)DLQK 164.48 0.00034602 2739970000 4508980 2829760 3880690 2879170 5445390 5481430 4878970 4024890 4143260 2539120 TRUE FALSE 4686998.012 3315749.268 3981823.969 3448661.233 4519784.553 4208450.954 4496543.583 3970942.933 3994144.882 3036611.95 1.543495873 1.091923934 1.311271916 1.135693757 1.488430075 1.385903442 1.480776489 1.307688634 1.31532937 1 21.53403113 0.539017991 2.268468587 1.000022541 1.337978987 0.354394125 0.138052413 5.442774628 25.4136289 0.128083931 0.03460854 3.459537092 -0.539017991 0.337956446 TVATPLNQVANPNSAIFGGARPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056;Q15056-2 EIF4H Eukaryotic translation initiation factor 4H 0 ; 192.09 9.31E-18 1560990000 175359 165711 189793 178747 265340 241520 161003 221787 236290 179630 FALSE TRUE 182282.3087 194170.5752 194739.1615 214102.6231 220237.6016 185430.6403 148383.1642 218814.308 227785.9691 214825.0593 0.84851511 0.903854401 0.906501142 0.996637095 1.025195116 0.863170437 0.690716272 1.018569755 1.060332392 1 17.71280277 1.576359241 13.41142234 1.031289834 0.896813914 0.340520303 0.086254595 0.159245408 56.03034383 0.049209195 0.02293145 37.70155306 -1.576359241 -0.13447592 TVCIYGHLDVQPAALEDGWDSEPFTLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVCIYGHLDVQPAALEDGWDSEPFTLVER 29 0 Q96KP4;J3QKT2;J3QRH4;A0A087WYZ1;J3KSV5;J3QRD0;J3QKQ0;J3QLU1;J3QR27;A0A087WVS2;J3KRD5 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 139.16 3.47E-07 129450000 49467 65026 81413 63874 67480 78337 77271 62146 64252 67583 FALSE TRUE 51419.99536 76193.70967 83534.68966 76508.08656 56009.7737 60144.41896 71214.29711 61313.03452 61939.58307 80824.5949 0.636192429 0.942704504 1.03353057 0.946594123 0.692979331 0.744135112 0.881096864 0.758593775 0.766345729 1 16.30250675 3.259831194 24.98821761 0.79507802 0.903807145 0.085881827 0.125043113 466.0318193 547480.6209 0.034112834 0.046145137 1818.993696 -3.259831194 0.108729124 TVDGPS(ph)GK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 TVDGPS(1)GK;TVDGPS(1)GK 104.95 0.0047008 227480000 1323500 1041320 1236320 870870 1434770 1670710 1518010 1249100 1321230 1079250 TRUE FALSE 1375752.802 1220158.61 1268539.515 1043125.487 1190888.308 1282712.922 1399024.41 1232357.858 1273679.19 1290708.374 1.065889731 0.945340275 0.98282427 0.808180614 0.922662572 0.993805377 1.083919836 0.954791867 0.986806327 1 20.29973164 2.658523355 6.046489983 1.00457902 0.939634049 0.161473855 0.066763016 0.431904233 26.05250355 0.022537093 0.021247065 455.5366825 -2.658523355 -0.064944971 TVDGPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 TVDGPSGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;; 150.05 0.0011524 10624800000 15424210 12267840 14977420 11811990 17521360 17154550 17167020 15242590 15206010 11012710 FALSE TRUE 16033169.72 14374746.09 15367743.87 14148366.37 14543085.49 13170665.74 15821424.11 15038288.01 14658748.67 13170439.67 1.217360249 1.091440107 1.166836055 1.074251636 1.104221715 1.000017165 1.201282911 1.141821259 1.113003744 1 23.65080017 -2.604150008 1.507039149 5.45E-05 1.122887884 0.274138146 0.060215004 493498.4642 26379.30416 1675790.59 0.015653398 0.002487998 2.604150008 1.122833345 TVDKFNEWFVSAFVTAGHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVDKFNEWFVSAFVTAGHMR 20 1 F5H785;P0DI82;P0DI81;P0DI81-3 F5H785 TRAPPC2;TRAPPC2B Trafficking protein particle complex subunit 2B;Trafficking protein particle complex subunit 2 0 166.25 9.29E-12 61882000 108720 90012 130580 102930 161480 159580 138120 131060 142110 99556 FALSE TRUE 113012.3496 105470.8608 133983.0221 123289.2468 134031.6873 122519.9635 127293.7935 129303.3551 136995.4889 119062.0921 0.94918834 0.885847535 1.125320576 1.035503783 1.125729314 1.029042589 1.069137886 1.086016152 1.150622221 1 16.86135462 4.241696624 24.99998289 1.079104686 0.917517895 0.648421972 0.047161941 41.77611195 333020.062 0.010626491 0.026698965 17446.03037 -4.241696624 -0.161586791 TVDLKPDWGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVDLKPDWGK 10 1 P31948;P31948-2;P31948-3;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 148.28 2.32E-05 4368600000 3114660 1904590 2797390 1881930 3882800 3419000 3280300 2808120 3358500 1902900 FALSE TRUE 3237629.182 2231688.517 2870292.281 2254170.137 3222803.043 2624989.065 3023181.515 2770481.745 3237628.241 2275736.822 1.422672934 0.980644377 1.261258443 0.990523208 1.41615806 1.153467765 1.328440743 1.217399885 1.422672521 1 21.1179023 3.233686869 24.99997248 1.263820219 1.157657133 0.067663259 0.166368341 293.9404058 1507773.206 0.043169073 0.053167157 1712.721973 -3.233686869 -0.106163086 TVDSTPLSVHT(ph)PTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TVDSTPLSVHTPTLR 15 0 Q5VT25-2;H0Y5V1;A0A0A0MRJ1;A0A0A0MRJ0;Q5VT25;H0Y6V3 Q5VT25-2 CDC42BPA Serine/threonine-protein kinase MRCK alpha;Non-specific serine/threonine protein kinase 1 TVDSTPLS(0.009)VHT(0.989)PT(0.002)LR;TVDSTPLSVHT(0.998)PT(0.002)LR;TVDSTPLSVHT(0.998)PT(0.002)LR;TVDSTPLSVHT(1)PTLR;TVDSTPLSVHT(0.998)PT(0.002)LR 286.68 1.05E-33 3971620000 1606250 3640250 3333620 4266610 3184380 4666490 3454800 3468860 2729060 3018330 TRUE FALSE 1669665.99 4265434.62 3420496.876 5110532.723 2643100.225 3582768.419 3184003.749 3422365.606 2630841.664 3609713.974 0.462548003 1.181654461 0.947581138 1.415772208 0.732218742 0.992535266 0.882065386 0.948098833 0.72882275 1 21.78345309 TVDVPASLPT(ph)PPHNNQEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVDVPASLPTPPHNNQEELR 20 0 Q8NEZ4;Q8NEZ4-3;Q8NEZ4-2;H7BY37;H0Y765;H7C2V8 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 TVDVPAS(0.001)LPT(0.999)PPHNNQEELR;TVDVPASLPT(1)PPHNNQEELR 193.54 2.57E-17 346060000 149508 193658 192128 193161 230570 221720 182819 218870 200782 255720 TRUE FALSE 155410.6913 226917.255 197135.0135 231367.6693 191377.7938 170228.8902 168489.1691 215936.4056 193555.895 305823.4379 0.508171291 0.741987784 0.644604007 0.756540018 0.625778701 0.556624735 0.55093609 0.706081938 0.632900789 1 18.22233945 -0.159760167 1.168545528 1.002531987 0.639361651 0.661406156 0.078071317 11.45810738 10.61829715 0.206950971 0.022448069 0.69221313 0.159760167 -0.363170336 TVEAEAAHGTVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVEAEAAHGTVTR 13 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;;;;; 252.99 9.02E-24 6130310000 1936830 3253010 3165610 3370750 3466270 4192430 3425050 3604610 3172340 3391760 FALSE TRUE 2013297.544 3811689.163 3248108.397 4037474.289 2877074.664 3218801.669 3156585.631 3556296.099 3058168.103 4056310.433 0.496337146 0.939693652 0.800754393 0.995356336 0.709283649 0.793529421 0.778191335 0.876731739 0.753928516 1 21.95173664 -5 0.252883164 2.180599078 0.789285838 0.184970938 0.129127122 325.7150896 3.221681403 199.4110547 0.169522177 1.00E-05 5 -1.39131324 TVECEEGSEDDESLREMVELAAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVECEEGSEDDESLREMVELAAQR 24 1 G5E9W3;Q9UKF6 G5E9W3 CPSF3 Cleavage and polyadenylation specificity factor subunit 3 0 58.914 0.070556 28907000 7833.8 15229 7946.1 8488.8 8713.1 11531 7180.5 7718.9 8003.1 9043 FALSE TRUE 8143.084473 17844.46228 8153.181894 10167.8593 7232.050374 8853.100004 6617.673647 7615.440771 7715.069994 10814.80271 0.752957284 1.650003496 0.75389095 0.940179823 0.668717735 0.818609478 0.611908865 0.704168257 0.713380558 1 13.40071973 4.131378348 24.97119744 0.757930063 1.201829246 0.349983753 0.230654565 7.122057238 1629.875014 0.051752227 0.111797655 13532.50972 -4.131378348 0.443899183 TVEEAENIAVTSGVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVEEAENIAVTSGVVR 16 0 O76070 O76070 SNCG Gamma-synuclein 0 ;;; 242.4 1.40E-19 388178000 182136 208896 202335 194436 236050 259951 200557 225846 204268 223227 FALSE TRUE 189326.8699 244772.263 207608.0163 232894.8605 195926.3053 199581.3198 184836.8183 222818.9038 196916.4346 266964.0567 0.70918487 0.916873477 0.777662802 0.872382834 0.733905185 0.747596221 0.692365933 0.834640088 0.737614033 1 18.02628599 -1.339052319 3.619914151 1.00087201 0.784451277 0.473841026 0.069342823 7665097.207 5740661.751 48143.79874 0.015537927 0.04580867 1.339052319 -0.216420733 TVEIVHIDIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVEIVHIDIADR 12 0 A0A0A0MSW4;P48739;P48739-3;P48739-2;B3KYB7;B3KYB6 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;;; 132.47 0.00018035 2075410000 1599270 1795440 1813250 1822420 2094840 2340950 1992940 1964190 1889510 1767060 FALSE TRUE 1662410.415 2103792.853 1860504.785 2182889.237 1738759.845 1797299.84 1836728.155 1937863.246 1821506.904 2113281.575 0.7866488 0.995509959 0.880386602 1.032938186 0.822777176 0.850478167 0.869135555 0.916992449 0.861932894 1 21.01105357 -1.414353322 2.896483593 1.002098489 0.895240941 0.172812217 0.071095753 17257122.99 20040496.73 299500.5634 0.016606386 0.038516488 1.414353322 -0.106857548 TVEMHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TVEMHNK 7 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 ;;;;;; 97.071 0.012267 1188119000 2422569 2122146 2432100 1991277 2966560 2939060 2670880 2282970 2219870 1819239 FALSE TRUE 2518213.895 2486608.067 2495482.524 2385145.647 2462305.191 2256507.857 2461529.447 2252370.521 2139977.312 2175684.051 1.157435471 1.142908625 1.146987552 1.096273904 1.131738402 1.037148687 1.13138185 1.035247062 0.98358827 1 21.05303764 2.102401579 0.476684931 0.984997548 1.155518451 0.738312426 0.032013603 0.488736592 0.245788085 0.03111724 0.02711806 126.5906351 -2.102401579 0.170520904 TVENIKDPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVENIKDPLFR 11 1 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 84.188 0.014727 1857200000 4004900 3318700 4168000 3699500 5058600 5280100 4467800 4309800 4597200 3303500 FALSE TRUE 4163016.544 3888660.909 4276621.504 4431250.058 4198740.979 4053876.796 4117602.162 4252034.18 4431747.67 3950757.576 1.053726144 0.984282339 1.082481378 1.121620341 1.06276857 1.026101126 1.042231036 1.076257933 1.121746294 1 21.91369789 4.222897421 24.99969572 1.068803385 1.019004227 0.187823493 0.039428878 319.595166 510101.3528 0.009751819 0.021184102 16706.95955 -4.222897421 -0.049799158 TVEVPFKGDVEHTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 178.01 4.38E-07 619470000 676160 608670 739380 536260 933750 864390 747180 750970 803630 629250 FALSE TRUE 702855.3189 713204.3377 758648.8502 642330.6274 775031.5085 663648.5225 688614.0792 740904.4755 774707.5133 752539.4898 0.933977988 0.947730116 1.008118325 0.853550725 1.029888157 0.881878667 0.915053746 0.984538998 1.029457622 1 19.52140776 1.536413266 4.444638206 1.013141576 0.939867927 0.281507409 0.049775651 0.208090336 9.051173023 0.028395679 0.012113289 34.38850263 -1.536413266 -0.073273649 TVFAEHISDECK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVFAEHISDECK 12 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;;;;; 206.1 9.41E-08 4434380000 2592410 4736690 5428550 4916590 6897510 7191380 6337640 6447510 5970380 4160850 FALSE TRUE 2694760.349 5550179.661 5570022.473 5889076.827 5725073.714 5521290.981 5840879.216 6361091.674 5755507.19 4976088.893 0.541541843 1.115369878 1.11935751 1.183475005 1.150516769 1.109564379 1.173789163 1.2783316 1.156632712 1 22.24658083 4.74816733 3.763649816 1.162238112 0.470891547 0.877558616 0.067272589 0.085865747 2.302410278 0.01658757 0.167079168 55997.33129 -4.74816733 -0.691346565 TVFAEHISDECKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVFAEHISDECKR 13 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2;F8WCR1 P39023 RPL3 60S ribosomal protein L3 0 ;; 198.14 8.33E-08 1234020000 597530 1440480 1580920 1465240 1925290 2087690 1651450 1904340 1628090 1369350 FALSE TRUE 621120.9458 1687871.235 1622120.074 1755060.099 1598029.893 1602855.637 1522005.034 1878815.437 1569495.359 1637647.915 0.379276241 1.030667959 0.990518206 1.071695621 0.975807974 0.978754726 0.929384772 1.147264574 0.958383878 1 20.64319379 4.739390089 24.99762552 1.015483782 0.379276043 0.910149 0.059343215 18.21919618 548977.2262 0.014241463 0.085937885 54876.96561 -4.739390089 -0.636207739 TVFDEAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 101.33 0.017934 49142000 179649 183467 176309 194976 248160 289940 230370 179787 175793 207661 FALSE TRUE 186741.6812 214976.0301 180903.7574 233541.6709 205977.8518 222605.8291 212312.9974 177377.2493 169466.2443 248348.197 0.751934918 0.865623478 0.728427907 0.940379973 0.829391372 0.896345662 0.854900498 0.714228053 0.682373564 1 17.92200475 -1.039162626 6.749466199 1.000000063 0.808858488 0.338611871 0.080856888 7.79E-08 1.10E-08 0.079864352 0.018824202 0.091377101 1.039162626 -0.191141575 TVFPGAVPVLPAS(ph)PPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVFPGAVPVLPASPPPK 17 0 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 TVFPGAVPVLPAS(1)PPPK;TVFPGAVPVLPAS(1)PPPK 147.24 4.27E-07 327380000 612800 399210 557150 535010 637870 691460 803420 620150 583620 304150 TRUE FALSE 636993.8172 467771.2121 571669.7867 640833.3812 529445.0852 530878.8942 740445.8411 611837.9036 562615.6302 363742.3692 1.751222489 1.285995946 1.571633758 1.761778213 1.455549669 1.459491495 2.035632645 1.682063888 1.546742084 1 18.47255746 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVFPGAVPVLPASPPPKDSLR 21 1 Q9UBC2;Q9UBC2-2;Q9UBC2-3;M0R165;Q9UBC2-4;M0R2S2 Q9UBC2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR 183.58 2.58E-17 9550254000 3152850 2646794 3214750 2649372 4096270 3985180 3326220 3546970 3482010 2727199 TRUE FALSE 3277326.953 3101360.28 3298529.026 3173409.874 3399987.489 3059682.341 3065502.185 3499428.669 3356693.14 3261541.429 1.004839897 0.9508879 1.011340527 0.972978557 1.042448046 0.938109298 0.939893683 1.072937059 1.029173847 1 21.63712252 1.734703713 24.99999995 1.038575881 0.980663698 0.32587334 0.035381892 0.476353084 3052.269416 0.016012604 0.008879792 54.28798386 -1.734703713 -0.057912184 TVFS(ph)PTLPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVFSPTLPAAR 11 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-3 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 TVFS(0.999)PT(0.001)LPAAR;TVFS(0.996)PT(0.004)LPAAR;T(0.015)VFS(0.958)PT(0.027)LPAAR;TVFS(0.953)PT(0.047)LPAAR 197.43 5.99E-08 750080000 792590 827960 861210 791350 956030 1033210 815250 834850 891630 844910 TRUE FALSE 823882.0652 970155.6894 883653.8401 947876.6681 793524.3621 793262.6359 751348.5747 823660.2013 859540.4105 1010453.938 0.81535836 0.960118669 0.874511749 0.938070141 0.785314731 0.785055712 0.743575285 0.815138791 0.850647791 1 19.94657213 3.234216979 24.9999488 0.81261193 0.8999148 0.138465915 0.074641407 150.0997774 863903.8829 0.019936595 0.024621316 1714.813836 -3.234216979 0.08730287 TVHTEWTQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVHTEWTQR 9 0 C9JIF9;P13798;H7C393 C9JIF9 APEH Acylamino-acid-releasing enzyme 0 ;;; 168.8 5.90E-05 2192920000 193499 300903 240301 356349 489507 505445 376184 289887 270347 540881 FALSE TRUE 201138.4899 352580.7495 246563.4415 426833.7686 406300.775 388063.0588 346697.7151 286001.5389 260617.2643 646856.2762 0.310947729 0.545068143 0.381171909 0.659858742 0.628115997 0.59992161 0.535973334 0.442140781 0.402898254 1 19.30308567 -1.440659671 3.143406584 1.008570397 0.50671494 0.65457601 0.108737909 51067993.63 65404524.07 3906003.097 0.027109662 0.036252698 1.440659671 -0.501855457 TVIDKCS(ph)PPLEFLDDSDSHLEIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVIDKCSPPLEFLDDSDSHLEIQK 24 1 Q93075;H7C1W4 Q93075 TATDN2 Putative deoxyribonuclease TATDN2 1 T(0.111)VIDKCS(0.889)PPLEFLDDSDSHLEIQK 117.8 0.00038608 77000000 115210 71266 89800 68021 141260 136210 119270 96754 115060 64458 TRUE FALSE 119758.5798 83505.38113 92140.26177 81475.35078 117248.6757 104577.2918 109921.3057 95457.17089 110919.0131 77087.31098 1.553544653 1.083257154 1.195271447 1.056922984 1.520985415 1.356608376 1.425932548 1.238299399 1.43887511 1 16.23420578 3.245243702 24.99978629 1.342425374 1.210394146 0.073358477 0.182799474 355.0492135 1328142.272 0.04798346 0.063533102 1758.910339 -3.245243702 -0.132031228 TVIDSQTHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVIDSQTHYR 10 0 Q9Y3Q3 Q9Y3Q3 TMED3 Transmembrane emp24 domain-containing protein 3 0 ; 199.03 2.86E-07 711220000 444670 858400 719730 1066970 1345190 1347600 973230 697500 663390 1178430 FALSE TRUE 462225.915 1005823.523 738486.7551 1278013.481 1116535.084 1034640.323 896945.6895 688151.1534 639514.7235 1409320.796 0.327977786 0.713693806 0.524001886 0.906829364 0.792250485 0.734141103 0.63643827 0.488285673 0.453775127 1 20.42656861 4.742811071 24.23737292 0.672965933 0.327977573 0.289109383 0.169395787 396.4855973 2260746.793 0.041127907 0.319978043 55310.94409 -4.742811071 -0.34498836 TVIDYNGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVIDYNGER 9 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ;;; 143.21 0.00023841 2864200000 3786600 4484870 4181910 4172100 5319380 5468350 4387320 4244550 4064160 4826180 FALSE TRUE 3936097.892 5255111.535 4290894.01 4997328.928 4415193.688 4198408.586 4043430.394 4187658.75 3917891.675 5771777.568 0.681955922 0.910484071 0.74342678 0.865821468 0.76496255 0.727403046 0.700552013 0.725540564 0.67880157 1 22.46058427 TVIIHDRPDITHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVIIHDRPDITHPR 14 1 Q9NWH9;Q9NWH9-3;H7C3F4 Q9NWH9 SLTM SAFB-like transcription modulator 0 ;; 155.98 3.68E-06 508680000 153715 187621 167051 175445 208423 238603 189141 177458 187135 180753 FALSE TRUE 159783.7869 219843.4473 171404.4863 210147.4973 172995.3329 183191.0693 174315.6342 175079.4658 180400.0479 216168.0896 0.739164542 1.017002314 0.792922242 0.972148561 0.800281546 0.847447325 0.806389299 0.809922806 0.834535977 1 17.72179404 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVIQIHMCEEEEGDLLLFLTGQEEIDEACKR 31 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 99.34 0.0001714 15765000 9033.6 8417.2 8223.2 7908.5 13649 14605 11289 11309 10335 8760.3 FALSE TRUE 9390.253503 9862.788623 8437.503347 9472.777695 11328.94786 11213.21009 10404.13868 11157.42135 9963.045369 10476.71306 0.89629767 0.941401045 0.805357873 0.904174586 1.081345627 1.070298483 0.993072791 1.06497346 0.95097053 1 13.35489854 3.324584559 6.317019101 1.031742309 0.882539872 0.663564957 0.048858994 0.119334377 7.089708397 0.013328867 0.018054467 2111.468269 -3.324584559 -0.149202438 TVKEEAEKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 130.1 0.00013005 4822700000 8063890 4412920 5578990 4137430 9465550 7933920 7054260 5583780 6620530 3110390 FALSE TRUE 8382258.604 5170804.682 5724383.063 4955801.305 7856599.192 6091387.32 6501328.668 5508938.562 6382258.419 3719811.368 2.253409588 1.390071746 1.538890684 1.332272208 2.112096129 1.637552746 1.747757621 1.480972559 1.715747866 1 21.82679803 -2.438059683 0.363655867 4.98E-15 1.695211761 0.354318448 0.280103424 66.7801949 2.900635023 53.3361671 0.195381836 0.003647038 2.438059683 1.695211761 TVKPVENKDDDDSIADFLNS(ph)DEEEDRVSLQNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVKPVENKDDDDSIADFLNSDEEEDRVSLQNLK 33 3 Q15649-2;Q15649 Q15649-2 ZNHIT3 Zinc finger HIT domain-containing protein 3 1 TVKPVENKDDDDSIADFLNS(1)DEEEDRVSLQNLK 249.39 9.93E-48 376140000 855840 259950 422070 219050 661560 622820 688300 405880 508880 180880 TRUE FALSE 889629.2241 304594.3904 433069.4909 262377.4362 549108.2675 478179.4939 634349.2475 400439.8425 490565.5082 216319.9728 4.112561648 1.408073357 2.001985694 1.212913596 2.53840762 2.210519388 2.932458058 1.851145954 2.267777227 1 17.72280735 0.031062566 1.22501557 0.996187995 2.231794918 0.193956706 0.7772298 18.62540433 21.55468986 0.932324739 0.210241017 1.074144147 -0.031062566 1.235606924 TVLELQYVLDKLGDDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVLELQYVLDKLGDDEVR 18 1 Q14444-2;Q14444;G3V153;E9PLA9 Q14444-2 CAPRIN1 Caprin-1 0 ; 213.69 5.00E-17 2609400000 1274070 988530 1229280 995360 1659980 1641010 1411990 1307950 1402350 1079300 FALSE TRUE 1324371.267 1158302.338 1261316.047 1192239.237 1377817.193 1259910.297 1301314.534 1290419.07 1351879.697 1290768.171 1.02603341 0.89737442 0.977182484 0.923666437 1.067439703 0.976093404 1.00817061 0.99972954 1.047345084 1 20.29979848 3.253988543 24.99111287 1.012909473 0.953380514 0.354639218 0.039676442 254.4165351 412117.3426 0.010136781 0.013676961 1794.686283 -3.253988543 -0.059528959 TVLPTVPES(ph)PEEEVK ddPTM_MDA-MB-175_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 315.47 2.76E-56 315860000 876750 514220 641390 513724 816860 994060 911140 656240 734100 403085 TRUE FALSE 911364.767 602533.2849 658105.1503 615337.0739 678010.429 763204.6301 839722.466 647444.1762 707679.8844 482061.7882 1.890555919 1.249908828 1.365188377 1.276469301 1.406480342 1.583209142 1.741939491 1.343073009 1.468027339 1 18.87885855 0.269631169 1.482387017 0.999898738 1.471305539 0.352568722 0.195028031 8.065571066 15.07945731 0.184461837 0.052933524 1.860506404 -0.269631169 0.4714068 TVLS(ph)LFDEEEDKMEDQNIIQAPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVLSLFDEEEDKMEDQNIIQAPQK 24 1 Q641Q2;Q641Q2-2;F8W7U3;E7ESD2;A0A087WYF6;B1AP61;A0A0A0MR88;A0A096LPC5;Q9Y4E1-6;Q9Y4E1;J3KP36;Q9Y4E1-3;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1-5 Q641Q2;A0A0A0MR88 FAM21A;FAM21C WASH complex subunit FAM21A;WASH complex subunit FAM21C 1 T(0.149)VLS(0.851)LFDEEEDKMEDQNIIQAPQK;T(0.016)VLS(0.984)LFDEEEDKMEDQNIIQAPQK;T(0.011)VLS(0.989)LFDEEEDKMEDQNIIQAPQK 217.84 7.37E-33 122882000 202816 71821 111767 82978 214886 200385 162160 135966 144817 77796 TRUE FALSE 210823.3323 84155.69806 114679.7398 99390.80074 178359.7545 153848.6206 149449.4755 134143.5982 139605.0645 93038.63671 2.265976155 0.904524196 1.232603399 1.068274475 1.917050387 1.653599258 1.606316266 1.441805286 1.500506342 1 16.50554234 -1.177347222 3.190922496 0.998844822 1.487833521 0.139667843 0.376158304 39275522.62 57503402.6 459790.6563 0.090994229 0.066474148 1.177347222 0.488988699 TVLS(ph)SAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 1 T(0.016)VLS(0.57)S(0.414)AR 79.713 0.03344 794230000 694480 723010 661140 604460 564920 808740 626100 671320 706350 826060 TRUE FALSE 721898.6067 847181.3433 678369.8515 724020.3839 468895.1002 620922.3916 577024.646 662322.0535 680928.6015 987910.6411 0.730732696 0.857548556 0.686671267 0.732880438 0.47463311 0.628520805 0.58408587 0.670427087 0.689261329 1 19.91402103 0.639692808 3.159705179 0.999996401 0.667804598 0.516556711 0.09509378 4.968330255 42.58145153 0.097471134 0.025351156 4.362071782 -0.639692808 -0.332191803 TVLSNVQEELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVLSNVQEELDR 12 0 O43237;O43237-2;J3KRI4 O43237 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 0 126.12 0.00068204 32042000 25814 25985 24373 24848 30770 32745 28902 27574 26596 29910 FALSE TRUE 26833.15665 30447.72161 25008.1804 29762.86024 25539.72639 25140.47001 26636.58572 27204.41563 25638.81516 35770.29184 0.750152019 0.851201375 0.699132691 0.832055281 0.713992676 0.702831001 0.744656651 0.760530995 0.716762817 1 15.12647427 -0.755640607 5.349968498 1.000000054 0.753652 0.694309085 0.049287163 3.49E-06 33405286.63 5.210609927 0.010965233 0.17553325 0.755640607 -0.246348054 TVLSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVLSSAR 7 0 Q6GYQ0-2;A0A1B0GUI1;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6 Q6GYQ0-2 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 0 ;;; 128.75 0.0086702 3169570000 734712 725253 701306 641116 1112250 965000 805519 742675 741190 1070660 FALSE TRUE 763718.9971 849809.5611 719582.6105 767926.8313 923190.1423 740893.3747 742380.3159 732720.6564 714514.7167 1280435.328 0.596452613 0.663687999 0.561982784 0.599738866 0.720997088 0.578626158 0.579787436 0.572243393 0.558024838 1 20.28820296 -2.137887489 2.516406342 1.881921261 0.603331834 0.85786715 0.048416817 5062462.935 1459587.552 25477990.94 0.011846243 0.007279684 2.137887489 -1.278589427 TVNSTRET(ph)PPKSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;TVNSTRET(1)PPKSK 120.24 0.013594 644260000 496820 243166 378450 197574 531350 391860 387370 329080 383470 234441 TRUE FALSE 516434.8372 284927.8689 388312.7179 236653.5475 441031.3168 300856.4537 357006.9272 324669.2209 369668.9896 280375.2253 1.841941765 1.016237682 1.384975143 0.844060124 1.573003878 1.073049352 1.273318378 1.157981132 1.31847951 1 18.09699935 4.748411496 24.86617942 1.194215721 1.841942142 0.487951222 0.202377739 1004.605519 2535829.517 0.042605317 0.575306615 56028.82255 -4.748411496 0.647726421 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVR 32 1 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 TVPLFPHPPVPSLSTSESKPPPQPS(0.997)PPT(0.645)S(0.358)PVR 106.93 7.90E-05 747670000 306790 286130 296930 320540 355460 385320 413090 298190 323220 232170 TRUE FALSE 318902.3061 335270.6017 304668.2397 383941.8553 295039.0362 295835.2696 380710.9264 294193.2508 311587.3753 277659.2663 1.148538316 1.207489331 1.097273805 1.38278063 1.062593877 1.06546154 1.371144322 1.05954775 1.122193325 1 18.08295602 1.140595854 1.589877515 1.010789127 1.183292469 0.198024128 0.11163335 0.557264317 2.718812336 0.099359457 0.029458899 13.82279459 -1.140595854 0.172503342 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPT(ph)SPVRTPLEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVPLFPHPPVPSLSTSESKPPPQPSPPTSPVRTPLEVR 38 2 E9PKC0;Q6IQ23;Q6IQ23-2;H0YDE2;Q6IQ23-3;A0A1B0GUN0;A0A1B0GUM1 E9PKC0 PLEKHA7 Pleckstrin homology domain-containing family A member 7 2 TVPLFPHPPVPS(0.001)LS(0.001)T(0.001)S(0.001)ES(0.002)KPPPQPS(0.994)PPT(0.536)S(0.461)PVRT(0.003)PLEVR 167.82 1.03E-17 506510000 142620 115140 166030 135690 225800 198610 175450 163060 185170 158440 TRUE FALSE 148250.7477 134914.3993 170356.8782 162529.077 187418.5967 152485.8375 161697.7705 160874.4474 178505.7679 189483.2845 0.782394859 0.712012142 0.899060192 0.85774889 0.989103589 0.804745589 0.853361662 0.849016566 0.942066042 1 17.53171106 8 0.073825302 1.108567903 0.258092685 0.432158968 0.065204204 244.4925669 1.325348271 2.517411879 21.42588811 100000000 -8 -0.850475218 TVPLFPHPPVPSLSTSESKPPPQPS(ph)PPTSPVR ddPTM_MDA-MB-175_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(0.992)PPT(0.004)S(0.005)PVR;TVPLFPHPPVPSLSTSESKPPPQPS(0.976)PPT(0.01)S(0.013)PVR 146.48 2.63E-10 2186000000 1211560 986860 1138060 986330 1419070 1349080 1134170 1056260 1178470 739520 TRUE FALSE 1259393.324 1156345.528 1167718.779 1181423.13 1177856.988 1035776.616 1045270.792 1042102.562 1136057.095 884414.785 1.423984928 1.307469694 1.320329328 1.335824717 1.331792512 1.171143487 1.181878469 1.17829618 1.284529741 1 19.75436362 2.751205458 6.38777814 1.175625527 1.340625755 0.611712556 0.071630903 0.112013123 21.87534763 0.020960688 0.021387745 563.9043667 -2.751205458 0.165000228 TVPS(ph)TPTLVVPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.011)VPS(0.734)T(0.255)PTLVVPHR 154.65 2.98E-05 118650000 42769 66233 62163 79469 90230 94497 70587 91644 70847 105510 TRUE FALSE 44457.55314 77608.00253 63783.01885 95187.73101 74892.73683 72551.50387 65054.2065 90415.66208 68297.23031 126182.6644 0.352326949 0.615044887 0.50548163 0.754364567 0.593526355 0.574972039 0.515555816 0.716545831 0.541256841 1 16.94515419 -5 0.208660558 2.962527577 0.52489781 0.606434717 0.104280345 96.870242 0.964998729 79.56735918 0.215992719 1.00E-05 5 -2.437629767 TVPST(ph)PTLVVPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 T(0.006)VPS(0.196)T(0.798)PTLVVPHR;T(0.001)VPS(0.012)T(0.987)PTLVVPHR;T(0.005)VPS(0.123)T(0.872)PTLVVPHR;TVPS(0.018)T(0.982)PTLVVPHR;TVPS(0.027)T(0.972)PTLVVPHR 189.1 2.04E-05 2789310000 1090801 931365 1137924 1319992 2274770 1855800 1379860 1684440 1543990 1825640 TRUE FALSE 1133866.666 1091319.694 1167579.234 1581082.478 1888105.408 1424818.575 1271702.968 1661862.837 1488422.102 2183339.204 0.519326847 0.499839737 0.534767677 0.724157966 0.864778778 0.652586906 0.582457808 0.761156505 0.681718213 1 21.05810485 -5 0.052086659 2.340086037 1.25E-16 0.611548696 0.095476873 383.2233318 1.473055052 70.54590634 14.85673779 1.00E-05 5 -2.340086037 TVQGS(ph)GHQEHINIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 1 T(0.008)VQGS(0.992)GHQEHINIHK;TVQGS(1)GHQEHINIHK;T(0.026)VQGS(0.974)GHQEHINIHK 175.59 1.42E-06 1089630000 370808 317826 428758 399800 620255 665021 502885 517028 572758 470377 TRUE FALSE 385447.7862 372410.1432 439931.7857 478879.2467 514824.2766 510579.9512 463467.5597 510098.0853 552144.5515 562538.3672 0.685193773 0.662017322 0.78204761 0.851282818 0.915180735 0.907635783 0.823886132 0.906779191 0.981523366 1 19.10159197 6.093379243 0.28525221 0.970850461 4.76E-13 0.833399356 0.044407453 7.484941566 0.272665346 0.054260056 2.925839508 1239878.826 -6.093379243 -0.970850461 TVQGSGHQEHINIHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVQGSGHQEHINIHK 15 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;; 148.7 1.21E-06 4071500000 2974950 4004580 4668300 3922640 5406200 5808380 4925130 5157110 4707500 3689360 FALSE TRUE 3092403.323 4692335.464 4789959.733 4698526.484 4487256.055 4459471.772 4539085.441 5087987.376 4538077.995 4412219.455 0.70087251 1.063486418 1.085612305 1.064889571 1.017006543 1.010709421 1.028753326 1.153158275 1.028524995 1 22.07307312 4.739128468 24.95143318 1.057666655 0.700872398 0.85293836 0.043421811 16.77390324 736864.5848 0.011075768 0.0661874 54843.91737 -4.739128468 -0.356794257 TVQS(ph)LEIDLDSMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 19 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 T(0.001)VQS(0.999)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.028)VQS(0.972)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;TVQS(1)LEIDLDSMR;T(0.002)VQS(0.998)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;T(0.003)VQS(0.997)LEIDLDSMR;TVQS(1)LEIDLDSMR 400.82 1.74E-109 7630376900 4291186.6 4854740.3 4925186.4 4627642 5614145 6204420 5362570 5087699.2 5008498 4877119.5 TRUE FALSE 4460605.96 5688504.182 5053540.804 5542975.775 4659854.638 4763537.484 4942237.751 5019506.914 4828243.135 5832697.688 0.764758642 0.975278419 0.866415692 0.950327974 0.79891928 0.816695419 0.847333089 0.860580675 0.827789026 1 22.47573187 4.810215783 21.43375509 0.873083171 0.764749442 0.209378103 0.066418195 45247.80811 13530331.69 0.015143953 75.48742532 64597.51075 -4.810215783 -0.108333729 TVQS(ph)PNSSVPSPGLAGPVTMTSVHPPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVQSPNSSVPSPGLAGPVTMTSVHPPIR 28 0 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 T(0.036)VQS(0.869)PNS(0.041)S(0.054)VPSPGLAGPVTMTSVHPPIR 121.2 3.19E-05 354310000 33056 69013 73714 65394 77623 96355 68618 63065 70988 79147 TRUE FALSE 34361.0764 80865.4459 75635.0474 78328.73802 64428.67019 73978.01152 63239.54186 62219.71683 68433.15575 94654.33929 0.363016389 0.854323706 0.799065822 0.827524006 0.680673181 0.781559642 0.66811033 0.657336127 0.722979594 1 16.53038103 -1.523750175 2.501833137 1.018478682 0.712567172 0.307947939 0.131867448 5949186.764 5460139.39 744494.9011 0.032617985 0.029939864 1.523750175 -0.305911511 TVQSLEIDLDSMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;;;;;;; 318.79 1.58E-50 8387297000 5312167 6179349 6086634 6006800 7310042 7856070 6518250 6421387 6232309 6436931 FALSE TRUE 5521895.455 7240604.122 6245256.682 7194927.111 6067483.672 6031616.802 6007332.533 6335318.811 6008009.417 7698124.387 0.717304005 0.940567307 0.81126991 0.934633782 0.788176881 0.783517711 0.780363142 0.822969141 0.78045107 1 22.87607555 TVQTDHNAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVQTDHNAVQR 11 0 O43747;O43747-2 O43747 AP1G1 AP-1 complex subunit gamma-1 0 ;;; 187.58 3.53E-06 1237010000 880460 987760 973580 1044380 1110500 1299310 1048050 1038200 963100 898150 FALSE TRUE 915221.2407 1157400.096 998952.2946 1250955.247 921737.6067 997564.9437 965901.1024 1024284.627 928438.2191 1074125.296 0.8520619 1.077528013 0.930014681 1.16462693 0.858128572 0.928723071 0.899244349 0.953598831 0.864366776 1 20.03473086 TVS(ph)AS(ph)STGDLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 2 T(0.063)VS(0.93)AS(0.77)S(0.196)T(0.041)GDLPK;T(0.005)VS(0.995)AS(0.539)S(0.389)T(0.073)GDLPK 120.59 0.00057491 467190000 1237590 765660 1080930 821660 1476100 1553560 1388780 1136250 1285750 739450 TRUE FALSE 1286451.009 897156.149 1109099.924 984181.8956 1225193.049 1192769.234 1279923.795 1121020.427 1239476.109 884331.0699 1.454716511 1.014502577 1.25416822 1.112911136 1.38544612 1.348781328 1.447335549 1.267647904 1.401597378 1 19.75422705 3.230671077 24.99988703 1.32915133 1.198397576 0.077912187 0.156470046 329.1976728 1043140.154 0.041201178 0.050095503 1700.869827 -3.230671077 -0.130753754 TVS(ph)ASS(ph)TGDLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSASSTGDLPK 12 0 P78362;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 2 T(0.007)VS(0.992)AS(0.002)S(0.857)T(0.142)GDLPK;TVS(0.999)AS(0.001)S(0.876)T(0.123)GDLPK 183.81 2.21E-05 468410000 1267590 707660 977900 738010 1483660 1533480 1327290 1145800 1238910 727770 TRUE FALSE 1317635.432 829195.1002 1003384.877 883986.1753 1231468.003 1177352.51 1223253.542 1130442.425 1194321.871 870362.5975 1.513892527 0.952700751 1.152835474 1.015652761 1.414890767 1.352714964 1.405452791 1.29881779 1.372211851 1 19.73125703 3.230517946 24.9996985 1.32910014 1.14362719 0.135207545 0.17743777 269.9159724 839001.2844 0.047380316 0.057576726 1700.270213 -3.230517946 -0.18547295 TVS(ph)DLALQNAFGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSDLALQNAFGDR 14 0 A0A1X7SBR1;Q7Z3G6 A0A1X7SBR1 PRICKLE2 Prickle-like protein 2 1 T(0.002)VS(0.998)DLALQNAFGDR;T(0.006)VS(0.994)DLALQNAFGDR;T(0.001)VS(0.999)DLALQNAFGDR;TVS(1)DLALQNAFGDR 282.19 2.40E-33 394765000 326264 356795 335277 318662 411381 425971 346911 361850 318799 318018 TRUE FALSE 339145.1547 418071.7658 344014.5941 381692.3925 341454.6046 327045.6909 319719.2093 356999.9926 307325.4863 380327.5383 0.891718639 1.099241374 0.904521917 1.003588628 0.897790904 0.859905366 0.840641755 0.93866459 0.808054783 1 18.53688288 3.167110474 6.190342755 0.885673978 0.978476484 0.240667207 0.072719451 0.259152936 17.1366747 0.019522265 0.023572564 1469.299984 -3.167110474 0.092802507 TVS(ph)DNS(ph)LSNSRGEGKPDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSDNSLSNSRGEGKPDLK 19 2 Q96RU3-5;Q96RU3-2;Q96RU3;H0Y7W6;Q96RU3-3;B7ZL14;Q96RU3-4 Q96RU3-5 FNBP1 Formin-binding protein 1 2 T(0.139)VS(0.861)DNS(0.996)LS(0.003)NSRGEGKPDLK 66.853 0.014261 313050000 162340 88407 135740 64513 209710 151990 104580 112200 122300 77751 TRUE FALSE 168749.3086 103590.2145 139277.4959 77273.47885 174063.5691 116692.6259 96382.74633 110696.1425 117898.4469 92984.81982 1.814804921 1.114055119 1.497851974 0.83103327 1.871956836 1.254964264 1.036542809 1.190475421 1.267932197 1 16.50470759 8 0.143882394 0.989891274 2.853674935 0.192424794 0.292417249 131.7435527 1.254249263 1.091519988 50.84213721 100000000 -8 1.863783661 TVS(ph)DNSLSNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;T(0.001)VS(0.999)DNSLSNSR;T(0.049)VS(0.951)DNSLSNSR;T(0.003)VS(0.994)DNS(0.003)LSNSR 283 1.75E-27 3601540000 2226260 2485940 2325880 2222330 2598890 3050620 2713110 2568610 2374620 2173064 TRUE FALSE 2314154.464 2912880.857 2386494.344 2661900.241 2157131.606 2342159.738 2500449.349 2534181.984 2289157.89 2598834.285 0.890458648 1.120841323 0.918294159 1.024267017 0.830038152 0.901234739 0.962142667 0.975122577 0.880840269 1 21.30943321 TVS(ph)EPNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSEPNLK 8 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;H0YI41;F8VWY3;C9JEB6;C9JF80;C9JAH2 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 T(0.004)VS(0.996)EPNLK 73.327 0.038781 0 226950 211510 247420 238170 283060 309050 327330 250220 269710 187960 TRUE FALSE 235910.1612 247835.1972 253867.9685 285279.3151 234945.5623 237277.8212 301673.0193 246866.2102 260003.1898 224787.1633 1.049482354 1.102532696 1.1293704 1.269108569 1.045191188 1.055566598 1.342038464 1.09822201 1.156663868 1 17.77820013 4.492180533 2.434466161 1.147214347 1.049217744 0.064298305 0.09799761 0.883000666 8.917560068 0.0239514 0.143782588 31058.50397 -4.492180533 -0.097996603 TVS(ph)FEALPIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSFEALPIMR 11 0 O15084-2;O15084;O15084-4;O15084-1 O15084-2 ANKRD28 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit A 1 TVS(1)FEALPIMR;TVS(1)FEALPIMR 140.14 4.06E-05 87964000 100559 87778 111187 63028 174376 134690 83539 101458 123975 126540 TRUE FALSE 104529.147 102853.1887 114084.6246 75494.75028 144735.6298 103410.2887 76990.99489 100098.1215 119513.164 151333.0902 0.690722345 0.679647713 0.753864369 0.49886479 0.956404376 0.683328997 0.508751885 0.661442394 0.789735832 1 17.20736795 0.930034939 3.461646318 0.999547167 0.676662273 0.399717738 0.120285729 0.302205564 8.952799794 0.112704816 0.029159169 8.512065149 -0.930034939 -0.322884894 TVS(ph)LCDITITQMLEEDSNQGHLIGDFSK ddPTM_MDA-MB-175_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(0.042)VS(0.958)LCDITITQMLEEDSNQGHLIGDFSK;T(0.031)VS(0.969)LCDITITQMLEEDSNQGHLIGDFSK 227.77 6.83E-35 139830000 66174 71682 84978 67292 113803 108940 97223 91718 88082 77620 TRUE FALSE 68786.60062 83992.82589 87192.59649 80602.15675 94458.80671 83640.336 89602.40721 90488.67023 84911.94603 92828.15288 0.741010119 0.90482061 0.939290439 0.868294308 1.017566372 0.901023379 0.965250352 0.974797703 0.914721918 1 16.50227479 5.531813236 1.043954174 0.952144631 1.61E-13 0.680629144 0.042516057 4.359975934 1.145489624 0.011692358 6.875493782 340261.8318 -5.531813236 -0.952144631 TVS(ph)PGSVS(ph)PIHGQGQVVENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 2 T(0.003)VS(0.997)PGS(0.015)VS(0.985)PIHGQGQVVENLK;T(0.001)VS(0.999)PGS(0.046)VS(0.954)PIHGQGQVVENLK;T(0.14)VS(0.86)PGS(0.023)VS(0.977)PIHGQGQVVENLK 273.56 5.40E-45 1121120000 1587280 1299400 1586370 1294910 1898200 2020210 1892970 1675790 1748360 1266110 TRUE FALSE 1649947.04 1522561.842 1627712.105 1551039.333 1575544.642 1551046.844 1744594.065 1653328.776 1685436.865 1514180.013 1.089663729 1.005535556 1.074979257 1.024342759 1.04052664 1.02434772 1.152170845 1.091897107 1.113102042 1 20.5301053 2.264964172 24.99991135 1.098381345 1.041980501 0.207522378 0.042598023 255.9877046 242378.2025 0.013479755 0.011274705 184.0620149 -2.264964172 -0.056400844 TVS(ph)PPIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.001)VS(0.999)PPIR;TVS(1)PPIR;TVS(1)PPIR;TVS(1)PPIR;T(0.001)VS(0.999)PPIR 128.93 0.0038912 7479910000 852353 773858 795792 716610 1003973 1133222 934335 836062 861638 815191 TRUE FALSE 886004.5546 906762.0917 816530.9933 858353.3191 833318.0281 870048.3646 861099.3813 824855.9564 830627.8167 974912.0687 0.908804582 0.930096283 0.83754322 0.880441782 0.854762245 0.892437782 0.88325851 0.846082414 0.852002805 1 19.89491258 -0.866506129 5.889715987 1.000000026 0.874768444 0.63973723 0.027862573 9.88E-09 1.92E-09 0.027633507 0.006513279 0.135985897 0.866506129 -0.125231583 TVS(ph)PPIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 TVSPPIRK 8 1 Q9UHB6;Q9UHB6-4;Q9UHB6-2;Q9UHB6-5;F8VQE1;Q9UHB6-3;F8VS07 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 T(0.073)VS(0.927)PPIRK;T(0.046)VS(0.954)PPIRK;T(0.032)VS(0.968)PPIRK;T(0.008)VS(0.992)PPIRK;T(0.05)VS(0.95)PPIRK;TVS(1)PPIRK;T(0.172)VS(0.828)PPIRK 103.26 0.0029449 11778140000 7279810 5711260 6683110 5302500 8358100 8366040 7553240 6766240 6894000 5460140 TRUE FALSE 7567222.52 6692124.478 6857277.337 6351318.674 6937393.147 6423153.999 6961197.312 6675549.62 6645886.287 6529949.892 1.158848482 1.024835502 1.050127099 0.97264432 1.062396077 0.98364522 1.066041459 1.02229722 1.017754561 1 22.63864049 4.738819358 8.132247365 1.024141761 1.159862107 0.655551373 0.029687175 0.051162905 44.0852859 0.006366347 0.037839361 54804.89601 -4.738819358 0.135720346 TVS(ph)PSTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVSPSTIR 8 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 T(0.002)VS(0.989)PS(0.009)TIR;T(0.003)VS(0.987)PS(0.01)TIR;T(0.471)VS(0.521)PS(0.007)T(0.001)IR;T(0.001)VS(0.998)PS(0.001)TIR;T(0.007)VS(0.975)PS(0.017)T(0.002)IR;T(0.125)VS(0.862)PS(0.01)T(0.003)IR 129.83 0.0011267 2450520000 3202820 4392850 4282090 4542770 4646350 5457280 4151530 4568730 4011120 4328430 TRUE FALSE 3329269.807 5147287.816 4393684.783 5441316.347 3856565.087 4189909.426 3826122.231 4507493.647 3866760.575 5176502.986 0.643150369 0.994356196 0.848774703 1.051156806 0.745013593 0.809409255 0.739132623 0.870760368 0.746983163 1 22.30354638 TVS(ph)SPIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.056)VS(0.472)S(0.472)PIPY(0.004)T(0.031)PS(0.96)PS(0.009)S(0.194)S(0.172)RPIS(0.627)PGLS(0.001)YAS(0.001)HTVGFTPPTSLTR 167.82 2.36E-17 3452000000 27200 44161 38892 33537 32315 43927 29126 34870 28012 38434 TRUE FALSE 28273.877 51745.30823 39905.55747 40170.5185 26822.10784 33725.61997 26843.02801 34402.62469 27003.85359 45964.40644 0.615125468 1.125769095 0.868183896 0.873948379 0.583540829 0.733733395 0.583995968 0.748462285 0.587494883 1 15.48822949 3.32575664 7.899916426 0.69082175 0.890610446 0.189241157 0.163151271 0.319792734 25.27562865 0.041447378 0.056124976 2117.174428 -3.32575664 0.199788695 TVS(ph)SPIPYTPSPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.783)S(0.217)PIPYTPSPSSSR 372.27 2.34E-104 141880000 115910 114830 129780 150920 154440 190040 207660 164510 144820 114560 TRUE FALSE 120486.2163 134551.1592 133162.1734 180771.5255 128188.344 145906.0901 191383.0666 162305.0125 139607.9565 137005.8386 0.879423954 0.982083396 0.971945245 1.319443955 0.935641468 1.064962571 1.396897158 1.184657633 1.018992752 1 17.06387785 3.926381986 10.39754236 1.146972224 0.942229802 0.278165305 0.137306025 0.724010272 99.90222059 0.035796704 0.064658877 8440.768427 -3.926381986 -0.204742422 TVS(ph)SPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.049)VS(0.877)S(0.073)PIPY(0.001)T(0.005)PS(0.037)PS(0.091)S(0.083)S(0.076)RPIS(0.656)PGLS(0.039)YAS(0.009)HT(0.002)VGFTPPTSLTR 90.349 0.00053624 1935200000 122120 165680 154730 187750 216770 237480 179120 201640 171310 248760 TRUE FALSE 126941.3919 194134.2512 158762.3909 224886.3896 179923.5128 182328.869 165080.1064 198937.3456 165144.5866 297499.7592 0.4266941 0.652552633 0.533655527 0.755921249 0.604785407 0.612870644 0.554891563 0.668697501 0.555108303 1 18.18252898 -1.643929765 2.562847162 1.048368455 0.604427699 0.673229136 0.084233304 7184970.789 6079399.26 2292335.735 0.019803633 0.02270232 1.643929765 -0.443940756 TVS(ph)SPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.499)S(0.499)PIPYT(0.001)PSPSSSRPISPGLSYASHTVGFTPPTSLTR 231.78 8.04E-41 866290000 102790 222390 229210 227580 328080 282840 267200 247890 259840 295750 TRUE FALSE 106848.2286 260583.7525 235183.4009 272594.6447 272313.0788 217154.6965 246256.1658 244567.44 250488.4092 353696.55 0.302090107 0.736743835 0.66492987 0.770702018 0.769905951 0.613957633 0.696235702 0.691461197 0.708201449 1 18.43215262 -5 0.088365662 1.945208093 0.415276653 0.473096709 0.118864223 215.5163634 1.328332555 39.78752032 2.931048968 1.00E-05 5 -1.52993144 TVS(ph)SPPTSPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 T(0.096)VS(0.388)S(0.388)PPT(0.096)S(0.029)PRPGSAATVSASTSNIIPPR 53.482 0.046833 299160000 20024 22488 21353 19512 23971 30501 21228 22791 16527 18296 TRUE FALSE 20814.56298 26350.13907 21909.47672 23371.41536 19896.41798 23417.605 19564.09389 22485.52392 15932.1965 21880.7509 0.951272791 1.204261188 1.001312835 1.068126751 0.90931148 1.070237722 0.894123514 1.0276395 0.728137557 1 14.41737463 2.782376614 0.681104458 0.913695502 1.073521108 0.21797994 0.106728692 1.09768433 1.103674242 0.073216512 0.078665986 605.8660457 -2.782376614 0.159825605 TVS(ph)SSGCEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSSGCEGKR 11 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 T(0.012)VS(0.894)S(0.047)S(0.047)GCEGKR 62.162 0.050669 118040000 87821 72052 91828 69327 151090 124470 93815 108300 111840 95038 TRUE FALSE 91288.24089 84426.37051 94221.11312 83039.67368 125407.7758 95563.72886 86461.53516 106848.4156 107814.9002 113658.8765 0.8031774 0.742804901 0.828981563 0.730604386 1.103369835 0.840794242 0.760710803 0.940079816 0.948583195 1 16.79435083 7.999999997 0.105767676 1.066041923 0.152406361 0.295324768 0.098255928 150.0806057 1.113989819 1.015024639 19.96614115 99999999.39 -7.999999997 -0.913635563 TVSASS(ph)TGDLPK ddPTM_MDA-MB-175_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 1 TVSASS(0.997)T(0.003)GDLPK;TVSASS(0.997)T(0.003)GDLPK;TVS(0.001)AS(0.024)S(0.965)T(0.01)GDLPK;TVSAS(0.034)S(0.96)T(0.005)GDLPK 326.99 4.94E-58 978100000 3588420 2216580 2866530 2116670 3593580 3712170 3432310 2856270 3093800 1970590 TRUE FALSE 3730093.592 2597260.372 2941234.127 2535341.008 2982744.555 2850074.776 3163276.574 2817986.373 2982454.742 2356689.381 1.582768447 1.102080059 1.248036398 1.075806183 1.265650271 1.209355292 1.34225435 1.195739411 1.265527297 1 21.16833019 -2.084649547 2.142478933 0.630297982 1.243480883 0.243487479 0.133200351 4550700.399 1324960.901 8204360.803 0.031179763 0.008229064 2.084649547 0.613182902 TVSDNS(ph)LSNSR ddPTM_MDA-MB-175_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 1 T(0.001)VS(0.339)DNS(0.66)LSNSR 187.6 3.69E-06 381560000 288130 290560 300420 277910 334540 386480 319860 322800 286270 235070 TRUE FALSE 299505.5949 340461.4198 308249.192 332879.7685 277675.0103 296725.8772 294788.5374 318473.394 275967.1986 281127.4658 1.06537294 1.211057122 1.096474836 1.184088391 0.987719252 1.055485192 1.04859387 1.132843399 0.981644386 1 18.10086488 3.097733708 0.235394733 0.994669069 1.193250095 0.286513287 0.063956499 6.567545744 0.663276724 0.127391697 0.397071254 1252.373036 -3.097733708 0.198581026 TVSGPGTPEPRPAT(ph)PGASSVEQLRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSGPGTPEPRPATPGASSVEQLRK 25 2 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 TVSGPGT(0.001)PEPRPAT(0.998)PGAS(0.001)S(0.001)VEQLRK;TVSGPGTPEPRPAT(1)PGASSVEQLRK 192.42 2.48E-16 1569880000 1136030 1041150 1126560 779620 1699420 1637030 1012100 1170830 1266810 1173970 TRUE FALSE 1180881.342 1219959.413 1155919.079 933826.5091 1410553.195 1256854.592 932768.9574 1155136.939 1221217.756 1403986.944 0.841091398 0.868925041 0.823311843 0.665124781 1.00467686 0.895203903 0.664371532 0.822754758 0.869821305 1 20.42109809 0.882603452 3.325905364 0.99982874 0.820709152 0.238137358 0.095292432 0.722710889 16.22558568 0.091185074 0.023655938 7.631386537 -0.882603452 -0.179119588 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIK;TVSLGAGAKDELHIVEAEAMNY(0.001)EGS(0.999)PIK 179.2 2.03E-17 421234000 718425 321421 516523 358190 693879 644070 701745 517209 601602 265909 TRUE FALSE 746788.9737 376622.5564 529984.0137 429038.9129 575933.6954 494494.5035 646740.3932 510276.6593 579950.4615 318008.7774 2.348328181 1.184314972 1.666570395 1.349141732 1.811062261 1.554971242 2.033718687 1.604599293 1.823693252 1 18.27870706 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 1 TVSLGAGAKDELHIVEAEAMNY(0.003)EGS(0.997)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.002)EGS(0.998)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.152)EGS(0.84)PIKVT(0.008)LATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.016)EGS(0.983)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK;TVSLGAGAKDELHIVEAEAMNY(0.01)EGS(0.957)PIKVT(0.033)LATLK;TVSLGAGAKDELHIVEAEAMNY(0.161)EGS(0.834)PIKVT(0.005)LAT(0.001)LK;TVSLGAGAKDELHIVEAEAMNYEGS(1)PIKVTLATLK 382.89 5.77E-167 10325321000 11108138 4976608 8488718 4213900.5 12972651 9856700 9720363 7909752 9926870 4222979.4 TRUE FALSE 11546695.87 5831301.711 8709940.965 5047397.442 10767564.42 7567630.805 8958455.549 7803734.712 9569603.888 5050391.36 2.286297248 1.15462373 1.724607133 0.999407191 2.132025748 1.49842463 1.773814129 1.545174256 1.894824224 1 22.26796376 -0.774589327 6.152232018 0.999999982 1.640565004 0.216923629 0.377424893 8.74E-08 1.74E-08 0.325894874 0.076814156 0.168039226 0.774589327 0.640565022 TVSLGAGAKDELHIVEAEAMNYEGSPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ;;; 182.54 7.69E-18 1298330000 998920 745860 1010760 673286 1375390 1207850 1088890 1050100 1162440 697745 FALSE TRUE 1038358.133 873955.653 1037101.236 806459.9612 1141601.699 927345.1426 1003539.957 1036025.127 1120604.011 834454.7736 1.244355195 1.047337352 1.242848946 0.966451372 1.368080974 1.111318638 1.202629535 1.241559351 1.342917611 1 19.67047433 3.233723428 24.99999841 1.21903086 1.128083219 0.098964923 0.125400158 263.6363155 1362550.584 0.033124875 0.040809478 1712.866153 -3.233723428 -0.090947642 TVSLPLSS(ph)PNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSLPLSSPNIK 12 0 Q8IWZ3-6;Q8IWZ3;Q8IWZ3-4;H0Y785;H0Y472;H0Y4P6;H0Y7Y3;A0A0A0MQZ8 Q8IWZ3-6;A0A0A0MQZ8 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 TVSLPLS(0.355)S(0.645)PNIK 152.55 7.33E-05 209110000 909360 618470 804480 618860 932620 978850 919130 763190 809390 511330 TRUE FALSE 945262.235 724687.4115 825445.4097 741268.6609 774093.5855 751526.9221 847086.1889 752960.6864 780260.212 611515.3235 1.545770316 1.185068278 1.349836019 1.212183297 1.265861305 1.228958447 1.385224795 1.231303056 1.275945478 1 19.22202913 -4.299332789 0.214146961 4.23E-14 1.332865052 0.469422923 0.098362197 93.04699748 1.220523137 40.3568566 0.187793849 5.02E-05 4.299332789 1.332865052 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 3 T(0.011)VS(0.047)LT(0.942)PS(0.657)PT(0.171)T(0.171)QVET(0.014)PDLVDHDNT(0.524)S(0.463)PLFR 89.186 0.0034311 68437000 27815 39845 39077 48135 39521 45550 39478 43179 43323 41347 TRUE FALSE 28913.15768 46688.0688 40095.37872 57655.95933 32803.23454 34971.70282 36383.6112 42600.25613 41763.81369 49448.15301 0.584716636 0.944182259 0.810856954 1.165988127 0.663386447 0.70723982 0.735793128 0.861513596 0.844598052 1 15.59362901 0.686004232 1.647869003 0.999574918 0.814977838 0.12145797 0.1535105 2.706593094 10.82658404 0.143455574 0.040940516 4.852932296 -0.686004232 -0.18459708 TVSLT(ph)PS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_MDA-MB-175_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(0.02)LT(0.977)PS(0.796)PT(0.111)T(0.093)QVETPDLVDHDNTSPLFR 148.94 1.22E-07 101820000 28497 34310 38750 37799 37506 45101 38634 43452 38463 32877 TRUE FALSE 29622.08356 40202.47561 39759.85683 45275.52938 31130.74352 34626.97626 35605.76613 42869.59701 37078.72414 39318.61868 0.753385662 1.022479348 1.011222117 1.15150356 0.791755778 0.880676316 0.905570117 1.090312896 0.943032217 1 15.26292502 1.756685877 25 1.018827373 0.938746632 0.090753788 0.113655963 18.9649646 26184.99589 0.053636265 0.029744263 57.10654387 -1.756685877 -0.080080742 TVSLTPS(ph)PTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 2 TVSLT(0.002)PS(0.974)PT(0.011)T(0.012)QVETPDLVDHDNT(0.529)S(0.471)PLFR;T(0.006)VS(0.007)LT(0.14)PS(0.845)PT(0.002)T(0.002)QVETPDLVDHDNT(0.512)S(0.488)PLFR 98.627 0.0029851 889004000 89922 105496 102593 113459 113349 134580 124992 122940 110842 103652 TRUE FALSE 93472.18999 123614.1174 105266.6579 135900.8516 94081.97747 103325.8346 115194.8004 121292.1904 106852.8181 123960.6249 0.754047425 0.997204697 0.849194315 1.096322737 0.758966628 0.833537542 0.929285413 0.978473532 0.861989992 1 16.91952241 -5 0.164472475 1.369540491 0.87880169 0.086268221 0.102193226 362.856668 3.378184546 43.62133672 0.387798502 1.00E-05 5 -0.490738801 TVSLTPS(ph)PTTQVETPDLVDHDNTSPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLT(0.002)PS(0.748)PT(0.125)T(0.125)QVETPDLVDHDNTSPLFR 201.53 2.64E-25 168560000 20772 19261 18959 19777 18746 27931 21944 19963 25852 19676 TRUE FALSE 21592.0946 22568.92692 19453.08711 23688.83157 15559.56162 21444.44855 20223.97194 19695.42864 24921.59157 23531.13548 0.917596799 0.959109132 0.82669564 1.006701593 0.661232928 0.911322302 0.859455846 0.836994401 1.059090055 1 14.52228332 1.237757696 24.99986636 1.029545085 0.870220709 0.33322301 0.088880848 22.84108495 710962.899 0.066825118 0.020416575 17.28851521 -1.237757696 -0.159324375 TVSLTPSPTTQVETPDLVDHDNT(ph)SPLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPS(0.017)PT(0.017)T(0.017)QVET(0.171)PDLVDHDNT(0.601)S(0.176)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.619)S(0.381)PLFR 288.04 4.13E-62 1479830000 144341 181315 165542 190143 188347 207474 192882 188174 155583 172132 TRUE FALSE 150039.6941 212454.4408 169856.1605 227752.7179 156331.8442 159291.3078 177763.4048 185651.8353 149983.5982 205857.9697 0.728850548 1.032043797 0.825113357 1.106358516 0.75941604 0.77379228 0.863524522 0.901844294 0.72857805 1 17.65128978 TVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 TVSLTPSPTTQVETPDLVDHDNT(0.413)S(0.587)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.25)S(0.75)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.061)S(0.939)PLFR;TVSLTPSPTTQVETPDLVDHDNT(0.079)S(0.921)PLFR 310.75 7.40E-83 5953110000 1010961 1101810 1057994 1153414 1201621 1491713 1215245 1095553 988429 935576 TRUE FALSE 1050874.521 1291037.297 1085566.193 1381555.847 997369.8916 1145285.263 1119990.921 1080868.904 952855.6334 1118884.205 0.939216513 1.153861402 0.970222109 1.234762133 0.891396882 1.023595881 1.000989126 0.966023919 0.851612374 1 20.09362931 2.504403012 0.968725539 0.941492926 1.060769783 0.164927225 0.099599692 0.917134841 1.743556861 0.060338019 0.04382792 319.450088 -2.504403012 0.119276857 TVSPDRLELEAAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSPDRLELEAAQK 14 1 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 ;;; 206.63 9.64E-09 2020350000 1215801 884045 1066676 927774 1444657 1404673 1198379 1212173 1259258 817243 FALSE TRUE 1263801.762 1035872.852 1094474.453 1111284.928 1199094.719 1078458.984 1104446.923 1195925.804 1213937.551 977366.1188 1.293068931 1.059861634 1.119820333 1.137020106 1.2268634 1.103433977 1.130023746 1.223621098 1.242049962 1 19.89853957 1.778196566 25 1.179743445 1.148356756 0 0.087377546 257.1112408 162233.2776 0.037955713 0.021085577 60.00626092 -1.778196566 -0.031386689 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 TVS(0.001)PGS(0.428)VS(0.571)PIHGQGQVVENLK;TVSPGS(0.07)VS(0.93)PIHGQGQVVENLK;TVSPGS(0.097)VS(0.903)PIHGQGQVVENLK;TVSPGS(0.14)VS(0.86)PIHGQGQVVENLK;TVSPGS(0.132)VS(0.868)PIHGQGQVVENLK;TVSPGS(0.392)VS(0.608)PIHGQGQVVENLK 359.9 4.49E-96 7584250000 4419030 3740030 4429530 3649987 5517670 5789490 5257340 4328110 4779530 3315227 TRUE FALSE 4593496.717 4382351.059 4544967.191 4371943.534 4579778.424 4444968.688 4845255.953 4270098.765 4607515.649 3964782.257 1.158574776 1.105319479 1.146334627 1.102694486 1.15511474 1.121112939 1.222073657 1.077007131 1.162110641 1 21.91881021 -1.504617903 3.037381298 0.995736364 1.136312001 0.538919999 0.038482479 888294.0464 904365.6968 22094.33399 0.008252506 0.031288309 1.504617903 0.140575637 TVSS(ph)DGCSTPSREEGGCSLASTPATTLHLLQLSGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQR 36 1 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 T(0.012)VS(0.448)S(0.51)DGCS(0.014)T(0.014)PS(0.002)REEGGCS(0.001)LASTPATTLHLLQLSGQR 173.3 2.36E-18 1241900000 32322 71152 67194 75418 58833 95445 50752 78857 64307 95826 TRUE FALSE 33598.09752 83371.80251 68945.13084 90335.4553 48832.58767 73279.34523 46773.92562 77800.0509 61992.60363 114601.27 0.293173867 0.727494578 0.601608785 0.788258763 0.426108608 0.639428736 0.408144915 0.678875992 0.540941681 1 16.80626351 -1.661994682 2.388407451 1.065769866 0.57790039 0.437527883 0.146787527 4897310.659 3734061.964 1962812.738 0.034684831 0.021777364 1.661994682 -0.487869477 TVSS(ph)PIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 4 T(0.028)VS(0.16)S(0.812)PIPY(0.112)T(0.567)PS(0.321)PS(0.001)S(0.001)S(0.004)RPIS(0.909)PGLS(0.065)Y(0.016)AS(0.007)HT(0.008)VGFT(0.986)PPT(0.002)S(0.001)LT(0.001)R 171.32 2.36E-18 147310000 18717 26359 28040 31749 29690 32164 38194 32260 29144 34933 TRUE FALSE 19455.96161 30885.95321 28770.74544 38028.85744 24643.3044 24694.39845 35200.25448 31827.60747 28095.11313 41777.45252 0.465704835 0.739297189 0.688666821 0.910272292 0.589870921 0.591093927 0.842565843 0.761836961 0.672494646 1 15.3504369 -5 0.151714578 2.040295941 0.61749852 0.387282382 0.119437803 146.7820728 1.315865474 46.13552524 0.580679494 1.00E-05 5 -1.422797421 TVSS(ph)PIPYTPS(ph)PS(ph)SSRPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.279)VS(0.342)S(0.379)PIPY(0.001)T(0.006)PS(0.952)PS(0.321)S(0.292)S(0.264)RPIS(0.146)PGLS(0.003)Y(0.011)AS(0.003)HTVGFTPPTSLTR 125.44 6.62E-08 243670000 58703 78154 93447 83417 97271 98079 73087 92581 92863 86846 TRUE FALSE 61020.63977 91576.34155 95882.30559 99916.63363 80736.91016 75301.63865 67358.24996 91340.10313 89520.87877 103861.8109 0.58751758 0.881713314 0.923171902 0.962015131 0.77734934 0.725017578 0.648537218 0.879438769 0.861922953 1 16.66430576 0.938128716 1.799250674 0.997072555 0.801277864 0.233778414 0.112909514 0.668714921 4.482108546 0.111117833 0.031566357 8.672188643 -0.938128716 -0.195794691 TVSS(ph)PIPYTPS(ph)PSSS(ph)RPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.032)VS(0.171)S(0.797)PIPY(0.054)T(0.054)PS(0.833)PS(0.091)S(0.149)S(0.496)RPIS(0.32)PGLS(0.004)YASHTVGFTPPTSLTR 119.44 3.58E-05 411260000 18464 30573 30533 29089 31307 39214 20130 23149 30709 30076 TRUE FALSE 19192.97298 35823.67493 31328.71506 34842.71738 25985.44732 30107.14279 18552.158 22838.72552 29603.78909 35968.81636 0.533600349 0.995964798 0.870996553 0.968692354 0.722443771 0.837034572 0.515784501 0.634959051 0.823040402 1 15.13445906 2.791790542 2.181657481 0.704082167 0.849833862 0 0.173127106 0.670116779 6.282497903 0.059075484 0.060647917 619.1423945 -2.791790542 0.145751695 TVSS(ph)PIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.078)VS(0.442)S(0.479)PIPY(0.045)T(0.046)PS(0.893)PS(0.18)S(0.166)S(0.154)RPIS(0.496)PGLS(0.004)Y(0.01)AS(0.003)HT(0.001)VGFT(0.001)PPTSLTR 92.121 0.0022266 231940000 17780 28914 23929 20836 30812 36089 24077 29514 29375 26137 TRUE FALSE 18481.96813 33879.75458 24552.6094 24957.29861 25574.58725 27707.87668 22189.78183 29118.41311 28317.79949 31258.04473 0.591270769 1.083873124 0.785481293 0.798428015 0.818176168 0.886423861 0.70989027 0.931549409 0.905936367 1 14.93193992 1.598785633 10.84778588 0.940553676 0.822459485 0.204922641 0.120523128 0.157259367 61.43902009 0.058061036 0.028241969 39.69955448 -1.598785633 -0.118094191 TVSS(ph)PIPYTPSPS(ph)SSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 T(0.015)VS(0.128)S(0.857)PIPYTPS(0.015)PS(0.378)S(0.377)S(0.269)RPIS(0.847)PGLS(0.055)Y(0.022)AS(0.036)HT(0.001)VGFTPPTSLTR 185.3 6.08E-23 3450400000 39141 70611 51551 70526 64427 79239 70265 63765 50338 85104 TRUE FALSE 40686.3169 82737.88997 52894.46141 84475.8323 53475.72155 60836.94313 64757.4457 62910.33447 48526.34521 101778.4994 0.399753555 0.812921103 0.519701722 0.829996834 0.525412753 0.597738653 0.636258602 0.618110258 0.476783854 1 16.6350733 -2.209458043 2.462696909 2.272423418 0.612096296 0.457453993 0.129648399 13176083.84 2231244.935 93783338.52 0.029492052 0.006173649 2.209458043 -1.660327122 TVSS(ph)PIPYTPSPSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSS(1)PIPYTPSPSSSR;TVSS(1)PIPYTPSPSSSR;TVS(0.001)S(0.999)PIPYTPSPSSSR;TVS(0.017)S(0.983)PIPYTPSPSSSR 399.27 3.73E-122 2020820000 828280 843670 891860 992380 913590 1134310 1161670 1003410 891270 685040 TRUE FALSE 860981.134 988563.7597 915102.6043 1188669.802 758298.2981 870883.6931 1070615.27 989960.9302 859193.3668 819260.4721 1.050924783 1.206653797 1.116986154 1.450905838 0.925588777 1.063011976 1.306806939 1.208359202 1.048742611 1 19.64396268 3.208753283 24.99999847 1.122802416 1.200004587 0.115042979 0.140115567 643.1972849 539460.9205 0.041679816 0.049823584 1617.16109 -3.208753283 0.077202171 TVSS(ph)PIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 T(0.001)VS(0.101)S(0.897)PIPYTPSPSSS(0.001)RPIS(0.999)PGLSYASHTVGFTPPTSLTR;T(0.066)VS(0.446)S(0.488)PIPYT(0.044)PS(0.037)PS(0.149)S(0.136)S(0.124)RPIS(0.503)PGLS(0.004)YAS(0.003)HTVGFTPPTSLTR 305.39 3.93E-93 7811400000 395816 627430 578380 641000 615020 777770 584870 624620 588460 575260 TRUE FALSE 411443.1213 735186.2218 593453.0579 767787.8868 510479.1201 597144.7047 539026.3611 616247.9906 567281.4395 687971.183 0.598052842 1.068629384 0.86261325 1.11601751 0.742006544 0.86797924 0.783501365 0.895746807 0.824571513 1 19.39198861 TVSS(ph)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVS(0.031)S(0.969)PIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR;T(0.013)VS(0.055)S(0.246)PIPY(0.208)T(0.065)PS(0.058)PS(0.058)S(0.058)S(0.058)RPIS(0.004)PGLS(0.084)Y(0.093)ASHTVGFTPPTSLTR 266.42 2.80E-63 4213300000 156254 298120 322135 228735 274368 313571 202463 272704 253345 260513 TRUE FALSE 162423.0286 349319.7909 330530.1027 273978.1003 227731.0254 240748.8875 186593.421 269048.8489 244227.1629 311555.5345 0.5213293 1.121211958 1.060902684 0.879387685 0.730948419 0.772731859 0.598909024 0.863566264 0.783896082 1 18.24912982 4.781605494 23.30118523 0.851056213 0.521326622 0.315701753 0.151265456 18474.41723 10000074.17 0.038612899 16.17722822 60479.12432 -4.781605494 -0.329729591 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 T(0.033)VS(0.163)S(0.803)PPT(0.524)S(0.476)PRPGSAATVSASTSNIIPPR;T(0.027)VS(0.154)S(0.819)PPT(0.534)S(0.465)PRPGSAATVSASTSNIIPPR;T(0.001)VS(0.12)S(0.879)PPT(0.546)S(0.454)PRPGSAATVSASTSNIIPPR 154.43 6.24E-08 3590770000 511065 580036 584939 518225 670570 710400 577392 586792 592176 516570 TRUE FALSE 531242.2408 679652.6709 600182.9909 620728.3583 556586.7509 545420.3662 532134.5063 578927.013 570863.7014 617782.0012 0.859918612 1.10014968 0.971512588 1.00476925 0.900943617 0.882868658 0.861362917 0.937105665 0.924053631 1 19.23673831 3.237063922 24.99983499 0.910758205 0.991479483 0.193840032 0.064685297 51.53165293 860760.9521 0.017261514 0.021706282 1726.091931 -3.237063922 0.080721278 TVSS(ph)PPTS(ph)PRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 TVS(0.035)S(0.965)PPT(0.21)S(0.79)PRPGSAATVSASTSNIIPPR;T(0.005)VS(0.123)S(0.872)PPT(0.193)S(0.807)PRPGSAATVSASTSNIIPPR;T(0.003)VS(0.126)S(0.866)PPT(0.051)S(0.95)PRPGS(0.003)AATVSASTSNIIPPR;T(0.003)VS(0.132)S(0.865)PPT(0.084)S(0.916)PRPGSAATVSASTSNIIPPR;T(0.007)VS(0.152)S(0.841)PPT(0.019)S(0.981)PRPGSAATVSASTSNIIPPR 207.39 1.25E-25 9004540000 1383273 1470164 1516515 1416218 1727375 1958210 1431825 1602520 1494921 1453305 TRUE FALSE 1437885.686 1722653.231 1556036.627 1696341.693 1433756.415 1503445.404 1319594.815 1581040.841 1441119.085 1738052.29 0.827297139 0.991140049 0.895276072 0.97600153 0.824921335 0.865017361 0.759237696 0.909662414 0.829157497 1 20.72904006 3.228693014 24.99956254 0.856455403 0.925397182 0.126803969 0.072190053 331.5687271 840028.4246 0.019208893 0.023217903 1693.140562 -3.228693014 0.06894178 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.045)S(0.931)PPT(0.022)S(0.001)PRPGSAATVSASTSNIIPPR;T(0.027)VS(0.135)S(0.589)PPT(0.206)S(0.042)PRPGSAATVSASTSNIIPPR 170.01 2.45E-12 1591400000 90228 115648 113488 115832 114719 141144 111687 91993 107463 93341 TRUE FALSE 93790.27111 135509.6444 116445.5905 138743.2239 95219.10536 108365.4451 102932.6811 90759.98431 103595.4276 111629.3818 0.840193411 1.213924526 1.043144633 1.242891626 0.852993216 0.970760953 0.922093085 0.813047451 0.928030111 1 16.76835728 3.217475035 24.99996108 0.902149685 1.091252325 0.347472758 0.113619212 228.398597 270798.4127 0.031119394 0.03722946 1649.966151 -3.217475035 0.18910264 TVSSPIPYT(ph)PSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 2 TVSSPIPY(0.245)T(0.441)PS(0.314)PS(0.001)S(0.001)S(0.002)RPIS(0.988)PGLS(0.004)YAS(0.004)HT(0.001)VGFTPPTSLTR;T(0.01)VS(0.046)S(0.066)PIPY(0.178)T(0.513)PS(0.169)PS(0.015)S(0.002)S(0.003)RPIS(0.92)PGLS(0.055)Y(0.022)AS(0.001)HTVGFTPPTSLTR 150.94 2.79E-12 4229300000 147255 217756 210735 178061 186934 243854 165657 189198 172370 156202 TRUE FALSE 153068.7411 255153.8991 216226.9272 213280.9343 155159.0255 187222.6041 152672.3715 186662.1103 166166.4374 186806.7912 0.819396019 1.365870574 1.157489649 1.141719383 0.830585571 1.002225898 0.817274203 0.999225505 0.889509617 1 17.51118738 3.254770324 24.78008357 0.924666526 1.141199176 0.323671376 0.138985666 225.4425003 344635.8112 0.035882647 0.048435306 1797.919836 -3.254770324 0.21653265 TVSSPIPYTPS(ph)PSSSRPIS(ph)PGLSYASHTVGFT(ph)PPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 3 TVSS(0.001)PIPY(0.028)T(0.329)PS(0.6)PS(0.026)S(0.028)S(0.031)RPIS(0.699)PGLS(0.199)Y(0.235)AS(0.17)HT(0.292)VGFT(0.318)PPT(0.015)S(0.015)LT(0.015)R 86.891 0.00076795 535060000 44857 79924 79723 87586 84753 125470 99312 93983 91808 105830 TRUE FALSE 46627.989 93650.32528 81800.64687 104910.2494 70346.71533 96331.49402 91527.66594 92723.31161 88503.84801 126565.3623 0.368410347 0.739936453 0.646311482 0.828901743 0.555813329 0.761120517 0.723165203 0.732612067 0.699273849 1 16.9495231 -5 0.063526463 2.045511818 0.255270042 0.501004797 0.110987912 315.9424927 1.459623396 51.28391253 7.727892835 1.00E-05 5 -1.790241776 TVSSPIPYTPSPSSSRPIS(ph)PGLSYASHTVGFTPPTSLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 TVSSPIPYTPSPS(0.017)S(0.008)S(0.008)RPIS(0.967)PGLSYASHTVGFTPPTSLTR 351.7 1.11E-145 7339700000 936270 1645200 1717100 1490800 1586500 1737500 1425500 1600100 1580900 1543000 TRUE FALSE 973234.6626 1927750.302 1761849.037 1785675.79 1316827.297 1333991.957 1313765.585 1578653.277 1524003.718 1845321.307 0.527406614 1.044669183 0.954765454 0.967677435 0.713603258 0.722904977 0.711944082 0.855489649 0.825874449 1 20.81544061 4.762952733 24.41907503 0.851658137 0.527406083 0.421574352 0.117977203 5961.570065 5968026.421 0.029917424 1.899624196 57936.5637 -4.762952733 -0.324252053 TVSSPPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 TVS(0.001)S(0.023)PPT(0.483)S(0.483)PRPGS(0.007)AAT(0.003)VSASTSNIIPPR 118.63 0.00027063 272010000 31445 28459 31483 30592 40744 43916 36153 28777 29141 27550 TRUE FALSE 32686.47288 33346.61187 32303.47284 36643.00629 33818.34943 33717.17455 33319.23339 28391.29138 28092.2211 32947.89502 0.992065589 1.012101436 0.980441173 1.112150147 1.026419121 1.023348367 1.011270473 0.861702739 0.852625671 1 15.00789868 1.793045949 6.509102454 0.892794859 1.024672417 0.534129064 0.050040481 0.142795086 12.13558418 0.022389088 0.012886845 62.09347269 -1.793045949 0.131877558 TVSTLHHVLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVSTLHHVLQR 11 0 O00764;F2Z2Y4;O00764-3;O00764-2 O00764 PDXK Pyridoxal kinase 0 ; 198.62 3.07E-08 3182300000 556920 1281090 1201750 1128530 1356190 1492070 1154200 1214170 1112870 1296520 FALSE TRUE 578907.6316 1501107.242 1233068.592 1351749.866 1125665.308 1145559.355 1063730.788 1197896.037 1072818.026 1550548.271 0.37335673 0.968113841 0.795246827 0.871788316 0.725978887 0.738809218 0.686035261 0.77256288 0.691895923 1 20.56434701 -1.968441395 2.454936074 1.210696232 0.748104466 0.222545976 0.146473969 22088631.01 10394529.59 26469260.23 0.033473506 0.010753717 1.968441395 -0.462591766 TVT(ph)PASSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TVTPASSAK 9 0 A0A1C7CYX9;Q16555-2;Q16555 A0A1C7CYX9 DPYSL2 Dihydropyrimidinase-related protein 2 1 T(0.003)VT(0.995)PAS(0.001)S(0.001)AK;T(0.002)VT(0.998)PASSAK;T(0.003)VT(0.997)PASSAK;TVT(1)PASSAK;T(0.005)VT(0.991)PAS(0.003)S(0.001)AK 157.25 0.00077128 1383925000 2986710 2176690 2604210 1970400 3036640 3196020 3027160 2428340 2590660 1730790 TRUE FALSE 3104627.617 2550519.575 2672077.852 2360139.239 2520473.017 2453792.791 2789883.289 2395792.074 2497422.653 2069905.163 1.499888823 1.232191514 1.290918009 1.140216123 1.217675603 1.185461458 1.347831456 1.157440504 1.206539651 1 20.98113324 8 0.025837306 4.52E-12 2.923999817 0.514682784 0.087927889 1638.617729 3.253158937 124.9247521 268.4026695 99999999.96 -8 2.923999817 TVTCVTVVEPEAPPS(ph)PDVLQAATHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 206.31 2.46E-25 6800100000 2768595 3038590 3055750 2974270 3382250 3916880 2960050 3243260 3064150 3099450 TRUE FALSE 2877901.268 3560444.196 3135385.355 3562571.729 2807336.353 3007243.981 2728033.546 3199789.405 2953871.84 3706727.885 0.77639939 0.960535628 0.845863374 0.961109593 0.757362407 0.81129343 0.735968118 0.86323828 0.796894709 1 21.82171478 5.05116215 14.96377463 0.849206196 0.352083441 0.067116578 0.085612774 1098000.86 8929152.203 0.019652507 15606700.96 112502.494 -5.05116215 -0.497122755 TVTEGGAAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVTEGGAAHR 10 0 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 ; 151.22 2.02E-05 90905000 81741 83796 94117 86069 115055 132930 109515 95611 99864 87668 FALSE TRUE 84968.1978 98187.31116 96569.76634 103093.1913 95497.9922 102059.0221 100930.9281 94329.49093 96269.91415 104844.8661 0.810418297 0.936500897 0.921072914 0.983292699 0.910850438 0.973428894 0.962669245 0.899705388 0.918212953 1 16.67789669 4.74376635 4.658129232 0.941622414 0.801946725 0.612362655 0.032058136 0.130002594 7.613604741 0.0074781 0.059482562 55432.7405 -4.74376635 -0.139675689 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TVTLPHEAERPDGSEDAEDDDDDDALSDWNLR 32 1 O14787-2;O14787;A0A075B780 O14787-2 TNPO2 Transportin-2 0 ;;;; 267.77 3.86E-60 1040177000 260050 298756 319171 323738 311448 361195 323430 289668 302197 283387 FALSE TRUE 270316.9748 350065.019 327488.8585 387772.4101 258508.1802 277312.9352 298078.7115 285785.4743 291320.989 338911.2569 0.797604002 1.032910568 0.966296787 1.144170936 0.762760678 0.818246457 0.879518474 0.843245742 0.85957897 1 18.37054803 3.219416749 24.99998167 0.85162227 0.987296823 0.279189905 0.097494879 279.186115 364588.419 0.02692418 0.032227139 1657.359605 -3.219416749 0.135674554 TVTNAVVTVPAYFNDSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVTNAVVTVPAYFNDSQR 18 0 P11142;P11142-2;E9PN89;E9PLF4;E9PQQ4;E9PQK7;E9PK54;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 144.18 2.75E-06 0 165180 177950 170700 159610 179150 213580 154580 194400 149510 154140 FALSE TRUE 171701.4339 208511.5282 175148.5822 191180.3816 148698.147 163979.2818 142463.6157 191794.386 144129.1643 184340.7818 0.93143488 1.131119908 0.950134748 1.03710302 0.80664813 0.889544246 0.772827446 1.040433832 0.781862607 1 17.49201575 3.256124163 24.9922201 0.887446302 1.016473773 0.306288074 0.095965343 298.3500256 424537.4427 0.025425579 0.034350581 1803.53329 -3.256124163 0.129027471 TVVDESENFFSAFLSPTDVQTIQKS(ph)PVVSKPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVVDESENFFSAFLSPTDVQTIQKSPVVSKPPAK 34 2 A0A2R8Y7M0;P82094;P82094-2;F8WF45 A0A2R8Y7M0 TMF1 TATA element modulatory factor 1 TVVDESENFFSAFLSPTDVQT(0.064)IQKS(0.935)PVVSKPPAK;TVVDESENFFSAFLSPT(0.003)DVQT(0.042)IQKS(0.954)PVVS(0.001)KPPAK 263.76 4.08E-60 440950000 566340 248083 396002 220754 605930 528140 462660 424832 499360 260534 TRUE FALSE 588699.5405 290689.3254 406322.1374 264418.4823 502934.235 405487.489 426395.5003 419137.8219 481388.1311 311580.6491 1.88939699 0.93295051 1.304067305 0.848635764 1.614138222 1.30138855 1.368491598 1.345198501 1.544987253 1 18.24924611 TVVLHIDGLDDTSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVVLHIDGLDDTSRR 15 1 Q9NVT9;E5RJ86 Q9NVT9 ARMC1 Armadillo repeat-containing protein 1 0 ;; 134.9 2.10E-05 264853000 58407 81922 70516 72168 75636 100635 61687 76236 69167 82282 FALSE TRUE 60712.95346 95991.46624 72353.70489 86442.615 62779.41974 77264.04639 56851.81175 75214.18112 66677.69318 98403.58252 0.616979097 0.975487516 0.735275109 0.878449877 0.637979006 0.785175137 0.57774128 0.764343931 0.677594164 1 16.58642322 TVVNKDVFRDPALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVVNKDVFRDPALK 14 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 144.68 4.94E-06 1520430000 1227100 1069460 1395310 692280 2356200 1764510 1136810 1514480 1637490 1475530 FALSE TRUE 1275546.856 1253131.436 1431672.925 829210.9178 1955693.966 1354729.294 1047703.862 1494180.873 1578557.055 1764631.853 0.722840208 0.710137604 0.811315359 0.469905899 1.108273073 0.767712139 0.593723762 0.846738015 0.894553191 1 20.7509358 1.214427467 2.187632363 0.986911075 0.746913013 0.224303424 0.155646067 0.435312893 3.607325197 0.139257064 0.039920428 16.384284 -1.214427467 -0.239998062 TVWDWELMNDIKPIWQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TVWDWELMNDIKPIWQR 17 1 P14625 P14625 HSP90B1 Endoplasmin 0 132.51 2.13E-05 249710000 200900 181780 189330 232400 221660 295250 297740 240940 228230 149940 FALSE TRUE 208831.6871 212999.3009 194264.0953 278368.0264 183982.3124 226682.6621 274402.3608 237710.5934 220016.0469 179317.8722 1.164589366 1.187830852 1.083350438 1.552371902 1.026012132 1.264138701 1.530256619 1.325638044 1.226961062 1 17.45215976 TVWDWELMNDIKPIWQRPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVWDWELMNDIKPIWQRPSK 20 2 P14625 P14625 HSP90B1 Endoplasmin 0 ; 271.95 1.16E-44 5977900000 6683400 5677800 6411500 5594500 9160900 8443100 7560100 6556100 7113300 4507800 FALSE TRUE 6947265.793 6652917.983 6578588.957 6701075.402 7603733.49 6482317.981 6967519.607 6468226.203 6857293.723 5391017.103 1.288674412 1.234074731 1.220287161 1.243007632 1.410445069 1.202429497 1.292431368 1.19981556 1.271985154 1 22.36212606 -0.80318618 0.538728088 0.939642384 1.267161378 0.646177531 0.058316413 9.642324244 1.901514624 1.045366008 0.025183661 0.157330825 0.80318618 0.327518994 TVWIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 2092842000 1217183 1514210 1347766 1369560 1618180 1796340 1436413 1407864 1388045 1488650 FALSE TRUE 1265238.325 1774263.789 1382889.889 1640454.88 1343122.342 1379167.259 1323823.196 1388993.886 1338089.532 1780322.466 0.710679301 0.996596865 0.776763713 0.921436937 0.754426441 0.774672727 0.743586188 0.780192304 0.751599532 1 20.76370715 3.220015503 24.96019224 0.784271106 0.856413672 0.041642584 0.100857877 507.2794963 682754.9553 0.026408767 0.031616464 1659.64615 -3.220015503 0.072142566 TVYCNVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVYCNVHK 8 0 Q13263;Q13263-2;M0R3C0;M0R2I3 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 93.551 0.010989 534790000 1294920 993600 1102130 971780 1952010 1657840 1601560 1235840 1351390 1231550 FALSE TRUE 1346044.441 1164243.071 1130852.413 1163995.184 1620208.037 1272831.785 1476025.542 1219275.586 1302753.738 1472848.643 0.913905477 0.790470274 0.767799474 0.79030197 1.100050603 0.864197276 1.002156976 0.827834952 0.884512977 1 20.49017775 TVYFAEEVQCEGNSFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TVYFAEEVQCEGNSFHK 17 0 P21291;E9PS42 P21291 CSRP1 Cysteine and glycine-rich protein 1 0 ;; 301.61 2.02E-46 1625600000 939120 1546200 1522260 1693780 1657690 2104070 1579160 1707630 1609720 1406320 FALSE TRUE 976197.1828 1811747.822 1561931.346 2028804.629 1375916.446 1615431.63 1455381.313 1684742.013 1551786.492 1681861.478 0.580426626 1.07722773 0.928692027 1.206285211 0.81809142 0.960502188 0.865339584 1.001712706 0.922660107 1 20.68162746 4.74814272 24.88535116 0.972276321 0.580426404 0.567325372 0.103498075 872.8813736 2266880.525 0.023340959 0.303564344 55994.15824 -4.74814272 -0.391849917 TVYGGGCSEMLMAHAVTQLANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TVYGGGCSEMLMAHAVTQLANR 22 0 P78371;P78371-2;F5GWF6 P78371 CCT2 T-complex protein 1 subunit beta 0 ; 294.88 1.68E-55 1325700000 298320 398760 334390 335020 406370 440620 339490 345130 365160 329560 FALSE TRUE 310097.904 467243.9281 343104.4781 401285.9561 337295.3726 338292.6827 312879.8867 340504.0969 352017.9629 394130.9722 0.786788976 1.185504213 0.870534168 1.018153823 0.855795145 0.858325548 0.793847499 0.863936409 0.893149709 1 18.5883156 3.226662731 24.64571526 0.863822739 0.974212994 0.127197978 0.108095964 283.9434412 588169.777 0.028671755 0.034534552 1685.243774 -3.226662731 0.110390255 TVYGNHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TVYGNHER 8 0 Q9NR19;Q9NR19-2 Q9NR19 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 0 ;;; 125.16 0.0012738 566206000 711110 782650 821020 743100 993180 1078970 850170 855970 855770 793940 FALSE TRUE 739185.1719 917064.0493 842416.4557 890082.9621 824359.6184 828395.5694 783531.4539 844497.1222 824971.0049 949497.3421 0.77850157 0.965841618 0.887223606 0.937425438 0.868206346 0.872456965 0.825206579 0.889414941 0.868850252 1 19.85680444 -1.435300285 6.120808932 1.000042032 0.879774532 0.356763959 0.049416779 2.64E-05 2.44E-06 0.044623108 0.010514095 0.036702844 1.435300285 -0.1202675 TWDHFWLNEGHTVYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TWDHFWLNEGHTVYLER 17 0 P09960-4;P09960;P09960-3;P09960-2 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;; 266.28 7.16E-28 1006004000 616558 678313 735993 755472 789457 903336 795272 745112 721736 652020 FALSE TRUE 640900.1859 794807.9812 755173.5822 904902.1067 655265.3811 693549.9042 732936.5026 735124.9924 695760.8623 779770.8353 0.821908382 1.019284058 0.968455792 1.160471854 0.840330712 0.889427859 0.939938337 0.942744918 0.892263253 1 19.57269067 TWEQQQEVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TWEQQQEVVSR 11 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4;Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 0 ; 256.96 3.82E-20 206380000 109071 125812 118807 118385 137604 158645 121130 137095 124006 129002 FALSE TRUE 113377.2073 147419.2323 121903.208 141801.1997 114214.1212 121802.103 111635.5141 135257.4658 119543.0483 154277.472 0.734891529 0.955546072 0.790155597 0.919130952 0.740316261 0.789500252 0.723602174 0.876715596 0.774857448 1 17.23516789 -1.480671604 3.154590062 1.004205865 0.816277473 0.354770796 0.075976856 29326533.81 41489374.11 1108477.55 0.017696581 0.033061945 1.480671604 -0.187928392 TWESVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TWESVKR 7 1 A6NFX8;Q9UKK9;A6NCQ0;A6NJU6;C9JYY9 A6NFX8 NUDT5 ADP-sugar pyrophosphatase 0 ; 85.265 0.033572 1107070000 1332150 1099090 1219930 1019020 1871770 1612560 1372050 1370350 1419770 1340870 FALSE TRUE 1384744.311 1287850.158 1251722.378 1220579.115 1553607.204 1238067.379 1264505.136 1351982.7 1368672.755 1603587.804 0.863528837 0.803105483 0.78057614 0.761155149 0.968832015 0.77206086 0.788547489 0.843098642 0.853506588 1 20.61287192 0.629696284 1.489645402 0.999878401 0.819911867 0.46104904 0.057430073 1.240105506 3.854151405 0.053382389 0.015512486 4.262813021 -0.629696284 -0.179966534 TWNHFSDNEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TWNHFSDNEAER 12 0 Q99543 Q99543 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 0 100.22 0.0033546 226090000 39006 165200 150570 139440 137560 184460 118710 147290 137150 164480 FALSE TRUE 40545.987 193571.8149 154493.9779 167020.8158 114177.6003 141621.9605 109405.2 145315.8185 132213.9983 196706.7068 0.20612407 0.984063116 0.785402696 0.849085517 0.580445894 0.719965083 0.556184391 0.738743588 0.672137724 1 17.58568662 -1.456014573 2.61002736 1.011742305 0.691015383 0.19162764 0.197172294 9144313.966 9217065.141 781464.9335 0.045182267 0.034993342 1.456014573 -0.320726922 TWPDHGVPSDPGGVLDFLEEVHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TWPDHGVPSDPGGVLDFLEEVHHK 24 0 Q06124;Q06124-1;Q06124-3;A0A0U1RRI0 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 149.32 5.09E-08 307895000 264796 241894 330216 289635 366546 398244 383805 324459 332801 227090 FALSE TRUE 275250.3505 283437.4128 338821.7002 346923.9385 304240.6418 305757.8664 353721.3612 320110.1578 320823.557 271583.9376 1.01350011 1.043645715 1.24757636 1.277409635 1.120245345 1.125831922 1.302438444 1.178678535 1.181305345 1 18.05103863 4.316100554 6.562534493 1.190628199 1.023536194 0.338074379 0.083248169 0.201635069 13.53532302 0.019273513 0.053587699 20706.20713 -4.316100554 -0.167092005 TWS(ph)PTACGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TWSPTACGGK 10 0 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 T(0.001)WS(0.791)PT(0.208)ACGGK;TWS(0.965)PT(0.035)ACGGK;TWS(0.815)PT(0.185)ACGGK;TWS(0.856)PT(0.144)ACGGK 164.48 6.44E-06 502620000 1034770 733680 873570 729010 1051110 1132550 1001290 845690 886550 565000 TRUE FALSE 1075623.519 859683.8328 896335.9518 873206.0021 872442.6976 869532.4265 922806.2734 834354.9088 854643.2387 675700.9324 1.591863304 1.272284515 1.326527623 1.292296577 1.291166929 1.286859888 1.365702235 1.234799108 1.264824714 1 19.36602532 -5 0.102968403 1.02E-11 1.522781836 0.648739221 0.0808794 114.1703658 0.795076967 24.47949463 1.191918257 1.00E-05 5 1.522781836 TWTDFEHMETIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TWTDFEHMETIEK 13 0 C9J6P4;Q7Z2W4;Q7Z2W4-2;Q7Z2W4-4;H7C5K1;Q7Z2W4-5 C9J6P4 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 0 141.38 3.98E-05 52424000 65654 54135 76191 59806 83295 86914 90053 72003 79071 56638 FALSE TRUE 68246.07062 63432.26514 78176.60005 71635.4483 69136.54565 66729.54069 82994.41055 71037.91756 76225.25016 67735.1317 1.007543189 0.936475113 1.154151444 1.057581885 1.020689617 0.98515407 1.225278647 1.048760308 1.125342909 1 16.04761668 TWTLCGT(ph)PEYLAPEIILSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.294)WT(0.294)LCGT(0.373)PEY(0.038)LAPEIILSK 79.545 0.031515 8280500 11551 6609.4 17717 9688 27842 15880 15392 11787 16835 9833.8 TRUE FALSE 12007.0424 7744.513036 18178.71957 11604.25748 23109.42678 12192.11066 14185.53482 11629.01454 16229.11164 11760.54483 1.020959707 0.658516518 1.545737875 0.986710875 1.964996275 1.036696075 1.206197079 0.98881597 1.379962567 1 13.52166728 4.248146768 24.99984137 1.253236308 0.839738112 0.235971804 0.304645177 279.9859938 730163.393 0.071192497 0.189681465 17707.07259 -4.248146768 -0.413498197 TWYVQATCATQGTGLYDGLDWLSHELSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TWYVQATCATQGTGLYDGLDWLSHELSK 28 0 P84085 P84085 ARF5 ADP-ribosylation factor 5 0 ;; 309.25 1.26E-82 848759000 738612 622678 774420 654230 902065 990049 915139 817138 852658 511677 FALSE TRUE 767772.9721 729618.1027 794602.0214 783634.7413 748732.3135 760125.1241 843408.0139 806185.6017 821971.0051 611930.3115 1.25467387 1.192322212 1.298517178 1.280594745 1.22355814 1.242175963 1.378274614 1.317446753 1.343242833 1 19.22300784 TYAHYFDLTIINNEIDETIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYAHYFDLTIINNEIDETIR 20 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;Q5JS79;A0A2R8Y7X6;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4;Q5JS72;O14936-5 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 258.95 2.83E-36 35155000 39651 44078 41882 52325 43120 55536 60591 40264 36101 34163 FALSE TRUE 41216.4521 51648.05362 42973.47933 62674.72883 35790.4778 42638.60566 55841.71909 39724.32694 34801.73206 40856.58576 1.008808037 1.264130437 1.051812787 1.534017776 0.87600266 1.043616466 1.366773999 0.972286994 0.851802259 1 15.31828103 1.569870861 7.582710344 0.922937838 1.162708662 0.239509085 0.182569043 0.163329602 18.19791045 0.094811026 0.044434328 37.14247678 -1.569870861 0.239770825 TYDATTHFETTCDDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 TYDATTHFETTCDDIK 16 0 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 ;;;; 268.56 1.54E-27 4387470000 6034390 3948390 5291030 4060550 6725450 6723460 6136160 5079220 5543290 3474960 FALSE TRUE 6272632.377 4626495.268 5428918.588 4863714.67 5582260.411 5162038.31 5655191.745 5011141.364 5343788.076 4155811.88 1.509363888 1.11325907 1.306343681 1.170340432 1.343241844 1.242125115 1.360791082 1.205815256 1.285858992 1 21.98669892 -3.374163238 0.402711465 7.32E-10 1.279916287 0.392887951 0.105150647 170.4958398 4.261621967 144.893741 0.058111143 0.00042251 3.374163238 1.279916286 TYDATTHFETTCDDIKNIYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYDATTHFETTCDDIKNIYK 20 1 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 186.23 2.02E-17 430820000 198640 148620 242190 114750 329870 237460 152540 212110 250090 170920 FALSE TRUE 206482.4606 174144.3289 248501.6704 137447.2075 273798.8152 182313.5137 140583.5162 209267.0124 241089.3098 204408.5015 1.010146149 0.851942691 1.215711032 0.672414339 1.339468824 0.891907687 0.687757677 1.023768634 1.179448545 1 17.64109567 1.47747658 24.9999994 1.093688131 0.952347796 0.070991787 0.200200078 0.146625151 7858.368483 0.10257582 0.047486849 30.02455507 -1.47747658 -0.141340335 TYEDIKENLESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TYEDIKENLESR 12 1 P25325-2;P25325;B1AH49 P25325-2 MPST 3-mercaptopyruvate sulfurtransferase;Sulfurtransferase 0 ;;; 184.21 1.33E-05 1665028000 2480990 1796270 2235090 1680700 2913020 2884400 2474780 2294680 2547100 1548740 FALSE TRUE 2578941.401 2104765.399 2293338.282 2013137.444 2417865.901 2214541.814 2280800.277 2263923.568 2455430.369 1852185.951 1.392377153 1.1363683 1.238179288 1.086898129 1.305412073 1.19563687 1.231409987 1.222298208 1.325693226 1 20.82079751 -1.018398129 4.576527309 0.999993529 1.229671524 0.411015992 0.084739472 5.80E-06 1.24E-06 0.074448721 0.017547167 0.095852153 1.018398129 0.229677995 TYEDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TYEDLKR 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 107.32 0.012033 331250000 792180 887250 1006360 911070 1235750 1260230 1212050 1088840 1132690 858050 FALSE TRUE 823455.8781 1039628.286 1032586.568 1091276.927 1025697.656 967560.6815 1117046.354 1074245.881 1091924.708 1026168.469 0.802456812 1.013116576 1.00625443 1.063448117 0.999541194 0.942886778 1.088560395 1.046851383 1.06407938 1 19.96883617 4.75087122 3.730097051 1.028990638 0.775497958 0.73684743 0.039931272 0.145913994 3.773057052 0.009942712 0.103745554 56347.05467 -4.75087122 -0.253492679 TYEDMTLEELEDHEDEFNEEDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 229.38 5.44E-33 80324000 22153 25127 32592 28481 36723 35055 27333 30818 25530 25485 FALSE TRUE 23027.61755 29442.36679 33441.37429 34114.45679 30480.83758 26914.00751 25190.56804 30404.93512 24611.18029 30478.29781 0.755541457 0.966010864 1.097219225 1.119303217 1.00008333 0.883054811 0.826508363 0.997592953 0.807498517 1 14.89549471 2.747052166 22.8632892 0.90431716 0.999833772 0.126803284 0.108772878 396.5441734 1067683.552 0.034633889 0.036116029 558.5372798 -2.747052166 0.095516612 TYEEGLKHEANNPQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TYEEGLKHEANNPQLK 16 1 P31948;P31948-2;F5H783;F5GXD8 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ;;; 202.82 1.77E-11 2750640000 4132440 2393050 3422440 2263940 4800490 4191830 4007750 3453800 4033360 2012630 FALSE TRUE 4295591.922 2804037.722 3511631.598 2711740.575 3984504.424 3218341.01 3693612.083 3407507.46 3888200.161 2406966.314 1.784649788 1.16496758 1.458945053 1.126621739 1.655405147 1.33709433 1.5345508 1.415685562 1.615394506 1 21.19878452 -0.852143251 6.021966047 0.999999946 1.440667152 0.320936976 0.197509624 1.30E-07 2.42E-08 0.171677211 0.040464702 0.140558382 0.852143251 0.440667206 TYGADLASVDFQHASEDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TYGADLASVDFQHASEDAR 19 0 P30740 P30740 SERPINB1 Leukocyte elastase inhibitor 0 ;; 275.23 1.97E-39 944320000 219514 840160 719370 874160 828480 1028320 701520 922590 730350 763950 FALSE TRUE 228180.5822 984450.9445 738117.3732 1047066.239 687655.2655 789508.2643 646533.0293 910224.1901 704064.8462 913631.3758 0.249751254 1.077514379 0.807894073 1.146048906 0.752661614 0.864143116 0.707651955 0.996270722 0.770622447 1 19.80125267 4.748600059 24.82238735 0.896803649 0.249750864 0.660732382 0.14027523 727.7567719 1799329.363 0.031032039 0.421666286 56053.15453 -4.748600059 -0.647052785 TYGEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYGEHK 6 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 72.234 0.086135 98921000 79486 66119 87804 76121 98887 105250 107890 88989 89699 59662 FALSE TRUE 82624.16866 77474.42392 90092.24437 91177.5066 82078.22306 80807.28258 99433.29988 87796.24801 86470.75051 71351.6266 1.157985775 1.085811601 1.262651584 1.27786164 1.150334295 1.13252194 1.393567388 1.230472972 1.211895995 1 16.1226587 4.239606899 24.99989151 1.223505629 1.121898678 0.088004004 0.099891304 49.18720542 1175133.286 0.023566302 0.057608006 17362.28572 -4.239606899 -0.101606951 TYGGDTGS(ph)PEISFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TYGGDTGSPEISFTK 15 0 O94915;H0Y9X0;A0A286YEZ9;A0A2C9F2R7 O94915 FRYL Protein furry homolog-like 1 TYGGDT(0.029)GS(0.971)PEISFTK;TYGGDT(0.029)GS(0.971)PEISFTK 137.75 1.55E-05 307040000 430370 336260 409740 320340 489110 521920 461950 415610 438690 289250 TRUE FALSE 447361.3399 394010.0393 420418.161 383702.2959 405971.2569 400711.9898 425741.1519 410039.4278 422901.6326 345922.9995 1.293239653 1.13901082 1.215351861 1.109213023 1.173588508 1.158384931 1.230739652 1.185348845 1.222531122 1 18.40009141 -2.380396331 1.90486119 2.88E-05 1.18853492 0.574225635 0.049503947 776551.541 70776.48897 3345289.063 0.012061347 0.004164891 2.380396331 1.188506141 TYIPPKGETK ddPTM_MDA-MB-175_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 ; 103.34 0.0025784 1243140000 1217410 778260 1004540 764360 1717850 1617680 1660050 1350210 1489700 878770 FALSE TRUE 1265474.287 911920.101 1030719.138 915548.1266 1425850.471 1241998.336 1529930.943 1332112.643 1436085.988 1050948.156 1.204126273 0.867711785 0.980751649 0.87116393 1.356727696 1.181788396 1.455762526 1.267534117 1.366467013 1 20.00326007 3.234542364 24.99999916 1.291777602 0.972837439 0.488075651 0.144725187 73.44534301 456948.8917 0.038271644 0.047354956 1716.099102 -3.234542364 -0.318940163 TYLGEEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TYLGEEGKR 9 1 Q9BV86;S4R338;Q9BV86-2 Q9BV86 NTMT1 "N-terminal Xaa-Pro-Lys N-methyltransferase 1;N-terminal Xaa-Pro-Lys N-methyltransferase 1, N-terminally processed" 0 ; 111.06 0.003506 406010000 364600 288870 316210 285440 517130 521480 485850 369610 442550 339690 FALSE TRUE 378994.6895 338481.1754 324450.6924 341899.18 429228.4273 400374.1731 447767.8075 364655.9825 426622.7119 406245.7517 0.932919761 0.833193145 0.79865621 0.841606783 1.056573331 0.985546732 1.102209206 0.897624113 1.050159196 1 18.6319932 3.248423694 24.9994638 1.007239025 0.846498318 0.640833335 0.059826615 130.8328558 331613.7493 0.01657303 0.022171797 1771.836706 -3.248423694 -0.160740708 TYLPDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TYLPDFR 7 0 Q13630;H0YCP7 Q13630 TSTA3 GDP-L-fucose synthase 0 ;;; 111.04 0.015516 2483680000 4583550 5847100 5382700 5204530 7049000 7182100 5709500 5706100 5306900 6401500 FALSE TRUE 4764512.093 6851293.941 5522977.584 6233970.5 5850813.498 5514166.121 5261974.471 5629619.063 5115905.706 7655751.361 0.622344153 0.894921167 0.721415485 0.814285915 0.764237659 0.720264525 0.687323062 0.735345076 0.668243451 1 22.86811254 -0.990006454 4.573715175 1.000005918 0.740822598 0.54190049 0.072586391 8655880.24 1892527.042 540.1356657 0.015927406 0.102327779 0.990006454 -0.259183321 TYQEHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TYQEHK 6 0 P09960-4;P09960 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ;;; 123.99 0.01855 1732000000 2243580 1700540 2108580 1665730 2800700 2513450 2449810 2315770 2265130 1727610 FALSE TRUE 2332158.271 1992594.517 2163531.327 1995206.422 2324638.014 1929739.329 2257787.491 2284730.891 2183608.414 2066102.102 1.128772033 0.964422094 1.047156055 0.965686265 1.125132205 0.933999983 1.092776339 1.10581703 1.056873429 1 20.97848012 TYS(ph)APAINAIQVPKPFSGPVR ddPTM_MDA-MB-175_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(0.009)YS(0.991)APAINAIQVPKPFSGPVR;T(0.001)YS(0.999)APAINAIQVPKPFSGPVR 232.19 1.59E-26 984130000 944230 768070 906730 736890 1094710 1073870 883540 799870 825660 678890 TRUE FALSE 981508.9295 899980.0477 930360.1287 882644.6426 908631.5852 824479.9672 814285.8261 789149.051 795944.6579 811905.4974 1.208895534 1.10847882 1.145897068 1.087127314 1.119134663 1.015487603 1.002931781 0.971971558 0.980341506 1 19.63095229 2.858589027 0.859613521 0.973988737 1.156739655 0.858298606 0.02889022 0.19515684 0.315332118 0.016087964 0.017301977 722.0861694 -2.858589027 0.182750918 TYS(ph)FEQPWPNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 TYS(1)FEQPWPNAR;TYS(1)FEQPWPNAR;TYS(1)FEQPWPNAR;T(0.001)YS(0.999)FEQPWPNAR;T(0.014)YS(0.986)FEQPWPNAR;TYS(1)FEQPWPNAR 242.35 2.87E-16 947857000 1006779 1111325 1222568 1221645 1485926 1652330 1425739 1366165 1388388 1100075 TRUE FALSE 1046527.412 1302186.424 1254429.126 1463282.735 1233348.829 1268601.399 1313985.852 1347853.793 1338420.187 1315613.634 0.795467138 0.989793956 0.953493559 1.112243517 0.937470392 0.964265926 0.99876272 1.024505796 1.017335297 1 20.32730443 4.899598175 2.162636021 1.003426437 0.667611132 0.639253675 0.045945731 0.767691633 2.716850033 0.01128148 0.580849611 79359.36332 -4.899598175 -0.335815305 TYS(ph)FTSAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TYSFTSAMSR 10 0 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 T(0.006)YS(0.994)FTSAMSR;T(0.079)YS(0.916)FT(0.005)SAMSR;T(0.014)YS(0.961)FT(0.025)SAMSR 203.03 2.23E-07 1093150000 520670 542950 641660 579210 949350 774650 589160 552120 591580 759470 TRUE FALSE 541226.4536 636197.4389 658382.1867 693776.0092 787979.8261 594749.2774 542980.0997 544719.7345 570289.1514 908273.6056 0.59588482 0.700446908 0.72487209 0.763840328 0.867557773 0.654812904 0.597815566 0.599730886 0.627882554 1 19.79276743 -2.291459472 2.382852266 2.580139372 0.680725334 0.572335737 0.082612468 3276092.823 660896.7648 27908729.31 0.022344691 0.005111408 2.291459472 -1.899414039 TYS(ph)LTTPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 TYSLTTPAR 9 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 T(0.003)YS(0.982)LT(0.015)TPAR;T(0.001)YS(0.993)LT(0.006)TPAR;T(0.007)YS(0.594)LT(0.398)T(0.001)PAR;T(0.003)YS(0.952)LT(0.045)TPAR 163.65 6.59E-05 1144900000 744840 780950 829780 821130 1149720 1174870 964040 946640 919350 942030 TRUE FALSE 774246.8583 915072.0876 851404.7485 983547.0632 954291.0051 902024.2478 888476.0258 933951.8392 886262.7731 1126602.742 0.687240346 0.812240245 0.755727566 0.873020299 0.84705191 0.800658665 0.788632934 0.828998372 0.786668397 1 20.10354746 -5 0.237764463 2.102244009 0.781601999 0.622071137 0.04772612 112.6065424 1.124319948 60.04550758 0.075700565 1.00E-05 5 -1.320642009 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYSHLNIAGLVGSIDNDFCGTDMTIGTDSALHR 33 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 179.08 8.03E-20 258320000 70278 83367 86023 91447 103190 122060 83737 88723 83132 81895 FALSE TRUE 73052.62971 97684.63374 88264.83005 109534.9437 85649.80066 93713.41484 77173.47513 87533.81331 80140.09556 97940.75728 0.745885898 0.997384914 0.901206326 1.118379587 0.874506212 0.95683776 0.787960776 0.89374246 0.818250724 1 16.57962173 2.280270203 24.99924277 0.866299574 0.93973091 0.064261204 0.102917869 323.7564797 194046.7815 0.033821535 0.028296908 190.6646597 -2.280270203 0.073431336 TYSSS(ph)LKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYSSSLKR 8 1 O00515;E9PDI4 O00515 LAD1 Ladinin-1 1 T(0.003)Y(0.002)S(0.025)S(0.121)S(0.849)LKR 54.066 0.081226 331820000 216090 171950 235140 170860 323840 276550 243100 237340 242250 178820 TRUE FALSE 224621.4001 201481.0749 241267.9416 204655.598 268793.7925 212325.4537 224045.1868 234158.8455 233531.4698 213856.3553 1.050337736 0.942132744 1.128177562 0.956976929 1.25688943 0.992841449 1.047643342 1.094935174 1.092001542 1 17.70628256 4.238536017 25 1.074130232 0.996235251 0.113784867 0.0833415 1.198484837 1222024.03 0.018938362 0.045608545 17319.5266 -4.238536017 -0.077894981 TYSYLT(ph)PDLWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYSYLTPDLWK 11 0 P15880;H0YEN5;E9PQD7 P15880 RPS2 40S ribosomal protein S2 1 TYSYLT(1)PDLWK 217.88 1.23E-10 32161000 104020 85279 90559 71687 113110 139630 114360 99482 106160 83238 TRUE FALSE 108126.7899 99925.00487 92919.04194 85866.47464 93883.6026 107203.0486 105396.1644 98148.60651 102339.3223 99546.89241 1.086189506 1.003798335 0.933419815 0.862573131 0.943109326 1.076910047 1.058758961 0.985953495 1.028051402 1 16.60308866 2.756525798 24.66924022 1.027891331 0.96039231 0.228172936 0.058477525 1122.482597 1541357.309 0.019503941 0.020648168 570.8549845 -2.756525798 -0.067499021 TYT(ph)HEVVTLWYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 T(0.425)YT(0.575)HEVVTLWYR;T(0.03)YT(0.97)HEVVTLWYR;T(0.144)YT(0.856)HEVVTLWYR 207.52 2.85E-07 816540000 482458 468904 557755 422580 773220 713759 580396 557148 581683 457671 TRUE FALSE 501505.8144 549434.6144 572290.5535 506165.0627 641788.3406 547999.2894 534903.0449 549680.3424 560748.3425 547342.8698 0.916255316 1.003821635 1.045579627 0.924767802 1.172552665 1.001199284 0.977272336 1.004270582 1.024491911 1 19.06208533 4.723854323 3.919145934 1.017883094 0.908061617 0.206409224 0.05988036 0.354089704 11.08263829 0.013899451 0.108597181 52948.58062 -4.723854323 -0.109821477 TYYVDHNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 TYYVDHNTR 9 0 Q9H0M0-3;Q9H0M0;Q9H0M0-6 Q9H0M0-3 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 0 ; 118.4 0.000995 124490000 129199 189734 178889 192131 195801 245670 185947 197351 182677 206860 FALSE TRUE 134299.8763 222319.3386 183550.9943 230133.9383 162518.816 188616.8657 171371.9883 194705.8326 176102.4905 247390.2564 0.542866474 0.898658427 0.741949165 0.930246573 0.65693297 0.762426412 0.692719231 0.787039213 0.71184085 1 17.91642915 -0.914846968 4.062243037 1.00000921 0.754748011 0.335474473 0.10626646 25690989.68 52224776.41 3548.97067 0.023237854 0.121661462 0.914846968 -0.245261199 TYYYNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 TYYYNNR 7 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 111.73 0.015154 146170000 92118 89399 97756 74127 124150 124950 96189 87610 91894 93612 FALSE TRUE 95754.88977 104752.5828 100303.6017 88789.09935 103047.0273 95932.25614 88649.45484 86435.73125 88586.75289 111953.4791 0.855309639 0.935679567 0.895940014 0.793089237 0.920445065 0.856893925 0.791841893 0.772068291 0.791281822 1 16.77253984 2.421973208 5.807782551 0.81424507 0.880153432 0.026657754 0.071051195 0.354374607 25.28890831 0.023647288 0.019800135 264.2245748 -2.421973208 0.065908362 VAAAAGSGPS(ph)PPGS(ph)PGHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 2 VAAAAGSGPS(1)PPGS(1)PGHDR;VAAAAGS(0.001)GPS(0.999)PPGS(1)PGHDR;VAAAAGSGPS(1)PPGS(1)PGHDR 243.99 2.52E-24 812580000 722130 813030 745470 925780 847360 1024120 926500 795790 771070 722290 TRUE FALSE 750640.25 952661.578 764897.5606 1108896.521 703326.0499 786283.6507 853878.509 785123.7367 743319.3413 863808.8964 0.868988793 1.102861503 0.88549396 1.283728988 0.814214872 0.910251855 0.988503953 0.908909065 0.860513644 1 19.72035265 VAAAAGSGPS(ph)PPGSPGHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR;VAAAAGSGPS(1)PPGSPGHDR 189.07 9.53E-15 679430000 206423 391248 347904 395014 357411 492962 324842 366497 319976 358509 TRUE FALSE 214572.7394 458441.8005 356970.664 473146.5902 296658.4059 378479.0464 299380.0352 361584.7072 308460.1263 428751.9745 0.500458895 1.069247089 0.832580805 1.103543816 0.691911463 0.882745897 0.698259257 0.843342372 0.719437215 1 18.70978379 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 331.56 5.49E-95 224410000 87614 96668 103230 96386 107280 129250 108950 107150 118790 101210 FALSE TRUE 91073.06837 113269.977 105920.2586 115450.8631 89044.58392 99233.6463 100410.2143 105713.8295 114514.7711 121040.1617 0.752420247 0.935804905 0.875083585 0.953822776 0.735661475 0.819840662 0.829561138 0.873378125 0.946089046 1 16.88512629 1.149410584 2.248568661 0.998495366 0.847238096 0.39205198 0.065262963 0.294572194 2.729770176 0.060629161 0.017044175 14.10621776 -1.149410584 -0.15125727 VAAASGHCGAFSGSDSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAAASGHCGAFSGSDSSR 18 0 Q9NZB2;Q9NZB2-6;A0A494C0Y9 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 ; 127.22 2.59E-05 280750000 62370 119482 113853 124682 140085 145821 120354 138664 120027 126980 FALSE TRUE 64832.41576 140002.1041 116820.1027 149343.7275 116273.4017 111956.2827 110920.339 136805.4359 115707.2517 151859.2998 0.426924237 0.921919858 0.769265385 0.983434848 0.765665335 0.737236921 0.730415188 0.900869661 0.761937213 1 17.21237574 -5 0.028174695 2.121011379 2.88E-17 0.224283099 0.139321398 2868.597951 6.092571332 348.2270382 149.115109 1.00E-05 5 -2.121011379 VAAETQS(ph)PSLFGSTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAAETQSPSLFGSTK 15 0 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 1 VAAETQS(0.994)PS(0.006)LFGSTK 215.23 2.48E-12 81536000 168860 104560 127110 109010 137210 144540 179330 125830 136700 100490 TRUE FALSE 175526.7232 122517.3666 130422.591 130571.8526 113887.0932 110972.7755 165273.646 124143.4547 131780.1937 120179.0915 1.460542936 1.019456589 1.085235288 1.086477282 0.947644817 0.923395028 1.375227953 1.032987129 1.096531785 1 16.8748264 4.743171343 24.66166164 1.070262637 1.460543128 0.503678507 0.118192131 336.2894105 1798654.036 0.027970882 0.225527151 55356.84672 -4.743171343 0.39028049 VAALAAS(ph)PASVAVDSGSELNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VAALAASPASVAVDSGSELNSR 22 0 O15119;O15119-2 O15119 TBX3 T-box transcription factor TBX3 1 VAALAAS(0.859)PAS(0.141)VAVDSGSELNSR;VAALAAS(1)PASVAVDSGSELNSR;VAALAAS(1)PASVAVDSGSELNSR 387.88 9.59E-132 163831000 169847 169549 166687 155774 172185 199170 165302 159787 164844 176999 TRUE FALSE 176552.6907 198667.7218 171031.0002 186585.6323 142917.0552 152915.786 152345.1973 157645.3166 158911.2966 211678.5652 0.834060315 0.938534904 0.807975054 0.881457374 0.675160733 0.722396176 0.719700633 0.744739159 0.750719831 1 17.69151566 3.258379369 24.99717748 0.750088386 0.866613819 0.203432087 0.089263924 293.5277958 370220.9799 0.022646174 0.030622157 1812.923042 -3.258379369 0.116525434 VAALFPALRPGGFQAHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAALFPALRPGGFQAHYR 18 1 Q13501;E7EMC7;E3W990;D6RBF1;C9J6J8 Q13501 SQSTM1 Sequestosome-1 0 97.631 0.00082397 137120000 170570 163350 160700 153460 186510 220110 173780 185160 161810 158810 FALSE TRUE 177304.2353 191404.0918 164887.974 183813.93 154807.0968 168992.7883 160158.6695 182678.2331 155986.4897 189925.7789 0.933544863 1.007783635 0.868170582 0.967819803 0.815092599 0.889783311 0.843269779 0.961840115 0.821302356 1 17.53507621 4.233726078 24.9999878 0.894801208 0.970664253 0.187140715 0.062284689 161.8696962 837066.225 0.014286288 0.03248854 17128.76605 -4.233726078 0.075863044 VAAQS(ph)PPSPASAEALLPALPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQS(0.911)PPS(0.078)PAS(0.011)AEALLPALPLR 69.148 0.019828 54007000 22246 26818 25231 22869 29588 29320 27942 25826 24694 26038 TRUE FALSE 23124.28926 31423.78288 25888.54059 27392.41994 24558.64233 22510.87435 25751.83303 25479.84471 23805.26776 31139.64757 0.742599582 1.009124551 0.831369094 0.879663775 0.788661537 0.722900742 0.826978949 0.818244479 0.764468118 1 14.926465 VAAQSPPS(ph)PASAEALLPALPLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VAAQSPPSPASAEALLPALPLR 22 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 VAAQSPPS(0.998)PAS(0.001)AEALLPALPLR;VAAQS(0.001)PPS(0.999)PASAEALLPALPLR;VAAQSPPS(0.962)PAS(0.038)AEALLPALPLR;VAAQSPPS(1)PASAEALLPALPLR;VAAQSPPS(0.997)PAS(0.003)AEALLPALPLR 237.14 1.71E-30 491701000 254741 280099 278482 269226 301099 331063 285589 276859 276533 288831 TRUE FALSE 264798.3714 328203.8244 285739.4697 322478.0992 249918.2995 254178.6356 263203.7879 273148.158 266580.6313 345421.9044 0.766594035 0.950153479 0.827218732 0.933577446 0.723516072 0.735849789 0.761977699 0.790766753 0.771753696 1 18.39800005 VAAYDKLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VAAYDKLEK 9 1 P35579 P35579 MYH9 Myosin-9 0 ;; 143.61 9.26E-05 5319260000 6353360 4071300 5362230 3702410 9405060 6744830 6979760 5358930 6417210 4327520 FALSE TRUE 6604195.559 4770514.105 5501974.119 4434735.647 7806391.261 5178445.451 6432668.173 5287102.309 6186255.866 5175414.689 1.276070799 0.921764611 1.063098215 0.856885083 1.508360533 1.000585608 1.242928067 1.02158042 1.195315977 1 22.30324303 5.130998992 8.992525963 1.096526185 3.980991013 0.089222054 0.177208198 34930.5707 72230.42643 0.039672389 1897473.706 135206.9425 -5.130998992 2.884464828 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861-2;P13861 P13861-2 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR 213.08 1.10E-25 8085383000 6661420 3059770 4055600 2890970 5532710 6879680 4988080 4098360 4314240 2621770 TRUE FALSE 6924418.005 3585261.696 4161292.268 3462795.237 4592261.93 5281978.583 4597101.256 4043428.188 4158971.345 3135455.635 2.208424807 1.143457957 1.327173066 1.104399373 1.464623476 1.684596817 1.466166896 1.289582332 1.326432847 1 21.58024368 7.999961247 0.034470617 2.68E-30 3.535594188 0.230613995 0.288150265 1947.238936 5.130298411 156.6661664 433.7186917 99991077.1 -7.999961247 3.535594188 VADEDDVDNEEAALLHEEATMTIEELLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VADEDDVDNEEAALLHEEATMTIEELLTR 29 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;;;;; 289.88 1.24E-80 338137000 236805.3 244013.5 268844.7 286005 278386.4 314289 334934 260137.7 260719.9 205997.8 FALSE TRUE 246154.5561 285920.9205 275851.0137 342575.9354 231066.3792 241300.1428 308680.9979 256650.9796 251336.6417 246359.1248 0.999169632 1.160585875 1.119710966 1.390555091 0.937924988 0.979465011 1.252971645 1.041775821 1.020204313 1 17.91040338 VADKIQLINNMLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VADKIQLINNMLDK 14 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;; 179.14 1.73E-06 632550000 1194990 799200 1110450 801149 1429540 1224080 1396510 1087240 1275800 648321 FALSE TRUE 1242169.128 936456.3831 1139389.239 959613.881 1186547.301 939805.9711 1287047.897 1072667.326 1229884.207 775347.0871 1.602081376 1.207789903 1.469521532 1.237657169 1.530343405 1.212110017 1.659963542 1.383467281 1.586236961 1 19.56448276 VADMALHYANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VADMALHYANK 11 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 116.77 0.00094491 1035400000 2399000 1696800 2160700 1876200 2962300 2727900 2992700 2105700 2333400 1730600 FALSE TRUE 2493714.372 1988212.201 2217009.617 2247306.76 2458769.304 2094386.567 2758124.354 2077476.536 2249421.39 2069677.936 1.204880397 0.960638448 1.071185801 1.085824379 1.187996094 1.011938394 1.332634564 1.003768026 1.086846099 1 20.98097486 5.07696407 18.88416083 1.090370231 4.457862198 0.10761368 0.103572464 459.5437822 116044.2726 0.022586759 1896.031011 119388.9328 -5.07696407 3.367491967 VADNS(ph)FDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VADNSFDAK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAK;VADNS(1)FDAK 142.29 0.0001098 293120000 670790 390980 497000 352870 673750 745890 672830 525390 550300 371490 TRUE FALSE 697273.3072 458127.7736 509952.2283 422666.6328 559226.2157 572668.3516 620091.8265 518348.0064 530494.8105 444276.3529 1.56945852 1.031177488 1.147826629 0.951359734 1.258735046 1.288991295 1.395734485 1.166724277 1.194064926 1 18.76109783 -2.562666624 0.968706206 0.249333573 1.213959973 0.137192369 0.166257298 12304.06997 823.775893 19802.04299 0.05000974 0.002737369 2.562666624 0.964626399 VADNS(ph)FDAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VADNSFDAKR 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 VADNS(1)FDAKR 54.598 0.083343 151080000 90401 61808 68003 55305 93947 100530 89041 73363 74746 68194 TRUE FALSE 93970.10128 72423.0432 69775.21405 66244.16393 77977.9225 77183.43105 82061.73375 72379.68898 72055.90606 81555.30865 1.152225439 0.888023654 0.855556986 0.8122606 0.956135459 0.946393709 1.006209591 0.887492061 0.883521959 1 16.31549117 VADPDHDHTGFLT(ph)EY(ph)VATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 2 VADPDHDHTGFLT(0.98)EY(0.967)VAT(0.053)R;VADPDHDHTGFLT(1)EY(1)VATR;VADPDHDHT(0.001)GFLT(0.999)EY(1)VATR 221.14 2.93E-19 495459000 240442 200263 283559 161433 347835 258223 254431 310681 305638 287351 TRUE FALSE 249934.8358 234656.6124 290948.7805 193363.9656 288710.1309 198254.6217 234488.0334 306516.8294 294638.1481 343651.9268 0.727290658 0.682832233 0.846638001 0.562673887 0.840123708 0.576905311 0.682341681 0.891939796 0.85737377 1 18.39058852 1.681119667 4.67029884 0.911378762 0.702458823 0.522948369 0.093554242 0.126935061 6.42060895 0.047567416 0.022901055 47.98656542 -1.681119667 -0.208919939 VADPDHDHTGFLT(ph)EYVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLT(0.991)EY(0.009)VATR;VADPDHDHTGFLT(0.84)EY(0.16)VATR;VADPDHDHTGFLT(0.862)EY(0.138)VATR;VADPDHDHTGFLT(0.889)EY(0.111)VATR;VADPDHDHTGFLT(0.773)EY(0.227)VATR 266.16 6.42E-31 40527700000 5780150 5937490 6465930 6618660 7936990 8783400 8486560 8067640 7810610 7821720 TRUE FALSE 6008354.785 6957207.72 6634437.448 7927811.193 6587863.275 6743588.464 7821361.252 7959506.482 7529507.672 9354236.278 0.642313772 0.743749411 0.70924416 0.847510257 0.70426522 0.720912778 0.836130393 0.850898592 0.804930242 1 23.15718844 -4.999999977 0.068365193 1.86862381 0.449756273 0.735184933 0.050394729 163.0132708 0.804759864 22.22527901 2.909830552 1.00E-05 4.999999977 -1.418867537 VADPDHDHTGFLTEY(ph)VATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLTEY(1)VATR;VADPDHDHTGFLT(0.01)EY(0.99)VATR;VADPDHDHTGFLT(0.008)EY(0.992)VATR;VADPDHDHTGFLTEY(1)VATR 296.17 6.16E-49 22431253000 10204402 10497118 11857990 12108992 14308921 16623210 14610359 14314652 13788452 14496499 TRUE FALSE 10607279.67 12299916.36 12167018.96 14504114.48 11876695.72 12762721.4 13465160.88 14122787.5 13292208.31 17336810.43 0.611835707 0.709468239 0.701802619 0.83660801 0.68505656 0.736163175 0.776680402 0.81461279 0.766704369 1 24.04733516 -5 0.102429187 1.83774319 0.570414997 0.758013461 0.049364177 86.48968343 0.599887405 15.34845537 0.758777099 1.00E-05 5 -1.267328193 VADPDHDHTGFLTEYVAT(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 1 VADPDHDHT(0.004)GFLT(0.032)EYVAT(0.964)R 165.66 2.39E-10 157320000 64808 69604 59344 74045 88134 98171 89956 83512 85660 84298 TRUE FALSE 67366.66988 81557.94556 60890.55339 88690.88 73153.01416 75372.27305 82905.01366 82392.65824 82577.11333 100814.5791 0.66822349 0.808989595 0.603985593 0.8797426 0.725619398 0.747632671 0.822351434 0.817269278 0.819098925 1 16.62134476 -5 0.108070469 1.785489959 0.623459599 0.575373072 0.068504382 113.8491174 0.822321564 19.61524627 0.827301188 1.00E-05 5 -1.16203036 VADPDHDHTGFLTEYVATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VADPDHDHTGFLTEYVATR 19 0 P28482;P28482-2 P28482 MAPK1 Mitogen-activated protein kinase 1 0 ;;; 204.13 2.74E-16 3529040000 2261140 2730140 2641410 2584270 2776920 3059000 2588840 2506840 2402630 2558510 FALSE TRUE 2350411.553 3199020.307 2710247.315 3095430.893 2304900.13 2348593.61 2385919.956 2473239.91 2316159.816 3059801.049 0.768158294 1.045499448 0.885759326 1.011644497 0.753284313 0.767564156 0.779763102 0.80830089 0.756964188 1 21.54500642 3.229693446 24.99923011 0.797981402 0.933174538 0.251391724 0.097009475 211.3012536 595721.075 0.025481197 0.030881027 1697.045341 -3.229693446 0.135193136 VADWTGATYQDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VADWTGATYQDKR 13 1 O15371-2;O15371;O15371-3;B0QYA5;B0QYA6;B0QYA8 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ;; 179.5 2.20E-05 1497530000 549780 583170 701600 506590 851390 868720 674870 674150 788290 740510 FALSE TRUE 571485.7389 683324.9111 719884.2724 606791.99 706671.0319 666972.9456 621971.926 665114.1219 759919.5969 885598.7566 0.645310006 0.771596511 0.812878594 0.685177102 0.797958473 0.753132206 0.702317976 0.751033261 0.858085664 1 19.75629367 0.982748231 2.505105586 0.999175248 0.74152724 0.741896467 0.04837028 0.135715471 1.942655631 0.044041342 0.011893448 9.610549752 -0.982748231 -0.257648008 VAEAHVPNFIFDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAEAHVPNFIFDEFR 15 0 Q12768;E7EQI7 Q12768 KIAA0196 WASH complex subunit strumpellin 0 126.77 8.23E-05 58124000 68785 71967 83413 75841 92167 97188 94159 82753 78543 82211 FALSE TRUE 71500.68491 84326.77242 85586.8113 90842.12344 76500.48626 74617.5599 86778.57154 81643.83139 75716.25277 98318.67143 0.727234043 0.857688282 0.870504148 0.92395597 0.778087063 0.758935804 0.882625551 0.830400068 0.770110618 1 16.5851778 -1.413510558 4.068583457 1.000709196 0.827437067 0.442137594 0.059661688 0.00038107 5.49E-05 0.057356091 0.013464228 0.038591303 1.413510558 -0.173272129 VAEEHAPSIVFIDEIDAIGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTK 21 0 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 184.78 3.83E-17 145907000 90967 75552 98443 70352 116616 128751 107228 95860 104686 73281 FALSE TRUE 94558.4474 88527.46829 101008.5055 84267.41562 96793.65397 98850.53149 98823.18917 94575.1535 100918.3713 87639.0089 1.078953865 1.010137716 1.152551891 0.961528624 1.104458565 1.12792845 1.127616462 1.079144489 1.151523421 1 16.41928555 3.089447678 23.6024968 1.104090882 1.052386582 0.128448014 0.059672768 23.77994412 6265.775371 0.015896661 0.019000143 1228.705149 -3.089447678 -0.0517043 VAEEHAPSIVFIDEIDAIGTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAEEHAPSIVFIDEIDAIGTKR 22 1 P62191;P62191-2 P62191 PSMC1 26S protease regulatory subunit 4 0 ; 168.27 6.24E-12 131989000 88222 80688 96872 68369 129654 110198 87348 94549 98976 77232 FALSE TRUE 91705.07268 94545.53633 99396.5639 81892.18414 107615.4594 84606.18457 80501.43552 93281.72531 95413.87309 92364.1317 0.992864557 1.023617443 1.076138129 0.886623223 1.165121757 0.916006928 0.871565986 1.009934523 1.033018677 1 16.49504509 VAEFHTELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VAEFHTELER 10 0 K7EJR3;R4GMR5;P48556;K7EJC1;K7ERW6 K7EJR3 PSMD8 26S proteasome non-ATPase regulatory subunit 8 0 ;;;; 192.1 7.20E-07 1938210000 1699690 1875450 1959920 2003320 2182150 2349510 2179220 2102550 1976030 1720590 FALSE TRUE 1766795.074 2197543.949 2010997.125 2399570.717 1811228.922 1803871.91 2008407.042 2074368.756 1904913.066 2057706.668 0.858623389 1.06795783 0.977300194 1.166138378 0.880217259 0.876641913 0.976041471 1.008097407 0.925745684 1 20.97260591 VAEIEHAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAEIEHAEK 9 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 183.67 4.49E-05 3359270000 7973400 5716800 7185400 6072600 9029200 8891200 9179400 7531700 7602100 4647700 FALSE TRUE 8288195.989 6698615.929 7372657.427 7273742.155 7494419.809 6826353.547 8459894.642 7430749.881 7328501.906 5558327.829 1.49113119 1.205149487 1.326416443 1.308620574 1.34832274 1.22813079 1.522021533 1.336867869 1.318472413 1 22.4062195 0.68229911 3.406428674 1.000006189 1.343343687 0.54812531 0.093645643 3.472241904 36.45858131 0.08478535 0.021908919 4.811706289 -0.68229911 0.343337498 VAEKLDEIYVAGLVAHSDLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ; 210.88 2.38E-23 570520000 1062020 761410 991760 733640 1315340 1226340 1192230 1122570 1156100 797080 FALSE TRUE 1103949.37 892176.2446 1017606.08 878751.8023 1091758.977 941541.1204 1098779.897 1107523.785 1114492.187 953252.565 1.158086965 0.935928501 1.067509407 0.921845725 1.145298756 0.987714227 1.152663982 1.16183667 1.169146801 1 19.86249898 2.228225061 24.91473312 1.137990452 1.032715141 0.178012276 0.086072422 260.7468989 628547.7159 0.029519811 0.022037596 169.1317184 -2.228225061 -0.105275311 VAELALSLSSTS(ph)DDEPPSSVSHGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VAELALSLSSTSDDEPPSSVSHGAK 25 0 Q8N1G2;Q5T7F5 Q8N1G2 CMTR1 Cap-specific mRNA (nucleoside-2-O-)-methyltransferase 1 1 VAELALS(0.005)LS(0.031)S(0.157)T(0.13)S(0.678)DDEPPSSVSHGAK;VAELALSLSS(0.004)T(0.142)S(0.854)DDEPPSSVSHGAK;VAELALSLSST(0.063)S(0.937)DDEPPSSVSHGAK 221.85 7.04E-34 408410000 115805 201434 250916 198046 299721 312492 266674 249631 243034 198528 TRUE FALSE 120377.0708 236028.7226 257455.0771 237218.9077 248774.5315 239920.4689 245771.3951 246285.1048 234287.2538 237425.7606 0.507009309 0.994115895 1.084360334 0.999128768 1.04779924 1.010507319 1.035150501 1.037314166 0.986781103 1 17.85711695 4.736833213 4.754190657 1.027629985 0.477915083 0.970212386 0.027098375 0.023420802 1.501324877 0.00589959 0.042701604 54554.83079 -4.736833213 -0.549714902 VAELSSDDFHLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAELSSDDFHLDR 13 0 Q92896;Q92896-3;Q92896-2;H3BM42 Q92896 GLG1 Golgi apparatus protein 1 0 ; 226.04 1.14E-11 251914000 117726 142698 131436 190499 248546 268580 205896 146473 131537 244195 FALSE TRUE 122373.9134 167205.2715 134861.3301 228179.1336 206298.2397 206206.3654 189757.3335 144509.769 126803.0091 292040.3349 0.419030862 0.572541706 0.461790082 0.781327462 0.706403243 0.706088649 0.649764128 0.494828117 0.434196903 1 18.15580811 3.764004703 24.76879494 0.6516167 0.493262942 0.247301725 0.151264043 1184.823019 1153373.049 0.039019575 0.070309709 5807.707072 -3.764004703 -0.158353757 VAERLDEIFQTGLVAYVDLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VAERLDEIFQTGLVAYVDLDER 22 1 O43390;O43390-3;O43390-2 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;; 173.8 3.05E-12 74933000 36357.1 55016 53007.8 37017.2 61770 67601 40850.3 54733.1 50800.5 74858 FALSE TRUE 37792.50638 64464.57003 54389.22681 44339.09167 51270.35746 51901.69225 37648.34674 53999.49232 48972.19993 89524.99186 0.422144762 0.720073453 0.607531212 0.495270547 0.572693238 0.579745289 0.420534489 0.603177852 0.547022668 1 16.45000286 -0.914248625 1.631531178 1.007503275 0.55603979 0.712876964 0.085256356 977.7508167 798.1057702 42.57642133 0.022069377 0.121829195 0.914248625 -0.451463485 VAESCKPGAGLLLVETLLDEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAESCKPGAGLLLVETLLDEEKR 23 2 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 0 140.66 1.08E-07 123610000 169390 108590 210000 118270 314750 189290 313400 182300 279030 107840 FALSE TRUE 176077.648 127239.4878 215472.7725 141663.453 261248.9074 145330.2662 288834.8891 179856.5667 268987.7648 128969.1833 1.365269156 0.986588304 1.67073069 1.098428705 2.02566924 1.126860406 2.239565156 1.394570099 2.085674717 1 16.97666685 3.574214418 1.240821316 1.658942465 1.229453285 0.100865299 0.428153301 0.926842999 2.831915869 0.131569269 0.294110864 3751.581776 -3.574214418 -0.429489181 VAGHPLAQNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAGHPLAQNER 11 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 ;;; 96.229 0.0071678 985470000 415194 490269 401769 379659 812250 691536 485523 432803 441250 811495 FALSE TRUE 431586.1797 574468.887 412239.4302 454754.417 674184.0351 530937.2443 447466.4386 427001.9837 425369.4987 970491.9082 0.444708684 0.591935782 0.424773691 0.468581359 0.694682799 0.547080547 0.461071787 0.439985105 0.438302983 1 19.88835666 -1.231189722 5.198910371 1.000050204 0.501444246 0.769185411 0.08196571 4.93E-05 7.29E-06 0.082003703 0.019326519 0.058723276 1.231189722 -0.498605958 VAGIESHSELQISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAGIESHSELQISR 14 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 188.13 8.68E-07 142800000 99327 209640 209990 196790 226240 260570 178160 231800 200150 224190 FALSE TRUE 103248.5067 245644.0392 215462.5119 235714.4746 187783.8056 200056.5665 164195.3537 228693.1001 192946.6406 268115.7381 0.385089318 0.916186573 0.803617547 0.879151952 0.700383375 0.746157491 0.612404758 0.852964103 0.719639369 1 18.03249638 -4.999999992 0.364044439 4.193266443 0.74122058 0.227437859 0.14560683 763.2490072 6.000500989 1912.755158 0.097708346 1.00E-05 4.999999992 -3.452045863 VAHALAEGLGVIACIGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAHALAEGLGVIACIGEK 18 0 P60174;P60174-3;P60174-4;U3KPZ0;U3KQF3 P60174 TPI1 Triosephosphate isomerase 0 202.33 1.31E-15 464260000 465950 456520 435770 354610 625630 560100 439930 448740 443630 486860 FALSE TRUE 484346.0658 534923.7588 447126.5242 424750.7996 519285.6361 430025.2634 405447.1371 442725.3743 427663.843 582250.8955 0.831851131 0.918716936 0.767927585 0.72949789 0.891858888 0.738556637 0.696344377 0.760368731 0.734500962 1 19.15128143 4.225352417 24.77778023 0.775417219 0.875284031 0.111758532 0.089132163 294.4305409 552337.0253 0.020713931 0.045174474 16801.66872 -4.225352417 0.099866812 VAHEPVAPPEDKESESEAKVDGET(ph)ASDSESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAHEPVAPPEDKESESEAKVDGETASDSESR 31 2 O95674 O95674 CDS2 Phosphatidate cytidylyltransferase 2 1 VAHEPVAPPEDKESESEAKVDGET(0.499)AS(0.499)DS(0.002)ESR 132.9 0.00014491 79723000 49442 18797 27155 24301 42969 52553 44064 28482 31802 19018 TRUE FALSE 51394.00834 22025.23853 27862.68161 29107.66527 35665.14473 40348.3622 40610.14854 28100.24538 30657.45223 22744.21298 2.259652088 0.968388686 1.225044878 1.279783358 1.568097554 1.774005644 1.785515664 1.235489898 1.347923195 1 14.47321189 1.048473502 1.538719136 1.019637311 1.504265262 0.177975394 0.346098111 0.716250518 3.433174328 0.322416114 0.095227908 11.18081604 -1.048473502 0.484627951 VAHFLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAHFLEK 7 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 107.43 0.0074794 1906550000 2872600 2466650 2813500 2320710 4022900 3540900 3302800 2742000 2968700 2589300 FALSE TRUE 2986012.466 2890277.95 2886822.121 2779739.511 3339088.895 2718579.638 3043917.906 2705247.975 2861857.067 3096623.76 0.964280035 0.933364262 0.932248263 0.897667824 1.078299837 0.877917322 0.982979574 0.873612097 0.924186239 1 21.56226468 -0.469236556 7.568160013 1 0.938101764 0.089135614 0.056587239 0 0 0.051549365 0.012150302 0.339440333 0.469236556 -0.061898236 VAHSFNCTPIEGMLSHQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAHSFNCTPIEGMLSHQLK 19 0 Q9UQ80;Q9UQ80-2;F8VR77;F8W0A3 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 ; 275.49 1.12E-39 1613680000 1027020 911810 1110530 909120 1322740 1343950 1217020 1135560 1141990 986410 FALSE TRUE 1067567.543 1068406.275 1139471.324 1088941.223 1097901.127 1031837.98 1121626.792 1120339.676 1100890.003 1179678.154 0.904965087 0.905676071 0.96591712 0.923083317 0.930678528 0.874677536 0.950790509 0.949699435 0.933212164 1 20.16996188 0.484204192 0.569186591 1.002452312 0.920910259 0.468345509 0.024399923 1.680344277 0.945229279 0.035018172 0.011095421 3.049328355 -0.484204192 -0.081542053 VAIEHLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VAIEHLDK 8 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 162.25 0.0003428 5512080000 12345490 9454050 11434490 8875820 14874210 14592250 13310520 11488980 12103290 8415970 FALSE TRUE 12832899.48 11077709.55 11732482.2 10631430.7 12345897.1 11203421.09 12267206.66 11334989.02 11667694.96 10064918.19 1.275012796 1.100625891 1.165680832 1.056285854 1.226626672 1.113115961 1.218808383 1.126187894 1.159243894 1 23.26283211 -0.218796203 1.085653444 0.998174263 1.157394985 0.371972984 0.062335702 18.69912807 15.10023718 0.206255285 0.016721573 0.604232104 0.218796203 0.159220722 VAILVDDMADTCGTICHAADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAILVDDMADTCGTICHAADK 21 0 B1ALA9;P60891;A0A2R8Y7H4;P60891-2;B7ZB02;P11908;P11908-2 B1ALA9;P11908 PRPS1;PRPS2 Ribose-phosphate pyrophosphokinase 1;Ribose-phosphate pyrophosphokinase 2 0 254.44 2.17E-36 78857000 86976 69818 100570 72758 101490 102860 117520 100110 107000 64355 FALSE TRUE 90409.87964 81808.69839 103190.9368 87149.31524 84238.76605 78972.32386 108308.4753 98768.1892 103149.0909 76964.1301 1.174701507 1.062945794 1.340766623 1.13233678 1.094519823 1.026092593 1.407259137 1.283301573 1.340222916 1 16.2318986 2.239841282 24.99989592 1.286016729 1.142029937 0.15962676 0.127303451 49.79657288 972103.2526 0.043704335 0.034689999 173.7165843 -2.239841282 -0.143986792 VAKPVVEMDGDEMTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAKPVVEMDGDEMTR 15 1 P48735;H0YL11 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 171.26 9.97E-07 1126350000 757190 763130 798490 809430 716880 1231640 880920 683430 810060 666630 FALSE TRUE 787084.4459 894191.6412 819299.3054 969532.8381 595024.9937 945610.2757 811871.1885 674269.7387 780906.0988 797243.3851 0.987257418 1.121604341 1.027665228 1.216106469 0.746353002 1.18609987 1.018347977 0.845751437 0.979507781 1 19.6046607 1.979341697 23.20676557 0.926473123 1.04880981 0.11772154 0.127509433 535.0936121 601102.0791 0.049141254 0.032180838 95.35461052 -1.979341697 0.122336687 VALAAGS(ph)PARPPPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VALAAGSPARPPPAR 15 1 C9J069 C9J069 C9orf172 Uncharacterized protein C9orf172 1 VALAAGS(1)PARPPPAR;VALAAGS(1)PARPPPAR;VALAAGS(1)PARPPPAR 158.45 1.10E-06 726170000 304042 349483 360421 369704 373259 455114 352719 328828 375029 411814 TRUE FALSE 316045.8129 409503.9866 369813.8673 442830.3477 309812.5685 349420.6708 325071.9631 324420.5985 361531.7795 492501.0686 0.641715994 0.831478372 0.750889472 0.899145963 0.629059688 0.709482056 0.660043163 0.658720598 0.734073086 1 18.90976733 0.938906475 21.71054195 1.000000001 0.721547091 0.505347874 0.082030245 4923.216743 1749545.464 0.080569329 0.020142332 8.687733202 -0.938906475 -0.27845291 VALENDDRS(ph)EEEKYTAVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 180.83 1.71E-14 118390000 112100 62630 74241 53562 113920 121960 97580 77508 85707 65520 TRUE FALSE 116525.7946 73386.21531 76175.78145 64156.40373 94555.91909 93636.63832 89931.42462 76469.13204 82622.42181 78357.38954 1.487106644 0.936557684 0.972158234 0.818766476 1.206726253 1.194994357 1.147708278 0.975901986 1.054430505 1 16.25778171 1.720899018 11.99427822 1.012115718 1.093110112 0.059047639 0.172963994 0.403447128 184.8767253 0.082371019 0.045063685 52.58949712 -1.720899018 0.080994394 VALS(ph)DDETKETENMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 217.26 1.27E-12 6323810000 3839080 1890663 2560120 1954828 3410830 3791400 3515180 2660270 2926700 1819059 TRUE FALSE 3990649.843 2215369.663 2626838.83 2341487.144 2831058.335 2910904.809 3239651.006 2624613.432 2821368.639 2175468.783 1.834386167 1.018341279 1.207481739 1.076313833 1.301355532 1.338058644 1.48917375 1.206458788 1.296901459 1 21.05289488 0.208155026 1.495295366 0.999896248 1.293514454 0.150328091 0.216986138 18.60154687 32.72966446 0.198837503 0.056492043 1.614934923 -0.208155026 0.293618205 VALSEPQPERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VALSEPQPERR 11 1 Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;Q9BXP5-5;H7C3A1;H7C1K0 Q9BXP5-4 SRRT Serrate RNA effector molecule homolog 0 ; 108.7 0.0032521 332680000 236880 307490 285810 274330 313110 346390 269340 289830 266460 325710 FALSE TRUE 246232.2053 360299.0156 293258.4434 328591.6552 259887.674 265946.1721 248228.427 285945.3029 256870.1567 389526.6384 0.632131878 0.924966305 0.752858507 0.843566583 0.66718845 0.682741938 0.637256615 0.734084077 0.659441823 1 18.57136247 4.009274417 24.98137069 0.728938879 0.793639889 0 0.122128756 678.7274163 1828172.412 0.028286222 0.060983763 10215.84788 -4.009274417 0.06470101 VALVTFNSAAHNKPSLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VALVTFNSAAHNKPSLIR 18 1 Q86VP6;Q86VP6-2;A0A0C4DGH5 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 268.55 1.04E-31 1113730000 834800 1122890 1275030 1180020 1538030 1605570 1311830 1335820 1328640 1339400 FALSE TRUE 867758.5486 1315737.623 1308258.329 1413424.434 1276596.21 1232700.7 1209005.337 1317915.518 1280822.506 1601829.786 0.541729562 0.821396652 0.816727433 0.882381166 0.796961214 0.769557859 0.754765174 0.822756281 0.799599631 1 20.61128942 -5 0.158817157 1.769652443 0.727195623 0.424224336 0.082330409 140.1232005 1.284374161 34.2038197 0.354637345 1.00E-05 5 -1.04245682 VANEAEFILSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VANEAEFILSR 11 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 145.91 8.38E-05 69661000 47130 52933 53388 48814 58318 66526 45056 52949 46520 47349 FALSE TRUE 48990.72879 62023.83099 54779.33514 58469.2635 48405.12719 51076.34471 41524.39299 52239.30526 44845.75429 56626.13 0.865161168 1.095321736 0.967386172 1.03254917 0.854819625 0.901992503 0.73330798 0.922530027 0.791962196 1 15.78918031 3.230375744 24.86707175 0.860096184 0.995997334 0.32188274 0.086665898 169.2254261 514135.722 0.022966207 0.027896553 1699.713579 -3.230375744 0.13590115 VANILHDDCAFLSAFGDVSKPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VANILHDDCAFLSAFGDVSKPER 23 1 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ; 206.49 8.19E-25 715310000 467520 523200 503090 492130 871660 727770 628930 523110 578830 478450 FALSE TRUE 485978.0506 613055.5301 516200.9387 589471.8451 723495.5445 558756.447 579632.8232 516098.5661 557998.0214 572193.117 0.84932523 1.071413675 0.902144614 1.030197371 1.264425459 0.976517246 1.01300209 0.901965701 0.975191775 1 19.12614262 -0.681966093 10.31629241 1 0.999212923 0 0.109150595 0 0 0.1060807 0.025003461 0.207985906 0.681966093 -0.000787077 VANS(ph)PTMVNLLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VANSPTMVNLLLGK 14 0 Q6UB99;A0A087WTN8;A0A2R8Y438 Q6UB99 ANKRD11 Ankyrin repeat domain-containing protein 11 1 VANS(0.977)PT(0.023)MVNLLLGK;VANS(0.5)PT(0.5)MVNLLLGK 140.81 1.03E-05 166263000 271820 236810 263830 234220 317180 358570 279930 285600 323510 242370 TRUE FALSE 282551.6635 277480.2754 270705.6265 280548.0169 263265.8569 275297.5517 257988.3551 281771.9991 311866.9383 289857.761 0.974794197 0.957298071 0.933925749 0.967881681 0.908258782 0.949767744 0.890051569 0.97210438 1.075930957 1 18.14498559 1.423554335 5.839951511 1.036032792 0.940355468 0.627552594 0.029734844 0.115039973 7.050173509 0.018633727 0.007054193 26.51882849 -1.423554335 -0.095677323 VAPEEHPVLLTEAPLNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 ;;;;;;;; 316.79 2.33E-61 44051539000 16588543 12942663 15578388 12808678 19743293 19347496 18726939 16438774 16855930 12140613 FALSE TRUE 17243471.49 15165464.69 15984373.59 15342196.28 16387335.11 14854333.27 17259072.59 16218439.12 16249288.37 14519333.67 1.187621407 1.044501424 1.100902696 1.056673579 1.128656141 1.023072656 1.188695913 1.117023652 1.119148353 1 23.79147191 2.243516918 24.99925662 1.11867934 1.088864451 0 0.061485121 399.0265648 2012663.049 0.020021162 0.016262264 175.193068 -2.243516918 -0.029814889 VAPLWHSS(ph)SEVISMADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAPLWHSSSEVISMADR 17 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 VAPLWHS(0.009)S(0.952)S(0.039)EVISMADR;VAPLWHS(0.15)S(0.839)S(0.011)EVISMADR 196.31 1.04E-11 545050000 115799 150843 150315 140339 166627 171673 145549 156624 147807 151073 TRUE FALSE 120370.8339 176749.1119 154232.3324 168097.6353 138303.8021 131804.5475 134140.4891 154524.7115 142487.4549 180672.8619 0.666236383 0.978282571 0.853655224 0.930397812 0.76549295 0.72952045 0.742449572 0.855273503 0.788648906 1 17.4630203 4.783032253 22.95958603 0.837120211 0.666234618 0.25599007 0.091531673 17878.30747 9229490.092 0.021716254 9.907326201 60678.1391 -4.783032253 -0.170885593 VAPSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAPSGSK 7 0 A0A0U1RQK4 A0A0U1RQK4 0 82.263 0.058079 156590000 461030 429550 495300 423310 568110 578040 544190 528190 510580 486430 FALSE TRUE 479231.8204 503321.8711 508207.9249 507039.4545 471542.8651 443798.9703 501534.9658 521110.477 492204.3255 581736.6452 0.823795139 0.865205717 0.873604799 0.871596209 0.810577895 0.762886392 0.862134043 0.895784168 0.846094757 1 19.15000666 0.254476622 0.735793256 1.002822438 0.841472885 0.624218049 0.036056189 2.006170013 1.408196565 0.054202025 0.013915 1.796704363 -0.254476622 -0.161349554 VAPVINNGS(ph)PTILGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAPVINNGSPTILGK 15 0 E7ESY4;Q13330-3;Q13330;H0Y4T7;F8W9Y9 E7ESY4 MTA1 Metastasis-associated protein MTA1 1 VAPVINNGS(0.684)PT(0.316)ILGK;VAPVINNGS(0.994)PT(0.006)ILGK;VAPVINNGS(0.787)PT(0.213)ILGK;VAPVINNGS(0.986)PT(0.014)ILGK 243.99 5.50E-18 1144690000 1718850 1277470 1474940 1293290 1770900 1904410 1885500 1575140 1620000 1178290 TRUE FALSE 1786711.525 1496865.535 1513378.148 1549098.902 1469883.051 1462139.639 1737709.583 1554027.825 1561696.516 1409153.366 1.267932624 1.062244587 1.073962696 1.099311785 1.043096576 1.037601495 1.233158594 1.102809575 1.108251631 1 20.42639721 4.744750927 24.35925458 1.092413093 1.267932737 0.456091473 0.059534026 462.9552983 1821684.044 0.014260172 0.129648941 55558.55306 -4.744750927 0.175519644 VAQGATEKS(ph)PEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAQGATEKSPEDK 13 1 P49321;P49321-3;P49321-4 P49321 NASP Nuclear autoantigenic sperm protein 1 VAQGAT(0.007)EKS(0.993)PEDK 81.346 0.0092773 278260000 495860 126030 215800 145430 309100 428660 359140 231000 233080 98200 TRUE FALSE 515436.9357 147674.6721 221423.9253 174195.6199 256559.2924 329110.2114 330989.6684 227903.8228 224691.4963 117440.4098 4.388923168 1.257443433 1.885415127 1.483268154 2.184591256 2.802359187 2.818362681 1.940591174 1.913238353 1 16.84156938 0.873746908 1.643673804 1.009295588 2.298453172 0.197318405 0.831658862 0.904241953 4.765148052 0.759515119 0.218561683 7.477336202 -0.873746908 1.289157584 VAQRS(ph)PVDSGTILREPTTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAQRSPVDSGTILREPTTK 19 2 P49454 P49454 CENPF Centromere protein F 1 VAQRS(1)PVDSGTILREPTTK 97.253 0.00059798 138970000 119310 80452 99383 65617 125780 141020 92220 93015 100310 119740 TRUE FALSE 124020.4509 94269.00517 101973.0026 78595.84675 104399.9605 108270.2422 84991.55543 91768.28607 96699.86269 143200.7604 0.866060002 0.658299613 0.712098192 0.548850764 0.729046132 0.756073095 0.593513297 0.640836583 0.675274785 1 17.12767963 -0.847289678 13.18311495 1 0.678802405 0.553923395 0.084086314 0 0 0.078490274 0.018500335 0.14213804 0.847289678 -0.321197595 VAQSIEDHHQEVIGFCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAQSIEDHHQEVIGFCR 17 0 Q9NZB2;Q9NZB2-4;Q9NZB2-6;Q9NZB2-2;Q9NZB2-5;A0A0C4DH52 Q9NZB2 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 0 141.86 3.52E-07 108400000 29245 27013 33874 34730 33222 41374 34895 34418 33851 26509 FALSE TRUE 30399.61518 31652.27262 34756.78427 41599.49034 27574.93631 31765.51553 32159.83872 33956.68301 32632.70912 31702.931 0.958889737 0.998402091 1.096327159 1.312165438 0.869791386 1.001974093 1.01441216 1.071089705 1.029327828 1 14.95232861 VARPLPAEEPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VARPLPAEEPER 12 1 P26358;P26358-2;K7ENQ6 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ; 64.827 0.056907 114000000 69100 96895 92727 101741 101854 114080 92862 91704 84903 106054 FALSE TRUE 71828.12136 113535.9625 95143.5418 121865.0661 84540.89346 87586.6489 85583.23379 90474.85788 81847.35761 126833.2508 0.566319328 0.895159288 0.750146679 0.960829005 0.666551499 0.690565355 0.674769694 0.713337057 0.645314672 1 16.95257349 -1.175963145 4.952129935 1.000022033 0.734659076 0.346236175 0.111399272 2.63E-05 4.37E-06 0.104641863 0.024662277 0.066686336 1.175963145 -0.265362956 VARPTSSEVDRFS(ph)PSGSVVPLTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VARPTSSEVDRFSPSGSVVPLTER 24 2 Q5TC79;Q5TC79-2 Q5TC79 ZBTB37 Zinc finger and BTB domain-containing protein 37 1 VARPTSSEVDRFS(0.996)PS(0.004)GSVVPLTER;VARPT(0.009)S(0.012)S(0.044)EVDRFS(0.874)PS(0.044)GS(0.016)VVPLT(0.002)ER 198.02 9.40E-25 355646000 101888 114749 128620 130020 145812 152393 111742 109144 118426 129885 TRUE FALSE 105910.6169 134456.2481 131971.9429 155737.5679 121026.9283 117002.0353 102983.3701 107681.1032 114163.8714 155333.479 0.681827367 0.865597352 0.849603986 1.002601429 0.779142585 0.753231281 0.662982448 0.693225336 0.734959856 1 17.24500928 3.011568532 24.99586032 0.739655364 0.855989742 0.077610683 0.113128586 364.3858941 787314.1127 0.031627584 0.037774405 1026.995481 -3.011568532 0.116334378 VARS(ph)PDKPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VARSPDKPGK 10 2 P55317-2;P55317;P55318 P55317-2 FOXA1;FOXA3 Hepatocyte nuclear factor 3-alpha;Hepatocyte nuclear factor 3-gamma 1 VARS(1)PDKPGK;VARS(1)PDKPGK 68.809 0.030714 126942000 607550 314120 398190 276975 585940 640660 508250 392860 469180 291107 TRUE FALSE 631536.5431 368067.6665 408567.1585 331759.8283 486342.1281 491876.4243 468412.0369 387594.3543 452294.3034 348143.8431 1.814010374 1.057228711 1.173558478 0.95293895 1.396957429 1.412854009 1.345455467 1.113316699 1.299159277 1 18.40932398 -4.951606401 0.175031011 3.19E-15 1.322053847 0.132530462 0.226184914 307.3362113 2.977734311 107.5672429 0.74672882 1.12E-05 4.951606401 1.322053847 VAS(ph)FRK ddPTM_MDA-MB-175_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 85.642 0.033371 545930000 727570 618980 681900 521130 981260 837520 771700 675130 783350 570710 TRUE FALSE 756295.0254 725285 699670.8742 624207.9586 814465.7757 643018.6727 711212.1375 666080.9866 755157.3865 682529.6976 1.108076364 1.062642406 1.025114184 0.914550621 1.193304524 0.942110907 1.042023724 0.975900373 1.106409566 1 19.3805323 4.496836945 2.774959784 1.02188402 1.106939029 0.105356312 0.075801165 0.635500863 8.781217194 0.01769388 0.094667367 31393.29821 -4.496836945 0.085055009 VAS(ph)GSDLHLTDIDSDSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VAS(0.574)GS(0.426)DLHLTDIDSDSNR 148.01 4.66E-08 801050000 190780 240970 247860 235420 211050 289610 236300 169400 214990 209050 TRUE FALSE 198312.1417 282354.723 254319.4352 281985.3733 175175.7964 222352.4666 217778.1885 167129.4701 207252.5519 250009.345 0.793218916 1.129376676 1.017239716 1.127899333 0.700676994 0.889376621 0.871080193 0.668492892 0.82897922 1 17.9316225 3.239023873 24.99999822 0.806502131 1.024987167 0.353435367 0.124296174 11.75296071 634229.2457 0.033923582 0.043255661 1733.899306 -3.239023873 0.218485036 VAS(ph)PGSTIDTAPLSSVDSLINK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASPGSTIDTAPLSSVDSLINK 22 0 Q9P2M7;Q9P2M7-2;A6PVU7 Q9P2M7 CGN Cingulin 1 VAS(0.33)PGS(0.33)T(0.33)IDT(0.009)APLSSVDSLINK 93.269 0.001254 38856000 32085 41255 42899 47176 40512 49677 47200 45882 48242 39544 TRUE FALSE 33351.74058 48340.22533 44016.98318 56507.27199 33625.78471 38140.26961 43500.34067 45267.02684 46505.77984 47291.88968 0.705231717 1.022167345 0.930751202 1.194861791 0.711026456 0.806486479 0.919826654 0.957183719 0.983377491 1 15.52930517 1.59599034 2.72577508 0.988321377 0.905106187 0.072409749 0.136370822 0.782807921 13.33158379 0.095501662 0.037219314 39.44485284 -1.59599034 -0.08321519 VASEAPLEHKPQVEAS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.5)S(0.5)PR;VASEAPLEHKPQVEAS(0.844)S(0.156)PR 232.87 2.85E-22 5116300000 2152410 1698440 2263860 1958680 2611710 2700420 2448940 2147240 2349910 1701640 TRUE FALSE 2237388.809 1990133.858 2322858.051 2346101.058 2167772.467 2073288.38 2256985.684 2118459.76 2265337.198 2035043.778 1.099430309 0.977931718 1.141429033 1.152850412 1.06522154 1.018793012 1.109060015 1.040989773 1.113163865 1 20.9566284 3.026953268 24.99164555 1.059804905 1.090772313 0.088813514 0.054875869 665.2823896 616859.011 0.015952682 0.019066258 1064.028517 -3.026953268 0.030967408 VASEAPLEHKPQVEASS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 VASEAPLEHKPQVEAS(0.168)S(0.832)PR;VASEAPLEHKPQVEAS(0.197)S(0.803)PR 177.6 2.40E-14 2087480000 824070 794090 924270 763180 1102170 1114150 972880 868920 925840 685340 TRUE FALSE 856604.9199 930468.7803 948357.2355 914134.7261 914823.5371 855405.5476 896623.1235 857273.5487 892519.1993 819619.2514 1.045125427 1.13524515 1.157070474 1.115316319 1.116156722 1.043662098 1.093950785 1.045941207 1.088943674 1 19.64459435 2.749961197 23.46293853 1.05962625 1.117465244 0.394875102 0.036275596 334.9881776 689420.8981 0.010711864 0.011253511 562.2910836 -2.749961197 0.057838994 VASGPSPGEGIS(ph)PQSAQAPQAPGDNHVVPVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VASGPSPGEGISPQSAQAPQAPGDNHVVPVLR 32 0 Q14764 Q14764 MVP Major vault protein 1 VAS(0.007)GPS(0.007)PGEGIS(0.94)PQS(0.045)AQAPQAPGDNHVVPVLR;VASGPSPGEGIS(1)PQSAQAPQAPGDNHVVPVLR;VASGPSPGEGIS(0.932)PQS(0.068)AQAPQAPGDNHVVPVLR 303.87 3.47E-90 1505595000 130801 170834 153122 158860 161103 196898 180777 173268 141701 136213 TRUE FALSE 135965.1245 200173.4106 157112.4851 190282.0339 133718.7696 151171.4235 166607.2264 170945.6259 136601.2087 162901.3294 0.834647114 1.228801578 0.964464107 1.168081529 0.820857449 0.927993799 1.022749335 1.049381405 0.838551835 1 17.31363885 3.24733696 24.99975712 0.957462393 1.055803433 0.146695312 0.121646103 390.0034538 1110933.396 0.032410183 0.043220896 1767.408585 -3.24733696 0.09834104 VASGSDLHLTDIDS(ph)DSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(1)DSNR;VASGSDLHLTDIDS(1)DSNR 158.37 2.94E-11 901530000 492136 726060 675040 703240 809940 959830 823260 824390 812450 704950 TRUE FALSE 511565.9093 850755.157 692632.097 842338.773 672266.6881 736924.0289 758730.73 813340.4005 783210.0832 843071.4554 0.606788317 1.009113939 0.821557998 0.999130937 0.797401791 0.874094389 0.89996017 0.964734834 0.928996087 1 19.68529539 4.749395917 24.96720334 0.915850967 0.606788138 0.63920792 0.070848099 959.4696267 2210811.363 0.015822491 0.2364377 56155.96785 -4.749395917 -0.309062829 VASGSDLHLTDIDSDSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VASGSDLHLTDIDSDSNR 18 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3 Q92614 MYO18A Unconventional myosin-XVIIIa 0 ; 178.14 9.03E-14 324700000 138704 268382 266841 278536 294965 349590 269766 280408 272342 291036 FALSE TRUE 144180.141 314474.5208 273795.0957 333629.5895 244826.9547 268403.0206 248621.036 276649.5894 262540.4646 348058.932 0.414240601 0.903509411 0.786634304 0.958543393 0.703406614 0.771142459 0.7143073 0.794835483 0.754298886 1 18.40897207 -2.864731211 1.656858541 7.332740189 0.766237015 0.219235358 0.137029863 2653725.42 53496.85874 63443575.85 0.031660222 0.001365428 2.864731211 -6.566503174 VASLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASLEK 6 0 Q92805;H0YE54 Q92805 GOLGA1 Golgin subfamily A member 1 0 72.021 0.086696 259110000 305390 1226000 1052000 1307400 731800 1433100 794980 1261600 950980 1468400 FALSE TRUE 317447.033 1436555.963 1079415.984 1565999.818 607408.8974 1100284.244 732667.3903 1244690.316 916754.4156 1756104.866 0.180767697 0.81803541 0.614664879 0.891746187 0.345884183 0.626548144 0.41721164 0.708779037 0.522038537 1 20.74394757 -1.60290162 2.71757416 1.034538836 0.585324192 0.281905873 0.204722916 30544034.45 28935859.59 7518934.95 0.045616203 0.024951599 1.60290162 -0.449214644 VASPSQGQVGSS(ph)SPKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.038)S(0.656)S(0.305)PKR 189.77 1.02E-09 43581000 90695 59434 68312 43837 80302 87233 79894 63185 67564 46123 TRUE FALSE 94275.70863 69641.32717 70092.26684 52507.82776 66652.29472 66974.45778 73631.69952 62338.10842 65132.38484 55159.91877 1.70913429 1.262534984 1.270710117 0.951919962 1.208346499 1.214187027 1.334876866 1.130134159 1.180791892 1 15.75133271 4.89328988 1.795676514 1.167717053 2.05956682 0.696325256 0.108335763 0.775907094 1.824625847 0.027405087 1.32939928 78214.96949 -4.89328988 0.891849767 VASPSQGQVGSSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASPSQGQVGSSSPK 15 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGS(0.006)S(0.025)S(0.969)PK 141.86 1.39E-05 0 150400 70041 75261 67118 112370 144850 114870 91823 88805 54431 TRUE FALSE 156337.9081 82069.99691 77222.36349 80393.74007 93269.38754 111210.7827 105866.1892 90592.26288 85608.9254 65095.71231 2.401662146 1.260758873 1.186289554 1.235008224 1.432803855 1.708419476 1.626315859 1.39167788 1.315123875 1 15.9902749 7.999999978 0.036243685 3.82E-12 3.731880011 0.234043074 0.32501924 1849.419528 5.116681698 152.6952814 445.2280653 99999994.95 -7.999999978 3.731880011 VASPSQGQVGSSS(ph)PKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VASPSQGQVGSS(0.008)S(0.992)PKR;VASPSQGQVGSS(0.027)S(0.973)PKR 233.29 7.33E-20 1382820000 578000 375230 410480 356050 522990 631310 504160 435960 450000 312870 TRUE FALSE 600819.8863 439672.8336 421177.446 426475.6273 434092.3466 484697.8201 464642.6218 430116.6693 433804.5879 374170.8862 1.605736599 1.17505891 1.125628587 1.139788377 1.160144636 1.295391592 1.241792558 1.149519338 1.159375579 1 18.51333778 4.738397152 7.71273492 1.170264354 1.609914825 0.768867391 0.073031468 0.04408546 28.25515111 0.017039348 0.101340248 54751.64246 -4.738397152 0.43965047 VASPT(ph)SGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASPTSGVK 9 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 VAS(0.351)PT(0.542)S(0.106)GVK 108.47 0.0080766 0 372510 258340 322720 250130 456160 461270 453050 332830 387340 248520 TRUE FALSE 387216.9824 302707.8854 331130.3483 299604.9674 378622.0861 354147.0331 417538.7572 328368.9583 373399.7091 297212.7358 1.302827691 1.018488944 1.114118974 1.008048887 1.27390936 1.191560759 1.404848134 1.104828019 1.256338185 1 18.18113641 3.225993372 24.99057711 1.216152557 1.104504369 0.115886387 0.125061395 401.437259 798276.1869 0.033978908 0.040879082 1682.648381 -3.225993372 -0.111648189 VASS(ph)PVMVSNPATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VASSPVMVSNPATR 14 0 P51610-2;P51610;A6NEM2;P51610-4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 VAS(0.027)S(0.973)PVMVSNPATR;VAS(0.015)S(0.985)PVMVSNPATR;VAS(0.025)S(0.975)PVMVSNPATR;VAS(0.034)S(0.966)PVMVSNPATR 260.96 1.83E-24 704340000 953180 972680 921820 832200 1018230 1190290 945860 925310 906190 1112880 TRUE FALSE 990812.2824 1139730.224 945843.3865 996806.6761 845151.6283 913863.1865 871721.0217 912907.733 873576.3989 1330927.529 0.744452467 0.856342813 0.71066483 0.748956389 0.635009503 0.686636325 0.654972568 0.685918439 0.656366617 1 20.34400059 -1.117104543 4.069716209 1.00007163 0.707578463 0.674757552 0.060643384 7435336.693 4081883.337 4580.144915 0.015211289 0.076365194 1.117104543 -0.292493167 VASSTLLDDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VASSTLLDDRR 11 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;;;; 168.3 2.92E-05 2401380000 884084 963650 1021997 1027788 1259914 1260295 936616 938182 970365 1142168 FALSE TRUE 918988.319 1129149.391 1048631.081 1231081.399 1045754.268 967610.5862 863201.5905 925607.2048 935441.7532 1365953.951 0.672781332 0.826637963 0.767691385 0.901261274 0.765585302 0.708377164 0.631940476 0.677626946 0.684826712 1 20.38147742 2.855997221 4.409865653 0.708611172 0.79674793 0.003846715 0.109814726 0.477786294 15.13969611 0.032108072 0.034250398 717.7896989 -2.855997221 0.088136759 VASVESQGQEISGNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VASVESQGQEISGNRR 16 1 Q5VU43-13;Q5VU43-2;E9PQG4;Q5VU43-6;Q5VU43-7;A0A087WX83;A0A075B749;Q5VU43-3;Q5VU43;Q5VU43-4 Q5VU43-13;A0A087WX83 PDE4DIP Myomegalin 0 85.976 0.011169 146090000 72636 72943 69074 69299 76483 86373 80521 74913 73750 87432 FALSE TRUE 75503.72537 85470.39283 70874.12518 83006.13536 63482.44698 66314.17975 74209.55362 73908.91377 71095.75191 104562.6264 0.722090942 0.817408626 0.677815082 0.793841339 0.607123684 0.634205375 0.70971394 0.706838727 0.679934642 1 16.67400776 -1.161607773 5.036617653 1.000017619 0.70580497 0.679658569 0.060666767 1.20E-05 2.01E-06 0.058954828 0.013894955 0.068927452 1.161607773 -0.294212649 VATLNS(ph)EEESDPPTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VATLNSEEESDPPTYK 16 0 Q00341;A0A024R4E5;Q00341-2;C9JIZ1;C9JZI8;C9J5E5;C9JHZ8;C9JES8;C9JK79;C9JHS7;C9JT62;C9JQ82;C9JHN6;C9JEJ8;C9JBS3;C9JMQ6 Q00341 HDLBP Vigilin 1 VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK;VATLNS(1)EEESDPPTYK 315.28 8.85E-58 1349550000 2776540 1995000 2603820 2124030 2908600 3075800 3209860 2652620 2801390 1657440 TRUE FALSE 2886159.943 2337625.731 2671677.688 2544156.794 2414197.211 2361492.064 2958262.786 2617065.968 2700568.521 1982183.634 1.456050738 1.17931845 1.3478457 1.283512158 1.217948312 1.191358875 1.492426198 1.320294408 1.362420955 1 20.91865919 -2.248694257 2.021453288 2.55E-05 1.314246863 0.477260212 0.099432196 2868077.249 398976.4924 13121903.6 0.023623883 0.005640346 2.248694257 1.314221367 VATPVDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VATPVDWK 8 0 P30041 P30041 PRDX6 Peroxiredoxin-6 0 ;;; 119.41 0.0039554 1251016000 3849970 2843770 3661590 3140660 4163090 4376170 4388440 3528280 3806670 2360720 FALSE TRUE 4001969.788 3332165.376 3757014.043 3761873.174 3455449.449 3359870.839 4044462.606 3480989.178 3669668.69 2823257.885 1.417500615 1.180255404 1.330737112 1.332458219 1.223922712 1.190068699 1.432551602 1.232968903 1.299799324 1 21.42892948 -0.609395 1.152463368 0.992769142 1.289677865 0.525353395 0.083569506 60.6502977 39.77041586 2.08369717 0.022657763 0.245813087 0.609395 0.296908724 VATT(ph)PGSPSLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VAT(0.006)T(0.535)PGS(0.459)PSLGR 126.5 0.0032015 435170000 184880 186740 181790 218720 219880 239770 223880 185150 188550 176270 TRUE FALSE 192179.2052 218811.1424 186527.5967 261982.1632 182504.8761 184087.0512 206331.7006 182668.3671 181764.1223 210806.7316 0.911636947 1.037970376 0.884827516 1.24275995 0.865745011 0.873250346 0.978771878 0.86652056 0.862231111 1 17.68556141 VATTAGLYGSNLMEHTEIDHWLEFSATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VATTAGLYGSNLMEHTEIDHWLEFSATK 28 0 P07814;V9GYZ6;V9GZ76 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 215.28 2.11E-34 487030000 103710 114930 142130 138000 156250 191160 162590 132200 139740 96992 FALSE TRUE 107804.5509 134668.3335 145834.0246 165295.9881 129690.6808 146765.9871 149845.771 130428.0752 134710.7847 115995.7254 0.929383825 1.160976691 1.257236196 1.425017927 1.118064311 1.265270652 1.291821491 1.124421394 1.161342664 1 16.82371212 -0.763781877 6.833947545 0.999999999 1.199332138 0.175284863 0.124575935 1.78E-09 2.61E-10 0.119738711 0.028222685 0.17227336 0.763781877 0.199332139 VATTPGS(ph)PSLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VATTPGSPSLGR 12 0 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;A0A087WWW7;H0Y4U1 E9PGF5 TNS1 Tensin-1 1 VAT(0.036)T(0.382)PGS(0.574)PS(0.009)LGR;VAT(0.001)T(0.119)PGS(0.856)PS(0.023)LGR 118.73 0.00062306 586530000 292640 327240 355550 334290 389240 418910 378590 314760 321260 300800 TRUE FALSE 304193.6532 383440.9244 364815.9251 400411.5642 323077.1238 321624.5011 348915.1265 310541.157 309697.9154 359736.0008 0.845602476 1.065895333 1.014121256 1.113070594 0.898095056 0.894057032 0.969919957 0.863247371 0.860903314 1 18.45657902 3.195923428 24.99857132 0.907532791 1.014006297 0.270882869 0.075970133 162.0822576 95029.80783 0.021202429 0.025341933 1570.085954 -3.195923428 0.106473506 VAVAT(ph)PAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAVATPAKK 9 1 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK;VAVAT(1)PAKK 97.911 0.0037331 6475100000 15736900 7646900 10617600 6408990 12770100 12227100 12285100 9586500 10239400 6046970 TRUE FALSE 16358204.96 8960195.59 10894303.38 7676669.093 10599442.96 9387541.328 11322161.76 9458008.648 9870885.994 7231757.995 2.261995627 1.239006559 1.506452979 1.061521845 1.465679987 1.298099485 1.565616793 1.307843633 1.364935884 1 22.78591497 4.742157926 24.98464158 1.334625288 2.261995981 0.72994892 0.17283803 165.16703 1147097.441 0.037155391 0.275259985 55227.82319 -4.742157926 0.927370694 VAVEEVDEEGKFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 229.97 9.90E-13 9304720000 5313480 3549200 4455900 3111090 5850530 5676660 5232200 4556190 4799510 3153270 FALSE TRUE 5523260.293 4158747.491 4572024.415 3726454.316 4856059 4358341.746 4822086.492 4495121.725 4626776.573 3771092.883 1.464631199 1.102796356 1.212387113 0.988162963 1.287706018 1.155723786 1.278697354 1.191994434 1.226906023 1 21.84655125 -2.099911324 2.406995004 0.643746188 1.204772893 0.221878605 0.118450454 3430655.237 1521107.126 6667868.489 0.026333236 0.007944904 2.099911324 0.561026705 VAVNDAHLLQYNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VAVNDAHLLQYNHR 14 0 P17931 P17931 LGALS3 Galectin-3 0 ;;;; 330.9 1.17E-68 6378130000 2192540 3052003 2478482 2731302 2863373 3162280 2385275 2525626 2352880 3872020 FALSE TRUE 2279103.172 3576160.774 2543073.277 3271545.383 2376657.88 2427888.395 2198310.913 2491774.115 2268200.308 4630668.185 0.492175876 0.772277484 0.549180631 0.706495316 0.513242967 0.524306277 0.474728662 0.538102497 0.489821386 1 22.14278895 -0.935281527 4.861001083 1.00000291 0.5639957 0.663733884 0.093464965 2.93E-06 6.42E-07 0.089931388 0.02119689 0.116069596 0.935281527 -0.43600721 VAVTASEVQQAESEVS(ph)DIESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VAVTASEVQQAESEVSDIESR 21 0 Q9BV36-2;Q9BV36-5;H7C3K9;H7C052;H7C190;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36 MLPH Melanophilin 1 VAVTASEVQQAESEVS(1)DIESR;VAVTASEVQQAESEVS(0.998)DIES(0.002)R;VAVTASEVQQAESEVS(1)DIESR;VAVTASEVQQAESEVS(1)DIESR 316.88 1.02E-66 459963000 301678 345008 342734 347491 439353 425280 344079 370948 350106 358775 TRUE FALSE 313588.4804 404260.4402 351665.9296 416223.6826 364671.934 326515.1652 317109.1889 365976.0488 337505.7534 429070.0921 0.730856068 0.942178091 0.819600191 0.970059881 0.849912265 0.760983278 0.739061507 0.852951664 0.78659818 1 18.71085382 2.992141843 24.85140551 0.813532539 0.873114561 0.022891268 0.090898973 856.3358001 2708172.608 0.025027675 0.028692853 982.0686389 -2.992141843 0.059582023 VAWHIDPFGHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VAWHIDPFGHSR 12 0 O00754;O00754-2 O00754 MAN2B1 Lysosomal alpha-mannosidase;Lysosomal alpha-mannosidase A peptide;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha-mannosidase D peptide;Lysosomal alpha-mannosidase E peptide 0 184.03 8.58E-06 302390000 202150 287060 240350 254100 305580 338460 249230 252620 217240 276950 FALSE TRUE 210131.0381 336360.322 246613.7184 304360.2216 253637.6208 259857.7944 229694.7014 249234.0421 209421.5748 331213.05 0.63442862 1.015540668 0.7445773 0.918925814 0.765783899 0.784563876 0.693495324 0.752488593 0.632286605 1 18.33739999 3.03044422 24.43293105 0.753015742 0.836577877 0.032414025 0.129712098 382.0157312 306582.6539 0.034237688 0.040921426 1072.615873 -3.03044422 0.083562135 VAYVSFGPHAGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 ; 186.46 1.17E-05 2457000000 1488610 1781340 2253500 1651220 3401400 2765400 2659000 2476000 2626800 2455200 FALSE TRUE 1547381.472 2087271.288 2312228.061 1977826.388 2823231.243 2123177.76 2450580.632 2442813.27 2532261.981 2936249.432 0.526992515 0.710863071 0.787476716 0.673589364 0.961509336 0.723091757 0.834595523 0.831950189 0.862413783 1 21.4855431 6.316591406 0.210160072 0.9476917 3.07E-39 0.616021748 0.082198359 18.22664862 0.415974736 0.140063074 5.016175938 2072962.309 -6.316591406 -0.9476917 VCDGAIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCDGAIR 7 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 0 80.377 0.069972 14061000 1322.2 1539 2214.9 2855.5 2385.5 2836.8 1783 2268.6 2838.4 2706.2 FALSE TRUE 1374.401477 1803.311278 2272.622114 3420.309377 1980.013562 2177.996192 1643.243801 2238.193128 2736.246538 3236.428077 0.424666158 0.557191829 0.702200716 1.056816124 0.611789762 0.672962952 0.507733761 0.691562758 0.845452602 1 11.66018673 -5 0.177512527 2.323466835 0.602859578 0.304190896 0.162549656 191.2469232 1.833615614 89.10226217 0.55658202 1.00E-05 5 -1.720607257 VCDSCYDSIKDEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VCDSCYDSIKDEDR 14 1 Q8IWB7 Q8IWB7 WDFY1 WD repeat and FYVE domain-containing protein 1 0 ;; 155.28 5.37E-06 412270000 670040 421010 519000 384033 667780 699900 615250 516390 589120 339851 FALSE TRUE 696493.6966 493315.1925 532525.5664 459993.5812 554270.9941 537358.8321 567025.0973 509468.6367 567917.6863 406438.2966 1.713651746 1.213751747 1.310224875 1.131767319 1.363727283 1.322116633 1.395107454 1.25349565 1.397303578 1 18.63267682 -2.26388816 1.825737786 5.33E-05 1.329761975 0.326577739 0.147062581 1382659.88 207880.3476 5686254.372 0.035079815 0.005446429 2.26388816 1.329708694 VCEEIAIIPSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCEEIAIIPSKK 12 1 H3BNC9;P08708;H0YN88;A0A075B716;H0YN73 H3BNC9 RPS17 40S ribosomal protein S17 0 121.04 0.00061462 982280000 687080 459880 683680 486580 843540 726660 720770 617760 719600 482340 FALSE TRUE 714206.4489 538860.8126 701497.2624 582824.0717 700155.3721 557904.2276 664274.164 609479.9377 693701.7366 576845.288 1.238124786 0.934151364 1.216092559 1.010364623 1.213766302 0.967164401 1.151563821 1.056574354 1.202578492 1 19.13782491 VCEIHFHEINNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCEIHFHEINNK 12 0 H0YHB7;O43347;B4DM51;Q96DH6-3;B4DHE8;Q96DH6-2;Q96DH6 H0YHB7;B4DHE8 MSI1;MSI2 RNA-binding protein Musashi homolog 1;RNA-binding protein Musashi homolog 2 0 161.99 3.69E-05 241310000 414370 333620 456630 362080 519410 485510 485470 379190 468000 341990 FALSE TRUE 430729.6476 390916.6398 468530.1529 433698.3433 431120.8737 372757.6605 447417.5929 374107.5783 451156.7714 408996.3927 1.053138011 0.955794835 1.1455606 1.0603965 1.054094563 0.911395961 1.093940193 0.914696523 1.10308252 1 18.64172859 VCENIPIVLCGNKVDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCENIPIVLCGNKVDIK 17 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 170.89 1.64E-09 287760000 390110 194020 304610 174530 394340 411720 300180 345960 332060 202610 FALSE TRUE 405511.844 227341.4257 312548.3868 209051.5131 327310.2277 316104.2697 276651.1072 341322.9721 320109.2255 242307.5503 1.673541924 0.938235005 1.289882987 0.862752782 1.350804906 1.304558068 1.141735397 1.408635314 1.321086467 1 17.88647983 VCEVCSAYLGLHDNDR ddPTM_MDA-MB-175_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 ; 136.63 1.64E-05 1300620000 214915 189469 268614 241803 304548 305112 294440 271859 282379 238071 FALSE TRUE 223400.0102 222008.8269 275614.3015 289630.9117 252781.0397 234254.362 271361.0234 268215.1748 272216.2349 284716.4543 0.784640321 0.779754115 0.968030816 1.017260883 0.88783432 0.822763695 0.953092171 0.942043112 0.956095901 1 18.11916635 4.244652984 24.9979036 0.938465591 0.782197136 0.60189184 0.052315626 100.6436917 412944.7853 0.013489895 0.035012612 17565.19534 -4.244652984 -0.156268455 VCEVCSAYLGLHDNDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VCEVCSAYLGLHDNDRR 17 1 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 183.36 4.52E-10 5236300000 1384485 1792975 1778915 1726531 1917240 2119856 1747253 1848643 1747623 1871423 FALSE TRUE 1439145.537 2100904.509 1825274.986 2068033.679 1591348.23 1627551.571 1610298.744 1823864.964 1684726.39 2238092.506 0.643023259 0.93870316 0.815549394 0.924016176 0.7110288 0.727204781 0.719496062 0.814919383 0.752751008 1 21.09383824 -1.371975707 2.866947968 1.00332808 0.788142247 0.347118221 0.089040834 35594417.9 42528423.56 994167.22 0.022206816 0.042464332 1.371975707 -0.215185834 VCGTLLEYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VCGTLLEYLGK 11 0 F8VWW7;Q8NCJ5 F8VWW7 SPRYD3 SPRY domain-containing protein 3 0 ; 68.893 0.055992 1117280000 326960 4218600 2653000 3971900 1611950 4296500 1423050 3004500 1658300 6149700 FALSE TRUE 339868.6333 4943111.734 2722139.359 4757529.965 1337951.315 3298702.989 1311507.623 2964229.592 1598618.107 7354615.972 0.046211608 0.672110108 0.370126648 0.646876735 0.181919943 0.448521446 0.178324419 0.403043422 0.217362553 1 22.81021858 -1.711344833 4.262079832 1.037452987 0.363559464 0.502265584 0.193308293 0.05838822 0.003954421 0.158855207 0.040157319 0.019438161 1.711344833 -0.673893523 VCHANPSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VCHANPSER 9 0 P53618;E9PP73 P53618 COPB1 Coatomer subunit beta 0 ;;; 153.24 7.85E-05 897040000 206898 193318 201603 207007 207009 248289 240079 209953 188591 172044 FALSE TRUE 215066.4928 226518.8627 206856.9398 247952.3667 171821.6841 190627.6426 221260.9807 207138.9234 181803.6467 205752.7278 1.045266787 1.100927628 1.005366694 1.205098807 0.835088244 0.926489017 1.075373255 1.006737192 0.883602607 1 17.65055203 3.24126247 24.99999999 0.965375592 1.08401955 0.404575453 0.079257227 83.63120062 773822.4043 0.022736798 0.029450951 1742.859871 -3.24126247 0.118643958 VCIESEHSMDTLLATLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VCIESEHSMDTLLATLK 17 0 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 206.1 7.28E-12 351850000 399650 472970 555440 438340 709740 689060 653650 580260 619330 534400 FALSE TRUE 415428.4906 554198.9183 569915.2227 525042.3437 589098.6483 529036.2578 602415.205 572482.5638 597040.4343 639105.4483 0.650015567 0.867147855 0.891738952 0.821526941 0.921755009 0.827776166 0.942591253 0.895756037 0.934181419 1 19.28569446 5.296499833 1.391172032 0.900848362 1.50E-13 0.694777022 0.050138444 2.765590079 1.614037083 0.012648823 5.117884572 197924.6258 -5.296499833 -0.900848362 VCIESEHSMDTLLATLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCIESEHSMDTLLATLKK 18 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 203.99 7.28E-16 576230000 391490 390000 499300 363040 693260 683130 453320 478010 603580 431670 FALSE TRUE 406946.3275 456979.4662 512312.1682 434848.2284 575419.9128 524483.4104 417787.5939 471603.0578 581857.2737 516247.4717 0.788277618 0.885194585 0.992377099 0.842325149 1.114620302 1.01595347 0.809277753 0.913521293 1.127089827 1 18.97770329 4.646589701 1.836362747 0.965165377 0.748014079 0.264004914 0.097881496 1.027349019 4.138364988 0.025945895 0.360750076 44318.9743 -4.646589701 -0.217151299 VCSTLLGLEEHLNALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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) 0 143.43 5.49E-07 44440000 29122 34916 36326 35121 39883 37798 33888 30595 36688 36504 FALSE TRUE 30271.75905 40912.55139 37272.6854 42067.82897 33103.70191 29019.98733 31231.77001 30184.92407 35367.60605 43656.25989 0.693411646 0.937152003 0.853776423 0.963615048 0.75828076 0.664738285 0.715401871 0.691422585 0.810138251 1 15.41390092 3.090235089 9.741780458 0.743517968 0.866587004 0.098890595 0.111572353 0.474157929 47.09399435 0.030285621 0.036224308 1230.934911 -3.090235089 0.123069036 VCTFSPQRVS(ph)PTTSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCTFSPQRVSPTTSPR 16 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VCTFSPQRVS(0.976)PT(0.022)T(0.001)SPR 72.086 0.023519 161220000 36529 32674 34568 44659 36845 40128 39057 31566 33756 38064 TRUE FALSE 37971.19313 38285.50533 35468.87048 53492.41691 30582.10006 30808.88015 35995.61028 31142.9094 32541.12815 45521.91202 0.834130014 0.84103465 0.779160385 1.17509161 0.671810535 0.676792313 0.790731511 0.684130082 0.714845372 1 15.47427353 VCTFSPQRVSPT(ph)TSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VCTFSPQRVSPTTSPR 16 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VCTFSPQRVS(0.366)PT(0.502)T(0.115)S(0.017)PR 77.391 0.038887 233390000 45262 68239 51508 76855 50716 81623 50770 57017 46864 69810 TRUE FALSE 47048.97871 79958.51742 52850.34079 92056.68961 42095.31244 62667.29526 46790.51474 56252.78038 45177.37379 83487.93291 0.563542264 0.957725442 0.633029696 1.102634673 0.504208344 0.750615006 0.560446439 0.673783365 0.541124594 1 16.34928007 VCTIS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VCTISPAPR 9 0 O43439-2;O43439-5;O43439;O43439-4 O43439-2 CBFA2T2 Protein CBFA2T2 1 VCT(0.002)IS(0.998)PAPR;VCT(0.005)IS(0.995)PAPR 135.87 0.00021878 336900000 380250 405530 408790 439540 423440 513350 450270 441400 413510 414120 TRUE FALSE 395262.5636 475176.6229 419443.4032 526479.7001 351463.82 394132.2424 414976.6608 435483.755 398627.8559 495258.8852 0.798092827 0.95945098 0.846917472 1.063039384 0.709656769 0.795810543 0.837898467 0.879305285 0.804887843 1 18.91782333 5.06299809 13.03225081 0.869973191 0.322116713 0.049451645 0.099635737 2542527.132 16120011.69 0.022860258 35202300.89 115610.7157 -5.06299809 -0.547856478 VCTLAIIDPGDSDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VCTLAIIDPGDSDIIR 16 0 E5RI99;P62888;A0A0C4DH44;A0A0B4J213 E5RI99 RPL30 60S ribosomal protein L30 0 ;; 115.14 0.0012307 99598000 310035 305336 314759 330413 386886 402107 363387 358178 358923 294764 FALSE TRUE 322275.4212 357775.0828 322961.8781 395767.7052 321123.2559 308723.7432 334903.7774 353377.2098 346005.4313 352517.3622 0.914211485 1.014914785 0.916158785 1.122689966 0.910943092 0.875768902 0.950034845 1.002439164 0.981527347 1 18.42733479 1.733601539 9.534126717 0.993542729 0.959800621 0.060944591 0.065853265 0.346024399 121.5537093 0.031692014 0.017103178 54.15038381 -1.733601539 -0.033742108 VDATEESDLAQQYGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDATEESDLAQQYGVR 16 0 P07237;H7BZ94;I3L3U6;I3NI03 P07237 P4HB Protein disulfide-isomerase 0 ; 347.73 9.38E-87 297730000 151923 162262 185120 157385 198043 245450 177270 159333 170370 161942 FALSE TRUE 157921.0374 190129.2363 189944.3793 188515.2833 164379.7216 188447.9573 163375.1142 157197.4018 164238.417 193671.4343 0.81540697 0.981710271 0.980755783 0.973376812 0.848755637 0.973029182 0.843568463 0.811670561 0.848026027 1 17.56325165 2.224145755 24.80314902 0.854339678 0.931986477 0.085259215 0.072083418 333.4103554 573683.3561 0.025948046 0.019254568 167.5505103 -2.224145755 0.077646799 VDAYGNLLVCAHGFNFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VDAYGNLLVCAHGFNFIR 18 0 P49902-2;P49902;Q5JUV4;Q5JUV3;H0YHR8 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;;;; 210.75 3.78E-16 1056560000 791114 796030 901883 840279 950358 1121898 1025888 928283 948618 772772 FALSE TRUE 822347.7916 932741.9602 925386.8119 1006483.678 788816.4866 861354.192 945476.2179 915840.8847 914477.4235 924181.8778 0.889811639 1.009262335 1.001303785 1.089053683 0.85352949 0.93201805 1.023041287 0.990974728 0.989499411 1 19.81781727 2.225110668 24.9983814 0.999964546 0.967185733 0.08086431 0.062169458 790.9587279 1470083.359 0.024002813 0.017826722 167.9231869 -2.225110668 -0.032778813 VDCDQHSDIAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDCDQHSDIAQR 12 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 ;;; 198.14 1.87E-07 2259450000 1676860 1827240 1835690 2018160 2536810 2710990 2012600 1854440 1812220 2175980 FALSE TRUE 1743063.728 2141054.256 1883529.589 2417346.024 2105603.942 2081403.658 1854847.153 1829584.265 1746998.556 2602321.619 0.669811031 0.82274775 0.723788165 0.928919011 0.809125178 0.79982568 0.7127663 0.703058473 0.671323077 1 21.31136784 2.25678703 23.82490911 0.741105213 0.797601413 0 0.106742626 421.2375066 550624.4544 0.035022087 0.029236596 180.6288137 -2.25678703 0.0564962 VDCGYPHVTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDCGYPHVTPK 11 0 X6R3S7;Q07654 X6R3S7 TFF3 Trefoil factor 3 0 ;;; 160.18 2.78E-05 3226770000 3876540 3489690 4053500 3010500 4747840 4500320 3918820 3744380 3650770 3012540 FALSE TRUE 4029588.793 4089017.111 4159137.54 3605967.915 3940803.853 3455188.883 3611652.648 3694192.711 3519379.501 3602789.534 1.118463556 1.13495864 1.154421456 1.0008822 1.093820168 0.959031564 1.00246007 1.025370113 0.976848486 1 21.78068295 3.569087085 1.408083313 1.003011841 1.139969381 0.685364997 0.038052375 0.235105396 0.92521894 0.011686506 0.024266114 3707.55058 -3.569087085 0.13695754 VDCTAHSDVCSAQGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDCTAHSDVCSAQGVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 252.17 1.60E-26 1840860000 1389650 977970 1142670 1026840 1234900 1626040 1289480 1046280 1101510 871890 FALSE TRUE 1444514.455 1145928.74 1172448.919 1229945.887 1024992.139 1248416.853 1188407.188 1032256.328 1061866.87 1042720.152 1.385332826 1.098980141 1.124413791 1.179555113 0.982998302 1.197269325 1.139718251 0.989964878 1.018362279 1 19.99192059 7.721447775 1.034854663 1.07340118 199.9999824 0.58995541 0.075897271 794.2959398 1.725022641 0.022497351 373891.4804 52655989.08 -7.721447775 198.9265813 VDCTQHYELCSGNQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDCTQHYELCSGNQVR 16 0 Q8NBS9;Q8NBS9-2 Q8NBS9 TXNDC5 Thioredoxin domain-containing protein 5 0 ;; 232.78 9.80E-17 1338230000 508110 572460 582340 601990 649860 692210 587510 589460 593960 538910 FALSE TRUE 528170.5751 670775.5519 597516.2588 721061.8252 539397.0293 531454.718 541459.431 581559.2529 572583.4956 644499.0964 0.819505532 1.040770353 0.927101779 1.11879416 0.836924415 0.824601184 0.840124422 0.902343007 0.888416289 1 19.29781881 3.151810199 23.03036877 0.873538766 0.977758336 0.222333948 0.085656042 16.02342953 4248.778379 0.023366924 0.027928842 1418.437484 -3.151810199 0.10421957 VDDDS(ph)LGEFPVTNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDDDSLGEFPVTNSR 15 0 Q92785;J3KMZ8;Q92785-2 Q92785 DPF2 Zinc finger protein ubi-d4 1 VDDDS(1)LGEFPVTNSR 149 3.60E-06 150420000 87742 73266 81183 68112 104680 119530 94362 76986 90319 94725 TRUE FALSE 91206.12191 85848.86557 83298.69567 81584.35031 86886.53099 91770.96899 86965.65987 75954.12859 87068.43683 113284.5501 0.805106449 0.757816185 0.735304996 0.720171905 0.766975999 0.81009254 0.767674496 0.670472086 0.768581742 1 16.78959159 -1.83196651 2.298880962 1.102422276 0.750684513 0.780609839 0.038752915 2996335.522 1704558.187 1692185.04 0.01071908 0.01472426 1.83196651 -0.351737762 VDDHLMGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDDHLMGK 8 0 O95232;J3KPP4;H0YA81 O95232 LUC7L3 Luc7-like protein 3 0 90.657 0.014703 0 277060 223440 287120 222700 365510 347260 339510 279990 322140 226350 FALSE TRUE 287998.5427 261814.0819 294602.5831 266749.3953 303380.7408 266614.1278 312898.3191 276237.192 310546.2443 270698.9488 1.063907134 0.967178052 1.088303388 0.985409794 1.120731137 0.984910097 1.155890411 1.02045905 1.147201516 1 18.04632976 3.24564688 24.9991436 1.07079409 1.026419765 0.107495083 0.063969493 369.1467025 1302281.411 0.016136209 0.021383175 1760.543984 -3.24564688 -0.044374325 VDDKPSS(ph)PGDSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDDKPSSPGDSSK 13 1 Q9HC52;C9JM54;C9J6K3 Q9HC52 CBX8 Chromobox protein homolog 8 1 VDDKPS(0.479)S(0.517)PGDS(0.003)S(0.001)K;VDDKPS(0.031)S(0.969)PGDSSK;VDDKPS(0.067)S(0.932)PGDSSK;VDDKPS(0.365)S(0.622)PGDS(0.01)S(0.003)K;VDDKPS(0.183)S(0.817)PGDSSK;VDDKPS(0.013)S(0.987)PGDSSK 202.81 5.51E-08 1952730000 6302910 1966249 3251016 1958791 5234450 5226080 5089510 3361980 3954180 1456884 TRUE FALSE 6551753.754 2303936.97 3335740.148 2346234.013 4344700.059 4012402.122 4690580.907 3316918.157 3811869.834 1742332.526 3.76033487 1.322329082 1.914525556 1.346605185 2.49361129 2.302891131 2.69212727 1.903722801 2.187796977 1 20.73258856 4.752139057 24.84654449 1.980763507 3.760336151 0.527633917 0.521880554 1739.530352 3183023.884 0.121479611 2.417225965 56511.78907 -4.752139057 1.779572644 VDDKWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDDKWEK 7 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;; 105.78 0.0071582 983740000 1738130 843550 1207150 887600 1751240 1497200 1669210 1202440 1338440 682620 FALSE TRUE 1806752.715 988423.1506 1238609.321 1063164.631 1453564.85 1149497.99 1538372.959 1186323.259 1290269.806 816366.3195 2.213164203 1.210759345 1.517222466 1.302313196 1.780530156 1.408066407 1.884415025 1.453175162 1.580503476 1 19.63885714 0.087357101 1.396574977 0.999333282 1.579092066 0.283846619 0.282322882 16.25034088 23.21890169 0.272115786 0.071905066 1.222804705 -0.087357101 0.579758784 VDDQIYSEFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDDQIYSEFRK 11 1 Q9BVG4;A6NDF3 Q9BVG4;A6NDF3 PBDC1 Protein PBDC1 0 ; 169.23 2.75E-05 491730000 557170 448360 606650 425060 786730 711980 622570 567850 657830 521850 FALSE TRUE 579167.5018 525362.3422 622459.7974 509135.5993 653001.9156 546633.4352 573771.3366 560238.8996 634154.8268 624096.5161 0.92800951 0.841796627 0.997377459 0.815796253 1.046315592 0.875879645 0.919363146 0.897679902 1.016116595 1 19.25140963 1.235221776 24.95195244 1.008058351 0.914668264 0.249683456 0.064327948 109.4819837 818117.2196 0.048164018 0.013939682 17.18785875 -1.235221776 -0.093390087 VDDSSGSIGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDDSSGSIGRR 11 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 105.03 0.004041 343400000 169429 191719 183682 152976 245510 272970 161746 209510 204076 237040 FALSE TRUE 176118.1877 224645.2469 188468.9038 183234.1962 203778.2979 209576.8544 149067.9259 206701.8611 196731.3446 283483.4496 0.621264444 0.792445722 0.664832124 0.646366469 0.718836666 0.739291323 0.525843488 0.729149661 0.693978237 1 18.11290498 0.377121393 1.763736742 0.999990295 0.680223326 0.65383796 0.06967263 3.843663051 10.18027664 0.063426395 0.017780774 2.382985462 -0.377121393 -0.319766969 VDEFPLCGHMVSDEYEQLSSEALEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 VDEFPLCGHMVSDEYEQLSSEALEAAR 27 0 P27635;X1WI28;A6QRI9;B8A6G2 P27635 RPL10 60S ribosomal protein L10 0 ;;;;;;;;; 353.43 2.74E-110 3424713000 959634.6 1150598.5 1250684.7 1119210.2 1452370.1 1546659 1301408 1325541.8 1335336 1147229 FALSE TRUE 997521.715 1348204.842 1283278.571 1340586.637 1205496.749 1187470.887 1199400.24 1307775.08 1287277.518 1372006.558 0.727053169 0.982651894 0.935329765 0.977099293 0.878637746 0.865499425 0.874194248 0.953184278 0.938244436 1 20.38785595 -4.999999472 0.012680897 2.056589062 1.93E-09 0.210489648 0.068133769 15369.70078 14.79593115 1450.910049 989.6094199 1.00E-05 4.999999472 -2.05658906 VDFGS(ph)SER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDFGSSER 8 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 VDFGS(0.5)S(0.5)ER;VDFGS(0.92)S(0.08)ER;VDFGS(0.926)S(0.074)ER 108.43 0.0039985 1052750000 2168360 1418130 1342560 1280190 1433280 1662080 1621330 1602700 1365080 1010830 TRUE FALSE 2253968.527 1661682.796 1377548.217 1533407.761 1189651.578 1276087.109 1494245.918 1581218.428 1315951.037 1208882.785 1.864505439 1.374560724 1.139521742 1.268450325 0.984091752 1.055592093 1.236055254 1.307999789 1.088567935 1 20.20524293 4.742467603 1.915832484 1.153133027 2.093151047 0.815086482 0.105597968 0.350242586 1.333669248 0.028887966 0.587912214 55267.21789 -4.742467603 0.94001802 VDFGSS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDFGSSER 8 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 1 VDFGS(0.092)S(0.908)ER 123.42 0.0014144 652720000 639740 591870 642410 633560 738920 713540 732120 637680 637210 491890 TRUE FALSE 664997.4292 693519.0684 659151.7323 758876.277 613318.6423 547831.1488 674734.5214 629132.9426 614276.9366 588266.4277 1.130435799 1.178920019 1.12049864 1.290021394 1.042586511 0.931263664 1.14698798 1.069469399 1.044215525 1 19.16611018 3.194279504 24.99923307 1.046772046 1.175646246 0.515931974 0.066550673 114.8611715 64845.36062 0.019247171 0.023004883 1564.153978 -3.194279504 0.128874199 VDFTEEEINNMKTELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDFTEEEINNMKTELEK 17 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 191.37 2.24E-10 63424000 32599 20003 30266 18054 43574 38026 40605 28741 38741 20421 FALSE TRUE 33886.03369 23438.35965 31054.75682 21625.02731 36167.30704 29195.03779 37422.274 28355.77391 37346.71898 24422.10397 1.387514922 0.9597191 1.271584007 0.885469464 1.480925112 1.195434997 1.532311633 1.161070068 1.529217918 1 14.57589987 3.223529642 24.9965807 1.322429814 1.124583173 0.166943925 0.208124044 380.9212937 633472.5931 0.054428053 0.065295932 1673.129831 -3.223529642 -0.197846642 VDGAEWGVDLPSVEAQLGSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 245.61 3.12E-30 1111382000 955001 1014411 1043094 987199 1229929 1329302 1117965 1071334 1128040 967990 FALSE TRUE 992705.1769 1188628.198 1070277.887 1182464.016 1020866.108 1020591.756 1030335.982 1056974.52 1087442.061 1157649.107 0.857518198 1.026760346 0.924527026 1.021435605 0.881844163 0.881607173 0.890024426 0.913035317 0.939353777 1 20.1427666 5.050735339 15.09873854 0.934641642 0.407560303 0.172546394 0.053360126 1805679.698 14844630.47 0.012758944 27466945.84 112391.9844 -5.050735339 -0.527081339 VDGPRS(ph)PS(ph)YGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VDGPRS(0.987)PS(0.941)Y(0.071)GR 108.09 0.025229 2713200000 1482900 1436400 1403000 1396400 1521100 1747500 1667700 1576600 1357700 1203300 TRUE FALSE 1541446.037 1683090.526 1439563.333 1672603.752 1262543.965 1341669.609 1536981.316 1555468.256 1308836.642 1439063.596 1.071145181 1.169573416 1.000347265 1.162286195 0.877337158 0.932321276 1.068042663 1.08088917 0.909505769 1 20.45669892 3.257129343 24.99962132 0.992767976 1.098569757 0.380045024 0.075429251 314.8239501 423853.8547 0.02197088 0.029695586 1807.712425 -3.257129343 0.105801782 VDGPRS(ph)PSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDGPRSPSYGR 11 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VDGPRS(0.998)PS(0.002)YGR;VDGPRS(0.997)PS(0.003)YGR;VDGPRS(0.989)PS(0.011)YGR;VDGPRS(0.971)PS(0.029)YGR 173.06 7.65E-06 2957320000 2619770 3287310 3273140 2002260 3760800 4045700 2433710 2867090 3063820 3667900 TRUE FALSE 2723200.543 3851879.921 3358440.717 2398301.052 3121540.559 3106147.488 2242949.451 2828661.348 2953553.717 4386554.779 0.620806232 0.878110525 0.765621515 0.546739109 0.711615543 0.708106394 0.511323707 0.644848062 0.673319693 1 22.06465685 -0.852143433 5.546545929 1.000000141 0.67141031 0.492225622 0.099500952 1.80E-07 3.70E-08 0.099159088 0.023372011 0.140558323 0.852143433 -0.328589832 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDHQTGPIVWGEPGTNGQHAFYQLIHQGTK 30 0 P06744;A0A2U3TZU2;P06744-2;K7EQ48;K7ESF4 P06744;K7ESF4 GPI Glucose-6-phosphate isomerase 0 ; 310.83 1.08E-92 8073000000 1605480 1650850 2024450 1640490 2320000 2371900 2171880 1947330 2136000 1559900 FALSE TRUE 1668865.59 1934370.646 2077208.83 1964974.026 1925647.229 1821062.171 2001642.37 1921229.227 2059125.777 1865532.539 0.894578655 1.036899976 1.113466952 1.053304611 1.032223876 0.976162106 1.07296031 1.029855651 1.103773713 1 20.83115609 4.732555526 5.226656906 1.047961334 0.88854376 0.564256893 0.040136832 0.106485528 10.03856893 0.009435943 0.060765729 54020.11767 -4.732555526 -0.159417574 VDHSQNQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDHSQNQK 8 0 E7EQ69;Q9GZZ1 E7EQ69 NAA50 N-alpha-acetyltransferase 50 0 ;;; 135.83 0.00081697 200260000 387734 311969 411320 331393 470574 458270 513630 414479 436016 315857 FALSE TRUE 403042.0377 365547.249 422039.3371 396941.5463 390585.9996 351843.7376 473370.3385 408923.587 420323.8693 377743.1317 1.066973835 0.96771382 1.117265416 1.050823994 1.033998945 0.931436492 1.253154058 1.082544069 1.112724055 1 18.527046 2.252532526 24.99999808 1.11987174 1.03065638 0.227552698 0.075247757 318.4359771 569778.2009 0.024964668 0.020790822 178.8679484 -2.252532526 -0.08921536 VDIAPHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDIAPHVR 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 71.501 0.053351 0 223220 246380 254830 274550 360770 341720 274820 244510 260680 299050 FALSE TRUE 232032.898 288693.8484 261471.0791 328855.1706 299446.4443 262360.7088 253278.8903 241232.7434 251298.1777 357643.1218 0.648783337 0.80721208 0.731094947 0.919506487 0.837277235 0.733582426 0.708188903 0.674506872 0.702650666 1 18.44816117 2.701041546 21.00644004 0.733629716 0.793857519 0 0.109037846 253.7440047 142065.7867 0.033974849 0.032034447 502.3906477 -2.701041546 0.060227803 VDIDAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;;;; 267.62 1.53E-31 4678810000 3583760 2888360 3185900 2742020 3906020 4077170 4000330 3324770 3396170 2525380 FALSE TRUE 3725249.612 3384413.362 3268927.171 3284383.372 3242076.116 3130309.058 3686773.682 3280206.896 3273942.505 3020179.86 1.233452902 1.120599937 1.082361754 1.087479397 1.073471206 1.03646445 1.220713286 1.08609654 1.084022362 1 21.52620304 -4.999999993 0.014674867 3.23E-06 1.959765327 0.300972603 0.058167231 9269.561452 10.31954395 858.3285009 551.2783769 1.00E-05 4.999999993 1.959762096 VDIDAPDVEVHDPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 233.49 5.56E-24 1224480000 944780 733260 856510 684810 1039830 1089210 1049200 846030 941650 654260 FALSE TRUE 982080.6439 859191.701 878831.3542 820263.374 863080.068 836257.4846 966960.9624 834690.3517 907760.2004 782449.7204 1.255135785 1.098079121 1.123179332 1.048327263 1.103048599 1.068768335 1.235812266 1.06676548 1.160151479 1 19.57763852 -1.148171364 0.011765373 3.16E-05 2.124386464 0.208962196 0.068254921 7547.810075 16.16641168 1568.642012 1354.963321 0.071093294 1.148171364 2.124354894 VDIDTPDIDIHGPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 159.88 8.98E-09 278460000 245590 177280 203240 191590 266280 264120 299830 221470 225640 146700 FALSE TRUE 255286.0828 207726.461 208536.6014 229485.9302 221017.8207 202782.1328 276328.5411 218501.5569 217519.2605 175443.0563 1.455093683 1.184010729 1.188628412 1.308036551 1.259769554 1.155828775 1.575032646 1.245427215 1.239828267 1 17.42064332 0.774144774 2.446770575 1.000315648 1.294308198 0.343518623 0.122755413 1.128399622 10.28924225 0.113668493 0.030501494 5.944903019 -0.774144774 0.29399255 VDIDVPDVDVQGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 227.04 3.19E-19 815810000 1451910 1143270 1301060 1160900 1669070 1778180 1733830 1389950 1573570 1188750 FALSE TRUE 1509232.528 1339617.729 1334966.692 1390522.555 1385362.078 1365224.644 1597927.874 1371319.994 1516937.523 1421662.803 1.061596692 0.942289358 0.939017811 0.978095898 0.974466009 0.960301304 1.123985147 0.964588784 1.067016398 1 20.43914789 VDIIENQVMDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VDIIENQVMDFR 12 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;;; 149.23 0.00015609 446357000 324979.9 321293 359569 392070 383618 452232 521848 407121 367828 264118 FALSE TRUE 337810.3574 376472.5734 368939.6635 469620.2758 318410.7494 347207.9716 480944.1902 401664.2089 354589.9421 315866.8653 1.0694707 1.191871053 1.168022683 1.486766507 1.008053659 1.09922252 1.522616783 1.27162502 1.122593032 1 18.26895708 VDIIPGFEFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDIIPGFEFDR 11 0 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ;;; 140.16 9.01E-05 409775000 324179 321717 349152 366401 387259 418825 392602 364851 347314 293816 FALSE TRUE 336977.8372 376969.3921 358251.188 438874.0242 321432.8535 321559.2411 361828.8294 359960.7691 334814.237 351383.6198 0.959002692 1.072814357 1.019544361 1.248988284 0.91476334 0.915123025 1.029725943 1.024409645 0.952845318 1 18.42268741 VDIKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDIKDR 6 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 ; 80.18 0.059458 851490000 4092200 2803400 3732000 2852900 4990100 4614600 4485000 3653000 4083100 2555300 FALSE TRUE 4253763.216 3284862.143 3829258.986 3417195.105 4141884.584 3542929.085 4133453.981 3604037.51 3936150.029 3055962.111 1.391955483 1.074902772 1.253045308 1.118205979 1.355345529 1.159349808 1.35258679 1.179346268 1.288023178 1 21.54319523 -1.315775168 3.770371054 0.999381841 1.234899405 0.333243888 0.102071436 7052177.592 2461153.171 35449.37808 0.021117238 0.048330894 1.315775168 0.235517565 VDINAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDINAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 186.11 2.87E-14 440250000 580180 485480 551670 454370 675060 690980 672460 591090 615880 453600 FALSE TRUE 603085.9544 568857.4135 566046.9734 544243.0298 560313.5423 530510.3669 619750.8281 583167.4054 593714.5991 542474.2353 1.111731978 1.048634896 1.043454116 1.003260606 1.032885077 0.977945739 1.142452098 1.075014014 1.094456769 1 19.04919509 2.238232668 24.99999986 1.085323542 1.035544185 0.157320992 0.045977047 13.71552403 1045453.874 0.016118785 0.012664058 173.0743336 -2.238232668 -0.049779357 VDINAPDVDVQGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDINAPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;; 200.73 1.48E-15 874256000 948720 789000 866330 774470 1058360 1212640 1036260 834330 934230 735850 FALSE TRUE 986176.1982 924504.6124 888907.2715 927657.8544 878460.3452 931022.7377 955035.2334 823147.171 900607.2448 880025.7188 1.120622019 1.05054272 1.010092379 1.054125845 0.998221218 1.057949464 1.085235594 0.935367176 1.023387414 1 19.74718616 7.999999997 0.799956103 1.01546031 27.24745095 0.371875723 0.039010118 552.2638794 1.901496353 0.013622053 26255.54466 99999999.3 -7.999999997 26.23199064 VDISAPDVDVHGPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDISAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ;;; 250.95 2.00E-25 711469000 1028430 899174 969785 838053 1162910 1299060 1142160 1003302 1064276 816032 FALSE TRUE 1069033.211 1053600.14 995058.3938 1003817.382 965238.9736 997373.0024 1052634.515 989854.3778 1025972.915 975917.8465 1.095413117 1.079599214 1.019612867 1.028587996 0.989057611 1.021984592 1.078609761 1.014280435 1.051290248 1 19.89640018 4.31322413 4.636764817 1.026756363 1.091225432 0.520918477 0.023914445 0.157347042 6.188327234 0.005884816 0.017050998 20569.51869 -4.31322413 0.06446907 VDIVAINDPFIDLNYMVYMFQYDSTHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 VDIVAINDPFIDLNYMVYMFQYDSTHGK 28 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;; 302.16 9.29E-72 35312698000 14121783 14305940.6 20226239 15300929.9 22561896 22752492 24668024 19482469 21581970 15838029 FALSE TRUE 14679321.9 16762874.61 20753351.4 18327408.17 18726832.98 17468570.55 22734479.82 19221338.37 20805239.12 18941187.55 0.774994802 0.884995968 1.095673191 0.967595518 0.988683151 0.922253185 1.200266866 1.014790563 1.098412603 1 24.17502345 4.432718677 3.94013689 1.035632812 0.792469629 0.561388757 0.075501371 0.142112424 4.552034207 0.018498044 0.064060054 27084.36616 -4.432718677 -0.243163183 VDKETNTETPAPS(ph)PTVVRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDKETNTETPAPSPTVVRPK 20 2 H0YAU4;H3BLZ3;Q8IX03-2;H0YBE8;Q8IX03 H0YAU4;H0YBE8 WWC1 Protein KIBRA 1 VDKETNTET(0.001)PAPS(0.951)PT(0.048)VVRPK 84.68 0.0014376 103720000 93347 34720 53488 42470 81921 85828 99691 67931 85919 33904 TRUE FALSE 97032.41164 40682.88992 54881.94122 50870.43924 67996.09768 65895.74774 91876.95893 67020.49606 82826.79197 40546.83967 2.393094318 1.003355385 1.353544238 1.254609229 1.67697651 1.625175927 2.265946241 1.652915409 2.04274347 1 15.30730185 2.883835838 2.697843185 1.797415987 1.45851977 0.027209845 0.459099903 0.649952807 9.205022858 0.141911039 0.154155838 765.3072686 -2.883835838 -0.338896217 VDKGVVPLAGTDGETTTQGLDGLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDKGVVPLAGTDGETTTQGLDGLSER 26 1 P09972;A8MVZ9;C9J8F3;J3KSV6;J3QKP5;K7EKH5 P09972 ALDOC Fructose-bisphosphate aldolase C;Fructose-bisphosphate aldolase 0 192.18 4.29E-18 92902000 111350 102790 127090 85210 175840 171780 119680 113710 136060 126850 FALSE TRUE 115746.184 120443.3829 130402.0698 102064.2837 145950.7796 131886.6984 110299.1689 112185.9034 131163.2272 151703.8288 0.762974705 0.79393766 0.859583247 0.672786471 0.9620771 0.869369609 0.727069117 0.739506078 0.864600638 1 17.21089797 VDKGVVPLAGTNGETTTQGLDGLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDKGVVPLAGTNGETTTQGLDGLSER 26 1 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ; 337.48 2.83E-95 2149700000 810940 771230 875280 649490 1128060 988620 830180 908800 914430 870860 FALSE TRUE 842956.5374 903682.7532 898090.5159 777957.1835 936312.7641 759027.9877 765108.3223 896619.0225 881519.8429 1041488.343 0.809376833 0.867683982 0.862314515 0.74696677 0.899014156 0.72879163 0.734629751 0.86090164 0.846403945 1 19.99021526 0.70702177 1.545388672 0.99946269 0.811894538 0.49279428 0.056838861 0.871301841 3.246231966 0.053756708 0.015544128 5.093564029 -0.70702177 -0.187568152 VDKITEYLCEPLRK ddPTM_MDA-MB-175_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 82.529 0.005882 476200000 535530 404870 475500 368510 645040 617510 522620 440660 489870 398250 FALSE TRUE 556673.1379 474403.273 487891.9206 441400.1781 535396.3312 474102.661 481655.6788 434753.6735 472239.6744 476279.4625 1.168795175 0.996060738 1.024381606 0.926767188 1.124122229 0.995429571 1.011287945 0.912812136 0.99151803 1 18.86144881 2.144026389 2.555805456 0.960278647 1.036953832 0.173611355 0.067667086 0.454146264 5.931289954 0.030282766 0.019595237 139.3241457 -2.144026389 0.076675185 VDKLDASESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDKLDASESLR 11 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;;;; 172.33 1.23E-05 5671270000 5832188 4069646 5377402 4387118 6677210 6723280 6687790 5093715 5653634 3487041 FALSE TRUE 6062447.286 4768576.043 5517541.514 5254876.846 5542220.229 5161900.112 6163583.545 5025442.082 5450160.817 4170259.921 1.453733676 1.143472142 1.323068974 1.260083771 1.328986762 1.237788582 1.477985464 1.205066873 1.30691154 1 21.99170587 0.049426463 1.129485519 0.998614069 1.301327713 0.464684306 0.097833247 7.10822197 7.56464541 0.116417068 0.026074669 1.120537674 -0.049426463 0.302713644 VDKWWGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDKWWGNR 8 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 80.688 0.022618 653620000 704670 578250 665200 589110 860790 837640 896490 653390 713380 534060 FALSE TRUE 732490.9157 677559.9393 682535.6585 705634.1997 714473.2233 643110.8046 826220.7713 644632.3758 687705.5932 638698.8318 1.146848686 1.060844181 1.068634581 1.104799578 1.118638688 1.006907751 1.293599941 1.00929005 1.076729061 1 19.28477629 1.599099955 25 1.032251259 1.109412605 0.221167535 0.073150953 1.166166577 3316.213347 0.036392906 0.017248054 39.72829753 -1.599099955 0.077161345 VDKWWGNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDKWWGNRK 9 2 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 119.16 0.00049103 2205700000 1646170 1105900 1292940 1121520 2606000 1902040 1746450 1442570 1562540 1557720 FALSE TRUE 1711162.063 1295829.722 1326635.079 1343353.309 2163033.051 1460320.036 1609558.686 1423234.709 1506304.491 1862925.41 0.918534931 0.695588624 0.712124636 0.721098817 1.161094824 0.783885403 0.86399524 0.763978365 0.808569405 1 20.82913848 VDLENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDLENR 6 0 P20700;E9PBF6;A0A0D9SFE5;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 0 ;; 110.34 0.066976 1036430000 1556060 2125920 1873330 1956960 2183640 2451470 1882510 1930870 1764570 1996640 FALSE TRUE 1617494.45 2491030.223 1922150.519 2344040.847 1812465.653 1882153.245 1734953.947 1904989.846 1701063.47 2387843.38 0.677387162 1.043213405 0.804973448 0.981656028 0.759038749 0.788223072 0.726577782 0.797786765 0.712384859 1 21.18727678 3.205739732 24.99729604 0.782935893 0.883562789 0.089387474 0.118273159 339.2454714 258377.8047 0.030995859 0.037049546 1605.978519 -3.205739732 0.100626896 VDLHFIALVHVDGHLYELDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDLHFIALVHVDGHLYELDGR 21 0 A0A087WTB8;P15374;Q5TBK7 A0A087WTB8;Q5TBK7 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 0 113.54 6.90E-05 9215900 8181.1 7733.8 8805.5 10141 9413.3 8864.8 9327.3 8370 8782.3 5623.3 FALSE TRUE 8504.096145 9062.019989 9034.978564 12146.85953 7813.230628 6806.084547 8596.201854 8257.813841 8466.226739 6725.07797 1.264534952 1.347496643 1.34347566 1.806203524 1.161805211 1.012045448 1.278230809 1.227913472 1.258903878 1 12.71533528 VDLNSNGFICDYELHELFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 208.28 2.78E-16 125540000 91039 92072 97782 102310 166250 131980 122780 110810 133070 103670 FALSE TRUE 94633.29002 107884.6498 100330.2792 122546.6126 137990.8844 101329.6452 113156.1828 109324.7732 128280.8367 123982.1516 0.763281559 0.870162748 0.809231635 0.988421406 1.112989915 0.817292198 0.912681231 0.881778319 1.034671806 1 16.91977292 3.745603039 24.63004144 0.951817477 0.819819045 0.407326193 0.081780224 520.7876043 1821386.166 0.021854017 0.038343137 5566.766932 -3.745603039 -0.131998431 VDLTLLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDLTLLSPK 9 0 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VDLT(0.001)LLS(0.999)PK;VDLTLLS(1)PK 99.215 0.0057564 40780000 237758 105134 140071 114072 204098 235977 187944 149779 165641 99333 TRUE FALSE 247144.8694 123189.9467 143721.3653 136635.1011 169405.4949 181174.918 173212.4582 147771.4575 159679.6128 118795.3995 2.080424583 1.03699257 1.209822652 1.150171654 1.426027401 1.525100457 1.458073788 1.243915658 1.344156537 1 16.85811944 -3.556102609 0.261546285 3.61E-10 1.398108561 0.162087628 0.270449559 169.5224609 3.308980328 91.57613737 0.348930305 0.000277906 3.556102609 1.39810856 VDLVDENFTELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDLVDENFTELR 12 0 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ;;; 144.1 0.00013664 144559000 174548.3 182816.2 177525.1 214538.4 216445 243667.2 241158.8 201155.7 177887.5 155275.7 FALSE TRUE 181439.6017 214213.4602 182151.5499 256973.4552 179653.7562 187079.1856 222256.1431 198459.5369 171485.3636 185699.0005 0.977062888 1.153552037 0.980896771 1.383817115 0.967446005 1.007432378 1.196862355 1.068716236 0.923458733 1 17.50260652 1.350914656 5.786012876 0.96390616 1.09859766 0.153771893 0.122997665 0.351751953 15.44223371 0.081522681 0.029060011 22.43441017 -1.350914656 0.134691501 VDLVDENFTELRGEIAGPPDTPYEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDLVDENFTELRGEIAGPPDTPYEGGR 27 1 D6RDM7;P61086;P61086-3 D6RDM7 UBE2K Ubiquitin-conjugating enzyme E2 K 0 ;; 192.18 3.61E-18 434108000 144116 142106 149172 131406 192533 201104 158101 155762 161293 150563 FALSE TRUE 149805.811 166511.6001 153059.5449 157397.7146 159806.3094 154400.6438 145708.6305 153674.2652 155488.0964 180062.9371 0.831963609 0.924741108 0.85003359 0.874126109 0.887502514 0.857481535 0.809209451 0.853447509 0.863520827 1 17.45814173 0.906450765 18.32019787 1 0.860892794 0.666721669 0.029415748 2389.718504 467993.062 0.028488138 0.007122035 8.062147972 -0.906450765 -0.139107207 VDNDENEHQLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VDNDENEHQLSLR 13 0 P06748;P06748-3;P06748-2;E5RGW4 P06748 NPM1 Nucleophosmin 0 ;;;;;;; 276.31 3.14E-32 54377770000 19929170 20240570 22094720 20951010 23991390 27339700 26119230 22561110 21369390 16543770 FALSE TRUE 20715989.02 23716730.45 22670526.55 25095057.25 19913342.1 20990469.01 24071936.5 22258715.22 20600309.83 19785204.98 1.047044448 1.198710373 1.145832281 1.268374893 1.006476411 1.06091744 1.216663488 1.125018176 1.041197695 1 24.23791868 3.230971567 24.99983789 1.093149008 1.16603062 0.218747302 0.078934271 319.4668324 1052387.044 0.023037947 0.028039484 1702.047072 -3.230971567 0.072881612 VDNEFDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDNEFDQR 8 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542;A0A2R8Y6I5 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 101.64 0.012211 1206210000 1239860 1366050 1474590 1537390 1816470 1963590 1462680 1459380 1479640 1496220 FALSE TRUE 1288810.63 1600658.461 1513019.027 1841481.153 1507707.078 1507575.981 1348031.32 1439819.398 1426388.045 1789375.662 0.720257159 0.894534611 0.84555695 1.02911937 0.842588345 0.842515081 0.753352886 0.804649034 0.797142867 1 20.77102487 2.800042428 3.704188409 0.817959313 0.87749336 0 0.093869749 0.64695227 17.83772323 0.029143515 0.030420274 631.0189889 -2.800042428 0.059534047 VDNLTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDNLTYR 7 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 133.6 0.0075747 537100000 370630 351850 359830 382280 438680 500240 453840 424760 371940 363830 FALSE TRUE 385262.7586 412277.5005 369207.4654 457893.843 364113.3303 384066.8412 418266.8349 419066.787 358553.9521 435115.5226 0.885426372 0.947512739 0.848527451 1.052350053 0.836819905 0.882677867 0.961277668 0.96311615 0.824043118 1 18.73103896 -1.210719363 4.160695177 1.000043007 0.917301357 0.12978434 0.067307357 2.51E-05 4.76E-06 0.060852297 0.014335571 0.061557452 1.210719363 -0.08274165 VDNLTYRT(ph)SPDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.277)YRT(0.597)S(0.1)PDT(0.025)LR 97.235 0.019457 823530000 438830 519500 555050 407590 681510 609570 435610 531280 617650 588160 TRUE FALSE 456155.3473 608720.0839 569515.059 488210.0855 565667.1736 468006.6056 401465.7499 524159.0606 595420.8972 703398.691 0.648501843 0.865398375 0.809661812 0.694073065 0.804191394 0.665350407 0.570751346 0.745180603 0.846491335 1 19.42398312 0.987395768 2.798487247 0.99839746 0.725564034 0.524178116 0.082237785 0.212817319 3.939201151 0.081787464 0.021745584 9.71394786 -0.987395768 -0.272833426 VDNLTYRT(ph)SPDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.807)S(0.193)PDTLRR;VDNLT(0.002)YRT(0.542)S(0.022)PDT(0.434)LRR 138.82 0.000393 1631100000 717320 1059780 851180 540550 1328770 1103920 544100 883090 981060 1434680 TRUE FALSE 745640.3475 1241788.971 873362.4501 647469.1766 1102906.15 847551.3101 501452.0203 871253.623 945751.8422 1715778.077 0.434578549 0.723746845 0.509018306 0.377361843 0.642802332 0.493974903 0.292259254 0.507789227 0.551208723 1 20.71043153 0.706041787 3.038648712 0.999969822 0.497450503 0.627648221 0.115351743 1.748058565 17.31087605 0.111011834 0.02899363 5.082083393 -0.706041787 -0.502519319 VDNLTYRTS(ph)PDTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDNLTYRTSPDTLR 14 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLTYRT(0.339)S(0.661)PDT(0.001)LR;VDNLTYRT(0.146)S(0.691)PDT(0.164)LR;VDNLTYRT(0.039)S(0.961)PDT(0.001)LR;VDNLTYRT(0.341)S(0.659)PDTLR;VDNLTYRT(0.197)S(0.803)PDTLR;VDNLTYRT(0.247)S(0.734)PDT(0.018)LR 207.43 5.73E-09 20942200000 3760070 4433630 4610340 2947410 5209730 4906640 3358300 4126360 4365880 4724370 TRUE FALSE 3908520.467 5195071.464 4730489.248 3530398.901 4324181.955 3767147.221 3095067.671 4071052.894 4208752.832 5650019.848 0.691771104 0.919478445 0.837251793 0.624847168 0.76533925 0.666749378 0.547797663 0.720537804 0.744909389 1 22.4298245 3.76040113 24.01733597 0.702525829 0.826498282 0.084389008 0.123581677 823.6755576 905765.5472 0.02965702 0.053395776 5759.716805 -3.76040113 0.123972453 VDNLTYRTS(ph)PDTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDNLTYRTSPDTLRR 15 2 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 1 VDNLT(0.001)YRT(0.198)S(0.8)PDT(0.001)LRR 104.45 0.001097 840960000 303190 414940 348230 243390 589650 474320 195830 378700 421630 592170 TRUE FALSE 315160.1753 486202.7172 357305.1599 291531.8156 489421.5036 364166.3684 180480.3329 373624.1459 406455.6187 708194.3737 0.445019315 0.68653852 0.504529792 0.411655086 0.691083581 0.514218104 0.254845759 0.527572881 0.57393229 1 19.43378586 0.73218865 2.771462753 0.999904036 0.50371095 0.604500859 0.119579645 1.169129485 11.19665423 0.115294971 0.030425008 5.397450269 -0.73218865 -0.496193086 ASSHS(ph)SQTQGGGSVTKK ddPTM_MDA-MB-175_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(0.268)S(0.268)HS(0.459)S(0.006)QTQGGGSVTKK 134.32 8.17E-06 431910000 226930 449650 478130 457600 658460 787480 555780 663130 649340 538650 TRUE FALSE 235889.3716 526873.8897 490590.4606 548111.9142 546535.2044 604599.7044 512216.5113 654241.827 625970.3802 644188.1544 0.366180859 0.817888199 0.761563927 0.850856866 0.848409274 0.938545206 0.795134943 1.015606733 0.971719793 1 19.29712261 4.958484187 1.0188044 0.917115802 9.32E-52 0.794730254 0.080631925 1.235727762 0.770650787 0.024182427 1.369506249 90883.32074 -4.958484187 -0.917115802 down VDPSLMEDS(ph)DDGPSLPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDPSLMEDSDDGPSLPTK 18 0 O15258;Q5T092;A0A0A0MR06;Q5T091 O15258 RER1 Protein RER1 1 VDPSLMEDS(1)DDGPSLPTK;VDPSLMEDS(1)DDGPSLPTK 219.95 7.39E-19 74931000 165654 122214 140874 133397 160390 174222 175790 142863 150849 92587 TRUE FALSE 172194.1478 143203.3038 144545.2922 159782.5284 133126.9651 133761.5809 162011.1205 140948.1552 145419.974 110727.65 1.555114264 1.293293083 1.305412805 1.443022845 1.202291976 1.208023298 1.463149633 1.272926457 1.313312203 1 16.756656 -4.088672014 0.20482264 1.38E-15 1.389535383 0.506514756 0.104391244 80.47205744 1.12037794 33.60205313 0.236406688 8.15E-05 4.088672014 1.389535383 VDQDSALHNDLQILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDQDSALHNDLQILK 15 0 Q7Z7E8;Q7Z7E8-2 Q7Z7E8 UBE2Q1 Ubiquitin-conjugating enzyme E2 Q1 0 112.5 0.00075881 102530000 103650 99422 126510 111280 145400 130270 139620 106940 125050 106230 FALSE TRUE 107742.182 116496.9551 129806.9545 133290.8519 120684.9599 100016.7668 128676.2196 105506.6442 120549.4749 127043.7346 0.84807159 0.91698308 1.021750147 1.049172966 0.949948144 0.787262489 1.012849787 0.83047499 0.9488817 1 16.9549657 2.980751843 24.86237744 0.903553986 0.965361738 0.047367369 0.082745216 1622.008919 2095112.906 0.024782985 0.026676806 956.647285 -2.980751843 0.061807752 VDQICHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VDQICHK 7 0 Q9UBE0;M0QX65;B3KNJ4;Q9UBE0-2;Q9UBE0-3;A0A590UK93;A0A590UKC5;M0QYM8;M0R054;M0R286;M0QYP2 Q9UBE0 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 ;;; 94.302 0.02039 632390000 1125360 886920 1085760 916100 1376310 1327310 1372130 1100190 1145730 883710 FALSE TRUE 1169790.082 1039241.611 1114055.798 1097301.846 1142365.318 1019062.368 1264578.865 1085443.753 1104495.401 1056856.055 1.106858476 0.983333166 1.054122548 1.038269915 1.080909091 0.964239513 1.196547874 1.027049755 1.045076476 1 20.01134746 VDRDYVLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDRDYVLK 8 1 Q9BUP3-3;Q9BUP3 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 ; 123.86 0.0012125 963160000 359630 379030 401660 344200 556050 521630 448810 389000 440590 357000 FALSE TRUE 373828.4701 444125.4541 412127.5896 412281.7327 461532.8196 400489.3379 413631.0995 383786.0913 424733.252 426947.3148 0.875584544 1.040234799 0.965289101 0.965650136 1.081006493 0.938029879 0.968810636 0.898907378 0.994814201 1 18.70369853 -0.358949188 7.9069129 1.000002302 0.968768786 0.024025476 0.057370457 0 0 0.053860171 0.012694964 0.437573298 0.358949188 -0.031233516 VDS(ph)EGDFS(ph)ENDDAAGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 2 VDS(1)EGDFS(1)ENDDAAGDFR;VDS(1)EGDFS(1)ENDDAAGDFR 291.03 5.24E-49 428700000 424680 334280 384510 363320 466430 678880 534180 393790 403500 239550 TRUE FALSE 441446.6943 391689.9897 394530.6465 435183.6116 387146.3952 521220.4085 492309.5758 388511.8892 388978.1138 286485.236 1.540905564 1.367225743 1.377141286 1.519043765 1.351365957 1.819362197 1.718446586 1.356132325 1.35775972 1 18.12810127 0.897763646 1.635096143 1.004961865 1.513427036 0.523324033 0.148459476 0.41498363 2.209275917 0.14868027 0.042887182 7.902484381 -0.897763646 0.508465171 VDS(ph)LVSLSEEDLESDQR ddPTM_MDA-MB-175_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 VDS(1)LVSLSEEDLESDQR 107.34 0.0014131 0 5367.4 6453.7 4675.7 4027.7 8207 10945 6057.6 4906 5927.8 5947.1 TRUE FALSE 5579.309097 7562.072772 4797.552583 4824.367039 6811.977071 8403.189623 5582.789483 4840.243095 5714.459636 7112.320381 0.784456942 1.063235677 0.674541124 0.678311266 0.957771403 1.181497623 0.784946288 0.680543456 0.803459255 1 12.7961046 -2.528592473 1.987073013 2.791220388 0.840567355 0.073947429 0.163300316 6574168.706 310736.4342 53256828.88 0.043171449 0.002960789 2.528592473 -1.950653033 VDS(ph)PSHGLVTSSLCIPSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.933)PS(0.067)HGLVTSSLCIPSPAR;VDS(1)PSHGLVTSSLCIPSPAR 312.63 1.64E-66 506070000 308740 304640 348570 311540 366370 470210 409200 326250 353600 249620 TRUE FALSE 320929.2936 356959.5502 357654.0206 373161.6821 304094.5583 361010.8536 377125.8348 321877.1524 340874.0051 298528.2597 1.075038236 1.195731187 1.1980575 1.250004547 1.018645801 1.209302107 1.263283533 1.078213341 1.141848364 1 18.18750798 0.778153091 1.101113322 1.001764296 1.169273098 0.294141044 0.075546807 0.9939154 2.215171299 0.069824585 0.022017617 6.000025425 -0.778153091 0.167508802 VDS(ph)PTVNTTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDSPTVNTTLR 11 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 VDS(0.708)PT(0.292)VNTTLR;VDS(0.982)PT(0.018)VNTTLR 140.53 4.04E-05 236630000 327120 261160 311110 279450 389290 448380 359350 283070 295800 232420 TRUE FALSE 340034.9502 306012.1985 319217.7822 334724.3759 323118.6249 344250.5403 331183.208 279275.9097 285154.2158 277958.2491 1.223331027 1.100928645 1.14843788 1.204225372 1.162471796 1.238497297 1.191485445 1.004740498 1.02588866 1 18.08450867 1.723423534 5.974019948 1.011876577 1.179446876 0.811978004 0.037662365 0.06089894 5.521311124 0.019692413 0.01010922 52.89608546 -1.723423534 0.167570299 VDS(ph)PTVTTTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VDSPTVTTTLK 11 0 Q07866-6;Q07866-4;Q07866-9;G3V5R9;Q07866-7;G3V3H3;Q07866-5;Q07866-10;G3V2E7;F8W6L3;Q07866-8;Q07866;Q07866-3;Q07866-2;E7EVH7;H0YG16;G5E9S8;H0YJU9;H0YJT3;H0YJL0 Q07866-6 KLC1 Kinesin light chain 1 1 VDS(1)PTVTTTLK;VDS(0.894)PT(0.106)VTTTLK;VDS(0.951)PT(0.049)VTTTLK 259.47 1.40E-20 467149000 1478920 784520 1031390 841360 1339870 1494760 1558880 1070720 1100640 532060 TRUE FALSE 1537308.904 919255.2073 1058268.871 1007778.497 1112119.376 1147624.643 1436690.912 1056368.75 1061028.181 636306.9701 2.41598627 1.444672541 1.663142037 1.583792956 1.747771796 1.803570756 2.257858203 1.660155867 1.667478483 1 19.2793634 0.710726612 1.910175485 1.001004833 1.80887759 0.432112269 0.282324969 1.112778976 5.903378248 0.259904389 0.072311255 5.137201631 -0.710726612 0.807872757 VDS(ph)TTCLFPVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.974)T(0.025)T(0.001)CLFPVEEK;VDS(0.96)T(0.039)T(0.001)CLFPVEEK;VDS(0.999)T(0.001)TCLFPVEEK;VDS(0.995)T(0.005)TCLFPVEEK;VDS(0.9)T(0.1)TCLFPVEEK;VDS(0.495)T(0.495)T(0.01)CLFPVEEK;VDS(0.486)T(0.486)T(0.029)CLFPVEEK;VDS(0.922)T(0.065)T(0.013)CLFPVEEK 327.94 2.53E-62 8069977000 10392130 5166318 7756000 5698507 12902870 11337680 9013770 7343130 8120060 4147326 TRUE FALSE 10802419.32 6053592.928 7958127.732 6825654.676 10709644.77 8704675.644 8307247.154 7244707.353 7827820.627 4959915.124 2.177944389 1.22050333 1.604488692 1.376163605 2.159239523 1.75500496 1.674876877 1.460651477 1.578216649 1 22.241884 0.582195038 0.860252333 1.000319492 1.685937296 0.341840812 0.286876598 1.582058516 1.923284323 0.275132669 0.091267203 3.82115837 -0.582195038 0.685617804 VDSDKTQASESFS(ph)SDEEADLELQALTTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSDKTQASESFSSDEEADLELQALTTSR 29 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 1 VDSDKTQASESFS(0.575)S(0.425)DEEADLELQALTTSR 169.27 1.90E-12 45033000 54588 48782 67521 43140 84546 82168 70510 60878 71071 48410 TRUE FALSE 56743.17639 57159.92903 69280.65273 51672.96324 70174.90112 63085.72727 64983.24196 60062.02999 68513.16859 57895.01263 0.980104741 0.987303162 1.196660119 0.89252875 1.212106154 1.089657371 1.122432469 1.037430121 1.183403638 1 15.82115145 4.425901733 24.91613873 1.089316869 0.981903778 0.178397039 0.09270782 133.16336 64777.98365 0.020533847 0.056234283 26662.55307 -4.425901733 -0.10741309 VDSEGDFS(ph)ENDDAAGDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDSEGDFSENDDAAGDFR 18 0 O43823;M0QYL4 O43823 AKAP8 A-kinase anchor protein 8 1 VDSEGDFS(1)ENDDAAGDFR;VDSEGDFS(1)ENDDAAGDFR 242.22 1.16E-20 136790000 127742 123627 126551 119271 120247 153761 152092 120811 126131 106912 TRUE FALSE 132785.3528 144858.9756 129849.023 142862.4478 99807.45789 118052.338 140170.6316 119191.7262 121591.5699 127859.3594 1.038526654 1.132955586 1.015561345 1.117340556 0.780603456 0.923298369 1.09628761 0.93220963 0.950979033 1 16.96419825 VDSGTEKPGLVAPES(ph)PVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSGTEKPGLVAPESPVRK 19 2 O15021-2;H7C1I9;O15021-3;O15021-6;O15021 O15021-2 MAST4 Microtubule-associated serine/threonine-protein kinase 4 1 VDSGTEKPGLVAPES(1)PVRK 56.461 0.049484 130190000 105790 120370 152150 96101 154670 175830 143620 145290 141980 109450 TRUE FALSE 109966.6709 141042.6112 156115.154 115109.491 128379.2486 134996.1472 132362.6891 143342.6252 136870.1675 130894.632 0.840115972 1.077527849 1.192678047 0.879405742 0.980783144 1.03133448 1.011215564 1.095099341 1.045651495 1 16.99804641 1.88456741 9.59768407 1.056741712 1.00744826 0.040309397 0.094716528 1.28580924 99.61396476 0.040065024 0.025393313 76.65975197 -1.88456741 -0.049293452 VDSIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSIDDR 7 0 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 81.784 0.090384 0 670740 460180 521680 427470 710260 862840 664000 525310 586980 403340 FALSE TRUE 697221.3331 539212.3353 535275.4094 512022.2901 589530.2589 662458.4865 611953.945 518269.0787 565854.7045 482366.7506 1.44541748 1.117847229 1.109685543 1.061479237 1.222161889 1.373350227 1.268648687 1.074429525 1.173079827 1 18.87977094 1.039480757 1.189485495 1.010562848 1.211726705 0.228817279 0.119024196 0.781591112 2.296175154 0.115920837 0.036487803 10.95168028 -1.039480757 0.201163857 VDSPDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSPDVKR 8 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;K7ERA4;K7EPS6 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 79.906 0.043011 72125000 36947 30788 31374 29194 44945 42352 38607 35369 31262 29143 FALSE TRUE 38405.69609 36075.5995 32191.63221 34968.48606 37305.26495 32516.38985 35580.88246 34894.93641 30136.88673 34853.01287 1.101933317 1.035078363 0.923639868 1.003313148 1.070359831 0.93295779 1.020883979 1.001202867 0.864685267 1 15.08899576 4.51169311 4.526516848 0.982682839 1.091958562 0.332617943 0.05507161 0.232959229 10.94858734 0.012981429 0.053027664 32485.76587 -4.51169311 0.109275724 VDSPS(ph)HGLVTSSLCIPSPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSPSHGLVTSSLCIPSPAR 20 0 Q9UER7-3;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 VDS(0.347)PS(0.499)HGLVT(0.111)S(0.021)S(0.021)LCIPSPAR 84.829 0.0028679 79549000 27076 28285 31268 33422 39049 40209 34884 37079 28251 31665 TRUE FALSE 28144.98139 33142.72872 32082.86977 40032.77185 32411.46493 30871.06912 32149.70093 36582.01665 27234.25203 37869.15049 0.743216603 0.875190711 0.847203313 1.05713414 0.855880433 0.815203635 0.848968105 0.966011019 0.719167229 1 15.20873544 4.848401157 2.183779849 0.891165861 0.673717601 0.180463168 0.09235418 1.67386878 7.005874347 0.022361114 0.7842649 70534.42935 -4.848401157 -0.21744826 VDST(ph)TCLFPVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.27)T(0.688)T(0.042)CLFPVEEK 313.83 1.25E-49 4546200000 843670 432700 664330 465340 1082700 933970 819940 673670 707550 362290 TRUE FALSE 876978.7431 507012.8591 681642.9856 557382.8631 898663.0407 717069.622 755670.9603 664640.5556 682085.4137 433273.789 2.024075227 1.170190471 1.573238453 1.286444916 2.074122791 1.655003465 1.744095718 1.533996684 1.574259581 1 18.72491944 0.370399413 1.372725441 0.999854959 1.623111399 0.334959277 0.265997902 4.443773649 8.532563409 0.243325732 0.07123918 2.346385753 -0.370399413 0.62325644 VDSTT(ph)CLFPVEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDSTTCLFPVEEK 13 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 1 VDS(0.179)T(0.179)T(0.642)CLFPVEEK;VDS(0.007)T(0.282)T(0.712)CLFPVEEK 322.02 4.40E-50 2013130000 1398060 701490 1049990 786590 1716940 1454420 1241240 977490 1093710 582030 TRUE FALSE 1453256.488 821965.4507 1077353.602 942175.1543 1425095.152 1116652.997 1143948.365 964388.3454 1054347.591 696067.6349 2.08780931 1.18087009 1.547771435 1.353568399 2.047351551 1.604230596 1.643444269 1.385480803 1.514720033 1 19.40886797 0.620807019 0.832343569 1.0006644 1.615296398 0.327750221 0.265947855 1.484058725 1.771138543 0.251879573 0.085031488 4.176447424 -0.620807019 0.614631998 VDTFPQPLAAPQCHTLLAPEMEDNEMS(ph)CSP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDTFPQPLAAPQCHTLLAPEMEDNEMSCSP 30 0 B7Z4K4;Q9UET6-2;Q9UET6 B7Z4K4 FTSJ1 Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase 1 VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.581)CS(0.419)P;VDTFPQPLAAPQCHTLLAPEMEDNEMS(0.5)CS(0.5)P 78.286 0.0021369 58742000 76343 95882 87916 90716 105461 118782 78698 90919 103218 105864 TRUE FALSE 79357.08059 112348.9876 90207.16318 108659.354 87534.77689 91196.68066 72529.44512 89700.37952 99503.20434 126606.0239 0.626803355 0.887390538 0.712502932 0.858247899 0.691395039 0.720318653 0.572875151 0.708500091 0.785927883 1 16.94998652 0.863574651 3.807583223 0.999929469 0.723346206 0.469588026 0.088591762 0.646569671 16.41747297 0.084714911 0.021725561 7.304233548 -0.863574651 -0.276583263 VDTFPQPLAAPQCHTLLAPEMEDNEMSCS(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDTFPQPLAAPQCHTLLAPEMEDNEMSCSP 30 0 B7Z4K4;Q9UET6-2;Q9UET6 B7Z4K4 FTSJ1 Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase 1 VDTFPQPLAAPQCHTLLAPEMEDNEMSCS(1)P;VDTFPQPLAAPQCHTLLAPEMEDNEMSCS(1)P 249.46 1.70E-46 148426000 120100 162564 147685 166115 194087 236020 151480 175384 172396 187396 TRUE FALSE 124841.6407 190483.1024 151533.7924 198972.0512 161096.1611 181207.9319 139606.6018 173033.2644 166191.5016 224112.6583 0.557048592 0.849943523 0.676150083 0.887821566 0.718817769 0.808557327 0.622930462 0.77208162 0.741553391 1 17.77386461 0.121156987 1.948835579 1.00001789 0.741527886 0.40392074 0.095640506 35.09032739 75.59505095 0.083150748 0.022754105 1.321773338 -0.121156987 -0.258490004 VDTPHYPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 164.72 0.00032843 831360000 1351410 1443480 1423380 1463660 1810760 2015670 1653990 1554850 1531190 1438730 FALSE TRUE 1404764.71 1691386.461 1460474.452 1753167.579 1502967.662 1547561.19 1524345.942 1534009.779 1476082.771 1720621.597 0.816428617 0.983008968 0.8488063 1.018915247 0.87350273 0.899419833 0.885927472 0.891543952 0.857877626 1 20.71449842 VDVADQAQDKDRDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDVADQAQDKDRDDR 15 2 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ;;;;; 242.19 3.65E-18 7457410000 9024870 5088450 7046500 5906560 9083600 9195880 10063750 7141710 7618530 4222810 FALSE TRUE 9381178.836 5962351.705 7230137.579 7074859.939 7539572.917 7060276.235 9274926.978 7045987.059 7344340.593 5050188.769 1.857589739 1.180619572 1.431656896 1.400909998 1.49292893 1.398022244 1.836550553 1.39519281 1.454270509 1 22.26790588 0.541375435 1.960501516 1.000133699 1.490798225 0.368837707 0.1947079 3.533497633 13.87077715 0.174791359 0.048263544 3.478367263 -0.541375435 0.490664525 VDVEVPDVS(ph)LEGPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVEVPDVS(1)LEGPEGK 115.31 0.00054063 18378000 97810 70234 79301 72580 107160 118340 113590 80995 97240 52113 TRUE FALSE 101671.6143 82296.14316 81367.64921 86936.10737 88944.98148 90857.32846 104686.519 79909.39451 93740.35139 62323.54459 1.631351602 1.320466345 1.305568381 1.394915966 1.427148954 1.457833136 1.679726654 1.282170246 1.504092105 1 15.92748967 -1.148844463 3.562425504 0.999618141 1.434465793 0.527354382 0.125989224 20618678.75 37258415.06 97645.45808 0.029229883 0.070983194 1.148844463 0.434847652 VDVFREDLCTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VDVFREDLCTK 11 1 Q06323;Q06323-3;Q06323-2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;;;;; 204.48 3.01E-08 4291067000 6278820 5102303 6265366 4292644 8578160 7651890 5657923 6032570 6722430 5387698 FALSE TRUE 6526712.662 5978583.85 6428646.585 5141716.171 7120047.427 5874854.513 5214440.211 5951713.266 6480491.057 6443314.269 1.0129434 0.92787401 0.997723581 0.797992455 1.105028737 0.911775255 0.809279199 0.923703706 1.005769824 1 22.61937153 VDVGKDQEFTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDVGKDQEFTVK 12 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 132.86 0.00023429 0 210160 111170 168680 101600 234530 200680 217620 178290 177240 117200 FALSE TRUE 218457.2791 130262.5827 173075.9394 121696.1768 194664.6744 154075.1113 200562.3758 175900.3142 170861.167 140163.0961 1.558593419 0.929364336 1.234818181 0.868246922 1.388843996 1.099255907 1.430921415 1.254968812 1.219016787 1 17.09674702 VDVKS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDVKSPK 7 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VDVKS(1)PK;VDVKS(1)PK 74.162 0.028421 275680000 1024770 273750 436150 292870 634240 819780 751450 457040 518240 191670 TRUE FALSE 1065228.711 320764.433 447516.4273 350798.8119 526432.1113 629398.5189 692549.3855 450914.1264 499588.6436 229224.0668 4.647106763 1.399348845 1.952309954 1.530375134 2.296583072 2.745778521 3.021276933 1.967132565 2.179477272 1 17.806399 0.65130115 1.397954773 1.003800146 2.391131062 0.19555971 0.876988693 2.106925916 6.113628923 0.799402449 0.23559728 4.480238664 -0.65130115 1.387330916 VDVNAPDVQAPDWHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDVNAPDVQAPDWHLK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 193.9 3.00E-10 129340000 123930 117980 132820 117880 136560 155540 146380 131430 150290 110230 FALSE TRUE 128822.8521 138242.1472 136281.3983 141196.3122 113347.58 119418.1922 134906.3531 129668.3958 144881.0923 131827.458 0.977208042 1.048659735 1.033786135 1.071069065 0.859817687 0.905867367 1.023355492 0.98362206 1.099020602 1 17.00829137 -0.895269903 5.718165887 1.000000001 0.997791859 0 0.069472942 1.02E-09 1.79E-10 0.068639882 0.016178567 0.127271188 0.895269903 -0.002208142 VDVRPLPAS(ph)PARPCPSPGPAAASSPARPPGLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDVRPLPASPARPCPSPGPAAASSPARPPGLQR 33 3 Q9BQ89;V9GZ26 Q9BQ89 FAM110A Protein FAM110A 1 VDVRPLPAS(0.993)PARPCPS(0.007)PGPAAASSPARPPGLQR 147.12 1.66E-09 658430000 100650 86206 87843 85511 98894 128700 104010 106750 88281 84534 TRUE FALSE 104623.7397 101011.2099 90132.26074 102424.8206 82084.0332 98811.37547 95857.42442 105319.1909 85103.78405 101096.8188 1.034886567 0.999153199 0.891543985 1.01313594 0.811934878 0.977393519 0.948174488 1.041765627 0.841804768 1 16.62537808 4.463303276 21.05254321 0.946784193 1.025953349 0.162056878 0.070378344 53.55616341 81597.29518 0.01649809 0.045296945 29060.51297 -4.463303276 0.079169156 VDVS(ph)CEPLEGVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDVSCEPLEGVEK 13 0 Q12888;Q12888-2;A6NNK5;Q12888-3;C9JXV0;H7C3N7 Q12888 TP53BP1 Tumor suppressor p53-binding protein 1 1 VDVS(1)CEPLEGVEK 119.32 0.00021898 0 38613 29463 30863 28086 40072 37717 30748 31537 34789 30416 TRUE FALSE 40137.47106 34523.04106 31667.31513 33641.32697 33260.57575 28957.79836 28337.89142 31114.2981 33536.95069 36375.43285 1.1034225 0.949075746 0.870568751 0.924836472 0.914369209 0.796081203 0.779039291 0.855365714 0.921967055 1 15.1506768 VDVSAPDVEAHGPEWNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDVSAPDVEAHGPEWNLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 198.96 1.68E-15 274590000 470470 381070 438340 361910 578000 581320 515060 426840 498670 391290 FALSE TRUE 489044.5189 446515.8082 449763.5005 433494.7178 479751.7665 446317.24 474688.2513 421118.908 480722.9641 467955.7838 1.045065658 0.954183758 0.961123927 0.926358286 1.025207473 0.953759427 1.014386974 0.899911749 1.027282877 1 18.83601269 4.7453389 23.9676783 0.968366245 1.045065721 0.206450735 0.040912513 626.6870649 2215826.928 0.009115597 0.088475304 55633.82244 -4.7453389 0.076699476 VDWDKAWEITK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDWDKAWEITK 11 1 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 73.624 0.028955 0 147170 97209 118530 90037 164630 158880 132330 94421 135400 83967 FALSE TRUE 152980.3852 113903.8896 121618.9892 107846.0499 136646.2514 121982.5278 121957.6288 93155.44094 130526.9804 100418.726 1.523424876 1.134289331 1.211118623 1.073963534 1.360764639 1.214738851 1.214490899 0.927670014 1.29982709 1 16.6156688 4.740685654 24.45147581 1.156237817 1.523425044 0.432428311 0.124972433 134.335919 1545569.61 0.029912583 0.197142352 55040.9162 -4.740685654 0.367187226 VDYIMQLPVPMDAALNKEELLEYEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VDYIMQLPVPMDAALNKEELLEYEEK 26 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 184.06 1.49E-17 201730000 160130 74078 121770 75337 166340 156250 160860 125120 143680 67291 FALSE TRUE 166452.056 86800.32025 124943.4262 90238.43374 138065.5862 119963.3055 148251.3729 123442.9711 138508.9849 80475.38309 2.068359909 1.078594682 1.552567027 1.121317231 1.715625088 1.490683249 1.842195305 1.53392213 1.721134831 1 16.29625992 VDYKADEWLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VDYKADEWLMK 11 1 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ; 129.37 0.00022476 1856470000 2244230 1546640 2220390 1150930 3486000 2460600 1907770 1954850 2436500 1882340 FALSE TRUE 2332833.933 1812263.389 2278255.187 1378580.519 2893450.965 1889162.941 1758234.002 1928648.433 2348810.841 2251148.483 1.036286123 0.805039473 1.012041278 0.612389866 1.285322131 0.839199615 0.781038663 0.85673977 1.043383348 1 21.10222979 4.778913573 21.47006086 0.904935981 1.03628847 0.039207483 0.173760539 11483.83685 6109245.268 0.038738079 8.655987912 60105.41128 -4.778913573 0.131352489 VEADIPGHGQEVLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEADIPGHGQEVLIR 15 0 B0QYF8;P02144;F2Z2F1;F2Z337 B0QYF8 MB Myoglobin 0 ;;; 197.14 8.57E-09 2343730000 2545880 3522960 3440180 3214360 3649270 3890890 3129710 3079830 2709710 3710360 FALSE TRUE 2646393.308 4128000.975 3529833.917 3850150.814 3028968.389 2987289.765 2884395.152 3038549.916 2612188.066 4437334.003 0.596392633 0.930288541 0.795485288 0.867672078 0.682609961 0.673217243 0.650028857 0.684769259 0.588684121 1 22.08126172 3.221185019 24.47787132 0.690823238 0.806806387 0.073857751 0.130941031 330.7108732 465887.5382 0.034786133 0.041675915 1664.12145 -3.221185019 0.115983149 VEADRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEADRPGK 8 1 P38159;P38159-2;H3BT71;H3BR27;P38159-3;H3BNC1;O75526;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA-binding motif protein, X-linked-like-2;RNA binding motif protein, X-linked-like-1" 0 ; 108.74 0.0034219 279270000 998630 842950 966970 745040 1032990 1143130 1029670 997730 1024980 693740 FALSE TRUE 1038056.684 987720.1053 992170.0326 892406.6883 857402.7288 877655.3818 948961.7749 984357.0613 988091.17 829665.0705 1.251175589 1.190504627 1.195868149 1.075622827 1.033432356 1.057842993 1.143788992 1.186451131 1.190951873 1 19.66216952 3.863445781 4.779482858 1.10934361 1.214659281 0.417857706 0.061085329 0.270307998 9.327848308 0.017570036 0.032843606 7302.066456 -3.863445781 0.105315671 VEAEAGGSGART(ph)PPLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VEAEAGGSGARTPPLSR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 VEAEAGGSGART(1)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.002)GART(0.998)PPLSR;VEAEAGGSGART(1)PPLSR;VEAEAGGS(0.005)GART(0.992)PPLS(0.003)R 192.64 2.83E-10 8984770000 472133 565615 530634 479799 622810 730973 503195 539170 564258 663548 TRUE FALSE 490773.1754 662754.9764 544462.758 574701.8101 516944.9787 561215.5988 463753.261 531943.3081 543950.4648 793557.5262 0.618446879 0.835169417 0.686103704 0.724209388 0.651427227 0.707214764 0.584397786 0.670327343 0.685458139 1 19.59797528 0.856035911 17.54868613 1 0.684526125 0.688462247 0.063619745 15171.88045 1849407.826 0.060334004 0.015083501 7.17853646 -0.856035911 -0.315473875 VEAFEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEAFEHR 7 0 P42285 P42285 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 147.34 0.0021584 66212000 165750 225430 202350 221100 204920 247540 203330 207970 186230 199220 FALSE TRUE 172293.938 264145.8489 207623.4072 264832.9201 170087.7716 190052.5865 187392.4633 205182.5023 179527.6187 238253.3447 0.723154331 1.108676351 0.871439633 1.111560135 0.713894581 0.797691158 0.786526055 0.861194635 0.753515628 1 17.86213694 3.225049267 24.99966301 0.812224245 0.958900561 0.212389206 0.126731365 309.9706685 573528.8504 0.033519198 0.040273276 1678.994475 -3.225049267 0.146676317 VEAKEES(ph)EES(ph)DEDMGFGLFD ddPTM_MDA-MB-175_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 93.633 0.00097257 18300000 120697 60036 79362 57963 123376 137526 98274 84290 93273 51440 TRUE FALSE 125462.2108 70346.71598 81430.23892 69427.9084 102404.5916 105587.6707 90571.02709 83160.23042 89916.12295 61518.68312 2.039416392 1.143501655 1.323666808 1.128566232 1.664609618 1.716351283 1.472252371 1.351788208 1.461606757 1 15.908737 0.109780641 0.947572073 0.995733404 1.466769769 0.230946972 0.261103225 7.939607736 7.084591894 0.346967546 0.079548132 1.287599029 -0.109780641 0.471036365 VEAKPEVQSQPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEAKPEVQSQPPR 13 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 162.87 3.62E-05 401260000 344849 278807 298951 265130 454000 447977 421608 355460 401042 290867 FALSE TRUE 358463.9048 326689.9334 306741.9087 317571.9227 376829.2422 343941.1309 388561.2633 350695.6401 386608.5768 347856.8197 1.030492676 0.939150579 0.881805074 0.912938614 1.083288356 0.988743389 1.117014936 1.008160888 1.111401459 1 18.40813408 3.241323616 24.99999396 1.050477054 0.936722594 0.494829544 0.054539563 58.01308052 524905.7056 0.014817139 0.019201594 1743.105271 -3.241323616 -0.11375446 VEAMNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEAMNKR 7 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 80.098 0.04944 583560000 650100 563690 542870 542860 872910 808190 652900 591410 571240 702300 FALSE TRUE 675766.45 660499.3726 557017.6382 650236.0877 724533.07 620500.1207 601723.992 583483.1163 550681.184 839902.2387 0.804577508 0.7864003 0.66319342 0.774180682 0.862639765 0.738776601 0.716421465 0.694703609 0.655649144 1 19.67986189 4.459351703 24.96274914 0.748539877 0.800033313 0.000977816 0.098421056 742.0715076 1042465.783 0.022701079 0.062195646 28797.29552 -4.459351703 0.051493435 VEAPSLDVHMDS(ph)PDINIEGPDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VEAPSLDVHMDS(1)PDINIEGPDVK 138.11 3.15E-06 94616000 64382 51654 64810 50554 78881 90017 77281 63569 67488 52358 TRUE FALSE 66923.85107 60525.17269 66499.00184 60553.43031 65472.8358 69111.91597 71223.51328 62716.96153 65059.12006 62616.54765 1.06878858 0.966600283 1.062003645 0.967051564 1.045615548 1.103732457 1.137455129 1.001603632 1.039008417 1 15.93425635 3.013132178 24.77791322 1.060246939 1.014662696 0.124189818 0.050119351 397.9016744 750758.7736 0.014458332 0.01727056 1030.699768 -3.013132178 -0.045584243 VEAQHILASAPTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEAQHILASAPTDR 14 0 A0A0A0MQS1;Q53H96-2;Q53H96 A0A0A0MQS1 PYCRL Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 3 0 70.281 0.044649 163530000 82967 87680 87400 87710 99740 108700 104410 91694 92732 81000 FALSE TRUE 86242.60122 102738.3579 89677.7158 105058.7762 82786.23043 83456.07236 96226.07138 90464.99191 89394.59343 96870.39916 0.890288488 1.060575355 0.92574942 1.084529197 0.854608127 0.861522953 0.993348559 0.933876527 0.922826727 1 16.56376827 5.093914912 12.05883904 0.955921226 6.56E-05 0.074167417 0.072459077 850525.5582 2627995.491 0.016849735 20518091.73 124140.9064 -5.093914912 -0.955855579 VEAVNMAEGIIHDTETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEAVNMAEGIIHDTETK 17 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 159.81 3.17E-09 66938000 78773 81172 93290 95223 101232 139100 111557 92830 95161 71588 FALSE TRUE 81883.01887 95112.65957 95721.21404 114057.8252 84024.6208 106796.1331 102812.8708 91585.76569 91736.1742 85614.29796 0.956417571 1.110943637 1.118051731 1.332228704 0.981432107 1.247410019 1.200884353 1.069748487 1.071505302 1 16.38556413 1.241768134 1.916821999 1.011647646 1.138067216 0.127616255 0.107269132 0.624788276 4.021380485 0.096267402 0.028203144 17.44890321 -1.241768134 0.12641957 VECQSHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VECQSHR 7 0 O14818;H0Y586;O14818-2;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 133.79 0.0032373 48069000 74858 74735 81974 80380 106230 106310 99501 81453 89983 94159 FALSE TRUE 77813.45164 87570.15489 84110.30978 96278.92409 88173.06254 81621.11364 91701.85162 80361.25577 86744.52941 112607.6533 0.691013882 0.777657223 0.746932445 0.854994499 0.783011278 0.72482741 0.814348305 0.713639379 0.770325345 1 16.78094536 -1.380100748 2.726683944 1.004791834 0.764535914 0.703669396 0.045927822 4313815.819 4835475.725 163273.7612 0.010982097 0.041677269 1.380100748 -0.24025592 VECYDYDNDGSHDLIGTFQTTMTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VECYDYDNDGSHDLIGTFQTTMTK 24 0 O75131;H0YB26 O75131 CPNE3 Copine-3 0 97.509 0.0058704 27827000 25484 34813 33049 35219 36245 50858 38191 32909 32803 32497 FALSE TRUE 26490.128 40791.86194 33910.28409 42185.21308 30084.08785 39047.00026 35197.48963 32467.90868 31622.42644 38864.16496 0.681608058 1.049600885 0.872533454 1.085452708 0.77408296 1.00470447 0.905654082 0.835420206 0.813665403 1 15.2461529 1.98183982 23.10290857 0.866190676 0.920665654 0.001570379 0.12385636 1042.078595 1325701.294 0.046289309 0.030582417 95.90468427 -1.98183982 0.054474979 VEDKWYSLSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEDKWYSLSGR 11 1 E9PP67;E9PQ25;F2Z2Y8;E7EN89;Q9H0E2-2;Q9H0E2 E9PP67 TOLLIP Toll-interacting protein 0 136.3 9.31E-05 616490000 444240 485000 597860 494060 791220 741180 631830 605320 684070 664970 FALSE TRUE 461778.9382 568294.9772 613440.7227 591783.5934 656728.707 569052.1777 582305.5136 597206.6755 659450.4543 795258.1399 0.580665466 0.714604414 0.771373083 0.744140253 0.825805703 0.715556558 0.73222201 0.750959526 0.829228173 1 19.60106371 -5 0.14403784 1.908381725 0.65271018 0.714756016 0.054397089 79.24748209 0.691140633 20.60118412 0.320012728 1.00E-05 5 -1.255671545 VEDLAWHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEDLAWHR 8 0 Q9NZU5;B4DEY6;Q9NZU5-2 Q9NZU5 LMCD1 LIM and cysteine-rich domains protein 1 0 ;;; 103.56 0.0047486 1082140000 1224110 1299500 1342380 1198250 1473250 1633330 1450280 1329730 1369890 1298590 FALSE TRUE 1272438.808 1522679.016 1377363.526 1435260.274 1222827.491 1254013.861 1336603.264 1311907.144 1320587.926 1553023.847 0.819329858 0.980460808 0.88689142 0.924171432 0.787384877 0.80746594 0.860645679 0.844743721 0.850333321 1 20.56664855 5.08791346 13.4474903 0.873189962 0.000122638 0.060693526 0.065989238 1419906.13 4407359.697 0.015574584 35286766.61 122437.2199 -5.08791346 -0.873067324 VEDMAELTCLNEASVLHNLK ddPTM_MDA-MB-175_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 ;; 364.88 5.85E-112 1139810000 1073900 943490 1250540 975190 1566400 1481900 1422270 1249080 1395700 807480 FALSE TRUE 1116298.401 1105527.068 1283130.1 1168079.671 1300143.888 1137751.183 1310788.761 1232338.126 1345469.03 965690.2459 1.155959073 1.144805048 1.328718091 1.209580066 1.346336357 1.178174045 1.357359429 1.276121542 1.393271844 1 19.88120098 4.253187636 24.74027702 1.274303918 1.150381951 0.13414786 0.108599931 327.2252562 553460.734 0.023526377 0.06379583 17913.79648 -4.253187636 -0.123921966 VEDVEALDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VEDVEALDR 9 0 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;; 152.79 0.00018523 1308376000 1151850 1236990 1279730 1219330 1500480 1691720 1318190 1285290 1226810 1172960 FALSE TRUE 1197325.927 1449433.41 1313080.815 1460509.835 1245428.946 1298843.668 1214866.823 1268062.79 1182657.348 1402779.054 0.853538498 1.03325852 0.936056759 1.041154578 0.887829728 0.925907515 0.866042888 0.903964731 0.843081699 1 20.41985636 3.190603187 24.99990091 0.898425531 0.968667568 0.184485843 0.06250737 159.2635993 83022.50646 0.01658444 0.019822223 1550.969249 -3.190603187 0.070242037 VEDVEALDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VEDVEALDRK 10 1 P11216;H0Y4Z6 P11216 PYGB "Glycogen phosphorylase, brain form;Alpha-1,4 glucan phosphorylase" 0 ;;;; 134.75 0.00026041 1332653000 1566240 1154630 1423410 1106660 1890800 1707670 1653860 1361410 1596650 1063180 FALSE TRUE 1628076.365 1352928.721 1460505.234 1325554.045 1569402.491 1311089.522 1524226.132 1343162.526 1539186.878 1271489.765 1.280447872 1.064050028 1.148656697 1.042520421 1.234302103 1.031144378 1.198771845 1.056369121 1.210538158 1 20.27808842 -2.238999745 2.471831964 0.484657906 1.132226557 0.192854087 0.084786258 24051097.44 16578212.6 65863863.59 0.017888016 0.005767668 2.238999745 0.647568651 VEEAS(ph)PGRPS(ph)SVDTLLSPTALIDSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VEEAS(0.503)PGRPS(0.549)S(0.54)VDT(0.406)LLS(0.002)PTALIDSILR 104.4 0.0012453 446860000 234610 233840 253170 228690 286840 317810 294800 246600 255360 234060 TRUE FALSE 243872.584 274000.201 259767.8182 273924.1994 238083.0393 244003.444 271692.8057 243294.7304 246169.6435 279919.5757 0.871223756 0.978853302 0.92800876 0.97858179 0.850540869 0.871691247 0.970610237 0.8691594 0.879429897 1 18.09465286 3.250455402 24.99996814 0.901127269 0.94120462 0.076830893 0.052352479 477.3403016 1003248.881 0.013770171 0.018496133 1780.145096 -3.250455402 0.040077351 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VEEAS(0.945)PGRPS(0.027)S(0.027)VDT(0.001)LLSPTALIDSILR;VEEAS(0.943)PGRPS(0.028)S(0.028)VDTLLSPTALIDSILR 144.26 1.06E-07 1932060000 59529.7 52392.3 63819.3 51757.9 62868.3 67652.9 68958 60924.5 57953.6 42912.3 TRUE FALSE 61879.97852 61390.26997 65482.48339 61995.45814 52181.96882 51941.53926 63552.89177 60107.90673 55867.86126 51320.14358 1.20576394 1.196221711 1.275960643 1.208014121 1.016793118 1.012108222 1.238361535 1.171234189 1.088614672 1 15.64723759 5.409280744 0.019680488 1.12E-07 2.454587971 0.344020559 0.078944758 2610.601019 6.617570474 345.5863569 489.7719211 256614.2349 -5.409280744 2.454587859 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEEEDDAEHVLALTMLCLTEGAKDECNVVEVVAR 34 1 O75607 O75607 NPM3 Nucleoplasmin-3 0 179.49 5.25E-20 170200000 55599 36039 46584 51862 70430 72279 68434 59284 66520 39145 FALSE TRUE 57794.09145 42228.41791 47798.01731 62120.14881 58458.33376 55493.29765 63069.96426 58489.39495 64125.95819 46814.71327 1.234528365 0.902033035 1.021004167 1.326936437 1.248717116 1.185381556 1.34722526 1.249380608 1.369782141 1 15.5146744 3.746671337 24.70142449 1.260025287 1.037472952 0.332855674 0.124498821 486.8547056 1482724.942 0.029583362 0.052166444 5580.477185 -3.746671337 -0.222552335 VEEEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VEEEEER 7 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 ;;;;; 181.49 0.0015614 19486480000 4723850 5491230 5674400 5216820 6416210 7012540 5862060 5743290 5453590 5578530 FALSE TRUE 4910351.246 6434306.037 5822279.526 6248691.425 5325584.916 5383983.861 5402576.42 5666310.592 5257316.361 6671536.146 0.736015085 0.964441456 0.872704486 0.936619586 0.798254675 0.807008123 0.809794971 0.849326222 0.788021866 1 22.66958755 4.786742643 22.40427721 0.859738491 0.736013031 0.229341255 0.07142942 16791.37097 7807088.786 0.016515913 9.695921302 61198.76285 -4.786742643 -0.12372546 VEEESTGDPFGFDS(ph)DDESLPVSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEEESTGDPFGFDSDDESLPVSSK 24 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 VEEESTGDPFGFDS(0.996)DDES(0.004)LPVSSK;VEEESTGDPFGFDS(0.86)DDES(0.14)LPVSSK 181.83 2.07E-17 166669000 364510 252010 379480 238490 450350 466760 428470 331380 396080 273580 TRUE FALSE 378901.1363 295290.7571 389369.5605 285662.6102 373799.6679 358362.0638 394885.4018 326938.3931 381825.1582 327182.763 1.158071815 0.902525409 1.190067463 0.873097982 1.142479709 1.095296282 1.206926056 0.999253109 1.167008783 1 18.31973722 VEEFLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEEFLYEK 8 0 B7ZC38;Q9NR46;Q9NR46-2;B7ZC39;F8WFB9;H7C1Z6 B7ZC38 SH3GLB2 Endophilin-B2 0 105.78 0.015296 0 28068 26852 31148 29022 38746 44506 39818 34803 31348 26978 FALSE TRUE 29176.14631 31463.62212 31959.74247 34762.46498 32159.96876 34170.15599 36696.96112 34336.52271 30219.7916 32263.82257 0.904299118 0.975198213 0.990575199 1.077444091 0.996781106 1.059085789 1.137402768 1.064242237 0.936646348 1 14.97762976 4.550725631 1.091159935 1.048716918 0.863712343 0.374532128 0.052683018 1.262294805 1.554911224 0.016278304 0.250596768 35540.67169 -4.550725631 -0.185004575 VEEGGRHPS(ph)PCQFTIATPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEEGGRHPSPCQFTIATPK 19 1 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VEEGGRHPS(0.999)PCQFT(0.001)IATPK;VEEGGRHPS(1)PCQFTIATPK 159.74 1.98E-11 1683000000 1580800 1137770 1430660 1047470 1819500 1783390 1422210 1502730 1570860 1129790 TRUE FALSE 1643211.205 1333173.147 1467944.175 1254656.44 1510222.04 1369224.7 1310733.464 1482588.362 1514325.055 1351150.719 1.216156851 0.986694621 1.086439991 0.92858363 1.117730256 1.013376732 0.97008679 1.097278298 1.120766939 1 20.36575718 4.74921857 24.44212111 1.038450833 1.21615699 0.420232418 0.063525687 1082.478309 2482405.553 0.014462702 0.204066145 56133.04086 -4.74921857 0.177706157 VEELARSLRADIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEELARSLRADIER 14 2 Q9BX97 Q9BX97 PLVAP Plasmalemma vesicle-associated protein 0 65.043 0.035595 107130000 227990 114100 148970 115110 231780 178940 194390 95194 190290 123480 FALSE TRUE 236991.2212 133695.7874 152852.2806 137878.4144 192382.1184 137383.8969 179153.2039 93918.08014 183441.5001 147673.5418 1.604831971 0.905346928 1.035068833 0.933670397 1.302752788 0.930321675 1.213170631 0.635984476 1.242209659 1 17.17205184 4.744552027 24.62745117 1.006091378 1.604832296 0.467438512 0.185912046 458.8365495 1885962.945 0.042749035 0.386743043 55533.11405 -4.744552027 0.598740918 VEELDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEELDRK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 101.33 0.014656 124050000 234620 209180 210320 206370 261160 255790 242810 229270 245360 203510 FALSE TRUE 243882.9788 245105.0378 215801.112 247189.37 216768.1165 196386.649 223777.9177 226197.0107 236529.5415 243383.8881 1.002050632 1.007071749 0.886669671 1.015635719 0.890642837 0.80690078 0.919444255 0.929383668 0.971837304 1 17.89287414 4.25363431 24.91915697 0.922578255 1.00456126 0.220449971 0.05730584 325.0445202 537339.2188 0.014064904 0.038184681 17932.2304 -4.25363431 0.081983006 VEELEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEELEHR 7 0 Q08379;Q08379-2;A0A087WYC0 Q08379 GOLGA2 Golgin subfamily A member 2 0 ; 143.85 0.0023936 506360000 599740 694740 747980 664020 808130 868370 721410 710890 686430 702290 FALSE TRUE 623418.1983 814056.1907 767472.9733 795361.1741 670764.3513 666704.2278 664863.9991 701361.6823 661725.5184 839890.2793 0.742261476 0.969241115 0.913777659 0.946982235 0.798633307 0.793799195 0.791608161 0.83506346 0.787871386 1 19.67984135 3.227782479 24.99928274 0.822263478 0.899986163 0.095937425 0.082047211 353.939897 820942.2854 0.022087423 0.026651942 1689.594468 -3.227782479 0.077722685 VEELKFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEELKFDR 8 1 Q9BUP3-3;Q9BUP3;E9PI87 Q9BUP3-3 HTATIP2 Oxidoreductase HTATIP2 0 ; 131.5 0.00091405 400720000 563880 411040 473170 410890 697370 637190 621280 471850 555850 376330 FALSE TRUE 586142.4178 481632.9226 485501.1989 492162.8156 578831.2965 489212.2792 572582.4502 465525.6225 535845.0671 450064.6582 1.302351578 1.07014162 1.078736555 1.093538021 1.286106976 1.086982215 1.272222646 1.034352763 1.190595745 1 18.77977275 -1.342367558 2.743971244 0.997670555 1.148744604 0.192707255 0.095125854 7394273.513 8461680.141 138871.6816 0.022061724 0.045460315 1.342367558 0.151074049 VEEPSKYGVVVCEADTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEEPSKYGVVVCEADTGR 18 1 Q9Y5P6;Q9Y5P6-2 Q9Y5P6 GMPPB Mannose-1-phosphate guanyltransferase beta 0 ; 145.9 8.00E-08 507440000 214750 200429 239180 166177 316430 281490 205403 211740 246740 224240 FALSE TRUE 223228.4958 234851.1216 245413.2273 199046.3146 262643.3416 216118.2135 189302.9761 208901.9716 237859.8756 268175.5347 0.832396945 0.875736565 0.915121611 0.742223987 0.979371 0.805883407 0.705892043 0.778974756 0.886955911 1 18.0328181 VEERDPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEERDPPR 8 1 Q14152-2;Q14152 Q14152-2 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 ; 99.802 0.0059781 1085340000 1461140 1516840 1568290 1691330 1710260 1972580 1807410 1554770 1611120 1345130 FALSE TRUE 1518826.935 1777345.471 1609160.926 2025870.026 1419550.616 1514478.19 1665740.481 1533930.851 1553136.106 1608682.469 0.9441434 1.104845427 1.000297421 1.259334931 0.882430587 0.941440103 1.035468785 0.953532397 0.965470896 1 20.61744816 3.175983673 25 0.964250322 1.07366038 0.304336134 0.084431203 80.89276807 32316.62066 0.023332024 0.027887115 1499.628459 -3.175983673 0.109410058 VEESGEHVILGTGELYLDCVMHDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VEESGEHVILGTGELYLDCVMHDLR 25 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;; 254.25 4.53E-45 534506000 143339.9 179808 175591.9 196798.3 215480.7 243483.4 202855.3 196800.1 182791.1 169552.9 FALSE TRUE 148999.0699 210688.6253 180167.9692 235724.4164 178853.3676 186938.0704 186954.9715 194162.3166 176212.484 202773.5445 0.734805274 1.03903409 0.888518123 1.162500843 0.882035021 0.921905621 0.921988971 0.957532784 0.869011214 1 17.62950991 7.999955603 0.005189022 1.826051176 1.41E-05 0.023302545 0.106888233 367489.2286 147.5298952 24030.00506 28029.02014 99989777.67 -7.999955603 -1.826037077 VEFATLQEALAHALTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEFATLQEALAHALTEK 17 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 ; 292.55 5.00E-46 2005810000 1740850 1442610 1832930 1452750 2053800 2150600 2100000 1887500 1849150 1207140 FALSE TRUE 1809580.102 1690367.046 1880697.662 1740099.614 1704695.81 1651155.743 1935396.513 1862201.15 1782599.453 1443655.971 1.253470452 1.17089326 1.302732576 1.205342304 1.180818591 1.143732147 1.340621694 1.289920305 1.234781339 1 20.46129555 -1.018241372 5.131675915 0.99999781 1.239060838 0.584939025 0.059535545 1.56E-06 2.99E-07 0.060445373 0.01424698 0.095886756 1.018241372 0.239063028 VEFEELCADLFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEFEELCADLFER 13 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 227.37 2.14E-11 237798000 174234 228696 207882 235930 257340 292272 226251 187884 208315 193585 FALSE TRUE 181112.8929 267972.759 213299.5757 282596.2498 213597.4387 224396.2574 208516.8554 185365.7223 200817.7838 231514.2743 0.782296873 1.157478344 0.921323648 1.220642877 0.922610234 0.969254522 0.900665223 0.800666494 0.867409944 1 17.82074162 2.447824013 1.840235616 0.866026736 1.018661655 0.133137213 0.124996866 0.50435568 3.47310451 0.051438306 0.04003863 280.4297037 -2.447824013 0.152634919 VEFMDDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VEFMDDTSR 9 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 ;;;;;;; 229.33 3.04E-07 4918480000 3534060 4126500 4115250 3819210 4745640 5121640 4239660 4127380 4197820 4199170 FALSE TRUE 3673587.418 4835194.275 4222496.796 4574638.339 3938977.808 3932216.729 3907344.371 4072059.222 4046741.278 5021916.964 0.731510984 0.962818444 0.840813742 0.910934683 0.784357415 0.783011101 0.778058339 0.810857537 0.805816047 1 22.25980674 5.02905685 15.88527412 0.839936068 0.41767638 0.168606472 0.076111854 5830929.96 88420054.94 0.017596383 65077908.52 106919.483 -5.02905685 -0.422259688 VEGEEEDKEET(ph)QR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEGEEEDKEETQR 13 1 Q2M329 Q2M329 CCDC96 Coiled-coil domain-containing protein 96 1 VEGEEEDKEET(1)QR 65.374 0.086139 1193200000 0 536280 236970 483000 155580 547220 110770 348920 147080 593510 TRUE FALSE 0 628381.9183 243145.6329 578535.9584 129134.5672 420136.4482 102087.558 344243.2981 141786.6195 709796.9211 0 0.885298174 0.342556618 0.81507251 0.181931709 0.591910779 0.143826431 0.484988435 0.1997566 1 19.43704679 -1.44405948 3.221532378 1.009322903 0.421694564 0.290844908 0.277614247 111767594.4 144757633.4 9490867.316 0.059375674 0.035970007 1.44405948 -0.587628339 VEGFLEEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEGFLEEDRR 10 1 A0A0G2JM25;A0A0G2JNK1;K7ERG0;A0A0G2JMB6;A0A0G2JPH3;A0A0G2JNK3;Q8WX94;Q8WX94-2;Q8WX94-3;Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8 A0A0G2JM25;Q9NX02 NLRP7;NLRP2 "NACHT, LRR and PYD domains-containing protein 7;NACHT, LRR and PYD domains-containing protein 2" 0 ;;; 179.31 3.40E-06 1159160000 334244 363014 388038 360634 458040 471870 404664 377115 385990 408631 FALSE TRUE 347440.2112 425358.8306 398150.5891 431966.3288 380182.5244 362285.3438 372945.3783 372060.3903 372098.2953 488694.4207 0.71095596 0.870398377 0.814723009 0.883919092 0.777955525 0.741333087 0.76314638 0.761335457 0.761413021 1 18.89857311 -0.964345793 5.87247838 1.000000175 0.78866464 0.601597468 0.051929923 1.22E-07 2.15E-08 0.051430552 0.012122287 0.108556094 0.964345793 -0.211335535 VEGGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEGGAR 6 0 A0A494C0Y0 A0A494C0Y0 0 99.511 0.090068 150190000 344110 369600 386260 379610 423910 458980 413120 387370 376760 369700 FALSE TRUE 357695.7285 433075.9249 396326.2529 454695.725 351853.9296 352388.8509 380738.5749 382177.9388 363200.4812 442135.6367 0.80901809 0.979509203 0.896390655 1.028407772 0.795805405 0.797015263 0.861135234 0.864390714 0.821468461 1 18.7541295 3.216267967 24.99999669 0.848597292 0.929705588 0.17218338 0.075770041 347.2434652 389413.7039 0.020548178 0.024577126 1645.386641 -3.216267967 0.081108296 VEGHVFPEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEGHVFPEFK 10 0 O14964-2;O14964;I3L1P5 O14964-2 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0 ; 79.693 0.02624 204830000 767990 640890 719730 603550 890900 923890 810100 739970 737090 580520 FALSE TRUE 798310.8382 750957.8721 738486.7551 722930.3886 739465.1362 709330.5492 746602.2452 730051.9125 710562.2749 694261.7793 1.149870066 1.081663854 1.063700721 1.041293659 1.06510996 1.021704738 1.075390101 1.051551352 1.02347889 1 19.40512022 7.999999948 0.72831192 1.042545219 17.59033513 0.725854791 0.02066379 170.1083175 0.797461028 0.006975275 4604.947141 99999988.14 -7.999999948 16.54778991 VEGQKEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEGQKEEK 8 1 A0A1W2PNT1 A0A1W2PNT1 0 ; 69.423 0.032419 208600000 12208.1 444820 315510 437860 189407 461100 202340 351650 236600 507470 FALSE TRUE 12690.08521 521214.3748 323732.4498 524467.4011 157211.6658 354016.513 186480.0621 346936.7069 228084.8122 606899.0304 0.020909714 0.858815633 0.533420608 0.864175711 0.259040891 0.583320281 0.307267029 0.571654739 0.375820031 1 19.21109699 -1.223577255 3.700542254 1.000645629 0.503113456 0.276373334 0.248111036 63826187.66 109853368.9 491516.8135 0.054525727 0.059761673 1.223577255 -0.497532172 VEGS(ph)PTEEANLPTELQDNSLSPAASEAGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEGSPTEEANLPTELQDNSLSPAASEAGEK 30 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 VEGS(0.5)PT(0.5)EEANLPTELQDNSLSPAASEAGEK 103.43 0.00023522 110700000 210830 110610 158530 160830 182590 212920 305590 175690 173140 69204 TRUE FALSE 219153.7312 129606.4071 162661.422 192641.694 151553.417 163472.5568 281637.0573 173335.1629 166908.7252 82763.19881 2.647961103 1.56599079 1.96538346 2.32762504 1.831169157 1.97518413 3.402926196 2.094350695 2.016702201 1 16.33670179 VEHES(ph)FEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 83.614 0.018919 12732510000 4926715 2907317 3765309 2709259 5163910 4370638 3707348 4233403 4752221 3018030 TRUE FALSE 5121225.512 3406626.079 3863436.046 3245142.344 4286150.423 3355623.562 3416756.376 4176661.157 4581189.495 3609355.195 1.41887546 0.943832318 1.070395081 0.89909199 1.187511395 0.929701673 0.946638996 1.15717654 1.26925427 1 21.78330969 -1.394452149 4.785065621 0.999901156 1.078079596 0.022244456 0.161348012 0.000160646 2.03E-05 0.14750806 0.034724065 0.040322537 1.394452149 0.078178441 VEHTNTGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEHTNTGTK 9 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 ; 123.75 0.000549 225573000 232930 174801 227400 197020 306990 280280 272810 252310 263080 179165 FALSE TRUE 242126.2563 204821.712 233326.2308 235989.968 254807.9495 215189.2177 251426.4393 248928.1971 253611.8022 214268.9514 1.130010926 0.955909434 1.088940928 1.101372674 1.189196791 1.004294912 1.173415176 1.1617558 1.183614334 1 17.70906329 3.87614104 3.209385553 1.127181402 1.040214041 0.108462116 0.076174156 0.407730508 7.873749164 0.019173043 0.038777091 7518.670288 -3.87614104 -0.08696736 VEHTPDGVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEHTPDGVK 9 0 P11216 P11216 PYGB "Glycogen phosphorylase, brain form" 0 ;;; 111.46 0.002122 2257310000 1953950 1487710 1722380 1447610 2546690 2310820 2144090 1761590 1851590 1411920 FALSE TRUE 2031093.455 1743212.62 1767266.638 1733942.937 2113804.543 1774167.076 1976030.623 1737978.767 1784951.638 1688558.691 1.202856297 1.032367207 1.046612503 1.026877506 1.251839545 1.050699087 1.170246929 1.029267609 1.057085932 1 20.68736089 1.61883539 11.35647409 1.032065327 1.105691273 0.205080857 0.073990375 0.155714214 69.42486674 0.035499736 0.018485505 41.57529988 -1.61883539 0.073625946 VEIAGPGFINVHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEIAGPGFINVHLR 14 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ; 222.81 3.75E-12 1337190000 1238100 1391190 1413610 1412790 1473750 1704880 1501130 1482800 1486690 1351900 FALSE TRUE 1286981.144 1630116.061 1450449.838 1692235.645 1223242.501 1308947.458 1383467.508 1462925.491 1433184.317 1616778.921 0.796015539 1.008249204 0.897123174 1.046671022 0.756592312 0.809602006 0.855693682 0.904839537 0.886444212 1 20.62469099 5.038178816 14.22198421 0.898766298 0.437391911 0.123664632 0.086209605 48268619.22 566310070.2 0.020487532 549045880.7 109188.9817 -5.038178816 -0.461374387 VEILANDQGNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 ;;;;;;; 215.06 3.05E-11 8032520000 4459930 4825140 4737520 4538160 5246130 5769740 4827940 4716700 4525080 4717700 FALSE TRUE 4636011.48 5653820.261 4860983.663 5435794.503 4354394.696 4429805.326 4449513.447 4653480.351 4362223.255 5642042.989 0.821690209 1.002087413 0.86156445 0.963444361 0.771776235 0.785142073 0.788635155 0.824786405 0.773163775 1 22.42778623 3.235733476 24.99999809 0.811844168 0.915000799 0.224678372 0.078368729 87.31310372 772099.0979 0.02028873 0.025292853 1720.8122 -3.235733476 0.103156631 VEKIPGGIIEDSCVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEKIPGGIIEDSCVLR 16 1 P49368;P49368-2;B4DUR8;Q5SZX6;E9PRC8;E9PQ35 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 151.95 5.42E-07 1270950000 786960 788150 825920 672520 1084740 983150 818910 835300 892050 801640 FALSE TRUE 818029.7885 923508.6315 847444.1537 805542.4487 900356.2823 754828.3123 754721.6944 824104.1698 859945.2948 958706.0097 0.853264484 0.963286578 0.883945803 0.840239281 0.939136996 0.787340754 0.787229544 0.859600505 0.896985401 1 19.87072895 2.756159712 24.86159273 0.851295224 0.895949499 0.024344891 0.066282305 1864.746331 2634255.623 0.019597028 0.020743986 570.3739897 -2.756159712 0.044654275 VEKPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VEKPDTK 7 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 83.005 0.020932 4231430000 9479810 5209500 7517960 5202310 9442550 8717630 9555730 7215680 7936080 4082150 FALSE TRUE 9854080.219 6104191.101 7713884.214 6231311.391 7837508.724 6693092.549 8806726.913 7118965.612 7650462.031 4881969.135 2.01846426 1.2503543 1.5800764 1.276393033 1.605399073 1.370982152 1.803929249 1.458216022 1.567085293 1 22.21903174 -1.898085185 2.192736399 0.680789322 1.534092756 0.351624055 0.222484631 5739803.449 2703248.472 9454071.873 0.050434601 0.012644883 1.898085185 0.853303434 VELAQLQEEWNEHNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VELAQLQEEWNEHNAK 16 0 Q9H307 Q9H307 PNN Pinin 0 188.9 1.10E-09 260470000 85203 63483 70288 66574 91606 101360 70594 74251 80161 71979 FALSE TRUE 88566.88023 74385.71142 72119.76302 79742.1385 76034.84484 77820.67613 65060.65782 73255.7868 77276.02127 86081.90693 1.028867545 0.864127133 0.837803966 0.926351905 0.883284857 0.904030579 0.755799449 0.851000976 0.897703409 1 16.39342242 VELS(ph)PGPPKPAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 130.27 8.72E-05 1169940000 1525630 1029990 1317770 1073530 1659370 1662480 1644390 1372400 1455510 869080 TRUE FALSE 1585863.05 1206882.77 1352112.169 1285871.03 1377310.88 1276394.215 1515498.415 1354005.223 1403126.479 1039359.586 1.525807883 1.161179236 1.300908931 1.237176283 1.325153391 1.228058346 1.458107891 1.302730297 1.349991377 1 19.98726344 -1.237187602 4.061313806 0.999763456 1.315661241 0.471169034 0.101884741 0.000212902 4.00E-05 0.090389455 0.021288134 0.057917845 1.237187602 0.315897785 VEMLETER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEMLETER 8 0 Q14980;Q14980-2;A0A087WY61;Q14980-3;Q14980-4;F5H4J1;F5H6Y5 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 79.474 0.065008 188810000 90266 116630 92660 102870 105130 141800 104140 108070 96208 95481 FALSE TRUE 93829.77138 136660.2952 95074.79572 123217.379 87260.04015 108869.099 95977.23468 106621.4984 92745.49287 114188.6739 0.821708215 1.196793785 0.832611436 1.079068307 0.764174215 0.953414164 0.840514487 0.933730946 0.812212716 1 16.80106003 3.24846516 24.99955865 0.88457512 0.987139286 0.137360441 0.120749471 374.2492967 944617.8463 0.0302634 0.040493665 1772.005885 -3.24846516 0.102564166 VENFEAAVHFYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VENFEAAVHFYGK 13 0 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 0 ; 160.48 4.38E-05 1765610000 1984160 1613480 1932430 1765460 2220830 2196980 2463780 2045570 1969750 1329170 FALSE TRUE 2062496.169 1890582.639 1982790.713 2114662.719 1843334.11 1686764.691 2270662.486 2018152.48 1898859.082 1589595.413 1.297497559 1.189348323 1.247355583 1.330315061 1.159624704 1.061128308 1.428453094 1.269601349 1.194554958 1 20.60022818 0.875140996 4.358943581 1.000037058 1.248968068 0.384221355 0.094054654 0.838833558 27.64357398 0.090941123 0.023129825 7.501377059 -0.875140996 0.248931011 VENMSSNQDGNDS(ph)DEFM ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;VENMSSNQDGNDS(1)DEFM 393.76 3.07E-122 757444000 722365 878017 915359 868098 1042548 1154160 934724 953930 929021 881727 TRUE FALSE 750884.528 1028809.59 939214.0075 1039805.193 865336.0633 886123.8315 861457.8904 941144.1287 895585.7157 1054484.524 0.712086817 0.975651673 0.890685436 0.986079141 0.820624716 0.840338394 0.816946926 0.892515829 0.849311389 1 20.00810649 -1.118628091 4.733153748 1.000006854 0.870078063 0.220903942 0.075548423 6.56E-06 1.22E-06 0.068827662 0.016221743 0.076097766 1.118628091 -0.12992879 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 VENS(0.171)PQVDGS(0.829)PPGLEGLLGGIGEK;VENSPQVDGS(1)PPGLEGLLGGIGEK 255.39 5.01E-44 68697000 110900 85989 103137 87396 134074 141941 127744 98402 109735 73789 TRUE FALSE 115278.4176 100756.9418 105824.8349 104682.6679 111284.1494 108977.3539 117731.0915 97083.08214 105785.6588 88246.54177 1.306322212 1.141766463 1.199195264 1.186252354 1.261059608 1.234919258 1.334115639 1.100134693 1.198751324 1 16.42925212 0.72917944 1.013541574 1.002260004 1.225657777 0.513873565 0.065277037 0.748799224 1.378301925 0.060565238 0.019527198 5.360180816 -0.72917944 0.223397773 VEPPKEEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEPPKEEQK 9 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 98.943 0.0051732 339870000 707950 309800 403170 283220 798320 639380 578620 512800 595870 320660 FALSE TRUE 735900.4127 363005.7401 413676.9414 339240.0707 662621.8516 490893.6849 533266.2525 505926.7548 574424.7551 383487.1876 1.918970011 0.946591573 1.078724283 0.884619048 1.727885241 1.280078451 1.390571236 1.319279421 1.497898166 1 18.54881885 3.248507501 24.99994406 1.377785093 1.179430894 0.056644292 0.314807916 537.6026442 1351172.654 0.083635708 0.111905766 1772.178654 -3.248507501 -0.198354199 VEPSSQS(ph)PGRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 2 VEPS(0.152)S(0.195)QS(0.653)PGRS(1)PR 67.449 0.030225 276620000 229210 214120 201590 217170 236790 277140 257830 212170 175770 181450 TRUE FALSE 238259.3878 250893.4444 206843.601 260125.5778 196540.5204 212778.4351 237620.6109 209326.2082 169444.072 217001.6534 1.097961163 1.156182178 0.953189055 1.198726248 0.905709783 0.980538313 1.095017513 0.964629554 0.780842309 1 17.72734651 3.115120277 0.484751125 0.929232505 1.131631881 0.277346026 0.101117214 1.756814651 0.812638161 0.085586406 0.166980266 1303.527738 -3.115120277 0.202399376 VEPSSQSPGRS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VEPSSQSPGRSPR 13 1 G8JLD3;X6RLX0;Q8IUD2-3;Q8IUD2;Q8IUD2-2;X6RM00;Q8IUD2-4;Q8IUD2-5;K7EKH8;K7EIZ7 G8JLD3 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR;VEPSSQS(0.001)PGRS(0.999)PR;VEPSSQSPGRS(1)PR;VEPSSQSPGRS(1)PR 149.97 2.44E-05 4906905000 2061145 2142472 2148274 2099789 2325785 2667545 2085295 2073902 1984501 1851365 TRUE FALSE 2142520.596 2510424.9 2204259.785 2515120.997 1930448.896 2048048.101 1921844.129 2046104.736 1913079.197 2214104.525 0.967669128 1.133833056 0.995553625 1.135954047 0.871886975 0.925000639 0.868000633 0.924122919 0.864041952 1 21.0782919 3.228335472 24.99999983 0.904384905 1.059172594 0.585422124 0.061525764 124.8555755 305265.6815 0.015919815 0.019231154 1691.74722 -3.228335472 0.154787689 VEPVGEDLGS(ph)PPPPADFAPEDYSSFQHIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEPVGEDLGSPPPPADFAPEDYSSFQHIR 29 0 O95644-6;O95644;K7ER53;O95644-8;O95644-11;O95644-3;O95644-10;O95644-2;O95644-5;O95644-4 O95644-6 NFATC1 "Nuclear factor of activated T-cells, cytoplasmic 1" 1 VEPVGEDLGS(1)PPPPADFAPEDYSSFQHIR 123.42 1.63E-05 160820000 35209 37075 55994 42254 52095 63091 56461 49697 56491 56790 TRUE FALSE 36599.07851 43442.34285 57453.24964 50611.71508 43239.91051 48439.0714 52035.43929 49030.893 54457.89994 67916.91319 0.538880182 0.639639536 0.845934347 0.745200462 0.636658948 0.713210732 0.766163196 0.721924639 0.801831199 1 16.05148327 -5 0.138106968 1.995638395 0.605982782 0.632265918 0.073170692 98.21191727 0.836243269 26.834478 0.490724878 1.00E-05 5 -1.389655613 VEQALSEVASS(ph)LQSSAPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEQALSEVASSLQSSAPK 18 0 Q86TV6;Q86TV6-2;H0YK02;H0YJS2;A0A0C4DGK5 Q86TV6 TTC7B Tetratricopeptide repeat protein 7B 1 VEQALSEVAS(0.001)S(0.999)LQSSAPK 298.76 2.02E-49 91149000 123850 99272 116360 78943 134220 143200 121430 105170 130000 82453 TRUE FALSE 128739.6936 116321.1938 119392.4372 94557.68978 111405.3323 109943.9702 111911.9993 103760.3682 125321.3254 98608.08669 1.30556933 1.179631384 1.210777343 0.958924293 1.129778866 1.114958964 1.134917055 1.052250091 1.270903124 1 16.58941834 4.44960532 1.575697798 1.100795297 1.313778106 0.351456493 0.085149573 0.666286872 2.355706742 0.02188729 0.185661985 28158.22795 -4.44960532 0.212982808 VEQAT(ph)KPSFESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.704)KPS(0.275)FES(0.021)GR 125.22 0.0012912 187310000 164530 99078 135040 128540 185210 195990 181120 162280 157760 86807 TRUE FALSE 171025.7714 116093.8758 138559.2533 153964.8283 153728.0704 150474.2928 166923.3411 160104.902 152082.2484 103815.1696 1.647406367 1.118274682 1.334672513 1.48306677 1.480786198 1.449444174 1.607889692 1.542211053 1.464932812 1 16.66365774 5.061258547 21.16816516 1.422912374 6.0941873 0.12771176 0.183665904 1238.262745 425493.9543 0.041644717 1500.864516 115148.5696 -5.061258547 4.671274925 VEQATKPS(ph)FESGR ddPTM_MDA-MB-175_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(0.991)FES(0.008)GR;VEQAT(0.005)KPS(0.994)FES(0.002)GR;VEQAT(0.006)KPS(0.993)FES(0.001)GR 98.035 0.0021223 2335150000 1177964 881392 1101470 910708 1325889 1504010 1499063 1236842 1233557 739062 TRUE FALSE 1224470.928 1032764.22 1130175.213 1090843.324 1100514.861 1154726.471 1381562.525 1220264.156 1189161.525 883867.0487 1.385356463 1.16846105 1.278671057 1.234171277 1.245113576 1.30644815 1.56308862 1.380596955 1.34540769 1 19.75346985 2.471427352 24.99411915 1.373115817 1.258409252 0 0.141954167 306.0242061 1343317.539 0.045726554 0.038364096 296.0924627 -2.471427352 -0.114706565 VEQATKPS(ph)FESGRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEQATKPSFESGRR 14 2 P38159;P38159-2;H3BT71;H0Y6E7 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 VEQAT(0.105)KPS(0.893)FES(0.002)GRR 61.096 0.045765 105300000 167430 93773 120520 97899 176790 170050 176740 129680 141800 79394 TRUE FALSE 174040.2657 109877.7833 123660.8502 117263.13 146739.2989 130558.4646 162886.657 127941.8517 136696.6457 94949.73421 1.832972647 1.157220546 1.302382268 1.235002193 1.545441914 1.375027173 1.715504086 1.347469298 1.439673811 1 16.53487634 -0.27183352 1.916186544 0.999791108 1.428168642 0.303136314 0.199051851 347.4663965 513.3524722 0.76855556 0.05012074 0.534769316 0.27183352 0.428377533 VEQATKPSFESGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 4627370000 2823604 2399863 2973480 2621575 3249910 3610090 3804470 3254495 3118370 2074212 FALSE TRUE 2935082.066 2812020.802 3050971.332 3140114.71 2697491.459 2771701.309 3506265.7 3210873.818 3006140.473 2480614.128 1.183207833 1.13359864 1.229925806 1.265861818 1.087428886 1.117344805 1.413466795 1.294386653 1.211853322 1 21.2422659 VEQHVVDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEQHVVDGK 9 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ;;; 85.958 0.014463 2686090000 3552350 3571890 4066630 3253740 5113510 5271210 4354060 4242170 4298110 3642980 FALSE TRUE 3692599.521 4185334.322 4172609.719 3897320.061 4244317.397 4047051.363 4012777.4 4185310.65 4143421.861 4356752.182 0.847557852 0.960654668 0.957734006 0.894547107 0.974192981 0.92891475 0.921047889 0.960649235 0.951034552 1 22.05482162 0.95630565 0.010447463 1.917465325 2.26E-07 0.366196483 0.032969908 1592.003232 10.74655401 999.6438743 971.2035138 9.042856736 -0.95630565 -1.917465099 VEQIAAIAQELNELDYYDSHNVNTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VEQIAAIAQELNELDYYDSHNVNTR 25 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 310.8 1.74E-74 1613561000 666928 890952 641658 923043 819521 1043643 1079584 789294 644984 1124894 FALSE TRUE 693258.8324 1043966.075 658380.1346 1105618.15 680219.1131 801272.7298 994963.3851 778714.805 621771.1518 1345295.442 0.515320881 0.776012497 0.489394459 0.821840405 0.505628052 0.595610975 0.739587271 0.578842967 0.462181862 1 20.35949161 -1.327789349 3.7758192 1.001106786 0.616617578 0.481909969 0.121296621 13060366.37 9186449.949 110296.3796 0.025818652 0.047012208 1.327789349 -0.384489207 VEQMPQAS(ph)PGLAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEQMPQASPGLAPR 14 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 VEQMPQAS(1)PGLAPR 172.42 3.00E-06 336580000 262030 232620 233930 245700 302700 296590 255400 274800 254860 248890 TRUE FALSE 272375.1467 272570.6755 240026.408 294298.7267 251247.1621 227711.4674 235381.0806 271116.7555 245687.6384 297655.2302 0.915069245 0.915726142 0.806390695 0.988723519 0.844087846 0.765017524 0.790784293 0.910841564 0.825410117 1 18.18328272 VERLS(ph)SGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.955)S(0.045)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.842)S(0.158)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK;VERLS(0.961)S(0.039)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 293.99 1.80E-92 1392610000 163504 241675 278965 281993 322719 374576 299723 306774 306051 218779 TRUE FALSE 169959.2642 283180.8013 286235.0571 337770.3737 267863.3397 287586.4008 276229.9281 302662.1963 295036.2843 261644.5563 0.649580739 1.082311076 1.093984378 1.290951276 1.023768059 1.099149185 1.055744985 1.156768559 1.127622483 1 17.99724872 4.742438537 4.184606523 1.113358544 0.610615502 0.760402843 0.076428157 0.099613426 3.914082536 0.017617146 0.151113598 55263.51909 -4.742438537 -0.502743042 VERLSS(ph)GPEQITLEASSTEGHPGAPSPQHTDQTEAFQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VERLSSGPEQITLEASSTEGHPGAPSPQHTDQTEAFQK 38 1 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 VERLS(0.272)S(0.328)GPEQIT(0.29)LEAS(0.034)S(0.034)T(0.041)EGHPGAPSPQHTDQTEAFQK 71.383 0.0018186 1017800000 135710 111760 155820 121540 179720 192530 171030 149680 164690 90036 TRUE FALSE 141067.9356 130953.9106 159880.7972 145580.2492 149171.2586 147817.8253 157624.2217 147673.7844 158762.8391 107676.8304 1.310104831 1.216175385 1.484820798 1.352010909 1.385360788 1.372791387 1.463863871 1.371453672 1.474438266 1 16.71634832 -1.292050424 4.665713171 0.999810226 1.381351361 0.687020466 0.077192459 0.000149561 2.27E-05 0.073358252 0.017282179 0.051044573 1.292050424 0.381541134 VES(ph)LESLYFTPIPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VESLESLYFTPIPAR 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VES(1)LESLYFTPIPAR;VES(1)LESLYFTPIPAR 145.43 4.26E-06 35351000 16199.6 7409.5 13910.9 10362 15654.1 21634.2 12894.3 17371 12543.4 9545.3 TRUE FALSE 16839.17272 8682.023987 14273.42948 12411.57267 12993.22167 16609.98492 11883.61107 17138.17016 12091.96548 11415.51878 1.475112349 0.760545723 1.250353116 1.087254369 1.13820685 1.455035486 1.041004908 1.501304539 1.059256764 1 13.4787088 2.965424621 24.88916958 1.253890815 1.122259703 0.002096918 0.228541328 1578.010899 1135935.16 0.064312727 0.068247204 923.4738894 -2.965424621 -0.131631112 VES(ph)MEALPILSR ddPTM_MDA-MB-175_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 117.93 0.00071349 43638000 38630 39756 43334 37308 44005 42542 38686 32988 31868 23734 TRUE FALSE 40155.14223 46583.78374 44463.31964 44687.41105 36525.04582 32662.26523 35653.69023 32545.84982 30721.07691 28384.22289 1.41469937 1.641185807 1.566480077 1.574375005 1.286808026 1.150719023 1.256109437 1.14661761 1.082329329 1 14.79280162 3.085427188 2.787911809 1.148525149 1.559950938 0.852227383 0.082422554 0.094896092 1.495003331 0.0248648 0.030305543 1217.382875 -3.085427188 0.41142579 VES(ph)NRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESNRR 6 1 A0A1W2PRI8 A0A1W2PRI8 1 VES(1)NRR 56.721 0.089982 0 89236 104800 111110 100760 112660 148010 103360 109730 103690 106700 TRUE FALSE 92759.10619 122798.5848 114005.6179 120690.0273 93510.09344 113636.9206 95258.37312 108259.2488 99958.21715 127605.8221 0.726919075 0.962327445 0.89342019 0.945803454 0.732804287 0.890530845 0.746504913 0.848388005 0.783335866 1 16.96133463 3.259316772 24.99619928 0.824361312 0.888654117 0.054137591 0.093170171 551.4177466 664056.224 0.023653531 0.031993463 1816.840371 -3.259316772 0.064292805 VESGDPSLHPPPS(ph)PGTPSAT(ph)PASPPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 2 VESGDPS(0.026)LHPPPS(0.914)PGT(0.369)PS(0.103)AT(0.508)PAS(0.077)PPAS(0.004)ATPSQR 93.656 0.00037913 285920000 63922 95270 119710 113410 111390 160980 118330 118030 127630 140800 TRUE FALSE 66445.68992 111631.8814 122829.7409 135842.1595 92455.96759 123594.8347 109054.9854 116448.0009 123036.6212 168387.0642 0.394600917 0.662948083 0.729448794 0.806725624 0.549068113 0.733992455 0.647644675 0.691549564 0.730677394 1 17.36142179 -5 0.162245753 2.248377558 0.577824748 0.53609675 0.102007523 109.3267586 1.011820734 43.95769994 0.415164837 1.00E-05 5 -1.67055281 VESGDPSLHPPPS(ph)PGTPSATPAS(ph)PPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 2 VESGDPS(0.323)LHPPPS(0.674)PGT(0.015)PS(0.008)AT(0.082)PAS(0.877)PPAS(0.015)AT(0.004)PS(0.001)QR 73.982 0.0015275 124790000 31538 58157 60085 57906 50561 64568 55525 67532 58796 63454 TRUE FALSE 32783.14459 68145.01235 61650.86446 69359.63397 41966.65928 49573.06054 51172.80541 66626.844 56679.94345 75886.5964 0.432001778 0.89798483 0.812407821 0.913990576 0.553018073 0.653251864 0.674332594 0.877979079 0.746903223 1 16.21155747 0.709861369 0.882252769 0.996989434 0.724159551 0.242455968 0.147245189 1.539352489 2.193781309 0.140788347 0.047455296 5.126977 -0.709861369 -0.272829883 VESGDPSLHPPPS(ph)PGTPSATPASPPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPS(0.012)LHPPPS(0.985)PGT(0.003)PSATPASPPASATPSQR;VESGDPSLHPPPS(0.994)PGT(0.005)PS(0.001)ATPASPPASATPSQR 169.94 1.49E-14 529960000 56545 100174 93829 96140 102313 136199 102458 109260 101307 117858 TRUE FALSE 58777.44026 117378.1053 96274.26082 115156.2051 84921.87281 104568.8464 94427.07424 107795.5484 97660.98086 140950.0186 0.417009099 0.832764028 0.683038298 0.817000283 0.602496358 0.741886006 0.669933039 0.764778533 0.69287668 1 17.10482414 -4.999999998 0.22311361 2.5430296 0.664025996 0.422513083 0.110954494 145.8662597 1.459965584 101.3010784 0.187630466 1.00E-05 4.999999998 -1.879003604 VESGDPSLHPPPSPGTPS(ph)ATPASPPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPS(0.147)PGT(0.204)PS(0.356)AT(0.26)PAS(0.032)PPAS(0.001)ATPSQR 130.19 4.43E-08 723990000 47772 80084 78788 63583 83777 86710 75673 77412 74827 67611 TRUE FALSE 49658.07545 93837.80403 80841.28001 76159.52762 69536.61546 66572.9166 69741.55253 76374.41876 72133.99089 80858.08096 0.614138684 1.160524748 0.999792217 0.941891357 0.8599835 0.823330406 0.862518028 0.944548991 0.892106145 1 16.30310434 4.770263865 24.39651228 0.933359793 0.614137889 0.531787981 0.092123321 9239.531903 7109894.379 0.022973122 3.39630261 58920.15284 -4.770263865 -0.319221904 VESGDPSLHPPPSPGTPSAT(ph)PASPPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGT(0.011)PS(0.156)AT(0.447)PAS(0.361)PPAS(0.022)AT(0.002)PS(0.001)QR 102.17 4.89E-05 322110000 35175 59166 58500 62126 59401 77469 64520 66217 51309 62281 TRUE FALSE 36563.73616 69327.30025 60024.55806 74414.33737 49304.03924 59477.9988 59462.75381 65329.46942 49462.39911 74483.76951 0.490895351 0.930770565 0.805874333 0.999067822 0.661943395 0.798536368 0.798331693 0.877096713 0.664069494 1 16.18463847 -2.454115677 2.302192767 3.262225234 0.796283029 0.174331506 0.139509816 5735740.888 670293.1469 68429867.25 0.031123456 0.003514668 2.454115677 -2.465942205 VESGDPSLHPPPSPGTPSATPAS(ph)PPASATPSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VESGDPSLHPPPSPGTPSATPASPPASATPSQR 33 0 H3BLU1;Q4KMQ1 H3BLU1 TPRN Taperin 1 VESGDPSLHPPPSPGTPS(0.033)AT(0.263)PAS(0.557)PPAS(0.115)AT(0.027)PS(0.005)QR 107.15 6.27E-06 178310000 61340 119680 115950 109570 114410 148470 122470 119220 109150 118610 TRUE FALSE 63761.75056 140234.109 118971.7523 131242.619 94962.62907 113990.0926 112870.4814 117622.0509 105221.7128 141849.3586 0.44950327 0.988612923 0.838719001 0.925225326 0.66946111 0.803599634 0.795706674 0.829203967 0.741784904 1 17.1140001 -2.392762134 2.005609291 2.257872682 0.794934389 0.17401532 0.139837539 7574137.845 654458.161 43258293.63 0.03193826 0.004047975 2.392762134 -1.462938292 VESTDVSDLLHQYR ddPTM_MDA-MB-175_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 ; 207.8 8.93E-09 400750000 326550 399900 381980 388200 431970 495390 428890 385150 403790 368240 FALSE TRUE 339442.4462 468579.7142 391934.7126 464984.8013 358543.8937 380343.1802 395272.4811 379987.6942 389257.6768 440389.5776 0.770777656 1.064011816 0.889972725 1.055848787 0.814151633 0.863651638 0.897551852 0.86284443 0.883893935 1 18.7484208 3.215263736 24.99953055 0.878789617 0.949701375 0.087350012 0.089245118 450.0528337 482943.4854 0.023610816 0.028235643 1641.586366 -3.215263736 0.070911758 VET(ph)PQPGGASALQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VETPQPGGASALQR 14 0 Q86XN8-2 Q86XN8-2 MEX3D RNA-binding protein MEX3D 1 VET(0.837)PQPGGAS(0.163)ALQR 96.143 0.038996 633590000 253400 305200 310560 280790 371170 487750 310780 305650 307630 284120 TRUE FALSE 263404.4277 357615.7259 318653.4487 336329.4239 308078.656 374477.4544 286420.2515 301553.2617 296558.4564 339787.8742 0.775202553 1.052467592 0.937801119 0.989821737 0.906679371 1.102091872 0.842938413 0.887475053 0.872775278 1 18.37427484 -0.75187687 4.89942189 1.000000027 0.932603221 0.048652623 0.092464899 5.00E-08 1.25E-08 0.084925958 0.020017225 0.177061089 0.75187687 -0.067396806 VETGILRPGMVVTFAPVNITTEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VETGILRPGMVVTFAPVNITTEVK 24 1 A0A2U3TZH3;Q05639 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 233.22 2.29E-37 226520000 254020 158250 203960 162810 300180 254690 258190 248720 250540 164530 FALSE TRUE 264048.9057 185428.2065 209275.3652 195013.3321 249155.5108 195542.1074 237952.3931 245386.3152 241523.1143 196766.5034 1.341940326 0.942376895 1.06357211 0.991090093 1.266249623 0.993777416 1.209313522 1.247093946 1.227460519 1 17.58612512 2.195057656 24.99778231 1.198142696 1.093650213 0.047832579 0.133551903 284.0206428 163202.9606 0.047126042 0.034805091 156.6959084 -2.195057656 -0.104492483 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_MDA-MB-175_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 ; 164.66 1.39E-11 974080000 533860 308580 350220 297362 599970 484950 479820 403320 480840 273406 FALSE TRUE 554937.205 361576.2146 359347.0209 356179.3161 497987.3137 372327.712 442210.4546 397914.1551 463534.6623 326974.671 1.697187135 1.105823315 1.099005681 1.08931776 1.523014954 1.138705059 1.352430307 1.216957123 1.417647003 1 18.31881936 -1.719838384 2.710433826 0.951982777 1.276310279 0.163918686 0.195370873 33313140.94 27537235.38 10847613.12 0.045605465 0.019061699 1.719838384 0.324327502 VETLKEEEEELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VETLKEEEEELKR 13 2 Q9Y3L3;Q6ZT62-2;Q6ZT62;Q9Y3L3-2 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 0 ; 74.789 0.018647 79729000 168206 136227 122257 147801 165235 212616 169567 136149 132998 158665 FALSE TRUE 174846.9028 159622.9276 125443.1179 177035.5967 137148.4137 163239.1562 156275.8955 134324.1453 128211.428 189752.3689 0.921447799 0.841217048 0.661088547 0.932982274 0.722775766 0.860274668 0.8235781 0.707891797 0.675677614 1 17.53375837 1.78714985 25 0.762436174 0.819555057 0 0.112609038 357.6750253 184085.7809 0.048363185 0.027162365 61.25617149 -1.78714985 0.057118883 VEVGKDQEFTVDTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VEVGKDQEFTVDTR 14 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 ;;;; 214.53 6.24E-12 4396100000 5832140 4138740 5050260 4193490 6682030 6451450 6460140 5348680 5753840 3675610 FALSE TRUE 6062397.391 4849536.4 5181873.924 5022949.806 5546220.927 4953198.51 5953777.346 5276989.693 5546760.422 4395775.406 1.379141751 1.10322661 1.178830456 1.142676625 1.261716174 1.126808823 1.354431652 1.200468451 1.261838905 1 22.06768625 -1.207934587 4.928810123 0.999972716 1.218708212 0.366056721 0.087951656 2.43E-05 3.91E-06 0.078588399 0.018521154 0.061953438 1.207934587 0.218735497 VEVNNLNNLNNHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEVNNLNNLNNHDR 14 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 0 ; 185.67 1.15E-06 331580000 109275 115751 122664 135745 136967 173002 170383 126533 131322 102760 FALSE TRUE 113589.2614 135630.3338 125860.7246 162594.9558 113685.3983 132824.9074 157027.9352 124837.0321 126595.7469 122893.8545 0.924287563 1.103638049 1.024141728 1.323051966 0.925069839 1.080810004 1.277752544 1.015811837 1.030122681 1 16.90705325 4.740951961 23.69732132 1.092659647 0.924287447 0.144410854 0.117806731 195.6710661 1938761.363 0.026662798 0.17817004 55074.67734 -4.740951961 -0.1683722 VEVT(ph)PTVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEVTPTVPR 9 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 VEVT(0.996)PT(0.004)VPR 98.04 0.070237 143440000 60270 77680 72149 79617 92648 76136 73227 75033 60026 65119 TRUE FALSE 62649.50614 91020.93573 74029.26221 95365.00497 76899.72605 58454.56785 67487.2764 74027.30536 57865.67599 77877.82127 0.804458896 1.168765821 0.950582091 1.224546391 0.987440645 0.750593261 0.866578896 0.950556964 0.743031521 1 16.2489249 2.987991015 24.4533348 0.867328812 1.048524654 0.29202558 0.129695245 508.0097611 1034440.048 0.036382362 0.040569562 972.7270984 -2.987991015 0.181195841 VEVTEFEDIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VEVTEFEDIK 10 0 Q01105-2;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105 Q01105-2;Q01105 SET;SETSIP Protein SET;Protein SETSIP 0 ;;;;; 204.07 4.51E-07 815624000 1822190 1127825 1467489 1111654 1893310 1949130 1788270 1418960 1593560 1012402 FALSE TRUE 1894131.468 1321520.17 1505732.969 1331535.843 1571485.842 1496474.097 1648100.725 1399941.162 1536208.087 1210762.788 1.564411697 1.091477359 1.243623428 1.09974956 1.29793041 1.235976288 1.361208604 1.156247265 1.268793608 1 20.20748481 -3.73355177 0.342808255 1.03E-10 1.255963743 0.259681123 0.130444323 211.3063113 4.073688799 151.1356399 0.095726071 0.000184692 3.73355177 1.255963743 VEWSAFLEAADNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VEWSAFLEAADNLR 14 0 F5GYQ2;Q9UI30;F5GX77 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 73.781 0.046662 0 9908.7 16754 16855 14890 18144 24614 15116 19035 13899 23300 FALSE TRUE 10299.90313 19631.36917 17294.25515 17835.19756 15059.88936 18897.77153 13931.16842 18779.86696 13398.77771 27865.18889 0.36963335 0.704512331 0.620640155 0.640052993 0.540455312 0.67818566 0.499948824 0.673954411 0.480842881 1 14.76617631 -1.95756088 2.978838462 1.306378538 0.590092596 0.607536592 0.101213537 73427815.5 78525901.77 156633008.3 0.021822957 0.011026537 1.95756088 -0.716285941 VEYEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VEYEKR 6 1 P63279 P63279 UBE2I SUMO-conjugating enzyme UBC9 0 ; 86.086 0.086548 347810000 630170 509590 562600 434090 736930 815640 593510 553370 614740 643200 FALSE TRUE 655049.5982 597108.1184 577261.8182 519951.7064 611666.9018 626219.9711 546989.1354 545952.9803 592615.6275 769222.7252 0.851573383 0.776248671 0.750448211 0.675944287 0.795175288 0.814094476 0.711093312 0.709746296 0.770408372 1 19.55304186 0.947524869 22.45716948 1 0.7551852 0.670012679 0.050114081 3077.375339 1316990.392 0.050029562 0.01250739 8.861859673 -0.947524869 -0.2448148 VEYSEEELKTHISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VEYSEEELKTHISK 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 256.77 1.52E-24 2607710000 831330 1240190 1737140 1179510 2329060 2080360 1755460 1882180 1895960 1200650 FALSE TRUE 864151.5503 1453182.985 1782411.295 1412813.558 1933167.213 1597227.918 1617862.458 1856952.456 1827724.77 1435894.38 0.601821111 1.012040304 1.241324794 0.983925822 1.346315746 1.112357525 1.126728039 1.293237499 1.27288246 1 20.4535182 4.708481852 2.276841834 1.184132144 0.476854607 0.687744991 0.115621721 0.287341111 1.840630504 0.027609321 0.396269072 51107.17219 -4.708481852 -0.707277537 VFAENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VFAENK 6 0 O95994;B5MC07;C9J3E2;H7C3Z9 O95994 AGR2 Anterior gradient protein 2 homolog 0 ;; 122.15 0.045 563060000 1349590 1240200 1230990 1129090 1886290 1765800 1515420 1275950 1247540 1191730 FALSE TRUE 1402872.855 1453194.703 1263070.611 1352420.632 1565659.1 1355719.711 1396637.421 1258847.977 1202641.279 1425226.676 0.984315603 1.019623563 0.886224368 0.948916165 1.098533395 0.95123094 0.979940555 0.883261588 0.843824564 1 20.44275996 1.760391607 7.548087045 0.89832079 0.981283587 0.21036457 0.063061415 0.210514992 37.43768126 0.029942636 0.016267494 57.59590508 -1.760391607 0.082962798 VFCMTEEELKEHLLGDSAIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFCMTEEELKEHLLGDSAIDR 21 1 Q86TU7 Q86TU7 SETD3 Histone-lysine N-methyltransferase setd3 0 ; 126.69 1.26E-05 94609000 83577 64399 74679 73408 87696 103872 106680 83792 90942 44063 FALSE TRUE 86876.6845 75459.0273 76625.19609 87927.8833 72789.46524 79749.3022 98318.14284 82668.9053 87669.01518 52696.30121 1.648629648 1.431960604 1.454090597 1.668577894 1.381301222 1.513375709 1.865750358 1.568780036 1.663665441 1 15.68541408 2.421296881 24.9999933 1.595533316 1.510142966 0 0.224314431 358.090242 160361.8011 0.071827265 0.060095006 263.8134183 -2.421296881 -0.08539035 VFDAIMNFKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFDAIMNFKK 10 1 P13639 P13639 EEF2 Elongation factor 2 0 113.63 0.0039428 0 193590 160100 218050 146350 368330 269480 231570 219320 259170 254860 FALSE TRUE 201233.0827 187595.9296 223732.5621 175297.5932 305721.3982 206897.354 213418.9383 216380.3741 249842.5223 304794.9374 0.660224492 0.615482433 0.734042908 0.57513289 1.00303962 0.678808368 0.700204997 0.709921155 0.81970693 1 18.21747941 -5 0.148716576 2.003939269 0.628443305 0.417597878 0.107257252 134.7565793 1.195680397 39.93262738 0.545589537 1.00E-05 5 -1.375495963 VFDDES(ph)DEKEDEEYADEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK;VFDDES(1)DEKEDEEYADEK 257.1 7.86E-31 2753070000 4556730 772980 1270410 969150 2018080 3547680 2993180 1444740 1615450 463760 TRUE FALSE 4736633.219 905733.3021 1303517.928 1160844.977 1675047.482 2723785.086 2758566.73 1425375.623 1557310.27 554624.8928 8.540246355 1.633055627 2.350269426 2.093027184 3.020144794 4.911040094 4.973752109 2.569981337 2.807862197 1 19.08115284 4.747161126 24.97351779 2.980513562 8.540249199 0.663555611 1.217487895 714.8640385 2075722.838 0.303610705 3.582793199 55867.74294 -4.747161126 5.559735637 VFDFAGEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFDFAGEEVR 10 0 Q9UEE9;Q9UEE9-2 Q9UEE9 CFDP1 Craniofacial development protein 1 0 ; 111.65 0.0040131 63186000 66098 99925 85773 86131 90453 105875 79082 88078 84743 104261 FALSE TRUE 68707.60008 117086.3414 88008.31484 103167.4547 75077.83137 81287.1358 72883.3462 86897.45848 81693.11598 124688.9468 0.551032003 0.939027432 0.705822907 0.827398558 0.602120984 0.651919339 0.584521308 0.696913886 0.655175283 1 16.92797406 -1.159853757 4.383313574 1.000063529 0.694087528 0.413553851 0.110513754 15507322.71 4103342.834 9439.034467 0.025123377 0.069206398 1.159853757 -0.305976001 VFDGIPPPYDKK ddPTM_MDA-MB-175_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 69.602 0.079424 388850000 293840 275640 273010 226200 354110 363140 301530 316640 313070 265410 FALSE TRUE 305441.0301 322979.0258 280124.8649 270941.6849 293918.5087 278806.2384 277895.2907 312395.9587 301802.6719 317412.0079 0.962285681 1.017538775 0.882527623 0.853596203 0.925984214 0.878373318 0.875503395 0.98419704 0.950823108 1 18.27599718 1.670552271 8.146777239 0.975392168 0.913410013 0.284448923 0.046811183 0.178648262 20.67033687 0.024961712 0.013083996 46.83303152 -1.670552271 -0.061982155 VFDKDGNGYISAAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;Q96HY3;G3V361;A0A590UJI2 P0DP25 CALM2;CALM1 0 ;;;;;; 243.86 4.61E-20 41138130000 14096760 14390220 16736350 15186720 15912670 19241050 20926450 16607060 16728200 12433470 FALSE TRUE 14653310.97 16861628.34 17172513.03 18190607.89 13207840.04 14772607.74 19286180.17 16384469.52 16126155.35 14869570.39 0.985456243 1.133968763 1.154876205 1.223344549 0.888246243 0.993479122 1.297023361 1.101879146 1.084507146 1 23.82585963 -0.716833434 7.739898814 0.999999999 1.102291392 0.058140714 0.113121776 0 0 0.109854565 0.02589297 0.191940475 0.716833434 0.102291393 VFDKEGNGTVMGAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VFDKEGNGTVMGAELR 16 1 P08590;P05976-2;P05976 P08590 MYL3;MYL1 "Myosin light chain 3;Myosin light chain 1/3, skeletal muscle isoform" 0 ;;;;; 193.9 2.74E-10 5726700000 3655080 3488110 3813430 3034060 5176510 4825170 3751020 3951700 4193380 3900450 FALSE TRUE 3799385.381 4087165.759 3912811.119 3634188.012 4296608.679 3704597.394 3457005.251 3898733.925 4042461.073 4664668.499 0.814502763 0.876196403 0.83881869 0.779088163 0.921096254 0.794182351 0.741104165 0.835800856 0.866612724 1 22.15334313 0.82428278 2.571481911 0.999833318 0.824477491 0.553087743 0.047271025 0.530117104 6.095455651 0.045327693 0.012097144 6.672410851 -0.82428278 -0.175355828 VFDMLNRR ddPTM_MDA-MB-175_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 ; 143.01 0.00097537 2292800000 2447700 3137500 2811000 2232600 5979500 4124300 2712300 2755100 2693900 6810600 FALSE TRUE 2544337.086 3676341.219 2884256.969 2674201.616 4963106.726 3166493.829 2499702.839 2718172.391 2596947.065 8145006.673 0.312379988 0.451361351 0.354113518 0.328324055 0.609343482 0.388765038 0.306900036 0.333722549 0.318839157 1 22.95748445 -1.709318602 3.13375664 1.076255099 0.378828094 0.819042341 0.087681702 413792488.1 416106090.2 248928391.7 0.021531161 0.019529063 1.709318602 -0.697427005 VFEEDALSWEDKLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;; 296.49 4.01E-44 1007220000 697020 488691 680730 597430 783500 764400 778110 696410 754380 452433 FALSE TRUE 724538.8878 572619.8778 698470.383 715599.8708 650320.9499 586879.6846 717119.705 687075.763 727230.0112 541078.584 1.339064064 1.058293369 1.290885287 1.322543327 1.201897412 1.084647779 1.325352225 1.269826202 1.344037692 1 19.04547861 5.074922619 20.33462326 1.226454837 5.098369165 0.083049196 0.117959382 1152.355659 325628.1627 0.026010605 8346.32789 118829.0483 -5.074922619 3.871914328 VFEHIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFEHIGK 7 0 P04040 P04040 CAT Catalase 0 ; 70.268 0.057489 490420000 641450 702430 645360 767810 793320 972830 769080 639580 669600 644250 FALSE TRUE 666774.9413 823066.8884 662178.6118 919680.5263 658471.7498 746904.9759 708797.5 631007.4762 645501.2268 770478.4526 0.865403749 1.068254259 0.859438197 1.1936486 0.85462708 0.969404106 0.919944611 0.818981341 0.837792705 1 19.55539508 2.052417674 3.614665017 0.865760807 0.97303801 0.09698222 0.108378206 0.399840106 10.67810837 0.043621567 0.028752622 112.8282037 -2.052417674 0.107277203 VFELMTSLHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VFELMTSLHTK 11 0 Q06323;Q06323-3;Q06323-2;H0YLU2 Q06323 PSME1 Proteasome activator complex subunit 1 0 ;; 218.18 1.08E-11 2415500000 1702087 2351609 2809343 2611295 3589360 3526130 3211630 2932758 2930410 2432566 FALSE TRUE 1769286.709 2755479.553 2882556.786 3127801.357 2979241.869 2707239.747 2959894.049 2893449.176 2824945.117 2909180.733 0.608173528 0.94716685 0.990848301 1.075148519 1.024082772 0.930584929 1.017432164 0.994592444 0.971044901 1 21.4721815 4.755779667 2.914936846 1.001280978 0.53126934 0.917280273 0.035128377 0.112463645 1.32201771 0.008927913 0.126751557 56987.50805 -4.755779667 -0.470011637 VFELQTSACQILHGHTDIVLALDVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFELQTSACQILHGHTDIVLALDVFR 26 0 Q12788;J3KNP2;A0A087WYP7 Q12788 TBL3 Transducin beta-like protein 3 0 ; 76.198 0.013566 9979500 8301.6 8381.2 9320.9 7445.6 11189.5 12667.6 9615.9 7886.4 9545.2 6859.2 FALSE TRUE 8629.353578 9820.605903 9563.810311 8918.317457 9287.512787 9725.741879 8862.180632 7780.695708 9201.670117 8203.128913 1.051958792 1.197178053 1.165873463 1.087184848 1.132191495 1.185613683 1.080341505 0.948503405 1.12172687 1 13.00195859 1.99595796 10.25841424 1.016830475 1.137886586 0.442641524 0.057025112 0.107346203 196.9821908 0.021275717 0.014883428 99.07360363 -1.99595796 0.121056111 VFEVSLADLQNDEVAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFEVSLADLQNDEVAFR 17 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RI02;D6RED7;D6RGE0 P61247 RPS3A 40S ribosomal protein S3a 0 80.469 0.026414 53216000 12651 16331 15292 15543 16530 19676 15629 15568 17271 17224 FALSE TRUE 13150.47125 19135.72221 15690.52208 18617.35901 13720.2365 15106.54719 14403.95814 15359.33642 16649.42008 20598.71303 0.638412275 0.928976591 0.761723417 0.903811757 0.666072511 0.733373351 0.699264955 0.745645439 0.808274772 1 14.33026658 -1.297718492 9.24279774 1.000000076 0.765656496 0.384396655 0.089191176 1.32E-07 1.00E-08 0.082007098 0.019329252 0.050382708 1.297718492 -0.234343579 VFFRPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 60.358 0.089365 715760000 1494500 1467200 1345600 1420500 2220400 2315700 1884400 1804700 2028300 2039700 FALSE TRUE 1553504.014 1719180.187 1380667.441 1701470.66 1842977.201 1777913.77 1736695.804 1780510.948 1955301.879 2439340.163 0.636854194 0.704772632 0.566000373 0.697512666 0.755522837 0.728850284 0.711953105 0.729914989 0.801569994 1 21.21805952 -5 0.136001828 2.060439643 0.583131492 0.841887946 0.042855177 52.70677802 0.444711327 15.02691023 0.291225007 1.00E-05 5 -1.477308152 VFGALGPIGPSS(ph)PGLTLGGLAVSEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFGALGPIGPSSPGLTLGGLAVSEHR 26 0 Q86YD1;M0QZB9;M0QYQ4;M0QYH7;A0A0C4DGR2;M0QY25;Q86YD1-2 Q86YD1 PTOV1 Prostate tumor-overexpressed gene 1 protein 1 VFGALGPIGPS(0.007)S(0.986)PGLT(0.008)LGGLAVSEHR;VFGALGPIGPS(0.026)S(0.968)PGLT(0.006)LGGLAVSEHR 135.41 2.04E-05 317920000 275230 379630 434790 471210 484590 564780 415930 480110 422100 484680 TRUE FALSE 286096.2929 444828.4994 446120.9846 564413.9316 402219.5649 433618.4043 383328.3198 473674.9108 406908.7035 579643.7662 0.493572621 0.767417033 0.769646825 0.973725527 0.693908204 0.748077405 0.661317075 0.817182791 0.701997894 1 19.144807 -2.637811533 1.916554132 5.233261461 0.746340072 0.315908385 0.115563384 9265549.2 327917.3251 171065050.3 0.027574683 0.002302441 2.637811533 -4.486921389 VFGS(ph)LER ddPTM_MDA-MB-175_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 142.04 0.0026391 1233190000 772600 817610 865380 829140 980130 1076210 924390 918690 877720 881830 TRUE FALSE 803102.8446 958028.1574 887932.5137 993141.4173 813527.8527 826276.5376 851933.8964 906376.4632 846131.0287 1054607.705 0.76151809 0.908421352 0.841955269 0.941716444 0.77140329 0.783491846 0.807820664 0.859444189 0.802318269 1 20.00827501 -1.594984566 4.24033115 1.003172691 0.834488831 0.450152754 0.055940718 0.001661952 0.000158741 0.053650656 0.012419629 0.02541063 1.594984566 -0.16868386 VFGWVHR ddPTM_MDA-MB-175_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 787550000 658170 610160 687540 750630 883890 939940 924840 728040 701460 646080 FALSE TRUE 684155.0598 714950.2336 705457.8572 899102.3736 733646.6935 721653.1799 852348.6242 718281.8146 676214.5916 772667.0061 0.885446194 0.92530188 0.91301667 1.163635003 0.949499186 0.933976958 1.103125431 0.929613674 0.875169493 1 19.55948727 3.948823554 24.99997462 0.99299676 0.908819145 0.190813413 0.080863348 566.7598804 276865.4906 0.020759844 0.037425935 8888.399252 -3.948823554 -0.084177615 VFHTEDDQYCWQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFHTEDDQYCWQHR 14 0 Q8IWR0;Q8IWR0-2 Q8IWR0 ZC3H7A Zinc finger CCCH domain-containing protein 7A 0 ; 203.82 8.39E-09 317890000 76111 132274 125648 120457 127761 158382 125097 125136 118894 161660 FALSE TRUE 79115.92105 154991.0306 128922.4901 144283.0351 106044.2309 121600.1808 115291.5703 123458.7566 114615.0282 193334.1818 0.409218485 0.801674226 0.666837539 0.746288285 0.548502235 0.628963692 0.596333091 0.638576973 0.592833751 1 17.56073721 -1.920179496 2.545826864 1.230143538 0.632524801 0.550804979 0.101287243 15153564.9 7223353.137 20748653.75 0.023825727 0.012017676 1.920179496 -0.597618738 VFIDQNLS(ph)PGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFIDQNLSPGK 11 0 F5H452;Q5JSB6;Q5JSB5;Q14186 F5H452 TFDP1 Transcription factor Dp-1 1 VFIDQNLS(1)PGK;VFIDQNLS(1)PGK 152.16 3.47E-05 185041000 359610 213000 228132 212658 309641 328406 361510 262777 256226 168652 TRUE FALSE 373807.6805 249581.0931 234077.3073 254721.1177 257008.3334 252138.6835 333173.9016 259254.9041 247004.4763 201696.1304 1.853321032 1.23741141 1.160544364 1.262895412 1.274235321 1.250091824 1.651860653 1.285373714 1.224636664 1 17.62182388 -3.500462485 0.288468713 2.26E-11 1.3720444 0.226185213 0.206252547 152.069973 3.189985796 90.81542342 0.223304064 0.000315891 3.500462485 1.372044399 KPLSTHSTEYNLDSVPS(ph)PAEEFADFATFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KPLSTHSTEYNLDSVPSPAEEFADFATFSK 30 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 KPLSTHSTEYNLDSVPS(1)PAEEFADFATFSK 206.64 5.73E-26 267680000 124590 218850 250010 239670 320330 312740 283580 319510 324100 217780 TRUE FALSE 129508.9094 256435.7851 256525.466 287076.0107 265880.421 240110.8746 261352.2586 315227.4911 312435.7043 260449.8214 0.497250905 0.984588063 0.984932394 1.102231551 1.020850848 0.921908387 1.003464918 1.210319475 1.199600379 1 17.99064592 4.966037619 1.704562389 1.066943754 1.60E-10 0.780648391 0.088086124 0.915243686 1.620339148 0.025540338 1.909158157 92477.82763 -4.966037619 -1.066943753 down VFIGEFAYTYAAMYDKGPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VFIGEFAYTYAAMYDKGPFR 20 1 P15559-2;P15559;H3BNV2 P15559-2 NQO1 NAD(P)H dehydrogenase [quinone] 1 0 ;;; 254.58 3.58E-36 2071767000 1277871 1179207 1360535 1297776 1704318 1793283 1760221 1474200 1599029 1162877 FALSE TRUE 1328322.334 1381726.629 1395991.66 1554472.219 1414618.635 1376820.201 1622250.279 1454440.76 1541480.259 1390720.484 0.955132501 0.993532953 1.003790249 1.117745972 1.017184008 0.990004977 1.166481905 1.045818177 1.10840408 1 20.40740106 3.938926164 5.57659075 1.0657592 0.97943835 0.326844816 0.053202037 0.229619677 14.65424773 0.013364944 0.025113661 8688.127059 -3.938926164 -0.08632085 VFIPHGLIMDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFIPHGLIMDR 11 0 P00492 P00492 HPRT1 Hypoxanthine-guanine phosphoribosyltransferase 0 ; 160.77 2.71E-05 1752830000 1043630 1254050 1182530 1119170 1512000 1481620 1230900 1159700 1131080 1615470 FALSE TRUE 1084833.318 1469423.332 1213347.703 1340538.486 1254990.78 1137536.209 1134418.842 1144156.118 1090372.652 1931990.416 0.561510714 0.760574856 0.628029877 0.693863942 0.649584371 0.588789778 0.587176226 0.592216249 0.564377878 1 20.88165651 -1.886438571 3.125910154 1.164852196 0.626681096 0.781864733 0.05939742 7268016.568 18372584.08 8387713.84 0.0145453 0.012988573 1.886438571 -0.5381711 VFITDDFHDMMPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFITDDFHDMMPK 13 0 P14625 P14625 HSP90B1 Endoplasmin 0 ; 162.31 4.07E-05 1775040000 3016600 2552300 2937100 3134100 4030000 3910300 3879900 3041100 3285800 2180360 FALSE TRUE 3135697.697 2990637.671 3013643.239 3754015.626 3344982.039 3002192.086 3575783.3 3000339.029 3167544.7 2607559.796 1.202541051 1.146910485 1.155733128 1.43966617 1.282801662 1.151341607 1.371314017 1.150630959 1.214754386 1 21.31426891 0.54697606 1.076278848 1.000332137 1.243872084 0.359966013 0.0953715 1.742319499 2.923340115 0.092005612 0.028714411 3.523514474 -0.54697606 0.243539947 VFLAQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 118.18 0.051381 141300000 413400 453140 431590 412850 767170 624300 501370 415910 486890 740070 FALSE TRUE 429721.3512 530963.2701 442837.59 494510.4978 636766.7174 479315.7864 462071.3093 410335.4067 469366.924 885072.547 0.485521049 0.59990932 0.500340443 0.558723123 0.719451439 0.541555365 0.522071677 0.463617822 0.530314634 1 19.75543619 -1.148426282 4.500262 1.000063206 0.545184622 0.798825572 0.068219783 4.83E-05 9.13E-06 0.069598478 0.016402114 0.071051576 1.148426282 -0.454878584 VFLKYPESLRPAFPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFLKYPESLRPAFPR 15 2 O14617-5;O14617;O14617-4;A0A2R8Y4J3 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 135.47 1.62E-05 295140000 135690 141180 150490 120190 195520 189120 157880 150190 157610 163500 FALSE TRUE 141047.146 165426.5668 154411.893 143963.2233 162285.5802 145199.7461 145504.9531 148176.9487 151937.6469 195534.6946 0.721340764 0.846021557 0.789690512 0.736254114 0.82995798 0.742577917 0.7441388 0.757803872 0.777036767 1 17.57706509 0.913839684 18.7514583 1 0.771635683 0.759944594 0.038514817 1653.345516 359827.264 0.035663185 0.008915796 8.200487753 -0.913839684 -0.228364317 VFLLDR ddPTM_MDA-MB-175_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 ; 126.68 0.040453 739870000 638670 803350 702730 712280 935930 932450 775710 744640 719540 903200 FALSE TRUE 663885.1848 941319.1133 721043.7211 853166.8581 776840.9529 715902.6189 714907.8233 734659.3188 693643.896 1080164.747 0.614614749 0.871458836 0.667531247 0.789848827 0.719187471 0.662771694 0.661850727 0.680136359 0.642164908 1 20.04281994 -1.000188429 4.97124045 1.000003173 0.703683598 0.603426047 0.072674888 2.44E-06 4.90E-07 0.067056468 0.015805192 0.099956622 1.000188429 -0.296319575 VFNAGDDPSVPLHVLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFNAGDDPSVPLHVLSR 17 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 145.91 4.57E-07 127240000 40805 51081 56981 53991 71338 64685 58283 59763 54291 52280 FALSE TRUE 42416.01291 59853.76439 58465.97167 64670.25865 59211.99224 49662.88906 53714.62617 58961.97474 52337.07752 62523.26504 0.678403677 0.957303883 0.935107462 1.034339115 0.947039349 0.79431055 0.859114221 0.943040558 0.837081644 1 15.9321055 -0.23023223 0.010068573 1.866091284 1.41E-05 0.083471876 0.096931249 13694.40191 37.22870768 3592.917672 3307.267884 0.588528868 0.23023223 -1.866077211 VFNGSGKPIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFNGSGKPIDR 11 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 ; 117.93 0.00071892 815040000 1688390 1445640 1704140 1486680 2154620 2277700 2096770 1934110 1945060 1454230 FALSE TRUE 1755048.941 1693917.424 1748551.288 1780740.867 1788378.462 1748738.694 1932419.689 1908186.419 1875057.671 1739158.526 1.009136841 0.973986787 1.005400751 1.02390946 1.028301006 1.005508508 1.111123374 1.097189469 1.078140746 1 20.72995801 2.251236259 24.98480937 1.082706864 1.00774217 0.489353179 0.03116795 153.7818559 303117.2302 0.01054218 0.008766859 178.3348658 -2.251236259 -0.074964695 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 ; 231.89 8.91E-34 1191530000 752820 725720 842040 714610 953840 1120350 907820 925320 835270 925340 FALSE TRUE 782541.9149 850356.7647 863984.2541 855957.7251 791706.6175 860165.6916 836662.6963 912917.5989 805208.7959 1106642.656 0.70713153 0.768411338 0.780725602 0.773472557 0.715413068 0.777275019 0.756036912 0.824943439 0.727614096 1 20.07775801 -5 0.293262847 2.88475662 0.750237894 0.820776224 0.033684353 97.70104463 0.915169702 112.7986516 0.03394868 1.00E-05 5 -2.134518726 VFNYNTLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFNYNTLER 9 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 129.42 0.0009067 140120000 75555 46315 60272 58074 71047 74687 73575 56273 60887 72633 FALSE TRUE 78537.96974 54269.24097 61842.73783 69560.86387 58970.45632 57342.07614 67807.99925 55518.75248 58695.68876 86864.04571 0.90414819 0.624760688 0.711948624 0.800801566 0.678882221 0.660135913 0.780622163 0.639145368 0.675719031 1 16.40647153 -1.703973839 8.041282775 1.001194558 0.713161583 0.510936606 0.082091968 0.001633091 6.01E-05 0.073834946 0.01733937 0.019770887 1.703973839 -0.288032975 VFPEPT(ph)ESGDEGEELGLPLLSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.527)ES(0.473)GDEGEELGLPLLSTR 83.453 0.028463 22779000 13238 10261 10546 11033 11034 14536 13966 12250 11161 11245 TRUE FALSE 13760.64646 12023.24693 10820.83742 13215.29447 9158.444621 11160.2343 12871.30843 12085.80879 10759.31779 13448.24245 1.0232301 0.894038531 0.804628372 0.982678184 0.681014241 0.829865637 0.957099671 0.898690578 0.800053823 1 13.71513002 -1.636704243 8.540084092 1.000098956 0.874680509 0.134017645 0.095637887 0.000174826 7.44E-06 0.089843062 0.021159585 0.023083186 1.636704243 -0.125418447 VFPEPTES(ph)GDEGEELGLPLLSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VFPEPTESGDEGEELGLPLLSTR 23 0 Q9BUR4;E9PMG4 Q9BUR4 WRAP53 Telomerase Cajal body protein 1 1 VFPEPT(0.492)ES(0.508)GDEGEELGLPLLSTR;VFPEPT(0.146)ES(0.854)GDEGEELGLPLLSTR;VFPEPT(0.36)ES(0.64)GDEGEELGLPLLSTR 98.269 0.0019543 61505000 37752.3 43228 43408 41613.9 47083 51393 54947 48564 49310 41525.1 TRUE FALSE 39242.78996 50652.07273 44539.24814 49845.00521 39079.84848 39457.75462 50640.11056 47913.07901 47535.34273 49661.1483 0.790211087 1.019953716 0.896863034 1.003702228 0.786930021 0.794539715 1.01971284 0.964800063 0.95719379 1 15.59983 2.212764573 24.99991511 0.98192691 0.890183957 0.288287662 0.078888831 338.9186249 328456.6531 0.03003026 0.022186288 163.2166924 -2.212764573 -0.091742953 VFPLS(ph)PASNLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VFPLSPASNLR 11 0 A0A2R8YH03;Q5VWN6;J3KPH3 A0A2R8YH03 FAM208B Protein FAM208B 1 VFPLS(0.996)PAS(0.004)NLR;VFPLS(0.993)PAS(0.007)NLR;VFPLS(0.94)PAS(0.06)NLR 112.02 0.001659 85162000 132566 154307 152205 151734 190562 191814 150856 156447 143172 147078 TRUE FALSE 137799.808 180808.0269 156171.5873 181746.5323 158170.3393 147268.1055 139031.5125 154350.0839 138019.2677 175895.1181 0.78342031 1.027930899 0.887867662 1.033266496 0.899230979 0.837249533 0.790422804 0.87751204 0.784667984 1 17.42435592 2.996619641 24.98777267 0.849272588 0.940359508 0.138136536 0.086593064 214.9573332 1588994.865 0.023268133 0.027290699 992.246649 -2.996619641 0.091086921 VFQGTDEQLNDLYHNHQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VFQGTDEQLNDLYHNHQR 18 0 Q92878-2;Q92878;A0A1W2PQ90;Q92878-3;A0A494C1B7;E7EN38;A0A494BZX5;A0A494C122;A0A494C0Y7;E7ESD9 Q92878-2 RAD50 DNA repair protein RAD50 0 ;; 250.41 3.67E-25 768490000 140724 166214 158294 159651 208701 188842 143774 169514 154644 169439 FALSE TRUE 146279.8922 194759.9615 162419.2717 191229.4913 173226.0786 144986.3074 132504.6182 167241.9421 149078.3926 202637.3279 0.721880286 0.961125788 0.801526912 0.943703183 0.854857692 0.715496542 0.653900343 0.825326428 0.735690675 1 17.62854043 2.844818806 7.235921087 0.768826229 0.865012075 0.08571621 0.106660798 0.47321958 28.44763994 0.030423529 0.032315595 699.5500731 -2.844818806 0.096185846 VFQSLPHENKPLTLSNYQTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFQSLPHENKPLTLSNYQTNK 21 1 P04080;A0A1W2PQG6 P04080 CSTB Cystatin-B 0 266.35 3.25E-37 708030000 557260 432280 530810 478290 568650 713280 631730 451550 505660 456960 FALSE TRUE 579261.0551 506520.7273 544643.3447 572894.3344 471991.0761 547631.5299 582213.3519 445497.7108 487461.3954 546492.563 1.05996146 0.926857494 0.996616206 1.04831131 0.863673375 1.00208414 1.065363724 0.815194462 0.891981755 1 19.05984234 1.737415755 25 0.887691886 0.989467613 0.2468246 0.072134652 0.195766133 4058.060947 0.032011866 0.017752174 54.62805714 -1.737415755 0.101775727 VFQSWWDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFQSWWDR 8 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 0 78.516 0.059644 0 82062 96355 93282 98064 100570 112870 95487 93072 81603 105210 FALSE TRUE 85301.87113 112903.2217 95713.00555 117460.7665 83475.14732 86657.65306 88002.47943 91824.52208 78666.12397 125823.8851 0.677946568 0.897311521 0.760690273 0.933533139 0.663428468 0.688721803 0.699409968 0.729786097 0.625208194 1 16.94104629 4.018793561 24.65661197 0.747864858 0.797971981 0 0.122746106 915.0848758 1200545.053 0.029190178 0.063042484 10442.23737 -4.018793561 0.050107123 VFS(ph)LSEADSHGGHWV ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 VFS(0.999)LS(0.001)EADSHGGHWV;VFS(0.981)LS(0.019)EADSHGGHWV;VFS(0.998)LS(0.002)EADSHGGHWV;VFS(0.985)LS(0.015)EADSHGGHWV 267.07 1.41E-25 556170000 261118 372888 423388 424280 520430 554030 452891 491826 452570 434385 TRUE FALSE 271427.1403 436928.6133 434421.8391 508201.3177 431967.4945 425364.9289 417392.22 485233.8769 436282.0941 519494.4239 0.52248326 0.841065069 0.836239657 0.978261352 0.83151517 0.818805572 0.803458518 0.934050212 0.839820552 1 18.98674874 4.777712322 2.884123913 0.875920942 0.440527185 0.726500043 0.065370914 0.248304583 2.675395315 0.015417518 0.263361745 59939.39046 -4.777712322 -0.435393757 VFS(ph)PVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFSPVIR 7 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 VFS(1)PVIR 117.04 0.0055819 28499000 45808 47653 51657 47493 55292 57706 51145 45356 46839 37500 TRUE FALSE 47616.53521 55837.03206 53003.22386 56886.97365 45893.48559 44304.65604 47136.12126 44748.07701 45153.27354 44847.40702 1.061745558 1.245044826 1.181857043 1.268456248 1.023325285 0.987897829 1.051033368 0.997785156 1.006820161 1 15.45273695 3.187439581 9.368391525 1.011474438 1.19261089 0.728743402 0.053229708 0.164092974 28.49296128 0.014545079 0.017436284 1539.712307 -3.187439581 0.181136451 VFS(ph)QENVCDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFSQENVCDR 10 0 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 1 VFS(1)QENVCDR 64.374 0.076045 232500000 212570 146500 218240 114430 265930 197320 267720 167000 182910 157240 TRUE FALSE 220962.4277 171660.2354 223927.5137 137063.9125 220727.3136 151495.4204 246735.4068 164761.6382 176327.1048 188048.1675 1.175031008 0.912852477 1.190798702 0.728876619 1.173780721 0.805620296 1.312086207 0.87616721 0.937669892 1 17.52074272 4.757959462 22.61665282 0.996211185 1.175031618 0.089611168 0.173714021 2740.845537 3195292.38 0.037072311 1.164605905 57274.25675 -4.757959462 0.178820433 VFSWGFGGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFSWGFGGYGR 11 0 Q9P258 Q9P258 RCC2 Protein RCC2 0 ; 145.17 8.46E-05 564330000 184050 230900 193553 178906 255140 251840 216750 229530 197845 248060 FALSE TRUE 191316.4361 270555.2788 198597.1502 214293.0728 211771.3939 193353.9767 199760.5686 226453.5258 190724.5971 296662.6076 0.644895687 0.911996564 0.669437756 0.722346084 0.713845926 0.651763895 0.673359444 0.763336936 0.642900697 1 18.17846357 -1.673878179 5.263433158 1.00545855 0.715817242 0.559560707 0.076937768 0.004710328 0.000291851 0.071201477 0.016538247 0.021189554 1.673878179 -0.289641309 VFSWLQQEGHLSEEEMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFSWLQQEGHLSEEEMAR 18 0 P22102 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 199.41 1.63E-15 92705000 16092 49127 43211 44769 42896 56749 43217 42834 43094 45539 FALSE TRUE 16727.32459 57564.18009 44337.11416 53624.17458 35604.55324 43569.90479 39829.53861 42259.88029 41543.05536 54461.49515 0.307140385 1.056970249 0.814100201 0.984625457 0.653756441 0.800013012 0.731333918 0.775958871 0.762796821 1 15.73294897 -1.927441134 2.516725261 1.145780939 0.777956929 0.117449591 0.190224769 34362352.84 16042300.31 29423231.39 0.041945366 0.011818405 1.927441134 -0.36782401 VFTESEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFTESEDR 8 0 Q9Y263;E5RIM3 Q9Y263 PLAA Phospholipase A-2-activating protein 0 77.282 0.062646 0 102730 117800 107140 107350 145860 150100 107570 117180 131600 126920 FALSE TRUE 106785.8597 138031.2336 109932.1564 128583.5096 121066.7693 115241.5498 99138.38232 115609.3938 126863.7417 151787.544 0.703521889 0.909371283 0.724250182 0.847128205 0.797606748 0.759229294 0.653139116 0.761652707 0.835798106 1 17.21169388 0.890970262 3.443111904 0.999835259 0.770186012 0.511105672 0.068225977 0.372277875 9.257858401 0.064647084 0.016719997 7.77983277 -0.890970262 -0.229649246 VFTTQELVQAFTHAPATLEADR ddPTM_MDA-MB-175_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 ;; 257.86 3.70E-37 2094704000 1394704 1580918 1553667 1491007 1754825 1873488 1664102 1710522 1522039 1537199 FALSE TRUE 1449767.991 1852428.369 1594156.838 1785923.734 1456540.473 1438398.805 1533665.337 1687595.25 1467261.114 1838383.713 0.788610115 1.007639676 0.867151307 0.971464076 0.792294048 0.782425777 0.834246587 0.917977699 0.798125605 1 20.81000649 5.032807947 16.42072498 0.879718957 0.47363141 0.109021264 0.081672745 8804802.84 120703003.5 0.018968203 101988118.2 107846.9698 -5.032807947 -0.406087547 VFTTVGSAEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VFTTVGSAEKR 11 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ; 242.45 1.45E-15 5485100000 3307700 3035300 3375400 2951000 6017900 5393200 4264500 4264100 4927200 4626000 FALSE TRUE 3438290.55 3556589.164 3463365.697 3534698.992 4994979.508 4140711.035 3930237.347 4206946.714 4749871.034 5532376.13 0.62148532 0.642868287 0.626017757 0.638911547 0.902863325 0.748450745 0.71040675 0.760423119 0.858558949 1 22.39946781 -4.388273208 0.044877559 2.259858827 8.60E-13 0.708359097 0.067239899 349.0906899 1.292973192 58.93949624 17.40838506 4.09E-05 4.388273208 -2.259858827 VFVEEQVYSEFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFVEEQVYSEFVR 13 0 H0Y2X5;P47895 H0Y2X5 ALDH1A3 Aldehyde dehydrogenase family 1 member A3 0 134.98 0.00020778 14795000 5840.5 7298.8 9680.3 6538.2 9667 10283 6953.2 7643.1 7469.9 7104 FALSE TRUE 6071.08745 8552.312123 9932.57657 7831.436445 8023.806793 7894.92909 6408.190015 7540.656746 7201.059758 8495.892786 0.714590874 1.006640778 1.169103333 0.921790875 0.944433622 0.929264209 0.754269172 0.887564961 0.847593059 1 13.05254984 2.463830285 24.79762305 0.859241354 0.962045577 0.083533962 0.118235428 423.3949826 789943.4058 0.040955177 0.034282766 290.9579881 -2.463830285 0.102804223 VFVGGLS(ph)PDTSEEQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFVGGLSPDTSEEQIK 16 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 VFVGGLS(1)PDTSEEQIK 105.14 0.0013709 35991000 85487 61006 78310 61271 80546 112470 109130 75763 98058 43543 TRUE FALSE 88862.09277 71483.30594 80350.82293 73390.22092 66854.81969 86350.547 100576.1054 74747.52091 94528.91173 52074.41717 1.706444308 1.37271447 1.542999947 1.409333506 1.283832318 1.658214373 1.93139186 1.435398128 1.815265861 1 15.66828717 2.695070328 24.96782447 1.611466342 1.459500971 0.02665621 0.256870464 1224.554754 703017.2264 0.077510994 0.07307839 495.5304281 -2.695070328 -0.151965371 VFVGGLSPDT(ph)SEEQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFVGGLSPDTSEEQIK 16 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 VFVGGLS(0.254)PDT(0.632)S(0.114)EEQIK 147.64 1.13E-05 32334000 71902 45944 57382 48352 65155 64595 87972 57452 56470 38527 TRUE FALSE 74740.74648 53834.52461 58877.42206 57915.88128 54079.97637 49593.7902 81076.52477 56681.94991 54437.65573 46075.62801 1.62213191 1.168394809 1.277843073 1.256974322 1.173721959 1.07635625 1.759640145 1.230193757 1.181484835 1 15.49171621 1.013556614 2.629388549 1.005134916 1.316996406 0.203274336 0.200221495 0.41837972 6.512310801 0.184980903 0.049734785 10.31707563 -1.013556614 0.311861489 YSSS(ph)GS(ph)PANSFHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 Y(0.001)S(0.029)S(0.304)S(0.668)GS(0.998)PANSFHFK 118.13 0.00038511 97910000 86837 144900 174140 147370 199580 229620 204560 202650 197620 167480 TRUE FALSE 90265.39181 169785.4478 178678.2315 176519.3461 165655.4629 176294.2349 188526.0527 199933.8082 190507.6948 200294.4994 0.450663359 0.847679034 0.892077576 0.881299021 0.827059472 0.880175119 0.941244284 0.998199196 0.951137926 1 17.61176328 4.985141007 1.682818702 0.923539666 6.48E-12 0.880715082 0.051668748 0.706924182 1.165303186 0.015359811 1.282488513 96636.45874 -4.985141007 -0.923539666 down VFVHYTGWLLDGTKFDSSLDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 247.89 2.51E-31 1345158000 805195.4 966717 1402219 939491 2065526 1717686 1483796 1602275 1732871 1233514 FALSE TRUE 836985.1361 1132743.125 1438761.979 1125319.516 1714428.628 1318779.458 1367492.192 1580799.124 1670505.311 1475197.451 0.567371599 0.767858651 0.975301291 0.762826369 1.16216892 0.893968097 0.926989259 1.071584772 1.132394385 1 20.49247664 5.222476796 0.607171535 1.027928981 5.37E-13 0.636450341 0.105946466 3.769553734 0.689846 0.04631422 3.077550934 166907.8626 -5.222476796 -1.027928981 VFVLDEADVMIATQGHQDQSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 213.15 1.25E-23 92630000 84269 107368 93785 104745 106496 123118 96783 99421 97697 102645 FALSE TRUE 87596.00519 125807.6188 96229.11415 125463.2484 88393.84796 94525.71037 89196.89556 98088.42411 94180.90405 122756.3225 0.713576323 1.024856531 0.783903527 1.022051213 0.720075725 0.770027225 0.726617528 0.799049875 0.767218357 1 16.90543781 3.210463217 24.99995684 0.782115666 0.888708994 0.116814799 0.115338382 350.8210735 312145.7935 0.030191682 0.03609265 1623.540837 -3.210463217 0.106593328 VFVTPQAPLEAIQAYLAGHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VFVTPQAPLEAIQAYLAGHYR 21 0 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 0 149.94 5.29E-11 0 99485 120830 234290 198950 241030 248230 238930 170790 262890 139980 FALSE TRUE 103412.7446 141581.6126 240395.7899 238301.7162 200059.8067 190582.3445 220202.0423 168500.8394 253428.6403 167406.4009 0.617734711 0.845735956 1.436001184 1.423492261 1.195054703 1.138441203 1.31537409 1.006537614 1.513852749 1 17.35299517 4.407007492 4.905921021 1.243165171 0.666282035 0.618582836 0.16771333 0.113966714 5.05762197 0.040571871 0.121790692 25527.45341 -4.407007492 -0.576883136 VGCYDANDAS(ph)DEEEFDREGDCISLPGALPGPIRPLSEDDPRR ddPTM_MDA-MB-175_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(0.169)DANDAS(0.83)DEEEFDREGDCIS(0.001)LPGALPGPIRPLSEDDPRR 49.385 0.021766 35024000 4659 7711.6 6455.6 4983.8 7050.4 9785.3 6041.7 5480.1 6943.5 6426 TRUE FALSE 4842.940918 9036.007312 6623.838239 5969.580765 5851.975526 7512.812373 5568.135767 5406.648223 6693.604791 7685.051667 0.630176754 1.175790054 0.861911998 0.776778221 0.761475105 0.977587751 0.724541097 0.703527895 0.870990213 1 12.90783924 4.005060668 24.99950784 0.809574461 0.931950265 0.014464248 0.155129955 319.0327987 1575965.039 0.036290166 0.077980086 10117.20776 -4.005060668 0.122375805 VGDAIPAVEVFEGEPGNKVNLAELFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDAIPAVEVFEGEPGNKVNLAELFK 26 1 P30044-2;P30044;P30044-3 P30044-2 PRDX5 "Peroxiredoxin-5, mitochondrial" 0 165.62 1.14E-11 223780000 93046 64945 85541 56267 113650 102800 83043 79154 85629 61316 FALSE TRUE 96719.52793 76098.79855 87770.26873 67396.44466 94331.81359 78926.25795 76533.87267 78093.0701 82547.22902 73329.69623 1.31896807 1.037762359 1.196926665 0.919088011 1.286406714 1.076320536 1.043695482 1.06495832 1.125699863 1 16.16210994 4.746213753 24.48487696 1.087036905 1.318968221 0.346352918 0.096958717 756.3204833 2419638.344 0.021167512 0.223009881 55746.00547 -4.746213753 0.231931315 VGDNDFLEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDNDFLEVR 10 0 O00178;F5H716;F5H257 O00178 GTPBP1 GTP-binding protein 1 0 83 0.04096 0 19473 21697 23587 23488 25838 30946 27657 22580 20819 21633 FALSE TRUE 20241.80908 25423.29097 24201.6966 28133.8563 21446.06599 23759.26049 25489.17207 22277.35203 20069.72826 25871.57216 0.782395788 0.982672828 0.935455196 1.087442855 0.828943284 0.91835395 0.985219294 0.861074538 0.77574444 1 14.65908011 1.635225518 8.623327573 0.863404216 0.934967124 0.052712131 0.09445697 0.252944905 39.70825879 0.044923131 0.023194354 43.17432116 -1.635225518 0.071562908 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VGDPPQPLPEEPMEVQGAERASPEPQR 27 1 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR;VGDPPQPLPEEPMEVQGAERAS(1)PEPQR 177.86 1.29E-17 3402380000 172645.1 168963.9 191747.7 201487.4 213367.8 221520.8 195145.6 188836.7 181035.6 155866.3 TRUE FALSE 179461.2619 197982.1355 196744.8026 241341.0063 177099.6176 170075.9514 179849.578 186305.6529 174520.1641 186405.3172 0.962747547 1.062105622 1.05546776 1.294710955 0.950078143 0.912398605 0.964830728 0.999465335 0.936240268 1 17.50808349 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENAS(ph)PAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 44 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 2 VGDPPQPLPEEPMEVQGAERAS(1)PEPQRENAS(0.974)PAPGT(0.019)T(0.006)AEEAMS(0.001)R 84.17 7.96E-05 130090000 18135 20599 19801 23528 24120 31893 15681 23292 21147 22022 TRUE FALSE 18850.9838 24136.71801 20317.03033 28181.76818 20020.09102 24486.33409 14451.88225 22979.80884 20385.9236 26336.78926 0.715766209 0.916463954 0.771431556 1.070053297 0.760156859 0.929738771 0.54873364 0.872536459 0.774047413 1 14.68479186 VGDPPQPLPEEPMEVQGAERAS(ph)PEPQRENASPAPGTTAEEAMSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDPPQPLPEEPMEVQGAERASPEPQRENASPAPGTTAEEAMSR 44 2 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;H0Y710 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 1 VGDPPQPLPEEPMEVQGAERAS(0.925)PEPQRENAS(0.041)PAPGT(0.011)T(0.011)AEEAMS(0.012)R 51.511 0.011737 85628000 3555.5 1686.6 0 0 2560.2 4394.5 0 2104.2 0 0 TRUE FALSE 3695.873885 1976.26043 0 0 2125.018118 3373.943974 0 2075.996641 0 0 0 VGDPQELNGITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGDPQELNGITR 12 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;; 227.72 2.85E-11 2300080000 952440 993340 1067490 1025910 1145150 1289390 1000750 984590 1024950 924350 FALSE TRUE 990043.0666 1163938.418 1095309.666 1228831.936 950497.812 989948.7134 922308.6 971393.1815 988062.2497 1105458.685 0.895594815 1.052900876 0.990819179 1.111603674 0.859822104 0.895509463 0.83432209 0.878724094 0.893802965 1 20.07621368 3.216190157 24.97360687 0.88319747 1.014034008 0.439822428 0.06516087 182.5410406 203781.9509 0.01766181 0.021124664 1645.091875 -3.216190157 0.130836538 VGDQVWLFIDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGDQVWLFIDEPR 13 0 P49588;P49588-2;H3BPK7 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;;; 178.32 3.42E-05 277339000 215463 216427 241925 224703 273620 305488 271541 269228 268320 209028 FALSE TRUE 223969.6456 253596.6537 248229.7642 269148.5827 227110.1701 234543.0417 250256.9069 265619.439 258663.2156 249983.0345 0.895939383 1.014455458 0.992986443 1.076667396 0.908502333 0.938235837 1.001095564 1.062549863 1.034723081 1 17.93147066 1.984735834 10.27854889 1.037526454 0.975505867 0.21959051 0.051291313 0.579864116 376.5901456 0.02088945 0.01406756 96.54634429 -1.984735834 -0.062020587 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8;Q9H8Y8-3;Q9H8Y8-2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 1 VGDSTPVSEKPVSAAVDANAS(0.003)ES(0.997)P;VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANAS(0.004)ES(0.996)P;VGDSTPVSEKPVSAAVDANASES(1)P;VGDSTPVSEKPVSAAVDANASES(1)P 288.61 9.51E-54 2711870000 5564730 4204750 5462270 4188750 6427340 6713920 6363720 5409440 6086550 4018360 TRUE FALSE 5784429.837 4926883.104 5604621.244 5017272.248 5334823.043 5154713.83 5864914.998 5336935.305 5867496.254 4805680.706 1.203665035 1.025220651 1.166249193 1.044029463 1.110107677 1.072629279 1.220412956 1.110547211 1.220950083 1 22.19630937 VGDTEKPEPERS(ph)PPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 VGDTEKPEPERSPPNR 16 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDT(0.207)EKPEPERS(0.793)PPNR;VGDTEKPEPERS(1)PPNR;VGDT(0.003)EKPEPERS(0.997)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR;VGDTEKPEPERS(1)PPNR 172.3 2.41E-09 9859190000 6733730 4146350 5305570 4115740 7318900 7002500 6686810 5150980 5992840 3845180 TRUE FALSE 6999582.86 4858453.358 5443837.513 4929821.088 6074835.992 5376275.499 6162680.359 5081939.538 5777158.859 4598569.401 1.522121828 1.056514088 1.183811103 1.072033639 1.321027359 1.169119139 1.340129902 1.105113155 1.256294807 1 22.13275368 -3.824655988 0.361936798 3.04E-09 1.219555303 0.195527261 0.135530519 314.5605448 5.719984224 238.8127864 0.090576897 0.000149742 3.824655988 1.2195553 VGDTEKPEPERS(ph)PPNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDTEKPEPERSPPNRK 17 3 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 1 VGDTEKPEPERS(1)PPNRK 111.13 0.00037422 79318000 203350 88112 122740 81354 195550 180900 168400 125860 134790 76203 TRUE FALSE 211378.415 103244.5506 125938.7052 97445.57838 162310.4808 138888.7166 155200.368 124173.0526 129938.9342 91133.51886 2.319436555 1.132893274 1.381914216 1.069261668 1.781018476 1.524013539 1.702999839 1.362539866 1.425808373 1 16.47569415 0.662724857 1.266969618 1.001589445 1.517257965 0.18588382 0.336622411 1.976020543 4.953050039 0.302959296 0.091376334 4.599650748 -0.662724857 0.51566852 VGDVT(ph)PQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDVTPQVK 9 0 Q13428-4;Q13428;Q13428-3;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGDVT(1)PQVK 131.17 0.0038071 271400000 386930 232090 273980 203780 338830 349610 315010 269530 289760 209080 TRUE FALSE 402206.2952 271949.6521 281120.1439 244087.0758 281235.7976 268418.3759 290318.6931 265917.3912 279331.5942 250045.2229 1.60853421 1.08760187 1.124277203 0.976171722 1.124739734 1.07347932 1.161064745 1.063477191 1.117124298 1 17.93182952 4.738652101 8.33716581 1.084581934 1.612006082 0.894395939 0.054380795 0.023932382 24.05312986 0.011998071 0.070839698 54783.79338 -4.738652101 0.527424148 VGDVVEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGDVVEFR 8 0 Q9UHQ9;H7C0R7 Q9UHQ9 CYB5R1 NADH-cytochrome b5 reductase 1 0 85.212 0.043352 0 127720 135880 145200 162680 154830 207190 131500 130090 122080 147710 FALSE TRUE 132762.4842 159216.333 148984.0313 194857.6184 128512.0519 159073.2625 121192.6864 128346.3563 117686.3646 176650.9464 0.751552635 0.901304727 0.843380884 1.103065805 0.727491443 0.900494822 0.686057385 0.72655346 0.666208515 1 17.43054195 2.246921609 24.98944651 0.74256217 0.875323367 0.114961165 0.129198396 285.5616094 853491.0056 0.042782028 0.035244711 176.5719077 -2.246921609 0.132761198 VGDVYIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VGDVYIPR 8 0 Q01130;Q01130-2;J3KP15;J3QL05;Q9BRL6-2;Q9BRL6 Q01130;Q9BRL6-2 SRSF2;SRSF8 Serine/arginine-rich splicing factor 2;Serine/arginine-rich splicing factor 8 0 ;;;;;; 154.31 0.00099363 3423100000 2310454 2639330 2605210 2486580 3039350 3230070 2752940 2783050 2644700 2626900 FALSE TRUE 2401672.508 3092614.396 2673103.913 2978418.102 2522722.373 2479935.195 2537157.369 2745747.767 2549517.764 3141590.76 0.764476563 0.98441033 0.850875915 0.948060499 0.803007955 0.789388365 0.80760276 0.873999186 0.811537198 1 21.58306383 5.040431207 15.37647037 0.865091378 0.343430755 0.154193869 0.074404933 894520.0405 9861186.726 0.01705749 12948539.39 109756.742 -5.040431207 -0.521660623 VGEAWQDRPGAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGEAWQDRPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;H7C1R1;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ;; 112.08 0.00084697 802030000 325667 377840 377530 347190 454540 462820 414300 368330 392410 372530 FALSE TRUE 338524.5846 442731.0808 387368.7419 415863.1457 377277.4532 355337.0691 381826.0834 363393.1388 378287.2408 445520.121 0.759841293 0.993739811 0.869475302 0.933432916 0.846824723 0.797578049 0.857034431 0.815660442 0.84909126 1 18.76513106 3.191388245 19.85070345 0.846401447 0.895191429 0.008017188 0.075628631 37.22688281 15664.13157 0.02009379 0.024017334 1553.775415 -3.191388245 0.048789981 VGEAWQERPGAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGEAWQERPGAPR 13 1 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;H7BZT5;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 0 ;;; 148.96 3.97E-05 695970000 416138 448979 450040 373185 537180 677070 506650 459266 481260 454157 FALSE TRUE 432567.4496 526087.6507 461768.4121 446999.8792 445870.3355 519830.7536 466937.4491 453110.2905 463939.5466 543140.3688 0.796419258 0.968603479 0.850182455 0.822991449 0.820911796 0.957083626 0.8596994 0.8342416 0.854179828 1 19.05096557 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK;VGEDEDGS(1)DEEVVHNEDIHFEPIVSLPEVEVK 284.3 1.08E-73 2294110000 543201 258263 387760 233967 551768 599164 480651 364156 428501 214916 TRUE FALSE 564646.9949 302617.6612 397865.3441 280244.9743 457978.6724 460017.2414 442976.3187 359275.0845 413079.3327 257024.6754 2.196859092 1.177387583 1.547965554 1.090342683 1.7818471 1.789778513 1.723477787 1.397823318 1.60715827 1 17.97154734 -0.20322894 0.988964381 0.990550878 1.572012779 0.250355112 0.304309863 19.74463102 14.3311672 1.03465793 0.088886919 0.62628363 0.20322894 0.581461901 VGEEEHVY(ph)SFPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGEEEHVYSFPNK 13 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 VGEEEHVY(0.954)S(0.046)FPNK;VGEEEHVY(0.984)S(0.016)FPNK 171.29 0.00014713 876360000 1385760 932560 1138020 953470 1627260 1567360 1409380 1118150 1281770 798220 TRUE FALSE 1440470.875 1092719.926 1167677.736 1142063.52 1350658.926 1203364.394 1298909.113 1103163.028 1235639.348 954615.9262 1.508953324 1.1446697 1.223191133 1.196359173 1.414871562 1.260574395 1.360661474 1.155609285 1.294383756 1 19.86456088 -0.201914135 0.568838732 0.973310475 1.286658113 0.377315042 0.109998917 6.408798882 2.092089159 0.479568999 0.044782223 0.628182545 0.201914135 0.313347637 VGEEEHVYS(ph)FPNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGEEEHVYSFPNK 13 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;F5H836;P49023-3 F5GZ78;P49023-3 PXN Paxillin 1 VGEEEHVYS(1)FPNK 94.922 0.0031776 100390000 104700 73512 101180 79531 148640 140940 135870 100120 126080 72414 TRUE FALSE 108833.6368 86137.11416 103816.8339 95261.99442 123374.2259 108208.821 125220.1544 98778.05516 121542.4054 86602.13685 1.256708446 0.994630355 1.198779126 1.099995888 1.424609489 1.24949366 1.445924534 1.140596049 1.403457349 1 16.402115 3.269235617 24.99981769 1.284641629 1.131696418 0.186515622 0.142353754 297.7921632 242695.6503 0.036163041 0.048959812 1858.812642 -3.269235617 -0.152945211 VGEEFEEQTVDGRPCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VGEEFEEQTVDGRPCK 16 1 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;;;; 271.19 3.48E-35 12635000000 6947550 3900620 5118640 3580760 7297210 6750990 6722030 5080050 5929000 2977025 FALSE TRUE 7221844.639 4570521.142 5252035.963 4289023.64 6056832.851 5183174.885 6195139.724 5011960.239 5715616.448 3560316.05 2.028427965 1.283740285 1.475160039 1.204674973 1.701206512 1.455818756 1.740053309 1.407729024 1.605367717 1 21.76357388 -1.13022344 4.878833899 0.999969942 1.526570523 0.33743303 0.227705498 6.80E-05 1.21E-05 0.201487162 0.047488274 0.074092894 1.13022344 0.526600581 VGEFCHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VGEFCHNR 8 0 P22314;P22314-2;Q5JRR9;Q5JRS0;Q5JRS2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ;;;; 190.52 0.00018602 5766840000 5840680 5727370 5866620 5208920 8276190 7856480 6692200 6254520 6006830 5842550 FALSE TRUE 6071274.556 6711001.245 6019508.937 6239228.829 6869406.18 6031931.586 6167647.877 6170688.39 5790645.362 6987285.81 0.868903137 0.960458957 0.861494592 0.892940263 0.983129411 0.863272485 0.882695806 0.883130955 0.828740303 1 22.73630072 VGEGDKEDATRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGEGDKEDATRR 12 2 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 83.53 0.0071695 136300000 222380 127350 181250 122630 242780 241590 221190 161480 196270 109440 FALSE TRUE 231159.7341 149221.3719 185973.5239 146885.848 201512.3423 185484.3838 203852.5498 159315.6247 189206.281 130882.6726 1.766159946 1.140115562 1.420917835 1.122271153 1.539641102 1.417180595 1.557521295 1.217240002 1.445617492 1 16.99791459 -0.841700298 0.661827263 0.933102 1.391432701 0.284127864 0.190198821 31.27663928 8.144306752 4.650396673 0.065382441 0.143979182 0.841700298 0.458330701 VGEGFEEETVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGEGFEEETVDGR 13 0 P29762;B5MCB5 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 ; 191.53 8.12E-06 820550000 502190 467340 543510 445898 610070 687580 594260 527450 562090 466567 FALSE TRUE 522016.849 547602.0096 557674.3171 534095.2935 506370.5193 527899.9654 547680.3484 520380.3955 541860.4907 557981.8707 0.935544462 0.981397494 0.999448811 0.957191123 0.907503534 0.946088024 0.981537891 0.932611654 0.971107699 1 19.08985872 0.988640549 23.7980605 1.000000003 0.955604164 0.222976461 0.025686573 459.8478191 963385.4029 0.025696639 0.00642416 9.741830061 -0.988640549 -0.044395839 VGEGFEEETVDGRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGEGFEEETVDGRK 14 1 P29762;B5MCB5 P29762 CRABP1 Cellular retinoic acid-binding protein 1 0 ; 168.89 5.48E-06 411820000 278080 171628 253750 170572 371680 330330 279550 212825 280790 170330 FALSE TRUE 289058.8131 201103.7739 260362.9335 204310.6325 308501.9664 253615.8637 257638.1405 209972.429 270684.4227 203702.9023 1.419021574 0.987240592 1.278150338 1.002983414 1.514470156 1.245028229 1.264774029 1.030777797 1.328819667 1 17.63610701 -1.050516158 4.420520229 0.99998639 1.214327102 0.138469443 0.168101121 0.191388293 46431820.1 1381.509674 0.036891489 0.089019232 1.050516158 0.214340712 VGELKDDDFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGELKDDDFER 11 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 ;; 151.16 3.06E-05 1745090000 3996240 2033030 2785620 1910210 4101390 3953380 3758240 2664110 3062310 1433890 FALSE TRUE 4154014.641 2382187.088 2858215.546 2288043.837 3404237.193 3035267.409 3463659.328 2628401.963 2952098.061 1714833.292 2.422401443 1.389165407 1.666760005 1.334266046 1.985170925 1.770007279 2.019822769 1.532744889 1.721507318 1 20.7096369 0.255759786 1.055097412 0.997500812 1.752435892 0.359134803 0.305654928 4.167976192 4.952404707 0.299188666 0.086493137 1.802020745 -0.255759786 0.75493508 VGEVCHITCKPEYAYGSAGSPPK ddPTM_MDA-MB-175_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 ; 253.84 1.00E-43 2987800000 1538370 1059220 1480250 1142180 1866910 1860180 2072460 1648800 1745680 724220 FALSE TRUE 1599106.035 1241132.795 1518826.531 1368099.795 1549573.305 1428181.386 1910015.17 1626700.533 1682853.318 866117.043 1.846293233 1.432985075 1.753604254 1.579578425 1.789103814 1.648947331 2.205262193 1.878153243 1.942986033 1 19.72420247 VGFAEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VGFAEAAR 8 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;; 180.01 0.00056145 2197080000 1320810 1595620 1109510 1053430 2965240 2179690 1485860 1175810 1185900 3408110 FALSE TRUE 1372956.599 1869655.323 1138424.742 1261795.31 2461209.564 1673490.031 1369394.411 1160050.19 1143219.691 4075863.902 0.336850452 0.458713875 0.279308821 0.30957739 0.603849791 0.410585356 0.335976481 0.284614555 0.280485246 1 21.95867445 -1.51409901 6.002944226 1.00076776 0.366039507 0.794206417 0.096717178 0.001036109 8.39E-05 0.09763373 0.02298726 0.030612654 1.51409901 -0.634728254 VGFQYEGTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGFQYEGTYK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 142.43 8.32E-05 295480000 273550 213770 284570 217410 380780 343270 339870 296090 295670 281110 FALSE TRUE 284349.9652 250483.3346 291986.128 260413.0491 316055.1516 263550.7448 313230.1013 292121.3979 285028.8945 336188.1223 0.845806102 0.74506896 0.868520059 0.774605145 0.940113974 0.783938299 0.931710791 0.868922423 0.847825594 1 18.35890923 -4.99999999 0.091601963 1.501855191 0.721595213 0.433197169 0.057309221 175.9024678 1.116669227 17.15243308 1.152319445 1.00E-05 4.99999999 -0.780259977 VGGS(ph)DEEASGIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 245.93 1.14E-17 4422580000 2259400 2207110 2512240 2126790 3030300 3255200 2749670 2538300 2559710 2088910 TRUE FALSE 2348602.857 2586163.974 2577711.038 2547462.714 2515210.688 2499229.133 2534143.68 2504278.24 2467586.537 2498191.92 0.940121068 1.03521429 1.031830668 1.019722582 1.006812434 1.000415186 1.014391112 1.00243629 0.987748987 1 21.25245288 4.750870287 24.75371571 1.011240379 0.940121018 0.695873926 0.014046633 977.7175994 1966067.122 0.003570965 0.059473435 56346.9336 -4.750870287 -0.071119362 VGGS(ph)SVDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.593)S(0.407)VDLHR;VGGS(0.914)S(0.086)VDLHR;VGGS(0.961)S(0.039)VDLHR;VGGS(0.584)S(0.416)VDLHR;VGGS(0.997)S(0.003)VDLHR 145.08 2.00E-05 4193890000 3383102 4022459 3911300 3833212 5209030 5165972 3525510 3760562 3228391 4046790 TRUE FALSE 3516669.479 4713285.043 4013231.691 4591409.893 4323600.941 3966253.294 3249171.314 3710157.817 3112201.839 4839681.02 0.726632492 0.973883407 0.829234752 0.948700932 0.893364857 0.819527832 0.671360633 0.766612056 0.64305929 1 22.20648053 2.472294878 6.149200247 0.748724232 0.879482223 0.15521439 0.10974086 0.205480979 32.68819709 0.034450237 0.029888369 296.6845141 -2.472294878 0.130757991 VGGSS(ph)VDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 1 VGGS(0.36)S(0.64)VDLHR;VGGS(0.128)S(0.872)VDLHR 108.98 0.001339 320320000 126702 171744 184492 149538 177952 223590 164330 165602 159972 158047 TRUE FALSE 131704.2928 201239.696 189300.0131 179116.1701 147703.7826 171664.611 151449.3852 163382.3761 154214.639 189013.2837 0.696799136 1.064685466 1.00151698 0.947638 0.781446572 0.908214532 0.801263183 0.864396263 0.815893127 1 17.5281281 3.273304683 24.86876234 0.853851842 0.942723036 0.074669369 0.106164504 332.2960156 237845.2981 0.027686317 0.037485729 1876.310387 -3.273304683 0.088871194 VGGSSVDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGGSSVDLHR 10 0 O60716-13;O60716-5;O60716-19;O60716-21;A0A669KB05;O60716-3;O60716-11;O60716-7;O60716-15;O60716-16;O60716-24;O60716-23;O60716-8;A0A669KB62;O60716-17;O60716-2;O60716-9;O60716-10;O60716;C9JZR2;O60716-18;O60716-14;O60716-22;O60716-12;O60716-4;O60716-6;O60716-20 O60716-13 CTNND1 Catenin delta-1 0 ;; 169.76 4.53E-06 670950000 612350 1008310 891260 869590 1084190 1245000 939550 1030230 921480 997850 FALSE TRUE 636526.0508 1181479.399 914486.9678 1041592.307 899899.7711 955867.6182 865905.6159 1016421.452 888316.1148 1193359.603 0.533389977 0.990044741 0.766312992 0.872823501 0.754089353 0.800988752 0.725603258 0.851731071 0.744382593 1 20.18659741 -2.045607946 2.581628172 1.272504263 0.792224739 0.250451557 0.111845956 12594589.47 5817633.156 20245947.94 0.023679697 0.0090031 2.045607946 -0.480279524 KKGEDLVGS(ph)LNGGHANVHPSQEQGEALSGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KKGEDLVGSLNGGHANVHPSQEQGEALSGHR 31 2 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 KKGEDLVGS(1)LNGGHANVHPSQEQGEALSGHR 190.15 7.38E-19 298460000 34489 53167 65095 60156 97518 92546 70049 79532 94956 77969 TRUE FALSE 35850.65235 62298.01867 66791.42918 72054.67725 80941.92519 71053.59405 64558.37634 78466.00363 91538.55211 93245.53274 0.384475817 0.668107274 0.71629629 0.772741333 0.868051507 0.762005342 0.692348196 0.841498797 0.981693701 1 16.50874699 5.004041704 0.828148482 0.837326897 1.74E-32 0.715677871 0.089291504 2.033175244 0.799328227 0.030567487 1.722772925 100934.9807 -5.004041704 -0.837326897 down VGGVS(ph)PEEHPAPEVSTPFPPLPPEPEGGGEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGGVSPEEHPAPEVSTPFPPLPPEPEGGGEEK 32 0 Q8TE77;Q8TE77-3 Q8TE77 SSH3 Protein phosphatase Slingshot homolog 3 1 VGGVS(1)PEEHPAPEVSTPFPPLPPEPEGGGEEK;VGGVS(0.989)PEEHPAPEVS(0.005)T(0.005)PFPPLPPEPEGGGEEK 138.29 6.85E-09 793930000 201145 130593 198560 140956 248990 273040 244200 172762 216243 102041 TRUE FALSE 209086.3599 153021.3319 203734.6367 168836.6761 206666.7687 209630.598 225058.9659 170446.408 208460.4567 122033.9803 1.71334541 1.253923961 1.669491041 1.383521833 1.693518218 1.717805135 1.844231954 1.396712683 1.708216484 1 16.8969234 -1.455415916 5.071936826 0.998985475 1.586630277 0.499882261 0.179084215 0.001969644 0.000211485 0.166237859 0.039120544 0.035041613 1.455415916 0.587644802 VGHFDPVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGHFDPVTR 9 0 Q9UNE7;Q9UNE7-2;H3BTA3 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ;;; 134.25 0.00025426 1674440000 442306 515303 521536 453531 552282 629502 509849 497699 496506 474000 FALSE TRUE 459768.5824 603802.2817 535127.6566 543238.0781 458405.3029 483309.7007 469885.7031 491028.159 478636.846 566871.2247 0.81106354 1.065148936 0.944002153 0.958309497 0.808658621 0.852591699 0.82891084 0.866207593 0.844348461 1 19.11266151 3.255667576 24.9928394 0.857437664 0.953194569 0.195079036 0.07525596 303.0282 442713.9401 0.019184737 0.025912502 1801.638176 -3.255667576 0.095756905 VGHSELVGEIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGHSELVGEIIR 12 0 P38606;P38606-2;C9JVW8;C9JA17 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 ;; 224.82 1.92E-11 942360000 549610 600970 622690 624560 725410 788870 691360 644830 641980 613390 FALSE TRUE 571309.0272 704181.9226 638917.8129 748096.1039 602105.0673 605666.8979 637169.3967 636187.1086 618875.2652 733572.0264 0.778804271 0.959935626 0.870968071 1.019799116 0.820785207 0.825640668 0.868584643 0.867245595 0.843646217 1 19.4845791 VGIDTPDIDIHGPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 ; 73.166 0.035824 117451000 209784 135486 161000 139901 237580 236270 207120 176415 190381 149404 FALSE TRUE 218066.4343 158754.6666 165195.7923 167573.0002 197196.2365 181399.8732 190885.3932 174050.4455 183529.225 178676.8533 1.220451504 0.888501581 0.924550602 0.937855112 1.103647355 1.015239914 1.068327484 0.974107403 1.027157249 1 17.44699323 4.757027414 24.21903537 0.995212145 1.220451804 0.545568416 0.062180397 2157.38232 2829316.564 0.015583768 0.50573085 57151.47113 -4.757027414 0.22523966 VGIIAWHPTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGIIAWHPTAR 11 0 Q9BR76;A0A087WW53;F5H390 Q9BR76 CORO1B Coronin-1B;Coronin 0 ; 159.83 2.82E-05 3327600000 1434840 2530600 2468460 2573150 2861000 3163800 2561870 2640300 2350790 2565930 FALSE TRUE 1491488.591 2965210.865 2532790.095 3082111.39 2374688.242 2429055.398 2361063.935 2604911.097 2266185.527 3068674.856 0.486036697 0.966283821 0.825369325 1.004378611 0.773848111 0.79156493 0.76940831 0.848871653 0.738489946 1 21.54918436 -2.545897898 2.157865394 3.824938619 0.812513628 0.162602826 0.133342889 6309359.963 532526.0667 86896131.8 0.029785649 0.00284513 2.545897898 -3.012424991 VGILSGHDNRVS(ph)CLGVT(ph)ADGMAVAT(ph)GSWDSFLK ddPTM_MDA-MB-175_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(0.522)GHDNRVS(0.6)CLGVT(0.621)ADGMAVAT(0.606)GS(0.59)WDS(0.061)FLK 42.761 0.05298 298030000 70015 47777 62454 47146 92855 90256 92919 83504 94601 45368 TRUE FALSE 72779.24626 55982.3281 64081.60255 56471.33808 77071.54027 69295.41184 85635.76598 82384.76546 91196.32849 54256.99098 1.341380068 1.031799351 1.181075496 1.040812199 1.4204905 1.277170197 1.578336071 1.518417516 1.680821712 1 15.72752142 2.906141012 1.654115827 1.479454093 1.146071361 0.251687222 0.199095616 0.391750954 2.160495744 0.068786112 0.075991196 805.6399829 -2.906141012 -0.333382732 VGLQS(ph)PSVEAWEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGLQSPSVEAWEAK 14 0 E9PEZ1;Q8IWT3-3;Q8IWT3 E9PEZ1 CUL9 Cullin-9 1 VGLQS(0.991)PS(0.009)VEAWEAK 152.94 6.85E-06 107910000 111270 86923 110980 85930 144250 143420 120900 105840 122040 92389 TRUE FALSE 115663.0255 101851.3491 113872.23 102926.6975 119730.4365 110112.8786 111423.5421 104421.3879 117647.8042 110490.8557 1.046810841 0.921807949 1.030603205 0.931540415 1.083623037 0.99657911 1.0084413 0.945068144 1.064774126 1 16.75356745 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 VGLSPDSPAGDRNS(1)VGSEGSVGSIR;VGLSPDSPAGDRNS(1)VGSEGSVGSIR;VGLSPDS(0.001)PAGDRNS(0.993)VGS(0.006)EGSVGSIR 171.94 3.95E-12 1436360000 658220 855770 789120 766970 799850 938010 721390 775060 788140 877760 TRUE FALSE 684207.0339 1002741.841 809685.1155 918674.3768 663891.7827 720171.3932 664845.5668 764671.5884 759774.9954 1049740.266 0.651786976 0.95522852 0.771319479 0.875144458 0.632434331 0.686047222 0.633342921 0.728438846 0.72377427 1 20.00160098 5.038932509 16.66427506 0.760007468 0.169893211 0.070882192 0.12214357 13297364.05 150928936.4 0.028611715 239371497.6 109378.6375 -5.038932509 -0.590114257 VGLVEDSPSTAGDGDDSPVVSLTVPS(ph)TSPPSSSGLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLTVPS(0.252)T(0.252)S(0.184)PPS(0.051)S(0.07)S(0.095)GLS(0.095)R;VGLVEDSPSTAGDGDDSPVVSLT(0.001)VPS(0.353)T(0.353)S(0.269)PPS(0.014)S(0.003)S(0.003)GLS(0.003)R 138.84 4.15E-10 204917000 91100 103145 118330 122199 147462 171659 136815 134631 136612 139494 TRUE FALSE 94696.69834 120859.3514 121413.777 146369.5975 122396.4619 131793.7988 126091.0828 132826.4917 131695.3608 166825.1785 0.567640324 0.724467089 0.727790482 0.877383131 0.733680989 0.790011436 0.755827651 0.796201705 0.789421369 1 17.34797752 -5 0.03427906 2.17600792 1.78E-09 0.648707121 0.062677782 765.4898396 1.969725491 103.6756778 36.99530845 1.00E-05 5 -2.176007918 VGLVEDSPSTAGDGDDSPVVSLTVPSTS(ph)PPSSSGLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 Q6VY07-2;Q6VY07;B4DF77 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VGLVEDSPSTAGDGDDSPVVSLTVPS(0.108)T(0.108)S(0.568)PPS(0.153)S(0.021)S(0.021)GLS(0.021)R 152.49 1.10E-13 92915000 44203 58598 58043 49500 66223 75337 63585 67222 62014 69921 TRUE FALSE 45948.16857 68661.75067 59555.64826 59290.95226 54966.43811 57841.12349 58601.04155 66320.99904 59782.12825 83620.68123 0.549483308 0.821109678 0.712211948 0.709046511 0.657330666 0.691708351 0.700796031 0.793117182 0.714920369 1 16.35157218 -1.160044583 0.351292481 1.157506092 0.688631705 0.644093459 0.06699415 10.27796793 0.88140441 1.606849706 0.051391268 0.069175995 1.160044583 -0.468874387 VGMVETNSQDRPVDDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGMVETNSQDRPVDDVK 17 1 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 195.46 1.57E-11 266850000 142700 92331 117960 89168 168070 158220 126520 133300 153650 94607 FALSE TRUE 148333.9062 108188.131 121034.1345 106805.1643 139501.5214 121475.8028 116603.0318 131513.3315 148120.1665 113143.4303 1.311025358 0.956203385 1.069740719 0.943980256 1.232961747 1.073644334 1.030577131 1.162359416 1.309136254 1 16.78779329 1.601531607 6.716016166 1.180286407 1.082194788 0.049042351 0.127327285 0.283349809 27.44492663 0.064051211 0.030656787 39.9513636 -1.601531607 -0.09809162 VGNES(ph)PVQELK ddPTM_MDA-MB-175_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 278.45 3.07E-27 3150920000 7862570 4208500 5774200 4229120 7414140 7943220 7945710 5999260 6361250 2926820 TRUE FALSE 8172990.335 4931277.137 5924680.396 5065627.313 6153887.131 6098527.536 7322904.488 5918849.733 6132309.855 3500274.342 2.334957074 1.408825897 1.692633153 1.447208652 1.758115659 1.742299871 2.09209444 1.69096738 1.751951206 1 21.73903657 0.238964667 2.368751191 0.99999743 1.755691058 0.440929691 0.259331522 40.45014194 123.5062167 0.235658961 0.063226686 1.733662944 -0.238964667 0.755693628 VGPAT(ph)PSAQVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGPATPSAQVGK 12 0 Q13428-4;Q13428;Q13428-2;Q13428-3;Q13428-8;A0A6I8PRA0;Q13428-6 Q13428-4;Q13428-3;Q13428-6 TCOF1 Treacle protein 1 VGPAT(0.696)PS(0.304)AQVGK 95.631 0.066379 110790000 362820 258110 288680 289630 356410 385700 428510 322790 360270 230980 TRUE FALSE 377144.4138 302438.3847 296203.238 346917.9495 295827.5555 296127.0203 394922.2665 318463.528 347303.9531 276236.1086 1.365297302 1.094854638 1.072282836 1.255874734 1.070922831 1.072006921 1.429654756 1.152867124 1.257272103 1 18.07554239 VGPCS(ph)SPPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.586)S(0.414)PPAAR 86.014 0.01551 367640000 269820 257790 245280 278890 311770 387150 292930 296600 260100 261200 TRUE FALSE 280472.7019 302063.4272 251672.1983 334053.6096 258775.4468 297240.2798 269969.3812 292624.5621 250739.0518 312377.139 0.897865647 0.966983141 0.805667787 1.069391988 0.828407122 0.951542999 0.864241801 0.936766894 0.802680544 1 18.25292935 VGPCSS(ph)PPAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGPCSSPPAAR 11 0 Q8TDM6-4;Q8TDM6;Q8TDM6-2;A0A0J9YYG8;A0A0A0MSL1 Q8TDM6-4 DLG5 Disks large homolog 5 1 VGPCS(0.433)S(0.567)PPAAR 118.97 0.00068109 322150000 215370 242240 241920 236850 296510 337970 247970 247470 268460 212920 TRUE FALSE 223872.9739 283842.8356 248224.6339 283698.2231 246109.3361 259481.5895 228533.4635 244153.0694 258798.177 254637.5974 0.879182714 1.114693347 0.974815332 1.114125431 0.96650824 1.019023083 0.897485155 0.958825688 1.01633922 1 17.95808592 2.686479433 2.281120679 0.963711125 1.022131564 0.048285409 0.072360743 0.657072484 6.742750248 0.024490859 0.023504738 485.8245233 -2.686479433 0.058420439 VGPDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGPDTER 7 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 ; 104.76 0.018793 1065040000 1263340 1268410 1225410 1181810 1530890 1611740 1423560 1293300 1375760 1179200 FALSE TRUE 1313217.639 1486249.551 1257345.191 1415568.491 1270669.865 1237437.811 1311977.647 1275965.429 1326246.666 1410241.663 0.931200427 1.053897066 0.891581368 1.003777245 0.901029872 0.877465078 0.930321151 0.904784948 0.940439289 1 20.42751098 4.223742016 24.99150558 0.926263774 0.992548785 0.196384962 0.048859284 277.3923389 467823.2511 0.011372601 0.024726114 16739.48205 -4.223742016 0.066285011 VGPGNHGTEGSGGERHS(ph)DTDSDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGPGNHGTEGSGGERHSDTDSDRR 24 2 Q99442 Q99442 SEC62 Translocation protein SEC62 1 VGPGNHGTEGS(0.006)GGERHS(0.994)DTDSDRR 162.91 8.28E-12 95339000 16067 35555 28852 48310 28455 55456 35382 32935 31849 34536 TRUE FALSE 16701.33757 41661.29467 29603.90682 57865.57381 23618.22926 42577.18444 32608.66639 32493.5602 30702.76071 41302.66797 0.404364618 1.008682894 0.716755316 1.401012977 0.571833018 1.03085797 0.789505085 0.78671819 0.743360229 1 15.33394736 7.999999679 0.017897183 1.52924072 1.96E-09 0.032304543 0.259623145 26167.92368 36.11605559 1180.521803 2006.506515 99999926.12 -7.999999679 -1.529240718 VGPPVSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGPPVSLER 9 0 P08151-3;P08151-2;P08151 P08151-3 GLI1 Zinc finger protein GLI1 0 67.993 0.05933 164900000 102660 192570 183360 199580 194600 240560 211700 222470 208920 214190 FALSE TRUE 106713.0961 225642.3995 188138.5122 239056.3283 161521.9615 184693.5857 195106.4008 219488.1535 201401.01 256156.4296 0.416593471 0.88087736 0.734467265 0.933243521 0.630559857 0.721018739 0.761668958 0.856852018 0.78624226 1 17.96666558 -5 0.035113748 2.202951861 1.28E-08 0.329271206 0.128888322 1372.964079 3.616555573 190.3975481 66.27166257 1.00E-05 5 -2.202951848 VGQEIEVRPGIVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGQEIEVRPGIVSK 14 1 P41091 P41091 EIF2S3 Eukaryotic translation initiation factor 2 subunit 3 0 ; 96.673 0.0029897 533210000 464920 400940 447020 339910 561450 546240 515430 445890 494810 356560 FALSE TRUE 483275.4006 469798.3261 458669.7084 407143.1835 466014.9295 419384.0383 475029.2498 439913.5739 477001.8848 426421.1052 1.13332899 1.101723907 1.075626189 0.954791352 1.092851465 0.983497377 1.113990944 1.031641184 1.11861697 1 18.70191932 4.217858671 3.068062907 1.045212693 1.123118385 0.24750352 0.052130598 0.32756043 6.212232168 0.012379779 0.03632919 16514.24302 -4.217858671 0.077905692 VGQGYPHDPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGQGYPHDPPK 11 0 P61081;M0QYI6 P61081 UBE2M NEDD8-conjugating enzyme Ubc12 0 98.353 0.0055837 175660000 449140 331890 416160 351920 582060 545470 517300 448630 471180 300120 FALSE TRUE 466872.394 388889.5258 427005.4715 421528.7256 483121.6491 418792.8592 476752.6743 442616.8487 454222.3238 358922.7679 1.30076004 1.083490825 1.189686221 1.174427379 1.346032329 1.166804942 1.328287635 1.233181309 1.265515494 1 18.45331392 5.075432598 20.73972141 1.213857344 4.489578018 0.067583359 0.1003443 1560.608105 454808.9425 0.02176798 14250.80301 118968.6677 -5.075432598 3.275720674 VGQQAIVLCIS(ph)PSKPNPVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGQQAIVLCISPSKPNPVFK 20 1 Q16656-2;Q16656;Q16656-4;C9JP85 Q16656-2 NRF1 Nuclear respiratory factor 1 1 VGQQAIVLCIS(0.898)PS(0.102)KPNPVFK 210.36 2.29E-22 190870000 263630 153410 200200 147880 242950 270110 247140 212800 218870 124210 TRUE FALSE 274038.316 179756.9741 205417.3765 177130.2226 201653.4458 207381.0461 227768.521 209947.7641 210992.9115 148546.5714 1.844797315 1.210105171 1.382848319 1.192422154 1.357509931 1.396067537 1.533313889 1.413346415 1.420382238 1 17.18055578 -1.716583231 2.40709916 0.915631185 1.406240812 0.344191363 0.172029899 7821712.671 5680342.226 3973138.829 0.041441148 0.019205109 1.716583231 0.490609627 VGQTIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGQTIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 92.491 0.036363 786630000 370050 383850 411790 371240 472860 511530 413640 394220 413770 379480 FALSE TRUE 384659.8597 449773.2516 422521.5857 444670.164 392483.4261 392734.9098 381217.816 388936.1257 398878.4985 453831.8404 0.847582354 0.991057065 0.931009127 0.979812619 0.864821265 0.865375399 0.839997951 0.857004932 0.878912546 1 18.79179831 3.221104717 24.938668 0.872100937 0.940746408 0.159341632 0.055310919 296.0762987 422993.3464 0.014832892 0.017767364 1663.81378 -3.221104717 0.068645471 VGRLS(ph)PCVPAKPPLAEFEEGLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGRLSPCVPAKPPLAEFEEGLLDR 24 2 Q15742 Q15742 NAB2 NGFI-A-binding protein 2 1 VGRLS(1)PCVPAKPPLAEFEEGLLDR 127 4.58E-05 28465000 33498 24921 30268 26593 35561 37186 32060 33008 32328 26279 TRUE FALSE 34820.52691 29200.98789 31056.80895 31853.01603 29516.35392 28550.11506 29547.05343 32565.58175 31164.52159 31427.86691 1.107950693 0.92914317 0.988193346 1.013527775 0.939177769 0.908433116 0.940154593 1.036200829 0.991620643 1 14.93975674 1.73331192 24.99999895 1.010789459 0.971469759 0.072952078 0.054400153 1.369647687 6469.02828 0.024963496 0.013843598 54.11428446 -1.73331192 -0.039319699 VGRPSNIGQAQPIIDQLAEEAR ddPTM_MDA-MB-175_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 ; 129.56 1.36E-05 269270000 168906 192804 182894 199474 205068 224770 170176 182844 188186 193267 FALSE TRUE 175574.5393 225916.5872 187660.3679 238929.3618 170210.6146 172570.5739 156837.1604 180393.2753 181413.2226 231133.9683 0.759622398 0.977427026 0.811911677 1.033726732 0.736415404 0.746625756 0.678555219 0.780470636 0.784883433 1 17.81836977 3.196613182 24.99999696 0.768022047 0.895529319 0.181873191 0.10722994 186.5205207 111162.675 0.028530592 0.034100836 1572.581571 -3.196613182 0.127507273 VGRPTASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGRPTASK 8 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ;;; 102.62 0.004496 5601130000 5528430 4443800 4529820 3625330 6495090 6193960 5768060 4898510 4928260 4627310 FALSE TRUE 5746696.685 5206988.082 4647870.83 4342409.453 5391056.922 4755506.66 5315944.385 4832853.486 4750892.885 5533942.799 1.038445263 0.940918306 0.839884148 0.784686364 0.974180095 0.859334264 0.960607035 0.873311066 0.858500541 1 22.3998763 4.620486671 3.340128662 0.88979057 1.042213556 0.320388854 0.063499136 0.28896756 5.209447929 0.014786295 0.092241472 41733.67894 -4.620486671 0.152422986 VGS(ph)GSLDNLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.993)GS(0.007)LDNLGR 78.287 0.031776 224300000 124240 110630 110660 103660 160740 226380 159830 122430 132900 102650 TRUE FALSE 129145.0911 129629.8419 113543.8905 124163.6386 133417.4722 173806.6758 147302.107 120789.0261 128116.955 122762.3021 1.05199307 1.055941764 0.924908449 1.011415039 1.086795131 1.41579844 1.19989691 0.983926042 1.043618055 1 16.90550808 3.134325578 4.898952133 1.132910025 1.008571682 0.172844797 0.120034325 0.394476444 15.48883754 0.038666432 0.046882247 1362.465699 -3.134325578 -0.124338343 VGS(ph)LDNVGHLPAGGAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VGSLDNVGHLPAGGAVK 17 0 E7EVA0;P27816-4;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK 186.63 3.30E-10 7076940000 18810100 5627660 8187770 5474250 12945330 15943390 11127740 8299040 9618850 4296680 TRUE FALSE 19552737.27 6594166.828 8401150.013 6557040.311 10744887.43 12240779.3 10255518.66 8187804.943 9272669.467 5138532.181 3.805121109 1.283278297 1.634931867 1.276053176 2.09104216 2.382154838 1.995807032 1.593413188 1.804536615 1 22.29292488 7.999999994 0.055048315 4.66E-10 5.54081812 0.225874182 0.661867116 768.909143 3.177191404 69.73370946 350.2826441 99999998.55 -7.999999994 5.54081812 VGS(ph)PLDYSLVDLPSTNGQS(ph)PGKAIENLIGKPTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGSPLDYSLVDLPSTNGQSPGKAIENLIGKPTEK 34 2 Q96T23-2;Q96T23;Q96T23-3 Q96T23-2 RSF1 Remodeling and spacing factor 1 2 VGS(0.885)PLDY(0.048)S(0.057)LVDLPS(0.036)T(0.053)NGQS(0.91)PGKAIENLIGKPT(0.011)EK;VGS(0.995)PLDY(0.004)S(0.001)LVDLPS(0.24)T(0.22)NGQS(0.54)PGKAIENLIGKPTEK 72.366 0.0019741 259650000 441450 83749 138747 68277 287130 285310 179740 140879 157723 60075 TRUE FALSE 458878.7869 98132.23927 142362.8608 81781.98681 238323.7452 219051.0764 165651.5091 138990.7474 152046.58 71845.54604 6.387017876 1.36587784 1.981512684 1.138302808 3.317167984 3.048916578 2.305661495 1.934577091 2.116297925 1 16.1326111 4.744575969 24.97975494 2.100169927 6.38701977 0.768737677 0.71693377 319.4131291 1326378.986 0.17256571 1.583698484 55536.17552 -4.744575969 4.286849843 VGS(ph)PLTLTDAQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 VGS(0.997)PLT(0.002)LT(0.001)DAQTR;VGS(1)PLTLTDAQTR;VGS(1)PLTLTDAQTR 216.83 2.81E-11 229158000 314303 233681 241344 234606 317640 526227 285476 264657 243829 178033 TRUE FALSE 326711.9251 273813.894 247633.6229 281010.3666 263647.6663 404018.7543 263099.6452 261109.7058 235053.6419 212915.1577 1.534470015 1.286023489 1.16306244 1.319823208 1.238275701 1.8975575 1.235701807 1.226355646 1.103977962 1 17.69991914 1.488160342 1.912899804 1.040720981 1.382152417 0.318191406 0.197686531 0.414509952 2.939652507 0.1716637 0.056211775 30.77232725 -1.488160342 0.341431436 VGS(ph)PQPSSSGGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGSPQPSSSGGEK 13 0 V9GYB6;O94761 V9GYB6 RECQL4 ATP-dependent DNA helicase Q4 1 VGS(1)PQPSSSGGEK;VGS(0.998)PQPSS(0.001)SGGEK;VGS(1)PQPSSSGGEK 104.94 0.00092721 75147000 659915 253255 343422 253746 484865 626067 461645 333546 389722 207699 TRUE FALSE 685968.9538 296749.5762 352371.8594 303936.2014 402447.8205 480672.4274 425460.0586 329075.3614 375695.9813 248393.6424 2.761620415 1.194674603 1.41860257 1.223607007 1.620201776 1.935123712 1.712846007 1.324813945 1.512502404 1 17.92226872 7.999999998 0.044040494 2.36E-12 4.24025318 0.231761863 0.415599429 1166.578725 3.897410229 96.63321522 353.5594646 99999999.53 -7.999999998 4.24025318 VGS(ph)PSGDAASSTPPSTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGSPSGDAASSTPPSTR 17 0 Q9NP87 Q9NP87 POLM DNA-directed DNA/RNA polymerase mu 1 VGS(0.976)PS(0.024)GDAASSTPPSTR;VGS(0.7)PS(0.3)GDAASSTPPSTR;VGS(0.976)PS(0.024)GDAASSTPPSTR 184.37 2.61E-14 63143000 162745 143350 157028 133676 190989 284345 194118 157359 160316 129469 TRUE FALSE 169170.2983 167969.2474 161120.2787 160116.7138 158524.758 218310.183 178902.5239 155249.86 154546.2585 154835.9717 1.092577496 1.084820572 1.040586867 1.034105396 1.023823833 1.409944864 1.155432565 1.002673076 0.998128902 1 17.24038115 1.670002896 6.154305373 0.999164611 1.119655478 0.214363803 0.105046231 0.235637724 18.64453559 0.058659467 0.029344518 46.77382607 -1.670002896 0.120490866 VGS(ph)TENIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VGSTENIK 8 0 E7EVA0;H0Y2V1;F8W9U4;H7C4C5;P27816-6;P27816;P27816-2;P27816-5 E7EVA0;P27816-6 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 VGS(0.935)T(0.065)ENIK;VGS(0.983)T(0.017)ENIK;VGS(0.799)T(0.201)ENIK;VGS(0.814)T(0.186)ENIK;VGS(0.859)T(0.141)ENIK;VGS(0.955)T(0.045)ENIK 178.54 0.00026126 1989730000 4886420 1514191 1986850 1508996 2919750 4215590 3010700 2018850 2193070 1027070 TRUE FALSE 5079339.635 1774241.525 2038628.943 1807470.905 2423451.938 3236583.11 2774713.467 1991790.618 2114141.839 1228304.702 4.135243988 1.444463676 1.659709468 1.471516719 1.973005504 2.635000179 2.258978137 1.621576971 1.7211868 1 20.22823706 4.744128559 24.72359663 1.809939804 4.135245156 0.729810459 0.433472395 281.926255 1251806.485 0.106062338 0.928949966 55478.9917 -4.744128559 2.325305352 VGSEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGSEIER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;;; 125.01 0.0095177 2397160000 1728400 1921670 1845350 1764510 2144800 2311410 2032260 1922220 1914240 2046670 FALSE TRUE 1796638.567 2251701.874 1893441.337 2113524.811 1780227.662 1774620.057 1872966.151 1896455.785 1845346.876 2447675.801 0.734018192 0.919934688 0.773567045 0.863482333 0.727313504 0.725022512 0.765201891 0.774798601 0.753918013 1 21.22298105 -1.487600768 3.01784965 1.006141036 0.783496937 0.547062295 0.05951537 18712032.06 23101453.21 967506.5095 0.014297435 0.032538628 1.487600768 -0.222644099 VGSGDTNNFPYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGSGDTNNFPYLEK 14 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 170.95 7.20E-06 115401000 67716 65772 75880 63231 76185 91740 77293 71997 73143 71658 FALSE TRUE 70389.47997 77067.82936 77857.49514 75737.90307 63235.10091 70434.77533 71234.57269 71031.99798 70510.59772 85698.01312 0.821366534 0.899295404 0.908509921 0.883776651 0.737882929 0.82189508 0.831227821 0.828864 0.822779842 1 16.38697414 6.591077883 12.01446658 0.848346234 0.427798431 0 0.067398527 0 0 0.014352444 0 3900119.225 -6.591077883 -0.420547803 VGSGS(ph)LDNLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGSGSLDNLGR 11 0 Q13136-2;A0A2R8Y7R9;Q13136;H0YDW2 Q13136-2 PPFIA1 Liprin-alpha-1 1 VGS(0.001)GS(0.999)LDNLGR;VGS(0.003)GS(0.997)LDNLGR;VGS(0.001)GS(0.999)LDNLGR 161.87 2.71E-05 1026100000 1720050 1818280 1839080 1661850 2108230 2136740 1971640 1755480 1794940 1647090 TRUE FALSE 1787958.902 2130555.446 1887007.936 1990558.97 1749873.818 1640514.518 1817097.705 1731950.662 1730340.46 1969805.75 0.907682853 1.081606877 0.957966508 1.010535668 0.888348416 0.832830607 0.922475582 0.87924947 0.878432028 1 20.90962194 3.233985978 24.97640239 0.891757985 0.993782085 0.359318501 0.057591426 100.7684559 550171.2479 0.015179635 0.018725312 1713.901971 -3.233985978 0.1020241 VGSLT(ph)PPS(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.848)S(0.152)PK;VGSLT(1)PPS(0.727)S(0.273)PK 174.9 5.55E-05 1385350000 2181260 829420 1084770 801100 1652210 1870060 1466680 1163790 1215920 636540 TRUE FALSE 2267377.829 971866.433 1113039.997 959555.189 1371367.934 1435766.906 1351717.789 1148191.299 1172159.277 761257.8257 2.978462424 1.276658709 1.462106477 1.260486469 1.801450032 1.886045513 1.775637299 1.508281767 1.539766472 1 19.53802563 8 0.046570073 1.25E-08 4.556274111 0.257536959 0.442762586 987.4172086 3.480479769 84.39498856 332.2442021 99999999.98 -8 4.556274098 VGSLT(ph)PPSS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGSLTPPSSPK 11 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 2 VGSLT(1)PPS(0.101)S(0.899)PK;VGSLT(1)PPS(0.03)S(0.97)PK;VGSLT(1)PPS(0.162)S(0.838)PK 156.52 0.00016459 1764920000 3018690 1098120 1499550 1084790 2241660 2631150 2155570 1604720 1768140 876400 TRUE FALSE 3137870.212 1286713.568 1538629.505 1299358.224 1860623.434 2020105.288 1986610.791 1583211.353 1704504.987 1048113.8 2.993825872 1.227646814 1.467998517 1.239711016 1.775211273 1.927372092 1.895415164 1.51053383 1.626259464 1 19.99936394 -2.512932033 0.2393706 2.00E-27 1.803588835 0.196366123 0.472525094 79.07491479 2.275238798 43.11929173 0.77883907 0.003069502 2.512932033 1.803588835 VGTEGLVDS(ph)FSQGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGTEGLVDSFSQGLER 16 0 O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170;T1ECW5 O75170-6 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 1 VGTEGLVDS(0.999)FS(0.001)QGLER;VGTEGLVDS(0.998)FS(0.002)QGLER;VGTEGLVDS(1)FSQGLER 217.91 1.45E-14 111019000 112925 106860 116134 114181 118900 141756 131283 99314 107012 89490 TRUE FALSE 117383.3662 125212.3737 119160.5474 136765.661 98689.42047 108835.3173 120992.6954 97982.85827 103160.659 107023.8521 1.096796311 1.169948299 1.11340178 1.277898882 0.922125475 1.016925808 1.130520842 0.915523562 0.963903438 1 16.70757284 3.228882479 24.99999628 0.993114242 1.161249002 0.582092136 0.071787475 145.5483283 375971.3604 0.02076754 0.025120914 1693.879372 -3.228882479 0.16813476 VGTLWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 124.86 0.064292 200660000 281620 307520 294360 275050 354640 371350 276330 276840 272600 311620 FALSE TRUE 292738.5751 360334.1678 302031.2634 329454.0691 294358.4195 285109.5904 254670.5325 273129.4126 262789.1792 372675.9727 0.785504289 0.966883283 0.810439324 0.884022833 0.789850812 0.765033464 0.683356458 0.732887099 0.705141191 1 18.50756228 3.057768929 2.905698279 0.751494168 0.865993447 0.124586346 0.094562551 0.36321682 6.24176156 0.027183222 0.032569687 1142.270416 -3.057768929 0.11449928 VGVAYFFS(ph)DDEEDLDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGVAYFFSDDEEDLDER 17 0 Q96KN4;Q96KN4-2 Q96KN4 FAM84A Protein FAM84A 1 VGVAYFFS(1)DDEEDLDER 140.96 6.73E-07 11704000 9139.6 10218 11187 6366.8 9982.2 12425 11619 9959.8 8002.8 9776.3 TRUE FALSE 9500.438465 11972.86201 11478.54241 7626.134037 8285.42921 9539.482053 10708.27242 9826.305172 7714.780791 11691.77881 0.812574256 1.024041099 0.981761852 0.652264652 0.70865429 0.815913661 0.915880517 0.840445696 0.659846625 1 13.51320682 3.773231971 24.96412905 0.799173779 0.947917303 0.240185943 0.114184677 836.7728511 602491.9897 0.029216415 0.052667561 5932.421106 -3.773231971 0.148743524 VGVEASEETPQTSSSSARPGT(ph)PSDHQSQEASQFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 VGVEASEETPQTS(0.001)S(0.002)S(0.002)S(0.002)ARPGT(0.865)PS(0.127)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.982)PS(0.018)DHQSQEASQFER;VGVEASEETPQTSSSSARPGT(0.5)PS(0.5)DHQSQEASQFER 340.82 5.48E-118 5171750000 183926 905580 801410 900310 757780 1116060 720420 903530 676640 927860 TRUE FALSE 191187.5405 1061106.321 822295.403 1078388.631 628972.8263 856871.9791 663951.5979 891419.6582 652287.8586 1109656.402 0.172294361 0.956247644 0.741036055 0.971822114 0.566817643 0.772195769 0.598339807 0.803329442 0.58782868 1 20.08168159 -2.477988877 2.163210345 4.177987516 0.706213534 0.151143572 0.218681362 7899294.028 503317.2453 123542598.8 0.048073332 0.003326681 2.477988877 -3.471773982 VGVNGFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;; 174.64 0.00062991 32739170000 6349760 7714750 7457180 7078090 8277120 9208190 7902070 7865550 6872640 7291440 FALSE TRUE 6600453.428 9039698.3 7651520.237 8478115.076 6870178.099 7069727.424 7282685.105 7760125.168 6625295.029 8720058.065 0.756927692 1.036655746 0.877462074 0.972254429 0.787859215 0.810743159 0.835164749 0.889916685 0.759776481 1 23.05590631 3.238552579 25 0.842666497 0.917429826 0.102288448 0.090837939 0.422955643 1298355.978 0.023775349 0.030205235 1732.018708 -3.238552579 0.074763329 VGWEQLLTTIAR ddPTM_MDA-MB-175_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 ; 164.04 0.0001358 318490000 178751 200960 170939 167870 190011 227380 207249 185394 177997 229530 FALSE TRUE 185808.2275 235473.3167 175393.8108 201074.185 157712.9981 174574.441 191004.2818 182909.0967 171590.9227 274502.0089 0.67689205 0.857820013 0.63895274 0.732505331 0.574542236 0.635967808 0.695821071 0.666330631 0.625098969 1 18.06645718 -1.6223829 6.640656665 1.000995944 0.679476079 0.639313455 0.072504063 0.001062662 6.04E-05 0.069780377 0.016400255 0.02385707 1.6223829 -0.321519865 VGWLVEWQDYKPVEYTAVSVLAGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VGWLVEWQDYKPVEYTAVSVLAGPR 25 1 Q9BW91-2;Q9BW91;D6RAW2;H7C386 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 63.63 0.048751 202030000 151610 127110 142950 118480 220410 218130 198160 176490 187830 135280 FALSE TRUE 157595.6799 148940.1537 146675.3944 141914.9904 182944.7869 167472.6133 182627.7014 174124.4402 181070.035 161785.5259 0.974102467 0.920602464 0.906603935 0.87717977 1.130785872 1.035152016 1.128825959 1.076267109 1.119197987 1 17.30372302 3.239247919 25 1.085897533 0.918762294 0.759270106 0.044671978 7.92133383 288124.8491 0.011812878 0.015083513 1734.794032 -3.239247919 -0.167135239 VGWSVDFSRPQLGEDEFSYGFDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VGWSVDFSRPQLGEDEFSYGFDGR 24 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 214.57 1.35E-32 740187000 208451 245809 230760 237817 269814 276045 251446 246245 242155 279471 FALSE TRUE 216680.8064 288024.7836 236773.7952 284856.4928 223951.1127 211937.7323 231737.0055 242944.4886 233439.8889 334227.9917 0.648302392 0.861761405 0.708420004 0.852281975 0.670054927 0.634111258 0.693350082 0.726882531 0.698445058 1 18.35047304 -1.365855547 5.620516226 1.000075277 0.724019164 0.563617328 0.073484035 6.77E-05 7.64E-06 0.069496028 0.01637592 0.043066983 1.365855547 -0.276056112 VGYTPDWIFLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 122.26 0.0008415 1123100000 291630 277610 402120 403230 413330 433820 430450 382150 343020 285500 FALSE TRUE 303143.7776 325287.358 412599.5775 482987.6905 343072.3142 333071.8796 396710.2042 377027.9043 330674.7772 341438.2588 0.887843614 0.952697449 1.208416359 1.414568163 1.004785801 0.975496656 1.161879766 1.104234498 0.968476053 1 18.3812652 1.241039108 24.81272408 0.984237995 1.096403219 0.076321863 0.143450993 151.8424516 1520275.573 0.112863185 0.036850574 17.41963731 -1.241039108 0.112165223 VHAEEKLDR ddPTM_MDA-MB-175_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 ; 133.23 0.00016998 247690000 190951 154927 201385 123044 288420 248810 196125 176670 215672 176952 FALSE TRUE 198489.8929 181534.5071 206633.2585 147381.736 239394.4714 191027.6483 180752.21 174302.0276 207910.0068 211622.3564 0.937943874 0.857822917 0.976424523 0.696437458 1.131234315 0.902681793 0.854126251 0.823646568 0.982457668 1 17.69113252 VHAELADVLTEAVVDSILAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 76.155 0.011398 566100000 131510 95347 127120 121700 156210 166930 149010 119140 157620 90354 FALSE TRUE 136702.1163 111722.1056 130432.8516 145771.8968 129657.48 128163.0373 137330.2068 117543.1232 151947.287 108057.1364 1.265091052 1.033916956 1.207072999 1.349026095 1.199897428 1.186067313 1.27090363 1.087786768 1.4061754 1 16.72143483 -0.976199561 7.993011489 1.000000001 1.211656002 0.282223478 0.105272375 1.44E-09 3.61E-10 0.096736907 0.022801107 0.105633201 0.976199561 0.211656001 VHATSTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHATSTYR 8 0 Q9H074;Q9H074-3;Q9H074-2;D6REB4 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 114.28 0.0026864 59572000 8409.6 26149 22386 21856 36609 31762 22951 24897 18977 42839 FALSE TRUE 8741.617502 30639.88734 22969.39755 26179.05157 30386.21526 24385.75686 21152.04065 24563.29644 18294.02148 51232.48185 0.17062647 0.598055886 0.448336616 0.510985426 0.593104495 0.475982345 0.412863869 0.479447717 0.357078572 1 15.64477116 -2.146053112 2.421280918 2.217682651 0.460661777 0.664942739 0.116972148 13554829.98 3536351.472 90578286.47 0.02780084 0.00714409 2.146053112 -1.757020874 VHCCLYFIPATGHSLRPLDIEFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHCCLYFIPATGHSLRPLDIEFMK 24 1 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18 Q9UHD8 9-Sep Septin-9 0 ; 217.11 8.24E-33 1424370000 611890 655770 678690 705390 1025740 948050 884670 769800 842110 695040 FALSE TRUE 636047.8897 768393.3963 696377.219 844914.0366 851385.0812 727879.7553 815327.2537 759482.0901 811802.6256 831219.7807 0.765198212 0.924416639 0.837777487 1.016474892 1.02425989 0.875676653 0.980880476 0.913695881 0.976640167 1 19.66487046 5.716713021 0.860398911 0.957894181 9.73E-16 0.525880322 0.055478328 8.521855716 1.385677632 0.017526842 11.46250494 520850.423 -5.716713021 -0.957894181 VHCLNTLFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHCLNTLFSR 10 0 P26196 P26196 DDX6 Probable ATP-dependent RNA helicase DDX6 0 ; 152.54 1.79E-05 592980000 218675 160556 174274 132104 209260 219252 207369 184832 149296 208917 FALSE TRUE 227308.4579 188130.244 178815.7236 158233.7769 173690.0599 168334.0458 191114.8759 182354.6294 143922.8661 249850.2862 0.909778657 0.752971897 0.71569149 0.633314371 0.69517655 0.673739656 0.764917579 0.729855595 0.576036427 1 17.93070435 -0.493393075 7.774800448 1 0.716593222 0.507107365 0.083751208 0 0 0.079443346 0.018724976 0.321075321 0.493393075 -0.283406778 VHDAES(ph)S(ph)DEDGYDWGPATDL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;VHDAES(0.888)S(0.947)DEDGY(0.165)DWGPATDL;VHDAES(1)S(1)DEDGYDWGPATDL;VHDAES(1)S(1)DEDGYDWGPATDL;VHDAES(1)S(1)DEDGYDWGPATDL 254.72 5.68E-36 558382000 602903 586730 610613 520568 673019 777944 599863 600058 615564 569591 TRUE FALSE 626706.076 687496.3134 626526.0764 623534.7967 558619.4708 597278.2959 552844.1706 592015.204 593409.9719 681191.451 0.920014594 1.009255639 0.919750351 0.915359105 0.820062363 0.876814139 0.811584129 0.869087836 0.871135378 1 19.3777008 3.686005582 2.20940649 0.864871086 0.961695426 0.264515523 0.05388592 0.314071424 2.989734386 0.01408246 0.026920477 4852.947377 -3.686005582 0.09682434 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHDRSEEEEEEEEEEEEEQPR 21 1 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR 363.48 4.20E-97 13334900000 1190910 1317730 1252690 1208010 1670360 1484550 1258850 1313270 1268010 1110352 TRUE FALSE 1237928.046 1544039.877 1285336.13 1446950.772 1386432.804 1139785.761 1160178.048 1295667.764 1222374.568 1327904.215 0.932241973 1.162764497 0.967943407 1.089649958 1.044075911 0.858334319 0.873691065 0.975723813 0.920529172 1 20.34071966 2.761668224 23.36924769 0.924148965 1.045021432 0.392100662 0.070583479 324.9550337 328633.372 0.020305321 0.021519995 577.6545835 -2.761668224 0.120872467 VHDRS(ph)EEEEEEEEEEEEEQPRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHDRSEEEEEEEEEEEEEQPRR 22 2 Q5TAQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;V9GYQ9 Q5TAQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 VHDRS(1)EEEEEEEEEEEEEQPRR 209.4 2.99E-23 519380000 37613 40753 41384 41474 66638 56454 45410 46506 41598 42215 TRUE FALSE 39097.99028 47752.01074 42462.50104 49677.43341 55310.89656 43343.41407 41850.64554 45882.66314 40100.89611 50486.221 0.774428934 0.945842446 0.841071092 0.983980033 1.095564205 0.858519676 0.828951835 0.908815559 0.794293875 1 15.62360207 -0.148986509 7.613514545 0.999999989 0.898190198 0.107016009 0.091892121 0 0 0.088869561 0.020946756 0.709599812 0.148986509 -0.101809791 VHDYDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHDYDMR 7 0 Q96MU7-2;Q96MU7;J3QR07 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ; 102.72 0.0085375 150750000 171544 224300 226290 218909 227940 266070 203224 221610 201904 224690 FALSE TRUE 178316.6896 262821.7802 232187.3033 262208.5468 189194.8402 204279.2748 187294.7719 218639.6804 194637.5145 268713.7036 0.663593584 0.978073603 0.864069455 0.975791496 0.704075891 0.760211601 0.697004914 0.813652886 0.724330438 1 18.03571037 3.227795918 24.99949037 0.76989448 0.877623403 0.113566922 0.115064284 355.0154795 824471.869 0.030758265 0.037108615 1689.646751 -3.227795918 0.107728923 VHEIFQVDPETEQEITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHEIFQVDPETEQEITR 17 0 Q92817;K7EKI0 Q92817 EVPL Envoplakin 0 159.8 3.17E-09 216730000 157720 174020 170210 161620 225990 240560 183820 186610 172830 163970 FALSE TRUE 163946.9074 203906.5813 174645.8124 193587.9536 187576.3005 184693.5857 169411.7081 184108.7982 166609.8821 196096.7821 0.836050983 1.039826249 0.890610292 0.987206172 0.95654961 0.941849141 0.863918858 0.938867003 0.849630883 1 17.58120634 2.445960043 24.98282592 0.908884052 0.947338593 0.042373341 0.063690789 507.1904402 406626.4543 0.020019606 0.016749722 279.2286929 -2.445960043 0.038454541 VHELNEEIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VHELNEEIGK 10 0 Q9Y383;Q96HJ9-2;A0A0A6YYJ8;Q9Y383-3;Q9Y383-2;B8ZZ09;Q9NQ29-3;Q9NQ29;Q9NQ29-2;A8MYV2;B8ZZ10 Q9Y383;Q9NQ29-3 LUC7L2;LUC7L Putative RNA-binding protein Luc7-like 2;Putative RNA-binding protein Luc7-like 1 0 ;;;;; 162.38 6.79E-06 4043570000 6941210 4727680 6084530 4700270 8143410 8045680 7452930 6382500 6936500 4385850 FALSE TRUE 7215254.331 5539622.264 6243097.85 5629969.377 6759196.077 6177192.753 6868749.872 6296953.027 6686856.72 5245173.335 1.375598835 1.056137121 1.190255774 1.073361931 1.288650659 1.177690871 1.309537251 1.200523343 1.274859055 1 22.32255902 3.220137717 24.99583172 1.22259491 1.166603782 0.011224372 0.114822122 763.4602989 1035845.124 0.030447113 0.036454062 1660.113254 -3.220137717 -0.055991127 VHEMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHEMEK 6 0 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 ; 143.97 0.011331 517310000 1172830 916360 1175880 963490 1376610 1480160 1516040 1200130 1212200 706210 FALSE TRUE 1219134.234 1073737.702 1206524.399 1154065.446 1142614.324 1136415.272 1397208.823 1184044.22 1168573.159 844578.3283 1.443482734 1.271329924 1.428552401 1.366439805 1.352881415 1.345541596 1.654327108 1.401935357 1.383617268 1 19.6878717 0.680596782 3.561701982 1.000005218 1.410032825 0.62305393 0.094746028 3.75009296 41.13849142 0.09230646 0.023767497 4.7928825 -0.680596782 0.410027606 VHEMEKEHLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHEMEKEHLNK 11 1 P33176 P33176 KIF5B Kinesin-1 heavy chain 0 147.71 2.27E-05 48768000 207670 133440 197220 114070 266620 236160 173910 170070 211110 135660 FALSE TRUE 215868.972 156357.282 202359.7152 136632.7055 221300.0276 181315.419 160278.4798 167790.4898 203512.1923 162239.9796 1.330553495 0.963740764 1.24728637 0.842164218 1.364028941 1.117575455 0.987909886 1.034211729 1.254389903 1 17.30776985 2.518457249 0.014238819 6.32E-07 2.207075981 0.049037413 0.162778073 3686.042048 24.34647966 1825.409583 1944.174386 329.9569259 -2.518457249 2.207075349 VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(ph)SPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;VHEPPREDAAPTKPAPPAPPPPQNLQPESDAPQQPGS(0.5)S(0.5)PR 197.72 2.40E-31 733880000 202274 165856 209187 171078 216153 252549 221263 205064 218250 193986 TRUE FALSE 210259.9337 194340.4778 214638.5851 204916.7178 179411.3903 193898.3222 203919.8279 202315.4525 210395.2251 231993.8426 0.906316872 0.837696706 0.92519087 0.883285157 0.773345483 0.835790812 0.878988104 0.872072509 0.90690004 1 17.82372699 0.796424972 1.373987846 0.999859765 0.860796515 0.520510052 0.039786729 0.593487036 2.022511614 0.038857251 0.011565924 6.257847454 -0.796424972 -0.13906325 VHFEESSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHFEESSK 8 0 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ; 109.71 0.0035651 496650000 925320 701320 830950 831020 1071620 1201560 1523020 890300 944020 460840 FALSE TRUE 961852.3481 821766.2545 852605.2396 995393.2757 889466.4152 922515.8998 1403641.713 878366.9847 910044.9046 551132.7747 1.745227996 1.491049512 1.547005148 1.806086158 1.613887716 1.673854182 2.546830414 1.593748413 1.65122625 1 19.0720404 3.740488894 24.14873628 1.759586843 1.584089748 0 0.360930302 382.0678646 4784755.002 0.091239522 0.154583369 5501.598515 -3.740488894 -0.175497095 VHFEESSKLEDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHFEESSKLEDLLR 14 1 P12956;B1AHC9;P12956-2 P12956 XRCC6 X-ray repair cross-complementing protein 6 0 ;;; 232.53 7.89E-14 2207278000 2922258 2102999 2791975 2252343 3525356 3630984 3661038 3007125 3250337 1883849 FALSE TRUE 3037631.002 2464172.719 2864736.162 2697849.723 2926117.246 2787742.994 3374076.275 2966819.408 3133358.006 2252953.143 1.348288584 1.093752316 1.271547156 1.197472629 1.298791879 1.237372824 1.497623812 1.316858017 1.390778151 1 21.10338588 2.860983854 1.95186811 1.329206958 1.223027664 0.006629806 0.135789442 0.743291447 5.614005444 0.044784343 0.047994451 726.0789633 -2.860983854 -0.106179294 VHFTAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VHFTAER 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;;;; 132.96 0.0033181 2028710000 245506.4 344782.9 331141.5 327289.2 454044.7 434797 357432.6 357084.2 326554.2 441526 FALSE TRUE 255199.1822 403996.681 339771.3195 392026.0269 376866.3441 333821.9862 329416.0988 352298.0704 314801.5781 528034.5662 0.483300145 0.765095141 0.643464162 0.742424932 0.713715291 0.632197223 0.623853285 0.667187516 0.596176081 1 19.01027285 -1.741145095 2.555008487 1.074468225 0.658413519 0.651129135 0.07630042 10932649.64 7989545.413 5145592.542 0.016947707 0.018149092 1.741145095 -0.416054706 VHGEPT(ph)SDLS(ph)DID ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.5)S(0.5)DLS(1)DID 117.79 0.0025384 830600000 214510 214100 254180 208510 284770 308600 248010 224430 240350 210900 TRUE FALSE 222979.0204 250870.0095 260804.1396 249752.6557 236364.8971 236932.3269 228570.3281 221421.8829 231699.8504 252221.8171 0.88405921 0.994640402 1.034026884 0.990210358 0.937131053 0.939380778 0.906227426 0.877885528 0.918635244 1 17.94433355 2.930019841 2.124338525 0.914110933 0.980448645 0.150004967 0.046888575 0.419240796 3.762860232 0.016042287 0.017981267 851.1769229 -2.930019841 0.066337712 VHGEPTS(ph)DLS(ph)DID ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 2 VHGEPT(0.078)S(0.922)DLS(1)DID 130.1 0.00021345 705410000 302270 266240 301090 263680 340400 389840 346990 275320 285340 265280 TRUE FALSE 314203.853 311964.6489 308936.6527 315835.117 282538.9296 299305.5681 319792.0171 271629.7857 275070.6691 317256.5369 0.990377869 0.983319846 0.973775531 0.995519651 0.890569292 0.943418128 1.007991893 0.856183417 0.867029161 1 18.27529036 3.274760327 0.829335563 0.91643668 0.993026829 0.179904919 0.050009045 1.004338296 1.496391544 0.025621535 0.046682792 1882.60985 -3.274760327 0.076590149 VHGEPTSDLS(ph)DID ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHGEPTSDLSDID 13 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 VHGEPTSDLS(0.999)DID;VHGEPTSDLS(0.999)DID 85.845 0.0095439 102491000 118846 195325 189803 166262 207150 252230 153773 201119 175340 249152 TRUE FALSE 123538.1318 228870.5493 194749.4221 199148.1274 171938.717 193653.4051 141719.8704 198423.3288 169029.5477 297968.5641 0.414601226 0.768103005 0.653590498 0.668352811 0.577036432 0.6499122 0.475620208 0.665920344 0.567273089 1 18.18480061 -1.833756864 2.455054513 1.151753332 0.611568206 0.597970081 0.097134072 14246984.72 8744359.855 12730536.06 0.022048968 0.014663685 1.833756864 -0.540185127 VHGLPT(ph)TSPSGMNMAELAQQVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHGLPTTSPSGMNMAELAQQVVK 23 0 B1AKB5;B0QYS6;B0QYS7;P19484-2;P19484 B1AKB5 TFEB Transcription factor EB 1 VHGLPT(0.322)T(0.322)S(0.322)PS(0.035)GMNMAELAQQVVK 132.13 0.00010321 120440000 66959 53800 69428 36211 72616 80402 93868 59011 69208 58531 TRUE FALSE 69602.59302 63039.73149 71237.35072 43373.42772 60272.75826 61729.854 86510.38088 58220.05407 66717.2176 69999.02881 0.994336553 0.900580088 1.017690558 0.619628993 0.86105135 0.881867292 1.235879731 0.831726598 0.953116332 1 16.09504729 2.43326862 24.99994756 0.992323177 0.873032915 0.165894318 0.13691732 267.3528769 152413.7733 0.047874814 0.04005496 271.1868457 -2.43326862 -0.119290262 VHGPGIQSGTTNKPNKFTVETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHGPGIQSGTTNKPNKFTVETR 22 2 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 258.95 2.03E-37 1212710000 1258760 1603680 1938620 1298130 2424290 2292010 1890640 1938850 2210510 1814370 FALSE TRUE 1308456.817 1879099.565 1989142.03 1554896.239 2012210.052 1759725.413 1742446.697 1912862.887 2130954.177 2169861.063 0.6030141 0.865999947 0.916714007 0.716587926 0.927345112 0.810985294 0.803022242 0.881560077 0.982069411 1 21.04917124 8 0.072161876 1.171942217 0.067482492 0.430239988 0.087426775 250.585271 1.330593841 3.440834082 27.97201077 100000000 -8 -1.104459725 VHHEPQLSDK ddPTM_MDA-MB-175_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 ; 91.095 0.0060041 445300000 443740 370840 453830 398170 542100 625860 511480 400650 484790 338470 FALSE TRUE 461259.1978 434528.8853 465657.1826 476926.8376 449954.0356 480513.5 471388.8611 395279.9421 467342.5026 404786.7161 1.139511697 1.073476149 1.150376641 1.178217611 1.111583008 1.187078234 1.16453639 0.976514116 1.154540117 1 18.62680242 1.756026354 25 1.044020132 1.142887457 0.425695214 0.053145657 6.232742221 8930.941548 0.023458255 0.013008711 57.01988728 -1.756026354 0.098867324 VHIDIGADGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHIDIGADGR 10 0 P31942;P31942-3;P31942-2;P31942-4;P31942-5;P31942-6 P31942 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 ;;; 169.37 4.65E-06 1744980000 781981 961852 894305 854570 978095 1144940 913998 871637 814395 1095300 FALSE TRUE 812854.2137 1127042.599 917611.323 1023601.395 811838.7613 879045.0367 842356.4485 859954.1317 785085.083 1309903.064 0.620545318 0.860401529 0.700518495 0.781432934 0.619770106 0.671076403 0.643067775 0.656502115 0.59934594 1 20.32102862 -1.12014294 4.65419537 1.000025227 0.686028841 0.604710374 0.076714418 2.00E-05 3.78E-06 0.074043114 0.017450728 0.075832794 1.12014294 -0.313996386 VHIEIGPDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 201.61 2.39E-07 15784830000 5654530 6136930 5845340 5897890 6162530 7036800 6270200 6235230 5504360 5965590 FALSE TRUE 5877775.211 7190899.989 5997674.362 7064475.039 5115025.352 5402609.844 5778725.34 6151656.941 5306259.159 7134433.142 0.823860157 1.007914693 0.840665858 0.990194301 0.71694909 0.757258459 0.809976802 0.862248874 0.743753435 1 22.76636738 3.244667023 24.99991103 0.809018446 0.916891814 0.225193417 0.091020591 200.0026645 818814.6521 0.023735905 0.031350486 1756.576318 -3.244667023 0.107873368 VHIGQVIMSIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHIGQVIMSIR 11 0 P27635;X1WI28;A0A087WV22;H7C123;H7C2C5;Q96L21;F8W7C6 P27635;F8W7C6 RPL10;RPL10L 60S ribosomal protein L10;60S ribosomal protein L10-like 0 143 3.74E-05 412750000 209350 177660 108630 113530 422150 287100 183650 143690 126380 477650 FALSE TRUE 217615.2997 208171.723 111460.987 135985.8951 350393.0938 220425.376 169255.0331 141764.0706 121831.6085 571236.3723 0.380954908 0.364423088 0.195122356 0.238055386 0.613394228 0.385874196 0.296295967 0.248170595 0.21327705 1 19.12372832 -1.544466326 6.016211311 1.001228232 0.324123417 0.751346039 0.116285742 0.002006774 0.000151948 0.117944876 0.027757523 0.028545238 1.544466326 -0.677104815 VHLENMGSHDIVDGNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHLENMGSHDIVDGNHR 17 0 Q01082;A0A087WUZ3;Q01082-2;F8W6C1;P11277-3;P11277;P11277-2;Q01082-3;O15020;O15020-2;A4QPE4 Q01082;Q01082-3;O15020 SPTBN1;SPTB;SPTBN2 "Spectrin beta chain, non-erythrocytic 1;Spectrin beta chain, erythrocytic;Spectrin beta chain, non-erythrocytic 2" 0 ;;; 268.26 2.19E-28 1483710000 314130 539077 451489 520258 404373 566157 424996 458639 408758 503052 FALSE TRUE 326532.095 631659.2813 463255.1742 623163.4796 335637.8219 434675.6169 391683.703 452491.6944 394046.8794 601615.4079 0.542758863 1.04993867 0.7700188 1.035817021 0.557894325 0.722514103 0.651053311 0.752127835 0.654981362 1 19.19848199 3.232310523 24.99999264 0.708869413 0.858254108 0.112426321 0.170718768 265.0945757 1060361.606 0.044757371 0.054760517 1707.302685 -3.232310523 0.149384695 VHLSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHLSQK 6 0 P43243;A0A0R4J2E8;D6REM6;P43243-2;B3KM87;H0Y8T4;D6RBK5;A8MXP9 P43243;A8MXP9 MATR3 Matrin-3 0 149.06 0.010686 196030000 104720 602320 501630 501470 600490 910040 508810 676150 532960 792670 FALSE TRUE 108854.4265 705763.7746 514702.8899 600659.2693 498418.9243 698697.0018 468928.1427 667087.3152 513778.8737 947978.5099 0.114827947 0.744493432 0.542947846 0.633621188 0.525770278 0.737038862 0.494661153 0.703694554 0.541973123 1 19.85449483 -5 0.11507216 2.293849285 0.360614869 0.429938367 0.163686915 154.4520982 1.167663343 47.43744458 1.64420288 1.00E-05 5 -1.933234416 VHLVGIDIFTGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHLVGIDIFTGK 12 0 P63241;P63241-2;I3L397;I3L504;Q6IS14;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 P63241 EIF5A;EIF5AL1;EIF5A2 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1-like;Eukaryotic translation initiation factor 5A-2 0 ; 178.81 2.15E-05 7066300000 5710120 4918560 5859700 5078500 6818200 7085300 6928800 6030880 6501900 5149860 FALSE TRUE 5935559.947 5763284.419 6012408.596 6083012.142 5659244.799 5439846.454 6385702.551 5950045.918 6267897.889 6158876.467 0.963740705 0.935768796 0.976218411 0.987682116 0.918876167 0.883253055 1.036829134 0.966092752 1.017701511 1 22.55423576 2.220353918 24.99998173 0.999679746 0.946143762 0.452958627 0.032525435 264.6404183 363380.8587 0.012622464 0.009339699 166.0939901 -2.220353918 -0.053535984 VHMFEAHSDYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHMFEAHSDYIR 12 0 P35606;P35606-2;D6R997;D6RBT6;D6RBZ7;D6RCL6;D6RBG7 P35606 COPB2 Coatomer subunit beta 0 ;;; 226.73 8.45E-12 1063660000 359338 396898 406827 397168 540375 556047 477971 379097 403231 454166 FALSE TRUE 373524.9417 465062.1441 417429.2458 475726.645 448522.2505 426913.5112 440506.3841 374015.8248 388718.7951 543151.1322 0.687699831 0.856229724 0.768532405 0.875864224 0.825777991 0.785993964 0.811019913 0.6886036 0.715673359 1 19.05099416 VHNDAQSFDYDHDAFLGAEEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 215.08 8.41E-26 1144320000 638550 415050 531231 483306 731200 702070 761340 556136 519073 323696 FALSE TRUE 663760.4471 486331.6089 545075.3163 578902.4843 606910.8852 539024.8825 701664.1814 548681.9066 500391.6641 387118.0337 1.714620321 1.256287661 1.408033904 1.495415956 1.567767018 1.392404475 1.812532924 1.417350417 1.292607475 1 18.56241399 0.986763064 2.306484978 1.004239642 1.507481656 0.524517659 0.15205881 0.233851655 2.759520657 0.139600233 0.038192995 9.699806354 -0.986763064 0.503242013 VHNGMDDLILDGHNILDGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHNGMDDLILDGHNILDGLR 20 0 O14653-3;O14653-2;E7EQ34;A0A1W2PS81;A0A1W2PQM3;A0A1W2PQP2;A0A1W2PRC2;I3L4Z6;A0A1W2PPG1;A0A1W2PPP5;A0A1W2PPG5;I3L0K1;A0A1W2PRV0;A0A1W2PRL0;A0A1W2PS12;A0A1W2PNV3;A0A1X7SBU8;A0A1W2PPJ0;O14653;I3NI02;A0A1W2PRE6;A0A1W2PQQ4;A0A1W2PQS3;A0A1W2PP28 O14653-3 GOSR2 Golgi SNAP receptor complex member 2 0 ; 255.98 2.07E-36 50039000 34540 43344 41674 43117 51060 58881 44782 40052 45131 44413 FALSE TRUE 35903.66587 50787.99483 42760.05868 51645.41391 42380.83944 45206.7801 41271.86982 39515.16845 43506.74413 53114.87701 0.675962515 0.956191517 0.805048624 0.972334246 0.79790902 0.851113335 0.777030319 0.743956697 0.819106559 1 15.69682838 VHNNS(ph)PDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VHNNSPDTSR 10 0 Q9BRD0 Q9BRD0 BUD13 BUD13 homolog 1 VHNNS(0.495)PDT(0.415)S(0.09)R;VHNNS(0.861)PDT(0.044)S(0.096)R;VHNNS(0.871)PDT(0.049)S(0.08)R 92.747 0.0097096 261290000 195555 229570 231927 234017 234440 286894 265140 236952 229786 221296 TRUE FALSE 203275.6624 268996.8617 237971.2082 280304.8641 194589.9725 220267.2164 244357.634 233776.046 221516.0467 264654.7142 0.768078751 1.01640684 0.899176154 1.059134219 0.735259801 0.832281477 0.923307316 0.8833247 0.837000192 1 18.01375183 6.000549086 12.14087232 0.894669462 0.617587906 0 0.101285222 0 0 0.021157065 0 1001265.118 -6.000549086 -0.277081556 VHPAVVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHPAVVIR 8 0 J3KTJ3;P62829;J3KT29;J3QQT9;C9JD32 J3KTJ3 RPL23 60S ribosomal protein L23 0 ; 117.93 0.0019836 985100000 732500 860580 915790 862230 1013560 1103750 987580 885930 903300 1054480 FALSE TRUE 761419.6656 1008377.921 939656.2397 1032776.521 841275.4332 847420.79 910170.899 874055.5574 870790.4095 1261085.167 0.603781319 0.799611277 0.745117193 0.818958582 0.667104376 0.671977446 0.721736266 0.693097961 0.690508803 1 20.26623428 -1.477519862 6.525895767 1.000110818 0.715383274 0.670524463 0.060441671 9.47E-05 7.58E-06 0.056864674 0.013397953 0.033302753 1.477519862 -0.284727544 VHPEEQGWICDPCHLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHPEEQGWICDPCHLAR 17 0 Q9BV36-2;Q9BV36-5;C9JKV5;Q9BV36-3;Q9BV36;Q9BV36-4 Q9BV36-2;Q9BV36-3;Q9BV36 MLPH Melanophilin 0 ;;; 234.48 2.26E-20 1590880000 602511 744850 727318 731943 769632 833534 655474 705068 702144 715675 FALSE TRUE 626298.5995 872772.1934 746272.5046 876719.1408 638810.2275 639958.3608 604096.2351 695617.7167 676873.9746 855897.8138 0.731744595 1.019715414 0.87191776 1.024326884 0.746362728 0.747704166 0.705804157 0.812734541 0.790835032 1 19.70707904 3.218218415 24.99398513 0.784025832 0.916767694 0.196223436 0.107137351 301.5152694 370463.8365 0.028726031 0.03437271 1652.792811 -3.218218415 0.132741862 VHPEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHPEGK 6 0 P62195-2;P62195;J3QSA9;J3KRP2;J3QLH6;J3QRW1 P62195-2 PSMC5 26S protease regulatory subunit 8 0 ; 121.87 0.019465 534190000 2107400 1694680 2047700 1598790 2564800 2414700 2560400 2147300 2286100 1747220 FALSE TRUE 2190601.779 1985728.107 2101064.744 1915025.89 2128836.212 1853922.52 2359709.158 2118518.956 2203823.708 2089554.306 1.048358386 0.950311797 1.005508561 0.916475769 1.018799179 0.887233471 1.129288265 1.01386164 1.054686016 1 20.99476382 2.236609121 24.99999969 1.049486127 0.971416224 0.329375524 0.054764535 57.60569223 737952.5736 0.018317211 0.014212654 172.4285283 -2.236609121 -0.078069902 VHPEIINENGNPSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHPEIINENGNPSYK 15 0 O95881 O95881 TXNDC12 Thioredoxin domain-containing protein 12 0 167.71 9.52E-10 0 74728 63332 71717 51743 81256 93630 73265 71713 64771 67581 FALSE TRUE 77678.31914 74208.77835 73586.00394 61977.61096 67444.13414 71885.85148 67522.29786 70751.80453 62439.90436 80822.20303 0.961101235 0.91817317 0.910467683 0.766838921 0.834475325 0.889431973 0.835442432 0.875400594 0.772558802 1 16.30246406 3.980852586 22.5342114 0.84876153 0.933308114 0.243703363 0.062560361 251.5264521 296020.6311 0.014829096 0.027380475 9568.692224 -3.980852586 0.084546584 VHQLEQEQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHQLEQEQAR 10 0 Q9NW68-9;Q9NW68-8;Q9NW68;Q9NW68-7;Q9NW68-4;Q9NW68-3;Q9NW68-2;E9PQA7 Q9NW68-9 BSDC1 BSD domain-containing protein 1 0 104.95 0.004214 0 66434 60961 76381 71850 69551 80400 75906 67197 63743 63779 FALSE TRUE 69056.86562 71430.57754 78371.55161 86061.71555 57728.74586 61728.31847 69956.28938 66296.33413 61448.90188 76275.27393 0.905363718 0.936484051 1.027483057 1.128304247 0.756847441 0.809283472 0.917155531 0.869172023 0.805620206 1 16.21892784 3.230472508 24.99986403 0.856008325 0.996919459 0.4023979 0.083325857 182.713935 564757.4294 0.024314954 0.029539575 1700.092331 -3.230472508 0.140911134 VHQLYETIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHQLYETIQR 10 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 0 ;;; 176.95 2.38E-06 1311760000 455639 477542 465406 439812 665176 596378 484830 524293 551313 551099 FALSE TRUE 473627.9795 559556.1237 477534.8627 526805.5009 552109.6211 457878.2477 446827.7577 517265.7099 531471.3528 659076.2976 0.7186239 0.849000527 0.724551716 0.799308825 0.837702134 0.694727226 0.677960593 0.784834338 0.806388205 1 19.33008596 0.73326711 2.107474005 0.999826972 0.761082115 0.631425659 0.05472067 0.730398237 4.749520505 0.052490928 0.014383107 5.410870129 -0.73326711 -0.238744857 VHS(ph)PSGAVEECHVSELEPDKYAVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHSPSGAVEECHVSELEPDKYAVR 24 1 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 1 VHS(0.559)PS(0.441)GAVEECHVSELEPDKYAVR 160.16 1.26E-11 224430000 29678 78262 80935 67064 98132 121270 84983 84267 81695 77265 TRUE FALSE 30849.71036 91702.88971 83044.23259 80329.05903 81451.55769 93106.88036 78321.8104 83137.5387 78754.81291 92403.59742 0.333858326 0.992416878 0.898712116 0.869328265 0.881476046 1.007610991 0.847605641 0.899721883 0.852291633 1 16.4956614 4.743596222 24.99598984 0.909568561 0.333858088 0.898699341 0.058649269 145.0774313 720119.7193 0.013228862 0.110744651 55411.02982 -4.743596222 -0.575710473 VHSFPTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHSFPTLK 8 0 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 ; 155.75 0.00040391 4202600000 3899900 3950800 3975900 3972200 5412200 5203500 4376700 3972000 4082000 3573400 FALSE TRUE 4053871.063 4629319.167 4079515.22 4757889.304 4492236.177 3995065.985 4033642.818 3918761.837 3935089.617 4273539.313 0.948598051 1.083251803 0.954598735 1.113336969 1.051174647 0.934837775 0.94386468 0.916982751 0.920803421 1 22.02699996 2.732732971 24.66929568 0.936539982 1.033559341 0.405020459 0.052260077 348.1545455 1473786.287 0.015818623 0.015279832 540.4219392 -2.732732971 0.097019359 VHSPSGAVEECHVSELEPDKYAVR ddPTM_MDA-MB-175_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 ;;; 372.13 5.49E-119 2423566000 384773 1346400 1344724 1285674 1663668 1834338 1418485 1570410 1530943 1362100 FALSE TRUE 399964.1351 1577633.726 1379768.612 1539976.48 1380878.308 1408340.799 1307300.439 1549361.223 1475844.66 1628977.416 0.245530804 0.96848103 0.847015188 0.945363923 0.84769641 0.864555141 0.802528277 0.951125048 0.90599455 1 20.63553517 4.742412823 24.99460369 0.89660337 0.245530554 0.915312908 0.060019807 93.62754622 607467.4464 0.013459429 0.102134999 55260.2472 -4.742412823 -0.651072817 VHSYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHSYLER 7 0 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 0 ; 139.31 0.0027006 250210000 95536 101730 105532 94429 135429 149034 124393 102083 105125 124101 FALSE TRUE 99307.83505 119201.3362 108282.2506 113106.7744 112408.827 114423.1121 114642.7516 100714.7444 101341.5718 148416.2149 0.669117152 0.803155748 0.729585044 0.76209176 0.757389124 0.770960991 0.77244088 0.678596637 0.68282008 1 17.17928919 -1.434839977 3.24868988 1.003804494 0.737689106 0.76850926 0.043421751 18184133.2 25457696.75 646761.3527 0.010518169 0.036741766 1.434839977 -0.266115388 VHTGFDQHEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VHTGFDQHEQK 11 0 O96013;O96013-4;O96013-2;O96013-3;M0R2X4;M0R0L9;M0R3G6 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 170.04 9.36E-06 771220000 716730 573551 684740 570850 955020 968560 826160 646250 718060 625650 FALSE TRUE 745027.0538 672053.9226 702584.8869 683762.4262 792686.0415 743626.6187 761403.4204 637588.0758 692217.1609 748234.1387 0.995713795 0.898186661 0.938990686 0.913834842 1.059409081 0.993842141 1.017600482 0.852123744 0.925134427 1 19.51313027 -1.417943606 3.292196721 1.000590231 0.951263363 0.046608076 0.058961799 9971693.286 4372816.722 41212.27923 0.01453779 0.038199387 1.417943606 -0.049326868 VHTVEDYQAIVDAEWNILYDKLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHTVEDYQAIVDAEWNILYDKLEK 24 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ; 229.76 1.52E-33 3273500000 3626800 2115040 3104630 2210820 3930300 3519500 3741300 2921070 3834800 1777940 FALSE TRUE 3769988.864 2478281.667 3185539.208 2648113.597 3262229.01 2702149.464 3448047.13 2881917.835 3696786.297 2126293.302 1.773033316 1.165540833 1.498165472 1.24541313 1.534232839 1.270826306 1.621623473 1.355371731 1.738606002 1 21.01990919 4.766024039 23.77142122 1.401730646 1.77303434 0.230173932 0.212034854 6994.477691 6053991.863 0.045024344 3.714749749 58347.73998 -4.766024039 0.371303694 VHVGDEDFVHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 ;;;;;;; 208.72 3.68E-08 7210340000 2855213 3951880 2955470 3735430 3203170 3857850 3279510 3094480 2781620 3849840 FALSE TRUE 2967939.014 4630584.649 3032491.976 4474286.905 2658696.308 2961922.804 3022453.437 3053003.557 2681510.04 4604142.438 0.64462363 1.005743135 0.658644257 0.971795935 0.57745744 0.643316935 0.656463929 0.663099285 0.582412485 1 22.13450104 3.224126996 24.99775104 0.666091432 0.821914916 0.141687303 0.155344821 357.7868444 619653.8987 0.040501133 0.048612525 1675.432734 -3.224126996 0.155823483 VHVIFNYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VHVIFNYK 8 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 ; 131.04 0.0010222 785010000 465230 464860 339960 317070 1942080 934310 606960 370530 437260 1781940 FALSE TRUE 483597.6396 544696.0889 348819.6369 379785.4996 1611965.935 717330.6621 559384.8892 365563.6514 421523.098 2131077.026 0.226926401 0.255596622 0.163682322 0.178212939 0.756409044 0.336604756 0.262489287 0.171539389 0.197798152 1 21.02315131 -1.398314732 3.135605913 1.009312363 0.282246244 0.626010771 0.166196828 69523703.29 90146041.43 5840914.577 0.041889494 0.039965502 1.398314732 -0.727066119 VHVQFFDDS(ph)PTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VHVQFFDDSPTR 12 0 P52701;P52701-2;A0A087WWJ1;A0A494C0M1;F8WAX8;C9J7Y7;C9J8Y8;C9JH55 P52701 MSH6 DNA mismatch repair protein Msh6 1 VHVQFFDDS(0.991)PT(0.009)R 143.93 4.03E-05 213920000 110250 120880 132670 132430 139110 174950 116540 117130 134810 140720 TRUE FALSE 114602.7551 141640.1997 136127.4892 158624.2587 115464.1319 134320.5139 107405.2903 115560.0639 129958.2144 168291.3898 0.680978125 0.841636639 0.808879702 0.942557186 0.68609649 0.79814252 0.638210252 0.686666526 0.772221411 1 17.36060184 3.191576523 24.9999556 0.737097117 0.819478274 0.023974051 0.111326221 259.4479219 138049.7611 0.030598776 0.036572647 1554.449163 -3.191576523 0.082381157 VIAHTQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIAHTQMR 8 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;; 157.86 0.00037013 529987000 134093 195469 149665 147657 318136 255084 158041 145856 145178 398791 FALSE TRUE 139387.0952 229039.2802 153565.3929 176863.1139 264059.3564 195844.6068 145653.3335 143901.0389 139953.0721 476926.4611 0.29226119 0.480240244 0.321989668 0.370839382 0.553668915 0.410639004 0.305399984 0.301725844 0.293447908 1 18.8634073 -1.366757127 3.560809135 1.003495505 0.37056745 0.834991151 0.084014959 54159753.81 81731437.64 1970222.697 0.021665017 0.042977671 1.366757127 -0.632928055 VIAIDSDAES(ph)PAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIAIDSDAESPAKR 14 1 P28749 P28749 RBL1 Retinoblastoma-like protein 1 1 VIAIDSDAES(1)PAKR 121.82 6.88E-05 219740000 270440 211150 238680 195920 266100 329220 266770 226030 242840 178140 TRUE FALSE 281117.18 247413.37 244900.1969 234672.3912 220868.417 252763.6444 245859.8703 223000.4376 234100.2358 213043.1223 1.319531825 1.161330004 1.149533457 1.10152531 1.036731037 1.186443578 1.154038054 1.046738497 1.098839678 1 17.70078595 7.999999698 0.756404119 1.091663472 43.31445979 0.635741012 0.0523228 253.6701229 1.057254461 0.018096218 18266.21862 99999930.5 -7.999999698 42.22279631 VIAINVDDPDAANYNDINDVKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VIAINVDDPDAANYNDINDVKR 22 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ;;;;; 266.18 1.97E-37 8015440000 4976930 3970680 4805040 3795840 5893250 5852550 5384870 4807810 5159460 3861740 FALSE TRUE 5173423.039 4652613.402 4930263.29 4546645.823 4891517.47 4493383.959 4962789.819 4743369.171 4973772.042 4618374.016 1.120182779 1.007413732 1.067532269 0.984468951 1.059142775 0.97293635 1.074575121 1.027064754 1.076953063 1 22.13895358 4.748502036 24.45488591 1.031584293 1.120182845 0.355618723 0.036359195 1057.889704 2602228.995 0.007779681 0.10365051 56040.50448 -4.748502036 0.088598552 VIDFDENTALDDAEEESFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIDFDENTALDDAEEESFR 19 0 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 220.21 6.87E-19 47410000 39155 47724 45666 50149 53383 50953 40431 49342 45888 53118 FALSE TRUE 40700.86963 55920.22576 46856.09348 60068.32252 44308.97673 39119.93795 37261.91257 48680.6512 44236.49984 63525.45509 0.64070174 0.880280601 0.737595558 0.945578783 0.697499556 0.615815155 0.586566637 0.766317237 0.696358645 1 15.95504719 -1.378402941 2.888386474 1.004252993 0.732570955 0.365065626 0.106904163 13447631.81 16049329.96 481398.5003 0.026934504 0.041840519 1.378402941 -0.271682038 VIDFDENTALDDAEEESFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 ; 288.78 4.78E-46 328080000 262396 228325 259843 214418 358880 315889 266254 245547 247622 229272 FALSE TRUE 272755.5967 267538.0426 266614.722 256829.2404 297877.7058 242528.5671 245384.3158 242255.8441 238710.1326 274193.4587 0.994756031 0.975727298 0.972359892 0.936671654 1.08637787 0.88451624 0.894931327 0.883521603 0.87059018 1 18.06483463 2.676475894 24.99917068 0.897326539 0.987913697 0.426294469 0.049371349 197.0926065 79361.37798 0.014972751 0.014116447 474.7619381 -2.676475894 0.090587157 VIDGPHSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIDGPHSGR 9 0 O00267;O00267-2 O00267 SUPT5H Transcription elongation factor SPT5 0 ; 143.39 0.00010205 246360000 418610 532660 509260 492760 517210 623000 539500 496590 467390 556620 FALSE TRUE 435137.046 624140.2115 522531.734 590226.4573 429294.8289 478317.6917 497212.5803 489934.0233 450568.7252 665679.0319 0.653673956 0.937599326 0.784960482 0.88665322 0.644897628 0.718541022 0.746925405 0.735991371 0.676855817 1 19.3444672 5.02922703 16.28154364 0.777332774 0.283779541 0.112090728 0.110000036 26469471.24 401197960.2 0.025072553 357072125.3 106961.3881 -5.02922703 -0.493553233 VIDRELYQQLQR ddPTM_MDA-MB-175_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 ; 218.06 6.47E-08 242460000 169193 180774 202765 117629 276360 228720 158934 183266 195908 297000 FALSE TRUE 175872.8703 211820.5283 208049.2225 140895.6651 229384.4259 175603.2463 146476.3378 180809.619 188857.3093 355191.4636 0.495149485 0.596355909 0.585738239 0.396675257 0.645805008 0.49439039 0.412386988 0.509048323 0.531705654 1 18.43823738 0.692931145 4.792825535 0.999999864 0.516049259 0.794212607 0.073548942 7.145803924 111.2887887 0.069348283 0.017556106 4.930956197 -0.692931145 -0.483950605 VIDTLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIDTLHR 7 0 Q9H993 Q9H993 ARMT1 Protein-glutamate O-methyltransferase 0 ;;; 158.36 0.0014236 1850330000 2898240 3471010 3324840 3507780 3940850 4154890 3339770 3370550 3305460 3792190 FALSE TRUE 3012664.753 4067128.967 3411488.062 4201608.414 3270985.725 3189979.765 3077990.101 3325373.29 3186497.14 4535197.025 0.664285308 0.896792123 0.752224885 0.926444516 0.721244459 0.703382841 0.67868939 0.733236786 0.70261493 1 22.1127338 VIEEEWQQVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 ;;; 178.84 1.71E-05 735530000 243514 309335 282947 286077 321567 367259 269124 300949 270992 301153 FALSE TRUE 253128.1208 362460.88 290320.8313 342662.1767 266907.1562 281968.6631 248029.3577 296915.2709 261239.0509 360158.1644 0.702824886 1.006393623 0.8060926 0.951421377 0.741083176 0.782902322 0.688667875 0.824402444 0.725345353 1 18.45827108 3.222410597 24.99173137 0.780186988 0.872334572 0.087392304 0.109791034 436.8954674 676082.9522 0.028843079 0.034573107 1668.824231 -3.222410597 0.092147583 VIEETEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIEETEER 8 0 A0A075B730;P58107 A0A075B730;P58107 EPPK1 Epiplakin 0 ; 150.4 0.0011395 763690000 1065390 1104270 1093000 1149640 1109140 1330590 1232010 1031350 982250 1044050 FALSE TRUE 1107452.42 1293919.782 1121484.478 1377035.361 920608.779 1021580.638 1135441.837 1017526.44 946899.0144 1248611.608 0.88694708 1.036286844 0.898185209 1.102853243 0.737305959 0.818173266 0.909363512 0.814926302 0.758361534 1 20.25189335 3.231873738 24.99945743 0.833360284 0.979092086 0.366178037 0.090880003 155.3775961 580891.7476 0.024380262 0.029778131 1705.586454 -3.231873738 0.145731802 VIEHGEQNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIEHGEQNR 9 0 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 0 78.655 0.024406 0 31554 37082 35105 31900 41133 40657 33446 33000 35927 33310 FALSE TRUE 32799.77628 43450.54504 36019.86514 38209.72479 34141.22735 31215.02791 30824.41513 32557.68898 34633.99429 39836.45674 0.823360785 1.090723136 0.904193497 0.959164743 0.85703474 0.783579426 0.773774016 0.817283756 0.869404488 1 15.28180171 3.159622545 4.208288003 0.829038814 0.952355015 0.203197243 0.086268744 0.252347513 8.471900485 0.023769339 0.029272726 1444.184053 -3.159622545 0.123316201 VIEPLKDFHKDEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VIEPLKDFHKDEVR 14 2 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 ;; 189.37 4.36E-07 1290415000 2573310 1570611 2198880 1395818 3129160 2732720 2634530 2209940 2561540 1513394 FALSE TRUE 2674906.266 1840351.222 2256184.619 1671906.634 2597266.501 2098087.195 2428028.655 2180319.369 2469350.676 1809914.579 1.477918515 1.016816618 1.24656967 0.923748918 1.435021593 1.159218904 1.341515607 1.204653189 1.36434653 1 20.78749018 3.212802649 24.99996298 1.258972271 1.161324337 0.050398673 0.177116293 624.4323676 606055.0833 0.046939498 0.056120567 1632.31003 -3.212802649 -0.097647934 VIET(ph)PENDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIETPENDFK 10 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 VIET(1)PENDFK 117.79 0.0073308 0 192240 147590 169190 139950 199000 217540 213590 170360 195400 141690 TRUE FALSE 199829.7836 172937.4344 173599.2304 167631.6923 165174.0511 167019.6319 196848.2577 168076.6029 188367.5922 169451.4427 1.179274608 1.020572216 1.024477736 0.989260933 0.97475742 0.985648922 1.161679444 0.991886526 1.111631682 1 17.37051239 -0.203876607 7.853373119 1.000000001 1.042625588 0.033649347 0.071902002 0 0 0.066592168 0.015695925 0.625350344 0.203876607 0.042625587 VIFGLFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIFGLFGK 8 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 146.21 0.0012957 131534000 404870 429530 367600 340680 544780 532090 374100 379230 370900 457160 FALSE TRUE 420854.5802 503298.4362 377179.958 408065.4872 452178.4902 408520.1614 344777.0645 374147.0421 357551.3815 546731.7491 0.769764296 0.920558276 0.689881205 0.746372399 0.827057311 0.747204021 0.630614675 0.684333849 0.653979547 1 19.06047363 4.227684307 24.99626065 0.730523977 0.845161303 0.102766384 0.106518135 322.9256689 742162.7192 0.025248892 0.05538363 16892.1258 -4.227684307 0.114637326 VIFLEDDDVAAVVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIFLEDDDVAAVVDGR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;;; 230.14 5.90E-15 128202000 84241.8 93527.8 90938.9 102335 95676 103399 95408 91897 79043.9 93293 FALSE TRUE 87567.73131 109590.4721 93308.84244 122576.5576 79413.02769 79386.14928 87929.67166 90665.27103 76199.12548 111571.9771 0.784854168 0.982240119 0.836310737 1.098632118 0.711764994 0.711524088 0.788098176 0.812616872 0.682959354 1 16.76761519 3.204160838 24.99995351 0.774822899 0.923190647 0.266602313 0.113878487 217.6369627 158166.5157 0.030594919 0.036569553 1600.150525 -3.204160838 0.148367748 VIFWSALAGAIPLNGDS(ph)EEEANRDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIFWSALAGAIPLNGDSEEEANRDDR 26 1 Q9H089 Q9H089 LSG1 Large subunit GTPase 1 homolog 1 VIFWSALAGAIPLNGDS(1)EEEANRDDR 187.43 6.97E-18 307320000 83708 73696 77888 97438 84375 97580 87526 78135 78017 78828 TRUE FALSE 87012.85648 86352.71472 79917.82527 116710.9456 70032.96764 74918.52384 80665.48341 77087.72813 75209.18341 94272.83735 0.922989685 0.915987226 0.847729076 1.238012442 0.742875356 0.794698939 0.855659866 0.817708794 0.797782113 1 16.52455453 VIGELVGHTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIGELVGHTER 11 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 147.91 0.0018547 0 60687 60261 74075 78792 72908 91233 69863 69533 63395 65471 FALSE TRUE 63082.96962 70610.35798 76005.45535 94376.82243 60515.1242 70045.5184 64386.95551 68601.02387 61113.42633 78298.78893 0.8056698 0.901806515 0.970710485 1.205342046 0.772874332 0.894592616 0.822323773 0.876144124 0.780515601 1 16.25670237 VIGQDSSEIHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIGQDSSEIHFK 12 0 B8ZZN6;P63165;B8ZZJ0;B9A032;G2XKQ0 B8ZZN6;G2XKQ0 SUMO1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 0 ;;; 179.67 2.04E-05 1984310000 1868050 2085540 2387410 2129930 2966000 3119910 2674330 2575700 2696630 2319810 FALSE TRUE 1941802.056 2443715.272 2449627.866 2551223.797 2461840.379 2395358.185 2464709.027 2541176.954 2599578.813 2774332.354 0.699916884 0.880830038 0.882961215 0.919581172 0.88736318 0.863399867 0.888397175 0.915959817 0.937010596 1 21.4037092 4.908481047 1.965073873 0.906615971 0.561258906 0.751723344 0.036199796 0.648871405 1.802977653 0.008725563 0.470745388 80999.25927 -4.908481047 -0.345357065 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIGTLEEVHMPQNGINHPGITALAQAFAVNPLLR 34 0 P46060;H0Y4Q3 P46060 RANGAP1 Ran GTPase-activating protein 1 0 64.984 0.0033003 114830000 29871 36750 40640 38099 46329 49298 33566 35467 41741 43486 FALSE TRUE 31050.33015 43061.52662 41699.11179 45634.86849 38454.01313 37849.28662 30935.00921 34991.62288 40238.74956 52006.24911 0.597049983 0.828006775 0.801809638 0.877488172 0.739411394 0.727783435 0.594832539 0.672834966 0.773729124 1 15.66639737 0.9652678 20.72342437 1.000000003 0.730594546 0.461620489 0.087077982 484.1191619 288857.7365 0.08996671 0.022491678 9.231404897 -0.9652678 -0.269405457 VIHCSGYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIHCSGYLK 9 0 H7BZX8;Q14190-2;Q14190;P81133 H7BZX8 SIM2;SIM1 Single-minded homolog 2;Single-minded homolog 1 0 65.06 0.067627 32580000000 0 2818400 1541800 2082400 802090 2266800 721050 1664000 1067500 3045000 FALSE TRUE 0 3302438.276 1581980.575 2494292.505 665751.0283 1740370.054 664532.2169 1641696.802 1029080.884 3641609.45 0 0.906862287 0.434417967 0.684942342 0.1828178 0.477912329 0.18248311 0.450816273 0.28258958 1 21.79614478 -1.361676785 5.351739815 1.000224863 0.413784532 0.342630921 0.248563358 0.000613011 7.31E-05 0.221227698 0.05212428 0.043483372 1.361676785 -0.586440331 VIHDNFGIVEGLMTTVHAIT(ph)ATQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIHDNFGIVEGLMTTVHAIT(0.999)AT(0.001)QK;VIHDNFGIVEGLMTTVHAIT(0.984)AT(0.015)QK;VIHDNFGIVEGLMTTVHAIT(0.999)AT(0.001)QK 246.36 1.33E-37 827690000 556048 513862 633870 439930 734760 688260 545291 624370 659690 540765 TRUE FALSE 578001.2044 602113.8012 650389.1729 526946.8409 609865.7576 528422.0457 502549.6666 616001.3414 635947.8858 646717.5482 0.893745973 0.93103056 1.005677324 0.814802138 0.943017179 0.817083203 0.777077517 0.952504448 0.983347193 1 19.30277623 -1.19800714 4.247409548 1.000039084 0.900370678 0.139896189 0.072770284 2.71E-05 5.11E-06 0.070860536 0.016695441 0.063385929 1.19800714 -0.099668406 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 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;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.01)AT(0.989)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.999)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK;VIHDNFGIVEGLMTTVHAIT(0.001)AT(0.999)QK;VIHDNFGIVEGLMTTVHAIT(0.287)AT(0.713)QK;VIHDNFGIVEGLMTTVHAITAT(1)QK 402.72 6.75E-157 49170464000 9310422 4100865.4 7510563 5232708 5854027 7306110 9943920 7038940 8683294 2501444.7 TRUE FALSE 9678004.65 4805157.132 7706294.442 6267722.024 4858961.582 5609376.678 9164489.567 6944594.523 8370783.945 2991554.896 3.235108493 1.606240667 2.576016389 2.095138563 1.624226113 1.875070615 3.063453584 2.321399661 2.798138171 1 21.51246411 -1.261247942 5.655449814 0.999911939 2.326659685 0.360166768 0.540610219 0.000575612 7.52E-05 0.501958899 0.118305151 0.054796404 1.261247942 1.326747746 VIHDNFGIVEGLMTTVHAITATQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 32 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 386.55 2.24E-137 2.32628E+11 15626082 15296765 17619853 15105456.2 20518934 20186232 18771534 17725960 17924731 15670669 FALSE TRUE 16243011.78 17923865.4 18079040.84 18093270.35 17031132.93 15498285.54 17300172.11 17488372.5 17279623.43 18741036.56 0.866708292 0.956396694 0.964676676 0.965435946 0.908761523 0.826970562 0.923117143 0.933159297 0.922020689 1 24.15969741 0.255083954 1.306503031 1.000061202 0.919669452 0.257800025 0.041442754 8.582580982 13.4964191 0.042757391 0.01240623 1.799218692 -0.255083954 -0.08039175 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIHDNFGIVEGLMTTVHAITATQKTVDGPSGK 32 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 176.87 1.39E-19 170080000 243320 137090 197490 149020 299380 179010 810210 190140 255330 103060 FALSE TRUE 252926.4615 160634.1411 202636.7516 178495.7112 248491.4945 137437.6404 746703.6231 187591.4843 246140.7232 123252.6338 2.052097823 1.303291752 1.644076442 1.448210117 2.016115087 1.115088872 6.058317783 1.522007916 1.997042299 1 16.91125895 VIHELANER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIHELANER 9 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 0 87.258 0.013583 98517000 130450 147710 162120 156490 163920 180180 155280 163370 143080 159130 FALSE TRUE 135600.2667 173078.0435 166344.9804 187443.2549 136056.937 138335.9257 143108.7479 161180.2924 137930.5787 190308.4768 0.71252878 0.909460505 0.874080772 0.984944329 0.714928411 0.726903646 0.751983045 0.846942265 0.724773699 1 17.5379803 4.7726721 22.44143926 0.827889327 0.712527867 0.11382727 0.101386269 9359.215862 6156849.1 0.024113325 3.38643767 59247.78246 -4.7726721 -0.11536146 VIHLVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VIHLVER 7 0 P46379-3;P46379;P46379-2;A0A0G2JK23;A0A024RCR6;P46379-5;A0A0G2JL47;P46379-4;A0A0G2JJM1;X6REW1;F6S6P2;F6U341;F6TC96;F6WML8;F6VEM6;F6X9W3;A0A1B0GX79;A0A0G2JJR8;F6XTU0;F6U1F2;F6UR09 P46379-3 BAG6;BAT3 Large proline-rich protein BAG6 0 ;;; 143.23 0.0024359 465181000 548035 681950 606250 636210 732140 762140 608660 630910 598600 790460 FALSE TRUE 569671.845 799069.6077 622049.373 762050.4391 607691.1043 585144.5353 560951.6388 622453.6834 577056.5029 945335.5027 0.602613404 0.845276207 0.658019689 0.806116386 0.642831146 0.61898081 0.593388947 0.658447378 0.610425083 1 19.85046691 -1.071886776 4.582764722 1.000014454 0.672658979 0.593396394 0.081766796 1.52E-05 3.07E-06 0.078608197 0.018527096 0.084744832 1.071886776 -0.327355474 VIISAPSADAPMFVMGVNHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 VIISAPSADAPMFVMGVNHEK 21 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;; 381.64 1.73E-113 98162180000 42135461 35254301 42976549 36620594 45801809 48727080 47681213 41404217 43099618 31658459 FALSE TRUE 43799001.54 41308952.96 44096553.17 43864038.19 38016433.87 37410954.14 43943834.93 40849261.19 41548471.17 37861327.9 1.156826872 1.091059275 1.164685858 1.158544632 1.004096686 0.988104649 1.160652237 1.078917816 1.097385471 1 25.17422168 8 0.012459193 1.41E-10 2.367715912 0.266621034 0.057939627 12395.33367 11.93005568 941.1978317 1361.915347 99999999.92 -8 2.367715912 VIISAPSADAPMFVMGVNHEKYDNSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VIISAPSADAPMFVMGVNHEKYDNSLK 27 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;; 361.92 3.08E-111 22660710000 6688000 4800390 6822720 3229810 9554930 7816360 5683720 5825260 7797820 6612760 FALSE TRUE 6952047.404 5624819.641 7000525.688 3868656.778 7930786.412 6001128.848 5238215.175 5747181.918 7517177.981 7908403.713 0.879070879 0.71124589 0.88520085 0.489183016 1.002830242 0.75882935 0.662360619 0.726718327 0.950530379 1 22.91495509 1.165088922 5.23163725 0.991190668 0.758753764 0.28896311 0.132623226 0.238995781 11.18351171 0.116619319 0.029932857 14.62476585 -1.165088922 -0.232436904 VIKDFMIQGGDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIKDFMIQGGDFTR 14 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 ; 179.81 1.66E-06 3515500000 2528700 3226200 2768900 2593400 3602600 3769200 2202900 2545400 2540300 3815200 FALSE TRUE 2628535.029 3780274.754 2841059.809 3106366.779 2990231.339 2893860.423 2030230.942 2511283.076 2448875.099 4562715.394 0.57609007 0.828514257 0.622668644 0.680815372 0.655362231 0.634240835 0.444961118 0.550392225 0.53671441 1 22.12146124 -1.102166325 5.036763612 1.00001164 0.612619474 0.590598224 0.096298588 1.35E-05 2.41E-06 0.100117584 0.023597232 0.079037587 1.102166325 -0.387392166 VILEDVAMLHIKPDQFTYTSDHFETIMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VILEDVAMLHIKPDQFTYTSDHFETIMK 28 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 66.886 0.0088676 413120000 469740 124650 144930 93521 197560 307470 193410 128850 196060 70934 FALSE TRUE 488285.6979 146057.6679 148706.9949 112019.1747 163978.8218 236064.7523 178250.0188 127122.9765 189003.8389 84832.15919 5.755903216 1.721725219 1.752955439 1.32048006 1.932979466 2.782727146 2.101208086 1.498523411 2.227973928 1 16.37232366 4.739649084 24.99484213 1.844205267 5.755904464 0.862225956 0.472422241 31.32223027 719171.466 0.112668466 0.69340838 54909.70164 -4.739649084 3.911699196 VILGSEAAQQHPEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VILGSEAAQQHPEEVR 16 0 G3V1D3;G3V180;Q9NY33-4;Q9NY33;Q9NY33-2;E9PKK8;E9PPK9;E9PQ14;E9PNX5 G3V1D3 DPP3 Dipeptidyl peptidase 3 0 ;;; 312.49 1.05E-57 1937110000 705880 826045 783955 785253 849888 980300 756451 761317 729084 841660 FALSE TRUE 733748.6875 967911.803 804385.5113 940573.6997 705424.3413 752640.1816 697158.394 751112.7909 702844.4093 1006567.162 0.728961479 0.96159684 0.799137446 0.934437099 0.70082193 0.747729719 0.692609912 0.746212294 0.69825883 1 19.94101201 3.229205022 24.9998496 0.74586697 0.859509497 0.143220117 0.104135806 276.4715959 738781.6003 0.02716485 0.032880787 1695.137854 -3.229205022 0.113642527 VILHLK ddPTM_MDA-MB-175_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 17703600000 15021100 12993800 14899600 14909800 16806800 18246700 20187500 16565600 15928500 11793200 FALSE TRUE 15614144.63 15225384.07 15287895.82 17858913.94 13949986.14 14009180.46 18605151 16343565.23 15355236.4 14103851.75 1.107083718 1.079519577 1.083951823 1.266243737 0.989090526 0.993287558 1.319153897 1.158801547 1.088726447 1 23.74958588 2.283511797 24.99999923 1.161190229 1.089833646 0.0505406 0.103547623 315.4818758 175456.785 0.035804275 0.029955896 192.0931139 -2.283511797 -0.071356583 VILHLKEDQTEYLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 30 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; 326.53 1.19E-71 13947509500 7957658.1 6811237.5 8200072.5 6387985.5 10501896.2 9570606.2 8051413.6 8274061.5 9418371.1 8045646 FALSE TRUE 8271832.586 7981014.557 8413773.126 7651509.966 8716787.635 7347977.954 7420322.764 8163161.239 9079405.764 9622036.291 0.859675887 0.829451721 0.874427499 0.795206933 0.905919222 0.763661426 0.771180085 0.84838188 0.943605438 1 23.19791081 1.147311478 2.946742564 0.996908237 0.827995827 0.652767753 0.042220237 0.141732021 2.227228931 0.039241127 0.010652202 14.03820169 -1.147311478 -0.16891241 VILSNMVSISSEPFGHLVDDDDIS(ph)DQEDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VILSNMVSISSEPFGHLVDDDDISDQEDHR 30 0 A8MUM1;Q53HC9;C9JVR6 A8MUM1 TSSC1 Protein TSSC1 1 VILSNMVSISSEPFGHLVDDDDIS(1)DQEDHR 137.44 3.31E-06 349750000 39392 41249 37369 46211 50824 57755 54758 48886 52078 35003 TRUE FALSE 40947.22658 48333.19488 38342.86684 55351.39787 42184.95463 44342.27654 50465.92488 48230.76313 50203.72295 41861.16768 0.978167329 1.154606944 0.915953113 1.322261202 1.007734781 1.059269939 1.205554639 1.152160004 1.199291031 1 15.35332493 6.673481691 0.526782878 1.136400166 3.36E-08 0.095919176 0.114490902 62.75924709 2.533634505 0.053788237 67.68550529 4714999.939 -6.673481691 -1.136400133 SLHDALCVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 SLHDALCVVK 10 0 P17987;F5H282;E7EQR6;E7ERF2;F5GZ03 P17987 TCP1 T-complex protein 1 subunit alpha 0 100.88 0.0037132 425350000 468990 770410 784290 829380 1170800 1172300 992400 914060 923270 911970 FALSE TRUE 487506.0873 902721.9245 804729.2417 993428.8885 971787.8342 900051.0914 914613.0948 901808.5208 890041.6931 1090653.061 0.446985485 0.827689351 0.737841639 0.910856921 0.891014631 0.825240513 0.83859215 0.826851868 0.816063077 1 20.05676082 5.030503442 1.699638644 0.852441067 1.30E-15 0.771386128 0.066159319 1.020945891 1.538072599 0.015991211 1.796832196 107276.215 -5.030503442 -0.852441067 down VIMELFDNDQVGKDEFLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIMELFDNDQVGKDEFLGR 19 1 Q9NZM1-6;Q9NZM1-3;Q9NZM1;Q9NZM1-2;H0YD14 Q9NZM1-6 MYOF Myoferlin 0 174.65 3.72E-12 194740000 190130 129380 166570 142460 231630 248120 213370 176380 202880 150940 FALSE TRUE 197636.4792 151600.0086 170910.951 170638.1628 192257.6153 190497.8903 196645.5019 174015.9146 195578.3884 180513.8031 1.094855218 0.839825022 0.946802672 0.945291495 1.065057697 1.055309273 1.089365459 0.964003371 1.083453925 1 17.46174963 3.247604309 24.68049511 1.039587957 0.947639323 0.275295351 0.067735357 201.9121702 551019.5412 0.018044346 0.024082441 1768.496924 -3.247604309 -0.091948635 VINAAHSFYNGTTTLPIS(ph)DEDRTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGT(0.002)T(0.001)T(0.008)LPIS(0.706)DEDRT(0.283)PR 119.89 0.00022826 272800000 57914 59514 64389 50689 56245 66297 54507 61823 52331 60088 TRUE FALSE 60200.48944 69735.06655 66067.03024 60715.13291 46684.49499 50900.52649 50234.59891 60994.36381 50447.61753 71861.09315 0.837734117 0.970414775 0.91937135 0.84489576 0.649649107 0.708318288 0.699051416 0.848781463 0.702015727 1 16.13292326 3.471919057 24.1993062 0.758201727 0.90977024 0.293464758 0.098263875 101.7766228 473435.3687 0.025946691 0.035260265 2964.278864 -3.471919057 0.151568513 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 1 VINAAHSFYNGTTTLPIS(0.001)DEDRT(0.999)PR;VINAAHSFYNGTTTLPISDEDRT(1)PR 206 5.81E-25 432430000 93870 100939 98306 106825 102523 131091 98447 95330 88557 105218 TRUE FALSE 97576.06008 118274.4881 100867.9351 127954.6662 85096.17708 100647.102 90730.4669 94052.25728 85369.85087 125833.4526 0.775438153 0.939928816 0.801598725 1.01685731 0.676260369 0.799843761 0.72103614 0.747434449 0.678435258 1 16.94115599 3.221975332 24.99992721 0.755409742 0.881642664 0.203285771 0.107051575 313.2532801 472183.2528 0.028121927 0.033699866 1667.152515 -3.221975332 0.126232922 VINAAHSFYNGTTTLPISDEDRTPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915;P49915-2 P49915 GMPS GMP synthase [glutamine-hydrolyzing] 0 144.5 1.81E-07 185650000 34545 26539 37240 26150 47881 35946 25470 39220 22205 48081 FALSE TRUE 35908.86327 31096.86681 38210.50499 31322.39195 39742.20472 27598.08627 23473.59485 38694.32005 21405.84639 57501.55138 0.624485121 0.540800484 0.664512593 0.544722554 0.69115013 0.479953768 0.408225418 0.672926541 0.372265545 1 15.81131326 -1.487999666 3.062620543 1.011845401 0.561470013 0.616447444 0.105101386 17015974.51 20234965.4 1704721.205 0.023520482 0.032508755 1.487999666 -0.450375388 VINDKHDDVMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VINDKHDDVMAK 12 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 ;;; 145.71 8.62E-05 791280000 2356780 1351090 1970390 1252530 2904780 2352620 2384330 1940510 2315550 1233100 FALSE TRUE 2449827.494 1583129.197 2021739.982 1500276.696 2411026.533 1806259.659 2197439.984 1914500.637 2232213.808 1474702.336 1.661235244 1.073524574 1.37094784 1.017342049 1.634924198 1.224829998 1.490090529 1.298228524 1.513670762 1 20.49199235 -1.180630194 4.921507921 0.999967381 1.351573803 0.21573651 0.207351698 6.64E-05 1.10E-05 0.179519955 0.04230934 0.065973543 1.180630194 0.351606423 VINIDFRDPEESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VINIDFRDPEESK 13 1 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 77.776 0.022828 99027000 268180 187060 234690 209370 296920 286350 317330 234280 232130 208650 FALSE TRUE 278767.9535 219186.0999 240806.2142 250782.7611 246449.6445 219849.5522 292456.8454 231139.8598 223775.6866 249530.9727 1.117167743 0.87839236 0.965035369 1.005016565 0.98765152 0.881051157 1.172026231 0.926297274 0.896785214 1 17.92885937 4.767042541 23.39440244 0.972038364 1.117168261 0.228867219 0.081829645 6562.947067 5390439.494 0.018763567 1.673902761 58484.7369 -4.767042541 0.145129897 VIPAKS(ph)PPPPTHSTQLGAPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VIPAKSPPPPTHSTQLGAPSR 21 1 Q14814-4;Q14814;Q14814-6;Q14814-3;Q14814-5;Q14814-2 Q14814-4 MEF2D Myocyte-specific enhancer factor 2D 1 VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(0.998)PPPPT(0.002)HSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(0.999)PPPPTHSTQLGAPSR;VIPAKS(1)PPPPTHSTQLGAPSR;VIPAKS(0.999)PPPPTHSTQLGAPSR 258.05 1.01E-36 6140410000 1103351 2098629 2386757 1986862 2535790 2857756 2282146 2557122 2376953 2086672 TRUE FALSE 1146912.149 2459052.206 2448957.848 2379857.373 2104757.322 2194085.479 2103265.433 2522847.962 2291406.926 2495515.427 0.459589285 0.985388501 0.981343502 0.953653641 0.843415873 0.879211347 0.842818045 1.010952661 0.918209882 1 21.25090639 4.74248915 24.99787602 0.932182752 0.459589102 0.851796357 0.059480535 146.2655948 930674.6235 0.014845463 0.113508063 55269.95992 -4.74248915 -0.47259365 VIPDSDAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIPDSDAHR 9 0 Q5EBL8;Q5EBL8-2 Q5EBL8 PDZD11 PDZ domain-containing protein 11 0 ; 157.96 6.73E-05 249230000 221815 321780 272950 339570 304660 390930 276720 307140 264100 411130 FALSE TRUE 230572.4275 377043.2119 280063.3012 406735.9325 252874.002 300142.4321 255029.9633 303023.2907 254595.0926 491683.0519 0.468945241 0.766841994 0.569601291 0.827231955 0.514302864 0.61043884 0.518687724 0.616298019 0.517803271 1 18.9073691 -1.886689063 2.748048835 1.191996123 0.60660131 0.545839347 0.109048064 14048044.25 8449341.157 17480763.12 0.024697802 0.012981083 1.886689063 -0.585394813 VIPELNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIPELNGK 8 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 129.56 0.0025249 6834600000 5378600 4527300 5369000 4428900 6809200 6304300 6202700 5326500 5367200 4581900 FALSE TRUE 5590951.281 5304828.557 5508920.551 5304923.201 5651774.616 4840221.868 5716516.166 5255106.98 5174035.52 5479635.579 1.020314435 0.968098787 1.005344328 0.968116059 1.031414322 0.883310906 1.043229259 0.959024903 0.944229857 1 22.38564852 VIPELNGKLT(ph)GMAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIPELNGKLTGMAFR 15 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VIPELNGKLT(1)GMAFR;VIPELNGKLT(1)GMAFR 161.95 1.79E-06 437110000 363340 407010 471320 373420 571870 563680 397070 484270 476950 519700 TRUE FALSE 377684.9438 476910.8014 483602.9864 447281.3615 474663.7417 432773.8627 365946.6159 477779.1528 459784.6627 621525.2647 0.607674322 0.767323275 0.778090633 0.719651134 0.763707879 0.696309365 0.588787997 0.768720404 0.739768258 1 19.24545351 0.502984004 1.569599051 0.999881768 0.712872313 0.654024182 0.062745038 1.655961415 4.559558045 0.059456351 0.01704827 3.184080242 -0.502984004 -0.287009454 VIPEYCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VIPEYCR 7 0 B0YIW6;P48444;Q6P1Q5 B0YIW6 ARCN1 Coatomer subunit delta 0 ;; 110.9 0.015585 686286000 714460 617480 571730 611750 726050 803500 591110 545410 571770 704950 FALSE TRUE 742667.4325 723527.3867 586629.7535 732752.3241 602636.2803 616899.3022 544777.2536 538099.6711 551192.1094 843071.4554 0.880906865 0.858204108 0.695824476 0.869146167 0.714810443 0.73172837 0.64618159 0.638261048 0.653790501 1 19.68529539 4.28009302 7.005546714 0.724341137 0.871860241 0.160825838 0.108002896 0.289429461 36.65441003 0.025650152 0.069868087 19058.68884 -4.28009302 0.147519104 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VIPNLPSEGQPALVEVHSMEALLQHTSEQEEMR 33 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 82.364 0.00039556 85865000 5085.3 41250 35594 41249 32147 51796 32562 43946 30928 48075 FALSE TRUE 5286.071571 48334.36662 36521.60888 49407.92908 26682.66442 39767.16398 30009.70536 43356.97575 29814.90732 57494.3758 0.091940672 0.840679909 0.635220548 0.859352387 0.464091732 0.691670506 0.521958973 0.754108122 0.51857085 1 15.81113322 -5 0.264959841 3.507016322 0.589756676 0.242732601 0.212025026 292.5418867 2.858846871 400.8065892 0.249238491 1.00E-05 5 -2.917259646 VIPSQEHLNGPLPVPFTNGEIQKENS(ph)REALAEAALESPRPALVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVR 44 3 O14745;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 VIPSQEHLNGPLPVPFTNGEIQKENS(1)REALAEAALESPRPALVR;VIPSQEHLNGPLPVPFT(0.132)NGEIQKENS(0.706)REALAEAALES(0.162)PRPALVR 200.29 4.06E-36 955610000 154318 139508 173521 118026 213398 222681 182817 191548 217138 168279 TRUE FALSE 160410.5938 163467.4138 178043.0998 141371.1905 177124.6842 170966.7125 168487.3258 188980.6124 209323.2458 201250.0482 0.797071083 0.812260247 0.884685999 0.702465375 0.880122444 0.849523834 0.837203903 0.939033874 1.040115258 1 17.6186296 1.583215848 2.115824033 1.022058185 0.82106747 0.726198359 0.049352589 0.143631649 1.369663272 0.03683222 0.013257646 38.30150574 -1.583215848 -0.200990715 VIQLMPS(ph)PIMHPLILNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR;VIQLMPS(1)PIMHPLILNPR 200.17 9.94E-16 1355136000 746620 853769 908324 840256 1000665 1044168 806003 884007 786939 873077 TRUE FALSE 776097.1341 1000397.184 931995.6696 1006456.129 830572.3207 801675.8065 742826.3788 872158.3321 758617.2191 1044139.722 0.743288583 0.958106624 0.892596699 0.963909434 0.795460898 0.767785948 0.711424308 0.835288912 0.72654761 1 19.99388335 3.1694062 11.31346533 0.792277575 0.894558413 0.149012276 0.093914306 0.793313328 126.3743859 0.025267269 0.030216027 1477.087421 -3.1694062 0.102280838 VIQPMGMS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VIQPMGMSPR 10 0 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2;H0YE35 Q9NPQ8-4 RIC8A Synembryn-A 1 VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR;VIQPMGMS(1)PR 136.27 0.00012797 1429542000 1022178 1200152 1152851 1245639 1461626 1606390 1229007 1241418 1228070 1323550 TRUE FALSE 1062534.377 1406268.77 1182895.244 1492022.676 1213179.335 1233330.268 1132674.22 1224778.822 1183872.001 1582874.282 0.671268962 0.888427329 0.747308398 0.942603398 0.766440739 0.779171335 0.715580658 0.773768856 0.747925476 1 20.59411524 VIQYLAYVASSHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VIQYLAYVASSHK 13 0 P35579;P35579-2;Q5BKV1 P35579 MYH9 Myosin-9 0 ; 214.23 3.12E-11 1691980000 1969480 3122000 3024200 2878800 5240800 5023100 3711400 3499300 3546500 4961900 FALSE TRUE 2047236.591 3658179.214 3103013.136 3448218.048 4349970.688 3856561.151 3420490.77 3452397.607 3418862.158 5934089.304 0.344995919 0.616468514 0.522913117 0.581086308 0.733047729 0.649899412 0.576413767 0.581790639 0.576139317 1 22.50059521 -5 0.243154663 3.401820173 0.541363634 0.666612745 0.091277558 107.7961852 1.073511014 128.4532018 0.140669826 1.00E-05 5 -2.860456539 VIREPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VIREPK 6 1 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 ;;;;; 110.61 0.026042 3117450000 4545830 3191320 4417450 4445460 5208530 5466470 5549480 4320380 4532920 3038030 FALSE TRUE 4725302.879 3739404.385 4532572.376 5324758.72 4323185.931 4196965.188 5114497.257 4262472.373 4369781.095 3633273.812 1.300563383 1.029210728 1.247517421 1.465553932 1.18988718 1.155146957 1.407682856 1.173176753 1.202711747 1 21.79283866 0.702671474 1.508856303 1.000681201 1.247645835 0.281752866 0.118374187 1.387163244 4.929840029 0.111750962 0.032465331 5.042796859 -0.702671474 0.246964634 VIREPKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 145.17 0.00032263 32719980000 2939630 2399147 3111920 2831930 3776430 3678560 2987770 2990770 3061870 2798390 FALSE TRUE 3055688.862 2811181.834 3193019.192 3392077.302 3134513.778 2824270.189 2753580.78 2950683.62 2951673.897 3346680.942 0.913050546 0.839990989 0.95408533 1.013564591 0.936603707 0.843901835 0.822779592 0.881674612 0.88197051 1 21.67429959 2.755627473 23.88673593 0.873851976 0.932195919 0.110248324 0.059610032 818.2092047 1145161.933 0.018603168 0.019681221 569.6754098 -2.755627473 0.058343942 VIS(ph)PSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VISPSQK 7 0 E7EWD6;Q76L83;A0A5F9ZHC8 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 VIS(0.99)PS(0.01)QK 65.157 0.074839 79298000 160990 144440 161380 141680 204950 213550 177970 165100 169540 155340 TRUE FALSE 167346.0095 169246.4464 165585.6954 169703.8811 170112.6722 163956.2489 164020.2464 162887.1045 163438.2885 185775.8988 0.900795047 0.911024775 0.891319576 0.913487068 0.915687521 0.882548543 0.882893031 0.876793521 0.879760451 1 17.50320382 2.742770876 24.1125679 0.893461667 0.906265186 0 0.035303885 984.5265581 5638457.564 0.010119518 0.010367825 553.0582511 -2.742770876 0.01280352 VISGTTLGYLS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VISGTTLGYLSPK 13 0 E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3;H0YBY0;E5RJN7;E5RJ67 E7EPX0 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 VISGTTLGYLS(1)PK;VISGTTLGYLS(1)PK 192.65 2.66E-06 429600000 494060 228532 257993 233286 424576 443142 419657 340339 361824 229849 TRUE FALSE 513565.8703 267780.5933 264716.5095 279429.2745 352406.7232 340228.9864 386763.1878 335777.3124 348802.0249 274883.5108 1.868303663 0.974160263 0.963013419 1.016537055 1.282022054 1.237720609 1.407007596 1.221525843 1.268908506 1 18.06846084 VITEEEKNFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VITEEEKNFK 10 1 P26373;P26373-2;J3KS98;H3BUK8 P26373 RPL13 60S ribosomal protein L13 0 ;; 107.83 0.0020354 725870000 584300 597070 623700 435730 955330 859530 492810 625230 647490 734380 FALSE TRUE 607368.6152 699612.1279 639954.1344 521916.0935 792943.3478 659917.1838 454182.2645 616849.8145 624186.9614 878267.7004 0.691552945 0.796581871 0.728654981 0.594256277 0.902849265 0.751385009 0.5171342 0.702348287 0.710702399 1 19.74430122 0.862261165 14.6603051 1 0.707949703 0.435080872 0.098890756 1902.385 202487.962 0.095871249 0.023968942 7.282175893 -0.862261165 -0.292050298 VIY(ph)DFIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VIYDFIEK 8 0 O00401 O00401 WASL Neural Wiskott-Aldrich syndrome protein 1 VIY(1)DFIEK;VIY(1)DFIEK;VIY(1)DFIEK 143.01 0.0062692 126599000 247550 185226 204513 182735 306668 282437 246774 220117 236113 209920 TRUE FALSE 257323.4652 217037.1246 209842.7768 218879.4376 254540.6829 216845.2871 227431.2091 217166.6917 227615.3393 251049.8048 1.024989704 0.864518197 0.835861143 0.871856633 1.013905122 0.863754056 0.905920677 0.865034298 0.906654117 1 17.93761408 4.747688809 24.43324125 0.896745778 1.024989796 0.289059391 0.056594345 1064.979356 2850523.723 0.013035991 0.160022308 55935.66546 -4.747688809 0.128244019 VKADRDESSPYAAMLAAQDVAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKADRDESSPYAAMLAAQDVAQR 23 2 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 ;;; 177.03 2.68E-16 1438780000 841266 851630 1005180 636157 1155670 1057240 820883 868053 958750 1057330 FALSE TRUE 874479.8313 997890.8277 1031375.817 761986.9559 959229.6262 811712.0326 756540.0455 856418.1694 924244.7748 1264493.57 0.691565266 0.789162438 0.815643386 0.602602476 0.758587983 0.64192658 0.598294893 0.677281554 0.730920897 1 20.27012827 -1.793230537 8.065352049 1.006498252 0.697681264 0.619037886 0.070411742 0.008537298 0.000218869 0.070743212 0.016561149 0.016097909 1.793230537 -0.308816988 VKAEAEAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKAEAEAAR 9 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ;;; 107.06 0.0025861 753170000 732250 617772 640270 478765 1253200 921510 774570 637750 721890 913490 FALSE TRUE 761159.7954 723869.5354 656955.9622 573463.288 1040181.512 707503.2681 713857.1794 629202.0044 695909.3199 1092470.876 0.696732345 0.662598474 0.60134872 0.524923182 0.952136606 0.64761751 0.653433602 0.575943962 0.637004917 1 20.05916339 -1.20863063 4.190691144 1.000165051 0.657329243 0.469913901 0.107843901 8672780547 1637748996 14334094.72 0.025168226 0.061854225 1.20863063 -0.342835807 VKAFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKAFDR 6 1 P62316;P62316-2 P62316 SNRPD2 Small nuclear ribonucleoprotein Sm D2 0 69.998 0.083928 593010000 423760 494150 518700 407120 727310 652910 449900 493360 561170 577110 FALSE TRUE 440490.372 579016.4185 532217.7481 487647.1209 603682.106 501281.5474 414635.6624 486747.3162 540973.6013 690183.6551 0.63822197 0.838930934 0.771124822 0.706546898 0.874668795 0.726301679 0.600761347 0.705243181 0.783811088 1 19.39662078 0.873037759 4.960666657 0.99998804 0.73357516 0.51258946 0.077942731 0.948453834 36.20140664 0.076619558 0.019374364 7.465136597 -0.873037759 -0.26641288 VKANLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKANLEK 7 1 P35579 P35579 MYH9 Myosin-9 0 ; 90.657 0.015484 1748430000 1921870 1335490 1678930 1066040 3148800 2441400 2006410 1766790 2063670 1821350 FALSE TRUE 1997746.912 1564850.019 1722684.295 1276899.53 2613568.101 1874421.85 1849142.341 1743109.07 1989398.92 2178208.661 0.917151303 0.718411439 0.790872025 0.586215432 1.199870402 0.86053365 0.848928009 0.800248893 0.9133188 1 21.05471073 3.275967844 24.99999988 0.909239698 0.753374126 0.313072593 0.129615981 240.4829081 160717.9962 0.035950723 0.048676355 1887.851564 -3.275967844 -0.155865573 VKAPVHFVEPLS(ph)PTGVAGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKAPVHFVEPLSPTGVAGHR 20 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 VKAPVHFVEPLS(1)PTGVAGHR;VKAPVHFVEPLS(1)PTGVAGHR 227.44 2.25E-25 3643200000 2071670 1931490 2093630 1694930 2795200 2723200 2330470 2335310 2378440 2190830 TRUE FALSE 2153461.131 2263208.383 2148191.718 2030182.095 2320072.902 2090778.07 2147801.672 2304008.989 2292840.409 2620081.193 0.821906259 0.863793225 0.819895095 0.77485465 0.885496567 0.797982168 0.819746227 0.879365493 0.875102808 1 21.32118009 0.731175134 0.882087645 0.999872291 0.826421311 0.734276143 0.031040871 0.476607967 0.691465783 0.028982818 0.009799935 5.384868891 -0.731175134 -0.17345098 VKAQT(ph)PPGPSLSGSK ddPTM_MDA-MB-175_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 109.03 0.0016692 1110110000 2849860 1325710 2147270 1364380 2854640 2439340 2709200 2117950 2417530 1160420 TRUE FALSE 2962374.673 1553390.38 2203229.62 1634250.292 2369409.312 1872840.254 2496845.825 2089562.345 2330523.568 1387782.081 2.134610839 1.119333072 1.58759048 1.17759864 1.707335283 1.349520417 1.799162749 1.50568477 1.679315217 1 20.40434961 -2.052338979 2.458297044 0.268296173 1.544021899 0.256807777 0.285428291 9234939.069 3854327.532 37916193.74 0.062681919 0.008864638 2.052338979 1.275725726 VKAS(ph)PITNDGEDEFVPSDGLDKDEYTFSPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKASPITNDGEDEFVPSDGLDKDEYTFSPGK 31 2 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VKAS(0.951)PIT(0.049)NDGEDEFVPSDGLDKDEYTFSPGK;VKAS(0.826)PIT(0.174)NDGEDEFVPSDGLDKDEYTFSPGK 184.78 1.24E-18 1113920000 497014 177948 299141 168208 436808 372274 435212 270722 314777 101324 TRUE FALSE 516636.4965 208509.1848 306936.8602 201479.0403 362559.5322 285819.0054 401098.9462 267093.4144 303448.2373 121176.4978 4.26350411 1.720706478 2.53297352 1.662690736 2.991995467 2.358699999 3.310039103 2.204168458 2.504183919 1 16.88675039 0.328906984 1.276947164 0.999051832 2.590401231 0.30878298 0.727401312 4.76734706 7.919409454 0.647043129 0.19089171 2.132588114 -0.328906984 1.591349399 VKDDIESLHDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKDDIESLHDK 11 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;; 183.79 3.12E-06 773750000 1377660 791650 1318170 1062340 1798310 1597220 1983600 1301300 1526320 711550 FALSE TRUE 1432051.081 927609.7293 1352522.593 1272467.681 1492633.909 1226289.861 1828120.249 1283858.202 1471388.041 850964.5991 1.682856234 1.09006853 1.589399365 1.495323874 1.754049358 1.441058609 2.148291775 1.508709297 1.729082553 1 19.69873959 4.031205189 24.9510089 1.625128272 1.374779991 0.04986302 0.305314319 407.3062295 325668.2581 0.06946006 0.15004855 10744.96954 -4.031205189 -0.250348281 VKDEPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VKDEPQR 7 1 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;; 113.26 0.0056276 2550400000 2027300 1530370 2010920 1640270 2146440 2266260 2457310 2097530 2050800 1285370 FALSE TRUE 2107339.369 1793199.143 2063326.227 1964710.51 1781588.895 1739955.461 2264699.621 2069416.041 1976992.109 1537213.642 1.370882558 1.16652565 1.342250792 1.27809854 1.158972863 1.131889162 1.473249755 1.346212384 1.286088059 1 20.55188625 2.265624138 24.99902986 1.315629385 1.240532194 0 0.133774254 625.4559454 577742.4534 0.044413662 0.037150973 184.3419333 -2.265624138 -0.075097191 VKDEPQRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 VKDEPQRR 8 2 P05204;O00479 P05204 HMGN2;HMGN4 Non-histone chromosomal protein HMG-17;High mobility group nucleosome-binding domain-containing protein 4 0 ;;;;;;;; 127.3 0.00066493 12839798000 10224960 8178610 10565070 7376780 12728230 11276760 10769060 10295890 10606010 8442380 FALSE TRUE 10628649.32 9583222.647 10840404.4 8835885.067 10564690.01 8657903.391 9924952.937 10157890.44 10224301.77 10096502.72 1.052706032 0.949162587 1.073679144 0.875143137 1.046371234 0.857515085 0.983008989 1.006080097 1.012657754 1 23.26735232 1.782311909 5.048283125 1.006799429 0.973405013 0.03764414 0.067435323 0.689756445 35.43496082 0.031009511 0.016886164 60.57757849 -1.782311909 -0.033394416 VKDGPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKDGPGGK 8 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 ; 66.568 0.055949 1814700000 3690200 2480500 3150200 2248690 4517600 3738100 4206900 3411100 3828200 2162750 FALSE TRUE 3835891.945 2906506.579 3232296.8 2693474.17 3749699.966 2869982.926 3877152.185 3365379.784 3690423.83 2586499.454 1.483043787 1.123722093 1.249680063 1.041358878 1.449719991 1.109601211 1.498995942 1.301132996 1.426802478 1 21.30256946 3.2213646 24.99987836 1.316803829 1.219058223 0.032206972 0.178268264 689.9549871 1003067.184 0.04779423 0.057255501 1664.809709 -3.2213646 -0.097745607 VKDLESLFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKDLESLFHR 10 1 Q03252 Q03252 LMNB2 Lamin-B2 0 ; 188.61 6.62E-07 1282430000 2136600 2904800 2633100 2427500 3747100 3826200 2982100 2899100 2899800 3282500 FALSE TRUE 2220954.618 3403676.804 2701720.749 2907652.255 3110169.28 2937623.037 2748355.21 2860242.306 2795436.764 3925643.028 0.565755623 0.867036758 0.688223746 0.740681777 0.79227002 0.748316395 0.700103191 0.728604788 0.712096527 1 21.90449756 -1.07687438 4.548110878 1.000016995 0.731596165 0.557188071 0.072905987 1.12E-05 2.27E-06 0.062768941 0.014793845 0.083777157 1.07687438 -0.26842083 VKDS(ph)SPGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.623)S(0.377)PGEK 119.21 0.002272 106900000 472810 164240 267750 157330 412180 401580 400360 307080 337830 127150 TRUE FALSE 491476.9039 192446.9424 274727.785 188449.4044 342117.7908 308319.131 368978.7371 302964.0949 325671.5643 152062.6081 3.23206941 1.26557702 1.806675477 1.239288256 2.249848238 2.027580185 2.426492231 1.99236419 2.141693927 1 17.21430591 VKDSS(ph)PGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKDSSPGEK 9 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 VKDS(0.141)S(0.859)PGEK;VKDS(0.139)S(0.861)PGEK;VKDS(0.144)S(0.856)PGEK;VKDS(0.179)S(0.821)PGEK 85.402 0.0089867 1953760000 8822500 3232590 5022590 3060700 7648900 7152100 7728200 5307030 6176930 2602810 TRUE FALSE 9170819.112 3787762.186 5153482.822 3666097.325 6348742.71 5491133.166 7122443.49 5235897.943 5954623.496 3112780.786 2.946182126 1.216841932 1.655588098 1.177756346 2.0395727 1.764060351 2.288128841 1.682064464 1.912959474 1 21.56977255 4.752604727 24.56042101 1.690742612 2.946183217 0.502731067 0.38723146 1628.454776 2847788.114 0.089479456 1.842633969 56572.41604 -4.752604727 1.255440605 VKEDPDGEHAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKEDPDGEHAR 11 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ;; 133.05 0.000102 5469100000 10314600 8812400 9643500 8292000 12098100 12733500 12033400 10437000 10575000 7338300 FALSE TRUE 10721828.37 10325861.15 9894817.532 9932132.851 10041669.28 9776337.603 11090190.66 10297109.09 10194407.82 8776099.385 1.22170772 1.176588903 1.127473277 1.131725202 1.144206423 1.113972982 1.26368107 1.173312725 1.161610343 1 23.06514843 -2.483920501 1.598243316 1.94E-05 1.168489372 0.577684923 0.043157199 558673.1915 41993.83588 2009186.479 0.011240356 0.003281554 2.483920501 1.168470013 VKEDPDGEHARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKEDPDGEHARR 12 2 A0A087X0X3;P52272-2;P52272;M0R2T0;M0R019;M0R0N3;M0QYQ7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 ; 107.17 0.0011071 338820000 935930 794360 944230 656530 1230510 1093020 813210 888970 975080 974510 FALSE TRUE 972881.2391 930785.1507 968837.4095 786389.6745 1021348.35 839182.6699 749468.4753 877054.8112 939987.0613 1165446.576 0.834771202 0.798651066 0.831301433 0.674753944 0.87635793 0.720052456 0.643074072 0.752548275 0.806546675 1 20.15245144 0.834307015 3.807446664 0.999968259 0.762655547 0.502239975 0.069355248 0.887991329 19.25518622 0.067134254 0.017213073 6.828212286 -0.834307015 -0.237312712 VKEEIIEAFVQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 212.25 2.47E-09 2230300000 1865610 1719570 2159340 1774710 2571800 2552330 2482500 2160720 2575200 1791560 FALSE TRUE 1939265.723 2014892.771 2215614.174 2125742.341 2134646.355 1959590.038 2287915.163 2131759.083 2482519.055 2142581.881 0.905106937 0.940404094 1.034086116 0.992140539 0.996296279 0.914592836 1.067830912 0.994948712 1.158657729 1 21.03091891 1.941466761 1.805863019 1.061435414 0.969997958 0.324745275 0.058617848 0.436986916 2.647742968 0.0362036 0.017330732 87.39101041 -1.941466761 -0.091437456 VKEEPPS(ph)PPQS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR;VKEEPPS(1)PPQS(1)PR 61.942 0.045753 3039590000 2574880 1737500 2154910 1928900 2558670 2827170 2755540 2309520 2392450 1524390 TRUE FALSE 2676538.251 2035902.109 2211068.725 2310430.663 2123748.187 2170602.614 2539553.575 2278564.662 2306346.192 1823065.034 1.468152918 1.116746836 1.212830417 1.267333101 1.164932763 1.190633671 1.393013155 1.249853746 1.265092659 1 20.7979346 -1.089455854 3.567613399 0.999869752 1.254233296 0.380086375 0.098977971 6270870608 10259743829 10476283.63 0.022532717 0.081384958 1.089455854 0.254363544 VKEEPPS(ph)PPQSPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 VKEEPPS(0.997)PPQS(0.003)PR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR;VKEEPPS(1)PPQSPR 137.45 3.67E-05 2520030000 2639820 2016040 2436150 2013480 3008030 3136490 2824160 2472290 2630760 1787360 TRUE FALSE 2744042.132 2362279.187 2499638.07 2411740.334 2496726.135 2408087.731 2602794.96 2439152.996 2536079.461 2137558.971 1.283726985 1.105129365 1.169389057 1.128268444 1.168026786 1.126559671 1.217648259 1.141092728 1.186437191 1 21.02753279 -1.205908304 3.945330296 0.999878504 1.165428139 0.514219174 0.049300238 4.71E-05 9.48E-06 0.042545076 0.010020605 0.062243169 1.205908304 0.165549634 VKEFCENLSADCR ddPTM_MDA-MB-175_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 ; 197.14 1.24E-07 1085530000 1753610 1597010 1692120 1446560 2332820 2182850 1662860 1802120 2019970 1778080 FALSE TRUE 1822843.877 1871284.044 1736218.037 1732685.25 1936288.09 1675916.169 1532520.688 1777965.529 1947271.674 2126460.733 0.857219627 0.879999342 0.816482529 0.814821183 0.910568467 0.788124673 0.720690801 0.836114912 0.915733662 1 21.02002278 1.037224493 3.006327633 0.998336789 0.82540543 0.560521788 0.048889427 0.172337309 3.43775512 0.049260624 0.01302851 10.89493124 -1.037224493 -0.172931359 VKEFLHNQGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKEFLHNQGK 10 1 Q9H4A4;A6NKB8 Q9H4A4 RNPEP Aminopeptidase B 0 ; 129.16 0.00018661 1804440000 1222180 743170 1120950 765451 1595960 1320720 1156960 1084550 1307180 778680 FALSE TRUE 1270432.61 870803.6664 1150162.878 916854.9232 1324679.289 1014002.796 1066274.452 1070013.381 1260134.847 931247.4373 1.364226691 0.935093759 1.23507763 0.984544909 1.422478319 1.088865059 1.144995851 1.14901082 1.35316866 1 19.82880502 VKEGMNIVEAMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 16 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 ;;;;;;;;;;;;;;; 195.84 1.34E-07 55636660000 43181350 42466390 48531330 39076280 64839040 58933760 48157590 48038550 52468330 50413720 FALSE TRUE 44886183.04 49759662.14 49796096.33 46805451.55 53817723.14 45247287.39 44382872.26 47394671.81 50580005.05 60291323.21 0.744488272 0.825320452 0.825924755 0.776321518 0.892627998 0.750477598 0.736140292 0.786094405 0.83892677 1 25.84544706 0.840053011 3.297063795 0.999941694 0.793064604 0.662376182 0.044504959 0.471205572 8.585831882 0.042845445 0.011116662 6.919154227 -0.840053011 -0.206877091 VKELEEQLENETLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKELEEQLENETLHK 15 1 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-2 A0MZ66 KIAA1598 Shootin-1 0 ;;; 211.17 9.10E-10 415883000 581396 317755 466035 324041 625905 573951 577157 454594 529702 273056 FALSE TRUE 604349.963 372326.9495 478180.255 388135.3426 519513.8917 440659.5786 531917.9262 448500.911 510638.1285 326556.0952 1.850677332 1.140162303 1.464312753 1.188571729 1.590887138 1.349414649 1.628871529 1.373426855 1.563707234 1 18.31697131 -1.200645921 4.897948223 0.999945768 1.446119933 0.317633135 0.201682294 0.000106355 1.74E-05 0.173885252 0.040980181 0.063001963 1.200645921 0.446174165 VKELLTLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKELLTLIR 9 1 Q15067-2;Q15067;Q15067-3;K7ENF1;K7ESC7 Q15067-2 ACOX1 Peroxisomal acyl-coenzyme A oxidase 1 0 ; 138.25 0.0013905 0 262793 270018 231406 233828 557610 424760 295400 234547 279426 408820 FALSE TRUE 273168.2706 316391.4911 237436.6305 280078.4805 462827.6514 326115.9273 272245.7761 231403.2811 269369.5128 488920.4517 0.55871721 0.647122635 0.485634482 0.572850818 0.946631808 0.667012243 0.556830411 0.473294337 0.550947525 1 18.89924023 3.435771106 24.99956752 0.657880101 0.565000403 0.107184218 0.164105752 456.1949076 275805.9857 0.047681896 0.064561655 2727.539861 -3.435771106 -0.092879698 VKELLVDCYKPTEAFISGLLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKELLVDCYKPTEAFISGLLDK 22 2 B5MC51;P53671-3;F5GXC4;F5H2U0;Q96C90 B5MC51;Q96C90 LIMK2;PPP1R14B LIM domain kinase 2;Protein phosphatase 1 regulatory subunit 14B 0 128.12 9.64E-06 152060000 441870 131170 231380 129220 366530 347700 318980 165380 300470 140680 FALSE TRUE 459315.3688 153697.4271 237409.9529 154779.3303 304227.3615 266951.9444 293977.5141 163163.3516 289656.1434 168243.5525 2.730062234 0.913541261 1.411108773 0.919971838 1.808255692 1.586699404 1.747333016 0.969804484 1.721647808 1 17.36019169 4.750177237 24.73560528 1.353136277 2.730063186 0.58907985 0.347672541 1060.664663 2258454.952 0.079931261 1.279282166 56257.08658 -4.750177237 1.376926909 VKELQAEQEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKELQAEQEDR 11 1 Q00341;A0A024R4E5;Q00341-2;H0Y394 Q00341 HDLBP Vigilin 0 153.39 2.96E-05 524240000 1129800 1011200 1146100 917520 1481300 1470300 1277200 1194400 1233500 1000400 FALSE TRUE 1174405.376 1184865.734 1175968.308 1099002.717 1229509.155 1128845.108 1177089.727 1178391.022 1189106.576 1196409.226 0.981608425 0.990351552 0.982914777 0.918584288 1.02766606 0.943527585 0.983852098 0.984939765 0.993896194 1 20.19027951 1.445007263 1.69531901 0.99855574 0.974852902 0.093990233 0.027122373 0.846525078 4.561820721 0.022596541 0.007227385 27.8616776 -1.445007263 -0.023702838 VKELVEFAQDDDRLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKELVEFAQDDDRLR 15 2 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 ; 233.84 6.88E-18 392910000 229804 225547 253122 186376 304790 315220 231713 246889 269513 277790 FALSE TRUE 238876.8394 264282.9427 259718.5673 223240.6165 252981.9047 242014.9322 213550.7296 243579.8568 259813.2798 332217.6319 0.719037211 0.795511488 0.781772375 0.671971007 0.761494516 0.728483106 0.64280372 0.733193646 0.782057467 1 18.34176912 0.789854486 2.763430664 0.999910822 0.728663931 0.774689992 0.043677516 0.473693876 5.453804334 0.043242461 0.011425585 6.163884414 -0.789854486 -0.27124689 VKENDQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKENDQK 7 1 P46778;M0R181 P46778 RPL21 60S ribosomal protein L21 0 ; 99.802 0.0093578 336220000 653590 228160 455490 256192 802660 494520 710730 429690 539320 235135 FALSE TRUE 679394.2379 267344.7052 467360.4436 306866.0129 666224.1399 379675.2245 655021.1255 423930.7084 519909.9786 281205.2013 2.416008789 0.950710385 1.661990751 1.091252976 2.369174314 1.350171415 2.329335028 1.507549314 1.848863307 1 18.10126375 -1.379176864 6.070239049 0.999880434 1.701704014 0.159300429 0.497072904 0.00072546 7.42E-05 0.434093743 0.102299734 0.041766024 1.379176864 0.70182358 VKENFDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 94.85 0.012675 421620000 817960 518100 682290 408800 964010 682460 665140 659080 812650 452460 FALSE TRUE 850253.6924 607079.6447 700071.0379 489659.4199 800147.9245 523969.0078 613004.5888 650246.1106 783402.8852 541110.8741 1.571311413 1.121913593 1.293766345 0.904915135 1.478713444 0.968320972 1.132863186 1.201687384 1.447767773 1 19.04556471 4.743504193 24.41889207 1.176443309 1.571311642 0.301054925 0.182327613 447.1509308 2208607.252 0.039780218 0.328243003 55399.28927 -4.743504193 0.394868333 VKESITR ddPTM_MDA-MB-175_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 ; 79.906 0.028595 229480000 387159 396360 428652 339766 522820 504640 422864 411440 412340 414220 FALSE TRUE 402444.3363 464431.7467 439823.0233 406970.7007 433951.2431 387445.0079 389718.8147 405925.3198 397499.9639 495378.4783 0.8123977 0.937529116 0.887852506 0.821534884 0.875999387 0.782119177 0.786709217 0.819424617 0.8024167 1 18.91817167 3.7415852 23.53146345 0.828898302 0.885086716 0.040875554 0.066595273 231.3627449 1799991.994 0.016075036 0.02747419 5515.503955 -3.7415852 0.056188414 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKESSIIAPAPAEDVDTPPR 20 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR 109.05 0.00032833 592270000 1199950 1058940 1248010 1040950 1584350 1579890 1447390 1340500 1429900 1151720 TRUE FALSE 1247324.953 1240804.708 1280534.166 1246846.803 1315042.753 1212984.491 1333939.79 1322532.79 1378438.178 1377377.483 0.905579602 0.900845791 0.929690068 0.905232457 0.954743902 0.88064783 0.968463479 0.960181799 1.000770083 1 20.39349257 1.742028203 1.272963956 1.000672089 0.914287487 0.703199992 0.021981353 0.224629875 0.686224919 0.016779929 0.006536978 55.21132925 -1.742028203 -0.086384602 VKEVHDELEDLPS(ph)PPPPLS(ph)PPPTTSPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 2 VKEVHDELEDLPS(1)PPPPLS(0.98)PPPT(0.007)T(0.007)S(0.006)PHK;VKEVHDELEDLPS(0.994)PPPPLS(0.988)PPPT(0.006)T(0.006)S(0.006)PHK 82.384 0.0023359 575320000 412980 346520 454940 323350 649020 560330 547600 465480 519890 329850 TRUE FALSE 429284.7693 406032.1144 466796.1101 387307.6649 538699.8122 430201.8494 504677.6811 459241.002 501179.2605 394477.7921 1.088235581 1.029290172 1.183326716 0.981823749 1.365602381 1.090560376 1.279356382 1.164174539 1.270487897 1 18.58958456 3.260515157 24.99998647 1.201389914 1.075760443 0.242672545 0.107123726 315.7915415 359594.6879 0.026722604 0.036152739 1821.860657 -3.260515157 -0.125629471 VKEVHDELEDLPSPPPPLS(ph)PPPTTSPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKEVHDELEDLPSPPPPLSPPPTTSPHK 28 1 F5H039;Q9NQX3;Q9NQX3-2;H0YJ30;G3V582 F5H039 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 VKEVHDELEDLPSPPPPLS(0.377)PPPT(0.208)T(0.208)S(0.208)PHK 58.26 0.025222 119520000 131940 110880 132780 125460 194900 160350 159710 161180 176250 84793 TRUE FALSE 137149.0931 129922.7775 136240.3559 150275.6135 161770.9676 123111.1426 147191.5129 159019.6457 169906.7969 101406.5649 1.352467596 1.28120677 1.343506271 1.48191208 1.595271152 1.214035233 1.451498855 1.568139557 1.675500961 1 16.62979153 3.833536409 4.861007426 1.456182144 1.316744604 0.042451404 0.18712386 0.536952947 20.78006397 0.04658581 0.086375775 6816.107157 -3.833536409 -0.13943754 VKEYQVETIVDTLCTNMLSDKEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKEYQVETIVDTLCTNMLSDKEQLR 25 2 Q86VP6;Q86VP6-2 Q86VP6 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 ; 271.51 3.48E-53 980640000 991990 575530 849640 604460 1139250 943830 889350 827850 895280 627060 FALSE TRUE 1031154.531 674372.8005 871782.3164 724020.3839 945600.6919 724639.7864 819640.4231 816754.0248 863059.0477 749920.4012 1.375018641 0.899259174 1.1624998 0.965462978 1.260934748 0.966288936 1.092969896 1.089120957 1.15086754 1 19.51637795 4.762188302 24.07183085 1.072931058 1.375019218 0.441631249 0.104167422 3597.733888 3665264.862 0.022206012 1.260253088 57834.67537 -4.762188302 0.302088159 VKFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKFEER 6 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;;; 94.407 0.0406 4281390000 9764030 8048510 9998860 7316850 12256990 11355480 10822240 9772590 10266470 8088040 FALSE TRUE 10149521.44 9430778.984 10259438.51 8764101.091 10173551.22 8718341.864 9973964.55 9641604.416 9896981.75 9672736.583 1.04929162 0.974985611 1.060655216 0.906062211 1.051775899 0.901331468 1.031141959 0.996781452 1.023183219 1 23.20549268 -0.758928305 6.325788267 1 0.997752859 0 0.054329113 0 5.18E-18 0.046619803 0.010988393 0.174209444 0.758928305 -0.002247141 VKFQGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKFQGGR 7 1 Q9UK45;K7ENY5;K7EML7 Q9UK45 LSM7 U6 snRNA-associated Sm-like protein LSm7 0 ; 110.61 0.0061693 1091070000 686470 730300 722200 621550 981680 930110 743630 773080 784660 827120 FALSE TRUE 713572.3657 855723.3441 741021.1253 744490.7349 814814.3842 714106.0485 685342.3375 762718.1271 756420.2399 989178.3278 0.721378892 0.86508501 0.749127942 0.75263551 0.823728504 0.721918413 0.692840025 0.771062311 0.764695524 1 19.91587111 0.335483286 2.924502381 0.999999962 0.762779137 0.689967469 0.047763456 34.44461717 149.976424 0.045286608 0.011861055 2.165126552 -0.335483286 -0.237220825 VKGEEIYSMDEGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKGEEIYSMDEGIR 14 1 Q96P70 Q96P70 IPO9 Importin-9 0 107.98 0.00077744 547690000 314790 259610 345270 271550 387580 349610 302350 253690 332570 241780 FALSE TRUE 327218.1523 304195.998 354268.0198 325261.7795 321699.29 268418.3759 278651.017 250289.7005 320600.8707 289152.1618 1.131646916 1.052027403 1.225195819 1.124881023 1.112560556 0.92829455 0.96368298 0.865598579 1.108761797 1 18.14146936 2.789755918 5.604950205 0.956014992 1.131507642 0.54486833 0.070462517 0.145499237 10.68765991 0.021532616 0.022645149 616.2485601 -2.789755918 0.175492651 VKGNNVYCLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKGNNVYCLDR 11 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 73.466 0.039655 551000000 138240 127900 144030 124310 238400 200770 127230 159710 137530 206620 FALSE TRUE 143697.8219 149865.8301 147783.5401 148898.147 197876.8532 154144.2102 117257.3801 157569.3487 132580.3222 247103.233 0.58152951 0.60649077 0.598063968 0.602574661 0.800786176 0.623804911 0.474527908 0.637666075 0.536538193 1 17.91475436 -1.153665989 4.903187648 1.000027698 0.608989557 0.691342985 0.078789424 2.40E-05 4.15E-06 0.076898508 0.01812387 0.070199499 1.153665989 -0.391038141 VKGPVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKGPVR 6 1 P60866;P60866-2;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 ; 83.229 0.05219 630980000 1827270 1650290 1420990 1245210 4895400 2777900 2117700 1558340 1746580 4677400 FALSE TRUE 1899412.031 1933714.47 1458022.167 1491508.821 4063281.657 2132774.824 1951709.14 1537453.001 1683720.927 5593846.976 0.339553806 0.345685979 0.260647489 0.266633826 0.726384128 0.381271571 0.348902848 0.274847168 0.300995171 1 22.41540936 -1.52394522 5.759676315 1.001161185 0.359051698 0.690718591 0.128364349 0.001974194 0.000163173 0.12819597 0.030168636 0.029926421 1.52394522 -0.642109487 VKIEPGVDPDDTYNETPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKIEPGVDPDDTYNETPYEK 20 1 Q9H4A4;A6NKB8;C9JMZ3 Q9H4A4 RNPEP Aminopeptidase B 0 219.34 8.46E-25 791630000 936220 444860 719960 480080 1010300 858960 814750 644900 861670 422800 FALSE TRUE 973182.6885 521261.2445 738722.7491 575038.3911 838569.5669 659479.5577 750887.766 636256.1703 830658.665 505639.565 1.924656921 1.030894891 1.460967061 1.137249596 1.658433447 1.304248329 1.485025734 1.25831959 1.642788109 1 18.94774983 -1.241165148 4.083474918 0.999676851 1.407580054 0.202505535 0.253454759 0.000661354 0.000122899 0.216600176 0.051012999 0.057389819 1.241165148 0.407903202 VKIPEGTILTMDMLTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKIPEGTILTMDMLTVK 17 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;; 146.1 4.10E-07 370690000 1134920 994190 1413830 910970 1876360 1484910 1513280 1276270 1720490 940100 FALSE TRUE 1179727.518 1164934.399 1450675.571 1091157.147 1557416.997 1140062.157 1394665.159 1259163.688 1658569.901 1124294.596 1.049304624 1.036146934 1.290298447 0.970526009 1.385239245 1.014024403 1.240480177 1.119958855 1.475209351 1 20.10058868 4.269243424 24.93406051 1.183920559 1.042725501 0.116332427 0.158839545 399.6120103 324733.9436 0.034817532 0.095328824 18588.46054 -4.269243424 -0.141195058 VKKDDEEEDPLDQLISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKKDDEEEDPLDQLISR 17 2 Q9NYJ1;Q9NYJ1-2 Q9NYJ1 COA4 "Cytochrome c oxidase assembly factor 4 homolog, mitochondrial" 0 140.75 3.65E-07 85277000 151520 51908 75687 49764 132540 122490 111870 69132 81168 43062 FALSE TRUE 157502.1266 60822.79521 77659.4654 59607.17067 110010.8981 94043.55385 103101.3371 68205.39862 78246.77954 51499.17443 3.058342747 1.181044082 1.507974958 1.157439344 2.136168188 1.826117698 2.001999803 1.324397903 1.519379299 1 15.65226168 8 0.048693878 4.32E-14 4.681619185 0.220435191 0.51471576 982.1156327 3.612532115 83.35921199 348.9158716 100000000 -8 4.681619185 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK 39 3 P06748;P06748-3;P06748-2 P06748 NPM1 Nucleophosmin 0 ; 406.67 1.15E-199 593800000 494450 87259 193508 56615 315450 292900 243860 166957 208841 56070 FALSE TRUE 513971.2678 102245.0545 198550.9774 67813.27802 261829.9217 224878.4139 224745.616 164719.2145 201324.8532 67055.84298 7.664824495 1.524774724 2.960979516 1.011295586 3.904654838 3.353599089 3.351618681 2.456448345 3.002346168 1 16.03307543 4.746240312 24.965155 2.620477304 7.664826968 0.716522092 0.970865441 479.9016841 1560027.276 0.220287718 2.361606882 55749.41464 -4.746240312 5.044349664 VKLDGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VKLDGSR 7 1 P62081;B5MCP9;A0A2R8Y623 P62081 RPS7 40S ribosomal protein S7 0 ;;;;; 123.92 0.0038278 4414190000 6006110 4917320 5653360 4307180 7554690 6934290 6437120 5545340 5819080 5023690 FALSE TRUE 6243235.861 5761831.459 5800691.206 5159127.348 6270546.492 5323906.238 5932561.714 5471013.788 5609652.447 6007985.871 1.039156215 0.959028796 0.965496812 0.858711631 1.043701937 0.886138275 0.987446016 0.910623611 0.933699341 1 22.51844999 4.836926598 2.023260689 0.943523426 1.084041344 0.209034402 0.052219447 1.417655212 5.059750622 0.012013368 0.400646033 68695.23259 -4.836926598 0.140517918 VKLEAEIATYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VKLEAEIATYR 11 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;; 183.79 4.74E-06 34732890000 14665344 12213297 14314397 11610104 18083603 16977611 17131918 14615406 16148947 11962745 FALSE TRUE 15244343.11 14310835.75 14687441.95 13906547.92 15009758.62 13034818.14 15789073.5 14419510.39 15567749.55 14306615.84 1.065545009 1.000294962 1.026618881 0.972036159 1.049148086 0.911104225 1.103620428 1.007891073 1.088150386 1 23.77017911 2.18481875 24.99999997 1.047894295 1.005558245 0.168817809 0.04963388 174.9354037 81376.34411 0.017152029 0.012667628 153.0448604 -2.18481875 -0.04233605 VKLEAEIATYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKLEAEIATYRR 12 2 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 134.21 8.41E-05 4701620000 2466620 2784750 3060810 1749140 5236240 4081880 2606870 3073290 3687360 4563350 FALSE TRUE 2564004.062 3263009.15 3140577.223 2095114.671 4346185.795 3133925.231 2402536.718 3032097.574 3554652.634 5457451.062 0.469817142 0.597899846 0.575465943 0.383899855 0.796376504 0.574247061 0.440230556 0.555588596 0.651339351 1 22.37979586 0.809261589 2.670620501 0.999805094 0.55041844 0.623710854 0.10507531 0.521746371 6.085126801 0.097576712 0.025902361 6.445573854 -0.809261589 -0.449386654 VKLEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKLEER 6 1 P38432;H0YJ39;F8W9L6;F5H006;A0A1B0GU45;Q12912-2;Q12912 P38432 COIL;LRMP Coilin;Lymphoid-restricted membrane protein;Processed lymphoid-restricted membrane protein 0 69.176 0.085905 47230000 112830 102580 116570 87079 109530 124320 128020 100690 119760 88633 FALSE TRUE 117284.6155 120197.317 119607.91 104302.9663 90912.12972 95448.56409 117985.4579 99340.41525 115449.861 105998.9394 1.106469708 1.133948299 1.1283878 0.984000094 0.857670183 0.900467162 1.113081495 0.937183106 1.08916053 1 16.6936903 3.7301832 8.064497976 0.977401144 1.124201853 0.431841901 0.0733115 0.128084682 74.95063876 0.019673518 0.032187817 5372.583825 -3.7301832 0.14680071 VKLPSGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKLPSGSK 8 1 P62917;E9PKZ0;G3V1A1 P62917 RPL8 60S ribosomal protein L8 0 63.076 0.068952 660470000 886970 642770 821660 714150 1092100 985440 1079700 897670 867050 614930 FALSE TRUE 921988.2605 753160.7474 843073.1346 855406.7385 906465.2321 756586.4945 995070.2927 885638.2019 835845.0399 735413.76 1.25370004 1.024131976 1.146392929 1.163163902 1.232592156 1.028790234 1.353075434 1.204272003 1.13656432 1 19.48819664 3.734743731 3.793852521 1.179693284 1.128474408 0 0.108301407 0.844558818 27.6312385 0.027796529 0.048793318 5429.298648 -3.734743731 -0.051218876 VKNQYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKNQYEK 7 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 84.476 0.037389 0 153980 124690 149980 116630 176700 199960 164300 154690 144610 114940 FALSE TRUE 160059.2493 146104.5375 153888.602 139699.0659 146664.5971 153522.3204 151421.7367 152616.6336 139405.5143 137460.2923 1.164403528 1.062885398 1.119513129 1.016286693 1.066959735 1.116848494 1.101567108 1.110259777 1.014151156 1 17.06865541 1.192465671 6.873200924 1.004723087 1.092995629 0.462677103 0.037811977 0.195053175 21.59357503 0.034552734 0.008900546 15.57634906 -1.192465671 0.088272543 VKPAPDETSFSEALLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKPAPDETSFSEALLKR 17 2 Q12905;B4DY09;A0A0A0MRL0;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 130.77 1.64E-05 746670000 443850 333760 431730 322560 629410 499020 441430 459170 481600 359750 FALSE TRUE 461373.5407 391080.6837 442981.2385 386361.4053 522423.113 383130.1677 406829.5631 453015.5772 464267.3101 430236.1247 1.072372854 0.908990811 1.029623532 0.898021768 1.214270683 0.890511386 0.945596011 1.052946397 1.079098856 1 18.71476914 1.625002094 10.45420846 1.049743846 0.993223963 0.054253998 0.09422719 0.276462585 82.5267588 0.043926084 0.022976827 42.16985365 -1.625002094 -0.056519882 VKPAPLEIKPLPEWEELQAPVRS(ph)PITR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPAPLEIKPLPEWEELQAPVRSPITR 27 3 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VKPAPLEIKPLPEWEELQAPVRS(0.988)PIT(0.012)R;VKPAPLEIKPLPEWEELQAPVRS(1)PITR 251.01 1.38E-46 2205290000 1593100 992930 1422920 1170320 1953560 1791920 1969000 1443440 1899240 1338990 TRUE FALSE 1655996.818 1163458.004 1460002.464 1401805.803 1621494.569 1375773.737 1814664.635 1424093.048 1830886.723 1601339.454 1.034132278 0.726553012 0.91173827 0.875395782 1.01258641 0.859139349 1.133216715 0.889313658 1.143347039 1 20.61084773 2.788301658 0.890741308 1.022746258 0.873233732 0.22450045 0.108789688 0.847813358 1.450285729 0.059930896 0.059155388 614.1884688 -2.788301658 -0.149512526 VKPAS(ph)PVAQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPASPVAQPK 11 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 VKPAS(1)PVAQPK;VKPAS(1)PVAQPK 134.88 7.97E-05 1101540000 3619800 1538450 2477310 1579970 3438600 3178280 3246430 2459780 2874220 1301580 TRUE FALSE 3762712.499 1802666.82 2541870.734 1892483.35 2854108 2440172.637 2991966.334 2426810.672 2770777.384 1556599.681 2.417264082 1.158079911 1.632963674 1.215780379 1.833552991 1.56763018 1.922116759 1.559046107 1.780019242 1 20.56996654 -0.639203638 6.149695578 0.999999997 1.651337709 0.259497806 0.340382371 8.87E-09 2.89E-09 0.297731658 0.070176024 0.229507225 0.639203638 0.651337712 VKPEELESFCEGGMLDSDTLNPDWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKPEELESFCEGGMLDSDTLNPDWK 25 1 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 0 71.052 0.03458 18448000 15777 16346 18781 16454 16653 26396 20301 16589 19490 17946 FALSE TRUE 16399.88814 19153.29835 19270.44829 19708.55209 13822.32901 20265.92904 18709.75457 16366.65159 18788.55871 21462.1751 0.764129827 0.89242112 0.897879558 0.918292391 0.644032068 0.944262589 0.871754819 0.762581216 0.875426587 1 14.38950867 -1.066223233 8.379356716 1.000000002 0.839536487 0.230873799 0.086906342 3.93E-09 4.29E-10 0.080411558 0.018953186 0.085857209 1.066223233 -0.160463516 VKPET(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;VKPET(1)PPR 94.692 0.016456 15060640000 9127400 5102450 6567090 5706690 8164850 9291030 9639420 6998080 7064250 3842900 TRUE FALSE 9487756.8 5978756.096 6738233.76 6835456.249 6776991.713 7133329.089 8883857.072 6904282.184 6810009.022 4595842.678 2.064421579 1.3009053 1.46615849 1.487312932 1.474591753 1.552126474 1.933020274 1.502288626 1.481775922 1 22.13189798 0.735356346 2.163974092 1.000530528 1.586471804 0.402793203 0.217733572 1.15006661 7.828917916 0.199874431 0.05454789 5.436962604 -0.735356346 0.585941276 VKPET(ph)PPRQSHSGSIS(ph)PYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 VKPET(0.993)PPRQS(0.006)HS(0.002)GS(0.001)IS(0.975)PY(0.023)PK;VKPET(0.995)PPRQS(0.004)HS(0.001)GS(0.002)IS(0.997)PY(0.001)PK 148.05 2.17E-07 1567270000 1766320 812580 1196300 591560 2067470 1812290 1255590 1226370 1451260 780930 TRUE FALSE 1836055.677 952134.294 1227476.561 708568.8024 1716042.188 1391413.113 1157173.575 1209932.516 1399029.436 933938.2817 1.965928278 1.019483099 1.314301582 0.758689109 1.837425686 1.489834115 1.239025745 1.295516567 1.497989175 1 19.83296769 -1.979192782 2.518100783 0.685562977 1.354767881 0.098897117 0.336377926 19243354.14 8738022.987 35211763.77 0.077114949 0.010490766 1.979192782 0.669204904 VKPET(ph)PPRQSHSGSISPYPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKPETPPRQSHSGSISPYPK 20 2 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKPET(0.93)PPRQS(0.024)HS(0.045)GSISPYPK 186.4 1.57E-15 952110000 754640 458270 784070 443970 1080400 942110 720170 831380 885910 541840 TRUE FALSE 784433.7699 536974.3077 804503.5083 531785.9409 896753.9939 723319.2303 663721.1936 820236.711 854026.2722 648003.1738 1.210540012 0.828659996 1.241511679 0.820653297 1.383872842 1.116227913 1.024256084 1.265791194 1.317935323 1 19.30564135 3.236309596 24.99999977 1.188242702 1.026733357 0.173318964 0.170362835 100.9837095 1121535.144 0.045499965 0.056923946 1723.096482 -3.236309596 -0.161509345 VKPFMTGAAEQIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPFMTGAAEQIK 13 1 Q5W0H4;A0A0B4J2C3;P13693;J3KPG2;E9PJF7;P13693-2;Q56UQ5 Q5W0H4 TPT1 Translationally-controlled tumor protein;TPT1-like protein 0 ; 173.44 1.98E-05 820250000 994460 560140 790490 602460 1268640 1044490 1098900 847430 926440 694720 FALSE TRUE 1033722.049 656339.6877 811090.8188 721624.7898 1052997.026 801923.0269 1012765.347 836071.587 893097.6054 830837.0828 1.244193441 0.789973993 0.97623329 0.868551494 1.267392907 0.965198886 1.218969841 1.006300278 1.074937101 1 19.66420608 3.269391142 24.99998935 1.086718529 0.957361768 0.144549497 0.140556499 347.9682319 282159.5911 0.035872439 0.048566238 1859.478416 -3.269391142 -0.129356761 VKPFVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPFVVR 7 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 122.78 0.0039289 899990000 505630 685680 578350 678090 778630 852160 661500 595430 617750 660420 FALSE TRUE 525592.6628 803440.2061 593422.2761 812214.1781 646278.7507 654258.7546 609649.9015 587449.2348 595517.2982 789816.6545 0.66546161 1.017249005 0.751341812 1.028357877 0.818264273 0.828367889 0.771887878 0.743779245 0.753994354 1 19.59115826 3.017864553 24.97237825 0.797899963 0.875152725 0.015772559 0.122584167 605.9212587 846995.2425 0.032755002 0.039142666 1041.992404 -3.017864553 0.077252762 VKPLLQVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPLLQVSR 9 1 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 128.81 0.0013272 0 1171730 1150870 836620 772070 2755200 1782660 1171380 989040 982090 2798000 FALSE TRUE 1217990.805 1348522.97 858423.0045 924783.1416 2286872.088 1368664.231 1079564.175 975783.5365 946744.7727 3346214.529 0.363990651 0.402999556 0.256535556 0.276366961 0.683420644 0.409018675 0.322622523 0.291608182 0.282930088 1 21.67409851 -0.944187462 4.21678654 1.000021756 0.364160393 0.723702397 0.117612183 47636768.58 100312245.2 15849.95101 0.030497245 0.113713634 0.944187462 -0.635861363 VKPPGGHS(ph)PQVNHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKPPGGHSPQVNHLK 15 1 Q92610 Q92610 ZNF592 Zinc finger protein 592 1 VKPPGGHS(1)PQVNHLK;VKPPGGHS(1)PQVNHLK 172.95 6.02E-07 689130000 1322430 733370 1119110 825330 1360580 1249980 1270560 1047570 1211350 647190 TRUE FALSE 1374640.558 859320.5927 1148274.926 988577.8106 1129309.098 959691.0886 1170970.187 1033529.038 1167753.75 773994.4893 1.776034037 1.110241229 1.483569899 1.277241407 1.45906607 1.239919795 1.51289215 1.335318341 1.508736517 1 19.56196377 -2.188405718 2.130326922 2.14E-05 1.396853647 0.329584548 0.174934049 3673346.624 861968.9316 17646683.61 0.037169192 0.006480288 2.188405718 1.396832209 VKQELLEEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKQELLEEVKK 11 2 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 87.18 0.0078275 206310000 331420 182830 221250 173220 341680 273700 281050 256740 278000 141310 FALSE TRUE 344504.7175 214229.6303 227015.9568 207482.399 283601.3556 210137.323 259020.5666 253298.8202 267994.8343 168996.989 2.038525773 1.267653534 1.343313619 1.227728377 1.67814443 1.243438266 1.532693382 1.498836292 1.585796504 1 17.36663802 -2.153014469 2.120396068 2.90E-05 1.47374445 0.280036264 0.23462057 2430581.995 544600.8581 11678135.65 0.052957515 0.007030489 2.153014469 1.473715426 VKQIESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKQIESK 7 1 P10599;P10599-2 P10599 TXN Thioredoxin 0 ; 103.56 0.0076133 3097800000 5961400 3847000 4988600 3688300 6912000 6095100 5414400 4892500 5857100 4082900 FALSE TRUE 6196760.675 4507692.324 5118607.014 4417834.732 5737100.709 4679605.397 4990005.18 4826924.04 5646304.115 4882866.083 1.26908266 0.923165257 1.048279213 0.904762624 1.174945332 0.958372668 1.021941846 0.988543195 1.156350393 1 22.21929678 4.752800008 24.3282233 1.018226831 1.269082911 0.440046694 0.084417089 1498.823027 2560698.385 0.01839647 0.380482317 56597.85972 -4.752800008 0.25085608 VKS(ph)PGGPGSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VKSPGGPGSHVR 12 1 O75382;O75382-3;O75382-2;O75382-4;A0A1W2PPI7 O75382 TRIM3 Tripartite motif-containing protein 3 1 VKS(0.895)PGGPGS(0.105)HVR;VKS(0.999)PGGPGS(0.001)HVR;VKS(1)PGGPGSHVR;VKS(0.994)PGGPGS(0.006)HVR;VKS(0.996)PGGPGS(0.004)HVR;VKS(1)PGGPGSHVR 139.29 3.59E-05 8966450000 2248530 1726510 1994240 1574340 2716980 2629910 2255600 2133400 2094530 1486900 TRUE FALSE 2337303.701 2023024.662 2046211.533 1885739.753 2255148.71 2019153.259 2078800.178 2104805.263 2019148.274 1778229.587 1.314399287 1.137662244 1.150701545 1.060459103 1.268198846 1.135485133 1.169028001 1.183652144 1.13548233 1 20.76201017 -4.687822581 0.276072161 7.01E-09 1.18252465 0.388082399 0.066964165 190.8591396 2.166238479 108.5132424 0.075231833 2.05E-05 4.687822581 1.182524643 VKS(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.857)PS(0.143)K;VKS(0.858)PS(0.142)K;VKS(0.976)PS(0.024)K 89.355 0.030438 632426000 1610960 601710 1084900 708410 1701110 1549020 1623350 1017320 1315480 557850 TRUE FALSE 1674561.945 705049.0118 1113173.385 848531.3836 1411955.93 1189283.581 1496107.585 1003684.489 1268136.132 667150.0268 2.510023049 1.05680729 1.668550312 1.271874915 2.11639942 1.78263289 2.242535449 1.504435958 1.900826022 1 19.3476517 -1.279046528 3.283580487 0.996766604 1.75509483 0.237479539 0.418506716 38266139.91 55838567.59 1237804.351 0.100388563 0.052596091 1.279046528 0.758328226 VKS(ph)S(ph)TPPRQS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKSSTPPRQSPSR 13 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 VKS(0.884)S(0.555)T(0.556)PPRQS(0.874)PS(0.13)R 48.314 0.093892 0 263540 171090 197070 152110 268590 291670 245790 203840 207370 134140 TRUE FALSE 273944.7627 200473.3766 202205.8061 182196.904 222935.1677 223934.0628 226524.3375 201107.8582 199906.7942 160422.1647 1.707649084 1.249661335 1.260460526 1.135733982 1.389678092 1.395904757 1.41205137 1.25361641 1.246129514 1 17.29151396 -4.229745398 0.1828792 7.61E-13 1.402058827 0.375644695 0.141756038 115.0413124 1.437341081 42.53889123 0.43651924 5.89E-05 4.229745398 1.402058827 VKSGT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VKSGTPPR 8 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VKS(0.005)GT(0.995)PPR;VKS(0.019)GT(0.981)PPR;VKS(0.003)GT(0.997)PPR 92.866 0.01855 2194490000 1525400 1252060 1459700 1196320 1860550 1807630 1659610 1522020 1677840 1106390 TRUE FALSE 1585623.97 1467091.565 1497740.981 1432948.525 1544294.376 1387835.327 1529525.432 1501619.811 1617454.866 1323165.937 1.198356098 1.10877368 1.131937377 1.08296963 1.167120716 1.048874739 1.155958893 1.134868854 1.222412715 1 20.33556257 4.745169635 23.77162389 1.122375375 1.198356166 0.138290922 0.059582617 759.6565571 2732216.338 0.012966626 0.122215496 55612.14347 -4.745169635 0.075980791 VKT(ph)PEMIIQKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKTPEMIIQKPK 12 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VKT(1)PEMIIQKPK 118.2 0.031031 1848500000 3446200 1088000 1789300 1081400 2685500 2268800 2653500 1781500 2143800 721140 TRUE FALSE 3582258.637 1274855.537 1835930.628 1295297.692 2229019.669 1741905.584 2445511.736 1757621.906 2066645.057 862433.5759 4.153663235 1.478207217 2.128779165 1.501910093 2.584569678 2.019756225 2.835594305 2.037979452 2.396294758 1 19.71805382 -1.851073086 2.352878613 0.423932831 2.29088405 0.232277407 0.72874487 6766366.371 3928492.97 21892137.21 0.164236854 0.014090517 1.851073086 1.86695122 VKT(ph)PTSQSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKTPTSQSYR 10 1 Q9Y2X9-2;Q9Y2X9 Q9Y2X9-2 ZNF281 Zinc finger protein 281 1 VKT(0.915)PT(0.065)S(0.018)QS(0.002)YR 84.173 0.024415 249260000 50727 192220 89069 146190 69556 106850 65979 85966 70116 193730 TRUE FALSE 52729.74113 225232.2897 91390.21131 175105.9457 57732.89596 82035.70683 60807.39358 84813.76638 67592.53886 231687.6843 0.227589746 0.972137515 0.394454334 0.755784435 0.249184138 0.354078841 0.262454147 0.366069378 0.291739887 1 17.82182183 -1.317219304 3.714702755 1.001638598 0.434860311 0.35415402 0.230693225 140233928.4 224233884.6 2546499.994 0.054539704 0.048170449 1.317219304 -0.566778287 VKTDDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKTDDIAR 8 1 Q52LJ0;Q52LJ0-1 Q52LJ0 FAM98B Protein FAM98B 0 ; 101.11 0.0051353 156692000 283070 246450 249960 216640 446110 358870 300950 248860 275740 335770 FALSE TRUE 294245.8222 288775.8704 256474.1629 259490.7454 370280.3815 275527.8812 277360.7526 245524.4388 265816.1713 401557.7028 0.732760996 0.719139163 0.638698153 0.646210354 0.92211002 0.686147668 0.690712071 0.611430031 0.661962576 1 18.61524779 VKTSEDADELHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKTSEDADELHK 12 1 Q9UKX7-2;Q9UKX7 Q9UKX7-2 NUP50 Nuclear pore complex protein Nup50 0 ; 97.121 0.0030644 233480000 1671820 1128130 1451000 1123130 2004280 1765300 1772500 1409960 1518340 1136870 FALSE TRUE 1737824.745 1321877.552 1488814.252 1345281.762 1663593.202 1355335.828 1633566.818 1391061.792 1463695.24 1359617.91 1.278171413 0.972241938 1.095024007 0.989455752 1.223574057 0.996850526 1.201489629 1.023126999 1.076548955 1 20.37476984 -5 0.158633037 0.662923831 1.114809778 0.089884408 0.100474874 361.3330024 3.310208636 38.17656837 0.39781825 1.00E-05 5 0.451885947 VKTSTVDLPIENQLLWQIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKTSTVDLPIENQLLWQIDR 20 1 P34932 P34932 HSPA4 Heat shock 70 kDa protein 4 0 137.43 3.29E-06 206510000 62626 87829 117580 74156 155470 149450 111530 194980 212410 122060 FALSE TRUE 65098.52284 102912.9475 120644.2314 88823.83547 129043.2649 114742.5024 102787.9872 192366.612 204765.4056 145975.32 0.445955678 0.705002377 0.826470059 0.608485294 0.884007412 0.786040424 0.704146339 1.317802297 1.402739899 1 17.15536495 1.741854753 6.375117794 1.266481479 0.71816339 0.724211831 0.149763846 0.06978575 7.854625823 0.072212382 0.037918431 55.18928309 -1.741854753 -0.548318089 VKVDGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VKVDGPR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 ;;; 98.392 0.010302 910350000 2492880 2026020 2109580 2009050 3834180 3191430 3113110 2291460 2384240 2472690 FALSE TRUE 2591300.827 2373973.175 2164557.388 2406434.094 3182447.453 2450268.749 2869096.304 2260746.727 2298431.668 2957166.263 0.876278368 0.802786507 0.731970135 0.813763542 1.076181442 0.828586739 0.970218124 0.764497673 0.777241272 1 21.49578393 3.44945556 24.99953231 0.888969936 0.798468519 0.181016347 0.098028013 399.4248575 360930.802 0.0276798 0.037479347 2814.851968 -3.44945556 -0.090501417 VKVDGPRS(ph)PS(ph)YGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 VKVDGPRS(1)PS(0.989)Y(0.011)GR 80.545 0.08607 6561600000 1739700 1328800 1555000 1284900 1984200 1907200 1751100 1532000 1607700 1091300 TRUE FALSE 1808384.699 1557011.063 1595524.577 1539049.385 1646926.393 1464281.704 1613844.206 1511466.046 1549839.191 1305119.341 1.385608689 1.193002827 1.2225124 1.179240347 1.261897162 1.121952344 1.236549146 1.158105622 1.187507642 1 20.3157503 -5 0.078117531 0.321897224 1.426097406 0.620223825 0.057915146 171.6655756 0.953171109 20.40343141 2.015701485 1.00E-05 5 1.104200182 VKVDGPRS(ph)PS(ph)YGRS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKVDGPRSPSYGRSR 15 3 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 VKVDGPRS(0.984)PS(0.78)Y(0.243)GRS(0.993)R 77.221 0.051734 880280000 1088100 809300 1075800 571330 1532400 1247000 953240 980650 1126700 1108400 TRUE FALSE 1131059.028 948290.9795 1103836.232 684337.3688 1271923.195 957403.1485 878522.558 967505.9908 1086150.287 1325569.758 0.853262547 0.715383686 0.832725871 0.516259038 0.95952943 0.722257838 0.662750906 0.729879348 0.819383726 1 20.33818116 0.895222582 3.474020591 0.999839917 0.744653744 0.312468466 0.112366058 0.494912039 12.77080755 0.099758823 0.025782463 7.856381823 -0.895222582 -0.255186173 VKVDGPRS(ph)PSYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VKVDGPRSPSYGR 13 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 1 VKVDGPRS(0.936)PS(0.062)Y(0.002)GR;VKVDGPRS(0.995)PS(0.005)YGR;VKVDGPRS(0.954)PS(0.046)YGR;VKVDGPRS(0.984)PS(0.016)YGR;VKVDGPRS(0.853)PS(0.147)YGR;VKVDGPRS(0.773)PS(0.227)YGR;VKVDGPRS(0.82)PS(0.18)YGR 130.01 7.67E-05 13617520000 5335726 5450840 6247640 3383420 8202740 7493420 4507520 5659890 6454980 7046550 TRUE FALSE 5546384.583 6386979.368 6410458.631 4052650.377 6808441.185 5753186.769 4154208.804 5584028.432 6222666.531 8427186.558 0.658153767 0.757901741 0.760687874 0.480901942 0.807913903 0.682693652 0.492953227 0.662620721 0.738403794 1 23.00661963 0.838603149 3.110376331 0.999837865 0.661208155 0.500207884 0.101047702 0.606899491 10.0457057 0.095770737 0.024992186 6.896093631 -0.838603149 -0.33862971 VKVDPSHDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 109.24 0.0011751 1724890000 2488250 1750190 2100940 1564400 2310270 2547690 2290480 2013320 2339080 1291920 FALSE TRUE 2586488.031 2050771.518 2155692.222 1873833.651 1917571.131 1956027.608 2110946.193 1986334.739 2254896.968 1545046.989 1.674051372 1.327319837 1.395227613 1.212800429 1.241108617 1.265998783 1.366266662 1.285614453 1.459435852 1 20.55921928 5.959198956 1.1791236 1.283969008 6.971511084 0.505869213 0.116947803 18.81996139 2.148765615 0.030251553 246.9316564 910330.2117 -5.959198956 5.687542076 VKVEPAVDTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 150.69 3.08E-05 2775850000 4679760 4321670 4440960 3768440 5172740 5641870 4789480 4441110 4615400 4679560 FALSE TRUE 4864520.538 5063883.205 4556695.066 4513826.184 4293479.502 4331631.196 4414068.043 4381584.185 4449292.656 5596430.186 0.86921848 0.904841664 0.814214582 0.806554542 0.767181821 0.773998969 0.788729225 0.782924836 0.795023347 1 22.41607543 4.163346197 5.457311694 0.801731097 0.886760847 0.132377765 0.065243915 0.257793186 13.29029113 0.01472282 0.033431652 14566.1976 -4.163346197 0.08502975 VKVETYNDESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 190.85 1.90E-06 715010000 1308700 907270 1267120 1066070 1436190 1467040 1573340 1254390 1437550 862660 FALSE TRUE 1360368.487 1063086.565 1300142.188 1276935.464 1192066.937 1126342.193 1450017.5 1237576.954 1385812.856 1031681.71 1.318593199 1.030440449 1.260216378 1.237722305 1.155459988 1.091753573 1.405489198 1.199572447 1.343256202 1 19.97656652 2.284927292 24.99999532 1.253333496 1.18029092 0.037178614 0.125710115 329.5204992 177669.4876 0.040265166 0.033688151 192.7202241 -2.284927292 -0.073042576 VKVFGPGVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKVFGPGVER 10 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 ; 72.652 0.043178 685180000 347350 340590 342790 313410 390340 452580 289040 386620 415670 393760 FALSE TRUE 361063.6462 399083.6831 351723.389 375401.5626 323990.1462 347475.1539 266384.2895 381437.9913 400710.1179 470909.733 0.766736427 0.847473847 0.746901931 0.797183698 0.688009025 0.737880595 0.565680152 0.810002352 0.850927662 1 18.84509102 1.013421667 2.119640168 0.996264769 0.740077232 0.554251586 0.072095654 0.23390347 2.244194448 0.070013893 0.019462511 10.31387032 -1.013421667 -0.256187537 VKVGVNGFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKVGVNGFGR 10 1 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 179.1 1.95E-06 14776800000 4151000 3621600 4559300 3716200 5562700 5427400 4823400 4649200 4890700 4594400 FALSE TRUE 4314884.685 4243581.628 4678119.104 4451253.268 4617154.241 4166968.603 4445329.304 4586885.079 4714684.662 5494584.715 0.78529769 0.772320721 0.851405401 0.810116414 0.840309956 0.758377351 0.809038269 0.834801048 0.858060237 1 22.38957901 0.679913689 1.107605869 0.99991363 0.804599076 0.824319245 0.027009766 0.411619808 0.83961928 0.025750896 0.008053508 4.785349793 -0.679913689 -0.195314554 VKVNKDDIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKVNKDDIQK 10 2 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 130.56 0.00015372 4635500000 8940800 4781700 6810700 4032200 11205800 8743600 8284400 6780500 9146300 4684600 FALSE TRUE 9293789.688 5602919.779 6988192.437 4829757.125 9301042.119 6713031.411 7635047.081 6689618.488 8817126.45 5602457.678 1.658877268 1.000082482 1.247344083 0.862078288 1.660171777 1.198229741 1.36280317 1.194050696 1.573796172 1 22.41762841 4.763145883 23.81026791 1.243906616 1.658878229 0.222732051 0.237814539 5791.173272 5608445.82 0.052939617 3.218853551 57962.3364 -4.763145883 0.414971613 VKVPEVDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKVPEVDVR 9 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 79.974 0.023188 214270000 427060 403770 434740 397910 560190 593860 508990 457710 513930 493070 FALSE TRUE 443920.6586 473114.3566 446069.6815 476615.4104 464969.1039 455945.015 469094.0338 451575.1461 495433.7597 589677.6261 0.752819234 0.802327129 0.756463637 0.808264362 0.788514068 0.773210641 0.795509297 0.765800034 0.840177307 1 19.16956693 0.869064947 3.225340474 0.999935749 0.781452553 0.931315782 0.017997336 0.115755897 2.317153994 0.015724273 0.004090512 7.397158886 -0.869064947 -0.218483196 VKVPLQDLMVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VKVPLQDLMVR 11 1 E5RIA4;E7ETB3;Q9ULA0-2;Q9ULA0;E7EMB6 E5RIA4 DNPEP Aspartyl aminopeptidase 0 142.91 3.41E-05 277410000 202140 207440 217700 165280 310530 290670 242480 210660 221220 290730 FALSE TRUE 210120.6433 243066.2063 223373.4408 197971.8907 257746.2215 223166.2976 223473.784 207836.4473 213258.3354 347692.9771 0.60432812 0.699082876 0.6424445 0.569387085 0.741304077 0.641848735 0.642733097 0.597758543 0.613352439 1 18.4074544 -1.527898316 2.86426912 1.0160334 0.639146712 0.838840393 0.047451634 7261903.08 7685133.599 901880.7056 0.011148854 0.029655256 1.527898316 -0.376886688 VKWGDIEFPPPFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKWGDIEFPPPFGR 14 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 87.932 0.006153 675190000 800620 733130 844940 631980 1114850 1008500 750210 843570 937830 852090 FALSE TRUE 832229.0958 859039.3745 866959.8305 756983.7577 925348.1952 774291.159 691406.5799 832263.324 904077.6815 1019040.721 0.81667894 0.84298827 0.850760733 0.742839557 0.908058114 0.75982357 0.678487685 0.816712528 0.887185038 1 19.95878027 0.986142889 2.763925522 0.99877212 0.799777959 0.514848704 0.06019764 0.211974976 3.813903987 0.058530305 0.015587238 9.685964849 -0.986142889 -0.19899416 VKYTPHHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VKYTPHHR 8 1 P47897;A0A1B0GVU9;P47897-2;B4DDN1;A0A1B0GTT3 P47897 QARS Glutamine--tRNA ligase 0 ; 128.69 0.00067467 131610000 190677 158303 135856 110958 420920 263330 152512 122205 134059 389190 FALSE TRUE 198205.0752 185490.3088 139396.519 132905.1612 349372.1687 202175.5983 140557.7109 120567.0419 129234.2428 465444.329 0.425840563 0.398523083 0.299491282 0.2855447 0.750620744 0.434371171 0.301986085 0.25903644 0.277657788 1 18.82824909 -0.989374881 4.567404075 1.000013563 0.376898244 0.644872408 0.137667658 60537036.51 178042260.2 15654.11673 0.035219994 0.102476697 0.989374881 -0.623115319 VLAEDEELYGDFEDLETGDVHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLAEDEELYGDFEDLETGDVHK 22 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 ; 119.62 6.06E-05 36490000 35180 31785 31638 26280 39992 40319 38394 35036 34702 27107 FALSE TRUE 36568.93356 37243.8265 32462.51227 31478.10556 33194.17412 30955.52329 35384.57796 34566.39973 33453.0818 32418.09766 1.1280407 1.1488591 1.001370056 0.971004095 1.023939606 0.954884016 1.091506921 1.066268604 1.031926122 1 14.98451181 4.24178733 24.99957395 1.022515258 1.138449943 0.604444979 0.038939632 59.42879849 460414.6575 0.010604216 0.026652556 17449.67449 -4.24178733 0.115934684 VLAGDKNFITAEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLAGDKNFITAEELR 15 1 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;;; 244.05 4.74E-18 6512250000 5252300 4957750 4772550 4949750 6321910 6745580 6492750 5554430 5542140 5566230 FALSE TRUE 5459664.86 5809204.997 4896926.574 5928795.776 5247313.996 5179021.275 5983831.289 5479981.951 5342679.464 6656826.197 0.820160343 0.87266887 0.73562482 0.890634005 0.788260628 0.778001576 0.898901535 0.823212412 0.802586594 1 22.66640307 -1.811168026 2.36340298 1.06260469 0.825047929 0.537785646 0.049110662 8500351.695 5234589.32 3038576.214 0.011872647 0.015446567 1.811168026 -0.23755676 VLAGDKNFITAEELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;F5GXS2;O43707-3;H7C144 O43707 ACTN4 Alpha-actinin-4 0 ;; 216.93 8.28E-15 4320428000 5068349 5072159 5497401 3975959 6760072 6517923 5055107 5357047 5652870 6214882 FALSE TRUE 5268451.332 5943262.852 5640667.786 4762391.823 5610997.376 5004234.163 4658874.504 5285244.547 5449424.313 7432569.137 0.708833142 0.799624294 0.758912253 0.640746387 0.754920307 0.673284576 0.626818859 0.711092551 0.733181786 1 22.82542955 -1.496982091 5.111897461 1.000777503 0.71021361 0.741409963 0.051028292 0.000467212 4.60E-05 0.051052133 0.012001917 0.031843288 1.496982091 -0.290563893 VLAMSGDPNYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLAMSGDPNYLHR 13 0 P30153;B3KQV6;E9PH38 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ;; 188.09 1.76E-06 841390000 639078 1136725 966938 1020526 1041760 1327201 928859 1149110 916644 1442110 FALSE TRUE 664309.2929 1331948.676 992137.1986 1222382.997 864682.0073 1018978.682 856052.6045 1133708.06 883654.1615 1724663.844 0.385181898 0.77229466 0.575264103 0.708765944 0.501362634 0.590827416 0.496359107 0.657350164 0.512363128 1 20.71788376 -1.648530843 2.808248509 1.042507635 0.587103776 0.578943025 0.107763953 32122737.81 30144055.93 9873391.361 0.023143504 0.022463072 1.648530843 -0.455403858 VLAPILPDNFST(ph)PTGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 VLAPILPDNFS(0.208)T(0.789)PT(0.002)GS(0.001)R;VLAPILPDNFS(0.184)T(0.815)PT(0.001)GSR;VLAPILPDNFS(0.048)T(0.951)PT(0.001)GSR;VLAPILPDNFS(0.026)T(0.972)PT(0.001)GS(0.001)R 288.42 5.00E-36 200823000 182328 212631 176581 181729 178119 209449 173614 171424 155821 200853 TRUE FALSE 189526.4502 249148.7202 181182.8459 217674.4538 147842.396 160807.644 160005.681 169126.3417 150213.0326 240206.2998 0.789015319 1.037228084 0.754280159 0.906197939 0.615480927 0.669456397 0.666117754 0.704087869 0.625350096 1 17.87391446 3.247907264 24.99565475 0.69410599 0.875119512 0.271423626 0.124592206 214.3593046 573255.734 0.031644002 0.042275211 1769.731021 -3.247907264 0.181013522 VLATVTKPVGGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLATVTKPVGGDK 13 1 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 ; 140.31 4.17E-06 0 1930190 1117180 1600830 1192910 2189060 1963950 1968540 1597740 1754800 967460 FALSE TRUE 2006395.392 1309046.975 1642548.945 1428864.038 1816964.363 1507852.376 1814240.691 1576324.909 1691645.091 1157015.264 1.734113157 1.131399918 1.419643281 1.234956947 1.570389277 1.303226002 1.568035226 1.362406321 1.462076728 1 20.14197647 -1.026934201 5.794974354 0.999999057 1.41045624 0.360906269 0.167449139 1.81E-06 3.04E-07 0.143855368 0.033906958 0.09398657 1.026934201 0.410457182 VLATVTKPVGGDKNGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLATVTKPVGGDKNGGTR 18 2 Q02878;F8VZ45;U3KQR5;F8VZA3;F8VWR1;F8VU16 Q02878 RPL6 60S ribosomal protein L6 0 109.72 0.00019931 342350000 209640 210210 240190 112030 348360 270600 138520 173050 223190 323770 FALSE TRUE 217916.7491 246311.9323 246449.5487 134189.1996 289145.8916 207757.251 127662.4404 170730.5478 215157.4355 387206.5325 0.562792026 0.636125457 0.636480865 0.346557169 0.746748485 0.536554096 0.329701154 0.440928893 0.55566582 1 18.56274377 0.947323739 21.37742416 1.000000001 0.522431476 0.563179919 0.123612114 2003.761173 813181.5298 0.12295318 0.030738295 8.857756539 -0.947323739 -0.477568525 VLAVNQENEHLMEDYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VLAVNQENEHLMEDYEK 17 0 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 ;;;;; 331.02 5.25E-72 3339170000 3625720 3066550 3259960 3270980 3752120 4517080 4891080 3623720 3616500 3206540 FALSE TRUE 3768866.225 3593206.108 3344917.236 3917970.081 3114335.983 3468056.627 4507704.369 3575149.961 3486342.871 3834800.12 0.982806432 0.936999582 0.872253346 1.021688213 0.812124722 0.904364378 1.175473096 0.932291084 0.909132878 1 21.87071995 VLDAPGGGSVLVMEHMDMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLDAPGGGSVLVMEHMDMR 19 0 Q9HA64;I3L3W5;I3L139;I3L2G3 Q9HA64 FN3KRP Ketosamine-3-kinase 0 124.84 2.85E-05 61287000 35121 49326 51781 43405 52805 53738 45189 46878 45254 45568 FALSE TRUE 36507.6042 57797.3568 53130.4554 51990.37945 43829.22496 41258.16391 41646.9681 46249.67709 43625.31738 54496.17715 0.669911288 1.060576353 0.974939127 0.954018835 0.804262377 0.757083635 0.764218158 0.848677458 0.800520691 1 15.73386741 3.234616732 24.97961231 0.815881419 0.929560884 0.108863719 0.113451668 161.7900256 1024740.102 0.030852715 0.038190094 1716.39299 -3.234616732 0.113679465 VLDEEGS(ph)ER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLDEEGSER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 VLDEEGS(1)ER;VLDEEGS(1)ER;VLDEEGS(1)ER;VLDEEGS(1)ER 183.08 4.78E-05 1740470000 1846410 1500380 1457500 2495730 1640240 1828550 3026310 1705240 1611780 837960 TRUE FALSE 1919307.693 1758058.594 1495483.647 2989377.945 1361432.591 1403896.974 2789099.914 1682384.047 1553772.353 1002142.218 1.915204906 1.754300499 1.492286843 2.982987734 1.358522339 1.40089595 2.783137826 1.678787717 1.550450948 1 19.93465583 VLDFEHFLPMLQTVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 244.17 4.86E-20 4745520000 4107920 3536720 3856810 3261700 5440520 5093600 4846160 3815530 4229090 4177740 FALSE TRUE 4270103.854 4144124.148 3957321.637 3906854.525 4515742.354 3910688.594 4466305.316 3764389.061 4076885.877 4996288.165 0.854655239 0.829440579 0.792052321 0.7819514 0.903819436 0.782718783 0.893924683 0.753437139 0.815982934 1 22.25242526 -0.845171668 5.13063421 1.000000213 0.820511387 0.562907982 0.046711679 4.31E-05 30146343.91 17.11718451 0.010318523 0.142832926 0.845171668 -0.179488826 VLDGLHNELQTIGFQIETIGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLDGLHNELQTIGFQIETIGK 21 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 179.36 5.78E-17 676350000 479080 430310 508090 486740 591630 665890 591820 534730 620490 420790 FALSE TRUE 497994.4483 504212.3952 521331.2428 583015.7192 491064.9439 511247.1392 545431.602 527562.819 598158.6861 503235.744 0.98958481 1.001940743 1.035958294 1.158534 0.975814913 1.015919766 1.083849088 1.04834131 1.188625199 1 18.94087487 2.229163188 24.82877668 1.080373198 1.032068433 0.128589534 0.064314008 417.3530411 1102671.675 0.0238113 0.017821104 169.4974573 -2.229163188 -0.048304766 VLDGLHNELQTIGFQIETIGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLDGLHNELQTIGFQIETIGKK 22 1 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ; 199.33 1.16E-22 315380000 386710 305650 365390 271165 527590 444000 419860 364640 426120 351610 FALSE TRUE 401977.6094 358143.0099 374912.3636 324800.6277 437910.4403 340887.7289 386950.2761 359752.5972 410784.0244 420501.2475 0.955948673 0.851704988 0.891584426 0.772412994 1.041401049 0.810669959 0.920211957 0.85553277 0.976891334 1 18.68175056 1.139744476 5.446867967 0.997393562 0.885448703 0.243554336 0.07145693 0.261516544 11.14529775 0.061585947 0.01561659 13.79572332 -1.139744476 -0.111944859 VLDHAMEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLDHAMEAER 10 0 O15020;O15020-2;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 104.79 0.0026344 61254000 33318 43796 40548 53802 53766 61069 47834 44840 44252 62023 FALSE TRUE 34633.42037 51317.62231 41604.71419 64443.87502 44626.87452 46886.65026 44084.64609 44238.99314 42659.37916 74175.21935 0.466913623 0.691843216 0.560897757 0.868805992 0.601641288 0.632106661 0.594331186 0.59641203 0.57511632 1 16.17864967 -1.393607598 3.114671062 1.004841936 0.625056277 0.569006254 0.098922357 35364067.52 44985299.26 1532882.176 0.023095298 0.040401027 1.393607598 -0.379785659 VLDLDLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLDLDLFR 8 0 P49591;Q5T5C7 P49591;Q5T5C7 SARS "Serine--tRNA ligase, cytoplasmic" 0 ;; 111.04 0.0077015 130717200 244291 282120 247589 242965 449735 359371 271200 246000 258252 454368 FALSE TRUE 253935.7973 330571.9154 254041.3727 291022.7518 373289.2053 275912.5316 249942.6354 242702.7724 248957.561 543392.7102 0.467315429 0.608348086 0.467509718 0.535566169 0.686960274 0.507758986 0.459966854 0.446643409 0.458154032 1 19.05163569 -1.01591357 4.914984856 1.000005628 0.514649192 0.795848103 0.073637524 6.00E-06 1.20E-06 0.075021211 0.017682412 0.096402086 1.01591357 -0.485356436 VLDPFTIKPLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 208.08 6.47E-08 9291800000 12180800 11457100 14132100 12093500 29068000 19107800 17419200 14971000 14821000 18150000 FALSE TRUE 12661707.39 13424767.8 14500394.14 14485558.2 24127031.74 14670303.03 16053837.59 14770338.23 14287595.11 21706145 0.583323634 0.618477754 0.668031755 0.667348265 1.111530018 0.675859441 0.739598744 0.680468053 0.658228124 1 24.37160019 3.456921803 24.99996064 0.785931605 0.630279569 0.268577291 0.140464348 370.9505811 459107.6178 0.039368963 0.053311169 2863.662306 -3.456921803 -0.155652036 VLDPFTIKPLDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLDPFTIKPLDRK 13 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 ; 173.06 1.26E-05 2434600000 1597830 1197690 1569580 1037800 3471300 1962340 1607670 1423280 1664020 1848900 FALSE TRUE 1660913.562 1403383.941 1610484.544 1243073.742 2881249.666 1506616.275 1481656.625 1404203.26 1604132.245 2211156.556 0.751151499 0.63468321 0.728344875 0.5621826 1.303050957 0.681370241 0.670082189 0.635053749 0.725472035 1 21.07636974 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 2 VLDTSSLT(0.001)QS(0.999)APAS(0.998)PT(0.002)NK;VLDTSSLT(0.001)QS(0.999)APAS(1)PTNK;VLDTSSLT(0.007)QS(0.993)APAS(1)PTNK;VLDTSSLT(0.002)QS(0.998)APAS(1)PTNK 354.55 2.29E-90 555254000 2048670 1309610 1771780 1421700 2424400 2411390 2036220 1859840 1980280 1425730 TRUE FALSE 2129553.074 1534525.33 1817954.042 1702908.017 2012301.354 1851381.217 1876615.756 1834911.887 1909010.11 1705074.496 1.248950165 0.899975534 1.06620212 0.998729393 1.180183833 1.085806645 1.100606314 1.076147635 1.119605105 1 20.70140334 4.797330126 22.62178558 1.066293258 1.248954875 0.372291607 0.073545735 28101.08228 10815454.93 0.017030271 30.94379742 62709.03616 -4.797330126 0.182661617 VLDTSSLTQSAPAS(ph)PTNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(1)PTNK;VLDTSSLTQSAPAS(0.991)PT(0.009)NK;VLDTSSLTQSAPAS(1)PTNK 491.21 3.49E-240 1748310000 2217270 1510750 1861330 1526620 2362060 2518880 2276770 1901380 2023190 1310730 TRUE FALSE 2304809.532 1770209.56 1909837.789 1828580.879 1960557.885 1933908.294 2098310.818 1875895.111 1950375.787 1567542.448 1.47033309 1.129289712 1.21836432 1.166527185 1.250720762 1.233719888 1.338599041 1.196710886 1.244225182 1 20.58007308 0.021640197 1.267373228 0.999347768 1.244499617 0.404546316 0.090730812 12.28517783 14.68631419 0.106809712 0.024039574 1.051090708 -0.021640197 0.245151849 VLEALLPLKGLEER ddPTM_MDA-MB-175_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 ; 140.93 8.95E-06 5329700000 1586920 1631570 1798740 1285240 2586540 2236490 1423380 1843920 2029490 1886110 FALSE TRUE 1649572.827 1911779.456 1845616.642 1539456.636 2146880.855 1717099.092 1311811.756 1819205.268 1956449.051 2255657.143 0.73130477 0.847548778 0.818216832 0.682486982 0.951776231 0.761241174 0.581565226 0.806507884 0.867352141 1 21.10511637 0.984496727 2.623806396 0.99811451 0.771183435 0.367609735 0.09332398 0.297235559 4.736982047 0.088923333 0.023853859 9.649320389 -0.984496727 -0.226931076 VLEDSDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLEDSDLK 8 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;; 133.55 0.002128 471710000 956820 680150 748690 686270 1028830 1069920 897110 730920 733740 570330 FALSE TRUE 994595.9924 796960.4717 768201.4765 822012.1577 853949.8441 821447.2948 826792.174 721123.2129 707332.8407 682075.2439 1.458191015 1.16843483 1.126270867 1.205163455 1.251987741 1.204335302 1.212171504 1.05724877 1.037030514 1 19.37957137 7.999999999 0.099383423 0.874419175 2.152465154 0.573837099 0.081309734 104.4178705 0.735258444 1.08592081 18.20361147 99999999.8 -7.999999999 1.278045979 VLEEMESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLEEMESR 8 0 Q9NUP9;G3V1D4 Q9NUP9 LIN7C Protein lin-7 homolog C 0 ; 101.54 0.012379 568180000 437230 485740 458560 439790 571190 552700 468890 469390 421860 466800 FALSE TRUE 454492.178 569162.0665 470510.4503 526779.1494 474099.3278 424343.8012 432137.1766 463098.5948 406677.341 558260.5226 0.814122009 1.0195277 0.842815193 0.943608097 0.849243872 0.760117873 0.774077978 0.829538497 0.728472325 1 19.09057901 3.026843337 5.804907665 0.805892725 0.908043999 0.176238914 0.086100665 0.236183286 24.06478219 0.023145951 0.027268541 1063.759219 -3.026843337 0.102151274 VLEENQEHYHIVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLEENQEHYHIVQK 14 0 P57740;P57740-2;P57740-3 P57740 NUP107 Nuclear pore complex protein Nup107 0 105.03 0.00059186 139660000 68766 69921 78992 64869 92277 88309 82526 70860 72244 81569 FALSE TRUE 71480.93478 81929.38784 81050.59641 77699.89459 76591.7885 67800.57309 76057.39648 69910.2376 69643.95255 97550.88382 0.732755378 0.839863102 0.830854558 0.796506311 0.785147048 0.695027768 0.779668964 0.716654067 0.713924363 1 16.57386732 2.991489968 20.86944097 0.757856967 0.803269431 0 0.085908253 138.9891776 340859.6346 0.023421196 0.026661763 980.5956617 -2.991489968 0.045412464 VLEFNCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLEFNCR 7 0 P22102;P22102-2;F8WD69 P22102 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 ; 129.39 0.0085261 234970000 94534 113024 98277 100411 124600 130255 93394 96821 82275 115914 FALSE TRUE 98266.27532 132434.9928 100838.1794 120271.9961 103420.5365 100005.2503 86073.53424 95523.27286 79313.93882 138625.129 0.708863364 0.955346219 0.727416307 0.867606018 0.746044655 0.721407807 0.620908596 0.689076169 0.572146907 1 17.08082928 2.938843831 2.715297173 0.691910784 0.818518151 0.088003227 0.12537526 0.45792323 6.676558932 0.037211756 0.0416565 868.6480148 -2.938843831 0.126607367 VLEGMEVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLEGMEVVR 9 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 114.5 0.0037886 85854000 88511 112240 86158 87349 121370 119780 79021 84511 80297 121370 FALSE TRUE 92005.48263 131516.3469 88403.34826 104626.3715 100739.5708 91962.91028 72827.12754 83378.26828 77407.12666 145150.1277 0.63386429 0.906071176 0.609047678 0.720814877 0.69403708 0.633570991 0.501736572 0.574427798 0.533290104 1 17.14718632 4.198723912 24.99990831 0.634595695 0.769968587 0.06724461 0.146193023 264.4896113 165982.7597 0.034313135 0.074126467 15802.43133 -4.198723912 0.135372892 VLELEGEKGEWGFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLELEGEKGEWGFK 14 1 P61201;P61201-2;H0YKU5 P61201 COPS2 COP9 signalosome complex subunit 2 0 67.115 0.048777 306030000 200090 129170 184580 122060 259530 226730 229410 185140 217370 129970 FALSE TRUE 207989.7077 151353.9427 189390.3064 146203.1037 215415.1833 174075.3936 211428.2447 182658.5011 209546.8962 155435.1331 1.338112585 0.97374345 1.218452371 0.94060526 1.385884768 1.119923084 1.360234592 1.175142952 1.348130838 1 17.24595311 3.230768013 24.99902076 1.239367287 1.114638337 0.115748405 0.153118005 327.9604502 1052111.361 0.039712752 0.048303003 1701.249511 -3.230768013 -0.124728949 VLEQLEDLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLEQLEDLDSR 11 0 P26358;P26358-2;P26358-3 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 0 ;; 135.66 0.00026835 107292000 129077 150634 155514 150184 158114 179870 162673 162074 158230 157116 FALSE TRUE 134173.0596 176504.2177 159566.8226 179889.9469 131237.8388 138097.9185 149922.2652 159901.6631 152535.3332 187899.872 0.714066796 0.939352517 0.849211981 0.957371312 0.698445599 0.73495483 0.797883807 0.850993997 0.811790511 1 17.51960456 -1.650718008 7.915507988 1.000307217 0.821273916 0.303268677 0.08294399 0.00044696 1.97E-05 0.079823534 0.018782891 0.02235023 1.650718008 -0.179033301 VLETAEDIQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLETAEDIQER 11 0 A0A0D9SGF6;Q13813;Q13813-2;A0A0D9SF54;Q13813-3;A0A0D9SFF6;A0A1B0GTB7 A0A0D9SGF6 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 ; 163.38 5.59E-05 97857000 107081 128307 112987 130569 125001 152492 132013 126520 126781 145750 FALSE TRUE 111308.6406 150342.7292 115931.534 156395.1585 103753.3747 117078.044 121665.4761 124824.2063 122218.1766 174306.9219 0.63857843 0.862517263 0.665100001 0.897240091 0.595233818 0.671677537 0.697995666 0.716117323 0.701166513 1 17.41127034 -1.677482316 5.080690448 1.006469469 0.718498207 0.475107779 0.08946585 0.006173316 0.000391876 0.081566419 0.018901299 0.021014433 1.677482316 -0.287971262 VLFNITLDSIKGEVDEEDAALYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLFNITLDSIKGEVDEEDAALYR 23 1 Q9NPQ8-4;Q9NPQ8;Q9NPQ8-3;Q9NPQ8-2 Q9NPQ8-4 RIC8A Synembryn-A 0 101.22 0.0019131 76231000 56905 37627 60004 53896 71142 83963 87803 74043 80468 50650 FALSE TRUE 59151.65334 44089.14455 61567.75353 64556.46794 59049.30825 64463.86572 80920.77143 73050.57469 77571.9724 60573.89775 0.976520507 0.72785715 1.016407328 1.065747299 0.974830916 1.064218552 1.335901674 1.205974478 1.280617152 1 15.88640863 3.067923217 0.887239552 1.221920603 0.880811112 0.48642527 0.119049564 0.440173544 0.765967753 0.0604202 0.082780127 1169.292644 -3.067923217 -0.341109491 VLGDHLLLDPTHELPPYTPPPMLS(ph)PVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLGDHLLLDPTHELPPYTPPPMLSPVR 27 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8;Q96PN7 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 VLGDHLLLDPTHELPPYTPPPMLS(1)PVR;VLGDHLLLDPTHELPPYT(0.001)PPPMLS(0.999)PVR;VLGDHLLLDPTHELPPYTPPPMLS(1)PVR 102.07 0.0041608 162145000 97994 114389 105381 107919 124249 139495 116925 110939 113134 112757 TRUE FALSE 101862.8788 134034.4209 108127.3154 129265.0561 103129.1994 107099.4003 107760.113 109452.0442 109062.3294 134849.5753 0.755381532 0.993955084 0.801836529 0.958587046 0.764772148 0.79421385 0.799113477 0.811660281 0.808770285 1 17.04099145 5.045091439 15.54506913 0.84709182 0.294755868 0.101696389 0.086039189 3939953.618 37930148.82 0.019405591 63146623.28 110940.8372 -5.045091439 -0.552335952 VLGEMGEAPAPEQYLVLEELIDMNQHHLNALGVGHASLDQLCQVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLGEMGEAPAPEQYLVLEELIDMNQHHLNALGVGHASLDQLCQVTR 46 0 F5H8H2;Q03426;A0A1B0GWC2 F5H8H2 MVK Mevalonate kinase 0 71.255 0.00025162 80744000 7830.7 6559.8 8031.4 8594.5 8459.1 11538 4357.9 7271.8 9445.1 5461 FALSE TRUE 8139.862083 7686.394622 8240.704882 10294.46645 7021.225204 8858.47436 4016.316411 7174.333415 9105.172696 6530.978393 1.246346503 1.176913191 1.261787191 1.5762518 1.075064834 1.356377839 0.614963972 1.098508215 1.394151404 1 12.67308342 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_MDA-MB-175_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 208.62 7.33E-12 335040000 629060 300790 423100 327820 575750 647840 587990 462440 480330 255051 TRUE FALSE 653895.7745 352448.3427 434126.3336 392661.8176 477884.2207 497388.9781 541901.8074 456241.7482 463043.0171 305023.3602 2.14375638 1.155479837 1.42325602 1.287317199 1.566713514 1.630658641 1.776591167 1.495760023 1.518057557 1 18.21856021 VLGS(ph)EGEEEDEALSPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLGSEGEEEDEALSPAK 17 0 P18858;P18858-3;P18858-2;M0R0Q7;F5GZ28;B4E135;M0QY71;M0R1G7 P18858 LIG1 DNA ligase 1;DNA ligase 1 VLGS(1)EGEEEDEALSPAK 120.99 6.47E-05 208360000 102760 128720 134910 123890 162610 174050 149540 129450 147070 120100 TRUE FALSE 106817.0441 150826.6587 138425.8654 148395.0722 134969.6103 133629.5253 137818.664 127714.9345 141776.9794 143631.2955 0.743689206 1.050096068 0.963758385 1.033166704 0.939695 0.930364965 0.959530884 0.889185981 0.987089749 1 17.1320106 7.999973589 0.005741743 1.833593049 1.63E-05 0.058958797 0.079902881 205919.094 91.44440799 13405.17447 15895.12454 99993918.71 -7.999973589 -1.833576741 VLGTEDLYDYIDKYNIELDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLGTEDLYDYIDKYNIELDPR 21 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;P68400-2 P68400 CSNK2A1 Casein kinase II subunit alpha 0 ;;; 174.02 3.24E-12 1359306000 2311334 2148015 2530280 2016655 3107420 2857770 2670190 2592029 2679520 2209695 FALSE TRUE 2402587.251 2516919.867 2596221.175 2415543.34 2579221.858 2194096.227 2460893.531 2557287.091 2583084.599 2642642.428 0.909160931 0.952425436 0.982433775 0.914063634 0.976001078 0.830266026 0.931224559 0.967700762 0.977462774 1 21.3335498 1.605390715 3.202344186 0.985171764 0.928605036 0.280395044 0.040325908 0.293565597 7.068195709 0.026350626 0.010907415 40.30795036 -1.605390715 -0.056566728 VLGTPVETIELTEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLGTPVETIELTEDRR 16 1 F8VPD4;P27708 F8VPD4 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 0 208.81 2.23E-11 239060000 42965 67248 69891 69480 65088 93551 58672 65887 64750 78375 FALSE TRUE 44661.29138 78797.32088 71712.41688 83222.93662 54024.36501 71825.19803 54073.13533 65003.89253 62419.66015 93731.08067 0.476483265 0.840674409 0.765086846 0.887890506 0.57637621 0.766290088 0.576896531 0.693514809 0.6659441 1 16.5162399 -1.117121284 6.894553558 1.000000246 0.69952556 0.365924319 0.12053028 4.30E-07 5.53E-08 0.110199257 0.025974193 0.07636225 1.117121284 -0.300474686 VLGTVHTHAFHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLGTVHTHAFHFK 13 0 O75106-2;O75106 O75106-2 AOC2 Retina-specific copper amine oxidase 0 ; 56.225 0.071573 1644240000 12907400 329490 386753 216882 1066950 2454630 732610 638100 608410 211539 FALSE TRUE 13416994.12 386077.3444 396832.1009 259780.6123 885590.2201 1884579.383 675186.1139 629547.3132 586513.4429 252986.0169 53.03452848 1.526081754 1.568593023 1.026857593 3.500550074 7.449342086 2.668867324 2.488466837 2.318363086 1 17.94869812 4.73940461 24.99998693 2.747386768 53.03454418 0.986278027 1.784030851 7.47045272 221246.974 0.449904522 2.727141646 54878.80043 -4.73940461 50.28715741 VLHEAEGHIVTCETNTGEVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLHEAEGHIVTCETNTGEVYR 21 0 P62318;P62318-2;H3BT13 P62318 SNRPD3 Small nuclear ribonucleoprotein Sm D3 0 178.88 3.44E-17 103690000 99539 97163 96535 84757 132860 136710 114500 95726 101550 103560 FALSE TRUE 103468.8766 113849.9894 99050.7814 101521.6816 110276.5047 104961.1744 105525.1908 94442.94955 97895.23534 123850.5992 0.835432991 0.919252633 0.799760211 0.819710863 0.890399444 0.847482168 0.852036175 0.762555451 0.79043005 1 16.91824132 1.93301834 24.99980686 0.820283269 0.852698897 0 0.068255835 648.0433942 241869.5524 0.026509114 0.017111168 85.70740379 -1.93301834 0.032415627 VLHEEHVELLMEEFAFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLHEEHVELLMEEFAFLK 18 0 P53004 P53004 BLVRA Biliverdin reductase A 0 ;; 123.88 1.91E-05 522280000 219360 199402 245372 255916 248340 283777 328241 235966 253336 144466 FALSE TRUE 228020.5022 233647.7424 251766.5959 306535.421 206127.2555 217874.0924 302512.6127 232803.2617 244218.4868 172771.3467 1.319781934 1.352352382 1.457224248 1.774226032 1.193063893 1.261054547 1.750942031 1.347464531 1.413535818 1 17.39850445 0.470486597 1.822540501 1.000083407 1.438543787 0.334418097 0.182162273 4.961154664 15.74503996 0.1714476 0.047858285 2.954517705 -0.470486597 0.43846038 VLHEEHVELLMEEFAFLKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLHEEHVELLMEEFAFLKK 19 1 P53004 P53004 BLVRA Biliverdin reductase A 0 ; 170.91 4.59E-12 1334680000 1378803 970203 1428399 993525 1808305 1578023 1534355 1303754 1642515 865926 FALSE TRUE 1433239.207 1136827.818 1465624.251 1190041.28 1500929.962 1211551.073 1414088.246 1286279.31 1583401.206 1035587.621 1.383986423 1.097761112 1.415258567 1.149145911 1.449351008 1.169916528 1.365493578 1.242076754 1.528988156 1 19.98201819 -1.322002755 4.61117563 0.99977489 1.301133319 0.320356624 0.13530843 0.000274935 4.04E-05 0.11502972 0.02709267 0.047642796 1.322002755 0.301358429 VLHNAQEVEKEPGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLHNAQEVEKEPGQR 15 1 P49916-3;P49916;P49916-4;P49916-2;K7ERZ5 P49916-3 LIG3 DNA ligase 3 0 206.2 2.41E-09 236720000 106900 86477 99496 110880 151770 139580 110290 110020 106460 78938 FALSE TRUE 111120.4945 101328.7521 102088.9475 132811.7331 125972.1896 107164.6604 101645.1816 108545.3619 102628.5254 94404.38974 1.177069147 1.073347885 1.081400428 1.406838532 1.33438911 1.135166073 1.076699737 1.149791468 1.08711603 1 16.52656633 2.490545582 23.57290212 1.097844722 1.212513873 0.27928108 0.101618971 505.2551894 887222.9625 0.037108111 0.033563884 309.4180052 -2.490545582 0.114669151 VLHNDSDILFPVSGVGSYSPADAPLGS(ph)LENGTGPEDHVLPDPGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLHNDSDILFPVSGVGSYSPADAPLGSLENGTGPEDHVLPDPGLR 45 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 VLHNDSDILFPVSGVGS(0.002)Y(0.006)S(0.027)PADAPLGS(0.483)LENGT(0.483)GPEDHVLPDPGLR 86.808 0.00011633 31817000 3341.7 4394.2 5240 4016.7 4222.2 5670.2 3879.8 4576 4363.8 4848.1 TRUE FALSE 3473.632896 5148.869668 5376.558705 4811.191271 3504.511952 4353.381983 3575.691138 4514.666205 4206.74769 5797.992373 0.599109601 0.888043539 0.927313863 0.829802967 0.60443542 0.750842999 0.616711942 0.778660253 0.725552471 1 12.50133772 4.767539969 22.88622669 0.774947172 0.599108756 0.173573771 0.121165845 6418.980876 5069075.431 0.029164241 2.56953204 58551.76203 -4.767539969 -0.175838416 VLHYGDLDDNPQGEVTFESLQEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLHYGDLDDNPQGEVTFESLQEK 23 0 H0YCM7;Q5JVZ5;Q96JJ3-3;Q96JJ3;Q5JW01 H0YCM7 ELMO2 Engulfment and cell motility protein 2 0 ; 225.3 1.18E-32 285081000 112972 98577 120967 98155 120596 144206 110239 113082 129177 112279 FALSE TRUE 117432.2218 115506.8329 124119.4994 117569.766 100097.135 110716.342 101598.1791 111566.3208 124527.945 134277.9203 0.874546027 0.860207193 0.924347794 0.875570352 0.745447463 0.824531253 0.7566261 0.83086125 0.927389586 1 17.03486257 1.052211132 3.403712328 0.998501442 0.834082026 0.519118686 0.051247049 0.175176475 4.289323662 0.053138536 0.013858899 11.27745576 -1.052211132 -0.164419416 VLIAAHGNSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 ;; 186.87 3.84E-06 7758800000 2384928 3366487 3164517 3597428 4599386 4209182 3248262 3127970 2969836 4511183 FALSE TRUE 2479086.799 3944654.955 3246986.913 4308988.521 3817584.011 3231663.271 2993654.737 3086044.678 2862952.182 5395062.937 0.459510265 0.731160137 0.601844121 0.798691057 0.707606946 0.599003813 0.554887825 0.57201273 0.530661498 1 22.36320836 -1.486958704 3.007771985 1.010841524 0.621300133 0.585857872 0.096484433 34076707.09 38934419.22 3057680.491 0.023823339 0.032586769 1.486958704 -0.389541391 VLIDPVSVQDKDTLSIHYLMLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLIDPVSVQDKDTLSIHYLMLPR 23 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 129.32 2.34E-05 273650000 187170 218990 262050 235930 328320 341770 330610 282770 296620 240310 FALSE TRUE 194559.6161 256599.829 268879.2383 282596.2498 272512.2837 262399.0971 304695.9243 278979.9307 285944.7041 287394.1435 0.676978361 0.892849889 0.935576609 0.983305527 0.948217943 0.913028686 1.060202273 0.970722393 0.994956615 1 18.13267114 5.338086146 1.034623845 0.982511158 1.37E-18 0.864459072 0.03608102 1.820949537 0.658169027 0.010654089 2.66180812 217814.1784 -5.338086146 -0.982511158 VLIGGDETPEGQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLIGGDETPEGQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 136.49 0.00016691 70126000 64285 55648 43963 62754 52190 70398 53296 54320 52183 52865 FALSE TRUE 66823.02144 65205.11112 45108.7119 75166.5539 43318.76244 54049.13139 49118.52026 53591.92925 50304.94402 63222.88459 1.056943572 1.031352991 0.713487089 1.188913704 0.685175356 0.854898218 0.776910459 0.847666626 0.795676191 1 15.94815924 5.407924405 0.621176667 0.836043749 1.48915583 0.172817583 0.14289804 11.04887431 1.760541329 0.057460017 6.188934828 255814.0568 -5.407924405 0.653112081 VLKDSLHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLKDSLHEK 9 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 93.058 0.005802 357500000 741750 683190 838810 589010 1199000 980470 954880 914220 976210 583270 FALSE TRUE 771034.8628 800522.568 860670.0777 705514.42 995194.4083 752770.7017 880034.0105 901966.3763 941076.3928 697550.5891 1.105346157 1.147619371 1.233846105 1.011416851 1.426698542 1.079162879 1.261606003 1.293047974 1.349115616 1 19.41193833 3.257920781 24.99998575 1.24695849 1.13401086 0.148833286 0.126581416 439.7358693 567831.9318 0.03281012 0.044360133 1811.009718 -3.257920781 -0.11294763 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLLALFCHEPCRPLHQLATDSTFSLDQPGGTLDLTLIR 38 1 Q13263;Q13263-2;M0R0K9 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ; 256.89 1.77E-62 1879890000 319190 370070 383930 414870 405140 472110 387870 386810 418720 472420 FALSE TRUE 331791.8677 433626.6438 393935.5312 496930.0477 336274.4475 362469.6074 357467.7359 381625.4446 403650.349 564981.654 0.587261313 0.767505707 0.697253669 0.879550768 0.59519534 0.64155996 0.632706803 0.675465198 0.714448595 1 19.1078445 -1.423371444 2.975358532 1.005958801 0.688656407 0.563412095 0.082422932 41709097.5 50310561.32 2112177.488 0.020262327 0.03772494 1.423371444 -0.317302394 VLLMELEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLLMELEEAR 10 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 0 ; 114.84 0.0030291 13029500 15125.1 15471.3 18726.1 13064.7 16884.2 18686.5 16828.6 15398.3 16507.8 17829.3 FALSE TRUE 15722.25063 18128.37542 19214.11755 15648.85867 14014.22971 14346.84357 15509.53036 15191.91098 15913.6875 21322.60997 0.737351133 0.850194955 0.901114712 0.733909155 0.657247388 0.672846504 0.727374856 0.71247896 0.74632925 1 14.38009642 5.112051962 13.18484072 0.761927902 4.05E-05 0 0.103635587 1414542.107 2280844.074 0.024745677 31230049.1 129435.0698 -5.112051962 -0.761887446 VLLPLHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLLPLHK 7 0 E9PFR3;Q14738;H0Y8C4;Q14738-2;Q14738-3;H0YJU0;H0YJ75;Q13362-3;Q13362;Q13362-4;Q13362-5;Q96B13;Q13362-2 E9PFR3;H0YJ75 PPP2R5D;PPP2R5C Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform;Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform 0 90.285 0.031398 0 118070 481560 332520 493940 253590 523100 254950 382010 256590 510870 FALSE TRUE 122731.4948 564264.184 341185.7444 591639.8577 210484.8624 401617.9527 234966.3528 376889.7808 247355.376 610965.1953 0.20088132 0.923561912 0.558437284 0.968369168 0.344512034 0.65734997 0.384582223 0.616876025 0.404860012 1 19.22073067 -1.754529267 5.954564232 1.014632144 0.576377322 0.238965781 0.233168526 0.040934853 0.001687497 0.204041981 0.048360178 0.017598301 1.754529267 -0.438254821 VLLSLEHGLWAPNLHFHS(ph)PNPEIPALLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR 30 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 VLLS(0.001)LEHGLWAPNLHFHS(0.999)PNPEIPALLDGR;VLLSLEHGLWAPNLHFHS(1)PNPEIPALLDGR 122.35 7.87E-06 2972100000 541740 863680 757990 1055710 1057690 1114310 906690 720340 817200 1135130 TRUE FALSE 563128.3135 1012010.322 777743.8421 1264526.287 877904.2316 855528.39 835621.2686 710685.0205 787789.1316 1357536.99 0.414816184 0.74547532 0.57290803 0.931485695 0.646688995 0.630206319 0.615542173 0.523510612 0.580307673 1 20.37256008 -1.458419431 2.906111342 1.009808248 0.631713253 0.424079853 0.129671166 28981361.38 32541019.93 2303654.395 0.031364032 0.034800106 1.458419431 -0.378094996 VLLSLEHGLWAPNLHFHSPNPEIPALLDGR ddPTM_MDA-MB-175_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 ;; 201.08 1.23E-25 47619100000 3270241 6380690 5941610 7367050 6907630 7876750 5745700 7004430 5991450 7444180 FALSE TRUE 3399352.64 7476523.873 6096453.238 8824230.502 5733473.52 6047494.186 5295337.02 6910547.073 5775818.885 8902724.544 0.381832845 0.839801775 0.684785114 0.991183144 0.644013357 0.67928578 0.594799603 0.776228338 0.648769807 1 23.08581549 -1.298378628 4.597122233 1.000175312 0.705387186 0.266097724 0.151578398 0.000253597 3.87E-05 0.13665655 0.032191215 0.050306184 1.298378628 -0.294788126 VLMATNRPDTLDPALMRPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLMATNRPDTLDPALMRPGR 20 2 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 ; 142.98 9.74E-08 1218350000 950320 1089050 1091420 1115420 1180290 1307490 1211770 1097960 1126790 1073600 FALSE TRUE 987839.3674 1276085.866 1119863.302 1336046.747 979664.7274 1003845.263 1116788.301 1083243.642 1086237.048 1283951.365 0.769374444 0.99387399 0.872200718 1.040574264 0.763007661 0.781840567 0.869805767 0.843679653 0.846011055 1 20.29215912 5.037259005 12.76222683 0.879663692 0.43974039 0.132919846 0.08898048 347536.8027 4104411.084 0.020957153 3250414.452 108957.9704 -5.037259005 -0.439923302 VLMKS(ph)PSPALHPPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLMKSPSPALHPPQK 15 1 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 VLMKS(0.835)PS(0.165)PALHPPQK;VLMKS(0.973)PS(0.027)PALHPPQK 117.18 0.00023588 1024180000 735680 565720 771300 575630 928660 1016460 839840 773110 813340 629060 TRUE FALSE 764725.2145 662878.0093 791400.7116 689487.8959 770806.7049 780402.5696 774011.1463 762747.725 784068.0523 752312.2629 1.016499733 0.881120835 1.051957745 0.916491635 1.024583465 1.037338627 1.028842921 1.013871184 1.042210915 1 19.52097208 3.154617469 13.61852244 1.025306631 0.966528948 0.279144757 0.045615754 1.010967819 160.7429189 0.012003434 0.014348534 1427.635927 -3.154617469 -0.058777683 VLMSVQYFLEDVDCKQS(ph)MR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLMSVQYFLEDVDCKQSMR 19 1 Q05655;Q05655-2;A0A494C1T7;C9K0E3 Q05655 PRKCD Protein kinase C delta type;Protein kinase C delta type regulatory subunit;Protein kinase C delta type catalytic subunit 1 VLMSVQYFLEDVDCKQS(1)MR 132.26 8.47E-06 48361000 44437 34285 64159 50008 72884 59827 71200 48212 54199 50675 TRUE FALSE 46191.40707 40173.18205 65831.03625 59899.43314 60495.20371 45933.08594 65619.15795 47565.797 52248.38858 60603.79602 0.762186696 0.662882273 1.086252687 0.988377578 0.99820816 0.757924238 1.082756564 0.784864978 0.862130626 1 15.88712054 4.256058396 24.99986727 0.933745072 0.712534375 0.415757628 0.109604091 238.4198479 340635.3147 0.026300961 0.071676417 18032.60193 -4.256058396 -0.221210697 VLNEAVGALMYHTITLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLNEAVGALMYHTITLTR 18 0 Q13363-2;Q13363;E9PGB1;E7ESU7;D6RAX2;E7EPF8 Q13363-2 CTBP1 C-terminal-binding protein 1 0 176.42 9.12E-13 74066000 36092 48963 56789 54289 52723 67023 63344 51268 64929 46328 FALSE TRUE 37516.94003 57372.01437 58268.96799 65027.20216 43761.16329 51457.92399 58378.93176 50580.83632 62592.21797 55405.0846 0.677138936 1.035500889 1.051689902 1.173668493 0.789840203 0.928758152 1.053674625 0.912927698 1.129719744 1 15.75773076 4.742318949 24.7082202 1.00100374 0.67713879 0.470768388 0.105110492 285.5474733 1877168.603 0.024902952 0.186236075 55248.30377 -4.742318949 -0.32386495 VLNSYWVGEDSTYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLNSYWVGEDSTYK 14 0 P61313;A0A2R8YEM3;E7EQV9;E7ENU7;E7EX53;A0A2R8Y738 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 ; 243.88 3.43E-17 241870000 397590 244450 297200 288150 388150 375210 411660 344210 360880 263740 FALSE TRUE 413287.1602 286432.3859 304945.2762 345145.21 322172.4016 288073.1639 379393.0135 339596.428 347891.9993 315414.8034 1.310297284 0.908113325 0.966807115 1.094258121 1.02142448 0.913315294 1.202838324 1.076666105 1.102966619 1 18.26689085 2.231174069 24.99986122 1.102892645 1.028784085 0.056090321 0.116871819 442.5001799 1497632.576 0.041355356 0.03115266 170.2840884 -2.231174069 -0.074108561 VLNT(ph)GSDVEEAVADALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.731)GS(0.269)DVEEAVADALK;VLNT(0.609)GS(0.391)DVEEAVADALK 138.55 3.68E-05 48749000 87637 59446 82751 67079 99442 94150 102862 77611 88609 55200 TRUE FALSE 91096.97643 69655.38807 84907.55904 80347.02599 82538.88436 72285.08936 94799.40766 76570.75149 85419.9794 66015.38313 1.379935586 1.055138738 1.286178388 1.217095504 1.25029774 1.094973413 1.436019957 1.159892556 1.293940523 1 16.01051462 -1.321898844 4.166216691 0.999666772 1.235496176 0.293437779 0.112074078 0.00032607 5.31E-05 0.096498509 0.02271121 0.047654197 1.321898844 0.235829404 VLNT(ph)GSDVEEAVADALKKPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLNTGSDVEEAVADALKKPAR 21 2 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.648)GS(0.352)DVEEAVADALKKPAR 102.27 0.022197 110810000 145620 110960 182640 102540 232350 209550 167700 159310 171670 129970 TRUE FALSE 151369.19 130016.5169 187399.7484 122822.1059 192855.23 160885.1883 154555.2358 157174.71 165491.6302 155435.1331 0.973841544 0.836468013 1.205646013 0.790182396 1.240744137 1.035063213 0.994339135 1.011191659 1.064698997 1 17.24595311 4.272976274 24.99999606 1.037036056 0.905154817 0.171613489 0.120387159 304.6937608 221328.8521 0.026640353 0.07295 18748.92078 -4.272976274 -0.131881239 VLNTGS(ph)DVEEAVADALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 VLNT(0.31)GS(0.69)DVEEAVADALK;VLNT(0.101)GS(0.899)DVEEAVADALK 169.28 2.09E-09 42310000 61532 43000 52837 46673 68009 63418 76599 52547 54580 35762 TRUE FALSE 63961.33087 50384.91551 54213.97563 55904.78009 56448.85447 48690.13061 70594.97023 51842.69341 52615.67646 42768.8792 1.495511037 1.178074255 1.267603375 1.307136898 1.319858166 1.138447664 1.65061539 1.212159271 1.230232764 1 15.38427378 0.888195725 1.977524685 1.002512855 1.320563136 0.318836896 0.143470203 0.541720338 4.280678921 0.128236914 0.035725554 7.7302889 -0.888195725 0.318050281 VLNTNIDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLNTNIDGR 9 0 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 ;; 133.13 0.0006642 373430000 330987 376110 363628 355726 436090 444460 390230 389670 376420 431690 FALSE TRUE 344054.6223 440703.9668 373104.4444 426087.5411 361963.5776 341240.9009 359642.7529 384447.111 362872.7177 516271.3903 0.666422019 0.853628489 0.722690529 0.825316973 0.701111052 0.660971937 0.696615694 0.744660886 0.702872025 1 18.97777013 -0.716442479 5.602560793 1.000000017 0.733143432 0.643453486 0.060159541 1.27E-08 2.95E-09 0.056820161 0.013392639 0.192113339 0.716442479 -0.266856585 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLPAQATEYAFAFIQVPQDDDARTDAVDSVVR 32 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;; 274.13 1.87E-73 574778000 128653.9 133795.2 140558.4 115848.7 156088.4 161940.6 128663.1 135830.5 138225.4 171993.8 FALSE TRUE 133733.2553 156773.4848 144221.4674 138763.2271 129556.5495 124332.3499 118578.15 134009.9143 133250.6949 205692.6921 0.65016046 0.762173334 0.701150177 0.674614279 0.629854898 0.604456817 0.576482075 0.651505471 0.647814434 1 17.65013101 -1.290888635 5.161399503 1.000075596 0.654454781 0.820115659 0.048421152 4.69E-05 6.44E-06 0.052177765 0.012295737 0.051181306 1.290888635 -0.345620815 VLPEFDTPGHTLSWGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLPEFDTPGHTLSWGK 16 0 P07686;Q5URX0 P07686 HEXB Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A 0 ; 235.22 1.07E-19 1202940000 890760 921150 973830 793780 1144540 1239600 1085690 1047210 976250 896870 FALSE TRUE 925927.8926 1079350.347 999208.8098 950787.3148 949991.4996 951721.6863 1000590.781 1033173.863 941114.9532 1072594.505 0.863259963 1.006298598 0.931581138 0.886436869 0.885694916 0.887308001 0.932869576 0.963247395 0.877419145 1 20.03267334 -1.031269063 5.306747139 1.000000581 0.919641366 0.259829636 0.042415128 2.91E-07 5.31E-08 0.040975605 0.009657973 0.09305312 1.031269063 -0.080359215 VLPFFERPDFQLFTGNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLPFFERPDFQLFTGNK 17 1 Q96HE7 Q96HE7 ERO1L ERO1-like protein alpha 0 182.18 6.95E-10 163400000 293850 266540 301460 311740 397410 412160 394590 302210 319720 227840 FALSE TRUE 305451.4249 312316.1716 309316.2953 373401.2415 329858.3902 316442.0863 363661.0047 298159.3693 308213.3397 272480.8857 1.121001292 1.14619479 1.135185297 1.370375909 1.21057442 1.161336824 1.334629414 1.094239577 1.13113747 1 18.0557955 1.107164982 1.480215775 1.008396221 1.207561999 0.358583051 0.083730636 0.414137433 1.801829159 0.078540685 0.023535907 12.79867414 -1.107164982 0.199165778 VLPPPAGYVPIRT(ph)PAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLPPPAGYVPIRTPAR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR;VLPPPAGYVPIRT(1)PAR 172.95 7.10E-09 1213540000 1496070 1269600 1326580 1154740 1700530 1795480 1459200 1330250 1389100 1200330 TRUE FALSE 1555135.999 1487643.924 1361151.765 1383144.125 1411474.518 1378506.981 1344824.091 1312420.175 1339106.562 1435511.682 1.083332179 1.036316139 0.948199713 0.963519937 0.983255334 0.960289629 0.936825599 0.914252521 0.932842679 1 20.45313364 5.250579746 0.764311099 0.944284493 1.314956406 0.716325274 0.0261859 2.674275238 0.687997236 0.009665915 1.013519281 178065.4844 -5.250579746 0.370671914 VLPSDLDLLLHMNNAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLPSDLDLLLHMNNAR 16 0 Q8WUY1 Q8WUY1 THEM6 Protein THEM6 0 200.44 3.55E-11 179680000 77292 121650 105690 143450 110100 173740 100070 91759 93158 153630 FALSE TRUE 80343.54784 142542.4412 108444.3682 171823.9818 91385.24133 133391.5181 92226.25192 90529.12069 89805.26178 183730.8571 0.437289354 0.775822001 0.590234923 0.935193928 0.497386464 0.72601587 0.501963869 0.492726819 0.48878704 1 17.48723442 2.240685766 24.98399157 0.566659445 0.667475674 0 0.194479018 171.5549499 2016891.831 0.064561594 0.051554086 174.0547043 -2.240685766 0.10081623 VLPSISLS(ph)PGPQPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLPSISLSPGPQPPK 15 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 VLPSIS(0.188)LS(0.811)PGPQPPK 164.09 1.57E-06 92165000 84739 73579 82149 95377 95590 104530 112780 99037 85422 72398 TRUE FALSE 88084.56115 86215.62088 84289.87043 114242.2859 79341.64594 80254.49167 103940.0089 97709.57101 82347.67891 86583.00196 1.017342425 0.995756891 0.973515223 1.319453973 0.916365154 0.926908167 1.20046668 1.128507545 0.951083666 1 16.4017962 2.242935182 24.99498727 1.090119695 1.029687147 0.020068023 0.123665612 391.3662712 2236166.452 0.044539853 0.036076134 174.9585544 -2.242935182 -0.060432548 VLPYIFEDPDWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VLPYIFEDPDWR 12 0 Q8IV36-2;Q8IV36;J3KSF1;E9PIM7 Q8IV36-2 HID1 Protein HID1 0 ;;;;; 159.11 0.00014371 1007388000 951024 1265735 1177291 1325709 1373936 1542469 1081647 1238555 1188353 1455713 FALSE TRUE 988571.1619 1483115.14 1207972.171 1587930.283 1140394.849 1184253.951 996864.6818 1221954.196 1145584.408 1740932.091 0.567840163 0.851908669 0.693865187 0.912115005 0.655048439 0.680241324 0.572604002 0.701896531 0.658029347 1 20.7314285 -1.077992375 5.090619167 1.000006026 0.702429777 0.433911657 0.10298703 6.84E-06 1.24E-06 0.096818168 0.022819799 0.083561769 1.077992375 -0.297576248 VLQCHKPVHAEYLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLQCHKPVHAEYLEK 15 1 Q9NZJ9;F8VRL4;F8VRR0;A0A0C4DGJ4;A0A024RBG1;Q9NZJ9-2;Q9NZJ9-3;Q96G61;Q8NFP7 Q9NZJ9 NUDT4;NUDT11;NUDT10 Diphosphoinositol polyphosphate phosphohydrolase 2;Diphosphoinositol polyphosphate phosphohydrolase 3-beta;Diphosphoinositol polyphosphate phosphohydrolase 3-alpha 0 ; 158.17 1.10E-06 1817860000 2090250 1267220 1677020 1276770 2142480 2087710 1965970 1699690 1992420 1395550 FALSE TRUE 2172774.684 1484855.177 1720724.519 1529311.295 1778302.015 1602870.992 1811872.134 1676908.436 1920713.193 1668981.303 1.301856815 0.889677538 1.031002873 0.916314217 1.06550146 0.960388825 1.085615597 1.004749683 1.150829665 1 20.67053636 2.205895867 24.99801859 1.055590459 1.01803266 0.015045603 0.113476549 934.5072069 715164.8025 0.039776647 0.029379405 160.6555995 -2.205895867 -0.037557799 VLQGDLVMNVYR ddPTM_MDA-MB-175_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 850540000 395740 433970 417310 408660 728500 598590 433180 382290 433150 701400 FALSE TRUE 411364.1208 508500.9717 428185.4414 489491.7283 604669.8302 459576.5442 399226.2197 377166.0279 417561.0161 838825.9009 0.490404648 0.606205616 0.510458059 0.583543889 0.720852598 0.547880727 0.47593454 0.449635648 0.49779223 1 19.67801188 -1.436616648 6.064333109 1.000176124 0.540418214 0.769480316 0.075110334 0.000197377 1.83E-05 0.080256318 0.018909464 0.036591764 1.436616648 -0.45975791 VLQLYPNNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLQLYPNNK 9 0 Q02790;H0YFG2 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 124.08 0.0012556 126970000 379440 272570 304480 270320 463070 438000 359150 349940 329650 318150 FALSE TRUE 394420.5842 319381.7772 312414.9989 323788.4892 384357.5268 336281.138 330998.8845 345249.6267 317785.9609 380485.4012 1.036624751 0.839406128 0.82109589 0.850987944 1.010176805 0.883821395 0.869938462 0.907392572 0.835211969 1 18.53748157 4.750889448 23.94447735 0.88804602 1.036624919 0.327035204 0.062595961 1239.989331 2408168.71 0.014579826 0.240008775 56349.41971 -4.750889448 0.148578899 VLQNFHPDEAES(ph)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLQNFHPDEAESDEDNDVVIEGTLEPARPPQTPGAPAGSLSR 42 1 Q9BYG4 Q9BYG4 PARD6G Partitioning defective 6 homolog gamma 1 VLQNFHPDEAES(1)DEDNDVVIEGTLEPARPPQTPGAPAGSLSR 229.12 6.80E-45 167170000 22945 26432 21254 27103 27639 30235 29445 27965 26435 30844 TRUE FALSE 23850.88632 30971.49039 21807.8967 32463.89251 22940.93265 23213.37947 27137.02396 27590.17492 25483.60951 36887.29126 0.646588175 0.839624958 0.591203527 0.880083395 0.621919688 0.629305614 0.735674077 0.747958822 0.69085066 1 15.17083623 -1.52519658 3.024921251 1.010469476 0.713477002 0.484574014 0.089864975 42251913.25 49973670.32 3660725.819 0.019795147 0.029840316 1.52519658 -0.296992473 VLRHEEFEEGCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLRHEEFEEGCK 12 1 Q9HC38-2;F6TLX2;I3L3Q4;Q9HC38-3;I3L1F4 Q9HC38-2 GLOD4 Glyoxalase domain-containing protein 4 0 ;; 117.79 0.00041778 424378000 487660 337924 377409 343499 523240 506570 430039 404632 465425 406329 FALSE TRUE 506913.1934 395959.8183 387244.5886 411442.077 434299.8517 388926.7946 396331.4195 399208.5699 448674.4452 485941.3879 1.043157068 0.814830406 0.796895671 0.846690747 0.893728879 0.800357418 0.815595109 0.821515886 0.923309799 1 18.89042279 -1.050665908 8.098232388 1.000000003 0.852720235 0.238219021 0.072534826 3.78E-09 4.90E-10 0.066606397 0.015699278 0.088988542 1.050665908 -0.147279768 VLRPPGGGSNFSLGFDEPTEQPVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLRPPGGGSNFSLGFDEPTEQPVRK 25 2 Q9UK76;J3KT51;Q9UK76-2 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 136.56 1.61E-05 380800000 105780 80799 95446 86626 129430 132570 118850 94015 108900 109520 FALSE TRUE 109956.2761 94675.59972 97933.40117 103760.3642 107429.5348 101782.6266 109534.2264 92754.8827 104980.7103 130978.3471 0.839499646 0.722833978 0.747706803 0.79219479 0.820208357 0.777095061 0.836277361 0.708169593 0.801511949 1 16.9989688 0.962028835 23.92701856 1.000000001 0.777010227 0.703113775 0.042481722 2212.034968 1393885.615 0.039939199 0.0099848 9.162813256 -0.962028835 -0.222989773 VLS(ph)AMIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLSAMIR 7 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 VLS(1)AMIR;VLS(1)AMIR;VLS(1)AMIR;VLS(1)AMIR 100.98 0.0098527 208319000 305995 314511 359448 262544 399509 365162 319726 348725 357846 259865 TRUE FALSE 318075.9189 368525.8177 368815.5102 314474.4196 331600.6029 280358.6596 294665.0407 344050.9118 344967.1924 310780.5713 1.023474272 1.185807131 1.186739276 1.011885712 1.066992706 0.902111282 0.948144987 1.10705412 1.11000244 1 18.24553679 3.72614162 24.32108997 1.022981936 1.137386916 0.318650416 0.074293671 622.2005035 1218504.22 0.020945623 0.032724693 5322.818041 -3.72614162 0.11440498 VLS(ph)LQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLSLQGR 7 0 Q8N5J2;Q8N5J2-3;Q8N5J2-2;Q8N5J2-4 Q8N5J2 FAM63A Protein FAM63A 1 VLS(1)LQGR;VLS(1)LQGR;VLS(1)LQGR;VLS(1)LQGR 150.27 0.0020563 1006420000 501632 451529 585437 582492 742940 829210 703840 656150 665840 591966 TRUE FALSE 521436.8187 529075.5933 600693.9692 697707.179 616655.3242 636638.5443 648671.1817 647355.3825 641876.5485 707950.4038 0.736544278 0.747334263 0.848497248 0.985531155 0.871043114 0.899269978 0.916266419 0.914407816 0.906668808 1 19.43328877 4.102071221 3.257589028 0.919798853 0.739526638 0.792198294 0.037674946 0.095628135 1.993472746 0.009039611 0.022654953 12649.43773 -4.102071221 -0.180272215 VLS(ph)PLIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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;VLS(1)PLIIK 163.64 0.00035113 2297374000 2930704 2447565 2938888 2299416 3483710 3712100 3539610 3067235 3097817 2380516 TRUE FALSE 3046410.457 2867915.249 3015477.836 2754233.622 2891550.219 2850021.032 3262166.119 3026123.732 2986327.171 2846932.532 1.070067668 1.007370289 1.059202423 0.967439021 1.015672197 1.001084852 1.145852978 1.06294185 1.048963099 1 21.44097687 VLS(ph)PPHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSPPHIK 8 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 1 VLS(1)PPHIK;VLS(1)PPHIK 77.662 0.021019 165868000 435070 367000 467720 381400 577360 625470 619290 531930 550590 406390 TRUE FALSE 452246.8995 430029.3951 479909.1674 456839.7816 479220.5534 480214.0716 570748.4316 524800.3484 530774.3735 486014.3397 0.93052172 0.88480804 0.987438288 0.939971816 0.986021428 0.988065644 1.174344839 1.079804248 1.092096118 1 18.89063936 2.412928541 5.953223886 1.094507888 0.948218907 0.657180555 0.047941672 0.114010259 7.687528704 0.016462726 0.013755679 258.7787087 -2.412928541 -0.146288981 VLS(ph)PPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSPPK 6 0 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0;K7EL01;Q5XUX1;Q5XUX1-2 Q9H6Z4 RANBP3;FBXW9 Ran-binding protein 3;F-box/WD repeat-containing protein 9 1 VLS(1)PPK;VLS(1)PPK 81.548 0.064604 188608000 969510 497740 589990 554400 723480 868670 864610 646500 623430 435090 TRUE FALSE 1007787.003 583222.9731 605365.6241 664058.6653 600503.128 666934.5573 796839.609 637834.725 600992.8761 520337.5552 1.93679467 1.120855044 1.163409441 1.276207452 1.154064553 1.281734425 1.53138977 1.225809513 1.155005765 1 18.98908831 4.744260078 24.79956257 1.234189766 1.936795009 0.724801491 0.133346805 300.6036726 1307947.324 0.031900422 0.281992663 55495.79505 -4.744260078 0.702605243 VLS(ph)PPKLNEVSSDANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VLSPPKLNEVSSDANR 16 1 Q9H6Z4;Q9H6Z4-2;Q9H6Z4-3;B7Z7F3;K7ESQ0 Q9H6Z4 RANBP3 Ran-binding protein 3 1 VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR;VLS(1)PPKLNEVSSDANR 192.09 3.58E-10 10532150000 3120570 1496517 2040120 1603870 2797970 3297060 2748150 2207680 2267340 1231807 TRUE FALSE 3243772.513 1753532.153 2093287.203 1921110.699 2322372.059 2531367.782 2532742.822 2178089.661 2185738.876 1473155.997 2.201920584 1.190323467 1.420954201 1.304078253 1.576460377 1.718329754 1.719263151 1.478519359 1.483711759 1 20.49047878 0.593359098 1.68096185 1.000324872 1.558890065 0.299267916 0.262676233 2.432493435 8.527752709 0.239875646 0.068043182 3.920659242 -0.593359098 0.558565192 VLS(ph)SPQLAQQGQGLMGHR ddPTM_MDA-MB-175_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 89.917 0.0013694 0 45961 40566 41404 32318 35717 53589 47731 44874 46073 35211 TRUE FALSE 47775.57577 47532.89494 42483.02225 38710.40394 29645.8371 41143.7669 43989.7195 44272.53743 44414.84173 42109.92129 1.134544409 1.128781377 1.008860168 0.919270394 0.704010746 0.977056371 1.044640269 1.051356452 1.054735805 1 15.36187256 4.168220654 3.646767049 0.966425528 1.135127113 0.316557292 0.096760209 0.295287224 7.700499083 0.02790128 0.071270065 14730.60737 -4.168220654 0.168701584 VLS(ph)TSTDLEAAVADALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLS(0.331)T(0.331)S(0.331)T(0.007)DLEAAVADALK 95.428 0.0026965 15839000 68222 38031 54754 43253 59998 70242 68520 51760 62299 33873 TRUE FALSE 70915.45724 44562.52841 56180.93422 51808.3143 49799.56139 53929.36003 63149.22336 51066.24186 60056.87116 40509.76581 1.750576826 1.100044089 1.386849148 1.278909252 1.229322372 1.331268126 1.558864192 1.260590893 1.482528224 1 15.30598212 -1.923086058 2.500618699 0.768977261 1.359806275 0.286915417 0.176017774 25791609.13 13386197.23 34858813.9 0.038414085 0.011937515 1.923086058 0.590829014 VLSAPPHFHFGQTNRT(ph)PEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSAPPHFHFGQTNRTPEFLR 21 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 1 VLSAPPHFHFGQT(0.163)NRT(0.837)PEFLR;VLSAPPHFHFGQT(0.25)NRT(0.75)PEFLR 202.15 9.59E-22 1719070000 253530 326650 325270 367810 338350 423530 348550 349740 302860 341860 TRUE FALSE 263539.5602 382749.5965 333746.8034 440561.7202 280837.3879 325171.5762 321229.7402 345052.3074 291960.1278 408840.9217 0.644601717 0.936182207 0.816324359 1.077587142 0.68691115 0.795349875 0.785708385 0.843976933 0.714116695 1 18.64118008 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 438.22 4.29E-181 1408761000 1081608 931071 1080964 934289 1187848 1293714 1186027 1055673 1209834 880392 FALSE TRUE 1124310.719 1090975.202 1109134.81 1119088.576 985938.0212 993268.5299 1093063.105 1041523.43 1166292.311 1052887.956 1.067835103 1.036174072 1.0534215 1.062875275 0.936413049 0.943375336 1.038157097 0.989206329 1.107707904 1 20.00592049 VLSEDEEDVDFDIIHNANDTFTVKYVPPAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSEDEEDVDFDIIHNANDTFTVKYVPPAAGR 32 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 ; 143.92 3.19E-10 154385000 88940 74021 86902 81345 122066 123743 110272 90442 83407 69500 FALSE TRUE 92451.41988 86733.53095 89166.73751 97434.79821 101317.2649 95005.56359 101628.5925 89229.77292 80405.19836 83117.19434 1.11230198 1.043508887 1.072783294 1.172258027 1.218968779 1.143031407 1.222714425 1.073541686 0.967371421 1 16.34285934 1.434963407 4.383344515 0.987979699 1.139341858 0.569862073 0.054316385 0.164665211 5.740479258 0.041915186 0.015414833 27.22471909 -1.434963407 0.151362159 VLSLNFSECHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSLNFSECHTK 12 0 Q9UN86-2;Q9UN86;D6RB17;D6RAC7;D6RE13;D6RBW8;D6RGJ4;D6RBM9;D6REX8;D6RBR0 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 145.71 6.41E-05 554770000 349710 381110 490920 361090 537170 600650 520450 558370 471930 438560 FALSE TRUE 363516.8208 446562.6779 503713.7785 432512.5243 445862.0353 461158.1404 479655.7691 550885.9635 454945.3315 524487.4353 0.693089665 0.851426837 0.960392461 0.824638485 0.850090975 0.879254887 0.914522898 1.050332051 0.8674094 1 19.00054869 7.396420304 0.220884132 0.996548827 4.82E-13 0.482999586 0.068253556 35.19984828 0.56947767 0.112118578 11.86363236 24912671.66 -7.396420304 -0.996548827 VLSNRPIMFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSNRPIMFR 10 1 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 105.98 0.0022599 233950000 95502 103660 84574 79073 199970 166850 105220 88918 81835 261350 FALSE TRUE 99272.4927 121462.7986 86778.06792 94713.40339 165979.1708 128101.6161 96972.58146 87726.19965 78889.77434 312556.5287 0.317614523 0.388610659 0.277639595 0.303028076 0.531037286 0.409851033 0.310256138 0.280673067 0.252401621 1 18.25375761 -1.042143069 4.964698943 1.000011565 0.341404709 0.863848333 0.078459327 0.373137734 110646632.8 2822.378741 0.019569022 0.090752152 1.042143069 -0.658606856 VLSPT(ph)AAKPSPFEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 VLS(0.348)PT(0.652)AAKPSPFEGK;VLS(0.448)PT(0.552)AAKPSPFEGK 209.25 4.01E-09 5159100000 4988600 2873100 4377300 3008700 5856400 5044800 5195000 4288000 4658400 2659400 TRUE FALSE 5185553.78 3366532.575 4491376.034 3603811.88 4860931.22 3873221.655 4787802.325 4230526.374 4490745.094 3180458.513 1.630442202 1.058505421 1.412178784 1.133110797 1.528374352 1.217818638 1.50538116 1.330162414 1.411980403 1 21.60080334 -1.290256904 3.471966051 0.998798173 1.350481341 0.282775952 0.170914837 3128619.393 1948688.62 26269.69077 0.035313648 0.051255809 1.290256904 0.351683169 VLSQSTPGT(ph)PSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSQSTPGTPSK 12 0 Q6MZP7-3;Q6MZP7 Q6MZP7-3 LIN54 Protein lin-54 homolog 1 VLSQSTPGT(0.985)PS(0.015)K;VLSQSTPGT(0.993)PS(0.006)K 172.43 0.00040002 222319000 516670 347300 385260 317760 499810 555390 455700 397060 393990 300350 TRUE FALSE 537068.5306 406946.0734 395300.1921 380611.9796 414852.4747 426409.0895 419981.0432 391738.0602 379810.3769 359197.832 1.495188675 1.132930205 1.100508291 1.059616584 1.154941477 1.187114875 1.169219316 1.090591383 1.057384937 1 18.45441912 4.7387681 4.767960014 1.111542737 1.516991096 0.822132047 0.054365357 0.07152736 4.631772671 0.013093644 0.096593334 54798.42805 -4.7387681 0.40544836 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSS(0.001)AAS(0.999)LPGS(0.001)ELPSSRPEGSQGGELSR;VLSS(0.034)AAS(0.961)LPGS(0.005)ELPSSRPEGSQGGELSR 201.79 2.43E-25 1071040000 390030 439250 458580 448320 505050 525790 459620 463700 473220 461120 TRUE FALSE 405428.6856 514687.7706 470530.9715 536996.3579 419201.7814 403683.2409 423593.7834 457484.86 456188.9046 551467.6353 0.735181286 0.933305488 0.853234064 0.97375861 0.760156634 0.732016197 0.76812084 0.829576988 0.827226977 1 19.07291669 4.794324473 21.48657331 0.840514 0.735177421 0.127732947 0.087021828 22942.6502 8838431.449 0.020837489 21.34599869 62276.53964 -4.794324473 -0.105336579 VLSSAASLPGSELPSSRPEGS(ph)QGGELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSSAASLPGSELPS(0.001)S(0.001)RPEGS(0.998)QGGELSR 224.78 1.02E-34 238800000 42925 51117 43829 51798 50105 59310 47213 45810 41300 48976 TRUE FALSE 44619.71215 59895.94711 44971.21975 62043.4898 41588.17 45536.15135 43512.32169 45195.99188 39813.62107 58571.9095 0.761793708 1.022605335 0.767795008 1.059270397 0.710036097 0.777440103 0.742887197 0.77163255 0.679739169 1 15.83792131 3.205025676 24.99999333 0.766638973 0.901771367 0.196491177 0.119527779 249.2005249 185776.0449 0.031141907 0.037223736 1603.340181 -3.205025676 0.135132394 VLSSAASLPGSELPSSRPEGSQGGELS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 VLSSAASLPGSELPSSRPEGS(0.003)QGGELS(0.997)R;VLSSAASLPGSELPSSRPEGSQGGELS(1)R 207.23 1.36E-25 343430000 111301 117000 124380 115679 153866 148413 101319 120009 104752 123897 TRUE FALSE 115695.2494 137093.8399 127621.445 138559.9609 127711.9123 113946.33 93377.35203 118400.4757 100981.996 148172.245 0.780815931 0.925232927 0.861304659 0.935127634 0.861915214 0.769012645 0.630194623 0.799073238 0.681517621 1 17.17691571 2.746746012 4.479487848 0.753690877 0.879796352 0.176573646 0.099309519 0.259094894 13.81572185 0.029429956 0.029677972 558.1436811 -2.746746012 0.126105475 VLSSIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSSIEQK 8 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ; 157.58 0.00087158 519630000 394580 310600 397420 317130 471320 460510 460880 385150 426310 300070 FALSE TRUE 410158.3231 363943.1339 407777.0917 379857.3675 391205.1948 353563.5316 424755.0213 379987.6942 410967.1864 358862.9713 1.142938547 1.014156274 1.136303058 1.058502542 1.090124159 0.985232693 1.183613399 1.058865708 1.145192509 1 18.45307354 -1.028284035 8.1996759 0.999999999 1.087546938 0.170423909 0.059602343 7.47E-10 9.37E-11 0.051560448 0.012152914 0.093694903 1.028284035 0.087546939 VLSSTINNQAVETDEGIEEEIPDS(ph)PGIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSSTINNQAVETDEGIEEEIPDSPGIEK 29 0 Q1RLN5;Q8IWW6-3;Q8IWW6-4;Q8IWW6;Q8IWW6-2 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 VLSSTINNQAVETDEGIEEEIPDS(1)PGIEK 150.14 2.48E-08 127280000 160330 121320 171630 132960 200030 244890 238840 193250 188710 121580 TRUE FALSE 166659.9522 142155.7663 176102.8188 159259.0912 166028.972 188018.0088 220119.0967 190659.7998 181918.364 145401.2732 1.146206966 0.977678965 1.211150459 1.095307404 1.141867388 1.293097403 1.513873241 1.311266371 1.251146981 1 17.14968038 2.763741538 3.996205905 1.315754381 1.108039521 0.244577292 0.131418109 0.238586015 8.732843082 0.040529141 0.041405857 580.4188894 -2.763741538 -0.20771486 VLSTNTDDNIGGAHFTETLAQYLASEFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLSTNTDDNIGGAHFTETLAQYLASEFQR 29 0 Q0VDF9 Q0VDF9 HSPA14 Heat shock 70 kDa protein 14 0 260.82 3.94E-58 83344000 58651 91727 86424 90886 95576 121600 91719 93761 92544 84693 FALSE TRUE 60966.58677 107480.3987 88676.28044 108862.9795 79330.02566 93360.24287 84529.82512 92504.28716 89213.35952 101286.9718 0.601919336 1.06114732 0.875495425 1.074797455 0.78322043 0.921739896 0.834557729 0.913289098 0.880797974 1 16.62808909 -4.679243721 0.011283734 1.982553522 7.42E-07 0.074107292 0.127157574 37614.16331 33.88714307 3496.74191 2529.340781 2.09E-05 4.679243721 -1.98255278 VLSTS(ph)TDLEAAVADALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 VLSTS(0.995)T(0.005)DLEAAVADALK;VLS(0.003)T(0.032)S(0.943)T(0.022)DLEAAVADALK 352.05 1.08E-87 85222000 301340 193169 253678 221062 320254 315532 313761 237223 267289 161545 TRUE FALSE 313237.1359 226344.2731 260289.0571 264787.4038 265817.3395 242254.4749 289167.593 234043.4137 257669.3211 193196.6498 1.621338342 1.171574524 1.347275211 1.370558983 1.375890005 1.253926894 1.496752626 1.21142584 1.333715266 1 17.55971055 -3.781698599 0.232865348 8.17E-15 1.387603403 0.445459929 0.12218372 77.74079647 1.299270123 36.95236553 0.193169171 0.000165311 3.781698599 1.387603403 VLT(ph)IDPTEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLTIDPTEFK 10 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 1 VLT(0.944)IDPT(0.056)EFK;VLT(1)IDPTEFK 122.33 0.0054944 45369000 236760 134294 201001 148550 308880 265530 264870 202472 223716 121795 TRUE FALSE 246107.4676 157357.9498 206239.2512 177932.7466 256376.6879 203864.6816 244108.7973 199758.194 215664.5049 145658.3983 1.689620855 1.080321846 1.415910469 1.221575609 1.760122937 1.399608151 1.675899228 1.371415561 1.480618401 1 17.15222936 -0.989459766 4.618507601 0.999993422 1.447366829 0.314719184 0.201141444 0.133329593 58147085.92 1302.387912 0.044219123 0.102456669 0.989459766 0.447373407 VLT(ph)PEEQLADKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 VLT(1)PEEQLADKLR;VLT(1)PEEQLADKLR 88.283 0.012901 313860000 573350 357020 477110 403740 612130 634020 641800 516290 537540 313590 TRUE FALSE 595986.3007 418335.4078 489543.8786 483598.567 508080.3612 486778.4637 591494.039 509369.977 518194.0404 375031.9565 1.589161378 1.11546603 1.305339105 1.289486292 1.354765514 1.297965294 1.577183034 1.358204196 1.381733027 1 18.51665401 -1.139847142 5.505360138 0.999993394 1.359228303 0.408370332 0.131088561 1.02E-05 1.59E-06 0.121443796 0.028624051 0.072469098 1.139847142 0.359234908 VLT(ph)PPHDVDSLPHLR ddPTM_MDA-MB-175_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 113.88 0.0012131 78990000 37923 38014 42029 40695 55232 69100 44251 45165 46505 48272 TRUE FALSE 39420.22932 44542.60879 43124.31027 48744.34954 45843.68437 53052.57222 40782.49099 44559.63705 44831.29413 57729.97418 0.68283816 0.77156814 0.747000339 0.844350794 0.794105402 0.918977931 0.706435289 0.771863104 0.776568754 1 15.81703296 -2.636742584 1.968122584 4.928170019 0.78073434 0.524286286 0.063054894 1531589.881 58779.58351 26972743.07 0.015236272 0.002308115 2.636742584 -4.147435679 VLTANSNPSS(ph)PSAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 VLTANSNPS(0.209)S(0.79)PS(0.001)AAK;VLTANSNPS(0.007)S(0.992)PS(0.001)AAK;VLTANSNPS(0.002)S(0.998)PSAAK;VLTANSNPS(0.002)S(0.996)PS(0.002)AAK 352.05 2.23E-82 1133430000 2660800 1885480 2390860 2059650 3005500 3082240 3043070 2542760 2664730 1808480 TRUE FALSE 2765850.439 2209296.523 2453167.776 2467042.623 2494626.184 2366436.472 2804546.222 2508678.461 2568826.888 2162817.031 1.278818504 1.021490256 1.134246559 1.140661733 1.153415267 1.094145477 1.296709884 1.159912478 1.187722702 1 21.04448019 VLTEDEMGHPEIGDAIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 VLTEDEMGHPEIGDAIAR 18 0 P14324-2;P14324;A0A087WVN4;A0A087X1D8;A0A087WTP2 P14324-2 FDPS Farnesyl pyrophosphate synthase 0 ;;;;;;;;; 246.45 2.74E-24 12239970000 4292810 5381610 5360540 5483450 5830950 6150680 5318100 5577690 5163800 5566510 FALSE TRUE 4462293.454 6305859.654 5500240.076 6568060.044 4839807.202 4722277.784 4901253.426 5502930.189 4977955.847 6657161.057 0.670299759 0.947229547 0.826214062 0.986615764 0.727007678 0.709353093 0.736237772 0.826618155 0.747759564 1 22.66647564 4.784472324 22.34665544 0.821799972 0.670297504 0.172740328 0.104464123 17138.47125 8341027.322 0.024614583 11.61202542 60879.6748 -4.784472324 -0.151502468 VLTEIIASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLTEIIASR 9 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 ; 113.74 0.0040745 221130000 375940 513900 483610 481580 517060 626190 429810 489270 466340 550450 FALSE TRUE 390782.4015 602158.3274 496213.2739 576835.0866 429170.3259 480766.8625 396120.3691 482712.1359 449556.5145 658300.1385 0.593623453 0.914716999 0.753779689 0.876249378 0.651937165 0.730315603 0.601732167 0.733270598 0.682905089 1 19.32838598 -1.097271876 3.764671283 1.000105707 0.729954555 0.403298122 0.099722422 28315273.03 48516597.36 37299.8478 0.023287823 0.07993337 1.097271876 -0.270151152 VLTLSDDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ;;;; 221.94 1.20E-08 536941000 477033 627774 588307 629425 620840 709869 597228 623502 571844 681857 FALSE TRUE 495866.6312 735589.3011 603638.7637 753923.3864 515309.8386 545012.6829 550415.7088 615144.9755 551263.4461 815453.8242 0.608086708 0.902061256 0.74024886 0.924544547 0.631930127 0.668355052 0.674980842 0.754359054 0.676020432 1 19.63724366 -1.138189696 4.336233747 1.000048314 0.736313038 0.387109872 0.101290489 4.55E-05 9.05E-06 0.094413485 0.022249401 0.072746199 1.138189696 -0.263735276 VLTLSERPLDFLDLERPPTT(ph)PQNEEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLTLSERPLDFLDLERPPTTPQNEEIR 27 2 Q9GZY8-5;Q9GZY8-2;Q9GZY8;C9JHF5;A0A0A0MS29;Q9GZY8-4;Q9GZY8-3 Q9GZY8-5 MFF Mitochondrial fission factor 1 VLTLSERPLDFLDLERPPT(0.397)T(0.603)PQNEEIR 157.73 1.83E-07 181400000 45863 57156 48424 58997 57605 85564 55027 58349 55183 81866 TRUE FALSE 47673.70665 66972.09839 49685.96922 70666.43051 47813.32268 65693.05773 50713.83995 57566.92709 53196.97461 97906.07528 0.486933079 0.684044358 0.507486068 0.721777789 0.488359099 0.670980402 0.517984607 0.587981154 0.543347024 1 16.57911076 -1.54362761 5.921563414 1.000829667 0.581840507 0.704816458 0.08175928 0.000774529 5.97E-05 0.068467018 0.016107947 0.028600419 1.54362761 -0.41898916 VLTPEEQLADKLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 ;; 222.74 1.55E-11 938190000 520770 542070 526930 424150 718490 701340 545980 570720 566040 613630 FALSE TRUE 541330.4017 635166.3058 540662.2287 508045.604 596361.3264 538464.4139 503184.6609 563070.4319 545668.331 733859.0498 0.73764901 0.865515396 0.736738518 0.692293165 0.812637422 0.733743645 0.685669354 0.767273269 0.743560131 1 19.48514347 -0.687699149 6.623265529 1.000000001 0.753134863 0.682393973 0.050595935 3.59E-10 1.08E-10 0.048156255 0.011350538 0.205258358 0.687699149 -0.246865137 VLTPPHDVDSLPHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLTPPHDVDSLPHLR 15 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 0 151.54 1.73E-06 92611000 26907 42513 34651 29431 35261 43003 39076 31338 32562 38419 FALSE TRUE 27969.30914 49814.27704 35554.03353 35252.36396 29267.34781 33016.20497 36013.12101 30917.96537 31390.09998 45946.46747 0.608736877 1.084180782 0.773814299 0.767248624 0.636987987 0.718579834 0.78380609 0.672912785 0.683188539 1 15.48766633 4.014658874 24.97866223 0.733671164 0.867093493 0.050117297 0.142920432 436.1501184 743186.7496 0.032262278 0.069653029 10343.29412 -4.014658874 0.133422329 VLTSEDEYNLLSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLTSEDEYNLLSDR 14 0 Q9BZQ8 Q9BZQ8 FAM129A Protein Niban 0 128.57 0.00016981 38539000 13790 19400 11328 9497.9 19546 19314 10646 19168 15432 15778 FALSE TRUE 14334.43985 22731.79909 11623.21699 11376.55627 16223.5779 14828.61621 9811.538702 18911.08431 14876.60533 18869.39701 0.759666026 1.204691336 0.615982428 0.60291043 0.85978253 0.78585533 0.519970972 1.002209255 0.788398555 1 14.2037607 1.052312443 1.306038245 0.983714744 0.783481244 0.095331013 0.190079986 1.099341183 3.841736299 0.17834459 0.054750041 11.28008683 -1.052312443 -0.200233499 VLVDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLVDVER 7 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 113.7 0.014125 112057000 145616 180889 160685 161780 185972 205754 162845 164894 158146 195408 FALSE TRUE 151365.0321 211955.2786 164872.5831 193779.6011 154360.5459 157970.7517 150080.7834 162683.8656 152454.3564 233694.4563 0.647704847 0.906976066 0.705504896 0.829200676 0.660522925 0.675971327 0.642209429 0.696139173 0.652366166 1 17.83426399 -1.136224936 3.832770627 1.000137014 0.714767347 0.519447105 0.08281033 18738023.82 35698738.96 32680.78721 0.020498719 0.07307605 1.136224936 -0.285369667 VLVQNAAGS(ph)QEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLVQNAAGSQEK 12 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 VLVQNAAGS(1)QEK 153.09 7.38E-05 77641000 108880 69941 76850 64161 107070 113420 109910 85503 87041 56314 TRUE FALSE 113178.6665 81952.82268 78852.77413 76851.8543 88870.27964 87079.9239 101294.967 84356.97214 83908.41141 67347.6501 1.680513964 1.216862393 1.170831855 1.141121541 1.319575063 1.292991274 1.504060897 1.252559993 1.245899616 1 16.03933999 0.774384566 1.975099694 1.000631403 1.313421492 0.286361357 0.152947276 1.126117301 7.228039467 0.14406015 0.039938289 5.948186356 -0.774384566 0.312790089 VLVTAVY(ph)LALFVVGT(ph)VGNTVTAFT(ph)LARK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VLVTAVYLALFVVGTVGNTVTAFTLARK 28 1 P30989 P30989 NTSR1 Neurotensin receptor type 1 3 VLVTAVY(0.665)LALFVVGT(0.693)VGNT(0.337)VT(0.337)AFT(0.967)LARK 78.837 0.0021071 224310000 281660 204620 295350 143510 453190 366520 262400 270050 371400 312230 TRUE FALSE 292780.1543 239761.8933 303047.0636 171895.8497 376156.9257 281401.2847 241832.4023 266430.4215 358033.3865 373405.4905 0.78408101 0.642095254 0.811576346 0.460346337 1.007368491 0.753607785 0.647640189 0.713515008 0.958832678 1 18.51038362 1.208402971 5.750603904 0.988575394 0.723951804 0.367404482 0.132345291 0.182556445 16.36340219 0.112128243 0.030364651 16.15857176 -1.208402971 -0.26462359 VLVTVEEDDTIMEELVDNHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 VLVTVEEDDTIMEELVDNHGK 21 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;;;;;;;; 389.62 3.66E-131 1709345300 816872 745594 875630 804240 1107179 1109709 1209450 972840 1035545 689231 FALSE TRUE 849122.7373 873643.9696 898449.6371 963316.2716 918981.1091 851995.9026 1114650.149 959800.671 998275.9377 824272.6183 1.030147937 1.059896872 1.089990881 1.168686488 1.114899475 1.033633635 1.352283363 1.164421394 1.211099235 1 19.65276204 2.291607798 24.9999995 1.19790424 1.08751089 0.221874907 0.088654413 123.013113 57972.7664 0.029174279 0.024408933 195.7076481 -2.291607798 -0.110393351 VLVTVEEDDTIMEELVDNHGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VLVTVEEDDTIMEELVDNHGKK 22 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ;;;; 385.57 6.95E-132 1456507000 1116564 815344 1112215 696960 1585159 1311358 1136263 983383 1291841 833385 FALSE TRUE 1160646.809 955372.9895 1141200.237 834816.6078 1315714.239 1006814.978 1047199.737 970202.3594 1245347.895 996670.8346 1.164523701 0.958564208 1.145012171 0.837605134 1.320109101 1.010178028 1.050697683 0.973443112 1.249507713 1 19.92675759 5.195372186 7.302158025 1.057727793 4.017380137 0.049760478 0.135749623 12664.01119 12286.31031 0.029682983 591689.1516 156809.4337 -5.195372186 2.959652344 VLVWDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLVWDLR 7 0 O43684;O43684-2;J3QT28 O43684 BUB3 Mitotic checkpoint protein BUB3 0 ; 105.12 0.018609 419790000 882240 1000190 969360 993860 1427100 1310770 1158180 1022440 975880 1442560 FALSE TRUE 917071.5164 1171964.852 994622.3179 1190442.542 1184522.052 1006363.532 1067398.825 1008735.864 940758.2694 1725202.013 0.53157341 0.67932036 0.576525132 0.69003081 0.686599044 0.583330836 0.618709471 0.58470594 0.545303253 1 20.71833387 -1.543306322 3.059330995 1.015468445 0.613720278 0.819436692 0.054809399 13161400.68 15615645.15 1688391.684 0.012909966 0.028621585 1.543306322 -0.401748167 VLWLADCDVSDSSCSSLAATLLANHSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VLWLADCDVSDSSCSSLAATLLANHSLR 28 0 P13489;H0YCR7 P13489 RNH1 Ribonuclease inhibitor 0 ;;; 401.97 8.01E-166 1207931000 467921 525042 503936 598415 580141 621687 564859 552273 516591 551464 FALSE TRUE 486394.8824 615213.8792 517068.9861 716779.7009 481528.84 477309.616 520583.8756 544870.6838 497998.9908 659512.8124 0.737506343 0.932830823 0.78401659 1.086832109 0.730128105 0.723730619 0.789346114 0.826171491 0.755101313 1 19.33104116 VLYQVEGFVDKNNDLLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VLYQVEGFVDKNNDLLYR 18 1 E9PDF6;O43795;O43795-2;A0A0U1RRI3 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 142.58 1.02E-07 343070000 304850 275320 308340 232790 375890 388040 332710 324280 376910 281500 FALSE TRUE 316885.7134 322604.0683 316375.5937 278835.1672 311996.3521 297923.5908 306631.3208 319933.557 363345.0827 336654.5354 0.941278611 0.958264436 0.939763349 0.828253114 0.926755232 0.884953445 0.910818922 0.950331938 1.07928171 1 18.36090938 1.419037602 4.057951347 1.03819888 0.912873444 0.620536014 0.038933881 0.138964712 3.939312399 0.028584008 0.010134038 26.24445761 -1.419037602 -0.125325436 VMDDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VMDDLDR 7 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 111.01 0.01553 391740000 1203500 1046400 1144000 1003300 1541600 1405100 1260300 1071600 1252300 1124800 FALSE TRUE 1251015.109 1226111.06 1173813.58 1201749.745 1279559.383 1078786.819 1161514.393 1057236.955 1207229.968 1345183.024 0.929996206 0.911482704 0.872605109 0.893372667 0.951215827 0.801962856 0.863461976 0.785942831 0.897446627 1 20.35937105 2.741981964 24.99626214 0.850360718 0.908526555 0.065780026 0.059232348 494.8556588 3615401.806 0.017428649 0.017797522 552.0545119 -2.741981964 0.058165837 VMDQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VMDQHK 6 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ;;;;; 100.82 0.037225 2564360000 3002240 2417070 2351210 2010160 4850730 3506040 3460660 2581000 2815580 3856510 FALSE TRUE 3120770.753 2832182.97 2412484.464 2407763.648 4026204.647 2691815.345 3189404.426 2546405.917 2714247.826 4612119.297 0.676645714 0.614074092 0.523075035 0.522051468 0.872961948 0.583639575 0.691526871 0.552111893 0.588503387 1 22.1369984 -1.869886768 2.654865869 1.170387625 0.622420613 0.563297898 0.099044352 11014296.68 8141041.721 11886922.13 0.02345479 0.013493146 1.869886768 -0.547967012 VMDS(ph)DEDDDY ddPTM_MDA-MB-175_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 167.1 5.61E-06 1470860000 1171740 1178740 1303340 1105290 1508750 1687250 1367240 1386010 1306130 1145230 TRUE FALSE 1218001.2 1381179.426 1337306.111 1323913.063 1252293.214 1295411.758 1260072.156 1367432.803 1259122.636 1369615.892 0.889301305 1.008442903 0.976409604 0.966630915 0.914338992 0.945821209 0.920018644 0.998406058 0.91932537 1 20.38533992 -1.106584284 3.877212083 1.000016189 0.952882548 0.139045263 0.036994656 10226.50824 18252846.49 609.3660319 0.008268402 0.078237635 1.106584284 -0.04713364 VMEGLDAFDDLMQHTHIQPWYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VMEGLDAFDDLMQHTHIQPWYLR 23 0 Q9H7Z7;A6NHH0 Q9H7Z7 PTGES2 Prostaglandin E synthase 2;Prostaglandin E synthase 2 truncated form 0 ; 244.74 1.05E-37 1801940000 784590 818340 752740 832010 793520 931310 683080 654100 681050 748930 FALSE TRUE 815566.219 958883.5292 772357.0228 996579.0947 658637.7538 715027.3666 629538.4047 645332.8594 656539.1435 895668.4944 0.91056705 1.070578607 0.862324652 1.112665122 0.73535885 0.798316979 0.702869877 0.720504141 0.733015784 1 19.77260533 3.221620403 24.99518643 0.760185366 0.985807831 0.478572255 0.104578903 172.5609346 254612.1109 0.027703266 0.033191747 1665.790586 -3.221620403 0.225622465 VMEHFIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VMEHFIK 7 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 114.02 0.0059982 4750000000 7740900 8151300 8276100 8407100 10641800 10913500 8829800 8173100 8111600 7460300 FALSE TRUE 8046516.709 9551222.367 8491781.965 10069999.29 8832910.637 8379005.021 8137697.204 8063552.963 7819665.101 8922002.949 0.901873352 1.070524457 0.951779776 1.128670249 0.990014315 0.939139459 0.912093086 0.903782818 0.876447267 1 23.08893619 2.724299669 3.224965023 0.915533666 1.017063454 0.286028685 0.064865661 0.27309491 5.897213407 0.020461495 0.020243007 530.0290446 -2.724299669 0.101529788 VMES(ph)MLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VMESMLK 7 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 VMES(1)MLK;VMES(1)MLK 62.842 0.055285 646130000 35233 778540 619700 699140 547200 815270 445390 596360 510230 830530 TRUE FALSE 36624.02605 912248.1888 635849.8911 837427.8053 454187.1395 625935.898 410479.168 588366.7696 491866.922 993256.452 0.036872679 0.918441745 0.640166887 0.843113381 0.457270767 0.630185585 0.413266047 0.592361387 0.49520637 1 19.92180673 -1.296917326 3.758391802 1.000954481 0.574184318 0.2451941 0.230902803 81264068.24 106458125.5 834369.0166 0.051184968 0.050475738 1.296917326 -0.426770163 VMEYINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VMEYINR 7 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 164.89 0.0027471 278310000 312520 326020 354960 344080 394860 425750 372360 329380 350560 339440 FALSE TRUE 324858.5309 382011.3989 364210.5492 412137.997 327741.8382 326876.0148 343173.4502 324965.1999 337943.4141 405946.769 0.800249086 0.941038156 0.897187949 1.01525133 0.80735176 0.80521891 0.84536564 0.800511852 0.832482088 1 18.63093104 3.181915542 24.99998849 0.833969831 0.914246056 0.139635306 0.073864037 120.3721402 53124.89965 0.020001521 0.023906405 1520.251857 -3.181915542 0.080276225 VMGLVPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VMGLVPAK 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 ; 115.3 0.0057942 117850000 704170 668650 702880 665910 982650 976830 720820 736670 717730 688910 FALSE TRUE 731971.1753 783485.4361 721197.6302 797625.0105 815619.504 749976.0365 664320.2449 726796.1436 691899.0375 823888.7245 0.88843451 0.950960261 0.875358054 0.968122256 0.989963183 0.910288021 0.806322778 0.882153284 0.839796707 1 19.65208997 2.468778944 24.87500511 0.869373348 0.935660332 0.145400289 0.056727514 255.816025 762782.5368 0.018523834 0.015522652 294.2923307 -2.468778944 0.066286984 VMIGS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VMIGSPK 7 0 Q68CZ2;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 VMIGS(1)PK 65.404 0.090637 0 468240 253450 265550 240520 412700 496410 400880 314100 313290 228480 TRUE FALSE 486726.4768 296978.0659 272470.4512 288094.1381 342549.4014 381126.3007 369457.9781 309890.0033 302014.7541 273246.2815 1.781273927 1.086851262 0.997160692 1.054338733 1.253628776 1.394808737 1.352106152 1.134105107 1.105284041 1 18.05984234 1.315430348 2.199634698 1.025451623 1.250201275 0.149854003 0.211821681 0.652953695 5.333989914 0.193661796 0.057550006 20.67427782 -1.315430348 0.224749651 VMLGETNPADSKPGTIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 192.24 1.80E-10 5866530000 2058220 1699360 2018640 1676950 2459720 2339280 2205090 2006710 2086580 1509170 FALSE TRUE 2139480.115 1991211.861 2071247.417 2008645.705 2041617.673 1796017.672 2032249.284 1979813.335 2011484.393 1804862.967 1.185397537 1.103248223 1.147592618 1.112907596 1.131176001 0.995099188 1.125985364 1.096932771 1.114480396 1 20.78345787 -4.999999996 0.01658281 2.30E-06 1.928796277 0.446328145 0.042477754 4575.602128 5.752559222 428.6637856 259.9514497 1.00E-05 4.999999996 1.928793979 VMQEQGTHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 VMQEQGTHPK 10 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;;;; 150.21 2.20E-05 6652039000 7665600 6586410 8009600 6436200 9375940 9655790 8856170 7898360 8354420 6732260 FALSE TRUE 7968243.807 7717574.682 8218336.756 7709261.15 7782221.068 7413379.107 8162000.254 7792495.403 8053746.056 8051317.45 0.989681981 0.958548055 1.020744345 0.957515487 0.966577348 0.920765968 1.013747167 0.967853454 1.000301641 1 22.94079344 1.311158884 1.391615498 1.000972453 0.972723873 0.108895424 0.027529972 0.889938875 3.26428822 0.024616538 0.007750424 20.47193453 -1.311158884 -0.02824858 VMS(ph)SSNPDLAGTHSAADEEVKNIMSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VMSSSNPDLAGTHSAADEEVKNIMSSK 27 1 Q8NF50-3;Q8NF50;A2A369;Q8NF50-4;Q8NF50-2;A2A370 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 VMS(0.371)S(0.315)S(0.315)NPDLAGTHSAADEEVKNIMSSK;VMS(0.408)S(0.328)S(0.264)NPDLAGTHSAADEEVKNIMSSK 234.39 7.08E-45 136172000 164434 119111 160657 87716 252170 196079 135175 150145 197673 132835 TRUE FALSE 170925.9813 139567.3877 164843.8534 105065.963 209306.2335 150542.6239 124579.6303 148132.5519 190558.7873 158861.475 1.075943562 0.878547727 1.03765783 0.661368422 1.317539281 0.94763456 0.784202906 0.932463657 1.199528 1 17.27740978 1.260533576 24.79165253 1.099764045 0.94761939 0.101797768 0.171745636 396.1163044 446932.5328 0.10957377 0.039937643 18.21937925 -1.260533576 -0.152144655 VMSSS(ph)NPDLAGTHSAADEEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VMSSSNPDLAGTHSAADEEVK 21 0 Q8NF50-3;Q8NF50;A2A369;Q8NF50-4;Q8NF50-2;A2A370 Q8NF50-3 DOCK8 Dedicator of cytokinesis protein 8 1 VMS(0.025)S(0.099)S(0.876)NPDLAGTHSAADEEVK;VMS(0.016)S(0.118)S(0.866)NPDLAGTHSAADEEVK;VMS(0.015)S(0.133)S(0.851)NPDLAGTHSAADEEVK 261.46 7.81E-37 798050000 549890 433650 567620 493490 713010 845450 718770 567830 600440 405110 TRUE FALSE 571600.0818 508126.0142 582412.6435 591100.8491 591812.8149 649107.0504 662430.9292 560219.1676 578830.2817 484483.5482 1.179813193 1.048799316 1.202130899 1.220063821 1.221533357 1.339791728 1.367292928 1.156322376 1.194736713 1 18.88608815 4.073605094 6.70451257 1.229526379 1.114952093 0.123450248 0.099577103 0.343974448 25.1472846 0.024190057 0.052981361 11846.91013 -4.073605094 -0.114574286 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 VMTIPYQPMPAS(0.043)S(0.957)PVICAGGQDR;VMTIPYQPMPAS(0.073)S(0.927)PVICAGGQDR;VMTIPYQPMPAS(0.208)S(0.792)PVICAGGQDR;VMTIPYQPMPAS(0.184)S(0.816)PVICAGGQDR;VMTIPYQPMPAS(0.295)S(0.705)PVICAGGQDR;VMTIPYQPMPAS(0.009)S(0.991)PVICAGGQDR 206.4 8.88E-25 1100980000 809818 898994 847420 874572 919885 1058431 777989 895421 863655 1038330 TRUE FALSE 841790.24 1053389.226 869504.4614 1047559.731 763523.2763 812626.4409 717008.1893 883419.3461 832572.2253 1241770.883 0.677894973 0.848295962 0.700213278 0.843601461 0.614866467 0.654409321 0.577407796 0.711418956 0.670471692 1 20.24396758 -1.069536119 3.785273424 1.000088354 0.700049591 0.542213413 0.082740137 24030270.8 42540713.33 27070.64765 0.020308278 0.085204765 1.069536119 -0.300038763 VMYMGEEHLFSVEQITAMLLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VMYMGEEHLFSVEQITAMLLTK 22 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 98.269 0.00010513 0 13884 8398 9763.7 9436.9 14186 14290 11192 11832 11849 10862 FALSE TRUE 14432.15104 9840.291173 10018.15004 11303.49065 11774.66879 10971.36407 10314.7418 11673.41139 11422.5568 12990.20093 1.11100291 0.757516471 0.771208243 0.870155182 0.906426994 0.844587711 0.794040204 0.898632088 0.879321025 1 13.66513613 0.607417648 1.408933671 0.999757392 0.859857492 0.141414884 0.094621136 2.682168724 7.393592243 0.085318509 0.02506597 4.049651476 -0.607417648 -0.1398999 VNAVPRPIPEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNAVPRPIPEKK 12 2 Q9HD45 Q9HD45 TM9SF3 Transmembrane 9 superfamily member 3 0 ; 109.18 0.00091457 837220000 2150880 1255840 1607980 1447640 2272250 2437680 2015060 1580170 1712300 1287260 FALSE TRUE 2235798.403 1471520.751 1649885.28 1733978.871 1886013.757 1871565.763 1857114.332 1558990.406 1650674.657 1539473.951 1.452313241 0.955859467 1.071720167 1.126345055 1.225102741 1.215717721 1.206330468 1.012677353 1.072232925 1 20.55400603 1.715007984 7.682068477 1.033270649 1.1674085 0.240321109 0.12130344 0.1909724 27.96563514 0.058215487 0.03064726 51.88095767 -1.715007984 0.134137851 VNCLDKFWHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNCLDKFWHK 10 1 Q14847;Q14847-2;F6S2S5;K7ESD6 Q14847 LASP1 LIM and SH3 domain protein 1 0 81.017 0.013383 1453000000 541680 614100 620210 496460 891140 778900 558970 671550 639310 695350 FALSE TRUE 563065.9447 719566.898 636373.1821 594658.3062 739664.3411 598012.2793 515156.4708 662548.9707 616301.358 831590.5192 0.677095195 0.865289925 0.765248241 0.715085481 0.8894574 0.719118683 0.619483338 0.796725017 0.741111573 1 19.66551378 -1.118336757 4.046054204 1.000062948 0.756696718 0.476476366 0.077229328 12475774756 45108668110 13694290.69 0.018035465 0.076148831 1.118336757 -0.24336623 VNDAEPGS(ph)PEAPQGK ddPTM_MDA-MB-175_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 313.66 3.22E-56 2106350000 3273590 2140560 2877790 2217350 3451850 3640080 3433990 2829810 2971440 1851900 TRUE FALSE 3402833.861 2508184.529 2952787.572 2655935.212 2865105.77 2794726.586 3164824.891 2791881.026 2864498.455 2214744.348 1.536445443 1.132493929 1.33324082 1.199206226 1.293650787 1.261873222 1.42897978 1.260588396 1.293376573 1 21.07870874 0.269927865 1.825632655 0.999986804 1.299426627 0.420091753 0.107205925 11.81104799 28.19744821 0.093037822 0.02589489 1.861777874 -0.269927865 0.299439823 VNDDIIVNWVNETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNDDIIVNWVNETLR 15 0 P13796;P13796-2 P13796 LCP1 Plastin-2 0 171.76 2.48E-06 31485000 31452 38726 30531 46192 75362 78367 75002 45814 45044 58853 FALSE TRUE 32693.74925 45376.88925 31326.66294 55328.63973 62551.99416 60167.45191 69123.14726 45199.93827 43422.87524 70384.11854 0.464504634 0.644703524 0.445081413 0.786095512 0.88872313 0.854844149 0.982084435 0.642189448 0.61694138 1 16.10296232 3.676104097 6.680593922 0.81401115 0.531233545 0.544762918 0.12797216 0.197188087 17.51253397 0.035162642 0.054985564 4743.556705 -3.676104097 -0.282777605 VNDGGGSHPSRPNSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNDGGGSHPSRPNSR 15 1 F8VRJ4;A0A5K1VW50;P11473;P11473-2 F8VRJ4 VDR Vitamin D3 receptor 0 62.377 0.049025 11517000 3274.5 10653 10431 10156 10119 14701 6838.7 9875.3 9755.5 12269 FALSE TRUE 3403.779788 12482.56988 10702.84043 12164.82649 8398.975994 11286.91555 6302.664824 9742.937756 9404.401461 14672.87565 0.231977689 0.850724165 0.729430324 0.82906901 0.572415128 0.769236775 0.429545304 0.664010109 0.640937856 1 13.84086402 -1.822932568 2.080783075 1.152111398 0.644645992 0.270131076 0.17926538 2398545.125 1207715.22 1823089.325 0.044412164 0.015033754 1.822932568 -0.507465406 VNDKEVSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNDKEVSDR 9 1 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 0 ; 62.303 0.076158 149415000 231760 214600 232590 202835 341110 322600 317390 239940 243900 210040 FALSE TRUE 240910.0638 251455.8806 238651.4865 242955.1576 283128.244 247681.0391 292512.1425 236723.9968 235122.0866 251193.3165 0.959062395 1.001045267 0.950071004 0.967203909 1.127132871 0.986017632 1.164490148 0.942397672 0.936020472 1 17.93843855 VNFDDYTVNLGGLKDHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNFDDYTVNLGGLKDHIK 18 1 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ; 282.06 1.40E-39 1145900000 1783740 1044380 1457230 1098110 1940590 1779600 1892140 1452610 1735390 893610 FALSE TRUE 1854163.433 1223744.141 1495206.611 1315312.88 1610729.205 1366314.87 1743829.123 1433140.139 1672933.653 1068695.77 1.734977796 1.14508186 1.399094721 1.230764561 1.507191522 1.278488142 1.631735777 1.341017883 1.565397468 1 20.02741978 -0.999843863 4.535617725 0.999987993 1.412833844 0.341351012 0.176666133 1.92E-05 4.24E-06 0.153495675 0.036178226 0.100035958 0.999843863 0.412845851 VNFEDDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 201.07 0.00026684 2518420000 3433190 4013700 4026680 3950790 4356990 4821250 4114010 4204830 3815460 3638870 FALSE TRUE 3568734.992 4703021.753 4131618.589 4732244.47 3616390.396 3701587.754 3791543.146 4148471.132 3678142.34 4351836.906 0.820052559 1.080698072 0.949396468 1.087413102 0.8310032 0.850580533 0.871251204 0.953268981 0.845193057 1 22.05319306 3.223948038 24.99611555 0.890660042 0.988769681 0.221986287 0.08466491 325.0478605 556022.1145 0.023119666 0.027745793 1674.742485 -3.223948038 0.098109639 VNFNDCS(ph)FDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNFNDCSFDLK 11 0 A0A087WVX1;P0C875 A0A087WVX1 FAM228B Protein FAM228B 1 VNFNDCS(1)FDLK;VNFNDCS(1)FDLK 69.01 0.03586 56757000 7456.4 69486 51278 74845 38312 81529 24474.1 54555 48258 99583 TRUE FALSE 7750.78443 81419.67997 52614.34681 89649.11761 31799.73992 62595.12533 22555.75609 53823.77946 46521.20401 119094.3822 0.065081025 0.683656764 0.441786975 0.752756897 0.26701293 0.525592594 0.189393955 0.45194222 0.390624672 1 16.86174584 -1.186815074 3.517675094 1.000783906 0.427452686 0.433251677 0.199244174 93487814.49 150723698.9 820484.5642 0.046786074 0.065040658 1.186815074 -0.573331219 VNFPENGFLS(ph)PDKLSLLEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNFPENGFLSPDKLSLLEK 19 1 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 1 VNFPENGFLS(1)PDKLSLLEK 208.89 1.51E-16 319750000 848140 352900 473800 322350 775410 832000 711720 525350 633570 296690 TRUE FALSE 881625.2221 413507.8298 486147.6172 386109.8679 643606.0852 638780.6091 655933.5267 518308.5425 610767.9395 354820.725 2.484706106 1.165399315 1.370121819 1.088182963 1.813890903 1.800291144 1.848633635 1.460761748 1.721342347 1 18.43673075 -1.421020016 5.433130467 0.999564612 1.608964747 0.197315297 0.382435273 0.001932684 0.000205957 0.35479527 0.0835688 0.03792975 1.421020016 0.609400136 VNGDAS(ph)PAAAESGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK 259.34 7.77E-25 1228590000 3009520 1726450 2440700 1999430 3245420 3330380 3620200 2508960 2645430 1357320 TRUE FALSE 3128338.173 2022954.358 2504306.647 2394911.286 2693764.668 2556949.717 3336439.264 2475331.495 2550221.491 1623260.867 1.927193736 1.246228748 1.542762903 1.475370555 1.659477366 1.575193347 2.055393149 1.524912937 1.571048464 1 20.63046344 0.582011234 2.221504769 1.000116132 1.62008386 0.429713042 0.215083526 3.269545637 16.23041877 0.200276291 0.054298046 3.819541509 -0.582011234 0.619967728 VNGDDHHEEDMDMS(ph)D ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VNGDDHHEEDMDMSD 15 0 Q05519-2;Q05519;Q5T757 Q05519-2 SRSF11 Serine/arginine-rich splicing factor 11 1 VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D;VNGDDHHEEDMDMS(1)D 304.03 5.66E-44 9036906000 3129928 3568199 3847228 3522390 4232024 4753417 4142908 3804828 3948129 3458186 TRUE FALSE 3253499.974 4181009.422 3947489.922 4219108.229 3512666.072 3649507.94 3818176.045 3753830.504 3806036.609 4135751.336 0.786676884 1.010943135 0.954479513 1.020155199 0.8493417 0.882429248 0.923212189 0.907653821 0.920276946 1 21.97971801 0.086470468 15.18076552 1 0.920466876 0.121584403 0.066225173 0 0 0.061270891 0.014441687 1.220310836 -0.086470468 -0.079533124 VNGRPLEMIEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VNGRPLEMIEPR 12 1 P62249;M0R3H0;M0R1M5;Q6IPX4 P62249 RPS16 40S ribosomal protein S16 0 ;;;;; 145.6 5.40E-05 4189630000 3166390 3881590 3869200 3587720 4768230 4783130 3929840 4076590 3971520 4112420 FALSE TRUE 3291401.522 4548222.888 3970034.531 4297360.308 3957727.968 3672320.547 3621808.872 4021949.979 3828585.771 4918169.962 0.669232976 0.924779526 0.807217839 0.873772224 0.804715575 0.746684351 0.73641393 0.817773686 0.778457394 1 22.22969016 -0.925510806 5.416625594 1.000000303 0.799537976 0.450132924 0.067687837 2.35E-07 4.67E-08 0.062147798 0.014648354 0.118710516 0.925510806 -0.200462327 VNGTSS(ph)PQSPLSTSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNGTSSPQSPLSTSGR 16 0 Q96KQ4;A0A3B3ISJ2 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 VNGTS(0.005)S(0.995)PQSPLSTSGR 225.01 7.93E-14 0 171890 186300 182270 165480 213290 246300 185220 171450 187280 157600 TRUE FALSE 178676.3499 218295.5758 187020.1059 198211.4501 177035.042 189100.5577 170701.9724 169151.9932 180539.8294 188478.7026 0.947992253 1.158197573 0.992261212 1.051638447 0.939284065 1.003299339 0.905683083 0.897459452 0.957879203 1 17.52404199 3.131059042 1.318081045 0.933455625 1.049080938 0.284567816 0.061692946 0.427803372 1.563375304 0.021982298 0.029925202 1352.256389 -3.131059042 0.115625314 VNGTSSPQS(ph)PLSTSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNGTSSPQSPLSTSGR 16 0 Q96KQ4;A0A3B3ISJ2 Q96KQ4 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 VNGTS(0.001)S(0.008)PQS(0.982)PLS(0.003)T(0.003)S(0.003)GR;VNGTSS(0.001)PQS(0.999)PLSTSGR 107.03 0.0012168 115550000 99210 105127 117693 102486 152683 172783 136248 130706 135510 128225 TRUE FALSE 103126.8874 123181.7445 120760.1763 122757.4249 126729.9982 132656.7668 125568.5257 128954.0999 130633.0216 153348.2337 0.672501306 0.803281143 0.787489841 0.80051411 0.82641968 0.865068763 0.818845595 0.840923281 0.851871707 1 17.22645202 -5 0.028071837 2.166921584 6.67E-16 0.815670827 0.032964362 693.3919197 1.46740204 85.87194971 36.88478491 1.00E-05 5 -2.166921584 VNHPGSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNHPGSK 7 0 P80303-2;P80303;E9PKG6;Q2L696;H0YEG8 P80303-2 NUCB2;Nucb2 Nucleobindin-2;Nesfatin-1 0 ; 98.997 0.010852 400260000 320000 340590 356730 417500 634910 583670 480560 410400 404750 563130 FALSE TRUE 332633.8471 399083.6831 366026.6769 500080.2539 526988.225 448121.4881 442892.4515 404899.2593 390183.1266 673464.5417 0.493914418 0.592583066 0.543498067 0.74254875 0.782503298 0.665397301 0.657632918 0.601218378 0.579366993 1 19.36124246 -2.386112578 2.30511318 3.848520529 0.633111537 0.642619123 0.083001624 3525905.554 413314.4696 52467339.97 0.021655522 0.004110432 2.386112578 -3.215408992 VNIAFNYDMPEDSDTYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VNIAFNYDMPEDSDTYLHR 19 0 Q13838-2;Q13838;Q5STU3;A0A0G2JJZ9;A0A140T9X3;H0Y400 Q13838-2 DDX39B Spliceosome RNA helicase DDX39B 0 ;;;;;; 191.07 7.92E-15 2902080000 1853687 2173708 2161193 2179550 2445422 2858090 2251393 2239618 2039481 2278884 FALSE TRUE 1926871.994 2547025.44 2217515.465 2610658.485 2029750.042 2194341.912 2074922.934 2209599.584 1966080.477 2725387.688 0.707008402 0.934555275 0.813651384 0.957903529 0.744756444 0.805148538 0.761331293 0.810746887 0.721394789 1 21.37803004 3.196459899 24.99999344 0.795643076 0.856255448 0.044180475 0.095871188 345.9848356 205449.4654 0.025287287 0.030224341 1572.026632 -3.196459899 0.060612372 VNIEGGAIALGHPLGASGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNIEGGAIALGHPLGASGCR 20 0 Q9BWD1;Q9BWD1-2 Q9BWD1 ACAT2 "Acetyl-CoA acetyltransferase, cytosolic" 0 142.99 1.73E-07 277080000 56919 80079 66507 90211 85935 112730 85605 90472 73260 79309 FALSE TRUE 59166.20607 93831.94532 68240.22706 108054.4665 71327.7994 86550.16594 78895.05641 89259.37082 70623.38691 94848.08009 0.623799723 0.989286712 0.719468723 1.139237257 0.752021541 0.912513631 0.831804464 0.941077255 0.744594797 1 16.53333095 4.753032376 24.01438997 0.888636883 0.623799402 0.288147022 0.126456494 1768.892983 2935207.142 0.026784228 0.559804852 56628.15031 -4.753032376 -0.264837482 VNIGQGSHPQKVKVFGPGVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNIGQGSHPQKVKVFGPGVER 21 2 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 190.37 1.10E-17 472220000 502310 339690 438550 322150 777520 578070 532800 447160 387970 430040 FALSE TRUE 522141.5867 398029.1151 449978.9733 385870.3085 645357.4281 443822.0032 491037.7438 441166.5516 374007.0355 514298.1044 1.015250848 0.773926856 0.874938036 0.750285302 1.254831435 0.862966438 0.954772611 0.857803184 0.727218382 1 18.97224531 -1.299741474 3.619986385 1.000287561 0.897488728 0.042777619 0.146303387 608642.7464 67589522.95 34112.19499 0.032848746 0.050148567 1.299741474 -0.102798833 VNIKPQVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VNIKPQVDR 9 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ;;;; 140.17 0.00010008 12135680000 12238520 10550270 11856260 11442400 16050740 15896450 14920520 13306690 13302050 10553440 FALSE TRUE 12721706.22 12362196.8 12165243.88 13705672.57 13322440.95 12204740.4 13751010.65 13128335.59 12823311.82 12621184.51 1.007964523 0.979479921 0.963874973 1.085926012 1.055561856 0.967004356 1.089518234 1.040182526 1.016014924 1 23.58934398 3.757085827 24.96405408 1.039227833 0.983343815 0.301829928 0.036430202 931.0862454 1254702.788 0.009167121 0.016491542 5715.915859 -3.757085827 -0.055884018 VNIVDLQQVINVDLIHIENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNIVDLQQVINVDLIHIENR 20 0 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 0 118.37 6.66E-05 39705000 27328 25497 24185 25622 26872 33732 29614 28577 29791 23731 FALSE TRUE 28406.93054 29875.91141 24815.28097 30689.95513 22304.30704 25898.25421 27292.7773 28193.97206 28718.82773 28380.63509 1.000926528 1.0526865 0.874373702 1.081369569 0.785898799 0.912532582 0.961669012 0.993422873 1.011916317 1 14.79261925 -0.451267432 6.637547393 1.00000218 0.962703041 0.016672933 0.082816311 0 0 0.07730542 0.018221062 0.353779422 0.451267432 -0.037299139 VNIVFNYDMPEDSDTYLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNIVFNYDMPEDSDTYLHR 19 0 O00148 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 ; 128.14 2.20E-05 455170000 184913 244220 225533 214184 245070 282370 255430 242910 220672 252100 FALSE TRUE 192213.508 286162.8852 231410.5753 256548.9559 203413.0889 216793.8469 235408.7292 239654.1888 212730.0578 301494.1683 0.637536405 0.94914899 0.767545776 0.850925102 0.674683328 0.71906481 0.780806908 0.794888306 0.705585979 1 18.20177057 -1.34478191 5.432550324 1.00006311 0.771120998 0.404612483 0.085372067 6.10E-05 7.36E-06 0.077306575 0.018216323 0.045208291 1.34478191 -0.228942112 VNKDDIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VNKDDIQK 8 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ;;; 121.73 0.0012956 9626600000 17778800 10105700 14072700 10153300 20828400 18259100 19477200 14601500 17541800 8483100 FALSE TRUE 18480720.75 11841275.36 14439446.12 12161592.44 17287996.01 14018700.74 17950526.17 14405790.78 16910474.04 10145201.03 1.821621938 1.167179964 1.423278463 1.198753224 1.704056525 1.381806108 1.769361309 1.419961097 1.666844649 1 23.27429412 -1.308040071 5.908847352 0.99995983 1.492711356 0.325282346 0.217830697 0.000106625 1.25E-05 0.195086784 0.045978662 0.049199414 1.308040071 0.492751527 VNLEESSGVENS(ph)PAGARPK ddPTM_MDA-MB-175_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 299.94 4.33E-50 1122570000 668960 485460 653500 503220 750560 804430 709610 548630 616430 441860 TRUE FALSE 695371.0573 568833.9786 670530.7469 602755.414 622980.0793 617613.3238 653988.914 541276.5122 594244.8047 528434.0071 1.315908984 1.076452255 1.268901581 1.140644633 1.178917464 1.168761502 1.237598083 1.02430295 1.124539293 1 19.01136379 1.725963159 9.030426984 1.057591679 1.192074999 0.482930592 0.070027758 0.088643445 22.53418072 0.030336529 0.016277681 53.20631229 -1.725963159 0.13448332 VNLFPGLS(ph)PSALK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VNLFPGLS(0.886)PS(0.114)ALK;VNLFPGLS(0.85)PS(0.15)ALK 93.768 0.0057302 732750000 2823800 1863100 2314200 1966910 2849100 2829500 2526400 2326300 2348900 1846750 TRUE FALSE 2935285.804 2183072.932 2374509.953 2355958.927 2364811 2172391.506 2328374.166 2295119.754 2264363.548 2208585.304 1.329034382 0.988448546 1.075127118 1.066727612 1.07073564 0.983612226 1.054237825 1.03918094 1.025255191 1 21.07469113 4.744513588 24.97113188 1.037808439 1.329034511 0.881365828 0.032474156 198.6464572 833244.8637 0.007427877 0.067899822 55528.19909 -4.744513588 0.291226072 VNLFTDFDKYMTISDEWDIPEKQPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNLFTDFDKYMTISDEWDIPEKQPFK 26 2 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 114.88 0.0007345 26620000 28414 17419 25359 14931 35386 28028 25971 22180 27858 14057 FALSE TRUE 29535.80666 20410.57775 26019.87637 17884.30724 29371.10036 21518.92177 23935.32516 21882.71338 26855.39602 16811.20001 1.756912454 1.214105937 1.547770317 1.063832875 1.747115039 1.280034843 1.423772553 1.301674679 1.597470496 1 14.03713509 -1.10963192 4.467520252 0.999956023 1.417799225 0.263159969 0.217233443 8.39E-05 1.67E-05 0.185388995 0.043692015 0.077690529 1.10963192 0.417843202 VNLS(ph)PNRNQSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VNLSPNRNQSAK 12 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 VNLS(1)PNRNQSAK;VNLS(1)PNRNQSAK;VNLS(1)PNRNQSAK 167.29 3.01E-05 592406000 463026 416185 488998 299504 662099 564405 377204 460276 562550 531695 TRUE FALSE 481306.624 487661.5363 501741.6896 358744.9973 549555.6485 433330.4924 347637.7648 454106.7531 542303.9354 635870.4553 0.756925597 0.766919633 0.789062749 0.564179377 0.864257246 0.68147606 0.546711617 0.714149791 0.852852858 1 19.27837335 1.020347023 3.101622165 0.997912846 0.706587053 0.502015491 0.091927221 0.179905264 3.998975225 0.087456962 0.02300007 10.47965591 -1.020347023 -0.291325793 VNMEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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 ;;;; 107.59 0.017314 797602000 1699900 1989670 1872810 1837700 2430630 2506960 2097690 1925460 1949860 2292400 FALSE TRUE 1767013.365 2331380.345 1921616.967 2201191.575 2017472.381 1924756.533 1933267.577 1899652.358 1879684.919 2741551.889 0.644530338 0.850387094 0.70092307 0.802899841 0.735886995 0.702068249 0.70517271 0.692911327 0.685628066 1 21.38656135 -0.792181894 5.689477753 1.000000037 0.726206269 0.67763163 0.056997275 2.55E-08 5.37E-09 0.052591539 0.012395943 0.161368256 0.792181894 -0.273793767 VNMS(ph)KYDAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNMSKYDAAR 10 1 Q86UK0-2;Q86UK0 Q86UK0-2 ABCA12 ATP-binding cassette sub-family A member 12 1 VNMS(0.997)KY(0.003)DAAR 69.864 0.084494 362580000 181340 165530 198330 172950 251060 234050 196270 199180 205260 170320 TRUE FALSE 188499.4432 193958.4899 203498.6427 207158.9938 208384.9109 179695.4346 180885.8445 196510.3179 197872.7327 203690.943 0.925418874 0.952219509 0.999055921 1.017026043 1.023044558 0.882196488 0.888040685 0.96474745 0.971436087 1 17.63602231 2.75070827 24.9985615 0.936843986 0.984366452 0.188354877 0.04314937 1248.167722 2568594.433 0.014040602 0.014799947 563.259169 -2.75070827 0.047522467 VNNGNTAPEDS(ph)SPAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNNGNTAPEDSSPAKK 16 1 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 VNNGNTAPEDS(0.619)S(0.381)PAKK 89.344 0.0035663 247910000 121750 44763 65415 44931 103860 100660 84658 66757 65684 29822 TRUE FALSE 126556.784 52450.69704 67119.76864 53818.21769 86205.9143 77283.24052 78022.28475 65862.23161 63320.04567 35665.04992 3.548481897 1.470646954 1.881947979 1.508990393 2.417097817 2.166918052 2.187639858 1.846688334 1.775408861 1 15.12222337 -1.664533105 0.220745112 5.65E-19 2.278943265 0.304805566 0.542931524 35.52532646 1.33806535 20.91262147 1.145392399 0.021650448 1.664533105 2.278943265 VNNGNTAPEDSS(ph)PAKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNNGNTAPEDSSPAKK 16 1 G3V167;Q9UGN5-2;Q9UGN5;E9PJ27 G3V167 PARP2 Poly [ADP-ribose] polymerase 2 1 VNNGNTAPEDS(0.229)S(0.771)PAKK 145.17 7.63E-07 151370000 148690 56062 84047 55463 115570 133680 124390 87525 91872 38629 TRUE FALSE 154560.396 65690.2124 86237.33387 66433.41586 95925.45268 102634.8459 114639.9868 86351.87054 88565.54467 46197.61295 3.345635978 1.421939538 1.866705406 1.438027024 2.076415783 2.221648249 2.481513209 1.869184683 1.917102184 1 15.49553069 4.749937016 24.58910122 1.878695187 3.345637067 0.550676618 0.411913675 1060.871183 2292926.543 0.096245514 1.488818858 56225.97766 -4.749937016 1.46694188 VNNVVWDLDRPLEEDCTLELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNNVVWDLDRPLEEDCTLELLK 22 1 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 ; 246.16 5.61E-31 83358000 104637 76264 86119 97838 107535 122478 129045 101535 105587 57661 FALSE TRUE 108768.1496 89361.74875 88363.33189 117190.0644 89256.23911 94034.34067 118930.1157 100174.0894 101786.9445 68958.56896 1.577297081 1.295875916 1.281397413 1.699427151 1.294345872 1.363635326 1.724660437 1.452670653 1.476059408 1 16.07344222 VNPCIGGVILFHETLYQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VNPCIGGVILFHETLYQK 18 0 H3BPS8;P04075;J3KPS3;P04075-2;H3BQN4;H3BUH7;H3BR04;H3BMQ8;H3BU78 H3BPS8;P04075 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 ;;; 258.61 1.15E-30 7524213000 1316116 1414349 1498446 1597504 2083873 2267293 2057162 1784549 1717203 1379763 FALSE TRUE 1368077.276 1657252.439 1537496.734 1913485.523 1729657.012 1740748.562 1895916.267 1760630.04 1655401.199 1650101.143 0.829086921 1.004333853 0.931759087 1.159617113 1.048212723 1.054934462 1.148969732 1.066983104 1.003211959 1 20.65412303 5.013987369 0.948093024 1.071749105 0.599711404 0.554090479 0.061669611 2.203909658 1.107385733 0.018473224 1.204478492 103273.137 -5.013987369 -0.4720377 VNPFRPGDSEPPPAPGAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNPFRPGDSEPPPAPGAQR 19 1 Q15942;H0Y2Y8;C9IZ41 Q15942 ZYX Zyxin 0 ; 149.34 7.89E-08 851640000 260330 312120 264980 308190 314820 366840 305050 278970 302970 299660 FALSE TRUE 270608.0294 365724.182 271885.5965 369149.0621 261307.0089 281646.9695 281139.3839 275230.8635 292066.1689 358372.6397 0.75510237 1.020513682 0.758667282 1.030070439 0.72914888 0.785905335 0.784488973 0.768001887 0.814978982 1 18.45110097 3.203921647 24.99999143 0.796828022 0.89087499 0.095699333 0.109263915 318.1504448 229617.8876 0.028536268 0.034108872 1599.269471 -3.203921647 0.094046968 VNPHKVS(ph)PASSVDSNIPSSQGYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNPHKVSPASSVDSNIPSSQGYKK 24 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 VNPHKVS(0.991)PAS(0.008)S(0.001)VDSNIPSSQGYKK 235.63 1.14E-37 326460000 650330 366940 576720 311520 806430 684870 638940 590210 688640 332580 TRUE FALSE 676005.5306 429959.0906 591749.797 373137.7262 669353.3166 525819.3218 588858.2132 582299.2003 663855.9809 397742.6834 1.699605194 1.080998114 1.487770415 0.938138505 1.682880276 1.322008786 1.480500429 1.464009835 1.669058939 1 18.60147587 2.23898028 24.98281348 1.445784455 1.355635964 0 0.272733698 54.04820651 3217855.275 0.091138339 0.071919292 173.3725273 -2.23898028 -0.090148491 VNPTVFFDIAVDGEPLGR ddPTM_MDA-MB-175_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 ;;; 220.21 1.75E-18 799276000 182418.9 247057 243296.5 203981 226065.9 283307 193187.2 218358 224022 268137 FALSE TRUE 189620.939 289487.1179 249637.0067 244327.833 187639.2991 217513.2428 178044.6825 215431.2682 215959.492 320673.3114 0.591321237 0.902747774 0.778477653 0.761921321 0.585141614 0.678301671 0.555221392 0.671809161 0.673456394 1 18.29074476 -1.114340901 3.336183774 1.000342058 0.689281657 0.471144489 0.098939408 15384924.02 23711099.21 57426.31863 0.024712703 0.076852695 1.114340901 -0.311060402 VNQSALEAVTPS(ph)PSFQQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 VNQSALEAVT(0.005)PS(0.995)PSFQQR;VNQSALEAVT(0.057)PS(0.943)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVT(0.01)PS(0.99)PSFQQR;VNQSALEAVT(0.006)PS(0.723)PS(0.271)FQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVTPS(1)PSFQQR;VNQSALEAVT(0.448)PS(0.545)PS(0.007)FQQR;VNQSALEAVTPS(0.999)PS(0.001)FQQR 410 2.52E-147 8786341000 2949665 3166751 3228823 3143425 3721180 3909375 3080374 3247807 3048564 2660133 TRUE FALSE 3066120.052 3710615.85 3312968.78 3765185.083 3088655.153 3001481.903 2838926.237 3204275.46 2938846.777 3181335.13 0.963784049 1.166370627 1.041376857 1.183523561 0.970867584 0.943466117 0.892369436 1.007210913 0.923777803 1 21.60120093 3.107034991 8.088162978 0.953616632 1.090611063 0.498011727 0.065327071 0.186004135 12.80768664 0.01755351 0.021019025 1279.484387 -3.107034991 0.136994431 VNRNSGS(ph)CLGGDEIFLLCDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VNRNSGSCLGGDEIFLLCDK 20 1 Q04206;Q04206-4;Q04206-2;A0A087X0W8;E9PKH5;Q2TAM5;Q04206-3;A0A087WVP0;E9PKV4 Q04206 RELA Transcription factor p65 1 VNRNS(0.445)GS(0.555)CLGGDEIFLLCDK 56.947 0.052495 45228000 45746 34581 40321 38864 47066 57882 52922 49638 46122 43392 TRUE FALSE 47552.0874 40520.01775 41371.79838 46551.1832 39065.73813 44439.78271 48773.83535 48972.6838 44462.07823 51893.83161 0.916334098 0.780825321 0.797239231 0.897046561 0.752801189 0.856359635 0.93987732 0.943709152 0.856789272 1 15.66327544 2.341967431 4.468249962 0.932059806 0.826287999 0.44018034 0.056621673 0.194025938 6.761620475 0.019308931 0.015830665 219.7695055 -2.341967431 -0.105771808 VNS(ph)GDTEVGSSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 VNS(0.995)GDT(0.005)EVGSSLLR;VNS(0.968)GDT(0.032)EVGSSLLR;VNS(0.976)GDT(0.024)EVGSSLLR;VNS(0.994)GDT(0.006)EVGSSLLR 273.43 5.47E-33 428886000 632977 502196 598246 566383 800360 1008070 870700 636650 673824 444611 TRUE FALSE 657967.4207 588444.2565 613836.7822 678411.8669 664315.0931 773961.0199 802452.2588 628116.7481 649573.2059 531724.0129 1.237422807 1.106672338 1.154427424 1.275872164 1.249360715 1.455569057 1.509151815 1.181283397 1.221636018 1 19.02031809 3.677481673 3.819155905 1.294226304 1.159365406 0.09155249 0.137054687 0.434398193 12.7437983 0.037413594 0.062084432 4758.627094 -3.677481673 -0.134860897 VNS(ph)KEDTEAQGIFIDLSK ddPTM_MDA-MB-175_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 347740000 10832 267570 145670 211970 97442 245210 67884 160360 101050 323410 TRUE FALSE 11259.65572 313523.0661 149466.2799 253897.0333 80878.84365 188263.6937 62563.0747 158210.6365 97413.23024 386775.9974 0.029111568 0.810606315 0.386441457 0.656444648 0.209110297 0.486751233 0.161755319 0.40904978 0.251859554 1 18.56113874 -1.323074378 3.462403925 1.002739498 0.389388941 0.413842133 0.221731607 159388766.6 237380122.7 4539005.708 0.050347488 0.047525383 1.323074378 -0.613350557 VNTLIRPDGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNTLIRPDGEK 11 1 P62750;H7BY10;K7EJV9;K7ERT8;A8MUS3;K7EMA7 P62750 RPL23A 60S ribosomal protein L23a 0 ; 114.7 0.0011141 442360000 448620 424960 463790 426780 605940 632900 637270 552340 548010 421950 FALSE TRUE 466331.864 497943.5743 475876.7484 511195.8102 502942.5352 485918.5667 587319.1122 544936.7857 528287.2271 504623.0238 0.924119277 0.986763486 0.943034158 1.013025142 0.996669814 0.962933802 1.163876963 1.079888868 1.046894815 1 18.94484651 2.265545901 24.99920792 1.082403064 0.973596762 0.543452646 0.045223393 147.9131008 137026.4775 0.015169244 0.01268832 184.3087275 -2.265545901 -0.108806303 VNVEHMTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VNVEHMTEK 9 0 P17858;P17858-2 P17858 PFKL "ATP-dependent 6-phosphofructokinase, liver type" 0 ; 147.74 9.17E-05 679990000 1155760 1170030 1415760 1154820 1934310 1810960 1633140 1407090 1492720 1284300 FALSE TRUE 1201390.297 1370973.551 1452655.869 1383239.949 1605516.677 1390391.985 1505130.219 1388230.26 1438997.299 1535933.996 0.782188753 0.892599262 0.94578014 0.900585542 1.045303172 0.905242015 0.979944596 0.903834581 0.936887459 1 20.55068479 4.864757621 1.437546929 0.949617871 0.673943464 0.585793467 0.043834814 1.103602283 1.660191822 0.011213393 0.474353331 73241.56599 -4.864757621 -0.275674407 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 VNVTVDYIRPAS(0.995)PAT(0.005)ETVPAFSER;VNVTVDYIRPAS(0.989)PAT(0.011)ETVPAFSER;VNVTVDYIRPAS(0.996)PAT(0.003)ET(0.001)VPAFSER 248.88 2.25E-38 1794540000 758817 904404 861891 837505 923512 1065211 939892 838487 890318 766744 TRUE FALSE 788775.6811 1059728.352 884352.5875 1003160.989 766533.7601 817831.8887 866220.8091 827248.4533 858275.6291 916972.8066 0.860195281 1.155681329 0.964426187 1.093992081 0.835939468 0.891882379 0.944652669 0.902151566 0.935988094 1 19.80651942 3.241076309 24.99978019 0.913458313 1.024499432 0.258468624 0.082592542 78.19086272 777016.4466 0.02133139 0.027595281 1742.11295 -3.241076309 0.11104112 VNYEEFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VNYEEFAR 8 0 Q9NZT1 Q9NZT1 CALML5 Calmodulin-like protein 5 0 ;; 214.25 0.00014213 966490000 729640 802620 770020 811490 874740 998540 927600 833750 783950 726260 FALSE TRUE 758446.7506 940463.7415 790087.3538 972000.2999 726052.0072 766644.218 854892.2882 822574.945 755735.7926 868556.7419 0.873226485 1.082789064 0.909655427 1.119098216 0.835929275 0.882664518 0.984267633 0.947059536 0.870105263 1 19.72826058 3.219683705 24.99997314 0.922127013 0.996196666 0.170896421 0.082131008 425.9203874 564073.9759 0.022414396 0.026831955 1658.378676 -3.219683705 0.074069653 VPAAFPTKVPVPGPGS(ph)GGNGPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPAAFPTKVPVPGPGSGGNGPER 23 1 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPAAFPTKVPVPGPGS(1)GGNGPER;VPAAFPTKVPVPGPGS(1)GGNGPER 163.49 9.32E-12 2773700000 2154450 2199900 2284500 1857240 2788400 2894000 1957580 2209220 2418800 2103710 TRUE FALSE 2239509.35 2577715.712 2344035.947 2224596.529 2314428.764 2221912.359 1804139.764 2179609.019 2331747.86 2515891.697 0.890145372 1.024573401 0.931691913 0.884217922 0.919923845 0.883151036 0.717097547 0.866336585 0.926807725 1 21.26263839 3.467436926 1.350093831 0.861604777 0.958355655 0.093708144 0.075359187 0.696112747 2.576644182 0.02527458 0.048000272 2933.843384 -3.467436926 0.096750879 VPAFLSAAEVEEHLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPAFLSAAEVEEHLR 15 0 Q14894;I3NI53;I3L2W5;I3L3J9 Q14894 CRYM Ketimine reductase mu-crystallin 0 ;;; 237.21 9.91E-18 508210000 284077 364954 336811 341157 362246 388145 333517 354265 317517 379528 FALSE TRUE 295292.5793 427632.0106 345588.5714 408636.8363 300671.5543 298004.2061 307375.0661 349516.6571 306089.6252 453889.2451 0.650582896 0.942150569 0.761394052 0.900300769 0.662433749 0.656557099 0.677202796 0.770048334 0.674370738 1 18.79198078 5.031431287 17.92447503 0.767992302 0.221003755 0.088194803 0.119281228 25469937.45 366284916.8 0.027442508 440200899.3 107505.6493 -5.031431287 -0.546988548 VPAHPDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPAHPDSR 8 0 O76071 O76071 CIAO1 Probable cytosolic iron-sulfur protein assembly protein CIAO1 0 67.897 0.057906 164440000 220790 268990 265250 267660 332580 354240 263100 300230 276100 347760 FALSE TRUE 229506.9597 315186.94 272162.6329 320602.3491 276048.1704 271973.1286 242477.5345 296205.9079 266163.2149 415896.9137 0.551836169 0.757848711 0.654399261 0.770869748 0.66374181 0.653943609 0.583023164 0.712209921 0.639974008 1 18.66586645 -1.595975252 2.834288716 1.023606219 0.669983385 0.702341101 0.065300811 11070129.98 11030601.99 1948967.306 0.014575819 0.025352731 1.595975252 -0.353622834 VPAS(ph)PLPGLER ddPTM_MDA-MB-175_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 160.56 2.87E-05 9650930000 2243960 2487304 2229757 2424923 2471299 2648371 2173796 2232766 1970462 2249606 TRUE FALSE 2332553.274 2914479.113 2287866.299 2904565.532 2051228.479 2033326.972 2003408.189 2202839.424 1899545.458 2690373.224 0.866999884 1.083299182 0.85038993 1.079614347 0.762432684 0.755778772 0.744658091 0.818785812 0.706052766 1 21.3593749 3.220752852 24.99972036 0.785584273 0.969614233 0.397754161 0.103087097 206.57614 290004.6424 0.026943798 0.03226781 1662.466305 -3.220752852 0.184029961 VPCNVEGIS(ph)PELEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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;VPCNVEGIS(1)PELEK 201.04 1.93E-08 766000000 1257214 1027853 1211402 988443 1429210 1587097 1231050 1173757 1181024 942353 TRUE FALSE 1306849.78 1204378.757 1242972.131 1183954.075 1186273.395 1218517.774 1134557.084 1158024.707 1138519.177 1126989.028 1.159594057 1.068669461 1.102914137 1.050546231 1.052604209 1.081215295 1.006715288 1.027538582 1.010230933 1 20.10404204 8 0.218965635 0.995803208 1.7569197 0.774717633 0.022383709 22.36785129 0.285400938 0.033191792 6.012173724 100000000 -8 0.761116492 VPDDPEHLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPDDPEHLAAR 11 0 Q9Y2S2-2;Q9Y2S2;A0A2R8Y4K2 Q9Y2S2-2 CRYL1 Lambda-crystallin homolog 0 87.667 0.013553 192230000 262050 300470 322510 301790 366000 369390 314110 307740 333490 353660 FALSE TRUE 272395.9363 352073.3852 330914.8755 361483.1612 303787.4507 283604.7707 289489.2374 303615.2487 321487.76 422952.9058 0.644033727 0.832417464 0.782391777 0.854665274 0.718253608 0.670535104 0.684447922 0.717846466 0.76010297 1 18.69013751 -1.516014026 8.748465525 1.00001511 0.740934284 0.590771449 0.064787348 1.98E-05 1.09E-06 0.064944355 0.01530664 0.030477966 1.516014026 -0.259080827 VPDEEENEES(ph)DNEKETEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPDEEENEESDNEKETEK 18 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 VPDEEENEES(1)DNEKETEK;VPDEEENEES(1)DNEKETEK 226.56 2.09E-19 799960000 1957200 548190 933140 563600 1012270 1731360 1567420 927530 1021840 182221 TRUE FALSE 2034471.767 642337.3682 957458.395 675078.3978 840204.707 1329277.879 1444561.525 915097.9775 985064.178 217923.7161 9.335706106 2.947533108 4.393548403 3.09777389 3.855499172 6.099739407 6.628748584 4.199166542 4.520224763 1 17.73346368 4.748641497 24.35645925 4.326891232 9.335710083 0.511533151 1.523267867 829.9624196 2005217.265 0.357550312 4.781821167 56058.50314 -4.748641497 5.00881885 VPDGKPENEFAFNAEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPDGKPENEFAFNAEFK 17 1 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 145.61 4.27E-07 302820000 285000 161200 208680 150250 283700 311770 316350 212810 229880 126740 FALSE TRUE 296252.0201 188884.846 214118.3722 179969.0015 235476.7753 239366.1424 291553.6604 209957.63 221606.6637 151572.2764 1.954526428 1.246170147 1.412648654 1.187347751 1.553560987 1.579221135 1.923528941 1.385198105 1.462052751 1 17.20964637 VPDHHPC ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VPDHHPC 7 0 P78371;P78371-2 P78371 CCT2 T-complex protein 1 subunit beta 0 ;; 111.69 0.0065229 282232000 518470 571637 493550 570974 588780 683280 539000 546790 551280 566813 FALSE TRUE 538939.5959 669811.208 506412.3185 683910.953 488699.3859 524598.5752 496751.7716 539461.1744 531439.5405 677869.1551 0.795049593 0.988112828 0.747064997 1.008912926 0.720934685 0.773893562 0.732813653 0.795819031 0.783985429 1 19.3706473 3.212231629 24.99997992 0.785681871 0.882328674 0.125646022 0.103097982 359.5766481 341425.3408 0.027031752 0.032318178 1630.16524 -3.212231629 0.096646803 VPDS(ph)PENELK ddPTM_MDA-MB-175_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 116.71 0.0011053 78694000 79546 53109 60322 50504 81415 105380 76050 54819 65872 49519 TRUE FALSE 82686.5375 62230.05762 61894.04088 60493.54046 67576.10738 80907.09205 70089.00228 54084.24097 63501.27959 59221.29995 1.396229694 1.05080533 1.045131413 1.02148282 1.141077745 1.366182305 1.183510027 0.913256565 1.07227095 1 15.85382854 1.750833515 25 0.991815495 1.162997718 0.294690683 0.124819876 4.808615077 9811.191637 0.060160216 0.033361991 56.3421629 -1.750833515 0.171182223 VPEASSEPFDTSS(ph)PQAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VPEASSEPFDTSSPQAGR 18 0 H0Y6F5;Q9H4I2 H0Y6F5 ZHX3 Zinc fingers and homeoboxes protein 3 1 VPEASSEPFDT(0.002)S(0.105)S(0.893)PQAGR;VPEASSEPFDTS(0.002)S(0.998)PQAGR;VPEASSEPFDTS(0.012)S(0.988)PQAGR 242.67 4.97E-24 1431420000 958370 1004770 976270 931350 1115450 1187230 1046460 1061430 922300 950830 TRUE FALSE 996207.1876 1177331.431 1001712.398 1115568.25 925846.2074 911513.8251 964435.7308 1047203.267 889106.6032 1137126.934 0.876073865 1.035356209 0.880915198 0.981041093 0.814197765 0.801593734 0.84813375 0.920920291 0.781888615 1 20.11696188 3.241841837 24.99981158 0.858013524 0.945459324 0.232072029 0.073103255 116.6810689 888992.8931 0.019429045 0.025253722 1745.18647 -3.241841837 0.087445799 VPEEDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPEEDLKR 8 1 Q99832-3;Q99832;Q99832-4;Q99832-2 Q99832-3 CCT7 T-complex protein 1 subunit eta 0 ;;; 149.94 0.00079724 4543440000 2782520 2347740 2618940 2239600 3266010 3132430 2871120 2567780 2642910 2298170 FALSE TRUE 2892376.038 2750946.082 2687191.728 2682586.195 2710854.787 2404970.605 2646074.112 2533363.109 2547792.185 2748452.41 1.052365334 1.0009073 0.977710845 0.976035163 0.986320439 0.875027196 0.962750565 0.921741668 0.926991559 1 21.39018807 4.777616808 0.62424358 0.936680907 1.12513884 0.493749723 0.033533257 2.742723382 0.782505079 0.014660503 0.376540173 59926.20942 -4.777616808 0.188457932 VPEPCHPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPEPCHPK 8 0 P35321;P22528 P35321 SPRR1A;SPRR1B Cornifin-A;Cornifin-B 0 ; 72.547 0.045871 373854000 257115 183186 238289 184627 279610 281810 264800 245058 258386 179580 FALSE TRUE 267266.0987 214646.7705 244499.0071 221145.6695 232081.9921 216363.8984 244044.2841 241773.3983 249086.7383 214765.2627 1.244456833 0.999448271 1.138447643 1.029708747 1.08063096 1.007443642 1.13633034 1.125756537 1.15980925 1 17.71240114 -0.556078983 7.284257475 1.000001685 1.098351744 0.151651751 0.072108853 0 0 0.06485012 0.01528532 0.277920778 0.556078983 0.098350059 VPESGEHYELHLLHYLQENLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPESGEHYELHLLHYLQENLGSR 23 0 Q6V1X1-5;Q6V1X1-3;Q6V1X1;H3BNM2;Q6V1X1-6;Q6V1X1-4;Q6V1X1-2 Q6V1X1-5 DPP8 Dipeptidyl peptidase 8 0 77.045 0.0053007 37416000 9738.3 31273 23404 21452 22579 35481 14432 24399 24605 27453 FALSE TRUE 10122.7756 36643.89448 24013.92747 25695.14157 18741.02965 27241.07547 13300.78213 24071.97131 23719.47086 32831.88973 0.308321443 1.116106772 0.731420813 0.782627555 0.570817879 0.829713906 0.405117775 0.733188723 0.722452197 1 15.00281017 0.663482169 2.671535683 0.999950269 0.693830428 0.161857402 0.213226453 5.217695269 39.22606712 0.189071407 0.050072848 4.607678504 -0.663482169 -0.30611984 VPFS(ph)LLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPFSLLR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VPFS(1)LLR;VPFS(1)LLR 110.41 0.0071437 39747000 16311.5 24589 23212 23458.7 28690 29561 21997 24674 21417.6 28374 TRUE FALSE 16955.49062 28811.96947 23816.92379 28098.76084 23813.28405 22695.90575 20272.81766 24343.28539 20646.78476 33933.34205 0.499670519 0.849075503 0.701873802 0.828057573 0.70176654 0.668837915 0.597430622 0.717385436 0.608451261 1 15.05041591 -1.590947592 2.988918017 1.018356331 0.693246343 0.475018451 0.098805237 39192998.13 42208048.14 5684731.764 0.023168822 0.025647935 1.590947592 -0.325109988 VPFS(ph)PGPAPPPHMGELDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPFSPGPAPPPHMGELDQER 20 0 Q6Y7W6;I1E4Y6;Q6Y7W6-3;Q6Y7W6-4;Q6Y7W6-5;E7ESB6;C9JHW1 Q6Y7W6;Q6Y7W6-4 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 VPFS(1)PGPAPPPHMGELDQER;VPFS(1)PGPAPPPHMGELDQER 180.9 3.41E-17 230580000 116630 125245 121290 114782 131257 162960 129862 139840 130235 112472 TRUE FALSE 121234.6425 146754.8545 124450.917 137485.537 108945.982 125115.0097 119683.0771 137965.6735 125547.8678 134508.735 0.901314271 1.091043303 0.925225541 1.02213092 0.809954699 0.930162712 0.889779219 1.025700476 0.933380779 1 17.03734034 5.524425889 0.001283186 1.21371265 0.692680512 0.001151853 0.077503595 17472613.28 2905.668407 583470.8605 596421.825 334522.928 -5.524425889 -0.521032137 VPFSLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPFSLLR 7 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ; 110.9 0.015585 144917000 402970 333740 307920 311580 493190 356210 316620 316500 333530 433330 FALSE TRUE 418879.5668 391057.2489 315944.6482 373209.594 409357.74 273485.6259 291802.4971 312257.8352 321526.3205 518232.7169 0.808284682 0.754597763 0.609657858 0.720158303 0.789911032 0.527727442 0.563072318 0.602543655 0.620428448 1 18.98324057 -1.109260776 4.641824664 1.000019744 0.65950457 0.537838178 0.0926194 0.834434079 61041347.76 3126.293033 0.023093472 0.077756951 1.109260776 -0.340515175 VPGGGEQPAQPNGWQYHS(ph)PSRPGSTAFPSQDGETGGHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPGGGEQPAQPNGWQYHSPSRPGSTAFPSQDGETGGHRR 39 2 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 VPGGGEQPAQPNGWQYHS(0.58)PS(0.419)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.994)PS(0.006)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQYHS(0.873)PS(0.127)RPGSTAFPSQDGETGGHRR;VPGGGEQPAQPNGWQY(0.246)HS(0.264)PS(0.264)RPGS(0.065)T(0.065)AFPS(0.045)QDGET(0.05)GGHRR 194.2 7.97E-25 4495870000 63071 52771 109774 79078 128308 117897 71137 116200 55599 100712 TRUE FALSE 65561.09178 61834.00875 112634.8006 94719.39238 106498.252 90517.2085 65561.09606 114642.5291 53598.00285 120444.5882 0.544325758 0.513381379 0.935158668 0.786414681 0.884209524 0.751525742 0.544325794 0.95182798 0.445001338 1 16.87801005 -4.999999441 0.030486625 2.005481211 7.00E-08 0.12668364 0.184174298 3271.687161 7.507584115 387.7284563 154.9383094 1.00E-05 4.999999441 -2.005481141 VPGGS(ph)PLGVSLVYSDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPGGSPLGVSLVYSDKK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 VPGGS(0.998)PLGVS(0.001)LVYSDKK 80.752 0.0065859 268910000 440890 230050 263580 217710 412210 402700 337660 300160 362080 191720 TRUE FALSE 458296.6776 269559.298 270449.1113 260772.3882 342142.6914 309179.028 311193.3269 296136.8462 349048.8115 229283.8633 1.998817845 1.175657519 1.179538357 1.137334239 1.492223162 1.348455245 1.35724042 1.291572996 1.522343555 1 17.8067753 -2.200053441 2.192799036 0.000211385 1.364098663 0.186259699 0.238929323 4540225.996 720386.5669 22606325.09 0.058336197 0.006308797 2.200053441 1.363887278 VPGGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPGGSPR 7 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 VPGGS(1)PR 93.429 0.015673 1247300000 535010 605530 500230 514910 543070 612260 433300 429180 422880 486960 TRUE FALSE 556132.6079 709525.0671 513266.4047 616757.6611 450759.1554 470071.8939 399336.8138 423427.5441 407660.6314 582370.4886 0.954946411 1.218339667 0.881339997 1.059046901 0.774007551 0.80716984 0.685709221 0.727075895 0.700002214 1 19.15157772 3.232696991 22.53114006 0.760696085 1.031478521 0.515155165 0.115808597 28.32993362 108858.9354 0.031250357 0.038408138 1708.822645 -3.232696991 0.270782436 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPHDPVALEEHFRDDDEGPVSNQGYMPYLNR 31 1 Q9UH65;E7EMB1;E9PJK8 Q9UH65 SWAP70 Switch-associated protein 70 0 111.43 6.10E-05 264750000 84818 107120 105390 114240 95845 129670 115630 108780 91332 97317 FALSE TRUE 88166.68013 125517.0267 108136.55 136836.331 79553.30113 99556.10767 106566.6185 107321.982 88044.97916 116384.4029 0.757547214 1.078469482 0.929132661 1.175727397 0.683539196 0.855407642 0.915643469 0.922133717 0.756501533 1 16.8285382 3.235615219 24.99999992 0.860631113 0.98787372 0.192569483 0.129792884 128.48809 1090585.292 0.035440257 0.044145334 1720.343689 -3.235615219 0.127242607 VPKPEPIPEPKEPS(ph)PEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VPKPEPIPEPKEPSPEK 17 2 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK 187.83 2.32E-10 3033250000 7224310 1151473 2075550 1151317 3704330 4980590 3685900 2409640 2641090 705812 TRUE FALSE 7509531.337 1349229.531 2129640.538 1379044.066 3074669.31 3823923.454 3396989.527 2377342.717 2546037.687 844102.3478 8.896470146 1.598419355 2.522964832 1.633740351 3.642531404 4.530165642 4.02438109 2.816415241 3.016266562 1 19.68705841 4.746266535 24.97599837 2.904754849 8.896473057 0.744955022 1.07498484 489.4455257 1586326.204 0.263106702 2.831981377 55752.78093 -4.746266535 5.991718207 VPLAPITDPQQLQLS(ph)PLK ddPTM_MDA-MB-175_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 251.75 1.91E-30 3821026000 2492292 1344910 1628073 1484877 2113445 2587112 2391096 1903727 1782999 1140416 TRUE FALSE 2590689.613 1575887.831 1670501.92 1778581.239 1754202.374 1986294.446 2203675.648 1878210.653 1718829.214 1363858.681 1.899529364 1.155462698 1.224835053 1.304080301 1.286205381 1.45637849 1.615765386 1.377129962 1.260269292 1 20.37926273 0.92286249 2.714776461 1.001123184 1.402097028 0.282873855 0.202934952 0.464070608 7.749447773 0.188658086 0.050170978 8.372641388 -0.92286249 0.400973844 VPLDLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPLDLSPR 8 0 R4GNG2;Q9UKV5 R4GNG2 AMFR E3 ubiquitin-protein ligase AMFR 1 VPLDLS(1)PR;VPLDLS(1)PR 64.297 0.071197 44871100 71593 84680 80181 120083 93513 127671 90403 85755 77579 117218 TRUE FALSE 74419.54692 99223.13128 82270.58273 143835.059 77617.69366 98021.34512 83316.97664 84605.59449 74786.94694 140184.6228 0.530868118 0.707803247 0.58687309 1.026040204 0.553681938 0.699230366 0.594337488 0.603529779 0.533488948 1 17.09696858 -1.248049449 3.596614385 1.000654204 0.652264419 0.364679584 0.139128897 38947929.27 49437888.63 279448.8195 0.032310001 0.056487265 1.248049449 -0.348389785 VPLS(ph)PLSLLAGPADAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VPLSPLSLLAGPADAR 16 0 Q53ET0;H0YDQ8;Q5T4K5 Q53ET0 CRTC2 CREB-regulated transcription coactivator 2 1 VPLS(0.999)PLS(0.001)LLAGPADAR;VPLS(0.995)PLS(0.005)LLAGPADAR;VPLS(0.999)PLS(0.001)LLAGPADAR;VPLS(0.977)PLS(0.023)LLAGPADAR;VPLS(1)PLSLLAGPADAR 217.32 1.51E-14 2366992000 174336.9 175309.7 172006.3 190031.6 218254.2 228201.5 222321.4 199902.8 211538.6 197933.7 TRUE FALSE 181219.8554 205417.7773 176488.9255 227619.2833 181155.429 175205.1601 204895.2677 197223.4299 203925.3671 236715.0188 0.765561291 0.867785146 0.745575529 0.961575165 0.765289122 0.740152276 0.865577811 0.833168216 0.861480476 1 17.85279172 0.545314742 0.940347702 1.000473413 0.815908244 0.420030622 0.064763457 1.424760009 1.92844898 0.059894621 0.019308834 3.510061634 -0.545314742 -0.184565169 VPLVAEKPLKEPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 122.64 0.00013088 534280000 883370 409220 656310 444870 878180 840180 1037300 618100 806030 279980 FALSE TRUE 918246.1297 479500.3517 673413.9778 532863.9582 728907.2773 645060.9281 955993.7155 609815.3805 777021.1377 334836.7205 2.742369859 1.432042313 2.011171227 1.591414339 2.176903645 1.926493985 2.855104166 1.821232091 2.320597146 1 18.35309823 VPMDIPVFTGTHADLLIVVFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPMDIPVFTGTHADLLIVVFHK 22 0 Q8IV36-2;Q8IV36;Q8IV36-3;X6R4D2 Q8IV36-2 HID1 Protein HID1 0 ; 212.83 9.37E-24 121045000 175613 125039 202525 147953 218126 244499 214599 157159 208844 129391 FALSE TRUE 182546.3368 146513.4756 207802.9679 177217.6618 181049.0204 187717.8127 197778.1696 155052.5407 201327.7452 154742.6891 1.179676648 0.946820017 1.342893607 1.145240934 1.170000479 1.213096488 1.278109943 1.002002366 1.301048511 1 17.23951172 -1.356525451 5.32897718 0.999938182 1.166024704 0.161300809 0.118271324 8.17E-05 9.87E-06 0.107726716 0.025381994 0.044002216 1.356525451 0.166086521 VPMYEEQWSYYDDKQPYPSRPPFDNQHS(ph)QDLDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPMYEEQWSYYDDKQPYPSRPPFDNQHSQDLDSR 34 2 A0A087X0K9;G5E9E7;Q07157-2;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 1 VPMYEEQWSYYDDKQPYPS(0.082)RPPFDNQHS(0.918)QDLDSR 118.48 1.12E-06 115180000 48330 37740 53120 46136 68829 43864 50783 55008 60589 43137 TRUE FALSE 50238.10572 44221.55142 54504.35084 55261.5631 57129.47117 33677.25077 46802.49576 54270.70773 58408.41373 51588.86924 0.973816764 0.857191717 1.056513772 1.071191594 1.107399174 0.652800716 0.90722081 1.051984828 1.13219023 1 15.6547722 1.62528949 5.551457282 1.073600284 0.947416034 0.147765567 0.126109318 0.277755116 18.30299398 0.071946233 0.034310833 42.19776901 -1.62528949 -0.12618425 VPPELLGGS(ph)PPWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPPELLGGSPPWK 13 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 VPPELLGGS(1)PPWK 106.42 0.0014424 316120000 742650 589080 796240 619770 982590 1026200 966920 885590 1022500 652970 TRUE FALSE 771970.3955 690249.9076 816990.6685 742358.6562 815569.7028 787880.6022 891130.2838 873720.1146 985700.4247 780906.9696 0.98855616 0.883907987 1.046207423 0.950636484 1.044387788 1.008930171 1.141147817 1.118853011 1.262250771 1 19.57479116 2.470439584 1.273258516 1.145891997 0.968807754 0.467413387 0.074159557 0.3501557 1.145964057 0.037519802 0.027120388 295.4197894 -2.470439584 -0.177084243 VPPELNNIS(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPPELNNISK 10 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 VPPELNNIS(1)K 59.757 0.054535 0 334200 236510 289740 233560 466160 419500 338800 279760 305700 282120 TRUE FALSE 347394.4741 277128.7527 297290.8624 279757.4709 386922.2897 322077.4826 312243.9707 276010.2748 294697.9167 337396.0125 1.029634202 0.821375305 0.881133302 0.8291665 1.146789753 0.954597774 0.925452463 0.818060275 0.873448132 1 18.3640834 -1.096375176 8.011365728 1.000000005 0.91403792 0.05317105 0.098510294 8.55E-09 1.08E-09 0.096826468 0.022822216 0.080098581 1.096375176 -0.085962085 VPPGYHPLDVEKEWGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPPGYHPLDVEKEWGK 16 1 Q15149-3;Q15149-2;Q15149;Q15149-6;Q15149-7;Q15149-9;H0YDN1;E9PMV1;Q15149-4;Q15149-5;Q15149-8 Q15149-3;Q15149-4;Q15149-5;Q15149-8 PLEC Plectin 0 ; 199.68 2.25E-11 770600000 1595660 890770 1390300 901040 1890960 1592070 1515160 1344960 1660710 922550 FALSE TRUE 1658657.889 1043752.818 1426532.36 1079263.023 1569535.295 1222335.871 1396397.8 1326933.011 1600941.372 1103306.009 1.503352538 0.946022961 1.292961652 0.978208234 1.422574772 1.107884721 1.265648685 1.202688103 1.451040199 1 20.07340156 3.231523669 24.99911799 1.243753921 1.171472913 0.023223781 0.191851315 673.3259946 2392026.891 0.050374173 0.061452254 1704.212194 -3.231523669 -0.072281008 VPPS(ph)PDDLPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VPPSPDDLPSR 11 0 A0A087X1N4;Q8IYJ3-2;Q8IYJ3 A0A087X1N4 SYTL1 Synaptotagmin-like protein 1 1 VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR;VPPS(1)PDDLPSR 125.82 0.00074964 332460000 726270 588212 527443 426750 653406 676025 642033 772679 415732 508397 TRUE FALSE 754943.7004 689232.8353 541188.5979 511159.8763 542340.2815 519028.439 591708.7758 762322.5019 400769.8865 608007.6583 1.241668078 1.133592358 0.890101614 0.840712891 0.891995806 0.853654443 0.973192965 1.253804112 0.659152695 1 19.21372997 4.392296184 4.122682258 0.942734584 1.220806057 0.357784645 0.143629597 0.247725544 7.703186574 0.037943021 0.120529286 24677.21725 -4.392296184 0.278071473 VPPVPDYVAHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPPVPDYVAHPER 13 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1 Q9Y5U2-2 TSSC4 Protein TSSC4 0 93.494 0.0022432 0 48503 58425 57024 58951 67109 72816 57655 58754 49856 61774 FALSE TRUE 50417.93589 68459.03927 58510.09229 70611.33185 55701.83615 55905.58754 53135.85045 57966.49873 48061.6923 73877.43257 0.682453818 0.92665699 0.791988707 0.955790279 0.753976339 0.756734304 0.719243328 0.784630661 0.650559862 1 16.17284611 VPS(ph)GIFDVNSR ddPTM_MDA-MB-175_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 147.52 3.70E-05 483367000 139410 190558 176351 162390 193352 207113 171992 183521 168460 159054 TRUE FALSE 144914.0144 223284.8542 180946.8519 194510.2573 160486.0961 159014.1446 158510.8176 181061.2012 162397.1575 190217.586 0.761832896 1.173839175 0.951262476 1.022567163 0.84369747 0.835959219 0.83331316 0.951863626 0.853744183 1 17.53729111 3.240536941 24.99981709 0.882787315 0.989543348 0.144121643 0.10672181 84.70319915 1071452.795 0.028172793 0.036319179 1739.950693 -3.240536941 0.106756033 VPS(ph)PDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 74.267 0.030045 3432365000 556910 595536 585092 525309 640375 742185 608574 607195 569943 540935 TRUE FALSE 578897.2368 697814.6754 600339.9782 629213.5523 531524.2862 569823.7817 560872.3797 599056.5442 549430.8628 646920.8564 0.894850168 1.078670858 0.927996017 0.97262833 0.821621812 0.880824565 0.866987629 0.926012105 0.849301514 1 19.3032297 3.282073795 20.93588646 0.887753748 0.973508371 0.265461163 0.063017924 31.09674807 14960.7511 0.016231679 0.021977119 1914.581223 -3.282073795 0.085754623 VPS(ph)PDHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VPSPDHRR 8 1 Q8NAV1;Q8NAV1-2 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 1 VPS(1)PDHRR;VPS(1)PDHRR;VPS(1)PDHRR 68.893 0.03389 476940000 193932 255880 262019 222910 282994 260253 185116 236593 242104 306959 TRUE FALSE 201588.5851 299825.3995 268847.4304 267000.9327 234890.781 199813.1849 170606.1242 233421.8578 233390.7243 367101.739 0.549135468 0.816736528 0.732351285 0.727321351 0.639851998 0.544299206 0.46473799 0.635850591 0.635765783 1 18.48582042 -0.97148245 4.070472087 1.000021544 0.638484567 0.551861042 0.097741963 25413494.01 46743301.67 8191.774539 0.025523679 0.106786795 0.97148245 -0.361536977 VPS(ph)PGMEEAGCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 184.17 3.78E-07 1209360000 135969 136733 144661 137977 174597 185365 167748 168939 160556 120880 TRUE FALSE 141337.1611 160215.8291 148430.9845 165268.4388 144919.0643 142316.788 154599.4734 166674.649 154777.6209 144564.1216 0.977677999 1.108268271 1.026748427 1.143218919 1.002455261 0.984454416 1.069417997 1.152946161 1.070650305 1 17.14135002 1.998735328 24.99978753 1.096440153 1.044293049 0.028058013 0.060921545 94.73803384 1872785.385 0.022494208 0.016403616 99.70922218 -1.998735328 -0.052147104 VPS(ph)PYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VPSPYVR 7 0 A0A2R8Y8C6;Q8WXX7-2;Q8WXX7;A0A087WVB5;Q75MD7;A0A2R8Y568;A0A024RDL5;A0A2R8Y522;Q8WXX7-5 A0A2R8Y8C6 AUTS2 Autism susceptibility gene 2 protein 1 VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR;VPS(1)PYVR 99.136 0.011277 2596080000 2815090 2941110 2884290 2886620 3115360 3544220 3021810 2912100 2731850 2892710 TRUE FALSE 2926231.927 3446222.764 2959456.967 3457584.82 2585812.22 2721128.618 2784952.636 2873068.063 2633531.252 3459481.14 0.845858615 0.996167525 0.855462668 0.999451848 0.74745666 0.786571312 0.805020326 0.830491032 0.761250357 1 21.72212425 3.235306879 24.99952355 0.811940842 0.924460867 0.275068292 0.080519681 94.0024773 722253.3857 0.020924232 0.026015606 1719.122716 -3.235306879 0.112520025 VPS(ph)S(ph)DEEVVEEPQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR;VPS(1)S(1)DEEVVEEPQSR 199.37 1.09E-08 3366690000 688430 691850 773130 698510 805230 902590 822290 727460 684360 624980 TRUE FALSE 715609.748 810669.8557 793278.4029 836673.1932 668357.2922 692977.1514 757836.7611 717709.5886 659730.0173 747432.865 0.957423444 1.084605579 1.061337332 1.119395778 0.894203779 0.927143003 1.013919506 0.960232848 0.882661237 1 19.51158448 3.236578026 24.99990851 0.94923116 1.058159236 0.492902848 0.054256519 44.81660911 565127.5422 0.015397511 0.01930013 1724.161829 -3.236578026 0.108928076 VPS(ph)SDEEVVEEPQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.984)S(0.016)DEEVVEEPQSR 262.42 8.48E-21 0 47024 43674 47106 48033 51901 57946 53771 45673 42707 40045 TRUE FALSE 48880.54383 51174.66976 48333.62106 57533.78404 43078.88656 44488.91968 49556.28852 45060.82814 41169.98341 47891.05104 1.02066133 1.068564349 1.009241184 1.201347283 0.899518503 0.928961021 1.03477137 0.940902886 0.859659216 1 15.54746848 3.209392109 24.99999676 0.946582456 1.069803612 0.481783873 0.066432127 185.1774475 158713.0198 0.018873139 0.022560802 1619.541602 -3.209392109 0.123221155 VPS(ph)SQS(ph)MEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 2 VPS(0.991)S(0.083)QS(0.925)MEDR;VPS(0.997)S(0.145)QS(0.858)MEDR;VPS(0.996)S(0.442)QS(0.562)MEDR 96.464 0.011024 719850000 592130 665710 672880 738050 695710 802860 809590 715750 670060 558030 TRUE FALSE 615507.7496 780040.514 690415.8056 884034.0871 577453.4627 616407.9325 746132.2203 706156.542 645944.6715 667365.2944 0.922295113 1.168835899 1.034539571 1.324662961 0.865273438 0.923643974 1.118026704 1.058125959 0.967902702 1 19.34811714 3.20807243 24.99998811 1.002041801 1.111027534 0.21152399 0.115356758 357.93305 293500.3839 0.033330008 0.039841178 1614.627817 -3.20807243 0.108985734 VPS(ph)VESLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 VPSVESLFR 9 0 Q13439-5;Q13439-3;Q13439-4;Q13439;E7EVX2;Q86W71 Q13439-5 GOLGA4 Golgin subfamily A member 4 1 VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR;VPS(1)VESLFR 233.14 4.03E-10 5912715000 861080 866319 920559 805665 1056209 1061605 925286 900386 981944 880209 TRUE FALSE 895076.1033 1015102.549 944549.5238 965023.1323 876674.9714 815063.3275 852759.6655 888317.7984 946604.0273 1052669.101 0.850291989 0.964313048 0.897290063 0.916739298 0.832811537 0.774282561 0.810092806 0.843871828 0.899241772 1 20.00562058 5.077950088 14.86600641 0.871568654 0.543823187 0 0.066390515 5751849.389 21063158.3 0.016374752 59183967.74 119660.3001 -5.077950088 -0.327745467 VPS(ph)WGLEDNVVCSQPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 219.23 4.61E-15 568640000 67074.8 54168 46124.1 49276.8 69104.7 74054.7 71269.1 53832.6 67682 53139 TRUE FALSE 69722.9649 63470.93263 47326.13194 59023.60396 57358.30778 56856.61823 65682.84171 53111.06205 65246.13804 63550.56964 1.097125727 0.998746872 0.744700358 0.928765931 0.902561662 0.894667326 1.033552368 0.835729126 1.026680617 1 15.95561744 -0.440413014 8.032371513 1 0.93046343 0.023372861 0.098928906 0 0 0.092498108 0.021802013 0.362732932 0.440413014 -0.06953657 VPSS(ph)DEEVVEEPQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VPS(0.004)S(0.996)DEEVVEEPQSR;VPS(0.028)S(0.972)DEEVVEEPQSR 292.82 6.11E-44 300440000 202970 196448 198195 190655 216070 242760 191189 197219 194916 191598 TRUE FALSE 210983.4123 230186.4158 203360.1245 228365.99 179342.4986 186382.6691 176203.1066 194575.6019 187901.0112 229137.9597 0.920770232 1.004575654 0.887500808 0.996630983 0.782683492 0.813408085 0.768982611 0.849163544 0.820034408 1 17.80585695 3.238305947 24.99999998 0.826936691 0.951464969 0.394835338 0.067739904 5.865586723 575825.2028 0.017615609 0.022347028 1731.035391 -3.238305947 0.124528278 VPSS(ph)QSMEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPS(0.122)S(0.637)QS(0.242)MEDR;VPS(0.006)S(0.7)QS(0.294)MEDR 167.71 5.41E-06 1349050000 403110 512020 479450 494960 451310 566640 512040 451520 449110 447590 TRUE FALSE 419025.0941 599955.452 491944.8609 592861.6107 374596.4874 435046.4475 471904.9668 445468.1129 432946.6188 535286.6909 0.782804993 1.12081145 0.919030623 1.107559035 0.699805345 0.812735409 0.881592939 0.832204724 0.808812597 1 19.02995226 3.241547496 24.99999977 0.832776809 0.987890007 0.277009699 0.113046291 90.97408891 761439.9433 0.02938488 0.038134261 1744.004079 -3.241547496 0.155113198 VPSSQS(ph)MEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPSSQSMEDR 10 0 O95049;O95049-4;O95049-3;O95049-5 O95049 TJP3 Tight junction protein ZO-3 1 VPSS(0.001)QS(0.998)MEDR 163.51 6.76E-06 1134700000 161130 216400 186040 198420 230590 242570 230090 180350 220500 177880 TRUE FALSE 167491.5368 253565.0166 190888.3552 237666.8838 191394.3942 186236.7937 212054.9446 177932.7032 212564.2481 212732.1803 0.787335215 1.191944803 0.897317721 1.117211714 0.899696482 0.875451911 0.996816487 0.836416489 0.999210593 1 17.69867876 VPT(ph)ANVSVVDLTCR ddPTM_MDA-MB-175_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 212.95 1.92E-08 772980000 169069 223448 198697 188804 254940 263960 133682 212630 164552 271490 TRUE FALSE 175743.9747 261823.4558 203875.2071 226148.8677 211605.3899 202659.2904 123203.6555 209780.0426 158629.8057 324683.2675 0.5412782 0.806396516 0.627920276 0.696521473 0.651728657 0.624175345 0.379457976 0.646106725 0.488567849 1 18.30867351 -1.042362236 4.721410006 1.000011725 0.610490419 0.531931734 0.110576745 0.228320326 69280168.87 1791.26709 0.025768617 0.090706365 1.042362236 -0.389521306 VPTANVS(ph)VVDLTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR;VPTANVS(1)VVDLTCR 228.23 1.82E-12 2625620000 537913 706868 566204 542745 656237 774690 453892 623889 555134 831963 TRUE FALSE 559150.2206 828267.0803 580959.7414 650098.3411 544690.0691 594779.988 418314.759 615526.7884 535154.8358 994970.221 0.56197684 0.832454141 0.583896612 0.653384722 0.547443589 0.597786723 0.420429426 0.618638403 0.537860154 1 19.92429382 -1.539734946 6.254786727 1.000534056 0.595939382 0.60216252 0.098785182 0.000733119 5.39E-05 0.095314619 0.02243755 0.028857922 1.539734946 -0.404594674 VPTANVSVVDLTCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VPTANVSVVDLTCR 14 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;; 243.75 3.49E-17 9401800000 735116 863390 729673 746506 851535 927010 724085 835091 735586 874915 FALSE TRUE 764138.9473 1011670.516 748688.8778 894162.6587 706791.3849 711725.9765 667329.3257 823897.9711 709112.4035 1046337.843 0.730298491 0.966867941 0.715532639 0.854564006 0.675490607 0.680206667 0.637776154 0.787411042 0.677708838 1 19.99691732 5.087335399 15.17170006 0.764855885 0.000133527 0.004070886 0.120824749 8362832.393 21565562.26 0.027538299 210152810.3 122274.3601 -5.087335399 -0.764722359 VPTANVSVVDLTCRLEKPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPTANVSVVDLTCRLEKPAK 20 2 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 263.24 9.92E-37 1258410000 572140 352720 531230 232802 877920 702100 370060 430370 709500 786590 FALSE TRUE 594728.529 413296.9162 545074.2902 278849.5408 728691.472 539047.9154 341053.7302 424601.5941 683965.2336 940707.2503 0.63221425 0.439347008 0.579430306 0.296425419 0.774620874 0.573024089 0.362550337 0.45136422 0.727075542 1 19.8433863 0.981784021 3.796040072 0.998871553 0.507804844 0.576405233 0.130587948 0.136491345 5.476225081 0.122232303 0.031415289 9.589236298 -0.981784021 -0.49106671 VPVASPS(ph)AHNISSSGGAPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPVASPSAHNISSSGGAPDR 20 0 E9PC69;Q7KZI7-14;E7ETY4;Q7KZI7-12;Q7KZI7-3;Q7KZI7-6;Q7KZI7-11;Q7KZI7-8;Q7KZI7;Q7KZI7-13;Q7KZI7-15;Q7KZI7-16 E9PC69;Q7KZI7-12;Q7KZI7-13 MARK2 Serine/threonine-protein kinase MARK2 1 VPVAS(0.001)PS(0.999)AHNISSSGGAPDR;VPVAS(0.001)PS(0.999)AHNISSSGGAPDR 294.36 9.45E-55 1113540000 134178 270000 284750 311550 267780 289320 237990 255850 213540 250650 TRUE FALSE 139475.451 316370.3997 292170.8189 373173.6601 222262.8512 222129.8147 219335.7219 252420.7492 205854.7371 299760.0685 0.465290296 1.055412088 0.974682253 1.244907842 0.741469177 0.741025367 0.731704269 0.842075966 0.686731686 1 18.19344869 VPVDVAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 101.33 0.012733 804240000 377820 354400 383150 339370 463600 481570 442800 374960 395560 354190 FALSE TRUE 392736.6253 415265.4432 393135.2038 406496.3731 384797.4376 369732.6658 408092.179 369934.2745 381323.8729 423586.7491 0.92716929 0.980355132 0.92811025 0.959653185 0.908426523 0.872861737 0.96342055 0.873337694 0.900226161 1 18.69229793 3.232221205 24.97195292 0.911643395 0.949594927 0.095100227 0.039511605 245.7296589 967967.605 0.01058274 0.012943862 1706.951593 -3.232221205 0.037951532 VPVDVAYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 108.98 0.0040468 174440000 29603 40449 38998 32547 58131 55374 30941 36912 36949 75382 FALSE TRUE 30771.7493 47395.8011 40014.31992 38984.69946 48249.91338 42514.2277 28515.76357 36417.25502 35619.21271 90151.65962 0.341333143 0.525734094 0.44385561 0.432434629 0.535208266 0.471585636 0.316308803 0.403955459 0.395103239 1 16.46006643 -1.274273946 3.55960988 1.001486293 0.430270186 0.867221455 0.066968461 137371320.5 207909326 2191132.289 0.016535062 0.053177272 1.274273946 -0.571216106 VPVHDVTDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPVHDVTDASK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 170.52 1.56E-05 924750000 1283360 1049900 1296650 1077140 1501630 1695600 1586070 1342950 1415410 982910 FALSE TRUE 1334028.044 1230212.158 1330441.764 1290195.077 1246383.469 1301822.597 1461749.689 1324949.952 1364469.671 1175492.396 1.134867438 1.046550503 1.131816564 1.097578412 1.060307556 1.107470029 1.243521178 1.127144639 1.160764354 1 20.16483378 2.458956364 24.99939266 1.149056492 1.092854201 0.056035295 0.061860675 425.6067803 585737.2263 0.019789416 0.016560423 287.7109318 -2.458956364 -0.056202291 VPVLIS(ph)PTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VPVLISPTLK 10 0 P42684-2;P42684-6;P42684-3;P42684;P42684-4;P42684-7;P42684-10;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 VPVLIS(0.987)PT(0.013)LK;VPVLIS(0.998)PT(0.002)LK 118.9 0.00080043 230211000 672370 440530 584480 500500 766460 802310 831630 663840 745740 446680 TRUE FALSE 698915.6868 516187.6007 599712.029 599497.4062 636177.403 615985.6616 766444.6675 654942.3106 718900.9631 534198.3938 1.308344793 0.966284449 1.122639147 1.122237381 1.190901003 1.153102796 1.434756593 1.226028229 1.345756504 1 19.02701611 2.444551573 24.86751522 1.274370856 1.134319154 0.130494315 0.130552807 267.4669891 204214.2604 0.041889585 0.035047515 278.3245867 -2.444551573 -0.140051702 VPVPDERFDFLCQYHKPASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPVPDERFDFLCQYHKPASK 20 2 J3KQ32;Q9NTK5;Q9NTK5-3;C9JTK6 J3KQ32 OLA1 Obg-like ATPase 1 0 184.26 2.45E-17 421260000 663720 499610 603370 349350 806940 725650 562390 608370 655300 588540 FALSE TRUE 689924.1781 585414.1311 619094.3179 418450.3873 669776.627 557128.7848 518308.4023 600215.7952 631715.881 703853.1447 0.980210408 0.831727663 0.879578819 0.594513771 0.951585756 0.791541231 0.736387137 0.852757141 0.897510917 1 19.42491492 0.991347617 2.179676309 0.99848219 0.820165272 0.214270773 0.102923894 0.457621016 4.735181476 0.093268936 0.025757431 9.802743001 -0.991347617 -0.178316918 VPVPGPGS(ph)GGNGPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VPVPGPGSGGNGPER 15 0 A0A494C1T9;Q6ZRV2;J3KPS2 A0A494C1T9 FAM83H Protein FAM83H 1 VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER;VPVPGPGS(1)GGNGPER 160.79 1.77E-06 1465090000 529680 532205 491619 580270 503777 635990 573077 504627 517130 441690 TRUE FALSE 550592.1754 623607.0688 504430.995 695045.6741 418145.1655 488290.961 528157.7273 497863.3005 498518.5923 528230.6988 1.042332785 1.180558173 0.954944489 1.315799471 0.79159573 0.924389594 0.999861857 0.942511107 0.943751648 1 19.01080862 3.22732368 24.99999503 0.935763209 1.115457706 0.451178758 0.102344888 195.5927027 435154.8798 0.027717861 0.033408338 1687.810482 -3.22732368 0.179694497 VPWSHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VPWSHVR 7 0 Q8NDH3-3;Q8NDH3-2;Q8NDH3 Q8NDH3-3 NPEPL1 Probable aminopeptidase NPEPL1 0 81.784 0.026263 200620000 40905 92192 74757 93951 88140 99820 59515 81350 56468 128400 FALSE TRUE 42519.96099 108025.2588 76705.22883 112534.2274 73157.99428 76638.31779 54850.05879 80259.63631 54435.72771 153557.5216 0.27689924 0.703483995 0.499521144 0.73284738 0.47642078 0.499085404 0.35719552 0.522668219 0.354497306 1 17.22841966 -1.446289456 3.450298205 1.006104208 0.500602208 0.552256885 0.137160162 43399572.76 59863753.58 2576840.244 0.031352557 0.035785785 1.446289456 -0.505502 VQAERPDTMLGVVCGALHVADVSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQAERPDTMLGVVCGALHVADVSLR 25 1 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 169.7 5.73E-12 372930000 96661 116060 135840 157740 131630 144490 137250 111900 138830 132110 FALSE TRUE 100477.2509 135992.4022 139380.102 188940.5012 109255.5796 110934.3873 126491.9864 110400.1635 133833.5354 157994.4251 0.635954407 0.860741777 0.882183671 1.195868152 0.69151541 0.70214115 0.800610441 0.698759867 0.847077581 1 17.26951413 VQAGPGS(ph)PR ddPTM_MDA-MB-175_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 84.605 0.016132 285200000 260480 312130 301060 274810 311160 365790 299230 295810 292550 304420 TRUE FALSE 270763.9515 365735.8995 308905.8709 329166.5978 258269.1343 280840.8161 275775.5707 291845.1508 282021.1826 364065.2705 0.743723649 1.004588817 0.848490356 0.904141714 0.709403382 0.77140238 0.757489365 0.801628649 0.774644564 1 18.4738376 3.263643259 24.99720323 0.788882383 0.882565229 0.114359339 0.093987882 360.0623815 358833.3144 0.023798301 0.0322102 1835.03038 -3.263643259 0.093682846 VQAMQIS(ph)SEKEEDDNEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 1 VQAMQIS(0.586)S(0.414)EKEEDDNEKR 74.444 0.0096729 178980000 318620 117840 159310 126830 243970 312360 288220 166750 178640 74146 TRUE FALSE 331199.3636 138078.1033 163461.7495 151916.5955 202500.0665 239819.1239 265628.5633 164514.989 172210.7813 88673.48909 3.735043777 1.557152028 1.843411725 1.713213239 2.283659622 2.704518863 2.99558037 1.855289452 1.942077424 1 16.43621522 4.749743703 24.68836753 2.069444292 3.735044936 0.476376943 0.543430458 1314.552588 2902009.42 0.13117789 2.002165779 56200.956 -4.749743703 1.665600644 VQAMQISS(ph)EKEEDDNEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 1 VQAMQIS(0.19)S(0.81)EKEEDDNEKR 94.384 0.0010298 164480000 307220 87499 151170 102170 221450 274460 259190 180540 187080 78516 TRUE FALSE 319349.2828 102526.2726 155109.6144 122378.9211 183808.0081 210720.8245 238874.0105 178120.1566 180347.0273 93899.70692 3.400961444 1.091869996 1.651864734 1.303293962 1.957492884 2.244105242 2.543927115 1.896919197 1.920634614 1 16.51883303 3.016712899 24.86055621 2.028827389 1.771780795 0 0.689175709 1002.109197 1490633.381 0.190315852 0.227423002 1039.232929 -3.016712899 -0.257046594 VQAMQISSEKEEDDNEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQAMQISSEKEEDDNEKR 18 2 Q9UKY7;Q9UKY7-2;H0Y8K3 Q9UKY7 CDV3 Protein CDV3 homolog 0 231.21 5.14E-20 268730000 387010 109540 200250 152530 299660 286060 318890 202310 249930 75548 FALSE TRUE 402289.4536 128352.6429 205468.6795 182699.9787 248723.9002 219626.9003 293894.5685 199598.3654 240935.0681 90350.18415 4.452558204 1.420612964 2.274136809 2.022131781 2.752887585 2.430840649 3.252838622 2.209163902 2.666680432 1 16.46323992 -1.097130348 4.161652528 0.999737419 2.548564731 0.279205763 0.770107876 56173300.05 133927575.3 218228.789 0.169542784 0.079959423 1.097130348 1.548827312 VQAYEEPSVASS(ph)PNGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 VQAYEEPSVAS(0.008)S(0.992)PNGK;VQAYEEPSVAS(0.319)S(0.681)PNGK;VQAYEEPSVAS(0.01)S(0.99)PNGK 297.56 1.01E-45 1933500000 2900730 1960270 2566120 2030880 3055420 3041820 3031770 2591090 2626230 1745160 TRUE FALSE 3015253.06 2296931.124 2632995.195 2432582.002 2536060.8 2335403.404 2794131.945 2556360.677 2531712.495 2087090.689 1.44471588 1.100542078 1.261562427 1.165537279 1.215117682 1.118975527 1.338768823 1.224844081 1.213034253 1 20.99306186 0.67527998 3.450794826 1.000003047 1.228326502 0.343222231 0.096198471 5.817971708 60.68511998 0.083944626 0.021668134 4.734563878 -0.67527998 0.228323454 VQCCLYFIAPSGHGLKPLDIEFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQCCLYFIAPSGHGLKPLDIEFMK 24 1 E7EPK1;E7ES33;Q16181;Q16181-2;G3V1Q4;A0A0U1RRH9;A0A0U1RRE1 E7EPK1 7-Sep Septin-7 0 181.26 2.01E-17 780180000 398750 472230 598530 477500 803580 699760 678290 635210 678250 478410 FALSE TRUE 414492.9579 553331.8291 614128.1835 571948.0748 666987.7586 537251.345 625123.8574 626696.0489 653839.915 572145.2798 0.724454037 0.967117704 1.073378048 0.999655324 1.165766427 0.939012107 1.092596373 1.095344261 1.142786523 1 19.126022 4.789051514 1.798861213 1.068641445 0.579233785 0.710211387 0.065409221 0.50101765 1.483282247 0.016045175 0.433445133 61524.98465 -4.789051514 -0.48940766 VQDDEVGDGTTSVTVLAAELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VQDDEVGDGTTSVTVLAAELLR 22 0 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 255.93 9.94E-37 123464000 119231 128977 127660 121458 154346 160995 134721 134552 136774 137747 FALSE TRUE 123938.3319 151127.7964 130986.9245 145482.0299 128110.3221 123606.3512 124161.216 132748.5505 131851.5305 164735.8873 0.752345673 0.917394497 0.795132904 0.883122872 0.777670999 0.750330442 0.753698651 0.805826543 0.800381341 1 17.32979535 -1.507567365 2.602622829 1.010197194 0.804902157 0.552564876 0.052908722 6137790.459 5987223.409 444436.1773 0.013423773 0.031076538 1.507567365 -0.205295037 VQDNFDKIEFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQDNFDKIEFNR 12 1 Q9UH65 Q9UH65 SWAP70 Switch-associated protein 70 0 137.46 8.38E-05 279610000 319030 245510 308250 245140 412860 400290 357190 318840 342200 244260 FALSE TRUE 331625.5507 287674.4327 316283.2482 293627.9603 342682.2047 307328.714 329192.5145 314566.4713 329884.2888 292118.0704 1.135244904 0.984788214 1.082724009 1.005168766 1.173094853 1.052070191 1.126915956 1.076847012 1.129284089 1 18.15619208 3.269380398 24.99999857 1.095872777 1.049377895 0.104197685 0.058418223 392.8114152 318633.2556 0.014557488 0.019708783 1859.432415 -3.269380398 -0.046494882 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.574)S(0.366)NT(0.061)GLGEDIIHQLSK 162.65 1.00E-10 42250000 33937 31177 37917 32871 42128 45706 42099 38771 33982 33063 TRUE FALSE 35276.85897 36531.40723 38905.14817 39372.78569 34967.09761 35091.47418 38799.17037 38251.33816 32758.99446 39541.06182 0.892157604 0.923885337 0.983917638 0.995744269 0.884323688 0.887469192 0.981237443 0.967382675 0.828480394 1 15.27106399 -1.243740714 4.911166021 1.000012879 0.933317991 0.140192112 0.052144673 7.34E-06 1.13E-06 0.050397486 0.011876508 0.057050478 1.243740714 -0.066694888 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 VQDT(0.036)S(0.684)NT(0.28)GLGEDIIHQLSK;VQDT(0.197)S(0.79)NT(0.012)GLGEDIIHQLSK;VQDT(0.07)S(0.921)NT(0.009)GLGEDIIHQLSK 270.46 1.71E-39 357839000 509744 444909 545295 459501 606123 681536 624695 545838 568611 448884 TRUE FALSE 529869.0867 521318.6598 559505.8357 550388.9263 503094.429 523259.5928 575729.7736 538521.9344 548146.8012 536834.2254 0.987025532 0.971098032 1.042232051 1.025249323 0.937150437 0.974713548 1.072453555 1.003143818 1.021072754 1 19.03411713 VQEAPIDEHWIIECNDGVFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQEAPIDEHWIIECNDGVFQR 21 0 A0A1W2PR36;Q14353;Q14353-2 A0A1W2PR36 GAMT Guanidinoacetate N-methyltransferase 0 ; 283.64 3.56E-45 863810000 508980 617270 571500 596640 604810 680100 577500 619020 613440 662130 FALSE TRUE 529074.9234 723281.3208 586393.7595 714653.6112 502004.6122 522157.082 532234.041 610723.0494 591362.4142 791861.6963 0.668140568 0.913393493 0.740525476 0.902498018 0.633954912 0.659404394 0.672130049 0.771249642 0.746800126 1 19.59488895 -1.164700661 9.422948712 1.000000003 0.747510708 0.407527305 0.092081759 6.20E-09 5.58E-10 0.088139396 0.020774655 0.06843832 1.164700661 -0.252489295 VQEAVLDKWVNDPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQEAVLDKWVNDPHR 15 1 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 160.25 1.03E-06 624200000 1267340 1130170 1256490 986190 1636430 1611080 1222280 1297370 1407200 1188510 FALSE TRUE 1317375.562 1324267.906 1289235.162 1181255.439 1358270.213 1236931.086 1126474.5 1279980.877 1356555.147 1421375.779 0.9268313 0.931680366 0.907033299 0.831064843 0.955602475 0.870235095 0.792524058 0.900522505 0.954395851 1 20.43885659 1.101827574 3.135077516 0.997522679 0.886613875 0.386805743 0.046011095 0.233893825 4.363066718 0.044743991 0.011884534 12.64234315 -1.101827574 -0.110908805 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 VQEHEDS(1)GDS(1)EVENEAK;VQEHEDS(1)GDS(1)EVENEAK 155.91 4.38E-08 441820000 967220 589020 767040 560040 945090 1010480 893310 742120 771670 520880 TRUE FALSE 1005406.592 690179.6031 787029.6925 670814.2404 784443.9394 775811.334 823290.028 732173.0953 743897.7474 622936.4631 1.613979357 1.107945423 1.263418886 1.076858203 1.259267976 1.245410054 1.321627608 1.175357582 1.194179168 1 19.2487255 -4.999999999 0.038837921 5.16E-11 1.848752623 0.302426303 0.132950258 1285.152418 3.732891341 157.2544336 48.99436107 1.00E-05 4.999999999 1.848752623 VQEKPDS(ph)PGGSTQIQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQEKPDSPGGSTQIQR 16 1 M0R300;Q13459-2;Q13459;M0R0P8 M0R300 MYO9B Unconventional myosin-IXb 1 VQEKPDS(0.996)PGGS(0.001)T(0.002)QIQR;VQEKPDS(0.999)PGGS(0.001)TQIQR 127.63 3.95E-05 1964420000 2348900 1382700 1811070 1369620 2371800 2656100 2108330 1788730 2052700 1297450 TRUE FALSE 2441636.386 1620167.969 1858267.972 1640526.748 1968642.283 2039261.029 1943073.586 1764755 1978823.728 1551660.486 1.573563552 1.044151078 1.197599596 1.057271718 1.268732626 1.314244351 1.252254345 1.137333209 1.275294271 1 20.56538149 -3.424995271 0.456159258 1.86E-10 1.224374536 0.190463517 0.14307542 485.4831957 11.71772065 472.1326207 0.070422957 0.000375841 3.424995271 1.224374536 VQENSPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VQENSPGHR 9 0 Q9H8Y8;F8WEG2 Q9H8Y8 GORASP2 Golgi reassembly-stacking protein 2 0 ;;; 173.32 5.55E-05 1430900000 757730 1027450 1103990 1026830 1207070 1367590 1019430 1122230 1053720 1069500 FALSE TRUE 787645.7655 1203906.545 1132760.886 1229933.909 1001892.673 1049987.949 939524.4128 1107188.342 1015796.823 1279048.048 0.615806237 0.941252009 0.885628095 0.961601021 0.783311209 0.820913608 0.734549741 0.865634676 0.794181911 1 20.28663903 -1.179915327 4.004796274 1.000086999 0.82964591 0.231557159 0.096202292 13252808.13 3904620.098 10166.1588 0.021436915 0.066082227 1.179915327 -0.170441089 VQESTKGPDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQESTKGPDEAK 12 1 O43390;O43390-3;B4DT28;O43390-2;O43390-4 O43390;O43390-2 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ; 155.42 6.60E-05 425260000 390020 174654 277350 166780 410160 371590 335470 252460 324520 164054 FALSE TRUE 405418.2908 204649.4659 284577.9688 199768.5862 340441.1497 285293.854 309174.9848 249076.1866 312840.5886 196197.2403 2.06638121 1.043080247 1.450468765 1.018202835 1.735198462 1.454117568 1.575837582 1.269519318 1.594520841 1 17.58194522 -1.227563284 4.73079847 0.999902332 1.440572306 0.176646859 0.297720447 0.000277801 4.54E-05 0.26110349 0.061529113 0.059215679 1.227563284 0.440669974 VQGGHS(ph)PDDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQGGHSPDDHR 11 0 A2AJT9-3;A2AJT9-2;A2AJT9 A2AJT9-3 CXorf23 Uncharacterized protein CXorf23 1 VQGGHS(1)PDDHR 68.919 0.03602 81228000 65941 163240 145960 155730 117530 180260 130390 131130 141660 318580 TRUE FALSE 68544.4016 191275.2002 149763.8375 186532.9292 97552.29258 138397.3469 120169.6911 129372.4168 136561.6843 380999.6514 0.17990673 0.502035105 0.393081298 0.489588189 0.256042997 0.363247962 0.315406302 0.33956046 0.358429945 1 18.53943015 -1.429617039 3.470916421 1.006717614 0.358830642 0.817251496 0.09145158 152291624.2 224345002.3 10155053.1 0.02075126 0.037186299 1.429617039 -0.647886971 VQGGVPAGS(ph)DEYEDECPHLIALSSLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQGGVPAGSDEYEDECPHLIALSSLNR 27 0 Q9BVS4-2;Q9BVS4;H0Y919;H0Y8R4 Q9BVS4-2 RIOK2 Serine/threonine-protein kinase RIO2 1 VQGGVPAGS(1)DEYEDECPHLIALSSLNR 140.49 1.43E-07 247700000 93290 72410 72887 82877 103790 104040 107690 85009 84517 95973 TRUE FALSE 96973.16124 84845.85423 74786.4951 99269.82324 86147.81287 79878.28674 99248.9764 83869.5934 81475.24968 114777.0718 0.84488269 0.739223025 0.651580441 0.864892453 0.750566394 0.695942887 0.864710824 0.730717312 0.709856493 1 16.80847495 -1.154250847 4.384916938 1.000046828 0.760643952 0.511645768 0.069935892 3.02E-05 5.83E-06 0.063875465 0.01505265 0.070105026 1.154250847 -0.239402876 VQHQDALQISDVVMASLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQHQDALQISDVVMASLLR 19 0 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 ; 179.41 3.59E-14 751300000 494150 491170 596300 666470 619900 675900 732400 543080 518110 430390 FALSE TRUE 513659.4236 575524.6267 611840.0679 798295.7768 514529.6194 518932.4684 674992.5742 535800.9009 499463.3223 514716.6802 0.997945945 1.118138675 1.188692909 1.550942115 0.999636575 1.008190502 1.311386633 1.040962769 0.970365526 1 18.97341901 VQHRPSGLIMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQHRPSGLIMAR 12 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 78.903 0.014707 261740000 231220 257490 276820 282620 355010 343790 308580 282800 276340 315300 FALSE TRUE 240348.7441 301711.9045 284034.1566 338521.3925 294665.527 263949.9827 284392.6933 279009.5286 266394.5774 377076.9982 0.637399643 0.80013341 0.753252407 0.897751372 0.78144657 0.699989615 0.754203239 0.739927203 0.706472627 1 18.52449962 -1.12334145 4.398142906 1.000026754 0.756261792 0.56371293 0.065293289 9105276.757 2325603.555 2973.933696 0.015162853 0.07527635 1.12334145 -0.243764962 VQIPVSRPDPEPVS(ph)DNEEDS(ph)YDEEIHDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVSRPDPEPVS(0.998)DNEEDS(0.652)Y(0.35)DEEIHDPR;VQIPVSRPDPEPVS(1)DNEEDS(0.901)Y(0.099)DEEIHDPR;VQIPVS(0.001)RPDPEPVS(0.999)DNEEDS(0.729)Y(0.271)DEEIHDPR 96.55 0.0014236 7335500000 1720746 1577878 1564447 1627999 1704280 2240452 1713416 1642250 1556156 1693451 TRUE FALSE 1788682.381 1848866.272 1605217.774 1950012.343 1414587.094 1720140.977 1579113.977 1620238.325 1500150.25 2025250.3 0.883190774 0.912907541 0.792602166 0.962850045 0.698475193 0.849347351 0.779712995 0.800018805 0.740723381 1 20.94966879 3.248428628 24.99994653 0.801081676 0.882868634 0.156078192 0.084837831 332.6081986 842635.5673 0.021449082 0.028693365 1771.856835 -3.248428628 0.081786959 VQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 A0A087X0K9;G5E9E7;Q07157-2;H0YKB1;G3V1L9;Q07157 A0A087X0K9;G3V1L9 TJP1 Tight junction protein ZO-1 2 VQIPVS(0.002)RPDPEPVS(0.978)DNEEDS(0.396)Y(0.624)DEEIHDPR 70.217 0.018469 2359600000 480940 582120 553120 565340 634390 689590 561610 594460 564250 627620 TRUE FALSE 499927.8826 682094.5817 567534.7616 677162.5646 526556.6144 529443.1733 517589.5407 586492.236 543942.7527 750590.1225 0.666046445 0.908744415 0.756118079 0.902173562 0.701523506 0.705369225 0.689576808 0.781374839 0.724686798 1 19.51766578 -1.137612422 3.742856253 1.000137507 0.763015892 0.446619506 0.080222338 23719036.28 38836118.98 39378.09295 0.018749873 0.072842959 1.137612422 -0.237121615 VQIS(ph)PDSGGLPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.982)PDS(0.018)GGLPER;VQIS(0.997)PDS(0.003)GGLPER;VQIS(0.937)PDS(0.063)GGLPER;VQIS(0.89)PDS(0.11)GGLPER;VQIS(0.916)PDS(0.084)GGLPER 230.38 4.40E-12 5620390000 2409510 2569950 2444960 2409370 2653330 3002530 2487250 2502110 2449650 2562280 TRUE FALSE 2504639.315 3011318.921 2508677.666 2885936.195 2202317.914 2305237.911 2292292.846 2468573.308 2361487.575 3064309.708 0.817358411 0.982707105 0.818676278 0.941789985 0.718699519 0.752286202 0.748061738 0.805588711 0.770642592 1 21.54713069 3.243936895 24.99969025 0.785190312 0.891641336 0.198507344 0.08677725 170.6734733 793625.5115 0.022192537 0.029198142 1753.625673 -3.243936895 0.106451024 VQISPDS(ph)GGLPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QYH3;M0QXW7 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 VQIS(0.196)PDS(0.804)GGLPER 253.82 9.01E-24 1211300000 469310 517540 541910 495070 527210 656720 482310 483400 520120 507220 TRUE FALSE 487838.7212 606423.4691 556032.6198 592993.3684 437595.0325 504206.7327 444505.2819 476920.8137 501400.9828 606600.0477 0.804218073 0.999708904 0.916637943 0.977568945 0.72138971 0.831201274 0.732781482 0.786219545 0.826575904 1 19.21038609 3.246724934 24.99903716 0.79956482 0.92933918 0.257703459 0.08703381 193.7199524 593164.4321 0.022290786 0.029674928 1764.919632 -3.246724934 0.129774359 VQIYHNPTANSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQIYHNPTANSFR 13 0 P50552;K7ENR7;K7ENL7 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 95.264 0.0047758 1946370000 1003540 1204330 1208380 1017560 1570680 1438330 1102780 1169000 1136910 1688530 FALSE TRUE 1043160.534 1411164.309 1239871.375 1218830.331 1303696.375 1104299.656 1016341.222 1153331.467 1095992.831 2019365.125 0.516578464 0.698815827 0.613990685 0.603571051 0.645597153 0.546854871 0.503297403 0.571135677 0.542741289 1 20.94547036 -1.687731408 2.589348949 1.064643464 0.583871167 0.828090219 0.057063257 11650740.68 9709055.598 4942897.163 0.015324612 0.020524311 1.687731408 -0.480772297 VQLEELRDDLELYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQLEELRDDLELYYK 15 1 Q14746-2;Q14746;V9GY21 Q14746-2 COG2 Conserved oligomeric Golgi complex subunit 2 0 ; 215.79 2.09E-12 143206000 208840 176585 228450 168415 272410 241190 219440 216870 256640 197982 FALSE TRUE 217085.1645 206912.1001 234403.5947 201726.9843 226105.8455 185177.2778 202239.7194 213963.2124 247403.5765 236772.7823 0.916850165 0.87388465 0.989993835 0.85198553 0.954948636 0.782088532 0.854151045 0.90366473 1.044898717 1 17.85314372 1.284521247 6.406936962 1.02237593 0.889150811 0.474238742 0.055425565 0.143429469 13.83026177 0.038605053 0.013467323 19.25401241 -1.284521247 -0.133225119 VQLPTETLQELLDLHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQLPTETLQELLDLHR 16 0 P32456;P32455 P32456 GBP2;GBP1 Interferon-induced guanylate-binding protein 2;Interferon-induced guanylate-binding protein 1 0 ; 289.98 1.67E-45 659890000 388930 455940 494410 463950 522900 621510 504820 513290 469830 472860 FALSE TRUE 404285.2567 534244.1483 507294.7308 555717.9252 434017.6448 477173.7216 465250.8893 506410.1871 452920.9101 565507.8635 0.714906516 0.944715684 0.897060436 0.982688237 0.767482952 0.843796793 0.822713386 0.895496278 0.800910013 1 19.10918756 -1.304574936 4.934155339 1.000052289 0.858829605 0.244694942 0.077114547 4.20E-05 5.92E-06 0.070703703 0.016658858 0.049593535 1.304574936 -0.141222684 VQNS(ph)PPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 151.92 8.57E-05 3546890000 3428190 3687590 3544510 3558400 3995600 4638000 3733380 3669110 3562680 3606520 TRUE FALSE 3563537.588 4320904.897 3636882.842 4262240.899 3316429.339 3560894.79 3440747.92 3619931.582 3434459.843 4313148.543 0.826203307 1.001798304 0.843208344 0.988197104 0.768911459 0.825590576 0.797734621 0.839278208 0.796276736 1 22.04030997 3.233130419 24.99820807 0.827443771 0.915944844 0.181086137 0.078188594 180.7809202 832234.5756 0.020218793 0.024825684 1710.528912 -3.233130419 0.088501073 VQPNEAVYTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQPNEAVYTK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 123.79 0.0069899 0 73815 57212 70566 55119 82824 94237 82126 68875 76091 68078 FALSE TRUE 76729.2732 67037.71595 72405.00793 66021.37369 68745.60606 72351.88493 75688.74952 67951.84328 73352.49977 81416.58067 0.942428097 0.823391444 0.889315264 0.81090821 0.844368622 0.88866278 0.929647854 0.834619223 0.900952842 1 16.31303501 2.596794435 5.687653624 0.89765984 0.858795732 0.157564076 0.052129006 0.522942978 22.35133197 0.01646332 0.015442615 395.1795255 -2.596794435 -0.038864109 VQPQWS(ph)PPAGTQPCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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;VQPQWS(1)PPAGTQPCR;VQPQWS(1)PPAGTQPCR 209.42 2.51E-09 2531320000 1266760 1269820 1273400 1280720 1387000 1600970 1313840 1278200 1285720 1284980 TRUE FALSE 1316772.663 1487901.707 1306585.85 1534042.593 1151238.235 1229168.98 1210857.788 1261067.82 1239447.188 1536747.229 0.856857028 0.968214993 0.850228213 0.998240026 0.74913962 0.799851113 0.78793556 0.820608488 0.8065394 1 20.55144845 3.23325171 24.99956223 0.81479538 0.917075998 0.249548732 0.075469162 149.2467276 702801.038 0.019678941 0.024187776 1711.0067 -3.23325171 0.102280619 VQPSGGPAADQDVLGEES(ph)PLGKPAMLHLPSEQGAPETLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQPSGGPAADQDVLGEESPLGKPAMLHLPSEQGAPETLQR 40 1 C9J2V2 C9J2V2 IKBKG 1 VQPS(0.001)GGPAADQDVLGEES(0.999)PLGKPAMLHLPSEQGAPETLQR 60.88 0.0072782 57311000 20222 16542 19673 17488 29540 23680 23105 21369 18674 19096 TRUE FALSE 21020.38017 19382.95982 20185.69454 20947.0742 24518.80135 18180.67887 21293.96973 21082.58351 18001.92639 22837.49558 0.920432807 0.848734037 0.883883895 0.917222912 1.073620409 0.796088993 0.932412648 0.923156544 0.788261844 1 14.47911683 3.747686674 7.155805545 0.918046797 0.880648257 0.035853252 0.080918741 0.553519274 185.5861461 0.020515234 0.035187127 5593.539044 -3.747686674 -0.03739854 VQPTHVIHLAAMVGGLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQPTHVIHLAAMVGGLFR 18 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9 Q13630 TSTA3 GDP-L-fucose synthase 0 ; 188.96 2.03E-14 303070000 269810 282030 281670 344280 328560 391130 346250 323150 319570 317830 FALSE TRUE 280462.3071 330466.4586 289010.5516 412377.5564 272711.4886 300295.9851 319110.0202 318818.7028 308068.7381 380102.7033 0.73785928 0.869413597 0.760348582 1.084910875 0.717467901 0.790039067 0.839536308 0.838769891 0.810488154 1 18.53602976 -2.139417773 1.926152523 1.313069946 0.831247471 0.219316659 0.097339594 3431037.864 757111.4845 4688543.206 0.024815326 0.007254078 2.139417773 -0.481822474 VQQAELHTGSLPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQQAELHTGSLPR 13 0 Q13085;Q13085-4;Q13085-3;Q13085-2 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 101.3 0.0020043 466780000 406310 416190 497440 491680 590080 578210 516130 501910 491310 493930 FALSE TRUE 422351.4325 487667.395 510403.6951 588932.8365 489778.4124 443929.4904 475674.3819 495182.7174 473627.8491 590706.1266 0.714994163 0.825566848 0.864056884 0.996998016 0.829140566 0.751523423 0.805264006 0.838289456 0.801799453 1 19.17208105 -1.274840678 3.317379056 1.000669363 0.829272328 0.353986435 0.070620449 34162827.25 48915571.99 229805.5883 0.017691264 0.053107924 1.274840678 -0.171397035 VQQLLHICSEHFDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQQLLHICSEHFDSK 15 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 203.37 3.15E-09 2093990000 1422140 1794310 2129200 1840210 2553800 2603200 2271800 2352000 2267400 1530690 FALSE TRUE 1478287.185 2102468.785 2184688.701 2204198.046 2119705.988 1998646.252 2093730.38 2320475.287 2185796.717 1830599.399 0.807542702 1.148513862 1.193428067 1.20408542 1.157930014 1.091798814 1.143740341 1.267604091 1.194033341 1 20.80388468 4.737907637 4.771205455 1.170002986 0.787212276 0.69315434 0.069045162 0.093633933 6.084326394 0.016344473 0.119362908 54689.96399 -4.737907637 -0.38279071 VQQSSESSTSS(ph)PSQHEATPGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQQSSESSTSSPSQHEATPGAR 22 0 O75152;E9PBY7;E9PQ61;A0A1B0GTU1;A0A494C0C4 O75152 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 VQQSSES(0.043)S(0.218)T(0.014)S(0.043)S(0.68)PS(0.002)QHEATPGAR 136.74 2.62E-06 196490000 23277 60540 60639 62001 51737 75834 55786 61744 54739 87381 TRUE FALSE 24195.99393 70937.27406 62219.30216 74264.61275 42942.76322 58222.70278 51413.34755 60916.42267 52768.95408 104501.6339 0.231536992 0.678814975 0.595390711 0.710655039 0.410929108 0.557146339 0.491986064 0.58292316 0.504958172 1 16.67316597 -2.028697217 2.287641024 1.534958488 0.540034571 0.539988953 0.129979186 9144847.399 3236510.224 25656333.23 0.03164852 0.009360581 2.028697217 -0.994923918 VQRPHS(ph)SPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQRPHSSPPR 10 1 R4GNF5;E9PP52;E9PMB0;E9PJ55;Q9NUJ3 R4GNF5 TCP11L1 T-complex protein 11-like protein 1 1 VQRPHS(0.5)S(0.5)PPR;VQRPHS(0.5)S(0.5)PPR 86.772 0.0080727 364090000 85698.4 134719 115306 134020 117084 151824 104085 133008 102017 129955 TRUE FALSE 89081.83901 157855.9403 118310.9691 160528.756 97182.1035 116565.1769 95926.54572 131225.2453 98345.4281 155417.1941 0.573178788 1.015691611 0.76124762 1.032889295 0.625298276 0.750014679 0.617219647 0.844341877 0.632783449 1 17.2457866 4.888418134 15.77078004 0.795428141 0.569330465 0.16798563 0.15476836 31622.48552 3229520.832 0.034835601 7643.975639 77342.48726 -4.888418134 -0.226097676 VQRPHSS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQRPHSSPPR 10 1 R4GNF5;E9PP52;E9PMB0;E9PJ55;Q9NUJ3 R4GNF5 TCP11L1 T-complex protein 11-like protein 1 1 VQRPHS(0.191)S(0.809)PPR;VQRPHS(0.089)S(0.911)PPR 87.831 0.0076358 377610000 81740.8 110993 114554 121312 120327 140277 102431 112374 94758 112308 TRUE FALSE 84967.9899 130055.1843 117539.3713 145307.1515 99873.85952 107699.7927 94402.19057 110867.8103 91347.67809 134312.6023 0.632613682 0.96830217 0.875117966 1.081857912 0.743592617 0.801859176 0.702854304 0.825446074 0.680112488 1 17.03523515 VQS(ph)LPSVPLSCAAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VQSLPSVPLSCAAYR 15 0 Q96AD5-2;Q96AD5 Q96AD5-2 PNPLA2 Patatin-like phospholipase domain-containing protein 2 1 VQS(0.969)LPS(0.031)VPLSCAAYR;VQS(0.855)LPS(0.145)VPLSCAAYR;VQS(0.864)LPS(0.136)VPLSCAAYR;VQS(1)LPSVPLSCAAYR;VQS(0.999)LPS(0.001)VPLSCAAYR;VQS(0.996)LPS(0.004)VPLSCAAYR;VQS(1)LPSVPLSCAAYR 289.59 7.44E-44 3644596000 801739 829493 883784 857228 1158359 1170166 985869 948445 920475 898303 TRUE FALSE 833392.2748 971951.9702 906816.1371 1026785.14 961461.5509 898412.6805 908594.0117 935732.6461 887347.2846 1074308.274 0.775747795 0.904723527 0.84409304 0.955763969 0.894958714 0.836270838 0.845747942 0.871009438 0.825970819 1 20.0349766 -2.497994852 2.196084097 2.673334707 0.865133717 0.439100058 0.046776504 3088309.505 168460.2538 26103699.79 0.0111134 0.003176912 2.497994852 -1.808200989 VQS(ph)SPNLLAAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQSSPNLLAAGR 12 0 O94875-12;O94875-9;O94875-11;C9JN77;C9IZT7;C9JWC3;C9JG84;C9JI79;C9JEA9;C9J372;C9JZ60;C9JBB0;C9JDX2;C9J4Z9;C9J9D3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 VQS(0.919)S(0.081)PNLLAAGR 94.059 0.0019598 0 105010 98611 106250 118520 140630 143270 102640 94841 104290 108930 TRUE FALSE 109155.8759 115546.6722 109018.9623 141962.9023 116725.7628 109997.7138 94594.8086 93569.81152 100536.6233 130272.7479 0.837902613 0.88695966 0.836851637 1.089735993 0.896010599 0.844364731 0.726128911 0.718260826 0.771739484 1 16.99117579 2.52853242 3.357269524 0.772429469 0.913393627 0.169302484 0.100449687 0.310476329 7.022364956 0.034716318 0.031043331 337.7010571 -2.52853242 0.140964158 VQSFLASLDGEKLELLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQSFLASLDGEKLELLK 17 1 Q8IWE2;Q8IWE2-2 Q8IWE2 FAM114A1 Protein NOXP20 0 ; 157.42 2.41E-08 62986000 192384 121653 163975 139907 204433 194613 199477 164177 200643 103897 FALSE TRUE 199979.4689 142545.9564 168248.3232 167580.187 169683.5517 149417.0801 183841.4715 161976.4759 193421.8976 124253.6279 1.609445714 1.147217661 1.354071716 1.34869452 1.365622514 1.202516841 1.479566227 1.303595545 1.556670021 1 16.92292845 -1.989572728 3.18426655 0.66550638 1.361073993 0.397815093 0.137254644 0.080808334 0.000264617 0.032948871 0.028100527 0.010243002 1.989572728 0.695567613 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 VQSGMGLILQGY(0.075)ES(0.934)GS(0.991)EEEGEIHEK;VQSGMGLILQGY(0.008)ES(0.993)GS(0.998)EEEGEIHEK 86.675 0.0087081 84629000 146519 102008 126580 109223 162546 149995 157611 138711 158926 100700 TRUE FALSE 152303.6833 119527.0805 129878.7788 130826.9834 134916.489 115160.9344 145257.038 136851.8059 153206.2843 120430.237 1.264663153 0.992500584 1.078456557 1.086330034 1.120287499 0.956246017 1.206150894 1.136357524 1.272157958 1 16.87783814 VQT(ph)TPPPAVQGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.715)T(0.285)PPPAVQGQK 122.51 0.0026179 237090000 507570 394830 482960 410450 568830 602150 535130 499230 532180 409300 TRUE FALSE 527609.2555 462638.9811 495546.3344 491635.7849 472140.4798 462309.7882 493185.1123 492538.6384 513026.9458 489494.4985 1.077865547 0.945136222 1.01236344 1.004374485 0.964547061 0.944463706 1.007539643 1.006218946 1.048074998 1 18.90093312 1.664387103 2.718061748 1.023594733 0.98954157 0.082534696 0.038291947 0.500798475 8.450831605 0.023806058 0.010014294 46.17289478 -1.664387103 -0.034053163 VQT(ph)TPSKPGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.494)T(0.494)PS(0.012)KPGGDR 70.529 0.076042 217510000 333200 244450 280830 227150 363030 400040 343390 293970 331000 250900 TRUE FALSE 346354.9933 286432.3859 288148.6605 272079.592 301322.2903 307136.7727 316474.1945 290029.813 319087.3747 300059.0512 1.154289437 0.954586721 0.960306511 0.90675349 1.004209968 1.023587762 1.054706376 0.966575785 1.063415262 1 18.19488692 3.006685298 24.97423265 1.017557624 0.984604084 0.02926939 0.065400292 578.7039609 2161839.956 0.018855824 0.022484703 1015.512558 -3.006685298 -0.03295354 VQTEKEEKEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VQTEKEEKEEAR 12 2 O75400-3;O75400;O75400-2 O75400-3 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 ;;; 121.56 0.00021042 578927000 1598440 746724 1106547 653155 1631910 1441900 1319690 1093313 1303590 632015 FALSE TRUE 1661547.645 874968.0383 1135384.524 782347.1095 1354518.521 1107040.577 1216249.249 1078658.928 1256674.051 755846.2386 2.198261446 1.157600572 1.502136898 1.035061193 1.792055648 1.464637278 1.60912258 1.427087776 1.662605417 1 19.52773325 -1.028923425 4.5348796 0.999979744 1.513294481 0.213015935 0.307166593 0.809264144 84437534.7 3825.122017 0.065396368 0.093557062 1.028923425 0.513314737 VQTLNEQDWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VQTLNEQDWER 11 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 0 103.08 0.0064718 80173000 18253 22055 21429 20978 24658 26853 19896 20726 25636 24503 FALSE TRUE 18973.64253 25842.77469 21987.45734 25127.38579 20466.64197 20616.79771 18336.49953 20448.20187 24713.36537 29303.89371 0.647478547 0.881888767 0.750325454 0.857476008 0.698427389 0.703551477 0.625735942 0.697798118 0.843347495 1 14.83880475 0.966308821 4.069623273 0.999610453 0.734030397 0.534271087 0.077633513 0.167275639 8.197293052 0.077125297 0.019713528 9.25355949 -0.966308821 -0.265580056 VQTT(ph)PPPAVQGQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VQTTPPPAVQGQK 13 0 Q2M2I8;Q2M2I8-2;E9PG46 Q2M2I8 AAK1 AP2-associated protein kinase 1 1 VQT(0.015)T(0.985)PPPAVQGQK;VQTT(1)PPPAVQGQK;VQT(0.004)T(0.996)PPPAVQGQK;VQT(0.194)T(0.806)PPPAVQGQK 236.05 1.18E-15 1410350000 1713160 1341610 1548190 1257400 1832600 1936760 1782210 1574990 1683680 1236050 TRUE FALSE 1780796.88 1572021.081 1588537.103 1506109.967 1521095.307 1486976.842 1642515.723 1553879.835 1623084.686 1478230.332 1.204681599 1.063447994 1.074620828 1.018860143 1.028997494 1.005916879 1.111136531 1.051175721 1.097991734 1 20.49543965 4.820125067 2.540551244 1.050526049 1.25941019 0.631537141 0.03547268 0.472504242 3.156181042 0.008678099 0.230641599 66088.37409 -4.820125067 0.208884141 VQTT(ph)PSKPGGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 VQT(0.33)T(0.594)PS(0.075)KPGGDR;VQT(0.378)T(0.62)PS(0.002)KPGGDR 106.42 0.0031097 703050000 1234950 938920 1115600 890770 1389150 1467480 1296600 1142760 1214720 934440 TRUE FALSE 1283706.78 1100172.206 1144673.452 1066961.647 1153022.779 1126680.01 1194969.104 1127443.171 1171002.464 1117525.627 1.148704556 0.984471568 1.024292799 0.954753628 1.031764061 1.008191654 1.069299061 1.008874556 1.047852896 1 20.09187648 VQVAALQAS(ph)PPLDQDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VQVAALQASPPLDQDDR 17 0 Q9UDY2-7;Q9UDY2;Q9UDY2-3;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-6;A0A3B3IRI3;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3ISZ5;Q9UDY2-5;A0A3B3ISF1;A0A3B3IRV6;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR 307.82 5.15E-58 507560000 576880 638880 610560 653240 652350 823250 698740 662840 632260 608440 TRUE FALSE 599655.6678 748602.6702 626471.6952 782448.9223 541463.78 632062.664 643970.933 653955.714 609505.0861 727652.1687 0.824096586 1.028791918 0.860949396 1.075306246 0.744124464 0.868632969 0.884998301 0.898720216 0.837632474 1 19.47288945 VQVEYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 121.29 0.045867 631350000 1132220 945390 1000210 964790 1279440 1449100 1401210 1104190 1142620 802260 FALSE TRUE 1176920.92 1107753.378 1026276.294 1155622.582 1061961.246 1112568.486 1291379.499 1089390.139 1101497.329 959447.4868 1.22666528 1.154574267 1.069653429 1.204466736 1.10684666 1.159592892 1.345961625 1.135434877 1.148053796 1 19.87184432 0.729483557 2.197631366 1.000214665 1.175461642 0.352461469 0.0711278 1.388154546 9.533838944 0.068087977 0.018535818 5.363935623 -0.729483557 0.175246977 VQVEYKGETK ddPTM_MDA-MB-175_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 ;;;;; 125.28 0.0003768 4002140000 4905300 3117580 3954950 2220505 7070350 5399720 4338990 4023740 4991780 3672500 FALSE TRUE 5098965.032 3653000.114 4058019.246 2659714.261 5868534.432 4145716.864 3998888.626 3969808.347 4812126.813 4392056.061 1.160951719 0.831728936 0.92394523 0.605573842 1.336170202 0.943912556 0.910482146 0.903861037 1.095643304 1 22.06646504 3.25487075 24.99999705 1.006340856 0.880162584 0.145666803 0.17288589 568.713161 871712.0763 0.047403455 0.064001355 1798.335636 -3.25487075 -0.126178272 VQVNHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VQVNHEK 7 0 P19367-4;P19367-2;P19367;P19367-3;B1AR62 P19367-4 HK1 Hexokinase-1 0 ;;;; 107.9 0.0073747 1587220000 2610481 2080800 2350964 2022114 2740570 2881790 2561679 2187007 2177538 1652243 FALSE TRUE 2713544.806 2438161.214 2412232.053 2422082.114 2274728.89 2212537.946 2360887.906 2157693.748 2099168.833 1975968.382 1.373273394 1.233906998 1.220784743 1.225769671 1.151197009 1.119723355 1.194800447 1.09196775 1.062349404 1 20.91412843 8 0.14447827 0.965529401 2.280311213 0.875749029 0.035442377 23.44510814 0.223922426 0.136044103 6.414795283 99999999.97 -8 1.314781812 VQYAPERPGPQPTAETTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VQYAPERPGPQPTAETTR 18 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ; 139.11 5.41E-07 747540000 241683 218290 198032 211310 258036 285260 231461 202167 212559 239500 FALSE TRUE 251224.8315 255779.6094 203192.8766 253106.4873 214175.1329 219012.6882 213318.482 199457.282 204909.0431 286425.4395 0.877103765 0.893005907 0.709409321 0.883673209 0.747751782 0.764641187 0.744760949 0.696367203 0.71540099 1 18.12780011 4.254671025 24.97167634 0.768004652 0.885054929 0.158582003 0.089231021 340.8834094 528371.3111 0.020319774 0.055276889 17975.08799 -4.254671025 0.117050277 VRDALTAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRDALTAEK 9 1 Q9HB71;B2ZWH1;Q9HB71-2 Q9HB71 CACYBP Calcyclin-binding protein 0 ; 142.71 9.46E-05 653980000 675850 421250 508510 393450 1181860 813540 766940 573800 584710 773430 FALSE TRUE 702533.0799 493596.4106 521762.1883 471273.2357 980967.8593 624607.6643 706825.2388 566109.1495 563666.4013 924968.8003 0.75952084 0.53363574 0.564086257 0.509501764 1.060541565 0.675274306 0.764161168 0.612030535 0.609389637 1 19.81904518 VRDFWDGFEIICK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRDFWDGFEIICK 13 1 Q7LBC6;Q7LBC6-2;Q7LBC6-3 Q7LBC6 KDM3B Lysine-specific demethylase 3B 0 106.61 0.0008285 0 79612 68105 89322 84227 104630 131860 87001 81866 98586 84821 FALSE TRUE 82755.14323 79801.50397 91649.8047 100886.8492 86845.02997 101237.5134 80181.63429 80768.72018 95037.90912 101440.051 0.815803447 0.786686355 0.903487369 0.994546515 0.856121711 0.998003376 0.790433695 0.796221211 0.936887435 1 16.63026785 4.236283274 24.98344979 0.895065977 0.801244883 0.233768865 0.074821357 90.76414755 995773.4577 0.019570104 0.045769169 17229.92052 -4.236283274 -0.093821094 VRDGPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRDGPGK 7 1 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 71.296 0.049888 51222000 70993 55460 74297 56725 83974 81225 83262 72487 78814 67846 FALSE TRUE 73795.85846 64984.82358 76233.24086 67945.03569 69700.12947 62361.72473 76735.70688 71515.43033 75977.49954 81139.12471 0.909497837 0.800906145 0.939537383 0.83738931 0.859019982 0.768577735 0.94573003 0.881392677 0.936385496 1 16.30811012 1.118409247 0.995041177 0.99812393 0.858305815 0.409230329 0.052484607 0.482039766 1.027513088 0.046351403 0.015695305 13.13437001 -1.118409247 -0.139818115 VRDVFEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VRDVFEAK 8 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 ;;; 150.27 0.00044863 2062420000 1965380 1361193 1681000 1319300 2937710 2352920 2088030 1870790 1968310 1636760 FALSE TRUE 2042974.72 1594967.309 1724808.241 1580253.602 2438359.104 1806489.989 1924364.753 1845715.12 1897470.908 1957451.784 1.043690954 0.814818184 0.881149796 0.807301419 1.245680289 0.922878409 0.983096885 0.942917284 0.969357673 1 20.90054534 VREAAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VREAAEK 7 1 P38646;H0YBG6;A0A3B3ITN1 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 66.299 0.062245 415890000 745650 581730 702810 582330 818360 855520 827300 658790 718650 605940 FALSE TRUE 775088.8378 681637.6023 721125.806 697513.1359 679255.4595 656838.4455 762454.0643 649959.9976 692785.9269 724662.3416 1.069586197 0.94062788 0.995119747 0.962535371 0.937340635 0.906406209 1.052150803 0.896914273 0.956012045 1 19.4669494 4.744036837 24.46265272 0.957742197 1.069586262 0.355445503 0.043779334 454.6832775 2031017.986 0.009846732 0.084326428 55467.2759 -4.744036837 0.111844064 VREEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VREEAER 7 1 Q14244-6;Q14244;Q14244-7;A0A087WZ40;Q14244-5;Q14244-3;Q14244-2;Q14244-4 Q14244-6 MAP7 Ensconsin 0 83.429 0.020325 37761000 22065 47565 48709 48278 54879 55194 38783 46875 44095 56815 FALSE TRUE 22936.14324 55733.91875 49978.39655 57827.2443 45550.68718 42376.02997 35743.08712 46246.7173 42508.02956 67946.81146 0.337560258 0.820258045 0.735551757 0.851066342 0.670387413 0.623664732 0.526045098 0.680631163 0.625607422 1 16.05211823 -1.302239955 3.49833052 1.001220102 0.661219182 0.358954852 0.138934223 45451576.05 60782717.96 568360.6745 0.0324174 0.049860892 1.302239955 -0.34000092 VREEEIEVDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 ;;;;; 151.16 3.06E-05 2080900000 3443000 3683040 3771560 3622550 4415550 4641190 3924230 3932950 3817710 3926410 FALSE TRUE 3578932.299 4315573.47 3869849.952 4339079.578 3664996.388 3563343.96 3616638.599 3880235.238 3680311.363 4695714.864 0.762169851 0.919045043 0.824123709 0.924050907 0.78049807 0.758850157 0.770199789 0.826335361 0.783759549 1 22.16291338 3.20613634 24.99963814 0.806314412 0.859381392 0.035186706 0.078155216 436.9486708 336893.3208 0.020814702 0.024880133 1607.445806 -3.20613634 0.05306698 VREEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VREEFK 6 1 P02545;P02545-6;P02545-3;P02545-2;Q3BDU5 P02545;P02545-2 LMNA Prelamin-A/C;Lamin-A/C 0 ;;; 97.068 0.037842 12361000000 7376610 5583150 6608920 5105070 9398310 7909360 8641040 6852050 7241750 5486140 FALSE TRUE 7667844.259 6542012.582 6781153.884 6114837.609 7800788.623 6072531.008 7963732.706 6760209.477 6981120.832 6561044.095 1.168692688 0.997099316 1.033547982 0.931991543 1.188955372 0.925543392 1.213790456 1.030355745 1.064025898 1 22.64549399 3.254842227 24.99978818 1.072278728 1.030331638 0.035078873 0.0959945 899.2058984 1380686.378 0.024739838 0.033403962 1798.21753 -3.254842227 -0.04194709 VREEILAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VREEILAK 8 1 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 119.75 0.0014909 371060000 505460 378430 495650 372400 649610 595060 545470 511620 543560 426170 FALSE TRUE 525415.9511 443422.4087 508567.0462 446059.6085 539189.5242 456866.3332 502714.6361 504762.5707 523997.3818 509669.852 1.030894704 0.870018909 0.997836235 0.875193239 1.057919204 0.896396621 0.986353488 0.990371647 1.028111394 1 18.95920349 1.773061602 2.352020819 1.010813797 0.953710437 0.124559684 0.060249336 0.525818675 5.788797227 0.034459134 0.015496177 59.30094336 -1.773061602 -0.057103361 VREELIDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VREELIDK 8 1 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 98.048 0.0071125 256520000 216910 143440 211790 157550 238500 239840 221550 191320 203570 166030 FALSE TRUE 225473.7743 168074.7042 217309.4214 188712.9198 197959.8552 184140.7948 204184.3321 188755.6683 196243.5555 198560.3997 1.135542508 0.846466387 1.094424778 0.95040562 0.996975507 0.927379251 1.028323535 0.950620913 0.988331791 1 17.5992184 4.782829131 23.29866289 0.97755901 1.135543884 0.373764342 0.061965757 14416.41791 7586974.35 0.013066427 6.286136278 60649.76618 -4.782829131 0.157984874 VREITENLMATGDLDQDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VREITENLMATGDLDQDGR 19 1 P13796;Q5TBN3 P13796 LCP1 Plastin-2 0 172.57 7.37E-12 191810000 102200 90773 105440 95061 128060 116770 112910 114350 113450 129680 FALSE TRUE 106234.9349 106362.5566 108187.853 113863.7821 106292.4069 89651.93717 104059.8192 112817.3253 109366.9567 155088.3131 0.684996392 0.685819289 0.697588689 0.734186734 0.685366968 0.578070232 0.670971378 0.727439244 0.705191477 1 17.24273045 0.210309643 1.03341888 1.001511244 0.680268909 0.852561848 0.039425798 1.612523771 1.780038693 0.046093192 0.01278116 1.622966826 -0.210309643 -0.321242335 VRELELELDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRELELELDR 10 1 O94992 O94992 HEXIM1 Protein HEXIM1 0 ; 176.18 2.35E-06 188989000 183635 178007 200820 159791 270170 247590 210057 215883 211031 214847 FALSE TRUE 190885.0516 208578.3175 206053.5342 191397.1829 224246.5999 190090.9748 193592.1835 212989.4415 203436.0355 256942.1562 0.742910601 0.811771492 0.801945221 0.744903778 0.872751296 0.739820112 0.753446559 0.828939263 0.791758108 1 17.97108409 -0.268524245 0.768402327 1.00995255 0.78600583 0.707387089 0.041070415 5.004219326 2.444912337 0.1899778 0.013242384 0.538859762 0.268524245 -0.22394672 VREYELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VREYELR 7 1 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 ;;;;; 152.63 0.0016423 5401920000 3596453 3796445 3868253 3352482 4723870 4799900 4174729 3945400 4166740 4140070 FALSE TRUE 3738443.742 4448454.897 3969062.851 4015592.933 3920908.265 3685195.968 3847502.832 3892518.366 4016779.841 4951237.45 0.755052404 0.898453153 0.801630479 0.811028147 0.791904712 0.744297967 0.777079038 0.786170812 0.811267866 1 22.23935771 0.800759596 5.564082562 0.999999812 0.796612596 0.704441022 0.039474103 3.483354966 97.12177171 0.038257833 0.009637739 6.320618765 -0.800759596 -0.203387216 VRGEVAPDAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VRGEVAPDAK 10 1 P09382;F8WEI7 P09382 LGALS1 Galectin-1 0 ;;;; 125.24 0.00037782 9968280000 11075470 7881110 9360250 7547470 12583570 12700220 12251830 9574550 9722110 7595960 FALSE TRUE 11512738.11 9234629.336 9604185.805 9040337.039 10444619.27 9750786.379 11291499.55 9446218.818 9372213.16 9084242.929 1.267330497 1.016554644 1.057235686 0.995166808 1.149751206 1.073373583 1.242976398 1.039846566 1.03169997 1 23.11493486 1.53602871 10.7890355 1.022749122 1.106319386 0.194193631 0.08425739 0.207908254 33.09741361 0.044550172 0.020698672 34.35806602 -1.53602871 0.083570264 VRGGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.73)S(0.27)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.67)S(0.33)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.598)S(0.402)PDAR 224.08 1.10E-34 2287000000 754643 759380 726265 615255 1108080 1045327 809178 832281 832664 1109000 TRUE FALSE 784436.8884 889797.6078 745192.0625 736950.6026 919728.9574 802565.6463 745752.514 821125.6345 802696.5853 1326287.317 0.591453208 0.670893551 0.56186322 0.555649287 0.693461323 0.605122009 0.562285792 0.619115952 0.605220735 1 20.33896191 -1.078965951 3.238934754 1.000401972 0.607594529 0.881706509 0.043159528 3573499.359 5594026.234 15709.50778 0.010387751 0.083374655 1.078965951 -0.392807442 VRGGAPDPSPGATATPGAPAQPS(ph)SPDARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRGGAPDPSPGATATPGAPAQPSSPDARR 29 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDARR;VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDARR 99.226 0.00044033 210406000 45073 63742 47212 38208 106378 89907 50014 56075 61882 124689 TRUE FALSE 46852.51684 74689.19266 48442.38351 45765.42836 88295.90556 69027.4618 46093.77199 55323.40635 59654.87891 149119.4222 0.314194597 0.500868308 0.324856298 0.306904545 0.592115395 0.462900545 0.309106428 0.371000675 0.40004768 1 17.18610865 0.861066711 17.44094433 1 0.397785181 0.799539627 0.090430638 8289.443187 1040620.02 0.087070464 0.021767616 7.262175018 -0.861066711 -0.602214819 VRGGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 VRGGAPDPSPGATATPGAPAQPS(0.287)S(0.713)PDAR 198.63 3.05E-25 598110000 206290 239690 227400 195680 366330 342130 277090 275100 240180 335890 TRUE FALSE 214434.4885 280854.893 233326.2308 234384.92 304061.3574 262675.4925 255370.9618 271412.7345 231535.9687 401701.2145 0.533815883 0.699163664 0.580845221 0.583480735 0.756934125 0.653907638 0.635723649 0.675658237 0.576388521 1 18.6157633 -2.192930671 2.497017043 2.09457339 0.639022651 0.748905481 0.063683348 2850774.515 769195.1422 17680035.9 0.014981264 0.006413119 2.192930671 -1.455550739 VRGQTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRGQTPK 7 1 P62861;E9PR30;E9PM49 P62861 FAU 40S ribosomal protein S30 0 ; 96.492 0.011575 599960000 745040 590140 648450 583260 883970 853370 893750 736350 705770 749910 FALSE TRUE 774454.7545 691491.9543 665349.1397 698627.0871 733713.0951 655187.7504 823695.5396 726480.4327 680369.4756 896840.5066 0.86353677 0.771031136 0.741881232 0.77898699 0.818108783 0.730551024 0.918441499 0.81004418 0.758629289 1 19.77449191 -5 0.293463748 2.592086669 0.788885613 0.537367994 0.055270374 193.0038672 1.807214782 188.4199835 0.056418902 1.00E-05 5 -1.803201056 VFVHYTGWLLDGTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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" 0 234.82 3.20E-17 1521300000 2069700 3338600 3586200 3519600 4739500 4936100 4651300 4314900 4045100 3694200 FALSE TRUE 2151413.354 3911978.579 3679659.318 4215766.375 3933881.483 3789765.582 4286718.952 4257065.823 3899517.641 4418007.76 0.486964594 0.885462134 0.832877514 0.954223397 0.890419777 0.857799666 0.970283255 0.963571377 0.882641646 1 22.07496452 5.030657141 1.688424025 0.923770167 2.11E-12 0.861087937 0.051617994 0.777980497 1.156972073 0.013198276 1.474361467 107314.1873 -5.030657141 -0.923770167 down VRHFSQS(ph)EETGNEVFGALNEEQPLPR ddPTM_MDA-MB-175_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(0.1)QS(0.533)EET(0.367)GNEVFGALNEEQPLPR 121.62 8.58E-05 78017000 24655 25328 37706 17428 61139 40504 26594 42018 31888 66382 TRUE FALSE 25628.39844 29677.88698 38688.64934 20875.20638 50746.61462 31097.55984 24509.49279 41454.81744 30740.35711 79388.28194 0.322823442 0.373832085 0.487334508 0.262950726 0.639220467 0.391714735 0.308729351 0.52217804 0.387215296 1 16.27663845 -5 0.355104893 7.973267109 0.398773203 0.735076438 0.106150273 219.6928374 1.77387535 1168.644542 0.074456852 1.00E-05 5 -7.574493906 VRIEAENEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRIEAENEK 9 1 Q06787;Q06787-2;R9WNI0;G3V0J0;Q06787-9;Q06787-7;Q06787-6;Q06787-5;Q06787-8;Q06787-3;Q06787-4;A8MQB8;Q06787-10;Q06787-11;A0A087WXI3 Q06787 FMR1 Fragile X mental retardation protein 1 0 72.848 0.041579 124130000 151570 200430 210130 241890 255500 327220 260850 232560 257950 305940 FALSE TRUE 157554.1006 234852.2934 215606.1604 289735.12 212070.2013 251228.1141 240403.8954 229442.9136 248666.4299 365883.0854 0.430613239 0.641877973 0.589276108 0.791878968 0.57961193 0.68663495 0.657051132 0.627093524 0.679633576 1 18.4810232 -5 0.212924585 2.769627186 0.584374333 0.659803688 0.082256534 89.62262789 0.894744381 67.85576617 0.164507997 1.00E-05 5 -2.185252854 VRLDDDDEGVPSSALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VRLDDDDEGVPSSALR 16 1 Q00535;Q00535-2 Q00535 CDK5 Cyclin-dependent-like kinase 5 0 ;;; 237.34 8.50E-20 635330000 471530 555780 544060 514080 632310 675030 526230 517590 519310 599170 FALSE TRUE 490146.3685 651230.8916 558238.6506 615763.4896 524830.1721 518264.5127 484982.7176 510652.5527 500620.1345 716565.8897 0.684021352 0.908822065 0.779047201 0.859325707 0.732424163 0.723261489 0.676815244 0.712638656 0.698637964 1 19.45073984 3.215916505 24.6274546 0.734155128 0.812965583 0.026018625 0.102431565 396.1012152 430793.4716 0.027158565 0.032483869 1644.055616 -3.215916505 0.078810455 VRPAS(ph)TGGLSLLPPPPGGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRPASTGGLSLLPPPPGGK 19 1 Q9NVZ3;Q9NVZ3-2;D6RB24;Q9NVZ3-4 Q9NVZ3 NECAP2 Adaptin ear-binding coat-associated protein 2 1 VRPAS(0.489)T(0.489)GGLS(0.021)LLPPPPGGK;VRPAS(0.493)T(0.493)GGLS(0.015)LLPPPPGGK 107.39 0.00017888 1642040000 1394590 1179280 1443530 1234120 1837510 1911900 1716080 1553820 1605940 1376410 TRUE FALSE 1449649.49 1381812.166 1481149.578 1478225.253 1525170.707 1467890.2 1581569.165 1532993.584 1548142.533 1646091.187 0.880661717 0.839450559 0.899798012 0.898021485 0.926540837 0.891742944 0.960802888 0.931293234 0.940496217 1 20.65061283 8 0.082104369 1.075227471 0.480520234 0.778976016 0.020102382 74.62077495 0.444947906 0.471199766 5.024605066 100000000 -8 -0.594707237 VRPCVVYGGADIGQQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRPCVVYGGADIGQQIR 17 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 ; 149.73 3.24E-07 0 342410 358380 319600 300200 371840 428310 332710 345930 328410 325930 FALSE TRUE 355928.6112 419928.9772 327929.0386 359578.664 308634.7696 328841.4936 306631.3208 341293.3742 316590.5883 389789.7432 0.913129751 1.077321773 0.841297249 0.922493909 0.791798078 0.843638139 0.786658259 0.87558326 0.812208617 1 18.5723366 4.219441679 24.94776989 0.851596913 0.995225763 0.365328452 0.071146698 180.1501435 235073.5746 0.016108707 0.034886306 16574.54744 -4.219441679 0.143628851 VRPEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VRPEEK 6 1 Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3;A0A087WT54;K7ERA4 Q7Z4V5-2 HDGFRP2 Hepatoma-derived growth factor-related protein 2 0 ;; 107.67 0.028332 501179000 520874 426001 492789 395100 613333 615356 581211 516352 559888 434009 FALSE TRUE 541438.5077 499163.3579 505631.4862 473249.6007 509078.8757 472448.8948 535654.1631 509431.146 539737.7402 519044.7539 1.043144167 0.961696182 0.974157782 0.911770319 0.980799578 0.910227666 1.031999956 0.981478268 1.039867441 1 18.98549941 2.212816546 24.99887546 1.009266615 0.962445914 0.286317593 0.038200583 307.5384237 298634.4078 0.013896086 0.010266592 163.2362261 -2.212816546 -0.0468207 VRPGETLLIHSGSGGVGQAAIAIALSLGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 125.42 8.55E-06 960887000 287882 336636 383633 463523 425549 515911 372535 396621 412014 361920 FALSE TRUE 299247.8037 394450.6143 393630.7911 555206.4659 353214.333 396098.489 343334.7333 391304.9442 397185.6966 432831.2946 0.691372845 0.911326467 0.909432372 1.282731801 0.816055441 0.915133665 0.79322992 0.904058808 0.917645516 1 18.72344529 VRPSS(ph)DLNNSTGQSPHHK ddPTM_MDA-MB-175_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(0.18)S(0.82)DLNNSTGQSPHHK 209.24 3.29E-16 190580000 7490.2 55299 53319 47283 59939 77095 48569 67101 51230 58328 TRUE FALSE 7785.91888 64796.17308 54708.53694 56635.43627 49750.59019 59190.85464 44762.03487 66201.62085 49386.24231 69756.25484 0.111616068 0.928894093 0.784281454 0.811904773 0.713206153 0.848538311 0.64169206 0.949042075 0.707982996 1 16.09003496 4.744368131 24.8841897 0.813226466 0.111615744 0.791149077 0.109224566 241.5874848 1035128.65 0.023602067 0.212432144 55509.60418 -4.744368131 -0.701610722 VRPSSDLNNSTGQS(ph)PHHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRPSSDLNNSTGQSPHHK 18 1 J3KNR0;P27448-8;P27448-3;P27448-4;P27448-2;P27448 J3KNR0 MARK3 MAP/microtubule affinity-regulating kinase 3 1 VRPSSDLNNSTGQS(1)PHHK;VRPSSDLNNSTGQS(1)PHHK 168.05 1.31E-11 220490000 112294 124753 148316 111842 148870 161379 122933 123268 131133 121491 TRUE FALSE 116727.4538 146178.3573 152181.2368 133964.0138 123565.1306 123901.173 113297.1902 121615.7941 126413.5489 145294.8354 0.803383366 1.00608089 1.047396051 0.922014974 0.850444066 0.852756897 0.77977438 0.837027646 0.870048468 1 17.1486239 3.350617352 4.019062788 0.849239706 0.961266046 0.182323415 0.079196475 0.275832125 8.17658887 0.021898872 0.030092734 2241.905757 -3.350617352 0.11202634 VRS(ph)LETENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRSLETENR 9 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 VRS(1)LETENR 84.365 0.009412 264190000 105150 89100 101930 87394 123940 125960 106390 104090 110510 68839 TRUE FALSE 109301.4032 104402.2319 104586.3795 104680.2724 102872.7231 96707.69894 98050.8738 102694.8438 106532.7667 82326.68405 1.327654629 1.268145719 1.27038251 1.271523001 1.249567188 1.174682305 1.190997487 1.247406536 1.294024749 1 16.3290725 -4.51403327 0.226131691 2.74E-13 1.281584594 0.763250326 0.042587892 62.89020882 0.769957144 28.86374253 0.081563722 3.06E-05 4.51403327 1.281584594 VRS(ph)PDEALPGGLS(ph)GCSSGSGHSPYALER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRSPDEALPGGLSGCSSGSGHSPYALER 28 1 Q5JSZ5-5 Q5JSZ5-5 PRRC2B Protein PRRC2B 2 VRS(0.997)PDEALPGGLS(0.306)GCS(0.241)S(0.223)GS(0.191)GHS(0.042)PYALER 50.166 0.054675 73773000 24833 41967 39141 37227 41267 50320 40243 44875 40957 40757 TRUE FALSE 25813.42602 49174.50579 40161.04661 44590.38949 34252.45008 38633.94261 37088.6485 44273.52403 39482.96557 48742.55381 0.529587065 1.008861907 0.823942192 0.914814387 0.702721696 0.792612196 0.760909013 0.90831359 0.810030712 1 15.57289422 0.386214605 0.71358544 1.002713775 0.805785323 0.186301712 0.123367072 3.58885297 2.697001057 0.140006327 0.041788869 2.433406173 -0.386214605 -0.196928452 VRTELADK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VRTELADK 8 1 P35579 P35579 MYH9 Myosin-9 0 ;;;;; 166.66 0.00028928 7007660000 5671340 3441100 4499120 3924160 6869510 6319000 7282760 5146860 5033300 3735670 FALSE TRUE 5895248.882 4032082.157 4616370.763 4700347.136 5701833.144 4851508.015 6711918.241 5077874.76 4852152.516 4467603.013 1.319555221 0.902515766 1.033299232 1.052095972 1.276262266 1.085930868 1.502353325 1.136599368 1.086075129 1 22.09106956 3.256224062 24.6445404 1.201937369 1.061300907 0.079765635 0.161393964 392.3022984 547347.329 0.042939471 0.058009419 1803.948195 -3.256224062 -0.140636461 VRVDSTAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VRVDSTAK 8 1 P78371;P78371-2;F5GWF6;F8VQ14 P78371 CCT2 T-complex protein 1 subunit beta 0 ;;; 99.013 0.0064886 1488240000 1417280 1107900 1250170 1031540 2178890 1807220 1576370 1344800 1403120 1543290 FALSE TRUE 1473235.309 1298173.207 1282750.457 1235575.533 1808523.056 1387520.544 1452810 1326775.156 1352621.985 1845668.127 0.798212467 0.703362207 0.695006019 0.66944621 0.979874458 0.751771417 0.787145846 0.718859006 0.732863057 1 20.81571173 -1.105071741 3.868820096 1.000080246 0.757970796 0.430757232 0.082881625 24808498.01 46608334.65 26320.72396 0.01996783 0.078510593 1.105071741 -0.24210945 VRVELSNGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VRVELSNGEK 10 1 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;;;; 184.44 1.42E-06 5926120000 3672980 2567210 3094844 2657487 4804630 4445600 4761970 3949550 4268810 2845692 FALSE TRUE 3817992.087 3008108.347 3175498.177 3183129.997 3987940.709 3413176.774 4388714.348 3896612.742 4115176.362 3403250.863 1.121866192 0.883892627 0.933077902 0.935320411 1.171803334 1.002916597 1.289565338 1.144967826 1.209189839 1 21.69848207 3.238414344 24.9999987 1.147955149 0.959960116 0.398007976 0.100318158 3.457228615 590943.3495 0.027221891 0.034572874 1731.4675 -3.238414344 -0.187995032 VRVELSNGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VRVELSNGEKR 11 2 P84103;P84103-2 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ; 107.97 0.0011959 282930000 92293 85886 92982 63680 125045 108454 69529 84223 100604 95467 FALSE TRUE 95936.79891 100636.2524 95405.18731 76275.71393 103789.8956 83267.20214 64079.1353 83094.12845 96983.28169 114171.9308 0.840283581 0.88144478 0.835627344 0.668077639 0.909066658 0.729314128 0.561251219 0.727798224 0.849449431 1 16.80084848 3.97442212 20.1267498 0.754940237 0.860282342 0.056820523 0.118339749 122.6764349 96534.76459 0.029941096 0.054487054 9428.055272 -3.97442212 0.105342105 VRVELSTGMPR ddPTM_MDA-MB-175_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 ; 174.05 1.05E-05 1008430000 403290 473550 465390 485590 631780 654130 477000 578980 517780 642850 FALSE TRUE 419212.2006 554878.5288 477518.4457 581638.2527 524390.2613 502218.2209 439611.4936 571219.7201 499145.1989 768804.1494 0.545278275 0.72174237 0.621118455 0.756549315 0.682085628 0.653245981 0.571812072 0.742997707 0.649248836 1 19.5522566 -4.999999774 0.406707953 6.645435527 0.659783658 0.706066877 0.065706631 415.2704526 2.832818339 2086.206936 0.037544533 1.00E-05 4.999999774 -5.985651869 VRYDS(ph)SNQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VRYDSSNQVK 10 1 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 VRYDS(0.884)S(0.116)NQVK;VRYDS(0.907)S(0.093)NQVK;VRYDS(0.968)S(0.032)NQVK;VRYDS(0.974)S(0.026)NQVK;VRYDS(0.886)S(0.114)NQVK 204.94 1.08E-07 2665590000 1250570 1000910 1348820 1051060 1886520 1773500 1635700 1481970 1628600 1164010 TRUE FALSE 1299943.469 1172808.507 1383971.357 1258956.531 1565850.004 1361631.503 1507489.56 1462106.616 1569987.004 1392075.473 0.933816804 0.842489168 0.994178393 0.904373761 1.124831257 0.978130517 1.082907923 1.050307002 1.127803078 1 20.408806 3.251556343 24.99994411 1.060009057 0.918660101 0.604325898 0.05626765 149.2220931 287057.5035 0.014675557 0.019751102 1784.663505 -3.251556343 -0.141348955 VRYDSS(ph)NQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VRYDSSNQVK 10 1 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 VRYDS(0.452)S(0.548)NQVK 166.86 3.28E-06 582960000 214100 160510 208100 163430 290790 311840 278630 243930 270640 207400 TRUE FALSE 222552.8333 188076.3439 213523.257 195755.9662 241361.6197 239419.886 256790.2525 240660.5173 260899.7193 248036.0591 0.897259996 0.758262103 0.860855707 0.789223821 0.97309085 0.965262417 1.035294035 0.970264236 1.051862057 1 17.92019035 3.161426974 5.197338566 0.9991607 0.824174041 0.794747007 0.043152287 0.082172976 3.919405604 0.011677557 0.014197893 1450.196905 -3.161426974 -0.174986659 VS(ph)LDVNHFAPDELTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK;VS(1)LDVNHFAPDELTVK 263.52 4.06E-27 2087457000 5613938 3588210 4848366 3458309 6794600 6450650 6639750 4994562 6043230 3428062 TRUE FALSE 5835580.607 4204457.155 4974718.401 4142352.198 5639656.319 4952584.298 6119309.045 4927618.066 5825735.333 4099725.115 1.423407776 1.025546113 1.213427306 1.010397547 1.37561816 1.208028382 1.492614474 1.201938649 1.421006328 1 21.96709575 3.217843916 24.99691156 1.297700654 1.161236301 0.098334005 0.166651136 450.0600891 543044.2003 0.04409653 0.052759156 1651.368194 -3.217843916 -0.136464353 VS(ph)LERLDLDLTADSQPPVFK ddPTM_MDA-MB-175_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 256.57 2.07E-36 373187000 900996 565099 784198 507053 1011352 1007545 806587 757625 900614 631022 TRUE FALSE 936568.0178 662150.3574 804634.8441 607346.57 839442.7483 773557.9432 743364.6033 747470.2761 868201.0781 754658.6793 1.241048495 0.877417004 1.066223534 0.804796376 1.11234757 1.025043459 0.985034193 0.99047463 1.150455301 1 19.52546476 VS(ph)PAAAQLADTLFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSPAAAQLADTLFSK 15 0 O14686;O14686-3 O14686 KMT2D Histone-lysine N-methyltransferase 2D 1 VS(1)PAAAQLADTLFSK;VS(1)PAAAQLADTLFSK 176.69 8.23E-07 344440000 609220 376850 525440 520040 614800 599560 759280 575600 535140 273783 TRUE FALSE 633272.476 441571.056 539133.3981 622902.3598 510296.5156 460321.2764 699765.6496 567885.0235 515880.4159 327425.537 1.934096167 1.3486152 1.646583229 1.902424489 1.558511655 1.405880802 2.137174932 1.734394418 1.57556561 1 18.32080732 0.836434065 3.837138042 1.00010162 1.706925132 0.462877614 0.22815584 0.946822149 20.96926454 0.215811652 0.055304378 6.861736942 -0.836434065 0.706823512 VS(ph)PAHS(ph)PPENGLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSPAHSPPENGLDK 14 0 H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;H0YNT2;A0A0D9SES8;H0YLI3;H0YKH0;H0YLW9 H0YKT5 TLE3 Transducin-like enhancer protein 3 2 VS(1)PAHS(1)PPENGLDK;VS(1)PAHS(1)PPENGLDK 228.3 9.03E-13 852870000 829460 394200 558220 514820 698940 846170 977550 628280 696820 280150 TRUE FALSE 862207.7213 461900.7835 572767.6718 616649.8594 580134.4285 649659.8413 900927.0766 619858.9343 671741.5843 335040.0287 2.573446894 1.378643577 1.709549972 1.840525927 1.731537663 1.939051414 2.689013251 1.85010411 2.004959189 1 18.35397395 2.48581426 24.91324199 2.014378735 1.815021005 0 0.479118986 1595.979579 4573928.064 0.152284452 0.133550193 306.0654167 -2.48581426 -0.19935773 VS(ph)PCHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSPCHSR 7 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-2;Q674X7;Q674X7-5 A0A1B0GWK2 KAZN Kazrin 1 VS(1)PCHSR 61.65 0.058103 85805000 37743 37211 40194 44054 42822 47526 52579 36071 34944 51049 TRUE FALSE 39233.12278 43601.69979 41241.48866 52767.74971 35543.13174 36488.80676 48457.72059 35587.52725 33686.37227 61051.07416 0.642627887 0.714183991 0.675524374 0.864321397 0.582186837 0.597676737 0.793724292 0.582914023 0.551773621 1 15.89772906 -2.216219503 2.537987354 2.169909508 0.669349008 0.524631971 0.095013111 6871369.779 1687048.911 46344458.57 0.022508318 0.006078277 2.216219503 -1.5005605 VS(ph)PENLVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 171.32 5.98E-05 704480000 1251243 656197 879651 750058 1284286 1338026 1370910 916740 1039208 485200 TRUE FALSE 1300643.04 768893.7302 902575.4277 898417.2337 1065983.524 1027289.739 1263454.492 904452.5998 1001807.107 580265.6503 2.241461371 1.325071939 1.555452106 1.548286088 1.837061222 1.770378341 2.177372539 1.558687128 1.726462882 1 19.146354 0.307076494 1.570039072 0.99995531 1.739691665 0.409226819 0.269915937 6.856956601 14.38588092 0.251125485 0.071637095 2.028039894 -0.307076494 0.739736354 VS(ph)PGLPS(ph)PNLENGAPAVGPVQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 2 VS(1)PGLPS(1)PNLENGAPAVGPVQPR;VS(1)PGLPS(1)PNLENGAPAVGPVQPR;VS(1)PGLPS(1)PNLENGAPAVGPVQPR 130.09 1.90E-05 156686000 109249 101826 103696 106668 117231 153692 115552 116856 103135 89980 TRUE FALSE 113562.2349 119313.8234 106398.4029 127766.612 97304.11649 117999.3622 106494.7323 115289.7365 99423.1915 107609.8582 1.055314418 1.108762946 0.988742153 1.187313264 0.904230505 1.096547883 0.989637326 1.071367794 0.923922707 1 16.71545072 2.560069911 0.431378143 0.987520616 1.081331912 0.12918237 0.077496748 2.713315794 1.062015255 0.072130125 0.095954643 363.1365061 -2.560069911 0.093811296 VS(ph)PGLPSPNLENGAPAVGPVQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 Q9UGP4;C9JRJ5 Q9UGP4 LIMD1 LIM domain-containing protein 1 1 VS(1)PGLPSPNLENGAPAVGPVQPR;VS(1)PGLPSPNLENGAPAVGPVQPR 180.8 4.66E-17 842990000 137623 109773 122805 118412 147787 169192 162615 130922 117675 99151 TRUE FALSE 143056.4623 128625.6588 126005.3992 141833.5402 122666.2185 129899.7221 149868.8114 129167.2047 113439.8997 118577.7401 1.206436066 1.084736973 1.062639574 1.196122814 1.034479308 1.095481513 1.263886555 1.089303984 0.956671123 1 16.85547368 1.346512657 5.128535382 0.980315617 1.130577269 0.448776582 0.06805272 0.182964535 6.86913486 0.047991574 0.01677979 22.20816404 -1.346512657 0.150261652 VS(ph)PPAS(ph)PTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 2 VS(0.984)PPAS(0.941)PT(0.059)LEVELGS(0.016)AELPLQGAVGPELPPGGGHGR;VS(0.982)PPAS(0.824)PT(0.19)LEVELGS(0.005)AELPLQGAVGPELPPGGGHGR;VS(0.966)PPAS(0.813)PT(0.22)LEVELGS(0.001)AELPLQGAVGPELPPGGGHGR 56.933 0.00092138 85266000 15495.5 21355.5 22256.3 23581.3 24181.1 27060.5 23939.5 19949.8 19069.9 22588.7 TRUE FALSE 16107.27431 25023.141 22836.31746 28245.61076 20070.80526 20776.10898 22063.05944 19682.40556 18383.57802 27014.52328 0.596244995 0.926284752 0.845334831 1.04557132 0.742963518 0.769071835 0.816711041 0.728586078 0.680507216 1 14.7214476 VS(ph)PPASPTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 VS(0.941)PPAS(0.029)PT(0.029)LEVELGS(0.001)AELPLQGAVGPELPPGGGHGR;VS(0.831)PPAS(0.084)PT(0.084)LEVELGSAELPLQGAVGPELPPGGGHGR;VS(1)PPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 116.27 4.69E-06 152655000 17684.4 19677 22484.9 18320.5 21699.8 25948.7 22488.9 22667.4 19724.9 20848.8 TRUE FALSE 18382.59377 23056.37168 23070.87497 21944.24022 18011.27575 19922.50768 20726.16125 22363.58058 19015.0047 24933.72319 0.737258276 0.924706331 0.925288004 0.880102825 0.722366075 0.799018563 0.831250155 0.896921026 0.762621954 1 14.60581071 -1.540219758 5.867148483 1.000324397 0.838312756 0.330009614 0.071546163 0.000307081 2.41E-05 0.070070254 0.016482964 0.028825725 1.540219758 -0.162011641 VS(ph)PQPMISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSPQPMISR 9 0 D6RIF6;Q9P270 D6RIF6;Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 VS(1)PQPMISR;VS(1)PQPMISR;VS(1)PQPMISR;VS(1)PQPMISR 171.32 5.98E-05 997180000 500397 438801 433820 473303 593460 657441 590817 524638 504643 387730 TRUE FALSE 520153.06 514161.6584 445125.7056 566920.9207 492583.8812 504760.2914 544507.2197 517606.0857 486480.997 463698.27 1.121748977 1.108828071 0.959946876 1.222607367 1.062293981 1.08855332 1.174270544 1.116256237 1.049132655 1 18.82282682 4.469934335 24.99955492 1.094170607 1.11851883 0.015132852 0.073055057 880.3139799 3062164.657 0.017006729 0.046799614 29507.63041 -4.469934335 0.024348223 VS(ph)PSDTTPLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSPSDTTPLVSR 12 0 Q9HCK8-2;Q9HCK8;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 VS(0.995)PS(0.005)DTTPLVSR;VS(1)PSDTTPLVSR;VS(0.94)PS(0.06)DTTPLVSR 263.7 1.81E-21 1064240000 561240 808400 736950 824990 683720 998660 810910 725740 676720 1013170 TRUE FALSE 583398.1886 947236.4115 756155.5224 988170.5597 567501.5186 766736.3498 747348.7553 716012.6424 652364.9794 1211681.263 0.481478262 0.781753783 0.624054812 0.815536717 0.468358747 0.632787164 0.616786591 0.590924911 0.538396523 1 20.20857881 -1.923554361 2.600040789 1.239456161 0.621533775 0.535795655 0.106953245 33332383.66 18594193.01 48570081.71 0.024022851 0.01192465 1.923554361 -0.617922386 VS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSPSPSQESLSSSK 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 VS(0.501)PS(0.496)PS(0.003)QESLSSSK;VS(0.926)PS(0.074)PSQESLSSSK;VS(0.999)PS(0.001)PSQESLSSSK;VS(0.975)PS(0.025)PSQESLSSSK 293.92 1.55E-43 625138000 642720 365643 481114 447279 556825 674163 768539 501733 531345 269375 TRUE FALSE 668095.0819 428439.3409 493652.2261 535749.4512 462176.0854 517598.8603 708298.905 495008.0898 512221.9972 322153.8738 2.073838424 1.329921431 1.532349186 1.663023464 1.434643886 1.606682093 2.198635381 1.536557931 1.589991737 1 18.29739042 2.459718712 24.9986836 1.670098896 1.583397273 0 0.329922722 1516.073527 2177819.973 0.108510249 0.090803536 288.2164148 -2.459718712 -0.086701623 VS(ph)PSSTEADGELYVFNTPSGTSSVETQMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSPSSTEADGELYVFNTPSGTSSVETQMR 29 0 B7Z3B9;Q13480;Q13480-2 B7Z3B9 GAB1 GRB2-associated-binding protein 1 1 VS(0.749)PS(0.084)S(0.084)T(0.084)EADGELYVFNTPSGTSSVETQMR 112.13 0.00019028 53201000 32920 31253 36155 26731 38572 41693 33039 30342 33525 29354 TRUE FALSE 34219.70702 36620.45964 37097.229 32018.31202 32015.54522 32010.43261 30449.31685 29935.31512 32318.4418 35105.35428 0.974771733 1.043158811 1.056739912 0.912063492 0.911984678 0.911839042 0.867369593 0.852727902 0.920612894 1 15.09940347 3.678610221 6.022907501 0.898812379 1.026547005 0.591307437 0.042618197 0.129022548 9.822719869 0.011341283 0.017845834 4771.008839 -3.678610221 0.127734626 VS(ph)SGYVPPPVATPFSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSGYVPPPVATPFSSK 17 0 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 VS(0.5)S(0.5)GYVPPPVATPFSSK;VS(0.993)S(0.007)GYVPPPVATPFSSK 179.74 9.43E-10 224440000 642900 512540 656710 498130 933700 919400 862730 712210 785900 616970 TRUE FALSE 668282.1884 600564.758 673824.4021 596658.6272 774990.0075 705883.2836 795106.9683 702663.9899 757615.6125 737853.4589 0.905711263 0.813935004 0.913222529 0.808641093 1.05033052 0.956671376 1.077594689 0.952308323 1.026783304 1 19.49297479 3.236544221 24.99999919 1.006586318 0.860834794 0.705914374 0.047462427 27.24023661 337735.3283 0.012313738 0.015433061 1724.027625 -3.236544221 -0.145751524 VS(ph)SPTKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.621)S(0.379)PTKPK 123.75 0.00080807 1456300000 3280800 1269900 2079300 1312100 3141300 2644600 3143600 2318800 2562100 1144100 TRUE FALSE 3410328.517 1487995.447 2133488.266 1571629.464 2607342.948 2030431.729 2897196.418 2287720.279 2469890.521 1368264.49 2.492448311 1.087505711 1.559265977 1.14862987 1.905584021 1.483946813 2.117424255 1.671986882 1.805126523 1 20.3839157 VS(ph)SSGLTDSLFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 VS(0.542)S(0.449)S(0.008)GLT(0.001)DSLFILK 77.078 0.026931 15986000 33023 24195 31705 28305 44787 46157 43800 37503 41923 30277 TRUE FALSE 34326.77354 28350.30304 32531.25835 33903.64452 37174.12174 35437.73627 40366.84155 37000.33363 40414.19942 36209.19846 0.948012522 0.782958592 0.898425255 0.936326844 1.026648568 0.978694303 1.114822842 1.021849011 1.116130738 1 15.14406862 3.341332736 1.289202658 1.054868161 0.860264459 0.653545931 0.055650659 0.24054386 0.832324878 0.018437346 0.031205926 2194.485601 -3.341332736 -0.194603702 VS(ph)SSSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.671)S(0.11)S(0.11)S(0.11)ELDLPSGDHCEAGLLQLDVPLLR;VS(0.435)S(0.435)S(0.065)S(0.065)ELDLPSGDHCEAGLLQLDVPLLR 181.9 8.65E-18 176967000 34361.4 41183.2 40815 43063 50427 62031 47310 45118.1 46216.6 42013.1 TRUE FALSE 35718.0146 48256.09424 41878.67243 51580.73287 41855.43655 47625.24034 43601.71858 44513.36567 44553.27359 50244.76256 0.710880354 0.960420386 0.83349329 1.026589245 0.833030836 0.947864771 0.86778634 0.885930461 0.886724732 1 15.6166856 2.56194434 0.015251736 1.79110613 8.87E-06 0.189436677 0.079426335 1857.358174 12.68466816 717.662744 770.1369356 364.7072022 -2.56194434 -1.791097259 VS(ph)VS(ph)PGR ddPTM_MDA-MB-175_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 76.827 0.058046 877360000 2488800 2071960 2170270 2221840 2639600 3165500 2971200 2378800 2352000 1562300 TRUE FALSE 2587059.746 2427803.012 2226829.019 2661313.32 2190921.735 2430360.599 2738309.58 2346916.077 2267351.979 1868402.773 1.384637072 1.29940024 1.191835642 1.424378811 1.172617471 1.300769103 1.46558848 1.256108218 1.2135242 1 20.83337406 0.882487384 1.992345618 1.001271654 1.312786857 0.53955758 0.088188696 0.356539862 2.84117991 0.080773585 0.022467434 7.629347289 -0.882487384 0.311515203 VSAGEPGSHPS(ph)PAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSAGEPGSHPSPAPR 15 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68;C9JME2 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 VSAGEPGS(0.001)HPS(0.999)PAPR;VSAGEPGSHPS(1)PAPR;VSAGEPGS(0.002)HPS(0.998)PAPR;VSAGEPGS(0.001)HPS(0.999)PAPR 186.98 2.32E-07 2138860000 1441570 2678620 1880630 3083520 2251130 3399860 2310220 2224910 1839900 2909740 TRUE FALSE 1498484.297 3138652.148 1929640.763 3693431.053 1868483.727 2610294.04 2129138.92 2195088.721 1773682.358 3479847.843 0.430617764 0.901950973 0.554518717 1.061377169 0.536944088 0.750117292 0.611848281 0.630800202 0.509701124 1 21.73059279 VSALNSVHCEHVEDEGESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSALNSVHCEHVEDEGESR 19 0 Q13085;Q13085-4;Q13085-3;Q13085-2;Q59FY4;A0A087WWN5 Q13085 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 0 ; 257.75 3.05E-31 777700000 91098 210010 192723 212451 214517 266046 160401 193064 184142 199733 FALSE TRUE 94694.61938 246077.5838 197745.5197 254473.1737 178053.477 204260.8485 147828.3505 190476.2929 177514.7654 238866.8572 0.396432642 1.030187221 0.827848292 1.065334792 0.745408882 0.855124276 0.618873427 0.797416163 0.743153602 1 17.86584717 VSAQEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSAQEVR 7 0 P15311;E7EQR4 P15311 EZR Ezrin 0 ; 96.253 0.029935 243750000 338100 428630 385620 367330 520750 566480 423570 435920 387610 450600 FALSE TRUE 351448.4491 502243.8682 395669.574 439986.7776 432233.101 434923.6051 390369.4766 430077.2054 373659.9918 538886.4427 0.65217534 0.932003161 0.734235532 0.816474015 0.802085684 0.807078395 0.724400255 0.798085035 0.693392823 1 19.03962177 -1.416115217 4.015264279 1.000998672 0.779263347 0.455381839 0.074111705 0.000592287 8.61E-05 0.064147525 0.015052921 0.038360546 1.416115217 -0.221735325 VSAS(ph)LPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSASLPR 7 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 VS(0.013)AS(0.987)LPR;VS(0.227)AS(0.773)LPR;VS(0.002)AS(0.998)LPR 80.219 0.032 1093810000 358279 407952 467518 424206 562599 539320 380062 428714 402350 493116 TRUE FALSE 372424.1316 478014.5826 479701.9032 508112.6807 466968.6229 414071.1035 350271.7473 422967.7901 387869.5021 589732.6389 0.631513515 0.810561517 0.813422679 0.86159837 0.791831064 0.702133605 0.593950079 0.717219571 0.657703977 1 19.16970152 2.739024034 22.2241653 0.705388643 0.789575789 0.008999845 0.11524925 19.80577027 949847.5425 0.034100413 0.034193322 548.3073077 -2.739024034 0.084187146 VSDEVGFGLEHVS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSDEVGFGLEHVSR 14 0 Q6VY07-2;Q6VY07 Q6VY07-2 PACS1 Phosphofurin acidic cluster sorting protein 1 1 VSDEVGFGLEHVS(1)R;VSDEVGFGLEHVS(1)R 147.92 5.09E-06 164046000 134873 148089 153422 162011 162724 191560 170416 160601 149183 127807 TRUE FALSE 140197.8902 173522.1338 157420.3034 194056.2922 135064.2326 147073.0931 157058.3486 158448.4063 143813.933 152848.3346 0.917235314 1.135256947 1.029911799 1.269600305 0.883648703 0.962215869 1.027543735 1.036638094 0.940893032 1 17.22174131 3.200928172 24.9999713 0.983997594 1.08722843 0.261275701 0.092236115 241.5336145 160454.8799 0.026005572 0.031083298 1588.284039 -3.200928172 0.103230835 VSDGIYQHVDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSDGIYQHVDVR 12 0 Q7KZ85;Q7KZ85-2 Q7KZ85;Q7KZ85-2 SUPT6H Transcription elongation factor SPT6 0 63.8 0.068115 99325000 33812 43492 49643 52896 46689 49360 36668 39473 37458 56541 FALSE TRUE 35146.92387 50961.41268 50936.73736 63358.67092 38752.82046 37896.88806 33793.86635 38943.929 36109.8939 67619.12641 0.519777846 0.753653816 0.7532889 0.936993337 0.573104423 0.560446283 0.499767864 0.575930673 0.534018935 1 16.04514376 -1.042008214 4.673404244 1.000012142 0.635775319 0.409194463 0.131881904 1.80E-05 3.69E-06 0.137629616 0.032438531 0.090780336 1.042008214 -0.364236823 VSDILHSIFSSYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSDILHSIFSSYK 13 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 ; 192.15 2.96E-06 573430000 848010 1202230 1422940 1278530 2232600 2078400 1660480 1447770 1397350 1570260 FALSE TRUE 881490.0896 1408703.65 1460022.985 1531419.418 1853103.449 1595723.098 1530327.239 1428365.011 1347059.646 1877922.383 0.469396445 0.750139443 0.777467162 0.815486003 0.986783834 0.84972793 0.814904414 0.760609184 0.717313803 1 20.840706 5.07376855 1.342627162 0.835412636 0.007389072 0.634657287 0.085087265 1.927863417 1.699946324 0.023848331 2.694286496 118513.698 -5.07376855 -0.828023565 VSDQNS(ph)PVLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VSDQNSPVLPK 11 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK 201.33 4.59E-08 7467060000 8411850 5582910 7745860 6039130 9442530 9500730 9117000 7319120 8066070 4541081 TRUE FALSE 8743956.333 6541731.363 7947723.475 7233651.889 7837492.123 7294329.442 8402385.717 7221019.168 7775773.716 5430818.878 1.610062226 1.204557086 1.463448451 1.331963384 1.443151079 1.343136202 1.547167362 1.329637267 1.431786604 1 22.37273832 -1.48392037 2.933170729 0.987648971 1.404050818 0.5527352 0.110901553 12896639.4 14728266.38 1294574.497 0.023158499 0.032815546 1.48392037 0.416401847 VSDS(ph)PSHIATK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSDSPSHIATK 11 0 Q9P2D3 Q9P2D3 HEATR5B HEAT repeat-containing protein 5B 1 VS(0.015)DS(0.984)PSHIATK;VS(0.205)DS(0.772)PS(0.023)HIATK 198.14 3.52E-08 642410000 1577990 1946050 2320720 2137100 2619660 2758950 2475270 2262400 2315860 1966720 TRUE FALSE 1640290.264 2280268.949 2381199.87 2559812.001 2174371.129 2118225.675 2281251.869 2232076.229 2232512.651 2352061.129 0.697384198 0.969476907 1.012388598 1.088327157 0.924453494 0.900582748 0.969894805 0.948987338 0.949172887 1 21.16549412 4.7383803 8.135324965 0.971973114 0.695342547 0.738179172 0.049360521 0.048564221 42.50501555 0.012589902 0.0741942 54749.51794 -4.7383803 -0.276630567 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFR 39 0 Q5JP53;P07437;Q5ST81;P68371;M0R2D3;Q9BVA1;P04350;M0QYM7;M0R042;K7ESM5;Q9BUF5 Q5JP53;P68371;Q9BVA1;P04350;K7ESM5 TUBB;TUBB4B;TUBB4A;TUBB2B;TUBB6 Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-2B chain;Tubulin beta-4A chain;Tubulin beta-6 chain 0 263.74 4.53E-63 40326000 7003.8 18356 13955 18985 17662 22493 13099 18512 15687 22113 FALSE TRUE 7280.315432 21508.50021 14318.67876 22740.17634 14659.81955 17269.34163 12072.26615 18263.87692 15122.42793 26445.61897 0.275293819 0.813310524 0.541438594 0.859884443 0.554338303 0.653013327 0.456493991 0.690620134 0.571831121 1 14.69074112 -2.225850894 2.118482985 2.16359529 0.613387466 0.354562283 0.160492477 8797169.263 1483464.217 49034834.94 0.035051478 0.005944962 2.225850894 -1.550207824 VSELHLEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSELHLEVK 9 0 Q9UNF0-2;Q9UNF0;A0A0U1RR22;B0QYG7;B0QYG8 Q9UNF0-2 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 ; 121.73 0.0006056 493680000 816510 786070 963170 783080 1269380 1240280 1142350 1034280 1046210 765880 FALSE TRUE 848746.4453 921071.4077 988271.0015 937970.8867 1053611.241 952243.7666 1052809.622 1020417.168 1008557.106 915939.5223 0.926640269 1.005602865 1.078969711 1.024053296 1.15030656 1.039636071 1.149431372 1.114066097 1.101117576 1 19.80489282 5.231019955 0.762967914 1.09870091 0.665512592 0.509073941 0.048120304 3.577014566 0.938344273 0.015897049 1.570070901 170223.6721 -5.231019955 -0.433188319 VSELKEELKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSELKEELKK 10 2 Q00839;A0A1X7SBS1;Q00839-2;A0A1W2PPS1 Q00839;Q00839-2 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 83.314 0.0088233 1076400000 5613400 2102500 3479300 1949600 6181700 4440900 5316700 3661000 4688100 1703100 FALSE TRUE 5835021.366 2463588.02 3569973.416 2335225.061 5130936.842 3409568.277 4899963.161 3611930.283 4519376.197 2036789.837 2.864812687 1.209544537 1.752745105 1.146522345 2.519129244 1.673991207 2.405728403 1.773344612 2.218872126 1 20.9578657 3.236368367 24.9999366 1.976779084 1.705940357 0.018768722 0.594007361 201.1938458 2294379.494 0.156273351 0.195579914 1723.329679 -3.236368367 -0.270838727 VSELYDVTWEEMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSELYDVTWEEMR 13 0 Q15006 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;; 254.19 1.95E-23 137616000 40952.5 53929 61081 46503.9 53031 66065 51673 50685 53501 57797 FALSE TRUE 42569.33632 63190.88624 62672.82104 55702.23262 44016.80956 50722.40497 47622.73524 50005.65048 51575.50946 69121.21556 0.615864984 0.91420392 0.906708896 0.805863036 0.636806069 0.733818185 0.688974215 0.723448656 0.746160336 1 16.07684097 4.789596057 22.00085227 0.776271425 0.61586129 0.177072406 0.109334368 19480.83513 8396893.49 0.026602896 19.0494856 61602.17651 -4.789596057 -0.160410135 VSEYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSEYAR 6 0 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 105.27 0.077053 300220000 149280 203960 160370 188660 202130 275180 180750 176300 135830 299460 FALSE TRUE 155173.6897 238988.5434 164549.3739 225976.3849 167772.0148 211273.6154 166582.3427 173936.9869 130941.5048 358133.4535 0.433284543 0.667317005 0.459463846 0.630983737 0.468462282 0.589929852 0.465140414 0.485676457 0.365622099 1 18.45013776 -1.415571857 3.197320813 1.006594768 0.511824977 0.733007309 0.08916616 29060307.77 37918983.32 1750256.385 0.019763582 0.03840857 1.415571857 -0.494769791 VSFELFADKVPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSFELFADKVPK 12 1 P62937;F8WE65;C9J5S7 P62937 PPIA "Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed;Peptidyl-prolyl cis-trans isomerase" 0 ; 166.7 4.67E-05 24882000000 14024900 8786700 11738600 7840400 16413800 13921600 13856000 11430700 12434300 7887800 FALSE TRUE 14578613.88 10295747.37 12044517.56 9391207.719 13623788.14 10688519.38 12769930.51 11277490.16 11986791.97 9433263.389 1.545447559 1.091430076 1.276813449 0.995541769 1.444228532 1.133066993 1.353712919 1.195502521 1.270694083 1 23.16932552 -1.867511811 2.379051711 0.880632142 1.246658898 0.192833549 0.156183185 16605546.7 9270702.9 11195821.51 0.034782622 0.013567136 1.867511811 0.366026757 VSGAGFS(ph)PSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(0.972)PS(0.025)S(0.002)K;VSGAGFS(0.909)PS(0.088)S(0.003)K;VSGAGFS(0.99)PS(0.009)S(0.001)K;VSGAGFS(1)PSSK;VSGAGFS(0.969)PS(0.031)SK;VSGAGFS(0.954)PS(0.036)S(0.01)K 284.67 1.26E-27 1277784000 2766124 1909744 2451517 1831880 3169045 3097672 2972347 2571024 2745739 1810429 TRUE FALSE 2875332.711 2237727.676 2515405.547 2194220.396 2630371.863 2378284.624 2739366.675 2536563.629 2646920.39 2165147.9 1.328007529 1.033521856 1.161770772 1.013427488 1.214869369 1.098439799 1.265209954 1.17154289 1.222512508 1 21.04603415 VSGAGFSPS(ph)SK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 VSGAGFS(0.271)PS(0.679)S(0.05)K 251.14 4.78E-17 1114900000 2708000 1782400 2411000 1831200 3044000 3187400 2843500 2473300 2660800 1623700 TRUE FALSE 2814913.931 2088513.335 2473832.641 2193405.894 2526581.967 2447174.656 2620619.04 2440149.459 2565038.328 1941832.927 1.449616953 1.075537089 1.273967809 1.129554383 1.301132518 1.26023955 1.349559482 1.256621733 1.320936674 1 20.88898765 -1.150969594 5.077380539 0.999987158 1.262717319 0.391844631 0.100138369 1.34E-05 2.23E-06 0.088953728 0.020965571 0.070636701 1.150969594 0.262730161 VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(ph)PPAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 VSGEEELHTGPPAPQGPLSVPQGLPT(0.004)QS(0.077)LAS(0.919)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPTQS(0.007)LAS(0.993)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPTQS(0.006)LAS(0.994)PPAR;VSGEEELHTGPPAPQGPLSVPQGLPT(0.001)QS(0.025)LAS(0.974)PPAR 303.81 7.81E-91 1281490000 275104 299172 337316 312825 348500 425856 343635 333554 346442 338405 TRUE FALSE 285965.3183 350552.4638 346106.7321 374700.8513 289262.0945 326957.3979 316699.9908 329083.2542 333973.6201 404708.9806 0.706594941 0.86618405 0.855199041 0.925852574 0.714740983 0.807882734 0.782537591 0.813135537 0.825219197 1 18.62652534 0.615111907 2.855616251 0.999997507 0.812015775 0.452163993 0.062627225 4.802839206 34.53529468 0.058652108 0.015409951 4.122037202 -0.615111907 -0.187981732 VSGRT(ph)SPPLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.103)GRT(0.652)S(0.245)PPLLDR;VS(0.012)GRT(0.613)S(0.375)PPLLDR 95.662 0.0095724 6592900000 2723700 3338700 3535100 2159050 4210900 4047200 2191600 3228700 3320200 4027800 TRUE FALSE 2831233.779 3912095.754 3627227.61 2586103.646 3495132.722 3107299.136 2019816.665 3185424.558 3200706.651 4816970.293 0.58776235 0.812148615 0.753010168 0.536873489 0.725587353 0.645073344 0.419312668 0.661292133 0.664464685 1 22.1996946 -1.869475916 6.372816436 1.052489021 0.643651853 0.501557116 0.106143076 0.057717198 0.001182128 0.074935845 0.02452043 0.013505917 1.869475916 -0.408837168 VSGRTS(ph)PPLLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 VS(0.019)GRT(0.367)S(0.614)PPLLDR;VS(0.032)GRT(0.297)S(0.671)PPLLDR;VS(0.05)GRT(0.32)S(0.63)PPLLDR 92.427 0.0046881 6385500000 2676570 3438850 3624990 2078900 4564800 3933160 2313330 3185140 3144270 4183200 TRUE FALSE 2782243.05 4029445.737 3719460.217 2490100.215 3788876.927 3019743.198 2132005.15 3142448.408 3031108.337 5002817.948 0.556135178 0.805435213 0.74347303 0.497739522 0.757348552 0.603608452 0.42616085 0.628135671 0.6058802 1 22.25430952 -1.499335104 8.723364365 1.000016103 0.624692645 0.502433551 0.111989574 3.52E-05 2.02E-06 0.108930918 0.025674164 0.031671228 1.499335104 -0.375323458 VSHEQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSHEQFR 7 0 O96013;O96013-4;O96013-2;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 0 ;;; 125.25 0.0040673 682050000 1064070 1072610 1098260 992730 1418940 1320720 1188130 1060030 1099000 1201500 FALSE TRUE 1106080.305 1256822.424 1126881.558 1189089.031 1177749.086 1014002.796 1095001.266 1045822.032 1059447.205 1436910.921 0.769762613 0.874669686 0.784238982 0.827531487 0.819639595 0.705682434 0.762052296 0.727826629 0.737308896 1 20.4545392 2.866436218 18.2827981 0.764306306 0.817461989 0 0.082347866 5.753452772 808.0390995 0.022972188 0.024365853 735.2520063 -2.866436218 0.053155683 VSHLLGINVTDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ; 213.99 2.62E-10 14073300000 2271330 2511800 2470400 2498200 2870000 2945400 2574100 2529400 2248550 2641800 FALSE TRUE 2361003.862 2943182.111 2534780.653 2992336.504 2382158.425 2261375.488 2372335.316 2495497.53 2167625.125 3159410.13 0.747292616 0.931560636 0.802295539 0.947118728 0.753988348 0.715758764 0.750879189 0.78986185 0.686085388 1 21.5912238 3.19795011 24.9999816 0.768475066 0.85847585 0.114586133 0.096366308 246.2495498 151591.4175 0.025429142 0.030393955 1577.430049 -3.19795011 0.090000784 VSHS(ph)PPPKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSHSPPPKQR 10 1 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.002)HS(0.998)PPPKQR 72.958 0.028117 35582000 46593 54736 50601 24264 89558 68922 30623 44775 61318 90943 TRUE FALSE 48432.52762 64136.48221 51919.70363 29063.34678 74334.96315 52915.91002 28222.68924 44174.86436 59111.17716 108761.5396 0.445309323 0.589698182 0.477371907 0.267220811 0.683467367 0.486531454 0.259491446 0.406162551 0.543493383 1 16.73080895 0.846316521 4.418028425 0.999972115 0.449224592 0.644220453 0.121598241 0.809770883 22.5930506 0.118511997 0.030117899 7.019667175 -0.846316521 -0.550747523 VSHYIINSSGPRPPVPPSPAQPPPGVS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSHYIINSSGPRPPVPPSPAQPPPGVSPSR 30 1 P46108-2;P46108;I3L297 P46108-2 CRK Adapter molecule crk 1 VSHYIINSSGPRPPVPPSPAQPPPGVS(0.944)PS(0.056)R;VSHYIINSSGPRPPVPPSPAQPPPGVS(0.867)PS(0.133)R 167.5 1.51E-12 1221920000 497090 634430 658970 676080 705190 809110 680240 679370 642310 664330 TRUE FALSE 516715.497 743388.4173 676143.2995 809806.6061 585322.0557 621206.4647 626921.0113 670264.1564 619193.3886 794492.7441 0.650371575 0.935676786 0.851037728 1.019275018 0.736724231 0.781890671 0.789083369 0.843637857 0.779356883 1 19.59967452 -1.347134148 3.526037982 1.000861308 0.82718018 0.231485816 0.097337102 10568721.23 8171468.926 63385.2459 0.021805613 0.044964095 1.347134148 -0.173681128 VSIGNITLS(ph)PAISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSIGNITLSPAISR 14 0 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 VSIGNITLS(1)PAISR;VSIGNITLS(1)PAISR;VSIGNITLS(1)PAISR;VSIGNITLS(1)PAISR 303.96 4.24E-44 2433120000 1189170 1250840 1272960 1408430 1244540 1535850 1366440 1299010 1109240 939580 TRUE FALSE 1236119.35 1465662.04 1306134.383 1687013.25 1032993.535 1179172.114 1259334.862 1281598.896 1069318.669 1123672.712 1.100070632 1.304349589 1.16237973 1.501338631 0.919301078 1.049391074 1.120731018 1.140544647 0.951628226 1 20.09979046 3.219102011 24.99997391 1.051210815 1.26222479 0.488598759 0.117460409 221.7664905 284920.0048 0.033282882 0.039835663 1656.158933 -3.219102011 0.211013974 VSIGNITLS(ph)PAISRHS(ph)PVQMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSIGNITLSPAISRHSPVQMNR 22 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 2 VSIGNIT(0.001)LS(0.999)PAIS(0.291)RHS(0.709)PVQMNR 93.596 0.007043 151850000 14619 42026 40145 36147 38582 43363 23645 41583 30173 36827 TRUE FALSE 15196.16941 49243.63858 41191.21168 43296.76871 32023.84542 33292.60042 21791.64312 41025.6479 29087.07962 44042.54555 0.345033858 1.118092471 0.935259558 0.9830669 0.727111592 0.755919078 0.494786186 0.93150038 0.660431391 1 15.42661024 4.76324687 23.6941445 0.832082046 0.345032652 0.416355621 0.177024438 3740.950017 3590487.481 0.042544474 2.591957376 57975.81597 -4.76324687 -0.487049395 VSIGNITLSPAIS(ph)RHSPVQMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSIGNITLSPAISRHSPVQMNR 22 1 Q0JRZ9;Q0JRZ9-3 Q0JRZ9 FCHO2 F-BAR domain only protein 2 1 VSIGNITLS(0.008)PAIS(0.496)RHS(0.496)PVQMNR;VSIGNITLSPAIS(0.602)RHS(0.398)PVQMNR 119.75 3.40E-05 1425090000 226260 615030 602400 487890 596840 713620 447460 570520 453920 648860 TRUE FALSE 235192.9195 720656.6182 618099.0389 584393.1858 495389.35 547892.57 412386.916 562873.1126 437583.5079 775991.6938 0.303086903 0.92869115 0.796527906 0.753092063 0.638395171 0.706054684 0.531432126 0.725359713 0.563902309 1 19.56568168 -2.114313917 2.446353872 1.620390853 0.674248183 0.280774891 0.161602207 17592005.92 5630071.538 60564464.06 0.040926373 0.007685747 2.114313917 -0.946142671 VSILESLDKWER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSILESLDKWER 12 1 P10644;P10644-2;K7EPB2;K7EM13 P10644 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 ; 138.01 7.48E-05 949160000 605450 525250 670340 521470 913400 859410 790620 699570 720970 605350 FALSE TRUE 629353.6335 615457.6016 687809.6111 624615.2096 758140.5943 659825.052 728649.1385 690193.4084 695022.4305 723956.7424 0.869324915 0.850130354 0.95007004 0.862779739 1.047218086 0.911415024 1.006481597 0.953362774 0.960033093 1 19.46554397 3.823413836 1.055616932 0.973127362 0.855455919 0.446479144 0.047075633 0.552554996 1.104021065 0.014933536 0.051918117 6659.073918 -3.823413836 -0.117671443 VSISEGDDKIEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VSISEGDDKIEYR 13 1 P22087;M0QXL5;M0R0P1;M0R2Q4;M0R299;M0R2U2;M0R1H0;M0R2B0 P22087 FBL rRNA 2-O-methyltransferase fibrillarin 0 ;;;;; 188.13 5.81E-06 4329240000 3933880 2515460 3404080 2701640 4364510 4195860 4087980 3290960 3539610 2279080 FALSE TRUE 4089192.62 2947470.687 3492793.121 3236016.328 3622632.149 3221435.104 3767553.446 3246850.064 3412220.128 2725622.09 1.500278646 1.081393748 1.281466398 1.187257889 1.329102872 1.181908202 1.382272861 1.191232664 1.251905075 1 21.37815411 0.162059674 1.033520543 0.998583114 1.26220328 0.336730019 0.111981247 5.387356279 5.676523455 0.11500878 0.030137683 1.452311158 -0.162059674 0.263620166 VSITEAMHR ddPTM_MDA-MB-175_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 ; 172.94 6.59E-05 196670000 212140 263480 240070 208630 528340 419570 274900 214246 234380 577550 FALSE TRUE 220515.451 308730.6404 246326.4214 249896.3913 438532.9555 322131.2261 253352.6197 211374.3828 225944.7096 690709.8646 0.31925916 0.446975867 0.356627919 0.361796471 0.634901828 0.466377046 0.366800349 0.30602485 0.327119564 1 19.3977203 -0.994326022 4.602952552 1.000012571 0.398321971 0.789431571 0.09320639 22340340.75 9709147.672 3029.04772 0.02331772 0.101315054 0.994326022 -0.6016906 VSIVNHLEFLRDEELEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSIVNHLEFLRDEELEER 18 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 0 ; 140.16 7.76E-08 88981000 30679 61994 55847 57147 60938 68246 51177 53386 49163 63474 FALSE TRUE 31890.23061 72640.98725 57302.4187 68450.50603 50579.78053 52396.90078 47165.61301 52670.44799 47393.63323 75910.51502 0.420102941 0.956929185 0.754868001 0.901726276 0.666307962 0.690245624 0.621331748 0.693849172 0.624335551 1 16.21201212 -1.106563773 4.795525193 1.000014968 0.711827416 0.280248392 0.142055419 2.15E-05 4.00E-06 0.129921143 0.030621118 0.07824133 1.106563773 -0.288187552 VSKEEEEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSKEEEEKER 10 2 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 77.64 0.018219 68371000 140920 73206 93996 65000 136150 116710 124540 83786 98347 52457 FALSE TRUE 146483.6304 85778.56104 96445.61298 77856.80599 113007.2716 89605.87126 114778.2294 82662.98572 94807.51068 62734.9448 2.334960697 1.367317072 1.537350727 1.241043668 1.80134488 1.428324701 1.829574087 1.317654554 1.511239246 1 15.93698166 -2.209782313 0.089498986 1.87E-25 2.118857469 0.331469831 0.289950808 134.7554876 1.605661167 37.92790376 8.384318848 0.006169041 2.209782313 2.118857469 VSLDVNHFAPDELTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 ;;;;;;;;;;; 227 5.43E-15 96973369000 42616647 36516513 43773845 34032914 55393400 52103840 53210580 45179421 49347650 34275532 FALSE TRUE 44299185.13 42787940.05 44914627.36 40764522.81 45977649.65 40003512.8 49039795.7 44573864.76 47571637.72 40991166.25 1.080700775 1.043833195 1.095714796 0.99447092 1.121647756 0.9759057 1.19635034 1.087401722 1.160533892 1 25.2888097 2.238685156 25 1.117824081 1.054203923 0.170781113 0.062911572 5.152024974 1034494.387 0.02044041 0.01609925 173.2547524 -2.238685156 -0.063620159 VSLEPHQGPGT(ph)PESK ddPTM_MDA-MB-175_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(0.996)PES(0.004)K;VSLEPHQGPGT(0.999)PES(0.001)K;VSLEPHQGPGT(0.991)PES(0.009)K;VSLEPHQGPGT(1)PESK;VSLEPHQGPGT(1)PESK 168.99 4.50E-06 8816620000 1406520 1272722 1605531 1170180 1867780 1906240 1833920 1561388 1572535 1074390 TRUE FALSE 1462050.496 1491302.103 1647372.457 1401638.111 1550295.423 1463544.649 1690172.558 1540460.148 1515939.773 1284896.15 1.137874447 1.160640183 1.282105528 1.090857118 1.206553092 1.139037306 1.315415692 1.198898563 1.179815017 1 20.29322033 0.759014598 4.430647413 1.00000138 1.194920103 0.444693358 0.063760649 4.199559706 76.57153265 0.058974074 0.01498245 5.741357607 -0.759014598 0.194918723 VSLEPHQGPGT(ph)PESKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSLEPHQGPGTPESKK 16 1 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 1 VSLEPHQGPGT(0.9)PES(0.1)KK 90.316 0.004186 246630000 423260 338410 455280 299520 672040 586760 496380 445000 482520 297540 TRUE FALSE 439970.6316 396529.285 467144.9708 358764.162 557806.8808 450493.8824 457472.4386 439035.5029 465154.1995 355837.2663 1.236437758 1.114355698 1.31280508 1.008225377 1.567589833 1.26601097 1.28562262 1.23380979 1.307210468 1 18.44085808 4.235184623 24.99638772 1.259953564 1.175396733 0.028978809 0.154738693 268.4864427 1987976.756 0.035900565 0.082955148 17186.38845 -4.235184623 -0.08455683 VSLEPHQGPGTPESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSLEPHQGPGTPESK 15 0 Q14980;Q14980-2;A0A087WY61;Q14980-5;H0YFY6 Q14980 NUMA1 Nuclear mitotic apparatus protein 1 0 118.21 0.00030912 58510000 47745 54004 61999 59614 72427 87015 67664 62841 74456 50446 FALSE TRUE 49630.00947 63278.76691 63614.74487 71405.47127 60115.88441 66807.08498 62360.31887 61998.71918 71776.3431 60329.92785 0.822643276 1.048878544 1.054447554 1.183582905 0.996452118 1.107362255 1.033654789 1.027661086 1.189730299 1 15.88058624 4.752604125 3.396968569 1.072237136 0.786249691 0.570985528 0.064965965 0.229970407 4.359252731 0.014861684 0.173638026 56572.33769 -4.752604125 -0.285987446 VSLERDDVWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSLERDDVWK 10 1 Q9Y3R5-2;Q9Y3R5 Q9Y3R5-2 DOPEY2 Protein dopey-2 0 78.692 0.02356 0 42052 102480 91111 71381 106450 119730 62808 84662 92886 157960 FALSE TRUE 43712.24543 120080.1428 93485.42751 85499.94875 88355.66702 91924.52203 57884.94484 83527.24437 89543.051 188909.2377 0.231392842 0.635649925 0.49486954 0.45259803 0.46771491 0.486606813 0.306416698 0.442155426 0.474000383 1 17.52733373 0.662206613 3.669314435 0.999997953 0.444612404 0.725175085 0.10293423 3.842053128 41.22607077 0.093621264 0.024051795 4.59416526 -0.662206613 -0.555385549 VSLQVHPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSLQVHPDR 9 0 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 ; 85.963 0.014459 1239620000 667050 895930 816290 880350 968950 1102960 859390 825610 801730 1099180 FALSE TRUE 693385.6491 1049799.008 837563.188 1054480.602 804248.2251 846814.2555 792028.7662 814544.0484 772875.8939 1314543.276 0.527472668 0.798603612 0.637151476 0.802164997 0.611808101 0.644188952 0.602512508 0.619640345 0.587942526 1 20.32613021 -2.12808929 2.690493616 1.771387745 0.65114562 0.617673546 0.083060084 3722628.209 2789011.971 17574851.82 0.019204851 0.007445789 2.12808929 -1.120242125 VSNEEVTEELLHVNDDLNNVFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSNEEVTEELLHVNDDLNNVFLR 23 0 Q6ZVM7-2;Q6ZVM7;Q6ZVM7-4;Q6ZVM7-3;Q6ZVM7-5;F5H3S6;B7Z2U2 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 0 ; 331.6 1.47E-86 268000000 110906 118938 117162 113029 136594 144582 127736 120725 114722 120703 FALSE TRUE 115284.6545 139364.6763 120215.338 135385.7988 113375.8007 111005.0217 117723.7185 119106.8788 110593.1776 144352.4419 0.798633214 0.965447307 0.832790471 0.937883676 0.785409649 0.768986103 0.815529804 0.825111632 0.766133057 1 17.13923599 3.227338417 24.99754312 0.815389573 0.885892991 0.105072677 0.076889473 363.0661498 808731.5823 0.020231217 0.024390433 1687.867755 -3.227338417 0.070503417 VSNGS(ph)PSLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSNGSPSLER 10 0 P46527;E7ES52 P46527 CDKN1B Cyclin-dependent kinase inhibitor 1B 1 VSNGS(0.995)PS(0.005)LER;VSNGS(0.75)PS(0.25)LER 156.02 1.22E-05 870260000 172443 441210 276910 446070 244140 438430 233830 293040 260510 512590 TRUE FALSE 179251.1828 516984.3854 284126.5021 534301.3146 202641.17 336611.277 215501.7936 289112.2781 251134.296 613022.1964 0.292405697 0.843337139 0.463484852 0.871585593 0.330560902 0.549101287 0.351539952 0.471617961 0.40966591 1 19.22557979 -1.053653272 4.743773869 1.000015744 0.514286736 0.374285 0.190254714 2.97E-05 5.92E-06 0.172459207 0.040647708 0.088378521 1.053653272 -0.485729009 VSNLQVS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSNLQVSPK 9 0 O00443;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK;VSNLQVS(1)PK 172.74 5.87E-05 2042460000 5769900 2515530 3312370 2520580 5078440 5420800 4527260 3650260 3934340 2080740 TRUE FALSE 5997700.107 2947552.709 3398693.083 3019143.201 4215208.583 4161901.353 4172401.531 3601334.235 3792743.872 2488421.165 2.410243166 1.184507169 1.365802996 1.213276612 1.693928923 1.672506813 1.676726428 1.44723662 1.524156733 1 21.24679925 0.287953776 1.147925785 0.99898288 1.560819565 0.217714391 0.328174437 6.16240555 8.488701483 0.310469778 0.091588505 1.940679312 -0.287953776 0.561836686 VSNS(ph)PEPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSNSPEPQK 9 0 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 VS(0.001)NS(0.999)PEPQK;VS(0.002)NS(0.998)PEPQK;VSNS(1)PEPQK;VSNS(1)PEPQK;VS(0.001)NS(0.999)PEPQK 215.79 6.57E-07 1360070000 3857140 2714060 3297340 2771190 3975230 4313330 4586190 3444550 3720990 2110410 TRUE FALSE 4009422.866 3180178.693 3383271.389 3319323.111 3299521.825 3311624.477 4226712.444 3398381.441 3587072.297 2523904.433 1.588579509 1.260023419 1.340491084 1.31515404 1.307308542 1.312103752 1.674672142 1.34647786 1.42123935 1 21.26722585 -0.891892463 4.162994402 0.999990915 1.391984244 0.467113077 0.126888846 16578237.53 34365830.32 2348.681549 0.029834356 0.128264814 0.891892463 0.391993329 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-3;Q96C92;Q96C92-2;Q96C92-4 A0A0A0MRP9;Q96C92-4 SDCCAG3 Serologically defined colon cancer antigen 3 2 VS(0.028)PAS(0.972)PAGS(0.993)PS(0.007)ADFAVHGESLGDR;VS(0.001)PAS(0.995)PAGS(0.973)PS(0.031)ADFAVHGESLGDR;VSPAS(1)PAGS(0.997)PS(0.003)ADFAVHGESLGDR 214.91 7.69E-33 786760000 210214 268254 274317 259238 331496 354003 306683 311220 304234 273738 TRUE FALSE 218513.411 314324.5378 281465.9264 310514.5027 275148.4283 271791.1682 282644.3851 307048.605 293284.6778 327371.7201 0.66747797 0.960145665 0.859774712 0.948507411 0.840477083 0.83022189 0.863374469 0.93792037 0.895876644 1 18.32057017 -1.001103059 0.020374562 1.927275881 1.58E-06 0.309303623 0.073874217 1628.369654 6.383290995 339.1973458 266.9385776 0.099746334 1.001103059 -1.927274299 VSPNELILGWYATGHDITEHSVLIHEYYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSPNELILGWYATGHDITEHSVLIHEYYSR 30 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 118.05 2.46E-05 1126920000 265108 190167 195171 195602 207384 259654 207331 225799 194012 143783 FALSE TRUE 275574.6685 222826.703 200257.3166 234291.4918 172132.9418 199353.2936 191079.8545 222772.5337 187029.546 171954.526 1.602602008 1.295846688 1.164594625 1.362520064 1.001037575 1.159337287 1.111223176 1.295531667 1.087668644 1 17.39166756 7.999999993 0.806675797 1.15088902 120.2856456 0.633661872 0.106422478 336.2529646 1.124150959 0.034303146 73257.69865 99999998.45 -7.999999993 119.1347566 VSPS(ph)PTTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSPSPTTYR 9 0 P11274-2;P11274 P11274-2 BCR Breakpoint cluster region protein 1 VS(0.406)PS(0.592)PT(0.002)TYR 102.42 0.0037626 195450000 201710 251410 254770 257280 268210 310110 289960 261760 239710 260690 TRUE FALSE 209673.6666 294587.7118 261409.5155 308169.2161 222619.76 238091.6523 267232.1775 258251.5354 231082.8839 311767.2143 0.672532765 0.944896379 0.838476605 0.988459344 0.714057636 0.763684061 0.857152918 0.828347317 0.741203287 1 18.2501097 -1.459865976 3.012066613 1.004155522 0.823683406 0.252175099 0.094059403 78737468.31 87918195.53 2728126.849 0.021557014 0.034684387 1.459865976 -0.180472116 VSPSTSYT(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 VSPS(0.003)T(0.002)S(0.008)YT(0.964)PS(0.023)R 90.697 0.017932 0 77655 88663 81576 94051 102640 111180 76792 96946 79534 89594 TRUE FALSE 80720.87936 103890.1805 83701.93758 112654.0071 85193.28946 85360.12995 70772.84238 95646.59744 76671.58688 107148.2289 0.753357103 0.969593073 0.781178918 1.051384687 0.795097505 0.796654605 0.660513413 0.892656821 0.715565601 1 16.70924848 VSPTTSPRPAS(ph)PVPGSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSPTTSPRPASPVPGSER 18 1 A0A5E8;Q99501;Q99501-4;Q99501-2 A0A5E8 GAS2L1 GAS2-like protein 1 1 VSPT(0.005)T(0.005)S(0.005)PRPAS(0.982)PVPGS(0.003)ER;VSPTTSPRPAS(0.996)PVPGS(0.003)ER 99.957 0.00056921 514450000 185340 280260 227040 248250 251620 284330 222876 233890 228150 335920 TRUE FALSE 192657.3663 328392.4749 232956.8489 297353.109 208849.7223 218298.6666 205406.3967 230755.0871 219938.9261 401737.0924 0.479560812 0.817431303 0.579873886 0.74016842 0.519866665 0.543386883 0.511295573 0.574393282 0.547469801 1 18.61589215 -1.033473862 5.188333001 1.000003936 0.592888711 0.596834558 0.100979372 4.46E-06 8.30E-07 0.094827579 0.022350859 0.09258191 1.033473862 -0.407115225 VSQGSAESLS(ph)PSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 VSQGSAESLS(0.999)PS(0.001)FR;VSQGSAESLS(0.955)PS(0.045)FR;VSQGSAES(0.001)LS(0.999)PSFR;VSQGSAES(0.004)LS(0.969)PS(0.027)FR 321.06 3.69E-56 965920000 917350 973400 1071930 1023040 1121800 1334920 1117830 1132630 1015540 1022910 TRUE FALSE 953567.6863 1140573.878 1099865.376 1225394.259 931116.8367 1024905.061 1030211.564 1117448.947 978990.9138 1223329.63 0.779485482 0.932352042 0.899075237 1.001687713 0.761133234 0.837799589 0.842137343 0.913448772 0.800267475 1 20.22238176 -1.207010552 3.466429221 1.000226944 0.868917678 0.246850861 0.071104342 25872371.99 42981920.86 66530.78407 0.016621815 0.062085395 1.207010552 -0.131309266 VSQGVEDGPDTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 97.273 0.0061798 314830000 401860 319210 372500 268890 477390 460360 401410 360010 362360 267790 FALSE TRUE 417725.7431 374031.8344 382207.656 322075.6394 396243.4183 353448.3668 369946.4353 355184.6548 349318.7344 320258.3234 1.304340005 1.167906678 1.193435512 1.005674532 1.23726189 1.103635225 1.155150103 1.109056749 1.090740533 1 18.28887654 8 0.094931877 0.940307893 1.761681964 0.466136675 0.066394925 134.6954969 0.911926731 0.962926979 14.40356787 100000000 -8 0.821374071 VSQPIEGHAASFAQFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSQPIEGHAASFAQFK 16 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ; 186.98 1.41E-09 1968890000 1871310 1696410 1908580 1799750 2359200 2473100 2350150 1992900 2169900 1687900 FALSE TRUE 1945190.764 1987755.221 1958319.163 2155735.178 1958184.027 1898760.005 2165939.102 1966188.435 2091805.723 2018611.688 0.96362801 0.984714016 0.970131687 1.067929603 0.970064742 0.940626677 1.072984524 0.974030046 1.036259591 1 20.94493198 VSQSALNPHQS(ph)PDFKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSQSALNPHQSPDFKR 16 1 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 VSQSALNPHQS(1)PDFKR;VSQSALNPHQS(1)PDFKR;VSQSALNPHQS(1)PDFKR 192.11 2.77E-10 460220000 677430 532020 617350 525090 836590 858400 729050 632360 698190 482380 TRUE FALSE 704175.4595 623390.2965 633438.6482 628951.2348 694386.7306 659049.6092 671905.156 623884.2485 673062.2783 576893.1253 1.220634167 1.080599281 1.098017328 1.090238741 1.203666156 1.142411966 1.16469607 1.081455509 1.166701853 1 19.13794455 -1.123579346 4.245880347 0.999977286 1.133635543 0.423100677 0.048265672 1.12E-05 2.31E-06 0.045044462 0.010615065 0.075235126 1.123579346 0.133658257 VSRPENEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSRPENEQLR 10 1 Q8ND56-2;Q8ND56;Q8ND56-3;A0A140TA76;K7EMZ9 Q8ND56-2 LSM14A Protein LSM14 homolog A 0 ;;; 208.17 1.08E-07 2484340000 1129920 1281270 1163080 1075960 1546970 1635830 1209750 1185650 1149960 1573060 FALSE TRUE 1174530.114 1501318.156 1193390.82 1288781.677 1284016.592 1255933.274 1114926.634 1169758.301 1108573.164 1881270.989 0.624327979 0.79803397 0.634353491 0.685059029 0.682526122 0.667598279 0.592645419 0.621791495 0.589268197 1 20.84327625 -1.916338666 4.708151827 1.139092887 0.655495269 0.76464333 0.057409838 0.036688259 0.000651931 0.024330779 0.013346749 0.01212443 1.916338666 -0.483597618 VSRS(ph)PGASR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSRSPGASR 9 1 Q12872-2;Q12872 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 VS(0.042)RS(0.958)PGASR;VS(0.132)RS(0.867)PGAS(0.001)R;VS(0.006)RS(0.994)PGASR 77.813 0.019102 498230000 35205 139584 79229 112262 62447 116048 40253 78172 47441 211457 TRUE FALSE 36594.92058 163556.4662 81293.77283 134467.0885 51832.28125 89097.61072 37097.86468 77124.2322 45733.60768 252887.9506 0.144708044 0.646754683 0.32146163 0.531725961 0.204961451 0.352320506 0.146696846 0.30497393 0.180845341 1 17.94813877 -1.583264645 4.013908443 1.014433187 0.320640264 0.631509347 0.156936356 0.019456367 0.002020015 0.145853318 0.034267846 0.026105701 1.583264645 -0.693792923 VSS(ph)GVYEPVVIESH ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSSGVYEPVVIESH 14 0 Q5T9C2-3;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 VS(0.018)S(0.982)GVYEPVVIESH;VS(0.013)S(0.987)GVYEPVVIESH;VS(0.012)S(0.988)GVYEPVVIESH;VS(0.002)S(0.998)GVYEPVVIESH;VS(0.005)S(0.995)GVYEPVVIESH 309.45 2.62E-56 2118330000 1416467 1409124 1436972 1473415 2010532 2148111 1683407 1627114 1560873 1638305 TRUE FALSE 1472390.211 1651130.086 1474420.671 1764852.089 1668782.489 1649244.775 1551457.161 1605305.198 1504697.486 1959299.498 0.751488077 0.842714494 0.752524396 0.900756669 0.851724043 0.841752258 0.79184278 0.819326091 0.767977273 1 20.90190651 -2.244219454 2.41961469 1.716361715 0.816274153 0.598969047 0.045762735 2251311.792 654814.5153 8806765.559 0.01071654 0.005698762 2.244219454 -0.900087563 VSS(ph)PIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSSPIEK 7 0 Q06190 Q06190 PPP2R3A Serine/threonine-protein phosphatase 2A regulatory subunit B subunit alpha 1 VS(0.004)S(0.996)PIEK;VS(0.003)S(0.997)PIEK;VS(0.016)S(0.984)PIEK;VS(0.001)S(0.999)PIEK 156.62 0.0016064 411806000 2327750 1415160 1931730 1512860 2664650 2827110 2626980 2098500 2217520 1328650 TRUE FALSE 2419651.367 1658202.722 1982072.471 1812099.193 2211713.745 2170556.548 2421070.443 2070373.04 2137711.888 1588973.529 1.522776386 1.0435685 1.24739175 1.140421259 1.391913524 1.366011773 1.523669463 1.302962574 1.34534141 1 20.59966366 3.226112774 24.99409803 1.349937216 1.22524527 0.037249395 0.169146066 479.8327842 963457.313 0.045458864 0.054686712 1683.111059 -3.226112774 -0.124691946 VSS(ph)PSPELGTTPASIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VS(0.169)S(0.772)PS(0.059)PELGTTPASIFR;VSS(0.998)PS(0.002)PELGTTPASIFR;VS(0.022)S(0.976)PS(0.002)PELGTTPASIFR;VSS(1)PSPELGTTPASIFR;VS(0.001)S(0.999)PSPELGTTPASIFR 431.31 8.87E-161 1086064000 564438 543244 583036 504701 703794 715688 675247 607515 563628 535452 TRUE FALSE 586722.4481 636541.9311 598230.3971 604529.3514 584163.3473 549480.3084 622319.3757 599372.2551 543343.1384 640363.5676 0.916233337 0.994032083 0.934204298 0.944040826 0.912237012 0.858075531 0.971821957 0.935987438 0.848491647 1 19.2885317 3.510324611 2.582519713 0.920170629 0.952908412 0.064381357 0.046689142 0.739295289 9.806877213 0.013077335 0.020905358 3238.356157 -3.510324611 0.032737783 VSS(ph)PTKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSSPTKPK 8 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 VS(0.181)S(0.818)PT(0.001)KPK;VS(0.113)S(0.887)PTKPK;VS(0.037)S(0.963)PTKPK;VS(0.398)S(0.602)PTKPK 113.93 0.0016682 3091350000 5600100 2334920 3384970 2349230 5374700 4763510 5234900 3831060 4131540 1935350 TRUE FALSE 5821196.272 2735924.347 3473185.099 2813900.682 4461110.414 3657256.994 4824574.859 3779710.907 3982846.682 2314544.778 2.515050185 1.182057212 1.500591016 1.215746919 1.927424544 1.580119352 2.084459504 1.633025614 1.720790507 1 21.14229704 VSS(ph)PTVNTTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSSPTVNTTLR 11 0 Q9NSK0-3;Q9NSK0;Q9NSK0-5 Q9NSK0-3 KLC4 Kinesin light chain 4 1 VS(0.006)S(0.994)PTVNTTLR;VSS(0.996)PT(0.004)VNTTLR;VSS(1)PTVNTTLR 271.44 5.10E-27 407907000 545187 589853 626100 569575 708290 776960 628730 635110 592840 540225 TRUE FALSE 566711.4037 691155.6643 642416.6803 682235.235 587895.1188 596522.8149 579448.4997 626597.3893 571503.8042 646071.7455 0.877164816 1.069781598 0.994342633 1.055974417 0.909953303 0.923307387 0.896879493 0.969857285 0.884582569 1 19.30133486 3.222318478 24.99359381 0.929409535 1.003993911 0.251287618 0.057715896 292.0029517 449336.6331 0.015589079 0.018687105 1668.470292 -3.222318478 0.074584376 VSS(ph)QAEDTSSSFDNLFIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 VS(0.023)S(0.977)QAEDTSSSFDNLFIDR;VS(0.021)S(0.979)QAEDTSSSFDNLFIDR;VS(0.121)S(0.879)QAEDTSSSFDNLFIDR;VS(0.05)S(0.95)QAEDTSSSFDNLFIDR 252.58 7.81E-31 250273000 196147 189630 213487 220948 273097 288148 262898 256347 260354 223451 TRUE FALSE 203891.035 222197.4774 219050.6466 264650.8549 226676.0695 221229.9939 242291.3678 252911.0878 250983.9104 267231.9452 0.762974033 0.831477978 0.819702324 0.990341386 0.848237172 0.827857589 0.906670674 0.946410384 0.939198756 1 18.02773295 8 0.130032808 1.028772172 0.226147187 0.578707365 0.04946725 63.47894744 0.558077874 0.269530192 9.350489236 99999999.94 -8 -0.802624985 VSS(ph)SGLTDSLFILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 VS(0.169)S(0.805)S(0.026)GLTDSLFILK;VS(0.008)S(0.991)SGLTDSLFILK 333.71 1.70E-68 308980000 623190 442540 614870 493270 797730 799900 811840 629660 680670 457650 TRUE FALSE 647794.0224 518542.8025 630894.0173 590837.3337 662132.1395 614135.3476 748205.8595 621220.4376 656172.8197 547317.7553 1.183579404 0.947425508 1.152701536 1.079514282 1.209776466 1.122081902 1.367041088 1.135027014 1.198888239 1 19.06201913 3.244622704 24.95588558 1.186757057 1.084984924 0.117888938 0.104007403 236.0843816 971884.9901 0.027140168 0.035834925 1756.397069 -3.244622704 -0.101772133 VSS(ph)SSELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.098)S(0.63)S(0.136)S(0.136)ELDLPSGDHCEAGLLQLDVPLLR 331.6 4.21E-96 161650000 45143 82483 76365 93024 110230 105360 82539 77599 65229 55731 TRUE FALSE 46925.2805 96648.81362 78355.13463 111423.8696 91493.14397 80891.73675 76069.3775 76558.91233 62881.42103 66650.42242 0.704050759 1.450085538 1.175613474 1.671765392 1.372731645 1.213671779 1.141318761 1.148663573 0.9434512 1 16.0243264 1.714651976 1.283169281 0.980520949 1.29212273 0.175754543 0.235067828 0.699030014 2.179829895 0.191375152 0.07326115 51.83844631 -1.714651976 0.31160178 VSSDNVADLHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSSDNVADLHEK 12 0 P28074;P28074-3 P28074 PSMB5 Proteasome subunit beta type-5 0 ;;;; 194.3 1.71E-06 1928943000 3630460 2703280 3545210 2688160 4265950 4140580 4324710 3458920 3769420 2423510 FALSE TRUE 3773793.364 3167547.311 3637601.085 3219870.025 3540825.343 3178993.046 3985727.93 3412558.835 3633759.311 2898350.384 1.302048705 1.09287936 1.255059121 1.110931944 1.221669182 1.096828411 1.375171184 1.177414178 1.253733617 1 21.46680058 4.790832642 21.3520247 1.189465958 1.302052428 0.108501515 0.102018209 15927.20234 6504725.863 0.022135247 15.07599794 61777.82898 -4.790832642 0.11258647 VSSPLSPLSPGIKS(ph)PTIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 VSSPLSPLS(0.023)PGIKS(0.966)PT(0.012)IPR;VSSPLSPLSPGIKS(0.957)PT(0.043)IPR 218.69 2.00E-19 1067580000 1225710 843050 1035370 779340 1251500 1319240 1151700 1063200 1174930 672920 TRUE FALSE 1274101.977 987837.2795 1062352.593 933491.1259 1038770.477 1012866.503 1061426.745 1048949.543 1132644.499 804765.7902 1.583195997 1.227484184 1.32007673 1.159953787 1.290773651 1.258585436 1.318926273 1.303422133 1.40742128 1 19.61820945 4.743150031 24.75256035 1.26841955 1.583196143 0.460927683 0.105760133 356.6134812 1923282.935 0.022904061 0.18460947 55354.13018 -4.743150031 0.314776594 VSSPS(ph)PELGTTPASIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 VS(0.217)S(0.136)PS(0.646)PELGTTPASIFR 84.508 0.0055239 55580000 24072 21788 21802 21726 28767 33034 24284 24993 21505 21792 TRUE FALSE 25022.38115 25529.91951 22370.17803 26023.33795 23877.19562 25362.35414 22380.55663 24658.00972 20731.03925 26061.72517 0.960119907 0.97959438 0.858353693 0.998527066 0.916178628 0.973164822 0.858751924 0.946138813 0.795459208 1 14.66964497 2.249184783 24.99784351 0.899698054 0.945930417 0.124221193 0.061771458 442.1192924 1040271.709 0.019969648 0.016543332 177.4944521 -2.249184783 0.046232363 VSSPSCDS(ph)QGLHAEEAPSSEPQS(ph)PVAQTSGWPACSTPLPLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSPSCDSQGLHAEEAPSSEPQSPVAQTSGWPACSTPLPLVSR 43 0 Q96RE7;K7ENW4 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 2 VS(0.242)S(0.242)PS(0.242)CDS(0.268)QGLHAEEAPS(0.009)S(0.009)EPQS(0.984)PVAQT(0.002)S(0.002)GWPACSTPLPLVSR 106.19 2.21E-06 41237000 15132 15856 19769 20053 22784 30711 20349 20958 18877 24769 TRUE FALSE 15729.42304 18579.14466 20284.19638 24019.42355 18911.18382 23578.83568 18753.99221 20677.09229 18197.62046 29622.01132 0.531004559 0.627207398 0.684767694 0.810864032 0.638416602 0.795990368 0.633110021 0.698031341 0.614327645 1 14.85438198 -2.295523151 2.295766754 2.543089699 0.676476344 0.604833515 0.079786049 4376720.759 724018.9651 34974330.57 0.019295022 0.005063804 2.295523151 -1.866613354 VSSPSCDSQGLHAEEAPSSEPQS(ph)PVAQTSGWPACSTPLPLVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSPSCDSQGLHAEEAPSSEPQSPVAQTSGWPACSTPLPLVSR 43 0 Q96RE7;K7ENW4 Q96RE7 NACC1 Nucleus accumbens-associated protein 1 1 VSSPSCDSQGLHAEEAPSSEPQS(1)PVAQTSGWPACSTPLPLVSR 273.85 1.27E-80 125840000 17530 32742 34468 31153 35878 42670 30156 36886 35491 40499 TRUE FALSE 18222.09794 38365.1838 35366.2644 37314.97042 29779.47038 32760.53917 27792.29392 36391.6035 34213.68584 48434.00365 0.376225308 0.792112584 0.73019494 0.770429194 0.61484635 0.676395439 0.57381781 0.751364759 0.706398052 1 15.56373264 0.422381516 1.015489195 1.000717064 0.664278812 0.44125612 0.114731963 2.021361379 2.707042144 0.106635976 0.03304733 2.644731062 -0.422381516 -0.336438251 VSSQS(ph)FSEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 VSSQS(0.887)FS(0.113)EIER;VSSQS(0.75)FS(0.25)EIER 204.18 3.57E-08 1102320000 353610 373600 471920 357940 464190 484660 449610 397030 448260 354540 TRUE FALSE 367570.7958 437762.8938 484218.6229 428739.4637 385287.1496 372105.0601 414368.3934 391708.4623 432127.2102 424005.3249 0.866901367 1.032446689 1.142010712 1.011165281 0.908684696 0.877595252 0.977271673 0.923829111 1.019155149 1 18.69372286 3.352307399 6.751321631 0.944448851 1.025303744 0.134991601 0.073974099 0.352085022 19.51550356 0.020809455 0.028220226 2250.647076 -3.352307399 0.080854894 VSSQSFSEIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VSSQSFSEIER 11 0 Q8N6H7;G5E9L0;A0A0D9SF70;Q8N6H7-2;E9PQP3;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 0 ; 100.88 0.005681 0 28962 26977 32478 28015 31324 40957 33620 24260.8 29691 28827 FALSE TRUE 30105.44212 31610.0899 33324.40336 33556.28338 25999.55767 31445.35746 30984.77655 23935.62366 28622.42671 34475.09872 0.873251803 0.916896284 0.96662242 0.973348435 0.754154698 0.912117981 0.898758167 0.694287313 0.8302348 1 15.07326706 3.251365314 24.99998537 0.830210556 0.933848257 0.175026926 0.084314539 326.7968407 638037.0378 0.023749057 0.031950192 1783.878676 -3.251365314 0.1036377 VSSS(ph)SELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.081)S(0.225)S(0.347)S(0.347)ELDLPSGDHCEAGLLQLDVPLLR 193.97 9.49E-19 87071000 28087 42695 41802 43204 45395 46418 43063 32671 43499 34096 TRUE FALSE 29195.89645 50027.53413 42891.39446 51749.62225 37678.77411 35638.12297 39687.60954 32233.09868 41933.47949 40776.45839 0.715998829 1.226872958 1.051866595 1.269105368 0.924032532 0.873987697 0.97329712 0.790483037 1.028374732 1 15.31544886 3.043860215 24.99952967 0.911629761 1.078963265 0.148167314 0.15226415 198.3016933 113027.1025 0.04170495 0.049846931 1106.267657 -3.043860215 0.167333504 VSSSS(ph)ELDLPSGDHCEAGLLQLDVPLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSSSSELDLPSGDHCEAGLLQLDVPLLR 28 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 VS(0.002)S(0.014)S(0.12)S(0.864)ELDLPSGDHCEAGLLQLDVPLLR 208.15 1.26E-25 116310000 41716 55808 54396 52735 54733 72098 55378 49237 58204 41356 TRUE FALSE 43362.97989 65392.58987 55813.60445 63165.8256 45429.50421 55354.33216 51037.32766 48577.05855 56109.24941 49458.91639 0.876747472 1.322159777 1.128484175 1.277137273 0.918530116 1.11919824 1.031913584 0.982169892 1.134461761 1 15.59394301 3.237771948 24.9999956 1.030968834 1.161730703 0.179776382 0.124842293 32.42899064 1027973.465 0.033008277 0.041716747 1728.908254 -3.237771948 0.130761869 VSTEVDAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VSTEVDAR 8 0 P37837;F2Z393 P37837 TALDO1 Transaldolase 0 ;;; 142.79 0.0014234 2735060000 3711810 4441960 4266540 4224690 5126300 5391760 4660550 4495150 4432970 4543740 FALSE TRUE 3858355.125 5204832.076 4377729.537 5060321.073 4254933.357 4139605.453 4295243.913 4434899.867 4273428.276 5433998.858 0.710039738 0.95782723 0.805618413 0.931233371 0.783020657 0.761797262 0.790438869 0.816139271 0.786424213 1 22.37358283 VSVGAPDLSLEASEGS(ph)IKLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSVGAPDLSLEASEGSIKLPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 VSVGAPDLS(0.001)LEAS(0.057)EGS(0.942)IKLPK 120.08 2.64E-05 66425000 63055 22677 45248 25240 70727 56704 47785 35621 42663 27236 TRUE FALSE 65544.46009 26571.59835 46427.20005 30232.39667 58704.8498 43535.35536 44039.48684 35143.55876 41127.56696 32572.37274 2.012271584 0.815771039 1.425355175 0.928160712 1.802289636 1.336573043 1.352050316 1.078937634 1.262651858 1 14.9913612 1.765170073 8.271853783 1.129484808 1.358882728 0.113178047 0.338541591 0.426844162 92.93518729 0.149599106 0.08218324 58.23312185 -1.765170073 0.22939792 VSVGIHKEDIDAAIETYNLLSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSVGIHKEDIDAAIETYNLLSER 23 1 P23921 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 149.85 5.44E-08 11311000 17751 16476 22681 14903 26320 27071 26222 22706 21463 17672 FALSE TRUE 18451.82319 19305.62483 23272.08549 17850.76892 21846.1358 20784.17051 24166.65112 22401.66321 20690.55082 21134.49005 0.873066875 0.913465373 1.101142513 0.844627378 1.033672246 0.983424273 1.143469801 1.059957593 0.978994562 1 14.36731168 2.907492981 2.390555979 1.050181881 0.94432726 0.237569901 0.07980537 0.405362644 4.565787904 0.026148517 0.028844936 808.1518674 -2.907492981 -0.10585462 VSVHVIEGDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 18 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 ;;;;;;;;;;;;;;;;; 221.55 4.82E-12 84390571000 4096214.6 15958395.4 14569111 18245606 14660678.3 19732329 13230732 16173668.5 13236951.5 16927537.1 FALSE TRUE 4257936.315 18699125.67 14948794 21854532.41 12168661.44 15149794.64 12193672.65 15956886.93 12760556.2 20244163.9 0.210329077 0.92367982 0.738424865 1.079547297 0.60109479 0.748353684 0.602330267 0.788221584 0.630332587 1 24.27100272 4.747906189 24.88226234 0.775806608 0.21032876 0.54761313 0.157630499 893.7292399 2379470.428 0.035695869 0.455235008 55963.67025 -4.747906189 -0.565477849 VSVHVLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSVHVLAR 8 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 73.26 0.043548 0 63286 143970 114230 145260 136560 181480 104970 120960 112180 185270 FALSE TRUE 65784.58015 168695.7276 117206.9276 173991.9944 113347.58 139334.0204 96742.17711 119338.7291 108142.6637 221570.1093 0.296901872 0.761365006 0.528983481 0.785268351 0.511565302 0.628848453 0.436621065 0.538604821 0.488074245 1 17.75740374 -1.009235458 5.105800621 1.000000847 0.55961589 0.4866134 0.137611099 5.54E-06 1.08E-06 0.122566688 0.028888993 0.097895909 1.009235458 -0.440384957 VSVS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VSVSPGR 7 0 A9Z1X7;Q8IYB3-2;E9PCT1;Q8IYB3 A9Z1X7;Q8IYB3 SRRM1 Serine/arginine repetitive matrix protein 1 1 VS(0.002)VS(0.998)PGR;VS(0.002)VS(0.998)PGR;VS(0.005)VS(0.995)PGR;VS(0.01)VS(0.99)PGR;VS(0.009)VS(0.991)PGR;VS(0.007)VS(0.993)PGR 100.02 0.010597 4725020000 3349090 3752480 3660060 3551540 4079810 4317400 3932320 3731070 3516820 3538940 TRUE FALSE 3481314.659 4396939.25 3755444.17 4254024.012 3386325.353 3314749.281 3624094.483 3681061.109 3390250.335 4232327.536 0.822553224 1.038893898 0.887323615 1.00512637 0.800109473 0.783197721 0.856288757 0.869748638 0.801036854 1 22.01301985 3.231718023 24.99997003 0.844233945 0.94199349 0.218443838 0.079516039 204.4585842 747005.1604 0.021149044 0.025812773 1704.975029 -3.231718023 0.097759546 VSVT(ph)PPEESQNSDTPPRPDRLPLDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209;Q05209-2;Q05209-3;H3BM04 Q05209 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 VS(0.002)VT(0.998)PPEESQNSDTPPRPDRLPLDEK 135.49 0.0014809 347040000 248930 175540 227610 167210 326270 295310 228880 220970 256820 181970 TRUE FALSE 258757.9486 205687.6295 233541.7036 200283.6389 270810.7419 226728.728 210939.7875 218008.2586 247577.0984 217623.5375 1.18901637 0.945153414 1.073145425 0.920321585 1.244400055 1.041839181 0.96928756 1.001767829 1.137639344 1 17.73147508 -1.739296058 6.598614126 0.999073854 1.048636746 0.021382628 0.101125974 0.001315197 5.20E-05 0.093463643 0.021622018 0.018226528 1.739296058 0.049562892 VSYGIGDEEHDQEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VSYGIGDEEHDQEGR 15 0 P27695;G3V3M6;G3V3C7;G3V5M0;G3V359 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;; 268.61 1.15E-25 2856300000 1405587 1605388 1611045 1413525 1898588 2050150 1751560 1661426 1761789 1441300 FALSE TRUE 1461080.66 1881100.901 1653030.156 1693116.026 1575866.69 1574033.733 1614268.15 1639157.302 1698382.558 1723695.14 0.847644474 1.091318794 0.959003781 0.982259558 0.914237474 0.913174085 0.936516042 0.950955459 0.985314931 1 20.7170732 6.130417156 12.92255787 0.957459214 0.624066399 0 0.061229873 0 0 0.012685131 0 1350259.235 -6.130417156 -0.333392815 VSYLVFDEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VSYLVFDEADR 11 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 ;;;; 157.75 7.08E-05 576273000 365927 402006 393830 398778 464863 497301 493413 447720 407022 364176 FALSE TRUE 380374.0805 471047.4033 404093.5333 477655.0982 385845.7533 381810.3794 454737.9998 441719.0457 392373.3577 435529.3146 0.873360455 1.081551545 0.927821664 1.096723187 0.885923726 0.876658279 1.04410423 1.014211974 0.900911476 1 18.7324103 -1.548932821 3.010623637 1.001124284 0.974282342 0.007132083 0.082481951 18332565.21 31477571.09 175342.7413 0.020128037 0.02825317 1.548932821 -0.026841943 VT(ph)PTKESYTEEIVSEAESHVSGISR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTPTKESYTEEIVSEAESHVSGISR 25 1 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 VT(0.922)PT(0.05)KES(0.01)Y(0.008)T(0.01)EEIVSEAESHVSGISR 91.416 0.018954 22720000 4893.1 11205 12036 12281 13412 17740 13793 13268 12719 9541.2 TRUE FALSE 5086.283366 13129.37159 12349.66805 14710.14514 11132.23303 13620.15385 12711.86862 13090.16416 12261.24567 11410.61546 0.445750134 1.150627819 1.082296401 1.289163165 0.975603206 1.193638844 1.114038823 1.147191771 1.074547268 1 13.47808899 4.740015451 24.93592019 1.122384162 0.445749903 0.84294706 0.086483045 39.13678439 670738.7131 0.018465009 0.116336655 54956.0426 -4.740015451 -0.676634258 VTAAMVLTSLST(ph)SPLVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTAAMVLTSLSTSPLVR 17 0 Q6ZNC4;E5RGL7 Q6ZNC4 ZNF704 Zinc finger protein 704 1 VTAAMVLT(0.006)S(0.003)LS(0.041)T(0.91)S(0.04)PLVR;VTAAMVLT(0.001)S(0.001)LS(0.004)T(0.861)S(0.133)PLVR 144.97 1.74E-05 0 153019 139700 180069 181331 186481 224854 217726 179596 181216 130716 TRUE FALSE 159060.3083 163692.3883 184761.7461 217197.7306 154783.0262 172635.0662 200660.0672 177188.8094 174694.0716 156327.2975 1.01748262 1.047113274 1.181890489 1.389378145 0.990121551 1.104318113 1.283589433 1.133447659 1.117489232 1 17.25421019 0.814060102 2.75544842 1.00013715 1.148950299 0.120840386 0.114935856 1.770645376 22.05882503 0.110737887 0.029284413 6.517185789 -0.814060102 0.148813148 VTAEADSSS(ph)PTGILATSESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTAEADSSSPTGILATSESK 20 0 A0MZ66;A0MZ66-3;A0MZ66-4;A0MZ66-6;A0MZ66-5;A0MZ66-8;A0MZ66-7 A0MZ66 KIAA1598 Shootin-1 1 VTAEADS(0.003)S(0.116)S(0.865)PT(0.016)GILATSESK;VTAEADSS(0.005)S(0.995)PTGILATSESK;VTAEADSS(0.02)S(0.979)PT(0.001)GILATSESK;VTAEADSS(0.007)S(0.988)PT(0.005)GILATSESK 260.97 2.44E-36 944210000 1804730 1248620 1677540 1322800 1960370 2083250 2028220 1672110 1830490 1215820 TRUE FALSE 1875982.134 1463060.772 1721258.071 1584445.892 1627147.008 1599446.759 1869242.817 1649698.1 1764611.022 1454036.651 1.290189029 1.006206254 1.183779012 1.089687726 1.119055016 1.100004432 1.285554127 1.134564318 1.213594597 1 20.4716322 VTAGWPSEPGQGDLNPES(ph)PAALGQDLLEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 119.97 2.06E-05 8277300 12947 20987 16110 16757 17989 15743 15924 16933 17510 16151 TRUE FALSE 13458.15756 24591.35399 16529.83983 20071.48459 14931.23621 12086.92684 14675.83527 16706.04083 16879.81852 19315.47922 0.696755043 1.273142318 0.855782021 1.039139871 0.773019195 0.625763757 0.759796591 0.86490429 0.873901099 1 14.23746985 3.232489136 24.99115473 0.800903354 0.980241584 0.162278094 0.163499271 214.0769309 881173.6112 0.044614411 0.054620521 1708.004993 -3.232489136 0.17933823 VTAIHIDPATHR ddPTM_MDA-MB-175_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 ;;;;;;;;;;;; 201 8.87E-08 72048432000 29085267 31520431 34141269 36628990 35896375 41321382 31969345 32201175 31089878 32409806 FALSE TRUE 30233575.8 36933819.83 35031018.52 43874094.9 29794722 31725117.26 29463504.2 31769570.92 29970959.36 38759886.96 0.78002229 0.952887707 0.903795683 1.131945894 0.76869992 0.818503864 0.760154544 0.819650763 0.773246821 1 25.20806103 VTANNDKNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTANNDKNR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 ; 172.27 5.14E-05 147250000 114170 109867 94956 87539 147090 133515 124152 107841 104785 134029 FALSE TRUE 118677.5198 128735.8026 97430.63137 104853.9529 122087.6943 102508.1647 114420.6418 106395.5678 101013.8083 160289.4164 0.740395233 0.803145994 0.60784195 0.654153938 0.76167034 0.639519233 0.713837784 0.663771634 0.63019637 1 17.29031964 -1.232216273 4.409780106 1.000127525 0.690003184 0.706029356 0.059911717 7.40E-05 1.29E-05 0.057150327 0.013464945 0.058584635 1.232216273 -0.310124341 VTAS(ph)PGTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTASPGTLR 9 0 Q12872-2 Q12872-2 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 VT(0.001)AS(0.998)PGT(0.001)LR 106.16 0.0031272 143550000 132940 184510 169630 164640 200450 245100 167010 174910 158750 166800 TRUE FALSE 138188.5739 216198.1572 174050.6972 197205.3006 166377.5806 188179.2395 153919.3198 172565.6175 153036.6185 199481.2664 0.692739606 1.083801808 0.872516504 0.988590579 0.834051155 0.943342916 0.771597868 0.865071797 0.767172884 1 17.60589374 2.25777071 24.96754794 0.8400004 0.910185805 0.041473602 0.113180718 592.5392663 770127.4652 0.035906211 0.029998033 181.0384029 -2.25777071 0.070185405 VTDALPEPEPPGAMAAS(ph)EDEEEEEEALEAMQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTDALPEPEPPGAMAASEDEEEEEEALEAMQSR 33 0 Q9Y3E7-2;Q9Y3E7-4;Q9Y3E7;Q9Y3E7-3 Q9Y3E7-2 CHMP3 Charged multivesicular body protein 3 1 VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR;VTDALPEPEPPGAMAAS(1)EDEEEEEEALEAMQSR 244.91 2.71E-47 462175000 461274 608307 580299 528646 577434 701444 562373 561950 551439 627124 TRUE FALSE 479485.4537 712778.9953 595422.0687 633210.6009 479281.9749 538544.2615 518292.7348 554417.9794 531592.8181 749996.9408 0.639316546 0.95037587 0.79389933 0.844284245 0.63904524 0.718061944 0.691059798 0.739226988 0.708793315 1 19.51652519 5.024375583 18.35143113 0.770107912 0.272961102 0.122408679 0.110572597 24126060.8 435290443.2 0.025508204 364536152.4 105773.1852 -5.024375583 -0.49714681 VTDKLTPIHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VTDKLTPIHDR 11 1 P28072;A0A087X2I4;I3L3X7 P28072 PSMB6 Proteasome subunit beta type-6;Proteasome subunit beta type 0 ;;;;; 193.23 6.28E-07 3388923000 6705080 6600592 7169459 5487542 9168538 8780224 6578212 7448329 7836176 7499552 FALSE TRUE 6969801.736 7734192.331 7356300.991 6572961.429 7610073.186 6741150.042 6062594.554 7348496.333 7554153.556 8968945.627 0.777103801 0.862330161 0.820196855 0.732857763 0.848491395 0.751610091 0.675953987 0.819326668 0.84225659 1 23.09650696 0.833903096 2.069589948 0.999440876 0.784524171 0.600391977 0.052840533 0.421486237 3.339248701 0.051470828 0.014193516 6.821864615 -0.833903096 -0.214916705 VTEGLTDVILYHQPDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VTEGLTDVILYHQPDDK 17 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 ;;;;; 246.03 1.27E-20 2869750000 6237980 4036710 5369280 4126070 6926450 6983150 6651700 5537470 5991320 3426518 FALSE TRUE 6484260.267 4729983.541 5509207.848 4942194.331 5749094.503 5361419.243 6130322.373 5463249.272 5775693.564 4097878.597 1.582345624 1.15425175 1.344404847 1.206037274 1.402944076 1.308340185 1.495974619 1.333189635 1.40943501 1 21.96644581 -1.162694049 4.195033635 0.999896272 1.352880089 0.449110246 0.119287348 6.723843607 30716880.49 6420.537874 0.025717309 0.068755264 1.162694049 0.352983817 VTEGLVDVILYHQPDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VTEGLVDVILYHQPDDK 17 0 O43390;O43390-3;B4DT28 O43390 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 ;;;; 199.49 1.32E-11 1115823000 1539675 1004809 1355893 1039052 1712873 1699050 1775410 1416346 1489866 870317 FALSE TRUE 1600462.558 1177377.129 1391228.685 1244573.384 1421719.459 1304471.387 1636248.725 1397362.199 1436246.014 1040838.953 1.537665893 1.131180886 1.33664164 1.195740591 1.365936061 1.253288401 1.572047933 1.342534495 1.379892643 1 19.98931543 VTEGQQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTEGQQER 8 0 Q13263;Q13263-2 Q13263 TRIM28 Transcription intermediary factor 1-beta 0 ;;; 154.28 0.00099468 1186718000 443883 613973 578404 572100 617430 791080 516671 596934 591850 608606 FALSE TRUE 461407.8436 719418.0867 593477.6834 685259.6725 512479.4691 607363.6589 476172.977 588933.0761 570549.4341 727850.6932 0.633931997 0.988414373 0.815383827 0.941483849 0.70409972 0.834461882 0.654217934 0.809139954 0.783882518 1 19.47328301 4.795787282 22.44446947 0.820378167 0.633927185 0.226829248 0.108617763 32992.29538 12938040.69 0.024776244 37.89240452 62486.6558 -4.795787282 -0.186450981 VTEHGT(ph)PKPFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VTEHGTPKPFR 11 1 Q9NZN5-2;E9PMR6;Q9NZN5 Q9NZN5-2 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 VT(0.002)EHGT(0.998)PKPFR;VT(0.028)EHGT(0.972)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR;VTEHGT(1)PKPFR 169.04 2.54E-05 1069008000 896582 717801 714540 698027 961180 999670 942990 837890 710039 615905 TRUE FALSE 931979.7497 841077.738 733161.4994 836094.6572 797798.9669 767511.7926 869075.9798 826659.4551 684484.8351 736579.7925 1.265280095 1.141869145 0.995359236 1.135103984 1.083112753 1.041994093 1.179880291 1.122294507 0.929274523 1 19.49048229 4.619985431 3.421684194 1.076164165 1.269278491 0.420082378 0.072167112 0.257660576 4.873195901 0.017233929 0.104675873 41685.53991 -4.619985431 0.193114327 VTEKIPVR ddPTM_MDA-MB-175_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 ; 102.61 0.0044983 1531240000 2688800 2268260 2763200 1923070 3704400 3474000 2593300 2673500 3104700 2505040 FALSE TRUE 2794955.9 2657816.01 2835211.262 2303447.506 3074727.411 2667216.149 2390030.37 2637666.105 2992962.453 2995854.626 0.932941097 0.887164546 0.946378118 0.768878265 1.026327307 0.890302262 0.797779154 0.880438618 0.999034608 1 21.51453619 1.235879968 24.49291522 0.999517402 0.888343908 0.284643564 0.068511677 67.09544602 612969.476 0.054335095 0.01598884 17.21392744 -1.235879968 -0.111173494 VTEQEWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTEQEWR 7 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 ;;; 151.56 0.0043572 2004160000 2832870 2919530 2886750 2655610 3273390 3801190 2731550 2775820 2758380 3595890 FALSE TRUE 2944713.895 3420936.567 2961981.076 3180881.732 2716980.337 2918421.23 2517443.973 2738614.673 2659106.443 4300435.798 0.684747787 0.795486022 0.688763003 0.739664974 0.631791861 0.678633833 0.585392758 0.636822592 0.61833418 1 22.03605144 -1.045434518 4.682187313 1.00001006 0.67176101 0.74107793 0.057927467 7.27E-06 1.48E-06 0.060525275 0.01426546 0.090066955 1.045434518 -0.32824905 VTFEDATDFFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTFEDATDFFGR 12 0 Q86WQ0;Q86WQ0-2 Q86WQ0 NR2C2AP Nuclear receptor 2C2-associated protein 0 ; 168.46 0.00010809 117690000 85404 91840 92350 104859 100812 112288 107716 98872 98326 103337 FALSE TRUE 88775.81587 107612.8056 94756.71687 125599.7972 83676.01225 86210.81374 99272.93846 97546.78256 94787.26647 123583.9066 0.71834447 0.870767145 0.766739938 1.016311918 0.677078549 0.697589323 0.803283705 0.789316224 0.766987135 1 16.91513136 -1.160739834 3.909726247 1.000106695 0.792387728 0.317524156 0.092456411 10240269.3 6080375.574 8738.392731 0.02095502 0.069065342 1.160739834 -0.207718966 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_MDA-MB-175_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 238.44 9.00E-31 799080000 756280 475075 679873 479481 843900 861890 825475 658006 757621 508101 TRUE FALSE 786138.5184 556665.4357 697591.0489 574320.9107 700454.1794 661729.1096 760772.1125 649186.5059 730354.3682 607653.6628 1.293727935 0.916089986 1.148007643 0.945145147 1.152719423 1.088990572 1.251983094 1.068349531 1.201925394 1 19.21288976 VTFFEPGSGDENGTSNKEDEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTFFEPGSGDENGTSNKEDEFR 22 1 O95793-2;O95793-3;O95793;Q5JW30 O95793-2 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 0 ;;; 288.96 8.04E-48 918290000 864650 623952 803530 612314 990820 989160 929440 761930 878210 628270 FALSE TRUE 898787.0497 731110.9023 824470.6519 733427.8816 822400.7703 759442.5809 856588.0642 751717.5746 846603.3936 751367.4775 1.196201694 0.973040389 1.097293504 0.976124072 1.094538684 1.010747209 1.140038782 1.000465947 1.126750118 1 19.51915915 4.758751278 24.22376585 1.048438903 1.196201909 0.358433647 0.060014928 3302.778507 3962414.15 0.012603682 0.507058496 57378.77575 -4.758751278 0.147763006 VTGGLLDRLDDS(ph)PDQCR ddPTM_MDA-MB-175_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 119.01 8.53E-05 98363000 54357 56437 52408 60813 57237 78042 54878 54698 60974 48735 TRUE FALSE 56503.05633 66129.61573 53773.79553 72841.62989 47507.87518 59917.92824 50576.51896 53964.86278 58779.55765 58283.69016 0.969448849 1.134616143 0.92262167 1.249777248 0.815114401 1.028039372 0.867764529 0.925899898 1.008507826 1 15.8308046 3.218685972 24.9999519 0.935473408 1.063330825 0.270317367 0.102803443 297.8837424 374701.5736 0.02718745 0.032535116 1654.573147 -3.218685972 0.127857417 VTGPPPGT(ph)PQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTGPPPGTPQPR 12 0 F5GYK2;Q9NRL3;Q9NRL3-3;R4GN16;M0QZM0 F5GYK2 STRN4 Striatin-4 1 VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR;VTGPPPGT(1)PQPR 207.73 8.39E-07 1077620000 368565 370305 385990 411179 443440 507270 481370 443640 425980 369811 TRUE FALSE 383116.2308 433902.0032 396049.2165 492508.979 368064.2272 389464.2303 443638.9616 437693.7314 410649.063 442268.385 0.866252809 0.981083021 0.895495201 1.113597525 0.832219168 0.880606083 1.00309897 0.989656386 0.928506484 1 18.75456259 2.212162683 24.97448411 0.98139114 0.933188884 0.099811893 0.075752785 588.7892278 557036.5433 0.028066973 0.02073509 162.9906467 -2.212162683 -0.048202256 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 VTGTEGSSSTLVDYTST(0.001)S(0.023)S(0.088)T(0.339)GGS(0.55)PVRK;VTGTEGSSSTLVDYTST(0.004)S(0.163)S(0.078)T(0.03)GGS(0.725)PVRK 270.95 5.81E-61 835610000 263880 189427 230390 192113 268050 255380 303840 205827 235580 149400 TRUE FALSE 274298.1862 221959.6137 236394.1527 230112.378 222486.9567 196071.8653 280024.2269 203068.2257 227101.5218 178672.0696 1.535204617 1.242273704 1.323061591 1.287903468 1.245225162 1.097383972 1.567252383 1.136541521 1.27105217 1 17.4469546 -5 0.12900805 0.037510299 1.417025592 0.338578581 0.136987571 171.5454278 1.400899028 42.87839655 1.008312444 1.00E-05 5 1.379515293 VTHAVVTVPAYFNDAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ; 176.21 1.13E-09 6307000000 2821000 3616800 3065200 3351300 3551200 4140500 3192800 2992600 2742900 3212400 FALSE TRUE 2932375.258 4237957.265 3145081.63 4014177.137 2947568.292 3178931.625 2942539.993 2952489.092 2644183.565 3841808.275 0.763279958 1.103115242 0.81864617 1.044866597 0.767234615 0.827457124 0.765925778 0.76851547 0.688265362 1 21.87335409 3.215127422 24.99293785 0.788628576 0.936534696 0.216661684 0.11875849 284.0625511 302969.341 0.031226514 0.03734349 1641.071194 -3.215127422 0.14790612 VTHDMDMCYGMMGSLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTHDMDMCYGMMGSLFR 17 0 P49902-2;P49902 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 173.34 1.49E-09 2786200000 1203520 1185310 1378400 1243110 1434710 1595390 1461650 1393840 1369170 1327940 FALSE TRUE 1251035.899 1388877.772 1414322.236 1488993.448 1190838.507 1224884.851 1347082.054 1375157.855 1319893.839 1588124.418 0.787744263 0.87453965 0.890561357 0.937579846 0.749839555 0.771277639 0.84822199 0.86590058 0.831102289 1 20.59889251 -1.558114138 3.469681509 1.004612536 0.842532888 0.436786812 0.054539272 202900052.5 25840609.06 7599069.368 0.013283597 0.027662146 1.558114138 -0.162079648 VTIPPPSSSVAISNHVT(ph)PPPIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTIPPPSSSVAISNHVTPPPIPK 23 0 F5H2U7;A0A1W2PNT6;F5GYH1;A0A1W2PRM0;A0A1W2PRL5;A0A1W2PR09;Q8NC96;A0A1W2PRW5 F5H2U7 NECAP1 Adaptin ear-binding coat-associated protein 1 1 VTIPPPSSSVAIS(0.001)NHVT(0.999)PPPIPK;VTIPPPSSSVAIS(0.002)NHVT(0.998)PPPIPK 147.41 4.32E-07 1164460000 348540 723100 807280 745030 953950 1037080 872190 869510 804710 617510 TRUE FALSE 362300.6283 847286.8001 828318.38 892394.7103 791797.9197 796233.8871 803825.4688 857855.6407 775748.6443 738499.2616 0.490590373 1.147308933 1.121623843 1.208389442 1.07217158 1.078178312 1.088458054 1.161620174 1.050439296 1 19.49423695 4.740548473 24.99353009 1.111813819 0.490590161 0.911598304 0.057167459 43.73559235 549852.7374 0.012940597 0.084973601 55023.53306 -4.740548473 -0.621223658 VTKNEEPS(ph)EEEIDAPKPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTKNEEPSEEEIDAPKPK 18 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 VT(0.002)KNEEPS(0.998)EEEIDAPKPK 52.909 0.067045 204620000 211340 104620 121220 82243 221410 179710 144330 128180 154720 90730 TRUE FALSE 219683.8664 122587.6712 124379.0928 98510.41993 183774.8073 137975.076 133017.0375 126461.9568 149151.6574 108506.8064 2.024609089 1.129769415 1.146279178 0.907873185 1.693670779 1.271579919 1.225886577 1.165474877 1.374583424 1 16.72742602 4.742541856 24.90477002 1.221096233 2.024609419 0.58898694 0.203342259 262.1834947 1640029.328 0.047355794 0.362329953 55276.66797 -4.742541856 0.803513186 VTKS(ph)PAPVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VTKSPAPVHR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 VT(0.14)KS(0.86)PAPVHR;VT(0.143)KS(0.857)PAPVHR;VTKS(1)PAPVHR;VT(0.201)KS(0.799)PAPVHR;VTKS(1)PAPVHR;VT(0.443)KS(0.557)PAPVHR 157.22 5.78E-06 6434410000 7541240 5840770 7016020 5400880 8701630 8487090 7761510 6987580 7280390 5250740 TRUE FALSE 7838973.978 6843876.813 7198863.245 6469157.944 7222530.041 6516091.971 7153142.565 6893922.919 7018370.186 6279521.972 1.248339287 1.089872262 1.146403067 1.03019911 1.150171952 1.03767325 1.139122149 1.097841994 1.117659946 1 22.58222331 8 0.013033454 2.02E-10 2.407282112 0.342454474 0.055623461 9153.647122 9.214636026 700.486427 1030.997142 100000000 -8 2.407282112 VTKS(ph)PGETSKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTKSPGETSKPR 12 2 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-4;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VT(0.208)KS(0.711)PGET(0.041)S(0.041)KPR 65.038 0.03226 214600000 489420 239930 361340 246300 486630 423870 448400 320450 408400 175270 TRUE FALSE 508742.6795 281136.1111 370756.8172 295017.4049 403912.8064 325432.6163 413253.2363 316154.8919 393701.7638 209610.8008 2.427082372 1.341229126 1.768786799 1.40745326 1.926965619 1.552556524 1.971526443 1.508294853 1.878251323 1 17.67735353 -1.868516309 2.510742045 0.661477763 1.724207145 0.347493424 0.307427331 25545700.32 15185417.64 51562180.45 0.067715957 0.013535793 1.868516309 1.062729381 VTKS(ph)PGETSKPRPFAGGGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTKSPGETSKPRPFAGGGYR 20 3 Q9UNZ2;Q9UNZ2-5;F2Z2K0;Q9UNZ2-6 Q9UNZ2 NSFL1C NSFL1 cofactor p47 1 VTKS(0.999)PGETSKPRPFAGGGYR;VT(0.05)KS(0.929)PGET(0.016)S(0.004)KPRPFAGGGYR 130.29 1.17E-05 3924960000 1675090 923610 1382090 818250 1955140 1631960 1287960 1287510 1567930 995220 TRUE FALSE 1741223.847 1082232.833 1418108.401 980097.4078 1622806.001 1252962.023 1187006.33 1270253.034 1511500.506 1190214.304 1.462949857 0.909275606 1.191473162 0.823462971 1.36345698 1.052719681 0.997304708 1.067247327 1.269939792 1 20.18278993 4.755222425 24.28053762 1.077053794 1.462950308 0.362883636 0.154196937 2302.421239 3355137.234 0.033825403 0.898711891 56914.4345 -4.755222425 0.385896514 VTKS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTKSPQK 7 1 Q9NVP1 Q9NVP1 DDX18 ATP-dependent RNA helicase DDX18 1 VT(0.02)KS(0.98)PQK 63.184 0.049031 101760000 720400 306850 429000 276810 617070 603980 679850 435070 488820 287100 TRUE FALSE 748841.9483 359549.1005 440180.0924 331562.1918 512180.6618 463714.7984 626561.5805 429238.5983 471227.4637 343351.7481 2.180976076 1.047174224 1.282009178 0.965663328 1.491708327 1.350553189 1.824838766 1.250142458 1.372433565 1 18.38932778 0.595172406 1.716150843 1.000567608 1.403936461 0.12066642 0.338887298 4.399387105 15.93395628 0.307325804 0.086855585 3.937063379 -0.595172406 0.403368853 VTLLEGDHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 ;; 154.24 1.48E-05 622632000 310525 363580 337080 351525 378553 437316 378369 377570 340944 365299 FALSE TRUE 322784.7668 426022.0367 345864.5817 421055.5958 314206.6963 335755.9866 348711.4491 372509.2917 328673.492 436872.345 0.738853742 0.975163664 0.791683396 0.96379549 0.719218554 0.76854484 0.79819987 0.852673089 0.752333023 1 18.73685226 5.029691382 17.19261827 0.837530121 0.419259509 0.096292545 0.095485936 19715533.67 297732161.1 0.021249757 242945382.6 107075.8132 -5.029691382 -0.418270611 VTLTSEEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 ; 194.84 9.75E-07 570260000 248140 273500 266510 284680 296640 326260 279040 283060 279930 294830 FALSE TRUE 257936.7588 320471.4975 273455.4695 340988.8543 246217.2388 250491.0595 257168.1157 279266.0437 269855.374 352596.2936 0.73153565 0.908890715 0.775548338 0.967080087 0.698297864 0.710418867 0.729355697 0.792027735 0.76533809 1 18.42765778 5.045891546 15.61477656 0.802965469 0.35963473 0.044594182 0.102079432 5952725.795 55775743.93 0.023390321 77405746.4 111145.4135 -5.045891546 -0.443330739 VTLVFEHVDQDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTLVFEHVDQDLR 13 0 F8W1L8;F8VYH9;F8VTV8;F8VWX7;P11802;F8VXD2;F8VZZ0;F8VZ51 F8W1L8 CDK4 Cyclin-dependent kinase 4 0 ;;; 159.02 4.27E-05 276622000 327340 344885 376721 384994 434503 455235 419463 404088 390658 354667 FALSE TRUE 340263.636 404116.3159 386538.6587 461144.6641 360646.3353 349513.5704 386584.394 398671.8613 376598.2949 424157.2081 0.802211136 0.952751263 0.91130989 1.087202234 0.850265723 0.824018934 0.911417716 0.939915328 0.887874325 1 18.69423955 -1.340424879 2.734216685 1.001375723 0.912315626 0.115603894 0.075730312 8869587.01 10090387.26 98107.47782 0.019172458 0.045664123 1.340424879 -0.089060097 VTLYNTDQDGSDS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTLYNTDQDGSDSPR 15 0 Q9UPW0-2;Q9UPW0;C9JXI1;C9JVP0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 VTLYNTDQDGS(0.02)DS(0.98)PR;VTLYNTDQDGS(0.008)DS(0.992)PR 145.91 4.17E-06 455760000 161788 139000 125244 122167 166037 187953 137818 140133 141884 116722 TRUE FALSE 168175.5152 162872.1687 128507.9615 146331.268 137814.09 144303.7642 127015.465 138254.7463 136777.6226 139591.4411 1.204769532 1.166777615 0.920600579 1.048282522 0.987267478 1.033757966 0.909908688 0.990424235 0.979842471 1 17.09085096 4.312179262 6.385092305 0.984212771 1.19213229 0.794501491 0.041164407 0.079295014 5.321466311 0.00957079 0.02663494 20520.09003 -4.312179262 0.207919519 VTNDIS(ph)PESS(ph)PGVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTNDISPESSPGVGR 15 0 A0A4W8VX11;A0A5H1ZRS1;Q15154-4;Q15154-2;Q15154-5;Q15154;E7EV93;E9PGW9;E5RGQ4;Q15154-3 A0A4W8VX11 PCM1 Pericentriolar material 1 protein 2 VTNDIS(0.999)PES(0.001)S(1)PGVGR;VTNDIS(1)PESS(1)PGVGR;VTNDIS(1)PES(0.03)S(0.97)PGVGR;VTNDIS(1)PES(0.005)S(0.995)PGVGR 302.64 2.91E-44 892618000 1468450 1681090 1556900 1514850 1713540 1963830 1601180 1541880 1414180 1475040 TRUE FALSE 1526425.54 1969804.13 1597474.093 1814482.809 1422273.083 1507760.245 1475675.328 1521213.621 1363283.938 1764045.847 0.865298112 1.116639987 0.905574022 1.028591639 0.806256303 0.854717153 0.836528898 0.862343586 0.772816614 1 20.75045663 3.237814511 24.99999252 0.84833441 0.983608956 0.339174454 0.084059474 19.39861385 650007.1431 0.02162203 0.027338361 1729.077703 -3.237814511 0.135274546 VTNDIS(ph)PESSPGVGR ddPTM_MDA-MB-175_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 1 VTNDIS(0.652)PES(0.337)S(0.01)PGVGR 119.85 0.00018875 152440000 147770 128710 137520 131750 146470 187120 155520 137460 130750 129750 TRUE FALSE 153604.0737 150814.9413 141103.8842 157809.7568 121573.0817 143664.2158 143329.936 135617.5735 126044.333 155172.0283 0.989895379 0.971920925 0.909338402 1.016998737 0.783472918 0.925838358 0.923684105 0.87398209 0.81228772 1 17.24350899 3.263564437 24.99999934 0.884277894 0.967551387 0.311793721 0.062027526 278.3373537 278292.8785 0.01629965 0.022060714 1834.697365 -3.263564437 0.083273492 VTNDISPES(ph)SPGVGR ddPTM_MDA-MB-175_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(0.045)PES(0.862)S(0.092)PGVGR;VTNDIS(0.029)PES(0.876)S(0.096)PGVGR;VTNDIS(0.072)PES(0.925)S(0.002)PGVGR 230.48 3.39E-13 4182540000 2767380 3010270 3044500 3020250 3273090 3706480 3259690 3129250 2954690 3019640 TRUE FALSE 2876638.299 3527260.456 3123842.171 3617646.435 2716731.331 2845706.192 3004186.98 3087307.522 2848351.284 3611280.643 0.796570132 0.976733963 0.865023375 1.001762752 0.752290281 0.78800472 0.831889647 0.854906563 0.788737173 1 21.78407911 3.232554023 24.99999433 0.828208683 0.911573428 0.160391134 0.081822522 224.1819647 933065.7597 0.021800421 0.026700449 1708.260201 -3.232554023 0.083364745 VTNDISPESS(ph)PGVGR ddPTM_MDA-MB-175_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 1 VTNDIS(0.038)PES(0.445)S(0.517)PGVGR 250.94 4.72E-19 1764600000 1025200 1088300 1016000 980440 1136400 1274600 1095600 1075100 1021000 1055500 TRUE FALSE 1065675.688 1275207.059 1042477.795 1174368.106 943235.1339 978593.4667 1009724.009 1060690.043 984254.4094 1262305.016 0.84422994 1.010221019 0.825852533 0.930336242 0.747232342 0.775243269 0.799904933 0.840280304 0.779727876 1 20.26762913 3.255435463 24.99859806 0.813771245 0.904856639 0.182281104 0.080196672 341.6428625 506110.6177 0.020541644 0.027741528 1800.675531 -3.255435463 0.091085394 VTNEFVHINNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTNEFVHINNLK 12 0 O00743;O00743-2;O00743-3 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ; 176.05 2.60E-05 1128300000 2173880 1713390 1977280 1798120 2428550 2572000 2431650 2154110 2195930 1515040 FALSE TRUE 2259706.461 2007651.404 2028809.541 2153782.769 2015745.938 1974691.979 2241050.919 2125237.679 2116898.908 1811883.081 1.247159094 1.108046885 1.119724315 1.188698538 1.112514356 1.089856183 1.236862876 1.17294416 1.168341893 1 20.78905843 4.751549245 24.1335744 1.143806346 1.247159202 0.216890221 0.062092343 2055.251915 3818658.33 0.01418507 0.247218644 56435.09299 -4.751549245 0.103352857 VTNGAFTGEIS(ph)PGMIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 VTNGAFTGEISPGMIK 16 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 VTNGAFTGEIS(1)PGMIK;VTNGAFT(0.001)GEIS(0.999)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK;VTNGAFTGEIS(1)PGMIK 204.05 2.75E-11 649796000 1324370 1075971 1259966 979992 1614870 1615360 1399990 1270590 1354900 1000810 TRUE FALSE 1376657.15 1260760.649 1292801.749 1173831.493 1340374.974 1240217.121 1290255.126 1253559.819 1306137.414 1196899.558 1.15018603 1.053355431 1.080125513 0.980726816 1.119872562 1.036191477 1.07799783 1.047339195 1.091267354 1 20.19087066 0.808808148 0.007764433 4.12E-06 2.092688652 0.192580155 0.043968248 5390.345492 23.39390908 3193.489258 3109.215587 6.438847626 -0.808808148 2.092684528 VTPDTDWAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTPDTDWAR 9 0 P53396;P53396-2;P53396-3;K7ESG8 P53396 ACLY ATP-citrate synthase 0 ;;; 172.11 0.00013131 3575110000 1731680 2024100 1892060 1898700 2334630 2376800 2089340 1961430 1928520 2194250 FALSE TRUE 1800048.064 2371723.43 1941368.638 2274257.193 1937790.427 1824824.221 1925572.071 1935140.239 1859112.942 2624171.276 0.685949153 0.903799021 0.739802564 0.8666573 0.738439005 0.69539067 0.733782924 0.737429091 0.708457165 1 21.32343046 -1.113614243 3.789508846 1.000104121 0.758818232 0.534535549 0.068102173 16602179.65 33587858.94 22424.45132 0.01601641 0.076981391 1.113614243 -0.241285889 VTQHES(ph)DNENEIQIQNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 VT(0.165)QHES(0.835)DNENEIQIQNK;VTQHES(1)DNENEIQIQNK 307.04 1.48E-47 1050160000 558670 415430 573950 448580 625300 649740 563540 511140 537200 382280 TRUE FALSE 580726.723 486776.8709 588907.6085 537307.7851 519011.7294 498847.7319 519368.2623 504289.0044 517866.2769 457180.4468 1.270235258 1.064736855 1.288129474 1.175264141 1.13524481 1.091139692 1.136024661 1.103041497 1.132739339 1 18.80240418 -4.999995764 0.030301807 0.051665895 1.782609464 0.47604237 0.060238375 1211.750265 2.76411113 123.6310621 49.67733958 1.00E-05 4.999995764 1.730943569 VTRS(ph)PPETAAPVEDMAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTRSPPETAAPVEDMAR 17 1 Q9Y3L3;Q6ZT62-2;Q6ZT62;A0A2R8Y5V0;A0A3B3IU28 Q9Y3L3 SH3BP1 SH3 domain-binding protein 1 1 VT(0.353)RS(0.646)PPET(0.001)AAPVEDMAR;VT(0.143)RS(0.857)PPETAAPVEDMAR 114.88 0.00051905 413930000 214230 416890 353080 383000 373090 479800 318420 383930 352260 462650 TRUE FALSE 222687.9658 488487.6145 362281.5549 458756.2569 309672.2951 368373.7214 293461.4084 378784.0463 339582.2314 553297.4095 0.402474261 0.88286626 0.654768211 0.829131402 0.559685062 0.665778865 0.530386377 0.684593927 0.613742674 1 19.07769564 -1.788562072 3.131743009 1.075164672 0.654710425 0.391719979 0.131636252 666780661.1 50395985.98 363067609.9 0.029078735 0.016271887 1.788562072 -0.420454248 VTRS(ph)QEELREDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTRSQEELREDK 12 2 P55196-5;P55196;J3KN01;P55196-3;A8MQ02;Q5TIG5;P55196-6;P55196-2;P55196-1 P55196-5;P55196-1 MLLT4 Afadin 1 VT(0.021)RS(0.979)QEELREDK;VT(0.011)RS(0.989)QEELREDK;VT(0.01)RS(0.99)QEELREDK;VT(0.06)RS(0.94)QEELREDK 106.82 0.0014811 1787280000 1181220 800600 962490 583780 1494410 1246760 834700 847880 1050110 807330 TRUE FALSE 1227855.478 938096.8222 987573.2801 699249.9416 1240390.722 957218.8848 769274.0329 836515.5555 1012316.746 965510.8562 1.271715869 0.971606706 1.022850519 0.724227943 1.284698887 0.99141183 0.796753375 0.866396841 1.04847785 1 19.88093296 2.467425354 24.630146 0.905463605 1.041004782 0.112168084 0.161506033 356.3012056 905090.9025 0.055131658 0.046180371 293.3765212 -2.467425354 0.135541177 VTRVEFEELCADLFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTRVEFEELCADLFER 16 1 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ;;; 156.22 1.68E-07 124030000 76829 110848 90149 80018 132978 138375 65896 90977 98558 142523 FALSE TRUE 79862.26824 129885.2817 92498.357 95845.32157 110374.4471 106239.5033 60730.89933 89757.60212 95010.91683 170447.6531 0.468544253 0.762024465 0.542678971 0.562315291 0.647556274 0.623296956 0.35630235 0.526599226 0.557419918 1 17.37896921 -1.54677901 3.222551638 1.015267518 0.559139907 0.625868074 0.10187702 29088003.79 33434206.65 3819943.959 0.024538927 0.028393635 1.54677901 -0.456127611 VTRYPILGIPQAHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTRYPILGIPQAHR 14 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 ; 77.754 0.014292 495900000 287650 306490 304390 250440 441920 448830 294370 318240 326440 449500 FALSE TRUE 299006.6441 359127.2733 312322.6535 299976.2845 366802.5962 344596.0346 271296.5102 313974.5133 314691.4882 537570.9188 0.556218042 0.66805562 0.580988745 0.558021787 0.682333406 0.641024324 0.504671106 0.584061567 0.585395298 1 19.03609557 -0.862926167 5.870332449 1.000000086 0.595274837 0.847305518 0.05149655 5.78E-08 1.12E-08 0.050015376 0.011788734 0.137111484 0.862926167 -0.404725248 VTS(ph)TQQQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTSTQQQTR 9 0 F5GZ78;A0A1B0GTU4;P49023;P49023-2;A0A1B0GU60;A0A1B0GV30;P49023-3;P49023-4 F5GZ78;P49023-3;P49023-4 PXN Paxillin 1 VT(0.043)S(0.914)T(0.043)QQQTR;VT(0.184)S(0.816)TQQQTR;VT(0.001)S(0.997)T(0.001)QQQTR 161.7 6.75E-05 1296770000 1371080 1837740 1932380 1924760 2205820 2599190 2059430 2145250 1951100 2360850 TRUE FALSE 1425211.297 2153357.549 1982739.41 2305471.783 1830875.504 1995567.514 1898006.495 2116496.433 1880880.292 2823413.356 0.504783082 0.762678814 0.702249072 0.816554819 0.648461728 0.706792546 0.672238265 0.749623298 0.666172485 1 21.42900893 -4.999999997 0.406772959 6.061946165 0.694523805 0.575096614 0.079149979 552.7793048 3.769996081 2490.701427 0.044753851 1.00E-05 4.999999997 -5.36742236 VTSAHKGPDETLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VTSAHKGPDETLR 13 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ;;;; 218.68 1.43E-11 2789420000 1168320 1749970 2010230 1579650 2560350 2477900 1935470 2143280 2138990 2003330 FALSE TRUE 1214446.176 2050513.735 2062618.245 1892100.055 2125142.622 1902445.278 1783762.804 2114552.837 2062008.168 2395844.157 0.506896983 0.855862736 0.86091503 0.789742542 0.887012043 0.794060529 0.74452372 0.882591979 0.86066039 1 21.19210264 4.739838415 24.8448167 0.843561846 0.506896865 0.70947686 0.066169799 51.58445712 1002859.649 0.014662445 0.091179358 54933.64476 -4.739838415 -0.33666498 VTSLEEELTDLRVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTSLEEELTDLRVEK 15 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 0 142.19 4.22E-06 55721000 58744 42361 54906 36349 73044 70386 73002 53166 61964 51711 FALSE TRUE 61063.25848 49636.17223 56336.89547 43538.72371 60628.00697 54039.91821 67279.91248 52453.39673 59733.92774 61842.78038 0.987395103 0.802618704 0.910969641 0.70402274 0.98035707 0.873827436 1.087918623 0.848173326 0.965899776 1 15.91631756 VTSSMS(ph)SPSMQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.719)S(0.239)PS(0.041)MQPK;VTSS(0.003)MS(0.544)S(0.386)PS(0.067)MQPK;VTSS(0.001)MS(0.669)S(0.324)PS(0.007)MQPK 150.49 8.49E-05 419660000 945420 622650 769180 607510 956930 984250 866630 779980 807410 519890 TRUE FALSE 982745.9116 729585.294 789225.4627 727673.6648 794271.3804 755672.854 798701.2761 769525.6439 778351.4718 621752.4916 1.58060631 1.173433647 1.269356333 1.170359065 1.27747197 1.215391758 1.284596824 1.237671991 1.251867073 1 19.24598086 -5 0.134899092 0.153954461 1.363730621 0.417574881 0.104509727 146.7631804 1.232252307 33.93031543 0.677902431 1.00E-05 5 1.20977616 VTSSMSS(ph)PSMQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 11 VTSSMSSPSMQPK 13 0 Q13136-2;A0A2R8Y7R9;Q13136 Q13136-2 PPFIA1 Liprin-alpha-1 1 VTSSMS(0.087)S(0.672)PS(0.24)MQPK;VTSSMS(0.417)S(0.581)PS(0.002)MQPK;VTSSMS(0.419)S(0.472)PS(0.11)MQPK;VTSSMS(0.007)S(0.991)PS(0.003)MQPK;VTSSMS(0.002)S(0.994)PS(0.004)MQPK;VTSSMS(0.002)S(0.997)PSMQPK;VTSSMS(0.002)S(0.998)PSMQPK;VTSSMS(0.025)S(0.975)PSMQPK;VTSSMS(0.032)S(0.967)PS(0.001)MQPK;VTSSMS(0.002)S(0.998)PS(0.001)MQPK;VTSSMS(0.342)S(0.629)PS(0.029)MQPK 363.82 2.45E-78 7872270000 9884910 7218140 8673420 7042490 10393660 10450280 9605090 8646680 8316390 5774520 TRUE FALSE 10275173.88 8457799.396 8899456.45 8435473.502 8626949.386 8023360.846 8852217.948 8530785.398 8017084.748 6905926.634 1.487877648 1.22471608 1.288669417 1.22148322 1.249209533 1.161808005 1.281829133 1.235284684 1.160899206 1 22.71940358 -4.344890803 0.045565132 1.02E-14 1.836784399 0.650715833 0.068779568 390.0377208 1.477459427 54.14088065 15.84178056 4.52E-05 4.344890803 1.836784399 VTSSVPLPSGSTS(ph)SPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPS(0.008)GS(0.008)T(0.01)S(0.487)S(0.487)PGR 102.52 0.00098995 114380000 148530 144470 170100 159350 177090 181580 172380 167940 154240 133950 TRUE FALSE 154394.0791 169281.5987 174532.9457 190868.9544 146988.3051 139410.7969 158868.4052 165689.039 148688.9325 160194.9379 0.963788751 1.056722521 1.089503502 1.191479312 0.917558988 0.870257192 0.99171926 1.034296347 0.928174975 1 17.28946903 3.21245735 24.99995607 0.962254413 1.075050709 0.423322404 0.067516834 240.6165344 230445.7386 0.021041304 0.025156721 1631.012727 -3.21245735 0.112796296 VTSSVPLPSGSTSS(ph)PGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 VTSSVPLPSGS(0.02)T(0.008)S(0.225)S(0.747)PGR;VTSSVPLPSGSTSS(1)PGR;VTSSVPLPSGSTSS(1)PGR;VTSSVPLPSGSTS(0.015)S(0.985)PGR;VTSSVPLPSGSTSS(1)PGR 335.95 3.59E-72 5681210000 3655650 3946240 4013420 4133460 4348560 4909200 4326680 4171700 3772170 3166340 TRUE FALSE 3799977.885 4623976.023 4118013.022 4951046.051 3609393.324 3769112.7 3987543.516 4115785.185 3636410.339 3786723.7 1.003500172 1.221102037 1.08748706 1.307474863 0.953170501 0.995349278 1.053032603 1.086898731 0.960305168 1 21.85251873 3.212399188 24.99999348 1.019927908 1.154806002 0.421788018 0.083499702 222.5457094 212665.2891 0.023291791 0.027847613 1630.794312 -3.212399188 0.134878094 VTSVAGVYFTDTYGDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTSVAGVYFTDTYGDRDR 18 1 A6NFQ2-2;A6NFQ2 A6NFQ2-2 TCAF2 TRPM8 channel-associated factor 2 0 191.36 2.09E-14 72866000 36149 43233 36587 48627 40805 43477 37740 45480 38457 37882 FALSE TRUE 37576.19043 50657.93144 37540.48728 58245.27546 33868.98068 33380.12565 34781.84018 44870.41499 37072.94008 45304.25261 0.829418615 1.118171662 0.828630539 1.285646978 0.747589436 0.736798948 0.767738969 0.99042391 0.818310378 1 15.46735886 VTTEIQLPSQS(ph)PVEEQSPASLSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VTTEIQLPSQSPVEEQSPASLSSLR 25 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 1 VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPS(0.02)QS(0.98)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR;VTTEIQLPSQS(1)PVEEQSPASLSSLR 289.87 5.33E-63 4013210000 2499060 2951830 2804200 2745760 2961450 3520310 2731250 2988860 2889690 3190880 TRUE FALSE 2597724.818 3458783.84 2877279.756 3288863.133 2458063.787 2702771.353 2517167.488 2948799.22 2785690.621 3816071.843 0.680732682 0.906372831 0.753989934 0.861845182 0.644134568 0.708260081 0.659622667 0.772731579 0.72998904 1 21.8636569 -1.09675258 3.632692157 1.000129802 0.74858059 0.475727286 0.079835457 170307043.3 300476251 269659.5645 0.018979258 0.080029006 1.09675258 -0.251549213 VTTHIPQTPVRPET(ph)PNRTPSATLSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTTHIPQTPVRPETPNRTPSATLSEK 26 2 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 VTTHIPQT(0.014)PVRPET(0.958)PNRT(0.014)PS(0.007)AT(0.007)LSEK;VTTHIPQT(0.001)PVRPET(0.567)PNRT(0.116)PS(0.157)AT(0.157)LS(0.002)EK 96.123 0.0072845 560720000 408060 323256 405560 303567 477980 489270 392100 377090 463010 332136 TRUE FALSE 424170.5239 378772.7034 416129.2268 363611.6465 396733.1303 375644.4575 361366.1774 372035.7253 446346.3605 397211.6901 1.067870192 0.953578943 1.047625831 0.915410235 0.998795202 0.945703429 0.909757156 0.936618268 1.123698954 1 18.59954856 4.746424717 24.03380663 0.973743534 1.067870273 0.137075541 0.062713942 1029.04447 3144778.339 0.014458149 0.155827096 55773.09135 -4.746424717 0.094126739 VTTHPLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTTHPLAK 8 0 Q99497;K7ELW0;K7EN27 Q99497 PARK7 Protein deglycase DJ-1 0 ; 106.36 0.0042112 3301500000 6242000 5551300 6508500 5087300 8058000 7684300 6940400 6383200 6539000 5677100 FALSE TRUE 6488438.98 6504692.592 6678116.857 6093552.756 6688304.038 5899737.782 6396393.313 6297643.645 6303662.667 6789419.05 0.955669245 0.958063207 0.983606522 0.89750724 0.985106971 0.868960619 0.942112022 0.927567381 0.92845391 1 22.6948567 3.757097574 24.94593227 0.932126094 0.965008011 0.120661237 0.036355903 1485.654458 1999297.149 0.008526766 0.01533961 5716.070467 -3.757097574 0.032881917 VTTVTEIGKDVIGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTTVTEIGKDVIGLR 15 1 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITI7 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 203.04 5.11E-09 385520000 387140 304600 411250 301250 513820 437270 380630 339330 407970 297780 FALSE TRUE 402424.5861 356912.6805 421967.5128 360836.3509 426481.0599 335720.6694 350795.226 334781.8364 393287.2394 356124.2897 1.130011622 1.002213808 1.184888324 1.013231507 1.197562403 0.942706463 0.985035944 0.940070212 1.104353875 1 18.44202131 2.7199251 24.89616747 0.985790495 1.099114266 0.36386814 0.07278445 794.3595287 1061225.514 0.021905669 0.020686388 524.7169578 -2.7199251 0.113323771 VTVAGGVHISGLHTESAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 244.1 9.85E-25 2822070000 233891 1239390 1155710 1637690 1024920 1973720 1026210 1495030 990990 1632840 FALSE TRUE 243125.1973 1452245.591 1185828.752 1961620.194 850704.4645 1515353.442 945772.9787 1474991.568 955324.4635 1952763.735 0.12450313 0.743687301 0.607256644 1.004535346 0.435641265 0.776004498 0.48432535 0.755335395 0.489216614 1 20.89708598 -2.690847275 1.995063028 9.99996088 0.623429664 0.209432427 0.22851666 6748897.312 202551.9793 276308780.2 0.052558007 0.002037759 2.690847275 -9.376531216 VTVAGLAGKDPVQCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTVAGLAGKDPVQCSR 16 1 Q99497;K7ELW0 Q99497 PARK7 Protein deglycase DJ-1 0 ; 185.99 1.43E-09 4271700000 1137960 1131940 1147760 1022230 1547950 1565950 1454800 1447200 1419320 1127810 FALSE TRUE 1182887.539 1326341.89 1177671.568 1224424.043 1284830.012 1202281.845 1340768.975 1427802.651 1368238.95 1348782.776 0.87700374 0.98336212 0.873136571 0.907799287 0.95258483 0.891382857 0.994058493 1.058586065 1.014424987 1 20.36322659 2.084075443 4.642070632 1.030032212 0.917292226 0.681131865 0.034663394 0.10889809 4.250079911 0.012862239 0.009196191 121.359965 -2.084075443 -0.112739986 VTVLFAGQHISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 94.728 0.0064465 833960000 690320 1552850 1450810 1492180 2028040 2336600 1841600 1865500 1627100 1862890 FALSE TRUE 717574.3666 1819539.908 1488619.3 1787328.75 1683314.485 1793960.062 1697250.58 1840496.024 1568540.989 2227887.628 0.322087325 0.816710809 0.668175217 0.802252648 0.755565256 0.80522915 0.761820551 0.826117081 0.704048521 1 21.08724504 4.741019734 24.98256246 0.784088344 0.322087161 0.736097317 0.084484918 102.3098913 1039320.477 0.017873782 0.121257809 55083.27251 -4.741019734 -0.462001182 VTYAEKLS(ph)PLTGQACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VTYAEKLSPLTGQACR 16 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 VTYAEKLS(0.982)PLT(0.018)GQACR 118.37 0.00016813 220910000 176710 131010 174450 149830 199500 244250 213980 176770 168710 135710 TRUE FALSE 183686.6472 153509.9484 178996.3103 179465.9268 165589.0613 187526.6391 197207.6885 174400.6873 162638.1601 162299.7762 1.131773879 0.945842021 1.102874659 1.105768172 1.020266726 1.155433751 1.215082936 1.074559013 1.002084931 1 17.30830148 VTYLVHNFEEGGGVAMGMYNQDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTYLVHNFEEGGGVAMGMYNQDK 23 0 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 ;; 308.79 4.08E-73 2225893000 1891926 1532391 1968147 1542186 2329066 2340838 2244997 1834062 2118361 1546579 FALSE TRUE 1966620.699 1795567.234 2019438.528 1847225.788 1933172.193 1797213.85 2069028.269 1809479.399 2042121.601 1849601.544 1.063267224 0.970785973 1.091823552 0.998715531 1.045183056 0.971676227 1.118634592 0.978307682 1.104087314 1 20.81878308 VTYMEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VTYMEEER 8 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 ;;; 147.04 0.0012649 1748230000 1493820 1551380 1539060 1611070 1803400 1815970 1724290 1608310 1641680 1443600 FALSE TRUE 1552797.167 1817817.447 1579169.168 1929734.837 1496858.712 1394238.489 1589135.644 1586753.235 1582596.257 1726445.781 0.899418438 1.052924724 0.914693752 1.117750038 0.867017504 0.807577339 0.920466581 0.91908663 0.916678806 1 20.7193736 3.172844646 24.9999998 0.899021429 0.994436666 0.264163531 0.074008083 70.81037518 26937.25281 0.020319291 0.024286207 1488.828403 -3.172844646 0.095415237 VTYS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VTYSPR 6 0 Q96K76-2;Q96K76-4;Q96K76;Q96K76-3 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 VTYS(1)PR;VTYS(1)PR;VTYS(1)PR 107.9 0.032388 1723940000 1910820 2167750 2069870 1942450 2449820 2737250 2190930 2103790 2035870 2279610 TRUE FALSE 1986260.649 2540044.2 2123812.513 2326660.812 2033400.471 2101565.171 2019199.182 2075592.136 1962599.436 2726255.934 0.728567199 0.931696899 0.779021693 0.853427143 0.745858247 0.770861292 0.740649165 0.761334294 0.719888185 1 21.37848957 5.047810611 15.93984286 0.798109947 0.326511057 0.056692957 0.087335551 10438813.6 91407071.86 0.019532927 149998460.1 111637.6307 -5.047810611 -0.47159889 VTYVVLDEADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VTYVVLDEADR 11 0 A0A0C4DG89;Q7L014 A0A0C4DG89 DDX46 Probable ATP-dependent RNA helicase DDX46 0 ; 139.15 9.92E-05 103117000 234753 238012 251893 241995 281310 325300 290840 264130 265840 249057 FALSE TRUE 244021.2297 278888.7095 258457.5385 289860.8887 233493.0267 249754.005 268043.2008 260589.7694 256272.4703 297854.9507 0.819261957 0.936323902 0.867729537 0.973161225 0.783915212 0.838508826 0.899911854 0.874888159 0.860393523 1 18.18425041 -1.910954986 4.516027537 1.049530859 0.874972485 0.349923833 0.05197759 0.027188482 0.00053609 0.052788194 0.011251661 0.012275665 1.910954986 -0.174558374 VVACTSAFLLWDPTKVPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVACTSAFLLWDPTKVPPR 19 1 P30043 P30043 BLVRB Flavin reductase (NADPH) 0 ; 192.96 5.76E-15 227390000 342220 334850 378330 326060 467220 444760 439990 390220 391400 337670 FALSE TRUE 355731.1099 392357.8827 388189.5906 390553.6948 387802.1113 341471.2304 405502.4341 384989.7392 377313.5905 403829.9714 0.880893284 0.971591785 0.961269886 0.967124093 0.960310375 0.845581692 1.004141502 0.953346127 0.934337759 1 18.62338846 -5 0.240215462 1.314526807 0.939610403 0.134778237 0.043938903 369.2833457 3.683172967 56.70669976 0.067053402 1.00E-05 5 -0.374916404 VVASGPGLEHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVASGPGLEHGK 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 ; 152.4 6.38E-05 868980000 342640 430120 430220 355160 509810 543920 462330 460970 424420 430400 FALSE TRUE 356167.6918 503989.7641 441431.8866 425409.588 423152.6783 417602.8232 426091.3665 454791.4511 409145.2071 514728.6395 0.69195235 0.979136822 0.857601176 0.826473515 0.822088856 0.811306757 0.827798055 0.883555754 0.794875544 1 18.97345253 -1.970774758 2.298211849 1.137232654 0.839765555 0.344942258 0.068531869 7179880.691 2926603.164 5241937.36 0.015260602 0.010696095 1.970774758 -0.297467099 VVDDEIYYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVDDEIYYFR 10 0 Q86U86-8;Q86U86;E7EVG2;Q86U86-5;Q86U86-7;Q86U86-3;Q86U86-2;Q86U86-4;Q86U86-9 Q86U86-8 PBRM1 Protein polybromo-1 0 ;;; 180.44 4.65E-06 224952000 185632 225870 215971 215578 255877 243893 221223 242928 226638 246616 FALSE TRUE 192960.8947 264661.4155 221599.3817 258218.685 212383.1189 187252.547 203882.9632 239671.9475 218481.3427 294935.6835 0.654247368 0.897352983 0.751348155 0.875508456 0.720099774 0.634892817 0.691279403 0.81262445 0.740776227 1 18.17004086 -1.80011099 4.586598034 1.029329204 0.757835314 0.444335189 0.082671684 0.02511421 0.001094505 0.081079832 0.018678706 0.015844882 1.80011099 -0.271493889 VVDLLAQDADIVCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVDLLAQDADIVCR 14 0 P30520 P30520 ADSS Adenylosuccinate synthetase isozyme 2 0 ; 118.37 0.00058055 87804000 60552 62275 58196 60621 69511 76328 63624 62917 59774 61452 FALSE TRUE 62942.63972 72970.24682 59712.63557 72611.65286 57695.54505 58601.97876 58636.98463 62073.70053 57622.74542 73492.34283 0.85645167 0.992895913 0.812501456 0.988016575 0.785055188 0.797388905 0.797865225 0.844628136 0.784064614 1 16.16530632 3.222360899 24.98958701 0.824216514 0.911071039 0.183805862 0.078225029 330.4972779 509821.9503 0.020561362 0.024644654 1668.633273 -3.222360899 0.086854525 VVDLMAHMASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 VVDLMAHMASK 11 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;; 181.31 6.28E-06 71730320000 26300020 25081920 27332410 27795350 35528030 35929280 37556000 31993770 29111500 25387120 FALSE TRUE 27338365.1 29389544.65 28044715.06 33293187.27 29488988.15 27585249.23 34612262.59 31564945.84 28063782.8 30361240.1 0.900436379 0.967995528 0.923701238 1.096568755 0.971270872 0.908567935 1.140014784 1.039646132 0.924329267 1 24.85572738 3.781636211 24.89039889 1.016545018 0.934439453 0.222647226 0.068604708 687.6173455 397324.1839 0.017876738 0.032227347 6048.340203 -3.781636211 -0.082105565 VVDLMAHMASKE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 22 VVDLMAHMASKE 12 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;;;;;;;;;;;;;; 184.34 2.24E-05 1.42683E+11 55849040 56848360 63168500 46474840 84446510 78407830 63233990 64001000 66235680 68283080 FALSE TRUE 58054003.22 66611623.61 64814723 55667424.64 70092322.39 60198799.76 58277544.63 63143171.28 63851870.82 81661842.17 0.710907343 0.815700722 0.793696557 0.681682205 0.858324041 0.737171709 0.713644746 0.773227368 0.781905834 1 26.28315878 0.539851012 2.117995738 0.999986545 0.761625822 0.668657349 0.05027562 2.276643031 9.806522984 0.04534694 0.012374052 3.466179202 -0.539851012 -0.238360723 VVDNS(ph)PPPALPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVDNSPPPALPPK 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 VVDNS(1)PPPALPPK;VVDNS(1)PPPALPPK 114.69 0.00030125 149440000 406930 319650 354940 308550 473570 488780 423470 365470 405910 304970 TRUE FALSE 422995.9106 374547.401 364190.028 369580.2691 393072.7406 375268.2525 390277.3149 360571.4724 391301.3784 364723.0325 1.159772959 1.026936518 0.998538605 1.013317603 1.077729415 1.028912953 1.070064899 0.988617225 1.072872683 1 18.47644178 4.739438563 24.75494608 1.030179665 1.159773004 0.60906784 0.031000583 41.20835977 1161709.287 0.007099596 0.042990182 54883.091 -4.739438563 0.129593339 VVDPFSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVDPFSKK 8 1 P61247;E9PFI5;H0Y8L7;H0Y9Y4;D6RI02 P61247 RPS3A 40S ribosomal protein S3a 0 ; 96.331 0.014458 1211190000 2253600 1482070 2028750 1364110 2665600 2280600 2274200 2104080 2378600 1646280 FALSE TRUE 2342573.868 1736603.994 2081620.892 1633926.887 2212502.264 1750965.213 2095942.261 2075878.249 2292994.651 1968837.046 1.189826183 0.88204557 1.0572845 0.829894424 1.123760988 0.889339835 1.064558525 1.054367731 1.164644202 1 20.90891228 2.035602221 24.99151366 1.074149562 0.990139059 0.098814739 0.111283451 355.7468112 249720.4751 0.038138272 0.028166904 108.5431 -2.035602221 -0.084010503 VVDRDSEEAEIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;;; 260.97 4.44E-24 4054100000 1528880 1753990 1829590 1738090 1994350 1898120 1920720 1832050 1778650 1801790 FALSE TRUE 1589241.363 2055224.138 1877270.618 2081879.014 1655351.099 1457310.396 1770168.948 1807494.366 1714636.734 2154816.253 0.737529876 0.953781621 0.87119754 0.966151527 0.768209863 0.676303789 0.821494151 0.838816008 0.795722945 1 21.03913342 5.021206744 15.46635003 0.843819872 0.511378055 0.112778428 0.094241017 8950148.897 164929493.4 0.022771323 70266110.67 105004.2178 -5.021206744 -0.332441817 VVDRDSEEAEIIRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVDRDSEEAEIIRK 14 2 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 ;; 196.8 1.37E-08 1136880000 853030 815920 818000 716860 1325840 1239060 940700 1025940 1097690 1052740 FALSE TRUE 886708.2831 956047.913 839317.752 858652.7684 1100474.19 951307.0931 866965.4759 1012188.952 1058184.351 1259004.247 0.704293322 0.759368299 0.666652042 0.68200943 0.874082985 0.755602767 0.688612034 0.803959919 0.840493075 1 20.26385172 -0.388367325 0.297735006 1.09861868 0.706480519 0.670160606 0.057137137 5.065568662 0.534419161 0.563370896 0.071195425 0.408914654 0.388367325 -0.39213816 VVDYSQFQES(ph)DDADEDYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 69 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.003)QFQES(0.997)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.002)QFQES(0.998)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDY(0.002)S(0.021)QFQES(0.976)DDADEDYGR;VVDY(0.002)S(0.131)QFQES(0.867)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.001)QFQES(0.999)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYS(0.005)QFQES(0.995)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR 386.09 7.78E-127 53691929000 5469207.2 5391975.7 5540652.4 5809781.7 5787070 6669216 6045951.8 5740275 5593220.2 5178498.6 TRUE FALSE 5685135.723 6318005.583 5685046.353 6958939.18 4803385.908 5120391.657 5572054.3 5663336.003 5391921.298 6193126.252 0.917975105 1.020164183 0.917960675 1.123655307 0.775599546 0.826786254 0.899715923 0.914455119 0.870629966 1 22.56223643 3.229216714 24.99995006 0.87836631 0.991242203 0.344271684 0.076773919 219.3801598 586958.7666 0.02136016 0.025856683 1695.183489 -3.229216714 0.112875892 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 332.46 3.11E-95 28288800000 4688050 4355740 5030310 3574570 6038480 6309760 4490500 4950970 5386830 4811990 TRUE FALSE 4873137.834 5103804.462 5161404.011 4281609.277 5012061.326 4844413.865 4138522.876 4884610.345 5192959.041 5754807.309 0.846794266 0.886876691 0.896885636 0.744005672 0.870934691 0.841802967 0.719141868 0.848787819 0.902368882 1 22.45633619 0.981855346 2.650268279 0.998885045 0.829745922 0.481338068 0.054536716 0.235751507 3.852279307 0.052596891 0.014085852 9.590811293 -0.981855346 -0.169139123 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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;VVDY(0.001)S(0.239)QFQES(0.76)DDADEDYGRDSGPPTKK;VVDY(0.001)S(0.01)QFQES(0.989)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK;VVDY(0.002)S(0.076)QFQES(0.921)DDADEDY(0.001)GRDSGPPTKK;VVDYSQFQES(1)DDADEDYGRDSGPPTKK 201.01 2.47E-25 32401282000 1916023 1400204 1772526 964232 2823314 2065663 1483333 1687813 2039001 1711481 TRUE FALSE 1991669.068 1640678.145 1818719.484 1154954.212 2343408.095 1585944.074 1367065.483 1665190.627 1965617.752 2046812.934 0.973058668 0.801576987 0.888561653 0.564269549 1.144905847 0.774835867 0.667899573 0.813552914 0.960330922 1 20.96494782 1.17688066 4.974222505 0.9918889 0.821255541 0.140687796 0.149933766 0.372351476 17.23171955 0.133692594 0.034793133 15.02728972 -1.17688066 -0.170633359 VVDYSQFQESDDADEDYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 ; 296.25 2.45E-49 187455000 71786 79741 70144 72741 65533 90701 73540 69841 68335 58164 FALSE TRUE 74620.16671 93435.89645 71972.01026 87128.95269 54393.72407 69637.06734 67775.74264 68904.89563 65875.6367 69560.12218 1.072743468 1.343239395 1.034673431 1.252570438 0.781967058 1.001106168 0.974347665 0.990580428 0.947031642 1 16.08597285 3.255180381 24.99976039 0.955644409 1.177685237 0.550782128 0.100161759 175.6660663 264238.5485 0.025791974 0.034826712 1799.618217 -3.255180381 0.222040828 VVEAVNS(ph)DS(ph)DSEFGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 VVEAVNS(1)DS(0.998)DS(0.003)EFGIPK;VVEAVNS(1)DS(0.998)DS(0.002)EFGIPK 112.3 0.00068365 50474000 79171 63604 76472 68560 101422 96191 88943 76510 81861 63526 TRUE FALSE 82296.73221 74527.49223 78464.92314 82120.96337 84182.32467 73852.09804 81971.41525 75484.5086 78914.8386 75972.70342 1.083240802 0.980977231 1.032804147 1.080927223 1.108060144 0.972087272 1.078958778 0.993574076 1.038726214 1 16.21319354 1.800305049 1.142378353 1.009613276 1.047368428 0.100069468 0.043992525 1.209044019 2.927572494 0.035987782 0.014671523 63.14006853 -1.800305049 0.037755151 VVEAVNS(ph)DSDSEFGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VVEAVNS(0.499)DS(0.499)DS(0.002)EFGIPK;VVEAVNS(0.904)DS(0.094)DS(0.003)EFGIPK;VVEAVNS(0.971)DS(0.029)DSEFGIPK 254.71 5.28E-22 91060000 155915 132528 152552 114668 184731 182831 176208 140187 155559 105391 TRUE FALSE 162070.6446 155288.6531 156527.6304 137348.9882 153330.4906 140371.2711 162396.3565 138308.0226 149960.462 126040.3486 1.285863189 1.23205509 1.241885096 1.089722376 1.216519093 1.11370107 1.288447377 1.097331324 1.189781396 1 16.94352612 -5 0.098787776 0.404712769 1.322393035 0.488108928 0.064991938 158.9310388 1.071769254 19.66780477 1.077659146 1.00E-05 5 0.917680266 VVEAVNSDS(ph)DSEFGIPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 VVEAVNS(0.034)DS(0.872)DS(0.093)EFGIPK 238.65 3.10E-20 24847000 41659 34289 34885 27931 49213 49648 44797 36256 40167 24743 TRUE FALSE 43303.72949 40177.86902 35794.13176 33455.66843 40847.79184 38118.00442 41285.69408 35770.04762 38721.39752 29590.91712 1.463412888 1.357777079 1.209632389 1.130606 1.380416554 1.288165699 1.39521509 1.208818486 1.308556858 1 14.85286679 -3.677666961 0.300386214 2.04E-09 1.31611167 0.485541502 0.094704424 101.5640373 1.971955154 63.09595371 0.097637252 0.000210055 3.677666961 1.316111668 VVEELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVEELTR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 ; 90.777 0.039293 234400000 265880 309040 296100 272810 348020 366360 314510 312490 297110 320060 FALSE TRUE 276377.1477 362115.216 303816.6092 326771.0037 288863.6847 281278.4422 289857.8844 308301.5827 286417.0691 382769.6291 0.722045655 0.946039572 0.793732277 0.853701493 0.754667201 0.734850471 0.757264585 0.805449438 0.748275326 1 18.54611684 5.040217391 16.44827064 0.80934737 0.321623465 0.094856611 0.084995068 14574317.75 159609366.8 0.019041622 215107829 109702.7187 -5.040217391 -0.487723905 VVEHNIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VVEHNIR 7 0 O00232-2;O00232 O00232-2 PSMD12 26S proteasome non-ATPase regulatory subunit 12 0 ;;;; 172.03 0.0009156 1181070000 1392960 1400930 1507110 1567570 1456690 1675770 1637930 1566140 1473270 1256720 FALSE TRUE 1447955.136 1641528.83 1546386.525 1877630.667 1209082.354 1286597.814 1509544.767 1545148.455 1420247.3 1502950.223 0.963408578 1.092204389 1.028900692 1.249296643 0.804472654 0.856048188 1.004387733 1.028076933 0.944972947 1 20.5193658 3.231656256 24.99999986 0.947577187 1.080181143 0.363041385 0.092913544 200.6232996 726436.4547 0.027937143 0.034076477 1704.73256 -3.231656256 0.132603956 VVEHPEFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVEHPEFLK 9 0 P06396-2;Q5T0I0 P06396-2 GSN Gelsolin 0 ; 113.62 0.0017705 651850000 936090 903140 939570 847200 1298780 1190120 1091430 970490 1003960 936340 FALSE TRUE 973047.556 1058247.27 964055.9661 1014773.631 1078013.84 913732.6664 1005880.865 957482.169 967827.6757 1119797.896 0.868949263 0.945034165 0.860919609 0.906211411 0.962686074 0.815979982 0.898270008 0.855049088 0.864287814 1 20.09480694 2.745722577 24.9968255 0.876988245 0.907975926 0.025641694 0.052968337 1519.343093 5302849.401 0.015095894 0.015730477 556.8299384 -2.745722577 0.030987681 VVELRPPS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 99.752 0.0031034 1495600000 360610 529960 458940 495110 488790 586160 440920 469000 457080 532730 TRUE FALSE 374847.1613 620976.5075 470900.3534 593041.2802 405705.6504 450033.2233 406359.5383 462713.8221 440629.7801 637108.2438 0.588357104 0.974679756 0.739121426 0.930832847 0.636792342 0.706368545 0.637818679 0.726271912 0.691608976 1 19.28117898 3.224306284 24.99736065 0.712516277 0.815198219 0.053564424 0.138085195 485.5048648 851412.5937 0.036299041 0.043577319 1676.124538 -3.224306284 0.102681942 VVES(ph)PDFSKDEDYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 1 VVES(0.782)PDFS(0.218)KDEDYLGK 185.23 1.03E-09 286400000 1057300 428020 633520 485390 869910 883180 1021200 644560 773220 305610 TRUE FALSE 1099043.02 501529.1055 650030.0516 581398.6933 722043.0089 678074.8297 941155.6756 635920.7275 745391.9632 365488.4282 3.007052852 1.3722161 1.778524302 1.590744462 1.975556415 1.85525663 2.575062855 1.739920277 2.039440665 1 18.4794662 VVESLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VVESLR 6 0 Q12905;B4DY09;X6R6Z1 Q12905 ILF2 Interleukin enhancer-binding factor 2 0 ;;;; 129.96 0.037149 873477000 695997 821742 745633 793636 761433 927632 787936 768464 720201 867188 FALSE TRUE 723475.499 962869.7962 765064.8085 950614.832 632004.8906 712203.5264 726175.5174 758163.997 694281.1067 1037096.885 0.697596829 0.928428009 0.737698492 0.916611404 0.609398119 0.686728055 0.700200268 0.731044522 0.669446719 1 19.98411925 VVESPDFSKDEDYLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ; 219.95 1.09E-14 323650000 608260 295547 441610 313450 572340 555310 633310 469760 490290 219429 FALSE TRUE 632274.5745 346304.8982 453118.7194 375449.4744 475053.8512 426347.6683 583669.5074 463463.6356 472644.5587 262421.9113 2.40938179 1.319649325 1.726680204 1.430709321 1.810267477 1.6246649 2.224164531 1.766101135 1.801086488 1 18.00152866 VVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCR 46 2 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 39.12 0.06031 101870000 39386 27754 29264 20433 43612 53682 28160 33102 45858 38367 FALSE TRUE 40940.98969 32520.5336 30026.64388 24474.58641 36198.84782 41215.16906 25952.74562 32658.32183 44207.57954 45884.27907 0.892266164 0.708751107 0.654399382 0.533398081 0.788916129 0.898241618 0.565613019 0.711754058 0.963458083 1 15.48571232 1.222299302 6.103614065 0.988492805 0.710803915 0.457969181 0.114130113 0.141185042 18.16146962 0.099619747 0.028169161 16.68396623 -1.222299302 -0.277688891 VVEVLAGHGHLYSR ddPTM_MDA-MB-175_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 ;;;;;;; 222.29 2.28E-12 17598569200 2309583.8 3061650.6 2979710 3619014.4 3524470.5 3837395.2 3049465.9 3059929.2 2925906.8 3303115.3 FALSE TRUE 2400767.952 3587465.274 3057363.69 4334844.647 2925382.263 2946218.321 2810440.794 3018915.854 2820603.986 3950297.501 0.607743582 0.908150658 0.773957832 1.097346376 0.740547329 0.745821883 0.711450414 0.764224936 0.714023181 1 21.91352988 VVFQEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 VVFQEFR 7 0 P35579;P35579-2 P35579 MYH9 Myosin-9 0 ;;;;;;; 189.31 0.0012958 2930844000 2349462 2846459 1936159 1956383 6590920 4126100 2773805 2090308 2111306 7247470 FALSE TRUE 2442220.574 3335316.191 1986616.894 2343349.718 5470597.773 3167875.807 2556386.916 2062290.84 2035320.509 8667472.985 0.281768467 0.384808375 0.229203702 0.270361352 0.631164098 0.365490128 0.294940281 0.237934499 0.234822827 1 23.04718 -1.513741023 5.927556854 1.000884711 0.325270986 0.759522176 0.113841038 0.001389366 0.000113975 0.115059847 0.027088327 0.030637899 1.513741023 -0.675613725 VVGAMQLYSVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVGAMQLYSVDR 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 0 162.38 0.00014618 135500000 73233 65978 68550 70048 95499 86994 70376 58883 55863 88254 FALSE TRUE 76124.29539 77309.20826 70336.46931 83903.28533 79266.11409 66790.96191 64859.74523 58093.7697 53852.50154 105545.6816 0.721245003 0.732471543 0.666407837 0.794947591 0.751012385 0.632815677 0.614518228 0.550413516 0.510229322 1 16.68750803 -1.04194138 4.625206086 1.000012558 0.661045819 0.582985473 0.085278881 1.25E-05 2.58E-06 0.093267282 0.021982495 0.090794307 1.04194138 -0.338966739 VVGAMQLYSVDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVGAMQLYSVDRK 13 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 170.18 4.37E-05 1351390000 682750 657520 697540 606650 1139240 1043510 845820 808050 977760 891350 FALSE TRUE 709705.4972 770443.9452 715718.4654 726643.5593 945592.3917 801170.617 779522.4183 797219.4115 942570.6086 1065992.967 0.665769399 0.722747682 0.67141012 0.681658868 0.887053125 0.751572142 0.731264129 0.747865546 0.884218412 1 20.02376649 -5 0.114119598 1.865490375 0.602281987 0.689729095 0.059056811 96.91848795 0.728384082 19.27065768 0.685966583 1.00E-05 5 -1.263208387 VVGSELVDTYTVYIIQVTDGSHEWTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVGSELVDTYTVYIIQVTDGSHEWTVK 27 0 Q9Y2I1;C9J715;Q9Y2I1-4;Q9Y2I1-3 Q9Y2I1 NISCH Nischarin 0 246.77 1.58E-45 81979000 137650 129690 159050 117890 179430 179190 187640 154600 179890 107100 FALSE TRUE 143084.5283 151963.2487 163194.9737 141208.2901 148930.5527 137575.8382 172932.2865 152527.8399 173415.794 128084.1944 1.117113075 1.186432481 1.274122653 1.1024646 1.162755118 1.074104723 1.350145404 1.190840451 1.353920324 1 16.96673293 2.251136949 24.99959708 1.238349482 1.158034242 0.090471698 0.105372923 468.9370011 932166.0412 0.034181186 0.028416713 178.2940904 -2.251136949 -0.08031524 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVGYAFDQVDDHLQTPYHETVYSLLDTLSPAYR 33 0 Q9P0R6 Q9P0R6 GSKIP GSK3-beta interaction protein 0 196.45 4.30E-27 180240000 35616 67480 60220 67426 76613 90694 58451 71716 69847 73413 FALSE TRUE 37022.14718 79069.16508 61789.38267 80762.66155 63590.34963 69631.69298 53869.45789 70754.76432 67333.22011 87796.87177 0.421679571 0.900592054 0.703776586 0.919880856 0.724289469 0.793099931 0.613569217 0.805891633 0.766920492 1 16.42188192 -5 0.279444487 2.838052101 0.730982511 0.259056535 0.135082128 312.513349 2.995475997 333.0731742 0.142689788 1.00E-05 5 -2.10706959 VVHIIQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVHIIQSR 8 0 O60885;O60885-2;O60885-3;Q58F21-5;Q58F21-4;Q58F21;Q58F21-3;Q58F21-2;Q15059 O60885;Q15059 BRD4;BRDT;BRD3 Bromodomain-containing protein 4;Bromodomain testis-specific protein;Bromodomain-containing protein 3 0 91.853 0.013281 0 150870 186310 177530 174210 246290 223740 193360 169260 171340 213320 FALSE TRUE 156826.4641 218307.2932 182156.5776 208668.218 204425.7138 171779.7758 178203.9379 166991.3466 165173.5069 255115.9697 0.614726174 0.855717866 0.714014798 0.817934754 0.801305046 0.673339956 0.698521297 0.654570338 0.647444796 1 17.96079369 -1.097997236 4.734546737 1.000014929 0.721645702 0.549398962 0.076128586 1.21E-05 2.31E-06 0.074628484 0.017589159 0.079799977 1.097997236 -0.278369226 VVHLLNDQHMGVVTAAVSLITCLCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVHLLNDQHMGVVTAAVSLITCLCK 25 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 0 104.53 0.0025346 169480000 70956 70415 56979 54335 80568 91294 67860 59655 67024 69134 FALSE TRUE 73757.39767 82508.2285 58463.91955 65082.30083 66873.08014 70092.35207 62540.95588 58855.4223 64611.81933 82679.48365 0.892088272 0.997928686 0.707115199 0.787163852 0.808823147 0.847759916 0.756426542 0.711850385 0.781473426 1 16.33524176 4.244110645 24.99985932 0.785328335 0.945008501 0.317498931 0.082767518 128.5354461 578965.0645 0.019074362 0.049239154 17543.27394 -4.244110645 0.159680166 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVKPKSPEPEATLTFPFLDK 20 2 Q9UPQ0-4;Q9UPQ0-5;Q9UPQ0-10;Q9UPQ0-2;E7EPK0;Q9UPQ0-9;Q9UPQ0-8;Q9UPQ0;E9PDJ9;Q9UPQ0-6;Q9UPQ0-3;G5EA03;H0Y8P3 Q9UPQ0-4 LIMCH1 LIM and calponin homology domains-containing protein 1 1 VVKPKS(1)PEPEATLTFPFLDK;VVKPKS(1)PEPEATLTFPFLDK 179.2 4.65E-17 608190000 1518960 347390 664290 374570 1156000 1045830 1006610 693150 880490 278960 TRUE FALSE 1578929.714 407051.5302 681601.9431 448658.828 959503.5329 802951.8322 927709.2779 683859.458 848801.3369 333616.871 4.732763391 1.220116743 2.043067969 1.344832552 2.876064181 2.406808234 2.780762481 2.049834758 2.544239847 1 18.34783272 -0.907018797 5.949296502 0.999999571 2.366169188 0.174404492 0.928818385 4.86E-06 8.93E-07 0.824983676 0.194450456 0.123874297 0.907018797 1.366169617 VVLAS(ph)ASPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVLASASPR 9 0 O95671;O95671-2 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 VVLAS(0.5)AS(0.5)PR 68.484 0.060776 268480000 97395 1224400 925060 1295800 613530 1345200 613630 1011400 781980 1422300 TRUE FALSE 101240.2298 1434681.175 949167.8235 1552105.372 509242.3897 1032797.687 565532.0772 997843.8373 753836.6926 1700972.453 0.05951903 0.843447625 0.558014812 0.912481192 0.29938309 0.607180725 0.332475741 0.586631392 0.443179836 1 20.69792835 -1.285186079 4.14951355 1.000507134 0.530909441 0.266249356 0.239962466 5868549646 1010944250 29279946.86 0.051392985 0.05185778 1.285186079 -0.469597694 VVLASAS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVLASASPR 9 0 O95671;O95671-2 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 VVLASAS(1)PR;VVLASAS(1)PR;VVLAS(0.053)AS(0.947)PR 149.95 9.06E-05 475600000 365810 1101620 871270 1206080 821080 1283020 692420 943670 723210 1207430 TRUE FALSE 380252.4613 1290814.666 893976.012 1444639.024 681513.1149 985058.0494 638146.3111 931021.6472 697181.8134 1444002.791 0.26333222 0.893914246 0.619095765 1.000440604 0.471961079 0.682171846 0.441928724 0.644750587 0.482811957 1 20.4616421 -1.145792138 4.791638856 1.000030394 0.623432616 0.240888495 0.206046754 6.17E-05 1.10E-05 0.184127269 0.043395716 0.071483838 1.145792138 -0.376597778 VVLDDKDYFLFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 ;;; 147.24 5.97E-05 3514331000 2748579 2018215 2157864 2210642 2526541 3091259 2557564 1885018 2123177 2129026 FALSE TRUE 2857095.021 2364827.727 2214099.709 2647900.389 2097080.463 2373360.946 2357095.451 1859752.417 2046764.275 2546167.882 1.122115726 0.928779184 0.869581195 1.039955145 0.823622228 0.93213058 0.925742355 0.730412331 0.803860692 1 21.27989612 8 0.508685341 0.855458013 8.890722754 0.349903763 0.089458856 119.1840634 1.234535176 0.046694916 1027.69074 100000000 -8 8.035264741 VVLEHEEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVLEHEEVR 9 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 ;; 200.05 2.37E-05 1562230000 967770 1142290 1109530 1118620 1384640 1512940 1307990 1197050 1164010 1180010 FALSE TRUE 1005978.307 1338469.422 1138445.263 1339879.697 1149279.387 1161582.614 1205466.326 1181005.503 1122117.507 1411210.367 0.712847872 0.948454924 0.806715491 0.949454262 0.814392676 0.823110885 0.854207391 0.836874169 0.795145454 1 20.42850163 -1.522426231 5.81663756 1.00026224 0.842756503 0.345692985 0.066599376 0.00020274 1.66E-05 0.057723536 0.013583083 0.030031275 1.522426231 -0.157505737 VVLGDGVQLPPGDYS(ph)TTPGGTLFS(ph)TTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.226)S(0.258)T(0.258)T(0.258)PGGT(0.072)LFS(0.303)T(0.303)T(0.303)PGGT(0.011)RIIY(0.008)DRK 106.69 1.07E-05 127400000 25846 23695 26329 15303 39319 30879 24905 22678 35050 37509 TRUE FALSE 26866.42004 27764.43193 27015.15537 18329.88773 32635.57042 23707.82023 22952.88102 22374.0385 33788.55735 44858.1704 0.598919211 0.618938126 0.602234891 0.40861871 0.727527898 0.528506179 0.51167671 0.498772872 0.75323084 1 15.45308316 0.978078697 3.901161372 0.999221331 0.559996317 0.741909294 0.080921818 0.09469104 4.118533299 0.076176024 0.019534488 9.507770655 -0.978078697 -0.439225014 VVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTRIIYDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDY(0.121)S(0.269)T(0.287)T(0.306)PGGT(0.099)LFS(0.31)T(0.292)T(0.275)PGGT(0.013)RIIY(0.028)DRK 61.871 0.02961 174290000 33889 25205 32142 17989 49166 35368 22453 34727 37696 36578 TRUE FALSE 35226.96389 29533.76268 32979.64692 21547.17051 40808.78088 27154.31801 20693.07519 34261.54137 36339.32832 43744.75877 0.805284219 0.675138314 0.753910819 0.492565764 0.932883893 0.620744491 0.473041246 0.783214774 0.830712738 1 15.41682255 1.069435826 2.084563039 0.992671098 0.682001095 0.358879168 0.131609883 0.310290344 2.722677723 0.119412719 0.033492956 11.73372285 -1.069435826 -0.310670003 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 VVLGDGVQLPPGDYS(0.011)T(0.055)T(0.929)PGGT(0.012)LFS(0.014)T(0.053)T(0.897)PGGT(0.028)R;VVLGDGVQLPPGDYS(0.001)T(0.052)T(0.927)PGGT(0.02)LFS(0.043)T(0.177)T(0.755)PGGT(0.024)R;VVLGDGVQLPPGDYS(0.007)T(0.035)T(0.948)PGGT(0.01)LFS(0.005)T(0.025)T(0.935)PGGT(0.035)R;VVLGDGVQLPPGDY(0.002)S(0.045)T(0.2)T(0.704)PGGT(0.048)LFS(0.047)T(0.036)T(0.75)PGGT(0.168)R 142.59 3.79E-08 508820000 464677 529116 525679 550688 567559 670719 545353 580426 519641 567100 TRUE FALSE 483022.8068 619987.557 539378.6266 659612.4428 471085.5239 514954.6771 502606.8068 572646.3389 500939.2219 678212.3872 0.712199918 0.914149562 0.795294567 0.972575045 0.69459882 0.759282323 0.741075829 0.844346623 0.738617034 1 19.37137761 -1.528150021 3.039037117 1.007274172 0.802077772 0.33665755 0.085247745 20698028.13 23567738.97 1240357.316 0.020816816 0.029638074 1.528150021 -0.205196401 VVLIGGKPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVLIGGKPDR 10 1 P61978;P61978-2;P61978-3;Q5T6W2 P61978;P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 ; 140.49 3.58E-05 11844200000 8182900 6711900 7876300 6620100 9094600 8980700 8659000 7927000 7400900 6038100 FALSE TRUE 8505967.211 7864616.614 8081562.848 7929536.021 7548703.141 6895068.529 7980284.954 7820751.531 7134543.055 7221150.089 1.177924168 1.089108593 1.119151762 1.098098769 1.045360233 0.954843542 1.105126587 1.083034065 0.988006476 1 22.7837972 7.999999999 0.325272265 1.027695611 2.444689848 0.509167314 0.045381127 55.48687959 0.793634429 0.043871985 47.02160937 99999999.8 -7.999999999 1.416994237 VVLLGEFLHPCEDDIVCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVLLGEFLHPCEDDIVCK 18 0 Q9NY12-2;Q9NY12 Q9NY12-2 GAR1 H/ACA ribonucleoprotein complex subunit 1 0 118.47 0.00013955 0 110840 94794 106960 93214 134510 135990 122180 113260 112970 99018 FALSE TRUE 115216.0488 111074.1321 109747.4655 111651.451 111646.0382 104408.3834 112603.2123 111741.935 108904.2318 118418.6813 0.972955006 0.937978121 0.926774933 0.942853355 0.942807647 0.881688449 0.950890612 0.943617458 0.919654151 1 16.85353717 -1.100585924 4.413731968 1.000004922 0.935420591 0.426373696 0.022454775 1.48E-06 3.02E-07 0.021083331 0.004968856 0.07932573 1.100585924 -0.064584332 VVLQELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 79.469 0.075704 66994000 72815 88324 66676 76952 144150 110440 81002 75554 63420 141640 FALSE TRUE 75689.79243 103492.9599 68413.63133 92172.87592 119647.4345 84791.98373 74652.85158 74541.32221 61137.52659 169391.6461 0.446833089 0.6109685 0.403878425 0.544140623 0.706336099 0.500567682 0.44071153 0.440053119 0.360924095 1 17.3700032 -1.3196811 4.382833649 1.000524667 0.496953636 0.706934023 0.097549998 0.000513936 7.98E-05 0.097063203 0.022854836 0.047898168 1.3196811 -0.50357103 VVNGAAASQPPS(ph)KR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 VVNGAAASQPPS(1)KR;VVNGAAASQPPS(1)KR;VVNGAAAS(0.028)QPPS(0.972)KR 181.86 9.73E-07 573650000 446059 310151 411356 303107 515801 524605 495136 376742 404574 343523 TRUE FALSE 463669.7538 363417.0216 422076.2753 363060.6599 428125.3303 402773.4392 456325.9465 371692.3897 390013.4608 410829.7547 1.128617751 0.884592748 1.027375136 0.883725328 1.042099131 0.980390136 1.110742202 0.904735807 0.949331095 1 18.64818115 1.631831757 24.99999994 0.945265236 1.000230449 0.089779082 0.079486345 1.939671343 2017.310233 0.034462544 0.019097465 42.83825351 -1.631831757 0.054965213 VVNGGVPWPS(ph)PCPSPSS(ph)RPPSR ddPTM_MDA-MB-175_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(0.998)PCPS(0.314)PS(0.314)S(0.334)RPPS(0.04)R 51.568 0.070392 121880000 50844 56638 64101 56229 58254 61663 44299 52969 48760 69516 TRUE FALSE 52851.36038 66365.13592 65771.52472 67350.92837 48352.00589 47342.70276 40826.72863 52259.03719 47005.13712 83136.32924 0.635719196 0.798268778 0.791128563 0.810126319 0.581598999 0.569458661 0.491081685 0.628594475 0.565398275 1 16.34319143 3.234214959 24.9841033 0.608452881 0.763937572 0.128858959 0.138592051 153.3380354 881572.7607 0.03666392 0.045284782 1714.805859 -3.234214959 0.155484691 VVNRCVY(ph)S(ph)T(ph)T(ph)KAAVIGLT(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVNRCVYSTTKAAVIGLTK 19 2 D6R9P2 D6R9P2 SLC9B2 5 VVNRCVY(1)S(1)T(1)T(1)KAAVIGLT(1)K 55.061 0.033261 479390000 663130 275410 476500 296770 690690 623680 643970 484330 548800 216270 TRUE FALSE 689310.8844 322709.5251 488917.9814 355470.2202 573286.7605 478839.772 593493.9487 477838.3486 529048.7952 258643.9658 2.665095559 1.24769787 1.890312732 1.374361158 2.216509319 1.851347162 2.294636749 1.84747534 2.045471247 1 17.98060801 3.213044094 24.99254533 1.939922988 1.762171566 0 0.485806777 942.9317137 923566.44 0.128984468 0.154217104 1633.217762 -3.213044094 -0.177751422 VVNSCHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VVNSCHR 7 0 P48643;B7ZAR1;E9PCA1;E7ENZ3;P48643-2 P48643 CCT5 T-complex protein 1 subunit epsilon 0 ;;;;; 117.16 0.0052935 644500000 124537 471545 360789 390313 539121 567839 352764 421166 334789 725384 FALSE TRUE 129453.8169 552529.1856 370191.4577 467515.7464 447481.405 435966.9979 325113.4359 415520.9587 322740.0093 867509.1065 0.149224735 0.636914566 0.426729189 0.538917393 0.515823294 0.502550342 0.374766597 0.478981668 0.372030687 1 19.72651938 -1.135722505 3.905025102 1.000213153 0.454676507 0.642521218 0.124187992 67697259.08 116901052.1 193327.3133 0.02699575 0.07316064 1.135722505 -0.545536646 VVNTDHGS(ph)PEQLQIPVTDSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVNTDHGSPEQLQIPVTDSGR 21 0 Q6IQ49-3;Q6IQ49-2;Q6IQ49 Q6IQ49-3 SDE2 Protein SDE2 homolog 1 VVNTDHGS(1)PEQLQIPVTDSGR;VVNT(0.002)DHGS(0.998)PEQLQIPVTDSGR;VVNT(0.041)DHGS(0.959)PEQLQIPVTDSGR;VVNT(0.008)DHGS(0.992)PEQLQIPVTDSGR 241.22 3.48E-30 2375530000 990410 1114130 1061980 1006560 1056300 1370680 1052850 1052610 1096960 1142000 TRUE FALSE 1029512.152 1305473.161 1089656.071 1205654.564 876750.5033 1052360.343 970324.8659 1038501.485 1057480.624 1365753.035 0.753805502 0.955863269 0.797842687 0.882776412 0.641953912 0.770534874 0.71046876 0.760387462 0.774283927 1 20.3812652 3.298390082 24.99997679 0.759546709 0.85175511 0.09576522 0.099345271 124.6004762 52063.48379 0.025038994 0.033902947 1987.879623 -3.298390082 0.092208401 VVPEDGS(ph)PEKR ddPTM_MDA-MB-175_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 161.48 2.78E-05 4233950000 5931890 3537680 4277940 3238110 5897630 6634220 5539560 4469340 4959250 3302190 TRUE FALSE 6166085.598 4145249.021 4389426.631 3878598.493 4895152.959 5093522.948 5105354.812 4409435.808 4780767.561 3949190.906 1.561354147 1.049645135 1.111474916 0.982124842 1.239533129 1.289763668 1.29275969 1.116541568 1.210568867 1 21.91312568 1.609453478 25 1.122658578 1.202210736 0.083389916 0.157797299 0.56166736 8583.722064 0.077345754 0.040020215 40.68679478 -1.609453478 0.079552158 VVPGQFDDADS(ph)SDSENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.631)S(0.369)DSENR 149.09 3.54E-07 75919000 74371 79458 72601 88628 83859 100700 95066 86613 75031 65331 TRUE FALSE 77307.22451 93104.2934 74493.0417 106158.3539 69604.67713 77313.95112 87614.47851 85452.09441 72330.64897 78131.35861 0.989451942 1.191637968 0.953433334 1.358716343 0.890867359 0.989538036 1.121374056 1.093697792 0.925756959 1 16.25361408 VVPGQFDDADS(ph)SDSENRDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.61)S(0.389)DSENRDLK;VVPGQFDDADS(0.553)S(0.447)DSENRDLK 211.5 1.61E-22 356830000 332740 228190 274310 194938 379290 377850 280460 285390 310620 268900 TRUE FALSE 345876.8321 267379.8574 281458.7439 233496.1546 314818.4213 290100.0639 258476.8124 281564.8139 299440.8469 321585.8066 1.075535129 0.831441724 0.875221288 0.726077301 0.978956206 0.90209225 0.803756904 0.875551122 0.931138255 1 18.29484421 0.98398648 3.241805404 0.999484129 0.876431458 0.135743224 0.08986656 0.416920711 11.0508834 0.081685007 0.021317583 9.637990194 -0.98398648 -0.123052671 VVPGQFDDADSS(ph)DSENRDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 VVPGQFDDADS(0.078)S(0.922)DSENRDLK 202.76 6.83E-22 113010000 93728 63591 90277 57383 120440 130780 102750 94509 90605 81690 TRUE FALSE 97428.45381 74512.25958 92629.69278 68733.18613 99967.65182 100408.327 94696.18651 93242.26144 87344.14375 97695.59145 0.997265612 0.76269828 0.948146087 0.703544399 1.023256529 1.027767226 0.969298462 0.954416264 0.894043861 1 16.57600584 3.196721426 24.99999066 0.9760956 0.853271085 0.339772012 0.085481905 158.0362599 94430.21443 0.023195123 0.027723704 1572.97357 -3.196721426 -0.122824515 VVPSFLPVDQGGS(ph)LVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVPSFLPVDQGGSLVGR 17 0 Q14126 Q14126 DSG2 Desmoglein-2 1 VVPSFLPVDQGGS(1)LVGR 62.377 0.065404 17470000 14344 22614 23265 25903 19284 29244 20227 21665 22720 27827 TRUE FALSE 14910.3122 26497.77859 23871.30501 31026.53609 16006.11257 22452.5242 18641.55489 21374.61611 21902.31164 33279.16787 0.44803741 0.796227198 0.717304745 0.932311054 0.480964928 0.674672044 0.560156881 0.642282169 0.658138801 1 15.02233174 -1.728481151 4.158203123 1.025224333 0.660491845 0.366032393 0.13546571 0.030824948 0.002012781 0.127632489 0.029639145 0.018686108 1.728481151 -0.364732488 VVPTTDHIDTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVPTTDHIDTEK 12 0 O75663;O75663-2 O75663 TIPRL TIP41-like protein 0 84.169 0.012388 318650000 606930 652080 741760 710460 903980 1073600 814620 772890 800640 739770 FALSE TRUE 630892.0651 764069.6675 761090.875 850986.8675 750321.8025 824272.6706 750767.9558 762530.6737 771825.1228 884713.7677 0.713103026 0.863634879 0.860267922 0.961878179 0.848095542 0.931682879 0.848599833 0.86189534 0.87240094 1 19.75485125 -4.999999998 0.017402299 2.059229378 1.48E-27 0.394648323 0.057453411 5201.016794 6.86003158 526.3900185 311.4428236 1.00E-05 4.999999998 -2.059229378 VVSETNDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;; 229.55 2.86E-07 1060670000 1778730 1232990 1514680 1253150 1955820 1931240 1880350 1521180 1723930 1197620 FALSE TRUE 1848955.634 1444746.441 1554153.805 1501019.33 1623370.415 1482738.778 1732963.254 1500791.07 1661886.096 1432270.709 1.290926095 1.008710457 1.085097807 1.047999739 1.133424292 1.035236404 1.209941139 1.04784037 1.160315634 1 20.44987277 4.752587378 24.5387227 1.085940249 1.290926276 0.484532031 0.064788501 1554.14253 2718790.787 0.014056942 0.289892898 56570.15616 -4.752587378 0.204986027 VVSHLIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVSHLIEK 8 0 Q9Y446;Q9Y446-2 Q9Y446 PKP3 Plakophilin-3 0 70.256 0.051802 432030000 821080 847280 884040 783300 1154800 1179300 1083000 960680 1022600 962600 FALSE TRUE 853496.8724 992793.7491 907078.8086 938234.4021 958507.5085 905425.4475 998111.6301 947803.656 985796.8258 1151203.04 0.741395603 0.86239674 0.7879399 0.815003409 0.832613775 0.786503698 0.867016152 0.823315804 0.856318817 1 20.13471088 -5 0.195098623 1.80914477 0.788779762 0.75556132 0.032523918 60.93675478 0.600039813 19.11350783 0.074460412 1.00E-05 5 -1.020365008 VVSHPTLPVTITAHEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVSHPTLPVTITAHEDR 17 0 Q13033-2;Q13033 Q13033-2 STRN3 Striatin-3 0 ; 270.26 9.59E-30 530470000 126120 179095 171309 182679 174080 200028 171630 171744 169703 229677 FALSE TRUE 131099.315 209853.1731 175773.4533 218812.361 144489.9438 153574.5285 158177.1921 169442.0526 163595.4222 274677.8107 0.477283966 0.763997545 0.639925929 0.796614624 0.526034278 0.55910788 0.575864471 0.616875648 0.595590236 1 18.06738084 -1.286601363 3.211403757 1.001935071 0.620709716 0.600491617 0.093717211 17332745.1 24192120.69 325804.5934 0.021847241 0.05168906 1.286601363 -0.381225355 VVSQSQPGS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 VVSQSQPGS(1)R 94.538 0.008429 100900000 118980 114600 110240 110790 93429 158780 111830 105830 103560 101990 TRUE FALSE 123677.4223 134281.6585 113112.945 132703.9313 77547.97195 121905.7513 103064.4724 104411.522 99832.89583 121972.9878 1.013973868 1.100913087 0.927360615 1.087978033 0.635779883 0.99944876 0.844977845 0.85602168 0.818483647 1 16.89620216 3.302573196 24.99999875 0.857768431 1.029925374 0.395082786 0.105107663 59.99713241 23430.97717 0.026769235 0.036245706 2007.11934 -3.302573196 0.172156942 VVSS(ph)TSEEEEAFTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVSSTSEEEEAFTEK 15 0 Q8N573-2;Q8N573-3;Q8N573-5;Q8N573-8;Q8N573 Q8N573-2 OXR1 Oxidation resistance protein 1 1 VVSS(0.928)T(0.036)S(0.036)EEEEAFTEK;VVSS(0.474)T(0.474)S(0.053)EEEEAFTEK;VVS(0.049)S(0.9)T(0.049)S(0.001)EEEEAFTEK 471.33 4.38E-199 777248000 1053400 794430 934410 807700 1288740 1288550 1243060 1106630 1113740 871930 TRUE FALSE 1094989.045 930867.1727 958761.4922 967460.6493 1069680.435 989303.7907 1145625.709 1091797.435 1073656.715 1042767.989 1.050079266 0.892688673 0.919438938 0.927781308 1.025808661 0.948728577 1.098639123 1.047018556 1.029621858 1 19.99198677 2.697325081 1.460219458 1.045859646 0.945560313 0.31750907 0.053206662 0.401040647 1.728721772 0.022237599 0.020537978 498.109794 -2.697325081 -0.100299333 VVSSIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VVSSIEQK 8 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;; 157.86 0.0014138 0 517020 401700 454614 401281 587650 642910 558160 497737 515610 423304 FALSE TRUE 537432.3488 470688.8502 466461.6143 480653.1841 487761.4629 493603.8959 514409.9607 491065.6496 497053.2968 506242.3142 1.06161088 0.929769869 0.921419647 0.949452803 0.963494061 0.975034844 1.016133868 0.970020948 0.981848579 1 18.94946857 2.579764939 3.799086178 0.988999464 0.959978879 0.089983669 0.037625362 0.551319125 14.35435938 0.01274582 0.011767457 379.9836749 -2.579764939 -0.029020585 GSDPS(ph)THQRPPSEMADFLSDAIPGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 GSDPSTHQRPPSEMADFLSDAIPGLK 26 1 Q8TC07-2;Q8TC07-3;Q8TC07;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 GS(0.07)DPS(0.308)T(0.308)HQRPPS(0.308)EMADFLS(0.005)DAIPGLK 53.266 0.064257 18298000 18877 27977 32433 31749 37730 42859 37753 37750 39199 33537 TRUE FALSE 19622.27854 32781.83212 33278.23062 38028.85744 31316.66808 32905.64678 34793.82121 37244.023 37788.23565 40107.93305 0.489236843 0.817340352 0.829716919 0.948162983 0.780809822 0.820427389 0.86750472 0.928594923 0.942163626 1 15.2916 5.057819818 1.505920115 0.887179712 1.02E-12 0.781887119 0.063320361 1.190763381 1.341532856 0.016917477 1.978696843 114240.4271 -5.057819818 -0.887179712 down VVTDTDETELAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 ; 210.08 1.11E-07 605280000 231960 275810 251980 238360 270460 303530 262630 266510 233120 280170 FALSE TRUE 241117.9599 323178.222 258546.8058 285506.8966 224487.3058 233039.7575 242044.3743 262937.8694 224730.0567 335063.9473 0.719617738 0.964526994 0.771634215 0.852096738 0.669983469 0.695508303 0.722382627 0.784739365 0.67070796 1 18.35407694 3.26369187 24.98920236 0.744131602 0.832842048 0.083655908 0.107294771 434.3673645 431909.1072 0.027294134 0.036941464 1835.23579 -3.26369187 0.088710447 VVTEKSPT(ph)DWALFTYEGNSNDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVTEKSPTDWALFTYEGNSNDIR 23 1 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;F8WBG8;F8WC20;F8WBB2;F8WFE1;Q9UJU6 Q9UJU6-2;Q9UJU6 DBNL Drebrin-like protein 1 VVT(0.064)EKS(0.37)PT(0.566)DWALFTYEGNSNDIR 188.41 3.46E-17 346590000 54869 29606 50035 38119 52766 51882 47582 46203 60998 42733 TRUE FALSE 57035.27049 34690.6002 51338.9532 45658.82443 43796.85417 39833.19178 43852.39851 45583.72436 58802.6939 51105.71318 1.116025331 0.678800824 1.004563874 0.893419181 0.856985481 0.779427373 0.858072332 0.891949677 1.150609007 1 15.64119696 1.296201454 8.132232016 1.074525148 0.876881598 0.299118179 0.116096207 0.243204457 30.29055301 0.071735957 0.025953801 19.77886898 -1.296201454 -0.19764355 VVTSTDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVTSTDVAK 9 0 Q5T5Q6;P51801-2;P51801 Q5T5Q6 CLCNKB Chloride channel protein ClC-Kb 0 87.323 0.029096 0 157520 124220 123910 116210 172900 172600 177420 135350 137710 110960 FALSE TRUE 163739.0112 145553.8187 127139.1964 139195.9911 143510.5198 132516.2658 163513.3568 133535.8546 132753.844 132700.4875 1.233899093 1.096859713 0.958091404 1.048948604 1.081461888 0.998611748 1.232198614 1.006295132 1.000402082 1 17.01781415 4.673255703 3.641544987 1.048150927 1.243307045 0.389486899 0.072334243 0.242674064 5.528401927 0.017137686 0.112510939 47125.47086 -4.673255703 0.195156118 VVTTS(ph)AR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 1 VVT(0.131)T(0.131)S(0.737)AR 64.207 0.078459 622540000 380380 449250 382620 353100 289920 467390 346330 393750 374900 462740 TRUE FALSE 395397.6961 526405.1928 392591.3915 422942.1261 240639.502 358845.7559 319183.7496 388472.4253 361407.4222 553405.0433 0.714481555 0.951211412 0.709410578 0.764254195 0.434834313 0.648432392 0.576763355 0.701967627 0.653061309 1 19.07797627 3.817167624 2.379587326 0.652040869 0.826779168 0.106713494 0.14809327 0.469056445 5.171297512 0.037944223 0.079894999 6563.985664 -3.817167624 0.174738299 VVTTSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VVTTSAR 7 0 F8VTQ9;F8VXU8;Q8IUR5 F8VTQ9 TMTC1 Transmembrane and TPR repeat-containing protein 1 0 ;;;;; 132.94 0.0077236 3593580000 1860990 1972640 1837800 1594420 2991580 2475900 2111810 1902620 1834590 2824710 FALSE TRUE 1934463.322 2311425.575 1885694.578 1909791.517 2483072.3 1900909.748 1946280.814 1877118.491 1768563.464 3378157.842 0.572638524 0.684226636 0.558202034 0.565335193 0.735037383 0.562706018 0.57613673 0.555663346 0.523528961 1 21.68780531 -1.254018856 4.277021434 1.00025971 0.593313756 0.795858846 0.06189765 9471576.97 2777085.936 23209.21816 0.014404181 0.055716156 1.254018856 -0.406945954 VVTVFSVADGYSENNVFYGHHAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVTVFSVADGYSENNVFYGHHAK 23 0 O75083;O75083-3 O75083 WDR1 WD repeat-containing protein 1 0 ; 199.12 1.54E-24 922814000 167135 529291 422936 458134 404935 565095 332029 453562 374936 636886 FALSE TRUE 173733.6189 620192.6119 433958.0596 548751.5378 336104.2933 433860.2503 306003.6994 447482.7433 361442.1266 761671.6178 0.228095172 0.814251966 0.569744296 0.720456854 0.441271915 0.569615882 0.401752792 0.587500877 0.474538001 1 19.53880961 -1.49132818 2.985866591 1.013742064 0.544677931 0.444434551 0.155857972 25037006.49 29818320.05 2854140.355 0.038120926 0.032260554 1.49132818 -0.469064132 VVVHPLVLLSVVDHFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVVHPLVLLSVVDHFNR 17 0 P51665;H3BNT7;H3BTM8;H3BQV2 P51665 PSMD7 26S proteasome non-ATPase regulatory subunit 7 0 ; 293.78 2.65E-46 1387790000 624820 835670 806420 731530 951140 1003220 819040 767940 738020 851500 FALSE TRUE 649488.3761 979189.8219 827435.9677 876224.4506 789465.5625 770237.3589 754841.5046 757647.0204 711458.8044 1018335.122 0.637794339 0.961559511 0.812537985 0.860448031 0.775251236 0.756369237 0.741250585 0.744005587 0.69864899 1 19.95778098 3.119091016 6.932159654 0.766274318 0.82772856 0 0.107574344 0.615627682 34.9495511 0.028804379 0.034556081 1315.500496 -3.119091016 0.061454242 VVVLMGSTSDLGHCEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VVVLMGSTSDLGHCEK 16 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 ; 215.48 1.61E-14 805020000 572990 638160 859800 771400 1039230 1131350 981980 909420 963170 710430 FALSE TRUE 595612.0876 747759.0158 882207.0943 923980.6176 862582.0558 868611.1083 905009.8417 897230.7124 928505.6998 849625.1565 0.701029252 0.880104609 1.038348603 1.087515607 1.015250136 1.022346268 1.0651872 1.056031246 1.092841582 1 19.69646696 4.532307799 2.050234861 1.051603353 0.671115022 0.934071651 0.029214575 0.102129508 0.642630767 0.007550831 0.061724843 34064.95337 -4.532307799 -0.380488331 VVVS(ph)PTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VVVSPTK 7 0 P19338;C9J1H7;C9JWL1;C9JYW2;C9JLB1 P19338 NCL Nucleolin 1 VVVS(0.989)PT(0.011)K;VVVS(0.991)PT(0.009)K;VVVS(1)PTK 139.98 0.0027853 1541800000 3638470 2330450 2896400 2363740 3872080 4574980 4012450 3171630 3302780 2246520 TRUE FALSE 3782119.605 2730686.659 2971882.563 2831280.717 3213905.225 3512510.229 3697943.684 3129119.488 3183913.593 2686682.582 1.407728487 1.016378592 1.10615321 1.053820327 1.196235553 1.307378197 1.376397684 1.164677774 1.185072481 1 21.35739445 3.011810392 24.26051197 1.229024161 1.132801818 0.027911416 0.135081401 372.1412158 764432.0957 0.037853752 0.045204754 1027.567576 -3.011810392 -0.096222344 VVVSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VVVSNR 6 0 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;; 127.1 0.040029 2012330000 1360358 1359006 1383935 1361520 1612870 1797760 1548260 1431504 1461844 1426690 FALSE TRUE 1414065.984 1592404.709 1420001.483 1630824.592 1338714.934 1380257.485 1426903.336 1412317.03 1409232.52 1706222.59 0.828769935 0.933292478 0.832248671 0.955809987 0.784607437 0.808955111 0.836293778 0.82774489 0.82593709 1 20.70237444 VVWVEESDKR ddPTM_MDA-MB-175_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 ;;;; 195.27 5.97E-07 2007060000 1265100 882391 1056000 885270 1570850 1405670 1287080 1081600 1196130 921370 FALSE TRUE 1315047.125 1033934.79 1083520.228 1060373.764 1303837.478 1079224.446 1186195.306 1067102.921 1153081.515 1101894.811 1.193441617 0.938324403 0.983324558 0.962318502 1.183268553 0.979426017 1.07650503 0.968425398 1.046453349 1 20.07155508 1.243953023 0.005478383 1.29E-07 2.038553867 0.029569672 0.085285026 20208.96585 95.50766186 17835.61085 17695.37976 17.53690796 -1.243953023 2.038553738 VVYAFS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 140.07 0.00068746 2435130000 5159100 2953360 3143990 2424980 5437500 5380590 4329480 3359440 3492250 2754150 TRUE FALSE 5362785.252 3460576.606 3225924.962 2904633.806 4513235.692 4131029.516 3990124.045 3314412.202 3366564.605 3293772.961 1.628158745 1.05064212 0.979401131 0.881856109 1.370232783 1.254193767 1.211414415 1.006266139 1.022099776 1 21.65130968 4.741317994 24.69892126 1.092552625 1.628158974 0.572266216 0.140459955 169.9964053 1522627.218 0.035718544 0.246226678 55121.115 -4.741317994 0.53560635 VWAEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWAEDLR 7 0 A0A590UJL7 A0A590UJL7 0 93.593 0.03448 540820000 874630 1099000 1081200 1016600 1192000 1284200 1161900 1038700 1062300 1078100 FALSE TRUE 909161.0678 1287744.701 1109376.96 1217680.446 989384.2658 985964.0122 1070827.242 1024777.925 1024068.031 1289333.054 0.705140588 0.998768082 0.860426991 0.944426611 0.767361283 0.764708552 0.830528031 0.794812421 0.79426183 1 20.29819355 3.231025057 24.99875248 0.811479459 0.88467728 0.053625798 0.09487846 347.5071375 1152832.648 0.025137398 0.03059904 1702.25672 -3.231025057 0.073197821 VWAHYEEQPVEEVMPVLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VWAHYEEQPVEEVMPVLEEK 20 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 199.12 1.49E-21 400410000 400757 280182 367876 319655 441666 447182 452042 366532 384223 259213 FALSE TRUE 416579.1958 328301.079 377463.1508 382881.8049 366591.7711 343330.7576 416609.7668 361619.2381 370394.8893 310000.8244 1.343800284 1.059032922 1.217619829 1.235099312 1.182550955 1.107515628 1.3438989 1.166510569 1.194819046 1 18.24191253 0.437203418 1.911519099 1.000019478 1.203836571 0.345134147 0.085097472 6.342743823 20.22716944 0.07495549 0.02075531 2.73655019 -0.437203418 0.203817093 VWDAVSGDELMTLAHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWDAVSGDELMTLAHK 16 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 157.37 7.32E-08 1566500000 955100 932490 1060970 853620 1297620 1229240 1206980 1047450 1184690 976650 FALSE TRUE 992808.0855 1092637.904 1088619.75 1022463.488 1077051.016 943767.6393 1112373.754 1033410.646 1142053.238 1168005.868 0.850002652 0.935472957 0.932032774 0.875392424 0.922128086 0.808016179 0.952370004 0.884764943 0.977780394 1 20.15561609 1.151812317 4.309648827 0.998687649 0.897015659 0.451268246 0.041549931 0.179930853 5.646876284 0.036620593 0.009507146 14.184444 -1.151812317 -0.10167199 VWDEANLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VWDEANLR 8 0 Q96GA7;F8VYZ3 Q96GA7 SDSL Serine dehydratase-like 0 ;; 171.38 0.00067396 420130000 621000 723270 675550 670590 864330 862030 703910 666530 682650 850380 FALSE TRUE 645517.5595 847485.9962 693155.388 803230.7005 717411.4953 661836.5967 648735.6949 657596.2556 658081.5598 1016995.679 0.634729894 0.833323104 0.681571615 0.789807387 0.705422363 0.650776213 0.637894249 0.646606735 0.647083929 1 19.95588212 -1.080742866 5.183504413 1.00000529 0.692108482 0.671384347 0.064662502 4.06E-06 7.21E-07 0.064346749 0.015166414 0.083034225 1.080742866 -0.307896808 VWDISGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWDISGLR 8 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3ITV3;A0A3B3ISK1;A0A3B3IU78 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ; 138.83 0.0031234 0 864530 1059080 1028620 1030680 1278120 1356980 1073660 1044700 981310 1058750 FALSE TRUE 898662.312 1240968.752 1055426.682 1234545.428 1060865.619 1041841.96 989503.7237 1030697.505 945992.8448 1266191.792 0.709736327 0.980079605 0.833544088 0.975006659 0.837839596 0.822815285 0.781480128 0.814013732 0.747116551 1 20.27206452 3.014373498 24.90123505 0.818209307 0.882598124 0.028493271 0.094773077 529.9905754 918170.1762 0.025204398 0.030113976 1033.649975 -3.014373498 0.064388817 VWDLFPEADKVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWDLFPEADKVR 12 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 ; 90.861 0.0078638 495550000 293927 306700 365830 273065 505940 464090 373520 360320 410140 323110 FALSE TRUE 305531.4649 359373.3392 375363.8303 327076.442 419940.4995 356312.1309 344242.5264 355490.4998 395379.1415 386417.2182 0.790677668 0.930013784 0.971395198 0.846433406 1.086754109 0.922091755 0.89085711 0.919965475 1.02319235 1 18.55979985 4.732411454 3.759124796 0.949280358 0.775160181 0.360597789 0.065597351 0.278831547 7.59782048 0.015255475 0.133792757 54002.20019 -4.732411454 -0.174120177 VWDLSDIDKDGHLDRDEFAVAMHLVYR ddPTM_MDA-MB-175_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 ; 187.51 3.09E-18 1059940000 672229 542375 688753 531587 783882 829393 760045 633031 690663 479556 FALSE TRUE 698769.12 635523.6872 706702.469 636733.322 650638.0176 636779.0453 700470.6869 624546.2549 665806.1735 573515.8165 1.218395552 1.10811885 1.232228386 1.110228007 1.134472666 1.110307732 1.221362457 1.088978258 1.160920334 1 19.12947375 -4.999999998 0.205877237 0.29249668 1.173496541 0.474007604 0.049564666 119.3537484 1.186848491 34.78433107 0.101670774 1.00E-05 4.999999998 0.880999861 VWDPDNPLTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWDPDNPLTDR 11 0 O94776;O94776-2 O94776 MTA2 Metastasis-associated protein MTA2 0 ; 183.03 1.29E-05 162521000 233830 254480 273840 265040 298990 296530 283730 282370 266310 254510 FALSE TRUE 243061.789 298184.9604 280976.4954 317464.1209 248167.7866 227665.4015 261490.5012 278585.292 256725.5551 304376.3616 0.79855672 0.979658732 0.923121933 1.042998606 0.815331996 0.747973332 0.859102526 0.915265859 0.843447743 1 18.2154968 4.789074442 21.33278647 0.896674879 0.798553716 0.114698059 0.085435199 15619.2521 6595083.944 0.021096887 12.32908803 61528.23288 -4.789074442 -0.098121162 VWDVGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWDVGTR 7 0 H3BQA8;H0YL19;H0YN81;Q9GZS3 H3BQA8 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 ; 104.45 0.042826 71495000 621240 688670 631050 650190 717350 770940 655940 661220 641950 666750 FALSE TRUE 645767.0349 806943.7154 647495.6814 778795.6414 595415.1032 591900.8687 604525.7088 652357.4274 618846.3449 797386.8968 0.809854084 1.011985171 0.812021973 0.976684774 0.74670791 0.742300721 0.758133487 0.818119071 0.776092945 1 19.60492037 3.230158876 24.99366627 0.793130046 0.903974658 0.199022716 0.091618953 236.2444066 702783.8175 0.024156037 0.029319555 1698.865025 -3.230158876 0.110844612 VWDVIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWDVIGR 7 0 J3KNF4;O14618;E9PP76 J3KNF4 CCS Copper chaperone for superoxide dismutase;Superoxide dismutase [Cu-Zn] 0 94.262 0.033338 308310000 273990 340450 314310 296740 327050 377410 304520 311530 273430 329320 FALSE TRUE 284807.3368 398919.6392 322501.1768 355434.2863 271458.1578 289762.2472 280650.9267 307354.4499 263589.3077 393843.9488 0.723147677 1.012887567 0.818855229 0.90247492 0.689253088 0.735728575 0.712594233 0.780396527 0.669273474 1 18.58726458 3.247602464 24.98944208 0.750788586 0.871702798 0.157277733 0.109927921 275.6704802 761880.8169 0.027789831 0.037096927 1768.489412 -3.247602464 0.120914213 VWEDRPS(ph)SAGSTPFPYNPLIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.627)S(0.373)AGSTPFPYNPLIMR;VWEDRPS(0.476)S(0.476)AGS(0.04)T(0.008)PFPYNPLIMR;VWEDRPS(0.58)S(0.418)AGS(0.001)TPFPYNPLIMR 178.95 3.54E-17 1076050000 349583 380760 366122 376611 412203 449598 348948 396091 420917 415665 TRUE FALSE 363384.8068 446152.5681 375663.4401 451103.5317 342136.8813 345185.6782 321596.544 390782.048 405768.2794 497106.5984 0.730999765 0.897498785 0.755699967 0.907458346 0.688256568 0.694389653 0.646936784 0.786113178 0.816260095 1 18.92319573 0.800028229 2.379196719 0.999747155 0.763108253 0.440167309 0.080139554 0.7779918 7.303456563 0.078881129 0.021265551 6.309983585 -0.800028229 -0.236638901 VWEDRPSS(ph)AGSTPFPYNPLIMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWEDRPSSAGSTPFPYNPLIMR 22 1 C9J0Q5;C9JE98;Q9Y618;Q9Y618-4;Q9Y618-5 C9J0Q5;Q9Y618 NCOR2 Nuclear receptor corepressor 2 1 VWEDRPS(0.2)S(0.8)AGS(0.001)TPFPYNPLIMR;VWEDRPS(0.018)S(0.98)AGS(0.001)TPFPYNPLIMR 206.96 5.24E-23 888520000 151748 200501 157962 168561 212093 204995 163065 174277 173734 201351 TRUE FALSE 157739.1282 234935.4871 162078.6195 201901.8627 176041.5076 157388.018 150283.5392 171941.1019 167481.3473 240801.8734 0.655057729 0.97563812 0.673078732 0.838456362 0.731063696 0.653599641 0.624096221 0.714035566 0.695515134 1 17.87748709 3.055526936 7.897093604 0.708402855 0.790695909 0.00911165 0.128085249 0.615253268 76.37605247 0.034160518 0.040840778 1136.388776 -3.055526936 0.082293053 VWGSPGGEGTGDLDEFDF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWGSPGGEGTGDLDEFDF 18 0 Q13438-4;Q13438;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;B4E321 Q13438-4 OS9 Protein OS-9 0 124.1 7.57E-05 10005000 17386 25585 18835 22172 23651 27032 18734 19302 17363 19833 FALSE TRUE 18072.4127 29979.02473 19325.85557 26557.55542 19630.81147 20754.22767 17265.58013 19043.28826 16738.10902 23718.89662 0.761941544 1.263929988 0.814787293 1.11967921 0.827644379 0.875008142 0.727925097 0.80287412 0.705686664 1 14.53374928 3.11880759 7.856048142 0.80685516 0.996707887 0.219076837 0.152722863 0.299446199 19.35664583 0.040349114 0.048334617 1314.642263 -3.11880759 0.189852727 VWLDPNETNEIANANSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWLDPNETNEIANANSR 17 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 258.91 8.15E-27 145180000 118920 133860 114720 115330 132020 144740 121520 126300 129290 125470 FALSE TRUE 123615.0534 156849.4137 117709.6974 138141.9298 109579.2876 111126.3286 111994.9449 124607.1551 124636.8782 150053.4442 0.823806838 1.045290327 0.78445182 0.920618187 0.730268393 0.740578326 0.746367039 0.830418493 0.830616577 1 17.19511691 3.255545276 24.99755603 0.798678246 0.896588851 0.131970271 0.096907901 392.8622019 578200.2688 0.025361753 0.034253334 1801.130896 -3.255545276 0.097910605 VWNWQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWNWQSR 7 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ITV3;A0A3B3ISK1 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 83.753 0.051295 247160000 384160 187470 221200 157680 470420 448910 312600 179260 205960 346470 FALSE TRUE 399326.9334 219666.5142 226964.6537 188868.6334 390458.1764 344657.4558 288097.5952 176857.3129 198547.5398 414354.1629 0.963733369 0.530141926 0.547755215 0.455814495 0.942329561 0.83179436 0.695293111 0.426826442 0.479173513 1 18.66050489 1.945010482 24.8177932 0.569000329 0.700743269 0 0.217081868 811.8077092 366381.9687 0.089226204 0.057588473 88.10701381 -1.945010482 0.13174294 VWPHKDYPLIPVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWPHKDYPLIPVGK 14 1 P04040 P04040 CAT Catalase 0 ; 94.728 0.0024334 562420000 1373230 1220550 1257250 1220670 1668810 1708270 1508710 1185610 1470430 1070580 FALSE TRUE 1427446.181 1430169.968 1290014.968 1462114.883 1385146.272 1311550.182 1390453.368 1169718.837 1417509.512 1280339.654 1.114896486 1.11702388 1.007556834 1.141974224 1.081858449 1.024376757 1.086003518 0.913600414 1.107135523 1 20.28809515 2.419037839 1.51913105 1.004629428 1.092056181 0.224066544 0.059359119 0.506652387 2.366057859 0.028742755 0.020654116 262.4447197 -2.419037839 0.087426753 VWQLGSSSPNFTLEGHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWQLGSSSPNFTLEGHEK 18 0 P35606;P35606-2 P35606 COPB2 Coatomer subunit beta 0 ; 222.6 5.61E-19 2643400000 1464700 1129240 1467250 1121370 2011340 1802970 1611630 1561980 1739320 1126180 FALSE TRUE 1522527.487 1323178.186 1505487.74 1343173.639 1669453.145 1384257.542 1485306.229 1541044.213 1676722.213 1346833.409 1.130449747 0.982436415 1.117798037 0.997282686 1.239539452 1.027786757 1.102813622 1.144198089 1.244936606 1 20.36113998 3.270737768 24.99998988 1.128196858 1.056009704 0.139217248 0.084654228 369.5951286 287153.9373 0.022040022 0.02983995 1865.253088 -3.270737768 -0.072187155 VWS(ph)PLVTEEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWSPLVTEEGK 11 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(0.969)PLVT(0.031)EEGK 95.183 0.008337 14901000 99588 62861 83902 66196 102120 122360 118080 86922 98145 55986 TRUE FALSE 103519.8111 73656.88776 86088.55505 79289.37122 84761.67888 93943.74438 108824.5811 85756.95277 94612.78062 66955.38478 1.546101355 1.100089082 1.285759993 1.184212016 1.265942674 1.403079748 1.625329784 1.280807407 1.413072017 1 16.03091247 2.748778639 21.546653 1.378159996 1.262020858 0.014547836 0.181375862 272.3934068 574390.2002 0.052361299 0.0547759 560.7620814 -2.748778639 -0.116139138 VWS(ph)PLVTEEGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 VWS(1)PLVTEEGKR 98.654 0.00072694 0 33058 25422 30680 26031 36113 38096 38662 32683 34697 24996 TRUE FALSE 34363.15537 29788.03074 31479.546 31179.85411 29974.52516 29248.78135 35631.57142 32244.93784 33448.26175 29893.48762 1.149519782 0.996472246 1.053056987 1.043031663 1.002710876 0.97843322 1.191950965 1.078660953 1.118914667 1 14.8675436 2.25535074 24.99994553 1.104372013 1.034770292 0.179488668 0.062188967 344.4148085 512821.3287 0.020388978 0.017014071 180.0324284 -2.25535074 -0.069601721 VWSEVNQAVLDYENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VWSEVNQAVLDYENR 15 0 Q9NWU2 Q9NWU2 GID8 Glucose-induced degradation protein 8 homolog 0 126.71 0.00019232 26135000 25701 33656 32369 32689 24551 37664 35137 35575 28305 30597 FALSE TRUE 26715.69533 39436.15619 33212.56273 39154.78663 20377.82979 28917.1068 32382.87013 35098.17531 27286.30858 36591.89634 0.730098683 1.077729228 0.907648033 1.070039833 0.556894609 0.790259858 0.884973816 0.959178912 0.745692662 1 15.15923656 VWYVSNIDGTHIAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VWYVSNIDGTHIAK 14 0 P06744;A0A2U3TZU2;P06744-2;A0A0J9YXP8;A0A2R8Y6C7;A0A0J9YYH3;K7EQ48;A0A0J9YX90;K7EPY4;K7ENA0 P06744 GPI Glucose-6-phosphate isomerase 0 ; 201.3 1.80E-08 6195600000 2766000 3205800 3776200 3334600 4342600 4452700 3923100 4174600 4184000 3261400 FALSE TRUE 2875203.816 3756371.212 3874610.874 3994173.927 3604446.403 3418627.906 3615597.171 4118646.315 4033418.657 3900408.887 0.737154462 0.963071135 0.993385818 1.024039798 0.924120139 0.876479366 0.926979011 1.055952449 1.034101494 1 21.89519394 4.737923432 4.612599841 0.978702179 0.72224183 0.652153991 0.052790774 0.128514866 7.31320053 0.014222813 0.106755548 54691.95306 -4.737923432 -0.256460349 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYAEADSQESADHLAHEVSLAVFQLAGGIGERPQPGF 37 1 O95394-4;O95394;A0A494C0G1;A0A087WT27;A0A494C1E2;A0A494C1Q4;H0Y8I3 O95394-4 PGM3 Phosphoacetylglucosamine mutase 0 ; 160.9 8.26E-18 587640000 376750 559260 553970 589950 584740 718100 533570 570210 526290 639870 FALSE TRUE 391624.3809 655308.5546 568406.9133 706640.3492 485346.1037 551332.1579 491747.3892 562567.2676 507348.9257 765240.2754 0.511766557 0.856343524 0.742782276 0.923422841 0.634240146 0.720469342 0.642605212 0.735151149 0.662992974 1 19.54555328 -1.669492045 6.922722964 1.001435669 0.721343497 0.376527165 0.109920923 0.002293589 0.000109502 0.100223279 0.023514089 0.021404641 1.669492045 -0.280092172 VYCGHEYTINNLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYCGHEYTINNLK 13 0 H3BPK3;Q16775-2;Q16775;H3BPQ4 H3BPK3 HAGH "Hydroxyacylglutathione hydrolase, mitochondrial" 0 193.23 2.04E-06 517740000 304970 288900 290410 243900 382710 365410 290580 289260 321590 275170 FALSE TRUE 317010.4511 338516.3277 297978.3232 292142.692 317657.0909 280549.0653 267803.5803 285382.9428 310016.0387 329084.2931 0.963310792 1.028661455 0.905477197 0.887744259 0.965275759 0.852514299 0.813784146 0.867203172 0.942056626 1 18.32809764 4.160092379 6.337034809 0.892534989 0.995439903 0.29340393 0.054752699 0.201581604 12.70650357 0.01372861 0.030482398 14457.47263 -4.160092379 0.102904913 VYEDSGIPLPAES(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 VYEDSGIPLPAESPK 15 0 F8W038;F8W1H0;H0YIS7;Q8IXM2;Q8IXM2-3;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK;VYEDSGIPLPAES(1)PK 235.78 1.14E-17 519901000 3068170 900529 1243970 1023046 1743700 2037910 1919200 1402680 1488840 752947 TRUE FALSE 3189303.721 1055187.851 1276388.88 1225401.445 1447306.497 1564636.287 1768768.089 1383879.369 1435256.939 900472.5486 3.541811159 1.171815679 1.417465621 1.360842646 1.607274424 1.737572444 1.964266531 1.536836821 1.593893053 1 19.78032277 4.744851361 24.99907108 1.531810245 3.541812051 0.844936767 0.263373126 266.5376785 1059177.366 0.063101407 0.592142161 55571.40295 -4.744851361 2.010001806 VYEFLDKLDVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYEFLDKLDVVR 12 1 O43242;O43242-2;H0YGV8 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ; 164.68 5.17E-05 1213560000 1988980 1620600 1993640 1695930 2624800 2392180 2321500 2076600 2203320 1590930 FALSE TRUE 2067506.466 1898925.443 2045595.896 2031379.892 2178637.434 1836632.449 2139534.764 2048766.574 2124022.944 1902642.273 1.086650126 0.99804649 1.075134262 1.067662545 1.145058882 0.965306235 1.12450711 1.076800722 1.116354332 1 20.85957291 4.071338152 24.99999642 1.075679589 1.040908395 0.037322841 0.055458727 125.104071 43838.02867 0.012786691 0.027622409 11785.23242 -4.071338152 -0.034771194 VYEGERPLTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VYEGERPLTK 10 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 ;;;; 165.63 5.28E-06 9075590000 4759440 5040160 4934130 4969320 6183990 6478050 5340980 4966060 4812380 4518700 FALSE TRUE 4947346.366 5905768.273 5062717.481 5952236.664 5132837.589 4973621.063 4922340.032 4899498.089 4639183.384 5404052.749 0.915488171 1.092840604 0.936837169 1.101439409 0.949812636 0.920350206 0.910860841 0.906634024 0.858463749 1 22.36561033 3.010400491 24.93526168 0.914598273 1.013796634 0.320963431 0.063302086 210.9446195 505737.4469 0.016713297 0.019957674 1024.237071 -3.010400491 0.099198361 VYELPFLVALDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYELPFLVALDHR 13 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 0 76.262 0.029147 54089000 59002 54737 66487 70021 76215 82069 79477 76324 63956 54905 FALSE TRUE 61331.44452 64137.65396 68219.70584 83870.94481 63260.00152 63009.71852 73247.38507 75301.00162 61654.23605 65662.58353 0.934039467 0.976776278 1.03894337 1.277301932 0.963410182 0.959598528 1.115511774 1.146787068 0.93895538 1 16.00278389 4.255140066 3.672906923 1.069658952 0.947736426 0.135824617 0.098620739 0.377035536 10.71084159 0.025100223 0.072071503 17994.51168 -4.255140066 -0.121922527 VYGGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYGGDDR 7 0 H3BPK3;Q16775-2;Q16775;H3BPQ4;H3BQW8;Q16775-3 H3BPK3 HAGH "Hydroxyacylglutathione hydrolase, mitochondrial" 0 98.133 0.026723 201800000 391550 488150 454210 419150 479720 558390 469920 501110 465710 511910 FALSE TRUE 407008.6963 571985.9652 466047.0857 502056.619 398177.3658 428712.385 433086.4425 494393.4401 448949.1881 612208.9634 0.664819891 0.93429858 0.76125492 0.820073944 0.650394538 0.70027133 0.707416043 0.807556684 0.733326715 1 19.22366464 -1.735182509 4.085542333 1.020047693 0.757904084 0.45975252 0.080096387 0.014936882 0.000968182 0.0792009 0.017853066 0.018399986 1.735182509 -0.262143609 VYHAWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYHAWK 6 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ; 85.077 0.055124 582670000 719290 704780 706320 634730 1241960 1032460 921570 749930 783860 1066440 FALSE TRUE 747688.1246 825820.4826 724727.2794 760277.6995 1030852.083 792686.8121 849334.9353 739878.415 755649.0317 1275388.5 0.586243427 0.647505041 0.568240406 0.596114595 0.808265155 0.621525764 0.665942131 0.58012003 0.592485374 1 20.28250535 -1.190912225 4.150078774 1.000161926 0.630283056 0.736281591 0.066500933 9812370.678 2815781.924 14359.357 0.015660825 0.064429947 1.190912225 -0.36987887 VYISSPHS(ph)SPAHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYISSPHSSPAHNK 14 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 VYISSPHS(0.655)S(0.345)PAHNK 145.69 1.42E-05 93532000 84175 91991 86516 73159 107550 108390 91064 83992 96789 77025 TRUE FALSE 87498.294 107789.7387 88770.67803 87629.63184 89268.68942 83218.06517 83926.16573 82866.22462 93305.5828 92116.57402 0.949864831 1.170144893 0.96367759 0.95129061 0.969083907 0.903399481 0.911086486 0.899579967 1.012907653 1 16.49117314 4.025419549 24.93625679 0.940895546 1.061731589 0.328461964 0.061523044 195.1113463 191398.9602 0.014252991 0.030788362 10602.7751 -4.025419549 0.120836043 VYISSPHSS(ph)PAHNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYISSPHSSPAHNK 14 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 VYISSPHS(0.234)S(0.765)PAHNK 93.909 0.0020248 0 58650 80501 88751 70821 99674 111330 100780 99445 91483 77211 TRUE FALSE 60965.54729 94326.42054 91063.92397 84829.18242 82731.44908 85475.29472 92880.60026 98112.10243 88190.5447 92339.01716 0.660236043 1.021522899 0.986191177 0.918671056 0.895953321 0.925668232 1.00586516 1.062520541 0.955073461 1 16.49465276 4.743523266 24.99242077 0.976646485 0.660235912 0.788730352 0.048800805 266.5482693 1342320.852 0.013523056 0.113277758 55401.72234 -4.743523266 -0.316410573 VYLLYRPGHYDILYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYLLYRPGHYDILYK 15 1 J3KR44;Q96FW1;F5GYN4;F5H6Q1;F5H3F0;Q96FW1-2 J3KR44 OTUB1 Ubiquitin thioesterase OTUB1 0 ; 127.26 4.76E-05 1615700000 1561530 1613840 1735160 1427800 2322740 2275240 1908010 1644250 1742940 1868940 FALSE TRUE 1623180.41 1891004.466 1780379.695 1710214.578 1927921.484 1746849.992 1758455.191 1622211.518 1680211.93 2235123.01 0.726215248 0.846040445 0.796546627 0.765154567 0.862557218 0.781545348 0.786737545 0.725781763 0.751731302 1 21.0919228 -1.743751456 2.884881008 1.039609393 0.782592642 0.699480783 0.042773057 806722550.9 675496132.3 228147780.9 0.010545258 0.018040499 1.743751456 -0.257016751 VYMGHGGKPWVSDFSHPHYLAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYMGHGGKPWVSDFSHPHYLAGR 23 1 Q96KP4;Q96KP4-2 Q96KP4 CNDP2 Cytosolic non-specific dipeptidase 0 ; 209.01 3.07E-25 2636700000 784890 1482120 1589580 1530820 1618790 1865070 1503080 1595320 1731920 1797390 FALSE TRUE 815878.0633 1736662.581 1631005.761 1833611.627 1343628.654 1431935.758 1385264.662 1573937.345 1669588.538 2149554.157 0.379556877 0.807917574 0.758764675 0.853019507 0.625073181 0.666154771 0.644442782 0.73221572 0.776713874 1 21.03560603 0.783052794 1.560359635 0.999454188 0.6898579 0.383177039 0.12218176 0.793689817 3.37559264 0.111607436 0.032304539 6.068100903 -0.783052794 -0.309596289 VYNLLT(ph)PDSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYNLLTPDSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;E5RJ97;H0YC29 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 VYNLLT(1)PDSK;VYNLLT(0.981)PDS(0.019)K 114.87 0.014515 227750000 670390 554620 662960 547780 750390 838850 736090 652170 692370 589330 TRUE FALSE 696857.5149 649871.6707 680237.2822 656129.249 622838.9758 644039.8004 678393.3424 643428.7279 667451.7389 704797.9301 0.98873377 0.922068075 0.965152213 0.930946617 0.883712833 0.913793547 0.962535946 0.912926529 0.947011491 1 19.42685016 -0.526595727 6.367219936 0.999998783 0.933956572 0.297862317 0.029128269 0 0 0.027455154 0.006471242 0.297443356 0.526595727 -0.066042211 VYNVTQHAVGIVVNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYNVTQHAVGIVVNK 15 0 P46778;M0R181;G3V1B3 P46778 RPL21 60S ribosomal protein L21 0 166.9 1.34E-06 506690000 889160 868230 1076400 808400 1083900 1141400 1063700 981340 992610 916010 FALSE TRUE 924264.7234 1017341.749 1104451.868 968299.1072 899659.0652 876327.1481 980324.4145 968186.7424 956886.16 1095484.621 0.843703969 0.928668216 1.008185644 0.883900228 0.821242989 0.799944729 0.894877386 0.883797658 0.873482057 1 20.0631378 6.917138548 11.30060015 0.889662122 0.313840935 0 0.065530812 0 0 0.014735262 0 8263015.122 -6.917138548 -0.575821187 VYNWDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYNWDVK 7 0 P61758;P61758-2 P61758 VBP1 Prefoldin subunit 3 0 86.011 0.047436 163980000 338030 254040 310900 251280 392740 397310 346490 299670 306370 272250 FALSE TRUE 351375.6854 297669.3938 319002.3094 300982.434 325982.1951 305040.7738 319331.2084 295653.4138 295343.8035 325592.175 1.079189589 0.914240012 0.979760369 0.924415441 1.001197879 0.936879929 0.980770525 0.908048278 0.907097364 1 18.3127065 4.747824926 24.93053386 0.948257632 1.07918966 0.540315751 0.035630766 892.7455158 2402353.102 0.00806802 0.103400851 55953.19959 -4.747824926 0.130932028 VYNYNHLMPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYNYNHLMPTR 11 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ; 143.79 3.70E-05 2670100000 1274700 1724390 1343860 1185610 2560500 1954870 1523450 1481830 1391150 2719800 FALSE TRUE 1325026.14 2020540.569 1378882.096 1420120.119 2125267.125 1500881.069 1404038.008 1461968.493 1341082.783 3252692.736 0.407362837 0.621190113 0.423920182 0.4365983 0.653386993 0.461427251 0.431654055 0.449464063 0.412299252 1 21.63320311 -1.606200244 3.233062686 1.027749605 0.479432589 0.782035678 0.082751291 75302296.41 91350220.61 17851377.51 0.019260167 0.0247628 1.606200244 -0.548317016 VYQSLCPTSWVTDWDEQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYQSLCPTSWVTDWDEQR 18 0 P14854 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 0 216.54 2.07E-18 123760000 91150 127060 84152 126600 89041 117770 108200 97038 86508 90163 FALSE TRUE 94748.67238 148881.5666 86345.07025 151641.1021 73905.84262 90419.70232 99719.00127 95737.36433 83394.59398 107828.7136 0.878696121 1.38072283 0.800761387 1.406314674 0.685400393 0.838549393 0.924790791 0.887865218 0.773398766 1 16.71838188 3.220251354 24.99997549 0.853427867 1.112926527 0.311217897 0.193060612 276.1780779 377100.3584 0.050825368 0.060856593 1660.547693 -3.220251354 0.25949866 VYQWDDPDPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 153.24 3.86E-05 82969600000 21158300 23336100 22396300 25353300 24433100 27567200 21198300 21558200 21422100 23396100 FALSE TRUE 21993646.02 27343893.65 22979965.98 30368107.07 20279970.39 21165135.58 19536721.85 21269247.59 20651122.81 27980117.85 0.786045511 0.977261561 0.821296254 1.085345931 0.72479932 0.756434826 0.698235867 0.760155754 0.738064182 1 24.7378987 3.191884127 24.99999897 0.760783878 0.91488729 0.263847896 0.110124181 133.4228771 71461.0344 0.029099535 0.034780698 1555.550543 -3.191884127 0.154103412 VYRDDIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYRDDIGR 8 1 A0A087WY71;Q96CW1-2;Q96CW1;C9JJ47;C9JJD3;C9JGT8 A0A087WY71 AP2M1 AP-2 complex subunit mu 0 ; 141.52 0.00057656 800430000 322930 347260 340560 320260 403660 436480 377250 358250 325300 355410 FALSE TRUE 335679.5258 406899.2037 349435.2734 383606.4721 335046.0174 335114.1349 347680.1592 353448.2447 313592.5165 425045.7848 0.789749099 0.957306761 0.822112078 0.902506238 0.788258652 0.788418911 0.817982843 0.831553346 0.737785264 1 18.69725873 3.237146347 24.99930309 0.817557891 0.871031525 0.053605677 0.076802604 84.67224568 1496715.842 0.019911637 0.025043436 1726.419555 -3.237146347 0.053473634 VYSGHQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 VYSGHQGR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 ;;;;; 150.4 0.0004898 374161000 220091 363814 364690 338452 361540 405834 365534 370107 335109 332265 FALSE TRUE 228780.3626 426296.2244 374194.121 405396.7954 300085.5599 311585.204 336882.4899 365146.321 323048.4925 397365.9652 0.575742219 1.072805076 0.941686389 1.020210161 0.755186871 0.784126552 0.847788989 0.918916951 0.812974741 1 18.60010878 -1.439841636 2.869634928 1.003183142 0.870314021 0.084198071 0.13497333 24028666.06 27255858.79 620719.5145 0.03173583 0.036321047 1.439841636 -0.132869121 VYSLDDIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VYSLDDIRR 9 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ;; 171.56 9.12E-05 405050000 223392 318524 280261 261739 394220 376860 256430 299796 264264 472300 FALSE TRUE 232211.6887 373228.0192 287564.8319 313510.193 327210.6252 289339.9764 236330.3465 295777.725 254753.1903 564838.1423 0.411111912 0.660769858 0.509110151 0.555044303 0.579299804 0.5122529 0.418403661 0.52365041 0.451019808 1 19.10747799 -1.46054992 3.351653835 1.007511392 0.517088804 0.805516705 0.071707841 54498375.37 77532721.12 3882757.051 0.01658457 0.034629808 1.46054992 -0.490422588 VYSS(ph)SEFLAVQPTPTFAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 VYS(0.002)S(0.998)SEFLAVQPTPTFAER;VYS(0.059)S(0.941)SEFLAVQPTPTFAER;VY(0.001)S(0.184)S(0.776)S(0.038)EFLAVQPTPTFAER 310.15 1.76E-61 81458000 85724 97220 102540 93625 98864 116620 90193 87825 93935 103387 TRUE FALSE 89108.44971 113916.7787 105212.2766 112143.7456 82059.13259 89536.77239 83123.43698 86647.84953 90554.2977 123643.7032 0.720687325 0.921331016 0.850931135 0.906991158 0.663674174 0.724151494 0.672282007 0.700786593 0.73238099 1 16.91582924 3.241285897 24.9991903 0.725653034 0.855148864 0.164294771 0.103820706 91.07868431 835463.2192 0.026857964 0.03479341 1742.953885 -3.241285897 0.129495831 VYTDVNTHRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VYTDVNTHRPR 11 1 P68400;E7EU96;A0A2R8YD58;A0A2R8Y5A0;Q8NEV1;A0A2R8YFU2;A0A2R8YF43;A0A2R8YDP2;A0A2R8Y4H0;A0A2R8Y4D6;V9GYA2;A0A2R8YEW1;A0A2R8YDY7;A0A2R8YCK2;V9GY80;A0A2R8Y7T1;A0A2R8YF47;A0A2R8YEL7;A0A2R8Y797;A0A2R8Y3W6;A0A2R8YCC9 P68400 CSNK2A1;CSNK2A3 Casein kinase II subunit alpha;Casein kinase II subunit alpha 3 0 ;; 149.96 2.05E-05 1049680000 868700 1039940 1046310 1128030 1233420 1309750 1164970 1198540 1086850 1024180 FALSE TRUE 902996.9468 1218541.605 1073577.698 1351150.967 1023763.709 1005580.412 1073656.607 1182475.532 1047734.481 1224848.462 0.737231564 0.994850909 0.876498385 1.103116842 0.835828873 0.820983528 0.876562808 0.965405573 0.855399271 1 20.22417184 -1.490565809 3.010751537 1.002778126 0.90436861 0.087426498 0.097440693 29238513.28 35673785.22 683256.3548 0.022929921 0.032317235 1.490565809 -0.098409517 VYTDVQQVASSLTHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYTDVQQVASSLTHPR 16 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 218.78 1.30E-14 740280000 378940 792320 704870 801680 778580 864870 661910 779590 667820 809160 FALSE TRUE 393900.8438 928394.7966 723239.4913 960249.9112 646237.2497 664017.0497 610027.7646 769140.8712 643785.2887 967699.4097 0.407048759 0.959383448 0.747380317 0.992301847 0.667807837 0.686181104 0.630389725 0.794813827 0.665274033 1 19.88419946 -1.151953139 3.989998119 1.000091617 0.739928233 0.206314967 0.158553391 16989582.71 9810143.015 14718.47079 0.0345356 0.070476911 1.151953139 -0.260163383 VYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 VYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIK 34 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 0 56.435 0.013297 280230000 33793 35021 64007 61315 72748 78206 68018 62387 75970 54982 FALSE TRUE 35127.17373 41035.58432 65675.075 73442.92399 60382.32094 60043.84172 62686.57143 61550.80431 73235.85454 65754.67021 0.534215648 0.624071023 0.998789513 1.116923311 0.918297069 0.913149462 0.953340215 0.936067417 1.11377419 1 16.00480574 4.284633334 4.684640658 0.986442228 0.560354244 0.849587305 0.070016419 0.068845044 3.235329817 0.017897789 0.050464901 19258.9823 -4.284633334 -0.426087984 VYTVGPDYAHAEAR ddPTM_MDA-MB-175_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 0 147.35 3.67E-06 0 83877 105820 105600 97456 112320 119440 97075 97919 98668 116910 FALSE TRUE 87188.52873 123993.7618 108352.0228 116732.5059 93227.88652 91701.87013 89466.00784 96606.55597 95116.95795 139816.2761 0.623593555 0.886833531 0.77496001 0.834899263 0.666788511 0.65587407 0.63988264 0.690953576 0.680299609 1 17.09317279 -1.285714247 3.672558357 1.000669717 0.718578266 0.510358962 0.083112442 1494106849 2846063219 11602162.22 0.020951643 0.051794751 1.285714247 -0.282091451 VYVGNLGNNGNKTELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 VYVGNLGNNGNKTELER 17 1 P84103;P84103-2;A0A087X2D0 P84103 SRSF3 Serine/arginine-rich splicing factor 3 0 ;;;; 309.55 4.06E-58 4447860000 1213209 1095767 1301258 936283 1628121 1492640 1219428 1283310 1372530 1134349 FALSE TRUE 1261107.428 1283956.458 1335169.852 1121476.983 1351373.574 1145996.981 1123846.047 1266109.329 1323132.913 1356602.968 0.929606862 0.94644969 0.984200893 0.826680325 0.996145229 0.844754883 0.828426646 0.93329394 0.97532804 1 20.37156712 1.243981437 3.427880306 0.994469443 0.908477661 0.232252947 0.057246001 0.337294866 7.100382292 0.050293071 0.01449362 17.53805536 -1.243981437 -0.085991781 VYVGNLGTGAGKGELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYVGNLGTGAGKGELER 17 1 Q16629;Q16629-4;C9JAB2;A0A0B4J1Z1;Q16629-3;Q16629-2 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 0 ; 163.45 2.48E-09 1566200000 405780 554780 591960 383430 937670 840680 536400 670640 772450 843100 FALSE TRUE 421800.5077 650059.1494 607386.9639 459271.3096 778285.1883 645444.8106 494355.5664 661651.1677 744649.6754 1008289.303 0.41833282 0.644714912 0.602393541 0.455495569 0.771886785 0.640138509 0.490291393 0.656211631 0.738527795 1 19.94347821 -5 0.176427236 2.642852741 0.512629356 0.63328362 0.098386146 86.20813574 0.824788794 49.32352743 0.317256604 1.00E-05 5 -2.130223385 VYWNDGLDQYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 VYWNDGLDQYR 11 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 ; 175.65 2.23E-05 154628000 172839 186612 171289 179625 236190 247140 204525 163362 174573 258120 FALSE TRUE 179662.8172 218661.1594 175752.9321 215154.2889 196042.5082 189745.4804 188493.7961 161172.3996 168290.1518 308693.672 0.582010043 0.708343511 0.569344136 0.696983153 0.635071354 0.614672401 0.610617622 0.522111123 0.545168778 1 18.23581638 -1.534131331 4.93447479 1.001968534 0.608294032 0.809773252 0.056797007 0.001300184 0.000122752 0.058130653 0.013639884 0.029232682 1.534131331 -0.393674502 VYYS(ph)PPVAR ddPTM_MDA-MB-175_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 131.09 0.00035976 3064671000 1880010 2093890 2012020 1954400 2141100 2280980 1978980 2000190 1835160 2083630 TRUE FALSE 1954234.246 2453499.319 2064454.894 2340974.487 1777156.587 1751256.964 1823862.376 1973380.725 1769112.95 2491877.405 0.78424173 0.984598726 0.8284737 0.939442078 0.713179783 0.702786164 0.731922996 0.791925285 0.709951841 1 21.24880166 3.237247386 24.99996501 0.760444637 0.887381513 0.226048589 0.096730935 42.09549534 801380.1756 0.02519595 0.031730985 1726.821255 -3.237247386 0.126936876 VYYTAGYNS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK;VYYTAGYNS(1)PVK 205.26 1.09E-07 649640000 895890 615090 739160 604770 975460 943410 871270 779510 859360 638480 TRUE FALSE 931260.429 720726.9228 758423.1168 724391.7009 809651.6576 724317.325 802977.5808 769061.9435 828431.8015 763577.9316 1.219601026 0.94388129 0.993249131 0.948680771 1.060339258 0.948583367 1.051598727 1.007181994 1.084934186 1 19.54241588 -0.156810072 7.614717317 1.000000001 1.021228782 0.003792783 0.079602303 0 0 0.070250102 0.016558108 0.696931233 0.156810072 0.021228781 WAEALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WAEALR 6 0 P38606;P38606-2 P38606 ATP6V1A V-type proton ATPase catalytic subunit A 0 102.12 0.08331 103120000 131230 159670 112610 137500 257620 209930 136020 131350 131180 278630 FALSE TRUE 136411.0617 187092.0804 115544.7091 164697.0896 213829.8444 161176.939 125358.397 129589.4681 126458.8574 333222.2138 0.409369652 0.56146341 0.346749719 0.494256033 0.641703451 0.48369206 0.376200601 0.388898047 0.379503083 1 18.34612505 -1.753825145 2.935486739 1.103550748 0.453053301 0.773678497 0.088667137 21902797.91 20260237.14 16514743.73 0.022624987 0.017626856 1.753825145 -0.650497447 WAELLS(ph)PLDESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WAELLSPLDESR 12 0 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 WAELLS(1)PLDESR;WAELLS(1)PLDESR;WAELLS(1)PLDESR 119.39 0.0005488 137439000 108251 127583 150482 142085 158030 173579 169369 157043 153338 170256 TRUE FALSE 112524.8331 149494.3878 154403.6845 170188.9889 131168.117 133267.9079 156093.4152 154938.0955 147819.3953 203614.4035 0.552636902 0.734203402 0.758314156 0.835839636 0.644198617 0.654511202 0.766612836 0.760938779 0.725977106 1 17.63548009 -4.999999984 0.230712152 2.515526198 0.689224635 0.587805969 0.073195817 118.7841512 1.188419633 83.99595418 0.127393179 1.00E-05 4.999999984 -1.826301563 WAEYHADIYDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WAEYHADIYDK 11 0 Q9NRX4;Q9NRX4-2 Q9NRX4 PHPT1 14 kDa phosphohistidine phosphatase 0 ;;; 174.24 1.12E-05 1889970000 6266400 4842660 5278620 5325700 6760100 7011400 6949100 5638230 5852160 4403770 FALSE TRUE 6513802.311 5674349.184 5416185.174 6379107.564 5611020.617 5383108.609 6404411.384 5562658.749 5641541.905 5266604.416 1.236812526 1.077420808 1.028401745 1.211237272 1.065396254 1.022121311 1.216041851 1.056213512 1.071191504 1 22.32844167 -0.379068478 0.014288299 6.38E-07 2.096780038 0.216210871 0.074166216 3372.660899 12.08295924 943.2802426 830.570204 0.41776449 0.379068478 2.0967794 WAHDKFS(ph)GEEGEIEDDES(ph)GTENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.908)GT(0.092)ENR;WAHDKFS(1)GEEGEIEDDES(0.86)GT(0.14)ENR;WAHDKFS(1)GEEGEIEDDES(0.864)GT(0.136)ENR;WAHDKFS(1)GEEGEIEDDES(0.856)GT(0.144)ENR 154.43 2.27E-08 1585240000 1740930 1043926 1290430 1193880 1673710 1846360 2059350 1464670 1600510 769057 TRUE FALSE 1809663.261 1223212.17 1324059.666 1430025.901 1389213.372 1417570.872 1897932.766 1445038.494 1542907.958 919738.9947 1.96758349 1.329955756 1.439603707 1.554817083 1.51044305 1.541275166 2.063555831 1.57113975 1.67754979 1 19.81086498 WAHDKFS(ph)GEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 2 WAHDKFS(1)GEEGEIEDDES(0.978)GT(0.022)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.961)GT(0.039)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.867)GT(0.133)ENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDES(0.545)GT(0.453)ENREEKDNIQPT(0.001)T(0.001)E;WAHDKFS(1)GEEGEIEDDES(0.986)GT(0.014)ENREEKDNIQPTTE 193.49 1.55E-20 4331640000 2186790 900315 1415450 803121 2242810 1980880 1717700 1434667 1701542 791299 TRUE FALSE 2273126.158 1054937.098 1452337.79 961975.9367 1861577.957 1520850.641 1583062.186 1415437.636 1640303.836 946338.8887 2.402021289 1.114756152 1.534691015 1.01652373 1.967136699 1.607088812 1.672827995 1.495698478 1.73331547 1 19.85199739 -1.287578518 5.340617134 0.999908032 1.586690653 0.192780225 0.373849413 0.000374866 5.00E-05 0.331460635 0.078113878 0.051572892 1.287578518 0.586782622 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(0.726)GEEGEIEDDES(0.267)GT(0.008)ENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR;WAHDKFS(1)GEEGEIEDDESGTENR 262.76 4.62E-44 4375520000 3551220 2185343 2683900 2568340 3303280 3636040 4481140 2935130 3102430 1512443 TRUE FALSE 3691424.908 2560658.661 2753844.639 3076349.986 2741789.646 2791624.815 4129896.538 2895789.383 2990774.15 1808777.248 2.040839971 1.415684913 1.522489649 1.700789851 1.51582493 1.543376785 2.283253254 1.600965175 1.653478422 1 20.78658332 0.582387141 2.500904327 1.000063381 1.697674539 0.408655865 0.252342019 4.662580724 26.69616036 0.237914424 0.063479303 3.822848972 -0.582387141 0.697611158 WAHDKFS(ph)GEEGEIEDDESGTENREEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENREEK 26 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEK;WAHDKFS(1)GEEGEIEDDESGTENREEK 281.13 3.92E-61 239260000 291260 134301 191426 118303 245440 260810 288300 189467 229806 92964 TRUE FALSE 302759.1697 157366.152 196414.7188 141702.9803 203720.1965 200240.8301 265702.2927 186927.5048 221535.327 111178.5159 2.723180529 1.415436703 1.766660737 1.274553624 1.832370174 1.801074861 2.389870835 1.681327577 1.99260914 1 16.7625185 3.028140619 24.97603276 1.850811445 1.739282484 0 0.485327124 1491.893093 1324110.815 0.133269614 0.159285288 1066.941527 -3.028140619 -0.111528961 WAHDKFS(ph)GEEGEIEDDESGTENREEKDNIQPTTE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE;WAHDKFS(1)GEEGEIEDDESGTENREEKDNIQPTTE 263.97 5.41E-60 3434230000 2127113 983697 1607966 804805 2293511 2123414 1680852 1477828 1708852 859957 TRUE FALSE 2211093.064 1152639.308 1649870.915 963993.0269 1903660.819 1630283.279 1549102.428 1458020.133 1647350.75 1028449.109 2.149929485 1.120754831 1.604231945 0.937326911 1.851001476 1.585186145 1.506250931 1.417688167 1.601781494 1 19.97203898 -1.168657288 4.355997034 0.999878933 1.506237563 0.192787223 0.322220907 0.00034303 6.55E-05 0.282487399 0.066567101 0.067817646 1.168657288 0.506358631 WAHDKFSGEEGEIEDDES(ph)GTENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.942)GT(0.058)ENR;WAHDKFSGEEGEIEDDES(0.999)GT(0.001)ENR 190.28 9.48E-18 171830000 214085 173789 225285 181412 271460 251410 242412 222175 231662 165291 TRUE FALSE 222537.2411 203635.9089 231156.1122 217294.7521 225317.3262 193023.8377 223411.114 219197.1075 223324.5299 197676.6068 1.12576417 1.030146724 1.169365035 1.099243637 1.139827974 0.976462723 1.13018489 1.108867211 1.129746881 1 17.59278263 WAHDKFSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WAHDKFSGEEGEIEDDESGTENREEKDNIQPTTE 34 3 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 WAHDKFSGEEGEIEDDES(0.968)GT(0.032)ENREEKDNIQPTTE;WAHDKFSGEEGEIEDDES(0.955)GT(0.045)ENREEKDNIQPTTE;WAHDKFSGEEGEIEDDES(0.823)GT(0.177)ENREEKDNIQPTTE 225.58 1.30E-36 1493070000 1513241 878376 1280371 638647 1971917 1567866 1142677 1191063 1490634 952231 TRUE FALSE 1572984.923 1029230.245 1313738.52 764969.4704 1636731.253 1203752.883 1053110.991 1175098.749 1436986.374 1138802.433 1.381262349 0.90378297 1.153614079 0.671731503 1.437238985 1.057033993 0.924753022 1.031872355 1.261839922 1 20.11908605 2.121448486 0.007905886 1.71E-06 2.129657941 0.009079836 0.219877456 21112.0993 111.697276 14882.96641 15192.19385 132.266081 -2.121448486 2.12965623 WAHLDIAGVMTNKDEVPYLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WAHLDIAGVMTNKDEVPYLR 20 1 P28838-2;P28838 P28838-2 LAP3 Cytosol aminopeptidase 0 181.41 3.07E-17 15859000 40378 38909 45142 37168 58351 57083 48214 45180 50886 36050 FALSE TRUE 41972.15462 45591.31808 46318.4376 44519.71946 48432.51786 43826.33835 44434.8607 44574.436 49054.6228 43113.30728 0.973531312 1.057476704 1.074342019 1.032621301 1.123377465 1.016538538 1.030653028 1.033890435 1.137807 1 15.39584562 4.73931496 23.22561393 1.055814839 0.973531253 0.255679088 0.042359299 31.65121775 973968.926 0.009520555 0.05715145 54867.47318 -4.73931496 -0.082283586 WASLADSYS(ph)DPGLTEDGLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 WASLADS(0.004)YS(0.996)DPGLTEDGLGR;WASLADS(0.079)YS(0.921)DPGLTEDGLGR;WASLADS(0.121)Y(0.013)S(0.867)DPGLTEDGLGR 217.91 1.08E-24 199410000 379785 414222 403562 382389 459879 518272 388308 403503 404646 415879 TRUE FALSE 394779.2051 485361.4063 414079.1572 458024.4029 381708.9318 397911.1825 357871.4043 398094.7023 390082.8695 497362.5276 0.793745373 0.975870476 0.83254997 0.920906537 0.767466206 0.800042545 0.719538334 0.800411531 0.784302894 1 18.92393829 3.235030244 24.99989517 0.795257424 0.884116968 0.122328935 0.083182384 133.2568537 943642.4744 0.021688069 0.026926285 1718.028027 -3.235030244 0.088859544 WATHGEPSPVNSHPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WATHGEPSPVNSHPQR 16 0 Q06210-2;Q06210;A0A6I8PRN4;A0A6I8PTT9 Q06210-2 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 ;; 160.8 5.00E-09 678290000 208771 319793 298641 299477 342142 416300 281179 301537 304449 316370 FALSE TRUE 217013.4403 374714.9601 306423.8298 358712.6568 283984.8251 319620.6341 259139.4553 297495.3897 293491.94 378356.6442 0.573568467 0.990374996 0.809880927 0.948080765 0.750574437 0.844760199 0.684907902 0.78628298 0.775701826 1 18.52938725 WCDKSDEDDWSKPLPPSER ddPTM_MDA-MB-175_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 ; 184.8 1.36E-14 421010000 599510 278690 423830 275800 598240 535310 534410 440680 510280 249060 FALSE TRUE 623179.1177 326552.8396 434875.358 330352.4168 496551.3785 410992.3652 492521.5478 434773.4054 491915.1225 297858.5385 2.092198266 1.096335332 1.460006351 1.109091646 1.667071158 1.379824018 1.653541813 1.459664066 1.651505863 1 18.18426779 -1.42414079 6.465720018 0.999907841 1.487486581 0.230606495 0.27599022 0.000332444 2.96E-05 0.242253588 0.057089032 0.03765817 1.42414079 0.487578741 WCNEHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WCNEHLK 7 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4;Q14315-2;Q14315 Q60FE5;O75369-8;Q14315-2 FLNA;FLNB;FLNC Filamin-A;Filamin-B;Filamin-C 0 ;;; 73.616 0.048409 2085110000 1626570 1729440 1512900 1555400 3684550 2798010 2424930 1940120 1871720 2779920 FALSE TRUE 1690788.24 2026457.867 1552327.417 1863053.478 3058251.507 2148214.582 2234857.65 1914115.865 1804357.163 3324592.099 0.508570131 0.609535789 0.466922669 0.560385582 0.919887738 0.646158842 0.672220105 0.575744575 0.542730389 1 21.66474591 3.449866328 24.99986366 0.693514554 0.532660622 0.29256559 0.139746706 312.0412306 286222.1761 0.038088933 0.05157377 2817.515589 -3.449866328 -0.160853933 WDAWNELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDAWNELK 8 0 P07108;B8ZWD1;A0A0A0MTI5;P07108-3;P07108-2;P07108-4;P07108-5 P07108 DBI Acyl-CoA-binding protein 0 ; 158.61 0.00084673 1055130000 1318050 945660 1012030 1015520 1191570 1287510 1485790 1053450 986310 693740 FALSE TRUE 1370087.632 1108069.749 1038404.333 1216386.825 989027.357 988505.3149 1369329.897 1039330.226 950812.8958 829665.0705 1.651374368 1.335562733 1.251594613 1.466117917 1.192080265 1.191451045 1.650461067 1.252710597 1.146020159 1 19.66216952 -4.438700702 0.117763032 1.86E-13 1.53631476 0.371725581 0.161468351 160.1727842 1.402952754 39.36863384 1.7083869 3.64E-05 4.438700702 1.53631476 WDDPYYDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 WDDPYYDIAR 10 0 Q07960;H0YE29;E9PNR6 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ;;;;;;; 229.55 3.66E-09 4875890000 3924180 4465900 4390680 4232080 5332380 5568420 4659670 4386890 4236550 4337190 FALSE TRUE 4079109.657 5232883.585 4505104.728 5069172.793 4425983.952 4275238.845 4294432.89 4328090.915 4084077.393 5186979.34 0.786413323 1.008849899 0.868541097 0.977288025 0.853287369 0.824225154 0.827925582 0.834414527 0.787371055 1 22.30646319 3.03076938 23.07596768 0.8413623 0.914452856 0.097611807 0.077436777 142.619801 106957.9179 0.02037233 0.024349154 1073.419251 -3.03076938 0.073090556 WDEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WDEAFR 6 0 P27695;G3V3M6;G3V5Q1;H7C4A8 P27695 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 ;;;; 163.34 0.018421 641187000 834382 846089 917990 956120 1005240 1157810 1119110 934400 881020 774953 FALSE TRUE 867324.0456 991398.2041 941913.5735 1145237.682 834369.6639 888926.1743 1031391.234 921875.8964 849312.2623 926790.203 0.935836442 1.069711571 1.016318009 1.235703268 0.900278899 0.959144984 1.112863764 0.994697498 0.916401856 1 19.82188327 WDEMNILATYHPADKDYGLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDEMNILATYHPADKDYGLMK 21 1 P41236;E7EMN6;E7EUI7 P41236 PPP1R2 Protein phosphatase inhibitor 2 0 113.99 0.00011298 202760000 155800 114130 189710 118800 215970 205810 224890 177920 191510 121960 FALSE TRUE 161951.1043 133730.9397 194653.9984 142298.2854 179259.4965 158013.7466 207262.5342 175535.2734 184617.5925 145855.7269 1.110351357 0.916871367 1.334565344 0.975609861 1.229019253 1.083356478 1.421010601 1.203485644 1.265754841 1 17.15418251 3.199019971 24.9886456 1.219612239 1.0902592 0.123382648 0.145990135 277.7204843 175511.1689 0.039984803 0.047791587 1581.320753 -3.199019971 -0.129353039 WDEQTSNTKGDDDEES(ph)DEEAVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDEQTSNTKGDDDEESDEEAVKK 23 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 WDEQTSNTKGDDDEES(1)DEEAVKK;WDEQTSNTKGDDDEES(1)DEEAVKK 224.91 6.45E-33 253580000 720590 127500 276670 134709 407130 454630 433220 251450 305940 77600 TRUE FALSE 749039.4496 149397.1332 283880.2475 161354.0381 337926.188 349049.0725 399263.0844 248079.724 294929.2792 92804.23426 8.071177523 1.609809449 3.05891482 1.738649528 3.641279848 3.761133048 4.302207626 2.673150918 3.177972229 1 16.50190301 8 0.070552647 8.66E-15 11.02678984 0.217993497 1.657890693 500.840922 2.605407641 70.45040212 547.7636747 100000000 -8 11.02678984 WDET(ph)PGR ddPTM_MDA-MB-175_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 125.82 0.044852 3061090000 2829940 2914610 3030200 2890950 3498010 3690690 2799010 2775430 2566610 2816670 TRUE FALSE 2941668.216 3415171.595 3109169.501 3462771.281 2903419.51 2833583.18 2579616.282 2738229.901 2474238.207 3368542.558 0.873276251 1.013842496 0.923001401 1.027973143 0.861921576 0.841189663 0.76579596 0.812882679 0.734512973 1 21.6836931 3.052541734 5.046775723 0.8165849 0.960623918 0.375765375 0.077555282 0.174510273 9.564553788 0.021196543 0.025256422 1128.604387 -3.052541734 0.144039018 WDETPASQMGGST(ph)PVLTPGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDETPASQMGGSTPVLTPGK 20 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDETPASQMGGS(0.013)T(0.987)PVLTPGK 250.39 1.28E-29 168530000 318010 246670 306620 273120 348860 364410 371260 316010 327280 193540 TRUE FALSE 330565.2804 289033.6537 314610.7691 327142.3208 289560.9018 279781.3002 342159.6711 311774.4028 315501.2567 231460.4575 1.428171723 1.248738799 1.359241974 1.413383195 1.251016718 1.208765001 1.478264041 1.346987759 1.36308923 1 17.82040622 -1.307783506 3.310873553 0.998253281 1.34330518 0.615682648 0.081576421 32905756.55 49383883.27 577738.3314 0.019281629 0.049228488 1.307783506 0.345051899 WDETPGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDETPGR 7 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 ; 148.54 0.0048322 399000000 500250 550890 571570 594080 647660 731750 676290 575220 567860 549310 FALSE TRUE 520000.2563 645501.0722 586465.5837 711587.2508 537570.9845 561812.1523 623280.6226 567510.1168 547422.8295 656936.7773 0.791552969 0.982592381 0.892727587 1.083189852 0.818299421 0.855199726 0.948768046 0.863873262 0.833296062 1 19.32539501 WDGS(ph)EEDEDNSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 WDGSEEDEDNSK 12 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK 364.02 2.55E-86 5254460000 7836750 3992770 5564730 3896410 7952250 8029810 7290410 5525570 6113450 3151950 TRUE FALSE 8146150.941 4678497.188 5709751.435 4667108.268 6600529.385 6165008.32 6718968.614 5451508.772 5893428.129 3769514.255 2.161061185 1.241140601 1.514718091 1.238119278 1.751029162 1.635491446 1.782449451 1.446209884 1.563444977 1 21.8459472 0.234757458 1.224685224 0.999148572 1.581842853 0.322720709 0.257596771 6.230286047 8.824869002 0.241991552 0.069867514 1.71694925 -0.234757458 0.582694281 WDGS(ph)EEDEDNSKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDGSEEDEDNSKK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK 207.39 3.32E-08 1493600000 1789770 471370 876380 476660 1368590 1353520 1295170 816380 1072910 356970 TRUE FALSE 1860431.502 552324.1308 899219.1828 570941.9253 1135957.561 1039185.493 1193651.191 805437.7614 1034296.179 426911.4369 4.357886299 1.293767473 2.106336596 1.33737791 2.660874042 2.434194549 2.79601596 1.886662412 2.42274179 1 18.70357729 -0.845056005 8.616955634 1.000001996 2.295300045 0.19385551 0.824471353 0 0 0.733508421 0.172889593 0.142870971 0.845056005 1.295298049 WDGVPFILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDGVPFILR 9 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 136.16 0.00046688 2678600000 2042090 2265000 2056620 2462100 3481800 3138500 2491600 2267700 2448500 3094200 FALSE TRUE 2122713.29 2653996.131 2110217.207 2949096.031 2889964.88 2409630.939 2296301.881 2237305.191 2360378.963 3700449.248 0.573636645 0.717209169 0.570259735 0.796956216 0.780976764 0.651172541 0.620546784 0.604603669 0.637862812 1 21.819269 -1.102988818 3.572086828 1.000202578 0.661627133 0.642657151 0.07573064 68918345.17 120639804.1 172536.8789 0.018847989 0.078888043 1.102988818 -0.338575446 WDHSLAWDVPAAEDFPNGS(ph)GSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.481)GS(0.481)PS(0.036)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.324)GS(0.324)PS(0.324)AAIY(0.009)NIDT(0.009)S(0.007)S(0.002)ES(0.001)PDHY(0.001)LVDHT(0.001)LDGR;WDHS(0.096)LAWDVPAAEDFPNGS(0.758)GS(0.124)PS(0.022)AAIY(0.001)NIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.373)GS(0.373)PS(0.033)AAIY(0.062)NIDT(0.038)S(0.038)S(0.038)ES(0.038)PDHY(0.006)LVDHT(0.001)LDGR 103.89 5.66E-08 787729000 24527.9 38602.4 43961.5 46653.4 45479.4 50178.1 37681.8 41261.94 40503.9 45898 TRUE FALSE 25496.28043 45232.06192 45107.1728 55881.30327 37748.82783 38524.99673 34728.20205 40708.89119 39046.17255 54890.83433 0.46449067 0.824036699 0.821761472 1.018044341 0.687707307 0.701847534 0.632677613 0.741633675 0.711342304 1 15.74427765 -1.82124163 2.354184136 1.098330586 0.740753406 0.256597663 0.135492989 10040272.91 5904517.507 5592274.751 0.033662054 0.015092402 1.82124163 -0.35757718 WDHSLAWDVPAAEDFPNGSGS(ph)PSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_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(0.164)GS(0.708)PS(0.128)AAIYNIDTSSESPDHYLVDHTLDGR;WDHSLAWDVPAAEDFPNGS(0.001)GS(0.972)PS(0.027)AAIYNIDTSSESPDHYLVDHTLDGR 245.63 1.65E-61 4425400000 50955 89995 91556 102872 101554 122328 87038 84550 89922 91182 TRUE FALSE 52966.74275 105450.9412 93942.02457 123219.7746 84291.88735 93919.1759 80215.73413 83416.74555 86685.72479 109047.3671 0.485722344 0.967019599 0.861479072 1.129965609 0.772984159 0.861269542 0.735604502 0.764958823 0.794936431 1 16.73459541 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDT(ph)SSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR 48 0 P49327;A0A0U1RQF0 P49327 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 1 WDHSLAWDVPAAEDFPNGS(0.037)GS(0.037)PS(0.037)AAIY(0.177)NIDT(0.192)S(0.192)S(0.192)ES(0.043)PDHY(0.04)LVDHT(0.05)LDGR 74.949 0.00026117 519140000 6891 14540 15137 11506 13870 18166 13943 13151 10285 15843 TRUE FALSE 7163.062001 17037.13189 15531.48266 13781.85246 11512.38235 13947.22181 12850.11123 12974.73236 9914.844859 18947.13252 0.378055201 0.899193156 0.819727346 0.727384603 0.607605523 0.736112538 0.678208759 0.684786067 0.523289994 1 14.20969191 -1.868641403 3.842920738 1.098322174 0.685621974 0.327392432 0.139635786 0.082794774 0.002830088 0.095164349 0.029987866 0.013531894 1.868641403 -0.4127002 WDHSLAWDVPAAEDFPNGSGSPSAAIYNIDTSSESPDHYLVDHTLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 ;;;;; 383.49 1.93E-206 35807700000 715807 1597868 1598416 1862397 1760406 2112936 1441030 1641781 1482758 1753735 FALSE TRUE 744067.6131 1872289.399 1640072.034 2230773.568 1461172.817 1622238.636 1328078.303 1619775.611 1429393.829 2097345.796 0.354766302 0.892694663 0.781975026 1.063617441 0.696677114 0.773472185 0.633218569 0.772297832 0.681525112 1 21.00013331 4.746325323 24.73991438 0.796551414 0.354766054 0.516822215 0.131596366 680.8312289 2169206.002 0.030778967 0.329525243 55760.32843 -4.746325323 -0.441785359 WDKDDFES(ph)EEEDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WDKDDFESEEEDVK 14 1 Q7Z6E9;A0A2R8Y880;Q7Z6E9-2;Q7Z6E9-4 Q7Z6E9 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK;WDKDDFES(1)EEEDVK 190.83 3.38E-07 667590000 2904400 734710 1248110 805080 1856420 2092260 2280660 1336410 1511460 487790 TRUE FALSE 3019067.955 860890.7272 1280636.772 964322.4211 1540866.391 1606364.324 2101895.91 1318497.61 1457062.85 583363.1112 5.175280879 1.475737342 2.19526526 1.653039766 2.641350408 2.753626845 3.603066203 2.26016624 2.497694527 1 19.15403464 WDKDNLQILR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDKDNLQILR 10 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 ; 150.09 2.02E-05 809330000 1628880 1315460 1572010 1428060 1980720 1978020 2027160 1562840 1670330 1131800 FALSE TRUE 1693189.44 1541380.022 1612977.872 1710526.006 1644037.922 1518654.832 1868265.902 1541892.686 1610215.15 1353554.54 1.250920735 1.13876462 1.191660789 1.263728911 1.214607814 1.121975352 1.380266437 1.139143374 1.189619702 1 20.36832159 0.600576891 1.449059587 1.000399524 1.214097589 0.442832561 0.071551766 1.391129327 3.96332135 0.064134032 0.018727038 3.986363435 -0.600576891 0.213698064 WDLPDSDWDNDSSSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDLPDSDWDNDSSSAR 16 0 O15020;O15020-2;A4QPE4;E9PJZ2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 104.87 0.0030895 23384000 19321 22561 18339 22322 23846 28074 24677 20558 21059 20691 FALSE TRUE 20083.808 26435.67625 18816.92941 26737.22498 19792.66544 21554.23897 22742.75226 20282.45364 20301.0907 24745.0053 0.811630782 1.068323726 0.760433436 1.080509972 0.799865072 0.871054126 0.919084558 0.819658488 0.820411653 1 14.59484973 WDNGPDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDNGPDGR 8 0 Q14166;V9GY16 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 97.431 0.019163 281200000 421680 381550 390130 403460 619510 547630 495230 456220 413450 355070 FALSE TRUE 438328.252 447078.2445 400297.1083 483263.1838 514205.9115 420451.2319 456412.5786 450105.1171 398570.0153 424639.1683 1.032236978 1.052842691 0.942675896 1.138056072 1.210924356 0.990137659 1.074824493 1.059970796 0.938608694 1 18.69587792 1.252677082 23.57290218 0.969304394 1.063807423 0.216795722 0.070988589 157.6355194 263239.3164 0.049015794 0.017671796 17.89274951 -1.252677082 0.094503029 WDPTANEDPEWILVEKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDPTANEDPEWILVEKDR 18 1 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 ; 154.74 2.18E-08 349320000 262390 286100 307450 200741 443780 375360 219880 264640 304610 307610 FALSE TRUE 272749.3598 335235.4495 315462.3996 240446.9706 368346.4341 288188.3286 202645.2311 261092.9337 293647.1456 367880.29 0.741407918 0.911262328 0.85751373 0.653601123 1.001267108 0.783375289 0.550845578 0.70972254 0.798213858 1 18.48887686 2.474299586 24.99678111 0.722518503 0.835108817 0.018623854 0.137111602 178.2655249 1579196.971 0.045176607 0.037994996 298.0571787 -2.474299586 0.112590314 WDQTADQTPGAT(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK;WDQTADQTPGAT(1)PK 317.76 6.34E-55 1965310000 3233380 1412500 1693190 1400590 2285300 2379900 2205850 1754040 1780760 1012220 TRUE FALSE 3361036.339 1655085.887 1737315.922 1677622.522 1896845.522 1827204.293 2032949.713 1730529.963 1716670.795 1210545.129 2.77646513 1.367223615 1.435151719 1.385840545 1.566934992 1.509406175 1.679367142 1.429546013 1.418097314 1 20.20722543 4.740796924 24.86712616 1.451910328 2.776465626 0.851864498 0.169102763 62.35339531 693303.4459 0.037164995 0.248090209 55055.01997 -4.740796924 1.324555299 WDS(ph)CDSLNGLDPSEKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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;WDS(0.999)CDS(0.001)LNGLDPSEKEK 121.48 3.64E-05 621110000 806590 301990 447260 260466 660290 615270 564800 394370 480870 185942 TRUE FALSE 838434.796 353854.4333 458915.963 311985.3974 548054.1416 472382.867 520529.5002 389084.1152 463563.5826 222373.7748 3.770385229 1.591259732 2.063714408 1.402977476 2.464562838 2.124274175 2.340786366 1.749685256 2.084614442 1 17.76262713 7.999999993 0.055764721 5.46E-11 6.125953419 0.308771931 0.590468522 584.8255247 2.446147661 57.96718445 297.195657 99999998.3 -7.999999993 6.125953419 WDS(ph)YDNFSGHRDDGMEEVVGHTQGPLDGSLYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDSYDNFSGHRDDGMEEVVGHTQGPLDGSLYAK 33 1 E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;E7ERH1;E7EMG1 E9PGF5 TNS1 Tensin-1 1 WDS(0.814)Y(0.006)DNFS(0.18)GHRDDGMEEVVGHTQGPLDGSLYAK 118.31 1.08E-06 51320000 31390 31354 36887 30432 46857 47680 37889 43695 38665 31114 TRUE FALSE 32629.30144 36738.8056 37848.30552 36451.35877 38892.26388 36607.0426 34919.16118 43109.34 37273.4542 37210.19259 0.876891496 0.987331778 1.017148875 0.979606829 1.045204584 0.983790732 0.938430004 1.158535794 1.001700115 1 15.18341024 5.954569043 0.821612073 1.028628341 2.32E-18 0.345580551 0.055605056 16.98491796 1.876943216 0.019368103 25.08970573 900676.9394 -5.954569043 -1.028628341 WDS(ph)YENLSADGEVLHTQGPVDGSLY(ph)AK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 2 WDS(1)YENLSADGEVLHTQGPVDGS(0.001)LY(0.999)AK 234.62 9.98E-44 41663000 50548 37512 39912 32884 61072 63656 55542 45079 54544 25094 TRUE FALSE 52543.67407 43954.3942 40952.13951 39388.35705 50691.00325 48872.85872 51188.47291 44474.78974 52580.97209 30010.68885 1.75083199 1.464624635 1.364585122 1.312477606 1.689098291 1.628515059 1.705674707 1.481964975 1.752074815 1 14.87318881 -1.318503984 5.642125776 0.999919956 1.560340745 0.560084096 0.151808368 0.000154887 1.87E-05 0.14893217 0.035098673 0.048028167 1.318503984 0.560420789 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK;WDS(1)YENLSADGEVLHTQGPVDGSLYAK 339.59 7.99E-96 7169330000 3134561 2091386 2663874 2273007 3321416 3275189 3574110 2918543 2815555 1622725 TRUE FALSE 3258315.889 2450565.277 2733296.745 2722601 2756842.895 2514575.991 3293961.919 2879424.705 2714223.726 1940666.895 1.67896711 1.262743897 1.408431685 1.402920309 1.420564705 1.295727771 1.697335039 1.483729491 1.39860361 1 20.88812108 0.830623898 5.084125308 1.000004728 1.453072357 0.50940043 0.133489453 2.091401878 62.28993327 0.124687854 0.031499008 6.770549196 -0.830623898 0.453067629 WDSNVIETFDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WDSNVIETFDIAR 13 0 Q9Y365;F5H8H3;F5H0V7;F5H8G1;F5GY11;F5H1Z6;H0YGA9;H0YFF3;F5GWK5;H0YH17 Q9Y365 STARD10 PCTP-like protein 0 ; 171.26 1.49E-06 111660000 191362 196783 205272 219940 250430 243640 272780 211625 206808 185089 FALSE TRUE 198917.1195 230578.9495 210621.557 263443.4755 207861.9981 187058.3024 251398.7908 208788.513 199365.0205 221353.6458 0.898639455 1.041676764 0.951516096 1.190147443 0.939049354 0.845065378 1.13573368 0.943235031 0.900662918 1 17.75599361 WDYLTQVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WDYLTQVEK 9 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 123.63 0.0012853 316420000 208870 250230 228590 275230 280410 347460 247330 242860 219800 246790 FALSE TRUE 217116.3489 293205.056 234547.2432 329669.6725 232746.0084 266767.6808 227943.6283 239604.8589 211889.4409 295143.7754 0.735629097 0.993431271 0.79468809 1.116979926 0.788585184 0.903856707 0.77231386 0.811824199 0.717919396 1 18.17105839 2.574949951 1.940886503 0.811612069 0.902628513 0.036628992 0.124258517 0.800585134 6.030263354 0.046117563 0.040300829 375.7940946 -2.574949951 0.091016444 WEADTLDKEGLSES(ph)VR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WEADTLDKEGLSESVR 16 1 Q6PHR2-3;Q6PHR2;Q6PHR2-4 Q6PHR2-3 ULK3 Serine/threonine-protein kinase ULK3 1 WEADTLDKEGLS(0.002)ES(0.998)VR 133.84 1.91E-05 114390000 301500 217970 309050 206940 378020 339870 344730 307520 337760 215670 TRUE FALSE 313403.4528 255404.6519 317104.0969 247872.1143 313764.2954 260940.3433 317709.1618 303398.1974 325604.0836 257926.4072 1.215088661 0.990222966 1.229436335 0.961018753 1.216487675 1.011685256 1.231782217 1.176297536 1.26239142 1 17.97659996 2.217726686 24.99655236 1.183432017 1.103135625 0.065194238 0.111765044 517.6550265 621078.3259 0.037556327 0.027767892 165.0922498 -2.217726686 -0.080296392 WEAERDDWLHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WEAERDDWLHNR 12 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 121.28 0.00022776 81359000 43742 54061 46219 42894 51084 61004 45124 51527 47488 57907 FALSE TRUE 45468.96794 63345.55621 47423.50511 51378.30517 42400.75993 46836.74552 41587.06297 50836.36485 45778.91616 69252.76795 0.656565352 0.914700713 0.684788587 0.741895331 0.61226087 0.676315863 0.600511203 0.73406979 0.661040959 1 16.07958411 -1.81512354 6.326457016 1.020277358 0.700343018 0.53666263 0.084153757 0.023297994 0.000680831 0.078873441 0.018930828 0.01530652 1.81512354 -0.31993434 WEETRTPESQPDT(ph)PPGTPLVSQDEKR ddPTM_MDA-MB-175_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(1)PPGTPLVSQDEKR 192.1 2.29E-16 768890000 391290 382300 434880 226460 643410 491170 256320 410530 495700 542730 TRUE FALSE 406738.4313 447957.0511 446213.3301 271253.1121 534043.398 377103.2113 236228.9686 405027.5168 477859.8538 649067.5523 0.626650385 0.690154745 0.687468243 0.417911989 0.822785542 0.58099224 0.363951283 0.624014427 0.736225147 1 19.30800911 0.91749756 2.738703596 0.998924719 0.597965465 0.487580447 0.124856373 0.301352644 5.081614418 0.118708117 0.031523717 8.26984863 -0.91749756 -0.400959253 WEFGTCQPLSDEKDLTQLFMFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WEFGTCQPLSDEKDLTQLFMFAR 23 1 Q9UHL4;R4GMR2 Q9UHL4 DPP7 Dipeptidyl peptidase 2 0 ; 221.83 1.56E-32 610060000 183175 161112 187914 155904 181222 230691 210412 166479 176162 143017 FALSE TRUE 190406.8904 188781.7327 192811.1932 186741.3459 150417.9492 177116.5114 193919.3576 164247.6213 169821.964 171038.4429 1.113240317 1.103738607 1.127297407 1.091809202 0.879439421 1.035536271 1.133776444 0.960296519 0.992887687 1 17.3839611 3.452552801 24.99990783 1.004749971 1.112972911 0.444808517 0.059773139 216.9101312 220718.7535 0.01693697 0.022933785 2834.998285 -3.452552801 0.10822294 WEFKHPQPFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WEFKHPQPFLR 11 1 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 96.604 0.0041388 327460000 535040 530040 469650 315220 928600 817600 369440 471530 514130 866150 FALSE TRUE 556163.7923 621070.2469 481889.4648 377569.5752 770756.9037 627724.7908 340482.3274 465209.9116 495626.5617 1035855.509 0.536912521 0.599572278 0.465209154 0.364500234 0.744077622 0.605996479 0.328696739 0.449106953 0.478470749 1 19.98239135 -1.448745176 6.013490913 1.000240588 0.503133234 0.619417372 0.115623997 0.000386482 3.54E-05 0.116014716 0.027332002 0.035584005 1.448745176 -0.497107354 WENPGLGAESHTDS(ph)LRNSSTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WENPGLGAESHTDSLRNSSTEIR 23 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 WENPGLGAESHTDS(0.561)LRNS(0.415)S(0.022)T(0.001)EIR 243.78 1.25E-37 181900000 82046 109140 102890 125180 129990 159540 124570 115190 102650 111710 TRUE FALSE 85285.23943 127883.946 105571.3979 149940.2304 107894.3462 122489.2529 114805.8779 113646.0665 98955.64655 133597.4357 0.638374824 0.957233538 0.790220242 1.122328656 0.807607913 0.916853323 0.859341928 0.850660538 0.740700194 1 17.02753279 -0.621603288 0.010354828 1.810601435 7.18E-06 0.059198236 0.127008086 19261.53132 44.67525388 4110.555381 3704.991624 0.238999346 0.621603288 -1.810594253 WENPGLGAESHTDSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WENPGLGAESHTDSLR 16 0 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 0 ;; 177.64 2.92E-09 598550000 228892 474140 415698 503270 434020 498880 423540 450520 416000 481630 FALSE TRUE 237928.8329 555569.8567 426531.4314 602815.3039 360245.4354 383022.6806 390341.8281 444481.5163 401028.2413 575996.1771 0.413073632 0.964537403 0.740510872 1.046561293 0.625430254 0.664974345 0.677681283 0.771674421 0.696234206 1 19.13569971 -1.090865023 5.128012189 1.000005571 0.744159869 0.184847344 0.166578714 9.88E-06 1.75E-06 0.150255421 0.035414771 0.081121314 1.090865023 -0.255845702 WENPGLGAESHTDSLRNS(ph)STEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WENPGLGAESHTDSLRNSSTEIR 23 1 Q9UHB6;Q9UHB6-4;F8VRN8;F8VTU2;F8VVQ7 Q9UHB6 LIMA1 LIM domain and actin-binding protein 1 1 WENPGLGAESHTDS(0.1)LRNS(0.3)S(0.3)T(0.3)EIR;WENPGLGAESHTDS(0.278)LRNS(0.683)S(0.037)T(0.002)EIR 227.25 5.28E-33 204578000 102159 153942 166913 176720 193912 199370 180122 173642 159194 168258 TRUE FALSE 106192.3162 180380.341 171262.8899 211674.6885 160950.9075 153069.339 166003.567 171314.613 153464.639 201224.9336 0.527729414 0.896411482 0.851101734 1.051930716 0.799855687 0.760687735 0.824965197 0.851358775 0.762652204 1 17.61844955 -4.999998884 0.018562573 1.991211978 1.70E-07 0.152040991 0.125260705 9561.809183 13.44640199 951.4885015 543.6438662 1.00E-05 4.999998884 -1.991211808 WES(ph)QQDVSQTTVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 WESQQDVSQTTVSR 14 0 Q9NQT8;H0YBA8 Q9NQT8 KIF13B Kinesin-like protein KIF13B 1 WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR;WES(0.999)QQDVS(0.001)QTTVSR;WES(1)QQDVSQTTVSR;WES(1)QQDVSQTTVSR 364.38 6.44E-97 5825700000 2283410 2097460 2431310 2097320 2756240 3018820 2200810 2193750 2034490 1720770 TRUE FALSE 2373560.79 2457682.439 2494671.936 2512163.636 2287735.309 2317744.806 2028304.761 2164346.37 1961269.102 2057921.935 1.153377467 1.194254455 1.212228653 1.220728344 1.111672542 1.126254969 0.985608213 1.051714515 0.953033771 1 20.97275683 2.528989844 1.230862083 0.996733457 1.195080364 0.84739168 0.03638248 0.162167287 0.498795608 0.018715605 0.014251185 338.0569306 -2.528989844 0.198346907 WESENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WESENK 6 0 P29373 P29373 CRABP2 Cellular retinoic acid-binding protein 2 0 ;;;; 143.37 0.02654 4329270000 7384600 5368280 7095140 5188340 8950410 8645420 8632390 6987720 7537540 5266690 FALSE TRUE 7676149.71 6290240.331 7280045.177 6214578.166 7429022.505 6637652.228 7955760.715 6894061.043 7266265.408 6298597.069 1.218707853 0.998673238 1.155820113 0.986660696 1.179472575 1.053830267 1.263100438 1.094539144 1.153632361 1 22.58659909 WESGSLLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WESGSLLER 9 0 O14776;O14776-2;G3V220 O14776 TCERG1 Transcription elongation regulator 1 0 81.548 0.048788 89356000 87928 123120 98165 98059 110390 118060 113790 105200 102190 94194 FALSE TRUE 91399.46534 144264.9023 100723.2605 117454.7775 91625.94723 90642.35422 104870.8425 103789.9661 98512.20186 112649.5108 0.811361404 1.280652718 0.894129586 1.042656791 0.813371905 0.80464046 0.93094805 0.921353012 0.874501816 1 16.78148152 3.252833495 24.98018026 0.888131396 1.018656014 0.170081439 0.124857211 363.6766309 636497.4817 0.032477383 0.043771033 1789.91948 -3.252833495 0.130524618 WESPAQNTAHLDQFER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WESPAQNTAHLDQFER 16 0 P17612-2;P17612;Q15136 P17612-2 PRKACA;KIN27 cAMP-dependent protein kinase catalytic subunit alpha 0 144.3 1.33E-06 204370000 135940 119740 143510 118480 144690 169200 139490 130860 141760 110180 FALSE TRUE 141307.0162 140304.4136 147249.9885 141914.9904 120095.6455 129905.8643 128556.4093 129106.0357 136658.0853 131767.6615 1.072395264 1.064786397 1.117497168 1.077009251 0.911419723 0.985870606 0.975629436 0.979800615 1.037113991 1 17.00763682 3.340805991 8.629112689 0.980494576 1.085063118 0.710224599 0.03170658 0.135743978 10.35469571 0.008657013 0.011724286 2191.825577 -3.340805991 0.104568543 WETFCTSSLGETNKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WETFCTSSLGETNKR 15 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PQP7;H0YEN2;H0YDW1 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 211.13 2.46E-09 1574620000 687790 538690 724640 534010 872180 917450 879920 722640 803690 545140 FALSE TRUE 714944.4803 631205.8171 743524.7137 639635.5841 723927.1551 704386.1416 810949.5712 712954.1928 774765.3539 651949.7457 1.096625139 0.968181706 1.140463231 0.981111793 1.110403309 1.080430119 1.243883561 1.093572315 1.188382017 1 19.31440124 2.829529742 2.329032673 1.136863463 1.048737681 0.15280881 0.077701756 0.451379213 4.810488754 0.0244207 0.025712531 675.3513021 -2.829529742 -0.088125782 WEWLVNQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 154.56 7.96E-05 946120000 876220 918260 1008980 1002590 1279190 1350470 1173840 1042540 1011550 1081530 FALSE TRUE 910813.8422 1075964.012 1035274.848 1200899.31 1061753.741 1036843.809 1081831.354 1028566.457 975144.5131 1293435.096 0.7041821 0.831865484 0.800407265 0.92845734 0.820879025 0.801620284 0.836401731 0.795220773 0.753918396 1 20.30277623 -2.359910466 2.372077446 2.340088776 0.81235392 0.522163628 0.054935429 6234815.348 528134.5844 45906615.7 0.014660456 0.004366058 2.359910466 -1.527734856 WFCHIQHYPGIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WFCHIQHYPGIR 12 0 O43324 O43324 EEF1E1 Eukaryotic translation elongation factor 1 epsilon-1 0 ; 77.305 0.016643 476240000 340040 478890 361370 481900 526620 588180 412380 399770 349590 586850 FALSE TRUE 353465.0418 561135.6323 370787.5991 577218.3817 437105.3205 451584.109 380056.578 394411.737 337008.3242 701832.0216 0.503631967 0.799529823 0.528313881 0.822445206 0.62280618 0.643436171 0.541520715 0.561974554 0.480183739 1 19.42076625 -1.153679274 4.558212496 1.000053405 0.61514654 0.521979986 0.111475242 5.79E-05 1.08E-05 0.10337639 0.024362676 0.070197351 1.153679274 -0.384906866 WFDFPFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WFDFPFTR 8 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 86.011 0.038005 64532000 171910 182160 214700 223830 205610 245930 205340 186510 178640 186730 FALSE TRUE 178697.1395 213444.563 220295.2584 268102.9059 170660.4856 188816.4846 189244.9142 184010.1385 172210.7813 223316.1683 0.800197947 0.955795385 0.986472498 1.200553045 0.764210164 0.845511931 0.84743042 0.823989324 0.77115232 1 17.76872818 WFHPNITGVEAENLLLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WFHPNITGVEAENLLLTR 18 0 Q06124;Q06124-1;Q06124-3;A0A1W2PPU4 Q06124 PTPN11 Tyrosine-protein phosphatase non-receptor type 11 0 ; 249.86 9.23E-25 628890000 540130 672290 572260 604170 671740 795090 614720 604930 590080 680910 FALSE TRUE 561454.7495 787750.5778 587173.5657 723673.0227 557557.8747 610442.3972 566536.6401 596821.9028 568843.1361 814321.2777 0.68947572 0.967370741 0.721058852 0.888682443 0.684690294 0.749633362 0.695716366 0.73290717 0.698548781 1 19.63523857 5.036972697 16.84987689 0.777571683 0.319713414 0.056345252 0.111975298 1012752.841 12219575.47 0.025053442 14144541.58 108886.1637 -5.036972697 -0.457858269 WFLTCINQPQFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WFLTCINQPQFR 12 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 ; 219.7 7.28E-11 2089460000 805090 909930 1015210 822250 1011610 1090310 961740 877180 855110 935430 FALSE TRUE 836875.5749 1066203.399 1041667.207 984888.5958 839656.8935 837102.0263 886356.3058 865422.8369 824334.7581 1118709.599 0.748072222 0.953065389 0.931132805 0.880379141 0.750558406 0.748274644 0.792302405 0.773590249 0.736862148 1 20.09340415 3.277868719 9.912413615 0.785270581 0.887474466 0.143355224 0.087693564 0.563065043 136.6572311 0.022627424 0.030525597 1896.132659 -3.277868719 0.102203885 WFNGQPIHAELSPVTDFR ddPTM_MDA-MB-175_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 ;;; 216.96 8.68E-19 2396897000 1513728 1842270 1787290 1848380 1933020 2295710 1829430 1925300 1886620 2150070 FALSE TRUE 1573491.15 2158665.542 1833868.246 2213984.047 1604445.951 1762566.144 1686034.496 1899494.503 1818720.915 2571335.051 0.611935481 0.839511576 0.713196923 0.861025111 0.623973896 0.685467319 0.655703929 0.738719173 0.70730608 1 21.29408618 -1.53114605 3.968131687 1.003882289 0.718445753 0.5450902 0.078001246 0.002562642 0.000302789 0.072243418 0.016817679 0.029434316 1.53114605 -0.285436536 WFSNPS(ph)R ddPTM_MDA-MB-175_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 112.8 0.0065797 2250030000 867792 1086840 993490 1135269 1140065 1229090 1042435 1055466 898047 1067093 TRUE FALSE 902053.0982 1273496.316 1019381.166 1359821.82 946277.1585 943652.4745 960726.2208 1041319.205 865726.4639 1276169.443 0.706844301 0.997905351 0.798781989 1.065549585 0.741498054 0.739441365 0.752820267 0.815972527 0.678378932 1 20.28338846 WFTPWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WFTPWSR 7 0 Q6IA69;H0YCQ6;E9PKY6 Q6IA69 NADSYN1 Glutamine-dependent NAD(+) synthetase 0 ; 120.65 0.010504 433580000 250630 258500 246440 238380 323220 329420 269770 249580 257590 328140 FALSE TRUE 260525.0659 302895.3641 252862.4289 285530.8525 268279.1799 252917.1974 248624.7225 246234.7883 248319.3862 392432.7504 0.663871875 0.771840179 0.644345888 0.727591803 0.683630965 0.644485449 0.633547333 0.627457286 0.632769273 1 18.58208592 -1.923430637 5.055027851 1.13581023 0.668874407 0.832272787 0.044447603 0.02894003 0.00043836 0.018307423 0.010683344 0.011928048 1.923430637 -0.466935823 WFVLVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WFVLVDR 7 0 A0A1B0GUN5;A0A5F9ZH45;Q5VTI5;Q9Y2H5 A0A1B0GUN5;Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 0 ; 110.63 0.015726 151853000 232670 317930 268470 298770 320680 375830 302380 282250 273670 359340 FALSE TRUE 241855.9913 372532.0043 275466.5488 357865.8143 266170.9281 288549.1783 278678.6655 278466.9004 263820.6702 429745.793 0.562788502 0.866865971 0.640998826 0.832738377 0.619368316 0.671441543 0.648473284 0.647980515 0.613899367 1 18.71312399 -1.071729834 4.999416093 1.00000728 0.681603843 0.526400962 0.091497622 6.90E-06 1.28E-06 0.082328611 0.019404596 0.084775462 1.071729834 -0.318403437 WFVVLEETPWDATSHIDNMENER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WFVVLEETPWDATSHIDNMENER 23 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 0 61.222 0.041128 38660000 12955 15894 17041 18595 17323 18548 19069 14776 18560 18416 FALSE TRUE 13466.4734 18623.67086 17485.10246 22273.0355 14378.44265 14240.5081 17574.32195 14577.95189 17892.02923 22024.2626 0.611438106 0.84559793 0.793901833 1.011295402 0.652845587 0.646582742 0.797952797 0.661904199 0.812378128 1 14.4268061 0.977029729 22.48411791 1.000000008 0.755260198 0.300293597 0.11345944 647.5219645 633819.8876 0.108913759 0.02722844 9.484833883 -0.977029729 -0.24473981 WGDEHIPGSPYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WGDEHIPGSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;;; 150.06 6.78E-05 2386340000 2386750 3115020 2727830 2523370 3984840 3908080 3188290 2922210 2893090 3947650 FALSE TRUE 2480980.733 3650000.454 2798919.491 3022485.054 3307498.32 3000487.648 2938383.499 2883042.555 2788968.256 4721116.435 0.525507211 0.773122312 0.592851189 0.640205573 0.70057546 0.635546208 0.622391661 0.610669657 0.590743375 1 22.17069663 -1.187779517 4.338603943 1.000099583 0.635483342 0.752812231 0.063170245 6.11E-05 1.14E-05 0.056041526 0.013205178 0.064896382 1.187779517 -0.364616241 WGDIEFPPPFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 ; 152.97 0.00014273 674950000 537120 535470 577000 555450 585300 673180 638300 576010 601870 521490 FALSE TRUE 558325.9123 627432.8071 592037.094 665316.3521 485810.9151 516844.1471 588268.3781 568289.5281 580208.8163 623665.981 0.895232271 1.006039813 0.949285534 1.066783138 0.7789601 0.82871948 0.943242691 0.911208155 0.930319809 1 19.25041404 3.251006177 24.99999913 0.89540701 0.97909622 0.240415374 0.070028901 326.9037581 656663.2396 0.019342917 0.026010102 1782.40412 -3.251006177 0.08368921 WGEDNHWICKPWNLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGEDNHWICKPWNLAR 16 1 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 ; 182.35 1.30E-09 1889850000 2020710 1870870 1947100 1596950 3730300 2827200 2351140 2020600 2173260 2793100 FALSE TRUE 2100489.191 2192177.369 1997843.026 1912821.944 3096224.938 2170625.647 2166851.503 1993517.162 2095044.797 3340354.468 0.628822244 0.656270881 0.59809312 0.572640407 0.926915083 0.649818954 0.648689091 0.596798089 0.627192359 1 21.67156977 -2.260428428 2.2391028 2.320762796 0.655124662 0.544901534 0.094271517 4746104.261 637367.7308 31829201.76 0.02334291 0.00548999 2.260428428 -1.665638134 WGEEHIPGSPFHVTVP ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WGEEHIPGSPFHVTVP 16 0 O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;E7EN95;O75369-7 O75369-8 FLNB Filamin-B 0 ;; 105 0.0013175 568201000 236407 722830 646463 638018 813589 891509 657338 783241 715921 779732 FALSE TRUE 245740.5309 846970.4297 663310.3569 764216.0561 675295.4324 684469.5457 605814.1299 772742.9355 690155.1431 932505.5565 0.263527149 0.908273869 0.711320541 0.819529761 0.724173092 0.734011225 0.649662756 0.828673813 0.740108344 1 19.8307528 -4.999939211 0.03944039 2.214812871 8.02E-06 0.309536898 0.154643756 1170.076664 3.449592947 172.9081238 52.91644569 1.00E-05 4.999939211 -2.214804849 WGEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGEEKR 6 1 Q15126 Q15126 PMVK Phosphomevalonate kinase 0 ; 91.26 0.077118 492620000 510080 439610 531650 401540 679420 615470 553640 529750 538940 384660 FALSE TRUE 530218.3523 515109.5978 545505.2358 480963.4135 563932.4311 472536.42 510244.2501 522649.5677 519543.6547 460026.7622 1.152581536 1.119738328 1.185811958 1.045511811 1.225868748 1.027193326 1.109162101 1.136128614 1.129377022 1 18.81135827 -5 0.255357704 0.22138147 1.135880122 0.320561627 0.05539089 215.8839606 2.130731766 88.06329378 0.070207056 1.00E-05 5 0.914498652 WGNNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGNNNR 6 0 Q9BUJ2-2;Q9BUJ2;A0A0A0MRA5;B7Z4B8;Q9BUJ2-4;Q9BUJ2-3;M0R3F1;Q9BUJ2-5 Q9BUJ2-2 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 0 ; 119.23 0.049289 334480000 258550 306410 302470 274540 350850 387700 309540 329310 302170 311060 FALSE TRUE 268757.7536 359033.534 310352.6167 328843.1926 291212.6423 297662.5507 285277.446 324896.1381 291294.9607 372006.2514 0.722454939 0.96512769 0.834267208 0.883972222 0.782816529 0.8001547 0.766861968 0.873362039 0.783037811 1 18.50496734 -1.29399616 3.392544275 1.000682923 0.828783381 0.38793096 0.066195254 18594004.63 27681674.12 130882.0707 0.014979505 0.050816394 1.29399616 -0.171899542 WGQPPS(ph)PTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_MDA-MB-175_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(0.986)PT(0.014)PVPRPPDADPNT(0.62)PS(0.38)PKPLEGRPER 116.84 2.85E-06 721140000 224170 135790 168360 117430 234740 265620 217250 187690 202030 124350 TRUE FALSE 233020.4047 159110.8762 172747.5999 140657.3035 194838.9786 203933.7805 200221.3773 185174.3225 194758.9798 148714.0017 1.566902928 1.069911874 1.161609519 0.945824212 1.310158939 1.371315264 1.346351891 1.245170734 1.309621001 1 17.18218096 WGQPPS(ph)PTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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(0.999)PT(0.001)PVPRPPDADPNT(0.049)PS(0.951)PKPLEGRPER;WGQPPS(0.975)PT(0.025)PVPRPPDADPNT(0.05)PS(0.95)PKPLEGRPER;WGQPPS(0.927)PT(0.062)PVPRPPDADPNT(0.073)PS(0.938)PKPLEGRPER 217.02 4.01E-36 1047070000 1025830 553980 715770 505561 891580 928520 855190 760260 772700 449986 TRUE FALSE 1066330.561 649121.7556 734423.5542 605559.4569 740029.5501 712885.3019 788157.9732 750069.9582 744890.6779 538152.1412 1.981466725 1.206204911 1.364713615 1.125256987 1.375130736 1.324691007 1.464563481 1.393787929 1.384163735 1 19.03765457 -2.263180591 1.565540357 0.000237658 1.387146909 0.235845516 0.215670371 432550.3776 60763.81073 1522098.372 0.056110578 0.00545531 2.263180591 1.386909251 WGQPPS(ph)PTPVPRPPDADPNTPSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.5)PT(0.5)PVPRPPDADPNTPSPK 171.99 3.63E-12 368220000 771820 498360 698280 580290 799490 860420 894030 711640 749880 389020 TRUE FALSE 802292.0496 583949.4533 716477.7504 695069.63 663592.9754 660600.4948 823953.5925 702101.6298 722891.9653 465241.0208 1.724465414 1.255154699 1.54001414 1.493999022 1.42634236 1.419910251 1.771025244 1.509113768 1.553801004 1 18.82761878 WGQPPSPT(ph)PVPRPPDADPNTPSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WGQPPSPTPVPRPPDADPNTPSPK 24 1 Q14839-2;Q14839;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8YDJ9;A0A2R8YFD8;A0A2R8YD40;A0A2R8Y8C1;A0A2R8Y445;A0A2R8YER1;A0A2R8Y5Z7;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 WGQPPS(0.129)PT(0.871)PVPRPPDADPNTPSPK 222.13 1.41E-32 362660000 616500 385540 566560 488270 636090 641710 742390 576310 642510 305570 TRUE FALSE 640839.896 451753.4959 581325.019 584848.3487 527967.649 492682.5777 684199.5319 568585.5071 619386.1906 365440.591 1.753608964 1.236188609 1.590751092 1.600392411 1.444742763 1.348187886 1.872259264 1.555890399 1.694902553 1 18.47927736 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_MDA-MB-175_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 1 WGQPPS(0.442)PT(0.447)PVPRPPDADPNT(0.056)PS(0.056)PKPLEGRPER;WGQPPS(0.401)PT(0.58)PVPRPPDADPNT(0.011)PS(0.008)PKPLEGRPER 173.01 9.19E-15 4365600000 1741730 1035140 1509190 1021740 1742200 1681670 1677970 1471890 1530940 1040380 TRUE FALSE 1810494.845 1212917.243 1548520.731 1223837.122 1446061.466 1291127.628 1546446.327 1452161.722 1475841.768 1244222.542 1.455121399 0.97483947 1.244568941 0.983615938 1.162220919 1.03769831 1.242901712 1.167123785 1.186155787 1 20.24681312 4.755455732 24.8798284 1.123754141 1.455121678 0.511002484 0.10029055 2623.463677 3863258.22 0.022134043 0.641804852 56945.01766 -4.755455732 0.331367537 WGQPPSPTPVPRPPDADPNT(ph)PSPKPLEGRPER ddPTM_MDA-MB-175_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(0.007)PT(0.04)PVPRPPDADPNT(0.803)PS(0.15)PKPLEGRPER 73.665 0.0013854 1050600000 86909 48979 69001 52901 75075 81718 57517 54292 59936 48757 TRUE FALSE 90340.23443 57390.76225 70799.22274 63364.65991 62313.77832 62740.23295 53008.66725 53564.30454 57778.91507 58310.00064 1.54930944 0.984235322 1.214186623 1.086685975 1.068663653 1.07597723 0.909083633 0.918612656 0.990892033 1 15.83145572 8 0.762767968 0.993881819 96.37454674 0.711894828 0.095598882 230.0660415 0.932337131 0.034021378 37768.44889 100000000 -8 95.38066493 WGQPPSPTPVPRPPDADPNTPS(ph)PKPLEGRPER ddPTM_MDA-MB-175_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 1 WGQPPS(0.02)PT(0.117)PVPRPPDADPNT(0.29)PS(0.572)PKPLEGRPER;WGQPPS(0.029)PT(0.029)PVPRPPDADPNT(0.322)PS(0.621)PKPLEGRPER 90.724 0.00073039 1229670000 649380 417820 516670 403360 675530 641670 632490 521610 583080 348960 TRUE FALSE 675018.0238 489577.3348 530134.8446 483143.4041 560703.6519 492651.8671 582913.7811 514618.6711 562095.0647 417332.0308 1.617460377 1.173112291 1.270295126 1.157695476 1.343543295 1.180479404 1.396762621 1.233115681 1.346877362 1 18.67083613 -2.27578459 1.946160985 2.44E-05 1.290585697 0.3208254 0.130916625 1547528.752 226075.4383 6792345.388 0.031060372 0.005299262 2.27578459 1.290561247 WGRDDIENIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 ;;; 228.93 2.65E-12 1491820000 635550 823430 852790 736760 928440 961200 732210 741010 739500 807790 FALSE TRUE 660642.0048 964847.6971 875014.408 882488.929 770624.1004 737975.8671 674817.4669 731077.973 712885.5395 966060.9844 0.683851243 0.998744088 0.905754835 0.913491946 0.797697157 0.763901947 0.698524708 0.756761721 0.737930163 1 19.88175474 3.110389955 4.631467501 0.768429035 0.8860276 0.104356106 0.106985321 0.322413768 11.70066335 0.029494729 0.035678431 1289.406796 -3.110389955 0.117598565 WGTDEDKFTEILCLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGTDEDKFTEILCLR 15 1 P12429;D6RA82;D6RFJ9 P12429 ANXA3 Annexin A3;Annexin 0 ; 125.28 8.34E-05 836050000 896280 823300 1099290 899390 1320990 1351590 1086690 1185490 1215700 918790 FALSE TRUE 931665.8265 964695.3706 1127938.4 1077286.658 1096448.592 1037703.706 1001512.398 1169600.446 1171947.194 1098809.309 0.847886725 0.877946121 1.026509687 0.980412751 0.997851568 0.944389256 0.911452415 1.064425315 1.066561035 1 20.06750961 4.312153491 5.520126517 0.99743615 0.857040604 0.587654715 0.045703382 0.14370686 7.625054312 0.012078859 0.034054426 20518.87241 -4.312153491 -0.140395546 WGTDEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WGTDEEK 7 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ;;; 157.9 0.0033611 1833600000 2012460 1043490 1541040 1195110 1936440 1983700 1647570 1543860 1682170 750790 FALSE TRUE 2091913.475 1222701.29 1581200.768 1431499.191 1607284.62 1523015.738 1518429.158 1523167.082 1621629.03 897892.9258 2.329802825 1.361745098 1.761012614 1.594287192 1.790062684 1.696210867 1.691102708 1.696379421 1.806038319 1 19.77618389 -1.457847988 4.083663256 0.99556001 1.726690174 0.485323176 0.230014077 0.00823238 0.00109294 0.197186275 0.046276894 0.034845926 1.457847988 0.731130164 WGTDEEKFITIFGTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGTDEEKFITIFGTR 15 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 193.69 7.54E-08 1978860000 2130000 2074740 2370000 1587060 3674000 3233500 2336200 2663900 2948600 2699200 FALSE TRUE 2214094.045 2431060.456 2431764.147 1900975.731 3049494.792 2482568.629 2153082.539 2628194.778 2842480.462 3228056.561 0.685890722 0.753103426 0.753321418 0.588891705 0.944684436 0.76905983 0.666990339 0.814172468 0.880554727 1 21.62223443 1.105632758 1.754579464 0.996622539 0.742104528 0.479059685 0.087265711 0.286328755 1.718564618 0.080091414 0.023213305 12.75359901 -1.105632758 -0.254518011 WGTLTDCVVMRDPQTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WGTLTDCVVMRDPQTK 16 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ; 213.83 8.24E-13 2425100000 2564430 2073390 2562250 1802860 3220200 2941400 2519860 2656370 2738110 2165890 FALSE TRUE 2665675.677 2429478.604 2629024.34 2159460.327 2672831.554 2258304.427 2322346.789 2620765.705 2639565.956 2590254.677 1.029117214 0.937930399 1.01496751 0.833686489 1.031879829 0.871846482 0.896570831 1.011779161 1.019037232 1 21.30466252 1.628049532 8.316039339 1.012246867 0.943939794 0.181977723 0.063148917 0.177185123 27.36325075 0.030373804 0.01544656 42.46679951 -1.628049532 -0.068307072 WHLVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WHLVYR 6 0 Q99829;B0QZ18;F2Z2V0;A6PVH9;E7ENH5;Q5JX45;Q5JX60;Q5JX52;Q5JX44;Q5JX61;Q5JX59;Q5JX58 Q99829 CPNE1 Copine-1 0 ; 150.22 0.010539 2758900000 1425410 1611850 1443580 1351190 2308200 2215400 1731600 1361450 1469770 2338000 FALSE TRUE 1481686.287 1888672.699 1481200.881 1618451.349 1915852.988 1700906.925 1595872.667 1343201.99 1416873.265 2796086.336 0.529914355 0.675470094 0.529740753 0.578827387 0.685190927 0.608317026 0.570752286 0.48038645 0.506734448 1 21.41497748 -1.531726123 6.122805999 1.0005797 0.573073387 0.799125353 0.06408446 0.000542146 4.15E-05 0.066335625 0.015615303 0.029395028 1.531726123 -0.427506313 WHPDKNPENKEEAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 156.17 1.30E-06 622290000 688700 432748 537510 386560 751470 679300 650660 543790 571740 348565 FALSE TRUE 715890.4078 507069.1027 551517.9522 463020.4142 623735.3978 521542.8699 599659.569 536501.3845 551163.1891 416859.6381 1.717341624 1.216402492 1.323030348 1.110734578 1.496271984 1.251123453 1.438516743 1.287007269 1.322179311 1 18.66920217 -3.572099427 0.2819648 1.18E-13 1.366721924 0.3168413 0.158045232 114.3277747 2.291645407 66.73340876 0.168912861 0.000267856 3.572099427 1.366721924 WHQPPPS(ph)PLPLR ddPTM_MDA-MB-175_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 63.062 0.042043 0 110660 211160 148610 187020 134260 197660 131790 159850 99942 264550 TRUE FALSE 115028.9422 247425.0874 152482.8987 224011.9978 111438.5332 151756.4606 121459.9554 157707.4722 96345.10694 316383.5074 0.363574395 0.782041673 0.481955902 0.708039429 0.352226113 0.479659834 0.383901033 0.498469321 0.304520004 1 18.27131487 -1.68244188 6.407464501 1.004695313 0.491364192 0.528046321 0.146241672 0.009383487 0.000465052 0.135455844 0.031787328 0.020775817 1.68244188 -0.513331121 WIAQDLSSLAGLLDQHGVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WIAQDLSSLAGLLDQHGVR 19 0 A0A2P0CU24;A0A0A0MRV4;J3KPF5;A0A2P0CTB1;A0A0A0MT35;J3KPF6;A0A0G2JRR6;A0A0G2JSF1;J3QKK8;J3KRV9;A0A2P0CTH9;Q8TBF2-2;Q8TBF2;Q8TBF2-7;Q8TBF2-3;Q8TBF2-4;Q8TBF2-6 A0A2P0CU24 FAM213B Prostamide/prostaglandin F synthase 0 73.138 0.017665 112910000 33449 31036 38422 33044 43709 43628 38957 41942 40029 29367 FALSE TRUE 34769.59235 36366.19157 39423.30888 39580.00457 36279.35979 33496.05819 35903.44854 41379.83609 38588.36411 35120.90138 0.989997152 1.035457239 1.122502764 1.126964372 1.032984871 0.953735721 1.022281523 1.178211107 1.09872932 1 15.10004225 1.767707542 25 1.11092507 1.04320826 0.098063888 0.064592964 39.78221266 34141.46548 0.031368582 0.017398319 58.57435867 -1.767707542 -0.06771681 WIDDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 103.71 0.080148 243510000 609590 911190 780410 1042800 865820 1104000 822360 869860 770680 923930 FALSE TRUE 633657.0839 1067679.794 800748.1257 1249062.728 718648.2257 847612.7313 757901.2744 858200.9495 742943.3773 1104956.394 0.573467955 0.96626419 0.724687535 1.130418118 0.650386051 0.767100617 0.685910574 0.776683093 0.672373481 1 20.07555801 WIDFDNDYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WIDFDNDYK 9 0 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 115.71 0.0033294 138110000 295850 172030 224170 195840 265110 278050 314890 251980 239910 114890 FALSE TRUE 307530.3864 201574.8143 230012.0544 234576.5675 220046.6969 213477.1014 290208.099 248602.6203 231275.686 137400.4958 2.238204343 1.467060312 1.674026378 1.707246878 1.601498565 1.553685088 2.112132837 1.809328408 1.683223082 1 17.06802768 0.823392245 5.326050647 1.000003619 1.761131915 0.503933206 0.227735242 2.867164735 86.09200298 0.211950738 0.05346174 6.658742869 -0.823392245 0.761128296 WIDFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WIDFVR 6 0 P05455 P05455 SSB Lupus La protein 0 ; 148.37 0.025066 3047900000 1419170 1605210 1583430 1556180 1715010 1829350 1650060 1616800 1529480 1771790 FALSE TRUE 1475199.927 1880892.331 1624695.487 1863987.759 1423493.213 1404511.187 1520723.986 1595129.441 1474434.314 2118938.328 0.69619767 0.887657893 0.766749775 0.879680043 0.67179549 0.662837218 0.717682042 0.75279654 0.695836351 1 21.01491017 -1.266965009 3.205619773 1.00111204 0.750581497 0.502031145 0.075276818 19020349.66 27084142.91 207392.663 0.019046641 0.054079789 1.266965009 -0.250530544 WIDLTMEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WIDLTMEDIR 10 0 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ; 108.98 0.0048383 39414000 57440 82605 78059 80859 88118 101747 91244 78337 84721 91859 FALSE TRUE 59707.77555 96791.76617 80093.28167 96852.66886 73139.73383 78117.80124 84092.05686 77287.02065 81671.90776 109857.0123 0.543504455 0.88107044 0.72906845 0.881624821 0.6657721 0.711086162 0.765468267 0.703523781 0.743438275 1 16.74526744 -1.803755292 2.794413252 1.073476736 0.740258446 0.41808664 0.093297448 13614305.25 10964805.74 6791066.832 0.020373917 0.015712479 1.803755292 -0.333218289 WIDLTMEDIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WIDLTMEDIRR 11 1 A0A0A0MSW4;P48739;P48739-3;P48739-2 A0A0A0MSW4 PITPNB Phosphatidylinositol transfer protein beta isoform 0 ;; 185.99 6.77E-06 375293000 254555 284165 290851 282620 337249 358301 339186 305002 292679 301605 FALSE TRUE 264605.028 332968.1283 298430.816 338521.3925 279923.5354 275091.0229 312599.715 300913.9471 282145.54 360698.7252 0.733590139 0.923119781 0.827368646 0.938515633 0.776059121 0.762661478 0.866650457 0.834252871 0.782219399 1 18.4604348 -2.002478244 6.067753814 1.174072837 0.831851253 0.394500008 0.064002058 0.04217344 1.72E-05 0.01734061 0.013788052 0.009943099 2.002478244 -0.342221584 WIDNPTVDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WIDNPTVDDR 10 0 P18206;P18206-2 P18206 VCL Vinculin 0 ;;; 208.75 2.51E-07 1359840000 1226600 1424790 1168150 1520420 1267260 1475520 1480300 1314810 1131170 1290830 FALSE TRUE 1275027.115 1669486.599 1198592.949 1821154.538 1051851.598 1132852.842 1364270.218 1297187.123 1090459.413 1543743.424 0.825932014 1.081453416 0.776419792 1.179700272 0.681364261 0.733834926 0.883741557 0.840286736 0.706373479 1 20.55800156 3.213654705 24.99997879 0.804407638 0.960599556 0.239622463 0.137926406 313.7988301 314983.1771 0.037183825 0.044460405 1635.515655 -3.213654705 0.156191917 WIGLDLSNGKPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WIGLDLSNGKPR 12 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 ; 205.46 9.25E-08 3211000000 3372400 3117100 3548100 3081000 4338600 4235700 3775000 3483500 3481100 3213100 FALSE TRUE 3505544.956 3652437.677 3640566.401 3690412.604 3601126.322 3252022.868 3479105.636 3436809.38 3355815.891 3842645.426 0.912273855 0.950500833 0.947411483 0.960383328 0.9371477 0.846297929 0.905393355 0.894386288 0.873308754 1 21.87366843 2.969420881 24.78325832 0.896783011 0.944196997 0.179151667 0.038941711 783.1443062 634709.7852 0.010917459 0.011594204 932.0106618 -2.969420881 0.047413986 WIPLSSDAQAPLAQPES(ph)PTASAGDEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WIPLSSDAQAPLAQPESPTASAGDEPR 27 0 Q6GQQ9;Q6GQQ9-2 Q6GQQ9 OTUD7B OTU domain-containing protein 7B 1 WIPLSSDAQAPLAQPES(0.788)PT(0.211)AS(0.001)AGDEPR 118.85 0.00021035 66869000 27946 28749 28943 32430 29727 31950 27579 29270 31638 27727 TRUE FALSE 29049.32966 33686.41711 29697.27836 38844.55721 24674.01516 24530.09671 25417.28592 28877.68353 30499.35456 33159.57478 0.876046507 1.015888091 0.895586827 1.171443164 0.744099263 0.739759085 0.766514229 0.87087014 0.919775201 1 15.01713789 3.211203484 24.99999222 0.826807262 0.984883741 0.315008472 0.106873228 240.1522741 219459.6658 0.030181821 0.036082208 1626.310566 -3.211203484 0.158076479 WIQDEIEFGYIEAPHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WIQDEIEFGYIEAPHK 16 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ;; 189.42 1.02E-09 878580000 990420 922900 1068490 935040 1197190 1256140 1069440 992040 1009950 866620 FALSE TRUE 1029522.546 1081400.896 1096335.727 1119988.121 993692.0714 964420.522 985614.4983 978743.3265 973602.0968 1036417.597 0.993347228 1.043402678 1.05781273 1.080634027 0.958775763 0.930532756 0.950982019 0.944352286 0.939391709 1 19.98317398 3.166717968 7.160908299 0.948959848 1.044585602 0.72705581 0.026871283 0.106276938 8.797465259 0.007638138 0.009180723 1467.972663 -3.166717968 0.095625754 WIQEAETTVNVLVDASHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WIQEAETTVNVLVDASHR 18 0 P46939-4;P46939;P46939-2 P46939-4 UTRN Utrophin 0 81.51 0.0068265 6965700 3976.8 4879.7 4805.7 6055.7 3911.1 5247.1 3659.3 3744.2 3970.7 4299.4 FALSE TRUE 4133.807135 5717.750516 4930.94049 7253.499386 3246.292619 4028.540546 3372.474504 3694.015123 3827.795283 5141.785113 0.803963418 1.112016623 0.958993887 1.410696718 0.631355171 0.783490647 0.655895653 0.718430475 0.744448708 1 12.3280536 3.206520387 24.99999862 0.734739581 1.066287898 0.448469485 0.170598919 157.3802247 122798.4924 0.046333686 0.055383645 1608.8679 -3.206520387 0.331548317 WIS(ph)ENQDSADVDPQEHSFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WISENQDSADVDPQEHSFTR 20 0 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 WIS(1)ENQDSADVDPQEHSFTR 89.565 0.001189 0 14997 12342 13910 14878 19487 19921 20139 17534 13241 18264 TRUE FALSE 15589.09314 14461.64249 14272.50603 17820.82399 16174.6067 15294.64966 18560.45256 17298.98541 12764.459 21842.48111 0.713705236 0.662087902 0.653428791 0.815879107 0.74051142 0.700224923 0.849741037 0.791988113 0.584386862 1 14.41484912 -5 0.28623575 3.002872644 0.716014658 0.506898203 0.079105427 202.8460424 1.923456084 242.6037495 0.087350729 1.00E-05 5 -2.286857986 WISIMTER ddPTM_MDA-MB-175_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 ; 157.33 0.0008809 906960000 716260 842770 835290 839270 914400 1062490 879850 783110 696610 972720 FALSE TRUE 744538.4979 987509.1917 857058.3436 1005275.101 758970.6146 815742.7997 810885.0579 772613.6914 671539.1422 1163305.86 0.640019554 0.848881816 0.736743769 0.864153732 0.652425678 0.701228136 0.697052328 0.664153528 0.57726791 1 20.14979903 -1.187296419 4.569145445 1.00005124 0.712643744 0.513496212 0.084881514 4.82E-05 8.57E-06 0.082415568 0.019421785 0.064968611 1.187296419 -0.287407495 KTATNDEESPLSVS(ph)SPEGTGTWLHYTSGVGTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 KTATNDEESPLSVSSPEGTGTWLHYTSGVGTGR 33 1 A0A087WZV0;O43314-2;O43314;A0A087WWN8 A0A087WZV0 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 KTATNDEESPLSVS(0.5)S(0.5)PEGTGTWLHYTSGVGTGR 326.33 1.31E-106 403130000 112150 143870 207810 149210 272860 256220 200030 232240 241020 228050 TRUE FALSE 116577.7686 168578.5533 213225.6993 178723.2927 226479.3547 196716.7881 184351.1259 229127.2027 232345.7373 272732.0312 0.42744436 0.618110578 0.781813923 0.655307306 0.830409812 0.721282305 0.675942335 0.840118418 0.851919506 1 18.05712462 5.434232622 0.140186298 1.05186908 8.82E-17 0.706218756 0.081166065 21.88229021 0.411457466 0.449958937 4.290611497 271789.467 -5.434232622 -1.05186908 down WIVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 WIVEER 6 0 O95433;O95433-2;G3V3W9 O95433 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 ;;;;;; 129.16 0.037954 3096550000 2954450 3582500 3320330 3452600 3671790 3903150 3294110 3390000 3191300 3568020 FALSE TRUE 3071093.967 4197766.507 3406860.527 4135513.975 3047660.447 2996702.565 3035909.051 3344562.595 3076445.736 4267105.205 0.719713675 0.983750413 0.798400875 0.969161475 0.714222008 0.702279982 0.711468057 0.783801297 0.720967867 1 22.02482625 3.219930509 24.99937184 0.755781946 0.871087936 0.146060567 0.108950374 351.7514092 472007.3216 0.028788601 0.034466726 1659.32138 -3.219930509 0.11530599 WIVNLIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WIVNLIR 7 0 P60228;E5RGA2;H0YAW4 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 126.16 0.0092578 49501000 58143 65972 68524 72725 75148 89790 80976 67144 66418 77554 FALSE TRUE 60438.53054 77302.17781 70309.79173 87109.78794 62374.3698 68937.63328 74628.88953 66244.04451 64027.62915 92749.22144 0.651633832 0.833453657 0.758063417 0.939196972 0.672505589 0.743269132 0.8046309 0.714227499 0.690330637 1 16.50104755 -0.99922798 4.606784333 1.000005645 0.760026077 0.446282257 0.081321421 0.040427498 47739145.44 647.4889884 0.018198289 0.100177922 0.99922798 -0.239979568 WIYEDVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 WIYEDVER 8 0 O43852;O43852-3;O43852-6;O43852-5;O43852-10;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 ;;;;; 151.56 0.0010961 1853660000 1916420 2937510 2341490 2854940 3154530 3283220 2286810 2468340 2211320 3313100 FALSE TRUE 1992081.741 3442004.492 2402511.153 3419638.611 2618324.117 2520741.913 2107563.857 2435255.94 2131735.025 3962238.512 0.50276674 0.868701993 0.606351976 0.863057234 0.66081941 0.636191361 0.531912415 0.61461619 0.538012797 1 21.9178843 -1.236804481 5.176475488 1.000039096 0.651022818 0.436020145 0.120381936 5.28E-05 7.78E-06 0.113234696 0.02668669 0.057968961 1.236804481 -0.349016279 WKAGLYGLPR ddPTM_MDA-MB-175_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 ; 147.95 2.37E-05 2081800000 1702720 2561600 2178700 1670150 5626000 3609700 2011600 2339870 2418040 6882900 FALSE TRUE 1769944.7 3001534.874 2235478.712 2000500.685 4669694.53 2771401.881 1853925.536 2308507.87 2331015.213 8231472.474 0.215021639 0.364641306 0.271577014 0.24303072 0.567297594 0.336683612 0.225224046 0.280448957 0.28318326 1 22.9727191 -1.730794741 2.666224241 1.132025744 0.31065314 0.820746489 0.096782655 21214003.01 17117106.55 18595865.12 0.025865807 0.018586827 1.730794741 -0.821372604 WKDSDEADLVLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WKDSDEADLVLAK 13 1 Q13185 Q13185 CBX3 Chromobox protein homolog 3 0 ;; 145.29 3.72E-05 5449940000 4360920 2362460 3468350 2315150 4519470 4303070 4195830 3422310 3932730 2288210 FALSE TRUE 4533092.489 2768194.128 3558738.05 2773079.76 3751252.104 3303747.206 3866949.881 3376439.532 3791191.816 2736540.939 1.65650454 1.011566861 1.300451237 1.013352192 1.370800652 1.207271252 1.413079492 1.233834833 1.385395614 1 21.38392201 -2.182101282 2.373172853 0.257115857 1.27456718 0.180821019 0.181897204 5143944.207 1329356.827 20547118.73 0.040251803 0.006575045 2.182101282 1.017451323 WKDTDEADLVLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WKDTDEADLVLAK 13 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 ;;; 163.99 3.45E-05 1538830000 2863760 1694460 2352530 1557030 3281110 2775430 3004990 2491950 2745560 1483040 FALSE TRUE 2976823.456 1985470.324 2413838.864 1865005.887 2723388.094 2130878.445 2769451.032 2458549.486 2646747.832 1773613.293 1.678394872 1.119449393 1.36097247 1.051529042 1.535502753 1.20143351 1.561473993 1.386181247 1.492291381 1 20.75826006 3.161889026 24.09830216 1.388168023 1.293494587 0.009135016 0.221286318 95.51912465 30016.71261 0.059069035 0.070601039 1451.740613 -3.161889026 -0.094673435 WKEPGSGGPQNLS(ph)GPGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WKEPGSGGPQNLSGPGGR 18 1 Q9H0W8-2;Q9H0W8;M0R2N0;M0QZC7;M0QZH1;M0QX70;M0QYR7 Q9H0W8-2 SMG9 Protein SMG9 1 WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR 210.14 2.69E-16 1409660000 536200 439330 494140 448217 629450 690800 559920 517030 593790 477440 TRUE FALSE 557369.59 514781.51 507017.6943 536872.9848 522456.3138 530372.1692 516032.0073 510100.0585 572419.6139 570985.2269 0.976154135 0.901567126 0.887969899 0.940257225 0.915008461 0.928871964 0.903757196 0.893368225 1.002512126 1 19.12309389 1.229689904 24.99996635 1.001256142 0.915944546 0.644589681 0.024566169 121.7467187 343101.144 0.021784039 0.005769261 16.97031501 -1.229689904 -0.085311595 WKGYDS(ph)EDDTWEPEQHLVNCEEYIHDFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WKGYDSEDDTWEPEQHLVNCEEYIHDFNR 29 1 Q9Y232;Q9Y232-2 Q9Y232 CDYL Chromodomain Y-like protein 1 WKGYDS(0.866)EDDT(0.134)WEPEQHLVNCEEYIHDFNR 155.28 8.10E-09 77233000 20428 15959 16294 13851 20923 21152 20197 17494 18304 13560 TRUE FALSE 21234.51321 18699.83411 16718.63503 16590.68646 17366.51593 16239.76856 18613.90636 17259.52154 17645.24262 16216.82238 1.309412702 1.153113333 1.030943957 1.02305409 1.070895119 1.001414962 1.147814654 1.064297378 1.088082622 1 13.98520354 4.613325716 2.599803827 1.058841776 1.328925175 0.771663125 0.042847022 0.167174 1.724311029 0.010557392 0.086094514 41051.18671 -4.613325716 0.270083399 WKGYT(ph)SDDDTWEPEIHLEDCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WKGYTSDDDTWEPEIHLEDCK 21 1 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 WKGY(0.005)T(0.492)S(0.492)DDDT(0.012)WEPEIHLEDCK;WKGYT(0.5)S(0.5)DDDTWEPEIHLEDCK;WKGYT(0.5)S(0.5)DDDTWEPEIHLEDCK 176.09 1.26E-12 331784000 419568 285343 336582 259469 497920 452551 412948 349576 399984 232458 TRUE FALSE 436132.8686 334348.4406 345353.6034 310791.1938 413283.7363 347452.8887 380580.0567 344890.5055 385588.654 278003.6944 1.56880242 1.20267625 1.24226264 1.117939078 1.486612389 1.249813926 1.368974817 1.240596843 1.386991115 1 18.08474453 -1.287678536 3.566230728 0.999116824 1.306896307 0.34677051 0.130215124 4771020.026 5168348.352 27153.84757 0.028283602 0.051561016 1.287678536 0.307779483 WKLGDDIDLIVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WKLGDDIDLIVR 12 1 O15371-2;O15371;O15371-3 O15371-2 EIF3D Eukaryotic translation initiation factor 3 subunit D 0 ; 136.99 9.14E-05 416000000 524360 502210 542140 431980 746990 643800 538310 562680 583950 500660 FALSE TRUE 545062.1377 588460.6608 556268.6138 517424.3547 620016.9066 494287.2069 496115.8556 555138.195 562933.7536 598754.7413 0.910326216 0.982807517 0.92904252 0.864167445 1.035510642 0.825525332 0.828579419 0.92715457 0.940174189 1 19.19160565 4.000679526 24.98294716 0.909940581 0.948906408 0.021707018 0.066005607 73.6252091 2706340.813 0.016139252 0.034363606 10015.6589 -4.000679526 0.038965827 WKPDYDSAASEYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WKPDYDSAASEYGK 14 1 Q99747;J3KTJ6 Q99747 NAPG Gamma-soluble NSF attachment protein 0 ; 169.25 3.07E-06 645040000 924220 603510 800240 583300 1057710 936770 936510 770510 920760 602700 FALSE TRUE 960708.9193 707158.1478 821094.9118 698674.999 877920.832 719219.3644 863103.8991 760182.5738 887622.0275 720787.5256 1.33286008 0.981090991 1.139163599 0.969321713 1.218002256 0.997824378 1.197445667 1.054655563 1.231461417 1 19.45921452 4.756346281 24.27180925 1.09188283 1.332860381 0.362835416 0.097333786 2571.03692 3508566.669 0.020539171 0.627050108 57061.90687 -4.756346281 0.240977551 WKS(ph)DVALNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WKSDVALNGR 10 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 WKS(1)DVALNGR;WKS(1)DVALNGR 143.58 2.04E-05 874910000 1164470 812880 1030300 800440 1427990 1329390 1155950 894680 969730 790300 TRUE FALSE 1210444.175 952485.8167 1057150.464 958764.6429 1185260.77 1020659.32 1065343.618 882688.278 934829.6067 945144.1538 1.280697944 1.007767771 1.118507119 1.014411018 1.254052903 1.07989804 1.127175801 0.933919206 0.9890868 1 19.85017486 1.756283516 10.19112354 0.9723446 1.120110842 0.401214959 0.08469747 0.141451823 62.47450725 0.037491079 0.020481332 57.05366083 -1.756283516 0.147766242 WLAES(ph)PVGLPPEEEDKLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WLAESPVGLPPEEEDKLTR 19 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 WLAES(1)PVGLPPEEEDKLTR;WLAES(1)PVGLPPEEEDKLTR 112.47 0.00011867 131866000 167747 122801 139814 121163 177854 173251 154597 154950 137607 122876 TRUE FALSE 174369.7811 143891.1165 143457.6677 145128.6798 147622.4406 133016.0809 142479.2832 152873.1487 132654.551 146951.1996 1.186582903 0.979176195 0.976226585 0.987597789 1.004567782 0.905171793 0.969568697 1.040298746 0.902711589 1 17.16497761 4.738570781 7.625546879 0.97706777 1.188709531 0.715553266 0.040182077 0.051972236 31.1220841 0.00947869 0.056671307 54773.53631 -4.738570781 0.211641761 WLAVDYENVRPDIVLLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WLAVDYENVRPDIVLLGK 18 1 P04181;P04181-2 P04181 OAT "Ornithine aminotransferase, mitochondrial;Ornithine aminotransferase, hepatic form;Ornithine aminotransferase, renal form" 0 156.49 1.02E-08 114600000 96488 71597 86245 73238 80964 118210 69949 63531 87734 74776 FALSE TRUE 100297.4207 83893.2278 88492.61555 87724.25781 67201.7682 90757.51899 64466.2146 62679.47086 84576.47048 89426.92553 1.121557296 0.938120452 0.989552252 0.980960234 0.751471302 1.014879114 0.720881482 0.700901552 0.945760686 1 16.44842166 3.886206934 0.75471057 0.82075704 1.092551226 0.259230006 0.115951915 1.267959402 1.139129111 0.05160514 0.242582086 7694.970053 -3.886206934 0.271794186 WLDDLLAS(ph)PPPSGGGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WLDDLLAS(0.999)PPPS(0.001)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 208.43 5.44E-12 1883081000 797385 933374 896365 921054 1093569 1198245 964311 1023275 1001496 1142284 TRUE FALSE 828866.3755 1093673.724 919725.0083 1103235.732 907684.532 919970.7583 888725.7841 1009559.672 965452.3546 1366092.679 0.606742418 0.800585305 0.673252278 0.807584836 0.664438472 0.673432171 0.650560388 0.739012578 0.70672537 1 20.38162393 -0.061425623 1.277757135 1.000976854 0.70432364 0.682649654 0.060855265 9.523154661 10.66977591 0.092206878 0.016113449 0.868109237 0.061425623 -0.296653214 WLDES(ph)DAEMELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 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;WLDES(1)DAEMELR;WLDES(1)DAEMELR 265.34 1.36E-21 4514140000 3929848 5351273 3742627 5608328 4374305 6127660 3928048 4003338 3710921 6803944 TRUE FALSE 4085001.434 6270312.511 3840162.934 6717638.539 3630762.199 4704603.831 3620157.334 3949679.802 3577365.678 8137046.557 0.502025078 0.770588255 0.471935721 0.825562259 0.446201478 0.578170937 0.444898196 0.485394765 0.439639328 1 22.95607381 -1.016143738 9.205812287 1 0.551848359 0.512780329 0.131123704 8.98E-10 9.91E-11 0.1224464 0.028860893 0.096351008 1.016143738 -0.448151642 WLEKEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WLEKEER 7 1 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-6;B4DWJ1 E7ESA6 PTK2 Focal adhesion kinase 1 0 66.429 0.061922 135650000 782190 501320 657680 454910 915170 795590 793310 694450 804430 567600 FALSE TRUE 813071.4652 587417.8103 674819.6811 544889.8402 759609.7303 610826.2798 731128.2893 685142.0336 775478.7214 678810.3526 1.19778884 0.865363659 0.99412108 0.80271292 1.119030856 0.899848209 1.07707298 1.009327614 1.142408507 1 19.37264904 2.213000023 24.99756128 1.053448792 0.973537474 0.096750328 0.114659845 522.5061925 510993.3266 0.040157429 0.029668432 163.3052035 -2.213000023 -0.079911318 WLFETQPMESLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WLFETQPMESLYEK 14 0 A0A5F9ZH43;A4UGR9-2;A4UGR9-3;A4UGR9;A4UGR9-8 A0A5F9ZH43 XIRP2 Xin actin-binding repeat-containing protein 2 0 54.524 0.080944 471440000 402110 518470 1331900 384500 1293700 760030 1189000 729280 918810 594430 FALSE TRUE 417985.6133 607513.1894 1366610.408 460552.9524 1073797.336 583524.5509 1095803.073 719505.1945 885742.2076 710897.1775 0.587969156 0.854572516 1.922374222 0.64784749 1.510481924 0.820828341 1.541436804 1.012108667 1.245949816 1 19.43928138 4.467154656 24.99502119 1.209425422 0.65461962 0.248187325 0.355543142 208.528294 522964.7043 0.077196987 0.211928814 29319.37147 -4.467154656 -0.554805802 WLFTEIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WLFTEIR 7 0 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 ; 122.79 0.010019 216220000 370100 642200 593750 610340 650010 807530 522540 577180 546950 893060 FALSE TRUE 384711.8338 752492.8544 609223.6128 731063.4303 539521.5324 619993.3957 481581.9494 569443.8462 527265.3763 1068038.008 0.360204254 0.70455625 0.570413794 0.684491961 0.505151997 0.580497502 0.450903381 0.533168147 0.493676603 1 20.02653156 -1.679698986 2.888841009 1.053762139 0.547321628 0.666010543 0.097127798 22919883.58 22936766.93 9104282.239 0.021969115 0.020907447 1.679698986 -0.506440511 WLHNEDQMAVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 13 WLHNEDQMAVEK 12 0 P37837 P37837 TALDO1 Transaldolase 0 ;;;;;;;;;;;; 231.52 3.24E-12 11358620000 14252110 12613920 14527530 11810210 19748420 18827050 16755930 15026710 15637860 13588960 FALSE TRUE 14814794.31 14780262.64 14906129.37 14146234.29 16391590.62 14454752.96 15442556.42 14825301.53 15075056.47 16251456.54 0.91159794 0.909473105 0.917218056 0.870459473 1.008622863 0.889443536 0.950225993 0.912244481 0.927612638 1 23.95406569 -5 0.222016659 1.398641951 0.912098457 0.31778345 0.03496854 179.2304689 1.793725095 32.01095238 0.061030427 1.00E-05 5 -0.486543494 WLIS(ph)PVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WLISPVK 7 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 WLIS(1)PVK;WLIS(1)PVK 92.051 0.016735 587230000 1717890 1177740 1376250 1042480 1751530 1840290 1695080 1397330 1421610 1108330 TRUE FALSE 1785713.624 1380007.683 1412116.206 1248679.433 1453805.556 1412910.537 1562215.2 1378601.077 1370446.534 1325486.043 1.347214203 1.041133319 1.06535728 0.942054003 1.096809403 1.065956556 1.178598001 1.040072118 1.033920003 1 20.33809005 4.740437867 24.92338578 1.056763425 1.347214306 0.697407785 0.058335902 91.16178736 1210216.034 0.013938331 0.090608852 55009.52143 -4.740437867 0.290450881 WLKEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WLKEDK 6 1 A0A087WVQ6;Q00610-2;Q00610;P53675;P53675-2;A0A087WX41 A0A087WVQ6;P53675 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 ; 78.496 0.063503 952540000 1193780 549780 844300 683960 1076830 967090 1159390 758930 910640 446540 FALSE TRUE 1240911.356 644200.4383 866303.1516 819245.2466 893790.8212 742498.0039 1068513.982 748757.7847 877866.2443 534030.9635 2.323669302 1.206297916 1.622196485 1.534078176 1.673668537 1.390365081 2.000846497 1.402086838 1.643848961 1 19.02656387 -2.539535688 0.355926708 2.23E-11 1.648665206 0.292945796 0.302075762 77.65019074 3.122512694 60.29434417 0.206990814 0.002887117 2.539535688 1.648665206 WLKEDKLECSEELGDLVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 172.84 5.51E-12 1156400000 1739700 594080 1142600 672340 1678600 1301900 1364500 1045500 1234900 508580 FALSE TRUE 1808384.699 696108.6187 1172377.095 805326.8453 1393272.172 999553.4555 1257546.925 1031486.783 1190456.19 608226.5136 2.973209255 1.144489106 1.927533687 1.324057448 2.290712654 1.64339014 2.067563476 1.6958925 1.957257968 1 19.21424918 -1.652037818 2.400175009 0.875207835 1.853988312 0.229538836 0.485657633 7499090.236 5814309.668 5754190.344 0.110332535 0.022282411 1.652037818 0.978780477 WLPEEDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WLPEEDFR 8 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 ;;; 102.72 0.011425 228957000 374278 520534 439501 437125 506317 534485 454960 448141 440293 500736 FALSE TRUE 389054.7844 609931.6653 450954.7571 523587.0203 420253.4172 410358.9589 419299.0464 442134.4029 424446.9409 598845.632 0.64967458 1.018512339 0.753040071 0.874327193 0.701772535 0.685249983 0.700178851 0.738311143 0.708775214 1 19.19182463 WLPLGLGLNHLGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WLPLGLGLNHLGK 13 0 Q13200;Q13200-3;Q13200-2;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 ; 209.85 3.46E-08 475940000 876430 740730 881620 800900 1110550 1152360 1121610 963380 990290 754510 FALSE TRUE 911032.1332 867944.6154 904595.7415 959315.6296 921779.1077 884741.8542 1033695.277 950467.4669 954649.6563 902341.7885 1.009630879 0.961880106 1.002497893 1.063139978 1.021540972 0.980495268 1.145569551 1.053334201 1.057969018 1 19.78331447 3.603626919 0.820704302 1.05938357 0.979367995 0.200780396 0.044711731 1.067893364 1.37441975 0.020041169 0.058260435 4014.458001 -3.603626919 -0.080015576 WLSTSIPEAQWHSS(ph)LAR ddPTM_MDA-MB-175_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 1 WLSTSIPEAQWHS(0.115)S(0.885)LAR;WLSTSIPEAQWHS(0.007)S(0.993)LAR 208.98 3.02E-12 275940000 207589 290260 307650 268060 373270 333920 239480 265550 267720 338940 TRUE FALSE 215784.774 340109.8971 315667.6117 321081.4679 309821.6987 256372.1406 220708.9318 261990.7366 258084.8095 405348.8036 0.532343434 0.839054893 0.778755504 0.792111547 0.764333571 0.632472918 0.544491386 0.646334057 0.636698091 1 18.62880436 -1.127764354 5.039163226 1.000012587 0.687196857 0.47146141 0.099980024 1.50E-05 2.59E-06 0.102470824 0.024151633 0.074513617 1.127764354 -0.31281573 WLSTSIPEAQWHSSLAR ddPTM_MDA-MB-175_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 ; 244.97 1.51E-20 15869900000 273380 2659100 2026870 2790100 1913730 3494500 1429010 2514700 1663900 3270100 FALSE TRUE 284173.2535 3115779.74 2079691.897 3341973.452 1588434.858 2682955.335 1317000.462 2480994.56 1604016.564 3910813.485 0.072663464 0.796708857 0.531779873 0.854546878 0.406164821 0.686035104 0.336758699 0.634393476 0.410149083 1 21.8990373 -2.107179798 2.492127232 1.845022471 0.5431655 0.289466248 0.221482502 34016393.7 11680133.06 162522639.7 0.048978531 0.007813043 2.107179798 -1.301856971 WLVEYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WLVEYGR 7 0 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5;Q9UPT5-4;C9JKC2 A0A0A0MRE1 EXOC7 Exocyst complex component 7 0 95.62 0.031016 23123000 40107 44815 39173 40855 51155 57143 54057 46910 42785 45379 FALSE TRUE 41690.45533 52511.62764 40193.88056 48935.99706 42459.69137 43872.40426 49819.87109 46281.24818 41245.17621 54270.14622 0.768202377 0.967596944 0.740625986 0.90171117 0.78237658 0.808407703 0.917997731 0.852793873 0.759997514 1 15.72787118 -1.526119728 3.168150711 1.005068687 0.839134147 0.322115033 0.072102665 27912910.48 27721666.52 1182003.18 0.016037216 0.029776954 1.526119728 -0.16593454 WMDEAQALDTADRFINSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WMDEAQALDTADRFINSK 18 1 A0A0B4J1W3;Q9BXJ9;Q9BXJ9-4 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 0 113.47 0.0002243 138830000 107460 107500 119200 89941 170690 165310 97065 128180 146560 167800 FALSE TRUE 111702.6038 125962.2888 122306.4499 107731.0614 141676.1748 126919.2578 89456.79167 126461.9568 141285.3342 200677.1973 0.556628283 0.627686107 0.609468597 0.536837582 0.7059904 0.632454806 0.445774572 0.630176016 0.704042792 1 17.61451717 0.833714204 2.179547769 0.999377978 0.591787025 0.779536583 0.065460973 0.271242918 2.371672392 0.062189327 0.017008264 6.81889815 -0.833714204 -0.407590952 WMGGAELSDDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WMGGAELSDDGR 12 0 P48147;A0A499FJL1 P48147 PREP Prolyl endopeptidase 0 129.16 0.00048861 0 82394 83247 81488 88426 98303 100630 83486 88566 80285 83537 FALSE TRUE 85646.97874 97544.02468 83611.64422 105916.3989 81593.49117 77260.20756 76942.14917 87378.91763 77395.55853 99904.47574 0.857288706 0.97637292 0.8369159 1.060176715 0.816715073 0.773340804 0.770157179 0.874624655 0.774695608 1 16.60826169 WMHPQVTPTDDSNPWWAAFSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WMHPQVTPTDDSNPWWAAFSR 21 0 A0A1B0GW23;Q03154;A0A1B0GU86;Q03154-2;Q03154-3;Q03154-4;C9JMV9 A0A1B0GW23 ACY1;ABHD14A-ACY1 Aminoacylase-1 0 111.11 0.0002562 377510000 659030 615250 755730 527500 843440 756660 811920 741410 709760 667450 FALSE TRUE 685049.0133 720914.4015 775424.9446 631837.9256 700072.3701 580937.1823 748279.5888 731472.6117 684215.8762 798224.0484 0.858216455 0.903147936 0.971437714 0.79155461 0.877037433 0.727787121 0.937430525 0.916375062 0.857172717 1 19.60643422 -1.219285293 5.329305752 1.000008657 0.874681305 0.248247465 0.067021733 6.86E-06 1.01E-06 0.064618184 0.0152296 0.060355202 1.219285293 -0.125327352 WMKWYGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WMKWYGK 7 1 Q8TEK3;Q8TEK3-1;C9JH95 Q8TEK3 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 0 74.639 0.02742 461650000 259140 219260 231800 247640 345230 330930 338800 257660 252080 223550 FALSE TRUE 269371.0473 256916.1994 237840.8984 296622.4529 286547.9279 254076.5228 312243.9707 254206.4891 243007.69 267350.3424 1.007558266 0.960972023 0.889622569 1.109489706 1.071806849 0.950350467 1.167920594 0.950836595 0.90894849 1 18.028372 3.749422807 24.96497278 1.024199533 0.953543069 0.14239196 0.078714362 1433.107396 3293754.537 0.020330365 0.036189799 5615.944494 -3.749422807 -0.070656463 WNDNCPSWNTIDPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WNDNCPSWNTIDPEER 16 0 P17655;P17655-2 P17655 CAPN2 Calpain-2 catalytic subunit 0 ; 147.18 2.45E-06 188509000 115648 105963 117591 129038 122641 132122 108477 120671 102426 120939 FALSE TRUE 120213.8723 124161.321 120655.5181 154561.3313 101794.5266 101438.6678 99974.28929 119053.6026 98739.70827 144634.6815 0.831155232 0.858447778 0.834208758 1.068632569 0.703804409 0.701344012 0.691219341 0.823133161 0.682683484 1 17.14205401 3.180126029 24.99992516 0.754661687 0.890720105 0.252121273 0.109064454 98.79857045 42268.14326 0.02990036 0.035737784 1514.000537 -3.180126029 0.136058418 WNGHTDMIDQDGLYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WNGHTDMIDQDGLYEK 16 0 Q9UHG3;Q9UHG3-2 Q9UHG3 PCYOX1 Prenylcysteine oxidase 1 0 81.157 0.013563 108450000 273660 121120 189020 122890 245590 245770 263100 156450 186760 90388 FALSE TRUE 284464.3081 141921.4178 193946.0165 147197.2752 203844.6995 188693.6422 242477.5345 154353.0437 180038.5441 108097.798 2.631545816 1.312898324 1.79417176 1.361704659 1.885743311 1.745582663 2.243131118 1.42790183 1.66551537 1 16.72197761 0.721222523 1.165611335 1.00530352 1.793494345 0.29043809 0.380206294 1.17599905 2.739029122 0.335936513 0.103831926 5.26286855 -0.721222523 0.788190825 WNRPGDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WNRPGDR 7 1 F8VX55;Q12800-2;Q12800-3;Q12800-4;Q12800;F8VWL0;C9JWL3;Q9NZI7-4;Q9NZI7 F8VX55 TFCP2;UBP1 Alpha-globin transcription factor CP2;Upstream-binding protein 1 0 ; 75.738 0.038902 174367000 157415 304020 261883 287858 264038 343340 225760 263946 224303 332100 FALSE TRUE 163629.8658 356233.0701 268707.8861 344795.4532 219156.9151 263604.4884 208064.3413 260408.2356 216230.3788 397168.6366 0.411990904 0.896931523 0.676558674 0.868133638 0.55179814 0.663709226 0.523869012 0.65566163 0.544429643 1 18.59939218 -1.140658317 5.000749651 1.000017563 0.651703777 0.358939507 0.142495248 2.62E-05 4.50E-06 0.129588644 0.030542797 0.072333867 1.140658317 -0.348313786 WNS(ph)NDFIDAFASPVEAEGTPEPGAEAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WNSNDFIDAFASPVEAEGTPEPGAEAAK 28 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK;WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK;WNS(1)NDFIDAFASPVEAEGTPEPGAEAAK 204.89 1.94E-25 274400000 452595 274396 368574 292593 513206 512988 498590 366951 409389 231870 TRUE FALSE 470463.8001 321521.3785 378179.3412 350467.0221 425971.4274 393854.3114 459509.213 362032.6221 394655.1699 277300.4871 1.696584831 1.159469217 1.363788954 1.26385289 1.5361366 1.420315974 1.657080439 1.305560715 1.423204027 1 18.08109062 0.148747322 1.409025962 0.999660534 1.418651998 0.388730339 0.159680696 10.56212189 16.23666765 0.152159156 0.042356829 1.408469094 -0.148747322 0.418991464 WNSIEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WNSIEER 7 0 Q9UNE7;Q9UNE7-2;H3BTA3;H3BS86;H3BUD0 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 ; 126.04 0.0092852 251500000 462600 567470 530720 521630 615300 709090 543050 517940 508350 606190 FALSE TRUE 480863.8052 664928.5582 544550.9992 624806.8571 510711.5258 544414.5939 500484.322 510997.8615 490054.5828 724961.3243 0.663295805 0.917191767 0.751144897 0.861848538 0.704467271 0.750956742 0.690360031 0.704862238 0.675973416 1 19.46754451 3.222818123 24.85461374 0.733114158 0.80348428 0.015152296 0.108160168 528.9355923 835093.8082 0.028532453 0.034213785 1670.390928 -3.222818123 0.070370122 WNSPAEEGSSDCEVFSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WNSPAEEGSSDCEVFSK 17 0 P34932;A0A087WYC1;A0A087WTS8 P34932 HSPA4 Heat shock 70 kDa protein 4 0 107.74 0.0031488 0 18285 37270 41563 33532 51410 53508 43765 45262 46760 42568 FALSE TRUE 19006.90592 43670.83258 42646.16592 40164.52952 42671.34656 41081.57792 40334.58494 44655.33692 45077.11673 50908.38459 0.373355118 0.857831827 0.837704167 0.788957062 0.838198794 0.806970762 0.792297482 0.877170574 0.885455649 1 15.63561567 4.73955822 24.98194863 0.84432243 0.373354967 0.857345236 0.058683321 27.14276864 679613.6548 0.012977542 0.079355501 54898.21454 -4.73955822 -0.470967463 WNTEDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WNTEDK 6 0 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ;;;; 157.86 0.022264 4825380000 3183100 2061050 2637330 2205470 3182890 3192720 3752200 2654260 2678510 1608060 FALSE TRUE 3308771.246 2415019.305 2706060.986 2641705.383 2641863.495 2451259.166 3458092.759 2618683.986 2582110.948 1923128.569 1.720514842 1.255776314 1.407113924 1.373649909 1.373732125 1.274620535 1.798159944 1.361679104 1.342661635 1 20.87502379 0.803403117 2.256167996 1.000820219 1.440913891 0.388397931 0.168299724 0.763820439 6.609401925 0.153003115 0.041576458 6.359209271 -0.803403117 0.440093672 WNTEDKVSHVSTGGGASLELLEGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WNTEDKVSHVSTGGGASLELLEGK 24 1 P00558;P00558-2;P07205 P00558;P07205 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 ; 147.93 1.02E-07 832294000 412207 1121321 1276347 868594 1805110 1610320 1184445 1485330 1459790 1110681 FALSE TRUE 428481.2507 1313899.159 1309609.651 1040399.301 1498278.047 1236347.585 1091605.106 1465421.581 1407252.443 1328297.677 0.322579237 0.989160173 0.985930845 0.783257638 1.127968582 0.93077599 0.821807585 1.103232812 1.059440566 1 20.34114707 4.739203942 24.74876382 0.977160277 0.32257901 0.778421007 0.104897211 20.58894208 791862.3006 0.024685248 0.147497971 54853.44926 -4.739203942 -0.654581267 WNTTLYEGTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WNTTLYEGTWR 11 0 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 197.21 0.0020022 0 142360 125830 100990 144230 147520 161230 133040 137920 133930 115430 FALSE TRUE 147980.4827 147440.3237 103621.8824 172758.2635 122444.6031 123786.776 122611.9772 136071.408 129109.8855 138046.2985 1.071962699 1.068049816 0.750631372 1.251451618 0.886982154 0.896704782 0.888194602 0.985693999 0.935265102 1 17.07479268 WNWLTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WNWLTR 6 0 A0A0A0MSJ0;Q86XP3-2;Q86XP3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 0 114.54 0.058621 305610000 165410 181250 185350 173890 248600 256260 211220 202890 191470 194120 FALSE TRUE 171940.5145 212378.2776 190180.3733 208284.923 206343.0608 196747.4987 194664.0245 200170.5914 184579.0321 232154.0973 0.740630971 0.914815978 0.819198866 0.89718392 0.88881938 0.847486652 0.838512121 0.862231568 0.79507118 1 17.82472322 -2.468637977 2.226838166 2.66074826 0.849797328 0.470443444 0.049123777 2966516.091 211656.9627 25072587.69 0.011425051 0.003399085 2.468637977 -1.810950932 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WNYRDEADVLEVDQGFDDHNLPCDVIWLDIEHADGKR 37 2 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ;; 284.3 3.23E-77 878860000 341061 343597 370085 313157 504397 486270 307921 339409 394575 316935 FALSE TRUE 354526.3516 402607.1119 379729.7191 375098.5199 418659.7781 373341.162 283785.3474 334859.7775 380374.3228 379032.3452 0.935345904 1.062197243 1.00183988 0.9896214 1.104548948 0.984984967 0.748710106 0.883459636 1.003540536 1 18.53196144 2.46017471 24.98710812 0.888989349 1.021192646 0.288610924 0.079072605 243.8200192 359502.3349 0.026782831 0.022412423 288.5191936 -2.46017471 0.132203296 WPAS(ph)PGSHSNDDFDNWSTFRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPASPGSHSNDDFDNWSTFRPR 22 1 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 WPAS(0.999)PGS(0.001)HSNDDFDNWSTFRPR 169.01 5.30E-12 136550000 82852 64712 66183 67215 78419 92517 66635 59953 71012 72230 TRUE FALSE 86123.06094 75825.78261 67907.78335 80509.92638 65089.36639 71031.32886 61411.97458 59149.4281 68456.29199 86382.08557 0.997001408 0.877795229 0.786132714 0.9320211 0.753505382 0.822292358 0.71093415 0.684741839 0.79248251 1 16.39844453 3.230075393 24.96221998 0.767837117 0.888769952 0.190165338 0.095947963 239.3679649 704182.4574 0.027001732 0.032765663 1698.538492 -3.230075393 0.120932835 WPFSGKT(ph)SPPCSPANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.019)GKT(0.68)S(0.301)PPCS(0.001)PANLSR 92.336 0.0038052 1998800000 710040 605910 896690 602170 982330 944850 743130 776170 837660 691440 TRUE FALSE 738072.9275 709970.3292 920058.478 721277.4287 815353.8975 725422.9068 684881.5288 765766.7107 807512.7802 826914.4296 0.892562641 0.858577749 1.112640492 0.872251593 0.986019675 0.877264782 0.828237487 0.926053148 0.976537295 1 19.65737852 2.730143496 24.74229135 0.910098183 0.944979239 0.009531431 0.08113378 2152.125145 6326196.361 0.025788992 0.024678686 537.2092669 -2.730143496 0.034881056 WPFSGKTS(ph)PPCS(ph)PANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 2 WPFS(0.022)GKT(0.072)S(0.906)PPCS(0.999)PANLS(0.001)R;WPFS(0.001)GKT(0.173)S(0.826)PPCS(1)PANLSR 117.4 7.54E-05 1745300000 2328400 1823190 1924560 1303750 2770800 2660100 1721090 1862280 2229800 2008650 TRUE FALSE 2420327.03 2136308.7 1974715.615 1561627.859 2299820.406 2042332.089 1586186.469 1837319.183 2149549.934 2402206.51 1.007543282 0.889311011 0.822042404 0.650080604 0.957378309 0.850190057 0.660303959 0.764846476 0.894823124 1 21.19592875 4.567753275 2.317999306 0.805426337 1.021149395 0.193591897 0.108650254 0.576397454 4.7327221 0.026989608 0.215645899 36961.81383 -4.567753275 0.215723058 WPFSGKTS(ph)PPCSPANLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPFSGKTSPPCSPANLSR 18 1 P49585;C9JEJ2 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 1 WPFS(0.002)GKT(0.271)S(0.723)PPCS(0.004)PANLSR 86.073 0.002129 2135800000 627130 590130 760100 456510 849680 880800 643600 676890 756770 561790 TRUE FALSE 651889.5766 691480.2369 779908.8304 546806.3155 705251.6971 676247.5487 593152.9503 667817.3967 729533.9955 671861.9944 0.970273035 1.02919981 1.160817008 0.813867014 1.049697264 1.006527463 0.882849388 0.993980017 1.085839059 1 19.3578054 5.145998453 10.63527094 0.997445001 0.000357103 0.008194127 0.092291197 12133501.38 13246677.38 0.021973939 283876387.5 139958.2338 -5.145998453 -0.997087898 WPS(ph)DSWIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPSDSWIR 8 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 WPS(0.993)DS(0.007)WIR 85.29 0.017672 65508000 54137 63998 61753 57273 74944 78776 64633 66178 64674 56542 TRUE FALSE 56274.37056 74989.15866 63362.33391 68601.42846 62205.04565 60481.46786 59566.89657 65290.99216 62346.39537 67620.32234 0.832210919 1.108973694 0.937030936 1.014509042 0.919916432 0.894427382 0.880902287 0.965552809 0.922006776 1 16.04516927 3.218550075 24.75225941 0.926276344 0.980298461 0.073068434 0.071860518 447.3119426 553305.9705 0.019326788 0.023128292 1654.055488 -3.218550075 0.054022117 WPS(ph)VSSLDSALESSPSLHSPADPSHLSPPAS(ph)SPRPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 2 WPS(0.673)VS(0.149)S(0.176)LDS(0.003)ALESSPSLHSPADPS(0.001)HLS(0.285)PPAS(0.503)S(0.202)PRPS(0.009)R 153.44 7.09E-14 39728000 2163 7168.8 5987.4 5573.3 5684.7 7316.2 4733.8 7454.8 5481.4 8918.6 TRUE FALSE 2248.39691 8399.985634 6143.436563 6675.682105 4718.416725 5617.123428 4362.752387 7354.8806 5284.125485 10666.02891 0.210799814 0.78754574 0.575981615 0.625882619 0.442378017 0.526636809 0.409032492 0.689561285 0.495416385 1 13.38073552 -1.041220662 0.617944435 1.118104387 0.537540225 0.461951287 0.151741747 26.37075345 5.40224428 5.847268999 0.055089969 0.090945107 1.041220662 -0.580564162 WPSVSS(ph)LDSALESSPSLHSPADPSHLSPPASS(ph)PRPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 2 WPS(0.314)VS(0.269)S(0.329)LDS(0.088)ALESSPSLHSPADPS(0.001)HLS(0.031)PPAS(0.332)S(0.589)PRPS(0.047)R 83.947 0.00046658 40983000 0 5939.8 5183.4 9919.9 8585.5 8692.2 6899.5 4913 3920.7 5680.1 TRUE FALSE 0 6959.914445 5318.483662 11882.02661 7126.139777 6673.568282 6358.699162 4847.149271 3779.594773 6793.006843 0 1.024570504 0.782935125 1.749155696 1.049040571 0.982417424 0.936065473 0.713549888 0.55639496 1 12.72983459 -1.41590424 3.750600336 1.000685792 0.893291144 0.005408661 0.417099856 68261399.5 25770844.77 381644.2246 0.096729806 0.038379186 1.41590424 -0.107394648 WPSVSSLDSALESSPSLHSPADPSHLSPPAS(ph)SPRPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WPSVSSLDSALESSPSLHSPADPSHLSPPASSPRPSR 37 1 O15211 O15211 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 WPSVSSLDSALESSPSLHSPADPSHLS(0.079)PPAS(0.539)S(0.368)PRPS(0.014)R 201.96 1.41E-30 87812000 3301.2 5816.2 5168 4231.6 5135.9 7852.8 4255.9 7345.8 6542.1 7178.2 TRUE FALSE 3431.533925 6815.087106 5302.682326 5068.59785 4262.901552 6029.10621 3922.311437 7247.341566 6306.651099 8584.630855 0.399729934 0.793870723 0.617694857 0.590427001 0.496573659 0.702313974 0.456899254 0.844222855 0.734644413 1 13.06754038 1.155706 1.046192275 0.985696227 0.591550507 0.512132013 0.124363569 0.373026769 0.865049397 0.10833923 0.036170676 14.31218692 -1.155706 -0.394145719 WQDEDGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WQDEDGKK 8 1 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;;; 107.15 0.0065062 4645970000 8698010 3651930 5333710 3419940 8081500 6393920 7348930 5489710 6359780 3147840 FALSE TRUE 9041414.151 4279120.569 5472710.864 4096393.924 6707809.517 4909028.981 6772901.664 5416129.417 6130892.76 3764598.979 2.401693833 1.136673678 1.453730104 1.088135535 1.7818125 1.303997852 1.799103092 1.43870023 1.628564634 1 21.84406476 -2.128771961 2.126688969 0.00023837 1.532138614 0.172375985 0.363247778 5878223.678 1391121.581 28367349.69 0.079910057 0.007434094 2.128771961 1.531900244 WQGGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 872430000 560170 794950 662590 822760 800150 961510 678090 731210 679280 951080 FALSE TRUE 582285.9441 931476.4786 679857.6397 985499.4723 664140.7888 738213.8743 624939.5339 721409.326 654832.8455 1137425.916 0.511933072 0.818933757 0.597715974 0.866429592 0.583898062 0.6490215 0.549433176 0.634247308 0.575714722 1 20.11734115 -1.900400661 4.944970688 1.113606758 0.6468819 0.494440286 0.108223704 0.062697579 0.001262826 0.048469345 0.023074388 0.012577645 1.900400661 -0.466724857 WQMNPYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WQMNPYDR 8 0 F1T0B3;A0A087X2G1;Q92499;Q92499-2 F1T0B3 DDX1 ATP-dependent RNA helicase DDX1 0 78.77 0.069246 99079000 103160 89923 73513 45768 164660 128230 79901 54549 64761 192620 FALSE TRUE 107232.8365 105366.5757 75428.80917 54820.7738 136671.152 98450.52584 73638.15084 53817.85988 62430.26426 230360.2011 0.465500707 0.457399218 0.327438545 0.237978494 0.593293248 0.427376454 0.319665248 0.233624817 0.271011503 1 17.81353196 -1.398082294 3.538693846 1.00471015 0.364080849 0.747446824 0.109743725 65843386.78 104846856.3 3211656.569 0.029164993 0.039986897 1.398082294 -0.640629301 WQPDTEEEYEDSSGNVVNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WQPDTEEEYEDSSGNVVNKK 20 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 189.48 3.49E-17 637130000 253585 143499 210703 136239 299875 265568 248644 198432 228699 138917 FALSE TRUE 263596.7316 168143.837 216194.0933 163186.6676 248902.3546 203893.8567 229154.6336 195772.3436 220468.1677 166135.1264 1.58664057 1.012090824 1.301314767 0.982252646 1.498192224 1.227277224 1.379326808 1.178392239 1.327041261 1 17.34199761 -1.393807274 3.086660273 0.996448222 1.264269006 0.17038595 0.181401437 31618522.52 37087246.49 982761.5902 0.039424845 0.040382456 1.393807274 0.267820784 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR;WQRPS(0.596)S(0.404)PPPFLPAASEEAEPAEGLR 163.29 1.10E-11 5043152000 881217 998118 996589 1136343 1091134 1221751 1148536 1045435 1009522 1030774 TRUE FALSE 916008.1276 1169537.002 1022560.928 1361108.254 905663.4324 938017.8461 1058510.747 1031422.654 973189.5004 1232734.43 0.743070126 0.948733948 0.829506261 1.104137453 0.73467846 0.760924513 0.858668925 0.836694935 0.789455926 1 20.2334306 4.771791023 22.25748488 0.864629069 0.743069114 0.110106563 0.108676326 7678.549444 5142637.56 0.025187065 3.135535042 59127.70513 -4.771791023 -0.121559955 WQRPS(ph)SPPPFLPAASEEAEPAEGLRVPGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLRVPGLAK 124.97 3.53E-06 49337000 35411 31746 32289 25633 48996 49995 31405 38735 42540 44574 TRUE FALSE 36809.05362 37198.12855 33130.47787 30703.13089 40667.67742 38384.41893 28943.39404 38215.82068 41008.99371 53307.42188 0.69050523 0.697803931 0.621498409 0.57596353 0.762889594 0.720057688 0.542952426 0.716894934 0.769292385 1 15.70204879 0.863404511 1.8124983 0.998968496 0.661573036 0.719206594 0.063762806 0.277095723 1.766385604 0.060671664 0.017136476 7.301372587 -0.863404511 -0.337395461 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.415)S(0.585)PPPFLPAASEEAEPAEGLR;WQRPS(0.198)S(0.802)PPPFLPAASEEAEPAEGLR;WQRPS(0.177)S(0.823)PPPFLPAASEEAEPAEGLR 203.96 3.00E-25 4819130000 1088240 1116980 1083650 1188530 1094550 1421190 1295010 1152630 1165500 1061240 TRUE FALSE 1131204.556 1308812.626 1111890.809 1423617.687 908498.782 1091140.161 1193503.732 1137180.88 1123553.883 1269169.659 0.891294987 1.031235357 0.876077364 1.121692184 0.715821384 0.859727581 0.940381551 0.896003834 0.885266894 1 20.27545351 3.246301957 24.99994434 0.881905143 0.976300825 0.206171899 0.093316061 284.9921594 920349.7621 0.024747122 0.032896661 1763.201542 -3.246301957 0.094395682 WQRPSS(ph)PPPFLPAASEEAEPAEGLRVPGLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3 H3BLU1 TPRN Taperin 1 WQRPS(0.423)S(0.577)PPPFLPAASEEAEPAEGLRVPGLAK;WQRPS(0.412)S(0.588)PPPFLPAASEEAEPAEGLRVPGLAK;WQRPS(0.426)S(0.574)PPPFLPAASEEAEPAEGLRVPGLAK 161.3 1.01E-12 1738258000 681482 678293 776155 524269 999840 1039185 656424 744076 855985 908103 TRUE FALSE 708387.4356 794784.5464 796382.2369 627967.8434 829887.5539 797850.0328 604971.7716 734102.8783 825178.2671 1086028.396 0.652273401 0.731826672 0.733297803 0.578224147 0.764149038 0.734649329 0.557049681 0.675951827 0.759812791 1 20.05063039 0.85497779 3.034655709 0.999807573 0.677882246 0.69099594 0.064737993 0.339211938 5.76485225 0.061704189 0.016149955 7.161067865 -0.85497779 -0.321925327 WQS(ph)PVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 WQSPVTK 7 0 A9Z1X7 A9Z1X7 SRRM1 1 WQS(0.999)PVT(0.001)K;WQS(0.999)PVT(0.001)K;WQS(0.998)PVT(0.002)K;WQS(1)PVTK;WQS(1)PVTK;WQS(0.999)PVT(0.001)K;WQS(1)PVTK;WQS(0.998)PVT(0.002)K 142.98 0.0025726 33018640000 18979290 13991520 16946070 13240450 19333580 19624120 19197490 16362110 17024960 12409880 TRUE FALSE 19728607.02 16394454.72 17387698.51 15859371.49 16047264.98 15066715.54 17692740.57 16142802.68 16412235.02 14841358.38 1.329299281 1.104646509 1.171570557 1.068592987 1.081253115 1.015184402 1.192124071 1.087690376 1.105844532 1 23.82311981 WQTMIEAHVDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WQTMIEAHVDVK 12 0 P61247;E9PFI5;D6RG13;H0Y8L7;D6RAT0;D6RB09;D6RAS7;D6RED7 P61247 RPS3A 40S ribosomal protein S3a 0 ; 94.728 0.0021111 287260000 477660 615130 707420 690550 764880 947480 762520 788420 750420 641820 FALSE TRUE 496518.3856 720773.7925 725855.9464 827138.7289 634865.9708 727442.1292 702751.6899 777852.5195 723412.5308 767572.3406 0.646868522 0.93903044 0.945651514 1.077603615 0.827108974 0.947718007 0.915551086 1.013393108 0.942468211 1 19.5499432 4.741660096 4.345365564 0.958204994 0.623288193 0.691897129 0.062107596 0.114330986 5.165079508 0.014446236 0.118770466 55164.55209 -4.741660096 -0.334916801 WQVVDTPGILDHPLEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WQVVDTPGILDHPLEDR 17 0 Q9BZE4-2;Q9BZE4;Q9BZE4-3 Q9BZE4-2 GTPBP4 Nucleolar GTP-binding protein 1 0 ;; 194.51 7.04E-11 237564000 159740 189682 185648 186536 189649 223332 223817 193895 180446 150737 FALSE TRUE 166046.6585 222258.408 190486.1394 223432.264 157412.5307 171466.5276 206273.6387 191296.1547 173951.7837 180271.0291 0.921094528 1.232912515 1.056665291 1.239424133 0.873199268 0.951159643 1.144241755 1.06115861 0.964945863 1 17.45980804 3.244799732 24.99999981 1.013842466 1.117133332 0.202667 0.107695147 265.7193137 1064724.933 0.029765048 0.039334355 1757.113164 -3.244799732 0.103290867 WRCPVPT(ph)LPGCQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WRCPVPTLPGCQK 13 1 E5RJ64 E5RJ64 C8orf58 1 WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK;WRCPVPT(1)LPGCQK 75.78 0.049241 1526440000 166065 3278530 1136110 2524760 571020 1907060 461050 1071100 694750 6332400 TRUE FALSE 172621.3744 3841592.024 1165717.96 3024149.992 473958.2244 1464174.217 424911.6963 1056743.656 669746.0832 7573112.539 0.02279398 0.507267257 0.153928514 0.399327222 0.062584337 0.1933385 0.056107934 0.139538882 0.08843736 1 22.85245494 -1.539152753 4.244529287 1.009029799 0.183872969 0.7331327 0.148339277 0.012141831 0.001318292 0.137581731 0.032326095 0.028896633 1.539152753 -0.82515683 WREEQMER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 WREEQMER 8 1 P09496-2;F8WF69;P09496-4;P09496-3;P09496 P09496-2 CLTA Clathrin light chain A 0 ;;;;;; 186.78 0.00018757 4793950000 3244680 2544860 2553210 2239760 3543290 3643770 2733050 2445140 2448450 3210630 FALSE TRUE 3372782.472 2981919.909 2619748.75 2682777.843 2941002.831 2797559.639 2518826.4 2412366.898 2360330.763 3839691.477 0.878399343 0.776604039 0.682281055 0.6986962 0.765947694 0.728589694 0.655997081 0.628271024 0.614718859 1 21.87255896 4.579011931 2.556695763 0.702426039 0.888695876 0.15251439 0.10459268 0.535443986 5.522420957 0.02457951 0.182452029 37932.54056 -4.579011931 0.186269837 WREEQR ddPTM_MDA-MB-175_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 ;;;;;;; 162.07 0.0075784 3813559000 2533600 2990530 2928620 2629860 3312430 3479420 2658640 2867350 2741490 3458620 FALSE TRUE 2633628.484 3504130.264 3004942.243 3150038.459 2749384.332 2671377.436 2450248.85 2828917.863 2642824.31 4136270.37 0.636715748 0.847171474 0.726485934 0.761564931 0.66470131 0.645842074 0.592381211 0.68392963 0.638938965 1 21.97989906 -1.106326461 4.461307521 1.000025443 0.68992654 0.64147993 0.069825887 2.32E-05 4.65E-06 0.070651751 0.016651063 0.078284096 1.106326461 -0.310098903 WRPDEEILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WRPDEEILK 9 1 P10155-3;P10155-5;P10155-4;P10155;G5E9R9 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 ;;; 130.94 0.00031655 1036070000 1236740 1130900 1281210 1043210 1956890 1755340 1702040 1324930 1486120 1266740 FALSE TRUE 1285567.45 1325123.278 1314599.385 1249553.824 1624258.537 1347688.887 1568629.657 1307171.48 1432634.831 1514933.45 0.84859665 0.874707254 0.867760485 0.824824235 1.072164944 0.8896027 1.035444598 0.862857362 0.945675093 1 20.53082299 3.283724646 24.9999969 0.955325422 0.856438046 0.451336233 0.060458495 131.0266825 72527.28434 0.016083927 0.021777644 1921.872827 -3.283724646 -0.098887376 WRPHS(ph)PDGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 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 119.25 0.00043291 12967470000 4646800 5378500 5062410 4843750 5534910 5936160 4944130 5102020 4721680 4932980 TRUE FALSE 4830259.252 6302215.536 5194340.563 5801829.293 4594087.975 4557576.803 4556596.172 5033635.767 4551747.659 5899502.983 0.818756981 1.068262115 0.880470877 0.983443742 0.778724579 0.772535723 0.7723695 0.853230481 0.771547649 1 22.49216199 3.237174931 24.99999656 0.814063174 0.942966731 0.273498244 0.089048861 40.25900259 726343.0399 0.023221291 0.02921935 1726.533187 -3.237174931 0.128903557 WRPHS(ph)PGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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;WRPHS(1)PGWR 100.31 0.0028732 919100000 579940 641920 614170 571830 692870 769170 563700 582160 644890 641540 TRUE FALSE 602836.479 752164.7666 630175.7747 684936.2673 575096.2049 590541.9244 519515.721 574357.0974 621680.5349 767237.48 0.785723449 0.980354566 0.82135687 0.892730458 0.749567402 0.769699004 0.677125055 0.748604066 0.810284366 1 19.54931367 3.239009964 24.99995612 0.769215286 0.874443401 0.11347357 0.092995145 17.1188146 952390.2369 0.024513479 0.0312465 1733.843775 -3.239009964 0.105228115 WRS(ph)LQQLAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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;WRS(1)LQQLAEER;WRS(1)LQQLAEER 278.85 1.70E-27 1418659000 1364625 1397242 1425111 1204869 1988069 1761948 1196689 1301938 1274963 1480138 TRUE FALSE 1418501.449 1637207.444 1462250.563 1443188.492 1650137.742 1352762.28 1102889.389 1284487.651 1229077.331 1770142.702 0.801348641 0.924901389 0.826063662 0.815294999 0.932206053 0.764210862 0.623051118 0.725640735 0.694337993 1 20.75543424 2.526898373 8.640480779 0.72767537 0.858329187 0.162754553 0.10112149 0.472126083 78.02151789 0.03036558 0.028451616 336.4328331 -2.526898373 0.130653817 WRVS(ph)LDVNHFAPDELTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 WRVSLDVNHFAPDELTVK 18 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK;WRVS(1)LDVNHFAPDELTVK 272.79 3.29E-39 7486899000 5231170 4299506 5261270 4280853 6850490 6420740 6478140 5436720 6031980 4778210 TRUE FALSE 5437700.631 5037912.71 5398383.018 5127592.946 5686046.157 4929620.442 5970366.459 5363849.661 5814890.218 5714408.765 0.951577119 0.88161574 0.944696685 0.897309443 0.99503665 0.862665001 1.044791632 0.938653478 1.017583876 1 22.44617281 2.234975507 24.99999844 0.990865452 0.923516386 0.429977758 0.043506288 95.87941908 668585.5144 0.014730548 0.011308678 171.7811505 -2.234975507 -0.067349066 WS(ph)DQGPAQTSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSDQGPAQTSR 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 WS(1)DQGPAQTSR;WS(1)DQGPAQTSR 160.65 2.86E-05 1297380000 896650 919130 1128160 1023170 1254020 1437100 1135860 1119300 1080230 1026220 TRUE FALSE 932050.4344 1076983.428 1157560.776 1225549.972 1040862.128 1103355.304 1046828.325 1104297.614 1041352.733 1227288.161 0.759438952 0.877531017 0.943185809 0.998583716 0.848099217 0.899018942 0.852960502 0.899786741 0.848498964 1 20.2270426 4.708449364 3.578545344 0.905065028 0.747010688 0.41640854 0.053406638 0.249814126 5.761283748 0.012748973 0.100813168 51103.34928 -4.708449364 -0.15805434 WS(ph)GNEPTDEFSDLPLR ddPTM_MDA-MB-175_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 209.23 1.34E-11 435293000 195835 177403 185890 193553 220603 281834 277746 213658 209570 159401 TRUE FALSE 203566.717 207870.5852 190734.4461 231837.2057 183104.9809 216382.3247 255975.5428 210794.264 202027.6166 190632.574 1.067848546 1.090425318 1.00053439 1.216146857 0.960512556 1.135075293 1.342769168 1.10576204 1.059774898 1 17.54043513 2.500132342 24.83427103 1.152409525 1.070454866 0.059692208 0.104321892 1491.229126 1609378.852 0.032969164 0.030884215 316.3241443 -2.500132342 -0.081954658 WS(ph)GSHQFEQLSGSILWMAPEVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WSGSHQFEQLSGSILWMAPEVIR 23 0 P15056;H7C560;A0A2U3TZI2;A0A2R8Y8E0;A0A2R8Y492;H7C4S5 P15056 BRAF Serine/threonine-protein kinase B-raf 1 WS(0.95)GS(0.05)HQFEQLSGSILWMAPEVIR;WS(0.832)GS(0.168)HQFEQLSGSILWMAPEVIR;WS(0.751)GS(0.228)HQFEQLS(0.018)GS(0.003)ILWMAPEVIR 165.02 8.78E-12 478176000 276866 268142 321906 335133 311253 396779 354887 315229 318555 250332 TRUE FALSE 287796.8835 314193.3026 330295.1348 401421.3071 258346.3262 304633.0905 327070.0296 311003.8709 307090.2678 299379.7625 0.961310414 1.049480767 1.103264737 1.340843161 0.86293851 1.017547372 1.092492114 1.038827302 1.025754931 1 18.19161718 WS(ph)IPADGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSIPADGR 8 0 E5RJF9;P55040 E5RJF9 GEM GTP-binding protein GEM 1 WS(1)IPADGR;WS(1)IPADGR 106.29 0.0044306 87431000 213364 229805 254250 216710 285410 314910 267290 254580 268780 233130 TRUE FALSE 221787.7755 269272.2211 260875.9639 259574.5912 236896.1101 241776.925 246339.1114 251167.7715 259106.6603 278807.36 0.795487521 0.965800261 0.935685356 0.931017715 0.849676673 0.867182721 0.883545942 0.900864925 0.929339385 1 18.08890912 0.874419315 2.015872862 0.99982598 0.8935908 0.348933462 0.045563305 0.572617735 4.623609575 0.042733835 0.01185817 7.488922139 -0.874419315 -0.10623518 WS(ph)NSQPADLAHMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSNSQPADLAHMGR 14 0 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 WS(0.5)NS(0.5)QPADLAHMGR;WS(0.64)NS(0.36)QPADLAHMGR 110.56 0.00045238 873710000 458783 609080 559813 628355 609000 723240 594760 631053 568657 585517 TRUE FALSE 476896.1071 713684.752 574402.1867 752641.7435 505482.3975 555278.4708 548141.1571 622594.7667 548191.1457 700237.8457 0.681048746 1.019203341 0.820295833 1.074837283 0.721872433 0.792985518 0.782792819 0.889118991 0.782864207 1 19.41748551 4.785733792 21.52765212 0.866437887 0.681044252 0.207460318 0.112927164 9200.02632 4197841.668 0.025649262 11.4313425 61056.76521 -4.785733792 -0.185393635 WS(ph)PIASTLPELVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 WSPIASTLPELVQR 14 0 Q13561;Q13561-3;Q13561-2;H0YI98 Q13561 DCTN2 Dynactin subunit 2 1 WS(1)PIASTLPELVQR;WS(1)PIASTLPELVQR;WS(1)PIASTLPELVQR 154.72 2.83E-07 97688000 247376 212123 257016 210324 277720 342065 289943 248365 284236 210167 TRUE FALSE 257142.5955 248553.4752 263714.0481 251925.4594 230513.2536 262625.5878 267216.51 245036.0734 274006.4019 251345.1998 1.023065472 0.988892867 1.049210601 1.002308617 0.917118186 1.044880062 1.063145468 0.97489856 1.090159677 1 17.93931061 WS(ph)PPQNYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 114.89 0.0026942 10253870000 2570200 1868430 2325770 1904640 2762270 2987430 2884090 2414430 2553810 1529850 TRUE FALSE 2671673.481 2189318.318 2386381.477 2281372.107 2292740.332 2293644.657 2658027.49 2382068.515 2461898.877 1829594.817 1.460254181 1.196613752 1.304322386 1.246927509 1.253141029 1.253635306 1.452795704 1.301965054 1.345597864 1 20.80309275 -1.010543042 4.084048973 0.999972805 1.309291792 0.565360441 0.082228778 7005546.112 12172313.54 2541.404646 0.019231047 0.097601605 1.010543042 0.309318988 WS(ph)TTAGFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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(0.998)T(0.001)TAGFLK 147.62 9.65E-05 323880000 486270 330980 385930 359610 722430 587330 575460 438710 431740 406590 TRUE FALSE 505468.3151 387823.2403 395987.6528 430739.7847 599631.6066 450931.5086 530353.9415 432829.81 416201.7617 486253.5259 1.039515989 0.797574145 0.814364589 0.885833751 1.233166599 0.927358846 1.090694285 0.890131972 0.85593572 1 18.89134919 5.067693686 20.28617879 0.945676787 3.256077836 0.048504467 0.126832246 1324.032347 434880.5836 0.030204756 13163.30481 116867.4816 -5.067693686 2.310401049 WSAEASGKPSPSDPGSGTATMMNS(ph)SSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGS(0.018)GT(0.004)AT(0.011)MMNS(0.322)S(0.322)S(0.322)R;WSAEASGKPSPSDPGS(0.009)GT(0.028)AT(0.035)MMNS(0.309)S(0.309)S(0.309)R 97.077 0.002587 668800000 736500 745450 691650 956270 798680 1128470 793060 691270 663470 648850 TRUE FALSE 765577.5887 873475.2387 709674.9672 1145417.352 662920.6589 866399.9446 730897.8849 682004.6563 639591.8443 775979.7345 0.986594823 1.125641817 0.914553481 1.476091837 0.85430151 1.116523932 0.941903316 0.878894932 0.824237819 1 19.56565945 2.110788682 3.920388854 0.8915336 1.081567835 0.204431846 0.162583969 0.331691154 9.512920191 0.062392705 0.043938709 129.0591149 -2.110788682 0.190034236 WSAEASGKPSPSDPGSGTATMMNSS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WSAEASGKPSPSDPGSGTATMMNSSSR 27 1 Q5JRA6-2;Q5JRA6;Q5JRA6-4 Q5JRA6-2 MIA3 Melanoma inhibitory activity protein 3 1 WSAEASGKPSPSDPGSGTATMMNS(0.133)S(0.434)S(0.434)R 156.23 1.38E-08 536380000 461280 470230 467830 624430 508450 730020 522310 491780 489920 447480 TRUE FALSE 479491.6906 550988.3446 480022.0341 747940.3903 422023.8506 560483.9186 481369.9774 485188.4935 472287.8749 535155.1385 0.895986334 1.029586198 0.896977343 1.397614143 0.78860095 1.04732979 0.899496133 0.906631477 0.882525161 1 19.02959766 WSDEACR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSDEACR 7 0 J3KNC9;O75596 J3KNC9 CLEC3A C-type lectin domain family 3 member A 0 ; 120.49 0.010575 279790000 358510 578150 547300 572340 629880 649550 491850 573630 526300 764010 FALSE TRUE 372664.2516 677442.7651 561563.0876 685547.1437 522813.2226 498701.8565 453297.5118 565941.4281 507358.5658 913703.1316 0.407861414 0.74142546 0.614601251 0.750295276 0.572191563 0.545802941 0.496110275 0.619393114 0.555277254 1 19.80136597 -1.620908754 2.871343893 1.032976121 0.595162231 0.612516369 0.097914195 21873330.4 21271678.15 5386981.574 0.022961993 0.023938186 1.620908754 -0.43781389 WSEPWVPVEALPPS(ph)PLELSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WSEPWVPVEALPPSPLELSR 20 0 O43379-4;O43379 O43379-4 WDR62 WD repeat-containing protein 62 1 WSEPWVPVEALPPS(0.978)PLELS(0.022)R;WSEPWVPVEALPPS(0.974)PLELS(0.026)R;WSEPWVPVEALPPS(0.971)PLELS(0.029)R;WSEPWVPVEALPPS(0.998)PLELS(0.002)R;WSEPWVPVEALPPS(0.984)PLELS(0.016)R 186.89 8.38E-17 0 174604 208133 194548 203424 211153 252198 204225 205113 191105 209201 TRUE FALSE 181497.5007 243878.2237 199618.0807 243660.66 175261.2885 193628.8366 188217.3109 202363.7957 184227.1684 250189.9306 0.725438871 0.974772339 0.797866166 0.973902745 0.700512959 0.773927377 0.752297706 0.808840689 0.736349253 1 17.9326642 5.049750882 15.66684131 0.823677478 0.134346787 0.082171877 0.103797464 5203409.134 43295561.05 0.023528789 108023880 112137.5032 -5.049750882 -0.689330691 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK 32 0 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 220.01 3.92E-36 1583870000 499740 820380 656460 560880 969240 1015990 633700 782610 702050 1056300 FALSE TRUE 519470.1211 961273.8833 673567.8869 671820.3899 804488.931 780041.72 584028.9381 772120.393 676783.3576 1263261.761 0.411213366 0.76094592 0.5331974 0.531814079 0.636834705 0.617482254 0.462318227 0.611211719 0.535742772 1 20.26872218 -1.465013291 4.104599562 1.002723939 0.572335065 0.662649101 0.092660958 3969.536497 45981999.01 154189.9923 0.01967301 0.03427573 1.465013291 -0.430388875 WSHDGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 WSHDGK 6 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;; 144.29 0.011291 2003160000 5622780 4496270 5583300 4590620 6724350 6962990 6631470 5685320 6081860 3853590 FALSE TRUE 5844771.696 5268469.396 5728805.385 5498630.934 5581347.389 5345941.098 6111678.053 5609117.585 5862975.047 4608627.179 1.268224022 1.143175439 1.243061146 1.193116892 1.211065068 1.159985586 1.326138526 1.217090766 1.272173864 1 22.13590563 -1.011259216 4.664097933 0.999994508 1.224567577 0.631154808 0.051820646 2.79E-06 5.92E-07 0.04734376 0.011158758 0.097440787 1.011259216 0.224573069 WSLALGLPLPLGEHAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WSLALGLPLPLGEHAGR 17 0 Q96F86 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 70.96 0.031528 79671000 43666 84064 70194 78201 55263 81323 64726 57413 62810 104550 FALSE TRUE 45389.9674 98501.33807 72023.31331 93668.92439 45869.415 62436.96571 59652.60699 56643.47264 60549.48037 125034.5708 0.36301934 0.787792828 0.576027197 0.749144207 0.366853861 0.49935762 0.477088909 0.45302249 0.484261912 1 16.93196751 -1.593171069 6.302090426 1.001281701 0.530474178 0.522420342 0.135229376 0.002409252 0.000155528 0.129537335 0.030459694 0.02551696 1.593171069 -0.470807523 WSLELEDQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WSLELEDQER 10 0 P37198 P37198 NUP62 Nuclear pore glycoprotein p62 0 ;;; 194.06 1.17E-06 539530000 369615 429317 402324 417455 460251 504423 438003 442161 447762 449735 FALSE TRUE 384207.6856 503048.8551 412808.894 500026.353 382017.6994 387278.4029 403671.1804 436234.555 431647.1331 537851.9626 0.714337238 0.935292404 0.767513968 0.929672824 0.710265512 0.720046462 0.750524695 0.811068073 0.80253892 1 19.03684962 -1.626280381 9.220972889 1.000073201 0.795556352 0.389175914 0.077582087 0.000112126 4.54E-06 0.072143572 0.016998358 0.023643928 1.626280381 -0.204516848 WSNS(ph)QPADLAHMGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WSNSQPADLAHMGR 14 0 Q9BRG2;Q9BRG2-2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 WS(0.002)NS(0.998)QPADLAHMGR;WS(0.001)NS(0.999)QPADLAHMGR;WS(0.003)NS(0.997)QPADLAHMGR;WS(0.018)NS(0.982)QPADLAHMGR 226.57 1.52E-12 1654180000 1054650 1228980 1228080 1278980 1285030 1451960 1268340 1273670 1249840 1164880 TRUE FALSE 1096288.396 1440047.755 1260084.774 1531958.427 1066601.06 1114764.295 1168924.197 1256598.537 1204858.503 1393115.933 0.786932638 1.033688382 0.904508192 1.099663273 0.765622612 0.800194921 0.83907173 0.902005718 0.864865927 1 20.40988389 5.03977425 14.67890715 0.90369817 0.339097704 0.118674107 0.100019819 1629004.966 18322637.54 0.024009502 23906479.47 109590.8384 -5.03977425 -0.564600466 WSPAYSFSSDS(ph)PLDSSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WSPAYSFSSDSPLDSSPK 18 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 1 WSPAYSFS(0.003)S(0.029)DS(0.968)PLDSSPK 256.33 1.44E-30 38942000 65194 34270 36548 33629 50904 59363 43771 44162 46094 31211 TRUE FALSE 67767.90946 40155.60592 37500.4709 40280.71583 42251.35626 45576.8429 40340.11465 43570.08062 44435.08594 37326.19788 1.815558865 1.075802203 1.00466892 1.079154002 1.131949104 1.221041668 1.080745346 1.167278831 1.190453046 1 15.18790094 4.740382741 24.99766936 1.112629642 1.815559102 0.902403675 0.070002771 46.51815527 638131.5277 0.017132541 0.111015446 55002.53937 -4.740382741 0.702929459 WTDGSLS(ph)PPAKEPLASDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WTDGSLSPPAKEPLASDSR 19 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 WTDGS(0.051)LS(0.949)PPAKEPLASDSR;WT(0.003)DGS(0.202)LS(0.795)PPAKEPLASDSR;WTDGS(0.007)LS(0.993)PPAKEPLASDSR;WTDGS(0.087)LS(0.912)PPAKEPLASDSR 171.72 5.89E-12 2214590000 4032200 3203930 3584480 3179250 4699570 4729490 4404590 3907070 4111170 3299750 TRUE FALSE 4191394.37 3754180.054 3677894.493 3808096.161 3900738.77 3631137.624 4059346.727 3854702.117 3963209.795 3946272.835 1.062114695 0.951322985 0.931991945 0.964985524 0.988461501 0.920143582 1.028653339 0.976795645 1.004291888 1 21.91205927 2.215457363 24.99992307 0.998967007 0.967900994 0.145573698 0.038150746 486.8540681 526818.9984 0.013962986 0.010318804 164.2318417 -2.215457363 -0.031066013 WTELDTNQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WTELDTNQHR 10 0 Q5VSL9;Q5VSL9-2;Q5VSL9-4 Q5VSL9 STRIP1 Striatin-interacting protein 1 0 171.87 0.0027376 0 55282 96060 104340 86294 111970 100440 97890 88629 93447 90364 FALSE TRUE 57464.57605 112557.5578 107059.1861 103362.6956 92937.37939 77114.33218 90217.12601 87441.07322 90083.86072 108069.0957 0.531739215 1.041533262 0.990654964 0.956450084 0.859981096 0.713565073 0.834809669 0.809121911 0.83357652 1 16.72159449 3.000759198 24.98028361 0.821089249 0.900609507 0.003569718 0.145330333 80.41465877 2645746.383 0.040677894 0.048226419 1001.749648 -3.000759198 0.079520258 WTETYVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WTETYVR 7 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;; 117.16 0.012315 447407000 430534 508788 482469 467467 718610 683560 538798 490371 439675 724840 FALSE TRUE 447531.8148 596168.3812 495042.5385 559930.5774 596460.9289 524813.5495 496565.6049 483798.3788 423851.1826 866858.5201 0.516268577 0.68773435 0.57107651 0.645930754 0.688071831 0.605420074 0.572833506 0.558105351 0.488950818 1 19.72543702 -1.373162 3.464160563 1.002720754 0.595997846 0.789063894 0.063154257 17685821.45 29338565.55 498070.4218 0.015304056 0.042348497 1.373162 -0.406722907 WTGPEISPNTSGSS(ph)PVIHFTPSDLEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WTGPEISPNTSGSSPVIHFTPSDLEVR 27 0 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 1 WTGPEISPNTSGS(0.251)S(0.749)PVIHFTPSDLEVR 175.95 4.38E-13 215490000 50168 93388 94104 109000 97452 127530 79389 79061 85438 108260 TRUE FALSE 52148.67138 109426.6625 96556.42755 130559.8747 80887.14385 97913.09024 73166.28274 78001.31661 82363.10307 129471.4742 0.402781166 0.845179706 0.745773755 1.008406488 0.624748767 0.756252223 0.565115082 0.602459477 0.636148646 1 16.98227475 WTKPSSFS(ph)DSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WTKPSSFSDSER 12 1 Q8NC56;H0Y9B7;Q8NC56-2 Q8NC56 LEMD2 LEM domain-containing protein 2 1 WTKPS(0.001)S(0.005)FS(0.993)DSER;WTKPSS(0.001)FS(0.999)DSER 173.51 1.99E-05 818300000 1102020 1067670 973350 1355590 1245940 1706780 1231190 1098590 1129180 1272980 TRUE FALSE 1145528.601 1251034.017 998716.3006 1623721.656 1034155.564 1310406.212 1134686.111 1083865.198 1088541.032 1522396.058 0.752451108 0.821753321 0.656016084 1.066556661 0.679294694 0.860752499 0.745329118 0.711946929 0.715018294 1 20.5379123 2.193494837 24.99918756 0.762101046 0.80609547 0 0.131970459 628.2517829 348504.1312 0.046318231 0.034208432 156.1330475 -2.193494837 0.043994424 WTLGFCDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WTLGFCDER 9 0 M0R1L2;O95336;M0R0U3;M0R261 M0R1L2 PGLS 6-phosphogluconolactonase 0 ;;; 229.44 2.95E-07 1350150000 1163550 1831970 1411290 1406870 1972350 2066260 1159138 1573260 1384980 2374260 FALSE TRUE 1209487.852 2146596.597 1448069.377 1685144.687 1637090.652 1586402.429 1068281.735 1552173.023 1335134.84 2839450.789 0.425958378 0.755990069 0.509982206 0.593475574 0.576551866 0.558700449 0.376228297 0.546645509 0.470208832 1 21.43718048 -1.346076013 3.234224865 1.003542316 0.537968886 0.66810218 0.09833057 28914169.69 39361392.38 973577.7698 0.022790679 0.045073781 1.346076013 -0.46557343 WTPKS(ph)PLDPDSGLLSCTLPNGFGGQSGPEGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WTPKSPLDPDSGLLSCTLPNGFGGQSGPEGER 32 1 A0A087X0R7;Q9H4L4 A0A087X0R7 SENP3-EIF4A1;SENP3 Sentrin-specific protease 3 1 WT(0.032)PKS(0.967)PLDPDSGLLSCTLPNGFGGQSGPEGER 98.987 2.39E-05 333400000 119200 93933 124460 75265 126860 153130 103520 108860 125560 86577 TRUE FALSE 123906.108 110065.2621 127703.5298 90152.19236 105296.3825 117567.8782 95405.8319 107400.9098 121041.1201 103540.1055 1.196696752 1.06302057 1.233372607 0.870698285 1.016962287 1.135481537 0.921438426 1.037288007 1.169026432 1 16.65983017 3.760023565 24.99835848 1.022327153 1.154229026 0.334375769 0.091995529 991.961697 1155355.662 0.022983682 0.04138849 5754.711613 -3.760023565 0.131901873 WTQLGAFYPFMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WTQLGAFYPFMR 12 0 P10253 P10253 GAA Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase 0 74.841 0.041343 0 297980 68541 69648 68211 98653 174390 108680 104410 74591 57230 FALSE TRUE 309744.4805 80312.38358 71463.0841 81702.93221 81883.9983 133890.5654 100161.3776 103010.5547 71906.48448 68443.12277 4.52557493 1.173417874 1.044123664 1.193734723 1.19638022 1.956231101 1.46342501 1.505053402 1.050602041 1 16.06261796 4.740223608 24.99337678 1.32638657 4.525575996 0.924698337 0.277048912 37.03237485 556518.5802 0.068928623 0.441332313 54982.38926 -4.740223608 3.199189426 WTS(ph)QDSLLGMEFSGR ddPTM_MDA-MB-175_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(0.057)S(0.942)QDSLLGMEFSGR;WT(0.029)S(0.971)QDSLLGMEFSGR 113.47 0.00071559 80243000 175075 163577 175086 190020 195854 218330 198981 182131 168159 143073 TRUE FALSE 181987.0962 191670.0773 179648.885 227605.3888 162562.807 167626.1663 183384.3493 179689.8319 162106.9904 171105.4151 1.063596357 1.120187092 1.049931032 1.330205644 0.950074005 0.979666051 1.071762394 1.05017034 0.947410054 1 17.38452589 WTSQDSLLGMEFSGR ddPTM_MDA-MB-175_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 ;;;;;;;;;;;; 345.15 2.00E-71 5302829000 2156955 2532142 2618139 2951394 2788948 3218083 2661012 2606619 2415090 2613789 FALSE TRUE 2242113.249 2967017.691 2686369.853 3535170.924 2314883.615 2470731.994 2452434.926 2571681.536 2328171.383 3125910.911 0.717267162 0.949168987 0.859387849 1.130925041 0.740546894 0.790403842 0.784550487 0.822698282 0.74479774 1 21.57584523 WTVHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WTVHGK 6 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 69.39 0.09363 269230000 476010 327620 429520 477760 503830 522180 580680 480980 503800 320710 FALSE TRUE 494803.2424 383886.1865 440713.6441 572259.502 418189.1566 400911.6087 535164.7843 474533.2498 485668.3364 383546.9841 1.290072045 1.000884383 1.149047346 1.492019298 1.090320544 1.045273787 1.395304373 1.237223259 1.26625513 1 18.54904379 2.244880966 24.99992627 1.249075612 1.178869297 0.011216124 0.158915942 574.6473875 2273004.001 0.055556873 0.045436241 175.7441859 -2.244880966 -0.070206315 WVCSSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 149.4 0.004697 1584673000 644039 794830 681160 656900 2473670 1252310 662029 686947 637831 3596740 FALSE TRUE 669466.157 931335.8696 698911.5892 786832.8593 2053196.457 961479.9814 610137.4371 677739.5991 614875.5869 4301452.339 0.155637237 0.216516608 0.1624827 0.182922603 0.47732633 0.2235245 0.141844519 0.157560644 0.142946042 1 22.03639242 -1.30104779 3.39397236 1.003326345 0.206992351 0.863618957 0.094568472 49235674.66 71842384.33 1683945.053 0.025495122 0.049997951 1.30104779 -0.796333993 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGR 39 1 Q99447-3;Q99447;Q99447-4;I3L1R7;Q99447-2;I3L2Q1;I3L1C4 Q99447-3 PCYT2 Ethanolamine-phosphate cytidylyltransferase 0 97.1 0.00010721 86207000 36482 40917 42253 37656 48678 50958 48138 40088 43331 38685 FALSE TRUE 37922.33753 47944.17646 43354.14789 45104.24441 40403.73095 39123.77678 44364.81777 39550.68593 41771.52577 46264.58508 0.819683943 1.036304041 0.937091467 0.974919462 0.873318779 0.845652819 0.9589369 0.854880377 0.902883398 1 15.49762063 3.236463671 24.99947503 0.896739815 0.948385161 0.052031479 0.066786885 114.698934 1367432.375 0.017699098 0.022181882 1723.707897 -3.236463671 0.051645346 WVDINDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVDINDK 7 0 Q9BW91-2;Q9BW91 Q9BW91-2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 0 82.452 0.056881 60784000 108900 111970 114310 100120 136910 148230 126650 123750 106770 116850 FALSE TRUE 113199.4561 131199.9765 117289.0125 119923.4372 113638.0871 113805.8289 116722.8421 122091.3337 102927.3686 139744.5203 0.81004576 0.938855965 0.83931028 0.858162001 0.813184566 0.814384913 0.835258813 0.873675286 0.736539568 1 17.09243219 7.020502282 10.82934738 0.848927014 0.267999303 0 0.069642441 0 0 0.013883804 0 10483403.01 -7.020502282 -0.580927711 WVEENVPSSVTDVALPALLDS(ph)DEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVEENVPSSVTDVALPALLDSDEER 25 0 Q8NBN3-3;Q8NBN3 Q8NBN3-3 TMEM87A Transmembrane protein 87A 1 WVEENVPSSVTDVALPALLDS(1)DEER;WVEENVPSSVTDVALPALLDS(1)DEER 86.18 0.010859 60180000 40039 42445 39927 52442 45930 50738 51707 44939 41170 40033 TRUE FALSE 41619.77064 49734.59857 40967.53042 62814.87108 38122.83501 38954.86844 47654.07023 44336.66621 39688.29974 47876.69987 0.869311601 1.038805906 0.855688269 1.312013385 0.796271153 0.813649824 0.995349938 0.926059364 0.828968994 1 15.54703609 WVEQHLGPQFVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVEQHLGPQFVER 13 0 Q8TCD5;J3KSY6;J3KRC4 Q8TCD5 NT5C "5(3)-deoxyribonucleotidase, cytosolic type" 0 153.09 1.45E-06 0 181220 212920 203920 169220 238920 244530 172450 209010 191120 229120 FALSE TRUE 188374.7055 249487.3537 209234.3227 202691.2109 198308.4637 187741.6134 158932.9184 206208.5628 184241.6285 274011.6772 0.687469627 0.910498984 0.763596372 0.73971742 0.723722674 0.68515917 0.580022428 0.752553924 0.672386047 1 18.06387785 -1.441411004 3.319562687 1.003836666 0.725541472 0.518560963 0.079795289 29456189.93 33239257.3 1026137.634 0.019921435 0.036190034 1.441411004 -0.278295193 WVESLK ddPTM_MDA-MB-175_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 7946127000 15502840 12505700 14913750 14179880 18148900 17695070 16291410 13969250 15477150 12481560 FALSE TRUE 16114904.09 14653456.69 15302414.58 16984617.94 15063956.46 13585658.16 15014446.71 13782015.05 14920130.39 14927082.71 1.079574918 0.981669157 1.025144355 1.137839072 1.009169491 0.910134849 1.005852718 0.923289254 0.999534248 1 23.8314289 2.998419929 24.9998486 0.962636983 1.051656539 0.429524371 0.047684081 55.86894104 883987.5328 0.013565571 0.015998858 996.3683632 -2.998419929 0.089019556 WVGGQHPCFIIAEIGQNHQGDLDVAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAK 26 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 291.15 1.77E-70 1656600000 932660 666850 878290 912560 1048820 1131910 1112180 943140 1030110 738440 FALSE TRUE 969482.137 781376.3001 901178.9589 1093061.644 870541.951 869041.0568 1025004.425 930498.751 993036.5423 883123.1797 1.097788122 0.884787443 1.020445369 1.237722743 0.98575371 0.98405418 1.1606585 1.053645485 1.124459832 1 19.75225516 3.992539908 24.97352475 1.080070029 0.981619931 0.13598148 0.090230256 558.8690047 1870905.219 0.021649115 0.043915418 9829.691962 -3.992539908 -0.098450098 WVGGQHPCFIIAEIGQNHQGDLDVAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVGGQHPCFIIAEIGQNHQGDLDVAKR 27 1 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 ; 317.8 1.19E-82 4183900000 1982430 1664360 2052490 1419520 2482730 2256770 1840590 2002430 2057200 1917740 FALSE TRUE 2060697.867 1950200.883 2105979.576 1700296.819 2060716.441 1732669.369 1696319.746 1975590.701 1983161.774 2293484.436 0.898500916 0.850322266 0.918244547 0.74135965 0.898509015 0.755474658 0.739625576 0.861392679 0.864693801 1 21.12910969 0.762376205 1.970383143 0.99968083 0.829568212 0.385208857 0.063239248 0.916005221 5.706386118 0.059486747 0.016491457 5.78597037 -0.762376205 -0.170112618 WVNDPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVNDPHR 7 0 Q9H4A6 Q9H4A6 GOLPH3 Golgi phosphoprotein 3 0 ; 110.81 0.0067205 276032000 292810 331120 328510 370480 343110 409590 385590 324730 317210 310330 FALSE TRUE 304370.3649 387987.2842 337071.2405 443759.8382 284788.2848 314468.9299 355366.4482 320377.5255 305793.6741 371133.2219 0.820110804 1.045412432 0.908221686 1.195688804 0.767347863 0.847320885 0.957517213 0.863241302 0.82394584 1 18.50157762 3.194711609 24.99999944 0.873628277 0.99014077 0.213200409 0.108856429 199.9103136 113975.8453 0.029825934 0.035648997 1565.711022 -3.194711609 0.116512492 WVNEAQEAASSDNIMVQYHALGLLYHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVNEAQEAASSDNIMVQYHALGLLYHVR 28 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 0 155.56 1.08E-08 299590000 120780 111930 107190 109840 113860 143320 105700 111070 112260 117320 FALSE TRUE 125548.4877 131153.1068 109983.4595 131566.0242 94506.11787 110036.102 97414.9578 109581.2883 108219.7845 140306.6078 0.894815217 0.934760728 0.7838794 0.937703692 0.673568547 0.784254596 0.69430057 0.781013026 0.771309251 1 17.09822343 3.251146784 24.99979156 0.767798899 0.883722657 0.222829765 0.09179708 286.1289579 568331.8385 0.023384711 0.031449214 1782.981281 -3.251146784 0.115923759 WVNPHKL ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVNPHKL 7 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 ; 83.614 0.035516 3608200000 3333700 3143600 2812400 2377600 10439100 5579100 4338500 2940700 3255200 10333900 FALSE TRUE 3465317.05 3683488.846 2885693.454 2847882.184 8664665.511 4283438.577 3998437.033 2901284.727 3138045.988 12358629.85 0.28039654 0.298049937 0.233496228 0.230436725 0.701102437 0.34659494 0.323534007 0.234757798 0.253915363 1 23.55901547 -1.07697744 4.061289893 1.000111018 0.321909103 0.702334663 0.132323354 510809312.9 889946774.7 806537.245 0.032984769 0.083757279 1.07697744 -0.678201915 WVPEITHHCPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WVPEITHHCPK 11 0 A0A590UJK8;P60953-1;P60953;A0A494C1M1;Q5JYX0;A0A494BZX6 A0A590UJK8 CDC42 Cell division control protein 42 homolog 0 ; 189.58 1.53E-06 1375200000 1299940 1080860 1385990 1270370 1648740 1632730 1542720 1419660 1600340 1520460 FALSE TRUE 1351262.635 1266489.297 1422110.038 1521645.394 1368487.764 1253553.202 1421797.575 1400631.78 1542744.076 1818365.026 0.743119569 0.696498931 0.782081715 0.836820645 0.752592436 0.689384796 0.781909878 0.770269863 0.848423751 1 20.79421041 0.871282604 1.537078809 0.999929287 0.753895989 0.779949501 0.039993178 0.258172292 1.183140695 0.039806988 0.011607524 7.435027917 -0.871282604 -0.246033298 WVPFDGDDIQLEFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVPFDGDDIQLEFVR 15 0 A0A0C4DGS1;P39656-2;P39656-3;P39656 A0A0C4DGS1 DDOST Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit 0 149.38 7.83E-06 21487000 13568 14890 15977 20501 16320 25772 18714 13679 14910 27922 FALSE TRUE 14103.67512 17447.24167 16393.37375 24556.03661 13545.93223 19786.84358 17247.14778 13495.65538 14373.39201 33392.7813 0.422357006 0.522485429 0.490925676 0.735369611 0.405654507 0.592548533 0.516493299 0.404148886 0.430434107 1 15.02724864 -1.886044579 2.529476077 1.256125355 0.502592973 0.704022966 0.09681686 6841941.638 4073420.497 10479373.21 0.023835089 0.013000361 1.886044579 -0.753532382 WVTTASLLDYDTVAGADKFGNICVVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WVTTASLLDYDTVAGADKFGNICVVR 26 1 Q15393;Q15393-3 Q15393 SF3B3 Splicing factor 3B subunit 3 0 91.813 0.008876 144000000 71486 91171 102760 85901 129530 153430 99447 100620 111240 113640 FALSE TRUE 74308.32248 106828.91 105438.01 102891.9614 107512.5369 117798.2078 91652.08428 99271.35348 107236.4941 135905.5822 0.546764314 0.786052407 0.775818096 0.757084144 0.791082567 0.866765042 0.674380572 0.730443532 0.789051431 1 17.05224519 -5 0.304319672 3.139413061 0.736150388 0.48427391 0.079981918 247.3174885 2.267663879 338.3619618 0.076900711 1.00E-05 5 -2.403262674 WVWDQEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 WVWDQEEER 9 0 E9PMS6;E9PMT2;Q8WWI1-5;A0A0A0MTE2;H0Y424;H0YDG6;H0YDQ3;U3KQE6;Q8WWI1-3;F8WD26;J3KP06;Q8WWI1;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6;Q8WWI1-3 LMO7 LIM domain only protein 7 0 ;;; 234.47 8.29E-10 1054930000 1091090 1382280 1268470 1194670 1380420 1598870 1301060 1324850 1191890 1456020 FALSE TRUE 1134167.076 1619675.837 1301527.37 1430972.16 1145776.701 1227556.674 1199079.518 1307092.553 1148994.112 1741299.242 0.651333814 0.930153645 0.747446125 0.821784175 0.658001034 0.70496595 0.688611979 0.750642119 0.659848741 1 20.73173272 -1.146930745 3.865688727 1.000126313 0.739173249 0.482141715 0.082353935 24843433.57 44921056.39 40441.97797 0.019272839 0.071296671 1.146930745 -0.260953064 WWDNLNHLNQFVDHEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WWDNLNHLNQFVDHEK 16 0 Q13907;Q13907-2 Q13907 IDI1 Isopentenyl-diphosphate Delta-isomerase 1 0 240.79 4.09E-20 469020000 222510 131040 195990 163160 212500 216360 273170 184760 211710 121680 FALSE TRUE 231294.8666 153545.1007 201097.6604 195432.561 176379.3259 166113.669 251758.2216 182283.5944 204090.5985 145520.8663 1.589427499 1.055141469 1.381916323 1.342986515 1.212055222 1.141510996 1.730048948 1.252628568 1.402483394 1 17.15086651 WWGNRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WWGNRK 6 1 A0A2R8Y5Y7;P32969;D6RAN4;E7ESE0;H0Y9R4 A0A2R8Y5Y7 RPL9 60S ribosomal protein L9 0 ; 103.7 0.05526 1286870000 1218730 1066280 1166030 957500 1928210 1594970 1371830 1237390 1404960 1339060 FALSE TRUE 1266846.401 1249405.295 1196417.7 1146890.642 1600453.553 1224562.39 1264302.38 1220804.811 1354395.764 1601423.169 0.791075355 0.780184351 0.747096534 0.716169632 0.999394528 0.764671333 0.789486754 0.762324934 0.845745079 1 20.61092315 -4.999999987 0.342214683 3.23215836 0.789620432 0.405081646 0.073610587 403.8558917 3.381642052 659.1689459 0.057839721 1.00E-05 4.999999987 -2.442537928 WWTCFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WWTCFVK 7 0 O15145 O15145 ARPC3 Actin-related protein 2/3 complex subunit 3 0 108.09 0.017057 109290000 130950 151960 110600 115370 294410 224800 156520 139130 156810 223960 FALSE TRUE 136120.0071 178057.9479 113482.3269 138189.8417 244366.2934 172593.6069 144251.5534 137265.1899 151166.4387 267840.674 0.508212607 0.664790546 0.423693404 0.515940464 0.912356924 0.644389085 0.538572246 0.512488219 0.564389405 1 18.03101554 -2.059133354 2.51202668 1.582542397 0.586243 0.48699264 0.127100112 27007096.93 10439596.54 90172611.43 0.032540579 0.008727034 2.059133354 -0.996299397 WYEIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WYEIEK 6 0 C9JX71;C9JF17;P05090 C9JX71 APOD Apolipoprotein D 0 100.07 0.088599 177400000 611690 309740 395800 285150 545010 506900 440380 361580 425370 286490 FALSE TRUE 635839.9935 362935.4356 406114.8732 341551.8189 452369.3949 389180.1571 405861.8649 356733.6115 410061.0168 342622.2303 1.855804841 1.05928747 1.185313845 0.996875826 1.320315364 1.135887058 1.184575398 1.041186415 1.196831322 1 18.38625924 4.741892788 24.99841642 1.128795267 1.855805111 0.836339766 0.097037388 111.8813259 839311.5541 0.021446863 0.155528827 55194.11675 -4.741892788 0.727009844 WYHPGCFVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WYHPGCFVK 9 0 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 114.93 0.001558 730620000 826990 853270 658820 634560 1563200 1306100 896180 773260 861020 1524700 FALSE TRUE 859640.2038 999812.485 675989.3904 760074.074 1297487.822 1002778.069 825935.0699 762895.7145 830032.0584 1823435.773 0.471439804 0.548312422 0.370722896 0.416836219 0.711562119 0.549938794 0.452955395 0.41838365 0.455202246 1 20.79822795 -1.325550662 3.175228914 1.003704466 0.486356257 0.737748707 0.091505225 30315848.13 40782573.79 1056641.86 0.025020555 0.047255171 1.325550662 -0.517348209 WYMQFDDDEKQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 WYMQFDDDEKQK 12 1 M0R0N4;M0QYZ2;P53680;X6R390;P53680-2 M0R0N4 AP2S1 AP-2 complex subunit sigma 0 206.53 8.12E-08 593010000 694650 245730 428070 264290 622610 522050 604190 410020 488540 199450 FALSE TRUE 722075.3184 287932.216 439225.8559 316565.7732 516778.9746 400811.7992 556832.009 404524.3526 470957.5408 238528.4088 3.027208885 1.207119175 1.841398507 1.32716172 2.166530088 1.680352463 2.334447338 1.69591687 1.974429558 1 17.86380158 -1.190212416 4.683607918 0.999857961 1.881325526 0.233565725 0.494609997 0.000658868 0.000113916 0.430123164 0.10136491 0.064533851 1.190212416 0.881467566 WYNHIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WYNHIK 6 0 P24534;C9JZW3;F2Z2G2 P24534 EEF1B2 Elongation factor 1-beta 0 ; 97.306 0.041221 3611600000 5671700 5499400 5595900 4781700 9257300 7895600 6773900 5674700 5800000 7077100 FALSE TRUE 5895623.096 6443879.171 5741733.751 5727505.988 7683747.453 6061966.559 6242944.018 5598639.928 5591259.133 8463722.246 0.696575682 0.761352864 0.678393452 0.676712423 0.907844945 0.716229383 0.737612109 0.661486727 0.660614676 1 23.01286085 -2.328192371 2.305046004 2.587148683 0.721975966 0.589938998 0.069564998 2480176.56 291115.2413 20712135.5 0.017216546 0.00469686 2.328192371 -1.865172717 WYQMGAYQPFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 WYQMGAYQPFFR 12 0 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 ; 122.13 0.00084657 338930000 201030 269104 203034 231695 348430 359860 233460 246873 196883 351230 FALSE TRUE 208966.8196 315320.5187 208325.2328 277523.5795 289203.9931 276287.9687 215160.7952 243564.0712 189797.2193 420046.7938 0.49748462 0.750679504 0.495957203 0.660696817 0.688504227 0.657755214 0.512230538 0.579849852 0.451847799 1 18.68019053 -1.211633293 4.057972968 1.000245939 0.593238353 0.633953671 0.093777172 54.36385691 48476355.61 22627.03887 0.020978516 0.061428047 1.211633293 -0.407007586 Y(ph)ATPQVIQAPGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YATPQVIQAPGPR 13 0 A0A5F9ZHP4;C9J1X3;A0A5F9ZI29;A0A5F9ZGX5;A0A5F9ZHJ2;A0A499FJ16;Q07912;Q07912-3;A0A5F9ZHD0 A0A5F9ZHP4 TNK2 Activated CDC42 kinase 1 1 Y(1)ATPQVIQAPGPR;Y(1)ATPQVIQAPGPR;Y(1)ATPQVIQAPGPR;Y(0.995)AT(0.005)PQVIQAPGPR 276 3.31E-31 2666660000 1363580 1210390 1369600 1250100 1766710 1703140 1506290 1495220 1478500 1212460 TRUE FALSE 1417415.191 1418265.067 1405292.901 1497366.049 1466405.265 1307611.546 1388223.054 1475179.022 1425289.074 1450018.323 0.977515366 0.978101479 0.969155271 1.032653191 1.011301197 0.901789671 0.957383111 1.017351987 0.982945561 1 20.4676397 1.735941544 24.99999977 1.000563644 0.976026771 0.104343912 0.033099654 0.847782068 7949.156163 0.01645413 0.009124443 54.44293672 -1.735941544 -0.024536873 Y(ph)EDVKAGETVRS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YEDVKAGETVRSR 13 2 O75376;O75376-2;A0A088AWL3;E7EVK1 O75376 NCOR1 Nuclear receptor corepressor 1 2 Y(0.997)EDVKAGET(0.003)VRS(1)R 83.204 0.0033588 0 257210 233010 206930 230730 253280 384170 299990 243020 220960 164390 TRUE FALSE 267364.8494 273027.6549 212322.7658 276367.7053 210227.5561 294952.3397 276475.9999 239762.7144 213007.6928 196599.0731 1.359949695 1.388753521 1.079978468 1.405742667 1.069321197 1.500273298 1.406293507 1.219551601 1.083462345 1 17.58489699 1.257566192 2.549553213 1.010933651 1.310213555 0.403704192 0.132710472 0.267719179 2.90536091 0.116420764 0.033607518 18.09531683 -1.257566192 0.299279904 Y(ph)KVAKRGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKVAKRGR 8 3 A0A1B0GX95;A0A0J9YYF1 A0A1B0GX95 1 Y(1)KVAKRGR 42.599 0.09456 644220000 4618.4 456280 224030 423010 97939 339160 77366 256150 98943 587460 TRUE FALSE 4800.737998 534642.5406 229868.4058 506680.1154 81291.36376 260395.23 71301.85076 252716.7282 95382.06076 702561.5394 0.006833192 0.760990334 0.327186151 0.721189657 0.115707108 0.370636899 0.101488406 0.359707604 0.135763283 1 19.42226508 -4.71627366 5.943588842 0.953002012 0.369612179 0 0.316025877 0 0 0 0.062945095 1.92E-05 4.71627366 -0.583389833 Y(ph)LRAFLPES(ph)GFT(ph)ILPCT(ph)RYSMETNGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLRAFLPESGFTILPCTRYSMETNGAK 27 2 Q86Y97 Q86Y97 SUV420H2 Histone-lysine N-methyltransferase SUV420H2 4 Y(0.762)LRAFLPES(0.73)GFT(0.758)ILPCT(0.758)RY(0.512)S(0.48)MET(0.001)NGAK 46.772 0.065439 41771000 15706 7329.8 9485.5 7096.3 11796 12209 15229 9209.6 9573.5 3365.4 TRUE FALSE 16326.08501 8588.636132 9732.699922 8499.92696 9790.920133 9373.644779 14035.31119 9086.160376 9228.951605 4024.785696 4.056386164 2.133936259 2.418190845 2.11189554 2.432656264 2.328979848 3.487219506 2.257551349 2.29302932 1 11.97469625 0.732698828 1.677584298 1.00351479 2.624764261 0.409703896 0.597632815 0.938538781 4.195657103 0.542318101 0.154488853 5.403794536 -0.732698828 1.621249471 Y(ph)MEDSTYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 Y(0.995)MEDS(0.005)TYYK;Y(1)MEDSTYYK;Y(0.976)MEDS(0.024)TYYK 172.21 0.00058086 539620000 577670 475680 563800 440940 735730 712310 666490 582380 606070 417250 TRUE FALSE 600476.8577 557374.3397 578493.0912 528156.6159 610670.8774 546886.7977 614248.7723 574574.1487 584257.6591 499002.1488 1.203355254 1.116977835 1.1592998 1.058425534 1.223784064 1.095960807 1.230954163 1.151446241 1.17085199 1 18.9286865 -0.882664748 4.166413751 0.999996704 1.155907276 0.447032482 0.052304043 4939171.471 13250642.71 277.3221177 0.011493974 0.131019293 0.882664748 0.155910572 Y(ph)RALFRLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRALFRLPK 9 2 Q6ZT07 Q6ZT07 TBC1D9 TBC1 domain family member 9 1 Y(1)RALFRLPK;Y(1)RALFRLPK 50.909 0.052108 0 848540 296610 490440 317610 730800 679650 770850 521220 638380 230660 TRUE FALSE 882041.0144 347550.4602 503221.2693 380432.31 606578.877 521811.5877 710428.7628 514233.8984 615404.8285 275853.4107 3.197499034 1.259909962 1.824234357 1.379110409 2.198917445 1.891626376 2.575385096 1.86415639 2.230912523 1 18.07354229 YAALSVDGEDENEGEDYAE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 351.37 1.35E-69 0 112160 146900 140170 133290 153240 164430 138570 148980 144370 136220 FALSE TRUE 116588.1634 172128.9323 143822.9454 159654.3642 127192.3195 126243.6245 127708.5213 146983.1668 139174.1519 162909.7009 0.71566127 1.056591052 0.882838435 0.980017539 0.780753502 0.774930061 0.78392214 0.902237043 0.854302421 1 17.31371299 5.038461583 14.70220237 0.879697257 0.11258867 0.233461344 0.093236279 1393211.568 16239847.87 0.022320835 27576778.54 109260.0974 -5.038461583 -0.767108587 YADEEIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 157.21 0.00088539 1242311000 1160221 1261892 1166868 1075795 1280180 1502829 1173086 1165054 1068577 1190040 FALSE TRUE 1206027.421 1478612.135 1197277.539 1288584.04 1062575.461 1153819.74 1081136.454 1149438.357 1030119.123 1423205.553 0.847402133 1.038930836 0.841254122 0.905409649 0.746607163 0.81071897 0.759648844 0.807640438 0.723802068 1 20.44071261 3.295206252 8.725544423 0.796184753 0.913270642 0.23277373 0.087341657 0.354005156 50.02301509 0.022215136 0.030034737 1973.359685 -3.295206252 0.11708589 YADEEIPRS(ph)PFK ddPTM_MDA-MB-175_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 201.16 9.18E-08 2045520000 2731930 1397690 1874930 1427240 2445800 2359560 2355390 1891720 2013490 1377970 TRUE FALSE 2839788.706 1637732.385 1923792.216 1709543.812 2030063.79 1811587.949 2170768.377 1866364.588 1941024.888 1647956.839 1.72321789 0.993795679 1.16738022 1.037371715 1.231867087 1.099293323 1.31724832 1.132532445 1.177837212 1 20.65224703 4.747635225 24.87350402 1.14162041 1.723218214 0.768098309 0.097783095 502.0686938 1376139.289 0.021836458 0.269079313 55928.76436 -4.747635225 0.581597804 YADLSDAANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YADLSDAANR 10 0 H7C5W5;P41219;P41219-2;F8W835 H7C5W5 PRPH Peripherin 0 81.784 0.046466 1543000000 1246500 1569300 1335700 1318100 1604700 1744000 1409400 1292900 1365900 1649300 FALSE TRUE 1295712.783 1838815.068 1370509.439 1578816.246 1331933.667 1338982.431 1298927.545 1275570.79 1316741.526 1972448.757 0.656905675 0.932249855 0.694826385 0.800434607 0.675269085 0.678842695 0.658535508 0.646694007 0.667566912 1 20.91155639 3.236590533 24.96661499 0.693822977 0.777166134 0.009340824 0.120126414 116.542566 1476933.344 0.031356198 0.03931508 1724.211481 -3.236590533 0.083343157 YADLSHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YADLSHNR 8 0 P54136;P54136-2 P54136 RARS "Arginine--tRNA ligase, cytoplasmic" 0 ;;;; 179.68 0.00024309 1459390000 1412580 1632360 1516850 1425740 2400290 2198090 1694510 1549550 1562190 2245150 FALSE TRUE 1468349.749 1912705.132 1556380.357 1707747.117 1992289.563 1687616.91 1561689.878 1528780.817 1505967.087 2685044.157 0.546862421 0.712355187 0.579647956 0.636021986 0.741995084 0.628524825 0.581625399 0.569368967 0.560872373 1 21.35651438 -0.910916294 5.001221908 0.999999841 0.618506337 0.775124148 0.061808922 9.56E-07 2.08E-07 0.06089692 0.01435349 0.122767583 0.910916294 -0.381493504 YADLTEDQLPSCESLKDTIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YADLTEDQLPSCESLKDTIAR 21 1 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 ;;;; 246.22 2.55E-30 7307964000 3283128 2630029 3192520 2574134 3976590 3888448 3486371 3277628 3472238 2598074 FALSE TRUE 3412748.429 3081716.022 3275719.694 3083290.022 3300650.652 2985414.882 3213100.131 3233696.758 3347272.833 3107116.857 1.098365007 0.99182495 1.054263436 0.992331529 1.06228726 0.96083122 1.034109845 1.0407387 1.077292225 1 21.56714507 -1.012118288 3.881586551 0.999995419 1.031963401 0.058996005 0.040254049 1547.189912 9531971.704 101.5143152 0.008625321 0.097248231 1.012118288 0.031967982 YADSPGAS(ph)SPEQPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 YADS(0.021)PGAS(0.759)S(0.221)PEQPK 217.39 4.92E-08 0 183390 107450 116460 96499 174220 185810 152470 122760 145770 99289 TRUE FALSE 190630.3788 125903.7017 119495.0433 115586.2142 144606.1466 142658.4435 140519.003 121114.603 140523.7662 118742.7785 1.605406081 1.060306178 1.006335246 0.973416789 1.217810029 1.201407321 1.183389885 1.019974473 1.183429998 1 16.85748025 4.741011913 24.82938401 1.095947057 1.605406279 0.744974737 0.089757374 105.9925302 1073536.519 0.022291469 0.151328663 55082.28058 -4.741011913 0.509459223 YAEAVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YAEAVTR 7 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 ;;; 141.83 0.0058871 1750340000 1357320 1496160 1476840 1470470 1772890 1891860 1586940 1577720 1401370 1533880 FALSE TRUE 1410908.042 1753113.841 1515327.664 1761324.577 1471534.791 1452504.186 1462551.496 1556573.244 1350934.967 1834414.418 0.76913266 0.955680365 0.826055252 0.960156309 0.802182308 0.791808095 0.797285216 0.848539582 0.736439353 1 20.80688817 YAEEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAEEDRR 7 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 ; 97.068 0.019673 1519680000 2712500 1545620 1466550 1457030 1786430 2400400 1831330 1315230 1596050 1466060 FALSE TRUE 2819591.595 1811068.212 1504769.498 1745226.185 1482773.267 1842943.478 1687785.569 1297601.493 1538608.472 1753306.388 1.608156803 1.032944512 0.858246744 0.995391449 0.845701172 1.051124602 0.962630138 0.740088271 0.877546836 1 20.7416467 4.734653675 2.902378602 0.906252761 1.726857689 0.848622294 0.087116116 0.144922484 1.75253718 0.02258622 0.277750099 54281.72931 -4.734653675 0.820604928 YAEIVHLTLPDGTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAEIVHLTLPDGTKR 15 1 P21281;H0YC04 P21281 ATP6V1B2 "V-type proton ATPase subunit B, brain isoform" 0 105.46 0.00085253 282710000 405990 450890 510890 453470 682410 731760 557990 544970 505040 508550 FALSE TRUE 422018.7987 528326.8501 524204.2131 543165.0125 566414.192 561819.8299 514253.2858 537665.5685 486863.7091 608190.6357 0.693892299 0.868686262 0.861907735 0.893083485 0.931310281 0.923756133 0.845546208 0.884041182 0.800511682 1 19.21416408 4.953467151 1.89634849 0.889061411 0.532371974 0.573494849 0.050916994 1.189607411 2.716685684 0.012394506 0.903009726 89839.4637 -4.953467151 -0.356689436 YAELLEEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 ; 113.22 0.0018358 313390000 101874 122857 117658 122429 129620 140638 112597 125674 111878 124086 FALSE TRUE 105896.0642 143956.7341 120724.2641 146645.0908 107587.2387 107976.9559 103771.3529 123989.5456 107851.5326 148398.2759 0.713593628 0.970070125 0.813515274 0.988185947 0.724989816 0.727615973 0.699276001 0.835518774 0.726770793 1 17.17911481 5.037975126 16.04825684 0.820375634 0.279183528 0.084050266 0.111462922 7801348.499 91916264.3 0.026026888 121741616.6 109137.7827 -5.037975126 -0.541192105 YAEQLLQEYVQLQGDPFGLPSFS(ph)PPRLPVAGLSAPAPSHAGLPVHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAEQLLQEYVQLQGDPFGLPSFSPPRLPVAGLSAPAPSHAGLPVHER 47 1 Q16619-2;Q16619 Q16619-2 CTF1 Cardiotrophin-1 1 YAEQLLQEYVQLQGDPFGLPS(0.054)FS(0.689)PPRLPVAGLS(0.191)APAPS(0.065)HAGLPVHER 104.07 8.13E-08 134990000 20581 24219 30288 20365 26078 37679 28425 27695 30518 21302 TRUE FALSE 21393.55377 28378.42485 31077.33016 24393.13622 21645.27087 28928.62328 26196.97423 27323.79382 29419.66314 25475.71905 0.83976251 1.113940093 1.219880393 0.957505308 0.849643177 1.135537067 1.028311475 1.072542595 1.154811885 1 14.63683525 YAGALRAS(ph)GEMASAQYITAALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAGALRASGEMASAQYITAALR 22 1 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 1 YAGALRAS(1)GEMASAQYITAALR 114.21 0.00014255 20812000 4282.8 5154.4 4469 5845.5 4913.8 7760.3 5512.4 4047.5 5306.5 3078.3 TRUE FALSE 4451.888251 6039.628104 4585.465811 7001.722453 4078.554031 5958.087933 5080.323684 3993.249883 5115.520102 3681.433947 1.209281034 1.640564028 1.245565146 1.901900877 1.107871033 1.618415003 1.379985016 1.084699587 1.389545534 1 11.8460521 1.908474369 5.448650869 1.176744049 1.460733082 0.23327622 0.239023109 0.318362041 14.53108426 0.097711108 0.058636981 80.99801365 -1.908474369 0.283989033 YAGGVAEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAGGVAEYR 9 0 A0A087WWM4;Q9P2T1;Q9P2T1-3;F8WAN9;H0YNJ6;Q9P2T1-2;H0YMB3;H0YLV5;H0YLB8;H0YK13;H0YK71 A0A087WWM4 GMPR2 GMP reductase;GMP reductase 2 0 77.674 0.052331 0 76620 78384 79255 75741 96949 109010 93451 90192 85124 95197 FALSE TRUE 79645.01676 91845.84226 81320.45041 90722.34374 80469.64361 83694.07956 86126.06643 88983.12376 82060.40387 113849.0295 0.699566936 0.806733642 0.714283211 0.796865324 0.706810097 0.73513213 0.756493637 0.781588777 0.720782638 1 16.79676247 -1.883246457 2.643086774 1.12279126 0.750091832 0.81367009 0.036359659 5149803.565 3518545.287 3963386.407 0.008184013 0.013084392 1.883246457 -0.372699427 YAGKDGYNYTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAGKDGYNYTLSK 13 1 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 ; 167.88 2.84E-05 9467900000 3931300 3735900 4421200 2053810 7989200 5082700 2866300 4036000 4892400 5659900 FALSE TRUE 4086510.76 4377511.764 4536420.104 2460047.488 6631198.638 3902319.954 2641631.916 3981904.022 4716323.48 6768849.04 0.603723135 0.646714344 0.670190763 0.363436601 0.979664135 0.576511595 0.390263086 0.588268995 0.696768897 1 22.69047911 0.862746708 3.452153853 0.999827073 0.599748488 0.361457122 0.158754374 0.687346033 14.96227358 0.148368689 0.038347261 7.290321961 -0.862746708 -0.400078585 YAHDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAHDLK 6 0 Q5T0N5-3;Q5T0N5-4;S4R347;Q5T0N5-2;Q5T0N5-5;Q5T0N5 Q5T0N5-3 FNBP1L Formin-binding protein 1-like 0 81.672 0.06126 214360000 143810 109570 144310 118810 189270 201280 183260 154800 148180 115050 FALSE TRUE 149487.7298 128387.7952 148070.8372 142310.2634 157097.953 154535.7704 168895.6023 152725.1592 142847.0307 137591.8447 1.086457778 0.93310614 1.076159982 1.034292866 1.14176791 1.123146293 1.227511723 1.109987002 1.038194022 1 17.07003544 3.250732658 21.10835842 1.120963721 1.028522334 0.198993973 0.069395245 43.60022022 75606.51956 0.018784333 0.025156065 1781.281913 -3.250732658 -0.092441386 YAHQSGFHVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAHQSGFHVDR 11 0 A0A0A0MSX9;P41252;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 130.56 0.00012813 152920000 11585 59756 37056 53389 34832 57041 29267 54427 34856 51322 FALSE TRUE 12042.38475 70018.62816 38021.7098 63949.18485 28911.26908 43794.09221 26972.97606 53697.49509 33601.53937 61377.56328 0.196201741 1.140785401 0.619472455 1.041898398 0.471039701 0.713519564 0.439459871 0.874871732 0.547456392 1 15.90542375 -1.739379145 4.25691051 1.023820099 0.693533345 0.110966188 0.272560936 0.056194145 0.003440374 0.240678469 0.055509433 0.018223041 1.739379145 -0.330286754 YAHVVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 ;;;; 133.99 0.0032182 2386853000 2492190 2890550 2903140 3090710 3006260 3656990 3104650 3036570 2791500 2574300 FALSE TRUE 2590583.586 3386979.477 2978798.213 3702043.213 2495256.999 2807709.495 2861299.421 2995869.746 2691034.46 3078684.797 0.841457881 1.100138436 0.967555437 1.202475556 0.810494469 0.911983421 0.929390181 0.97310051 0.874085734 1 21.55388274 3.214958059 24.99988307 0.919817457 1.028755636 0.233457064 0.098774682 334.9591989 354788.6549 0.02711716 0.032428547 1640.431343 -3.214958059 0.108938179 YALGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YALGER 6 0 P09960-4;P09960;P09960-3;P09960-2;B4DEH5 P09960-4 LTA4H Leukotriene A-4 hydrolase 0 ; 112.56 0.06256 333730000 419710 506500 476940 467460 602830 608820 480960 470000 471110 581070 FALSE TRUE 436280.4749 593487.435 489369.4482 559922.1928 500361.1719 467430.7818 443261.0984 463700.4188 454154.8431 694919.5412 0.627814371 0.854037626 0.704210227 0.805736721 0.720027488 0.672640146 0.637859597 0.667272096 0.653535864 1 19.40648642 -1.166723398 5.201627577 1.000013619 0.705861785 0.61943333 0.069412547 1.12E-05 1.79E-06 0.068370355 0.016114301 0.068120308 1.166723398 -0.294151834 YALPLVGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YALPLVGHR 9 0 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 ; 151.27 8.33E-05 2043600000 1603960 1983350 1642550 1920230 2176100 2425500 1693200 1632440 1585280 1897420 FALSE TRUE 1667285.579 2323974.934 1685356.202 2300045.763 1806207.299 1862214.384 1560482.56 1610559.812 1528226.082 2269183.121 0.734751446 1.024146052 0.742714939 1.013600772 0.795972473 0.820654079 0.68768472 0.709753125 0.673469703 1 21.11374161 2.691865125 2.205682052 0.74093602 0.877986272 0.09018708 0.126723457 0.491577404 4.717889254 0.042351351 0.040718515 491.8867514 -2.691865125 0.137050252 YALQMEQLNGILLHLESELAQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YALQMEQLNGILLHLESELAQTR 23 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;; 257.91 9.54E-44 11734821800 1492092.8 2116333.8 2040335.8 2331941.5 2285521.8 2724929.3 2103612.9 2378007.8 2396040.9 2286398.7 FALSE TRUE 1551001.776 2479797.667 2093508.627 2793192.569 1897029.621 2092105.767 1938726.224 2346134.495 2309807.856 2734374.75 0.567223559 0.906897516 0.765626082 1.021510519 0.693770896 0.765113036 0.709019941 0.85801498 0.844729808 1 21.38277955 0.837486211 1.401347333 0.998372659 0.788761344 0.239395925 0.117094457 0.925535262 3.419149666 0.104939379 0.031160558 6.878380722 -0.837486211 -0.209611315 YALTGDEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 149.23 3.80E-05 1213190000 1623170 858170 1176540 807920 1746520 1482990 1688870 1240600 1329010 697330 FALSE TRUE 1687254.005 1005554.022 1207201.599 967724.1646 1449647.154 1138588.047 1556491.956 1223971.786 1281179.19 833958.4623 2.023187102 1.205760319 1.447556028 1.160398519 1.738272612 1.365281484 1.866390266 1.467665167 1.536262593 1 19.669616 3.199699066 24.99998538 1.534347243 1.440284576 0 0.307175025 813.7211799 523471.4797 0.082948716 0.099144068 1583.795359 -3.199699066 -0.094062667 YALYDATYETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YALYDATYETK 11 0 G3V1A4;E9PQB7;E9PLJ3;P23528;E9PP50;E9PK25;Q9Y281;Q9Y281-3 G3V1A4;P23528;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 ;;;;; 278.16 6.99E-27 4185370000 2752220 2027130 2497440 1965260 3079420 3063860 2965040 2550050 2658990 1895210 FALSE TRUE 2860879.771 2375273.809 2562525.338 2353982.562 2555981.288 2352324.948 2732632.417 2515870.751 2563293.469 2266540.114 1.262223313 1.047973426 1.130589008 1.038579705 1.127701766 1.037848364 1.205640439 1.110004952 1.130927908 1 21.11206026 4.750292198 24.7313826 1.100176135 1.262223426 0.426075328 0.058554978 1469.56095 3097919.436 0.013003189 0.207915863 56271.98024 -4.750292198 0.16204729 YAPLHLVPLIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAPLHLVPLIER 12 0 Q7L576;Q7L576-2;Q7L576-3;Q96F07;Q96F07-2;E7EVJ5;H7C229;H0YL50;E7EW33 Q7L576 CYFIP1;CYFIP2 Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2 0 ; 78.692 0.025044 237610000 438340 463600 470360 485140 600060 631380 460690 442360 426050 588210 FALSE TRUE 455646.0017 543219.6937 482617.968 581099.244 498062.0155 484751.5637 424579.914 436430.8878 410716.5437 703458.4875 0.647722658 0.772212864 0.686064603 0.826060463 0.708019058 0.689097612 0.603560724 0.620407452 0.583853278 1 19.42410576 -1.133306606 4.93910274 1.000016667 0.681911401 0.643801198 0.070985658 1.41E-05 2.48E-06 0.074510745 0.017561432 0.073568753 1.133306606 -0.318105266 YAS(ph)SPKPNNSYMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YASSPKPNNSYMFK 14 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 YAS(0.5)S(0.5)PKPNNSYMFK 129.62 4.05E-05 490870000 919290 448490 622350 433660 1046300 792860 754800 623730 672420 420940 TRUE FALSE 955584.279 525514.6687 638568.9523 519436.6537 868450.2997 608730.2809 695636.8037 615369.9196 648219.7356 503415.1336 1.898203322 1.043899227 1.268473889 1.031825662 1.725117585 1.209201393 1.381835303 1.222390585 1.287644515 1 18.94138906 -4.688733028 0.141545454 2.90E-15 1.440190738 0.163340842 0.256719973 251.1364877 2.354894478 71.98429697 1.462810176 2.05E-05 4.688733028 1.440190738 YASICQQNGIVPIVEPEILPDGDHDLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YASICQQNGIVPIVEPEILPDGDHDLK 27 0 H3BPS8;P04075;P04075-2;H3BQN4;P09972 H3BPS8;P04075;P09972 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 ;;; 273.53 8.13E-61 2608820000 1205140 748540 889690 984710 1388510 1511190 1635550 972360 1062080 628209 FALSE TRUE 1252719.858 877095.9222 912876.0523 1179482.699 1152491.566 1160239.025 1507351.317 959327.1047 1023855.948 751294.5258 1.667415128 1.167446177 1.215070816 1.569933839 1.534007672 1.544319817 2.006338747 1.276898835 1.362789044 1 19.51901906 0.924804102 1.817959628 1.007607658 1.501893015 0.307096912 0.229447524 0.552596137 3.762436473 0.223886017 0.063428023 8.410156985 -0.924804102 0.494285358 YASICQQNGIVPIVEPEILPDGDHDLKR ddPTM_MDA-MB-175_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 ;;;;; 205 1.93E-25 34091250000 22775940 17423930 21176280 17074960 28771910 29240180 24974830 22997700 23971390 19079130 FALSE TRUE 23675151.7 20416354.44 21728151.25 20452336.12 23881271.02 22449591.33 23017237.57 22689453.45 23108664.36 22817320.23 1.037595627 0.894774418 0.952265693 0.896351365 1.046629086 0.983883782 1.008761648 0.994396065 1.012768551 1 24.44362603 3.235968283 24.99999942 1.005560625 0.942142961 0.368776229 0.039910669 68.31146613 658785.4795 0.010609649 0.013246395 1721.742828 -3.235968283 -0.063417664 YASPEMCFVFSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YASPEMCFVFSDR 13 0 A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566;A0A1B0GTG9;A0A1B0GWF8;P30566-2;A0A096LNY5;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4 A0A1B0GWJ0 ADSL Adenylosuccinate lyase 0 106.62 0.0031633 43915000 12244 13777 17558 12558 17853 16269 14645 12985 15688 19510 FALSE TRUE 12727.40257 16143.09258 18015.5759 15041.93492 14818.35344 12490.77131 13497.08663 12810.95731 15123.39194 23332.61096 0.545476998 0.691868244 0.772120014 0.644674312 0.635091952 0.535335344 0.578464479 0.549058026 0.648165436 1 14.51006014 0.951912414 22.29003089 1.000000001 0.618348974 0.726552357 0.069726295 1928.114811 893740.4259 0.074020307 0.018505077 8.951842125 -0.951912414 -0.381651027 YASS(ph)PKPNNSYMFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YASSPKPNNSYMFK 14 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 YAS(0.008)S(0.992)PKPNNSYMFK 220.1 2.89E-12 487890000 1157100 559250 780780 505310 1307400 1038300 1034200 788090 923710 553850 TRUE FALSE 1202783.201 655296.8371 801127.7682 605258.8098 1085168.615 797170.5606 953136.7016 777526.9426 890465.8575 662366.3034 1.815888271 0.989326954 1.209493545 0.91378261 1.638320986 1.203519195 1.438987305 1.173862466 1.34437071 1 19.33726975 -0.655894048 5.785182081 0.999999995 1.284173237 0.104053348 0.26155435 1.38E-08 3.58E-09 0.231659941 0.054602771 0.220854347 0.655894048 0.284173242 YATDTFAGLCHQLTNALVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YATDTFAGLCHQLTNALVER 20 0 Q9UNS2-2;Q9UNS2;H7C3P9;J3QKR0;K7ES36;C9JLV5 Q9UNS2-2 COPS3 COP9 signalosome complex subunit 3 0 ; 216.16 1.15E-24 487070000 377360 431670 428490 445020 467670 508750 388820 405530 497890 471130 FALSE TRUE 392258.4642 505805.9646 439656.8014 533043.6277 388175.6204 390600.5227 358343.2724 400094.5337 479971.0362 563438.9032 0.696186334 0.897712177 0.780309629 0.946053999 0.68894004 0.693243794 0.635993131 0.71009391 0.85185995 1 19.10389965 3.207487004 24.99593315 0.73467549 0.83134368 0.040286157 0.11692534 381.38477 306788.8253 0.031996699 0.038247088 1612.452774 -3.207487004 0.09666819 YAVTTGDHGIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YAVTTGDHGIIR 12 0 P53621;A0A3B3IT15;P53621-2;A0A3B3IS84;A0A3B3ISC6;A0A3B3IU89 P53621 COPA Coatomer subunit alpha;Xenin;Proxenin 0 ;;;; 261.22 2.37E-21 1853870000 809832 987301 1008465 1015062 1248951 1225930 1060884 988402 946529 1130200 FALSE TRUE 841804.7927 1156862.267 1034746.426 1215838.234 1036654.755 941226.3366 977729.14 975154.0879 912463.6062 1351641.051 0.622802032 0.855894593 0.765548239 0.899527454 0.7669601 0.696358205 0.72336449 0.72145936 0.675078347 1 20.36628064 -1.059921791 4.824400965 1.000007245 0.75149895 0.486711834 0.077707625 6.02E-06 1.17E-06 0.074821965 0.017635192 0.087112045 1.059921791 -0.248508295 YAVWFGGSMLASTPEFYQVCHTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YAVWFGGSMLASTPEFYQVCHTK 23 0 B4DXW1;P61158 B4DXW1 ACTR3 Actin-related protein 3 0 298.76 8.64E-62 193410000 186680 171640 203720 170930 237420 238020 231580 207870 227290 154380 FALSE TRUE 194050.2705 201117.8348 209029.1106 204739.4438 197063.4332 182743.4622 213428.1545 205083.8427 219109.8773 184627.8052 1.05103492 1.089314985 1.132164845 1.108930714 1.06735512 0.989793829 1.155991397 1.110796082 1.186765325 1 17.49426032 YAWQGVALLPFVDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAWQGVALLPFVDER 15 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 ; 129.34 0.00015461 152688000 222520 242710 267440 240370 294330 342170 246080 254290 244810 311110 FALSE TRUE 231305.2614 284393.5545 274409.7061 287914.4686 244299.8917 262706.2031 226791.6066 250881.6585 235999.3359 372066.0479 0.621677959 0.764363091 0.737529553 0.773826234 0.65660356 0.706074109 0.609546633 0.674293341 0.634294199 1 18.50519922 -0.627561231 6.122385949 1.000000001 0.688140997 0.743003495 0.055310802 7368436.716 1203523.793 0.117489831 0.013285063 0.23574298 0.627561231 -0.311859004 YAYDKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAYDKR 6 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 ; 119.7 0.033331 1217630000 1956270 1626180 1752120 1382800 2991900 2437200 2066300 1645480 1736650 2156900 FALSE TRUE 2033505.05 1905463.765 1797781.687 1656313.713 2483337.907 1871197.236 1904338.007 1623425.032 1674148.306 2579503.259 0.788332034 0.738694072 0.696948795 0.642105687 0.96271943 0.725409914 0.738257647 0.629355682 0.649019651 1 21.29866184 2.501043741 24.96331416 0.716005226 0.762613879 0 0.123795538 3285.712419 3428665.92 0.039163087 0.036720452 316.988671 -2.501043741 0.046608653 YAYYDTER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YAYYDTER 8 0 O00303 O00303 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 ; 147.34 0.0012538 809670000 491930 595330 548120 567750 835460 769960 671220 588790 604270 667220 FALSE TRUE 511351.7763 697573.2965 562404.4575 680049.2554 693448.8076 591148.4589 618608.0225 580898.2331 582522.4407 797948.9843 0.640832668 0.874207888 0.704812549 0.852246533 0.869039025 0.740834904 0.775247584 0.727989188 0.730024666 1 19.60593699 -2.309182809 2.357594384 2.224928487 0.771380285 0.47791508 0.07257072 2701893.915 514542.465 17709234.76 0.017026336 0.004907013 2.309182809 -1.453548202 YCDPDSYHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YCDPDSYHR 9 0 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ;;; 183.47 4.51E-05 1853760000 1495750 2477320 2162930 2542730 2145520 2808870 2346080 2400370 2087150 2270610 FALSE TRUE 1554803.365 2902780.439 2219297.733 3045674.405 1780825.277 2156552.511 2162188.119 2368196.966 2012033.879 2715492.556 0.572567714 1.068970133 0.817272626 1.121591881 0.655801936 0.794166239 0.796241593 0.872105858 0.740946196 1 21.37278248 4.770854089 23.60681528 0.863669082 0.572566576 0.290869404 0.140402779 8753.794245 6398860.342 0.031847389 4.370556623 59000.28226 -4.770854089 -0.291102506 YCDPDSYHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YCDPDSYHRR 10 1 P26368-2;P26368;K7ENG2 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 0 ; 70.1 0.035699 333640000 152095 271220 258100 220290 258090 291950 193208 246370 233470 327120 FALSE TRUE 158099.828 317799.9252 264826.298 263862.7045 214219.954 224149.037 178063.8521 243067.8131 225067.4603 391212.9009 0.404127338 0.812345208 0.676936516 0.674473423 0.547578961 0.572959216 0.455158436 0.621318501 0.575306846 1 18.57759442 -1.039191998 6.86745973 1.000000101 0.59835946 0.552674865 0.109668871 1.65E-07 2.33E-08 0.10341777 0.024375796 0.091370921 1.039191998 -0.401640641 YCFPNYVGRPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YCFPNYVGRPK 11 1 P61163;R4GMT0;A0A1B0GVS3;P42025 P61163;P42025 ACTR1A;ACTR1B Alpha-centractin;Beta-centractin 0 ; 185.14 4.19E-06 2813000000 1586720 1446120 1681570 1410430 2142690 2035130 1775010 1666820 1610390 1603570 FALSE TRUE 1649364.931 1694479.861 1725393.096 1689408.844 1778476.319 1562501.9 1635880.078 1644479.004 1552432.378 1917758.839 0.860048144 0.883572963 0.899692422 0.880928722 0.927372244 0.814754112 0.853016576 0.857500417 0.809503441 1 20.87098988 2.743792291 24.99121275 0.857088864 0.889946531 0.031476231 0.051969678 1089.89561 5206323.41 0.014756264 0.015266919 554.3605167 -2.743792291 0.032857667 YCHDNNIIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YCHDNNIIHR 10 0 A0A2U3TZM1;A0A2R8YE77;O14936;A0A2R8YEK3;O14936-6;O14936-2;A0A2U3TZN6;A0A2R8YGH2;A0A2R8Y6F8;O14936-3;A0A2U3TZM4;A0A2R8YFN5;O14936-4 A0A2U3TZM1;A0A2R8Y6F8 CASK Peripheral plasma membrane protein CASK 0 67.726 0.035918 71868000 42709 168150 123590 131700 102880 161110 93418 136780 107080 187610 FALSE TRUE 44395.1843 197028.4545 126810.8569 157749.8669 85392.49435 123694.6441 86095.65306 134946.6878 103226.2117 224368.5875 0.197867201 0.878146342 0.565189888 0.703083567 0.380590239 0.551301078 0.383724184 0.601450895 0.460074259 1 17.77551118 -1.56852506 3.875604668 1.009853951 0.536716878 0.38860098 0.178309098 0.014062584 0.001565602 0.159915281 0.037195858 0.027006913 1.56852506 -0.473137073 YCLS(ph)ILTSHVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YCLSILTSHVK 11 0 O95163;F5H2T0 O95163 IKBKAP Elongator complex protein 1 1 Y(0.239)CLS(0.283)ILT(0.239)S(0.239)HVK;Y(0.22)CLS(0.26)ILT(0.26)S(0.26)HVK 58.223 0.055676 0 552360 391450 448900 377870 458420 568350 469800 468210 541130 359670 TRUE FALSE 574167.5993 458678.4924 460598.7028 452611.5582 380497.9321 436359.3259 432975.8484 461934.4108 521654.837 430140.4502 1.334837491 1.06634587 1.070810017 1.052241327 0.88458998 1.014457779 1.006591796 1.0739153 1.212754664 1 18.71444828 4.859357359 2.233370305 1.035787054 1.482314346 0.563000205 0.07743645 0.768555154 3.297181428 0.020106783 0.760449112 72336.47784 -4.859357359 0.446527292 YCQVIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YCQVIR 6 0 P39023;H7C422;G5E9G0;H7C3M2;B5MCW2 P39023 RPL3 60S ribosomal protein L3 0 ;;; 112.27 0.06314 876760000 600250 725300 641130 655950 758220 888420 673410 695130 667470 741610 FALSE TRUE 623948.3335 849864.6329 657838.3745 785694.9522 629338.0352 682097.9191 620626.3646 685812.9194 643447.8851 886914.2805 0.703504665 0.958226349 0.741715844 0.885874734 0.709581579 0.769068594 0.699759129 0.773257275 0.7254905 1 19.75843515 5.035593771 17.47048158 0.792768853 0.329888532 0.070777618 0.101309308 870526.3458 10930446.69 0.022413855 12749439.78 108540.9882 -5.035593771 -0.462880321 YCRPESQEHPEADPGSAAPYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YCRPESQEHPEADPGSAAPYLK 22 1 P40763;P40763-3;G8JLH9 P40763 STAT3 Signal transducer and activator of transcription 3;Signal transducer and activator of transcription 0 ; 161.58 1.03E-11 335450000 204748 198756 219570 214634 301650 281200 252670 224733 207336 204827 FALSE TRUE 212831.6091 232890.7969 225292.1746 257087.9646 250375.6407 215895.5616 232865.0652 221720.8217 199874.0179 244958.929 0.868846096 0.950734059 0.919714074 1.049514568 1.022112734 0.881354121 0.950629014 0.90513468 0.815949101 1 17.90218035 2.716574192 24.94442839 0.908221166 0.964040415 0.137700228 0.06430346 1565.061987 1775619.484 0.021105139 0.019912035 520.6839515 -2.716574192 0.055819249 YDAVQHCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDAVQHCR 8 0 P49585;C9JEJ2;C9J050;H7C1T3;C9J2E1;H7BZN1 P49585 PCYT1A Choline-phosphate cytidylyltransferase A 0 94.302 0.01079 0 88430 112630 94332 82649 127700 136870 108710 102820 102180 113770 FALSE TRUE 91921.28468 131973.3264 96790.36941 98996.72552 105993.5996 105084.0168 100189.0261 101441.8661 98502.56176 136061.0532 0.675588513 0.969956672 0.711374542 0.727590469 0.779014987 0.772329879 0.736353451 0.745561376 0.723958542 1 17.05389464 -1.219138185 8.92672951 1.000000025 0.762607929 0.474532647 0.07566659 3.61E-08 3.10E-09 0.068688258 0.016189976 0.060375649 1.219138185 -0.237392096 YDCGEEILITVLSAMTEEAAVAIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDCGEEILITVLSAMTEEAAVAIK 24 0 P63241;P63241-2;Q6IS14 P63241 EIF5A;EIF5AL1 Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-1-like 0 63.69 0.044802 110100000 7155.2 7228 7630.6 6223.7 7767.8 7857.7 7865.1 5918.6 9040.2 8867.5 FALSE TRUE 7437.692821 8469.352774 7829.459705 7454.729284 6447.432131 6032.86826 7248.61291 5839.270848 8714.844968 10604.91685 0.701343813 0.7986251 0.738285818 0.702950282 0.607966307 0.568874641 0.683514356 0.550619202 0.821774003 1 13.37244569 -1.647056925 5.554450633 1.003547945 0.676121729 0.54485838 0.085670645 0.00395705 0.00025144 0.087204265 0.020373486 0.022539438 1.647056925 -0.327426216 YDDAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 110.61 0.066431 1195220000 1906090 2164320 2168850 2197160 2278970 2829150 2657640 2390150 2158010 1887340 FALSE TRUE 1981343.905 2536025.124 2225372.013 2631751.69 1891591.493 2172122.789 2449327.232 2358113.949 2080343.642 2257128.138 0.877816315 1.123562762 0.985930739 1.165973542 0.838052329 0.962339157 1.085152053 1.044740841 0.921677244 1 21.10605689 YDDAERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDDAERR 7 1 P29692;P29692-2;E9PRY8;P29692-4;E9PK01;E9PQ49;A0A087X1X7;E9PQZ1;E9PI39;E9PPR1;E9PL12;E9PMW7;E9PK06;H0YCK7;E9PIZ1;E9PK72;E9PKK3;E9PJD0;E9PNW6;P29692-3;E9PL71;E9PN91 P29692;P29692-3 EEF1D Elongation factor 1-delta 0 ;;; 117.39 0.0084057 4616548000 4873520 5441000 5295490 4620310 6367770 6310090 4976170 5247130 5281130 5585510 FALSE TRUE 5065930.333 6375449.425 5433494.82 5534193.528 5285378.73 4844667.228 4586124.793 5176800.805 5091063.163 6679883.743 0.758386003 0.954425207 0.813411584 0.828486504 0.791238131 0.725262207 0.686557576 0.774983668 0.762148468 1 22.67139156 5.057381076 21.71798574 0.801334585 0.000457005 0.01367358 0.092239036 646.8416969 1547677.298 0.02121358 179492.2535 114125.0749 -5.057381076 -0.80087758 YDDAIQLYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDDAIQLYDR 10 0 Q15006;H0YAS9 Q15006 EMC2 ER membrane protein complex subunit 2 0 ;;; 187.22 2.92E-06 563921000 740564 789631 806850 752404 1014900 1036510 871240 833490 787276 820470 FALSE TRUE 769802.0386 925243.9818 827877.1738 901227.2655 842387.6605 795796.261 802949.9322 822318.4299 758942.0905 981225.3877 0.78453131 0.942947455 0.843717646 0.918471206 0.858505774 0.811022902 0.81831345 0.838052541 0.773463569 1 19.90422504 2.996398635 24.82020898 0.835734377 0.877040307 0.009337693 0.068926739 365.1234156 2516426.424 0.018341923 0.021476081 991.7418374 -2.996398635 0.04130593 YDDIKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDDIKK 6 1 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ; 95.62 0.069169 85562000000 69828000 30917000 49141000 35558000 65822000 59727000 79088000 50122000 53090000 21849300 FALSE TRUE 72584863.36 36226754.25 50421654.83 42591266.27 54633599.95 45856309.42 72888875.9 49450196.57 51179301.27 26130252 2.777809542 1.386391308 1.929627576 1.629960027 2.090817951 1.754912636 2.789444047 1.892450045 1.958622567 1 24.6392177 YDDMAACMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YDDMAACMK 9 0 P63104;E7EX29;E7ESK7;E9PD24;E7EVZ2;E5RIR4;E5RGE1 P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;;; 155.1 0.00025346 1284726000 1808150 1636750 1934950 1537727 2598360 2367740 2153920 1893470 2037730 1769030 FALSE TRUE 1879537.158 1917849.08 1985376.387 1841884.811 2156691.695 1817868.268 1985090.122 1868091.132 1964392.495 2115637.558 0.888402246 0.906511171 0.938429354 0.870605082 1.01940509 0.859253165 0.938294045 0.882992044 0.928510882 1 21.01266106 YDDMATCMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDDMATCMK 9 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 114.89 0.0036388 90406000 96037 98982 111970 98527 136640 135850 120940 118730 115110 91425 FALSE TRUE 99828.61492 115981.3885 114888.0302 118015.3465 113413.9816 104300.8963 111460.4068 117138.6186 110967.2136 109337.9783 0.91302781 1.060760317 1.050760513 1.079362801 1.037278934 0.953931085 1.019411631 1.071344288 1.014900909 1 16.73843508 4.746064293 24.74791895 1.035060675 0.913027743 0.499872223 0.035571938 680.9430883 2245760.106 0.008929313 0.092772015 55726.82414 -4.746064293 -0.122032932 YDDPPDWQEILTYFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDDPPDWQEILTYFR 15 0 P61221;D6R9I9;D6RGF4;H0Y990 P61221 ABCE1 ATP-binding cassette sub-family E member 1 0 80.318 0.04031 176620000 64777 63273 98836 81874 84563 121640 119870 79038 78260 71582 FALSE TRUE 67334.44598 74139.64555 101411.7474 98068.43283 70189.01147 93390.95347 110474.2762 77978.62489 75443.43789 85607.12238 0.786551914 0.866045295 1.184618108 1.145563945 0.819896867 1.090925041 1.290479964 0.910889453 0.881275247 1 16.38544321 4.413889378 7.301306034 1.041095667 0.805790193 0.286274055 0.137744916 0.243661219 23.11903355 0.034368383 0.095816676 25935.18666 -4.413889378 -0.235305474 YDDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 110.34 0.066976 548170000 561740 683420 712960 626930 776910 827280 723770 725520 646620 593210 FALSE TRUE 583917.929 800792.0687 731540.3233 750934.8828 644851.1157 635156.7575 667039.0162 715795.5911 623348.2725 709438.1418 0.823070955 1.128769404 1.031154487 1.058492402 0.908960313 0.895295474 0.940235627 1.008961245 0.878650633 1 19.43631737 3.236284098 24.99996846 0.942016449 1.020313261 0.149800483 0.082085387 104.6274305 1148988.952 0.022608166 0.028271549 1722.99532 -3.236284098 0.078296811 YDDYRDYDS(ph)PERER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 160.43 3.75E-06 1905340000 1367530 1461970 1522750 1297010 1873150 1902860 1473090 1556760 1489250 1532410 TRUE FALSE 1421521.14 1713051.975 1562434.116 1553554.707 1554752.632 1460949.603 1357625.357 1535894.179 1435652.183 1832656.4 0.77566157 0.934737125 0.852551584 0.847706481 0.848360136 0.797175948 0.740796451 0.838069907 0.783372259 1 20.80550489 2.901406752 5.062270011 0.815936994 0.85742715 0 0.073633834 0.654861687 26.30275748 0.021097889 0.022612548 796.9053677 -2.901406752 0.041490155 YDDYSSSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDDYSSSR 8 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 ;;; 210.1 9.75E-05 7380800000 5549850 6488070 6446850 5854700 7396650 7594260 6695860 6597520 6263140 6135220 FALSE TRUE 5768962.363 7602345.552 6614860.207 7012742.185 6139370.075 5830608.207 6171020.997 6509091.036 6037730.815 7337298.893 0.786251514 1.036123192 0.901538877 0.955766187 0.836734357 0.794653222 0.84104806 0.887123604 0.822881949 1 22.80681763 3.23362276 24.99596388 0.855516264 0.926907244 0.103516119 0.077713917 212.4285216 1075335.972 0.020734741 0.025530748 1712.469164 -3.23362276 0.07139098 YDEEFQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDEEFQR 7 0 P55060-3;P55060 P55060-3 CSE1L Exportin-2 0 ; 152.39 0.004227 889750000 1072440 845620 1093550 1243080 1124050 1322720 1422280 1055310 1079160 667280 FALSE TRUE 1114780.759 990848.657 1122048.811 1488957.514 932984.3825 1015538.326 1310797.977 1041165.296 1040321.242 798020.7402 1.396932064 1.241632713 1.406039662 1.865813053 1.169122976 1.272571344 1.642561291 1.304684507 1.303626823 1 19.60606672 0.824118639 1.535426921 1.001810565 1.419836055 0.296774639 0.193620042 0.81930277 3.565578594 0.182191613 0.053007146 6.669889497 -0.824118639 0.418025491 YDEELEGERPHSFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDEELEGERPHSFR 14 1 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 0 ; 143.93 5.40E-06 189044000 223560 242730 261930 225106 283580 305720 291540 273560 246490 226590 FALSE TRUE 232386.3214 284416.9893 268756.111 269631.2949 235377.1729 234721.1632 268688.333 269893.3757 237618.873 270985.9722 0.857558491 1.049563514 0.991771304 0.995000932 0.868595415 0.86617459 0.991521188 0.99596807 0.876867799 1 18.04785865 4.83355329 0.001137213 1.841227958 0.060389906 0.002486221 0.068879553 7515851.383 1357.509358 1054421.127 1071441.684 68163.72101 -4.83355329 -1.780838052 YDEFHDYLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDEFHDYLER 10 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 ;;; 141.1 3.81E-05 389319000 546322 622390 632255 636330 768184 833142 739058 661674 673607 597528 FALSE TRUE 567891.2144 729280.641 648732.0847 762194.1747 637608.3581 639657.3969 681128.7028 652805.3423 649364.0157 714602.1712 0.794695618 1.020540757 0.907822717 1.066599299 0.892256396 0.89512378 0.953157897 0.913522752 0.908707029 1 19.44678077 YDEGS(ph)GGS(ph)GDEGRDEAHKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDEGSGGSGDEGRDEAHKR 19 2 O94762-4;O94762 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 2 Y(0.129)DEGS(0.874)GGS(0.997)GDEGRDEAHKR;Y(0.049)DEGS(0.964)GGS(0.987)GDEGRDEAHKR 58.284 0.042945 468390000 150080 109315 117394 99328 148761 164608 120168 117038 136572 86687 TRUE FALSE 156005.2743 128089.0009 120453.3841 118974.7819 123474.6584 126380.2867 110748.9182 115469.297 131656.8004 103671.6579 1.504801576 1.235525731 1.161873809 1.147611452 1.191016531 1.21904375 1.068266104 1.113798114 1.269940146 1 16.66166201 4.844371529 1.766760112 1.146953587 1.697089024 0.694230445 0.071609897 0.65159648 1.64562044 0.017817594 0.65254015 69882.99822 -4.844371529 0.550135437 YDEIRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDEIRR 6 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 88.591 0.081983 37794000 103060 108150 111130 118720 135450 150000 143090 127880 123970 104260 FALSE TRUE 107128.8884 126723.9212 114026.1391 142202.4617 112426.2574 115164.7733 131874.2319 126165.9778 119508.3439 124687.7508 0.859177326 1.016330156 0.914493512 1.140468576 0.901662406 0.923625396 1.057635823 1.01185543 0.958460981 1 16.92796022 4.744762785 24.37147779 0.993233502 0.859177241 0.249583561 0.068841494 681.9422845 2679592.054 0.015719816 0.144462075 55560.07008 -4.744762785 -0.134056261 YDEMVESMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDEMVESMK 9 0 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 118.26 0.0023673 238400000 471710 407040 473180 408550 551620 609760 609240 499380 512400 351570 FALSE TRUE 490333.475 476945.9537 485511.4595 489359.9706 457855.8294 468152.481 561486.1768 492686.6279 493958.8241 420453.4103 1.166201684 1.134361006 1.154733075 1.163886316 1.088957345 1.113446745 1.335430188 1.171798387 1.174824159 1 18.68158642 YDEMVESMKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDEMVESMKK 10 1 P62258;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 ; 161.62 1.13E-05 3313100000 6965400 4222600 5948500 4124500 8455000 7237200 7771100 5996900 7128700 4006700 FALSE TRUE 7240399.37 4947798.703 6103522.797 4940313.79 7017822.12 5556469.981 7161980.876 5916521.364 6872139.48 4791736.152 1.511017957 1.032569103 1.273760199 1.031007057 1.464567726 1.159594311 1.494652595 1.234734379 1.434164833 1 22.19211704 3.232193937 24.99996489 1.311434087 1.203670878 0.043777799 0.188805337 408.4879925 1604002.196 0.049263674 0.060242843 1706.844422 -3.232193937 -0.107763208 YDERPGPS(ph)PLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 146.76 2.39E-05 19694140000 8859180 9475040 9865140 8970970 11084740 12194650 10264840 9920630 9740970 9102520 TRUE FALSE 9208947.267 11102304.41 10122233.65 10745401.09 9200559.854 9362627.349 9460255.019 9787660.182 9390394.392 10885984.52 0.845945284 1.019871413 0.929840901 0.987085833 0.845174806 0.860062527 0.869030725 0.899106568 0.862613242 1 23.37596855 3.238710461 25 0.882697212 0.949853042 0.176415265 0.058331622 5.559815735 927467.5586 0.015209893 0.019350937 1732.648477 -3.238710461 0.067155831 YDERPGPS(ph)PLPHRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDERPGPSPLPHRDR 15 2 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 YDERPGPS(1)PLPHRDR;Y(0.001)DERPGPS(0.999)PLPHRDR;YDERPGPS(1)PLPHRDR;YDERPGPS(1)PLPHRDR 131.11 2.90E-05 702778000 354173 487488 465887 375937 563170 528362 372298 457394 442667 647513 TRUE FALSE 368156.0235 571210.2719 478028.398 450296.2165 467442.5646 405657.9329 343116.3099 451263.3816 426735.5011 774380.775 0.475419891 0.737634882 0.617304062 0.581491988 0.603634 0.523848146 0.443084747 0.582740941 0.551066755 1 19.56268361 -1.064687138 6.587354105 1.000000296 0.5703908 0.738549921 0.077018343 3.38E-07 4.80E-08 0.075209997 0.017727154 0.086161423 1.064687138 -0.429609497 YDERPGPSPLPHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 ; 97.69 0.0022008 801100000 479600 1025670 1076060 1049550 1145060 1291120 986630 1074920 920410 1054700 FALSE TRUE 498534.9783 1201820.844 1104103.008 1257147.857 950423.1102 991276.9471 909295.3625 1060512.456 887284.6239 1261348.272 0.395239752 0.95280651 0.875335569 0.996669901 0.75349777 0.785886792 0.720891591 0.840776873 0.703441424 1 20.26653524 -2.598056662 2.013126952 4.278410106 0.795030964 0.142438568 0.157993627 5105393.411 230122.4337 76657098.04 0.038707949 0.002523152 2.598056662 -3.483379143 YDFGIYDDDPEIITLER ddPTM_MDA-MB-175_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 0 112.51 0.0010644 35879000 41841 51570 42255 47705 49055 63593 43909 41679 44856 40191 FALSE TRUE 43492.91499 60426.74634 43356.20001 57140.90661 40716.64862 48824.48951 40467.29785 41120.36118 43241.64132 48065.65695 0.904864674 1.257170924 0.902020336 1.188809438 0.847104798 1.015787417 0.841917086 0.855503987 0.899636956 1 15.55271883 3.222776917 24.99888916 0.899876068 1.065556267 0.29052739 0.116639019 261.2730503 413814.4455 0.030963082 0.037122703 1670.232449 -3.222776917 0.165680199 YDFIDLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDFIDLDR 8 0 Q6V1X1-5;Q6V1X1-3;Q6V1X1;H3BNM2;Q6V1X1-6;H0YK36 Q6V1X1-5 DPP8 Dipeptidyl peptidase 8 0 96.711 0.02035 57589000 133190 153400 152220 158360 169570 201850 175970 164400 152640 122670 FALSE TRUE 138448.444 179745.2567 156186.9783 189683.1353 140746.552 154973.3966 162177.0116 162196.4869 147146.5162 146704.8378 0.943721053 1.225216969 1.064634136 1.292957602 0.959385894 1.056361868 1.105464646 1.105597397 1.00301066 1 17.16255692 3.19871732 24.99998721 1.053091647 1.133532858 0.172047524 0.097064938 296.8570746 186264.3682 0.026723792 0.031941506 1580.219148 -3.19871732 0.08044121 YDGSTIVPGEQGAEYQHFIQQCTDDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDGSTIVPGEQGAEYQHFIQQCTDDVR 27 0 Q14019 Q14019 COTL1 Coactosin-like protein 0 ; 314.51 4.04E-82 707560000 322060 339820 353740 370350 395260 444600 388750 366920 392970 343870 FALSE TRUE 334775.1775 398181.4416 362958.755 443604.1246 328073.8464 341348.388 358278.7592 362002.0376 378827.0865 411244.7427 0.814053391 0.968234728 0.882585763 1.078686433 0.797758153 0.830037086 0.871205688 0.880259369 0.921171865 1 18.64963771 0.897308279 4.190393775 0.999974473 0.892494307 0.154049616 0.077552699 1.013210948 36.73008604 0.072817054 0.018563289 7.894202803 -0.897308279 -0.107480166 YDHQAEEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDHQAEEDLR 10 0 Q15417;Q15417-3 Q15417 CNN3 Calponin-3 0 96.756 0.0065239 239290000 551350 328960 417730 334650 609320 597120 504620 463890 526580 305020 FALSE TRUE 573117.7237 385456.321 428616.387 400842.7712 505748.004 458447.9294 465066.5658 457672.3133 507628.4887 364782.829 1.571120344 1.056673424 1.174990578 1.098853179 1.386435884 1.256769488 1.274913534 1.254643248 1.391590964 1 18.4766783 -1.081965161 4.17605602 0.999962611 1.261685358 0.244562884 0.143002486 1.118277663 37364318.1 3030.782735 0.031424951 0.082800858 1.081965161 0.261722747 YDIDLPNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDIDLPNKK 9 1 O00244;E5RGN3;E5RIM7 O00244 ATOX1 Copper transport protein ATOX1 0 ; 111.06 0.003506 4587500000 16540900 10915900 14748400 11302900 18936700 18353500 19684600 16015500 16486000 9060800 FALSE TRUE 17193947.5 12790620.91 15132755.42 13538579.88 15717846.5 14091177.77 18141669.62 15800838.42 15892672.08 10836090.28 1.586729813 1.18037231 1.396514336 1.24939711 1.450509002 1.300393169 1.674189597 1.458167846 1.466642642 1 23.36934098 YDLDFKSPDDPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 136.83 6.19E-05 2421000000 4717340 3662610 4352400 2794500 6938190 5605490 3943730 4085290 4897130 4086960 FALSE TRUE 4903584.226 4291634.776 4465827.12 3347243.759 5758838.942 4303699.9 3634610.138 4030533.37 4720883.248 4887721.562 1.003245411 0.878044038 0.913682799 0.684827013 1.178225656 0.880512493 0.743620538 0.824624177 0.965865831 1 22.22073067 2.486131066 24.98221816 0.853739707 0.925468328 0.012232904 0.133105234 1371.746213 3803562.135 0.044152548 0.038784814 306.2887644 -2.486131066 0.071728621 YDLIQNSESPAS(ph)PPVAVPHSWSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDLIQNSESPASPPVAVPHSWSR 23 0 A0A1B0GU24;Q9HCJ0-2;Q9HCJ0 A0A1B0GU24 TNRC6C Trinucleotide repeat-containing gene 6C protein 1 YDLIQNSESPAS(1)PPVAVPHSWSR;YDLIQNSESPAS(1)PPVAVPHSWSR 188.8 1.30E-17 249540000 102346 99156 122348 128343 129004 157150 134769 124715 116571 108919 TRUE FALSE 106386.6991 116185.2717 125536.4894 153728.8623 107075.9462 120654.2941 124205.4536 123043.3994 112375.6325 130259.5927 0.816728326 0.89195175 0.963740841 1.180173062 0.822019661 0.926260336 0.953522509 0.944601445 0.862705235 1 16.99103009 7.999926834 0.006530321 1.804400975 2.47E-05 0.0302534 0.098224897 183671.3032 92.75420656 11627.1301 14113.17083 99983154.41 -7.999926834 -1.804376305 YDLSGRPLNIKEDPDGENAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDLSGRPLNIKEDPDGENAR 20 2 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ; 89.028 0.001202 348430000 331860 255104 321470 236465 370030 397560 382570 338800 342620 238568 FALSE TRUE 344962.0891 298916.1276 329847.7723 283237.0712 307132.4328 305232.7151 352583.1637 334258.9402 330289.1731 285310.8319 1.209074632 1.047685871 1.156099718 0.992731574 1.076483605 1.06982519 1.235786112 1.171560638 1.157646805 1 18.12217499 2.276525512 24.99991573 1.160127015 1.087668267 0.064700967 0.078726917 282.1092581 185768.1924 0.025767248 0.021557943 189.027727 -2.276525512 -0.072458749 YDLSGRPLNIKEDPDGENARR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDLSGRPLNIKEDPDGENARR 21 3 A0A0A0MQW0;A0A0A0MR39;Q9P2K5-2;Q9P2K5;A0A087WUT0 A0A0A0MQW0 MYEF2 Myelin expression factor 2 0 ; 93.776 0.00073192 201600000 348396 306565 343488 244443 464190 427450 326054 369579 391260 317959 FALSE TRUE 362150.9431 359215.154 352439.5795 292793.0958 385287.1496 328181.2156 300497.0355 364625.398 377178.629 380256.9784 0.952384739 0.944664199 0.92684579 0.769987436 1.013228347 0.863051132 0.790247261 0.958892062 0.991904555 1 18.5366152 1.522001209 7.833506675 0.989201312 0.894760943 0.265678106 0.069642559 0.161146436 18.94282405 0.037904462 0.01751691 33.26604795 -1.522001209 -0.094440369 YDNGSGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YDNGSGYR 8 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;; 194.22 0.00038737 838660000 837440 1018840 978930 1002650 1102120 1223160 969340 963500 966820 947540 FALSE TRUE 870502.7778 1193817.845 1004441.72 1200971.177 914782.0361 939099.6272 893360.5979 950585.8585 932024.3371 1133192.321 0.768186266 1.053499765 0.886382392 1.059812315 0.807261061 0.828720429 0.78835744 0.838856601 0.82247675 1 20.1119613 3.202560092 24.99878729 0.834791547 0.945966279 0.184022286 0.094917503 226.933074 157581.8017 0.025052778 0.029944769 1594.26346 -3.202560092 0.111174732 YDNSLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 YDNSLK 6 0 P04406;E7EUT5;P04406-2 P04406;P04406-2 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 ;;;;;;;;; 146.94 0.025485 48397760000 20204220 15867440 19531240 15319660 22569560 22317200 22676590 19145800 18706300 12862410 FALSE TRUE 21001898.21 18592549.39 20040240.16 18349843.02 18733194.25 17134368.52 20899139.62 18889181.87 18033063.92 15382552.97 1.365306412 1.208677742 1.302790258 1.192899713 1.217820883 1.113883277 1.358626208 1.227961438 1.17230631 1 23.87479163 -4.549301462 0.225875321 2.39E-12 1.270122409 0.518709 0.07272612 103.454452 1.248092889 47.16131188 0.129307674 2.82E-05 4.549301462 1.270122409 YDPQKEAELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDPQKEAELR 10 1 B4DDF4;B4DUT8;Q99439;H3BVI6;Q99439-2;A0A087X271;K7ES69 B4DDF4 CNN2 Calponin;Calponin-2 0 ;;; 101.93 0.0027493 3143810000 6982200 6057400 7388600 4419120 10165400 8674100 6344700 7014000 8088600 7344900 FALSE TRUE 7257862.647 7097711.33 7581152.986 5293208.746 8437488.939 6659671.732 5847385.835 6919988.803 7797492.866 8783992.528 0.826260112 0.808027933 0.863064599 0.602597137 0.960552837 0.758159995 0.665686568 0.787795388 0.887693477 1 23.0664454 1.013897423 3.03868162 0.998548327 0.78092925 0.349614374 0.093546886 0.241833485 5.210885873 0.085301994 0.022479871 10.32517505 -1.013897423 -0.217619077 YDPSIGIYGLDFYVVLGRPGFSIADKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDPSIGIYGLDFYVVLGRPGFSIADKK 27 2 Q5VVC8;P62913-2;P62913 Q5VVC8 RPL11 60S ribosomal protein L11 0 206.46 1.54E-25 209210000 247870 140960 214520 158000 351010 301450 293530 240070 273510 177020 FALSE TRUE 257656.099 165168.7835 220110.5674 189251.9284 291345.4456 231442.806 270522.3516 236852.2543 263666.4285 211703.6797 1.217060087 0.780188534 1.039710636 0.893947279 1.376194528 1.09323941 1.277834905 1.118791391 1.245450381 1 17.69168682 3.257991087 24.99905988 1.188250144 0.972329894 0.325038214 0.142620255 250.9564651 322876.1506 0.035799283 0.048401035 1811.302917 -3.257991087 -0.21592025 YDPSLLDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDPSLLDVR 9 0 P35219 P35219 CA8 Carbonic anhydrase-related protein 0 87.616 0.031035 46454000 62159 69376 66679 66512 81631 85261 61611 61554 54695 66523 FALSE TRUE 64613.08532 81290.78833 68416.70952 79667.87508 67755.39178 65460.42489 56781.76883 60728.96931 52726.53763 79556.90819 0.812161845 1.021794212 0.859971951 1.001394812 0.851659439 0.82281258 0.713725183 0.763339988 0.662752473 1 16.27969959 2.784759374 2.305841707 0.765219279 0.92547964 0.251747357 0.101741433 0.327249755 3.427059901 0.032503292 0.033270107 609.1992695 -2.784759374 0.160260362 YDS(ph)DGDKSDDLVVDVSNEDPATPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 120.13 0.00013252 34086000 59101 27889 38786 30909 55735 76425 56809 40934 38242 24910 TRUE FALSE 61434.35312 32678.7188 39796.79502 37022.70795 46261.18461 58676.45198 52356.16214 40385.34668 36865.67789 29790.63757 2.062203368 1.096945936 1.335882622 1.242763196 1.552876621 1.969627264 1.757470347 1.355638885 1.237492075 1 14.86257138 1.182901284 2.1070318 1.023495164 1.544798919 0.286468169 0.29088857 0.412624755 3.26788364 0.279724828 0.079884068 15.23706373 -1.182901284 0.521303754 YDS(ph)SNQVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDSSNQVK 8 0 O95983-2;O95983;K7EIE8;A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YDS(0.666)S(0.334)NQVK;YDS(0.5)S(0.5)NQVK;YDS(0.5)S(0.5)NQVK;YDS(0.907)S(0.093)NQVK 140.48 0.0006806 891470000 1093190 838170 1174510 916420 1621450 1577860 1493430 1330550 1392060 897780 TRUE FALSE 1136349.985 982119.1774 1205118.695 1097685.141 1345836.508 1211425.928 1376371.054 1312716.154 1341960.033 1073682.802 1.058366571 0.914720042 1.122415944 1.022355149 1.253476824 1.128290334 1.281915899 1.222629394 1.249866376 1 20.03413641 3.247094036 24.95658925 1.20528519 1.027907748 0.424076354 0.09014159 150.2579633 439437.0117 0.023432351 0.031231591 1766.420256 -3.247094036 -0.177377442 YDSDGVWDPEKWHASLYPAS(ph)GR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDSDGVWDPEKWHASLYPASGR 22 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 YDSDGVWDPEKWHASLYPAS(1)GR;YDSDGVWDPEKWHASLYPAS(1)GR 212.28 1.38E-23 228580000 90266 277320 292050 360210 340310 372470 338870 365600 289740 218451 TRUE FALSE 93829.77138 324947.5527 299661.0629 431458.4629 282464.2278 285969.4873 312308.4839 360699.73 279312.314 261252.291 0.35915387 1.243807477 1.147017934 1.651501165 1.081193304 1.094610448 1.19542869 1.380656716 1.069128669 1 17.99508416 4.73913308 24.61751482 1.22968063 0.359153548 0.662163433 0.181039995 21.51655706 924993.1207 0.041734141 0.248066164 54844.49978 -4.73913308 -0.870527082 YDSDRTELGFTNYIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDSDRTELGFTNYIR 15 1 Q14554 Q14554 PDIA5 Protein disulfide-isomerase A5 0 100.23 0.0020409 55560000 43504 44374 41088 54006 46911 58814 57094 46032 49799 43229 FALSE TRUE 45221.57151 51994.88932 42158.78703 64688.22561 38937.08498 45155.33983 52618.82309 45415.01633 48006.74372 51698.89488 0.874710603 1.005725353 0.815467857 1.251249679 0.753151205 0.873429499 1.017793963 0.878452362 0.928583557 1 15.65784582 YDSSREAGTVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDSSREAGTVK 11 1 Q96J01;D6REC9 Q96J01 THOC3 THO complex subunit 3 0 ; 80.014 0.015362 757620000 36860 806080 856550 825040 805950 1041270 621390 811470 720680 841500 FALSE TRUE 38315.26126 944517.9696 878872.3967 988230.4495 668954.9069 799450.8231 572683.8281 800593.5719 694742.8676 1006375.814 0.038072518 0.938534051 0.873304371 0.981969594 0.664716797 0.794385966 0.569055635 0.795521475 0.69034138 1 19.94073772 4.745160776 24.94440787 0.796477994 0.038072164 0.746554692 0.135004746 373.4596293 1411402.095 0.032212453 0.311279745 55611.00912 -4.745160776 -0.75840583 YDSWHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDSWHK 6 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ; 119.7 0.020787 623230000 662270 1115420 1345300 1315700 1540660 1727770 1446480 1381980 1328490 991460 FALSE TRUE 688416.931 1306984.708 1380359.623 1575941.533 1278779.164 1326521.602 1333101.118 1363456.819 1280677.904 1185717.604 0.580590967 1.102273175 1.16415546 1.329103597 1.078485433 1.118750027 1.124299001 1.149900123 1.080086776 1 20.17732902 4.738434535 4.46776038 1.140490287 0.542634426 0.807351089 0.08012734 0.076989651 3.875177059 0.018750063 0.145412171 54756.35557 -4.738434535 -0.597855861 YDVDTLDMVFLDHWK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YDVDTLDMVFLDHWK 15 0 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;;;;; 300.61 2.78E-44 3476833000 2898610.8 2334705.6 2980992.9 2708290 3569604 3940329 4099523 3201481 3505762.5 1746178 FALSE TRUE 3013050.193 2735673.125 3058680.024 3243981.679 2962843.987 3025247.306 3778191.675 3158570.384 3379590.792 2088308.147 1.442818771 1.30999495 1.464668913 1.553401821 1.418777201 1.448659438 1.809211769 1.512502065 1.618339132 1 20.99390318 4.035120283 6.368303029 1.516686811 1.37738394 0.018740169 0.196800261 0.458609386 53.34965463 0.045963242 0.09948214 10842.27161 -4.035120283 -0.139302871 YDVDTLDMVFLDHWKDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YDVDTLDMVFLDHWKDR 17 1 P21964-2;P21964;E7EMS6;E7EUU8;H7BZ45 P21964-2 COMT Catechol O-methyltransferase 0 ;;; 215.79 3.31E-15 827463000 819373 832871 1007643 551077 1519339 1243825 654708 922628 1084485 1035288 FALSE TRUE 851722.4787 975910.1154 1033903.004 660078.3858 1261082.299 954965.4941 603390.2762 910261.6808 1045454.597 1238132.862 0.68790879 0.788211141 0.835050128 0.533124034 1.018535521 0.771294845 0.487338875 0.735189016 0.844379976 1 20.23973471 0.975117857 3.291769872 0.998819675 0.730425682 0.259818799 0.141033838 0.318855592 8.854730044 0.133084763 0.0346584 9.443171067 -0.975117857 -0.268393993 YDVEIVEEYFAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YDVEIVEEYFAR 12 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 73.781 0.089041 8110700 9611.3 11844 11697 13527 15735 14903 14687 12164 12298 12403 FALSE TRUE 9990.761546 13878.11487 12001.83343 16202.60023 13060.37032 11442.00411 13535.79456 12000.96148 11855.39738 14833.13038 0.673543702 0.935616051 0.809123437 1.092325073 0.880486451 0.771381618 0.912537962 0.809064652 0.799251209 1 13.85653548 YDVYLYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YDVYLYDR 8 0 Q9Y6Y8;Q9Y6Y8-2;H7C0V8;A0A0C4DH82;H7C4C4 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 ;; 111.95 0.0072944 432901000 508535 483270 555741 580192 668500 708630 672010 570764 541223 523365 FALSE TRUE 528612.3545 566267.8632 570224.067 694952.2459 554868.6088 544061.4219 619336.1002 563113.8422 521744.49 625908.3513 0.844552327 0.904713704 0.911034444 1.110309911 0.886501367 0.869234962 0.989499659 0.899674594 0.833579691 1 19.2555919 3.835086317 0.004516783 1.839363179 8.57E-08 0.031704034 0.079208574 156825.8954 151.9222538 30204.10771 31670.29236 6840.475904 -3.835086317 -1.839363093 YDWDLLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YDWDLLAAR 9 0 Q15029;Q15029-3;Q15029-2;K7EP67;K7EJ74 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;;;; 136.27 0.0004595 398518000 720803 796869 781239 708131 1171294 1128266 856258 773821 763130 1044631 FALSE TRUE 749260.859 933725.052 801598.7301 848197.1982 972197.8643 866243.3205 789142.2605 763449.1952 735665.1004 1249306.444 0.599741451 0.74739473 0.641634992 0.678934462 0.778190066 0.693379374 0.631664284 0.611098421 0.588858806 1 20.25269597 -1.023674741 4.626214231 1.000009033 0.66465183 0.743264392 0.059338389 8067903.094 1785241.086 836.0017776 0.014518205 0.09469461 1.023674741 -0.335357204 YDYNSGEELESYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDYNSGEELESYK 13 0 Q9Y3F4;Q9Y3F4-2;H0YH33 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 ; 210.64 6.58E-08 189766000 118752 91547 110317 96512 141627 134559 153190 126825 124034 82327 FALSE TRUE 123440.4207 107269.4851 113191.9516 115601.7855 117553.2931 103309.7115 141182.5675 125125.1183 119570.0406 98457.3994 1.253744476 1.089501508 1.149654087 1.174129992 1.193950824 1.049283367 1.433945731 1.270855406 1.214434276 1 16.58721201 2.2653456 24.99998849 1.260844429 1.151728652 0.07809472 0.112836802 359.2058872 335266.5942 0.036793443 0.030775766 184.2237421 -2.2653456 -0.109115777 YDYVLTGYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YDYVLTGYTR 10 0 O00764;F2Z2Y4;O00764-3 O00764 PDXK Pyridoxal kinase 0 ; 174.02 7.52E-06 200262000 194440 222990 204980 190150 246940 256890 214890 215703 216060 220420 FALSE TRUE 202116.6413 261286.7979 210321.9472 227761.1025 204965.227 197231.1907 198046.3603 212811.8541 208284.0428 263607.0788 0.766734498 0.991197957 0.79786153 0.864017399 0.777540679 0.74820142 0.751293786 0.807307054 0.790130689 1 18.00802959 5.080467761 13.97889595 0.824261408 7.89E-05 0.038600593 0.087048226 846326.2601 3092598.42 0.020074422 20445704.6 120356.0043 -5.080467761 -0.82418252 YEAHSDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YEAHSDK 7 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 0 109.01 0.0071238 144450000 274610 196030 239540 210510 313940 312420 317930 271590 274940 199260 FALSE TRUE 285451.8148 229696.6276 245782.6092 252148.2497 260576.5909 239865.1898 293009.8158 267949.7803 265044.9631 238301.1819 1.197861515 0.963892104 1.031394839 1.058107424 1.093475865 1.006563156 1.229577686 1.124416497 1.112226809 1 17.86242658 2.267139481 24.99999097 1.130321114 1.054579785 0.10693534 0.077666061 344.0893205 300998.4153 0.025368343 0.021221273 184.9862638 -2.267139481 -0.075741329 YEAQKLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 79.148 0.026455 0 282090 249870 248950 192770 379910 346910 272150 237960 316340 257090 FALSE TRUE 293227.131 292783.2288 255437.8415 230899.3306 315333.0339 266345.41 250818.1719 234770.5354 304954.9852 307461.8632 0.953702446 0.952258682 0.830795204 0.750985271 1.025600478 0.866271372 0.815770025 0.763576116 0.99184654 1 18.23004795 2.498795579 24.89748721 0.857027776 0.898296855 0 0.098740882 3066.704561 3522749.191 0.032582987 0.030457457 315.3519922 -2.498795579 0.04126908 YEAVS(ph)PERLELER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEAVSPERLELER 13 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 YEAVS(1)PERLELER;YEAVS(1)PERLELER 220.64 1.24E-11 167799000 181216 208469 193654 196381 218554 267520 208189 213943 209272 221958 TRUE FALSE 188370.5476 244271.9291 198700.7823 235224.5757 181404.2691 205392.5343 191870.6022 211075.444 201740.3416 265446.4205 0.709636797 0.920230639 0.748553256 0.8861471 0.683393164 0.773762682 0.722822338 0.795171559 0.760004001 1 18.01806116 -1.839336538 8.842961545 1.008346312 0.780094829 0.469649458 0.070814356 0.010829266 0.000196752 0.063722214 0.014887768 0.014476496 1.839336538 -0.228251483 YEAWLAEAESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YEAWLAEAESR 11 0 Q15642;M0R0F9;W4VSQ9;Q15642-4;Q15642-2;Q15642-3 Q15642 TRIP10 Cdc42-interacting protein 4 0 ;;; 164.97 5.15E-05 156256000 151265.2 187184 180863 186659 219515 230749 199919 192427 186525 204674 FALSE TRUE 157237.2669 219331.3959 185576.4384 223579.5931 182201.9187 177161.0418 184248.8264 189847.8308 179812.0017 244775.9516 0.642372202 0.89604961 0.758148164 0.913405061 0.744362008 0.723768167 0.75272438 0.775598377 0.734598315 1 17.9011023 -1.750533013 6.642811255 1.004938284 0.775747066 0.449636416 0.07578332 0.005254055 0.000197313 0.069558611 0.01613331 0.017760983 1.750533013 -0.229191218 YEDFKEEGSENAVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YEDFKEEGSENAVK 14 1 J3KQ32;Q9NTK5;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 212.39 2.28E-09 380400000 1088900 421140 683510 441140 1034900 942490 922520 733010 839300 332210 FALSE TRUE 1131890.613 493467.519 701322.8321 528396.1753 858988.0677 723610.9811 850210.4718 723185.1999 809093.7569 397300.189 2.848955637 1.242052062 1.765221491 1.329967088 2.162063074 1.821320506 2.139969966 1.820248819 2.036479668 1 18.59986995 YEDICPSTHNMDVPNIKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YEDICPSTHNMDVPNIKR 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 86.488 0.0016411 60255000 49766 66014 85376 58960 87236 90340 63039 87736 81194 70914 FALSE TRUE 51730.80011 77351.39098 87600.9687 70622.11202 72407.65588 69359.90412 58097.83846 86560.04243 78271.8438 84808.24057 0.609973745 0.912073997 1.032929915 0.832727003 0.853780899 0.817843922 0.685049449 1.020656033 0.922927339 1 16.37191683 1.648392718 11.51945277 0.978318295 0.834335418 0.297738254 0.111456474 0.158804539 34.86412402 0.053749585 0.029125544 44.50335141 -1.648392718 -0.143982876 YEDRYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEDRYDR 7 1 E7EX17;P23588-2;P23588;F8VX11;F8VP89 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 ; 178.65 0.00064989 2769000000 3163200 3289500 3309800 3756400 3662300 4092400 4428700 3657200 3169200 2747300 FALSE TRUE 3288085.579 3854446.036 3396056.107 4499404.708 3039783.554 3142002.121 4081566.922 3608181.216 3055141.111 3285580.835 1.000762344 1.17313992 1.033624275 1.369439662 0.925189094 0.956300356 1.242266475 1.098186713 0.929863322 1 21.64771701 YEDYDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YEDYDYR 7 0 Q13595;Q13595-3;Q13595-4 Q13595 TRA2A Transformer-2 protein homolog alpha 0 ;; 96.19 0.030042 1462650000 3062650 3140580 3156230 3433150 3666920 4015770 3973620 3475050 3068670 2721740 FALSE TRUE 3183565.787 3679950.185 3238483.947 4112216.823 3043618.248 3083168.277 3662157.281 3428472.639 2958229.166 3255012.842 0.978050146 1.130548592 0.994922018 1.263348878 0.935055681 0.947206179 1.125082284 1.05329005 0.908822579 1 21.6342318 YEEEEEQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 ; 257.93 1.15E-14 630850000 438600 495170 463780 426730 501170 608820 535960 491530 494780 435820 FALSE TRUE 455916.2667 580211.5956 475866.4878 511135.9203 415981.3024 467430.7818 493950.0547 484941.8443 476972.9644 521210.5847 0.874725648 1.113199948 0.913002348 0.980670645 0.798106014 0.896817516 0.947697666 0.930414421 0.915125246 1 18.99150686 YEEIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YEEIVK 6 0 P68104;A0A087WVQ9;Q5VTE0;A0A087WV01 P68104 EEF1A1;EEF1A1P5 Elongation factor 1-alpha 1;Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 0 ;;;;; 129.96 0.037149 6635450000 8124110 6403550 7879250 6276640 9401140 9135210 9468170 7832690 8024410 5173180 FALSE TRUE 8444856.136 7503309.9 8084589.728 7518140.658 7803137.581 7013695.923 8726030.095 7727705.602 7735613.052 6186765.574 1.364987251 1.212800099 1.306755465 1.215197274 1.26126285 1.133661174 1.410434902 1.249070376 1.250348499 1 22.56075394 0.58645204 2.641719447 1.000010426 1.26765447 0.537875394 0.07447694 3.852441595 23.71209758 0.066527944 0.017631941 3.858797959 -0.58645204 0.267644043 YEELFPAFSDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YEELFPAFSDSR 12 0 P54920;M0R0Y2;M0R2M1;M0R213;M0R0I4 P54920 NAPA Alpha-soluble NSF attachment protein 0 ;;;;; 238.01 9.34E-16 720129000 558468 623398 662524 643553 786873 795444 713014 690617 685568 633264 FALSE TRUE 580516.7479 730461.7571 679789.9197 770845.8626 653120.6085 610714.1861 657126.0996 681360.4087 660894.5416 757339.9562 0.766520693 0.964509731 0.89760208 1.017833347 0.862387628 0.806393722 0.867676522 0.899675771 0.872652415 1 19.53058152 -1.126666858 3.893983171 1.00003919 0.887921846 0.207907802 0.067568235 7439879.596 4305240.669 2585.59651 0.015479606 0.074702157 1.126666858 -0.112117345 YEEVAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 137.44 0.029627 2084250000 2166840 2063900 2331100 1996550 2466370 2605440 2567690 2404890 2353410 2002650 FALSE TRUE 2252388.516 2418358.77 2391850.381 2391461.631 2047137.308 2000366.046 2366427.748 2372656.383 2268711.234 2395030.924 0.940442352 1.009740102 0.998672024 0.998509709 0.854743581 0.835215122 0.988057283 0.990657932 0.947257595 1 21.19161285 -0.670272357 15.76535526 0.999999999 0.954041622 0.057472727 0.058120758 0 0 0.061063939 0.014392909 0.213662174 0.670272357 -0.045958377 YEEVSVSGFEEFHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YEEVSVSGFEEFHR 14 0 Q9BRA2;I3L2R6;I3L0K2;I3L3M7 Q9BRA2 TXNDC17 Thioredoxin domain-containing protein 17 0 ;;; 192.18 4.03E-07 1393270000 844070 1062640 995740 991250 1143840 1233370 979840 1077970 1035380 1080010 FALSE TRUE 877394.5354 1245140.154 1021689.802 1187316.291 949410.4854 946938.5094 903037.5805 1063521.575 998116.8761 1291617.281 0.679299161 0.964016332 0.791015897 0.919247759 0.735055576 0.733141715 0.6991526 0.823403024 0.772765192 1 20.30074722 5.022213226 16.32012873 0.812289613 0.373021277 0.154374066 0.098419491 23474323.34 432234889.5 0.022529793 263447229.8 105247.8484 -5.022213226 -0.439268336 YEFTDALLCHDDELEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YEFTDALLCHDDELEGR 17 0 A0A0A0MTR2;Q8N543;H3BR79;H3BUA6;Q8N543-2 A0A0A0MTR2 OGFOD1 Prolyl 3-hydroxylase OGFOD1 0 ;; 178.03 9.95E-10 87512000 73245 89706.5 76034.4 92207.8 103295 114848 96661 85267 86567 82750 FALSE TRUE 76136.76916 105112.8936 78015.91893 110446.2276 85736.9528 88176.29254 89084.45824 84124.13533 83451.47058 98963.27816 0.769343645 1.062140377 0.788331999 1.116032428 0.86635118 0.891000118 0.900176913 0.850054049 0.843256935 1 16.59460567 YEHANDDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YEHANDDK 8 0 H3BND4;Q6P996-3;Q6P996-5;Q6P996;Q6P996-4 H3BND4;Q6P996-4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 0 ;;; 120.99 0.0014525 1669730000 2909350 1809660 2277670 1967060 2883930 3370540 3161820 2463800 2440800 1324360 FALSE TRUE 3024213.385 2120455.028 2337027.951 2356138.597 2393720.609 2587783.166 2913988.287 2430776.791 2352956.085 1583842.986 1.909414893 1.338803813 1.475542697 1.487608695 1.511337065 1.633863451 1.839821443 1.534733438 1.485599334 1 20.59499789 0.728977282 2.338105692 1.000270002 1.583930658 0.543548327 0.161949704 1.017499117 7.645653528 0.152759628 0.041210515 5.35768631 -0.728977282 0.583660655 YEKDIAAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YEKDIAAYR 9 1 P26583;P09429 P26583;P09429 HMGB2;HMGB1 High mobility group protein B2;High mobility group protein B1 0 ;;; 126.39 0.00043313 2602690000 2949900 3046360 3229700 2241810 5021010 3885140 2732940 3090270 3369280 4281400 FALSE TRUE 3066364.33 3569548.633 3313868.635 2685233.327 4167540.514 2982875.115 2518725.022 3048849.985 3248020.271 5120258.358 0.598869064 0.697142289 0.647207309 0.524433171 0.813931685 0.582563399 0.491913659 0.595448466 0.63434695 1 22.28778518 -1.980150115 1.91577356 1.349936986 0.618037024 0.640835594 0.085178672 743999.6824 246988.5565 1152430.52 0.022710984 0.010467667 1.980150115 -0.731899962 YEKDVADYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEKDVADYK 9 1 O15347;E7ES08;E7EQU1 O15347 HMGB3 High mobility group protein B3 0 ; 107.06 0.0025861 1114990000 1161710 662120 997870 638920 1413410 1149760 1246370 1009910 1180540 619280 FALSE TRUE 1207575.208 775833.9594 1023875.312 765296.469 1173159.073 882745.6648 1148676.263 996373.8083 1138052.596 740616.0592 1.630500977 1.047552169 1.382464368 1.033324162 1.584031373 1.191907269 1.550974015 1.345331088 1.53662965 1 19.49836631 2.262905863 24.99186681 1.388401617 1.302577934 0.001982002 0.233243959 955.5344922 980910.9656 0.07406826 0.061943466 183.1917295 -2.262905863 -0.085823683 YELGRPAANTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YELGRPAANTK 11 1 P62241;Q5JR95 P62241 RPS8 40S ribosomal protein S8 0 ; 145.09 3.32E-05 559680000 849130 787410 909770 680620 1221520 1151490 1008760 1003340 986930 818230 FALSE TRUE 882654.3081 922641.5423 933479.3536 815244.6046 1013886.467 884073.8985 929690.7553 989891.8684 951410.5821 978546.5025 0.90200548 0.942869388 0.953944806 0.833117897 1.036114752 0.903456194 0.950073147 1.0115941 0.972269156 1 19.90028089 2.058126758 0.891600385 1.001705894 0.923781416 0.244277643 0.04948286 0.802599508 1.183028966 0.038714171 0.019638123 114.3211957 -2.058126758 -0.077924478 YELHLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YELHLK 6 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 ;;; 102.81 0.035225 7866400000 13753100 10965900 12298900 11609400 16657400 16487100 17117800 13661100 14124300 10265190 FALSE TRUE 14296083.01 12849208.02 12619419.44 13905704.67 13825981.1 12658220.89 15776062.11 13477995.3 13615969.2 12276457.44 1.164512081 1.046654386 1.027936561 1.132713141 1.12621912 1.0310972 1.28506633 1.097873337 1.109112239 1 23.54939097 3.697361939 24.93091449 1.122147823 1.076396275 0.021598533 0.07850952 1351.40146 817784.1507 0.020126615 0.031180671 4981.520693 -3.697361939 -0.045751549 YELPTDDDTYEEHRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YELPTDDDTYEEHRR 15 1 C9J1C6;Q9P0P0 C9J1C6 RNF181 E3 ubiquitin-protein ligase RNF181 0 ;;; 77.146 0.017367 827010000 352721 458687 427989 396934 479380 534119 439258 453452 429929 452688 FALSE TRUE 366646.6974 537462.9242 439142.7449 475446.3605 397895.1588 410077.9569 404827.8102 447374.2176 414455.9393 541383.5464 0.677240193 0.992758143 0.811149042 0.878206151 0.734959829 0.757462911 0.747765263 0.826353554 0.765549567 1 19.04629152 5.024705836 15.8892907 0.821720737 0.320493644 0.19732722 0.092001224 6579823.104 112207131.7 0.020874706 83603639.74 105853.6496 -5.024705836 -0.501227092 YELYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YELYSR 6 0 A0A0G2JQD6;Q8IXL6 A0A0G2JQD6 FAM20C Extracellular serine/threonine protein kinase FAM20C 0 ;;; 114.67 0.058367 2745820000 1505130 1342360 1448910 1242620 1391370 1596500 1537190 1523660 1495420 1137140 FALSE TRUE 1564553.695 1572899.888 1486669.785 1488406.527 1154865.424 1225737.07 1416701.031 1503237.83 1441600.126 1359940.811 1.150457198 1.156594372 1.093187125 1.094464196 0.849202712 0.901316484 1.041737272 1.105370041 1.060046227 1 20.37511243 3.4597936 24.91190305 1.001834678 1.128746863 0.446368626 0.071843915 262.7590241 377766.48 0.023439718 0.031744691 2882.661184 -3.4597936 0.126912184 YEMACAIADAFNLPSSHLRPITDS(ph)PVLGAQRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEMACAIADAFNLPSSHLRPITDSPVLGAQRPR 33 2 Q9NZL9;Q9NZL9-2 Q9NZL9 MAT2B Methionine adenosyltransferase 2 subunit beta 1 YEMACAIADAFNLPS(0.07)S(0.07)HLRPIT(0.07)DS(0.791)PVLGAQRPR;YEMACAIADAFNLPS(0.002)S(0.002)HLRPIT(0.037)DS(0.959)PVLGAQRPR 179.58 6.39E-20 1222940000 142766 273977 268112 237748 278215 314889 218110 276783 259565 308821 TRUE FALSE 148402.5119 321030.4185 275099.219 284773.8448 230924.1137 241760.8019 201013.9683 273073.1766 250223.3064 369328.5622 0.401817046 0.869227163 0.744863103 0.771058277 0.625253872 0.654595465 0.544268678 0.739377358 0.677508679 1 18.49454531 0.131984514 1.436221633 1.000256524 0.676244298 0.393507098 0.122763418 11.87626329 18.35066341 0.117289338 0.032376138 1.35514109 -0.131984514 -0.324012225 YEPFSFADDIGSNNCGYYDLQAVLTHQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEPFSFADDIGSNNCGYYDLQAVLTHQGR 29 0 P54578-2;P54578;A6NJA2;P54578-3 P54578-2 USP14 Ubiquitin carboxyl-terminal hydrolase 14;Ubiquitin carboxyl-terminal hydrolase 0 ; 301.55 4.28E-81 273078000 74716 63653 88332 76453 108907 113153 90060 97245 84403 98873 FALSE TRUE 77665.84537 74584.9076 90634.00449 91575.17521 90395.02704 86874.9306 83000.86187 95941.58984 81365.35252 118245.2713 0.656819884 0.6307644 0.766491577 0.774451056 0.764470545 0.734701097 0.701938107 0.811377815 0.688106608 1 16.85142297 -5 0.201615239 2.217636989 0.688374661 0.707360562 0.053150986 79.48110043 0.787736838 39.07361498 0.127923928 1.00E-05 5 -1.529262327 YEPQS(ph)PGYEPR ddPTM_MDA-MB-175_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(1)PGYEPR 192.65 1.36E-06 2060040000 1045600 1015810 1089680 1006330 1180020 1313820 1115140 1052190 1109860 1006260 TRUE FALSE 1086881.095 1190267.466 1118077.956 1205379.07 979440.6219 1008705.216 1027732.413 1038087.114 1069916.355 1203417.381 0.903162205 0.989072856 0.929085763 1.001630099 0.813882729 0.838200638 0.854011608 0.862616022 0.889065068 1 20.19870567 3.241091534 24.99990884 0.865867559 0.956215098 0.334444132 0.053704224 63.38309796 626079.6786 0.014003879 0.018116851 1742.174023 -3.241091534 0.090347538 YEPSDKDRQS(ph)PPPAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YEPSDKDRQSPPPAK 15 2 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK;YEPSDKDRQS(1)PPPAK 182.7 2.80E-07 2919510000 6210430 2785560 4240110 3009050 5562440 5502710 6184660 4385620 5024430 2283130 TRUE FALSE 6455622.572 3263958.261 4350610.75 3604231.109 4616938.436 4224788.997 5699890.189 4326837.937 4843601.746 2730465.61 2.364293675 1.19538523 1.593358559 1.320006044 1.690897852 1.547277864 2.087515831 1.584652054 1.773910548 1 21.38071556 YEQGTGCWQGPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YEQGTGCWQGPNR 13 0 K7ELL7;P14314-2;P14314;A0A0C4DGP4 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 ;;;;; 268.91 1.70E-24 1584860000 328525 365465 342894 344074 467720 463500 323445 312802 309353 366154 FALSE TRUE 341495.4207 428230.7708 351830.0993 412130.8102 388217.1215 355859.1494 298092.5357 308609.4008 298219.446 437894.8659 0.779857101 0.977930559 0.803457923 0.941163833 0.886553261 0.812658876 0.680739965 0.704756838 0.681029784 1 18.74022501 2.491314897 4.054236593 0.735912921 0.881382321 0.181537995 0.103116163 0.251221411 9.492260067 0.033104888 0.029166517 309.9665985 -2.491314897 0.1454694 YESLELCRPVLQQGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YESLELCRPVLQQGR 15 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;;; 228.03 5.93E-13 2384570000 1052782 722628 885588 890065 1013925 1158410 1125789 857173 884464 607868 FALSE TRUE 1094346.646 846733.7377 908667.1508 1066117.2 841578.3907 889386.8334 1037546.716 845683.998 852632.3134 726968.0963 1.505357184 1.164746764 1.249940892 1.466525431 1.157655191 1.223419347 1.427224553 1.163302767 1.172860704 1 19.47153253 1.07572385 1.261583899 1.004857661 1.3013399 0.394566141 0.119500973 0.445524937 1.456183873 0.106622114 0.033122365 11.90484788 -1.07572385 0.296482239 YESLTDPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YESLTDPSK 9 0 P08238;Q58FF7;Q58FF6;P07900;P07900-2;G3V2J8;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AA1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-beta 2 0 ; 113.71 0.0040871 350000000 838970 542130 691040 630820 946660 953610 993090 793950 750700 480020 FALSE TRUE 872093.1834 635236.6103 709049.0701 755594.3132 785747.0713 732148.5296 915249.0108 783308.3989 723682.4536 574070.7285 1.519138915 1.106547641 1.235124933 1.316204216 1.368728682 1.275362936 1.59431402 1.364480647 1.260615492 1 19.13086897 3.506270002 5.546317259 1.348296843 1.269344069 0 0.168999403 0.689293614 62.04384325 0.043858053 0.06594809 3208.263292 -3.506270002 -0.078952774 YESLTDPSKLDSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 158.81 4.57E-06 14520400000 14675700 8081150 10920250 7463320 16086800 13654800 13492900 11151310 12846700 6168770 FALSE TRUE 15255107.97 9469024.65 11204840.69 8939542.42 13352371.48 10483679.64 12435291.24 11001844.93 12384349.78 7377422.373 2.067810029 1.283513966 1.51880157 1.211743339 1.809896575 1.421049129 1.685587542 1.49128576 1.678682492 1 22.8146854 -1.261519585 5.5054332 0.999952224 1.555741986 0.338145449 0.239768013 0.000126786 1.70E-05 0.209335955 0.049336735 0.05476214 1.261519585 0.555789762 YESQEPLAGQES(ph)PLPLATR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YESQEPLAGQESPLPLATR 19 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR 384.06 8.83E-127 8136520000 3825847 4181340 4094660 4063703 4182170 4749090 4132881 4395530 4000780 3919901 TRUE FALSE 3976894.394 4899452.619 4201370.203 4867491.324 3471286.237 3646185.821 3808934.988 4336615.11 3856792.709 4687930.55 0.848326218 1.045120564 0.896209993 1.03830278 0.740473051 0.777781535 0.812498169 0.925059589 0.822706878 1 22.16051977 3.245576058 24.99999855 0.842942518 0.958943501 0.274317209 0.087970822 207.5957622 739776.6558 0.023763213 0.031505634 1760.256912 -3.245576058 0.116000983 YETSSTSAGDRYDS(ph)LLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YETSSTSAGDRYDSLLGR 18 1 O14974;O14974-5;O14974-2;O14974-3;O14974-4;H0YIS3;H0YIM2 O14974 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 YETSSTSAGDRYDS(1)LLGR 76.417 0.0092462 101000000 25368 29203 36211 28969 37529 42877 29194 30198 37314 45043 TRUE FALSE 26369.54823 34218.38808 37154.68841 34698.98174 31149.83399 32919.46656 26905.698 29793.2452 35971.07643 53868.31345 0.489518727 0.635222933 0.689731793 0.644144572 0.578258943 0.611110028 0.499471698 0.553075515 0.66775947 1 15.71714928 0.856546116 4.32725072 0.999971222 0.589347021 0.812125452 0.059332677 0.450515149 13.04026418 0.060876715 0.015488011 7.186974692 -0.856546116 -0.410624201 YETSSTSAGDRYDSLLGR ddPTM_MDA-MB-175_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 ;; 340.55 1.99E-75 829290000 267690 299508 298706 311083 356181 399566 301227 321141 301032 333219 FALSE TRUE 278258.6079 350946.1692 306490.5237 372614.2889 295637.4808 306772.852 277616.0406 316836.6302 290197.9171 398506.8832 0.698252953 0.880652716 0.769097189 0.93502598 0.741862922 0.769805654 0.696640516 0.795059367 0.728213061 1 18.60424512 -1.720746681 6.424186569 1.003494007 0.782580131 0.454445162 0.072435514 0.003509249 0.000152544 0.067897925 0.015792621 0.019021875 1.720746681 -0.220913876 YEWDVAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YEWDVAEAR 9 0 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;; 190.26 8.67E-05 8253000000 5597660 6131300 6133440 7003050 6840530 8031020 7889370 6425230 5857270 5513630 FALSE TRUE 5818659.939 7184303.08 6293282.485 8388232.388 5677779.154 6165937.316 7270980.564 6339110.301 5646467.997 6593920.234 0.882428014 1.089534423 0.954406827 1.272116145 0.86106276 0.935094314 1.102679485 0.961356837 0.856314271 1 22.652705 YEWVVIKHPELTKPPPLMAAEPTAPLSHSASSDPADRLS(ph)PFLAAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YEWVVIKHPELTKPPPLMAAEPTAPLSHSASSDPADRLSPFLAAR 45 3 Q9ULP9-2;Q9ULP9 Q9ULP9-2 TBC1D24 TBC1 domain family member 24 1 YEWVVIKHPELTKPPPLMAAEPTAPLSHS(0.003)AS(0.22)S(0.22)DPADRLS(0.557)PFLAAR;YEWVVIKHPELTKPPPLMAAEPTAPLSHSAS(0.02)S(0.005)DPADRLS(0.975)PFLAAR 165.74 6.84E-21 609310000 930560 1188060 1400240 871830 1813710 1703600 1015250 1369030 1416070 1547920 TRUE FALSE 967299.2273 1392100.063 1436731.405 1044275.372 1505416.222 1307964.718 935672.0521 1350680.392 1365105.917 1851205.287 0.522524019 0.75199659 0.776105932 0.564105655 0.813208688 0.706547635 0.50543938 0.729622156 0.73741466 1 20.82003346 0.733206928 1.897044191 0.999552524 0.67350276 0.486586881 0.10141014 0.859242629 4.724703586 0.092764676 0.025856288 5.410120374 -0.733206928 -0.326049764 YEYDPDIS(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YEYDPDISPPR 11 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR 132.5 0.00019004 465197000 379954 434900 410437 460495 458520 544330 511550 419360 424060 379351 TRUE FALSE 394954.8773 509590.6919 421133.3254 551579.5366 380580.9342 417917.6069 471453.3743 413739.1651 408798.1634 453677.5653 0.870562945 1.123244196 0.928265706 1.215796369 0.838879776 0.921177591 1.039181591 0.911967434 0.901076435 1 18.79130779 YEYHWADGTNIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YEYHWADGTNIK 12 0 Q9H8S9;Q7L9L4;Q7L9L4-2;D6RCK3;Q9H8S9-2 Q9H8S9 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 0 ;; 256.47 3.60E-21 1165510000 1435610 1172400 1291740 1124010 1707940 1698570 1649810 1402050 1518450 1171590 FALSE TRUE 1492288.991 1373750.58 1325403.806 1346335.823 1417624.969 1304102.86 1520493.581 1383257.813 1463801.281 1401140.629 1.065052972 0.980451606 0.945946308 0.960885578 1.011764943 0.930743733 1.085182707 0.987236958 1.044721173 1 20.41817033 2.245629191 24.99999145 1.025864734 0.981072004 0.222191692 0.042667052 257.7265407 911523.0601 0.01450493 0.011905896 176.0472281 -2.245629191 -0.04479273 YFAES(ph)DEEEDDVDFAMFN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFAESDEEEDDVDFAMFN 18 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 Y(0.063)FAES(0.937)DEEEDDVDFAMFN;Y(0.001)FAES(0.999)DEEEDDVDFAMFN 122.34 0.00014191 10180000 60057 52288 62547 49121 74923 76916 65368 65013 59042 44776 TRUE FALSE 62428.09673 61268.05726 64177.0262 58836.98719 62187.61522 59053.42467 60244.28535 64141.60707 56917.08995 53548.99991 1.165812561 1.144149421 1.198472918 1.09875044 1.161321693 1.102792298 1.125031008 1.197811484 1.062897347 1 15.70857201 1.028659351 5.254530783 1.000334802 1.148756786 0.694909629 0.032541996 0.080341034 5.903160794 0.030723566 0.007758511 10.68216671 -1.028659351 0.148421984 YFDACADAVSKDELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFDACADAVSKDELQR 16 1 Q9Y5P4-3;Q9Y5P4;Q9Y5P4-2;A0A2R8Y7C5;A0A2R8YE18;A0A2R8Y7Q9;A0A2R8Y5S9;A0A2R8YEA4;A0A2R8YE59;A0A2U3TZL3;A0A2R8YEK8;A0A2R8Y5H3;A0A2R8YFI2;A0A2R8YCI0;A0A2R8YDX6 Q9Y5P4-3 COL4A3BP Collagen type IV alpha-3-binding protein 0 94.922 0.0035823 308460000 267360 222890 258820 220480 341950 322830 303490 255780 270290 222620 FALSE TRUE 277915.5792 261169.6237 265565.0618 264090.2859 283825.4611 247857.625 279701.6608 252351.6875 260562.3157 266238.1267 1.043860933 0.98096252 0.997471944 0.991932633 1.066058662 0.930962173 1.050569519 0.947842034 0.978681449 1 18.02235766 1.703764127 17.35537728 0.972518259 1.005877441 0.130408287 0.038681298 0.378259189 177.1799073 0.016533021 0.009145739 50.55500142 -1.703764127 0.033359182 YFDDEFTAQS(ph)ITITPPDRYDSLGLLELDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFT(0.063)AQS(0.333)IT(0.333)IT(0.272)PPDRYDSLGLLELDQR 88.683 0.00070409 1948400000 16698 20555 21181 20686 21493 23562 18712 18861 16978 21840 TRUE FALSE 17357.24993 24085.16135 21732.99426 24777.62906 17839.62754 18090.08259 17245.30455 18608.19915 16366.9651 26119.12985 0.664541661 0.922127249 0.83207191 0.948639147 0.683010025 0.692598976 0.660255707 0.712435646 0.626627502 1 14.67281921 3.217032711 24.99984551 0.7085843 0.84688139 0.161638181 0.12015981 319.2959879 370789.9001 0.03199283 0.038271597 1648.286536 -3.217032711 0.13829709 YFDDEFTAQSITIT(ph)PPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSIT(0.059)IT(0.941)PPDR;YFDDEFTAQSIT(0.001)IT(0.999)PPDR;YFDDEFTAQSIT(0.001)IT(0.999)PPDR;YFDDEFTAQSITIT(1)PPDR;YFDDEFTAQSIT(0.001)IT(0.999)PPDR;YFDDEFTAQSITIT(1)PPDR 193.27 1.48E-13 260077000 137300.6 148825.1 149306.7 180214.7 155525.8 181936 184536 156526.8 143948.4 125063.8 TRUE FALSE 142721.3337 174384.6532 153197.7553 215860.6298 129089.5801 139684.1213 170071.5861 154428.8143 138767.7252 149567.6571 0.95422591 1.165924884 1.024270609 1.443230669 0.863084858 0.933919298 1.137087987 1.032501393 0.927792331 1 17.19043871 YFDDEFTAQSITIT(ph)PPDRYDSLGLLELDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 YFDDEFTAQSITITPPDRYDSLGLLELDQR 30 1 P31751;P31751-2 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 YFDDEFT(0.152)AQS(0.106)IT(0.106)IT(0.634)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.004)IT(0.996)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(0.764)PPDRY(0.108)DS(0.128)LGLLELDQR;YFDDEFTAQS(0.001)IT(0.116)IT(0.882)PPDRYDSLGLLELDQR;YFDDEFTAQSITIT(1)PPDRYDSLGLLELDQR;YFDDEFTAQSIT(0.128)IT(0.871)PPDRYDSLGLLELDQR;YFDDEFTAQS(0.001)IT(0.003)IT(0.996)PPDRYDSLGLLELDQR;YFDDEFT(0.001)AQS(0.006)IT(0.03)IT(0.963)PPDRYDSLGLLELDQR;YFDDEFT(0.001)AQSIT(0.003)IT(0.996)PPDRYDSLGLLELDQR 221.64 1.91E-34 3913652000 320648.3 388738.6 380150.1 388865.2 413170.9 444716.1 365854.6 393550.6 367326.9 422070.4 TRUE FALSE 333307.7425 455501.4306 390057.1239 465781.5759 342940.258 341437.5255 337177.9605 388275.6979 354106.8766 504767.0139 0.660319976 0.902399361 0.772746858 0.92276548 0.679403068 0.676425987 0.667987311 0.769217653 0.701525391 1 18.94525811 3.213745138 24.999633 0.731142254 0.817845923 0.060390046 0.113699839 462.7357061 466168.301 0.030386087 0.036332883 1635.856251 -3.213745138 0.086703669 YFDEEFTAQMITIT(ph)PPDQDDSMECVDSER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFDEEFTAQMITITPPDQDDSMECVDSER 29 0 P31749;P31749-2;G3V2I6 P31749 AKT1 RAC-alpha serine/threonine-protein kinase 1 YFDEEFTAQMIT(0.001)IT(0.74)PPDQDDS(0.258)MECVDS(0.001)ER 110.61 0.0012616 26997000 3480 8668.4 6171.4 7931.3 7771.3 8759.1 6863 6383.1 5668.4 7976.8 TRUE FALSE 3617.393087 10157.13027 6332.231754 9500.087467 6450.337202 6724.93177 6325.060127 6297.544985 5464.395391 9539.701235 0.379193541 1.064722051 0.663776737 0.995847483 0.67615715 0.70494155 0.66302497 0.660140693 0.572805715 1 13.21972837 YFDGSGGNNHAVEHYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YFDGSGGNNHAVEHYR 16 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 0 ;;;; 188.9 6.39E-10 3785876000 1169177 1605540 1491580 1562710 1688810 1892330 1601100 1619850 1459760 1484130 FALSE TRUE 1215337.011 1881279.006 1530451.8 1871809.374 1401746.679 1452865.036 1475601.598 1598138.56 1407223.523 1774916.858 0.684728981 1.059925144 0.862266755 1.05458989 0.789753432 0.818553855 0.831363786 0.900401928 0.792839122 1 20.75932002 YFDLGLPNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFDLGLPNR 9 0 P48735;P48735-2 P48735 IDH2 "Isocitrate dehydrogenase [NADP], mitochondrial" 0 ; 116.73 0.0029479 379310000 238742 269960 225123 283850 227618 351740 237801 216762 227956 254090 FALSE TRUE 248167.7185 316323.53 230989.8903 339994.6828 188927.5737 270053.7157 219161.5362 213856.6599 219751.9081 303874.0707 0.816679482 1.04096914 0.760150051 1.118867043 0.621729828 0.888702728 0.721224867 0.703767385 0.723167685 1 18.21311405 3.227610189 24.99999578 0.759351663 0.929365481 0.234286247 0.137525991 267.8611147 611530.1016 0.036315414 0.043797425 1688.924319 -3.227610189 0.170013818 YFDNKDDDS(ph)DTETSNDLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFDNKDDDSDTETSNDLPK 19 1 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 YFDNKDDDS(0.984)DT(0.01)ET(0.005)S(0.001)NDLPK;YFDNKDDDS(0.995)DT(0.004)ETSNDLPK 202.15 3.43E-16 262240000 517130 139219 207641 139649 338440 358410 308340 221203 264640 107595 TRUE FALSE 537546.6917 163128.7803 213052.295 167271.1554 280912.0897 275174.7093 284171.5051 218238.1356 255115.6581 128676.1802 4.177515145 1.267746525 1.655724429 1.29993877 2.183093166 2.138505423 2.208423537 1.69602591 1.982617588 1 16.97338549 8 0.055899198 1.58E-09 5.787804827 0.208588339 0.747486159 787.8265584 3.302718024 73.61842638 378.8897566 99999999.99 -8 5.787804825 YFDPANGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFDPANGK 8 0 P13639 P13639 EEF2 Elongation factor 2 0 ; 122.74 0.0032044 286970000 1035970 915650 1080290 901510 1284800 1374570 1198510 1072820 1104190 970680 FALSE TRUE 1076870.896 1072905.765 1108443.245 1079825.987 1066410.155 1055346.949 1104567.654 1058440.603 1064450.418 1160866.161 0.927644316 0.92422865 0.95484155 0.930189908 0.918633164 0.909103034 0.951503017 0.911767987 0.916944996 1 20.14677022 -1.02209352 4.880804692 1.000001228 0.927173352 0.692578645 0.014549468 1.92E-07 3.86E-08 0.013941002 0.00328587 0.095040011 1.02209352 -0.072827877 YFDS(ph)GDYNMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 14 YFDSGDYNMAK 11 0 A6NMQ3;Q5T5H1;O43768-2;O43768;O43768-9;O43768-3;O43768-4;O43768-6;O43768-5;O43768-7;P56211;H3BMD8;P56211-2;H3BQ52;H3BTD3 A6NMQ3;P56211 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 1 YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(0.999)GDY(0.001)NMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK;YFDS(1)GDYNMAK 286.09 8.50E-28 15454833000 21607830 16120720 16296620 14896690 23327930 23061060 18455730 17777860 16391410 15524310 TRUE FALSE 22460923.81 18889328.26 16721323.31 17843210.82 19362656.79 17705478.31 17009121.66 17539576.87 15801486.36 18566001.31 1.209787904 1.017415002 0.900642148 0.961069135 1.042909373 0.953650601 0.916143513 0.944714835 0.851097988 1 24.14615979 4.683781427 2.898167551 0.946936374 1.239360888 0.715668912 0.049977927 0.180157033 2.293386228 0.012385821 0.115165951 48281.57478 -4.683781427 0.292424514 YFDSGDYNMAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 0 ; 101.3 0.012046 363380000 363660 512270 461730 430950 557370 639890 466450 485970 476930 624550 FALSE TRUE 378017.5776 600248.3876 473763.0631 516190.6237 462628.4465 491285.2451 429888.4302 479456.367 459765.3825 746918.6148 0.506102767 0.80363292 0.634290074 0.691093532 0.619382671 0.657749366 0.575549225 0.641912462 0.615549503 1 19.51059153 -1.988834603 2.553623096 1.33529207 0.641945586 0.689575557 0.072755941 33306985.07 14802089.33 65793123.11 0.01595755 0.010260426 1.988834603 -0.693346484 YFEADPPGQVAAS(ph)PDPTT ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFEADPPGQVAASPDPTT 18 0 O43598;H0Y8X4 O43598 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 YFEADPPGQVAAS(1)PDPTT;YFEADPPGQVAAS(1)PDPTT 237.89 7.64E-24 220990000 549870 631820 608620 643150 626020 732090 624980 639330 596750 645730 TRUE FALSE 571579.2922 740330.1701 624481.1372 770363.1504 519609.344 562073.1924 575992.4345 630760.8271 575273.0841 772248.4303 0.740149503 0.958668404 0.808653165 0.997558713 0.672852574 0.727839864 0.74586417 0.816784861 0.744932669 1 19.55870551 5.069450616 13.99854101 0.819054563 0.000100128 0.047156383 0.111694396 1522651.822 7657969.426 0.025925356 35415246.6 117341.2244 -5.069450616 -0.818954435 YFEGEFTGLPPALT(ph)PPAPHSLLTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFEGEFTGLPPALTPPAPHSLLTAR 25 0 Q6P5Z2 Q6P5Z2 PKN3 Serine/threonine-protein kinase N3 1 YFEGEFTGLPPALT(0.999)PPAPHS(0.001)LLTAR 102.06 0.018488 103960000 142700 211420 180300 177360 191980 230730 159370 197610 184930 213070 TRUE FALSE 148333.9062 247729.7404 184998.7661 212441.2786 159347.3082 177146.4542 146878.163 194961.3612 178274.4054 254816.987 0.582119379 0.972186914 0.726006411 0.833701399 0.62534021 0.695190915 0.576406482 0.765103471 0.699617429 1 17.95910193 -1.102576679 3.573828299 1.000168781 0.723800335 0.354929414 0.113305385 27665964.62 46964466.84 55632.38177 0.026204647 0.078962942 1.102576679 -0.276368446 YFEITDESPYVHYLNTFSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFEITDESPYVHYLNTFSSK 20 0 Q9ULV4;Q9ULV4-2;Q9ULV4-3;B4E3S0 Q9ULV4 CORO1C Coronin-1C;Coronin 0 ; 324.12 4.29E-67 369540000 575300 656970 793860 734200 930300 1048080 886440 868780 771480 652470 FALSE TRUE 598013.2882 769799.487 814548.6438 879422.5686 772167.9383 804679.3038 816958.5165 857135.4251 743714.5855 780309.0042 0.766380094 0.986531596 1.04387959 1.127018353 0.989566869 1.031231601 1.046967947 1.098456407 0.953102657 1 19.57368602 4.739159575 2.557919265 1.044192627 0.706915025 0.7350687 0.048234007 0.235970938 1.968601792 0.011659804 0.172287334 54847.84575 -4.739159575 -0.337277602 YFEITEEPPYIHFLNTFTSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YFEITEEPPYIHFLNTFTSK 20 0 Q9BR76 Q9BR76 CORO1B Coronin-1B 0 ;; 211.49 2.66E-22 1004720000 1250910 1220730 1431620 1270730 1542540 1615820 1559610 1380540 1439740 1173670 FALSE TRUE 1300296.893 1430380.882 1468929.193 1522076.601 1280339.602 1240570.293 1437363.693 1362036.119 1387924.039 1403628.165 0.926382731 1.019059689 1.046523025 1.084387332 0.912164371 0.883831148 1.024034519 0.970368188 0.988811762 1 20.42072937 4.756568197 23.12508326 0.990482887 0.926382577 0.108072442 0.056486495 3476.672873 4464487.085 0.014358053 0.408770583 57091.07194 -4.756568197 -0.06410031 YFGTDAVPDGS(ph)DEEEVAYTG ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFGTDAVPDGSDEEEVAYTG 20 0 Q9NWZ5;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 YFGTDAVPDGS(1)DEEEVAYTG 113.69 0.00014181 37605000 114990 120460 125170 128840 130820 168320 141450 140660 128810 119530 TRUE FALSE 119529.894 141148.068 128432.033 154324.1675 108583.2631 129230.2309 130362.7794 138774.6828 124174.1533 142949.615 0.836168002 0.987397329 0.898442665 1.079570361 0.759591155 0.904026436 0.911949147 0.97079438 0.868656787 1 17.12514721 -1.435961059 3.055141854 1.001527419 0.918714622 0.086782288 0.082835174 25784572.06 30559089.52 339305.6491 0.018682744 0.036647043 1.435961059 -0.082812797 YFHVVIAGPQDSPFEGGTFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFHVVIAGPQDSPFEGGTFK 20 0 P61088;F8VSD4;F8VV71;F8VZ29 P61088 UBE2N Ubiquitin-conjugating enzyme E2 N 0 ; 290.92 1.84E-54 2107100000 1696550 1365830 1767900 1522550 1907440 1988450 1946710 1677140 1743700 1264480 FALSE TRUE 1763531.104 1600400.678 1813972.926 1823705.846 1583214.03 1526662.623 1794121.783 1654660.682 1680944.578 1512230.646 1.166178657 1.058304619 1.199534562 1.205970697 1.046939522 1.009543502 1.186407502 1.094185392 1.111566269 1 20.52824677 3.231096042 24.9984353 1.085024767 1.15341463 0.284546218 0.062882416 271.8904474 910543.1587 0.018509448 0.022536951 1702.534975 -3.231096042 0.068389863 YFIRDEFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 131.62 0.00029924 223580000 90924 157350 127440 155850 157960 204930 132150 147140 114880 197320 FALSE TRUE 94513.74973 184373.6385 130761.1911 186676.6648 131110.0156 157338.1132 121791.7377 145167.829 110745.4912 235981.0761 0.400514106 0.781306881 0.554117276 0.79106625 0.555595465 0.666740384 0.51610807 0.615167247 0.469298187 1 17.84831165 -1.371911256 5.173607956 1.000223473 0.603073558 0.508479599 0.119351647 0.00027682 3.36E-05 0.103983358 0.024495498 0.042470634 1.371911256 -0.397149915 YFLNLVLVDEEDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFLNLVLVDEEDRR 14 1 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 0 ; 219.61 7.93E-12 863460000 418150 408700 512860 513080 491380 582660 502280 450370 472710 403090 FALSE TRUE 434658.8849 478891.0458 526225.5529 614565.6926 407855.4031 447346.0453 462909.9811 444333.5268 455697.2594 482067.7679 0.901655149 0.993410217 1.091600783 1.274853316 0.846054083 0.927973358 0.960259142 0.921724198 0.945297093 1 18.87887645 3.166847874 24.99999991 0.930754625 1.062163811 0.316846511 0.094728738 55.32922641 19287.30663 0.028298773 0.033823515 1468.411829 -3.166847874 0.131409186 YFNEMSAQGLRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFNEMSAQGLRPR 13 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 0 ; 197.38 1.22E-07 1082420000 487940 431430 457490 493900 525740 605360 532530 471490 453430 430730 FALSE TRUE 507204.248 505524.7464 469412.5652 591591.9459 436374.9026 464774.3143 490788.9071 465170.4478 437111.1429 515123.2967 0.984626887 0.981366499 0.911262543 1.148447274 0.847127096 0.902258386 0.952760068 0.903027393 0.848556347 1 18.97455826 YFPSSCLDLNSPTS(ph)PTPTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFPSSCLDLNSPTSPTPTR 19 0 A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A096LNR9 CDKL5 Cyclin-dependent kinase-like 5 1 YFPSSCLDLNSPT(0.012)S(0.988)PT(0.001)PTR;YFPSSCLDLNSPT(0.001)S(0.996)PT(0.003)PTR 256.4 6.13E-31 135090000 126170 149847 134995 123737 138496 171063 122284 136596 120143 136612 TRUE FALSE 131151.289 175582.0566 138513.0806 148211.8093 114954.4994 131336.2107 112699.0606 134765.154 115819.0769 163378.5058 0.802745064 1.074694959 0.847804795 0.907168348 0.703608463 0.803876924 0.689803472 0.82486465 0.708900331 1 17.31785867 3.31432022 8.409458217 0.777124673 0.916573984 0.227406622 0.106348972 0.328522075 32.56710729 0.026950594 0.036480808 2062.149848 -3.31432022 0.13944931 YFPSSLS(ph)PVTPSESLPRPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFPSSLSPVTPSESLPRPR 19 1 Q9P0U4;Q9P0U4-2;K7EKZ6;K7EQ21 Q9P0U4 CXXC1 CXXC-type zinc finger protein 1 1 YFPSS(0.009)LS(0.991)PVTPSESLPRPR;YFPSS(0.003)LS(0.997)PVTPSESLPRPR 208.89 1.51E-16 426550000 126903 139369 114133 130278 134665 153220 124958 126763 127011 149724 TRUE FALSE 131913.2284 163304.5416 117107.3997 156046.5996 111774.6914 117636.9771 115163.4654 125063.9493 122439.8989 179059.5512 0.736700319 0.912012459 0.654013701 0.871478782 0.624231942 0.65697125 0.643157345 0.698448916 0.683794291 1 17.45007995 4.229162067 25 0.711994301 0.824356406 0.078492096 0.119815923 334.8666895 890748.3494 0.027466839 0.060601852 16949.70198 -4.229162067 0.112362105 YFQFQEEGKEGENR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YFQFQEEGKEGENR 14 1 O15144 O15144 ARPC2 Actin-related protein 2/3 complex subunit 2 0 ;;; 265.99 7.36E-25 1988150000 1340760 908260 1140940 827300 1460430 1452080 1252930 1181250 1294170 873050 FALSE TRUE 1393694.24 1064246.59 1170673.834 990937.4708 1212186.63 1114856.426 1154722.073 1165417.276 1247593.075 1044107.432 1.33481881 1.019288396 1.121219712 0.949076159 1.160978835 1.067760263 1.105941819 1.116185213 1.194889564 1 19.99383873 4.74839634 24.7062767 1.086895018 1.334818968 0.529442358 0.071436474 888.2804417 2231211.329 0.016042537 0.211374855 56026.86732 -4.74839634 0.24792395 YFQHLLGK ddPTM_MDA-MB-175_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 ; 86.833 0.015753 1050310000 3210800 3481500 3331800 3383500 4605500 4687900 3610500 3342500 3259700 3119000 FALSE TRUE 3337564.863 4079420.543 3418629.445 4052746.201 3822658.755 3599206.271 3327499.576 3297699.255 3142384.034 3730108.333 0.89476352 1.093646666 0.916496021 1.086495576 1.024811725 0.964906633 0.89206513 0.884076 0.84243774 1 21.8307861 2.38843197 3.279493613 0.893353408 1.007519089 0.298677567 0.070084139 0.25209398 5.441058761 0.024187605 0.019777549 244.5862114 -2.38843197 0.114165682 YFQINQDEEEEEDED ddPTM_MDA-MB-175_Trastuzumab_2h_R1 15 YFQINQDEEEEEDED 15 0 P35268;K7ERI7 P35268 RPL22 60S ribosomal protein L22 0 ;;;;;;;;;;;;;; 308.91 9.78E-56 6563510000 5322966 6195792 6500981 6039790 6496439 7402066 6391964 6639349 6397278 6554499 FALSE TRUE 5533120.808 7259871.079 6670401.905 7234442.435 5392176.619 5683048.351 5890945.159 6550359.386 6167041.214 7838727.586 0.705869766 0.926154277 0.850954678 0.922910301 0.687889273 0.724996281 0.751518036 0.835640646 0.786740086 1 22.90218806 -1.526162689 2.431136543 1.013877408 0.802980642 0.358922202 0.080369968 3529574.071 3117900.532 321548.4749 0.020841944 0.029774009 1.526162689 -0.210896766 YFQS(ph)PSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YFQSPSR 7 0 Q16629;Q16629-4;H7BZZ6 Q16629 SRSF7 Serine/arginine-rich splicing factor 7 1 YFQS(0.98)PS(0.02)R;YFQS(0.994)PS(0.005)R;YFQS(0.994)PS(0.006)R;YFQS(0.998)PS(0.002)R 137.69 0.002998 1013530000 1373150 1525180 1322610 1452550 1581780 1701330 1667060 1420930 1253450 1416550 TRUE FALSE 1427363.022 1787117.801 1357078.303 1739860.055 1312909.601 1306221.891 1536391.481 1401884.758 1208338.579 1694095.851 0.842551513 1.054909496 0.801063471 1.02701394 0.774991332 0.771043675 0.906909417 0.827512066 0.713264588 1 20.69208407 3.222681499 24.99994824 0.826425058 0.930899189 0.182847829 0.102178401 367.8912245 579203.4952 0.027449889 0.032908414 1669.865526 -3.222681499 0.104474131 YFSDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YFSDLR 6 0 E7ESC6;Q9UIA9 E7ESC6 XPO7 Exportin-7 0 ;;;; 113.25 0.061181 833830000 1320320 1419200 1502040 1547070 1608990 1738310 1535670 1507330 1382660 1248640 FALSE TRUE 1372447.253 1662936.56 1541184.396 1853075.828 1335494.455 1334613.847 1415300.173 1487126.707 1332898.337 1493287.101 0.919077954 1.113608065 1.032075074 1.24093741 0.89433201 0.893742299 0.947774993 0.995874608 0.892593484 1 20.51006014 3.191059639 24.99999239 0.939911004 1.075914412 0.403865448 0.08271975 117.2255928 61695.96848 0.023251386 0.027790782 1552.600204 -3.191059639 0.136003408 YFTWDPSRFPQPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YFTWDPSRFPQPR 13 1 Q14697;F5H6X6;Q14697-2;E9PKU7 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 64.65 0.055387 353660000 244970 380850 271850 236410 383280 360470 218650 273350 258720 432250 FALSE TRUE 254641.6048 446258.0249 278934.6343 283171.1924 318130.2025 276756.3055 201511.6417 269686.1904 249408.7177 516941.1116 0.492593061 0.863266656 0.539586866 0.547782303 0.615408981 0.535372984 0.389815469 0.521696155 0.48247027 1 18.97964042 -1.176609846 7.057480364 1.000000689 0.554287767 0.566429377 0.117003121 1.29E-06 1.51E-07 0.115550446 0.027235459 0.066587108 1.176609846 -0.445712922 YFVAFDGDLVQEFDMTSATHVLGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YFVAFDGDLVQEFDMTSATHVLGSR 25 0 P49916-3;P49916 P49916-3 LIG3 DNA ligase 3 0 ; 178.53 2.89E-17 25664300 12687.7 19678.2 21910.3 23856.6 23828.2 28395 22929.3 21122.9 21235.9 22920 FALSE TRUE 13188.62019 23057.77777 22481.30042 28575.36428 19777.89108 21800.69158 21132.04155 20839.78208 20471.62411 27410.73517 0.481147992 0.841195161 0.820164081 1.042488065 0.721538147 0.795334071 0.770940342 0.760278115 0.746846955 1 14.7424534 -2.514918383 2.143258078 3.7445126 0.783822889 0.209036123 0.130088995 5093100.936 445567.7181 67687955.45 0.030413847 0.003055495 2.514918383 -2.960689711 YGADALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGADALR 7 0 A0A0A0MSX9;P41252;J3KR24 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 88.734 0.042782 60077000 101160 161790 106070 93395 154540 137800 114090 100620 87855 142270 FALSE TRUE 105153.8749 189576.1739 108834.2713 111868.2522 128271.346 105798.0384 105147.3277 99271.35348 84693.11571 170145.0826 0.618024766 1.114203074 0.639655697 0.657487425 0.753893936 0.621810732 0.617986286 0.583451205 0.497769988 1 17.37640593 YGAFGLPITVAHVDGQTHMLFGSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGAFGLPITVAHVDGQTHMLFGSDR 25 0 Q9Y2Q3-3;Q9Y2Q3;Q9Y2Q3-2;Q9Y2Q3-4 Q9Y2Q3-3 GSTK1 Glutathione S-transferase kappa 1 0 ; 239.19 9.17E-39 2067500000 752160 1136920 1119280 1221250 1295670 1398850 1133230 1073660 1180200 1112750 FALSE TRUE 781855.8576 1332177.166 1148449.356 1462809.605 1075432.476 1073988.287 1044404.471 1059269.344 1137724.833 1330772.058 0.587520495 1.00105586 0.862994793 1.099218755 0.808126734 0.807041507 0.784810941 0.795981053 0.854935919 1 20.34383205 YGDAFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGDAFIR 7 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 ;;; 148.28 0.0048727 722640000 1153140 1381540 1339080 1266670 1632020 1747450 1390510 1435420 1303670 1391500 FALSE TRUE 1198666.858 1618808.748 1373977.525 1517213.545 1354609.823 1341631.22 1281518.193 1416180.543 1256751.171 1664137.783 0.720293037 0.972761249 0.825639282 0.911711495 0.814001002 0.806202007 0.77007938 0.850999573 0.755196585 1 20.66634346 3.168307116 24.99966369 0.821738746 0.863547908 0.007991084 0.087314048 150.8650504 53682.49494 0.023042457 0.027541014 1473.354031 -3.168307116 0.041809161 YGDFFIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGDFFIR 7 0 B0QY89;Q9Y262-2;Q9Y262;B0QY90;H0Y7E6 B0QY89 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 ; 124.37 0.009661 137821000 124152 128200 139224 129410 222641 201425 154840 146915 147283 181685 FALSE TRUE 129053.6168 150217.3527 142852.2918 155006.9117 184796.5623 154647.0964 142703.2362 144945.8447 141982.3136 217282.6972 0.593943367 0.691345214 0.657448999 0.713388198 0.850489085 0.71173222 0.656763001 0.667084156 0.653445099 1 17.72921377 -2.137392567 2.329408663 1.646370891 0.69067157 0.68558205 0.063288027 6787247.742 1614946.906 23202748.67 0.016181617 0.007287984 2.137392567 -0.955699321 YGDGGSSFQSTTGHCVHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YGDGGSSFQSTTGHCVHMR 19 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 ;;;;;; 214.5 2.48E-19 1494470000 190886 474873 415360 449658 451078 580695 375034 486208 401661 564725 FALSE TRUE 198422.3267 556428.7438 426184.6228 538599.0103 374403.9227 445837.3868 345637.8551 479691.177 387205.2991 675372.0514 0.293797065 0.823884765 0.631036807 0.797484896 0.554366918 0.660135974 0.511773998 0.710262108 0.573321473 1 19.36532295 -1.83676377 2.483825919 1.145465718 0.629956042 0.384205706 0.144542857 15117390.78 9722085.248 13108935.33 0.034607651 0.01456251 1.83676377 -0.515509675 YGDGGSTFQSTTGHCVHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGDGGSTFQSTTGHCVHMR 19 0 P31943;G8JLB6;E9PCY7;H0YB39;H0YBD7;D6RIT2;H0YBG7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 ;;;;; 129.32 1.14E-05 1904576000 207827 411057 366275 377698 378530 477667 361569 371377 332126 383976 FALSE TRUE 216032.1704 481652.8422 375820.4274 452405.5371 314187.6058 366736.0784 333228.277 366399.2988 320172.8501 459208.7455 0.470444373 1.048875586 0.818408689 0.985184933 0.684193428 0.798626076 0.725657515 0.797892685 0.697227249 1 18.80879059 3.208032686 24.99975816 0.772392565 0.845430798 0.013079378 0.164627693 706.1795866 578298.5607 0.044057878 0.052665164 1614.480063 -3.208032686 0.073038232 YGDGPRPPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGDGPRPPK 9 1 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 67.563 0.055219 222560000 558140 375240 460100 389410 611000 555590 563900 493470 548920 334600 FALSE TRUE 580175.7982 439684.551 472090.584 466434.1357 507142.4382 426562.6425 519700.0445 486855.8418 529164.4764 400158.4637 1.449865118 1.098776087 1.179759087 1.165623567 1.267354022 1.065984307 1.298735605 1.216657614 1.322387315 1 18.6102119 4.751832355 24.62051569 1.191597097 1.449865327 0.399616475 0.098422769 1786.982305 3314973.989 0.021776477 0.410851666 56471.89419 -4.751832355 0.25826823 YGDSEFTVQSTTGHCVHMR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YGDSEFTVQSTTGHCVHMR 19 0 P52597 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ;; 165.8 1.22E-11 629503000 274103 513500 476560 525450 477021 574110 469941 522920 454753 470340 FALSE TRUE 284924.7981 601689.6305 488979.5451 629382.4417 395937.1408 440781.6532 433105.7965 515911.1127 438386.5284 562494.1178 0.506538271 1.06968164 0.86930606 1.118913819 0.703895611 0.783620022 0.769973912 0.917184903 0.779361978 1 19.10147848 -0.961579341 3.852746309 1.000014741 0.848576915 0.075310176 0.167397057 41664928.64 80982274.06 8504.351426 0.037682785 0.109249802 0.961579341 -0.151437825 YGEAGEGPGWGGAHPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGEAGEGPGWGGAHPR 16 0 P26640;A0A140T954;A2ABF4;A0A0G2JJT9 P26640 VARS Valine--tRNA ligase 0 ;;; 234.66 1.11E-19 1580620000 977884 997115 1020064 885282 1242188 1386227 1153341 1014551 1065839 868804 FALSE TRUE 1016491.615 1168361.745 1046647.706 1060388.137 1031041.327 1064296.788 1062939.119 1000952.603 1027479.663 1039029.51 0.978308706 1.124474073 1.007332031 1.020556324 0.992311881 1.024318153 1.023011482 0.963353393 0.988884005 1 19.9868052 3.219535006 0.682923738 0.98792151 1.048751139 0.159764135 0.038439329 1.213453061 1.224895732 0.023109149 0.0419545 1657.810959 -3.219535006 0.060829628 YGEDYSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGEDYSR 7 0 Q9H201;I6L9I8;Q9H201-2 Q9H201 EPN3 Epsin-3 0 91.626 0.037841 66051000 204560 122810 162370 133320 183050 204650 152620 129390 157800 138910 FALSE TRUE 212636.1868 143901.6622 166601.4956 159690.2981 151935.2264 157123.139 140657.2456 127655.7387 152120.8088 166126.7549 1.279963525 0.866216054 1.002857702 0.961255748 0.914574094 0.945802734 0.846686289 0.768423718 0.915691208 1 17.34192491 6.771475269 1.533213846 0.897570765 199.9785596 0.678665206 0.073344724 463.2948482 2.685188998 0.021349415 322896.1539 5908473.193 -6.771475269 199.0809888 YGEPSEVFINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YGEPSEVFINR 11 0 Q8WXF1;Q8WXF1-2;X6RDA4 Q8WXF1 PSPC1 Paraspeckle component 1 0 ;; 223.08 1.68E-11 399430000 709896 481897 561811 475575 687986 714196 644864 544539 532856 430467 FALSE TRUE 737923.2422 564659.0611 576452.2562 569642.3156 571042.3855 548334.8027 594317.8746 537240.3454 513678.6166 514808.7669 1.433392921 1.096832644 1.119740559 1.106512461 1.109232053 1.065123281 1.154443966 1.043572643 0.997804718 1 18.9736771 YGEVEEMNVCDNLGDHLVGNVYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGEVEEMNVCDNLGDHLVGNVYVK 24 0 P0DN76;Q01081;Q01081-2;Q01081-4 P0DN76;Q01081-2;Q01081-4 U2AF1 Splicing factor U2AF 35 kDa subunit 0 256.9 6.99E-44 65654000 57960 43260 57686 47937 62692 68024 64075 55447 62239 37452 FALSE TRUE 60248.30555 50689.56848 59189.34455 57418.79552 52035.63623 52226.45691 59052.63407 54703.82366 59999.03055 44790.00234 1.345128431 1.131716138 1.321485632 1.281955627 1.161769 1.166029341 1.318433378 1.221340049 1.339563014 1 15.45088912 -1.354885916 3.600516717 0.998819571 1.248783827 0.501033005 0.075919704 13788137.72 22819007.51 173497.2379 0.017135623 0.044168646 1.354885916 0.249964256 YGEYFPGTGDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGEYFPGTGDLR 12 0 Q92769;Q92769-3;Q13547;Q5TEE2 Q92769;Q13547 HDAC2;HDAC1 Histone deacetylase 2;Histone deacetylase 1 0 ;;; 179.72 4.74E-05 1550150000 1528020 1583570 1671130 1644140 1956860 2110420 1863390 1763570 1676330 1390730 FALSE TRUE 1588347.409 1855535.829 1714681.021 1969345.985 1624233.636 1620306.939 1717332.623 1739932.229 1615999.211 1663216.916 0.954985122 1.115630686 1.030942509 1.184058414 0.976561518 0.974200613 1.03253677 1.046124659 0.971610615 1 20.66554491 YGGDEIPFS(ph)PYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGGDEIPFSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR 206.32 9.60E-08 510671000 930440 1012930 950970 990590 1051280 1210520 1088500 1011780 912660 929890 TRUE FALSE 967174.4897 1186892.848 975753.0594 1186525.745 872583.8011 929395.0756 1003180.526 998218.744 879813.5449 1112084.142 0.869695424 1.067268926 0.877409382 1.066938823 0.784638292 0.835723702 0.902072503 0.897610807 0.791139368 1 20.08483452 3.233748958 24.99999747 0.866655169 0.970615424 0.259598284 0.084185506 154.0502416 800401.311 0.022367562 0.027557643 1712.966848 -3.233748958 0.103960254 YGGELVPHFPAR ddPTM_MDA-MB-175_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 ;;;; 110.86 0.0014446 1950900000 2457340 3230720 2634990 2623730 3658350 3819120 2947020 2858920 2747990 4061820 FALSE TRUE 2554357.681 3785571.028 2703660.004 3142695.963 3036504.974 2932187.259 2716024.872 2820600.854 2649090.377 4857655.861 0.525841631 0.779299962 0.556577098 0.646957309 0.625096767 0.603621859 0.559122538 0.580650613 0.545343362 1 22.21182886 -1.998254251 3.267725984 1.39012072 0.604705465 0.749942335 0.068848804 3776202.079 22161624.31 11049952.36 0.015228569 0.010040278 1.998254251 -0.785415255 YGGGGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGGGGYGR 8 0 Q01130;J3KP15 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 124.86 0.0029931 2436000000 2124140 2353850 2404670 2287150 2577980 2996800 2499180 2406360 2295519 2370610 FALSE TRUE 2208002.687 2758105.427 2467337.676 2739541.444 2139775.88 2300838.617 2303287.741 2374106.68 2212903.72 2835085.641 0.7788134 0.972847305 0.870286823 0.966299361 0.754748234 0.81155877 0.812422633 0.837402104 0.780542107 1 21.43496089 3.239850731 24.99994404 0.823350892 0.900562475 0.128192566 0.079677884 55.89318659 1083084.107 0.020571119 0.026383102 1737.203643 -3.239850731 0.077211583 YGGPPPGWEGPHPQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGGPPPGWEGPHPQR 15 0 B7Z8Z7;A0AV96;A0AV96-2;D6R9D6;D6RBS9;D6REZ6;D6R9M7;D6RBP6;D6RFL5;D6RA49 B7Z8Z7 RBM47 RNA-binding protein 47 0 159.02 1.79E-06 135800000 95870 93594 95803 93118 110780 119670 104670 101650 92168 88489 FALSE TRUE 99655.02163 109668.0414 98299.70488 111536.4625 91949.65517 91878.45612 96465.6919 100287.548 88850.89168 105826.7253 0.941681048 1.036298167 0.928874106 1.053953641 0.86886989 0.868197101 0.911543767 0.947658049 0.839588407 1 16.69134448 3.226237691 24.99989962 0.905101341 0.989113807 0.360890818 0.054894621 233.9421785 474604.8583 0.0149326 0.017968446 1683.595245 -3.226237691 0.084012465 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;Q04323;E9PJ81;E9PRQ7;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 YGGSVGSQPPPVAPEPGPVPS(0.161)S(0.709)PS(0.11)QEPPT(0.021)KR;YGGSVGSQPPPVAPEPGPVPS(0.118)S(0.762)PS(0.118)QEPPT(0.001)KR 217.65 4.74E-35 1062470000 304580 271410 330760 270080 395400 399060 343130 354050 362600 310230 TRUE FALSE 316605.0536 318022.5562 339379.8773 323501.0179 328190.0492 306384.3628 316234.574 349304.5389 349550.0968 371013.6288 0.853351546 0.857172167 0.914736956 0.871938368 0.884576802 0.825803526 0.852352985 0.941487082 0.942148939 1 18.50111266 1.608233602 3.390992624 0.964893283 0.866701231 0.745290795 0.025836547 0.105528788 2.852009752 0.016894187 0.007135716 40.57267121 -1.608233602 -0.098192052 YGIDKDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGIDKDK 7 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 79.906 0.028595 500650000 1432100 675590 914320 734460 1281200 1136700 1487000 979930 1004100 459950 FALSE TRUE 1488640.414 791617.3271 938147.9303 879733.9959 1063422.082 872718.6519 1370445.054 966795.6412 967962.6371 550068.3962 2.70628239 1.439125266 1.705511418 1.59931747 1.933254281 1.586563885 2.491408457 1.757591688 1.759713235 1 19.06925149 4.751165 24.11379103 1.758035185 2.706283378 0.404160853 0.360862106 1252.256926 2395655.336 0.081513187 1.404054918 56385.18376 -4.751165 0.948248193 YGIICMEDLIHEIYTVGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGIICMEDLIHEIYTVGK 18 0 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 200.71 1.48E-15 284440000 629680 524810 658210 561363 879590 912120 769330 721840 762950 550130 FALSE TRUE 654540.2526 614942.035 675363.4933 672398.9259 730077.606 700293.9533 709027.9043 712164.9155 735491.5785 657917.4406 0.994866851 0.934679638 1.026517085 1.022011098 1.109679666 1.064410077 1.077685224 1.082453316 1.117908621 1 19.32754703 3.75895977 1.67329395 1.078517589 0.966701927 0.561818692 0.036188181 0.236339338 1.276318418 0.009804078 0.022823738 5740.632828 -3.75895977 -0.111815662 YGIICMEDLIHEIYTVGKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGIICMEDLIHEIYTVGKR 19 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 ; 244.97 9.77E-25 2200680000 2016450 2020610 2282560 1563770 3284900 2827200 1749990 2250430 2489500 2944800 FALSE TRUE 2096061.003 2367634.049 2342045.389 1873079.039 2726533.871 2170625.647 1612821.211 2220266.667 2399903.381 3521777.178 0.595171386 0.672283887 0.665018049 0.531856203 0.774192612 0.616343833 0.457956631 0.630439279 0.681446684 1 21.7478722 0.760479994 2.745450684 0.99989802 0.616934801 0.67302758 0.079529529 0.763694449 7.899868253 0.076245534 0.02015114 5.760762807 -0.760479994 -0.382963218 YGIKPEWMMIHR ddPTM_MDA-MB-175_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 0 122.42 0.00021557 419120000 451650 466110 527890 438260 878450 682680 558080 533860 531650 747840 FALSE TRUE 469481.4907 546160.7667 541647.2471 524946.5199 729131.3828 524137.9161 514336.2313 526704.4799 512516.0204 894364.9297 0.524932804 0.610668809 0.60562219 0.586948909 0.815250418 0.5860448 0.57508542 0.588914505 0.573050221 1 19.77050409 -1.246030561 4.636624178 1.000124691 0.609416771 0.721654941 0.073139293 9.42E-05 1.53E-05 0.070777902 0.016677218 0.056750467 1.246030561 -0.39070792 YGISSMIQSQEKPDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGISSMIQSQEKPDR 15 1 P14868;H7C278 P14868 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 ; 238.67 8.12E-18 992840000 700220 513330 661530 545500 870260 863010 871050 806400 849270 575910 FALSE TRUE 727865.2263 601490.4343 678770.0153 653398.2718 722333.516 662589.0065 802774.8249 795591.527 818704.9386 688748.538 1.05679386 0.873309199 0.985512096 0.948674641 1.048762322 0.962018748 1.165555759 1.155126266 1.18868483 1 19.39361783 2.240312565 24.99986023 1.142763881 0.976430478 0.526169742 0.06822558 30.73912234 438647.6096 0.022892688 0.018234273 173.9051988 -2.240312565 -0.166333403 YGKIETIEVMEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGKIETIEVMEDR 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;;;; 161.49 3.84E-05 2346040000 2817240 2985220 3800910 2158880 5026810 4245800 2615790 3390420 3870190 4053410 FALSE TRUE 2928466.811 3497908.313 3899964.837 2585900.02 4172354.632 3259777.296 2410757.545 3344976.966 3730902.618 4847598.082 0.604106768 0.721575563 0.80451489 0.533439443 0.860705562 0.672452056 0.497309699 0.690027702 0.769639429 1 22.20883866 0.879356111 2.746497023 0.99949232 0.673136326 0.471540216 0.104988604 0.405470958 6.243064963 0.097962435 0.02596479 7.574537343 -0.879356111 -0.326355993 YGLQDS(ph)DEEEEEHPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 290.71 1.03E-45 2260830000 1076438 947305 1111966 965681 1430245 1505204 1355795 1181258 1251272 769267 TRUE FALSE 1118936.603 1109997.265 1140944.747 1156689.82 1187132.466 1155643.183 1249524.245 1165425.169 1206238.965 919990.1401 1.216248473 1.206531697 1.240170625 1.257285018 1.290375205 1.256147357 1.358193083 1.266780064 1.311143362 1 19.81125887 3.940662235 2.194995331 1.26855963 1.210917211 0 0.090981663 0.93657241 8.811759543 0.022702289 0.056130755 8722.926949 -3.940662235 -0.057642419 YGNPWEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 ;; 120.92 0.010442 678290000 591078 501061 599635 490100 720078 699436 672723 596683 634008 477894 FALSE TRUE 614414.2159 587114.329 615261.9807 587040.3172 597679.3988 537002.5891 619993.2134 588685.4404 611190.1759 571528.1795 1.075037484 1.027271008 1.076520814 1.02714151 1.045756658 0.939590747 1.084799028 1.030019974 1.069396397 1 19.12446511 3.710186945 24.08239168 1.029911874 1.056375897 0.115936328 0.039349923 1110.545451 942586.6905 0.010168316 0.015756836 5130.821958 -3.710186945 0.026464023 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 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(0.999)DDEEES(0.001)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(0.997)DDEEES(0.003)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(0.999)DDEEES(0.001)EEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR;YGPADVEDTTGSGATDSKDDDDIDLFGS(1)DDEEESEEAKR 314.51 1.89E-110 35211384000 9035453 2322349.3 3807477 2149778.6 5825451 6616927 5726270 3641137 4258719 1646042.7 TRUE FALSE 9392179.661 2721194.727 3906702.978 2574998.391 4835242.92 5080245.985 5277429.995 3592333.514 4105448.535 1968553.252 4.771107743 1.382332291 1.984555396 1.308066413 2.45624187 2.580700309 2.680867277 1.824859709 2.08551561 1 20.90870431 8 0.060105575 4.10E-12 6.762868858 0.222309885 0.888730244 665.5358593 2.986296601 67.90840991 393.9021211 100000000 -8 6.762868858 YGPLS(ph)EPGSAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YGPLSEPGSAR 11 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 YGPLS(0.976)EPGS(0.024)AR;YGPLS(1)EPGSAR;YGPLS(0.999)EPGS(0.001)AR 135.26 0.00012974 252760000 313393 408830 437570 371240 503080 528810 437680 436650 413490 385410 TRUE FALSE 325765.9976 479043.3722 448973.4337 444670.164 417566.6413 406001.8917 403373.4979 430797.421 398608.5757 460923.7104 0.706767715 1.039311629 0.9740732 0.964737014 0.905934392 0.880844015 0.875141566 0.934639315 0.864803799 1 18.81416846 3.061504995 24.8701159 0.905118493 0.933670426 0 0.088447465 329.8710218 133382.8343 0.024445133 0.029217519 1152.139312 -3.061504995 0.028551933 YGPQYGHPPPPPPPPEYGPHADSPVLMVYGLDQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGPQYGHPPPPPPPPEYGPHADSPVLMVYGLDQSK 35 0 A0A3B3ITJ4;P14866;M0QXS5;P14866-2 A0A3B3ITJ4;P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 199.21 1.09E-27 870300000 412130 390010 445890 365990 530560 535030 463430 448540 496070 396870 FALSE TRUE 428401.2106 456991.1836 457510.2597 438381.7296 440375.6007 410777.391 427105.1457 442528.055 478216.5376 474629.078 0.902602117 0.962838572 0.963932218 0.923630157 0.92783106 0.865470343 0.899871427 0.932366084 1.007558449 1 18.85644096 1.273167981 5.165644313 1.004777698 0.922154893 0.584339328 0.027562771 0.132148828 8.173301136 0.02308563 0.007536689 18.75719876 -1.273167981 -0.082622806 YGQFSGLNPGGRPIT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 1 YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR;YGQFSGLNPGGRPIT(1)PPR 184.2 9.60E-14 6004700000 3012830 3309740 3243360 3449480 4019810 4408760 3820600 3640720 3337110 3575310 TRUE FALSE 3131778.855 3878162.099 3327884.626 4131776.848 3336524.132 3384892.305 3521131.389 3591922.103 3217008.063 4275823.541 0.732438751 0.906997696 0.778302611 0.966311357 0.780323159 0.791635172 0.823497826 0.840053868 0.752371568 1 22.02777089 -1.090991663 4.397671381 1.00001734 0.82429854 0.388449267 0.067811302 8498800.219 2108415.988 1442.755834 0.014522077 0.081097663 1.090991663 -0.1757188 YGQFSGLNPGGRPITPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGQFSGLNPGGRPITPPR 18 1 P62136;P62136-2;P62136-3 P62136 PPP1CA Serine/threonine-protein phosphatase PP1-alpha catalytic subunit 0 ; 197.45 1.68E-15 1629620000 354200 413270 425680 359220 471430 484610 390810 430010 349610 384690 FALSE TRUE 368184.0895 484245.9077 436773.5705 430272.6438 391296.497 372066.6718 360177.291 424246.4193 337027.6044 460062.6402 0.800291215 1.052565163 0.949378481 0.935247956 0.850528739 0.808730463 0.782887502 0.922149252 0.732568948 1 18.81147078 3.247865579 4.670365421 0.843895201 0.945170656 0.172677974 0.089661503 0.282948983 15.50946139 0.024173899 0.031419732 1769.561166 -3.247865579 0.101275455 YGQNCHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGQNCHK 7 0 O15355 O15355 PPM1G Protein phosphatase 1G 0 ;;; 104.11 0.0082248 765250000 562646 479742 569782 448666 654340 678370 643519 563507 585943 466069 FALSE TRUE 584859.6985 562133.9566 584630.987 537410.7957 543115.5205 520828.8483 593078.2993 555954.1104 564855.0259 557386.2971 1.049289696 1.008517718 1.048879368 0.964162195 0.974396973 0.934412724 1.064034588 0.997430531 1.013399556 1 19.08831801 3.751476109 24.79180732 0.993921061 1.032857807 0.254616063 0.033573426 1143.176374 2194366.396 0.008907565 0.015921831 5642.559007 -3.751476109 0.038936746 YGQNGDFTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGQNGDFTR 9 0 O76094-2;O76094;R4GNC1 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 ; 108.81 0.0059357 536320000 381130 364600 401560 361440 519800 520440 455070 416990 432310 378730 FALSE TRUE 396177.3067 427217.2138 412024.9835 432931.7532 431444.5817 399575.6973 419400.4243 411400.9311 416751.2475 452934.8923 0.874689306 0.943219922 0.909678169 0.955836613 0.952553201 0.882192351 0.925961836 0.908300372 0.920112923 1 18.78894416 -2.536299973 2.051465399 2.007376987 0.92002244 0.469183347 0.025777767 1813091.48 97728.49437 8528705.889 0.006015046 0.002908707 2.536299973 -1.087354547 YGREDLDVLGLTFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGREDLDVLGLTFR 14 1 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ;;;;; 235.93 2.73E-17 1776907000 992610 984576 1166378 1124673 1319529 1383932 1303484 1141598 1181879 933302 FALSE TRUE 1031799.009 1153669.269 1196774.769 1347129.963 1095235.932 1062534.767 1201313.518 1126296.746 1139343.406 1116164.658 0.924414693 1.033601325 1.072220627 1.206927628 0.981249428 0.951951631 1.076287006 1.009077593 1.020766423 1 20.09011844 YGREDLDVLGLTFRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGREDLDVLGLTFRK 15 2 P49407-2;P49407;E9PM35 P49407-2 ARRB1 Beta-arrestin-1 0 ; 212.69 4.23E-10 395410000 350240 371150 423000 248128 678150 492600 322000 458010 492600 519680 FALSE TRUE 364067.7456 434892.1254 434023.7275 297206.9778 562878.3052 378201.1154 296760.7986 451871.1251 474871.4222 621501.3461 0.585787542 0.699744462 0.698347204 0.4782081 0.905675118 0.608528232 0.477490194 0.727063791 0.76407143 1 19.24539799 0.906591987 1.829360198 0.997788968 0.644840265 0.458976653 0.117905726 0.395231071 2.691996965 0.10778294 0.030466719 8.064770011 -0.906591987 -0.352948703 YGRPPDSHHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YGRPPDSHHSR 11 1 Q01130;Q01130-2;J3KP15;J3QL05 Q01130 SRSF2 Serine/arginine-rich splicing factor 2 0 ;;;;; 133.32 9.86E-05 455513000 62853.1 570128 462554 542204 525212 786152 411802 543360 385782 717605 FALSE TRUE 65334.58892 668043.049 474608.5372 649450.3329 435936.6518 603580.1122 379523.8832 536077.148 371897.7812 858205.9604 0.076129265 0.778418095 0.553024052 0.756753463 0.507962741 0.703304498 0.442229372 0.624648596 0.433343275 1 19.7109644 -2.196807323 2.238494791 2.214116101 0.55977412 0.329948237 0.194386111 8321439.852 1803477.831 51088590.89 0.042305568 0.006356129 2.196807323 -1.654341981 YGS(ph)FEEAEASYPILNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR;YGS(1)FEEAEASYPILNR 266.07 3.92E-27 143541000 140881 121691 159493 98764 232488 230462 170977 148586 165787 115483 TRUE FALSE 146443.0907 142590.4826 163649.5186 118299.2244 192969.7728 176940.6932 157575.376 146594.4477 159820.3583 138109.6828 1.060339056 1.032443778 1.184924296 0.85655996 1.397221172 1.281160666 1.140943725 1.061434975 1.157198793 1 17.07545494 3.24949144 24.99998908 1.170911011 1.044297902 0.222777528 0.126914223 380.2302431 869623.3776 0.036020088 0.048301856 1776.198261 -3.24949144 -0.126613109 YGS(ph)PPQRDPNWNGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGSPPQRDPNWNGER 15 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 YGS(1)PPQRDPNWNGER;YGS(1)PPQRDPNWNGER 124.73 5.74E-05 1091730000 805080 650180 763800 614720 975900 1279770 840170 786370 759720 572440 TRUE FALSE 836865.1801 761843.3573 783705.2555 736309.7812 810016.8666 982562.8126 774315.28 775829.9964 732377.8256 684598.658 1.222417208 1.112832093 1.144765983 1.075534947 1.183199612 1.435239174 1.131049953 1.133262514 1.069791501 1 19.38489894 -0.78379023 6.618881667 0.999999999 1.166821722 0.203380406 0.099479815 2.93E-09 4.43E-10 0.098475047 0.023210791 0.164516617 0.78379023 0.166821723 YGSIIDRDDRDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YGSIIDRDDRDER 13 2 P52756;C9JR02;C9J9P7;C9JFQ5;P52756-4;P52756-2;P52756-5;F8W910;P52756-3;F8WE23 P52756 RBM5 RNA-binding protein 5 0 112.08 0.00052233 208460000 145630 219090 195260 176230 199330 223150 203250 210090 187310 240230 FALSE TRUE 151379.5849 256717.0032 200348.636 211087.768 165447.9578 171326.7944 187318.7339 207274.0872 180568.7497 287298.469 0.526907036 0.893555069 0.69735365 0.734733355 0.575874833 0.596337304 0.65200046 0.721459073 0.628505785 1 18.13219078 -1.31875877 4.835082989 1.000164361 0.676657841 0.507708618 0.097372046 0.000166374 2.34E-05 0.090920109 0.02141926 0.047999999 1.31875877 -0.32350652 YGTCPHGGYGLGLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGTCPHGGYGLGLER 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 ;;; 225.85 9.44E-13 1359490000 883901 959511 999307 946687 1219049 1243627 1138663 1053105 1038628 1033106 FALSE TRUE 918798.094 1124299.55 1025349.761 1133938.863 1011835.486 954813.4766 1049411.619 1038989.85 1001247.981 1235523.341 0.74365094 0.909978398 0.829891049 0.917780203 0.818952951 0.772800841 0.849366082 0.840930977 0.810383704 1 20.23669083 -1.437885985 6.057950876 1.000064383 0.836305151 0.492138777 0.050881901 4.15E-05 3.85E-06 0.046245612 0.010895919 0.036484972 1.437885985 -0.163759232 YGVIILDEAHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 ;;;;;;; 211.46 3.16E-08 4083239000 2607537 3046559 3033929 3103726 3278615 3579369 3210526 3097386 2953725 2891001 FALSE TRUE 2710484.574 3569781.809 3112995.682 3717633.739 2721317.193 2748114.796 2958876.583 3055870.607 2847421.014 3457437.294 0.783957696 1.03249358 0.900376613 1.075257025 0.787090831 0.794841543 0.855800505 0.883854238 0.823564037 1 21.72127166 3.213998542 24.99957781 0.85107417 0.950651925 0.18775656 0.091557458 330.8924655 336785.4731 0.024836595 0.029698272 1636.811027 -3.213998542 0.099577755 YGVQADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGVQADR 7 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;; 127.12 0.01051 1712600000 849330 977600 855510 970560 908130 1258290 991220 931250 880280 916470 FALSE TRUE 882862.2042 1145495.195 877805.2934 1162533.871 753766.387 966071.2171 913525.5863 918768.117 848598.8948 1096034.75 0.805505669 1.045126713 0.800891846 1.060672457 0.687721249 0.881423894 0.83348232 0.8382655 0.774244516 1 20.06386211 3.241988 24.99998059 0.830578354 0.927329148 0.146962152 0.108361551 154.9357736 1130119.654 0.027513452 0.035795818 1745.773914 -3.241988 0.096750795 YGVQADRVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YGVQADRVDK 10 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 ;;;;;;; 158.05 7.39E-06 11805540000 8276020 6997480 7696490 5882830 10524890 9538770 8194460 7653140 7974290 7223250 FALSE TRUE 8602763.66 8199242.757 7897066.852 7046436.216 8735872.957 7323535.229 7552156.813 7550562.176 7687296.861 8638507.54 0.995862262 0.949150385 0.914170279 0.81570065 1.011271092 0.847777836 0.874243239 0.874058643 0.889887151 1 23.04235065 4.41222351 2.346373701 0.89451873 0.99391291 0.194226769 0.058517453 0.464408412 4.573221546 0.014037793 0.07079811 25835.89494 -4.41222351 0.09939418 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENYEVGS(1)DDEEIPFK;YGVYEDENY(0.001)EVGS(0.999)DDEEIPFK 130.14 9.88E-06 432879000 595914 431870 535066 429050 665880 633830 620880 534640 585395 403568 TRUE FALSE 619441.1449 506040.313 549010.2595 513914.8094 552693.9554 486632.5883 572213.8032 527474.0253 564326.7483 482639.4228 1.283444981 1.048485244 1.137516402 1.064800729 1.145148799 1.0082736 1.185592756 1.092894613 1.16925125 1 18.88058624 -0.232109382 0.011736292 4.08E-07 2.143896647 0.183664333 0.075454555 5375.137627 17.01693994 1629.425239 1479.313286 0.585990557 0.232109382 2.143896239 YGYIHLYDLETGTCIYMNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YGYIHLYDLETGTCIYMNR 19 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 ;; 290.63 1.57E-49 2204380000 1773900 1903860 2254080 2203820 2231410 2775390 2354060 2345680 2204560 1725540 FALSE TRUE 1843934.942 2230833.145 2312823.177 2639729.018 1852115.725 2130847.734 2169542.626 2314239.996 2125218.316 2063626.526 0.893541016 1.08102562 1.120756662 1.27916994 0.897505291 1.032574309 1.051325227 1.12144323 1.029846384 1 20.97675047 1.003562382 24.28433284 0.999999966 1.066279355 0.028803999 0.105467321 210.9379106 1437916.323 0.099926478 0.024981619 10.08236423 -1.003562382 0.06627939 YGYTHLSAGELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YGYTHLSAGELLR 13 0 P30085;P30085-3;Q5T0D2 P30085 CMPK1 UMP-CMP kinase 0 ; 176.05 1.72E-05 400765000 164502 353819 338053 322323 454264 494358 295810 355118 302412 476653 FALSE TRUE 170996.666 414584.6609 346862.9389 386077.5274 377048.3675 379550.8466 272623.6392 350358.2241 291528.2512 570044.0293 0.29997098 0.727285332 0.60848447 0.67727668 0.661437272 0.665827247 0.478250144 0.614616075 0.511413568 1 19.12071383 -2.121872671 2.398080717 1.798886406 0.59244199 0.524279512 0.118919775 4288360.673 1221871.653 18657354.34 0.026947494 0.007553136 2.121872671 -1.206444416 YGYTHLSTGDLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YGYTHLSTGDLLR 13 0 P00568;Q5T9B7 P00568 AK1 Adenylate kinase isoenzyme 1 0 ;; 124.86 0.00020692 612470000 221610 741520 640392 694811 1000290 1065640 662063 767583 622819 1314980 FALSE TRUE 230359.3339 868870.2918 657081.1416 832242.542 830261.0631 818161.2599 610168.7721 757294.8054 600403.8659 1572625.154 0.146480764 0.552496753 0.417824387 0.52920592 0.527945939 0.520251923 0.387993776 0.481548196 0.381784473 1 20.5847434 -2.115727799 2.438654804 2.055060751 0.449171733 0.684633069 0.114138427 15155826.47 4173774.73 88617189.02 0.026665474 0.007660766 2.115727799 -1.605889017 YHDGNRNPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YHDGNRNPK 9 1 P13674;P13674-2;P13674-3 P13674;P13674-2 P4HA1 Prolyl 4-hydroxylase subunit alpha-1 0 ; 141.48 6.41E-05 80298000 105269 98343 109683 72601 173856 133424 75183 83457 99989 113737 FALSE TRUE 109425.1014 115232.6452 112541.4291 86961.26111 144304.0192 102438.2981 69289.96001 82338.39542 96390.41542 136021.5875 0.804468639 0.84716439 0.827379177 0.639319557 1.060890568 0.753103238 0.509404141 0.605333292 0.708640571 1 17.05347611 2.473843613 24.98592217 0.656292275 0.833276199 0.107135154 0.153470941 142.7450332 1088146.589 0.050331825 0.042310809 297.7444078 -2.473843613 0.176983924 YHDLECQLIQEFTSAQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YHDLECQLIQEFTSAQR 17 0 F8W9B8;A0A0A0MSI8;O00471 F8W9B8 EXOC5 Exocyst complex component 5 0 ; 159.81 3.17E-09 167710000 164389 192046 190064 202500 221198 255683 204055 195790 197397 189579 FALSE TRUE 170879.2047 225028.4066 195017.224 242553.8956 183598.843 196304.4982 188060.6359 193165.7553 190292.7205 226723.3753 0.753690282 0.992524067 0.860154908 1.069823062 0.809792297 0.865832638 0.829471754 0.851988707 0.839316723 1 17.79057362 YHEDFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 154.35 0.0087287 0 561090 439190 539800 426510 711700 713060 637540 552730 573860 394390 FALSE TRUE 583242.2665 514617.4661 553867.6315 510872.405 590725.4882 547462.6215 587567.9489 545321.5584 553206.8907 471663.1694 1.236565211 1.091069855 1.174286371 1.083129738 1.252430816 1.160706744 1.245736337 1.156167354 1.172885497 1 18.84739742 0.185364543 2.099941784 0.99999611 1.173600723 0.471134687 0.055541197 30.32265444 76.18065167 0.050043181 0.013631623 1.532373184 -0.185364543 0.173604613 YHEEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YHEEFEK 7 0 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;;;;; 170.06 0.00098884 6998914000 12228318 9711388 11696683 8897076 14825888 14674895 13810640 11408695 12236735 8297387 FALSE TRUE 12711101.44 11379243.34 12001508.17 10656891.08 12305788.85 11266873.04 12728125.95 11255780.1 11796337.3 9923101.12 1.280960587 1.146742657 1.209451362 1.073947645 1.240115233 1.135418545 1.282676232 1.134300655 1.188775279 1 23.24235962 -0.052524421 1.062222766 0.998438244 1.186381079 0.435675989 0.064168336 9.129638904 8.21456206 0.109667493 0.017426147 0.886085397 0.052524421 0.187942834 YHEEKER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YHEEKER 7 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ; 116.73 0.0032392 125213000 114701 129475 123131 105914 143369 154549 120472 98508 113065 112350 FALSE TRUE 119229.484 151711.3241 126339.895 126863.4731 118999.1886 118657.337 111029.0898 97187.66139 108995.8127 134362.8314 0.887369541 1.129116754 0.940289019 0.944185767 0.885655559 0.883111317 0.826337825 0.723322517 0.81120509 1 17.03577458 3.114795351 1.102814258 0.81235039 1.002635096 0.301075687 0.088140367 0.453093891 1.184240503 0.036186197 0.050060616 1302.552842 -3.114795351 0.190284706 YHGHS(ph)MSDPGVSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YHGHSMSDPGVSYR 14 0 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3;P29803 P08559-3 PDHA1;PDHA2 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial;Pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial" 1 YHGHS(0.997)MS(0.003)DPGVSYR 114.01 0.00032344 979170000 247880 403990 371360 393490 425700 613140 382650 333410 352560 400840 TRUE FALSE 257666.4938 473372.1399 381037.9467 471321.1475 353339.6661 470747.5272 352656.8931 328941.1843 339871.4345 479376.9235 0.537502915 0.987473774 0.794860845 0.98319532 0.737081092 0.981998724 0.735656799 0.686184854 0.708985806 1 18.87080094 YHGNVMLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 ;;;;;; 196.95 2.88E-05 10271500000 1311808 1405044 1284790 1435219 3143575 2267135 1419919 1201776 1314452 3593753 FALSE TRUE 1363599.193 1646349.377 1318272.683 1719101.034 2609231.244 1740627.255 1308622.039 1185668.158 1267145.129 4297880.094 0.317272507 0.383060798 0.306726259 0.399988133 0.607097264 0.4049967 0.304480816 0.275872787 0.294830266 1 22.0351938 -1.270887943 3.478416116 1.001845145 0.364756914 0.811588878 0.091635155 60175110.8 92758468.71 1178598.521 0.024503276 0.053593492 1.270887943 -0.637088231 YHIDLDPHFNDILGQHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YHIDLDPHFNDILGQHSR 18 0 P19784;H3BSA1;H3BV19 P19784 CSNK2A2 Casein kinase II subunit alpha 0 ; 109.42 0.00012616 113968000 95374 113206 104972 101383 107244 121420 110150 89139 98287 102748 FALSE TRUE 99139.43916 132648.2499 107707.6566 121436.2548 89014.70319 93222.04514 101516.1552 87944.23751 94749.67007 122879.5034 0.806802082 1.079498584 0.876530696 0.988254766 0.724406437 0.758646012 0.826143925 0.71569493 0.771077905 1 16.90688476 3.241027299 24.99970066 0.780682125 0.94352056 0.30072259 0.100898968 63.79840404 646586.3544 0.026022247 0.033644699 1741.916363 -3.241027299 0.162838435 YHIEVNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YHIEVNR 7 0 Q15029;Q15029-3;Q15029-2 Q15029 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 ;;; 149.4 0.002019 789540000 579360 944393 827427 1027140 700553 1001590 854380 761695 680286 1166460 FALSE TRUE 602233.5802 1106585.151 848990.4274 1230305.226 581473.2513 768985.9017 787411.4631 751485.7244 655802.6397 1395005.504 0.431706956 0.793247875 0.608592887 0.881935751 0.416825059 0.551242199 0.564450435 0.538697319 0.470107564 1 20.41183938 -1.645548972 8.545615248 1.000384142 0.589324468 0.436058746 0.141782041 0.001004819 4.17E-05 0.132932714 0.031305051 0.022617835 1.645548972 -0.411059674 YHNTICGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YHNTICGR 8 0 Q9Y316-2;Q9Y316;Q9Y316-3 Q9Y316-2 MEMO1 Protein MEMO1 0 101.54 0.005321 58667000 28652 52176 48586 50530 60315 71991 58887 63941 53913 70556 FALSE TRUE 29783.20308 61136.82213 49852.19107 60524.68318 50062.67784 55272.18128 54271.28307 63083.97548 51972.68166 84380.09732 0.352964787 0.724540787 0.590805091 0.717286245 0.593299598 0.655038131 0.643176351 0.747616766 0.615935313 1 16.36461513 -5 0.141801892 2.242912922 0.511419757 0.593524666 0.098008363 92.01926007 0.795533925 32.35546547 0.534455969 1.00E-05 5 -1.731493165 YHNVGLSK ddPTM_MDA-MB-175_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 ; 107.57 0.0039768 1973070000 3926400 3669000 4161000 3185800 4941800 5254400 4371900 4355100 4141400 3266700 FALSE TRUE 4081417.304 4299122.209 4269439.078 3815941.731 4101794.601 4034145.231 4029219.054 4296727.008 3992351.823 3906747.32 1.044709824 1.100435185 1.092837271 0.976756728 1.049925748 1.032609714 1.031348773 1.099822091 1.021911963 1 21.89753652 YHPDKNKEPGAEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YHPDKNKEPGAEEK 14 2 P25685 P25685 DNAJB1 DnaJ homolog subfamily B member 1 0 64.675 0.036213 50930000 51503 27031 38224 25704 46592 45823 34615 30868 37182 24659 FALSE TRUE 53536.37821 31673.36398 39220.14884 30788.17448 38672.30848 35181.3027 31901.78585 30454.26495 35843.82708 29490.45892 1.815379623 1.074020722 1.329926704 1.04400459 1.311349836 1.192972371 1.081766341 1.032681961 1.21543809 1 14.84796065 4.742253234 24.9884099 1.144973222 1.81537988 0.769572112 0.110457594 162.9918366 1102940.575 0.025640067 0.191266867 55239.94455 -4.742253234 0.670406658 YHPDKNPEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YHPDKNPEGR 10 1 O75165 O75165 DNAJC13 DnaJ homolog subfamily C member 13 0 ;; 150.46 1.29E-05 344120000 276836 350332 341069 321090 407650 416920 327099 329353 322954 373726 FALSE TRUE 287765.699 410498.7958 349957.5383 384600.6436 338357.7986 320096.6485 301460.1257 324938.5617 311330.9486 446950.4543 0.643842503 0.918443626 0.782989557 0.860499503 0.75703648 0.716179266 0.6744822 0.727012488 0.696567026 1 18.76975539 3.021517374 19.29456376 0.737259633 0.808518962 0.002633129 0.108505427 42.73292749 38314.08487 0.028841625 0.034458622 1050.793491 -3.021517374 0.071259329 YHPGYFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YHPGYFGK 8 0 P46776;E9PLL6 P46776 RPL27A 60S ribosomal protein L27a 0 ;; 140.53 0.00064813 6131757000 7776100 6795700 7794810 7266660 8648860 9097580 9608860 7873590 7462050 6478020 FALSE TRUE 8083106.432 7962808.612 7997949.152 8703983.659 7178729.866 6984804.92 8855692.445 7768057.405 7193492.278 7747263.99 1.043349813 1.027822031 1.032357896 1.123491296 0.926614851 0.90158344 1.143073536 1.002683969 0.928520351 1 22.88525547 3.23576361 24.9974701 0.992287833 1.052945923 0.212268892 0.067553116 146.9820951 1313616.852 0.02024542 0.025231322 1720.931604 -3.23576361 0.06065809 YHQIGSGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YHQIGSGK 8 0 A0A087WUK2;O14979;O14979-2;O14979-3 A0A087WUK2;O14979-2 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 ;; 153.08 0.00044675 2984300000 4787160 4298990 5232990 4408220 6236700 6505400 5672540 5116820 5338960 4260960 FALSE TRUE 4976160.773 5037308.091 5369366.018 5280152.759 5176587.962 4994619.44 5227911.492 5048237.397 5146811.873 5095813.531 0.9765194 0.988518921 1.053681809 1.036174642 1.015851135 0.98014172 1.025922841 0.990663682 1.01000789 1 22.28088106 2.934732104 24.99973227 1.001587227 1.016182166 0.067302941 0.02321464 562.7694422 215557.1877 0.007471184 0.007924414 860.4628086 -2.934732104 0.014594939 YHRPEETHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YHRPEETHK 9 1 Q8IX12-2;Q8IX12;A0A0C4DGG8;F5H1H2;F5H2E6 Q8IX12-2 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 76.465 0.021243 19548000 16096 15996 20937 16851 22895 25626 20142 19679 21786 15571 FALSE TRUE 16731.48251 18743.18857 21482.63542 20184.0775 19003.31608 19674.74987 18563.21741 19415.23519 21001.92612 18621.83933 0.898487105 1.006516501 1.153625861 1.083892797 1.02048545 1.056541705 0.99685198 1.042605666 1.127811585 1 14.18470796 4.63588351 3.742033153 1.05790469 0.895976225 0.499338749 0.048920426 0.192892361 4.351949594 0.01197028 0.068697902 43239.78342 -4.63588351 -0.161928466 YHSDDYIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YHSDDYIK 8 0 Q13547;Q5TEE2 Q13547 HDAC1 Histone deacetylase 1 0 ;;;;; 130.28 0.0010547 1392390000 1613360 1542615 1562964 1339972 2414810 2255143 1882760 1637309 1634455 1753740 FALSE TRUE 1677056.699 1807547.126 1603696.126 1605014.462 2004341.459 1731420.215 1735184.352 1615363.551 1575631.284 2097351.776 0.799606779 0.861823537 0.764629064 0.765257636 0.955653449 0.825526855 0.827321564 0.770191996 0.75124798 1 21.00013743 -2.390689304 2.367355748 2.565061161 0.813975819 0.482809944 0.057914015 2316949.478 606632.0847 19275139.24 0.014513 0.004067342 2.390689304 -1.751085342 YHSDEYIK ddPTM_MDA-MB-175_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 ; 163.9 0.00033324 741300000 680490 785310 869610 753930 1048960 1042070 910140 841540 848840 832920 FALSE TRUE 707356.2707 920180.8836 892272.751 903055.1037 870658.1539 800065.0352 838800.8486 830260.5328 818290.4142 996114.7268 0.710115262 0.923769982 0.895752996 0.906577405 0.874054093 0.803185631 0.84207253 0.833498904 0.821482097 1 19.92595239 YHSDFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YHSDFNR 7 0 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ;; 128.57 0.0037452 312280000 180209 229515 205276 212835 289307 282162 217545 228478 207641 274016 FALSE TRUE 187323.7905 268932.4159 210625.6612 254933.1278 240130.6995 216634.1517 200493.2545 225415.6261 200168.041 327704.1888 0.571624645 0.820656022 0.642731062 0.777936738 0.732766646 0.661066166 0.611811693 0.687863121 0.610819293 1 18.32203459 -0.854964769 6.208454654 1.000000025 0.684009948 0.624930097 0.07437522 2.42E-08 4.38E-09 0.067601425 0.015933807 0.139648164 0.854964769 -0.315990077 YHSDFNRQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YHSDFNRQDR 10 1 Q15424;Q15424-3;Q15424-4;Q15424-2;K7EII0 Q15424 SAFB Scaffold attachment factor B1 0 ; 97.456 0.0036328 166319000 25568.6 50851 35031 45290 53322 55153 25988 37330 32040 79905 FALSE TRUE 26578.06807 59584.26368 35943.93664 54248.22682 44258.34549 42344.5516 23950.99265 36829.65241 30886.88666 95560.85488 0.278127148 0.623521669 0.376136617 0.567682519 0.463143047 0.443116082 0.250636023 0.385405221 0.323216935 1 16.54413214 -1.157084221 4.543809928 1.000085923 0.4151673 0.710738393 0.112458806 9.68E-05 1.80E-05 0.106926892 0.025199204 0.069649143 1.157084221 -0.584918622 YHTINGHNAEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 ;;;;;;; 268.08 3.36E-22 31328310000 3329140 3618540 3520830 3664350 4751310 5069880 3917030 3251240 3402790 3852680 FALSE TRUE 3460577.018 4239996.097 3612585.722 4389147.493 3943684.023 3892477.205 3610002.953 3207662.446 3280324.253 4607538.882 0.751068435 0.920230128 0.784059737 0.952601292 0.855919858 0.844806155 0.783499184 0.696176967 0.711947167 1 22.13556491 2.218374388 3.931933124 0.762757158 0.857229885 0.023125974 0.096492243 0.372342955 12.64169093 0.034905205 0.026171582 165.3386502 -2.218374388 0.094472727 YHTINGHNCEVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YHTINGHNCEVK 12 0 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 ;;; 233.37 3.11E-16 2600060000 1706460 1259120 1581480 1337580 2129570 2319870 2071500 1599150 1719270 1165470 FALSE TRUE 1773832.358 1475364.065 1622694.668 1602149.332 1767586.452 1781115.35 1909130.417 1577716.01 1657393.809 1393821.532 1.272639515 1.058502851 1.164205481 1.14946519 1.268158377 1.277864712 1.369709373 1.131935455 1.189100448 1 20.41061442 5.075870675 20.85193106 1.191724003 4.364739257 0.057327002 0.102748152 2107.299829 575066.3866 0.023659281 2211.055379 119088.7332 -5.075870675 3.173015254 YHTINGHNCEVKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YHTINGHNCEVKK 13 1 P51991;P51991-2 P51991;P51991-2 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 125.82 7.96E-05 461810000 169450 113740 162280 122070 261630 243990 183010 161290 205370 154090 FALSE TRUE 176140.0168 133273.9602 166509.1501 146215.0817 217158.2261 187327.0202 168665.198 159128.1714 197978.7738 184280.9853 0.955823069 0.723210591 0.90356121 0.793435532 1.17840821 1.016529296 0.915260995 0.86350836 1.074330993 1 17.49154769 YHTSQSGDEMTSLSEYVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 YHTSQSGDEMTSLSEYVSR 19 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 ;;;;;;;;;;; 329.93 3.08E-75 7450895000 282742.2 2803871 2226587 2826174 2233148 3647496 1981384 2983638 2128636 3076465 FALSE TRUE 293905.0804 3285414.033 2284613.686 3385182.782 1853558.301 2800420.332 1826077.945 2943647.213 2052026.806 3679239.414 0.079882021 0.89296011 0.620947274 0.920076788 0.503788444 0.761141099 0.496319413 0.800069493 0.557731252 1 21.81097613 -5 0.185350776 2.419460289 0.581118811 0.194895067 0.231727645 230.7705478 2.242898946 121.6927255 0.615574879 1.00E-05 5 -1.838341478 YHTVNGHNCEVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 243.4 1.40E-16 27384650000 2353439 2434125 2572570 2571852 3280468 3889995 2780284 2413056 2546102 2704077 FALSE TRUE 2446354.589 2852167.034 2639613.288 3080556.649 2722855.221 2986602.615 2562358.075 2380712.931 2454468.286 3233889.115 0.756474481 0.881961914 0.81623494 0.952585738 0.841975443 0.923532783 0.792345682 0.736176426 0.75898344 1 21.62483878 2.195918285 23.95211253 0.792794838 0.864138812 0.006518833 0.085632242 178.858011 100462.4942 0.030202836 0.022306511 157.0067359 -2.195918285 0.071343974 YHYLGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 ;;;;; 132.01 0.0034109 2831460000 2304060 3278580 2992000 3226170 3522630 4017680 2916610 3052330 2760220 3681920 FALSE TRUE 2395026.068 3841650.611 3069973.978 3864296.797 2923854.611 3084634.709 2687998.487 3011418.509 2660880.221 4403321.729 0.543913485 0.87244377 0.697195019 0.877586748 0.664011124 0.70052449 0.610447896 0.683896997 0.604289304 1 22.07016083 -0.994036003 4.996140412 1.000000716 0.700002833 0.444528696 0.102166497 3.07E-06 6.18E-07 0.094408035 0.022251978 0.101382734 0.994036003 -0.299997883 YIAIVSTTVETKEPEKEIRPALELLEPIEQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIAIVSTTVETKEPEKEIRPALELLEPIEQK 31 3 P50395;P50395-2 P50395 GDI2 Rab GDP dissociation inhibitor beta 0 134.97 9.06E-07 352590000 1657100 593270 1096800 466980 1664200 1165500 1188600 988630 1182400 511950 FALSE TRUE 1722523.588 695159.5075 1125383.509 559347.2502 1381319.878 894830.2883 1095434.426 975379.0319 1139845.655 612256.8006 2.813400498 1.135405122 1.838090664 0.913582748 2.25611194 1.461527724 1.789174779 1.593088114 1.86171171 1 19.22377737 -2.072661384 2.117371422 0.000167846 1.701596705 0.155439088 0.51053682 10503315.96 3030566.177 50693558.5 0.111808191 0.008459382 2.072661384 1.70142886 YIASTQRPDGTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YIASTQRPDGTWR 13 1 Q9BRP8-2;Q9BRP8 Q9BRP8-2 WIBG Partner of Y14 and mago 0 ;;; 187.63 6.20E-06 1682310000 708170 887410 846510 771370 940070 1015810 825110 803520 800740 992810 FALSE TRUE 736129.0984 1039815.764 868570.746 923944.6837 780277.2372 779903.5222 760435.7222 792750.1287 771921.5238 1187332.111 0.619985842 0.875758143 0.731531421 0.778168699 0.657168479 0.656853727 0.640457472 0.667673452 0.650131094 1 20.1792921 -1.039225484 4.339504028 1.000019732 0.698959313 0.598898629 0.074252626 9994650.054 2393521.433 1927.987697 0.017857916 0.091363876 1.039225484 -0.301060419 YIDENQDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 176.75 0.00060136 2228790000 1284840 1396980 1441390 1251080 2194850 1682580 1747430 1453830 1375540 1431210 FALSE TRUE 1335566.475 1636900.448 1478953.808 1498539.89 1821770.181 1291826.295 1610461.871 1434343.787 1326034.584 1711628.197 0.780290064 0.956341132 0.86406254 0.875505494 1.064349246 0.754735343 0.940894683 0.837999625 0.774721161 1 20.70693792 -0.056658787 7.991805891 0.999999999 0.876889797 0.150524442 0.090510074 11048584.24 1382488.567 0.081251623 0.019706413 0.877690128 0.056658787 -0.123110202 YIDQEELNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YIDQEELNK 9 0 P08238;P07900;P07900-2;Q14568;Q58FF8 P08238;P07900;Q58FF8 HSP90AB1;HSP90AA1;HSP90AA2P;HSP90AB2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2;Putative heat shock protein HSP 90-beta 2 0 ;;;;; 222.42 8.93E-07 5267280000 6780170 4711550 5894270 4711150 7414120 7307400 7104100 6046380 6359290 4291480 FALSE TRUE 7047856.347 5520722.062 6047879.518 5643001.409 6153870.531 5610367.095 6547262.079 5965338.166 6130420.395 5132313.341 1.37323189 1.075679074 1.178392494 1.09950446 1.199044197 1.093145863 1.275694145 1.162309814 1.194475081 1 22.29117782 -2.447582013 1.672972468 4.47E-05 1.178319981 0.293342629 0.085100485 1118481.433 90043.63088 4215753.454 0.021275735 0.003567944 2.447582013 1.17827533 YIDTEHGGSQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YIDTEHGGSQAR 12 0 F5H365;Q15436;Q15436-2 F5H365 SEC23A Protein transport protein Sec23A 0 ;;; 162.22 6.33E-05 2015060000 1629860 2189890 2051930 2262350 2240410 2647830 2001760 2052540 1872510 2250940 FALSE TRUE 1694208.131 2565986.573 2105404.981 2709836.078 1859585.908 2032911.611 1844856.821 2025029.059 1805118.731 2691968.596 0.629356573 0.953200783 0.782106071 1.006637329 0.690790342 0.75517657 0.685318849 0.752248396 0.670557128 1 21.36023015 YIEIDS(ph)DEEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIEIDSDEEPR 11 0 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 YIEIDS(1)DEEPR 175.74 9.93E-06 287350000 182790 208580 197870 235910 204510 243670 277890 203300 189380 164610 TRUE FALSE 190006.6903 244401.9925 203026.6548 282572.2939 169747.4632 187081.3354 256108.2557 200575.096 182564.2508 196862.1779 0.965176208 1.241487802 1.031313668 1.435381326 0.862265495 0.950316294 1.300952059 1.018860495 0.927370878 1 17.58682643 YIEIDS(ph)DEEPRGELLSLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.986)DEEPRGELLS(0.014)LR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR 276.77 2.48E-39 3139400000 799724 1020384 1004579 917423 968895 1095392 913654 904387 868128 1000831 TRUE FALSE 831297.721 1195627.015 1030759.154 1098886.531 804202.574 841003.8088 842039.4121 892265.1715 836884.2429 1196924.672 0.694528019 0.99891584 0.861172952 0.918091636 0.671890715 0.702637207 0.703502427 0.745464767 0.699195415 1 20.19090093 3.244255102 24.99960665 0.735892014 0.877015307 0.186160248 0.112934524 176.063864 772940.1582 0.028941268 0.038134282 1754.911023 -3.244255102 0.141123293 YIEIFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIEIFK 6 0 P31943;G8JLB6;E9PCY7;H0YB39;D6RBM0;E7EN40;E5RGV0;P55795 P31943;P55795 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 97.596 0.095131 531680000 835620 777660 953940 843830 1138900 1119300 1062800 888460 967740 839630 FALSE TRUE 868610.9228 911217.0556 978800.4601 1010737.055 945310.1848 859359.5382 979494.9589 876551.6469 932911.2264 1004139.423 0.865030197 0.907460692 0.974765494 1.006570435 0.941413277 0.85581695 0.975457129 0.872938187 0.929065432 1 19.93752817 3.159638228 0.004470833 1.853965443 5.22E-06 0.080222458 0.051083645 77914.41899 103.8241969 21170.64083 21882.06863 1444.236204 -3.159638228 -1.853960221 YIELFR ddPTM_MDA-MB-175_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 ;;;;;; 137.5 0.029562 2339322000 1964058 2305039 2164049 2093922 2259849 2645131 2101589 2217078 2005786 2367616 FALSE TRUE 2041600.526 2700911.518 2220445.895 2508093.522 1875720.674 2030839.413 1936860.963 2187361.696 1933598.154 2831505.024 0.721030162 0.953878412 0.784192815 0.88578106 0.662446529 0.717229669 0.684039388 0.772508499 0.682887064 1 21.43313766 3.249159338 24.98661681 0.737813333 0.84090847 0.116277366 0.10692111 342.1864508 806703.9839 0.026990683 0.036171814 1774.840533 -3.249159338 0.103095136 YIEQATVHSSMNEMLEEGQEYAVMLYTWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIEQATVHSSMNEMLEEGQEYAVMLYTWR 29 0 Q7L576;A0A087WU52;A0A0G2JRX2;A0A087WWL1;A0A0G2JRV9;A0A0G2JR96;A0A0G2JQT1 Q7L576;A0A0G2JR96 CYFIP1 Cytoplasmic FMR1-interacting protein 1 0 199.64 3.63E-25 48263000 13004 21097 28867 32368 31864 40299 29897 29229 31489 34374 FALSE TRUE 13517.40796 24720.24564 29619.29773 38770.29379 26447.76866 30940.16799 27553.59502 28837.23306 30355.71704 41108.92717 0.328819283 0.601335217 0.72050768 0.943111301 0.64335828 0.752638663 0.670258188 0.701483474 0.738421533 1 15.3271641 4.647306906 2.083555418 0.753913261 0.257531309 0.607748263 0.109266826 0.371585878 2.078448414 0.026635037 0.322936771 44392.22426 -4.647306906 -0.496381952 YIEVFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIEVFK 6 0 P52597;A0A1B0GW42 P52597 HNRNPF "Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 0 ; 116.35 0.055015 1510560000 2544900 2295400 2519900 2178030 2932500 2966200 2751500 2567100 2569500 2278700 FALSE TRUE 2645374.617 2689617.094 2585570.664 2608837.833 2434034.697 2277345.003 2535830.24 2532692.223 2477024.197 2725167.637 0.970719959 0.986954732 0.948774904 0.95731279 0.893168796 0.835671528 0.930522661 0.929371166 0.908943789 1 21.37791355 3.355015262 5.254126111 0.91140931 0.967852929 0.275450167 0.039212177 0.258257186 10.84366853 0.011007176 0.014987684 2264.723895 -3.355015262 0.05644362 YIGTGHADTTKWEWLVNQHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIGTGHADTTKWEWLVNQHR 20 1 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 217.09 6.98E-25 1700590000 1140610 1216210 1375190 1119560 1736850 1614370 1102720 1474270 1465430 1671060 FALSE TRUE 1185642.164 1425084.607 1411028.581 1341005.626 1441620.857 1239457.034 1016285.925 1454509.822 1412689.461 1998472.213 0.59327428 0.713087026 0.70605364 0.671015398 0.721361472 0.620202285 0.508531426 0.727810881 0.706884715 1 20.93046608 0.623750344 1.60796397 0.999621285 0.657116185 0.716552942 0.064471214 0.842256408 2.914358502 0.062525876 0.017895654 4.204848418 -0.623750344 -0.3425051 YIHILGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIHILGR 7 0 Q9Y2J8;Q9Y2J8-2 Q9Y2J8 PADI2 Protein-arginine deiminase type-2 0 ; 172.15 0.00091122 2650200000 1890190 2070970 2132140 2247500 2288700 2449100 2179600 2186400 1972360 1884050 FALSE TRUE 1964816.161 2426642.988 2187705.32 2692048.792 1899667.592 1880333.641 2008757.257 2157094.884 1901375.149 2253193.525 0.872013939 1.07697939 0.970935384 1.194770339 0.843100058 0.83451937 0.891515635 0.957350028 0.843857897 1 21.1035398 3.193068257 24.99994973 0.894372548 1.028002326 0.34402323 0.090384749 138.6505234 76193.73249 0.0251341 0.030041096 1559.797635 -3.193068257 0.133629779 YIHLENLLAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 ; 215.06 8.36E-09 791800000 696420 862880 855180 740670 924080 916410 749880 810000 724280 896270 FALSE TRUE 723915.1994 1011072.928 877466.6933 887172.3153 767005.2117 703587.6658 691102.4462 799143.2749 698213.3043 1071876.946 0.675371554 0.943273322 0.818626332 0.827681124 0.715572076 0.656407126 0.644759129 0.745555054 0.651393154 1 20.03170786 -1.548565549 6.326321054 1.000354992 0.745236192 0.415919916 0.091627437 0.000483973 3.45E-05 0.093591333 0.022029584 0.028277073 1.548565549 -0.2551188 YIHPDDELVLEDELQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIHPDDELVLEDELQR 16 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 ; 166.9 6.51E-09 150166000 137599 181439 146512 179752 151606 213622 154720 164896 140912 186381 FALSE TRUE 143031.5148 212599.7369 150330.2231 215306.4091 125836.0663 164011.528 142592.6421 162685.8388 135840.6046 222898.7885 0.641688166 0.953794941 0.674432661 0.965937996 0.564543518 0.735811662 0.639719234 0.729864168 0.60942729 1 17.76602925 5.036455155 16.3295969 0.748362478 0.221881929 0.047997462 0.149574105 17675891.68 217692782.5 0.032987589 271378615.7 108756.483 -5.036455155 -0.526480549 YIHSADIIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YIHSADIIHR 10 0 Q16539-2;Q16539;B4E0K5;Q16539-5;Q16539-3;Q16539-4;E7EX54;B5TY33 Q16539-2 MAPK14 Mitogen-activated protein kinase 14 0 ;; 188.04 6.73E-07 445740000 434940 487610 495600 516850 560190 624400 535280 503130 484160 495690 FALSE TRUE 452111.767 571353.2244 508515.7431 619081.3874 464969.1039 479392.5629 493323.3549 496386.3653 466735.1762 592810.9649 0.762657565 0.963803401 0.857804213 1.044315008 0.784346329 0.80867695 0.832176502 0.837343428 0.787325478 1 19.17721261 YIHSANVLHR ddPTM_MDA-MB-175_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 ; 156.48 6.28E-06 982170000 720800 677550 751960 764720 856330 948480 984250 832050 764580 701830 FALSE TRUE 749257.7406 793913.9419 771556.6953 915979.3335 710771.3325 728209.8944 907101.9131 820897.7307 737062.9152 839340.1512 0.892674727 0.945878665 0.919241972 1.091308848 0.846821556 0.867598069 1.080732182 0.978027477 0.878145665 1 19.67889607 2.261661901 24.99999136 0.985439461 0.931537422 0.114209233 0.07714838 571.1688299 618111.5688 0.027195273 0.022739117 182.6677592 -2.261661901 -0.053902039 YIKDYMK ddPTM_MDA-MB-175_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 ; 109.86 0.0063228 1674960000 2101460 1750220 1660800 1161170 5643400 2994200 2102300 1780180 1919250 4264300 FALSE TRUE 2184427.263 2050806.67 1704081.812 1390845.96 4684136.884 2298842.428 1937516.233 1756319.599 1850176.567 5099807.94 0.428335202 0.402134099 0.334146272 0.272725165 0.918492802 0.450770393 0.379919451 0.344389361 0.362793381 1 22.28201149 -1.580859301 2.863649296 1.035874375 0.430284435 0.501353161 0.169735217 51254948.28 52804811.65 13970336.21 0.04225083 0.026250689 1.580859301 -0.60558994 YIKNPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIKNPR 6 1 P49368;P49368-2;B4DUR8;Q5SZX6 P49368 CCT3 T-complex protein 1 subunit gamma 0 ; 109.88 0.026612 3402800000 2883900 3097800 3063900 2891300 4688900 4493700 4037500 4003600 3960700 3955500 FALSE TRUE 2997758.599 3629823.052 3143747.751 3463190.51 3891882.453 3450106.278 3721030.2 3949938.291 3818155.181 4730504.492 0.633708012 0.76732261 0.664569235 0.7320975 0.82272038 0.729331572 0.786603248 0.834993032 0.807134881 1 22.17356262 -5 0.074639918 1.871016233 0.470037877 0.809066146 0.042304189 108.9927689 0.581650246 15.79281056 1.724553662 1.00E-05 5 -1.400978356 YILHDASS(ph)AEETITAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YILHDASSAEETITAK 16 0 A6NM62 A6NM62 LRRC53 Leucine-rich repeat-containing protein 53 1 YILHDAS(0.055)S(0.379)AEET(0.283)IT(0.283)AK 73.464 0.022541 280800000 305460 251020 302370 255270 379680 405620 357850 327820 365460 235760 TRUE FALSE 317519.7967 294130.7323 310250.0106 305761.6441 315142.1292 311420.9022 329800.7819 323426.1091 352307.166 281952.6581 1.126145782 1.043191911 1.10036207 1.084443205 1.117712922 1.104514865 1.169702688 1.147093669 1.249525961 1 18.10509342 2.574241534 1.682024022 1.15332335 1.088189631 0.096627594 0.061512545 0.614201094 3.497156619 0.024346745 0.020730948 375.1816026 -2.574241534 -0.065133719 YIMIFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIMIFR 6 0 P55060-3;P55060;P55060-4 P55060-3 CSE1L Exportin-2 0 150.22 0.024519 143160000 100130 121830 101500 129250 192490 177760 131160 116990 103600 199410 FALSE TRUE 104083.2097 142753.3548 104145.1734 154815.2642 159770.6186 136477.934 120879.3365 115421.9404 99871.45624 238480.5716 0.436443141 0.598595323 0.436702968 0.649173487 0.669952347 0.572281143 0.50687289 0.483988862 0.418782359 1 17.86351221 -1.482695394 3.337981617 1.008721856 0.53376012 0.73142358 0.085362002 36206383.05 39032875.7 2835873.698 0.021130623 0.032908236 1.482695394 -0.474961736 YINTEHGGSQAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YINTEHGGSQAR 12 0 A0A2R8YFH5;Q15437;Q5QPE1 A0A2R8YFH5 SEC23B Protein transport protein Sec23B 0 ;;; 202.61 1.35E-07 2494690000 1076430 1423500 1301570 1351450 1475600 1686980 1264020 1367470 1207040 1373240 FALSE TRUE 1118928.288 1667975.052 1335489.983 1618762.776 1224778.039 1295204.461 1164942.809 1349141.301 1163598.866 1642300.086 0.681317804 1.015633541 0.813182679 0.985668082 0.745769942 0.788652739 0.709336144 0.821494995 0.708517814 1 20.64728633 3.207732624 24.99836695 0.783077689 0.879730367 0.092134252 0.11594817 365.9978345 296786.0188 0.030458308 0.036408517 1613.364971 -3.207732624 0.096652678 YIPFTHGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YIPFTHGK 8 0 O15258 O15258 RER1 Protein RER1 0 96.492 0.0089028 472400000 581940 709230 709120 679810 742360 941390 774500 587440 699520 673190 FALSE TRUE 604915.4406 831034.7355 727600.2497 814274.389 616173.9124 722766.4394 713792.6662 579566.3277 674344.4118 805088.6915 0.75136497 1.03222756 0.90375167 1.011409547 0.765349109 0.897747599 0.886601282 0.719878858 0.837602638 1 19.6187882 3.234289722 24.99999955 0.83404024 0.930874317 0.097825259 0.100918578 185.392817 1085211.673 0.027726193 0.034259439 1715.101087 -3.234289722 0.096834077 YIQDIYSCGEIVEHLEESTAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIQDIYSCGEIVEHLEESTAFR 22 0 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 0 ; 161.2 1.76E-11 56263000 31585.7 37927 34920 37629 35917 41288 42985 37975 38389 36019 FALSE TRUE 32832.72783 44440.66722 35830.04389 45071.90389 29811.84117 31699.48773 39615.72338 37466.00724 37007.38739 43076.23342 0.762200527 1.031674863 0.831782193 1.046328806 0.692071678 0.735892747 0.919665445 0.869760521 0.859113819 1 15.39460449 -1.504235629 2.506975173 1.007717634 0.864920038 0.12399488 0.110428496 9618135.688 9017426.705 508173.4045 0.027658017 0.031315862 1.504235629 -0.142797596 YIQELWR ddPTM_MDA-MB-175_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 ;;;;; 165.11 0.0027282 8341490000 3378660 3821740 3495380 3293350 4636100 4636740 3759600 3534260 3445090 4719180 FALSE TRUE 3512052.106 4478094.116 3586472.474 3944764.8 3848057.378 3559927.405 3464912.728 3486889.026 3321101.884 5643812.967 0.622283574 0.793451899 0.63546976 0.69895385 0.681818728 0.630766368 0.613931175 0.617825049 0.588450025 1 22.42823875 -1.843907999 5.473539659 1.048342001 0.654299202 0.774981263 0.055985921 0.027998239 0.000798441 0.045953869 0.013027475 0.014324913 1.843907999 -0.394042799 YIQHTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YIQHTYR 7 0 P52565;J3KTF8;J3QQX2;J3KRY1;P52565-2 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ;;;;; 159.2 0.0013924 6646420000 2032670 2312030 2253410 2186450 3392650 2986060 2499660 2228150 2135070 3231340 FALSE TRUE 2112921.381 2709103.167 2312135.716 2618923.284 2815968.565 2292592.819 2303730.118 2198285.294 2058229.248 3864459.205 0.546757326 0.701030344 0.598307704 0.677694638 0.728683734 0.59325062 0.596132601 0.568846811 0.532604729 1 21.88183511 -1.360324111 3.236469753 1.003247395 0.617922458 0.773040369 0.062424308 13912941.49 19548015.02 430336.3952 0.015475105 0.043619018 1.360324111 -0.385324937 YIQQTKPLTLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIQQTKPLTLER 12 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 ; 156.08 6.15E-05 1179380000 712080 684480 727930 626990 973570 973680 772250 742310 673410 833970 FALSE TRUE 740193.4682 802034.1155 746900.4538 751006.7506 808082.9192 747557.5763 711719.0271 732360.5486 649174.1056 997370.4542 0.742144972 0.804148661 0.748869641 0.752986764 0.810213412 0.749528496 0.713595459 0.734291402 0.650885639 1 19.92776994 -1.252453735 4.94679456 1.000050719 0.746996167 0.765962486 0.042245028 2.39E-05 3.62E-06 0.041436482 0.009764718 0.055917309 1.252453735 -0.253054552 YIS(ph)PDQLADLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 YIS(1)PDQLADLYK;Y(0.005)IS(0.995)PDQLADLYK 98.531 0.0045174 43937000 120091 92094 102142 84943 150272 132135 125867 105557 124065 94621 TRUE FALSE 124832.2854 107910.4281 104803.9044 101744.4719 124728.8191 101448.6488 116001.2156 104142.1811 119599.9249 113160.1733 1.103146821 0.953607837 0.92615539 0.899119088 1.102232486 0.89650489 1.02510638 0.92030772 1.056908286 1 16.78800677 -1.106187111 7.108989988 1.000000009 0.97959209 0 0.076668421 1.01E-08 1.29E-09 0.068133329 0.016059173 0.078309218 1.106187111 -0.020407919 YISFEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YISFEER 7 0 Q14192 Q14192 FHL2 Four and a half LIM domains protein 2 0 ; 97.068 0.028543 68927000 102849 129510 112103 124461 148965 160978 131775 123173 124832 148047 FALSE TRUE 106909.5579 151752.3351 115024.4963 149079.0143 123643.9825 123593.2991 121446.1312 121522.0674 120339.3207 177053.9751 0.603824669 0.857096459 0.649657802 0.841997556 0.698340619 0.698054359 0.685927165 0.686356052 0.679675905 1 17.43382971 -1.918859804 2.692470519 1.173088102 0.71368665 0.570985718 0.075069009 12203643.89 7792460.282 13344300.6 0.016434715 0.01205425 1.918859804 -0.459401451 YISKPENLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YISKPENLK 9 1 Q9H9S4;Q5TAW7;B7ZBJ4;Q9Y376;A0A087X0K1 Q9H9S4;Q9Y376 CAB39L;CAB39 Calcium-binding protein 39-like;Calcium-binding protein 39 0 ; 117.67 0.0010155 1514000000 2068930 1368260 1826960 1244620 2420700 2340200 2210900 1803390 2059400 1340320 FALSE TRUE 2150612.954 1603248.011 1874572.078 1490802.121 2009230.279 1796724.016 2037603.881 1779218.507 1985282.596 1602930.042 1.341676117 1.000198368 1.169465934 0.930048151 1.253473468 1.120899833 1.271174554 1.109978889 1.238533526 1 20.61228003 YISPDQLADLYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;; 178.81 5.01E-05 1877590000 2450079 1833462 2154667 1744422 3291440 2794905 2588363 2069684 2408125 2186807 FALSE TRUE 2546810.011 2148344.836 2210819.392 2089463.465 2731962.204 2145830.671 2385480.345 2041943.271 2321457.052 2615269.963 0.973822988 0.821461978 0.845350355 0.798947525 1.044619578 0.820500637 0.912135412 0.780777243 0.887654844 1 21.31852845 4.757347982 23.04118188 0.869526681 0.973823262 0.096580766 0.082450646 2883.03924 3535643.332 0.01861336 0.573959974 57193.67224 -4.757347982 0.104296581 YISQEEGPLS(ph)PFLGQLDEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YISQEEGPLSPFLGQLDEDYR 21 0 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 YISQEEGPLS(1)PFLGQLDEDYR 152.35 3.44E-08 16942000 18920 22813 21945 24239 21886 30401 23908 21982 23855 26044 TRUE FALSE 19666.97621 26730.95529 22516.90473 29033.40185 18165.82554 23340.82848 22034.02849 21687.36725 22996.46321 31146.82316 0.631427999 0.858224133 0.722927812 0.932146489 0.583232051 0.749380711 0.707424586 0.696294679 0.738324518 1 14.9267974 -1.858322113 8.19352931 1.018209912 0.736275936 0.41045634 0.095098456 0.028150499 0.000486762 0.08193915 0.020196404 0.013857277 1.858322113 -0.281933975 YITDWQNVFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YITDWQNVFR 10 0 O75340-2;O75340;A0A024QZ42 O75340-2 PDCD6 Programmed cell death protein 6 0 ; 193.38 1.35E-06 2118700000 1278910 1583050 1434150 1451600 1626830 1848060 1442930 1532300 1391730 1788780 FALSE TRUE 1329402.354 1854926.523 1471525.127 1738722.147 1350302.018 1418876.073 1329829.376 1511762.025 1341641.909 2139257.193 0.621431756 0.867089067 0.687867327 0.812769102 0.631201345 0.663256423 0.621631368 0.706676144 0.62715316 1 21.02867851 -0.940853985 4.300751222 1.000007906 0.696626327 0.568438563 0.080139488 21043770.25 48588471.58 2745.803078 0.018707629 0.114589814 0.940853985 -0.303381579 YIVNGSHEANK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YIVNGSHEANK 11 0 P55010;H0YLZ1;H0YN40;H0YMJ8;H0YM54 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 131.42 0.00020376 291420000 616280 485650 594410 518680 761520 796120 832080 650440 626230 516920 FALSE TRUE 640611.2103 569056.6097 609900.8129 621273.3559 632077.1024 611233.1953 766859.3954 641721.9157 603692.1046 618200.577 1.036251395 0.920504818 0.986574318 1.004970521 1.022446639 0.988729578 1.240470203 1.03804807 0.976531125 1 19.23771548 2.382315298 21.64870873 1.075607023 0.991435006 0.178181005 0.072348479 8.722312072 1981.598504 0.024895867 0.02082938 241.1655659 -2.382315298 -0.084172016 YIYFYEKENDAVTIQVLNQLIQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YIYFYEKENDAVTIQVLNQLIQK 23 1 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 ;;;;;;; 228.63 6.01E-33 567243000 542921.1 344867.3 533372.2 383524.5 621591.2 616497.1 589465.3 507220.3 618559.3 346209.6 FALSE TRUE 564356.0443 404095.5761 547272.3177 459384.5014 515933.3499 473324.9916 543261.4695 500421.8415 596297.4716 414042.7425 1.363038127 0.975975508 1.321777347 1.109509851 1.246087171 1.143179056 1.312090308 1.208623628 1.440183368 1 18.65942018 2.245521839 24.991695 1.254306868 1.187820509 0.020196728 0.144807573 542.0092026 1945884.257 0.046143731 0.037829897 176.0037166 -2.245521839 -0.066486359 YKAEDEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YKAEDEK 7 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;;;;;;; 105.78 0.0071582 13944260000 20842130 8174120 11205210 8323240 16524680 16574450 20290080 12578980 14179050 6268390 FALSE TRUE 21664993.39 9577961.524 11497226.98 9969552.03 13715820.8 12725285.18 18699690.51 12410379.35 13668748.76 7496561.005 2.88999094 1.27764738 1.533666833 1.329883399 1.829615044 1.697483042 2.494435849 1.655476336 1.823335894 1 22.83779749 3.093992108 21.76127593 1.821857864 1.691531953 0 0.54169739 43.36687089 9995.698689 0.150581887 0.179979772 1241.629744 -3.093992108 -0.130325911 YKAEDEKQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YKAEDEKQR 9 2 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PS65;E9PM13 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 ;; 119.16 0.00049103 1100400000 2408770 1449510 1845990 1069690 2961030 2365090 1859990 1825810 2154220 1591050 FALSE TRUE 2503870.1 1698452.067 1894098.016 1281271.489 2457715.178 1815833.691 1714199.124 1801338.003 2076690.043 1902785.785 1.315896997 0.892613388 0.995434184 0.673366124 1.291640498 0.954302741 0.900889179 0.946684602 1.091394554 1 20.85968172 4.74627826 24.29371171 0.966816606 1.31589725 0.326355975 0.148147888 721.9911506 2272612.52 0.033496048 0.353839838 55754.28619 -4.74627826 0.349080644 YKAEDEVQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 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 17983686000 10104923 7450229 9144181 7520573 11224842 10547759 10099056 9038551 9772270 6804815 FALSE TRUE 10503873.16 8729747.876 9382485.869 9008119.893 9316847.366 8098201.825 9307465.602 8917404.008 9420567.912 8138088.213 1.290705248 1.072702537 1.152910318 1.106908608 1.144844725 0.995098801 1.143691904 1.095761532 1.157589801 1 22.95625849 4.744000503 24.85046421 1.10185967 1.290705335 0.512652576 0.056564797 411.8983411 1881570.186 0.012335529 0.104569111 55462.63555 -4.744000503 0.188845665 YKAEDEVQRER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKAEDEVQRER 11 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 ; 101.6 0.0017808 514250000 588930 550000 815320 401350 1390700 981640 616500 704630 924770 1012160 FALSE TRUE 612181.4112 644458.2216 836567.909 480735.8321 1154309.311 753668.9869 568177.1191 695185.5874 891487.7083 1210473.373 0.505737197 0.532401816 0.691108064 0.39714697 0.953601571 0.62262335 0.469384236 0.574308864 0.736478578 1 20.20713991 0.926580501 3.313891327 0.999484992 0.594580256 0.429696376 0.14358223 0.298103477 7.904428129 0.134045562 0.034823378 8.444627568 -0.926580501 -0.404904736 YKCEGR ddPTM_MDA-MB-175_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 ; 88.591 0.046631 322620000 439800 423050 458030 362670 590110 591140 503060 474100 522300 492170 FALSE TRUE 457163.6436 495705.5466 469966.6381 434405.0435 489803.313 453856.6938 463628.8427 467745.465 503502.525 588601.2883 0.776694942 0.842175436 0.798446499 0.738029379 0.832147878 0.771076623 0.787678946 0.794672853 0.855422057 1 19.16693117 0.84870501 2.237054021 0.999875219 0.792508068 0.83515301 0.027962333 0.201291129 1.91354434 0.02565178 0.006991632 7.058379578 -0.84870501 -0.207367151 YKDAIHFYNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKDAIHFYNK 10 1 P31948;P31948-2;P31948-3 P31948 STIP1 Stress-induced-phosphoprotein 1 0 ; 129.89 0.00017494 2159900000 5311600 4045400 4972600 3730100 9592100 6773500 6325400 5265400 5739500 6427500 FALSE TRUE 5521306.069 4740165.981 5102190.041 4467902.647 7961638.268 5200457.278 5829598.62 5194825.925 5532936.516 7686845.563 0.718279823 0.616659453 0.663756023 0.581240069 1.035748436 0.676539841 0.758386333 0.675807245 0.719792855 1 22.87396025 -5 0.277034906 3.027140578 0.695612007 0.346159462 0.117303455 255.6477527 2.459176948 297.8783683 0.135748639 1.00E-05 5 -2.331528571 YKDDDDDQLFYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKDDDDDQLFYTR 13 1 O60568;H7C2V1 O60568 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 ; 125.73 0.00017949 451590000 418640 346500 348050 364950 474750 480020 443910 332570 356620 234490 FALSE TRUE 435168.2305 406008.6796 357120.4689 437136.0207 394052.1646 368542.6298 409115.1743 328112.4431 343785.3159 280433.8259 1.551767976 1.447787828 1.273457179 1.558784927 1.405152047 1.314187504 1.458865288 1.170017355 1.225905308 1 18.09730085 1.299313052 0.640521922 0.998792805 1.452371044 0.700931518 0.092372237 0.367463467 0.359928202 0.087184122 0.03973299 19.9210879 -1.299313052 0.453578238 YKDEDGDLITIFDSSDLSFAIQCSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKDEDGDLITIFDSSDLSFAIQCSR 25 1 Q92734-2;Q92734;Q92734-4;Q92734-3;C9JTY3;C9JUE0;C9JJP5 Q92734-2 TFG Protein TFG 0 ; 102.67 0.0044372 55282000 58126 43919 49173 40396 59825 55750 53475 54191 56479 42411 FALSE TRUE 60420.85936 51461.74661 50454.48878 48386.20823 49655.96787 42802.9074 49283.48977 53464.65828 54446.33182 50720.62344 1.191248357 1.01461187 0.99475293 0.953975029 0.979009415 0.84389553 0.971665694 1.054100968 1.073455493 1 15.63028486 4.782277968 2.492498764 0.982785307 1.251682932 0.529415625 0.058321955 0.540069069 3.806193943 0.015989708 0.322472991 60572.84444 -4.782277968 0.268897625 YKDIIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKDIIR 6 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 81.381 0.056569 502250000 1034000 1036600 1160300 977790 1456700 1498400 1313700 1224600 1260200 1057800 FALSE TRUE 1074823.118 1214627.986 1190538.371 1171193.944 1209090.654 1150419.308 1210728.761 1208186.24 1214845.648 1265055.657 0.849625163 0.960137982 0.941095646 0.925804281 0.955760837 0.909382367 0.957055727 0.955045917 0.96031004 1 20.27076943 8 0.061832712 1.078345824 0.649905231 0.488746075 0.027200174 288.5314417 1.329262022 1.813968616 11.04868982 99999999.97 -8 -0.428440593 YKDIIRQPS(ph)EEEIIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YKDIIRQPSEEEIIK 15 2 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK;YKDIIRQPS(1)EEEIIK 227.4 3.84E-13 2824370000 2977650 2283480 3943400 1294650 5270550 3474140 2261390 2989790 4357740 2871640 TRUE FALSE 3095209.921 2675649.927 4046168.244 1550727.906 4374663.794 2667323.636 2084136.343 2949716.755 4200905.789 3434282.877 0.901268193 0.77910004 1.178169763 0.45154344 1.273821625 0.776675577 0.606862165 0.858903259 1.22322649 1 21.71157745 1.257835146 22.6787979 1.111612831 0.848030764 0.163938698 0.233101824 116.5967811 137193.072 0.146009819 0.053055951 18.10652657 -1.257835146 -0.263582067 YKDLDEDELLGNLS(ph)ETELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 YKDLDEDELLGNLS(0.999)ET(0.001)ELK;YKDLDEDELLGNLS(0.998)ET(0.002)ELK;YKDLDEDELLGNLS(0.976)ET(0.024)ELK;YKDLDEDELLGNLS(0.999)ET(0.001)ELK;YKDLDEDELLGNLS(0.999)ET(0.001)ELK 235.23 2.25E-24 528218000 1112980 385639 607586 395777 876764 828337 872809 613190 695089 321151 TRUE FALSE 1156921.31 451869.4984 623420.1903 474060.5093 727731.9685 635968.2853 804395.9499 604971.191 670072.8827 384074.3896 3.012232372 1.176515567 1.623175632 1.234293465 1.894768274 1.655846634 2.094375391 1.575140669 1.744643488 1 18.55102624 -2.237090241 0.528836696 3.41E-06 1.749617227 0.184412295 0.488154952 209.3133835 14.47009195 247.2710435 0.201500332 0.005793083 2.237090241 1.749613814 YKDLDEDELLGNLSETELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 0 ;; 242.2 1.95E-24 492577000 471985 223204 328699 214672 488698 414632 433969 317887 385669 179080 FALSE TRUE 490619.3323 261537.5507 337265.166 257133.4809 405629.2885 318340.0018 399953.3758 313626.2447 371788.848 214167.2973 2.290822821 1.221183411 1.574774348 1.200619722 1.893983319 1.486408083 1.867481081 1.464398387 1.735973945 1 17.70837868 -1.318401959 5.690193508 0.999918988 1.612392273 0.268289229 0.313320056 0.000289913 3.47E-05 0.273102749 0.064362493 0.048039452 1.318401959 0.612473285 YKDNEAIEFSFDLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKDNEAIEFSFDLER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 0 59.862 0.09323 46061000 20396 23219 25535 20935 31830 33557 26890 25325 27191 22400 FALSE TRUE 21201.24983 27206.68263 26200.46308 25075.88052 26419.54797 25763.89531 24782.29154 24985.5598 26212.40122 26788.85113 0.791420645 1.015597216 0.978036085 0.936056586 0.986214297 0.961739464 0.925097214 0.932685007 0.978481724 1 14.70934509 4.749738955 24.97514644 0.962444927 0.791420544 0.770742264 0.028771766 819.9220245 1831871.891 0.007118203 0.109928561 56200.34149 -4.749738955 -0.171024383 YKDNPFSLGES(ph)FGSR ddPTM_MDA-MB-175_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 YKDNPFSLGES(0.999)FGSR;YKDNPFSLGES(0.999)FGS(0.001)R;YKDNPFS(0.002)LGES(0.894)FGS(0.104)R 132.13 2.99E-05 556680000 488980 362800 584440 421940 855180 651120 608160 532960 686740 474400 TRUE FALSE 508285.308 425108.0778 599670.9865 505398.4726 709816.8091 499907.2478 560490.8301 525816.5429 662024.3615 567349.5971 0.895894367 0.749287706 1.056969089 0.890806084 1.251110096 0.881127351 0.987910863 0.9267946 1.166872004 1 19.11387846 4.233609765 24.99889524 1.010222228 0.822591023 0.315236797 0.115752475 126.7176204 639862.5912 0.027140464 0.061681574 17124.17925 -4.233609765 -0.187631205 YKDPQDENK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YKDPQDENK 9 1 C9JVE2;Q96GG9;C9J8R4;C9JRU6;C9J0B2;C9JRE2;C9JAV2;H7C216;Q6PH85-2;Q6PH85 C9JVE2 DCUN1D1;DCUN1D2 DCN1-like protein;DCN1-like protein 1;DCN1-like protein 2 0 ;;; 95.642 0.007211 891020000 2455060 983680 1415500 930390 2257410 2013460 1979290 1419150 1775550 773640 FALSE TRUE 2551987.665 1152619.388 1452389.093 1114418.365 1873696.255 1545864.429 1824148.078 1400128.616 1711648.302 925219.9458 2.758249729 1.245778794 1.56977711 1.204490208 2.025136037 1.670807505 1.971583175 1.513292728 1.849990708 1 19.81943684 -1.201969342 4.276636885 0.999722621 1.718997617 0.217254359 0.425474067 156.0449482 111691012 57028.3367 0.091727528 0.06281027 1.201969342 0.719274996 YKEALLGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKEALLGR 8 1 P52565;J3KTF8;J3QQX2;J3KRE2;J3KRY1;P52565-2;J3KS60 P52565 ARHGDIA Rho GDP-dissociation inhibitor 1 0 ; 126.07 0.0011263 2895900000 2159680 2016580 2304700 1906180 2990600 2726000 2199710 2229260 2300000 2251060 FALSE TRUE 2244945.834 2362911.928 2364762.375 2283216.715 2482258.88 2092927.813 2027290.982 2199380.416 2217223.449 2692112.108 0.833897603 0.877716764 0.878404123 0.848113534 0.922048853 0.777429665 0.753048499 0.816972075 0.823599969 1 21.36030706 2.730670961 24.71042384 0.815841867 0.871376503 0.041144246 0.066330459 981.443869 3073879.82 0.019890867 0.019091039 537.8621218 -2.730670961 0.055534636 YKEEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKEEAR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ; 88.734 0.046482 1009340000 1691750 1480910 1739230 1402300 2064530 1992940 1907750 1748600 1799900 1424730 FALSE TRUE 1758541.596 1735244.773 1784555.763 1679670.755 1713601.928 1530109.888 1758215.57 1725162.877 1735121.951 1703878.565 1.03208153 1.01840871 1.047349147 0.985792526 1.005706605 0.898015809 1.031890186 1.012491683 1.018336627 1 20.70039109 3.730777052 24.64714189 0.993826431 1.031192687 0.210081554 0.034995304 818.4917524 2591803.387 0.009584027 0.01517455 5379.935291 -3.730777052 0.037366257 YKEEFEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YKEEFEK 7 1 Q14847;Q14847-2;C9J9W2;Q14847-3 Q14847 LASP1 LIM and SH3 domain protein 1 0 ;;; 101.64 0.0081244 6570100000 5904900 3259010 4779020 3286760 6665700 6042200 6531700 4893200 5899300 2908540 FALSE TRUE 6138030.012 3818719.616 4903565.187 3936871.318 5532666.695 4638990.62 6019728.287 4827614.658 5686985.345 3478412.726 1.764606588 1.09783396 1.409713445 1.131801091 1.590572233 1.333651578 1.730596327 1.387878621 1.634936908 1 21.72999769 YKEELIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKEELIEK 8 1 Q9UNX3 Q9UNX3 RPL26L1 60S ribosomal protein L26-like 1 0 73.499 0.039587 177050000 137130 102010 135200 107860 190240 178480 181260 147980 169110 109050 FALSE TRUE 142543.9983 119529.424 138723.4231 129194.3861 157903.0728 137030.7249 167052.3676 145996.5701 163023.7641 130416.2596 1.092992536 0.916522405 1.063697299 0.990630972 1.210762164 1.050718103 1.280916721 1.119466013 1.250026374 1 16.99276422 3.245687937 24.98214178 1.159383018 1.012267786 0.345943036 0.091229208 160.1896366 561481.1743 0.023181538 0.030736116 1760.71043 -3.245687937 -0.147115232 YKEENNDHLDDFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKEENNDHLDDFK 13 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 0 67.964 0.031075 117650000 264910 155660 191580 161530 281460 284230 249650 213450 220210 146890 FALSE TRUE 275368.8514 182393.3941 196572.7322 193480.1519 233617.5297 218221.89 230081.7807 210589.0519 212284.6851 175670.2831 1.567532348 1.038271191 1.118986824 1.101382365 1.329863683 1.242224275 1.309736494 1.198774478 1.20842684 1 17.42251064 0.511591911 1.788338349 1.000047427 1.228649934 0.201892946 0.140392439 5.437709257 18.02600009 0.128028693 0.035871553 3.247819693 -0.511591911 0.228602507 YKEETIEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YKEETIEK 8 1 P61254 P61254 RPL26 60S ribosomal protein L26 0 ;;;;; 136.63 0.00071367 5312900000 6169840 3496530 5140420 3477960 7402080 6393150 6845380 5444270 6200130 3347430 FALSE TRUE 6413430.047 4097031.828 5274383.568 4165890.107 6143877.086 4908437.802 6308821.229 5371298.466 5976988.532 4003294.818 1.602037906 1.023414966 1.317510653 1.040615367 1.534705128 1.226099507 1.575907225 1.341719436 1.493017328 1 21.93275643 3.227941906 24.9990787 1.384481998 1.235118706 0.0577236 0.216748439 470.2311843 1107039.157 0.056974769 0.068762594 1690.214824 -3.227941906 -0.149363292 YKELGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YKELGEK 7 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 ;;;; 90.629 0.015502 8204770000 12197430 8685190 10213430 8117550 16203010 13873000 12871630 10919570 12902840 7187330 FALSE TRUE 12678993.95 10176803.82 10479600.38 9723177.162 13448828.15 10651206 11862718.01 10773211.02 12438469.31 8595549.704 1.475064934 1.183961954 1.219189085 1.131187358 1.564626884 1.239153558 1.380099984 1.253347534 1.447082471 1 23.03515848 -1.351664395 4.608078456 0.999679213 1.311743859 0.338935099 0.134084836 0.000415008 5.84E-05 0.121928248 0.02870956 0.044497499 1.351664395 0.312064646 YKETDLLILFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKETDLLILFK 11 1 P05455 P05455 SSB Lupus La protein 0 ; 122.35 0.00035811 651980000 2326600 1645970 2027540 1750790 3073500 2659100 2889700 2186000 2461400 1612100 FALSE TRUE 2418455.965 1928652.544 2080379.358 2097091.036 2551067.568 2041564.324 2663197.763 2156700.246 2372814.695 1927960.129 1.254411815 1.000359143 1.079057251 1.087725314 1.323195189 1.058924556 1.381355207 1.118643593 1.230738467 1 20.87864379 YKETDLLILFKDDYFAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKETDLLILFKDDYFAK 17 2 P05455 P05455 SSB Lupus La protein 0 ; 190.71 1.59E-10 1605110000 2310300 1186300 2122290 1076520 2815900 2113430 2083260 2072680 2428000 1148710 FALSE TRUE 2401512.428 1390037.797 2177598.621 1289452.443 2337254.324 1622617.912 1919968.638 2044899.115 2340616.754 1373777.731 1.748108427 1.011836024 1.585117135 0.938617954 1.701333681 1.181135693 1.397583171 1.488522538 1.70378126 1 20.38971717 1.999729472 24.99883076 1.449549394 1.346419612 0 0.303003128 45.40582246 4196044.997 0.104218321 0.076179548 99.93772798 -1.999729472 -0.103129782 YKEVAELTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKEVAELTR 9 1 Q01082;A0A087WUZ3;Q01082-2;Q01082-3 Q01082;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 ; 120.09 0.00065789 346950000 381880 545710 426840 320750 657610 638200 397320 432420 372730 581040 FALSE TRUE 396956.9173 639431.4475 437963.8011 384193.3927 545829.6871 489987.722 366177.0202 426624.1172 359315.5201 694883.6633 0.571256655 0.920199281 0.630269244 0.552888797 0.785497941 0.705136338 0.526961619 0.61395042 0.517087304 1 19.40641194 YKLDEDEDEDDADLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKLDEDEDEDDADLSK 16 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 178.66 2.51E-09 122070000 279670 66448 122180 91395 184590 229070 237890 134340 160350 42236 FALSE TRUE 290711.5876 77859.92711 125364.1112 109472.6582 153213.4577 175871.9641 219243.5602 132539.392 154579.0348 50511.33554 5.755373213 1.541434735 2.481900544 2.167288927 3.033248994 3.481831597 4.340482346 2.623953428 3.060284056 1 15.62431957 3.019525364 24.5086258 3.105267452 2.816366795 0 1.308807639 1433.712162 1799608.264 0.361914722 0.432512545 1045.984777 -3.019525364 -0.288900657 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLS(0.227)KY(0.213)NLDAS(0.552)EEEDS(0.008)NK;YKLDEDEDEDDADLS(0.226)KY(0.211)NLDAS(0.558)EEEDS(0.005)NK 57.184 0.02633 353592000 441666 65179 105859 71376 202550 255695 219915 114212 144725 36722 TRUE FALSE 459103.3147 76372.98623 108617.7725 85493.95976 168120.6233 196313.7113 202677.4877 112681.175 139516.3755 43916.97281 10.45389255 1.739031207 2.473252721 1.946717961 3.8281469 4.470110273 4.615014986 2.565777369 3.176821319 1 15.42249099 4.744610485 24.86535274 3.014700313 10.45389607 0.802609148 1.126447542 275.14525 1130830.905 0.27504076 2.512504474 55540.58949 -4.744610485 7.439195758 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNKK 30 3 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YKLDEDEDEDDADLSKYNLDAS(1)EEEDSNKK 107.73 0.0015392 97988000 114600 10582 23396 10748 51176 68997 46455 23844 30272 6422.7 TRUE FALSE 119124.4965 12399.37618 24005.71898 12873.92232 42477.1218 52973.49241 42813.73571 23524.41018 29182.51663 7681.105095 15.50877055 1.614269826 3.125294952 1.676050798 5.530079497 6.896597788 5.573903128 3.062633552 3.799260168 1 12.90709817 4.745113854 24.98698484 3.796462618 15.50877585 0.79028224 1.83964302 349.1163627 1331118.534 0.456754899 4.408947727 55605.00115 -4.745113854 11.71231323 YKPESEELTAER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 ;;;;; 189.61 7.03E-06 13982260000 11526550 12644750 12445000 12449610 15565650 17074000 13962480 13151150 12180350 12265750 FALSE TRUE 11981627.09 14816387.45 12769326.92 14912105.7 12919806.37 13108822.26 12868064.33 12974880.35 11741981.58 14668988.87 0.816799794 1.010048312 0.870498099 1.016573523 0.880756437 0.893641844 0.877229129 0.884510886 0.800462914 1 23.80626609 YKPVCNQVECHPYFNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKPVCNQVECHPYFNR 16 1 A0A0A0MSS8;P42330;S4R3Z2;P42330-2 A0A0A0MSS8 AKR1C3 Aldo-keto reductase family 1 member C3 0 ; 141 9.89E-07 1597100000 1336740 1330680 1372670 1219530 1833580 1944570 1586420 1684290 1705400 1370840 FALSE TRUE 1389515.527 1559213.939 1408442.908 1460749.394 1521908.727 1492973.088 1462072.255 1661714.847 1644022.987 1639429.852 0.847560221 0.951070848 0.85910532 0.891010611 0.928315856 0.910666038 0.891817514 1.013593138 1.002801666 1 20.64476274 1.73117103 6.295332797 1.005560494 0.899102767 0.748533864 0.028722689 0.065101819 6.889101481 0.013584805 0.007054399 53.84818009 -1.73117103 -0.106457727 YKPYEEALLQAEAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKPYEEALLQAEAPR 15 1 A0A499FI31;Q15020-4;Q15020;Q15020-2 A0A499FI31 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 0 143.67 3.99E-06 184950000 116860 102640 110510 104720 142770 138550 137770 119100 124960 100670 FALSE TRUE 121473.723 120267.6216 113389.9814 125433.3034 118502.0064 106373.8622 126971.2274 117503.6593 120462.714 120394.3591 1.008965237 0.998947314 0.94182138 1.041853658 0.984282049 0.883545235 1.054627712 0.975989741 1.000567759 1 16.87740827 YKQDVYLLPK ddPTM_MDA-MB-175_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 0 100.72 0.0048294 0 817530 585870 761770 626440 1097400 1011700 862620 778540 854760 620050 FALSE TRUE 849806.7157 686488.6151 781622.352 750347.9623 910864.34 776748.0075 795005.5904 768104.9447 823997.3546 741536.9259 1.14600728 0.925764572 1.054057222 1.011882128 1.228346571 1.047483922 1.072105195 1.035828315 1.111202053 1 19.50015901 YKQENTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKQENTR 7 1 Q9H2M9 Q9H2M9 RAB3GAP2 Rab3 GTPase-activating protein non-catalytic subunit 0 ; 103.56 0.0076133 285960000 260850 211580 281980 232690 332030 330300 291850 275630 262300 240690 FALSE TRUE 271148.5594 247917.2191 289328.6304 278715.3875 275591.6592 253592.8307 268974.0344 271935.6307 252859.8742 287848.5972 0.941983258 0.861276454 1.005141707 0.968270786 0.957418802 0.880993804 0.934428853 0.944717582 0.878447478 1 18.13495066 -1.096283304 4.082970457 1.000013428 0.932071527 0.193970228 0.04248795 40585181914 8983308102 5552978.052 0.00975168 0.080115527 1.096283304 -0.067941902 YKSEDEANR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKSEDEANR 9 1 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 73.067 0.041014 27689000 31993 24779 24328 35901 34620 47141 48219 32803 33232 24963 FALSE TRUE 33256.10834 29034.6005 24962.00767 43002.11065 28735.30477 36193.21718 44439.46878 32363.32944 32035.98681 29854.0219 1.113957391 0.972552395 0.836135504 1.440412645 0.962527088 1.212339741 1.488558859 1.084052579 1.073087804 1 14.86563768 3.759244999 24.87765414 1.188491286 0.974048848 0.225896771 0.174208111 1099.768514 1322716.307 0.043659885 0.078600759 5744.404304 -3.759244999 -0.214442438 YKSEDEANRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YKSEDEANRDR 11 2 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 ;;;; 152.47 1.85E-05 4094400000 4857840 3793790 4546490 3813550 5503190 5613950 5410610 4566730 4736530 3236350 FALSE TRUE 5049631.274 4445343.921 4664975.264 4567858.808 4567759.729 4310195.193 4986512.25 4505520.454 4566063.211 3870450.819 1.304662302 1.148533886 1.205279561 1.180187792 1.180162194 1.113615802 1.288354376 1.164081567 1.179723868 1 21.88407019 -4.008508962 0.348166142 7.74E-11 1.200544662 0.534891125 0.055340205 148.1074195 2.394953239 107.9617333 0.039840879 9.81E-05 4.008508962 1.200544662 YKVDHDER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YKVDHDER 8 1 A0A0G2JRG8;A0A0G2JNY3;E9PIR1;Q6ZUM4-3;Q6ZUM4;A0A0C4DGE6;E9PNT2;Q6ZUM4-2 A0A0G2JRG8 ARHGAP27 Rho GTPase-activating protein 27 0 ;;; 130.28 0.0006338 270346000 575080 525290 613090 596040 746020 801430 772010 619510 685380 491720 FALSE TRUE 597784.6025 615504.4713 629067.6291 713934.933 619211.7869 615310.0283 711497.8389 611206.4818 660713.3077 588063.1195 1.01653136 1.046663957 1.069728076 1.214044733 1.052968238 1.046333307 1.20990046 1.039355235 1.12354148 1 19.16561149 4.188669333 3.453045652 1.101049602 1.028231058 0.130298927 0.067160392 0.413134777 9.919849196 0.016200131 0.043308784 15440.78347 -4.188669333 -0.072818543 YKVEGFPTIYFAPSGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKVEGFPTIYFAPSGDK 17 1 P13667;A0A499FI48 P13667 PDIA4 Protein disulfide-isomerase A4 0 135.71 1.16E-05 479060000 639650 400240 518620 427410 710400 716410 730750 485310 545890 359120 FALSE TRUE 664903.8759 468978.1066 532135.6633 511950.4223 589646.4617 550034.6348 673471.9055 478805.2133 526243.5255 429482.6882 1.548150587 1.091960443 1.239015397 1.192016434 1.372922537 1.28069105 1.568100238 1.114841707 1.225296246 1 18.71224045 1.014113735 1.492968 1.010854454 1.30341408 0.279863491 0.150422174 0.538142038 2.447652973 0.135791758 0.040238705 10.33031906 -1.014113735 0.292559626 YKVPDGKPENEFAFNAEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKVPDGKPENEFAFNAEFK 19 2 Q15181 Q15181 PPA1 Inorganic pyrophosphatase 0 ; 230.01 3.76E-20 3768900000 4046100 1489810 2546500 1498960 3493400 2987100 3440300 2500200 3146900 1078640 FALSE TRUE 4205843.152 1745673.278 2612863.882 1795449.814 2899593.116 2293391.295 3170640.296 2466688.909 3033643.684 1289978.856 3.260396969 1.35325728 2.025509077 1.391844374 2.247783444 1.777851849 2.457900981 1.912193286 2.351700316 1 20.29891599 YKWCEYGLTFTEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKWCEYGLTFTEK 13 1 Q5JSD2;Q5JSD1;A0A0A0MR02;P45880-2;P45880;P45880-1;A2A3S1 Q5JSD2 VDAC2 Voltage-dependent anion-selective channel protein 2 0 ; 59.898 0.057625 2787600000 1726330 2038510 1983050 1782650 2835100 2577500 2372100 2227000 2381200 2212950 FALSE TRUE 1794486.841 2388608.235 2034729.912 2135252.849 2353190.715 1978914.687 2186168.604 2197150.708 2295501.077 2646535.183 0.678051383 0.902541652 0.768827834 0.806810679 0.889159052 0.74773791 0.826049326 0.830198942 0.867360877 1 21.3356734 -5 0.188405607 1.805627646 0.779853002 0.494990511 0.060792253 110.5755491 1.079594467 33.25940809 0.15499652 1.00E-05 5 -1.025774644 YKYEDKDGKQPVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YKYEDKDGKQPVGR 14 3 A0A499FJT0;Q8NHP1;O43488;H3BLU7 A0A499FJT0;O43488 AKR7L;AKR7A2 Aflatoxin B1 aldehyde reductase member 4;Aflatoxin B1 aldehyde reductase member 2 0 95.538 0.0016333 771780000 1135400 541860 864620 427800 1429100 1054700 954410 770260 1040900 483270 FALSE TRUE 1180226.469 634920.2399 887152.7075 512417.5631 1186182.092 809761.9091 879600.8503 759935.9246 1003438.212 577957.5037 2.042064444 1.098558693 1.534979132 0.886600762 2.052369049 1.401075172 1.521912675 1.314864708 1.73617992 1 19.14060389 -1.585351457 6.039250438 0.998494039 1.480817424 0.153886693 0.352791171 0.00648873 0.00044551 0.309846887 0.072835644 0.025980562 1.585351457 0.482323385 YKYPNISCELLTSDVSQMNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YKYPNISCELLTSDVSQMNDR 21 1 Q5H9R7-2;Q5H9R7;Q5H9R7-5;H7BXH2;E9PKF6;Q5H9R7-4;Q5H9R7-6;Q5H9R7-3;E9PNN8 Q5H9R7-2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 ; 189.79 1.86E-17 1169120000 2294810 2178850 2509230 2134480 2898900 2969200 2628410 2680860 2702590 2076410 FALSE TRUE 2385410.871 2553050.538 2574622.595 2556673.773 2406146.013 2279648.299 2422388.356 2644927.457 2605324.314 2483242.784 0.960603162 1.02811153 1.036798581 1.029570604 0.968953188 0.918012654 0.975493968 1.065110296 1.04916214 1 21.24379389 1.744241904 23.23267599 1.042830198 0.989772217 0.264705459 0.037780667 0.969803991 3987.473094 0.019282969 0.010691324 55.49347276 -1.744241904 -0.053057981 YLAEFATGNDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLAEFATGNDR 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 247.51 9.38E-16 1456260000 652205 713820 659271 769309 750585 876197 785124 742324 659441 626421 FALSE TRUE 677954.557 836413.0323 676452.1439 921476.024 623000.8298 672713.5256 723583.9293 732374.361 635707.8472 749156.2014 0.904957545 1.116473481 0.902952071 1.230018549 0.831603381 0.897961633 0.965865233 0.97759901 0.848565154 1 19.51490703 YLAEFATGNDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 ;;; 224.24 3.29E-11 4251640000 2894520 1811060 2585340 2251520 3277970 3010350 3238760 2769710 2882920 1721960 FALSE TRUE 3008797.885 2122095.467 2652716.084 2696863.936 2720781.83 2311241.835 2984897.528 2732586.568 2779164.272 2059345.093 1.461045987 1.030471034 1.288135773 1.309573585 1.321187906 1.122318859 1.449440183 1.326920183 1.34953791 1 20.97375418 4.049690637 24.9998664 1.291773426 1.224145049 0 0.154302027 432.1196346 217397.8825 0.035462045 0.076606763 11212.19486 -4.049690637 -0.067628377 YLAEKYEWDVAEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 ;;;;;;; 224.67 2.79E-12 9036160000 7867335 7103861 8629720 6020973 9486070 9298440 7632796 8410583 8890230 7362329 FALSE TRUE 8177943.461 8323893.866 8854617.593 7211903.489 7873631.21 7139018.229 7034517.505 8297852.892 8570272.359 8804836.407 0.928801295 0.945377459 1.005653846 0.819084325 0.894239353 0.810806459 0.7989379 0.942419882 0.973359636 1 23.06986477 1.50309406 6.556361802 0.97805076 0.886731744 0.304237605 0.061619964 0.179954221 17.66318773 0.037820495 0.017054607 31.84887236 -1.50309406 -0.091319016 YLAEVAAGDDKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLAEVAAGDDKK 12 1 B7Z2E6;H0YB80;P63104-2;P63104;E7EX29;B0AZS6 B7Z2E6;P63104 YWHAZ 14-3-3 protein zeta/delta 0 ;;;; 195.88 3.42E-07 13161420000 9312650 3438070 5520800 3629450 7682250 6965770 8329920 5165770 6612300 2676280 FALSE TRUE 9680320.613 4028531.778 5664676.583 4347344.377 6376423.889 5348075.485 7676999.104 5096531.303 6374324.615 3200645.826 3.024489788 1.258662157 1.769854239 1.358270991 1.992230392 1.67093636 2.398578138 1.592344664 1.991574502 1 21.60993161 -1.46923263 2.95630154 0.976986021 1.855541855 0.226646161 0.491197957 41172367.68 47740540.09 7812017.831 0.108728058 0.03394434 1.46923263 0.878555834 YLAEVACGDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YLAEVACGDDR 11 0 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;;; 213.31 6.91E-09 2967680000 1435460 1565430 1573850 1736110 1791790 2046010 1675370 1646560 1571840 1566500 FALSE TRUE 1492133.069 1834280.425 1614865.824 2079507.376 1487222.176 1570855.185 1544050.122 1624490.556 1515269.785 1873425.683 0.796473051 0.979104985 0.861985527 1.110002599 0.793851707 0.838493461 0.824185414 0.867123031 0.808823002 1 20.83724732 YLAEVACGDDRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLAEVACGDDRK 12 1 P27348;E9PG15 P27348 YWHAQ 14-3-3 protein theta 0 ;;;; 198.49 2.93E-07 5206020000 3310120 2110880 2702960 2421000 3681320 3694570 3986430 3286960 3331780 2139390 FALSE TRUE 3440806.094 2473407.22 2773401.358 2899866.574 3055570.541 2836562.109 3673963.2 3242903.678 3211869.889 2558562.509 1.344820023 0.966717526 1.083968575 1.133396805 1.194252839 1.108654605 1.435948188 1.267470959 1.255341574 1 21.28690205 YLAEVASGEKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLAEVASGEKK 11 1 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 140.39 0.0024122 0 340510 174210 232880 177780 386460 333370 351940 261320 376240 194610 FALSE TRUE 353953.5977 204129.2123 238949.0441 212944.3534 320769.6672 255949.8698 324354.0232 257817.4328 362699.1959 232740.1035 1.52081052 0.877069355 1.026677571 0.914944826 1.378231179 1.099723967 1.39363186 1.107748209 1.55838719 1 17.8283603 3.233708553 24.99733024 1.253304964 1.065875271 0.120397454 0.224553109 230.9416388 1189787.917 0.060233659 0.07418487 1712.807487 -3.233708553 -0.187429693 YLAEVATGDDKKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLAEVATGDDKKR 13 2 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 ;; 183.89 5.61E-06 1707150000 1345410 697290 1096370 698940 1676940 1238830 1184690 1048300 1395560 822610 FALSE TRUE 1398527.826 817044.1333 1124942.303 837188.2459 1391894.338 951130.5072 1091830.902 1034249.253 1345334.068 983784.6797 1.421579188 0.830511137 1.143484267 0.850987277 1.414836363 0.966807602 1.109827104 1.05129636 1.367508659 1 19.90798306 YLAEVATGEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 ;; 179.19 1.16E-05 1097250000 1142430 1021424 1003494 1030205 1513860 1425030 1345454 1166013 1374451 1131126 FALSE TRUE 1187534.019 1196845.626 1029645.878 1233976.474 1256534.618 1094088.379 1239993.8 1150384.503 1324984.777 1352748.483 0.877867566 0.884751039 0.761151013 0.912199488 0.928875274 0.808789212 0.91664771 0.850405317 0.979476077 1 20.36746219 1.187026157 5.627681119 0.995608392 0.867699493 0.50133739 0.04878095 0.158424409 10.49384632 0.043739393 0.011378445 15.38247284 -1.187026157 -0.127908899 YLAFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLAFLR 6 0 P40429;M0QYS1 P40429 RPL13A 60S ribosomal protein L13a 0 ; 128.65 0.038468 570690000 329090 355020 284030 252770 1220920 590150 458990 300470 312840 1471210 FALSE TRUE 342082.7273 415991.9233 291432.0551 302767.1516 1013388.455 453096.6063 423013.1645 296442.6911 301580.9495 1759465.431 0.194424239 0.236430859 0.165636704 0.172079057 0.575963833 0.257519471 0.240421413 0.168484521 0.171404873 1 20.74670574 -1.11236408 4.432758232 1.000085481 0.242682452 0.792554033 0.116265377 31132100.77 11727503.6 25860.74133 0.028047733 0.07720331 1.11236408 -0.75740303 YLDEDTIYHLQPSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 ;;;; 194.55 4.72E-08 2490080000 1055758 2534040 2531743 2639728 2601480 3099030 2211371 2585954 2500158 3124320 FALSE TRUE 1097440.141 2969241.658 2597722.302 3161858.32 2159281.359 2379327.249 2038037.963 2551293.516 2410177.802 3736470.685 0.293710358 0.794664781 0.695234225 0.846215208 0.577893296 0.636784669 0.545444655 0.682808386 0.645041272 1 21.83324477 0.01437876 1.608659826 1.000201415 0.644354347 0.367655569 0.14304336 31.04216873 48.55358059 0.14689873 0.036775335 1.033662497 -0.01437876 -0.355847068 YLDESSGGWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YLDESSGGWR 10 0 K7ENE5;O00115-2;O00115 K7ENE5 DNASE2 Deoxyribonuclease-2-alpha 0 ;;;;; 269.38 5.65E-18 1564604000 1098641 1396320 1220429 1260973 1466540 1646310 1269636 1178644 1047553 1436390 FALSE TRUE 1142016.195 1636127.098 1252234.382 1510389.696 1217258.055 1263979.453 1170118.613 1162846.205 1009851.772 1717823.119 0.664804299 0.952442123 0.728965845 0.879246343 0.708605002 0.735803028 0.681163619 0.676930117 0.587867145 1 20.71215006 3.210033368 23.99448028 0.710044486 0.811270259 0.06341279 0.12424745 256.2676052 215547.4021 0.033009209 0.03946226 1621.934711 -3.210033368 0.101225774 YLDIHER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLDIHER 7 0 P62072 P62072 TIMM10 Mitochondrial import inner membrane translocase subunit Tim10 0 ; 107.9 0.0073747 515830000 762690 1090550 925300 1067980 970290 1180300 867610 873150 746910 972550 FALSE TRUE 792801.5901 1277843.479 949414.0781 1279223.256 805360.4524 906193.2126 799604.4611 861446.8524 720028.855 1163102.552 0.681626559 1.09865074 0.816277186 1.09983703 0.692424285 0.779117208 0.687475459 0.740645656 0.619058787 1 20.14954688 3.211111587 24.99990227 0.737186715 0.928864595 0.236628031 0.148704953 255.4273709 232636.2657 0.039004477 0.046629406 1625.966475 -3.211111587 0.19167788 YLDLHDCYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLDLHDCYLK 10 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 0 ;; 164.97 6.00E-06 553680000 2280280 1968820 2135120 1877330 3317080 2882210 2708500 2346420 2445700 2330240 FALSE TRUE 2370307.215 2306949.52 2190762.981 2248660.271 2753243.926 2212860.408 2496200.693 2314970.078 2357679.735 2786805.913 0.850546213 0.827811334 0.786119683 0.806895184 0.987956827 0.794048985 0.895721041 0.830689381 0.846015047 1 21.4101811 -5 0.287162419 2.164656154 0.837840646 0.404705096 0.055632433 240.3428446 2.275480867 167.5262843 0.058907447 1.00E-05 5 -1.326815509 YLDPEYIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLDPEYIDR 9 0 X6RA56;X6RLR1;O75935-2;O75935;X6RCK5;A0A0A0MRV8;O75935-3 X6RA56 DCTN3 Dynactin subunit 3 0 ;;; 134.48 0.00057639 832490000 1580100 1858720 1759990 1832890 1894260 2148570 1870230 1788870 1744860 1847470 FALSE TRUE 1642483.568 2177940.701 1805856.785 2195430.171 1572274.362 1649597.179 1723636.486 1764893.124 1682062.829 2209446.375 0.743391461 0.985740467 0.817334517 0.993656237 0.711614629 0.746611096 0.780121439 0.798794279 0.761305116 1 21.07525349 5.066573914 13.87723238 0.83197431 0.000103259 0.066993448 0.10430203 2927926.493 16108446.29 0.024302603 67705639.15 116566.5422 -5.066573914 -0.831871052 YLDQMEDLYEDFHIVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YLDQMEDLYEDFHIVK 16 0 O43681 O43681 ASNA1 ATPase ASNA1 0 ;;;;;; 227.29 5.16E-15 1520775000 1757301 1707355 2022065 1778181 2427320 2418420 2157370 2030106 2152312 1692300 FALSE TRUE 1826680.6 2000579.94 2074761.675 2129899.894 2014725.013 1856778.607 1988269.702 2002895.75 2074850.712 2023873.784 0.902566462 0.988490466 1.025143807 1.052387709 0.995479575 0.917437946 0.982407953 0.989634712 1.0251878 1 20.94868789 4.731815149 4.767871358 0.996452051 0.897702998 0.418890221 0.033593582 0.184299194 11.9154323 0.008754445 0.060022007 53928.10371 -4.731815149 -0.098749053 YLDYAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLDYAR 6 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 102.98 0.081604 163520000 251210 296170 284070 250630 412410 362230 317640 296790 248640 387860 FALSE TRUE 261127.9648 347034.8936 291473.0976 300203.8659 342308.6955 278107.5721 292742.5468 292812.0155 239691.495 463853.741 0.562953237 0.748155858 0.628372851 0.647195095 0.737966875 0.599558757 0.631109595 0.63125936 0.516739381 1 18.82331045 -1.522679646 3.477987924 1.007898565 0.638777646 0.731331288 0.066541216 11333740.92 5677642.668 667791.4589 0.014774538 0.030013756 1.522679646 -0.369120919 YLEES(ph)DEDDLF ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLEESDEDDLF 11 0 P11388;P11388-2;P11388-3;P11388-4;J3QR57 P11388 TOP2A DNA topoisomerase 2-alpha 1 Y(0.008)LEES(0.992)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF 171.73 1.49E-05 506974000 1120151 1317304 1383885 1303003 1461794 1460897 1337964 1370522 1251436 1271946 TRUE FALSE 1164375.426 1543540.715 1419950.18 1560733.104 1213318.778 1121625.812 1233090.886 1352152.394 1206397.063 1521159.466 0.765452573 1.014713283 0.933465696 1.026015444 0.797627603 0.737349264 0.810625653 0.888895888 0.793077314 1 20.53673997 3.220335424 24.99805791 0.829920654 0.940508593 0.201818506 0.093412576 330.9573196 453947.1012 0.02600431 0.031137663 1660.869173 -3.220335424 0.110587939 YLELLGYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLELLGYR 8 0 D6REX3;O94979-8;O94979;O94979-2;O94979-3;O94979-9;O94979-10;O94979-6;O94979-4;D6RHZ5;O94979-7;H7BXG7;O94979-5;H0YAB3;H0Y8V7;H0Y9K1 D6REX3 SEC31A Protein transport protein Sec31A 0 103.91 0.016407 0 129900 135620 118270 129490 219870 189330 154730 122110 126910 199800 FALSE TRUE 135028.5523 158911.68 121352.2134 155102.7355 182496.5759 145360.9768 142601.8583 120473.3152 122342.5339 238946.9846 0.565098373 0.665049949 0.507862502 0.649109407 0.763753417 0.608339867 0.596792877 0.504184288 0.512007022 1 17.86633104 -1.333316116 3.305404961 1.002502898 0.59628773 0.708763643 0.077515623 22577775.65 32275439.51 558987.7752 0.019762926 0.046417729 1.333316116 -0.406215168 YLEMIYS(ph)MCKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLEMIYSMCKK 11 1 O95373 O95373 IPO7 Importin-7 1 YLEMIY(0.448)S(0.552)MCKK 49.35 0.070185 200660000 9609.1 471010 108770 280490 40015 201300 23112 98288 25463 811210 TRUE FALSE 9988.474688 551902.3036 111604.6356 335970.0848 33213.26459 154551.1257 21300.42105 96970.61013 24546.5916 970151.0679 0.010295793 0.568882849 0.115038409 0.346306978 0.034235147 0.159306247 0.021955778 0.099954134 0.025301824 1 19.88784989 -1.774231757 6.075229638 1.035830778 0.156956114 0.695230908 0.168129966 0.065841369 0.002446803 0.1313603 0.037169628 0.016817764 1.774231757 -0.878874664 YLEQLHQLYSDSFPMELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLEQLHQLYSDSFPMELR 18 0 P40763;P40763-2;P40763-3;K7EP08 P40763 STAT3 Signal transducer and activator of transcription 3 0 ; 221.79 6.05E-19 507320000 292070 499120 484850 464400 515600 587190 462970 504170 417920 427300 FALSE TRUE 303601.1491 584839.9774 497485.5893 556256.9339 427958.4962 450824.0215 426681.2017 497412.4258 402879.1408 511021.2538 0.594106697 1.144453333 0.973512521 1.088520154 0.837457333 0.882202096 0.834957839 0.97336935 0.788380401 1 18.96302377 3.18098957 24.99999011 0.887143847 0.965701809 0.038752292 0.148432725 240.537334 104450.9508 0.040590889 0.048515418 1517.013936 -3.18098957 0.078557962 YLFDLPLKVLVVS(ph)NNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLFDLPLKVLVVSNNK 16 1 Q5VUJ6-2;Q5VUJ6 Q5VUJ6-2 LRCH2 Leucine-rich repeat and calponin homology domain-containing protein 2 1 Y(0.007)LFDLPLKVLVVS(0.993)NNK 57.159 0.072845 1110300000 847730 691100 867310 595610 1032500 990930 885450 795530 1043300 827060 TRUE FALSE 881199.035 809791.049 889912.8111 713419.8803 856996.0188 760801.5252 816046.1153 784867.2216 1005751.837 989106.572 0.890904034 0.818709603 0.899713778 0.72127706 0.86643446 0.769180538 0.825033559 0.79351128 1.016828586 1 19.91576645 1.235105959 24.99998659 1.008414412 0.820544545 0.672679569 0.051683976 47.99784651 347314.3816 0.040061798 0.011583304 17.18327575 -1.235105959 -0.187869867 YLFLGDYVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLFLGDYVDR 10 0 P16298-3;P16298;P16298-4;G3V111;Q5F2F8;P48454-2;P48454;P16298-2;P48454-3;H0YB02;Q08209-3;Q08209-2;Q08209;E7ETC2;Q08209-5;E9PPC8;E9PK68 P16298-3;Q08209-3 PPP3CB;PPP3CC;PPP3CA Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform;Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform;Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 0 83.647 0.035968 59993000 129670 99905 147230 112380 142270 151650 170440 124410 139860 108650 FALSE TRUE 134789.4717 117062.9066 151066.9348 134608.4286 118086.9962 116431.5858 157080.4674 122742.4874 134826.4659 129937.8873 1.03733772 0.900914345 1.162608827 1.035944415 0.908795723 0.89605571 1.208888883 0.944624313 1.037622427 1 16.98746263 -0.717233063 8.117818108 1.000004425 1.013266403 0.001685437 0.102100657 0 0 0.0945011 0.022274123 0.191763937 0.717233063 0.013261978 YLGDAFGS(ph)PQTDHGFETDPDPFLLDEPAPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLGDAFGSPQTDHGFETDPDPFLLDEPAPR 30 0 Q9H8N7 Q9H8N7 ZNF395 Zinc finger protein 395 1 YLGDAFGS(0.825)PQT(0.175)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.964)PQT(0.036)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.985)PQT(0.015)DHGFETDPDPFLLDEPAPR;YLGDAFGS(0.955)PQT(0.045)DHGFETDPDPFLLDEPAPR 230.29 1.76E-35 564294000 205110 217135 236060 251359 275670 286431 247136 268286 244612 287012 TRUE FALSE 213207.9012 254426.2472 242211.9175 301077.06 228811.7119 219911.7412 227764.8346 264690.065 235808.4619 343246.5062 0.621150973 0.741234776 0.705650059 0.877145301 0.666610461 0.640681659 0.663560533 0.771136953 0.6869945 1 18.38888551 -1.869282419 2.452779565 1.137010543 0.713250028 0.603737169 0.070806438 12091598.45 6872410.305 9641597.78 0.016929416 0.013511936 1.869282419 -0.423760515 YLGEGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLGEGPR 7 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 ; 106.76 0.01775 213884000 282340 354570 327950 355220 392620 400960 352450 368910 346570 365130 FALSE TRUE 293487.0012 415464.6393 336496.6464 425481.4558 325882.5926 307843.1166 324824.048 363965.3649 334097.0134 436670.2327 0.672102148 0.951437969 0.770596714 0.974377056 0.746289919 0.704978479 0.743865791 0.833501662 0.765101416 1 18.73618466 -1.492717552 3.156463842 1.004960257 0.800944068 0.297505885 0.093833742 23656138.29 32620226.07 1044271.987 0.021473107 0.032157513 1.492717552 -0.204016189 YLGGS(ph)MDLSTFDFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLGGSMDLSTFDFR 14 0 O95983-2;O95983 O95983-2 MBD3 Methyl-CpG-binding domain protein 3 1 YLGGS(1)MDLSTFDFR;YLGGS(1)MDLSTFDFR 192.46 3.90E-07 55711000 51800 60686 79999 55300 99370 68149 60253 70180 83004 81060 TRUE FALSE 53845.104 71108.34843 82083.83966 66238.17495 82479.12289 52322.42756 55530.21242 69239.35189 80016.70225 96942.15501 0.555435393 0.73351318 0.84673009 0.683275247 0.850807607 0.539728331 0.572818011 0.714233678 0.825406679 1 16.56483653 0.983959008 2.564027655 0.998334592 0.689016142 0.475023027 0.10348713 0.252374448 3.811883537 0.100693487 0.027101317 9.637380553 -0.983959008 -0.30931845 YLGHVEVDESR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLGHVEVDESR 11 0 P49757-3;P49757;P49757-8;P49757-7;P49757-6;P49757-5;P49757-4;P49757-2;G3V4S6;G3V433;G3V3R1 P49757-3 NUMB Protein numb homolog 0 134.75 0.00013437 135310000 152270 214140 206440 200920 245820 247170 226880 216320 245550 222520 FALSE TRUE 158281.7372 250916.8792 211819.996 240661.3763 204035.6042 189768.5134 209096.5528 213420.5842 236712.7035 266118.5336 0.594779082 0.942876379 0.795961082 0.904339029 0.766709486 0.713097697 0.785727134 0.801975651 0.889501006 1 18.02170946 0.990545578 2.346159027 0.999406344 0.793181686 0.356775618 0.090207483 0.321731831 3.94157378 0.080665559 0.022017847 9.784656367 -0.990545578 -0.206224658 YLGQDYEQLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLGQDYEQLR 10 0 P07384;E9PRM1;E9PJJ3;E9PLC9;E9PMC6;E9PJA6;E9PSA6;E9PQB3;E9PLX0;E9PIA9 P07384 CAPN1 Calpain-1 catalytic subunit 0 ;;; 153.05 3.94E-05 651860000 511395 654000 551131 517122 864310 794540 622100 557940 537124 903380 FALSE TRUE 531585.2695 766319.4126 565493.9266 619407.1881 717394.8949 610020.1264 573338.1764 550461.7269 517793.0122 1080380.015 0.492035453 0.709305432 0.523421314 0.573323441 0.664020886 0.564634775 0.530681953 0.509507506 0.479269336 1 20.04310743 -1.231537153 5.197367326 1.00004438 0.562308273 0.779194219 0.070153006 3.59E-05 5.31E-06 0.067609509 0.015934103 0.058676317 1.231537153 -0.437736107 YLGS(ph)PITTVPK ddPTM_MDA-MB-175_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(0.947)PIT(0.043)T(0.01)VPK 83.182 0.01773 65571000 190650 164100 158380 143660 212700 228760 211000 196300 211500 199470 TRUE FALSE 198177.0092 192282.8985 162507.5129 172075.5192 176545.33 175633.9569 194461.2687 193668.9196 203888.1563 238552.3274 0.830748588 0.806040757 0.681223758 0.721332385 0.740069619 0.736249186 0.815172381 0.811850891 0.854689445 1 17.86394624 0.912907913 0.799823895 0.999306239 0.75086083 0.755098086 0.042077547 0.377369173 0.521101224 0.043105731 0.015618652 8.182912603 -0.912907913 -0.248445409 YLHDESGLNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLHDESGLNR 10 0 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;;; 229.17 1.75E-09 1542190000 840490 982840 994180 1036120 1017200 1208360 1225100 994430 950310 799150 FALSE TRUE 873673.1942 1151635.125 1020089.148 1241061.443 844296.7073 927736.7029 1129073.461 981101.2924 916108.5287 955728.1418 0.91414405 1.204981913 1.067342378 1.298550696 0.883406766 0.970711923 1.181375133 1.026548502 0.958545101 1 19.86624077 3.224188848 24.99939102 1.016859509 1.123384451 0.192614434 0.116209733 426.3496655 741624.6997 0.033108987 0.0397386 1675.671364 -3.224188848 0.106524942 YLHDESGLNRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YLHDESGLNRR 11 1 Q15019-2;Q15019-3;Q15019;B5MCX3;C9J2Q4;C9J938;C9JB25;C9IY94;H7C310 Q15019-2 2-Sep Septin-2 0 ;;;;; 199.68 3.21E-08 2976270000 1353114 1537507 1660875 1454480 1680560 1971000 1605730 1539084 1586171 1502768 FALSE TRUE 1406535.986 1801561.867 1704158.767 1742171.803 1394899.011 1513265.121 1479868.687 1518455.096 1529085.016 1797206.617 0.782623418 1.002423344 0.948226403 0.969377581 0.776148384 0.842009542 0.82342713 0.844897343 0.850812033 1 20.77732485 3.252269899 24.99996276 0.845512578 0.932757286 0.155173114 0.076275917 330.4398359 602579.7869 0.019729691 0.026573588 1787.59816 -3.252269899 0.087244708 YLIT(ph)T(ph)FS(ph)LAHELQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLITTFSLAHELQK 14 0 Q9NX02;J3KN39;Q9NX02-2;Q9NX02-3;A0A0G2JNC8;A0A0G2JP37;A0A0G2JPB6;A0A0G2JLX3;A0A0G2JPQ2;Q9NX02-4;Q9NX02-5;A0A0G2JLQ8;A0A0G2JMG8;F5H5B1;K7ELX1;K7EJ90;F5H7Q5 Q9NX02 NLRP2 "NACHT, LRR and PYD domains-containing protein 2" 3 Y(0.717)LIT(0.761)T(0.761)FS(0.761)LAHELQK 42.743 0.082144 0 6034.3 6844.2 7642.9 6633.8 7378.8 8466.3 7270.7 7233.2 7572.5 7464.7 TRUE FALSE 6272.538823 8019.63811 7842.080253 7945.94584 6124.554212 6500.130133 6700.803536 7136.250785 7299.967204 8927.265045 0.702627153 0.898330908 0.878441517 0.890076166 0.686050451 0.72812111 0.75059982 0.799377049 0.817715971 1 13.12400254 0.664964441 2.549666117 0.999983057 0.794142283 0.418668449 0.073144664 2.683396134 19.12200488 0.073784562 0.019654098 4.623431639 -0.664964441 -0.205840773 YLKDVTLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 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 0 131.82 0.0012216 0 883420 954810 1029700 788400 1889500 1640100 1257100 1332900 1458000 1544700 FALSE TRUE 918298.1037 1118791.19 1056534.828 944343.1669 1568323.465 1259211.631 1158565.217 1315034.656 1405526.865 1847354.39 0.497088219 0.605618065 0.571917783 0.511186793 0.848956472 0.681629707 0.627148328 0.711847528 0.760832287 1 20.81702922 -5 0.077101165 2.214693195 0.261148815 0.70978297 0.079983398 149.027222 0.818133567 30.97557766 3.150947561 1.00E-05 5 -1.95354438 YLLEGTAETHELAEGSTADVLHSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLLEGTAETHELAEGSTADVLHSR 24 0 Q709C8-3;Q709C8;Q709C8-4;Q709C8-2;A0A3B3IU50 Q709C8-3 VPS13C Vacuolar protein sorting-associated protein 13C 0 258.4 3.59E-44 57056000 46782 64646 68525 59382 72290 73123 70451 62135 58505 64188 FALSE TRUE 48628.98948 75748.44762 70310.81779 71127.58236 60002.17162 56141.29144 64928.86653 61302.18196 56399.41648 76764.40965 0.633483534 0.986765195 0.915929897 0.926569783 0.781640501 0.731345316 0.845819916 0.798575567 0.734707877 1 16.22814997 3.225347736 24.89152063 0.803308252 0.877924315 0.035241389 0.11237433 526.3136549 991511.3865 0.030740035 0.036947265 1680.148759 -3.225347736 0.074616063 YLLGDAPVS(ph)PSSQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.997)PS(0.002)S(0.001)QK;YLLGDAPVS(0.999)PS(0.001)SQK;YLLGDAPVS(0.742)PS(0.23)S(0.028)QK;YLLGDAPVS(0.992)PS(0.007)S(0.001)QK;YLLGDAPVS(0.944)PS(0.056)SQK;YLLGDAPVS(0.865)PS(0.133)S(0.002)QK;YLLGDAPVS(0.525)PS(0.474)S(0.001)QK 288.45 2.01E-34 3385956000 6949340 5247940 6405370 5001480 7816570 7838130 7226040 6464790 6857190 4871180 TRUE FALSE 7223705.309 6149232.872 6572299.204 5990757.816 6487912.223 6017843.096 6659644.103 6378140.064 6610401.071 5825594.457 1.239994538 1.055554573 1.128176575 1.028351331 1.113691018 1.03300069 1.143169878 1.094847936 1.134717001 1 22.47397384 -4.999984799 0.011019034 4.14E-07 2.002322767 0.216238431 0.059514442 20081.45625 16.80390699 1801.222772 1291.611259 1.00E-05 4.999984799 2.002322353 YLLGDAPVSPS(ph)SQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 YLLGDAPVS(0.395)PS(0.599)S(0.006)QK 316.32 6.93E-56 1473800000 2058400 1468300 1887300 1530800 2355400 2348900 2288300 2083600 2109400 1506300 TRUE FALSE 2139667.221 1720469.103 1936484.588 1833587.671 1955029.949 1803403.573 2108937.067 2055672.75 2033483.106 1801430.645 1.187759977 0.955057086 1.074970382 1.017850826 1.085265178 1.001095201 1.170701227 1.141133441 1.128815651 1 20.78071168 2.236775891 24.99928649 1.125723937 1.049960884 0.11400911 0.0716677 71.28739551 998526.0226 0.023916313 0.018557417 172.4947536 -2.236775891 -0.075763053 YLLGDMEGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLLGDMEGR 9 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 ;;; 119.29 0.0019799 429850000 740740 866780 860680 886200 989080 1078310 932830 946800 806070 887610 FALSE TRUE 769984.9872 1015642.722 883110.0279 1061487.715 820956.5349 827888.8444 859712.3471 934109.6947 777059.6982 1061520.185 0.725360665 0.956781356 0.831929567 0.999969412 0.773378167 0.779908716 0.809887894 0.879973558 0.732025362 1 20.01770037 4.778119988 22.75462904 0.855632748 0.7253595 0.166114202 0.091066821 13701.11632 7880379.031 0.020573572 5.522251309 59995.6811 -4.778119988 -0.130273248 YLLHGLECVVAMHQAQLISK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLLHGLECVVAMHQAQLISK 20 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 0 ; 226.45 2.55E-25 600620000 403890 342980 503710 420800 537320 579000 592380 478350 557340 417690 FALSE TRUE 419835.8891 401884.147 516837.0964 504032.984 445986.5383 444536.0248 545947.7077 471938.5007 537281.4423 499528.3583 0.840464574 0.804527191 1.034650161 1.009017758 0.892815254 0.889911488 1.092926355 0.944768185 1.075577459 1 18.93020706 4.244882911 24.99310832 0.987068485 0.822495814 0.518468117 0.065353634 115.8743913 458058.8481 0.015911137 0.04138315 17574.49727 -4.244882911 -0.164572671 YLLSQS(ph)SPAPLTAAEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLS(0.003)QS(0.899)S(0.098)PAPLTAAEEELR 74.12 0.017067 17651000 20317 20297 19591 24650 23301 25763 22231 23579 23367 22069 TRUE FALSE 21119.13085 23782.85186 20101.55755 29525.69643 19340.30434 19779.93369 20488.47613 23262.96207 22526.02623 26392.99801 0.800179307 0.901104598 0.761624638 1.1186943 0.732781639 0.749438684 0.776284533 0.881406578 0.853484937 1 14.68786762 0.516501414 1.520124976 0.999861259 0.840523187 0.166321196 0.106996988 4.459240406 11.99511005 0.099529154 0.028721891 3.284743141 -0.516501414 -0.159338072 YLLSQSS(ph)PAPLTAAEEELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YLLSQSSPAPLTAAEEELR 19 0 Q12792;Q12792-3;Q12792-4;F8VS81 Q12792 TWF1 Twinfilin-1 1 YLLSQS(0.134)S(0.866)PAPLTAAEEELR;YLLS(0.002)QS(0.118)S(0.88)PAPLTAAEEELR;YLLSQS(0.006)S(0.994)PAPLTAAEEELR;YLLSQS(0.002)S(0.998)PAPLTAAEEELR;YLLSQS(0.017)S(0.983)PAPLTAAEEELR;YLLSQS(0.059)S(0.941)PAPLTAAEEELR 341.19 8.44E-76 469621000 512702 582868 550554 550398 601408 682750 570049 582454 576184 672803 TRUE FALSE 532943.8709 682971.0449 564901.8895 659265.0816 499180.883 524191.6597 525367.0698 574647.1568 555447.2504 804625.8663 0.662349911 0.848805729 0.702067772 0.819343634 0.620388809 0.651472544 0.652933359 0.714179323 0.690317418 1 19.61795859 -1.178118083 5.416120479 1.000010323 0.708125065 0.614032506 0.069713503 8.63E-06 1.31E-06 0.067008884 0.015793587 0.066356263 1.178118083 -0.291885258 YLMAS(ph)DPNLQVLGAAYIQHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLMASDPNLQVLGAAYIQHK 20 0 Q9Y446;Q9Y446-2;E9PKC4 Q9Y446 PKP3 Plakophilin-3 1 YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK;YLMAS(1)DPNLQVLGAAYIQHK 337.4 2.77E-80 3438489000 2779930 2591897 2890669 2301689 3378566 3196702 2814858 2953527 2788380 2234089 TRUE FALSE 2889683.783 3037035.148 2966002.209 2756956.214 2804278.558 2454316.407 2594222.075 2913939.802 2688026.748 2671815.965 1.081542973 1.13669324 1.110107226 1.03186606 1.049577738 0.918594858 0.97095837 1.09062145 1.006067328 1 21.34938921 3.613907847 2.247530713 1.009524444 1.114302753 0.521113889 0.04429262 0.278642432 2.749088897 0.014016032 0.0250493 4110.624886 -3.613907847 0.104778309 YLMDEGAHLHIYDPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLMDEGAHLHIYDPK 15 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;; 189.1 1.57E-07 970390000 1789510 1187850 1627140 1300010 2078330 1957430 2011420 1644290 1798580 1190840 FALSE TRUE 1860161.237 1391853.997 1669544.605 1557148.098 1725056.209 1502846.548 1853759.645 1622250.982 1733849.457 1424162.298 1.306144138 0.977314172 1.172299398 1.093378262 1.211277824 1.055249496 1.30164915 1.139091369 1.217452154 1 20.44168213 3.249685623 24.93213524 1.164982352 1.128358695 0 0.110037048 1005.937147 2254381.504 0.028046967 0.037619984 1776.992613 -3.249685623 -0.036623657 YLMEEDEDAYKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 YLMEEDEDAYKK 12 1 P46777;A0A2R8Y6J3 P46777 RPL5 60S ribosomal protein L5 0 ;;;;;;;;; 229.54 1.27E-11 12105400000 10265740 4547349 6754860 4684275 9872520 8933330 9447800 7146390 8075350 3723609 FALSE TRUE 10671039.34 5328320.817 6930897.201 5610810.614 8194392.577 6858699.493 8707256.749 7050604.331 7784719.731 4453178.891 2.396274572 1.196520721 1.556393168 1.259956259 1.840122029 1.540180546 1.955290134 1.583274444 1.748126433 1 22.08640414 YLMGER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLMGER 6 0 P00338;P00338-3;P00338-4;P00338-2;P00338-5 P00338 LDHA L-lactate dehydrogenase A chain 0 103.28 0.080999 2292900000 716190 1138300 1030900 1061300 1558600 1626600 1075500 1122600 965380 1781400 FALSE TRUE 744465.7342 1333794.17 1057766.101 1271221.972 1293669.729 1248846.801 991199.4997 1107553.383 930636.1624 2130431.223 0.349443684 0.626067697 0.496503285 0.596697025 0.607233744 0.586194376 0.465257685 0.519872865 0.436829949 1 21.02271405 -1.005220456 4.75447341 1.000006349 0.526737937 0.749557437 0.083086161 7.34E-06 1.54E-06 0.075996003 0.017912096 0.098805141 1.005220456 -0.473268411 YLNEYGAPDAGGLEHVPLGWSYWYALEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLNEYGAPDAGGLEHVPLGWSYWYALEK 28 0 H7C3P4;F6S8M0;P15586-2;P15586;F5H4C6 H7C3P4 GNS N-acetylglucosamine-6-sulfatase 0 64.176 0.016831 69116000 78773 109200 97675 109490 132490 168580 120760 106010 108800 130040 FALSE TRUE 81883.01887 127954.2505 100220.4907 131146.7952 109969.3971 129429.8499 111294.5157 104589.1093 104884.3093 155518.8482 0.52651508 0.82275719 0.644426652 0.843285535 0.707112986 0.832245424 0.715633616 0.672517258 0.674415419 1 17.24672991 -2.037208375 2.357810029 1.34260017 0.720036076 0.457985817 0.09275011 10454659.94 3835787.854 19334228.05 0.021387403 0.009178921 2.037208375 -0.622564094 YLNFFTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLNFFTK 7 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 ; 114.93 0.013479 306190000 316210 306710 323280 308770 440820 440140 388770 318080 346220 356510 FALSE TRUE 328694.215 359385.0566 331704.9424 369843.7844 365889.5739 337924.1554 358297.1915 313816.6579 333759.6098 426361.3087 0.770928807 0.842911984 0.777990253 0.867442183 0.858167865 0.792576973 0.840360474 0.736034559 0.782809329 1 18.701717 -2.176486665 2.386113856 1.509334847 0.806871767 0.666551848 0.040801651 4263277.621 684416.8497 11805174.19 0.01096087 0.0066606 2.176486665 -0.70246308 YLPDTLLLEECGLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLPDTLLLEECGLLR 15 0 P21964-2;P21964;E7EMS6 P21964-2 COMT Catechol O-methyltransferase 0 ;;;; 242.82 1.41E-17 596781000 127121.7 173713.6 158226.9 186559.8 163494.8 207925.7 146913.4 135087.1 127093 175487.6 FALSE TRUE 132140.5629 203547.5595 162350.423 223460.7716 135704.0123 159638.1073 135397.9438 133276.4784 122518.9478 209871.0353 0.629627441 0.969869707 0.773572317 1.064752796 0.646606675 0.760648591 0.64514831 0.635039886 0.583782072 1 17.67914355 3.179411271 24.99999964 0.687710977 0.861213524 0.172157268 0.153123774 103.3979856 43701.41586 0.041078136 0.049097787 1511.510857 -3.179411271 0.173502547 YLPENDLKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLPENDLKR 9 1 O00743;O00743-2 O00743 PPP6C "Serine/threonine-protein phosphatase 6 catalytic subunit;Serine/threonine-protein phosphatase 6 catalytic subunit, N-terminally processed" 0 ;; 147.95 0.00014621 1478900000 773500 607250 708650 618540 928120 844400 797510 719160 735180 577700 FALSE TRUE 804038.3773 711540.4638 727118.0012 740885.3658 770358.4939 648300.897 734999.0823 709520.8365 708721.0154 690889.2543 1.16377317 1.029890767 1.05243785 1.072364871 1.11502457 0.938357187 1.063845005 1.026967538 1.025809869 1 19.39809495 2.770806478 24.99917876 1.018229132 1.080842618 0.404588519 0.045218524 784.2316061 607988.3704 0.013390157 0.014201553 589.9381442 -2.770806478 0.062613486 YLPHSAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 ;;;;;; 194.44 0.00016534 6176130000 3302140 4532200 4322610 4309000 5285550 5636170 4216470 4367940 4019840 5074990 FALSE TRUE 3432511.037 5310570.094 4435260.768 5161307.339 4387114.099 4327254.934 3885972.064 4309394.909 3875166.744 6069337.124 0.565549576 0.874983542 0.730765268 0.850390617 0.722832495 0.712969942 0.640263011 0.710027277 0.638482698 1 22.53310753 -1.049707975 4.658801091 1.000009424 0.721283274 0.479998972 0.088461177 9.18E-06 1.87E-06 0.082121662 0.019355538 0.089185043 1.049707975 -0.27872615 YLQAHTQSVYNYHLS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YLQAHTQSVYNYHLSPR 17 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR;YLQAHTQSVYNYHLS(1)PR 200.23 4.20E-14 1275270000 466948 752494 716234 798764 729594 911778 700815 782688 674549 853239 TRUE FALSE 485383.4676 881728.9909 734899.6464 956757.1351 605577.8725 700031.3776 645883.2891 772197.3476 650272.1133 1020414.846 0.475672683 0.864088752 0.720196937 0.937615852 0.593462429 0.686026257 0.632961478 0.756748445 0.637262498 1 19.96072436 -2.007163341 2.869503616 1.304206111 0.709855821 0.335875017 0.125740935 94397427.78 104595017.7 189214643.2 0.02920023 0.009836411 2.007163341 -0.594350291 YLQDLLAWVEENQHR ddPTM_MDA-MB-175_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 ; 256.26 9.49E-25 7248300000 1351000 1609470 1459280 1581800 1726560 1947400 1587180 1668280 1601560 1623150 FALSE TRUE 1404338.523 1885883.953 1497310.036 1894675.319 1433079.948 1495145.863 1462772.684 1645919.435 1543920.168 1941175.165 0.723447604 0.971516629 0.771342052 0.976045517 0.738253803 0.770227175 0.753550071 0.847898461 0.795353349 1 20.88849888 -1.625701599 2.625551606 1.018720422 0.82001001 0.290075251 0.085999566 24312710.45 21318786.13 3096722.714 0.020245358 0.023675459 1.625701599 -0.198710412 YLQEEVNINR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLQEEVNINR 10 0 Q9UHD8;Q9UHD8-5;Q9UHD8-2;Q9UHD8-7;Q9UHD8-3;Q9UHD8-8;Q9UHD8-9;Q9UHD8-4;K7EL40;K7EK18;K7EIE4;K7EQD7;K7ER52 Q9UHD8 9-Sep Septin-9 0 170.47 1.00E-05 53514000 49382 54401 54263 57951 59456 67235 56928 49065 51658 60516 FALSE TRUE 51331.63949 63743.94857 55677.13836 69413.53483 49349.69036 51620.69021 52465.83461 48407.36393 49798.83867 72372.95155 0.709265525 0.880770332 0.76930866 0.959108802 0.681880306 0.71325943 0.724937058 0.668859883 0.688086331 1 16.14316299 3.196106561 24.99963638 0.722903785 0.828960755 0.100704883 0.109637385 225.3332427 132689.7706 0.029157212 0.034849794 1570.748163 -3.196106561 0.10605697 YLQEVIDVLETDGHFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLQEVIDVLETDGHFR 16 0 Q02818;H7BZI1;C9JKZ2;C9JBD3;C9J3C1 Q02818 NUCB1 Nucleobindin-1 0 ;;; 194.58 1.90E-10 345615000 196769 255259 231674 307147 362179 381521 287878 260752 236419 351450 FALSE TRUE 204537.5921 299097.7476 237711.6148 367899.7599 300615.9429 292918.5298 265313.3701 257257.0459 227910.3264 420309.8986 0.486635201 0.711612428 0.565562733 0.875305961 0.715224514 0.696910853 0.631232743 0.612065161 0.542243538 1 18.68109391 5.205477806 1.854157254 0.689886162 2.36E-16 0.180456293 0.134089774 8.366936893 8.925383701 0.032681486 15.50154081 160501.0235 -5.205477806 -0.689886162 YLQLAEELIRPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 ; 193.06 1.99E-06 67845000 55529 59198 65312 66630 68292 80991 68598 66710 61351 75206 FALSE TRUE 57721.3278 69364.796 67014.08437 79809.21513 56683.75023 62182.06768 63221.10951 65815.86157 59142.98949 89941.17579 0.641767547 0.771224029 0.745087929 0.88734903 0.630231368 0.69136374 0.7029162 0.731765634 0.65757412 1 16.45669412 -1.325421762 6.004637193 1.000024755 0.721857869 0.585374766 0.071199084 2.30E-05 2.58E-06 0.067147985 0.015825525 0.047269198 1.325421762 -0.278166887 YLQSLLAEVERR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLQSLLAEVERR 12 1 O95232;J3KPP4;D6RDI2;D6RHH0;U3KQT3 O95232 LUC7L3 Luc7-like protein 3 0 166.6 8.25E-05 167450000 76047 107260 86709 72455 119280 118460 86715 79972 67380 135600 FALSE TRUE 79049.39428 125681.0706 88968.70777 86786.38274 99004.82821 90949.46028 79918.05171 78900.10615 64955.00696 162168.2238 0.487453044 0.775004299 0.548619857 0.535162689 0.610506953 0.560834041 0.492809564 0.486532468 0.400540904 1 17.30713163 -1.767637688 4.388772628 1.043319536 0.546612912 0.680135911 0.093767709 0.037208757 0.001970007 0.084996796 0.021796382 0.017075063 1.767637688 -0.496706624 YLQTYGEWNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLQTYGEWNR 10 0 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 0 90.149 0.023061 0 94093 71492 95213 67830 111060 123240 114840 94374 101850 71538 FALSE TRUE 97807.8643 83770.19487 97694.329 81246.57155 92182.06087 94619.37772 105838.5407 93109.07089 98184.4384 85554.50142 1.143222889 0.979144212 1.141895837 0.949646952 1.077465935 1.105954405 1.237089095 1.088301251 1.147624459 1 16.38455614 2.753730433 3.759839303 1.129500581 1.051145473 0.107998398 0.079523286 0.385344195 12.19112008 0.02403492 0.024327569 567.1924387 -2.753730433 -0.078355108 YLS(ph)FHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLSFHFK 7 0 P53004 P53004 BLVRA Biliverdin reductase A 1 YLS(1)FHFK;YLS(1)FHFK 79.474 0.020951 501240000 534720 522020 651140 457010 1111550 719110 720310 668640 718080 544830 TRUE FALSE 555831.1585 611672.8742 668109.2433 547405.214 922609.128 552107.6007 663850.22 659677.9745 692236.4411 651579.0071 0.853052588 0.938754729 1.025369504 0.840121011 1.415958952 0.84733792 1.018833039 1.012429755 1.062398318 1 19.3135806 4.61735929 1.151469231 1.034263696 0.792376075 0.128190815 0.148297694 2.72868381 3.535252439 0.041612933 0.757086651 41434.23163 -4.61735929 -0.241887621 YLS(ph)FTPPEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.999)FT(0.001)PPEK;YLS(1)FTPPEK;YLS(1)FTPPEK;YLS(1)FTPPEK;YLS(0.999)FT(0.001)PPEK 189.58 3.99E-05 2554930000 4911230 3628160 4560880 4352290 5917190 5576230 6051510 4603240 4685990 2932970 TRUE FALSE 5105129.153 4251268.257 4679740.28 5213159.972 4911388.157 4281235.091 5577176.834 4541541.097 4517342.135 3507629.316 1.455435764 1.212006137 1.334160442 1.486234577 1.400201593 1.220549467 1.590013177 1.294760845 1.287861894 1 21.74206486 0.779391492 1.779880321 1.000938413 1.375530841 0.509885247 0.110798877 0.614405733 3.310449898 0.100891552 0.028480772 6.017159061 -0.779391492 0.374592428 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 YLS(0.995)FT(0.005)PPEKDGFPSGTPALNAK;YLS(0.962)FT(0.038)PPEKDGFPSGTPALNAK 285.84 2.77E-46 11683000000 5448500 3297200 4822100 3194700 7446400 5640700 5194600 4262500 5154500 3172600 TRUE FALSE 5663610.987 3863468.451 4947767.887 3826602.125 6180663.588 4330732.911 4787433.678 4205368.16 4968990.552 3794210.227 1.492698256 1.01825366 1.304031035 1.008537191 1.62897236 1.141405629 1.261773437 1.108364563 1.309624469 1 21.85536819 -4.373658492 0.244223731 5.01E-07 1.263980321 0.139280482 0.187941248 250.5600782 3.306828686 123.9769076 0.265675013 4.23E-05 4.373658492 1.26397982 YLSDSCS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YLSDSCSPR 9 0 P83436 P83436 COG7 Conserved oligomeric Golgi complex subunit 7 1 YLSDSCS(1)PR;YLSDSCS(1)PR;YLSDSCS(1)PR;YLSDS(0.002)CS(0.998)PR;YLSDSCS(1)PR 145.75 0.00010115 2458780000 2313210 2962480 2664140 3078910 2972600 3406640 2506710 2693960 2585930 3103930 TRUE FALSE 2404537.317 3471262.895 2733569.677 3687909.208 2467318.514 2615499.488 2310227.52 2657851.873 2492862.884 3712085.655 0.647759115 0.935124676 0.736397252 0.993487099 0.664671762 0.704590285 0.622352967 0.715999608 0.671553169 1 21.82379857 5.029649 16.41503963 0.764947236 0.288372936 0.069161435 0.135057511 49044693.42 737189851 0.031520853 648126624.9 107065.3646 -5.029649 -0.4765743 YLSEVASGDNK ddPTM_MDA-MB-175_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 ; 229.48 5.82E-12 695980000 923520 588160 778440 668570 1042830 948740 1031510 805350 858370 564890 FALSE TRUE 959981.2827 689171.9048 798726.7859 800811.1505 865570.1291 728409.5133 950657.5509 794555.6005 827477.4314 675569.38 1.420995846 1.020134904 1.18230164 1.185386985 1.281245353 1.078215702 1.407194552 1.176127314 1.22485929 1 19.36574441 -0.969615507 4.830353579 0.999997737 1.21466054 0.230670738 0.120011425 2.65E-06 5.66E-07 0.105432104 0.024850323 0.107246837 0.969615507 0.214662803 YLSFHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLSFHFK 7 0 P53004 P53004 BLVRA Biliverdin reductase A 0 97.071 0.024502 0 119090 252280 224050 216260 730830 455050 286420 248170 236140 821680 FALSE TRUE 123791.7652 295607.1275 229888.9271 259035.5825 606603.7776 349371.5338 263969.652 244843.6871 227641.3675 982672.464 0.125974594 0.30081959 0.233942575 0.263603176 0.617300067 0.355532028 0.268624248 0.249161034 0.231655385 1 19.9063511 -1.129703347 4.1560522 1.000155009 0.298246514 0.75205331 0.121580193 9747161.447 5298988.551 14010.86318 0.029445059 0.074181678 1.129703347 -0.701908496 YLSHSEFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLSHSEFK 8 0 Q92616 Q92616 GCN1L1 Translational activator GCN1 0 ; 155.75 0.00040391 637600000 784040 698300 811560 716440 1064680 1087120 837780 772820 848310 717830 FALSE TRUE 814994.5046 818227.593 832709.9203 858149.6936 883706.0739 834652.8555 772112.6145 762461.612 817779.4888 858475.0448 0.949351422 0.953117505 0.969987334 0.999621013 1.029390521 0.972250574 0.899400185 0.888158155 0.952595528 1 19.71141667 2.328366424 6.479305373 0.920945369 0.981205122 0.223271793 0.036619558 0.231636338 13.79895528 0.013184337 0.010958828 212.9935363 -2.328366424 0.060259753 YLSLGEHDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLSLGEHDR 9 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 0 145.89 9.61E-05 63801000 55461 142350 126570 144820 98677 171540 101540 124840 102220 125370 FALSE TRUE 57650.64311 166797.5052 129868.5182 173464.9638 81903.91879 131702.4347 93581.02947 123166.724 98541.12217 149933.8511 0.384507185 1.11247396 0.866172096 1.156943295 0.546267025 0.878403601 0.624148775 0.821473757 0.657230648 1 17.19396662 3.223658464 24.99955985 0.747767465 0.895638372 0.064715723 0.229700254 579.3883213 971968.4639 0.061778274 0.074123857 1673.626192 -3.223658464 0.147870906 YLSVPPS(ph)PNISTSES(ph)RSPPEGDTTLFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 Y(0.004)LS(0.047)VPPS(0.866)PNIS(0.128)T(0.123)S(0.118)ES(0.367)RS(0.328)PPEGDT(0.007)T(0.007)LFLS(0.006)R;YLS(0.001)VPPS(0.961)PNIS(0.106)T(0.115)S(0.108)ES(0.384)RS(0.325)PPEGDTTLFLSR;YLSVPPS(0.963)PNIS(0.036)T(0.035)S(0.034)ES(0.558)RS(0.374)PPEGDTTLFLSR 92.846 0.0007903 173456000 153320 174059 164653 144569 160824 183039 141989 161893 163412 142328 TRUE FALSE 159373.192 203952.2793 168943.9924 173164.3167 133487.1939 140530.9662 130859.5312 159723.0891 157530.834 170214.4466 0.936308258 1.19820781 0.992536156 1.017330316 0.784229521 0.825611275 0.768792155 0.938363884 0.925484512 1 17.37699396 3.363820033 5.970094389 0.866427654 1.049370024 0.43225235 0.091007905 0.18083071 8.786044273 0.024961107 0.033923595 2311.106895 -3.363820033 0.18294237 YLSVPPSPNISTSESRS(ph)PPEGDTTLFLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLSVPPSPNISTSESRSPPEGDTTLFLSR 29 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 YLSVPPSPNISTSES(0.018)RS(0.982)PPEGDTTLFLSR;YLSVPPSPNIS(0.002)T(0.002)S(0.002)ES(0.03)RS(0.89)PPEGDT(0.069)T(0.006)LFLSR;YLSVPPS(0.003)PNIS(0.006)T(0.004)S(0.013)ES(0.028)RS(0.945)PPEGDTTLFLSR 183.9 5.16E-18 964720000 226977 256077 239063 227026 234477 269239 211811 239657 251177 243351 TRUE FALSE 235938.2272 300056.2327 245293.1782 271931.0652 194620.6833 206712.3226 195208.7004 236444.7899 242137.1888 291030.9692 0.810698009 1.031011351 0.842842186 0.934371575 0.668728431 0.710276034 0.670748893 0.812438589 0.831998015 1 18.15081316 3.257420236 24.90414105 0.765002977 0.90933025 0.232002223 0.106156539 281.665872 371937.6265 0.028005386 0.037855842 1808.923646 -3.257420236 0.144327273 YLTESYGTGQDIDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YLTESYGTGQDIDDR 15 0 Q9UM54-1;A0A590UJ40;E7EW20;Q9UM54;Q9UM54-2;A0A0A0MRM8;A0A1Y0BRN3;Q9UM54-5;Q9UM54-4;Q9UM54-6;A0A0D9SGC1;A0A590UJ75;A0A590UK22;A0A590UKB0;A0A590UK86;A0A5F9ZI03;A0A590UJY4;A0A590UK71 Q9UM54-1 MYO6 Unconventional myosin-VI 0 ;; 232.6 8.86E-14 620530000 201767 213215 209452 204924 319489 259994 295691 240050 219386 191309 FALSE TRUE 209732.917 249833.0177 214910.4912 245457.3556 265182.3739 199614.3337 272513.9668 236832.5224 211490.3407 228792.3357 0.916695554 1.091964103 0.93932557 1.072839065 1.159052698 0.872469496 1.191097446 1.035141853 0.924376859 1 17.8036792 4.756582334 23.36906818 1.037558494 0.916695301 0.110429042 0.096783466 3201.004021 4150630.156 0.02162003 0.62432013 57092.93033 -4.756582334 -0.120863193 YLTVAAVFR ddPTM_MDA-MB-175_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 ; 153.71 0.00018014 428320000 138278 147647 122583 107311 557600 254043 135206 113648 123590 620770 FALSE TRUE 143737.3222 173004.2237 125777.6137 128536.7955 462819.3512 195045.3633 124608.2004 112124.7345 119142.02 742397.9961 0.193612217 0.233034336 0.169420734 0.173137315 0.623411369 0.262723451 0.167845551 0.151030492 0.16048268 1 19.50183329 -1.562180991 2.998919154 1.037120482 0.235976838 0.745727913 0.133626331 46528006.22 51083790.13 13852884.32 0.034592692 0.027404319 1.562180991 -0.801143644 YLVEFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLVEFR 6 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 0 110.23 0.067187 222680000 463270 547040 522390 598610 608060 663520 626290 586300 568280 583600 FALSE TRUE 481560.2573 640989.8646 536003.9125 717013.2713 504702.1784 509427.5357 577199.7533 578441.6075 547827.7138 697945.2463 0.689968532 0.918395631 0.767974158 1.027320231 0.723125748 0.729896132 0.826998617 0.828777917 0.78491503 1 19.41275434 -1.459844218 4.672693046 1.000550992 0.815868628 0.260876713 0.095188993 0.000512558 5.93E-05 0.086459792 0.020318688 0.034686125 1.459844218 -0.184682365 YLVLDEADR ddPTM_MDA-MB-175_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 ;;; 157.68 0.00015813 1385190000 1865400 2367820 2174320 2261380 2429650 2664540 2244050 2169750 2042300 2536090 FALSE TRUE 1939047.432 2774474.666 2230984.565 2708674.214 2016658.961 2045740.966 2068155.497 2140668.05 1968798.022 3032988.279 0.639319131 0.914766036 0.735573092 0.893071112 0.664908261 0.674496826 0.681887072 0.705795029 0.649128134 1 21.53230849 4.065206631 24.99999856 0.73439586 0.789074116 0 0.12377827 234.6194348 89947.28759 0.02898778 0.062620758 11620.01344 -4.065206631 0.054678256 YLYPNIDKDHAFGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLYPNIDKDHAFGK 14 1 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;J3KPM9;A0A669KBI6;P42224-2 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 171.76 1.78E-06 322190000 523130 373320 441730 336070 594580 539350 457730 444040 460300 321310 FALSE TRUE 543783.5763 437434.806 453241.8467 402543.6429 493513.504 414094.1364 421851.9265 438088.3701 443733.8929 384264.5426 1.415128163 1.138368903 1.179504733 1.047569053 1.284306641 1.077627755 1.097816425 1.140069721 1.154761482 1 18.55174033 4.741851585 5.143313199 1.129999503 1.428622067 0.581991624 0.073797935 0.110809327 9.702178786 0.016155367 0.117385499 55188.8806 -4.741851585 0.298622565 YLYTLVITDKEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YLYTLVITDKEK 12 1 J3KT73;J3QL01;P63173 J3KT73 RPL38 60S ribosomal protein L38 0 158.58 6.66E-05 639670000 1163900 797610 1109200 709750 1623500 1257300 1211700 987950 1151900 820070 FALSE TRUE 1209851.671 934593.313 1138106.663 850136.4316 1347538.05 965311.1296 1116723.788 974708.1462 1110443.344 980747.0153 1.233602195 0.952940257 1.160448766 0.866825408 1.373991487 0.984261093 1.138646124 0.993842582 1.132242389 1 19.90352151 -4.999999915 0.188986846 0.629883968 1.100968014 0.036585966 0.141254832 555.1241685 5.424336611 77.00069993 0.353292047 1.00E-05 4.999999915 0.471084046 YLYVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLYVDK 6 0 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 102.98 0.081604 563150000 1286620 1013040 1206590 1259570 1290460 1561900 1684160 1255470 1303910 869940 FALSE TRUE 1337416.751 1187021.74 1238034.727 1508709.187 1071108.07 1199172.396 1552151.138 1238642.478 1256982.534 1040388.087 1.285497948 1.140941303 1.189973955 1.450140775 1.029527427 1.152620268 1.491896301 1.190558114 1.208186204 1 19.98869035 0.713094099 2.278389003 1.000208837 1.242445478 0.227978298 0.132728877 2.150218616 14.93746981 0.123755309 0.033498888 5.165282733 -0.713094099 0.24223664 YLYVDKNFINNPLAQADWAAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YLYVDKNFINNPLAQADWAAK 21 1 P35579;Q5BKV1;B1AH99 P35579 MYH9 Myosin-9 0 ; 287.14 1.14E-45 795590000 867540 652460 837470 643050 1140180 984090 881270 834180 952610 716690 FALSE TRUE 901791.1491 764514.9296 859295.1562 770243.3707 946372.6109 755550.0115 812193.7546 822999.1815 918325.7522 857111.6836 1.052127939 0.891966525 1.002547477 0.898649949 1.104141536 0.881507073 0.947593844 0.960200633 1.071419011 1 19.70912368 1.25518795 24.85512235 1.035709499 0.96427215 0.13368087 0.069265146 342.7179323 512310.4818 0.042399469 0.015391546 17.99649582 -1.25518795 -0.071437349 YLYYTGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YLYYTGR 7 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 ;;; 167.25 0.0025431 1271129000 728063 734257 755233 756503 979164 965590 781028 717866 776348 717602 FALSE TRUE 756807.4894 860359.928 774914.9924 906137.0355 812726.053 741346.3562 719808.9845 708244.1805 748407.3871 858202.3726 0.881852013 1.00251404 0.902951352 1.055854731 0.947009795 0.863836293 0.83874038 0.825264766 0.872063992 1 19.71095836 2.772565195 4.826427845 0.861930366 0.963917296 0.246910579 0.064452329 0.211191252 12.58834856 0.019135291 0.019808658 592.3319997 -2.772565195 0.101986929 YMACCLLYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 159.19 0.0001541 1063420000 216110 290490 188070 175867 1035450 469070 265790 195954 198470 1336010 FALSE TRUE 224642.1897 340379.3978 192971.2587 210652.9677 859444.5789 360135.6013 244956.6853 193327.5571 191327.1035 1597775.58 0.140596835 0.213033296 0.120774946 0.131841399 0.537900685 0.225398113 0.153311071 0.120997942 0.119745918 1 20.60763335 -1.775846647 2.822622864 1.187327816 0.195894736 0.80143494 0.120065591 56430618.63 46060487.96 73157702.5 0.031076517 0.016755344 1.775846647 -0.991433081 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 A0A0A0MSJ0;Q86XP3-2;Q86XP3;J3KRE3 A0A0A0MSJ0 DDX42 ATP-dependent RNA helicase DDX42 1 YMAENPTAGVVQEEEEDNLEY(0.001)DS(0.999)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.022)DS(0.978)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEYDS(1)DGNPIAPTKK;YMAENPTAGVVQEEEEDNLEY(0.045)DS(0.951)DGNPIAPT(0.005)KK 270.02 2.51E-61 489877000 550356 320251 445812 313085 627024 562925 553526 457203 523659 311355 TRUE FALSE 572084.4798 375251.618 457430.227 375012.2785 520442.6844 432194.2 510139.1857 451074.9416 504812.6149 372359.051 1.536378606 1.00776822 1.228465444 1.007125455 1.397690436 1.160692076 1.370019567 1.211397817 1.355714635 1 18.5063349 3.218638323 24.99821546 1.260488996 1.183960315 0.018577602 0.175672039 854.5187133 1072236.553 0.046670287 0.055847965 1654.391625 -3.218638323 -0.07652868 YMDNDYAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YMDNDYAK 8 0 Q99747;Q99747-2 Q99747 NAPG Gamma-soluble NSF attachment protein 0 79.906 0.056261 0 181400 98308 119440 102290 194440 189430 145340 119170 140330 106420 FALSE TRUE 188561.8121 115191.6343 122552.7045 122522.6567 161389.1583 145437.7533 133947.871 117572.7211 135279.5507 127270.9615 1.481577651 0.905089684 0.962927467 0.962691373 1.268075266 1.142741059 1.05246216 0.923798483 1.062925503 1 16.95754376 4.748715305 24.65411536 1.031375224 1.481577953 0.628791022 0.103815762 832.9260224 2022175.172 0.026824378 0.364614282 56068.03098 -4.748715305 0.450202729 YMEAFKPFLGIGLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YMEAFKPFLGIGLK 14 1 Q14974;Q14974-2;J3KTM9 Q14974 KPNB1 Importin subunit beta-1 0 86.944 0.0065105 101750000 246740 120710 201750 207760 246770 239170 361270 233180 230380 113580 FALSE TRUE 256481.4857 141441.0035 207007.7707 248854.3079 204824.1235 183626.3922 332952.7134 230054.6035 222088.6688 135833.8264 1.888200403 1.041279682 1.523978057 1.832049605 1.507902185 1.351845833 2.451176723 1.693647375 1.63500267 1 17.05148327 YMEDS(ph)TYYK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 Y(0.166)MEDS(0.827)T(0.007)YYK;YMEDS(0.384)T(0.384)Y(0.231)Y(0.001)K 151.07 8.78E-05 235410000 379040 298260 361750 299900 495440 482580 413270 388940 434600 297120 TRUE FALSE 394004.7919 349483.8349 371177.5022 359219.3249 411225.2858 370508.1086 380876.8175 383726.8955 418958.8309 355334.9753 1.108826373 0.983533452 1.044584766 1.010931515 1.157289078 1.042700928 1.071881025 1.079901845 1.179053175 1 18.43882017 3.281726551 24.99992277 1.088307374 1.033696168 0.164947864 0.056576995 232.5979452 134709.6381 0.014697472 0.019900363 1913.051012 -3.281726551 -0.054611205 YMEDSTY(ph)YK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YMEDSTYYK 9 0 E7ESA6;Q05397;Q05397-7;H0YBP1;Q05397-5;E9PEI4;H0YB16;H0YBZ1;Q05397-2;Q05397-4;Q05397-3 E7ESA6 PTK2 Focal adhesion kinase 1 1 YMEDS(0.168)T(0.168)Y(0.663)Y(0.001)K 113.26 0.004409 145400000 304950 227710 265170 213740 423600 375260 349600 294380 310270 267110 TRUE FALSE 316989.6615 266817.4212 272080.548 256017.134 351596.6233 288111.5521 322197.4385 290434.3176 299103.4433 319445.0904 0.992313456 0.835252847 0.851728689 0.801443321 1.100648074 0.9019126 1.008616029 0.909183852 0.936321929 1 18.28520844 3.268370805 24.99947528 0.966265807 0.866371212 0.342157648 0.071095971 243.8586154 204503.5694 0.018948114 0.025652501 1855.114863 -3.268370805 -0.099894594 YMEDYHQFHEDVKDAQELLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YMEDYHQFHEDVKDAQELLR 20 1 O60437;K7EKI8 O60437 PPL Periplakin 0 252.4 2.88E-36 73875000 89198 78452 92374 70169 114150 110690 90670 98811 101840 77170 FALSE TRUE 92719.60592 91925.52073 94781.34233 84048.21877 94746.82377 84983.92502 83563.04848 97486.60017 98174.79829 92289.98399 1.004655131 0.99605089 1.026994894 0.910697078 1.026620871 0.920835841 0.905440058 1.056307477 1.063764388 1 16.49388646 1.63657131 10.73441779 1.045013622 0.971584034 0.325292366 0.045814322 0.117845248 29.1715717 0.022064342 0.011776457 43.30831732 -1.63657131 -0.073429588 YMEEMADTADAIEMATLDKEMAEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YMEEMADTADAIEMATLDKEMAEER 25 1 E7EX90;Q14203-3;Q14203-4;Q14203-6;Q14203;Q14203-5;Q14203-2;Q6AWB1 E7EX90 DCTN1;DKFZp686E0752 Dynactin subunit 1 0 ;; 235.95 1.82E-38 159859000 81722 92794 116448 83599 133299 127620 111432 98196 119948 96636 FALSE TRUE 84948.44766 108730.6477 119482.7305 100134.6327 110640.8836 97982.1891 102697.6687 96879.84324 115631.0949 115569.974 0.735039083 0.940820906 1.033856169 0.866441596 0.957349732 0.847817004 0.888618948 0.838278663 1.000528865 1 16.8184071 1.219136839 24.63674827 1.000264649 0.892540572 0.258440001 0.075464739 331.7815799 420812.2135 0.070732183 0.01779508 16.56291752 -1.219136839 -0.107724077 YMHSGPVVAMVWEGLNVVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 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 1377310000 612560 599730 716690 558540 784890 788590 758440 656280 667060 587070 FALSE TRUE 636744.3418 702728.9622 735367.5302 669017.5449 651474.6782 605451.9237 698991.491 647483.6401 643052.6409 702095.1264 0.906920327 1.000902778 1.047390165 0.952887322 0.927900869 0.862350273 0.995579466 0.9222164 0.915905291 1 19.42130699 3.48885995 23.70652084 0.933912721 0.988901677 0.155873187 0.049065859 439.3133112 887200.4459 0.012986557 0.018928857 3082.193856 -3.48885995 0.054988955 YMIGVTYGGDDIPLSPYR ddPTM_MDA-MB-175_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 0 233.37 2.25E-23 62349000 52349 71104 55078 61980 62837 79276 49664 53573 49410 65513 FALSE TRUE 54415.77894 83315.55889 56513.37793 74239.45901 52155.98918 60865.35044 45771.20591 52854.94156 47631.74375 78349.01803 0.694530452 1.063389957 0.721302951 0.947548047 0.665687848 0.776848925 0.584196293 0.674608858 0.607943085 1 16.25762757 3.226156074 24.99093157 0.693978184 0.861786228 0.163529338 0.147260233 304.3542165 613169.0176 0.038936921 0.046843604 1683.278877 -3.226156074 0.167808044 YMLTHQELAS(ph)DGEIETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YMLTHQELASDGEIETK 17 0 Q02241;H7BYN4;A0A2U3TZL8;Q02241-2;Q02241-3 Q02241;Q02241-2 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 YMLTHQELAS(1)DGEIETK 186.63 3.30E-10 153020000 192810 139250 187360 141550 200660 199620 184370 159720 186710 126190 TRUE FALSE 200422.2877 163165.1043 192242.7555 169548.1675 166551.8849 153261.2803 169918.5976 157579.2146 179990.3436 150914.5144 1.328051768 1.08117569 1.273851996 1.123471577 1.103617405 1.015550299 1.125926146 1.044162089 1.192664233 1 17.20337204 8 0.369364352 1.067622737 3.945843807 0.440961788 0.076373146 61.2518412 0.84902157 0.055710246 124.9739161 99999999.99 -8 2.87822107 YMNSDTTS(ph)PELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YMNSDTTSPELR 12 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 YMNSDTTS(1)PELR;YMNSDTT(0.016)S(0.984)PELR;YMNSDTT(0.002)S(0.998)PELR;YMNSDT(0.002)T(0.011)S(0.987)PELR 316.12 1.92E-46 2123370000 1943570 2313920 2222090 2194140 2340590 2699680 2249410 2197010 2174600 2231930 TRUE FALSE 2020303.644 2711317.76 2279999.491 2628134.343 1942737.348 2072720.234 2073095.366 2167562.675 2096336.571 2669233.951 0.756885189 1.01576625 0.854177466 0.984602471 0.727825805 0.776522505 0.776663044 0.812054213 0.785370114 1 21.34799433 3.237046321 24.99999012 0.800316352 0.907445555 0.169173927 0.094766947 55.95820119 923836.9903 0.024583353 0.030917597 1726.021978 -3.237046321 0.107129202 YMS(ph)FTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YMSFTDK 7 0 E9PM17;B3KNX7;Q13153;Q13153-2;H0YCM0 E9PM17 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 YMS(0.994)FT(0.006)DK;YMS(0.998)FT(0.002)DK;YMS(0.997)FT(0.003)DK 104.89 0.0084442 689880000 1039270 668580 918910 823170 1383780 1211960 1127600 914410 1038630 643060 TRUE FALSE 1080301.182 783403.4142 942857.5495 985990.5691 1148565.57 930500.6574 1039215.766 902153.8296 1001249.909 769055.2949 1.404711975 1.018656811 1.225994484 1.282080204 1.493475928 1.209926859 1.351288747 1.173067575 1.301921872 1 19.55272781 -1.147620139 3.871516507 0.999867528 1.265919714 0.30198495 0.124249747 6832649.626 4050763.847 7058.189257 0.028260703 0.071183586 1.147620139 0.266052186 YMTISGFQIEETIDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YMTISGFQIEETIDR 15 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 ; 107.65 0.0026548 51272000 32063.2 22614.6 28763 25710.6 31847.6 40669 31342.6 23557.5 24905 20469 FALSE TRUE 33329.07989 26498.48163 29512.58741 30796.07994 26434.15633 31224.24109 28885.88511 23241.75024 24008.67391 24479.50865 1.361509349 1.082476042 1.205603749 1.258035052 1.079848322 1.275525647 1.180002652 0.949436959 0.980766169 1 14.57928698 1.774300136 5.46719201 0.974447646 1.202283318 0.630033667 0.080554491 0.113687061 7.465354883 0.036597211 0.019919664 59.47030096 -1.774300136 0.227835671 YMVADKFTELQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YMVADKFTELQK 12 1 P30153;B3KQV6;C9J9C1 P30153 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 ; 175.74 2.45E-05 1831980000 1721710 1242840 1683020 1205290 2207480 1900250 1869000 1599580 1741730 1319040 FALSE TRUE 1789684.44 1456288.102 1726880.884 1443692.765 1832253.338 1458945.736 1722502.896 1578140.246 1679045.478 1577480.633 1.134520705 0.923173363 1.094708136 0.915188899 1.161506074 0.924858097 1.091932832 1.000418143 1.06438421 1 20.58919086 YNADEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 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 ;;; 130.22 0.0083387 3089830000 3911590 4290490 4004990 4092950 4930070 5362970 4406940 4395540 4259930 4615410 FALSE TRUE 4066022.594 5027348.282 4109363.33 4902523.294 4092058.462 4117501.494 4061512.527 4336624.976 4106615.951 5519711.222 0.736636833 0.910799149 0.744488826 0.888184743 0.741353723 0.745963209 0.735819749 0.785661568 0.743991087 1 22.39616136 -1.37773881 3.133521086 1.002413582 0.783260273 0.531326776 0.06156131 11922255.03 16328031.5 265990.4898 0.015100212 0.041904551 1.37773881 -0.219153309 YNDWS(ph)DDDDDSNESK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YNDWSDDDDDSNESK 15 0 H3BV87;Q9UH62 H3BV87 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK;YNDWS(1)DDDDDSNESK 388.56 2.93E-87 906640000 1352150 732415 1001940 788670 1365660 1688120 1292750 968180 1126550 658200 TRUE FALSE 1405533.926 858201.5789 1028051.38 944666.5721 1133525.601 1296079.714 1191420.877 955203.1307 1086005.686 787161.688 1.785572072 1.090248156 1.30602314 1.200092162 1.440016223 1.64652286 1.513565631 1.21347767 1.379647539 1 19.58630048 0.513030328 1.062271017 1.001152618 1.394647818 0.262693446 0.200611026 2.473496946 3.914494165 0.191901277 0.059871279 3.258594563 -0.513030328 0.3934952 YNEDLELEDAIHTAILTLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YNEDLELEDAIHTAILTLK 19 0 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 228.38 1.05E-19 1052500000 421140 362100 468810 376240 566790 499520 557970 475200 500460 380030 FALSE TRUE 437766.9324 424287.8583 481027.5737 450659.149 470447.2383 383514.0503 514234.8534 468830.7213 482448.5424 454489.6024 0.963205605 0.933547998 1.058390712 0.991571967 1.035111113 0.843834597 1.131455705 1.031554339 1.061517227 1 18.79388776 2.205534906 24.99962756 1.058442458 0.977072772 0.302932209 0.062856479 243.989321 184692.2908 0.022702923 0.016768324 160.5221269 -2.205534906 -0.081369686 YNEEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNEEER 6 0 K7EP07;Q99426-2;Q99426;A0A494C0X0;K7EK42 K7EP07 TBCB Tubulin-folding cofactor B 0 ; 145.04 0.038633 258240000 473690 552730 532530 502280 588150 646080 543920 576730 518320 528010 FALSE TRUE 492391.647 647657.0779 546408.1693 601629.4848 488176.4731 496037.7114 501286.1291 568999.8777 499665.7644 631463.4501 0.779762703 1.0256446 0.865304507 0.952754248 0.773087457 0.785536695 0.793848209 0.901081254 0.791282163 1 19.26833971 YNEQHVPGSPFTAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YNEQHVPGSPFTAR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ;; 91.657 0.0052687 1411000000 2006480 2285040 2118140 2117030 2316100 2866970 2208850 2307290 2308220 2319880 FALSE TRUE 2085697.38 2677477.845 2173340.468 2535772.215 1922410.149 2201159.667 2035714.565 2276364.552 2225147.613 2774416.069 0.751760849 0.965059954 0.783350591 0.913984115 0.692906219 0.793377638 0.733745233 0.820484201 0.802023762 1 21.40375273 5.916858075 12.90276769 0.817646891 0.586909224 0 0.096551638 0 0 0.01962471 0 825768.0495 -5.916858075 -0.230737667 YNGGVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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 ; 148.07 0.0049053 588550000 388710 466880 486940 455380 550630 602140 447470 514070 483150 528950 FALSE TRUE 404056.5709 547063.0082 499630.0564 545452.8048 457034.1093 462302.1105 412396.1322 507179.7325 465761.5259 632587.6251 0.638736129 0.864801944 0.789819523 0.862256521 0.722483481 0.730811183 0.65191938 0.801754116 0.736279857 1 19.27090581 -1.810715615 5.376586265 1.023070595 0.759695095 0.501931059 0.072977169 0.019817526 0.000697682 0.069385426 0.016137058 0.015462666 1.810715615 -0.263375501 YNGLIHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YNGLIHR 7 0 P46779;H0YKD8;P46779-2;P46779-3;H0YLP6;H0YMF4;P46779-4;P46779-5 P46779 RPL28 60S ribosomal protein L28 0 ;;;;; 134.44 0.0031745 2727780000 3899430 4686670 4623410 4586500 5984570 6161690 5038130 5135370 4792860 5351380 FALSE TRUE 4053382.507 5491569.115 4743899.863 5493696.011 4967314.929 4730730.879 4643228.206 5066538.765 4620365.905 6399880.453 0.633352847 0.858073702 0.7412482 0.858406036 0.776157456 0.739190507 0.725517959 0.79166147 0.721945658 1 22.60961353 -1.266429167 3.460838753 1.000673752 0.766032445 0.560167105 0.063472458 19543621.06 27014925.56 136079.7642 0.013998091 0.054146555 1.266429167 -0.234641308 YNHDGEAGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YNHDGEAGR 9 0 Q9BUK6-2;Q9BUK6;A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-5 Q9BUK6-2 MSTO1 Protein misato homolog 1 0 74.162 0.041871 103340000 61512 74104 78160 78755 79522 84809 92043 80120 81737 80848 FALSE TRUE 63940.54126 86830.78555 80196.91381 94332.50394 66004.87884 65113.39504 84828.42915 79046.12245 78795.30134 96688.61767 0.661303707 0.898045578 0.829434899 0.975631943 0.682654075 0.673433922 0.877336249 0.817532863 0.814938751 1 16.56105844 -0.020593883 0.895151535 1.00320324 0.805090675 0.265704329 0.098286828 9.544103689 7.032445202 0.195508951 0.031037196 0.953687558 0.020593883 -0.198112565 YNHIDESEMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YNHIDESEMK 10 0 Q92598-2;Q92598;Q92598-4;A0A0A0MSM0;Q92598-3;Q5TBM3 Q92598-2 HSPH1 Heat shock protein 105 kDa 0 ;;; 183.03 1.71E-06 1986150000 3495650 2341130 3119240 2363840 4398920 4223440 3916860 3197630 3397660 2352860 FALSE TRUE 3633660.961 2743200.866 3200529.957 2831400.497 3651193.15 3242610.067 3609846.278 3154771 3275378.88 2813857.869 1.291344883 0.974889633 1.137417064 1.006234369 1.297575542 1.152371661 1.282881527 1.121155064 1.164017173 1 21.42411803 3.251317551 24.99818195 1.178799316 1.095854653 0.075873634 0.11124663 489.1626443 958546.3439 0.028475851 0.038308091 1783.682499 -3.251317551 -0.082944663 YNLDAS(ph)EEEDSNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YNLDASEEEDSNKK 14 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK;YNLDAS(1)EEEDSNKK 175.59 1.44E-06 1007990000 1884750 590020 854850 662780 1272810 1234680 1616730 893870 1058580 365475 TRUE FALSE 1959161.385 691351.3453 877128.0933 793875.9058 1056458.211 947944.2818 1490006.478 881889.1347 1020481.913 437082.8288 4.482357247 1.581739889 2.006777744 1.816305408 2.41706638 2.16879781 3.408979671 2.017670511 2.334756356 1 18.73754718 4.747695732 24.80146092 2.171261012 4.482358596 0.592434238 0.592885391 761.5521044 2067533.553 0.136252644 1.681687181 55936.55707 -4.747695732 2.311097584 YNLDAS(ph)EEEDSNKKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YNLDASEEEDSNKKK 15 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 YNLDAS(1)EEEDSNKKK;YNLDAS(1)EEEDSNKKK;YNLDAS(1)EEEDSNKKK;YNLDAS(1)EEEDSNKKK 180.05 3.37E-07 1376820000 2566050 474720 911120 542470 1539960 1377310 1705840 950350 1171500 267855 TRUE FALSE 2667359.635 556249.4672 934864.5357 649768.9469 1278198.149 1057450.626 1572131.803 937612.1127 1129337.944 320336.0589 8.326754237 1.736455987 2.918386831 2.028397768 3.990178795 3.301066479 4.907757837 2.926964002 3.525478673 1 18.28922668 0.278989259 1.181925554 0.996004054 3.643963308 0.178031588 1.761297241 7.431618674 10.54045918 1.626798268 0.477952715 1.901031264 -0.278989259 2.647959254 YNLDFWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YNLDFWR 7 0 Q13630;E9PP14;A0A0J9YX13;E9PKL9;E9PLH9;H0YE90 Q13630 TSTA3 GDP-L-fucose synthase 0 76.774 0.092701 525820000 786350 975070 594430 620350 2949600 1667400 993560 696320 717450 3181600 FALSE TRUE 817395.7052 1142530.688 609921.3341 743053.3784 2448228.046 1280171.62 915682.171 686986.9693 691629.1146 3804973.605 0.214822963 0.30027296 0.160295812 0.195284766 0.643428391 0.336446912 0.240654014 0.180549733 0.181769754 1 21.85945501 -1.098578245 4.027621474 1.000135099 0.272462782 0.723449519 0.134917796 89836481.23 177882474.1 204682.7243 0.034168633 0.07969329 1.098578245 -0.727672317 YNLINEGS(ph)PPSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNLINEGSPPSK 12 0 Q68D06 Q68D06 SLFN13 Schlafen family member 13 1 YNLINEGS(1)PPSK;YNLINEGS(0.942)PPS(0.058)K 133.47 0.0001706 123830000 410800 287920 372630 289800 472000 463440 445120 365740 392700 274740 TRUE FALSE 427018.7012 337368.0203 382341.0439 347121.575 391769.6086 355813.0835 410230.3313 360837.8535 378566.8037 328570.0428 1.299627615 1.026776566 1.163651563 1.056461423 1.192347316 1.082913952 1.248532361 1.098206795 1.152164697 1 18.32584142 -1.034087892 1.314150074 0.992384846 1.141773087 0.226729876 0.080825594 965.6997165 563.8102756 31.82245371 0.020363666 0.092451105 1.034087892 0.149388241 YNMGLPVDFDQYNELHLPAVILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNMGLPVDFDQYNELHLPAVILK 23 0 Q07960;H0YE29 Q07960 ARHGAP1 Rho GTPase-activating protein 1 0 ; 198.64 2.75E-24 1653940000 1561610 1427170 1668960 1514830 1939520 2029120 1869260 1643710 1670580 1319860 FALSE TRUE 1623263.569 1672275.346 1712454.469 1814458.853 1609841.083 1557887.632 1722742.517 1621678.756 1610456.152 1578461.297 1.02838351 1.059433861 1.084888475 1.149511145 1.019879985 0.986966 1.091406245 1.027379486 1.020269648 1 20.59008746 YNPTWHCIVGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNPTWHCIVGR 11 0 P63167;Q96FJ2 P63167;Q96FJ2 DYNLL1;DYNLL2 "Dynein light chain 1, cytoplasmic;Dynein light chain 2, cytoplasmic" 0 ; 179.35 7.14E-06 4313000000 711550 1036280 918870 786250 1322260 1290590 679250 972670 954020 1456380 FALSE TRUE 739642.5434 1214253.029 942816.5071 941767.9033 1097502.717 990870.0316 626008.6101 959632.9496 919685.0066 1741729.777 0.424659757 0.697153511 0.541310437 0.54070839 0.630122268 0.568899978 0.359417757 0.550965461 0.528029674 1 20.73208938 -1.452855337 2.612191157 1.017134584 0.53940378 0.706523575 0.0893389 3921758.497 3982213.191 490347.6909 0.022485231 0.035248826 1.452855337 -0.477730804 YNQATPNFHQWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNQATPNFHQWR 12 0 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 ; 143.42 6.22E-05 818540000 828790 1050280 960720 856670 1630550 1543850 1074610 968080 987160 1542120 FALSE TRUE 861511.2692 1230657.42 985757.1524 1026116.769 1353389.693 1185314.235 990379.2602 955104.4711 951632.3044 1844268.888 0.467128885 0.667287415 0.534497523 0.556381326 0.733835344 0.642701421 0.537003724 0.517877017 0.515994338 1 20.81461758 -1.362633286 3.102735724 1.004455321 0.576472836 0.730068548 0.077567454 18986483.78 24187108.26 763172.5895 0.020504538 0.043387709 1.362633286 -0.427982485 YNQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YNQLLR 6 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 ;;;;; 156.22 0.022749 10179670000 6447850 7144760 7006730 6663460 9924270 9403450 7392630 7274950 7103890 8380350 FALSE TRUE 6702416.097 8371816.951 7189331.14 7981472.5 8237346.13 7219641.248 6813176.344 7177441.195 6848222.387 10022319.13 0.66874902 0.835317339 0.717332091 0.796369822 0.821900203 0.720356352 0.679800379 0.716145744 0.683297179 1 23.25671305 -1.395922617 4.884606751 1.000291917 0.739420698 0.656859513 0.056863199 0.000181849 2.25E-05 0.055386772 0.013040321 0.040186241 1.395922617 -0.260871219 YNSLQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNSLQK 6 0 Q86VH5-2;Q86VH5 Q86VH5-2 LRRTM3 Leucine-rich repeat transmembrane neuronal protein 3 0 ; 109.7 0.029331 172368000 389700 354590 383320 335080 609640 565190 482750 457170 494500 431230 FALSE TRUE 405085.6569 415488.0742 393309.6341 401357.8239 506013.6106 433933.188 444910.7936 451042.3839 476703.0416 515721.2621 0.785474028 0.805644647 0.762639943 0.77824564 0.981176554 0.841410312 0.86269624 0.874585589 0.924342424 1 18.976232 7.999999655 0.055132216 1.254341374 0.074115033 0.607905249 0.049950681 279.2571434 1.155568852 5.38736428 27.12647386 99999920.63 -7.999999655 -1.18022634 YNSPELDEEGYSIR ddPTM_MDA-MB-175_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 51.546 0.05689 1327500000 194710 345640 353670 105010 498550 406390 117400 248470 367110 696070 FALSE TRUE 202397.3011 405000.9813 362886.9307 125780.6646 413806.6491 312012.0814 108197.8812 245139.6661 353897.7828 832451.5894 0.24313402 0.486515957 0.435925567 0.151096672 0.49709395 0.374811083 0.129974983 0.294479186 0.425127163 1 19.66700685 0.807499038 3.933201729 0.999968222 0.326656538 0.733620704 0.12103316 0.840581771 16.6192631 0.116500568 0.029800556 6.419467994 -0.807499038 -0.673311684 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 YNTEGRVS(0.984)PS(0.016)PSQESLSSSK;YNTEGRVS(0.986)PS(0.014)PSQESLSSSK;YNTEGRVS(0.999)PS(0.001)PSQESLSSSK 284.75 3.12E-45 2408600000 1074690 686260 910730 737380 1089630 1143320 1110230 832520 979930 570600 TRUE FALSE 1117119.591 804119.8166 934464.372 883231.5631 904415.0818 877801.2572 1023207.272 821361.4311 944662.5107 682398.1452 1.637049571 1.178373391 1.369382931 1.29430534 1.325348095 1.28634766 1.499428565 1.203639601 1.384327489 1 19.3802542 -3.505034268 0.296148963 1.37E-12 1.36299828 0.407184585 0.128159055 93.06661704 1.969187749 57.19049649 0.121237739 0.000312583 3.505034268 1.36299828 YNVYPTYDFACPIVDSIEGVTHALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YNVYPTYDFACPIVDSIEGVTHALR 25 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 215.42 1.73E-33 745110000 251128 283183 291223 332641 317254 377210 338550 318901 292664 276651 FALSE TRUE 261042.7274 331817.4774 298812.5106 398436.397 263327.2784 289608.6942 312013.5664 314626.6537 282131.0798 330855.4666 0.788993242 1.002907647 0.903151197 1.204261187 0.795898224 0.875332958 0.943050963 0.950948935 0.852732109 1 18.33584159 YNYHLDSSGSYVFENTVATVMALR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YNYHLDSSGSYVFENTVATVMALR 24 0 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 ;; 259.77 5.50E-44 197809000 72173.6 98240.6 110406.2 111425.1 123999.5 140683.3 132232.5 114869.3 111910.8 99608.5 FALSE TRUE 75023.06946 115112.6588 113283.4763 133464.6522 102922.1093 108011.7357 121867.7711 113329.6649 107883.1522 119124.8785 0.629785066 0.966319213 0.950964045 1.120375978 0.86398501 0.906710144 1.023025355 0.951351778 0.905630743 1 16.86211522 4.738668653 24.48057641 0.965295282 0.629784994 0.686697687 0.068002869 3.621955744 819304.89 0.015838384 0.091742596 54785.88135 -4.738668653 -0.335510289 YPALHKPENQDIDWGALEGETR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YPALHKPENQDIDWGALEGETR 22 1 P13796 P13796 LCP1 Plastin-2 0 ;; 201.32 9.26E-23 1022543000 294559 356538 286091 526651 952790 920339 704980 381012 365002 967170 FALSE TRUE 306188.4168 417770.628 293546.7665 630820.9959 790835.0961 706604.2151 649721.8255 375905.1573 351865.6493 1156668.444 0.264715804 0.361184426 0.25378644 0.545377545 0.683718053 0.610896077 0.561718294 0.32498955 0.304206146 1 20.14154395 3.732292728 23.86324463 0.540091647 0.30002444 0.313938468 0.186195931 364.5905389 1388080.556 0.049686792 0.079232152 5398.74392 -3.732292728 -0.240067206 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPDSHQLFVGNLPHDIDENELKEFFMSFGNVVELR 35 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 ; 373.63 4.98E-149 1292440000 335060 322420 411810 366160 425030 464010 492380 371110 432170 313030 FALSE TRUE 348288.4275 377793.1269 422542.1069 438585.3551 352783.5524 356250.7096 453785.969 366135.8775 416616.2861 374362.2352 0.930351394 1.009164631 1.128698536 1.171553415 0.942358815 0.951620319 1.212157441 0.978025674 1.112869427 1 18.51407538 YPDVAS(ph)PTLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YPDVASPTLR 10 0 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 YPDVAS(0.856)PT(0.144)LR;YPDVAS(0.973)PT(0.027)LR;YPDVAS(0.984)PT(0.016)LR;YPDVAS(0.943)PT(0.057)LR 214.04 1.17E-08 1844610000 1212850 1477760 1313460 1467190 1536510 1732860 1504210 1445600 1375790 1416780 TRUE FALSE 1260734.255 1731553.785 1347689.847 1757395.803 1275334.579 1330429.527 1386306.09 1426224.097 1326275.587 1694370.915 0.744072176 1.021944941 0.795392458 1.03719663 0.752689135 0.785205597 0.818183361 0.841742551 0.782753985 1 20.6923183 YPDVAS(ph)PTLRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YPDVASPTLRR 11 1 Q8IVL1-9;Q8IVL1-13;A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-5;Q8IVL1-4;Q8IVL1-10;Q8IVL1-8;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;E9PNV5 Q8IVL1-9 NAV2 Neuron navigator 2 1 YPDVAS(0.999)PT(0.001)LRR;YPDVAS(0.999)PT(0.001)LRR;YPDVAS(0.999)PT(0.001)LRR;YPDVAS(1)PTLRR;YPDVAS(1)PTLRR 146.77 2.18E-05 2263730000 2028930 2349530 2199920 2142150 2715600 2860410 2227020 2347570 2251490 2643510 TRUE FALSE 2109033.723 2753043.501 2257251.722 2565860.876 2254003.282 2196123.127 2052460.353 2316104.664 2170459.315 3161455.171 0.667108533 0.87081529 0.713991374 0.811607547 0.71296386 0.694655786 0.649213809 0.73260715 0.686538065 1 21.59215733 -1.07838895 4.58727427 1.000012695 0.72855213 0.623536548 0.063712236 0.221005724 38184710.12 1302.104377 0.014618024 0.0834855 1.07838895 -0.271460565 YPEPERPS(ph)SR ddPTM_MDA-MB-175_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(0.908)S(0.092)R 110.31 0.0050075 2104300000 568210 651110 593870 673700 599140 733440 647790 685920 567120 529260 TRUE FALSE 590643.3696 762933.0776 609346.7401 806955.8492 497298.3968 563109.6754 597014.5271 676726.3643 546709.462 632958.3637 0.933147271 1.205344808 0.962696403 1.274895626 0.785673158 0.889647262 0.943212953 1.069148309 0.863736848 1 19.27175108 3.231699702 24.99959251 0.937799714 1.092592397 0.324496842 0.118465394 203.1227501 740131.9707 0.03318025 0.040486347 1704.903106 -3.231699702 0.154792683 YPEPERPS(ph)SRAS(ph)HSSERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 YPEPERPS(0.74)S(0.296)RAS(0.715)HS(0.054)S(0.195)ERPPPR 82.773 0.0053241 878480000 108100 232300 232890 215660 236740 478680 193790 227050 195740 234250 TRUE FALSE 112367.8715 272195.718 238959.3047 258316.9043 196499.0194 367513.8245 178600.2334 224006.7661 188695.3556 280146.8025 0.40110353 0.97161815 0.852978876 0.922076933 0.701414464 1.311861571 0.637523726 0.799604936 0.673558841 1 18.0958235 4.746998188 24.55248425 0.863398302 0.401103231 0.36273619 0.187725687 920.1928703 2677591.584 0.042763666 0.488141389 55846.78644 -4.746998188 -0.462295071 YPEPERPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YPEPERPSSR 10 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YPEPERPS(0.019)S(0.981)R;YPEPERPS(0.004)S(0.996)R;YPEPERPS(0.281)S(0.719)R 124.04 0.0011735 3090110000 1018850 1189810 1111090 1214300 1175870 1371570 1259900 1151950 1057030 927540 TRUE FALSE 1059074.985 1394150.612 1140045.918 1454484.916 975996.0374 1053043.654 1161145.746 1136509.994 1018987.697 1109273.704 0.954746318 1.256813902 1.027740867 1.311204719 0.879851414 0.949309129 1.046762167 1.024553264 0.918607998 1 20.08118395 3.221147312 24.99999239 0.979003994 1.138290947 0.375911103 0.105510361 254.2023958 364953.4475 0.028701625 0.034379962 1663.976975 -3.221147312 0.159286954 YPEPERPSS(ph)RAS(ph)HS(ph)SERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 3 YPEPERPS(0.481)S(0.537)RAS(0.981)HS(0.529)S(0.472)ERPPPR 86.48 0.0053539 626510000 142800 165810 156140 172150 213280 206930 107480 145070 149980 165480 TRUE FALSE 148437.8543 194286.5777 160209.1367 206200.7562 177026.7418 158873.6436 99055.43675 143125.5739 144582.2491 197902.6377 0.750054956 0.981728086 0.809535126 1.041930308 0.894514312 0.802786893 0.500526107 0.723212058 0.730572623 1 17.59443132 2.476086568 24.97962786 0.701533657 0.898189171 0.208895894 0.137206582 40.22313089 971027.1472 0.044509945 0.03753112 299.2861146 -2.476086568 0.196655514 YPEPERPSS(ph)RAS(ph)HSS(ph)ERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 3 YPEPERPS(0.248)S(0.763)RAS(0.959)HS(0.313)S(0.718)ERPPPR 71.295 0.033234 420230000 105120 130530 115640 122250 137410 129190 89931 115720 77086 140010 TRUE FALSE 109270.2188 152947.5121 118653.6734 146430.6851 114053.0973 99187.58039 82881.97323 114168.9627 74311.68992 167442.2788 0.652584398 0.913434248 0.708624334 0.874514407 0.68114874 0.592368792 0.494988326 0.681840712 0.443804817 1 17.35330433 3.036900884 5.986879003 0.617592492 0.790350425 0.152324529 0.156268437 0.265480336 25.72033661 0.04178738 0.049577428 1088.681604 -3.036900884 0.172757933 YPEPERPSS(ph)RAS(ph)HSSERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 YPEPERPS(0.486)S(0.554)RAS(0.945)HS(0.007)S(0.008)ERPPPR;YPEPERPS(0.501)S(0.544)RAS(0.687)HS(0.139)S(0.129)ERPPPR 92.819 0.002601 896142000 129602 218743 234719 212939 230979 440184 199873 222018 207312 206395 TRUE FALSE 134718.787 256310.4087 240835.97 255057.6986 191717.2721 337957.9371 184206.432 219042.2119 199850.8816 246834.1486 0.545786666 1.038391204 0.975699559 1.033316095 0.776704817 1.369170105 0.746276125 0.887406435 0.809656536 1 17.91318247 4.746181932 24.25029047 0.953020103 0.545786364 0.347780263 0.169801768 687.3317275 2186941.709 0.038793606 0.405937608 55741.92113 -4.746181932 -0.407233739 YPEPERPSSRAS(ph)HS(ph)SERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 Y(0.001)PEPERPS(0.295)S(0.313)RAS(0.674)HS(0.491)S(0.226)ERPPPR 63.932 0.041961 596270000 42455 129560 123470 119880 130890 167640 101120 127360 105150 145180 TRUE FALSE 44131.15618 151810.9222 126687.7296 143591.9062 108641.3646 128708.1506 93193.95017 125652.9475 101365.672 173625.2414 0.254174772 0.874359747 0.729661935 0.827022068 0.625723332 0.741298613 0.536753466 0.723702075 0.583818754 1 17.40561717 -1.571312336 2.774806041 1.021337777 0.66949987 0.274567454 0.166693555 30335715.32 30643912.23 4786023.579 0.041270958 0.026834139 1.571312336 -0.351837907 YPEPERPSSRAS(ph)HSS(ph)ERPPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPEPERPSSRASHSSERPPPR 21 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 2 YPEPERPS(0.026)S(0.102)RAS(0.902)HS(0.441)S(0.529)ERPPPR 101.86 0.00068834 627350000 28303 79569 72874 79894 75463 101780 60375 86223 74698 92520 TRUE FALSE 29420.42429 93234.35679 74773.15631 95696.79474 62635.82621 78143.13749 55642.64974 85067.32172 72009.63357 110647.5226 0.265893204 0.842624892 0.675777953 0.864879687 0.566084308 0.706234859 0.502882021 0.768813614 0.650802041 1 16.75561162 -4.999999984 0.327033063 4.350205626 0.648974457 0.287304078 0.166314777 441.4107859 3.84469762 1026.564242 0.131626256 1.00E-05 4.999999984 -3.701231169 YPES(ph)NRTPVKPSSVEEEDSFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.864)NRT(0.135)PVKPS(0.001)SVEEEDSFFR 226.23 2.84E-26 554850000 1175000 975910 1152600 907410 1374700 1425600 1377400 1168600 1190300 948620 TRUE FALSE 1221389.907 1143514.951 1182637.703 1086892.99 1141028.985 1094526.005 1269435.789 1152936.828 1147461.336 1134483.927 1.076603977 1.007960469 1.042445534 0.958050585 1.005769195 0.964778768 1.118954407 1.016265459 1.011439042 1 20.11360474 YPESNRT(ph)PVKPSSVEEEDSFFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPESNRTPVKPSSVEEEDSFFR 22 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 YPES(0.043)NRT(0.951)PVKPS(0.005)S(0.001)VEEEDSFFR;YPES(0.296)NRT(0.704)PVKPSSVEEEDSFFR 200.06 8.06E-21 1325520000 826660 679630 734340 600360 848850 954620 923220 775970 803820 678480 TRUE FALSE 859297.1751 796351.1657 753477.5037 719109.4161 704562.7802 732923.9724 850855.604 765569.3914 774890.6752 811415.1657 1.059010494 0.981434905 0.928596772 0.886241035 0.868313546 0.903266297 1.048606977 0.943498993 0.95498668 1 19.63008074 0.937845937 15.84823387 1.000000002 0.950335387 0.052368664 0.060004363 524.690225 133792.6557 0.060762631 0.015190599 8.66654381 -0.937845937 -0.049664616 YPEYDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPEYDGR 7 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8;A0A494C1S4 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ; 120.45 0.010595 456470000 443020 548520 486780 531170 570660 615020 495610 529740 469180 536350 FALSE TRUE 460510.7717 642724.0431 499465.8867 636233.8406 473659.417 472190.9257 456762.7932 522639.7018 452294.3034 641437.5135 0.717935515 1.002005698 0.778666474 0.991887483 0.738434231 0.736144856 0.712092423 0.814794412 0.705126055 1 19.2909492 3.199592632 24.99909393 0.770956579 0.875154553 0.120423561 0.113223888 262.1449042 168172.8314 0.029731369 0.035536303 1583.407259 -3.199592632 0.104197974 YPFILPHQQVDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPFILPHQQVDK 12 0 Q9ULC4-2;Q9ULC4;Q9ULC4-3;A0A3B3IRV3 Q9ULC4-2 MCTS1 Malignant T-cell-amplified sequence 1 0 ; 172.11 3.66E-05 721040000 1364790 1050700 1323510 1053680 1393350 1527310 1522490 1117100 1309220 992870 FALSE TRUE 1418672.963 1231149.552 1358001.758 1262094.759 1156508.865 1172615.399 1403153.256 1102127.102 1262101.428 1187403.867 1.19476869 1.036841454 1.143673013 1.062902686 0.97398105 0.987545545 1.181698405 0.928182173 1.062908302 1 20.17937929 7.999999999 0.458398194 1.01887033 4.730026334 0.296978994 0.072164729 114.9680925 1.358907531 0.04109567 401.3921261 99999999.84 -7.999999999 3.711156004 YPGSTFMDHVLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPGSTFMDHVLR 12 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 ; 159.99 6.93E-05 592850000 343290 395710 408500 460030 462820 528140 469270 460120 399200 435650 FALSE TRUE 356843.3543 463670.1143 419145.8456 551022.5609 384150.0217 405487.489 432487.3912 453952.844 384832.87 521007.2765 0.6849105 0.889949402 0.804491347 1.057610106 0.737321798 0.778276057 0.830098562 0.871298472 0.738632429 1 18.990944 -1.307912486 3.657162666 1.000499454 0.829689132 0.222120424 0.099183118 22655596.43 45851408.77 123721.7491 0.022655523 0.04921387 1.307912486 -0.170810322 YPHLGQKPGGSDFLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPHLGQKPGGSDFLR 15 1 P56211;H3BMD8;P56211-2;H3BTD3 P56211 ARPP19 cAMP-regulated phosphoprotein 19 0 ; 164.09 9.02E-07 1115860000 897520 801540 959470 794060 1195220 1148950 929570 961770 990370 957620 FALSE TRUE 932954.7826 939198.2599 984474.5764 951122.698 992056.9313 882123.775 856707.8744 948879.0463 954726.7772 1145247.304 0.814631721 0.820083362 0.859617458 0.83049547 0.866238172 0.770247414 0.748054915 0.828536372 0.833642457 1 20.12722774 0.616659563 2.426030674 0.999983195 0.816663535 0.721062411 0.033905967 1.844773367 10.99856442 0.034777972 0.009318791 4.136752738 -0.616659563 -0.183319659 YPHVEDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPHVEDYR 8 0 K7ESG5;K9J957;P61289;P61289-2;A0A087WTV2;B3KQ25;P61289-3 K7ESG5 PSME3 Proteasome activator complex subunit 3 0 ; 111.95 0.0031354 375580000 296460 252760 306690 311890 493850 363610 412450 323130 361890 252130 FALSE TRUE 308164.4697 296169.5638 314682.5933 373580.9111 409905.5534 279167.0881 380121.0913 318798.9709 348865.6496 301530.0462 1.022002529 0.982222394 1.043619358 1.238950864 1.359418601 0.925835059 1.260640842 1.057270991 1.156984699 1 18.20194224 3.943213339 7.345232611 1.146713559 1.004513962 0.192380707 0.120814617 0.38623934 44.13632856 0.030014382 0.055029447 8774.31738 -3.943213339 -0.142199596 YPHYFPLLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPHYFPLLK 9 0 P52888;K7EP46 P52888 THOP1 Thimet oligopeptidase 0 68.227 0.058667 72338000 6302.7 495060 369970 527990 220520 567590 255620 403040 369260 896140 FALSE TRUE 6551.535463 580082.704 379611.7221 632424.8461 183036.0892 435775.8244 235583.8365 397637.908 355970.4047 1071721.475 0.006113095 0.541262555 0.354207442 0.590101869 0.170786994 0.406612944 0.219818154 0.371027284 0.332148243 1 20.03149859 -1.114770027 4.880791838 1.000031469 0.341569527 0.60303606 0.16233102 5.03E-05 9.13E-06 0.142333879 0.033546818 0.076776794 1.114770027 -0.658461942 YPIEHGIITNWDDMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 28 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 ;;;;;;;;;;;;;;;;;;;;;;;;;;; 224.59 5.81E-15 3.50682E+11 125541969 85526220 107241207 83120927 132757655 124931989 131449127 105578769 113944276 79857255 FALSE TRUE 130498462.9 100214683 110036001 99561998.27 110191556.2 95918427.92 121145800.9 104163658.3 109843443.8 95503755.16 1.366422322 1.049327148 1.15216413 1.042493021 1.153792917 1.004341952 1.26849254 1.090676049 1.150147903 1 26.50905412 7.999997497 0.013366965 2.41E-07 2.457665977 0.170110684 0.101806886 15212.33963 15.7037906 1182.420429 1757.608993 99999423.58 -7.999997497 2.457665735 YPIEHGIITNWDDMEKIWHHTFYNELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YPIEHGIITNWDDMEKIWHHTFYNELR 27 1 P68133;P68032;A6NL76 P68133 ACTA1;ACTC1 "Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1" 0 ;; 215.68 1.29E-34 4072190000 739371 1131269 1108976 601973 1775360 1364521 607603 1013117 1232212 2114170 FALSE TRUE 768561.938 1325555.651 1137876.826 721041.4627 1473584.941 1047631.677 559977.4892 999537.8237 1187864.931 2528401.133 0.303971521 0.524266357 0.450038093 0.285176847 0.582812957 0.414345518 0.22147494 0.395324069 0.469808732 1 21.26979394 0.735665132 3.217537285 0.999968629 0.398169441 0.753153956 0.102888877 1.102964691 12.87018419 0.097823193 0.02541238 5.440829692 -0.735665132 -0.601799188 YPLAAAAERPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPLAAAAERPPR 12 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 0 145.28 5.81E-05 86641000 83734 45439 43139 44532 53859 71470 53300 37631 46463 45651 FALSE TRUE 87039.88298 53242.79478 44263.23778 53340.29669 44704.06642 54872.17564 49122.20673 37126.618 44790.80571 54595.43941 1.594270216 0.975224219 0.81074973 0.977010118 0.818824189 1.005068852 0.89974927 0.68003149 0.820412954 1 15.73649282 4.736034842 3.168631467 0.863200508 1.700509234 0.829786125 0.096766718 0.134078989 2.105547936 0.024996038 0.27773738 54454.63377 -4.736034842 0.837308726 YPLFEGQETGKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 ; 125.03 0.00050098 1037360000 834620 552610 745260 559870 1056190 895230 923820 729840 840020 510590 FALSE TRUE 867571.4421 647516.4688 764682.0878 670610.615 876659.2011 687326.3998 851408.5744 720057.6886 809787.8443 610630.3347 1.420780123 1.060406652 1.252283165 1.098226827 1.43566271 1.125601466 1.39431097 1.179203927 1.326150698 1 19.21993974 -1.019036182 4.833470637 0.999995522 1.246931575 0.253816298 0.130414889 5.57E-06 1.13E-06 0.111651391 0.026316008 0.095711433 1.019036182 0.246936053 YPNKYESVIATLCENLDSLDEPEAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPNKYESVIATLCENLDSLDEPEAR 25 1 Q10567-4;Q10567-3;Q10567-2;Q10567;C9J1E7;H7C034 Q10567-4 AP1B1 AP-1 complex subunit beta-1 0 156.43 3.26E-08 65098000 42834 35568 48809 41390 43409 51782 62625 41230 45394 34986 FALSE TRUE 44525.1194 41676.52732 50081.00264 49576.81846 36030.35369 39756.41526 57716.28886 40677.37929 43760.27881 41840.83685 1.064154609 0.996072986 1.19694075 1.1848907 0.861128897 0.950182125 1.37942482 0.972193253 1.045874846 1 15.35262409 YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPS(ph)QAPSPNQPTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPSQAPSPNQPTK 48 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVT(0.004)HNLPT(0.09)VAHPS(0.446)QAPS(0.37)PNQPT(0.09)K 96.474 3.61E-06 239640000 41763 93161 112180 96776 122340 126100 92230 122560 111690 102330 TRUE FALSE 43411.83549 109160.6771 115103.503 115918.004 101544.6905 96815.18606 85000.7716 120917.2837 107670.2987 122379.6043 0.354730968 0.89198423 0.940544821 0.94720035 0.829751747 0.791105566 0.694566485 0.988050945 0.879805907 1 16.90100361 4.739380077 24.81826665 0.879694412 0.354730787 0.761226682 0.089016883 30.22445654 915210.5774 0.02178877 0.131444148 54875.70046 -4.739380077 -0.524963626 S(ph)FSKEVEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 SFSKEVEER 9 1 Q04637-9;Q04637-4;Q04637-5;Q04637;Q04637-8;Q04637-3;E7EUU4;E9PGM1;E7EX73;Q04637-6;Q04637-7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 S(0.998)FS(0.002)KEVEER;S(0.998)FS(0.002)KEVEER;S(0.998)FS(0.002)KEVEER;S(0.949)FS(0.051)KEVEER;S(0.998)FS(0.002)KEVEER;S(1)FSKEVEER;S(0.819)FS(0.181)KEVEER 160.52 3.95E-05 5048870000 12341800 7802160 8319490 4813320 9042830 9094130 6285690 5804850 6382440 4323530 TRUE FALSE 12829063.79 9142120.288 8536302.744 5765380.33 7505732.987 6982156.13 5793001.193 5727045.481 6152737.231 5170642.925 2.481135128 1.768081923 1.650917085 1.115021945 1.451605361 1.350345834 1.120363807 1.107608002 1.189936594 1 22.30191225 8 0.501765624 1.13052393 44.73663059 0.911310079 0.126907354 27.94906796 0.295236999 0.065267429 1285.682907 100000000 -8 43.60610666 up YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPSQAPSPNQPT(ph)K ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTVAHPSQAPSPNQPTK 48 0 P56545;P56545-3;P56545-2 P56545 CTBP2 C-terminal-binding protein 2 1 YPPGIVGVAPGGLPAAMEGIIPGGIPVT(0.055)HNLPT(0.055)VAHPS(0.287)QAPS(0.287)PNQPT(0.315)K 46.645 0.013989 457910000 9427 175730 136270 150710 81918 93349 75700 87844 101560 165740 TRUE FALSE 9799.185239 205910.2605 139821.3081 180519.9882 67993.60762 71670.10947 69766.43619 86666.59486 97904.87544 198213.5797 0.049437507 1.03883024 0.70540731 0.910734716 0.343032035 0.361580219 0.351976067 0.437238432 0.493936266 1 17.59669628 -1.433598524 3.045443988 1.008848429 0.52936564 0.210667979 0.277560825 87454251.61 105703491.2 6659073.786 0.070005146 0.036846944 1.433598524 -0.479482789 YPPYTT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPPYTTPPR 9 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 YPPYT(0.005)T(0.995)PPR;YPPYT(0.001)T(0.999)PPR 136.84 0.0020282 1468000000 655050 784970 801600 810690 839430 867590 741150 754740 737190 772760 TRUE FALSE 680911.8798 919782.4913 822490.3545 971042.0623 696743.9884 666105.371 683056.7264 744623.9448 710658.6759 924167.5266 0.736784036 0.995255151 0.889979718 1.050720821 0.753915246 0.72076258 0.739104877 0.805723988 0.768971702 1 19.81779487 3.206856622 24.99995902 0.782234727 0.921675435 0.228176002 0.105757535 232.9267089 183672.0358 0.028596639 0.034182335 1610.113985 -3.206856622 0.139440709 YPQQYQPS(ph)PLPVHYELLTDGYTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPQQYQPSPLPVHYELLTDGYTR 23 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 YPQQY(0.001)QPS(0.999)PLPVHYELLTDGYTR;YPQQYQPS(1)PLPVHYELLTDGYTR 114.03 0.00045645 94371000 71250 58464 59532 63943 69739 86824 68436 67698 67888 60603 TRUE FALSE 74063.00502 68504.73721 61083.45283 76590.73455 57884.78969 66660.44183 63071.8075 66790.61904 65444.72414 72476.99754 1.021882908 0.945192813 0.842797783 1.056759208 0.798664289 0.919746183 0.870232069 0.9215423 0.902972341 1 16.14523557 4.643408723 3.666709332 0.910022155 1.024769562 0.174707904 0.069740196 0.3590192 7.864524495 0.015374046 0.091673351 43995.54716 -4.643408723 0.114747407 YPRPASVPPS(ph)PSLSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPRPASVPPSPSLSR 15 1 P13807;P13807-2 P13807 GYS1 "Glycogen [starch] synthase, muscle" 1 YPRPAS(0.001)VPPS(0.937)PS(0.058)LS(0.004)R 64.249 0.040115 108720000 42044 37391 38037 42479 53657 57787 44066 43659 37152 34309 TRUE FALSE 43703.92959 43812.61339 39028.27547 50881.21941 44536.40231 44366.84502 40611.99177 43073.82252 35814.90678 41031.19166 1.065139174 1.067787983 0.951185522 1.240061947 1.085427951 1.081295552 0.989783385 1.049782392 0.872870256 1 15.32443343 1.734557764 1.402415238 0.951771103 1.080971065 0.301709425 0.077148249 0.512358858 1.927379284 0.061067813 0.023663427 54.26974287 -1.734557764 0.129199962 YPS(ph)CESVTDEYAGHLIQILK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YPSCESVTDEYAGHLIQILK 20 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 YPS(0.997)CES(0.001)VT(0.001)DEYAGHLIQILK;YPS(0.994)CES(0.005)VT(0.001)DEYAGHLIQILK;YPS(0.999)CES(0.001)VTDEYAGHLIQILK 220.13 5.63E-25 410560000 485870 404560 429540 411820 544850 585560 536810 487030 505740 311884 TRUE FALSE 505052.5228 474040.033 440734.1653 493276.7668 452236.5916 449572.5642 494733.4295 480502.1595 487538.5162 372991.6984 1.354058347 1.270913093 1.181619235 1.322487254 1.212457525 1.205315202 1.326392602 1.288238214 1.307102861 1 18.508784 -0.972690318 4.466364976 0.999993374 1.272464715 0.693714598 0.054664271 0.019300215 16052958.91 266.9379038 0.012623645 0.10649021 0.972690318 0.272471342 YPS(ph)LGQKPGGSDFLMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPSLGQKPGGSDFLMK 16 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 1 YPS(1)LGQKPGGSDFLMK;YPS(1)LGQKPGGSDFLMK 117.37 0.00021505 472260000 492220 265189 395310 302840 474130 488100 529240 347150 438590 289069 TRUE FALSE 511653.2257 310733.1479 405612.1034 362740.8481 393537.552 374746.1722 487756.7859 342497.0221 422805.2316 345706.536 1.480021846 0.898835039 1.173284451 1.049273908 1.13835728 1.084000831 1.410898364 0.990716074 1.223017755 1 18.39918835 0.358847759 0.011282232 6.14E-05 2.212059271 0.052738006 0.170859418 9260.554811 40.3963789 4081.06538 3834.852791 2.284797731 -0.358847759 2.211997897 YPS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPSPQK 6 0 Q9P2N5;U3KPZ7 Q9P2N5 RBM27 RNA-binding protein 27 1 YPS(1)PQK;YPS(1)PQK 80.438 0.067671 595420000 1887830 1037230 1470030 1075750 1970750 2080630 1823860 1484620 1621060 884830 TRUE FALSE 1962362.986 1215366.184 1508340.189 1288530.139 1635762.619 1597435.215 1680901.087 1464721.097 1562718.367 1058195.497 1.854442767 1.148527079 1.425388969 1.21766738 1.545803798 1.509584211 1.588459875 1.384168711 1.476776617 1 20.01317475 -1.223622924 4.760052862 0.999909625 1.448403924 0.354208243 0.186101937 0.000164626 2.69E-05 0.166187208 0.039162846 0.059755389 1.223622924 0.448494299 YPSPFFVFGEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPSPFFVFGEK 11 0 Q08211;Q08211-2 Q08211 DHX9 ATP-dependent RNA helicase A 0 104.52 0.0060221 98301000 45065 50767 65168 42089 85581 70308 62831 63108 69778 52677 FALSE TRUE 46844.201 59485.83734 66866.33162 50414.07858 71033.97219 53980.03253 57906.14204 62262.14048 67266.70341 62998.04959 0.743581766 0.944248873 1.061403203 0.800248244 1.127558276 0.85685244 0.919173568 0.988318541 1.067758508 1 15.94301954 4.724975724 4.389060051 0.971610905 0.729866608 0.354328302 0.093865544 0.198019254 9.225428517 0.020876487 0.145364615 53085.47703 -4.724975724 -0.241744297 YPSSISS(ph)SPQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.003)S(0.499)S(0.499)PQK 221.27 8.95E-12 473380000 682980 400130 458410 478700 615850 717080 868550 565130 557620 290080 TRUE FALSE 709944.5778 468849.2149 470356.5412 573385.4312 511168.037 550549.0375 800470.7815 557555.3567 537551.3651 346915.6221 2.046447414 1.351479106 1.355824043 1.652809487 1.473465028 1.586982547 2.307393298 1.60717858 1.549516167 1 18.40422528 2.453913841 24.99973198 1.716142504 1.553031406 0 0.352325839 831.3633277 895564.5328 0.117115859 0.097991081 284.3896854 -2.453913841 -0.163111099 YPSSISSS(ph)PQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPSSISSSPQK 11 0 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.004)S(0.057)S(0.939)PQK;YPSSIS(0.013)S(0.029)S(0.958)PQK 101.56 0.0033524 876930000 1230390 702160 963180 886630 1210900 1304480 1540140 1111120 1111800 549400 TRUE FALSE 1278966.747 822750.518 988281.2621 1062002.768 1005071.651 1001534.29 1419419.802 1096227.254 1071786.535 657044.4111 1.946545356 1.252199249 1.504131601 1.61633331 1.529686021 1.524302273 2.16031029 1.668421853 1.631223882 1 19.32563136 YPSSISSS(ph)PQKDLTQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YPSSISSSPQKDLTQAK 17 1 Q14157-4;Q14157-1;F8W726;Q14157-3;Q14157;Q14157-5 Q14157-4 UBAP2L Ubiquitin-associated protein 2-like 1 YPSSIS(0.001)S(0.424)S(0.575)PQKDLTQAK;YPSSIS(0.138)S(0.116)S(0.745)PQKDLTQAK;YPS(0.001)S(0.005)IS(0.326)S(0.264)S(0.404)PQKDLTQAK;YPSS(0.001)IS(0.049)S(0.341)S(0.609)PQKDLTQAK 190.83 1.67E-10 4123320000 4053200 1933980 2916960 2145490 3770860 3797230 4273640 3293830 3543020 1616310 TRUE FALSE 4213223.466 2266126.021 2992978.374 2569861.518 3129890.564 2915380.88 3938660.93 3249681.596 3415507.402 1932994.998 2.179634955 1.172339309 1.548363227 1.329471375 1.619192272 1.508219567 2.037594993 1.681163996 1.766950978 1 20.88240647 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YPSVLLLVCQDSEQSKPDVHFFHCDEVEAELVHEDIESALADCR 44 1 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 0 ; 61.782 0.0020892 164114000 46182 49231 47702 40356 60703 69580 46462 52816 55689 47599 FALSE TRUE 48005.30102 57686.04129 48945.15331 48338.29635 50384.72574 53421.0995 42820.18703 52108.08791 53684.76377 56925.11271 0.843306209 1.013367186 0.859816537 0.849155918 0.885105419 0.938445212 0.752219627 0.915379618 0.943076987 1 15.79677762 1.097667783 2.608117306 0.996405571 0.880939936 0.263800153 0.064149452 0.337541533 4.490998742 0.058896437 0.016044206 12.52182942 -1.097667783 -0.115465635 YQAVTATLEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQAVTATLEEK 11 0 P40429;M0QYS1;Q8J015;Q6NVV1 P40429 RPL13A;RPL13a;RPL13AP3 60S ribosomal protein L13a;Putative 60S ribosomal protein L13a protein RPL13AP3 0 183.99 0.001869 0 104230 87576 88511 89635 114120 126040 107100 101580 110130 101170 FALSE TRUE 108345.0809 102616.4968 90817.66937 107364.5355 94721.92316 96769.12015 98705.22215 100218.4863 106166.4428 120992.3245 0.895470695 0.848124021 0.750606865 0.8873665 0.782875472 0.799795529 0.815797387 0.828304495 0.877464279 1 16.884556 0.84585258 2.109994754 0.999864357 0.823084232 0.613456648 0.041821051 0.355932543 2.999323793 0.038208478 0.010509031 7.012172316 -0.84585258 -0.176780126 YQCGFCNCVNDVPPFYFQHLDHIGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQCGFCNCVNDVPPFYFQHLDHIGR 25 0 O94855;O94855-2;E9PDM8 O94855 SEC24D Protein transport protein Sec24D 0 117.43 0.00058961 494370000 118570 123640 122850 99008 131500 129780 140370 111820 100900 104380 FALSE TRUE 123251.2352 144874.2082 126051.5719 118591.4869 109147.677 99640.56183 129367.4326 110321.2358 97268.62871 124831.2625 0.987342695 1.160560306 1.009775671 0.950014319 0.874361716 0.798201987 1.036338414 0.883762878 0.779200873 1 16.92961976 3.745538345 2.405650464 0.895839114 1.074322244 0.413176419 0.084452419 0.268444782 3.044941582 0.022910387 0.044946516 5565.937755 -3.745538345 0.17848313 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YQDEVFGGFVTEPQEESEEEVEEPEER 27 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVT(0.001)EPQEES(0.999)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER 222.04 1.56E-34 4933550000 2524514 3242054 3214193 3118304 3304894 3897291 3056807 3346762 3193763 3320339 TRUE FALSE 2624183.762 3798851.555 3297957.51 3735095.224 2743129.298 2992204.229 2817206.48 3301904.13 3078820.093 3970895.855 0.660854341 0.956673681 0.830532361 0.940617775 0.690808673 0.753533796 0.709463704 0.831526247 0.775346472 1 21.92103309 4.794676855 21.17280639 0.818353263 0.660847318 0.195536572 0.100784055 14230.21677 5367900.234 0.023396128 22.8781469 62327.09059 -4.794676855 -0.157505945 YQDTHPER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQDTHPER 8 0 C9JAH0;F8WD54;A0A087WUI8;Q96IJ6;Q96IJ6-2 C9JAH0 GMPPA Mannose-1-phosphate guanyltransferase alpha 0 ; 85.355 0.016802 1166220000 1131480 1108250 1195350 1240290 1375260 1564530 1338250 1323000 1282440 1120520 FALSE TRUE 1176151.704 1298583.317 1226501.803 1485615.66 1141493.796 1201191.618 1233354.468 1305267.349 1236285.235 1340064.44 0.877682945 0.969045426 0.915255838 1.10861509 0.851820078 0.896368549 0.920369522 0.97403327 0.922556556 1 20.35387095 -1.47465309 2.616010298 1.002502211 0.940666228 0.07045131 0.067330513 11671996.43 11484230.05 210962.3674 0.015971329 0.033523311 1.47465309 -0.061835983 YQDTPGVEHIPVVQIDLSVPLKVPGLPMSDQYVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQDTPGVEHIPVVQIDLSVPLKVPGLPMSDQYVK 34 1 O14617-5;O14617-2;O14617;A0A2R8Y611;O14617-3;O14617-4 O14617-5 AP3D1 AP-3 complex subunit delta-1 0 129.46 3.19E-08 68732000 69726 47740 70183 46091 76252 75378 72154 68632 72091 47353 FALSE TRUE 72478.83632 55938.97363 72012.02664 55207.66223 63290.71228 57872.60186 66498.38094 67712.1003 69496.45899 56630.91372 1.279845787 0.987781584 1.271602768 0.974867941 1.117600055 1.021925978 1.17424171 1.195673809 1.227182371 1 15.78930219 YQEALHLGSQLLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQEALHLGSQLLR 13 0 O00231;O00231-2 O00231 PSMD11 26S proteasome non-ATPase regulatory subunit 11 0 ; 153.14 4.56E-05 1211310000 1079360 1922040 1737940 2037880 1909250 2432110 1764840 1910380 1658500 1962210 FALSE TRUE 1121973.966 2252135.419 1783232.144 2440966.582 1584716.367 1867289.311 1626507.229 1884774.481 1598810.909 2346667.481 0.47811374 0.959716465 0.759899798 1.040184262 0.675305036 0.795719601 0.693113636 0.803170665 0.681311231 1 21.162182 -1.961729678 2.596642023 1.178072276 0.776056266 0.181061247 0.148207355 18965025.52 7041875.48 20300154.73 0.033014228 0.010921199 1.961729678 -0.40201601 YQEGGVESAFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQEGGVESAFHK 12 0 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 ; 91.202 0.0084305 371870000 171613 358800 293830 348160 328060 414380 260870 325960 300980 517780 FALSE TRUE 178388.4138 420421.1089 301487.4512 417025.0088 272296.4784 318146.525 240422.3277 321591.0394 290147.7886 619229.0775 0.288081455 0.678942776 0.486875475 0.673458376 0.439734645 0.513778401 0.38826072 0.519340986 0.468562926 1 19.24011369 -1.303670224 3.018290509 1.003938789 0.50124001 0.646920244 0.111794557 11965730.2 15504515.56 426229.6279 0.025047924 0.049696955 1.303670224 -0.502698779 YQELINDIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YQELINDIAR 10 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 ;;; 147.74 6.13E-05 768400000 462385 1704660 1184340 1537360 1096420 1727460 929200 1281380 971240 2050720 FALSE TRUE 480640.3168 1997422.095 1215204.873 1841445.219 910050.92 1326283.595 856366.876 1264205.197 936285.2621 2452519.321 0.195978198 0.814436844 0.495492477 0.750838211 0.371067788 0.540784158 0.349178442 0.515472064 0.381764683 1 21.22583307 -1.681259739 4.06002443 1.02536003 0.500836275 0.428989771 0.175966284 0.036797543 0.002888863 0.155211776 0.036781499 0.020832446 1.681259739 -0.524523755 YQELLER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQELLER 7 0 Q9H074;Q9H074-3;Q9H074-2;H0YA44 Q9H074 PAIP1 Polyadenylate-binding protein-interacting protein 1 0 ;; 137.62 0.0066656 529520000 673740 620280 628220 649680 680900 783330 715200 714370 606950 541720 FALSE TRUE 700339.7754 726808.2649 644591.9293 778184.7649 565160.8612 601413.479 659140.7552 704795.0386 585105.9881 647859.6621 1.081005373 1.121860655 0.99495611 1.201162552 0.872350749 0.928308265 1.017412865 1.087882268 0.903136933 1 19.30532181 3.239246387 24.99998897 0.981882122 1.093840756 0.417729441 0.074927206 22.18896368 808883.2112 0.02214074 0.028275916 1734.787909 -3.239246387 0.111958634 YQEQGGEAS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQEQGGEASPQR 12 0 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR 177.21 2.47E-05 641950000 567860 570140 511230 568750 563480 642570 624770 538020 547920 513350 TRUE FALSE 590279.5513 668057.1099 524553.0738 681247.0525 467699.8709 493342.8557 575798.8949 530808.7219 528200.4662 613931.1038 0.961475233 1.088162997 0.85441684 1.109647399 0.761811656 0.803580162 0.937888456 0.864606335 0.860357885 1 19.22771724 3.236879493 24.99999986 0.866211926 0.998834793 0.340996262 0.089669996 49.1067279 730271.0227 0.024144369 0.030315887 1725.359078 -3.236879493 0.132622867 YQEQGGEAS(ph)PQRTWEQQQEVVSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQEQGGEASPQRTWEQQQEVVSR 23 1 Q9UJU6;H0Y5J4;Q9UJU6-5 Q9UJU6 DBNL Drebrin-like protein 1 YQEQGGEAS(1)PQRTWEQQQEVVSR 287.17 8.22E-53 204480000 54619 79524 72626 41064 75358 87425 47233 66359 71629 125210 TRUE FALSE 56775.4003 93181.62839 74518.69322 49186.33664 62548.67408 67121.86869 43530.75404 65469.56615 69051.08628 149742.5022 0.379153543 0.622279093 0.497645572 0.328472784 0.41770822 0.448248611 0.290704065 0.437214319 0.461132179 1 17.19212424 0.595688855 2.9153314 0.999993903 0.427775472 0.797092048 0.086213419 2.906423193 20.42060181 0.085177539 0.022327675 3.94174799 -0.595688855 -0.57221843 YQEQGGEAS(ph)PQSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQEQGGEASPQSR 13 0 Q9UJU6-2;Q9UJU6-3;B4DDD6;Q9UJU6-6;Q9UJU6-4 Q9UJU6-2 DBNL Drebrin-like protein 1 YQEQGGEAS(0.998)PQS(0.002)R;YQEQGGEAS(0.967)PQS(0.033)R;YQEQGGEAS(0.99)PQS(0.01)R 220.96 2.09E-11 616333000 479743 564005 525544 501393 575655 701617 525413 541371 517638 573372 TRUE FALSE 498683.6241 660868.4714 539240.1084 600567.0389 477805.3687 538677.0849 484229.7561 534114.8072 499008.3095 685713.2655 0.727248034 0.963767955 0.786392995 0.875828235 0.696800533 0.785571918 0.706169445 0.778918586 0.727721534 1 19.38724591 YQEQHSVMCK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQEQHSVMCK 10 0 Q5QNY5;P40855;P40855-5;H0YJ60;H0YDY4 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 0 91.937 0.0074402 37821000 86556 89511 87810 88754 127960 124240 92905 109770 106960 108510 FALSE TRUE 89973.29772 104883.818 90098.40074 106309.2763 106209.4049 95387.14288 85622.86334 108298.7127 103110.5305 129770.457 0.693326508 0.808225696 0.694290541 0.819210156 0.818440556 0.735045134 0.659802434 0.834540582 0.794560896 1 16.98560246 0.614461871 1.172396428 0.999463498 0.755579218 0.61784677 0.057459774 0.846130773 1.759281764 0.053400499 0.016384207 4.115872104 -0.614461871 -0.24388428 YQETFNVIER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQETFNVIER 10 0 Q13011;M0R248;M0QZW4 Q13011 ECH1 "Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial" 0 ;; 207.34 3.11E-07 574650000 246816 443250 348371 396980 275299 432500 312821 330835 289000 483254 FALSE TRUE 256560.4863 519374.7395 357449.8344 475501.4591 228503.7743 332058.4296 288301.2726 326400.698 278598.9465 577938.3688 0.443923609 0.898668037 0.618491268 0.822754613 0.395377408 0.574556817 0.49884432 0.56476731 0.482056499 1 19.14055613 -1.16426418 4.387584965 1.000087523 0.593565348 0.397309917 0.151823822 0.000126316 2.41E-05 0.142853018 0.033663557 0.068507137 1.16426418 -0.406522175 YQEVDRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQEVDRR 7 1 Q96MU7-2;Q96MU7 Q96MU7-2 YTHDC1 YTH domain-containing protein 1 0 ;; 98.523 0.017959 391013000 233807 273306 268031 252919 318023 355003 269702 294809 280579 270924 FALSE TRUE 243037.8809 320244.1795 275016.108 302945.6233 263965.5641 272558.9334 248562.0525 290857.5676 270481.0166 324006.3706 0.750102167 0.988388527 0.848798459 0.934998971 0.814692512 0.841214735 0.767151745 0.897690891 0.834801538 1 18.30566265 -1.38303073 2.859345783 1.002446025 0.857126851 0.290370502 0.068637155 12576819.18 14649948.09 254781.8021 0.017416037 0.041397038 1.38303073 -0.145319173 YQHDDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQHDDGR 7 0 P60983;G3V4P8 P60983 GMFB Glia maturation factor beta 0 ; 121.99 0.0043845 124507000 64310 132404 94067 127841 89199 126328 86684 104546 84383 141759 FALSE TRUE 66849.00846 155143.357 96518.4633 153127.5682 74036.98584 96990.23652 79889.48157 103144.7319 81346.07231 169533.9619 0.394310424 0.915116684 0.569316391 0.903226507 0.436708875 0.572099156 0.471229957 0.608401589 0.479821691 1 17.37121478 -1.078868546 4.391676923 1.000031879 0.602083621 0.334616014 0.171253783 21839728.93 5365194.561 7509.191977 0.037694828 0.083393356 1.078868546 -0.397948258 YQHTGAVLDCAFYDPTHAWSGGLDHQLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQHTGAVLDCAFYDPTHAWSGGLDHQLK 28 0 O43684;O43684-2;J3QT28;J3QSX4 O43684 BUB3 Mitotic checkpoint protein BUB3 0 237.13 1.28E-45 261300000 79092 116780 122900 128750 111290 140240 100820 113840 114320 126260 FALSE TRUE 82214.61323 136836.0566 126102.875 154216.3657 92372.96555 107671.3854 92917.46496 112314.161 110205.6455 150998.2296 0.544474021 0.906209675 0.835128169 1.02131241 0.611748666 0.713063892 0.615354665 0.743811112 0.729847269 1 17.20417211 3.207079959 24.99996104 0.715322814 0.833051332 0.070866984 0.150620618 401.0044077 318451.4549 0.041319008 0.049390036 1610.942203 -3.207079959 0.117728519 YQILPLHSQIPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQILPLHSQIPR 12 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ; 191.26 5.60E-06 1936400000 1749870 2135700 2068510 2112140 2241800 2635500 2029650 2122940 1968200 2095150 FALSE TRUE 1818956.219 2502489.862 2122417.07 2529914.988 1860739.637 2023445.066 1870560.729 2094485.462 1897364.866 2505654.528 0.725940547 0.99873699 0.847050958 1.009682284 0.742616197 0.807551497 0.746535769 0.835903529 0.757233228 1 21.25675608 3.218790106 24.99964855 0.803937952 0.899287233 0.124393945 0.10176785 394.3988764 498713.0081 0.026845698 0.032127037 1654.969924 -3.218790106 0.095349282 YQLDKDGVVLFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQLDKDGVVLFK 12 1 P07237;H7BZ94;I3L398;I3L312;I3L3U6 P07237 P4HB Protein disulfide-isomerase 0 ; 196.57 1.87E-07 5058000000 5336400 3591900 4310590 3870460 6057600 5667700 5502500 4534550 4757430 2811310 FALSE TRUE 5547085.193 4208780.884 4422927.517 4636025.436 5027931.316 4351462.57 5071199.672 4473771.774 4586211.024 3362132.369 1.649871149 1.251818912 1.315512607 1.378894382 1.495459061 1.294256767 1.508328381 1.330635229 1.364078067 1 21.68094509 0.234357109 1.065397749 0.998454951 1.399058083 0.53168535 0.113112905 3.101540957 3.654422184 0.110027343 0.031369821 1.71536723 -0.234357109 0.400603132 YQLQSQENFEAFMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQLQSQENFEAFMK 14 0 A8MW49;P07148 A8MW49 FABP1 "Fatty acid-binding protein, liver" 0 ; 66.989 0.040837 1359200000 781180 395180 690690 399180 723210 712640 815830 665890 698260 287230 FALSE TRUE 812021.5896 463049.0909 708689.9488 478136.6126 600279.0225 547140.1602 751883.1128 656964.8337 673129.759 343507.2191 2.36391419 1.348003958 2.063100597 1.391925951 1.747500457 1.592805419 2.188842245 1.912521185 1.959579658 1 18.38998089 YQPLASTAS(ph)DNDFVTPEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLAST(0.006)AS(0.994)DNDFVTPEPR 181.26 3.34E-14 78397000 22484 22762 22382 26422 30425 36132 25544 26558 24988 30669 TRUE FALSE 23371.68568 26671.19644 22965.29331 31648.19274 25253.36937 27740.89059 23541.79453 26202.03345 24088.68676 36678.00336 0.637212595 0.727171438 0.626132592 0.862865746 0.688515379 0.756335897 0.641850493 0.714380039 0.656761125 1 15.16262748 -1.197173444 3.920059187 1.000193567 0.703983967 0.638307815 0.067438103 7290572.556 4466635.829 12139.6408 0.014675086 0.063507725 1.197173444 -0.296209601 YQPLASTASDNDFVT(ph)PEPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 YQPLASTASDNDFVT(1)PEPR 92.307 0.021657 35043000 33299 32430 35283 36107 29642 40282 25223 31449 37285 40680 TRUE FALSE 34613.67023 37999.60023 36202.50397 43248.85683 24603.46343 30927.11598 23245.95535 31027.4776 35943.12013 48650.46713 0.711476626 0.781073697 0.744134766 0.88897105 0.505718956 0.635700288 0.477815666 0.6377632 0.738803186 1 15.57016604 0.874478866 4.492417125 0.999964074 0.668677342 0.417210687 0.115653413 0.888918395 30.34256816 0.118579581 0.030113153 7.489949089 -0.874478866 -0.331286732 YQQETSVSQLPGRPKS(ph)PLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQQETSVSQLPGRPKSPLSK 20 2 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 YQQETSVSQLPGRPKS(0.986)PLS(0.014)K 137.89 1.46E-06 431700000 108710 51997 78875 46444 111640 108090 90126 84544 99237 48108 TRUE FALSE 113001.9547 60927.08027 80930.5473 55630.48458 92663.47268 82987.73562 83061.68862 83410.82597 95665.47975 57533.84152 1.964095422 1.058978136 1.406659892 0.966917611 1.610590745 1.442416036 1.443701419 1.449769801 1.662768855 1 15.81212318 YQQEVDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQQEVDR 7 0 P33176;O60282;O60282-2;Q12840;J3KNA1;A0A0G2JMZ6 P33176;Q12840 KIF5B;KIF5C;KIF5A Kinesin-1 heavy chain;Kinesin heavy chain isoform 5C;Kinesin heavy chain isoform 5A;Kinesin-like protein 0 ;; 205.13 0.00057649 875138000 1135120 1417230 1368100 1261850 1447070 1731040 1439070 1327070 1301570 1404800 FALSE TRUE 1179935.414 1660628.228 1403753.81 1511440.164 1201097.558 1329032.194 1326271.933 1309282.797 1254726.75 1680043.663 0.702324255 0.988443494 0.835546028 0.899643382 0.714920442 0.791070032 0.789427062 0.779314744 0.74684175 1 20.6800673 3.2597143 24.99769788 0.790373586 0.864418639 0.05371111 0.097665909 498.0477243 588548.3717 0.024661492 0.033360291 1818.504166 -3.2597143 0.074045053 YQQGDFGYCPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YQQGDFGYCPR 11 0 P67870;Q5SRQ3;Q5SRQ6;N0E472;A0A0G2JM12 P67870 CSNK2B;CSNK2B-LY6G5B-1181;CSNK2B-LY6G5B--991 Casein kinase II subunit beta 0 ;;;; 201.33 1.02E-07 1486630000 1000740 1099621 995994 922564 1133980 1248868 1005451 993857 980516 1179787 FALSE TRUE 1040249.988 1288472.353 1021950.422 1105044.406 941226.4846 958837.3338 926641.1234 980535.9725 945227.4207 1410943.674 0.737272513 0.913199 0.724302777 0.783195266 0.667090049 0.679571659 0.65675274 0.694950472 0.669925694 1 20.42822897 4.108164147 9.752207288 0.715395479 0.825019513 0.085507215 0.105174997 0.482851966 40.35167227 0.023888888 0.051754078 12828.15346 -4.108164147 0.109624034 YQQPFEDFRIS(ph)QEHLADHFDSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQQPFEDFRISQEHLADHFDSR 22 1 P19174-2;P19174;V9GY71;V9GYH5 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 YQQPFEDFRIS(1)QEHLADHFDSR;YQQPFEDFRIS(1)QEHLADHFDSR 186.43 1.93E-17 974000000 319410 382180 433680 430910 521820 564300 431430 494120 492310 524760 TRUE FALSE 332020.5534 447816.4421 444982.0571 516142.7119 433121.2228 433249.877 397613.3893 487497.1296 474591.8593 627576.6749 0.529051774 0.713564509 0.709048113 0.822437692 0.690148694 0.690353696 0.633569419 0.776792939 0.756229284 1 19.25943221 -5 0.19805547 2.333415735 0.657235729 0.637190291 0.070713801 92.48315415 0.913555309 48.63733418 0.175088902 1.00E-05 5 -1.676180005 YQVAGAEYWDNNDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQVAGAEYWDNNDHR 15 0 O95685 O95685 PPP1R3D Protein phosphatase 1 regulatory subunit 3D 0 ; 145.69 4.02E-06 329480000 275110 258139 236232 251455 324620 335120 290550 289000 270720 198683 FALSE TRUE 285971.5552 302472.3652 242388.4 301192.0485 269441.2084 257293.4588 267775.9318 285126.4277 260976.8401 237611.1298 1.20352761 1.272972211 1.020105414 1.267583925 1.133958702 1.082834205 1.12695029 1.199970843 1.098335925 1 17.85824289 -5 0.129419114 0.480167118 1.225110621 0.334982541 0.07329081 174.6995989 1.429549171 23.66906508 0.550289301 1.00E-05 5 0.744943503 YQVFFFGTHETAFLGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YQVFFFGTHETAFLGPK 17 0 P51858;P51858-2;P51858-3 P51858 HDGF Hepatoma-derived growth factor 0 ;; 258.2 3.72E-27 4467250000 1510730 1990030 2292110 1984210 2586100 2776570 2573160 2326040 2200440 1783690 FALSE TRUE 1570374.787 2331802.172 2351844.27 2376680.816 2146515.646 2131753.697 2371468.995 2294863.238 2121246.594 2133169.905 0.736169577 1.093116009 1.102511462 1.114154485 1.006256295 0.999336102 1.111711257 1.075799557 0.99441052 1 21.02456745 4.742032392 24.88724355 1.060917979 0.736169447 0.796648203 0.04828742 133.5587182 957364.0564 0.011663307 0.085093197 55211.86178 -4.742032392 -0.324748532 YQVGVHYELTEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YQVGVHYELTEEEK 14 0 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 155.98 3.03E-07 0 279640 215460 238880 220530 271400 340760 287770 275570 232010 174870 FALSE TRUE 290680.4031 252463.579 245105.409 264150.1758 225267.5249 261623.6543 265213.8355 271876.4349 223660.0054 209132.4284 1.389934623 1.207194795 1.172010534 1.263076118 1.077152533 1.250995153 1.268162176 1.300020456 1.069465922 1 17.67405726 1.091487958 4.951508611 1.002717237 1.237202428 0.537389337 0.077630038 0.144969239 5.485056065 0.074158423 0.018805096 12.34491084 -1.091487958 0.234485191 YQYAIDEYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQYAIDEYYR 10 0 G3V583;Q8N128;Q8N128-2 G3V583 FAM177A1 Protein FAM177A1 0 ; 142 8.50E-05 254870000 259170 263410 231762 221579 302730 317460 280370 223905 230000 303060 FALSE TRUE 269402.2317 308648.6185 237801.9081 265406.6649 251272.0627 243734.7262 258393.8668 220903.9197 221722.3449 362438.8046 0.743304051 0.851588226 0.656116026 0.732279937 0.693281347 0.672485184 0.71293102 0.609493015 0.611751121 1 18.4673779 -1.077778108 4.668838174 1.000015046 0.695793599 0.646632172 0.066924573 1.11E-05 2.20E-06 0.068833395 0.016223385 0.083603006 1.077778108 -0.304221447 YQYGGLNSGRPVT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 1 YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR;YQYGGLNSGRPVT(1)PPR 151.58 1.02E-06 8760170000 1914100 2133420 2004724 2124239 2390250 2745910 2384463 2176038 2010557 2172225 TRUE FALSE 1989670.146 2499818.289 2056968.754 2544407.134 1983956.159 2108214.017 2197562.559 2146871.77 1938197.446 2597830.899 0.765896713 0.962271367 0.791802405 0.979435242 0.76369719 0.811528579 0.845922096 0.82640936 0.746082991 1 21.30887609 3.193772948 24.99999789 0.823970813 0.875165245 0.047653716 0.088700104 344.9136991 192525.9302 0.023364124 0.027925584 1562.330631 -3.193772948 0.051194432 YQYGGLNSGRPVTPPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 0 ; 114.35 0.00053835 774380000 464330 367120 453960 358540 580860 601180 544070 492420 516020 382010 FALSE TRUE 482662.1069 430170.0042 465790.5705 429458.1419 482125.6247 461565.056 501424.3717 485819.9153 497448.541 456857.5455 1.05648273 0.941584545 1.019553196 0.940026374 1.055308442 1.01030411 1.097550816 1.06339475 1.088848255 1 18.80138486 2.793850624 1.701731491 1.065456911 0.990280937 0.281495271 0.044628643 0.376529569 2.17535109 0.015654452 0.015905371 622.0862813 -2.793850624 -0.075175974 YRADTLGELDLER ddPTM_MDA-MB-175_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 ; 164.15 3.09E-06 211670000 167951 236860 205344 212345 278040 276660 209750 223240 194777 285260 FALSE TRUE 174581.8352 277538.8625 210695.4333 254346.2072 230778.8601 212409.9078 193309.2469 220247.8329 187767.0138 341151.2354 0.51174323 0.81353615 0.617601262 0.745552649 0.676470832 0.622626817 0.56663798 0.645601745 0.550392302 1 18.38005191 -2.076237469 2.626080704 1.564258202 0.644173276 0.614306257 0.085744601 20022658.04 11104014.25 67223305.08 0.019586503 0.008390011 2.076237469 -0.920084926 YRCELLYEGPPDDEAAMGIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRCELLYEGPPDDEAAMGIK 20 1 P13639 P13639 EEF2 Elongation factor 2 0 117.38 3.49E-05 0 54433 69877 71786 65261 99070 99358 65163 77641 73150 96168 FALSE TRUE 56582.05687 81877.83118 73656.80213 78169.43102 82230.11679 76283.61029 60055.35379 76600.34939 70517.34579 115010.2784 0.491973915 0.711917512 0.640436691 0.679673436 0.714980591 0.66327646 0.522173797 0.666030467 0.613139511 1 16.81140327 -1.130271017 4.297285294 1.00006625 0.638039686 0.707205866 0.070652291 13940597.1 38631577.74 13192.5771 0.016244782 0.074084778 1.130271017 -0.362026564 YRDELKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRDELKR 7 2 P33992;B1AHB1 P33992 MCM5 DNA replication licensing factor MCM5;DNA helicase 0 80.684 0.016449 53557000 23448 246800 74688 201370 57697 162140 41309 73333 42254 503410 FALSE TRUE 24373.74515 289185.9802 76634.43064 241200.385 47889.68455 124485.4423 38071.09264 72350.09108 40733.28679 602043.5511 0.04048502 0.480340633 0.12729051 0.400636108 0.079545216 0.20677149 0.063236443 0.120174182 0.067658372 1 19.19950833 -1.503064543 5.167854499 1.002219167 0.179119111 0.751693432 0.142026831 0.003472061 0.00033387 0.131483523 0.030929154 0.03140042 1.503064543 -0.823100056 YRDILEPQNER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRDILEPQNER 11 1 A0A494C1L5;P50851-2;P50851;E9PEM5;A0A494BZW2;A0A494C0R9;H0YAC6 A0A494C1L5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 0 106.54 0.0021135 169400000 149750 167290 188120 154250 184250 205290 184950 187850 175640 150410 FALSE TRUE 155662.2456 196020.7562 193022.5617 184760.1896 152931.2508 157614.5087 170453.1357 185332.178 169318.7507 179879.9597 0.865367359 1.089730932 1.073063181 1.027130481 0.85018504 0.876220502 0.947593806 1.030310315 0.941287462 1 17.45667494 3.363869724 19.37184721 0.945292286 1.023540101 0.17974475 0.074784841 3.320373742 551.0280344 0.021698195 0.02937946 2311.371339 -3.363869724 0.078247815 YRDQFTDQQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRDQFTDQQK 10 1 E9PDF6;O43795;O43795-2;H7C2Y7 E9PDF6 MYO1B Unconventional myosin-Ib 0 ; 100.69 0.0048369 0 303290 214675 253490 184972 350470 355360 293270 257040 279640 214823 FALSE TRUE 315264.1234 251543.7613 260096.1576 221558.9095 290897.2346 272833.0255 270282.7311 253594.7992 269575.811 256913.4538 1.227121891 0.979099216 1.012388233 0.862387338 1.132277155 1.061964726 1.052038058 0.987082597 1.04928647 1 17.97092292 1.849160344 0.00690535 6.45E-08 2.049248568 0.041137995 0.090028655 10708.21621 64.85397491 9574.694708 9664.419989 70.65783794 -1.849160344 2.049248503 YRDYYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YRDYYR 6 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;; 100.07 0.034732 484500000 285897 359650 285760 275504 483430 432890 325595 319707 299353 523200 FALSE TRUE 297184.4343 421417.0898 293207.1404 329997.8689 401256.7413 332357.858 300074.0131 315421.8506 288579.344 625711.0227 0.474954769 0.673501144 0.46859833 0.527396605 0.641281241 0.531168296 0.479572841 0.504101477 0.46120227 1 19.25513699 -1.363236873 3.492979526 1.002797978 0.53074693 0.806926704 0.069100248 25019820.46 31524000 691489.8691 0.016308381 0.04332745 1.363236873 -0.472051047 YREDIINVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YREDIINVR 9 1 Q15276-2;Q15276 Q15276-2 RABEP1 Rab GTPase-binding effector protein 1 0 ; 180.67 4.41E-05 414320000 119775 190934 157899 179629 163558 196498 146651 165480 133150 204068 FALSE TRUE 124503.8095 223725.4292 162013.9777 215159.0801 135756.4696 150864.3175 135156.1114 163262.0113 128357.9575 244051.2175 0.510154429 0.916715071 0.663852364 0.881614451 0.55626221 0.618166625 0.553802242 0.668966182 0.525946803 1 17.89682442 -1.145986054 4.361878586 1.000063682 0.661838074 0.37273764 0.133984466 18440957.74 4844952.458 11188.18303 0.030209687 0.071451927 1.145986054 -0.338225608 YREQEYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YREQEYR 7 1 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 0 143.89 0.0021809 88654000 46202 59310 49985 51001 70942 74217 61856 56261 55273 78699 FALSE TRUE 48026.09064 69496.03113 51287.65016 61088.84558 58883.30418 56981.22652 57007.56509 55506.91332 53283.73553 94118.56227 0.510272251 0.738388151 0.544925984 0.649062673 0.625629023 0.605419645 0.605699489 0.589755219 0.566134185 1 16.52219166 -1.553923177 6.071741301 1.000768993 0.607006184 0.803259741 0.058788201 0.000543997 4.00E-05 0.050599283 0.011904456 0.027930379 1.553923177 -0.39376281 YRESNTAGNDVFHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YRESNTAGNDVFHK 14 1 O95833 O95833 CLIC3 Chloride intracellular channel protein 3 0 ;; 132.31 3.07E-05 485470000 551380 512904 561593 453961 783130 710680 575970 593990 676460 624990 FALSE TRUE 573148.9082 600991.2722 576228.5749 543753.1309 650013.8423 545635.3405 530823.9664 586028.5356 652114.3367 747444.8243 0.766810993 0.804061053 0.770931253 0.727482636 0.869647927 0.730000828 0.710184818 0.784042536 0.872458161 1 19.51160756 0.985899652 2.49037976 0.998980233 0.768934993 0.741433038 0.042670317 0.13857842 1.953641406 0.040316916 0.010900165 9.680541527 -0.985899652 -0.23004524 YREWHHFLVVNMK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YREWHHFLVVNMK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 77.527 0.016585 757840000 725440 847510 730680 612080 1186160 1066250 762050 835170 884490 1322250 FALSE TRUE 754080.9314 993063.2498 749722.1211 733147.5971 984536.9469 818629.5967 702318.5298 823975.9122 852657.3777 1581319.571 0.476868145 0.627996559 0.474111707 0.463630256 0.622604668 0.51768764 0.44413447 0.52106856 0.539206238 1 20.59269752 0.573396394 3.135797664 0.999998674 0.519014825 0.855104471 0.059229981 3.5757422 25.84499522 0.055424016 0.014422506 3.744522062 -0.573396394 -0.480983849 YREYS(ph)PPYAPSHQQYPPSHATPLPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YREYSPPYAPSHQQYPPSHATPLPK 25 1 Q9UPT8 Q9UPT8 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 YREYS(0.998)PPYAPS(0.002)HQQYPPSHATPLPK;Y(0.001)REY(0.001)S(0.988)PPYAPS(0.009)HQQYPPSHATPLPK 141.84 2.18E-07 489280000 347610 467630 545870 444640 654330 701180 505800 568350 616730 526390 TRUE FALSE 361333.9112 547941.8148 560095.8206 532588.4649 543107.2203 538341.5715 466154.0743 560732.1979 594534.0078 629526.0422 0.573977702 0.870403729 0.889710327 0.846014985 0.862723992 0.855153775 0.740484179 0.89072121 0.944415271 1 19.26390653 8 0.074132437 1.131152224 0.141450244 0.420470658 0.084559866 262.0283826 1.425751587 3.124302532 26.81685094 100000000 -8 -0.989701981 YRGDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YRGDYDR 7 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 ;;;;; 122.18 0.0039818 1719740000 1258160 1627560 1496510 1447810 1775180 1866250 1535420 1435430 1329990 1664640 FALSE TRUE 1307833.128 1907080.769 1535510.28 1734182.497 1473435.538 1432841.721 1415069.768 1416190.409 1282123.92 1990794.337 0.65694035 0.957949666 0.771305329 0.871100779 0.740124437 0.719733673 0.710806607 0.711369519 0.644026305 1 20.92491276 3.151494197 8.225572532 0.733295952 0.821352942 0.042427722 0.114439134 0.519597536 43.26676117 0.03031579 0.03632014 1417.405773 -3.151494197 0.08805699 YRGFTIPEAFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRGFTIPEAFR 11 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 ; 72.659 0.04167 439720000 528990 574790 466550 463930 717610 593370 476060 479870 461350 746590 FALSE TRUE 549874.9337 673505.7113 478708.6763 555693.9693 595630.9085 455568.8101 438745.1732 473438.1276 444746.1036 892870.0162 0.615851046 0.754315521 0.536145987 0.622368272 0.667096999 0.510229711 0.491387509 0.530243058 0.498108454 1 19.76809064 -1.470295303 8.666928643 1.000010809 0.578613474 0.709118453 0.080567123 1.79E-05 1.09E-06 0.083001584 0.01956316 0.033861383 1.470295303 -0.421397334 YRHDENILESEPIVYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRHDENILESEPIVYR 16 1 Q96F86;H3BSQ0;H3BPN4 Q96F86 EDC3 Enhancer of mRNA-decapping protein 3 0 76.85 0.015358 108980000 32809 166140 105510 174950 84906 159800 88490 123060 80019 169580 FALSE TRUE 34104.32465 194673.2526 108259.6773 209554.5878 70473.70845 122688.8718 81553.92257 121410.582 77139.13182 202805.9542 0.168162344 0.959899099 0.533809166 1.033276309 0.347493291 0.604956951 0.402127851 0.598653932 0.380359305 1 17.62974048 -1.020973882 4.575502556 1.000013489 0.574041005 0.211332539 0.254183362 0.674042296 142351546.3 4531.145402 0.054635813 0.095285346 1.020973882 -0.425972485 YRLEVGIQAMEHLIHVLQTDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YRLEVGIQAMEHLIHVLQTDR 21 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 0 ;; 218.44 3.51E-25 320429300 164300.1 158412.6 189240.6 188652.8 211044.2 232190 222362.5 191289.1 190814.2 149160.5 FALSE TRUE 170786.7948 185618.7318 194172.3655 225967.7608 175170.9823 178267.3914 204933.1462 188725.1825 183946.8342 178385.6441 0.957402125 1.040547476 1.088497712 1.266737365 0.981979145 0.999337095 1.148820844 1.057961718 1.031175099 1 17.44463999 1.103698184 2.929241642 1.001925125 1.072529493 0.061440253 0.084719678 0.696071055 11.4464027 0.080890361 0.021699288 12.69691416 -1.103698184 0.070604367 YRPAS(ph)ASVSALIGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YRPASASVSALIGGR 15 1 P46108-2 P46108-2 CRK Adapter molecule crk 1 YRPAS(0.94)AS(0.049)VS(0.011)ALIGGR;YRPAS(1)ASVSALIGGR;YRPAS(0.999)AS(0.001)VSALIGGR;YRPAS(1)ASVSALIGGR;YRPAS(0.999)AS(0.001)VSALIGGR 211.67 7.65E-10 2072890000 706465 862616 927124 927350 1106141 1172070 933815 1010242 928608 1115980 TRUE FALSE 734356.7837 1010763.588 951285.6131 1110777.062 918119.5479 899874.5054 860620.1402 996701.3584 895187.5795 1334634.914 0.550230461 0.757333393 0.712768415 0.832270346 0.687918125 0.674247688 0.644835626 0.746797006 0.670735922 1 20.34801372 -2.322512406 2.235163783 2.558626671 0.70361652 0.618700962 0.071104292 4442654.627 480335.8572 35104614.81 0.016474702 0.004758692 2.322512406 -1.855010151 YRPETK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YRPETK 6 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 ;;;;; 120.52 0.018319 5558520000 6055690 4735340 5869900 4593670 7378610 7049870 6802650 6178610 6177350 4947550 FALSE TRUE 6294773.317 5548597.809 6022874.416 5502284.215 6124396.508 5412644.534 6269440.518 6095795.839 5955028.38 5916927.696 1.063858414 0.937749808 1.017905698 0.929922503 1.035063604 0.914772803 1.059577003 1.030229902 1.006439268 1 22.49641683 2.200271452 24.99992301 1.028150097 0.982657029 0.150344853 0.047163792 264.1059681 172439.5726 0.016054928 0.01185755 158.5884127 -2.200271452 -0.045493068 YRPLFDYFLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRPLFDYFLK 10 1 A0A0A0MSX9;P41252;J3KR24;Q5TCD1 A0A0A0MSX9 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 ; 108.7 0.0019307 219362000 674400 690150 623760 536410 1720030 1166120 877300 658660 749510 1451160 FALSE TRUE 701025.8328 808677.8939 640015.698 642510.297 1427659.915 895306.3027 808534.9336 649831.7401 722535.2815 1735487.018 0.403936086 0.465965971 0.368781611 0.370219017 0.822627827 0.515881878 0.465883597 0.374437684 0.416329983 1 20.72690914 -1.174098787 4.252840899 1.00016356 0.466405191 0.610581704 0.127668734 31853196.42 17587733.4 45663.72796 0.031084146 0.066973225 1.174098787 -0.533758369 YRPSMEGYRAPS(ph)RQDVYGPQPQVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRPSMEGYRAPSRQDVYGPQPQVR 24 3 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 YRPS(0.208)MEGYRAPS(0.792)RQDVYGPQPQVR;YRPS(0.037)MEGYRAPS(0.963)RQDVYGPQPQVR 91.1 0.051502 327640000 29010 53711 33259 30451 53581 53106 20295.7 33855.8 38953 87127 TRUE FALSE 30155.3372 62935.44644 34125.75686 36474.11691 44473.32076 40772.93633 18704.87 33402.01838 37551.08914 104197.8675 0.289404552 0.603999371 0.327509168 0.350046674 0.426816036 0.391302983 0.179512983 0.320563359 0.360382511 1 16.66896623 -1.125788277 3.627071222 1.000428795 0.358860138 0.777254447 0.102607401 41198705.55 70795637.32 210501.3326 0.024634419 0.074853433 1.125788277 -0.641568657 YRPYDGAASAYAQNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRPYDGAASAYAQNYR 16 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 0 ; 285.18 7.50E-36 697760000 218020 268750 261450 219960 311750 350140 254100 224620 245330 324230 FALSE TRUE 226627.5979 314905.7219 268263.6018 263467.4315 258758.8464 268825.2914 234182.978 221609.3363 236500.6212 387756.6607 0.584458298 0.812122018 0.691834929 0.679465908 0.667322763 0.693283491 0.603943147 0.571516517 0.609920203 1 18.56479204 -1.129434481 5.248475652 1.000009274 0.656120471 0.702490419 0.066943133 7.79E-06 1.29E-06 0.0694756 0.016375115 0.074227617 1.129434481 -0.343888803 YRPYDGAASAYAQNYRYPEPERPS(ph)SR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRPYDGAASAYAQNYRYPEPERPSSR 26 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YRPYDGAASAYAQNYRYPEPERPS(0.735)S(0.265)R 141.9 1.60E-06 798230000 62322 84911 92813 42556 100910 94931 35597 67136 81742 139440 TRUE FALSE 64782.52068 99493.80373 95231.78303 50973.44978 83757.35424 72884.71394 32806.81412 66236.15173 78800.12139 166760.5983 0.388476183 0.59662657 0.57106885 0.305668427 0.502261056 0.43706196 0.19673001 0.397193057 0.472534413 1 17.34741893 0.787832664 4.782631277 0.999997011 0.422026714 0.701457582 0.111990029 2.377342593 53.23977472 0.113090931 0.02863405 6.135255649 -0.787832664 -0.577970297 YRPYDGAASAYAQNYRYPEPERPSS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRPYDGAASAYAQNYRYPEPERPSSR 26 3 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0 O15027 SEC16A Protein transport protein Sec16A 1 YRPYDGAASAYAQNYRYPEPERPS(0.164)S(0.836)R 105.71 0.017429 622330000 31658 62723 59354 28599 63865 69899 29503 40026 37102 95017 TRUE FALSE 32907.88229 73495.18733 60900.814 34255.79684 53009.25011 53666.01658 27190.47777 39489.51694 35766.70627 113633.7619 0.289595994 0.646772456 0.535939433 0.301457914 0.466492081 0.472271759 0.239281683 0.347515705 0.314754221 1 16.79403201 -1.084025474 4.992643953 1.00001216 0.402580255 0.687122145 0.121144228 2.21E-05 4.06E-06 0.120482152 0.028397158 0.082408977 1.084025474 -0.597431905 YRQDDDQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YRQDDDQR 8 1 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ;;; 115.7 0.0022012 6001220000 3736410 4233210 4086090 3941220 4518260 5004090 4320730 4345500 4007390 4104060 FALSE TRUE 3883926.352 4960230.888 4192576.862 4720781.553 3750247.779 3841965.935 3982059.892 4287255.68 3863164.817 4908171.98 0.791318309 1.010606578 0.854203333 0.961820729 0.76408239 0.782769216 0.811312217 0.873493369 0.787088316 1 22.22675437 3.243695492 24.99992817 0.829077614 0.908475474 0.133461177 0.083416152 214.4902328 1044270.311 0.021630656 0.028421523 1752.65119 -3.243695492 0.07939786 YRS(ph)PEPDPYLSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YRSPEPDPYLSYR 13 1 H3BUL5;H3BVF8;P49761-3;P49761-1;P49761;H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BQG1;P49761-2 H3BUL5 CLK3 Dual specificity protein kinase CLK3 1 YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR;YRS(1)PEPDPYLSYR 174.78 1.17E-05 5104450000 1847190 2151900 2057710 2048320 2209060 2444660 2014140 1988250 2008100 2173870 TRUE FALSE 1920118.488 2521472.086 2111335.613 2453471.582 1833564.77 1876924.764 1856266.444 1961600.761 1935828.873 2599798.205 0.738564433 0.969872231 0.81211519 0.943716161 0.705271958 0.721950173 0.714004048 0.754520392 0.744607358 1 21.30996822 3.230953193 24.99974436 0.754559955 0.869627965 0.153699779 0.100747571 233.7909924 768290.1032 0.026388595 0.032119086 1701.975064 -3.230953193 0.115068011 YRS(ph)PYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YRSPYR 6 1 Q14498-3 Q14498-3 RBM39 RNA-binding protein 39 1 YRS(0.998)PY(0.002)R;YRS(0.997)PY(0.003)R;YRS(0.999)PYR 76.478 0.045391 1258470000 278463 326869 300474 360152 391660 415550 297119 311717 343640 391330 TRUE FALSE 289456.9343 383006.2081 308304.5993 431388.9907 325085.7731 319044.8102 273830.0364 307538.9435 331272.4635 468003.621 0.618492937 0.818383001 0.658765414 0.921764216 0.694622346 0.681714405 0.585102388 0.65712941 0.707841668 1 18.83616017 0.908750385 19.78428344 1 0.70327916 0.474573767 0.093161322 8902.286388 1930155.896 0.090645398 0.022661349 8.104950839 -0.908750385 -0.29672084 YRS(ph)PYSGPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.734)PYS(0.265)GPK;YRS(0.882)PYS(0.118)GPK;YRS(0.988)PYS(0.012)GPK;YRS(0.985)PY(0.003)S(0.013)GPK;YRS(0.959)PY(0.001)S(0.041)GPK 147.72 0.00024128 5959570000 3194670 2436500 2941040 2267820 3738530 3597120 3387800 2978250 3106410 2120790 TRUE FALSE 3320798.038 2854949.922 3017685.918 2716388.027 3103056.006 2761743.395 3122255.384 2938331.43 2994610.911 2536318.196 1.309298669 1.125627662 1.189789958 1.070996546 1.223449018 1.088878911 1.231018801 1.158502681 1.180692121 1 21.27430432 -1.311335751 3.146090971 0.998839901 1.171563615 0.380524551 0.066966174 8534453.99 12139859.76 94683.11384 0.014857664 0.048827473 1.311335751 0.172723714 YRS(ph)QSGEDESMNQPGPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRSQSGEDESMNQPGPIK 18 1 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 YRS(0.838)QS(0.159)GEDES(0.002)MNQPGPIK 118.35 6.38E-05 362540000 149730 132940 172870 134700 216510 223190 189710 174910 192240 157270 TRUE FALSE 155641.456 155771.4109 177375.1342 161343.258 179707.7075 171357.505 174840.0345 172565.6175 185321.32 188084.0454 0.827510147 0.828201087 0.94306316 0.857825328 0.955464921 0.911068797 0.929584613 0.917492056 0.985311219 1 17.52101795 8 0.163344511 1.00145253 0.319752408 0.672003621 0.033040144 36.87816601 0.386577397 0.08914752 6.08817366 100000000 -8 -0.681700121 YRSDS(ph)QDEVEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRSDSQDEVEK 11 1 H0YBZ4;Q15390-2;Q15390;H7C5V5;H0YF01 H0YBZ4 MTFR1 Mitochondrial fission regulator 1 1 YRS(0.021)DS(0.979)QDEVEK 98.694 0.0032279 103800000 62924 53833 64782 40735 78702 80343 65102 59569 59305 46830 TRUE FALSE 65408.28811 63078.39899 66470.27214 48792.26142 65324.26215 61684.55586 59999.13513 58770.57499 57170.62463 56005.44189 1.167891653 1.126290533 1.186853811 0.871205722 1.166391335 1.101402896 1.071309021 1.049372579 1.020804813 1 15.7732794 8 0.33233498 1.037903857 2.47754495 0.218801337 0.080799805 95.35108091 1.360500244 0.070026872 84.4938979 100000000 -8 1.439641093 YRSPYS(ph)GPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 YRS(0.093)PYS(0.907)GPK;YRS(0.13)PYS(0.87)GPK 145.15 0.00025741 2063850000 1659470 1368840 1640620 1331440 1992850 1870990 1870020 1604190 1711750 1195410 TRUE FALSE 1724987.157 1603927.622 1683375.905 1594794.858 1654106.069 1436480.928 1723442.946 1582688.457 1650144.452 1429627.702 1.206598861 1.121919797 1.177492506 1.115531586 1.157018758 1.004793714 1.205518712 1.107063367 1.154247676 1 20.44720806 -5 0.216398431 0.336356684 1.154339415 0.367451108 0.055258591 160.4553994 1.603953853 46.50112118 0.102834039 1.00E-05 5 0.81798273 YRSQS(ph)GEDESMNQPGPIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRSQSGEDESMNQPGPIK 18 1 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 YRS(0.069)QS(0.931)GEDESMNQPGPIK 262.05 4.92E-31 323630000 362200 333980 401240 292350 580740 492010 384970 452270 462640 421370 TRUE FALSE 376499.9357 391338.467 411696.644 350175.9574 482026.0222 377748.134 354795.0455 446208.0604 445989.6768 503929.3839 0.747128363 0.776574019 0.816972888 0.694890928 0.956534859 0.749605294 0.70405707 0.885457516 0.885024154 1 18.94286206 1.169973745 1.51976212 0.991676617 0.78361039 0.472559151 0.072909227 0.312833677 1.387370137 0.065773215 0.019761219 14.79018971 -1.169973745 -0.208066227 YRVPDVLVADPPIAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YRVPDVLVADPPIAR 15 1 Q14697;F5H6X6;Q14697-2 Q14697;Q14697-2 GANAB Neutral alpha-glucosidase AB 0 75.463 0.028962 809850000 560580 773630 657230 804810 850270 1063300 709240 825710 752960 798360 FALSE TRUE 582712.1313 906494.9345 674357.9537 963999.0159 705741.4091 816364.6895 653647.9155 814642.708 725861.1167 954783.3565 0.610308221 0.949424734 0.706294207 1.009652095 0.739163921 0.8550261 0.684603383 0.853222569 0.760236458 1 19.86481389 -1.772648573 2.343174174 1.05764009 0.803425484 0.21342155 0.116546073 9073072.965 5782541.533 2996440.328 0.025604714 0.016879183 1.772648573 -0.254214606 YS(ph)GAYGASVSDEELK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSGAYGASVSDEELK 15 0 C9JRZ6;Q9NX63;A0A286YEX5;F8WAR4 C9JRZ6 CHCHD3 MICOS complex subunit MIC19 1 YS(1)GAYGASVSDEELK;YS(1)GAYGASVSDEELK;YS(1)GAYGASVSDEELK;Y(0.001)S(0.999)GAYGASVSDEELK 313.32 3.30E-56 249426000 630292 378409 467948 418024 618513 724727 711183 474304 509396 320656 TRUE FALSE 655176.4149 443397.8021 480143.1093 500707.8995 513378.3812 556420.1376 655438.6181 467946.7307 491062.9375 383482.4039 1.708491467 1.15624028 1.252060341 1.305686765 1.338727347 1.450966542 1.70917521 1.220256069 1.280535776 1 18.54880086 0.925115411 1.694995195 1.005945328 1.390437334 0.318142236 0.177198314 0.552223438 3.231109457 0.166435738 0.047760703 8.416187672 -0.925115411 0.384492005 YS(ph)NVSSIEDSFAMEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSNVSSIEDSFAMEK 15 0 O15231-3;O15231-4;O15231-7;O15231;O15231-8;O15231-6;H0Y704;O15231-2;O15231-9;O15231-5 O15231-3;O15231-5 ZNF185 Zinc finger protein 185 1 Y(0.004)S(0.987)NVS(0.007)S(0.003)IEDSFAMEK;Y(0.001)S(0.998)NVSSIEDSFAMEK 97.352 0.0035107 51712000 71952 59075 84023 71068 96527 103086 94915 72668 88764 82447 TRUE FALSE 74792.72052 69220.67171 86212.70841 85125.03828 80119.37502 79145.83878 87475.31429 71694.00432 85569.40098 98600.91111 0.758539852 0.702028723 0.87436016 0.863329125 0.812562218 0.802688717 0.887165375 0.727113 0.867835804 1 16.58931336 -5 0.283696734 2.434797475 0.795768318 0.48446006 0.059985126 210.2415063 2.001877359 178.0000373 0.068388057 1.00E-05 5 -1.639029157 YS(ph)PAPGGPPGAPTELLQQLEAEEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSPAPGGPPGAPTELLQQLEAEEKR 25 1 Q92817;K7EKI0 Q92817 EVPL Envoplakin 1 YS(0.999)PAPGGPPGAPTELLQQLEAEEKR 83.22 0.011686 52448000 30474 75658 47161 80716 56757 80370 48450 58561 52618 73791 TRUE FALSE 31677.13705 88651.67296 48390.0544 96681.38389 47109.46541 61705.28552 44652.3624 57776.08558 50724.28846 88248.93364 0.358952066 1.004563674 0.548335854 1.095552999 0.533824755 0.699218483 0.505981892 0.654694433 0.574786418 1 16.42929123 -1.148651198 4.96232391 1.000019531 0.672359345 0.179853612 0.21458932 4.22E-05 7.24E-06 0.189188801 0.044589572 0.071014789 1.148651198 -0.327660187 YS(ph)PPAISPLVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YS(1)PPAISPLVSEK;YS(1)PPAISPLVSEK 142.45 4.11E-05 117034000 264140 189394 256370 232990 313040 348860 376960 241620 264360 173309 TRUE FALSE 274568.4512 221920.9462 263051.2128 279074.7266 259829.5726 267842.552 347412.8902 238381.4791 254845.7352 207265.5803 1.324718029 1.070708151 1.26915049 1.346459582 1.253606953 1.292267397 1.676172617 1.150125741 1.229561294 1 17.66112103 0.903757591 1.828115047 1.004498386 1.303115122 0.272376201 0.148345807 0.619569251 4.203548114 0.141430502 0.039975767 8.01230717 -0.903757591 0.298616736 YS(ph)PPRDDDKVDNQAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSPPRDDDKVDNQAK 15 2 Q14669-3;Q14669;Q14669-2;Q14669-4 Q14669-3 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 YS(1)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK;YS(1)PPRDDDKVDNQAK 122.19 5.76E-05 1074890000 3851660 1264390 2237260 1373570 3243930 3125760 3126770 2127590 2463890 826580 TRUE FALSE 4003726.511 1481539.147 2295564.834 1645258.046 2692527.937 2399849.611 2881685.597 2099073.136 2375215.08 988532.5252 4.050171754 1.498725747 2.322194541 1.664343868 2.723762617 2.427689075 2.9151146 2.123423441 2.402768771 1 19.91492891 0.09550752 1.197548246 0.995834549 2.422300171 0.297087131 0.671454248 10.2582625 12.26673737 0.70871115 0.179290657 1.245969811 -0.09550752 1.426465622 YS(ph)PQSLTDPQIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YSPQSLTDPQIR 12 0 Q9ULL0 Q9ULL0 KIAA1210 Uncharacterized protein KIAA1210 1 YS(0.999)PQS(0.001)LTDPQIR;YS(0.997)PQS(0.002)LT(0.002)DPQIR;Y(0.052)S(0.942)PQS(0.005)LTDPQIR;YS(0.926)PQS(0.07)LT(0.004)DPQIR;Y(0.007)S(0.986)PQS(0.003)LT(0.004)DPQIR;Y(0.008)S(0.99)PQS(0.001)LT(0.001)DPQIR 230.5 5.95E-12 1072713000 1421013 1427396 1483405 1393249 1696520 1993150 1703820 1542634 1622811 1349731 TRUE FALSE 1477115.691 1672540.159 1522063.753 1668829.494 1408146.136 1530271.119 1570270.136 1521957.514 1564406.349 1614184.947 0.91508454 1.036151503 0.942930211 1.033852717 0.872357371 0.948014737 0.972794437 0.942864395 0.969161775 1 20.62237446 7.129347688 8.423490233 0.961823533 0.004838135 0 0.048415205 0 0 0.009917306 0 13469382.56 -7.129347688 -0.956985398 YS(ph)PRHS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YSPRHSR 7 1 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 2 Y(0.029)S(0.971)PRHS(1)R;Y(0.007)S(0.993)PRHS(1)R;Y(0.021)S(0.979)PRHS(1)R;Y(0.066)S(0.934)PRHS(1)R;Y(0.044)S(0.956)PRHS(1)R 99.343 0.0060304 57211610000 9565950 9310480 9095250 9672490 9917470 11524800 11563210 9864310 8867410 6695190 TRUE FALSE 9943621.093 10909482.51 9332279.687 11585679.65 8231701.992 8848339.86 10656855.39 9732095.059 8548273.646 8006984.293 1.24186844 1.362495806 1.165517421 1.446946719 1.02806521 1.105077709 1.330944959 1.215450749 1.06760215 1 22.93282755 -4.999999997 0.086193285 0.219414181 1.435784987 0.314856233 0.118133079 281.1308682 1.697249166 40.29329013 3.158173936 1.00E-05 4.999999997 1.216370806 YS(ph)PRHS(ph)RS(ph)R ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPRHSRSR 9 2 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 3 Y(0.12)S(0.88)PRHS(1)RS(1)R;Y(0.035)S(0.965)PRHS(1)RS(1)R 61.444 0.05886 1354860000 1478470 1600730 1521440 1186800 1891330 2019560 1380440 1617110 1493350 1467300 TRUE FALSE 1536841.137 1875642.926 1561089.976 1421545.498 1569842.402 1550547.797 1272237.506 1595435.286 1439604.625 1754789.342 0.87579808 1.068870708 0.889616741 0.810094673 0.894604477 0.88360908 0.725008681 0.909189068 0.820386009 1 20.74286642 4.016491952 24.22880046 0.855967374 0.974061835 0.218073878 0.080622479 199.1090938 292510.7292 0.018322837 0.03956333 10387.04353 -4.016491952 0.118094461 YS(ph)PSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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(0.058)S(0.927)PS(0.015)QNS(1)PIHHIPSR;Y(0.166)S(0.82)PS(0.015)QNS(0.999)PIHHIPSR;Y(0.145)S(0.631)PS(0.224)QNS(1)PIHHIPSR;Y(0.258)S(0.729)PS(0.059)QNS(0.954)PIHHIPSR;Y(0.002)S(0.722)PS(0.276)QNS(1)PIHHIPSR;Y(0.24)S(0.511)PS(0.25)QNS(1)PIHHIPSR;Y(0.06)S(0.648)PS(0.293)QNS(1)PIHHIPSR;Y(0.362)S(0.63)PS(0.205)QNS(0.803)PIHHIPSR 201.12 3.47E-09 10894420000 2007393 2233315 2248502 2581985 2255270 2948266 3144127 2507493 2302496 1727853 TRUE FALSE 2086646.426 2616869.478 2307099.809 3092693.927 1871920.011 2263575.903 2897682.11 2473884.158 2219629.619 2066392.714 1.009801483 1.266395038 1.116486617 1.496663198 0.90588783 1.09542387 1.402290131 1.19719942 1.07415672 1 20.97868303 1.085550775 3.814792699 1.003466252 1.194998296 0.120874643 0.165294178 0.402268973 10.73236375 0.151292054 0.039116782 12.17729355 -1.085550775 0.191532044 YS(ph)PSQNS(ph)PIHHIPSRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 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 Y(0.084)S(0.742)PS(0.174)QNS(1)PIHHIPSRR;Y(0.005)S(0.753)PS(0.242)QNS(1)PIHHIPSRR;YS(0.999)PS(0.001)QNS(1)PIHHIPSRR;YS(0.997)PS(0.003)QNS(1)PIHHIPSRR;Y(0.001)S(0.96)PS(0.039)QNS(1)PIHHIPSRR;Y(0.009)S(0.714)PS(0.277)QNS(0.999)PIHHIPS(0.001)RR 208.72 1.44E-11 7446660000 1770066 1819780 1828600 1584632 2169740 2431740 1774990 1895060 1871390 1768320 TRUE FALSE 1839949.572 2132313.059 1876254.818 1898067.48 1800928.37 1867005.238 1635861.646 1869659.82 1804039.039 2114788.447 0.870039542 1.008286697 0.88720686 0.897521207 0.851587955 0.882833099 0.773534416 0.884088346 0.853058868 1 21.01208192 3.812774131 2.205850853 0.864657931 0.93815193 0.095265733 0.062400686 0.496278283 4.693602253 0.016105148 0.034748872 6497.916569 -3.812774131 0.073493999 YS(ph)PSQNSPIHHIPSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPSQNSPIHHIPSR 15 0 E9PK91;Q9NYF8-3;E9PQN2;E9PKI6;A0A1W2PQ43;E9PK09;H0YF00;Q9NYF8;Q9NYF8-2;Q9NYF8-4;E9PJA7 E9PK91;Q9NYF8;Q9NYF8-4 BCLAF1 Bcl-2-associated transcription factor 1 1 YS(0.889)PS(0.111)QNSPIHHIPSR;YS(0.707)PS(0.292)QNSPIHHIPSR 187.57 2.16E-07 1238550000 98266 181059 197341 261670 206891 284670 269540 234020 189175 158830 TRUE FALSE 102145.6176 212154.4748 202483.8686 313427.545 171723.7417 218559.7067 248412.7505 230883.3447 182366.6287 189949.6975 0.537750883 1.116898198 1.065986791 1.65005551 0.904048514 1.150618872 1.307781764 1.215497301 0.960078542 1 17.53525789 4.802212626 2.58878903 1.180979827 0.33721542 0.450402201 0.2025313 0.554860926 4.111230325 0.047860343 1.088143609 63418.01234 -4.802212626 -0.843764406 YS(ph)PSQNSPIHHIPSRR ddPTM_MDA-MB-175_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 YS(0.977)PS(0.023)QNSPIHHIPSRR;Y(0.001)S(0.897)PS(0.102)QNSPIHHIPSRR;YS(0.992)PS(0.008)QNSPIHHIPSRR;YS(0.988)PS(0.012)QNSPIHHIPSRR 181.4 1.09E-09 964400000 152730 326079 271081 303697 261413 378255 248557 300246 229785 338141 TRUE FALSE 158759.8983 382080.5317 278145.5936 363767.3602 216978.1116 290411.0088 229074.4529 296221.6935 221515.0827 404393.2548 0.392587899 0.944824196 0.687809676 0.899538644 0.536552252 0.718140091 0.566464574 0.732508987 0.547771458 1 18.62539941 -1.141352963 4.896964587 1.000019855 0.681845209 0.274178964 0.160167533 3.15E-05 5.52E-06 0.140486936 0.033111024 0.072218263 1.141352963 -0.318174646 YS(ph)PTVQTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSPTVQTR 8 0 O60437;K7EKI8 O60437 PPL Periplakin 1 Y(0.001)S(0.98)PT(0.019)VQTR 97.472 0.0086097 162730000 90622 102960 106760 97082 125060 163120 116080 107760 105080 105330 TRUE FALSE 94199.82654 120642.5791 109542.2533 116284.5298 103802.3459 125237.8521 106981.3463 106315.6535 101298.1913 125967.3968 0.747811171 0.957728604 0.869607978 0.923131959 0.824041367 0.994208464 0.849278059 0.843993415 0.804161981 1 16.94269085 4.758207126 24.10688087 0.888039582 0.747810959 0.300208158 0.066939131 3611.103921 4430821.07 0.01513205 0.557141898 57306.92766 -4.758207126 -0.140228623 YS(ph)PVSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 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(0.857)PVS(0.143)K;YS(0.976)PVS(0.023)K 79.713 0.069677 2150220000 3548200 2387390 2952090 2600620 3250000 3741300 4206900 3283600 3117600 1749400 TRUE FALSE 3688285.676 2797405.661 3029023.891 3115014.874 2697566.161 2872439.775 3877152.185 3239588.713 3005398.185 2092161.436 1.762906826 1.337088818 1.447796446 1.488897951 1.289368074 1.372953218 1.853180218 1.54844108 1.436503959 1 20.99656275 0.844758058 4.958712852 1.000011236 1.509963397 0.450715826 0.168794765 1.766679102 55.72085265 0.165126349 0.04175315 6.99452228 -0.844758058 0.509952161 YS(ph)SQDADEQDWEFQKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSSQDADEQDWEFQKR 16 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 YS(0.824)S(0.176)QDADEQDWEFQKR;YS(0.884)S(0.116)QDADEQDWEFQKR 145.9 7.20E-07 224573000 156737 118337 134714 120419 173807 193317 205107 165473 191396 107087 TRUE FALSE 162925.0978 138660.4592 138224.7575 144237.5188 144263.3482 148422.0565 189030.1774 163255.1051 184507.6953 128068.6473 1.272170052 1.082704175 1.07930208 1.126251598 1.126453283 1.158925776 1.476006668 1.274746852 1.440693715 1 16.96655781 2.404639205 10.70313274 1.321275176 1.131709033 0.253106053 0.129816276 0.491017117 69.65703354 0.04125689 0.034504597 253.8862642 -2.404639205 -0.189566144 YS(ph)SSGSPANSFHFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSSSGSPANSFHFK 14 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 YS(0.579)S(0.102)S(0.16)GS(0.16)PANSFHFK 73.498 0.011838 0 46494 97361 113850 96168 110510 128620 98643 89314 97045 103450 TRUE FALSE 48329.61902 114081.9944 116817.0245 115189.7434 91725.54967 98749.95425 90911.1039 88116.89192 93552.36941 123719.0468 0.390640085 0.922105345 0.944212128 0.931059092 0.741402007 0.798179074 0.734818981 0.712233841 0.75616788 1 16.9167081 YS(ph)TPHAFTFNTSSPSSEGSLSQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSTPHAFTFNTSSPSSEGSLSQR 23 0 P04049;P04049-2;H7C155 P04049 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 YS(0.961)T(0.039)PHAFTFNTSSPSSEGSLSQR 140.82 1.23E-07 140040000 37311 36723 28960 35058 41342 41976 37306 38943 34168 38038 TRUE FALSE 38784.06709 43029.88958 29714.72139 41992.36776 34314.70161 32227.71015 34381.85824 38421.03278 32938.30035 45490.81782 0.852569133 0.945902748 0.65320262 0.923095468 0.754321493 0.70844429 0.755797761 0.844588746 0.72406481 1 15.47328775 4.280643549 24.99988961 0.790718758 0.899235985 0.144198261 0.100621408 243.5745326 144694.6949 0.022275564 0.061003138 19082.86373 -4.280643549 0.108517227 YSAPPDVYLDEAPSS(ph)PDVK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSAPPDVYLDEAPSSPDVK 19 0 Q9Y3S1;Q9Y3S1-4;Q9Y3S1-2;H0Y7T5;F8W9F9;H0Y7R3;H0Y493;H0Y7J9;E9PCD1 Q9Y3S1 WNK2 Serine/threonine-protein kinase WNK2 1 YSAPPDVYLDEAPS(0.023)S(0.977)PDVK 173.37 6.87E-12 49223000 118040 73553 84680 70046 108530 122190 109650 95855 104240 68435 TRUE FALSE 122700.3103 86185.15559 86886.83037 83900.88973 90082.10937 93813.22431 101055.3465 94570.22051 100488.4228 81843.52798 1.499206026 1.053047904 1.061621273 1.025137745 1.100662589 1.146250982 1.234738396 1.155500292 1.227811474 1 16.32058072 2.469141704 24.56812303 1.171328729 1.130287346 0 0.139832463 882.6834163 2717653.789 0.047328023 0.039666043 294.5382514 -2.469141704 -0.041041383 YSASKPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSASKPLK 8 1 P23526;P23526-2 P23526 AHCY Adenosylhomocysteinase 0 ; 63.283 0.067753 2046130000 2694600 1765310 2347180 1770100 3248700 2810600 2802900 2222050 2424700 1625450 FALSE TRUE 2800984.889 2068488.26 2408349.439 2120220.497 2696487.134 2157880.745 2583201.374 2192267.054 2337435.521 1943925.806 1.44089084 1.064077782 1.238910164 1.09069003 1.3871348 1.110063325 1.328858008 1.127752431 1.202430418 1 20.89054173 0.340207165 0.761114796 0.996803514 1.224033621 0.235972815 0.122026828 3.291701613 2.62808202 0.131340093 0.038040325 2.188805467 -0.340207165 0.227230108 YSCPESPSQELGGPLPS(ph)PGPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSCPESPSQELGGPLPSPGPR 21 0 A0A494BZV2;A0A1W2PPU9 A0A494BZV2 1 YSCPESPSQELGGPLPS(1)PGPR;YSCPESPSQELGGPLPS(1)PGPR 127.07 2.14E-05 201346000 116990 144211 159971 134406 169782 202529 151481 165419 157939 204492 TRUE FALSE 121608.8555 168978.1174 164139.9757 160991.1056 140922.5163 155494.7091 139607.5234 163201.8289 152254.8062 244558.2922 0.497259179 0.690952312 0.671169128 0.658293384 0.576232828 0.635818592 0.570855816 0.667333041 0.622570615 1 17.89981886 -0.634074043 0.861754537 1.025044857 0.623322914 0.806288333 0.055700717 12.06396338 5.310227672 1.018093838 0.016989571 0.232234082 0.634074043 -0.401721944 YSDFEWLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSDFEWLR 8 0 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 0 ; 161.9 0.00080229 423710000 415440 499280 449550 419980 770980 665280 533300 455340 450760 769290 FALSE TRUE 431841.892 585027.4561 461265.6423 503050.7905 639929.095 510778.8024 491498.5525 449236.9121 434537.2357 920017.6466 0.469384358 0.635887212 0.501366081 0.54678385 0.695561762 0.555183701 0.53422731 0.488291625 0.472314023 1 19.81130201 -1.770929406 2.812033779 1.102992034 0.545940344 0.79801541 0.068769361 10469613.46 8866607.055 7461786.191 0.016800159 0.016946132 1.770929406 -0.55705169 YSDPGPVYDCLVWHDGEVWR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YSDPGPVYDCLVWHDGEVWR 20 0 A0A494C0U1;Q5VZU9;P29144;A0A494C1B8 A0A494C0U1 TPP2 Tripeptidyl-peptidase 2 0 ;;;; 280.43 1.03E-44 699651000 250009.5 315500 297556 353059 333860 386956 320714 298756 286894 285825 FALSE TRUE 259880.0681 369684.6708 305310.5538 422893.0164 277110.5965 297091.3334 295575.5986 294751.6645 276568.741 341826.9363 0.760267962 1.081496604 0.893172894 1.237155331 0.810675131 0.869127918 0.864693701 0.862283317 0.809089956 1 18.38290656 YSEKEDKYEEEIK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSEKEDKYEEEIK 13 2 P67936;A0A2R8Y5V9;A0A2R8YH90;A0A2R8YE05;K7ENT6;A0A5F9UN72;K7EPB9;P67936-2;A0A2R8YHD2 P67936;P67936-2 TPM4 Tropomyosin alpha-4 chain 0 ;;; 185.12 5.02E-06 6716780000 6346900 1364316 2764915 1501181 4718480 4356290 4744090 2788277 3293110 888726 FALSE TRUE 6597480.513 1598626.66 2836970.956 1798110.121 3916434.455 3344607.668 4372235.829 2750904.708 3174591.614 1062854.844 6.20732036 1.504087476 2.669198877 1.691773934 3.684825333 3.146815096 4.11367164 2.588222393 2.986853409 1 20.01951315 YSEKQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSEKQER 7 1 B4DDF4;B4DUT8;Q99439;A0A087X1X5;H3BVI6;A0A087X271 B4DDF4 CNN2 Calponin;Calponin-2 0 ;; 106.36 0.0070411 1389110000 711950 901160 945480 695090 1271660 1247470 834940 914490 1034620 1059360 FALSE TRUE 740058.3357 1055927.22 970119.9855 832576.7274 1055503.687 957763.9981 769495.2211 902232.7574 997384.2283 1266921.309 0.584139149 0.833459199 0.765730262 0.657165304 0.833124899 0.755977495 0.607374125 0.712145854 0.787250337 1 20.27289549 0.856080003 3.413803178 0.99989903 0.721607528 0.526413195 0.080200423 0.530770224 10.99020886 0.074631617 0.019306516 7.179265309 -0.856080003 -0.278291502 YSESNFS(ph)VDDQDLSR ddPTM_MDA-MB-175_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 400.72 9.51E-116 689340000 368670 438190 498960 462020 581640 572990 474680 448040 537280 470880 TRUE FALSE 383225.3763 513445.7239 511963.3075 553406.177 482773.0406 439921.7562 437473.3413 442034.7566 517943.3978 563139.9205 0.680515379 0.911755152 0.90912274 0.982715231 0.857287901 0.781194407 0.776846615 0.784946584 0.919741931 1 19.1031339 2.996924222 24.92023664 0.827715361 0.882075398 0 0.098538899 379.076319 3071359.493 0.028298809 0.03319801 992.9427802 -2.996924222 0.054360037 YSGGNYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSGGNYR 7 0 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;; 125.08 0.0095001 3202610000 1804650 1966840 1909820 1977120 2010610 2419410 2170720 1963230 1660180 1827520 FALSE TRUE 1875898.975 2304629.47 1959591.478 2368188.435 1668847.23 1857538.694 2000573.294 1936916.113 1600430.446 2185587.554 0.858304199 1.05446678 0.896597107 1.083547731 0.76356915 0.849903583 0.915348045 0.886222155 0.732265538 1 21.05958974 3.233907378 24.99999909 0.858200306 0.973557948 0.268716073 0.093215953 151.0717971 811648.4726 0.025037784 0.030872025 1713.591811 -3.233907378 0.115357642 YSGGNYRDNYDN ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSGGNYRDNYDN 12 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;; 199.68 1.38E-06 1202100000 810580 1514770 1223800 1032480 1308190 1583450 720152 1150940 1007550 2060220 FALSE TRUE 842582.3243 1774919.964 1255693.233 1236701.462 1085824.331 1215717.735 663704.6045 1135513.532 971288.4723 2463880.664 0.341973675 0.720375784 0.509640443 0.501932371 0.440696803 0.493415835 0.269373681 0.460863851 0.394210843 1 21.23250095 -1.088432851 4.953787948 1.000012747 0.461659201 0.672532933 0.113205373 2.04E-05 3.75E-06 0.108897067 0.025666503 0.081576891 1.088432851 -0.538353546 YSGKEGDKFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSGKEGDKFK 10 2 P26447 P26447 S100A4 Protein S100-A4 0 ; 75.695 0.021498 3007200000 6263400 3229780 5159600 1971800 8026000 5239200 3808880 4794300 6029500 3262440 FALSE TRUE 6510683.868 3784469.591 5294063.415 2361816.155 6661743.387 4022475.201 3510330.033 4730040.25 5812499.473 3901652.655 1.668698996 0.969965788 1.356877171 0.605337369 1.707415799 1.030967017 0.899703368 1.212317105 1.489753186 1 21.89565392 4.751265843 23.57647623 1.144057523 1.668699744 0.217414186 0.300101316 1361.831892 2526982.735 0.066489485 1.12310499 56398.27784 -4.751265843 0.524642222 YSGLCPHVVVLVATVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSGLCPHVVVLVATVR 16 0 V9GYY3;A0A384N5Y3;F5H2F4;P11586;V9GZ78;A0A494C1T2 V9GYY3 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 119.47 0.0001915 322920000 153210 148700 180310 165540 194360 213240 186420 175680 181000 154060 FALSE TRUE 159258.8491 174238.0683 185009.0267 198283.3179 161322.7566 163718.2417 171807.9133 173325.297 174485.8454 184245.1073 0.864385771 0.94568627 1.004146213 1.076193125 0.875587737 0.888589358 0.932496476 0.940732155 0.947031093 1 17.49126678 0.789000658 5.430180047 0.999999947 0.943258789 0.079662417 0.059410474 21.32419998 547.8121794 0.059494125 0.014997669 6.151778053 -0.789000658 -0.056741158 YSGREGDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSGREGDK 8 1 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 59.35 0.090452 59010000 46023 47226 52719 31961 81162 63856 38002 49880 52075 72496 FALSE TRUE 47840.02358 55336.69813 54092.90045 38282.79041 67366.11223 49026.41175 35023.30394 49211.44019 50200.83092 86700.20318 0.551786753 0.638253385 0.623907424 0.441553641 0.777000627 0.565470552 0.40395873 0.56760467 0.579016301 1 16.40374775 -1.764319065 2.423019011 1.11547691 0.56991087 0.634485474 0.097429262 10674858.2 7208101.783 7329174.393 0.024178368 0.01720604 1.764319065 -0.54556604 YSGREGDKHTLSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSGREGDKHTLSK 13 2 P06703;R4GN98 P06703 S100A6 Protein S100-A6;Protein S100 0 88.075 0.0048497 190370000 288720 189720 319360 117250 509920 335430 234260 290350 371920 292230 FALSE TRUE 300118.8885 222302.9342 327682.784 140441.7 423243.9805 257531.466 215898.0891 286458.3332 358534.6719 349486.8734 0.858741519 0.636083788 0.937611135 0.401851144 1.211043998 0.736884517 0.617757362 0.819654056 1.025888808 1 18.41487874 1.298587446 4.835427434 1.01466076 0.770391535 0.18037767 0.202299366 0.305798508 13.10104793 0.14250017 0.047487508 19.88783214 -1.298587446 -0.244269225 YSGTLNLDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 204.36 3.89E-05 11051690000 4072350 4258650 4178880 4158950 8089230 6461670 4486220 3808060 3932520 7948080 FALSE TRUE 4233129.523 4990040.01 4287785.046 4981577.897 6714225.574 4961045.07 4134578.354 3757019.184 3790989.373 9505354.101 0.445341591 0.524971501 0.451091564 0.524081254 0.706362488 0.521921121 0.434973627 0.395252943 0.398826738 1 23.18030894 -1.223151214 4.653431899 1.000124174 0.488263589 0.760265433 0.086048906 0.000122307 2.04E-05 0.091924075 0.021661495 0.059820328 1.223151214 -0.511860585 YSHDFNFHINYGDLGFLGPEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSHDFNFHINYGDLGFLGPEDLR 23 0 A0A494C039;Q9Y4L1;A0A087X054;E9PJ21;A0A087WWI4;K7EQK2;Q9Y4L1-2 A0A494C039 HYOU1 Hypoxia up-regulated protein 1 0 ; 109.75 0.00064923 683110000 320400 459750 431660 511940 542530 642890 437290 438450 404330 450370 FALSE TRUE 333049.6394 538708.4861 442909.4142 613200.204 450310.9444 493588.5406 403014.0672 432573.2949 389778.2423 538611.3786 0.618348688 1.000180292 0.822317225 1.138483568 0.8360591 0.916409419 0.748246478 0.803126915 0.723672499 1 19.03888518 2.251594468 24.97064891 0.800505583 0.899656152 0.044972985 0.14318636 520.9145898 997983.1254 0.04699877 0.039092878 178.4820182 -2.251594468 0.09915057 YSHLQPGDHLTDITLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSHLQPGDHLTDITLK 16 0 Q15046;Q15046-2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 ; 169.25 3.29E-09 189648000 234561 221759 299380 260170 342500 365610 340070 299480 316940 209802 FALSE TRUE 243821.6494 259844.3832 307182.0887 311630.8495 284281.9723 280702.6184 313414.4248 295465.9605 305533.3913 250908.685 0.971754523 1.035613348 1.224278421 1.242009018 1.133009694 1.118744129 1.249117482 1.177583631 1.217707515 1 17.93680288 4.368777922 4.640048567 1.179625192 0.986235904 0.47038389 0.071333712 0.146733342 5.167069222 0.016393708 0.04886649 23376.4157 -4.368777922 -0.193389288 YSHS(ph)GSSSPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHS(0.25)GS(0.25)S(0.25)S(0.25)PDTK 89.548 0.0098195 16765000 56702 43996 52449 39883 75848 70101 70130 58159 63215 41710 TRUE FALSE 58940.63874 51551.97076 53815.86403 47771.73836 62955.38405 53821.10514 64633.02735 57379.47373 60939.9045 49882.27591 1.181594818 1.033472708 1.078857431 0.95768963 1.262079224 1.0789625 1.295711276 1.15029783 1.2216745 1 15.60623967 3.232362376 24.99995248 1.178384079 1.061940993 0.220986564 0.095614339 190.9825781 770307.7255 0.02530443 0.030972744 1707.506541 -3.232362376 -0.116443087 YSHSGS(ph)SS(ph)PDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHSGS(0.716)S(0.567)S(0.716)PDTK 203.32 1.85E-07 230190000 666560 436610 567040 447890 797190 904170 728240 616330 625100 376740 TRUE FALSE 692876.3035 511594.3711 581817.5282 536481.3052 661683.9285 694190.2203 671158.6459 608069.1045 602602.7731 450554.9899 1.537828498 1.135475985 1.291335223 1.19071216 1.468597493 1.540744717 1.489626485 1.3496002 1.33746776 1 18.78134367 0.610490982 2.411689356 1.000031132 1.371354957 0.417258647 0.132264533 3.568224066 20.82674782 0.131956364 0.035383356 4.078410927 -0.610490982 0.371323825 YSHSGS(ph)SSPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHS(0.007)GS(0.746)S(0.132)S(0.115)PDTK 138.2 8.24E-05 150740000 277790 246680 353590 268520 437810 458280 452580 370460 412460 260390 TRUE FALSE 288757.3637 289045.3711 362804.8459 321632.4545 363391.2126 351851.4153 417105.597 365494.5897 397615.6452 311408.435 0.927262499 0.928187353 1.165045018 1.032831543 1.166927969 1.129871178 1.339416503 1.173682369 1.276830042 1 18.2484485 4.315650743 0.693343821 1.204444298 0.81317413 0.458359819 0.097505565 1.477774387 0.782142035 0.040096834 0.416684059 20684.77221 -4.315650743 -0.391270168 YSHSGSS(ph)S(ph)PDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 YSHS(0.05)GS(0.533)S(0.663)S(0.752)PDT(0.002)K 92.636 0.011146 183230000 448230 354140 475350 285590 527970 608620 521990 431260 418460 281670 TRUE FALSE 465926.4665 414960.7902 487738.0115 342078.8496 438225.848 467277.2287 481075.0598 425479.6651 403399.7063 336857.8436 1.383154572 1.23185729 1.447904571 1.015499137 1.300922203 1.38716446 1.428124857 1.26308374 1.197536925 1 18.36178037 0.9196507 2.133809463 1.001351722 1.307526612 0.39309461 0.117726824 0.406069351 3.926263658 0.110031492 0.030327853 8.310950576 -0.9196507 0.30617489 YSHSGSS(ph)SPDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YS(0.002)HS(0.074)GS(0.252)S(0.336)S(0.336)PDTK 77.062 0.030875 21676000 58254 46835 60725 45272 80421 82270 82597 65717 67584 44876 TRUE FALSE 60553.9129 54878.54692 62307.54339 54226.66648 66751.06715 63164.03931 76122.83131 64836.17111 65151.66504 53668.593 1.128293281 1.022544916 1.160968453 1.010398511 1.24376406 1.176927432 1.418386938 1.208084049 1.213962606 1 15.71179045 3.223794069 24.9952483 1.232186085 1.082152062 0.254305217 0.104749389 262.1480286 443735.5407 0.028534225 0.034237281 1674.14885 -3.223794069 -0.150034023 YSHSGSSS(ph)PDTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YSHSGSSSPDTK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 YSHS(0.001)GS(0.002)S(0.051)S(0.946)PDTK;YSHSGS(0.007)S(0.209)S(0.783)PDTK;YSHSGS(0.123)S(0.056)S(0.82)PDTK;YSHSGS(0.316)S(0.014)S(0.67)PDTK;YSHS(0.001)GS(0.051)S(0.074)S(0.874)PDTK 260.67 2.63E-21 1957230000 3070730 2761340 3527470 2898680 4495100 4735060 4564160 4005030 4153880 2424200 TRUE FALSE 3191964.792 3235578.665 3619398.766 3472030.252 3731024.508 3635414.076 4206409.213 3951349.124 4004382.67 2899175.576 1.100990508 1.116034052 1.248423447 1.197592268 1.286926028 1.253947538 1.450898403 1.362921638 1.381214268 1 21.46721128 3.877847161 0.832299461 1.327569455 1.077899004 0.212630467 0.117747631 1.085055184 1.226717297 0.04518286 0.200007094 7548.265385 -3.877847161 -0.249670451 YSHSYLS(ph)DSDTEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-4;Q92614-3;Q92614-2;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 YSHSYLS(1)DSDTEAK;YSHSYLS(1)DSDTEAK;YSHSYLS(1)DSDTEAK;YSHSYLS(1)DSDTEAK 347.55 8.59E-82 266982000 547945 342388 440350 342890 618500 646242 608017 464322 535070 301903 TRUE FALSE 569578.2917 401190.4756 451825.8828 410712.6186 513367.5909 496162.0894 560359.0388 458098.5231 515812.9352 361055.1126 1.577538364 1.11116132 1.251404196 1.137534421 1.42185382 1.374200426 1.552004166 1.268777278 1.428626593 1 18.46185955 3.215876934 24.99931562 1.364115297 1.256819931 0.02536853 0.179695251 616.7649903 679724.7966 0.048574617 0.058095891 1643.905823 -3.215876934 -0.107295366 YSHVNKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSHVNKK 7 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 68.915 0.0397 140080000 180390 124400 166420 124160 209450 193690 187840 154410 178320 131850 FALSE TRUE 187511.9365 145764.7323 170757.0419 148718.4774 173847.7638 148708.4329 173116.61 152340.3865 171902.298 157683.4831 1.189166632 0.924413448 1.082910135 0.943145563 1.102510932 0.943081862 1.097874087 0.966115052 1.090173141 1 17.26667202 4.760406512 23.99050997 1.017188824 1.189166944 0.368274369 0.067765391 3154.875257 3464492.749 0.013973772 0.643454504 57597.88172 -4.760406512 0.17197812 YSHVQEVQER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSHVQEVQER 10 0 Q93008;Q93008-3;O00507;O00507-2 Q93008 USP9X;USP9Y Probable ubiquitin carboxyl-terminal hydrolase FAF-X;Probable ubiquitin carboxyl-terminal hydrolase FAF-Y 0 ;; 171.92 3.87E-06 382490000 218212 302916 287010 303985 322061 377883 285752 297612 277632 345846 FALSE TRUE 226827.1783 354939.4666 294489.7164 364112.3257 267317.1863 290125.4001 263354.0116 293622.9979 267640.0786 413607.9021 0.548411133 0.858154462 0.712002152 0.880332131 0.646305801 0.701450332 0.63672384 0.709906645 0.647086473 1 18.65790422 -1.195347202 5.155567111 1.000020625 0.709700449 0.46400696 0.095134846 2.12E-05 3.30E-06 0.086469354 0.020379576 0.063775342 1.195347202 -0.290320177 YSPKT(ph)PPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSPKTPPR 8 1 P49792;J3KNE0;A6NKT7;Q7Z3J3;F8VYC4;A0A286YES2;P0DJD0;A0A1W2PNU4;P0DJD1 P49792;F8VYC4 RANBP2;RGPD3;RGPD4;RGPD1;RGPD2 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 YS(0.001)PKT(0.999)PPR;YS(0.002)PKT(0.998)PPR;YS(0.001)PKT(0.999)PPR 102.52 0.0080004 875430000 1617480 1117170 1363870 1111350 1839010 1875420 1811910 1441190 1582390 973770 TRUE FALSE 1681339.359 1309035.257 1399413.573 1331171.713 1526415.737 1439882.127 1669887.76 1421873.205 1525440.093 1164561.588 1.443753063 1.124058419 1.201665577 1.143066822 1.310721351 1.236415611 1.433919663 1.22095149 1.309883573 1 20.15135551 -0.84334249 9.191330677 1 1.263680353 0.379708881 0.103059235 0 0 0.095171232 0.022432074 0.143435783 0.84334249 0.263680353 YSPPAIS(ph)PLVSEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK;YSPPAIS(1)PLVSEK 220.46 2.18E-11 407790000 542900 460894 533750 475790 653380 753310 675260 599180 641620 491480 TRUE FALSE 564334.1112 540048.9592 547659.9635 569899.8419 542318.701 578365.169 622331.3567 591148.9722 618528.2215 587776.096 0.960117492 0.91880048 0.931749296 0.969586626 0.922662056 0.983988925 1.058789837 1.005738369 1.052319456 1 19.16490716 2.482199361 4.693688217 1.028023465 0.941120083 0.778331817 0.022273061 0.082087341 4.84955543 0.00722034 0.006336526 303.5284201 -2.482199361 -0.086903382 YSPSQNS(ph)PIHHIPSR ddPTM_MDA-MB-175_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(0.03)PS(0.136)QNS(0.834)PIHHIPSR;YSPS(0.002)QNS(0.998)PIHHIPSR;YSPSQNS(1)PIHHIPSR;YS(0.017)PS(0.015)QNS(0.969)PIHHIPSR 255.69 6.36E-25 1697450000 465564 661829 619581 663416 692495 747921 684442 704480 583995 602209 TRUE FALSE 483944.8262 775492.9824 635727.7899 794637.7047 574784.9473 574227.6826 630793.6476 695037.5979 562977.134 720200.3236 0.671958635 1.076773999 0.88270967 1.103356495 0.798090376 0.797316613 0.875858601 0.965061491 0.781695197 1 19.45803872 4.767050419 24.03642015 0.916191233 0.671958018 0.316916366 0.109153922 7896.557946 6662018.705 0.025266479 2.465774002 58485.79789 -4.767050419 -0.244233215 YSPT(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.651)S(0.349)PK;YSPT(0.616)S(0.384)PK 110.41 0.076129 964200000 3704030 1899750 2434320 1840310 3272330 3693300 3084840 2418000 2415860 1330150 TRUE FALSE 3850267.965 2226017.284 2497760.379 2204317.825 2716100.515 2835587.048 2843042.18 2385590.665 2328913.671 1590767.425 2.420383963 1.399335471 1.570160628 1.385694596 1.707415221 1.78252773 1.787214231 1.499647671 1.464018959 1 20.60129149 -2.572803405 0.196856981 3.75E-14 1.802215939 0.39496869 0.2726375 50.55158672 1.182624923 22.7066385 0.734805837 0.002674217 2.572803405 1.802215939 YSPTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSPTSPK 7 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.226)S(0.773)PK;YSPT(0.04)S(0.96)PK;YSPT(0.001)S(0.999)PK 140.88 0.0027215 2950460000 6259500 3236700 4063330 3193050 5398930 6298500 5232630 4062400 3975670 2196940 TRUE FALSE 6506629.893 3792578.047 4169223.718 3824625.76 4481221.807 4835768.83 4822482.788 4007950.173 3832586.413 2627388.33 2.476462965 1.443478303 1.586831939 1.455675857 1.705580312 1.840523068 1.835466319 1.525450245 1.458705731 1 21.32519802 -2.422841915 0.19111228 1.38E-11 1.862275451 0.419078219 0.276167147 45.63910467 1.095835645 20.3655335 0.819489901 0.003777097 2.422841915 1.862275451 YSPTS(ph)PTYSPTS(ph)PK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 YSPT(0.026)S(0.927)PT(0.046)Y(0.001)SPT(0.01)S(0.99)PK;YSPT(0.002)S(0.997)PT(0.001)YSPT(0.002)S(0.998)PK;YSPT(0.011)S(0.919)PT(0.046)Y(0.023)SPT(0.006)S(0.994)PK;YSPT(0.025)S(0.531)PT(0.443)YSPTS(1)PK 269.87 1.20E-25 1629420000 2399810 1146060 1454410 1136530 1944530 2355780 1857840 1504120 1428460 802090 TRUE FALSE 2494556.352 1342886.89 1492313.119 1361332.242 1613999.485 1808685.797 1712217.646 1483959.732 1377050.004 959244.1786 2.600543644 1.399942705 1.555717671 1.419171752 1.682574178 1.885532211 1.784965376 1.547009369 1.435557321 1 19.87153858 -2.421334428 0.16098321 3.75E-23 1.926753942 0.364422425 0.316743277 60.25549217 1.221128534 23.77318256 1.515160006 0.00379023 2.421334428 1.926753942 YSPTS(ph)PTYSPTSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.003)S(0.966)PT(0.031)YSPTSPK 167.22 1.71E-07 0 163730 110090 139860 122010 173290 192210 145860 142130 140280 92040 TRUE FALSE 170194.1868 128997.1011 143504.8665 146143.2138 143834.2277 147572.1405 134427.1121 140224.9798 135231.3502 110073.4758 1.546187086 1.171918123 1.303718861 1.327687827 1.306711055 1.340669398 1.221248908 1.273921613 1.228555283 1 16.74810734 -4.716590594 0.153454168 2.73E-11 1.389641199 0.573405201 0.086074454 86.00443884 0.840043501 26.28295449 0.384406243 1.92E-05 4.716590594 1.389641199 YSPTS(ph)PTYSPTTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPT(0.012)S(0.982)PT(0.006)YSPTTPK;YSPT(0.001)S(0.998)PT(0.002)YSPTTPK 247.11 8.98E-18 1343200000 1810620 1484700 1730400 1465910 2178800 2193500 1927960 1750450 1767670 1265090 TRUE FALSE 1882104.676 1739685.676 1775495.646 1755862.623 1808448.354 1684092.868 1776841.457 1726988.081 1704051.902 1512960.164 1.243988256 1.149855573 1.173524385 1.160547822 1.195304673 1.113111176 1.174413907 1.141463022 1.126303218 1 20.52894257 -4.999999999 0.155855494 0.388999601 1.211310709 0.783024061 0.028178825 56.42584017 0.512622522 10.606383 0.119218327 1.00E-05 4.999999999 0.822311108 YSPTSPTYS(ph)PTSPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.99)PT(0.005)S(0.005)PK;YSPTSPTYS(0.999)PTSPK 330.57 2.17E-68 822940000 537010 379580 421990 378370 590700 581490 495150 442310 442220 305230 TRUE FALSE 558211.5695 444769.9123 432987.4061 453210.4567 490293.025 446447.7601 456338.8492 436381.5579 426304.5886 365033.9745 1.529204426 1.218434292 1.186156457 1.241556919 1.343143541 1.223030707 1.250127059 1.195454638 1.167849073 1 18.47767122 -5 0.057560477 0.022986731 1.686629594 0.571101606 0.083515481 339.6297358 1.43312253 47.61278224 8.539626483 1.00E-05 5 1.663642863 YSPTSPTYSPT(ph)SPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 YSPTSPTYS(0.101)PT(0.888)S(0.011)PK;YSPTSPTYS(0.222)PT(0.699)S(0.079)PK 187.49 1.05E-05 352300000 584330 397140 466600 333380 602300 603140 497710 421900 470780 305230 TRUE FALSE 607399.7996 465345.7057 478759.9793 399321.569 499921.2611 463069.8757 458698.1897 416245.1206 453836.7198 365033.9745 1.663954158 1.274801082 1.311549096 1.093929872 1.369519815 1.268566512 1.256590404 1.140291451 1.243272548 1 18.47767122 7.401306349 1.098647087 1.210856899 199.5126102 0.640270454 0.101762794 421.4466004 1.547107486 0.027502527 209324.828 25194535.09 -7.401306349 198.3017533 YSQKEDKYEEEIK ddPTM_MDA-MB-175_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 ;;;;; 198.16 7.20E-08 10129900000 10025550 2616412 4890200 2630885 8394220 7319660 8072020 4904420 6231710 1902313 FALSE TRUE 10421366.46 3065760.408 5017642.629 3151266.201 6967373.483 5619779.896 7439313.98 4838684.272 6007431.974 2275034.81 4.580750329 1.347566373 2.205523452 1.385150762 3.06253489 2.470195124 3.269978088 2.126861642 2.640589035 1 21.11745719 YSQKEDKYEEEIKILTDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSQKEDKYEEEIKILTDK 18 3 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 0 143.6 4.57E-08 455150000 664560 205540 395560 120610 836210 495220 249650 322450 503700 208680 FALSE TRUE 690797.342 240839.8961 405868.6186 144466.298 694071.3229 380212.6601 230081.7807 318128.0852 485571.9354 249566.8506 2.767985172 0.965031596 1.626292184 0.578868138 2.781103826 1.523490236 0.921924447 1.274720919 1.945658785 1 17.92906679 4.750797693 24.12673437 1.409726883 2.76798655 0.321719554 0.594968466 1401.729227 2763579.538 0.136833687 2.262576016 56337.51576 -4.750797693 1.358259667 YSQKEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSQKEDR 7 1 H7BYY1;P09493-2;F5H7S3;B7Z596;H0YKJ4;H0YK48;A0A494BZZ2;P09493-5;A0A494C0V8;H0YL42;P09493-3;Q6ZN40;P09493-9;P09493-4;P09493-10;A0A0S2Z4G6;P09493;P09493-8;P09493-7;P09493-6 H7BYY1;P09493-3 TPM1 Tropomyosin alpha-1 chain 0 65.252 0.064833 46776000 106660 97596 96496 105890 110090 129210 169990 115430 129090 75918 FALSE TRUE 110871.0192 114357.3538 99010.76503 126834.7259 91376.94112 99202.9357 156665.7396 113882.8497 124444.0761 90792.67856 1.221144931 1.259543783 1.090514859 1.396970857 1.006435129 1.092631446 1.725532742 1.254317545 1.370639991 1 16.47028834 YSS(ph)PTAGSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSSPTAGSAK 10 0 P28749;P28749-2 P28749 RBL1 Retinoblastoma-like protein 1 1 YS(0.043)S(0.939)PT(0.019)AGSAK;YSS(0.987)PT(0.013)AGSAK;YSS(0.999)PT(0.001)AGSAK 208.82 1.12E-07 672110000 1634020 1279970 1622900 1284230 2173090 2191850 1976960 1690590 1706500 1388920 TRUE FALSE 1698532.371 1499794.891 1665194.107 1538246.861 1803708.938 1682826.055 1822000.709 1667930.406 1645083.398 1661052.282 1.022564064 0.902918534 1.002493495 0.926067697 1.085883303 1.013108422 1.096895462 1.004140824 0.990386285 1 20.66366605 3.246625949 24.99972148 1.033638482 0.961967388 0.34537176 0.045950793 188.088935 583006.0635 0.01203226 0.01601974 1764.517417 -3.246625949 -0.071671094 YSSDYFQAPSDYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSSDYFQAPSDYR 13 0 Q08380 Q08380 LGALS3BP Galectin-3-binding protein 0 ; 248.69 4.58E-17 470780000 319420 325120 279570 302760 366260 408850 289220 297220 279150 342640 FALSE TRUE 332030.9482 380956.8309 286855.8239 362645.0244 304003.256 313900.7837 266550.1807 293236.2521 269103.446 409773.7478 0.810278721 0.92967603 0.700034654 0.884988427 0.741880752 0.766034392 0.65048135 0.715605267 0.656712265 1 18.64446804 4.235779149 24.99965144 0.750161668 0.869977379 0.127765602 0.105081716 108.5992279 976120.831 0.02457375 0.057133591 17209.93177 -4.235779149 0.11981571 YSSNLGNFNYER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSSNLGNFNYER 12 0 Q9BZZ5-2;Q9BZZ5-5 Q9BZZ5-2 API5 Apoptosis inhibitor 5 0 ; 111.52 0.0031929 141073000 119808 94067 96079 78343 131538 130558 119857 94145 98001 104734 FALSE TRUE 124538.1124 110222.2755 98582.89767 93839.01157 109179.2177 100237.8831 110462.2952 92883.14027 94473.96315 125254.622 0.994279575 0.879985694 0.787059959 0.749186018 0.871658195 0.800272928 0.881901948 0.741554593 0.754255305 1 16.93450432 4.608779216 2.772231286 0.812165684 1.004817568 0.312614994 0.075564762 0.346725838 4.192331634 0.0174771 0.130116832 40623.67568 -4.608779216 0.192651883 KAASLT(ph)EDRDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 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(0.37)LT(0.63)EDRDR;KAAS(0.379)LT(0.621)EDRDR;KAAS(0.138)LT(0.862)EDRDR;KAAS(0.103)LT(0.897)EDRDR;KAAS(0.372)LT(0.628)EDRDR 139.66 6.26E-05 9940600000 7039470 4471040 5100720 3110310 4983950 4942670 4384010 3494660 4098490 2859950 TRUE FALSE 7317393.711 5238906.34 5233648.953 3725520.035 4136779.959 3794809.799 4040379.841 3447819.799 3950986.145 3420302.445 2.139399608 1.531708503 1.530171392 1.089237018 1.209477824 1.109495391 1.181293147 1.008045298 1.155156951 1 21.70569247 8 0.526158757 1.067955895 41.99610164 0.928702716 0.088971209 25.52035641 0.251106194 0.04017575 1168.764712 100000000 -8 40.92814574 up YSSSS(ph)IPEPFGSR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSSSSIPEPFGSR 13 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSS(0.036)S(0.963)IPEPFGSR 88.101 0.0056396 0 66856 94855 78540 79108 154090 113940 88244 89375 76454 131240 TRUE FALSE 69495.5265 111145.6084 80586.81692 94755.32629 127897.8368 87479.16178 81327.2047 88177.07431 73702.43547 156953.9653 0.442776494 0.708141449 0.513442376 0.603714128 0.814874837 0.557355538 0.518159605 0.561802145 0.469579952 1 17.25998195 -1.226402753 3.571050155 1.000699223 0.581911463 0.588923105 0.106027309 36021141.5 57200672.75 287347.1107 0.02504166 0.059374128 1.226402753 -0.41878776 YSSSSIPEPFGSRGS(ph)PR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSSSSIPEPFGSRGSPR 17 1 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 YSSS(0.004)S(0.01)IPEPFGS(0.208)RGS(0.778)PR 187.56 9.76E-18 0 134400 164730 172010 142640 145940 178120 122090 142990 143690 179780 TRUE FALSE 139706.2158 193021.0961 176492.7219 170853.7663 121133.1709 136754.3294 112520.2668 141073.4529 138518.625 215004.4489 0.649782907 0.897753963 0.820879395 0.794652237 0.563398439 0.636053487 0.523339249 0.656142018 0.644259343 1 17.71400699 3.261772997 22.38322979 0.642318048 0.800560285 0.140166475 0.13460422 96.51066402 93061.06643 0.034334742 0.046439673 1827.14493 -3.261772997 0.158242237 YSTSPYLLEAASHLS(ph)PENFVEDEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSTSPYLLEAASHLSPENFVEDEAK 25 0 Q9BX63;Q9BX63-2 Q9BX63 BRIP1 Fanconi anemia group J protein 1 YSTSPYLLEAAS(0.003)HLS(0.997)PENFVEDEAK 73.936 0.021543 14796000 18816 11716 15473 12909 21757 21497 22308 18938 18180 9485.5 TRUE FALSE 19558.87021 13728.13186 15876.23909 15462.36167 18058.75291 16504.64754 20559.44067 18684.16709 17525.70535 11344.00211 1.724159605 1.210166547 1.399527163 1.363042912 1.591920799 1.454922819 1.812362204 1.647052504 1.544931425 1 13.46964209 3.234624503 24.99062333 1.565666679 1.407170162 0 0.232839632 237.6812395 1509053.772 0.062765976 0.077712262 1716.4237 -3.234624503 -0.158496516 YSTVS(ph)LQEDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YSTVSLQEDR 10 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 YS(0.001)T(0.009)VS(0.99)LQEDR 63.16 0.084568 0 118240 127340 151400 131400 175260 198770 144280 147240 145380 129720 TRUE FALSE 122908.2065 149209.6544 155345.6084 157390.5278 145469.3678 152608.6799 132970.9566 145266.4886 140147.8022 155136.1504 0.792260258 0.961798099 1.001350156 1.014531606 0.937688395 0.98370805 0.85712425 0.936380646 0.903385844 1 17.24317538 4.740857718 24.42440162 0.951524042 0.79226018 0.523800697 0.046468522 129.8889774 1380946.776 0.011647341 0.077591925 55062.72721 -4.740857718 -0.159263861 YSVDIPLDK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSVDIPLDK 9 0 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 ;; 145.72 0.00022448 278866000 995190 752540 911510 700070 1167810 1099940 1054970 927640 1003670 685580 FALSE TRUE 1034480.87 881782.8911 935264.6994 838541.7565 969306.0733 844495.6048 972278.6947 915206.5031 967548.1128 819906.2748 1.261706248 1.075467914 1.140697087 1.022728795 1.182215703 1.029990416 1.185841266 1.116233076 1.180071604 1 19.64509948 4.74688964 24.28381715 1.110138652 1.261706363 0.333384575 0.066471327 769.8256265 2244400.824 0.014251672 0.157210497 55832.82983 -4.74688964 0.151567711 YSVEASS(ph)PGHGSPLSSLLPSASVPESMTISELR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSVEASSPGHGSPLSSLLPSASVPESMTISELR 33 0 Q8TEQ0;Q8TEQ0-2;H3BQF0 Q8TEQ0 SNX29 Sorting nexin-29 1 YSVEAS(0.144)S(0.852)PGHGS(0.003)PLSSLLPSASVPESMTISELR;Y(0.003)S(0.013)VEAS(0.19)S(0.775)PGHGS(0.012)PLS(0.003)S(0.003)LLPSASVPESMTISELR 154.99 5.41E-11 220130000 18651.9 77070 70293 72288 73043 106403 75716 83784 64991 95194 TRUE FALSE 19388.29141 90306.17298 72124.89333 86586.35064 60627.17695 81692.5158 69781.18207 82661.01252 62651.98661 113845.4417 0.170303625 0.79323486 0.633533431 0.76056054 0.532539345 0.717573884 0.61294665 0.726081003 0.550324946 1 16.796717 -5 0.153834869 2.277928555 0.522705009 0.345083718 0.166063572 155.4090503 1.402915739 61.32753481 0.728431474 1.00E-05 5 -1.755223546 YSVLNNDDYFADVS(ph)PLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YSVLNNDDYFADVSPLR 17 0 Q1ED39;H3BMC9 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR 240.42 2.67E-20 249540000 242896 251533 287782 279532 296663 328251 278753 280429 255614 262835 TRUE FALSE 252485.7216 294731.8361 295281.8353 334822.5953 246236.3292 252019.6799 256903.6115 276670.3079 246414.5021 314332.486 0.803244122 0.937643576 0.939393313 1.065186101 0.78336265 0.801761482 0.817298952 0.880183628 0.783929479 1 18.26193186 3.204793073 24.99997133 0.837626265 0.936674547 0.222243218 0.083684551 254.3414459 188302.2764 0.023440468 0.028018116 1602.481678 -3.204793073 0.099048283 YSYLTEPGMS(ph)PQS(ph)PCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 2 YSYLTEPGMS(1)PQS(1)PCER;YSYLTEPGMS(1)PQS(1)PCER;YSYLTEPGMS(1)PQS(1)PCER;YSYLTEPGMS(1)PQS(1)PCER;YSYLTEPGMS(1)PQS(1)PCER 227.46 2.55E-15 299599000 444840 542865 522889 547354 638655 771572 559266 643804 627184 618843 TRUE FALSE 462402.6267 636097.8408 536515.9169 655618.9875 530096.6512 592386.0963 515429.2696 635174.8604 604611.7704 740093.4374 0.624789524 0.859483153 0.724929975 0.88585975 0.716256387 0.800420685 0.696438103 0.858236039 0.816939781 1 19.4973479 0.671479474 0.905572493 0.999820389 0.767160866 0.457079002 0.076797974 0.932767216 1.342605732 0.06717147 0.022321992 4.693312516 -0.671479474 -0.232659523 YSYLTEPGMS(ph)PQSPCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.999)PQS(0.001)PCER;YSYLTEPGMS(1)PQSPCER 343.31 7.20E-73 1556790000 309980 390880 380660 387940 412110 472740 348110 396530 350070 340330 TRUE FALSE 322218.2498 458010.5994 390580.3123 464673.3741 342059.6894 362953.2994 320824.2286 391215.1639 337471.0491 407011.1475 0.791669348 1.125302347 0.959630503 1.141672352 0.840418479 0.891752724 0.788244328 0.961190293 0.829144487 1 18.63470878 3.208189761 24.99989002 0.882242973 1.009982797 0.229441698 0.106972539 263.5954091 216978.9343 0.028673714 0.034275439 1615.064089 -3.208189761 0.127739824 YSYLTEPGMSPQS(ph)PCER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 YSYLTEPGMSPQSPCER 17 0 Q12955-4;Q12955-5;Q12955-6;H0Y3A4;H0YA66 Q12955-4 ANK3 Ankyrin-3 1 YSYLTEPGMS(0.004)PQS(0.996)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMS(0.004)PQS(0.996)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMSPQS(1)PCER;YSYLTEPGMS(0.001)PQS(0.999)PCER 392.82 5.44E-122 2047050000 1499840 1711820 1690650 1739340 1974500 2451030 1961170 2005330 1954880 1952700 TRUE FALSE 1559054.841 2005811.769 1734709.728 2083376.261 1638875.195 1881815.428 1807448.371 1978451.831 1884524.251 2335294.178 0.66760533 0.858911818 0.742822786 0.892125831 0.70178533 0.80581515 0.773970315 0.847195976 0.806975099 1 21.15517287 -5 0.205036878 1.981924114 0.760709909 0.51376729 0.064077642 109.2241511 1.085470907 43.87807039 0.131148903 1.00E-05 5 -1.221214205 YTCGEAPDYDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YTCGEAPDYDR 11 0 P21266;A0A0A0MTN3 P21266 GSTM3 Glutathione S-transferase Mu 3 0 ;;;;; 294.13 3.61E-35 10082910000 4298570 4773910 5003520 4546380 5044930 5740220 5077690 4907230 4761980 3975760 FALSE TRUE 4468280.863 5593791.907 5133915.842 5445640.394 4187394.601 4407140.899 4679687.39 4841456.608 4590597.27 4754734.051 0.939754109 1.176467884 1.079748265 1.145309146 0.880679036 0.926895353 0.984216433 1.018239202 0.965479293 1 22.18093322 3.247856729 24.99989702 0.967061176 1.091432455 0.436347114 0.06808284 184.5303719 496251.9028 0.018687587 0.024965006 1769.525108 -3.247856729 0.124371279 YTEFYHVPTHSDASK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YTEFYHVPTHSDASK 15 0 Q96HC4;Q96HC4-4;Q96HC4-7;H0YBI4;Q96HC4-3;Q96HC4-2;Q96HC4-6 Q96HC4;Q96HC4-6 PDLIM5 PDZ and LIM domain protein 5 0 ;;; 224.34 6.63E-13 1072900000 1269220 1174070 1327060 1154630 1756020 1694960 1628130 1393100 1545400 1160550 FALSE TRUE 1319329.786 1375707.39 1361644.274 1383012.368 1457532.348 1301331.227 1500512.916 1374427.773 1489781.356 1387937.552 0.950568549 0.991188247 0.981055863 0.996451436 1.050142598 0.937600705 1.081109819 0.990266292 1.0733778 1 20.40451123 5.807156828 0.386720075 1.026838595 0.814150128 0.236763301 0.040121089 18.61079109 1.162334285 0.028756693 2.167452695 641441.1661 -5.807156828 -0.212688467 YTGEDFDEDLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YTGEDFDEDLR 11 0 Q14204;A0A2R8Y706;A0A2R8YFZ7;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 ;;;; 225.87 1.20E-11 1793200000 1043250 1068850 1134820 1275380 1328070 1426610 1264460 1132000 1177650 1158003 FALSE TRUE 1084438.316 1252416.673 1164394.341 1527646.357 1102325.136 1095301.448 1165348.321 1116827.392 1135266.607 1384891.517 0.783049288 0.904342801 0.840783792 1.103080161 0.795964971 0.790893319 0.84147264 0.806436734 0.81975129 1 20.40134154 YTGEEDGAGGHS(ph)PAPPQTEECLR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YTGEEDGAGGHSPAPPQTEECLR 23 0 O94762-4;O94762;J3KS37;J3KSV9 O94762-4 RECQL5 ATP-dependent DNA helicase Q5 1 YTGEEDGAGGHS(1)PAPPQTEECLR;YTGEEDGAGGHS(1)PAPPQTEECLR 178.55 6.43E-20 607940000 188623 237796 219161 271930 232617 274740 232119 230400 210529 208388 TRUE FALSE 196069.9817 278635.6132 224872.5157 325716.9424 193076.8454 210935.7987 213924.9062 227311.8649 202952.1024 249217.6388 0.786741992 1.118041301 0.902313804 1.306957822 0.774731862 0.846391932 0.858385896 0.912101832 0.814356895 1 17.92704666 YTIAALLSPY(ph)SYSTTAVVT(ph)NPKE ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTIAALLSPYSYSTTAVVTNPKE 23 1 A0A087WT59;P02766 A0A087WT59 TTR Transthyretin 2 Y(0.001)T(0.001)IAALLS(0.008)PY(0.275)S(0.275)Y(0.275)S(0.297)T(0.3)T(0.296)AVVT(0.273)NPKE 42.321 0.09563 173730000 4767.2 49344 31843 49359 19189 37183 17478 39622 24534 65182 TRUE FALSE 4955.412737 57818.44816 32672.85474 59122.06288 15927.26063 28547.81176 16108.02869 39090.9319 23651.02613 77953.16492 0.063569103 0.741707514 0.419134422 0.758430565 0.204318332 0.366217482 0.206637264 0.501466899 0.30340046 1 16.25031998 -1.56671661 3.855644259 1.012604016 0.409668822 0.416901205 0.213718873 0.021753952 0.00244463 0.194408994 0.045433043 0.027119607 1.56671661 -0.602935194 YTIENPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YTIENPR 7 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 ; 130.77 0.0082156 587630000 517080 661980 601610 598840 713980 821370 647690 633150 626040 666180 FALSE TRUE 537494.7177 775669.9155 617288.4508 717288.7646 592617.9346 630619.2655 596922.3654 624663.6599 603508.9427 796705.2162 0.674646917 0.973597134 0.774801568 0.900318901 0.743835891 0.791533999 0.749238681 0.784058705 0.757505951 1 19.6036865 5.019049364 16.26152902 0.815762039 0.386681415 0.194832404 0.09070158 5670472.59 113312362.7 0.020073443 59710543.28 104483.8973 -5.019049364 -0.429080624 YTIGDIFVHS(ph)PQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YTIGDIFVHSPQR 13 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 YTIGDIFVHS(1)PQR;YTIGDIFVHS(1)PQR;YTIGDIFVHS(1)PQR;YTIGDIFVHS(1)PQR 176.04 1.11E-05 523338000 448917 488058 472673 486752 561963 675372 555674 520927 522499 589266 TRUE FALSE 466640.5898 571878.1649 484991.2467 583030.0928 466440.73 518527.0884 512118.8199 513944.8256 503694.3631 704721.3905 0.662163227 0.811495398 0.688202818 0.827319989 0.661879625 0.735790194 0.726696857 0.729287961 0.714742549 1 19.42669348 -1.222294909 5.13650421 1.000027246 0.730852474 0.707327007 0.052352029 1.44E-05 2.18E-06 0.044601574 0.010511629 0.059938393 1.222294909 -0.269174772 YTIHSQLEHLQSK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YTIHSQLEHLQSK 13 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 ; 253.69 5.01E-24 928080000 929210 825170 1032100 955390 1185780 1287990 1250090 1089050 1095080 850850 FALSE TRUE 965895.9283 966886.5286 1058997.374 1144363.29 984221.5391 988873.8422 1152104.679 1074453.066 1055668.285 1017557.767 0.949229577 0.950203084 1.040724574 1.124617518 0.967238982 0.971811011 1.132225331 1.055913581 1.037452928 1 19.95667927 4.231175383 6.419135206 1.046616412 0.948914092 0.323031096 0.052595403 0.14905802 26.11423436 0.013369471 0.03237833 17028.46039 -4.231175383 -0.09770232 YTLETRPNQEGIDVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YTLETRPNQEGIDVR 15 1 A0A3B3ISG5;P14735;Q5T5N3 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ;;; 101.39 0.0016335 1884300000 1762350 2008400 2092080 2118980 2270020 2622580 2211910 2190500 2138650 1994790 FALSE TRUE 1831928.939 2353327.077 2146601.323 2538107.919 1884162.811 2013525.541 2038534.714 2161139.93 2061680.404 2385630.908 0.767901243 0.986458999 0.899804457 1.063914754 0.789796445 0.844022239 0.854505493 0.905898697 0.864207618 1 21.18593942 4.764045906 23.31695262 0.904996142 0.767900806 0.22705241 0.07883313 4932.221176 4512395.43 0.018485052 1.175009831 58082.58085 -4.764045906 -0.137095336 YTPAS(ph)PSSPDFTTWSCAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTPASPSSPDFTTWSCAK 18 0 A0A1B0GVE3;O75808-2;O75808 A0A1B0GVE3 CAPN15 Calpain-15 1 YTPAS(0.991)PS(0.009)SPDFTTWSCAK 260.25 1.04E-30 62217000 237790 205370 247550 196260 279930 302290 243850 252850 267160 230990 TRUE FALSE 247178.1328 240640.6999 254001.3564 235079.6422 232347.5986 232087.7287 224736.3998 249460.9593 257544.9638 276248.0679 0.89476873 0.871103649 0.919468354 0.850972982 0.841083162 0.840142451 0.813531119 0.903032413 0.932295982 1 18.07560485 1.097147588 1.892874726 0.997177384 0.862660803 0.685668297 0.029370571 0.187014013 1.311121356 0.029309991 0.008378177 12.50683983 -1.097147588 -0.134516581 YTPASPSS(ph)PDFTTWSCAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTPASPSSPDFTTWSCAK 18 0 A0A1B0GVE3;O75808-2;O75808 A0A1B0GVE3 CAPN15 Calpain-15 1 YTPASPS(0.226)S(0.774)PDFTTWSCAK 278.89 3.56E-39 104220000 149470 138800 143890 133910 182080 201080 178870 165910 168410 131900 TRUE FALSE 155371.191 162637.8203 147639.8916 160396.9983 151130.1066 154382.2174 164849.702 163686.2478 162348.957 157743.2796 0.984962348 1.031028521 0.935950438 1.016823022 0.958076357 0.978692834 1.045050556 1.037674938 1.029197297 1 17.26721902 2.243641667 24.99859055 1.032320073 0.984476309 0.374303775 0.027466163 116.5011717 573183.9574 0.009203809 0.007477489 175.2433987 -2.243641667 -0.047843765 YTPSGQAGAAASESLFVSNHAY ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTPSGQAGAAASESLFVSNHAY 22 0 P04075;J3KPS3;P04075-2;H3BR68 P04075 ALDOA Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase 0 84.653 0.0075805 33430000 13327 27351 23631 25849 24439 35184 23694 26866 19241 29133 FALSE TRUE 13853.16025 32048.32149 24246.84327 30961.85505 20284.86751 27013.04922 21836.80237 26505.90521 18548.52017 34841.05357 0.397610257 0.919843639 0.695927384 0.888660126 0.582211656 0.775322399 0.626754938 0.760766467 0.53237541 1 15.08850063 -1.220105853 3.788837503 1.000321976 0.701178628 0.271221931 0.152440019 29207304.17 62061089.86 119807.4956 0.033215181 0.060241274 1.220105853 -0.299143348 YTQLQYIGEGAYGMVSSAYDHVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YTQLQYIGEGAYGMVSSAYDHVR 23 0 P27361;E9PBK7;E9PQW4;P27361-3;P27361-2;E9PJF0 P27361 MAPK3 Mitogen-activated protein kinase 3;Mitogen-activated protein kinase 0 ; 160.92 1.84E-11 430650000 334020 485190 473590 518070 537840 622420 496370 547890 550610 530870 FALSE TRUE 347207.3675 568517.6082 485932.1445 620542.6997 446418.1489 477872.3879 457463.2224 540546.4307 530793.6537 634883.8124 0.546883321 0.895467166 0.765387517 0.977411438 0.703149364 0.752692664 0.720546364 0.851410006 0.836048492 1 19.27613307 -4.999999998 0.207670134 2.013125178 0.757818174 0.283273805 0.10956422 195.622429 1.947570705 82.20669105 0.229103611 1.00E-05 4.999999998 -1.255307004 YTQSNGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YTQSNGR 7 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 ; 143.94 0.0055544 91666000 68345 111052 91182 87017 107187 129666 92812 111805 93872 126768 FALSE TRUE 71043.31337 130124.3171 93558.27783 104228.7029 88967.39203 99553.03661 85537.15292 110306.4369 90493.56506 151605.7625 0.468605627 0.858307198 0.617115579 0.687498293 0.586833842 0.656657339 0.564207795 0.727587362 0.596900564 1 17.20996507 -1.657861619 2.784376296 1.039139468 0.648967586 0.539301807 0.099422672 13342142.9 12263590.12 3725859.535 0.021581737 0.021985603 1.657861619 -0.390171882 YTQVGPDHNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 ;;;;; 122.51 0.00048667 5185520000 2984310 3486800 3601760 3713420 3918350 4525070 3889150 3675850 3405680 3274760 FALSE TRUE 3102132.863 4085630.776 3695624.824 4447923.393 3252310.267 3474191.071 3584308.261 3626581.243 3283110.242 3916386.523 0.792090578 1.04321439 0.943631279 1.135721249 0.830436487 0.887090958 0.915207996 0.92600187 0.838300873 1 21.90109173 YTRPTPVQK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTRPTPVQK 9 1 A0A0D9SFB3;O00571;A0A0D9SG12;A0A0D9SF53;A0A2R8YF78;A0A2R8Y645;A0A2U3TZJ9;O00571-2;F6S8Q4;A0A2R8YDH3;A0A2R8Y7T2;A0A2R8Y4D2;A0A2R8YFS5;A0A2R8Y4A4;A0A2R8YCW1;A0A2R8YFR4;A0A2R8Y5G6;A0A2R8YDT5;O15523-2;O15523;O15523-3;C9J8G5;C9J081 A0A0D9SFB3;A0A2R8YFS5;O15523-2 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 97.597 0.0060042 412180000 267050 211670 283800 163030 324180 346500 351840 255900 309740 257170 FALSE TRUE 277593.3402 248022.6759 291196.0611 195276.8474 269075.9994 266030.6263 324261.8614 252470.0791 298592.5179 307557.5377 0.902573685 0.806426914 0.9468019 0.634927854 0.874880198 0.864978398 1.054312841 0.820887308 0.970850918 1 18.23049681 2.463264665 24.96526254 0.939801213 0.831242331 0.278736532 0.095573546 344.0268558 619825.4053 0.032196269 0.026949034 290.5792942 -2.463264665 -0.108558882 YTS(ph)PPWVTPK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTSPPWVTPK 10 0 Q9ULL0 Q9ULL0 KIAA1210 Uncharacterized protein KIAA1210 1 YT(0.029)S(0.971)PPWVTPK 105.13 0.0027163 202760000 582590 463700 553790 484030 694160 678610 683950 576240 622810 445210 TRUE FALSE 605591.1031 543336.8679 568222.2223 579769.6893 576166.9311 521013.1119 630340.2118 568516.4453 600395.1898 532440.3754 1.137387642 1.020465188 1.067203481 1.088891294 1.082124793 0.978537947 1.183870046 1.067756075 1.127628966 1 19.02226045 2.238215334 24.99999998 1.099935012 1.062841639 0.065540568 0.0586208 23.24671013 1683032.067 0.019662254 0.015441742 173.0674258 -2.238215334 -0.037093373 YTSCETGFKDGDLFMSYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YTSCETGFKDGDLFMSYR 18 1 P49902-2;P49902;Q5JUV4;Q5JUV3 P49902-2 NT5C2 Cytosolic purine 5-nucleotidase 0 ;; 128.14 2.18E-05 868979000 240332 220648 241341 172216 315371 305093 214001 238674 266567 249151 FALSE TRUE 249820.4929 258542.5776 247630.5447 206279.8108 261764.3501 234239.7745 197227.0424 235474.9654 256973.3057 297967.3682 0.838415611 0.867687556 0.831065986 0.692289938 0.878500058 0.786125595 0.661908194 0.790270985 0.862420967 1 18.18479482 0.923557454 3.182356909 0.999615376 0.790272915 0.475374056 0.066259232 0.290629989 6.967714938 0.065287591 0.017030846 8.386050135 -0.923557454 -0.209342461 YTVQDESHSEWVSCVR ddPTM_MDA-MB-175_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 ;;;; 280.15 1.90E-35 3617260000 1598470 1682350 1746640 1938410 1964240 2248450 1989110 1837270 1980480 1492070 FALSE TRUE 1661578.83 1971280.526 1792158.873 2321821.712 1630359.186 1726281.563 1833198.361 1812644.401 1909202.912 1784412.549 0.931162937 1.104722407 1.004341106 1.301168675 0.913667183 0.9674229 1.027339985 1.01582137 1.069933583 1 20.76701777 YTWHGRHNLNK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YTWHGRHNLNK 11 1 A0AVK6 A0AVK6 E2F8 Transcription factor E2F8 0 56.783 0.07536 20249000 1145 38631 27557 34222 15727 37586 12763 26610 19988 47786 FALSE TRUE 1190.205484 45265.57374 28275.15806 40991.00946 13053.73016 28857.22112 11762.60271 26253.33648 19268.63578 57148.75178 0.020826448 0.792065834 0.494764228 0.717268675 0.228416715 0.504949281 0.205824315 0.459386 0.337166345 1 15.80243437 -1.353822703 3.615490799 1.002611929 0.429907492 0.382058739 0.221630726 731722088.4 1074187745 20210953.84 0.049638815 0.044276909 1.353822703 -0.572704437 YVASYLLAALGGNS(ph)SPSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNS(0.497)S(0.497)PS(0.007)AK 97.095 0.0012286 86599000 73607 53688 56328 51938 88386 82837 74988 61700 66034 56296 TRUE FALSE 76513.0612 62908.49637 57795.95395 62211.18138 73362.17929 63599.36216 69110.24462 60873.01242 63657.44924 67326.12335 1.136454282 0.934384652 0.858447674 0.92402738 1.089653995 0.944646134 1.026499688 0.904151456 0.945508906 1 16.03887878 4.742782287 24.56817243 0.95584891 1.136454374 0.42322092 0.06221738 333.2586754 1939318.593 0.01515971 0.117322661 55307.27823 -4.742782287 0.180605464 YVASYLLAALGGNSS(ph)PSAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 YVASYLLAALGGNSS(1)PSAK;YVASYLLAALGGNS(0.001)S(0.998)PS(0.001)AK 386 7.83E-127 3816500000 2238720 1529400 1802930 1678100 2579840 2493640 2537530 2007910 1888400 1664780 TRUE FALSE 2327106.394 1792062.553 1849915.837 2010023.171 2141319.718 1914529.901 2338631.768 1980997.251 1820436.853 1990961.767 1.1688353 0.900098928 0.929156887 1.009573968 1.075520261 0.961610581 1.174624147 0.994995124 0.914350483 1 20.92503409 4.76510739 23.79537376 1.0030905 1.168835731 0.304861729 0.077753332 6110.443913 5476962.47 0.018909986 1.41045924 58224.71743 -4.76510739 0.16574523 YVATLGVEVHPLVFHTNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 3 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 ;; 331.34 3.78E-75 13389596000 4832746 5677544 5329653 5918328 5959990 6639619 6165348 5644860 5727079 5738838 FALSE TRUE 5023546.544 6652618.017 5468548.136 7088955.614 4946913.029 5097668.112 5682091.914 5569199.885 5520962.546 6863253.429 0.73194828 0.969309685 0.796786567 1.032885597 0.720782509 0.742748052 0.827900641 0.811451878 0.804423529 1 22.7104612 5.035891989 14.72196341 0.84399569 0.353684902 0.105658312 0.103085265 2202837.896 27477764.82 0.023511503 27387190.2 108615.5459 -5.035891989 -0.490310788 YVAVMPPHIGDQPLTGAYTVTLDGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVAVMPPHIGDQPLTGAYTVTLDGR 25 0 P30043;A0A2R8YEP4 P30043 BLVRB Flavin reductase (NADPH) 0 ; 254.68 7.63E-45 2113200000 1286570 1566850 1525170 1531940 1661020 1808860 1488800 1519670 1499520 1824240 FALSE TRUE 1337364.777 1835944.299 1564917.183 1834953.16 1378680.414 1388779.679 1372103.966 1499301.309 1445552.568 2181664.901 0.613001922 0.841533591 0.717304102 0.841079287 0.631939586 0.636568741 0.628925169 0.687228047 0.662591477 1 21.05699809 -0.965809271 4.380580647 1.000008414 0.697511082 0.569864549 0.079328817 8833121.319 4033404.332 708.9578329 0.018744645 0.108190899 0.965809271 -0.302497332 YVDEASKK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YVDEASKK 8 1 P62249;M0R210 P62249 RPS16 40S ribosomal protein S16 0 ;;; 108.98 0.0059437 1648200000 2560300 1234860 1845990 1297770 2519600 2073330 2801450 1948880 2290170 996010 FALSE TRUE 2661382.621 1446937.599 1894098.016 1554465.033 2091319.292 1591830.529 2581865.029 1922758.451 2207747.229 1191159.09 2.23427974 1.214730771 1.590130178 1.305002032 1.755701073 1.336371055 2.167523256 1.614191142 1.853444471 1 20.18393468 YVDEENS(ph)DGETSNHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVDEENSDGETSNHR 15 0 A0A494C108;Q8N9T8;H0YFD2;H0YH26;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR 199.01 4.92E-09 1326320000 428692 926590 889500 960070 923140 1088870 902890 955790 867110 1057610 TRUE FALSE 445617.0912 1085724.625 912681.1007 1149968.98 766224.9925 835996.4445 832119.1225 942979.1984 835902.8805 1264828.43 0.352314259 0.858396758 0.721584903 0.909189699 0.605793619 0.660956399 0.657890906 0.745539218 0.660882425 1 20.27051027 -1.950474645 2.244763709 1.233860302 0.697895834 0.298700105 0.143346109 6791627.969 2910225.813 8287308.201 0.035259321 0.011207929 1.950474645 -0.535964468 YVEQYVGTEGASS(ph)SPTEGFLLKPVFLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVEQYVGTEGASSSPTEGFLLKPVFLQR 28 1 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 YVEQYVGTEGAS(0.001)S(0.499)S(0.499)PT(0.001)EGFLLKPVFLQR 273.06 1.10E-61 306580000 189760 145940 178260 165580 197930 272640 195750 201620 170970 171120 TRUE FALSE 197251.8713 171004.0597 182905.602 198331.2298 164285.9293 209323.4919 180406.6035 198917.6137 164816.8231 204647.6877 0.963860738 0.835602208 0.893758459 0.969134966 0.802774422 1.022848068 0.881547236 0.972000299 0.805368607 1 17.64278284 2.73706392 24.99994075 0.933200785 0.894104893 0.077407631 0.074345585 405.2419297 6768870.876 0.021869068 0.021692077 545.8381925 -2.73706392 -0.039095892 YVEQYVGTEGASSS(ph)PTEGFLLKPVFLQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVEQYVGTEGASSSPTEGFLLKPVFLQR 28 1 O75182-2;O75182;M0QYC5 O75182-2 SIN3B Paired amphipathic helix protein Sin3b 1 YVEQYVGTEGAS(0.001)S(0.172)S(0.825)PT(0.003)EGFLLKPVFLQR 203.83 2.03E-25 372770000 452840 416780 461020 398420 532030 592050 478150 437070 445390 385540 TRUE FALSE 470718.4729 488358.7229 473034.5599 477226.2868 441595.7306 454555.3601 440671.3536 431211.7916 429360.5009 461079.1814 1.020905935 1.059164548 1.025929122 1.035020244 0.957743807 0.985850974 0.955738995 0.935222862 0.931207737 1 18.814655 3.23965715 7.228393275 0.956905593 1.036515457 0.736785317 0.021670038 0.063307899 19.17665862 0.006290122 0.008035946 1736.429479 -3.23965715 0.079609864 YVGEGAR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVGEGAR 7 0 P35998;P35998-2 P35998 PSMC2 26S protease regulatory subunit 7 0 84.359 0.050259 87624000 168430 265530 219290 236910 246750 296870 243870 228860 207880 241010 FALSE TRUE 175079.7465 311132.712 225004.8775 283770.0909 204807.5231 227926.4416 224754.8322 225792.506 200398.4394 288231.2951 0.607427956 1.079454998 0.780639998 0.984522138 0.710566571 0.790776177 0.779772481 0.783372624 0.695269538 1 18.13686746 3.221777041 24.99950522 0.781733594 0.872587927 0.051241247 0.139411919 567.5634807 845396.6685 0.03660875 0.043865024 1666.391496 -3.221777041 0.090854334 YVGSMVADVHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YVGSMVADVHR 11 0 P09467;A0A3B3IUC7;O00757 P09467 FBP1;FBP2 "Fructose-1,6-bisphosphatase 1;Fructose-1,6-bisphosphatase isozyme 2" 0 ;;;;; 164.64 2.25E-05 4209470000 2553900 3038060 2461550 2283670 5363790 4121470 2912430 2701560 2665540 5407820 FALSE TRUE 2654729.944 3559823.172 2525700.015 2735373.11 4452054.892 3164321.054 2684146.126 2665350.007 2569607.736 6467378.79 0.410480046 0.550427505 0.390529161 0.422949266 0.68838629 0.489274118 0.415028439 0.412122143 0.397318267 1 22.62474968 -1.119419567 4.956780961 1.000023114 0.464554446 0.768337499 0.088285553 2.30E-05 4.09E-06 0.087306417 0.020577433 0.075959209 1.119419567 -0.535468667 YVIS(ph)DEEEEDDD ddPTM_MDA-MB-175_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 268.91 3.84E-22 508400000 399780 457720 414910 429540 487730 520730 441960 455540 428490 465190 TRUE FALSE 415563.6231 536329.8494 425722.8955 514501.73 404825.8288 399798.3492 407318.0204 449434.2314 413068.7286 556335.0739 0.746966428 0.964041051 0.765227496 0.924805489 0.72766548 0.718628697 0.73214514 0.807848098 0.742481911 1 19.08559454 5.034277388 18.26269093 0.808713974 0.486109959 0.034693508 0.100508505 5330.233005 48985.83834 0.022161822 59483.46246 108212.4893 -5.034277388 -0.322604015 YVIYIER ddPTM_MDA-MB-175_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 ;;;;; 168.38 0.0024455 2053626000 1692690 1689251 1756503 1728730 1923133 2086568 1922858 1873895 1721037 1706612 FALSE TRUE 1759518.708 1979366.719 1802278.911 2070667.634 1596239.54 1601994.204 1772139.366 1848778.503 1659097.215 2040989.946 0.862090826 0.969807187 0.883041543 1.01454083 0.782090839 0.784910385 0.868274422 0.905824404 0.81288848 1 20.96083765 5.129842604 11.87467929 0.886877176 0.000169814 0.009242155 0.079714286 1424610.528 1781318.95 0.018829051 33116037.36 134847.4085 -5.129842604 -0.886707362 YVLHCQGTEEEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YVLHCQGTEEEK 12 0 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 ;;;; 230.59 4.05E-11 896370000 2554394 1441390 1806405 1598218 2328859 2662640 2594026 2001712 2167984 1042601 FALSE TRUE 2655243.448 1688937.52 1853481.398 1914340.75 1933000.379 2044282.213 2390699.464 1974882.325 2089958.679 1246878.704 2.129512228 1.354532333 1.486496956 1.535306316 1.550271388 1.639519711 1.917347258 1.583860818 1.676152357 1 20.2498897 -1.543868819 4.867761622 0.996149829 1.639466604 0.461610252 0.210995883 0.008402823 0.000787382 0.19471533 0.045705828 0.028584538 1.543868819 0.643316775 YVLLNDQPDDDDGNPNEHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVLLNDQPDDDDGNPNEHR 19 0 Q8NEU8-2;Q8NEU8;Q8NEU8-3;F8VS86 Q8NEU8-2 APPL2 DCC-interacting protein 13-beta 0 135.18 8.29E-06 118780000 61593 44771 46307 52865 66604 78760 49810 46862 47929 44252 FALSE TRUE 64024.7392 52460.07098 47513.79846 63321.53921 55282.67587 60469.18362 45905.76205 46233.89154 46204.04465 52922.33214 1.209786807 0.991265291 0.897802431 1.196499411 1.044600146 1.142602398 0.867417595 0.873617803 0.873053828 1 15.69158902 2.229098811 24.99941566 0.890001462 1.071719853 0.450194662 0.095014646 178.1213491 470618.0713 0.034962433 0.02616163 169.472334 -2.229098811 0.181718391 YVPPSSTDRS(ph)PYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YVPPSSTDRSPYEK 14 1 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10;V9GZ38 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 1 YVPPSSTDRS(1)PYEK;YVPPSSTDRS(1)PYEK;YVPPSSTDRS(1)PYEK;YVPPS(0.001)S(0.001)T(0.001)DRS(0.998)PYEK 143.83 5.46E-06 1312900000 784620 764760 676930 879570 926910 1180720 975180 760360 670023 802690 TRUE FALSE 815597.4035 896101.581 694571.3519 1053546.321 769354.1693 906515.674 898742.8434 750168.6179 645909.0031 959961.7371 0.849614492 0.933476353 0.723540663 1.097487827 0.801442536 0.944324799 0.936227777 0.78145679 0.672848696 1 19.87261738 1.70295631 7.729516358 0.79635763 0.898297371 0.076403777 0.119918833 0.23842997 30.84368154 0.054502577 0.028625529 50.46105311 -1.70295631 0.101939741 YVPPSSTDRSPYEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVPPSSTDRSPYEK 14 1 P15941-2;A0A087WWM1;A0A087X2A4;A0A0C4DGW3;P15941-7;P15941-11;P15941-4;P15941-3;P15941;P15941-8;A0A087WVJ0;A0A0A0MSH4;A0A0A0MRB3;B1AVQ7;A0A087X0L2;P15941-15;P15941-17;P15941-6;A6ZIE3;A6ZIE4;P15941-12;P15941-16;P15941-9;P15941-10;V9GZ38 P15941-2 MUC1 Mucin-1;Mucin-1 subunit alpha;Mucin-1 subunit beta 0 74.678 0.016436 0 131650 142340 130250 154350 185670 213850 142320 142770 129350 170810 FALSE TRUE 136847.6437 166785.7877 133644.422 184879.9693 154109.8797 164186.5784 131164.5865 140856.4017 124694.7188 204276.9491 0.669912314 0.816468958 0.654231535 0.905045675 0.754416396 0.803745009 0.642091959 0.689536447 0.610419919 1 17.64016689 2.255452793 24.98234325 0.705073696 0.770073734 0 0.120561004 693.5573122 1025720.732 0.038649609 0.032255063 180.0747384 -2.255452793 0.065000038 YVQHTYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 7 YVQHTYR 7 0 P52566;F5H3P3;H0YGX7 P52566 ARHGDIB Rho GDP-dissociation inhibitor 2 0 ;;;;;; 157.34 0.0014824 4316720000 1807089 2370882 1897658 1804021 4362502 3116294 2196981 2015050 1913501 5069444 FALSE TRUE 1878434.269 2778062.541 1947112.526 2160850.969 3620965.468 2392581.946 2024775.888 1988041.551 1844634.473 6062704.491 0.309834377 0.458221664 0.321162367 0.356417004 0.597252509 0.394639381 0.333972387 0.327913319 0.304259341 1 22.53153007 -0.985980617 4.892756087 1.000006388 0.379429218 0.826542737 0.085454863 6.45E-06 1.34E-06 0.084443979 0.019903419 0.10328075 0.985980617 -0.62057717 YVSDRPQAFK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVSDRPQAFK 10 1 Q9Y6D6;E5RIF2;E5RHL7 Q9Y6D6 ARFGEF1 Brefeldin A-inhibited guanine nucleotide-exchange protein 1 0 67.726 0.064814 0 650200 289450 424960 267460 689400 557720 479390 371480 477060 338350 FALSE TRUE 675870.3981 339160.7859 436034.8067 320362.7897 572216.0342 428197.9823 441814.1591 366500.9182 459890.7038 404643.2044 1.670287282 0.83817245 1.077578474 0.791716718 1.414124908 1.058211228 1.091861063 0.905738473 1.136533862 1 18.62629084 4.749722975 24.90488398 1.03487002 1.670287671 0.568775148 0.165979212 1122.439531 2504280.096 0.037998981 0.580575978 56198.27367 -4.749722975 0.635417651 YVSGSS(ph)PDLVTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVSGSSPDLVTR 12 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 1 YVSGS(0.003)S(0.997)PDLVTR;YVSGS(0.001)S(0.999)PDLVTR 315.7 2.00E-46 355220000 509070 581900 577210 643850 650660 765790 683310 640760 607100 591310 TRUE FALSE 529168.4767 681836.7984 592252.5668 771201.6083 540061.0456 587946.8782 629750.3767 632171.6603 585250.5896 707165.8732 0.748294702 0.964182272 0.837501623 1.090552638 0.763697834 0.831412969 0.890527103 0.893951029 0.82760016 1 19.43168913 -1.458572972 5.40535136 1.000144685 0.87781046 0.139326713 0.094464904 0.000152669 1.53E-05 0.084777306 0.019958634 0.034787805 1.458572972 -0.122334225 YVTAFNGELEDYMSDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVTAFNGELEDYMSDR 16 0 F5H8D7 F5H8D7 XRCC1 0 80.469 0.036013 17394000 9251.2 7884.6 9921.8 8217.7 10490 10871 8510.3 10326 7494.5 8109 FALSE TRUE 9616.444519 9238.718716 10180.37026 9843.136533 8706.913547 8346.375002 7843.240448 10187.59686 7224.774409 9697.803294 0.991610598 0.952660972 1.049760441 1.014986202 0.897823278 0.860645937 0.808764646 1.05050562 0.744990818 1 13.24344228 3.234707971 24.78230169 0.899465797 1.00210544 0.281681608 0.084564097 122.4413058 787609.5909 0.023777867 0.02946584 1716.753618 -3.234707971 0.102639643 YVVGCR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YVVGCR 6 0 A0A087X2I1;P62333;H0YJC0;H0YJS8;H0YJT1 A0A087X2I1 PSMC6 26S protease regulatory subunit 10B 0 109.53 0.068583 90882000 67874 97979 98449 94735 77895 109520 71873 79466 84571 96970 FALSE TRUE 70553.71793 114806.1311 101014.6618 113473.3002 64654.43572 84085.63979 66239.40645 78400.88825 81527.30623 115969.4149 0.608382115 0.989969046 0.871045714 0.978476095 0.557512822 0.72506738 0.571179966 0.676047976 0.703006964 1 16.82338484 3.241518027 24.99999702 0.680472847 0.871759541 0.194438794 0.150468577 97.22432039 821862.1061 0.039181568 0.050835256 1743.885741 -3.241518027 0.191286694 YVVLCRGAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVVLCRGAK 9 1 O75426-2;O75426-4;O75426;O75426-3 O75426-2 FBXO24 F-box only protein 24 0 ; 83.265 0.0097856 2832300000 4724700 3726800 4422900 3301200 6805100 5840400 5025700 4428200 4656600 4997300 FALSE TRUE 4911234.804 4366848.91 4538164.407 3954167.507 5648371.533 4484055.612 4631772.502 4368847.222 4489009.876 5976425.256 0.821767962 0.73067908 0.759344292 0.661627534 0.945108705 0.750290587 0.775007183 0.731013446 0.751119554 1 22.51085138 -1.330062764 5.647390593 1.000038353 0.76708249 0.493034442 0.07006442 3.21E-05 3.81E-06 0.064406708 0.015178311 0.046766755 1.330062764 -0.232955864 YVWLVYEQDRPLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVWLVYEQDRPLK 13 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 203.82 7.55E-08 5410300000 2305570 2525690 2339210 1844990 3009400 3537800 2199850 2228730 2164770 3484200 FALSE TRUE 2396595.684 2959457.61 2400171.734 2209923.515 2497863.263 2716199.566 2027420.009 2198857.52 2086860.351 4166862.281 0.575155962 0.710236483 0.576014174 0.530356745 0.59945904 0.651857293 0.486557959 0.527701031 0.500822972 1 21.99052999 -2.079295606 2.64486223 1.693752836 0.571986061 0.794828667 0.065061465 9608106.641 5489103.473 39913758.92 0.016729609 0.008331139 2.079295606 -1.121766774 YVWLVYEQDRPLKCDEPILSNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YVWLVYEQDRPLKCDEPILSNR 22 2 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 0 ; 309.91 2.05E-67 2278400000 719990 743850 665630 528450 984650 1048120 612550 717760 763780 1197510 FALSE TRUE 748415.7612 871600.4512 682976.8646 632975.8327 817279.5447 804710.0144 564536.7304 708139.6012 736291.707 1432139.157 0.522585922 0.608600391 0.476892808 0.44197928 0.570670483 0.561893731 0.394191254 0.494462845 0.514120226 1 20.44974025 0.89617064 17.28802648 1 0.506336183 0.858542043 0.059727506 1120.461946 186563.6073 0.059058445 0.014764611 7.873550905 -0.89617064 -0.493663817 YWCDAEYDAYR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWCDAEYDAYR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ; 140.45 8.98E-05 428880000 243610 290980 266330 292530 332020 384930 308760 266220 277760 298450 FALSE TRUE 253227.9109 340953.5515 273270.7786 350391.5609 275583.359 295535.8412 284558.5844 262651.7563 267763.4719 356925.5633 0.709469808 0.955251141 0.765624003 0.981693655 0.77210317 0.828004132 0.797249101 0.735872639 0.750194156 1 18.44526371 YWCDAEYDAYRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YWCDAEYDAYRR 12 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-4;O15027-3;A0A3F2YNX0;A0A3F2YNZ0;X6RGP5 O15027 SEC16A Protein transport protein Sec16A 0 ;;;; 214.04 2.47E-09 1498470000 792903 1015150 918070 891763 1119623 1183380 768615 940050 908758 1154010 FALSE TRUE 824207.4227 1189494.116 941995.6584 1068151.06 929309.8824 908557.9293 708368.9479 927450.1674 876051.9771 1380116.165 0.597201485 0.861879707 0.682548095 0.773957357 0.673356277 0.658319896 0.513267626 0.672008771 0.63476684 1 20.39635827 -0.985558647 4.383348637 1.000010739 0.675052857 0.547758714 0.088821702 9949409.166 4539638.549 1043.472441 0.021109811 0.103381149 0.985558647 -0.324957882 YWDAEK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWDAEK 6 0 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 ; 126.24 0.040887 326140000 677990 522730 635580 545510 812310 801080 840180 662570 700850 478600 FALSE TRUE 704757.5687 612504.8112 652143.7369 653410.2498 674233.8363 615041.3105 774324.4962 653689.3329 675626.5454 572372.5066 1.231291791 1.07011571 1.13936943 1.141582173 1.177963352 1.074547263 1.352833141 1.142069763 1.180396573 1 19.12659485 3.253730503 18.89689291 1.170109106 1.139754157 0 0.092543565 67.31636816 83842.92962 0.024391803 0.03274472 1793.62027 -3.253730503 -0.030354948 YWDAEKR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YWDAEKR 7 1 P17174;P17174-2 P17174 GOT1 "Aspartate aminotransferase, cytoplasmic" 0 98.997 0.017401 220130000 213390 192530 219430 143090 359100 296110 193300 200030 227390 246480 FALSE TRUE 221814.802 225595.5298 225148.5261 171392.7749 298060.3103 227342.9401 178148.6409 197348.925 219206.2783 294773.0369 0.752493526 0.765319421 0.763802987 0.581439798 1.01115188 0.771247406 0.604358671 0.669494494 0.743644265 1 18.16924504 YWDGWFR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWDGWFR 7 0 Q9Y570;Q9Y570-4;Q9Y570-2;Q9Y570-3 Q9Y570 PPME1 Protein phosphatase methylesterase 1 0 ; 108.24 0.016978 996330000 1016660 1189630 1291340 1265440 1455150 1516210 1352020 1255600 1281200 1241430 FALSE TRUE 1056798.522 1393939.698 1324993.381 1515740.255 1207804.123 1164093.206 1246045.14 1238770.736 1235089.862 1484664.44 0.711809681 0.93889209 0.8924531 1.020931205 0.813519938 0.784078324 0.839277285 0.834377589 0.831898326 1 20.50170546 YWEAFLPEAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWEAFLPEAK 10 0 Q13596-2;Q13596;H0YK42;O60749;O60749-2 Q13596-2;O60749 SNX1;SNX2 Sorting nexin-1;Sorting nexin-2 0 ; 138.66 0.0092133 0 219769 209552 249237 234153 292042 314620 332110 273404 302650 206882 FALSE TRUE 228445.6498 245540.9259 255732.321 280467.7645 242400.8052 241554.2731 306078.3504 269739.4666 291757.6856 247416.5669 0.923323982 0.992419097 1.033610336 1.133585224 0.979727462 0.976305977 1.237097233 1.090223949 1.17921645 1 17.91658258 2.260800678 24.99990435 1.133123007 1.011648092 0.370545626 0.076346087 244.4235157 274754.0369 0.025921827 0.021672099 182.3058808 -2.260800678 -0.121474915 YWGEIISQQYNFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YWGEIISQQYNFDR 14 0 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 93.766 0.008658 0 95041 66115 90405 62425 135340 108190 99099 92698 104610 77659 FALSE TRUE 98793.29207 77469.73695 92761.02857 74772.47868 112334.9551 83064.51214 91331.36143 91455.53493 100845.1065 92874.79418 1.063725556 0.834130914 0.998775065 0.805089038 1.209531134 0.894370888 0.983381576 0.984718575 1.08581782 1 16.50299949 YWGEIISQQYNFDRDNTEVAYLK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWGEIISQQYNFDRDNTEVAYLK 23 1 A0A3B3ISG5;P14735;P14735-2 A0A3B3ISG5 IDE Insulin-degrading enzyme 0 ; 298.23 8.35E-62 443660000 268502 246272 284700 214309 337250 327370 279725 280980 283510 254837 FALSE TRUE 279102.6663 288567.3003 292119.5159 256698.6806 279924.3655 251343.2788 257799.4236 277213.9227 273306.5305 304767.431 0.915789018 0.946844285 0.958499781 0.842277273 0.918485169 0.824705179 0.84588902 0.90959169 0.896770792 1 18.21734921 3.755071954 24.83675511 0.884583094 0.941024356 0.172088595 0.048055018 1102.382008 1658225.38 0.011652787 0.020919337 5689.471868 -3.755071954 0.056441262 YWGPAS(ph)PTHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 10 YWGPASPTHK 10 0 Q9H6S3;Q9H6S3-3;A0A3B3ISQ4;Q9H6S3-2 Q9H6S3 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 YWGPAS(0.948)PT(0.052)HK;YWGPAS(0.758)PT(0.242)HK;YWGPAS(0.945)PT(0.055)HK;YWGPAS(0.997)PT(0.003)HK;YWGPAS(0.818)PT(0.182)HK;YWGPAS(0.819)PT(0.181)HK;YWGPAS(0.993)PT(0.007)HK;YWGPAS(0.949)PT(0.051)HK;YWGPAS(0.945)PT(0.055)HK;YWGPAS(0.956)PT(0.044)HK 164.9 6.31E-06 21305240000 9879260 7035750 8986180 8342170 10380270 11725070 14086950 10886230 10874760 6311450 TRUE FALSE 10269300.81 8244085.332 9220367.233 9992226.327 8615835.413 9002100.188 12982778.05 10740317.89 10483379.51 7548057.787 1.360522283 1.0922128 1.221554934 1.323814233 1.141463891 1.192637953 1.72001572 1.422924704 1.388884374 1 22.84767404 YWGPAS(ph)PTHKLPPSFPGNKDELMQHMDEVNDELIR ddPTM_MDA-MB-175_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(0.5)PT(0.5)HKLPPSFPGNKDELMQHMDEVNDELIR;YWGPAS(0.813)PT(0.187)HKLPPSFPGNKDELMQHMDEVNDELIR 220.77 6.66E-37 4442900000 685130 887310 1031850 876150 1190080 1247220 1002060 1075660 1342100 1349820 TRUE FALSE 712179.4614 1039698.59 1058740.859 1049449.855 987790.6267 957572.0568 923515.9188 1061242.537 1293798.083 1614291.385 0.441171568 0.644058811 0.655854865 0.650099396 0.611903548 0.593184146 0.572087498 0.657404572 0.801465024 1 20.62246958 1.024670525 1.826323883 0.998611027 0.601968711 0.826242816 0.058700221 0.131202051 0.903182901 0.054346171 0.015504738 10.58450433 -1.024670525 -0.396642316 YWLEEAECR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YWLEEAECR 9 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 ;;;;; 231.3 1.36E-07 1127799000 847035 980463 926370 1014557 1096539 1220530 1042124 987921 939637 1024323 FALSE TRUE 880476.5959 1148849.893 950511.9632 1215233.346 910149.6925 937080.4048 960439.5978 974679.5349 905819.6479 1225019.48 0.718744975 0.937821734 0.775915795 0.992011447 0.742967526 0.764951431 0.784019857 0.795644111 0.739432852 1 20.22437326 YWPQEAGEYAVHVLCNSEDIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWPQEAGEYAVHVLCNSEDIR 21 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 ; 185.71 3.50E-17 322520000 104821 159404 105306 123698 154650 159772 94759 129015 101857 265630 FALSE TRUE 108959.414 186780.397 108050.3609 148165.0952 128362.6482 122667.3744 87331.54197 127285.765 98191.18647 317675.1127 0.342990085 0.587960434 0.340128504 0.466404478 0.404068947 0.386140964 0.274908353 0.400679058 0.309093103 1 18.27719255 -1.268113543 3.553827008 1.001508536 0.39266348 0.827186099 0.08360213 34523494.38 55655395.8 572584.4041 0.019316129 0.053936959 1.268113543 -0.608845056 YWPTADGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YWPTADGR 8 0 P52788;H7C2R7;P52788-2 P52788 SMS Spermine synthase 0 ;;;; 161.6 0.00080627 1344480000 988910 1293530 1179680 1200392 1356560 1524180 1166380 1217110 1127160 1543940 FALSE TRUE 1027952.93 1515683.715 1210423.43 1437825.955 1125972.416 1170212.294 1074956.088 1200796.631 1086593.732 1846445.482 0.556719892 0.820865674 0.655542469 0.778699381 0.609805394 0.633764877 0.582175915 0.650328776 0.588478643 1 20.81631924 -1.906198011 6.845781395 1.078347993 0.656302963 0.625741936 0.080485883 0.045167338 0.00061889 0.03657277 0.017712188 0.012410863 1.906198011 -0.42204503 YWQQVIDMNDYQR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YWQQVIDMNDYQR 13 0 O60701-2;O60701;O60701-3 O60701-2 UGDH UDP-glucose 6-dehydrogenase 0 ;;;; 258.48 1.43E-23 1334682000 1202590 1387670 1423410 1420558 1511050 1753600 1360901 1467750 1393667 1539910 FALSE TRUE 1250069.182 1625991.528 1460505.234 1701540.132 1254202.261 1346352.976 1254230.024 1448077.212 1343509.197 1841625.881 0.678785629 0.88291088 0.793052079 0.923933656 0.681029884 0.73106758 0.681044959 0.786303682 0.729523412 1 20.81254858 -1.34489391 3.059307236 1.002274285 0.768396555 0.434427452 0.080269428 23166928.96 30637278.06 480285.1238 0.019545693 0.045196634 1.34489391 -0.23387773 YWSQFDENIR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YWSQFDENIR 10 0 Q5VTR2;C9J0A5;C9JXC9 Q5VTR2 RNF20 E3 ubiquitin-protein ligase BRE1A 0 95.573 0.017053 108690000 75714 76168 79759 65889 63715 86343 82848 79228 76281 93567 FALSE TRUE 78703.24718 89249.2615 81837.58506 78921.64754 52884.74706 66291.14679 76354.15728 78166.07825 73535.66171 111899.6622 0.703337666 0.797582939 0.731347919 0.705289417 0.472608639 0.592415969 0.682344842 0.698537214 0.657157138 1 16.77184616 -1.086387271 8.114042114 1.000000013 0.6719714 0.586844814 0.08276784 2.09E-08 2.24E-09 0.087097522 0.020529082 0.081962034 1.086387271 -0.328028612 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 9 YWSQQIEESTTVVTTQSAEVGAAETTLTELRR 32 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 ;;;;;;;; 268.77 6.23E-60 4107824000 385059.2 450986 459962.6 462465.9 410764.1 578935 516396.5 418940.8 425422.6 367283.9 FALSE TRUE 400261.6345 528439.3373 471949.6032 553940.2747 340942.565 444486.1201 475919.993 413325.5838 410111.7237 439246.1481 0.911246772 1.203059696 1.074453596 1.261115839 0.776199328 1.011929466 1.083492695 0.940988522 0.933671759 1 18.74467011 3.248924798 24.99997295 0.964931126 1.116224304 0.310258378 0.112676638 259.6162066 626229.6244 0.030145887 0.040378782 1773.882293 -3.248924798 0.151293178 YWVSGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YWVSGR 6 0 P26640;A0A140T936;H0Y426 P26640 VARS Valine--tRNA ligase 0 ; 117.56 0.052613 134656000 73908 146148 121658 145436 146091 165459 143242 135703 122593 160745 FALSE TRUE 76825.94491 171247.7821 124828.5074 174202.8067 121258.504 127033.6548 132014.3177 133884.1233 118180.9019 192239.9051 0.399635783 0.890802469 0.649337126 0.906174015 0.630766562 0.660807935 0.686716515 0.696442932 0.614757388 1 17.55254832 -1.241058098 3.944815812 1.000310684 0.692094233 0.329637655 0.135441488 18397115.18 5787891.73 49023.66144 0.02860884 0.057403966 1.241058098 -0.308216451 YYAFDEAFVR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYAFDEAFVR 10 0 O43427-2;O43427;E9PSD3;E9PJW6 O43427-2 FIBP Acidic fibroblast growth factor intracellular-binding protein 0 87.639 0.029636 17292000 83817 52915 62479 56771 102120 81098 72300 61083 69838 57272 FALSE TRUE 87126.15988 62002.73963 64107.25407 68000.13436 84761.67888 62264.21855 66632.93708 60264.2823 67324.54402 68493.35186 1.272038198 0.90523734 0.93596316 0.992799046 1.237516877 0.909054921 0.972838024 0.879855937 0.982935456 1 16.06367634 YYDDIYFDS(ph)DS(ph)EDEDRAVQVTK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YYDDIYFDSDSEDEDRAVQVTK 22 1 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 2 YYDDIYFDS(1)DS(1)EDEDRAVQVTK;YYDDIY(0.096)FDS(0.907)DS(0.996)EDEDRAVQVT(0.001)K 166.23 6.79E-12 39798000 133378 113242 128258 96976 140365 155105 129676 127534 113526 111332 TRUE FALSE 138643.8664 132690.4326 131600.5088 116157.5634 116505.8074 119084.2144 119511.6563 125824.6153 109440.2214 133145.3738 1.041296911 0.996583124 0.988397156 0.872411561 0.875027078 0.89439243 0.897602769 0.945016802 0.821960375 1 17.02264278 3.879798635 4.001022009 0.900084552 1.01422533 0.545121506 0.045532745 0.166422162 4.55891364 0.011295549 0.021794258 7582.259353 -3.879798635 0.114140778 YYDSRPGGYGYGYGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 ;;;;; 175.29 7.88E-07 12132890000 4468470 5452790 4768720 4760920 5052470 5961390 4804240 5066160 4251690 5290370 FALSE TRUE 4644888.646 6389264.266 4892996.761 5702615.766 4193652.954 4576947.518 4427671.115 4998256.412 4098672.507 6326916.711 0.734147272 1.009854335 0.773361968 0.901326195 0.662827274 0.723408846 0.699814984 0.789998769 0.647815151 1 22.59307117 3.250019126 24.99329366 0.7418056 0.85994898 0.148624985 0.115614646 336.747245 734508.5983 0.029210903 0.039212324 1778.357726 -3.250019126 0.11814338 YYEGYYAAGPGYGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYEGYYAAGPGYGGR 15 0 Q93052;A0A087WZF1;C9JUT4;C9JXK9 Q93052 LPP Lipoma-preferred partner 0 125.23 0.0012312 0 78971 62520 69134 62985 85189 102120 88489 77296 78450 72291 FALSE TRUE 82088.83606 73257.32366 70935.68883 75443.24501 70708.60421 78404.17764 81553.00096 76259.97355 75626.59982 86455.03736 0.949497433 0.847345926 0.820492258 0.872629835 0.817865637 0.906878073 0.943299586 0.882076694 0.874750647 1 16.39966241 2.57650135 8.458190736 0.914183119 0.859203434 0.279344859 0.047413775 0.466866617 36.12226128 0.014956952 0.014082534 377.1389176 -2.57650135 -0.054979684 YYFQVER ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYFQVER 7 0 Q96PQ1-2;Q96PQ1 Q96PQ1-2 SIGLEC12 Sialic acid-binding Ig-like lectin 12 0 81.381 0.063639 299030000 250830 397180 338030 310330 276230 376590 265310 336020 297880 270030 FALSE TRUE 260732.9621 465392.5754 346839.3395 371712.3478 229276.5233 289132.6798 244514.3089 331516.2015 287159.357 322937.2085 0.807379748 1.441124043 1.074014794 1.151035985 0.709972457 0.895321667 0.757157437 1.026565514 0.88921112 1 18.30089415 3.264385694 24.91381547 0.883279821 1.138271773 0.320947284 0.169049651 233.2968734 225063.0941 0.044184246 0.059805378 1838.170083 -3.264385694 0.254991951 YYFSHDTD ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YYFSHDTD 8 0 A0AVT1;A0AVT1-2 A0AVT1 UBA6 Ubiquitin-like modifier-activating enzyme 6 0 ;;; 224.29 9.61E-06 1195620000 1880880 2430860 2285300 2210470 2700110 2852730 2187530 2349030 2267850 2442270 FALSE TRUE 1955138.595 2848341.296 2344856.795 2647694.368 2241146.267 2190226.691 2016065.683 2317545.095 2186230.522 2920786.046 0.669387817 0.975196831 0.802817036 0.906500622 0.76730929 0.749875772 0.690247642 0.793466231 0.748507589 1 21.47792525 5.026412988 15.74127168 0.81088651 0.300818443 0.172045752 0.098152221 1220647.094 19823265.21 0.022764562 15862365.35 106270.5647 -5.026412988 -0.510068067 YYGGGSEGGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YYGGGSEGGR 10 0 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 ; 148.04 6.01E-05 1557100000 979390 1176200 1162770 1174990 1174280 1347770 1117280 1262090 1102880 1156230 FALSE TRUE 1018057.073 1378203.2 1193072.741 1407399.515 974676.305 1034770.843 1029704.674 1245173.748 1063187.564 1382771.131 0.73624409 0.996696539 0.86281288 1.01781089 0.704871749 0.748331246 0.744667466 0.900491571 0.768881806 1 20.39913096 5.040093181 14.18576207 0.851909405 0.307761224 0.096673862 0.11119329 1076096.896 12008669.23 0.026289974 14586102.72 109671.3478 -5.040093181 -0.544148181 YYHSPTNTVHMYPPEMAPSSAPPS(ph)TPPTHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSSAPPS(0.494)T(0.494)PPT(0.012)HK;YYHSPTNTVHMYPPEMAPSS(0.005)APPS(0.589)T(0.402)PPT(0.003)HK 129.23 1.73E-05 133505000 79584 83858 105804 99922 121804 133768 125530 110506 109307 92914 TRUE FALSE 82726.03777 98259.95918 108561.3392 119686.2734 101099.7996 102702.4093 115690.6306 109024.8478 105373.0624 111118.7194 0.744483362 0.884279082 0.976985154 1.077102707 0.909835896 0.924258396 1.041144384 0.981156447 0.948292628 1 16.76174235 4.584270181 2.253949999 0.983528956 0.722793677 0.706263035 0.047706373 0.237842062 1.78172307 0.0123324 0.107610678 38394.60297 -4.584270181 -0.260735279 YYHSPTNTVHMYPPEMAPSSAPPSTPPT(ph)HK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYHSPTNTVHMYPPEMAPSSAPPSTPPTHK 30 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 YYHSPTNTVHMYPPEMAPSS(0.001)APPS(0.312)T(0.312)PPT(0.376)HK 63.491 0.0088985 118050000 83073 92164 101830 92368 117210 125440 118160 104430 105410 87576 TRUE FALSE 86352.78619 107992.4501 104483.7735 110638.1147 97286.68607 96308.46106 108898.3104 103030.2867 101616.3147 104734.8405 0.824489595 1.0311034 0.997602832 1.056363997 0.928885609 0.919545594 1.039752483 0.983725055 0.970224562 1 16.67638191 4.7471009 24.77475366 0.991263235 0.8244895 0.58590413 0.042221935 700.5376745 2032158.523 0.010192597 0.117842685 55859.99598 -4.7471009 -0.166773736 YYIADR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYIADR 6 0 Q9H0D6;Q9H0D6-2 Q9H0D6 XRN2 5-3 exoribonuclease 2 0 100.82 0.086601 433090000 320270 408280 336930 382790 499350 521290 440910 373350 342850 493910 FALSE TRUE 332914.5069 478398.914 345710.6726 458504.7195 414470.6654 400228.2977 406350.3221 368345.8539 330510.8955 590682.208 0.563610182 0.809909131 0.58527355 0.776229101 0.70168131 0.677569584 0.687933912 0.623593954 0.55954097 1 19.17202263 -1.205376502 4.400836917 1.000105275 0.669377042 0.607832366 0.080648467 7.74E-05 1.40E-05 0.072512515 0.017085943 0.062319434 1.205376502 -0.330728233 YYITIIDAPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 5 YYITIIDAPGHR 12 0 A0A2U3TZH3;Q05639;A0A2R8Y488;A0A2R8Y660;A0A2R8YDN5 A0A2U3TZH3 EEF1A2 Elongation factor 1-alpha 2 0 ;;;; 166.14 5.27E-05 3929230000 2382005 2791190 3077280 3157110 3052850 3647830 3538640 3159420 3055430 2686940 FALSE TRUE 2476048.397 3270555.17 3157476.445 3781576.935 2533927.647 2800676.766 3261272.15 3117073.143 2945465.671 3213394.448 0.770539825 1.017788268 0.982598463 1.176816913 0.788551698 0.87156333 1.014899416 0.97002506 0.916621261 1 21.61566665 -1.309319177 5.164004507 1.00001271 0.95313731 0.016554273 0.112959296 1.60E-05 2.14E-06 0.105815496 0.024934189 0.049054722 1.309319177 -0.0468754 YYKVDENGK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 ;;; 156.12 6.54E-05 4183220000 8116100 6034820 6807000 4951700 12171600 10111400 9298800 8388600 9682400 6676960 FALSE TRUE 8436529.895 7071253.391 6984396.012 5931131.481 10102675.78 7763180.59 8569935.758 8276164.538 9333932.315 7985182.474 1.056523119 0.885546876 0.874669556 0.742767182 1.265177823 0.97219827 1.073229796 1.036440252 1.168906577 1 22.92889395 3.246233414 24.99999985 1.078227357 0.888481223 0.450864361 0.105818807 162.5590531 529656.7826 0.028516296 0.037896945 1762.923286 -3.246233414 -0.189746134 YYLHDDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 ;;; 140.98 0.0025874 988800000 1458800 1915050 1752560 2055490 1906500 2335210 1985600 1923710 1697470 1759230 FALSE TRUE 1516394.55 2243944.94 1798233.153 2462059.787 1582433.811 1792892.868 1829963.484 1897925.814 1636378.386 2103917.436 0.720748127 1.066555608 0.854707092 1.170226428 0.75213684 0.852168834 0.869788639 0.902091395 0.777776902 1 21.00464666 YYPTEDVPR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YYPTEDVPR 9 0 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;;;; 236.09 7.51E-10 3878560000 2688110 3331180 3062500 3130780 3402450 3776090 3171290 3279120 2925990 3359640 FALSE TRUE 2794238.658 3903284.252 3142311.266 3750038.94 2824102.764 2899150.325 2922716.003 3235168.76 2820684.191 4017897.134 0.695448033 0.971474411 0.782078575 0.933333735 0.702880803 0.721559121 0.727424298 0.805189544 0.702029967 1 21.9380092 YYPTEDVPRK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YYPTEDVPRK 10 1 Q02878;F8VZ45;U3KQR5;F8VR69 Q02878 RPL6 60S ribosomal protein L6 0 ;;; 163.16 1.05E-05 1623060000 1077250 940581 1070880 854866 1332120 1198710 947384 995240 1082311 979200 FALSE TRUE 1119780.662 1102118.47 1098788.013 1023955.943 1105686.718 920327.7691 873125.5666 981900.4357 1043358.839 1171055.492 0.956214859 0.941132574 0.938288595 0.874387209 0.94417961 0.785895951 0.74558855 0.838474728 0.890955933 1 20.15937801 2.750677213 24.8131597 0.833184174 0.928689833 0.231434105 0.06730197 807.5118948 1653674.379 0.02011705 0.021195369 563.2188909 -2.750677213 0.09550566 YYQLFLDSLRDPNKVFPEHIGEDVLRPAMLAK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYQLFLDSLRDPNKVFPEHIGEDVLRPAMLAK 32 3 A0A1B0GUA3;Q96EK5 A0A1B0GUA3 KIAA1279 KIF1-binding protein 0 47.429 0.054086 88915000 62332 53602 62921 48482 104200 79511 82182 68293 72315 42197 FALSE TRUE 64792.91549 62807.72653 64560.77295 58071.5949 86488.12122 61045.77525 75740.3601 67377.64404 69712.39728 50464.69424 1.283925653 1.244587478 1.279325555 1.15073708 1.713834246 1.209672944 1.500858397 1.335144204 1.381409287 1 15.62298679 YYTLFGR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 2 YYTLFGR 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 ; 166.34 0.0026222 1270470000 734370 863110 762420 743150 1484580 1241020 919480 725520 734060 1531110 FALSE TRUE 763363.4947 1011342.428 782289.2915 890142.8519 1232231.622 952811.9128 847408.755 715795.5911 707641.324 1831101.69 0.416887549 0.552313634 0.427223292 0.486124204 0.672945489 0.520348989 0.462786289 0.390909798 0.386456595 1 20.80428048 -1.163039237 4.809815116 1.000049025 0.479955474 0.782208378 0.082386127 4.62E-05 8.03E-06 0.085019915 0.020037503 0.068700637 1.163039237 -0.520093551 YYTSASGDEMVS(ph)LKDYCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 4 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 1 YYTSASGDEMVS(1)LKDYCTR;YYTSASGDEMVS(1)LKDYCTR;YYTSASGDEMVS(1)LKDYCTR;YYTSASGDEMVS(1)LKDYCTR 291.91 8.79E-50 843780000 1077960 603422 784250 582257 1133120 1057920 852690 822130 834490 555075 TRUE FALSE 1120518.693 707055.0345 804688.1993 697425.6967 940512.6671 812234.1129 785853.9297 811110.6921 804456.8679 663831.3187 1.687956958 1.065112499 1.21218776 1.050606799 1.41679466 1.223554976 1.183815689 1.221862647 1.211839281 1 19.34045717 7.994700574 0.024087109 2.42E-06 2.875576973 0.231267022 0.166288138 3764.276394 6.9791121 290.3855947 592.1920482 98787176.72 -7.994700574 2.875574552 YYTSASGDEMVSLKDYCTR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 6 YYTSASGDEMVSLKDYCTR 19 1 P07900;P07900-2 P07900 HSP90AA1 Heat shock protein HSP 90-alpha 0 ;;;;; 340.85 7.96E-76 3791500000 1693990 1943160 2088670 1377022 2749010 2503690 1661700 2053070 2268400 2462900 FALSE TRUE 1760870.033 2276882.614 2143102.456 1649392.842 2281734.262 1922245.941 1531451.612 2025551.955 2186760.727 2945458.1 0.597825524 0.77301477 0.727595635 0.559978375 0.774661932 0.652613575 0.519936648 0.687686562 0.742417869 1 21.4900606 0.811054755 2.393110347 0.999663968 0.661935932 0.615882354 0.080380488 0.485315843 4.745333369 0.075870052 0.02044362 6.472242112 -0.811054755 -0.337728036 YYTVFDR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 YYTVFDR 7 0 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;;;; 199.65 0.00086569 46502775000 14169720 16506410 14679783 16555900 16905060 20142460 17911720 15596860 14143726 16711230 FALSE TRUE 14729151.49 19341257.52 15062350.2 19830607.61 14031543.94 15464678.93 16507752.58 15387809.6 13634696.06 19985475.56 0.736992795 0.967765688 0.753664838 0.992250975 0.702087068 0.773795894 0.825987479 0.769949634 0.682230254 1 24.25244857 3.213248371 24.99965045 0.781809231 0.862389732 0.084398057 0.110249255 473.4820375 467633.3545 0.029137904 0.034839177 1633.98615 -3.213248371 0.080580501 YYTVFDRDNNR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 12 YYTVFDRDNNR 11 1 A0A1B0GW44;A0A1B0GVD5;A0A1B0GWE8;P07339;A0A1B0GVP3;A0A1B0GV23;H7C469;H7C1V0 A0A1B0GW44 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 ;;;;;;;;;;; 262.54 8.71E-21 50587625000 8183060 11192519 8968745 7491051 13323280 12533130 7341393 8651646 8422443 16698490 FALSE TRUE 8506133.527 13114747.07 9202477.863 8972758.529 11058593.62 9622500.499 6765955.433 8535684.837 8119320.922 19970239.4 0.425940489 0.656714564 0.460809592 0.449306508 0.553753683 0.48184202 0.338801919 0.427420256 0.406571036 1 24.25134829 -1.635507123 4.206604326 1.015635561 0.466185002 0.791430782 0.08211657 0.012554399 0.00108781 0.082896284 0.019421056 0.023146902 1.635507123 -0.549450558 YYVGHK ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYVGHK 6 0 P61326;Q96A72;F5H6N1;P61326-2;F5H124 P61326 MAGOH;MAGOHB Protein mago nashi homolog;Protein mago nashi homolog 2 0 112.58 0.077439 0 139560 126280 139780 122850 189560 188950 162290 164000 148970 123600 FALSE TRUE 145069.9366 147967.6077 143422.7816 147149.3633 157338.6589 145069.2261 149569.2857 161801.8482 143608.5988 147817.0535 0.981415426 1.001018517 0.970272226 0.995482996 1.064414796 0.981410619 1.01185406 1.094608804 0.971529302 1 17.1734532 3.456089553 24.0624831 1.027794362 0.985407679 0.164656138 0.035549645 222.6912194 254780.9844 0.009993548 0.01353309 2858.179851 -3.456089553 -0.042386683 YYVTIIDAPGHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 8 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 ;;;;;;; 194.17 1.88E-06 71049380000 19446660 19377500 21756110 22580770 22381460 24871640 24714870 21878020 21370030 16490430 FALSE TRUE 20214429.15 22705434.89 22323092.1 27047178.91 18577067.42 19095578.54 22777653.91 21584780.93 20600926.79 19721414.03 1.024998974 1.151308667 1.131921477 1.371462455 0.941974414 0.968266196 1.154970626 1.094484447 1.044596841 1 24.23325966 3.19558322 24.99999717 1.047718794 1.165881196 0.307855567 0.098462583 200.3908325 116566.8387 0.029433139 0.035179524 1568.856495 -3.19558322 0.118162402 YYYVQNVYTPVDEHVYPDHR ddPTM_MDA-MB-175_Trastuzumab_2h_R1 1 YYYVQNVYTPVDEHVYPDHR 20 0 A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7 A0A087WXK2 PEG10 Retrotransposon-derived protein PEG10 0 101.13 0.00024109 98163000 45407 52132 47335 52848 56684 71950 54367 49186 54090 62899 FALSE TRUE 47199.70342 61085.26547 48568.58899 63301.17666 47048.87393 55240.70291 50105.57248 48526.74212 52143.31147 75222.85478 0.627464932 0.812057262 0.645662666 0.841515213 0.62545983 0.734360629 0.666095067 0.645106361 0.693184427 1 16.19888344 -2.177551388 2.260629439 1.759962696 0.698435642 0.611819289 0.071928465 5740043.557 1320352.618 22297973.26 0.016091937 0.00664429 2.177551388 -1.061527054